Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	G	C	tCw	wGa	tC	Ga	tC_mutation	tC_mutation_to_G	tC_mutation_to_T	APOBEC_mutation	APOBEC_mutation_to_G	APOBEC_mutation_to_T	[tCw_to_G+tCw_to_T]_per_mut	tCw_to_G+tCw_to_T	BH_Fisher_p-value_tCw	APOBEC_enrich	tCw_to_G_enrich	tCw_to_T_enrich	p-value_GvT_skew	BH_p-value_GvT_skew	APOBEC_MutLoad_MinEstimate	"CONTEXT(+/-20)"	g_counts	c_counts	tcw_counts	wga_counts	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_CancerGermlineMut	i_CGC_CancerMolecularGenetics	i_CGC_CancerSomaticMut	i_CGC_CancerSyndrome	i_CGC_Chr	i_CGC_ChrBand	i_CGC_GeneID	i_CGC_Name	i_CGC_OtherGermlineMut	i_CGC_TissueType	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_AccessionNumbers	i_HGNC_CCDSIDs	i_HGNC_Chromosome	i_HGNC_DateModified	i_HGNC_DateNameChanged	i_HGNC_DateSymbolChanged	i_HGNC_EnsemblGeneID	i_HGNC_EnsemblIDsuppliedbyEnsembl	i_HGNC_EnzymeIDs	i_HGNC_Genefamilydescription	i_HGNC_HGNCID	i_HGNC_LocusGroup	i_HGNC_LocusType	i_HGNC_NameSynonyms	i_HGNC_OMIMIDsuppliedbyNCBI	i_HGNC_PreviousNames	i_HGNC_PreviousSymbols	i_HGNC_PrimaryIDs	i_HGNC_PubmedIDs	i_HGNC_RecordType	i_HGNC_RefSeqsuppliedbyNCBI	i_HGNC_SecondaryIDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSCIDsuppliedbyUCSC	i_HGNC_UniProtIDsuppliedbyUniProt	i_HGNC_VEGAIDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP_NR	i_dbNSFP_GERP_RS	i_dbNSFP_GERP_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos1coor	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	newbase	end	tum_allele1	tum_allele2	start	effect_idx	newbase_idx	pat_idx	is_coding	is_flank	is_indel	is_ins	is_del	is_missense	is_nonsense	is_splice	is_silent	gene_idx	context_and_effect	context65	categ_idx	trackpos	categ	gene	chr	pos	type	classification	ref_allele	patient	DistBetween_Mutations	Distance_to_LT_end	Distance_to_RT_end	Strain_Mutation_ID	Dataset_Mutation_ID	Complex_ID	Complex_Size	StrainCluster_ID	Dataset_Cluster_ID	Distance_Between_Clusters	Cluster_Size_Mutations	Cluster_Size_Complexes	Cluster_Length	Cluster_Coordination	Content_of_non_coordinated_cluster	Cluster_Pvalue
CASP9	842	hgsc.bcm.edu	37	chr1	15820444	15820444	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	cactgctcaaagatgtcgtcCagggtctcaacgtaccagga	10	12	2	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:15820444C>A	ENST00000333868.5	-	8	1195	c.1101G>T	c.(1099-1101)ctG>ctT	p.L367L	CASP9_ENST00000348549.5_Silent_p.L217L|CASP9_ENST00000375890.4_Silent_p.L284L|CASP9_ENST00000546424.1_Silent_p.L367L	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	367					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		AGATGTCGTCCAGGGTCTCAA	0.597																																					p.L367L		Atlas-SNP	.											.	CASP9	40	.	0			c.G1101T						.						71	52	59					1																	15820444		2203	4300	6503	SO:0001819	synonymous_variant	842	exon8			GTCGTCCAGGGTC	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"Caspases", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1511	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 56"	602234	"caspase 9, apoptosis-related cysteine protease"			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.1101G>T	chr1.hg19:g.15820444C>A		23.0	0.0		27.0	11.0	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Silent	SNP	ENST00000333868.5	hg19	CCDS158.1	.	.	.	.	.	.	.	.	.	.	C	1.412	-0.575360	0.03882	.	.	ENSG00000132906	ENST00000424908	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7195	0.46032	0.0:0.914:0.0:0.086	.	.	.	.	X	149	.	.	G	-	1	0	CASP9	15693031	1.000000	0.71417	1.000000	0.80357	0.194000	0.23727	4.088000	0.57678	2.703000	0.92315	0.655000	0.94253	GGA	.	.		0.597	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996		A	15820444	C	A	15820444	2	1	1	1	0	0	0	0	0	0	0	1	2681	581	21	3		3	CASP9	1	15820444	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10		15820444	233430177	1	1										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27102134	27102134	+	Frame_Shift_Del	DEL	C	C	-													0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	cctggcagagagcacatgggCattagataccatcaacatcc							TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:27102134delC	ENST00000324856.7	+	19	5431	c.5060delC	c.(5059-5061)gcafs	p.A1687fs	ARID1A_ENST00000457599.2_Frame_Shift_Del_p.A1470fs|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.A1304fs|ARID1A_ENST00000540690.1_Frame_Shift_Del_p.A15fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1687					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGCACATGGGCATTAGATACC	0.502			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.A1687fs		Atlas-Indel,Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.5059delG						.						149	118	129					1																	27102134		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon19			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5060delC	chr1.hg19:g.27102134delC	ENSP00000320485:p.Ala1687fs	70.0	0.0		112.0	22.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.502	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27102134	C	-	27102134	7	5	1	1	0	1	0	1	0	0	0	0	913	710	25	0	5134	0	ARID1A	1	27102134	Frame_Shift_Del	DEL	C	TCGA-2V-A95S-01A-11D-A36X-10	11281690	27102134	222148487	2	2										
C1orf113	79729	hgsc.bcm.edu	37	chr1	36786280	36786280	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tcccaagagacgctcgcgctCccctcgctggtcccgcaaaa	9	18	0	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:36786280C>T	ENST00000426732.2	+	13	1953	c.1668C>T	c.(1666-1668)ctC>ctT	p.L556L	SH3D21_ENST00000453908.2_Silent_p.L672L|SH3D21_ENST00000474766.1_3'UTR|SH3D21_ENST00000505871.1_Silent_p.L561L|EVA1B_ENST00000490466.1_5'Flank|SH3D21_ENST00000312808.4_Silent_p.L318L			A4FU49	SH321_HUMAN	SH3 domain containing 21	556						extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(6)|lung(4)|pancreas(1)	12						CGCTCGCGCTCCCCTCGCTGG	0.567																																					p.L672L		Atlas-SNP	.											.	SH3D21	73	.	0			c.C2016T						.						49	52	51					1																	36786280		2201	4298	6499	SO:0001819	synonymous_variant	79729	exon14			CGCGCTCCCCTCG	AK056459	CCDS30674.1, CCDS30674.2	1p34.3	2011-02-21	2011-02-21	2011-02-21	ENSG00000214193	ENSG00000214193			26236	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 113"	C1orf113		12477932	Standard	NM_024676		Approved	FLJ22938	uc010oia.1	A4FU49	OTTHUMG00000007868	ENST00000426732.2:c.1668C>T	chr1.hg19:g.36786280C>T		231.0	0.0		229.0	42.0	NM_001162530	B4DLI6|D3DPS6|J3KQM5|Q5VTK7|Q86XZ6|Q8N445|Q96DN4|Q9H5W5	Silent	SNP	ENST00000426732.2	hg19																																																																																				.	.		0.567	SH3D21-202	KNOWN	basic	protein_coding	protein_coding		NM_024676		T	36786280	C	T	36786280	2	4	1	1	0	0	0	0	0	0	0	1	1988	842	30	3		3	C1orf113	1	36786280	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	9684146	36786280	212464341	3	3										
ZC3H12A	80149	hgsc.bcm.edu	37	chr1	37947212	37947212	+	Frame_Shift_Del	DEL	C	C	-													0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	cacctcccagaccagcacatCctgcgggaactggagaagaa							TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:37947212delC	ENST00000373087.6	+	4	710	c.594delC	c.(592-594)atcfs	p.I198fs		NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A											NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ACCAGCACATCCTGCGGGAAC	0.597																																					p.I198fs		Atlas-Indel,Pindel	.											.	ZC3H12A	58	.	0			c.593delT						.						153	142	146					1																	37947212		2203	4300	6503	SO:0001589	frameshift_variant	80149	exon4			.		CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"Zinc fingers, CCCH-type domain containing"	26259	protein-coding gene	gene with protein product	"MCP induced protein 1"	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.594delC	chr1.hg19:g.37947212delC	ENSP00000362179:p.Ile198fs	101.0	0.0		75.0	12.0	NM_025079		Frame_Shift_Del	DEL	ENST00000373087.6	hg19	CCDS417.1																																																																																			.	.		0.597	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		-	37947212	C	-	37947212	7	5	1	1	0	1	0	1	0	0	0	0	17576	845	30	0	604	0	ZC3H12A	1	37947212	Frame_Shift_Del	DEL	C	TCGA-2V-A95S-01A-11D-A36X-10	1160932	37947212	211303409	4	4										
FHL3	2275	hgsc.bcm.edu	37	chr1	38463418	38463418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gttctccaaaacaggccacaCagtagggatcttcatcccgg	9	13	3	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:38463418C>T	ENST00000373016.3	-	5	794	c.626G>A	c.(625-627)tGt>tAt	p.C209Y	FHL3_ENST00000485803.1_5'UTR	NM_001243878.1|NM_004468.4	NP_001230807.1|NP_004459.2	Q13643	FHL3_HUMAN	four and a half LIM domains 3	209	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|muscle organ development (GO:0007517)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)|Z disc (GO:0030018)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				ACAGGCCACACAGTAGGGATC	0.582																																					p.C209Y		Atlas-SNP	.											.	FHL3	9	.	0			c.G626A						.						76	75	75					1																	38463418		2203	4300	6503	SO:0001583	missense	2275	exon5			GCCACACAGTAGG	BC011697	CCDS30678.1	1p34.3	2008-02-05			ENSG00000183386	ENSG00000183386			3704	protein-coding gene	gene with protein product		602790				8753811, 10226657	Standard	NM_004468		Approved	SLIM2	uc001cck.3	Q13643	OTTHUMG00000004434	ENST00000373016.3:c.626G>A	chr1.hg19:g.38463418C>T	ENSP00000362107:p.Cys209Tyr	141.0	0.0		129.0	31.0	NM_004468	D3DPT6|Q6I9T0|Q9BVA2	Missense_Mutation	SNP	ENST00000373016.3	hg19	CCDS30678.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.722473	0.68959	.	.	ENSG00000183386	ENST00000373016	D	0.99319	-5.74	5.18	4.2	0.49525	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.99711	0.9889	H	0.99697	4.71	0.80722	D	1	D;D	0.71674	0.998;0.996	D;D	0.70487	0.969;0.948	D	0.96840	0.9617	10	0.87932	D	0	.	15.1367	0.72572	0.0:0.8582:0.1418:0.0	.	101;209	Q96C98;Q13643	.;FHL3_HUMAN	Y	209	ENSP00000362107:C209Y	ENSP00000362107:C209Y	C	-	2	0	FHL3	38236005	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	6.041000	0.70988	2.426000	0.82243	0.313000	0.20887	TGT	.	.		0.582	FHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012958.1	NM_004468		T	38463418	C	T	38463418	3	4	1	1	0	0	0	0	1	0	0	0	5888	478	17	3	224	3	FHL3	1	38463418	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	516206	38463418	210787203	5	5										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144857701	144857701	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ctggggaattcataccaacaTcccggactggaggggacaca	12	11	1	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:144857701T>C	ENST00000369354.3	-	39	6542	c.6353A>G	c.(6352-6354)gAt>gGt	p.D2118G	PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.D2012G|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.D2203G|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.D2118G|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.D2254G			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2118					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CATACCAACATCCCGGACTGG	0.522			T	PDGFRB	MPD																																p.D2118G		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6353G						.						140	155	150					1																	144857701		2203	4296	6499	SO:0001583	missense	9659	exon39			CCAACATCCCGGA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6353A>G	chr1.hg19:g.144857701T>C	ENSP00000358360:p.Asp2118Gly	111.0	0.0		128.0	12.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	19.55|19.55	3.848492|3.848492	0.71603|0.71603	.|.	.|.	ENSG00000178104|ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359|ENST00000530130	T;T;T;T;T|.	0.02067|.	4.47;4.5;4.5;4.56;4.51|.	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	.|.	.|.	.|.	.|.	T|T	0.68109|0.68109	0.2965|0.2965	M|M	0.80183|0.80183	2.485|2.485	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.998|.	D;D|.	0.87578|.	0.998;0.992|.	T|T	0.71600|0.71600	-0.4544|-0.4544	9|5	0.72032|.	D|.	0.01|.	.|.	12.746|12.746	0.57281|0.57281	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2012;2118|.	Q5VU43-3;Q5VU43|.	.;MYOME_HUMAN|.	G|V	2012;2118;2118;2203;2254|195	ENSP00000327209:D2012G;ENSP00000358360:D2118G;ENSP00000358363:D2118G;ENSP00000435654:D2203G;ENSP00000358366:D2254G|.	ENSP00000327209:D2012G|.	D|M	-|-	2|1	0|0	PDE4DIP|PDE4DIP	143569058|143569058	1.000000|1.000000	0.71417|0.71417	0.949000|0.949000	0.38748|0.38748	0.551000|0.551000	0.35334|0.35334	5.010000|5.010000	0.64004|0.64004	1.966000|1.966000	0.57179|0.57179	0.454000|0.454000	0.30748|0.30748	GAT|ATG	.	.		0.522	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144857701	T	C	144857701	3	2	1	1	0	0	0	0	1	0	0	0	11652	1435	50	2	711	2	PDE4DIP	1	144857701	Missense_Mutation	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	106394283	144857701	104392920	6	6										
SYT11	23208	hgsc.bcm.edu	37	chr1	155851003	155851003	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ccccagatccttatgtcaagGtgaacgtctactacggcaga	9	12	2	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:155851003G>T	ENST00000368324.4	+	4	1253	c.1000G>T	c.(1000-1002)Gtg>Ttg	p.V334L	SYT11_ENST00000539162.1_Missense_Mutation_p.V27L	NM_152280.4	NP_689493.3	Q9BT88	SYT11_HUMAN	synaptotagmin XI	334	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				negative regulation of neurotransmitter secretion (GO:0046929)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(1)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;0.000162)			TTATGTCAAGGTGAACGTCTA	0.438																																					p.V334L		Atlas-SNP	.											.	SYT11	55	.	0			c.G1000T						.						191	203	199					1																	155851003		2203	4300	6503	SO:0001583	missense	23208	exon4			GTCAAGGTGAACG	D38522	CCDS1122.1	1q22	2013-01-21			ENSG00000132718	ENSG00000132718		"Synaptotagmins"	19239	protein-coding gene	gene with protein product		608741				11543631	Standard	NM_152280		Approved	KIAA0080, MGC10881, MGC17226, DKFZp781D015	uc001fmg.3	Q9BT88	OTTHUMG00000014105	ENST00000368324.4:c.1000G>T	chr1.hg19:g.155851003G>T	ENSP00000357307:p.Val334Leu	243.0	1.0		317.0	141.0	NM_152280	Q14998|Q5W0D4|Q68CT5|Q8IXU3|Q96SU2	Missense_Mutation	SNP	ENST00000368324.4	hg19	CCDS1122.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.703944	0.48412	.	.	ENSG00000132718	ENST00000368324;ENST00000539162	T;T	0.71579	-0.58;-0.58	5.17	4.18	0.49190	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.139246	0.49305	D	0.000152	T	0.41719	0.1171	N	0.16656	0.425	0.54753	D	0.999989	B	0.02656	0.0	B	0.06405	0.002	T	0.42413	-0.9453	10	0.48119	T	0.1	.	13.9537	0.64135	0.0856:0.0:0.9144:0.0	.	334	Q9BT88	SYT11_HUMAN	L	334;27	ENSP00000357307:V334L;ENSP00000441657:V27L	ENSP00000357307:V334L	V	+	1	0	SYT11	154117627	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.387000	0.73191	2.691000	0.91804	0.655000	0.94253	GTG	.	.		0.438	SYT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039597.1	NM_152280		T	155851003	G	T	155851003	3	4	1	1	0	0	0	0	1	0	0	0	15482	1261	44	3	1014	3	SYT11	1	155851003	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	10993302	155851003	93399618	7	7										
KIAA0907	22889	hgsc.bcm.edu	37	chr1	155891652	155891652	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	acacttcaagatgtacacacCtggtaaaggtacagcagtat	8	9	1	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:155891652C>T	ENST00000368321.3	-	9	1035	c.1012G>A	c.(1012-1014)Ggc>Agc	p.G338S	KIAA0907_ENST00000368319.3_Splice_Site_p.A338T|KIAA0907_ENST00000482337.1_5'UTR|KIAA0907_ENST00000368320.3_Splice_Site_p.G338S|SNORA42_ENST00000384744.1_RNA	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	338	Pro-rich.						RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			ATGTACACACCTGGTAAAGGT	0.383																																					p.G338S		Atlas-SNP	.											.	KIAA0907	58	.	0			c.G1012A						.						86	86	86					1																	155891652		2203	4300	6503	SO:0001630	splice_region_variant	22889	exon9			ACACACCTGGTAA	BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.1012+1G>A	chr1.hg19:g.155891652C>T		465.0	0.0		623.0	91.0	NM_014949	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Missense_Mutation	SNP	ENST00000368321.3	hg19	CCDS30885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.6|24.6	4.544143|4.544143	0.86022|0.86022	.|.	.|.	ENSG00000132680|ENSG00000132680	ENST00000368319|ENST00000368321;ENST00000368320	.|.	.|.	.|.	5.94|5.94	5.94|5.94	0.96194|0.96194	.|.	.|0.160586	.|0.56097	.|D	.|0.000031	T|T	0.36276|0.36276	0.0961|0.0961	L|L	0.29908|0.29908	0.895|0.895	0.20975|0.20975	N|N	0.999814|0.999814	D|P;P	0.60575|0.47962	0.988|0.844;0.903	P|P;P	0.62885|0.56398	0.908|0.797;0.795	T|T	0.21109|0.21109	-1.0255|-1.0255	7|8	.|.	.|.	.|.	-7.9971|-7.9971	18.1253|18.1253	0.89584|0.89584	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	338|338;338	Q7Z7F0-3|Q7Z7F0-2;Q7Z7F0	.|.;K0907_HUMAN	T|S	338|338	.|.	.|.	A|G	-|-	1|1	0|0	KIAA0907|KIAA0907	154158276|154158276	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.652000|5.652000	0.67959|0.67959	2.821000|2.821000	0.97095|0.97095	0.484000|0.484000	0.47621|0.47621	GCA|GGC	.	.		0.383	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949	Missense_Mutation	T	155891652	C	T	155891652	5	4	1	1	0	0	0	0	0	0	1	0	8208	695	24	3	856	3	KIAA0907	1	155891652	Splice_Site	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	40649	155891652	93358969	8	8										
UBQLN4	56893	hgsc.bcm.edu	37	chr1	156021615	156021615	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	caggaccagctgatcctgctGagccttaaacctccgggaga	11	13	0	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:156021615G>A	ENST00000368309.3	-	2	234	c.142C>T	c.(142-144)Cag>Tag	p.Q48*	LAMTOR2_ENST00000368305.4_5'Flank|LAMTOR2_ENST00000368304.5_5'Flank|UBQLN4_ENST00000472638.1_5'UTR	NM_020131.3	NP_064516.2	Q9NRR5	UBQL4_HUMAN	ubiquilin 4	48	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|polyubiquitin binding (GO:0031593)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)	16	Hepatocellular(266;0.133)|all_neural(408;0.195)					TGATCCTGCTGAGCCTTAAAC	0.562																																					p.Q48X		Atlas-SNP	.											.	UBQLN4	47	.	0			c.C142T						.						82	70	74					1																	156021615		2203	4300	6503	SO:0001587	stop_gained	56893	exon2			CCTGCTGAGCCTT	BC018403	CCDS1127.1	1q21	2013-02-12	2004-11-05	2004-11-06	ENSG00000160803	ENSG00000160803		"Ubiquilin family"	1237	protein-coding gene	gene with protein product	"ataxin-1 ubiquitin-like interacting protein"	605440	"chromosome 1 open reading frame 6"	C1orf6		10575211, 11001934	Standard	NM_020131		Approved	A1U, UBIN	uc001fna.3	Q9NRR5	OTTHUMG00000017461	ENST00000368309.3:c.142C>T	chr1.hg19:g.156021615G>A	ENSP00000357292:p.Gln48*	67.0	0.0		151.0	15.0	NM_020131	A6ND44|B2RAY7|Q5VYA0|Q5VYA1|Q9BR98|Q9UHX4	Nonsense_Mutation	SNP	ENST00000368309.3	hg19	CCDS1127.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.218699	0.79464	.	.	ENSG00000160803	ENST00000368309;ENST00000368307	.	.	.	5.04	5.04	0.67666	.	0.053007	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-14.3825	10.8654	0.46851	0.0:0.0:0.7145:0.2855	.	.	.	.	X	48	.	ENSP00000357290:Q48X	Q	-	1	0	UBQLN4	154288239	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.558000	0.60789	2.618000	0.88619	0.561000	0.74099	CAG	.	.		0.562	UBQLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046193.1	NM_020131		A	156021615	G	A	156021615	4	1	1	1	0	0	0	0	0	1	0	0	16914	1299	45	3	1703	3	UBQLN4	1	156021615	Nonsense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	129963	156021615	93229006	9	9										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157497415	157497415	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	aggtcaacttacctataacaCtgagtgatattgtgtcactg	8	8	2	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:157497415C>A	ENST00000361835.3	-	9	2109	c.1952G>T	c.(1951-1953)aGt>aTt	p.S651I	FCRL5_ENST00000368190.3_Missense_Mutation_p.S651I|FCRL5_ENST00000368191.3_Missense_Mutation_p.S566I|FCRL5_ENST00000356953.4_Missense_Mutation_p.S651I	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	651	Ig-like C2-type 6.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				ACCTATAACACTGAGTGATAT	0.443																																					p.S651I		Atlas-SNP	.											.	FCRL5	177	.	0			c.G1952T						.						105	103	104					1																	157497415		2203	4300	6503	SO:0001583	missense	83416	exon9			ATAACACTGAGTG	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.1952G>T	chr1.hg19:g.157497415C>A	ENSP00000354691:p.Ser651Ile	95.0	0.0		154.0	28.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	hg19	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.424059	0.43020	.	.	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191	T;T;T;T	0.03212	4.01;4.01;4.01;4.01	3.53	-4.6	0.03390	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.06872	0.0175	M	0.90483	3.12	0.09310	N	1	D;D;P;D	0.67145	0.996;0.976;0.768;0.981	D;D;B;P	0.67725	0.953;0.912;0.253;0.827	T	0.02424	-1.1161	9	0.48119	T	0.1	.	5.3737	0.16154	0.0:0.2293:0.4445:0.3261	.	566;651;651;651	F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9	.;.;.;FCRL5_HUMAN	I	651;651;651;566	ENSP00000354691:S651I;ENSP00000349434:S651I;ENSP00000357173:S651I;ENSP00000357174:S566I	ENSP00000349434:S651I	S	-	2	0	FCRL5	155764039	0.000000	0.05858	0.001000	0.08648	0.039000	0.13416	-1.347000	0.02632	-0.713000	0.04981	0.650000	0.86243	AGT	.	.		0.443	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		A	157497415	C	A	157497415	3	1	1	1	0	0	0	0	1	0	0	0	5806	565	20	3	1017	3	FCRL5	1	157497415	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	1475800	157497415	91753206	10	10										
FCRL1	115350	hgsc.bcm.edu	37	chr1	157765893	157765893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	agaatcttccataaccttacAtagcatcttcatagtccaca	3	12	3	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:157765893A>G	ENST00000368176.3	-	11	1353	c.1286T>C	c.(1285-1287)aTg>aCg	p.M429T	FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000358292.3_3'UTR|FCRL1_ENST00000491942.1_Missense_Mutation_p.M428T	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	429						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			ATAACCTTACATAGCATCTTC	0.443																																					p.M429T	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.T1286C						.						191	162	172					1																	157765893		2203	4300	6503	SO:0001583	missense	115350	exon11			CCTTACATAGCAT	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.1286T>C	chr1.hg19:g.157765893A>G	ENSP00000357158:p.Met429Thr	126.0	0.0		205.0	19.0	NM_052938	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Missense_Mutation	SNP	ENST00000368176.3	hg19	CCDS1170.1	.	.	.	.	.	.	.	.	.	.	A	8.914	0.959393	0.18507	.	.	ENSG00000163534	ENST00000368176;ENST00000491942	T;T	0.39056	1.1;1.1	4.37	2.1	0.27182	.	1.292250	0.05210	N	0.506600	T	0.18964	0.0455	L	0.51422	1.61	0.09310	N	1	B;B	0.26547	0.152;0.003	B;B	0.25140	0.058;0.002	T	0.36866	-0.9730	10	0.87932	D	0	.	5.3852	0.16215	0.7755:0.0:0.2245:0.0	.	428;429	Q96LA6-2;Q96LA6	.;FCRL1_HUMAN	T	429;428	ENSP00000357158:M429T;ENSP00000418130:M428T	ENSP00000357158:M429T	M	-	2	0	FCRL1	156032517	0.309000	0.24518	0.040000	0.18447	0.047000	0.14425	1.434000	0.34958	0.835000	0.34877	0.454000	0.30748	ATG	.	.		0.443	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938		G	157765893	A	G	157765893	3	3	1	1	0	0	0	0	1	0	0	0	5802	217	8	2	7	2	FCRL1	1	157765893	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	268478	157765893	91484728	11	11										
NR1I3	9970	hgsc.bcm.edu	37	chr1	161200931	161200931	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	agagaagagggccatggcagCcaagagcacatactcaggct	13	10	1	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:161200931C>G	ENST00000367982.4	-	7	954	c.799G>C	c.(799-801)Gct>Cct	p.A267P	NR1I3_ENST00000508740.1_Missense_Mutation_p.A234P|NR1I3_ENST00000515621.1_Missense_Mutation_p.A188P|NR1I3_ENST00000502985.1_Intron|NR1I3_ENST00000511676.1_Missense_Mutation_p.A234P|NR1I3_ENST00000412844.2_Missense_Mutation_p.A238P|NR1I3_ENST00000442691.2_Missense_Mutation_p.A267P|NR1I3_ENST00000367985.3_Intron|NR1I3_ENST00000505005.1_Intron|NR1I3_ENST00000367980.2_Missense_Mutation_p.A267P|NR1I3_ENST00000504010.1_Intron|NR1I3_ENST00000428574.2_Missense_Mutation_p.A263P|NR1I3_ENST00000506209.1_Missense_Mutation_p.A234P|NR1I3_ENST00000367984.4_Intron|NR1I3_ENST00000479324.1_5'UTR|NR1I3_ENST00000511944.1_Intron|NR1I3_ENST00000367981.3_Missense_Mutation_p.A234P|NR1I3_ENST00000512372.1_Intron|NR1I3_ENST00000367979.2_Missense_Mutation_p.A267P|NR1I3_ENST00000437437.2_Missense_Mutation_p.A234P|NR1I3_ENST00000511748.1_Intron|NR1I3_ENST00000367983.4_Missense_Mutation_p.A263P|NR1I3_ENST00000508387.1_Intron			Q14994	NR1I3_HUMAN	nuclear receptor subfamily 1, group I, member 3	267					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	15	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCCATGGCAGCCAAGAGCACA	0.537																																					p.A267P		Atlas-SNP	.											.	NR1I3	74	.	0			c.G799C						.						53	55	54					1																	161200931		2203	4300	6503	SO:0001583	missense	9970	exon7			TGGCAGCCAAGAG	Z30425	CCDS1228.1, CCDS41427.1, CCDS41428.1, CCDS41429.1, CCDS41430.1, CCDS44260.1, CCDS44261.1, CCDS44262.1, CCDS53405.1, CCDS53406.1, CCDS53407.1, CCDS53408.1, CCDS53409.1, CCDS53410.1, CCDS53411.1	1q23.3	2013-01-16			ENSG00000143257	ENSG00000143257		"Nuclear hormone receptors"	7969	protein-coding gene	gene with protein product	"constitutive androstane receptor"	603881				8114692	Standard	NM_001077480		Approved	MB67, CAR1, CAR	uc001fzp.3	Q14994	OTTHUMG00000034347	ENST00000367982.4:c.799G>C	chr1.hg19:g.161200931C>G	ENSP00000356961:p.Ala267Pro	134.0	0.0		177.0	23.0	NM_001077478	E9PB75|E9PC13|E9PDU3|E9PGH6|E9PH10|E9PHC8|E9PHN4|F1D8Q0|F1D8Q1|Q0VAC9|Q4U0F0|Q5VTW5|Q5VTW6|Q6GZ68|Q6GZ76|Q6GZ77|Q6GZ78|Q6GZ79|Q6GZ82|Q6GZ83|Q6GZ84|Q6GZ85|Q6GZ87|Q6GZ89	Missense_Mutation	SNP	ENST00000367982.4	hg19	CCDS41430.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.685655	0.68157	.	.	ENSG00000143257	ENST00000367983;ENST00000367980;ENST00000437437;ENST00000442691;ENST00000412844;ENST00000428574;ENST00000508740;ENST00000367982;ENST00000511676;ENST00000367981;ENST00000515621;ENST00000367979;ENST00000506209	D;D;D;D;D;D;D;D;D;D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13	5.38	5.38	0.77491	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.264976	0.37530	N	0.002052	D	0.97430	0.9159	M	0.71036	2.16	0.37677	D	0.923342	D;D;D;D;D;D;D;D;D;D;D;D	0.76494	0.99;0.999;0.986;0.986;0.999;0.986;0.993;0.968;0.995;0.998;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D;D	0.74674	0.95;0.984;0.965;0.928;0.982;0.928;0.952;0.928;0.95;0.937;0.935;0.982	D	0.97199	0.9863	9	0.46703	T	0.11	.	16.633	0.85039	0.0:1.0:0.0:0.0	.	234;238;263;267;267;267;188;234;234;234;234;263	E9PCF2;E9PHN4;F1D8Q1;Q14994;E9PC13;Q4U0F0;D6REZ7;Q6GZ68;E9PH10;Q6GZ84;E9PGH6;E9PB75	.;.;.;NR1I3_HUMAN;.;.;.;.;.;.;.;.	P	263;267;234;267;238;263;234;267;234;234;188;267;234	ENSP00000356962:A263P;ENSP00000356959:A267P;ENSP00000407446:A234P;ENSP00000406493:A267P;ENSP00000399361:A238P;ENSP00000412672:A263P;ENSP00000423666:A234P;ENSP00000356961:A267P;ENSP00000427175:A234P;ENSP00000356960:A234P;ENSP00000421588:A188P;ENSP00000356958:A267P;ENSP00000423089:A234P	ENSP00000356958:A267P	A	-	1	0	NR1I3	159467555	0.826000	0.29277	1.000000	0.80357	0.990000	0.78478	0.682000	0.25335	2.512000	0.84698	0.561000	0.74099	GCT	.	.		0.537	NR1I3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083048.2			G	161200931	C	G	161200931	3	3	1	1	0	0	0	0	1	0	0	0	10630	739	26	4	381	4	NR1I3	1	161200931	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	3435038	161200931	88049690	12	12										
RFWD2	64326	hgsc.bcm.edu	37	chr1	175958611	175958611	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	agatcatagtagtggacacaGtgatctaaaacaaaacaaaa	7	6	2	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:175958611G>C	ENST00000367669.3	-	16	2248	c.1734C>G	c.(1732-1734)caC>caG	p.H578Q	RFWD2_ENST00000308769.8_Missense_Mutation_p.H554Q	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	578					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						AGTGGACACAGTGATCTAAAA	0.333																																					p.H578Q	Ovarian(134;1413 1765 5706 35534 51541)	Atlas-SNP	.											RFWD2,NS,carcinoma,0,1	RFWD2	67	.	0			c.C1734G						.						94	84	88					1																	175958611		2203	4300	6503	SO:0001583	missense	64326	exon16			GACACAGTGATCT	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	17440	protein-coding gene	gene with protein product		608067	"ring finger and WD repeat domain 2"			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.1734C>G	chr1.hg19:g.175958611G>C	ENSP00000356641:p.His578Gln	93.0	0.0		113.0	16.0	NM_022457	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Missense_Mutation	SNP	ENST00000367669.3	hg19	CCDS30944.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.038117	0.75617	.	.	ENSG00000143207	ENST00000367665;ENST00000367669;ENST00000367666;ENST00000308769	T;T;T	0.70282	-0.47;-0.47;-0.47	5.79	4.88	0.63580	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.82719	0.5098	M	0.73319	2.225	0.80722	D	1	D;P;D;D;D	0.89917	1.0;0.845;1.0;0.968;0.968	D;P;D;D;D	0.97110	1.0;0.855;0.999;0.978;0.967	D	0.84490	0.0610	10	0.62326	D	0.03	-12.7373	14.4669	0.67490	0.0714:0.0:0.9286:0.0	.	353;338;554;578;578	Q8NHY2-3;B1AMD2;Q8NHY2-2;Q8NHY2;Q504W6	.;.;.;RFWD2_HUMAN;.	Q	353;578;413;554	ENSP00000356641:H578Q;ENSP00000356638:H413Q;ENSP00000310943:H554Q	ENSP00000310943:H554Q	H	-	3	2	RFWD2	174225234	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.723000	0.84788	1.460000	0.47911	-0.136000	0.14681	CAC	.	.		0.333	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457		C	175958611	G	C	175958611	3	2	1	1	0	0	0	0	1	0	0	0	13275	1020	36	4	481	4	RFWD2	1	175958611	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	14757680	175958611	73292010	13	13										
IGFN1	91156	hgsc.bcm.edu	37	chr1	201195085	201195085	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gtgttcacacgctcctcagcGcacggtccctggcacgaggc	12	16	2	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:201195085G>T	ENST00000335211.4	+	22	10750	c.10620G>T	c.(10618-10620)gcG>gcT	p.A3540A	RP11-567E21.3_ENST00000453155.1_RNA|IGFN1_ENST00000295591.8_3'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	1083						nucleus (GO:0005634)|Z disc (GO:0030018)		p.A3540A(1)|p.A700A(1)		autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GCTCCTCAGCGCACGGTCCCT	0.667																																					p.A3540A		Atlas-SNP	.											.	IGFN1	220	.	2	Substitution - coding silent(2)	lung(2)	c.G10620T						.						79	63	68					1																	201195085		2203	4300	6503	SO:0001819	synonymous_variant	91156	exon22			CTCAGCGCACGGT	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.10620G>T	chr1.hg19:g.201195085G>T		146.0	0.0		148.0	37.0	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	hg19	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	G	0.054	-1.240670	0.01493	.	.	ENSG00000163395	ENST00000412892	T	0.55588	0.51	5.0	-10.0	0.00425	.	1.450430	0.03910	N	0.281704	T	0.19765	0.0475	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.08493	-1.0719	7	0.05351	T	0.99	.	6.5254	0.22299	0.084:0.3982:0.3879:0.1299	.	.	.	.	S	958	ENSP00000387975:A958S	ENSP00000387975:A958S	A	+	1	0	IGFN1	199461708	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.499000	0.02285	-4.425000	0.00050	-2.516000	0.00186	GCA	.	.		0.667	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		T	201195085	G	T	201195085	2	4	1	1	0	0	0	0	0	0	0	1	7599	1074	38	1		1	IGFN1	1	201195085	Silent	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	25236474	201195085	48055536	14	14										
RYR2	6262	hgsc.bcm.edu	37	chr1	237754162	237754162	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	atgatgctgattctgactttGaggttctgatgaagacagct	11	6	2	7			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:237754162G>A	ENST00000366574.2	+	31	4347	c.4030G>A	c.(4030-4032)Gag>Aag	p.E1344K	RYR2_ENST00000360064.6_Missense_Mutation_p.E1342K|RYR2_ENST00000542537.1_Missense_Mutation_p.E1328K	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1344	4 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTCTGACTTTGAGGTTCTGAT	0.493																																					p.E1344K		Atlas-SNP	.											.	RYR2	1273	.	0			c.G4030A						.						83	80	81					1																	237754162		1927	4142	6069	SO:0001583	missense	6262	exon31			GACTTTGAGGTTC	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.4030G>A	chr1.hg19:g.237754162G>A	ENSP00000355533:p.Glu1344Lys	143.0	0.0		184.0	24.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	g	24.2	4.499794	0.85176	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.97186	-4.28;-4.25;-4.27	5.87	5.87	0.94306	B30.2/SPRY domain (1);	0.000000	0.64402	D	0.000016	D	0.98046	0.9356	L	0.59436	1.845	0.80722	D	1	D	0.63880	0.993	D	0.72625	0.978	D	0.97650	1.0154	10	0.46703	T	0.11	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	1344	Q92736	RYR2_HUMAN	K	1344;1342;1328	ENSP00000355533:E1344K;ENSP00000353174:E1342K;ENSP00000443798:E1328K	ENSP00000353174:E1342K	E	+	1	0	RYR2	235820785	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.534000	0.98061	2.941000	0.99782	0.655000	0.94253	GAG	.	.		0.493	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237754162	G	A	237754162	3	1	1	1	0	0	0	0	1	0	0	0	13784	1291	45	3	4152	3	RYR2	1	237754162	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	36559077	237754162	11496459	15	15										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370837	240370837	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tgcagggtacagaaatgctgCcaccccctccccctcctctt	7	18	1	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:240370837C>T	ENST00000319653.9	+	5	2955	c.2725C>T	c.(2725-2727)Cca>Tca	p.P909S		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	909	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AGAAATGCTGCCACCCCCTCC	0.662																																					p.P909S		Atlas-SNP	.											FMN2,right_upper_lobe,carcinoma,0,1	FMN2	451	.	0			c.C2725T						.						49	52	51					1																	240370837		2203	4299	6502	SO:0001583	missense	56776	exon5			ATGCTGCCACCCC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2725C>T	chr1.hg19:g.240370837C>T	ENSP00000318884:p.Pro909Ser	141.0	0.0		136.0	22.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	C	8.718	0.913558	0.17907	.	.	ENSG00000155816	ENST00000319653	T	0.25579	1.79	4.05	3.13	0.36017	Actin-binding FH2/DRF autoregulatory (1);	0.221828	0.31246	N	0.007990	T	0.17534	0.0421	L	0.43152	1.355	0.80722	D	1	B	0.27498	0.18	B	0.23150	0.044	T	0.04752	-1.0929	9	.	.	.	.	6.9284	0.24428	0.0:0.7473:0.0:0.2527	.	909	Q9NZ56	FMN2_HUMAN	S	909	ENSP00000318884:P909S	.	P	+	1	0	FMN2	238437460	0.007000	0.16637	0.874000	0.34290	0.429000	0.31625	1.218000	0.32467	2.256000	0.74724	0.484000	0.47621	CCA	.	.		0.662	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240370837	C	T	240370837	3	4	1	1	0	0	0	0	1	0	0	0	5958	739	26	3	2743	3	FMN2	1	240370837	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	2616675	240370837	8879784	16	16										
SDCCAG8	10806	hgsc.bcm.edu	37	chr1	243589807	243589807	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ttacagagaagaaatgaagaAttggaggaacagtgtgtcca	12	4	0	4			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:243589807A>C	ENST00000366541.3	+	16	2050	c.1932A>C	c.(1930-1932)gaA>gaC	p.E644D	SDCCAG8_ENST00000355875.4_Missense_Mutation_p.E601D|SDCCAG8_ENST00000343783.6_Missense_Mutation_p.E499D	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	644	Gln-rich.|Mediates interaction with OFD1.|Sufficient for homodimerization. {ECO:0000250}.				establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		GAAATGAAGAATTGGAGGAAC	0.373																																					p.E644D		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.A1932C						.						141	125	130					1																	243589807		2203	4300	6503	SO:0001583	missense	10806	exon16			TGAAGAATTGGAG	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.1932A>C	chr1.hg19:g.243589807A>C	ENSP00000355499:p.Glu644Asp	614.0	1.0		871.0	156.0	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	hg19	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.479405	0.44044	.	.	ENSG00000054282	ENST00000355875;ENST00000366541;ENST00000343783;ENST00000435549	T;T;T;T	0.53423	0.9;0.85;0.87;0.62	6.17	-0.274	0.12910	.	0.386686	0.28538	N	0.014994	T	0.27278	0.0669	L	0.29908	0.895	0.36156	D	0.847776	B;B	0.29115	0.096;0.233	B;B	0.26202	0.039;0.067	T	0.11817	-1.0572	10	0.20519	T	0.43	-9.2946	6.4011	0.21638	0.6307:0.1177:0.2517:0.0	.	601;644	E9PFS7;Q86SQ7	.;SDCG8_HUMAN	D	601;644;499;345	ENSP00000348137:E601D;ENSP00000355499:E644D;ENSP00000341260:E499D;ENSP00000410200:E345D	ENSP00000341260:E499D	E	+	3	2	SDCCAG8	241656430	0.997000	0.39634	0.579000	0.28588	0.213000	0.24496	1.070000	0.30653	-0.012000	0.14223	-0.250000	0.11733	GAA	.	.		0.373	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		C	243589807	A	C	243589807	3	2	1	1	0	0	0	0	1	0	0	0	13974	98	4	5	1994	5	SDCCAG8	1	243589807	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	3218970	243589807	5660814	17	17										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245775173	245775173	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	atgccgccattgcctcccgcAggagccaccaacaggactgt	10	16	0	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr1:245775173A>G	ENST00000407071.2	+	9	2433	c.1993A>G	c.(1993-1995)Agg>Ggg	p.R665G	KIF26B_ENST00000366518.4_Missense_Mutation_p.R284G|RP11-522M21.2_ENST00000418402.1_RNA	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	665	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TGCCTCCCGCAGGAGCCACCA	0.592																																					p.R665G		Atlas-SNP	.											.	KIF26B	343	.	0			c.A1993G						.						45	52	50					1																	245775173		2025	4174	6199	SO:0001583	missense	55083	exon9			TCCCGCAGGAGCC	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.1993A>G	chr1.hg19:g.245775173A>G	ENSP00000385545:p.Arg665Gly	102.0	0.0		134.0	22.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	A	13.63	2.294550	0.40594	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.75704	-0.96;-0.96	5.12	3.18	0.36537	Kinesin, motor domain (4);	.	.	.	.	T	0.77110	0.4082	L	0.49699	1.58	0.37717	D	0.924762	P;D	0.53619	0.813;0.961	P;P	0.55713	0.782;0.687	T	0.76756	-0.2842	9	0.35671	T	0.21	.	12.8117	0.57643	0.4486:0.5514:0.0:0.0	.	284;665	B7WPD9;Q2KJY2	.;KI26B_HUMAN	G	665;284;281	ENSP00000385545:R665G;ENSP00000355475:R284G	ENSP00000355475:R284G	R	+	1	2	KIF26B	243841796	0.291000	0.24352	0.548000	0.28192	0.989000	0.77384	0.863000	0.27913	0.506000	0.28125	-0.213000	0.12676	AGG	.	.		0.592	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		G	245775173	A	G	245775173	3	3	1	1	0	0	0	0	1	0	0	0	8304	179	7	2	2027	2	KIF26B	1	245775173	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	2185366	245775173	3475448	18	18										
TPO	7173	hgsc.bcm.edu	37	chr2	1481106	1481106	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ctccgcgtccacgcgcgcctCcgggactccggccgcgccta	12	21	0	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:1481106C>T	ENST00000345913.4	+	8	1159	c.1068C>T	c.(1066-1068)ctC>ctT	p.L356L	TPO_ENST00000346956.3_Silent_p.L356L|TPO_ENST00000497517.2_Intron|TPO_ENST00000349624.3_Intron|TPO_ENST00000329066.4_Silent_p.L356L|TPO_ENST00000382201.3_Silent_p.L356L|TPO_ENST00000382198.1_Intron|TPO_ENST00000337415.3_Silent_p.L356L	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	356					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	ACGCGCGCCTCCGGGACTCCG	0.751																																					p.L356L		Atlas-SNP	.											.	TPO	224	.	0			c.C1068T						.						6	6	6					2																	1481106		2099	4130	6229	SO:0001819	synonymous_variant	7173	exon8			GCGCCTCCGGGAC		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.1068C>T	chr2.hg19:g.1481106C>T		983.0	0.0		957.0	221.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	hg19	CCDS1643.1																																																																																			.	.		0.751	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1481106	C	T	1481106	2	4	1	1	0	0	0	0	0	0	0	1	16425	842	30	3		3	TPO	2	1481106	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10		1481106	241718267	19	19										
SOS1	6654	hgsc.bcm.edu	37	chr2	39250230	39250230	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tacacgtgtaagagttccttCcattataaattcattacaac	4	9	1	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:39250230C>T	ENST00000426016.1	-	11	1425	c.1339G>A	c.(1339-1341)Gaa>Aaa	p.E447K	SOS1_ENST00000472480.1_5'UTR|SOS1_ENST00000395038.2_Missense_Mutation_p.E447K|SOS1_ENST00000402219.2_Missense_Mutation_p.E447K			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	447	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				AGAGTTCCTTCCATTATAAAT	0.388									Noonan syndrome																												p.E447K		Atlas-SNP	.											.	SOS1	134	.	0			c.G1339A						.						121	113	116					2																	39250230		2203	4300	6503	SO:0001583	missense	6654	exon10	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TTCCTTCCATTAT	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1339G>A	chr2.hg19:g.39250230C>T	ENSP00000387784:p.Glu447Lys	105.0	0.0		112.0	16.0	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	hg19	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.694414	0.88830	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	D;D;D	0.89810	-2.57;-2.57;-2.57	5.52	5.52	0.82312	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.92008	0.7468	M	0.84082	2.675	0.80722	D	1	B;P	0.35107	0.08;0.484	B;B	0.40677	0.19;0.337	D	0.92194	0.5762	10	0.87932	D	0	.	19.8	0.96502	0.0:1.0:0.0:0.0	.	179;447	F5GX06;Q07889	.;SOS1_HUMAN	K	447;447;179;447;447	ENSP00000387784:E447K;ENSP00000384675:E447K;ENSP00000378479:E447K	ENSP00000263879:E447K	E	-	1	0	SOS1	39103734	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.666000	0.83877	2.753000	0.94483	0.557000	0.71058	GAA	.	.		0.388	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		T	39250230	C	T	39250230	3	4	1	1	0	0	0	0	1	0	0	0	14951	864	30	3	2718	3	SOS1	2	39250230	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	37769124	39250230	203949143	20	20										
EPB41L5	57669	hgsc.bcm.edu	37	chr2	120922447	120922447	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ttggatgccttgcttgcatcTctaactgagaatctaattga	8	8	2	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:120922447T>C	ENST00000263713.5	+	22	2137	c.1923T>C	c.(1921-1923)tcT>tcC	p.S641S	EPB41L5_ENST00000488691.1_3'UTR|EPB41L5_ENST00000452780.1_Silent_p.S641S|EPB41L5_ENST00000443902.2_Silent_p.S641S	NM_020909.3	NP_065960.2	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	641					actomyosin structure organization (GO:0031032)|apical constriction (GO:0003383)|axial mesoderm morphogenesis (GO:0048319)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ectoderm development (GO:0007398)|embryonic foregut morphogenesis (GO:0048617)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|in utero embryonic development (GO:0001701)|left/right axis specification (GO:0070986)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of protein binding (GO:0032091)|neural plate morphogenesis (GO:0001839)|paraxial mesoderm development (GO:0048339)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein binding (GO:0032092)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of establishment of protein localization (GO:0070201)|somite rostral/caudal axis specification (GO:0032525)|substrate-dependent cell migration, cell attachment to substrate (GO:0006931)|unidimensional cell growth (GO:0009826)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(12)|ovary(1)	26						TGCTTGCATCTCTAACTGAGA	0.348																																					p.S641S		Atlas-SNP	.											.	EPB41L5	98	.	0			c.T1923C						.						120	114	116					2																	120922447		2203	4300	6503	SO:0001819	synonymous_variant	57669	exon22			TGCATCTCTAACT	AK023019	CCDS2130.1, CCDS54392.1, CCDS54393.1	2q14.2	2009-07-28			ENSG00000115109	ENSG00000115109			19819	protein-coding gene	gene with protein product		611730					Standard	NM_001184937		Approved	KIAA1548, FLJ12957, BE37, YMO1	uc002tmg.3	Q9HCM4	OTTHUMG00000131433	ENST00000263713.5:c.1923T>C	chr2.hg19:g.120922447T>C		272.0	0.0		284.0	78.0	NM_020909	Q7Z5S1|Q8IZ12|Q9H975	Silent	SNP	ENST00000263713.5	hg19	CCDS2130.1																																																																																			.	.		0.348	EPB41L5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254230.2	NM_020909		C	120922447	T	C	120922447	2	2	1	1	0	0	0	0	0	0	0	1	5159	1538	54	2		2	EPB41L5	2	120922447	Silent	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	81672217	120922447	122276926	21	21										
SCRN3	79634	hgsc.bcm.edu	37	chr2	175287757	175287757	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ttgcattcacttctttacagGgactcctgatcctgagaggt	9	10	2	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:175287757G>A	ENST00000272732.6	+	6	981	c.899G>A	c.(898-900)gGg>gAg	p.G300E	SCRN3_ENST00000409673.3_Missense_Mutation_p.G293E|SCRN3_ENST00000548921.1_3'UTR	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	300							dipeptidase activity (GO:0016805)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			TTCTTTACAGGGACTCCTGAT	0.433																																					p.G300E		Atlas-SNP	.											.	SCRN3	76	.	0			c.G899A						.						87	86	86					2																	175287757		2203	4300	6503	SO:0001583	missense	79634	exon6			TTACAGGGACTCC	AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.899G>A	chr2.hg19:g.175287757G>A	ENSP00000272732:p.Gly300Glu	217.0	0.0		211.0	49.0	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Missense_Mutation	SNP	ENST00000272732.6	hg19	CCDS2258.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.405641	0.42715	.	.	ENSG00000144306	ENST00000409673;ENST00000272732	T;T	0.11821	2.74;2.74	5.16	3.31	0.37934	.	0.224693	0.45361	D	0.000364	T	0.14614	0.0353	L	0.50333	1.59	0.43133	D	0.994879	B;B	0.34329	0.449;0.256	B;B	0.30495	0.116;0.055	T	0.02821	-1.1106	10	0.52906	T	0.07	-4.5348	15.4901	0.75600	0.0:0.2617:0.7383:0.0	.	293;300	B4DI11;Q0VDG4	.;SCRN3_HUMAN	E	293;300	ENSP00000387142:G293E;ENSP00000272732:G300E	ENSP00000272732:G300E	G	+	2	0	SCRN3	174996003	1.000000	0.71417	0.987000	0.45799	0.975000	0.68041	3.346000	0.52190	0.537000	0.28751	0.561000	0.74099	GGG	.	.		0.433	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583		A	175287757	G	A	175287757	3	1	1	1	0	0	0	0	1	0	0	0	13955	1232	43	3	917	3	SCRN3	2	175287757	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	54365310	175287757	67911616	22	22										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178936399	178936399	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tgcatgcacatcaaagaattTggagaccaaggtcttcttgc	9	9	3	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:178936399T>A	ENST00000286063.6	-	1	1083	c.766A>T	c.(766-768)Aaa>Taa	p.K256*	PDE11A_ENST00000358450.4_Intron	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	256	GAF 1.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	TCAAAGAATTTGGAGACCAAG	0.517									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.K256X		Atlas-SNP	.											.	PDE11A	283	.	0			c.A766T						.						70	67	68					2																	178936399		2203	4300	6503	SO:0001587	stop_gained	50940	exon1	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AGAATTTGGAGAC	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.766A>T	chr2.hg19:g.178936399T>A	ENSP00000286063:p.Lys256*	56.0	0.0		66.0	24.0	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Nonsense_Mutation	SNP	ENST00000286063.6	hg19	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	T	42	9.294755	0.99128	.	.	ENSG00000128655	ENST00000286063	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8099	0.69985	0.0:0.0:0.0:1.0	.	.	.	.	X	256	.	ENSP00000286063:K256X	K	-	1	0	PDE11A	178644645	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.093000	0.63338	0.533000	0.62120	AAA	.	.		0.517	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			A	178936399	T	A	178936399	4	1	1	1	0	0	0	0	0	1	0	0	11640	1821	63	4	2115	4	PDE11A	2	178936399	Nonsense_Mutation	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	3648642	178936399	64262974	23	23										
PRKRA	8575	hgsc.bcm.edu	37	chr2	179315144	179315144	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	atcatcttccccaaactgcaAaaaccacaaaaaggtgtgct	5	12	2	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:179315144A>G	ENST00000325748.4	-	2	266				DFNB59_ENST00000375129.4_5'Flank|DFNB59_ENST00000409117.3_5'Flank|PRKRA_ENST00000487082.1_Intron|PRKRA_ENST00000432031.2_Silent_p.F9F|PRKRA_ENST00000438687.3_Intron|PRKRA_ENST00000470200.1_Intron	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator						cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CCAAACTGCAAAAACCACAAA	0.478																																					p.F9F	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											.	PRKRA	56	.	0			c.T27C						.						143	151	148					2																	179315144		2203	4300	6503	SO:0001627	intron_variant	8575	exon1			ACTGCAAAAACCA	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"protein activator of the interferon-induced protein kinase"	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.66-6T>C	chr2.hg19:g.179315144A>G		151.0	0.0		151.0	9.0	NM_001139517	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Silent	SNP	ENST00000325748.4	hg19	CCDS2279.1																																																																																			.	.		0.478	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690		G	179315144	A	G	179315144	1	3	1	0	1	0	0	0	0	0	0	0	12536	11	1	2		2	PRKRA	2	179315144	Intron	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	378745	179315144	63884229	24	24										
TTN	7273	hgsc.bcm.edu	37	chr2	179479398	179479398	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ggttcaggttttccggttacGgtggcaggaagttcaatctt	13	7	3	0	rs547682223		TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:179479398G>A	ENST00000591111.1	-	211	44144	c.43920C>T	c.(43918-43920)acC>acT	p.T14640T	TTN_ENST00000342992.6_Silent_p.T13713T|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Silent_p.T7341T|TTN_ENST00000460472.2_Silent_p.T7216T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.T7408T|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Silent_p.T16281T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14640	Ig-like 96.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCCGGTTACGGTGGCAGGAA	0.423													g|||	1	0.000199681	0	0	5008	,	,		19341	0.001		0	False		,,,				2504	0				p.T16281T		Atlas-SNP	.											.	TTN	18412	.	0			c.C48843T						.						90	81	84					2																	179479398		1865	4103	5968	SO:0001819	synonymous_variant	7273	exon261			GGTTACGGTGGCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.43920C>T	chr2.hg19:g.179479398G>A		133.0	0.0		135.0	43.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179479398	G	A	179479398	2	1	1	1	0	0	0	0	0	0	0	1	16750	1103	39	1		1	TTN	2	179479398	Silent	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	164254	179479398	63719975	25	25										
TTN	7273	hgsc.bcm.edu	37	chr2	179574397	179574397	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ctgctttcctgacttgcagcActaacgtgttgttcttgaat	8	10	1	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:179574397A>T	ENST00000591111.1	-	97	27922	c.27698T>A	c.(27697-27699)gTg>gAg	p.V9233E	TTN_ENST00000342992.6_Missense_Mutation_p.V8306E|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V9550E|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13356	Ig-like 75.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GACTTGCAGCACTAACGTGTT	0.438																																					p.V9550E		Atlas-SNP	.											.	TTN	18412	.	0			c.T28649A						.						190	192	191					2																	179574397		2025	4179	6204	SO:0001583	missense	7273	exon99			TGCAGCACTAACG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.27698T>A	chr2.hg19:g.179574397A>T	ENSP00000465570:p.Val9233Glu	121.0	0.0		131.0	28.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.99	1.508527	0.27036	.	.	ENSG00000155657	ENST00000342992	T	0.65549	-0.16	5.91	5.91	0.95273	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.62780	0.2456	L	0.56124	1.755	0.80722	D	1	B	0.21381	0.055	B	0.29440	0.102	T	0.61893	-0.6969	9	0.87932	D	0	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	9233	Q8WZ42	TITIN_HUMAN	E	8306	ENSP00000343764:V8306E	ENSP00000343764:V8306E	V	-	2	0	TTN	179282642	0.993000	0.37304	0.953000	0.39169	0.103000	0.19146	4.213000	0.58520	2.254000	0.74563	0.533000	0.62120	GTG	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179574397	A	T	179574397	3	4	1	1	0	0	0	0	1	0	0	0	16750	159	6	4	75936	4	TTN	2	179574397	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	94999	179574397	63624976	26	26										
PDE1A	5136	hgsc.bcm.edu	37	chr2	183129032	183129032	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gaaggttaaaacttaccttgTttcatcgatataaactgctt	6	7	1	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:183129032T>C	ENST00000410103.1	-	3	294	c.211A>G	c.(211-213)Aca>Gca	p.T71A	PDE1A_ENST00000435564.1_Missense_Mutation_p.T71A|PDE1A_ENST00000358139.2_Missense_Mutation_p.T71A|PDE1A_ENST00000409365.1_Missense_Mutation_p.T55A|PDE1A_ENST00000351439.5_Missense_Mutation_p.T55A|PDE1A_ENST00000456212.1_Missense_Mutation_p.T71A|PDE1A_ENST00000331935.6_Missense_Mutation_p.T71A|PDE1A_ENST00000536095.1_5'UTR	NM_001003683.2	NP_001003683.1	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	71					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	ACTTACCTTGTTTCATCGATA	0.388																																					p.T75A		Atlas-SNP	.											.	PDE1A	184	.	0			c.A223G						.						105	100	102					2																	183129032		2202	4300	6502	SO:0001583	missense	5136	exon3			ACCTTGTTTCATC		CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	3.1.4.17	"Phosphodiesterases"	8774	protein-coding gene	gene with protein product		171890				8557689, 11342109	Standard	NM_005019		Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000410103.1:c.211A>G	chr2.hg19:g.183129032T>C	ENSP00000387037:p.Thr71Ala	219.0	0.0		262.0	36.0	NM_001258312	D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	Missense_Mutation	SNP	ENST00000410103.1	hg19	CCDS33344.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336046	0.60963	.	.	ENSG00000115252	ENST00000435564;ENST00000409365;ENST00000331935;ENST00000351439;ENST00000410103;ENST00000358139;ENST00000456212	T;T;T;T;T;T;T	0.71103	-0.54;-0.51;-0.54;-0.51;-0.53;-0.53;-0.53	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.66713	0.2817	L	0.50333	1.59	0.80722	D	1	B;B;B	0.25521	0.052;0.128;0.086	B;B;B	0.30782	0.023;0.12;0.075	T	0.61917	-0.6964	10	0.22109	T	0.4	.	15.1461	0.72653	0.0:0.0:0.0:1.0	.	71;55;71	P54750;P54750-2;P54750-4	PDE1A_HUMAN;.;.	A	71;55;71;55;71;71;71	ENSP00000410309:T71A;ENSP00000386767:T55A;ENSP00000331574:T71A;ENSP00000309269:T55A;ENSP00000387037:T71A;ENSP00000350858:T71A;ENSP00000408874:T71A	ENSP00000331574:T71A	T	-	1	0	PDE1A	182837277	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.372000	0.79612	2.308000	0.77769	0.533000	0.62120	ACA	.	.		0.388	PDE1A-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334356.1			C	183129032	T	C	183129032	3	2	1	1	0	0	0	0	1	0	0	0	11642	1725	60	2	1526	2	PDE1A	2	183129032	Missense_Mutation	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	3554635	183129032	60070341	27	27										
STAT1	6772	hgsc.bcm.edu	37	chr2	191859857	191859857	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tttgttttttgtgatagggtCatgttcgtaggtgtatttct	11	3	2	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:191859857C>G	ENST00000361099.3	-	10	1261	c.874G>C	c.(874-876)Gac>Cac	p.D292H	STAT1_ENST00000540176.1_3'UTR|STAT1_ENST00000409465.1_Missense_Mutation_p.D292H|STAT1_ENST00000392323.2_Missense_Mutation_p.D294H|STAT1_ENST00000392322.3_Missense_Mutation_p.D292H	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	292					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			GTGATAGGGTCATGTTCGTAG	0.443																																					p.D292H		Atlas-SNP	.											.	STAT1	93	.	0			c.G874C						.						158	137	144					2																	191859857		2203	4300	6503	SO:0001583	missense	6772	exon10			TAGGGTCATGTTC		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"SH2 domain containing"	11362	protein-coding gene	gene with protein product	"transcription factor ISGF-3 components p91/p84"	600555	"signal transducer and activator of transcription 1, 91kD"			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.874G>C	chr2.hg19:g.191859857C>G	ENSP00000354394:p.Asp292His	68.0	0.0		65.0	21.0	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	hg19	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.661128	0.88154	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	5.66	5.66	0.87406	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.000000	0.85682	D	0.000000	D	0.84257	0.5432	M	0.85462	2.755	0.80722	D	1	D;D	0.76494	0.999;0.981	D;P	0.71870	0.975;0.891	D	0.86021	0.1507	10	0.72032	D	0.01	-25.2597	19.7589	0.96306	0.0:1.0:0.0:0.0	.	292;292	P42224-2;P42224	.;STAT1_HUMAN	H	292;292;292;294	ENSP00000354394:D292H;ENSP00000386244:D292H;ENSP00000376136:D292H;ENSP00000376137:D294H	ENSP00000354394:D292H	D	-	1	0	STAT1	191568102	1.000000	0.71417	0.952000	0.39060	0.722000	0.41435	7.696000	0.84270	2.662000	0.90505	0.557000	0.71058	GAC	.	.		0.443	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		G	191859857	C	G	191859857	3	3	1	1	0	0	0	0	1	0	0	0	15279	826	29	4	1446	4	STAT1	2	191859857	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	8730825	191859857	51339516	28	28										
ANKZF1	55139	hgsc.bcm.edu	37	chr2	220099637	220099637	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tggatctttgtgagtctgaaGtattgcccaagcggaggagg	15	6	2	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:220099637G>T	ENST00000323348.5	+	10	1468	c.1294G>T	c.(1294-1296)Gta>Tta	p.V432L	ANKZF1_ENST00000409849.1_Missense_Mutation_p.V222L|ANKZF1_ENST00000410034.3_Missense_Mutation_p.V432L|GLB1L_ENST00000497855.1_5'Flank	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	432						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGAGTCTGAAGTATTGCCCAA	0.507																																					p.V432L		Atlas-SNP	.											.	ANKZF1	45	.	0			c.G1294T						.						61	69	66					2																	220099637		2138	4259	6397	SO:0001583	missense	55139	exon10			TCTGAAGTATTGC	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"Zinc fingers, C2H2-type", "Ankyrin repeat domain containing"	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.1294G>T	chr2.hg19:g.220099637G>T	ENSP00000321617:p.Val432Leu	129.0	0.0		150.0	35.0	NM_001042410	Q9NVZ4	Missense_Mutation	SNP	ENST00000323348.5	hg19	CCDS42821.1	.	.	.	.	.	.	.	.	.	.	G	8.035	0.762632	0.15914	.	.	ENSG00000163516	ENST00000323348;ENST00000409849;ENST00000410034	T;T;T	0.27104	1.69;1.89;1.69	5.41	2.37	0.29283	.	0.114147	0.64402	D	0.000016	T	0.21631	0.0521	L	0.53249	1.67	0.40514	D	0.98076	B	0.14012	0.009	B	0.12156	0.007	T	0.05971	-1.0853	10	0.32370	T	0.25	-5.8995	8.1423	0.31091	0.0792:0.0:0.6294:0.2915	.	432	Q9H8Y5	ANKZ1_HUMAN	L	432;222;432	ENSP00000321617:V432L;ENSP00000386815:V222L;ENSP00000386337:V432L	ENSP00000321617:V432L	V	+	1	0	ANKZF1	219807881	0.984000	0.35163	0.708000	0.30435	0.601000	0.36947	2.031000	0.41117	0.825000	0.34637	0.591000	0.81541	GTA	.	.		0.507	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089		T	220099637	G	T	220099637	3	4	1	1	0	0	0	0	1	0	0	0	693	1029	36	3	1328	3	ANKZF1	2	220099637	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	28239780	220099637	23099736	29	29										
ANO7	50636	hgsc.bcm.edu	37	chr2	242135166	242135166	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	cctgaagctagacaggcagcAggacagtgccgcccgggaca	14	13	0	2	rs199644599		TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr2:242135166A>G	ENST00000274979.8	+	4	480	c.377A>G	c.(376-378)cAg>cGg	p.Q126R	ANO7_ENST00000402530.3_Missense_Mutation_p.Q125R|ANO7_ENST00000402430.3_Missense_Mutation_p.Q125R	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	126					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						GACAGGCAGCAGGACAGTGCC	0.607																																					p.Q126R		Atlas-SNP	.											.	ANO7	136	.	0			c.A377G						.	A	ARG/GLN,ARG/GLN	0,4406		0,0,2203	88	77	81		377,374	-1.9	0	2		81	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	ANO7	NM_001001891.3,NM_001001666.3	43,43	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign	126/934,125/180	242135166	1,13005	2203	4300	6503	SO:0001583	missense	50636	exon4			GGCAGCAGGACAG	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	31677	protein-coding gene	gene with protein product		605096	"transmembrane protein 16G"	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.377A>G	chr2.hg19:g.242135166A>G	ENSP00000274979:p.Gln126Arg	115.0	0.0		99.0	29.0	NM_001001891	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	hg19	CCDS33423.1	.	.	.	.	.	.	.	.	.	.	A	8.261	0.811176	0.16537	0.0	1.16E-4	ENSG00000146205	ENST00000274979;ENST00000402530;ENST00000402430	T;T;T	0.70164	-0.25;0.89;-0.46	2.98	-1.91	0.07641	.	.	.	.	.	T	0.42108	0.1188	L	0.29908	0.895	0.09310	N	1	B;B	0.27656	0.001;0.184	B;B	0.19666	0.001;0.026	T	0.19451	-1.0305	9	0.17369	T	0.5	.	1.2421	0.01965	0.5301:0.1729:0.1123:0.1847	.	126;125	Q6IWH7;Q6IWH7-2	ANO7_HUMAN;.	R	126;125;125	ENSP00000274979:Q126R;ENSP00000383985:Q125R;ENSP00000385418:Q125R	ENSP00000274979:Q126R	Q	+	2	0	ANO7	241783839	0.001000	0.12720	0.000000	0.03702	0.017000	0.09413	0.310000	0.19356	-0.499000	0.06623	0.383000	0.25322	CAG	.	.		0.607	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891		G	242135166	A	G	242135166	3	3	1	1	0	0	0	0	1	0	0	0	702	188	7	2	391	2	ANO7	2	242135166	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	22035529	242135166	1064207	30	30										
SLC6A6	6533	hgsc.bcm.edu	37	chr3	14487226	14487226	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	cccattctgctctctgcaggTgcgtttctcataccgtattt	7	13	3	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr3:14487226T>C	ENST00000454876.2	+	4	560	c.231T>C	c.(229-231)ggT>ggC	p.G77G	SLC6A6_ENST00000360861.3_Splice_Site_p.G77G|SLC6A6_ENST00000484191.1_3'UTR|SLC6A6_ENST00000416216.2_Splice_Site_p.G77G			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	77					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|taurine transport (GO:0015734)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|taurine binding (GO:0030977)|taurine:sodium symporter activity (GO:0005369)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)	28						TCTCTGCAGGTGCGTTTCTCA	0.542																																					p.G77G		Atlas-SNP	.											.	SLC6A6	58	.	0			c.T231C						.						170	152	158					3																	14487226		2203	4300	6503	SO:0001630	splice_region_variant	6533	exon4			TGCAGGTGCGTTT		CCDS33705.1, CCDS46765.1	3p25.1	2013-07-19	2013-07-19		ENSG00000131389	ENSG00000131389		"Solute carriers"	11052	protein-coding gene	gene with protein product	"taurine transporter"	186854	"solute carrier family 6 (neurotransmitter transporter, taurine), member 6"			8010975, 8382624	Standard	XM_006713307		Approved	TAUT	uc010heg.4	P31641	OTTHUMG00000155525	ENST00000454876.2:c.230-1T>C	chr3.hg19:g.14487226T>C		96.0	0.0		73.0	20.0	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Silent	SNP	ENST00000454876.2	hg19	CCDS33705.1																																																																																			.	.		0.542	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043	Silent	C	14487226	T	C	14487226	5	2	1	1	0	0	0	0	0	0	1	0	14703	1710	59	2	237	2	SLC6A6	3	14487226	Splice_Site	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10		14487226	183535204	31	31										
BSN	8927	hgsc.bcm.edu	37	chr3	49700756	49700756	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ccatcatgcctctgacagcaAgaagggctcccggcaagccc	10	16	2	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr3:49700756A>G	ENST00000296452.4	+	7	11279	c.11165A>G	c.(11164-11166)aAg>aGg	p.K3722R		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3722					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		TCTGACAGCAAGAAGGGCTCC	0.632																																					p.K3722R		Atlas-SNP	.											.	BSN	272	.	0			c.A11165G						.						82	82	82					3																	49700756		2203	4300	6503	SO:0001583	missense	8927	exon7			ACAGCAAGAAGGG	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.11165A>G	chr3.hg19:g.49700756A>G	ENSP00000296452:p.Lys3722Arg	80.0	0.0		77.0	15.0	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	hg19	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.309986	0.40895	.	.	ENSG00000164061	ENST00000296452	T	0.18016	2.24	4.99	4.99	0.66335	.	0.396353	0.25601	N	0.029541	T	0.12347	0.0300	L	0.40543	1.245	0.33399	D	0.577052	P	0.44734	0.842	B	0.35114	0.196	T	0.22521	-1.0214	10	0.25751	T	0.34	-19.339	11.2828	0.49206	0.8476:0.1524:0.0:0.0	.	3722	Q9UPA5	BSN_HUMAN	R	3722	ENSP00000296452:K3722R	ENSP00000296452:K3722R	K	+	2	0	BSN	49675760	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	1.919000	0.40015	1.861000	0.53984	0.260000	0.18958	AAG	.	.		0.632	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		G	49700756	A	G	49700756	3	3	1	1	0	0	0	0	1	0	0	0	1532	72	3	2	11191	2	BSN	3	49700756	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	35213530	49700756	148321674	32	32										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78706316	78706316	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tgctggctgccacttccacaCtgtatcggattccaggaaca	9	13	0	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr3:78706316C>T	ENST00000464233.1	-	18	2659	c.2546G>A	c.(2545-2547)aGt>aAt	p.S849N	ROBO1_ENST00000467549.1_Missense_Mutation_p.S813N|ROBO1_ENST00000495273.1_Missense_Mutation_p.S813N|ROBO1_ENST00000436010.2_Missense_Mutation_p.S810N	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	849	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		CACTTCCACACTGTATCGGAT	0.512																																					p.S849N		Atlas-SNP	.											.	ROBO1	833	.	0			c.G2546A						.						54	58	56					3																	78706316		1983	4173	6156	SO:0001583	missense	6091	exon18			TCCACACTGTATC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2546G>A	chr3.hg19:g.78706316C>T	ENSP00000420321:p.Ser849Asn	146.0	0.0		144.0	34.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.740716	0.69304	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	6.04	6.04	0.98038	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.109901	0.85682	D	0.000000	T	0.66396	0.2785	L	0.44542	1.39	0.54753	D	0.999987	P;D;D;P;P	0.67145	0.939;0.987;0.996;0.888;0.935	P;D;D;P;P	0.65573	0.503;0.926;0.936;0.777;0.669	T	0.59830	-0.7380	9	.	.	.	.	20.6396	0.99537	0.0:1.0:0.0:0.0	.	813;849;813;813;810	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	N	810;813;849;813;813;853	ENSP00000406043:S810N;ENSP00000420321:S849N;ENSP00000420637:S813N;ENSP00000417992:S813N	.	S	-	2	0	ROBO1	78789006	1.000000	0.71417	0.997000	0.53966	0.228000	0.25075	4.836000	0.62789	2.881000	0.98747	0.650000	0.86243	AGT	.	.		0.512	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78706316	C	T	78706316	3	4	1	1	0	0	0	0	1	0	0	0	13528	565	20	3	2465	3	ROBO1	3	78706316	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	29005560	78706316	119316114	33	33										
ADCY5	111	hgsc.bcm.edu	37	chr3	123046605	123046605	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	agccttggtgatgtggatgcGtctacaggggggcagggatc	18	7	1	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr3:123046605G>A	ENST00000462833.1	-	7	3019	c.1807C>T	c.(1807-1809)Cgc>Tgc	p.R603C	ADCY5_ENST00000491190.1_Splice_Site_p.R236C|ADCY5_ENST00000309879.5_Splice_Site_p.R253C	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	603					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		ATGTGGATGCGTCTACAGGGG	0.557																																					p.R603C		Atlas-SNP	.											.	ADCY5	169	.	0			c.C1807T						.						68	56	60					3																	123046605		2203	4300	6503	SO:0001630	splice_region_variant	111	exon7			GGATGCGTCTACA	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.1806-1C>T	chr3.hg19:g.123046605G>A		77.0	0.0		96.0	24.0	NM_183357	B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	hg19	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382739	0.82792	.	.	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879;ENST00000466617	D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54	5.52	4.63	0.57726	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.000000	0.64402	D	0.000001	D	0.90614	0.7057	M	0.86573	2.825	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.97110	0.89;1.0	D	0.91789	0.5442	10	0.56958	D	0.05	.	15.5175	0.75837	0.0:0.0:0.8606:0.1394	.	603;236	O95622;B3KWA8	ADCY5_HUMAN;.	C	603;236;253;162	ENSP00000419361:R603C;ENSP00000418537:R236C;ENSP00000308685:R253C;ENSP00000420082:R162C	ENSP00000308685:R253C	R	-	1	0	ADCY5	124529295	1.000000	0.71417	0.986000	0.45419	0.847000	0.48162	7.915000	0.87484	1.274000	0.44362	0.655000	0.94253	CGC	.	.		0.557	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048	Missense_Mutation	A	123046605	G	A	123046605	5	1	1	1	0	0	0	0	0	0	1	0	297	1159	40	1	2038	1	ADCY5	3	123046605	Splice_Site	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	44340289	123046605	74975825	34	34										
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6602390	6602390	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tttgcctcggtctacaacccGctggcctggacggtcaccac	10	16	2	0	rs376601093		TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr4:6602390G>A	ENST00000285599.3	+	10	1482	c.1446G>A	c.(1444-1446)ccG>ccA	p.P482P	MAN2B2_ENST00000504248.1_Silent_p.P431P	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	482					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						TCTACAACCCGCTGGCCTGGA	0.592																																					p.P482P		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G1446A						.						149	117	128					4																	6602390		2203	4300	6503	SO:0001819	synonymous_variant	23324	exon10			CAACCCGCTGGCC	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"core-specific lysosomal alpha-1,6-Mannosidase"					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1446G>A	chr4.hg19:g.6602390G>A		103.0	0.0		76.0	4.0	NM_015274	Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	hg19	CCDS33951.1	.	.	.	.	.	.	.	.	.	.	g	1.930	-0.446246	0.04604	.	.	ENSG00000013288	ENST00000505907	.	.	.	4.67	-2.0	0.07433	.	.	.	.	.	T	0.38719	0.1051	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27434	-1.0074	4	.	.	.	-29.3766	1.041	0.01559	0.2933:0.2926:0.2471:0.167	.	.	.	.	H	481	.	.	R	+	2	0	MAN2B2	6653291	0.051000	0.20477	0.987000	0.45799	0.139000	0.21198	-1.276000	0.02815	-0.462000	0.06984	-2.005000	0.00442	CGC	.	.		0.592	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		A	6602390	G	A	6602390	2	1	1	1	0	0	0	0	0	0	0	1	9226	1074	38	1		1	MAN2B2	4	6602390	Silent	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10		6602390	184551886	35	35										
COX18	285521	hgsc.bcm.edu	37	chr4	73931079	73931079	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ttgaaagggtggcagttatcTcgcacatatagctctgaaat	10	7	2	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr4:73931079T>G	ENST00000295890.4	-	3	577	c.486A>C	c.(484-486)cgA>cgC	p.R162R	COX18_ENST00000507544.2_Silent_p.R162R	NM_173827.2	NP_776188.1	Q8N8Q8	COX18_HUMAN	COX18 cytochrome C oxidase assembly factor	162					protein insertion into mitochondrial membrane (GO:0051204)|protein transport (GO:0015031)|respiratory chain complex IV assembly (GO:0008535)	integral component of mitochondrial inner membrane (GO:0031305)	protein transporter activity (GO:0008565)			large_intestine(4)|lung(2)	6	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GGCAGTTATCTCGCACATATA	0.433																																					p.R162R		Atlas-SNP	.											.	COX18	20	.	0			c.A486C						.						122	115	118					4																	73931079		2203	4300	6503	SO:0001819	synonymous_variant	285521	exon3			GTTATCTCGCACA	AY957564	CCDS3554.1, CCDS75139.1	4q13.3	2013-06-12	2013-06-12		ENSG00000163626	ENSG00000163626		"Mitochondrial respiratory chain complex assembly factors"	26801	protein-coding gene	gene with protein product		610428	"COX18 cytochrome c oxidase assembly homolog (S. cerevisiae)", "cytochrome c oxidase assembly homolog 18 (yeast)"			16212937, 16911509	Standard	XM_005265679		Approved	FLJ38991	uc003hgm.1	Q8N8Q8	OTTHUMG00000129917	ENST00000295890.4:c.486A>C	chr4.hg19:g.73931079T>G		188.0	0.0		161.0	7.0	NM_173827	Q2PB66|Q2PB67|Q2PB68|Q49B97|Q6IPP9	Silent	SNP	ENST00000295890.4	hg19	CCDS3554.1																																																																																			.	.		0.433	COX18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252169.2	NM_173827		G	73931079	T	G	73931079	2	3	1	1	0	0	0	0	0	0	0	1	3769	1538	54	5		5	COX18	4	73931079	Silent	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	67328689	73931079	117223197	36	36										
ALB	213	hgsc.bcm.edu	37	chr4	74280813	74280813	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tcgtgctgctgctgagacttGccaagacatatgaaaccact	9	11	0	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr4:74280813G>T	ENST00000503124.1	+	7	877	c.670G>T	c.(670-672)Gcc>Tcc	p.A224S	ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Missense_Mutation_p.A259S|ALB_ENST00000295897.4_Missense_Mutation_p.A374S|ALB_ENST00000509063.1_Missense_Mutation_p.A374S|ALB_ENST00000415165.2_Missense_Mutation_p.A182S			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GCTGAGACTTGCCAAGACATA	0.388																																					p.A374S		Atlas-SNP	.											.	ALB	132	.	0			c.G1120T						.						146	143	144					4																	74280813		2203	4300	6503	SO:0001583	missense	213	exon9			AGACTTGCCAAGA	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.670G>T	chr4.hg19:g.74280813G>T	ENSP00000421027:p.Ala224Ser	131.0	0.0		137.0	38.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.49|19.49	3.838263|3.838263	0.71373|0.71373	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202|ENST00000511370	T;T;T;T;T|.	0.76709|.	-1.04;-1.04;-1.04;-1.04;-1.04|.	5.84|5.84	5.84|5.84	0.93424|0.93424	Serum albumin-like (1);Serum albumin, N-terminal (3);|.	0.138111|.	0.49916|.	D|.	0.000136|.	T|T	0.79046|0.79046	0.4380|0.4380	M|M	0.80982|0.80982	2.52|2.52	0.52099|0.52099	D|D	0.999941|0.999941	P;P;P;P;P|.	0.50528|.	0.936;0.673;0.723;0.535;0.535|.	D;P;P;P;P|.	0.67231|.	0.95;0.844;0.761;0.784;0.784|.	T|T	0.78785|0.78785	-0.2068|-0.2068	10|5	0.66056|.	D|.	0.02|.	-13.5493|-13.5493	18.6984|18.6984	0.91611|0.91611	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	259;182;224;374;374|.	B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768|.	.;.;.;.;ALBU_HUMAN|.	S|F	374;182;224;374;259;383|218	ENSP00000295897:A374S;ENSP00000401820:A182S;ENSP00000421027:A224S;ENSP00000422784:A374S;ENSP00000384695:A259S|.	ENSP00000295897:A374S|.	A|C	+|+	1|2	0|0	ALB|ALB	74499677|74499677	1.000000|1.000000	0.71417|0.71417	0.958000|0.958000	0.39756|0.39756	0.299000|0.299000	0.27559|0.27559	2.901000|2.901000	0.48695|0.48695	2.765000|2.765000	0.95021|0.95021	0.655000|0.655000	0.94253|0.94253	GCC|TGC	.	.		0.388	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		T	74280813	G	T	74280813	3	4	1	1	0	0	0	0	1	0	0	0	486	1319	46	3	1154	3	ALB	4	74280813	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	349734	74280813	116873463	37	37										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90816240	90816240	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ggaactctcagaagactatgCcttctgcttcagttcctcca	7	13	3	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr4:90816240C>T	ENST00000394980.1	+	2	437	c.118C>T	c.(118-120)Cct>Tct	p.P40S	MMRN1_ENST00000264790.2_Missense_Mutation_p.P40S|MMRN1_ENST00000394981.1_Missense_Mutation_p.P40S			Q13201	MMRN1_HUMAN	multimerin 1	40					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		GAAGACTATGCCTTCTGCTTC	0.448																																					p.P40S		Atlas-SNP	.											.	MMRN1	174	.	0			c.C118T						.						80	88	85					4																	90816240		2203	4300	6503	SO:0001583	missense	22915	exon1			ACTATGCCTTCTG	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.118C>T	chr4.hg19:g.90816240C>T	ENSP00000378431:p.Pro40Ser	101.0	0.0		92.0	18.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	hg19	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	C	7.804	0.714296	0.15306	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000394981	T;T;T	0.69435	0.28;0.28;-0.4	4.67	-4.62	0.03370	.	0.778991	0.11199	N	0.589080	T	0.32194	0.0821	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.09377	0.0;0.004	T	0.19910	-1.0291	10	0.17832	T	0.49	.	0.4684	0.00528	0.2632:0.1518:0.2937:0.2913	.	40;40	Q13201-2;Q13201	.;MMRN1_HUMAN	S	40	ENSP00000378431:P40S;ENSP00000264790:P40S;ENSP00000378432:P40S	ENSP00000264790:P40S	P	+	1	0	MMRN1	91035263	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.081000	0.14823	-0.506000	0.06558	-0.363000	0.07495	CCT	.	.		0.448	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		T	90816240	C	T	90816240	3	4	1	1	0	0	0	0	1	0	0	0	9679	739	26	3	120	3	MMRN1	4	90816240	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	16535427	90816240	100338036	38	38										
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1053548	1053548	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ctgggacttgttgaggacgaCgccattgagcttcacagccg	13	11	1	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr5:1053548C>T	ENST00000264930.5	-	23	3119	c.3076G>A	c.(3076-3078)Gtc>Atc	p.V1026I		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	1026					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	TTGAGGACGACGCCATTGAGC	0.632																																					p.V1026I		Atlas-SNP	.											SLC12A7,NS,neuroblastoma,0,1	SLC12A7	97	.	0			c.G3076A						.						170	133	145					5																	1053548		2203	4300	6503	SO:0001583	missense	10723	exon23			GGACGACGCCATT	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.3076G>A	chr5.hg19:g.1053548C>T	ENSP00000264930:p.Val1026Ile	80.0	0.0		72.0	13.0	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	hg19	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	C	12.97	2.096368	0.36952	.	.	ENSG00000113504	ENST00000264930	T	0.63913	-0.07	3.88	3.88	0.44766	.	0.077059	0.52532	D	0.000075	T	0.53514	0.1801	L	0.48174	1.505	0.50039	D	0.999842	B	0.20887	0.049	B	0.20184	0.028	T	0.50841	-0.8780	10	0.23891	T	0.37	.	13.6707	0.62422	0.0:1.0:0.0:0.0	.	1026	Q9Y666	S12A7_HUMAN	I	1026	ENSP00000264930:V1026I	ENSP00000264930:V1026I	V	-	1	0	SLC12A7	1106548	0.997000	0.39634	0.084000	0.20598	0.549000	0.35272	3.833000	0.55790	1.885000	0.54596	0.491000	0.48974	GTC	.	.		0.632	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		T	1053548	C	T	1053548	3	4	1	1	0	0	0	0	1	0	0	0	14403	536	19	1	183	1	SLC12A7	5	1053548	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10		1053548	179861712	39	39										
EDIL3	10085	hgsc.bcm.edu	37	chr5	83402637	83402637	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tccaccttcaattcccagtgGgcctgagcattctggaaaca	8	13	2	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr5:83402637G>T	ENST00000296591.5	-	6	899	c.481C>A	c.(481-483)Cca>Aca	p.P161T	EDIL3_ENST00000380138.3_Missense_Mutation_p.P151T	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	161	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		ATTCCCAGTGGGCCTGAGCAT	0.368																																					p.P161T		Atlas-SNP	.											.	EDIL3	94	.	0			c.C481A						.						123	131	129					5																	83402637		2203	4299	6502	SO:0001583	missense	10085	exon6			CCAGTGGGCCTGA	U70312	CCDS4062.1, CCDS64195.1	5q14	2008-02-05			ENSG00000164176	ENSG00000164176			3173	protein-coding gene	gene with protein product		606018				9420328	Standard	NM_005711		Approved	DEL1	uc003kio.1	O43854	OTTHUMG00000119047	ENST00000296591.5:c.481C>A	chr5.hg19:g.83402637G>T	ENSP00000296591:p.Pro161Thr	136.0	0.0		131.0	21.0	NM_005711	B2R763|O43855|Q5D094|Q8N610	Missense_Mutation	SNP	ENST00000296591.5	hg19	CCDS4062.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.781884	0.49891	.	.	ENSG00000164176	ENST00000296591;ENST00000380138	D;D	0.99259	-5.64;-5.64	5.86	5.86	0.93980	Coagulation factor 5/8 C-terminal type domain (2);Galactose-binding domain-like (1);	0.215828	0.49305	D	0.000158	D	0.98789	0.9592	M	0.82923	2.615	0.80722	D	1	P;B	0.41848	0.763;0.107	B;B	0.39027	0.288;0.065	D	0.99924	1.1270	10	0.72032	D	0.01	-14.9132	20.1891	0.98225	0.0:0.0:1.0:0.0	.	151;161	O43854-2;O43854	.;EDIL3_HUMAN	T	161;151	ENSP00000296591:P161T;ENSP00000369483:P151T	ENSP00000296591:P161T	P	-	1	0	EDIL3	83438393	1.000000	0.71417	0.984000	0.44739	0.240000	0.25518	9.209000	0.95087	2.787000	0.95880	0.650000	0.86243	CCA	.	.		0.368	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711		T	83402637	G	T	83402637	3	4	1	1	0	0	0	0	1	0	0	0	4917	1232	43	3	985	3	EDIL3	5	83402637	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	82349089	83402637	97512623	40	40										
NEUROG1	4762	hgsc.bcm.edu	37	chr5	134870884	134870884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ggcaggggacgcactgcggcGgcaggaggcgctcccgggca	20	13	0	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr5:134870884G>A	ENST00000314744.4	-	1	755	c.497C>T	c.(496-498)cCg>cTg	p.P166L		NM_006161.2	NP_006152.2	Q92886	NGN1_HUMAN	neurogenin 1	166					cell fate commitment (GO:0045165)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perikaryon (GO:0043204)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)			endometrium(1)|liver(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCACTGCGGCGGCAGGAGGCG	0.746																																					p.P166L		Atlas-SNP	.											.	NEUROG1	18	.	0			c.C497T						.						11	15	14					5																	134870884		2151	4239	6390	SO:0001583	missense	4762	exon1			TGCGGCGGCAGGA	U63842	CCDS4187.1	5q23-q31	2013-05-21			ENSG00000181965	ENSG00000181965		"Basic helix-loop-helix proteins"	7764	protein-coding gene	gene with protein product	"neurogenic differentiation 3"	601726		NEUROD3		9119405	Standard	NM_006161		Approved	AKA, Math4C, ngn1, bHLHa6	uc003lax.3	Q92886	OTTHUMG00000129138	ENST00000314744.4:c.497C>T	chr5.hg19:g.134870884G>A	ENSP00000317580:p.Pro166Leu	80.0	0.0		82.0	25.0	NM_006161	Q5U0Q9|Q96HE1	Missense_Mutation	SNP	ENST00000314744.4	hg19	CCDS4187.1	.	.	.	.	.	.	.	.	.	.	G	5.123	0.208348	0.09757	.	.	ENSG00000181965	ENST00000314744	D	0.95853	-3.83	5.05	3.21	0.36854	Helix-loop-helix DNA-binding (1);	0.395940	0.22744	N	0.056170	D	0.82674	0.5088	N	0.01874	-0.695	0.24034	N	0.996109	B	0.11235	0.004	B	0.04013	0.001	T	0.71781	-0.4489	10	0.16896	T	0.51	-34.5207	4.858	0.13570	0.1504:0.0:0.5331:0.3165	.	166	Q92886	NGN1_HUMAN	L	166	ENSP00000317580:P166L	ENSP00000317580:P166L	P	-	2	0	NEUROG1	134898783	0.000000	0.05858	0.992000	0.48379	0.178000	0.23041	-0.251000	0.08818	1.060000	0.40578	0.655000	0.94253	CCG	.	.		0.746	NEUROG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251192.1	NM_006161		A	134870884	G	A	134870884	3	1	1	1	0	0	0	0	1	0	0	0	10361	1116	39	1	220	1	NEUROG1	5	134870884	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	51468247	134870884	46044376	41	41										
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140480872	140480872	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gaactcagcttaacgctcacCgcgctggacggcggctctcc	11	16	3	0	rs148121148		TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr5:140480872C>T	ENST00000231130.2	+	1	639	c.639C>T	c.(637-639)acC>acT	p.T213T	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	213	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TAACGCTCACCGCGCTGGACG	0.562																																					p.T213T		Atlas-SNP	.											PCDHB3,NS,adenoma,0,1	PCDHB3	208	.	0			c.C639T						.	C		1,4405	2.1+/-5.4	0,1,2202	51	51	51		639	-10.2	0	5	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous	PCDHB3	NM_018937.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		213/797	140480872	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	56132	exon1			GCTCACCGCGCTG	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.639C>T	chr5.hg19:g.140480872C>T		134.0	0.0		123.0	22.0	NM_018937	B2R8P2	Silent	SNP	ENST00000231130.2	hg19	CCDS4245.1																																																																																			.	C|1.000;T|0.000		0.562	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		T	140480872	C	T	140480872	2	4	1	1	0	0	0	0	0	0	0	1	11552	639	23	1		1	PCDHB3	5	140480872	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	5609988	140480872	40434388	42	42										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141329103	141329103	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tcctgttctgggtctgtctgGcctccagcccttgcacttgg	11	14	3	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr5:141329103G>A	ENST00000231484.3	-	3	4234	c.3024C>T	c.(3022-3024)ggC>ggT	p.G1008G	AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1008					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTCTGTCTGGCCTCCAGCCC	0.527																																					p.G1008G		Atlas-SNP	.											.	PCDH12	133	.	0			c.C3024T						.						139	131	134					5																	141329103		2203	4300	6503	SO:0001819	synonymous_variant	51294	exon3			TGTCTGGCCTCCA	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.3024C>T	chr5.hg19:g.141329103G>A		94.0	0.0		95.0	23.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	hg19	CCDS4269.1																																																																																			.	.		0.527	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141329103	G	A	141329103	2	1	1	1	0	0	0	0	0	0	0	1	11519	1190	42	3		3	PCDH12	5	141329103	Silent	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	848231	141329103	39586157	43	43										
STK10	6793	hgsc.bcm.edu	37	chr5	171471887	171471887	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ccacagccccgggcggttgtTaagaagcatccgcagaactg	12	13	0	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr5:171471887T>C	ENST00000176763.5	-	19	3249	c.2906A>G	c.(2905-2907)tAa>tGa	p.*969*		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	0					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GGGCGGTTGTTAAGAAGCATC	0.587																																					p.X969X		Atlas-SNP	.											.	STK10	100	.	0			c.A2906G						.						69	70	70					5																	171471887		2203	4300	6503	SO:0001819	synonymous_variant	6793	exon19			GGTTGTTAAGAAG	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.2906A>G	chr5.hg19:g.171471887T>C		63.0	0.0		72.0	22.0	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	hg19	CCDS34290.1																																																																																			.	.		0.587	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		C	171471887	T	C	171471887	2	2	1	1	0	0	0	0	0	0	0	1	15301	1761	61	2		2	STK10	5	171471887	Silent	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	30142784	171471887	9443373	44	44										
N4BP3	23138	hgsc.bcm.edu	37	chr5	177548182	177548182	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	cacgaggtgacccagaaggcTgagcgcagcgagcgcaacct	14	13	0	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr5:177548182T>A	ENST00000274605.5	+	4	1295	c.936T>A	c.(934-936)gcT>gcA	p.A312A		NM_015111.1	NP_055926.1	O15049	N4BP3_HUMAN	NEDD4 binding protein 3	312						cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)				breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCAGAAGGCTGAGCGCAGCG	0.672											OREG0017096	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A312A		Atlas-SNP	.											.	N4BP3	25	.	0			c.T936A						.						11	12	12					5																	177548182		2193	4289	6482	SO:0001819	synonymous_variant	23138	exon4			GAAGGCTGAGCGC	AB002339	CCDS34307.1	5q35.3	2012-05-17				ENSG00000145911			29852	protein-coding gene	gene with protein product						9205841, 11717310	Standard	XM_006714834		Approved	LZTS4	uc003mik.1	O15049		ENST00000274605.5:c.936T>A	chr5.hg19:g.177548182T>A		49.0	0.0	1939	77.0	14.0	NM_015111	B4DIL3|D3DWP3|Q6ZSQ6|Q7Z6I3	Silent	SNP	ENST00000274605.5	hg19	CCDS34307.1																																																																																			.	.		0.672	N4BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373552.2	NM_015111		A	177548182	T	A	177548182	2	1	1	1	0	0	0	0	0	0	0	1	10122	1567	55	4		4	N4BP3	5	177548182	Silent	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	6076295	177548182	3367078	45	45										
F13A1	2162	hgsc.bcm.edu	37	chr6	6225010	6225010	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	aatagaatgtcaacgcttccAgtccaggccgatggggggac	13	10	1	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr6:6225010A>T	ENST00000264870.3	-	7	1147	c.882T>A	c.(880-882)acT>acA	p.T294T		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	294					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	CAACGCTTCCAGTCCAGGCCG	0.498																																					p.T294T		Atlas-SNP	.											.	F13A1	135	.	0			c.T882A						.						99	99	99					6																	6225010		2203	4300	6503	SO:0001819	synonymous_variant	2162	exon7			GCTTCCAGTCCAG	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"Transglutaminases"	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.882T>A	chr6.hg19:g.6225010A>T		165.0	0.0		154.0	28.0	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Silent	SNP	ENST00000264870.3	hg19	CCDS4496.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.454408	0.26161	.	.	ENSG00000124491	ENST00000445223	.	.	.	5.51	-6.28	0.02020	.	.	.	.	.	T	0.17195	0.0413	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40327	-0.9569	4	.	.	.	.	0.4812	0.00548	0.207:0.1815:0.2471:0.3644	.	.	.	.	Q	11	.	.	L	-	2	0	F13A1	6170009	0.000000	0.05858	0.883000	0.34634	0.960000	0.62799	-6.324000	0.00070	-1.488000	0.01847	0.460000	0.39030	CTG	.	.		0.498	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129		T	6225010	A	T	6225010	2	4	1	1	0	0	0	0	0	0	0	1	5342	175	7	4		4	F13A1	6	6225010	Silent	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10		6225010	164890057	46	46										
HIST1H2BM	8342	hgsc.bcm.edu	37	chr6	27783152	27783152	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ccggggaattggccaagcacGccgtgtccgagggcaccaag	15	13	0	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr6:27783152G>A	ENST00000359465.4	+	1	331	c.331G>A	c.(331-333)Gcc>Acc	p.A111T	HIST1H2AJ_ENST00000333151.3_5'Flank	NM_003521.2	NP_003512.1	Q99879	H2B1M_HUMAN	histone cluster 1, H2bm	111					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	12						GGCCAAGCACGCCGTGTCCGA	0.617																																					p.A111T		Atlas-SNP	.											.	HIST1H2BM	36	.	0			c.G331A						.						56	58	57					6																	27783152		2203	4300	6503	SO:0001583	missense	8342	exon1			AAGCACGCCGTGT	Z83738	CCDS4629.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196374	ENSG00000273703		"Histones / Replication-dependent"	4750	protein-coding gene	gene with protein product		602802	"H2B histone family, member E", "histone 1, H2bm"	H2BFE		9439656, 12408966	Standard	NM_003521		Approved	H2B/e, dJ160A22.3	uc003njo.3	Q99879	OTTHUMG00000014489	ENST00000359465.4:c.331G>A	chr6.hg19:g.27783152G>A	ENSP00000352442:p.Ala111Thr	62.0	0.0		55.0	8.0	NM_003521	Q6NWQ3	Missense_Mutation	SNP	ENST00000359465.4	hg19	CCDS4629.1	.	.	.	.	.	.	.	.	.	.	.	9.718	1.158902	0.21454	.	.	ENSG00000196374	ENST00000359465	T	0.36340	1.26	4.34	4.34	0.51931	Histone-fold (2);	0.000000	0.56097	U	0.000026	T	0.33614	0.0869	M	0.86420	2.815	0.58432	D	0.999999	B	0.24317	0.101	B	0.14023	0.01	T	0.45906	-0.9229	10	0.59425	D	0.04	.	16.3606	0.83263	0.0:0.0:1.0:0.0	.	111	Q99879	H2B1M_HUMAN	T	111	ENSP00000352442:A111T	ENSP00000352442:A111T	A	+	1	0	HIST1H2BM	27891131	1.000000	0.71417	0.999000	0.59377	0.031000	0.12232	9.129000	0.94430	2.391000	0.81399	0.563000	0.77884	GCC	.	.		0.617	HIST1H2BM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040157.1	NM_003521		A	27783152	G	A	27783152	3	1	1	1	0	0	0	0	1	0	0	0	7161	1087	38	1	333	1	HIST1H2BM	6	27783152	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	21558142	27783152	143331915	47	47										
OR2H1	26716	hgsc.bcm.edu	37	chr6	29430083	29430083	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gatgactttttatgtgaggtCccatctctgattcgactctc	8	10	2	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr6:29430083C>T	ENST00000377136.1	+	4	1002	c.537C>T	c.(535-537)gtC>gtT	p.V179V	OR2H1_ENST00000377133.1_Silent_p.V179V|OR2H1_ENST00000473369.1_3'UTR|OR2H1_ENST00000377132.1_Silent_p.V179V|OR2H1_ENST00000442615.1_Silent_p.V179V|OR2H1_ENST00000396792.2_Silent_p.V179V			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						TATGTGAGGTCCCATCTCTGA	0.507																																					p.V179V		Atlas-SNP	.											.	OR2H1	38	.	0			c.C537T						.						196	206	202					6																	29430083		1511	2709	4220	SO:0001819	synonymous_variant	26716	exon3			TGAGGTCCCATCT	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"GPCR / Class A : Olfactory receptors"	8252	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily H, member 8"	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.537C>T	chr6.hg19:g.29430083C>T		115.0	0.0		111.0	26.0	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Silent	SNP	ENST00000377136.1	hg19	CCDS4660.1																																																																																			.	.		0.507	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			T	29430083	C	T	29430083	2	4	1	1	0	0	0	0	0	0	0	1	11010	842	30	3		3	OR2H1	6	29430083	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	1646931	29430083	141684984	48	48										
TAPBP	9278	hgsc.bcm.edu	37	chr6	33281114	33281114	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ccaagccccatccagggcccGcgggcagttctgcgcggggg	16	16	1	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr6:33281114G>T	ENST00000431845.2	-	0	2651				TAPBP_ENST00000489157.1_Intron|TAPBP_ENST00000434618.2_Silent_p.R117R|TAPBP_ENST00000456592.2_Silent_p.R117R|TAPBP_ENST00000475304.1_Silent_p.R117R|TAPBP_ENST00000426633.2_Silent_p.R117R	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(3)	21						TCCAGGGCCCGCGGGCAGTTC	0.692																																					p.R117R		Atlas-SNP	.											.	TAPBP	48	.	0			c.C349A						.						20	24	23					6																	33281114		2196	4292	6488	SO:0001628	intergenic_variant	6892	exon3			GGGCCCGCGGGCA	Z97183	CCDS4775.1	6p21.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000236104	ENSG00000236104		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13085	protein-coding gene	gene with protein product		611439	"zinc finger protein 297"	ZNF297			Standard	NM_005453		Approved	BING1, ZNF297A, fruitless, fru, ZBTB22A	uc010juu.3	O15209	OTTHUMG00000031110		chr6.hg19:g.33281114G>T		49.0	0.0		54.0	4.0	NM_172208	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Silent	SNP	ENST00000431845.2	hg19	CCDS4775.1																																																																																			.	.		0.692	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2			T	33281114	G	T	33281114	1	4	1	0	1	0	0	0	0	0	0	0	15567	1086	38	1		1	TAPBP	6	33281114	IGR	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	3851031	33281114	137833953	49	49										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87964507	87964507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tgatgatctggaagttaaacGtgcttgtcaactgagtgaat	11	5	2	4			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr6:87964507G>A	ENST00000369577.3	+	8	1203	c.1160G>A	c.(1159-1161)cGt>cAt	p.R387H	ZNF292_ENST00000339907.4_Missense_Mutation_p.R382H	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	387						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		GAAGTTAAACGTGCTTGTCAA	0.378																																					p.R387H		Atlas-SNP	.											.	ZNF292	479	.	0			c.G1160A						.						134	126	129					6																	87964507		1906	4130	6036	SO:0001583	missense	23036	exon8			TTAAACGTGCTTG	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.1160G>A	chr6.hg19:g.87964507G>A	ENSP00000358590:p.Arg387His	183.0	0.0		205.0	60.0	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	hg19	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.068105	0.76301	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.44083	0.93;0.93	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.62816	0.2459	M	0.73962	2.25	0.54753	D	0.999981	D	0.89917	1.0	D	0.83275	0.996	T	0.64437	-0.6408	10	0.87932	D	0	.	20.3172	0.98658	0.0:0.0:1.0:0.0	.	387	O60281	ZN292_HUMAN	H	387;382	ENSP00000358590:R387H;ENSP00000342847:R382H	ENSP00000342847:R382H	R	+	2	0	ZNF292	88021226	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.801000	0.96364	0.650000	0.86243	CGT	.	.		0.378	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		A	87964507	G	A	87964507	3	1	1	1	0	0	0	0	1	0	0	0	17841	1145	40	1	1190	1	ZNF292	6	87964507	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	54683393	87964507	83150560	50	50										
C6orf174	387104	hgsc.bcm.edu	37	chr6	127837105	127837105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tttgcccgcagaagaggaggAtggagaaggggaggccccct	17	9	0	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr6:127837105A>G	ENST00000525778.1	-	2	1400	c.655T>C	c.(655-657)Tcc>Ccc	p.S219P	SOGA3_ENST00000481848.2_Missense_Mutation_p.S219P|SOGA3_ENST00000368268.2_Missense_Mutation_p.S219P|SOGA3_ENST00000465909.2_Missense_Mutation_p.S219P|SOGA3_ENST00000556132.1_Missense_Mutation_p.S219P			Q5TF21	SOGA3_HUMAN	SOGA family member 3	219	Gly-rich.				regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GAAGAGGAGGATGGAGAAGGG	0.721																																					p.S219P		Atlas-SNP	.											.	.	.	.	0			c.T655C						.						10	11	11					6																	127837105		1744	3988	5732	SO:0001583	missense	387104	exon2			AGGAGGATGGAGA	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.655T>C	chr6.hg19:g.127837105A>G	ENSP00000434570:p.Ser219Pro	36.0	0.0		38.0	5.0	NM_001012279		Missense_Mutation	SNP	ENST00000525778.1	hg19	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	A	5.712	0.315943	0.10789	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	3.58	1.18	0.20946	.	1.067160	0.07444	N	0.897937	T	0.09247	0.0228	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31251	-0.9950	10	0.36615	T	0.2	-2.1391	3.1615	0.06522	0.5979:0.0:0.2229:0.1791	.	219	Q5TF21	CF174_HUMAN	P	219	ENSP00000451768:S219P;ENSP00000357251:S219P;ENSP00000434570:S219P;ENSP00000435559:S219P	ENSP00000435559:S219P	S	-	1	0	C6orf174	127878798	0.984000	0.35163	0.010000	0.14722	0.499000	0.33736	0.367000	0.20382	0.136000	0.18733	0.459000	0.35465	TCC	.	.		0.721	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		G	127837105	A	G	127837105	3	3	1	1	0	0	0	0	1	0	0	0	2347	333	12	2	2212	2	C6orf174	6	127837105	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	39872598	127837105	43277962	51	51										
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4815367	4815367	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	atgttctcggcaggagcggaGagtttgctccaccaggccag	14	11	1	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr7:4815367G>C	ENST00000348624.4	+	1	115	c.21G>C	c.(19-21)gaG>gaC	p.E7D	AP5Z1_ENST00000401897.1_Missense_Mutation_p.E7D	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	7					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CAGGAGCGGAGAGTTTGCTCC	0.687																																					p.E7D		Atlas-SNP	.											.	.	.	.	0			c.G21C						.						34	42	40					7																	4815367		2019	4164	6183	SO:0001583	missense	9907	exon1			AGCGGAGAGTTTG	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"KIAA0415"	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.21G>C	chr7.hg19:g.4815367G>C	ENSP00000297562:p.Glu7Asp	49.0	0.0		36.0	8.0	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	hg19	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.417901	0.25552	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.66638	-0.22;0.67	4.32	1.47	0.22746	.	0.063933	0.64402	D	0.000012	T	0.56761	0.2007	L	0.59436	1.845	0.42964	D	0.994419	P	0.41524	0.753	B	0.37091	0.241	T	0.55431	-0.8142	10	0.87932	D	0	.	7.8103	0.29228	0.2792:0.0:0.7208:0.0	.	7	O43299	K0415_HUMAN	D	7	ENSP00000297562:E7D;ENSP00000384980:E7D	ENSP00000297562:E7D	E	+	3	2	KIAA0415	4781893	1.000000	0.71417	0.467000	0.27180	0.027000	0.11550	0.930000	0.28858	0.109000	0.17891	-0.935000	0.02700	GAG	.	.		0.687	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			C	4815367	G	C	4815367	3	2	1	1	0	0	0	0	1	0	0	0	8184	933	33	4	23	4	KIAA0415	7	4815367	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10		4815367	154323296	52	52										
PION	54103	hgsc.bcm.edu	37	chr7	77010640	77010640	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	accactctatttccatcttcTtgggcgacatggatacgaaa	7	11	3	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr7:77010640T>C	ENST00000257626.7	-	8	636	c.558A>G	c.(556-558)caA>caG	p.Q186Q		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	186					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										TTCCATCTTCTTGGGCGACAT	0.299																																					p.Q186Q		Atlas-SNP	.											.	PION	74	.	0			c.A558G						.						78	73	74					7																	77010640		1807	4071	5878	SO:0001819	synonymous_variant	54103	exon8			ATCTTCTTGGGCG		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"pigeon homolog (Drosophila)"	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.558A>G	chr7.hg19:g.77010640T>C		70.0	0.0		73.0	19.0	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Silent	SNP	ENST00000257626.7	hg19	CCDS34672.2																																																																																			.	.		0.299	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439		C	77010640	T	C	77010640	2	2	1	1	0	0	0	0	0	0	0	1	11943	1606	56	2		2	PION	7	77010640	Silent	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	72195273	77010640	82128023	53	53										
MAGI2	9863	hgsc.bcm.edu	37	chr7	77998508	77998508	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ccataaatgggatcatcgatTttttcccagccatatggaag	8	9	1	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr7:77998508T>C	ENST00000354212.4	-	7	1321	c.1068A>G	c.(1066-1068)aaA>aaG	p.K356K	MAGI2_ENST00000535697.1_Silent_p.K193K|MAGI2_ENST00000522391.1_Silent_p.K356K|MAGI2_ENST00000419488.1_Silent_p.K356K|MAGI2_ENST00000536571.1_Silent_p.K188K	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	356	Interaction with DDN.|WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GATCATCGATTTTTTCCCAGC	0.249																																					p.K356K		Atlas-SNP	.											.	MAGI2	246	.	0			c.A1068G						.						61	63	62					7																	77998508		2202	4300	6502	SO:0001819	synonymous_variant	9863	exon7			ATCGATTTTTTCC	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1068A>G	chr7.hg19:g.77998508T>C		483.0	1.0		525.0	124.0	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	hg19	CCDS5594.1																																																																																			.	.		0.249	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		C	77998508	T	C	77998508	2	2	1	1	0	0	0	0	0	0	0	1	9200	1838	64	2		2	MAGI2	7	77998508	Silent	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	987868	77998508	81140155	54	54										
GNAI1	2770	hgsc.bcm.edu	37	chr7	79846776	79846776	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gctgtaacagatgtcatcatAaaaaataatctaaaagattg	6	5	3	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr7:79846776A>G	ENST00000351004.3	+	8	1405	c.1032A>G	c.(1030-1032)atA>atG	p.I344M	GNAI1_ENST00000457358.2_Missense_Mutation_p.I292M	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	344					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						ATGTCATCATAAAAAATAATC	0.323																																					p.I344M		Atlas-SNP	.											.	GNAI1	44	.	0			c.A1032G						.						94	90	91					7																	79846776		2203	4299	6502	SO:0001583	missense	2770	exon8			CATCATAAAAAAT	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"Gi1 protein alpha subunit"	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.1032A>G	chr7.hg19:g.79846776A>G	ENSP00000343027:p.Ile344Met	214.0	0.0		220.0	44.0	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Missense_Mutation	SNP	ENST00000351004.3	hg19	CCDS5595.1	.	.	.	.	.	.	.	.	.	.	A	15.06	2.720670	0.48728	.	.	ENSG00000127955	ENST00000351004;ENST00000457358	T;T	0.70631	-0.5;-0.5	5.9	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.79070	0.4384	M	0.79805	2.47	0.80722	D	1	P	0.46327	0.876	P	0.54815	0.761	T	0.78465	-0.2193	9	.	.	.	.	8.7936	0.34866	0.7436:0.1237:0.0:0.1327	.	344	P63096	GNAI1_HUMAN	M	344;292	ENSP00000343027:I344M;ENSP00000410572:I292M	.	I	+	3	3	GNAI1	79684712	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.581000	0.53914	1.019000	0.39547	0.460000	0.39030	ATA	.	.		0.323	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		G	79846776	A	G	79846776	3	3	1	1	0	0	0	0	1	0	0	0	6512	352	13	2	1062	2	GNAI1	7	79846776	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	1848268	79846776	79291887	55	55										
SLC26A3	1811	hgsc.bcm.edu	37	chr7	107431676	107431676	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	atcatactcagaatcggaaaCggacctaattaacagtgggt	9	8	2	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr7:107431676C>T	ENST00000340010.5	-	5	571	c.387G>A	c.(385-387)ccG>ccA	p.P129P	SLC26A3_ENST00000422236.2_Silent_p.P94P	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	129			P -> L (in DIAR1). {ECO:0000269|PubMed:21394828}.		anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						GAATCGGAAACGGACCTAATT	0.433																																					p.P129P		Atlas-SNP	.											SLC26A3,NS,haematopoietic_neoplasm,0,2	SLC26A3	120	.	0			c.G387A						.						175	157	163					7																	107431676		2203	4300	6503	SO:0001819	synonymous_variant	1811	exon5			CGGAAACGGACCT	L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"Solute carriers"	3018	protein-coding gene	gene with protein product		126650	"congenital chloride diarrhea", "solute carrier family 26, member 3"	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.387G>A	chr7.hg19:g.107431676C>T		163.0	0.0		142.0	30.0	NM_000111		Silent	SNP	ENST00000340010.5	hg19	CCDS5748.1																																																																																			.	.		0.433	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111		T	107431676	C	T	107431676	2	4	1	1	0	0	0	0	0	0	0	1	14533	523	19	1		1	SLC26A3	7	107431676	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	27584900	107431676	51706987	56	56										
NCAPG2	54892	hgsc.bcm.edu	37	chr7	158449049	158449049	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gatgagtcagcagatactcaAtgtagaccaatgccaattca	8	9	3	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr7:158449049A>G	ENST00000409423.1	-	20	2463	c.2291T>C	c.(2290-2292)aTt>aCt	p.I764T	NCAPG2_ENST00000449727.2_Missense_Mutation_p.I764T|NCAPG2_ENST00000541468.1_Missense_Mutation_p.I265T|NCAPG2_ENST00000275830.10_Missense_Mutation_p.I556T|NCAPG2_ENST00000356309.3_Missense_Mutation_p.I764T|NCAPG2_ENST00000409339.3_Missense_Mutation_p.I764T	NM_001281932.1	NP_001268861.1	Q86XI2	CNDG2_HUMAN	non-SMC condensin II complex, subunit G2	764					chromosome condensation (GO:0030261)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	39	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		CAGATACTCAATGTAGACCAA	0.463																																					p.I764T		Atlas-SNP	.											.	NCAPG2	80	.	0			c.T2291C						.						157	161	160					7																	158449049		2007	4178	6185	SO:0001583	missense	54892	exon19			TACTCAATGTAGA	BC043404	CCDS43686.1, CCDS64816.1	7q36.3	2006-09-04	2006-09-04	2006-09-04	ENSG00000146918	ENSG00000146918			21904	protein-coding gene	gene with protein product		608532	"leucine zipper protein 5"	LUZP5		14532007	Standard	NM_001281933		Approved	FLJ20311, MTB, CAP-G2, hCAP-G2	uc003wnv.1	Q86XI2	OTTHUMG00000151438	ENST00000409423.1:c.2291T>C	chr7.hg19:g.158449049A>G	ENSP00000386569:p.Ile764Thr	187.0	0.0		183.0	47.0	NM_017760	A4D228|Q7Z3J9|Q8WUG8|Q9BRX6|Q9H8S2|Q9H9K6	Missense_Mutation	SNP	ENST00000409423.1	hg19	CCDS43686.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.804492	0.31869	.	.	ENSG00000146918	ENST00000541468;ENST00000356309;ENST00000409423;ENST00000275830;ENST00000409339;ENST00000545393;ENST00000449727	T;T;T;T;T;T	0.33865	1.4;1.41;1.41;1.41;1.39;1.39	5.91	5.91	0.95273	.	0.454398	0.26931	N	0.021765	T	0.32704	0.0838	L	0.48642	1.525	0.30241	N	0.795049	B;B;B;B	0.27068	0.045;0.167;0.007;0.055	B;B;B;B	0.26864	0.019;0.074;0.014;0.02	T	0.34900	-0.9810	10	0.49607	T	0.09	-4.5291	11.387	0.49791	0.9303:0.0:0.0697:0.0	.	764;207;556;764	Q86XI2-2;B4DHE5;E7EUH9;Q86XI2	.;.;.;CNDG2_HUMAN	T	265;764;764;556;764;207;764	ENSP00000442337:I265T;ENSP00000348657:I764T;ENSP00000386569:I764T;ENSP00000275830:I556T;ENSP00000387007:I764T;ENSP00000388326:I764T	ENSP00000275830:I556T	I	-	2	0	NCAPG2	158141810	0.943000	0.32029	0.129000	0.21949	0.407000	0.30961	6.421000	0.73353	2.254000	0.74563	0.533000	0.62120	ATT	.	.		0.463	NCAPG2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327111.1	NM_017760		G	158449049	A	G	158449049	3	3	1	1	0	0	0	0	1	0	0	0	10217	101	4	2	1180	2	NCAPG2	7	158449049	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	51017373	158449049	689614	57	57										
GSR	2936	hgsc.bcm.edu	37	chr8	30539480	30539480	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	cactgtcccaataggggggtGgctgaagaccacagttggga	15	9	0	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr8:30539480G>A	ENST00000221130.5	-	11	1342	c.1252C>T	c.(1252-1254)Cac>Tac	p.H418Y	GSR_ENST00000541648.1_Missense_Mutation_p.H365Y|GSR_ENST00000537535.1_Missense_Mutation_p.H336Y|GSR_ENST00000414019.1_Missense_Mutation_p.H375Y|GSR_ENST00000546342.1_Missense_Mutation_p.H389Y	NM_000637.3|NM_001195102.1|NM_001195103.1	NP_000628.2|NP_001182031.1|NP_001182032.1	P00390	GSHR_HUMAN	glutathione reductase	418					cell redox homeostasis (GO:0045454)|glutathione metabolic process (GO:0006749)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|glutathione-disulfide reductase activity (GO:0004362)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	23				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Flavin adenine dinucleotide(DB03147)|Glutathione(DB00143)	ATAGGGGGGTGGCTGAAGACC	0.438																																					p.H418Y		Atlas-SNP	.											.	GSR	53	.	0			c.C1252T						.						94	101	98					8																	30539480		2203	4300	6503	SO:0001583	missense	2936	exon11			GGGGGTGGCTGAA		CCDS34877.1, CCDS56530.1, CCDS56531.1, CCDS56532.1	8p21.1	2012-10-02			ENSG00000104687	ENSG00000104687	1.8.1.7		4623	protein-coding gene	gene with protein product		138300					Standard	NM_000637		Approved		uc003xih.2	P00390	OTTHUMG00000163946	ENST00000221130.5:c.1252C>T	chr8.hg19:g.30539480G>A	ENSP00000221130:p.His418Tyr	108.0	0.0		100.0	23.0	NM_000637	C8KIL8|C8KIL9|C8KIM0|D3DSV3|Q7Z5C9|Q9NP63	Missense_Mutation	SNP	ENST00000221130.5	hg19	CCDS34877.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.813187	0.90707	.	.	ENSG00000104687	ENST00000221130;ENST00000414019;ENST00000546342;ENST00000541648;ENST00000537535	D;D;D;D;D	0.93133	-3.17;-3.17;-3.17;-3.17;-3.17	5.56	5.56	0.83823	FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (2);	0.000000	0.85682	D	0.000000	D	0.98046	0.9356	H	0.97491	4.015	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99308	1.0903	10	0.87932	D	0	-23.1765	17.0923	0.86625	0.0:0.0:1.0:0.0	.	418	P00390	GSHR_HUMAN	Y	418;375;389;365;336	ENSP00000221130:H418Y;ENSP00000390065:H375Y;ENSP00000445516:H389Y;ENSP00000444559:H365Y;ENSP00000438845:H336Y	ENSP00000221130:H418Y	H	-	1	0	GSR	30659022	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	8.746000	0.91604	2.622000	0.88805	0.644000	0.83932	CAC	.	.		0.438	GSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376519.1			A	30539480	G	A	30539480	3	1	1	1	0	0	0	0	1	0	0	0	6837	1348	47	3	328	3	GSR	8	30539480	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10		30539480	115824542	58	58										
FNTA	2339	hgsc.bcm.edu	37	chr8	42911566	42911566	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ggcgcaacccccgccccagcCgcacccaccgccgccccagc	9	26	0	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr8:42911566C>G	ENST00000302279.3	+	1	271	c.77C>G	c.(76-78)cCg>cGg	p.P26R	FNTA_ENST00000342116.4_Missense_Mutation_p.P26R|FNTA_ENST00000524546.1_3'UTR|FNTA_ENST00000529687.1_5'Flank|RP11-598P20.5_ENST00000534420.1_Intron	NM_002027.2	NP_002018.1	P49354	FNTA_HUMAN	farnesyltransferase, CAAX box, alpha	26	Pro-rich.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|phototransduction, visible light (GO:0007603)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of tubulin deacetylation (GO:0090044)|protein farnesylation (GO:0018343)|protein geranylgeranylation (GO:0018344)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transforming growth factor beta receptor signaling pathway (GO:0007179)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|protein farnesyltransferase complex (GO:0005965)	alpha-tubulin binding (GO:0043014)|CAAX-protein geranylgeranyltransferase activity (GO:0004662)|microtubule binding (GO:0008017)|protein farnesyltransferase activity (GO:0004660)|protein geranylgeranyltransferase activity (GO:0004661)			cervix(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	16	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			CCGCCCCAGCCGCACCCACCG	0.746																																					p.P26R		Atlas-SNP	.											.	FNTA	34	.	0			c.C77G						.						5	6	6					8																	42911566		2067	4078	6145	SO:0001583	missense	2339	exon1			CCCAGCCGCACCC	L10413	CCDS6140.1	8p11.21	2011-06-27			ENSG00000168522	ENSG00000168522		"Prenyltransferase alpha subunit repeat containing"	3782	protein-coding gene	gene with protein product	"protein prenyltransferase alpha subunit repeat containing 2"	134635				8276393	Standard	NR_033698		Approved	FPTA, PGGT1A, PTAR2	uc003xps.3	P49354	OTTHUMG00000165279	ENST00000302279.3:c.77C>G	chr8.hg19:g.42911566C>G	ENSP00000303423:p.Pro26Arg	55.0	0.0		34.0	12.0	NM_002027	A6NJW0|Q53XJ9|Q9UDC1	Missense_Mutation	SNP	ENST00000302279.3	hg19	CCDS6140.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.331146	0.41297	.	.	ENSG00000168522	ENST00000302279;ENST00000342116;ENST00000531266	.	.	.	4.93	3.99	0.46301	.	0.000000	0.51477	D	0.000087	T	0.18257	0.0438	N	0.08118	0	0.09310	N	0.999999	P;B	0.34662	0.462;0.218	B;B	0.32211	0.142;0.067	T	0.17048	-1.0382	9	0.72032	D	0.01	-9.8866	9.7132	0.40258	0.2066:0.7933:0.0:0.0	.	26;26	P49354-2;P49354	.;FNTA_HUMAN	R	26;26;21	.	ENSP00000303423:P26R	P	+	2	0	FNTA	43030723	0.329000	0.24696	0.961000	0.40146	0.768000	0.43524	0.912000	0.28597	2.277000	0.76020	0.585000	0.79938	CCG	.	.		0.746	FNTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383178.1	NM_002027		G	42911566	C	G	42911566	3	3	1	1	0	0	0	0	1	0	0	0	5985	652	23	4	79	4	FNTA	8	42911566	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	12372086	42911566	103452456	59	59										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116427157	116427157	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tgatcttctgacctcctctcTaacgggcttccattgacttg	7	13	3	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr8:116427157T>C	ENST00000220888.5	-	6	3099	c.2940A>G	c.(2938-2940)ttA>ttG	p.L980L	TRPS1_ENST00000395715.3_Silent_p.L993L|TRPS1_ENST00000519076.1_Silent_p.L734L|TRPS1_ENST00000520276.1_Silent_p.L984L			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	980					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			ACCTCCTCTCTAACGGGCTTC	0.498									Langer-Giedion syndrome																												p.L993L		Atlas-SNP	.											.	TRPS1	516	.	0			c.A2979G						.						169	163	165					8																	116427157		1974	4151	6125	SO:0001819	synonymous_variant	7227	exon7	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	CCTCTCTAACGGG	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2940A>G	chr8.hg19:g.116427157T>C		105.0	0.0		168.0	21.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	T	3.363	-0.130165	0.06753	.	.	ENSG00000104447	ENST00000518018	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	T	0.73071	0.3540	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72250	-0.4348	4	.	.	.	.	16.1729	0.81831	0.0:0.0:0.0:1.0	.	.	.	.	G	105	.	.	R	-	1	2	TRPS1	116496333	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.495000	0.35627	2.214000	0.71695	0.533000	0.62120	AGA	.	.		0.498	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		C	116427157	T	C	116427157	2	2	1	1	0	0	0	0	0	0	0	1	16608	1519	53	2		2	TRPS1	8	116427157	Silent	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	73515591	116427157	29936865	60	60										
FAM135B	51059	hgsc.bcm.edu	37	chr8	139163633	139163633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	cacagataagttcacaacctCcacagccttcaggctgtcca	6	15	2	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr8:139163633C>T	ENST00000395297.1	-	13	3255	c.3085G>A	c.(3085-3087)Gag>Aag	p.E1029K		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1029										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TTCACAACCTCCACAGCCTTC	0.527										HNSCC(54;0.14)																											p.E1029K		Atlas-SNP	.											.	FAM135B	423	.	0			c.G3085A						.						70	70	70					8																	139163633		2203	4300	6503	SO:0001583	missense	51059	exon13			CAACCTCCACAGC	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3085G>A	chr8.hg19:g.139163633C>T	ENSP00000378710:p.Glu1029Lys	162.0	0.0		285.0	99.0	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	hg19	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	20.4	3.985026	0.74474	.	.	ENSG00000147724	ENST00000395297	T	0.18960	2.18	5.33	4.46	0.54185	.	0.119617	0.56097	D	0.000036	T	0.43722	0.1260	M	0.72894	2.215	0.41599	D	0.988847	D;D;P	0.76494	0.999;0.997;0.953	D;D;P	0.69479	0.964;0.935;0.551	T	0.44742	-0.9308	10	0.72032	D	0.01	-7.4971	13.0315	0.58845	0.0:0.9225:0.0:0.0775	.	1029;1029;1029	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	K	1029	ENSP00000378710:E1029K	ENSP00000276737:E1029K	E	-	1	0	FAM135B	139232815	1.000000	0.71417	0.986000	0.45419	0.472000	0.32918	7.487000	0.81328	1.259000	0.44117	0.655000	0.94253	GAG	.	.		0.527	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139163633	C	T	139163633	3	4	1	1	0	0	0	0	1	0	0	0	5454	864	30	3	1167	3	FAM135B	8	139163633	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	22736476	139163633	7200389	61	61										
TMEM215	401498	hgsc.bcm.edu	37	chr9	32784868	32784868	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	aatcagatacaaggcaggtgGgaccacgagaccatcgtcta	11	10	2	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr9:32784868G>A	ENST00000342743.5	+	2	1052	c.687G>A	c.(685-687)tgG>tgA	p.W229*		NM_212558.2	NP_997723.2	Q68D42	TM215_HUMAN	transmembrane protein 215	229						integral component of membrane (GO:0016021)				endometrium(4)|kidney(1)|large_intestine(3)|lung(2)|prostate(2)	12						AAGGCAGGTGGGACCACGAGA	0.478																																					p.W229X		Atlas-SNP	.											.	TMEM215	38	.	0			c.G687A						.						64	56	59					9																	32784868		2125	4164	6289	SO:0001587	stop_gained	401498	exon2			CAGGTGGGACCAC		CCDS6530.1	9p21.1	2008-08-08			ENSG00000188133	ENSG00000188133			33816	protein-coding gene	gene with protein product							Standard	NM_212558		Approved		uc003zri.4	Q68D42	OTTHUMG00000129521	ENST00000342743.5:c.687G>A	chr9.hg19:g.32784868G>A	ENSP00000345468:p.Trp229*	128.0	0.0		125.0	32.0	NM_212558	Q6ZUU2	Nonsense_Mutation	SNP	ENST00000342743.5	hg19	CCDS6530.1	.	.	.	.	.	.	.	.	.	.	G	38	7.213905	0.98139	.	.	ENSG00000188133	ENST00000342743	.	.	.	5.57	5.57	0.84162	.	0.094723	0.47455	D	0.000234	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.9916	17.0359	0.86476	0.0:0.0:1.0:0.0	.	.	.	.	X	229	.	ENSP00000345468:W229X	W	+	3	0	TMEM215	32774868	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.421000	0.52742	2.622000	0.88805	0.655000	0.94253	TGG	.	.		0.478	TMEM215-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251701.1	NM_212558		A	32784868	G	A	32784868	4	1	1	1	0	0	0	0	0	1	0	0	16153	1241	43	3	689	3	TMEM215	9	32784868	Nonsense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10		32784868	108428563	62	62										
GOLM1	51280	hgsc.bcm.edu	37	chr9	88692475	88692475	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ctctctctgcagccgccctgCggaccctgccttccagctcc	8	21	2	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr9:88692475C>A	ENST00000388712.3	-	3	329	c.161G>T	c.(160-162)cGc>cTc	p.R54L	GOLM1_ENST00000257504.6_5'UTR|GOLM1_ENST00000388711.3_Missense_Mutation_p.R54L	NM_016548.3	NP_057632.2	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	54					nucleus organization (GO:0006997)|regulation of lipid metabolic process (GO:0019216)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17						AGCCGCCCTGCGGACCCTGCC	0.607																																					p.R54L		Atlas-SNP	.											.	GOLM1	36	.	0			c.G161T						.						82	82	82					9																	88692475		2203	4300	6503	SO:0001583	missense	51280	exon3			GCCCTGCGGACCC	AF236056	CCDS35054.1	9q21.33	2012-12-13	2007-07-30	2007-07-30	ENSG00000135052	ENSG00000135052			15451	protein-coding gene	gene with protein product		606804	"golgi phosphoprotein 2", "chromosome 9 open reading frame 155"	GOLPH2, C9orf155		10831838, 18953438, 22542941	Standard	NM_016548		Approved	GP73, FLJ23608, bA379P1.3	uc004aol.3	Q8NBJ4	OTTHUMG00000020130	ENST00000388712.3:c.161G>T	chr9.hg19:g.88692475C>A	ENSP00000373364:p.Arg54Leu	52.0	0.0		64.0	15.0	NM_016548	Q6IAF4|Q9NRB9	Missense_Mutation	SNP	ENST00000388712.3	hg19	CCDS35054.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.419149	0.62622	.	.	ENSG00000135052	ENST00000388712;ENST00000388711;ENST00000486130;ENST00000466178	T;T;D	0.89875	1.0;1.0;-2.58	5.61	5.61	0.85477	.	0.057169	0.64402	D	0.000001	D	0.93074	0.7795	M	0.65498	2.005	0.48696	D	0.999695	D	0.89917	1.0	D	0.81914	0.995	D	0.92886	0.6327	10	0.62326	D	0.03	3.5297	12.9051	0.58147	0.0:0.9248:0.0:0.0752	.	54	Q8NBJ4	GOLM1_HUMAN	L	54	ENSP00000373364:R54L;ENSP00000373363:R54L;ENSP00000419076:R54L	ENSP00000373363:R54L	R	-	2	0	GOLM1	87882295	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	3.615000	0.54167	2.804000	0.96469	0.462000	0.41574	CGC	.	.		0.607	GOLM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052904.2	NM_177937		A	88692475	C	A	88692475	3	1	1	1	0	0	0	0	1	0	0	0	6575	768	27	1	1076	1	GOLM1	9	88692475	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	55907607	88692475	52520956	63	63										
CTNNAL1	8727	hgsc.bcm.edu	37	chr9	111739250	111739250	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	aactatacttacttctttctTaagttcattaagactgtgac	4	8	3	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr9:111739250T>A	ENST00000325551.4	-	8	1266	c.1180A>T	c.(1180-1182)Aag>Tag	p.K394*	CTNNAL1_ENST00000325580.6_Nonsense_Mutation_p.K394*|CTNNAL1_ENST00000374595.4_Nonsense_Mutation_p.K394*|CTNNAL1_ENST00000488130.1_5'UTR	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	394					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		ACTTCTTTCTTAAGTTCATTA	0.284																																					p.K394X		Atlas-SNP	.											.	CTNNAL1	51	.	0			c.A1180T						.						97	91	93					9																	111739250		2189	4288	6477	SO:0001587	stop_gained	8727	exon8			CTTTCTTAAGTTC	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.1180A>T	chr9.hg19:g.111739250T>A	ENSP00000320434:p.Lys394*	48.0	0.0		44.0	11.0	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Nonsense_Mutation	SNP	ENST00000325551.4	hg19	CCDS6775.1	.	.	.	.	.	.	.	.	.	.	T	38	6.721503	0.97788	.	.	ENSG00000119326	ENST00000374595;ENST00000325551;ENST00000325580	.	.	.	5.56	4.39	0.52855	.	0.145281	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	-7.0276	9.4249	0.38574	0.0:0.0:0.1794:0.8206	.	.	.	.	X	394	.	ENSP00000320434:K394X	K	-	1	0	CTNNAL1	110779071	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	5.755000	0.68750	0.896000	0.36366	0.533000	0.62120	AAG	.	.		0.284	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		A	111739250	T	A	111739250	4	1	1	1	0	0	0	0	0	1	0	0	4017	1763	61	4	1072	4	CTNNAL1	9	111739250	Nonsense_Mutation	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	23046775	111739250	29474181	64	64										
ADARB2	105	hgsc.bcm.edu	37	chr10	1405746	1405746	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	actgcacgaaggacctgagtGccagctccgccgcgcgcatc	12	16	0	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr10:1405746G>A	ENST00000381312.1	-	3	879	c.554C>T	c.(553-555)gCa>gTa	p.A185V	RP11-398B16.2_ENST00000432987.1_RNA	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	185	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		GGACCTGAGTGCCAGCTCCGC	0.701																																					p.A185V		Atlas-SNP	.											.	ADARB2	95	.	0			c.C554T						.						36	32	33					10																	1405746		2203	4299	6502	SO:0001583	missense	105	exon3			CTGAGTGCCAGCT	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.554C>T	chr10.hg19:g.1405746G>A	ENSP00000370713:p.Ala185Val	140.0	0.0		164.0	40.0	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	hg19	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	g	26.0	4.690510	0.88735	.	.	ENSG00000185736	ENST00000381312	D	0.85013	-1.93	5.14	5.14	0.70334	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.099447	0.64402	D	0.000002	D	0.91536	0.7327	M	0.73217	2.22	0.80722	D	1	D	0.76494	0.999	D	0.65573	0.936	D	0.92291	0.5841	10	0.66056	D	0.02	-30.0799	18.6205	0.91319	0.0:0.0:1.0:0.0	.	185	Q9NS39	RED2_HUMAN	V	185	ENSP00000370713:A185V	ENSP00000370713:A185V	A	-	2	0	ADARB2	1395746	1.000000	0.71417	0.945000	0.38365	0.594000	0.36715	9.713000	0.98740	2.393000	0.81446	0.556000	0.70494	GCA	.	.		0.701	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		A	1405746	G	A	1405746	3	1	1	1	0	0	0	0	1	0	0	0	283	1319	46	3	1697	3	ADARB2	10	1405746	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10		1405746	134129001	65	65										
KIAA0913	23053	hgsc.bcm.edu	37	chr10	75561253	75561253	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ctgtggcagcgggtctcactCgagatggccaccttctcccc	11	16	2	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr10:75561253C>T	ENST00000605216.1	+	26	5707	c.5490C>T	c.(5488-5490)ctC>ctT	p.L1830L	RP11-574K11.31_ENST00000603027.1_3'UTR|ZSWIM8_ENST00000604524.1_Silent_p.L1648L|ZSWIM8-AS1_ENST00000456638.2_RNA|ZSWIM8_ENST00000604729.1_Silent_p.L1827L|ZSWIM8_ENST00000603114.1_Silent_p.L1789L|ZSWIM8_ENST00000398706.2_Silent_p.L1835L	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	1830							zinc ion binding (GO:0008270)										GGGTCTCACTCGAGATGGCCA	0.592																																					p.R1800X		Atlas-SNP	.											.	.	.	.	0			c.C5398T						.						65	71	69					10																	75561253		2067	4212	6279	SO:0001819	synonymous_variant	23053	exon26			CTCACTCGAGATG	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"Zinc fingers, SWIM-type"	23528	protein-coding gene	gene with protein product			"KIAA0913"	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.5490C>T	chr10.hg19:g.75561253C>T		77.0	0.0		91.0	18.0	NM_001242488	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Nonsense_Mutation	SNP	ENST00000605216.1	hg19		.	.	.	.	.	.	.	.	.	.	C	3.374	-0.127854	0.06753	.	.	ENSG00000214655	ENST00000412198	.	.	.	5.99	1.43	0.22495	.	.	.	.	.	T	0.43366	0.1244	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24835	-1.0149	4	.	.	.	-4.5216	2.2063	0.03936	0.2036:0.3643:0.2793:0.1528	.	.	.	.	L	1105	.	.	S	+	2	0	KIAA0913	75231259	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.476000	0.22180	0.387000	0.25024	0.655000	0.94253	TCG	.	.		0.592	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		T	75561253	C	T	75561253	2	4	1	1	0	0	0	0	0	0	0	1	8209	871	31	1		1	KIAA0913	10	75561253	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	74155507	75561253	59973494	66	66										
LRIT2	340745	hgsc.bcm.edu	37	chr10	85982126	85982126	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	acctccttcctgaaggcttcAtccgatgcaatgtagagggt	10	11	1	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr10:85982126A>G	ENST00000372113.4	-	3	1208	c.1203T>C	c.(1201-1203)gaT>gaC	p.D401D	LRIT2_ENST00000538192.1_Silent_p.D411D	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	401	Fibronectin type-III.					integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						TGAAGGCTTCATCCGATGCAA	0.532																																					p.D401D		Atlas-SNP	.											.	LRIT2	81	.	0			c.T1203C						.						108	97	100					10																	85982126		2203	4300	6503	SO:0001819	synonymous_variant	340745	exon3			GGCTTCATCCGAT		CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"Immunoglobulin superfamily / I-set domain containing"	23443	protein-coding gene	gene with protein product			"leucine rich repeat containing 22"	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.1203T>C	chr10.hg19:g.85982126A>G		60.0	0.0		79.0	29.0	NM_001017924	B7ZME6	Silent	SNP	ENST00000372113.4	hg19	CCDS31234.1																																																																																			.	.		0.532	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697		G	85982126	A	G	85982126	2	3	1	1	0	0	0	0	0	0	0	1	8957	214	8	2		2	LRIT2	10	85982126	Silent	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	10420873	85982126	49552621	67	67										
EBF3	253738	hgsc.bcm.edu	37	chr10	131761669	131761669	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gtccacaaaagcggtcctttCaatctccaccggctgcccct	7	17	2	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr10:131761669C>T	ENST00000355311.5	-	2	325	c.253G>A	c.(253-255)Gaa>Aaa	p.E85K	EBF3_ENST00000368648.3_Missense_Mutation_p.E85K			Q9H4W6	COE3_HUMAN	early B-cell factor 3	85					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		GCGGTCCTTTCAATCTCCACC	0.557																																					p.E85K		Atlas-SNP	.											.	EBF3	193	.	0			c.G253A						.						79	86	84					10																	131761669		2203	4300	6503	SO:0001583	missense	253738	exon2			TCCTTTCAATCTC		CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.253G>A	chr10.hg19:g.131761669C>T	ENSP00000347463:p.Glu85Lys	78.0	0.0		88.0	34.0	NM_001005463	A0AUY1|Q5T6H9|Q9H4W5	Missense_Mutation	SNP	ENST00000355311.5	hg19		.	.	.	.	.	.	.	.	.	.	C	22.8	4.342455	0.81911	.	.	ENSG00000108001	ENST00000355311;ENST00000368648	T;T	0.58797	0.31;0.35	3.45	3.45	0.39498	.	0.000000	0.85682	U	0.000000	T	0.76630	0.4014	M	0.87456	2.885	0.80722	D	1	D;D	0.71674	0.998;0.997	D;P	0.64595	0.927;0.89	T	0.82657	-0.0349	10	0.87932	D	0	-6.2858	14.5175	0.67827	0.0:1.0:0.0:0.0	.	85;85	Q9H4W6;Q9H4W6-2	COE3_HUMAN;.	K	85	ENSP00000347463:E85K;ENSP00000357637:E85K	ENSP00000347463:E85K	E	-	1	0	EBF3	131651659	1.000000	0.71417	0.999000	0.59377	0.908000	0.53690	7.027000	0.76463	1.453000	0.47775	0.205000	0.17691	GAA	.	.		0.557	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		T	131761669	C	T	131761669	3	4	1	1	0	0	0	0	1	0	0	0	4884	835	29	3	1462	3	EBF3	10	131761669	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	45779543	131761669	3773078	68	68										
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	377314	377314	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	agtacatggagcggctgaacGcgcgccacggcgggtatggg	18	10	0	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr11:377314G>A	ENST00000329962.6	+	14	2191	c.2191G>A	c.(2191-2193)Gcg>Acg	p.A731T		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	731					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCGGCTGAACGCGCGCCACGG	0.701																																					p.A731T		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.G2191A						.						10	7	8					11																	377314		1972	3868	5840	SO:0001583	missense	338707	exon14			CTGAACGCGCGCC	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"Beta 4-glycosyltransferases"	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2191G>A	chr11.hg19:g.377314G>A	ENSP00000328277:p.Ala731Thr	68.0	0.0		74.0	6.0	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	hg19	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	g	9.533	1.111282	0.20714	.	.	ENSG00000182272	ENST00000329962	T	0.15256	2.44	3.28	0.294	0.15747	.	0.382752	0.24774	N	0.035713	T	0.11410	0.0278	L	0.39898	1.24	0.26844	N	0.9683	P	0.34837	0.472	B	0.30855	0.121	T	0.17319	-1.0373	10	0.34782	T	0.22	-8.9964	9.0266	0.36234	0.2727:0.0:0.7273:0.0	.	731	Q76KP1	B4GN4_HUMAN	T	731	ENSP00000328277:A731T	ENSP00000328277:A731T	A	+	1	0	B4GALNT4	367314	0.703000	0.27826	0.058000	0.19502	0.114000	0.19823	1.287000	0.33284	0.232000	0.21100	0.205000	0.17691	GCG	.	.		0.701	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		A	377314	G	A	377314	3	1	1	1	0	0	0	0	1	0	0	0	1269	1087	38	1	2245	1	B4GALNT4	11	377314	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10		377314	134629202	69	69										
SAA2	6289	hgsc.bcm.edu	37	chr11	18266987	18266987	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tctctgccactcctgccccaTttattggcagcctgatcggc	8	16	1	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr11:18266987T>C	ENST00000526900.1	-	4	489	c.306A>G	c.(304-306)aaA>aaG	p.K102K	SAA2_ENST00000414546.2_Intron|SAA2_ENST00000256733.4_Silent_p.K102K|SAA2_ENST00000528349.1_Intron|SAA2_ENST00000529528.1_Silent_p.K102K|SAA2_ENST00000530400.1_Intron|RNA5SP333_ENST00000363466.1_RNA|SAA2-SAA4_ENST00000524555.1_RNA			P0DJI9	SAA2_HUMAN	serum amyloid A2	102					acute-phase response (GO:0006953)	extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(1)	6						TCCTGCCCCATTTATTGGCAG	0.567																																					p.K102K		Atlas-SNP	.											.	SAA2	22	.	0			c.A306G						.						94	84	87					11																	18266987		2199	4293	6492	SO:0001819	synonymous_variant	6289	exon4			GCCCCATTTATTG	M26152	CCDS7833.1, CCDS44548.1	11p15.1-p14	2008-07-21			ENSG00000134339	ENSG00000134339			10514	protein-coding gene	gene with protein product		104751				7686132	Standard	NM_030754		Approved			P0DJI9	OTTHUMG00000166484	ENST00000526900.1:c.306A>G	chr11.hg19:g.18266987T>C		135.0	0.0		143.0	29.0	NM_030754	G3XAK9|P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Silent	SNP	ENST00000526900.1	hg19	CCDS7833.1																																																																																			.	.		0.567	SAA2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389983.1	NM_030754		C	18266987	T	C	18266987	2	2	1	1	0	0	0	0	0	0	0	1	13814	1490	52	2		2	SAA2	11	18266987	Silent	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	17889673	18266987	116739529	70	70										
C11orf30	56946	hgsc.bcm.edu	37	chr11	76175034	76175034	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	atgagcaacatcatgcagagCattgccaactccttaccacc	6	14	1	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr11:76175034C>T	ENST00000529032.1	+	6	741	c.741C>T	c.(739-741)agC>agT	p.S247S	C11orf30_ENST00000525038.1_Silent_p.S262S|C11orf30_ENST00000524490.1_Silent_p.S248S|C11orf30_ENST00000525919.1_Silent_p.S248S|C11orf30_ENST00000533248.1_Silent_p.S261S|C11orf30_ENST00000343878.3_Silent_p.S247S|C11orf30_ENST00000524767.1_Silent_p.S262S|C11orf30_ENST00000334736.3_Silent_p.S247S			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	247	Interaction with BRCA2.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						TCATGCAGAGCATTGCCAACT	0.453																																					p.S247S		Atlas-SNP	.											.	C11orf30	123	.	0			c.C741T						.						184	163	170					11																	76175034		2200	4292	6492	SO:0001819	synonymous_variant	56946	exon7			GCAGAGCATTGCC	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.741C>T	chr11.hg19:g.76175034C>T		177.0	0.0		212.0	29.0	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Silent	SNP	ENST00000529032.1	hg19	CCDS8244.1																																																																																			.	.		0.453	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193		T	76175034	C	T	76175034	2	4	1	1	0	0	0	0	0	0	0	1	1638	709	25	3		3	C11orf30	11	76175034	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	57908047	76175034	58831482	71	71										
KCNC2	3747	hgsc.bcm.edu	37	chr12	75601373	75601373	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ctcctcctcgaagagcggccCgcacacgtctgcggggcagt	13	16	1	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr12:75601373C>T	ENST00000549446.1	-	2	1071	c.391G>A	c.(391-393)Ggg>Agg	p.G131R	KCNC2_ENST00000341669.3_Missense_Mutation_p.G131R|KCNC2_ENST00000393288.2_Missense_Mutation_p.G131R|KCNC2_ENST00000548513.1_Missense_Mutation_p.G131R|KCNC2_ENST00000550433.1_Missense_Mutation_p.G131R|KCNC2_ENST00000298972.1_Missense_Mutation_p.G131R|KCNC2_ENST00000350228.2_Missense_Mutation_p.G131R|KCNC2_ENST00000540018.1_Missense_Mutation_p.G131R	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	131					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	AAGAGCGGCCCGCACACGTCT	0.672																																					p.G131R		Atlas-SNP	.											.	KCNC2	239	.	0			c.G391A						.						31	36	34					12																	75601373		2203	4299	6502	SO:0001583	missense	3747	exon2			GCGGCCCGCACAC	AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.391G>A	chr12.hg19:g.75601373C>T	ENSP00000449253:p.Gly131Arg	583.0	1.0		694.0	227.0	NM_139137	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Missense_Mutation	SNP	ENST00000549446.1	hg19	CCDS9007.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.460089	0.84317	.	.	ENSG00000166006	ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000350228;ENST00000540018;ENST00000393288	T;T;T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	3.38	3.38	0.38709	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.470849	0.17462	N	0.173406	T	0.64371	0.2592	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;0.999	D;D;D;D;D	0.97110	1.0;1.0;0.98;1.0;0.92	T	0.69967	-0.5001	10	0.66056	D	0.02	.	15.3106	0.74028	0.0:1.0:0.0:0.0	.	131;131;131;131;131	F5H030;Q96PR1-2;Q96PR1;Q96PR1-4;Q96PR1-3	.;.;KCNC2_HUMAN;.;.	R	131	ENSP00000448301:G131R;ENSP00000449941:G131R;ENSP00000449253:G131R;ENSP00000340121:G131R;ENSP00000298972:G131R;ENSP00000319877:G131R;ENSP00000438423:G131R;ENSP00000376966:G131R	ENSP00000298972:G131R	G	-	1	0	KCNC2	73887640	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.370000	0.79589	1.898000	0.54952	0.462000	0.41574	GGG	.	.		0.672	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		T	75601373	C	T	75601373	3	4	1	1	0	0	0	0	1	0	0	0	8024	652	23	1	1607	1	KCNC2	12	75601373	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10		75601373	58250522	72	72										
TBX5	6910	hgsc.bcm.edu	37	chr12	114793370	114793370	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ctccactctggcaccatgccAactccgtgcacagagtggta	9	15	1	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr12:114793370A>C	ENST00000310346.4	-	9	2190	c.1524T>G	c.(1522-1524)gtT>gtG	p.V508V	TBX5_ENST00000349716.5_Silent_p.V458V|TBX5_ENST00000405440.2_Silent_p.V508V	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	508				PRTLSPHQYHSVHGVGMVPEWSDNS -> QGLYPLISTTLC TELAWCRVERQ (in Ref. 1; CAA70592). {ECO:0000305}.	apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		GCACCATGCCAACTCCGTGCA	0.542																																					p.V508V	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											.	TBX5	188	.	0			c.T1524G						.						52	50	50					12																	114793370		2203	4300	6503	SO:0001819	synonymous_variant	6910	exon9			CATGCCAACTCCG	U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"T-boxes"	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.1524T>G	chr12.hg19:g.114793370A>C		93.0	0.0		121.0	44.0	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Silent	SNP	ENST00000310346.4	hg19	CCDS9173.1																																																																																			.	.		0.542	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		C	114793370	A	C	114793370	2	2	1	1	0	0	0	0	0	0	0	1	15676	117	5	5		5	TBX5	12	114793370	Silent	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	39191997	114793370	19058525	73	73										
RNF17	56163	hgsc.bcm.edu	37	chr13	25433158	25433158	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gaatttgagctaataaaaatGacaaatgaaattcaaagtaa	6	3	1	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr13:25433158G>T	ENST00000255324.5	+	26	3682	c.3630G>T	c.(3628-3630)atG>atT	p.M1210I	RNF17_ENST00000381921.1_Missense_Mutation_p.M1210I|RNF17_ENST00000339524.3_Missense_Mutation_p.M262I	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1210					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		TAATAAAAATGACAAATGAAA	0.299																																					p.M1210I		Atlas-SNP	.											RNF17_ENST00000255324,NS,carcinoma,0,1	RNF17	259	.	0			c.G3630T						.						36	38	37					13																	25433158		2203	4300	6503	SO:0001583	missense	56163	exon26			AAAAATGACAAAT	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.3630G>T	chr13.hg19:g.25433158G>T	ENSP00000255324:p.Met1210Ile	113.0	0.0		135.0	26.0	NM_031277	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	hg19	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	G	14.05	2.420515	0.42918	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000418120;ENST00000339524	T;T;T;T	0.09723	2.95;2.95;2.95;2.95	5.14	5.14	0.70334	Maternal tudor protein (1);	0.208576	0.43110	D	0.000619	T	0.09512	0.0234	N	0.24115	0.695	0.80722	D	1	P;B;B;P	0.40000	0.454;0.31;0.4;0.698	B;B;B;B	0.40702	0.192;0.171;0.121;0.338	T	0.10177	-1.0641	10	0.45353	T	0.12	-22.1835	12.9058	0.58152	0.0:0.0:0.8374:0.1626	.	1206;262;1210;1210	B7Z7S1;Q5T6R1;Q9BXT8-5;Q9BXT8	.;.;.;RNF17_HUMAN	I	1210;1210;534;262	ENSP00000255324:M1210I;ENSP00000371346:M1210I;ENSP00000388892:M534I;ENSP00000344776:M262I	ENSP00000255324:M1210I	M	+	3	0	RNF17	24331158	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	4.869000	0.63028	2.832000	0.97577	0.655000	0.94253	ATG	.	.		0.299	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		T	25433158	G	T	25433158	3	4	1	1	0	0	0	0	1	0	0	0	13476	1290	45	3	3732	3	RNF17	13	25433158	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10		25433158	89736720	74	74										
COL4A1	1282	hgsc.bcm.edu	37	chr13	110835346	110835346	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tctggcagggttacctttggGgccggggggccctggaaatc	17	10	1	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr13:110835346G>A	ENST00000375820.4	-	28	2210	c.2089C>T	c.(2089-2091)Ccc>Tcc	p.P697S		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	697	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TTACCTTTGGGGCCGGGGGGC	0.612																																					p.P697S		Atlas-SNP	.											.	COL4A1	372	.	0			c.C2089T						.						14	17	16					13																	110835346		2201	4299	6500	SO:0001583	missense	1282	exon28			CTTTGGGGCCGGG	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.2089C>T	chr13.hg19:g.110835346G>A	ENSP00000364979:p.Pro697Ser	103.0	0.0		106.0	27.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.227252	0.58668	.	.	ENSG00000187498	ENST00000375820	D	0.96587	-4.06	4.7	4.7	0.59300	.	0.194402	0.45361	D	0.000376	D	0.97049	0.9036	M	0.76938	2.355	0.80722	D	1	D	0.59767	0.986	P	0.62740	0.906	D	0.96032	0.9017	10	0.08837	T	0.75	.	13.7388	0.62836	0.0:0.1541:0.8459:0.0	.	697	P02462	CO4A1_HUMAN	S	697	ENSP00000364979:P697S	ENSP00000364979:P697S	P	-	1	0	COL4A1	109633347	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	4.589000	0.61006	2.328000	0.79073	0.561000	0.74099	CCC	.	.		0.612	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			A	110835346	G	A	110835346	3	1	1	1	0	0	0	0	1	0	0	0	3691	1232	43	3	3020	3	COL4A1	13	110835346	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	85402188	110835346	4334532	75	75										
PSMB5	5693	hgsc.bcm.edu	37	chr14	23504068	23504068	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ggttcaccggtagcggtctcTccaacacgctggcaagcgcc	12	15	2	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr14:23504068T>C	ENST00000361611.6	-	1	286	c.23A>G	c.(22-24)gAg>gGg	p.E8G	AL132780.1_ENST00000385031.1_RNA|PSMB5_ENST00000493471.2_Missense_Mutation_p.E8G|PSMB5_ENST00000460922.2_Missense_Mutation_p.E8G|PSMB5_ENST00000425762.2_Intron	NM_002797.3	NP_002788.1	P28074	PSB5_HUMAN	proteasome (prosome, macropain) subunit, beta type, 5	8					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to oxidative stress (GO:0006979)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)|Carfilzomib(DB08889)	TAGCGGTCTCTCCAACACGCT	0.577																																					p.E8G		Atlas-SNP	.											.	PSMB5	31	.	0			c.A23G						.						40	39	39					14																	23504068		2203	4300	6503	SO:0001583	missense	5693	exon1			GGTCTCTCCAACA	D29011	CCDS9584.1, CCDS45083.1, CCDS45084.1	14q11.2	2008-08-29			ENSG00000100804	ENSG00000100804		"Proteasome (prosome, macropain) subunits"	9542	protein-coding gene	gene with protein product		600306				8066462, 8811196	Standard	NM_001130725		Approved	X, MB1	uc001wii.3	P28074	OTTHUMG00000028713	ENST00000361611.6:c.23A>G	chr14.hg19:g.23504068T>C	ENSP00000355325:p.Glu8Gly	112.0	0.0		103.0	21.0	NM_001144932	B2R4N9|B4DUM9|D3DS43|E9PAV2|Q16242|Q6PEW2|Q7Z3B5|Q86T01|Q9TNN9	Missense_Mutation	SNP	ENST00000361611.6	hg19	CCDS9584.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.907091	0.33628	.	.	ENSG00000100804	ENST00000361611;ENST00000493471;ENST00000460922	T;T;T	0.51817	0.69;0.69;0.69	5.22	5.22	0.72569	.	0.405202	0.27891	N	0.017439	T	0.30510	0.0767	N	0.24115	0.695	0.80722	D	1	B;B	0.30281	0.275;0.023	B;B	0.30179	0.112;0.026	T	0.11991	-1.0565	10	0.02654	T	1	-15.9303	14.0914	0.64993	0.0:0.0:0.0:1.0	.	8;8	P28074-2;P28074	.;PSB5_HUMAN	G	8	ENSP00000355325:E8G;ENSP00000452424:E8G;ENSP00000451286:E8G	ENSP00000334973:E8G	E	-	2	0	PSMB5	22573908	1.000000	0.71417	0.992000	0.48379	0.747000	0.42532	1.140000	0.31516	1.967000	0.57214	0.454000	0.30748	GAG	.	.		0.577	PSMB5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071695.4	NM_002797		C	23504068	T	C	23504068	3	2	1	1	0	0	0	0	1	0	0	0	12692	1551	54	2	869	2	PSMB5	14	23504068	Missense_Mutation	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10		23504068	83845472	76	76										
SLC22A17	51310	hgsc.bcm.edu	37	chr14	23815958	23815958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gcgacacagctccccgtcccGgagcacctcgggcaggagct	13	17	0	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr14:23815958G>A	ENST00000206544.8	-	9	1852	c.1516C>T	c.(1516-1518)Cgg>Tgg	p.R506W	SLC22A17_ENST00000474057.1_5'UTR|SLC22A17_ENST00000397267.1_Missense_Mutation_p.R506W|SLC22A17_ENST00000397260.3_Missense_Mutation_p.R377W|SLC22A17_ENST00000354772.3_Missense_Mutation_p.R488W	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	506					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|vacuole (GO:0005773)	transmembrane signaling receptor activity (GO:0004888)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)		TCCCCGTCCCGGAGCACCTCG	0.692																																					p.R506W		Atlas-SNP	.											.	SLC22A17	32	.	0			c.C1516T						.						6	8	8					14																	23815958		2134	4208	6342	SO:0001583	missense	51310	exon9			CGTCCCGGAGCAC	AJ243653	CCDS9593.1, CCDS9594.2	14q11.2	2013-05-22	2008-01-11		ENSG00000092096	ENSG00000092096		"Solute carriers"	23095	protein-coding gene	gene with protein product	"neutrophil gelatinase-associated lipocalin receptor"	611461				16377569	Standard	NM_016609		Approved	BOCT, BOIT, NGALR	uc001wjl.3	Q8WUG5	OTTHUMG00000028740	ENST00000206544.8:c.1516C>T	chr14.hg19:g.23815958G>A	ENSP00000206544:p.Arg506Trp	82.0	0.0		61.0	12.0	NM_020372	A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	Missense_Mutation	SNP	ENST00000206544.8	hg19	CCDS9593.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.423948	0.62733	.	.	ENSG00000092096	ENST00000354772;ENST00000397260;ENST00000206544;ENST00000397267	T;T;T;T	0.71222	-0.32;-0.55;-0.27;-0.27	5.38	4.43	0.53597	.	0.154548	0.45126	D	0.000397	T	0.72867	0.3514	N	0.22421	0.69	0.36510	D	0.869537	D;D	0.89917	1.0;1.0	D;D	0.71184	0.951;0.972	T	0.78743	-0.2085	10	0.87932	D	0	-17.5241	13.0764	0.59089	0.0:0.0:0.7716:0.2284	.	488;506	Q8WUG5-2;Q8WUG5	.;S22AH_HUMAN	W	488;377;506;506	ENSP00000346824:R488W;ENSP00000380430:R377W;ENSP00000206544:R506W;ENSP00000380437:R506W	ENSP00000206544:R506W	R	-	1	2	SLC22A17	22885798	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.084000	0.41625	2.804000	0.96469	0.462000	0.41574	CGG	.	.		0.692	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157223.3	NM_020372		A	23815958	G	A	23815958	3	1	1	1	0	0	0	0	1	0	0	0	14463	1115	39	1	104	1	SLC22A17	14	23815958	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	311890	23815958	83533582	77	77										
FOXG1	2290	hgsc.bcm.edu	37	chr14	29236983	29236983	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ggcgagggcggcaaggacggGgaggggggcaaggagggcga	26	6	0	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr14:29236983G>A	ENST00000313071.4	+	1	697	c.498G>A	c.(496-498)ggG>ggA	p.G166G	RP11-966I7.1_ENST00000546560.1_RNA|RP11-966I7.1_ENST00000551395.1_RNA|FOXG1_ENST00000382535.3_Silent_p.G166G|RP11-966I7.1_ENST00000549487.1_RNA	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	166	Gly-rich.				aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G166G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		gcaaggacggggaggggggca	0.711																																					p.G166G		Atlas-SNP	.											FOXG1,arm,malignant_melanoma,0,1	FOXG1	92	.	1	Substitution - coding silent(1)	skin(1)	c.G498A						.						12	13	13					14																	29236983		2191	4294	6485	SO:0001819	synonymous_variant	2290	exon1			GGACGGGGAGGGG		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.498G>A	chr14.hg19:g.29236983G>A		376.0	0.0		340.0	71.0	NM_005249	A6NFY2|P55315|Q14488|Q86XT7	Silent	SNP	ENST00000313071.4	hg19	CCDS9636.1																																																																																			.	.		0.711	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			A	29236983	G	A	29236983	2	1	1	1	0	0	0	0	0	0	0	1	6015	1219	43	3		3	FOXG1	14	29236983	Silent	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	5421025	29236983	78112557	78	78										
ZBTB1	22890	hgsc.bcm.edu	37	chr14	64988788	64988796	+	In_Frame_Del	DEL	TATTTGATG	TATTTGATG	-													0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	aggtaattttcctgagccacTatttgatgtatgtaaaaaaa							TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	TATTTGATG	TATTTGATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr14:64988788_64988796delTATTTGATG	ENST00000554015.1	+	4	997_1005	c.566_574delTATTTGATG	c.(565-576)ctatttgatgta>cta	p.FDV190del	ZBTB1_ENST00000394712.2_In_Frame_Del_p.FDV190del|ZBTB1_ENST00000358738.3_In_Frame_Del_p.FDV190del|RP11-973N13.4_ENST00000554918.1_RNA			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	190					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		CCTGAGCCACTATTTGATGTATGTAAAAA	0.416																																					p.189_191del		Atlas-Indel,Pindel	.											.	ZBTB1	93	.	0			c.565_573del						.																																			SO:0001651	inframe_deletion	22890	exon2			.	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.566_574delTATTTGATG	chr14.hg19:g.64988788_64988796delTATTTGATG	ENSP00000451000:p.Phe190_Val192del	184.0	0.0		191.0	28.0	NM_001123329	A8K6S8|Q86SW8	In_Frame_Del	DEL	ENST00000554015.1	hg19	CCDS45126.1																																																																																			.	.		0.416	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1			-	64988796	TATTTGATG	-	64988788	7	5	1	1	0	1	0	1	0	0	0	0	17537	1522	53	0	568	0	ZBTB1	14	64988788	In_Frame_Del	DEL	TATTTGATG	TCGA-2V-A95S-01A-11D-A36X-10	35751805	64988788	42360752	79	79										
EML5	161436	hgsc.bcm.edu	37	chr14	89153622	89153622	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tcttgagacatctttcaaaaGagtcatcccaaagagctact	6	10	4	3			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr14:89153622G>T	ENST00000380664.5	-	19	2791	c.2792C>A	c.(2791-2793)tCt>tAt	p.S931Y	EML5_ENST00000352093.5_Missense_Mutation_p.S893Y|EML5_ENST00000554922.1_Missense_Mutation_p.S931Y			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	931						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						TCTTTCAAAAGAGTCATCCCA	0.343																																					p.S931Y		Atlas-SNP	.											.	EML5	141	.	0			c.C2792A						.						59	52	54					14																	89153622		1803	4074	5877	SO:0001583	missense	161436	exon19			TCAAAAGAGTCAT	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.2792C>A	chr14.hg19:g.89153622G>T	ENSP00000370039:p.Ser931Tyr	296.0	0.0		295.0	60.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509389	0.64522	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.44083	0.93;2.16;2.67	4.5	4.5	0.54988	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.323197	0.28104	N	0.016588	T	0.46870	0.1415	L	0.40543	1.245	0.41614	D	0.988924	P;B	0.35033	0.481;0.349	P;B	0.45195	0.473;0.206	T	0.52290	-0.8595	10	0.62326	D	0.03	-0.9106	17.3499	0.87321	0.0:0.0:1.0:0.0	.	931;931	Q05BV3-5;Q05BV3	.;EMAL5_HUMAN	Y	931;893;931	ENSP00000451998:S931Y;ENSP00000298315:S893Y;ENSP00000370039:S931Y	ENSP00000298315:S893Y	S	-	2	0	EML5	88223375	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.124000	0.64709	2.498000	0.84270	0.467000	0.42956	TCT	.	.		0.343	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89153622	G	T	89153622	3	4	1	1	0	0	0	0	1	0	0	0	5102	942	33	3	3241	3	EML5	14	89153622	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	24164834	89153622	18195918	80	80										
RTL1	388015	hgsc.bcm.edu	37	chr14	101349210	101349210	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	agtcctgtctgttggtcagcAtgtcctgcaggtcccagtat	11	11	2	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr14:101349210A>C	ENST00000534062.1	-	1	1974	c.1916T>G	c.(1915-1917)aTg>aGg	p.M639R	MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA|MIR432_ENST00000606207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	639					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						GTTGGTCAGCATGTCCTGCAG	0.542																																					p.M639R		Atlas-SNP	.											.	RTL1	120	.	0			c.T1916G						.						94	77	82					14																	101349210		692	1591	2283	SO:0001583	missense	388015	exon1			GTCAGCATGTCCT		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.1916T>G	chr14.hg19:g.101349210A>C	ENSP00000435342:p.Met639Arg	79.0	0.0		81.0	27.0	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	hg19	CCDS53910.1	.	.	.	.	.	.	.	.	.	.	A	15.72	2.917220	0.52546	.	.	ENSG00000254656	ENST00000534062	T	0.39997	1.05	3.4	3.4	0.38934	.	.	.	.	.	T	0.39064	0.1064	N	0.10685	0.025	0.33343	D	0.570139	D	0.61080	0.989	P	0.62382	0.901	T	0.54523	-0.8281	9	0.87932	D	0	.	10.4533	0.44535	1.0:0.0:0.0:0.0	.	639	E9PKS8	.	R	639	ENSP00000435342:M639R	ENSP00000435342:M639R	M	-	2	0	RTL1	100418963	1.000000	0.71417	0.939000	0.37840	0.992000	0.81027	5.553000	0.67287	1.782000	0.52362	0.383000	0.25322	ATG	.	.		0.542	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		C	101349210	A	C	101349210	3	2	1	1	0	0	0	0	1	0	0	0	13739	217	8	5	2164	5	RTL1	14	101349210	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	12195588	101349210	6000330	81	81										
MYO1E	4643	hgsc.bcm.edu	37	chr15	59466403	59466403	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tatcactcgagcatacccatCatactttctctctctcatct	2	15	6	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr15:59466403C>G	ENST00000288235.4	-	20	2485	c.2086G>C	c.(2086-2088)Gat>Cat	p.D696H	MIR2116_ENST00000517221.1_RNA	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	696	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		GCATACCCATCATACTTTCTC	0.408																																					p.D696H		Atlas-SNP	.											.	MYO1E	99	.	0			c.G2086C						.						135	140	138					15																	59466403		2191	4291	6482	SO:0001583	missense	4643	exon20			ACCCATCATACTT	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.2086G>C	chr15.hg19:g.59466403C>G	ENSP00000288235:p.Asp696His	78.0	0.0		73.0	18.0	NM_004998	Q14778	Missense_Mutation	SNP	ENST00000288235.4	hg19	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.279506	0.59758	.	.	ENSG00000157483	ENST00000288235	D	0.95137	-3.62	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.93184	0.7829	M	0.78916	2.43	0.80722	D	1	P	0.39157	0.662	B	0.37387	0.248	D	0.91497	0.5216	10	0.05721	T	0.95	.	19.15	0.93483	0.0:1.0:0.0:0.0	.	696	Q12965	MYO1E_HUMAN	H	696	ENSP00000288235:D696H	ENSP00000288235:D696H	D	-	1	0	MYO1E	57253695	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.908000	0.69916	2.750000	0.94351	0.655000	0.94253	GAT	.	.		0.408	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		G	59466403	C	G	59466403	3	3	1	1	0	0	0	0	1	0	0	0	10081	826	29	4	1276	4	MYO1E	15	59466403	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10		59466403	43064989	82	82										
MAN2C1	4123	hgsc.bcm.edu	37	chr15	75660853	75660889	+	Frame_Shift_Del	DEL	GAGCGGCGACACGAACTTCTCCACCCGCTCCAGCGTG	GAGCGGCGACACGAACTTCTCCACCCGCTCCAGCGTG	-													0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	aggttacagtcggtaaagtaGagcggcgacacgaacttctc					rs199781388		TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	GAGCGGCGACACGAACTTCTCCACCCGCTCCAGCGTG	GAGCGGCGACACGAACTTCTCCACCCGCTCCAGCGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr15:75660853_75660889delGAGCGGCGACACGAACTTCTCCACCCGCTCCAGCGTG	ENST00000267978.5	-	1	82_118	c.36_72delCACGCTGGAGCGGGTGGAGAAGTTCGTGTCGCCGCTC	c.(34-72)accacgctggagcgggtggagaagttcgtgtcgccgctcfs	p.TTLERVEKFVSPL12fs	MAN2C1_ENST00000565683.1_Frame_Shift_Del_p.TTLERVEKFVSPL12fs|RP11-817O13.8_ENST00000563278.1_lincRNA|MAN2C1_ENST00000563622.1_Frame_Shift_Del_p.TTLERVEKFVSPL12fs|MAN2C1_ENST00000563539.1_5'UTR|MAN2C1_ENST00000569482.1_Frame_Shift_Del_p.TTLERVEKFVSPL12fs	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	12					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.P23L(1)		central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						CGGTAAAGTAGAGCGGCGACACGAACTTCTCCACCCGCTCCAGCGTGGTGCGCCAGT	0.679																																					p.13_25del		Atlas-Indel,Pindel	.											.	MAN2C1	76	.	1	Substitution - Missense(1)	large_intestine(1)	c.37_73del						.																																			SO:0001589	frameshift_variant	4123	exon1			.	AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.36_72delCACGCTGGAGCGGGTGGAGAAGTTCGTGTCGCCGCTC	chr15.hg19:g.75660853_75660889delGAGCGGCGACACGAACTTCTCCACCCGCTCCAGCGTG	ENSP00000267978:p.Thr12fs	237.0	0.0		176.0	26.0	NM_001256494	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Frame_Shift_Del	DEL	ENST00000267978.5	hg19	CCDS32298.1																																																																																			.	.		0.679	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1			-	75660889	GAGCGGCGACACGAACTTCTCCACCCGCTCCAGCGTG	-	75660853	7	5	1	1	0	1	0	1	0	0	0	0	9227	929	33	0	3154	0	MAN2C1	15	75660853	Frame_Shift_Del	DEL	GAGCGGCGACACGAACTTCTCCACCCGCTCCAGCGTG	TCGA-2V-A95S-01A-11D-A36X-10	16194450	75660853	26870539	83	83										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94841718	94841718	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ctccgggccacagtcttcctAcacctcggtgcccagcagtc	9	18	1	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr15:94841718A>G	ENST00000357742.4	+	1	224	c.224A>G	c.(223-225)tAc>tGc	p.Y75C	MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Missense_Mutation_p.Y75C|MCTP2_ENST00000543482.1_Missense_Mutation_p.Y75C	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	75					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			CAGTCTTCCTACACCTCGGTG	0.587																																					p.Y75C		Atlas-SNP	.											.	MCTP2	122	.	0			c.A224G						.						55	59	57					15																	94841718		2197	4298	6495	SO:0001583	missense	55784	exon1			CTTCCTACACCTC	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.224A>G	chr15.hg19:g.94841718A>G	ENSP00000350377:p.Tyr75Cys	71.0	0.0		65.0	12.0	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	hg19	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.637714	0.47049	.	.	ENSG00000140563	ENST00000543482;ENST00000556363;ENST00000451018;ENST00000357742	T;T;T	0.69926	-0.44;-0.21;-0.05	5.04	3.87	0.44632	.	0.136830	0.32918	N	0.005496	T	0.58864	0.2152	N	0.24115	0.695	0.36343	D	0.859602	P;P;P;P;D	0.67145	0.944;0.904;0.845;0.906;0.996	P;P;B;B;P	0.56216	0.634;0.513;0.315;0.43;0.794	T	0.63972	-0.6516	10	0.39692	T	0.17	.	4.8741	0.13648	0.4753:0.3241:0.0:0.2006	.	75;75;75;75;75	F5H415;Q6DN12-2;Q6DN12;B7Z6H2;G3V2J2	.;.;MCTP2_HUMAN;.;.	C	75	ENSP00000438521:Y75C;ENSP00000395109:Y75C;ENSP00000350377:Y75C	ENSP00000350377:Y75C	Y	+	2	0	MCTP2	92642722	0.799000	0.28903	0.980000	0.43619	0.650000	0.38633	2.731000	0.47343	1.906000	0.55180	0.460000	0.39030	TAC	.	.		0.587	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		G	94841718	A	G	94841718	3	3	1	1	0	0	0	0	1	0	0	0	9410	391	14	2	226	2	MCTP2	15	94841718	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	19180865	94841718	7689674	84	84										
PKD1	5310	hgsc.bcm.edu	37	chr16	2140499	2140499	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ggtgacaggtgccaggactcGgcaggacacagggtagagag	18	8	0	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr16:2140499G>A	ENST00000262304.4	-	45	12439	c.12231C>T	c.(12229-12231)gcC>gcT	p.A4077A	PKD1_ENST00000423118.1_Silent_p.A4076A|MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	4077					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GCCAGGACTCGGCAGGACACA	0.682																																					p.A4077A		Atlas-SNP	.											.	PKD1	184	.	0			c.C12231T						.						25	28	27					16																	2140499		2185	4288	6473	SO:0001819	synonymous_variant	5310	exon45			GGACTCGGCAGGA	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.12231C>T	chr16.hg19:g.2140499G>A		113.0	0.0		90.0	4.0	NM_001009944	Q15140|Q15141	Silent	SNP	ENST00000262304.4	hg19	CCDS32369.1																																																																																			.	.		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2140499	G	A	2140499	2	1	1	1	0	0	0	0	0	0	0	1	11972	1103	39	1		1	PKD1	16	2140499	Silent	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10		2140499	88214254	85	85										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2819139	2819139	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tcctcctcctcctcctcctcCtcttcttcctcctcctcttc	0	24	3	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr16:2819139C>T	ENST00000301740.8	+	12	8424	c.7875C>T	c.(7873-7875)tcC>tcT	p.S2625S	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2625	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						cctcctcctcctcttcttcct	0.592																																					p.S2625S		Atlas-SNP	.											.	SRRM2	263	.	0			c.C7875T						.						141	121	128					16																	2819139		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon12			CTCCTCCTCTTCT	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.7875C>T	chr16.hg19:g.2819139C>T		56.0	0.0		69.0	4.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.		0.592	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2819139	C	T	2819139	2	4	1	1	0	0	0	0	0	0	0	1	15184	668	24	3		3	SRRM2	16	2819139	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	678640	2819139	87535614	86	86										
GLG1	2734	hgsc.bcm.edu	37	chr16	74524981	74524981	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gtagggtccgcccttttcgaTgtaatccggaacaatggtgt	12	9	0	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr16:74524981T>A	ENST00000422840.2	-	8	1366	c.1367A>T	c.(1366-1368)cAt>cTt	p.H456L	GLG1_ENST00000447066.2_Missense_Mutation_p.H445L|GLG1_ENST00000205061.5_Missense_Mutation_p.H456L	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	456					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						CCCTTTTCGATGTAATCCGGA	0.502																																					p.H456L		Atlas-SNP	.											.	GLG1	106	.	0			c.A1367T						.						164	142	149					16																	74524981		2198	4300	6498	SO:0001583	missense	2734	exon8			TTTCGATGTAATC		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.1367A>T	chr16.hg19:g.74524981T>A	ENSP00000405984:p.His456Leu	166.0	0.0		190.0	10.0	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	hg19	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	T	33	5.274972	0.95459	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.57710	0.2072	L	0.53249	1.67	0.80722	D	1	P;P;P	0.42620	0.785;0.758;0.714	B;B;B	0.43052	0.406;0.195;0.163	T	0.57081	-0.7872	9	0.33940	T	0.23	-3.1895	15.9905	0.80202	0.0:0.0:0.0:1.0	.	456;456;445	Q92896;Q92896-2;B7Z8Y4	GSLG1_HUMAN;.;.	L	456;445;456	.	ENSP00000205061:H456L	H	-	2	0	GLG1	73082482	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.825000	0.86693	2.176000	0.68965	0.533000	0.62120	CAT	.	.		0.502	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		A	74524981	T	A	74524981	3	1	1	1	0	0	0	0	1	0	0	0	6444	1464	51	4	2328	4	GLG1	16	74524981	Missense_Mutation	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	71705842	74524981	15829772	87	87										
OR1A1	8383	hgsc.bcm.edu	37	chr17	3118953	3118953	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tcctctacactggaattcatCctcctgggagttactggtca	8	12	3	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr17:3118953C>G	ENST00000304094.1	+	1	39	c.39C>G	c.(37-39)atC>atG	p.I13M		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						TGGAATTCATCCTCCTGGGAG	0.418																																					p.I13M		Atlas-SNP	.											.	OR1A1	54	.	0			c.C39G						.						109	94	99					17																	3118953		2203	4300	6503	SO:0001583	missense	8383	exon1			ATTCATCCTCCTG	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"GPCR / Class A : Olfactory receptors"	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.39C>G	chr17.hg19:g.3118953C>G	ENSP00000305207:p.Ile13Met	99.0	0.0		73.0	17.0	NM_014565	A5D914|Q6IFM1|Q6NTA9|Q96R87	Missense_Mutation	SNP	ENST00000304094.1	hg19	CCDS11022.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.742613	0.49151	.	.	ENSG00000172146	ENST00000304094	T	0.01034	5.42	4.76	-1.89	0.07689	.	0.278577	0.25951	N	0.027260	T	0.02304	0.0071	M	0.82630	2.6	0.21416	N	0.999693	D	0.53462	0.96	P	0.49502	0.613	T	0.23476	-1.0187	10	0.72032	D	0.01	.	8.8951	0.35458	0.0:0.4024:0.0:0.5976	.	13	Q9P1Q5	OR1A1_HUMAN	M	13	ENSP00000305207:I13M	ENSP00000305207:I13M	I	+	3	3	OR1A1	3065703	0.000000	0.05858	0.992000	0.48379	0.867000	0.49689	-0.944000	0.03913	-0.186000	0.10533	0.436000	0.28706	ATC	.	.		0.418	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565		G	3118953	C	G	3118953	3	3	1	1	0	0	0	0	1	0	0	0	10958	845	30	4	41	4	OR1A1	17	3118953	Missense_Mutation	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10		3118953	78076257	88	88										
COL1A1	1277	hgsc.bcm.edu	37	chr17	48263287	48263287	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	cgctgttcttgcagtggtagGtgatgttctgggaggcctcg	16	8	2	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr17:48263287G>A	ENST00000225964.5	-	50	4218	c.4100C>T	c.(4099-4101)aCc>aTc	p.T1367I		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	1367	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	GCAGTGGTAGGTGATGTTCTG	0.627			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.T1367I		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1	158	.	0			c.C4100T						.						104	78	87					17																	48263287		2203	4300	6503	SO:0001583	missense	1277	exon50			TGGTAGGTGATGT	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.4100C>T	chr17.hg19:g.48263287G>A	ENSP00000225964:p.Thr1367Ile	90.0	0.0		85.0	16.0	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Missense_Mutation	SNP	ENST00000225964.5	hg19	CCDS11561.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.874688	0.51695	.	.	ENSG00000108821	ENST00000225964	T	0.80909	-1.43	4.07	4.07	0.47477	Fibrillar collagen, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.92792	0.7708	H	0.96833	3.89	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.95224	0.8336	10	0.87932	D	0	.	15.1789	0.72938	0.0:0.0:1.0:0.0	.	1367	P02452	CO1A1_HUMAN	I	1367	ENSP00000225964:T1367I	ENSP00000225964:T1367I	T	-	2	0	COL1A1	45618286	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.534000	0.98061	2.094000	0.63399	0.313000	0.20887	ACC	.	.		0.627	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			A	48263287	G	A	48263287	3	1	1	1	0	0	0	0	1	0	0	0	3679	1261	44	3	302	3	COL1A1	17	48263287	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	45144334	48263287	32931923	89	89										
CCDC46	201134	hgsc.bcm.edu	37	chr17	63685338	63685338	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ctaattcatcttgtaaaaccTgaaacggtataaaataaaga	5	6	2	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr17:63685338T>A	ENST00000392769.2	-	24	2826		c.e24-2		CEP112_ENST00000535342.2_Splice_Site|CEP112_ENST00000580482.1_Splice_Site|CEP112_ENST00000537949.1_Splice_Site|CEP112_ENST00000541355.1_Splice_Site|CEP112_ENST00000317442.8_Splice_Site	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa						receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						TTGTAAAACCTGAAACGGTAT	0.353																																					.		Atlas-SNP	.											.	CEP112	192	.	0			c.376-2A>T						.						88	83	85					17																	63685338		2203	4299	6502	SO:0001630	splice_region_variant	201134	exon5			AAAACCTGAAACG	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"coiled-coil domain containing 46"	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.2608-2A>T	chr17.hg19:g.63685338T>A		83.0	0.0		110.0	24.0	NM_001037325	Q6PIB5|Q8NCR4|Q8NFR4	Splice_Site	SNP	ENST00000392769.2	hg19	CCDS32710.1	.	.	.	.	.	.	.	.	.	.	T	12.51	1.958452	0.34565	.	.	ENSG00000154240	ENST00000535342;ENST00000392769;ENST00000317442;ENST00000541355;ENST00000537949	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5364	0.67963	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CEP112	61115800	1.000000	0.71417	0.998000	0.56505	0.164000	0.22412	5.062000	0.64326	2.221000	0.72209	0.460000	0.39030	.	.	.		0.353	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	Intron	A	63685338	T	A	63685338	5	1	1	1	0	0	0	0	0	0	1	0	2819	1594	55	4	277	4	CCDC46	17	63685338	Splice_Site	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	15422051	63685338	17509872	90	90										
DSC1	1823	hgsc.bcm.edu	37	chr18	28720139	28720139	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gggccctcatcactgtctatAattttaacggtgacagttgt	9	9	3	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr18:28720139A>T	ENST00000257198.5	-	10	1647	c.1386T>A	c.(1384-1386)atT>atA	p.I462I	DSC1_ENST00000257197.3_Silent_p.I462I|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	462	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CACTGTCTATAATTTTAACGG	0.448																																					p.I462I		Atlas-SNP	.											.	DSC1	240	.	0			c.T1386A						.						105	100	102					18																	28720139		2203	4300	6503	SO:0001819	synonymous_variant	1823	exon10			GTCTATAATTTTA	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"Cadherins / Major cadherins"	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1386T>A	chr18.hg19:g.28720139A>T		109.0	0.0		126.0	21.0	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	hg19	CCDS11894.1																																																																																			.	.		0.448	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421		T	28720139	A	T	28720139	2	4	1	1	0	0	0	0	0	0	0	1	4767	358	13	4		4	DSC1	18	28720139	Silent	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10		28720139	49357109	91	91										
DPP9	91039	hgsc.bcm.edu	37	chr19	4682753	4682753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gggccacggaacccgcctcaTagccgtgctggttgttctca	12	14	2	0	rs376453990		TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr19:4682753T>C	ENST00000598800.1	-	21	2847	c.2342A>G	c.(2341-2343)tAt>tGt	p.Y781C	DPP9_ENST00000262960.9_Missense_Mutation_p.Y810C|DPP9_ENST00000594671.1_Missense_Mutation_p.Y781C|AC005594.3_ENST00000381796.1_RNA|DPP9_ENST00000601173.1_5'Flank			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	781						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		ACCCGCCTCATAGCCGTGCTG	0.667																																					p.Y810C		Atlas-SNP	.											.	DPP9	59	.	0			c.A2429G						.	T	CYS/TYR,	1,4261		0,1,2130	57	69	65		2429,	2.2	1	19		65	0,8496		0,0,4248	no	missense,intron	DPP9,LOC100131094	NM_139159.4,NM_001242901.1	194,	0,1,6378	CC,CT,TT		0.0,0.0235,0.0078	probably-damaging,	810/893,	4682753	1,12757	2131	4248	6379	SO:0001583	missense	91039	exon20			GCCTCATAGCCGT	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"dipeptidylpeptidase 9"				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.2342A>G	chr19.hg19:g.4682753T>C	ENSP00000469603:p.Tyr781Cys	81.0	0.0		70.0	17.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Missense_Mutation	SNP	ENST00000598800.1	hg19		.	.	.	.	.	.	.	.	.	.	t	17.15	3.314916	0.60524	2.35E-4	0.0	ENSG00000142002	ENST00000357909;ENST00000381797;ENST00000262960	T	0.40756	1.02	3.29	2.24	0.28232	.	0.000000	0.85682	D	0.000000	T	0.76154	0.3948	H	0.99516	4.605	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78448	-0.2200	10	0.87932	D	0	-24.3259	8.3565	0.32333	0.1756:0.0:0.0:0.8243	.	810	Q1ZZB8	.	C	889;751;810	ENSP00000262960:Y810C	ENSP00000262960:Y810C	Y	-	2	0	DPP9	4633753	1.000000	0.71417	0.995000	0.50966	0.916000	0.54674	7.691000	0.84191	0.451000	0.26802	0.444000	0.29173	TAT	.	.		0.667	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2			C	4682753	T	C	4682753	3	2	1	1	0	0	0	0	1	0	0	0	4735	1406	49	2	261	2	DPP9	19	4682753	Missense_Mutation	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10		4682753	54446230	92	92										
MUC16	94025	hgsc.bcm.edu	37	chr19	9063485	9063485	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	atgctctctggtaatgtggaGgaaacaggagaaggtgaagt	15	4	1	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr19:9063485G>T	ENST00000397910.4	-	3	24164	c.23961C>A	c.(23959-23961)tcC>tcA	p.S7987S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7989	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTAATGTGGAGGAAACAGGAG	0.473																																					p.S7987S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C23961A						.						88	85	86					19																	9063485		2002	4172	6174	SO:0001819	synonymous_variant	94025	exon3			TGTGGAGGAAACA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.23961C>A	chr19.hg19:g.9063485G>T		104.0	0.0		116.0	23.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9063485	G	T	9063485	2	4	1	1	0	0	0	0	0	0	0	1	9982	987	35	3		3	MUC16	19	9063485	Silent	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	4380732	9063485	50065498	93	93										
TSPAN16	26526	hgsc.bcm.edu	37	chr19	11411928	11411930	+	Missense_Mutation	TNP	AGA	AGA	TTT													0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tgaccctgaggaagaattacAgaggttacaacgagccagac							TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A|G|A	A|G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr19:11411928_11411930AGA>TTT	ENST00000316737.1	+	4	544_546	c.394_396AGA>TTT	c.(394-396)AGA>TTT	p.R132F	TSPAN16_ENST00000592955.1_Missense_Mutation_p.R107F|CTC-510F12.4_ENST00000586356.1_RNA|TSPAN16_ENST00000590327.1_Missense_Mutation_p.R132F	NM_012466.2	NP_036598.1	Q9UKR8	TSN16_HUMAN	tetraspanin 16	132						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	12						GAAGAATTACAGAGGTTACAACG	0.458																																					p.R132X|p.R132I|p.R132S		Atlas-SNP	.											.	TSPAN16	22	.	0			c.A394T|c.G395T|c.A396T						.																																			SO:0001583	missense	26526	exon4			AATTACAGAGGTT|ATTACAGAGGTTA|TTACAGAGGTTAC	BC029908	CCDS12256.1, CCDS62549.1, CCDS62550.1	19p13.2	2013-02-14	2005-03-21	2005-03-21	ENSG00000130167	ENSG00000130167		"Tetraspanins"	30725	protein-coding gene	gene with protein product			"transmembrane 4 superfamily member 16"	TM4SF16		10500248	Standard	NM_012466		Approved	TM4-B, TM-8	uc002mqv.1	Q9UKR8	OTTHUMG00000180833	ENST00000316737.1:c.394_396AGA>TTT	chr19.hg19:g.11411928AGA>TTT	ENSP00000319486:p.Arg132Phe	143.0|144.0|145.0	0.0		162.0|160.0|160.0	30.0|31.0|31.0	NM_012466	K7EN22|K7EPD8|Q8N6J7	Nonsense_Mutation|Missense_Mutation|Missense_Mutation	SNP	ENST00000316737.1	hg19	CCDS12256.1																																																																																			.	.		0.458	TSPAN16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453204.1	NM_012466		TTT	11411930	AGA	TTT	11411928	3	4	1	1	0	0	0	0	1	0	0	0	16655	180	7	4	408	4	TSPAN16	19	11411928	Missense_Mutation	TNP	AGA	TCGA-2V-A95S-01A-11D-A36X-10	2348443	11411928	47717055	94	94										
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47575379	47575379	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	gtccaccgggtccagggaacCtagaagagggaaaaggtgcc	15	10	0	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr19:47575379C>G	ENST00000253048.5	-	13	1840		c.e13-1		ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4								metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		TCCAGGGAACCTAGAAGAGGG	0.672																																					.		Atlas-SNP	.											.	ZC3H4	96	.	0			c.1803-1G>C						.						13	14	14					19																	47575379		1960	4127	6087	SO:0001630	splice_region_variant	23211	exon14			GGGAACCTAGAAG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"Zinc fingers, CCCH-type domain containing"	17808	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 7"	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1803-1G>C	chr19.hg19:g.47575379C>G		37.0	0.0		34.0	12.0	NM_015168	Q9Y420	Splice_Site	SNP	ENST00000253048.5	hg19	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	C	10.35	1.324898	0.24080	.	.	ENSG00000130749	ENST00000253048	.	.	.	5.21	4.18	0.49190	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0474	0.47867	0.0:0.9115:0.0:0.0884	.	.	.	.	.	-1	.	.	.	-	.	.	ZC3H4	52267219	1.000000	0.71417	0.987000	0.45799	0.219000	0.24729	4.618000	0.61211	1.192000	0.43071	-0.145000	0.13849	.	.	.		0.672	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		Intron	G	47575379	C	G	47575379	5	3	1	1	0	0	0	0	0	0	1	0	17585	695	24	4	2121	4	ZC3H4	19	47575379	Splice_Site	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	36163451	47575379	11553604	95	95										
ZNF836	162962	hgsc.bcm.edu	37	chr19	52659296	52659296	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	aaggttgctccccagtatgaAttcttaaatgtcttacaagg	8	8	2	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr19:52659296A>T	ENST00000322146.8	-	5	2161	c.1640T>A	c.(1639-1641)aTt>aAt	p.I547N	ZNF836_ENST00000597252.1_Missense_Mutation_p.I547N|CTC-471J1.8_ENST00000594362.1_RNA	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	547					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						CCCAGTATGAATTCTTAAATG	0.373																																					p.I547N		Atlas-SNP	.											.	ZNF836	158	.	0			c.T1640A						.						129	139	136					19																	52659296		2061	4238	6299	SO:0001583	missense	162962	exon5			GTATGAATTCTTA	BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"Zinc fingers, C2H2-type", "-"	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.1640T>A	chr19.hg19:g.52659296A>T	ENSP00000325038:p.Ile547Asn	141.0	0.0		137.0	29.0	NM_001102657		Missense_Mutation	SNP	ENST00000322146.8	hg19	CCDS46162.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.239099	0.39598	.	.	ENSG00000196267	ENST00000322146	T	0.07567	3.18	2.09	2.09	0.27110	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.14787	0.0357	L	0.31578	0.945	0.20821	N	0.999842	D	0.76494	0.999	D	0.87578	0.998	T	0.12041	-1.0563	9	0.59425	D	0.04	.	6.0777	0.19925	0.7365:0.2635:0.0:0.0	.	547	Q6ZNA1	ZN836_HUMAN	N	547	ENSP00000325038:I547N	ENSP00000325038:I547N	I	-	2	0	ZNF836	57351108	0.000000	0.05858	0.054000	0.19295	0.012000	0.07955	0.823000	0.27366	0.952000	0.37798	0.397000	0.26171	ATT	.	.		0.373	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		T	52659296	A	T	52659296	3	4	1	1	0	0	0	0	1	0	0	0	18202	101	4	4	1172	4	ZNF836	19	52659296	Missense_Mutation	SNP	A	TCGA-2V-A95S-01A-11D-A36X-10	5083917	52659296	6469687	96	96										
USP29	57663	hgsc.bcm.edu	37	chr19	57641665	57641665	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tttaagtttatcttcttattGcaatgaaagcaccaaaccac	4	9	2	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr19:57641665G>A	ENST00000254181.4	+	4	2076	c.1622G>A	c.(1621-1623)tGc>tAc	p.C541Y	USP29_ENST00000598197.1_Missense_Mutation_p.C541Y	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	541	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TCTTCTTATTGCAATGAAAGC	0.403																																					p.C541Y		Atlas-SNP	.											.	USP29	186	.	0			c.G1622A						.						139	148	145					19																	57641665		2203	4300	6503	SO:0001583	missense	57663	exon4			CTTATTGCAATGA		CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.1622G>A	chr19.hg19:g.57641665G>A	ENSP00000254181:p.Cys541Tyr	100.0	0.0		97.0	23.0	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	hg19	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.471022	0.26423	.	.	ENSG00000131864	ENST00000254181	T	0.31247	1.5	2.52	2.52	0.30459	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.	.	.	.	T	0.52435	0.1734	M	0.75447	2.3	0.35851	D	0.826793	D	0.89917	1.0	D	0.97110	1.0	T	0.65533	-0.6145	9	0.87932	D	0	-4.2598	11.1806	0.48625	0.0:0.0:1.0:0.0	.	541	Q9HBJ7	UBP29_HUMAN	Y	541	ENSP00000254181:C541Y	ENSP00000254181:C541Y	C	+	2	0	USP29	62333477	1.000000	0.71417	0.013000	0.15412	0.044000	0.14063	5.155000	0.64900	1.678000	0.50952	0.467000	0.42956	TGC	.	.		0.403	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			A	57641665	G	A	57641665	3	1	1	1	0	0	0	0	1	0	0	0	17074	1319	46	3	1624	3	USP29	19	57641665	Missense_Mutation	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	4982369	57641665	1487318	97	97										
RSPH1	89765	hgsc.bcm.edu	37	chr21	43912902	43912902	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ccatctggatatataaaagtGccttgaccgtgctttttatt	7	8	1	1			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr21:43912902G>T	ENST00000291536.3	-	3	407	c.240C>A	c.(238-240)ggC>ggA	p.G80G	RSPH1_ENST00000398352.3_Silent_p.G42G	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	80					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)				large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						ATATAAAAGTGCCTTGACCGT	0.318																																					p.G80G	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-SNP	.											.	RSPH1	36	.	0			c.C240A						.						157	158	157					21																	43912902		2203	4300	6503	SO:0001819	synonymous_variant	89765	exon3			AAAAGTGCCTTGA	AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"meichroacidin"	609314	"testis specific A2 homolog (mouse)"	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.240C>A	chr21.hg19:g.43912902G>T		86.0	0.0		90.0	5.0	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Silent	SNP	ENST00000291536.3	hg19	CCDS13688.1																																																																																			.	.		0.318	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1			T	43912902	G	T	43912902	2	4	1	1	0	0	0	0	0	0	0	1	13717	1306	46	3		3	RSPH1	21	43912902	Silent	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10		43912902	4216993	98	98										
TMPRSS6	164656	hgsc.bcm.edu	37	chr22	37482384	37482384	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tagtagctgtgcaggcccttCttccagacgaccgccatgat	10	13	1	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr22:37482384C>T	ENST00000346753.3	-	8	1055	c.939G>A	c.(937-939)aaG>aaA	p.K313K	TMPRSS6_ENST00000406725.1_Silent_p.K304K|TMPRSS6_ENST00000442782.2_Silent_p.K313K|TMPRSS6_ENST00000406856.1_Silent_p.K304K|TMPRSS6_ENST00000381792.2_Silent_p.K304K	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	313	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						GCAGGCCCTTCTTCCAGACGA	0.667																																					p.K313K		Atlas-SNP	.											.	TMPRSS6	99	.	0			c.G939A						.						32	30	30					22																	37482384		2203	4299	6502	SO:0001819	synonymous_variant	164656	exon8			GCCCTTCTTCCAG	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"Serine peptidases / Transmembrane"	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.939G>A	chr22.hg19:g.37482384C>T		264.0	0.0		296.0	71.0	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	hg19	CCDS13941.1																																																																																			.	.		0.667	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609		T	37482384	C	T	37482384	2	4	1	1	0	0	0	0	0	0	0	1	16266	912	32	3		3	TMPRSS6	22	37482384	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10		37482384	13822182	99	99										
EP300	2033	hgsc.bcm.edu	37	chr22	41574171	41574171	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ccccagcagcaaccacagcaGcaactccagccacccatggg	8	19	0	0			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chr22:41574171G>A	ENST00000263253.7	+	31	7675	c.6456G>A	c.(6454-6456)caG>caA	p.Q2152Q	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2152	Interaction with HTLV-1 Tax.|Interaction with NCOA2.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AACCACAGCAGCAACTCCAGC	0.587			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.Q2152Q		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.G6456A						.						76	60	65					22																	41574171		2203	4300	6503	SO:0001819	synonymous_variant	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	ACAGCAGCAACTC	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.6456G>A	chr22.hg19:g.41574171G>A		174.0	0.0		153.0	36.0	NM_001429	B1AKC2	Silent	SNP	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.		0.587	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		A	41574171	G	A	41574171	2	1	1	1	0	0	0	0	0	0	0	1	5150	962	34	3		3	EP300	22	41574171	Silent	SNP	G	TCGA-2V-A95S-01A-11D-A36X-10	4091787	41574171	9730395	100	100										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382417	24382418	+	IGR	INS	-	-	CTGCTGCTC													0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	tgctgctgctgctgctgctgINSctgctgctgctcctgctcct					rs185449787		TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chrX:24382417_24382418insCTGCTGCTC								AC004552.1 (15394 upstream) : PDK3 (100919 downstream)																							tgctgctgctgctgctgctgct	0.619																																					p.A514delinsAAAP		Atlas-INDEL	.											.	.	.	.	0			c.1540_1541insCTGCTGCTC						.																																			SO:0001628	intergenic_variant	100130302	exon1			.																													chrX.hg19:g.24382417_24382418insCTGCTGCTC		59.0	0.0		85.0	38.0	NM_001136234		In_Frame_Ins	INS		hg19																																																																																				.	.	0	0.619									CTGCTGCTC	24382418	-	CTGCTGCTC	24382417	6	5	1	0	1	1	1	0	0	0	0	0	5581	1319	46	0		0	FAM48B1	23	24382417	IGR	INS	-	TCGA-2V-A95S-01A-11D-A36X-10		24382417	130888143	101	101										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34148187	34148187	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	aatgaaatccttaaaggcaaTtggtccataaagatcgtcaa	7	7	1	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chrX:34148187T>C	ENST00000346193.3	-	1	2260	c.2209A>G	c.(2209-2211)Att>Gtt	p.I737V		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	737										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						TTAAAGGCAATTGGTCCATAA	0.423																																					p.I737V		Atlas-SNP	.											.	FAM47A	249	.	0			c.A2209G						.						132	127	129					X																	34148187		2202	4300	6502	SO:0001583	missense	158724	exon1			AGGCAATTGGTCC	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.2209A>G	chrX.hg19:g.34148187T>C	ENSP00000345029:p.Ile737Val	191.0	0.0		167.0	62.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.672427	0.29693	.	.	ENSG00000185448	ENST00000346193	T	0.15139	2.45	1.17	1.17	0.20885	.	.	.	.	.	T	0.26268	0.0641	L	0.49126	1.545	0.21105	N	0.999782	D	0.56968	0.978	D	0.67725	0.953	T	0.14035	-1.0487	9	0.25751	T	0.34	.	4.2137	0.10524	0.0:0.0:0.0:1.0	.	737	Q5JRC9	FA47A_HUMAN	V	737	ENSP00000345029:I737V	ENSP00000345029:I737V	I	-	1	0	FAM47A	34058108	0.949000	0.32298	0.765000	0.31456	0.166000	0.22503	0.853000	0.27777	0.724000	0.32296	0.441000	0.28932	ATT	.	.		0.423	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		C	34148187	T	C	34148187	3	2	1	1	0	0	0	0	1	0	0	0	5577	1493	52	2	170	2	FAM47A	23	34148187	Missense_Mutation	SNP	T	TCGA-2V-A95S-01A-11D-A36X-10	9765770	34148187	121122373	102	102										
OCRL	4952	hgsc.bcm.edu	37	chrX	128694557	128694557	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0679611650485437	7	1	1.14653296019901	2.9482276119403	0.786194029850746	1	1	0	ggaacttggaatgtgaatggCcagtctccagatagcgggtt	14	7	1	2			TCGA-2V-A95S-01A-11D-A36X-10	TCGA-2V-A95S-10D-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	163604c4-1a54-4072-9821-38e000866920	2143f2ba-4527-449c-975d-fbeff27126ca	g.chrX:128694557C>A	ENST00000371113.4	+	9	918	c.753C>A	c.(751-753)ggC>ggA	p.G251G	OCRL_ENST00000357121.5_Silent_p.G251G	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	251	5-phosphatase.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						ATGTGAATGGCCAGTCTCCAG	0.363																																					p.G251G		Atlas-SNP	.											.	OCRL	117	.	0			c.C753A						.						127	108	115					X																	128694557		2203	4300	6503	SO:0001819	synonymous_variant	4952	exon9			GAATGGCCAGTCT	U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.753C>A	chrX.hg19:g.128694557C>A		54.0	0.0		91.0	26.0	NM_000276	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Silent	SNP	ENST00000371113.4	hg19	CCDS35393.1																																																																																			.	.		0.363	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		A	128694557	C	A	128694557	2	1	1	1	0	0	0	0	0	0	0	1	10832	726	26	3		3	OCRL	23	128694557	Silent	SNP	C	TCGA-2V-A95S-01A-11D-A36X-10	94546370	128694557	26576003	103	103										
TNFRSF25	8718	hgsc.bcm.edu	37	chr1	6524730	6524730	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	aaccagcctggcttacagccAcagcgggtgtcggccactgc	12	15	0	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr1:6524730A>G	ENST00000356876.3	-	4	432	c.345T>C	c.(343-345)tgT>tgC	p.C115C	TNFRSF25_ENST00000461703.2_5'UTR|TNFRSF25_ENST00000348333.3_Silent_p.C70C|TNFRSF25_ENST00000377782.3_Silent_p.C115C|TNFRSF25_ENST00000351748.3_Intron|TNFRSF25_ENST00000351959.5_Silent_p.C115C	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	115					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|central_nervous_system(2)|endometrium(1)|lung(4)|prostate(1)|stomach(1)	10	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		GCTTACAGCCACAGCGGGTGT	0.622																																					p.C115C		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.T345C						.						47	48	48					1																	6524730		2203	4300	6503	SO:0001819	synonymous_variant	8718	exon4			ACAGCCACAGCGG	U72763	CCDS71.1, CCDS72.1, CCDS73.1, CCDS74.1, CCDS75.1	1p36.2	2008-02-05	2002-12-20	2002-12-20	ENSG00000215788	ENSG00000215788		"Tumor necrosis factor receptor superfamily"	11910	protein-coding gene	gene with protein product		603366	"tumor necrosis factor receptor superfamily, member 12 (translocating chain-association membrane protein)"	TNFRSF12		9052839, 8934525	Standard	NM_003790		Approved	DR3, TRAMP, WSL-1, LARD, WSL-LR, DDR3, TR3, APO-3	uc001anh.3	Q93038	OTTHUMG00000000831	ENST00000356876.3:c.345T>C	chr1.hg19:g.6524730A>G		83.0	0.0		139.0	14.0	NM_148966	B1ALX2|B1ALX3|B7ZLL7|O00275|O00276|O00277|O00278|O00279|O00280|O14865|O14866|P78507|P78515|Q17RU4|Q92983|Q93036|Q93037|Q99722|Q99830|Q99831|Q9BY86|Q9UME0|Q9UME1|Q9UME5	Silent	SNP	ENST00000356876.3	hg19	CCDS71.1																																																																																			.	.		0.622	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965		G	6524730	A	G	6524730	2	3	2	1	0	0	0	0	0	0	0	1	16311	157	6	2		2	TNFRSF25	1	6524730	Silent	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10		6524730	242725891	1	104										
LPHN2	23266	hgsc.bcm.edu	37	chr1	82302739	82302739	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tcagcttcttaccaaatacaGaaggtaagatccagtttaca	6	9	2	2			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr1:82302739G>A	ENST00000370728.1	+	5	715	c.70G>A	c.(70-72)Gaa>Aaa	p.E24K	LPHN2_ENST00000271029.4_Missense_Mutation_p.E24K|LPHN2_ENST00000359929.3_Missense_Mutation_p.E24K|LPHN2_ENST00000319517.6_Missense_Mutation_p.E24K|LPHN2_ENST00000394879.1_Missense_Mutation_p.E24K|LPHN2_ENST00000370713.1_Missense_Mutation_p.E24K|LPHN2_ENST00000370725.1_Missense_Mutation_p.E24K|LPHN2_ENST00000370730.1_Missense_Mutation_p.E24K|LPHN2_ENST00000370717.2_Missense_Mutation_p.E24K|LPHN2_ENST00000370723.1_Missense_Mutation_p.E24K|LPHN2_ENST00000335786.5_Missense_Mutation_p.E24K|LPHN2_ENST00000370727.1_Missense_Mutation_p.E24K|LPHN2_ENST00000370715.1_Missense_Mutation_p.E24K|LPHN2_ENST00000469377.2_3'UTR|LPHN2_ENST00000370721.1_Missense_Mutation_p.E24K			O95490	LPHN2_HUMAN	latrophilin 2	24					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		ACCAAATACAGAAGGTAAGAT	0.308																																					p.E24K		Atlas-SNP	.											.	LPHN2	464	.	0			c.G70A						.						139	135	136					1																	82302739		2203	4299	6502	SO:0001583	missense	23266	exon2			AATACAGAAGGTA	AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"-", "GPCR / Class B : Orphans"	18582	protein-coding gene	gene with protein product		607018	"latrophilin 1"	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.70G>A	chr1.hg19:g.82302739G>A	ENSP00000359763:p.Glu24Lys	83.0	0.0		176.0	28.0	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.01	2.108296	0.37242	.	.	ENSG00000117114	ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000370715;ENST00000370713;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68479	-0.3;-0.33;-0.32;-0.26;-0.27;-0.22;-0.28;-0.29;-0.28;-0.28;-0.27;-0.22;-0.26;-0.32	5.44	5.44	0.79542	.	0.630568	0.15695	N	0.249227	T	0.36220	0.0959	N	0.14661	0.345	0.37340	D	0.910351	B;B;B;B	0.12013	0.0;0.0;0.0;0.005	B;B;B;B	0.21546	0.001;0.0;0.001;0.035	T	0.24404	-1.0161	10	0.12103	T	0.63	.	19.2609	0.93967	0.0:0.0:1.0:0.0	.	24;24;24;24	O95490-3;O95490-4;O95490-2;B3KVU1	.;.;.;.	K	24	ENSP00000359756:E24K;ENSP00000359763:E24K;ENSP00000359765:E24K;ENSP00000359762:E24K;ENSP00000359760:E24K;ENSP00000359758:E24K;ENSP00000353006:E24K;ENSP00000359750:E24K;ENSP00000359748:E24K;ENSP00000322270:E24K;ENSP00000359752:E24K;ENSP00000378344:E24K;ENSP00000271029:E24K;ENSP00000337306:E24K	ENSP00000271029:E24K	E	+	1	0	LPHN2	82075327	1.000000	0.71417	0.992000	0.48379	0.792000	0.44763	5.308000	0.65768	2.560000	0.86352	0.467000	0.42956	GAA	.	.		0.308	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		A	82302739	G	A	82302739	3	1	2	1	0	0	0	0	1	0	0	0	8925	943	33	3	72	3	LPHN2	1	82302739	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	75778009	82302739	166947882	2	105										
CTBS	1486	hgsc.bcm.edu	37	chr1	85040007	85040007	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cggccgcgagccgcagcgccAgcagcgccagcagcgccagc	15	19	0	0	rs142534762|rs3217269|rs199701060	byFrequency	TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr1:85040007A>C	ENST00000370630.5	-	1	140	c.92T>G	c.(91-93)cTg>cGg	p.L31R	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	31					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		CCgcagcgccagcagcgccag	0.721																																					p.L31R		Atlas-SNP	.											.	CTBS	24	.	0			c.T92G						.						3	4	3					1																	85040007		1460	3157	4617	SO:0001583	missense	1486	exon1			AGCGCCAGCAGCG	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.92T>G	chr1.hg19:g.85040007A>C	ENSP00000359664:p.Leu31Arg	94.0	0.0		132.0	10.0	NM_004388	Q5VX50	Missense_Mutation	SNP	ENST00000370630.5	hg19	CCDS698.1	.	.	.	.	.	.	.	.	.	.	A	11.47	1.648232	0.29336	.	.	ENSG00000117151	ENST00000370630	T	0.37235	1.21	5.0	3.89	0.44902	.	406.533000	0.01622	U	0.023085	T	0.39358	0.1075	L	0.59436	1.845	0.25105	N	0.990754	D	0.58268	0.982	P	0.60236	0.871	T	0.15093	-1.0449	10	0.41790	T	0.15	-0.1024	8.619	0.33849	0.9087:0.0:0.0913:0.0	.	31	Q01459	DIAC_HUMAN	R	31	ENSP00000359664:L31R	ENSP00000359664:L31R	L	-	2	0	CTBS	84812595	0.406000	0.25344	0.074000	0.20217	0.092000	0.18411	1.052000	0.30429	2.225000	0.72522	0.482000	0.46254	CTG	.	.		0.721	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388		C	85040007	A	C	85040007	3	2	2	1	0	0	0	0	1	0	0	0	4001	188	7	5	1093	5	CTBS	1	85040007	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10	2737268	85040007	164210614	3	106										
ZNF326	284695	hgsc.bcm.edu	37	chr1	90473296	90473296	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	aggaccatcaacaggcagagGccgaggccgaggagtaagta	15	9	1	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr1:90473296G>T	ENST00000340281.4	+	5	745	c.602G>T	c.(601-603)gGc>gTc	p.G201V	ZNF326_ENST00000455342.2_Intron|ZNF326_ENST00000370447.3_Missense_Mutation_p.G112V	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	201	Gly-rich.				mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		ACAGGCAGAGGCCGAGGCCGA	0.453																																					p.G201V		Atlas-SNP	.											.	ZNF326	60	.	0			c.G602T						.						68	70	70					1																	90473296		2203	4300	6503	SO:0001583	missense	284695	exon5			GCAGAGGCCGAGG	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.602G>T	chr1.hg19:g.90473296G>T	ENSP00000340796:p.Gly201Val	118.0	0.0		177.0	60.0	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	hg19	CCDS727.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.190093	0.58017	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447	T;T	0.47177	0.85;0.85	5.84	5.84	0.93424	.	0.118601	0.64402	D	0.000017	T	0.58293	0.2112	L	0.43152	1.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.59295	-0.7481	10	0.72032	D	0.01	-6.5508	20.1319	0.98001	0.0:0.0:1.0:0.0	.	201;201	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	V	201;201;112	ENSP00000340796:G201V;ENSP00000359476:G112V	ENSP00000340796:G201V	G	+	2	0	ZNF326	90245884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.863000	0.69568	2.747000	0.94245	0.655000	0.94253	GGC	.	.		0.453	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		T	90473296	G	T	90473296	3	4	2	1	0	0	0	0	1	0	0	0	17861	1203	42	3	624	3	ZNF326	1	90473296	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	5433289	90473296	158777325	4	107										
NES	10763	hgsc.bcm.edu	37	chr1	156640363	156640363	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cctcctcagcttcctctgacCccagaggccaaggtgaaggg	11	15	2	3			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr1:156640363C>A	ENST00000368223.3	-	4	3749	c.3617G>T	c.(3616-3618)gGg>gTg	p.G1206V		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1206	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTCCTCTGACCCCAGAGGCCA	0.647																																					p.G1206V		Atlas-SNP	.											.	NES	196	.	0			c.G3617T						.						78	77	78					1																	156640363		2203	4300	6503	SO:0001583	missense	10763	exon4			TCTGACCCCAGAG	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3617G>T	chr1.hg19:g.156640363C>A	ENSP00000357206:p.Gly1206Val	94.0	0.0		84.0	29.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	C	16.43	3.120368	0.56613	.	.	ENSG00000132688	ENST00000368223	D	0.86432	-2.12	3.63	0.478	0.16789	.	.	.	.	.	D	0.83450	0.5257	L	0.59436	1.845	0.20196	N	0.99993	D	0.69078	0.997	P	0.60682	0.878	T	0.72931	-0.4142	9	0.87932	D	0	.	5.6659	0.17695	0.0:0.4756:0.0:0.5244	.	1206	P48681	NEST_HUMAN	V	1206	ENSP00000357206:G1206V	ENSP00000357206:G1206V	G	-	2	0	NES	154906987	0.000000	0.05858	0.001000	0.08648	0.635000	0.38103	0.317000	0.19487	0.145000	0.18977	0.455000	0.32223	GGG	.	.		0.647	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		A	156640363	C	A	156640363	3	1	2	1	0	0	0	0	1	0	0	0	10346	623	22	3	1252	3	NES	1	156640363	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	66167067	156640363	92610258	5	108										
FCRL4	83417	hgsc.bcm.edu	37	chr1	157559113	157559113	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tcagggtcaacttttctcccCagtagtgccgatgataccat	8	12	3	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr1:157559113C>A	ENST00000271532.1	-	3	323	c.188G>T	c.(187-189)tGg>tTg	p.W63L	FCRL4_ENST00000448509.2_5'Flank	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	63	Ig-like C2-type 1.				immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				CTTTTCTCCCCAGTAGTGCCG	0.517																																					p.W63L		Atlas-SNP	.											.	FCRL4	95	.	0			c.G188T						.						107	92	97					1																	157559113		2203	4300	6503	SO:0001583	missense	83417	exon3			TCTCCCCAGTAGT	AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.188G>T	chr1.hg19:g.157559113C>A	ENSP00000271532:p.Trp63Leu	202.0	0.0		250.0	80.0	NM_031282	Q96PJ3|Q96RE0	Missense_Mutation	SNP	ENST00000271532.1	hg19	CCDS1166.1	.	.	.	.	.	.	.	.	.	.	C	2.009	-0.427543	0.04701	.	.	ENSG00000163518	ENST00000271532	T	0.18960	2.18	4.06	-0.104	0.13605	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.056910	0.01476	N	0.016467	T	0.02380	0.0073	N	0.08118	0	0.09310	N	1	B	0.18863	0.031	B	0.11329	0.006	T	0.28554	-1.0040	10	0.13470	T	0.59	.	2.7602	0.05305	0.2055:0.4492:0.0:0.3453	.	63	Q96PJ5	FCRL4_HUMAN	L	63	ENSP00000271532:W63L	ENSP00000271532:W63L	W	-	2	0	FCRL4	155825737	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.011000	0.03652	0.097000	0.17492	0.557000	0.71058	TGG	.	.		0.517	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282		A	157559113	C	A	157559113	3	1	2	1	0	0	0	0	1	0	0	0	5805	595	21	3	1399	3	FCRL4	1	157559113	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	918750	157559113	91691508	6	109										
RXRG	6258	hgsc.bcm.edu	37	chr1	165386442	165386442	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tgcagccttcacaactgtatAccccgtagtgctttcctggt	8	13	1	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr1:165386442A>G	ENST00000359842.5	-	4	760	c.458T>C	c.(457-459)gTa>gCa	p.V153A	RXRG_ENST00000470566.1_5'UTR	NM_001256570.1|NM_006917.4	NP_001243499.1|NP_008848.1	P48443	RXRG_HUMAN	retinoid X receptor, gamma	153					gene expression (GO:0010467)|heart development (GO:0007507)|neuron differentiation (GO:0030182)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|skeletal muscle tissue development (GO:0007519)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	9-cis retinoic acid receptor activity (GO:0004886)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(3)|large_intestine(6)|lung(22)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	38	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tretinoin(DB00755)	ACAACTGTATACCCCGTAGTG	0.433																																					p.V153A		Atlas-SNP	.											.	RXRG	91	.	0			c.T458C						.						149	140	143					1																	165386442		2203	4300	6503	SO:0001583	missense	6258	exon4			CTGTATACCCCGT	U38480	CCDS1248.1, CCDS72970.1	1q22-q23	2013-01-16			ENSG00000143171	ENSG00000143171		"Nuclear hormone receptors"	10479	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 3"	180247				8034312	Standard	NR_033824		Approved	NR2B3	uc001gda.3	P48443	OTTHUMG00000034626	ENST00000359842.5:c.458T>C	chr1.hg19:g.165386442A>G	ENSP00000352900:p.Val153Ala	135.0	0.0		154.0	51.0	NM_006917	A6NIP1|Q6IBU7	Missense_Mutation	SNP	ENST00000359842.5	hg19	CCDS1248.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.277335	0.80580	.	.	ENSG00000143171	ENST00000359842	D	0.97665	-4.48	4.96	4.96	0.65561	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.000000	0.85682	D	0.000000	D	0.95758	0.8620	N	0.21324	0.655	0.58432	D	0.999998	D	0.76494	0.999	D	0.87578	0.998	D	0.96016	0.9005	9	0.39692	T	0.17	.	13.6338	0.62210	1.0:0.0:0.0:0.0	.	153	P48443	RXRG_HUMAN	A	153	ENSP00000352900:V153A	ENSP00000352900:V153A	V	-	2	0	RXRG	163653066	1.000000	0.71417	0.997000	0.53966	0.873000	0.50193	7.040000	0.76551	2.076000	0.62316	0.533000	0.62120	GTA	.	.		0.433	RXRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083794.2	NM_006917		G	165386442	A	G	165386442	3	3	2	1	0	0	0	0	1	0	0	0	13780	391	14	2	961	2	RXRG	1	165386442	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10	7827329	165386442	83864179	7	110										
ASTN1	460	hgsc.bcm.edu	37	chr1	176918372	176918372	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ggtcgtccgggaagggcgccAtctgctggaggcacagctgc	17	12	1	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr1:176918372A>C	ENST00000367654.3	-	12	2238	c.2027T>G	c.(2026-2028)aTg>aGg	p.M676R	ASTN1_ENST00000424564.2_Missense_Mutation_p.M668R|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000361833.2_Missense_Mutation_p.M668R|ASTN1_ENST00000367657.3_Missense_Mutation_p.M668R	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	676	EGF-like 3.				locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GAAGGGCGCCATCTGCTGGAG	0.617											OREG0014004	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M668R		Atlas-SNP	.											.	ASTN1	314	.	0			c.T2003G						.						74	72	73					1																	176918372		2203	4300	6503	SO:0001583	missense	460	exon12			GGCGCCATCTGCT	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.2027T>G	chr1.hg19:g.176918372A>C	ENSP00000356626:p.Met676Arg	60.0	0.0	1934	94.0	8.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	A	14.56	2.572003	0.45798	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	D;D;D;D	0.96200	-3.94;-3.94;-3.94;-3.94	5.3	5.3	0.74995	.	0.268407	0.46145	D	0.000307	D	0.85017	0.5601	N	0.03608	-0.345	0.52501	D	0.999958	P;B;B	0.38420	0.63;0.015;0.015	B;B;B	0.29353	0.101;0.029;0.029	D	0.85667	0.1292	10	0.33940	T	0.23	-20.4559	10.2105	0.43138	0.8517:0.0:0.0:0.1482	.	676;668;668	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	R	668;668;676;668;668	ENSP00000356629:M668R;ENSP00000354536:M668R;ENSP00000356626:M676R;ENSP00000395041:M668R	ENSP00000354536:M668R	M	-	2	0	ASTN1	175184995	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	4.443000	0.59994	2.008000	0.58898	0.533000	0.62120	ATG	.	.		0.617	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		C	176918372	A	C	176918372	3	2	2	1	0	0	0	0	1	0	0	0	1064	217	8	5	1933	5	ASTN1	1	176918372	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10	11531930	176918372	72332249	8	111										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228506637	228506637	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cctcagcccagcttgcccccCgaggcagcccaggagggtga	13	17	1	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr1:228506637C>A	ENST00000422127.1	+	54	14228	c.14184C>A	c.(14182-14184)ccC>ccA	p.P4728P	OBSCN_ENST00000284548.11_Silent_p.P4728P|OBSCN_ENST00000366707.4_Silent_p.P2362P|OBSCN_ENST00000366709.4_Silent_p.P1847P|OBSCN_ENST00000570156.2_Silent_p.P5685P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4728					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTTGCCCCCCGAGGCAGCCC	0.637																																					p.P5685P		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C17055A						.						12	15	14					1																	228506637		2090	4211	6301	SO:0001819	synonymous_variant	84033	exon65			GCCCCCCGAGGCA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.14184C>A	chr1.hg19:g.228506637C>A		101.0	0.0		144.0	43.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228506637	C	A	228506637	2	1	2	1	0	0	0	0	0	0	0	1	10821	639	23	1		1	OBSCN	1	228506637	Silent	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	51588265	228506637	20743984	9	112										
CEP68	23177	hgsc.bcm.edu	37	chr2	65309718	65309718	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	aaagcagtctggtgagctggAgagccacgcagatcgcctgt	14	10	1	3			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr2:65309718A>C	ENST00000377990.2	+	6	2356	c.2153A>C	c.(2152-2154)gAg>gCg	p.E718A	CEP68_ENST00000546106.1_3'UTR|CEP68_ENST00000260569.4_Missense_Mutation_p.E581A|RAB1A_ENST00000494188.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	718					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						GGTGAGCTGGAGAGCCACGCA	0.493																																					p.E718A		Atlas-SNP	.											.	CEP68	69	.	0			c.A2153C						.						163	150	154					2																	65309718		2203	4300	6503	SO:0001583	missense	23177	exon6			AGCTGGAGAGCCA	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"KIAA0582"	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.2153A>C	chr2.hg19:g.65309718A>C	ENSP00000367229:p.Glu718Ala	115.0	0.0		151.0	37.0	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	hg19	CCDS1880.2	.	.	.	.	.	.	.	.	.	.	A	21.9	4.211784	0.79240	.	.	ENSG00000011523	ENST00000377990;ENST00000260569	T;T	0.80566	-1.39;-1.39	5.73	4.56	0.56223	.	0.000000	0.64402	D	0.000003	T	0.77336	0.4115	M	0.62723	1.935	0.80722	D	1	P;P	0.40211	0.707;0.707	B;B	0.38655	0.278;0.278	T	0.74256	-0.3724	10	0.32370	T	0.25	-13.5397	12.9728	0.58522	0.8648:0.1352:0.0:0.0	.	718;581	Q76N32;Q76N32-2	CEP68_HUMAN;.	A	718;581	ENSP00000367229:E718A;ENSP00000260569:E581A	ENSP00000260569:E581A	E	+	2	0	CEP68	65163222	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.878000	0.75567	0.977000	0.38444	0.459000	0.35465	GAG	.	.		0.493	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		C	65309718	A	C	65309718	3	2	2	1	0	0	0	0	1	0	0	0	3260	304	11	5	2171	5	CEP68	2	65309718	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10		65309718	177889655	10	113										
MRPL19	9801	hgsc.bcm.edu	37	chr2	75881940	75881940	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	attagagaaacggctggatgAtagcttgctatacttacgag	11	6	0	2			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr2:75881940A>G	ENST00000393909.2	+	5	579	c.554A>G	c.(553-555)gAt>gGt	p.D185G	MRPL19_ENST00000409374.1_Missense_Mutation_p.D185G|MRPL19_ENST00000358788.6_Intron	NM_014763.3	NP_055578.2	P49406	RM19_HUMAN	mitochondrial ribosomal protein L19	185					translation (GO:0006412)	mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(6)	8						CGGCTGGATGATAGCTTGCTA	0.388																																					p.D185G		Atlas-SNP	.											.	MRPL19	21	.	0			c.A554G						.						137	127	131					2																	75881940		1871	4099	5970	SO:0001583	missense	9801	exon5			TGGATGATAGCTT	AB051621	CCDS1960.2	2p11.1-q11.2	2012-09-13			ENSG00000115364	ENSG00000115364		"Mitochondrial ribosomal proteins / large subunits"	14052	protein-coding gene	gene with protein product	"39S ribosomal protein L19"	611832				11543634, 17309879	Standard	XM_006712155		Approved	MRP-L15, RPML15, KIAA0104, RLX1	uc002snl.3	P49406	OTTHUMG00000129990	ENST00000393909.2:c.554A>G	chr2.hg19:g.75881940A>G	ENSP00000377486:p.Asp185Gly	113.0	0.0		155.0	43.0	NM_014763	Q53TX9|Q96Q52	Missense_Mutation	SNP	ENST00000393909.2	hg19	CCDS1960.2	.	.	.	.	.	.	.	.	.	.	A	13.29	2.192787	0.38707	.	.	ENSG00000115364	ENST00000393909;ENST00000409374	.	.	.	5.18	5.18	0.71444	Translation protein SH3-like (1);	0.233777	0.49916	D	0.000137	T	0.44244	0.1284	L	0.40543	1.245	0.80722	D	1	B	0.12013	0.005	B	0.14578	0.011	T	0.34453	-0.9828	9	0.21540	T	0.41	-12.0197	7.96	0.30066	0.9076:0.0:0.0924:0.0	.	185	P49406	RM19_HUMAN	G	185	.	ENSP00000377486:D185G	D	+	2	0	MRPL19	75735448	1.000000	0.71417	0.931000	0.37212	0.874000	0.50279	4.164000	0.58190	2.087000	0.62958	0.460000	0.39030	GAT	.	.		0.388	MRPL19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252256.1	NM_014763		G	75881940	A	G	75881940	3	3	2	1	0	0	0	0	1	0	0	0	9793	333	12	2	572	2	MRPL19	2	75881940	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10	10572222	75881940	167317433	11	114										
MGAT5	4249	hgsc.bcm.edu	37	chr2	135075151	135075151	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	attgcctcctatggacggctAccctcactgtgagggaaaga	11	11	1	2			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr2:135075151A>G	ENST00000409645.1	+	4	710	c.458A>G	c.(457-459)tAc>tGc	p.Y153C	MGAT5_ENST00000281923.2_Missense_Mutation_p.Y153C			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	153					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|pancreas(1)|skin(3)	36				BRCA - Breast invasive adenocarcinoma(221;0.0964)		ATGGACGGCTACCCTCACTGT	0.428																																					p.Y153C		Atlas-SNP	.											.	MGAT5	84	.	0			c.A458G						.						105	91	96					2																	135075151		2203	4300	6503	SO:0001583	missense	4249	exon3			ACGGCTACCCTCA	D17716	CCDS2171.1	2q21	2013-02-25			ENSG00000152127	ENSG00000152127	2.4.1.155	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7049	protein-coding gene	gene with protein product		601774				8292036	Standard	NM_002410		Approved	GNT-V	uc002ttw.4	Q09328	OTTHUMG00000131681	ENST00000409645.1:c.458A>G	chr2.hg19:g.135075151A>G	ENSP00000386377:p.Tyr153Cys	60.0	0.0		78.0	25.0	NM_002410	D3DP70	Missense_Mutation	SNP	ENST00000409645.1	hg19	CCDS2171.1	.	.	.	.	.	.	.	.	.	.	A	17.80	3.477450	0.63849	.	.	ENSG00000152127	ENST00000409645;ENST00000281923	.	.	.	5.44	4.24	0.50183	.	0.100947	0.64402	D	0.000002	T	0.50429	0.1615	L	0.52905	1.665	0.52501	D	0.999956	P	0.49447	0.924	P	0.45829	0.494	T	0.56408	-0.7984	9	0.87932	D	0	-19.619	9.5823	0.39495	0.7565:0.0:0.0:0.2434	.	153	Q09328	MGT5A_HUMAN	C	153	.	ENSP00000281923:Y153C	Y	+	2	0	MGAT5	134791621	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.879000	0.56138	2.068000	0.61886	0.533000	0.62120	TAC	.	.		0.428	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410		G	135075151	A	G	135075151	3	3	2	1	0	0	0	0	1	0	0	0	9557	391	14	2	468	2	MGAT5	2	135075151	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10	59193211	135075151	108124222	12	115										
LY75	4065	hgsc.bcm.edu	37	chr2	160708822	160708822	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ttcacagatgaagggcaactTggtactacagtctgttggtt	11	7	2	2			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr2:160708822T>A	ENST00000263636.4	-	21	2800	c.2773A>T	c.(2773-2775)Aag>Tag	p.K925*	LY75_ENST00000553424.1_Nonsense_Mutation_p.K925*|LY75-CD302_ENST00000504764.1_Nonsense_Mutation_p.K925*|LY75-CD302_ENST00000505052.1_Nonsense_Mutation_p.K925*|LY75_ENST00000554112.1_Nonsense_Mutation_p.K925*	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	925	C-type lectin 5. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		AAGGGCAACTTGGTACTACAG	0.358																																					p.K925X		Atlas-SNP	.											.	LY75	151	.	0			c.A2773T						.						82	85	84					2																	160708822		2203	4300	6503	SO:0001587	stop_gained	4065	exon21			GCAACTTGGTACT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.2773A>T	chr2.hg19:g.160708822T>A	ENSP00000263636:p.Lys925*	129.0	0.0		158.0	51.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Nonsense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	T	39	7.675614	0.98425	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	.	.	.	5.12	3.88	0.44766	.	0.000000	0.33496	U	0.004843	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-11.251	8.5401	0.33388	0.0:0.0:0.1955:0.8045	.	.	.	.	X	925	.	ENSP00000423463:K925X	K	-	1	0	LY75;LY75-CD302	160417068	0.994000	0.37717	1.000000	0.80357	0.862000	0.49288	1.919000	0.40015	2.058000	0.61347	0.477000	0.44152	AAG	.	.		0.358	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			A	160708822	T	A	160708822	4	1	2	1	0	0	0	0	0	1	0	0	9108	1821	63	4	2455	4	LY75	2	160708822	Nonsense_Mutation	SNP	T	TCGA-2Y-A9GS-01A-12D-A382-10	25633671	160708822	82490551	13	116										
TTN	7273	hgsc.bcm.edu	37	chr2	179474818	179474818	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	catccatgtccaaacttacgCtttggatcttgagcaatgac	7	11	1	2			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr2:179474818C>A	ENST00000591111.1	-	221	46736	c.46512G>T	c.(46510-46512)aaG>aaT	p.K15504N	TTN_ENST00000359218.5_Splice_Site_p.K8205N|TTN_ENST00000460472.2_Splice_Site_p.K8080N|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342175.6_Splice_Site_p.K8272N|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Splice_Site_p.K17145N|TTN_ENST00000342992.6_Splice_Site_p.K14577N|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15504					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAAACTTACGCTTTGGATCTT	0.358																																					p.K17145N		Atlas-SNP	.											.	TTN	18412	.	0			c.G51435T						.						60	60	60					2																	179474818		1898	4116	6014	SO:0001630	splice_region_variant	7273	exon271			CTTACGCTTTGGA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.46513+1G>T	chr2.hg19:g.179474818C>A		70.0	0.0		96.0	37.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.10	1.257136	0.22965	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53640	0.61;0.61;0.61;0.61	5.48	2.6	0.31112	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.57080	0.2029	L	0.45422	1.42	0.43890	D	0.996515	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.994;0.994;0.994;0.994	T	0.56980	-0.7889	9	0.87932	D	0	.	10.0869	0.42423	0.0:0.694:0.0:0.306	.	8080;8205;8272;15504	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	14577;8080;8272;8205;8080	ENSP00000343764:K14577N;ENSP00000434586:K8080N;ENSP00000340554:K8272N;ENSP00000352154:K8205N	ENSP00000340554:K8272N	K	-	3	2	TTN	179183063	0.984000	0.35163	1.000000	0.80357	0.997000	0.91878	0.225000	0.17757	0.632000	0.30432	0.655000	0.94253	AAG	.	.		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	Missense_Mutation	A	179474818	C	A	179474818	5	1	2	1	0	0	0	0	0	0	1	0	16750	811	28	3	56626	3	TTN	2	179474818	Splice_Site	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	18765996	179474818	63724555	14	117										
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197948210	197948210	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tacagtggaaatgacaattcGcagctgcatagtgcaaaggg	12	7	0	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr2:197948210G>A	ENST00000328737.2	-	14	1341	c.1265C>T	c.(1264-1266)gCg>gTg	p.A422V	ANKRD44_ENST00000539527.1_Missense_Mutation_p.A375V|ANKRD44_ENST00000450567.1_Missense_Mutation_p.A422V|ANKRD44_ENST00000477852.1_5'UTR|ANKRD44_ENST00000282272.8_Missense_Mutation_p.A439V|ANKRD44_ENST00000337207.5_Missense_Mutation_p.A422V|ANKRD44_ENST00000409153.1_Missense_Mutation_p.A447V			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	447										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ATGACAATTCGCAGCTGCATA	0.473																																					p.A447V		Atlas-SNP	.											.	ANKRD44	281	.	0			c.C1340T						.						119	104	109					2																	197948210		2203	4300	6503	SO:0001583	missense	91526	exon14			CAATTCGCAGCTG	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1265C>T	chr2.hg19:g.197948210G>A	ENSP00000331516:p.Ala422Val	97.0	0.0		89.0	39.0	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	hg19		.	.	.	.	.	.	.	.	.	.	G	19.96	3.923121	0.73213	.	.	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000422886;ENST00000409153;ENST00000539527	T;T;T;T;T;T;T;T	0.65916	-0.07;-0.18;-0.14;-0.14;-0.18;-0.18;-0.16;-0.18	5.65	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.50326	0.1609	L	0.37750	1.13	0.58432	D	0.999994	P;B;B	0.37731	0.607;0.053;0.022	B;B;B	0.32677	0.15;0.032;0.02	T	0.51293	-0.8724	10	0.35671	T	0.21	.	15.0175	0.71597	0.0679:0.0:0.9321:0.0	.	375;447;465	F5H682;Q8N8A2-3;Q8N8A2-2	.;.;.	V	262;439;422;422;422;122;447;375	ENSP00000403415:A262V;ENSP00000282272:A439V;ENSP00000331516:A422V;ENSP00000402420:A422V;ENSP00000338794:A422V;ENSP00000416319:A122V;ENSP00000387141:A447V;ENSP00000437825:A375V	ENSP00000282272:A439V	A	-	2	0	ANKRD44	197656455	1.000000	0.71417	0.979000	0.43373	0.941000	0.58515	7.827000	0.86722	1.627000	0.50400	0.655000	0.94253	GCG	.	.		0.473	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		A	197948210	G	A	197948210	3	1	2	1	0	0	0	0	1	0	0	0	672	1087	38	1	1546	1	ANKRD44	2	197948210	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	18473392	197948210	45251163	15	118										
CTDSP1	58190	hgsc.bcm.edu	37	chr2	219268014	219268014	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gccttccgggcccggctgttTcgagagtcctgcgtcttcca	12	15	1	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr2:219268014T>G	ENST00000273062.2	+	6	867	c.531T>G	c.(529-531)ttT>ttG	p.F177L	CTDSP1_ENST00000488627.1_3'UTR|CTDSP1_ENST00000443891.1_Missense_Mutation_p.F176L|MIR26B_ENST00000362251.2_RNA	NM_021198.2|NM_182642.2	NP_067021.1|NP_872580.1	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	177	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|protein dephosphorylation (GO:0006470)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			NS(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	8		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCGGCTGTTTCGAGAGTCCT	0.642																																					p.F177L		Atlas-SNP	.											.	CTDSP1	19	.	0			c.T531G						.						50	58	55					2																	219268014		2203	4300	6503	SO:0001583	missense	58190	exon6			GCTGTTTCGAGAG	AF229162	CCDS2416.1, CCDS56166.1	2q35	2010-06-21			ENSG00000144579	ENSG00000144579		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	21614	protein-coding gene	gene with protein product	"nuclear LIM interactor-interacting factor", "small CTD phosphatase 1"	605323				11950066, 12721286	Standard	NM_021198		Approved	NLIIF, SCP1	uc021vwv.1	Q9GZU7	OTTHUMG00000133109	ENST00000273062.2:c.531T>G	chr2.hg19:g.219268014T>G	ENSP00000273062:p.Phe177Leu	90.0	0.0		126.0	52.0	NM_021198	C9IYG0|Q7Z5Q3|Q7Z5Q4	Missense_Mutation	SNP	ENST00000273062.2	hg19	CCDS2416.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.5|24.5	4.540554|4.540554	0.85917|0.85917	.|.	.|.	ENSG00000144579|ENSG00000144579	ENST00000452977;ENST00000428361|ENST00000443891;ENST00000273062	T;T|T;T	0.19105|0.18502	2.17;2.17|2.21;2.21	4.64|4.64	-0.283|-0.283	0.12874|0.12874	.|NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.52435|0.52435	0.1734|0.1734	H|H	0.98388|0.98388	4.22|4.22	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.998	T|T	0.61312|0.61312	-0.7088|-0.7088	8|10	0.87932|0.87932	D|D	0|0	-15.0159|-15.0159	8.764|8.764	0.34692|0.34692	0.0:0.6021:0.0:0.3979|0.0:0.6021:0.0:0.3979	.|.	.|177;176	.|Q9GZU7;C9IYG0	.|CTDS1_HUMAN;.	C|L	170;178|176;177	ENSP00000404301:F170C;ENSP00000403256:F178C|ENSP00000392248:F176L;ENSP00000273062:F177L	ENSP00000403256:F178C|ENSP00000273062:F177L	F|F	+|+	2|3	0|2	CTDSP1|CTDSP1	218976258|218976258	0.996000|0.996000	0.38824|0.38824	0.974000|0.974000	0.42286|0.42286	0.975000|0.975000	0.68041|0.68041	0.522000|0.522000	0.22909|0.22909	0.173000|0.173000	0.19788|0.19788	0.402000|0.402000	0.26972|0.26972	TTC|TTT	.	.		0.642	CTDSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256774.1	NM_182642, NM_021198		G	219268014	T	G	219268014	3	3	2	1	0	0	0	0	1	0	0	0	4005	1780	62	5	553	5	CTDSP1	2	219268014	Missense_Mutation	SNP	T	TCGA-2Y-A9GS-01A-12D-A382-10	21319804	219268014	23931359	16	119										
PTPRN	5798	hgsc.bcm.edu	37	chr2	220167459	220167459	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tccacctttgcccactggtgGttgtggaagccgatgctggg	14	11	0	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr2:220167459G>A	ENST00000295718.2	-	5	718	c.478C>T	c.(478-480)Cca>Tca	p.P160S	AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000409251.3_Missense_Mutation_p.P160S|PTPRN_ENST00000423636.2_Missense_Mutation_p.P70S	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	160					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CCCACTGGTGGTTGTGGAAGC	0.647																																					p.P160S		Atlas-SNP	.											.	PTPRN	138	.	0			c.C478T						.						46	53	51					2																	220167459		2203	4299	6502	SO:0001583	missense	5798	exon5			CTGGTGGTTGTGG		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.478C>T	chr2.hg19:g.220167459G>A	ENSP00000295718:p.Pro160Ser	93.0	0.0		124.0	37.0	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	hg19	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	G	3.391	-0.124350	0.06795	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666;ENST00000412847;ENST00000446182;ENST00000440552;ENST00000442029	T;T;T	0.03580	3.88;3.97;3.99	4.79	3.91	0.45181	.	0.214419	0.31566	N	0.007434	T	0.03827	0.0108	L	0.44542	1.39	0.09310	N	0.999995	B;B	0.11235	0.004;0.002	B;B	0.10450	0.005;0.003	T	0.42732	-0.9434	10	0.12430	T	0.62	.	10.4929	0.44760	0.0916:0.0:0.9084:0.0	.	160;160	Q6NSL1;Q16849	.;PTPRN_HUMAN	S	160;160;160;70;70;70;127;70	ENSP00000386638:P160S;ENSP00000295718:P160S;ENSP00000444244:P70S	ENSP00000295718:P160S	P	-	1	0	PTPRN	219875703	0.994000	0.37717	0.118000	0.21660	0.021000	0.10359	2.871000	0.48459	1.231000	0.43661	0.561000	0.74099	CCA	.	.		0.647	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			A	220167459	G	A	220167459	3	1	2	1	0	0	0	0	1	0	0	0	12822	1261	44	3	2537	3	PTPRN	2	220167459	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	899445	220167459	23031914	17	120										
PRR21	643905	hgsc.bcm.edu	37	chr2	240981415	240981415	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gaagggccgtgggtgaagagAcgtggatgaagaggcatgga	20	4	0	4	rs113785129		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr2:240981415A>G	ENST00000408934.1	-	1	984	c.985T>C	c.(985-987)Tct>Cct	p.S329P		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	329										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GGGTGAAGAGACGTGGATGAA	0.597																																					p.S329P		Atlas-SNP	.											.	PRR21	53	.	0			c.T985C						.						196	173	181					2																	240981415		2203	4300	6503	SO:0001583	missense	643905	exon1			GAAGAGACGTGGA	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.985T>C	chr2.hg19:g.240981415A>G	ENSP00000386166:p.Ser329Pro	72.0	0.0		96.0	5.0	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	hg19	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	-	1.195	-0.634159	0.03584	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.14391	2.51;2.51	0.698	-1.4	0.08968	.	.	.	.	.	T	0.05456	0.0144	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.34925	-0.9809	8	0.44086	T	0.13	.	.	.	.	.	329	Q8WXC7	PRR21_HUMAN	P	329	ENSP00000386166:S329P;ENSP00000418240:S329P	ENSP00000386166:S329P	S	-	1	0	PRR21	240630088	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-5.007000	0.00160	-1.155000	0.02822	0.138000	0.15974	TCT	.	A|0.500;G|0.500		0.597	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835		G	240981415	A	G	240981415	3	3	2	1	0	0	0	0	1	0	0	0	12604	275	10	2	187	2	PRR21	2	240981415	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10	20813956	240981415	2217958	18	121										
CLASP2	23122	hgsc.bcm.edu	37	chr3	33725916	33725916	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tctcccacatgtctataaatCtccactatagccaatattgc	3	13	3	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr3:33725916C>G	ENST00000468888.2	-	6	625	c.579G>C	c.(577-579)gaG>gaC	p.E193D	CLASP2_ENST00000307312.7_5'UTR|CLASP2_ENST00000359576.5_Missense_Mutation_p.E193D|CLASP2_ENST00000399362.4_Missense_Mutation_p.E193D			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1246					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						GTCTATAAATCTCCACTATAG	0.323																																					p.E193D		Atlas-SNP	.											.	CLASP2	138	.	0			c.G579C						.						137	136	137					3																	33725916		1819	4079	5898	SO:0001583	missense	23122	exon6			ATAAATCTCCACT	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.579G>C	chr3.hg19:g.33725916C>G	ENSP00000419974:p.Glu193Asp	296.0	0.0		327.0	133.0	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	hg19		.	.	.	.	.	.	.	.	.	.	C	14.02	2.411477	0.42817	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576	T;T;T	0.45668	0.89;0.89;0.89	5.12	2.33	0.28932	.	0.062472	0.64402	D	0.000006	T	0.29491	0.0735	L	0.35854	1.095	0.80722	D	1	B	0.11235	0.004	B	0.11329	0.006	T	0.06991	-1.0796	10	0.35671	T	0.21	-13.6418	8.0237	0.30425	0.0:0.7373:0.0:0.2627	.	193	F5H604	.	D	193	ENSP00000419974:E193D;ENSP00000382297:E193D;ENSP00000352581:E193D	ENSP00000352581:E193D	E	-	3	2	CLASP2	33700920	0.999000	0.42202	1.000000	0.80357	0.970000	0.65996	0.412000	0.21131	0.677000	0.31305	0.650000	0.86243	GAG	.	.		0.323	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		G	33725916	C	G	33725916	3	3	2	1	0	0	0	0	1	0	0	0	3457	912	32	4	4073	4	CLASP2	3	33725916	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10		33725916	164296514	19	122										
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69230791	69230791	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tggcttatcgctgtccatctCggagagcaggtgggactggg	16	9	1	1	rs527581690	byFrequency	TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr3:69230791C>T	ENST00000398540.3	-	21	2193	c.2110G>A	c.(2110-2112)Gag>Aag	p.E704K	FRMD4B_ENST00000542259.1_Missense_Mutation_p.E650K|FRMD4B_ENST00000478263.1_Missense_Mutation_p.E356K	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	704					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		CTGTCCATCTCGGAGAGCAGG	0.517													C|||	2	0.000399361	0.0015	0	5008	,	,		19136	0		0	False		,,,				2504	0				p.E704K		Atlas-SNP	.											.	FRMD4B	90	.	0			c.G2110A						.						54	53	53					3																	69230791		1974	4153	6127	SO:0001583	missense	23150	exon21			CCATCTCGGAGAG	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.2110G>A	chr3.hg19:g.69230791C>T	ENSP00000381549:p.Glu704Lys	136.0	0.0		132.0	45.0	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	hg19	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.361359	0.82353	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000478263	D;D	0.86627	-2.15;-2.12	5.98	5.98	0.97165	.	0.100920	0.64402	D	0.000003	D	0.90068	0.6898	M	0.69823	2.125	0.58432	D	0.999999	D;D	0.62365	0.991;0.975	P;B	0.48089	0.566;0.434	D	0.90614	0.4554	10	0.72032	D	0.01	-27.5628	20.452	0.99131	0.0:1.0:0.0:0.0	.	548;704	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	K	704;650;356	ENSP00000381549:E704K;ENSP00000437658:E650K	ENSP00000381549:E704K	E	-	1	0	FRMD4B	69313481	1.000000	0.71417	0.975000	0.42487	0.877000	0.50540	5.750000	0.68712	2.838000	0.97847	0.591000	0.81541	GAG	.	.		0.517	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			T	69230791	C	T	69230791	3	4	2	1	0	0	0	0	1	0	0	0	6060	893	31	1	1006	1	FRMD4B	3	69230791	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	35504875	69230791	128791639	20	123										
IL1RAP	3556	hgsc.bcm.edu	37	chr3	190362044	190362045	+	Frame_Shift_Ins	INS	-	-	C													0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tgttcattccagtgccagctINSccaagatacacagtggaact							TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr3:190362044_190362045insC	ENST00000412504.2	+	9	1311_1312	c.1059_1060insC	c.(1060-1062)ccafs	p.P354fs	IL1RAP_ENST00000317757.3_Frame_Shift_Ins_p.P354fs|RN7SKP296_ENST00000411185.1_RNA|IL1RAP_ENST00000443369.2_Frame_Shift_Ins_p.P354fs|IL1RAP_ENST00000439062.1_Frame_Shift_Ins_p.P354fs|IL1RAP_ENST00000447382.1_Frame_Shift_Ins_p.P354fs|IL1RAP_ENST00000072516.3_Frame_Shift_Ins_p.P354fs			Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein	354					immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-2 biosynthetic process (GO:0042094)|protein complex assembly (GO:0006461)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		CAGTGCCAGCTCCAAGATACAC	0.47																																					p.A353fs		Atlas-Indel,Pindel	.											.	IL1RAP	96	.	0			c.1059_1060insC						.																																			SO:0001589	frameshift_variant	3556	exon10			.	AB006537	CCDS3298.1, CCDS46982.1, CCDS54696.1	3q28	2013-01-11			ENSG00000196083	ENSG00000196083		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5995	protein-coding gene	gene with protein product		602626				9479509, 9065432	Standard	NM_002182		Approved	IL-1RAcP, IL1R3, C3orf13	uc003fsq.3	Q9NPH3	OTTHUMG00000156211	ENST00000412504.2:c.1061dupC	chr3.hg19:g.190362046_190362046dupC	ENSP00000412053:p.Pro354fs	71.0	0.0		109.0	35.0	NM_001167931	B1NLD0|D3DNW0|O14915|Q86WJ7	Frame_Shift_Ins	INS	ENST00000412504.2	hg19	CCDS3298.1																																																																																			.	.		0.47	IL1RAP-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343497.1			C	190362045	-	C	190362044	7	5	2	1	0	1	1	0	0	0	0	0	7669	1538	54	0	1109	0	IL1RAP	3	190362044	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GS-01A-12D-A382-10	121131253	190362044	7660386	21	124										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46043212	46043212	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tacccataatcatcttcttgCggcacagaaatattattcat	4	10	4	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr4:46043212C>T	ENST00000295452.4	-	9	1358	c.1191G>A	c.(1189-1191)ccG>ccA	p.P397P		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	397					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.P397P(1)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CATCTTCTTGCGGCACAGAAA	0.408																																					p.P397P		Atlas-SNP	.											GABRG1,NS,lymphoid_neoplasm,-1,1	GABRG1	172	.	1	Substitution - coding silent(1)	prostate(1)	c.G1191A						.						82	84	83					4																	46043212		2203	4300	6503	SO:0001819	synonymous_variant	2565	exon9			TTCTTGCGGCACA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.1191G>A	chr4.hg19:g.46043212C>T		102.0	1.0		90.0	40.0	NM_173536	Q5H9T8	Silent	SNP	ENST00000295452.4	hg19	CCDS3470.1																																																																																			.	.		0.408	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		T	46043212	C	T	46043212	2	4	2	1	0	0	0	0	0	0	0	1	6179	755	27	1		1	GABRG1	4	46043212	Silent	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10		46043212	145111064	22	125										
ALB	213	hgsc.bcm.edu	37	chr4	74283353	74283360	+	Frame_Shift_Del	DEL	TGAAGCAA	TGAAGCAA	-													0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	agcaaatgttgtaaacatccTgaagcaaaaagaatgccctg							TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	TGAAGCAA	TGAAGCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr4:74283353_74283360delTGAAGCAA	ENST00000503124.1	+	9	1152_1159	c.945_952delTGAAGCAA	c.(943-954)cctgaagcaaaafs	p.EAK316fs	ALB_ENST00000415165.2_Frame_Shift_Del_p.EAK274fs|ALB_ENST00000509063.1_Frame_Shift_Del_p.EAK466fs|ALB_ENST00000505649.1_Intron|ALB_ENST00000295897.4_Frame_Shift_Del_p.EAK466fs|ALB_ENST00000401494.3_Frame_Shift_Del_p.EAK351fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTAAACATCCTGAAGCAAAAAGAATGCC	0.341																																					p.465_467del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.1394_1401del						.																																			SO:0001589	frameshift_variant	213	exon11			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.945_952delTGAAGCAA	chr4.hg19:g.74283353_74283360delTGAAGCAA	ENSP00000421027:p.Glu316fs	193.0	0.0		153.0	72.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.341	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74283360	TGAAGCAA	-	74283353	7	5	2	1	0	1	0	1	0	0	0	0	486	1567	55	0	1437	0	ALB	4	74283353	Frame_Shift_Del	DEL	TGAAGCAA	TCGA-2Y-A9GS-01A-12D-A382-10	28240141	74283353	116870923	23	126										
BASP1	10409	hgsc.bcm.edu	37	chr5	17275720	17275720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cgccgcggccccggccgagaGcgcggcccctgccgccgggg	18	20	0	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr5:17275720G>A	ENST00000322611.3	+	2	655	c.395G>A	c.(394-396)aGc>aAc	p.S132N		NM_001271606.1|NM_006317.3	NP_001258535.1|NP_006308.3	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein 1	132				APAES -> GPRPR (in Ref. 1; AAC67374). {ECO:0000305}.	diaphragm development (GO:0060539)|glomerular visceral epithelial cell differentiation (GO:0072112)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|metanephric mesenchyme development (GO:0072075)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of heart growth (GO:0060421)|positive regulation of metanephric ureteric bud development (GO:2001076)|substantia nigra development (GO:0021762)|thorax and anterior abdomen determination (GO:0007356)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(8)	9						ccggccgagagcgcggcccct	0.761																																					p.S132N		Atlas-SNP	.											.	BASP1	29	.	0			c.G395A						.						2	2	2					5																	17275720		1319	2883	4202	SO:0001583	missense	10409	exon2			CCGAGAGCGCGGC	AF039656	CCDS3888.1	5p15.1	2010-12-03			ENSG00000176788	ENSG00000176788			957	protein-coding gene	gene with protein product		605940				9310187, 9749536	Standard	NM_001271606		Approved	NAP-22, NAP22, CAP23, CAP-23	uc031siz.1	P80723	OTTHUMG00000131061	ENST00000322611.3:c.395G>A	chr5.hg19:g.17275720G>A	ENSP00000319281:p.Ser132Asn	78.0	0.0		103.0	43.0	NM_006317	B4DJA8|D3DTD5|O43596|Q5U0S0|Q9BWA5	Missense_Mutation	SNP	ENST00000322611.3	hg19	CCDS3888.1	.	.	.	.	.	.	.	.	.	.	G	9.050	0.991905	0.18966	.	.	ENSG00000176788	ENST00000322611	T	0.49432	0.78	4.16	3.29	0.37713	.	0.828878	0.09610	U	0.779067	T	0.28566	0.0707	N	0.08118	0	0.09310	N	1	B	0.30211	0.273	B	0.22601	0.04	T	0.18840	-1.0324	10	0.62326	D	0.03	-0.0563	11.2865	0.49224	0.0:0.7283:0.2717:0.0	.	132	P80723	BASP1_HUMAN	N	132	ENSP00000319281:S132N	ENSP00000319281:S132N	S	+	2	0	BASP1	17328720	0.033000	0.19621	0.005000	0.12908	0.696000	0.40369	1.555000	0.36277	0.743000	0.32719	0.298000	0.19748	AGC	.	.		0.761	BASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253716.2			A	17275720	G	A	17275720	3	1	2	1	0	0	0	0	1	0	0	0	1317	971	34	3	397	3	BASP1	5	17275720	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10		17275720	163639540	24	127										
PDZD2	23037	hgsc.bcm.edu	37	chr5	31983276	31983276	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tgcagttacctggctgagcaGtgctggaatggcggctttat	14	8	0	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr5:31983276G>A	ENST00000438447.1	+	3	880	c.492G>A	c.(490-492)caG>caA	p.Q164Q	PDZD2_ENST00000282493.3_Silent_p.Q164Q			O15018	PDZD2_HUMAN	PDZ domain containing 2	164	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						TGGCTGAGCAGTGCTGGAATG	0.532																																					p.Q164Q		Atlas-SNP	.											.	PDZD2	306	.	0			c.G492A						.						93	98	97					5																	31983276		2203	4300	6503	SO:0001819	synonymous_variant	23037	exon2			TGAGCAGTGCTGG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.492G>A	chr5.hg19:g.31983276G>A		61.0	0.0		80.0	26.0	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	hg19	CCDS34137.1																																																																																			.	.		0.532	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			A	31983276	G	A	31983276	2	1	2	1	0	0	0	0	0	0	0	1	11710	1020	36	3		3	PDZD2	5	31983276	Silent	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	14707556	31983276	148931984	25	128										
EDIL3	10085	hgsc.bcm.edu	37	chr5	83433153	83433153	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ccaccatttttgcaaggctcAacttcgcattcatttatgtc	5	12	2	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr5:83433153A>C	ENST00000296591.5	-	5	793	c.375T>G	c.(373-375)gtT>gtG	p.V125V	EDIL3_ENST00000380138.3_Silent_p.V115V	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	125	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		TGCAAGGCTCAACTTCGCATT	0.333																																					p.V125V		Atlas-SNP	.											.	EDIL3	94	.	0			c.T375G						.						172	153	159					5																	83433153		2203	4300	6503	SO:0001819	synonymous_variant	10085	exon5			AGGCTCAACTTCG	U70312	CCDS4062.1, CCDS64195.1	5q14	2008-02-05			ENSG00000164176	ENSG00000164176			3173	protein-coding gene	gene with protein product		606018				9420328	Standard	NM_005711		Approved	DEL1	uc003kio.1	O43854	OTTHUMG00000119047	ENST00000296591.5:c.375T>G	chr5.hg19:g.83433153A>C		41.0	0.0		72.0	25.0	NM_005711	B2R763|O43855|Q5D094|Q8N610	Silent	SNP	ENST00000296591.5	hg19	CCDS4062.1																																																																																			.	.		0.333	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711		C	83433153	A	C	83433153	2	2	2	1	0	0	0	0	0	0	0	1	4917	117	5	5		5	EDIL3	5	83433153	Silent	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10	51449877	83433153	97482107	26	129										
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121759066	121759066	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	caccattttgtgttctttctCccgtgaaaagccctcacttg	6	13	3	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr5:121759066C>A	ENST00000261368.8	+	4	896	c.634C>A	c.(634-636)Ccc>Acc	p.P212T	SNCAIP_ENST00000261367.7_Missense_Mutation_p.P259T|SNCAIP_ENST00000379536.2_Missense_Mutation_p.P212T|SNCAIP_ENST00000542191.1_Intron|SNCAIP_ENST00000379533.2_Missense_Mutation_p.P259T|SNCAIP_ENST00000504884.2_Intron|SNCAIP_ENST00000503116.2_Missense_Mutation_p.P259T|SNCAIP_ENST00000379538.3_Intron|SNCAIP_ENST00000414317.2_Intron	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	212					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		TGTTCTTTCTCCCGTGAAAAG	0.488																																					p.P212T		Atlas-SNP	.											.	SNCAIP	308	.	0			c.C634A						.						86	88	87					5																	121759066		2203	4300	6503	SO:0001583	missense	9627	exon4			CTTTCTCCCGTGA	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.634C>A	chr5.hg19:g.121759066C>A	ENSP00000261368:p.Pro212Thr	120.0	0.0		172.0	25.0	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	hg19	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	C	19.27	3.795912	0.70452	.	.	ENSG00000064692	ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000261367;ENST00000503116	T;T;T;T;T;T	0.41758	3.2;1.18;0.99;3.2;0.99;2.7	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.57330	0.2046	L	0.36672	1.1	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.996;0.997	T	0.48293	-0.9048	9	.	.	.	-20.4124	20.2405	0.98372	0.0:1.0:0.0:0.0	.	212;259;259;212	D6R9G8;Q9Y6H5-6;Q9Y6H5-3;Q9Y6H5	.;.;.;SNCAP_HUMAN	T	212;212;259;212;259;259	ENSP00000422106:P212T;ENSP00000261368:P212T;ENSP00000368848:P259T;ENSP00000368851:P212T;ENSP00000261367:P259T;ENSP00000423199:P259T	.	P	+	1	0	SNCAIP	121786965	1.000000	0.71417	0.999000	0.59377	0.684000	0.39900	5.915000	0.69973	2.797000	0.96272	0.561000	0.74099	CCC	.	.		0.488	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			A	121759066	C	A	121759066	3	1	2	1	0	0	0	0	1	0	0	0	14856	855	30	3	644	3	SNCAIP	5	121759066	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	38325913	121759066	59156194	27	130										
MEGF10	84466	hgsc.bcm.edu	37	chr5	126734452	126734452	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	aatggaggagtgtgtcatcaCgtcactggagaatgctcttg	13	7	4	1	rs190469012		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr5:126734452C>A	ENST00000274473.6	+	8	1011	c.744C>A	c.(742-744)caC>caA	p.H248Q	MEGF10_ENST00000418761.2_Missense_Mutation_p.H248Q|MEGF10_ENST00000508365.1_Missense_Mutation_p.H248Q|MEGF10_ENST00000503335.2_Missense_Mutation_p.H248Q	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	248	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.H248H(1)		breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		TGTGTCATCACGTCACTGGAG	0.527																																					p.H248Q		Atlas-SNP	.											MEGF10,rectum,carcinoma,0,1	MEGF10	152	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C744A						.						265	198	220					5																	126734452		2203	4300	6503	SO:0001583	missense	84466	exon8			TCATCACGTCACT	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.744C>A	chr5.hg19:g.126734452C>A	ENSP00000274473:p.His248Gln	127.0	0.0		139.0	38.0	NM_032446	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	hg19	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.198873	0.38806	.	.	ENSG00000145794	ENST00000503335;ENST00000508365;ENST00000418761;ENST00000274473	T;T;T;T	0.32515	2.18;1.45;1.45;2.18	5.75	-4.53	0.03462	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.44603	0.1301	M	0.73430	2.235	0.51767	D	0.999939	D;D	0.76494	0.97;0.999	P;D	0.63381	0.866;0.914	T	0.59440	-0.7454	10	0.13470	T	0.59	-21.0905	16.5156	0.84299	0.0:0.1875:0.0:0.8125	.	248;248	Q96KG7-2;Q96KG7	.;MEG10_HUMAN	Q	248	ENSP00000423354:H248Q;ENSP00000423195:H248Q;ENSP00000416284:H248Q;ENSP00000274473:H248Q	ENSP00000274473:H248Q	H	+	3	2	MEGF10	126762351	0.099000	0.21834	0.976000	0.42696	0.970000	0.65996	-0.593000	0.05740	-0.662000	0.05338	-0.769000	0.03391	CAC	.	C|1.000;T|0.000		0.527	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		A	126734452	C	A	126734452	3	1	2	1	0	0	0	0	1	0	0	0	9469	535	19	1	766	1	MEGF10	5	126734452	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	4975386	126734452	54180808	28	131										
LOC153328	153328	hgsc.bcm.edu	37	chr5	135188365	135188365	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ttcctcagccagcaccgctgCggggagccagaggccagtcc	13	16	1	1	rs368023667		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr5:135188365C>T	ENST00000420621.1	+	4	448	c.276C>T	c.(274-276)tgC>tgT	p.C92C	SLC25A48_ENST00000433282.2_Silent_p.C38C|SLC25A48_ENST00000274513.5_Silent_p.C92C|SLC25A48_ENST00000425402.1_Intron|SLC25A48_ENST00000412661.2_Silent_p.C92C			Q6ZT89	S2548_HUMAN	solute carrier family 25, member 48	92					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						AGCACCGCTGCGGGGAGCCAG	0.667													C|||	1	0.000199681	8e-04	0	5008	,	,		17722	0		0	False		,,,				2504	0				p.C92C		Atlas-SNP	.											.	SLC25A48	37	.	0			c.C276T						.						58	69	65					5																	135188365		1946	4122	6068	SO:0001819	synonymous_variant	153328	exon4			CCGCTGCGGGGAG		CCDS43366.2	5q31.1	2013-05-22			ENSG00000145832	ENSG00000145832		"Solute carriers"	30451	protein-coding gene	gene with protein product	"HCC-down-regulated mitochondrial carrier protein"					15322095, 19303656	Standard	NM_145282		Approved	FLJ44862, HDMCP	uc003lba.3	Q6ZT89	OTTHUMG00000157007	ENST00000420621.1:c.276C>T	chr5.hg19:g.135188365C>T		104.0	0.0		125.0	43.0	NM_145282	Q8TAV9	Silent	SNP	ENST00000420621.1	hg19																																																																																				.	.		0.667	SLC25A48-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_145282		T	135188365	C	T	135188365	2	4	2	1	0	0	0	0	0	0	0	1	8880	776	27	1		1	LOC153328	5	135188365	Silent	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	8453913	135188365	45726895	29	132										
WNT8A	7478	hgsc.bcm.edu	37	chr5	137420203	137420203	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ccaggcctatctgacctacaCgactagtgtggccttgggtg	12	12	1	1	rs528082347		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr5:137420203C>T	ENST00000398754.1	+	3	124	c.119C>T	c.(118-120)aCg>aTg	p.T40M	WNT8A_ENST00000506684.1_Missense_Mutation_p.T58M	NM_058244.2	NP_490645.1	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family, member 8A	40					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|endoderm development (GO:0007492)|establishment of organ orientation (GO:0048561)|neural crest cell fate commitment (GO:0014034)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|polarity specification of anterior/posterior axis (GO:0009949)|polarity specification of proximal/distal axis (GO:0010085)|regulation of protein localization (GO:0032880)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTGACCTACACGACTAGTGTG	0.577													C|||	1	0.000199681	8e-04	0	5008	,	,		20974	0		0	False		,,,				2504	0				p.T40M		Atlas-SNP	.											.	WNT8A	36	.	0			c.C119T						.						73	75	74					5																	137420203		2024	4215	6239	SO:0001583	missense	7478	exon3			CCTACACGACTAG	AB057725	CCDS43368.1, CCDS75311.1	5q31	2008-07-18			ENSG00000061492	ENSG00000061492		"Wingless-type MMTV integration sites"	12788	protein-coding gene	gene with protein product		606360				11408932	Standard	XM_005272076		Approved	WNT8D	uc003lcd.1	Q9H1J5	OTTHUMG00000129196	ENST00000398754.1:c.119C>T	chr5.hg19:g.137420203C>T	ENSP00000381739:p.Thr40Met	84.0	0.0		89.0	33.0	NM_058244	Q96S51	Missense_Mutation	SNP	ENST00000398754.1	hg19	CCDS43368.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.245629	0.39697	.	.	ENSG00000061492	ENST00000506684;ENST00000504809;ENST00000398754	T;T;T	0.75154	-0.91;-0.91;-0.91	4.96	4.09	0.47781	.	0.215692	0.49305	D	0.000144	T	0.66557	0.2801	N	0.02403	-0.565	0.41715	D	0.989479	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.68621	0.953;0.953;0.959	T	0.71279	-0.4640	10	0.30078	T	0.28	.	13.7291	0.62776	0.0:0.9259:0.0:0.0741	.	58;58;40	D6RF47;D6RF94;Q9H1J5	.;.;WNT8A_HUMAN	M	58;58;40	ENSP00000426653:T58M;ENSP00000424809:T58M;ENSP00000381739:T40M	ENSP00000354726:T40M	T	+	2	0	WNT8A	137448102	0.804000	0.28969	0.387000	0.26183	0.095000	0.18619	7.320000	0.79064	1.465000	0.48006	0.655000	0.94253	ACG	.	.		0.577	WNT8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280395.1	NM_058244		T	137420203	C	T	137420203	3	4	2	1	0	0	0	0	1	0	0	0	17411	536	19	1	129	1	WNT8A	5	137420203	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	2231838	137420203	43495057	30	133										
PCDHGA6	56109	hgsc.bcm.edu	37	chr5	140755818	140755818	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gcagcgctggcacaagtcacGcctgctgcaggcttcgggag	15	13	1	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr5:140755818G>A	ENST00000517434.1	+	1	2168	c.2168G>A	c.(2167-2169)cGc>cAc	p.R723H	PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	723					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACAAGTCACGCCTGCTGCAG	0.647																																					p.R723H		Atlas-SNP	.											.	PCDHGA6	219	.	0			c.G2168A						.						82	89	87					5																	140755818		2203	4300	6503	SO:0001583	missense	56109	exon1			AGTCACGCCTGCT	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"Cadherins / Protocadherins : Clustered"	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.2168G>A	chr5.hg19:g.140755818G>A	ENSP00000429601:p.Arg723His	164.0	0.0		164.0	59.0	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	hg19	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	13.25	2.182335	0.38511	.	.	ENSG00000253731	ENST00000517434	T	0.15372	2.43	5.15	-0.662	0.11413	.	0.819212	0.09410	U	0.805991	T	0.15349	0.0370	L	0.48935	1.535	0.09310	N	1	B;B	0.14438	0.01;0.005	B;B	0.13407	0.008;0.009	T	0.31280	-0.9949	10	0.48119	T	0.1	.	8.9657	0.35874	0.6259:0.0:0.3741:0.0	.	723;723	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	H	723	ENSP00000429601:R723H	ENSP00000429601:R723H	R	+	2	0	PCDHGA6	140736002	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	0.057000	0.14279	-0.047000	0.13423	-0.137000	0.14449	CGC	.	.		0.647	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		A	140755818	G	A	140755818	3	1	2	1	0	0	0	0	1	0	0	0	11567	1087	38	1	2170	1	PCDHGA6	5	140755818	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	3335615	140755818	40159442	31	134										
DRD1	1812	hgsc.bcm.edu	37	chr5	174869971	174869971	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	aacctgataacggcagcacaGaccagcgtgttccccaggag	11	13	0	2			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr5:174869971G>C	ENST00000393752.2	-	2	1124	c.132C>G	c.(130-132)gtC>gtG	p.V44V		NM_000794.3	NP_000785.1	P21728	DRD1_HUMAN	dopamine receptor D1	44					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult walking behavior (GO:0007628)|astrocyte development (GO:0014002)|behavioral fear response (GO:0001662)|behavioral response to cocaine (GO:0048148)|cellular response to catecholamine stimulus (GO:0071870)|cerebral cortex GABAergic interneuron migration (GO:0021853)|conditioned taste aversion (GO:0001661)|dentate gyrus development (GO:0021542)|dopamine metabolic process (GO:0042417)|dopamine transport (GO:0015872)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose import (GO:0046323)|grooming behavior (GO:0007625)|habituation (GO:0046959)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|maternal behavior (GO:0042711)|mating behavior (GO:0007617)|memory (GO:0007613)|neuronal action potential (GO:0019228)|operant conditioning (GO:0035106)|peristalsis (GO:0030432)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|prepulse inhibition (GO:0060134)|protein import into nucleus (GO:0006606)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|sensitization (GO:0046960)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|transmission of nerve impulse (GO:0019226)|vasodilation (GO:0042311)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.V44V(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acepromazine(DB01614)|Acetophenazine(DB01063)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Dopamine(DB00988)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Methylergometrine(DB00353)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Phenylpropanolamine(DB00397)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CGGCAGCACAGACCAGCGTGT	0.577																																					p.V44V		Atlas-SNP	.											DRD1,colon,carcinoma,0,2	DRD1	56	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C132G						.						97	84	88					5																	174869971		2203	4300	6503	SO:0001819	synonymous_variant	1812	exon2			AGCACAGACCAGC	X55760	CCDS4393.1	5q34-q35	2012-08-08			ENSG00000184845	ENSG00000184845		"GPCR / Class A : Dopamine receptors"	3020	protein-coding gene	gene with protein product		126449					Standard	NM_000794		Approved		uc003mcz.3	P21728	OTTHUMG00000130557	ENST00000393752.2:c.132C>G	chr5.hg19:g.174869971G>C		168.0	0.0		140.0	55.0	NM_000794	B2RA44|Q4QRJ0	Silent	SNP	ENST00000393752.2	hg19	CCDS4393.1																																																																																			.	.		0.577	DRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252982.2	NM_000794		C	174869971	G	C	174869971	2	2	2	1	0	0	0	0	0	0	0	1	4758	929	33	4		4	DRD1	5	174869971	Silent	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	34114153	174869971	6045289	32	135										
GFRAL	389400	hgsc.bcm.edu	37	chr6	55216306	55216306	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	agaagctcttcacagcaagaCatgtgcagtgaacatggttc	10	9	2	3			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr6:55216306C>G	ENST00000340465.2	+	5	712	c.626C>G	c.(625-627)aCa>aGa	p.T209R		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	209					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			CACAGCAAGACATGTGCAGTG	0.428																																					p.T209R		Atlas-SNP	.											.	GFRAL	91	.	0			c.C626G						.						115	112	113					6																	55216306		2203	4300	6503	SO:0001583	missense	389400	exon5			GCAAGACATGTGC	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.626C>G	chr6.hg19:g.55216306C>G	ENSP00000343636:p.Thr209Arg	97.0	0.0		112.0	43.0	NM_207410	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	hg19	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.431963	0.43122	.	.	ENSG00000187871	ENST00000340465	T	0.62498	0.02	6.05	4.22	0.49857	GDNF/GAS1 (2);	0.190419	0.45606	D	0.000352	T	0.25791	0.0628	N	0.08118	0	0.22947	N	0.998528	B	0.06786	0.001	B	0.06405	0.002	T	0.25082	-1.0142	10	0.56958	D	0.05	-2.7163	16.8145	0.85730	0.0:0.7721:0.2279:0.0	.	209	Q6UXV0	GFRAL_HUMAN	R	209	ENSP00000343636:T209R	ENSP00000343636:T209R	T	+	2	0	GFRAL	55324265	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	2.335000	0.43929	0.824000	0.34613	0.650000	0.86243	ACA	.	.		0.428	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		G	55216306	C	G	55216306	3	3	2	1	0	0	0	0	1	0	0	0	6359	478	17	4	644	4	GFRAL	6	55216306	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10		55216306	115898761	33	136										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138613011	138613012	+	Frame_Shift_Ins	INS	-	-	G													0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	agtgtgagggctcgccccccINSgagcacagcccggagcaggg							TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr6:138613011_138613012insG	ENST00000251691.4	+	19	3355_3356	c.3189_3190insG	c.(3190-3192)gagfs	p.E1064fs		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		GCTCGCCCCCCGAGCACAGCCC	0.728																																					p.P1063fs		Atlas-Indel,Pindel	.											.	KIAA1244	236	.	0			c.3189_3190insG						.																																			SO:0001589	frameshift_variant	57221	exon19			.	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.3190dupG	chr6.hg19:g.138613012_138613012dupG	ENSP00000251691:p.Glu1064fs	164.0	0.0		184.0	63.0	NM_020340		Frame_Shift_Ins	INS	ENST00000251691.4	hg19	CCDS5189.2																																																																																			.	.		0.728	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		G	138613012	-	G	138613011	7	5	2	1	0	1	1	0	0	0	0	0	8226	639	23	0	3263	0	KIAA1244	6	138613011	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GS-01A-12D-A382-10	83396705	138613011	32502056	34	137										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48626793	48626793	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cttacacctcgaagcccacgCggacaaacctgtggccacct	8	17	0	0	rs563692415		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr7:48626793C>T	ENST00000435803.1	+	57	14573	c.14549C>T	c.(14548-14550)gCg>gTg	p.A4850V	ABCA13_ENST00000544596.1_Missense_Mutation_p.A580V	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4850	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GAAGCCCACGCGGACAAACCT	0.557																																					p.A4850V		Atlas-SNP	.											ABCA13_ENST00000435803,rectum,carcinoma,+1,2	ABCA13	1192	.	0			c.C14549T						.						43	48	46					7																	48626793		2024	4188	6212	SO:0001583	missense	154664	exon57			CCCACGCGGACAA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.14549C>T	chr7.hg19:g.48626793C>T	ENSP00000411096:p.Ala4850Val	54.0	0.0		53.0	19.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	1.942	-0.443420	0.04604	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.94184	-3.37;-3.37;-3.37	5.71	-0.712	0.11226	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.760684	0.11485	N	0.559299	D	0.89174	0.6640	L	0.58428	1.81	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.002	T	0.76105	-0.3081	10	0.30854	T	0.27	.	7.0876	0.25266	0.1224:0.1475:0.0:0.7301	.	580;2552;4850	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	V	4850;623;580	ENSP00000411096:A4850V;ENSP00000391042:A623V;ENSP00000442634:A580V	ENSP00000391042:A623V	A	+	2	0	ABCA13	48597339	0.097000	0.21791	0.017000	0.16124	0.151000	0.21798	0.423000	0.21313	-0.283000	0.09115	-0.143000	0.13931	GCG	.	.		0.557	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48626793	C	T	48626793	3	4	2	1	0	0	0	0	1	0	0	0	31	768	27	1	14604	1	ABCA13	7	48626793	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10		48626793	110511870	35	138										
TECPR1	25851	hgsc.bcm.edu	37	chr7	97863212	97863212	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ccctcacctcatcaccgaagAagcagccggcactggggaca	10	16	3	1	rs375012059		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr7:97863212A>C	ENST00000447648.2	-	11	1492	c.1193T>G	c.(1192-1194)tTc>tGc	p.F398C	TECPR1_ENST00000379795.3_Missense_Mutation_p.F398C|TECPR1_ENST00000542604.1_Missense_Mutation_p.F328C			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	398					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						ATCACCGAAGAAGCAGCCGGC	0.642																																					p.F398C		Atlas-SNP	.											.	TECPR1	77	.	0			c.T1193G						.	A	CYS/PHE	1,4241		0,1,2120	8	8	8		1193	4.7	1	7		8	0,8346		0,0,4173	no	missense	TECPR1	NM_015395.1	205	0,1,6293	CC,CA,AA		0.0,0.0236,0.0079	probably-damaging	398/1166	97863212	1,12587	2121	4173	6294	SO:0001583	missense	25851	exon11			CCGAAGAAGCAGC		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.1193T>G	chr7.hg19:g.97863212A>C	ENSP00000404923:p.Phe398Cys	214.0	0.0		252.0	42.0	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Missense_Mutation	SNP	ENST00000447648.2	hg19	CCDS47648.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.715654	0.48622	2.36E-4	0.0	ENSG00000205356	ENST00000447648;ENST00000379795;ENST00000542604	T;T;T	0.37584	1.19;1.2;1.2	4.7	4.7	0.59300	.	0.051780	0.85682	D	0.000000	T	0.51907	0.1702	L	0.55990	1.75	0.47737	D	0.999501	D;B	0.89917	1.0;0.198	D;B	0.65573	0.936;0.04	T	0.51537	-0.8693	10	0.46703	T	0.11	-35.9513	13.3404	0.60540	1.0:0.0:0.0:0.0	.	328;398	F5GX57;Q7Z6L1	.;TCPR1_HUMAN	C	398;398;328	ENSP00000404923:F398C;ENSP00000369121:F398C;ENSP00000441121:F328C	ENSP00000369121:F398C	F	-	2	0	TECPR1	97701148	1.000000	0.71417	1.000000	0.80357	0.355000	0.29361	5.680000	0.68168	1.761000	0.52028	0.379000	0.24179	TTC	.	.		0.642	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395		C	97863212	A	C	97863212	3	2	2	1	0	0	0	0	1	0	0	0	15758	246	9	5	2368	5	TECPR1	7	97863212	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10	49236419	97863212	61275451	36	139										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107696204	107696204	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gtctgcctcacagacaggcaGggtctctcttttatcttcca	8	13	5	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr7:107696204G>A	ENST00000388781.3	-	25	3711	c.3628C>T	c.(3628-3630)Ctg>Ttg	p.L1210L	LAMB4_ENST00000205386.4_Silent_p.L1210L|LAMB4_ENST00000388780.3_Silent_p.L1210L	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1210	Domain II.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						CAGACAGGCAGGGTCTCTCTT	0.453																																					p.L1210L		Atlas-SNP	.											.	LAMB4	253	.	0			c.C3628T						.						77	75	76					7																	107696204		2203	4300	6503	SO:0001819	synonymous_variant	22798	exon25			CAGGCAGGGTCTC	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.3628C>T	chr7.hg19:g.107696204G>A		90.0	0.0		138.0	20.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	hg19	CCDS34732.1																																																																																			.	.		0.453	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		A	107696204	G	A	107696204	2	1	2	1	0	0	0	0	0	0	0	1	8622	991	35	3		3	LAMB4	7	107696204	Silent	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	9832992	107696204	51442459	37	140										
GEM	2669	hgsc.bcm.edu	37	chr8	95262710	95262710	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ccttgctgtcccgccgaaggCgcacctgtcgcacaatgccc	10	18	0	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr8:95262710C>T	ENST00000297596.2	-	5	983	c.719G>A	c.(718-720)cGc>cAc	p.R240H	GEM_ENST00000396194.2_Missense_Mutation_p.R240H	NM_005261.3	NP_005252.1	P55040	GEM_HUMAN	GTP binding protein overexpressed in skeletal muscle	240					cell surface receptor signaling pathway (GO:0007166)|chromosome organization (GO:0051276)|immune response (GO:0006955)|metaphase plate congression (GO:0051310)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic side of plasma membrane (GO:0009898)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle midzone (GO:0051233)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			CCGCCGAAGGCGCACCTGTCG	0.577																																					p.R240H	GBM(125;80 1653 28655 32188 47338)|Esophageal Squamous(19;97 579 13602 49091 51766)	Atlas-SNP	.											.	GEM	40	.	0			c.G719A						.						65	61	62					8																	95262710		2203	4300	6503	SO:0001583	missense	2669	exon5			CGAAGGCGCACCT		CCDS6261.1	8q13-q21	2014-05-09	2001-11-28		ENSG00000164949	ENSG00000164949			4234	protein-coding gene	gene with protein product	"kinase-inducible Ras-like protein"	600164	"GTP-binding protein overexpressed in skeletal muscle"			7912851, 11956230	Standard	NM_005261		Approved	KIR	uc003ygj.3	P55040	OTTHUMG00000164392	ENST00000297596.2:c.719G>A	chr8.hg19:g.95262710C>T	ENSP00000297596:p.Arg240His	89.0	0.0		103.0	42.0	NM_181702	B2RA31	Missense_Mutation	SNP	ENST00000297596.2	hg19	CCDS6261.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.683966	0.88639	.	.	ENSG00000164949	ENST00000396194;ENST00000297596	T;T	0.80123	-1.34;-1.34	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.92280	0.7551	M	0.91717	3.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93393	0.6753	10	0.87932	D	0	.	19.6814	0.95965	0.0:1.0:0.0:0.0	.	240	P55040	GEM_HUMAN	H	240	ENSP00000379497:R240H;ENSP00000297596:R240H	ENSP00000297596:R240H	R	-	2	0	GEM	95331886	1.000000	0.71417	0.998000	0.56505	0.800000	0.45204	7.445000	0.80570	2.733000	0.93635	0.557000	0.71058	CGC	.	.		0.577	GEM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378566.1	NM_181702		T	95262710	C	T	95262710	3	4	2	1	0	0	0	0	1	0	0	0	6337	768	27	1	175	1	GEM	8	95262710	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10		95262710	51101312	38	141										
RGS22	26166	hgsc.bcm.edu	37	chr8	101076177	101076177	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	acagacacctcttcttcttcTccttcttcttcttcaaattc	1	15	8	1	rs538962849	byFrequency	TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr8:101076177T>A	ENST00000360863.6	-	8	1013	c.819A>T	c.(817-819)ggA>ggT	p.G273G	RGS22_ENST00000523437.1_Silent_p.G261G|RGS22_ENST00000523287.1_Silent_p.G92G	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	273	Poly-Glu.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			cttcttcttctccttcttctt	0.373																																					p.G273G		Atlas-SNP	.											.	RGS22	319	.	0			c.A819T						.						105	108	107					8																	101076177		1822	4073	5895	SO:0001819	synonymous_variant	26166	exon8			TTCTTCTCCTTCT	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.819A>T	chr8.hg19:g.101076177T>A		59.0	0.0		57.0	7.0	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Silent	SNP	ENST00000360863.6	hg19	CCDS43758.1																																																																																			.	.		0.373	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		A	101076177	T	A	101076177	2	1	2	1	0	0	0	0	0	0	0	1	13320	1538	54	4		4	RGS22	8	101076177	Silent	SNP	T	TCGA-2Y-A9GS-01A-12D-A382-10	5813467	101076177	45287845	39	142										
ABRA	137735	hgsc.bcm.edu	37	chr8	107773510	107773510	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gtagatgtgctcctcagcacGcttggccctttcagcagttt	10	12	2	1	rs182944429		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr8:107773510G>T	ENST00000311955.3	-	2	955	c.901C>A	c.(901-903)Cgt>Agt	p.R301S		NM_139166.4	NP_631905.1			actin-binding Rho activating protein											breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			TCCTCAGCACGCTTGGCCCTT	0.517																																					p.R301S		Atlas-SNP	.											.	ABRA	57	.	0			c.C901A						.						140	110	120					8																	107773510		2203	4300	6503	SO:0001583	missense	137735	exon2			CAGCACGCTTGGC	AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"striated muscle activator of Rho-dependent signaling"	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.901C>A	chr8.hg19:g.107773510G>T	ENSP00000311436:p.Arg301Ser	118.0	0.0		114.0	51.0	NM_139166		Missense_Mutation	SNP	ENST00000311955.3	hg19	CCDS6305.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.418291	0.62622	.	.	ENSG00000174429	ENST00000311955	.	.	.	6.06	2.03	0.26663	.	0.000000	0.85682	D	0.000000	T	0.69324	0.3098	L	0.59912	1.85	0.58432	D	0.999997	D	0.76494	0.999	D	0.73380	0.98	T	0.70457	-0.4866	9	0.72032	D	0.01	-10.8748	12.4501	0.55673	0.0:0.0924:0.3144:0.5932	.	301	Q8N0Z2	ABRA_HUMAN	S	301	.	ENSP00000311436:R301S	R	-	1	0	ABRA	107842686	0.731000	0.28111	0.921000	0.36526	0.724000	0.41520	0.772000	0.26647	0.396000	0.25283	-0.169000	0.13324	CGT	.	G|1.000;A|0.000		0.517	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166		T	107773510	G	T	107773510	3	4	2	1	0	0	0	0	1	0	0	0	100	1087	38	1	248	1	ABRA	8	107773510	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	6697333	107773510	38590512	40	143										
CYC1	1537	hgsc.bcm.edu	37	chr8	145150769	145150769	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cgtcgaagtctggcctttccCgaggccggaaagtgatgctg	14	11	1	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr8:145150769C>G	ENST00000318911.4	+	2	236	c.163C>G	c.(163-165)Cga>Gga	p.R55G		NM_001916.3	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	55					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to glucagon (GO:0033762)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|respiratory chain (GO:0070469)	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity (GO:0045155)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	15	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGGCCTTTCCCGAGGCCGGAA	0.652											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R55G		Atlas-SNP	.											.	CYC1	34	.	0			c.C163G						.						88	86	87					8																	145150769		2203	4300	6503	SO:0001583	missense	1537	exon2			CTTTCCCGAGGCC	BC001006	CCDS6415.1	8q24	2011-07-04			ENSG00000179091	ENSG00000179091		"Mitochondrial respiratory chain complex / Complex III"	2579	protein-coding gene	gene with protein product		123980					Standard	NM_001916		Approved	UQCR4	uc003zaz.4	P08574	OTTHUMG00000165242	ENST00000318911.4:c.163C>G	chr8.hg19:g.145150769C>G	ENSP00000317159:p.Arg55Gly	28.0	0.0	1692	45.0	15.0	NM_001916	Q5U062|Q6FHS7	Missense_Mutation	SNP	ENST00000318911.4	hg19	CCDS6415.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.586119	0.46110	.	.	ENSG00000179091	ENST00000318911	T	0.32515	1.45	4.3	3.34	0.38264	.	0.075574	0.49916	D	0.000125	T	0.25158	0.0611	L	0.55990	1.75	0.40657	D	0.982093	P	0.48016	0.904	B	0.37601	0.254	T	0.10706	-1.0618	10	0.39692	T	0.17	-13.0053	11.0888	0.48104	0.1965:0.8035:0.0:0.0	.	55	P08574	CY1_HUMAN	G	55	ENSP00000317159:R55G	ENSP00000317159:R55G	R	+	1	2	CYC1	145222757	0.996000	0.38824	0.983000	0.44433	0.915000	0.54546	2.303000	0.43646	2.242000	0.73789	0.561000	0.74099	CGA	.	.		0.652	CYC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382895.1	NM_001916		G	145150769	C	G	145150769	3	3	2	1	0	0	0	0	1	0	0	0	4137	644	23	4	169	4	CYC1	8	145150769	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	37377259	145150769	1213253	41	144										
OR1L4	254973	hgsc.bcm.edu	37	chr9	125486542	125486542	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	attttctatcagagacaaagAttatctcttatgtgggctgc	8	7	3	2	rs143746640	byFrequency	TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr9:125486542A>T	ENST00000259466.1	+	1	274	c.274A>T	c.(274-276)Att>Ttt	p.I92F		NM_001005235.1	NP_001005235.1	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L, member 4	92						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(3)|lung(13)|prostate(1)|skin(1)	20						AGAGACAAAGATTATCTCTTA	0.453																																					p.I92F		Atlas-SNP	.											.	OR1L4	38	.	0			c.A274T						.						142	136	138					9																	125486542		2203	4300	6503	SO:0001583	missense	254973	exon1			ACAAAGATTATCT		CCDS35129.1	9q33.2	2013-09-20			ENSG00000136939	ENSG00000136939		"GPCR / Class A : Olfactory receptors"	8216	protein-coding gene	gene with protein product				OR1L5			Standard	NM_001005235		Approved	OR9-E	uc004bmu.1	Q8NGR5	OTTHUMG00000020620	ENST00000259466.1:c.274A>T	chr9.hg19:g.125486542A>T	ENSP00000259466:p.Ile92Phe	82.0	0.0		78.0	47.0	NM_001005235	Q6IFN0|Q96R81	Missense_Mutation	SNP	ENST00000259466.1	hg19	CCDS35129.1	.	.	.	.	.	.	.	.	.	.	.	5.611	0.297509	0.10622	.	.	ENSG00000136939	ENST00000259466	T	0.01838	4.61	4.01	-8.02	0.01118	GPCR, rhodopsin-like superfamily (1);	1.445290	0.04270	N	0.341889	T	0.01835	0.0058	L	0.28458	0.855	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43278	-0.9401	10	0.48119	T	0.1	0.0814	5.607	0.17385	0.4363:0.0:0.2515:0.3122	.	92	Q8NGR5	OR1L4_HUMAN	F	92	ENSP00000259466:I92F	ENSP00000259466:I92F	I	+	1	0	OR1L4	124526363	0.000000	0.05858	0.160000	0.22671	0.110000	0.19582	-0.375000	0.07475	-1.904000	0.01092	-0.711000	0.03637	ATT	.	A|0.984;G|0.016		0.453	OR1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053951.1			T	125486542	A	T	125486542	3	4	2	1	0	0	0	0	1	0	0	0	10974	333	12	4	276	4	OR1L4	9	125486542	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10		125486542	15726889	42	145										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7212949	7212949	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cagcttaatgaacctcaccaCgtcggtgaccgtccactcca	7	16	1	2			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr10:7212949C>T	ENST00000361972.4	-	20	2575	c.2485G>A	c.(2485-2487)Gtg>Atg	p.V829M	SFMBT2_ENST00000397167.1_Missense_Mutation_p.V829M	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	829	SAM.				negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						AACCTCACCACGTCGGTGACC	0.562																																					p.V829M		Atlas-SNP	.											.	SFMBT2	209	.	0			c.G2485A						.						275	230	246					10																	7212949		2203	4300	6503	SO:0001583	missense	57713	exon20			TCACCACGTCGGT	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.2485G>A	chr10.hg19:g.7212949C>T	ENSP00000355109:p.Val829Met	99.0	0.0		150.0	47.0	NM_001029880	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	hg19	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.985910	0.93044	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.69926	-0.44;-0.44	5.09	5.09	0.68999	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.87337	0.6152	H	0.94503	3.545	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90882	0.4754	10	0.87932	D	0	.	18.8635	0.92282	0.0:1.0:0.0:0.0	.	829	Q5VUG0	SMBT2_HUMAN	M	829	ENSP00000355109:V829M;ENSP00000380353:V829M	ENSP00000355109:V829M	V	-	1	0	SFMBT2	7252955	1.000000	0.71417	0.990000	0.47175	0.994000	0.84299	7.651000	0.83577	2.532000	0.85374	0.555000	0.69702	GTG	.	.		0.562	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		T	7212949	C	T	7212949	3	4	2	1	0	0	0	0	1	0	0	0	14173	536	19	1	207	1	SFMBT2	10	7212949	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10		7212949	128321798	43	146										
ST8SIA6	338596	hgsc.bcm.edu	37	chr10	17363216	17363216	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cttgctttagactcttcgagCgtgtagtatactttgaaaga	9	7	1	3			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr10:17363216C>G	ENST00000377602.4	-	8	932	c.858G>C	c.(856-858)acG>acC	p.T286T		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	286					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						ACTCTTCGAGCGTGTAGTATA	0.433																																					p.T286T		Atlas-SNP	.											.	ST8SIA6	85	.	0			c.G858C						.						139	146	144					10																	17363216		2203	4300	6503	SO:0001819	synonymous_variant	338596	exon8			TTCGAGCGTGTAG		CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.858G>C	chr10.hg19:g.17363216C>G		223.0	0.0		252.0	98.0	NM_001004470	B0YJ97|B9EH72|Q5VZH4	Silent	SNP	ENST00000377602.4	hg19	CCDS31158.1	.	.	.	.	.	.	.	.	.	.	C	0.015	-1.543833	0.00934	.	.	ENSG00000148488	ENST00000440449	.	.	.	5.18	-7.5	0.01351	.	.	.	.	.	T	0.30978	0.0782	.	.	.	0.32042	N	0.598104	.	.	.	.	.	.	T	0.36359	-0.9751	4	.	.	.	0.8831	5.9037	0.18980	0.2924:0.3042:0.0:0.4034	.	.	.	.	P	107	.	.	A	-	1	0	ST8SIA6	17403222	0.002000	0.14202	0.002000	0.10522	0.018000	0.09664	-1.684000	0.01932	-1.523000	0.01767	-1.154000	0.01816	GCT	.	.		0.433	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		G	17363216	C	G	17363216	2	3	2	1	0	0	0	0	0	0	0	1	15251	755	27	4		4	ST8SIA6	10	17363216	Silent	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	10150267	17363216	118171531	44	147										
CWF19L1	55280	hgsc.bcm.edu	37	chr10	102020773	102020773	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	attcagcatcttgggtggagCcaaagaaatttcctacacac	8	10	2	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr10:102020773C>G	ENST00000354105.4	-	3	223	c.137G>C	c.(136-138)gGc>gCc	p.G46A	RNU6-422P_ENST00000384632.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	46							catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		TTGGGTGGAGCCAAAGAAATT	0.289																																					p.G46A		Atlas-SNP	.											.	CWF19L1	39	.	0			c.G137C						.						54	53	53					10																	102020773		2203	4299	6502	SO:0001583	missense	55280	exon3			GTGGAGCCAAAGA	AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.137G>C	chr10.hg19:g.102020773C>G	ENSP00000326411:p.Gly46Ala	484.0	1.0		403.0	232.0	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	hg19	CCDS7489.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.421660	0.62622	.	.	ENSG00000095485	ENST00000354105	T	0.38887	1.11	5.83	4.93	0.64822	.	0.087163	0.85682	D	0.000000	T	0.38268	0.1034	L	0.39633	1.23	0.80722	D	1	P	0.50156	0.932	P	0.47206	0.541	T	0.09975	-1.0650	10	0.14252	T	0.57	-5.1579	12.8254	0.57716	0.0:0.9208:0.0:0.0792	.	46	Q69YN2	C19L1_HUMAN	A	46	ENSP00000326411:G46A	ENSP00000326411:G46A	G	-	2	0	CWF19L1	102010763	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.275000	0.65575	1.477000	0.48234	0.484000	0.47621	GGC	.	.		0.289	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294		G	102020773	C	G	102020773	3	3	2	1	0	0	0	0	1	0	0	0	4073	739	26	4	1527	4	CWF19L1	10	102020773	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	84657557	102020773	33513974	45	148										
OR52R1	119695	hgsc.bcm.edu	37	chr11	4824698	4824698	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	acaacatccttggataacccTgtccccgatctgtttggttc	7	13	1	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr11:4824698T>C	ENST00000356069.2	-	1	912	c.913A>G	c.(913-915)Agg>Ggg	p.R305G	OR52R1_ENST00000380382.1_Missense_Mutation_p.R384G|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	305						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGATAACCCTGTCCCCGATC	0.463																																					p.R305G		Atlas-SNP	.											.	OR52R1	81	.	0			c.A913G						.						87	87	87					11																	4824698		2201	4298	6499	SO:0001583	missense	119695	exon1			TAACCCTGTCCCC	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"GPCR / Class A : Olfactory receptors"	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.913A>G	chr11.hg19:g.4824698T>C	ENSP00000348368:p.Arg305Gly	117.0	0.0		152.0	56.0	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	hg19	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	T	13.30	2.195947	0.38806	.	.	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.37584	1.19;1.19	5.43	5.43	0.79202	.	0.000000	0.53938	D	0.000045	T	0.33352	0.0860	M	0.63208	1.945	0.32803	D	0.500364	P	0.42078	0.77	B	0.36186	0.219	T	0.52624	-0.8551	10	0.34782	T	0.22	.	11.7962	0.52102	0.0:0.0:0.0:1.0	.	305	Q8NGF1	O52R1_HUMAN	G	305;384	ENSP00000348368:R305G;ENSP00000369742:R384G	ENSP00000348368:R305G	R	-	1	2	OR52R1	4781274	0.000000	0.05858	0.611000	0.29010	0.009000	0.06853	0.239000	0.18023	2.271000	0.75665	0.528000	0.53228	AGG	.	.		0.463	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177		C	4824698	T	C	4824698	3	2	2	1	0	0	0	0	1	0	0	0	11140	1579	55	2	37	2	OR52R1	11	4824698	Missense_Mutation	SNP	T	TCGA-2Y-A9GS-01A-12D-A382-10		4824698	130181818	46	149										
NLRP14	338323	hgsc.bcm.edu	37	chr11	7091576	7091576	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tctctcctctgctcttatctGcaacaaaagactgataaaaa	4	11	4	2			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr11:7091576G>A	ENST00000299481.4	+	11	3381	c.3035G>A	c.(3034-3036)tGc>tAc	p.C1012Y		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	1012					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GCTCTTATCTGCAACAAAAGA	0.348																																					p.C1012Y		Atlas-SNP	.											.	NLRP14	187	.	0			c.G3035A						.						104	100	101					11																	7091576		2201	4296	6497	SO:0001583	missense	338323	exon11			TTATCTGCAACAA	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.3035G>A	chr11.hg19:g.7091576G>A	ENSP00000299481:p.Cys1012Tyr	72.0	0.0		99.0	35.0	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	hg19	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	G	8.559	0.877223	0.17395	.	.	ENSG00000158077	ENST00000299481	T	0.41065	1.01	4.13	1.67	0.24075	.	0.504141	0.18557	N	0.137736	T	0.28928	0.0718	L	0.48362	1.52	0.23607	N	0.997302	B	0.30542	0.284	B	0.27887	0.084	T	0.13176	-1.0519	10	0.35671	T	0.21	.	3.9463	0.09350	0.1833:0.221:0.5956:0.0	.	1012	Q86W24	NAL14_HUMAN	Y	1012	ENSP00000299481:C1012Y	ENSP00000299481:C1012Y	C	+	2	0	NLRP14	7048152	0.000000	0.05858	0.473000	0.27253	0.026000	0.11368	-0.991000	0.03728	0.421000	0.25980	0.557000	0.71058	TGC	.	.		0.348	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		A	7091576	G	A	7091576	3	1	2	1	0	0	0	0	1	0	0	0	10485	1319	46	3	3073	3	NLRP14	11	7091576	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	2266878	7091576	127914940	47	150										
DAK	26007	hgsc.bcm.edu	37	chr11	61113934	61113934	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	accccggggcggtggcagctGctgccatcctccgggccatc	14	17	0	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr11:61113934G>T	ENST00000394900.3	+	18	1916	c.1687G>T	c.(1687-1689)Gct>Tct	p.A563S	CYB561A3_ENST00000540317.1_5'Flank	NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	563	DhaL. {ECO:0000255|PROSITE- ProRule:PRU00813}.				carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)			NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						GGTGGCAGCTGCTGCCATCCT	0.622																																					p.A563S		Atlas-SNP	.											.	DAK	52	.	0			c.G1687T						.						73	86	82					11																	61113934		2203	4299	6502	SO:0001583	missense	26007	exon18			GCAGCTGCTGCCA		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"dihydroxyacetone kinase 2 homolog (yeast)"				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.1687G>T	chr11.hg19:g.61113934G>T	ENSP00000378360:p.Ala563Ser	26.0	0.0		28.0	15.0	NM_015533	Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Missense_Mutation	SNP	ENST00000394900.3	hg19	CCDS8003.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012156	0.75046	.	.	ENSG00000149476	ENST00000394900	T	0.32988	1.43	5.67	5.67	0.87782	Dak phosphatase (3);	0.049597	0.85682	D	0.000000	T	0.45836	0.1362	L	0.41492	1.28	0.58432	D	0.999998	D	0.67145	0.996	D	0.63192	0.912	T	0.17992	-1.0351	10	0.44086	T	0.13	-17.6	17.9412	0.89027	0.0:0.0:1.0:0.0	.	563	Q3LXA3	DHAK_HUMAN	S	563	ENSP00000378360:A563S	ENSP00000378360:A563S	A	+	1	0	DAK	60870510	1.000000	0.71417	0.192000	0.23308	0.960000	0.62799	4.875000	0.63072	2.686000	0.91538	0.561000	0.74099	GCT	.	.		0.622	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533		T	61113934	G	T	61113934	3	4	2	1	0	0	0	0	1	0	0	0	4230	1319	46	3	1753	3	DAK	11	61113934	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	54022358	61113934	73892582	48	151										
MAP4K2	5871	hgsc.bcm.edu	37	chr11	64567661	64567661	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cagctgtgtgaggagggcccGagggagctgctgagtcgtga	19	8	0	3			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr11:64567661G>A	ENST00000294066.2	-	12	926	c.835C>T	c.(835-837)Cgg>Tgg	p.R279W	MAP4K2_ENST00000468062.1_5'Flank|MAP4K2_ENST00000377350.3_Missense_Mutation_p.R279W	NM_004579.3	NP_004570.2	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase kinase 2	279					activation of JUN kinase activity (GO:0007257)|immune response (GO:0006955)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|positive regulation of JNK cascade (GO:0046330)|protein phosphorylation (GO:0006468)|vesicle targeting (GO:0006903)	Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(1)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(2)	8						AGGAGGGCCCGAGGGAGCTGC	0.642																																					p.R279W		Atlas-SNP	.											.	MAP4K2	83	.	0			c.C835T						.						28	33	31					11																	64567661		2201	4297	6498	SO:0001583	missense	5871	exon12			GGGCCCGAGGGAG	BC047865	CCDS8082.1	11q13.1	2011-06-09			ENSG00000168067	ENSG00000168067		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6864	protein-coding gene	gene with protein product		603166		RAB8IP		7515885	Standard	NM_004579		Approved	GCK, BL44	uc001obh.3	Q12851	OTTHUMG00000045328	ENST00000294066.2:c.835C>T	chr11.hg19:g.64567661G>A	ENSP00000294066:p.Arg279Trp	35.0	0.0		30.0	6.0	NM_004579	Q86VU3	Missense_Mutation	SNP	ENST00000294066.2	hg19	CCDS8082.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.165594	0.57476	.	.	ENSG00000168067	ENST00000294066;ENST00000377350;ENST00000439069	T;T;T	0.27557	1.66;1.66;1.66	4.12	3.19	0.36642	Protein kinase-like domain (1);	0.240072	0.30762	N	0.008928	T	0.35068	0.0919	L	0.31476	0.935	0.37252	D	0.90658	P;D	0.69078	0.955;0.997	B;P	0.57468	0.354;0.821	T	0.39272	-0.9622	10	0.72032	D	0.01	.	11.1656	0.48541	0.0:0.0:0.8144:0.1856	.	279;279	Q86VU3;Q12851	.;M4K2_HUMAN	W	279;279;235	ENSP00000294066:R279W;ENSP00000366567:R279W;ENSP00000403563:R235W	ENSP00000294066:R279W	R	-	1	2	MAP4K2	64324237	0.994000	0.37717	0.996000	0.52242	0.994000	0.84299	1.813000	0.38962	1.090000	0.41315	0.456000	0.33151	CGG	.	.		0.642	MAP4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105239.1	NM_004579		A	64567661	G	A	64567661	3	1	2	1	0	0	0	0	1	0	0	0	9269	1057	37	1	1711	1	MAP4K2	11	64567661	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	3453727	64567661	70438855	49	152										
KRT81	3887	hgsc.bcm.edu	37	chr12	52681039	52681039	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ccagctcggccagcttgcagCgggcatcactgagggccgcc	14	16	1	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr12:52681039C>T	ENST00000327741.5	-	7	1162	c.1094G>A	c.(1093-1095)cGc>cAc	p.R365H	KRT86_ENST00000423955.2_Intron|KRT86_ENST00000544024.1_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	365	Coil 2.|Rod.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		CAGCTTGCAGCGGGCATCACT	0.612																																					p.R365H		Atlas-SNP	.											.	KRT81	46	.	0			c.G1094A						.						37	36	37					12																	52681039		2202	4297	6499	SO:0001583	missense	3887	exon7			TTGCAGCGGGCAT	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"-", "Intermediate filaments type II, keratins (basic)"	6458	protein-coding gene	gene with protein product	"hard keratin type II 1"	602153	"keratin, hair, basic, 1"	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.1094G>A	chr12.hg19:g.52681039C>T	ENSP00000369349:p.Arg365His	89.0	0.0		92.0	22.0	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Missense_Mutation	SNP	ENST00000327741.5	hg19	CCDS31805.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.967990	0.34754	.	.	ENSG00000205426	ENST00000327741;ENST00000389388	D	0.90004	-2.6	5.1	-1.06	0.10002	Filament (1);	3.356480	0.01608	U	0.022403	D	0.87462	0.6183	M	0.62088	1.915	0.18873	N	0.999989	B	0.26602	0.154	B	0.24269	0.052	T	0.71066	-0.4700	10	0.37606	T	0.19	.	10.7506	0.46207	0.0:0.4193:0.0:0.5807	.	365	Q14533	KRT81_HUMAN	H	365	ENSP00000369349:R365H	ENSP00000369349:R365H	R	-	2	0	KRT81	50967306	0.000000	0.05858	0.095000	0.20976	0.658000	0.38924	-0.067000	0.11579	-0.036000	0.13669	0.561000	0.74099	CGC	.	.		0.612	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281		T	52681039	C	T	52681039	3	4	2	1	0	0	0	0	1	0	0	0	8504	768	27	1	435	1	KRT81	12	52681039	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10		52681039	81170856	50	153										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56995571	56995571	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	agctgctcaacagggagctaTggctctgagtctggctcagc	13	11	4	1	rs367656362		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr12:56995571T>C	ENST00000551812.1	-	20	4029	c.3836A>G	c.(3835-3837)cAt>cGt	p.H1279R	BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000549884.1_Missense_Mutation_p.H1277R|BAZ2A_ENST00000379441.3_Missense_Mutation_p.H1249R|BAZ2A_ENST00000179765.5_Missense_Mutation_p.H1247R	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1279					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						CAGGGAGCTATGGCTCTGAGT	0.587																																					p.H1279R		Atlas-SNP	.											.	BAZ2A	263	.	0			c.A3836G						.	T	ARG/HIS	0,4090		0,0,2045	103	109	107		3836	2.7	0.8	12		107	1,8399		0,1,4199	no	missense	BAZ2A	NM_013449.3	29	0,1,6244	CC,CT,TT		0.0119,0.0,0.0080	possibly-damaging	1279/1906	56995571	1,12489	2045	4200	6245	SO:0001583	missense	11176	exon20			GAGCTATGGCTCT	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.3836A>G	chr12.hg19:g.56995571T>C	ENSP00000446880:p.His1279Arg	72.0	0.0		108.0	31.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	T	9.935	1.215842	0.22373	0.0	1.19E-4	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.69435	-0.14;-0.15;-0.16;-0.4;-0.15	5.23	2.72	0.32119	.	0.147753	0.31660	N	0.007278	T	0.62368	0.2422	L	0.44542	1.39	0.09310	N	0.999998	D;D;D;D	0.56968	0.978;0.978;0.963;0.978	P;P;P;P	0.53649	0.731;0.731;0.543;0.731	T	0.51012	-0.8759	10	0.30854	T	0.27	-32.7742	5.5369	0.17016	0.0:0.0919:0.264:0.6442	.	1277;1279;1279;1252	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	R	1249;1247;1279;215;1277	ENSP00000368754:H1249R;ENSP00000179765:H1247R;ENSP00000446880:H1279R;ENSP00000448760:H215R;ENSP00000447941:H1277R	ENSP00000179765:H1247R	H	-	2	0	BAZ2A	55281838	0.751000	0.28327	0.757000	0.31301	0.746000	0.42486	0.858000	0.27845	0.952000	0.37798	-0.353000	0.07706	CAT	.	.		0.587	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		C	56995571	T	C	56995571	3	2	2	1	0	0	0	0	1	0	0	0	1331	1464	51	2	1921	2	BAZ2A	12	56995571	Missense_Mutation	SNP	T	TCGA-2Y-A9GS-01A-12D-A382-10	4314532	56995571	76856324	51	154										
HSP90B1	7184	hgsc.bcm.edu	37	chr12	104337556	104337556	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tcagcgcctgacagaatctcCgtgtgctttggtggccagcc	12	13	2	2			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr12:104337556C>A	ENST00000299767.5	+	14	2113	c.1931C>A	c.(1930-1932)cCg>cAg	p.P644Q		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	644					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	ACAGAATCTCCGTGTGCTTTG	0.443																																					p.P644Q		Atlas-SNP	.											.	HSP90B1	72	.	0			c.C1931A						.						82	75	77					12																	104337556		2203	4300	6503	SO:0001583	missense	7184	exon14			AATCTCCGTGTGC	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.1931C>A	chr12.hg19:g.104337556C>A	ENSP00000299767:p.Pro644Gln	93.0	0.0		86.0	18.0	NM_003299	Q96A97	Missense_Mutation	SNP	ENST00000299767.5	hg19	CCDS9094.1	.	.	.	.	.	.	.	.	.	.	C	32	5.139105	0.94560	.	.	ENSG00000166598	ENST00000299767;ENST00000421266	T	0.70986	-0.53	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.92499	0.7618	H	0.99863	4.86	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95613	0.8674	10	0.87932	D	0	.	19.961	0.97250	0.0:1.0:0.0:0.0	.	644	P14625	ENPL_HUMAN	Q	644;394	ENSP00000299767:P644Q	ENSP00000299767:P644Q	P	+	2	0	HSP90B1	102861686	1.000000	0.71417	0.970000	0.41538	0.979000	0.70002	7.818000	0.86416	2.783000	0.95769	0.655000	0.94253	CCG	.	.		0.443	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		A	104337556	C	A	104337556	3	1	2	1	0	0	0	0	1	0	0	0	7412	652	23	1	1985	1	HSP90B1	12	104337556	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	47341985	104337556	29514339	52	155										
EXD1	161829	hgsc.bcm.edu	37	chr15	41476594	41476594	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cttggagctttatctatcctAaaatttttaccaaataagaa	4	7	1	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr15:41476594A>G	ENST00000314992.5	-	10	1270	c.1080T>C	c.(1078-1080)ttT>ttC	p.F360F	EXD1_ENST00000458580.2_Silent_p.F418F	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	360							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						TATCTATCCTAAAATTTTTAC	0.378																																					p.F360F		Atlas-SNP	.											.	EXD1	52	.	0			c.T1080C						.						117	128	124					15																	41476594		2202	4300	6502	SO:0001819	synonymous_variant	161829	exon10			TATCCTAAAATTT	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"exonuclease 3'-5' domain-like 1"	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.1080T>C	chr15.hg19:g.41476594A>G		104.0	0.0		159.0	22.0	NM_152596	A8K909|B7Z839|Q6ZW94	Silent	SNP	ENST00000314992.5	hg19	CCDS10072.1																																																																																			.	.		0.378	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596		G	41476594	A	G	41476594	2	3	2	1	0	0	0	0	0	0	0	1	5299	359	13	2		2	EXD1	15	41476594	Silent	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10		41476594	61054798	53	156										
PDE8A	5151	hgsc.bcm.edu	37	chr15	85634396	85634396	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gctcgatactataaattcatGcatcaggataggcaaggtaa	9	7	2	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr15:85634396G>T	ENST00000310298.4	+	9	1088	c.836G>T	c.(835-837)tGc>tTc	p.C279F	PDE8A_ENST00000339708.5_Intron|PDE8A_ENST00000557819.2_Intron|PDE8A_ENST00000394553.1_Missense_Mutation_p.C279F|PDE8A_ENST00000557957.1_Missense_Mutation_p.C207F			O60658	PDE8A_HUMAN	phosphodiesterase 8A	279	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	ATAAATTCATGCATCAGGATA	0.388																																					p.C279F		Atlas-SNP	.											.	PDE8A	50	.	0			c.G836T						.						78	76	76					15																	85634396		2203	4299	6502	SO:0001583	missense	5151	exon8			ATTCATGCATCAG	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"Phosphodiesterases"	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.836G>T	chr15.hg19:g.85634396G>T	ENSP00000311453:p.Cys279Phe	173.0	0.0		271.0	77.0	NM_002605	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Missense_Mutation	SNP	ENST00000310298.4	hg19	CCDS10336.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434826	0.25813	.	.	ENSG00000073417	ENST00000310298;ENST00000394553	T;T	0.76186	-1.0;-1.0	4.61	1.11	0.20524	PAS (3);PAS fold (1);	0.461207	0.26804	N	0.022411	T	0.70011	0.3175	M	0.78637	2.42	0.52099	D	0.999947	P	0.47106	0.89	P	0.45071	0.468	T	0.66736	-0.5848	10	0.10111	T	0.7	.	7.4282	0.27111	0.3635:0.0:0.6365:0.0	.	279	O60658	PDE8A_HUMAN	F	279	ENSP00000311453:C279F;ENSP00000378056:C279F	ENSP00000311453:C279F	C	+	2	0	PDE8A	83435400	1.000000	0.71417	0.979000	0.43373	0.933000	0.57130	3.564000	0.53791	0.136000	0.18733	0.563000	0.77884	TGC	.	.		0.388	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		T	85634396	G	T	85634396	3	4	2	1	0	0	0	0	1	0	0	0	11662	1319	46	3	866	3	PDE8A	15	85634396	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	44157802	85634396	16896996	54	157										
STUB1	339123	hgsc.bcm.edu	37	chr16	731861	731892	+	3'UTR	DEL	CCTGCATTGAGGCCAAGCACGTGAGGGTGCCC	CCTGCATTGAGGCCAAGCACGTGAGGGTGCCC	-													0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ccacgtccgggcccagcaggCctgcattgaggccaagcacg					rs201741662|rs111699688|rs544433451	byFrequency	TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	CCTGCATTGAGGCCAAGCACGTGAGGGTGCCC	CCTGCATTGAGGCCAAGCACGTGAGGGTGCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr16:731861_731892delCCTGCATTGAGGCCAAGCACGTGAGGGTGCCC	ENST00000293882.4	-	0	1906_1937				JMJD8_ENST00000609261.1_3'UTR|LA16c-313D11.9_ENST00000571933.1_RNA|STUB1_ENST00000566181.2_3'UTR|JMJD8_ENST00000412368.2_3'UTR|STUB1_ENST00000564370.1_Splice_Site_p.ACIEAKH126fs|STUB1_ENST00000219548.4_Splice_Site_p.ACIEAKH198fs|LA16c-313D11.9_ENST00000567091.1_RNA|JMJD8_ENST00000454700.1_3'UTR|STUB1_ENST00000565677.1_Splice_Site_p.ACIEAKH126fs			Q96S16	JMJD8_HUMAN	jumonji domain containing 8							extracellular vesicular exosome (GO:0070062)				breast(1)	1						GCCCAGCAGGCCTGCATTGAGGCCAAGCACGTGAGGGTGCCCCCCACCCACA	0.659																																					p.198_204del		Atlas-Indel,Pindel	.											.	STUB1	26	.	0			c.592_612del						.																																			SO:0001624	3_prime_UTR_variant	10273	exon4			.		CCDS45369.1	16p13.3	2008-07-28	2008-07-28	2008-07-28		ENSG00000161999			14148	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 20"	C16orf20			Standard	NM_001005920		Approved		uc002ciw.1	Q96S16		ENST00000293882.4:c.*933GGGCACCCTCACGTGCTTGGCCTCAATGCAGG>-	chr16.hg19:g.731861_731892delCCTGCATTGAGGCCAAGCACGTGAGGGTGCCC		151.0	0.0		169.0	21.0	NM_005861	B2RNS7|D3DU58|Q4PKE3|Q4VBY1|Q6GMW5|Q71RB8	In_Frame_Del	DEL	ENST00000293882.4	hg19																																																																																				.	.		0.659	JMJD8-201	KNOWN	basic	protein_coding	protein_coding		NM_001005920		-	731892	CCTGCATTGAGGCCAAGCACGTGAGGGTGCCC	-	731861	6	5	2	0	1	1	0	1	0	0	0	0	15350	739	26	0		0	STUB1	16	731861	3'UTR	DEL	CCTGCATTGAGGCCAAGCACGTGAGGGTGCCC	TCGA-2Y-A9GS-01A-12D-A382-10		731861	89622892	55	158										
GSG1L	146395	hgsc.bcm.edu	37	chr16	28074601	28074601	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cgagttggggcagttggcgcGcccgccctggccgcagcccg	17	16	0	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr16:28074601G>A	ENST00000447459.2	-	1	229	c.145C>T	c.(145-147)Cgc>Tgc	p.R49C	GSG1L_ENST00000380898.2_5'UTR|GSG1L_ENST00000395724.3_Missense_Mutation_p.R49C	NM_001109763.1	NP_001103233.1	Q6UXU4	GSG1L_HUMAN	GSG1-like	49					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	asymmetric synapse (GO:0032279)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(4)	17						CAGTTGGCGCGCCCGCCCTGG	0.786																																					p.R49C		Atlas-SNP	.											.	GSG1L	82	.	0			c.C145T						.						1	2	1					16																	28074601		903	1984	2887	SO:0001583	missense	146395	exon1			TGGCGCGCCCGCC	AK128775	CCDS10631.1, CCDS45450.1	16p11.2	2014-01-20			ENSG00000169181	ENSG00000169181			28283	protein-coding gene	gene with protein product						22813734	Standard	NM_001109763		Approved	MGC18079, PRO19651, KTSR5831	uc002doz.2	Q6UXU4	OTTHUMG00000131676	ENST00000447459.2:c.145C>T	chr16.hg19:g.28074601G>A	ENSP00000394954:p.Arg49Cys	4.0	0.0		8.0	6.0	NM_001109763	Q7Z6F8|Q8TB81	Missense_Mutation	SNP	ENST00000447459.2	hg19	CCDS45450.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.053134	0.55218	.	.	ENSG00000169181	ENST00000447459;ENST00000395724	T;T	0.32023	1.47;1.47	2.95	-5.52	0.02560	.	0.771763	0.10741	U	0.639421	T	0.20333	0.0489	L	0.27053	0.805	0.80722	D	1	D;D	0.56035	0.969;0.974	B;P	0.48114	0.34;0.567	T	0.47711	-0.9096	10	0.59425	D	0.04	.	4.7527	0.13068	0.0:0.2233:0.2526:0.5241	.	49;49	Q6UXU4-3;Q6UXU4	.;GSG1L_HUMAN	C	49	ENSP00000394954:R49C;ENSP00000379074:R49C	ENSP00000379074:R49C	R	-	1	0	GSG1L	27982102	.	.	0.988000	0.46212	0.980000	0.70556	.	.	-0.552000	0.06167	0.305000	0.20034	CGC	.	.		0.786	GSG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433832.2	NM_144675		A	28074601	G	A	28074601	3	1	2	1	0	0	0	0	1	0	0	0	6830	1087	38	1	878	1	GSG1L	16	28074601	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	27342740	28074601	62280152	56	159										
IL27	55911	hgsc.bcm.edu	37	chr16	28511194	28511194	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ctctcctcctcctcctcctcCtcttcctcctcctcctcctc	0	26	2	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr16:28511194C>T	ENST00000431282.1	+	0	3414				IL27_ENST00000356897.1_Silent_p.E170E			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor						cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						cctcctcctcctcttcctcct	0.677																																					p.E170E		Atlas-SNP	.											.	IL27	27	.	0			c.G510A						.						9	10	9					16																	28511194		2158	4227	6385	SO:0001628	intergenic_variant	246778	exon5			CTCCTCCTCTTCC	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"apolipoprotein B48 receptor", "apolipoprotein B100 receptor"	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83			chr16.hg19:g.28511194C>T		67.0	0.0		94.0	5.0	NM_145659	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	hg19																																																																																				.	.		0.677	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804		T	28511194	C	T	28511194	1	4	2	0	1	0	0	0	0	0	0	0	7689	680	24	3		3	IL27	16	28511194	IGR	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	436593	28511194	61843559	57	160										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000420246.2_Missense_Mutation_p.R249S|TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	94.0	0.0		87.0	40.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	2	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10		7577534	73617676	58	161										
PTRF	284119	hgsc.bcm.edu	37	chr17	40556985	40556985	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ggtcgggcgtgaaggatttgCgcaacttgtcccgcgacgtc	15	11	0	1	rs144331065		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr17:40556985C>T	ENST00000357037.5	-	2	1312	c.893G>A	c.(892-894)cGc>cAc	p.R298H		NM_012232.5	NP_036364.2			polymerase I and transcript release factor									p.R298H(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		GAAGGATTTGCGCAACTTGTC	0.642																																					p.R298H		Atlas-SNP	.											PTRF,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	PTRF	48	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G893A						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	113	97	103		893	5.1	1	17	dbSNP_134	103	0,8600		0,0,4300	no	missense	PTRF	NM_012232.5	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	298/391	40556985	1,13005	2203	4300	6503	SO:0001583	missense	284119	exon2			GATTTGCGCAACT	AF000421	CCDS11425.1	17q21.31	2011-04-20				ENSG00000177469			9688	protein-coding gene	gene with protein product		603198				9582279	Standard	NM_012232		Approved	cavin-1, CAVIN1	uc002hzo.3	Q6NZI2		ENST00000357037.5:c.893G>A	chr17.hg19:g.40556985C>T	ENSP00000349541:p.Arg298His	85.0	0.0		106.0	11.0	NM_012232		Missense_Mutation	SNP	ENST00000357037.5	hg19	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148153	0.78001	2.27E-4	0.0	ENSG00000177469	ENST00000357037;ENST00000357684	T	0.60040	0.22	5.12	5.12	0.69794	.	0.065401	0.64402	D	0.000012	T	0.63200	0.2491	L	0.50333	1.59	0.38284	D	0.942509	D;D	0.69078	0.997;0.997	P;P	0.57548	0.823;0.823	T	0.68603	-0.5365	10	0.87932	D	0	-18.1461	9.4221	0.38557	0.0:0.8439:0.0:0.1561	.	280;298	B4DNU9;Q6NZI2	.;PTRF_HUMAN	H	298;253	ENSP00000349541:R298H	ENSP00000349541:R298H	R	-	2	0	PTRF	37810511	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.157000	0.50716	2.673000	0.90976	0.544000	0.68410	CGC	.	C|1.000;T|0.000		0.642	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232		T	40556985	C	T	40556985	3	4	2	1	0	0	0	0	1	0	0	0	12830	768	27	1	283	1	PTRF	17	40556985	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	32979451	40556985	40638225	59	162										
AATK	9625	hgsc.bcm.edu	37	chr17	79093297	79093297	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gggcgtgggcgcagccggggCgggtgcggccgggtctaggg	25	10	1	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr17:79093297C>T	ENST00000326724.4	-	13	3991	c.3967G>A	c.(3967-3969)Gcc>Acc	p.A1323T	AATK_ENST00000417379.1_Missense_Mutation_p.A1220T	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1323					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GCAGCCGGGGCGGGTGCGGCC	0.721																																					p.A1323T		Atlas-SNP	.											.	AATK	102	.	0			c.G3967A						.						11	16	15					17																	79093297		1997	4087	6084	SO:0001583	missense	9625	exon13			CCGGGGCGGGTGC	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.3967G>A	chr17.hg19:g.79093297C>T	ENSP00000324196:p.Ala1323Thr	141.0	0.0		178.0	51.0	NM_001080395	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	hg19	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	C	9.251	1.040858	0.19669	.	.	ENSG00000181409	ENST00000326724	T	0.10005	2.92	3.52	-5.79	0.02354	.	0.670270	0.13734	N	0.366449	T	0.04318	0.0119	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.41233	-0.9520	10	0.15952	T	0.53	.	8.0776	0.30726	0.1043:0.3037:0.0:0.592	.	1323	Q6ZMQ8	LMTK1_HUMAN	T	1323	ENSP00000324196:A1323T	ENSP00000324196:A1323T	A	-	1	0	AATK	76707892	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-2.052000	0.01401	-1.228000	0.02568	-0.898000	0.02899	GCC	.	.		0.721	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		T	79093297	C	T	79093297	3	4	2	1	0	0	0	0	1	0	0	0	26	768	27	1	165	1	AATK	17	79093297	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	38536312	79093297	2101913	60	163										
ZBTB7C	201501	hgsc.bcm.edu	37	chr18	45555810	45555810	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ctcagcctccagctgcgcgcGcccgaacagcttcatctgtg	10	17	3	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr18:45555810G>A	ENST00000588982.1	-	4	2182	c.1681C>T	c.(1681-1683)Cgc>Tgc	p.R561C	ZBTB7C_ENST00000535628.2_Missense_Mutation_p.R561C|ZBTB7C_ENST00000590800.1_Missense_Mutation_p.R561C|ZBTB7C_ENST00000586438.1_Missense_Mutation_p.R561C|ZBTB7C_ENST00000332053.2_Missense_Mutation_p.R561C			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	561							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						AGCTGCGCGCGCCCGAACAGC	0.721																																					p.R561C		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.C1681T						.						10	11	11					18																	45555810		2188	4265	6453	SO:0001583	missense	201501	exon3			GCGCGCGCCCGAA	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	31700	protein-coding gene	gene with protein product			"zinc finger and BTB domain containing 36"	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.1681C>T	chr18.hg19:g.45555810G>A	ENSP00000468782:p.Arg561Cys	53.0	0.0		89.0	33.0	NM_001039360	O73453	Missense_Mutation	SNP	ENST00000588982.1	hg19	CCDS32830.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.761613	0.49468	.	.	ENSG00000184828	ENST00000535628;ENST00000332053	T;T	0.11604	2.76;2.76	4.51	2.45	0.29901	.	0.659005	0.12970	N	0.424205	T	0.06690	0.0171	N	0.14661	0.345	0.43852	D	0.996445	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18209	-1.0344	10	0.87932	D	0	.	7.5778	0.27946	0.0966:0.0:0.6156:0.2878	.	561;561	B2RG49;A1YPR0	.;ZBT7C_HUMAN	C	561	ENSP00000439781:R561C;ENSP00000328732:R561C	ENSP00000328732:R561C	R	-	1	0	ZBTB7C	43809808	1.000000	0.71417	0.994000	0.49952	0.977000	0.68977	3.350000	0.52224	0.886000	0.36113	0.555000	0.69702	CGC	.	.		0.721	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360		A	45555810	G	A	45555810	3	1	2	1	0	0	0	0	1	0	0	0	17570	1087	38	1	182	1	ZBTB7C	18	45555810	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10		45555810	32521438	61	164										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10602490	10602514	+	Frame_Shift_Del	DEL	CTCCGCGGCACCTGCAGGTCCGCCA	CTCCGCGGCACCTGCAGGTCCGCCA	-													0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ccacgcagccggccaggccgCtccgcggcacctgcaggtcc					rs35450620		TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	CTCCGCGGCACCTGCAGGTCCGCCA	CTCCGCGGCACCTGCAGGTCCGCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr19:10602490_10602514delCTCCGCGGCACCTGCAGGTCCGCCA	ENST00000171111.5	-	3	1611_1635	c.1064_1088delTGGCGGACCTGCAGGTGCCGCGGAG	c.(1063-1089)ttggcggacctgcaggtgccgcggagcfs	p.LADLQVPRS355fs	KEAP1_ENST00000393623.2_Frame_Shift_Del_p.LADLQVPRS355fs|CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000588024.1_5'Flank	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	355					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)		p.R362Q(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GGCCAGGCCGCTCCGCGGCACCTGCAGGTCCGCCAACCGGAGCCA	0.693																																					p.355_363del		Atlas-Indel,Pindel	.											.	KEAP1	182	.	1	Substitution - Missense(1)	lung(1)	c.1065_1089del						.																																			SO:0001589	frameshift_variant	9817	exon3			.	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1064_1088delTGGCGGACCTGCAGGTGCCGCGGAG	chr19.hg19:g.10602490_10602514delCTCCGCGGCACCTGCAGGTCCGCCA	ENSP00000171111:p.Leu355fs	110.0	0.0		58.0	30.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Frame_Shift_Del	DEL	ENST00000171111.5	hg19	CCDS12239.1																																																																																			.	.		0.693	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		-	10602514	CTCCGCGGCACCTGCAGGTCCGCCA	-	10602490	7	5	2	1	0	1	0	1	0	0	0	0	8150	797	28	0	802	0	KEAP1	19	10602490	Frame_Shift_Del	DEL	CTCCGCGGCACCTGCAGGTCCGCCA	TCGA-2Y-A9GS-01A-12D-A382-10		10602490	48526493	62	165										
DNAJB1	3337	hgsc.bcm.edu	37	chr19	14627395	14627395	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ggaatgttgttggaggtctgGtctccttccttggggaaagt	15	6	2	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr19:14627395G>T	ENST00000254322.2	-	2	745	c.675C>A	c.(673-675)gaC>gaA	p.D225E	DNAJB1_ENST00000396969.4_Missense_Mutation_p.D125E	NM_006145.1	NP_006136.1	P25685	DNJB1_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 1	225					chaperone cofactor-dependent protein refolding (GO:0070389)|chaperone mediated protein folding requiring cofactor (GO:0051085)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(1328;0.0476)		TGGAGGTCTGGTCTCCTTCCT	0.438																																					p.D225E		Atlas-SNP	.											.	DNAJB1	38	.	0			c.C675A						.						131	119	123					19																	14627395		2203	4300	6503	SO:0001583	missense	3337	exon2			GGTCTGGTCTCCT	D49547	CCDS12312.1, CCDS74295.1	19p13.12	2014-08-12			ENSG00000132002	ENSG00000132002		"Heat shock proteins / DNAJ (HSP40)"	5270	protein-coding gene	gene with protein product	"radial spoke 16 homolog B (Chlamydomonas)"	604572		HSPF1		8975727, 8250930	Standard	XM_006722733		Approved	Hsp40, Sis1, RSPH16B	uc002myz.1	P25685	OTTHUMG00000183289	ENST00000254322.2:c.675C>A	chr19.hg19:g.14627395G>T	ENSP00000254322:p.Asp225Glu	81.0	0.0		52.0	15.0	NM_006145	B4DX52	Missense_Mutation	SNP	ENST00000254322.2	hg19	CCDS12312.1	.	.	.	.	.	.	.	.	.	.	g	22.3	4.265305	0.80358	.	.	ENSG00000132002	ENST00000254322;ENST00000396969	D;D	0.85013	-1.93;-1.93	5.19	5.19	0.71726	HSP40/DnaJ peptide-binding (1);	0.000000	0.85682	D	0.000000	D	0.87346	0.6154	M	0.73217	2.22	0.80722	D	1	P	0.40000	0.698	P	0.44477	0.451	D	0.89060	0.3462	10	0.87932	D	0	.	16.1946	0.82018	0.0:0.0:1.0:0.0	.	225	P25685	DNJB1_HUMAN	E	225;125	ENSP00000254322:D225E;ENSP00000444212:D125E	ENSP00000254322:D225E	D	-	3	2	DNAJB1	14488395	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.112000	0.41892	2.424000	0.82194	0.561000	0.74099	GAC	.	.		0.438	DNAJB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465987.1	NM_006145		T	14627395	G	T	14627395	3	4	2	1	0	0	0	0	1	0	0	0	4617	1252	44	3	355	3	DNAJB1	19	14627395	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	4024905	14627395	44501588	63	166										
LILRA4	23547	hgsc.bcm.edu	37	chr19	54849337	54849337	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	atggggaacagggcctggaaCtttccatggttgtgttggtg	16	6	0	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr19:54849337C>A	ENST00000291759.4	-	4	581	c.525G>T	c.(523-525)aaG>aaT	p.K175N	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	175	Ig-like C2-type 2.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		GGGCCTGGAACTTTCCATGGT	0.567																																					p.K175N		Atlas-SNP	.											.	LILRA4	91	.	0			c.G525T						.						91	80	84					19																	54849337		2203	4300	6503	SO:0001583	missense	23547	exon4			CTGGAACTTTCCA	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.525G>T	chr19.hg19:g.54849337C>A	ENSP00000291759:p.Lys175Asn	129.0	0.0		161.0	64.0	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	hg19	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	6.917	0.538785	0.13250	.	.	ENSG00000239961	ENST00000291759	T	0.02944	4.1	2.76	2.76	0.32466	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.03348	0.0097	N	0.24115	0.695	0.09310	N	1	B	0.29301	0.241	B	0.38755	0.281	T	0.46555	-0.9183	9	0.36615	T	0.2	.	9.1771	0.37118	0.0:1.0:0.0:0.0	.	175	P59901	LIRA4_HUMAN	N	175	ENSP00000291759:K175N	ENSP00000291759:K175N	K	-	3	2	LILRA4	59541149	0.000000	0.05858	0.002000	0.10522	0.278000	0.26855	0.026000	0.13599	1.855000	0.53841	0.563000	0.77884	AAG	.	.		0.567	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276		A	54849337	C	A	54849337	3	1	2	1	0	0	0	0	1	0	0	0	8796	564	20	3	994	3	LILRA4	19	54849337	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10	40221942	54849337	4279646	64	167										
PLAGL2	5326	hgsc.bcm.edu	37	chr20	30785139	30785139	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gtgccgccgtacatccttacGagtatagaaccgccggtcgc	11	14	0	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr20:30785139G>T	ENST00000246229.4	-	3	871	c.607C>A	c.(607-609)Cgt>Agt	p.R203S		NM_002657.3	NP_002648.1	Q9UPG8	PLAL2_HUMAN	pleiomorphic adenoma gene-like 2	203					chylomicron assembly (GO:0034378)|lipid metabolic process (GO:0006629)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|post-embryonic development (GO:0009791)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|liver(1)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			ACATCCTTACGAGTATAGAAC	0.627																																					p.R203S	Colon(163;15 1893 11280 16306 47518)	Atlas-SNP	.											.	PLAGL2	56	.	0			c.C607A						.						23	19	20					20																	30785139		2203	4300	6503	SO:0001583	missense	5326	exon3			CCTTACGAGTATA		CCDS13197.1	20q11.21	2013-01-08			ENSG00000126003	ENSG00000126003		"Zinc fingers, C2H2-type"	9047	protein-coding gene	gene with protein product	"C2H2-type zinc finger protein"	604866				15585652, 17950244	Standard	NM_002657		Approved	ZNF900	uc002wxn.2	Q9UPG8	OTTHUMG00000032210	ENST00000246229.4:c.607C>A	chr20.hg19:g.30785139G>T	ENSP00000246229:p.Arg203Ser	85.0	0.0		98.0	4.0	NM_002657	A8K8T5|E1P5M3|Q92584	Missense_Mutation	SNP	ENST00000246229.4	hg19	CCDS13197.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.447620	0.63178	.	.	ENSG00000126003	ENST00000246229	T	0.59906	0.23	5.13	4.12	0.48240	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.57651	0.2068	N	0.11789	0.175	0.58432	D	0.999997	D	0.89917	1.0	D	0.76575	0.988	T	0.55315	-0.8160	10	0.22706	T	0.39	.	16.2439	0.82431	0.0:0.0:0.8586:0.1414	.	203	Q9UPG8	PLAL2_HUMAN	S	203	ENSP00000246229:R203S	ENSP00000246229:R203S	R	-	1	0	PLAGL2	30248800	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.695000	0.84257	2.675000	0.91044	0.555000	0.69702	CGT	.	.		0.627	PLAGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078615.2	NM_002657		T	30785139	G	T	30785139	3	4	2	1	0	0	0	0	1	0	0	0	12029	1058	37	1	887	1	PLAGL2	20	30785139	Missense_Mutation	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10		30785139	32240381	65	168										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61510865	61510865	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	cgctcctctcccggtttctgTcccagtcccggctggagtcc	10	18	2	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr20:61510865T>C	ENST00000266070.4	-	16	6768	c.6443A>G	c.(6442-6444)gAc>gGc	p.D2148G	DIDO1_ENST00000395343.1_Missense_Mutation_p.D2148G	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	2148	Arg-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					ccggtttctgtcccagtcccg	0.726																																					p.D2148G	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.A6443G						.						18	16	17					20																	61510865		2177	4223	6400	SO:0001583	missense	11083	exon16			TTTCTGTCCCAGT	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.6443A>G	chr20.hg19:g.61510865T>C	ENSP00000266070:p.Asp2148Gly	81.0	0.0		102.0	35.0	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.076536	0.55753	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.47528	0.84;0.84	4.81	4.81	0.61882	.	.	.	.	.	T	0.64951	0.2645	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.69018	-0.5256	9	0.87932	D	0	-28.9568	14.0427	0.64687	0.0:0.0:0.0:1.0	.	2148	Q9BTC0	DIDO1_HUMAN	G	2148	ENSP00000266070:D2148G;ENSP00000378752:D2148G	ENSP00000266070:D2148G	D	-	2	0	DIDO1	60981310	1.000000	0.71417	0.918000	0.36340	0.073000	0.16967	3.241000	0.51376	1.794000	0.52575	0.533000	0.62120	GAC	.	.		0.726	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		C	61510865	T	C	61510865	3	2	2	1	0	0	0	0	1	0	0	0	4524	1667	58	2	283	2	DIDO1	20	61510865	Missense_Mutation	SNP	T	TCGA-2Y-A9GS-01A-12D-A382-10	30725726	61510865	1514655	66	169										
KRTAP13-3	337960	hgsc.bcm.edu	37	chr21	31798109	31798109	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gctggcaggtgctgggagagCagaggtcagtgctgtagacc	18	8	1	3			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr21:31798109C>A	ENST00000390690.2	-	1	177	c.122G>T	c.(121-123)tGc>tTc	p.C41F		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	41						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						GCTGGGAGAGCAGAGGTCAGT	0.587																																					p.C41F		Atlas-SNP	.											.	KRTAP13-3	47	.	0			c.G122T						.						67	73	71					21																	31798109		2203	4300	6503	SO:0001583	missense	337960	exon1			GGAGAGCAGAGGT	AP001708	CCDS13591.1	21q22.1	2006-03-13			ENSG00000240432	ENSG00000240432		"Keratin associated proteins"	18925	protein-coding gene	gene with protein product						12359730	Standard	NM_181622		Approved	KAP13.3	uc002yob.1	Q3SY46	OTTHUMG00000057776	ENST00000390690.2:c.122G>T	chr21.hg19:g.31798109C>A	ENSP00000375109:p.Cys41Phe	134.0	0.0		135.0	27.0	NM_181622	Q3LI78	Missense_Mutation	SNP	ENST00000390690.2	hg19	CCDS13591.1	.	.	.	.	.	.	.	.	.	.	-	9.141	1.013918	0.19277	.	.	ENSG00000240432	ENST00000390690;ENST00000448917	T	0.04454	3.62	4.78	3.89	0.44902	.	0.000000	0.45606	U	0.000359	T	0.06554	0.0168	L	0.56769	1.78	0.24308	N	0.995092	P	0.51653	0.947	B	0.41374	0.355	T	0.26121	-1.0112	10	0.62326	D	0.03	-4.7465	9.4006	0.38431	0.0:0.8982:0.0:0.1018	.	41	Q3SY46	KR133_HUMAN	F	41	ENSP00000375109:C41F	ENSP00000375109:C41F	C	-	2	0	KRTAP13-3	30719980	0.651000	0.27340	0.820000	0.32676	0.140000	0.21249	0.621000	0.24418	1.315000	0.45114	0.650000	0.86243	TGC	.	.		0.587	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2			A	31798109	C	A	31798109	3	1	2	1	0	0	0	0	1	0	0	0	8533	710	25	3	400	3	KRTAP13-3	21	31798109	Missense_Mutation	SNP	C	TCGA-2Y-A9GS-01A-12D-A382-10		31798109	16331786	67	170										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37617781	37617781	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	gctggcggccttccagtcagAaagcttcaaggctggggcca	14	12	2	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr21:37617781A>T	ENST00000399151.3	+	19	3588	c.3503A>T	c.(3502-3504)gAa>gTa	p.E1168V		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1168					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TTCCAGTCAGAAAGCTTCAAG	0.637																																					p.E1168V		Atlas-SNP	.											.	DOPEY2	184	.	0			c.A3503T						.						36	40	39					21																	37617781		2203	4300	6503	SO:0001583	missense	9980	exon19			AGTCAGAAAGCTT	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.3503A>T	chr21.hg19:g.37617781A>T	ENSP00000382104:p.Glu1168Val	64.0	0.0		63.0	23.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	A	3.484	-0.105369	0.06967	.	.	ENSG00000142197	ENST00000399151	T	0.34072	1.38	4.61	0.639	0.17747	.	0.412728	0.20393	N	0.093212	T	0.23210	0.0561	L	0.36672	1.1	0.09310	N	1	B;B	0.32753	0.383;0.265	B;B	0.29785	0.107;0.05	T	0.11421	-1.0588	10	0.37606	T	0.19	.	7.609	0.28118	0.6649:0.2621:0.073:0.0	.	1168;1168	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	V	1168	ENSP00000382104:E1168V	ENSP00000382104:E1168V	E	+	2	0	DOPEY2	36539651	0.564000	0.26602	0.005000	0.12908	0.011000	0.07611	1.715000	0.37971	0.374000	0.24650	0.528000	0.53228	GAA	.	.		0.637	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		T	37617781	A	T	37617781	3	4	2	1	0	0	0	0	1	0	0	0	4710	246	9	4	3573	4	DOPEY2	21	37617781	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10	5819672	37617781	10512114	68	171			1	1		2	2	17	N	G_A	3.721253e-05
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37617797	37617797	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	tcagaaagcttcaaggctggGgccaagttaagcctggtgcg	14	9	2	1			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr21:37617797G>T	ENST00000399151.3	+	19	3604	c.3519G>T	c.(3517-3519)ggG>ggT	p.G1173G		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1173					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TCAAGGCTGGGGCCAAGTTAA	0.642																																					p.G1173G		Atlas-SNP	.											.	DOPEY2	184	.	0			c.G3519T						.						36	40	39					21																	37617797		2203	4300	6503	SO:0001819	synonymous_variant	9980	exon19			GGCTGGGGCCAAG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.3519G>T	chr21.hg19:g.37617797G>T		53.0	0.0		55.0	26.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	hg19	CCDS13643.1																																																																																			.	.		0.642	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		T	37617797	G	T	37617797	2	4	2	1	0	0	0	0	0	0	0	1	4710	1219	43	3		3	DOPEY2	21	37617797	Silent	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	16	37617797	10512098	69	172			1	1		2	2	17	N	G_A	3.721253e-05
PLAC4	25825	hgsc.bcm.edu	37	chr21	42551433	42551433	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ggtgaggagtgacggtgtctGgggtgagtgagggtgtccag	22	4	1	4			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr21:42551433G>A	ENST00000330333.6	+	1	775				BACE2_ENST00000328735.6_Intron|PLAC4_ENST00000430327.2_RNA|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000440221.2_RNA|BACE2-IT1_ENST00000433378.1_RNA|PLAC4_ENST00000536486.1_RNA|PLAC4_ENST00000414699.1_RNA	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				GACGGTGTCTGGGGTGAGTGA	0.607																																					p.P41P		Atlas-SNP	.											.	.	.	.	0			c.C123T						.						124	109	114					21																	42551433		2196	4275	6471	SO:0001627	intron_variant	191585	exon1			GTGTCTGGGGTGA	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10931G>A	chr21.hg19:g.42551433G>A		92.0	0.0		85.0	6.0	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Silent	SNP	ENST00000330333.6	hg19	CCDS13668.1																																																																																			.	.		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			A	42551433	G	A	42551433	1	1	2	0	1	0	0	0	0	0	0	0	12023	1335	47	3		3	PLAC4	21	42551433	Intron	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10	4933636	42551433	5578462	70	173										
SMTN	6525	hgsc.bcm.edu	37	chr22	31494787	31494787	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	ctcagcctcccaggcgcgcaAggccatgattgagaagctgg	13	13	1	2			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chr22:31494787A>G	ENST00000347557.2	+	17	2512	c.2294A>G	c.(2293-2295)aAg>aGg	p.K765R	SMTN_ENST00000333137.7_Missense_Mutation_p.K765R|SMTN_ENST00000358743.1_Missense_Mutation_p.K765R|SMTN_ENST00000404574.1_Missense_Mutation_p.K288R	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	765					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						CAGGCGCGCAAGGCCATGATT	0.682																																					p.K850R		Atlas-SNP	.											.	SMTN	219	.	0			c.A2549G						.						13	18	16					22																	31494787		2198	4287	6485	SO:0001583	missense	6525	exon18			CGCGCAAGGCCAT	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.2294A>G	chr22.hg19:g.31494787A>G	ENSP00000328635:p.Lys765Arg	112.0	0.0		74.0	15.0	NM_001207017	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	hg19	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.907692	0.92107	.	.	ENSG00000183963	ENST00000358743;ENST00000347557;ENST00000333137;ENST00000329852;ENST00000404496;ENST00000455608;ENST00000404574;ENST00000403419	T;T;T;T;D	0.93659	-0.15;-0.55;-0.55;1.8;-3.26	5.34	5.34	0.76211	.	0.000000	0.39759	N	0.001269	D	0.94991	0.8379	L	0.41961	1.31	0.80722	D	1	P;D;D;D;D;P;D;P	0.76494	0.741;0.998;0.997;0.997;0.999;0.578;0.999;0.832	P;D;D;D;D;P;D;P	0.81914	0.545;0.995;0.985;0.985;0.991;0.458;0.991;0.733	D	0.95279	0.8384	10	0.56958	D	0.05	-39.4047	15.6299	0.76899	1.0:0.0:0.0:0.0	.	821;850;145;288;788;765;765;765	E7ETT8;B4E229;B5MBZ4;B5MCI0;B5MC56;E7EWD0;P53814;P53814-5	.;.;.;.;.;.;SMTN_HUMAN;.	R	765;765;765;763;788;166;288;145	ENSP00000351593:K765R;ENSP00000328635:K765R;ENSP00000329532:K765R;ENSP00000392329:K166R;ENSP00000383919:K288R	ENSP00000329393:K763R	K	+	2	0	SMTN	29824787	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.803000	0.69129	2.169000	0.68431	0.459000	0.35465	AAG	.	.		0.682	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		G	31494787	A	G	31494787	3	3	2	1	0	0	0	0	1	0	0	0	14829	72	3	2	2356	2	SMTN	22	31494787	Missense_Mutation	SNP	A	TCGA-2Y-A9GS-01A-12D-A382-10		31494787	19809779	71	174										
TKTL1	8277	hgsc.bcm.edu	37	chrX	153556300	153556300	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	3	1	0.890340909090909	2.96780303030303	0.370975378787879	1	1	0	acagtggaggatcactacccGcaaggtgtgtgtgggcattg	15	8	1	0			TCGA-2Y-A9GS-01A-12D-A382-10	TCGA-2Y-A9GS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ce44141-64e4-4d9d-9971-4dc79b316d4a	27ea2725-9c48-4965-a503-91d2302923b4	g.chrX:153556300G>A	ENST00000369915.3	+	12	1803	c.1614G>A	c.(1612-1614)ccG>ccA	p.P538P	TKTL1_ENST00000369912.2_Silent_p.P482P|TKTL1_ENST00000217905.7_Silent_p.P278P	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	538					glucose catabolic process (GO:0006007)|thiamine metabolic process (GO:0006772)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			NS(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(5)|prostate(1)|skin(1)|urinary_tract(2)	34	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ATCACTACCCGCAAGGTGTGT	0.493																																					p.P538P		Atlas-SNP	.											.	TKTL1	61	.	0			c.G1614A						.						171	139	150					X																	153556300		2203	4300	6503	SO:0001819	synonymous_variant	8277	exon12			CTACCCGCAAGGT	X91817	CCDS35448.1, CCDS55541.1	Xq28	2008-02-05			ENSG00000007350	ENSG00000007350			11835	protein-coding gene	gene with protein product		300044				8838793	Standard	NM_012253		Approved	TKR, TKT2	uc004fkg.3	P51854	OTTHUMG00000022707	ENST00000369915.3:c.1614G>A	chrX.hg19:g.153556300G>A		143.0	1.0		159.0	112.0	NM_012253	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Silent	SNP	ENST00000369915.3	hg19	CCDS35448.1																																																																																			.	.		0.493	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1	NM_012253		A	153556300	G	A	153556300	2	1	2	1	0	0	0	0	0	0	0	1	15950	1074	38	1		1	TKTL1	23	153556300	Silent	SNP	G	TCGA-2Y-A9GS-01A-12D-A382-10		153556300	1714260	72	175										
TMEM201	199953	hgsc.bcm.edu	37	chr1	9661209	9661209	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ggtccaggtcatcctgctccGtgccctcgccttcctggcct	10	18	1	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:9661209G>T	ENST00000340381.6	+	5	662	c.653G>T	c.(652-654)cGt>cTt	p.R218L	TMEM201_ENST00000340305.5_Missense_Mutation_p.R218L|TMEM201_ENST00000377376.4_Missense_Mutation_p.R218L	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	218					fibroblast migration (GO:0010761)|nuclear migration (GO:0007097)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				lung(3)|upper_aerodigestive_tract(1)	4	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)		ATCCTGCTCCGTGCCCTCGCC	0.667																																					p.R218L		Atlas-SNP	.											.	TMEM201	63	.	0			c.G653T						.						75	75	75					1																	9661209		2203	4300	6503	SO:0001583	missense	199953	exon5			TGCTCCGTGCCCT		CCDS30579.1, CCDS44055.1, CCDS44055.2	1p36.22	2009-11-06			ENSG00000188807	ENSG00000188807			33719	protein-coding gene	gene with protein product							Standard	NM_001130924		Approved	RP13-15M17.2, NET5	uc021ofy.1	Q5SNT2	OTTHUMG00000057457	ENST00000340381.6:c.653G>T	chr1.hg19:g.9661209G>T	ENSP00000344503:p.Arg218Leu	167.0	0.0		100.0	25.0	NM_001010866	B9EH90|Q5SNT3	Missense_Mutation	SNP	ENST00000340381.6	hg19	CCDS44055.2	.	.	.	.	.	.	.	.	.	.	G	27.5	4.837633	0.91117	.	.	ENSG00000188807	ENST00000377376;ENST00000340305;ENST00000340381	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.66867	0.2833	L	0.36672	1.1	0.53688	D	0.999976	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.65643	-0.6118	9	0.38643	T	0.18	-15.9352	15.4399	0.75176	0.0:0.0:1.0:0.0	.	218;218	E9PBR6;Q5SNT2-2	.;.	L	218	.	ENSP00000344772:R218L	R	+	2	0	TMEM201	9583796	1.000000	0.71417	0.936000	0.37596	0.974000	0.67602	8.751000	0.91628	2.314000	0.78098	0.563000	0.77884	CGT	.	.		0.667	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866		T	9661209	G	T	9661209	3	4	3	1	0	0	0	0	1	0	0	0	16141	1145	40	1	671	1	TMEM201	1	9661209	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10		9661209	239589412	1	176										
MIIP	60672	hgsc.bcm.edu	37	chr1	12082273	12082273	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	cgtgtggggcccaccagatgCctgtcgaggggacctccgtg	16	13	0	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:12082273C>T	ENST00000235332.4	+	3	405	c.236C>T	c.(235-237)gCc>gTc	p.A79V	MIIP_ENST00000436478.2_Missense_Mutation_p.A79V|Y_RNA_ENST00000365591.1_RNA	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein	79										autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						CCACCAGATGCCTGTCGAGGG	0.657																																					p.A79V		Atlas-SNP	.											.	MIIP	34	.	0			c.C236T						.						52	56	55					1																	12082273		2203	4300	6503	SO:0001583	missense	60672	exon3			CAGATGCCTGTCG	AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"invasion inhibitory protein 45"	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.236C>T	chr1.hg19:g.12082273C>T	ENSP00000235332:p.Ala79Val	178.0	0.0		133.0	43.0	NM_021933	C0KL22|Q96HU6|Q9H839|Q9HA00	Missense_Mutation	SNP	ENST00000235332.4	hg19	CCDS143.1	.	.	.	.	.	.	.	.	.	.	C	4.461	0.085321	0.08583	.	.	ENSG00000116691	ENST00000235332;ENST00000436478	T;T	0.19938	2.11;2.11	4.49	-2.92	0.05615	.	1.072830	0.07298	N	0.873639	T	0.10551	0.0258	L	0.36672	1.1	0.09310	N	1	B	0.20550	0.046	B	0.19666	0.026	T	0.36601	-0.9741	10	0.02654	T	1	0.0728	1.4506	0.02374	0.1343:0.3715:0.1397:0.3545	.	79	Q5JXC2	MIIP_HUMAN	V	79	ENSP00000235332:A79V;ENSP00000392417:A79V	ENSP00000235332:A79V	A	+	2	0	MIIP	12004860	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.338000	0.19858	-0.687000	0.05162	-0.229000	0.12294	GCC	.	.		0.657	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933		T	12082273	C	T	12082273	3	4	3	1	0	0	0	0	1	0	0	0	9594	739	26	3	242	3	MIIP	1	12082273	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	2421064	12082273	237168348	2	177										
NECAP2	55707	hgsc.bcm.edu	37	chr1	16767319	16767319	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gacgtccacgtctaccgcatCcctccgcgggctaccaaccg	9	19	1	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:16767319C>T	ENST00000337132.5	+	1	153	c.63C>T	c.(61-63)atC>atT	p.I21I	NECAP2_ENST00000504551.2_Silent_p.I21I|NECAP2_ENST00000443980.2_Silent_p.I21I|NECAP2_ENST00000486390.1_3'UTR|NECAP2_ENST00000406746.1_Silent_p.I21I|NECAP2_ENST00000457722.2_Intron	NM_001145278.1|NM_018090.4	NP_001138750.1|NP_060560.1	Q9NVZ3	NECP2_HUMAN	NECAP endocytosis associated 2	21					endocytosis (GO:0006897)|protein transport (GO:0015031)	clathrin vesicle coat (GO:0030125)|coated pit (GO:0005905)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|Kidney(64;0.000181)|KIRC - Kidney renal clear cell carcinoma(64;0.00268)|STAD - Stomach adenocarcinoma(196;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		TCTACCGCATCCCTCCGCGGG	0.637											OREG0013136	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I21I		Atlas-SNP	.											.	NECAP2	24	.	0			c.C63T						.						120	95	103					1																	16767319		2203	4300	6503	SO:0001819	synonymous_variant	55707	exon1			CCGCATCCCTCCG	AK021938	CCDS173.1, CCDS44066.1, CCDS44067.1	1p36.13	2008-02-05			ENSG00000157191	ENSG00000157191			25528	protein-coding gene	gene with protein product		611624				14555962, 15494011	Standard	NM_001145277		Approved	FLJ10420	uc001ayq.3	Q9NVZ3	OTTHUMG00000002313	ENST00000337132.5:c.63C>T	chr1.hg19:g.16767319C>T		97.0	0.0	712	72.0	13.0	NM_001145277	B4DY19|E9PGQ8|Q5VSU4|Q5VSU5|Q9H7L1|Q9H8L1	Silent	SNP	ENST00000337132.5	hg19	CCDS173.1																																																																																			.	.		0.637	NECAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006680.2	NM_018090		T	16767319	C	T	16767319	2	4	3	1	0	0	0	0	0	0	0	1	10317	845	30	3		3	NECAP2	1	16767319	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	4685046	16767319	232483302	3	178										
ZC3H12A	80149	hgsc.bcm.edu	37	chr1	37941375	37941375	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gaaacacgggacagccaccgAgcgggagcgccagacctcac	13	15	1	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:37941375A>G	ENST00000373087.6	+	2	394	c.278A>G	c.(277-279)gAg>gGg	p.E93G	RP11-422J8.1_ENST00000424989.1_RNA	NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A											NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ACAGCCACCGAGCGGGAGCGC	0.657																																					p.E93G		Atlas-SNP	.											.	ZC3H12A	58	.	0			c.A278G						.						42	41	41					1																	37941375		2203	4299	6502	SO:0001583	missense	80149	exon2			CCACCGAGCGGGA		CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"Zinc fingers, CCCH-type domain containing"	26259	protein-coding gene	gene with protein product	"MCP induced protein 1"	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.278A>G	chr1.hg19:g.37941375A>G	ENSP00000362179:p.Glu93Gly	183.0	0.0		80.0	19.0	NM_025079		Missense_Mutation	SNP	ENST00000373087.6	hg19	CCDS417.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.819342	0.32145	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	T	0.24538	1.85	4.8	4.8	0.61643	.	0.474047	0.22726	N	0.056384	T	0.22475	0.0542	L	0.41492	1.28	0.48040	D	0.99957	B	0.14438	0.01	B	0.15484	0.013	T	0.03433	-1.1037	10	0.25106	T	0.35	-26.5589	14.3326	0.66566	1.0:0.0:0.0:0.0	.	93	Q5D1E8	ZC12A_HUMAN	G	93	ENSP00000362179:E93G	ENSP00000362174:E93G	E	+	2	0	ZC3H12A	37713962	0.185000	0.23213	0.552000	0.28243	0.006000	0.05464	1.923000	0.40055	1.785000	0.52413	0.460000	0.39030	GAG	.	.		0.657	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		G	37941375	A	G	37941375	3	3	3	1	0	0	0	0	1	0	0	0	17576	304	11	2	280	2	ZC3H12A	1	37941375	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10	21174056	37941375	211309246	4	179										
C1orf175	374977	hgsc.bcm.edu	37	chr1	55118680	55118680	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	cccccctcctgtggggccccGggattagggtctggtaccat	13	15	1	0	rs371606173		TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:55118680G>A	ENST00000421030.2	+	3	366	c.81G>A	c.(79-81)ccG>ccA	p.P27P	MROH7_ENST00000545244.1_Intron|MROH7_ENST00000339553.5_Silent_p.P27P|MROH7_ENST00000409996.1_Intron|MROH7_ENST00000395690.2_Silent_p.P27P|MROH7_ENST00000454855.2_Intron|MROH7_ENST00000472987.1_3'UTR|MROH7-TTC4_ENST00000414150.2_Silent_p.P27P	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	27						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GTGGGGCCCCGGGATTAGGGT	0.592													G|||	1	0.000199681	8e-04	0	5008	,	,		17658	0		0	False		,,,				2504	0				p.P27P		Atlas-SNP	.											.	.	.	.	0			c.G81A						.	G		1,3737		0,1,1868	57	58	58		81	-7	0	1		58	1,8171		0,1,4085	no	coding-synonymous	HEATR8	NM_001039464.2		0,2,5953	AA,AG,GG		0.0122,0.0268,0.0168		27/1324	55118680	2,11908	1869	4086	5955	SO:0001819	synonymous_variant	374977	exon3			GGCCCCGGGATTA	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.81G>A	chr1.hg19:g.55118680G>A		105.0	0.0		99.0	35.0	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	hg19	CCDS41342.2																																																																																			.	.		0.592	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		A	55118680	G	A	55118680	2	1	3	1	0	0	0	0	0	0	0	1	2018	1103	39	1		1	C1orf175	1	55118680	Silent	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	17177305	55118680	194131941	5	180										
CLCA1	1179	hgsc.bcm.edu	37	chr1	86954813	86954813	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	cacacagtcgctttggggccCtctgcagctcaagaactaga	10	13	2	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:86954813C>T	ENST00000234701.3	+	9	1668	c.1317C>T	c.(1315-1317)ccC>ccT	p.P439P	CLCA1_ENST00000394711.1_Silent_p.P439P			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	439	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		CTTTGGGGCCCTCTGCAGCTC	0.512																																					p.P439P		Atlas-SNP	.											.	CLCA1	109	.	0			c.C1317T						.						70	69	69					1																	86954813		2203	4300	6503	SO:0001819	synonymous_variant	1179	exon8			GGGGCCCTCTGCA		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.1317C>T	chr1.hg19:g.86954813C>T		101.0	0.0		129.0	31.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Silent	SNP	ENST00000234701.3	hg19	CCDS709.1																																																																																			.	.		0.512	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		T	86954813	C	T	86954813	2	4	3	1	0	0	0	0	0	0	0	1	3459	668	24	3		3	CLCA1	1	86954813	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	31836133	86954813	162295808	6	181										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103496801	103496801	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aaaaactgctgaatgtccccCtgggaaaaaaaaaaaaacaa	6	8	0	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:103496801C>A	ENST00000370096.3	-	5	964		c.e5-1		COL11A1_ENST00000358392.2_Splice_Site|COL11A1_ENST00000353414.4_Splice_Site|COL11A1_ENST00000512756.1_Splice_Site	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1						cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.?(2)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GAATGTCCCCCTGGGAAAAAA	0.383																																					.		Atlas-SNP	.											COL11A1_ENST00000370096,NS,carcinoma,0,2	COL11A1	972	.	2	Unknown(2)	lung(2)	c.652-1G>T						.						46	44	45					1																	103496801		2203	4300	6503	SO:0001630	splice_region_variant	1301	exon6			GTCCCCCTGGGAA	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.652-1G>T	chr1.hg19:g.103496801C>A		27.0	0.0		36.0	8.0	NM_001190709	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Splice_Site	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.015912	0.75161	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239;ENST00000447608	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5892	0.95501	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL11A1	103269389	1.000000	0.71417	1.000000	0.80357	0.771000	0.43674	7.372000	0.79612	2.631000	0.89168	0.551000	0.68910	.	.	.		0.383	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	Intron	A	103496801	C	A	103496801	5	1	3	1	0	0	0	0	0	0	1	0	3669	695	24	3	5178	3	COL11A1	1	103496801	Splice_Site	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	16541988	103496801	145753820	7	182										
SEMA6C	10500	hgsc.bcm.edu	37	chr1	151105214	151105214	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aggcaacctccggcctccgcCgacgcccagccggggagcgg	15	18	0	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:151105214C>T	ENST00000341697.3	-	19	4230	c.2539G>A	c.(2539-2541)Ggc>Agc	p.G847S	SEMA6C_ENST00000479820.1_Intron|RP11-68I18.10_ENST00000563624.1_RNA			Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	847					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CGGCCTCCGCCGACGCCCAGC	0.791																																					p.G879S		Atlas-SNP	.											.	SEMA6C	70	.	0			c.G2635A						.						1	1	1					1																	151105214		902	2002	2904	SO:0001583	missense	10500	exon20			CTCCGCCGACGCC	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"Semaphorins"	10740	protein-coding gene	gene with protein product	"m-Sema Y2"	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.2539G>A	chr1.hg19:g.151105214C>T	ENSP00000344148:p.Gly847Ser	202.0	0.0		124.0	38.0	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	hg19	CCDS984.1	.	.	.	.	.	.	.	.	.	.	C	9.742	1.165184	0.21538	.	.	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697	T;T;T;T	0.18810	2.24;2.38;2.19;2.24	3.33	2.39	0.29439	.	12.152400	0.00166	U	0.000005	T	0.05090	0.0136	N	0.19112	0.55	0.23653	N	0.997192	B;B;B	0.26577	0.153;0.153;0.039	B;B;B	0.23716	0.048;0.048;0.022	T	0.24657	-1.0154	10	0.36615	T	0.2	.	6.6826	0.23129	0.0:0.8619:0.0:0.1381	.	839;879;847	Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;SEM6C_HUMAN	S	847;839;879;847	ENSP00000357910:G847S;ENSP00000357908:G839S;ENSP00000357909:G879S;ENSP00000344148:G847S	ENSP00000344148:G847S	G	-	1	0	SEMA6C	149371838	0.221000	0.23642	0.024000	0.17045	0.210000	0.24377	0.455000	0.21843	0.569000	0.29329	0.455000	0.32223	GGC	.	.		0.791	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		T	151105214	C	T	151105214	3	4	3	1	0	0	0	0	1	0	0	0	14056	652	23	1	257	1	SEMA6C	1	151105214	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	47608413	151105214	98145407	8	183										
TPR	7175	hgsc.bcm.edu	37	chr1	186295267	186295267	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	cagcttcataaccatcattgCcatcggcactaccagttcct	5	15	2	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:186295267C>T	ENST00000367478.4	-	41	6286	c.5990G>A	c.(5989-5991)gGc>gAc	p.G1997D		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1997					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		accatcattgccatcggcact	0.408			T	NTRK1	papillary thyroid																																p.G1997D		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.G5990A						.						159	159	159					1																	186295267		2080	4214	6294	SO:0001583	missense	7175	exon41			TCATTGCCATCGG	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.5990G>A	chr1.hg19:g.186295267C>T	ENSP00000356448:p.Gly1997Asp	90.0	0.0		63.0	11.0	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	hg19	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737583	0.69304	.	.	ENSG00000047410	ENST00000367478	T	0.21543	2.0	4.27	4.27	0.50696	.	0.143201	0.64402	D	0.000006	T	0.26448	0.0646	L	0.28740	0.885	0.52501	D	0.999958	D	0.64830	0.994	P	0.52646	0.705	T	0.01600	-1.1315	10	0.41790	T	0.15	.	17.6148	0.88064	0.0:1.0:0.0:0.0	.	1997	P12270	TPR_HUMAN	D	1997	ENSP00000356448:G1997D	ENSP00000356448:G1997D	G	-	2	0	TPR	184561890	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.650000	0.37292	2.660000	0.90430	0.655000	0.94253	GGC	.	.		0.408	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		T	186295267	C	T	186295267	3	4	3	1	0	0	0	0	1	0	0	0	16431	739	26	3	1145	3	TPR	1	186295267	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	35190053	186295267	62955354	9	184										
ESRRG	2104	hgsc.bcm.edu	37	chr1	216680527	216680527	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tcttctatgtgcatggagtcTgtgcaatgaagcaaaagata	10	6	3	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:216680527T>A	ENST00000408911.3	-	7	1286		c.e7-2		ESRRG_ENST00000366938.2_Splice_Site|ESRRG_ENST00000359162.2_Splice_Site|ESRRG_ENST00000463665.1_Splice_Site|ESRRG_ENST00000366940.2_Splice_Site|ESRRG_ENST00000487276.1_Splice_Site|ESRRG_ENST00000361525.3_Splice_Site|ESRRG_ENST00000493603.1_Splice_Site|ESRRG_ENST00000360012.3_Splice_Site|ESRRG_ENST00000366937.1_Splice_Site|ESRRG_ENST00000361395.2_Splice_Site|ESRRG_ENST00000493748.1_Splice_Site|ESRRG_ENST00000391890.3_Splice_Site	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma						gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	GCATGGAGTCTGTGCAATGAA	0.348																																					.		Atlas-SNP	.											.	ESRRG	111	.	0			c.1064-2A>T						.						74	71	72					1																	216680527		2203	4300	6503	SO:0001630	splice_region_variant	2104	exon9			GGAGTCTGTGCAA	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"Nuclear hormone receptors"	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.1133-2A>T	chr1.hg19:g.216680527T>A		165.0	0.0		170.0	48.0	NM_001243510	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Splice_Site	SNP	ENST00000408911.3	hg19	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	T	14.84	2.655255	0.47467	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5982	0.76602	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ESRRG	214747150	1.000000	0.71417	0.987000	0.45799	0.610000	0.37248	8.040000	0.89188	2.098000	0.63641	0.459000	0.35465	.	.	.		0.348	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595	Intron	A	216680527	T	A	216680527	5	1	3	1	0	0	0	0	0	0	1	0	5264	1594	55	4	249	4	ESRRG	1	216680527	Splice_Site	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	30385260	216680527	32570094	10	185										
ESRRG	2104	hgsc.bcm.edu	37	chr1	216737654	216737654	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tttgatgtcactgtcggggaCagtagggtcaggcatggcat	15	7	2	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:216737654C>T	ENST00000408911.3	-	5	922	c.769G>A	c.(769-771)Gtc>Atc	p.V257I	ESRRG_ENST00000366938.2_Missense_Mutation_p.V234I|ESRRG_ENST00000359162.2_Missense_Mutation_p.V234I|ESRRG_ENST00000463665.1_Missense_Mutation_p.V195I|ESRRG_ENST00000366940.2_Missense_Mutation_p.V234I|ESRRG_ENST00000487276.1_Missense_Mutation_p.V234I|ESRRG_ENST00000361525.3_Missense_Mutation_p.V234I|ESRRG_ENST00000493603.1_Missense_Mutation_p.V234I|ESRRG_ENST00000360012.3_Missense_Mutation_p.V234I|ESRRG_ENST00000366937.1_Missense_Mutation_p.V269I|ESRRG_ENST00000361395.2_Missense_Mutation_p.V234I|ESRRG_ENST00000493748.1_Missense_Mutation_p.V234I|ESRRG_ENST00000391890.3_Missense_Mutation_p.V241I	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	257					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CTGTCGGGGACAGTAGGGTCA	0.493																																					p.V269I		Atlas-SNP	.											.	ESRRG	111	.	0			c.G805A						.						179	151	160					1																	216737654		2203	4300	6503	SO:0001583	missense	2104	exon6			CGGGGACAGTAGG	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"Nuclear hormone receptors"	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.769G>A	chr1.hg19:g.216737654C>T	ENSP00000386171:p.Val257Ile	96.0	0.0		149.0	41.0	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	hg19	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.011126	0.75046	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748;ENST00000475275	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98701	-5.08;-5.08;-5.08;-5.08;-5.08;-5.08;-5.08;-5.08;-5.08;-5.08;-4.05;-5.08;-5.08;-5.08	5.56	5.56	0.83823	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.055638	0.64402	D	0.000001	D	0.98052	0.9358	N	0.17922	0.545	0.80722	D	1	B;P;D	0.53885	0.001;0.917;0.963	B;P;D	0.65874	0.007;0.781;0.939	D	0.98472	1.0601	10	0.34782	T	0.22	.	19.5216	0.95187	0.0:1.0:0.0:0.0	.	195;269;257	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	I	234;234;269;257;234;234;234;234;234;241;195;234;234;234;234	ENSP00000355225:V234I;ENSP00000355907:V234I;ENSP00000355904:V269I;ENSP00000386171:V257I;ENSP00000352077:V234I;ENSP00000354584:V234I;ENSP00000355905:V234I;ENSP00000353108:V234I;ENSP00000419594:V234I;ENSP00000375761:V241I;ENSP00000418629:V195I;ENSP00000419155:V234I;ENSP00000417374:V234I;ENSP00000419514:V234I	ENSP00000346386:V234I	V	-	1	0	ESRRG	214804277	1.000000	0.71417	0.974000	0.42286	0.990000	0.78478	6.079000	0.71291	2.605000	0.88082	0.655000	0.94253	GTC	.	.		0.493	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		T	216737654	C	T	216737654	3	4	3	1	0	0	0	0	1	0	0	0	5264	478	17	3	619	3	ESRRG	1	216737654	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	57127	216737654	32512967	11	186										
ZNF669	79862	hgsc.bcm.edu	37	chr1	247263872	247263872	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ggtgaagggaactgaggcgaCtgaaggcttgatcacattgt	15	6	1	4			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr1:247263872C>T	ENST00000343381.6	-	4	1371	c.1199G>A	c.(1198-1200)aGt>aAt	p.S400N	ZNF669_ENST00000358785.4_3'UTR|ZNF669_ENST00000448299.2_Missense_Mutation_p.S314N	NM_024804.2	NP_079080.2	Q96BR6	ZN669_HUMAN	zinc finger protein 669	400					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(4)|large_intestine(2)|lung(6)	17	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)			ACTGAGGCGACTGAAGGCTTG	0.433																																					p.S400N		Atlas-SNP	.											.	ZNF669	46	.	0			c.G1199A						.						151	152	151					1																	247263872		2203	4300	6503	SO:0001583	missense	79862	exon4			AGGCGACTGAAGG		CCDS31088.1, CCDS44345.1	1q44	2013-01-08			ENSG00000188295	ENSG00000188295		"Zinc fingers, C2H2-type", "-"	25736	protein-coding gene	gene with protein product						12477932	Standard	NM_024804		Approved	FLJ12606	uc001ice.2	Q96BR6	OTTHUMG00000040869	ENST00000343381.6:c.1199G>A	chr1.hg19:g.247263872C>T	ENSP00000342818:p.Ser400Asn	246.0	0.0		158.0	49.0	NM_024804	B3KP94|Q5VT39|Q9H9Q6	Missense_Mutation	SNP	ENST00000343381.6	hg19	CCDS31088.1	.	.	.	.	.	.	.	.	.	.	C	5.453	0.268687	0.10349	.	.	ENSG00000188295	ENST00000535105;ENST00000448299;ENST00000343381	T;T	0.07567	3.18;3.18	0.544	0.544	0.17185	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12347	0.0300	L	0.33668	1.02	0.09310	N	0.999998	D;D	0.56746	0.977;0.977	P;D	0.65443	0.905;0.935	T	0.28996	-1.0026	9	0.26408	T	0.33	.	4.3293	0.11055	1.0E-4:0.5644:0.4356:0.0	.	314;400	B3KP94;Q96BR6	.;ZN669_HUMAN	N	314;314;400	ENSP00000404370:S314N;ENSP00000342818:S400N	ENSP00000342818:S400N	S	-	2	0	ZNF669	245330495	0.000000	0.05858	0.010000	0.14722	0.027000	0.11550	-6.805000	0.00053	0.543000	0.28864	0.289000	0.19496	AGT	.	.		0.433	ZNF669-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000098394.4	NM_024804		T	247263872	C	T	247263872	3	4	3	1	0	0	0	0	1	0	0	0	18091	565	20	3	199	3	ZNF669	1	247263872	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	30526218	247263872	1986749	12	187										
PXDN	7837	hgsc.bcm.edu	37	chr2	1648512	1648512	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aacaggtcgatgttgagtgtCgagccatacaacctaaaaaa	9	8	0	1	rs61731247	byFrequency	TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr2:1648512C>G	ENST00000252804.4	-	18	3671	c.3621G>C	c.(3619-3621)tcG>tcC	p.S1207S		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1207					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TGTTGAGTGTCGAGCCATACA	0.468																																					p.S1207S		Atlas-SNP	.											.	PXDN	255	.	0			c.G3621C						.						19	24	22					2																	1648512		1880	4122	6002	SO:0001819	synonymous_variant	7837	exon18			GAGTGTCGAGCCA	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.3621G>C	chr2.hg19:g.1648512C>G		762.0	0.0		453.0	125.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	hg19	CCDS46221.1																																																																																			.	C|0.989;A|0.011		0.468	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		G	1648512	C	G	1648512	2	3	3	1	0	0	0	0	0	0	0	1	12862	871	31	4		4	PXDN	2	1648512	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10		1648512	241550861	13	188										
VWA3B	200403	hgsc.bcm.edu	37	chr2	98779440	98779440	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	cgtggccactgtggactgcgGttggtgctatttctggtcac	14	10	2	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr2:98779440G>A	ENST00000477737.1	+	8	1318		c.e8+1		VWA3B_ENST00000451075.2_Splice_Site|VWA3B_ENST00000435344.1_Splice_Site	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B											NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						GTGGACTGCGGTTGGTGCTAT	0.577																																					.		Atlas-SNP	.											.	VWA3B	138	.	0			c.1114+1G>A						.						65	71	69					2																	98779440		2008	4187	6195	SO:0001630	splice_region_variant	200403	exon8			ACTGCGGTTGGTG	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1114+1G>A	chr2.hg19:g.98779440G>A		58.0	0.0		46.0	14.0	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Splice_Site	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.582617	0.65992	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9809	0.58564	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	VWA3B	98145872	1.000000	0.71417	0.743000	0.31040	0.364000	0.29643	4.235000	0.58666	2.428000	0.82296	0.650000	0.86243	.	.	.		0.577	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	Intron	A	98779440	G	A	98779440	5	1	3	1	0	0	0	0	0	0	1	0	17256	1275	44	3	1141	3	VWA3B	2	98779440	Splice_Site	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	97130928	98779440	144419933	14	189										
NCK2	8440	hgsc.bcm.edu	37	chr2	106497846	106497846	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	cccccacgcccagcacggacGccgagtaccccgccaatggc	10	21	0	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr2:106497846G>A	ENST00000233154.4	+	4	731	c.289G>A	c.(289-291)Gcc>Acc	p.A97T	NCK2_ENST00000393349.2_Missense_Mutation_p.A97T|NCK2_ENST00000522586.1_Intron|NCK2_ENST00000451463.2_Intron	NM_003581.4	NP_003572.2	O43639	NCK2_HUMAN	NCK adaptor protein 2	97					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|lamellipodium assembly (GO:0030032)|negative regulation of cell proliferation (GO:0008285)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of translation (GO:0006417)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|lung(3)|ovary(1)	5						CAGCACGGACGCCGAGTACCC	0.672																																					p.A97T		Atlas-SNP	.											.	NCK2	75	.	0			c.G289A						.						31	32	32					2																	106497846		2203	4299	6502	SO:0001583	missense	8440	exon3			ACGGACGCCGAGT	AF043119	CCDS33266.1	2q12	2013-02-14			ENSG00000071051	ENSG00000071051		"SH2 domain containing"	7665	protein-coding gene	gene with protein product		604930				9737977, 16752908	Standard	NM_001004720		Approved	NCKbeta	uc002tdi.3	O43639	OTTHUMG00000153116	ENST00000233154.4:c.289G>A	chr2.hg19:g.106497846G>A	ENSP00000233154:p.Ala97Thr	61.0	0.0		46.0	18.0	NM_001004720	D3DVK1|Q9BWN9|Q9UIC3	Missense_Mutation	SNP	ENST00000233154.4	hg19	CCDS33266.1	.	.	.	.	.	.	.	.	.	.	G	13.74	2.326148	0.41197	.	.	ENSG00000071051	ENST00000233154;ENST00000393348;ENST00000425756;ENST00000393349	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.64	4.76	0.60689	.	0.102236	0.64402	D	0.000002	T	0.29093	0.0723	N	0.21448	0.665	0.80722	D	1	B	0.17667	0.023	B	0.11329	0.006	T	0.06516	-1.0822	10	0.15499	T	0.54	.	14.8665	0.70419	0.0691:0.0:0.9309:0.0	.	97	O43639	NCK2_HUMAN	T	97	ENSP00000233154:A97T;ENSP00000377017:A97T;ENSP00000408040:A97T;ENSP00000377018:A97T	ENSP00000233154:A97T	A	+	1	0	NCK2	105864278	1.000000	0.71417	0.751000	0.31187	0.754000	0.42855	6.109000	0.71528	1.524000	0.49035	0.563000	0.77884	GCC	.	.		0.672	NCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329634.1	NM_003581		A	106497846	G	A	106497846	3	1	3	1	0	0	0	0	1	0	0	0	10229	1087	38	1	295	1	NCK2	2	106497846	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	7718406	106497846	136701527	15	190										
GLI2	2736	hgsc.bcm.edu	37	chr2	121745883	121745883	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gtccgcgagcgaggtgaccaTgctgagccagctgcaggagc	16	12	0	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr2:121745883T>C	ENST00000452319.1	+	14	2453	c.2393T>C	c.(2392-2394)aTg>aCg	p.M798T	GLI2_ENST00000361492.4_Missense_Mutation_p.M798T|GLI2_ENST00000314490.11_Missense_Mutation_p.M470T					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GAGGTGACCATGCTGAGCCAG	0.706																																					p.M798T		Atlas-SNP	.											.	GLI2	187	.	0			c.T2393C						.						6	8	7					2																	121745883		2117	4190	6307	SO:0001583	missense	2736	exon13			TGACCATGCTGAG		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.2393T>C	chr2.hg19:g.121745883T>C	ENSP00000390436:p.Met798Thr	829.0	0.0		479.0	133.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	T	13.89	2.370595	0.42003	.	.	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	D;D;D	0.90563	-2.69;-2.69;-2.69	4.58	4.58	0.56647	.	0.579086	0.18934	N	0.127133	D	0.88477	0.6447	M	0.62723	1.935	0.30838	N	0.735947	B;B;B;B	0.28783	0.094;0.152;0.222;0.152	B;B;B;B	0.25614	0.026;0.058;0.062;0.036	D	0.86669	0.1909	10	0.40728	T	0.16	.	14.1388	0.65306	0.0:0.0:0.0:1.0	.	798;453;453;470	P10070;P10070-2;P10070-4;P10070-3	GLI2_HUMAN;.;.;.	T	798;798;470	ENSP00000390436:M798T;ENSP00000354586:M798T;ENSP00000312694:M470T	ENSP00000312694:M470T	M	+	2	0	GLI2	121462353	1.000000	0.71417	0.966000	0.40874	0.987000	0.75469	3.215000	0.51169	1.918000	0.55548	0.459000	0.35465	ATG	.	.		0.706	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		C	121745883	T	C	121745883	3	2	3	1	0	0	0	0	1	0	0	0	6446	1464	51	2	2443	2	GLI2	2	121745883	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	15248037	121745883	121453490	16	191										
MBD5	55777	hgsc.bcm.edu	37	chr2	149227600	149227600	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aagcagggtcagggttcattTcccatcagttcaatgtctca	9	10	5	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr2:149227600T>G	ENST00000407073.1	+	9	3085	c.2088T>G	c.(2086-2088)ttT>ttG	p.F696L	MBD5_ENST00000404807.1_Missense_Mutation_p.F696L	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	696					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		AGGGTTCATTTCCCATCAGTT	0.463																																					p.F696L		Atlas-SNP	.											.	MBD5	164	.	0			c.T2088G						.						89	88	88					2																	149227600		2203	4300	6503	SO:0001583	missense	55777	exon9			TTCATTTCCCATC	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.2088T>G	chr2.hg19:g.149227600T>G	ENSP00000386049:p.Phe696Leu	72.0	0.0		89.0	36.0	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	hg19	CCDS33302.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.326|9.326	1.059272|1.059272	0.19987|0.19987	.|.	.|.	ENSG00000204406|ENSG00000204406	ENST00000416015|ENST00000407073;ENST00000404807	T|T;T	0.48836|0.38887	0.8|1.11;1.13	4.84|4.84	2.39|2.39	0.29439|0.29439	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000016|0.000016	T|T	0.20292|0.20292	0.0488|0.0488	N|N	0.08118|0.08118	0|0	0.36271|0.36271	D|D	0.855151|0.855151	.|B;B	.|0.33103	.|0.04;0.397	.|B;B	.|0.33960	.|0.038;0.173	T|T	0.14420|0.14420	-1.0473|-1.0473	8|10	0.66056|0.27082	D|T	0.02|0.32	-6.1341|-6.1341	7.9096|7.9096	0.29782|0.29782	0.0:0.2612:0.0:0.7388|0.0:0.2612:0.0:0.7388	.|.	.|696;696	.|Q9P267-2;Q9P267	.|.;MBD5_HUMAN	C|L	436|696	ENSP00000393168:F436C|ENSP00000386049:F696L;ENSP00000384672:F696L	ENSP00000393168:F436C|ENSP00000384672:F696L	F|F	+|+	2|3	0|2	MBD5|MBD5	148944070|148944070	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.991000|0.991000	0.79684|0.79684	2.480000|2.480000	0.45206|0.45206	0.408000|0.408000	0.25621|0.25621	-0.408000|-0.408000	0.06270|0.06270	TTC|TTT	.	.		0.463	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			G	149227600	T	G	149227600	3	3	3	1	0	0	0	0	1	0	0	0	9356	1780	62	5	2102	5	MBD5	2	149227600	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	27481717	149227600	93971773	17	192										
PTPRN	5798	hgsc.bcm.edu	37	chr2	220167512	220167512	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	agccagtggggatgtcctgtAaaagcagctctccagcagga	13	10	1	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr2:220167512A>G	ENST00000295718.2	-	5	665	c.425T>C	c.(424-426)tTa>tCa	p.L142S	AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Missense_Mutation_p.L52S|PTPRN_ENST00000409251.3_Missense_Mutation_p.L142S	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	142					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		GATGTCCTGTAAAAGCAGCTC	0.607																																					p.L142S		Atlas-SNP	.											.	PTPRN	138	.	0			c.T425C						.						62	70	67					2																	220167512		2203	4300	6503	SO:0001583	missense	5798	exon5			TCCTGTAAAAGCA		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.425T>C	chr2.hg19:g.220167512A>G	ENSP00000295718:p.Leu142Ser	161.0	0.0		90.0	19.0	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	hg19	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.754351	0.00663	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666;ENST00000536579;ENST00000412847;ENST00000446182;ENST00000440552;ENST00000442029;ENST00000451506	T;T;T	0.03242	4.03;4.0;4.08	4.79	-0.283	0.12874	.	1.419410	0.04937	N	0.458049	T	0.02610	0.0079	N	0.11427	0.14	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.47100	-0.9143	10	0.28530	T	0.3	.	8.6577	0.34073	0.3482:0.0:0.6518:0.0	.	142;142	Q6NSL1;Q16849	.;PTPRN_HUMAN	S	142;142;142;52;142;52;52;109;52;52	ENSP00000386638:L142S;ENSP00000295718:L142S;ENSP00000444244:L52S	ENSP00000295718:L142S	L	-	2	0	PTPRN	219875756	0.062000	0.20869	0.885000	0.34714	0.254000	0.26022	0.579000	0.23788	0.034000	0.15491	0.459000	0.35465	TTA	.	.		0.607	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			G	220167512	A	G	220167512	3	3	3	1	0	0	0	0	1	0	0	0	12822	372	13	2	2590	2	PTPRN	2	220167512	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10	70939912	220167512	23031861	18	193										
EPM2AIP1	9852	hgsc.bcm.edu	37	chr3	37033593	37033593	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	cctttcaccatgctctgattCagattccgttagtaaagtct	6	11	4	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr3:37033593C>T	ENST00000322716.5	-	1	1202	c.976G>A	c.(976-978)Gaa>Aaa	p.E326K	MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000539477.1_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000455445.2_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	326					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						TGCTCTGATTCAGATTCCGTT	0.368																																					p.E326K		Atlas-SNP	.											.	EPM2AIP1	47	.	0			c.G976A						.						87	88	88					3																	37033593		1858	4102	5960	SO:0001583	missense	9852	exon1			CTGATTCAGATTC	AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.976G>A	chr3.hg19:g.37033593C>T	ENSP00000406027:p.Glu326Lys	128.0	0.0		110.0	24.0	NM_014805	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	hg19	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.026606	0.54683	.	.	ENSG00000178567	ENST00000322716	D	0.83335	-1.71	4.68	3.8	0.43715	.	.	.	.	.	T	0.74261	0.3693	N	0.19112	0.55	0.20764	N	0.999856	P	0.50528	0.936	P	0.45167	0.472	T	0.63305	-0.6667	9	0.35671	T	0.21	-12.5695	11.8881	0.52615	0.1757:0.8243:0.0:0.0	.	326	Q7L775	EPMIP_HUMAN	K	326	ENSP00000406027:E326K	ENSP00000406027:E326K	E	-	1	0	EPM2AIP1	37008597	0.965000	0.33210	0.786000	0.31890	0.722000	0.41435	2.978000	0.49305	1.158000	0.42547	0.467000	0.42956	GAA	.	.		0.368	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805		T	37033593	C	T	37033593	3	4	3	1	0	0	0	0	1	0	0	0	5186	835	29	3	851	3	EPM2AIP1	3	37033593	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10		37033593	160988837	19	194										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47046579	47046579	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ccaagcatgcccagctcgtgAgggagaagtgagcatgtggg	16	9	0	3			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr3:47046579A>C	ENST00000450053.3	+	39	6591	c.6412A>C	c.(6412-6414)Agg>Cgg	p.R2138R	NBEAL2_ENST00000292309.5_Silent_p.R1954R|NBEAL2_ENST00000383740.2_Silent_p.R417R	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2138	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CCAGCTCGTGAGGGAGAAGTG	0.627																																					p.R2138R		Atlas-SNP	.											.	NBEAL2	267	.	0			c.A6412C						.						58	64	62					3																	47046579		2083	4206	6289	SO:0001819	synonymous_variant	23218	exon39			CTCGTGAGGGAGA	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.6412A>C	chr3.hg19:g.47046579A>C		174.0	0.0		89.0	16.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.590|9.590	1.125767|1.125767	0.20959|0.20959	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000416683	.|.	.|.	.|.	4.86|4.86	0.792|0.792	0.18625|0.18625	.|.	.|.	.|.	.|.	.|.	T|.	0.61185|.	0.2327|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.58375|.	-0.7647|.	4|.	.|.	.|.	.|.	.|.	12.2457|12.2457	0.54568|0.54568	0.5882:0.4118:0.0:0.0|0.5882:0.4118:0.0:0.0	.|.	.|.	.|.	.|.	A|C	506|1425	.|.	.|.	E|X	+|+	2|3	0|0	NBEAL2|NBEAL2	47021583|47021583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	2.003000|2.003000	0.40844|0.40844	0.296000|0.296000	0.22592|0.22592	0.459000|0.459000	0.35465|0.35465	GAG|TGA	.	.		0.627	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		C	47046579	A	C	47046579	2	2	3	1	0	0	0	0	0	0	0	1	10198	295	11	5		5	NBEAL2	3	47046579	Silent	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10	10012986	47046579	150975851	20	195										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51284221	51284221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aactgattcgacaggaccacAttcaagaagctatgcgggta	10	9	1	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr3:51284221A>G	ENST00000266037.9	+	22	2190	c.2167A>G	c.(2167-2169)Att>Gtt	p.I723V		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	723					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.I712F(1)|p.I723F(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ACAGGACCACATTCAAGAAGC	0.443																																					p.I723V		Atlas-SNP	.											DOCK3_ENST00000266037,NS,carcinoma,0,2	DOCK3	397	.	2	Substitution - Missense(2)	lung(2)	c.A2167G						.						103	95	97					3																	51284221		1897	4132	6029	SO:0001583	missense	1795	exon22			GACCACATTCAAG	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.2167A>G	chr3.hg19:g.51284221A>G	ENSP00000266037:p.Ile723Val	147.0	0.0		93.0	23.0	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	A	19.32	3.805807	0.70682	.	.	ENSG00000088538	ENST00000266037	T	0.65178	-0.14	6.13	6.13	0.99165	.	0.000000	0.85682	D	0.000000	T	0.61652	0.2364	M	0.65975	2.015	0.58432	D	0.999999	B	0.33212	0.402	B	0.29942	0.109	T	0.61917	-0.6964	10	0.44086	T	0.13	.	16.4676	0.84087	1.0:0.0:0.0:0.0	.	723	Q8IZD9	DOCK3_HUMAN	V	723	ENSP00000266037:I723V	ENSP00000266037:I723V	I	+	1	0	DOCK3	51259261	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.926000	0.92839	2.367000	0.80283	0.529000	0.55759	ATT	.	.		0.443	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		G	51284221	A	G	51284221	3	3	3	1	0	0	0	0	1	0	0	0	4690	217	8	2	2253	2	DOCK3	3	51284221	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10	4237642	51284221	146738209	21	196										
ZBED2	79413	hgsc.bcm.edu	37	chr3	111312572	111312572	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gccctttccctcctaagcacCtccttttccctttggctggc	6	18	0	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr3:111312572C>A	ENST00000317012.4	-	2	1485	c.477G>T	c.(475-477)gaG>gaT	p.E159D	CD96_ENST00000283285.5_Intron|CD96_ENST00000438817.2_Intron|CD96_ENST00000352690.4_Intron	NM_024508.4	NP_078784.2	Q9BTP6	ZBED2_HUMAN	zinc finger, BED-type containing 2	159							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(1)|skin(2)	6						TCCTAAGCACCTCCTTTTCCC	0.617																																					p.E159D		Atlas-SNP	.											.	ZBED2	22	.	0			c.G477T						.						91	81	84					3																	111312572		2203	4300	6503	SO:0001583	missense	79413	exon2			AAGCACCTCCTTT	BC003536	CCDS2960.2	3p13-q13.2	2013-05-03			ENSG00000177494	ENSG00000177494		"Zinc fingers, BED-type"	20710	protein-coding gene	gene with protein product		615246				23533661	Standard	NM_024508		Approved	MGC10796	uc003dxy.3	Q9BTP6	OTTHUMG00000074061	ENST00000317012.4:c.477G>T	chr3.hg19:g.111312572C>A	ENSP00000321370:p.Glu159Asp	66.0	0.0		60.0	14.0	NM_024508	D3DN62	Missense_Mutation	SNP	ENST00000317012.4	hg19	CCDS2960.2	.	.	.	.	.	.	.	.	.	.	C	11.32	1.602509	0.28534	.	.	ENSG00000177494	ENST00000317012	.	.	.	3.74	0.155	0.14906	.	0.000000	0.32161	U	0.006498	T	0.35393	0.0930	L	0.61218	1.895	0.09310	N	1	P	0.52842	0.956	P	0.47528	0.549	T	0.24548	-1.0157	9	0.87932	D	0	-7.7783	5.7	0.17877	0.0:0.5138:0.0:0.4862	.	159	Q9BTP6	ZBED2_HUMAN	D	159	.	ENSP00000321370:E159D	E	-	3	2	ZBED2	112795262	0.000000	0.05858	0.357000	0.25798	0.781000	0.44180	-2.266000	0.01171	0.143000	0.18926	0.460000	0.39030	GAG	.	.		0.617	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	NM_024508		A	111312572	C	A	111312572	3	1	3	1	0	0	0	0	1	0	0	0	17533	680	24	3	183	3	ZBED2	3	111312572	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	60028351	111312572	86709858	22	197										
ATR	545	hgsc.bcm.edu	37	chr3	142272131	142272131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tttaacacttttagctgcaaCcagagctctaatttctgtgt	6	9	2	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr3:142272131C>T	ENST00000350721.4	-	13	2864	c.2743G>A	c.(2743-2745)Gtt>Att	p.V915I	ATR_ENST00000383101.3_Missense_Mutation_p.V851I	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	915					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TTAGCTGCAACCAGAGCTCTA	0.413								Other conserved DNA damage response genes																													p.V915I		Atlas-SNP	.											.	ATR	285	.	0			c.G2743A						.						79	79	79					3																	142272131		2203	4300	6503	SO:0001583	missense	545	exon13			CTGCAACCAGAGC	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.2743G>A	chr3.hg19:g.142272131C>T	ENSP00000343741:p.Val915Ile	133.0	0.0		124.0	26.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	19.33	3.806545	0.70682	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.63913	-0.07;-0.07	5.53	5.53	0.82687	Armadillo-like helical (1);Armadillo-type fold (1);	0.178956	0.47852	D	0.000214	T	0.46560	0.1399	N	0.08118	0	0.37655	D	0.92254	B	0.27791	0.189	B	0.24541	0.054	T	0.52946	-0.8507	10	0.66056	D	0.02	-16.5228	19.8241	0.96610	0.0:1.0:0.0:0.0	.	915	Q13535	ATR_HUMAN	I	915;851	ENSP00000343741:V915I;ENSP00000372581:V851I	ENSP00000343741:V915I	V	-	1	0	ATR	143754821	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.587000	0.82613	2.758000	0.94735	0.655000	0.94253	GTT	.	.		0.413	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142272131	C	T	142272131	3	4	3	1	0	0	0	0	1	0	0	0	1204	507	18	3	5331	3	ATR	3	142272131	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	30959559	142272131	55750299	23	198										
MAST4	375449	hgsc.bcm.edu	37	chr5	66461632	66461632	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ctccaaagactaagcaccccGaccggtccctctcctctcag	6	19	2	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr5:66461632G>T	ENST00000403625.2	+	29	6920	c.6625G>T	c.(6625-6627)Gac>Tac	p.D2209Y	MAST4_ENST00000261569.7_Missense_Mutation_p.D2015Y|MAST4_ENST00000403666.1_Missense_Mutation_p.D2020Y|MAST4_ENST00000404260.3_Missense_Mutation_p.D2212Y|MAST4_ENST00000405643.1_Missense_Mutation_p.D2030Y	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2212	Pro-rich.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TAAGCACCCCGACCGGTCCCT	0.652																																					p.D2209Y		Atlas-SNP	.											.	MAST4	218	.	0			c.G6625T						.						13	16	15					5																	66461632		1858	4099	5957	SO:0001583	missense	375449	exon29			CACCCCGACCGGT	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.6625G>T	chr5.hg19:g.66461632G>T	ENSP00000385727:p.Asp2209Tyr	139.0	0.0		94.0	23.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.28|12.28	1.890139|1.890139	0.33348|0.33348	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569|ENST00000443808	T;T;T;T;T|.	0.71934|.	-0.59;-0.59;-0.61;-0.61;-0.58|.	4.86|4.86	3.99|3.99	0.46301|0.46301	.|.	0.471987|.	0.19841|.	N|.	0.104851|.	T|T	0.37376|0.37376	0.1001|0.1001	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	0.999999|0.999999	D;D|.	0.56968|.	0.963;0.978|.	P;P|.	0.60415|.	0.752;0.874|.	T|T	0.21381|0.21381	-1.0247|-1.0247	10|5	0.87932|.	D|.	0|.	-19.2308|-19.2308	11.5466|11.5466	0.50696|0.50696	0.0832:0.0:0.9168:0.0|0.0832:0.0:0.9168:0.0	.|.	2212;2020|.	O15021;O15021-3|.	MAST4_HUMAN;.|.	Y|L	2212;2209;2020;2030;2030;2015|1265	ENSP00000385048:D2212Y;ENSP00000385727:D2209Y;ENSP00000384313:D2020Y;ENSP00000384099:D2030Y;ENSP00000261569:D2015Y|.	ENSP00000261569:D2015Y|.	D|R	+|+	1|2	0|0	MAST4|MAST4	66497388|66497388	1.000000|1.000000	0.71417|0.71417	0.847000|0.847000	0.33407|0.33407	0.009000|0.009000	0.06853|0.06853	4.745000|4.745000	0.62125|0.62125	1.270000|1.270000	0.44297|0.44297	0.561000|0.561000	0.74099|0.74099	GAC|CGA	.	.		0.652	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			T	66461632	G	T	66461632	3	4	3	1	0	0	0	0	1	0	0	0	9336	1058	37	1	6869	1	MAST4	5	66461632	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10		66461632	114453628	24	199										
PCDHB4	56131	hgsc.bcm.edu	37	chr5	140501893	140501893	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ttgaaccgtgtgtactgcatTtccaagtgttcctggaaatg	10	8	0	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr5:140501893T>C	ENST00000194152.1	+	1	313	c.313T>C	c.(313-315)Ttc>Ctc	p.F105L	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	105	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGTACTGCATTTCCAAGTGTT	0.463																																					p.F105L		Atlas-SNP	.											.	PCDHB4	177	.	0			c.T313C						.						54	59	57					5																	140501893		2203	4300	6503	SO:0001583	missense	56131	exon1			CTGCATTTCCAAG	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"Cadherins / Protocadherins : Clustered"	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.313T>C	chr5.hg19:g.140501893T>C	ENSP00000194152:p.Phe105Leu	91.0	0.0		81.0	4.0	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	hg19	CCDS4246.1	.	.	.	.	.	.	.	.	.	.	T	15.10	2.732086	0.48939	.	.	ENSG00000081818	ENST00000194152	T	0.25579	1.79	4.66	4.66	0.58398	Cadherin, N-terminal (1);	.	.	.	.	T	0.40448	0.1117	L	0.37750	1.13	0.32996	D	0.525613	D	0.69078	0.997	D	0.80764	0.994	T	0.50154	-0.8861	9	0.46703	T	0.11	.	14.2182	0.65807	0.0:0.0:0.0:1.0	.	105	Q9Y5E5	PCDB4_HUMAN	L	105	ENSP00000194152:F105L	ENSP00000194152:F105L	F	+	1	0	PCDHB4	140482077	0.013000	0.17824	1.000000	0.80357	0.917000	0.54804	0.850000	0.27737	2.078000	0.62432	0.533000	0.62120	TTC	.	.		0.463	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		C	140501893	T	C	140501893	3	2	3	1	0	0	0	0	1	0	0	0	11553	1841	64	2	315	2	PCDHB4	5	140501893	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	74040261	140501893	40413367	25	200										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169496161	169496161	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gccttcttcactgaagagtaTgtcagggaccaccctgagga	11	11	3	3			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr5:169496161T>A	ENST00000256935.8	+	46	4745	c.4665T>A	c.(4663-4665)taT>taA	p.Y1555*	DOCK2_ENST00000520908.1_Nonsense_Mutation_p.Y1047*|DOCK2_ENST00000540750.1_Nonsense_Mutation_p.Y616*|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1555	DHR-2.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTGAAGAGTATGTCAGGGACC	0.567																																					p.Y1555X		Atlas-SNP	.											.	DOCK2	389	.	0			c.T4665A						.						79	62	68					5																	169496161		2203	4300	6503	SO:0001587	stop_gained	1794	exon46			AGAGTATGTCAGG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4665T>A	chr5.hg19:g.169496161T>A	ENSP00000256935:p.Tyr1555*	246.0	0.0		174.0	41.0	NM_004946	Q2M3I0|Q96AK7	Nonsense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	T	50	17.150584	0.99880	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	.	.	.	4.62	-0.486	0.12064	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1691	0.42900	0.0:0.1661:0.0:0.8339	.	.	.	.	X	1555;1047;616	.	ENSP00000256935:Y1555X	Y	+	3	2	DOCK2	169428739	0.027000	0.19231	0.779000	0.31741	0.953000	0.61014	0.328000	0.19681	-0.136000	0.11475	-0.132000	0.14878	TAT	.	.		0.567	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169496161	T	A	169496161	4	1	3	1	0	0	0	0	0	1	0	0	4689	1471	51	4	4847	4	DOCK2	5	169496161	Nonsense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	28994268	169496161	11419099	26	201										
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74227933	74227933	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aatgtgagccgtgtggcaatCcaatacaggggcatagccgg	14	9	0	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr6:74227933C>A	ENST00000316292.9	-	6	2075	c.1084G>T	c.(1084-1086)Gat>Tat	p.D362Y	EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000309268.6_Missense_Mutation_p.D362Y|EEF1A1_ENST00000331523.2_Missense_Mutation_p.D362Y	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	362					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						GTGTGGCAATCCAATACAGGG	0.448																																					p.D362Y		Atlas-SNP	.											EEF1A1,NS,carcinoma,0,1	EEF1A1	56	.	0			c.G1084T						.						34	38	37					6																	74227933		2197	4298	6495	SO:0001583	missense	1915	exon7			GGCAATCCAATAC	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1084G>T	chr6.hg19:g.74227933C>A	ENSP00000339063:p.Asp362Tyr	190.0	0.0		190.0	40.0	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.830719	0.71258	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.44482	0.92;0.92;0.92	4.81	4.81	0.61882	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (2);Translation elongation factor EFTu/EF1A, C-terminal (2);	0.058657	0.64402	U	0.000003	T	0.79776	0.4504	H	0.99847	4.84	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.77004	0.989;0.989;0.989	D	0.89972	0.4094	10	0.87932	D	0	.	18.3119	0.90203	0.0:1.0:0.0:0.0	.	362;362;362	P68104;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;EF1A3_HUMAN	Y	362;360;362;362;341	ENSP00000339063:D362Y;ENSP00000339053:D362Y;ENSP00000330054:D362Y	ENSP00000339053:D362Y	D	-	1	0	EEF1A1	74284654	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	7.441000	0.80485	2.381000	0.81170	0.556000	0.70494	GAT	.	.		0.448	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		A	74227933	C	A	74227933	3	1	3	1	0	0	0	0	1	0	0	0	4925	855	30	3	312	3	EEF1A1	6	74227933	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10		74227933	96887134	27	202										
C6orf174	387104	hgsc.bcm.edu	37	chr6	127834064	127834064	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ttttttccagttcattctgtAaagcttgctttgcaatttca	5	8	3	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr6:127834064A>G	ENST00000525778.1	-	4	2202	c.1457T>C	c.(1456-1458)tTa>tCa	p.L486S	SOGA3_ENST00000368268.2_Missense_Mutation_p.L486S|SOGA3_ENST00000481848.2_Missense_Mutation_p.L486S|SOGA3_ENST00000556132.1_Missense_Mutation_p.L486S|SOGA3_ENST00000465909.2_Missense_Mutation_p.L486S			Q5TF21	SOGA3_HUMAN	SOGA family member 3	486					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											TTCATTCTGTAAAGCTTGCTT	0.318																																					p.L486S		Atlas-SNP	.											.	.	.	.	0			c.T1457C						.						146	128	133					6																	127834064		1821	4075	5896	SO:0001583	missense	387104	exon4			TTCTGTAAAGCTT	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1457T>C	chr6.hg19:g.127834064A>G	ENSP00000434570:p.Leu486Ser	142.0	0.0		137.0	18.0	NM_001012279		Missense_Mutation	SNP	ENST00000525778.1	hg19	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.520032	0.85495	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.59810	0.2221	M	0.79926	2.475	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.62548	-0.6831	10	0.44086	T	0.13	-4.2364	16.1814	0.81903	1.0:0.0:0.0:0.0	.	486	Q5TF21	CF174_HUMAN	S	486	ENSP00000451768:L486S;ENSP00000357251:L486S;ENSP00000434570:L486S;ENSP00000435559:L486S	ENSP00000435559:L486S	L	-	2	0	C6orf174	127875757	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.234000	0.73211	0.533000	0.62120	TTA	.	.		0.318	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		G	127834064	A	G	127834064	3	3	3	1	0	0	0	0	1	0	0	0	2347	372	13	2	1402	2	C6orf174	6	127834064	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10	53606131	127834064	43281003	28	203										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3245023	3245023	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gagctgtacctaccgtcgcaGctgggcaaggcgtggttcca	14	12	0	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr8:3245023G>T	ENST00000520002.1	-	19	3333	c.2778C>A	c.(2776-2778)agC>agA	p.S926R	CSMD1_ENST00000539096.1_Missense_Mutation_p.S925R|CSMD1_ENST00000537824.1_Missense_Mutation_p.S925R|CSMD1_ENST00000602723.1_Missense_Mutation_p.S926R|CSMD1_ENST00000400186.3_Missense_Mutation_p.S926R|CSMD1_ENST00000542608.1_Missense_Mutation_p.S925R|CSMD1_ENST00000602557.1_Missense_Mutation_p.S926R			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	926	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TACCGTCGCAGCTGGGCAAGG	0.587																																					p.S925R		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C2775A						.						37	42	40					8																	3245023		2108	4225	6333	SO:0001583	missense	64478	exon18			GTCGCAGCTGGGC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.2778C>A	chr8.hg19:g.3245023G>T	ENSP00000430733:p.Ser926Arg	78.0	0.0		70.0	18.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.84|13.84	2.357566|2.357566	0.41801|0.41801	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	.|T;T;T;T;T	.|0.63913	.|-0.07;-0.07;-0.07;-0.07;-0.07	5.11|5.11	4.22|4.22	0.49857|0.49857	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.62708|0.62708	0.2450|0.2450	L|L	0.31294|0.31294	0.92|0.92	0.45837|0.45837	D|D	0.998706|0.998706	.|D;P;P	.|0.76494	.|0.999;0.956;0.876	.|D;D;P	.|0.85130	.|0.997;0.93;0.541	T|T	0.56074|0.56074	-0.8039|-0.8039	5|10	.|0.13853	.|T	.|0.58	.|.	8.8091|8.8091	0.34956|0.34956	0.2268:0.0:0.7732:0.0|0.2268:0.0:0.7732:0.0	.|.	.|926;926;926	.|E5RIG2;Q96PZ7;Q96PZ7-4	.|.;CSMD1_HUMAN;.	M|R	406|926;926;788;925;925;925	.|ENSP00000383047:S926R;ENSP00000430733:S926R;ENSP00000441462:S925R;ENSP00000446243:S925R;ENSP00000441675:S925R	.|ENSP00000320445:S788R	L|S	-|-	1|3	2|2	CSMD1|CSMD1	3232430|3232430	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.568000|0.568000	0.35870|0.35870	1.904000|1.904000	0.39868|0.39868	2.374000|2.374000	0.81015|0.81015	0.650000|0.650000	0.86243|0.86243	CTG|AGC	.	.		0.587	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3245023	G	T	3245023	3	4	3	1	0	0	0	0	1	0	0	0	3946	962	34	3	8131	3	CSMD1	8	3245023	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10		3245023	143118999	29	204										
MTSS1	9788	hgsc.bcm.edu	37	chr8	125565324	125565324	+	Frame_Shift_Del	DEL	G	G	-													0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tcagcatgtcttctccttgtGgagtatcccttgggctcagg							TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr8:125565324delG	ENST00000518547.1	-	14	2650	c.2177delC	c.(2176-2178)ccafs	p.P726fs	MTSS1_ENST00000325064.5_Frame_Shift_Del_p.P730fs|MTSS1_ENST00000354184.4_Frame_Shift_Del_p.P444fs|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000431961.2_Frame_Shift_Del_p.P444fs|MTSS1_ENST00000395508.2_Frame_Shift_Del_p.P500fs|MTSS1_ENST00000378017.3_Frame_Shift_Del_p.P701fs|MTSS1_ENST00000524090.1_Frame_Shift_Del_p.P616fs	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	726	Pro-rich.				actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TTCTCCTTGTGGAGTATCCCT	0.557																																					p.P726fs	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-Indel,Pindel	.											.	MTSS1	79	.	0			c.2178delA						.						220	216	217					8																	125565324		2203	4300	6503	SO:0001589	frameshift_variant	9788	exon14			.	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.2177delC	chr8.hg19:g.125565324delG	ENSP00000429064:p.Pro726fs	148.0	0.0		110.0	23.0	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Frame_Shift_Del	DEL	ENST00000518547.1	hg19	CCDS6353.1																																																																																			.	.		0.557	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		-	125565324	G	-	125565324	7	5	3	1	0	1	0	1	0	0	0	0	9971	1348	47	0	94	0	MTSS1	8	125565324	Frame_Shift_Del	DEL	G	TCGA-2Y-A9GT-01A-11D-A382-10	122320301	125565324	20798698	30	205										
PPAPDC2	403313	hgsc.bcm.edu	37	chr9	4662813	4662813	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tcgggacacggcatcccctgGctgctgggcaccctctactg	12	16	1	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr9:4662813G>T	ENST00000381883.2	+	1	516	c.438G>T	c.(436-438)tgG>tgT	p.W146C	SPATA6L_ENST00000223517.5_Intron|SPATA6L_ENST00000454239.2_Intron|SPATA6L_ENST00000381890.5_Intron|SPATA6L_ENST00000475086.1_Intron|SPATA6L_ENST00000381895.5_Intron	NM_203453.3	NP_982278.3	Q8IY26	PPAC2_HUMAN	phosphatidic acid phosphatase type 2 domain containing 2	146						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(2)|lung(1)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.026)		GCATCCCCTGGCTGCTGGGCA	0.662																																					p.W146C	Melanoma(187;1057 3809 8526)	Atlas-SNP	.											.	PPAPDC2	12	.	0			c.G438T						.						45	42	43					9																	4662813		2203	4300	6503	SO:0001583	missense	403313	exon1			CCCCTGGCTGCTG	AK128369	CCDS34981.1	9p24	2010-04-23			ENSG00000205808	ENSG00000205808			23682	protein-coding gene	gene with protein product	"polyisoprenoid diphosphate phosphatase type 1"	611666				16464866	Standard	NM_203453		Approved	FLJ90191, FLJ46512, PDP1	uc003zin.4	Q8IY26	OTTHUMG00000019466	ENST00000381883.2:c.438G>T	chr9.hg19:g.4662813G>T	ENSP00000371307:p.Trp146Cys	61.0	0.0		50.0	13.0	NM_203453	B3KY05|Q5JVJ6|Q8NCK9	Missense_Mutation	SNP	ENST00000381883.2	hg19	CCDS34981.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.154749	0.78114	.	.	ENSG00000205808	ENST00000381883;ENST00000537542	T	0.75367	-0.93	5.35	4.45	0.53987	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.138236	0.52532	U	0.000065	T	0.82171	0.4979	M	0.82056	2.57	0.80722	D	1	D	0.64830	0.994	P	0.53722	0.733	D	0.85271	0.1056	10	0.72032	D	0.01	-6.9783	13.9758	0.64273	0.0:0.1524:0.8476:0.0	.	146	Q8IY26	PPAC2_HUMAN	C	146;55	ENSP00000371307:W146C	ENSP00000371307:W146C	W	+	3	0	PPAPDC2	4652813	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	7.351000	0.79395	1.480000	0.48289	0.655000	0.94253	TGG	.	.		0.662	PPAPDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051567.1	NM_203453		T	4662813	G	T	4662813	3	4	3	1	0	0	0	0	1	0	0	0	12304	1212	42	3	440	3	PPAPDC2	9	4662813	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10		4662813	136550618	31	206										
C9orf84	158401	hgsc.bcm.edu	37	chr9	114476836	114476836	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aactgtacaatctccagctgTctccaaatgtcacccaaata	4	13	3	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr9:114476836T>A	ENST00000318737.4	-	15	2240	c.2112A>T	c.(2110-2112)agA>agT	p.R704S	C9orf84_ENST00000394777.4_Missense_Mutation_p.R630S|C9orf84_ENST00000394779.3_Missense_Mutation_p.R665S|C9orf84_ENST00000374287.3_Missense_Mutation_p.R704S	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	704										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TCTCCAGCTGTCTCCAAATGT	0.363																																					p.R704S		Atlas-SNP	.											.	C9orf84	207	.	0			c.A2112T						.						115	109	111					9																	114476836		2203	4300	6503	SO:0001583	missense	158401	exon15			CAGCTGTCTCCAA	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.2112A>T	chr9.hg19:g.114476836T>A	ENSP00000322108:p.Arg704Ser	124.0	0.0		126.0	28.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	hg19	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	T	13.97	2.394642	0.42512	.	.	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.15718	2.4;2.52;2.42;2.42	5.87	2.26	0.28386	.	0.000000	0.64402	D	0.000018	T	0.25457	0.0619	L	0.34521	1.04	0.33138	D	0.544041	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.67382	0.951;0.951;0.951	T	0.22487	-1.0215	10	0.52906	T	0.07	-12.5672	9.6397	0.39831	0.0:0.2812:0.0:0.7188	.	630;704;665	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	S	665;630;318;704;704	ENSP00000378259:R665S;ENSP00000378257:R630S;ENSP00000363405:R704S;ENSP00000322108:R704S	ENSP00000322108:R704S	R	-	3	2	C9orf84	113516657	1.000000	0.71417	0.997000	0.53966	0.057000	0.15508	0.632000	0.24583	0.138000	0.18790	-0.912000	0.02778	AGA	.	.		0.363	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		A	114476836	T	A	114476836	3	1	3	1	0	0	0	0	1	0	0	0	2502	1664	58	4	2270	4	C9orf84	9	114476836	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	109814023	114476836	26736595	32	207										
SUSD1	64420	hgsc.bcm.edu	37	chr9	114905792	114905792	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tggtcgggtggaaaggttcaGgtccattccttggcaagtat	14	7	1	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr9:114905792G>A	ENST00000374270.3	-	4	657	c.485C>T	c.(484-486)cCt>cTt	p.P162L	SUSD1_ENST00000374264.2_Missense_Mutation_p.P162L|SUSD1_ENST00000374263.3_Missense_Mutation_p.P162L|SUSD1_ENST00000482851.1_5'UTR	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	162	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						GAAAGGTTCAGGTCCATTCCT	0.502																																					p.P162L		Atlas-SNP	.											.	SUSD1	51	.	0			c.C485T						.						171	154	159					9																	114905792		2203	4300	6503	SO:0001583	missense	64420	exon4			GGTTCAGGTCCAT	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.485C>T	chr9.hg19:g.114905792G>A	ENSP00000363388:p.Pro162Leu	109.0	0.0		74.0	23.0	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Missense_Mutation	SNP	ENST00000374270.3	hg19	CCDS6783.1	.	.	.	.	.	.	.	.	.	.	G	9.265	1.044158	0.19748	.	.	ENSG00000106868	ENST00000374270;ENST00000374263;ENST00000374264	T;T;T	0.74632	-0.81;-0.81;-0.86	5.87	5.87	0.94306	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.165825	0.28940	N	0.013646	T	0.57829	0.2080	N	0.04203	-0.255	0.29651	N	0.843962	P;P;P	0.36354	0.493;0.493;0.549	B;B;B	0.38378	0.178;0.079;0.272	T	0.54827	-0.8235	10	0.22109	T	0.4	-7.6297	18.9906	0.92789	0.0:0.0:1.0:0.0	.	162;162;162	F8WAQ1;Q6UWL2-2;Q6UWL2	.;.;SUSD1_HUMAN	L	162	ENSP00000363388:P162L;ENSP00000363381:P162L;ENSP00000363382:P162L	ENSP00000363381:P162L	P	-	2	0	SUSD1	113945613	0.263000	0.24083	0.938000	0.37757	0.045000	0.14185	1.901000	0.39838	2.780000	0.95670	0.655000	0.94253	CCT	.	.		0.502	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		A	114905792	G	A	114905792	3	1	3	1	0	0	0	0	1	0	0	0	15422	1000	35	3	1814	3	SUSD1	9	114905792	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	428956	114905792	26307639	33	208										
MAPKAP1	79109	hgsc.bcm.edu	37	chr9	128206874	128206874	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	acgtgagtttaaatattgcgTgacctgcagagacagaaaac	10	7	0	4			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr9:128206874T>C	ENST00000373498.1	-	10	1417	c.1349A>G	c.(1348-1350)cAc>cGc	p.H450R	MAPKAP1_ENST00000265960.3_Missense_Mutation_p.H450R|MAPKAP1_ENST00000394063.1_Missense_Mutation_p.H258R|MAPKAP1_ENST00000350766.3_Missense_Mutation_p.H414R|MAPKAP1_ENST00000373497.5_Missense_Mutation_p.H163R|MAPKAP1_ENST00000373511.2_Missense_Mutation_p.H403R|MAPKAP1_ENST00000373503.3_Missense_Mutation_p.H258R|MAPKAP1_ENST00000483937.1_5'UTR			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	450					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						AAATATTGCGTGACCTGCAGA	0.463																																					p.H450R		Atlas-SNP	.											.	MAPKAP1	68	.	0			c.A1349G						.						140	123	129					9																	128206874		2203	4300	6503	SO:0001583	missense	79109	exon11			ATTGCGTGACCTG	M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487			18752	protein-coding gene	gene with protein product	"stress-activated protein kinase-interacting 1"	610558				15363842	Standard	NM_001006620		Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000373498.1:c.1349A>G	chr9.hg19:g.128206874T>C	ENSP00000362597:p.His450Arg	82.0	0.0		40.0	12.0	NM_001006617	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Missense_Mutation	SNP	ENST00000373498.1	hg19	CCDS35140.1	.	.	.	.	.	.	.	.	.	.	T	11.71	1.718635	0.30503	.	.	ENSG00000119487	ENST00000373511;ENST00000350766;ENST00000373503;ENST00000373498;ENST00000265960;ENST00000394063;ENST00000373497;ENST00000420643	.	.	.	5.91	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.45558	0.1348	L	0.45137	1.4	0.80722	D	1	B;P;B;B	0.35011	0.04;0.48;0.42;0.321	B;B;B;B	0.28465	0.05;0.09;0.061;0.09	T	0.29640	-1.0005	9	0.20519	T	0.43	-12.7454	13.3363	0.60520	0.0:0.0:0.1318:0.8682	.	163;403;414;450	B7Z5E5;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7	.;.;.;SIN1_HUMAN	R	403;414;258;450;450;258;163;222	.	ENSP00000265960:H450R	H	-	2	0	MAPKAP1	127246695	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.409000	0.80053	1.038000	0.40049	0.533000	0.62120	CAC	.	.		0.463	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1			C	128206874	T	C	128206874	3	2	3	1	0	0	0	0	1	0	0	0	9297	1696	59	2	227	2	MAPKAP1	9	128206874	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	13301082	128206874	13006557	34	209										
EHMT1	79813	hgsc.bcm.edu	37	chr9	140669567	140669567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ttgtctgattgcagttgggcCggtgcacaaacagcgtggtc	14	9	1	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr9:140669567C>T	ENST00000460843.1	+	11	1681	c.1654C>T	c.(1654-1656)Cgg>Tgg	p.R552W	EHMT1_ENST00000334856.6_Missense_Mutation_p.R521W|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Missense_Mutation_p.R552W	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	552					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GCAGTTGGGCCGGTGCACAAA	0.612																																					p.R552W		Atlas-SNP	.											.	EHMT1	196	.	0			c.C1654T						.						131	105	114					9																	140669567		2203	4300	6503	SO:0001583	missense	79813	exon11			TTGGGCCGGTGCA	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	24650	protein-coding gene	gene with protein product		607001	"euchromatic histone methyltransferase 1"			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.1654C>T	chr9.hg19:g.140669567C>T	ENSP00000417980:p.Arg552Trp	101.0	0.0		69.0	18.0	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	hg19	CCDS7050.2	.	.	.	.	.	.	.	.	.	.	C	20.2	3.948844	0.73787	.	.	ENSG00000181090	ENST00000334856;ENST00000371400;ENST00000462484;ENST00000460843	T;T;T	0.71103	1.53;0.76;-0.54	5.34	1.94	0.25998	.	0.099176	0.64402	D	0.000004	D	0.82875	0.5132	M	0.71581	2.175	0.46298	D	0.998972	D;D;D	0.89917	0.998;1.0;1.0	P;D;D	0.73708	0.881;0.957;0.981	D	0.85071	0.0940	10	0.72032	D	0.01	.	18.6479	0.91418	0.1736:0.8264:0.0:0.0	.	552;521;552	Q9H9B1;Q9H9B1-2;Q9H9B1-4	EHMT1_HUMAN;.;.	W	521;521;552;552	ENSP00000334476:R521W;ENSP00000417328:R552W;ENSP00000417980:R552W	ENSP00000334476:R521W	R	+	1	2	EHMT1	139789388	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.316000	0.33620	0.207000	0.20607	0.491000	0.48974	CGG	.	.		0.612	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757		T	140669567	C	T	140669567	3	4	3	1	0	0	0	0	1	0	0	0	4985	643	23	1	1696	1	EHMT1	9	140669567	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	12462693	140669567	543864	35	210										
DIP2C	22982	hgsc.bcm.edu	37	chr10	468861	468861	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gtggtggacgtggtggagccGtggatggcctggctgatcca	19	8	0	1	rs145952021		TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr10:468861G>A	ENST00000280886.6	-	5	594	c.507C>T	c.(505-507)caC>caT	p.H169H	DIP2C_ENST00000381496.3_Silent_p.H62H	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	169						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		TGGTGGAGCCGTGGATGGCCT	0.657																																					p.H169H		Atlas-SNP	.											.	DIP2C	195	.	0			c.C507T						.	G		0,4406		0,0,2203	110	112	112		507	-6	0.9	10	dbSNP_134	112	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DIP2C	NM_014974.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		169/1557	468861	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	22982	exon5			GGAGCCGTGGATG	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.507C>T	chr10.hg19:g.468861G>A		101.0	0.0		64.0	19.0	NM_014974	B4DPI5|Q5SS78	Silent	SNP	ENST00000280886.6	hg19	CCDS7054.1																																																																																			.	G|1.000;A|0.000		0.657	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		A	468861	G	A	468861	2	1	3	1	0	0	0	0	0	0	0	1	4531	1136	40	1		1	DIP2C	10	468861	Silent	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10		468861	135065886	36	211										
NEBL	10529	hgsc.bcm.edu	37	chr10	21178791	21178791	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tacctcagaaataaaagcacCgatattttttacatggttta	5	7	1	1	rs369862013		TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr10:21178791C>A	ENST00000377122.4	-	3	637	c.241G>T	c.(241-243)Ggt>Tgt	p.G81C	NEBL_ENST00000377119.1_Missense_Mutation_p.G81C|NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	81					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						ATAAAAGCACCGATATTTTTT	0.318																																					p.G81C		Atlas-SNP	.											.	NEBL	199	.	0			c.G241T						.						91	93	93					10																	21178791		2202	4300	6502	SO:0001583	missense	10529	exon3			AAGCACCGATATT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.241G>T	chr10.hg19:g.21178791C>A	ENSP00000366326:p.Gly81Cys	207.0	0.0		196.0	40.0	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	hg19	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.816913	0.50633	.	.	ENSG00000078114	ENST00000377122;ENST00000377119;ENST00000434381	T;T;T	0.32515	1.45;1.45;1.45	6.17	4.25	0.50352	.	0.246860	0.41712	D	0.000824	T	0.30603	0.0770	L	0.51422	1.61	0.22866	N	0.998638	P	0.44521	0.837	P	0.45856	0.495	T	0.22068	-1.0227	10	0.72032	D	0.01	.	5.9825	0.19415	0.255:0.5988:0.0:0.1462	.	81	O76041	NEBL_HUMAN	C	81;81;65	ENSP00000366326:G81C;ENSP00000366323:G81C;ENSP00000396512:G65C	ENSP00000366323:G81C	G	-	1	0	NEBL	21218797	0.002000	0.14202	0.596000	0.28811	0.764000	0.43329	0.043000	0.13971	0.851000	0.35264	0.655000	0.94253	GGT	.	.		0.318	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		A	21178791	C	A	21178791	3	1	3	1	0	0	0	0	1	0	0	0	10312	652	23	1	2907	1	NEBL	10	21178791	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	20709930	21178791	114355956	37	212										
TSPAN4	7106	hgsc.bcm.edu	37	chr11	850322	850322	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ggcatggcgcgcgcctgcctCcaggccgtcaagtacctcat	12	16	2	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr11:850322C>T	ENST00000397404.1	+	3	277	c.18C>T	c.(16-18)ctC>ctT	p.L6L	TSPAN4_ENST00000397396.1_Intron|TSPAN4_ENST00000397411.2_Silent_p.L6L|TSPAN4_ENST00000525201.1_Intron|TSPAN4_ENST00000409543.2_Silent_p.L6L|TSPAN4_ENST00000409531.1_Silent_p.L25L|TSPAN4_ENST00000346501.4_Silent_p.L6L|TSPAN4_ENST00000397406.1_Silent_p.L6L|TSPAN4_ENST00000397408.1_Silent_p.L6L|TSPAN4_ENST00000397397.2_Silent_p.L6L	NM_001025237.1	NP_001020408.1	O14817	TSN4_HUMAN	tetraspanin 4	6					protein complex assembly (GO:0006461)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	antigen binding (GO:0003823)|integrin binding (GO:0005178)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)	3		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCGCCTGCCTCCAGGCCGTCA	0.647																																					p.L6L		Atlas-SNP	.											.	TSPAN4	14	.	0			c.C18T						.						18	20	19					11																	850322		2194	4297	6491	SO:0001819	synonymous_variant	7106	exon3			CTGCCTCCAGGCC	AF022813	CCDS7721.1, CCDS41589.1	11p15.5	2013-02-14	2005-03-21	2005-03-21	ENSG00000214063	ENSG00000214063		"Tetraspanins"	11859	protein-coding gene	gene with protein product		602644	"transmembrane 4 superfamily member 7"	TM4SF7		9360996	Standard	XM_005253102		Approved	NAG-2, TSPAN-4, TETRASPAN	uc001lsf.1	O14817	OTTHUMG00000133305	ENST00000397404.1:c.18C>T	chr11.hg19:g.850322C>T		66.0	0.0		47.0	9.0	NM_001025235	Q6IAP6	Silent	SNP	ENST00000397404.1	hg19	CCDS7721.1																																																																																			.	.		0.647	TSPAN4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257102.2			T	850322	C	T	850322	2	4	3	1	0	0	0	0	0	0	0	1	16664	842	30	3		3	TSPAN4	11	850322	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10		850322	134156194	38	213										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6662511	6662511	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	agtgaagcggtagcggtcccGctgctcacggtccaagacac	13	13	1	2	rs367639691		TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr11:6662511G>A	ENST00000299441.3	-	2	745	c.334C>T	c.(334-336)Cgg>Tgg	p.R112W		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	112	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TAGCGGTCCCGCTGCTCACGG	0.607																																					p.R112W		Atlas-SNP	.											.	DCHS1	277	.	0			c.C334T						.	G	TRP/ARG	1,4401	2.1+/-5.4	0,1,2200	79	63	68		334	4.5	1	11		68	0,8592		0,0,4296	no	missense	DCHS1	NM_003737.2	101	0,1,6496	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	112/3299	6662511	1,12993	2201	4296	6497	SO:0001583	missense	8642	exon2			GGTCCCGCTGCTC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.334C>T	chr11.hg19:g.6662511G>A	ENSP00000299441:p.Arg112Trp	117.0	0.0		84.0	6.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.253238	0.59212	2.27E-4	0.0	ENSG00000166341	ENST00000299441	T	0.39056	1.1	5.41	4.48	0.54585	Cadherin (3);Cadherin-like (1);	0.000000	0.42294	D	0.000728	T	0.68915	0.3053	M	0.88979	2.995	0.49915	D	0.999834	D	0.89917	1.0	D	0.80764	0.994	T	0.75682	-0.3233	10	0.66056	D	0.02	.	14.1642	0.65466	0.0:0.0:0.8443:0.1557	.	112	Q96JQ0	PCD16_HUMAN	W	112	ENSP00000299441:R112W	ENSP00000299441:R112W	R	-	1	2	DCHS1	6619087	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	2.692000	0.47018	1.218000	0.43458	0.643000	0.83706	CGG	.	.		0.607	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6662511	G	A	6662511	3	1	3	1	0	0	0	0	1	0	0	0	4289	1086	38	1	9642	1	DCHS1	11	6662511	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	5812189	6662511	128344005	39	214										
OR4A15	81328	hgsc.bcm.edu	37	chr11	55135909	55135909	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ggattggaggctttcttcacTcattggttcaatttctcttt	8	8	5	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr11:55135909T>C	ENST00000314706.3	+	1	550	c.550T>C	c.(550-552)Tca>Cca	p.S184P		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	184						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						CTTTCTTCACTCATTGGTTCA	0.423																																					p.S184P		Atlas-SNP	.											.	OR4A15	161	.	0			c.T550C						.						183	166	172					11																	55135909		2201	4296	6497	SO:0001583	missense	81328	exon1			CTTCACTCATTGG	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"GPCR / Class A : Olfactory receptors"	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.550T>C	chr11.hg19:g.55135909T>C	ENSP00000325065:p.Ser184Pro	69.0	0.0		73.0	22.0	NM_001005275	Q6IFL4|Q96R65	Missense_Mutation	SNP	ENST00000314706.3	hg19	CCDS31500.1	.	.	.	.	.	.	.	.	.	.	-	13.35	2.210424	0.39003	.	.	ENSG00000181958	ENST00000314706	T	0.46063	0.88	3.48	-1.26	0.09376	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42294	D	0.000729	T	0.53834	0.1821	M	0.70108	2.13	0.09310	N	1	D	0.67145	0.996	D	0.75020	0.985	T	0.48031	-0.9070	10	0.87932	D	0	.	5.9819	0.19411	0.1397:0.0:0.4134:0.4469	.	184	Q8NGL6	O4A15_HUMAN	P	184	ENSP00000325065:S184P	ENSP00000325065:S184P	S	+	1	0	OR4A15	54892485	0.000000	0.05858	0.000000	0.03702	0.635000	0.38103	-0.523000	0.06230	-0.550000	0.06183	0.403000	0.27427	TCA	.	.		0.423	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		C	55135909	T	C	55135909	3	2	3	1	0	0	0	0	1	0	0	0	11049	1551	54	2	552	2	OR4A15	11	55135909	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	48473398	55135909	79870607	40	215										
OR5B17	219965	hgsc.bcm.edu	37	chr11	58126247	58126247	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	caaagactgcacaaaagaacAtctgagcagcacaggcactg	9	11	1	3			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr11:58126247A>G	ENST00000357377.3	-	1	295	c.296T>C	c.(295-297)aTg>aCg	p.M99T		NM_001005489.1	NP_001005489.1	Q8NGF7	OR5BH_HUMAN	olfactory receptor, family 5, subfamily B, member 17	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ACAAAAGAACATCTGAGCAGC	0.478																																					p.M99T		Atlas-SNP	.											.	OR5B17	64	.	0			c.T296C						.						101	91	94					11																	58126247		2201	4295	6496	SO:0001583	missense	219965	exon1			AAGAACATCTGAG	AB065849	CCDS31548.1	11q12.1	2012-08-09			ENSG00000197786	ENSG00000197786		"GPCR / Class A : Olfactory receptors"	15267	protein-coding gene	gene with protein product				OR5B20P			Standard	NM_001005489		Approved		uc010rke.2	Q8NGF7	OTTHUMG00000167465	ENST00000357377.3:c.296T>C	chr11.hg19:g.58126247A>G	ENSP00000349945:p.Met99Thr	182.0	0.0		136.0	35.0	NM_001005489	Q6IEX1	Missense_Mutation	SNP	ENST00000357377.3	hg19	CCDS31548.1	.	.	.	.	.	.	.	.	.	.	a	9.218	1.032665	0.19590	.	.	ENSG00000197786	ENST00000357377	T	0.00402	7.56	3.6	3.6	0.41247	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	U	0.000404	T	0.00412	0.0013	M	0.62016	1.91	0.25300	N	0.989287	B	0.27229	0.172	B	0.24269	0.052	T	0.38866	-0.9641	10	0.66056	D	0.02	-15.3883	11.1791	0.48616	1.0:0.0:0.0:0.0	.	99	Q8NGF7	OR5BH_HUMAN	T	99	ENSP00000349945:M99T	ENSP00000349945:M99T	M	-	2	0	OR5B17	57882823	0.010000	0.17322	1.000000	0.80357	0.367000	0.29736	2.608000	0.46308	1.505000	0.48720	0.378000	0.23410	ATG	.	.		0.478	OR5B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394708.2	NM_001005489		G	58126247	A	G	58126247	3	3	3	1	0	0	0	0	1	0	0	0	11158	217	8	2	650	2	OR5B17	11	58126247	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10	2990338	58126247	76880269	41	216										
GPR152	390212	hgsc.bcm.edu	37	chr11	67220097	67220097	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	agcagggccaccaggaagacCgtgtcccagccaccttgggg	14	14	0	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr11:67220097C>A	ENST00000312457.2	-	1	103	c.99G>T	c.(97-99)acG>acT	p.T33T	CABP4_ENST00000542025.2_3'UTR|CABP4_ENST00000438189.2_De_novo_Start_InFrame|CABP4_ENST00000325656.5_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			CCAGGAAGACCGTGTCCCAGC	0.652																																					p.T33T	Pancreas(102;800 1581 2723 7382 33622)	Atlas-SNP	.											.	GPR152	41	.	0			c.G99T						.						43	44	44					11																	67220097		2198	4290	6488	SO:0001819	synonymous_variant	390212	exon1			GAAGACCGTGTCC	AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"GPCR / Class A : Orphans"	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.99G>T	chr11.hg19:g.67220097C>A		326.0	0.0		193.0	55.0	NM_206997	Q0VD88|Q86SM0	Silent	SNP	ENST00000312457.2	hg19	CCDS8165.1																																																																																			.	.		0.652	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1			A	67220097	C	A	67220097	2	1	3	1	0	0	0	0	0	0	0	1	6666	639	23	1		1	GPR152	11	67220097	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	9093850	67220097	67786419	42	217										
WNT11	7481	hgsc.bcm.edu	37	chr11	75907729	75907729	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ttgcagtgttgcgtctggttCagtgccagggccgatggtgt	16	8	2	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr11:75907729C>T	ENST00000322563.3	-	2	241	c.117G>A	c.(115-117)ctG>ctA	p.L39L	RP11-619A14.2_ENST00000527314.1_RNA	NM_004626.2	NP_004617.2	O96014	WNT11_HUMAN	wingless-type MMTV integration site family, member 11	39					adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|bone mineralization (GO:0030282)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|cloacal septation (GO:0060197)|embryonic skeletal system development (GO:0048706)|lung-associated mesenchyme development (GO:0060484)|mesonephric duct development (GO:0072177)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of fibroblast growth factor production (GO:0090272)|negative regulation of mesenchymal cell proliferation (GO:0072201)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroendocrine cell differentiation (GO:0061101)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway (GO:0035567)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta2 production (GO:0032915)|protein localization to cell surface (GO:0034394)|protein phosphorylation (GO:0006468)|response to nutrient levels (GO:0031667)|tight junction assembly (GO:0070830)|ureteric bud morphogenesis (GO:0060675)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|protein kinase activator activity (GO:0030295)|Ras GTPase activator activity (GO:0005099)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	20						GCGTCTGGTTCAGTGCCAGGG	0.627																																					p.L39L		Atlas-SNP	.											.	WNT11	44	.	0			c.G117A						.						53	36	42					11																	75907729		2200	4292	6492	SO:0001819	synonymous_variant	7481	exon2			CTGGTTCAGTGCC	Y12692	CCDS8242.1	11q13.5	2008-02-05			ENSG00000085741	ENSG00000085741		"Wingless-type MMTV integration sites"	12776	protein-coding gene	gene with protein product		603699				9757009	Standard	NM_004626		Approved		uc001oxe.3	O96014	OTTHUMG00000165264	ENST00000322563.3:c.117G>A	chr11.hg19:g.75907729C>T		150.0	0.0		109.0	25.0	NM_004626	B2R8Z6|Q14DE8|Q8WZ98	Silent	SNP	ENST00000322563.3	hg19	CCDS8242.1																																																																																			.	.		0.627	WNT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383083.1	NM_004626		T	75907729	C	T	75907729	2	4	3	1	0	0	0	0	0	0	0	1	17399	813	29	3		3	WNT11	11	75907729	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	8687632	75907729	59098787	43	218										
PVRL1	5818	hgsc.bcm.edu	37	chr11	119508882	119508883	+	Frame_Shift_Ins	INS	-	-	G													0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gagacccccagatcatagtaINSggggggctgcagggacagct							TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr11:119508882_119508883insG	ENST00000341398.2	-	8	1301_1302	c.1302_1303insC	c.(1300-1305)ccctacfs	p.Y435fs	RP11-196E1.3_ENST00000601999.1_RNA|RP11-196E1.3_ENST00000532153.1_RNA	NM_203285.1	NP_976030.1	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	0					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		AGATCATAGTAGGGGGGCTGCA	0.629																																					p.Y435fs		Atlas-Indel,Pindel	.											.	PVRL1	133	.	0			c.1303_1304insC						.																																			SO:0001589	frameshift_variant	5818	exon8			.	X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9706	protein-coding gene	gene with protein product	"nectin"	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000341398.2:c.1303dupC	chr11.hg19:g.119508888_119508888dupG	ENSP00000344974:p.Tyr435fs	104.0	0.0		51.0	16.0	NM_203285	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Frame_Shift_Ins	INS	ENST00000341398.2	hg19	CCDS8425.1																																																																																			.	.		0.629	PVRL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388230.1			G	119508883	-	G	119508882	7	5	3	1	0	1	1	0	0	0	0	0	12854	420	15	0	77	0	PVRL1	11	119508882	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GT-01A-11D-A382-10	43601153	119508882	15497634	44	219										
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128868356	128868356	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gtaatgagcttgccgtgcttTttagacactaaaaatcaata	7	7	1	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr11:128868356T>C	ENST00000310343.9	-	11	1010	c.1011A>G	c.(1009-1011)aaA>aaG	p.K337K	ARHGAP32_ENST00000524655.1_Silent_p.K263K|ARHGAP32_ENST00000527272.1_5'Flank|ARHGAP32_ENST00000392657.3_5'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	337					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						TGCCGTGCTTTTTAGACACTA	0.388																																					p.K337K		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.A1011G						.						67	62	63					11																	128868356		2201	4297	6498	SO:0001819	synonymous_variant	9743	exon11			GTGCTTTTTAGAC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.1011A>G	chr11.hg19:g.128868356T>C		78.0	0.0		59.0	12.0	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	hg19	CCDS44769.1																																																																																			.	.		0.388	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		C	128868356	T	C	128868356	2	2	3	1	0	0	0	0	0	0	0	1	881	1838	64	2		2	ARHGAP32	11	128868356	Silent	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	9359474	128868356	6138160	45	220										
KCNA5	3741	hgsc.bcm.edu	37	chr12	5153915	5153915	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	cgtgttcgcggacgagatacGcttctaccagctgggggacg	15	11	1	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr12:5153915G>C	ENST00000252321.3	+	1	831	c.602G>C	c.(601-603)cGc>cCc	p.R201P		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	201					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	GACGAGATACGCTTCTACCAG	0.637																																					p.R201P		Atlas-SNP	.											KCNA5,NS,carcinoma,0,1	KCNA5	138	.	0			c.G602C						.						46	49	48					12																	5153915		2203	4300	6503	SO:0001583	missense	3741	exon1			AGATACGCTTCTA	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.602G>C	chr12.hg19:g.5153915G>C	ENSP00000252321:p.Arg201Pro	98.0	0.0		52.0	16.0	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.790425	0.70337	.	.	ENSG00000130037	ENST00000252321	T	0.77620	-1.11	4.77	4.77	0.60923	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.64402	U	0.000002	D	0.88522	0.6459	M	0.86953	2.85	0.53005	D	0.999961	D	0.58970	0.984	P	0.62382	0.901	D	0.90614	0.4554	10	0.72032	D	0.01	.	16.9696	0.86295	0.0:0.0:1.0:0.0	.	201	P22460	KCNA5_HUMAN	P	201	ENSP00000252321:R201P	ENSP00000252321:R201P	R	+	2	0	KCNA5	5024176	0.177000	0.23109	1.000000	0.80357	0.993000	0.82548	0.851000	0.27751	2.478000	0.83669	0.561000	0.74099	CGC	.	.		0.637	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		C	5153915	G	C	5153915	3	2	3	1	0	0	0	0	1	0	0	0	8015	1087	38	4	604	4	KCNA5	12	5153915	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10		5153915	128697980	46	221										
KLRC3	3823	hgsc.bcm.edu	37	chr12	10573090	10573090	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ttgcctttaggtttcctttgCtgccactttgggtcctgggc	11	11	0	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr12:10573090C>G	ENST00000396439.2	-	1	104	c.60G>C	c.(58-60)caG>caC	p.Q20H	KLRC3_ENST00000381903.2_Missense_Mutation_p.Q20H|NKG2-E_ENST00000539033.1_Intron|KLRC3_ENST00000381904.2_Missense_Mutation_p.Q20H	NM_002261.2	NP_002252.2	Q07444	NKG2E_HUMAN	killer cell lectin-like receptor subfamily C, member 3	20					cellular defense response (GO:0006968)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						GTTTCCTTTGCTGCCACTTTG	0.428																																					p.Q20H		Atlas-SNP	.											.	KLRC3	25	.	0			c.G60C						.						91	88	89					12																	10573090		2203	4297	6500	SO:0001583	missense	3823	exon1			CCTTTGCTGCCAC	L14542	CCDS31744.1, CCDS41755.1	12p13	2008-08-05			ENSG00000205810	ENSG00000205810		"Killer cell lectin-like receptors"	6376	protein-coding gene	gene with protein product		602892				9598306	Standard	NM_002261		Approved	NKG2-E	uc001qyi.1	Q07444	OTTHUMG00000167149	ENST00000396439.2:c.60G>C	chr12.hg19:g.10573090C>G	ENSP00000379716:p.Gln20His	57.0	0.0		70.0	19.0	NM_007333	Q8WXA4|Q96RL0|Q9UP04	Missense_Mutation	SNP	ENST00000396439.2	hg19	CCDS41755.1	.	.	.	.	.	.	.	.	.	.	c	10.72	1.429946	0.25726	.	.	ENSG00000205810	ENST00000396439;ENST00000381904;ENST00000381903	T;T;T	0.06768	3.26;3.26;3.26	2.55	-3.38	0.04883	.	0.975336	0.08397	N	0.952023	T	0.26195	0.0639	M	0.90082	3.085	0.09310	N	1	P;D	0.65815	0.927;0.995	P;D	0.68353	0.681;0.957	T	0.15122	-1.0448	10	0.87932	D	0	.	2.6543	0.05008	0.3645:0.2247:0.0:0.4108	.	20;20	Q07444-2;Q07444	.;NKG2E_HUMAN	H	20	ENSP00000379716:Q20H;ENSP00000371329:Q20H;ENSP00000371328:Q20H	ENSP00000371328:Q20H	Q	-	3	2	KLRC3	10464357	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.574000	0.05868	-0.946000	0.03677	-0.302000	0.09304	CAG	.	.		0.428	KLRC3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393471.1	NM_002261		G	10573090	C	G	10573090	3	3	3	1	0	0	0	0	1	0	0	0	8426	796	28	4	786	4	KLRC3	12	10573090	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	5419175	10573090	123278805	47	222										
ALG10B	144245	hgsc.bcm.edu	37	chr12	38710750	38710750	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ccttgagctgtacctttttaGtgtcctgcctcctcttctcc	6	15	2	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr12:38710750G>C	ENST00000308742.4	+	1	371	c.55G>C	c.(55-57)Gtg>Ctg	p.V19L	ALG10B_ENST00000551464.1_Missense_Mutation_p.V19L	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	19					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				TACCTTTTTAGTGTCCTGCCT	0.597											OREG0021733	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V19L		Atlas-SNP	.											.	ALG10B	58	.	0			c.G55C						.						197	203	201					12																	38710750		2203	4300	6503	SO:0001583	missense	144245	exon1			TTTTTAGTGTCCT	AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"		"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.55G>C	chr12.hg19:g.38710750G>C	ENSP00000310120:p.Val19Leu	124.0	0.0	880	92.0	33.0	NM_001013620	B2RPF4	Missense_Mutation	SNP	ENST00000308742.4	hg19	CCDS31772.1	.	.	.	.	.	.	.	.	.	.	g	9.706	1.155724	0.21454	.	.	ENSG00000175548	ENST00000308742;ENST00000551464	T;T	0.42131	1.56;0.98	3.64	2.69	0.31865	.	0.276731	0.34484	N	0.003939	T	0.13243	0.0321	N	0.01789	-0.72	0.26874	N	0.967691	B	0.02656	0.0	B	0.04013	0.001	T	0.31916	-0.9926	10	0.02654	T	1	.	8.5725	0.33578	0.0:0.0:0.7473:0.2527	.	19	Q5I7T1	AG10B_HUMAN	L	19	ENSP00000310120:V19L;ENSP00000448819:V19L	ENSP00000310120:V19L	V	+	1	0	ALG10B	36997017	0.406000	0.25344	0.388000	0.26195	0.771000	0.43674	0.650000	0.24858	1.011000	0.39340	0.655000	0.94253	GTG	.	.		0.597	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620		C	38710750	G	C	38710750	3	2	3	1	0	0	0	0	1	0	0	0	512	1029	36	4	57	4	ALG10B	12	38710750	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	28137660	38710750	95141145	48	223										
GLIPR1L2	144321	hgsc.bcm.edu	37	chr12	75807475	75807475	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aattttcatatgcaactatgCgccagggtaagttacttaaa	7	7	1	0	rs550463995		TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr12:75807475C>T	ENST00000550916.1	+	3	625	c.578C>T	c.(577-579)gCg>gTg	p.A193V	GLIPR1L2_ENST00000320460.4_Missense_Mutation_p.A193V|GLIPR1L2_ENST00000547164.1_Intron|GLIPR1L2_ENST00000378692.3_Missense_Mutation_p.A86V|GLIPR1L2_ENST00000441218.1_Missense_Mutation_p.A128V|GLIPR1L2_ENST00000435775.1_Intron	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	193						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						TGCAACTATGCGCCAGGGTAA	0.289													C|||	1	0.000199681	0	0	5008	,	,		11243	0.001		0	False		,,,				2504	0				p.A193V		Atlas-SNP	.											GLIPR1L2_ENST00000550916,colon,carcinoma,0,2	GLIPR1L2	54	.	0			c.C578T						.						81	86	84					12																	75807475		2202	4295	6497	SO:0001583	missense	144321	exon3			ACTATGCGCCAGG	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.578C>T	chr12.hg19:g.75807475C>T	ENSP00000448248:p.Ala193Val	120.0	0.0		154.0	48.0	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Missense_Mutation	SNP	ENST00000550916.1	hg19	CCDS58258.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.250561	0.59212	.	.	ENSG00000180481	ENST00000550916;ENST00000378692;ENST00000320460;ENST00000441218	T;T;T;T	0.10099	2.91;2.91;2.91;2.91	5.14	3.16	0.36331	CAP domain (2);	0.062202	0.64402	D	0.000005	T	0.12603	0.0306	L	0.49350	1.555	0.31845	N	0.622947	D;D	0.58620	0.983;0.972	B;P	0.48400	0.353;0.576	T	0.07770	-1.0755	10	0.38643	T	0.18	.	6.321	0.21217	0.0:0.5334:0.3665:0.1001	.	193;193	Q4G1C9;Q4G1C9-2	GRPL2_HUMAN;.	V	193;86;193;128	ENSP00000448248:A193V;ENSP00000367963:A86V;ENSP00000317385:A193V;ENSP00000405273:A128V	ENSP00000317385:A193V	A	+	2	0	GLIPR1L2	74093742	0.809000	0.29036	1.000000	0.80357	0.987000	0.75469	0.328000	0.19681	1.376000	0.46267	0.591000	0.81541	GCG	.	.		0.289	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436		T	75807475	C	T	75807475	3	4	3	1	0	0	0	0	1	0	0	0	6451	768	27	1	588	1	GLIPR1L2	12	75807475	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	37096725	75807475	58044420	49	224										
CIT	11113	hgsc.bcm.edu	37	chr12	120213641	120213641	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ttgagctgctgctcagcattGatctataattaaaatcccag	7	9	2	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr12:120213641G>C	ENST00000261833.7	-	16	1942	c.1890C>G	c.(1888-1890)atC>atG	p.I630M	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Missense_Mutation_p.I630M	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	630					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		GCTCAGCATTGATCTATAATT	0.418																																					p.I630M		Atlas-SNP	.											.	CIT	535	.	0			c.C1890G						.						59	58	59					12																	120213641		2203	4300	6503	SO:0001583	missense	11113	exon16			AGCATTGATCTAT	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.1890C>G	chr12.hg19:g.120213641G>C	ENSP00000261833:p.Ile630Met	95.0	0.0		81.0	25.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.97|14.97	2.695389|2.695389	0.48202|0.48202	.|.	.|.	ENSG00000122966|ENSG00000122966	ENST00000392521;ENST00000261833|ENST00000392520	T;T|.	0.78364|.	-1.17;-0.08|.	5.96|5.96	3.99|3.99	0.46301|0.46301	.|.	0.275955|.	0.36268|.	N|.	0.002689|.	T|.	0.45316|.	0.1336|.	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B;B;B|.	0.27791|.	0.087;0.087;0.189|.	B;B;B|.	0.25614|.	0.062;0.062;0.06|.	T|.	0.40156|.	-0.9578|.	10|.	0.36615|.	T|.	0.2|.	.|.	18.2029|18.2029	0.89844|0.89844	0.0:0.2399:0.7601:0.0|0.0:0.2399:0.7601:0.0	.|.	630;630;163|.	Q2M5E1;O14578;O14578-3|.	.;CTRO_HUMAN;.|.	M|X	630|258	ENSP00000376306:I630M;ENSP00000261833:I630M|.	ENSP00000261833:I630M|.	I|S	-|-	3|2	3|0	CIT|CIT	118698024|118698024	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	1.463000|1.463000	0.35277|0.35277	1.477000|1.477000	0.48234|0.48234	0.655000|0.655000	0.94253|0.94253	ATC|TCA	.	.		0.418	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		C	120213641	G	C	120213641	3	2	3	1	0	0	0	0	1	0	0	0	3440	1280	45	4	4321	4	CIT	12	120213641	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	44406166	120213641	13638254	50	225										
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130926753	130926753	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gacgcactgcacggagatgcGgtaggtgcaggctgccatgt	16	10	0	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr12:130926753G>T	ENST00000261655.4	-	8	1256	c.1093C>A	c.(1093-1095)Cgc>Agc	p.R365S	RIMBP2_ENST00000536002.1_Missense_Mutation_p.R273S|RIMBP2_ENST00000535703.1_Missense_Mutation_p.R273S	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	365	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.R365S(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		ACGGAGATGCGGTAGGTGCAG	0.627																																					p.R365S		Atlas-SNP	.											RIMBP2,NS,carcinoma,0,1	RIMBP2	220	.	1	Substitution - Missense(1)	lung(1)	c.C1093A						.						158	151	153					12																	130926753		2203	4300	6503	SO:0001583	missense	23504	exon8			AGATGCGGTAGGT	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.1093C>A	chr12.hg19:g.130926753G>T	ENSP00000261655:p.Arg365Ser	120.0	0.0		99.0	31.0	NM_015347	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	hg19	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	g	23.4	4.415541	0.83449	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.52754	0.65;0.65;0.65	4.09	4.09	0.47781	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.70587	0.3241	M	0.85859	2.78	0.80722	D	1	D;D;D	0.69078	0.997;0.983;0.997	P;D;D	0.76071	0.866;0.921;0.987	T	0.73814	-0.3864	10	0.34782	T	0.22	-31.2126	16.3122	0.82883	0.0:0.0:1.0:0.0	.	273;273;365	C9JWN3;O15034-2;O15034	.;.;RIMB2_HUMAN	S	365;273;273;273	ENSP00000261655:R365S;ENSP00000440347:R273S;ENSP00000439159:R273S	ENSP00000261655:R365S	R	-	1	0	RIMBP2	129492706	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	5.581000	0.67471	1.795000	0.52594	0.431000	0.28591	CGC	.	.		0.627	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		T	130926753	G	T	130926753	3	4	3	1	0	0	0	0	1	0	0	0	13378	1116	39	1	2113	1	RIMBP2	12	130926753	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	10713112	130926753	2925142	51	226										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42873655	42873655	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ctcagtgaatgtcctgggacAtaaagaactaccttctgtga	9	9	2	3			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr13:42873655A>G	ENST00000025301.2	+	8	948	c.773A>G	c.(772-774)cAt>cGt	p.H258R		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	258	Ser-rich.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		GTCCTGGGACATAAAGAACTA	0.398																																					p.H258R		Atlas-SNP	.											.	AKAP11	146	.	0			c.A773G						.						103	98	99					13																	42873655		2203	4300	6503	SO:0001583	missense	11215	exon8			TGGGACATAAAGA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.773A>G	chr13.hg19:g.42873655A>G	ENSP00000025301:p.His258Arg	147.0	0.0		169.0	49.0	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.305891	0.00240	.	.	ENSG00000023516	ENST00000025301	T	0.44083	0.93	5.43	-0.549	0.11829	.	0.930262	0.09166	N	0.839504	T	0.19406	0.0466	N	0.13043	0.29	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24764	-1.0151	10	0.15952	T	0.53	.	2.4728	0.04568	0.579:0.0899:0.1468:0.1843	.	258	Q9UKA4	AKA11_HUMAN	R	258	ENSP00000025301:H258R	ENSP00000025301:H258R	H	+	2	0	AKAP11	41771655	0.035000	0.19736	0.799000	0.32177	0.032000	0.12392	0.327000	0.19663	-0.089000	0.12484	-1.256000	0.01477	CAT	.	.		0.398	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		G	42873655	A	G	42873655	3	3	3	1	0	0	0	0	1	0	0	0	447	217	8	2	795	2	AKAP11	13	42873655	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10		42873655	72296223	52	227										
NPAS3	64067	hgsc.bcm.edu	37	chr14	34145492	34145492	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	agatggctgagcagctgggcAtgaagctcccccctgggcgg	16	12	0	3			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr14:34145492A>C	ENST00000356141.4	+	6	634	c.634A>C	c.(634-636)Atg>Ctg	p.M212L	NPAS3_ENST00000551492.1_Missense_Mutation_p.M217L|NPAS3_ENST00000551008.1_Missense_Mutation_p.M110L|NPAS3_ENST00000548645.1_Missense_Mutation_p.M182L|NPAS3_ENST00000357798.5_Missense_Mutation_p.M199L|NPAS3_ENST00000341321.4_Missense_Mutation_p.M212L|NPAS3_ENST00000346562.2_Missense_Mutation_p.M180L|NPAS3_ENST00000547068.1_Missense_Mutation_p.M108L			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	212	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		GCAGCTGGGCATGAAGCTCCC	0.632																																					p.M212L		Atlas-SNP	.											.	NPAS3	266	.	0			c.A634C						.						73	72	73					14																	34145492		2203	4300	6503	SO:0001583	missense	64067	exon6			CTGGGCATGAAGC	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.634A>C	chr14.hg19:g.34145492A>C	ENSP00000348460:p.Met212Leu	69.0	0.0		58.0	18.0	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	A	3.275	-0.148321	0.06627	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000341321;ENST00000548645;ENST00000356141;ENST00000357798;ENST00000547068;ENST00000551008	T;T;T;T;T;T;T	0.40225	2.24;2.24;2.24;1.04;2.24;2.24;2.24	5.62	5.62	0.85841	PAS (2);PAS fold (1);	0.000000	0.85682	D	0.000000	T	0.13243	0.0321	N	0.00408	-1.53	0.80722	D	1	B;B;B;B;B	0.18310	0.002;0.022;0.027;0.022;0.022	B;B;B;B;B	0.21151	0.007;0.02;0.033;0.02;0.02	T	0.35025	-0.9805	10	0.02654	T	1	.	15.8164	0.78604	1.0:0.0:0.0:0.0	.	110;182;212;180;199	F8W0C2;Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;.;NPAS3_HUMAN;.;.	L	189;217;180;212;182;212;199;108;110	ENSP00000448373:M189L;ENSP00000450392:M217L;ENSP00000319610:M180L;ENSP00000344158:M212L;ENSP00000448916:M182L;ENSP00000348460:M212L;ENSP00000350446:M199L	ENSP00000344158:M212L	M	+	1	0	NPAS3	33215243	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.487000	0.81328	2.141000	0.66446	0.459000	0.35465	ATG	.	.		0.632	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			C	34145492	A	C	34145492	3	2	3	1	0	0	0	0	1	0	0	0	10573	217	8	5	711	5	NPAS3	14	34145492	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10		34145492	73204048	53	228										
C14orf104	55172	hgsc.bcm.edu	37	chr14	50092384	50092384	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tgctgtcgaatccaggtataTtgtgaaccgtagttttgttc	10	7	0	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr14:50092384T>C	ENST00000298292.8	-	3	2470	c.2390A>G	c.(2389-2391)aAt>aGt	p.N797S	RP11-649E7.5_ENST00000555043.1_RNA|DNAAF2_ENST00000406043.3_Missense_Mutation_p.N749S	NM_018139.2	NP_060609.2	Q9NVR5	KTU_HUMAN	dynein, axonemal, assembly factor 2	797					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)				kidney(1)|lung(4)	5						TCCAGGTATATTGTGAACCGT	0.358																																					p.N797S		Atlas-SNP	.											.	DNAAF2	47	.	0			c.A2390G						.						192	176	182					14																	50092384		2203	4300	6503	SO:0001583	missense	55172	exon3			GGTATATTGTGAA	AK001425	CCDS9691.2, CCDS45100.1	14q21.3	2012-05-03	2011-06-09	2011-06-09	ENSG00000165506	ENSG00000165506			20188	protein-coding gene	gene with protein product	"kintoun"	612517	"chromosome 14 open reading frame 104"	C14orf104			Standard	NM_001083908		Approved	FLJ10563, KTU, PF13, CILD10	uc001wws.4	Q9NVR5	OTTHUMG00000152331	ENST00000298292.8:c.2390A>G	chr14.hg19:g.50092384T>C	ENSP00000298292:p.Asn797Ser	153.0	0.0		108.0	23.0	NM_018139	B9WS54|C0JAP7|Q86TR1|Q86TY8|Q969Z5	Missense_Mutation	SNP	ENST00000298292.8	hg19	CCDS9691.2	.	.	.	.	.	.	.	.	.	.	T	6.121	0.390592	0.11581	.	.	ENSG00000165506	ENST00000298292;ENST00000406043	T;T	0.15139	2.45;2.45	5.17	-1.41	0.08941	.	0.960570	0.08691	N	0.908019	T	0.10508	0.0257	N	0.17474	0.49	0.09310	N	1	B;B	0.16603	0.018;0.01	B;B	0.14578	0.011;0.005	T	0.35871	-0.9771	10	0.34782	T	0.22	.	10.709	0.45971	0.0:0.4501:0.0:0.5499	.	749;797	Q9NVR5-2;Q9NVR5	.;KTU_HUMAN	S	797;749	ENSP00000298292:N797S;ENSP00000384862:N749S	ENSP00000298292:N797S	N	-	2	0	DNAAF2	49162134	0.000000	0.05858	0.001000	0.08648	0.272000	0.26649	0.238000	0.18004	-0.302000	0.08869	-0.388000	0.06559	AAT	.	.		0.358	DNAAF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276813.1			C	50092384	T	C	50092384	3	2	3	1	0	0	0	0	1	0	0	0	1738	1493	52	2	127	2	C14orf104	14	50092384	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	15946892	50092384	57257156	54	229										
DDX24	57062	hgsc.bcm.edu	37	chr14	94545834	94545834	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gactttccctcctcctcctcCtcttcttctgaaacagcttg	4	17	3	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr14:94545834C>T	ENST00000330836.5	-	2	386	c.255G>A	c.(253-255)gaG>gaA	p.E85E	IFI27L1_ENST00000557066.1_5'Flank|IFI27L1_ENST00000553664.1_5'Flank|IFI27L1_ENST00000556381.1_5'Flank|DDX24_ENST00000544005.1_Intron|IFI27L1_ENST00000393115.3_5'Flank|IFI27L1_ENST00000557218.1_5'Flank|DDX24_ENST00000555054.1_Silent_p.E42E|IFI27L1_ENST00000554544.1_5'Flank|IFI27L1_ENST00000555523.1_5'Flank	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	85	Poly-Glu.				RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		CCTCCTCCTCCTCTTCTTCTG	0.438																																					p.E85E		Atlas-SNP	.											.	DDX24	82	.	0			c.G255A						.						165	161	163					14																	94545834		2203	4300	6503	SO:0001819	synonymous_variant	57062	exon2			CTCCTCCTCTTCT	AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"DEAD-boxes"	13266	protein-coding gene	gene with protein product		606181	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.255G>A	chr14.hg19:g.94545834C>T		80.0	0.0		92.0	6.0	NM_020414	E7EMJ4|Q4V9L5	Silent	SNP	ENST00000330836.5	hg19	CCDS9918.1																																																																																			.	.		0.438	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		T	94545834	C	T	94545834	2	4	3	1	0	0	0	0	0	0	0	1	4353	680	24	3		3	DDX24	14	94545834	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	44453450	94545834	12803706	55	230										
PLCB2	5330	hgsc.bcm.edu	37	chr15	40588548	40588548	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gggctggatgtaattgactaGgctggacatctcctcataag	12	8	2	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr15:40588548G>A	ENST00000260402.3	-	16	1894	c.1645C>T	c.(1645-1647)Cta>Tta	p.L549L	PLCB2_ENST00000557821.1_Silent_p.L545L|PLCB2_ENST00000456256.2_Silent_p.L549L	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	549	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		TAATTGACTAGGCTGGACATC	0.537																																					p.L549L		Atlas-SNP	.											.	PLCB2	177	.	0			c.C1645T						.						64	65	65					15																	40588548		1977	4163	6140	SO:0001819	synonymous_variant	5330	exon16			TGACTAGGCTGGA		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1645C>T	chr15.hg19:g.40588548G>A		131.0	0.0		72.0	17.0	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	hg19	CCDS42020.1																																																																																			.	.		0.537	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			A	40588548	G	A	40588548	2	1	3	1	0	0	0	0	0	0	0	1	12037	991	35	3		3	PLCB2	15	40588548	Silent	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10		40588548	61942844	56	231										
INO80	54617	hgsc.bcm.edu	37	chr15	41280125	41280125	+	Frame_Shift_Del	DEL	G	G	-													0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aagcggtgggccctgtccatGgcctgctggtccacagtggg							TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr15:41280125delG	ENST00000361937.3	-	30	4042	c.3618delC	c.(3616-3618)gccfs	p.A1206fs	INO80_ENST00000561244.1_5'UTR|INO80_ENST00000401393.3_Frame_Shift_Del_p.A1206fs			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1206	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.|Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CCCTGTCCATGGCCTGCTGGT	0.498																																					p.M1207fs		Atlas-Indel,Pindel	.											.	INO80	122	.	0			c.3619delA						.						143	141	141					15																	41280125		2203	4300	6503	SO:0001589	frameshift_variant	54617	exon30			.	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.3618delC	chr15.hg19:g.41280125delG	ENSP00000355205:p.Ala1206fs	178.0	0.0		151.0	37.0	NM_017553	A6H8X4|Q9NTG6	Frame_Shift_Del	DEL	ENST00000361937.3	hg19	CCDS10071.1																																																																																			.	.		0.498	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		-	41280125	G	-	41280125	7	5	3	1	0	1	0	1	0	0	0	0	7755	1335	47	0	1080	0	INO80	15	41280125	Frame_Shift_Del	DEL	G	TCGA-2Y-A9GT-01A-11D-A382-10	691577	41280125	61251267	57	232										
TSPAN3	10099	hgsc.bcm.edu	37	chr15	77345132	77345132	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gactcacctcagcatagaggTcggaagggtgggccaggctg	16	10	2	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr15:77345132T>C	ENST00000267970.4	-	5	845	c.572A>G	c.(571-573)gAc>gGc	p.D191G	TSPAN3_ENST00000424443.3_Missense_Mutation_p.D127G|TSPAN3_ENST00000558745.1_5'UTR|TSPAN3_ENST00000561277.1_5'UTR|TSPAN3_ENST00000559494.1_Missense_Mutation_p.D102G|TSPAN3_ENST00000346495.2_Missense_Mutation_p.D166G|TSPAN3_ENST00000558394.1_5'Flank	NM_001168412.1|NM_005724.5|NM_198902.2	NP_001161884.1|NP_005715.1|NP_944492.1	O60637	TSN3_HUMAN	tetraspanin 3	191						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	10				all cancers(203;1.14e-19)		AGCATAGAGGTCGGAAGGGTG	0.478																																					p.D191G		Atlas-SNP	.											.	TSPAN3	21	.	0			c.A572G						.						99	79	85					15																	77345132		2196	4294	6490	SO:0001583	missense	10099	exon5			TAGAGGTCGGAAG		CCDS10292.1, CCDS10293.1, CCDS53963.1	15q23	2013-02-14	2005-03-21	2005-03-21	ENSG00000140391	ENSG00000140391		"Tetraspanins"	17752	protein-coding gene	gene with protein product		613134	"transmembrane 4 superfamily member 8"	TM4SF8			Standard	NM_005724		Approved	TM4-A, TSPAN-3	uc002bcj.3	O60637	OTTHUMG00000143728	ENST00000267970.4:c.572A>G	chr15.hg19:g.77345132T>C	ENSP00000267970:p.Asp191Gly	174.0	0.0		133.0	6.0	NM_005724	A6NEH4|B3KQQ2|B4DP19|Q9BW22|Q9NVX9	Missense_Mutation	SNP	ENST00000267970.4	hg19	CCDS10292.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470899	0.63625	.	.	ENSG00000140391	ENST00000267970;ENST00000424443;ENST00000423920;ENST00000346495	T;T;T	0.78924	-1.22;-1.22;-1.22	6.16	6.16	0.99307	Tetraspanin, EC2 domain (1);	0.177290	0.64402	D	0.000017	T	0.81083	0.4749	M	0.62723	1.935	0.80722	D	1	P;B;B;B	0.49559	0.925;0.367;0.018;0.018	P;B;B;B	0.49922	0.626;0.253;0.026;0.043	T	0.78411	-0.2214	10	0.25106	T	0.35	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	127;153;166;191	B4DP19;B4DEK8;A6NEH4;O60637	.;.;.;TSN3_HUMAN	G	191;127;153;166	ENSP00000267970:D191G;ENSP00000407243:D127G;ENSP00000341329:D166G	ENSP00000267970:D191G	D	-	2	0	TSPAN3	75132187	1.000000	0.71417	0.954000	0.39281	0.838000	0.47535	6.285000	0.72658	2.367000	0.80283	0.528000	0.53228	GAC	.	.		0.478	TSPAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289792.3	NM_005724		C	77345132	T	C	77345132	3	2	3	1	0	0	0	0	1	0	0	0	16660	1667	58	2	201	2	TSPAN3	15	77345132	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	36065007	77345132	25186260	58	233										
TM6SF1	53346	hgsc.bcm.edu	37	chr15	83781634	83781634	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tcgtcaaaagaaaaccacccCgggacccactgttctatggt	8	13	2	1	rs371581703		TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr15:83781634C>A	ENST00000322019.9	+	2	452	c.178C>A	c.(178-180)Cgg>Agg	p.R60R	TM6SF1_ENST00000379386.4_Silent_p.R60R|TM6SF1_ENST00000564988.1_3'UTR|RP11-382A20.2_ENST00000565513.1_RNA|TM6SF1_ENST00000379390.6_Silent_p.R60R|TM6SF1_ENST00000565774.1_Silent_p.R60R			Q9BZW5	TM6S1_HUMAN	transmembrane 6 superfamily member 1	60						integral component of membrane (GO:0016021)				endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						AAAACCACCCCGGGACCCACT	0.478																																					p.R60R		Atlas-SNP	.											.	TM6SF1	38	.	0			c.C178A						.						131	118	122					15																	83781634		2203	4300	6503	SO:0001819	synonymous_variant	53346	exon2			CCACCCCGGGACC	AF255922	CCDS10323.1, CCDS45338.1	15q24-q26	2003-04-04			ENSG00000136404	ENSG00000136404			11860	protein-coding gene	gene with protein product		606562				11124529	Standard	NM_001144903		Approved		uc002bjp.3	Q9BZW5	OTTHUMG00000147365	ENST00000322019.9:c.178C>A	chr15.hg19:g.83781634C>A		190.0	0.0		113.0	26.0	NM_001144903	A8K7T5|H3BU56|Q4U0U5	Silent	SNP	ENST00000322019.9	hg19	CCDS10323.1																																																																																			.	.		0.478	TM6SF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000304009.1	NM_023003		A	83781634	C	A	83781634	2	1	3	1	0	0	0	0	0	0	0	1	15987	643	23	1		1	TM6SF1	15	83781634	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	6436502	83781634	18749758	59	234										
AGBL1	123624	hgsc.bcm.edu	37	chr15	86800184	86800184	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	acttcccttggtcacagccaGcagtgcctatgccttcccgg	9	16	1	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr15:86800184G>T	ENST00000441037.2	+	7	793	c.698G>T	c.(697-699)aGc>aTc	p.S233I	AGBL1_ENST00000421325.2_Missense_Mutation_p.S233I	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	233					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GTCACAGCCAGCAGTGCCTAT	0.522																																					p.S233I		Atlas-SNP	.											.	AGBL1	151	.	0			c.G698T						.						86	87	87					15																	86800184		2061	4202	6263	SO:0001583	missense	123624	exon7			CAGCCAGCAGTGC	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.698G>T	chr15.hg19:g.86800184G>T	ENSP00000413001:p.Ser233Ile	77.0	0.0		81.0	19.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	hg19	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.245803	0.39697	.	.	ENSG00000166748	ENST00000441037;ENST00000421325	T	0.43294	0.95	5.93	5.02	0.67125	Armadillo-type fold (1);	0.319446	0.27851	N	0.017583	T	0.37210	0.0995	L	0.60455	1.87	0.80722	D	1	P	0.45902	0.868	B	0.34242	0.178	T	0.38478	-0.9659	10	0.54805	T	0.06	-8.8623	14.4644	0.67472	0.0:0.1559:0.844:0.0	.	233	Q96MI9	CBPC4_HUMAN	I	262;233	ENSP00000397173:S233I	ENSP00000397173:S233I	S	+	2	0	AGBL1	84601188	0.042000	0.20092	0.973000	0.42090	0.385000	0.30292	0.742000	0.26216	1.495000	0.48549	0.655000	0.94253	AGC	.	.		0.522	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		T	86800184	G	T	86800184	3	4	3	1	0	0	0	0	1	0	0	0	375	971	34	3	720	3	AGBL1	15	86800184	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	3018550	86800184	15731208	60	235										
SYNGR3	9143	hgsc.bcm.edu	37	chr16	2042999	2042999	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gcagcggcgtggagggcaccGagacctaccagagcccgccc	15	16	0	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr16:2042999G>C	ENST00000248121.2	+	4	774	c.616G>C	c.(616-618)Gag>Cag	p.E206Q	SYNGR3_ENST00000562045.1_3'UTR	NM_004209.5	NP_004200.2	O43761	SNG3_HUMAN	synaptogyrin 3	206					positive regulation of transporter activity (GO:0032411)|substantia nigra development (GO:0021762)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|synaptic vesicle (GO:0008021)				endometrium(1)|lung(2)	3						GGAGGGCACCGAGACCTACCA	0.692																																					p.E206Q		Atlas-SNP	.											.	SYNGR3	10	.	0			c.G616C						.						28	26	27					16																	2042999		2192	4294	6486	SO:0001583	missense	9143	exon4			GGCACCGAGACCT	AJ002309	CCDS10456.1	16p13.3	2008-05-19			ENSG00000127561	ENSG00000127561			11501	protein-coding gene	gene with protein product		603927				9760194	Standard	NM_004209		Approved		uc002cod.3	O43761	OTTHUMG00000128711	ENST00000248121.2:c.616G>C	chr16.hg19:g.2042999G>C	ENSP00000248121:p.Glu206Gln	199.0	0.0		104.0	24.0	NM_004209	B2R9S0	Missense_Mutation	SNP	ENST00000248121.2	hg19	CCDS10456.1	.	.	.	.	.	.	.	.	.	.	g	23.9	4.475559	0.84640	.	.	ENSG00000127561	ENST00000248121	T	0.14640	2.49	3.39	3.39	0.38822	.	0.188390	0.45606	D	0.000346	T	0.16981	0.0408	L	0.31664	0.95	0.80722	D	1	D	0.65815	0.995	P	0.56278	0.795	T	0.01172	-1.1429	10	0.59425	D	0.04	.	8.0574	0.30612	0.1132:0.0:0.8868:0.0	.	206	O43761	SNG3_HUMAN	Q	206	ENSP00000248121:E206Q	ENSP00000248121:E206Q	E	+	1	0	SYNGR3	1983000	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.640000	0.83355	1.733000	0.51620	0.462000	0.41574	GAG	.	.		0.692	SYNGR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250616.1			C	2042999	G	C	2042999	3	2	3	1	0	0	0	0	1	0	0	0	15465	1059	37	4	630	4	SYNGR3	16	2042999	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10		2042999	88311754	61	236										
EDC4	23644	hgsc.bcm.edu	37	chr16	67916488	67916488	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	atgatagcttccggctggggAcacaggaatgtgagtggggt	17	6	0	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr16:67916488A>G	ENST00000358933.5	+	25	3672	c.3433A>G	c.(3433-3435)Aca>Gca	p.T1145A	CTC-479C5.10_ENST00000572067.1_lincRNA|NRN1L_ENST00000339176.3_5'Flank|NRN1L_ENST00000576147.1_5'Flank	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	1145					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		CCGGCTGGGGACACAGGAATG	0.562																																					p.T1145A		Atlas-SNP	.											.	EDC4	101	.	0			c.A3433G						.						62	61	61					16																	67916488		2198	4300	6498	SO:0001583	missense	23644	exon25			CTGGGGACACAGG	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.3433A>G	chr16.hg19:g.67916488A>G	ENSP00000351811:p.Thr1145Ala	170.0	0.0		100.0	29.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	hg19	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.222523	0.79464	.	.	ENSG00000038358	ENST00000358933	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.67822	0.2934	M	0.65975	2.015	0.80722	D	1	D	0.63880	0.993	P	0.57911	0.829	T	0.64249	-0.6452	9	0.10902	T	0.67	-12.9179	16.0566	0.80812	1.0:0.0:0.0:0.0	.	1145	Q6P2E9	EDC4_HUMAN	A	1145	.	ENSP00000351811:T1145A	T	+	1	0	EDC4	66473989	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	9.258000	0.95555	2.272000	0.75746	0.460000	0.39030	ACA	.	.		0.562	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		G	67916488	A	G	67916488	3	3	3	1	0	0	0	0	1	0	0	0	4910	275	10	2	3531	2	EDC4	16	67916488	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10	65873489	67916488	22438265	62	237										
G6PC	2538	hgsc.bcm.edu	37	chr17	41056030	41056030	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ccgtgcccctgataaagcagTtccctgtaacctgtgagact	9	13	0	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr17:41056030T>C	ENST00000253801.2	+	2	392	c.313T>C	c.(313-315)Ttc>Ctc	p.F105L	G6PC_ENST00000585489.1_Missense_Mutation_p.F105L|G6PC_ENST00000592383.1_Missense_Mutation_p.F105L	NM_000151.3	NP_000142.2	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit	105					carbohydrate metabolic process (GO:0005975)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|hexose transport (GO:0008645)|multicellular organism growth (GO:0035264)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)|urate metabolic process (GO:0046415)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)|phosphate ion binding (GO:0042301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GATAAAGCAGTTCCCTGTAAC	0.493																																					p.F105L		Atlas-SNP	.											.	G6PC	48	.	0			c.T313C						.						143	122	129					17																	41056030		2203	4300	6503	SO:0001583	missense	2538	exon2			AAGCAGTTCCCTG	U01120	CCDS11446.1, CCDS59291.1	17q21	2014-09-17	2006-06-28			ENSG00000131482	3.1.3.9		4056	protein-coding gene	gene with protein product	"glycogen storage disease type I, von Gierke disease"	613742	"glucose-6-phosphatase, catalytic (glycogen storage disease type I, von Gierke disease)"	G6PT		7774924	Standard	NM_000151		Approved	GSD1a	uc002icb.2	P35575		ENST00000253801.2:c.313T>C	chr17.hg19:g.41056030T>C	ENSP00000253801:p.Phe105Leu	112.0	0.0		79.0	20.0	NM_001270397	A1L4C0|B4E1C3|K7EL82	Missense_Mutation	SNP	ENST00000253801.2	hg19	CCDS11446.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.940465	0.92526	.	.	ENSG00000131482	ENST00000253801	T	0.79033	-1.23	4.74	4.74	0.60224	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.059538	0.64402	D	0.000002	D	0.85314	0.5668	L	0.58101	1.795	0.53688	D	0.999979	D;D	0.76494	0.991;0.999	P;D	0.85130	0.881;0.997	D	0.86342	0.1705	10	0.56958	D	0.05	.	14.389	0.66965	0.0:0.0:0.0:1.0	.	107;105	E7ENG5;P35575	.;G6PC_HUMAN	L	105	ENSP00000253801:F105L	ENSP00000253801:F105L	F	+	1	0	G6PC	38309556	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	7.819000	0.86621	1.987000	0.57996	0.402000	0.26972	TTC	.	.		0.493	G6PC-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452451.1	NM_000151		C	41056030	T	C	41056030	3	2	3	1	0	0	0	0	1	0	0	0	6151	1725	60	2	319	2	G6PC	17	41056030	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10		41056030	40139180	63	238										
EPN3	55040	hgsc.bcm.edu	37	chr17	48614268	48614268	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tacatcgaccgcgacggcaaGgaccagggcgtcaacgtgcg	14	13	1	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr17:48614268G>C	ENST00000268933.3	+	2	930	c.351G>C	c.(349-351)aaG>aaC	p.K117N	RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000537145.1_Missense_Mutation_p.K172N|EPN3_ENST00000541226.1_Missense_Mutation_p.K61N	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	117	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.					clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			GCGACGGCAAGGACCAGGGCG	0.637																																					p.K117N		Atlas-SNP	.											.	EPN3	32	.	0			c.G351C						.						99	78	85					17																	48614268		2203	4300	6503	SO:0001583	missense	55040	exon2			CGGCAAGGACCAG	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.351G>C	chr17.hg19:g.48614268G>C	ENSP00000268933:p.Lys117Asn	222.0	0.0		119.0	5.0	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	hg19	CCDS11570.1	.	.	.	.	.	.	.	.	.	.	G	17.96	3.515288	0.64634	.	.	ENSG00000049283	ENST00000268933;ENST00000503246;ENST00000442715;ENST00000537145;ENST00000541226;ENST00000507467;ENST00000411703	T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63	5.47	1.06	0.20224	Epsin domain, N-terminal (1);ENTH/VHS (2);Epsin-like, N-terminal (2);	0.319446	0.32970	N	0.005439	T	0.69886	0.3161	M	0.90977	3.165	0.40759	D	0.982988	D;D;D	0.76494	0.985;0.982;0.999	P;P;D	0.80764	0.893;0.828;0.994	T	0.72408	-0.4303	10	0.87932	D	0	-28.2328	9.1479	0.36944	0.398:0.0:0.602:0.0	.	172;172;117	B4DK18;F6QWW5;Q9H201	.;.;EPN3_HUMAN	N	117;117;172;172;61;117;117	ENSP00000268933:K117N;ENSP00000426762:K117N;ENSP00000439512:K172N;ENSP00000440540:K61N;ENSP00000421515:K117N	ENSP00000268933:K117N	K	+	3	2	EPN3	45969267	1.000000	0.71417	0.997000	0.53966	0.640000	0.38277	0.836000	0.27545	0.216000	0.20781	0.561000	0.74099	AAG	.	.		0.637	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957		C	48614268	G	C	48614268	3	2	3	1	0	0	0	0	1	0	0	0	5189	991	35	4	353	4	EPN3	17	48614268	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	7558238	48614268	32580942	64	239										
CDR2L	30850	hgsc.bcm.edu	37	chr17	72999276	72999276	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tgcgactctcactacccgccAggtgcaaggatgctttccgc	10	15	1	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr17:72999276A>T	ENST00000337231.5	+	5	918		c.e5-1			NM_014603.2	NP_055418.2	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like													all_lung(278;0.226)					ACTACCCGCCAGGTGCAAGGA	0.697																																					.		Atlas-SNP	.											.	.	.	.	0			c.507-2A>T						.						17	17	17					17																	72999276		2144	4196	6340	SO:0001630	splice_region_variant	30850	exon5			CCCGCCAGGTGCA		CCDS11710.2	17q25.1	2006-03-28			ENSG00000109089	ENSG00000109089			29999	protein-coding gene	gene with protein product	"paraneoplastic antigen"						Standard	NM_014603		Approved	HUMPPA	uc002jml.4	Q86X02	OTTHUMG00000150435	ENST00000337231.5:c.507-1A>T	chr17.hg19:g.72999276A>T		222.0	0.0		132.0	37.0	NM_014603	B4DFA7|Q15175	Splice_Site	SNP	ENST00000337231.5	hg19	CCDS11710.2	.	.	.	.	.	.	.	.	.	.	A	19.46	3.832381	0.71258	.	.	ENSG00000109089	ENST00000337231	.	.	.	4.71	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4553	0.67413	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDR2L	70510871	1.000000	0.71417	0.989000	0.46669	0.835000	0.47333	8.620000	0.90943	1.876000	0.54355	0.379000	0.24179	.	.	.		0.697	CDR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318080.1	NM_014603	Intron	T	72999276	A	T	72999276	5	4	3	1	0	0	0	0	0	0	1	0	3175	202	7	4	523	4	CDR2L	17	72999276	Splice_Site	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10	24385008	72999276	8195934	65	240										
ZNF556	80032	hgsc.bcm.edu	37	chr19	2877815	2877815	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tgcacgccggagggagaccgTatgagtgcaagcagtgtggg	18	8	0	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr19:2877815T>A	ENST00000307635.2	+	4	946	c.859T>A	c.(859-861)Tat>Aat	p.Y287N	ZNF556_ENST00000586426.1_Missense_Mutation_p.Y286N	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	287					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGGAGACCGTATGAGTGCAA	0.522																																					p.Y287N		Atlas-SNP	.											.	ZNF556	73	.	0			c.T859A						.						61	55	57					19																	2877815		2203	4300	6503	SO:0001583	missense	80032	exon4			AGACCGTATGAGT	BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"Zinc fingers, C2H2-type", "-"	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.859T>A	chr19.hg19:g.2877815T>A	ENSP00000302603:p.Tyr287Asn	167.0	0.0		131.0	42.0	NM_024967	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	hg19	CCDS12097.1	.	.	.	.	.	.	.	.	.	.	T	13.26	2.184038	0.38609	.	.	ENSG00000172000	ENST00000307635	T	0.15017	2.46	2.3	1.17	0.20885	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40619	0.1124	M	0.88310	2.945	0.09310	N	1	D	0.67145	0.996	D	0.67382	0.951	T	0.10989	-1.0606	9	0.87932	D	0	.	5.5901	0.17297	0.0:0.1618:0.0:0.8382	.	287	Q9HAH1	ZN556_HUMAN	N	287	ENSP00000302603:Y287N	ENSP00000302603:Y287N	Y	+	1	0	ZNF556	2828815	0.001000	0.12720	0.002000	0.10522	0.009000	0.06853	0.956000	0.29202	0.902000	0.36520	0.334000	0.21626	TAT	.	.		0.522	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967		A	2877815	T	A	2877815	3	1	3	1	0	0	0	0	1	0	0	0	18002	1638	57	4	873	4	ZNF556	19	2877815	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10		2877815	56251168	66	241										
SLC7A9	11136	hgsc.bcm.edu	37	chr19	33355006	33355008	+	In_Frame_Del	DEL	GGC	GGC	-													0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gggctcaggtactcacagatGgcggcggcggccaggcattt					rs140134166	byFrequency	TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	GGC	GGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr19:33355006_33355008delGGC	ENST00000023064.4	-	4	663_665	c.472_474delGCC	c.(472-474)gccdel	p.A158del	RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000590341.1_In_Frame_Del_p.A158del|SLC7A9_ENST00000587772.1_In_Frame_Del_p.A158del	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	158			A -> AA (in CSNU). {ECO:0000269|PubMed:11157794}.		amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)	p.A158T(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	ACTCACAGATGGCGGCGGCGGCC	0.606																																					p.158_159del	GBM(181;1335 2108 9644 44178 46689)	Atlas-Indel,Pindel	.											.	SLC7A9	78	.	1	Substitution - Missense(1)	large_intestine(1)	c.473_475del						.																																			SO:0001651	inframe_deletion	11136	exon4			.	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"Solute carriers"	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.472_474delGCC	chr19.hg19:g.33355015_33355017delGGC	ENSP00000023064:p.Ala158del	142.0	0.0		72.0	23.0	NM_001243036	B2R9A6	In_Frame_Del	DEL	ENST00000023064.4	hg19	CCDS12425.1																																																																																			.	.		0.606	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			-	33355008	GGC	-	33355006	7	5	3	1	0	1	0	1	0	0	0	0	14720	1335	47	0	1029	0	SLC7A9	19	33355006	In_Frame_Del	DEL	GGC	TCGA-2Y-A9GT-01A-11D-A382-10	30477191	33355006	25773977	67	242										
SLC8A2	6543	hgsc.bcm.edu	37	chr19	47960478	47960478	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	cctggatgcggtagaaggcgCggctcttctgctggtgcagc	16	11	2	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr19:47960478C>T	ENST00000236877.6	-	3	1444	c.1049G>A	c.(1048-1050)cGc>cAc	p.R350H	SLC8A2_ENST00000539381.1_Intron|SLC8A2_ENST00000542837.1_Missense_Mutation_p.R106H	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	350					blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		GTAGAAGGCGCGGCTCTTCTG	0.687																																					p.R350H		Atlas-SNP	.											.	SLC8A2	77	.	0			c.G1049A						.						6	5	6					19																	47960478		2038	3910	5948	SO:0001583	missense	6543	exon3			AAGGCGCGGCTCT	AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"Solute carriers"	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.1049G>A	chr19.hg19:g.47960478C>T	ENSP00000236877:p.Arg350His	106.0	0.0		62.0	13.0	NM_015063	B4DYQ9	Missense_Mutation	SNP	ENST00000236877.6	hg19	CCDS33065.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.677031	0.68042	.	.	ENSG00000118160	ENST00000391903;ENST00000236877;ENST00000542837	T;T	0.55760	0.69;0.5	3.69	3.69	0.42338	.	0.000000	0.85682	D	0.000000	T	0.76321	0.3971	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	T	0.82810	-0.0273	10	0.87932	D	0	.	14.3677	0.66817	0.0:1.0:0.0:0.0	.	178;350	E9PGS7;Q9UPR5	.;NAC2_HUMAN	H	178;350;106	ENSP00000236877:R350H;ENSP00000437536:R106H	ENSP00000236877:R350H	R	-	2	0	SLC8A2	52652290	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.349000	0.79376	1.914000	0.55421	0.313000	0.20887	CGC	.	.		0.687	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1			T	47960478	C	T	47960478	3	4	3	1	0	0	0	0	1	0	0	0	14722	768	27	1	1748	1	SLC8A2	19	47960478	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	14605472	47960478	11168505	68	243										
LILRB5	10990	hgsc.bcm.edu	37	chr19	54756264	54756264	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ggatgtcagcaactgggctgGccctgggggaggacacggga	19	9	1	0	rs34318516		TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr19:54756264G>T	ENST00000316219.5	-	11	1645	c.1538C>A	c.(1537-1539)gCc>gAc	p.A513D	LILRB5_ENST00000450632.1_Missense_Mutation_p.A505D|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000345866.6_Missense_Mutation_p.A414D|LILRB5_ENST00000449561.2_Missense_Mutation_p.A514D	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	513					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AACTGGGCTGGCCCTGGGGGA	0.587																																					p.A514D		Atlas-SNP	.											.	LILRB5	176	.	0			c.C1541A						.						91	90	91					19																	54756264		2203	4300	6503	SO:0001583	missense	10990	exon11			GGGCTGGCCCTGG	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1538C>A	chr19.hg19:g.54756264G>T	ENSP00000320390:p.Ala513Asp	100.0	0.0		84.0	14.0	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	hg19	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.034677	0.35893	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00479	7.16;7.12;7.15;7.14	2.08	0.93	0.19454	.	.	.	.	.	T	0.00695	0.0023	L	0.44542	1.39	0.09310	N	1	P;D;B;P	0.62365	0.799;0.991;0.003;0.751	B;P;B;B	0.62885	0.214;0.908;0.01;0.17	T	0.55970	-0.8056	9	0.72032	D	0.01	.	5.5071	0.16860	0.0:0.0:0.6715:0.3285	.	505;414;514;513	C9JMK7;O75023-2;O75023-3;O75023	.;.;.;LIRB5_HUMAN	D	513;505;514;414	ENSP00000320390:A513D;ENSP00000414225:A505D;ENSP00000406478:A514D;ENSP00000263430:A414D	ENSP00000320390:A513D	A	-	2	0	LILRB5	59448076	0.786000	0.28738	0.004000	0.12327	0.030000	0.12068	0.905000	0.28504	0.363000	0.24346	0.585000	0.79938	GCC	.	.		0.587	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			T	54756264	G	T	54756264	3	4	3	1	0	0	0	0	1	0	0	0	8803	1203	42	3	246	3	LILRB5	19	54756264	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10	6795786	54756264	4372719	69	244										
BRSK1	84446	hgsc.bcm.edu	37	chr19	55815039	55815039	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aactgttgtccctcagacccCccccggaagcgtgtggattc	10	15	1	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr19:55815039C>T	ENST00000309383.1	+	12	1408	c.1131C>T	c.(1129-1131)ccC>ccT	p.P377P	BRSK1_ENST00000590333.1_Silent_p.P393P|BRSK1_ENST00000326848.7_Silent_p.P72P	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	377					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		CCTCAGACCCCCCCCGGAAGC	0.582																																					p.P377P		Atlas-SNP	.											.	BRSK1	192	.	0			c.C1131T						.						56	65	62					19																	55815039		2203	4300	6503	SO:0001819	synonymous_variant	84446	exon12			AGACCCCCCCCGG	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1131C>T	chr19.hg19:g.55815039C>T		371.0	0.0		217.0	59.0	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	hg19	CCDS12921.1																																																																																			.	.		0.582	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430		T	55815039	C	T	55815039	2	4	3	1	0	0	0	0	0	0	0	1	1525	610	22	3		3	BRSK1	19	55815039	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	1058775	55815039	3313944	70	245										
ABHD12	26090	hgsc.bcm.edu	37	chr20	25319898	25319898	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tcagtttggcctgtattccaGgacatagtttgatgagaaat	10	6	1	2	rs546873766		TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr20:25319898G>A	ENST00000339157.5	-	2	553	c.281C>T	c.(280-282)cCt>cTt	p.P94L	ABHD12_ENST00000376542.3_Missense_Mutation_p.P94L	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	94					adult walking behavior (GO:0007628)|phosphatidylserine catabolic process (GO:0006660)|response to auditory stimulus (GO:0010996)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)	acylglycerol lipase activity (GO:0047372)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	12						CTGTATTCCAGGACATAGTTT	0.408													G|||	1	0.000199681	0	0	5008	,	,		19215	0.001		0	False		,,,				2504	0				p.P94L		Atlas-SNP	.											.	ABHD12	46	.	0			c.C281T						.						116	103	107					20																	25319898		2203	4300	6503	SO:0001583	missense	26090	exon2			ATTCCAGGACATA	AL117442	CCDS13172.1, CCDS42857.1	20p11.21	2007-04-24	2006-03-10	2006-03-10	ENSG00000100997	ENSG00000100997		"Abhydrolase domain containing"	15868	protein-coding gene	gene with protein product		613599	"chromosome 20 open reading frame 22"	C20orf22			Standard	NM_015600		Approved	DKFZP434P106, dJ965G21.2, BEM46L2, ABHD12A	uc002wuq.3	Q8N2K0	OTTHUMG00000032121	ENST00000339157.5:c.281C>T	chr20.hg19:g.25319898G>A	ENSP00000341408:p.Pro94Leu	390.0	0.0		346.0	91.0	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Missense_Mutation	SNP	ENST00000339157.5	hg19	CCDS42857.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.672359	0.88348	.	.	ENSG00000100997	ENST00000376542;ENST00000339157;ENST00000526543;ENST00000450393	T;T;T	0.29655	1.56;1.56;1.56	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.55577	0.1929	M	0.78456	2.415	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.992;0.996;0.998	T	0.50988	-0.8762	10	0.12430	T	0.62	.	18.2043	0.89850	0.0:0.0:1.0:0.0	.	49;94;94	Q5T712;Q8N2K0;Q8N2K0-2	.;ABD12_HUMAN;.	L	94;94;56;49	ENSP00000365725:P94L;ENSP00000341408:P94L;ENSP00000413311:P49L	ENSP00000341408:P94L	P	-	2	0	ABHD12	25267898	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.692000	0.74578	2.584000	0.87258	0.563000	0.77884	CCT	.	.		0.408	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600		A	25319898	G	A	25319898	3	1	3	1	0	0	0	0	1	0	0	0	76	1000	35	3	1025	3	ABHD12	20	25319898	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10		25319898	37705622	71	246										
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42164801	42164808	+	Frame_Shift_Del	DEL	TGCCTCTC	TGCCTCTC	-													0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	gcaagttcacagctcaccatTgcctctcaggctgcccactg							TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	TGCCTCTC	TGCCTCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr20:42164801_42164808delTGCCTCTC	ENST00000427442.2	+	18	2083_2090	c.1924_1931delTGCCTCTC	c.(1924-1932)tgcctctcafs	p.CLS642fs	L3MBTL1_ENST00000373135.3_Frame_Shift_Del_p.CLS574fs|L3MBTL1_ENST00000444063.1_Frame_Shift_Del_p.CLS574fs|L3MBTL1_ENST00000418998.1_Frame_Shift_Del_p.CLS642fs|L3MBTL1_ENST00000373134.1_Frame_Shift_Del_p.CLS579fs			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	574					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						AGCTCACCATTGCCTCTCAGGCTGCCCA	0.591																																					p.641_644del		Atlas-Indel,Pindel	.											.	L3MBTL1	105	.	0			c.1923_1930del						.																																			SO:0001589	frameshift_variant	26013	exon18			.	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.1924_1931delTGCCTCTC	chr20.hg19:g.42164801_42164808delTGCCTCTC	ENSP00000402107:p.Cys642fs	108.0	0.0		88.0	17.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Frame_Shift_Del	DEL	ENST00000427442.2	hg19	CCDS46602.2																																																																																			.	.		0.591	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		-	42164808	TGCCTCTC	-	42164801	7	5	3	1	0	1	0	1	0	0	0	0	8600	1812	63	0	1778	0	L3MBTL	20	42164801	Frame_Shift_Del	DEL	TGCCTCTC	TCGA-2Y-A9GT-01A-11D-A382-10	16844903	42164801	20860719	72	247										
KRTAP6-1	337966	hgsc.bcm.edu	37	chr21	31986208	31986208	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ggtgccatagtagtttccgtAgtagctgccacacatggtgt	12	9	0	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr21:31986208A>G	ENST00000329122.2	-	1	41	c.16T>C	c.(16-18)Tac>Cac	p.Y6H	KRTAP20-1_ENST00000334664.2_5'Flank	NM_181602.1	NP_853633.1	Q3LI64	KRA61_HUMAN	keratin associated protein 6-1	6						cytosol (GO:0005829)|intermediate filament (GO:0005882)				breast(2)|endometrium(1)|lung(7)	10						TAGTTTCCGTAGTAGCTGCCA	0.552																																					p.Y6H		Atlas-SNP	.											.	KRTAP6-1	21	.	0			c.T16C						.						193	187	189					21																	31986208		2203	4300	6503	SO:0001583	missense	337966	exon1			TTCCGTAGTAGCT	AP001708	CCDS13602.1	21q22.1	2006-03-13			ENSG00000184724	ENSG00000184724		"Keratin associated proteins"	18931	protein-coding gene	gene with protein product						12359730	Standard	NM_181602		Approved	KAP6.1, C21orf103	uc002yop.3	Q3LI64	OTTHUMG00000057788	ENST00000329122.2:c.16T>C	chr21.hg19:g.31986208A>G	ENSP00000332690:p.Tyr6His	126.0	0.0		114.0	40.0	NM_181602		Missense_Mutation	SNP	ENST00000329122.2	hg19	CCDS13602.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.551515	0.27739	.	.	ENSG00000184724	ENST00000329122;ENST00000399871	T	0.26957	1.7	5.24	4.09	0.47781	.	0.248600	0.20725	U	0.086839	T	0.20700	0.0498	.	.	.	0.24342	N	0.994951	B	0.06786	0.001	B	0.12837	0.008	T	0.18777	-1.0326	9	0.87932	D	0	.	9.4424	0.38677	0.9163:0.0:0.0837:0.0	.	6	Q3LI64	KRA61_HUMAN	H	6;4	ENSP00000332690:Y6H	ENSP00000332690:Y6H	Y	-	1	0	KRTAP6-1	30908079	0.950000	0.32346	0.851000	0.33527	0.854000	0.48673	1.556000	0.36288	1.132000	0.42129	0.523000	0.50628	TAC	.	.		0.552	KRTAP6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128240.2	NM_181602		G	31986208	A	G	31986208	3	3	3	1	0	0	0	0	1	0	0	0	8578	420	15	2	203	2	KRTAP6-1	21	31986208	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10		31986208	16143687	73	248										
SERPIND1	3053	hgsc.bcm.edu	37	chr22	21140349	21140349	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	aagaactacaatctagtggaGtccctgaagttgatggggat	12	6	1	3			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr22:21140349G>T	ENST00000215727.5	+	4	1504	c.1221G>T	c.(1219-1221)gaG>gaT	p.E407D	PI4KA_ENST00000572273.1_Intron|SERPIND1_ENST00000406799.1_Missense_Mutation_p.E407D|PI4KA_ENST00000466162.1_Intron|PI4KA_ENST00000255882.6_Intron	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	407					blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)|Sulodexide(DB06271)	ATCTAGTGGAGTCCCTGAAGT	0.483																																					p.E407D		Atlas-SNP	.											.	SERPIND1	92	.	0			c.G1221T						.						190	174	180					22																	21140349		2203	4300	6503	SO:0001583	missense	3053	exon4			AGTGGAGTCCCTG	M12849	CCDS13783.1	22q11.21	2014-02-18	2005-08-18		ENSG00000099937	ENSG00000099937		"Serine (or cysteine) peptidase inhibitors"	4838	protein-coding gene	gene with protein product	"heparin cofactor II"	142360	"serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1"	HCF2		1671335, 24172014	Standard	XM_005261597		Approved	HC-II, HLS2, HC2, D22S673	uc002ztb.1	P05546	OTTHUMG00000150755	ENST00000215727.5:c.1221G>T	chr22.hg19:g.21140349G>T	ENSP00000215727:p.Glu407Asp	167.0	0.0		93.0	33.0	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Missense_Mutation	SNP	ENST00000215727.5	hg19	CCDS13783.1	.	.	.	.	.	.	.	.	.	.	G	12.23	1.875187	0.33162	.	.	ENSG00000099937	ENST00000215727;ENST00000406799	D;D	0.87571	-2.27;-2.27	5.28	1.85	0.25348	Serpin domain (3);	0.346134	0.33916	N	0.004427	T	0.70116	0.3187	N	0.17723	0.515	0.39723	D	0.971491	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.56177	-0.8022	10	0.20519	T	0.43	.	0.9117	0.01296	0.2544:0.1241:0.4104:0.2111	.	407;407	Q8IVC0;P05546	.;HEP2_HUMAN	D	407	ENSP00000215727:E407D;ENSP00000384050:E407D	ENSP00000215727:E407D	E	+	3	2	SERPIND1	19470349	0.385000	0.25172	1.000000	0.80357	0.887000	0.51463	0.352000	0.20113	0.801000	0.34066	0.655000	0.94253	GAG	.	.		0.483	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185		T	21140349	G	T	21140349	3	4	3	1	0	0	0	0	1	0	0	0	14125	1020	36	3	1231	3	SERPIND1	22	21140349	Missense_Mutation	SNP	G	TCGA-2Y-A9GT-01A-11D-A382-10		21140349	30164217	74	249										
ZNF280B	140883	hgsc.bcm.edu	37	chr22	22842186	22842186	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tggatgctacatccactgatCctggctgaagaggttccagt	11	10	0	3			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr22:22842186C>A	ENST00000406426.1	-	4	2280	c.1538G>T	c.(1537-1539)gGa>gTa	p.G513V	ZNF280B_ENST00000360412.2_Missense_Mutation_p.G513V			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	513					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G513E(1)		autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		ATCCACTGATCCTGGCTGAAG	0.408																																					p.G513V		Atlas-SNP	.											ZNF280B,NS,carcinoma,0,1	ZNF280B	67	.	1	Substitution - Missense(1)	kidney(1)	c.G1538T						.						144	131	135					22																	22842186		2203	4300	6503	SO:0001583	missense	140883	exon4			ACTGATCCTGGCT	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"zinc finger protein 279", "suppressor of hairy wing homolog 2 (Drosophila)"	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.1538G>T	chr22.hg19:g.22842186C>A	ENSP00000385998:p.Gly513Val	99.0	0.0		89.0	26.0	NM_080764		Missense_Mutation	SNP	ENST00000406426.1	hg19	CCDS13799.1	.	.	.	.	.	.	.	.	.	.	C	8.185	0.794612	0.16327	.	.	ENSG00000198477	ENST00000406426;ENST00000360412	T;T	0.03386	3.95;3.95	4.32	-0.452	0.12205	.	.	.	.	.	T	0.07728	0.0194	L	0.46157	1.445	0.21220	N	0.999759	D	0.64830	0.994	P	0.61070	0.883	T	0.30794	-0.9966	9	0.45353	T	0.12	-0.0804	4.1382	0.10181	0.0:0.412:0.1715:0.4165	.	513	Q86YH2	Z280B_HUMAN	V	513	ENSP00000385998:G513V;ENSP00000353586:G513V	ENSP00000353586:G513V	G	-	2	0	ZNF280B	21172186	0.000000	0.05858	0.149000	0.22428	0.155000	0.21991	-0.325000	0.07976	0.019000	0.15079	-0.345000	0.07892	GGA	.	.		0.408	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764		A	22842186	C	A	22842186	3	1	3	1	0	0	0	0	1	0	0	0	17830	855	30	3	97	3	ZNF280B	22	22842186	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	1701837	22842186	28462380	75	250										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46776800	46776800	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	cgggagcggagccccctcgcTgtacaccagcgtgctcacca	12	17	1	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr22:46776800T>C	ENST00000262738.3	-	22	7140	c.7141A>G	c.(7141-7143)Agc>Ggc	p.S2381G		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2381					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GCCCCCTCGCTGTACACCAGC	0.617																																					p.S2381G		Atlas-SNP	.											.	CELSR1	242	.	0			c.A7141G						.						39	40	40					22																	46776800		2203	4300	6503	SO:0001583	missense	9620	exon22			CCTCGCTGTACAC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.7141A>G	chr22.hg19:g.46776800T>C	ENSP00000262738:p.Ser2381Gly	103.0	0.0		70.0	17.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	T	10.62	1.400084	0.25291	.	.	ENSG00000075275	ENST00000262738	T	0.10960	2.82	4.28	1.92	0.25849	Domain of unknown function DUF3497 (1);	0.123909	0.52532	U	0.000079	T	0.16727	0.0402	M	0.66939	2.045	0.80722	D	1	P;P	0.51933	0.949;0.542	P;B	0.49922	0.626;0.309	T	0.05115	-1.0905	10	0.25106	T	0.35	.	10.2336	0.43268	0.0:0.0:0.3183:0.6817	.	702;2381	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	G	2381	ENSP00000262738:S2381G	ENSP00000262738:S2381G	S	-	1	0	CELSR1	45155464	0.952000	0.32445	0.330000	0.25442	0.582000	0.36321	1.028000	0.30128	0.516000	0.28340	0.260000	0.18958	AGC	.	.		0.617	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		C	46776800	T	C	46776800	3	2	3	1	0	0	0	0	1	0	0	0	3223	1580	55	2	1959	2	CELSR1	22	46776800	Missense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	23934614	46776800	4527766	76	251										
SAPS2	9701	hgsc.bcm.edu	37	chr22	50874856	50874856	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ggaggagacgctgacggagaCgaaccgcaggaacactgtgg	17	9	0	3			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chr22:50874856C>A	ENST00000216061.5	+	15	1947	c.1577C>A	c.(1576-1578)aCg>aAg	p.T526K	PPP6R2_ENST00000359139.3_Missense_Mutation_p.T526K|PPP6R2_ENST00000395741.3_Missense_Mutation_p.T527K|PPP6R2_ENST00000395744.3_Missense_Mutation_p.T526K			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	526						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						CTGACGGAGACGAACCGCAGG	0.692																																					p.T527K		Atlas-SNP	.											.	PPP6R2	71	.	0			c.C1580A						.						54	35	41					22																	50874856		2193	4291	6484	SO:0001583	missense	9701	exon14			CGGAGACGAACCG	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	19253	protein-coding gene	gene with protein product		610877	"KIAA0685", "SAPS domain family, member 2"	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.1577C>A	chr22.hg19:g.50874856C>A	ENSP00000216061:p.Thr526Lys	451.0	0.0		265.0	63.0	NM_001242899	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	hg19		.	.	.	.	.	.	.	.	.	.	C	24.0	4.479350	0.84747	.	.	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.38887	1.19;1.19;1.19;1.11	4.92	4.92	0.64577	.	0.049728	0.85682	D	0.000000	T	0.67804	0.2932	M	0.84511	2.7	0.51012	D	0.9999	D;D;D;D;D;D	0.76494	0.999;0.998;0.998;0.988;0.998;0.996	D;D;D;D;D;D	0.72625	0.976;0.973;0.978;0.956;0.963;0.972	T	0.74444	-0.3663	10	0.87932	D	0	-15.805	15.6017	0.76631	0.0:1.0:0.0:0.0	.	85;526;526;527;526;526	F2Z3M7;O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;.;PP6R2_HUMAN;.;.;.	K	526;527;526;526	ENSP00000352051:T526K;ENSP00000379090:T527K;ENSP00000379093:T526K;ENSP00000216061:T526K	ENSP00000216061:T526K	T	+	2	0	PPP6R2	49221722	1.000000	0.71417	0.985000	0.45067	0.764000	0.43329	4.428000	0.59894	2.285000	0.76669	0.561000	0.74099	ACG	.	.		0.692	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		A	50874856	C	A	50874856	3	1	3	1	0	0	0	0	1	0	0	0	13852	536	19	1	1623	1	SAPS2	22	50874856	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	4098056	50874856	429710	77	252										
ZNF645	158506	hgsc.bcm.edu	37	chrX	22291149	22291149	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tgaacaagaatgtgaatataAcaaagaagggaagtactact	9	4	0	4			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chrX:22291149A>G	ENST00000323684.1	+	1	85	c.41A>G	c.(40-42)aAc>aGc	p.N14S		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	14					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						TGTGAATATAACAAAGAAGGG	0.358																																					p.N14S		Atlas-SNP	.											.	ZNF645	67	.	0			c.A41G						.						83	81	82					X																	22291149		2203	4300	6503	SO:0001583	missense	158506	exon1			AATATAACAAAGA	AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.41A>G	chrX.hg19:g.22291149A>G	ENSP00000323348:p.Asn14Ser	327.0	0.0		201.0	111.0	NM_152577	A0AV29|A0AV31|E3SBK4|Q6DJY9	Missense_Mutation	SNP	ENST00000323684.1	hg19	CCDS14205.1	.	.	.	.	.	.	.	.	.	.	A	10.25	1.297863	0.23650	.	.	ENSG00000175809	ENST00000323684	T	0.30182	1.54	3.15	1.93	0.25924	.	0.146969	0.44483	U	0.000441	T	0.15652	0.0377	N	0.17474	0.49	0.09310	N	1	P	0.46512	0.879	B	0.42827	0.399	T	0.07635	-1.0762	10	0.32370	T	0.25	.	3.3512	0.07153	0.52:0.2417:0.0:0.2383	.	14	Q8N7E2	ZN645_HUMAN	S	14	ENSP00000323348:N14S	ENSP00000323348:N14S	N	+	2	0	ZNF645	22201070	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	1.226000	0.32563	0.434000	0.26340	0.430000	0.28490	AAC	.	.		0.358	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577		G	22291149	A	G	22291149	3	3	3	1	0	0	0	0	1	0	0	0	18076	43	2	2	43	2	ZNF645	23	22291149	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10		22291149	132979411	78	253										
CXorf36	79742	hgsc.bcm.edu	37	chrX	45017000	45017000	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	agttgacagccagcgtgtagAgcaggcgcagcttgtcacgg	15	10	1	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chrX:45017000A>G	ENST00000398000.2	-	3	706	c.632T>C	c.(631-633)cTc>cCc	p.L211P	CXorf36_ENST00000477281.1_Intron	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	211						extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						CAGCGTGTAGAGCAGGCGCAG	0.617																																					p.L211P		Atlas-SNP	.											.	CXorf36	53	.	0			c.T632C						.						55	50	51					X																	45017000		1567	3578	5145	SO:0001583	missense	79742	exon3			GTGTAGAGCAGGC	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.632T>C	chrX.hg19:g.45017000A>G	ENSP00000381086:p.Leu211Pro	92.0	0.0		59.0	32.0	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Missense_Mutation	SNP	ENST00000398000.2	hg19	CCDS48096.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.304888	0.81247	.	.	ENSG00000147113	ENST00000398000	T	0.39997	1.05	4.8	4.8	0.61643	.	0.000000	0.56097	D	0.000026	T	0.64886	0.2639	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70066	-0.4974	10	0.87932	D	0	.	13.5808	0.61901	1.0:0.0:0.0:0.0	.	211	Q9H7Y0	CX036_HUMAN	P	211	ENSP00000381086:L211P	ENSP00000381086:L211P	L	-	2	0	CXorf36	44901944	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	8.305000	0.89960	1.580000	0.49851	0.350000	0.21858	CTC	.	.		0.617	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689		G	45017000	A	G	45017000	3	3	3	1	0	0	0	0	1	0	0	0	4108	304	11	2	681	2	CXorf36	23	45017000	Missense_Mutation	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10	22725851	45017000	110253560	79	254										
CLCN5	1184	hgsc.bcm.edu	37	chrX	49840465	49840465	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	atcaggttcgttagctggttTgatagacatctctgctcatt	9	8	3	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chrX:49840465T>A	ENST00000307367.2	+	4	512	c.221T>A	c.(220-222)tTg>tAg	p.L74*	CLCN5_ENST00000376088.3_Nonsense_Mutation_p.L144*|CLCN5_ENST00000376091.3_Nonsense_Mutation_p.L144*|CLCN5_ENST00000376108.3_Nonsense_Mutation_p.L74*			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	74					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					TTAGCTGGTTTGATAGACATC	0.428																																					p.L144X		Atlas-SNP	.											.	CLCN5	137	.	0			c.T431A						.						124	113	116					X																	49840465		2203	4300	6503	SO:0001587	stop_gained	1184	exon7			CTGGTTTGATAGA	X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.221T>A	chrX.hg19:g.49840465T>A	ENSP00000304257:p.Leu74*	101.0	0.0		102.0	51.0	NM_001127898	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Nonsense_Mutation	SNP	ENST00000307367.2	hg19	CCDS14328.1	.	.	.	.	.	.	.	.	.	.	T	39	7.431091	0.98279	.	.	ENSG00000171365	ENST00000376088;ENST00000376091;ENST00000376108;ENST00000307367	.	.	.	5.27	5.27	0.74061	.	0.199991	0.43579	D	0.000545	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.003	13.4109	0.60942	0.0:0.0:0.0:1.0	.	.	.	.	X	144;144;74;74	.	ENSP00000304257:L74X	L	+	2	0	CLCN5	49727205	0.999000	0.42202	0.999000	0.59377	0.984000	0.73092	2.938000	0.48987	1.878000	0.54408	0.430000	0.28490	TTG	.	.		0.428	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			A	49840465	T	A	49840465	4	1	3	1	0	0	0	0	0	1	0	0	3468	1821	63	4	449	4	CLCN5	23	49840465	Nonsense_Mutation	SNP	T	TCGA-2Y-A9GT-01A-11D-A382-10	4823465	49840465	105430095	80	255										
FGD1	2245	hgsc.bcm.edu	37	chrX	54496732	54496732	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	tgggcaccttctcaccgtccCggggcccaggagccagcaga	13	16	1	1			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chrX:54496732C>A	ENST00000375135.3	-	4	1551	c.818G>T	c.(817-819)cGg>cTg	p.R273L		NM_004463.2	NP_004454.2	P98174	FGD1_HUMAN	FYVE, RhoGEF and PH domain containing 1	273	Pro-rich.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						CTCACCGTCCCGGGGCCCAGG	0.662																																					p.R273L		Atlas-SNP	.											.	FGD1	99	.	0			c.G818T						.						31	25	27					X																	54496732		2198	4298	6496	SO:0001583	missense	2245	exon4			CCGTCCCGGGGCC	U11690	CCDS14359.1	Xp11.21	2013-01-10	2008-08-01		ENSG00000102302	ENSG00000102302		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	3663	protein-coding gene	gene with protein product		300546	"faciogenital dysplasia (Aarskog-Scott syndrome)"	FGDY			Standard	NM_004463		Approved	ZFYVE3	uc004dtg.3	P98174	OTTHUMG00000021627	ENST00000375135.3:c.818G>T	chrX.hg19:g.54496732C>A	ENSP00000364277:p.Arg273Leu	88.0	0.0		60.0	4.0	NM_004463	Q5H999|Q8N4D9	Missense_Mutation	SNP	ENST00000375135.3	hg19	CCDS14359.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.952697	0.34471	.	.	ENSG00000102302	ENST00000375135	T	0.78003	-1.14	4.33	3.46	0.39613	.	0.000000	0.43110	D	0.000611	T	0.52757	0.1754	N	0.08118	0	0.34493	D	0.705188	B;P	0.35242	0.166;0.492	B;B	0.30029	0.02;0.11	T	0.60742	-0.7203	10	0.30078	T	0.28	-10.4729	8.1452	0.31108	0.0:0.7969:0.0:0.2031	.	31;273	B4DS99;P98174	.;FGD1_HUMAN	L	273	ENSP00000364277:R273L	ENSP00000364277:R273L	R	-	2	0	FGD1	54513457	0.961000	0.32948	1.000000	0.80357	0.855000	0.48748	2.565000	0.45939	1.186000	0.42985	0.436000	0.28706	CGG	.	.		0.662	FGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056801.1	NM_004463		A	54496732	C	A	54496732	3	1	3	1	0	0	0	0	1	0	0	0	5840	652	23	1	2127	1	FGD1	23	54496732	Missense_Mutation	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	4656267	54496732	100773828	81	256										
TAF1	6872	hgsc.bcm.edu	37	chrX	70643062	70643062	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ttcattctggacaacattgtCacccagaaaatgatggcagt	8	9	3	2			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chrX:70643062C>T	ENST00000373790.4	+	30	4596	c.4545C>T	c.(4543-4545)gtC>gtT	p.V1515V	TAF1_ENST00000276072.3_Silent_p.V1536V|TAF1_ENST00000423759.1_Silent_p.V1536V|TAF1_ENST00000449580.1_Silent_p.V1515V|TAF1_ENST00000461764.1_3'UTR	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1515	Interaction with ASF1A and ASF1B.|Protein kinase 2.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				ACAACATTGTCACCCAGAAAA	0.438																																					p.V1536V		Atlas-SNP	.											.	TAF1	439	.	0			c.C4608T						.						154	117	129					X																	70643062		2203	4300	6503	SO:0001819	synonymous_variant	6872	exon30			CATTGTCACCCAG		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.4545C>T	chrX.hg19:g.70643062C>T		97.0	0.0		93.0	38.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	9.798	1.179681	0.21787	.	.	ENSG00000147133	ENST00000437147	.	.	.	4.75	2.98	0.34508	.	.	.	.	.	T	0.54029	0.1833	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44174	-0.9345	4	.	.	.	.	5.6669	0.17700	0.0:0.6168:0.1381:0.2451	.	.	.	.	L	170	.	.	S	+	2	0	TAF1	70559787	0.995000	0.38212	1.000000	0.80357	0.990000	0.78478	0.379000	0.20585	0.386000	0.24997	0.544000	0.68410	TCA	.	.		0.438	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		T	70643062	C	T	70643062	2	4	3	1	0	0	0	0	0	0	0	1	15528	813	29	3		3	TAF1	23	70643062	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	16146330	70643062	84627498	82	257										
ARMCX6	54470	hgsc.bcm.edu	37	chrX	100871590	100871590	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	agtcctgccgccatccaaccCacttcccgagcccggcccat	7	21	0	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chrX:100871590C>A	ENST00000361910.4	-	3	365	c.21G>T	c.(19-21)gtG>gtT	p.V7V	ARMCX6_ENST00000497931.1_Intron|ARMCX6_ENST00000538627.1_Silent_p.V7V|ARMCX6_ENST00000539247.1_Silent_p.V7V	NM_019007.3	NP_061880.2	Q7L4S7	ARMX6_HUMAN	armadillo repeat containing, X-linked 6	7						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|liver(2)|lung(3)	9						CCATCCAACCCACTTCCCGAG	0.592																																					p.V7V		Atlas-SNP	.											.	ARMCX6	21	.	0			c.G21T						.						55	47	50					X																	100871590		2203	4300	6503	SO:0001819	synonymous_variant	54470	exon4			CCAACCCACTTCC	BC007677	CCDS14488.1	Xq21.33-q22.3	2014-03-21			ENSG00000198960	ENSG00000198960		"Armadillo repeat containing"	26094	protein-coding gene	gene with protein product						16221301, 22569362	Standard	NM_001184768		Approved	FLJ20811, GASP10	uc004ehy.3	Q7L4S7	OTTHUMG00000022034	ENST00000361910.4:c.21G>T	chrX.hg19:g.100871590C>A		96.0	0.0		120.0	49.0	NM_001184768	Q9NWJ3	Silent	SNP	ENST00000361910.4	hg19	CCDS14488.1																																																																																			.	.		0.592	ARMCX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057562.1	NM_019007		A	100871590	C	A	100871590	2	1	3	1	0	0	0	0	0	0	0	1	963	581	21	3		3	ARMCX6	23	100871590	Silent	SNP	C	TCGA-2Y-A9GT-01A-11D-A382-10	30228528	100871590	54398970	83	258										
SLC6A14	11254	hgsc.bcm.edu	37	chrX	115577963	115577963	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.20067567567568	1.37220077220077	1.15264864864865	0.485714285714286	1	0	ctactcatcctgttagtacgAggtgcaactctggagggtgc	12	10	2	0			TCGA-2Y-A9GT-01A-11D-A382-10	TCGA-2Y-A9GT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38c5baf0-5376-42d2-b545-89f5c606b05e	76f29a85-4ade-4630-b69b-5a23a1c16628	g.chrX:115577963A>G	ENST00000371900.4	+	7	934	c.846A>G	c.(844-846)cgA>cgG	p.R282R		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	282					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TGTTAGTACGAGGTGCAACTC	0.363																																					p.R282R		Atlas-SNP	.											.	SLC6A14	56	.	0			c.A846G						.						107	105	106					X																	115577963		2203	4300	6503	SO:0001819	synonymous_variant	11254	exon7			AGTACGAGGTGCA	AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"Solute carriers"	11047	protein-coding gene	gene with protein product		300444	"solute carrier family 6 (neurotransmitter transporter), member 14"			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.846A>G	chrX.hg19:g.115577963A>G		190.0	0.0		249.0	101.0	NM_007231	Q5H942	Silent	SNP	ENST00000371900.4	hg19	CCDS14570.1																																																																																			.	.		0.363	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			G	115577963	A	G	115577963	2	3	3	1	0	0	0	0	0	0	0	1	14692	291	11	2		2	SLC6A14	23	115577963	Silent	SNP	A	TCGA-2Y-A9GT-01A-11D-A382-10	14706373	115577963	39692597	84	259										
CCDC27	148870	hgsc.bcm.edu	37	chr1	3669193	3669193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gcctcatgttacctaaggagGccagcccatctcagaggcac	10	14	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:3669193G>A	ENST00000294600.2	+	1	232	c.148G>A	c.(148-150)Gcc>Acc	p.A50T		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	50										breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		ACCTAAGGAGGCCAGCCCATC	0.602																																					p.A50T		Atlas-SNP	.											.	CCDC27	79	.	0			c.G148A						.						142	119	127					1																	3669193		2203	4300	6503	SO:0001583	missense	148870	exon1			AAGGAGGCCAGCC		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.148G>A	chr1.hg19:g.3669193G>A	ENSP00000294600:p.Ala50Thr	182.0	0.0		111.0	19.0	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	hg19	CCDS50.1	.	.	.	.	.	.	.	.	.	.	G	8.945	0.966813	0.18659	.	.	ENSG00000162592	ENST00000294600	T	0.18810	2.19	3.95	-4.29	0.03721	.	2.345970	0.01967	N	0.043767	T	0.11879	0.0289	N	0.19112	0.55	0.09310	N	1	B	0.17268	0.021	B	0.16289	0.015	T	0.18304	-1.0341	10	0.49607	T	0.09	-1.5701	1.7556	0.02981	0.4643:0.1403:0.2525:0.1428	.	50	Q2M243	CCD27_HUMAN	T	50	ENSP00000294600:A50T	ENSP00000294600:A50T	A	+	1	0	CCDC27	3659053	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.140000	0.10342	-0.943000	0.03691	0.650000	0.86243	GCC	.	.		0.602	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492		A	3669193	G	A	3669193	3	1	4	1	0	0	0	0	1	0	0	0	2803	1203	42	3	150	3	CCDC27	1	3669193	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10		3669193	245581428	1	260										
AJAP1	55966	hgsc.bcm.edu	37	chr1	4772364	4772364	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ctccgcggtggccggtggggCcccggagcagcaggccctcc	17	17	0	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:4772364C>A	ENST00000378191.4	+	2	815	c.434C>A	c.(433-435)gCc>gAc	p.A145D	AJAP1_ENST00000378190.3_Missense_Mutation_p.A145D	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	145					cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		GCCGGTGGGGCCCCGGAGCAG	0.697																																					p.A145D		Atlas-SNP	.											.	AJAP1	68	.	0			c.C434A						.						6	7	7					1																	4772364		2080	4125	6205	SO:0001583	missense	55966	exon2			GTGGGGCCCCGGA	AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"transmembrane protein SHREW1"	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.434C>A	chr1.hg19:g.4772364C>A	ENSP00000367433:p.Ala145Asp	134.0	0.0		64.0	29.0	NM_018836	Q9Y229	Missense_Mutation	SNP	ENST00000378191.4	hg19	CCDS54.1	.	.	.	.	.	.	.	.	.	.	C	7.916	0.737537	0.15574	.	.	ENSG00000196581	ENST00000378190;ENST00000378191	T;T	0.49432	0.78;0.78	5.37	1.04	0.20106	.	1.811680	0.02513	N	0.091777	T	0.31263	0.0791	N	0.14661	0.345	0.09310	N	1	P	0.36535	0.557	B	0.30179	0.112	T	0.34179	-0.9839	10	0.56958	D	0.05	-2.9129	8.7351	0.34523	0.0:0.3558:0.5495:0.0947	.	145	Q9UKB5	AJAP1_HUMAN	D	145	ENSP00000367432:A145D;ENSP00000367433:A145D	ENSP00000367432:A145D	A	+	2	0	AJAP1	4672224	0.054000	0.20591	0.002000	0.10522	0.072000	0.16883	1.577000	0.36515	0.211000	0.20683	0.563000	0.77884	GCC	.	.		0.697	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836		A	4772364	C	A	4772364	3	1	4	1	0	0	0	0	1	0	0	0	438	739	26	3	440	3	AJAP1	1	4772364	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	1103171	4772364	244478257	2	261										
KAZ	23254	hgsc.bcm.edu	37	chr1	15441094	15441094	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	caggctggaacagtgccgtcTggaaggctacaacagcctgg	14	11	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:15441094T>A	ENST00000376030.2	+	15	2585	c.2291T>A	c.(2290-2292)cTg>cAg	p.L764Q	TMEM51-AS1_ENST00000310916.3_RNA	NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	764					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						CAGTGCCGTCTGGAAGGCTAC	0.547																																					p.L764Q		Atlas-SNP	.											.	KAZN	57	.	0			c.T2291A						.						45	37	39					1																	15441094		2203	4300	6503	SO:0001583	missense	23254	exon15			GCCGTCTGGAAGG	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.2291T>A	chr1.hg19:g.15441094T>A	ENSP00000365198:p.Leu764Gln	252.0	0.0		168.0	41.0	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	hg19	CCDS152.2	.	.	.	.	.	.	.	.	.	.	T	20.6	4.012698	0.75161	.	.	ENSG00000189337	ENST00000376030	T	0.20463	2.07	5.41	5.41	0.78517	.	0.000000	0.39083	N	0.001477	T	0.29850	0.0746	N	0.19112	0.55	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.08086	-1.0739	10	0.59425	D	0.04	-17.6005	11.8245	0.52259	0.0:0.0:0.0:1.0	.	764	Q674X7	KAZRN_HUMAN	Q	764	ENSP00000365198:L764Q	ENSP00000365198:L764Q	L	+	2	0	KAZN	15313681	0.983000	0.35010	0.997000	0.53966	0.994000	0.84299	2.402000	0.44521	2.037000	0.60232	0.533000	0.62120	CTG	.	.		0.547	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		A	15441094	T	A	15441094	3	1	4	1	0	0	0	0	1	0	0	0	7997	1580	55	4	2605	4	KAZ	1	15441094	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	10668730	15441094	233809527	3	262										
PDIK1L	149420	hgsc.bcm.edu	37	chr1	26448455	26448455	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gttgtccaggaaacccaatcGtaaaactaacaccagcttca	6	12	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:26448455G>C	ENST00000374271.4	+	4	700	c.413G>C	c.(412-414)cGt>cCt	p.R138P	PDIK1L_ENST00000374269.1_Missense_Mutation_p.R138P	NM_001243532.1|NM_001243533.1|NM_152835.4	NP_001230461.1|NP_001230462.1|NP_690048.1	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like	138	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)		AAACCCAATCGTAAAACTAAC	0.438																																					p.R138P		Atlas-SNP	.											.	PDIK1L	19	.	0			c.G413C						.						114	116	115					1																	26448455		2203	4300	6503	SO:0001583	missense	149420	exon3			CCAATCGTAAAAC	AF411102	CCDS274.1	1p35.1	2008-02-05			ENSG00000175087	ENSG00000175087			18981	protein-coding gene	gene with protein product		610785				14631099	Standard	NM_152835		Approved	CLIK1L	uc009vsb.3	Q8N165	OTTHUMG00000007511	ENST00000374271.4:c.413G>C	chr1.hg19:g.26448455G>C	ENSP00000363389:p.Arg138Pro	114.0	0.0		95.0	4.0	NM_001243532	B2R777|D3DPK2|Q5T2I0|Q8NDB3	Missense_Mutation	SNP	ENST00000374271.4	hg19	CCDS274.1	.	.	.	.	.	.	.	.	.	.	G	5.975	0.363901	0.11296	.	.	ENSG00000175087	ENST00000444713;ENST00000374271;ENST00000374269	T;T;T	0.21031	2.03;2.03;2.03	5.96	5.96	0.96718	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.12347	0.0300	N	0.04018	-0.295	0.42200	D	0.991765	B	0.09022	0.002	B	0.14023	0.01	T	0.25117	-1.0141	10	0.15952	T	0.53	-14.6606	20.0112	0.97449	0.0:0.0:1.0:0.0	.	138	Q8N165	PDK1L_HUMAN	P	138	ENSP00000406510:R138P;ENSP00000363389:R138P;ENSP00000363387:R138P	ENSP00000363387:R138P	R	+	2	0	PDIK1L	26321042	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.816000	0.75247	2.826000	0.97356	0.655000	0.94253	CGT	.	.		0.438	PDIK1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019752.1	NM_152835		C	26448455	G	C	26448455	3	2	4	1	0	0	0	0	1	0	0	0	11682	1145	40	4	419	4	PDIK1L	1	26448455	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	11007361	26448455	222802166	4	263										
CCDC23	374969	hgsc.bcm.edu	37	chr1	43273173	43273173	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ctctgttgagggcatagatcTgaatgagagaaagagataca	12	5	2	6			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:43273173T>G	ENST00000372521.4	-	3	213		c.e3-2		CCDC23_ENST00000372522.1_Splice_Site|CCDC23_ENST00000537227.1_Splice_Site	NM_199342.3	NP_955374.1	Q8N300	CCD23_HUMAN	coiled-coil domain containing 23						negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein ubiquitination (GO:0031397)|protein secretion (GO:0009306)	apical part of cell (GO:0045177)				large_intestine(1)	1	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GGCATAGATCTGAATGAGAGA	0.463																																					.		Atlas-SNP	.											.	CCDC23	3	.	0			c.115-2A>C						.						114	112	113					1																	43273173		2203	4300	6503	SO:0001630	splice_region_variant	374969	exon4			TAGATCTGAATGA	AL512353, CAH72714	CCDS474.1	1p34.2	2008-02-05			ENSG00000177868	ENSG00000177868			29204	protein-coding gene	gene with protein product							Standard	NM_199342		Approved	MGC45441	uc001cib.2	Q8N300	OTTHUMG00000007566	ENST00000372521.4:c.115-2A>C	chr1.hg19:g.43273173T>G		58.0	0.0		26.0	7.0	NM_199342	A8K5P1|D3DPW7	Splice_Site	SNP	ENST00000372521.4	hg19	CCDS474.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.033051	0.75504	.	.	ENSG00000177868	ENST00000372522;ENST00000372521;ENST00000537227	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6933	0.56988	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CCDC23	43045760	1.000000	0.71417	0.997000	0.53966	0.905000	0.53344	5.674000	0.68117	2.239000	0.73571	0.533000	0.62120	.	.	.		0.463	CCDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019997.1	NM_199342	Intron	G	43273173	T	G	43273173	5	3	4	1	0	0	0	0	0	0	1	0	2800	1594	55	5	91	5	CCDC23	1	43273173	Splice_Site	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	16824718	43273173	205977448	5	264										
SLC1A7	6512	hgsc.bcm.edu	37	chr1	53571448	53571448	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gttggctgggaacatgttccTaggaagagaatcagcaattg	13	6	1	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:53571448T>C	ENST00000371494.4	-	4	559		c.e4-2			NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7						dicarboxylic acid transport (GO:0006835)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Colorectal(1306;0.234)		AACATGTTCCTAGGAAGAGAA	0.572																																					.	NSCLC(128;80 1811 21245 38490 51715)	Atlas-SNP	.											.	SLC1A7	65	.	0			c.432-2A>G						.						145	135	139					1																	53571448		2203	4300	6503	SO:0001630	splice_region_variant	6512	exon5			TGTTCCTAGGAAG	U76362	CCDS574.1, CCDS72796.1, CCDS72797.1, CCDS72798.1	1p32.3	2013-05-22			ENSG00000162383	ENSG00000162383		"Solute carriers"	10945	protein-coding gene	gene with protein product		604471				9108121	Standard	NM_001287597		Approved	EAAT5	uc001cuy.3	O00341	OTTHUMG00000008937	ENST00000371494.4:c.432-2A>G	chr1.hg19:g.53571448T>C		149.0	0.0		85.0	17.0	NM_006671	Q5VVZ0|Q969Z8|Q9BW45	Splice_Site	SNP	ENST00000371494.4	hg19	CCDS574.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.397287	0.62177	.	.	ENSG00000162383	ENST00000371494	.	.	.	4.46	4.46	0.54185	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8011	0.63202	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC1A7	53344036	1.000000	0.71417	0.890000	0.34922	0.721000	0.41392	7.570000	0.82390	1.649000	0.50652	0.329000	0.21502	.	.	.		0.572	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1	NM_006671	Intron	C	53571448	T	C	53571448	5	2	4	1	0	0	0	0	0	0	1	0	14452	1536	53	2	1284	2	SLC1A7	1	53571448	Splice_Site	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	10298275	53571448	195679173	6	265										
SGIP1	84251	hgsc.bcm.edu	37	chr1	67148034	67148034	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ccggacctggctcgggccctGgtccggggaccaccagtggt	16	15	0	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:67148034G>A	ENST00000371037.4	+	15	1374	c.1297G>A	c.(1297-1299)Ggt>Agt	p.G433S	SGIP1_ENST00000237247.6_Missense_Mutation_p.G437S|SGIP1_ENST00000371039.1_Intron|SGIP1_ENST00000371035.3_Intron|SGIP1_ENST00000371036.3_Intron	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	433	Pro-rich.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021)	AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	71						CTCGGGCCCTGGTCCGGGGAC	0.592																																					p.G433S		Atlas-SNP	.											.	SGIP1	272	.	0			c.G1297A						.						106	123	117					1																	67148034		2195	4281	6476	SO:0001583	missense	84251	exon15			GGCCCTGGTCCGG	AL136561	CCDS30744.1	1p31.3	2008-02-05			ENSG00000118473	ENSG00000118473			25412	protein-coding gene	gene with protein product		611540				11230166	Standard	NM_032291		Approved	DKFZp761D221	uc001dcr.3	Q9BQI5	OTTHUMG00000009161	ENST00000371037.4:c.1297G>A	chr1.hg19:g.67148034G>A	ENSP00000360076:p.Gly433Ser	189.0	0.0		192.0	40.0	NM_032291	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Missense_Mutation	SNP	ENST00000371037.4	hg19	CCDS30744.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.205537	0.39003	.	.	ENSG00000118473	ENST00000237247;ENST00000371038;ENST00000407289;ENST00000371037	T;T	0.03468	3.92;4.13	5.39	5.39	0.77823	.	0.266825	0.43416	D	0.000579	T	0.06050	0.0157	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.986	T	0.56226	-0.8014	10	0.13470	T	0.59	-9.9881	18.7507	0.91814	0.0:0.0:1.0:0.0	.	436;433	A6NEV3;Q9BQI5	.;SGIP1_HUMAN	S	437;436;436;433	ENSP00000237247:G437S;ENSP00000360076:G433S	ENSP00000237247:G437S	G	+	1	0	SGIP1	66920622	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	5.442000	0.66575	2.523000	0.85059	0.455000	0.32223	GGT	.	.		0.592	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291		A	67148034	G	A	67148034	3	1	4	1	0	0	0	0	1	0	0	0	14221	1348	47	3	1355	3	SGIP1	1	67148034	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	13576586	67148034	182102587	7	266										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86591328	86591328	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	atatctgcagtagtctgcagAtgcttctgcagaaggaataa	10	7	3	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:86591328A>G	ENST00000370571.2	-	3	1057	c.691T>C	c.(691-693)Tct>Cct	p.S231P	COL24A1_ENST00000436319.1_Missense_Mutation_p.S231P	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	231					extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TAGTCTGCAGATGCTTCTGCA	0.358																																					p.S231P		Atlas-SNP	.											.	COL24A1	202	.	0			c.T691C						.						60	59	59					1																	86591328		1959	4154	6113	SO:0001583	missense	255631	exon3			CTGCAGATGCTTC	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.691T>C	chr1.hg19:g.86591328A>G	ENSP00000359603:p.Ser231Pro	58.0	0.0		52.0	15.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	hg19	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	A	12.53	1.965204	0.34659	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	T;T	0.02103	4.45;4.45	5.82	4.67	0.58626	Concanavalin A-like lectin/glucanase (1);	0.193385	0.25830	N	0.028037	T	0.03136	0.0092	L	0.38175	1.15	0.46044	D	0.998839	D;D	0.71674	0.996;0.998	D;P	0.65010	0.931;0.855	T	0.50996	-0.8761	10	0.72032	D	0.01	.	12.3364	0.55069	0.8587:0.1413:0.0:0.0	.	231;231	F8WDM8;Q17RW2	.;COOA1_HUMAN	P	231	ENSP00000359603:S231P;ENSP00000392531:S231P	ENSP00000359603:S231P	S	-	1	0	COL24A1	86363916	0.998000	0.40836	0.984000	0.44739	0.680000	0.39746	3.653000	0.54446	0.990000	0.38787	0.533000	0.62120	TCT	.	.		0.358	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		G	86591328	A	G	86591328	3	3	4	1	0	0	0	0	1	0	0	0	3685	333	12	2	4685	2	COL24A1	1	86591328	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	19443294	86591328	162659293	8	267										
FLG2	388698	hgsc.bcm.edu	37	chr1	152324873	152324873	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gtggccagatgaccttcttcCagtggtcctggaccctgtct	11	13	2	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:152324873C>A	ENST00000388718.5	-	3	5461	c.5389G>T	c.(5389-5391)Gga>Tga	p.G1797*	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1797					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACCTTCTTCCAGTGGTCCTG	0.547																																					p.G1797X		Atlas-SNP	.											.	FLG2	431	.	0			c.G5389T						.						279	243	255					1																	152324873		2203	4300	6503	SO:0001587	stop_gained	388698	exon3			TTCTTCCAGTGGT	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.5389G>T	chr1.hg19:g.152324873C>A	ENSP00000373370:p.Gly1797*	86.0	0.0		145.0	13.0	NM_001014342	Q9H4U1	Nonsense_Mutation	SNP	ENST00000388718.5	hg19	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	C	42	9.362916	0.99148	.	.	ENSG00000143520	ENST00000388718	.	.	.	3.65	0.637	0.17735	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	3.6427	0.08173	0.0:0.4153:0.2997:0.2849	.	.	.	.	X	1797	.	ENSP00000373370:G1797X	G	-	1	0	FLG2	150591497	0.000000	0.05858	0.001000	0.08648	0.035000	0.12851	-3.269000	0.00532	0.352000	0.24053	0.297000	0.19635	GGA	.	.		0.547	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152324873	C	A	152324873	4	1	4	1	0	0	0	0	0	1	0	0	5931	603	21	3	1790	3	FLG2	1	152324873	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	65733545	152324873	96925748	9	268										
KIAA0907	22889	hgsc.bcm.edu	37	chr1	155887335	155887335	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cgttcatctggtagctcctcTgtgaatcgtctcttctgtgc	9	12	5	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:155887335T>C	ENST00000368321.3	-	11	1418	c.1395A>G	c.(1393-1395)acA>acG	p.T465T	SNORA42_ENST00000384744.1_RNA|KIAA0907_ENST00000368320.3_Silent_p.T465T	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	465							RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			GTAGCTCCTCTGTGAATCGTC	0.527																																					p.T465T		Atlas-SNP	.											.	KIAA0907	58	.	0			c.A1395G						.						129	141	137					1																	155887335		2203	4300	6503	SO:0001819	synonymous_variant	22889	exon11			CTCCTCTGTGAAT	BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.1395A>G	chr1.hg19:g.155887335T>C		125.0	0.0		142.0	15.0	NM_014949	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Silent	SNP	ENST00000368321.3	hg19	CCDS30885.1																																																																																			.	.		0.527	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		C	155887335	T	C	155887335	2	2	4	1	0	0	0	0	0	0	0	1	8208	1567	55	2		2	KIAA0907	1	155887335	Silent	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	3562462	155887335	93363286	10	269										
C1orf111	284680	hgsc.bcm.edu	37	chr1	162344031	162344031	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ccctcttgatgtggctcttgAggaagtccagggtggggtac	15	9	2	2	rs377620109		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:162344031A>T	ENST00000367935.5	-	3	672	c.593T>A	c.(592-594)cTc>cAc	p.L198H	RP11-565P22.6_ENST00000431696.1_Intron	NM_182581.3	NP_872387.2	Q5T0L3	CA111_HUMAN	chromosome 1 open reading frame 111	198										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			GTGGCTCTTGAGGAAGTCCAG	0.597																																					p.L198H		Atlas-SNP	.											.	C1orf111	26	.	0			c.T593A						.						120	119	120					1																	162344031		2203	4300	6503	SO:0001583	missense	284680	exon3			CTCTTGAGGAAGT	BC032957	CCDS1238.1	1q23.3	2008-02-05			ENSG00000171722	ENSG00000171722			27648	protein-coding gene	gene with protein product						12477932	Standard	NM_182581		Approved		uc001gbx.2	Q5T0L3	OTTHUMG00000031375	ENST00000367935.5:c.593T>A	chr1.hg19:g.162344031A>T	ENSP00000356912:p.Leu198His	104.0	0.0		162.0	13.0	NM_182581	Q6X961|Q8NEC3	Missense_Mutation	SNP	ENST00000367935.5	hg19	CCDS1238.1	.	.	.	.	.	.	.	.	.	.	A	17.52	3.410537	0.62399	.	.	ENSG00000171722	ENST00000367935	T	0.32515	1.45	5.14	5.14	0.70334	.	0.128829	0.30949	N	0.008558	T	0.43964	0.1271	M	0.72118	2.19	0.29393	N	0.862517	D	0.89917	1.0	D	0.76575	0.988	T	0.53528	-0.8426	9	0.87932	D	0	-11.6173	12.3478	0.55130	1.0:0.0:0.0:0.0	.	198	Q5T0L3	CA111_HUMAN	H	198	ENSP00000356912:L198H	ENSP00000356912:L198H	L	-	2	0	C1orf111	160610655	0.951000	0.32395	0.992000	0.48379	0.658000	0.38924	5.564000	0.67359	1.939000	0.56221	0.533000	0.62120	CTC	.	.		0.597	C1orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076791.2	NM_182581		T	162344031	A	T	162344031	3	4	4	1	0	0	0	0	1	0	0	0	1986	304	11	4	196	4	C1orf111	1	162344031	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	6456696	162344031	86906590	11	270										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096100	167096100	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gtgcagaggaggcagtagggGagaagaacccctccgacgtc	16	10	0	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:167096100G>A	ENST00000361200.2	+	6	1898	c.1732G>A	c.(1732-1734)Gag>Aag	p.E578K	DUSP27_ENST00000443333.1_Missense_Mutation_p.E578K|DUSP27_ENST00000271385.5_Missense_Mutation_p.E578K|DUSP27_ENST00000485151.1_Intron			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	578					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GGCAGTAGGGGAGAAGAACCC	0.557																																					p.E578K		Atlas-SNP	.											.	DUSP27	235	.	0			c.G1732A						.						50	52	51					1																	167096100		2203	4300	6503	SO:0001583	missense	92235	exon5			GTAGGGGAGAAGA	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1732G>A	chr1.hg19:g.167096100G>A	ENSP00000354483:p.Glu578Lys	209.0	0.0		213.0	30.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	G	5.875	0.345614	0.11126	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03717	3.83;3.83;3.83	5.05	4.12	0.48240	.	1.757900	0.03021	N	0.150753	T	0.02083	0.0065	M	0.67953	2.075	0.09310	N	0.999999	P	0.35433	0.501	B	0.32980	0.156	T	0.45425	-0.9262	10	0.49607	T	0.09	-4.9355	4.8797	0.13674	0.1302:0.0:0.6635:0.2064	.	578	Q5VZP5	DUS27_HUMAN	K	578	ENSP00000354483:E578K;ENSP00000271385:E578K;ENSP00000404874:E578K	ENSP00000271385:E578K	E	+	1	0	DUSP27	165362724	0.305000	0.24481	0.050000	0.19076	0.180000	0.23129	2.660000	0.46749	1.092000	0.41356	0.643000	0.83706	GAG	.	.		0.557	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		A	167096100	G	A	167096100	3	1	4	1	0	0	0	0	1	0	0	0	4826	1175	41	3	1750	3	DUSP27	1	167096100	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	4752069	167096100	82154521	12	271										
DCAF6	55827	hgsc.bcm.edu	37	chr1	168032858	168032858	+	Splice_Site	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tttaatatgtaattcatataGacgctctgctgttgcccgta	7	8	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:168032858G>C	ENST00000312263.6	+	15	2231		c.e15-1		DCAF6_ENST00000367840.3_Splice_Site|DCAF6_ENST00000367843.3_Splice_Site|DCAF6_ENST00000432587.2_Splice_Site	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						AATTCATATAGACGCTCTGCT	0.303																																					.		Atlas-SNP	.											.	DCAF6	99	.	0			c.2088-1G>C						.						22	21	22					1																	168032858		2199	4295	6494	SO:0001630	splice_region_variant	55827	exon16			CATATAGACGCTC	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.2028-1G>C	chr1.hg19:g.168032858G>C		220.0	0.0		285.0	34.0	NM_018442	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Splice_Site	SNP	ENST00000312263.6	hg19	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.388316	0.82902	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6926	0.96008	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DCAF6	166299482	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.296000	0.96104	2.676000	0.91093	0.555000	0.69702	.	.	.		0.303	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442	Intron	C	168032858	G	C	168032858	5	2	4	1	0	0	0	0	0	0	1	0	4276	956	33	4	2149	4	DCAF6	1	168032858	Splice_Site	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	936758	168032858	81217763	13	272										
TNN	63923	hgsc.bcm.edu	37	chr1	175067608	175067608	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gagagaccagggaggttccgGtggggaaggagcagagcagc	20	7	0	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:175067608G>T	ENST00000239462.4	+	9	2109	c.1996G>T	c.(1996-1998)Gtg>Ttg	p.V666L		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	666	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GGAGGTTCCGGTGGGGAAGGA	0.617																																					p.V666L		Atlas-SNP	.											.	TNN	297	.	0			c.G1996T						.						102	95	97					1																	175067608		2203	4300	6503	SO:0001583	missense	63923	exon9			GTTCCGGTGGGGA	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1996G>T	chr1.hg19:g.175067608G>T	ENSP00000239462:p.Val666Leu	356.0	0.0		454.0	108.0	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.903822	0.52333	.	.	ENSG00000120332	ENST00000239462	T	0.59083	0.29	5.14	5.14	0.70334	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.69575	0.3126	L	0.53729	1.69	0.41988	D	0.990834	P;D	0.89917	0.938;1.0	D;D	0.87578	0.921;0.998	T	0.67979	-0.5530	10	0.38643	T	0.18	.	12.7044	0.57051	0.0:0.0:0.8356:0.1644	.	666;666	B3KXB6;Q9UQP3	.;TENN_HUMAN	L	666	ENSP00000239462:V666L	ENSP00000239462:V666L	V	+	1	0	TNN	173334231	1.000000	0.71417	0.686000	0.30086	0.075000	0.17131	4.444000	0.60001	2.551000	0.86045	0.460000	0.39030	GTG	.	.		0.617	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		T	175067608	G	T	175067608	3	4	4	1	0	0	0	0	1	0	0	0	16338	1261	44	3	2026	3	TNN	1	175067608	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	7034750	175067608	74183013	14	273										
RASAL2	9462	hgsc.bcm.edu	37	chr1	178408576	178408576	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ggtctcgtgggctgcctaaaCtaaaagagtcacgttcccat	10	11	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:178408576C>G	ENST00000462775.1	+	4	375	c.250C>G	c.(250-252)Cta>Gta	p.L84V	RASAL2_ENST00000367649.3_Missense_Mutation_p.L232V|RASAL2_ENST00000448150.3_Missense_Mutation_p.L214V	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	84	PH.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						GCTGCCTAAACTAAAAGAGTC	0.438																																					p.L232V		Atlas-SNP	.											.	RASAL2	334	.	0			c.C694G						.						122	106	112					1																	178408576		2203	4300	6503	SO:0001583	missense	9462	exon6			CCTAAACTAAAAG	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"Pleckstrin homology (PH) domain containing"	9874	protein-coding gene	gene with protein product	"Ras GTPase activating protein-like", "Ras protein activator like 1"	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.250C>G	chr1.hg19:g.178408576C>G	ENSP00000420558:p.Leu84Val	50.0	0.0		105.0	23.0	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000462775.1	hg19	CCDS1322.1	.	.	.	.	.	.	.	.	.	.	C	19.70	3.877248	0.72294	.	.	ENSG00000075391	ENST00000448150;ENST00000367649;ENST00000462775	T;T;T	0.22539	1.95;1.95;1.96	6.16	4.32	0.51571	Pleckstrin homology domain (1);	0.000000	0.64402	D	0.000001	T	0.46502	0.1396	M	0.78801	2.425	0.80722	D	1	B;D	0.67145	0.32;0.996	B;D	0.75484	0.288;0.986	T	0.48725	-0.9010	10	0.72032	D	0.01	.	12.8514	0.57860	0.0:0.8696:0.0:0.1304	.	84;232	Q9UJF2;F8W755	NGAP_HUMAN;.	V	214;232;84	ENSP00000407768:L214V;ENSP00000356621:L232V;ENSP00000420558:L84V	ENSP00000356621:L232V	L	+	1	2	RASAL2	176675199	1.000000	0.71417	0.988000	0.46212	0.994000	0.84299	2.998000	0.49465	0.948000	0.37687	0.650000	0.86243	CTA	.	.		0.438	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692		G	178408576	C	G	178408576	3	3	4	1	0	0	0	0	1	0	0	0	13079	564	20	4	733	4	RASAL2	1	178408576	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	3340968	178408576	70842045	15	274										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179561920	179561920	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tcggtccactatggagctggTattggacatgcctgatgttg	13	8	0	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:179561920T>C	ENST00000367614.1	+	2	529	c.170T>C	c.(169-171)gTa>gCa	p.V57A	TDRD5_ENST00000444136.1_Missense_Mutation_p.V57A|TDRD5_ENST00000294848.8_Missense_Mutation_p.V57A|RP11-545A16.4_ENST00000567150.1_RNA	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	57	HTH OST-type 1. {ECO:0000255|PROSITE- ProRule:PRU00975}.				DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						ATGGAGCTGGTATTGGACATG	0.463																																					p.V57A		Atlas-SNP	.											.	TDRD5	149	.	0			c.T170C						.						199	175	183					1																	179561920		2203	4300	6503	SO:0001583	missense	163589	exon2			AGCTGGTATTGGA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.170T>C	chr1.hg19:g.179561920T>C	ENSP00000356586:p.Val57Ala	119.0	0.0		156.0	19.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.038282	0.75617	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.50813	0.73;0.73;0.73	5.91	4.77	0.60923	.	0.071561	0.56097	D	0.000040	T	0.60843	0.2300	L	0.50333	1.59	0.36331	D	0.85887	D;D	0.76494	0.999;0.999	D;D	0.74674	0.975;0.984	T	0.69079	-0.5240	10	0.72032	D	0.01	-5.2049	11.4906	0.50379	0.1346:0.0:0.0:0.8654	.	57;57	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	A	57	ENSP00000356586:V57A;ENSP00000294848:V57A;ENSP00000406052:V57A	ENSP00000294848:V57A	V	+	2	0	TDRD5	177828543	1.000000	0.71417	0.954000	0.39281	0.989000	0.77384	4.087000	0.57671	1.035000	0.39972	0.533000	0.62120	GTA	.	.		0.463	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		C	179561920	T	C	179561920	3	2	4	1	0	0	0	0	1	0	0	0	15748	1638	57	2	172	2	TDRD5	1	179561920	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	1153344	179561920	69688701	16	275										
DHX9	1660	hgsc.bcm.edu	37	chr1	182850422	182850422	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gggagatgctatctgtaccaTtgctgctgctacctgctttc	10	11	1	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:182850422T>C	ENST00000367549.3	+	23	2758	c.2648T>C	c.(2647-2649)aTt>aCt	p.I883T	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	883					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						ATCTGTACCATTGCTGCTGCT	0.453																																					p.I883T	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.T2648C						.						141	139	140					1																	182850422		2019	4172	6191	SO:0001583	missense	1660	exon23			GTACCATTGCTGC	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.2648T>C	chr1.hg19:g.182850422T>C	ENSP00000356520:p.Ile883Thr	75.0	0.0		96.0	9.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.247143	0.80024	.	.	ENSG00000135829	ENST00000367549	T	0.40476	1.03	5.76	5.76	0.90799	Helicase-associated domain (2);	0.054581	0.64402	D	0.000001	T	0.70745	0.3259	M	0.90977	3.165	0.58432	D	0.999995	D;P	0.55605	0.972;0.949	D;P	0.64410	0.925;0.83	T	0.78311	-0.2253	10	0.87932	D	0	.	15.765	0.78120	0.0:0.0:0.0:1.0	.	162;883	B3KU66;Q08211	.;DHX9_HUMAN	T	883	ENSP00000356520:I883T	ENSP00000356520:I883T	I	+	2	0	DHX9	181117045	1.000000	0.71417	0.995000	0.50966	0.970000	0.65996	5.682000	0.68182	2.186000	0.69663	0.533000	0.62120	ATT	.	.		0.453	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		C	182850422	T	C	182850422	3	2	4	1	0	0	0	0	1	0	0	0	4518	1493	52	2	2734	2	DHX9	1	182850422	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	3288502	182850422	66400199	17	276										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186052065	186052066	+	Frame_Shift_Ins	INS	-	-	A													0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agaacacagctgggagtgccINSaaaaaatattttaacctcaa							TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:186052065_186052066insA	ENST00000271588.4	+	57	9085_9086	c.8856_8857insA	c.(8857-8859)aaafs	p.K2953fs	HMCN1_ENST00000367492.2_Frame_Shift_Ins_p.K2953fs	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2953	Ig-like C2-type 27.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTGGGAGTGCCAAAAAATATTT	0.351																																					p.A2952fs		Atlas-Indel,Pindel	.											.,1	HMCN1	797	.	0			c.8856_8857insA						.																																			SO:0001589	frameshift_variant	83872	exon57			.	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8862dupA	chr1.hg19:g.186052071_186052071dupA	ENSP00000271588:p.Lys2953fs	173.0	0.0		435.0	50.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Frame_Shift_Ins	INS	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.351	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186052066	-	A	186052065	7	5	4	1	0	1	1	0	0	0	0	0	7229	581	21	0	9082	0	HMCN1	1	186052065	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GU-01A-11D-A382-10	3201643	186052065	63198556	18	277										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208272269	208272269	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tggctgatgctggcagcaaaTcgattaggttcccaggcctg	13	10	0	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:208272269T>G	ENST00000367033.3	-	6	2410	c.1653A>C	c.(1651-1653)cgA>cgC	p.R551R		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	551					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TGGCAGCAAATCGATTAGGTT	0.552																																					p.R551R		Atlas-SNP	.											.	PLXNA2	178	.	0			c.A1653C						.						103	79	87					1																	208272269		2203	4300	6503	SO:0001819	synonymous_variant	5362	exon6			AGCAAATCGATTA	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.1653A>C	chr1.hg19:g.208272269T>G		66.0	0.0		116.0	12.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	hg19	CCDS31013.1																																																																																			.	.		0.552	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		G	208272269	T	G	208272269	2	3	4	1	0	0	0	0	0	0	0	1	12129	1422	50	5		5	PLXNA2	1	208272269	Silent	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	22220204	208272269	40978352	19	278										
RCOR3	55758	hgsc.bcm.edu	37	chr1	211462588	211462588	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agagagtatcagagtttacaAcatcgccatcattctcagcg	8	10	3	2	rs376624554		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:211462588A>G	ENST00000367005.4	+	7	756	c.615A>G	c.(613-615)caA>caG	p.Q205Q	RCOR3_ENST00000452621.2_Silent_p.Q263Q|RCOR3_ENST00000419091.2_Silent_p.Q263Q|RCOR3_ENST00000367006.4_Silent_p.Q263Q	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	205					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		AGAGTTTACAACATCGCCATC	0.438																																					p.Q263Q		Atlas-SNP	.											.	RCOR3	51	.	0			c.A789G						.	A	,,,	0,4406		0,0,2203	180	152	161		789,789,789,615	-4	1	1		161	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RCOR3	NM_001136223.1,NM_001136224.2,NM_001136225.1,NM_018254.3	,,,	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,,,	263/554,263/437,263/450,205/496	211462588	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55758	exon8			TTTACAACATCGC	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.615A>G	chr1.hg19:g.211462588A>G		278.0	0.0		391.0	79.0	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Silent	SNP	ENST00000367005.4	hg19	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	A	9.800	1.180277	0.21787	0.0	1.16E-4	ENSG00000117625	ENST00000534460	.	.	.	5.84	-4.04	0.04010	.	.	.	.	.	T	0.55465	0.1922	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55515	-0.8129	4	.	.	.	-0.995	11.9324	0.52853	0.2498:0.0:0.6395:0.1107	.	.	.	.	A	50	.	.	T	+	1	0	RCOR3	209529211	0.999000	0.42202	0.963000	0.40424	0.996000	0.88848	0.532000	0.23067	-0.740000	0.04803	-0.250000	0.11733	ACA	.	.		0.438	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		G	211462588	A	G	211462588	2	3	4	1	0	0	0	0	0	0	0	1	13199	40	2	2		2	RCOR3	1	211462588	Silent	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	3190319	211462588	37788033	20	279										
RD3	343035	hgsc.bcm.edu	37	chr1	211652629	211652629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gcggaagagctgggacacctCctgcacctcgggctcctgct	13	15	0	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:211652629C>T	ENST00000367002.4	-	3	1500	c.337G>A	c.(337-339)Gag>Aag	p.E113K	RD3_ENST00000484910.1_5'UTR	NM_001164688.1|NM_183059.2	NP_001158160.1|NP_898882.1	Q7Z3Z2	RD3_HUMAN	retinal degeneration 3	113					response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)					central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10				OV - Ovarian serous cystadenocarcinoma(81;0.00284)|all cancers(67;0.0279)|Epithelial(68;0.0689)		TGGGACACCTCCTGCACCTCG	0.697																																					p.E113K		Atlas-SNP	.											.	RD3	26	.	0			c.G337A						.						13	13	13					1																	211652629		2195	4299	6494	SO:0001583	missense	343035	exon3			ACACCTCCTGCAC	AY191519	CCDS1498.1	1q32.3	2008-02-05	2006-11-13	2006-11-13	ENSG00000198570	ENSG00000198570			19689	protein-coding gene	gene with protein product		180040	"chromosome 1 open reading frame 36"	C1orf36		12914764	Standard	NM_183059		Approved	LCA12	uc001hin.2	Q7Z3Z2	OTTHUMG00000037002	ENST00000367002.4:c.337G>A	chr1.hg19:g.211652629C>T	ENSP00000355969:p.Glu113Lys	159.0	0.0		145.0	30.0	NM_183059	A8K595	Missense_Mutation	SNP	ENST00000367002.4	hg19	CCDS1498.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.898891	0.72754	.	.	ENSG00000198570	ENST00000367002	T	0.20069	2.1	4.09	3.17	0.36434	.	0.054029	0.64402	N	0.000001	T	0.36082	0.0954	M	0.81497	2.545	0.47153	D	0.999336	P	0.48503	0.911	P	0.50192	0.634	T	0.34576	-0.9823	10	0.62326	D	0.03	-29.2847	12.2834	0.54779	0.0:0.9158:0.0:0.0842	.	113	Q7Z3Z2	RD3_HUMAN	K	113	ENSP00000355969:E113K	ENSP00000355969:E113K	E	-	1	0	RD3	209719252	0.998000	0.40836	1.000000	0.80357	0.443000	0.32047	2.599000	0.46231	0.863000	0.35553	-0.232000	0.12228	GAG	.	.		0.697	RD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089837.1	NM_183059		T	211652629	C	T	211652629	3	4	4	1	0	0	0	0	1	0	0	0	13202	864	30	3	254	3	RD3	1	211652629	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	190041	211652629	37597992	21	280										
RYR2	6262	hgsc.bcm.edu	37	chr1	237919659	237919659	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gatcgtggcgcggctgagatGgtgctacagacaatcagtgc	15	9	1	2	rs397516502		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:237919659G>T	ENST00000366574.2	+	81	11534	c.11217G>T	c.(11215-11217)atG>atT	p.M3739I	RYR2_ENST00000542537.1_Missense_Mutation_p.M3723I|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Missense_Mutation_p.M3745I	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3739					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CGGCTGAGATGGTGCTACAGA	0.488																																					p.M3739I		Atlas-SNP	.											.	RYR2	1273	.	0			c.G11217T						.						96	100	99					1																	237919659		1967	4168	6135	SO:0001583	missense	6262	exon81			TGAGATGGTGCTA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.11217G>T	chr1.hg19:g.237919659G>T	ENSP00000355533:p.Met3739Ile	43.0	0.0		72.0	6.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.557498	0.45590	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.89810	-2.57;-2.57;-2.57	5.44	5.44	0.79542	.	0.000000	0.85682	U	0.000000	D	0.94804	0.8322	M	0.83953	2.67	0.80722	D	1	D;D	0.67145	0.958;0.996	D;D	0.71184	0.943;0.972	D	0.95122	0.8247	10	0.87932	D	0	.	18.6247	0.91333	0.0:0.0:1.0:0.0	.	713;3739	B4DGV4;Q92736	.;RYR2_HUMAN	I	3739;3745;3723;713	ENSP00000355533:M3739I;ENSP00000353174:M3745I;ENSP00000443798:M3723I	ENSP00000353174:M3745I	M	+	3	0	RYR2	235986282	1.000000	0.71417	1.000000	0.80357	0.113000	0.19764	9.813000	0.99286	2.717000	0.92951	0.563000	0.77884	ATG	.	.		0.488	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237919659	G	T	237919659	3	4	4	1	0	0	0	0	1	0	0	0	13784	1348	47	3	11539	3	RYR2	1	237919659	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	26267030	237919659	11330962	22	281										
WDR64	128025	hgsc.bcm.edu	37	chr1	241958512	241958512	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	atccctttgttttgcagattCgaagatatcccttggaaggt	9	8	0	2	rs201917329	byFrequency	TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:241958512C>T	ENST00000366552.2	+	25	3178	c.2971C>T	c.(2971-2973)Cga>Tga	p.R991*	WDR64_ENST00000437684.2_Nonsense_Mutation_p.R824*	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	991										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			TTTGCAGATTCGAAGATATCC	0.418													C|||	3	0.000599042	0	0.0043	5008	,	,		20193	0		0	False		,,,				2504	0				p.R991X		Atlas-SNP	.											WDR64_ENST00000366552,colon,carcinoma,0,4	WDR64	234	.	0			c.C2971T						.	C	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	175	169	171		2971	3.5	0.7	1		171	2,8598	2.2+/-6.3	0,2,4298	yes	stop-gained	WDR64	NM_144625.4		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		991/1082	241958512	3,13003	2203	4300	6503	SO:0001587	stop_gained	128025	exon25			CAGATTCGAAGAT	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.2971C>T	chr1.hg19:g.241958512C>T	ENSP00000355510:p.Arg991*	127.0	0.0		152.0	22.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Nonsense_Mutation	SNP	ENST00000366552.2	hg19		.	.	.	.	.	.	.	.	.	.	C	41	8.655293	0.98901	2.27E-4	2.33E-4	ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635	.	.	.	5.62	3.55	0.40652	.	0.799060	0.11021	N	0.608373	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-0.7728	10.5595	0.45138	0.493:0.5069:0.0:0.0	.	.	.	.	X	991;824;595	.	ENSP00000355510:R991X	R	+	1	2	WDR64	240025135	0.935000	0.31712	0.690000	0.30148	0.889000	0.51656	1.268000	0.33062	1.313000	0.45069	0.462000	0.41574	CGA	.	.		0.418	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		T	241958512	C	T	241958512	4	4	4	1	0	0	0	0	0	1	0	0	17330	876	31	1	3069	1	WDR64	1	241958512	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	4038853	241958512	7292109	23	282										
OR2W3	343171	hgsc.bcm.edu	37	chr1	248059059	248059059	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ctggacccccacctccacacCcccatgtacttcttcctcgc	4	22	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr1:248059059C>A	ENST00000360358.3	+	1	171	c.171C>A	c.(169-171)acC>acA	p.T57T	OR2W3_ENST00000537741.1_Silent_p.T57T	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	57						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			ACCTCCACACCCCCATGTACT	0.567																																					p.T57T		Atlas-SNP	.											.	OR2W3	113	.	0			c.C171A						.						207	174	185					1																	248059059		2203	4300	6503	SO:0001819	synonymous_variant	343171	exon1			CCACACCCCCATG	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"GPCR / Class A : Olfactory receptors"	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.171C>A	chr1.hg19:g.248059059C>A		134.0	0.0		164.0	46.0	NM_001001957	Q6IF06|Q8NG86	Silent	SNP	ENST00000360358.3	hg19	CCDS31099.1																																																																																			.	.		0.567	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957		A	248059059	C	A	248059059	2	1	4	1	0	0	0	0	0	0	0	1	11042	610	22	3		3	OR2W3	1	248059059	Silent	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	6100547	248059059	1191562	24	283										
ALK	238	hgsc.bcm.edu	37	chr2	29551301	29551301	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tggaggactgtcccattccaAcaagtgaaggagctctgcag	12	10	1	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr2:29551301A>G	ENST00000389048.3	-	6	2235	c.1329T>C	c.(1327-1329)tgT>tgC	p.C443C	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	443	LDL-receptor class A.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TCCCATTCCAACAAGTGAAGG	0.582			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.C443C		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.T1329C						.						80	72	75					2																	29551301		2203	4300	6503	SO:0001819	synonymous_variant	238	exon6	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	ATTCCAACAAGTG	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1329T>C	chr2.hg19:g.29551301A>G		182.0	0.0		222.0	21.0	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	hg19	CCDS33172.1																																																																																			.	.		0.582	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		G	29551301	A	G	29551301	2	3	4	1	0	0	0	0	0	0	0	1	525	41	2	2		2	ALK	2	29551301	Silent	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10		29551301	213648072	25	284										
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43953414	43953414	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	actaatatttactttagtttCctttaggtcagatcaaactc	4	8	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr2:43953414C>T	ENST00000282406.4	+	17	2655	c.2545C>T	c.(2545-2547)Cct>Tct	p.P849S		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	849	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				ACTTTAGTTTCCTTTAGGTCA	0.333																																					p.P849S		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.C2545T						.						58	56	57					2																	43953414		2203	4300	6503	SO:0001583	missense	130271	exon17			TAGTTTCCTTTAG	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.2545C>T	chr2.hg19:g.43953414C>T	ENSP00000282406:p.Pro849Ser	168.0	0.0		187.0	38.0	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.367725	0.82463	.	.	ENSG00000152527	ENST00000282406	T	0.26518	1.73	4.48	4.48	0.54585	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.58736	0.2143	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.68138	-0.5488	10	0.66056	D	0.02	-18.0584	17.7963	0.88572	0.0:1.0:0.0:0.0	.	849;286	Q8IVE3;Q8IVE3-2	PKHH2_HUMAN;.	S	849	ENSP00000282406:P849S	ENSP00000282406:P849S	P	+	1	0	PLEKHH2	43806918	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.377000	0.79668	2.494000	0.84150	0.580000	0.79431	CCT	.	.		0.333	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		T	43953414	C	T	43953414	3	4	4	1	0	0	0	0	1	0	0	0	12086	855	30	3	2607	3	PLEKHH2	2	43953414	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	14402113	43953414	199245959	26	285										
DQX1	165545	hgsc.bcm.edu	37	chr2	74752293	74752293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aacctgtcctttctggaaccCtctggccagcgcaaactctg	8	15	3	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr2:74752293C>T	ENST00000404568.3	-	3	493	c.274G>A	c.(274-276)Ggg>Agg	p.G92R	DQX1_ENST00000393951.2_Missense_Mutation_p.G92R|DQX1_ENST00000495597.1_5'Flank	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	92	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						TTCTGGAACCCTCTGGCCAGC	0.562																																					p.G92R		Atlas-SNP	.											.	DQX1	95	.	0			c.G274A						.						44	44	44					2																	74752293		692	1591	2283	SO:0001583	missense	165545	exon3			GGAACCCTCTGGC	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.274G>A	chr2.hg19:g.74752293C>T	ENSP00000384621:p.Gly92Arg	150.0	0.0		138.0	6.0	NM_133637	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	hg19	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	C	11.91	1.780608	0.31502	.	.	ENSG00000144045	ENST00000393951;ENST00000404568	T;T	0.07327	3.2;3.2	5.16	5.16	0.70880	DEAD-like helicase (2);	.	.	.	.	T	0.05960	0.0155	N	0.21545	0.675	0.36229	D	0.852514	B	0.29612	0.251	B	0.26202	0.067	T	0.41466	-0.9507	9	0.17369	T	0.5	.	11.8575	0.52446	0.0:0.8241:0.1759:0.0	.	92	Q8TE96	DQX1_HUMAN	R	92	ENSP00000377523:G92R;ENSP00000384621:G92R	ENSP00000377523:G92R	G	-	1	0	DQX1	74605801	0.596000	0.26866	1.000000	0.80357	0.983000	0.72400	1.096000	0.30976	2.696000	0.92011	0.650000	0.86243	GGG	.	.		0.562	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		T	74752293	C	T	74752293	3	4	4	1	0	0	0	0	1	0	0	0	4753	681	24	3	1919	3	DQX1	2	74752293	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	30798879	74752293	168447080	27	286										
TMEM177	80775	hgsc.bcm.edu	37	chr2	120438742	120438742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tccctgctggggctgtggtgGgcatccctgccagtttcttg	14	12	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr2:120438742G>A	ENST00000424086.1	+	2	786	c.313G>A	c.(313-315)Ggc>Agc	p.G105S	TMEM177_ENST00000401466.1_Missense_Mutation_p.G105S|TMEM177_ENST00000496203.1_Intron|TMEM177_ENST00000272521.6_Missense_Mutation_p.G105S|TMEM177_ENST00000409951.1_Intron	NM_001105198.1	NP_001098668.1	Q53S58	TM177_HUMAN	transmembrane protein 177	105						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	13	Colorectal(110;0.196)					GGCTGTGGTGGGCATCCCTGC	0.582																																					p.G105S		Atlas-SNP	.											.	TMEM177	26	.	0			c.G313A						.						163	175	171					2																	120438742		2203	4300	6503	SO:0001583	missense	80775	exon2			GTGGTGGGCATCC	BC004404	CCDS2128.1	2q14.2	2008-02-05			ENSG00000144120	ENSG00000144120			28143	protein-coding gene	gene with protein product						12477932	Standard	NM_001105198		Approved	MGC10993	uc002tmc.1	Q53S58	OTTHUMG00000153312	ENST00000424086.1:c.313G>A	chr2.hg19:g.120438742G>A	ENSP00000402661:p.Gly105Ser	161.0	0.0		72.0	27.0	NM_030577	Q9BT20	Missense_Mutation	SNP	ENST00000424086.1	hg19	CCDS2128.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.930447	0.92389	.	.	ENSG00000144120	ENST00000401466;ENST00000424086;ENST00000272521;ENST00000445518;ENST00000415646	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	T	0.70482	0.3229	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75806	-0.3188	10	0.87932	D	0	-6.2826	15.0498	0.71858	0.0:0.0:1.0:0.0	.	105	Q53S58	TM177_HUMAN	S	105	ENSP00000385966:G105S;ENSP00000402661:G105S;ENSP00000272521:G105S;ENSP00000405898:G105S	ENSP00000272521:G105S	G	+	1	0	TMEM177	120155212	1.000000	0.71417	0.968000	0.41197	0.990000	0.78478	8.840000	0.92125	2.509000	0.84616	0.549000	0.68633	GGC	.	.		0.582	TMEM177-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330673.1	NM_030577		A	120438742	G	A	120438742	3	1	4	1	0	0	0	0	1	0	0	0	16109	1232	43	3	315	3	TMEM177	2	120438742	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	45686449	120438742	122760631	28	287										
TTN	7273	hgsc.bcm.edu	37	chr2	179615916	179615916	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gagaacagaatatctttatcActagcttcacttctcaaagt	5	9	4	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr2:179615916A>C	ENST00000591111.1	-	45	10585				TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.S3737R|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATCTTTATCACTAGCTTCAC	0.343																																					p.S3737R		Atlas-SNP	.											.	TTN	18412	.	0			c.T11211G						.						54	52	53					2																	179615916		2202	4295	6497	SO:0001627	intron_variant	7273	exon46			TTTATCACTAGCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+1934T>G	chr2.hg19:g.179615916A>C		75.0	0.0		102.0	21.0	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.22	2.471459	0.43942	.	.	ENSG00000155657	ENST00000360870	T	0.58060	0.36	5.77	1.96	0.26148	.	.	.	.	.	T	0.32704	0.0838	N	0.24115	0.695	0.09310	N	1	B	0.32526	0.374	B	0.29716	0.106	T	0.14476	-1.0471	9	0.22706	T	0.39	.	6.6757	0.23093	0.7316:0.1292:0.1392:0.0	.	3737	Q8WZ42-6	.	R	3737	ENSP00000354117:S3737R	ENSP00000354117:S3737R	S	-	3	2	TTN	179324161	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.124000	0.10595	0.153000	0.19213	-0.290000	0.09829	AGT	.	.		0.343	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179615916	A	C	179615916	1	2	4	0	1	0	0	0	0	0	0	0	16750	156	6	5		5	TTN	2	179615916	Intron	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	59177174	179615916	63583457	29	288										
BOLL	66037	hgsc.bcm.edu	37	chr2	198641827	198641827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ttcttgtgtttcaaaagtgaCgaaaccatacctaaataaat	5	7	2	1	rs577424738	byFrequency	TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr2:198641827C>T	ENST00000392296.4	-	4	541	c.232G>A	c.(232-234)Gtc>Atc	p.V78I	BOLL_ENST00000321801.7_Missense_Mutation_p.V90I|BOLL_ENST00000282278.8_Intron|BOLL_ENST00000430004.1_Missense_Mutation_p.V78I|BOLL_ENST00000433157.1_Missense_Mutation_p.V78I	NM_033030.5	NP_149019.1	Q8N9W6	BOLL_HUMAN	boule-like RNA-binding protein	78	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494)			central_nervous_system(1)|endometrium(2)|lung(6)|ovary(3)|prostate(1)	13						TCAAAAGTGACGAAACCATAC	0.209													C|||	5	0.000998403	0	0	5008	,	,		14472	0.001		0	False		,,,				2504	0.0041				p.V90I		Atlas-SNP	.											BOLL_ENST00000321801,colon,carcinoma,0,6	BOLL	67	.	0			c.G268A						.						53	54	54					2																	198641827		2202	4289	6491	SO:0001583	missense	66037	exon4			AAGTGACGAAACC		CCDS2324.1, CCDS2325.1, CCDS63081.1	2q33	2013-10-17	2013-10-17		ENSG00000152430	ENSG00000152430		"RNA binding motif (RRM) containing"	14273	protein-coding gene	gene with protein product		606165	"bol (Drosophila boule homolog)-like", "bol, boule-like (Drosophila)"			11390979, 16001084	Standard	NM_197970		Approved	BOULE	uc002uut.2	Q8N9W6	OTTHUMG00000132747	ENST00000392296.4:c.232G>A	chr2.hg19:g.198641827C>T	ENSP00000376116:p.Val78Ile	507.0	0.0		389.0	90.0	NM_197970	B4DZA4|Q0JW32|Q53T62|Q969U3	Missense_Mutation	SNP	ENST00000392296.4	hg19	CCDS2325.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.443393	0.25987	.	.	ENSG00000152430	ENST00000430004;ENST00000392296;ENST00000321801;ENST00000433157	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.96	-4.8	0.03190	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.532723	0.18574	N	0.137248	T	0.16514	0.0397	N	0.20807	0.61	0.50039	D	0.999843	B;B;B;B	0.30605	0.287;0.003;0.003;0.003	B;B;B;B	0.23716	0.048;0.009;0.016;0.018	T	0.00950	-1.1503	10	0.44086	T	0.13	-11.6757	15.2117	0.73230	0.0:0.288:0.0:0.712	.	84;90;78;84	Q8N9W6-2;Q8N9W6-3;Q8N9W6;Q8N9W6-4	.;.;BOLL_HUMAN;.	I	78;78;90;78	ENSP00000397711:V78I;ENSP00000376116:V78I;ENSP00000314792:V90I;ENSP00000396099:V78I	ENSP00000314792:V90I	V	-	1	0	BOLL	198350072	0.000000	0.05858	0.065000	0.19835	0.983000	0.72400	-1.594000	0.02094	-0.931000	0.03746	-0.897000	0.02905	GTC	.	.		0.209	BOLL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256107.3	NM_033030		T	198641827	C	T	198641827	3	4	4	1	0	0	0	0	1	0	0	0	1489	536	19	1	651	1	BOLL	2	198641827	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	19025911	198641827	44557546	30	289										
CASP10	843	hgsc.bcm.edu	37	chr2	202074072	202074072	+	Frame_Shift_Del	DEL	G	G	-													0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	actctttttcatccaggcctGccaaggtgaagagatacagc							TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr2:202074072delG	ENST00000272879.5	+	9	1386	c.1202delG	c.(1201-1203)tgcfs	p.C401fs	CASP10_ENST00000492363.1_3'UTR|CASP10_ENST00000448480.1_Frame_Shift_Del_p.C358fs|CASP10_ENST00000313728.7_Frame_Shift_Del_p.C334fs|CASP10_ENST00000346817.5_Frame_Shift_Del_p.C358fs|CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000286186.6_Frame_Shift_Del_p.C401fs	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	401					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						ATCCAGGCCTGCCAAGGTGAA	0.537																																					p.C401fs		Atlas-Indel,Pindel	.											.	CASP10	95	.	0			c.1201delT						.						75	69	71					2																	202074072		2203	4300	6503	SO:0001589	frameshift_variant	843	exon9			.	U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	3.4.22.63	"Caspases"	1500	protein-coding gene	gene with protein product		601762	"caspase 10, apoptosis-related cysteine protease"			8755496	Standard	NM_032974		Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000272879.5:c.1202delG	chr2.hg19:g.202074072delG	ENSP00000272879:p.Cys401fs	88.0	0.0		72.0	20.0	NM_032977	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Frame_Shift_Del	DEL	ENST00000272879.5	hg19	CCDS2338.1																																																																																			.	.		0.537	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977		-	202074072	G	-	202074072	7	5	4	1	0	1	0	1	0	0	0	0	2671	1319	46	0	1232	0	CASP10	2	202074072	Frame_Shift_Del	DEL	G	TCGA-2Y-A9GU-01A-11D-A382-10	3432245	202074072	41125301	31	290										
SGPP2	130367	hgsc.bcm.edu	37	chr2	223339386	223339386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tgttctacatcacgtttcttCcattcactcactggaatatt	4	11	5	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr2:223339386C>T	ENST00000321276.7	+	2	405	c.319C>T	c.(319-321)Cca>Tca	p.P107S		NM_152386.2	NP_689599.2	Q8IWX5	SGPP2_HUMAN	sphingosine-1-phosphate phosphatase 2	107					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	18		Renal(207;0.0376)		Epithelial(121;2.08e-09)|all cancers(144;9.25e-07)|LUSC - Lung squamous cell carcinoma(224;0.011)|Lung(261;0.0143)		CACGTTTCTTCCATTCACTCA	0.353																																					p.P107S		Atlas-SNP	.											.	SGPP2	39	.	0			c.C319T						.						139	131	134					2																	223339386		2202	4300	6502	SO:0001583	missense	130367	exon2			TTTCTTCCATTCA	AF542512	CCDS2453.1	2q36.3	2010-05-26	2010-05-26		ENSG00000163082	ENSG00000163082			19953	protein-coding gene	gene with protein product		612827				12411432	Standard	NM_152386		Approved	SPP2, FLJ39004	uc010zlo.2	Q8IWX5	OTTHUMG00000133156	ENST00000321276.7:c.319C>T	chr2.hg19:g.223339386C>T	ENSP00000315137:p.Pro107Ser	122.0	0.0		77.0	21.0	NM_152386	A3KPB4|Q8N8Q6	Missense_Mutation	SNP	ENST00000321276.7	hg19	CCDS2453.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.222191	0.79464	.	.	ENSG00000163082	ENST00000321276	T	0.74632	-0.86	5.37	5.37	0.77165	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.86859	0.6034	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.87097	0.2176	10	0.51188	T	0.08	-12.9899	19.0932	0.93238	0.0:1.0:0.0:0.0	.	107	Q8IWX5	SGPP2_HUMAN	S	107	ENSP00000315137:P107S	ENSP00000315137:P107S	P	+	1	0	SGPP2	223047630	1.000000	0.71417	0.984000	0.44739	0.831000	0.47069	6.010000	0.70753	2.505000	0.84491	0.561000	0.74099	CCA	.	.		0.353	SGPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256856.2			T	223339386	C	T	223339386	3	4	4	1	0	0	0	0	1	0	0	0	14235	855	30	3	325	3	SGPP2	2	223339386	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	21265314	223339386	19859987	32	291										
ARPP21	10777	hgsc.bcm.edu	37	chr3	35778748	35778748	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gcagcccctgcgaagcgccaTggtggggcagtcccaacagc	14	15	0	0	rs566433210	byFrequency	TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:35778748T>C	ENST00000187397.4	+	16	1994	c.1538T>C	c.(1537-1539)aTg>aCg	p.M513T	ARPP21_ENST00000337271.5_Missense_Mutation_p.M459T|ARPP21_ENST00000458225.1_Missense_Mutation_p.M479T|ARPP21_ENST00000444190.1_Missense_Mutation_p.M459T|ARPP21_ENST00000417925.1_Missense_Mutation_p.M479T	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	513	Gln-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						CGAAGCGCCATGGTGGGGCAG	0.622													T|||	2	0.000399361	0	0	5008	,	,		13856	0		0	False		,,,				2504	0.002				p.M513T		Atlas-SNP	.											.	ARPP21	153	.	0			c.T1538C						.						44	51	49					3																	35778748		2203	4300	6503	SO:0001583	missense	10777	exon16			GCGCCATGGTGGG	AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"R3H domain containing 3"	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.1538T>C	chr3.hg19:g.35778748T>C	ENSP00000187397:p.Met513Thr	179.0	0.0		126.0	8.0	NM_016300	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	hg19	CCDS2661.1	.	.	.	.	.	.	.	.	.	.	T	14.08	2.429191	0.43122	.	.	ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.91	5.91	0.95273	.	0.432629	0.27424	N	0.019428	T	0.39886	0.1095	L	0.57536	1.79	0.40029	D	0.975501	B;B;B;B	0.28820	0.008;0.027;0.224;0.008	B;B;B;B	0.24006	0.019;0.025;0.05;0.019	T	0.26608	-1.0098	10	0.17832	T	0.49	-1.8461	16.3512	0.83208	0.0:0.0:0.0:1.0	.	479;1;513;459	Q9UBL0-3;Q9UBL0-5;Q9UBL0;Q9UBL0-4	.;.;ARP21_HUMAN;.	T	479;459;459;513;479	ENSP00000414351:M479T;ENSP00000337792:M459T;ENSP00000405276:M459T;ENSP00000187397:M513T;ENSP00000412326:M479T	ENSP00000187397:M513T	M	+	2	0	ARPP21	35753752	0.799000	0.28903	0.289000	0.24876	0.554000	0.35429	3.978000	0.56881	2.266000	0.75297	0.533000	0.62120	ATG	.	.		0.622	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		C	35778748	T	C	35778748	3	2	4	1	0	0	0	0	1	0	0	0	978	1464	51	2	1605	2	ARPP21	3	35778748	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10		35778748	162243682	33	292										
ACAA1	30	hgsc.bcm.edu	37	chr3	38178099	38178099	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tcaccgacacagatgtccccCagctgttccggcctcagatt	8	16	2	2	rs11552535		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:38178099C>T	ENST00000333167.8	-	2	421	c.249G>A	c.(247-249)ctG>ctA	p.L83L	MYD88_ENST00000396334.3_5'Flank|ACAA1_ENST00000450296.1_Silent_p.L83L|ACAA1_ENST00000444607.2_Silent_p.L83L|MYD88_ENST00000424893.1_5'Flank|MYD88_ENST00000443433.2_5'Flank|ACAA1_ENST00000301810.7_Silent_p.L83L|MYD88_ENST00000417037.2_5'Flank|MYD88_ENST00000495303.1_5'Flank|ACAA1_ENST00000544624.1_5'UTR	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	83					alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		AGATGTCCCCCAGCTGTTCCG	0.632																																					p.L83L		Atlas-SNP	.											.	ACAA1	32	.	0			c.G249A						.						57	49	52					3																	38178099		2203	4300	6503	SO:0001819	synonymous_variant	30	exon2			GTCCCCCAGCTGT	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"peroxisomal 3-oxoacyl-Coenzyme A thiolase"	604054	"acetyl-Coenzyme A acyltransferase 1"				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087	ENST00000333167.8:c.249G>A	chr3.hg19:g.38178099C>T		247.0	0.0		130.0	31.0	NM_001130410	G5E935|Q96CA6	Silent	SNP	ENST00000333167.8	hg19	CCDS2673.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.488967	0.26686	.	.	ENSG00000060971	ENST00000421218	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.322	17.9617	0.89087	0.0:1.0:0.0:0.0	rs11552535	.	.	.	X	6	.	.	W	-	2	0	ACAA1	38153103	1.000000	0.71417	0.996000	0.52242	0.787000	0.44495	1.344000	0.33941	2.230000	0.72887	0.655000	0.94253	TGG	.	.		0.632	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		T	38178099	C	T	38178099	2	4	4	1	0	0	0	0	0	0	0	1	104	581	21	3		3	ACAA1	3	38178099	Silent	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	2399351	38178099	159844331	34	293										
KIF15	56992	hgsc.bcm.edu	37	chr3	44893334	44893334	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agatggaatgccttagaatgActgatgaagtcgaacgaacc	11	7	0	5			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:44893334A>T	ENST00000326047.4	+	33	4011	c.3862A>T	c.(3862-3864)Act>Tct	p.T1288S	KIF15_ENST00000425755.1_Missense_Mutation_p.T923S	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1288					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		CCTTAGAATGACTGATGAAGT	0.373																																					p.T1288S		Atlas-SNP	.											.	KIF15	103	.	0			c.A3862T						.						152	156	155					3																	44893334		2203	4300	6503	SO:0001583	missense	56992	exon33			AGAATGACTGATG	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.3862A>T	chr3.hg19:g.44893334A>T	ENSP00000324020:p.Thr1288Ser	183.0	0.0		186.0	8.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	hg19	CCDS33744.1	.	.	.	.	.	.	.	.	.	.	A	3.998	-0.003051	0.07773	.	.	ENSG00000163808	ENST00000326047;ENST00000425755	T;T	0.22336	1.96;1.96	5.68	-6.03	0.02185	.	0.955176	0.08653	N	0.913755	T	0.09202	0.0227	N	0.20685	0.6	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.42783	-0.9431	10	0.07990	T	0.79	.	7.7537	0.28911	0.4391:0.0:0.447:0.1139	.	1288	Q9NS87	KIF15_HUMAN	S	1288;923	ENSP00000324020:T1288S;ENSP00000389982:T923S	ENSP00000324020:T1288S	T	+	1	0	KIF15	44868338	0.004000	0.15560	0.001000	0.08648	0.213000	0.24496	0.013000	0.13310	-1.274000	0.02421	-0.375000	0.07067	ACT	.	.		0.373	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			T	44893334	A	T	44893334	3	4	4	1	0	0	0	0	1	0	0	0	8286	275	10	4	3992	4	KIF15	3	44893334	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	6715235	44893334	153129096	35	294										
BAP1	8314	hgsc.bcm.edu	37	chr3	52440899	52440899	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cccgccgggccttgtctgtcCactcctcgtcctccccccag	8	22	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:52440899C>A	ENST00000460680.1	-	8	1076	c.605G>T	c.(604-606)tGg>tTg	p.W202L	BAP1_ENST00000296288.5_Missense_Mutation_p.W202L	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CTTGTCTGTCCACTCCTCGTC	0.612			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.W202L	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.G605T						.						51	41	44					3																	52440899		2198	4297	6495	SO:0001583	missense	8314	exon8			TCTGTCCACTCCT	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.605G>T	chr3.hg19:g.52440899C>A	ENSP00000417132:p.Trp202Leu	134.0	0.0		46.0	29.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	C	34	5.400744	0.96030	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.51817	0.69;0.69	6.04	6.04	0.98038	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	T	0.76593	0.4009	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78979	-0.1990	10	0.59425	D	0.04	-3.2529	20.1995	0.98256	0.0:1.0:0.0:0.0	.	202	Q92560	BAP1_HUMAN	L	202	ENSP00000417132:W202L;ENSP00000296288:W202L	ENSP00000296288:W202L	W	-	2	0	BAP1	52415939	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.783000	0.85696	2.876000	0.98609	0.650000	0.86243	TGG	.	.		0.612	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52440899	C	A	52440899	3	1	4	1	0	0	0	0	1	0	0	0	1311	595	21	3	1624	3	BAP1	3	52440899	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	7547565	52440899	145581531	36	295										
FLNB	2317	hgsc.bcm.edu	37	chr3	57994371	57994371	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cacgttcacacgctggtgcaAcgagcacctcaagtgcgtga	11	13	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:57994371A>G	ENST00000295956.4	+	1	245	c.80A>G	c.(79-81)aAc>aGc	p.N27S	FLNB_ENST00000357272.4_Missense_Mutation_p.N27S|FLNB_ENST00000429972.2_Missense_Mutation_p.N27S|FLNB_ENST00000490882.1_Missense_Mutation_p.N27S|FLNB_ENST00000348383.5_Missense_Mutation_p.N27S|FLNB_ENST00000358537.3_Missense_Mutation_p.N27S	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	27	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CGCTGGTGCAACGAGCACCTC	0.617																																					p.N27S		Atlas-SNP	.											.	FLNB	430	.	0			c.A80G						.						100	84	89					3																	57994371		2203	4300	6503	SO:0001583	missense	2317	exon1			GGTGCAACGAGCA	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.80A>G	chr3.hg19:g.57994371A>G	ENSP00000295956:p.Asn27Ser	242.0	0.0		70.0	16.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	34	5.412446	0.96072	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272	D;D;D;D;D;D	0.98150	-4.75;-4.75;-4.75;-4.75;-4.75;-4.75	5.52	5.52	0.82312	Actinin-type, actin-binding, conserved site (1);Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.99187	0.9718	H	0.97732	4.065	0.80722	D	1	D;D;D;D	0.76494	0.997;0.999;0.997;0.997	D;D;D;D	0.70935	0.95;0.957;0.971;0.971	D	0.98968	1.0800	10	0.87932	D	0	.	15.3124	0.74045	1.0:0.0:0.0:0.0	.	27;27;27;27	O75369-2;B2ZZ83;Q60FE7;O75369	.;.;.;FLNB_HUMAN	S	27	ENSP00000295956:N27S;ENSP00000420213:N27S;ENSP00000351339:N27S;ENSP00000415599:N27S;ENSP00000232447:N27S;ENSP00000349819:N27S	ENSP00000295956:N27S	N	+	2	0	FLNB	57969411	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.100000	0.94213	2.112000	0.64535	0.477000	0.44152	AAC	.	.		0.617	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		G	57994371	A	G	57994371	3	3	4	1	0	0	0	0	1	0	0	0	5942	43	2	2	82	2	FLNB	3	57994371	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	5553472	57994371	140028059	37	296										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77623726	77623726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aggtctgcaggcgacatcttCgtggcagaatttagatgcca	12	9	2	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:77623726C>T	ENST00000461745.1	+	14	2948	c.2048C>T	c.(2047-2049)tCg>tTg	p.S683L	ROBO2_ENST00000332191.8_Missense_Mutation_p.S683L|ROBO2_ENST00000487694.3_Missense_Mutation_p.S699L	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	683	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)	p.S683L(1)|p.S699L(1)		NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GCGACATCTTCGTGGCAGAAT	0.448																																					p.S683L		Atlas-SNP	.											ROBO2_ENST00000487694,rectum,carcinoma,0,2	ROBO2	527	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2048T						.						101	91	94					3																	77623726		1917	4129	6046	SO:0001583	missense	6092	exon14			CATCTTCGTGGCA	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.2048C>T	chr3.hg19:g.77623726C>T	ENSP00000417164:p.Ser683Leu	109.0	1.0		159.0	36.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	C	8.393	0.840121	0.16891	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.57436	0.4;0.4;0.4	5.7	4.82	0.62117	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.147300	0.06721	N	0.774782	T	0.49389	0.1554	L	0.46157	1.445	0.25363	N	0.988766	B;B;B	0.27380	0.177;0.025;0.056	B;B;B	0.25884	0.064;0.05;0.041	T	0.49808	-0.8900	9	0.46703	T	0.11	.	10.706	0.45956	0.0:0.8315:0.0:0.1685	.	699;683;683	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	L	699;699;703;683;683;404	ENSP00000417335:S699L;ENSP00000417164:S683L;ENSP00000327536:S683L	ENSP00000327536:S683L	S	+	2	0	ROBO2	77706416	0.002000	0.14202	0.003000	0.11579	0.076000	0.17211	1.911000	0.39937	1.374000	0.46228	0.585000	0.79938	TCG	.	.		0.448	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		T	77623726	C	T	77623726	3	4	4	1	0	0	0	0	1	0	0	0	13529	893	31	1	2104	1	ROBO2	3	77623726	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	19629355	77623726	120398704	38	297										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77629133	77629133	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aatgaaacgcgattccatatCaacaaaactgtggatgcagc	8	9	1	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:77629133C>G	ENST00000461745.1	+	16	3264	c.2364C>G	c.(2362-2364)atC>atG	p.I788M	ROBO2_ENST00000332191.8_Missense_Mutation_p.I788M|ROBO2_ENST00000487694.3_Missense_Mutation_p.I804M	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	788	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GATTCCATATCAACAAAACTG	0.428																																					p.I788M		Atlas-SNP	.											.	ROBO2	527	.	0			c.C2364G						.						133	127	129					3																	77629133		1891	4109	6000	SO:0001583	missense	6092	exon16			CCATATCAACAAA	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.2364C>G	chr3.hg19:g.77629133C>G	ENSP00000417164:p.Ile788Met	63.0	0.0		84.0	19.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.434252	0.43224	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.57752	0.38;0.38;0.38	5.53	4.65	0.58169	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41194	U	0.000921	T	0.63977	0.2557	M	0.62723	1.935	0.37487	D	0.916220	D;P;D	0.52996	0.957;0.906;0.957	P;P;P	0.61397	0.888;0.859;0.839	T	0.73260	-0.4039	9	0.48119	T	0.1	.	9.6906	0.40125	0.1408:0.785:0.0:0.0743	.	804;788;788	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	M	804;804;808;788;788;509	ENSP00000417335:I804M;ENSP00000417164:I788M;ENSP00000327536:I788M	ENSP00000327536:I788M	I	+	3	3	ROBO2	77711823	1.000000	0.71417	1.000000	0.80357	0.490000	0.33462	0.699000	0.25586	1.322000	0.45245	0.563000	0.77884	ATC	.	.		0.428	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		G	77629133	C	G	77629133	3	3	4	1	0	0	0	0	1	0	0	0	13529	816	29	4	2428	4	ROBO2	3	77629133	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	5407	77629133	120393297	39	298										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78763622	78763622	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	acaagtgtatgaacccatgtCaccagctgtcaccttcctaa	6	13	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:78763622C>A	ENST00000464233.1	-	8	1083	c.970G>T	c.(970-972)Gac>Tac	p.D324Y	ROBO1_ENST00000467549.1_Missense_Mutation_p.D285Y|ROBO1_ENST00000495273.1_Missense_Mutation_p.D285Y|ROBO1_ENST00000436010.2_Missense_Mutation_p.D285Y	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	324	Ig-like C2-type 3.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GAACCCATGTCACCAGCTGTC	0.398																																					p.D324Y		Atlas-SNP	.											.	ROBO1	833	.	0			c.G970T						.						98	97	97					3																	78763622		1964	4165	6129	SO:0001583	missense	6091	exon8			CCATGTCACCAGC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.970G>T	chr3.hg19:g.78763622C>A	ENSP00000420321:p.Asp324Tyr	124.0	0.0		99.0	44.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.558596	0.86231	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54	5.31	5.31	0.75309	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93374	0.7887	H	0.96208	3.785	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.999	D	0.95288	0.8392	9	.	.	.	.	18.9684	0.92706	0.0:1.0:0.0:0.0	.	324;285;285;285	Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	ROBO1_HUMAN;.;.;.	Y	285;285;324;285;285;324	ENSP00000406043:D285Y;ENSP00000420321:D324Y;ENSP00000420637:D285Y;ENSP00000417992:D285Y	.	D	-	1	0	ROBO1	78846312	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.487000	0.81328	2.490000	0.84030	0.563000	0.77884	GAC	.	.		0.398	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78763622	C	A	78763622	3	1	4	1	0	0	0	0	1	0	0	0	13528	826	29	3	4094	3	ROBO1	3	78763622	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	1134489	78763622	119258808	40	299										
ABCC5	10057	hgsc.bcm.edu	37	chr3	183643410	183643410	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gcaggcgatgggcaatggtcAgcatggtacagtctgcaaat	14	8	2	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:183643410A>G	ENST00000334444.6	-	29	4385	c.4145T>C	c.(4144-4146)cTg>cCg	p.L1382P	ABCC5_ENST00000265586.6_Missense_Mutation_p.L1339P	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	1382	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	GGCAATGGTCAGCATGGTACA	0.507																																					p.L1382P		Atlas-SNP	.											.	ABCC5	142	.	0			c.T4145C						.						157	154	155					3																	183643410		2067	4210	6277	SO:0001583	missense	10057	exon29			ATGGTCAGCATGG	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.4145T>C	chr3.hg19:g.183643410A>G	ENSP00000333926:p.Leu1382Pro	100.0	0.0		64.0	13.0	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Missense_Mutation	SNP	ENST00000334444.6	hg19	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.580325	0.86645	.	.	ENSG00000114770	ENST00000334444;ENST00000265586	D;D	0.84589	-1.87;-1.87	4.91	4.91	0.64330	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.64402	D	0.000005	D	0.94069	0.8099	M	0.93507	3.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.95503	0.8579	10	0.87932	D	0	-10.8238	14.7136	0.69251	1.0:0.0:0.0:0.0	.	1339;1382	Q86UX3;O15440	.;MRP5_HUMAN	P	1382;1339	ENSP00000333926:L1382P;ENSP00000265586:L1339P	ENSP00000265586:L1339P	L	-	2	0	ABCC5	185126104	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.085000	0.94083	2.066000	0.61787	0.533000	0.62120	CTG	.	.		0.507	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		G	183643410	A	G	183643410	3	3	4	1	0	0	0	0	1	0	0	0	56	188	7	2	176	2	ABCC5	3	183643410	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	104879788	183643410	14379020	41	300										
ACAP2	23527	hgsc.bcm.edu	37	chr3	195063318	195063318	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cttgggcattttttactaacGcattttctttttcttcactg	5	9	3	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:195063318G>A	ENST00000326793.6	-	6	640	c.410C>T	c.(409-411)gCg>gTg	p.A137V		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	137	BAR.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						TTTTACTAACGCATTTTCTTT	0.333																																					p.A137V		Atlas-SNP	.											.	ACAP2	72	.	0			c.C410T						.						192	174	180					3																	195063318		2203	4300	6503	SO:0001583	missense	23527	exon6			ACTAACGCATTTT		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.410C>T	chr3.hg19:g.195063318G>A	ENSP00000324287:p.Ala137Val	139.0	0.0		102.0	39.0	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	hg19	CCDS33924.1	.	.	.	.	.	.	.	.	.	.	G	35	5.422139	0.96111	.	.	ENSG00000114331	ENST00000326793	T	0.00504	6.94	6.08	6.08	0.98989	.	0.509728	0.21860	N	0.068043	T	0.00998	0.0033	M	0.73430	2.235	0.80722	D	1	P	0.51653	0.947	P	0.44422	0.449	T	0.71494	-0.4576	10	0.62326	D	0.03	.	19.6516	0.95815	0.0:0.0:1.0:0.0	.	137	Q15057	ACAP2_HUMAN	V	137	ENSP00000324287:A137V	ENSP00000324287:A137V	A	-	2	0	ACAP2	196544607	1.000000	0.71417	0.990000	0.47175	0.902000	0.53008	9.414000	0.97362	2.894000	0.99253	0.655000	0.94253	GCG	.	.		0.333	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287		A	195063318	G	A	195063318	3	1	4	1	0	0	0	0	1	0	0	0	119	1087	38	1	1998	1	ACAP2	3	195063318	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	11419908	195063318	2959112	42	301										
MUC4	4585	hgsc.bcm.edu	37	chr3	195501076	195501076	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cggagagaggagccaaggggGaagccagtcgccggcttgaa	18	9	0	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr3:195501076G>C	ENST00000346145.4	-	3	375	c.336C>G	c.(334-336)ttC>ttG	p.F112L	MUC4_ENST00000463781.3_Missense_Mutation_p.F4348L|MUC4_ENST00000475231.1_Missense_Mutation_p.F4348L|MUC4_ENST00000349607.4_Missense_Mutation_p.F61L	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1105					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGCCAAGGGGGAAGCCAGTCG	0.652																																					p.F4348L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C13044G						.						42	41	41					3																	195501076		2202	4300	6502	SO:0001583	missense	4585	exon4			AAGGGGGAAGCCA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.336C>G	chr3.hg19:g.195501076G>C	ENSP00000304207:p.Phe112Leu	337.0	0.0		210.0	12.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	hg19	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	.	11.25	1.582544	0.28180	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.48522	0.81;1.18;1.12;0.97	5.27	1.38	0.22167	.	0.000000	0.50627	D	0.000115	T	0.61337	0.2339	M	0.74258	2.255	0.25756	N	0.985009	D;D;D;D	0.89917	0.993;1.0;1.0;1.0	D;D;D;D	0.91635	0.935;0.997;0.999;0.999	T	0.51180	-0.8738	10	0.32370	T	0.25	-23.5089	7.8608	0.29509	0.4503:0.0:0.5497:0.0	.	4220;1105;61;112	E7ESK3;Q99102;Q99102-12;Q99102-13	.;MUC4_HUMAN;.;.	L	61;112;4348;4348;1074	ENSP00000338109:F61L;ENSP00000304207:F112L;ENSP00000417498:F4348L;ENSP00000420243:F4348L	ENSP00000304207:F112L	F	-	3	2	MUC4	196986710	0.998000	0.40836	0.981000	0.43875	0.040000	0.13550	0.186000	0.16978	0.213000	0.20722	-0.155000	0.13514	TTC	.	.		0.652	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		C	195501076	G	C	195501076	3	2	4	1	0	0	0	0	1	0	0	0	9987	1165	41	4	3282	4	MUC4	3	195501076	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	437758	195501076	2521354	43	302										
C4orf22	255119	hgsc.bcm.edu	37	chr4	81256985	81256985	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	actcaattcaacgcctatgaAgatttcctggactcgcagat	7	11	2	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr4:81256985A>C	ENST00000358105.3	+	1	112	c.63A>C	c.(61-63)gaA>gaC	p.E21D	C4orf22_ENST00000508675.1_Missense_Mutation_p.E21D|C4orf22_ENST00000512931.1_3'UTR	NM_152770.2	NP_689983.2	Q6V702	CD022_HUMAN	chromosome 4 open reading frame 22	21										NS(1)|large_intestine(3)|lung(5)|prostate(1)|skin(5)	15						ACGCCTATGAAGATTTCCTGG	0.582											OREG0016247	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E21D		Atlas-SNP	.											.	C4orf22	35	.	0			c.A63C						.						121	113	116					4																	81256985		2203	4300	6503	SO:0001583	missense	255119	exon1			CTATGAAGATTTC	BC034296	CCDS3587.1, CCDS56336.1	4q21.21	2008-02-05			ENSG00000197826	ENSG00000197826			28554	protein-coding gene	gene with protein product						12477932	Standard	NM_152770		Approved		uc010ijp.3	Q6V702	OTTHUMG00000130289	ENST00000358105.3:c.63A>C	chr4.hg19:g.81256985A>C	ENSP00000350818:p.Glu21Asp	80.0	0.0	1204	39.0	10.0	NM_152770	E7EQ13|Q6ZQY4|Q8N4G9	Missense_Mutation	SNP	ENST00000358105.3	hg19	CCDS3587.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.621567	0.46736	.	.	ENSG00000197826	ENST00000358105;ENST00000508675	T;T	0.36878	1.23;1.23	5.44	0.00784	0.14072	.	0.000000	0.85682	D	0.000000	T	0.43456	0.1248	M	0.67700	2.07	0.31451	N	0.670712	D;P	0.53745	0.962;0.748	P;P	0.53490	0.727;0.536	T	0.51196	-0.8736	10	0.42905	T	0.14	.	9.2036	0.37275	0.5082:0.0:0.4918:0.0	.	21;21	E7EQ13;Q6V702	.;CD022_HUMAN	D	21	ENSP00000350818:E21D;ENSP00000425786:E21D	ENSP00000350818:E21D	E	+	3	2	C4orf22	81476009	0.998000	0.40836	0.994000	0.49952	0.175000	0.22909	0.245000	0.18142	-0.115000	0.11915	-0.912000	0.02778	GAA	.	.		0.582	C4orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252629.2	NM_152770		C	81256985	A	C	81256985	3	2	4	1	0	0	0	0	1	0	0	0	2257	69	3	5	65	5	C4orf22	4	81256985	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10		81256985	109897291	44	303										
ANK2	287	hgsc.bcm.edu	37	chr4	114276315	114276315	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tcaacacaacatttccactcGactacatgaaagatgagttc	5	11	1	3	rs552900652		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr4:114276315G>C	ENST00000357077.4	+	38	6594	c.6541G>C	c.(6541-6543)Gac>Cac	p.D2181H	ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.D2148H|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2181					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ATTTCCACTCGACTACATGAA	0.463																																					p.D2181H		Atlas-SNP	.											.	ANK2	576	.	0			c.G6541C						.						126	118	120					4																	114276315		2203	4300	6503	SO:0001583	missense	287	exon38			CCACTCGACTACA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.6541G>C	chr4.hg19:g.114276315G>C	ENSP00000349588:p.Asp2181His	79.0	0.0		132.0	15.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	G	8.875	0.950343	0.18431	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.69806	-0.42;-0.43	5.87	5.87	0.94306	.	0.195946	0.35291	N	0.003319	T	0.80330	0.4603	M	0.62723	1.935	0.41193	D	0.986311	D;D	0.76494	0.971;0.999	P;D	0.67382	0.68;0.951	T	0.77264	-0.2652	9	.	.	.	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	2148;2181	Q01484;Q01484-4	ANK2_HUMAN;.	H	2181;2148	ENSP00000349588:D2181H;ENSP00000264366:D2148H	.	D	+	1	0	ANK2	114495764	1.000000	0.71417	0.113000	0.21522	0.142000	0.21351	4.140000	0.58031	2.941000	0.99782	0.655000	0.94253	GAC	.	.		0.463	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		C	114276315	G	C	114276315	3	2	4	1	0	0	0	0	1	0	0	0	621	1058	37	4	6756	4	ANK2	4	114276315	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	33019330	114276315	76877961	45	304										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123122219	123122219	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	catgccgcagacatggcagtGtgaattagaggtttataaag	12	6	0	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr4:123122219G>T	ENST00000264501.4	+	15	1809	c.1436G>T	c.(1435-1437)tGt>tTt	p.C479F	KIAA1109_ENST00000388738.3_Missense_Mutation_p.C479F|KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000455637.1_Missense_Mutation_p.C479F			Q2LD37	K1109_HUMAN	KIAA1109	479					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ACATGGCAGTGTGAATTAGAG	0.358																																					p.C479F		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G1436T						.						91	84	86					4																	123122219		1884	4123	6007	SO:0001583	missense	84162	exon13			GGCAGTGTGAATT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1436G>T	chr4.hg19:g.123122219G>T	ENSP00000264501:p.Cys479Phe	97.0	0.0		71.0	16.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.786868	0.70337	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637	D;D;D	0.92752	-3.1;-3.1;-3.1	5.93	5.93	0.95920	.	7739.210000	0.00531	N	0.000208	D	0.95598	0.8569	L	0.39245	1.2	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	D	0.84544	0.0640	10	0.23891	T	0.37	.	20.3465	0.98790	0.0:0.0:1.0:0.0	.	479	Q2LD37	K1109_HUMAN	F	479	ENSP00000264501:C479F;ENSP00000373390:C479F;ENSP00000389925:C479F	ENSP00000264501:C479F	C	+	2	0	KIAA1109	123341669	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.750000	0.98875	2.798000	0.96311	0.655000	0.94253	TGT	.	.		0.358	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123122219	G	T	123122219	3	4	4	1	0	0	0	0	1	0	0	0	8217	1377	48	3	1486	3	KIAA1109	4	123122219	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	8845904	123122219	68032057	46	305										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123165177	123165177	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cccctggtggctgaagctttAgacaggtattgattttgtct	11	8	1	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr4:123165177A>T	ENST00000264501.4	+	31	5284	c.4911A>T	c.(4909-4911)ttA>ttT	p.L1637F	KIAA1109_ENST00000388738.3_Missense_Mutation_p.L1637F|KIAA1109_ENST00000455637.1_Missense_Mutation_p.L1637F			Q2LD37	K1109_HUMAN	KIAA1109	1637					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CTGAAGCTTTAGACAGGTATT	0.388																																					p.L1637F		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A4911T						.						155	143	147					4																	123165177		1862	4090	5952	SO:0001583	missense	84162	exon29			AGCTTTAGACAGG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.4911A>T	chr4.hg19:g.123165177A>T	ENSP00000264501:p.Leu1637Phe	133.0	0.0		163.0	63.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.1|20.1	3.936975|3.936975	0.73557|0.73557	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000446180	T;T;T|.	0.30714|.	2.11;2.11;1.52|.	5.65|5.65	1.98|1.98	0.26296|0.26296	.|.	0.000000|.	0.35646|.	U|.	0.003078|.	T|.	0.39655|.	0.1086|.	N|N	0.24115|0.24115	0.695|0.695	0.47819|0.47819	D|D	0.999524|0.999524	P;P|.	0.44627|.	0.835;0.839|.	P;P|.	0.49332|.	0.607;0.526|.	T|.	0.07424|.	-1.0773|.	10|.	0.87932|.	D|.	0|.	.|.	8.0898|8.0898	0.30795|0.30795	0.6201:0.0:0.3799:0.0|0.6201:0.0:0.3799:0.0	.|.	1636;1637|.	Q2LD37-2;Q2LD37|.	.;K1109_HUMAN|.	F|L	1637|210	ENSP00000264501:L1637F;ENSP00000373390:L1637F;ENSP00000389925:L1637F|.	ENSP00000264501:L1637F|.	L|X	+|+	3|2	2|0	KIAA1109|KIAA1109	123384627|123384627	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	1.712000|1.712000	0.37940|0.37940	0.427000|0.427000	0.26145|0.26145	0.460000|0.460000	0.39030|0.39030	TTA|TAG	.	.		0.388	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123165177	A	T	123165177	3	4	4	1	0	0	0	0	1	0	0	0	8217	417	15	4	5025	4	KIAA1109	4	123165177	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	42958	123165177	67989099	47	306										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155219388	155219388	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tcattaacatcagtgacataTacttttataattacagtggt	5	6	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr4:155219388T>C	ENST00000357232.4	-	18	4712	c.4713A>G	c.(4711-4713)gtA>gtG	p.V1571V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1571	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CAGTGACATATACTTTTATAA	0.448																																					p.V1571V		Atlas-SNP	.											.	DCHS2	594	.	0			c.A4713G						.						99	99	99					4																	155219388		2203	4300	6503	SO:0001819	synonymous_variant	54798	exon18			GACATATACTTTT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4713A>G	chr4.hg19:g.155219388T>C		185.0	0.0		168.0	65.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	hg19	CCDS3785.1																																																																																			.	.		0.448	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		C	155219388	T	C	155219388	2	2	4	1	0	0	0	0	0	0	0	1	4290	1393	49	2		2	DCHS2	4	155219388	Silent	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	32054211	155219388	35934888	48	307										
CARD6	84674	hgsc.bcm.edu	37	chr5	40853355	40853355	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tctcttcttgcctcagatgtGtgtctgtggaggatatggcc	12	9	4	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr5:40853355G>C	ENST00000254691.5	+	3	2120	c.1921G>C	c.(1921-1923)Gtg>Ctg	p.V641L	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	641					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						CCTCAGATGTGTGTCTGTGGA	0.507																																					p.V641L		Atlas-SNP	.											.	CARD6	141	.	0			c.G1921C						.						141	144	143					5																	40853355		2203	4300	6503	SO:0001583	missense	84674	exon3			AGATGTGTGTCTG	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.1921G>C	chr5.hg19:g.40853355G>C	ENSP00000254691:p.Val641Leu	100.0	0.0		74.0	12.0	NM_032587	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	hg19	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	G	10.82	1.458644	0.26248	.	.	ENSG00000132357	ENST00000254691	T	0.15487	2.42	5.0	2.19	0.27852	.	0.136498	0.33457	N	0.004897	T	0.14442	0.0349	L	0.58428	1.81	0.50039	D	0.999841	B	0.21309	0.054	B	0.18263	0.021	T	0.07635	-1.0762	10	0.38643	T	0.18	-5.2146	4.4097	0.11427	0.1869:0.0:0.6363:0.1768	.	641	Q9BX69	CARD6_HUMAN	L	641	ENSP00000254691:V641L	ENSP00000254691:V641L	V	+	1	0	CARD6	40889112	0.005000	0.15991	0.517000	0.27799	0.859000	0.49053	0.534000	0.23098	0.274000	0.22072	0.561000	0.74099	GTG	.	.		0.507	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			C	40853355	G	C	40853355	3	2	4	1	0	0	0	0	1	0	0	0	2652	1377	48	4	1931	4	CARD6	5	40853355	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10		40853355	140061905	49	308										
IL31RA	133396	hgsc.bcm.edu	37	chr5	55147432	55147432	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aactcaagtttttcaccacgGcatgtgtctgtgaatgtccg	9	10	3	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr5:55147432G>C	ENST00000447346.2	+	1	99	c.34G>C	c.(34-36)Gca>Cca	p.A12P	IL31RA_ENST00000354961.4_5'Flank|IL31RA_ENST00000396836.2_Missense_Mutation_p.A12P|IL31RA_ENST00000359040.5_Missense_Mutation_p.A12P|IL31RA_ENST00000490985.1_5'Flank|IL31RA_ENST00000297015.3_5'Flank|IL31RA_ENST00000396834.1_5'UTR	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	0					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				tttcaccacggcatgtgtctg	0.438																																					p.A12P		Atlas-SNP	.											.	IL31RA	84	.	0			c.G34C						.						149	152	151					5																	55147432		1989	4166	6155	SO:0001583	missense	133396	exon1			ACCACGGCATGTG	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.34G>C	chr5.hg19:g.55147432G>C	ENSP00000415900:p.Ala12Pro	70.0	0.0		69.0	30.0	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	hg19	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	.	9.523	1.108740	0.20714	.	.	ENSG00000164509	ENST00000396836;ENST00000447346;ENST00000359040	T;T;T	0.42513	1.11;1.0;0.97	1.91	-0.103	0.13609	.	1.979650	0.02851	N	0.129101	T	0.47820	0.1466	.	.	.	0.09310	N	1	D;D;D	0.53885	0.963;0.963;0.963	P;P;P	0.52343	0.696;0.696;0.696	T	0.29701	-1.0003	9	0.59425	D	0.04	.	4.6121	0.12408	0.3668:0.0:0.6332:0.0	.	12;12;12	Q8NI17-5;Q8NI17-2;Q8NI17-8	.;.;.	P	12	ENSP00000380048:A12P;ENSP00000415900:A12P;ENSP00000351935:A12P	ENSP00000351935:A12P	A	+	1	0	IL31RA	55183189	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.368000	0.07543	-0.047000	0.13423	0.491000	0.48974	GCA	.	.		0.438	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		C	55147432	G	C	55147432	3	2	4	1	0	0	0	0	1	0	0	0	7700	1203	42	4	36	4	IL31RA	5	55147432	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	14294077	55147432	125767828	50	309										
ERCC8	1161	hgsc.bcm.edu	37	chr5	60200668	60200668	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ggagacatatgatgactataAactgtttcctcaaaattaaa	6	6	1	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr5:60200668A>C	ENST00000265038.5	-	5	474	c.432T>G	c.(430-432)gtT>gtG	p.V144V	ERCC8_ENST00000426742.2_Silent_p.V86V|ERCC8_ENST00000462279.1_5'UTR|ERCC8_ENST00000543101.1_Intron	NM_000082.3	NP_000073.1	Q13216	ERCC8_HUMAN	excision repair cross-complementation group 8	144					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|positive regulation of DNA repair (GO:0045739)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|transcription-coupled nucleotide-excision repair (GO:0006283)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|protein complex (GO:0043234)	protein complex binding (GO:0032403)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)				GATGACTATAAACTGTTTCCT	0.308																																					p.V144V		Atlas-SNP	.											.	ERCC8	31	.	0			c.T432G						.						108	109	108					5																	60200668		2203	4298	6501	SO:0001819	synonymous_variant	1161	exon5			ACTATAAACTGTT	U28413	CCDS3978.1	5q12.1	2014-09-17	2014-03-07		ENSG00000049167	ENSG00000049167		"WD repeat domain containing"	3439	protein-coding gene	gene with protein product		609412	"Cockayne syndrome 1 (classical)", "excision repair cross-complementing rodent repair deficiency, complementation group 8"	CKN1		8596535	Standard	NM_000082		Approved	CSA	uc003jsm.3	Q13216	OTTHUMG00000097741	ENST00000265038.5:c.432T>G	chr5.hg19:g.60200668A>C		293.0	0.0		223.0	10.0	NM_000082	B2RB64|Q6FHX5|Q96GB9	Silent	SNP	ENST00000265038.5	hg19	CCDS3978.1																																																																																			.	.		0.308	ERCC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214971.2	NM_000082		C	60200668	A	C	60200668	2	2	4	1	0	0	0	0	0	0	0	1	5221	1	1	5		5	ERCC8	5	60200668	Silent	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	5053236	60200668	120714592	51	310										
ANKRA2	57763	hgsc.bcm.edu	37	chr5	72857113	72857113	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	atgtatggatattgcattcaGctaagtgaaaaacaaatgta	8	4	1	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr5:72857113G>C	ENST00000296785.3	-	3	948	c.290C>G	c.(289-291)gCt>gGt	p.A97G		NM_023039.4	NP_075526.1	Q9H9E1	ANRA2_HUMAN	ankyrin repeat, family A (RFXANK-like), 2	97						cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	low-density lipoprotein particle binding (GO:0030169)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		Lung NSC(167;0.0378)|Ovarian(174;0.0908)		OV - Ovarian serous cystadenocarcinoma(47;3.71e-54)		ATTGCATTCAGCTAAGTGAAA	0.363																																					p.A97G		Atlas-SNP	.											.	ANKRA2	23	.	0			c.C290G						.						138	121	127					5																	72857113		2203	4300	6503	SO:0001630	splice_region_variant	57763	exon3			CATTCAGCTAAGT	AA442702	CCDS4020.1	5q12-q13	2013-01-10			ENSG00000164331	ENSG00000164331		"Ankyrin repeat domain containing"	13208	protein-coding gene	gene with protein product		605787				10965114	Standard	NM_023039		Approved		uc003kcu.2	Q9H9E1	OTTHUMG00000102030	ENST00000296785.3:c.290-1C>G	chr5.hg19:g.72857113G>C		98.0	0.0		105.0	42.0	NM_023039		Missense_Mutation	SNP	ENST00000296785.3	hg19	CCDS4020.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.809262	0.50421	.	.	ENSG00000164331	ENST00000296785	T	0.40476	1.03	4.84	4.84	0.62591	Ankyrin repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.40119	0.1104	L	0.44542	1.39	0.80722	D	1	B;B	0.20780	0.043;0.048	B;B	0.28011	0.085;0.022	T	0.19128	-1.0315	10	0.25751	T	0.34	.	18.0124	0.89227	0.0:0.0:1.0:0.0	.	97;97	D6RBK8;Q9H9E1	.;ANRA2_HUMAN	G	97	ENSP00000296785:A97G	ENSP00000296785:A97G	A	-	2	0	ANKRA2	72892869	1.000000	0.71417	0.998000	0.56505	0.640000	0.38277	9.350000	0.97070	2.246000	0.74042	0.449000	0.29647	GCT	.	.		0.363	ANKRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219814.2	NM_023039	Missense_Mutation	C	72857113	G	C	72857113	5	2	4	1	0	0	0	0	0	0	1	0	636	985	34	4	679	4	ANKRA2	5	72857113	Splice_Site	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	12656445	72857113	108058147	52	311										
PHF15	23338	hgsc.bcm.edu	37	chr5	133873703	133873703	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tgcgacatctacatccgcatCaagatgctccaaactgccca	6	15	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr5:133873703C>A	ENST00000402835.1	+	3	338	c.83C>A	c.(82-84)tCa>tAa	p.S28*	PHF15_ENST00000395003.1_Nonsense_Mutation_p.S28*|PHF15_ENST00000361895.2_Nonsense_Mutation_p.S28*|PHF15_ENST00000282605.4_Nonsense_Mutation_p.S28*																NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACATCCGCATCAAGATGCTCC	0.572																																					p.S28X		Atlas-SNP	.											.	PHF15	60	.	0			c.C83A						.						89	83	85					5																	133873703		2203	4300	6503	SO:0001587	stop_gained	23338	exon3			CCGCATCAAGATG																												ENST00000402835.1:c.83C>A	chr5.hg19:g.133873703C>A	ENSP00000384671:p.Ser28*	151.0	0.0		117.0	10.0	NM_015288		Nonsense_Mutation	SNP	ENST00000402835.1	hg19		.	.	.	.	.	.	.	.	.	.	C	38	6.720166	0.97788	.	.	ENSG00000043143	ENST00000512386;ENST00000413974;ENST00000448712;ENST00000282605;ENST00000361895;ENST00000432594;ENST00000402835;ENST00000395003;ENST00000431355	.	.	.	5.77	4.9	0.64082	.	23.323500	0.00166	N	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.5355	0.56140	0.0:0.9239:0.0:0.0761	.	.	.	.	X	28;28;44;28;28;28;28;28;28	.	ENSP00000282605:S28X	S	+	2	0	PHF15	133901602	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	3.157000	0.50716	2.724000	0.93272	0.561000	0.74099	TCA	.	.		0.572	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1			A	133873703	C	A	133873703	4	1	4	1	0	0	0	0	0	1	0	0	11835	838	29	3	89	3	PHF15	5	133873703	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	61016590	133873703	47041557	53	312										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135651385	135651385	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	catcaccgtttaaaattgctTccacctcttctgtgtctcgg	6	13	4	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr5:135651385T>C	ENST00000513104.1	-	3	1145	c.863A>G	c.(862-864)gAa>gGa	p.E288G	TRPC7_ENST00000426057.2_Intron|TRPC7_ENST00000355180.3_Intron|TRPC7-AS2_ENST00000513958.1_RNA	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	288					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TAAAATTGCTTCCACCTCTTC	0.458																																					p.E288G		Atlas-SNP	.											.	TRPC7	126	.	0			c.A863G						.						101	105	103					5																	135651385		2070	4222	6292	SO:0001583	missense	57113	exon3			ATTGCTTCCACCT	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.863A>G	chr5.hg19:g.135651385T>C	ENSP00000426070:p.Glu288Gly	87.0	0.0		102.0	31.0	NM_020389	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	hg19	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	T	22.4	4.281495	0.80692	.	.	ENSG00000069018	ENST00000513104;ENST00000265193	T	0.63744	-0.06	5.64	5.64	0.86602	.	0.049405	0.85682	D	0.000000	T	0.73125	0.3547	M	0.83223	2.63	0.80722	D	1	P;B	0.43314	0.803;0.054	P;B	0.47626	0.552;0.094	T	0.77281	-0.2646	10	0.59425	D	0.04	-18.7765	16.0238	0.80522	0.0:0.0:0.0:1.0	.	288;288	Q70T25;Q9HCX4	.;TRPC7_HUMAN	G	288	ENSP00000426070:E288G	ENSP00000265193:E288G	E	-	2	0	TRPC7	135679284	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.138000	0.71717	2.367000	0.80283	0.528000	0.53228	GAA	.	.		0.458	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		C	135651385	T	C	135651385	3	2	4	1	0	0	0	0	1	0	0	0	16599	1783	62	2	1765	2	TRPC7	5	135651385	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	1777682	135651385	45263875	54	313										
PCDHGB6	56100	hgsc.bcm.edu	37	chr5	140787868	140787868	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cccaccctgagtgagccgatCcgctactcgattccggagga	11	15	0	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr5:140787868C>A	ENST00000520790.1	+	1	99	c.99C>A	c.(97-99)atC>atA	p.I33I	PCDHGA4_ENST00000571252.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	33	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGAGCCGATCCGCTACTCGA	0.652											OREG0016861	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I33I		Atlas-SNP	.											.	PCDHGB6	120	.	0			c.C99A						.						36	39	38					5																	140787868		1912	4129	6041	SO:0001819	synonymous_variant	56100	exon1			GCCGATCCGCTAC	AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"Cadherins / Protocadherins : Clustered"	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.99C>A	chr5.hg19:g.140787868C>A		199.0	0.0	1659	86.0	7.0	NM_032100	Q9Y5C5	Silent	SNP	ENST00000520790.1	hg19	CCDS54929.1																																																																																			.	.		0.652	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		A	140787868	C	A	140787868	2	1	4	1	0	0	0	0	0	0	0	1	11576	845	30	3		3	PCDHGB6	5	140787868	Silent	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	5136483	140787868	40127392	55	314										
EBF1	1879	hgsc.bcm.edu	37	chr5	158140067	158140067	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tcatccctgcgtggaccgagGtgttagcaagggccgggagt	16	10	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr5:158140067G>C	ENST00000313708.6	-	13	1562	c.1280C>G	c.(1279-1281)aCc>aGc	p.T427S	EBF1_ENST00000517373.1_Missense_Mutation_p.T419S|EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000380654.4_Missense_Mutation_p.T396S	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	427					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTGGACCGAGGTGTTAGCAAG	0.552			T	HMGA2	lipoma																																p.T427S		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	.	EBF1	110	.	0			c.C1280G						.						128	108	115					5																	158140067		2203	4300	6503	SO:0001583	missense	1879	exon13			ACCGAGGTGTTAG	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"early B-cell factor"	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1280C>G	chr5.hg19:g.158140067G>C	ENSP00000322898:p.Thr427Ser	116.0	0.0		130.0	31.0	NM_024007	Q8IW11	Missense_Mutation	SNP	ENST00000313708.6	hg19	CCDS4343.1	.	.	.	.	.	.	.	.	.	.	G	6.048	0.377166	0.11466	.	.	ENSG00000164330	ENST00000318060;ENST00000313708;ENST00000380654;ENST00000517373	T;T;T	0.28454	1.61;1.61;1.61	5.91	5.91	0.95273	.	0.295799	0.39020	N	0.001489	T	0.16514	0.0397	N	0.04746	-0.17	0.33396	D	0.576777	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.0;0.0;0.001;0.002	T	0.09618	-1.0666	10	0.02654	T	1	-7.445	20.2985	0.98592	0.0:0.0:1.0:0.0	.	427;414;427;396	A8K0Z7;B4E2U8;Q9UH73;Q9UH73-2	.;.;COE1_HUMAN;.	S	427;427;396;419	ENSP00000322898:T427S;ENSP00000370029:T396S;ENSP00000428020:T419S	ENSP00000322898:T427S	T	-	2	0	EBF1	158072645	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.151000	0.64875	2.793000	0.96121	0.655000	0.94253	ACC	.	.		0.552	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		C	158140067	G	C	158140067	3	2	4	1	0	0	0	0	1	0	0	0	4882	1261	44	4	511	4	EBF1	5	158140067	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	17352199	158140067	22775193	56	315										
TTC1	7265	hgsc.bcm.edu	37	chr5	159437674	159437674	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	attcccagagtaagctgctcAgggatgatgaggcccatctc	11	11	2	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr5:159437674A>T	ENST00000231238.5	+	2	249	c.139A>T	c.(139-141)Agg>Tgg	p.R47W	TTC1_ENST00000522793.1_Missense_Mutation_p.R47W|Y_RNA_ENST00000362528.1_RNA	NM_001282500.1|NM_003314.1	NP_001269429.1|NP_003305.1	Q99614	TTC1_HUMAN	tetratricopeptide repeat domain 1	47					protein folding (GO:0006457)	peroxisomal membrane (GO:0005778)	unfolded protein binding (GO:0051082)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|prostate(1)|skin(1)	12	Renal(175;0.00196)	all_hematologic(541;0.00014)|Breast(839;0.0101)|all_neural(177;0.0281)|Medulloblastoma(196;0.0425)|Lung NSC(249;0.119)|all_lung(500;0.163)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Epithelial(171;8.37e-05)|all cancers(165;0.000694)|OV - Ovarian serous cystadenocarcinoma(192;0.0402)		TAAGCTGCTCAGGGATGATGA	0.517																																					p.R47W		Atlas-SNP	.											.	TTC1	26	.	0			c.A139T						.						56	54	55					5																	159437674		2203	4300	6503	SO:0001583	missense	7265	exon2			CTGCTCAGGGATG	U46570	CCDS4348.1	5q32-q33.2	2013-01-10			ENSG00000113312	ENSG00000113312		"Tetratricopeptide (TTC) repeat domain containing"	12391	protein-coding gene	gene with protein product		601963				8836031	Standard	NM_003314		Approved	TPR1	uc003lxu.3	Q99614	OTTHUMG00000130326	ENST00000231238.5:c.139A>T	chr5.hg19:g.159437674A>T	ENSP00000231238:p.Arg47Trp	153.0	0.0		109.0	19.0	NM_003314	B2RCT2|D3DQJ8|Q9BVT3	Missense_Mutation	SNP	ENST00000231238.5	hg19	CCDS4348.1	.	.	.	.	.	.	.	.	.	.	A	9.392	1.075642	0.20227	.	.	ENSG00000113312	ENST00000231238;ENST00000522793	T;T	0.18174	2.23;2.23	5.09	-5.37	0.02681	.	1.622640	0.02937	N	0.139952	T	0.10680	0.0261	N	0.08118	0	0.09310	N	1	B	0.27679	0.185	B	0.16289	0.015	T	0.24297	-1.0164	10	0.66056	D	0.02	-7.8588	17.0131	0.86412	0.2469:0.7531:0.0:0.0	.	47	Q99614	TTC1_HUMAN	W	47	ENSP00000231238:R47W;ENSP00000429225:R47W	ENSP00000231238:R47W	R	+	1	2	TTC1	159370252	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-0.457000	0.06745	-1.283000	0.02393	0.454000	0.30748	AGG	.	.		0.517	TTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252675.3	NM_003314		T	159437674	A	T	159437674	3	4	4	1	0	0	0	0	1	0	0	0	16693	179	7	4	141	4	TTC1	5	159437674	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	1297607	159437674	21477586	57	316										
HLA-B	3106	hgsc.bcm.edu	37	chr6	31324656	31324656	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cgaactgggtgtcgtccacgTagcccactgagatgaagcgg	14	11	0	2	rs281864590		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr6:31324656T>C	ENST00000412585.2	-	2	180	c.152A>G	c.(151-153)tAc>tGc	p.Y51C		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	51	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GTCGTCCACGTAGCCCACTGA	0.677									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.Y51C		Atlas-SNP	.											.	HLA-B	54	.	0			c.A152G						.						33	26	28					6																	31324656		2144	4156	6300	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	TCCACGTAGCCCA	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4932	protein-coding gene	gene with protein product		142830	"ankylosing spondylitis"	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.152A>G	chr6.hg19:g.31324656T>C	ENSP00000399168:p.Tyr51Cys	190.0	0.0		113.0	28.0	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	hg19	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	7.967	0.748333	0.15710	.	.	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.01165	5.24;5.24	3.2	3.2	0.36748	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.265381	0.19817	U	0.105417	T	0.05640	0.0148	H	0.96662	3.86	0.30030	N	0.81353	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.06162	-1.0842	10	0.87932	D	0	.	9.7863	0.40677	0.0:0.0:0.0:1.0	.	51;51;26	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	C	51;62	ENSP00000399168:Y51C;ENSP00000405931:Y62C	ENSP00000399168:Y51C	Y	-	2	0	HLA-B	31432635	1.000000	0.71417	0.966000	0.40874	0.004000	0.04260	1.253000	0.32886	1.476000	0.48215	0.368000	0.22195	TAC	.	.		0.677	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		C	31324656	T	C	31324656	3	2	4	1	0	0	0	0	1	0	0	0	7205	1638	57	2	960	2	HLA-B	6	31324656	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10		31324656	139790411	58	317										
IBTK	25998	hgsc.bcm.edu	37	chr6	82906144	82906144	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agagattccacagaattggtCttaccagactttaataatcc	6	9	1	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr6:82906144C>G	ENST00000306270.7	-	22	3594	c.3045G>C	c.(3043-3045)aaG>aaC	p.K1015N	IBTK_ENST00000510291.1_Intron|IBTK_ENST00000503631.1_Missense_Mutation_p.K814N	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1015					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		CAGAATTGGTCTTACCAGACT	0.353																																					p.K1015N		Atlas-SNP	.											.	IBTK	128	.	0			c.G3045C						.						55	54	54					6																	82906144		2203	4300	6503	SO:0001583	missense	25998	exon22			ATTGGTCTTACCA	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3045G>C	chr6.hg19:g.82906144C>G	ENSP00000305721:p.Lys1015Asn	61.0	0.0		56.0	9.0	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	hg19	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.965176	0.53507	.	.	ENSG00000005700	ENST00000306270;ENST00000503631	T;T	0.36878	1.62;1.23	5.65	2.85	0.33270	.	0.046882	0.85682	D	0.000000	T	0.37293	0.0998	M	0.65498	2.005	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.71184	0.972;0.968;0.929	T	0.19095	-1.0316	10	0.27785	T	0.31	-14.0282	7.2579	0.26187	0.0:0.5682:0.0:0.4318	.	814;1015;1015	E9PDR5;Q9P2D0-2;Q9P2D0	.;.;IBTK_HUMAN	N	1015;814	ENSP00000305721:K1015N;ENSP00000422762:K814N	ENSP00000305721:K1015N	K	-	3	2	IBTK	82962863	0.931000	0.31567	1.000000	0.80357	0.831000	0.47069	0.031000	0.13710	0.840000	0.34995	0.563000	0.77884	AAG	.	.		0.353	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		G	82906144	C	G	82906144	3	3	4	1	0	0	0	0	1	0	0	0	7485	912	32	4	1048	4	IBTK	6	82906144	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	51581488	82906144	88208923	59	318										
QRSL1	55278	hgsc.bcm.edu	37	chr6	107111016	107111016	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	caaagaggacaacagaacccGaagtgcccaggatgatattt	10	9	0	3	rs530501491		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr6:107111016G>A	ENST00000369046.4	+	10	1426	c.1322G>A	c.(1321-1323)cGa>cAa	p.R441Q		NM_018292.4	NP_060762.3			glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1											endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		AACAGAACCCGAAGTGCCCAG	0.433													G|||	1	0.000199681	0	0	5008	,	,		18270	0		0	False		,,,				2504	0.001				p.R441Q	NSCLC(192;2127 2142 11668 26277 49545)	Atlas-SNP	.											.	QRSL1	30	.	0			c.G1322A						.						82	78	79					6																	107111016		2203	4300	6503	SO:0001583	missense	55278	exon10			GAACCCGAAGTGC	AK001851	CCDS5057.1	6q21	2014-08-04			ENSG00000130348	ENSG00000130348			21020	protein-coding gene	gene with protein product	"glutamyl-tRNA(Gln) amidotransferase, subunit A"					11230166, 19805282	Standard	NM_018292		Approved	GatA, FLJ10989, FLJ12189, DKFZP564C1278, FLJ13447	uc003prm.3	Q9H0R6	OTTHUMG00000015301	ENST00000369046.4:c.1322G>A	chr6.hg19:g.107111016G>A	ENSP00000358042:p.Arg441Gln	103.0	0.0		76.0	12.0	NM_018292		Missense_Mutation	SNP	ENST00000369046.4	hg19	CCDS5057.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647666	0.67358	.	.	ENSG00000130348	ENST00000369046	T	0.54479	0.57	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.15478	0.0373	N	0.02973	-0.45	0.80722	D	1	B	0.28470	0.213	B	0.28553	0.091	T	0.21280	-1.0250	10	0.09590	T	0.72	-11.0963	19.2883	0.94087	0.0:0.0:1.0:0.0	.	441	Q9H0R6	GATA_HUMAN	Q	441	ENSP00000358042:R441Q	ENSP00000358042:R441Q	R	+	2	0	QRSL1	107217709	1.000000	0.71417	0.988000	0.46212	0.991000	0.79684	9.476000	0.97823	2.578000	0.87016	0.484000	0.47621	CGA	.	.		0.433	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041667.1	NM_018292		A	107111016	G	A	107111016	3	1	4	1	0	0	0	0	1	0	0	0	12896	1058	37	1	1360	1	QRSL1	6	107111016	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	24204872	107111016	64004051	60	319										
WISP3	8838	hgsc.bcm.edu	37	chr6	112382473	112382473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cagtagacaggcctaggtacGagactggagtgtgtgcatgt	15	7	0	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr6:112382473G>A	ENST00000368666.2	+	2	614	c.328G>A	c.(328-330)Gag>Aag	p.E110K	WISP3_ENST00000368663.3_Missense_Mutation_p.E88K|WISP3_ENST00000409166.1_5'Flank|WISP3_ENST00000361714.1_Missense_Mutation_p.E128K|WISP3_ENST00000230529.5_Missense_Mutation_p.E110K|WISP3_ENST00000604763.1_Missense_Mutation_p.E110K	NM_198239.1	NP_937882.1	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	110	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	13		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		GCCTAGGTACGAGACTGGAGT	0.458																																					p.E128K		Atlas-SNP	.											.	WISP3	33	.	0			c.G382A						.						121	108	113					6																	112382473		2203	4300	6503	SO:0001583	missense	8838	exon2			AGGTACGAGACTG	AF100781	CCDS5097.1, CCDS5098.1	6q21	2014-05-06			ENSG00000112761	ENSG00000112761			12771	protein-coding gene	gene with protein product		603400				9843955	Standard	NM_003880		Approved	CCN6	uc003pvo.3	O95389	OTTHUMG00000185101	ENST00000368666.2:c.328G>A	chr6.hg19:g.112382473G>A	ENSP00000357655:p.Glu110Lys	107.0	0.0		115.0	20.0	NM_198239	Q3KR29|Q5H8W4|Q6UXH6	Missense_Mutation	SNP	ENST00000368666.2	hg19	CCDS5098.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.062988	0.55432	.	.	ENSG00000112761	ENST00000368666;ENST00000230529;ENST00000361714;ENST00000541400;ENST00000368663	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	4.51	3.57	0.40892	Insulin-like growth factor-binding protein, IGFBP (2);	0.255500	0.39985	N	0.001202	T	0.53981	0.1830	L	0.58302	1.8	0.50171	D	0.999858	D;D	0.63046	0.992;0.982	P;P	0.53593	0.73;0.464	T	0.53578	-0.8419	10	0.11794	T	0.64	-3.0554	14.2091	0.65753	0.0:0.1503:0.8497:0.0	.	128;110	O95389-2;O95389	.;WISP3_HUMAN	K	110;110;128;110;88	ENSP00000357655:E110K;ENSP00000230529:E110K;ENSP00000354734:E128K;ENSP00000357652:E88K	ENSP00000230529:E110K	E	+	1	0	WISP3	112489166	1.000000	0.71417	0.866000	0.34008	0.757000	0.42996	5.366000	0.66122	2.203000	0.70933	0.563000	0.77884	GAG	.	.		0.458	WISP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041873.2	NM_003880		A	112382473	G	A	112382473	3	1	4	1	0	0	0	0	1	0	0	0	17389	1059	37	1	388	1	WISP3	6	112382473	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	5271457	112382473	58732594	61	320										
SGK1	6446	hgsc.bcm.edu	37	chr6	134498800	134498800	+	5'Flank	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tatagtacggtaagtacgaaCctttcaaagggggttttata	10	5	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr6:134498800C>G	ENST00000237305.7	-	0	0				SGK1_ENST00000413996.3_5'Flank|SGK1_ENST00000528577.1_Splice_Site|SGK1_ENST00000475719.2_5'Flank|SGK1_ENST00000367857.5_5'Flank|SGK1_ENST00000367858.5_Intron	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1						apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TAAGTACGAACCTTTCAAAGG	0.488																																					.		Atlas-SNP	.											.	SGK1	387	.	0			c.160+1G>C						.						110	102	104					6																	134498800		1568	3582	5150	SO:0001631	upstream_gene_variant	6446	exon2			TACGAACCTTTCA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"serum/glucocorticoid regulated kinase"	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613		chr6.hg19:g.134498800C>G	Exception_encountered	123.0	0.0		76.0	27.0	NM_001143677	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Splice_Site	SNP	ENST00000237305.7	hg19	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	10.03	1.240050	0.22711	.	.	ENSG00000118515	ENST00000528577	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8313	0.78752	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SGK1	134540493	1.000000	0.71417	0.998000	0.56505	0.032000	0.12392	3.943000	0.56621	2.797000	0.96272	0.655000	0.94253	.	.	.		0.488	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			G	134498800	C	G	134498800	1	3	4	0	1	0	0	0	0	0	0	0	14222	521	18	4		4	SGK1	6	134498800	5'Flank	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	22116327	134498800	36616267	62	321										
IPCEF1	26034	hgsc.bcm.edu	37	chr6	154481159	154481159	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gcaactggttaatcatggccAgatcatgttctttacactgt	8	9	3	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr6:154481159A>G	ENST00000265198.4	-	12	1273	c.1118T>C	c.(1117-1119)cTg>cCg	p.L373P	OPRM1_ENST00000337049.4_Intron|IPCEF1_ENST00000367220.4_Missense_Mutation_p.L374P|IPCEF1_ENST00000519344.1_Missense_Mutation_p.L345P|IPCEF1_ENST00000422970.2_Missense_Mutation_p.L374P	NM_001130700.1|NM_015553.2	NP_001124172.1|NP_056368.1	Q8WWN9	ICEF1_HUMAN	interaction protein for cytohesin exchange factors 1	373					oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|positive regulation of GTP catabolic process (GO:0033126)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	oxygen transporter activity (GO:0005344)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	12						AATCATGGCCAGATCATGTTC	0.428																																					p.L374P		Atlas-SNP	.											.	IPCEF1	45	.	0			c.T1121C						.						52	54	53					6																	154481159		2203	4300	6503	SO:0001583	missense	26034	exon13			ATGGCCAGATCAT	AB007863	CCDS5245.1, CCDS47509.1	6q25.2	2013-01-10			ENSG00000074706	ENSG00000074706		"Pleckstrin homology (PH) domain containing"	21204	protein-coding gene	gene with protein product	"phosphoinositide binding protein PIP3-E"					11804589, 19756519	Standard	NM_001130699		Approved	PIP3-E, KIAA0403	uc021zhc.1	Q8WWN9	OTTHUMG00000015872	ENST00000265198.4:c.1118T>C	chr6.hg19:g.154481159A>G	ENSP00000265198:p.Leu373Pro	39.0	0.0		54.0	12.0	NM_001130699	A8K1K2|B7ZL78|B7ZL80|O43153|Q5HYL8	Missense_Mutation	SNP	ENST00000265198.4	hg19	CCDS5245.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.944813	0.73672	.	.	ENSG00000074706	ENST00000265198;ENST00000422970;ENST00000367220;ENST00000519344	T;T;T;T	0.39056	1.1;1.1;1.1;1.17	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000002	T	0.61236	0.2331	M	0.83603	2.65	0.54753	D	0.999987	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.68337	-0.5435	10	0.66056	D	0.02	-12.5156	15.5527	0.76167	1.0:0.0:0.0:0.0	.	373;374;345	Q8WWN9;Q8WWN9-2;G3V132	ICEF1_HUMAN;.;.	P	373;374;374;345	ENSP00000265198:L373P;ENSP00000394751:L374P;ENSP00000356189:L374P;ENSP00000430287:L345P	ENSP00000265198:L373P	L	-	2	0	IPCEF1	154522851	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	8.817000	0.91985	2.084000	0.62774	0.383000	0.25322	CTG	.	.		0.428	IPCEF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042789.2	NM_001130699		G	154481159	A	G	154481159	3	3	4	1	0	0	0	0	1	0	0	0	7800	188	7	2	199	2	IPCEF1	6	154481159	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	19982359	154481159	16633908	63	322										
TULP4	56995	hgsc.bcm.edu	37	chr6	158923744	158923744	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agcccctggccaagtccaagGgcgggcccgggggggtggtg	20	12	0	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr6:158923744G>A	ENST00000367097.3	+	13	4406	c.3049G>A	c.(3049-3051)Ggc>Agc	p.G1017S	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	1017					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CAAGTCCAAGGGCGGGCCCGG	0.721																																					p.G1017S		Atlas-SNP	.											.	TULP4	137	.	0			c.G3049A						.						5	7	6					6																	158923744		1967	3956	5923	SO:0001583	missense	56995	exon13			TCCAAGGGCGGGC		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"WD repeat domain containing"	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.3049G>A	chr6.hg19:g.158923744G>A	ENSP00000356064:p.Gly1017Ser	59.0	0.0		34.0	9.0	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	hg19	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.528053	0.00959	.	.	ENSG00000130338	ENST00000367097	T	0.58797	0.31	4.49	2.4	0.29515	.	0.687206	0.15355	N	0.266720	T	0.11495	0.0280	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24941	-1.0146	10	0.07325	T	0.83	-13.7441	5.6839	0.17792	0.7435:0.0:0.2565:0.0	.	1017	Q9NRJ4	TULP4_HUMAN	S	1017	ENSP00000356064:G1017S	ENSP00000356064:G1017S	G	+	1	0	TULP4	158843732	1.000000	0.71417	0.943000	0.38184	0.041000	0.13682	2.308000	0.43690	0.332000	0.23536	0.561000	0.74099	GGC	.	.		0.721	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		A	158923744	G	A	158923744	3	1	4	1	0	0	0	0	1	0	0	0	16791	1232	43	3	3099	3	TULP4	6	158923744	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	4442585	158923744	12191323	64	323										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159653615	159653615	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gaagctctgtgcaccccggcGcaaagccagcctcgccggcc	12	18	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr6:159653615G>A	ENST00000297267.9	+	11	2271	c.2071G>A	c.(2071-2073)Gca>Aca	p.A691T	FNDC1_ENST00000340366.6_Missense_Mutation_p.A628T	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	691	Ser-rich.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		GCACCCCGGCGCAAAGCCAGC	0.706																																					p.A691T		Atlas-SNP	.											.	FNDC1	250	.	0			c.G2071A						.						14	17	16					6																	159653615		1932	4116	6048	SO:0001583	missense	84624	exon11			CCCGGCGCAAAGC	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.2071G>A	chr6.hg19:g.159653615G>A	ENSP00000297267:p.Ala691Thr	173.0	0.0		82.0	17.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	hg19	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.718|6.718	0.501191|0.501191	0.12822|0.12822	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000297267;ENST00000340366|ENST00000329629	T;T|.	0.07216|.	3.21;4.0|.	4.13|4.13	-8.25|-8.25	0.01025|0.01025	.|.	1.699670|.	0.03305|.	N|.	0.189585|.	T|T	0.03348|0.03348	0.0097|0.0097	N|N	0.04203|0.04203	-0.255|-0.255	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.28839|0.28839	-1.0031|-1.0031	10|5	0.07030|.	T|.	0.85|.	0.4295|0.4295	8.3637|8.3637	0.32374|0.32374	0.1444:0.0:0.6126:0.2431|0.1444:0.0:0.6126:0.2431	.|.	628;691|.	Q4ZHG4-2;Q4ZHG4|.	.;FNDC1_HUMAN|.	T|H	691;628|586	ENSP00000297267:A691T;ENSP00000342460:A628T|.	ENSP00000297267:A691T|.	A|R	+|+	1|2	0|0	FNDC1|FNDC1	159573605|159573605	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.004000|0.004000	0.04260|0.04260	-2.067000|-2.067000	0.01383|0.01383	-2.374000|-2.374000	0.00599|0.00599	-1.093000|-1.093000	0.02169|0.02169	GCA|CGC	.	.		0.706	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159653615	G	A	159653615	3	1	4	1	0	0	0	0	1	0	0	0	5976	1087	38	1	2113	1	FNDC1	6	159653615	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	729871	159653615	11461452	65	324										
LPA	4018	hgsc.bcm.edu	37	chr6	161016462	161016462	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	acacttgattctgtcaccagGcattgtgtcaggttgcagta	10	9	3	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr6:161016462G>A	ENST00000316300.5	-	21	3437	c.3393C>T	c.(3391-3393)tgC>tgT	p.C1131C	LPA_ENST00000447678.1_Silent_p.C1131C			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3639	Kringle 10. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	CTGTCACCAGGCATTGTGTCA	0.517																																					p.C1131C		Atlas-SNP	.											.	LPA	237	.	0			c.C3393T						.						151	151	151					6																	161016462		2137	4271	6408	SO:0001819	synonymous_variant	4018	exon22			CACCAGGCATTGT	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.3393C>T	chr6.hg19:g.161016462G>A		40.0	0.0		61.0	25.0	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	hg19	CCDS43523.1																																																																																			.	.		0.517	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		A	161016462	G	A	161016462	2	1	4	1	0	0	0	0	0	0	0	1	8912	1195	42	3		3	LPA	6	161016462	Silent	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	1362847	161016462	10098605	66	325										
C7orf30	115416	hgsc.bcm.edu	37	chr7	23347541	23347541	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ttaagatagaagggaaggacActgatgactggctgtgcgtg	15	5	0	4			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr7:23347541A>G	ENST00000466681.1	+	3	643	c.490A>G	c.(490-492)Act>Gct	p.T164A		NM_138446.1	NP_612455.1	Q96EH3	MASU1_HUMAN	mitochondrial assembly of ribosomal large subunit 1	164					negative regulation of mitochondrial translation (GO:0070130)|ribosomal large subunit biogenesis (GO:0042273)	mitochondrion (GO:0005739)											AGGGAAGGACACTGATGACTG	0.418																																					p.T164A		Atlas-SNP	.											.	.	.	.	0			c.A490G						.						293	252	266					7																	23347541		2203	4300	6503	SO:0001583	missense	115416	exon3			AAGGACACTGATG	BC012331	CCDS5381.1	7p15.3	2013-05-24	2012-02-20	2012-02-20	ENSG00000156928	ENSG00000156928			21721	protein-coding gene	gene with protein product		614624	"chromosome 7 open reading frame 30"	C7orf30		22238376, 22238375	Standard	NM_138446		Approved	mtRsfA	uc003swd.1	Q96EH3	OTTHUMG00000128443	ENST00000466681.1:c.490A>G	chr7.hg19:g.23347541A>G	ENSP00000419370:p.Thr164Ala	139.0	0.0		130.0	19.0	NM_138446	A4D154	Missense_Mutation	SNP	ENST00000466681.1	hg19	CCDS5381.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.028370	0.35797	.	.	ENSG00000156928	ENST00000466681	.	.	.	5.04	2.36	0.29203	.	0.194714	0.43260	N	0.000595	T	0.25568	0.0622	N	0.14661	0.345	0.32287	N	0.566877	B	0.13145	0.007	B	0.21151	0.033	T	0.22312	-1.0220	9	0.15952	T	0.53	-21.2521	7.6888	0.28557	0.8029:0.0:0.0723:0.1247	.	164	Q96EH3	CG030_HUMAN	A	164	.	ENSP00000419370:T164A	T	+	1	0	C7orf30	23314066	1.000000	0.71417	0.994000	0.49952	0.987000	0.75469	1.867000	0.39499	0.814000	0.34374	0.528000	0.53228	ACT	.	.		0.418	MALSU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250241.2	NM_138446		G	23347541	A	G	23347541	3	3	4	1	0	0	0	0	1	0	0	0	2388	159	6	2	500	2	C7orf30	7	23347541	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10		23347541	135791122	67	326										
DPY19L1	23333	hgsc.bcm.edu	37	chr7	34979865	34979865	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gtttgcagatttgctgaaccTtgtattgacattgctgctaa	9	7	0	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr7:34979865T>G	ENST00000310974.4	-	19	1689	c.1545A>C	c.(1543-1545)caA>caC	p.Q515H	MIR548N_ENST00000408742.1_RNA	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	515						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						TTGCTGAACCTTGTATTGACA	0.378																																					p.Q515H		Atlas-SNP	.											.	DPY19L1	56	.	0			c.A1545C						.						82	70	74					7																	34979865		1842	4093	5935	SO:0001583	missense	23333	exon19			TGAACCTTGTATT	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.1545A>C	chr7.hg19:g.34979865T>G	ENSP00000308695:p.Gln515His	54.0	0.0		72.0	14.0	NM_015283	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	hg19	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.932899	0.52866	.	.	ENSG00000173852	ENST00000310974	T	0.56941	0.43	5.0	-1.62	0.08372	.	0.182084	0.48767	D	0.000172	T	0.59183	0.2175	L	0.55103	1.725	0.42466	D	0.992806	D	0.71674	0.998	D	0.66196	0.942	T	0.56492	-0.7970	10	0.29301	T	0.29	-10.8028	11.8054	0.52152	0.0:0.4572:0.0:0.5428	.	515	Q2PZI1	D19L1_HUMAN	H	515	ENSP00000308695:Q515H	ENSP00000308695:Q515H	Q	-	3	2	DPY19L1	34946390	0.914000	0.31030	0.994000	0.49952	0.996000	0.88848	-0.006000	0.12833	-0.189000	0.10482	0.482000	0.46254	CAA	.	.		0.378	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			G	34979865	T	G	34979865	3	3	4	1	0	0	0	0	1	0	0	0	4742	1606	56	5	498	5	DPY19L1	7	34979865	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	11632324	34979865	124158798	68	327										
MLXIPL	51085	hgsc.bcm.edu	37	chr7	73038554	73038554	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aggccaggctcaagcactcgAagaggcgtgtgagtgtgggg	18	8	1	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr7:73038554A>G	ENST00000313375.3	-	1	316	c.269T>C	c.(268-270)tTc>tCc	p.F90S	MLXIPL_ENST00000429400.2_Missense_Mutation_p.F90S|MLXIPL_ENST00000395189.1_Missense_Mutation_p.F90S|MLXIPL_ENST00000414749.2_Missense_Mutation_p.F90S|MLXIPL_ENST00000434326.1_Missense_Mutation_p.F90S|MLXIPL_ENST00000354613.1_Missense_Mutation_p.F90S	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	90					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				CAAGCACTCGAAGAGGCGTGT	0.731																																					p.F90S		Atlas-SNP	.											.	MLXIPL	54	.	0			c.T269C						.						14	11	12					7																	73038554		2191	4273	6464	SO:0001583	missense	51085	exon1			CACTCGAAGAGGC	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"carbohydrate response element binding protein"	605678	"Williams Beuren syndrome chromosome region 14"	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.269T>C	chr7.hg19:g.73038554A>G	ENSP00000320886:p.Phe90Ser	229.0	0.0		205.0	122.0	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Missense_Mutation	SNP	ENST00000313375.3	hg19	CCDS5553.1	.	.	.	.	.	.	.	.	.	.	A	32	5.165676	0.94768	.	.	ENSG00000009950	ENST00000414749;ENST00000429400;ENST00000313375;ENST00000354613;ENST00000395189;ENST00000434326;ENST00000453275	T;T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44;1.44	4.33	4.33	0.51752	.	0.000000	0.85682	D	0.000000	T	0.54464	0.1860	M	0.78456	2.415	0.44282	D	0.997145	D;D;D;D;D	0.76494	0.999;0.998;0.999;0.999;0.999	D;D;D;D;D	0.83275	0.996;0.991;0.996;0.996;0.996	T	0.59915	-0.7364	10	0.87932	D	0	-21.539	11.4764	0.50300	1.0:0.0:0.0:0.0	.	90;90;90;90;90	Q9NP71-6;Q9NP71;Q9NP71-2;Q9NP71-3;Q9NP71-4	.;MLXPL_HUMAN;.;.;.	S	90	ENSP00000412330:F90S;ENSP00000406296:F90S;ENSP00000320886:F90S;ENSP00000346629:F90S;ENSP00000378616:F90S;ENSP00000392636:F90S;ENSP00000395172:F90S	ENSP00000320886:F90S	F	-	2	0	MLXIPL	72676490	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.041000	0.93788	1.799000	0.52666	0.459000	0.35465	TTC	.	.		0.731	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951		G	73038554	A	G	73038554	3	3	4	1	0	0	0	0	1	0	0	0	9646	246	9	2	2357	2	MLXIPL	7	73038554	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	38058689	73038554	86100109	69	328										
LIMK1	3984	hgsc.bcm.edu	37	chr7	73525982	73525982	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tctttctccatcccaggacaGccagtacccatggagccaga	8	15	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr7:73525982G>C	ENST00000336180.2	+	11	1340	c.1289G>C	c.(1288-1290)aGc>aCc	p.S430T	LIMK1_ENST00000538333.3_Missense_Mutation_p.S396T|LIMK1_ENST00000418310.1_Missense_Mutation_p.S460T	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	430	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	TCCCAGGACAGCCAGTACCCA	0.597																																					p.S430T		Atlas-SNP	.											.	LIMK1	55	.	0			c.G1289C						.						47	40	42					7																	73525982		2203	4300	6503	SO:0001583	missense	3984	exon11			AGGACAGCCAGTA	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.1289G>C	chr7.hg19:g.73525982G>C	ENSP00000336740:p.Ser430Thr	117.0	0.0		96.0	9.0	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	ENST00000336180.2	hg19	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	G	10.67	1.414846	0.25465	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000538333	D;D;D	0.82803	-1.65;-1.65;-1.65	4.64	4.64	0.57946	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.091548	0.85682	D	0.000000	T	0.64549	0.2608	N	0.08118	0	0.45867	D	0.99872	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.59794	-0.7387	10	0.15066	T	0.55	-40.0184	11.0546	0.47911	0.0:0.1886:0.8114:0.0	.	396;430	B7Z6I8;P53667	.;LIMK1_HUMAN	T	460;430;430;396	ENSP00000409717:S460T;ENSP00000336740:S430T;ENSP00000444452:S396T	ENSP00000336740:S430T	S	+	2	0	LIMK1	73163918	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.334000	0.65923	2.128000	0.65567	0.543000	0.68304	AGC	.	.		0.597	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		C	73525982	G	C	73525982	3	2	4	1	0	0	0	0	1	0	0	0	8810	971	34	4	1331	4	LIMK1	7	73525982	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	487428	73525982	85612681	70	329										
SRPK2	6733	hgsc.bcm.edu	37	chr7	104844117	104844117	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ctcttgctcctcatcatctgAtcccaggatctcctcctctg	5	17	6	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr7:104844117A>T	ENST00000393651.3	-	3	274	c.187T>A	c.(187-189)Tca>Aca	p.S63T	SRPK2_ENST00000357311.3_Missense_Mutation_p.S52T|SRPK2_ENST00000489828.1_Missense_Mutation_p.S52T	NM_182692.1	NP_872634.1			SRSF protein kinase 2											NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						TCATCATCTGATCCCAGGATC	0.592																																					p.S63T		Atlas-SNP	.											.	SRPK2	76	.	0			c.T187A						.						127	105	112					7																	104844117		2203	4300	6503	SO:0001583	missense	6733	exon3			CATCTGATCCCAG	U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250			11306	protein-coding gene	gene with protein product	"SR protein kinase 2", "serine/arginine-rich splicing factor kinase 2"	602980	"SFRS protein kinase 2"			8208298, 9472028	Standard	NM_182692		Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.187T>A	chr7.hg19:g.104844117A>T	ENSP00000377262:p.Ser63Thr	48.0	0.0		67.0	21.0	NM_182692		Missense_Mutation	SNP	ENST00000393651.3	hg19	CCDS34724.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.032647	0.75504	.	.	ENSG00000135250	ENST00000393651;ENST00000357311;ENST00000489828;ENST00000482897;ENST00000460391	T;T;T;T;T	0.35236	1.32;1.33;1.33;3.25;2.82	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.53433	0.1796	L	0.48877	1.53	0.80722	D	1	D;P	0.61697	0.99;0.924	D;P	0.72982	0.979;0.878	T	0.53500	-0.8430	10	0.62326	D	0.03	-15.5324	14.818	0.70050	1.0:0.0:0.0:0.0	.	63;52	P78362-2;P78362	.;SRPK2_HUMAN	T	63;52;52;100;52	ENSP00000377262:S63T;ENSP00000349863:S52T;ENSP00000419791:S52T;ENSP00000419240:S100T;ENSP00000417357:S52T	ENSP00000349863:S52T	S	-	1	0	SRPK2	104631353	1.000000	0.71417	0.976000	0.42696	0.989000	0.77384	8.548000	0.90669	2.317000	0.78254	0.459000	0.35465	TCA	.	.		0.592	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348723.1	NM_182691		T	104844117	A	T	104844117	3	4	4	1	0	0	0	0	1	0	0	0	15175	333	12	4	1968	4	SRPK2	7	104844117	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	31318135	104844117	54294546	71	330										
TAS2R38	5726	hgsc.bcm.edu	37	chr7	141673139	141673139	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aaacggatgagcttggagcaGtaaagcaggctgaggcaggc	16	7	0	2	rs373253461		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr7:141673139G>C	ENST00000547270.1	-	1	434	c.351C>G	c.(349-351)taC>taG	p.Y117*		NM_176817.4	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	117					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			NS(2)|breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)|stomach(1)	21	Melanoma(164;0.0171)					GCTTGGAGCAGTAAAGCAGGC	0.512																																					p.Y117X		Atlas-SNP	.											.	TAS2R38	51	.	0			c.C351G						.						70	68	69					7																	141673139		2203	4300	6503	SO:0001587	stop_gained	5726	exon1			GGAGCAGTAAAGC	AF494231	CCDS34765.1	7q34	2012-10-03	2003-05-29	2003-05-30	ENSG00000257138	ENSG00000257138		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	9584	protein-coding gene	gene with protein product		607751	"phenylthiocarbamide tasting"	PTC		12624758, 12584440	Standard	NM_176817		Approved	T2R61	uc003vwx.1	P59533	OTTHUMG00000158374	ENST00000547270.1:c.351C>G	chr7.hg19:g.141673139G>C	ENSP00000448219:p.Tyr117*	78.0	0.0		99.0	22.0	NM_176817	A4D1U6|P59552|Q2M3E8|Q645W3|Q86UK3	Nonsense_Mutation	SNP	ENST00000547270.1	hg19	CCDS34765.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.523731	0.85600	.	.	ENSG00000257138	ENST00000547270	.	.	.	4.7	0.865	0.19074	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.8076	0.23786	0.3908:0.0:0.6092:0.0	.	.	.	.	X	117	.	ENSP00000331291:Y117X	Y	-	3	2	TAS2R38	141319608	1.000000	0.71417	0.997000	0.53966	0.909000	0.53808	0.507000	0.22675	0.046000	0.15833	0.655000	0.94253	TAC	.	.		0.512	TAS2R38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350810.2	NM_176817		C	141673139	G	C	141673139	4	2	4	1	0	0	0	0	0	1	0	0	15590	1024	36	4	654	4	TAS2R38	7	141673139	Nonsense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	36829022	141673139	17465524	72	331										
MTUS1	57509	hgsc.bcm.edu	37	chr8	17611234	17611234	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tatattacttaccaaaaacaGagaaccatattcaaaagtct	3	8	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr8:17611234G>A	ENST00000262102.6	-	2	2307	c.2083C>T	c.(2083-2085)Ctg>Ttg	p.L695L	MTUS1_ENST00000381869.3_Silent_p.L695L|MTUS1_ENST00000519263.1_Silent_p.L695L|MTUS1_ENST00000381862.3_Silent_p.L695L	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	695					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		ACCAAAAACAGAGAACCATAT	0.313																																					p.L695L		Atlas-SNP	.											.	MTUS1	144	.	0			c.C2083T						.						84	72	76					8																	17611234		1804	4069	5873	SO:0001819	synonymous_variant	57509	exon2			AAAACAGAGAACC	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2083C>T	chr8.hg19:g.17611234G>A		57.0	0.0		44.0	10.0	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	hg19	CCDS43717.1																																																																																			.	.		0.313	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		A	17611234	G	A	17611234	2	1	4	1	0	0	0	0	0	0	0	1	9974	933	33	3		3	MTUS1	8	17611234	Silent	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10		17611234	128752788	73	332										
PCM1	5108	hgsc.bcm.edu	37	chr8	17796420	17796420	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cgattggatcagcacagtgtAaagagttgtttgcttctgct	11	7	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr8:17796420A>G	ENST00000519253.1	+	5	765	c.514A>G	c.(514-516)Aaa>Gaa	p.K172E	PCM1_ENST00000325083.8_Missense_Mutation_p.K172E|PCM1_ENST00000518537.1_Missense_Mutation_p.K172E|PCM1_ENST00000524226.1_Missense_Mutation_p.K172E			Q15154	PCM1_HUMAN	pericentriolar material 1	172					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		AGCACAGTGTAAAGAGTTGTT	0.438			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.K172E		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.A514G						.						121	115	117					8																	17796420		1901	4124	6025	SO:0001583	missense	5108	exon5			CAGTGTAAAGAGT		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.514A>G	chr8.hg19:g.17796420A>G	ENSP00000431099:p.Lys172Glu	134.0	0.0		137.0	66.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.	.	.	.	.	.	.	.	.	.	A	22.4	4.290142	0.80914	.	.	ENSG00000078674	ENST00000325083;ENST00000325126;ENST00000517730;ENST00000518537;ENST00000523055;ENST00000519253;ENST00000524226	T;T;T;T;T;T	0.30182	3.2;2.36;1.54;1.58;3.2;2.96	5.62	4.44	0.53790	.	0.094403	0.64402	D	0.000001	T	0.38558	0.1045	N	0.24115	0.695	0.80722	D	1	P;D;P;P	0.63046	0.925;0.992;0.925;0.925	P;D;P;P	0.74674	0.54;0.984;0.54;0.54	T	0.08973	-1.0696	10	0.28530	T	0.3	-29.9836	13.0712	0.59061	0.8657:0.1343:0.0:0.0	.	172;172;172;172	E7ETA6;E7EV93;E7EV56;Q15154	.;.;.;PCM1_HUMAN	E	172	ENSP00000327077:K172E;ENSP00000428131:K172E;ENSP00000428123:K172E;ENSP00000429941:K172E;ENSP00000431099:K172E;ENSP00000430521:K172E	ENSP00000327077:K172E	K	+	1	0	PCM1	17840700	1.000000	0.71417	1.000000	0.80357	0.720000	0.41350	8.544000	0.90654	1.048000	0.40298	0.460000	0.39030	AAA	.	.		0.438	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		G	17796420	A	G	17796420	3	3	4	1	0	0	0	0	1	0	0	0	11593	363	13	2	524	2	PCM1	8	17796420	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	185186	17796420	128567602	74	333										
TAF2	6873	hgsc.bcm.edu	37	chr8	120744294	120744294	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tatgtttatgcttcttcttcTttttcttgtgctcatggtga	7	7	5	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr8:120744294T>C	ENST00000378164.2	-	26	3768	c.3470A>G	c.(3469-3471)aAg>aGg	p.K1157R		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	1157	His-rich.|Lys-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CTTCTTCTTCTTTTTCTTGTG	0.473																																					p.K1157R		Atlas-SNP	.											.	TAF2	204	.	0			c.A3470G						.						434	375	395					8																	120744294		2203	4300	6503	SO:0001583	missense	6873	exon26			TTCTTCTTTTTCT	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.3470A>G	chr8.hg19:g.120744294T>C	ENSP00000367406:p.Lys1157Arg	75.0	0.0		77.0	6.0	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	hg19	CCDS34937.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.670424	0.88348	.	.	ENSG00000064313	ENST00000378164;ENST00000529653	T;T	0.57273	1.37;0.41	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.58680	0.2139	L	0.27053	0.805	0.80722	D	1	P	0.52842	0.956	P	0.62184	0.899	T	0.62784	-0.6781	10	0.87932	D	0	-24.4748	14.2903	0.66273	0.0:0.0:0.0:1.0	.	1157	Q6P1X5	TAF2_HUMAN	R	1157;333	ENSP00000367406:K1157R;ENSP00000436750:K333R	ENSP00000367406:K1157R	K	-	2	0	TAF2	120813475	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.415000	0.59809	2.299000	0.77371	0.528000	0.53228	AAG	.	.		0.473	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		C	120744294	T	C	120744294	3	2	4	1	0	0	0	0	1	0	0	0	15539	1609	56	2	133	2	TAF2	8	120744294	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	102947874	120744294	25619728	75	334										
RECQL4	9684	hgsc.bcm.edu	37	chr8	145740426	145740426	+	5'Flank	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agcacagggacttgccggcaCctgtaggcagcaccagcagc	13	14	0	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr8:145740426C>G	ENST00000292524.1	+	0	0				RECQL4_ENST00000532237.1_5'UTR|CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000428558.2_Missense_Mutation_p.G505A|LRRC14_ENST00000529022.1_5'Flank	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CTTGCCGGCACCTGTAGGCAG	0.667																																					p.G505A		Atlas-SNP	.											.	RECQL4	75	.	0			c.G1514C						.						20	26	24					8																	145740426		2163	4267	6430	SO:0001631	upstream_gene_variant	9401	exon9			CCGGCACCTGTAG	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		chr8.hg19:g.145740426C>G	Exception_encountered	192.0	0.0		88.0	6.0	NM_004260	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1																																																																																			.	.		0.667	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		G	145740426	C	G	145740426	1	3	4	0	1	0	0	0	0	0	0	0	13217	507	18	4		4	RECQL4	8	145740426	5'Flank	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	24996132	145740426	623596	76	335										
RORB	6096	hgsc.bcm.edu	37	chr9	77249681	77249681	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tgtcttgccctaggaatgtcAagagatggtaagacattacc	10	8	2	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr9:77249681A>T	ENST00000396204.2	+	3	261	c.261A>T	c.(259-261)tcA>tcT	p.S87S	RORB_ENST00000376896.3_Silent_p.S76S			Q92753	RORB_HUMAN	RAR-related orphan receptor B	87					amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	TAGGAATGTCAAGAGATGGTA	0.438																																					p.S76S		Atlas-SNP	.											.	RORB	89	.	0			c.A228T						.						85	79	81					9																	77249681		2203	4300	6503	SO:0001819	synonymous_variant	6096	exon3			AATGTCAAGAGAT	Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"Nuclear hormone receptors"	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.261A>T	chr9.hg19:g.77249681A>T		61.0	0.0		56.0	6.0	NM_006914	Q8WX73	Silent	SNP	ENST00000396204.2	hg19																																																																																				.	.		0.438	RORB-201	KNOWN	basic	protein_coding	protein_coding				T	77249681	A	T	77249681	2	4	4	1	0	0	0	0	0	0	0	1	13544	117	5	4		4	RORB	9	77249681	Silent	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10		77249681	63963750	77	336										
MURC	347273	hgsc.bcm.edu	37	chr9	103340609	103340609	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aagagagacacagggaaatgGaaaatgccataaaatccgtc	10	7	0	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr9:103340609G>A	ENST00000307584.5	+	1	249	c.184G>A	c.(184-186)Gaa>Aaa	p.E62K	RN7SKP87_ENST00000364096.1_RNA	NM_001018116.1	NP_001018126.1	Q5BKX8	MURC_HUMAN	muscle-related coiled-coil protein	62					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Z disc (GO:0030018)				endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)	16		Acute lymphoblastic leukemia(62;0.0461)				CAGGGAAATGGAAAATGCCAT	0.448																																					p.E62K		Atlas-SNP	.											.	MURC	43	.	0			c.G184A						.						135	144	141					9																	103340609		2203	4300	6503	SO:0001583	missense	347273	exon1			GAAATGGAAAATG	BC090888	CCDS35083.1	9q31.1	2014-09-17			ENSG00000170681	ENSG00000170681			33742	protein-coding gene	gene with protein product	"muscle-restricted coiled-coil protein"					18508909, 18332105	Standard	NM_001018116		Approved	cavin-4, CAVIN4	uc004bba.3	Q5BKX8	OTTHUMG00000020368	ENST00000307584.5:c.184G>A	chr9.hg19:g.103340609G>A	ENSP00000418668:p.Glu62Lys	147.0	0.0		99.0	33.0	NM_001018116	B1PRL3|B4DT88	Missense_Mutation	SNP	ENST00000307584.5	hg19	CCDS35083.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.709396	0.68615	.	.	ENSG00000170681	ENST00000307584	T	0.65549	-0.16	5.39	5.39	0.77823	.	0.101290	0.64402	D	0.000003	T	0.73466	0.3590	M	0.75085	2.285	0.58432	D	0.999999	P	0.51791	0.948	P	0.52823	0.71	T	0.77381	-0.2609	10	0.72032	D	0.01	-10.4406	16.6642	0.85248	0.0:0.0:1.0:0.0	.	62	Q5BKX8	MURC_HUMAN	K	62	ENSP00000418668:E62K	ENSP00000418668:E62K	E	+	1	0	MURC	102380430	1.000000	0.71417	0.996000	0.52242	0.999000	0.98932	9.869000	0.99810	2.532000	0.85374	0.655000	0.94253	GAA	.	.		0.448	MURC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053419.2	NM_001018116		A	103340609	G	A	103340609	3	1	4	1	0	0	0	0	1	0	0	0	9996	1175	41	3	186	3	MURC	9	103340609	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	26090928	103340609	37872822	78	337										
ITIH2	3698	hgsc.bcm.edu	37	chr10	7749193	7749193	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ccaggagaatcggaagaaatGatggtaagttgacttgatgt	13	4	0	5			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr10:7749193G>T	ENST00000358415.4	+	3	355	c.189G>T	c.(187-189)atG>atT	p.M63I	ITIH2_ENST00000480387.1_3'UTR|ITIH2_ENST00000379587.4_Intron	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	63	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CGGAAGAAATGATGGTAAGTT	0.368																																					p.M63I		Atlas-SNP	.											.	ITIH2	144	.	0			c.G189T						.						172	170	171					10																	7749193		2203	4300	6503	SO:0001583	missense	3698	exon3			AGAAATGATGGTA	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.189G>T	chr10.hg19:g.7749193G>T	ENSP00000351190:p.Met63Ile	85.0	0.0		61.0	19.0	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	hg19	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	G	0.836	-0.743620	0.03088	.	.	ENSG00000151655	ENST00000358415;ENST00000429820	T;T	0.16196	4.95;2.36	5.62	-2.87	0.05700	Vault protein inter-alpha-trypsin (1);Vault protein inter-alpha-trypsin, metazoa (1);	6.159120	0.00166	N	0.000000	T	0.11879	0.0289	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.25950	-1.0117	10	0.32370	T	0.25	6.1894	7.1891	0.25816	0.3584:0.2036:0.438:0.0	.	63	P19823	ITIH2_HUMAN	I	63;38	ENSP00000351190:M63I;ENSP00000388826:M38I	ENSP00000351190:M63I	M	+	3	0	ITIH2	7789199	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.143000	0.10296	-0.702000	0.05056	-2.364000	0.00238	ATG	.	.		0.368	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		T	7749193	G	T	7749193	3	4	4	1	0	0	0	0	1	0	0	0	7913	1290	45	3	199	3	ITIH2	10	7749193	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10		7749193	127785554	79	338										
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24889744	24889744	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agcaagcattaacactgatgGgctgctcttcctcagacgga	10	11	2	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr10:24889744G>C	ENST00000396432.2	-	14	3449	c.2963C>G	c.(2962-2964)cCc>cGc	p.P988R	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.P775R|ARHGAP21_ENST00000493154.1_Intron	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	987	Interaction with ARF1 and ARF6.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						AACACTGATGGGCTGCTCTTC	0.458																																					p.P988R		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.C2963G						.						87	85	86					10																	24889744		2202	4280	6482	SO:0001583	missense	57584	exon14			CTGATGGGCTGCT	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.2963C>G	chr10.hg19:g.24889744G>C	ENSP00000379709:p.Pro988Arg	200.0	0.0		143.0	58.0	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	hg19	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	G	17.02	3.281738	0.59758	.	.	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94	5.67	4.76	0.60689	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.161907	0.56097	D	0.000034	D	0.82761	0.5107	M	0.69463	2.115	0.49299	D	0.999778	D;P	0.71674	0.998;0.932	D;P	0.71656	0.974;0.734	D	0.83710	0.0187	10	0.72032	D	0.01	.	11.2105	0.48795	0.1409:0.0:0.8591:0.0	.	978;987	F8W9U9;Q5T5U3	.;RHG21_HUMAN	R	988;775;978;988;823	ENSP00000379709:P988R;ENSP00000365604:P775R;ENSP00000365592:P978R;ENSP00000405018:P988R	ENSP00000365604:P775R	P	-	2	0	ARHGAP21	24929750	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.407000	0.66363	2.679000	0.91253	0.655000	0.94253	CCC	.	.		0.458	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		C	24889744	G	C	24889744	3	2	4	1	0	0	0	0	1	0	0	0	871	1232	43	4	2965	4	ARHGAP21	10	24889744	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	17140551	24889744	110645003	80	339										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108339221	108339221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	actgtgggttggagtgaggtCcaccaggggggcttgtgggg	21	6	0	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr10:108339221C>T	ENST00000263054.6	-	25	3284	c.3277G>A	c.(3277-3279)Gac>Aac	p.D1093N	SORCS1_ENST00000344440.6_Missense_Mutation_p.D1093N|SORCS1_ENST00000369698.1_Missense_Mutation_p.D628N	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1093					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GGAGTGAGGTCCACCAGGGGG	0.522																																					p.D1093N		Atlas-SNP	.											SORCS1_ENST00000344440,NS,carcinoma,0,2	SORCS1	534	.	0			c.G3277A						.						80	65	70					10																	108339221		2203	4300	6503	SO:0001583	missense	114815	exon25			TGAGGTCCACCAG	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3277G>A	chr10.hg19:g.108339221C>T	ENSP00000263054:p.Asp1093Asn	82.0	0.0		62.0	17.0	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.4|28.4	4.914391|4.914391	0.92178|0.92178	.|.	.|.	ENSG00000108018|ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440|ENST00000452214	T;T;T|.	0.23950|.	1.88;2.38;2.43|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.69269|.	0.3092|.	L|L	0.43923|0.43923	1.385|1.385	0.58432|0.58432	D|D	0.999998|0.999998	D;D;D;D;D|.	0.76494|.	0.999;0.999;0.999;0.999;0.999|.	D;D;D;D;D|.	0.76071|.	0.971;0.987;0.987;0.971;0.987|.	T|.	0.62714|.	-0.6796|.	9|.	.|.	.|.	.|.	-29.1402|-29.1402	20.3167|20.3167	0.98654|0.98654	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1093;1093;1093;1093;1093|.	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2|.	.;.;.;SORC1_HUMAN;.|.	N|X	628;1093;1093|107	ENSP00000358712:D628N;ENSP00000263054:D1093N;ENSP00000345964:D1093N|.	.|.	D|W	-|-	1|3	0|0	SORCS1|SORCS1	108329211|108329211	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.798000|0.798000	0.45092|0.45092	7.487000|7.487000	0.81328|0.81328	2.809000|2.809000	0.96659|0.96659	0.557000|0.557000	0.71058|0.71058	GAC|TGG	.	.		0.522	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		T	108339221	C	T	108339221	3	4	4	1	0	0	0	0	1	0	0	0	14945	855	30	3	471	3	SORCS1	10	108339221	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	83449477	108339221	27195526	81	340										
TACC2	10579	hgsc.bcm.edu	37	chr10	123844285	123844285	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tgatggggagggcttgctgaCgtccccagatcaaccccgcg	14	13	1	3	rs201466757		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr10:123844285C>T	ENST00000369005.1	+	4	2610	c.2270C>T	c.(2269-2271)aCg>aTg	p.T757M	TACC2_ENST00000515273.1_Missense_Mutation_p.T757M|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.T757M|TACC2_ENST00000334433.3_Missense_Mutation_p.T757M|TACC2_ENST00000453444.2_Missense_Mutation_p.T757M|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	757					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GGCTTGCTGACGTCCCCAGAT	0.602																																					p.T757M		Atlas-SNP	.											.	TACC2	271	.	0			c.C2270T						.						65	75	71					10																	123844285		2203	4300	6503	SO:0001583	missense	10579	exon4			TGCTGACGTCCCC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.2270C>T	chr10.hg19:g.123844285C>T	ENSP00000358001:p.Thr757Met	223.0	0.0		90.0	5.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	hg19	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.400186	0.42613	.	.	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.03152	4.06;4.04;4.03;4.06;4.04	5.21	1.83	0.25207	.	0.662651	0.12568	N	0.457581	T	0.01489	0.0048	N	0.14661	0.345	0.09310	N	1	P;P;P	0.40211	0.707;0.707;0.707	B;B;B	0.23018	0.043;0.043;0.043	T	0.46205	-0.9208	10	0.23891	T	0.37	-0.1967	2.8057	0.05427	0.2014:0.4109:0.0:0.3877	.	757;757;757	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	M	757;757;757;757;757;747	ENSP00000358001:T757M;ENSP00000424467:T757M;ENSP00000427618:T757M;ENSP00000334280:T757M;ENSP00000395048:T757M	ENSP00000334280:T757M	T	+	2	0	TACC2	123834275	0.000000	0.05858	0.001000	0.08648	0.166000	0.22503	-0.111000	0.10807	0.557000	0.29117	0.561000	0.74099	ACG	.	C|0.999;T|0.001		0.602	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123844285	C	T	123844285	3	4	4	1	0	0	0	0	1	0	0	0	15517	536	19	1	2280	1	TACC2	10	123844285	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	15505064	123844285	11690462	82	341										
TUBGCP2	10844	hgsc.bcm.edu	37	chr10	135094884	135094884	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aagttcttgtcaaacttgttGatggtggcctcgaagccgga	12	8	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr10:135094884G>A	ENST00000252936.3	-	16	2505	c.2466C>T	c.(2464-2466)atC>atT	p.I822I	TUBGCP2_ENST00000417178.2_Silent_p.I692I|TUBGCP2_ENST00000543663.1_Silent_p.I850I|TUBGCP2_ENST00000368563.2_Silent_p.I822I|TUBGCP2_ENST00000368562.1_Silent_p.I415I			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	822					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		CAAACTTGTTGATGGTGGCCT	0.617																																					p.I850I		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.C2550T						.						124	102	110					10																	135094884		2203	4300	6503	SO:0001819	synonymous_variant	10844	exon18			CTTGTTGATGGTG	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.2466C>T	chr10.hg19:g.135094884G>A		91.0	0.0		41.0	7.0	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	hg19	CCDS7676.1																																																																																			.	.		0.617	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1			A	135094884	G	A	135094884	2	1	4	1	0	0	0	0	0	0	0	1	16781	1280	45	3		3	TUBGCP2	10	135094884	Silent	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	11250599	135094884	439863	83	342										
OR51L1	119682	hgsc.bcm.edu	37	chr11	5020444	5020444	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	atgacctggggatgtccctgTctacacttcccaccatgctt	8	14	1	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr11:5020444T>C	ENST00000321543.1	+	1	232	c.232T>C	c.(232-234)Tct>Cct	p.S78P		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	78						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGTCCCTGTCTACACTTCC	0.458																																					p.S78P		Atlas-SNP	.											.	OR51L1	60	.	0			c.T232C						.						206	169	182					11																	5020444		2201	4298	6499	SO:0001583	missense	119682	exon1			TCCCTGTCTACAC	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"GPCR / Class A : Olfactory receptors"	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.232T>C	chr11.hg19:g.5020444T>C	ENSP00000322156:p.Ser78Pro	74.0	0.0		94.0	43.0	NM_001004755	Q6IFE5	Missense_Mutation	SNP	ENST00000321543.1	hg19	CCDS31369.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.284443	0.40394	.	.	ENSG00000176798	ENST00000321543	T	0.00912	5.55	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43919	D	0.000513	T	0.08492	0.0211	M	0.93197	3.39	0.24052	N	0.996046	D	0.71674	0.998	D	0.75484	0.986	T	0.10965	-1.0607	10	0.52906	T	0.07	.	14.7065	0.69194	0.0:0.0:0.0:1.0	.	78	Q8NGJ5	O51L1_HUMAN	P	78	ENSP00000322156:S78P	ENSP00000322156:S78P	S	+	1	0	OR51L1	4977020	0.000000	0.05858	0.780000	0.31762	0.520000	0.34377	0.507000	0.22675	2.340000	0.79590	0.528000	0.53228	TCT	.	.		0.458	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755		C	5020444	T	C	5020444	3	2	4	1	0	0	0	0	1	0	0	0	11111	1667	58	2	234	2	OR51L1	11	5020444	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10		5020444	129986072	84	343										
ZDHHC13	54503	hgsc.bcm.edu	37	chr11	19170829	19170829	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cagcagcatccacctggcagTattgtttcaacacatgccta	7	13	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr11:19170829T>C	ENST00000446113.2	+	5	591	c.470T>C	c.(469-471)gTa>gCa	p.V157A	ZDHHC13_ENST00000399351.3_Missense_Mutation_p.V27A|ZDHHC13_ENST00000532812.1_3'UTR	NM_019028.2	NP_061901.2	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC-type containing 13	157					metabolic process (GO:0008152)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	magnesium ion transmembrane transporter activity (GO:0015095)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6						CACCTGGCAGTATTGTTTCAA	0.413																																					p.V157A		Atlas-SNP	.											.	ZDHHC13	40	.	0			c.T470C						.						84	75	78					11																	19170829		1901	4116	6017	SO:0001583	missense	54503	exon5			TGGCAGTATTGTT	AB024495	CCDS44550.1, CCDS44551.1	11p15.1	2013-01-10			ENSG00000177054	ENSG00000177054		"Zinc fingers, DHHC-type", "Ankyrin repeat domain containing"	18413	protein-coding gene	gene with protein product		612815				18794299	Standard	NM_001001483		Approved	FLJ10852, FLJ10941, HIP14L	uc001mpi.3	Q8IUH4	OTTHUMG00000166099	ENST00000446113.2:c.470T>C	chr11.hg19:g.19170829T>C	ENSP00000400113:p.Val157Ala	67.0	0.0		61.0	19.0	NM_019028	Q7Z2D3|Q86VK2|Q9NV30|Q9NV99	Missense_Mutation	SNP	ENST00000446113.2	hg19	CCDS44550.1	.	.	.	.	.	.	.	.	.	.	T	14.68	2.606828	0.46527	.	.	ENSG00000177054	ENST00000446113;ENST00000399351	T;T	0.64618	-0.11;0.33	5.79	5.79	0.91817	Ankyrin repeat-containing domain (4);	0.055223	0.64402	D	0.000001	T	0.56673	0.2001	N	0.03115	-0.41	0.50313	D	0.999864	D	0.67145	0.996	D	0.65140	0.932	T	0.62277	-0.6888	9	.	.	.	-0.2223	15.7882	0.78326	0.0:0.0:0.0:1.0	.	157	Q8IUH4	ZDH13_HUMAN	A	157;27	ENSP00000400113:V157A;ENSP00000382288:V27A	.	V	+	2	0	ZDHHC13	19127405	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	5.967000	0.70403	2.205000	0.71048	0.455000	0.32223	GTA	.	.		0.413	ZDHHC13-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387821.1	NM_019028		C	19170829	T	C	19170829	3	2	4	1	0	0	0	0	1	0	0	0	17618	1638	57	2	488	2	ZDHHC13	11	19170829	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	14150385	19170829	115835687	85	344										
SLC22A8	9376	hgsc.bcm.edu	37	chr11	62760762	62760762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tagagggatcctctgggaggCcttttccacctctggctcct	11	13	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr11:62760762C>T	ENST00000336232.2	-	11	1711	c.1576G>A	c.(1576-1578)Gcc>Acc	p.A526T	SLC22A8_ENST00000430500.2_Missense_Mutation_p.A526T|SLC22A8_ENST00000535878.1_Missense_Mutation_p.A403T|SLC22A8_ENST00000311438.8_3'UTR|SLC22A8_ENST00000545207.1_Missense_Mutation_p.A435T|SLC22A8_ENST00000542795.1_5'Flank	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8	526				A -> T (in Ref. 3; BAG60589). {ECO:0000305}.	glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CTCTGGGAGGCCTTTTCCACC	0.622																																					p.A526T		Atlas-SNP	.											.	SLC22A8	60	.	0			c.G1576A						.						61	60	60					11																	62760762		2201	4298	6499	SO:0001583	missense	9376	exon11			GGGAGGCCTTTTC	AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"Solute carriers"	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.1576G>A	chr11.hg19:g.62760762C>T	ENSP00000337335:p.Ala526Thr	73.0	0.0		76.0	18.0	NM_001184732	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Missense_Mutation	SNP	ENST00000336232.2	hg19	CCDS8042.1	.	.	.	.	.	.	.	.	.	.	C	10.25	1.298422	0.23650	.	.	ENSG00000149452	ENST00000336232;ENST00000540631;ENST00000545207;ENST00000535878;ENST00000430500	T;T;T;T	0.66638	-0.17;-0.22;-0.15;-0.17	5.36	4.44	0.53790	.	0.484707	0.20326	N	0.094524	T	0.43322	0.1242	N	0.08118	0	0.09310	N	1	B	0.29955	0.263	B	0.29598	0.104	T	0.26121	-1.0112	10	0.19590	T	0.45	.	10.4805	0.44691	0.0:0.9095:0.0:0.0905	.	526	Q8TCC7	S22A8_HUMAN	T	526;512;435;403;526	ENSP00000337335:A526T;ENSP00000441658:A435T;ENSP00000443368:A403T;ENSP00000398548:A526T	ENSP00000337335:A526T	A	-	1	0	SLC22A8	62517338	0.000000	0.05858	0.484000	0.27391	0.467000	0.32768	-0.107000	0.10873	1.390000	0.46547	0.561000	0.74099	GCC	.	.		0.622	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254		T	62760762	C	T	62760762	3	4	4	1	0	0	0	0	1	0	0	0	14475	739	26	3	56	3	SLC22A8	11	62760762	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	43589933	62760762	72245754	86	345										
PPFIA1	8500	hgsc.bcm.edu	37	chr11	70201848	70201848	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agaaaggcattaagtcctccAttggccgcttgtttggcaag	11	9	0	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr11:70201848A>T	ENST00000253925.7	+	18	2634	c.2419A>T	c.(2419-2421)Att>Ttt	p.I807F	AP000487.4_ENST00000324630.5_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.I807F|AP000487.6_ENST00000528607.1_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	807					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TAAGTCCTCCATTGGCCGCTT	0.537																																					p.I807F		Atlas-SNP	.											.	PPFIA1	114	.	0			c.A2419T						.						100	97	98					11																	70201848		2200	4294	6494	SO:0001583	missense	8500	exon18			TCCTCCATTGGCC	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"Sterile alpha motif (SAM) domain containing"	9245	protein-coding gene	gene with protein product	"Liprin-alpha1"	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.2419A>T	chr11.hg19:g.70201848A>T	ENSP00000253925:p.Ile807Phe	201.0	0.0		125.0	17.0	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	hg19	CCDS31627.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.9|24.9	4.579215|4.579215	0.86645|0.86645	.|.	.|.	ENSG00000131626|ENSG00000131626	ENST00000530798|ENST00000253925;ENST00000389547;ENST00000544950	.|T;T	.|0.26810	.|1.71;1.71	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	.|0.067147	.|0.64402	.|U	.|0.000020	T|T	0.52075|0.52075	0.1712|0.1712	M|M	0.78456|0.78456	2.415|2.415	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.998;0.995	.|D;D	.|0.71414	.|0.973;0.92	T|T	0.58059|0.58059	-0.7703|-0.7703	5|10	.|0.87932	.|D	.|0	.|.	15.3826|15.3826	0.74673|0.74673	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|807;807	.|Q13136;Q13136-2	.|LIPA1_HUMAN;.	L|F	199|807;807;304	.|ENSP00000253925:I807F;ENSP00000374198:I807F	.|ENSP00000253925:I807F	H|I	+|+	2|1	0|0	PPFIA1|PPFIA1	69879496|69879496	1.000000|1.000000	0.71417|0.71417	0.872000|0.872000	0.34217|0.34217	0.442000|0.442000	0.32017|0.32017	5.830000|5.830000	0.69324|0.69324	2.106000|2.106000	0.64143|0.64143	0.482000|0.482000	0.46254|0.46254	CAT|ATT	.	.		0.537	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		T	70201848	A	T	70201848	3	4	4	1	0	0	0	0	1	0	0	0	12318	217	8	4	2485	4	PPFIA1	11	70201848	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	7441086	70201848	64804668	87	346										
TMEM135	65084	hgsc.bcm.edu	37	chr11	87032351	87032351	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agatacacaactgtaacaccAgagttgcccacagagttttc	7	11	0	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr11:87032351A>T	ENST00000305494.5	+	15	1392	c.1353A>T	c.(1351-1353)ccA>ccT	p.P451P	TMEM135_ENST00000340353.7_Silent_p.P429P|TMEM135_ENST00000532959.1_Silent_p.P322P|TMEM135_ENST00000535167.1_Silent_p.P312P	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	451					peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CTGTAACACCAGAGTTGCCCA	0.398																																					p.P451P		Atlas-SNP	.											.	TMEM135	40	.	0			c.A1353T						.						103	98	100					11																	87032351		2201	4299	6500	SO:0001819	synonymous_variant	65084	exon15			AACACCAGAGTTG	BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.1353A>T	chr11.hg19:g.87032351A>T		63.0	0.0		84.0	15.0	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Silent	SNP	ENST00000305494.5	hg19	CCDS8280.1																																																																																			.	.		0.398	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918		T	87032351	A	T	87032351	2	4	4	1	0	0	0	0	0	0	0	1	16066	175	7	4		4	TMEM135	11	87032351	Silent	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	16830503	87032351	47974165	88	347										
MMP3	4314	hgsc.bcm.edu	37	chr11	102713311	102713311	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ctggtgtataattcacaatcCtgtaggagaaaaattgaagc	9	6	1	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr11:102713311C>A	ENST00000299855.5	-	3	607		c.e3-1			NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)						cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	ATTCACAATCCTGTAGGAGAA	0.378																																					.		Atlas-SNP	.											MMP3,NS,carcinoma,0,1	MMP3	60	.	0			c.351-1G>T						.						90	92	91					11																	102713311		2203	4299	6502	SO:0001630	splice_region_variant	4314	exon4			ACAATCCTGTAGG	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"matrix metalloproteinase 3 (stromelysin 1, progelatinase)"	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.351-1G>T	chr11.hg19:g.102713311C>A		73.0	0.0		101.0	29.0	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Splice_Site	SNP	ENST00000299855.5	hg19	CCDS8323.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.397726	0.83120	.	.	ENSG00000149968	ENST00000299855	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MMP3	102218521	1.000000	0.71417	0.980000	0.43619	0.909000	0.53808	7.792000	0.85828	2.937000	0.99478	0.650000	0.86243	.	.	.		0.378	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	Intron	A	102713311	C	A	102713311	5	1	4	1	0	0	0	0	0	0	1	0	9675	695	24	3	1115	3	MMP3	11	102713311	Splice_Site	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	15680960	102713311	32293205	89	348										
CCDC15	80071	hgsc.bcm.edu	37	chr11	124857994	124857998	+	Frame_Shift_Del	DEL	CAAAT	CAAAT	-													0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aacgaccagaatattctaccCaaatgtcaggaccaagattt							TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	CAAAT	CAAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr11:124857994_124857998delCAAAT	ENST00000344762.5	+	8	2131_2135	c.1872_1876delCAAAT	c.(1870-1878)cccaaatgtfs	p.KC625fs	CCDC15_ENST00000529051.1_Frame_Shift_Del_p.KC625fs	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	625						centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		ATATTCTACCCAAATGTCAGGACCA	0.39																																					p.624_625del		Atlas-Indel,Pindel	.											.	CCDC15	134	.	0			c.1871_1875del						.																																			SO:0001589	frameshift_variant	80071	exon8			.	BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.1872_1876delCAAAT	chr11.hg19:g.124857994_124857998delCAAAT	ENSP00000341684:p.Lys625fs	141.0	0.0		111.0	49.0	NM_025004	Q9H8U7	Frame_Shift_Del	DEL	ENST00000344762.5	hg19	CCDS44756.1																																																																																			.	.		0.39	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004		-	124857998	CAAAT	-	124857994	7	5	4	1	0	1	0	1	0	0	0	0	2786	581	21	0	1898	0	CCDC15	11	124857994	Frame_Shift_Del	DEL	CAAAT	TCGA-2Y-A9GU-01A-11D-A382-10	22144683	124857994	10148522	90	349										
NINJ2	283358	hgsc.bcm.edu	37	chr12	674565	674565	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tacctcattcaggttcagccGtgctgcagggaagtggagtg	14	9	3	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr12:674565G>A	ENST00000266383.5	+	0	5068				NINJ2_ENST00000397265.3_Missense_Mutation_p.R82W|NINJ2_ENST00000305108.4_Missense_Mutation_p.R135W|NINJ2_ENST00000537416.1_5'Flank|NINJ2_ENST00000433832.2_3'UTR|NINJ2_ENST00000542920.1_Missense_Mutation_p.R53W	NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3						metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			AGGTTCAGCCGTGCTGCAGGG	0.567																																					p.R135W		Atlas-SNP	.											NINJ2,colon,carcinoma,+2,2	NINJ2	19	.	0			c.C403T						.						114	105	108					12																	674565		2203	4300	6503	SO:0001628	intergenic_variant	4815	exon3			TCAGCCGTGCTGC	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283		chr12.hg19:g.674565G>A		112.0	1.0		42.0	14.0	NM_016533	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	G	17.20	3.328066	0.60743	.	.	ENSG00000171840	ENST00000305108;ENST00000397265;ENST00000542920	T;T;T	0.46451	0.87;0.87;0.87	4.88	3.95	0.45737	.	0.284575	0.33631	N	0.004713	T	0.64000	0.2559	M	0.85197	2.74	0.25407	N	0.988397	D	0.71674	0.998	P	0.60886	0.88	T	0.62315	-0.6880	10	0.72032	D	0.01	-4.1378	13.9554	0.64144	0.0:0.0:0.842:0.158	.	89	Q9NZG7	NINJ2_HUMAN	W	135;82;53	ENSP00000307552:R135W;ENSP00000380435:R82W;ENSP00000438831:R53W	ENSP00000307552:R135W	R	-	1	2	NINJ2	544826	0.050000	0.20438	0.632000	0.29296	0.771000	0.43674	1.790000	0.38734	0.993000	0.38866	0.491000	0.48974	CGG	.	.		0.567	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		A	674565	G	A	674565	1	1	4	0	1	0	0	0	0	0	0	0	10428	1144	40	1		1	NINJ2	12	674565	IGR	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10		674565	133177330	91	350										
LPCAT3	10162	hgsc.bcm.edu	37	chr12	7087833	7087833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gatcagcatgtacatgcagcGgaaccagaaggggtggttct	14	8	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr12:7087833G>A	ENST00000261407.4	-	8	890	c.805C>T	c.(805-807)Cgc>Tgc	p.R269C	U47924.30_ENST00000606112.1_lincRNA|LPCAT3_ENST00000535021.1_5'UTR	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	269					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						TACATGCAGCGGAACCAGAAG	0.453																																					p.R269C		Atlas-SNP	.											.	LPCAT3	33	.	0			c.C805T						.						94	83	87					12																	7087833		2203	4300	6503	SO:0001583	missense	10162	exon8			TGCAGCGGAACCA	U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"O-acyltransferase (membrane bound) domain containing 5", "membrane bound O-acyltransferase domain containing 5"	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970	ENST00000261407.4:c.805C>T	chr12.hg19:g.7087833G>A	ENSP00000261407:p.Arg269Cys	162.0	0.0		111.0	25.0	NM_005768	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Missense_Mutation	SNP	ENST00000261407.4	hg19	CCDS8572.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.338122	0.81911	.	.	ENSG00000111684	ENST00000261407	T	0.75050	-0.9	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.88735	0.6517	M	0.88979	2.995	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	D	0.90395	0.4398	10	0.87932	D	0	-6.6008	19.5024	0.95100	0.0:0.0:1.0:0.0	.	269	Q6P1A2	MBOA5_HUMAN	C	269	ENSP00000261407:R269C	ENSP00000261407:R269C	R	-	1	0	LPCAT3	6958094	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.186000	0.77722	2.607000	0.88179	0.655000	0.94253	CGC	.	.		0.453	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768		A	7087833	G	A	7087833	3	1	4	1	0	0	0	0	1	0	0	0	8921	1116	39	1	678	1	LPCAT3	12	7087833	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	6413268	7087833	126764062	92	351										
KRT2	3849	hgsc.bcm.edu	37	chr12	53040621	53040621	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ctggtagtcacgcagcagccGcgccaagtcctccttggcct	11	16	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr12:53040621G>A	ENST00000309680.3	-	7	1393	c.1372C>T	c.(1372-1374)Cgg>Tgg	p.R458W		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	458	Coil 2.|Rod.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		CGCAGCAGCCGCGCCAAGTCC	0.622																																					p.R458W		Atlas-SNP	.											.	KRT2	94	.	0			c.C1372T						.						101	89	93					12																	53040621		2203	4300	6503	SO:0001583	missense	3849	exon7			GCAGCCGCGCCAA		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.1372C>T	chr12.hg19:g.53040621G>A	ENSP00000310861:p.Arg458Trp	62.0	0.0		48.0	12.0	NM_000423	Q4VAQ2	Missense_Mutation	SNP	ENST00000309680.3	hg19	CCDS8835.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.980621	0.74474	.	.	ENSG00000172867	ENST00000309680	T	0.71103	-0.54	4.48	2.63	0.31362	Filament (1);	.	.	.	.	D	0.84415	0.5467	M	0.89287	3.02	0.36609	D	0.875113	D	0.89917	1.0	D	0.85130	0.997	D	0.87279	0.2291	9	0.87932	D	0	.	10.4968	0.44783	0.159:0.0:0.841:0.0	.	458	P35908	K22E_HUMAN	W	458	ENSP00000310861:R458W	ENSP00000310861:R458W	R	-	1	2	KRT2	51326888	0.004000	0.15560	0.997000	0.53966	0.957000	0.61999	0.300000	0.19156	0.631000	0.30412	0.563000	0.77884	CGG	.	.		0.622	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		A	53040621	G	A	53040621	3	1	4	1	0	0	0	0	1	0	0	0	8466	1086	38	1	559	1	KRT2	12	53040621	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	45952788	53040621	80811274	93	352										
AMHR2	269	hgsc.bcm.edu	37	chr12	53819694	53819694	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cccctgctggtactggaactGcatcccaaggtgagcaccaa	10	14	0	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr12:53819694G>A	ENST00000257863.4	+	6	923	c.843G>A	c.(841-843)ctG>ctA	p.L281L	AMHR2_ENST00000379791.3_Silent_p.L281L|AMHR2_ENST00000550311.1_Silent_p.L281L	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	281	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	TACTGGAACTGCATCCCAAGG	0.577																																					p.L281L		Atlas-SNP	.											.	AMHR2	61	.	0			c.G843A						.						38	39	39					12																	53819694		2203	4300	6503	SO:0001819	synonymous_variant	269	exon6			GGAACTGCATCCC	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"Muellerian inhibiting substance type II receptor"	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.843G>A	chr12.hg19:g.53819694G>A		50.0	0.0		47.0	5.0	NM_020547	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Silent	SNP	ENST00000257863.4	hg19	CCDS8858.1																																																																																			.	.		0.577	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547		A	53819694	G	A	53819694	2	1	4	1	0	0	0	0	0	0	0	1	573	1306	46	3		3	AMHR2	12	53819694	Silent	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	779073	53819694	80032201	94	353										
NACA	4666	hgsc.bcm.edu	37	chr12	57114040	57114040	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gcatttgggccactaaaggaTaatgataagtggcattagga	12	5	0	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr12:57114040T>C	ENST00000454682.1	-	3	1555	c.1274A>G	c.(1273-1275)tAt>tGt	p.Y425C	NACA_ENST00000552540.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.Y425C	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	425	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						CACTAAAGGATAATGATAAGT	0.458			T	BCL6	NHL																																p.Y425C		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.A1274G						.						140	127	131					12																	57114040		1568	3582	5150	SO:0001583	missense	4666	exon3			AAAGGATAATGAT	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.1274A>G	chr12.hg19:g.57114040T>C	ENSP00000403817:p.Tyr425Cys	110.0	0.0		102.0	22.0	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.09	1.254109	0.22965	.	.	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.46063	0.88;0.96	3.53	2.23	0.28157	.	.	.	.	.	T	0.22551	0.0544	N	0.08118	0	0.09310	N	1	P;P	0.43094	0.799;0.706	B;B	0.40982	0.288;0.345	T	0.06197	-1.0840	9	0.62326	D	0.03	.	6.3344	0.21289	0.2199:0.0:0.0:0.7801	.	425;425	E9PAV3;F8VU71	.;.	C	425	ENSP00000403817:Y425C;ENSP00000448035:Y425C	ENSP00000403817:Y425C	Y	-	2	0	NACA	55400307	0.139000	0.22563	0.451000	0.26982	0.095000	0.18619	0.368000	0.20399	1.401000	0.46761	0.156000	0.16432	TAT	.	.		0.458	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		C	57114040	T	C	57114040	3	2	4	1	0	0	0	0	1	0	0	0	10142	1406	49	2	4990	2	NACA	12	57114040	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	3294346	57114040	76737855	95	354										
GRIP1	23426	hgsc.bcm.edu	37	chr12	66838478	66838478	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tggaattccattgatggccaTcactctgtctccaatctgta	7	11	4	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr12:66838478T>A	ENST00000398016.3	-	12	1485	c.1417A>T	c.(1417-1419)Atg>Ttg	p.M473L	GRIP1_ENST00000286445.7_Missense_Mutation_p.M525L|GRIP1_ENST00000359742.4_Missense_Mutation_p.M525L	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TTGATGGCCATCACTCTGTCT	0.458																																					p.M473L		Atlas-SNP	.											.	GRIP1	106	.	0			c.A1417T						.						130	124	126					12																	66838478		1958	4140	6098	SO:0001583	missense	23426	exon12			TGGCCATCACTCT	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.1417A>T	chr12.hg19:g.66838478T>A	ENSP00000381098:p.Met473Leu	183.0	0.0		133.0	12.0	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	hg19	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	2.531|2.531	-0.308479|-0.308479	0.05458|0.05458	.|.	.|.	ENSG00000155974|ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215|ENST00000538164	T;T;T;T;T;T|.	0.19105|.	2.17;2.17;2.17;2.17;2.17;2.17|.	5.57|5.57	4.43|4.43	0.53597|0.53597	PDZ/DHR/GLGF (4);|.	0.250420|.	0.46145|.	N|.	0.000306|.	T|.	0.03739|.	0.0106|.	N|N	0.00025|0.00025	-2.675|-2.675	0.27379|0.27379	N|N	0.955478|0.955478	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0|.	T|.	0.28235|.	-1.0050|.	9|.	.|.	.|.	.|.	-8.9594|-8.9594	6.9315|6.9315	0.24444|0.24444	0.0:0.0792:0.3022:0.6186|0.0:0.0792:0.3022:0.6186	.|.	473;525;473;525|.	F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2|.	.;GRIP1_HUMAN;.;.|.	L|C	473;525;525;473;417;365|339	ENSP00000381098:M473L;ENSP00000352780:M525L;ENSP00000286445:M525L;ENSP00000446047:M473L;ENSP00000446024:M417L;ENSP00000446011:M365L|.	.|.	M|X	-|-	1|3	0|0	GRIP1|GRIP1	65124745|65124745	0.992000|0.992000	0.36948|0.36948	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	0.385000|0.385000	0.20685|0.20685	0.956000|0.956000	0.37904|0.37904	0.441000|0.441000	0.28932|0.28932	ATG|TGA	.	.		0.458	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			A	66838478	T	A	66838478	3	1	4	1	0	0	0	0	1	0	0	0	6796	1435	50	4	1865	4	GRIP1	12	66838478	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	9724438	66838478	67013417	96	355										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80707414	80707414	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agatcatctactgtttgttgTaagtaccctacttagaacat	6	8	2	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr12:80707414T>C	ENST00000547103.1	+	30	3586		c.e30+2		OTOGL_ENST00000458043.2_Splice_Site			Q3ZCN5	OTOGL_HUMAN	otogelin-like						L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						CTGTTTGTTGTAAGTACCCTA	0.363																																					.		Atlas-SNP	.											.	OTOGL	235	.	0			c.3580+2T>C						.						161	170	167					12																	80707414		2149	4262	6411	SO:0001630	splice_region_variant	283310	exon30			TTGTTGTAAGTAC	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.3580+2T>C	chr12.hg19:g.80707414T>C		103.0	0.0		76.0	22.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Splice_Site	SNP	ENST00000547103.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.64	3.667181	0.67814	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1894	0.81975	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	OTOGL	79231545	1.000000	0.71417	1.000000	0.80357	0.619000	0.37552	7.588000	0.82629	2.217000	0.71921	0.528000	0.53228	.	.	.		0.363	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	Intron	C	80707414	T	C	80707414	5	2	4	1	0	0	0	0	0	0	1	0	1709	1652	57	2	3700	2	C12orf64	12	80707414	Splice_Site	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	13868936	80707414	53144481	97	356										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130185157	130185157	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	caggaagaaggagacgtccgCgttgttgatgtggtaggtca	16	6	1	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr12:130185157C>T	ENST00000422113.2	-	2	492	c.166G>A	c.(166-168)Gcg>Acg	p.A56T	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	56					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GAGACGTCCGCGTTGTTGATG	0.552																																					p.A56T		Atlas-SNP	.											TMEM132D,colon,carcinoma,0,1	TMEM132D	299	.	0			c.G166A						.						93	70	77					12																	130185157		2203	4300	6503	SO:0001583	missense	121256	exon2			CGTCCGCGTTGTT	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.166G>A	chr12.hg19:g.130185157C>T	ENSP00000408581:p.Ala56Thr	100.0	0.0		84.0	18.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.323844	0.41096	.	.	ENSG00000151952	ENST00000422113	T	0.14640	2.49	5.33	4.44	0.53790	.	0.323515	0.26463	N	0.024223	T	0.27205	0.0667	L	0.59436	1.845	0.41431	D	0.987863	D	0.76494	0.999	P	0.56865	0.808	T	0.01621	-1.1310	9	.	.	.	-41.0693	14.1315	0.65257	0.0:0.9274:0.0:0.0726	.	56	Q14C87	T132D_HUMAN	T	56	ENSP00000408581:A56T	.	A	-	1	0	TMEM132D	128751110	1.000000	0.71417	0.029000	0.17559	0.824000	0.46624	3.952000	0.56691	1.228000	0.43614	0.555000	0.69702	GCG	.	.		0.552	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	130185157	C	T	130185157	3	4	4	1	0	0	0	0	1	0	0	0	16062	768	27	1	3165	1	TMEM132D	12	130185157	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	49477743	130185157	3666738	98	357										
MTUS2	23281	hgsc.bcm.edu	37	chr13	29600032	29600032	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cacaccacccccaaacagggCtctgcttccttaggaggggc	10	16	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr13:29600032C>T	ENST00000431530.3	+	1	1285	c.1227C>T	c.(1225-1227)ggC>ggT	p.G409G		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	399						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CCAAACAGGGCTCTGCTTCCT	0.547																																					p.G409G		Atlas-SNP	.											.	MTUS2	279	.	0			c.C1227T						.						32	35	34					13																	29600032		1928	4151	6079	SO:0001819	synonymous_variant	23281	exon1			ACAGGGCTCTGCT	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.1227C>T	chr13.hg19:g.29600032C>T		221.0	0.0		195.0	93.0	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Silent	SNP	ENST00000431530.3	hg19	CCDS45022.1																																																																																			.	.		0.547	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		T	29600032	C	T	29600032	2	4	4	1	0	0	0	0	0	0	0	1	9975	784	28	3		3	MTUS2	13	29600032	Silent	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10		29600032	85569846	99	358										
PCDH8	5100	hgsc.bcm.edu	37	chr13	53422137	53422137	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gtgcccactgccgcaccctcGgacacctctaccgggatctg	10	18	2	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr13:53422137G>A	ENST00000377942.3	-	1	638	c.435C>T	c.(433-435)tcC>tcT	p.S145S	PCDH8_ENST00000338862.4_Silent_p.S145S	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	145	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.S145S(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		CCGCACCCTCGGACACCTCTA	0.711																																					p.S145S	GBM(36;25 841 9273 49207)	Atlas-SNP	.											.	PCDH8	95	.	1	Substitution - coding silent(1)	lung(1)	c.C435T						.						28	28	28					13																	53422137		2193	4292	6485	SO:0001819	synonymous_variant	5100	exon1			ACCCTCGGACACC	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"Cadherins / Protocadherins : Non-clustered"	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.435C>T	chr13.hg19:g.53422137G>A		127.0	0.0		68.0	11.0	NM_002590	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Silent	SNP	ENST00000377942.3	hg19	CCDS9438.1																																																																																			.	.		0.711	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590		A	53422137	G	A	53422137	2	1	4	1	0	0	0	0	0	0	0	1	11526	1103	39	1		1	PCDH8	13	53422137	Silent	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	23822105	53422137	61747741	100	359										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33046347	33046347	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ggtttgtaaacaaactggatGaattcattcaatggttaaat	8	4	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr14:33046347G>T	ENST00000280979.4	+	5	2538	c.2368G>T	c.(2368-2370)Gaa>Taa	p.E790*	AKAP6_ENST00000557272.1_Nonsense_Mutation_p.E790*|AKAP6_ENST00000557354.1_Nonsense_Mutation_p.E790*	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	790					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		CAAACTGGATGAATTCATTCA	0.378																																					p.E790X	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.G2368T						.						91	91	91					14																	33046347		2203	4300	6503	SO:0001587	stop_gained	9472	exon5			CTGGATGAATTCA	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.2368G>T	chr14.hg19:g.33046347G>T	ENSP00000280979:p.Glu790*	131.0	0.0		146.0	26.0	NM_004274	A7E242|A7E2D4|O15028	Nonsense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	G	41	8.601446	0.98881	.	.	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272	.	.	.	4.96	4.96	0.65561	.	0.145097	0.48286	D	0.000183	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-15.5508	11.6851	0.51481	0.0819:0.0:0.9181:0.0	.	.	.	.	X	790	.	ENSP00000280979:E790X	E	+	1	0	AKAP6	32116098	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.474000	0.73578	2.272000	0.75746	0.563000	0.77884	GAA	.	.		0.378	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33046347	G	T	33046347	4	4	4	1	0	0	0	0	0	1	0	0	455	1291	45	3	2382	3	AKAP6	14	33046347	Nonsense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10		33046347	74303193	101	360										
ADCK1	57143	hgsc.bcm.edu	37	chr14	78288800	78288800	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ggctgtcatcagttacgactAcctcacttccctgaagagtg	9	12	3	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr14:78288800A>G	ENST00000238561.5	+	3	257	c.158A>G	c.(157-159)tAc>tGc	p.Y53C	Y_RNA_ENST00000362570.1_RNA|ADCK1_ENST00000341211.5_Missense_Mutation_p.Y53C	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	53						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		AGTTACGACTACCTCACTTCC	0.507																																					p.Y53C		Atlas-SNP	.											.	ADCK1	81	.	0			c.A158G						.						175	131	146					14																	78288800		2203	4300	6503	SO:0001583	missense	57143	exon3			ACGACTACCTCAC	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.158A>G	chr14.hg19:g.78288800A>G	ENSP00000238561:p.Tyr53Cys	61.0	0.0		57.0	14.0	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Missense_Mutation	SNP	ENST00000238561.5	hg19	CCDS9869.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.056542	0.76074	.	.	ENSG00000063761	ENST00000238561;ENST00000557501;ENST00000341211	T;D;T	0.84516	-0.72;-1.86;0.16	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.93716	0.7992	M	0.91972	3.26	0.49051	D	0.999744	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.94792	0.7963	10	0.87932	D	0	-15.9498	14.0887	0.64975	1.0:0.0:0.0:0.0	.	53;53	Q9UIE6;Q86TW2-2	.;.	C	53	ENSP00000238561:Y53C;ENSP00000451549:Y53C;ENSP00000339663:Y53C	ENSP00000238561:Y53C	Y	+	2	0	ADCK1	77358553	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.983000	0.70540	2.302000	0.77476	0.533000	0.62120	TAC	.	.		0.507	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421		G	78288800	A	G	78288800	3	3	4	1	0	0	0	0	1	0	0	0	288	391	14	2	164	2	ADCK1	14	78288800	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	45242453	78288800	29060740	102	361										
TRPM1	4308	hgsc.bcm.edu	37	chr15	31360290	31360290	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ttggtgtcataggatacacgGatatactgtgaaagagtgtg	13	4	1	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr15:31360290G>A	ENST00000256552.6	-	5	432	c.285C>T	c.(283-285)atC>atT	p.I95I	TRPM1_ENST00000542188.1_Silent_p.I112I|MIR211_ENST00000384969.1_RNA|TRPM1_ENST00000397795.2_Silent_p.I73I	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		AGGATACACGGATATACTGTG	0.493																																					p.I112I		Atlas-SNP	.											.	TRPM1	183	.	0			c.C336T						.						89	91	90					15																	31360290		2051	4197	6248	SO:0001819	synonymous_variant	4308	exon4			TACACGGATATAC	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.285C>T	chr15.hg19:g.31360290G>A		49.0	0.0		43.0	12.0	NM_001252020		Silent	SNP	ENST00000256552.6	hg19	CCDS58346.1																																																																																			.	.		0.493	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		A	31360290	G	A	31360290	2	1	4	1	0	0	0	0	0	0	0	1	16600	1164	41	3		3	TRPM1	15	31360290	Silent	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10		31360290	71171102	103	362										
DUOX1	53905	hgsc.bcm.edu	37	chr15	45443417	45443417	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cccatggacacagaccctccCcaggagattcggcggaggtt	12	14	0	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr15:45443417C>T	ENST00000321429.4	+	24	3392	c.2985C>T	c.(2983-2985)ccC>ccT	p.P995P	CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000561166.1_Silent_p.P641P|DUOX1_ENST00000389037.3_Silent_p.P995P	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	995	Interaction with TXNDC11. {ECO:0000250}.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CAGACCCTCCCCAGGAGATTC	0.537																																					p.P995P		Atlas-SNP	.											.	DUOX1	125	.	0			c.C2985T						.						116	118	117					15																	45443417		2198	4298	6496	SO:0001819	synonymous_variant	53905	exon24			CCCTCCCCAGGAG	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.2985C>T	chr15.hg19:g.45443417C>T		118.0	0.0		72.0	36.0	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	hg19	CCDS32221.1																																																																																			.	.		0.537	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		T	45443417	C	T	45443417	2	4	4	1	0	0	0	0	0	0	0	1	4802	610	22	3		3	DUOX1	15	45443417	Silent	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	14083127	45443417	57087975	104	363										
DYX1C1	161582	hgsc.bcm.edu	37	chr15	55727133	55727134	+	Frame_Shift_Ins	INS	-	-	T													0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cttcaatagccttgtgtaagINSttttttagttttaggtggca							TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr15:55727133_55727134insT	ENST00000321149.3	-	8	1383_1384	c.1016_1017insA	c.(1015-1017)aacfs	p.N339fs	DYX1C1_ENST00000448430.2_Frame_Shift_Ins_p.N339fs|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000348518.3_Frame_Shift_Ins_p.N339fs|DYX1C1_ENST00000457155.2_Frame_Shift_Ins_p.N339fs|DYX1C1_ENST00000380679.1_Frame_Shift_Ins_p.N339fs	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	339					cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		CCTTGTGTAAGTTTTTTAGTTT	0.312																																					p.N339fs		Atlas-Indel,Pindel	.											.	DYX1C1	54	.	0			c.1017_1018insA						.																																			SO:0001589	frameshift_variant	161582	exon8			.		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"Tetratricopeptide (TTC) repeat domain containing"	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.1017dupA	chr15.hg19:g.55727139_55727139dupT	ENSP00000323275:p.Asn339fs	144.0	0.0		86.0	20.0	NM_001033560	Q6P5Y9|Q8N1S6	Frame_Shift_Ins	INS	ENST00000321149.3	hg19	CCDS10154.1																																																																																			.	.		0.312	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810		T	55727134	-	T	55727133	7	5	4	1	0	1	1	0	0	0	0	0	4864	1020	36	0	360	0	DYX1C1	15	55727133	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GU-01A-11D-A382-10	10283716	55727133	46804259	105	364										
TEX9	374618	hgsc.bcm.edu	37	chr15	56683537	56683537	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gcaaaaacaattagcaaaatTgaagggcaactggaggaaga	11	5	0	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr15:56683537T>A	ENST00000352903.2	+	7	516	c.492T>A	c.(490-492)atT>atA	p.I164I	TEX9_ENST00000537232.1_Silent_p.I89I|TEX9_ENST00000561221.2_Silent_p.I164I|RP11-48G14.2_ENST00000564401.1_lincRNA|TEX9_ENST00000558083.2_Silent_p.I89I	NM_198524.1	NP_940926.1	Q8N6V9	TEX9_HUMAN	testis expressed 9	164										cervix(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	14				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		TTAGCAAAATTGAAGGGCAAC	0.353																																					p.I164I		Atlas-SNP	.											.	TEX9	29	.	0			c.T492A						.						94	96	95					15																	56683537		2192	4292	6484	SO:0001819	synonymous_variant	374618	exon7			CAAAATTGAAGGG	BC028119	CCDS10157.1, CCDS66776.1	15q21.3	2007-03-13	2007-03-13		ENSG00000151575	ENSG00000151575			29585	protein-coding gene	gene with protein product			"testis expressed sequence 9"				Standard	XM_005254361		Approved		uc002adp.3	Q8N6V9	OTTHUMG00000132035	ENST00000352903.2:c.492T>A	chr15.hg19:g.56683537T>A		233.0	0.0		307.0	59.0	NM_198524	B4DH73	Silent	SNP	ENST00000352903.2	hg19	CCDS10157.1																																																																																			.	.		0.353	TEX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255048.2	NM_198524		A	56683537	T	A	56683537	2	1	4	1	0	0	0	0	0	0	0	1	15799	1800	63	4		4	TEX9	15	56683537	Silent	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	956404	56683537	45847855	106	365										
SMAD6	4091	hgsc.bcm.edu	37	chr15	67073814	67073814	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gctgggggccctgctactccCggcagttcatcacctcctgc	11	17	2	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr15:67073814C>T	ENST00000288840.5	+	4	2463	c.1432C>T	c.(1432-1434)Cgg>Tgg	p.R478W	SMAD6_ENST00000338426.4_Missense_Mutation_p.R217W	NM_005585.4	NP_005576.3	O43541	SMAD6_HUMAN	SMAD family member 6	478	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				BMP signaling pathway (GO:0030509)|cell-substrate adhesion (GO:0031589)|fat cell differentiation (GO:0045444)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|response to estrogen (GO:0043627)|response to laminar fluid shear stress (GO:0034616)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity (GO:0030617)|type I activin receptor binding (GO:0070698)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			lung(1)|skin(1)	2						CTGCTACTCCCGGCAGTTCAT	0.731																																					p.R478W	Esophageal Squamous(179;72 2004 22333 39628 47290)	Atlas-SNP	.											.	SMAD6	14	.	0			c.C1432T						.						10	14	13					15																	67073814		2140	4244	6384	SO:0001583	missense	4091	exon4			TACTCCCGGCAGT	BC012986	CCDS10221.1	15q22.31	2014-09-11	2006-11-06	2004-05-26	ENSG00000137834	ENSG00000137834		"SMADs"	6772	protein-coding gene	gene with protein product		602931	"MAD, mothers against decapentaplegic homolog 6 (Drosophila)", "SMAD, mothers against DPP homolog 6 (Drosophila)"	MADH7, MADH6		9256479	Standard	NR_027654		Approved	HsT17432	uc002aqf.3	O43541	OTTHUMG00000133218	ENST00000288840.5:c.1432C>T	chr15.hg19:g.67073814C>T	ENSP00000288840:p.Arg478Trp	68.0	0.0		54.0	8.0	NM_005585	A9J6M5|O43654|Q15799|Q7Z7L4|Q96E31|Q9UKZ3	Missense_Mutation	SNP	ENST00000288840.5	hg19	CCDS10221.1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.507623	0.64410	.	.	ENSG00000137834	ENST00000288840;ENST00000338426	D;D	0.99698	-6.44;-6.44	5.71	0.994	0.19832	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99764	0.9904	H	0.95365	3.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98012	1.0366	10	0.87932	D	0	.	14.829	0.70135	0.6061:0.3939:0.0:0.0	.	217;478	O43541-2;O43541	.;SMAD6_HUMAN	W	478;217	ENSP00000288840:R478W;ENSP00000345054:R217W	ENSP00000288840:R478W	R	+	1	2	SMAD6	64860868	0.571000	0.26659	0.962000	0.40283	0.998000	0.95712	1.286000	0.33273	0.274000	0.22072	0.561000	0.74099	CGG	.	.		0.731	SMAD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256953.2	NM_005585		T	67073814	C	T	67073814	3	4	4	1	0	0	0	0	1	0	0	0	14777	643	23	1	1484	1	SMAD6	15	67073814	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	10390277	67073814	35457578	107	366										
UACA	55075	hgsc.bcm.edu	37	chr15	70959216	70959216	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tccttctcatcttttgcagaTatttccttctttttggcatg	5	10	3	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr15:70959216T>C	ENST00000322954.6	-	16	3992	c.3807A>G	c.(3805-3807)atA>atG	p.I1269M	UACA_ENST00000539319.1_Missense_Mutation_p.I1160M|UACA_ENST00000560441.1_Missense_Mutation_p.I1254M|UACA_ENST00000379983.2_Missense_Mutation_p.I1256M	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1269					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						CTTTTGCAGATATTTCCTTCT	0.358																																					p.I1269M		Atlas-SNP	.											.	UACA	235	.	0			c.A3807G						.						177	168	171					15																	70959216		2199	4298	6497	SO:0001583	missense	55075	exon16			TGCAGATATTTCC	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.3807A>G	chr15.hg19:g.70959216T>C	ENSP00000314556:p.Ile1269Met	75.0	0.0		93.0	20.0	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	hg19	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	T	6.180	0.401451	0.11696	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000539319	T;T;T	0.34275	1.37;1.39;1.87	5.7	-11.4	0.00090	.	0.673298	0.13019	N	0.420253	T	0.10294	0.0252	N	0.08118	0	0.09310	N	1	B;B;B;B	0.30542	0.284;0.138;0.138;0.217	B;B;B;B	0.28916	0.096;0.044;0.044;0.096	T	0.09335	-1.0679	10	0.46703	T	0.11	-0.3482	1.314	0.02103	0.2079:0.4102:0.2358:0.1461	.	1160;1269;1269;1256	F5H2B9;B7ZKM6;Q9BZF9;G3XAG2	.;.;UACA_HUMAN;.	M	1269;1256;1160	ENSP00000314556:I1269M;ENSP00000369319:I1256M;ENSP00000438667:I1160M	ENSP00000314556:I1269M	I	-	3	3	UACA	68746270	0.000000	0.05858	0.000000	0.03702	0.538000	0.34931	-4.194000	0.00276	-2.183000	0.00763	-0.899000	0.02877	ATA	.	.		0.358	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			C	70959216	T	C	70959216	3	2	4	1	0	0	0	0	1	0	0	0	16839	1396	49	2	459	2	UACA	15	70959216	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	3885402	70959216	31572176	108	367										
C15orf39	56905	hgsc.bcm.edu	37	chr15	75500060	75500060	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	accctgcctgcccaggagggCccctcagggagtaaacccct	11	17	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr15:75500060C>T	ENST00000360639.2	+	2	1991	c.1671C>T	c.(1669-1671)ggC>ggT	p.G557G	C15orf39_ENST00000394987.4_Silent_p.G557G|C15orf39_ENST00000567617.1_Silent_p.G557G			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	557						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						CCCAGGAGGGCCCCTCAGGGA	0.617																																					p.G557G		Atlas-SNP	.											.	C15orf39	64	.	0			c.C1671T						.						22	24	23					15																	75500060		2196	4293	6489	SO:0001819	synonymous_variant	56905	exon2			GGAGGGCCCCTCA	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 38~Name Same As HGNC:28782"				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.1671C>T	chr15.hg19:g.75500060C>T		149.0	0.0		70.0	32.0	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Silent	SNP	ENST00000360639.2	hg19	CCDS10276.1																																																																																			.	.		0.617	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		T	75500060	C	T	75500060	2	4	4	1	0	0	0	0	0	0	0	1	1795	726	26	3		3	C15orf39	15	75500060	Silent	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	4540844	75500060	27031332	109	368										
EFTUD1	79631	hgsc.bcm.edu	37	chr15	82512452	82512452	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tccttttggacatgtttcaaTggcactcccatcttgggtgg	10	10	2	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr15:82512452T>G	ENST00000268206.7	-	13	1579	c.1411A>C	c.(1411-1413)Att>Ctt	p.I471L	EFTUD1_ENST00000359445.3_Missense_Mutation_p.I420L	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	471					GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						CATGTTTCAATGGCACTCCCA	0.498																																					p.I471L		Atlas-SNP	.											.	EFTUD1	74	.	0			c.A1411C						.						142	137	139					15																	82512452		1931	4135	6066	SO:0001583	missense	79631	exon13			TTTCAATGGCACT	AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"ribosome assembly 1 homolog (yeast)"					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.1411A>C	chr15.hg19:g.82512452T>G	ENSP00000268206:p.Ile471Leu	84.0	0.0		87.0	37.0	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Missense_Mutation	SNP	ENST00000268206.7	hg19	CCDS42071.1	.	.	.	.	.	.	.	.	.	.	t	1.422	-0.572524	0.03882	.	.	ENSG00000140598	ENST00000268206;ENST00000359445	T;T	0.61859	0.07;0.34	4.29	1.39	0.22231	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	2.054490	0.02795	N	0.122479	T	0.23886	0.0578	N	0.00538	-1.39	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19614	-1.0300	10	0.22706	T	0.39	-10.7283	3.8643	0.09010	0.3401:0.0:0.4888:0.1711	.	420;471	Q7Z2Z2-2;Q7Z2Z2	.;ETUD1_HUMAN	L	471;420	ENSP00000268206:I471L;ENSP00000352418:I420L	ENSP00000268206:I471L	I	-	1	0	EFTUD1	80299507	0.002000	0.14202	0.012000	0.15200	0.043000	0.13939	1.070000	0.30653	0.567000	0.29293	-0.207000	0.12724	ATT	.	.		0.498	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580		G	82512452	T	G	82512452	3	3	4	1	0	0	0	0	1	0	0	0	4962	1464	51	5	1983	5	EFTUD1	15	82512452	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	7012392	82512452	20018940	110	369										
BTBD12	84464	hgsc.bcm.edu	37	chr16	3658812	3658812	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aaagctagcgcagagttcttTaaagtcctcatcagactcat	7	10	4	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr16:3658812T>C	ENST00000294008.3	-	2	794	c.154A>G	c.(154-156)Aaa>Gaa	p.K52E		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	52	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CAGAGTTCTTTAAAGTCCTCA	0.473								Direct reversal of damage																													p.K52E		Atlas-SNP	.											.	SLX4	173	.	0			c.A154G						.						130	121	124					16																	3658812		2197	4300	6497	SO:0001583	missense	84464	exon2			GTTCTTTAAAGTC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.154A>G	chr16.hg19:g.3658812T>C	ENSP00000294008:p.Lys52Glu	135.0	0.0		88.0	18.0	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	hg19	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	T	17.43	3.388544	0.61956	.	.	ENSG00000188827	ENST00000294008	T	0.01464	4.86	5.52	3.2	0.36748	.	0.289012	0.25717	N	0.028779	T	0.01905	0.0060	N	0.22421	0.69	0.22034	N	0.999402	P	0.48407	0.91	B	0.42462	0.388	T	0.47837	-0.9086	10	0.59425	D	0.04	.	11.8887	0.52616	0.0:0.0:0.2758:0.7242	.	52	Q8IY92	SLX4_HUMAN	E	52	ENSP00000294008:K52E	ENSP00000294008:K52E	K	-	1	0	SLX4	3598813	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	2.367000	0.44213	0.427000	0.26145	0.533000	0.62120	AAA	.	.		0.473	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		C	3658812	T	C	3658812	3	2	4	1	0	0	0	0	1	0	0	0	1542	1763	61	2	5406	2	BTBD12	16	3658812	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10		3658812	86695941	111	370										
C16orf93	90835	hgsc.bcm.edu	37	chr16	30772547	30772547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gatccggggtcggggcagcgGcggctgcggaaagaaagcga	20	9	0	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr16:30772547G>A	ENST00000543610.1	-	2	1169	c.208C>T	c.(208-210)Ccg>Tcg	p.P70S	RNF40_ENST00000324685.6_5'Flank|C16orf93_ENST00000541260.1_Missense_Mutation_p.P70S|RNF40_ENST00000357890.5_5'Flank|RNF40_ENST00000402121.3_5'Flank|C16orf93_ENST00000545825.1_Missense_Mutation_p.P70S|RNF40_ENST00000563683.1_5'Flank	NM_001014979.2	NP_001014979.2	A1A4V9	CP093_HUMAN	chromosome 16 open reading frame 93	70										breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)	11						CGGGGCAGCGGCGGCTGCGGA	0.552																																					p.P70S		Atlas-SNP	.											.	C16orf93	33	.	0			c.C208T						.						34	38	37					16																	30772547		2197	4298	6495	SO:0001583	missense	90835	exon2			GCAGCGGCGGCTG	BC042548	CCDS32434.1, CCDS32434.2, CCDS55993.1	16p11.2	2012-10-10			ENSG00000196118	ENSG00000196118			28078	protein-coding gene	gene with protein product							Standard	NM_001195620		Approved	MGC104706	uc002dzm.3	A1A4V9	OTTHUMG00000167926	ENST00000543610.1:c.208C>T	chr16.hg19:g.30772547G>A	ENSP00000437532:p.Pro70Ser	271.0	0.0		146.0	32.0	NM_001195620	A1A4V8|F5GX13|Q569G2	Missense_Mutation	SNP	ENST00000543610.1	hg19	CCDS32434.2	.	.	.	.	.	.	.	.	.	.	G	25.2	4.615554	0.87359	.	.	ENSG00000196118	ENST00000354963;ENST00000543610;ENST00000545825	.	.	.	5.41	5.41	0.78517	.	0.074009	0.53938	D	0.000057	T	0.66177	0.2763	L	0.38531	1.155	0.39550	D	0.968956	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.62905	-0.6755	9	0.32370	T	0.25	-31.6405	14.5573	0.68109	0.0:0.0:1.0:0.0	.	70;33;70	F5GX13;A1A4V9-2;A1A4V9	.;.;CP093_HUMAN	S	33;70;70	.	ENSP00000347050:P33S	P	-	1	0	C16orf93	30680048	0.998000	0.40836	0.995000	0.50966	0.996000	0.88848	4.594000	0.61041	2.815000	0.96918	0.561000	0.74099	CCG	.	.		0.552	C16orf93-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397089.1	NM_001014979		A	30772547	G	A	30772547	3	1	4	1	0	0	0	0	1	0	0	0	1848	1203	42	3	819	3	C16orf93	16	30772547	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	27113735	30772547	59582206	112	371										
TRIM72	260434	hgsc.bcm.edu	37	chr16	31226233	31226233	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ctctgcccctgctgccaggcCcccacgcggccgcaggcact	11	21	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr16:31226233C>T	ENST00000302964.3	-	0	813				TRIM72_ENST00000322122.3_Silent_p.A58A|PYDC1_ENST00000568383.1_5'Flank	NM_152901.2	NP_690865.1	Q8WXC3	PYDC1_HUMAN	PYD (pyrin domain) containing 1						innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of interleukin-1 beta secretion (GO:0050718)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						GCTGCCAGGCCCCCACGCGGC	0.746																																					p.A58A		Atlas-SNP	.											.	TRIM72	32	.	0			c.C174T						.						2	3	3					16																	31226233		1673	3378	5051	SO:0001628	intergenic_variant	493829	exon2			CCAGGCCCCCACG		CCDS10710.1	16p11.2	2008-02-05	2005-12-02		ENSG00000169900	ENSG00000169900			30261	protein-coding gene	gene with protein product		615700	"pyrin domain containing 1"			11786556, 16905547	Standard	NM_152901		Approved	ASC2, POP1	uc002ebo.3	Q8WXC3	OTTHUMG00000132407		chr16.hg19:g.31226233C>T		39.0	0.0		25.0	6.0	NM_001008274	B2R8L4|Q8NFP8	Silent	SNP	ENST00000302964.3	hg19	CCDS10710.1																																																																																			.	.		0.746	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901		T	31226233	C	T	31226233	1	4	4	0	1	0	0	0	0	0	0	0	16560	610	22	3		3	TRIM72	16	31226233	IGR	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	453686	31226233	59128520	113	372										
ABCC11	85320	hgsc.bcm.edu	37	chr16	48258272	48258272	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ttgttctctggaacctcagcAtcaccagaagcactgaagct	8	12	3	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr16:48258272A>G	ENST00000394747.1	-	4	813	c.464T>C	c.(463-465)aTg>aCg	p.M155T	ABCC11_ENST00000537808.1_Missense_Mutation_p.M155T|ABCC11_ENST00000353782.5_Missense_Mutation_p.M155T|ABCC11_ENST00000356608.2_Missense_Mutation_p.M155T|ABCC11_ENST00000394748.1_Missense_Mutation_p.M155T	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	155					organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	GAACCTCAGCATCACCAGAAG	0.493																																					p.M155T		Atlas-SNP	.											.	ABCC11	177	.	0			c.T464C						.						128	109	115					16																	48258272		2200	4300	6500	SO:0001583	missense	85320	exon4			CTCAGCATCACCA	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.464T>C	chr16.hg19:g.48258272A>G	ENSP00000378230:p.Met155Thr	91.0	0.0		71.0	8.0	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	hg19	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	A	11.17	1.559711	0.27827	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14	4.45	4.45	0.53987	ABC transporter, transmembrane domain, type 1 (1);	0.325266	0.32444	N	0.006082	T	0.34483	0.0899	L	0.45581	1.43	0.20403	N	0.999904	P;P	0.41910	0.764;0.457	B;B	0.42738	0.304;0.396	T	0.27331	-1.0077	10	0.59425	D	0.04	-19.2298	10.3605	0.43991	1.0:0.0:0.0:0.0	.	155;155	Q96J66-2;Q96J66	.;ABCCB_HUMAN	T	155	ENSP00000311326:M155T;ENSP00000349017:M155T;ENSP00000378231:M155T;ENSP00000378230:M155T;ENSP00000438530:M155T	ENSP00000311326:M155T	M	-	2	0	ABCC11	46815773	0.338000	0.24775	0.850000	0.33497	0.149000	0.21700	1.681000	0.37618	1.753000	0.51906	0.377000	0.23210	ATG	.	.		0.493	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		G	48258272	A	G	48258272	3	3	4	1	0	0	0	0	1	0	0	0	51	217	8	2	3788	2	ABCC11	16	48258272	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	17032039	48258272	42096481	114	373										
ZNF19	7567	hgsc.bcm.edu	37	chr16	71512898	71512898	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gcacagccacatcctcgaagGtcaccatctcctaaaacaac	5	16	2	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr16:71512898G>C	ENST00000288177.5	-	4	299	c.44C>G	c.(43-45)aCc>aGc	p.T15S	ZNF19_ENST00000565100.2_Intron|AC010547.9_ENST00000561908.1_Missense_Mutation_p.T15S|ZNF19_ENST00000564230.1_Missense_Mutation_p.T15S|ZNF19_ENST00000567225.1_Missense_Mutation_p.T15S|ZNF19_ENST00000565637.1_5'UTR	NM_006961.3	NP_008892.2	P17023	ZNF19_HUMAN	zinc finger protein 19	15	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|prostate(1)|stomach(1)	22		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		ATCCTCGAAGGTCACCATCTC	0.567																																					p.T15S		Atlas-SNP	.											.	ZNF19	46	.	0			c.C44G						.						95	91	93					16																	71512898		2198	4300	6498	SO:0001583	missense	7567	exon4			TCGAAGGTCACCA	X52343	CCDS10901.1	16q22	2013-01-08	2006-05-10		ENSG00000157429	ENSG00000157429		"Zinc fingers, C2H2-type", "-"	12981	protein-coding gene	gene with protein product		194525	"zinc finger protein 19 (KOX 12)"			1505991, 1946370	Standard	NM_006961		Approved	KOX12, MGC51021	uc002fam.1	P17023	OTTHUMG00000137593	ENST00000288177.5:c.44C>G	chr16.hg19:g.71512898G>C	ENSP00000288177:p.Thr15Ser	88.0	0.0		50.0	19.0	NM_006961	A8K895|Q86Y66|Q8NDE2|Q96M79|Q96NE5	Missense_Mutation	SNP	ENST00000288177.5	hg19	CCDS10901.1	.	.	.	.	.	.	.	.	.	.	G	18.68	3.676438	0.67928	.	.	ENSG00000157429	ENST00000288177	T	0.02631	4.22	3.0	3.0	0.34707	Krueppel-associated box (4);	0.227955	0.22658	N	0.057232	T	0.06142	0.0159	M	0.61703	1.905	0.24791	N	0.992756	P	0.47253	0.892	P	0.46253	0.509	T	0.11966	-1.0566	10	0.62326	D	0.03	.	12.243	0.54553	0.0:0.0:1.0:0.0	.	15	P17023	ZNF19_HUMAN	S	15	ENSP00000288177:T15S	ENSP00000288177:T15S	T	-	2	0	ZNF19	70070399	1.000000	0.71417	0.968000	0.41197	0.977000	0.68977	0.838000	0.27572	1.977000	0.57605	0.563000	0.77884	ACC	.	.		0.567	ZNF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268993.2	NM_006961		C	71512898	G	C	71512898	3	2	4	1	0	0	0	0	1	0	0	0	17770	1261	44	4	1344	4	ZNF19	16	71512898	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	23254626	71512898	18841855	115	374										
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44128014	44128015	+	Frame_Shift_Ins	INS	-	-	A													0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tgatgctgcctgaaccacacINSagtgcgcaggagggattcac							TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr17:44128014_44128015insA	ENST00000262419.6	-	7	2374_2375	c.1904_1905insT	c.(1903-1905)ctgfs	p.L635fs	KANSL1_ENST00000572904.1_Frame_Shift_Ins_p.L635fs|KANSL1_ENST00000575318.1_Frame_Shift_Ins_p.L635fs|KANSL1_ENST00000432791.1_Frame_Shift_Ins_p.L635fs|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Frame_Shift_Ins_p.L635fs	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	635					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CTGAACCACACAGTGCGCAGGA	0.49																																					p.L635fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1905_1906insT						.																																			SO:0001589	frameshift_variant	284058	exon7			.	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"centromere protein 36"	612452	"KIAA1267"	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.1905dupT	chr17.hg19:g.44128015_44128015dupA	ENSP00000262419:p.Leu635fs	92.0	0.0		76.0	28.0	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Frame_Shift_Ins	INS	ENST00000262419.6	hg19	CCDS11503.1																																																																																			.	.		0.49	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		A	44128015	-	A	44128014	7	5	4	1	0	1	1	0	0	0	0	0	8228	465	17	0	1448	0	KIAA1267	17	44128014	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GU-01A-11D-A382-10		44128014	37067196	116	375										
C17orf80	55028	hgsc.bcm.edu	37	chr17	71232524	71232524	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aaacaagagaaaggacttacCctgggagtagagacgtgtgg	14	6	0	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr17:71232524C>T	ENST00000535032.2	+	2	1016	c.903C>T	c.(901-903)acC>acT	p.T301T	C17orf80_ENST00000577615.1_Silent_p.T301T|C17orf80_ENST00000426147.2_Silent_p.T301T|C17orf80_ENST00000359042.2_Silent_p.T301T|C17orf80_ENST00000268942.8_Silent_p.T301T|C17orf80_ENST00000582793.1_Intron|FAM104A_ENST00000583178.1_Intron|C17orf80_ENST00000255557.4_Silent_p.T301T			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	301						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			AAGGACTTACCCTGGGAGTAG	0.438																																					p.T301T		Atlas-SNP	.											.	C17orf80	37	.	0			c.C903T						.						68	63	65					17																	71232524		2203	4300	6503	SO:0001819	synonymous_variant	55028	exon3			ACTTACCCTGGGA	AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219			29601	protein-coding gene	gene with protein product	"sperm-expressed protein 1", "migration-inducing protein 3"					12477932	Standard	NM_017941		Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.903C>T	chr17.hg19:g.71232524C>T		183.0	0.0		145.0	58.0	NM_001100621	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Silent	SNP	ENST00000535032.2	hg19	CCDS11694.1																																																																																			.	.		0.438	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1	NM_017941		T	71232524	C	T	71232524	2	4	4	1	0	0	0	0	0	0	0	1	1887	610	22	3		3	C17orf80	17	71232524	Silent	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	27104510	71232524	9962686	117	376										
RNMT	8731	hgsc.bcm.edu	37	chr18	13746225	13746225	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tcttttttggacagaatggcAaagaagtacaatatgaaact	8	5	1	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr18:13746225A>G	ENST00000383314.2	+	9	1386	c.1146A>G	c.(1144-1146)gcA>gcG	p.A382A	RNMT_ENST00000589866.1_Silent_p.A382A|RNMT_ENST00000262173.3_Silent_p.A382A|RNMT_ENST00000543302.2_Silent_p.A382A|RNMT_ENST00000592764.1_Silent_p.A382A|RNMT_ENST00000535051.1_Silent_p.A140A			O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	382	mRNA cap 0 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00895}.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA (guanine-N7)-methylation (GO:0036265)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|receptor complex (GO:0043235)	mRNA (guanine-N7-)-methyltransferase activity (GO:0004482)|RNA binding (GO:0003723)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						ACAGAATGGCAAAGAAGTACA	0.303																																					p.A382A	GBM(29;474 594 19092 36647 41529)	Atlas-SNP	.											.	RNMT	42	.	0			c.A1146G						.						66	71	69					18																	13746225		2200	4298	6498	SO:0001819	synonymous_variant	8731	exon9			AATGGCAAAGAAG	AF067791	CCDS11867.1	18p11.21	2008-05-14			ENSG00000101654	ENSG00000101654	2.1.1.56		10075	protein-coding gene	gene with protein product		603514				9828141, 9705270	Standard	NM_003799		Approved	RG7MT1	uc002ksl.1	O43148	OTTHUMG00000131718	ENST00000383314.2:c.1146A>G	chr18.hg19:g.13746225A>G		817.0	0.0		599.0	97.0	NM_003799	B0YJ90|D3DUJ5|O94996|Q9UIJ9	Silent	SNP	ENST00000383314.2	hg19	CCDS11867.1																																																																																			.	.		0.303	RNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254636.1	NM_003799		G	13746225	A	G	13746225	2	3	4	1	0	0	0	0	0	0	0	1	13521	117	5	2		2	RNMT	18	13746225	Silent	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10		13746225	64331023	118	377										
MEP1B	4225	hgsc.bcm.edu	37	chr18	29787402	29787403	+	Frame_Shift_Del	DEL	TC	TC	-													0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	atggatttcagtgactctgaTctcctaaagttgaatcaact							TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr18:29787402_29787403delTC	ENST00000269202.6	+	8	782_783	c.735_736delTC	c.(733-738)gatctcfs	p.L247fs	MEP1B_ENST00000581447.1_Frame_Shift_Del_p.L247fs	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	247	Metalloprotease.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						GTGACTCTGATCTCCTAAAGTT	0.396																																					p.245_245del		Atlas-Indel,Pindel	.											.	MEP1B	54	.	0			c.734_735del						.																																			SO:0001589	frameshift_variant	4225	exon8			.	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.735_736delTC	chr18.hg19:g.29787404_29787405delTC	ENSP00000269202:p.Leu247fs	176.0	0.0		132.0	24.0	NM_005925	B7ZM35|B9EGL6|Q670J1	Frame_Shift_Del	DEL	ENST00000269202.6	hg19	CCDS45846.1																																																																																			.	.		0.396	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		-	29787403	TC	-	29787402	7	5	4	1	0	1	0	1	0	0	0	0	9485	1432	50	0	765	0	MEP1B	18	29787402	Frame_Shift_Del	DEL	TC	TCGA-2Y-A9GU-01A-11D-A382-10	16041177	29787402	48289846	119	378										
AP3D1	8943	hgsc.bcm.edu	37	chr19	2108726	2108726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	catggtggccctggatggagCggctgtacatggaggcgcag	18	9	0	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:2108726C>T	ENST00000345016.5	-	29	3557	c.3326G>A	c.(3325-3327)cGc>cAc	p.R1109H	AP3D1_ENST00000350812.6_Missense_Mutation_p.R940H|AP3D1_ENST00000355272.6_Missense_Mutation_p.R1171H|AP3D1_ENST00000356926.4_Missense_Mutation_p.R1068H	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	1109					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGGATGGAGCGGCTGTACAT	0.637																																					p.R1171H		Atlas-SNP	.											.	AP3D1	81	.	0			c.G3512A						.						31	40	37					19																	2108726		2131	4233	6364	SO:0001583	missense	8943	exon31			ATGGAGCGGCTGT	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.3326G>A	chr19.hg19:g.2108726C>T	ENSP00000344055:p.Arg1109His	148.0	0.0		65.0	4.0	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	hg19	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	C	19.06	3.753710	0.69648	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	T;T;T;T	0.19938	2.11;2.63;2.6;2.14	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.36524	0.0970	L	0.39898	1.24	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.85130	0.997;0.99;0.997;0.994	T	0.08994	-1.0695	10	0.52906	T	0.07	.	13.8204	0.63315	0.0:1.0:0.0:0.0	.	940;1171;1109;1068	E7EMM2;O14617-5;O14617;G5E988	.;.;AP3D1_HUMAN;.	H	1068;1109;1171;977;940	ENSP00000349398:R1068H;ENSP00000344055:R1109H;ENSP00000347416:R1171H;ENSP00000342321:R940H	ENSP00000341579:R977H	R	-	2	0	AP3D1	2059726	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.372000	0.79612	2.052000	0.61016	0.561000	0.74099	CGC	.	.		0.637	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1			T	2108726	C	T	2108726	3	4	4	1	0	0	0	0	1	0	0	0	746	768	27	1	143	1	AP3D1	19	2108726	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10		2108726	57020257	120	379										
EMR1	2015	hgsc.bcm.edu	37	chr19	6924851	6924851	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tcctcttggcgaagactctcTtcctcgccggtatacacaag	8	14	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:6924851T>C	ENST00000312053.4	+	15	1991	c.1954T>C	c.(1954-1956)Ttc>Ctc	p.F652L	EMR1_ENST00000381404.4_Missense_Mutation_p.F600L|EMR1_ENST00000381407.5_Missense_Mutation_p.F511L|EMR1_ENST00000450315.3_Missense_Mutation_p.F475L|EMR1_ENST00000250572.8_Intron	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	652					cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					GAAGACTCTCTTCCTCGCCGG	0.567																																					p.F652L		Atlas-SNP	.											.	EMR1	153	.	0			c.T1954C						.						207	131	157					19																	6924851		2203	4300	6503	SO:0001583	missense	2015	exon15			ACTCTCTTCCTCG	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.1954T>C	chr19.hg19:g.6924851T>C	ENSP00000311545:p.Phe652Leu	67.0	0.0		106.0	14.0	NM_001974	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	hg19	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	T	15.31	2.794504	0.50102	.	.	ENSG00000174837	ENST00000312053;ENST00000381404;ENST00000381407;ENST00000450315	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	3.61	3.61	0.41365	GPCR, family 2-like (1);	.	.	.	.	T	0.55000	0.1893	L	0.49640	1.575	0.33527	D	0.593117	D;D;D;D	0.89917	0.997;0.994;1.0;0.999	D;D;D;D	0.87578	0.985;0.955;0.998;0.996	T	0.65721	-0.6099	9	0.87932	D	0	.	8.9222	0.35619	0.0:0.0:0.0:1.0	.	475;511;600;652	E7EPX9;B7Z486;E9PD45;Q14246	.;.;.;EMR1_HUMAN	L	652;600;511;475	ENSP00000311545:F652L;ENSP00000370811:F600L;ENSP00000370814:F511L;ENSP00000405974:F475L	ENSP00000311545:F652L	F	+	1	0	EMR1	6875851	1.000000	0.71417	0.947000	0.38551	0.053000	0.15095	5.786000	0.69006	1.402000	0.46780	0.533000	0.62120	TTC	.	.		0.567	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			C	6924851	T	C	6924851	3	2	4	1	0	0	0	0	1	0	0	0	5106	1609	56	2	2012	2	EMR1	19	6924851	Missense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	4816125	6924851	52204132	121	380										
ACTL9	284382	hgsc.bcm.edu	37	chr19	8807887	8807887	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ggactggaaggcgcgcagggAggccaggatggagcccccga	19	11	0	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:8807887A>T	ENST00000324436.3	-	1	1285	c.1165T>A	c.(1165-1167)Tcc>Acc	p.S389T		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	389						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						GCGCGCAGGGAGGCCAGGATG	0.647																																					p.S389T		Atlas-SNP	.											.	ACTL9	74	.	0			c.T1165A						.						37	39	38					19																	8807887		2203	4299	6502	SO:0001583	missense	284382	exon1			GCAGGGAGGCCAG		CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.1165T>A	chr19.hg19:g.8807887A>T	ENSP00000316674:p.Ser389Thr	207.0	0.0		173.0	22.0	NM_178525	A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	hg19	CCDS12207.1	.	.	.	.	.	.	.	.	.	.	a	23.0	4.365919	0.82463	.	.	ENSG00000181786	ENST00000324436	D	0.95342	-3.68	4.51	4.51	0.55191	.	0.000000	0.39615	U	0.001309	D	0.96907	0.8990	M	0.80332	2.49	0.47949	D	0.99955	D	0.76494	0.999	D	0.87578	0.998	D	0.97394	0.9991	10	0.87932	D	0	.	13.0887	0.59156	1.0:0.0:0.0:0.0	.	389	Q8TC94	ACTL9_HUMAN	T	389	ENSP00000316674:S389T	ENSP00000316674:S389T	S	-	1	0	ACTL9	8668887	1.000000	0.71417	0.998000	0.56505	0.783000	0.44284	8.535000	0.90623	2.027000	0.59764	0.375000	0.23000	TCC	.	.		0.647	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525		T	8807887	A	T	8807887	3	4	4	1	0	0	0	0	1	0	0	0	203	304	11	4	89	4	ACTL9	19	8807887	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	1883036	8807887	50321096	122	381										
ZNF431	170959	hgsc.bcm.edu	37	chr19	21350459	21350459	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aagagacatgagatggtggaTgaacccccaggtaggtgaga	15	6	0	4			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:21350459T>C	ENST00000311048.7	+	4	453	c.309T>C	c.(307-309)gaT>gaC	p.D103D	ZNF431_ENST00000600692.1_Silent_p.D103D|ZNF431_ENST00000599296.1_Silent_p.D103D|ZNF431_ENST00000594425.1_Intron	NM_133473.2	NP_597730.2	Q8TF32	ZN431_HUMAN	zinc finger protein 431	103	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23						AGATGGTGGATGAACCCCCAG	0.418																																					p.D103D		Atlas-SNP	.											.	ZNF431	71	.	0			c.T309C						.						73	77	76					19																	21350459		2203	4300	6503	SO:0001819	synonymous_variant	170959	exon4			GGTGGATGAACCC	AB075849	CCDS32979.1	19p12	2013-01-08				ENSG00000196705		"Zinc fingers, C2H2-type", "-"	20809	protein-coding gene	gene with protein product						11853319	Standard	NM_133473		Approved	KIAA1969	uc002npp.2	Q8TF32		ENST00000311048.7:c.309T>C	chr19.hg19:g.21350459T>C		94.0	0.0		171.0	78.0	NM_133473	A8KAK7|Q8IWC4	Silent	SNP	ENST00000311048.7	hg19	CCDS32979.1																																																																																			.	.		0.418	ZNF431-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463943.1	XM_086098		C	21350459	T	C	21350459	2	2	4	1	0	0	0	0	0	0	0	1	17920	1461	51	2		2	ZNF431	19	21350459	Silent	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	12542572	21350459	37778524	123	382										
ZNF43	7594	hgsc.bcm.edu	37	chr19	21990788	21990788	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aggacagtttaaaagctttgCcacattcttcacatttgtag	7	8	2	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:21990788C>A	ENST00000354959.4	-	4	2220	c.2051G>T	c.(2050-2052)gGc>gTc	p.G684V	ZNF43_ENST00000598381.1_Missense_Mutation_p.G678V|ZNF43_ENST00000595461.1_Missense_Mutation_p.G678V|ZNF43_ENST00000594012.1_Missense_Mutation_p.G678V	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	684					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		AAAAGCTTTGCCACATTCTTC	0.368																																					p.G693V		Atlas-SNP	.											.	ZNF43	152	.	0			c.G2078T						.						49	53	52					19																	21990788		2165	4278	6443	SO:0001583	missense	7594	exon4			GCTTTGCCACATT	X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"Zinc fingers, C2H2-type", "-"	13109	protein-coding gene	gene with protein product		603972	"zinc finger protein 39-like 1 (KOX 27)", "zinc finger protein 43 (HTF6)"	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.2051G>T	chr19.hg19:g.21990788C>A	ENSP00000347045:p.Gly684Val	36.0	0.0		44.0	6.0	NM_001256653	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	hg19	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	C	14.88	2.667505	0.47677	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.07444	3.19	1.76	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33030	0.0849	M	0.92691	3.335	0.58432	D	0.999999	D	0.71674	0.998	D	0.74348	0.983	T	0.38542	-0.9656	9	0.87932	D	0	.	10.4707	0.44635	0.0:1.0:0.0:0.0	.	684	P17038	ZNF43_HUMAN	V	683;684	ENSP00000347045:G684V	ENSP00000347045:G684V	G	-	2	0	ZNF43	21782628	0.622000	0.27085	0.647000	0.29507	0.841000	0.47740	2.428000	0.44749	0.976000	0.38417	0.305000	0.20034	GGC	.	.		0.368	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		A	21990788	C	A	21990788	3	1	4	1	0	0	0	0	1	0	0	0	17918	739	26	3	382	3	ZNF43	19	21990788	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	640329	21990788	37138195	124	383										
FFAR2	2867	hgsc.bcm.edu	37	chr19	35940790	35940790	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	acgctggccgacctcctcctGctgctgctgctgcccttcaa	9	18	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:35940790G>C	ENST00000599180.2	+	2	254	c.174G>C	c.(172-174)ctG>ctC	p.L58L	FFAR2_ENST00000601590.1_Intron|FFAR2_ENST00000246549.2_Silent_p.L58L			O15552	FFAR2_HUMAN	free fatty acid receptor 2	58					cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			ACCTCCTCCTGCTGCTGCTGC	0.647																																					p.L58L	GBM(40;139 809 9833 23358 48736)	Atlas-SNP	.											.	FFAR2	39	.	0			c.G174C						.						39	34	36					19																	35940790		2203	4300	6503	SO:0001819	synonymous_variant	2867	exon1			CCTCCTGCTGCTG	AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"GPCR / Class A : Fatty acid receptors"	4501	protein-coding gene	gene with protein product		603823	"G protein-coupled receptor 43"	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.174G>C	chr19.hg19:g.35940790G>C		58.0	0.0		39.0	4.0	NM_005306	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Silent	SNP	ENST00000599180.2	hg19	CCDS12461.1																																																																																			.	.		0.647	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306		C	35940790	G	C	35940790	2	2	4	1	0	0	0	0	0	0	0	1	5836	1306	46	4		4	FFAR2	19	35940790	Silent	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	13950002	35940790	23188193	125	384										
ATP4A	495	hgsc.bcm.edu	37	chr19	36042401	36042401	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gcgcgtcttgcggatgaggaCatcggcgatctggcacacct	14	12	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:36042401C>T	ENST00000262623.3	-	19	2861	c.2833G>A	c.(2833-2835)Gtc>Atc	p.V945I		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	945					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CGGATGAGGACATCGGCGATC	0.607																																					p.V945I		Atlas-SNP	.											.	ATP4A	123	.	0			c.G2833A						.						124	90	101					19																	36042401		2203	4300	6503	SO:0001583	missense	495	exon19			TGAGGACATCGGC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.2833G>A	chr19.hg19:g.36042401C>T	ENSP00000262623:p.Val945Ile	133.0	0.0		107.0	32.0	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	C	13.27	2.186691	0.38609	.	.	ENSG00000105675	ENST00000262623	D	0.95788	-3.81	5.03	5.03	0.67393	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.64402	D	0.000020	D	0.93475	0.7918	N	0.25286	0.73	0.44227	D	0.997061	B	0.24426	0.103	B	0.39805	0.31	D	0.91841	0.5483	10	0.87932	D	0	.	15.9034	0.79400	0.0:1.0:0.0:0.0	.	945	P20648	ATP4A_HUMAN	I	945	ENSP00000262623:V945I	ENSP00000262623:V945I	V	-	1	0	ATP4A	40734241	0.517000	0.26226	0.569000	0.28460	0.188000	0.23474	1.172000	0.31908	2.623000	0.88846	0.313000	0.20887	GTC	.	.		0.607	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		T	36042401	C	T	36042401	3	4	4	1	0	0	0	0	1	0	0	0	1145	478	17	3	290	3	ATP4A	19	36042401	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	101611	36042401	23086582	126	385										
PSG6	5675	hgsc.bcm.edu	37	chr19	43420365	43420365	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gtgtaggatcctgcatcctcCtgtgtgacattctggatcag	11	10	2	1	rs386809476		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:43420365C>T	ENST00000292125.2	-	2	383	c.339G>A	c.(337-339)caG>caA	p.Q113Q	PSG6_ENST00000601833.1_Silent_p.Q42Q|PSG6_ENST00000187910.2_Silent_p.Q113Q|PSG6_ENST00000402603.4_Silent_p.Q113Q	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	113	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				CTGCATCCTCCTGTGTGACAT	0.453																																					p.Q113Q		Atlas-SNP	.											.	PSG6	89	.	0			c.G339A						.						360	324	336					19																	43420365		2201	4299	6500	SO:0001819	synonymous_variant	5675	exon2			ATCCTCCTGTGTG		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.339G>A	chr19.hg19:g.43420365C>T		93.0	0.0		133.0	32.0	NM_001031850	O75244|Q15224|Q15235|Q549K1	Silent	SNP	ENST00000292125.2	hg19	CCDS12613.1																																																																																			.	.		0.453	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782		T	43420365	C	T	43420365	2	4	4	1	0	0	0	0	0	0	0	1	12671	680	24	3		3	PSG6	19	43420365	Silent	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	7377964	43420365	15708618	127	386										
CD3EAP	10849	hgsc.bcm.edu	37	chr19	45912584	45912584	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aggggagggacagcctgaagCcagggcaactccgggatcca	16	11	0	1	rs368905711		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:45912584C>G	ENST00000309424.3	+	3	1846	c.1358C>G	c.(1357-1359)gCc>gGc	p.A453G	ERCC1_ENST00000588738.1_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.A455G|PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000423698.2_3'UTR|ERCC1_ENST00000300853.3_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	453					rRNA transcription (GO:0009303)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		CAGCCTGAAGCCAGGGCAACT	0.567																																					p.A453G		Atlas-SNP	.											.	CD3EAP	27	.	0			c.C1358G						.						49	57	54					19																	45912584		2200	4299	6499	SO:0001583	missense	10849	exon3			CTGAAGCCAGGGC	U86751	CCDS12661.1, CCDS74397.1	19q13.3	2008-02-05	2006-03-28			ENSG00000117877			24219	protein-coding gene	gene with protein product	"CD3 epsilon associated protein", "antisense to ERCC 1"	107325	"CD3e antigen, epsilon polypeptide associated protein"			10373416, 9426281, 15226435	Standard	XM_005258425		Approved	ASE-1, CAST, PAF49	uc002pbq.1	O15446		ENST00000309424.3:c.1358C>G	chr19.hg19:g.45912584C>G	ENSP00000310966:p.Ala453Gly	194.0	0.0		172.0	49.0	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	hg19	CCDS12661.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.105165	0.37145	.	.	ENSG00000117877	ENST00000309424	T	0.15487	2.42	4.24	1.9	0.25705	.	0.532266	0.14198	N	0.334898	T	0.12774	0.0310	L	0.27053	0.805	0.20196	N	0.999928	D;P	0.52996	0.957;0.928	P;B	0.45946	0.498;0.302	T	0.14587	-1.0467	10	0.32370	T	0.25	.	6.9953	0.24779	0.169:0.7327:0.0:0.0983	.	455;453	O15446-2;O15446	.;RPA34_HUMAN	G	453	ENSP00000310966:A453G	ENSP00000310966:A453G	A	+	2	0	CD3EAP	50604424	0.006000	0.16342	0.011000	0.14972	0.254000	0.26022	1.047000	0.30367	0.760000	0.33108	0.561000	0.74099	GCC	.	.		0.567	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099		G	45912584	C	G	45912584	3	3	4	1	0	0	0	0	1	0	0	0	3014	739	26	4	1368	4	CD3EAP	19	45912584	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	2492219	45912584	13216399	128	387										
EML2	24139	hgsc.bcm.edu	37	chr19	46124887	46124887	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cagcaccgcctgtgtgatacGgttcccacctgcagggtggc	13	14	0	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:46124887G>A	ENST00000245925.3	-	10	900	c.850C>T	c.(850-852)Cgt>Tgt	p.R284C	EML2_ENST00000586902.1_5'UTR|EML2_ENST00000536630.1_Missense_Mutation_p.R431C|EML2_ENST00000587152.1_Missense_Mutation_p.R485C|EML2_ENST00000589876.1_Missense_Mutation_p.R284C	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	284	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		TGTGTGATACGGTTCCCACCT	0.662																																					p.R485C		Atlas-SNP	.											.	EML2	64	.	0			c.C1453T						.						20	21	21					19																	46124887		2202	4295	6497	SO:0001583	missense	24139	exon13			TGATACGGTTCCC	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"WD repeat domain containing"	18035	protein-coding gene	gene with protein product	"echinoderm MT-associated protein (EMAP)-like protein 70", "microtubule-associated protein like echinoderm EMAP"					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.850C>T	chr19.hg19:g.46124887G>A	ENSP00000245925:p.Arg284Cys	256.0	0.0		171.0	30.0	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	hg19	CCDS12670.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.083522	0.55861	.	.	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055;ENST00000399594	T;T;T	0.39406	1.08;1.08;5.0	3.1	3.1	0.35709	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.069226	0.56097	U	0.000031	T	0.58850	0.2151	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.962;0.972;0.996;0.95	T	0.60642	-0.7223	10	0.62326	D	0.03	-16.5272	7.354	0.26709	0.0:0.0:0.739:0.261	.	284;450;431;284	B7Z918;B7Z3Q9;B7Z3I2;O95834	.;.;.;EMAL2_HUMAN	C	431;284;485;442	ENSP00000442365:R431C;ENSP00000245925:R284C;ENSP00000382503:R442C	ENSP00000245925:R284C	R	-	1	0	EML2	50816727	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	3.887000	0.56197	1.565000	0.49641	0.195000	0.17529	CGT	.	.		0.662	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155		A	46124887	G	A	46124887	3	1	4	1	0	0	0	0	1	0	0	0	5099	1116	39	1	1139	1	EML2	19	46124887	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	212303	46124887	13004096	129	388										
PNMAL2	57469	hgsc.bcm.edu	37	chr19	46997933	46997933	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cttctctgcctcttctttctTcgatttgtcggtgacggtga	9	11	4	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:46997933T>G	ENST00000377655.2	-	1	734				PNMAL2_ENST00000599531.1_Missense_Mutation_p.K264Q|AC011484.1_ENST00000377652.3_Missense_Mutation_p.F15C|PNMAL2_ENST00000594749.1_Intron			Q9ULN7	PNML2_HUMAN	paraneoplastic Ma antigen family-like 2											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)	8		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		TCTTCTTTCTTCGATTTGTCG	0.592																																					p.K264Q		Atlas-SNP	.											.	PNMAL2	44	.	0			c.A790C						.						74	63	67					19																	46997933		2203	4300	6503	SO:0001627	intron_variant	57469	exon1			CTTTCTTCGATTT	AB033009	CCDS59400.1	19q13.32	2014-02-12	2012-02-09		ENSG00000204851	ENSG00000204851		"Paraneoplastic Ma antigens"	29206	protein-coding gene	gene with protein product			"PNMA-like 2"			10574461	Standard	NM_020709		Approved	KIAA1183	uc002pes.2	Q9ULN7		ENST00000377655.2:c.734+55A>C	chr19.hg19:g.46997933T>G		155.0	0.0		117.0	5.0	NM_020709	C9JGD5|M0R374|Q08E79|Q0D2F9|Q6ZVD1	Missense_Mutation	SNP	ENST00000377655.2	hg19		.	.	.	.	.	.	.	.	.	.	T	6.437	0.448769	0.12223	.	.	ENSG00000204850	ENST00000377652	.	.	.	2.32	1.29	0.21616	.	.	.	.	.	T	0.24699	0.0599	N	0.19112	0.55	0.26138	N	0.980323	B	0.13145	0.007	B	0.04013	0.001	T	0.21861	-1.0233	8	0.87932	D	0	-5.8825	4.2223	0.10563	0.0:0.1731:0.0:0.8269	.	15	Q6ZVU4	.	C	15	.	ENSP00000366880:F15C	F	+	2	0	AC011484.1	51689773	0.062000	0.20869	0.310000	0.25168	0.042000	0.13812	0.327000	0.19663	0.318000	0.23185	0.402000	0.26972	TTC	.	.		0.592	PNMAL2-201	KNOWN	basic	protein_coding	protein_coding		NM_020709		G	46997933	T	G	46997933	1	3	4	0	1	0	0	0	0	0	0	0	12167	1792	62	5		5	PNMAL2	19	46997933	Intron	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	873046	46997933	12131050	130	389										
CABP5	56344	hgsc.bcm.edu	37	chr19	48533839	48533839	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gagacatcatcttcacaaacTctgcaaagaaaaaaaaaaat	4	8	4	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:48533839T>A	ENST00000293255.2	-	6	627	c.497A>T	c.(496-498)gAg>gTg	p.E166V		NM_019855.4	NP_062829.1	Q9NP86	CABP5_HUMAN	calcium binding protein 5	166	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				signal transduction (GO:0007165)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	11		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)		CTTCACAAACTCTGCAAAGAA	0.488																																					p.E166V		Atlas-SNP	.											.	CABP5	28	.	0			c.A497T						.						81	82	82					19																	48533839		2203	4300	6503	SO:0001630	splice_region_variant	56344	exon6			ACAAACTCTGCAA	AF169159	CCDS12709.1	19q13.33	2014-08-12			ENSG00000105507	ENSG00000105507		"EF-hand domain containing"	13714	protein-coding gene	gene with protein product		607315	"calcium binding protein 3"	CABP3		10625670	Standard	NM_019855		Approved	CaBP3	uc002phu.2	Q9NP86	OTTHUMG00000183139	ENST00000293255.2:c.497-1A>T	chr19.hg19:g.48533839T>A		129.0	0.0		151.0	20.0	NM_019855	A0AUY4	Missense_Mutation	SNP	ENST00000293255.2	hg19	CCDS12709.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.550428	0.86127	.	.	ENSG00000105507	ENST00000293255	D	0.86865	-2.18	5.31	5.31	0.75309	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.95439	0.8519	H	0.96833	3.89	0.80722	D	1	D	0.67145	0.996	D	0.70935	0.971	D	0.96697	0.9515	10	0.87932	D	0	.	13.5807	0.61901	0.0:0.0:0.0:1.0	.	166	Q9NP86	CABP5_HUMAN	V	166	ENSP00000293255:E166V	ENSP00000293255:E166V	E	-	2	0	CABP5	53225651	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.660000	0.74417	2.162000	0.67917	0.529000	0.55759	GAG	.	.		0.488	CABP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465212.1	NM_019855	Missense_Mutation	A	48533839	T	A	48533839	5	1	4	1	0	0	0	0	0	0	1	0	2536	1565	54	4	28	4	CABP5	19	48533839	Splice_Site	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	1535906	48533839	10595144	131	390										
HSPBP1	23640	hgsc.bcm.edu	37	chr19	55777301	55777301	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	tggaaggggctgtgctctgtCcgcaccagggccaccagctg	15	13	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:55777301C>A	ENST00000255631.5	-	7	1156	c.846G>T	c.(844-846)cgG>cgT	p.R282R	HSPBP1_ENST00000587922.1_Silent_p.R282R|HSPBP1_ENST00000376343.3_Intron|HSPBP1_ENST00000433386.2_Silent_p.R282R	NM_001130106.1|NM_012267.4	NP_001123578.1|NP_036399.3	Q9NZL4	HPBP1_HUMAN	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	285					negative regulation of catalytic activity (GO:0043086)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)		enzyme inhibitor activity (GO:0004857)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	8			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		TGTGCTCTGTCCGCACCAGGG	0.682																																					p.R282R		Atlas-SNP	.											.	HSPBP1	24	.	0			c.G846T						.						18	19	19					19																	55777301		2201	4298	6499	SO:0001819	synonymous_variant	23640	exon6			CTCTGTCCGCACC		CCDS33111.1	19q13.42	2008-12-16			ENSG00000133265	ENSG00000133265			24989	protein-coding gene	gene with protein product	"hsp70 interacting protein", "Hsp70 binding protein 1"	612939				10786638, 9830037	Standard	NM_001130106		Approved	HspBP1, FES1	uc002qkd.3	Q9NZL4		ENST00000255631.5:c.846G>T	chr19.hg19:g.55777301C>A		175.0	0.0		209.0	31.0	NM_012267	B3KQP0|B4DG11|O95351|Q6ZNU5	Silent	SNP	ENST00000255631.5	hg19	CCDS33111.1																																																																																			.	.		0.682	HSPBP1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452670.1	NM_012267		A	55777301	C	A	55777301	2	1	4	1	0	0	0	0	0	0	0	1	7435	842	30	3		3	HSPBP1	19	55777301	Silent	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	7243462	55777301	3351682	132	391										
NLRP9	338321	hgsc.bcm.edu	37	chr19	56244026	56244026	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agcacacaggctttttagtcGggctctgttcaccttaggtg	11	10	2	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr19:56244026G>A	ENST00000332836.2	-	2	1198	c.1171C>T	c.(1171-1173)Cga>Tga	p.R391*		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	391	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		CTTTTTAGTCGGGCTCTGTTC	0.418																																					p.R391X		Atlas-SNP	.											.	NLRP9	163	.	0			c.C1171T						.						88	89	89					19																	56244026		2203	4298	6501	SO:0001587	stop_gained	338321	exon2			TTAGTCGGGCTCT	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.1171C>T	chr19.hg19:g.56244026G>A	ENSP00000331857:p.Arg391*	119.0	0.0		180.0	17.0	NM_176820	B2RN12|Q86W27	Nonsense_Mutation	SNP	ENST00000332836.2	hg19	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.639125	0.67244	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	.	.	.	2.56	1.5	0.22942	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.9099	0.09199	0.1422:0.2557:0.6021:0.0	.	.	.	.	X	391	.	ENSP00000331857:R391X	R	-	1	2	NLRP9	60935838	0.007000	0.16637	0.001000	0.08648	0.000000	0.00434	0.105000	0.15333	0.667000	0.31107	-0.178000	0.13098	CGA	.	.		0.418	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		A	56244026	G	A	56244026	4	1	4	1	0	0	0	0	0	1	0	0	10493	1124	39	1	1836	1	NLRP9	19	56244026	Nonsense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	466725	56244026	2884957	133	392										
SRXN1	140809	hgsc.bcm.edu	37	chr20	629465	629465	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ctgcagttgctggtaggccgCgtagcggtggcagcccccaa	15	13	0	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr20:629465C>T	ENST00000381962.3	-	2	491	c.307G>A	c.(307-309)Gcg>Acg	p.A103T	RP5-850E9.3_ENST00000488788.2_3'UTR	NM_080725.1	NP_542763.1	Q9BYN0	SRXN1_HUMAN	sulfiredoxin 1	103					response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	ATP binding (GO:0005524)|oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)|sulfiredoxin activity (GO:0032542)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5						TGGTAGGCCGCGTAGCGGTGG	0.612																																					p.A103T		Atlas-SNP	.											SRXN1,NS,carcinoma,0,2	SRXN1	11	.	0			c.G307A						.						79	78	79					20																	629465		2203	4300	6503	SO:0001583	missense	140809	exon2			AGGCCGCGTAGCG	AF075053	CCDS13005.1	20p13	2013-05-22	2010-06-24	2005-05-10	ENSG00000271303	ENSG00000271303			16132	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 139", "sulfiredoxin 1 homolog (S. cerevisiae)"	C20orf139			Standard	NM_080725		Approved	Npn3, SRX1, YKL086W, dJ850E9.2	uc002wea.4	Q9BYN0	OTTHUMG00000031644	ENST00000381962.3:c.307G>A	chr20.hg19:g.629465C>T	ENSP00000371388:p.Ala103Thr	120.0	0.0		77.0	29.0	NM_080725	B2R543|Q8NDM3|Q96AK6	Missense_Mutation	SNP	ENST00000381962.3	hg19	CCDS13005.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.952875	0.73787	.	.	ENSG00000172070	ENST00000381962	.	.	.	5.69	4.75	0.60458	ParB-like nuclease (1);	0.000000	0.64402	U	0.000007	T	0.46502	0.1396	L	0.42245	1.32	0.53005	D	0.999961	P	0.43607	0.812	B	0.41988	0.372	T	0.46317	-0.9200	9	0.49607	T	0.09	-12.2745	11.4831	0.50337	0.0:0.9168:0.0:0.0832	.	103	Q9BYN0	SRXN1_HUMAN	T	103	.	ENSP00000371388:A103T	A	-	1	0	SRXN1	577465	1.000000	0.71417	0.583000	0.28640	0.970000	0.65996	7.015000	0.76387	1.422000	0.47177	0.650000	0.86243	GCG	.	.		0.612	SRXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077479.2	NM_080725		T	629465	C	T	629465	3	4	4	1	0	0	0	0	1	0	0	0	15188	768	27	1	110	1	SRXN1	20	629465	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10		629465	62396055	134	393										
C20orf3	57136	hgsc.bcm.edu	37	chr20	24944625	24944625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	taggacgaggctgtaccgcgGcacaaacttcatcaccgtct	10	13	3	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr20:24944625G>A	ENST00000217456.2	-	9	1365	c.1075C>T	c.(1075-1077)Ccg>Tcg	p.P359S	APMAP_ENST00000447138.1_3'UTR	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	359					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)	p.P359S(1)									CTGTACCGCGGCACAAACTTC	0.572																																					p.P359S		Atlas-SNP	.											C20orf3,NS,carcinoma,0,1	APMAP	3	.	1	Substitution - Missense(1)	prostate(1)	c.C1075T						.						89	82	84					20																	24944625		2203	4300	6503	SO:0001583	missense	57136	exon9			ACCGCGGCACAAA	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"chromosome 20 open reading frame 3"	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.1075C>T	chr20.hg19:g.24944625G>A	ENSP00000217456:p.Pro359Ser	170.0	0.0		101.0	41.0	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Missense_Mutation	SNP	ENST00000217456.2	hg19	CCDS13166.1	.	.	.	.	.	.	.	.	.	.	G	17.14	3.313619	0.60414	.	.	ENSG00000101474	ENST00000217456	T	0.23147	1.92	5.01	5.01	0.66863	Six-bladed beta-propeller, TolB-like (1);	0.114812	0.64402	D	0.000009	T	0.39963	0.1098	M	0.75150	2.29	0.80722	D	1	D;B	0.54047	0.964;0.409	P;B	0.52823	0.71;0.156	T	0.27872	-1.0061	10	0.11794	T	0.64	-7.486	15.8198	0.78631	0.0:0.0:1.0:0.0	.	351;359	A2A2F9;Q9HDC9	.;APMAP_HUMAN	S	359	ENSP00000217456:P359S	ENSP00000217456:P359S	P	-	1	0	C20orf3	24892625	1.000000	0.71417	0.939000	0.37840	0.820000	0.46376	9.749000	0.98871	2.298000	0.77334	0.561000	0.74099	CCG	.	.		0.572	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531		A	24944625	G	A	24944625	3	1	4	1	0	0	0	0	1	0	0	0	2111	1203	42	3	179	3	C20orf3	20	24944625	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	24315160	24944625	38080895	135	394										
ACSS1	84532	hgsc.bcm.edu	37	chr20	25028776	25028776	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gcgctcccagatcaaagcaaCgctctcgggggacttccgaa	11	14	2	1	rs113598729		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr20:25028776C>T	ENST00000323482.4	-	2	455	c.376G>A	c.(376-378)Gtt>Att	p.V126I	ACSS1_ENST00000432802.2_Missense_Mutation_p.V126I|ACSS1_ENST00000376726.3_Missense_Mutation_p.V126I	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	126					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	ATCAAAGCAACGCTCTCGGGG	0.547																																					p.V126I		Atlas-SNP	.											.	ACSS1	46	.	0			c.G376A						.						103	86	92					20																	25028776		2203	4300	6503	SO:0001583	missense	84532	exon2			AAGCAACGCTCTC		CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"Acyl-CoA synthetase family"	16091	protein-coding gene	gene with protein product		614355	"acetyl-Coenzyme A synthetase 2 (AMP forming)-like"	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.376G>A	chr20.hg19:g.25028776C>T	ENSP00000316924:p.Val126Ile	95.0	0.0		53.0	25.0	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Missense_Mutation	SNP	ENST00000323482.4	hg19	CCDS13167.1	.	.	.	.	.	.	.	.	.	.	C	8.990	0.977432	0.18812	.	.	ENSG00000154930	ENST00000323482;ENST00000376727;ENST00000432802;ENST00000376726	T;T;T	0.49432	0.78;0.78;2.84	5.39	-4.21	0.03812	Acyl-CoA synthase, domain of unknown function DUF3448 (1);	0.482252	0.22670	N	0.057076	T	0.34193	0.0889	L	0.39514	1.22	0.27613	N	0.948602	P;B;B	0.47034	0.889;0.053;0.065	B;B;B	0.42555	0.391;0.02;0.034	T	0.40720	-0.9548	10	0.38643	T	0.18	-9.1504	11.7706	0.51956	0.0:0.3746:0.0:0.6254	.	126;126;126	E9PC79;Q9NUB1-2;Q9NUB1	.;.;ACS2L_HUMAN	I	126	ENSP00000316924:V126I;ENSP00000388793:V126I;ENSP00000365916:V126I	ENSP00000316924:V126I	V	-	1	0	ACSS1	24976776	0.013000	0.17824	0.000000	0.03702	0.033000	0.12548	-0.003000	0.12901	-0.834000	0.04239	0.455000	0.32223	GTT	.	C|0.500;T|0.500		0.547	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501		T	25028776	C	T	25028776	3	4	4	1	0	0	0	0	1	0	0	0	188	536	19	1	1745	1	ACSS1	20	25028776	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	84151	25028776	37996744	136	395										
FAM83D	81610	hgsc.bcm.edu	37	chr20	37576553	37576553	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gactatcacaggaaatatctActatgcaaggtcaggaacta	8	8	3	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr20:37576553A>G	ENST00000217429.4	+	3	817	c.776A>G	c.(775-777)tAc>tGc	p.Y259C		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	229					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				GGAAATATCTACTATGCAAGG	0.433																																					p.Y259C		Atlas-SNP	.											.	FAM83D	60	.	0			c.A776G						.						135	128	130					20																	37576553		1934	4134	6068	SO:0001583	missense	81610	exon3			ATATCTACTATGC	AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 129"	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.776A>G	chr20.hg19:g.37576553A>G	ENSP00000217429:p.Tyr259Cys	83.0	0.0		87.0	18.0	NM_030919	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Missense_Mutation	SNP	ENST00000217429.4	hg19	CCDS42872.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.280881	0.80692	.	.	ENSG00000101447	ENST00000217429;ENST00000424027	T	0.18016	2.24	6.16	6.16	0.99307	.	0.058491	0.64402	D	0.000001	T	0.49150	0.1540	M	0.87827	2.91	0.58432	D	0.999993	D	0.89917	1.0	D	0.81914	0.995	T	0.55958	-0.8058	10	0.87932	D	0	.	16.4795	0.84153	1.0:0.0:0.0:0.0	.	229	Q9H4H8	FA83D_HUMAN	C	259;213	ENSP00000217429:Y259C	ENSP00000217429:Y259C	Y	+	2	0	FAM83D	37009967	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.731000	0.62022	2.367000	0.80283	0.528000	0.53228	TAC	.	.		0.433	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1			G	37576553	A	G	37576553	3	3	4	1	0	0	0	0	1	0	0	0	5644	391	14	2	786	2	FAM83D	20	37576553	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	12547777	37576553	25448967	137	396										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40979351	40979351	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ttcaatggggtgtctgtgtcGtactcaggcatggatggagc	15	7	3	0	rs377291418		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr20:40979351G>A	ENST00000373187.1	-	11	1781	c.1782C>T	c.(1780-1782)taC>taT	p.Y594Y	PTPRT_ENST00000373184.1_Silent_p.Y594Y|PTPRT_ENST00000373201.1_Silent_p.Y594Y|PTPRT_ENST00000356100.2_Silent_p.Y594Y|PTPRT_ENST00000373198.4_Silent_p.Y594Y|PTPRT_ENST00000373193.3_Silent_p.Y594Y|PTPRT_ENST00000373190.1_Silent_p.Y594Y			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	594	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TGTCTGTGTCGTACTCAGGCA	0.557																																					p.Y594Y		Atlas-SNP	.											PTPRT,colon,carcinoma,0,1	PTPRT	372	.	0			c.C1782T						.	G	,	1,4179		0,1,2089	146	153	151		1782,1782	-3.6	1	20		151	0,8446		0,0,4223	no	coding-synonymous,coding-synonymous	PTPRT	NM_007050.5,NM_133170.3	,	0,1,6312	AA,AG,GG		0.0,0.0239,0.0079	,	594/1442,594/1461	40979351	1,12625	2090	4223	6313	SO:0001819	synonymous_variant	11122	exon11			TGTGTCGTACTCA	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1782C>T	chr20.hg19:g.40979351G>A		35.0	0.0		52.0	9.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	hg19	CCDS42874.1																																																																																			.	.		0.557	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	40979351	G	A	40979351	2	1	4	1	0	0	0	0	0	0	0	1	12827	1140	40	1		1	PTPRT	20	40979351	Silent	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	3402798	40979351	22046169	138	397										
CDH22	64405	hgsc.bcm.edu	37	chr20	44815546	44815546	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ttgtcgttcacatccaggatTcggatccttagggatgcccg	11	11	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr20:44815546T>A	ENST00000372262.3	-	8	1864	c.1464A>T	c.(1462-1464)cgA>cgT	p.R488R	CDH22_ENST00000537909.1_Silent_p.R488R	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	488	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				CATCCAGGATTCGGATCCTTA	0.577																																					p.R488R		Atlas-SNP	.											.	CDH22	112	.	0			c.A1464T						.						244	220	228					20																	44815546		2203	4300	6503	SO:0001819	synonymous_variant	64405	exon9			CAGGATTCGGATC	AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"Cadherins / Major cadherins"	13251	protein-coding gene	gene with protein product		609920	"cadherin-like 22"	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.1464A>T	chr20.hg19:g.44815546T>A		83.0	0.0		69.0	14.0	NM_021248	B9EGK7|O43205	Silent	SNP	ENST00000372262.3	hg19	CCDS13395.1																																																																																			.	.		0.577	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		A	44815546	T	A	44815546	2	1	4	1	0	0	0	0	0	0	0	1	3109	1770	62	4		4	CDH22	20	44815546	Silent	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10	3836195	44815546	18209974	139	398										
GART	2618	hgsc.bcm.edu	37	chr21	34889352	34889352	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ggatgttctctagtaatcctCcaccagtaatatgggcaaag	9	9	1	0			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr21:34889352C>A	ENST00000381831.3	-	16	2314	c.2051G>T	c.(2050-2052)gGa>gTa	p.G684V	GART_ENST00000381815.4_Missense_Mutation_p.G684V|GART_ENST00000381839.3_Missense_Mutation_p.G684V|GART_ENST00000543717.1_Missense_Mutation_p.G236V	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	684	AIRS.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	TAGTAATCCTCCACCAGTAAT	0.458																																					p.G684V		Atlas-SNP	.											.	GART	81	.	0			c.G2051T						.						118	113	115					21																	34889352		2203	4300	6503	SO:0001583	missense	2618	exon16			AATCCTCCACCAG	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2051G>T	chr21.hg19:g.34889352C>A	ENSP00000371253:p.Gly684Val	215.0	0.0		163.0	26.0	NM_001136005	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	hg19	CCDS13627.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.432502	0.83776	.	.	ENSG00000159131	ENST00000381815;ENST00000381831;ENST00000381839;ENST00000543717	T;T;T;T	0.38560	1.13;1.13;1.13;1.13	4.6	4.6	0.57074	AIR synthase-related protein, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.80003	0.4544	H	0.99498	4.595	0.80722	D	1	D	0.76494	0.999	D	0.69654	0.965	D	0.89891	0.4037	10	0.87932	D	0	-9.2916	17.802	0.88590	0.0:1.0:0.0:0.0	.	684	P22102	PUR2_HUMAN	V	684;684;684;236	ENSP00000371236:G684V;ENSP00000371253:G684V;ENSP00000371261:G684V;ENSP00000443579:G236V	ENSP00000371236:G684V	G	-	2	0	GART	33811222	1.000000	0.71417	0.993000	0.49108	0.944000	0.59088	5.672000	0.68102	2.261000	0.74972	0.462000	0.41574	GGA	.	.		0.458	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819		A	34889352	C	A	34889352	3	1	4	1	0	0	0	0	1	0	0	0	6251	855	30	3	1009	3	GART	21	34889352	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10		34889352	13240543	140	399										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37612121	37612121	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	atggtgccatcggtgcggcaGcccagggctggctggtgcgt	18	11	0	0	rs559929390		TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr21:37612121G>C	ENST00000399151.3	+	18	3020	c.2935G>C	c.(2935-2937)Gcc>Ccc	p.A979P		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	979					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CGGTGCGGCAGCCCAGGGCTG	0.647																																					p.A979P		Atlas-SNP	.											.	DOPEY2	184	.	0			c.G2935C						.						50	39	43					21																	37612121		2192	4290	6482	SO:0001583	missense	9980	exon18			GCGGCAGCCCAGG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.2935G>C	chr21.hg19:g.37612121G>C	ENSP00000382104:p.Ala979Pro	57.0	0.0		34.0	6.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.813550	0.90790	.	.	ENSG00000142197	ENST00000399151	T	0.37752	1.18	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.61899	0.2384	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.65179	-0.6231	10	0.72032	D	0.01	-13.6637	18.878	0.92346	0.0:0.0:1.0:0.0	.	979;979	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	P	979	ENSP00000382104:A979P	ENSP00000382104:A979P	A	+	1	0	DOPEY2	36533991	1.000000	0.71417	0.950000	0.38849	0.683000	0.39861	9.253000	0.95501	2.470000	0.83445	0.561000	0.74099	GCC	.	.		0.647	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		C	37612121	G	C	37612121	3	2	4	1	0	0	0	0	1	0	0	0	4710	971	34	4	3001	4	DOPEY2	21	37612121	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	2722769	37612121	10517774	141	400										
ELFN2	114794	hgsc.bcm.edu	37	chr22	37769363	37769363	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	cgagtaggtggagtcacgctTggagcgggtcagcggcttga	18	8	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chr22:37769363T>A	ENST00000402918.2	-	3	2997	c.2212A>T	c.(2212-2214)Aag>Tag	p.K738*	ELFN2_ENST00000435824.1_5'Flank|RP1-63G5.8_ENST00000609322.1_RNA|RP1-63G5.5_ENST00000430883.1_RNA	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	738					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					GAGTCACGCTTGGAGCGGGTC	0.632																																					p.K738X		Atlas-SNP	.											.	ELFN2	89	.	0			c.A2212T						.						61	56	58					22																	37769363		2202	4300	6502	SO:0001587	stop_gained	114794	exon3			CACGCTTGGAGCG	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing"	29396	protein-coding gene	gene with protein product			"leucine rich repeat containing 62", "extracellular leucine-rich repeat and fibronectin type III containing 2", "extracellular leucine-rich repeat and fibronectin type III domain containing 2", "protein phosphatase 1, regulatory subunit 29"	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.2212A>T	chr22.hg19:g.37769363T>A	ENSP00000385277:p.Lys738*	138.0	0.0		101.0	11.0	NM_052906	Q96PY3	Nonsense_Mutation	SNP	ENST00000402918.2	hg19	CCDS33642.1	.	.	.	.	.	.	.	.	.	.	T	39	7.608802	0.98387	.	.	ENSG00000166897	ENST00000349653;ENST00000402918	.	.	.	4.63	4.63	0.57726	.	0.197550	0.40908	D	0.000987	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-28.6294	14.3358	0.66589	0.0:0.0:0.0:1.0	.	.	.	.	X	738	.	ENSP00000300147:K738X	K	-	1	0	ELFN2	36099309	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.138000	0.50570	1.837000	0.53436	0.459000	0.35465	AAG	.	.		0.632	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906		A	37769363	T	A	37769363	4	1	4	1	0	0	0	0	0	1	0	0	5060	1821	63	4	254	4	ELFN2	22	37769363	Nonsense_Mutation	SNP	T	TCGA-2Y-A9GU-01A-11D-A382-10		37769363	13535203	142	401										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12736467	12736467	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gacgctgactcgtccacctgCgaccatccttccaagcttcc	7	18	0	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chrX:12736467C>T	ENST00000380682.1	+	16	4028	c.3522C>T	c.(3520-3522)tgC>tgT	p.C1174C		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	1174					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						CGTCCACCTGCGACCATCCTT	0.552																																					p.C1174C		Atlas-SNP	.											.	FRMPD4	214	.	0			c.C3522T						.						144	127	133					X																	12736467		2203	4300	6503	SO:0001819	synonymous_variant	9758	exon16			CACCTGCGACCAT	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.3522C>T	chrX.hg19:g.12736467C>T		204.0	0.0		102.0	26.0	NM_014728	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	hg19	CCDS35201.1																																																																																			.	.		0.552	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		T	12736467	C	T	12736467	2	4	4	1	0	0	0	0	0	0	0	1	6067	776	27	1		1	FRMPD4	23	12736467	Silent	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10		12736467	142534093	143	402										
USP51	158880	hgsc.bcm.edu	37	chrX	55514722	55514722	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ggggtcccactccaaacgaaAcgctggtagatcaacctcag	10	13	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chrX:55514722A>G	ENST00000500968.3	-	2	733	c.651T>C	c.(649-651)cgT>cgC	p.R217R	USP51_ENST00000586165.1_Intron	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	217					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						TCCAAACGAAACGCTGGTAGA	0.488																																					p.R217R		Atlas-SNP	.											.	USP51	71	.	0			c.T651C						.						93	76	82					X																	55514722		2203	4300	6503	SO:0001819	synonymous_variant	158880	exon2			AACGAAACGCTGG	BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"Ubiquitin-specific peptidases"	23086	protein-coding gene	gene with protein product			"ubiquitin specific protease 51"			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.651T>C	chrX.hg19:g.55514722A>G		499.0	0.0		270.0	96.0	NM_201286	Q8IWJ8	Silent	SNP	ENST00000500968.3	hg19	CCDS14370.1																																																																																			.	.		0.488	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286		G	55514722	A	G	55514722	2	3	4	1	0	0	0	0	0	0	0	1	17098	30	2	2		2	USP51	23	55514722	Silent	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	42778255	55514722	99755838	144	403										
NONO	4841	hgsc.bcm.edu	37	chrX	70517737	70517737	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gagatgcggcggcagcaagaAgaaatgatgcggcgacagca	16	8	0	4			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chrX:70517737A>C	ENST00000276079.8	+	9	1285	c.1080A>C	c.(1078-1080)gaA>gaC	p.E360D	NONO_ENST00000535149.1_Missense_Mutation_p.E271D|NONO_ENST00000373856.3_Missense_Mutation_p.E360D|NONO_ENST00000490044.1_3'UTR|NONO_ENST00000373841.1_Missense_Mutation_p.E360D	NM_007363.4	NP_031389.3	Q15233	NONO_HUMAN	non-POU domain containing, octamer-binding	360	DBHS.				circadian rhythm (GO:0007623)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mRNA processing (GO:0006397)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)		NONO/TFE3(2)	endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	19	Renal(35;0.156)					GGCAGCAAGAAGAAATGATGC	0.517			T	TFE3	papillary renal cancer																																p.E360D		Atlas-SNP	.		Dom	yes		X	Xq13.1	4841	"non-POU domain containing, octamer-binding"		E	.	NONO	70	.	0			c.A1080C						.						89	68	75					X																	70517737		2203	4300	6503	SO:0001583	missense	4841	exon10			GCAAGAAGAAATG	L14599	CCDS14410.1, CCDS55445.1	Xq13.1	2014-06-13	2002-01-14		ENSG00000147140	ENSG00000147140		"RNA binding motif (RRM) containing"	7871	protein-coding gene	gene with protein product	"Nuclear RNA-binding protein, 54-kD", "non-Pou domain-containing octamer (ATGCAAAT) binding protein", "protein phosphatase 1, regulatory subunit 114"	300084	"non-POU-domain-containing, octamer-binding"			8371983, 9360842	Standard	NM_007363		Approved	NRB54, NMT55, P54NRB, P54, PPP1R114	uc004dzp.3	Q15233	OTTHUMG00000021798	ENST00000276079.8:c.1080A>C	chrX.hg19:g.70517737A>C	ENSP00000276079:p.Glu360Asp	257.0	0.0		216.0	84.0	NM_001145408	B7Z4C2|D3DVV4|F5GYZ3|O00201|P30807|Q12786|Q9BQC5	Missense_Mutation	SNP	ENST00000276079.8	hg19	CCDS14410.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	16.61|16.61	3.171919|3.171919	0.57584|0.57584	.|.	.|.	ENSG00000147140|ENSG00000147140	ENST00000535149;ENST00000276079;ENST00000373856;ENST00000373841|ENST00000418921	T;T;T;T|.	0.23147|.	1.96;1.92;1.92;1.92|.	5.23|5.23	1.34|1.34	0.21922|0.21922	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61788|0.61788	0.2375|0.2375	M|M	0.67625|0.67625	2.065|2.065	0.80722|0.80722	D|D	1|1	D|.	0.53151|.	0.958|.	B|.	0.40534|.	0.332|.	T|T	0.57236|0.57236	-0.7846|-0.7846	10|5	0.62326|.	D|.	0.03|.	-12.0954|-12.0954	8.9718|8.9718	0.35910|0.35910	0.612:0.0:0.388:0.0|0.612:0.0:0.388:0.0	.|.	360|.	Q15233|.	NONO_HUMAN|.	D|T	271;360;360;360|222	ENSP00000441364:E271D;ENSP00000276079:E360D;ENSP00000362963:E360D;ENSP00000362947:E360D|.	ENSP00000276079:E360D|.	E|K	+|+	3|2	2|0	NONO|NONO	70434462|70434462	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.975000|0.975000	0.68041|0.68041	2.426000|2.426000	0.44731|0.44731	0.275000|0.275000	0.22094|0.22094	0.430000|0.430000	0.28490|0.28490	GAA|AAG	.	.		0.517	NONO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057138.1	NM_007363		C	70517737	A	C	70517737	3	2	4	1	0	0	0	0	1	0	0	0	10543	69	3	5	1106	5	NONO	23	70517737	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	15003015	70517737	84752823	145	404			1	2		2	2	17	N	C_A	7.855826e-05
NONO	4841	hgsc.bcm.edu	37	chrX	70517753	70517753	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	aagaagaaatgatgcggcgaCagcaggaaggattcaaggga	15	5	1	3			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chrX:70517753C>T	ENST00000276079.8	+	9	1301	c.1096C>T	c.(1096-1098)Cag>Tag	p.Q366*	NONO_ENST00000535149.1_Nonsense_Mutation_p.Q277*|NONO_ENST00000373856.3_Nonsense_Mutation_p.Q366*|NONO_ENST00000490044.1_3'UTR|NONO_ENST00000373841.1_Nonsense_Mutation_p.Q366*	NM_007363.4	NP_031389.3	Q15233	NONO_HUMAN	non-POU domain containing, octamer-binding	366	DBHS.			QQ -> HE (in Ref. 3; CAA72157 and 4; AAA03427). {ECO:0000305}.	circadian rhythm (GO:0007623)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mRNA processing (GO:0006397)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)		NONO/TFE3(2)	endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	19	Renal(35;0.156)					GATGCGGCGACAGCAGGAAGG	0.522			T	TFE3	papillary renal cancer																																p.Q366X		Atlas-SNP	.		Dom	yes		X	Xq13.1	4841	"non-POU domain containing, octamer-binding"		E	.	NONO	70	.	0			c.C1096T						.						91	68	76					X																	70517753		2203	4300	6503	SO:0001587	stop_gained	4841	exon10			CGGCGACAGCAGG	L14599	CCDS14410.1, CCDS55445.1	Xq13.1	2014-06-13	2002-01-14		ENSG00000147140	ENSG00000147140		"RNA binding motif (RRM) containing"	7871	protein-coding gene	gene with protein product	"Nuclear RNA-binding protein, 54-kD", "non-Pou domain-containing octamer (ATGCAAAT) binding protein", "protein phosphatase 1, regulatory subunit 114"	300084	"non-POU-domain-containing, octamer-binding"			8371983, 9360842	Standard	NM_007363		Approved	NRB54, NMT55, P54NRB, P54, PPP1R114	uc004dzp.3	Q15233	OTTHUMG00000021798	ENST00000276079.8:c.1096C>T	chrX.hg19:g.70517753C>T	ENSP00000276079:p.Gln366*	262.0	0.0		214.0	84.0	NM_001145408	B7Z4C2|D3DVV4|F5GYZ3|O00201|P30807|Q12786|Q9BQC5	Nonsense_Mutation	SNP	ENST00000276079.8	hg19	CCDS14410.1	.	.	.	.	.	.	.	.	.	.	c	28.6	4.937907	0.92526	.	.	ENSG00000147140	ENST00000535149;ENST00000276079;ENST00000373856;ENST00000373841	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-9.9515	16.7805	0.85562	0.0:1.0:0.0:0.0	.	.	.	.	X	277;366;366;366	.	ENSP00000276079:Q366X	Q	+	1	0	NONO	70434478	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.488000	0.81441	2.427000	0.82271	0.529000	0.55759	CAG	.	.		0.522	NONO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057138.1	NM_007363		T	70517753	C	T	70517753	4	4	4	1	0	0	0	0	0	1	0	0	10543	479	17	3	1122	3	NONO	23	70517753	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	16	70517753	84752807	146	405			1	2		2	2	17	N	C_A	7.855826e-05
CYSLTR1	10800	hgsc.bcm.edu	37	chrX	77528345	77528345	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	acagccttttcctaaagttaCccccagaaaagaaatatagg	6	10	0	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chrX:77528345C>A	ENST00000373304.3	-	3	1191	c.899G>T	c.(898-900)gGt>gTt	p.G300V		NM_001282187.1|NM_001282188.1|NM_006639.3	NP_001269116.1|NP_001269117.1|NP_006630.1	Q9Y271	CLTR1_HUMAN	cysteinyl leukotriene receptor 1	300					defense response (GO:0006952)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|respiratory gaseous exchange (GO:0007585)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	leukotriene receptor activity (GO:0004974)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14					Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549)	CCTAAAGTTACCCCCAGAAAA	0.433																																					p.G300V		Atlas-SNP	.											.	CYSLTR1	59	.	0			c.G899T						.						55	54	54					X																	77528345		2202	4300	6502	SO:0001583	missense	10800	exon3			AAGTTACCCCCAG	AF119711	CCDS14439.1	Xq13-q21	2012-08-10			ENSG00000173198	ENSG00000173198		"GPCR / Class A : Leukotriene receptors"	17451	protein-coding gene	gene with protein product		300201				10391245, 10462554	Standard	NM_006639		Approved	CysLT1, CysLT(1), CYSLT1R	uc004edb.3	Q9Y271	OTTHUMG00000021889	ENST00000373304.3:c.899G>T	chrX.hg19:g.77528345C>A	ENSP00000362401:p.Gly300Val	526.0	0.0		440.0	168.0	NM_006639	B2R954|D3DTE4|Q5JS94|Q8IV19	Missense_Mutation	SNP	ENST00000373304.3	hg19	CCDS14439.1	.	.	.	.	.	.	.	.	.	.	C	9.578	1.122903	0.20959	.	.	ENSG00000173198	ENST00000373304	T	0.20463	2.07	4.07	4.07	0.47477	.	0.326050	0.32147	N	0.006519	T	0.10380	0.0254	N	0.08118	0	0.58432	D	0.999998	B	0.30068	0.267	B	0.30495	0.116	T	0.10222	-1.0639	10	0.62326	D	0.03	.	6.7907	0.23697	0.0:0.8695:0.0:0.1305	.	300	Q9Y271	CLTR1_HUMAN	V	300	ENSP00000362401:G300V	ENSP00000362401:G300V	G	-	2	0	CYSLTR1	77415001	1.000000	0.71417	0.951000	0.38953	0.512000	0.34134	5.426000	0.66476	1.855000	0.53841	0.468000	0.43344	GGT	.	.		0.433	CYSLTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057315.1			A	77528345	C	A	77528345	3	1	4	1	0	0	0	0	1	0	0	0	4203	507	18	3	118	3	CYSLTR1	23	77528345	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	7010592	77528345	77742215	147	406										
GPR174	84636	hgsc.bcm.edu	37	chrX	78427214	78427214	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gatgattctaacctgtgcagGggtattcctaatttgctttg	10	7	1	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chrX:78427214G>A	ENST00000276077.1	+	1	746	c.710G>A	c.(709-711)gGg>gAg	p.G237E		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.G237E(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						ACCTGTGCAGGGGTATTCCTA	0.408										HNSCC(63;0.18)																											p.G237E		Atlas-SNP	.											.	GPR174	79	.	1	Substitution - Missense(1)	lung(1)	c.G710A						.						102	95	98					X																	78427214		2203	4300	6503	SO:0001583	missense	84636	exon1			GTGCAGGGGTATT	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.710G>A	chrX.hg19:g.78427214G>A	ENSP00000276077:p.Gly237Glu	57.0	0.0		81.0	33.0	NM_032553	Q2M3F7	Missense_Mutation	SNP	ENST00000276077.1	hg19	CCDS14443.1	.	.	.	.	.	.	.	.	.	.	g	3.764	-0.049063	0.07407	.	.	ENSG00000147138	ENST00000276077	T	0.38401	1.14	5.18	3.34	0.38264	GPCR, rhodopsin-like superfamily (1);	0.603289	0.17071	N	0.188174	T	0.33933	0.0880	L	0.39245	1.2	0.09310	N	1	B	0.31256	0.316	B	0.41412	0.356	T	0.29549	-1.0008	10	0.49607	T	0.09	.	6.717	0.23308	0.0:0.3841:0.3517:0.2643	.	237	Q9BXC1	GP174_HUMAN	E	237	ENSP00000276077:G237E	ENSP00000276077:G237E	G	+	2	0	GPR174	78313870	0.981000	0.34729	0.673000	0.29887	0.444000	0.32077	2.228000	0.42981	0.941000	0.37499	0.488000	0.48403	GGG	.	.		0.408	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		A	78427214	G	A	78427214	3	1	4	1	0	0	0	0	1	0	0	0	6680	1232	43	3	712	3	GPR174	23	78427214	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	898869	78427214	76843346	148	407										
CUL4B	8450	hgsc.bcm.edu	37	chrX	119672026	119672026	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	agaaagttccatgtctttaaAcattccttcaagtttgctgg	7	8	2	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chrX:119672026A>G	ENST00000404115.3	-	16	2346	c.1945T>C	c.(1945-1947)Ttt>Ctt	p.F649L	CUL4B_ENST00000336592.6_Missense_Mutation_p.F636L|CUL4B_ENST00000371322.5_Missense_Mutation_p.F631L	NM_003588.3	NP_003579.3	Q13620	CUL4B_HUMAN	cullin 4B	649					cell cycle (GO:0007049)|histone H2A monoubiquitination (GO:0035518)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of protein catabolic process (GO:0045732)|ubiquitin-dependent protein catabolic process (GO:0006511)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						ATGTCTTTAAACATTCCTTCA	0.299																																					p.F649L		Atlas-SNP	.											.	CUL4B	181	.	0			c.T1945C						.						109	95	100					X																	119672026		2202	4298	6500	SO:0001583	missense	8450	exon16			CTTTAAACATTCC	U58091	CCDS35379.1, CCDS43987.1	Xq23	2011-05-24			ENSG00000158290	ENSG00000158290			2555	protein-coding gene	gene with protein product		300304				8681378	Standard	NM_003588		Approved		uc004esw.3	Q13620	OTTHUMG00000022302	ENST00000404115.3:c.1945T>C	chrX.hg19:g.119672026A>G	ENSP00000384109:p.Phe649Leu	101.0	0.0		106.0	29.0	NM_003588	B1APK5|B3KVX4|B7Z5K8|Q6PIE4|Q6UP07|Q7Z673|Q9BY37|Q9UEB7|Q9UED7	Missense_Mutation	SNP	ENST00000404115.3	hg19	CCDS35379.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.083071	0.76642	.	.	ENSG00000158290	ENST00000371322;ENST00000336592;ENST00000404115	T;T;T	0.71341	-0.56;-0.56;-0.56	5.87	4.69	0.59074	Cullin, N-terminal (1);Cullin homology (3);	0.046389	0.85682	D	0.000000	T	0.81758	0.4890	M	0.81682	2.555	0.80722	D	1	P;D;D	0.65815	0.913;0.995;0.993	P;P;P	0.62184	0.532;0.899;0.837	T	0.81771	-0.0780	9	.	.	.	-15.4884	11.477	0.50304	0.8515:0.1485:0.0:0.0	.	453;649;631	Q13620-3;Q13620;Q13620-1	.;CUL4B_HUMAN;.	L	631;636;649	ENSP00000360373:F631L;ENSP00000338919:F636L;ENSP00000384109:F649L	.	F	-	1	0	CUL4B	119556054	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.307000	0.96226	0.816000	0.34421	-0.508000	0.04489	TTT	.	.		0.299	CUL4B-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058103.1	NM_003588		G	119672026	A	G	119672026	3	3	4	1	0	0	0	0	1	0	0	0	4060	43	2	2	824	2	CUL4B	23	119672026	Missense_Mutation	SNP	A	TCGA-2Y-A9GU-01A-11D-A382-10	41244812	119672026	35598534	149	408										
GLUD2	2747	hgsc.bcm.edu	37	chrX	120181749	120181749	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	ccaacttcttcaagatggtgGagggcttcttcgatcgcggc	12	11	3	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chrX:120181749G>A	ENST00000328078.1	+	1	288	c.211G>A	c.(211-213)Gag>Aag	p.E71K		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	71					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						CAAGATGGTGGAGGGCTTCTT	0.677																																					p.E71K		Atlas-SNP	.											.	GLUD2	89	.	0			c.G211A						.						69	63	65					X																	120181749		2203	4298	6501	SO:0001583	missense	2747	exon1			ATGGTGGAGGGCT	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.211G>A	chrX.hg19:g.120181749G>A	ENSP00000327589:p.Glu71Lys	1229.0	0.0		782.0	88.0	NM_012084	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	hg19	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.782346	0.49891	.	.	ENSG00000182890	ENST00000328078	D	0.96856	-4.15	1.58	0.643	0.17770	.	0.000000	0.85682	U	0.000000	D	0.90580	0.7047	L	0.52126	1.63	0.53688	D	0.999974	P	0.44344	0.833	B	0.31442	0.13	D	0.84295	0.0502	10	0.33141	T	0.24	.	6.6429	0.22919	0.0:0.0:0.717:0.283	.	71	P49448	DHE4_HUMAN	K	71	ENSP00000327589:E71K	ENSP00000327589:E71K	E	+	1	0	GLUD2	120009430	1.000000	0.71417	0.007000	0.13788	0.455000	0.32408	6.227000	0.72282	0.162000	0.19483	-0.833000	0.03075	GAG	.	.		0.677	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		A	120181749	G	A	120181749	3	1	4	1	0	0	0	0	1	0	0	0	6485	1175	41	3	213	3	GLUD2	23	120181749	Missense_Mutation	SNP	G	TCGA-2Y-A9GU-01A-11D-A382-10	509723	120181749	35088811	150	409										
OR13H1	347468	hgsc.bcm.edu	37	chrX	130678588	130678588	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	accattttgcctgtgagattCtctccctcattaagctgacc	6	13	2	2			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chrX:130678588C>G	ENST00000338616.3	+	1	639	c.541C>G	c.(541-543)Ctc>Gtc	p.L181V		NM_001004486.1	NP_001004486.1	Q8NG92	O13H1_HUMAN	olfactory receptor, family 13, subfamily H, member 1	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15	Acute lymphoblastic leukemia(192;0.000636)					CTGTGAGATTCTCTCCCTCAT	0.473																																					p.L181V		Atlas-SNP	.											.	OR13H1	41	.	0			c.C541G						.						263	225	237					X																	130678588		2203	4300	6503	SO:0001583	missense	347468	exon1			GAGATTCTCTCCC		CCDS35396.1	Xq26.2	2012-08-23			ENSG00000171054	ENSG00000171054		"GPCR / Class A : Olfactory receptors"	14755	protein-coding gene	gene with protein product							Standard	NM_001004486		Approved		uc011muw.2	Q8NG92	OTTHUMG00000022411	ENST00000338616.3:c.541C>G	chrX.hg19:g.130678588C>G	ENSP00000340748:p.Leu181Val	83.0	0.0		109.0	19.0	NM_001004486	B2RNQ3|Q6IET8|Q96R12	Missense_Mutation	SNP	ENST00000338616.3	hg19	CCDS35396.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.385003	0.25031	.	.	ENSG00000171054	ENST00000338616	T	0.00115	8.71	4.78	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.464888	0.15868	U	0.240660	T	0.00271	0.0008	M	0.71871	2.18	0.09310	N	1	P	0.49447	0.924	P	0.49387	0.609	T	0.49214	-0.8963	10	0.39692	T	0.17	.	10.8765	0.46915	0.2042:0.7958:0.0:0.0	.	181	Q8NG92	O13H1_HUMAN	V	181	ENSP00000340748:L181V	ENSP00000340748:L181V	L	+	1	0	OR13H1	130506269	0.000000	0.05858	0.077000	0.20336	0.604000	0.37047	-0.735000	0.04888	0.967000	0.38186	-0.328000	0.08392	CTC	.	.		0.473	OR13H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058297.1			G	130678588	C	G	130678588	3	3	4	1	0	0	0	0	1	0	0	0	10952	913	32	4	543	4	OR13H1	23	130678588	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	10496839	130678588	24591972	151	410										
VGLL1	51442	hgsc.bcm.edu	37	chrX	135632968	135632968	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	6	1	0.633817215293396	1.46884624496565	0.296593953310371	0.628482972136223	1	0	gtggatctgccagtaccagcCttccaaatgaaagtaggtat	10	9	1	1			TCGA-2Y-A9GU-01A-11D-A382-10	TCGA-2Y-A9GU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	263e7d45-46a8-4d9d-a82a-0324d7f9a3ff	745978d5-14c9-407e-9db8-1a158a071ae7	g.chrX:135632968C>T	ENST00000370634.3	+	4	846	c.676C>T	c.(676-678)Ctt>Ttt	p.L226F	MIR934_ENST00000401241.1_RNA|VGLL1_ENST00000470358.1_3'UTR	NM_016267.3	NP_057351.1	Q99990	VGLL1_HUMAN	vestigial-like family member 1	226					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(192;0.000127)					CAGTACCAGCCTTCCAAATGA	0.403																																					p.L226F		Atlas-SNP	.											.	VGLL1	41	.	0			c.C676T						.						151	140	144					X																	135632968		2203	4300	6503	SO:0001583	missense	51442	exon4			ACCAGCCTTCCAA	AF137387	CCDS14658.1	Xq26.3	2014-03-03	2014-03-03		ENSG00000102243	ENSG00000102243			20985	protein-coding gene	gene with protein product		300583	"vestigial like 1 (Drosophila)"			10518497	Standard	NM_016267		Approved	TONDU, TDU	uc004ezy.3	Q99990	OTTHUMG00000022509	ENST00000370634.3:c.676C>T	chrX.hg19:g.135632968C>T	ENSP00000359668:p.Leu226Phe	183.0	0.0		147.0	20.0	NM_016267	Q5H915	Missense_Mutation	SNP	ENST00000370634.3	hg19	CCDS14658.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.95|10.95	1.494602|1.494602	0.26774|0.26774	.|.	.|.	ENSG00000102243|ENSG00000102243	ENST00000370634;ENST00000430688;ENST00000456412|ENST00000440515	T;T|.	0.60797|.	0.2;0.16|.	5.55|5.55	3.79|3.79	0.43588|0.43588	.|.	1.255470|.	0.05458|.	N|.	0.550611|.	T|T	0.25419|0.25419	0.0618|0.0618	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B|.	0.10296|.	0.003|.	B|.	0.12837|.	0.008|.	T|T	0.19712|0.19712	-1.0297|-1.0297	10|5	0.46703|.	T|.	0.11|.	-1.0884|-1.0884	7.2407|7.2407	0.26094|0.26094	0.0:0.8003:0.0:0.1997|0.0:0.8003:0.0:0.1997	.|.	226|.	Q99990|.	VGLL1_HUMAN|.	F|L	226;83;28|143	ENSP00000359668:L226F;ENSP00000388868:L28F|.	ENSP00000359668:L226F|.	L|P	+|+	1|2	0|0	VGLL1|VGLL1	135460634|135460634	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.163000|0.163000	0.22366|0.22366	-0.280000|-0.280000	0.08468|0.08468	0.684000|0.684000	0.31448|0.31448	0.600000|0.600000	0.82982|0.82982	CTT|CCT	.	.		0.403	VGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058493.1	NM_016267		T	135632968	C	T	135632968	3	4	4	1	0	0	0	0	1	0	0	0	17173	681	24	3	686	3	VGLL1	23	135632968	Missense_Mutation	SNP	C	TCGA-2Y-A9GU-01A-11D-A382-10	4954380	135632968	19637592	152	411										
ARHGEF16	27237	hgsc.bcm.edu	37	chr1	3390035	3390035	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gggggcctgcccatgctctcCttcctgatcctccccatgca	9	18	1	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr1:3390035C>T	ENST00000378378.4	+	8	1659	c.1254C>T	c.(1252-1254)tcC>tcT	p.S418S	ARHGEF16_ENST00000378371.2_Silent_p.S130S|ARHGEF16_ENST00000413250.2_Silent_p.S122S|ARHGEF16_ENST00000378373.1_Silent_p.S130S	NM_014448.3	NP_055263.2	Q5VV41	ARHGG_HUMAN	Rho guanine nucleotide exchange factor (GEF) 16	418	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.|Required for RHOG activation and mediates interaction with EPHA2.				activation of Cdc42 GTPase activity (GO:0032864)|activation of Rac GTPase activity (GO:0032863)|apoptotic signaling pathway (GO:0097190)|cell chemotaxis (GO:0060326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	PDZ domain binding (GO:0030165)|receptor tyrosine kinase binding (GO:0030971)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			lung(6)|ovary(1)	7	all_cancers(77;0.00276)|all_epithelial(69;0.00102)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.101)	all_epithelial(116;7.14e-21)|all_lung(118;2.24e-08)|Lung NSC(185;3.55e-06)|Breast(487;0.000765)|Renal(390;0.00121)|Hepatocellular(190;0.0046)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.211)		Epithelial(90;8.62e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.62e-22)|GBM - Glioblastoma multiforme(42;2.49e-12)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000681)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CCATGCTCTCCTTCCTGATCC	0.672																																					p.S418S		Atlas-SNP	.											.	ARHGEF16	76	.	0			c.C1254T						.						50	64	59					1																	3390035		2203	4298	6501	SO:0001819	synonymous_variant	27237	exon8			GCTCTCCTTCCTG	D89016	CCDS46.2	1p36.3	2013-01-10	2010-04-13		ENSG00000130762	ENSG00000130762		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15515	protein-coding gene	gene with protein product	"putative neuroblastoma protein"						Standard	NM_014448		Approved	NBR, GEF16	uc001akg.4	Q5VV41	OTTHUMG00000000625	ENST00000378378.4:c.1254C>T	chr1.hg19:g.3390035C>T		90.0	0.0		80.0	12.0	NM_014448	Q86TF0|Q99434	Silent	SNP	ENST00000378378.4	hg19	CCDS46.2																																																																																			.	.		0.672	ARHGEF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001515.1	NM_014448		T	3390035	C	T	3390035	2	4	5	1	0	0	0	0	0	0	0	1	899	668	24	3		3	ARHGEF16	1	3390035	Silent	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10		3390035	245860586	1	412										
SPOCD1	90853	hgsc.bcm.edu	37	chr1	32256885	32256885	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	agaggggagacaggaagagcCcaaaggcctgcggggaagaa	18	7	0	4			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr1:32256885C>G	ENST00000360482.2	-	16	3099	c.2970G>C	c.(2968-2970)tgG>tgC	p.W990C	RP11-84A19.3_ENST00000527035.1_RNA|SPOCD1_ENST00000257100.3_Intron|SPOCD1_ENST00000373648.2_3'UTR|SPOCD1_ENST00000533231.1_Intron	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	990					negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		CAGGAAGAGCCCAAAGGCCTG	0.577																																					p.W990C		Atlas-SNP	.											.	SPOCD1	109	.	0			c.G2970C						.						21	24	23					1																	32256885		2203	4299	6502	SO:0001583	missense	90853	exon16			AAGAGCCCAAAGG	AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 146"					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.2970G>C	chr1.hg19:g.32256885C>G	ENSP00000353670:p.Trp990Cys	85.0	0.0		62.0	14.0	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	hg19	CCDS347.1	.	.	.	.	.	.	.	.	.	.	C	8.624	0.892083	0.17613	.	.	ENSG00000134668	ENST00000360482	T	0.22743	1.94	4.44	2.06	0.26882	.	.	.	.	.	T	0.14527	0.0351	N	0.14661	0.345	0.09310	N	1	D	0.58620	0.983	P	0.46975	0.533	T	0.12142	-1.0559	9	0.45353	T	0.12	12.3231	7.7734	0.29021	0.0:0.8254:0.0:0.1746	.	990	Q6ZMY3	SPOC1_HUMAN	C	990	ENSP00000353670:W990C	ENSP00000353670:W990C	W	-	3	0	SPOCD1	32029472	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	0.588000	0.23924	0.335000	0.23614	0.655000	0.94253	TGG	.	.		0.577	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		G	32256885	C	G	32256885	3	3	5	1	0	0	0	0	1	0	0	0	15093	624	22	4	684	4	SPOCD1	1	32256885	Missense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10	28866850	32256885	216993736	2	413										
ATP1A1	476	hgsc.bcm.edu	37	chr1	116935513	116935514	+	Frame_Shift_Ins	INS	-	-	A													0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gcctctgagtcagcactcttINSaaagtgcatagagctgtgct							TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr1:116935513_116935514insA	ENST00000295598.5	+	11	1622_1623	c.1370_1371insA	c.(1369-1374)ttaaagfs	p.LK457fs	ATP1A1_ENST00000537345.1_Frame_Shift_Ins_p.LK457fs|ATP1A1_ENST00000369496.4_Frame_Shift_Ins_p.LK426fs	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	457					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	TCAGCACTCTTAAAGTGCATAG	0.45																																					p.L457fs		Atlas-Indel,Pindel	.											.	ATP1A1	87	.	0			c.1370_1371insA						.																																			SO:0001589	frameshift_variant	476	exon11			.	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1373dupA	chr1.hg19:g.116935516_116935516dupA	ENSP00000295598:p.Leu457fs	141.0	0.0		88.0	25.0	NM_000701	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Frame_Shift_Ins	INS	ENST00000295598.5	hg19	CCDS887.1																																																																																			.	.		0.45	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		A	116935514	-	A	116935513	7	5	5	1	0	1	1	0	0	0	0	0	1128	1764	61	0	1428	0	ATP1A1	1	116935513	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GV-01A-11D-A382-10	84678628	116935513	132315108	3	414										
KIAA0907	22889	hgsc.bcm.edu	37	chr1	155896529	155896529	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ctgagcgatgggtgctggctGgtgatagacagttactgttg	16	6	0	3			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr1:155896529G>C	ENST00000368321.3	-	6	642	c.619C>G	c.(619-621)Cag>Gag	p.Q207E	KIAA0907_ENST00000368320.3_Missense_Mutation_p.Q207E|KIAA0907_ENST00000482337.1_5'UTR|KIAA0907_ENST00000368319.3_Missense_Mutation_p.Q207E|SCARNA4_ENST00000516999.1_RNA	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	207							RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			GGTGCTGGCTGGTGATAGACA	0.463																																					p.Q207E		Atlas-SNP	.											.	KIAA0907	58	.	0			c.C619G						.						164	146	152					1																	155896529		2203	4300	6503	SO:0001583	missense	22889	exon6			CTGGCTGGTGATA	BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.619C>G	chr1.hg19:g.155896529G>C	ENSP00000357304:p.Gln207Glu	258.0	0.0		262.0	67.0	NM_014949	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Missense_Mutation	SNP	ENST00000368321.3	hg19	CCDS30885.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.689962	0.68271	.	.	ENSG00000132680	ENST00000368321;ENST00000368320;ENST00000368319	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.50650	0.1628	L	0.46157	1.445	0.80722	D	1	D;P;P;P	0.57257	0.979;0.73;0.677;0.949	P;B;B;P	0.56563	0.801;0.35;0.309;0.641	T	0.48658	-0.9016	9	0.02654	T	1	-6.8505	19.4873	0.95035	0.0:0.0:1.0:0.0	.	207;207;207;207	Q7Z7F0-4;Q7Z7F0-3;Q7Z7F0-2;Q7Z7F0	.;.;.;K0907_HUMAN	E	207	.	ENSP00000357302:Q207E	Q	-	1	0	KIAA0907	154163153	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.218000	0.89768	2.937000	0.99478	0.650000	0.86243	CAG	.	.		0.463	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		C	155896529	G	C	155896529	3	2	5	1	0	0	0	0	1	0	0	0	8208	1357	47	4	1261	4	KIAA0907	1	155896529	Missense_Mutation	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10	38961016	155896529	93354092	4	415										
C1orf49	84066	hgsc.bcm.edu	37	chr1	178491567	178491567	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ccccaaagtcccagactgagGgaaggtgaagcttaactgcc	11	12	0	3			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr1:178491567G>A	ENST00000319416.2	+	9	806	c.694G>A	c.(694-696)Gga>Aga	p.G232R	TEX35_ENST00000367642.3_3'UTR|TEX35_ENST00000258298.2_Intron|TEX35_ENST00000367641.3_3'UTR|TEX35_ENST00000367639.1_Intron	NM_032126.4	NP_115502.2			testis expressed 35																		ccagactgagggaaggtgaag	0.522																																					p.G232R		Atlas-SNP	.											.	TEX35	15	.	0			c.G694A						.						33	28	30					1																	178491567		2203	4300	6503	SO:0001583	missense	84066	exon9			ACTGAGGGAAGGT	AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"Testis-Specific Conserved gene 24kDa"		"chromosome 1 open reading frame 49"	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000319416.2:c.694G>A	chr1.hg19:g.178491567G>A	ENSP00000323795:p.Gly232Arg	81.0	0.0		92.0	30.0	NM_032126		Missense_Mutation	SNP	ENST00000319416.2	hg19	CCDS1323.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.920638	0.33908	.	.	ENSG00000240021	ENST00000319416	T	0.24538	1.85	2.47	0.564	0.17302	.	.	.	.	.	T	0.11836	0.0288	N	0.08118	0	0.09310	N	0.999998	B	0.13145	0.007	B	0.15870	0.014	T	0.25950	-1.0117	9	0.87932	D	0	6.3536	4.5613	0.12161	0.3277:0.0:0.6723:0.0	.	232	Q5T0J7	CA049_HUMAN	R	232	ENSP00000323795:G232R	ENSP00000323795:G232R	G	+	1	0	C1orf49	176758190	0.036000	0.19791	0.004000	0.12327	0.070000	0.16714	0.551000	0.23361	0.150000	0.19136	-0.324000	0.08512	GGA	.	.		0.522	TEX35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084917.1	NM_032126		A	178491567	G	A	178491567	3	1	5	1	0	0	0	0	1	0	0	0	2043	1233	43	3	809	3	C1orf49	1	178491567	Missense_Mutation	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10	22595038	178491567	70759054	5	416										
OR2M2	391194	hgsc.bcm.edu	37	chr1	248343868	248343868	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ctcatgcaatgacacatcaaTatttgaagaggttattttca	6	7	3	3			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr1:248343868T>C	ENST00000359682.2	+	1	581	c.581T>C	c.(580-582)aTa>aCa	p.I194T		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	194						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GACACATCAATATTTGAAGAG	0.413																																					p.I194T		Atlas-SNP	.											.	OR2M2	149	.	0			c.T581C						.						229	223	225					1																	248343868		2203	4300	6503	SO:0001583	missense	391194	exon1			CATCAATATTTGA	AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"GPCR / Class A : Olfactory receptors"	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.581T>C	chr1.hg19:g.248343868T>C	ENSP00000352710:p.Ile194Thr	159.0	0.0		159.0	10.0	NM_001004688	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	hg19	CCDS31106.1	.	.	.	.	.	.	.	.	.	.	t	0.391	-0.923547	0.02377	.	.	ENSG00000198601	ENST00000359682	T	0.00183	8.6	1.88	-3.75	0.04372	GPCR, rhodopsin-like superfamily (1);	0.265846	0.19632	N	0.109647	T	0.00073	0.0002	N	0.17901	0.54	0.09310	N	1	B	0.12013	0.005	B	0.16289	0.015	T	0.30822	-0.9965	10	0.30078	T	0.28	.	4.1381	0.10181	0.5105:0.2708:0.0:0.2187	.	194	Q96R28	OR2M2_HUMAN	T	194	ENSP00000352710:I194T	ENSP00000352710:I194T	I	+	2	0	OR2M2	246410491	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.006000	0.12833	-1.226000	0.02574	-0.478000	0.04885	ATA	.	.		0.413	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688		C	248343868	T	C	248343868	3	2	5	1	0	0	0	0	1	0	0	0	11019	1406	49	2	583	2	OR2M2	1	248343868	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10	69852301	248343868	906753	6	417										
TMEM150A	129303	hgsc.bcm.edu	37	chr2	85827014	85827014	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	caggggagaaggggaagcacCtgaaagttgccaaccaccaa	13	10	0	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr2:85827014C>A	ENST00000409668.1	-	5	863	c.396G>T	c.(394-396)caG>caT	p.Q132H	TMEM150A_ENST00000334462.5_Splice_Site_p.Q132H|TMEM150A_ENST00000306353.3_Splice_Site_p.Q79H			Q86TG1	T150A_HUMAN	transmembrane protein 150A	132					catabolic process (GO:0009056)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|lung(1)|skin(1)	7						GGGGAAGCACCTGAAAGTTGC	0.582																																					p.Q132H		Atlas-SNP	.											.	TMEM150A	15	.	0			c.G396T						.						95	89	91					2																	85827014		2203	4300	6503	SO:0001630	splice_region_variant	129303	exon6			AAGCACCTGAAAG	AK098152	CCDS33233.1	2p11.2	2009-06-12	2009-06-12	2009-06-12	ENSG00000168890	ENSG00000168890			24677	protein-coding gene	gene with protein product			"transmembrane protein 150"	TMEM150		10858565	Standard	NM_001031738		Approved	TM6P1, FLJ90024	uc002spy.2	Q86TG1	OTTHUMG00000130168	ENST00000409668.1:c.396+1G>T	chr2.hg19:g.85827014C>A		136.0	0.0		121.0	37.0	NM_001031738	A8K764|B7WPQ9|D6W5L2|Q8N2R6	Missense_Mutation	SNP	ENST00000409668.1	hg19	CCDS33233.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.924894	0.73213	.	.	ENSG00000168890	ENST00000306353;ENST00000334462;ENST00000409668	T;T;T	0.50277	0.75;0.75;0.75	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.75354	0.3838	M	0.91459	3.21	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.81210	-0.1036	9	.	.	.	-8.9487	16.3731	0.83371	0.0:1.0:0.0:0.0	.	79;132	Q86TG1-2;Q86TG1	.;T150A_HUMAN	H	79;132;132	ENSP00000302715:Q79H;ENSP00000334708:Q132H;ENSP00000387292:Q132H	.	Q	-	3	2	TMEM150A	85680525	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	3.570000	0.53834	2.472000	0.83506	0.561000	0.74099	CAG	.	.		0.582	TMEM150A-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329474.1	NM_153342	Missense_Mutation	A	85827014	C	A	85827014	5	1	5	1	0	0	0	0	0	0	1	0	16082	695	24	3	431	3	TMEM150A	2	85827014	Splice_Site	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10		85827014	157372359	7	418										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230723842	230723842	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	cccagctttggctgaggtggCtgattttgaagccagcttgg	14	9	0	3			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr2:230723842C>T	ENST00000283943.5	-	3	725	c.547G>A	c.(547-549)Gcc>Acc	p.A183T	TRIP12_ENST00000409677.1_Missense_Mutation_p.A225T|TRIP12_ENST00000389045.3_Intron|TRIP12_ENST00000543084.1_Missense_Mutation_p.A225T|TRIP12_ENST00000389044.4_Missense_Mutation_p.A225T	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	183					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		GCTGAGGTGGCTGATTTTGAA	0.512																																					p.A183T		Atlas-SNP	.											.	TRIP12	207	.	0			c.G547A						.						59	54	55					2																	230723842		2203	4300	6503	SO:0001583	missense	9320	exon3			AGGTGGCTGATTT	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.547G>A	chr2.hg19:g.230723842C>T	ENSP00000283943:p.Ala183Thr	91.0	0.0		86.0	27.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	hg19	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.860452	0.91433	.	.	ENSG00000153827	ENST00000283943;ENST00000389044;ENST00000543084;ENST00000409677;ENST00000453485	T;T	0.52295	0.67;0.67	5.72	5.72	0.89469	.	0.051447	0.85682	D	0.000000	T	0.35158	0.0922	N	0.24115	0.695	0.80722	D	1	B;B;B	0.26635	0.155;0.155;0.084	B;B;B	0.25759	0.063;0.063;0.063	T	0.19160	-1.0314	10	0.07644	T	0.81	.	19.8788	0.96888	0.0:1.0:0.0:0.0	.	183;225;183	D4HL82;Q14CA3;Q14669	.;.;TRIPC_HUMAN	T	183;225;225;225;53	ENSP00000283943:A183T;ENSP00000373696:A225T	ENSP00000283943:A183T	A	-	1	0	TRIP12	230432086	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	7.456000	0.80751	2.704000	0.92352	0.563000	0.77884	GCC	.	.		0.512	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		T	230723842	C	T	230723842	3	4	5	1	0	0	0	0	1	0	0	0	16571	797	28	3	5587	3	TRIP12	2	230723842	Missense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10	144896828	230723842	12475531	8	419										
SLC22A14	9389	hgsc.bcm.edu	37	chr3	38347652	38347652	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	cgcagattgagggctgtccaCaccaagcaggatgacaagtt	12	10	0	3			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr3:38347652C>T	ENST00000273173.4	+	1	226	c.135C>T	c.(133-135)caC>caT	p.H45H	RNU6-235P_ENST00000362644.1_RNA|SLC22A14_ENST00000448498.1_Silent_p.H45H	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	45					organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		GGGCTGTCCACACCAAGCAGG	0.542																																					p.H45H		Atlas-SNP	.											.	SLC22A14	64	.	0			c.C135T						.						194	166	176					3																	38347652		2203	4300	6503	SO:0001819	synonymous_variant	9389	exon1			TGTCCACACCAAG	AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"Solute carriers"	8495	protein-coding gene	gene with protein product		604048	"organic cationic transporter-like 4", "solute carrier family 22 (organic cation transporter), member 14"	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.135C>T	chr3.hg19:g.38347652C>T		190.0	0.0		140.0	35.0	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Silent	SNP	ENST00000273173.4	hg19	CCDS2677.1																																																																																			.	.		0.542	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803		T	38347652	C	T	38347652	2	4	5	1	0	0	0	0	0	0	0	1	14460	477	17	3		3	SLC22A14	3	38347652	Silent	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10		38347652	159674778	9	420										
DALRD3	55152	hgsc.bcm.edu	37	chr3	49055466	49055466	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ccccgctcacccgtgagcgcGcagggctcgcgccaggtgat	14	17	1	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr3:49055466G>C	ENST00000341949.4	-	2	457	c.451C>G	c.(451-453)Cgc>Ggc	p.R151G	NDUFAF3_ENST00000326912.4_5'Flank|DALRD3_ENST00000441576.2_Missense_Mutation_p.R151G|DALRD3_ENST00000313778.5_5'UTR|DALRD3_ENST00000395462.4_5'UTR|NDUFAF3_ENST00000326925.6_5'Flank|MIR191_ENST00000384873.1_RNA|MIR425_ENST00000362162.1_RNA|DALRD3_ENST00000496568.1_5'UTR|DALRD3_ENST00000440857.1_5'UTR	NM_001009996.1	NP_001009996.1	Q5D0E6	DALD3_HUMAN	DALR anticodon binding domain containing 3	151					arginyl-tRNA aminoacylation (GO:0006420)		arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)			breast(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCGTGAGCGCGCAGGGCTCGC	0.706																																					p.R151G		Atlas-SNP	.											.	DALRD3	57	.	0			c.C451G						.						5	6	6					3																	49055466		1921	3893	5814	SO:0001583	missense	55152	exon2			GAGCGCGCAGGGC	BC014099	CCDS2783.1, CCDS33754.1, CCDS63632.1	3p21.31	2005-01-10			ENSG00000178149	ENSG00000178149			25536	protein-coding gene	gene with protein product						12477932	Standard	NM_001009996		Approved	FLJ10496	uc003cvk.2	Q5D0E6	OTTHUMG00000156748	ENST00000341949.4:c.451C>G	chr3.hg19:g.49055466G>C	ENSP00000344989:p.Arg151Gly	57.0	0.0		42.0	16.0	NM_001009996	Q7Z5S7|Q86WY1|Q8N105|Q8NA89|Q9NVU8	Missense_Mutation	SNP	ENST00000341949.4	hg19	CCDS33754.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286814	0.80803	.	.	ENSG00000178149	ENST00000441576;ENST00000341949;ENST00000420952	T;T;T	0.56941	0.48;0.53;0.43	4.92	3.98	0.46160	.	0.184247	0.44097	D	0.000491	T	0.51975	0.1706	L	0.50333	1.59	0.80722	D	1	P;P;P	0.46512	0.879;0.667;0.796	P;B;P	0.45343	0.452;0.397;0.477	T	0.59899	-0.7367	10	0.72032	D	0.01	-8.3772	13.9758	0.64273	0.0:0.0:0.8478:0.1522	.	151;151;151	B7Z727;Q5D0E6-2;Q5D0E6	.;.;DALD3_HUMAN	G	151;151;116	ENSP00000410623:R151G;ENSP00000344989:R151G;ENSP00000397385:R116G	ENSP00000344989:R151G	R	-	1	0	DALRD3	49030470	0.359000	0.24955	0.094000	0.20943	0.010000	0.07245	2.099000	0.41767	2.270000	0.75569	0.655000	0.94253	CGC	.	.		0.706	DALRD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345581.1	NM_018114		C	49055466	G	C	49055466	3	2	5	1	0	0	0	0	1	0	0	0	4231	1087	38	4	1224	4	DALRD3	3	49055466	Missense_Mutation	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10	10707814	49055466	148966964	10	421										
GPM6A	2823	hgsc.bcm.edu	37	chr4	176556177	176556177	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	aggcgtctttcacataggccCagttggcagacagaaccata	10	11	2	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr4:176556177C>A	ENST00000280187.7	-	8	761	c.716G>T	c.(715-717)tGg>tTg	p.W239L	GPM6A_ENST00000506219.1_5'UTR|GPM6A_ENST00000506894.1_Missense_Mutation_p.W228L|GPM6A_ENST00000515090.1_Missense_Mutation_p.W232L|GPM6A_ENST00000393658.2_Missense_Mutation_p.W239L	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	239					neural retina development (GO:0003407)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|positive regulation of filopodium assembly (GO:0051491)|stem cell differentiation (GO:0048863)|synapse assembly (GO:0007416)	axonal growth cone (GO:0044295)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium channel activity (GO:0005262)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		CACATAGGCCCAGTTGGCAGA	0.428																																					p.W239L		Atlas-SNP	.											.	GPM6A	70	.	0			c.G716T						.						78	73	75					4																	176556177		2203	4300	6503	SO:0001583	missense	2823	exon7			TAGGCCCAGTTGG		CCDS3824.1, CCDS54822.1, CCDS58936.1	4q34	2008-08-29				ENSG00000150625			4460	protein-coding gene	gene with protein product		601275		GPM6		8661015, 18574501	Standard	NM_005277		Approved		uc003iug.4	P51674		ENST00000280187.7:c.716G>T	chr4.hg19:g.176556177C>A	ENSP00000280187:p.Trp239Leu	75.0	0.0		73.0	14.0	NM_201591	B7Z642|E9PHI5|Q92602	Missense_Mutation	SNP	ENST00000280187.7	hg19	CCDS3824.1	.	.	.	.	.	.	.	.	.	.	C	33	5.212976	0.95069	.	.	ENSG00000150625	ENST00000280187;ENST00000393658;ENST00000506894;ENST00000515090	D;D;D;D	0.99207	-5.56;-5.56;-5.56;-5.56	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.99165	0.9711	L	0.46157	1.445	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.81914	0.995;0.995;0.995	D	0.99906	1.1182	10	0.72032	D	0.01	-12.5234	20.3627	0.98863	0.0:1.0:0.0:0.0	.	232;228;239	B7Z642;E9PHI5;P51674	.;.;GPM6A_HUMAN	L	239;239;228;232	ENSP00000280187:W239L;ENSP00000377268:W239L;ENSP00000421578:W228L;ENSP00000423984:W232L	ENSP00000280187:W239L	W	-	2	0	GPM6A	176793171	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.445000	0.80570	2.885000	0.99019	0.655000	0.94253	TGG	.	.		0.428	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1			A	176556177	C	A	176556177	3	1	5	1	0	0	0	0	1	0	0	0	6623	595	21	3	124	3	GPM6A	4	176556177	Missense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10		176556177	14598099	11	422										
IRX4	50805	hgsc.bcm.edu	37	chr5	1878600	1878600	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gcacaaaccccagcttggccTcgcagacctgagggccgccc	11	18	0	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr5:1878600T>A	ENST00000505790.1	-	6	1499	c.1043A>T	c.(1042-1044)gAg>gTg	p.E348V	IRX4_ENST00000505938.1_5'Flank|IRX4_ENST00000231357.2_Missense_Mutation_p.E348V|IRX4_ENST00000513692.1_Missense_Mutation_p.E348V	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	348					establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		CAGCTTGGCCTCGCAGACCTG	0.771																																					p.E348V		Atlas-SNP	.											.	IRX4	45	.	0			c.A1043T						.						2	3	2					5																	1878600		1347	2831	4178	SO:0001583	missense	50805	exon5			TTGGCCTCGCAGA	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"Homeoboxes / TALE class"	6129	protein-coding gene	gene with protein product		606199	"iroquois homeobox protein 4"			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.1043A>T	chr5.hg19:g.1878600T>A	ENSP00000423161:p.Glu348Val	47.0	0.0		33.0	9.0	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Missense_Mutation	SNP	ENST00000505790.1	hg19	CCDS3867.1	.	.	.	.	.	.	.	.	.	.	t	12.68	2.011184	0.35511	.	.	ENSG00000113430	ENST00000231357;ENST00000505790;ENST00000513692	T;T;T	0.66099	-0.19;-0.19;-0.19	3.37	3.37	0.38596	.	0.290011	0.22703	U	0.056665	T	0.53786	0.1818	L	0.50333	1.59	0.44149	D	0.996948	B	0.14438	0.01	B	0.06405	0.002	T	0.52480	-0.8570	10	0.35671	T	0.21	-15.3684	11.6433	0.51246	0.0:0.0:0.0:1.0	.	348	P78413	IRX4_HUMAN	V	348	ENSP00000231357:E348V;ENSP00000423161:E348V;ENSP00000424235:E348V	ENSP00000231357:E348V	E	-	2	0	IRX4	1931600	1.000000	0.71417	0.776000	0.31678	0.008000	0.06430	3.155000	0.50700	1.399000	0.46721	0.373000	0.22412	GAG	.	.		0.771	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358		A	1878600	T	A	1878600	3	1	5	1	0	0	0	0	1	0	0	0	7855	1551	54	4	520	4	IRX4	5	1878600	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10		1878600	179036660	12	423										
MSH3	4437	hgsc.bcm.edu	37	chr5	79950707	79950733	+	In_Frame_Del	DEL	CTGCAGCGGCCGCAGCGGCCGCAGCGC	CTGCAGCGGCCGCAGCGGCCGCAGCGC	-													0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ggaccctggcgctgcagcggCtgcagcggccgcagcggccg					rs2431220|rs2001675|rs2405876|rs201874762|rs2405875|rs144776112|rs1574197|rs148550291|rs201906899|rs535056167|rs60484572|rs70991168|rs201149584	byFrequency	TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	CTGCAGCGGCCGCAGCGGCCGCAGCGC	CTGCAGCGGCCGCAGCGGCCGCAGCGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr5:79950707_79950733delCTGCAGCGGCCGCAGCGGCCGCAGCGC	ENST00000265081.6	+	1	241_267	c.161_187delCTGCAGCGGCCGCAGCGGCCGCAGCGC	c.(160-189)gctgcagcggccgcagcggccgcagcgccc>gcc	p.AAAAAAAAP55del	DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000439211.2_5'UTR	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	55	Poly-Ala.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		GCTgcagcggctgcagcggccgcagcggccgcagcgCCCCCAGCGCC	0.709								Mismatch excision repair (MMR)																													p.54_62del	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-INDEL	.											.	MSH3	129	.	0			c.160_186del						.																																			SO:0001651	inframe_deletion	4437	exon1			.	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.161_187delCTGCAGCGGCCGCAGCGGCCGCAGCGC	chr5.hg19:g.79950707_79950733delCTGCAGCGGCCGCAGCGGCCGCAGCGC	ENSP00000265081:p.Ala55_Pro63del	119.0	0.0		111.0	49.0	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	In_Frame_Del	DEL	ENST00000265081.6	hg19	CCDS34195.1																																																																																			.	.		0.709	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		-	79950733	CTGCAGCGGCCGCAGCGGCCGCAGCGC	-	79950707	7	5	5	1	0	1	0	1	0	0	0	0	9880	797	28	0	163	0	MSH3	5	79950707	In_Frame_Del	DEL	CTGCAGCGGCCGCAGCGGCCGCAGCGC	TCGA-2Y-A9GV-01A-11D-A382-10	78072107	79950707	100964553	13	424										
GPR98	84059	hgsc.bcm.edu	37	chr5	90106847	90106847	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gtttactggcaatgtcagcaTaacagttaaaactttcggtg	9	7	1	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr5:90106847T>C	ENST00000405460.2	+	74	15866	c.15770T>C	c.(15769-15771)aTa>aCa	p.I5257T	GPR98_ENST00000425867.2_Missense_Mutation_p.I918T	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5257					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AATGTCAGCATAACAGTTAAA	0.418																																					p.I5257T		Atlas-SNP	.											.	GPR98	605	.	0			c.T15770C						.						141	131	134					5																	90106847		1915	4127	6042	SO:0001583	missense	84059	exon74			TCAGCATAACAGT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.15770T>C	chr5.hg19:g.90106847T>C	ENSP00000384582:p.Ile5257Thr	264.0	0.0		221.0	52.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.274796	0.40194	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.30448	1.53;1.53	5.5	5.5	0.81552	.	0.477226	0.23369	N	0.048938	T	0.28400	0.0702	L	0.40543	1.245	0.09310	N	0.999999	B;B;B	0.28636	0.139;0.09;0.218	B;B;B	0.30572	0.055;0.024;0.117	T	0.14839	-1.0458	9	.	.	.	.	15.6013	0.76628	0.0:0.0:0.0:1.0	.	918;5257;918	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	T	5257;5257;918	ENSP00000384582:I5257T;ENSP00000392618:I918T	.	I	+	2	0	GPR98	90142603	0.967000	0.33354	0.034000	0.17996	0.909000	0.53808	3.998000	0.57024	2.096000	0.63516	0.533000	0.62120	ATA	.	.		0.418	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	90106847	T	C	90106847	3	2	5	1	0	0	0	0	1	0	0	0	6730	1406	49	2	16064	2	GPR98	5	90106847	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10	10156140	90106847	90808413	14	425										
RFESD	317671	hgsc.bcm.edu	37	chr5	94988893	94988893	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ggcatttcagctcagctgtcAtctcagtgaccagtttttat	8	10	4	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr5:94988893A>T	ENST00000311364.4	+	2	1416				SPATA9_ENST00000477047.2_5'UTR|RFESD_ENST00000380005.4_Missense_Mutation_p.I45F|RFESD_ENST00000458310.1_Missense_Mutation_p.I45F|RFESD_ENST00000513950.2_5'Flank	NM_173362.3	NP_775498.1	Q8TAC1	RFESD_HUMAN	Rieske (Fe-S) domain containing								2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			autonomic_ganglia(2)|endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	6		all_cancers(142;0.000215)|all_epithelial(76;7.43e-07)|all_lung(232;0.0318)|Lung NSC(167;0.041)|Ovarian(225;0.051)|Colorectal(57;0.162)		all cancers(79;5.94e-17)		ctcagctgtcatctcagtgaC	0.413																																					p.I45F		Atlas-SNP	.											.	RFESD	22	.	0			c.A133T						.						235	176	194					5																	94988893		692	1591	2283	SO:0001627	intron_variant	317671	exon3			GCTGTCATCTCAG	BC035110	CCDS4075.1, CCDS47248.1	5q15	2010-12-07			ENSG00000175449	ENSG00000175449			29587	protein-coding gene	gene with protein product						12477932	Standard	NM_173362		Approved		uc003klg.3	Q8TAC1	OTTHUMG00000121168	ENST00000311364.4:c.-2+858A>T	chr5.hg19:g.94988893A>T		95.0	0.0		73.0	17.0	NM_001131066	J3KPH1	Missense_Mutation	SNP	ENST00000311364.4	hg19	CCDS4075.1	.	.	.	.	.	.	.	.	.	.	A	14.71	2.615569	0.46631	.	.	ENSG00000175449	ENST00000380005;ENST00000458310	.	.	.	1.11	1.11	0.20524	.	.	.	.	.	T	0.28300	0.0699	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.22977	-1.0201	5	0.40728	T	0.16	.	4.4223	0.11486	1.0:0.0:0.0:0.0	.	.	.	.	F	45	.	ENSP00000369341:I45F	I	+	1	0	RFESD	95014649	0.029000	0.19370	0.057000	0.19452	0.190000	0.23558	-0.112000	0.10791	0.747000	0.32809	0.379000	0.24179	ATC	.	.		0.413	RFESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241654.1	NM_173362		T	94988893	A	T	94988893	1	4	5	0	1	0	0	0	0	0	0	0	13264	217	8	4		4	RFESD	5	94988893	Intron	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10	4882046	94988893	85926367	15	426										
CAMLG	819	hgsc.bcm.edu	37	chr5	134076873	134076873	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	cagtacaggaacaactgaccAgcagggtggtgtggccgagg	16	9	0	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr5:134076873A>T	ENST00000297156.2	+	2	413	c.293A>T	c.(292-294)cAg>cTg	p.Q98L	CAMLG_ENST00000514518.1_Intron	NM_001745.3	NP_001736.1	P49069	CAMLG_HUMAN	calcium modulating ligand	98					defense response (GO:0006952)|epidermal growth factor receptor signaling pathway (GO:0007173)|receptor recycling (GO:0001881)|signal transduction (GO:0007165)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|cervix(1)|kidney(3)|lung(3)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Cyclosporine(DB00091)	ACAACTGACCAGCAGGGTGGT	0.507																																					p.Q98L		Atlas-SNP	.											.	CAMLG	27	.	0			c.A293T						.						86	85	85					5																	134076873		2203	4300	6503	SO:0001583	missense	819	exon2			CTGACCAGCAGGG	AF068179.1	CCDS4178.1	5q23	2008-07-18			ENSG00000164615	ENSG00000164615			1471	protein-coding gene	gene with protein product	"calcium-modulating cyclophilin ligand", "calcium-signal modulating cyclophilin ligand", "cyclophilin B-binding protein"	601118				8824814	Standard	NM_001745		Approved	CAML	uc003kzt.3	P49069	OTTHUMG00000129116	ENST00000297156.2:c.293A>T	chr5.hg19:g.134076873A>T	ENSP00000297156:p.Gln98Leu	248.0	0.0		245.0	68.0	NM_001745	A1L3Y3	Missense_Mutation	SNP	ENST00000297156.2	hg19	CCDS4178.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.570005	0.45798	.	.	ENSG00000164615	ENST00000297156	T	0.29397	1.57	5.74	4.56	0.56223	.	0.296779	0.37955	N	0.001865	T	0.26629	0.0651	L	0.34521	1.04	0.80722	D	1	B	0.25609	0.13	B	0.32624	0.149	T	0.04281	-1.0963	10	0.39692	T	0.17	-6.6662	11.6308	0.51173	0.8514:0.1486:0.0:0.0	.	98	P49069	CAMLG_HUMAN	L	98	ENSP00000297156:Q98L	ENSP00000297156:Q98L	Q	+	2	0	CAMLG	134104772	0.974000	0.33945	0.990000	0.47175	0.986000	0.74619	1.498000	0.35660	0.970000	0.38263	0.533000	0.62120	CAG	.	.		0.507	CAMLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251161.1	NM_001745		T	134076873	A	T	134076873	3	4	5	1	0	0	0	0	1	0	0	0	2611	188	7	4	299	4	CAMLG	5	134076873	Missense_Mutation	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10	39087980	134076873	46838387	16	427										
PCDHGB1	56104	hgsc.bcm.edu	37	chr5	140731303	140731303	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	tctattctggccagtgacctGgagccgcgggagctgttgtc	14	11	2	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr5:140731303G>A	ENST00000523390.1	+	1	1476	c.1476G>A	c.(1474-1476)ctG>ctA	p.L492L	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	492	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAGTGACCTGGAGCCGCGGG	0.647																																					p.L492L		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.G1476A						.						35	41	39					5																	140731303		1977	4160	6137	SO:0001819	synonymous_variant	56104	exon1			TGACCTGGAGCCG	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"Cadherins / Protocadherins : Clustered"	8708	other	protocadherin	"protocadherin gamma subfamily B, 1, isoform 2"	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1476G>A	chr5.hg19:g.140731303G>A		139.0	0.0		107.0	31.0	NM_018922	Q3SY75|Q9Y5C8	Silent	SNP	ENST00000523390.1	hg19	CCDS54923.1																																																																																			.	.		0.647	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922		A	140731303	G	A	140731303	2	1	5	1	0	0	0	0	0	0	0	1	11571	1335	47	3		3	PCDHGB1	5	140731303	Silent	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10	6654430	140731303	40183957	17	428										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168135071	168135071	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	cacgggctggagaggcaggcAttgcatttggccacaatgtt	14	9	0	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr5:168135071A>G	ENST00000519560.1	-	26	3173	c.2754T>C	c.(2752-2754)aaT>aaC	p.N918N	SLIT3_ENST00000332966.8_Silent_p.N925N|SLIT3_ENST00000404867.3_Silent_p.N918N|CTC-558O2.1_ENST00000521870.1_RNA|CTC-558O2.1_ENST00000522615.1_RNA	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	918	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGAGGCAGGCATTGCATTTGG	0.582																																					p.N925N	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.T2775C						.						155	108	124					5																	168135071		2203	4300	6503	SO:0001819	synonymous_variant	6586	exon26			GCAGGCATTGCAT	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.2754T>C	chr5.hg19:g.168135071A>G		275.0	0.0		230.0	67.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.582	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		G	168135071	A	G	168135071	2	3	5	1	0	0	0	0	0	0	0	1	14756	214	8	2		2	SLIT3	5	168135071	Silent	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10	27403768	168135071	12780189	18	429										
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178634533	178634533	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	caatgttcatgagtgtcagcAggtacttctgtacgtgctcc	10	10	3	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr5:178634533A>G	ENST00000251582.7	-	4	973	c.872T>C	c.(871-873)cTg>cCg	p.L291P	ADAMTS2_ENST00000274609.5_Missense_Mutation_p.L291P	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	291	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GAGTGTCAGCAGGTACTTCTG	0.637																																					p.L291P		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.T872C						.						125	103	110					5																	178634533		2203	4300	6503	SO:0001583	missense	9509	exon4			GTCAGCAGGTACT	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.872T>C	chr5.hg19:g.178634533A>G	ENSP00000251582:p.Leu291Pro	77.0	0.0		72.0	30.0	NM_021599		Missense_Mutation	SNP	ENST00000251582.7	hg19	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.083629	0.76642	.	.	ENSG00000087116	ENST00000251582;ENST00000274609	T;T	0.65364	-0.15;-0.15	5.39	5.39	0.77823	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.41605	D	0.000855	T	0.81054	0.4743	M	0.85859	2.78	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.84451	0.0588	10	0.87932	D	0	.	14.8751	0.70488	1.0:0.0:0.0:0.0	.	291;291	O95450-2;O95450	.;ATS2_HUMAN	P	291	ENSP00000251582:L291P;ENSP00000274609:L291P	ENSP00000251582:L291P	L	-	2	0	ADAMTS2	178567139	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.051000	0.93849	2.171000	0.68590	0.459000	0.35465	CTG	.	.		0.637	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		G	178634533	A	G	178634533	3	3	5	1	0	0	0	0	1	0	0	0	265	188	7	2	2914	2	ADAMTS2	5	178634533	Missense_Mutation	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10	10499462	178634533	2280727	19	430										
PHIP	55023	hgsc.bcm.edu	37	chr6	79727292	79727292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	tgtgcttcccgtcgccagaaAcattccacctatgaagaata	7	12	0	3			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr6:79727292A>G	ENST00000275034.4	-	11	1170	c.1003T>C	c.(1003-1005)Ttt>Ctt	p.F335L		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	335					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		GTCGCCAGAAACATTCCACCT	0.313																																					p.F335L		Atlas-SNP	.											.	PHIP	177	.	0			c.T1003C						.						36	37	36					6																	79727292		2203	4296	6499	SO:0001583	missense	55023	exon11			CCAGAAACATTCC	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.1003T>C	chr6.hg19:g.79727292A>G	ENSP00000275034:p.Phe335Leu	369.0	0.0		374.0	105.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.014604	0.93404	.	.	ENSG00000146247	ENST00000275034	T	0.15256	2.44	5.14	5.14	0.70334	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.33352	0.0860	M	0.83483	2.645	0.80722	D	1	P;P	0.52842	0.956;0.956	D;D	0.65010	0.931;0.931	T	0.17018	-1.0383	9	.	.	.	-15.1063	14.1281	0.65235	1.0:0.0:0.0:0.0	.	335;335	A7J992;Q8WWQ0	.;PHIP_HUMAN	L	335	ENSP00000275034:F335L	.	F	-	1	0	PHIP	79784011	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.962000	0.93254	1.918000	0.55548	0.454000	0.30748	TTT	.	.		0.313	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			G	79727292	A	G	79727292	3	3	5	1	0	0	0	0	1	0	0	0	11851	43	2	2	4582	2	PHIP	6	79727292	Missense_Mutation	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10		79727292	91387775	20	431										
TSPYL1	7259	hgsc.bcm.edu	37	chr6	116600549	116600549	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	cacctcctccgcctcagcctCcgcccccgccgtcagctcag	7	24	3	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr6:116600549C>G	ENST00000368608.3	-	1	517	c.445G>C	c.(445-447)Gag>Cag	p.E149Q	RP1-93H18.1_ENST00000449314.1_lincRNA|DSE_ENST00000540275.1_Intron|DSE_ENST00000452085.3_5'Flank	NM_003309.3	NP_003300.1	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	149					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)	enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(3)|urinary_tract(1)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)		GCCTCAGCCTCCGCCCCCGCC	0.657																																					p.E149Q		Atlas-SNP	.											.	TSPYL1	28	.	0			c.G445C						.						49	56	54					6																	116600549		2202	4300	6502	SO:0001583	missense	7259	exon1			CAGCCTCCGCCCC	AF042181	CCDS34518.1	6q22.1	2014-09-17	2004-04-05	2004-04-07	ENSG00000189241	ENSG00000189241			12382	protein-coding gene	gene with protein product		604714	"TSPY-like"	TSPYL		9730615	Standard	NM_003309		Approved		uc003pwp.4	Q9H0U9	OTTHUMG00000015427	ENST00000368608.3:c.445G>C	chr6.hg19:g.116600549C>G	ENSP00000357597:p.Glu149Gln	37.0	0.0		26.0	8.0	NM_003309	O75885|Q5TFE6	Missense_Mutation	SNP	ENST00000368608.3	hg19	CCDS34518.1	.	.	.	.	.	.	.	.	.	.	C	9.084	0.999976	0.19121	.	.	ENSG00000189241	ENST00000368608;ENST00000545830	T	0.22743	1.94	1.42	-0.998	0.10212	.	.	.	.	.	T	0.03739	0.0106	N	0.22421	0.69	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.41858	-0.9485	9	0.49607	T	0.09	.	4.6634	0.12653	0.0:0.6187:0.0:0.3813	.	149	Q9H0U9	TSYL1_HUMAN	Q	149	ENSP00000357597:E149Q	ENSP00000357597:E149Q	E	-	1	0	TSPYL1	116707242	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.178000	0.16820	-0.328000	0.08539	-0.367000	0.07326	GAG	.	.		0.657	TSPYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041929.1			G	116600549	C	G	116600549	3	3	5	1	0	0	0	0	1	0	0	0	16674	864	30	4	872	4	TSPYL1	6	116600549	Missense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10	36873257	116600549	54514518	21	432										
CCR6	1235	hgsc.bcm.edu	37	chr6	167549735	167549735	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gtttcctttccaggaatcaaTgaatttcagcgatgttttcg	8	8	2	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr6:167549735T>C	ENST00000341935.5	+	3	569	c.17T>C	c.(16-18)aTg>aCg	p.M6T	CCR6_ENST00000349984.4_Missense_Mutation_p.M6T|CCR6_ENST00000400926.2_Missense_Mutation_p.M6T|RP11-517H2.6_ENST00000609590.1_RNA	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	6					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|humoral immune response (GO:0006959)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	14		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		CAGGAATCAATGAATTTCAGC	0.378																																					p.M6T		Atlas-SNP	.											.	CCR6	36	.	0			c.T17C						.						154	153	153					6																	167549735		2203	4300	6503	SO:0001583	missense	1235	exon3			AATCAATGAATTT	U68030	CCDS5298.1	6q27	2012-08-08			ENSG00000112486	ENSG00000112486		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1607	protein-coding gene	gene with protein product		601835		STRL22		8886020	Standard	NM_031409		Approved	CKR-L3, GPR-CY4, CMKBR6, GPR29, DRY-6, DCR2, BN-1, CD196	uc010kkm.3	P51684	OTTHUMG00000016015	ENST00000341935.5:c.17T>C	chr6.hg19:g.167549735T>C	ENSP00000343952:p.Met6Thr	78.0	0.0		91.0	34.0	NM_004367	E1P5C6|P78553|Q92846	Missense_Mutation	SNP	ENST00000341935.5	hg19	CCDS5298.1	.	.	.	.	.	.	.	.	.	.	T	7.859	0.725632	0.15439	.	.	ENSG00000112486	ENST00000400926;ENST00000341935;ENST00000349984	T;T;T	0.64991	-0.13;-0.13;-0.13	4.57	-1.22	0.09494	.	10.835500	0.00520	U	0.000196	T	0.16471	0.0396	N	0.08118	0	0.09310	N	1	B	0.23937	0.094	B	0.14023	0.01	T	0.14531	-1.0469	10	0.72032	D	0.01	.	1.0637	0.01606	0.1439:0.2519:0.149:0.4552	.	6	P51684	CCR6_HUMAN	T	6	ENSP00000383715:M6T;ENSP00000343952:M6T;ENSP00000339393:M6T	ENSP00000343952:M6T	M	+	2	0	CCR6	167469725	0.000000	0.05858	0.018000	0.16275	0.061000	0.15899	-0.287000	0.08388	-0.511000	0.06514	-0.496000	0.04628	ATG	.	.		0.378	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043118.1			C	167549735	T	C	167549735	3	2	5	1	0	0	0	0	1	0	0	0	2947	1464	51	2	23	2	CCR6	6	167549735	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10	50949186	167549735	3565332	22	433										
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	10	12	0	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000230354.6_Silent_p.Q60Q|TBP_ENST00000540980.1_Silent_p.Q40Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		81.0	0.0		66.0	7.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	5	1	0	0	0	0	0	0	0	1	15659	962	34	3		3	TBP	6	170871004	Silent	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10	3321269	170871004	244063	23	434										
SSPO	23145	hgsc.bcm.edu	37	chr7	149494390	149494390	+	RNA	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	acagccaagaccctggccctCtcctctgcccagccggggca	10	19	2	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr7:149494390C>A	ENST00000378016.2	+	0	6861							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCCTGGCCCTCTCCTCTGCCC	0.667																																					p.L2287L		Atlas-SNP	.											.	.	.	.	0			c.C6861A						.						53	61	59					7																	149494390		1972	4147	6119			23145	exon46			GGCCCTCTCCTCT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149494390C>A		83.0	0.0		99.0	19.0	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149494390	C	A	149494390	1	1	5	0	1	0	0	0	0	0	0	0	15204	900	32	3		3	SSPO	7	149494390	RNA	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10		149494390	9644273	24	435										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113812406	113812406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	attacctttgtagttaacctTgaaaccaacagatccaacac	4	11	0	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr8:113812406T>C	ENST00000297405.5	-	13	2201	c.1957A>G	c.(1957-1959)Aag>Gag	p.K653E	CSMD3_ENST00000343508.3_Missense_Mutation_p.K613E|CSMD3_ENST00000455883.2_Missense_Mutation_p.K549E|CSMD3_ENST00000352409.3_Missense_Mutation_p.K653E	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	653	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TAGTTAACCTTGAAACCAACA	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.K653E		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A1957G						.						124	113	117					8																	113812406		2203	4300	6503	SO:0001583	missense	114788	exon13			TAACCTTGAAACC	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1957A>G	chr8.hg19:g.113812406T>C	ENSP00000297405:p.Lys653Glu	118.0	0.0		118.0	31.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.804756	0.90623	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.18960	2.18;2.18;2.18;2.18	5.83	5.83	0.93111	CUB (5);	0.000000	0.85682	D	0.000000	T	0.37892	0.1020	L	0.58354	1.805	0.40474	D	0.980372	D;D;D	0.67145	0.989;0.996;0.992	P;D;D	0.67382	0.736;0.95;0.951	T	0.18178	-1.0345	10	0.07175	T	0.84	.	16.2002	0.82067	0.0:0.0:0.0:1.0	.	549;653;613	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	E	613;653;549;653	ENSP00000345799:K613E;ENSP00000297405:K653E;ENSP00000412263:K549E;ENSP00000343124:K653E	ENSP00000297405:K653E	K	-	1	0	CSMD3	113881582	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.864000	0.87037	2.231000	0.72958	0.454000	0.30748	AAG	.	.		0.363	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113812406	T	C	113812406	3	2	5	1	0	0	0	0	1	0	0	0	3948	1821	63	2	9402	2	CSMD3	8	113812406	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10		113812406	32551616	25	436										
NRBP2	340371	hgsc.bcm.edu	37	chr8	144917875	144917876	+	Frame_Shift_Ins	INS	-	-	AGGCGGCCAGCTTCAT													0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gaggaaggtgctctccaggaINSaggcggccagcttcatccgg							TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr8:144917875_144917876insAGGCGGCCAGCTTCAT	ENST00000442628.2	-	18	1601_1602	c.1462_1463insATGAAGCTGGCCGCCT	c.(1462-1464)ttcfs	p.F488fs	RP11-299M14.2_ENST00000534006.1_RNA|NRBP2_ENST00000327830.5_Frame_Shift_Ins_p.F245fs	NM_178564.3	NP_848659.2			nuclear receptor binding protein 2											central_nervous_system(2)|kidney(1)|large_intestine(2)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GCTCTCCAGGAAGGCGGCCAGC	0.738																																					p.F488fs		Atlas-Indel,Pindel	.											.	NRBP2	20	.	0			c.1463_1464insATGAAGCTGGCCGCCT						.																																			SO:0001589	frameshift_variant	340371	exon18			.	BC037396	CCDS34959.1, CCDS34959.2	8q24.3	2005-01-24							19339	protein-coding gene	gene with protein product		615563				14702039	Standard	NM_178564		Approved	DKFZp434P086	uc011lkt.2	Q9NSY0		ENST00000442628.2:c.1447_1462dupATGAAGCTGGCCGCCT	chr8.hg19:g.144917875_144917876insAGGCGGCCAGCTTCAT	ENSP00000414055:p.Phe488fs	181.0	0.0		126.0	10.0	NM_178564		Frame_Shift_Ins	INS	ENST00000442628.2	hg19	CCDS34959.2																																																																																			.	.		0.738	NRBP2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382247.1	NM_178564		AGGCGGCCAGCTTCAT	144917876	-	AGGCGGCCAGCTTCAT	144917875	7	5	5	1	0	1	1	0	0	0	0	0	10652	246	9	0	46	0	NRBP2	8	144917875	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GV-01A-11D-A382-10	31105469	144917875	1446147	26	437										
NRARP	441478	hgsc.bcm.edu	37	chr9	140196211	140196211	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ggttgccgtcgatgaccgacTggtgcagcgccgtctggccc	15	14	1	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr9:140196211T>C	ENST00000356628.2	-	1	492	c.170A>G	c.(169-171)cAg>cGg	p.Q57R		NM_001004354.2	NP_001004354.1	Q7Z6K4	NRARP_HUMAN	NOTCH-regulated ankyrin repeat protein	57					blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of Notch signaling pathway involved in somitogenesis (GO:1902367)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|patterning of blood vessels (GO:0001569)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of endothelial cell proliferation (GO:0001938)|regulation of cell-cell adhesion (GO:0022407)|somite rostral/caudal axis specification (GO:0032525)					lung(3)	3	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.185)	OV - Ovarian serous cystadenocarcinoma(145;9.07e-05)|Epithelial(140;0.000273)		GATGACCGACTGGTGCAGCGC	0.647																																					p.Q57R		Atlas-SNP	.											.	NRARP	7	.	0			c.A170G						.						47	36	40					9																	140196211		2202	4298	6500	SO:0001583	missense	441478	exon1			ACCGACTGGTGCA		CCDS35188.1	9q34.3	2013-01-10			ENSG00000198435	ENSG00000198435		"Ankyrin repeat domain containing"	33843	protein-coding gene	gene with protein product							Standard	NM_001004354		Approved	MGC61598	uc004cmo.2	Q7Z6K4	OTTHUMG00000156150	ENST00000356628.2:c.170A>G	chr9.hg19:g.140196211T>C	ENSP00000349041:p.Gln57Arg	117.0	0.0		87.0	26.0	NM_001004354	B8A4K5	Missense_Mutation	SNP	ENST00000356628.2	hg19	CCDS35188.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.618422	0.46736	.	.	ENSG00000198435	ENST00000356628	T	0.63913	-0.07	3.57	3.57	0.40892	Ankyrin repeat-containing domain (4);	0.000000	0.85682	U	0.000000	T	0.47284	0.1437	N	0.03608	-0.345	0.48511	D	0.999662	P	0.52061	0.95	P	0.54629	0.757	T	0.43814	-0.9368	10	0.25106	T	0.35	.	10.1757	0.42937	0.0:0.0:0.0:1.0	.	57	Q7Z6K4	NRARP_HUMAN	R	57	ENSP00000349041:Q57R	ENSP00000349041:Q57R	Q	-	2	0	NRARP	139316032	1.000000	0.71417	0.998000	0.56505	0.012000	0.07955	1.744000	0.38268	1.517000	0.48917	0.439000	0.28862	CAG	.	.		0.647	NRARP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343196.1	NM_001004354		C	140196211	T	C	140196211	3	2	5	1	0	0	0	0	1	0	0	0	10648	1580	55	2	178	2	NRARP	9	140196211	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10		140196211	1017220	27	438										
PPRC1	23082	hgsc.bcm.edu	37	chr10	103906507	103906507	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	actgctggccaaagccaaatCtcctaagtccaccgcccagg	8	16	1	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr10:103906507C>G	ENST00000278070.2	+	9	3797	c.3758C>G	c.(3757-3759)tCt>tGt	p.S1253C	PPRC1_ENST00000489648.1_Intron|PPRC1_ENST00000370012.1_Missense_Mutation_p.S220C|PPRC1_ENST00000413464.2_Intron	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	1253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		AAAGCCAAATCTCCTAAGTCC	0.617																																					p.S1253C		Atlas-SNP	.											.	PPRC1	151	.	0			c.C3758G						.						71	67	68					10																	103906507		2203	4300	6503	SO:0001583	missense	23082	exon9			CCAAATCTCCTAA	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.3758C>G	chr10.hg19:g.103906507C>G	ENSP00000278070:p.Ser1253Cys	118.0	0.0		92.0	27.0	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	hg19	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.373013	0.61624	.	.	ENSG00000148840	ENST00000278070;ENST00000370012	T;T	0.35236	1.67;1.32	5.31	5.31	0.75309	.	0.507716	0.22087	N	0.064812	T	0.57784	0.2077	L	0.56769	1.78	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.71870	0.975;0.945	T	0.59542	-0.7435	10	0.72032	D	0.01	.	17.9755	0.89126	0.0:1.0:0.0:0.0	.	1133;1253	Q5VV67-2;Q5VV67	.;PPRC1_HUMAN	C	1253;220	ENSP00000278070:S1253C;ENSP00000359029:S220C	ENSP00000278070:S1253C	S	+	2	0	PPRC1	103896497	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.458000	0.45014	2.492000	0.84095	0.462000	0.41574	TCT	.	.		0.617	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		G	103906507	C	G	103906507	3	3	5	1	0	0	0	0	1	0	0	0	12422	913	32	4	3792	4	PPRC1	10	103906507	Missense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10		103906507	31628240	28	439										
TDRD1	56165	hgsc.bcm.edu	37	chr10	115981225	115981225	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ttgttttatgctctaccaaaAgggatgccaggtaagaaacc	9	8	1	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr10:115981225A>G	ENST00000369280.1	+	20	3340	c.2880A>G	c.(2878-2880)aaA>aaG	p.K960K	TDRD1_ENST00000251864.2_Silent_p.K960K|TDRD1_ENST00000369282.1_Silent_p.K960K|TDRD1_ENST00000369281.2_Silent_p.K846K|TDRD1_ENST00000422662.1_Silent_p.K564K			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	960					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		CTCTACCAAAAGGGATGCCAG	0.368																																					p.K960K		Atlas-SNP	.											.	TDRD1	126	.	0			c.A2880G						.						99	103	101					10																	115981225		2203	4300	6503	SO:0001819	synonymous_variant	56165	exon20			ACCAAAAGGGATG	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.2880A>G	chr10.hg19:g.115981225A>G		189.0	0.0		112.0	5.0	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Silent	SNP	ENST00000369280.1	hg19																																																																																				.	.		0.368	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			G	115981225	A	G	115981225	2	3	5	1	0	0	0	0	0	0	0	1	15745	69	3	2		2	TDRD1	10	115981225	Silent	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10	12074718	115981225	19553522	29	440										
ZNF143	7702	hgsc.bcm.edu	37	chr11	9494252	9494252	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	aacttagaaaatatggaaggCgtaagcttgcaagcagtaac	10	6	0	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr11:9494252C>T	ENST00000396602.2	+	3	260	c.141C>T	c.(139-141)ggC>ggT	p.G47G	ZNF143_ENST00000299606.2_Silent_p.G47G|ZNF143_ENST00000396597.3_Intron|ZNF143_ENST00000396604.1_Silent_p.G47G|ZNF143_ENST00000530463.1_Silent_p.G47G	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	47					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		ATATGGAAGGCGTAAGCTTGC	0.338																																					p.G47G		Atlas-SNP	.											.	ZNF143	38	.	0			c.C141T						.						143	138	140					11																	9494252		2201	4294	6495	SO:0001819	synonymous_variant	7702	exon3			GGAAGGCGTAAGC	U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"Zinc fingers, C2H2-type"	12928	protein-coding gene	gene with protein product		603433	"zinc finger protein 143 (clone pHZ-1)"				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.141C>T	chr11.hg19:g.9494252C>T		135.0	0.0		101.0	23.0	NM_003442	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Silent	SNP	ENST00000396602.2	hg19	CCDS7799.2																																																																																			.	.		0.338	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442		T	9494252	C	T	9494252	2	4	5	1	0	0	0	0	0	0	0	1	17747	755	27	1		1	ZNF143	11	9494252	Silent	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10		9494252	125512264	30	441										
P4HA3	283208	hgsc.bcm.edu	37	chr11	74013578	74013578	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	catcagggcccttgctgctcCctcaaggtcctcaaaggctg	10	15	3	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr11:74013578C>G	ENST00000331597.4	-	3	448	c.403G>C	c.(403-405)Gga>Cga	p.G135R	P4HA3_ENST00000427714.2_Missense_Mutation_p.G135R	NM_182904.3	NP_878907.1	Q7Z4N8	P4HA3_HUMAN	prolyl 4-hydroxylase, alpha polypeptide III	135						endoplasmic reticulum (GO:0005783)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			NS(1)|biliary_tract(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(1)	15	Breast(11;2.31e-05)					CTTGCTGCTCCCTCAAGGTCC	0.522																																					p.G135R		Atlas-SNP	.											.	P4HA3	43	.	0			c.G403C						.						106	103	104					11																	74013578		2200	4293	6493	SO:0001583	missense	283208	exon3			CTGCTCCCTCAAG	AY327887	CCDS8230.1, CCDS73347.1	11q13	2008-12-09	2008-12-09			ENSG00000149380			30135	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(III)"	608987	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III"			14500733	Standard	XM_005273924		Approved	C-P4Halpha(III)	uc001ouz.3	Q7Z4N8		ENST00000331597.4:c.403G>C	chr11.hg19:g.74013578C>G	ENSP00000332170:p.Gly135Arg	129.0	0.0		113.0	37.0	NM_182904	A0AV13|B4DUD3|Q5EBL3|Q5JPA9	Missense_Mutation	SNP	ENST00000331597.4	hg19	CCDS8230.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.651672	0.88056	.	.	ENSG00000149380	ENST00000331597;ENST00000427714	T;T	0.61859	0.2;0.07	4.96	4.96	0.65561	Prolyl 4-hydroxylase alpha-subunit, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79179	0.4402	M	0.87328	2.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82705	-0.0325	10	0.87932	D	0	-16.4985	16.0853	0.81042	0.0:1.0:0.0:0.0	.	135;135	B4DUD3;Q7Z4N8	.;P4HA3_HUMAN	R	135	ENSP00000332170:G135R;ENSP00000401749:G135R	ENSP00000332170:G135R	G	-	1	0	P4HA3	73691226	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.520000	0.73773	2.727000	0.93392	0.563000	0.77884	GGA	.	.		0.522	P4HA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382988.1	NM_182904		G	74013578	C	G	74013578	3	3	5	1	0	0	0	0	1	0	0	0	11367	632	22	4	1275	4	P4HA3	11	74013578	Missense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10	64519326	74013578	60992938	31	442										
GRIK4	2900	hgsc.bcm.edu	37	chr11	120690494	120690494	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	tcaaagtggccccagaggagTtcgtcaagttccagttccag	11	11	2	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr11:120690494T>C	ENST00000527524.2	+	6	663	c.376T>C	c.(376-378)Ttc>Ctc	p.F126L	GRIK4_ENST00000438375.2_Missense_Mutation_p.F126L	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	126					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.F126L(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		CCCAGAGGAGTTCGTCAAGTT	0.532																																					p.F126L		Atlas-SNP	.											GRIK4,NS,carcinoma,-2,1	GRIK4	149	.	1	Substitution - Missense(1)	large_intestine(1)	c.T376C						.						235	241	239					11																	120690494		2203	4299	6502	SO:0001583	missense	2900	exon4			GAGGAGTTCGTCA	S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.376T>C	chr11.hg19:g.120690494T>C	ENSP00000435648:p.Phe126Leu	131.0	1.0		95.0	24.0	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	hg19	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.300088	0.23650	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.21361	2.01;2.01	4.27	4.27	0.50696	Extracellular ligand-binding receptor (1);	0.099966	0.64402	D	0.000002	T	0.12178	0.0296	N	0.16478	0.41	0.38613	D	0.950951	B;B	0.06786	0.0;0.001	B;B	0.08055	0.003;0.003	T	0.09662	-1.0664	10	0.09843	T	0.71	.	13.5674	0.61826	0.0:0.0:0.0:1.0	.	126;126	A6H8K8;Q16099	.;GRIK4_HUMAN	L	126	ENSP00000435648:F126L;ENSP00000404063:F126L	ENSP00000404063:F126L	F	+	1	0	GRIK4	120195704	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	5.933000	0.70130	1.782000	0.52362	0.459000	0.35465	TTC	.	.		0.532	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		C	120690494	T	C	120690494	3	2	5	1	0	0	0	0	1	0	0	0	6785	1725	60	2	390	2	GRIK4	11	120690494	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10	46676916	120690494	14316022	32	443										
KRT1	3848	hgsc.bcm.edu	37	chr12	53069229	53069229	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gagccatagctgccacctccGgagccgtagctgctacctcc	10	17	0	0	rs540699806|rs267607656	byFrequency	TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr12:53069229G>A	ENST00000252244.3	-	9	1741	c.1683C>T	c.(1681-1683)tcC>tcT	p.S561S		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	561	Gly/Ser-rich.|Tail.		Missing (in allele 1B). {ECO:0000269|PubMed:1281859}.		complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						tgccacctccggagccgtagc	0.692																																					p.S561S		Atlas-SNP	.											.	KRT1	110	.	0			c.C1683T						.						4	4	4					12																	53069229		1797	3656	5453	SO:0001819	synonymous_variant	3848	exon9			ACCTCCGGAGCCG	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1683C>T	chr12.hg19:g.53069229G>A		51.0	0.0		42.0	8.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Silent	SNP	ENST00000252244.3	hg19	CCDS8836.1																																																																																			.	.		0.692	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		A	53069229	G	A	53069229	2	1	5	1	0	0	0	0	0	0	0	1	8456	1103	39	1		1	KRT1	12	53069229	Silent	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10		53069229	80782666	33	444										
KRT79	338785	hgsc.bcm.edu	37	chr12	53225368	53225368	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ctgctcctgcagcagtgcccActtggtctccagcaccttat	8	16	1	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr12:53225368A>G	ENST00000330553.5	-	2	554	c.520T>C	c.(520-522)Tgg>Cgg	p.W174R		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	174	Coil 1A.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGCAGTGCCCACTTGGTCTCC	0.607																																					p.W174R		Atlas-SNP	.											.	KRT79	78	.	0			c.T520C						.						72	63	66					12																	53225368		2203	4300	6503	SO:0001583	missense	338785	exon2			GTGCCCACTTGGT	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"-", "Intermediate filaments type II, keratins (basic)"	28930	protein-coding gene	gene with protein product	"keratin 6-like"	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.520T>C	chr12.hg19:g.53225368A>G	ENSP00000328358:p.Trp174Arg	58.0	0.0		66.0	25.0	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	hg19	CCDS8839.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.155441	0.78114	.	.	ENSG00000185640	ENST00000330553	T	0.77229	-1.08	4.39	4.39	0.52855	Filament (1);	0.000000	0.46442	D	0.000287	D	0.88771	0.6527	M	0.86953	2.85	0.53688	D	0.99997	D	0.89917	1.0	D	0.85130	0.997	D	0.90735	0.4645	10	0.87932	D	0	.	13.8135	0.63276	1.0:0.0:0.0:0.0	.	174	Q5XKE5	K2C79_HUMAN	R	174	ENSP00000328358:W174R	ENSP00000328358:W174R	W	-	1	0	KRT79	51511635	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.139000	0.94554	2.200000	0.70718	0.459000	0.35465	TGG	.	.		0.607	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		G	53225368	A	G	53225368	3	3	5	1	0	0	0	0	1	0	0	0	8501	159	6	2	1119	2	KRT79	12	53225368	Missense_Mutation	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10	156139	53225368	80626527	34	445										
GNPTAB	79158	hgsc.bcm.edu	37	chr12	102190473	102190473	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	accgattctgaaaggactttCcagcaatattgtctctatag	7	9	2	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr12:102190473C>A	ENST00000299314.7	-	2	447	c.185G>T	c.(184-186)gGa>gTa	p.G62V	GNPTAB_ENST00000549165.1_Missense_Mutation_p.G62V|GNPTAB_ENST00000392919.4_Missense_Mutation_p.G62V|RNU6-172P_ENST00000411000.1_RNA|GNPTAB_ENST00000549940.1_Missense_Mutation_p.G62V	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	62					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						AAAGGACTTTCCAGCAATATT	0.353																																					p.G62V		Atlas-SNP	.											.	GNPTAB	120	.	0			c.G185T						.						119	118	118					12																	102190473		2203	4300	6503	SO:0001583	missense	79158	exon2			GACTTTCCAGCAA	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"EF-hand domain containing"	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.185G>T	chr12.hg19:g.102190473C>A	ENSP00000299314:p.Gly62Val	134.0	0.0		127.0	40.0	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Missense_Mutation	SNP	ENST00000299314.7	hg19	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.635587	0.87760	.	.	ENSG00000111670	ENST00000299314;ENST00000549940;ENST00000547090;ENST00000392919;ENST00000549165	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.80586	0.4651	M	0.76328	2.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.992;0.999	T	0.81493	-0.0908	10	0.87932	D	0	-22.1692	19.7169	0.96124	0.0:1.0:0.0:0.0	.	62;62	Q3T906-2;Q3T906	.;GNPTA_HUMAN	V	62	ENSP00000299314:G62V;ENSP00000449150:G62V;ENSP00000376651:G62V;ENSP00000450413:G62V	ENSP00000299314:G62V	G	-	2	0	GNPTAB	100714604	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.271000	0.78506	2.763000	0.94921	0.561000	0.74099	GGA	.	.		0.353	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			A	102190473	C	A	102190473	3	1	5	1	0	0	0	0	1	0	0	0	6553	855	30	3	3665	3	GNPTAB	12	102190473	Missense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10	48965105	102190473	31661422	35	446										
CARKD	55739	hgsc.bcm.edu	37	chr13	111287890	111287890	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	aagccctgggcaacgtgacgGtggtccagaaaggagagcgc	16	10	0	3			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr13:111287890G>T	ENST00000309957.2	+	8	741	c.727G>T	c.(727-729)Gtg>Ttg	p.V243L	CARKD_ENST00000470164.2_3'UTR|CARKD_ENST00000424185.2_Missense_Mutation_p.V133L|CARKD_ENST00000458711.2_Missense_Mutation_p.V112L	NM_001242881.1|NM_018210.3	NP_001229810.1|NP_060680.2			carbohydrate kinase domain containing											NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	15						CAACGTGACGGTGGTCCAGAA	0.602																																					p.V243L		Atlas-SNP	.											.	CARKD	36	.	0			c.G727T						.						155	140	145					13																	111287890		2203	4300	6503	SO:0001583	missense	55739	exon8			GTGACGGTGGTCC	AF151071	CCDS9513.1, CCDS55903.1	13q34	2008-12-19			ENSG00000213995	ENSG00000213995			25576	protein-coding gene	gene with protein product		615910					Standard	NM_018210		Approved	LP3298, FLJ10769	uc001vrc.3	Q8IW45	OTTHUMG00000017345	ENST00000309957.2:c.727G>T	chr13.hg19:g.111287890G>T	ENSP00000311984:p.Val243Leu	107.0	0.0		98.0	27.0	NM_018210		Missense_Mutation	SNP	ENST00000309957.2	hg19	CCDS9513.1	.	.	.	.	.	.	.	.	.	.	G	8.494	0.862762	0.17178	.	.	ENSG00000213995	ENST00000458711;ENST00000424185;ENST00000439607;ENST00000309957	T;T;T	0.32515	1.45;1.45;1.45	4.86	-0.414	0.12359	Uncharacterised domain, carbohydrate kinase-related (3);	0.546729	0.18973	N	0.126094	T	0.20047	0.0482	L	0.35542	1.07	0.36066	D	0.841801	B;B;B;B;B	0.30824	0.008;0.033;0.04;0.296;0.04	B;B;B;B;B	0.29353	0.022;0.044;0.06;0.101;0.074	T	0.14615	-1.0466	10	0.38643	T	0.18	-9.5232	10.0796	0.42381	0.596:0.0:0.404:0.0	.	112;133;225;243;243	B4DQR1;Q8IW45-4;B4DKX7;Q8IW45-2;Q8IW45	.;.;.;.;CARKD_HUMAN	L	112;133;225;243	ENSP00000412789:V112L;ENSP00000413191:V133L;ENSP00000311984:V243L	ENSP00000311984:V243L	V	+	1	0	CARKD	110085891	0.000000	0.05858	0.001000	0.08648	0.234000	0.25298	-0.335000	0.07873	0.044000	0.15775	0.462000	0.41574	GTG	.	.		0.602	CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210		T	111287890	G	T	111287890	3	4	5	1	0	0	0	0	1	0	0	0	2656	1261	44	3	757	3	CARKD	13	111287890	Missense_Mutation	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10		111287890	3881988	36	447										
JPH4	84502	hgsc.bcm.edu	37	chr14	24044991	24044991	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ctccttaaccttgccccgccGaagggccagaggcaggagac	12	15	0	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr14:24044991G>A	ENST00000397118.3	-	4	1956	c.1054C>T	c.(1054-1056)Cgg>Tgg	p.R352W	JPH4_ENST00000544177.1_5'Flank|JPH4_ENST00000356300.4_Missense_Mutation_p.R352W	NM_032452.2	NP_115828.2	Q96JJ6	JPH4_HUMAN	junctophilin 4	352					calcium ion transport into cytosol (GO:0060402)|learning (GO:0007612)|neuromuscular process controlling balance (GO:0050885)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic plasticity (GO:0048167)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)				endometrium(1)|large_intestine(2)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		TTGCCCCGCCGAAGGGCCAGA	0.721																																					p.R352W		Atlas-SNP	.											.	JPH4	64	.	0			c.C1054T						.						6	6	6					14																	24044991		1924	3854	5778	SO:0001583	missense	84502	exon3			CCCGCCGAAGGGC	AB058734	CCDS9603.1	14q11	2004-05-28	2004-05-28	2004-05-28	ENSG00000092051	ENSG00000092051			20156	protein-coding gene	gene with protein product			"junctophilin like 1"	JPHL1		11347906	Standard	NM_032452		Approved	KIAA1831	uc001wkr.2	Q96JJ6	OTTHUMG00000028769	ENST00000397118.3:c.1054C>T	chr14.hg19:g.24044991G>A	ENSP00000380307:p.Arg352Trp	156.0	0.0		139.0	39.0	NM_001146028	D3DS53|Q8ND44|Q96DQ0	Missense_Mutation	SNP	ENST00000397118.3	hg19	CCDS9603.1	.	.	.	.	.	.	.	.	.	.	.	11.05	1.524308	0.27299	.	.	ENSG00000092051	ENST00000356300;ENST00000397118;ENST00000543864;ENST00000267407	T;T	0.61859	0.07;0.07	4.07	0.146	0.14833	.	.	.	.	.	T	0.64713	0.2623	M	0.66439	2.03	0.09310	N	1	D;D	0.76494	0.999;0.981	P;P	0.57679	0.825;0.639	T	0.54788	-0.8241	9	0.87932	D	0	.	7.3026	0.26430	0.0:0.1334:0.4568:0.4098	.	352;352	A8K396;Q96JJ6	.;JPH4_HUMAN	W	352;352;352;353	ENSP00000348648:R352W;ENSP00000380307:R352W	ENSP00000267407:R353W	R	-	1	2	JPH4	23114831	0.002000	0.14202	0.235000	0.24058	0.002000	0.02628	0.410000	0.21098	0.190000	0.20209	-0.176000	0.13171	CGG	.	.		0.721	JPH4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413853.1	NM_032452		A	24044991	G	A	24044991	3	1	5	1	0	0	0	0	1	0	0	0	7972	1057	37	1	848	1	JPH4	14	24044991	Missense_Mutation	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10		24044991	83304549	37	448										
RGS6	9628	hgsc.bcm.edu	37	chr14	72976961	72976961	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	cagtttctacgattcctggaGtccgaattcagttcagaaaa	8	9	3	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr14:72976961G>T	ENST00000553530.1	+	14	1272	c.1065G>T	c.(1063-1065)gaG>gaT	p.E355D	RGS6_ENST00000407322.4_Missense_Mutation_p.E355D|RGS6_ENST00000555571.1_Missense_Mutation_p.E355D|RGS6_ENST00000343854.6_Missense_Mutation_p.E318D|RGS6_ENST00000355512.6_Missense_Mutation_p.E355D|RGS6_ENST00000434263.2_Missense_Mutation_p.E286D|RGS6_ENST00000554782.1_Missense_Mutation_p.E216D|RGS6_ENST00000404301.2_Missense_Mutation_p.E355D|RGS6_ENST00000402788.2_Missense_Mutation_p.E355D|RGS6_ENST00000406236.4_Missense_Mutation_p.E355D|RGS6_ENST00000553525.1_Missense_Mutation_p.E355D|RGS6_ENST00000556437.1_Missense_Mutation_p.E355D	NM_001204417.1|NM_001204418.1|NM_001204420.1|NM_001204421.1|NM_001204422.1|NM_004296.5	NP_001191346.1|NP_001191347.1|NP_001191349.1|NP_001191350.1|NP_001191351.1|NP_004287.3	P49758	RGS6_HUMAN	regulator of G-protein signaling 6	355	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neuron differentiation (GO:0045666)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		GATTCCTGGAGTCCGAATTCA	0.473																																					p.E355D	Ovarian(143;1926 2468 21071 48641)	Atlas-SNP	.											.	RGS6	92	.	0			c.G1065T						.						97	109	105					14																	72976961		2203	4300	6503	SO:0001583	missense	9628	exon14			CCTGGAGTCCGAA	AF073920	CCDS9808.1, CCDS55924.1, CCDS73655.1	14q24.3	2008-07-28	2007-08-14			ENSG00000182732		"Regulators of G-protein signaling"	10002	protein-coding gene	gene with protein product		603894	"regulator of G-protein signalling 6"			10083744, 14734556	Standard	NM_004296		Approved		uc010ttn.2	P49758		ENST00000553530.1:c.1065G>T	chr14.hg19:g.72976961G>T	ENSP00000452331:p.Glu355Asp	110.0	0.0		89.0	27.0	NM_001204424	C9JE95|F8W7W5|O75576|O75577|Q7Z4K3|Q7Z4K4|Q7Z4K5|Q7Z4K6|Q8TE13|Q8TE14|Q8TE15|Q8TE16|Q8TE17|Q8TE18|Q8TE19|Q8TE20|Q8TE21|Q8TE22|Q9UDS8|Q9UDT0|Q9Y245|Q9Y647	Missense_Mutation	SNP	ENST00000553530.1	hg19	CCDS9808.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.385715	0.42308	.	.	ENSG00000182732	ENST00000553525;ENST00000555571;ENST00000553530;ENST00000556437;ENST00000355512;ENST00000404301;ENST00000406236;ENST00000407322;ENST00000402788;ENST00000343854;ENST00000453330;ENST00000434263;ENST00000554782;ENST00000535521	T;T;T;T;T;T;T;T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43	5.72	3.88	0.44766	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.40595	0.1123	L	0.41124	1.26	0.58432	D	0.999993	D;B;D;B	0.63880	0.993;0.002;0.993;0.001	D;B;D;B	0.66084	0.941;0.028;0.941;0.026	T	0.10497	-1.0627	10	0.33141	T	0.24	-0.5822	10.4952	0.44772	0.2123:0.0:0.7877:0.0	.	286;355;360;355	B7Z7N5;P49758-2;Q59FJ8;P49758	.;.;.;RGS6_HUMAN	D	355;355;355;355;355;355;355;355;355;318;327;286;216;216	ENSP00000451030:E355D;ENSP00000450936:E355D;ENSP00000452331:E355D;ENSP00000451855:E355D;ENSP00000347699:E355D;ENSP00000385243:E355D;ENSP00000384218:E355D;ENSP00000384612:E355D;ENSP00000383953:E355D;ENSP00000341199:E318D;ENSP00000412144:E286D;ENSP00000451912:E216D	ENSP00000341199:E318D	E	+	3	2	RGS6	72046714	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	2.134000	0.42102	1.566000	0.49654	-0.140000	0.14226	GAG	.	.		0.473	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2			T	72976961	G	T	72976961	3	4	5	1	0	0	0	0	1	0	0	0	13324	1020	36	3	1115	3	RGS6	14	72976961	Missense_Mutation	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10	48931970	72976961	34372579	38	449										
TTBK2	146057	hgsc.bcm.edu	37	chr15	43045067	43045067	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	acaatgctgccctctacttaActtctcatcttcattatctg	3	13	5	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr15:43045067A>C	ENST00000267890.6	-	14	2485	c.2377T>G	c.(2377-2379)Tta>Gta	p.L793V		NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	793					cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		CCTCTACTTAACTTCTCATCT	0.408																																					p.L793V		Atlas-SNP	.											.	TTBK2	82	.	0			c.T2377G						.						143	130	134					15																	43045067		1880	4111	5991	SO:0001583	missense	146057	exon14			TACTTAACTTCTC	AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"spinocerebellar ataxia 11"	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.2377T>G	chr15.hg19:g.43045067A>C	ENSP00000267890:p.Leu793Val	110.0	0.0		113.0	41.0	NM_173500	O94932|Q6ZN52|Q8IVV1	Missense_Mutation	SNP	ENST00000267890.6	hg19	CCDS42029.1	.	.	.	.	.	.	.	.	.	.	A	9.946	1.218788	0.22373	.	.	ENSG00000128881	ENST00000267890;ENST00000399479;ENST00000263802	T	0.38560	1.13	5.87	3.54	0.40534	.	0.509864	0.19169	N	0.120996	T	0.29976	0.0750	L	0.41236	1.265	0.44668	D	0.997651	B;B	0.20052	0.041;0.024	B;B	0.14578	0.011;0.007	T	0.09422	-1.0675	10	0.37606	T	0.19	.	5.7807	0.18304	0.7151:0.0:0.2849:0.0	.	724;793	Q6IQ55-2;Q6IQ55	.;TTBK2_HUMAN	V	793;723;1198	ENSP00000267890:L793V	ENSP00000263802:L1198V	L	-	1	2	TTBK2	40832359	0.681000	0.27614	0.981000	0.43875	0.814000	0.46013	1.522000	0.35921	1.009000	0.39289	0.533000	0.62120	TTA	.	.		0.408	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500		C	43045067	A	C	43045067	3	2	5	1	0	0	0	0	1	0	0	0	16692	40	2	5	1365	5	TTBK2	15	43045067	Missense_Mutation	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10		43045067	59486325	39	450										
C16orf45	89927	hgsc.bcm.edu	37	chr16	15609232	15609232	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	attgagctggagatggcaaaAattcagcgtctccgggaagt	13	7	2	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr16:15609232A>C	ENST00000300006.4	+	2	536	c.177A>C	c.(175-177)aaA>aaC	p.K59N	C16orf45_ENST00000452191.2_Missense_Mutation_p.K42N|C16orf45_ENST00000566490.1_Missense_Mutation_p.K59N|C16orf45_ENST00000561692.1_Missense_Mutation_p.K11N	NM_033201.2	NP_149978.1	Q96MC5	CP045_HUMAN	chromosome 16 open reading frame 45	59										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)	11						AGATGGCAAAAATTCAGCGTC	0.522																																					p.K59N		Atlas-SNP	.											.	C16orf45	24	.	0			c.A177C						.						130	110	116					16																	15609232		2197	4300	6497	SO:0001583	missense	89927	exon2			GGCAAAAATTCAG	AK057180	CCDS10561.1, CCDS45422.1	16p13.2	2012-10-09			ENSG00000166780	ENSG00000166780			19213	protein-coding gene	gene with protein product							Standard	NM_033201		Approved	FLJ32618	uc002ddo.3	Q96MC5	OTTHUMG00000129883	ENST00000300006.4:c.177A>C	chr16.hg19:g.15609232A>C	ENSP00000300006:p.Lys59Asn	99.0	0.0		74.0	5.0	NM_033201	O00223|O75769|Q8IZ36|Q96H25	Missense_Mutation	SNP	ENST00000300006.4	hg19	CCDS10561.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.712557	0.68730	.	.	ENSG00000166780	ENST00000300006;ENST00000452191	T;T	0.47177	0.85;0.85	5.14	0.287	0.15714	Domain of unknown function DUF3585 (1);	0.050263	0.85682	D	0.000000	T	0.53158	0.1779	L	0.46741	1.465	0.42261	D	0.992014	D;P	0.67145	0.996;0.922	D;P	0.67382	0.951;0.537	T	0.48246	-0.9052	10	0.48119	T	0.1	-15.9761	8.0631	0.30644	0.6129:0.0:0.3871:0.0	.	3;59	B4DE25;Q96MC5	.;CP045_HUMAN	N	59;42	ENSP00000300006:K59N;ENSP00000408976:K42N	ENSP00000300006:K59N	K	+	3	2	C16orf45	15516733	0.997000	0.39634	0.998000	0.56505	0.982000	0.71751	0.251000	0.18257	-0.013000	0.14199	-0.250000	0.11733	AAA	.	.		0.522	C16orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252130.2	NM_033201		C	15609232	A	C	15609232	3	2	5	1	0	0	0	0	1	0	0	0	1816	11	1	5	242	5	C16orf45	16	15609232	Missense_Mutation	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10		15609232	74745521	40	451										
ABCC12	94160	hgsc.bcm.edu	37	chr16	48139142	48139159	+	In_Frame_Del	DEL	ACACCATGCTTGCAGTGT	ACACCATGCTTGCAGTGT	-													0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gacgccaaacaccagcatgaAcaccatgcttgcagtgtaca					rs139979809		TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	ACACCATGCTTGCAGTGT	ACACCATGCTTGCAGTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr16:48139142_48139159delACACCATGCTTGCAGTGT	ENST00000311303.3	-	19	2909_2926	c.2564_2581delACACTGCAAGCATGGTGT	c.(2563-2583)tacactgcaagcatggtgttc>ttc	p.YTASMV855del	ABCC12_ENST00000448542.1_In_Frame_Del_p.YTASMV852del|ABCC12_ENST00000416054.1_3'UTR	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	855	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				ACCAGCATGAACACCATGCTTGCAGTGTACACCCACTG	0.555																																					p.855_861del		Atlas-Indel,Pindel	.											.	ABCC12	190	.	0			c.2565_2582del						.																																			SO:0001651	inframe_deletion	94160	exon19			.	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.2564_2581delACACTGCAAGCATGGTGT	chr16.hg19:g.48139142_48139159delACACCATGCTTGCAGTGT	ENSP00000311030:p.Tyr855_Val860del	119.0	0.0		94.0	18.0	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	In_Frame_Del	DEL	ENST00000311303.3	hg19	CCDS10730.1																																																																																			.	.		0.555	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		-	48139159	ACACCATGCTTGCAGTGT	-	48139142	7	5	5	1	0	1	0	1	0	0	0	0	52	43	2	0	1542	0	ABCC12	16	48139142	In_Frame_Del	DEL	ACACCATGCTTGCAGTGT	TCGA-2Y-A9GV-01A-11D-A382-10	32529910	48139142	42215611	41	452										
CES2	8824	hgsc.bcm.edu	37	chr16	66971949	66971949	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	tctgcccacaggccaggactCagccagtcccatccggacca	9	18	2	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr16:66971949C>G	ENST00000317091.4	+	2	1262	c.278C>G	c.(277-279)tCa>tGa	p.S93*	CES2_ENST00000417689.1_Nonsense_Mutation_p.S93*	NM_003869.5	NP_003860.2	O00748	EST2_HUMAN	carboxylesterase 2	29					catabolic process (GO:0009056)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)			breast(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|urinary_tract(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0663)|Epithelial(162;0.166)	Dabigatran etexilate(DB06695)|Irinotecan(DB00762)|Mycophenolate mofetil(DB00688)|Prasugrel(DB06209)	GGCCAGGACTCAGCCAGTCCC	0.587																																					p.S93X	Ovarian(70;1230 1691 37888 38351)	Atlas-SNP	.											.	CES2	43	.	0			c.C278G						.						57	60	59					16																	66971949		2200	4300	6500	SO:0001587	stop_gained	8824	exon2			AGGACTCAGCCAG	BC032095	CCDS10825.1, CCDS45507.1	16q22.1	2010-10-12	2010-10-12		ENSG00000172831	ENSG00000172831		"Carboxylesterases"	1864	protein-coding gene	gene with protein product		605278	"carboxylesterase 2 (intestine, liver)"			9169443, 9144407, 20931200	Standard	NM_198061		Approved	CE-2, iCE, CES2A1	uc002eqr.3	O00748	OTTHUMG00000137517	ENST00000317091.4:c.278C>G	chr16.hg19:g.66971949C>G	ENSP00000317842:p.Ser93*	92.0	0.0		98.0	34.0	NM_003869	A8K367|Q16859|Q5MAB8|Q7Z366|Q8IUP4|Q8TCP8	Nonsense_Mutation	SNP	ENST00000317091.4	hg19	CCDS10825.1	.	.	.	.	.	.	.	.	.	.	C	44	10.684086	0.99449	.	.	ENSG00000172831	ENST00000417689;ENST00000317091	.	.	.	5.49	5.49	0.81192	.	0.478367	0.16025	N	0.233139	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	11.8073	0.52163	0.1747:0.8253:0.0:0.0	.	.	.	.	X	93	.	ENSP00000317842:S93X	S	+	2	0	CES2	65529450	0.001000	0.12720	0.981000	0.43875	0.819000	0.46315	0.725000	0.25970	2.878000	0.98634	0.650000	0.86243	TCA	.	.		0.587	CES2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268838.2	NM_003869		G	66971949	C	G	66971949	4	3	5	1	0	0	0	0	0	1	0	0	3272	838	29	4	284	4	CES2	16	66971949	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10	18832807	66971949	23382804	42	453										
ATAD5	79915	hgsc.bcm.edu	37	chr17	29203505	29203505	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ccaaaaccttggcaaattatTttaaagtatctcccaaacct	3	11	1	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr17:29203505T>A	ENST00000321990.4	+	15	4099	c.3721T>A	c.(3721-3723)Ttt>Att	p.F1241I		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1241					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				GGCAAATTATTTTAAAGTATC	0.323																																					p.F1241I		Atlas-SNP	.											.	ATAD5	150	.	0			c.T3721A						.						56	58	57					17																	29203505		2203	4300	6503	SO:0001583	missense	79915	exon15			AATTATTTTAAAG		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.3721T>A	chr17.hg19:g.29203505T>A	ENSP00000313171:p.Phe1241Ile	444.0	1.0		386.0	121.0	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	T	32	5.115396	0.94339	.	.	ENSG00000176208	ENST00000321990	T	0.12774	2.65	5.21	5.21	0.72293	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.37489	0.1005	M	0.69823	2.125	0.48696	D	0.999697	D	0.89917	1.0	D	0.87578	0.998	T	0.16100	-1.0414	10	0.66056	D	0.02	.	15.4007	0.74838	0.0:0.0:0.0:1.0	.	1241	Q96QE3	ATAD5_HUMAN	I	1241	ENSP00000313171:F1241I	ENSP00000313171:F1241I	F	+	1	0	ATAD5	26227631	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.230000	0.72301	2.088000	0.63022	0.533000	0.62120	TTT	.	.		0.323	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		A	29203505	T	A	29203505	3	1	5	1	0	0	0	0	1	0	0	0	1076	1841	64	4	3779	4	ATAD5	17	29203505	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10		29203505	51991705	43	454										
GGNBP2	79893	hgsc.bcm.edu	37	chr17	34945743	34945743	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	acagcaatagagaacaatacCgacagcatctgaaggagaaa	9	8	1	3			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr17:34945743C>T	ENST00000304718.4	+	14	2312	c.1996C>T	c.(1996-1998)Cga>Tga	p.R666*	DHRS11_ENST00000590554.1_5'Flank|DHRS11_ENST00000251312.5_5'Flank	NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	666					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)		p.R666R(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		AGAACAATACCGACAGCATCT	0.378																																					p.R666X		Atlas-SNP	.											.	GGNBP2	72	.	1	Substitution - coding silent(1)	lung(1)	c.C1996T						.						137	150	146					17																	34945743		2203	4300	6503	SO:0001587	stop_gained	79893	exon14			CAATACCGACAGC	AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.1996C>T	chr17.hg19:g.34945743C>T	ENSP00000307617:p.Arg666*	179.0	0.0		162.0	17.0	NM_024835	B2RPK7|Q96T90|Q9GZR8|Q9H767	Nonsense_Mutation	SNP	ENST00000304718.4	hg19	CCDS11314.1	.	.	.	.	.	.	.	.	.	.	C	38	6.947687	0.97956	.	.	ENSG00000005955	ENST00000304718	.	.	.	5.85	4.88	0.63580	.	0.124466	0.52532	D	0.000077	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.4774	11.9307	0.52845	0.1375:0.7305:0.1321:0.0	.	.	.	.	X	666	.	ENSP00000307617:R666X	R	+	1	2	GGNBP2	32019856	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.286000	0.51724	1.469000	0.48083	0.561000	0.74099	CGA	.	.		0.378	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		T	34945743	C	T	34945743	4	4	5	1	0	0	0	0	0	1	0	0	6367	644	23	1	2046	1	GGNBP2	17	34945743	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10	5742238	34945743	46249467	44	455										
PTRF	284119	hgsc.bcm.edu	37	chr17	40574761	40574761	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gcgcacggtcttcacgttgaCgctgaccttgcgcaccttct	10	15	3	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr17:40574761C>T	ENST00000357037.5	-	1	774	c.355G>A	c.(355-357)Gtc>Atc	p.V119I		NM_012232.5	NP_036364.2			polymerase I and transcript release factor											breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		TTCACGTTGACGCTGACCTTG	0.642																																					p.V119I		Atlas-SNP	.											.	PTRF	48	.	0			c.G355A						.						41	28	33					17																	40574761		2203	4300	6503	SO:0001583	missense	284119	exon1			CGTTGACGCTGAC	AF000421	CCDS11425.1	17q21.31	2011-04-20				ENSG00000177469			9688	protein-coding gene	gene with protein product		603198				9582279	Standard	NM_012232		Approved	cavin-1, CAVIN1	uc002hzo.3	Q6NZI2		ENST00000357037.5:c.355G>A	chr17.hg19:g.40574761C>T	ENSP00000349541:p.Val119Ile	138.0	0.0		120.0	34.0	NM_012232		Missense_Mutation	SNP	ENST00000357037.5	hg19	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.937490	0.92458	.	.	ENSG00000177469	ENST00000357037;ENST00000357684	T	0.60299	0.2	5.13	5.13	0.70059	.	0.061560	0.64402	D	0.000005	T	0.56140	0.1965	L	0.61218	1.895	0.58432	D	0.999999	B;P	0.35411	0.348;0.5	B;B	0.30401	0.115;0.115	T	0.60541	-0.7243	10	0.48119	T	0.1	-35.7366	18.5736	0.91145	0.0:1.0:0.0:0.0	.	101;119	B4DNU9;Q6NZI2	.;PTRF_HUMAN	I	119;74	ENSP00000349541:V119I	ENSP00000349541:V119I	V	-	1	0	PTRF	37828287	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.967000	0.70403	2.373000	0.80994	0.561000	0.74099	GTC	.	.		0.642	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232		T	40574761	C	T	40574761	3	4	5	1	0	0	0	0	1	0	0	0	12830	536	19	1	825	1	PTRF	17	40574761	Missense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10	5629018	40574761	40620449	45	456										
ITGB3	3690	hgsc.bcm.edu	37	chr17	45369918	45369918	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ttctcctgtgtccgctacaaGggggagatgtgctcaggtga	14	9	2	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr17:45369918G>T	ENST00000559488.1	+	10	1690	c.1674G>T	c.(1672-1674)aaG>aaT	p.K558N	ITGB3_ENST00000435993.2_Missense_Mutation_p.K511N|ITGB3_ENST00000560629.1_Missense_Mutation_p.G547W	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	558	Cysteine-rich tandem repeats.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	TCCGCTACAAGGGGGAGATGT	0.572																																					p.K558N		Atlas-SNP	.											.	ITGB3	157	.	0			c.G1674T						.						103	94	97					17																	45369918		2203	4300	6503	SO:0001583	missense	3690	exon10			CTACAAGGGGGAG		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.1674G>T	chr17.hg19:g.45369918G>T	ENSP00000452786:p.Lys558Asn	1609.0	1.0		1317.0	420.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	hg19	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.811619	0.32053	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.99023	-5.34	5.38	1.83	0.25207	.	0.088163	0.85682	D	0.000000	D	0.95404	0.8508	N	0.10629	0.0099999999999999	0.58432	D	0.999992	P	0.48350	0.909	P	0.45881	0.496	D	0.92662	0.6142	10	0.19147	T	0.46	.	10.8838	0.46955	0.2516:0.0:0.7484:0.0	.	558	P05106	ITB3_HUMAN	N	558;511	ENSP00000407801:K511N	ENSP00000262017:K558N	K	+	3	2	C17orf57	42724917	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.253000	0.32886	0.647000	0.30713	0.462000	0.41574	AAG	.	.		0.572	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		T	45369918	G	T	45369918	3	4	5	1	0	0	0	0	1	0	0	0	7904	991	35	3	1712	3	ITGB3	17	45369918	Missense_Mutation	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10	4795157	45369918	35825292	46	457										
MARCH10	162333	hgsc.bcm.edu	37	chr17	60814029	60814029	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gatttggtgtcccacgaaagAgggctctttttcgcattttc	10	9	1	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr17:60814029A>T	ENST00000311269.5	-	6	1474	c.1200T>A	c.(1198-1200)ccT>ccA	p.P400P	MARCH10_ENST00000544856.2_Silent_p.P399P|RP11-156L14.1_ENST00000582564.1_RNA|RP11-156L14.1_ENST00000584597.1_RNA|RP11-156L14.1_ENST00000577270.1_RNA|MARCH10_ENST00000583600.1_Silent_p.P438P|RP11-156L14.1_ENST00000579201.1_RNA|MARCH10_ENST00000456609.2_Silent_p.P400P	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	400					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						CCCACGAAAGAGGGCTCTTTT	0.517																																					p.P400P		Atlas-SNP	.											.	MARCH10	102	.	0			c.T1200A						.						86	73	78					17																	60814029		2203	4300	6503	SO:0001819	synonymous_variant	162333	exon6			CGAAAGAGGGCTC	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"RING-type (C3HC4) zinc fingers", "MARCH membrane-associated ring fingers"	26655	protein-coding gene	gene with protein product		613337	"ring finger protein 190", "membrane-associated ring finger (C3HC4) 10"	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.1200T>A	chr17.hg19:g.60814029A>T		98.0	0.0		117.0	42.0	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Silent	SNP	ENST00000311269.5	hg19	CCDS11635.1																																																																																			.	.		0.517	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598		T	60814029	A	T	60814029	2	4	5	1	0	0	0	0	0	0	0	1	9308	291	11	4		4	MARCH10	17	60814029	Silent	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10	15444111	60814029	20381181	47	458										
DYM	54808	hgsc.bcm.edu	37	chr18	46798586	46798586	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gttgaagccatcatcttccgTaaggatcaacaatattataa	6	8	3	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr18:46798586T>C	ENST00000269445.6	-	11	1670	c.1213A>G	c.(1213-1215)Acg>Gcg	p.T405A	DYM_ENST00000442713.2_Missense_Mutation_p.T215A	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	405					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						TCATCTTCCGTAAGGATCAAC	0.358																																					p.T405A		Atlas-SNP	.											.	DYM	52	.	0			c.A1213G						.						130	117	121					18																	46798586		2203	4299	6502	SO:0001583	missense	54808	exon11			CTTCCGTAAGGAT	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.1213A>G	chr18.hg19:g.46798586T>C	ENSP00000269445:p.Thr405Ala	297.0	0.0		274.0	67.0	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	hg19	CCDS11937.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.311599	0.81358	.	.	ENSG00000141627	ENST00000418472;ENST00000442713;ENST00000269445	D;D	0.83591	-1.74;-1.74	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.90400	0.6995	M	0.76328	2.33	0.80722	D	1	P;D;P	0.69078	0.762;0.997;0.9	B;D;P	0.80764	0.445;0.994;0.622	D	0.91568	0.5269	10	0.72032	D	0.01	-14.8141	15.0753	0.72071	0.0:0.0:0.0:1.0	.	215;227;405	Q7RTS9-2;Q9NXS9;Q7RTS9	.;.;DYM_HUMAN	A	10;215;405	ENSP00000395942:T215A;ENSP00000269445:T405A	ENSP00000269445:T405A	T	-	1	0	DYM	45052584	1.000000	0.71417	0.985000	0.45067	0.940000	0.58332	7.659000	0.83766	1.981000	0.57761	0.477000	0.44152	ACG	.	.		0.358	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		C	46798586	T	C	46798586	3	2	5	1	0	0	0	0	1	0	0	0	4842	1638	57	2	824	2	DYM	18	46798586	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10		46798586	31278662	48	459										
PLIN4	729359	hgsc.bcm.edu	37	chr19	4511406	4511406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ctttgtacctgttgcgatatTttgggtcgttttcagcccag	10	9	1	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr19:4511406T>C	ENST00000301286.3	-	3	2523	c.2524A>G	c.(2524-2526)Aat>Gat	p.N842D		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	842	27 X 33 AA approximate tandem repeat.			GLKTTQNIA -> SVDTTKTVL (in Ref. 2; BAB67774). {ECO:0000305}.		cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						GTTGCGATATTTTGGGTCGTT	0.597																																					p.N842D		Atlas-SNP	.											.	PLIN4	191	.	0			c.A2524G						.						74	87	83					19																	4511406		1915	4169	6084	SO:0001583	missense	729359	exon3			CGATATTTTGGGT	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"Perilipins"	29393	protein-coding gene	gene with protein product		613247	"KIAA1881"	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2524A>G	chr19.hg19:g.4511406T>C	ENSP00000301286:p.Asn842Asp	167.0	0.0		125.0	12.0	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	hg19	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	T	7.397	0.632036	0.14322	.	.	ENSG00000167676	ENST00000301286	T	0.05319	3.46	4.46	-0.135	0.13477	.	1.776240	0.03525	U	0.221644	T	0.04907	0.0132	L	0.34521	1.04	0.09310	N	1	B	0.21821	0.061	B	0.22386	0.039	T	0.39840	-0.9594	10	0.15952	T	0.53	-4.3924	0.8331	0.01134	0.1661:0.2976:0.1711:0.3651	.	842	Q96Q06	PLIN4_HUMAN	D	842	ENSP00000301286:N842D	ENSP00000301286:N842D	N	-	1	0	PLIN4	4462406	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.733000	0.01850	-0.150000	0.11195	0.379000	0.24179	AAT	.	.		0.597	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		C	4511406	T	C	4511406	3	2	5	1	0	0	0	0	1	0	0	0	12101	1841	64	2	1565	2	PLIN4	19	4511406	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10		4511406	54617577	49	460			1	3		2	2	21	N	T_G	3.940905e-05
PLIN4	729359	hgsc.bcm.edu	37	chr19	4511426	4511426	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	tttgggtcgttttcagcccaGtttgcacagcacccttggcc	10	13	1	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr19:4511426G>A	ENST00000301286.3	-	3	2503	c.2504C>T	c.(2503-2505)aCt>aTt	p.T835I		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	835	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TTTCAGCCCAGTTTGCACAGC	0.597																																					p.T835I		Atlas-SNP	.											.	PLIN4	191	.	0			c.C2504T						.						81	95	90					19																	4511426		1941	4187	6128	SO:0001583	missense	729359	exon3			AGCCCAGTTTGCA	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"Perilipins"	29393	protein-coding gene	gene with protein product		613247	"KIAA1881"	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2504C>T	chr19.hg19:g.4511426G>A	ENSP00000301286:p.Thr835Ile	157.0	0.0		114.0	9.0	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	hg19	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.628418	0.46944	.	.	ENSG00000167676	ENST00000301286	T	0.05319	3.46	4.61	-2.63	0.06133	.	0.782001	0.10634	N	0.651842	T	0.09113	0.0225	M	0.83852	2.665	0.09310	N	1	B	0.29716	0.255	B	0.28991	0.097	T	0.28396	-1.0045	10	0.37606	T	0.19	-0.7363	6.6746	0.23087	0.1849:0.3787:0.4364:0.0	.	835	Q96Q06	PLIN4_HUMAN	I	835	ENSP00000301286:T835I	ENSP00000301286:T835I	T	-	2	0	PLIN4	4462426	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.362000	0.07602	0.023000	0.15187	0.462000	0.41574	ACT	.	.		0.597	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		A	4511426	G	A	4511426	3	1	5	1	0	0	0	0	1	0	0	0	12101	1029	36	3	1585	3	PLIN4	19	4511426	Missense_Mutation	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10	20	4511426	54617557	50	461			1	3		2	2	21	N	T_G	3.940905e-05
EMR1	2015	hgsc.bcm.edu	37	chr19	6937618	6937618	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ccagctcccagtcccagaccTcaaggatcttgctgtcctcc	7	18	2	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr19:6937618T>A	ENST00000312053.4	+	20	2651	c.2614T>A	c.(2614-2616)Tca>Aca	p.S872T	EMR1_ENST00000450315.3_Missense_Mutation_p.S695T|EMR1_ENST00000250572.8_Missense_Mutation_p.S807T|EMR1_ENST00000381407.5_Missense_Mutation_p.S731T|EMR1_ENST00000381404.4_Missense_Mutation_p.S853T	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	872					cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					GTCCCAGACCTCAAGGATCTT	0.567																																					p.S872T		Atlas-SNP	.											.	EMR1	153	.	0			c.T2614A						.						168	137	148					19																	6937618		2203	4300	6503	SO:0001583	missense	2015	exon20			CAGACCTCAAGGA	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.2614T>A	chr19.hg19:g.6937618T>A	ENSP00000311545:p.Ser872Thr	113.0	0.0		93.0	30.0	NM_001974	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	hg19	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	t	10.05	1.244819	0.22796	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07	4.64	3.58	0.41010	.	.	.	.	.	T	0.57681	0.2070	M	0.73962	2.25	0.28012	N	0.934863	D;D;D;D;D	0.76494	0.999;0.999;0.996;0.997;0.997	D;D;D;D;D	0.83275	0.996;0.918;0.987;0.985;0.985	T	0.49826	-0.8898	9	0.17832	T	0.49	.	7.246	0.26121	0.1976:0.0:0.0:0.8024	.	695;731;807;853;872	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	T	807;872;853;807;731;695	ENSP00000311545:S872T;ENSP00000370811:S853T;ENSP00000250572:S807T;ENSP00000370814:S731T;ENSP00000405974:S695T	ENSP00000250572:S807T	S	+	1	0	EMR1	6888618	0.007000	0.16637	0.615000	0.29064	0.012000	0.07955	0.735000	0.26115	0.593000	0.29745	0.529000	0.55759	TCA	.	.		0.567	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			A	6937618	T	A	6937618	3	1	5	1	0	0	0	0	1	0	0	0	5106	1551	54	4	2692	4	EMR1	19	6937618	Missense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10	2426192	6937618	52191365	51	462										
APLP1	333	hgsc.bcm.edu	37	chr19	36363437	36363437	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gatatttactttggcatgccTggggaaatcagtgagcacga	12	7	1	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr19:36363437T>A	ENST00000221891.4	+	7	1095	c.903T>A	c.(901-903)ccT>ccA	p.P301P	APLP1_ENST00000586861.1_Silent_p.P295P|APLP1_ENST00000537454.2_Silent_p.P262P	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	301	O-glycosylated at three sites.				adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TTGGCATGCCTGGGGAAATCA	0.587																																					p.P301P		Atlas-SNP	.											.	APLP1	77	.	0			c.T903A						.						155	151	152					19																	36363437		2203	4300	6503	SO:0001819	synonymous_variant	333	exon7			CATGCCTGGGGAA	U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"amyloid-like protein 1", "amyloid precursor-like protein 1"	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.903T>A	chr19.hg19:g.36363437T>A		178.0	0.0		120.0	35.0	NM_005166	O00113|Q96A92	Silent	SNP	ENST00000221891.4	hg19	CCDS32997.1																																																																																			.	.		0.587	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807		A	36363437	T	A	36363437	2	1	5	1	0	0	0	0	0	0	0	1	778	1567	55	4		4	APLP1	19	36363437	Silent	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10	29425819	36363437	22765546	52	463										
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40581433	40581433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	catcccacattccttacataCaaagggtttctcattggaat	5	11	1	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr19:40581433C>T	ENST00000595687.2	-	6	1125	c.916G>A	c.(916-918)Gta>Ata	p.V306I	ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000450241.2_Missense_Mutation_p.V272I|ZNF780A_ENST00000340963.5_Missense_Mutation_p.V306I|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000455521.1_Missense_Mutation_p.V307I|ZNF780A_ENST00000594395.1_Missense_Mutation_p.V307I	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	306					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TCCTTACATACAAAGGGTTTC	0.383																																					p.V307I		Atlas-SNP	.											.	ZNF780A	156	.	0			c.G919A						.						175	171	173					19																	40581433		2203	4300	6503	SO:0001583	missense	284323	exon6			TACATACAAAGGG	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"Zinc fingers, C2H2-type", "-"	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.916G>A	chr19.hg19:g.40581433C>T	ENSP00000472189:p.Val306Ile	216.0	0.0		186.0	69.0	NM_001142577	E9PB48|Q6ZN87	Missense_Mutation	SNP	ENST00000595687.2	hg19	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	C	14.17	2.454668	0.43634	.	.	ENSG00000197782	ENST00000450241;ENST00000455521;ENST00000340963	T;T	0.07567	3.18;3.18	1.53	1.53	0.23141	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13970	0.0338	L	0.31845	0.965	0.09310	N	1	P;B	0.49185	0.92;0.064	D;B	0.65443	0.935;0.027	T	0.15549	-1.0433	9	0.66056	D	0.02	.	3.9199	0.09239	0.0:0.7579:0.0:0.2421	.	307;306	E9PB48;O75290	.;Z780A_HUMAN	I	306;307;306	ENSP00000400997:V307I;ENSP00000341507:V306I	ENSP00000341507:V306I	V	-	1	0	ZNF780A	45273273	.	.	0.589000	0.28718	0.967000	0.64934	.	.	0.795000	0.33922	0.305000	0.20034	GTA	.	.		0.383	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		T	40581433	C	T	40581433	3	4	5	1	0	0	0	0	1	0	0	0	18167	478	17	3	1140	3	ZNF780A	19	40581433	Missense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10	4217996	40581433	18547550	53	464										
ZNF225	7768	hgsc.bcm.edu	37	chr19	44635631	44635631	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	catactggggagaagccattCaaatgtgatatatgttgtaa	10	5	1	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr19:44635631C>T	ENST00000262894.6	+	5	1144	c.864C>T	c.(862-864)ttC>ttT	p.F288F	ZNF225_ENST00000590612.1_Silent_p.F288F|ZNF225_ENST00000592780.1_3'UTR	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	288					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				AGAAGCCATTCAAATGTGATA	0.413																																					p.F288F		Atlas-SNP	.											.	ZNF225	41	.	0			c.C864T						.						94	99	97					19																	44635631		2200	4298	6498	SO:0001819	synonymous_variant	7768	exon5			GCCATTCAAATGT	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.864C>T	chr19.hg19:g.44635631C>T		160.0	0.0		133.0	38.0	NM_013362	A8K8S2|Q53F12|Q9NS46|Q9UID8	Silent	SNP	ENST00000262894.6	hg19	CCDS46100.1																																																																																			.	.		0.413	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			T	44635631	C	T	44635631	2	4	5	1	0	0	0	0	0	0	0	1	17794	825	29	3		3	ZNF225	19	44635631	Silent	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10	4054198	44635631	14493352	54	465										
SLC23A2	9962	hgsc.bcm.edu	37	chr20	4854660	4854660	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gcgagcatagaagccatactTtgtgctgtcgggagggaaga	15	7	0	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr20:4854660T>A	ENST00000379333.1	-	11	1416	c.1024A>T	c.(1024-1026)Aag>Tag	p.K342*	SLC23A2_ENST00000338244.1_Nonsense_Mutation_p.K342*|SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000424750.2_Nonsense_Mutation_p.K228*	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	342					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						AAGCCATACTTTGTGCTGTCG	0.532																																					p.K342X		Atlas-SNP	.											.	SLC23A2	62	.	0			c.A1024T						.						131	115	120					20																	4854660		2203	4300	6503	SO:0001587	stop_gained	9962	exon11			CATACTTTGTGCT	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"Solute carriers"	10973	protein-coding gene	gene with protein product		603791	"solute carrier family 23 (nucleobase transporters), member 1"	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.1024A>T	chr20.hg19:g.4854660T>A	ENSP00000368637:p.Lys342*	127.0	0.0		114.0	35.0	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Nonsense_Mutation	SNP	ENST00000379333.1	hg19	CCDS13085.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.61|11.61	1.690244|1.690244	0.29962|0.29962	.|.	.|.	ENSG00000089057|ENSG00000089057	ENST00000423430|ENST00000379333;ENST00000338244;ENST00000424750	.|.	.|.	.|.	5.72|5.72	2.25|2.25	0.28309|0.28309	.|.	0.090711|0.090711	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.21227|.	0.0511|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.38090|.	-0.9677|.	4|.	.|0.02654	.|T	.|1	-6.499|-6.499	8.3503|8.3503	0.32299|0.32299	0.0:0.2351:0.0:0.7649|0.0:0.2351:0.0:0.7649	.|.	.|.	.|.	.|.	I|X	98|342;342;228	.|.	.|ENSP00000344322:K342X	K|K	-|-	2|1	0|0	SLC23A2|SLC23A2	4802660|4802660	1.000000|1.000000	0.71417|0.71417	0.029000|0.029000	0.17559|0.17559	0.001000|0.001000	0.01503|0.01503	3.357000|3.357000	0.52277|0.52277	0.125000|0.125000	0.18397|0.18397	-0.256000|-0.256000	0.11100|0.11100	AAA|AAG	.	.		0.532	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			A	4854660	T	A	4854660	4	1	5	1	0	0	0	0	0	1	0	0	14478	1850	64	4	956	4	SLC23A2	20	4854660	Nonsense_Mutation	SNP	T	TCGA-2Y-A9GV-01A-11D-A382-10		4854660	58170860	55	466										
PREX1	57580	hgsc.bcm.edu	37	chr20	47317318	47317318	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	tccgcttgcagtagacgagaAggttgtcgaagaggaagaag	15	6	0	4			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr20:47317318A>C	ENST00000371941.3	-	7	912	c.890T>G	c.(889-891)cTt>cGt	p.L297R	PREX1_ENST00000396220.1_Missense_Mutation_p.L297R	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	297	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GTAGACGAGAAGGTTGTCGAA	0.557																																					p.L297R		Atlas-SNP	.											.	PREX1	441	.	0			c.T890G						.						172	162	165					20																	47317318		2203	4300	6503	SO:0001583	missense	57580	exon7			ACGAGAAGGTTGT	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.890T>G	chr20.hg19:g.47317318A>C	ENSP00000361009:p.Leu297Arg	165.0	0.0		128.0	38.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.104309	0.76983	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.74209	-0.82;-0.82	5.11	5.11	0.69529	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.43919	U	0.000512	D	0.83229	0.5209	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85217	0.1024	10	0.87932	D	0	.	15.1983	0.73112	1.0:0.0:0.0:0.0	.	297	Q8TCU6	PREX1_HUMAN	R	297	ENSP00000361009:L297R;ENSP00000379522:L297R	ENSP00000361009:L297R	L	-	2	0	PREX1	46750725	1.000000	0.71417	0.998000	0.56505	0.655000	0.38815	9.277000	0.95755	2.043000	0.60533	0.374000	0.22700	CTT	.	.		0.557	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		C	47317318	A	C	47317318	3	2	5	1	0	0	0	0	1	0	0	0	12488	72	3	5	4225	5	PREX1	20	47317318	Missense_Mutation	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10	42462658	47317318	15708202	56	467										
KRTAP27-1	643812	hgsc.bcm.edu	37	chr21	31709506	31709506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	gttctgagactgacactgacAttggctagatgcacgttcca	10	10	1	4			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr21:31709506A>G	ENST00000382835.2	-	1	506	c.481T>C	c.(481-483)Tgt>Cgt	p.C161R		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	161						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						TGACACTGACATTGGCTAGAT	0.498																																					p.C161R		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.T481C						.						138	134	135					21																	31709506		2203	4300	6503	SO:0001583	missense	643812	exon1			ACTGACATTGGCT	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"Keratin associated proteins"	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.481T>C	chr21.hg19:g.31709506A>G	ENSP00000372286:p.Cys161Arg	167.0	0.0		133.0	53.0	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	hg19	CCDS33532.1	.	.	.	.	.	.	.	.	.	.	A	8.463	0.855791	0.17106	.	.	ENSG00000206107	ENST00000382835	T	0.03468	3.92	4.44	-1.24	0.09435	.	0.379473	0.08080	U	1.000000	T	0.09247	0.0228	M	0.75777	2.31	0.09310	N	1	D	0.55172	0.97	P	0.54100	0.742	T	0.27400	-1.0075	10	0.34782	T	0.22	1.1589	4.6064	0.12380	0.3442:0.2988:0.0:0.357	.	161	Q3LI81	KR271_HUMAN	R	161	ENSP00000372286:C161R	ENSP00000372286:C161R	C	-	1	0	KRTAP27-1	30631377	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.049000	0.11924	-0.171000	0.10797	-0.449000	0.05564	TGT	.	.		0.498	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711		G	31709506	A	G	31709506	3	3	5	1	0	0	0	0	1	0	0	0	8553	217	8	2	146	2	KRTAP27-1	21	31709506	Missense_Mutation	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10		31709506	16420389	57	468										
HLCS	3141	hgsc.bcm.edu	37	chr21	38126652	38126652	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	tggtgaacctggaggaagccAgaatcgtccaggccaacgat	13	10	0	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr21:38126652A>G	ENST00000399120.1	-	12	3306	c.2076T>C	c.(2074-2076)tcT>tcC	p.S692S	HLCS_ENST00000336648.4_Silent_p.S692S	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	692					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	GGAGGAAGCCAGAATCGTCCA	0.597																																					p.S692S		Atlas-SNP	.											.	HLCS	64	.	0			c.T2076C						.						75	56	63					21																	38126652		2203	4300	6503	SO:0001819	synonymous_variant	3141	exon12			GAAGCCAGAATCG		CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)", "holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.2076T>C	chr21.hg19:g.38126652A>G		2054.0	1.0		1851.0	154.0	NM_000411	B2RAH1|D3DSG6|Q99451	Silent	SNP	ENST00000399120.1	hg19	CCDS13647.1																																																																																			.	.		0.597	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2			G	38126652	A	G	38126652	2	3	5	1	0	0	0	0	0	0	0	1	7222	175	7	2		2	HLCS	21	38126652	Silent	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10	6417146	38126652	10003243	58	469										
FBLN1	2192	hgsc.bcm.edu	37	chr22	45931160	45931160	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ctctgggatccttccgctgcCgacccaagctacagtgcaag	10	15	1	0			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chr22:45931160C>G	ENST00000327858.6	+	8	960	c.865C>G	c.(865-867)Cga>Gga	p.R289G	FBLN1_ENST00000340923.5_Missense_Mutation_p.R289G|FBLN1_ENST00000402984.3_Missense_Mutation_p.R327G|FBLN1_ENST00000442170.2_Missense_Mutation_p.R289G|FBLN1_ENST00000348697.2_Missense_Mutation_p.R289G|FBLN1_ENST00000262722.7_Missense_Mutation_p.R289G	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	289	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CTTCCGCTGCCGACCCAAGCT	0.473																																					p.R289G		Atlas-SNP	.											.	FBLN1	143	.	0			c.C865G						.						102	91	95					22																	45931160		2203	4300	6503	SO:0001583	missense	2192	exon8			CGCTGCCGACCCA		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.865C>G	chr22.hg19:g.45931160C>G	ENSP00000331544:p.Arg289Gly	133.0	0.0		119.0	7.0	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	hg19	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	c	16.89	3.247191	0.59103	.	.	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923	D;D;D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05;-3.05;-3.05	5.56	1.98	0.26296	EGF-like calcium-binding (2);	0.176916	0.49916	D	0.000132	D	0.90400	0.6995	N	0.11284	0.12	0.35086	D	0.763899	D;D;D;D	0.89917	1.0;1.0;0.99;1.0	D;D;D;D	0.97110	1.0;0.999;0.964;0.999	D	0.90623	0.4561	10	0.33141	T	0.24	.	14.5479	0.68044	0.3537:0.6463:0.0:0.0	.	327;289;289;289	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	G	289;327;289;289;289;289	ENSP00000262723:R289G;ENSP00000385521:R327G;ENSP00000262722:R289G;ENSP00000331544:R289G;ENSP00000393812:R289G;ENSP00000342212:R289G	ENSP00000262722:R289G	R	+	1	2	FBLN1	44309824	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.900000	0.28431	0.388000	0.25054	-0.455000	0.05494	CGA	.	.		0.473	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		G	45931160	C	G	45931160	3	3	5	1	0	0	0	0	1	0	0	0	5706	644	23	4	895	4	FBLN1	22	45931160	Missense_Mutation	SNP	C	TCGA-2Y-A9GV-01A-11D-A382-10		45931160	5373406	59	470										
IRS4	8471	hgsc.bcm.edu	37	chrX	107977611	107977611	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	ctctgtcaacacaaaaataaAgtctgaatcttcccccagac	4	13	4	2			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chrX:107977611A>T	ENST00000372129.2	-	1	2040	c.1964T>A	c.(1963-1965)cTt>cAt	p.L655H	RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	655					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						ACAAAAATAAAGTCTGAATCT	0.522																																					p.L655H		Atlas-SNP	.											.	IRS4	253	.	0			c.T1964A						.						241	252	248					X																	107977611		2203	4300	6503	SO:0001583	missense	8471	exon1			AAATAAAGTCTGA	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1964T>A	chrX.hg19:g.107977611A>T	ENSP00000361202:p.Leu655His	246.0	0.0		197.0	9.0	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	hg19	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	A	11.13	1.549324	0.27652	.	.	ENSG00000133124	ENST00000372129	T	0.38240	1.15	4.9	4.9	0.64082	.	0.588692	0.15430	N	0.262757	T	0.47116	0.1428	L	0.51422	1.61	0.25666	N	0.985949	D	0.76494	0.999	D	0.68192	0.956	T	0.39121	-0.9629	10	0.41790	T	0.15	-7.0606	4.7439	0.13028	0.7413:0.0:0.0886:0.17	.	655	O14654	IRS4_HUMAN	H	655	ENSP00000361202:L655H	ENSP00000361202:L655H	L	-	2	0	IRS4	107864267	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	2.298000	0.43602	1.807000	0.52817	0.486000	0.48141	CTT	.	.		0.522	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		T	107977611	A	T	107977611	3	4	5	1	0	0	0	0	1	0	0	0	7851	72	3	4	1813	4	IRS4	23	107977611	Missense_Mutation	SNP	A	TCGA-2Y-A9GV-01A-11D-A382-10		107977611	47292949	60	471										
FMR1	2332	hgsc.bcm.edu	37	chrX	147014109	147014109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0491803278688525	3	1	1.04092071611253	1.99509803921569	0.53202614379085	1	1	0	cctgcacatttcatatttatGgagaggtaaatattttactg	7	6	1	1			TCGA-2Y-A9GV-01A-11D-A382-10	TCGA-2Y-A9GV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbb0ee98-a0a5-4308-96f6-1ba7f5b71fef	c00cd9c3-fd3e-497f-94dd-30cfb18e4aa2	g.chrX:147014109G>A	ENST00000370475.4	+	8	924	c.796G>A	c.(796-798)Gga>Aga	p.G266R	FMR1_ENST00000334557.6_Missense_Mutation_p.G266R|FMR1_ENST00000218200.8_Missense_Mutation_p.G266R|FMR1_ENST00000440235.2_5'UTR|FMR1_ENST00000439526.2_Missense_Mutation_p.G266R|FMR1_ENST00000370471.3_Missense_Mutation_p.G266R|FMR1_ENST00000370470.1_Missense_Mutation_p.G266R|FMR1_ENST00000370477.1_Missense_Mutation_p.G266R	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	266					central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					TCATATTTATGGAGAGGTAAA	0.353									Fragile X syndrome																												p.G266R		Atlas-SNP	.											.	FMR1	93	.	0			c.G796A						.						133	129	131					X																	147014109		2203	4300	6503	SO:0001583	missense	2332	exon8	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	ATTTATGGAGAGG	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"premature ovarian failure 1"	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.796G>A	chrX.hg19:g.147014109G>A	ENSP00000359506:p.Gly266Arg	689.0	1.0		666.0	200.0	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Missense_Mutation	SNP	ENST00000370475.4	hg19	CCDS14682.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.905707	0.92107	.	.	ENSG00000102081	ENST00000218200;ENST00000370471;ENST00000370477;ENST00000370475;ENST00000334557;ENST00000439526;ENST00000370470	T;T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;0.17;0.17	5.78	5.78	0.91487	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.79707	0.4492	M	0.85542	2.76	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;1.0	T	0.82839	-0.0259	10	0.87932	D	0	-36.5954	17.8786	0.88833	0.0:0.0:1.0:0.0	.	266;266;182;266;266	Q8IXW7;Q06787;Q59GC1;Q06787-8;G3V0J0	.;FMR1_HUMAN;.;.;.	R	266	ENSP00000218200:G266R;ENSP00000359502:G266R;ENSP00000359508:G266R;ENSP00000359506:G266R;ENSP00000355115:G266R;ENSP00000395923:G266R;ENSP00000359501:G266R	ENSP00000218200:G266R	G	+	1	0	FMR1	146821801	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.400000	0.97290	2.443000	0.82685	0.538000	0.68166	GGA	.	.		0.353	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		A	147014109	G	A	147014109	3	1	5	1	0	0	0	0	1	0	0	0	5968	1349	47	3	826	3	FMR1	23	147014109	Missense_Mutation	SNP	G	TCGA-2Y-A9GV-01A-11D-A382-10	39036498	147014109	8256451	61	472										
ANGPTL7	10218	hgsc.bcm.edu	37	chr1	11249872	11249872	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ggactgggtcagcgtggtcaTgcaggtgatggagctggaga	19	6	2	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:11249872T>C	ENST00000376819.3	+	1	475	c.236T>C	c.(235-237)aTg>aCg	p.M79T	MTOR_ENST00000361445.4_Intron	NM_021146.2	NP_066969.1	O43827	ANGL7_HUMAN	angiopoietin-like 7	79					response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|stomach(1)	10	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.39e-06)|COAD - Colon adenocarcinoma(227;0.000244)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0487)		AGCGTGGTCATGCAGGTGATG	0.542																																					p.M79T		Atlas-SNP	.											.	ANGPTL7	23	.	0			c.T236C						.						107	100	103					1																	11249872		2203	4300	6503	SO:0001583	missense	10218	exon1			TGGTCATGCAGGT	Y16132	CCDS128.1	1p36	2013-02-06			ENSG00000171819	ENSG00000171819		"Fibrinogen C domain containing"	24078	protein-coding gene	gene with protein product						9727400, 11682471	Standard	NM_021146		Approved	CDT6, AngX	uc001ase.4	O43827	OTTHUMG00000002002	ENST00000376819.3:c.236T>C	chr1.hg19:g.11249872T>C	ENSP00000366015:p.Met79Thr	187.0	0.0		178.0	10.0	NM_021146	B2R9B2|F1T0A6|Q4ZGK4	Missense_Mutation	SNP	ENST00000376819.3	hg19	CCDS128.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.151799	0.38021	.	.	ENSG00000171819	ENST00000376819	T	0.53640	0.61	5.07	5.07	0.68467	.	0.136234	0.64402	D	0.000001	T	0.33818	0.0876	L	0.29908	0.895	0.50313	D	0.999865	B	0.29716	0.255	B	0.24394	0.053	T	0.12760	-1.0535	10	0.14252	T	0.57	.	15.1471	0.72662	0.0:0.0:0.0:1.0	.	79	O43827	ANGL7_HUMAN	T	79	ENSP00000366015:M79T	ENSP00000366015:M79T	M	+	2	0	ANGPTL7	11172459	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.170000	0.58229	2.034000	0.60081	0.533000	0.62120	ATG	.	.		0.542	ANGPTL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005564.1	NM_021146		C	11249872	T	C	11249872	3	2	6	1	0	0	0	0	1	0	0	0	619	1464	51	2	238	2	ANGPTL7	1	11249872	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10		11249872	238000749	1	473										
RIMKLA	284716	hgsc.bcm.edu	37	chr1	42880608	42880608	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gcccgaacctggctacaacaTtaacaacaggattgcttctg	8	12	1	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:42880608T>C	ENST00000431473.3	+	5	1268	c.1139T>C	c.(1138-1140)aTt>aCt	p.I380T		NM_173642.3	NP_775913.2	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family member A	380					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)			NS(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						GGCTACAACATTAACAACAGG	0.468																																					p.I380T		Atlas-SNP	.											.	RIMKLA	32	.	0			c.T1139C						.						66	76	73					1																	42880608		2203	4300	6503	SO:0001583	missense	284716	exon5			ACAACATTAACAA	BC039737	CCDS466.2	1p34.2	2011-09-21	2008-10-13	2008-10-13	ENSG00000177181	ENSG00000177181	6.3.2.N6		28725	protein-coding gene	gene with protein product	"N-acetylaspartylglutamate synthetase II"		"family with sequence similarity 80, member A"	FAM80A		20657015, 21454531	Standard	NM_173642		Approved	MGC47816, RP11-157D18.1, NAAGS-II	uc001chi.2	Q8IXN7	OTTHUMG00000007335	ENST00000431473.3:c.1139T>C	chr1.hg19:g.42880608T>C	ENSP00000414330:p.Ile380Thr	56.0	0.0		53.0	7.0	NM_173642	Q5VUS5	Missense_Mutation	SNP	ENST00000431473.3	hg19	CCDS466.2	.	.	.	.	.	.	.	.	.	.	T	14.61	2.587225	0.46110	.	.	ENSG00000177181	ENST00000431473	.	.	.	5.38	5.38	0.77491	.	0.260843	0.37178	N	0.002217	T	0.39036	0.1063	L	0.34521	1.04	0.42964	D	0.994413	P	0.40144	0.704	B	0.30646	0.118	T	0.46925	-0.9156	9	0.87932	D	0	-11.314	13.3632	0.60667	0.0:0.0:0.0:1.0	.	380	Q8IXN7	RIMKA_HUMAN	T	380	.	ENSP00000414330:I380T	I	+	2	0	RIMKLA	42653195	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.033000	0.57282	2.043000	0.60533	0.459000	0.35465	ATT	.	.		0.468	RIMKLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019174.3	NM_173642		C	42880608	T	C	42880608	3	2	6	1	0	0	0	0	1	0	0	0	13380	1493	52	2	1157	2	RIMKLA	1	42880608	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	31630736	42880608	206370013	2	474										
MAST2	23139	hgsc.bcm.edu	37	chr1	46500510	46500510	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	cctgggcaggcaactctcacGgcccaagagtgcggagccac	13	15	1	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:46500510G>A	ENST00000361297.2	+	29	4452	c.4169G>A	c.(4168-4170)cGg>cAg	p.R1390Q	MAST2_ENST00000372009.2_Missense_Mutation_p.R1200Q	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CAACTCTCACGGCCCAAGAGT	0.617																																					p.R1390Q		Atlas-SNP	.											.	MAST2	136	.	0			c.G4169A						.						88	95	93					1																	46500510		2055	4189	6244	SO:0001583	missense	23139	exon29			TCTCACGGCCCAA	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.4169G>A	chr1.hg19:g.46500510G>A	ENSP00000354671:p.Arg1390Gln	115.0	0.0		119.0	27.0	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	hg19	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	g	28.1	4.887568	0.91814	.	.	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.51325	0.71;0.71	4.4	4.4	0.53042	.	0.227913	0.32624	N	0.005859	T	0.69287	0.3094	M	0.76574	2.34	0.38821	D	0.955632	D;D	0.89917	1.0;1.0	P;D	0.85130	0.86;0.997	T	0.75986	-0.3124	10	0.87932	D	0	-4.7446	17.5359	0.87830	0.0:0.0:1.0:0.0	.	1200;1390	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	Q	1390;1200	ENSP00000354671:R1390Q;ENSP00000361079:R1200Q	ENSP00000354671:R1390Q	R	+	2	0	MAST2	46273097	1.000000	0.71417	0.821000	0.32701	0.919000	0.55068	9.602000	0.98312	2.431000	0.82371	0.558000	0.71614	CGG	.	.		0.617	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		A	46500510	G	A	46500510	3	1	6	1	0	0	0	0	1	0	0	0	9334	1116	39	1	4283	1	MAST2	1	46500510	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	3619902	46500510	202750111	3	475										
MIER1	57708	hgsc.bcm.edu	37	chr1	67423897	67423897	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	aacagtggctgtagtggggaAaataaagtaagtctatatac	11	4	1	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:67423897A>C	ENST00000355356.3	+	4	485	c.336A>C	c.(334-336)gaA>gaC	p.E112D	MIER1_ENST00000371014.1_Missense_Mutation_p.E165D|MIER1_ENST00000479067.1_3'UTR|MIER1_ENST00000371018.3_Missense_Mutation_p.E129D|MIER1_ENST00000357692.2_Missense_Mutation_p.E129D|MIER1_ENST00000371016.1_Missense_Mutation_p.E129D|MIER1_ENST00000355977.6_Missense_Mutation_p.E49D|MIER1_ENST00000401042.3_Missense_Mutation_p.E112D|MIER1_ENST00000401041.1_Missense_Mutation_p.E165D	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	112	Glu-rich.				positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						GTAGTGGGGAAAATAAAGTAA	0.313																																					p.E165D		Atlas-SNP	.											.	MIER1	86	.	0			c.A495C						.						94	95	95					1																	67423897		1936	4141	6077	SO:0001583	missense	57708	exon5			TGGGGAAAATAAA		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.336A>C	chr1.hg19:g.67423897A>C	ENSP00000347514:p.Glu112Asp	98.0	0.0		97.0	21.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Missense_Mutation	SNP	ENST00000355356.3	hg19	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	A	13.57	2.277692	0.40294	.	.	ENSG00000198160	ENST00000371017;ENST00000371018;ENST00000355977;ENST00000357692;ENST00000401041;ENST00000371016;ENST00000371014;ENST00000401042;ENST00000355356	T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.25	4.13	0.48395	.	0.000000	0.64402	D	0.000008	T	0.26593	0.0650	L	0.42245	1.32	0.43275	D	0.995235	B;B;B;P;P;B;B;B;P	0.45044	0.013;0.034;0.046;0.849;0.765;0.067;0.046;0.114;0.788	B;B;B;P;B;B;B;B;B	0.47705	0.006;0.01;0.028;0.555;0.352;0.018;0.028;0.034;0.225	T	0.02610	-1.1134	10	0.30078	T	0.28	-41.7233	10.9968	0.47580	0.9266:0.0:0.0734:0.0	.	129;129;112;112;49;136;129;165;165	Q5TAD2;Q32NC4;Q8N108-3;Q8N108-6;Q08AE0;Q8N108;Q8N108-10;Q5TAD5;Q5TAD4	.;.;.;.;.;MIER1_HUMAN;.;.;.	D	133;129;49;129;165;129;165;112;112	ENSP00000360057:E129D;ENSP00000348253:E49D;ENSP00000350321:E129D;ENSP00000383820:E165D;ENSP00000360055:E129D;ENSP00000360053:E165D;ENSP00000383821:E112D;ENSP00000347514:E112D	ENSP00000347514:E112D	E	+	3	2	MIER1	67196485	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	6.212000	0.72188	0.954000	0.37851	0.383000	0.25322	GAA	.	.		0.313	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948		C	67423897	A	C	67423897	3	2	6	1	0	0	0	0	1	0	0	0	9589	11	1	5	590	5	MIER1	1	67423897	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	20923387	67423897	181826724	4	476										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103387110	103387110	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ccttgagggcctcttgggccTggaggaccaggtggcccctg	16	13	1	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:103387110T>A	ENST00000370096.3	-	48	3984	c.3672A>T	c.(3670-3672)ccA>ccT	p.P1224P	COL11A1_ENST00000358392.2_Silent_p.P1236P|COL11A1_ENST00000512756.1_Silent_p.P1108P|COL11A1_ENST00000353414.4_Silent_p.P1185P	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1224	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CTCTTGGGCCTGGAGGACCAG	0.358																																					p.P1236P		Atlas-SNP	.											.	COL11A1	972	.	0			c.A3708T						.						71	84	80					1																	103387110		2203	4300	6503	SO:0001819	synonymous_variant	1301	exon48			TGGGCCTGGAGGA	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3672A>T	chr1.hg19:g.103387110T>A		917.0	0.0		1076.0	94.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.358	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103387110	T	A	103387110	2	1	6	1	0	0	0	0	0	0	0	1	3669	1567	55	4		4	COL11A1	1	103387110	Silent	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	35963213	103387110	145863511	5	477										
FBXO28	23219	hgsc.bcm.edu	37	chr1	224345064	224345064	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	tcctccacagttccaggaccGtctgcagccctaacaacaat	6	16	1	0	rs201209850	byFrequency	TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:224345064G>A	ENST00000366862.5	+	5	766	c.723G>A	c.(721-723)ccG>ccA	p.P241P	FBXO28_ENST00000424254.2_Missense_Mutation_p.R176H	NM_015176.3	NP_055991.1	Q9NVF7	FBX28_HUMAN	F-box protein 28	241										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(2)|skin(1)	10	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		TTCCAGGACCGTCTGCAGCCC	0.418													G|||	3	0.000599042	0	0	5008	,	,		18746	0		0	False		,,,				2504	0.0031				p.R176H		Atlas-SNP	.											.	FBXO28	34	.	0			c.G527A						.	G	HIS/ARG,	0,4406		0,0,2203	107	107	107		527,723	-6	0.8	1		107	1,8599	1.2+/-3.3	0,1,4299	no	missense,coding-synonymous	FBXO28	NM_001136115.1,NM_015176.2	29,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	176/180,241/369	224345064	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23219	exon4			AGGACCGTCTGCA	AK001628	CCDS1539.1, CCDS44320.1	1q42.12	2011-08-12			ENSG00000143756	ENSG00000143756		"F-boxes /  "other""	29046	protein-coding gene	gene with protein product	"centromere protein 30"	609100				9455484	Standard	NM_015176		Approved	FLJ10766, KIAA0483, Fbx28, CENP-30	uc001hoh.3	Q9NVF7	OTTHUMG00000037495	ENST00000366862.5:c.723G>A	chr1.hg19:g.224345064G>A		131.0	0.0		169.0	12.0	NM_001136115	E9PEM8|O75070	Missense_Mutation	SNP	ENST00000366862.5	hg19	CCDS1539.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.624414	0.28889	0.0	1.16E-4	ENSG00000143756	ENST00000424254	.	.	.	6.17	-6.01	0.02199	.	.	.	.	.	T	0.24547	0.0595	.	.	.	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.28106	-1.0054	7	0.87932	D	0	-9.0138	3.0686	0.06222	0.1404:0.2011:0.4336:0.2249	.	176	E9PEM8	.	H	176	.	ENSP00000416888:R176H	R	+	2	0	FBXO28	222411687	0.017000	0.18338	0.786000	0.31890	0.973000	0.67179	-1.043000	0.03535	-1.467000	0.01895	-1.140000	0.01884	CGT	.	G|0.999;A|0.001		0.418	FBXO28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091283.2	NM_015176		A	224345064	G	A	224345064	2	1	6	1	0	0	0	0	0	0	0	1	5746	1145	40	1		1	FBXO28	1	224345064	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	120957954	224345064	24905557	6	478										
FSHR	2492	hgsc.bcm.edu	37	chr2	49210076	49210076	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gactggtccagaggctccgtGgaaaacatcattaggcaatt	11	9	1	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr2:49210076G>A	ENST00000406846.2	-	8	762	c.643C>T	c.(643-645)Cac>Tac	p.H215Y	FSHR_ENST00000541117.1_5'UTR|FSHR_ENST00000346173.3_Missense_Mutation_p.H215Y|FSHR_ENST00000469138.1_5'UTR|FSHR_ENST00000304421.4_Missense_Mutation_p.H189Y	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	215					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	GAGGCTCCGTGGAAAACATCA	0.418									Gonadal Dysgenesis, 46 XX																												p.H215Y		Atlas-SNP	.											.	FSHR	164	.	0			c.C643T						.						98	95	96					2																	49210076		2203	4300	6503	SO:0001583	missense	2492	exon8	Familial Cancer Database		CTCCGTGGAAAAC		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.643C>T	chr2.hg19:g.49210076G>A	ENSP00000384708:p.His215Tyr	272.0	0.0		268.0	57.0	NM_000145	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Missense_Mutation	SNP	ENST00000406846.2	hg19	CCDS1843.1	.	.	.	.	.	.	.	.	.	.	G	3.548	-0.092336	0.07053	.	.	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000454032	T;D;T;D	0.90788	0.39;-2.73;0.39;-2.73	5.38	4.49	0.54785	.	0.669321	0.15520	N	0.258061	D	0.85057	0.5610	N	0.22421	0.69	0.80722	D	1	B;B;P	0.35401	0.355;0.103;0.499	B;B;B	0.38985	0.287;0.05;0.183	T	0.81077	-0.1096	9	.	.	.	.	13.127	0.59360	0.0:0.0:0.8404:0.1596	.	189;215;215	Q05AH0;G5E967;P23945	.;.;FSHR_HUMAN	Y	215;215;189;215	ENSP00000384708:H215Y;ENSP00000333908:H215Y;ENSP00000306780:H189Y;ENSP00000415504:H215Y	.	H	-	1	0	FSHR	49063580	1.000000	0.71417	0.987000	0.45799	0.920000	0.55202	3.606000	0.54095	1.490000	0.48466	0.655000	0.94253	CAC	.	.		0.418	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2			A	49210076	G	A	49210076	3	1	6	1	0	0	0	0	1	0	0	0	6081	1348	47	3	1456	3	FSHR	2	49210076	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10		49210076	193989297	7	479										
EIF2AK3	9451	hgsc.bcm.edu	37	chr2	88857341	88857341	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	aaggagcgagacctctgtctGagcactgtttttcctggaaa	11	9	2	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr2:88857341G>A	ENST00000303236.3	-	17	3565	c.3264C>T	c.(3262-3264)ctC>ctT	p.L1088L	AC104134.2_ENST00000413234.1_RNA|EIF2AK3_ENST00000419748.1_Silent_p.L937L	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	1088					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						ACCTCTGTCTGAGCACTGTTT	0.453																																					p.L1088L	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											EIF2AK3_ENST00000303236,NS,carcinoma,0,2	EIF2AK3	160	.	0			c.C3264T						.						257	243	248					2																	88857341		2203	4300	6503	SO:0001819	synonymous_variant	9451	exon17			CTGTCTGAGCACT	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.3264C>T	chr2.hg19:g.88857341G>A		182.0	0.0		158.0	35.0	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Silent	SNP	ENST00000303236.3	hg19	CCDS33241.1																																																																																			.	.		0.453	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		A	88857341	G	A	88857341	2	1	6	1	0	0	0	0	0	0	0	1	5000	1277	45	3		3	EIF2AK3	2	88857341	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	39647265	88857341	154342032	8	480										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141526828	141526828	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	aatgaagttcctgatataggCatcaaagcatccattttgtc	7	8	1	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr2:141526828C>A	ENST00000389484.3	-	35	6683	c.5712G>T	c.(5710-5712)atG>atT	p.M1904I		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1904					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTGATATAGGCATCAAAGCAT	0.353										TSP Lung(27;0.18)																											p.M1904I	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G5712T						.						87	87	87					2																	141526828		2203	4300	6503	SO:0001583	missense	53353	exon35			TATAGGCATCAAA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.5712G>T	chr2.hg19:g.141526828C>A	ENSP00000374135:p.Met1904Ile	107.0	0.0		105.0	27.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.897607	0.72639	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90676	-2.71	5.59	5.59	0.84812	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.81494	0.4834	N	0.11023	0.085	0.80722	D	1	P	0.39831	0.69	B	0.36666	0.23	T	0.80448	-0.1378	10	0.11485	T	0.65	.	19.5947	0.95530	0.0:1.0:0.0:0.0	.	1904	Q9NZR2	LRP1B_HUMAN	I	1904;1842	ENSP00000374135:M1904I	ENSP00000374135:M1904I	M	-	3	0	LRP1B	141243298	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.640000	0.83355	2.636000	0.89361	0.655000	0.94253	ATG	.	.		0.353	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141526828	C	A	141526828	3	1	6	1	0	0	0	0	1	0	0	0	8964	710	25	3	8315	3	LRP1B	2	141526828	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10	52669487	141526828	101672545	9	481										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171355106	171355106	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ttcttttattttgcaggtatTattacttggcattcacagca	6	7	2	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr2:171355106T>C	ENST00000408978.4	+	26	3162	c.3019T>C	c.(3019-3021)Tat>Cat	p.Y1007H	MYO3B_ENST00000602629.1_Intron|MYO3B_ENST00000334231.6_Missense_Mutation_p.Y1016H|MYO3B_ENST00000409044.3_Missense_Mutation_p.Y1007H	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	1007	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TTGCAGGTATTATTACTTGGC	0.393																																					p.Y1007H		Atlas-SNP	.											.	MYO3B	320	.	0			c.T3019C						.						110	102	105					2																	171355106		1839	4088	5927	SO:0001583	missense	140469	exon26			AGGTATTATTACT		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.3019T>C	chr2.hg19:g.171355106T>C	ENSP00000386213:p.Tyr1007His	81.0	0.0		64.0	4.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	hg19	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.889567	0.33348	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22	5.66	5.66	0.87406	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.85182	0.5638	L	0.35249	1.045	0.52501	D	0.999952	B;B;B	0.27932	0.02;0.194;0.107	B;B;B	0.39531	0.033;0.159;0.302	T	0.82267	-0.0542	10	0.35671	T	0.21	.	16.1831	0.81925	0.0:0.0:0.0:1.0	.	1007;1007;1007	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	H	1007;1007;1006;1016;1016	ENSP00000386497:Y1007H;ENSP00000386213:Y1007H;ENSP00000446237:Y1016H;ENSP00000335100:Y1016H	ENSP00000314213:Y1006H	Y	+	1	0	MYO3B	171063352	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.579000	0.67457	2.285000	0.76669	0.482000	0.46254	TAT	.	.		0.393	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			C	171355106	T	C	171355106	3	2	6	1	0	0	0	0	1	0	0	0	10086	1754	61	2	3121	2	MYO3B	2	171355106	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	29828278	171355106	71844267	10	482										
FGD5	152273	hgsc.bcm.edu	37	chr3	14939057	14939057	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	agggccttggatgacatggaCcatgaaggcagagacacatt	13	8	0	3			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:14939057C>A	ENST00000285046.5	+	5	2900	c.2790C>A	c.(2788-2790)gaC>gaA	p.D930E	FGD5_ENST00000543601.1_Missense_Mutation_p.D689E|FGD5_ENST00000476851.1_3'UTR	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	930	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						ATGACATGGACCATGAAGGCA	0.552																																					p.D930E		Atlas-SNP	.											.	FGD5	248	.	0			c.C2790A						.						67	64	65					3																	14939057		1987	4176	6163	SO:0001583	missense	152273	exon5			CATGGACCATGAA	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.2790C>A	chr3.hg19:g.14939057C>A	ENSP00000285046:p.Asp930Glu	182.0	0.0		156.0	43.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.177|0.177	-1.066289|-1.066289	0.01934|0.01934	.|.	.|.	ENSG00000154783|ENSG00000154783	ENST00000285046;ENST00000543601|ENST00000457774	T;T|.	0.73363|.	-0.74;-0.58|.	4.96|4.96	0.67|0.67	0.17923|0.17923	Dbl homology (DH) domain (5);|.	0.584200|.	0.15967|.	N|.	0.235992|.	T|T	0.14141|0.14141	0.0342|0.0342	N|N	0.04880|0.04880	-0.145|-0.145	0.09310|0.09310	N|N	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.06405|.	0.0;0.002|.	T|T	0.25363|0.25363	-1.0134|-1.0134	10|5	0.06099|.	T|.	0.92|.	-21.2749|-21.2749	3.9498|3.9498	0.09364|0.09364	0.1448:0.4823:0.279:0.0938|0.1448:0.4823:0.279:0.0938	.|.	689;930|.	B7ZM68;Q6ZNL6|.	.;FGD5_HUMAN|.	E|T	930;689|114	ENSP00000285046:D930E;ENSP00000445949:D689E|.	ENSP00000285046:D930E|.	D|P	+|+	3|1	2|0	FGD5|FGD5	14914061|14914061	0.989000|0.989000	0.36119|0.36119	0.200000|0.200000	0.23457|0.23457	0.651000|0.651000	0.38670|0.38670	0.285000|0.285000	0.18883|0.18883	0.444000|0.444000	0.26612|0.26612	0.591000|0.591000	0.81541|0.81541	GAC|CCA	.	.		0.552	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		A	14939057	C	A	14939057	3	1	6	1	0	0	0	0	1	0	0	0	5844	506	18	3	2808	3	FGD5	3	14939057	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10		14939057	183083373	11	483										
SCN5A	6331	hgsc.bcm.edu	37	chr3	38640520	38640520	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ggtcagcatctggggcccgcCtggctcctccgatggcgtgg	16	14	2	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:38640520C>T	ENST00000333535.4	-	13	2061	c.1912G>A	c.(1912-1914)Ggc>Agc	p.G638S	SCN5A_ENST00000443581.1_Missense_Mutation_p.G638S|SCN5A_ENST00000450102.2_Missense_Mutation_p.G638S|SCN5A_ENST00000449557.2_Missense_Mutation_p.G638S|SCN5A_ENST00000451551.2_Missense_Mutation_p.G638S|SCN5A_ENST00000413689.1_Missense_Mutation_p.G638S|SCN5A_ENST00000423572.2_Missense_Mutation_p.G638S|SCN5A_ENST00000455624.2_Missense_Mutation_p.G638S|SCN5A_ENST00000425664.1_Missense_Mutation_p.G638S|SCN5A_ENST00000414099.2_Missense_Mutation_p.G638S			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	638					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	TGGGGCCCGCCTGGCTCCTCC	0.662																																					p.G638S		Atlas-SNP	.											.	SCN5A	634	.	0			c.G1912A						.						23	28	26					3																	38640520		2141	4247	6388	SO:0001583	missense	6331	exon13			GCCCGCCTGGCTC	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1912G>A	chr3.hg19:g.38640520C>T	ENSP00000328968:p.Gly638Ser	89.0	0.0		97.0	20.0	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	hg19	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.472782	0.43942	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.90444	-2.67;-2.67;-2.67;-2.67;-2.67;-2.67;-2.67;-2.67;-2.67;-2.67	3.55	2.65	0.31530	Domain of unknown function DUF3451 (1);	0.520160	0.18714	N	0.133205	T	0.77565	0.4149	N	0.16307	0.4	0.31810	N	0.627219	B;B;B;B;B;B;B	0.18013	0.001;0.025;0.019;0.024;0.011;0.006;0.009	B;B;B;B;B;B;B	0.19666	0.006;0.026;0.013;0.022;0.013;0.007;0.007	T	0.67515	-0.5651	10	0.14252	T	0.57	.	3.4381	0.07453	0.0:0.593:0.0:0.407	.	638;638;638;638;638;638;638	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	S	638	ENSP00000398962:G638S;ENSP00000398266:G638S;ENSP00000410257:G638S;ENSP00000388797:G638S;ENSP00000397915:G638S;ENSP00000416634:G638S;ENSP00000328968:G638S;ENSP00000399524:G638S;ENSP00000403355:G638S;ENSP00000413996:G638S	ENSP00000328968:G638S	G	-	1	0	SCN5A	38615524	0.983000	0.35010	1.000000	0.80357	0.884000	0.51177	1.951000	0.40333	1.989000	0.58080	0.561000	0.74099	GGC	.	.		0.662	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		T	38640520	C	T	38640520	3	4	6	1	0	0	0	0	1	0	0	0	13937	681	24	3	4202	3	SCN5A	3	38640520	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10	23701463	38640520	159381910	12	484										
CCK	885	hgsc.bcm.edu	37	chr3	42299622	42299622	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ctcatactcctcggcactgcGacggccaaaatccatccagc	7	17	1	0	rs533678433		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:42299622G>A	ENST00000396169.2	-	5	1221	c.316C>T	c.(316-318)Cgc>Tgc	p.R106C	CCK_ENST00000434608.1_Missense_Mutation_p.R106C|CCK_ENST00000334681.5_Missense_Mutation_p.R106C	NM_000729.4	NP_000720.1	P06307	CCKN_HUMAN	cholecystokinin	106					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axonogenesis (GO:0007409)|behavioral fear response (GO:0001662)|eating behavior (GO:0042755)|negative regulation of appetite (GO:0032099)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein oligomerization (GO:0032461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|release of cytochrome c from mitochondria (GO:0001836)|signal transduction (GO:0007165)	axon (GO:0030424)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|terminal bouton (GO:0043195)	hormone activity (GO:0005179)|neuropeptide hormone activity (GO:0005184)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6		Ovarian(412;0.0728)		KIRC - Kidney renal clear cell carcinoma(284;0.219)		TCGGCACTGCGACGGCCAAAA	0.562													G|||	1	0.000199681	0	0	5008	,	,		17782	0		0.001	False		,,,				2504	0				p.R106C		Atlas-SNP	.											CCK,colon,carcinoma,0,1	CCK	15	.	0			c.C316T						.						116	102	107					3																	42299622		2203	4300	6503	SO:0001583	missense	885	exon5			CACTGCGACGGCC		CCDS2696.1	3p22.1	2013-02-25			ENSG00000187094	ENSG00000187094		"Endogenous ligands"	1569	protein-coding gene	gene with protein product	"prepro-cholecystokinin", "cholecystokinin triacontatriapeptide"	118440				3856870	Standard	NM_001174138		Approved		uc021wwk.1	P06307	OTTHUMG00000131796	ENST00000396169.2:c.316C>T	chr3.hg19:g.42299622G>A	ENSP00000379472:p.Arg106Cys	138.0	0.0		139.0	18.0	NM_000729		Missense_Mutation	SNP	ENST00000396169.2	hg19	CCDS2696.1	.	.	.	.	.	.	.	.	.	.	G	33	5.260448	0.95368	.	.	ENSG00000187094	ENST00000396169;ENST00000334681;ENST00000434608	T;T;T	0.68765	-0.35;-0.35;-0.35	5.7	5.7	0.88788	Gastrin/cholecystokinin peptide hormone (2);	0.099413	0.64402	D	0.000001	D	0.85396	0.5687	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87529	0.2451	10	0.87932	D	0	-23.505	18.8882	0.92388	0.0:0.0:1.0:0.0	.	106	P06307	CCKN_HUMAN	C	106	ENSP00000379472:R106C;ENSP00000335657:R106C;ENSP00000409124:R106C	ENSP00000335657:R106C	R	-	1	0	CCK	42274626	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.471000	0.97696	2.698000	0.92095	0.650000	0.86243	CGC	.	.		0.562	CCK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343380.1	NM_000729		A	42299622	G	A	42299622	3	1	6	1	0	0	0	0	1	0	0	0	2881	1058	37	1	35	1	CCK	3	42299622	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	3659102	42299622	155722808	13	485										
DAG1	1605	hgsc.bcm.edu	37	chr3	49568955	49568955	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	atccaggagcccccatccagGatcgtgccaacccccacatc	7	19	0	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:49568955G>T	ENST00000539901.1	+	3	1569	c.1011G>T	c.(1009-1011)agG>agT	p.R337S	DAG1_ENST00000538711.1_Missense_Mutation_p.R337S|DAG1_ENST00000541308.1_Missense_Mutation_p.R337S|DAG1_ENST00000515359.2_Missense_Mutation_p.R337S|DAG1_ENST00000545947.1_Missense_Mutation_p.R337S|DAG1_ENST00000308775.2_Missense_Mutation_p.R337S	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	337	Mucin-like domain.|Required for laminin recognition.|Thr-rich.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CCCCATCCAGGATCGTGCCAA	0.617																																					p.R337S		Atlas-SNP	.											.	DAG1	60	.	0			c.G1011T						.						76	76	76					3																	49568955		2203	4300	6503	SO:0001583	missense	1605	exon4			ATCCAGGATCGTG	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.1011G>T	chr3.hg19:g.49568955G>T	ENSP00000439334:p.Arg337Ser	79.0	0.0		61.0	10.0	NM_001177642	A8K6M7|Q969J9	Missense_Mutation	SNP	ENST00000539901.1	hg19	CCDS2799.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.758102	0.49468	.	.	ENSG00000173402	ENST00000515359;ENST00000308775;ENST00000545947;ENST00000541308;ENST00000539901;ENST00000538711	T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77	5.74	1.42	0.22433	.	0.000000	0.85682	D	0.000000	T	0.60064	0.2240	M	0.67953	2.075	0.50313	D	0.999867	D	0.64830	0.994	D	0.75020	0.985	T	0.57423	-0.7814	9	.	.	.	-25.1431	8.5001	0.33152	0.4539:0.0:0.5461:0.0	.	337	Q14118	DAG1_HUMAN	S	337	ENSP00000440705:R337S;ENSP00000312435:R337S;ENSP00000442600:R337S;ENSP00000440590:R337S;ENSP00000439334:R337S;ENSP00000438421:R337S	.	R	+	3	2	DAG1	49543959	0.948000	0.32251	0.997000	0.53966	0.974000	0.67602	0.070000	0.14573	0.555000	0.29079	0.655000	0.94253	AGG	.	.		0.617	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			T	49568955	G	T	49568955	3	4	6	1	0	0	0	0	1	0	0	0	4227	1165	41	3	1017	3	DAG1	3	49568955	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	7269333	49568955	148453475	14	486										
ITIH1	3697	hgsc.bcm.edu	37	chr3	52824803	52824803	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	caagaagaggaacctggtggTgtctgtggacgacggtggca	17	7	1	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:52824803T>C	ENST00000273283.2	+	20	2384	c.2360T>C	c.(2359-2361)gTg>gCg	p.V787A	ITIH1_ENST00000540715.1_Missense_Mutation_p.V645A|ITIH1_ENST00000537050.1_Missense_Mutation_p.V499A|ITIH1_ENST00000405128.3_Missense_Mutation_p.V153A|ITIH1_ENST00000542827.1_3'UTR	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	787	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		AACCTGGTGGTGTCTGTGGAC	0.597																																					p.V787A		Atlas-SNP	.											.	ITIH1	108	.	0			c.T2360C						.						187	154	165					3																	52824803		2203	4300	6503	SO:0001583	missense	3697	exon20			TGGTGGTGTCTGT		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"inter-alpha (globulin) inhibitor, H1 polypeptide"			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2360T>C	chr3.hg19:g.52824803T>C	ENSP00000273283:p.Val787Ala	108.0	0.0		108.0	14.0	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	hg19	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.106103	0.77096	.	.	ENSG00000055957	ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133;ENST00000405128	T;T;T;T;T	0.20200	2.09;2.09;2.09;2.09;2.09	5.75	5.75	0.90469	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.204155	0.41294	D	0.000906	T	0.47488	0.1448	M	0.86502	2.82	0.26781	N	0.9696	B;P;P;P	0.47484	0.402;0.881;0.896;0.881	B;P;P;P	0.56343	0.292;0.723;0.471;0.796	T	0.51849	-0.8653	10	0.59425	D	0.04	-15.6007	14.8895	0.70597	0.0:0.0:0.0:1.0	.	645;153;388;787	F5H165;B5MCP1;Q9P1C5;P19827	.;.;.;ITIH1_HUMAN	A	787;645;499;340;153	ENSP00000273283:V787A;ENSP00000443973:V645A;ENSP00000443847:V499A;ENSP00000395836:V340A;ENSP00000384589:V153A	ENSP00000273283:V787A	V	+	2	0	ITIH1	52799843	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	2.204000	0.42761	2.195000	0.70347	0.533000	0.62120	GTG	.	.		0.597	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		C	52824803	T	C	52824803	3	2	6	1	0	0	0	0	1	0	0	0	7912	1696	59	2	2438	2	ITIH1	3	52824803	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	3255848	52824803	145197627	15	487										
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73673733	73673733	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gccgcgcgtcgcgtacgcgcActtgatgtccagcttgagga	14	13	0	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:73673733A>G	ENST00000263666.4	-	1	358	c.244T>C	c.(244-246)Tgc>Cgc	p.C82R	PDZRN3-AS1_ENST00000608743.1_RNA|PDZRN3-AS1_ENST00000608304.1_RNA|PDZRN3_ENST00000308537.4_Missense_Mutation_p.C82R|PDZRN3-AS1_ENST00000478988.1_RNA	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	82					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GCGTACGCGCACTTGATGTCC	0.716																																					p.C82R		Atlas-SNP	.											.	PDZRN3	196	.	0			c.T244C						.						9	8	8					3																	73673733		2160	4218	6378	SO:0001583	missense	23024	exon1			ACGCGCACTTGAT	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.244T>C	chr3.hg19:g.73673733A>G	ENSP00000263666:p.Cys82Arg	61.0	0.0		74.0	26.0	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	hg19	CCDS33789.1	.	.	.	.	.	.	.	.	.	.	A	18.74	3.688731	0.68271	.	.	ENSG00000121440	ENST00000263666;ENST00000416926;ENST00000308537	D;D	0.94576	-3.46;-3.46	4.49	4.49	0.54785	TRAF-like (1);Seven In Absentia Homolog-type (1);	0.108090	0.64402	N	0.000014	D	0.96503	0.8859	M	0.71581	2.175	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	D	0.96865	0.9635	10	0.87932	D	0	.	12.9606	0.58455	1.0:0.0:0.0:0.0	.	82	Q9UPQ7	PZRN3_HUMAN	R	82	ENSP00000263666:C82R;ENSP00000308831:C82R	ENSP00000263666:C82R	C	-	1	0	PDZRN3	73756423	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	6.538000	0.73852	1.638000	0.50547	0.260000	0.18958	TGC	.	.		0.716	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		G	73673733	A	G	73673733	3	3	6	1	0	0	0	0	1	0	0	0	11718	159	6	2	2996	2	PDZRN3	3	73673733	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	20848930	73673733	124348697	16	488										
CCDC54	84692	hgsc.bcm.edu	37	chr3	107097051	107097051	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	cagttatccaaagtccactgAccatcttgagaaaaaaacaa	5	10	1	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:107097051A>C	ENST00000261058.1	+	1	864	c.617A>C	c.(616-618)gAc>gCc	p.D206A		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	206										NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						AAGTCCACTGACCATCTTGAG	0.398																																					p.D206A		Atlas-SNP	.											.	CCDC54	56	.	0			c.A617C						.						73	72	72					3																	107097051		2203	4300	6503	SO:0001583	missense	84692	exon1			CCACTGACCATCT	AF367469	CCDS2949.1	3q13.12	2013-10-11			ENSG00000138483	ENSG00000138483			30703	protein-coding gene	gene with protein product	"sperm protein 17"					15257753	Standard	NM_032600		Approved	NYD-SP17, FLJ25362, SP17	uc003dwi.1	Q8NEL0	OTTHUMG00000159169	ENST00000261058.1:c.617A>C	chr3.hg19:g.107097051A>C	ENSP00000261058:p.Asp206Ala	383.0	0.0		442.0	44.0	NM_032600	Q96A43	Missense_Mutation	SNP	ENST00000261058.1	hg19	CCDS2949.1	.	.	.	.	.	.	.	.	.	.	A	0.038	-1.296348	0.01364	.	.	ENSG00000138483	ENST00000261058	T	0.42900	0.96	5.19	-5.25	0.02781	.	1.285700	0.05794	N	0.610844	T	0.31295	0.0792	L	0.60455	1.87	0.09310	N	1	B	0.13145	0.007	B	0.12156	0.007	T	0.33471	-0.9867	10	0.08837	T	0.75	3.0096	7.0425	0.25029	0.2386:0.3308:0.4306:0.0	.	206	Q8NEL0	CCD54_HUMAN	A	206	ENSP00000261058:D206A	ENSP00000261058:D206A	D	+	2	0	CCDC54	108579741	0.000000	0.05858	0.000000	0.03702	0.431000	0.31685	-0.604000	0.05667	-0.690000	0.05142	0.377000	0.23210	GAC	.	.		0.398	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1	NM_032600		C	107097051	A	C	107097051	3	2	6	1	0	0	0	0	1	0	0	0	2826	275	10	5	619	5	CCDC54	3	107097051	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	33423318	107097051	90925379	17	489										
POLQ	10721	hgsc.bcm.edu	37	chr3	121200637	121200637	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gagtcggctcctgagaatctGgatctagtaaccagcatgcc	11	11	2	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:121200637G>A	ENST00000264233.5	-	19	6121	c.5993C>T	c.(5992-5994)cCa>cTa	p.P1998L		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1998					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTGAGAATCTGGATCTAGTAA	0.418								DNA polymerases (catalytic subunits)																													p.P1998L	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C5993T						.						77	78	77					3																	121200637		2203	4300	6503	SO:0001583	missense	10721	exon19			GAATCTGGATCTA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.5993C>T	chr3.hg19:g.121200637G>A	ENSP00000264233:p.Pro1998Leu	146.0	0.0		155.0	39.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785376	0.90282	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.27104	1.69	5.17	5.17	0.71159	Ribonuclease H-like (1);	0.121109	0.64402	D	0.000020	T	0.51601	0.1684	M	0.68952	2.095	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.79108	0.963;0.992	T	0.52909	-0.8512	10	0.87932	D	0	.	18.8557	0.92251	0.0:0.0:1.0:0.0	.	1998;1170	O75417;O75417-2	DPOLQ_HUMAN;.	L	1621;1998;2134	ENSP00000264233:P1998L	ENSP00000264233:P1998L	P	-	2	0	POLQ	122683327	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.348000	0.90064	2.688000	0.91661	0.650000	0.86243	CCA	.	.		0.418	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121200637	G	A	121200637	3	1	6	1	0	0	0	0	1	0	0	0	12217	1348	47	3	1827	3	POLQ	3	121200637	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	14103586	121200637	76821793	18	490										
KCNMB3	27094	hgsc.bcm.edu	37	chr3	178960728	178960728	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	cttcctttgctcctcctcatAatgcacagtttgaactgatg	6	12	1	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:178960728A>G	ENST00000314235.5	-	4	1315	c.804T>C	c.(802-804)atT>atC	p.I268I	KCNMB3_ENST00000349697.2_Silent_p.I266I|KCNMB3_ENST00000485523.1_Silent_p.I246I|KCNMB3_ENST00000497599.1_Intron|KCNMB3_ENST00000486944.1_Intron|KCNMB3_ENST00000392685.2_Silent_p.I264I	NM_014407.3	NP_055222.3	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	268					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	TCCTCCTCATAATGCACAGTT	0.418																																					p.I268I		Atlas-SNP	.											.	KCNMB3	46	.	0			c.T804C						.						120	115	117					3																	178960728		2203	4300	6503	SO:0001819	synonymous_variant	27094	exon4			CCTCATAATGCAC	AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121		"Potassium channels"	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL		10585773	Standard	NM_001163677		Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000314235.5:c.804T>C	chr3.hg19:g.178960728A>G		242.0	0.0		242.0	46.0	NM_014407	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Silent	SNP	ENST00000314235.5	hg19	CCDS3226.1																																																																																			.	.		0.418	KCNMB3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348484.1			G	178960728	A	G	178960728	2	3	6	1	0	0	0	0	0	0	0	1	8085	358	13	2		2	KCNMB3	3	178960728	Silent	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	57760091	178960728	19061702	19	491										
HRG	3273	hgsc.bcm.edu	37	chr3	186386775	186386776	+	Frame_Shift_Ins	INS	-	-	C													0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	tgtgcaagaatcggactgttINScggtcctatccaggaaatac					rs4516605	byFrequency	TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:186386775_186386776insC	ENST00000232003.4	+	2	315_316	c.235_236insC	c.(235-237)tcgfs	p.S79fs		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	79	Cystatin 1.|Interaction with ATP5A1.		S -> L (in dbSNP:rs4516605).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		ATCGGACTGTTCGGTCCTATCC	0.436																																					p.S79fs		Atlas-Indel,Pindel	.											.	HRG	81	.	0			c.235_236insC						.																																			SO:0001589	frameshift_variant	3273	exon2			.		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.236dupC	chr3.hg19:g.186386776_186386776dupC	ENSP00000232003:p.Ser79fs	89.0	0.0		103.0	15.0	NM_000412	B9EK35|D3DNU7	Frame_Shift_Ins	INS	ENST00000232003.4	hg19	CCDS3280.1																																																																																			.	.		0.436	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		C	186386776	-	C	186386775	7	5	6	1	0	1	1	0	0	0	0	0	7363	1783	62	0	241	0	HRG	3	186386775	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GW-01A-11D-A382-10	7426047	186386775	11635655	20	492										
SENP5	205564	hgsc.bcm.edu	37	chr3	196613318	196613318	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	tctggagcagatacatctgtGagtagcgtagatgggcctgt	14	7	2	3			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:196613318G>T	ENST00000323460.5	+	2	1515	c.1266G>T	c.(1264-1266)gtG>gtT	p.V422V	SENP5_ENST00000445299.2_Silent_p.V422V|SENP5_ENST00000419026.1_Intron	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	422					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		ATACATCTGTGAGTAGCGTAG	0.438																																					p.V422V	Ovarian(47;891 1095 11174 13858 51271)	Atlas-SNP	.											.	SENP5	68	.	0			c.G1266T						.						96	96	96					3																	196613318		2203	4300	6503	SO:0001819	synonymous_variant	205564	exon2			ATCTGTGAGTAGC	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"SUMO1/sentrin specific protease 5"			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1266G>T	chr3.hg19:g.196613318G>T		93.0	0.0		81.0	12.0	NM_152699	B4DY82|Q96SA5	Silent	SNP	ENST00000323460.5	hg19	CCDS3322.1																																																																																			.	.		0.438	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699		T	196613318	G	T	196613318	2	4	6	1	0	0	0	0	0	0	0	1	14064	1277	45	3		3	SENP5	3	196613318	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	10226543	196613318	1409112	21	493										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85626603	85626603	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	actgagctaatcgttcatctGtttgtgctcccattggctta	8	10	2	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr4:85626603G>A	ENST00000295888.4	-	54	8686	c.8279C>T	c.(8278-8280)aCa>aTa	p.T2760I	WDFY3_ENST00000322366.6_Missense_Mutation_p.T2743I	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2760	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.|Interaction with SQSTM1.|Sufficient for translocalization to p62 bodies/ALIS.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TCGTTCATCTGTTTGTGCTCC	0.388																																					p.T2760I		Atlas-SNP	.											.	WDFY3	314	.	0			c.C8279T						.						233	203	213					4																	85626603		2203	4300	6503	SO:0001583	missense	23001	exon54			TCATCTGTTTGTG	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.8279C>T	chr4.hg19:g.85626603G>A	ENSP00000295888:p.Thr2760Ile	140.0	0.0		168.0	34.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	34	5.342568	0.95783	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000514711	T;T;T	0.64991	-0.13;-0.13;-0.13	5.64	5.64	0.86602	BEACH domain (4);	0.000000	0.85682	D	0.000000	D	0.83101	0.5181	M	0.91354	3.2	0.80722	D	1	D	0.62365	0.991	D	0.63192	0.912	D	0.85282	0.1062	10	0.59425	D	0.04	.	19.8946	0.96949	0.0:0.0:1.0:0.0	.	2760	Q8IZQ1	WDFY3_HUMAN	I	2743;2760;363	ENSP00000318466:T2743I;ENSP00000295888:T2760I;ENSP00000424987:T363I	ENSP00000295888:T2760I	T	-	2	0	WDFY3	85845627	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.544000	0.98092	2.937000	0.99478	0.650000	0.86243	ACA	.	.		0.388	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85626603	G	A	85626603	3	1	6	1	0	0	0	0	1	0	0	0	17285	1377	48	3	2361	3	WDFY3	4	85626603	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10		85626603	105527673	22	494										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123236737	123236737	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gggcaatactcttacaacacTgacaggagaggaagacatag	11	8	1	3			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr4:123236737T>A	ENST00000264501.4	+	61	10806	c.10433T>A	c.(10432-10434)cTg>cAg	p.L3478Q	KIAA1109_ENST00000455637.1_Missense_Mutation_p.L3478Q|KIAA1109_ENST00000388738.3_Missense_Mutation_p.L3478Q			Q2LD37	K1109_HUMAN	KIAA1109	3478					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CTTACAACACTGACAGGAGAG	0.418																																					p.L3478Q		Atlas-SNP	.											.	KIAA1109	424	.	0			c.T10433A						.						197	184	188					4																	123236737		2012	4175	6187	SO:0001583	missense	84162	exon59			CAACACTGACAGG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.10433T>A	chr4.hg19:g.123236737T>A	ENSP00000264501:p.Leu3478Gln	153.0	0.0		152.0	27.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.786466	0.90367	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637;ENST00000438707	T;T;T;T	0.46451	1.44;1.44;0.87;1.01	5.63	5.63	0.86233	.	0.000000	0.56097	D	0.000024	T	0.54255	0.1847	L	0.49126	1.545	0.54753	D	0.999985	D;P	0.54397	0.966;0.943	P;P	0.56700	0.804;0.642	T	0.57447	-0.7810	10	0.87932	D	0	.	15.8347	0.78789	0.0:0.0:0.0:1.0	.	3478;3478	Q2LD37-6;Q2LD37	.;K1109_HUMAN	Q	3478;3478;3478;94	ENSP00000264501:L3478Q;ENSP00000373390:L3478Q;ENSP00000389925:L3478Q;ENSP00000410874:L94Q	ENSP00000264501:L3478Q	L	+	2	0	KIAA1109	123456187	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	7.975000	0.88055	2.143000	0.66587	0.528000	0.53228	CTG	.	.		0.418	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123236737	T	A	123236737	3	1	6	1	0	0	0	0	1	0	0	0	8217	1580	55	4	10667	4	KIAA1109	4	123236737	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	37610134	123236737	67917539	23	495										
RXFP1	59350	hgsc.bcm.edu	37	chr4	159568324	159568324	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	agatacagaaagtattggagCccagatttattcagtggcaa	10	6	1	3			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr4:159568324C>T	ENST00000307765.5	+	16	1978	c.1727C>T	c.(1726-1728)gCc>gTc	p.A576V	RXFP1_ENST00000448688.2_Missense_Mutation_p.A471V|RXFP1_ENST00000470033.1_Missense_Mutation_p.A543V|RXFP1_ENST00000460056.2_Missense_Mutation_p.A495V|RXFP1_ENST00000343542.5_Missense_Mutation_p.A528V	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	576					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		AGTATTGGAGCCCAGATTTAT	0.328																																					p.A603V		Atlas-SNP	.											.	RXFP1	98	.	0			c.C1808T						.						51	48	49					4																	159568324		1806	4079	5885	SO:0001583	missense	59350	exon16			TTGGAGCCCAGAT	AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"GPCR / Class A : Relaxin family peptide receptors"	19718	protein-coding gene	gene with protein product		606654	"leucine-rich repeat-containing G protein-coupled receptor 7"	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.1727C>T	chr4.hg19:g.159568324C>T	ENSP00000303248:p.Ala576Val	71.0	0.0		95.0	21.0	NM_001253727	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Missense_Mutation	SNP	ENST00000307765.5	hg19	CCDS43276.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.957387	0.73902	.	.	ENSG00000171509	ENST00000460056;ENST00000307765;ENST00000448688;ENST00000343542;ENST00000470033;ENST00000440678	T;T;T;T;T	0.36699	1.24;1.24;1.24;1.24;1.24	5.64	4.8	0.61643	GPCR, rhodopsin-like superfamily (1);	0.101317	0.64402	D	0.000003	T	0.52677	0.1749	M	0.68317	2.08	0.44547	D	0.997509	P;P;P;B;P;B;P;P	0.49253	0.872;0.851;0.872;0.221;0.921;0.025;0.872;0.612	P;P;P;B;P;B;P;P	0.56474	0.742;0.799;0.678;0.224;0.628;0.043;0.678;0.685	T	0.51220	-0.8733	10	0.34782	T	0.22	.	15.8211	0.78644	0.0:0.6816:0.3184:0.0	.	587;603;471;528;543;495;446;576	B3KV27;B4DGP2;B4DHD1;Q9HBX9-4;Q9HBX9-2;E9PCA3;Q59H16;Q9HBX9	.;.;.;.;.;.;.;RXFP1_HUMAN	V	495;576;471;528;543;446	ENSP00000423306:A495V;ENSP00000303248:A576V;ENSP00000414885:A471V;ENSP00000345889:A528V;ENSP00000420712:A543V	ENSP00000303248:A576V	A	+	2	0	RXFP1	159787774	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	5.120000	0.64685	1.387000	0.46486	-0.156000	0.13503	GCC	.	.		0.328	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634		T	159568324	C	T	159568324	3	4	6	1	0	0	0	0	1	0	0	0	13774	739	26	3	1789	3	RXFP1	4	159568324	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10	36331587	159568324	31585952	24	496										
TLL1	7092	hgsc.bcm.edu	37	chr4	167020507	167020507	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gtttggtgataacaactaccCaggacaggttgactgtgaat	11	7	0	3			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr4:167020507C>A	ENST00000061240.2	+	20	3382	c.2735C>A	c.(2734-2736)cCa>cAa	p.P912Q	TLL1_ENST00000507499.1_Missense_Mutation_p.P935Q	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	912	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		AACAACTACCCAGGACAGGTT	0.453																																					p.P912Q		Atlas-SNP	.											.	TLL1	194	.	0			c.C2735A						.						173	159	164					4																	167020507		2203	4300	6503	SO:0001583	missense	7092	exon20			ACTACCCAGGACA	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2735C>A	chr4.hg19:g.167020507C>A	ENSP00000061240:p.Pro912Gln	289.0	0.0		274.0	78.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	hg19	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.679164	0.68042	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	T;T	0.40476	1.03;1.03	5.76	5.76	0.90799	CUB (5);	0.000000	0.85682	U	0.000000	T	0.71500	0.3347	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.74609	-0.3608	10	0.59425	D	0.04	.	19.9813	0.97326	0.0:1.0:0.0:0.0	.	935;912	E9PD25;O43897	.;TLL1_HUMAN	Q	912;935	ENSP00000061240:P912Q;ENSP00000426082:P935Q	ENSP00000061240:P912Q	P	+	2	0	TLL1	167239957	1.000000	0.71417	0.966000	0.40874	0.073000	0.16967	7.776000	0.85560	2.726000	0.93360	0.655000	0.94253	CCA	.	.		0.453	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			A	167020507	C	A	167020507	3	1	6	1	0	0	0	0	1	0	0	0	15960	594	21	3	2813	3	TLL1	4	167020507	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10	7452183	167020507	24133769	25	497										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72179050	72179050	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	atgatgatacaatttctgacTggaatctaagtaagtcagaa	8	5	3	4			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:72179050T>A	ENST00000337273.5	+	11	1567	c.1141T>A	c.(1141-1143)Tgg>Agg	p.W381R	TNPO1_ENST00000506351.2_Missense_Mutation_p.W373R|TNPO1_ENST00000454282.1_Missense_Mutation_p.W331R|TNPO1_ENST00000523768.1_Missense_Mutation_p.W331R	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	381					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		AATTTCTGACTGGAATCTAAG	0.383																																					p.W381R		Atlas-SNP	.											.	TNPO1	90	.	0			c.T1141A						.						37	32	34					5																	72179050		2203	4300	6503	SO:0001583	missense	3842	exon11			TCTGACTGGAATC	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.1141T>A	chr5.hg19:g.72179050T>A	ENSP00000336712:p.Trp381Arg	332.0	0.0		336.0	91.0	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.317790	0.81469	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	5.07	5.07	0.68467	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.87943	0.6305	H	0.97465	4.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75484	0.986;0.976	D	0.92253	0.5810	10	0.87932	D	0	-2.574	15.1295	0.72511	0.0:0.0:0.0:1.0	.	331;381	Q92973-3;Q92973	.;TNPO1_HUMAN	R	381;331;331;373	ENSP00000336712:W381R;ENSP00000398524:W331R;ENSP00000428899:W331R;ENSP00000425118:W373R	ENSP00000336712:W381R	W	+	1	0	TNPO1	72214806	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.668000	0.83897	2.037000	0.60232	0.397000	0.26171	TGG	.	.		0.383	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		A	72179050	T	A	72179050	3	1	6	1	0	0	0	0	1	0	0	0	16350	1580	55	4	1183	4	TNPO1	5	72179050	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10		72179050	108736210	26	498										
PSD2	84249	hgsc.bcm.edu	37	chr5	139219625	139219625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	tttgcaggaggagcaactgcGgtctcatgagaataagttga	13	6	1	2	rs200345805		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:139219625G>A	ENST00000274710.3	+	14	2187	c.1982G>A	c.(1981-1983)cGg>cAg	p.R661Q		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	661					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCAACTGCGGTCTCATGAG	0.562																																					p.R661Q		Atlas-SNP	.											PSD2,NS,adenocarcinoma,0,1	PSD2	88	.	0			c.G1982A						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	91	84	86		1982	4.9	1	5		86	2,8598	2.2+/-6.3	0,2,4298	no	missense	PSD2	NM_032289.2	43	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	possibly-damaging	661/772	139219625	3,13003	2203	4300	6503	SO:0001583	missense	84249	exon14			AACTGCGGTCTCA	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1982G>A	chr5.hg19:g.139219625G>A	ENSP00000274710:p.Arg661Gln	68.0	0.0		60.0	9.0	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.654046	0.47362	2.27E-4	2.33E-4	ENSG00000146005	ENST00000274710	T	0.12672	2.66	4.95	4.95	0.65309	.	0.222920	0.35291	N	0.003306	T	0.08537	0.0212	L	0.28556	0.865	0.36681	D	0.87907	P	0.34462	0.454	B	0.23150	0.044	T	0.22695	-1.0209	10	0.37606	T	0.19	.	9.3902	0.38367	0.16:0.0:0.84:0.0	.	661	Q9BQI7	PSD2_HUMAN	Q	661	ENSP00000274710:R661Q	ENSP00000274710:R661Q	R	+	2	0	PSD2	139199809	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	1.618000	0.36954	2.460000	0.83146	0.561000	0.74099	CGG	.	G|0.999;A|0.001		0.562	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		A	139219625	G	A	139219625	3	1	6	1	0	0	0	0	1	0	0	0	12659	1116	39	1	2032	1	PSD2	5	139219625	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	67040575	139219625	41695635	27	499										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140793290	140793290	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	cagccccaataagcacttctCcctaagagttcagagccgtg	8	14	2	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:140793290C>A	ENST00000398610.2	+	1	548	c.548C>A	c.(547-549)tCc>tAc	p.S183Y	PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	183	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGCACTTCTCCCTAAGAGTT	0.577																																					p.S183Y		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.C548A						.						34	36	36					5																	140793290		1971	4153	6124	SO:0001583	missense	56106	exon1			ACTTCTCCCTAAG		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.548C>A	chr5.hg19:g.140793290C>A	ENSP00000381611:p.Ser183Tyr	79.0	0.0		81.0	24.0	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	hg19	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	c	10.97	1.502992	0.26949	.	.	ENSG00000253846	ENST00000398610	T	0.52983	0.64	5.49	5.49	0.81192	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.71247	0.3317	M	0.90425	3.115	0.09310	N	1	D;D	0.64830	0.975;0.994	P;D	0.67231	0.819;0.95	T	0.66783	-0.5836	9	0.66056	D	0.02	.	9.9105	0.41403	0.0:0.7868:0.1397:0.0735	.	183;183	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	Y	183	ENSP00000381611:S183Y	ENSP00000381611:S183Y	S	+	2	0	PCDHGA10	140773474	0.000000	0.05858	0.947000	0.38551	0.350000	0.29205	0.287000	0.18920	2.590000	0.87494	0.557000	0.71058	TCC	.	.		0.577	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		A	140793290	C	A	140793290	3	1	6	1	0	0	0	0	1	0	0	0	11560	855	30	3	550	3	PCDHGA10	5	140793290	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10	1573665	140793290	40121970	28	500										
PCDHGB7	56099	hgsc.bcm.edu	37	chr5	140799322	140799322	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gtgcgcatggtgcgtgctttGggtgacaaggactcggtccg	17	9	0	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:140799322G>C	ENST00000398594.2	+	1	1896	c.1896G>C	c.(1894-1896)ttG>ttC	p.L632F	PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	632	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCGTGCTTTGGGTGACAAGG	0.647																																					p.L632F		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.G1896C						.						60	66	64					5																	140799322		2182	4289	6471	SO:0001583	missense	56099	exon1			TGCTTTGGGTGAC	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1896G>C	chr5.hg19:g.140799322G>C	ENSP00000381594:p.Leu632Phe	91.0	0.0		102.0	17.0	NM_018927	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	hg19	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	g	11.66	1.703845	0.30232	.	.	ENSG00000254122	ENST00000398594	T	0.74737	-0.87	5.57	4.71	0.59529	Cadherin (4);Cadherin-like (1);	0.000000	0.27700	U	0.018202	T	0.70954	0.3283	L	0.35249	1.045	0.21604	N	0.999624	P;P	0.50943	0.94;0.862	P;P	0.56434	0.798;0.551	T	0.60490	-0.7253	10	0.31617	T	0.26	.	5.6108	0.17404	0.0756:0.139:0.6419:0.1435	.	632;632	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	F	632	ENSP00000381594:L632F	ENSP00000381594:L632F	L	+	3	2	PCDHGB7	140779506	0.997000	0.39634	0.988000	0.46212	0.665000	0.39181	3.193000	0.50997	1.356000	0.45884	0.491000	0.48974	TTG	.	.		0.647	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		C	140799322	G	C	140799322	3	2	6	1	0	0	0	0	1	0	0	0	11577	1339	47	4	1898	4	PCDHGB7	5	140799322	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	6032	140799322	40115938	29	501										
MRPL22	29093	hgsc.bcm.edu	37	chr5	154320807	154320807	+	Frame_Shift_Del	DEL	G	G	-													0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gatacataacctgaggagccGggggaagctggccttggggt							TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:154320807delG	ENST00000523037.1	+	2	100	c.59delG	c.(58-60)cggfs	p.R20fs	MRPL22_ENST00000522038.1_Frame_Shift_Del_p.R20fs|MRPL22_ENST00000439747.3_Frame_Shift_Del_p.R46fs|MRPL22_ENST00000265229.8_5'UTR	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	20					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTGAGGAGCCGGGGGAAGCTG	0.537																																					p.R20fs		Atlas-Indel,Pindel	.											.	MRPL22	18	.	0			c.58delC						.						107	110	109					5																	154320807		2203	4300	6503	SO:0001589	frameshift_variant	29093	exon2			.	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"Mitochondrial ribosomal proteins / large subunits"	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.59delG	chr5.hg19:g.154320807delG	ENSP00000431040:p.Arg20fs	130.0	0.0		170.0	42.0	NM_014180	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Frame_Shift_Del	DEL	ENST00000523037.1	hg19	CCDS4331.1																																																																																			.	.		0.537	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2			-	154320807	G	-	154320807	7	5	6	1	0	1	0	1	0	0	0	0	9797	1116	39	0	65	0	MRPL22	5	154320807	Frame_Shift_Del	DEL	G	TCGA-2Y-A9GW-01A-11D-A382-10	13521485	154320807	26594453	30	502										
SLC34A1	6569	hgsc.bcm.edu	37	chr5	176825095	176825095	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	cccaagtggttacagacatgGgacttcctgcctcgctggat	11	12	0	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:176825095G>A	ENST00000324417.5	+	13	1819	c.1728G>A	c.(1726-1728)tgG>tgA	p.W576*	SLC34A1_ENST00000513614.1_3'UTR	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1	576					arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TACAGACATGGGACTTCCTGC	0.667																																					p.W576X		Atlas-SNP	.											.	SLC34A1	73	.	0			c.G1728A						.						74	78	77					5																	176825095		2203	4300	6503	SO:0001587	stop_gained	6569	exon13			GACATGGGACTTC	L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"Solute carriers"	11019	protein-coding gene	gene with protein product	"sodium/phosphate co-transporter", "solute carrier family 17 (sodium phosphate), member 2", "Na+-phosphate cotransporter type II"	182309	"solute carrier family 34 (sodium phosphate), member 1"	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.1728G>A	chr5.hg19:g.176825095G>A	ENSP00000321424:p.Trp576*	479.0	1.0		521.0	157.0	NM_003052	B4DPE3	Nonsense_Mutation	SNP	ENST00000324417.5	hg19	CCDS4418.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.647222	0.87958	.	.	ENSG00000131183	ENST00000324417	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.3697	19.057	0.93069	0.0:0.0:1.0:0.0	.	.	.	.	X	576	.	ENSP00000321424:W576X	W	+	3	0	SLC34A1	176757701	1.000000	0.71417	1.000000	0.80357	0.086000	0.17979	9.706000	0.98722	2.491000	0.84063	0.455000	0.32223	TGG	.	.		0.667	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052		A	176825095	G	A	176825095	4	1	6	1	0	0	0	0	0	1	0	0	14582	1241	43	3	1865	3	SLC34A1	5	176825095	Nonsense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	22504288	176825095	4090165	31	503										
TBC1D22B	55633	hgsc.bcm.edu	37	chr6	37281660	37281660	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ctggaagagcttgtcagccgGattgatggtaggttcagagg	16	6	2	3			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr6:37281660G>T	ENST00000373491.3	+	10	1304	c.1158G>T	c.(1156-1158)cgG>cgT	p.R386R		NM_017772.2	NP_060242.2	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B	386	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|prostate(1)	15			OV - Ovarian serous cystadenocarcinoma(102;0.241)			TTGTCAGCCGGATTGATGGTA	0.493																																					p.R386R		Atlas-SNP	.											TBC1D22B,colon,carcinoma,0,1	TBC1D22B	37	.	0			c.G1158T						.						185	165	172					6																	37281660		2203	4300	6503	SO:0001819	synonymous_variant	55633	exon10			CAGCCGGATTGAT	AK096340	CCDS4832.1	6p21.2	2005-01-05	2005-01-05	2005-01-05	ENSG00000065491	ENSG00000065491			21602	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 197"	C6orf197			Standard	NM_017772		Approved	FLJ20337, dJ744I24.2	uc003onn.3	Q9NU19	OTTHUMG00000014619	ENST00000373491.3:c.1158G>T	chr6.hg19:g.37281660G>T		170.0	0.0		191.0	35.0	NM_017772	A8KA28|Q32MQ8|Q5VUK9|Q6P4C3|Q7Z6P7|Q9BPV6|Q9BUT5|Q9NXB6	Silent	SNP	ENST00000373491.3	hg19	CCDS4832.1																																																																																			.	.		0.493	TBC1D22B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040402.1	NM_017772		T	37281660	G	T	37281660	2	4	6	1	0	0	0	0	0	0	0	1	15627	1161	41	3		3	TBC1D22B	6	37281660	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10		37281660	133833407	32	504										
NCOA7	135112	hgsc.bcm.edu	37	chr6	126176369	126176369	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gatcaggcgtacagaactaaAgagatattatagtattggtg	11	4	1	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr6:126176369A>G	ENST00000368357.3	+	4	606	c.254A>G	c.(253-255)aAg>aGg	p.K85R	NCOA7_ENST00000487635.1_3'UTR|NCOA7_ENST00000229634.9_Intron|NCOA7_ENST00000392477.2_Missense_Mutation_p.K85R	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	85					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		ACAGAACTAAAGAGATATTAT	0.313																																					p.K85R		Atlas-SNP	.											.	NCOA7	92	.	0			c.A254G						.						84	94	90					6																	126176369		2203	4300	6503	SO:0001583	missense	135112	exon4			AACTAAAGAGATA	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 4"	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.254A>G	chr6.hg19:g.126176369A>G	ENSP00000357341:p.Lys85Arg	92.0	0.0		99.0	23.0	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	hg19	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.248350	0.59103	.	.	ENSG00000111912	ENST00000368357;ENST00000431092;ENST00000392477;ENST00000453302;ENST00000417494;ENST00000428318;ENST00000419660	T;T;T;T	0.60548	2.56;2.56;0.67;0.18	5.39	5.39	0.77823	.	0.111289	0.64402	D	0.000013	T	0.57489	0.2057	L	0.29908	0.895	0.80722	D	1	D;P;D;P	0.76494	0.999;0.868;0.972;0.682	D;B;P;B	0.83275	0.996;0.359;0.737;0.141	T	0.63821	-0.6550	10	0.62326	D	0.03	-25.048	14.1421	0.65327	1.0:0.0:0.0:0.0	.	85;85;85;85	Q8NI08-6;Q8NI08-2;Q8NI08-4;Q8NI08	.;.;.;NCOA7_HUMAN	R	85	ENSP00000357341:K85R;ENSP00000376269:K85R;ENSP00000406363:K85R;ENSP00000408211:K85R	ENSP00000357341:K85R	K	+	2	0	NCOA7	126218062	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.487000	0.66863	2.267000	0.75376	0.528000	0.53228	AAG	.	.		0.313	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748		G	126176369	A	G	126176369	3	3	6	1	0	0	0	0	1	0	0	0	10243	72	3	2	260	2	NCOA7	6	126176369	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	88894709	126176369	44938698	33	505										
OSBPL3	26031	hgsc.bcm.edu	37	chr7	24870414	24870414	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gaaaaaaactggaagcccttGtcctcccgaatacattcata	6	11	1	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:24870414G>T	ENST00000313367.2	-	16	2308	c.1857C>A	c.(1855-1857)gaC>gaA	p.D619E	OSBPL3_ENST00000431825.2_Missense_Mutation_p.D552E|OSBPL3_ENST00000409069.1_Missense_Mutation_p.D552E|OSBPL3_ENST00000353930.1_Missense_Mutation_p.D583E|OSBPL3_ENST00000396431.1_Missense_Mutation_p.D588E|OSBPL3_ENST00000352860.1_Missense_Mutation_p.D588E|OSBPL3_ENST00000396429.1_Missense_Mutation_p.D583E	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	619					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						GGAAGCCCTTGTCCTCCCGAA	0.428																																					p.D619E		Atlas-SNP	.											.	OSBPL3	100	.	0			c.C1857A						.						183	198	193					7																	24870414		2203	4300	6503	SO:0001583	missense	26031	exon16			GCCCTTGTCCTCC	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.1857C>A	chr7.hg19:g.24870414G>T	ENSP00000315410:p.Asp619Glu	120.0	0.0		140.0	34.0	NM_015550	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	hg19	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.189334	0.57909	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33;1.33;1.33	5.74	3.86	0.44501	.	0.045811	0.85682	D	0.000000	T	0.34106	0.0886	L	0.48986	1.54	0.51482	D	0.999923	B;B;B;B	0.25563	0.022;0.041;0.041;0.129	B;B;B;B	0.37387	0.073;0.073;0.073;0.248	T	0.29579	-1.0007	10	0.48119	T	0.1	-17.1482	5.568	0.17180	0.0975:0.1389:0.6216:0.142	.	552;588;583;619	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	E	619;588;583;552;588;583;552	ENSP00000315410:D619E;ENSP00000315331:D588E;ENSP00000315277:D583E;ENSP00000389779:D552E;ENSP00000379708:D588E;ENSP00000379706:D583E;ENSP00000386953:D552E	ENSP00000315410:D619E	D	-	3	2	OSBPL3	24836939	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.538000	0.36094	2.732000	0.93576	0.591000	0.81541	GAC	.	.		0.428	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2			T	24870414	G	T	24870414	3	4	6	1	0	0	0	0	1	0	0	0	11288	1368	48	3	838	3	OSBPL3	7	24870414	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10		24870414	134268249	34	506										
POR	5447	hgsc.bcm.edu	37	chr7	75583458	75583458	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	actggttcctcttcagaaagAaaaaagaagaagtccccgag	9	9	2	4			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:75583458A>G	ENST00000461988.1	+	2	253	c.148A>G	c.(148-150)Aaa>Gaa	p.K50E	POR_ENST00000394893.1_Missense_Mutation_p.K50E|POR_ENST00000419840.1_5'UTR	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	47					carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	CTTCAGAAAGAAAAAAGAAGA	0.498																																					p.K50E		Atlas-SNP	.											.	POR	46	.	0			c.A148G						.						75	71	72					7																	75583458		1884	4113	5997	SO:0001583	missense	5447	exon2			AGAAAGAAAAAAG	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.148A>G	chr7.hg19:g.75583458A>G	ENSP00000419970:p.Lys50Glu	123.0	0.0		173.0	12.0	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Missense_Mutation	SNP	ENST00000461988.1	hg19	CCDS5579.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.70|17.70	3.454134|3.454134	0.63290|0.63290	.|.	.|.	ENSG00000127948|ENSG00000127948	ENST00000447222|ENST00000453773;ENST00000439963;ENST00000461988;ENST00000394893;ENST00000412521;ENST00000414186;ENST00000432753;ENST00000449920;ENST00000418341	.|T;T;T	.|0.46819	.|0.86;4.28;4.28	4.86|4.86	4.86|4.86	0.63082|0.63082	.|.	.|0.102540	.|0.64402	.|D	.|0.000004	T|T	0.51024|0.51024	0.1650|0.1650	M|M	0.76328|0.76328	2.33|2.33	0.80722|0.80722	D|D	1|1	.|B	.|0.31968	.|0.349	.|B	.|0.36885	.|0.235	T|T	0.52990|0.52990	-0.8501|-0.8501	5|10	.|0.40728	.|T	.|0.16	-2.0478|-2.0478	12.4164|12.4164	0.55496|0.55496	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|56	.|Q59ED7	.|.	G|E	22|50	.|ENSP00000390540:K50E;ENSP00000419970:K50E;ENSP00000378355:K50E	.|ENSP00000378355:K50E	E|K	+|+	2|1	0|0	POR|POR	75421394|75421394	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	6.192000|6.192000	0.72069|0.72069	1.823000|1.823000	0.53134|0.53134	0.533000|0.533000	0.62120|0.62120	GAA|AAA	.	.		0.498	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941		G	75583458	A	G	75583458	3	3	6	1	0	0	0	0	1	0	0	0	12266	247	9	2	150	2	POR	7	75583458	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	50713044	75583458	83555205	35	507										
GIGYF1	64599	hgsc.bcm.edu	37	chr7	100285497	100285497	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gaactccttgtcctgcagctCttccgggacctggcagtggg	13	13	1	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:100285497C>G	ENST00000275732.5	-	3	1384	c.175G>C	c.(175-177)Gag>Cag	p.E59Q	GIGYF1_ENST00000471340.2_5'UTR	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	59					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					TCCTGCAGCTCTTCCGGGACC	0.682																																					p.E59Q		Atlas-SNP	.											.	GIGYF1	113	.	0			c.G175C						.						58	62	61					7																	100285497		2203	4299	6502	SO:0001583	missense	64599	exon3			GCAGCTCTTCCGG	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"GYF domain containing 1"	612064	"PERQ amino acid rich, with GYF domain 1"	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.175G>C	chr7.hg19:g.100285497C>G	ENSP00000275732:p.Glu59Gln	95.0	0.0		121.0	38.0	NM_022574	Q6Y7W7|Q8WZ38	Missense_Mutation	SNP	ENST00000275732.5	hg19	CCDS34708.1	.	.	.	.	.	.	.	.	.	.	.	22.6	4.316445	0.81469	.	.	ENSG00000146830	ENST00000275732	D	0.83914	-1.78	5.01	5.01	0.66863	.	0.063489	0.64402	D	0.000008	D	0.84379	0.5459	L	0.52573	1.65	0.58432	D	0.999998	D	0.56521	0.976	P	0.52598	0.703	T	0.83303	-0.0027	10	0.35671	T	0.21	-23.1894	15.8586	0.79005	0.0:1.0:0.0:0.0	.	59	O75420	PERQ1_HUMAN	Q	59	ENSP00000275732:E59Q	ENSP00000275732:E59Q	E	-	1	0	GIGYF1	100123433	1.000000	0.71417	0.958000	0.39756	0.517000	0.34286	7.320000	0.79064	2.597000	0.87782	0.563000	0.77884	GAG	.	.		0.682	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		G	100285497	C	G	100285497	3	3	6	1	0	0	0	0	1	0	0	0	6385	922	32	4	3020	4	GIGYF1	7	100285497	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10	24702039	100285497	58853166	36	508										
DOCK4	9732	hgsc.bcm.edu	37	chr7	111398823	111398823	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ctcctggctctctggaatggGagtcacagcatatatctgca	10	11	3	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:111398823G>T	ENST00000437633.1	-	40	4415	c.4159C>A	c.(4159-4161)Ccc>Acc	p.P1387T	DOCK4_ENST00000428084.1_Missense_Mutation_p.P1396T|DOCK4_ENST00000494651.2_Missense_Mutation_p.P270T	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1387	DHR-2.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				TCTGGAATGGGAGTCACAGCA	0.483																																					p.P1387T		Atlas-SNP	.											.	DOCK4	365	.	0			c.C4159A						.						77	72	74					7																	111398823		1925	4117	6042	SO:0001583	missense	9732	exon40			GAATGGGAGTCAC		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.4159C>A	chr7.hg19:g.111398823G>T	ENSP00000404179:p.Pro1387Thr	99.0	0.0		143.0	28.0	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.660933	0.88154	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288	T;T;T	0.21932	2.57;1.98;2.55	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.57257	0.2041	M	0.91249	3.19	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.78314	0.96;0.982;0.988;0.988;0.991	T	0.66763	-0.5841	10	0.87932	D	0	.	19.1084	0.93307	0.0:0.0:1.0:0.0	.	294;270;1432;1387;1396	B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2	.;.;.;DOCK4_HUMAN;.	T	1375;1396;270;1387;1384	ENSP00000410746:P1396T;ENSP00000440944:P270T;ENSP00000404179:P1387T	ENSP00000345432:P1384T	P	-	1	0	DOCK4	111186059	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.585000	0.98223	2.820000	0.97059	0.650000	0.86243	CCC	.	.		0.483	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		T	111398823	G	T	111398823	3	4	6	1	0	0	0	0	1	0	0	0	4691	1174	41	3	1793	3	DOCK4	7	111398823	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	11113326	111398823	47739840	37	509										
C7orf58	79974	hgsc.bcm.edu	37	chr7	120906375	120906375	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ggaatggcagaaagtacatgGcactaaattctatcacaacg	9	8	2	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:120906375G>T	ENST00000310396.5	+	19	2872	c.2405G>T	c.(2404-2406)gGc>gTc	p.G802V		NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	802						endoplasmic reticulum (GO:0005783)											AAAGTACATGGCACTAAATTC	0.393																																					p.G802V		Atlas-SNP	.											.	.	.	.	0			c.G2405T						.						218	195	203					7																	120906375		2203	4300	6503	SO:0001583	missense	79974	exon19			TACATGGCACTAA		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.2405G>T	chr7.hg19:g.120906375G>T	ENSP00000309772:p.Gly802Val	116.0	0.0		160.0	19.0	NM_024913	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	hg19	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.665015	0.67700	.	.	ENSG00000106034	ENST00000310396	T	0.17528	2.27	5.94	5.94	0.96194	.	0.247982	0.41001	D	0.000967	T	0.32346	0.0826	L	0.56769	1.78	0.80722	D	1	D	0.63880	0.993	D	0.65874	0.939	T	0.05194	-1.0900	10	0.72032	D	0.01	-15.2066	6.9921	0.24761	0.1083:0.1734:0.7183:0.0	.	802	A4D0V7	CG058_HUMAN	V	802	ENSP00000309772:G802V	ENSP00000309772:G802V	G	+	2	0	C7orf58	120693611	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.588000	0.60999	2.816000	0.96949	0.561000	0.74099	GGC	.	.		0.393	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		T	120906375	G	T	120906375	3	4	6	1	0	0	0	0	1	0	0	0	2407	1203	42	3	2521	3	C7orf58	7	120906375	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	9507552	120906375	38232288	38	510										
AASS	10157	hgsc.bcm.edu	37	chr7	121758381	121758381	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	cttagaaacattaccagttcCtgtgaacacaaatgttaagg	7	8	0	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:121758381C>T	ENST00000393376.1	-	5	762	c.667G>A	c.(667-669)Gga>Aga	p.G223R	AASS_ENST00000473553.1_Intron|AASS_ENST00000417368.2_Missense_Mutation_p.G223R			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	223	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TTACCAGTTCCTGTGAACACA	0.403																																					p.G223R		Atlas-SNP	.											.	AASS	123	.	0			c.G667A						.						92	86	88					7																	121758381		2203	4300	6503	SO:0001583	missense	10157	exon6			CAGTTCCTGTGAA	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.667G>A	chr7.hg19:g.121758381C>T	ENSP00000377040:p.Gly223Arg	49.0	0.0		91.0	18.0	NM_005763	O95462	Missense_Mutation	SNP	ENST00000393376.1	hg19	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	.	27.9	4.868839	0.91587	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	D;D	0.94280	-3.39;-3.39	5.02	5.02	0.67125	Alanine dehydrogenase/PNT, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.97334	0.9128	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98055	1.0390	10	0.87932	D	0	-16.5808	18.1242	0.89581	0.0:1.0:0.0:0.0	.	223	Q9UDR5	AASS_HUMAN	R	223	ENSP00000377040:G223R;ENSP00000403768:G223R	ENSP00000351834:G223R	G	-	1	0	AASS	121545617	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.627000	0.83176	2.610000	0.88304	0.655000	0.94253	GGA	.	.		0.403	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		T	121758381	C	T	121758381	3	4	6	1	0	0	0	0	1	0	0	0	24	690	24	3	2189	3	AASS	7	121758381	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10	852006	121758381	37380282	39	511										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73848214	73848214	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ttcattgtgctttccaccatTgctttgtctctcaatacgct	5	12	3	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr8:73848214T>C	ENST00000523207.1	+	3	1212	c.624T>C	c.(622-624)atT>atC	p.I208I		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	208					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	TTTCCACCATTGCTTTGTCTC	0.483																																					p.I208I		Atlas-SNP	.											.	KCNB2	228	.	0			c.T624C						.						233	223	226					8																	73848214		2203	4300	6503	SO:0001819	synonymous_variant	9312	exon3			CACCATTGCTTTG	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.624T>C	chr8.hg19:g.73848214T>C		159.0	0.0		449.0	167.0	NM_004770	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	hg19	CCDS6209.1																																																																																			.	.		0.483	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		C	73848214	T	C	73848214	2	2	6	1	0	0	0	0	0	0	0	1	8022	1800	63	2		2	KCNB2	8	73848214	Silent	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10		73848214	72515808	40	512										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73848327	73848327	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gtgtattgcatggtttaccaTggagtaccttttgcgattct	10	7	1	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr8:73848327T>C	ENST00000523207.1	+	3	1325	c.737T>C	c.(736-738)aTg>aCg	p.M246T		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	246					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	TGGTTTACCATGGAGTACCTT	0.463																																					p.M246T		Atlas-SNP	.											.	KCNB2	228	.	0			c.T737C						.						202	173	183					8																	73848327		2203	4300	6503	SO:0001583	missense	9312	exon3			TTACCATGGAGTA	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.737T>C	chr8.hg19:g.73848327T>C	ENSP00000430846:p.Met246Thr	203.0	0.0		585.0	41.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.792524	0.70452	.	.	ENSG00000182674	ENST00000523207	D	0.98400	-4.91	5.93	5.93	0.95920	Ion transport (1);	0.000000	0.56097	D	0.000035	D	0.97657	0.9232	N	0.21097	0.63	0.58432	D	0.999994	D	0.67145	0.996	D	0.64877	0.93	D	0.99470	1.0945	10	0.66056	D	0.02	.	16.3871	0.83514	0.0:0.0:0.0:1.0	.	246	Q92953	KCNB2_HUMAN	T	246	ENSP00000430846:M246T	ENSP00000430846:M246T	M	+	2	0	KCNB2	74010881	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.289000	0.72696	2.265000	0.75225	0.533000	0.62120	ATG	.	.		0.463	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		C	73848327	T	C	73848327	3	2	6	1	0	0	0	0	1	0	0	0	8022	1464	51	2	743	2	KCNB2	8	73848327	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	113	73848327	72515695	41	513										
FBXO43	286151	hgsc.bcm.edu	37	chr8	101146559	101146559	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gcgatttaaaagctggagccGagtggcagcatcctcgacat	12	10	0	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr8:101146559G>T	ENST00000428847.2	-	4	2024	c.1708C>A	c.(1708-1710)Cgg>Agg	p.R570R		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	570					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			AGCTGGAGCCGAGTGGCAGCA	0.493																																					p.R570R		Atlas-SNP	.											.	FBXO43	155	.	0			c.C1708A						.						90	90	90					8																	101146559		1910	4137	6047	SO:0001819	synonymous_variant	286151	exon4			GGAGCCGAGTGGC	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"F-boxes /  "other""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.1708C>A	chr8.hg19:g.101146559G>T		120.0	0.0		384.0	42.0	NM_001029860		Silent	SNP	ENST00000428847.2	hg19	CCDS47904.1																																																																																			.	.		0.493	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918		T	101146559	G	T	101146559	2	4	6	1	0	0	0	0	0	0	0	1	5760	1057	37	1		1	FBXO43	8	101146559	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	27298232	101146559	45217463	42	514										
SLC30A8	169026	hgsc.bcm.edu	37	chr8	118159313	118159313	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	aagcccacagaaaagggggcGaatgagtacgcctatgccaa	12	10	0	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr8:118159313G>A	ENST00000456015.2	+	2	192	c.192G>A	c.(190-192)gcG>gcA	p.A64A	SLC30A8_ENST00000519688.1_Silent_p.A15A|SLC30A8_ENST00000427715.2_Silent_p.A15A|SLC30A8_ENST00000521243.1_Silent_p.A15A	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	64					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			AAAAGGGGGCGAATGAGTACG	0.507																																					p.A64A	Ovarian(162;1202 1922 6011 16223 52092)	Atlas-SNP	.											.	SLC30A8	102	.	0			c.G192A						.						174	147	156					8																	118159313		2203	4300	6503	SO:0001819	synonymous_variant	169026	exon2			GGGGGCGAATGAG		CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"Solute carriers"	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.192G>A	chr8.hg19:g.118159313G>A		172.0	0.0		488.0	97.0	NM_173851	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Silent	SNP	ENST00000456015.2	hg19	CCDS6322.1																																																																																			.	.		0.507	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851		A	118159313	G	A	118159313	2	1	6	1	0	0	0	0	0	0	0	1	14576	1045	37	1		1	SLC30A8	8	118159313	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	17012754	118159313	28204709	43	515										
AP2A2	161	hgsc.bcm.edu	37	chr11	1000560	1000560	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	tcagactcggcctctgtggtCgcgcctctcgctcctggctc	11	17	3	1	rs376836623		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr11:1000560C>T	ENST00000448903.2	+	15	2226	c.2085C>T	c.(2083-2085)gtC>gtT	p.V695V	AP2A2_ENST00000534328.1_Intron|AP2A2_ENST00000332231.5_Silent_p.V696V|AP2A2_ENST00000525891.1_3'UTR	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	695					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCTCTGTGGTCGCGCCTCTCG	0.697																																					p.V696V		Atlas-SNP	.											.	AP2A2	50	.	0			c.C2088T						.	C	,	1,3965		0,1,1982	11	11	11		2088,2085	-6.6	0	11		11	1,8253		0,1,4126	no	coding-synonymous,coding-synonymous	AP2A2	NM_001242837.1,NM_012305.3	,	0,2,6108	TT,TC,CC		0.0121,0.0252,0.0164	,	696/941,695/940	1000560	2,12218	1983	4127	6110	SO:0001819	synonymous_variant	161	exon15			TGTGGTCGCGCCT	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.2085C>T	chr11.hg19:g.1000560C>T		38.0	0.0		26.0	8.0	NM_001242837	O75403|Q53ET1|Q96SI8	Silent	SNP	ENST00000448903.2	hg19	CCDS44512.1																																																																																			.	.		0.697	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		T	1000560	C	T	1000560	2	4	6	1	0	0	0	0	0	0	0	1	740	871	31	1		1	AP2A2	11	1000560	Silent	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10		1000560	134005956	44	516										
TUB	7275	hgsc.bcm.edu	37	chr11	8118839	8118839	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ggacgttgaggtccaggatcTtgaggagtttgcactgaggc	16	7	1	3			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr11:8118839T>G	ENST00000299506.2	+	7	901	c.752T>G	c.(751-753)cTt>cGt	p.L251R	TUB_ENST00000305253.4_Missense_Mutation_p.L306R|TUB_ENST00000534099.1_Missense_Mutation_p.L257R	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	251					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		GTCCAGGATCTTGAGGAGTTT	0.602																																					p.L306R		Atlas-SNP	.											.	TUB	71	.	0			c.T917G						.						88	82	84					11																	8118839		2201	4296	6497	SO:0001583	missense	7275	exon8			AGGATCTTGAGGA	U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"tubby (mouse) homolog", "tubby homolog (mouse)"			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.752T>G	chr11.hg19:g.8118839T>G	ENSP00000299506:p.Leu251Arg	179.0	0.0		203.0	21.0	NM_003320	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000299506.2	hg19	CCDS7787.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.439687	0.83885	.	.	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	D;D;D	0.85773	-2.03;-2.03;-2.03	4.71	4.71	0.59529	Tubby, C-terminal (1);	0.061993	0.64402	D	0.000003	D	0.92645	0.7663	M	0.86651	2.83	0.80722	D	1	P;D;D	0.76494	0.901;0.999;0.999	B;D;D	0.71656	0.226;0.97;0.974	D	0.93879	0.7169	10	0.72032	D	0.01	-12.0625	14.6238	0.68605	0.0:0.0:0.0:1.0	.	257;251;306	E9PQR4;P50607;P50607-2	.;TUB_HUMAN;.	R	257;306;251	ENSP00000434400:L257R;ENSP00000305426:L306R;ENSP00000299506:L251R	ENSP00000299506:L251R	L	+	2	0	TUB	8075415	1.000000	0.71417	0.910000	0.35882	0.992000	0.81027	7.776000	0.85560	2.115000	0.64714	0.477000	0.44152	CTT	.	.		0.602	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320		G	8118839	T	G	8118839	3	3	6	1	0	0	0	0	1	0	0	0	16757	1609	56	5	989	5	TUB	11	8118839	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	7118279	8118839	126887677	45	517										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65350076	65350076	+	Frame_Shift_Del	DEL	G	G	-													0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	tgggggtcatagagaccccaGggacagagactgaggtattg							TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr11:65350076delG	ENST00000309295.4	+	9	2198	c.1933delG	c.(1933-1935)gggfs	p.G645fs		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	645	Glu-rich.					membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						AGAGACCCCAGGGACAGAGAC	0.547																																					p.P644fs		Atlas-Indel,Pindel	.											.	EHBP1L1	64	.	0			c.1932delA						.						51	56	54					11																	65350076		1914	4144	6058	SO:0001589	frameshift_variant	254102	exon9			.	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.1933delG	chr11.hg19:g.65350076delG	ENSP00000312671:p.Gly645fs	140.0	0.0		118.0	29.0	NM_001099409	Q8TB89|Q9H7M7	Frame_Shift_Del	DEL	ENST00000309295.4	hg19	CCDS44649.1																																																																																			.	.		0.547	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		-	65350076	G	-	65350076	7	5	6	1	0	1	0	1	0	0	0	0	4978	1000	35	0	1967	0	EHBP1L1	11	65350076	Frame_Shift_Del	DEL	G	TCGA-2Y-A9GW-01A-11D-A382-10	57231237	65350076	69656440	46	518										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73076531	73076531	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	cattgaaaggtagtgcccacGtgtgtctctaccatccagac	9	12	1	2	rs141322412	byFrequency	TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr11:73076531G>T	ENST00000263674.3	+	19	5997	c.5647G>T	c.(5647-5649)Gtg>Ttg	p.V1883L		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1883					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						TAGTGCCCACGTGTGTCTCTA	0.557																																					p.V1883L		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G5647T						.						160	116	131					11																	73076531		2200	4293	6493	SO:0001583	missense	9828	exon19			GCCCACGTGTGTC	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.5647G>T	chr11.hg19:g.73076531G>T	ENSP00000263674:p.Val1883Leu	100.0	0.0		93.0	22.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.367681	0.61513	.	.	ENSG00000110237	ENST00000263674	T	0.37058	1.22	5.8	4.9	0.64082	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.37404	0.1002	N	0.11000	0.08	0.58432	D	0.999995	D	0.89917	1.0	D	0.81914	0.995	T	0.19647	-1.0299	10	0.13853	T	0.58	-21.1515	14.2313	0.65895	0.0713:0.0:0.9287:0.0	.	1883	Q96PE2	ARHGH_HUMAN	L	1883	ENSP00000263674:V1883L	ENSP00000263674:V1883L	V	+	1	0	ARHGEF17	72754179	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.914000	0.87478	1.484000	0.48361	-0.119000	0.15052	GTG	.	G|0.999;A|0.001		0.557	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		T	73076531	G	T	73076531	3	4	6	1	0	0	0	0	1	0	0	0	900	1145	40	1	5721	1	ARHGEF17	11	73076531	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	7726455	73076531	61929985	47	519										
BACE1	23621	hgsc.bcm.edu	37	chr11	117162462	117162462	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	tgatggatttgactgcagctTcaaacactttcttgggcaaa	9	8	2	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr11:117162462T>G	ENST00000313005.6	-	6	1368	c.908A>C	c.(907-909)gAa>gCa	p.E303A	BACE1_ENST00000513780.1_Missense_Mutation_p.E278A|BACE1_ENST00000445823.2_Missense_Mutation_p.E259A|BACE1_ENST00000392937.6_Missense_Mutation_p.E203A|BACE1_ENST00000428381.2_Missense_Mutation_p.E234A|BACE1_ENST00000528053.1_Intron|BACE1_ENST00000514464.1_5'Flank|BACE1_ENST00000510630.1_Missense_Mutation_p.E178A	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	303					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		GACTGCAGCTTCAAACACTTT	0.483																																					p.E303A		Atlas-SNP	.											.	BACE1	33	.	0			c.A908C						.						169	140	150					11																	117162462		2201	4296	6497	SO:0001583	missense	23621	exon6			GCAGCTTCAAACA	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"beta-site APP-cleaving enzyme"	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.908A>C	chr11.hg19:g.117162462T>G	ENSP00000318585:p.Glu303Ala	128.0	0.0		127.0	12.0	NM_012104	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Missense_Mutation	SNP	ENST00000313005.6	hg19	CCDS8383.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.37|14.37	2.514037|2.514037	0.44763|0.44763	.|.	.|.	ENSG00000186318|ENSG00000186318	ENST00000313005;ENST00000392937;ENST00000510630;ENST00000428381;ENST00000513780;ENST00000445823;ENST00000292095|ENST00000530844	T;T;T;T;T|.	0.58060|.	0.36;0.36;0.36;0.36;0.36|.	5.88|5.88	4.7|4.7	0.59300|0.59300	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);|.	0.162995|.	0.53938|.	D|.	0.000042|.	T|.	0.39226|.	0.1070|.	N|N	0.12471|0.12471	0.22|0.22	0.51012|0.51012	D|D	0.9999|0.9999	B;B;B;B;B;B|.	0.10296|.	0.003;0.0;0.001;0.0;0.0;0.0|.	B;B;B;B;B;B|.	0.18871|.	0.022;0.002;0.023;0.005;0.001;0.002|.	T|.	0.23547|.	-1.0185|.	10|.	0.33141|.	T|.	0.24|.	.|.	12.1005|12.1005	0.53780|0.53780	0.0:0.0:0.1432:0.8568|0.0:0.0:0.1432:0.8568	.|.	203;178;303;259;234;278|.	F8W807;E9PE65;P56817;P56817-3;P56817-4;P56817-2|.	.;.;BACE1_HUMAN;.;.;.|.	A|C	303;203;178;234;278;259;69|172	ENSP00000318585:E303A;ENSP00000422461:E178A;ENSP00000402228:E234A;ENSP00000424536:E278A;ENSP00000403685:E259A|.	ENSP00000292095:E69A|.	E|X	-|-	2|3	0|0	BACE1|BACE1	116667672|116667672	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.502000|5.502000	0.66956|0.66956	2.239000|2.239000	0.73571|0.73571	0.533000|0.533000	0.62120|0.62120	GAA|TGA	.	.		0.483	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1			G	117162462	T	G	117162462	3	3	6	1	0	0	0	0	1	0	0	0	1281	1783	62	5	613	5	BACE1	11	117162462	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	44085931	117162462	17844054	48	520										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124268707	124268707	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	atgtgcgctttctctccaccGtggagcgttatttcaaggta	10	10	2	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr12:124268707G>C	ENST00000409039.3	+	8	1055	c.1030G>C	c.(1030-1032)Gtg>Ctg	p.V344L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	344	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TCTCTCCACCGTGGAGCGTTA	0.463																																					p.V344L		Atlas-SNP	.											.	DNAH10	888	.	0			c.G1030C						.						119	103	108					12																	124268707		2203	4300	6503	SO:0001583	missense	196385	exon8			TCCACCGTGGAGC	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.1030G>C	chr12.hg19:g.124268707G>C	ENSP00000386770:p.Val344Leu	91.0	0.0		131.0	38.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	2.529	-0.308906	0.05458	.	.	ENSG00000197653	ENST00000409039	T	0.31510	1.49	5.87	5.87	0.94306	Dynein heavy chain, domain-1 (1);	0.181280	0.35970	N	0.002870	T	0.09818	0.0241	N	0.00823	-1.155	0.37538	D	0.918198	B	0.10296	0.003	B	0.12837	0.008	T	0.24693	-1.0153	10	0.02654	T	1	.	14.5995	0.68429	0.0:0.2572:0.7428:0.0	.	344	Q8IVF4	DYH10_HUMAN	L	344	ENSP00000386770:V344L	ENSP00000386770:V344L	V	+	1	0	DNAH10	122834660	1.000000	0.71417	0.986000	0.45419	0.624000	0.37722	5.347000	0.65998	2.785000	0.95823	0.655000	0.94253	GTG	.	.		0.463	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			C	124268707	G	C	124268707	3	2	6	1	0	0	0	0	1	0	0	0	4600	1145	40	4	1060	4	DNAH10	12	124268707	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10		124268707	9583188	49	521										
DIS3	22894	hgsc.bcm.edu	37	chr13	73346861	73346861	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	atgctccagggcatctttggCagaaaactaagaacagcctg	10	10	1	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr13:73346861C>A	ENST00000377767.4	-	9	1456	c.1356G>T	c.(1354-1356)ctG>ctT	p.L452L	DIS3_ENST00000377780.4_Silent_p.L422L|DIS3_ENST00000545453.1_Silent_p.L290L	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	452					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		GCATCTTTGGCAGAAAACTAA	0.348										Multiple Myeloma(4;0.011)																											p.L452L		Atlas-SNP	.											.	DIS3	103	.	0			c.G1356T						.						103	106	105					13																	73346861		2203	4300	6503	SO:0001819	synonymous_variant	22894	exon9			CTTTGGCAGAAAA	AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"exosome component 11"	607533	"KIAA1008", "DIS3 mitotic control homolog (S. cerevisiae)"	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.1356G>T	chr13.hg19:g.73346861C>A		395.0	1.0		490.0	172.0	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Silent	SNP	ENST00000377767.4	hg19	CCDS9447.1																																																																																			.	.		0.348	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953		A	73346861	C	A	73346861	2	1	6	1	0	0	0	0	0	0	0	1	4537	697	25	3		3	DIS3	13	73346861	Silent	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10		73346861	41823017	50	522										
INSM2	84684	hgsc.bcm.edu	37	chr14	36005072	36005072	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	tccactttttttagctctccAgggctgacccggcacatcaa	7	14	2	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr14:36005072A>G	ENST00000307169.3	+	1	1825	c.1614A>G	c.(1612-1614)ccA>ccG	p.P538P		NM_032594.3	NP_115983.3	Q96T92	INSM2_HUMAN	insulinoma-associated 2	538					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	10	Breast(36;0.122)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(9;2.16e-07)|Lung(238;2.63e-07)|Epithelial(34;0.00145)|all cancers(34;0.00452)	GBM - Glioblastoma multiforme(112;0.0223)		TTAGCTCTCCAGGGCTGACCC	0.617																																					p.P538P		Atlas-SNP	.											.	INSM2	39	.	0			c.A1614G						.						33	36	35					14																	36005072		2197	4289	6486	SO:0001819	synonymous_variant	84684	exon1			CTCTCCAGGGCTG	AF260323	CCDS9657.1	14q13.1	2013-01-08			ENSG00000168348	ENSG00000168348		"Zinc fingers, C2H2-type"	17539	protein-coding gene	gene with protein product	"mlt 1"	614027					Standard	NM_032594		Approved	IA-6	uc001wth.1	Q96T92	OTTHUMG00000140223	ENST00000307169.3:c.1614A>G	chr14.hg19:g.36005072A>G		102.0	0.0		130.0	38.0	NM_032594	A1L432|J9Y024|Q8N8K7|Q96Q84	Silent	SNP	ENST00000307169.3	hg19	CCDS9657.1																																																																																			.	.		0.617	INSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276686.1			G	36005072	A	G	36005072	2	3	6	1	0	0	0	0	0	0	0	1	7781	175	7	2		2	INSM2	14	36005072	Silent	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10		36005072	71344468	51	523										
SNAPC1	6617	hgsc.bcm.edu	37	chr14	62248976	62248976	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	actcttaaggcatccaaatcAagaaggcatcgtcaagtcaa	7	10	4	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr14:62248976A>G	ENST00000216294.4	+	8	941	c.837A>G	c.(835-837)tcA>tcG	p.S279S		NM_003082.3	NP_003073.1	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex, polypeptide 1, 43kDa	279					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		CATCCAAATCAAGAAGGCATC	0.343																																					p.S279S	NSCLC(27;223 907 37180 39193 46568)	Atlas-SNP	.											.	SNAPC1	32	.	0			c.A837G						.						88	82	84					14																	62248976		2203	4300	6503	SO:0001819	synonymous_variant	6617	exon8			CAAATCAAGAAGG	Z47542	CCDS9755.1	14q22	2008-08-11	2002-08-29		ENSG00000023608	ENSG00000023608			11134	protein-coding gene	gene with protein product		600591	"small nuclear RNA activating complex, polypeptide 1, 43kD"			9644240	Standard	NM_003082		Approved	SNAP43, PTFgamma	uc001xft.3	Q16533	OTTHUMG00000140343	ENST00000216294.4:c.837A>G	chr14.hg19:g.62248976A>G		105.0	0.0		136.0	54.0	NM_003082		Silent	SNP	ENST00000216294.4	hg19	CCDS9755.1																																																																																			.	.		0.343	SNAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276976.2	NM_003082		G	62248976	A	G	62248976	2	3	6	1	0	0	0	0	0	0	0	1	14849	117	5	2		2	SNAPC1	14	62248976	Silent	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	26243904	62248976	45100564	52	524										
TECPR2	9895	hgsc.bcm.edu	37	chr14	102916924	102916924	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ctggaatcatgtggttccccGtgggacagcttctgctacaa	11	11	2	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr14:102916924G>A	ENST00000359520.7	+	15	3570	c.3344G>A	c.(3343-3345)cGt>cAt	p.R1115H	TECPR2_ENST00000558678.1_Missense_Mutation_p.R1115H	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	1115					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						GTGGTTCCCCGTGGGACAGCT	0.463																																					p.R1115H		Atlas-SNP	.											.	TECPR2	114	.	0			c.G3344A						.						110	89	96					14																	102916924		2203	4300	6503	SO:0001583	missense	9895	exon15			TTCCCCGTGGGAC	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"KIAA0329"	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.3344G>A	chr14.hg19:g.102916924G>A	ENSP00000352510:p.Arg1115His	97.0	0.0		107.0	10.0	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	hg19	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.842649	0.91197	.	.	ENSG00000196663	ENST00000359520	T	0.16897	2.31	5.38	4.49	0.54785	.	0.057959	0.64402	D	0.000003	T	0.28830	0.0715	L	0.27053	0.805	0.54753	D	0.999986	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.996;0.998	T	0.03910	-1.0993	10	0.56958	D	0.05	.	14.0237	0.64573	0.073:0.0:0.927:0.0	.	298;1115;1115	B4DSD3;A5PKY3;O15040	.;.;TCPR2_HUMAN	H	1115	ENSP00000352510:R1115H	ENSP00000352510:R1115H	R	+	2	0	TECPR2	101986677	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	6.980000	0.76160	1.279000	0.44446	0.655000	0.94253	CGT	.	.		0.463	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		A	102916924	G	A	102916924	3	1	6	1	0	0	0	0	1	0	0	0	15759	1145	40	1	3398	1	TECPR2	14	102916924	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	40667948	102916924	4432616	53	525										
HERC2	8924	hgsc.bcm.edu	37	chr15	28437148	28437148	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ctgccagcagggctcgctgcCgtcaatgagacgggatgcct	14	13	1	1	rs571204932		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr15:28437148C>A	ENST00000261609.7	-	53	8518	c.8410G>T	c.(8410-8412)Ggc>Tgc	p.G2804C		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GGCTCGCTGCCGTCAATGAGA	0.592											OREG0022997	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G2804C		Atlas-SNP	.											.	HERC2	501	.	0			c.G8410T						.						108	96	100					15																	28437148		2203	4300	6503	SO:0001583	missense	8924	exon53			CGCTGCCGTCAAT	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.8410G>T	chr15.hg19:g.28437148C>A	ENSP00000261609:p.Gly2804Cys	76.0	0.0	801	70.0	12.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957381	0.53400	.	.	ENSG00000128731	ENST00000261609	T	0.71934	-0.61	5.51	4.59	0.56863	Anaphase-promoting complex, subunit 10/DOC domain (2);Galactose-binding domain-like (1);	0.230238	0.45126	D	0.000382	T	0.67458	0.2895	L	0.52011	1.625	0.49798	D	0.999827	B;B	0.18968	0.02;0.032	B;B	0.20955	0.032;0.031	T	0.65553	-0.6140	10	0.54805	T	0.06	.	16.7446	0.85469	0.0:0.8707:0.1293:0.0	.	271;2804	A8KAQ8;O95714	.;HERC2_HUMAN	C	2804	ENSP00000261609:G2804C	ENSP00000261609:G2804C	G	-	1	0	HERC2	26110743	1.000000	0.71417	0.918000	0.36340	0.990000	0.78478	3.938000	0.56583	1.446000	0.47643	0.579000	0.79373	GGC	.	.		0.592	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28437148	C	A	28437148	3	1	6	1	0	0	0	0	1	0	0	0	7067	652	23	1	6258	1	HERC2	15	28437148	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10		28437148	74094244	54	526										
FAM98B	283742	hgsc.bcm.edu	37	chr15	38773609	38773609	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gaagatctatccaagatcatTaggacaagtagtggcaccag	10	8	2	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr15:38773609T>A	ENST00000491535.1	+	7	854	c.846T>A	c.(844-846)atT>atA	p.I282I	FAM98B_ENST00000397609.2_Silent_p.I282I	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B	282						cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		CCAAGATCATTAGGACAAGTA	0.418																																					p.I282I		Atlas-SNP	.											.	FAM98B	53	.	0			c.T846A						.						140	126	131					15																	38773609		2200	4297	6497	SO:0001819	synonymous_variant	283742	exon7			GATCATTAGGACA		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831	ENST00000491535.1:c.846T>A	chr15.hg19:g.38773609T>A		188.0	0.0		191.0	38.0	NM_001042429	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	hg19	CCDS42015.1																																																																																			.	.		0.418	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		A	38773609	T	A	38773609	2	1	6	1	0	0	0	0	0	0	0	1	5665	1742	61	4		4	FAM98B	15	38773609	Silent	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	10336461	38773609	63757783	55	527										
SEC14L5	9717	hgsc.bcm.edu	37	chr16	5050723	5050723	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ggcttgatgaaggccgtgggGgaggaggcgctgctgcggca	21	8	0	2	rs534122915		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr16:5050723G>A	ENST00000251170.7	+	9	1218	c.1038G>A	c.(1036-1038)ggG>ggA	p.G346G		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	346	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						AGGCCGTGGGGGAGGAGGCGC	0.657																																					p.G346G		Atlas-SNP	.											.	SEC14L5	79	.	0			c.G1038A						.						13	15	15					16																	5050723		2010	4126	6136	SO:0001819	synonymous_variant	9717	exon9			CGTGGGGGAGGAG	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1038G>A	chr16.hg19:g.5050723G>A		112.0	0.0		101.0	19.0	NM_014692		Silent	SNP	ENST00000251170.7	hg19	CCDS45403.1																																																																																			.	.		0.657	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1			A	5050723	G	A	5050723	2	1	6	1	0	0	0	0	0	0	0	1	14000	1219	43	3		3	SEC14L5	16	5050723	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10		5050723	85304030	56	528										
KIAA0430	9665	hgsc.bcm.edu	37	chr16	15706458	15706458	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	taataactcaatcagcttggAgtatccgtagtctgacactc	7	10	3	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr16:15706458A>G	ENST00000396368.3	-	17	3636	c.3430T>C	c.(3430-3432)Tcc>Ccc	p.S1144P	CTB-193M12.1_ENST00000549756.1_RNA|KIAA0430_ENST00000548025.1_Missense_Mutation_p.S1141P|KIAA0430_ENST00000602337.1_Missense_Mutation_p.S1141P|KIAA0430_ENST00000344181.3_Missense_Mutation_p.S746P|KIAA0430_ENST00000551742.1_Missense_Mutation_p.S1144P|KIAA0430_ENST00000540441.2_Missense_Mutation_p.S979P	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	1144	HTH OST-type 3. {ECO:0000255|PROSITE- ProRule:PRU00975}.				double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						ATCAGCTTGGAGTATCCGTAG	0.463																																					p.S1144P		Atlas-SNP	.											.	KIAA0430	154	.	0			c.T3430C						.						156	158	158					16																	15706458		2051	4211	6262	SO:0001583	missense	9665	exon17			GCTTGGAGTATCC	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29562	protein-coding gene	gene with protein product	"limkain b1", "protein phosphatase 1, regulatory subunit 34", "meiosis arrest female 1"	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.3430T>C	chr16.hg19:g.15706458A>G	ENSP00000379654:p.Ser1144Pro	102.0	0.0		116.0	29.0	NM_001184998	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Missense_Mutation	SNP	ENST00000396368.3	hg19	CCDS10562.2	.	.	.	.	.	.	.	.	.	.	A	19.38	3.817101	0.70912	.	.	ENSG00000166783	ENST00000396368;ENST00000540441;ENST00000321370;ENST00000344181;ENST00000548025;ENST00000551742;ENST00000551298	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.58264	0.2110	L	0.40543	1.245	0.58432	D	0.99999	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.87578	0.996;0.982;0.982;0.998	T	0.58842	-0.7565	10	0.49607	T	0.09	.	11.5189	0.50539	0.8659:0.0:0.0:0.1341	.	1143;1141;1140;1143	Q9Y4F3-5;F8VV09;Q9Y4F3-4;Q9Y4F3	.;.;.;LKAP_HUMAN	P	1144;979;1084;746;1141;1144;924	ENSP00000379654:S1144P;ENSP00000439819:S979P;ENSP00000341939:S746P;ENSP00000449376:S1141P;ENSP00000450309:S1144P	ENSP00000315718:S1084P	S	-	1	0	KIAA0430	15613959	1.000000	0.71417	0.994000	0.49952	0.886000	0.51366	5.497000	0.66924	2.124000	0.65301	0.523000	0.50628	TCC	.	.		0.463	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647		G	15706458	A	G	15706458	3	3	6	1	0	0	0	0	1	0	0	0	8186	304	11	2	1842	2	KIAA0430	16	15706458	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	10655735	15706458	74648295	57	529										
MTSS1L	92154	hgsc.bcm.edu	37	chr16	70710812	70710812	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gctggacttccgggagctggAgctgctgggtgatgagggtg	20	7	0	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr16:70710812A>C	ENST00000338779.6	-	10	1076	c.802T>G	c.(802-804)Tcc>Gcc	p.S268A		NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	268	Ser-rich.				filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						CGGGAGCTGGAGCTGCTGGGT	0.607																																					p.S268A		Atlas-SNP	.											.	MTSS1L	22	.	0			c.T802G						.						64	59	61					16																	70710812		2198	4300	6498	SO:0001583	missense	92154	exon10			AGCTGGAGCTGCT		CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613			25094	protein-coding gene	gene with protein product	"actin-bundling protein with BAIAP2 homology"					12477932	Standard	XM_006721335		Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.802T>G	chr16.hg19:g.70710812A>C	ENSP00000341171:p.Ser268Ala	109.0	0.0		103.0	24.0	NM_138383	A6NJI7|Q9BUA8	Missense_Mutation	SNP	ENST00000338779.6	hg19	CCDS32476.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.962178	0.53400	.	.	ENSG00000132613	ENST00000338779	T	0.32753	1.44	4.57	4.57	0.56435	.	0.059652	0.64402	D	0.000002	T	0.29652	0.0740	L	0.56769	1.78	0.31391	N	0.677799	B	0.20459	0.045	B	0.17098	0.017	T	0.25433	-1.0132	10	0.19147	T	0.46	-28.5471	13.6248	0.62157	1.0:0.0:0.0:0.0	.	268	Q765P7	MTSSL_HUMAN	A	268	ENSP00000341171:S268A	ENSP00000341171:S268A	S	-	1	0	MTSS1L	69268313	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.057000	0.41365	1.696000	0.51158	0.460000	0.39030	TCC	.	.		0.607	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434927.3	NM_138383		C	70710812	A	C	70710812	3	2	6	1	0	0	0	0	1	0	0	0	9972	304	11	5	1465	5	MTSS1L	16	70710812	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	55004354	70710812	19643941	58	530										
TAT	6898	hgsc.bcm.edu	37	chr16	71604656	71604657	+	Frame_Shift_Ins	INS	-	-	G													0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ccaggaaccagccagcgcttINSggccagccctccacaggaca							TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr16:71604656_71604657insG	ENST00000355962.4	-	8	970_971	c.837_838insC	c.(835-840)gccaagfs	p.K280fs	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	280					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	AGCCAGCGCTTGGCCAGCCCTC	0.52																																					p.K280fs	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-Indel,Pindel	.											.	TAT	80	.	0			c.838_839insC						.																																			SO:0001589	frameshift_variant	6898	exon8			.		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.838dupC	chr16.hg19:g.71604658_71604658dupG	ENSP00000348234:p.Lys280fs	159.0	0.0		124.0	25.0	NM_000353	B2R8I1|D3DWS2	Frame_Shift_Ins	INS	ENST00000355962.4	hg19	CCDS10903.1																																																																																			.	.		0.52	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1			G	71604657	-	G	71604656	7	5	6	1	0	1	1	0	0	0	0	0	15605	1821	63	0	546	0	TAT	16	71604656	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GW-01A-11D-A382-10	893844	71604656	18750097	59	531										
PRPF8	10594	hgsc.bcm.edu	37	chr17	1584925	1584925	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gctgattagccaggcggtagAgagtcgacatcataggtagt	14	7	1	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:1584925A>C	ENST00000572621.1	-	5	978	c.713T>G	c.(712-714)cTc>cGc	p.L238R	PRPF8_ENST00000304992.6_Missense_Mutation_p.L238R			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	238					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CAGGCGGTAGAGAGTCGACAT	0.468																																					p.L238R		Atlas-SNP	.											.	PRPF8	169	.	0			c.T713G						.						146	142	143					17																	1584925		2203	4300	6503	SO:0001583	missense	10594	exon6			CGGTAGAGAGTCG	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.713T>G	chr17.hg19:g.1584925A>C	ENSP00000460348:p.Leu238Arg	158.0	0.0		137.0	33.0	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.613477	0.87359	.	.	ENSG00000174231	ENST00000304992	D	0.88664	-2.41	5.84	5.84	0.93424	.	0.061562	0.64402	D	0.000003	D	0.95671	0.8592	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96508	0.9376	10	0.87932	D	0	.	16.2141	0.82191	1.0:0.0:0.0:0.0	.	238	Q6P2Q9	PRP8_HUMAN	R	238	ENSP00000304350:L238R	ENSP00000304350:L238R	L	-	2	0	PRPF8	1531675	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.307000	0.96226	2.230000	0.72887	0.528000	0.53228	CTC	.	.		0.468	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			C	1584925	A	C	1584925	3	2	6	1	0	0	0	0	1	0	0	0	12587	304	11	5	6446	5	PRPF8	17	1584925	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10		1584925	79610285	60	532										
TEKT3	64518	hgsc.bcm.edu	37	chr17	15234544	15234544	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ggcgagatgtatccactcttAgtttctccgaattatgtcgg	10	9	2	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:15234544A>T	ENST00000395930.1	-	3	545	c.359T>A	c.(358-360)cTa>cAa	p.L120Q	TEKT3_ENST00000338696.2_Missense_Mutation_p.L120Q	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	120					cilium morphogenesis (GO:0060271)|regulation of fertilization (GO:0080154)|sperm motility (GO:0030317)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				endometrium(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	23				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		ATCCACTCTTAGTTTCTCCGA	0.413																																					p.L120Q		Atlas-SNP	.											.	TEKT3	64	.	0			c.T359A						.						241	220	227					17																	15234544		2203	4300	6503	SO:0001583	missense	64518	exon3			ACTCTTAGTTTCT	AF334676	CCDS11169.1	17p12	2011-05-23			ENSG00000125409	ENSG00000125409			14293	protein-coding gene	gene with protein product		612683				11381029, 14735490	Standard	NM_031898		Approved	FLJ32828	uc002gon.3	Q9BXF9	OTTHUMG00000058965	ENST00000395930.1:c.359T>A	chr17.hg19:g.15234544A>T	ENSP00000379263:p.Leu120Gln	170.0	0.0		159.0	44.0	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Missense_Mutation	SNP	ENST00000395930.1	hg19	CCDS11169.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.505815	0.85282	.	.	ENSG00000125409	ENST00000395930;ENST00000338696;ENST00000536146;ENST00000539316	T;T;T;T	0.54479	4.03;4.03;4.03;0.57	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.73674	0.3617	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77448	-0.2584	10	0.87932	D	0	1.5702	16.1054	0.81216	1.0:0.0:0.0:0.0	.	120	Q9BXF9	TEKT3_HUMAN	Q	120	ENSP00000379263:L120Q;ENSP00000343995:L120Q;ENSP00000446111:L120Q;ENSP00000439713:L120Q	ENSP00000343995:L120Q	L	-	2	0	TEKT3	15175269	1.000000	0.71417	0.974000	0.42286	0.932000	0.56968	8.910000	0.92685	2.266000	0.75297	0.533000	0.62120	CTA	.	.		0.413	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898		T	15234544	A	T	15234544	3	4	6	1	0	0	0	0	1	0	0	0	15769	420	15	4	1141	4	TEKT3	17	15234544	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	13649619	15234544	65960666	61	533										
RNF112	7732	hgsc.bcm.edu	37	chr17	19319264	19319264	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ggggtgctgtgggggccgggCtcatgggcctggcagggggc	24	9	1	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:19319264C>T	ENST00000461366.1	+	14	1887	c.1672C>T	c.(1672-1674)Ctc>Ttc	p.L558F	CTB-187M2.2_ENST00000579897.1_RNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	558						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	12						GGGGGCCGGGCTCATGGGCCT	0.692																																					p.L558F		Atlas-SNP	.											.	RNF112	37	.	0			c.C1672T						.						10	11	11					17																	19319264		1932	4110	6042	SO:0001583	missense	7732	exon14			GCCGGGCTCATGG	AF054587	CCDS58529.1	17p11.2	2013-01-16	2008-06-13	2008-06-13	ENSG00000128482	ENSG00000128482		"RING-type (C3HC4) zinc fingers"	12968	protein-coding gene	gene with protein product		601237	"zinc finger protein 179"	ZNF179		8660987, 9806830	Standard	NM_007148		Approved	BFP	uc010vyw.2	Q9ULX5	OTTHUMG00000059601	ENST00000461366.1:c.1672C>T	chr17.hg19:g.19319264C>T	ENSP00000454919:p.Leu558Phe	39.0	0.0		38.0	10.0	NM_007148	O60633|Q7Z5V9	Missense_Mutation	SNP	ENST00000461366.1	hg19	CCDS58529.1																																																																																			.	.		0.692	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148		T	19319264	C	T	19319264	3	4	6	1	0	0	0	0	1	0	0	0	13441	797	28	3	1436	3	RNF112	17	19319264	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10	4084720	19319264	61875946	62	534										
IKZF3	22806	hgsc.bcm.edu	37	chr17	37922198	37922198	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	cacatagtccaggaagaggaCgcggcagtggtcacaccgat	13	11	1	1	rs149299224		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:37922198C>T	ENST00000346872.3	-	8	1436	c.1375G>A	c.(1375-1377)Gtc>Atc	p.V459I	IKZF3_ENST00000377945.3_Missense_Mutation_p.V325I|IKZF3_ENST00000377944.3_Missense_Mutation_p.V316I|RP11-94L15.2_ENST00000488188.2_lincRNA|IKZF3_ENST00000467757.1_Missense_Mutation_p.V403I|IKZF3_ENST00000351680.3_Missense_Mutation_p.V420I|IKZF3_ENST00000350532.3_Missense_Mutation_p.V420I|IKZF3_ENST00000377958.2_Missense_Mutation_p.V372I|IKZF3_ENST00000535189.1_Missense_Mutation_p.V425I|IKZF3_ENST00000346243.3_Missense_Mutation_p.V381I|IKZF3_ENST00000583368.1_Missense_Mutation_p.V212I|IKZF3_ENST00000377952.2_Missense_Mutation_p.V238I|IKZF3_ENST00000439167.2_Missense_Mutation_p.V386I|IKZF3_ENST00000439016.2_Missense_Mutation_p.V364I|IKZF3_ENST00000394189.2_Missense_Mutation_p.V277I	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	459					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			AGGAAGAGGACGCGGCAGTGG	0.547													C|||	1	0.000199681	0	0	5008	,	,		20447	0		0	False		,,,				2504	0.001				p.V459I		Atlas-SNP	.											.	IKZF3	79	.	0			c.G1375A						.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	161	145	150		1375,1207,1258,1258,1090,1141	3.5	1	17	dbSNP_134	150	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,missense,missense	IKZF3	NM_012481.3,NM_183228.1,NM_183229.1,NM_183230.1,NM_183231.1,NM_183232.1	29,29,29,29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	459/510,403/454,420/471,420/471,364/415,381/432	37922198	1,13005	2203	4300	6503	SO:0001583	missense	22806	exon8			AGAGGACGCGGCA	AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13178	protein-coding gene	gene with protein product		606221	"zinc finger protein, subfamily 1A, 3 (Aiolos)"	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.1375G>A	chr17.hg19:g.37922198C>T	ENSP00000344544:p.Val459Ile	113.0	0.0		123.0	19.0	NM_012481	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Missense_Mutation	SNP	ENST00000346872.3	hg19	CCDS11346.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.527813	0.44969	0.0	1.16E-4	ENSG00000161405	ENST00000488188;ENST00000346872;ENST00000377945;ENST00000394189;ENST00000377944;ENST00000377958;ENST00000377952;ENST00000535189;ENST00000351680;ENST00000346243;ENST00000350532;ENST00000467757	T;T;T;T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.51	3.54	0.40534	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.50627	D	0.000109	T	0.27559	0.0677	N	0.25332	0.735	0.50467	D	0.99987	B;B;P;B;B;B;B;B;B;B;B;B;B	0.37061	0.039;0.295;0.58;0.141;0.22;0.112;0.006;0.427;0.417;0.205;0.039;0.039;0.075	B;B;B;B;B;B;B;B;B;B;B;B;B	0.30029	0.023;0.038;0.088;0.038;0.036;0.102;0.007;0.061;0.102;0.11;0.023;0.023;0.029	T	0.06552	-1.0820	10	0.54805	T	0.06	-15.4234	12.4038	0.55428	0.0:0.8628:0.0:0.1372	.	372;238;277;325;316;425;381;364;420;403;420;386;459	Q9UKT9-9;Q9UKT9-12;Q9UKT9-11;Q9UKT9-13;Q9UKT9-10;Q9UKT9-7;Q9UKT9-6;Q9UKT9-5;Q9UKT9-4;Q9UKT9-2;Q9UKT9-3;Q9UKT9-8;Q9UKT9	.;.;.;.;.;.;.;.;.;.;.;.;IKZF3_HUMAN	I	459;364;325;277;316;372;238;425;420;381;420;403	ENSP00000367180:V325I;ENSP00000377741:V277I;ENSP00000367179:V316I;ENSP00000367194:V372I;ENSP00000367188:V238I;ENSP00000438972:V425I;ENSP00000345622:V420I;ENSP00000341977:V381I;ENSP00000344471:V420I;ENSP00000420463:V403I	ENSP00000341977:V381I	V	-	1	0	IKZF3	35175724	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	4.980000	0.63812	0.718000	0.32166	-0.942000	0.02676	GTC	.	C|1.000;T|0.000		0.547	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		T	37922198	C	T	37922198	3	4	6	1	0	0	0	0	1	0	0	0	7625	536	19	1	158	1	IKZF3	17	37922198	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10	18602934	37922198	43273012	63	535										
SLC39A11	201266	hgsc.bcm.edu	37	chr17	70845832	70845832	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	cgatcctcctccagctgctgCcgccgggctgtgccagattc	11	17	0	1	rs373163649		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:70845832C>T	ENST00000542342.2	-	6	651	c.563G>A	c.(562-564)gGc>gAc	p.G188D	SLC39A11_ENST00000255559.3_Missense_Mutation_p.G181D|SLC39A11_ENST00000579732.1_Missense_Mutation_p.G181D	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	188					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			endometrium(1)|large_intestine(4)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						CCAGCTGCTGCCGCCGGGCTG	0.597																																					p.G188D	NSCLC(95;736 1527 12296 39625 41839)	Atlas-SNP	.											.	SLC39A11	32	.	0			c.G563A						.						96	84	88					17																	70845832		2203	4300	6503	SO:0001583	missense	201266	exon6			CTGCTGCCGCCGG	AF331643	CCDS11690.1, CCDS54160.1	17q24.3-q25.1	2014-08-12	2013-07-17	2003-10-24	ENSG00000133195	ENSG00000133195		"Solute carriers"	14463	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 26"	C17orf26		11707075	Standard	NM_139177		Approved		uc002jjb.3	Q8N1S5	OTTHUMG00000178306	ENST00000542342.2:c.563G>A	chr17.hg19:g.70845832C>T	ENSP00000445829:p.Gly188Asp	74.0	0.0		62.0	14.0	NM_001159770	B2R8H7|Q8WZ81	Missense_Mutation	SNP	ENST00000542342.2	hg19	CCDS54160.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.272106	0.23221	.	.	ENSG00000133195	ENST00000542342;ENST00000255559	T;T	0.76448	-0.98;-1.02	5.79	2.56	0.30785	.	0.520844	0.20319	N	0.094663	T	0.52484	0.1737	N	0.02960	-0.455	0.09310	N	0.999999	B;B	0.23316	0.083;0.032	B;B	0.28784	0.094;0.038	T	0.39781	-0.9597	10	0.12430	T	0.62	.	11.1194	0.48279	0.1332:0.6095:0.2572:0.0	.	188;181	Q8N1S5;Q8N1S5-2	S39AB_HUMAN;.	D	188;181	ENSP00000445829:G188D;ENSP00000255559:G181D	ENSP00000255559:G181D	G	-	2	0	SLC39A11	68357427	0.089000	0.21612	0.011000	0.14972	0.044000	0.14063	1.079000	0.30766	0.757000	0.33036	-0.165000	0.13383	GGC	.	.		0.597	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1			T	70845832	C	T	70845832	3	4	6	1	0	0	0	0	1	0	0	0	14629	739	26	3	485	3	SLC39A11	17	70845832	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10	32923634	70845832	10349378	64	536										
COG1	9382	hgsc.bcm.edu	37	chr17	71202364	71202364	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ggacgttttcacgccacaccTcaacagcaaccttcatcgcc	6	17	3	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:71202364T>G	ENST00000299886.4	+	11	2662	c.2582T>G	c.(2581-2583)cTc>cGc	p.L861R		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	861					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			ACGCCACACCTCAACAGCAAC	0.443																																					p.L861R		Atlas-SNP	.											.	COG1	46	.	0			c.T2582G						.						132	114	120					17																	71202364		2203	4300	6503	SO:0001583	missense	9382	exon11			CACACCTCAACAG		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"Components of oligomeric golgi complex"	6545	protein-coding gene	gene with protein product		606973	"low density lipoprotein receptor defect B complementing"	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.2582T>G	chr17.hg19:g.71202364T>G	ENSP00000299886:p.Leu861Arg	88.0	0.0		95.0	23.0	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	hg19	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030189	0.35797	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.47528	0.84;0.85	5.7	5.7	0.88788	.	0.063724	0.64402	D	0.000006	T	0.72581	0.3478	M	0.85859	2.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.99;0.999;0.99	T	0.77816	-0.2447	10	0.87932	D	0	-20.1055	15.9745	0.80049	0.0:0.0:0.0:1.0	.	861;861;861	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	R	861	ENSP00000400111:L861R;ENSP00000299886:L861R	ENSP00000299886:L861R	L	+	2	0	COG1	68713959	1.000000	0.71417	0.999000	0.59377	0.333000	0.28666	5.748000	0.68697	2.168000	0.68352	0.533000	0.62120	CTC	.	.		0.443	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			G	71202364	T	G	71202364	3	3	6	1	0	0	0	0	1	0	0	0	3659	1551	54	5	2624	5	COG1	17	71202364	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	356532	71202364	9992846	65	537										
ME2	4200	hgsc.bcm.edu	37	chr18	48444552	48444552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	cacaacagtatgatgacctgAttgatgagtttatgaaagct	9	6	0	6	rs532005925		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr18:48444552A>G	ENST00000321341.5	+	7	975	c.703A>G	c.(703-705)Att>Gtt	p.I235V	ME2_ENST00000382927.3_Missense_Mutation_p.I235V	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	235					malate metabolic process (GO:0006108)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(3)	23		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)		TGATGACCTGATTGATGAGTT	0.353													A|||	1	0.000199681	0	0	5008	,	,		14551	0		0	False		,,,				2504	0.001				p.I235V		Atlas-SNP	.											.	ME2	49	.	0			c.A703G						.						71	67	68					18																	48444552		2203	4300	6503	SO:0001583	missense	4200	exon7			GACCTGATTGATG	M55905	CCDS11948.1, CCDS54187.1	18q21	2012-10-02			ENSG00000082212	ENSG00000082212	1.1.1.40		6984	protein-coding gene	gene with protein product		154270				1993674	Standard	NM_002396		Approved		uc002ley.3	P23368	OTTHUMG00000132694	ENST00000321341.5:c.703A>G	chr18.hg19:g.48444552A>G	ENSP00000321070:p.Ile235Val	351.0	0.0		351.0	29.0	NM_001168335	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	hg19	CCDS11948.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.387601	0.25031	.	.	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.39787	1.06;1.06	5.29	5.29	0.74685	Malic enzyme, N-terminal (2);	0.046188	0.85682	D	0.000000	T	0.25901	0.0631	N	0.16016	0.355	0.58432	D	0.999994	B;B	0.06786	0.0;0.001	B;B	0.20767	0.006;0.031	T	0.08889	-1.0700	10	0.08837	T	0.75	-14.2031	14.5043	0.67743	1.0:0.0:0.0:0.0	.	235;235	Q9BWL6;P23368	.;MAOM_HUMAN	V	235	ENSP00000321070:I235V;ENSP00000372384:I235V	ENSP00000321070:I235V	I	+	1	0	ME2	46698550	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.207000	0.77899	2.126000	0.65437	0.528000	0.53228	ATT	.	.		0.353	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396		G	48444552	A	G	48444552	3	3	6	1	0	0	0	0	1	0	0	0	9427	333	12	2	725	2	ME2	18	48444552	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10		48444552	29632696	66	538										
DCC	1630	hgsc.bcm.edu	37	chr18	50923690	50923690	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ttgtatagtcagaagacacaAcatctctaagttacacagca	6	9	2	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr18:50923690A>G	ENST00000442544.2	+	18	3317	c.2701A>G	c.(2701-2703)Aca>Gca	p.T901A	DCC_ENST00000581580.1_Missense_Mutation_p.T536A|DCC_ENST00000412726.1_Missense_Mutation_p.T729A	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	901	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		AGAAGACACAACATCTCTAAG	0.343																																					p.T901A		Atlas-SNP	.											.	DCC	360	.	0			c.A2701G						.						108	97	101					18																	50923690		2203	4300	6503	SO:0001583	missense	1630	exon18			GACACAACATCTC	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.2701A>G	chr18.hg19:g.50923690A>G	ENSP00000389140:p.Thr901Ala	122.0	0.0		133.0	13.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.54|14.54	2.567038|2.567038	0.45694|0.45694	.|.	.|.	ENSG00000187323|ENSG00000187323	ENST00000304775|ENST00000442544;ENST00000412726	.|T;T	.|0.59224	.|0.28;0.28	5.8|5.8	5.8|5.8	0.92144|0.92144	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.72003|0.72003	0.3407|0.3407	M|M	0.79475|0.79475	2.455|2.455	0.80722|0.80722	D|D	1|1	.|P;P;D	.|0.60160	.|0.947;0.947;0.987	.|D;D;D	.|0.65773	.|0.931;0.931;0.938	T|T	0.69924|0.69924	-0.5013|-0.5013	6|10	0.20046|0.08837	T|T	0.44|0.75	.|.	15.1301|15.1301	0.72517|0.72517	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|729;729;901	.|E7EQM8;B4DYX2;P43146	.|.;.;DCC_HUMAN	S|A	756|901;729	.|ENSP00000389140:T901A;ENSP00000397322:T729A	ENSP00000304146:N756S|ENSP00000397322:T729A	N|T	+|+	2|1	0|0	DCC|DCC	49177688|49177688	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.413000|7.413000	0.80104|0.80104	2.213000|2.213000	0.71641|0.71641	0.528000|0.528000	0.53228|0.53228	AAC|ACA	.	.		0.343	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		G	50923690	A	G	50923690	3	3	6	1	0	0	0	0	1	0	0	0	4284	43	2	2	2771	2	DCC	18	50923690	Missense_Mutation	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	2479138	50923690	27153558	67	539										
PPAP2C	8612	hgsc.bcm.edu	37	chr19	287737	287737	+	Frame_Shift_Del	DEL	T	T	-													0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	tctgtgtacaccaggtaggcTtccccggccgagacctgcaa							TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:287737delT	ENST00000269812.3	-	3	268	c.219delA	c.(217-219)gaafs	p.E73fs	PPAP2C_ENST00000327790.3_Frame_Shift_Del_p.E94fs|PPAP2C_ENST00000434325.2_Frame_Shift_Del_p.E17fs	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	73					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGGTAGGCTTCCCCGGCCG	0.642																																					p.A95fs		Atlas-INDEL	.											.	PPAP2C	38	.	0			c.283delG						.						114	134	127					19																	287737		2203	4300	6503	SO:0001589	frameshift_variant	8612	exon3			.	AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	3.1.3.4		9230	protein-coding gene	gene with protein product		607126				9570154, 9607309	Standard	NM_177543		Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.219delA	chr19.hg19:g.287737delT	ENSP00000269812:p.Glu73fs	75.0	0.0		81.0	11.0	NM_177543	A6NLV0|E9PAY8	Frame_Shift_Del	DEL	ENST00000269812.3	hg19	CCDS12023.1																																																																																			.	.		0.642	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451777.2			-	287737	T	-	287737	7	5	6	1	0	1	0	1	0	0	0	0	12301	1606	56	0	663	0	PPAP2C	19	287737	Frame_Shift_Del	DEL	T	TCGA-2Y-A9GW-01A-11D-A382-10		287737	58841246	68	540										
ZNF57	126295	hgsc.bcm.edu	37	chr19	2917323	2917323	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gtgtcggatggcgtttaatgGgttcgcaagcttcactagac	13	8	1	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:2917323G>A	ENST00000306908.5	+	4	852	c.704G>A	c.(703-705)gGg>gAg	p.G235E	ZNF57_ENST00000523428.1_Missense_Mutation_p.G203E|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	235					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGTTTAATGGGTTCGCAAGC	0.463																																					p.G235E	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.G704A						.						97	91	93					19																	2917323		2203	4300	6503	SO:0001583	missense	126295	exon4			TTAATGGGTTCGC	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"Zinc fingers, C2H2-type", "-"	13125	protein-coding gene	gene with protein product			"zinc finger protein 424"	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.704G>A	chr19.hg19:g.2917323G>A	ENSP00000303696:p.Gly235Glu	109.0	0.0		129.0	28.0	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	hg19	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	G	9.426	1.084342	0.20309	.	.	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.14766	2.48;2.48	1.98	-3.96	0.04106	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04452	0.0122	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35351	-0.9792	9	0.27785	T	0.31	.	2.5155	0.04667	0.3776:0.0:0.2684:0.3539	.	235	Q68EA5	ZNF57_HUMAN	E	235;237;203	ENSP00000303696:G235E;ENSP00000430223:G203E	ENSP00000303696:G235E	G	+	2	0	ZNF57	2868323	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.033000	0.00636	-1.772000	0.01292	-0.424000	0.05967	GGG	.	.		0.463	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		A	2917323	G	A	2917323	3	1	6	1	0	0	0	0	1	0	0	0	18016	1232	43	3	718	3	ZNF57	19	2917323	Missense_Mutation	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	2629586	2917323	56211660	69	541										
NRTN	4902	hgsc.bcm.edu	37	chr19	5827964	5827964	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ctacgcgtccgacgagacggTgctgttccgctactgcgcag	13	14	0	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:5827964T>C	ENST00000303212.2	+	2	738	c.374T>C	c.(373-375)gTg>gCg	p.V125A		NM_004558.3	NP_004549.1	Q99748	NRTN_HUMAN	neurturin	125					axon guidance (GO:0007411)|MAPK cascade (GO:0000165)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|extracellular region (GO:0005576)	receptor binding (GO:0005102)			large_intestine(1)	1						GACGAGACGGTGCTGTTCCGC	0.781																																					p.V125A		Atlas-SNP	.											.	NRTN	4	.	0			c.T374C						.																																			SO:0001583	missense	4902	exon2			AGACGGTGCTGTT	U78110	CCDS12151.1	19p13.3	2014-01-30				ENSG00000171119		"Endogenous ligands"	8007	protein-coding gene	gene with protein product	"prepro-neurturin"	602018				8945474	Standard	NM_004558		Approved	NTN	uc002mde.3	Q99748		ENST00000303212.2:c.374T>C	chr19.hg19:g.5827964T>C	ENSP00000302648:p.Val125Ala	24.0	0.0		35.0	8.0	NM_004558	B2RPE8	Missense_Mutation	SNP	ENST00000303212.2	hg19	CCDS12151.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.772326	0.90108	.	.	ENSG00000171119	ENST00000303212	D	0.84442	-1.85	4.47	2.26	0.28386	Transforming growth factor-beta, C-terminal (3);	0.155857	0.42420	D	0.000715	D	0.87410	0.6170	L	0.61218	1.895	0.37760	D	0.926282	D	0.53885	0.963	P	0.62491	0.903	D	0.85333	0.1091	10	0.72032	D	0.01	-13.1242	4.9046	0.13791	0.1634:0.0954:0.0:0.7412	.	125	Q99748	NRTN_HUMAN	A	125	ENSP00000302648:V125A	ENSP00000302648:V125A	V	+	2	0	NRTN	5778964	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	4.275000	0.58927	0.171000	0.19730	0.397000	0.26171	GTG	.	.		0.781	NRTN-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451882.2	NM_004558		C	5827964	T	C	5827964	3	2	6	1	0	0	0	0	1	0	0	0	10673	1696	59	2	380	2	NRTN	19	5827964	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	2910641	5827964	53301019	70	542										
FARSA	2193	hgsc.bcm.edu	37	chr19	13039211	13039211	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gggtgctgctggggctggaaGagggcgtcaaagttccagaa	18	7	1	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:13039211G>T	ENST00000314606.4	-	7	804	c.786C>A	c.(784-786)ctC>ctA	p.L262L	FARSA_ENST00000588025.1_Silent_p.L302L|CTC-425F1.2_ENST00000592636.1_RNA|FARSA_ENST00000423140.2_Silent_p.L231L	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	262					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	GGGGCTGGAAGAGGGCGTCAA	0.602																																					p.L262L		Atlas-SNP	.											.	FARSA	46	.	0			c.C786A						.						103	99	100					19																	13039211		2203	4300	6503	SO:0001819	synonymous_variant	2193	exon7			CTGGAAGAGGGCG	U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	3592	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 1, alpha, cytoplasmic"	602918	"phenylalanine-tRNA synthetase-like", "phenylalanyl-tRNA synthetase-like, alpha subunit"	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.786C>A	chr19.hg19:g.13039211G>T		133.0	0.0		117.0	21.0	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Silent	SNP	ENST00000314606.4	hg19	CCDS12287.1																																																																																			.	.		0.602	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461		T	13039211	G	T	13039211	2	4	6	1	0	0	0	0	0	0	0	1	5687	929	33	3		3	FARSA	19	13039211	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	7211247	13039211	46089772	71	543										
CEACAM7	1087	hgsc.bcm.edu	37	chr19	42192077	42192077	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	atgcacactctgtatggacaGgctgaaggggaccccatggt	13	10	1	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:42192077G>T	ENST00000006724.3	-	1	219	c.18C>A	c.(16-18)gcC>gcA	p.A6A	CEACAM7_ENST00000599715.1_Intron|CEACAM7_ENST00000401731.1_Silent_p.A6A|CEACAM7_ENST00000602225.1_Silent_p.A6A|CEACAM7_ENST00000338196.4_Silent_p.A6A	NM_006890.3	NP_008821.1	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 7	6						anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)		TGTATGGACAGGCTGAAGGGG	0.612																																					p.A6A		Atlas-SNP	.											.	CEACAM7	33	.	0			c.C18A						.						82	69	74					19																	42192077		2203	4300	6503	SO:0001819	synonymous_variant	1087	exon1			TGGACAGGCTGAA	X98311	CCDS12583.1	19q13.2	2013-01-29			ENSG00000007306	ENSG00000007306		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1819	protein-coding gene	gene with protein product	"carcinoembryonic antigen gene family member 2"			CGM2		7806520, 9135022	Standard	XM_005278379		Approved	CEA	uc002ori.1	Q14002	OTTHUMG00000151063	ENST00000006724.3:c.18C>A	chr19.hg19:g.42192077G>T		73.0	0.0		73.0	19.0	NM_006890	A8K848|O15148|O15149|Q0VAC1|Q13983|Q9UPJ2	Silent	SNP	ENST00000006724.3	hg19	CCDS12583.1																																																																																			.	.		0.612	CEACAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321145.1	NM_006890		T	42192077	G	T	42192077	2	4	6	1	0	0	0	0	0	0	0	1	3199	987	35	3		3	CEACAM7	19	42192077	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	29152866	42192077	16936906	72	544										
CD79A	973	hgsc.bcm.edu	37	chr19	42383663	42383663	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	accaagaaccgaatcatcacAgccgaggggatcatcctcct	8	14	3	1			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:42383663A>G	ENST00000221972.3	+	3	623	c.438A>G	c.(436-438)acA>acG	p.T146T	CD79A_ENST00000444740.2_Silent_p.T108T	NM_001783.3|NM_021601.3	NP_001774.1|NP_067612.1	P11912	CD79A_HUMAN	CD79a molecule, immunoglobulin-associated alpha	146					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)	B cell receptor complex (GO:0019815)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	11						GAATCATCACAGCCGAGGGGA	0.667			"O, S"		DLBCL																																p.T146T		Atlas-SNP	.		Dom	yes		19	19q13.2	973	"CD79a molecule, immunoglobulin-associated alpha"		L	.	CD79A	25	.	0			c.A438G						.						64	34	44					19																	42383663		2203	4297	6500	SO:0001819	synonymous_variant	973	exon3			CATCACAGCCGAG	M80462	CCDS12589.1, CCDS46088.1	19q13.2	2014-09-17	2006-03-28					"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1698	protein-coding gene	gene with protein product		112205	"CD79A antigen (immunoglobulin-associated alpha)"	IGA		1538135	Standard	NM_001783		Approved	MB-1	uc002orv.3	P11912		ENST00000221972.3:c.438A>G	chr19.hg19:g.42383663A>G		52.0	0.0		46.0	16.0	NM_001783	A0N775|Q53FB8	Silent	SNP	ENST00000221972.3	hg19	CCDS12589.1																																																																																			.	.		0.667	CD79A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463058.1			G	42383663	A	G	42383663	2	3	6	1	0	0	0	0	0	0	0	1	3038	175	7	2		2	CD79A	19	42383663	Silent	SNP	A	TCGA-2Y-A9GW-01A-11D-A382-10	191586	42383663	16745320	73	545										
ZNF772	400720	hgsc.bcm.edu	37	chr19	57985762	57985762	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	agctctgctcaaaaggtatcTcttcatcctccattccatgc	5	14	4	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:57985762T>C	ENST00000343280.4	-	5	610	c.350A>G	c.(349-351)gAg>gGg	p.E117G	AC004076.9_ENST00000415705.3_Intron|ZNF772_ENST00000600175.1_Intron|AC004076.9_ENST00000596831.1_Intron|ZNF772_ENST00000427512.2_Missense_Mutation_p.E5G|ZNF772_ENST00000601768.1_Intron|ZNF772_ENST00000425074.3_Missense_Mutation_p.R34G|ZNF772_ENST00000356584.3_Missense_Mutation_p.E76G	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	117					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)	9		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		AAAAGGTATCTCTTCATCCTC	0.468																																					p.E117G	Melanoma(5;289 436 14293 15924 30817)	Atlas-SNP	.											.	ZNF772	42	.	0			c.A350G						.						76	81	79					19																	57985762		2203	4300	6503	SO:0001583	missense	400720	exon5			GGTATCTCTTCAT	BX647068	CCDS33133.1, CCDS46210.1	19q13.43	2013-01-08				ENSG00000197128		"Zinc fingers, C2H2-type", "-"	33106	protein-coding gene	gene with protein product							Standard	NM_001024596		Approved	DKFZp686I1569	uc002qot.3	Q68DY9		ENST00000343280.4:c.350A>G	chr19.hg19:g.57985762T>C	ENSP00000341165:p.Glu117Gly	26.0	0.0		25.0	6.0	NM_001024596	A6NJK9|B4DH56|B4DYS0	Missense_Mutation	SNP	ENST00000343280.4	hg19	CCDS33133.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.597|9.597	1.127675|1.127675	0.20959|0.20959	.|.	.|.	ENSG00000197128|ENSG00000197128	ENST00000343280;ENST00000427512;ENST00000319969;ENST00000356584;ENST00000291809|ENST00000415705	T;T;T|.	0.08634|.	3.25;3.07;5.6|.	3.36|3.36	3.36|3.36	0.38483|0.38483	.|.	.|.	.|.	.|.	.|.	T|T	0.40670|0.40670	0.1126|0.1126	L|L	0.43923|0.43923	1.385|1.385	0.09310|0.09310	N|N	1|1	P;P;P|.	0.48016|.	0.904;0.734;0.734|.	B;B;B|.	0.42798|.	0.305;0.247;0.398|.	T|T	0.23048|0.23048	-1.0199|-1.0199	9|5	0.45353|.	T|.	0.12|.	.|.	10.0555|10.0555	0.42241|0.42241	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	5;76;117|.	Q68DY9-2;A6NJK9;Q68DY9|.	.;.;ZN772_HUMAN|.	G|G	117;5;63;76;96|34	ENSP00000341165:E117G;ENSP00000395967:E5G;ENSP00000348992:E76G|.	ENSP00000291809:E96G|.	E|R	-|-	2|1	0|2	ZNF772|ZNF772	62677574|62677574	0.173000|0.173000	0.23056|0.23056	0.010000|0.010000	0.14722|0.14722	0.201000|0.201000	0.24016|0.24016	3.454000|3.454000	0.52986|0.52986	1.553000|1.553000	0.49476|0.49476	0.402000|0.402000	0.26972|0.26972	GAG|AGA	.	.		0.468	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596		C	57985762	T	C	57985762	3	2	6	1	0	0	0	0	1	0	0	0	18160	1551	54	2	1123	2	ZNF772	19	57985762	Missense_Mutation	SNP	T	TCGA-2Y-A9GW-01A-11D-A382-10	15602099	57985762	1143221	74	546										
CYYR1	116159	hgsc.bcm.edu	37	chr21	27840930	27840930	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	acagtattccatctcgtggtCgtgaccgtagggtggtggtc	14	9	1	1	rs371412046		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr21:27840930C>A	ENST00000299340.4	-	4	698	c.355G>T	c.(355-357)Gac>Tac	p.D119Y	CYYR1_ENST00000435845.2_3'UTR|AP001596.6_ENST00000421771.1_RNA|AP001596.6_ENST00000429340.1_RNA|AP001596.6_ENST00000444306.1_RNA|AP001597.1_ENST00000414486.1_RNA|AP001597.1_ENST00000357401.3_RNA	NM_052954.2	NP_443186.1	Q96J86	CYYR1_HUMAN	cysteine/tyrosine-rich 1	119						integral component of membrane (GO:0016021)				large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	15						ATCTCGTGGTCGTGACCGTAG	0.532																																					p.D119Y		Atlas-SNP	.											.	CYYR1	38	.	0			c.G355T						.						114	93	100					21																	27840930		2203	4300	6503	SO:0001583	missense	116159	exon4			CGTGGTCGTGACC	AY061853	CCDS13578.1	21q21.2	2014-07-04	2005-07-24		ENSG00000166265	ENSG00000166265			16274	protein-coding gene	gene with protein product			"cysteine and tyrosine-rich 1"	C21orf95		12036297, 12062809, 24981926	Standard	NM_052954		Approved		uc002ymd.3	Q96J86	OTTHUMG00000078689	ENST00000299340.4:c.355G>T	chr21.hg19:g.27840930C>A	ENSP00000299340:p.Asp119Tyr	79.0	0.0		53.0	11.0	NM_052954	A0A059TD09|A8MTU9|B2R845|Q53ER3|Q5JPD0|Q96NV7|R9QAJ4|W8CQB3	Missense_Mutation	SNP	ENST00000299340.4	hg19	CCDS13578.1	.	.	.	.	.	.	.	.	.	.	C	11.18	1.562065	0.27915	.	.	ENSG00000166265	ENST00000299340	T	0.37752	1.18	3.99	2.18	0.27775	.	0.240351	0.47852	D	0.000201	T	0.46151	0.1378	L	0.53249	1.67	0.51233	D	0.999916	D;D	0.63880	0.993;0.989	P;P	0.62649	0.884;0.905	T	0.39800	-0.9596	10	0.87932	D	0	-18.5615	6.5007	0.22168	0.0:0.7817:0.0:0.2183	.	120;119	Q96J86-2;Q96J86	.;CYYR1_HUMAN	Y	119	ENSP00000299340:D119Y	ENSP00000299340:D119Y	D	-	1	0	CYYR1	26762801	0.922000	0.31269	0.609000	0.28983	0.139000	0.21198	1.633000	0.37113	0.652000	0.30806	0.555000	0.69702	GAC	.	.		0.532	CYYR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171654.2	NM_052954		A	27840930	C	A	27840930	3	1	6	1	0	0	0	0	1	0	0	0	4213	884	31	1	113	1	CYYR1	21	27840930	Missense_Mutation	SNP	C	TCGA-2Y-A9GW-01A-11D-A382-10		27840930	20288965	75	547										
FOXRED2	80020	hgsc.bcm.edu	37	chr22	36900813	36900813	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	ccagtggctacaaagaggacGctgcaggcggggacagagga	17	9	0	2			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr22:36900813G>A	ENST00000397224.4	-	3	621	c.528C>T	c.(526-528)agC>agT	p.S176S	FOXRED2_ENST00000216187.6_Splice_Site_p.S176S|FOXRED2_ENST00000397223.4_Splice_Site_p.S176S	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	176					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CAAAGAGGACGCTGCAGGCGG	0.562																																					p.S176S		Atlas-SNP	.											.	FOXRED2	48	.	0			c.C528T						.						36	39	38					22																	36900813		2203	4300	6503	SO:0001630	splice_region_variant	80020	exon3			GAGGACGCTGCAG	BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.528-1C>T	chr22.hg19:g.36900813G>A		105.0	0.0		116.0	29.0	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	hg19	CCDS13929.1																																																																																			.	.		0.562	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	Silent	A	36900813	G	A	36900813	5	1	6	1	0	0	0	0	0	0	1	0	6042	1101	38	1	1554	1	FOXRED2	22	36900813	Splice_Site	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10		36900813	14403753	76	548										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51117297	51117297	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gacttccgcactcgcgatggGctcactgccgtgcactgtgc	12	15	1	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr22:51117297G>A	ENST00000414786.2	+	5	776	c.549G>A	c.(547-549)ggG>ggA	p.G183G	SHANK3_ENST00000445220.2_Silent_p.G183G|SHANK3_ENST00000262795.3_Silent_p.G183G			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	183					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CTCGCGATGGGCTCACTGCCG	0.667																																					p.G183G		Atlas-SNP	.											.	SHANK3	96	.	0			c.G549A						.						32	35	34					22																	51117297		2118	4218	6336	SO:0001819	synonymous_variant	85358	exon5			CGATGGGCTCACT	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.549G>A	chr22.hg19:g.51117297G>A		97.0	0.0		93.0	17.0	NM_033517	D7UT47|Q8TET3	Silent	SNP	ENST00000414786.2	hg19																																																																																				.	.		0.667	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		A	51117297	G	A	51117297	2	1	6	1	0	0	0	0	0	0	0	1	14281	1190	42	3		3	SHANK3	22	51117297	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10	14216484	51117297	187269	77	549										
PRKX	5613	hgsc.bcm.edu	37	chrX	3573254	3573254	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.608356110894182	2.63620981387479	0.343853453983668	1	1	0	gtggccatccctatccagcaGgatgttctctggcttcaagt	10	12	2	0			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chrX:3573254G>A	ENST00000262848.5	-	3	889	c.535C>T	c.(535-537)Ctg>Ttg	p.L179L	PRKX_ENST00000425240.1_5'UTR	NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	179	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				CTATCCAGCAGGATGTTCTCT	0.522																																					p.L179L		Atlas-SNP	.											.	PRKX	29	.	0			c.C535T						.						157	128	138					X																	3573254		2203	4300	6503	SO:0001819	synonymous_variant	5613	exon3			CCAGCAGGATGTT		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.535C>T	chrX.hg19:g.3573254G>A		127.0	0.0		118.0	51.0	NM_005044		Silent	SNP	ENST00000262848.5	hg19	CCDS14125.1																																																																																			.	.		0.522	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044		A	3573254	G	A	3573254	2	1	6	1	0	0	0	0	0	0	0	1	12539	991	35	3		3	PRKX	23	3573254	Silent	SNP	G	TCGA-2Y-A9GW-01A-11D-A382-10		3573254	151697306	78	550										
CYP4A22	284541	hgsc.bcm.edu	37	chr1	47606450	47606450	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	atctgtctaccctcgttgacAgttccaacacgaccaggagc	8	14	2	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr1:47606450A>C	ENST00000371891.3	+	2	226		c.e2-1		CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000294337.3_Splice_Site|CYP4A22_ENST00000485117.1_Splice_Site|CYP4A22_ENST00000371890.3_Splice_Site	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22							endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCTCGTTGACAGTTCCAACAC	0.502																																					.	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.196-2A>C						.						153	134	140					1																	47606450		2203	4300	6503	SO:0001630	splice_region_variant	284541	exon2			GTTGACAGTTCCA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"Cytochrome P450s"	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.196-1A>C	chr1.hg19:g.47606450A>C		92.0	0.0		78.0	11.0	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Splice_Site	SNP	ENST00000371891.3	hg19	CCDS30707.1	.	.	.	.	.	.	.	.	.	.	a	3.871	-0.027890	0.07589	.	.	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	.	.	.	1.19	-0.103	0.13609	.	.	.	.	.	.	.	.	.	.	.	0.20403	N	0.999907	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.2145	0.10528	0.6951:0.0:0.0:0.3049	.	.	.	.	.	-1	.	.	.	+	.	.	CYP4A22	47379037	0.071000	0.21146	0.005000	0.12908	0.105000	0.19272	2.149000	0.42244	-0.049000	0.13379	0.172000	0.16884	.	.	.		0.502	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	Intron	C	47606450	A	C	47606450	5	2	7	1	0	0	0	0	0	0	1	0	4186	202	7	5	200	5	CYP4A22	1	47606450	Splice_Site	SNP	A	TCGA-2Y-A9GX-01A-11D-A382-10		47606450	201644171	1	551										
EVI5	7813	hgsc.bcm.edu	37	chr1	93091357	93091357	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	atatattaatatacctgccaGtgttcctctaaatccttgac	4	10	1	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr1:93091357G>C	ENST00000370331.1	-	13	1623	c.1614C>G	c.(1612-1614)caC>caG	p.H538Q	EVI5_ENST00000540033.1_Missense_Mutation_p.H538Q|EVI5_ENST00000491940.1_5'UTR|EVI5_ENST00000543509.1_Missense_Mutation_p.H549Q	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	538	Dimerization.|Interaction with AURKB and INCENP.|Targeting to the centrosomes.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		ATACCTGCCAGTGTTCCTCTA	0.358																																					p.H538Q		Atlas-SNP	.											.	EVI5	94	.	0			c.C1614G						.						135	136	136					1																	93091357		2202	4300	6502	SO:0001583	missense	7813	exon13			CTGCCAGTGTTCC	AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1614C>G	chr1.hg19:g.93091357G>C	ENSP00000359356:p.His538Gln	289.0	0.0		301.0	25.0	NM_005665	A6NKX8|B9A6J0|Q9H1Y9	Missense_Mutation	SNP	ENST00000370331.1	hg19	CCDS30774.1	.	.	.	.	.	.	.	.	.	.	G	1.040	-0.679072	0.03378	.	.	ENSG00000067208	ENST00000370331;ENST00000540033;ENST00000543509;ENST00000338689	T;T;T	0.29655	1.56;1.56;1.56	5.61	-0.176	0.13311	.	0.000000	0.85682	D	0.000000	T	0.10035	0.0246	L	0.33792	1.035	0.40241	D	0.977968	P;P	0.45902	0.868;0.67	P;P	0.50825	0.651;0.449	T	0.16748	-1.0392	10	0.02654	T	1	-12.2788	7.0901	0.25279	0.3719:0.1194:0.5087:0.0	.	549;538	F5H4R0;O60447	.;EVI5_HUMAN	Q	538;538;549;237	ENSP00000359356:H538Q;ENSP00000440826:H538Q;ENSP00000445019:H549Q	ENSP00000345500:H237Q	H	-	3	2	EVI5	92863945	1.000000	0.71417	0.999000	0.59377	0.509000	0.34042	1.128000	0.31369	0.065000	0.16485	-0.196000	0.12772	CAC	.	.		0.358	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665		C	93091357	G	C	93091357	3	2	7	1	0	0	0	0	1	0	0	0	5291	1020	36	4	842	4	EVI5	1	93091357	Missense_Mutation	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10	45484907	93091357	156159264	2	552										
ABCA4	24	hgsc.bcm.edu	37	chr1	94476366	94476366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	atggacgtaccattgggagaGgaagaagtggcgctggacca	16	7	0	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr1:94476366G>A	ENST00000370225.3	-	40	5790	c.5704C>T	c.(5704-5706)Ctc>Ttc	p.L1902F	ABCA4_ENST00000465352.1_5'UTR|ABCA4_ENST00000535881.1_Missense_Mutation_p.L21F|ABCA4_ENST00000536513.1_Missense_Mutation_p.L172F	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1902					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CATTGGGAGAGGAAGAAGTGG	0.572																																					p.L1902F		Atlas-SNP	.											.	ABCA4	275	.	0			c.C5704T						.						166	129	141					1																	94476366		2203	4300	6503	SO:0001583	missense	24	exon40			GGGAGAGGAAGAA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.5704C>T	chr1.hg19:g.94476366G>A	ENSP00000359245:p.Leu1902Phe	111.0	0.0		99.0	8.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	G	8.785	0.929285	0.18131	.	.	ENSG00000198691	ENST00000546054;ENST00000370225;ENST00000536513;ENST00000535881	D;D;D	0.91521	-2.86;-2.35;-2.39	4.74	0.647	0.17796	.	0.520502	0.22207	N	0.063143	T	0.74107	0.3673	L	0.43923	1.385	0.80722	D	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.10450	0.005;0.001;0.002	T	0.62445	-0.6853	10	0.18710	T	0.47	.	9.7315	0.40363	0.5594:0.0:0.4406:0.0	.	172;21;1902	B4DWY6;B4DX12;P78363	.;.;ABCA4_HUMAN	F	694;1902;172;21	ENSP00000359245:L1902F;ENSP00000439707:L172F;ENSP00000443203:L21F	ENSP00000359245:L1902F	L	-	1	0	ABCA4	94248954	0.094000	0.21725	0.991000	0.47740	0.936000	0.57629	-0.453000	0.06778	0.027000	0.15297	0.585000	0.79938	CTC	.	.		0.572	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94476366	G	A	94476366	3	1	7	1	0	0	0	0	1	0	0	0	34	1000	35	3	1161	3	ABCA4	1	94476366	Missense_Mutation	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10	1385009	94476366	154774255	3	553										
CAPZA1	829	hgsc.bcm.edu	37	chr1	113202330	113202330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	tgtgttttaataggaatggtCgttggagatcagagtggaag	15	2	1	2	rs145898509		TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr1:113202330C>T	ENST00000263168.3	+	7	1186	c.514C>T	c.(514-516)Cgt>Tgt	p.R172C	CAPZA1_ENST00000476936.1_3'UTR	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	172					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TAGGAATGGTCGTTGGAGATC	0.438																																					p.R172C		Atlas-SNP	.											.	CAPZA1	16	.	0			c.C514T						.						92	85	87					1																	113202330		2203	4300	6503	SO:0001583	missense	829	exon7			AATGGTCGTTGGA	U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.514C>T	chr1.hg19:g.113202330C>T	ENSP00000263168:p.Arg172Cys	65.0	0.0		69.0	9.0	NM_006135	Q53FQ6|Q6FHD5	Missense_Mutation	SNP	ENST00000263168.3	hg19	CCDS30805.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.447848	0.84101	.	.	ENSG00000116489	ENST00000263168	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.61652	0.2364	M	0.73319	2.225	0.80722	D	1	B	0.29612	0.251	B	0.31946	0.138	T	0.65158	-0.6236	9	0.62326	D	0.03	-28.1951	19.3394	0.94335	0.0:1.0:0.0:0.0	.	172	P52907	CAZA1_HUMAN	C	172	.	ENSP00000263168:R172C	R	+	1	0	CAPZA1	113003853	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.895000	0.63214	2.739000	0.93911	0.655000	0.94253	CGT	.	C|1.000;A|0.000		0.438	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135		T	113202330	C	T	113202330	3	4	7	1	0	0	0	0	1	0	0	0	2642	884	31	1	540	1	CAPZA1	1	113202330	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	18725964	113202330	136048291	4	554										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172548362	172548362	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	attatccactggattataatActggagaggataaatcctca	7	7	1	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr1:172548362A>G	ENST00000263688.3	+	15	1672	c.1453A>G	c.(1453-1455)Act>Gct	p.T485A	SUCO_ENST00000367723.4_Missense_Mutation_p.T636A|SUCO_ENST00000610051.1_Missense_Mutation_p.T448A|SUCO_ENST00000608151.1_Missense_Mutation_p.T637A	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	485					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											GGATTATAATACTGGAGAGGA	0.308																																					p.T485A		Atlas-SNP	.											.	.	.	.	0			c.A1453G						.						59	63	61					1																	172548362		2202	4296	6498	SO:0001583	missense	51430	exon15			TATAATACTGGAG	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1453A>G	chr1.hg19:g.172548362A>G	ENSP00000263688:p.Thr485Ala	162.0	0.0		231.0	17.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	hg19	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.792243	0.50102	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.22	5.22	0.72569	.	0.155109	0.56097	D	0.000023	T	0.18964	0.0455	N	0.14661	0.345	0.38557	D	0.949613	B;B;P;B	0.36315	0.084;0.03;0.547;0.125	B;B;B;B	0.32928	0.014;0.008;0.155;0.05	T	0.08848	-1.0702	9	0.24483	T	0.36	-5.1596	13.9322	0.64003	1.0:0.0:0.0:0.0	.	448;485;637;485	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	A	637;485	.	ENSP00000263688:T485A	T	+	1	0	C1orf9	170814985	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.257000	0.58816	1.980000	0.57719	0.377000	0.23210	ACT	.	.		0.308	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		G	172548362	A	G	172548362	3	3	7	1	0	0	0	0	1	0	0	0	2069	391	14	2	1511	2	C1orf9	1	172548362	Missense_Mutation	SNP	A	TCGA-2Y-A9GX-01A-11D-A382-10	59346032	172548362	76702259	5	555										
OR2G6	391211	hgsc.bcm.edu	37	chr1	248685675	248685675	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ggcctttgggacctgttcgtCtcacctggttgtggtcatca	12	11	3	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr1:248685675C>A	ENST00000343414.4	+	1	760	c.728C>A	c.(727-729)tCt>tAt	p.S243Y		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACCTGTTCGTCTCACCTGGTT	0.458																																					p.S243Y		Atlas-SNP	.											.	OR2G6	124	.	0			c.C728A						.						114	114	114					1																	248685675		2203	4300	6503	SO:0001583	missense	391211	exon1			GTTCGTCTCACCT		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"GPCR / Class A : Olfactory receptors"	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.728C>A	chr1.hg19:g.248685675C>A	ENSP00000341291:p.Ser243Tyr	58.0	0.0		83.0	10.0	NM_001013355	B2RP33	Missense_Mutation	SNP	ENST00000343414.4	hg19	CCDS31119.1	.	.	.	.	.	.	.	.	.	.	N	18.49	3.635631	0.67130	.	.	ENSG00000188558	ENST00000343414	T	0.39406	1.08	3.83	3.83	0.44106	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44097	U	0.000486	T	0.79246	0.4413	H	0.99435	4.565	0.34104	D	0.662163	D	0.89917	1.0	D	0.85130	0.997	D	0.91307	0.5071	10	0.87932	D	0	.	14.6536	0.68817	0.0:1.0:0.0:0.0	.	243	Q5TZ20	OR2G6_HUMAN	Y	243	ENSP00000341291:S243Y	ENSP00000341291:S243Y	S	+	2	0	OR2G6	246752298	0.206000	0.23470	0.952000	0.39060	0.693000	0.40251	5.535000	0.67173	1.964000	0.57103	0.400000	0.26472	TCT	.	.		0.458	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842		A	248685675	C	A	248685675	3	1	7	1	0	0	0	0	1	0	0	0	11009	913	32	3	730	3	OR2G6	1	248685675	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	76137313	248685675	564946	6	556										
NBAS	51594	hgsc.bcm.edu	37	chr2	15614384	15614384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	cagaatcagaatcctcttctCcttcatcttcttctccagct	3	15	7	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr2:15614384C>T	ENST00000281513.5	-	15	1431	c.1406G>A	c.(1405-1407)gGa>gAa	p.G469E	NBAS_ENST00000441750.1_Missense_Mutation_p.G469E	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	469					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						ATCCTCTTCTCCTTCATCTTC	0.388																																					p.G469E		Atlas-SNP	.											.	NBAS	246	.	0			c.G1406A						.						69	66	67					2																	15614384		2203	4300	6503	SO:0001583	missense	51594	exon15			TCTTCTCCTTCAT	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1406G>A	chr2.hg19:g.15614384C>T	ENSP00000281513:p.Gly469Glu	100.0	0.0		109.0	10.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.477767	0.63849	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.09350	2.99;3.14	5.74	5.74	0.90152	.	0.052751	0.85682	D	0.000000	T	0.32102	0.0818	L	0.54323	1.7	0.43863	D	0.996467	D	0.89917	1.0	D	0.91635	0.999	T	0.00587	-1.1657	10	0.87932	D	0	.	19.9219	0.97089	0.0:1.0:0.0:0.0	.	469	A2RRP1	NBAS_HUMAN	E	469	ENSP00000413201:G469E;ENSP00000281513:G469E	ENSP00000281513:G469E	G	-	2	0	NBAS	15531835	0.987000	0.35691	0.976000	0.42696	0.998000	0.95712	2.729000	0.47327	2.716000	0.92895	0.655000	0.94253	GGA	.	.		0.388	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15614384	C	T	15614384	3	4	7	1	0	0	0	0	1	0	0	0	10195	855	30	3	5861	3	NBAS	2	15614384	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10		15614384	227584989	7	557										
PASK	23178	hgsc.bcm.edu	37	chr2	242075394	242075394	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ggccaggtctgggagctgtaAtgagctgttgtacgcaaggt	16	7	1	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr2:242075394A>G	ENST00000405260.1	-	8	1896	c.1198T>C	c.(1198-1200)Tta>Cta	p.L400L	PASK_ENST00000358649.4_Silent_p.L400L|PASK_ENST00000234040.4_Silent_p.L400L|PASK_ENST00000539818.1_Silent_p.L184L|PASK_ENST00000403638.3_Silent_p.L400L|PASK_ENST00000544142.1_Silent_p.L214L	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	400	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GGGAGCTGTAATGAGCTGTTG	0.547																																					p.L400L		Atlas-SNP	.											.	PASK	230	.	0			c.T1198C						.						146	144	145					2																	242075394		2203	4300	6503	SO:0001819	synonymous_variant	23178	exon8			GCTGTAATGAGCT	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.1198T>C	chr2.hg19:g.242075394A>G		103.0	0.0		108.0	12.0	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	hg19	CCDS2545.1																																																																																			.	.		0.547	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		G	242075394	A	G	242075394	2	3	7	1	0	0	0	0	0	0	0	1	11481	98	4	2		2	PASK	2	242075394	Silent	SNP	A	TCGA-2Y-A9GX-01A-11D-A382-10	226461010	242075394	1123979	8	558										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48608074	48608074	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	tagggcacctctactcaccaCtgaccccggtggtccaggtg	11	15	2	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr3:48608074C>T	ENST00000328333.8	-	95	7449	c.7342G>A	c.(7342-7344)Gtg>Atg	p.V2448M	COL7A1_ENST00000454817.1_Missense_Mutation_p.V2416M	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2448	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTACTCACCACTGACCCCGGT	0.627																																					p.V2448M		Atlas-SNP	.											.	COL7A1	320	.	0			c.G7342A						.						18	19	19					3																	48608074		2201	4296	6497	SO:0001583	missense	1294	exon95			TCACCACTGACCC	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.7342G>A	chr3.hg19:g.48608074C>T	ENSP00000332371:p.Val2448Met	98.0	0.0		97.0	12.0	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	hg19	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	10.92	1.485734	0.26686	.	.	ENSG00000114270	ENST00000328333;ENST00000454817;ENST00000422991	D;D;D	0.94457	-3.43;-3.43;-3.21	4.35	1.42	0.22433	.	1.380920	0.05217	N	0.507854	D	0.90208	0.6939	L	0.32530	0.975	0.09310	N	0.999999	B	0.16802	0.019	B	0.19666	0.026	T	0.78984	-0.1988	10	0.46703	T	0.11	.	5.6707	0.17721	0.0:0.6566:0.1619:0.1815	.	2448	Q02388	CO7A1_HUMAN	M	2448;2416;113	ENSP00000332371:V2448M;ENSP00000412569:V2416M;ENSP00000391608:V113M	ENSP00000332371:V2448M	V	-	1	0	COL7A1	48583078	0.005000	0.15991	0.522000	0.27862	0.935000	0.57460	1.626000	0.37039	0.371000	0.24564	0.655000	0.94253	GTG	.	.		0.627	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		T	48608074	C	T	48608074	3	4	7	1	0	0	0	0	1	0	0	0	3706	565	20	3	1588	3	COL7A1	3	48608074	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10		48608074	149414356	9	559										
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69225699	69225699	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ttggagagggtaaaggattaTagacattgccatagcagctg	13	5	0	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr3:69225699T>C	ENST00000398540.3	-	22	3043	c.2960A>G	c.(2959-2961)tAt>tGt	p.Y987C	FRMD4B_ENST00000478263.1_Missense_Mutation_p.Y639C|FRMD4B_ENST00000542259.1_Missense_Mutation_p.Y933C	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	987					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TAAAGGATTATAGACATTGCC	0.458																																					p.Y987C		Atlas-SNP	.											.	FRMD4B	90	.	0			c.A2960G						.						144	145	145					3																	69225699		1936	4124	6060	SO:0001583	missense	23150	exon22			GGATTATAGACAT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.2960A>G	chr3.hg19:g.69225699T>C	ENSP00000381549:p.Tyr987Cys	126.0	0.0		145.0	11.0	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	hg19	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.320496	0.41096	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000478263	D;D	0.84146	-1.81;-1.81	5.69	5.69	0.88448	.	0.552403	0.18903	N	0.127996	D	0.90021	0.6884	L	0.60455	1.87	0.39400	D	0.966574	D;B	0.76494	0.999;0.017	D;B	0.64321	0.924;0.012	D	0.91129	0.4936	10	0.72032	D	0.01	-14.9811	14.5303	0.67920	0.0:0.0:0.0:1.0	.	831;987	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	C	987;933;639	ENSP00000381549:Y987C;ENSP00000437658:Y933C	ENSP00000381549:Y987C	Y	-	2	0	FRMD4B	69308389	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	2.031000	0.41117	2.180000	0.69256	0.482000	0.46254	TAT	.	.		0.458	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			C	69225699	T	C	69225699	3	2	7	1	0	0	0	0	1	0	0	0	6060	1406	49	2	152	2	FRMD4B	3	69225699	Missense_Mutation	SNP	T	TCGA-2Y-A9GX-01A-11D-A382-10	20617625	69225699	128796731	10	560										
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122645524	122645524	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	aggctgccacgaagtttggcTctgggtgggcagaagaggaa	17	7	1	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr3:122645524T>C	ENST00000357599.3	-	9	1237	c.851A>G	c.(850-852)gAg>gGg	p.E284G	AC078794.1_ENST00000408284.1_RNA|SEMA5B_ENST00000195173.4_Splice_Site_p.E284G|SEMA5B_ENST00000451055.2_Splice_Site_p.E338G	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	284	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GAAGTTTGGCTCTGGGTGGGC	0.577																																					p.E338G		Atlas-SNP	.											.	SEMA5B	303	.	0			c.A1013G						.						44	38	40					3																	122645524		2203	4300	6503	SO:0001630	splice_region_variant	54437	exon9			TTTGGCTCTGGGT	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.851-1A>G	chr3.hg19:g.122645524T>C		129.0	0.0		132.0	15.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	hg19	CCDS35491.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.199646	0.79015	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	4.69	4.69	0.59074	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.45216	0.1331	M	0.65498	2.005	0.80722	D	1	D;D;D	0.71674	0.998;0.996;0.996	D;D;D	0.66351	0.939;0.943;0.943	T	0.31052	-0.9957	10	0.30854	T	0.27	.	13.5066	0.61486	0.0:0.0:0.0:1.0	.	226;284;284	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	G	284;284;226;338;284	ENSP00000350215:E284G;ENSP00000195173:E284G;ENSP00000389588:E338G;ENSP00000377208:E284G	ENSP00000195173:E284G	E	-	2	0	SEMA5B	124128214	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.545000	0.82128	1.971000	0.57363	0.528000	0.53228	GAG	.	.		0.577	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	Missense_Mutation	C	122645524	T	C	122645524	5	2	7	1	0	0	0	0	0	0	1	0	14053	1565	54	2	2664	2	SEMA5B	3	122645524	Splice_Site	SNP	T	TCGA-2Y-A9GX-01A-11D-A382-10	53419825	122645524	75376906	11	561										
MCM2	4171	hgsc.bcm.edu	37	chr3	127327292	127327292	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	caaagtggcggctggccggcTgccccgctccaaggacgcca	14	16	0	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr3:127327292T>A	ENST00000265056.7	+	7	1413	c.1169T>A	c.(1168-1170)cTg>cAg	p.L390Q		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	390					cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						GCTGGCCGGCTGCCCCGCTCC	0.602																																					p.L390Q		Atlas-SNP	.											.	MCM2	79	.	0			c.T1169A						.						75	81	79					3																	127327292		2203	4300	6503	SO:0001583	missense	4171	exon7			GCCGGCTGCCCCG	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"mitotin"	116945	"minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)", "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.1169T>A	chr3.hg19:g.127327292T>A	ENSP00000265056:p.Leu390Gln	173.0	0.0		164.0	18.0	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	hg19	CCDS3043.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.3|24.3	4.512029|4.512029	0.85389|0.85389	.|.	.|.	ENSG00000073111|ENSG00000073111	ENST00000491422|ENST00000265056;ENST00000539922;ENST00000543142	.|T	.|0.29142	.|1.58	5.31|5.31	5.31|5.31	0.75309|0.75309	.|Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	.|0.067804	.|0.64402	.|D	.|0.000010	T|T	0.62588|0.62588	0.2440|0.2440	H|H	0.95079|0.95079	3.62|3.62	0.80722|0.80722	D|D	1|1	.|D;P;P	.|0.57571	.|0.98;0.763;0.558	.|P;P;P	.|0.56700	.|0.804;0.764;0.664	T|T	0.76132|0.76132	-0.3071|-0.3071	5|10	.|0.87932	.|D	.|0	-21.8617|-21.8617	15.2532|15.2532	0.73564|0.73564	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|371;260;390	.|F5H1E9;B4DSV5;P49736	.|.;.;MCM2_HUMAN	S|Q	253|390;294;371	.|ENSP00000265056:L390Q	.|ENSP00000265056:L390Q	C|L	+|+	1|2	0|0	MCM2|MCM2	128809982|128809982	1.000000|1.000000	0.71417|0.71417	0.908000|0.908000	0.35775|0.35775	0.978000|0.978000	0.69477|0.69477	5.899000|5.899000	0.69846|0.69846	2.004000|2.004000	0.58718|0.58718	0.482000|0.482000	0.46254|0.46254	TGC|CTG	.	.		0.602	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			A	127327292	T	A	127327292	3	1	7	1	0	0	0	0	1	0	0	0	9395	1580	55	4	1195	4	MCM2	3	127327292	Missense_Mutation	SNP	T	TCGA-2Y-A9GX-01A-11D-A382-10	4681768	127327292	70695138	12	562										
RTP1	132112	hgsc.bcm.edu	37	chr3	186917601	186917601	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	agtaccgcatccacgtggccAgccgccaggacaaccggcgg	13	16	0	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr3:186917601A>T	ENST00000312295.4	+	2	565	c.535A>T	c.(535-537)Agc>Tgc	p.S179C	RP11-208N14.4_ENST00000356133.3_RNA	NM_153708.2	NP_714919.2	P59025	RTP1_HUMAN	receptor (chemosensory) transporter protein 1	179					protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)			breast(2)|endometrium(4)|large_intestine(5)|lung(6)|ovary(3)|skin(2)	22	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		CCACGTGGCCAGCCGCCAGGA	0.682																																					p.S179C		Atlas-SNP	.											.	RTP1	51	.	0			c.A535T						.						24	25	25					3																	186917601		2200	4294	6494	SO:0001583	missense	132112	exon2			GTGGCCAGCCGCC	BC034744	CCDS3287.2	3q27.3	2014-02-20	2006-11-21		ENSG00000175077	ENSG00000175077		"Receptor transporter proteins"	28580	protein-coding gene	gene with protein product	"receptor transporting protein 1", "zinc finger, 3CxxC-type 1"	609137	"receptor transporter protein 1"			16271481, 15550249, 16720576	Standard	NM_153708		Approved	MGC35450, Z3CXXC1	uc003frg.3	P59025	OTTHUMG00000149886	ENST00000312295.4:c.535A>T	chr3.hg19:g.186917601A>T	ENSP00000311712:p.Ser179Cys	132.0	0.0		112.0	14.0	NM_153708		Missense_Mutation	SNP	ENST00000312295.4	hg19	CCDS3287.2	.	.	.	.	.	.	.	.	.	.	A	19.30	3.801615	0.70682	.	.	ENSG00000175077	ENST00000312295	T	0.24151	1.87	5.7	1.97	0.26223	.	0.683764	0.16626	N	0.206267	T	0.28499	0.0705	L	0.42245	1.32	0.25792	N	0.984601	P	0.44195	0.828	P	0.49752	0.621	T	0.07751	-1.0756	10	0.66056	D	0.02	.	7.6186	0.28173	0.7481:0.0:0.2519:0.0	.	179	P59025	RTP1_HUMAN	C	179	ENSP00000311712:S179C	ENSP00000311712:S179C	S	+	1	0	RTP1	188400295	0.953000	0.32496	1.000000	0.80357	0.969000	0.65631	0.640000	0.24705	0.443000	0.26582	0.459000	0.35465	AGC	.	.		0.682	RTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313731.2	NM_153708		T	186917601	A	T	186917601	3	4	7	1	0	0	0	0	1	0	0	0	13748	188	7	4	541	4	RTP1	3	186917601	Missense_Mutation	SNP	A	TCGA-2Y-A9GX-01A-11D-A382-10	59590309	186917601	11104829	13	563										
ZFYVE28	57732	hgsc.bcm.edu	37	chr4	2321941	2321941	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	aagggccggaacagctcggaCatgtcttccaccttgcggtc	12	13	1	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr4:2321941C>A	ENST00000290974.2	-	7	1098	c.759G>T	c.(757-759)atG>atT	p.M253I	RP11-478C1.7_ENST00000510632.1_RNA|ZFYVE28_ENST00000511071.1_Missense_Mutation_p.M223I|ZFYVE28_ENST00000515312.1_Missense_Mutation_p.M183I	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	253					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						ACAGCTCGGACATGTCTTCCA	0.607																																					p.M253I		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.G759T						.						116	101	106					4																	2321941		2203	4300	6503	SO:0001583	missense	57732	exon7			CTCGGACATGTCT	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"Zinc fingers, FYVE domain containing"	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.759G>T	chr4.hg19:g.2321941C>A	ENSP00000290974:p.Met253Ile	66.0	0.0		85.0	14.0	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Missense_Mutation	SNP	ENST00000290974.2	hg19	CCDS33942.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.379583	0.61845	.	.	ENSG00000159733	ENST00000290974;ENST00000511071;ENST00000515312	T;T;T	0.32023	1.47;1.47;1.47	5.41	5.41	0.78517	.	0.039280	0.85682	D	0.000000	T	0.46983	0.1421	L	0.41710	1.295	0.80722	D	1	D;P	0.61080	0.989;0.533	D;B	0.72982	0.979;0.083	T	0.17899	-1.0354	10	0.30854	T	0.27	.	17.8039	0.88596	0.0:1.0:0.0:0.0	.	223;253	Q9HCC9-2;Q9HCC9	.;LST2_HUMAN	I	253;223;183	ENSP00000290974:M253I;ENSP00000425706:M223I;ENSP00000426299:M183I	ENSP00000290974:M253I	M	-	3	0	ZFYVE28	2291739	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.942000	0.70203	2.536000	0.85505	0.650000	0.86243	ATG	.	.		0.607	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371		A	2321941	C	A	2321941	3	1	7	1	0	0	0	0	1	0	0	0	17685	478	17	3	1932	3	ZFYVE28	4	2321941	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10		2321941	188832335	14	564										
PRKG2	5593	hgsc.bcm.edu	37	chr4	82031670	82031670	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	acactgaagtcatgtcccttGttgagaatgacttcaggagc	10	9	2	3			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr4:82031670G>A	ENST00000395578.1	-	15	1988	c.1872C>T	c.(1870-1872)aaC>aaT	p.N624N	PRKG2_ENST00000264399.1_Silent_p.N624N|PRKG2_ENST00000418486.2_Silent_p.N595N|PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000545647.1_Silent_p.N204N			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	624	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						CATGTCCCTTGTTGAGAATGA	0.448																																					p.N624N		Atlas-SNP	.											.	PRKG2	195	.	0			c.C1872T						.						123	120	121					4																	82031670		2203	4300	6503	SO:0001819	synonymous_variant	5593	exon14			TCCCTTGTTGAGA	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.1872C>T	chr4.hg19:g.82031670G>A		77.0	0.0		106.0	12.0	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Silent	SNP	ENST00000395578.1	hg19	CCDS3589.1																																																																																			.	.		0.448	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		A	82031670	G	A	82031670	2	1	7	1	0	0	0	0	0	0	0	1	12535	1368	48	3		3	PRKG2	4	82031670	Silent	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10	79709729	82031670	109122606	15	565										
GRID2	2895	hgsc.bcm.edu	37	chr4	94693257	94693257	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	aaattgacctggagcacctcCatagacgtgtaaatagcttg	9	9	0	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr4:94693257C>T	ENST00000282020.4	+	16	2890	c.2632C>T	c.(2632-2634)Cat>Tat	p.H878Y	GRID2_ENST00000510992.1_Missense_Mutation_p.H783Y	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	878					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		GGAGCACCTCCATAGACGTGT	0.413																																					p.H878Y		Atlas-SNP	.											.	GRID2	233	.	0			c.C2632T						.						144	133	137					4																	94693257		2203	4300	6503	SO:0001583	missense	2895	exon16			CACCTCCATAGAC	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.2632C>T	chr4.hg19:g.94693257C>T	ENSP00000282020:p.His878Tyr	73.0	0.0		71.0	9.0	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	hg19	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.632972	0.87660	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.15256	2.48;2.44	5.42	5.42	0.78866	.	0.763557	0.12699	N	0.446513	T	0.34106	0.0886	L	0.34521	1.04	0.80722	D	1	P;D	0.57899	0.851;0.981	P;D	0.65140	0.775;0.932	T	0.07731	-1.0757	10	0.72032	D	0.01	.	19.2246	0.93814	0.0:1.0:0.0:0.0	.	783;878	E9PH24;O43424	.;GRID2_HUMAN	Y	878;783	ENSP00000282020:H878Y;ENSP00000421257:H783Y	ENSP00000282020:H878Y	H	+	1	0	GRID2	94912280	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.484000	0.81180	2.531000	0.85337	0.650000	0.86243	CAT	.	.		0.413	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			T	94693257	C	T	94693257	3	4	7	1	0	0	0	0	1	0	0	0	6781	594	21	3	2694	3	GRID2	4	94693257	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	12661587	94693257	96461019	16	566										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71492333	71492333	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	atgtgatggctgtggtcgacAaggctgcagaggctggtggt	18	6	0	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr5:71492333A>T	ENST00000296755.7	+	5	3449	c.3151A>T	c.(3151-3153)Aag>Tag	p.K1051*		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1051					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TGTGGTCGACAAGGCTGCAGA	0.542																																					p.K1051X	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A3151T						.						119	123	121					5																	71492333		2203	4300	6503	SO:0001587	stop_gained	4131	exon5			GTCGACAAGGCTG	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3151A>T	chr5.hg19:g.71492333A>T	ENSP00000296755:p.Lys1051*	54.0	0.0		50.0	6.0	NM_005909	A2BDK5	Nonsense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	41	8.928517	0.99006	.	.	ENSG00000131711	ENST00000296755	.	.	.	5.86	4.64	0.57946	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.627	11.6874	0.51494	0.8674:0.0:0.0:0.1326	.	.	.	.	X	1051	.	ENSP00000296755:K1051X	K	+	1	0	MAP1B	71528089	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	4.948000	0.63590	2.246000	0.74042	0.533000	0.62120	AAG	.	.		0.542	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71492333	A	T	71492333	4	4	7	1	0	0	0	0	0	1	0	0	9237	131	5	4	3169	4	MAP1B	5	71492333	Nonsense_Mutation	SNP	A	TCGA-2Y-A9GX-01A-11D-A382-10		71492333	109422927	17	567										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71495123	71495123	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	atgaaaagactgagaggtctAgaaggcttctggatgacatc	12	6	2	5			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr5:71495123A>T	ENST00000296755.7	+	5	6239	c.5941A>T	c.(5941-5943)Aga>Tga	p.R1981*		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1981					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TGAGAGGTCTAGAAGGCTTCT	0.498																																					p.R1981X	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A5941T						.						101	107	105					5																	71495123		2203	4300	6503	SO:0001587	stop_gained	4131	exon5			AGGTCTAGAAGGC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.5941A>T	chr5.hg19:g.71495123A>T	ENSP00000296755:p.Arg1981*	59.0	0.0		52.0	11.0	NM_005909	A2BDK5	Nonsense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	46	12.891367	0.99704	.	.	ENSG00000131711	ENST00000296755	.	.	.	5.11	0.985	0.19779	.	0.184821	0.37348	N	0.002137	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-6.3131	6.8591	0.24058	0.5445:0.317:0.0:0.1385	.	.	.	.	X	1981	.	ENSP00000296755:R1981X	R	+	1	2	MAP1B	71530879	0.103000	0.21917	0.967000	0.41034	0.992000	0.81027	0.713000	0.25794	0.243000	0.21327	0.450000	0.29827	AGA	.	.		0.498	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71495123	A	T	71495123	4	4	7	1	0	0	0	0	0	1	0	0	9237	412	15	4	5959	4	MAP1B	5	71495123	Nonsense_Mutation	SNP	A	TCGA-2Y-A9GX-01A-11D-A382-10	2790	71495123	109420137	18	568										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79034864	79034864	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	atgagtatgaatttacagaaTccctgcataatgaagtggtt	9	5	0	4			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr5:79034864T>A	ENST00000446378.2	+	2	10307	c.10276T>A	c.(10276-10278)Tcc>Acc	p.S3426T		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3426					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		ATTTACAGAATCCCTGCATAA	0.418																																					p.S3426T		Atlas-SNP	.											.	CMYA5	643	.	0			c.T10276A						.						87	83	84					5																	79034864		1888	4098	5986	SO:0001583	missense	202333	exon2			ACAGAATCCCTGC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.10276T>A	chr5.hg19:g.79034864T>A	ENSP00000394770:p.Ser3426Thr	103.0	0.0		101.0	7.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	T	7.625	0.677716	0.14841	.	.	ENSG00000164309	ENST00000446378	T	0.39229	1.09	5.48	3.08	0.35506	.	0.528214	0.17980	N	0.155542	T	0.53932	0.1827	M	0.65975	2.015	0.28432	N	0.917212	D	0.62365	0.991	P	0.58454	0.839	T	0.49560	-0.8927	10	0.59425	D	0.04	.	8.9859	0.35994	0.0:0.2113:0.0:0.7887	.	3426	Q8N3K9	CMYA5_HUMAN	T	3426	ENSP00000394770:S3426T	ENSP00000394770:S3426T	S	+	1	0	CMYA5	79070620	0.520000	0.26250	0.123000	0.21794	0.016000	0.09150	0.242000	0.18087	0.469000	0.27268	-0.256000	0.11100	TCC	.	.		0.418	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79034864	T	A	79034864	3	1	7	1	0	0	0	0	1	0	0	0	3592	1435	50	4	10282	4	CMYA5	5	79034864	Missense_Mutation	SNP	T	TCGA-2Y-A9GX-01A-11D-A382-10	7539741	79034864	101880396	19	569										
GPR98	84059	hgsc.bcm.edu	37	chr5	90052872	90052872	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	agttcctgtagtccggctggCtggaagctttggggcagtaa	15	8	0	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr5:90052872C>G	ENST00000405460.2	+	57	11930	c.11834C>G	c.(11833-11835)gCt>gGt	p.A3945G		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3945	Calx-beta 26. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GTCCGGCTGGCTGGAAGCTTT	0.448																																					p.A3945G		Atlas-SNP	.											.	GPR98	605	.	0			c.C11834G						.						93	92	92					5																	90052872		1857	4098	5955	SO:0001583	missense	84059	exon57			GGCTGGCTGGAAG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.11834C>G	chr5.hg19:g.90052872C>G	ENSP00000384582:p.Ala3945Gly	125.0	0.0		145.0	19.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.8|22.8	4.341999|4.341999	0.81911|0.81911	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.21031|.	2.03|.	5.3|5.3	5.3|5.3	0.74995|0.74995	Na-Ca exchanger/integrin-beta4 (2);|.	0.048166|.	0.85682|.	D|.	0.000000|.	T|T	0.60143|0.60143	0.2246|0.2246	L|L	0.33339|0.33339	1.005|1.005	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.998;0.999|.	D;D|.	0.74348|.	0.977;0.983|.	T|T	0.53995|0.53995	-0.8359|-0.8359	10|5	0.19147|.	T|.	0.46|.	.|.	19.3122|19.3122	0.94192|0.94192	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	3945;3945|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	G|V	3945|1511	ENSP00000384582:A3945G|.	ENSP00000296619:A3945G|.	A|L	+|+	2|1	0|2	GPR98|GPR98	90088628|90088628	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.921000|6.921000	0.75805|0.75805	2.636000|2.636000	0.89361|0.89361	0.467000|0.467000	0.42956|0.42956	GCT|CTG	.	.		0.448	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	90052872	C	G	90052872	3	3	7	1	0	0	0	0	1	0	0	0	6730	797	28	4	12060	4	GPR98	5	90052872	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	11018008	90052872	90862388	20	570										
PCDHGC4	56098	hgsc.bcm.edu	37	chr5	140867041	140867041	+	Frame_Shift_Del	DEL	C	C	-													0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	aagtttgttgatgtgggaggCcactctcatggctgtacacc							TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr5:140867041delC	ENST00000306593.1	+	1	2301	c.2301delC	c.(2299-2301)ggcfs	p.G767fs	PCDHGA11_ENST00000398587.2_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGC5_ENST00000252087.1_5'Flank|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA11_ENST00000518882.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	767					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGTGGGAGGCCACTCTCATG	0.557																																					p.G767fs		Atlas-Indel,Pindel	.											.	PCDHGC4	91	.	0			c.2300delG						.						88	74	79					5																	140867041		2203	4300	6503	SO:0001589	frameshift_variant	56098	exon1			.	AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"Cadherins / Protocadherins : Clustered"	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.2301delC	chr5.hg19:g.140867041delC	ENSP00000306918:p.Gly767fs	96.0	0.0		114.0	14.0	NM_018928	Q495T2|Q9Y5C3	Frame_Shift_Del	DEL	ENST00000306593.1	hg19	CCDS4262.1																																																																																			.	.		0.557	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928		-	140867041	C	-	140867041	7	5	7	1	0	1	0	1	0	0	0	0	11579	726	26	0	2303	0	PCDHGC4	5	140867041	Frame_Shift_Del	DEL	C	TCGA-2Y-A9GX-01A-11D-A382-10	50814169	140867041	40048219	21	571										
SYNPO	11346	hgsc.bcm.edu	37	chr5	150029676	150029676	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ctccctccatctcctgccctGcctcggccctcgcgctcctc	6	24	1	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr5:150029676G>A	ENST00000394243.1	+	3	2945	c.2571G>A	c.(2569-2571)ctG>ctA	p.L857L	SYNPO_ENST00000519664.1_Silent_p.L613L|SYNPO_ENST00000522122.1_Silent_p.L857L|SYNPO_ENST00000307662.4_Silent_p.L613L	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	857	Pro-rich.				positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)			NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTCCTGCCCTGCCTCGGCCCT	0.697																																					p.L857L		Atlas-SNP	.											.	SYNPO	147	.	0			c.G2571A						.						58	64	62					5																	150029676		2203	4299	6502	SO:0001819	synonymous_variant	11346	exon3			TGCCCTGCCTCGG	AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.2571G>A	chr5.hg19:g.150029676G>A		108.0	0.0		105.0	16.0	NM_001166209	A5PKZ8|D3DQG8|O15271|Q9UPX1	Silent	SNP	ENST00000394243.1	hg19	CCDS54937.1																																																																																			.	.		0.697	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286		A	150029676	G	A	150029676	2	1	7	1	0	0	0	0	0	0	0	1	15471	1306	46	3		3	SYNPO	5	150029676	Silent	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10	9162635	150029676	30885584	22	572										
SLC17A4	10050	hgsc.bcm.edu	37	chr6	25776866	25776866	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	gtttgttgttggatgtatctGcattatccttggaggtctac	11	6	2	0	rs560726056		TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr6:25776866G>T	ENST00000377905.4	+	9	1150	c.1031G>T	c.(1030-1032)tGc>tTc	p.C344F	SLC17A4_ENST00000439485.2_Missense_Mutation_p.C114F|SLC17A4_ENST00000397076.2_Missense_Mutation_p.C114F	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	344					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			breast(4)|endometrium(1)|kidney(4)|large_intestine(3)|lung(21)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GGATGTATCTGCATTATCCTT	0.507																																					p.C344F		Atlas-SNP	.											.	SLC17A4	79	.	0			c.G1031T						.						270	251	257					6																	25776866		2203	4300	6503	SO:0001583	missense	10050	exon9			GTATCTGCATTAT	AB020527	CCDS4564.1, CCDS75411.1	6p22.2	2013-07-18	2013-07-18		ENSG00000146039	ENSG00000146039		"Solute carriers"	10932	protein-coding gene	gene with protein product		604216	"solute carrier family 17 (sodium phosphate), member 4"			10319585	Standard	NM_005495		Approved	KIAA2138	uc003nfe.3	Q9Y2C5	OTTHUMG00000014410	ENST00000377905.4:c.1031G>T	chr6.hg19:g.25776866G>T	ENSP00000367137:p.Cys344Phe	87.0	0.0		75.0	11.0	NM_005495	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Missense_Mutation	SNP	ENST00000377905.4	hg19	CCDS4564.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.189166	0.38707	.	.	ENSG00000146039	ENST00000377905;ENST00000439485;ENST00000397076	T;T;T	0.57436	0.4;0.61;0.4	5.48	1.53	0.23141	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.352612	0.24825	N	0.035286	T	0.11367	0.0277	N	0.11313	0.125	0.09310	N	1	B;B;B	0.31790	0.002;0.34;0.0	B;B;B	0.29862	0.011;0.108;0.01	T	0.28459	-1.0043	10	0.24483	T	0.36	.	8.5519	0.33458	0.0:0.1428:0.4155:0.4417	.	114;114;344	E7EPE8;E7EU17;Q9Y2C5	.;.;S17A4_HUMAN	F	344;114;114	ENSP00000367137:C344F;ENSP00000391345:C114F;ENSP00000380266:C114F	ENSP00000367137:C344F	C	+	2	0	SLC17A4	25884845	0.000000	0.05858	0.008000	0.14137	0.996000	0.88848	0.415000	0.21181	0.057000	0.16193	0.655000	0.94253	TGC	.	.		0.507	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1			T	25776866	G	T	25776866	3	4	7	1	0	0	0	0	1	0	0	0	14434	1319	46	3	1061	3	SLC17A4	6	25776866	Missense_Mutation	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10		25776866	145338201	23	573										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51890835	51890835	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	cagtgggagcgcccgcatcgGgtatctggggggctggcagg	20	10	1	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr6:51890835G>C	ENST00000371117.3	-	32	4048	c.3773C>G	c.(3772-3774)cCc>cGc	p.P1258R	PKHD1_ENST00000340994.4_Missense_Mutation_p.P1258R	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1258	IPT/TIG 7.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GCCCGCATCGGGTATCTGGGG	0.597																																					p.P1258R		Atlas-SNP	.											.	PKHD1	927	.	0			c.C3773G						.						39	42	41					6																	51890835		2203	4300	6503	SO:0001583	missense	5314	exon32			GCATCGGGTATCT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.3773C>G	chr6.hg19:g.51890835G>C	ENSP00000360158:p.Pro1258Arg	90.0	0.0		86.0	9.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	16.05	3.011948	0.54468	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87491	-2.09;-2.26	5.69	4.82	0.62117	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.678460	0.14908	N	0.291409	D	0.87517	0.6197	M	0.77103	2.36	0.09310	N	1	P;D	0.54772	0.834;0.968	P;P	0.58331	0.483;0.837	T	0.80099	-0.1524	10	0.26408	T	0.33	.	12.0941	0.53744	0.0791:0.0:0.9209:0.0	.	1258;1258	P08F94-2;P08F94	.;PKHD1_HUMAN	R	1258	ENSP00000360158:P1258R;ENSP00000341097:P1258R	ENSP00000341097:P1258R	P	-	2	0	PKHD1	51998794	0.008000	0.16893	0.006000	0.13384	0.004000	0.04260	1.637000	0.37155	1.409000	0.46915	0.655000	0.94253	CCC	.	.		0.597	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		C	51890835	G	C	51890835	3	2	7	1	0	0	0	0	1	0	0	0	11980	1232	43	4	8634	4	PKHD1	6	51890835	Missense_Mutation	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10	26113969	51890835	119224232	24	574										
EYS	346007	hgsc.bcm.edu	37	chr6	65301270	65301270	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	gtttagatataattaccttaGcaggaaaaatgggagacatc	9	5	0	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr6:65301270G>T	ENST00000370621.3	-	26	5016	c.4490C>A	c.(4489-4491)gCt>gAt	p.A1497D	EYS_ENST00000503581.1_Missense_Mutation_p.A1497D|EYS_ENST00000370616.2_Missense_Mutation_p.A1497D			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1497					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AATTACCTTAGCAGGAAAAAT	0.413																																					p.A1497D		Atlas-SNP	.											.	EYS	527	.	0			c.C4490A						.						35	32	33					6																	65301270		692	1590	2282	SO:0001583	missense	346007	exon26			ACCTTAGCAGGAA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4490C>A	chr6.hg19:g.65301270G>T	ENSP00000359655:p.Ala1497Asp	84.0	0.0		109.0	8.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	G	17.12	3.307836	0.60305	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84660	-1.88;-1.85;-1.85	5.84	4.02	0.46733	.	.	.	.	.	T	0.69088	0.3072	N	0.08118	0	0.80722	D	1	D;D	0.76494	0.999;0.986	D;P	0.66979	0.948;0.809	T	0.69778	-0.5053	9	0.07175	T	0.84	.	9.3914	0.38374	0.0762:0.1453:0.7785:0.0	.	1497;1497	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	D	1497	ENSP00000424243:A1497D;ENSP00000359655:A1497D;ENSP00000359650:A1497D	ENSP00000359650:A1497D	A	-	2	0	EYS	65357991	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.041000	0.41213	1.447000	0.47661	0.591000	0.81541	GCT	.	.		0.413	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		T	65301270	G	T	65301270	3	4	7	1	0	0	0	0	1	0	0	0	5334	971	34	3	4861	3	EYS	6	65301270	Missense_Mutation	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10	13410435	65301270	105813797	25	575										
SCIN	85477	hgsc.bcm.edu	37	chr7	12684320	12684320	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	cggctgctctaacaaaactgGaagatttgttgtaagtgtcc	10	8	1	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr7:12684320G>T	ENST00000297029.5	+	13	1972	c.1871G>T	c.(1870-1872)gGa>gTa	p.G624V	SCIN_ENST00000519209.1_Missense_Mutation_p.G377V|SCIN_ENST00000445618.2_Missense_Mutation_p.G377V	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	624	Ca(2+)-dependent actin binding.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		AACAAAACTGGAAGATTTGTT	0.507																																					p.G624V		Atlas-SNP	.											.	SCIN	105	.	0			c.G1871T						.						38	39	39					7																	12684320		1874	4105	5979	SO:0001583	missense	85477	exon13			AAACTGGAAGATT	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.1871G>T	chr7.hg19:g.12684320G>T	ENSP00000297029:p.Gly624Val	75.0	0.0		53.0	6.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	hg19	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	G	37	6.355118	0.97498	.	.	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.33216	1.42;1.42;1.42	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.69070	0.3070	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80381	-0.1406	10	0.87932	D	0	-17.1973	18.4559	0.90720	0.0:0.0:1.0:0.0	.	624	Q9Y6U3	ADSV_HUMAN	V	624;377;377	ENSP00000297029:G624V;ENSP00000430997:G377V;ENSP00000390189:G377V	ENSP00000297029:G624V	G	+	2	0	SCIN	12650845	1.000000	0.71417	1.000000	0.80357	0.153000	0.21895	9.325000	0.96381	2.353000	0.79882	0.462000	0.41574	GGA	.	.		0.507	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		T	12684320	G	T	12684320	3	4	7	1	0	0	0	0	1	0	0	0	13920	1174	41	3	1921	3	SCIN	7	12684320	Missense_Mutation	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10		12684320	146454343	26	576										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128450355	128450355	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	gtttcaaagagtctcatttcCaggaagtgttggagaatccc	10	8	2	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr7:128450355C>T	ENST00000297788.4	+	12	2330	c.1963C>T	c.(1963-1965)Cag>Tag	p.Q655*	CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000378685.4_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	655						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						GTCTCATTTCCAGGAAGTGTT	0.433																																					p.Q655X		Atlas-SNP	.											.	CCDC136	170	.	0			c.C1963T						.						66	64	65					7																	128450355		1948	4146	6094	SO:0001587	stop_gained	64753	exon12			CATTTCCAGGAAG		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.1963C>T	chr7.hg19:g.128450355C>T	ENSP00000297788:p.Gln655*	147.0	0.0		138.0	18.0	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Nonsense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	C	38	7.063842	0.98036	.	.	ENSG00000128596	ENST00000297788;ENST00000397697;ENST00000320524;ENST00000464672	.	.	.	4.94	4.06	0.47325	.	0.782188	0.11602	N	0.547695	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.0858	9.393	0.38386	0.0:0.9033:0.0:0.0967	.	.	.	.	X	655;655;655;246	.	ENSP00000297788:Q655X	Q	+	1	0	CCDC136	128237591	0.983000	0.35010	0.885000	0.34714	0.012000	0.07955	1.171000	0.31896	1.448000	0.47680	-0.140000	0.14226	CAG	.	.		0.433	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		T	128450355	C	T	128450355	4	4	7	1	0	0	0	0	0	1	0	0	2772	595	21	3	2009	3	CCDC136	7	128450355	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	115766035	128450355	30688308	27	577										
LRGUK	136332	hgsc.bcm.edu	37	chr7	133906659	133906659	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	gggccaaactttcagccaaaAaaacaccagcggtaagagag	10	10	1	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr7:133906659A>G	ENST00000285928.2	+	16	2041	c.1972A>G	c.(1972-1974)Aaa>Gaa	p.K658E		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	658						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						TTCAGCCAAAAAAACACCAGC	0.388																																					p.K658E		Atlas-SNP	.											.	LRGUK	113	.	0			c.A1972G						.						52	53	53					7																	133906659		2203	4300	6503	SO:0001583	missense	136332	exon16			GCCAAAAAAACAC	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1972A>G	chr7.hg19:g.133906659A>G	ENSP00000285928:p.Lys658Glu	74.0	0.0		70.0	6.0	NM_144648	Q2M3I1	Missense_Mutation	SNP	ENST00000285928.2	hg19	CCDS5830.1	.	.	.	.	.	.	.	.	.	.	A	7.096	0.573080	0.13623	.	.	ENSG00000155530	ENST00000285928	T	0.42513	0.97	5.77	1.95	0.26073	.	0.775105	0.12121	N	0.497673	T	0.33147	0.0853	L	0.55103	1.725	0.09310	N	1	B	0.24721	0.11	B	0.19148	0.024	T	0.35051	-0.9804	10	0.72032	D	0.01	-2.2053	3.5337	0.07786	0.5946:0.2001:0.2052:0.0	.	658	Q96M69	LRGUK_HUMAN	E	658	ENSP00000285928:K658E	ENSP00000285928:K658E	K	+	1	0	LRGUK	133557199	0.060000	0.20803	0.005000	0.12908	0.033000	0.12548	0.591000	0.23969	1.026000	0.39733	0.528000	0.53228	AAA	.	.		0.388	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		G	133906659	A	G	133906659	3	3	7	1	0	0	0	0	1	0	0	0	8952	15	1	2	2034	2	LRGUK	7	133906659	Missense_Mutation	SNP	A	TCGA-2Y-A9GX-01A-11D-A382-10	5456304	133906659	25232004	28	578										
SLC26A7	115111	hgsc.bcm.edu	37	chr8	92346665	92346665	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	taaagttgttcttcctgtagAtttagttttggtaagtataa	8	3	1	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr8:92346665A>G	ENST00000276609.3	+	6	1024	c.785A>G	c.(784-786)gAt>gGt	p.D262G	SLC26A7_ENST00000523719.1_Missense_Mutation_p.D262G|SLC26A7_ENST00000309536.2_Missense_Mutation_p.D262G	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			CTTCCTGTAGATTTAGTTTTG	0.353																																					p.D262G		Atlas-SNP	.											.	SLC26A7	207	.	0			c.A785G						.						92	88	89					8																	92346665		2202	4298	6500	SO:0001583	missense	115111	exon6			CTGTAGATTTAGT	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"Solute carriers"	14467	protein-coding gene	gene with protein product		608479	"solute carrier family 26, member 7"			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.785A>G	chr8.hg19:g.92346665A>G	ENSP00000276609:p.Asp262Gly	42.0	0.0		48.0	14.0	NM_134266		Missense_Mutation	SNP	ENST00000276609.3	hg19	CCDS6254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.6|20.6	4.023216|4.023216	0.75275|0.75275	.|.	.|.	ENSG00000147606|ENSG00000147606	ENST00000523719;ENST00000276609;ENST00000309536|ENST00000520818	D;D;D|.	0.92752|.	-3.1;-3.1;-3.1|.	5.73|5.73	5.73|5.73	0.89815|0.89815	Sulphate transporter (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68952|0.68952	0.3057|0.3057	L|L	0.52573|0.52573	1.65|1.65	0.47214|0.47214	D|D	0.999357|0.999357	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.998;0.999|.	T|T	0.66496|0.66496	-0.5909|-0.5909	10|5	0.72032|.	D|.	0.01|.	.|.	16.3197|16.3197	0.82945|0.82945	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	262;262|.	Q8TE54-2;Q8TE54|.	.;S26A7_HUMAN|.	G|V	262|130	ENSP00000428849:D262G;ENSP00000276609:D262G;ENSP00000309504:D262G|.	ENSP00000276609:D262G|.	D|I	+|+	2|1	0|0	SLC26A7|SLC26A7	92415841|92415841	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	6.072000|6.072000	0.71238|0.71238	2.302000|2.302000	0.77476|0.77476	0.533000|0.533000	0.62120|0.62120	GAT|ATT	.	.		0.353	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1			G	92346665	A	G	92346665	3	3	7	1	0	0	0	0	1	0	0	0	14537	333	12	2	803	2	SLC26A7	8	92346665	Missense_Mutation	SNP	A	TCGA-2Y-A9GX-01A-11D-A382-10		92346665	54017357	29	579										
NIPAL2	79815	hgsc.bcm.edu	37	chr8	99208234	99208234	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ttcctgataaaatatgatacCtgtaacacaggaaaagaaga	7	6	0	4			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr8:99208234C>G	ENST00000341166.3	-	9	1136		c.e9-1		NIPAL2_ENST00000430223.2_Splice_Site|NIPAL2_ENST00000520545.1_Splice_Site	NM_024759.1	NP_079035.1	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2							integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(3)|kidney(1)|large_intestine(2)|lung(5)|stomach(1)	12						AATATGATACCTGTAACACAG	0.269																																					.		Atlas-SNP	.											.	NIPAL2	23	.	0			c.881-1G>C						.						48	48	48					8																	99208234		2203	4297	6500	SO:0001630	splice_region_variant	79815	exon10			TGATACCTGTAAC	AK024017	CCDS6278.1	8q22.2	2009-03-24		2009-03-24	ENSG00000104361	ENSG00000104361			25854	protein-coding gene	gene with protein product				NPAL2		14702039	Standard	NM_024759		Approved	FLJ13955	uc003yil.1	Q9H841	OTTHUMG00000164668	ENST00000341166.3:c.881-1G>C	chr8.hg19:g.99208234C>G		495.0	0.0		670.0	71.0	NM_024759	A2RTY8	Splice_Site	SNP	ENST00000341166.3	hg19	CCDS6278.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.385091	0.61956	.	.	ENSG00000104361	ENST00000430223;ENST00000341166	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4977	0.87723	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NIPAL2	99277410	1.000000	0.71417	0.988000	0.46212	0.749000	0.42624	6.634000	0.74290	2.553000	0.86117	0.563000	0.77884	.	.	.		0.269	NIPAL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379677.1	NM_024759	Intron	G	99208234	C	G	99208234	5	3	7	1	0	0	0	0	0	0	1	0	10434	695	24	4	242	4	NIPAL2	8	99208234	Splice_Site	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	6861569	99208234	47155788	30	580										
SLC45A4	57210	hgsc.bcm.edu	37	chr8	142222517	142222517	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	agaggccaccatggggatgaCgcggacagtccccacggcgt	15	13	0	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr8:142222517C>A	ENST00000024061.3	-	7	2234	c.1927G>T	c.(1927-1929)Gtc>Ttc	p.V643F	SLC45A4_ENST00000519067.1_Missense_Mutation_p.V643F|SLC45A4_ENST00000433583.2_Missense_Mutation_p.V636F|SLC45A4_ENST00000517878.1_Missense_Mutation_p.V694F	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			ATGGGGATGACGCGGACAGTC	0.612																																					p.V643F		Atlas-SNP	.											.	SLC45A4	71	.	0			c.G1927T						.						67	68	68					8																	142222517		2203	4300	6503	SO:0001583	missense	57210	exon7			GGATGACGCGGAC	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"Solute carriers"	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.1927G>T	chr8.hg19:g.142222517C>A	ENSP00000024061:p.Val643Phe	86.0	0.0		70.0	16.0	NM_001080431	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	hg19	CCDS34948.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.097849	0.76870	.	.	ENSG00000022567	ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061	T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.90618	0.7058	M	0.82323	2.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.91079	0.4898	10	0.52906	T	0.07	-63.0162	18.9005	0.92440	0.0:1.0:0.0:0.0	.	694;643;643	E7EV90;Q5BKX6-3;Q5BKX6-2	.;.;.	F	643;694;636;643	ENSP00000429059:V643F;ENSP00000428137:V694F;ENSP00000400799:V636F;ENSP00000024061:V643F	ENSP00000024061:V643F	V	-	1	0	SLC45A4	142291699	1.000000	0.71417	0.944000	0.38274	0.357000	0.29423	7.272000	0.78516	2.453000	0.82957	0.655000	0.94253	GTC	.	.		0.612	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325		A	142222517	C	A	142222517	3	1	7	1	0	0	0	0	1	0	0	0	14658	536	19	1	477	1	SLC45A4	8	142222517	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	43014283	142222517	4141505	31	581										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113261408	113261408	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	gactccagataaaatgaaccCttggcggcaacttacatagc	8	11	0	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr9:113261408C>A	ENST00000401783.2	-	7	1930	c.1594G>T	c.(1594-1596)Ggg>Tgg	p.G532W	SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374461.1_Missense_Mutation_p.G509W|SVEP1_ENST00000374469.1_Missense_Mutation_p.G509W|SVEP1_ENST00000302728.8_Missense_Mutation_p.G532W	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	532	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						AAAATGAACCCTTGGCGGCAA	0.468																																					p.G532W		Atlas-SNP	.											.	SVEP1	326	.	0			c.G1594T						.						66	63	64					9																	113261408		1965	4164	6129	SO:0001583	missense	79987	exon7			TGAACCCTTGGCG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.1594G>T	chr9.hg19:g.113261408C>A	ENSP00000384917:p.Gly532Trp	108.0	0.0		122.0	8.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.521262	0.85600	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.59364	0.27;0.27;0.27;0.27	5.91	5.91	0.95273	Complement control module (2);Sushi/SCR/CCP (2);	0.000000	0.85682	D	0.000000	T	0.70020	0.3176	L	0.36672	1.1	0.48135	D	0.999594	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;1.0	T	0.71174	-0.4670	10	0.87932	D	0	.	19.0678	0.93119	0.0:1.0:0.0:0.0	.	532;532;532	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	W	532;509;532;509	ENSP00000384917:G532W;ENSP00000363593:G509W;ENSP00000304118:G532W;ENSP00000363585:G509W	ENSP00000304118:G532W	G	-	1	0	SVEP1	112301229	1.000000	0.71417	0.994000	0.49952	0.978000	0.69477	5.599000	0.67592	2.813000	0.96785	0.655000	0.94253	GGG	.	.		0.468	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113261408	C	A	113261408	3	1	7	1	0	0	0	0	1	0	0	0	15435	681	24	3	9289	3	SVEP1	9	113261408	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10		113261408	27952023	32	582										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140970351	140970351	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	acgtttttgcaagccctgatGctgctgttcaggtgtgttgt	12	8	1	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr9:140970351G>A	ENST00000371372.1	+	35	5083	c.4938G>A	c.(4936-4938)atG>atA	p.M1646I	CACNA1B_ENST00000371365.2_Missense_Mutation_p.M10I|CACNA1B_ENST00000371357.1_Missense_Mutation_p.M1645I|CACNA1B_ENST00000277549.5_Missense_Mutation_p.M840I|CACNA1B_ENST00000371363.1_Missense_Mutation_p.M1644I|CACNA1B_ENST00000277551.2_Missense_Mutation_p.M1646I|CACNA1B_ENST00000371355.4_Missense_Mutation_p.M1647I	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1646					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	AAGCCCTGATGCTGCTGTTCA	0.537																																					p.M1646I		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G4938A						.						67	72	70					9																	140970351		2039	4180	6219	SO:0001583	missense	774	exon34			CCTGATGCTGCTG	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.4938G>A	chr9.hg19:g.140970351G>A	ENSP00000360423:p.Met1646Ile	98.0	0.0		68.0	15.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.12|16.12	3.034388|3.034388	0.54896|0.54896	.|.	.|.	ENSG00000148408|ENSG00000148408	ENST00000413253|ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355;ENST00000371365	.|D;D;D;D;D;D;D	.|0.97279	.|-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32	5.23|5.23	5.23|5.23	0.72850|0.72850	.|Ion transport (1);	.|0.050300	.|0.85682	.|D	.|0.000000	D|D	0.94768|0.94768	0.8311|0.8311	N|N	0.20304|0.20304	0.555|0.555	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.45902	.|0.74;0.868;0.868	.|P;P;P	.|0.45276	.|0.475;0.475;0.475	D|D	0.95661|0.95661	0.8715|0.8715	5|10	.|0.87932	.|D	.|0	.|.	19.1693|19.1693	0.93570|0.93570	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1646;1645;1644	.|Q00975;B1AQK7;B1AQK6	.|CAC1B_HUMAN;.;.	T|I	11|1646;1646;840;1644;1645;1647;10	.|ENSP00000360423:M1646I;ENSP00000277551:M1646I;ENSP00000277549:M840I;ENSP00000360414:M1644I;ENSP00000360408:M1645I;ENSP00000360406:M1647I;ENSP00000360416:M10I	.|ENSP00000277549:M840I	A|M	+|+	1|3	0|0	CACNA1B|CACNA1B	140090172|140090172	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	3.847000|3.847000	0.55895|0.55895	2.607000|2.607000	0.88179|0.88179	0.655000|0.655000	0.94253|0.94253	GCT|ATG	.	.		0.537	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		A	140970351	G	A	140970351	3	1	7	1	0	0	0	0	1	0	0	0	2541	1319	46	3	5072	3	CACNA1B	9	140970351	Missense_Mutation	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10	27708943	140970351	243080	33	583										
TIMM23	100287932	hgsc.bcm.edu	37	chr10	51592507	51592507	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	atgagttggcaaaatcttcaGagtgactgttggagcaagga	13	5	2	3			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr10:51592507G>C	ENST00000260867.4	-	7	750	c.627C>G	c.(625-627)ctC>ctG	p.L209L	TIMM23_ENST00000485812.1_5'UTR|TIMM23_ENST00000374064.3_Silent_p.L161L|TIMM23_ENST00000374065.3_Silent_p.L172L	NM_006327.3	NP_006318.1	O14925	TIM23_HUMAN	translocase of inner mitochondrial membrane 23 homolog (yeast)	209					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			endometrium(1)|large_intestine(1)|pancreas(1)	3						AAAATCTTCAGAGTGACTGTT	0.423																																					p.L209L		Atlas-SNP	.											.	TIMM23	4	.	0			c.C627G						.						134	127	129					10																	51592507		2203	4300	6503	SO:0001819	synonymous_variant	100287932	exon7			TCTTCAGAGTGAC	AF030162	CCDS73091.1	10q11.21-q11.23	2010-03-17			ENSG00000138297				17312	protein-coding gene	gene with protein product		605034				10339406	Standard	NM_006327		Approved	TIM23	uc010qha.2	O14925	OTTHUMG00000018213	ENST00000260867.4:c.627C>G	chr10.hg19:g.51592507G>C		97.0	0.0		125.0	12.0	NM_006327	Q53FF8|Q5T1E6|Q6P5S5	Silent	SNP	ENST00000260867.4	hg19	CCDS7238.1	.	.	.	.	.	.	.	.	.	.	G	8.452	0.853212	0.17106	.	.	ENSG00000138297	ENST00000444743	.	.	.	5.55	0.247	0.15521	.	0.106294	0.33199	N	0.005174	T	0.53965	0.1829	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52147	-0.8614	6	0.87932	D	0	-6.4792	1.7704	0.03010	0.3265:0.2213:0.3394:0.1128	.	.	.	.	V	107	.	ENSP00000408548:L107V	L	-	1	2	TIMM23	51262513	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	1.113000	0.31184	0.156000	0.19299	0.655000	0.94253	CTG	.	.		0.423	TIMM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048040.1	NM_006327.2		C	51592507	G	C	51592507	2	2	7	1	0	0	0	0	0	0	0	1	15926	929	33	4		4	TIMM23	10	51592507	Silent	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10		51592507	83942240	34	584										
FAM21A	387680	hgsc.bcm.edu	37	chr10	51829449	51829449	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	caatgacttccttatgctctCtaatacccagttcattgaga	5	11	2	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr10:51829449C>G	ENST00000282633.5	+	3	314	c.269C>G	c.(268-270)tCt>tGt	p.S90C	FAM21A_ENST00000492914.1_3'UTR|FAM21A_ENST00000351071.6_Missense_Mutation_p.S90C|RP11-324H6.5_ENST00000456967.1_RNA|FAM21A_ENST00000314664.7_Missense_Mutation_p.S90C	NM_001005751.1	NP_001005751.1	Q641Q2	FA21A_HUMAN	family with sequence similarity 21, member A	90					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)				breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	15						CTTATGCTCTCTAATACCCAG	0.358																																					p.S90C		Atlas-SNP	.											.	FAM21A	32	.	0			c.C269G						.						187	185	185					10																	51829449		1848	4098	5946	SO:0001583	missense	387680	exon3			TGCTCTCTAATAC	BC082258	CCDS41527.1	10q11.23	2014-06-19			ENSG00000099290	ENSG00000099290			23416	protein-coding gene	gene with protein product			"family with sequence similarity 21, member B"	FAM21B			Standard	XM_005269805		Approved	bA56A21.1, bA98I6.1, FLJ10824	uc001jjb.3	Q641Q2	OTTHUMG00000018225	ENST00000282633.5:c.269C>G	chr10.hg19:g.51829449C>G	ENSP00000282633:p.Ser90Cys	198.0	0.0		200.0	18.0	NM_001005751	A2A3S2|A2A3U6|Q6DHY0	Missense_Mutation	SNP	ENST00000282633.5	hg19	CCDS41527.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.575719	0.65878	.	.	ENSG00000099290	ENST00000351071;ENST00000314664;ENST00000434114;ENST00000282633	.	.	.	3.73	3.73	0.42828	.	0.000000	0.85682	D	0.000000	T	0.79227	0.4410	M	0.83012	2.62	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.82756	-0.0300	9	0.66056	D	0.02	-15.5385	13.3892	0.60813	0.0:1.0:0.0:0.0	.	90;90;90	E7ESD2;Q641Q2-2;Q641Q2	.;.;FA21A_HUMAN	C	90;90;89;90	.	ENSP00000282633:S90C	S	+	2	0	FAM21A	51499455	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	7.612000	0.82975	1.792000	0.52537	0.194000	0.17425	TCT	.	.		0.358	FAM21A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276917.2	NM_001005751		G	51829449	C	G	51829449	3	3	7	1	0	0	0	0	1	0	0	0	5545	913	32	4	279	4	FAM21A	10	51829449	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	236942	51829449	83705298	35	585										
KIAA1598	57698	hgsc.bcm.edu	37	chr10	118711419	118711419	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	tttcaggcctgagatacataCttcttcaattacttctacga	5	10	4	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr10:118711419C>T	ENST00000355371.4	-	6	1032		c.e6+1		KIAA1598_ENST00000260777.10_Splice_Site|KIAA1598_ENST00000497044.1_Splice_Site|KIAA1598_ENST00000392901.4_Splice_Site|KIAA1598_ENST00000392903.2_Splice_Site	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598						axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		GAGATACATACTTCTTCAATT	0.363																																					.		Atlas-SNP	.											.	KIAA1598	74	.	0			c.534+1G>A						.						82	74	77					10																	118711419		2202	4299	6501	SO:0001630	splice_region_variant	57698	exon7			TACATACTTCTTC	BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.534+1G>A	chr10.hg19:g.118711419C>T		115.0	0.0		119.0	14.0	NM_001127211	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Splice_Site	SNP	ENST00000355371.4	hg19	CCDS44482.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.161118	0.78226	.	.	ENSG00000187164	ENST00000392903;ENST00000260777;ENST00000355371;ENST00000392901	.	.	.	5.69	5.69	0.88448	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9862	0.89156	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA1598	118701409	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.418000	0.66429	2.682000	0.91365	0.655000	0.94253	.	.	.		0.363	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330	Intron	T	118711419	C	T	118711419	5	4	7	1	0	0	0	0	0	0	1	0	8255	579	20	3	1408	3	KIAA1598	10	118711419	Splice_Site	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	66881970	118711419	16823328	36	586										
C10orf90	118611	hgsc.bcm.edu	37	chr10	128153451	128153451	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	tggagagctatccccaatggGaaggaaatgtctagtgggct	14	7	1	1			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr10:128153451G>A	ENST00000284694.7	-	4	1468	c.1348C>T	c.(1348-1350)Ccc>Tcc	p.P450S	C10orf90_ENST00000480379.1_5'Flank|C10orf90_ENST00000356858.3_Missense_Mutation_p.P403S|C10orf90_ENST00000544758.1_Missense_Mutation_p.P547S|C10orf90_ENST00000454341.1_Intron	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	450					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TCCCCAATGGGAAGGAAATGT	0.473																																					p.P450S		Atlas-SNP	.											.	C10orf90	121	.	0			c.C1348T						.						115	109	111					10																	128153451		2203	4300	6503	SO:0001583	missense	118611	exon4			CAATGGGAAGGAA	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.1348C>T	chr10.hg19:g.128153451G>A	ENSP00000284694:p.Pro450Ser	126.0	0.0		154.0	8.0	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	hg19	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	G	9.752	1.167620	0.21621	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000544758;ENST00000432642	T;T;T	0.20200	2.09;2.11;2.09	4.34	3.42	0.39159	.	0.174621	0.27782	N	0.017875	T	0.28366	0.0701	L	0.55481	1.735	0.19775	N	0.99995	D;P	0.53312	0.959;0.705	P;B	0.51615	0.675;0.439	T	0.05209	-1.0899	10	0.44086	T	0.13	-4.2843	10.0054	0.41953	0.0:0.2057:0.7943:0.0	.	547;450	F5GZL2;Q96M02	.;CJ090_HUMAN	S	403;450;547;450	ENSP00000284694:P450S;ENSP00000444369:P547S;ENSP00000405995:P450S	ENSP00000284694:P450S	P	-	1	0	C10orf90	128143441	0.004000	0.15560	0.024000	0.17045	0.131000	0.20780	0.525000	0.22956	1.017000	0.39495	0.637000	0.83480	CCC	.	.		0.473	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		A	128153451	G	A	128153451	3	1	7	1	0	0	0	0	1	0	0	0	1625	1174	41	3	775	3	C10orf90	10	128153451	Missense_Mutation	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10	9442032	128153451	7381296	37	587										
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643035	1643035	+	Frame_Shift_Del	DEL	A	A	-													0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ggagccacagccccccttggAacccccacaggagacacagc							TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr11:1643035delA	ENST00000399682.1	-	1	333	c.289delT	c.(289-291)tccfs	p.S97fs		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCCCTTGGAACCCCCACAG	0.687																																					p.S97fs		Atlas-INDEL	.											.	KRTAP5-4	78	.	0			c.290delC						.						6	11	10					11																	1643035		647	1524	2171	SO:0001589	frameshift_variant	387267	exon1			.	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"Keratin associated proteins"	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.289delT	chr11.hg19:g.1643035delA	ENSP00000382590:p.Ser97fs	244.0	0.0		206.0	16.0	NM_001012709		Frame_Shift_Del	DEL	ENST00000399682.1	hg19																																																																																				.	.		0.687	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		-	1643035	A	-	1643035	7	5	7	1	0	1	0	1	0	0	0	0	8572	246	9	0	401	0	KRTAP5-4	11	1643035	Frame_Shift_Del	DEL	A	TCGA-2Y-A9GX-01A-11D-A382-10		1643035	133363481	38	588										
MMP13	4322	hgsc.bcm.edu	37	chr11	102824960	102824960	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	atttggcccaggaggaaaagCatgagccagcaggccagagg	15	9	0	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr11:102824960C>G	ENST00000260302.3	-	4	590	c.562G>C	c.(562-564)Gct>Cct	p.A188P	MMP13_ENST00000340273.4_Missense_Mutation_p.A188P	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	188	Interaction with TIMP2.				bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	GGAGGAAAAGCATGAGCCAGC	0.443																																					p.A188P		Atlas-SNP	.											.	MMP13	75	.	0			c.G562C						.						50	51	51					11																	102824960		2202	4299	6501	SO:0001583	missense	4322	exon4			GAAAAGCATGAGC	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"Endogenous ligands"	7159	protein-coding gene	gene with protein product	"collagenase 3"	600108	"matrix metalloproteinase 13 (collagenase 3)"			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.562G>C	chr11.hg19:g.102824960C>G	ENSP00000260302:p.Ala188Pro	245.0	0.0		289.0	36.0	NM_002427	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	hg19	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.966339	0.92855	.	.	ENSG00000137745	ENST00000260302;ENST00000546012;ENST00000340273	T;T	0.61980	0.06;0.06	5.88	5.88	0.94601	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.89132	0.6628	H	0.99197	4.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93066	0.6478	10	0.87932	D	0	.	20.2314	0.98350	0.0:1.0:0.0:0.0	.	188	P45452	MMP13_HUMAN	P	188	ENSP00000260302:A188P;ENSP00000339672:A188P	ENSP00000260302:A188P	A	-	1	0	MMP13	102330170	1.000000	0.71417	0.977000	0.42913	0.985000	0.73830	7.445000	0.80570	2.789000	0.95967	0.591000	0.81541	GCT	.	.		0.443	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		G	102824960	C	G	102824960	3	3	7	1	0	0	0	0	1	0	0	0	9661	710	25	4	881	4	MMP13	11	102824960	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	101181925	102824960	32181556	39	589										
NCAM1	4684	hgsc.bcm.edu	37	chr11	113075222	113075222	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	gccaccgtcaacgtgaagatCtttcgtaagagcctccttct	8	13	3	3			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr11:113075222C>A	ENST00000316851.7	+	2	312	c.312C>A	c.(310-312)atC>atA	p.I104I	NCAM1_ENST00000533760.1_5'UTR|NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Silent_p.I113I	NM_001242607.1|NM_181351.4	NP_001229536.1|NP_851996.2	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	114	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		ACGTGAAGATCTTTCGTAAGA	0.517																																					p.I114I		Atlas-SNP	.											.	NCAM1	372	.	0			c.C342A						.						71	75	73					11																	113075222		2126	4225	6351	SO:0001819	synonymous_variant	4684	exon4			GAAGATCTTTCGT		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000316851.7:c.312C>A	chr11.hg19:g.113075222C>A		72.0	0.0		61.0	4.0	NM_001242608	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Silent	SNP	ENST00000316851.7	hg19																																																																																				.	.		0.517	NCAM1-201	KNOWN	basic	protein_coding	protein_coding		NM_000615		A	113075222	C	A	113075222	2	1	7	1	0	0	0	0	0	0	0	1	10211	903	32	3		3	NCAM1	11	113075222	Silent	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	10250262	113075222	21931294	40	590										
SORL1	6653	hgsc.bcm.edu	37	chr11	121384869	121384869	+	Frame_Shift_Del	DEL	C	C	-													0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ttgattccaaaggaatattaCatcgcagatgcctccgagga							TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr11:121384869delC	ENST00000260197.7	+	8	1179	c.1050delC	c.(1048-1050)tacfs	p.Y350fs	SORL1_ENST00000532451.1_3'UTR	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	350					cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		AGGAATATTACATCGCAGATG	0.438																																					p.Y350fs		Atlas-Indel,Pindel	.											.	SORL1	218	.	0			c.1049delA						.						97	95	96					11																	121384869		2203	4299	6502	SO:0001589	frameshift_variant	6653	exon8			.	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.1050delC	chr11.hg19:g.121384869delC	ENSP00000260197:p.Tyr350fs	91.0	0.0		103.0	16.0	NM_003105	B2RNX7|Q92856	Frame_Shift_Del	DEL	ENST00000260197.7	hg19	CCDS8436.1																																																																																			.	.		0.438	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		-	121384869	C	-	121384869	7	5	7	1	0	1	0	1	0	0	0	0	14949	489	17	0	1080	0	SORL1	11	121384869	Frame_Shift_Del	DEL	C	TCGA-2Y-A9GX-01A-11D-A382-10	8309647	121384869	13621647	41	591										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85267040	85267040	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	caatgacaccaccaaatcccAgacctaaggcaaagaacact	5	14	0	3			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr12:85267040A>C	ENST00000266682.5	-	7	1476	c.935T>G	c.(934-936)cTg>cGg	p.L312R	SLC6A15_ENST00000551388.1_5'UTR|SLC6A15_ENST00000309283.7_Missense_Mutation_p.L20R|SLC6A15_ENST00000552192.1_Missense_Mutation_p.L205R	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	312					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						ACCAAATCCCAGACCTAAGGC	0.413																																					p.L312R		Atlas-SNP	.											.	SLC6A15	159	.	0			c.T935G						.						153	151	152					12																	85267040		2203	4300	6503	SO:0001583	missense	55117	exon7			AATCCCAGACCTA	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.935T>G	chr12.hg19:g.85267040A>C	ENSP00000266682:p.Leu312Arg	295.0	0.0		299.0	28.0	NM_182767	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	hg19	CCDS9026.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.0|28.0	4.879646|4.879646	0.91740|0.91740	.|.	.|.	ENSG00000072041|ENSG00000072041	ENST00000309283;ENST00000266682;ENST00000318721;ENST00000552192;ENST00000551818;ENST00000551612|ENST00000551388	T;T;T;T|.	0.78707|.	-1.2;-1.2;-1.2;-1.2|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.063145|.	0.64402|.	D|.	0.000004|.	D|D	0.87589|0.87589	0.6215|0.6215	H|H	0.95260|0.95260	3.645|3.645	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.91020|0.91020	0.4856|0.4856	10|6	0.72032|0.87932	D|D	0.01|0	.|.	16.8222|16.8222	0.85835|0.85835	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	20;312|.	F8WJN6;Q9H2J7|.	.;S6A15_HUMAN|.	R|G	20;312;28;205;20;28|7	ENSP00000311645:L20R;ENSP00000266682:L312R;ENSP00000450145:L205R;ENSP00000449263:L28R|.	ENSP00000266682:L312R|ENSP00000449619:W7G	L|W	-|-	2|1	0|0	SLC6A15|SLC6A15	83791171|83791171	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	8.962000|8.962000	0.93254|0.93254	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	CTG|TGG	.	.		0.413	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		C	85267040	A	C	85267040	3	2	7	1	0	0	0	0	1	0	0	0	14693	188	7	5	1281	5	SLC6A15	12	85267040	Missense_Mutation	SNP	A	TCGA-2Y-A9GX-01A-11D-A382-10		85267040	48584855	42	592										
WSCD2	9671	hgsc.bcm.edu	37	chr12	108603913	108603913	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	cccaggggttacctgtatggCgggctggagttcggcgccga	17	11	0	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr12:108603913C>T	ENST00000332082.4	+	5	1331	c.513C>T	c.(511-513)ggC>ggT	p.G171G	WSCD2_ENST00000261400.3_Silent_p.G171G|WSCD2_ENST00000547525.1_Silent_p.G171G|WSCD2_ENST00000549903.1_Silent_p.G171G			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	171	WSC 1. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)		p.G171G(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						ACCTGTATGGCGGGCTGGAGT	0.647																																					p.G171G		Atlas-SNP	.											WSCD2,colon,carcinoma,0,1	WSCD2	125	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C513T						.						28	32	31					12																	108603913		2144	4254	6398	SO:0001819	synonymous_variant	9671	exon4			GTATGGCGGGCTG		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.513C>T	chr12.hg19:g.108603913C>T		121.0	1.0		99.0	11.0	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Silent	SNP	ENST00000332082.4	hg19	CCDS41828.1																																																																																			.	.		0.647	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		T	108603913	C	T	108603913	2	4	7	1	0	0	0	0	0	0	0	1	17422	755	27	1		1	WSCD2	12	108603913	Silent	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10	23336873	108603913	25247982	43	593										
C14orf43	91748	hgsc.bcm.edu	37	chr14	74196641	74196641	+	Frame_Shift_Del	DEL	T	T	-													0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ggcctgggccgctgctttggTttccgcacggaaggctcccc							TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr14:74196641delT	ENST00000286523.5	-	4	2579	c.1797delA	c.(1795-1797)aaafs	p.K599fs	ELMSAN1_ENST00000394071.2_Frame_Shift_Del_p.K599fs	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	599					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										GCTGCTTTGGTTTCCGCACGG	0.607																																					p.P600fs		Atlas-INDEL	.											.	.	.	.	0			c.1798delC						.						46	45	45					14																	74196641		2203	4300	6503	SO:0001589	frameshift_variant	91748	exon4			.	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.1797delA	chr14.hg19:g.74196641delT	ENSP00000286523:p.Lys599fs	61.0	0.0		59.0	10.0	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Frame_Shift_Del	DEL	ENST00000286523.5	hg19	CCDS9819.1																																																																																			.	.		0.607	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		-	74196641	T	-	74196641	7	5	7	1	0	1	0	1	0	0	0	0	1776	1722	60	0	1376	0	C14orf43	14	74196641	Frame_Shift_Del	DEL	T	TCGA-2Y-A9GX-01A-11D-A382-10		74196641	33152899	44	594										
MESP2	145873	hgsc.bcm.edu	37	chr15	90320134	90320134	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	caggcggaggggcaggggcaAgggcaggggcaggggcaggg	26	7	0	0	rs56192595|rs200021459|rs199821487	byFrequency	TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr15:90320134A>G	ENST00000341735.3	+	1	546	c.546A>G	c.(544-546)caA>caG	p.Q182Q	MESP2_ENST00000558723.1_Intron|MESP2_ENST00000560219.1_Intron	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	182	13 X 2 AA tandem repeats of G-Q.				mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q198_G205delQGQGQGQG(1)		kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			ggcaggggcaagggcaggggc	0.786																																					p.Q182Q		Atlas-SNP	.											MESP2,NS,carcinoma,0,1	MESP2	20	.	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.A546G						.						3	3	3					15																	90320134		1211	2942	4153	SO:0001819	synonymous_variant	145873	exon1			GGGGCAAGGGCAG		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"Basic helix-loop-helix proteins"	29659	protein-coding gene	gene with protein product		605195	"mesoderm posterior 2 homolog (mouse)"			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.546A>G	chr15.hg19:g.90320134A>G		13.0	1.0		44.0	6.0	NM_001039958	Q7RTU2	Silent	SNP	ENST00000341735.3	hg19	CCDS42078.1																																																																																			.	.		0.786	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		G	90320134	A	G	90320134	2	3	7	1	0	0	0	0	0	0	0	1	9492	69	3	2		2	MESP2	15	90320134	Silent	SNP	A	TCGA-2Y-A9GX-01A-11D-A382-10		90320134	12211258	45	595										
ZCCHC14	23174	hgsc.bcm.edu	37	chr16	87445309	87445309	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	tgcatgggtggcacggcaaaCgtggactgcccactcaggac	14	12	1	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr16:87445309C>A	ENST00000268616.4	-	12	2824	c.2607G>T	c.(2605-2607)acG>acT	p.T869T		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	869							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		GCACGGCAAACGTGGACTGCC	0.627																																					p.T869T		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.G2607T						.						56	47	50					16																	87445309		2198	4300	6498	SO:0001819	synonymous_variant	23174	exon12			GGCAAACGTGGAC	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"Zinc fingers, CCHC domain containing", "Sterile alpha motif (SAM) domain containing"	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2607G>T	chr16.hg19:g.87445309C>A		50.0	0.0		68.0	9.0	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Silent	SNP	ENST00000268616.4	hg19	CCDS10961.1																																																																																			.	.		0.627	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144		A	87445309	C	A	87445309	2	1	7	1	0	0	0	0	0	0	0	1	17598	523	19	1		1	ZCCHC14	16	87445309	Silent	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10		87445309	2909444	46	596										
RNF135	84282	hgsc.bcm.edu	37	chr17	29325716	29325716	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ctttaacttgaagagcctttCctgcagcctggaggtgtcca	10	11	0	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr17:29325716C>T	ENST00000328381.5	+	5	1679	c.806C>T	c.(805-807)tCc>tTc	p.S269F	RNF135_ENST00000443677.2_3'UTR|RNF135_ENST00000535306.2_3'UTR|RNF135_ENST00000324689.4_3'UTR	NM_032322.3	NP_115698.3	Q8IUD6	RN135_HUMAN	ring finger protein 135	269	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-beta production (GO:0032728)|protein ubiquitination (GO:0016567)|regulation of innate immune response (GO:0045088)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|ribonucleoprotein complex binding (GO:0043021)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|skin(2)|urinary_tract(1)	10		all_cancers(10;8.65e-08)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Myeloproliferative disorder(56;0.0255)				AAGAGCCTTTCCTGCAGCCTG	0.493																																					p.S269F		Atlas-SNP	.											.	RNF135	19	.	1	Unknown(1)	central_nervous_system(1)	c.C806T						.						98	101	100					17																	29325716		2203	4300	6503	SO:0001583	missense	84282	exon5			GCCTTTCCTGCAG	AJ496729	CCDS11262.1, CCDS11263.1, CCDS54104.1	17q11.2	2013-01-09			ENSG00000181481	ENSG00000181481		"RING-type (C3HC4) zinc fingers"	21158	protein-coding gene	gene with protein product	"riplet"	611358				11468690, 19017631	Standard	NM_001184992		Approved	MGC13061	uc002hfz.3	Q8IUD6	OTTHUMG00000132867	ENST00000328381.5:c.806C>T	chr17.hg19:g.29325716C>T	ENSP00000328340:p.Ser269Phe	108.0	0.0		128.0	14.0	NM_032322	A0AVM5|B2R7G9|B6ZLM5|F5GX60|Q9BSE9	Missense_Mutation	SNP	ENST00000328381.5	hg19	CCDS11262.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.202202	0.58234	.	.	ENSG00000181481	ENST00000328381;ENST00000535605	T	0.62941	-0.01	4.93	2.84	0.33178	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	0.194775	0.25686	N	0.028975	T	0.75095	0.3803	M	0.70595	2.14	0.27650	N	0.94742	D	0.76494	0.999	D	0.67231	0.95	T	0.69760	-0.5058	10	0.62326	D	0.03	-8.2189	13.1279	0.59366	0.0:0.5276:0.4724:0.0	.	269	Q8IUD6	RN135_HUMAN	F	269;88	ENSP00000328340:S269F	ENSP00000328340:S269F	S	+	2	0	RNF135	26349842	0.001000	0.12720	0.037000	0.18230	0.174000	0.22865	0.918000	0.28678	0.546000	0.28920	0.563000	0.77884	TCC	.	.		0.493	RNF135-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256342.3	NM_032322		T	29325716	C	T	29325716	3	4	7	1	0	0	0	0	1	0	0	0	13455	855	30	3	893	3	RNF135	17	29325716	Missense_Mutation	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10		29325716	51869494	47	597										
CDC27	996	hgsc.bcm.edu	37	chr17	45216246	45216246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	atccttctaacctctgagaaTattctttcagcctgaaataa	4	10	4	2	rs199551316		TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr17:45216246T>C	ENST00000066544.3	-	13	1656	c.1563A>G	c.(1561-1563)atA>atG	p.I521M	CDC27_ENST00000446365.2_Missense_Mutation_p.I460M|CDC27_ENST00000531206.1_Missense_Mutation_p.I527M|CDC27_ENST00000527547.1_Missense_Mutation_p.I520M	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	521					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CCTCTGAGAATATTCTTTCAG	0.343																																					p.I527M		Atlas-SNP	.											.	CDC27	337	.	0			c.A1581G						.						26	30	29					17																	45216246		2179	4283	6462	SO:0001583	missense	996	exon13			TGAGAATATTCTT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1563A>G	chr17.hg19:g.45216246T>C	ENSP00000066544:p.Ile521Met	46.0	0.0		54.0	12.0	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	hg19	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	14.67	2.603451	0.46423	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83	5.22	2.78	0.32641	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.176402	0.53938	D	0.000051	T	0.67822	0.2934	L	0.57536	1.79	0.50313	D	0.999864	P;P;P;B	0.40266	0.71;0.624;0.624;0.306	B;B;B;B	0.42112	0.284;0.376;0.376;0.22	T	0.67987	-0.5528	10	0.48119	T	0.1	-1.4205	5.5829	0.17260	0.0:0.0929:0.2737:0.6334	.	460;520;527;521	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	M	521;527;460;520	ENSP00000066544:I521M;ENSP00000434614:I527M;ENSP00000392802:I460M;ENSP00000437339:I520M	ENSP00000066544:I521M	I	-	3	3	CDC27	42571245	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.459000	0.35234	1.972000	0.57404	0.528000	0.53228	ATA	.	.		0.343	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			C	45216246	T	C	45216246	3	2	7	1	0	0	0	0	1	0	0	0	3068	1396	49	2	939	2	CDC27	17	45216246	Missense_Mutation	SNP	T	TCGA-2Y-A9GX-01A-11D-A382-10	15890530	45216246	35978964	48	598										
ADNP2	22850	hgsc.bcm.edu	37	chr18	77895930	77895930	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	aagcgagtgtccacctgcccCttttgctttggcccctttgt	9	14	0	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr18:77895930C>T	ENST00000262198.4	+	4	3089	c.2634C>T	c.(2632-2634)ccC>ccT	p.P878P		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	878					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		CCACCTGCCCCTTTTGCTTTG	0.592																																					p.P878P		Atlas-SNP	.											.	ADNP2	102	.	0			c.C2634T						.						67	68	68					18																	77895930		2203	4300	6503	SO:0001819	synonymous_variant	22850	exon4			CTGCCCCTTTTGC	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	23803	protein-coding gene	gene with protein product			"zinc finger protein 508"	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.2634C>T	chr18.hg19:g.77895930C>T		52.0	0.0		46.0	4.0	NM_014913	A8K951|O94943|Q9H9P3	Silent	SNP	ENST00000262198.4	hg19	CCDS32853.1																																																																																			.	.		0.592	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913		T	77895930	C	T	77895930	2	4	7	1	0	0	0	0	0	0	0	1	324	668	24	3		3	ADNP2	18	77895930	Silent	SNP	C	TCGA-2Y-A9GX-01A-11D-A382-10		77895930	181318	49	599										
SYT3	84258	hgsc.bcm.edu	37	chr19	51129192	51129192	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ccatcgctttgaggttagagGctttgatgatggtcacggtg	14	7	1	4			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr19:51129192G>T	ENST00000338916.4	-	5	1997	c.1364C>A	c.(1363-1365)gCc>gAc	p.A455D	SYT3_ENST00000544769.1_Missense_Mutation_p.A455D|SYT3_ENST00000600079.1_Missense_Mutation_p.A455D|SYT3_ENST00000593901.1_Missense_Mutation_p.A455D	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	455	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		GAGGTTAGAGGCTTTGATGAT	0.602																																					p.A455D		Atlas-SNP	.											.	SYT3	85	.	0			c.C1364A						.						87	75	79					19																	51129192		2203	4300	6503	SO:0001583	missense	84258	exon5			TTAGAGGCTTTGA	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.1364C>A	chr19.hg19:g.51129192G>T	ENSP00000340914:p.Ala455Asp	94.0	0.0		113.0	5.0	NM_032298	Q8N5Z1|Q8N640	Missense_Mutation	SNP	ENST00000338916.4	hg19	CCDS12798.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.328003	0.81690	.	.	ENSG00000213023	ENST00000338916;ENST00000544769	D;D	0.82984	-1.67;-1.67	4.13	4.13	0.48395	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.089261	0.42964	U	0.000638	D	0.94739	0.8302	H	0.99026	4.405	0.58432	D	0.999995	D	0.65815	0.995	D	0.76071	0.987	D	0.97015	0.9739	10	0.87932	D	0	.	15.5391	0.76027	0.0:0.0:1.0:0.0	.	455	Q9BQG1	SYT3_HUMAN	D	455	ENSP00000340914:A455D;ENSP00000438883:A455D	ENSP00000340914:A455D	A	-	2	0	SYT3	55821004	0.505000	0.26131	1.000000	0.80357	0.997000	0.91878	1.991000	0.40727	2.044000	0.60594	0.555000	0.69702	GCC	.	.		0.602	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		T	51129192	G	T	51129192	3	4	7	1	0	0	0	0	1	0	0	0	15490	1203	42	3	424	3	SYT3	19	51129192	Missense_Mutation	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10		51129192	7999791	50	600										
KRTAP27-1	643812	hgsc.bcm.edu	37	chr21	31709461	31709461	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	ctcaggtgcaacattgaccaGaggtctacaggaactggatt	11	9	2	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr21:31709461G>T	ENST00000382835.2	-	1	551	c.526C>A	c.(526-528)Ctg>Atg	p.L176M		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	176						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						ACATTGACCAGAGGTCTACAG	0.458																																					p.L176M		Atlas-SNP	.											KRTAP27-1,NS,carcinoma,0,1	KRTAP27-1	53	.	0			c.C526A						.						106	102	103					21																	31709461		2203	4300	6503	SO:0001583	missense	643812	exon1			TGACCAGAGGTCT	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"Keratin associated proteins"	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.526C>A	chr21.hg19:g.31709461G>T	ENSP00000372286:p.Leu176Met	127.0	0.0		109.0	6.0	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	hg19	CCDS33532.1	.	.	.	.	.	.	.	.	.	.	G	9.967	1.224474	0.22457	.	.	ENSG00000206107	ENST00000382835	T	0.03272	3.99	4.17	-4.38	0.03622	.	1.199530	0.06361	N	0.711660	T	0.03783	0.0107	L	0.50333	1.59	0.09310	N	1	P	0.47409	0.895	B	0.42771	0.397	T	0.29761	-1.0001	10	0.34782	T	0.22	0.1228	1.841	0.03150	0.3244:0.1436:0.3894:0.1426	.	176	Q3LI81	KR271_HUMAN	M	176	ENSP00000372286:L176M	ENSP00000372286:L176M	L	-	1	2	KRTAP27-1	30631332	0.000000	0.05858	0.000000	0.03702	0.332000	0.28634	-0.923000	0.04000	-0.736000	0.04831	-0.482000	0.04802	CTG	.	.		0.458	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711		T	31709461	G	T	31709461	3	4	7	1	0	0	0	0	1	0	0	0	8553	933	33	3	101	3	KRTAP27-1	21	31709461	Missense_Mutation	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10		31709461	16420434	51	601										
TCF20	6942	hgsc.bcm.edu	37	chr22	42607813	42607813	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	cttgttaggcagaccatcacTagacattaggcagcgcccag	10	12	1	2			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chr22:42607813T>C	ENST00000359486.3	-	1	3635	c.3499A>G	c.(3499-3501)Agt>Ggt	p.S1167G	TCF20_ENST00000335626.4_Missense_Mutation_p.S1167G|TCF20_ENST00000404876.1_5'Flank	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1167					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						AGACCATCACTAGACATTAGG	0.507																																					p.S1167G		Atlas-SNP	.											.	TCF20	164	.	0			c.A3499G						.						73	70	71					22																	42607813		2203	4300	6503	SO:0001583	missense	6942	exon1			CATCACTAGACAT	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.3499A>G	chr22.hg19:g.42607813T>C	ENSP00000352463:p.Ser1167Gly	83.0	0.0		104.0	13.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	T	6.392	0.440410	0.12104	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.59083	0.29;0.29	5.53	0.912	0.19349	.	0.270733	0.37437	N	0.002100	T	0.28499	0.0705	N	0.08118	0	0.25551	N	0.987084	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12941	-1.0528	10	0.18276	T	0.48	-3.3979	5.425	0.16421	0.0:0.3002:0.1384:0.5614	.	1167;1167	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	G	1167	ENSP00000352463:S1167G;ENSP00000335561:S1167G	ENSP00000335561:S1167G	S	-	1	0	TCF20	40937757	0.001000	0.12720	0.513000	0.27749	0.861000	0.49209	0.086000	0.14935	-0.064000	0.13043	0.533000	0.62120	AGT	.	.		0.507	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		C	42607813	T	C	42607813	3	2	7	1	0	0	0	0	1	0	0	0	15705	1522	53	2	2421	2	TCF20	22	42607813	Missense_Mutation	SNP	T	TCGA-2Y-A9GX-01A-11D-A382-10		42607813	8696753	52	602										
KCNE1L	23630	hgsc.bcm.edu	37	chrX	108868238	108868238	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.713393476752255	2.24209378407852	0	0.444444444444444	1	0	gttcgcagccgctggctctcGctgcagttcatggctttcgg	13	13	2	0			TCGA-2Y-A9GX-01A-11D-A382-10	TCGA-2Y-A9GX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1ab7d98-d4e4-47e9-bcbd-a616ec8e29bb	e977b5c2-99d4-4352-b892-10503efd33a7	g.chrX:108868238G>A	ENST00000372101.2	-	1	155	c.12C>T	c.(10-12)agC>agT	p.S4S		NM_012282.2	NP_036414.1	Q9UJ90	KCE1L_HUMAN	KCNE1-like	4					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cation channel activity (GO:2001257)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						GCTGGCTCTCGCTGCAGTTCA	0.697																																					p.S4S		Atlas-SNP	.											.	KCNE1L	8	.	0			c.C12T						.						7	8	8					X																	108868238		2135	4173	6308	SO:0001819	synonymous_variant	23630	exon1			GCTCTCGCTGCAG	AJ012743	CCDS14547.1	Xq22.3	2008-02-05	2004-06-09		ENSG00000176076	ENSG00000176076		"Potassium channels"	6241	protein-coding gene	gene with protein product		300328	"potassium voltage-gated channel, Isk-related family, member 1-like"			10493825	Standard	NM_012282		Approved		uc004eoh.3	Q9UJ90	OTTHUMG00000022189	ENST00000372101.2:c.12C>T	chrX.hg19:g.108868238G>A		58.0	0.0		68.0	19.0	NM_012282		Silent	SNP	ENST00000372101.2	hg19	CCDS14547.1																																																																																			.	.		0.697	KCNE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057892.1	NM_012282		A	108868238	G	A	108868238	2	1	7	1	0	0	0	0	0	0	0	1	8031	1078	38	1		1	KCNE1L	23	108868238	Silent	SNP	G	TCGA-2Y-A9GX-01A-11D-A382-10		108868238	46402322	53	603										
NADK	65220	hgsc.bcm.edu	37	chr1	1686824	1686825	+	Frame_Shift_Ins	INS	-	-	TTTC													0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	caactcaccctctatcacctINSgagtaacttgggactgaaag							TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr1:1686824_1686825insTTTC	ENST00000341426.5	-	7	897_898	c.676_677insGAAA	c.(676-678)cagfs	p.Q226fs	NADK_ENST00000341991.3_Frame_Shift_Ins_p.Q226fs|NADK_ENST00000492768.1_5'Flank|NADK_ENST00000344463.4_Frame_Shift_Ins_p.Q371fs|NADK_ENST00000378625.1_Frame_Shift_Ins_p.Q371fs|NADK_ENST00000342348.5_Frame_Shift_Ins_p.Q194fs	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	226					ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		CTCTATCACCTGAGTAACTTGG	0.554																																					p.Q371fs		Atlas-INDEL	.											.	NADK	79	.	0			c.1112_1113insGAAA						.																																			SO:0001589	frameshift_variant	65220	exon9			.	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.676_677insGAAA	chr1.hg19:g.1686824_1686825insTTTC	ENSP00000341679:p.Gln226fs	48.0	0.0		100.0	36.0	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Frame_Shift_Ins	INS	ENST00000341426.5	hg19	CCDS30565.1																																																																																			.	.		0.554	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018		TTTC	1686825	-	TTTC	1686824	7	5	8	1	0	1	1	0	0	0	0	0	10146	1580	55	0	687	0	NADK	1	1686824	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GY-01A-11D-A382-10		1686824	247563797	1	604	1	2								
NADK	65220	hgsc.bcm.edu	37	chr1	1686825	1686825	+	Frame_Shift_Del	DEL	G	G	-													0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	caactcaccctctatcacctGagtaacttgggactgaaagt							TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr1:1686825delG	ENST00000341426.5	-	7	897	c.676delC	c.(676-678)cagfs	p.Q226fs	NADK_ENST00000341991.3_Frame_Shift_Del_p.Q226fs|NADK_ENST00000492768.1_5'Flank|NADK_ENST00000344463.4_Frame_Shift_Del_p.Q371fs|NADK_ENST00000378625.1_Frame_Shift_Del_p.Q371fs|NADK_ENST00000342348.5_Frame_Shift_Del_p.Q194fs	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	226					ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		TCTATCACCTGAGTAACTTGG	0.557																																					p.Q371fs		Pindel	.											.	NADK	79	.	0			c.1112delA						.						165	166	166					1																	1686825		2203	4300	6503	SO:0001589	frameshift_variant	65220	exon9			.	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.676delC	chr1.hg19:g.1686825delG	ENSP00000341679:p.Gln226fs	48.0	0.0		100.0	29.0	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Frame_Shift_Del	DEL	ENST00000341426.5	hg19	CCDS30565.1																																																																																			.	.		0.557	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018		-	1686825	G	-	1686825	7	5	8	1	0	1	0	1	0	0	0	0	10146	1299	45	0	688	0	NADK	1	1686825	Frame_Shift_Del	DEL	G	TCGA-2Y-A9GY-01A-11D-A382-10	1	1686825	247563796	2	605	1	2								
EPB41	2035	hgsc.bcm.edu	37	chr1	29314060	29314060	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	caagaacctcagcaggaggaAtcttgtcaaacagcagctga	10	10	3	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr1:29314060A>G	ENST00000343067.4	+	2	238	c.111A>G	c.(109-111)gaA>gaG	p.E37E	EPB41_ENST00000398863.2_Silent_p.E37E|EPB41_ENST00000356093.2_Silent_p.E37E|EPB41_ENST00000347529.3_Silent_p.E37E|EPB41_ENST00000349460.4_5'UTR|Y_RNA_ENST00000383977.1_RNA|EPB41_ENST00000373798.1_Silent_p.E37E|EPB41_ENST00000373797.1_Silent_p.E37E|EPB41_ENST00000373800.3_5'UTR	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	37					actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		AGCAGGAGGAATCTTGTCAAA	0.458																																					p.E37E		Atlas-SNP	.											.	EPB41	118	.	0			c.A111G						.						172	174	173					1																	29314060		2203	4300	6503	SO:0001819	synonymous_variant	2035	exon2			GGAGGAATCTTGT	BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023			3377	protein-coding gene	gene with protein product		130500	"elliptocytosis 1, RH-linked"	EL1			Standard	NM_001166005		Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.111A>G	chr1.hg19:g.29314060A>G		333.0	0.0		475.0	135.0	NM_203343	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	Silent	SNP	ENST00000343067.4	hg19	CCDS53288.1																																																																																			.	.		0.458	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010312.1	NM_203342		G	29314060	A	G	29314060	2	3	8	1	0	0	0	0	0	0	0	1	5153	98	4	2		2	EPB41	1	29314060	Silent	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	27627235	29314060	219936561	3	606										
CCDC24	149473	hgsc.bcm.edu	37	chr1	44457670	44457670	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gacctgagcctggagctgcgGgcggaggtggggagagggaa	22	7	0	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr1:44457670G>A	ENST00000372318.3	+	2	291	c.120G>A	c.(118-120)cgG>cgA	p.R40R	SLC6A9_ENST00000372307.3_Intron|SLC6A9_ENST00000372306.3_Intron	NM_152499.1	NP_689712.1	Q8N4L8	CCD24_HUMAN	coiled-coil domain containing 24	40										endometrium(3)|large_intestine(2)|lung(3)|stomach(1)	9	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				TGGAGCTGCGGGCGGAGGTGG	0.706																																					p.R40R		Atlas-SNP	.											.	CCDC24	22	.	0			c.G120A						.						12	12	12					1																	44457670		2050	4060	6110	SO:0001819	synonymous_variant	149473	exon2			GCTGCGGGCGGAG		CCDS507.1	1p34.1	2008-02-05			ENSG00000159214	ENSG00000159214			28688	protein-coding gene	gene with protein product						12477932	Standard	NM_152499		Approved	MGC45441	uc001clj.3	Q8N4L8	OTTHUMG00000008299	ENST00000372318.3:c.120G>A	chr1.hg19:g.44457670G>A		124.0	0.0		128.0	50.0	NM_152499	Q6RWT2	Silent	SNP	ENST00000372318.3	hg19	CCDS507.1																																																																																			.	.		0.706	CCDC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022865.1	NM_152499		A	44457670	G	A	44457670	2	1	8	1	0	0	0	0	0	0	0	1	2801	1219	43	3		3	CCDC24	1	44457670	Silent	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	15143610	44457670	204792951	4	607										
HFM1	164045	hgsc.bcm.edu	37	chr1	91841093	91841093	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	acaatccataccacaagtgtGggtttctgatcagagtacat	8	9	2	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr1:91841093G>T	ENST00000370425.3	-	12	1685	c.1587C>A	c.(1585-1587)ccC>ccA	p.P529P	HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Silent_p.P208P	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	529	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		CCACAAGTGTGGGTTTCTGAT	0.313																																					p.P529P		Atlas-SNP	.											.	HFM1	188	.	0			c.C1587A						.						84	77	79					1																	91841093		1823	4077	5900	SO:0001819	synonymous_variant	164045	exon12			AAGTGTGGGTTTC	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.1587C>A	chr1.hg19:g.91841093G>T		198.0	0.0		290.0	56.0	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	hg19	CCDS30769.2																																																																																			.	.		0.313	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		T	91841093	G	T	91841093	2	4	8	1	0	0	0	0	0	0	0	1	7092	1335	47	3		3	HFM1	1	91841093	Silent	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	47383423	91841093	157409528	5	608										
KCNA10	3744	hgsc.bcm.edu	37	chr1	111060812	111060812	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	aaagaggagccagaactgacGgtggatgtcattggtgggta	16	5	1	3	rs150505266		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr1:111060812G>T	ENST00000369771.2	-	1	985	c.598C>A	c.(598-600)Cgt>Agt	p.R200S		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	200			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	CAGAACTGACGGTGGATGTCA	0.547																																					p.R200S		Atlas-SNP	.											KCNA10,colon,carcinoma,+2,2	KCNA10	92	.	0			c.C598A						.						121	122	122					1																	111060812		2203	4300	6503	SO:0001583	missense	3744	exon1			ACTGACGGTGGAT	U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.598C>A	chr1.hg19:g.111060812G>T	ENSP00000358786:p.Arg200Ser	176.0	0.0		181.0	53.0	NM_005549		Missense_Mutation	SNP	ENST00000369771.2	hg19	CCDS826.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.173284	0.57584	.	.	ENSG00000143105	ENST00000369771	T	0.65178	-0.14	5.93	3.84	0.44239	.	0.050482	0.64402	D	0.000001	T	0.57359	0.2048	M	0.87758	2.905	0.40720	D	0.982654	P	0.44521	0.837	B	0.40677	0.337	T	0.69884	-0.5024	10	0.87932	D	0	.	13.2524	0.60060	0.0:0.0:0.604:0.396	.	200	Q16322	KCA10_HUMAN	S	200	ENSP00000358786:R200S	ENSP00000358786:R200S	R	-	1	0	KCNA10	110862335	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.620000	0.36976	1.460000	0.47911	0.655000	0.94253	CGT	.	G|1.000;A|0.000		0.547	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		T	111060812	G	T	111060812	3	4	8	1	0	0	0	0	1	0	0	0	8011	1116	39	1	941	1	KCNA10	1	111060812	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	19219719	111060812	138189809	6	609										
CD5L	922	hgsc.bcm.edu	37	chr1	157803136	157803136	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ccatagcatttccggtctctGaaggagggagagagggactt	14	8	1	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr1:157803136G>A	ENST00000368174.4	-	5	981	c.885C>T	c.(883-885)ttC>ttT	p.F295F	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	295	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TCCGGTCTCTGAAGGAGGGAG	0.582																																					p.F295F		Atlas-SNP	.											.	CD5L	112	.	0			c.C885T						.						117	119	118					1																	157803136		2203	4300	6503	SO:0001819	synonymous_variant	922	exon5			GTCTCTGAAGGAG	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.885C>T	chr1.hg19:g.157803136G>A		114.0	0.0		171.0	83.0	NM_005894	A8K7M5|Q6UX63	Silent	SNP	ENST00000368174.4	hg19	CCDS1171.1																																																																																			.	.		0.582	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		A	157803136	G	A	157803136	2	1	8	1	0	0	0	0	0	0	0	1	3029	1281	45	3		3	CD5L	1	157803136	Silent	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	46742324	157803136	91447485	7	610										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245847634	245847634	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gccgcggtcgggagctacgcGgagaccctgtccaccatcca	13	16	0	1	rs148065443		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr1:245847634G>T	ENST00000407071.2	+	11	2798	c.2358G>T	c.(2356-2358)gcG>gcT	p.A786A	KIF26B_ENST00000366518.4_Silent_p.A405A	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	786	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GGAGCTACGCGGAGACCCTGT	0.597																																					p.A786A		Atlas-SNP	.											.	KIF26B	343	.	0			c.G2358T						.						48	52	51					1																	245847634		2032	4179	6211	SO:0001819	synonymous_variant	55083	exon11			CTACGCGGAGACC	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2358G>T	chr1.hg19:g.245847634G>T		92.0	0.0		81.0	4.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	G|1.000;A|0.000		0.597	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		T	245847634	G	T	245847634	2	4	8	1	0	0	0	0	0	0	0	1	8304	1103	39	1		1	KIF26B	1	245847634	Silent	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	88044498	245847634	3402987	8	611										
TTC27	55622	hgsc.bcm.edu	37	chr2	33042572	33042572	+	Frame_Shift_Del	DEL	A	A	-													0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	cagttcccaagaagctgtacAaatgctttcttctgttcgac							TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:33042572delA	ENST00000317907.4	+	19	2588	c.2357delA	c.(2356-2358)caafs	p.Q786fs		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	786										breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						GAAGCTGTACAAATGCTTTCT	0.343																																					p.Q786fs		Atlas-Indel,Pindel	.											.	TTC27	71	.	0			c.2356delC						.						131	118	122					2																	33042572		2203	4300	6503	SO:0001589	frameshift_variant	55622	exon19			.	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.2357delA	chr2.hg19:g.33042572delA	ENSP00000313953:p.Gln786fs	101.0	0.0		128.0	33.0	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Frame_Shift_Del	DEL	ENST00000317907.4	hg19	CCDS33176.1																																																																																			.	.		0.343	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		-	33042572	A	-	33042572	7	5	8	1	0	1	0	1	0	0	0	0	16710	130	5	0	2431	0	TTC27	2	33042572	Frame_Shift_Del	DEL	A	TCGA-2Y-A9GY-01A-11D-A382-10		33042572	210156801	9	612										
VPS54	51542	hgsc.bcm.edu	37	chr2	64189527	64189527	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	aaaaatgcttctgaacgtagAgagatctggtgagcaatgtt	11	5	2	4			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:64189527A>C	ENST00000272322.4	-	7	829	c.675T>G	c.(673-675)tcT>tcG	p.S225S	VPS54_ENST00000354504.3_Silent_p.S108S|VPS54_ENST00000409558.4_Silent_p.S213S			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	225					growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						CTGAACGTAGAGAGATCTGGT	0.388																																					p.S225S		Atlas-SNP	.											.	VPS54	57	.	0			c.T675G						.						89	84	86					2																	64189527		2203	4300	6503	SO:0001819	synonymous_variant	51542	exon7			ACGTAGAGAGATC	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 164"	614633	"vacuolar protein sorting 54 (yeast)"			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.675T>G	chr2.hg19:g.64189527A>C		80.0	0.0		112.0	56.0	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Silent	SNP	ENST00000272322.4	hg19	CCDS33208.1																																																																																			.	.		0.388	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516		C	64189527	A	C	64189527	2	2	8	1	0	0	0	0	0	0	0	1	17231	291	11	5		5	VPS54	2	64189527	Silent	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	31146955	64189527	179009846	10	613										
DYSF	8291	hgsc.bcm.edu	37	chr2	71740979	71740979	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tcacgtcctccgccccactaCcccgggatcaaaagaaagcg	8	17	2	1	rs564416027		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:71740979C>A	ENST00000258104.3	+	6	868	c.591C>A	c.(589-591)taC>taA	p.Y197*	DYSF_ENST00000410041.1_Nonsense_Mutation_p.Y229*|DYSF_ENST00000429174.2_Nonsense_Mutation_p.Y197*|DYSF_ENST00000413539.2_Nonsense_Mutation_p.Y228*|DYSF_ENST00000409366.1_Nonsense_Mutation_p.Y198*|DYSF_ENST00000409762.1_Nonsense_Mutation_p.Y228*|DYSF_ENST00000409744.1_Nonsense_Mutation_p.Y198*|DYSF_ENST00000394120.2_Nonsense_Mutation_p.Y198*|DYSF_ENST00000409582.3_Nonsense_Mutation_p.Y228*|DYSF_ENST00000409651.1_Nonsense_Mutation_p.Y229*|DYSF_ENST00000410020.3_Nonsense_Mutation_p.Y229*	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	197					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.Y197Y(1)|p.Y229Y(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CGCCCCACTACCCCGGGATCA	0.582																																					p.Y229X		Atlas-SNP	.											DYSF_ENST00000410020,NS,carcinoma,0,2	DYSF	536	.	2	Substitution - coding silent(2)	lung(2)	c.C687A	GRCh37	CM090599	DYSF	M		.						58	60	60					2																	71740979		2203	4300	6503	SO:0001587	stop_gained	8291	exon7			CCACTACCCCGGG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.591C>A	chr2.hg19:g.71740979C>A	ENSP00000258104:p.Tyr197*	193.0	2.0		334.0	154.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Nonsense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.971787	0.92919	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	.	.	.	4.79	1.92	0.25849	.	0.467753	0.22878	N	0.054551	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	-13.1964	7.0741	0.25195	0.0:0.6012:0.0:0.3988	.	.	.	.	X	228;228;228;197;197;229;198;198;198;229;229	.	ENSP00000258104:Y197X	Y	+	3	2	DYSF	71594487	0.032000	0.19561	0.975000	0.42487	0.025000	0.11179	-0.500000	0.06405	0.545000	0.28902	0.549000	0.68633	TAC	.	.		0.582	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71740979	C	A	71740979	4	1	8	1	0	0	0	0	0	1	0	0	4861	518	18	3	805	3	DYSF	2	71740979	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	7551452	71740979	171458394	11	614										
CCT7	10574	hgsc.bcm.edu	37	chr2	73479950	73479950	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tcgactgtggatgctcccacAgcagcaggccggggccgtgg	16	13	0	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:73479950A>T	ENST00000258091.5	+	12	1734	c.1593A>T	c.(1591-1593)acA>acT	p.T531T	CCT7_ENST00000540468.1_Silent_p.T444T|CCT7_ENST00000398422.2_Silent_p.T327T|CCT7_ENST00000537131.1_Silent_p.T431T|CCT7_ENST00000538797.1_Silent_p.T403T|CCT7_ENST00000539919.1_Silent_p.T487T	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	531					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						ATGCTCCCACAGCAGCAGGCC	0.637																																					p.T531T		Atlas-SNP	.											.	CCT7	60	.	0			c.A1593T						.						32	34	34					2																	73479950		1962	4133	6095	SO:0001819	synonymous_variant	10574	exon12			TCCCACAGCAGCA	AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"Heat Shock Proteins / Chaperonins"	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	ENST00000258091.5:c.1593A>T	chr2.hg19:g.73479950A>T		169.0	0.0		208.0	91.0	NM_006429	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Silent	SNP	ENST00000258091.5	hg19	CCDS46336.1																																																																																			.	.		0.637	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2			T	73479950	A	T	73479950	2	4	8	1	0	0	0	0	0	0	0	1	2961	175	7	4		4	CCT7	2	73479950	Silent	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	1738971	73479950	169719423	12	615										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	catggccgggcgagctggagGaggaggaggaggaggaggag	24	5	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						.						3	4	4					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	139.0	0.0		231.0	13.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73613036	G	C	73613036	3	2	8	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	133086	73613036	169586337	13	616			1	4		2	2	30	G		7.681394e-05
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613065	73613065	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gaggaggaggaggaggaggaGgaggaagaggaggaggctgc	25	2	0	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:73613065G>A	ENST00000264448.6	+	1	180	c.69G>A	c.(67-69)gaG>gaA	p.E23E	ALMS1_ENST00000409009.1_Silent_p.E23E|ALMS1_ENST00000377715.1_Silent_p.E23E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	23	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						aggaggaggaggaggaagagg	0.687																																					p.E23E		Atlas-SNP	.											.	ALMS1	384	.	0			c.G69A						.						6	9	8					2																	73613065		1849	3831	5680	SO:0001819	synonymous_variant	7840	exon1			GGAGGAGGAGGAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.69G>A	chr2.hg19:g.73613065G>A		389.0	0.0		595.0	41.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.687	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73613065	G	A	73613065	2	1	8	1	0	0	0	0	0	0	0	1	535	991	35	3		3	ALMS1	2	73613065	Silent	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	29	73613065	169586308	14	617			1	4		2	2	30	G		7.681394e-05
CYTIP	9595	hgsc.bcm.edu	37	chr2	158272222	158272222	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tcttcctcttccacagcacgAtgaaggccagggataaattt	8	11	2	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:158272222A>G	ENST00000264192.3	-	8	1168	c.1047T>C	c.(1045-1047)caT>caC	p.H349H	CYTIP_ENST00000540637.1_Silent_p.H243H	NM_004288.4	NP_004279.3	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein	349					regulation of cell adhesion (GO:0030155)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	15						CCACAGCACGATGAAGGCCAG	0.473																																					p.H349H		Atlas-SNP	.											.	CYTIP	45	.	0			c.T1047C						.						89	84	86					2																	158272222		2203	4300	6503	SO:0001819	synonymous_variant	9595	exon8			AGCACGATGAAGG	L06633	CCDS2204.1	2q11.2	2011-09-08	2008-08-14	2008-08-19	ENSG00000115165	ENSG00000115165			9506	protein-coding gene	gene with protein product	"cytohesin binding protein HE", "cytohesin binder and regulator"	604448	"pleckstrin homology, Sec7 and coiled-coil domains, binding protein"	PSCDBP		18926288, 10343115, 11867758, 20530790, 21562043	Standard	NM_004288		Approved	B3-1, HE, CYBR, CASP, CYTHIP	uc002tzj.1	O60759	OTTHUMG00000154551	ENST00000264192.3:c.1047T>C	chr2.hg19:g.158272222A>G		348.0	0.0		489.0	233.0	NM_004288	B4DWH9|Q15630|Q8NE32	Silent	SNP	ENST00000264192.3	hg19	CCDS2204.1																																																																																			.	.		0.473	CYTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254926.1	NM_004288		G	158272222	A	G	158272222	2	3	8	1	0	0	0	0	0	0	0	1	4209	330	12	2		2	CYTIP	2	158272222	Silent	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	84659157	158272222	84927151	15	618										
STAT4	6775	hgsc.bcm.edu	37	chr2	192012877	192012877	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tgtcatcatagaattgatccAcctgctccaaaaacttgatt	5	10	2	3			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:192012877A>T	ENST00000392320.2	-	2	367	c.53T>A	c.(52-54)gTg>gAg	p.V18E	STAT4_ENST00000358470.4_Missense_Mutation_p.V18E|STAT4_ENST00000409995.1_Missense_Mutation_p.V18E	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	18					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			GAATTGATCCACCTGCTCCAA	0.368																																					p.V18E		Atlas-SNP	.											.	STAT4	85	.	0			c.T53A						.						121	117	119					2																	192012877		2203	4300	6503	SO:0001583	missense	6775	exon2			TGATCCACCTGCT		CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"SH2 domain containing"	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.53T>A	chr2.hg19:g.192012877A>T	ENSP00000376134:p.Val18Glu	100.0	0.0		166.0	76.0	NM_001243835	Q96NZ6	Missense_Mutation	SNP	ENST00000392320.2	hg19	CCDS2310.1	.	.	.	.	.	.	.	.	.	.	A	19.00	3.741572	0.69304	.	.	ENSG00000138378	ENST00000358470;ENST00000392320;ENST00000409995;ENST00000450994;ENST00000432798	T;T;T;T;T	0.60424	0.19;0.19;0.19;0.19;0.19	5.73	5.73	0.89815	STAT transcription factor, protein interaction (4);	0.075363	0.52532	D	0.000072	T	0.76285	0.3966	M	0.74647	2.275	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.995;0.997;0.997	T	0.79364	-0.1834	10	0.87932	D	0	-20.4535	16.0048	0.80354	1.0:0.0:0.0:0.0	.	18;18;18	B4DSY7;B4DV04;Q14765	.;.;STAT4_HUMAN	E	18	ENSP00000351255:V18E;ENSP00000376134:V18E;ENSP00000386288:V18E;ENSP00000412397:V18E;ENSP00000414322:V18E	ENSP00000351255:V18E	V	-	2	0	STAT4	191721122	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.288000	0.96055	2.190000	0.69967	0.533000	0.62120	GTG	.	.		0.368	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151		T	192012877	A	T	192012877	3	4	8	1	0	0	0	0	1	0	0	0	15282	159	6	4	2285	4	STAT4	2	192012877	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	33740655	192012877	51186496	16	619										
SP140	11262	hgsc.bcm.edu	37	chr2	231115713	231115714	+	Frame_Shift_Del	DEL	TC	TC	-													0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	cagagggcagtgatgactgtTcagaaatgtgtgatggagaa							TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:231115713_231115714delTC	ENST00000392045.3	+	10	1108_1109	c.994_995delTC	c.(994-996)tcafs	p.S332fs	SP140_ENST00000486687.2_Frame_Shift_Del_p.S256fs|SP140_ENST00000343805.6_Frame_Shift_Del_p.S306fs|SP140_ENST00000350136.5_Intron|SP140_ENST00000417495.3_Intron|SP140_ENST00000420434.3_Frame_Shift_Del_p.S332fs	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	332					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		TGATGACTGTTCAGAAATGTGT	0.485																																					p.331_332del		Atlas-INDEL	.											.	SP140	121	.	0			c.993_994del						.																																			SO:0001589	frameshift_variant	11262	exon10			.	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.994_995delTC	chr2.hg19:g.231115713_231115714delTC	ENSP00000375899:p.Ser332fs	80.0	0.0		122.0	18.0	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Frame_Shift_Del	DEL	ENST00000392045.3	hg19	CCDS42831.1																																																																																			.	.		0.485	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		-	231115714	TC	-	231115713	7	5	8	1	0	1	0	1	0	0	0	0	14977	1783	62	0	1149	0	SP140	2	231115713	Frame_Shift_Del	DEL	TC	TCGA-2Y-A9GY-01A-11D-A382-10	39102836	231115713	12083660	17	620	2	2								
SP140	11262	hgsc.bcm.edu	37	chr2	231115716	231115716	+	Frame_Shift_Del	DEL	G	G	-													0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	agggcagtgatgactgttcaGaaatgtgtgatggagaagag							TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:231115716delG	ENST00000392045.3	+	10	1111	c.997delG	c.(997-999)gaafs	p.E333fs	SP140_ENST00000486687.2_Frame_Shift_Del_p.E257fs|SP140_ENST00000343805.6_Frame_Shift_Del_p.E307fs|SP140_ENST00000350136.5_Intron|SP140_ENST00000417495.3_Intron|SP140_ENST00000420434.3_Frame_Shift_Del_p.E333fs	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	333					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		TGACTGTTCAGAAATGTGTGA	0.483																																					p.S332fs		Atlas-INDEL	.											.	SP140	121	.	0			c.996delA						.						90	84	86					2																	231115716		1862	4102	5964	SO:0001589	frameshift_variant	11262	exon10			.	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.997delG	chr2.hg19:g.231115716delG	ENSP00000375899:p.Glu333fs	76.0	0.0		123.0	18.0	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Frame_Shift_Del	DEL	ENST00000392045.3	hg19	CCDS42831.1																																																																																			.	.		0.483	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		-	231115716	G	-	231115716	7	5	8	1	0	1	0	1	0	0	0	0	14977	943	33	0	1152	0	SP140	2	231115716	Frame_Shift_Del	DEL	G	TCGA-2Y-A9GY-01A-11D-A382-10	3	231115716	12083657	18	621	2	2								
NGEF	25791	hgsc.bcm.edu	37	chr2	233759597	233759597	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ttcagactcttgtagtaggaCgcctcggaagtgaccagctc	11	11	2	2	rs527494178		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:233759597C>T	ENST00000264051.3	-	6	1136	c.858G>A	c.(856-858)gcG>gcA	p.A286A	NGEF_ENST00000539537.1_Silent_p.A9A|NGEF_ENST00000373552.4_Silent_p.A194A|NGEF_ENST00000409079.1_Silent_p.A194A	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	286	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		TGTAGTAGGACGCCTCGGAAG	0.582													C|||	1	0.000199681	8e-04	0	5008	,	,		18589	0		0	False		,,,				2504	0				p.A286A		Atlas-SNP	.											.	NGEF	198	.	0			c.G858A						.						121	106	111					2																	233759597		2203	4300	6503	SO:0001819	synonymous_variant	25791	exon6			GTAGGACGCCTCG	AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"Rho guanine nucleotide exchange factors"	7807	protein-coding gene	gene with protein product	"ephexin"	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.858G>A	chr2.hg19:g.233759597C>T		98.0	0.0		153.0	32.0	NM_019850	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Silent	SNP	ENST00000264051.3	hg19	CCDS2500.1	.	.	.	.	.	.	.	.	.	.	C	5.168	0.216573	0.09810	.	.	ENSG00000066248	ENST00000420650	.	.	.	5.22	-0.627	0.11541	.	.	.	.	.	T	0.50309	0.1608	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34477	-0.9827	4	.	.	.	-31.3689	5.3754	0.16162	0.0612:0.2032:0.3025:0.4331	.	.	.	.	I	79	.	.	V	-	1	0	NGEF	233467841	0.413000	0.25400	0.990000	0.47175	0.473000	0.32948	-0.301000	0.08232	-0.409000	0.07553	-2.275000	0.00273	GTC	.	.		0.582	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799		T	233759597	C	T	233759597	2	4	8	1	0	0	0	0	0	0	0	1	10403	523	19	1		1	NGEF	2	233759597	Silent	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	2643881	233759597	9439776	19	622										
PER2	8864	hgsc.bcm.edu	37	chr2	239161961	239161961	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	agcatgaatgccatgacaggCgccaaaggggcagggaaagg	16	8	0	2	rs575531966		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr2:239161961C>T	ENST00000254657.3	-	19	2982	c.2703G>A	c.(2701-2703)gcG>gcA	p.A901A	AC096574.4_ENST00000456601.1_RNA|PER2_ENST00000254658.3_3'UTR	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	901	Interaction with PPARG. {ECO:0000250|UniProtKB:O54943}.|Pro-rich.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		CCATGACAGGCGCCAAAGGGG	0.647																																					p.A901A		Atlas-SNP	.											.	PER2	85	.	0			c.G2703A						.						41	44	43					2																	239161961		2203	4300	6503	SO:0001819	synonymous_variant	8864	exon19			GACAGGCGCCAAA	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2703G>A	chr2.hg19:g.239161961C>T		125.0	0.0		161.0	12.0	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	hg19	CCDS2528.1																																																																																			.	.		0.647	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		T	239161961	C	T	239161961	2	4	8	1	0	0	0	0	0	0	0	1	11739	755	27	1		1	PER2	2	239161961	Silent	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	5402364	239161961	4037412	20	623										
CAND2	23066	hgsc.bcm.edu	37	chr3	12845054	12845054	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tccagctggacgaggacagcGagcgcaaggtggtgaagatg	17	8	0	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr3:12845054G>T	ENST00000456430.2	+	2	177	c.136G>T	c.(136-138)Gag>Tag	p.E46*	CAND2_ENST00000295989.5_Nonsense_Mutation_p.E46*	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	46					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CGAGGACAGCGAGCGCAAGGT	0.602																																					p.E46X	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.G136T						.						63	71	68					3																	12845054		2203	4300	6503	SO:0001587	stop_gained	23066	exon2			GACAGCGAGCGCA		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.136G>T	chr3.hg19:g.12845054G>T	ENSP00000387641:p.Glu46*	50.0	0.0		87.0	4.0	NM_012298	B9EGM9|E9KL24	Nonsense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	G	36	5.634867	0.96682	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	.	.	.	4.66	4.66	0.58398	.	0.149727	0.42964	D	0.000622	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-10.9323	15.4488	0.75257	0.0:0.0:1.0:0.0	.	.	.	.	X	46	.	ENSP00000295989:E46X	E	+	1	0	CAND2	12820054	1.000000	0.71417	0.965000	0.40720	0.933000	0.57130	9.532000	0.98057	2.572000	0.86782	0.655000	0.94253	GAG	.	.		0.602	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		T	12845054	G	T	12845054	4	4	8	1	0	0	0	0	0	1	0	0	2618	1059	37	1	142	1	CAND2	3	12845054	Nonsense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10		12845054	185177376	21	624										
CD80	941	hgsc.bcm.edu	37	chr3	119263513	119263513	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ggcgcagagccaggatcacaAtggagaggttattagtgata	14	6	1	3			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr3:119263513A>G	ENST00000264246.3	-	3	664	c.302T>C	c.(301-303)aTt>aCt	p.I101T	CD80_ENST00000478182.1_Missense_Mutation_p.I101T|CD80_ENST00000383668.3_Missense_Mutation_p.I101T|CD80_ENST00000383669.3_Missense_Mutation_p.I101T	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	101	Ig-like V-type.				cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of signal transduction (GO:0009967)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	12					Abatacept(DB01281)|Belatacept(DB06681)	CAGGATCACAATGGAGAGGTT	0.473																																					p.I101T	Melanoma(132;135 1764 1806 5833 14593)	Atlas-SNP	.											.	CD80	35	.	0			c.T302C						.						149	143	145					3																	119263513		2203	4300	6503	SO:0001583	missense	941	exon3			ATCACAATGGAGA		CCDS2989.1	3q13.3-q21	2013-01-11	2006-03-31		ENSG00000121594	ENSG00000121594		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	1700	protein-coding gene	gene with protein product	"B-lymphocyte activation antigen B7"	112203	"CD80 antigen (CD28 antigen ligand 1, B7-1 antigen)", "CD80 molecule "	CD28LG, CD28LG1		1370389	Standard	NM_005191		Approved	B7.1, B7-1	uc003ecq.3	P33681	OTTHUMG00000159419	ENST00000264246.3:c.302T>C	chr3.hg19:g.119263513A>G	ENSP00000264246:p.Ile101Thr	119.0	0.0		117.0	49.0	NM_005191	Q5DTA9|Q5DTB0	Missense_Mutation	SNP	ENST00000264246.3	hg19	CCDS2989.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.818243	0.32145	.	.	ENSG00000121594	ENST00000264246;ENST00000478182;ENST00000383669;ENST00000383668	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	5.13	5.13	0.70059	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.680401	0.12921	N	0.428161	T	0.69531	0.3121	M	0.80847	2.515	0.09310	N	1	D;D;D;D	0.71674	0.998;0.982;0.996;0.996	D;D;D;D	0.87578	0.998;0.986;0.994;0.994	T	0.61282	-0.7094	10	0.87932	D	0	-2.6865	11.2561	0.49054	1.0:0.0:0.0:0.0	.	101;101;101;101	Q5DTA9;Q5DTB0;A0N0P2;P33681	.;.;.;CD80_HUMAN	T	101	ENSP00000264246:I101T;ENSP00000418364:I101T;ENSP00000373165:I101T;ENSP00000373164:I101T	ENSP00000264246:I101T	I	-	2	0	CD80	120746203	0.054000	0.20591	0.026000	0.17262	0.039000	0.13416	3.767000	0.55288	2.152000	0.67230	0.528000	0.53228	ATT	.	.		0.473	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191		G	119263513	A	G	119263513	3	3	8	1	0	0	0	0	1	0	0	0	3040	101	4	2	580	2	CD80	3	119263513	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	106418459	119263513	78758917	22	625										
GPR156	165829	hgsc.bcm.edu	37	chr3	119886025	119886025	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	agagtcagaagagctctggaAgcagatttcacagtagggcc	13	8	3	4			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr3:119886025A>C	ENST00000464295.1	-	10	2744	c.2299T>G	c.(2299-2301)Ttc>Gtc	p.F767V	GPR156_ENST00000461057.1_Missense_Mutation_p.F763V|GPR156_ENST00000315843.3_Missense_Mutation_p.F767V			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	767						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		GAGCTCTGGAAGCAGATTTCA	0.557																																					p.F767V		Atlas-SNP	.											.	GPR156	85	.	0			c.T2299G						.						113	127	122					3																	119886025		2203	4300	6503	SO:0001583	missense	165829	exon9			TCTGGAAGCAGAT	AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"GPCR / Class C : Orphans"	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.2299T>G	chr3.hg19:g.119886025A>C	ENSP00000417261:p.Phe767Val	110.0	0.0		103.0	47.0	NM_153002	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Missense_Mutation	SNP	ENST00000464295.1	hg19	CCDS2997.1	.	.	.	.	.	.	.	.	.	.	A	19.57	3.851630	0.71719	.	.	ENSG00000175697	ENST00000464295;ENST00000315843;ENST00000461057	T;T;T	0.30448	1.53;1.53;1.54	5.11	5.11	0.69529	.	0.158034	0.44285	D	0.000464	T	0.29652	0.0740	L	0.27053	0.805	0.36555	D	0.872077	D;D	0.53151	0.958;0.958	P;P	0.51833	0.681;0.681	T	0.17776	-1.0358	9	.	.	.	-24.5545	10.5774	0.45235	0.9223:0.0:0.0777:0.0	.	763;767	E9PFZ4;Q8NFN8	.;GP156_HUMAN	V	767;767;763	ENSP00000417261:F767V;ENSP00000324553:F767V;ENSP00000418758:F763V	.	F	-	1	0	GPR156	121368715	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.672000	0.46850	2.281000	0.76405	0.533000	0.62120	TTC	.	.		0.557	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		C	119886025	A	C	119886025	3	2	8	1	0	0	0	0	1	0	0	0	6669	72	3	5	149	5	GPR156	3	119886025	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	622512	119886025	78136405	23	626										
OTOL1	131149	hgsc.bcm.edu	37	chr3	161221396	161221396	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	caaatttgaaaagattctctAtaatgaccaagggaattaca	6	6	1	3	rs570932275		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr3:161221396A>T	ENST00000327928.4	+	4	1100	c.1100A>T	c.(1099-1101)tAt>tTt	p.Y367F		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	367	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						AAGATTCTCTATAATGACCAA	0.468													A|||	1	0.000199681	0	0	5008	,	,		18186	0.001		0	False		,,,				2504	0				p.Y367F		Atlas-SNP	.											.	OTOL1	63	.	0			c.A1100T						.						57	52	54					3																	161221396		1879	4104	5983	SO:0001583	missense	131149	exon4			TTCTCTATAATGA		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"C1q and tumor necrosis factor related protein 15"		"otolin 1 homolog (zebrafish)"			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.1100A>T	chr3.hg19:g.161221396A>T	ENSP00000330808:p.Tyr367Phe	83.0	0.0		87.0	19.0	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	hg19	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.525009	0.27299	.	.	ENSG00000182447	ENST00000327928	T	0.75589	-0.95	5.23	4.06	0.47325	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.057841	0.64402	D	0.000001	D	0.82742	0.5103	M	0.76002	2.32	0.26282	N	0.978266	D	0.64830	0.994	D	0.66847	0.947	T	0.73898	-0.3837	10	0.31617	T	0.26	.	10.9923	0.47557	0.837:0.163:0.0:0.0	.	367	A6NHN0	OTOL1_HUMAN	F	367	ENSP00000330808:Y367F	ENSP00000330808:Y367F	Y	+	2	0	OTOL1	162704090	1.000000	0.71417	0.707000	0.30419	0.076000	0.17211	5.918000	0.69996	0.804000	0.34136	0.455000	0.32223	TAT	.	.		0.468	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440		T	161221396	A	T	161221396	3	4	8	1	0	0	0	0	1	0	0	0	11313	449	16	4	1114	4	OTOL1	3	161221396	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	41335371	161221396	36801034	24	627										
MARCH11	441061	hgsc.bcm.edu	37	chr5	16067614	16067614	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ctctcatcacaacctcccccGagctgttatcttctgataag	5	15	4	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr5:16067614G>T	ENST00000332432.8	-	4	1374	c.1175C>A	c.(1174-1176)tCg>tAg	p.S392*		NM_001102562.1	NP_001096032.1	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11	392					protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)|urinary_tract(1)	20						AACCTCCCCCGAGCTGTTATC	0.463																																					p.S392X		Atlas-SNP	.											MARCH11,rectum,carcinoma,0,1	MARCH11	50	.	0			c.C1175A						.						182	177	179					5																	16067614		1943	4147	6090	SO:0001587	stop_gained	441061	exon4			TCCCCCGAGCTGT	BC150513	CCDS47192.1	5p15.1	2013-01-09			ENSG00000183654	ENSG00000183654		"RING-type (C3HC4) zinc fingers", "MARCH membrane-associated ring fingers"	33609	protein-coding gene	gene with protein product		613338				17604280	Standard	NM_001102562		Approved	MARCH-XI	uc003jfo.2	A6NNE9	OTTHUMG00000161789	ENST00000332432.8:c.1175C>A	chr5.hg19:g.16067614G>T	ENSP00000333181:p.Ser392*	59.0	0.0		95.0	34.0	NM_001102562	A7E2S6	Nonsense_Mutation	SNP	ENST00000332432.8	hg19	CCDS47192.1	.	.	.	.	.	.	.	.	.	.	G	36	5.970353	0.97156	.	.	ENSG00000183654	ENST00000332432	.	.	.	5.12	5.12	0.69794	.	0.135742	0.50627	D	0.000113	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.7453	18.9417	0.92608	0.0:0.0:1.0:0.0	.	.	.	.	X	392	.	ENSP00000333181:S392X	S	-	2	0	MARCH11	16120614	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	6.707000	0.74654	2.525000	0.85131	0.655000	0.94253	TCG	.	.		0.463	MARCH11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000366096.2	NM_001102562		T	16067614	G	T	16067614	4	4	8	1	0	0	0	0	0	1	0	0	9309	1059	37	1	37	1	MARCH11	5	16067614	Nonsense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10		16067614	164847646	25	628										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128977574	128977574	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tgttatttgcacaggattatGgtgcaaggtagaaggtgaga	14	3	0	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr5:128977574G>T	ENST00000274487.4	+	11	1920	c.1775G>T	c.(1774-1776)tGg>tTg	p.W592L	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	592	Disintegrin.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		ACAGGATTATGGTGCAAGGTA	0.398																																					p.W592L		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.G1775T						.						214	180	191					5																	128977574		2203	4300	6503	SO:0001583	missense	171019	exon11			GATTATGGTGCAA	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1775G>T	chr5.hg19:g.128977574G>T	ENSP00000274487:p.Trp592Leu	90.0	0.0		123.0	41.0	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.192046	0.78902	.	.	ENSG00000145808	ENST00000274487	T	0.64991	-0.13	3.85	3.85	0.44370	.	0.000000	0.64402	D	0.000018	D	0.82490	0.5048	M	0.90595	3.13	0.58432	D	0.999994	D	0.89917	1.0	D	0.87578	0.998	D	0.86680	0.1916	9	.	.	.	.	17.0821	0.86601	0.0:0.0:1.0:0.0	.	592	Q8TE59	ATS19_HUMAN	L	592	ENSP00000274487:W592L	.	W	+	2	0	ADAMTS19	129005473	1.000000	0.71417	0.994000	0.49952	0.988000	0.76386	7.207000	0.77899	2.426000	0.82243	0.591000	0.81541	TGG	.	.		0.398	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		T	128977574	G	T	128977574	3	4	8	1	0	0	0	0	1	0	0	0	264	1357	47	3	1817	3	ADAMTS19	5	128977574	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	112909960	128977574	51937686	26	629										
ACSL6	23305	hgsc.bcm.edu	37	chr5	131310509	131310509	+	Intron	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	aggaaatgtgcacatccgcaCaagtgggagcccactgactc	11	12	0	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr5:131310509C>G	ENST00000379240.1	-	11	1147				ACSL6_ENST00000379249.3_Missense_Mutation_p.C312S|ACSL6_ENST00000379246.1_Intron|ACSL6_ENST00000357096.1_Intron|ACSL6_ENST00000379264.2_Intron|ACSL6_ENST00000544770.1_Intron|ACSL6_ENST00000296869.4_Missense_Mutation_p.C337S|ACSL6_ENST00000431707.1_Intron|ACSL6_ENST00000379244.1_Missense_Mutation_p.C312S|ACSL6_ENST00000543479.1_Missense_Mutation_p.C312S|ACSL6_ENST00000379272.2_Intron|ACSL6_ENST00000379255.1_Intron			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6						acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CACATCCGCACAAGTGGGAGC	0.522																																					p.C337S		Atlas-SNP	.											.	ACSL6	169	.	0			c.G1010C						.						62	57	59					5																	131310509		2203	4300	6503	SO:0001627	intron_variant	23305	exon11			TCCGCACAAGTGG	AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"Acyl-CoA synthetase family"	16496	protein-coding gene	gene with protein product		604443	"fatty-acid-Coenzyme A ligase, long-chain 6"	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.993+76G>C	chr5.hg19:g.131310509C>G		259.0	0.0		239.0	119.0	NM_015256	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Missense_Mutation	SNP	ENST00000379240.1	hg19		.	.	.	.	.	.	.	.	.	.	C	2.187	-0.386197	0.04966	.	.	ENSG00000164398	ENST00000379249;ENST00000296869;ENST00000379244;ENST00000543479;ENST00000434099	T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0	5.16	4.3	0.51218	.	0.670270	0.15722	N	0.247865	T	0.03390	0.0098	N	0.00894	-1.105	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.36962	-0.9726	10	0.11485	T	0.65	.	10.6827	0.45823	0.0:0.8461:0.0:0.1539	.	312;302;337	Q9UKU0-3;B4DFW3;Q9UKU0-8	.;.;.	S	312;337;312;312;277	ENSP00000368551:C312S;ENSP00000296869:C337S;ENSP00000368546:C312S;ENSP00000442124:C312S;ENSP00000397507:C277S	ENSP00000296869:C337S	C	-	2	0	ACSL6	131338408	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.087000	0.50167	1.194000	0.43101	0.555000	0.69702	TGT	.	.		0.522	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256		G	131310509	C	G	131310509	1	3	8	0	1	0	0	0	0	0	0	0	181	478	17	4		4	ACSL6	5	131310509	Intron	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	2332935	131310509	49604751	27	630										
H2AFY	9555	hgsc.bcm.edu	37	chr5	134705791	134705791	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gggtgtgacccgtcccttctTgttgtctctcgctgcattgc	11	13	2	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr5:134705791T>C	ENST00000511689.1	-	3	807	c.214A>G	c.(214-216)Aag>Gag	p.K72E	H2AFY_ENST00000312469.4_Missense_Mutation_p.K72E|H2AFY_ENST00000510038.1_Missense_Mutation_p.K72E|H2AFY_ENST00000304332.4_Missense_Mutation_p.K72E|H2AFY_ENST00000423969.2_Intron	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	72	Histone H2A.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CGTCCCTTCTTGTTGTCTCTC	0.577																																					p.K72E		Atlas-SNP	.											.	H2AFY	61	.	0			c.A214G						.						91	72	79					5																	134705791		2203	4300	6503	SO:0001583	missense	9555	exon3			CCTTCTTGTTGTC	AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"Histones / Replication-independent"	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.214A>G	chr5.hg19:g.134705791T>C	ENSP00000423563:p.Lys72Glu	53.0	0.0		42.0	19.0	NM_138610	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Missense_Mutation	SNP	ENST00000511689.1	hg19	CCDS4185.1	.	.	.	.	.	.	.	.	.	.	T	35	5.487474	0.96323	.	.	ENSG00000113648	ENST00000511689;ENST00000304332;ENST00000312469;ENST00000510038	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	6.06	6.06	0.98353	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.85682	D	0.000000	D	0.93003	0.7773	H	0.98577	4.27	0.80722	D	1	D;D;D	0.89917	0.998;0.999;1.0	D;D;D	0.80764	0.915;0.994;0.989	D	0.95541	0.8612	10	0.87932	D	0	.	16.6093	0.84858	0.0:0.0:0.0:1.0	.	72;72;72	O75367-3;O75367-2;O75367	.;.;H2AY_HUMAN	E	72	ENSP00000423563:K72E;ENSP00000302572:K72E;ENSP00000310169:K72E;ENSP00000424971:K72E	ENSP00000302572:K72E	K	-	1	0	H2AFY	134733690	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.015000	0.88690	2.324000	0.78689	0.533000	0.62120	AAG	.	.		0.577	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893		C	134705791	T	C	134705791	3	2	8	1	0	0	0	0	1	0	0	0	6938	1821	63	2	1027	2	H2AFY	5	134705791	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	3395282	134705791	46209469	28	631										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141060026	141060026	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	caccgtggccagccacacagCgatgtccaggtcctgagggg	14	14	0	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr5:141060026C>A	ENST00000239440.4	-	2	93	c.28G>T	c.(28-30)Gct>Tct	p.A10S	ARAP3_ENST00000508305.1_5'UTR	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	10	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.A10T(1)		NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						AGCCACACAGCGATGTCCAGG	0.682																																					p.A10S		Atlas-SNP	.											ARAP3,NS,NS,0,1	ARAP3	139	.	1	Substitution - Missense(1)	NS(1)	c.G28T						.						27	28	27					5																	141060026		2203	4293	6496	SO:0001583	missense	64411	exon2			ACACAGCGATGTC	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.28G>T	chr5.hg19:g.141060026C>A	ENSP00000239440:p.Ala10Ser	29.0	0.0		17.0	10.0	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	hg19	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.093123	0.36952	.	.	ENSG00000120318	ENST00000239440;ENST00000504448	D;T	0.85339	-1.97;-0.01	4.39	-0.788	0.10939	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.581772	0.15624	N	0.252737	T	0.71634	0.3363	N	0.25890	0.77	0.80722	D	1	B	0.28055	0.199	B	0.33121	0.158	T	0.57388	-0.7820	10	0.51188	T	0.08	.	1.3608	0.02191	0.2954:0.3899:0.1437:0.171	.	10	Q8WWN8	ARAP3_HUMAN	S	10	ENSP00000239440:A10S;ENSP00000421148:A10S	ENSP00000239440:A10S	A	-	1	0	ARAP3	141040210	0.998000	0.40836	0.990000	0.47175	0.989000	0.77384	0.326000	0.19646	-0.401000	0.07644	-0.361000	0.07541	GCT	.	.		0.682	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		A	141060026	C	A	141060026	3	1	8	1	0	0	0	0	1	0	0	0	840	768	27	1	4734	1	ARAP3	5	141060026	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	6354235	141060026	39855234	29	632										
TDRD6	221400	hgsc.bcm.edu	37	chr6	46657236	46657236	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gcaacagaggaggaggaaccAgaaacatctcagtctcagtc	11	10	2	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr6:46657236A>G	ENST00000316081.6	+	1	1371	c.1371A>G	c.(1369-1371)ccA>ccG	p.P457P	RP11-446F17.3_ENST00000422284.2_RNA|RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000434329.2_RNA|TDRD6_ENST00000544460.1_Silent_p.P457P	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	457	Poly-Glu.				germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			AGGAGGAACCAGAAACATCTC	0.468																																					p.P457P		Atlas-SNP	.											.	TDRD6	205	.	0			c.A1371G						.						88	80	83					6																	46657236		2203	4300	6503	SO:0001819	synonymous_variant	221400	exon1			GGAACCAGAAACA	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.1371A>G	chr6.hg19:g.46657236A>G		32.0	0.0		59.0	29.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Silent	SNP	ENST00000316081.6	hg19	CCDS34470.1																																																																																			.	.		0.468	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		G	46657236	A	G	46657236	2	3	8	1	0	0	0	0	0	0	0	1	15749	175	7	2		2	TDRD6	6	46657236	Silent	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10		46657236	124457831	30	633										
TNFRSF21	27242	hgsc.bcm.edu	37	chr6	47200685	47200685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	catcaaagataggctgcaagTcacaggggtccaggcgtacc	12	11	2	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr6:47200685T>C	ENST00000296861.2	-	6	2177	c.1784A>G	c.(1783-1785)gAc>gGc	p.D595G		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	595					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			AGGCTGCAAGTCACAGGGGTC	0.522																																					p.D595G		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.A1784G						.						80	81	81					6																	47200685		2203	4300	6503	SO:0001583	missense	27242	exon6			TGCAAGTCACAGG	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"Tumor necrosis factor receptor superfamily", "CD molecules"	13469	protein-coding gene	gene with protein product	"death receptor 6"	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1784A>G	chr6.hg19:g.47200685T>C	ENSP00000296861:p.Asp595Gly	80.0	0.0		120.0	26.0	NM_014452	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	hg19	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	T	19.58	3.853495	0.71719	.	.	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.70631	-0.5	5.84	5.84	0.93424	.	0.088018	0.85682	D	0.000000	T	0.69557	0.3124	L	0.27053	0.805	0.58432	D	0.999996	D	0.89917	1.0	D	0.74348	0.983	T	0.76184	-0.3052	10	0.87932	D	0	.	14.7818	0.69772	0.0:0.0:0.0:1.0	.	595	O75509	TNR21_HUMAN	G	595;284	ENSP00000296861:D595G	ENSP00000296861:D595G	D	-	2	0	TNFRSF21	47308644	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.232000	0.73038	0.533000	0.62120	GAC	.	.		0.522	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		C	47200685	T	C	47200685	3	2	8	1	0	0	0	0	1	0	0	0	16310	1667	58	2	187	2	TNFRSF21	6	47200685	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	543449	47200685	123914382	31	634										
PTP4A1	7803	hgsc.bcm.edu	37	chr6	64289208	64289208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	taattgaaggtggaatgaaaTacgaagatgcagtacaattc	10	4	0	3			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr6:64289208T>C	ENST00000370651.3	+	5	1529	c.376T>C	c.(376-378)Tac>Cac	p.Y126H	PTP4A1_ENST00000370650.2_Intron	NM_003463.3	NP_003454.1	Q93096	TP4A1_HUMAN	protein tyrosine phosphatase type IVA, member 1	126	Interaction with ATF5. {ECO:0000250}.|Tyrosine-protein phosphatase.				cell cycle (GO:0007049)|multicellular organismal development (GO:0007275)|positive regulation of cell migration (GO:0030335)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			large_intestine(3)|lung(4)|skin(1)	8	all_cancers(3;0.071)|all_epithelial(2;0.0146)|Lung NSC(77;0.175)		Epithelial(2;0.0365)|LUSC - Lung squamous cell carcinoma(74;0.0644)|all cancers(2;0.112)|Lung(124;0.13)			TGGAATGAAATACGAAGATGC	0.333																																					p.Y126H	Pancreas(91;1019 1502 28028 38110 51645)	Atlas-SNP	.											.	PTP4A1	13	.	0			c.T376C						.						123	114	117					6																	64289208		2203	4299	6502	SO:0001583	missense	7803	exon5			ATGAAATACGAAG	U48296	CCDS4965.1	6q12	2011-06-09			ENSG00000112245	ENSG00000112245		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"	9634	protein-coding gene	gene with protein product		601585				9642300	Standard	NM_003463		Approved	PTPCAAX1, PRL-1	uc003pel.3	Q93096	OTTHUMG00000014949	ENST00000370651.3:c.376T>C	chr6.hg19:g.64289208T>C	ENSP00000359685:p.Tyr126His	303.0	0.0		515.0	35.0	NM_003463	B2R6C8|O00648|Q49A54	Missense_Mutation	SNP	ENST00000370651.3	hg19	CCDS4965.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.458009	0.63401	.	.	ENSG00000112245	ENST00000370651	D	0.86164	-2.08	5.96	5.96	0.96718	Protein-tyrosine phosphatase, receptor/non-receptor type (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.86502	0.5948	M	0.84846	2.72	0.80722	D	1	B	0.19817	0.039	B	0.31016	0.123	D	0.84718	0.0738	10	0.46703	T	0.11	-12.6314	16.4221	0.83766	0.0:0.0:0.0:1.0	.	126	Q93096	TP4A1_HUMAN	H	126	ENSP00000359685:Y126H	ENSP00000359685:Y126H	Y	+	1	0	PTP4A1	64347167	1.000000	0.71417	0.992000	0.48379	0.846000	0.48090	8.015000	0.88690	2.283000	0.76528	0.477000	0.44152	TAC	.	.		0.333	PTP4A1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041083.2			C	64289208	T	C	64289208	3	2	8	1	0	0	0	0	1	0	0	0	12783	1406	49	2	390	2	PTP4A1	6	64289208	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	17088523	64289208	106825859	32	635										
SIM1	6492	hgsc.bcm.edu	37	chr6	100896042	100896042	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gcaaatggtgcgcgcagcgcAggtggaaggtgtcgcagccg	18	10	0	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr6:100896042A>C	ENST00000369208.3	-	8	1612	c.830T>G	c.(829-831)cTg>cGg	p.L277R	SIM1_ENST00000262901.4_Missense_Mutation_p.L277R			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	277	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		CGCGCAGCGCAGGTGGAAGGT	0.612																																					p.L277R		Atlas-SNP	.											SIM1,NS,lymphoid_neoplasm,0,1	SIM1	173	.	0			c.T830G						.						112	82	92					6																	100896042		2203	4300	6503	SO:0001583	missense	6492	exon7			CAGCGCAGGTGGA	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"Basic helix-loop-helix proteins"	10882	protein-coding gene	gene with protein product		603128	"single-minded (Drosophila) homolog 1", "single-minded homolog 1 (Drosophila)"			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.830T>G	chr6.hg19:g.100896042A>C	ENSP00000358210:p.Leu277Arg	36.0	0.0		48.0	16.0	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	hg19	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.645429	0.67358	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.22539	1.95;1.95	5.29	5.29	0.74685	PAS fold-3 (1);PAS (1);	0.000000	0.85682	D	0.000000	T	0.44582	0.1300	M	0.87381	2.88	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.55623	-0.8112	10	0.87932	D	0	.	15.2644	0.73649	1.0:0.0:0.0:0.0	.	277	P81133	SIM1_HUMAN	R	277	ENSP00000358210:L277R;ENSP00000262901:L277R	ENSP00000262901:L277R	L	-	2	0	SIM1	101002763	1.000000	0.71417	1.000000	0.80357	0.176000	0.22953	8.962000	0.93254	2.003000	0.58678	0.533000	0.62120	CTG	.	.		0.612	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		C	100896042	A	C	100896042	3	2	8	1	0	0	0	0	1	0	0	0	14338	188	7	5	1490	5	SIM1	6	100896042	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	36606834	100896042	70219025	33	636										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102516350	102516350	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	atcaacatgcacacatttaaCgacagaaggttgccaggtaa	8	9	1	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr6:102516350C>T	ENST00000421544.1	+	16	3181	c.2691C>T	c.(2689-2691)aaC>aaT	p.N897N	GRIK2_ENST00000369137.3_Silent_p.N821N|GRIK2_ENST00000413795.1_3'UTR|GRIK2_ENST00000369138.1_3'UTR|GRIK2_ENST00000369134.4_Silent_p.N848N	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	897					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	ACACATTTAACGACAGAAGGT	0.438																																					p.N897N		Atlas-SNP	.											.	GRIK2	487	.	0			c.C2691T						.						92	83	86					6																	102516350		2203	4300	6503	SO:0001819	synonymous_variant	2898	exon16			ATTTAACGACAGA		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2691C>T	chr6.hg19:g.102516350C>T		100.0	0.0		135.0	50.0	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Silent	SNP	ENST00000421544.1	hg19	CCDS5048.1																																																																																			.	.		0.438	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			T	102516350	C	T	102516350	2	4	8	1	0	0	0	0	0	0	0	1	6783	535	19	1		1	GRIK2	6	102516350	Silent	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	1620308	102516350	68598717	34	637										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3046528	3046528	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ttgagtgaaattgccactgcAgggtactaaaagacacaacc	9	9	0	3			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr8:3046528A>G	ENST00000520002.1	-	36	5962	c.5407T>C	c.(5407-5409)Tgc>Cgc	p.C1803R	CSMD1_ENST00000542608.1_Missense_Mutation_p.C1802R|CSMD1_ENST00000602557.1_Missense_Mutation_p.C1803R|CSMD1_ENST00000539096.1_Missense_Mutation_p.C1802R|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602723.1_Missense_Mutation_p.C1803R|CSMD1_ENST00000400186.3_Missense_Mutation_p.C1803R|CSMD1_ENST00000537824.1_Missense_Mutation_p.C1802R			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1803	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TTGCCACTGCAGGGTACTAAA	0.438																																					p.C1802R		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T5404C						.						68	64	65					8																	3046528		1928	4138	6066	SO:0001583	missense	64478	exon35			CACTGCAGGGTAC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.5407T>C	chr8.hg19:g.3046528A>G	ENSP00000430733:p.Cys1803Arg	99.0	0.0		84.0	25.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.31|17.31	3.357530|3.357530	0.61293|0.61293	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096|ENST00000335551	T;T;T;T;T|.	0.66280|.	-0.2;-0.2;-0.2;-0.2;-0.2|.	5.55|5.55	5.55|5.55	0.83447|0.83447	CUB (5);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88676|0.88676	0.6501|0.6501	H|H	0.98199|0.98199	4.17|4.17	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;0.966;1.0|.	D;D;D|.	0.97110|.	0.998;0.976;1.0|.	D|D	0.92872|0.92872	0.6315|0.6315	10|5	0.87932|.	D|.	0|.	.|.	15.7137|15.7137	0.77652|0.77652	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1803;1803;1803|.	E5RIG2;Q96PZ7;Q96PZ7-4|.	.;CSMD1_HUMAN;.|.	R|P	1803;1803;1665;1802;1802;1802|1282	ENSP00000383047:C1803R;ENSP00000430733:C1803R;ENSP00000441462:C1802R;ENSP00000446243:C1802R;ENSP00000441675:C1802R|.	ENSP00000320445:C1665R|.	C|L	-|-	1|2	0|0	CSMD1|CSMD1	3033935|3033935	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.150000|0.150000	0.21749|0.21749	9.050000|9.050000	0.93843|0.93843	2.095000|2.095000	0.63458|0.63458	0.519000|0.519000	0.50382|0.50382	TGC|CTG	.	.		0.438	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	3046528	A	G	3046528	3	3	8	1	0	0	0	0	1	0	0	0	3946	188	7	2	5434	2	CSMD1	8	3046528	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10		3046528	143317494	35	638										
BHLHE22	27319	hgsc.bcm.edu	37	chr8	65494023	65494023	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gcggtagcggcagcggcggcAgcagcagcagcagcagcagc	18	13	0	0	rs62519837		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr8:65494023A>G	ENST00000321870.1	+	1	1210	c.676A>G	c.(676-678)Agc>Ggc	p.S226G	RP11-21C4.1_ENST00000517909.1_RNA	NM_152414.4	NP_689627.1	Q8NFJ8	BHE22_HUMAN	basic helix-loop-helix family, member e22	226	Ser-rich.				anterior commissure morphogenesis (GO:0021960)|cerebral cortex regionalization (GO:0021796)|corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|retinal bipolar neuron differentiation (GO:0060040)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S234delS(1)|p.S226G(1)		NS(1)|central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	5						cagcggcggcagcagcagcag	0.706																																					p.S226G	Colon(113;104 1586 2865 9855 18065)	Atlas-SNP	.											BHLHE22,extremity,malignant_melanoma,0,1	BHLHE22	21	.	2	Substitution - Missense(1)|Deletion - In frame(1)	central_nervous_system(1)|skin(1)	c.A676G						.						3	4	4					8																	65494023		1652	3428	5080	SO:0001583	missense	27319	exon1			GGCGGCAGCAGCA	U80755	CCDS6179.1	8q12.1	2009-01-12	2009-01-12	2009-01-12		ENSG00000180828		"Basic helix-loop-helix proteins"	11963	protein-coding gene	gene with protein product		613483	"trinucleotide repeat containing 20", "basic helix-loop-helix domain containing, class B, 5"	TNRC20, BHLHB5		9225980, 12213201, 18557763	Standard	NM_152414		Approved	CAGL85, Beta3, bHLHe22	uc003xvi.3	Q8NFJ8		ENST00000321870.1:c.676A>G	chr8.hg19:g.65494023A>G	ENSP00000318799:p.Ser226Gly	21.0	2.0		39.0	8.0	NM_152414		Missense_Mutation	SNP	ENST00000321870.1	hg19	CCDS6179.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.714868	0.00005	.	.	ENSG00000180828	ENST00000321870	T	0.80033	-1.33	0.79	-1.26	0.09376	.	.	.	.	.	T	0.48642	0.1511	N	0.00926	-1.1	0.09310	N	1	B	0.26041	0.14	B	0.32805	0.153	T	0.47368	-0.9123	9	0.15499	T	0.54	.	3.5404	0.07809	0.3747:0.0:0.6253:0.0	rs62519837	226	Q8NFJ8	BHE22_HUMAN	G	226	ENSP00000318799:S226G	ENSP00000318799:S226G	S	+	1	0	BHLHE22	65656577	0.273000	0.24181	0.215000	0.23724	0.107000	0.19398	-0.535000	0.06142	-0.333000	0.08476	0.136000	0.15936	AGC	.	G|1.000;|0.000		0.706	BHLHE22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378549.1	NM_152414		G	65494023	A	G	65494023	3	3	8	1	0	0	0	0	1	0	0	0	1421	188	7	2	678	2	BHLHE22	8	65494023	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	62447495	65494023	80869999	36	639										
TIGD5	84948	hgsc.bcm.edu	37	chr8	144680335	144680335	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tcggcgtgccgggcgggacgCtgcgcggctggctcaaggac	19	13	1	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr8:144680335C>A	ENST00000504548.2	+	1	262	c.262C>A	c.(262-264)Ctg>Atg	p.L88M	EEF1D_ENST00000532400.1_5'Flank|EEF1D_ENST00000526838.1_5'Flank|EEF1D_ENST00000395119.3_5'Flank|EEF1D_ENST00000529272.1_5'Flank|EEF1D_ENST00000531770.1_5'Flank|EEF1D_ENST00000317198.6_5'Flank|EEF1D_ENST00000524624.1_5'Flank|EEF1D_ENST00000423316.2_5'Flank|EEF1D_ENST00000419152.2_5'Flank|EEF1D_ENST00000442189.2_5'Flank|TIGD5_ENST00000321385.3_Missense_Mutation_p.L39M|EEF1D_ENST00000531621.1_5'Flank|EEF1D_ENST00000528610.1_5'Flank	NM_032862.4	NP_116251.4	Q53EQ6	TIGD5_HUMAN	tigger transposable element derived 5	88	HTH psq-type. {ECO:0000255|PROSITE- ProRule:PRU00320}.					nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	7	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			GGGCGGGACGCTGCGCGGCTG	0.692																																					p.L88M		Atlas-SNP	.											.	TIGD5	22	.	0			c.C262A						.						13	13	13					8																	144680335		2168	4268	6436	SO:0001583	missense	84948	exon1			GGGACGCTGCGCG	AK027832	CCDS6406.1, CCDS6406.2	8q24.3	2008-02-01				ENSG00000179886			18336	protein-coding gene	gene with protein product							Standard	NM_032862		Approved	FLJ14926	uc003yyx.2	Q53EQ6		ENST00000504548.2:c.262C>A	chr8.hg19:g.144680335C>A	ENSP00000421489:p.Leu88Met	83.0	0.0		179.0	58.0	NM_032862	E7EWS2|Q6NT83|Q8N5A1|Q96JW8	Missense_Mutation	SNP	ENST00000504548.2	hg19	CCDS6406.2	.	.	.	.	.	.	.	.	.	.	c	15.64	2.891855	0.52014	.	.	ENSG00000179886	ENST00000504548;ENST00000321385	T;T	0.58060	0.36;0.36	4.31	4.31	0.51392	Homeodomain-related (1);Homeodomain-like (1);Helix-turn-helix, Psq-like (1);Centromere protein Cenp-B, DNA-binding domain 1 (1);	0.000000	0.37095	U	0.002254	T	0.67458	0.2895	L	0.52905	1.665	0.21841	N	0.999513	D	0.89917	1.0	D	0.75484	0.986	T	0.61481	-0.7054	10	0.54805	T	0.06	.	15.7972	0.78420	0.0:1.0:0.0:0.0	.	39	Q53EQ6	TIGD5_HUMAN	M	88;39	ENSP00000421489:L88M;ENSP00000315906:L39M	ENSP00000315906:L39M	L	+	1	2	TIGD5	144751478	0.961000	0.32948	1.000000	0.80357	0.522000	0.34438	1.196000	0.32198	1.934000	0.56057	0.165000	0.16767	CTG	.	.		0.692	TIGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368269.1	NM_032862		A	144680335	C	A	144680335	3	1	8	1	0	0	0	0	1	0	0	0	15914	796	28	3	264	3	TIGD5	8	144680335	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	79186312	144680335	1683687	37	640										
FAM83H	286077	hgsc.bcm.edu	37	chr8	144810307	144810307	+	Frame_Shift_Del	DEL	G	G	-													0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gaagtggctggtctggaagcGgaagtcgtcgccgtggctga							TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr8:144810307delG	ENST00000388913.3	-	5	1449	c.1324delC	c.(1324-1326)cgcfs	p.R442fs		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	442					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GTCTGGAAGCGGAAGTCGTCG	0.701																																					p.R442fs		Atlas-Indel,Pindel	.											.	FAM83H	68	.	0			c.1325delG						.						25	38	34					8																	144810307		2137	4225	6362	SO:0001589	frameshift_variant	286077	exon5			.	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.1324delC	chr8.hg19:g.144810307delG	ENSP00000373565:p.Arg442fs	930.0	0.0		1503.0	327.0	NM_198488	A0JLS2|Q8N4W0	Frame_Shift_Del	DEL	ENST00000388913.3	hg19	CCDS6410.2																																																																																			.	.		0.701	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		-	144810307	G	-	144810307	7	5	8	1	0	1	0	1	0	0	0	0	5648	1116	39	0	2219	0	FAM83H	8	144810307	Frame_Shift_Del	DEL	G	TCGA-2Y-A9GY-01A-11D-A382-10	129972	144810307	1553715	38	641										
SLC35D2	11046	hgsc.bcm.edu	37	chr9	99113414	99113414	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	atgaaagccccgagaataatGgcaaagacactgaggatgat	11	7	0	5			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr9:99113414G>A	ENST00000253270.7	-	6	521	c.459C>T	c.(457-459)gcC>gcT	p.A153A	SLC35D2_ENST00000375257.1_Silent_p.A153A|SLC35D2_ENST00000375259.4_Silent_p.A153A|SLC35D2_ENST00000482643.1_5'UTR	NM_007001.2	NP_008932.2	Q76EJ3	S35D2_HUMAN	solute carrier family 35 (UDP-GlcNAc/UDP-glucose transporter), member D2	153					carbohydrate derivative transport (GO:1901264)|carbohydrate metabolic process (GO:0005975)|carbohydrate transport (GO:0008643)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)			endometrium(3)|large_intestine(3)|lung(4)|skin(2)	12		Acute lymphoblastic leukemia(62;0.0167)				CGAGAATAATGGCAAAGACAC	0.413																																					p.A153A		Atlas-SNP	.											.	SLC35D2	20	.	0			c.C459T						.						138	124	129					9																	99113414		2203	4300	6503	SO:0001819	synonymous_variant	11046	exon6			AATAATGGCAAAG	AB122077	CCDS6717.1, CCDS69625.1	9q22.33	2013-07-17	2013-07-17		ENSG00000130958	ENSG00000130958		"Solute carriers"	20799	protein-coding gene	gene with protein product		609182	"solute carrier family 35, member D2"			15607426	Standard	NM_007001		Approved	UGTrel8, SQV7L	uc004awc.3	Q76EJ3	OTTHUMG00000020293	ENST00000253270.7:c.459C>T	chr9.hg19:g.99113414G>A		124.0	0.0		164.0	54.0	NM_007001	O95454|Q498C1|Q75W21|Q7Z5X5	Silent	SNP	ENST00000253270.7	hg19	CCDS6717.1																																																																																			.	.		0.413	SLC35D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053261.1			A	99113414	G	A	99113414	2	1	8	1	0	0	0	0	0	0	0	1	14597	1335	47	3		3	SLC35D2	9	99113414	Silent	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10		99113414	42100017	39	642										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113261434	113261434	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ggcaacttacatagcagatcGtcccaaatttggctggctgc	10	11	0	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr9:113261434G>A	ENST00000401783.2	-	7	1904	c.1568C>T	c.(1567-1569)aCg>aTg	p.T523M	SVEP1_ENST00000302728.8_Missense_Mutation_p.T523M|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.T500M|SVEP1_ENST00000374461.1_Missense_Mutation_p.T500M	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	523	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						ATAGCAGATCGTCCCAAATTT	0.483																																					p.T523M		Atlas-SNP	.											.	SVEP1	326	.	0			c.C1568T						.						61	60	60					9																	113261434		2006	4181	6187	SO:0001583	missense	79987	exon7			CAGATCGTCCCAA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.1568C>T	chr9.hg19:g.113261434G>A	ENSP00000384917:p.Thr523Met	92.0	0.0		116.0	46.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	1.137	-0.650572	0.03506	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.91	-1.35	0.09114	Complement control module (2);Sushi/SCR/CCP (2);	0.460626	0.25433	N	0.030719	T	0.20901	0.0503	N	0.11201	0.11	0.09310	N	1	B;B;B	0.22003	0.041;0.007;0.063	B;B;B	0.18263	0.004;0.004;0.021	T	0.15122	-1.0448	10	0.20519	T	0.43	.	6.3811	0.21536	0.485:0.0:0.3963:0.1187	.	523;523;523	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	M	523;500;523;500	ENSP00000384917:T523M;ENSP00000363593:T500M;ENSP00000304118:T523M;ENSP00000363585:T500M	ENSP00000304118:T523M	T	-	2	0	SVEP1	112301255	0.001000	0.12720	0.002000	0.10522	0.013000	0.08279	0.015000	0.13355	-0.577000	0.05967	-0.794000	0.03295	ACG	.	.		0.483	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113261434	G	A	113261434	3	1	8	1	0	0	0	0	1	0	0	0	15435	1145	40	1	9315	1	SVEP1	9	113261434	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	14148020	113261434	27951997	40	643										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26446318	26446318	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	catcaaaccaaatagtgagcGtcaggcaagaaaatatgaca	8	8	2	3			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr10:26446318G>C	ENST00000265944.5	+	26	3039	c.2873G>C	c.(2872-2874)cGt>cCt	p.R958P	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	958	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R958H(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AATAGTGAGCGTCAGGCAAGA	0.408																																					p.R958P		Atlas-SNP	.											MYO3A,caecum,carcinoma,0,2	MYO3A	371	.	1	Substitution - Missense(1)	breast(1)	c.G2873C						.						139	131	133					10																	26446318		2203	4300	6503	SO:0001583	missense	53904	exon26			GTGAGCGTCAGGC	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2873G>C	chr10.hg19:g.26446318G>C	ENSP00000265944:p.Arg958Pro	118.0	0.0		136.0	17.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.934020	0.92458	.	.	ENSG00000095777	ENST00000265944	D	0.87650	-2.28	5.31	5.31	0.75309	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.94361	0.8187	M	0.85299	2.745	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94745	0.7922	10	0.72032	D	0.01	.	19.3468	0.94367	0.0:0.0:1.0:0.0	.	958	Q8NEV4	MYO3A_HUMAN	P	958	ENSP00000265944:R958P	ENSP00000265944:R958P	R	+	2	0	MYO3A	26486324	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.809000	0.99208	2.640000	0.89533	0.655000	0.94253	CGT	.	.		0.408	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		C	26446318	G	C	26446318	3	2	8	1	0	0	0	0	1	0	0	0	10085	1145	40	4	2967	4	MYO3A	10	26446318	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10		26446318	109088429	41	644										
KIAA1462	57608	hgsc.bcm.edu	37	chr10	30318601	30318601	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tcttcatcacatgctctgacCttcctccaacttcccatgga	4	16	4	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr10:30318601C>T	ENST00000375377.1	-	3	577	c.476G>A	c.(475-477)aGg>aAg	p.R159K		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	159					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						ATGCTCTGACCTTCCTCCAAC	0.572																																					p.R159K		Atlas-SNP	.											.	KIAA1462	162	.	0			c.G476A						.						288	284	286					10																	30318601		2092	4224	6316	SO:0001583	missense	57608	exon3			TCTGACCTTCCTC	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"junctional protein associated with coronary artery disease"	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.476G>A	chr10.hg19:g.30318601C>T	ENSP00000364526:p.Arg159Lys	82.0	0.0		104.0	15.0	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	hg19	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	C	19.11	3.764313	0.69878	.	.	ENSG00000165757	ENST00000375377	T	0.15372	2.43	5.55	5.55	0.83447	.	0.211473	0.42964	D	0.000625	T	0.34803	0.0910	M	0.67953	2.075	0.09310	N	1	D	0.60575	0.988	P	0.57911	0.829	T	0.14144	-1.0483	10	0.41790	T	0.15	-34.187	15.0318	0.71713	0.0:0.8582:0.1418:0.0	.	159	Q9P266	K1462_HUMAN	K	159	ENSP00000364526:R159K	ENSP00000364526:R159K	R	-	2	0	KIAA1462	30358607	0.674000	0.27549	0.969000	0.41365	0.772000	0.43724	2.423000	0.44705	2.610000	0.88304	0.655000	0.94253	AGG	.	.		0.572	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		T	30318601	C	T	30318601	3	4	8	1	0	0	0	0	1	0	0	0	8243	681	24	3	3611	3	KIAA1462	10	30318601	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	3872283	30318601	105216146	42	645										
CYP2E1	1571	hgsc.bcm.edu	37	chr10	135340964	135340964	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	cttcctcctgctggtgtccaTgtggaggcaggtgcacagca	13	12	0	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr10:135340964T>C	ENST00000463117.2	+	3	337	c.65T>C	c.(64-66)aTg>aCg	p.M22T	SPRN_ENST00000541506.1_Intron|CYP2E1_ENST00000252945.3_Missense_Mutation_p.M22T			P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E, polypeptide 1	22					drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organonitrogen compound (GO:0010243)|response to ozone (GO:0010193)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|triglyceride metabolic process (GO:0006641)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(7)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Aldesleukin(DB00041)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminophylline(DB01223)|Amitriptyline(DB00321)|Antipyrine(DB01435)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupropion(DB01156)|Caffeine(DB00201)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Citalopram(DB00215)|Clevidipine(DB04920)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonazepam(DB01068)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Dacarbazine(DB00851)|Dalfampridine(DB06637)|Dapsone(DB00250)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Disulfiram(DB00822)|Econazole(DB01127)|Enflurane(DB00228)|Enfuvirtide(DB00109)|Estrone(DB00655)|Ethanol(DB00898)|Ethanolamine Oleate(DB06689)|Ethosuximide(DB00593)|Etoposide(DB00773)|Etoricoxib(DB01628)|Felbamate(DB00949)|Fingolimod(DB08868)|Flunitrazepam(DB01544)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluvoxamine(DB00176)|Folic Acid(DB00158)|Fomepizole(DB01213)|Glucosamine(DB01296)|Halothane(DB01159)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imipramine(DB00458)|Isoflurane(DB00753)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Itraconazole(DB01167)|Menadione(DB00170)|Meprobamate(DB00371)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Mexiletine(DB00379)|Miconazole(DB01110)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nitrazepam(DB01595)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Orphenadrine(DB01173)|Oxaliplatin(DB00526)|Paramethadione(DB00617)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Pimozide(DB01100)|Proguanil(DB01131)|Propofol(DB00818)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rufinamide(DB06201)|S-Adenosylmethionine(DB00118)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulfadiazine(DB00359)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiopental(DB00599)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Ursodeoxycholic acid(DB01586)|Zafirlukast(DB00549)|Zopiclone(DB01198)	CTGGTGTCCATGTGGAGGCAG	0.632									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.M22T		Atlas-SNP	.											.	CYP2E1	69	.	0			c.T65C						.						57	57	57					10																	135340964		2203	4300	6503	SO:0001583	missense	1571	exon1	Familial Cancer Database	incl.: Familial Head and Neck Cancer	TGTCCATGTGGAG	J02843	CCDS7686.1	10q26.3	2013-05-03	2003-01-14	2002-09-13	ENSG00000130649	ENSG00000130649		"Cytochrome P450s"	2631	protein-coding gene	gene with protein product		124040	"cytochrome P450, subfamily IIE (ethanol-inducible), polypeptide 1"	CYP2E			Standard	NM_000773		Approved		uc001lnj.1	P05181	OTTHUMG00000019322	ENST00000463117.2:c.65T>C	chr10.hg19:g.135340964T>C	ENSP00000440689:p.Met22Thr	57.0	0.0		77.0	17.0	NM_000773	Q5VZD5|Q6NWT9|Q9UK47	Missense_Mutation	SNP	ENST00000463117.2	hg19	CCDS7686.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.554352	0.27739	.	.	ENSG00000130649	ENST00000463117;ENST00000541261;ENST00000252945	T;T;T	0.67345	-0.26;1.98;-0.26	4.86	3.73	0.42828	.	1.055870	0.07266	N	0.868308	T	0.43787	0.1263	N	0.08118	0	0.18873	N	0.999981	B	0.09022	0.002	B	0.09377	0.004	T	0.31138	-0.9954	10	0.25751	T	0.34	.	4.3703	0.11244	0.1734:0.093:0.0:0.7336	.	22	P05181	CP2E1_HUMAN	T	22	ENSP00000440689:M22T;ENSP00000437799:M22T;ENSP00000252945:M22T	ENSP00000252945:M22T	M	+	2	0	CYP2E1	135190954	0.278000	0.24230	0.711000	0.30485	0.843000	0.47879	1.738000	0.38207	0.990000	0.38787	0.460000	0.39030	ATG	.	.		0.632	CYP2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051161.2	NM_000773		C	135340964	T	C	135340964	3	2	8	1	0	0	0	0	1	0	0	0	4172	1464	51	2	67	2	CYP2E1	10	135340964	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	105022363	135340964	193783	43	646										
GALNTL4	374378	hgsc.bcm.edu	37	chr11	11394087	11394087	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tcccaagctccacattctcgCccccgtagacttccatgcct	5	19	1	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr11:11394087C>A	ENST00000227756.4	-	6	1478	c.1067G>T	c.(1066-1068)gGc>gTc	p.G356V		NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	356	Catalytic subdomain B.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										CACATTCTCGCCCCCGTAGAC	0.597																																					p.G356V		Atlas-SNP	.											.	.	.	.	0			c.G1067T						.						99	79	86					11																	11394087		2201	4294	6495	SO:0001583	missense	374378	exon6			TTCTCGCCCCCGT	AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"Glycosyltransferase family 2 domain containing"	30488	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 18"	615136	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.1067G>T	chr11.hg19:g.11394087C>A	ENSP00000227756:p.Gly356Val	57.0	0.0		81.0	11.0	NM_198516	O95903|Q8NDY9	Missense_Mutation	SNP	ENST00000227756.4	hg19	CCDS7807.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.688022	0.88639	.	.	ENSG00000110328	ENST00000227756	T	0.67865	-0.29	6.0	6.0	0.97389	.	0.063492	0.64402	N	0.000008	D	0.85919	0.5809	M	0.90369	3.11	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87396	0.2366	10	0.66056	D	0.02	.	19.1107	0.93315	0.0:1.0:0.0:0.0	.	356	Q6P9A2	GLTL4_HUMAN	V	356	ENSP00000227756:G356V	ENSP00000227756:G356V	G	-	2	0	GALNTL4	11350663	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	7.818000	0.86416	2.850000	0.98022	0.650000	0.86243	GGC	.	.		0.597	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516		A	11394087	C	A	11394087	3	1	8	1	0	0	0	0	1	0	0	0	6231	739	26	3	780	3	GALNTL4	11	11394087	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10		11394087	123612429	44	647										
OR5W2	390148	hgsc.bcm.edu	37	chr11	55681443	55681443	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tgaaatggtactcagttcaaTaaaaccaaagacggtgaata	8	6	2	3			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr11:55681443T>C	ENST00000344514.1	-	1	615	c.616A>G	c.(616-618)Att>Gtt	p.I206V		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	206						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CTCAGTTCAATAAAACCAAAG	0.388																																					p.I206V	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.A616G						.						58	61	60					11																	55681443		2201	4296	6497	SO:0001583	missense	390148	exon1			GTTCAATAAAACC	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"GPCR / Class A : Olfactory receptors"	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.616A>G	chr11.hg19:g.55681443T>C	ENSP00000342448:p.Ile206Val	120.0	0.0		125.0	33.0	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	hg19	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	T	8.977	0.974421	0.18736	.	.	ENSG00000187612	ENST00000344514	T	0.00044	8.83	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41097	D	0.000959	T	0.00073	0.0002	N	0.12746	0.255	0.24431	N	0.994572	B	0.12013	0.005	B	0.20577	0.03	T	0.19582	-1.0301	10	0.02654	T	1	.	12.6626	0.56822	0.0:0.0:0.0:1.0	.	206	Q8NH69	OR5W2_HUMAN	V	206	ENSP00000342448:I206V	ENSP00000342448:I206V	I	-	1	0	OR5W2	55438019	0.000000	0.05858	0.879000	0.34478	0.601000	0.36947	0.255000	0.18333	1.870000	0.54199	0.443000	0.29094	ATT	.	.		0.388	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		C	55681443	T	C	55681443	3	2	8	1	0	0	0	0	1	0	0	0	11194	1406	49	2	318	2	OR5W2	11	55681443	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	44287356	55681443	79325073	45	648										
OR5I1	10798	hgsc.bcm.edu	37	chr11	55703115	55703115	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	taaataaagaggagagtcccTtggtagatcgtcactgaagt	11	6	1	4			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr11:55703115T>A	ENST00000301532.3	-	1	761	c.762A>T	c.(760-762)caA>caT	p.Q254H		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	254					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GGAGAGTCCCTTGGTAGATCG	0.433																																					p.Q254H		Atlas-SNP	.											.	OR5I1	110	.	0			c.A762T						.						74	73	73					11																	55703115		2201	4296	6497	SO:0001583	missense	10798	exon1			AGTCCCTTGGTAG	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"GPCR / Class A : Olfactory receptors"	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.762A>T	chr11.hg19:g.55703115T>A	ENSP00000301532:p.Gln254His	97.0	0.0		104.0	31.0	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	hg19	CCDS7949.1	.	.	.	.	.	.	.	.	.	.	T	7.091	0.572151	0.13623	.	.	ENSG00000167825	ENST00000301532	T	0.36699	1.24	5.16	2.02	0.26589	GPCR, rhodopsin-like superfamily (1);	0.155531	0.30374	N	0.009764	T	0.20618	0.0496	N	0.00690	-1.25	0.30772	N	0.74296	D	0.71674	0.998	D	0.83275	0.996	T	0.10109	-1.0644	10	0.31617	T	0.26	.	4.2144	0.10528	0.2718:0.5533:0.0:0.1749	.	254	Q13606	OR5I1_HUMAN	H	254	ENSP00000301532:Q254H	ENSP00000301532:Q254H	Q	-	3	2	OR5I1	55459691	0.000000	0.05858	0.779000	0.31741	0.032000	0.12392	-0.356000	0.07661	0.646000	0.30693	-0.925000	0.02716	CAA	.	.		0.433	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637		A	55703115	T	A	55703115	3	1	8	1	0	0	0	0	1	0	0	0	11173	1606	56	4	185	4	OR5I1	11	55703115	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	21672	55703115	79303401	46	649										
TCN1	6947	hgsc.bcm.edu	37	chr11	59623355	59623355	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	cttatacctgaagcagagacGcaagaagagtctttgttaat	9	7	1	4	rs146250932	byFrequency	TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr11:59623355G>T	ENST00000257264.3	-	6	1028	c.924C>A	c.(922-924)tgC>tgA	p.C308*	TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	308	Globular N-terminal alpha domain.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AAGCAGAGACGCAAGAAGAGT	0.443																																					p.C308X		Atlas-SNP	.											TCN1,bladder,carcinoma,0,1	TCN1	64	.	0			c.C924A						.						113	112	113					11																	59623355		2201	4295	6496	SO:0001587	stop_gained	6947	exon6			AGAGACGCAAGAA	J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"haptocorin", "haptocorrin"	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.924C>A	chr11.hg19:g.59623355G>T	ENSP00000257264:p.Cys308*	70.0	0.0		88.0	19.0	NM_001062	A8KAC5|Q8WV77	Nonsense_Mutation	SNP	ENST00000257264.3	hg19	CCDS7978.1	.	.	.	.	.	.	.	.	.	.	g	18.95	3.732387	0.69189	.	.	ENSG00000134827	ENST00000257264	.	.	.	4.83	2.35	0.29111	.	0.519912	0.16168	N	0.226457	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.7723	0.18259	0.7819:0.0:0.2181:0.0	.	.	.	.	X	308	.	ENSP00000257264:C308X	C	-	3	2	TCN1	59379931	0.005000	0.15991	0.369000	0.25952	0.289000	0.27227	-0.253000	0.08794	0.683000	0.31428	-0.451000	0.05528	TGC	.	G|0.999;A|0.001		0.443	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062		T	59623355	G	T	59623355	4	4	8	1	0	0	0	0	0	1	0	0	15721	1079	38	1	393	1	TCN1	11	59623355	Nonsense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	3920240	59623355	75383161	47	650										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62296756	62296756	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ggcattttcatcttgggcatTttcaggtgccaatctgggtc	11	9	4	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr11:62296756T>C	ENST00000378024.4	-	5	5407	c.5133A>G	c.(5131-5133)aaA>aaG	p.K1711K	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1711					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TCTTGGGCATTTTCAGGTGCC	0.483																																					p.K1711K		Atlas-SNP	.											.	AHNAK	532	.	0			c.A5133G						.						219	225	223					11																	62296756		2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			GGGCATTTTCAGG	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.5133A>G	chr11.hg19:g.62296756T>C		109.0	0.0		99.0	4.0	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.483	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62296756	T	C	62296756	2	2	8	1	0	0	0	0	0	0	0	1	414	1838	64	2		2	AHNAK	11	62296756	Silent	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	2673401	62296756	72709760	48	651										
ZC3H12C	85463	hgsc.bcm.edu	37	chr11	110035069	110035069	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	aattttactcttcttaggaaAgaagtgtacctatggacaca	7	7	2	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr11:110035069A>G	ENST00000278590.3	+	6	1310	c.1259A>G	c.(1258-1260)aAg>aGg	p.K420R	ZC3H12C_ENST00000453089.2_Missense_Mutation_p.K389R|ZC3H12C_ENST00000528673.1_Missense_Mutation_p.K421R	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	420							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		TTCTTAGGAAAGAAGTGTACC	0.428																																					p.K420R		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.A1259G						.						28	27	27					11																	110035069		1900	4117	6017	SO:0001583	missense	85463	exon6			TAGGAAAGAAGTG		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1259A>G	chr11.hg19:g.110035069A>G	ENSP00000278590:p.Lys420Arg	50.0	0.0		55.0	13.0	NM_033390	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	hg19	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.182575	0.57800	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.46819	0.86;0.86;0.86	5.76	5.76	0.90799	Zinc finger, CCCH-type (1);	0.000000	0.85682	D	0.000000	T	0.61286	0.2335	L	0.42245	1.32	0.53688	D	0.999973	P;D;P	0.76494	0.615;0.999;0.615	B;D;B	0.80764	0.219;0.994;0.219	T	0.59016	-0.7533	10	0.38643	T	0.18	-27.7098	16.0668	0.80887	1.0:0.0:0.0:0.0	.	421;420;420	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	R	420;421;389	ENSP00000278590:K420R;ENSP00000431821:K421R;ENSP00000413094:K389R	ENSP00000278590:K420R	K	+	2	0	ZC3H12C	109540279	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.576000	0.82467	2.192000	0.70111	0.459000	0.35465	AAG	.	.		0.428	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		G	110035069	A	G	110035069	3	3	8	1	0	0	0	0	1	0	0	0	17578	72	3	2	1281	2	ZC3H12C	11	110035069	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	47738313	110035069	24971447	49	652										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133790637	133790637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	caggggcggggacgacatgaCggagctcagggggctgccca	19	11	1	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr11:133790637C>T	ENST00000321016.8	-	18	3213	c.2983G>A	c.(2983-2985)Gtc>Atc	p.V995I	IGSF9B_ENST00000533871.2_Missense_Mutation_p.V995I			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	995	Pro-rich.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GACGACATGACGGAGCTCAGG	0.657																																					p.V995I		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G2983A						.						28	32	30					11																	133790637		2028	4170	6198	SO:0001583	missense	22997	exon18			ACATGACGGAGCT	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.2983G>A	chr11.hg19:g.133790637C>T	ENSP00000317980:p.Val995Ile	79.0	0.0		61.0	15.0	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	c	14.16	2.453566	0.43531	.	.	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.68624	-0.02;-0.34	4.93	4.0	0.46444	.	0.184196	0.26166	N	0.025944	T	0.48447	0.1500	N	0.24115	0.695	0.26237	N	0.978926	P	0.34587	0.458	B	0.20184	0.028	T	0.39781	-0.9597	10	0.44086	T	0.13	.	14.0103	0.64493	0.1527:0.8473:0.0:0.0	.	995	Q9UPX0	TUTLB_HUMAN	I	995;837	ENSP00000317980:V995I;ENSP00000436552:V837I	ENSP00000317980:V995I	V	-	1	0	IGSF9B	133295847	1.000000	0.71417	0.367000	0.25926	0.647000	0.38526	5.682000	0.68182	1.031000	0.39867	0.550000	0.68814	GTC	.	.		0.657	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		T	133790637	C	T	133790637	3	4	8	1	0	0	0	0	1	0	0	0	7615	536	19	1	1074	1	IGSF9B	11	133790637	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	23755568	133790637	1215879	50	653										
CHD4	1108	hgsc.bcm.edu	37	chr12	6682294	6682294	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tgccattgactccttggacaGgtgctgatgactttccgcca	10	12	0	3			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr12:6682294G>A	ENST00000357008.2	-	38	5666	c.5503C>T	c.(5503-5505)Ctg>Ttg	p.L1835L	CHD4_ENST00000309577.6_Silent_p.L1863L|CHD4_ENST00000544040.1_Silent_p.L1828L|CHD4_ENST00000544484.1_Silent_p.L1860L	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1835	Required for interaction with PCNT.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						TCCTTGGACAGGTGCTGATGA	0.567																																					p.L1835L	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.C5503T						.						149	125	133					12																	6682294		2203	4300	6503	SO:0001819	synonymous_variant	1108	exon38			TGGACAGGTGCTG	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.5503C>T	chr12.hg19:g.6682294G>A		73.0	0.0		130.0	20.0	NM_001273	Q8IXZ5	Silent	SNP	ENST00000357008.2	hg19	CCDS8552.1																																																																																			.	.		0.567	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6682294	G	A	6682294	2	1	8	1	0	0	0	0	0	0	0	1	3329	991	35	3		3	CHD4	12	6682294	Silent	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10		6682294	127169601	51	654										
NECAP1	25977	hgsc.bcm.edu	37	chr12	8245601	8245601	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ctcagttgccatcagcaatcAtgtcaccccaccacccattc	4	18	4	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr12:8245601A>G	ENST00000339754.5	+	6	704	c.626A>G	c.(625-627)cAt>cGt	p.H209R		NM_015509.3	NP_056324.2	Q8NC96	NECP1_HUMAN	NECAP endocytosis associated 1	209					endocytosis (GO:0006897)|protein transport (GO:0015031)	clathrin vesicle coat (GO:0030125)|coated pit (GO:0005905)|plasma membrane (GO:0005886)				cervix(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				Kidney(36;0.0915)		ATCAGCAATCATGTCACCCCA	0.493																																					p.H209R		Atlas-SNP	.											.	NECAP1	21	.	0			c.A626G						.						194	178	183					12																	8245601		2203	4300	6503	SO:0001583	missense	25977	exon6			GCAATCATGTCAC	AK074923	CCDS8589.1	12p13.31	2012-05-02			ENSG00000089818	ENSG00000089818			24539	protein-coding gene	gene with protein product		611623				14555962, 15494011	Standard	NM_015509		Approved	DKFZP566B183	uc001qtx.2	Q8NC96	OTTHUMG00000168568	ENST00000339754.5:c.626A>G	chr12.hg19:g.8245601A>G	ENSP00000341737:p.His209Arg	98.0	0.0		128.0	63.0	NM_015509	Q2NL73|Q5XG95|Q6NWY6|Q8N153|Q8NCB0|Q9BU52|Q9Y407	Missense_Mutation	SNP	ENST00000339754.5	hg19	CCDS8589.1	.	.	.	.	.	.	.	.	.	.	A	10.87	1.473367	0.26423	.	.	ENSG00000089818	ENST00000545179;ENST00000339754;ENST00000540291;ENST00000540083	T;T	0.30448	1.57;1.53	4.63	4.63	0.57726	.	0.234273	0.44285	D	0.000480	T	0.19565	0.0470	L	0.36672	1.1	0.49915	D	0.999831	P	0.43701	0.815	B	0.35931	0.214	T	0.03695	-1.1012	10	0.15952	T	0.53	.	10.6245	0.45500	1.0:0.0:0.0:0.0	.	209	Q8NC96	NECP1_HUMAN	R	209;209;67;67	ENSP00000341737:H209R;ENSP00000439319:H67R	ENSP00000341737:H209R	H	+	2	0	NECAP1	8136868	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	5.504000	0.66968	2.077000	0.62373	0.533000	0.62120	CAT	.	.		0.493	NECAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400244.1	NM_015509		G	8245601	A	G	8245601	3	3	8	1	0	0	0	0	1	0	0	0	10316	217	8	2	648	2	NECAP1	12	8245601	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10	1563307	8245601	125606294	52	655										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80746176	80746176	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tatgtggctctgtgcaacaaGtttgatatctgtattcagtg	10	6	3	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr12:80746176G>C	ENST00000547103.1	+	44	5310	c.5304G>C	c.(5302-5304)aaG>aaC	p.K1768N	OTOGL_ENST00000458043.2_Missense_Mutation_p.K1780N			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1768					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TGTGCAACAAGTTTGATATCT	0.343																																					p.K1780N		Atlas-SNP	.											.	OTOGL	235	.	0			c.G5340C						.						127	119	121					12																	80746176		1889	4113	6002	SO:0001583	missense	283310	exon44			CAACAAGTTTGAT	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5304G>C	chr12.hg19:g.80746176G>C	ENSP00000447211:p.Lys1768Asn	63.0	0.0		72.0	6.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.82|12.82	2.051617|2.051617	0.36181|0.36181	.|.	.|.	ENSG00000165899|ENSG00000165899	ENST00000547103;ENST00000458043|ENST00000298820	D;D|.	0.85861|.	-2.04;-2.04|.	6.04|6.04	-1.12|-1.12	0.09808|0.09808	.|.	.|.	.|.	.|.	.|.	T|T	0.38506|0.38506	0.1043|0.1043	L|L	0.55743|0.55743	1.74|1.74	0.26376|0.26376	N|N	0.976818|0.976818	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.37776|0.37776	-0.9691|-0.9691	7|5	0.46703|.	T|.	0.11|.	.|.	5.5859|5.5859	0.17274|0.17274	0.3311:0.0:0.4557:0.2132|0.3311:0.0:0.4557:0.2132	.|.	.|.	.|.	.|.	N|T	1768;1780|223	ENSP00000447211:K1768N;ENSP00000400895:K1780N|.	ENSP00000400895:K1780N|.	K|S	+|+	3|2	2|0	OTOGL|OTOGL	79270307|79270307	0.923000|0.923000	0.31300|0.31300	0.995000|0.995000	0.50966|0.50966	0.833000|0.833000	0.47200|0.47200	0.045000|0.045000	0.14013|0.14013	-0.086000|-0.086000	0.12550|0.12550	-0.222000|-0.222000	0.12452|0.12452	AAG|AGT	.	.		0.343	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		C	80746176	G	C	80746176	3	2	8	1	0	0	0	0	1	0	0	0	1709	1020	36	4	5514	4	C12orf64	12	80746176	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	72500575	80746176	53105719	53	656										
PAH	5053	hgsc.bcm.edu	37	chr12	103249042	103249042	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ttttatacaaggacttcagaGtcttgaacactgtgccccat	7	10	2	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr12:103249042G>A	ENST00000553106.1	-	6	1050	c.578C>T	c.(577-579)aCt>aTt	p.T193I	PAH_ENST00000307000.2_Missense_Mutation_p.T188I|PAH_ENST00000551988.1_5'Flank	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	193					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GGACTTCAGAGTCTTGAACAC	0.433																																					p.T193I		Atlas-SNP	.											.	PAH	77	.	0			c.C578T						.						130	122	124					12																	103249042		2203	4300	6503	SO:0001583	missense	5053	exon6			TTCAGAGTCTTGA	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"phenylalanine 4-monooxygenase"	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.578C>T	chr12.hg19:g.103249042G>A	ENSP00000448059:p.Thr193Ile	65.0	0.0		90.0	47.0	NM_000277	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	hg19	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.046551	0.36085	.	.	ENSG00000171759	ENST00000553106;ENST00000307000	D;D	0.99541	-6.12;-6.12	5.87	4.97	0.65823	Aromatic amino acid hydroxylase, C-terminal (3);	0.098161	0.64402	D	0.000003	D	0.98479	0.9493	N	0.25957	0.775	0.38386	D	0.945266	P;P	0.46512	0.879;0.562	P;B	0.48368	0.575;0.382	D	0.99854	1.1075	10	0.39692	T	0.17	-14.4771	13.2417	0.59999	0.0:0.0:0.5667:0.4333	.	193;193	B4DPN2;P00439	.;PH4H_HUMAN	I	193;188	ENSP00000448059:T193I;ENSP00000303500:T188I	ENSP00000303500:T188I	T	-	2	0	PAH	101773172	1.000000	0.71417	0.997000	0.53966	0.003000	0.03518	5.819000	0.69243	1.460000	0.47911	0.650000	0.86243	ACT	.	.		0.433	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			A	103249042	G	A	103249042	3	1	8	1	0	0	0	0	1	0	0	0	11403	1029	36	3	812	3	PAH	12	103249042	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	22502866	103249042	30602853	54	657										
STOML3	161003	hgsc.bcm.edu	37	chr13	39542580	39542580	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	cctcagcctcggctgccatgGatctctgcaactgcacggga	11	15	2	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr13:39542580G>C	ENST00000379631.4	-	6	952	c.608C>G	c.(607-609)tCc>tGc	p.S203C	STOML3_ENST00000423210.1_Missense_Mutation_p.S194C	NM_145286.2	NP_660329.1	Q8TAV4	STML3_HUMAN	stomatin (EPB72)-like 3	203					signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	11		Lung NSC(96;1.42e-05)|Prostate(109;0.00851)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;2.93e-08)|Epithelial(112;3.64e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00107)|BRCA - Breast invasive adenocarcinoma(63;0.00349)|GBM - Glioblastoma multiforme(144;0.0137)		GGCTGCCATGGATCTCTGCAA	0.557																																					p.S203C		Atlas-SNP	.											.	STOML3	47	.	0			c.C608G						.						105	99	101					13																	39542580		2203	4300	6503	SO:0001583	missense	161003	exon6			GCCATGGATCTCT	BC025760	CCDS9367.1, CCDS45040.1	13q13.2	2004-03-05			ENSG00000133115	ENSG00000133115			19420	protein-coding gene	gene with protein product		608327				12122055	Standard	NM_145286		Approved	SRO, Epb7.2l	uc001uwx.3	Q8TAV4	OTTHUMG00000016763	ENST00000379631.4:c.608C>G	chr13.hg19:g.39542580G>C	ENSP00000368952:p.Ser203Cys	52.0	0.0		50.0	24.0	NM_145286	B4E285|Q5JS35	Missense_Mutation	SNP	ENST00000379631.4	hg19	CCDS9367.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.428853	0.62844	.	.	ENSG00000133115	ENST00000379631;ENST00000423210	D;D	0.94966	-3.57;-3.57	5.92	5.92	0.95590	.	0.096682	0.64402	D	0.000001	D	0.97018	0.9026	M	0.85373	2.75	0.51012	D	0.999905	D;D	0.58970	0.984;0.984	D;D	0.64506	0.926;0.926	D	0.97115	0.9807	10	0.87932	D	0	-16.713	13.1665	0.59573	0.0767:0.0:0.9232:0.0	.	194;203	B4E285;Q8TAV4	.;STML3_HUMAN	C	203;194	ENSP00000368952:S203C;ENSP00000401989:S194C	ENSP00000368952:S203C	S	-	2	0	STOML3	38440580	1.000000	0.71417	0.999000	0.59377	0.200000	0.23975	7.634000	0.83273	2.795000	0.96236	0.655000	0.94253	TCC	.	.		0.557	STOML3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044604.2			C	39542580	G	C	39542580	3	2	8	1	0	0	0	0	1	0	0	0	15330	1174	41	4	275	4	STOML3	13	39542580	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10		39542580	75627298	55	658										
SYT16	83851	hgsc.bcm.edu	37	chr14	62551004	62551004	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ctcatggaggggcgccagagCtgttggtggggctctcgtac	17	10	2	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr14:62551004C>T	ENST00000430451.2	+	5	1722	c.1525C>T	c.(1525-1527)Ctg>Ttg	p.L509L		NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	509	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GGCGCCAGAGCTGTTGGTGGG	0.567																																					p.L509L		Atlas-SNP	.											.	SYT16	144	.	0			c.C1525T						.						90	90	90					14																	62551004		2002	4162	6164	SO:0001819	synonymous_variant	83851	exon5			CCAGAGCTGTTGG	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1525C>T	chr14.hg19:g.62551004C>T		93.0	0.0		74.0	44.0	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	hg19	CCDS45121.1																																																																																			.	.		0.567	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		T	62551004	C	T	62551004	2	4	8	1	0	0	0	0	0	0	0	1	15487	796	28	3		3	SYT16	14	62551004	Silent	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10		62551004	44798536	56	659										
NRXN3	9369	hgsc.bcm.edu	37	chr14	80158522	80158522	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tttaaactttaaaggcaacaCtgataatgaacgcttccaaa	5	8	0	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr14:80158522C>T	ENST00000557594.1	+	4	1554				NRXN3_ENST00000335750.5_Intron|NRXN3_ENST00000428277.2_Missense_Mutation_p.T203I|RP11-242P2.1_ENST00000553322.1_RNA|NRXN3_ENST00000281127.7_Intron|NRXN3_ENST00000556003.1_Intron|NRXN3_ENST00000554719.1_Intron	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3						adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		AAAGGCAACACTGATAATGAA	0.333																																					p.T203I		Atlas-SNP	.											.	NRXN3	342	.	0			c.C608T						.						56	52	53					14																	80158522		1803	4072	5875	SO:0001627	intron_variant	9369	exon4			GCAACACTGATAA	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000557594.1:c.602-5451C>T	chr14.hg19:g.80158522C>T		70.0	0.0		69.0	12.0	NM_001105250	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000557594.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.76	2.630539	0.46944	.	.	ENSG00000021645	ENST00000332068;ENST00000428277	T	0.78246	-1.16	5.72	5.72	0.89469	.	.	.	.	.	D	0.86543	0.5958	.	.	.	0.80722	D	1	D	0.60575	0.988	P	0.60789	0.879	D	0.85995	0.1491	7	.	.	.	.	18.0612	0.89378	0.0:1.0:0.0:0.0	.	203	Q9HDB5-4	.	I	1197;203	ENSP00000394426:T203I	.	T	+	2	0	NRXN3	79228275	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.831000	0.48144	2.704000	0.92352	0.650000	0.86243	ACT	.	.		0.333	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250		T	80158522	C	T	80158522	1	4	8	0	1	0	0	0	0	0	0	0	10676	565	20	3		3	NRXN3	14	80158522	Intron	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	17607518	80158522	27191018	57	660										
BAG5	9529	hgsc.bcm.edu	37	chr14	104026516	104026516	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ctgctcttctcctggcttccCggatgcaggggtttttttca	10	12	3	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr14:104026516C>T	ENST00000445922.2	-	2	1232	c.986G>A	c.(985-987)cGg>cAg	p.R329Q	RP11-894P9.2_ENST00000556332.1_RNA|RP11-73M18.2_ENST00000472726.2_5'Flank|BAG5_ENST00000299204.4_Missense_Mutation_p.R329Q|APOPT1_ENST00000556253.2_5'Flank|APOPT1_ENST00000247618.4_5'Flank|APOPT1_ENST00000409074.2_5'Flank|BAG5_ENST00000337322.4_Missense_Mutation_p.R370Q	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	329	BAG 4. {ECO:0000255|PROSITE- ProRule:PRU00369}.				negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)	p.R329L(1)		endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			CCTGGCTTCCCGGATGCAGGG	0.453																																					p.R370Q	NSCLC(171;1832 2055 18950 31566 41632)	Atlas-SNP	.											.	BAG5	47	.	1	Substitution - Missense(1)	lung(1)	c.G1109A						.						64	69	68					14																	104026516		2203	4300	6503	SO:0001583	missense	9529	exon2			GCTTCCCGGATGC	AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.986G>A	chr14.hg19:g.104026516C>T	ENSP00000391713:p.Arg329Gln	91.0	0.0		99.0	35.0	NM_001015049	O94950|Q86W59	Missense_Mutation	SNP	ENST00000445922.2	hg19	CCDS9982.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.399391	0.62177	.	.	ENSG00000166170	ENST00000299204;ENST00000445922;ENST00000337322	D;D;D	0.93366	-3.21;-3.21;-3.21	5.76	4.85	0.62838	BAG domain (3);	0.000000	0.85682	D	0.000000	D	0.94384	0.8194	L	0.32530	0.975	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.69307	0.961;0.963	D	0.95218	0.8331	10	0.87932	D	0	-17.4587	16.6082	0.84836	0.0:0.8697:0.1303:0.0	.	329;370	Q9UL15;Q9UL15-2	BAG5_HUMAN;.	Q	329;329;370	ENSP00000299204:R329Q;ENSP00000391713:R329Q;ENSP00000338814:R370Q	ENSP00000299204:R329Q	R	-	2	0	BAG5	103096269	1.000000	0.71417	0.963000	0.40424	0.240000	0.25518	7.013000	0.76373	1.403000	0.46800	0.655000	0.94253	CGG	.	.		0.453	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			T	104026516	C	T	104026516	3	4	8	1	0	0	0	0	1	0	0	0	1290	652	23	1	361	1	BAG5	14	104026516	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	23867994	104026516	3323024	58	661										
BAG5	9529	hgsc.bcm.edu	37	chr14	104028275	104028275	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	actgggagtccacaatggccTaatgcacgtttcaagctctt	9	11	2	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr14:104028275T>C	ENST00000445922.2	-	1	219				RP11-894P9.2_ENST00000556332.1_RNA|RP11-73M18.2_ENST00000472726.2_5'Flank|BAG5_ENST00000299204.4_Intron|APOPT1_ENST00000556253.2_5'Flank|APOPT1_ENST00000247618.4_5'Flank|APOPT1_ENST00000409074.2_5'Flank|BAG5_ENST00000337322.4_Missense_Mutation_p.R24G	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5						negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			CACAATGGCCTAATGCACGTT	0.493																																					p.R24G	NSCLC(171;1832 2055 18950 31566 41632)	Atlas-SNP	.											.	BAG5	47	.	0			c.A70G						.						107	108	108					14																	104028275		1917	4128	6045	SO:0001627	intron_variant	9529	exon1			ATGGCCTAATGCA	AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.27+161A>G	chr14.hg19:g.104028275T>C		78.0	0.0		99.0	4.0	NM_001015049	O94950|Q86W59	Missense_Mutation	SNP	ENST00000445922.2	hg19	CCDS9982.1	.	.	.	.	.	.	.	.	.	.	T	9.837	1.189976	0.21954	.	.	ENSG00000166170	ENST00000337322	T	0.80909	-1.43	2.78	-5.56	0.02529	.	1.637800	0.05073	U	0.481964	T	0.63224	0.2493	.	.	.	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.42699	-0.9436	9	0.35671	T	0.21	.	2.2259	0.03984	0.142:0.3842:0.2875:0.1863	.	24	Q9UL15-2	.	G	24	ENSP00000338814:R24G	ENSP00000338814:R24G	R	-	1	2	BAG5	103098028	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.742000	0.01835	-1.978000	0.00993	-1.614000	0.00798	AGG	.	.		0.493	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			C	104028275	T	C	104028275	1	2	8	0	1	0	0	0	0	0	0	0	1290	1521	53	2		2	BAG5	14	104028275	Intron	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	1759	104028275	3321265	59	662										
RYR3	6263	hgsc.bcm.edu	37	chr15	34130221	34130221	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	acgattcccgcctgaagtgtCtgttggacccagcagaaagt	11	11	1	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr15:34130221C>T	ENST00000389232.4	+	89	12110	c.12040C>T	c.(12040-12042)Ctg>Ttg	p.L4014L	RYR3_ENST00000415757.3_Silent_p.L4009L	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4014					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CCTGAAGTGTCTGTTGGACCC	0.473																																					p.L4014L		Atlas-SNP	.											.	RYR3	760	.	0			c.C12040T						.						121	120	120					15																	34130221		1942	4149	6091	SO:0001819	synonymous_variant	6263	exon89			AAGTGTCTGTTGG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.12040C>T	chr15.hg19:g.34130221C>T		108.0	0.0		140.0	18.0	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.473	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34130221	C	T	34130221	2	4	8	1	0	0	0	0	0	0	0	1	13785	912	32	3		3	RYR3	15	34130221	Silent	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10		34130221	68401171	60	663										
PDCD7	10081	hgsc.bcm.edu	37	chr15	65421369	65421369	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gaaatgcaaagccacagttaCctttcctcgctgcagcctct	7	14	1	0	rs543198741		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr15:65421369C>A	ENST00000204549.4	-	2	1064		c.e2+1			NM_005707.1	NP_005698.1	Q8N8D1	PDCD7_HUMAN	programmed cell death 7						apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of T cell apoptotic process (GO:0070234)|response to glucocorticoid (GO:0051384)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)				endometrium(4)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	7						GCCACAGTTACCTTTCCTCGC	0.428																																					.		Atlas-SNP	.											.	PDCD7	22	.	0			c.1009+1G>T						.						291	265	273					15																	65421369		2202	4299	6501	SO:0001630	splice_region_variant	10081	exon3			CAGTTACCTTTCC	AF083930	CCDS10201.1	15q22.2	2012-06-07			ENSG00000090470	ENSG00000090470			8767	protein-coding gene	gene with protein product	"U11/U12 snRNP 59K"	608138				10037816	Standard	NM_005707		Approved	HES18, ES18	uc002aol.3	Q8N8D1	OTTHUMG00000133117	ENST00000204549.4:c.1009+1G>T	chr15.hg19:g.65421369C>A		52.0	0.0		79.0	28.0	NM_005707	Q96AK8|Q9Y6D7	Splice_Site	SNP	ENST00000204549.4	hg19	CCDS10201.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.977925	0.74360	.	.	ENSG00000090470	ENST00000204549;ENST00000431964;ENST00000380204	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1162	0.97934	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDCD7	63208422	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	7.487000	0.81328	2.757000	0.94681	0.563000	0.77884	.	.	.		0.428	PDCD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256784.2	NM_005707	Intron	A	65421369	C	A	65421369	5	1	8	1	0	0	0	0	0	0	1	0	11634	521	18	3	463	3	PDCD7	15	65421369	Splice_Site	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	31291148	65421369	37110023	61	664										
DENND4A	10260	hgsc.bcm.edu	37	chr15	66021923	66021923	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	acggatggccgtagggaatgGataagaattttatgttctgt	13	4	1	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr15:66021923G>A	ENST00000431932.2	-	10	1468	c.1260C>T	c.(1258-1260)atC>atT	p.I420I	DENND4A_ENST00000443035.3_Silent_p.I420I	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	420	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						GTAGGGAATGGATAAGAATTT	0.398																																					p.I420I		Atlas-SNP	.											.	DENND4A	217	.	0			c.C1260T						.						64	60	61					15																	66021923		1882	4100	5982	SO:0001819	synonymous_variant	10260	exon10			GGAATGGATAAGA	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.1260C>T	chr15.hg19:g.66021923G>A		69.0	0.0		82.0	28.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	hg19	CCDS45285.1																																																																																			.	.		0.398	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		A	66021923	G	A	66021923	2	1	8	1	0	0	0	0	0	0	0	1	4435	1164	41	3		3	DENND4A	15	66021923	Silent	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	600554	66021923	36509469	62	665										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88679766	88679766	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	aggaaggggtgatccagagcCattgcaagtgataacagcgt	14	7	0	3			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr15:88679766C>T	ENST00000360948.2	-	7	858	c.697G>A	c.(697-699)Ggc>Agc	p.G233S	NTRK3_ENST00000542733.2_Missense_Mutation_p.G135S|NTRK3_ENST00000558676.1_Missense_Mutation_p.G233S|NTRK3_ENST00000357724.2_Missense_Mutation_p.G233S|NTRK3_ENST00000394480.2_Missense_Mutation_p.G233S|NTRK3_ENST00000540489.2_Missense_Mutation_p.G233S|NTRK3_ENST00000355254.2_Missense_Mutation_p.G233S|NTRK3_ENST00000317501.3_Missense_Mutation_p.G233S|NTRK3_ENST00000557856.1_Missense_Mutation_p.G233S	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	233	Ig-like C2-type 1.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			GATCCAGAGCCATTGCAAGTG	0.557			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.G233S		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.G697A						.						171	104	126					15																	88679766		2201	4299	6500	SO:0001583	missense	4916	exon8			CAGAGCCATTGCA	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.697G>A	chr15.hg19:g.88679766C>T	ENSP00000354207:p.Gly233Ser	51.0	0.0		97.0	38.0	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.541047	0.85917	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.64	5.64	0.86602	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75034	0.3795	L	0.40543	1.245	0.80722	D	1	D;D;P;D;D;P	0.89917	1.0;1.0;0.621;1.0;1.0;0.621	D;D;P;D;D;P	0.97110	1.0;1.0;0.593;1.0;0.998;0.593	T	0.68014	-0.5521	10	0.16896	T	0.51	.	18.6884	0.91574	0.0:1.0:0.0:0.0	.	135;233;233;233;233;233	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	S	233;233;233;233;135;233;233	ENSP00000377990:G233S;ENSP00000354207:G233S;ENSP00000350356:G233S;ENSP00000347397:G233S;ENSP00000437773:G135S;ENSP00000444673:G233S;ENSP00000318328:G233S	ENSP00000318328:G233S	G	-	1	0	NTRK3	86480770	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.359000	0.79477	2.657000	0.90304	0.655000	0.94253	GGC	.	.		0.557	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				T	88679766	C	T	88679766	3	4	8	1	0	0	0	0	1	0	0	0	10717	594	21	3	2136	3	NTRK3	15	88679766	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	22657843	88679766	13851626	63	666										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2814152	2814152	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	attcaaagacacacttagaaCcccgccaagggaaagaagtg	9	10	1	3			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr16:2814152C>G	ENST00000301740.8	+	11	4172	c.3623C>G	c.(3622-3624)aCc>aGc	p.T1208S		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1208	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						ACACTTAGAACCCCGCCAAGG	0.458																																					p.T1208S		Atlas-SNP	.											.	SRRM2	263	.	0			c.C3623G						.						105	110	108					16																	2814152		2198	4300	6498	SO:0001583	missense	23524	exon11			TTAGAACCCCGCC	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.3623C>G	chr16.hg19:g.2814152C>G	ENSP00000301740:p.Thr1208Ser	104.0	0.0		196.0	28.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	3.012	-0.203734	0.06180	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	D	0.92595	-3.07	5.97	2.73	0.32206	.	0.476475	0.21288	N	0.077040	T	0.75598	0.3871	N	0.02539	-0.55	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.62854	-0.6766	10	0.13853	T	0.58	-0.0106	6.9403	0.24488	0.0:0.6721:0.1601:0.1678	.	1208	Q9UQ35	SRRM2_HUMAN	S	1208;1208;460	ENSP00000301740:T1208S	ENSP00000301740:T1208S	T	+	2	0	SRRM2	2754153	0.001000	0.12720	0.012000	0.15200	0.016000	0.09150	0.907000	0.28531	0.846000	0.35142	0.655000	0.94253	ACC	.	.		0.458	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			G	2814152	C	G	2814152	3	3	8	1	0	0	0	0	1	0	0	0	15184	507	18	4	3661	4	SRRM2	16	2814152	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10		2814152	87540601	64	667										
LRRC50	123872	hgsc.bcm.edu	37	chr16	84203706	84203706	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gctgagaccctgctactgtcGtcacctgtggaggttaaagg	13	10	1	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr16:84203706G>A	ENST00000378553.5	+	8	1396	c.1272G>A	c.(1270-1272)tcG>tcA	p.S424S	DNAAF1_ENST00000563818.1_3'UTR|DNAAF1_ENST00000334315.5_Intron	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	424	Pro-rich.				axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						TGCTACTGTCGTCACCTGTGG	0.622																																					p.S424S		Atlas-SNP	.											DNAAF1,NS,carcinoma,0,3	DNAAF1	81	.	0			c.G1272A						.						61	64	63					16																	84203706		2200	4300	6500	SO:0001819	synonymous_variant	123872	exon8			ACTGTCGTCACCT	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"outer row dynein assembly 7 homolog (Chlamydomonas)"	613190	"leucine rich repeat containing 50"	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1272G>A	chr16.hg19:g.84203706G>A		110.0	0.0		105.0	50.0	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Silent	SNP	ENST00000378553.5	hg19	CCDS10943.2																																																																																			.	.		0.622	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452		A	84203706	G	A	84203706	2	1	8	1	0	0	0	0	0	0	0	1	9018	1132	40	1		1	LRRC50	16	84203706	Silent	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	81389554	84203706	6151047	65	668										
TP53	7157	hgsc.bcm.edu	37	chr17	7578211	7578211	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	agggcaccaccacactatgtCgaaaagtgtttctgtcatcc	8	12	2	0	rs587778720		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr17:7578211C>A	ENST00000269305.4	-	6	827	c.638G>T	c.(637-639)cGa>cTa	p.R213L	TP53_ENST00000359597.4_Missense_Mutation_p.R213L|TP53_ENST00000413465.2_Missense_Mutation_p.R213L|TP53_ENST00000420246.2_Missense_Mutation_p.R213L|TP53_ENST00000455263.2_Missense_Mutation_p.R213L|TP53_ENST00000445888.2_Missense_Mutation_p.R213L|TP53_ENST00000574684.1_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	213	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R213L(38)|p.R213Q(29)|p.0?(8)|p.R213P(5)|p.?(5)|p.R120L(4)|p.R81L(4)|p.R120Q(2)|p.R81Q(2)|p.D208_V216delDRNTFRHSV(1)|p.D207_R213delDDRNTFR(1)|p.T211_S215delTFRHS(1)|p.D208fs*1(1)|p.R213>L(1)|p.R209_R213delRNTFR(1)|p.R213fs*2(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213fs*32(1)|p.R209fs*6(1)|p.R213W(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CACACTATGTCGAAAAGTGTT	0.532		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R213L	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,-1,1	TP53	33396	.	110	Substitution - Missense(85)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(5)|Unknown(5)|Complex - deletion inframe(1)|Complex - compound substitution(1)	prostate(15)|large_intestine(14)|urinary_tract(9)|liver(9)|haematopoietic_and_lymphoid_tissue(8)|biliary_tract(6)|stomach(6)|oesophagus(6)|kidney(5)|lung(5)|central_nervous_system(4)|ovary(4)|pancreas(4)|bone(4)|upper_aerodigestive_tract(3)|soft_tissue(2)|eye(2)|vulva(1)|endometrium(1)|skin(1)|breast(1)	c.G638T	GRCh37	CM004906|CM022474	TP53	M		.						132	118	122					17																	7578211		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CTATGTCGAAAAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.638G>T	chr17.hg19:g.7578211C>A	ENSP00000269305:p.Arg213Leu	149.0	0.0		97.0	46.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	36	5.890676	0.97074	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99866	-7.3;-7.3;-7.3;-7.3;-7.3;-7.3;-7.3;-7.3	5.28	4.32	0.51571	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.057335	0.64402	D	0.000003	D	0.99871	0.9939	M	0.92507	3.315	0.53688	D	0.999978	D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.988;0.996;0.999;0.989;0.986;0.999	D	0.96662	0.9490	10	0.87932	D	0	-7.5444	11.7807	0.52013	0.0:0.9141:0.0:0.0859	.	174;213;213;120;213;213;213	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	L	213;213;213;213;213;213;202;120;81;120;81	ENSP00000410739:R213L;ENSP00000352610:R213L;ENSP00000269305:R213L;ENSP00000398846:R213L;ENSP00000391127:R213L;ENSP00000391478:R213L;ENSP00000425104:R81L;ENSP00000423862:R120L	ENSP00000269305:R213L	R	-	2	0	TP53	7518936	0.996000	0.38824	0.185000	0.23176	0.961000	0.63080	7.775000	0.85489	1.367000	0.46095	0.563000	0.77884	CGA	.	.		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578211	C	A	7578211	3	1	8	1	0	0	0	0	1	0	0	0	16396	884	31	1	656	1	TP53	17	7578211	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10		7578211	73616999	66	669										
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319642	21319642	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ggggtcaccgctttgagcccGtgctcttcgaggagaagaac	14	11	2	3	rs368741477		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr17:21319642G>A	ENST00000583088.1	+	3	1883	c.988G>A	c.(988-990)Gtg>Atg	p.V330M	KCNJ12_ENST00000331718.5_Missense_Mutation_p.V330M	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	330					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CTTTGAGCCCGTGCTCTTCGA	0.592										Prostate(3;0.18)																											p.V330M		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	.	0			c.G988A						.	G	MET/VAL	0,4406		0,0,2203	148	150	149		988	5.8	0.9	17		149	1,8599	1.2+/-3.3	0,1,4299	no	missense	KCNJ12	NM_021012.4	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	330/434	21319642	1,13005	2203	4300	6503	SO:0001583	missense	100134444	exon3			GAGCCCGTGCTCT	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.988G>A	chr17.hg19:g.21319642G>A	ENSP00000463778:p.Val330Met	118.0	0.0		94.0	15.0	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	hg19	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.989628	0.74589	0.0	1.16E-4	ENSG00000184185	ENST00000331718	D	0.95588	-3.75	5.76	5.76	0.90799	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.97120	0.9059	L	0.58669	1.825	0.80722	D	1	D	0.89917	1.0	D	0.68353	0.957	D	0.96931	0.9681	10	0.54805	T	0.06	.	19.9738	0.97296	0.0:0.0:1.0:0.0	.	330	Q14500	IRK12_HUMAN	M	330	ENSP00000328150:V330M	ENSP00000328150:V330M	V	+	1	0	KCNJ12	21260235	1.000000	0.71417	0.938000	0.37757	0.900000	0.52787	9.698000	0.98700	2.732000	0.93576	0.655000	0.94253	GTG	.	.		0.592	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21319642	G	A	21319642	3	1	8	1	0	0	0	0	1	0	0	0	8055	1145	40	1	990	1	KCNJ12	17	21319642	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	13741431	21319642	59875568	67	670										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27014460	27014460	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tccagtatgtttgtggcctgGgacctcggaaagggacccac	13	11	0	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr17:27014460G>T	ENST00000314616.6	+	23	3260	c.2977G>T	c.(2977-2979)Gga>Tga	p.G993*	SUPT6H_ENST00000347486.4_Nonsense_Mutation_p.G993*	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	993	Interaction with KDM6A. {ECO:0000250}.			YVCGLGP -> VCLWPGT (in Ref. 1; AAB18949). {ECO:0000305}.	chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					TTGTGGCCTGGGACCTCGGAA	0.458																																					p.G993X		Atlas-SNP	.											.	SUPT6H	165	.	0			c.G2977T						.						64	54	58					17																	27014460		2203	4300	6503	SO:0001587	stop_gained	6830	exon23			GGCCTGGGACCTC	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.2977G>T	chr17.hg19:g.27014460G>T	ENSP00000319104:p.Gly993*	49.0	0.0		75.0	25.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Nonsense_Mutation	SNP	ENST00000314616.6	hg19	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	44	10.989530	0.99499	.	.	ENSG00000109111	ENST00000314616	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-16.3759	19.3016	0.94146	0.0:0.0:1.0:0.0	.	.	.	.	X	993	.	ENSP00000319104:G993X	G	+	1	0	SUPT6H	24038587	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.160000	0.94734	2.649000	0.89929	0.557000	0.71058	GGA	.	.		0.458	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27014460	G	T	27014460	4	4	8	1	0	0	0	0	0	1	0	0	15415	1233	43	3	3063	3	SUPT6H	17	27014460	Nonsense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	5694818	27014460	54180750	68	671										
NAGLU	4669	hgsc.bcm.edu	37	chr17	40689495	40689495	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	cccgctgggagcgagagataGactggatggcgctgaatggc	17	9	0	3			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr17:40689495G>C	ENST00000225927.2	+	2	564	c.463G>C	c.(463-465)Gac>Cac	p.D155H	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	155					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	GCGAGAGATAGACTGGATGGC	0.622																																					p.D155H		Atlas-SNP	.											.	NAGLU	36	.	0			c.G463C						.						130	112	118					17																	40689495		2203	4300	6503	SO:0001583	missense	4669	exon2			GAGATAGACTGGA		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"Sanfilippo disease IIIB"	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.463G>C	chr17.hg19:g.40689495G>C	ENSP00000225927:p.Asp155His	66.0	0.0		109.0	46.0	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	hg19	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.979917	0.92982	.	.	ENSG00000108784	ENST00000225927	D	0.99479	-5.98	4.3	4.3	0.51218	Alpha-N-acetylglucosaminidase, tim-barrel domain (1);	0.000000	0.85682	D	0.000000	D	0.99661	0.9874	H	0.95611	3.695	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97379	0.9981	10	0.87932	D	0	-42.4756	15.8626	0.79038	0.0:0.0:1.0:0.0	.	155	P54802	ANAG_HUMAN	H	155	ENSP00000225927:D155H	ENSP00000225927:D155H	D	+	1	0	NAGLU	37943021	1.000000	0.71417	0.953000	0.39169	0.977000	0.68977	9.428000	0.97476	2.363000	0.80096	0.561000	0.74099	GAC	.	.		0.622	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		C	40689495	G	C	40689495	3	2	8	1	0	0	0	0	1	0	0	0	10152	942	33	4	469	4	NAGLU	17	40689495	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	13675035	40689495	40505715	69	672										
HOXB5	3215	hgsc.bcm.edu	37	chr17	46670974	46670974	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tcagagagctgccactgccaTaatttagcaactgatagtcc	8	11	1	2	rs199857901		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr17:46670974T>G	ENST00000239151.5	-	1	349	c.71A>C	c.(70-72)tAt>tCt	p.Y24S	HOXB-AS3_ENST00000480872.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000492897.3_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	24					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell differentiation (GO:0045446)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			large_intestine(1)|lung(2)	3						GCCACTGCCATAATTTAGCAA	0.517																																					p.Y24S		Atlas-SNP	.											.	HOXB5	20	.	0			c.A71C						.						46	47	47					17																	46670974		1908	3830	5738	SO:0001583	missense	3215	exon1			CTGCCATAATTTA		CCDS11530.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120075	ENSG00000120075		"Homeoboxes / ANTP class : HOXL subclass"	5116	protein-coding gene	gene with protein product		142960	"homeo box B5"	HOX2, HOX2A		1973146, 1358459	Standard	NM_002147		Approved		uc002inr.3	P09067	OTTHUMG00000159913	ENST00000239151.5:c.71A>C	chr17.hg19:g.46670974T>G	ENSP00000239151:p.Tyr24Ser	151.0	0.0		212.0	27.0	NM_002147	B2RC69|P09069|Q17RP4	Missense_Mutation	SNP	ENST00000239151.5	hg19	CCDS11530.1	.	.	.	.	.	.	.	.	.	.	T	19.86	3.904827	0.72868	.	.	ENSG00000120075	ENST00000239151	D	0.93604	-3.25	5.44	5.44	0.79542	.	0.000000	0.64402	D	0.000001	D	0.97259	0.9104	M	0.91612	3.225	0.80722	D	1	D	0.71674	0.998	D	0.73708	0.981	D	0.98200	1.0467	10	0.87932	D	0	.	15.4969	0.75662	0.0:0.0:0.0:1.0	.	24	P09067	HXB5_HUMAN	S	24	ENSP00000239151:Y24S	ENSP00000239151:Y24S	Y	-	2	0	HOXB5	44025973	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.062000	0.61559	0.454000	0.30748	TAT	.	T|0.999;C|0.001		0.517	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2			G	46670974	T	G	46670974	3	3	8	1	0	0	0	0	1	0	0	0	7313	1406	49	5	746	5	HOXB5	17	46670974	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	5981479	46670974	34524236	70	673										
TEX14	56155	hgsc.bcm.edu	37	chr17	56665261	56665261	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ccacaaggatccttacctggTagagtcccagtgacagctgg	11	12	0	2	rs369322235		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr17:56665261T>C	ENST00000240361.8	-	16	2801	c.2716A>G	c.(2716-2718)Acc>Gcc	p.T906A	TEX14_ENST00000349033.5_Missense_Mutation_p.T900A|TEX14_ENST00000389934.3_Missense_Mutation_p.T900A			Q8IWB6	TEX14_HUMAN	testis expressed 14	906					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCTTACCTGGTAGAGTCCCAG	0.582											OREG0024616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T906A		Atlas-SNP	.											.	TEX14	343	.	0			c.A2716G						.						132	126	128					17																	56665261		2203	4300	6503	SO:0001583	missense	56155	exon16			ACCTGGTAGAGTC	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2716A>G	chr17.hg19:g.56665261T>C	ENSP00000240361:p.Thr906Ala	63.0	0.0	1017	123.0	20.0	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	T	2.338	-0.351856	0.05173	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.78246	-1.16;-1.16;-1.11	5.0	-10.0	0.00425	.	1.931450	0.01822	N	0.034142	T	0.60457	0.2270	L	0.36672	1.1	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.08055	0.001;0.001;0.003	T	0.48375	-0.9041	10	0.15952	T	0.53	.	5.1361	0.14935	0.1897:0.5002:0.14:0.1701	.	906;900;900	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	A	906;900;900	ENSP00000240361:T906A;ENSP00000374584:T900A;ENSP00000268910:T900A	ENSP00000240361:T906A	T	-	1	0	TEX14	54020260	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-2.048000	0.01406	-3.012000	0.00272	0.455000	0.32223	ACC	.	.		0.582	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			C	56665261	T	C	56665261	3	2	8	1	0	0	0	0	1	0	0	0	15793	1638	57	2	1849	2	TEX14	17	56665261	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	9994287	56665261	24529949	71	674										
GPRC5C	55890	hgsc.bcm.edu	37	chr17	72436225	72436225	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ccctgggcctcttctgcctcGtgtttgcctgtgtggtgaag	13	12	2	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr17:72436225G>A	ENST00000392627.1	+	2	1571	c.445G>A	c.(445-447)Gtg>Atg	p.V149M	GPRC5C_ENST00000342648.5_Intron|GPRC5C_ENST00000392629.2_Missense_Mutation_p.V116M|GPRC5C_ENST00000481232.1_Intron	NM_022036.2	NP_071319.2	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	104					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						CTTCTGCCTCGTGTTTGCCTG	0.607																																					p.V149M		Atlas-SNP	.											.	GPRC5C	92	.	0			c.G445A						.						93	95	94					17																	72436225		2203	4300	6503	SO:0001583	missense	55890	exon2			TGCCTCGTGTTTG	AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"GPCR / Class C : Orphans"	13309	protein-coding gene	gene with protein product		605949	"G protein-coupled receptor, family C, group 5, member C"			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000392627.1:c.445G>A	chr17.hg19:g.72436225G>A	ENSP00000376403:p.Val149Met	35.0	0.0		67.0	36.0	NM_022036	B5BUN4|Q2NL85|Q9NZG5	Missense_Mutation	SNP	ENST00000392627.1	hg19	CCDS11699.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.456136	0.26161	.	.	ENSG00000170412	ENST00000392627;ENST00000342648;ENST00000392629;ENST00000392628	D	0.88975	-2.45	5.67	5.67	0.87782	GPCR, family 3, C-terminal (2);	0.233636	0.44483	D	0.000452	D	0.92476	0.7611	M	0.62723	1.935	0.41042	D	0.985232	D;D;D	0.76494	0.999;0.997;0.999	D;D;D	0.67548	0.952;0.919;0.92	D	0.92825	0.6275	10	0.87932	D	0	-7.1666	12.0466	0.53483	0.0867:0.0:0.9133:0.0	.	104;104;116	A8MXZ4;Q9NQ84;Q9NQ84-2	.;GPC5C_HUMAN;.	M	104;149;116;104	ENSP00000376405:V116M	ENSP00000340595:V149M	V	+	1	0	GPRC5C	69947820	1.000000	0.71417	0.997000	0.53966	0.870000	0.49936	4.859000	0.62954	2.676000	0.91093	0.561000	0.74099	GTG	.	.		0.607	GPRC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145094.2			A	72436225	G	A	72436225	3	1	8	1	0	0	0	0	1	0	0	0	6735	1145	40	1	459	1	GPRC5C	17	72436225	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	15770964	72436225	8758985	72	675										
ME2	4200	hgsc.bcm.edu	37	chr18	48452204	48452204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	caatgaaaggcctgtaatatTtgcattaagtaatcctacag	7	7	0	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr18:48452204T>C	ENST00000321341.5	+	12	1522	c.1250T>C	c.(1249-1251)tTt>tCt	p.F417S	ME2_ENST00000382927.3_Missense_Mutation_p.F417S	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	417					malate metabolic process (GO:0006108)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(3)	23		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)		CCTGTAATATTTGCATTAAGT	0.398																																					p.F417S		Atlas-SNP	.											.	ME2	49	.	0			c.T1250C						.						67	62	64					18																	48452204		2203	4300	6503	SO:0001583	missense	4200	exon12			TAATATTTGCATT	M55905	CCDS11948.1, CCDS54187.1	18q21	2012-10-02			ENSG00000082212	ENSG00000082212	1.1.1.40		6984	protein-coding gene	gene with protein product		154270				1993674	Standard	NM_002396		Approved		uc002ley.3	P23368	OTTHUMG00000132694	ENST00000321341.5:c.1250T>C	chr18.hg19:g.48452204T>C	ENSP00000321070:p.Phe417Ser	192.0	0.0		282.0	115.0	NM_001168335	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	hg19	CCDS11948.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.432115	0.83776	.	.	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.60040	0.22;0.22	5.59	5.59	0.84812	Malic enzyme, NAD-binding (2);NAD(P)-binding domain (1);	0.047369	0.85682	D	0.000000	D	0.84293	0.5440	H	0.97564	4.03	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89821	0.3989	10	0.87932	D	0	-23.0014	14.7442	0.69477	0.0:0.0:0.0:1.0	.	417;417	Q9BWL6;P23368	.;MAOM_HUMAN	S	417	ENSP00000321070:F417S;ENSP00000372384:F417S	ENSP00000321070:F417S	F	+	2	0	ME2	46706202	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.989000	0.70587	2.118000	0.64928	0.533000	0.62120	TTT	.	.		0.398	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396		C	48452204	T	C	48452204	3	2	8	1	0	0	0	0	1	0	0	0	9427	1841	64	2	1292	2	ME2	18	48452204	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10		48452204	29625044	73	676										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610255	10610255	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	caccgttcatgacgtggaggAcacacttctcgcccatggag	11	13	2	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr19:10610255A>C	ENST00000171111.5	-	2	1002	c.455T>G	c.(454-456)gTc>gGc	p.V152G	KEAP1_ENST00000393623.2_Missense_Mutation_p.V152G|KEAP1_ENST00000588024.1_5'Flank	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	152					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GACGTGGAGGACACACTTCTC	0.582																																					p.V152G		Atlas-SNP	.											.	KEAP1	182	.	0			c.T455G						.						182	143	156					19																	10610255		2203	4300	6503	SO:0001583	missense	9817	exon2			TGGAGGACACACT	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.455T>G	chr19.hg19:g.10610255A>C	ENSP00000171111:p.Val152Gly	107.0	0.0		67.0	27.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	A	15.53	2.859886	0.51482	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.70986	-0.53;-0.53	4.81	3.8	0.43715	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.128186	0.52532	D	0.000074	D	0.87249	0.6130	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87316	0.2315	10	0.87932	D	0	.	8.5797	0.33621	0.9066:0.0:0.0934:0.0	.	152	Q14145	KEAP1_HUMAN	G	152	ENSP00000171111:V152G;ENSP00000377245:V152G	ENSP00000171111:V152G	V	-	2	0	KEAP1	10471255	1.000000	0.71417	0.989000	0.46669	0.401000	0.30781	9.093000	0.94163	0.703000	0.31848	-0.379000	0.06801	GTC	.	.		0.582	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		C	10610255	A	C	10610255	3	2	8	1	0	0	0	0	1	0	0	0	8150	275	10	5	1439	5	KEAP1	19	10610255	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10		10610255	48518728	74	677										
TMED1	11018	hgsc.bcm.edu	37	chr19	10943770	10943770	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gccacgttgacagctgaccaGaagttgacccgctccaagtt	10	13	0	4			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr19:10943770G>T	ENST00000214869.2	-	4	683	c.585C>A	c.(583-585)ttC>ttA	p.F195L	TMED1_ENST00000591695.1_Missense_Mutation_p.S134Y|TMED1_ENST00000588289.1_Missense_Mutation_p.F50L	NM_006858.2	NP_006849.1	Q13445	TMED1_HUMAN	transmembrane emp24 protein transport domain containing 1	195					cell-cell signaling (GO:0007267)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|lung(2)|ovary(3)|prostate(1)|skin(1)	10						CAGCTGACCAGAAGTTGACCC	0.647																																					p.F195L		Atlas-SNP	.											.	TMED1	22	.	0			c.C585A						.						76	73	74					19																	10943770		2203	4300	6503	SO:0001583	missense	11018	exon4			TGACCAGAAGTTG	U41804	CCDS12249.1	19p13.2	2008-02-05	2005-08-26			ENSG00000099203			17291	protein-coding gene	gene with protein product		605395	"transmembrane emp24 domain containing 1"			11466339, 8621446	Standard	NM_006858		Approved	ST2L, MGC1270, IL1RL1LG, Il1rl1l	uc002mpy.3	Q13445		ENST00000214869.2:c.585C>A	chr19.hg19:g.10943770G>T	ENSP00000214869:p.Phe195Leu	102.0	0.0		68.0	33.0	NM_006858		Missense_Mutation	SNP	ENST00000214869.2	hg19	CCDS12249.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.693921	0.48202	.	.	ENSG00000099203	ENST00000214869	T	0.16196	2.36	5.24	4.2	0.49525	GOLD (1);	0.000000	0.85682	D	0.000000	T	0.21801	0.0525	M	0.71296	2.17	0.80722	D	1	P	0.36086	0.536	B	0.39531	0.302	T	0.03095	-1.1073	10	0.15952	T	0.53	-20.8576	12.7717	0.57426	0.0807:0.0:0.9193:0.0	.	195	Q13445	TMED1_HUMAN	L	195	ENSP00000214869:F195L	ENSP00000214869:F195L	F	-	3	2	TMED1	10804770	1.000000	0.71417	1.000000	0.80357	0.318000	0.28184	3.171000	0.50824	1.215000	0.43411	-0.140000	0.14226	TTC	.	.		0.647	TMED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452614.1	NM_006858		T	10943770	G	T	10943770	3	4	8	1	0	0	0	0	1	0	0	0	16017	933	33	3	102	3	TMED1	19	10943770	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	333515	10943770	48185213	75	678										
NXNL1	115861	hgsc.bcm.edu	37	chr19	17571528	17571528	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gaagtccttgaggatgggcaCgaaggcctggcactgtggac	16	9	0	1	rs374915427		TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr19:17571528C>A	ENST00000301944.2	-	1	235	c.151G>T	c.(151-153)Gtg>Ttg	p.V51L	CTD-2521M24.10_ENST00000594663.1_5'UTR	NM_138454.1	NP_612463.1	Q96CM4	NXNL1_HUMAN	nucleoredoxin-like 1	51	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				photoreceptor cell maintenance (GO:0045494)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	6						AGGATGGGCACGAAGGCCTGG	0.617																																					p.V51L		Atlas-SNP	.											.	NXNL1	13	.	0			c.G151T						.						82	79	80					19																	17571528		2203	4300	6503	SO:0001583	missense	115861	exon1			TGGGCACGAAGGC	BC014127	CCDS12360.1	19p13.11	2014-05-21	2007-08-16	2007-08-16	ENSG00000171773	ENSG00000171773			25179	protein-coding gene	gene with protein product		608791	"thioredoxin-like 6"	TXNL6		12477932	Standard	NM_138454		Approved	RDCVF	uc002ngs.3	Q96CM4	OTTHUMG00000182798	ENST00000301944.2:c.151G>T	chr19.hg19:g.17571528C>A	ENSP00000305631:p.Val51Leu	57.0	0.0		49.0	26.0	NM_138454	Q0QD37	Missense_Mutation	SNP	ENST00000301944.2	hg19	CCDS12360.1	.	.	.	.	.	.	.	.	.	.	c	7.195	0.592355	0.13812	.	.	ENSG00000171773	ENST00000301944	T	0.79033	-1.23	3.92	3.92	0.45320	Thioredoxin-like fold (3);	0.241819	0.41001	D	0.000969	T	0.51024	0.1650	N	0.01228	-0.945	0.09310	N	1	B	0.13594	0.008	B	0.12156	0.007	T	0.47611	-0.9104	10	0.36615	T	0.2	-8.9194	13.4448	0.61134	0.0:1.0:0.0:0.0	.	51	Q96CM4	NXNL1_HUMAN	L	51	ENSP00000305631:V51L	ENSP00000305631:V51L	V	-	1	0	NXNL1	17432528	0.006000	0.16342	0.209000	0.23619	0.092000	0.18411	0.983000	0.29552	2.018000	0.59344	0.467000	0.42956	GTG	.	.		0.617	NXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463803.1	NM_138454		A	17571528	C	A	17571528	3	1	8	1	0	0	0	0	1	0	0	0	10797	536	19	1	495	1	NXNL1	19	17571528	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	6627758	17571528	41557455	76	679										
R3HDML	140902	hgsc.bcm.edu	37	chr20	42979420	42979420	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	gggctgaaatccaacaagttCacgtggttctgaattttctc	9	9	3	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr20:42979420C>G	ENST00000217043.2	+	5	922	c.750C>G	c.(748-750)ttC>ttG	p.F250L	RP5-881L22.5_ENST00000438702.1_RNA|RP5-881L22.5_ENST00000430481.2_RNA	NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	250						extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)	21		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			CCAACAAGTTCACGTGGTTCT	0.522																																					p.F250L		Atlas-SNP	.											.	R3HDML	33	.	0			c.C750G						.						162	142	149					20																	42979420		2203	4300	6503	SO:0001583	missense	140902	exon5			CAAGTTCACGTGG	BC107048	CCDS13329.1	20q13.12	2007-04-26	2005-09-02		ENSG00000101074	ENSG00000101074			16249	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing-like"				Standard	NM_178491		Approved	dJ881L22.3	uc002xls.2	Q9H3Y0	OTTHUMG00000032524	ENST00000217043.2:c.750C>G	chr20.hg19:g.42979420C>G	ENSP00000217043:p.Phe250Leu	121.0	0.0		183.0	45.0	NM_178491		Missense_Mutation	SNP	ENST00000217043.2	hg19	CCDS13329.1	.	.	.	.	.	.	.	.	.	.	C	2.487	-0.318397	0.05386	.	.	ENSG00000101074	ENST00000217043	T	0.04156	3.69	4.64	2.2	0.27929	.	0.486384	0.19009	N	0.125123	T	0.00936	0.0031	N	0.00205	-1.85	0.20307	N	0.999914	B	0.02656	0.0	B	0.01281	0.0	T	0.46721	-0.9171	10	0.02654	T	1	.	5.9616	0.19303	0.0:0.4921:0.2832:0.2247	.	250	Q9H3Y0	CRSPL_HUMAN	L	250	ENSP00000217043:F250L	ENSP00000217043:F250L	F	+	3	2	R3HDML	42412834	0.001000	0.12720	0.167000	0.22817	0.005000	0.04900	-0.407000	0.07178	0.887000	0.36136	0.561000	0.74099	TTC	.	.		0.522	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491		G	42979420	C	G	42979420	3	3	8	1	0	0	0	0	1	0	0	0	12904	825	29	4	768	4	R3HDML	20	42979420	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10		42979420	20046100	77	680										
WDR4	10785	hgsc.bcm.edu	37	chr21	44272435	44272435	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	acggtgctctcaggaacagaCtgcaggcgacaaacaggaaa	12	10	1	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr21:44272435C>A	ENST00000398208.2	-	10	1035		c.e10-1		WDR4_ENST00000492742.1_Splice_Site|WDR4_ENST00000330317.2_Splice_Site	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4											haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		CAGGAACAGACTGCAGGCGAC	0.572																																					.		Atlas-SNP	.											.	WDR4	35	.	0			c.976-1G>T						.						77	62	67					21																	44272435		2203	4300	6503	SO:0001630	splice_region_variant	10785	exon11			AACAGACTGCAGG	AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"WD repeat domain containing"	12756	protein-coding gene	gene with protein product	"TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.976-1G>T	chr21.hg19:g.44272435C>A		76.0	0.0		89.0	14.0	NM_033661		Splice_Site	SNP	ENST00000398208.2	hg19	CCDS13691.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.967697	0.34754	.	.	ENSG00000160193	ENST00000330317;ENST00000398208	.	.	.	4.12	4.12	0.48240	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.065	0.53583	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR4	43145504	0.937000	0.31787	0.308000	0.25141	0.022000	0.10575	3.344000	0.52174	2.303000	0.77524	0.655000	0.94253	.	.	.		0.572	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		Intron	A	44272435	C	A	44272435	5	1	8	1	0	0	0	0	0	0	1	0	17308	579	20	3	271	3	WDR4	21	44272435	Splice_Site	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10		44272435	3857460	78	681										
ANKRD54	129138	hgsc.bcm.edu	37	chr22	38228664	38228664	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ctgctctttggtactggtcaTctgcaggcgggtgcagaggt	15	9	3	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chr22:38228664T>C	ENST00000215941.4	-	7	1000	c.808A>G	c.(808-810)Atg>Gtg	p.M270V	ANKRD54_ENST00000406423.1_Missense_Mutation_p.M150V|ANKRD54_ENST00000609454.1_Missense_Mutation_p.M77V|ANKRD54_ENST00000411961.2_Missense_Mutation_p.M254V|ANKRD54_ENST00000498417.1_5'UTR	NM_138797.2	NP_620152.1	Q6NXT1	ANR54_HUMAN	ankyrin repeat domain 54	270					nucleocytoplasmic transport (GO:0006913)|positive regulation of erythrocyte differentiation (GO:0045648)|regulation of intracellular signal transduction (GO:1902531)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)	protein kinase regulator activity (GO:0019887)			lung(1)	1	Melanoma(58;0.045)					GTACTGGTCATCTGCAGGCGG	0.617																																					p.M270V		Atlas-SNP	.											.	ANKRD54	7	.	0			c.A808G						.						76	70	72					22																	38228664		2203	4300	6503	SO:0001583	missense	129138	exon7			TGGTCATCTGCAG	BC014641	CCDS13959.1	22q13.1	2013-01-10			ENSG00000100124	ENSG00000100124		"Ankyrin repeat domain containing"	25185	protein-coding gene	gene with protein product		613383				15461802	Standard	NM_138797		Approved	LIAR	uc003auc.3	Q6NXT1	OTTHUMG00000150663	ENST00000215941.4:c.808A>G	chr22.hg19:g.38228664T>C	ENSP00000215941:p.Met270Val	37.0	0.0		55.0	21.0	NM_138797	Q6ZSB1|Q9UGV1	Missense_Mutation	SNP	ENST00000215941.4	hg19	CCDS13959.1	.	.	.	.	.	.	.	.	.	.	T	1.606	-0.525197	0.04141	.	.	ENSG00000100124	ENST00000215941;ENST00000406423;ENST00000411961	T;T;T	0.66638	-0.11;-0.03;-0.22	5.59	5.59	0.84812	.	0.238444	0.49916	D	0.000134	T	0.49745	0.1575	N	0.19112	0.55	0.36218	D	0.851827	B;B	0.19445	0.036;0.005	B;B	0.13407	0.009;0.002	T	0.54180	-0.8332	10	0.25751	T	0.34	-3.6261	11.7302	0.51732	0.0:0.0:0.1473:0.8527	.	150;270	B5MCX7;Q6NXT1	.;ANR54_HUMAN	V	270;150;254	ENSP00000215941:M270V;ENSP00000384392:M150V;ENSP00000405782:M254V	ENSP00000215941:M270V	M	-	1	0	ANKRD54	36558610	1.000000	0.71417	1.000000	0.80357	0.189000	0.23516	2.500000	0.45381	2.129000	0.65627	0.528000	0.53228	ATG	.	.		0.617	ANKRD54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319490.1	NM_138797		C	38228664	T	C	38228664	3	2	8	1	0	0	0	0	1	0	0	0	680	1435	50	2	102	2	ANKRD54	22	38228664	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10		38228664	13075902	79	682										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20211662	20211662	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tatgtagatggtctaaagcaAgtgcaagttcagccaagtag	11	6	2	1			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chrX:20211662A>C	ENST00000379565.3	-	7	743	c.536T>G	c.(535-537)cTt>cGt	p.L179R	RPS6KA3_ENST00000540702.1_Missense_Mutation_p.L151R|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.L151R|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.L150R	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	179	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	GTCTAAAGCAAGTGCAAGTTC	0.294																																					p.L179R		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.T536G						.						88	77	81					X																	20211662		2203	4299	6502	SO:0001583	missense	6197	exon7			AAAGCAAGTGCAA	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.536T>G	chrX.hg19:g.20211662A>C	ENSP00000368884:p.Leu179Arg	58.0	0.0		82.0	22.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	a	20.2	3.944526	0.73672	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702;ENST00000457145	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04	4.78	3.59	0.41128	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.074930	0.53938	D	0.000053	T	0.70011	0.3175	L	0.42008	1.315	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;0.999;1.0;0.999	T	0.69837	-0.5037	10	0.87932	D	0	.	10.1644	0.42871	0.8482:0.0:0.0:0.1518	.	151;150;151;179	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	R	179;151;150;151;150	ENSP00000368884:L179R;ENSP00000440220:L151R;ENSP00000368865:L150R;ENSP00000444837:L151R;ENSP00000407655:L150R	ENSP00000368865:L150R	L	-	2	0	RPS6KA3	20121583	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.280000	0.95786	0.567000	0.29293	0.483000	0.47432	CTT	.	.		0.294	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		C	20211662	A	C	20211662	3	2	8	1	0	0	0	0	1	0	0	0	13667	72	3	5	1750	5	RPS6KA3	23	20211662	Missense_Mutation	SNP	A	TCGA-2Y-A9GY-01A-11D-A382-10		20211662	135058898	80	683										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382426	24382426	+	IGR	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	ctgctgctgctgctgctgctGctcctgctcctgctctagct	10	16	1	0			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chrX:24382426G>C								AC004552.1 (15403 upstream) : PDK3 (100911 downstream)																							tgctgctgctgctcctgctcc	0.627																																					p.A517P		Atlas-SNP	.											.	.	.	.	0			c.G1549C						.						2	2	2					X																	24382426		1073	2483	3556	SO:0001628	intergenic_variant	100130302	exon1			GCTGCTGCTCCTG																													chrX.hg19:g.24382426G>C		168.0	0.0		171.0	9.0	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.627									C	24382426	G	C	24382426	1	2	8	0	1	0	0	0	0	0	0	0	5581	1319	46	4		4	FAM48B1	23	24382426	IGR	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	4170764	24382426	130888134	81	684										
ABCB7	22	hgsc.bcm.edu	37	chrX	74295382	74295382	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	aaagacatttttggctattcTtcggattgaattctgggcta	9	6	2	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chrX:74295382T>C	ENST00000373394.3	-	6	677	c.670A>G	c.(670-672)Aga>Gga	p.R224G	ABCB7_ENST00000253577.3_Missense_Mutation_p.R225G|ABCB7_ENST00000339447.4_Missense_Mutation_p.R184G|ABCB7_ENST00000534570.1_5'Flank			O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 7	224	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)			breast(1)|endometrium(5)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)	20						TTGGCTATTCTTCGGATTGAA	0.418																																					p.R225G		Atlas-SNP	.											.	ABCB7	69	.	0			c.A673G						.						104	89	94					X																	74295382		2203	4300	6503	SO:0001583	missense	22	exon6			CTATTCTTCGGAT	AF038950	CCDS14428.1, CCDS65290.1, CCDS65291.1, CCDS75994.1	Xq13.3	2012-03-14			ENSG00000131269	ENSG00000131269		"ATP binding cassette transporters / subfamily B"	48	protein-coding gene	gene with protein product		300135		ABC7		9143506	Standard	NM_004299		Approved	EST140535, Atm1p, ASAT	uc004ebz.4	O75027	OTTHUMG00000021862	ENST00000373394.3:c.670A>G	chrX.hg19:g.74295382T>C	ENSP00000362492:p.Arg224Gly	186.0	0.0		257.0	57.0	NM_004299	G3XAC4|O75345|Q5VWY7|Q5VWY8|Q9BRE1|Q9UND1|Q9UP01	Missense_Mutation	SNP	ENST00000373394.3	hg19		.	.	.	.	.	.	.	.	.	.	T	19.86	3.905816	0.72868	.	.	ENSG00000131269	ENST00000535115;ENST00000253577;ENST00000339447;ENST00000373394;ENST00000529949;ENST00000534524	D;D;D;D;D	0.92348	-2.66;-2.66;-2.66;-2.66;-3.02	5.58	5.58	0.84498	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.93530	0.7935	L	0.60012	1.86	0.80722	D	1	B;P;P;B;P	0.47677	0.103;0.876;0.899;0.126;0.745	B;P;P;B;P	0.54664	0.093;0.712;0.758;0.151;0.62	D	0.93740	0.7049	10	0.59425	D	0.04	-16.6247	13.8666	0.63592	0.0:0.0:0.0:1.0	.	198;184;225;224;225	G3V1J3;G3XAC4;B3KM98;O75027;O75027-2	.;.;.;ABCB7_HUMAN;.	G	198;225;184;224;198;169	ENSP00000253577:R225G;ENSP00000343849:R184G;ENSP00000362492:R224G;ENSP00000436586:R198G;ENSP00000435521:R169G	ENSP00000253577:R225G	R	-	1	2	ABCB7	74212107	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.084000	0.71335	1.871000	0.54225	0.417000	0.27973	AGA	.	.		0.418	ABCB7-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000057274.1	NM_004299		C	74295382	T	C	74295382	3	2	8	1	0	0	0	0	1	0	0	0	46	1617	56	2	1632	2	ABCB7	23	74295382	Missense_Mutation	SNP	T	TCGA-2Y-A9GY-01A-11D-A382-10	49912956	74295382	80975178	82	685										
FAM199X	139231	hgsc.bcm.edu	37	chrX	103420443	103420443	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	tcacttcttttgatttatttCctgaggggagtgtctgcagt	10	7	3	2			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chrX:103420443C>G	ENST00000493442.1	+	2	503	c.337C>G	c.(337-339)Cct>Gct	p.P113A		NM_207318.3	NP_997201.1	Q6PEV8	F199X_HUMAN	family with sequence similarity 199, X-linked	113										breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)	11						TGATTTATTTCCTGAGGGGAG	0.413																																					p.P113A		Atlas-SNP	.											.	FAM199X	38	.	0			c.C337G						.						167	133	145					X																	103420443		2203	4300	6503	SO:0001583	missense	139231	exon2			TTATTTCCTGAGG	BC016683	CCDS35364.1	Xq22	2010-02-11	2010-02-11	2010-02-11	ENSG00000123575	ENSG00000123575			25195	protein-coding gene	gene with protein product			"chromosome X open reading frame 39"	CXorf39			Standard	NM_207318		Approved		uc004elw.3	Q6PEV8	OTTHUMG00000022126	ENST00000493442.1:c.337C>G	chrX.hg19:g.103420443C>G	ENSP00000417581:p.Pro113Ala	65.0	0.0		84.0	15.0	NM_207318	Q8WVP6|Q96AV3	Missense_Mutation	SNP	ENST00000493442.1	hg19	CCDS35364.1	.	.	.	.	.	.	.	.	.	.	C	19.19	3.778991	0.70107	.	.	ENSG00000123575	ENST00000493442	T	0.58060	0.36	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.51193	0.1660	L	0.60455	1.87	0.80722	D	1	P	0.45715	0.865	B	0.41135	0.348	T	0.54833	-0.8234	9	.	.	.	-8.5331	16.1766	0.81857	0.0:1.0:0.0:0.0	.	113	Q6PEV8	F199X_HUMAN	A	113	ENSP00000417581:P113A	.	P	+	1	0	FAM199X	103307099	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	5.955000	0.70306	2.102000	0.63906	0.600000	0.82982	CCT	.	.		0.413	FAM199X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057764.1	NM_207318		G	103420443	C	G	103420443	3	3	8	1	0	0	0	0	1	0	0	0	5535	855	30	4	343	4	FAM199X	23	103420443	Missense_Mutation	SNP	C	TCGA-2Y-A9GY-01A-11D-A382-10	29125061	103420443	51850117	83	686										
DCX	1641	hgsc.bcm.edu	37	chrX	110654106	110654106	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0487804878048781	4	1	0.947562881909905	1.46872246696035	0.699391650933501	1	1	0	agcctgacaaaattccccttGaagagaacagaaggagctac	9	10	0	4			TCGA-2Y-A9GY-01A-11D-A382-10	TCGA-2Y-A9GY-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75a72b01-26d1-410f-a2f3-fabe09059eed	e1cd43c8-e295-4191-8754-0520f03119e1	g.chrX:110654106G>T	ENST00000338081.3	-	1	268	c.97C>A	c.(97-99)Caa>Aaa	p.Q33K	DCX_ENST00000356915.2_Intron|DCX_ENST00000371993.2_Intron|DCX_ENST00000488120.1_Intron|DCX_ENST00000496551.1_Intron|DCX_ENST00000356220.3_Intron	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	33					axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						AATTCCCCTTGAAGAGAACAG	0.413																																					p.Q33K		Atlas-SNP	.											.	DCX	158	.	0			c.C97A						.						193	170	178					X																	110654106		2203	4300	6503	SO:0001583	missense	1641	exon1			CCCCTTGAAGAGA	AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"doublecortex"	300121	"doublecortex; lissencephaly, X-linked (doublecortin)"			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.97C>A	chrX.hg19:g.110654106G>T	ENSP00000337697:p.Gln33Lys	349.0	0.0		484.0	186.0	NM_000555	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Missense_Mutation	SNP	ENST00000338081.3	hg19	CCDS14556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	11.01|11.01	1.513531|1.513531	0.27123|0.27123	.|.	.|.	ENSG00000077279|ENSG00000077279	ENST00000358070|ENST00000338081	.|T	.|0.25250	.|1.81	4.42|4.42	0.46|0.46	0.16684|0.16684	.|.	.|0.406541	.|0.18243	.|N	.|0.147198	T|T	0.09862|0.09862	0.0242|0.0242	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|B;B	.|0.06786	.|0.001;0.0	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.18304|0.18304	-1.0341|-1.0341	5|10	.|0.87932	.|D	.|0	.|.	0.7146|0.7146	0.00930|0.00930	0.3218:0.2098:0.3144:0.154|0.3218:0.2098:0.3144:0.154	.|.	.|21;33	.|B4DM53;O43602	.|.;DCX_HUMAN	L|K	24|33	.|ENSP00000337697:Q33K	.|ENSP00000337697:Q33K	F|Q	-|-	3|1	2|0	DCX|DCX	110540762|110540762	1.000000|1.000000	0.71417|0.71417	0.818000|0.818000	0.32626|0.32626	0.990000|0.990000	0.78478|0.78478	1.335000|1.335000	0.33839|0.33839	-0.044000|-0.044000	0.13491|0.13491	0.505000|0.505000	0.49811|0.49811	TTC|CAA	.	.		0.413	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153		T	110654106	G	T	110654106	3	4	8	1	0	0	0	0	1	0	0	0	4320	1299	45	3	1271	3	DCX	23	110654106	Missense_Mutation	SNP	G	TCGA-2Y-A9GY-01A-11D-A382-10	7233663	110654106	44616454	84	687										
ATAD3B	83858	hgsc.bcm.edu	37	chr1	1425945	1425945	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tgggaactccttccccaggcGcctgaagctggcccagtttg	12	14	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr1:1425945G>T	ENST00000308647.7	+	15	1624	c.1508G>T	c.(1507-1509)cGc>cTc	p.R503L		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	503						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TTCCCCAGGCGCCTGAAGCTG	0.662																																					p.R503L		Atlas-SNP	.											ATAD3B,NS,carcinoma,0,1	ATAD3B	68	.	0			c.G1508T						.						32	34	33					1																	1425945		2199	4291	6490	SO:0001583	missense	83858	exon15			CCAGGCGCCTGAA	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"ATPases / AAA-type"	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1508G>T	chr1.hg19:g.1425945G>T	ENSP00000311766:p.Arg503Leu	227.0	0.0		272.0	110.0	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	hg19	CCDS30.1	.	.	.	.	.	.	.	.	.	.	.	12.20	1.867062	0.32977	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	T	0.19938	2.11	2.51	2.51	0.30379	.	0.000000	0.85682	D	0.000000	T	0.40645	0.1125	M	0.81802	2.56	0.80722	D	1	D;D	0.65815	0.995;0.982	D;P	0.63192	0.912;0.863	T	0.31971	-0.9924	10	0.51188	T	0.08	.	8.7624	0.34683	0.127:0.0:0.873:0.0	.	457;503	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	L	337;503	ENSP00000311766:R503L	ENSP00000311766:R503L	R	+	2	0	ATAD3B	1415808	1.000000	0.71417	0.995000	0.50966	0.183000	0.23260	7.477000	0.81069	1.412000	0.46977	0.194000	0.17425	CGC	.	.		0.662	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		T	1425945	G	T	1425945	3	4	9	1	0	0	0	0	1	0	0	0	1074	1087	38	1	1566	1	ATAD3B	1	1425945	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10		1425945	247824676	1	688										
PRAMEF2	65122	hgsc.bcm.edu	37	chr1	12919905	12919905	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gagctggaaattcacaacacGtgctggccacatctgataag	10	10	2	1	rs376186859		TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr1:12919905G>T	ENST00000240189.2	+	3	732	c.645G>T	c.(643-645)acG>acT	p.T215T		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	215					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TTCACAACACGTGCTGGCCAC	0.373																																					p.T215T		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G645T						.	G		1,4401	2.1+/-5.4	0,1,2200	99	107	104		645	-1.3	0	1		104	0,8586		0,0,4293	no	coding-synonymous	PRAMEF2	NM_023014.1		0,1,6493	TT,TG,GG		0.0,0.0227,0.0077		215/475	12919905	1,12987	2201	4293	6494	SO:0001819	synonymous_variant	65122	exon3			CAACACGTGCTGG		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"-"	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.645G>T	chr1.hg19:g.12919905G>T		120.0	0.0		143.0	32.0	NM_023014		Silent	SNP	ENST00000240189.2	hg19	CCDS149.1																																																																																			.	.		0.373	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014		T	12919905	G	T	12919905	2	4	9	1	0	0	0	0	0	0	0	1	12447	1132	40	1		1	PRAMEF2	1	12919905	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	11493960	12919905	236330716	2	689										
EIF2C1	26523	hgsc.bcm.edu	37	chr1	36359333	36359333	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	agggctactaccacccgctgGggggtgggcgcgaggtctgg	19	11	1	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr1:36359333G>T	ENST00000373204.4	+	5	784	c.571G>T	c.(571-573)Ggg>Tgg	p.G191W	AGO1_ENST00000373206.1_Missense_Mutation_p.G116W	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	191					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										CCACCCGCTGGGGGGTGGGCG	0.632																																					p.G191W		Atlas-SNP	.											.	.	.	.	0			c.G571T						.						46	44	45					1																	36359333		2203	4300	6503	SO:0001583	missense	26523	exon5			CCGCTGGGGGGTG	AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"Argonaute/PIWI family"	3262	protein-coding gene	gene with protein product	"argonaute 1"	606228	"eukaryotic translation initiation factor 2C, 1"	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.571G>T	chr1.hg19:g.36359333G>T	ENSP00000362300:p.Gly191Trp	33.0	0.0		43.0	17.0	NM_012199	Q5TA57|Q6P4S0	Missense_Mutation	SNP	ENST00000373204.4	hg19	CCDS398.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327338	0.81690	.	.	ENSG00000092847	ENST00000373206;ENST00000373204	T;T	0.13420	2.62;2.59	5.93	5.93	0.95920	Argonaute/Dicer protein, PAZ (1);Domain of unknown function DUF1785 (1);	0.000000	0.85682	D	0.000000	T	0.57007	0.2024	H	0.97540	4.025	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72181	-0.4368	10	0.87932	D	0	-23.2269	20.3334	0.98727	0.0:0.0:1.0:0.0	.	191	Q9UL18	AGO1_HUMAN	W	116;191	ENSP00000362302:G116W;ENSP00000362300:G191W	ENSP00000362300:G191W	G	+	1	0	EIF2C1	36131920	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.818000	0.97014	0.591000	0.81541	GGG	.	.		0.632	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			T	36359333	G	T	36359333	3	4	9	1	0	0	0	0	1	0	0	0	5007	1232	43	3	589	3	EIF2C1	1	36359333	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	23439428	36359333	212891288	3	690										
ELAVL4	1996	hgsc.bcm.edu	37	chr1	50572025	50572025	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tatgagattacttcttttaaGggaaattgtcattaatgagt	8	3	2	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr1:50572025G>A	ENST00000371823.4	+	0	0				ELAVL4_ENST00000357083.4_Missense_Mutation_p.R7K|ELAVL4_ENST00000371824.1_5'Flank|ELAVL4_ENST00000448907.2_Intron|ELAVL4_ENST00000371827.1_Intron	NM_001144774.1|NM_021952.3	NP_001138246.1|NP_068771.2	P26378	ELAV4_HUMAN	ELAV like neuron-specific RNA binding protein 4						mRNA processing (GO:0006397)|RNA processing (GO:0006396)		AU-rich element binding (GO:0017091)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	32						CTTCTTTTAAGGGAAATTGTC	0.478																																					p.R7K		Atlas-SNP	.											.	ELAVL4	124	.	0			c.G20A						.						96	93	94					1																	50572025		1568	3582	5150	SO:0001631	upstream_gene_variant	1996	exon1			TTTTAAGGGAAAT	AY033998	CCDS553.1, CCDS44138.1, CCDS44139.1, CCDS44140.1, CCDS53315.1, CCDS72788.1	1p34	2013-10-03	2013-10-03		ENSG00000162374	ENSG00000162374		"RNA binding motif (RRM) containing"	3315	protein-coding gene	gene with protein product	"Hu antigen D"	168360	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)", "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4"	HUD		8222755	Standard	XM_005270581		Approved	PNEM	uc001csb.2	P26378	OTTHUMG00000007877		chr1.hg19:g.50572025G>A	Exception_encountered	57.0	0.0		61.0	31.0	NM_001144775	B1APY6|B1APY7|B7Z4G7|Q8IYD4|Q96J74|Q96J75|Q9UD24	Missense_Mutation	SNP	ENST00000371823.4	hg19	CCDS553.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.205822	0.39003	.	.	ENSG00000162374	ENST00000357083	T	0.08984	3.03	4.99	4.99	0.66335	.	.	.	.	.	T	0.05044	0.0135	.	.	.	0.80722	D	1	B	0.28667	0.219	B	0.32090	0.14	T	0.15867	-1.0422	8	0.02654	T	1	.	14.4472	0.67359	0.0:0.147:0.853:0.0	.	7	P26378-3	.	K	7	ENSP00000349594:R7K	ENSP00000349594:R7K	R	+	2	0	ELAVL4	50344612	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.962000	0.63687	2.752000	0.94435	0.655000	0.94253	AGG	.	.		0.478	ELAVL4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000021712.1	NM_021952		A	50572025	G	A	50572025	1	1	9	0	1	0	0	0	0	0	0	0	5054	1000	35	3		3	ELAVL4	1	50572025	5'Flank	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	14212692	50572025	198678596	4	691										
C1orf59	113802	hgsc.bcm.edu	37	chr1	109191343	109191343	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	atacgcaaggagtctctgcaGaggtacgaaaaatttatctc	9	8	2	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr1:109191343G>A	ENST00000370032.5	-	8	1447	c.1027C>T	c.(1027-1029)Ctg>Ttg	p.L343L	HENMT1_ENST00000402983.1_Silent_p.L343L|HENMT1_ENST00000370031.1_Silent_p.L374L|HENMT1_ENST00000493676.1_5'Flank	NM_144584.2	NP_653185.2	Q5T8I9	HENMT_HUMAN	HEN1 methyltransferase homolog 1 (Arabidopsis)	343					gene silencing by RNA (GO:0031047)|piRNA metabolic process (GO:0034587)|RNA methylation (GO:0001510)	P granule (GO:0043186)	metal ion binding (GO:0046872)|O-methyltransferase activity (GO:0008171)|RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	16						AGTCTCTGCAGAGGTACGAAA	0.473																																					p.L343L		Atlas-SNP	.											.	HENMT1	38	.	0			c.C1027T						.						116	107	110					1																	109191343		2203	4300	6503	SO:0001819	synonymous_variant	113802	exon8			TCTGCAGAGGTAC		CCDS787.1	1p13.3	2011-01-28	2011-01-28	2011-01-28	ENSG00000162639	ENSG00000162639			26400	protein-coding gene	gene with protein product	"HEN1 methyltransferase homolog (Arabidopsis)"	612178	"chromosome 1 open reading frame 59"	C1orf59			Standard	NM_144584		Approved	FLJ30525, HEN1	uc001dvt.4	Q5T8I9	OTTHUMG00000011123	ENST00000370032.5:c.1027C>T	chr1.hg19:g.109191343G>A		143.0	0.0		177.0	84.0	NM_144584	A8MRR6|B1AM16|B1AM17|Q96EJ7|Q96NN0	Silent	SNP	ENST00000370032.5	hg19	CCDS787.1																																																																																			.	.		0.473	HENMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030592.1	NM_144584		A	109191343	G	A	109191343	2	1	9	1	0	0	0	0	0	0	0	1	2053	933	33	3		3	C1orf59	1	109191343	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	58619318	109191343	140059278	5	692										
BCL9	607	hgsc.bcm.edu	37	chr1	147096555	147096555	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tgctgccgtgggcatgattcCtggcaaggatcgggggcctg	17	10	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr1:147096555C>A	ENST00000234739.3	+	10	4816	c.4076C>A	c.(4075-4077)cCt>cAt	p.P1359H		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	1359	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					GGCATGATTCCTGGCAAGGAT	0.612			T	"IGH@, IGL@"	B-ALL																																p.P1359H		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.C4076A						.						48	50	49					1																	147096555		2203	4300	6503	SO:0001583	missense	607	exon10			TGATTCCTGGCAA	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.4076C>A	chr1.hg19:g.147096555C>A	ENSP00000234739:p.Pro1359His	73.0	0.0		83.0	25.0	NM_004326	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	hg19	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	C	18.09	3.545510	0.65198	.	.	ENSG00000116128	ENST00000234739	T	0.56444	0.46	5.32	5.32	0.75619	.	0.059328	0.64402	D	0.000001	T	0.59293	0.2183	L	0.36672	1.1	0.44539	D	0.997491	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.63594	-0.6602	10	0.72032	D	0.01	-8.9403	18.9922	0.92798	0.0:1.0:0.0:0.0	.	1359;1359	Q1JQ81;O00512	.;BCL9_HUMAN	H	1359	ENSP00000234739:P1359H	ENSP00000234739:P1359H	P	+	2	0	BCL9	145563179	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.301000	0.59086	2.486000	0.83907	0.650000	0.86243	CCT	.	.		0.612	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		A	147096555	C	A	147096555	3	1	9	1	0	0	0	0	1	0	0	0	1381	681	24	3	4102	3	BCL9	1	147096555	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	37905212	147096555	102154066	6	693										
RFX5	5993	hgsc.bcm.edu	37	chr1	151315600	151315600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ctcaactacactcttcttccGctctccacgtgcgagaggac	7	16	4	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr1:151315600G>A	ENST00000290524.4	-	11	1091	c.913C>T	c.(913-915)Cgg>Tgg	p.R305W	RFX5_ENST00000368870.2_Missense_Mutation_p.R305W|RFX5_ENST00000452513.2_Missense_Mutation_p.R265W|RP11-126K1.8_ENST00000422153.1_RNA|RFX5_ENST00000452671.2_Missense_Mutation_p.R305W|RFX5_ENST00000478564.1_5'Flank	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	305					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CTCTTCTTCCGCTCTCCACGT	0.567																																					p.R305W		Atlas-SNP	.											.	RFX5	69	.	0			c.C913T						.						32	38	36					1																	151315600		2187	4265	6452	SO:0001583	missense	5993	exon11			TCTTCCGCTCTCC		CCDS994.1	1q21	2014-09-17			ENSG00000143390	ENSG00000143390			9986	protein-coding gene	gene with protein product		601863				9401005	Standard	XM_005245405		Approved		uc001exw.1	P48382	OTTHUMG00000012495	ENST00000290524.4:c.913C>T	chr1.hg19:g.151315600G>A	ENSP00000290524:p.Arg305Trp	62.0	0.0		54.0	11.0	NM_000449	B7Z848|D3DV19|E9PFU4|Q5VWC3	Missense_Mutation	SNP	ENST00000290524.4	hg19	CCDS994.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.681418	0.68042	.	.	ENSG00000143390	ENST00000290524;ENST00000368870;ENST00000436637;ENST00000452671;ENST00000452513;ENST00000392746	T;T;T;T;T;T	0.78126	0.11;0.11;-1.15;0.11;0.11;0.12	5.65	4.73	0.59995	.	0.098879	0.43260	D	0.000595	T	0.81113	0.4755	M	0.63428	1.95	0.34831	D	0.739687	D;D	0.89917	1.0;1.0	D;D	0.79784	0.972;0.993	D	0.84430	0.0576	10	0.72032	D	0.01	-14.5474	11.4842	0.50344	0.0:0.0:0.6729:0.3271	.	265;305	B7Z848;P48382	.;RFX5_HUMAN	W	305;305;197;305;265;305	ENSP00000290524:R305W;ENSP00000357864:R305W;ENSP00000390769:R197W;ENSP00000389130:R305W;ENSP00000398388:R265W;ENSP00000376502:R305W	ENSP00000290524:R305W	R	-	1	2	RFX5	149582224	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	1.118000	0.31246	1.611000	0.50210	0.655000	0.94253	CGG	.	.		0.567	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449		A	151315600	G	A	151315600	3	1	9	1	0	0	0	0	1	0	0	0	13281	1086	38	1	941	1	RFX5	1	151315600	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	4219045	151315600	97935021	7	694										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181726159	181726159	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ttatgtagtctactttgtggTcttccccttcttctttgtca	6	10	5	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr1:181726159T>C	ENST00000367573.2	+	30	4226	c.4226T>C	c.(4225-4227)gTc>gCc	p.V1409A	CACNA1E_ENST00000367567.4_Missense_Mutation_p.V1016A|CACNA1E_ENST00000357570.5_Missense_Mutation_p.V1360A|CACNA1E_ENST00000367570.1_Missense_Mutation_p.V1409A|CACNA1E_ENST00000526775.1_Missense_Mutation_p.V1390A|CACNA1E_ENST00000360108.3_Missense_Mutation_p.V1390A|CACNA1E_ENST00000358338.5_Missense_Mutation_p.V1341A	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1409					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TACTTTGTGGTCTTCCCCTTC	0.483																																					p.V1409A		Atlas-SNP	.											.	CACNA1E	778	.	0			c.T4226C						.						190	190	190					1																	181726159		1954	4168	6122	SO:0001583	missense	777	exon30			TTGTGGTCTTCCC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.4226T>C	chr1.hg19:g.181726159T>C	ENSP00000356545:p.Val1409Ala	118.0	0.0		103.0	21.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.948970	0.92660	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98684	-5.07;-5.07;-5.07;-5.07;-5.07;-5.07;-5.07	5.75	5.75	0.90469	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99324	0.9763	M	0.92880	3.355	0.80722	D	1	D;D;D	0.76494	0.989;0.999;0.996	P;D;D	0.85130	0.882;0.997;0.987	D	0.98900	1.0776	10	0.87932	D	0	.	15.7322	0.77814	0.0:0.0:0.0:1.0	.	1390;1409;1409	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	A	1409;1390;1360;1341;1016;1390;1409	ENSP00000356542:V1409A;ENSP00000434814:V1390A;ENSP00000350183:V1360A;ENSP00000351101:V1341A;ENSP00000356539:V1016A;ENSP00000353222:V1390A;ENSP00000356545:V1409A	ENSP00000350183:V1360A	V	+	2	0	CACNA1E	179992782	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.930000	0.87610	2.194000	0.70268	0.533000	0.62120	GTC	.	.		0.483	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		C	181726159	T	C	181726159	3	2	9	1	0	0	0	0	1	0	0	0	2544	1667	58	2	4344	2	CACNA1E	1	181726159	Missense_Mutation	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10	30410559	181726159	67524462	8	695										
LHX9	56956	hgsc.bcm.edu	37	chr1	197898219	197898219	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ataaagctgacggcacgtcgCttccggccccgccctcagca	10	17	1	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr1:197898219C>A	ENST00000367387.4	+	5	1449	c.1024C>A	c.(1024-1026)Ctt>Att	p.L342I	LHX9_ENST00000337020.2_Intron|LHX9_ENST00000561173.1_Intron|LHX9_ENST00000367391.1_Intron|LHX9_ENST00000367390.3_Missense_Mutation_p.L333I	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	342					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						CGGCACGTCGCTTCCGGCCCC	0.552																																					p.L342I		Atlas-SNP	.											.	LHX9	144	.	0			c.C1024A						.						72	75	74					1																	197898219		2203	4300	6503	SO:0001583	missense	56956	exon5			ACGTCGCTTCCGG	AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"Homeoboxes / LIM class"	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367387.4:c.1024C>A	chr1.hg19:g.197898219C>A	ENSP00000356357:p.Leu342Ile	170.0	0.0		203.0	121.0	NM_020204	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Missense_Mutation	SNP	ENST00000367387.4	hg19	CCDS1393.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.395909	0.62177	.	.	ENSG00000143355	ENST00000367390;ENST00000367387	D;D	0.89123	-2.46;-2.47	5.84	4.92	0.64577	.	0.127979	0.51477	N	0.000083	D	0.83862	0.5346	N	0.08118	0	0.45747	D	0.998646	P;P	0.46656	0.466;0.882	B;P	0.49752	0.294;0.621	D	0.84989	0.0893	10	0.36615	T	0.2	.	16.4627	0.84069	0.1321:0.8679:0.0:0.0	.	342;333	Q9NQ69;Q9NQ69-2	LHX9_HUMAN;.	I	333;342	ENSP00000356360:L333I;ENSP00000356357:L342I	ENSP00000356357:L342I	L	+	1	0	LHX9	196164842	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.656000	0.61483	1.460000	0.47911	0.591000	0.81541	CTT	.	.		0.552	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086547.2	NM_020204		A	197898219	C	A	197898219	3	1	9	1	0	0	0	0	1	0	0	0	8786	797	28	3	1074	3	LHX9	1	197898219	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	16172060	197898219	51352402	9	696										
LAD1	3898	hgsc.bcm.edu	37	chr1	201355885	201355885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ggccagcaccttctcagagaTggaggttttatcggagacca	12	10	1	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr1:201355885T>C	ENST00000391967.2	-	3	905	c.604A>G	c.(604-606)Atc>Gtc	p.I202V	LAD1_ENST00000367313.3_Missense_Mutation_p.I216V	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	202						basement membrane (GO:0005604)	structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						TTCTCAGAGATGGAGGTTTTA	0.473																																					p.I202V		Atlas-SNP	.											.	LAD1	42	.	0			c.A604G						.						95	105	102					1																	201355885		2203	4300	6503	SO:0001583	missense	3898	exon3			CAGAGATGGAGGT	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.604A>G	chr1.hg19:g.201355885T>C	ENSP00000375829:p.Ile202Val	80.0	0.0		76.0	30.0	NM_005558	O95614|Q96GD8	Missense_Mutation	SNP	ENST00000391967.2	hg19	CCDS1410.1	.	.	.	.	.	.	.	.	.	.	T	5.784	0.329037	0.10956	.	.	ENSG00000159166	ENST00000391967;ENST00000367313	T;T	0.10668	2.89;2.85	4.8	-9.59	0.00556	.	2.799430	0.00777	N	0.001256	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.28808	-1.0032	10	0.07175	T	0.84	0.7371	5.9283	0.19124	0.0818:0.5835:0.2345:0.1002	.	216;202	E9PDI4;O00515	.;LAD1_HUMAN	V	202;216	ENSP00000375829:I202V;ENSP00000356282:I216V	ENSP00000356282:I216V	I	-	1	0	LAD1	199622508	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.536000	0.00940	-2.860000	0.00327	-0.256000	0.11100	ATC	.	.		0.473	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558		C	201355885	T	C	201355885	3	2	9	1	0	0	0	0	1	0	0	0	8608	1464	51	2	981	2	LAD1	1	201355885	Missense_Mutation	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10	3457666	201355885	47894736	10	697										
SOX11	6664	hgsc.bcm.edu	37	chr2	5833474	5833474	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ggcagcctgcgcgtgagcggCtcgggcggcggcggcgcggg	23	13	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr2:5833474C>T	ENST00000322002.3	+	1	676	c.621C>T	c.(619-621)ggC>ggT	p.G207G	AC108025.2_ENST00000453678.1_RNA|AC107057.2_ENST00000458264.1_RNA|AC010729.1_ENST00000455579.2_RNA|AC108025.2_ENST00000420221.1_RNA	NM_003108.3	NP_003099.1	P35716	SOX11_HUMAN	SRY (sex determining region Y)-box 11	207	Poly-Gly.				cardiac ventricle formation (GO:0003211)|closure of optic fissure (GO:0061386)|cornea development in camera-type eye (GO:0061303)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|eyelid development in camera-type eye (GO:0061029)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|hard palate development (GO:0060022)|kidney development (GO:0001822)|lens morphogenesis in camera-type eye (GO:0002089)|limb bud formation (GO:0060174)|lung morphogenesis (GO:0060425)|negative regulation of cell death (GO:0060548)|negative regulation of gene expression (GO:0010629)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural crest cell development (GO:0014032)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|neuron differentiation (GO:0030182)|noradrenergic neuron differentiation (GO:0003357)|oligodendrocyte development (GO:0014003)|outflow tract morphogenesis (GO:0003151)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of hippo signaling (GO:0035332)|positive regulation of hormone secretion (GO:0046887)|positive regulation of lens epithelial cell proliferation (GO:2001111)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|signal transduction involved in cell cycle checkpoint (GO:0072395)|skeletal muscle cell differentiation (GO:0035914)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)|somite development (GO:0061053)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|translation (GO:0006412)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|translation factor activity, nucleic acid binding (GO:0008135)			central_nervous_system(5)|cervix(1)|endometrium(1)|liver(1)|lung(4)|stomach(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)		GCGTGAGCGGCTCGGGCGGCG	0.731																																					p.G207G		Atlas-SNP	.											.	SOX11	69	.	0			c.C621T						.						7	9	9					2																	5833474		1673	3501	5174	SO:0001819	synonymous_variant	6664	exon1			GAGCGGCTCGGGC		CCDS1654.1	2p25	2008-05-21			ENSG00000176887	ENSG00000176887		"SRY (sex determining region Y)-boxes"	11191	protein-coding gene	gene with protein product	"SRY-related HMG-box gene 11"	600898				8666406, 12637543	Standard	NM_003108		Approved		uc002qyj.3	P35716	OTTHUMG00000090333	ENST00000322002.3:c.621C>T	chr2.hg19:g.5833474C>T		9.0	0.0		23.0	14.0	NM_003108	Q4ZFV8	Silent	SNP	ENST00000322002.3	hg19	CCDS1654.1																																																																																			.	.		0.731	SOX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206698.1	NM_003108		T	5833474	C	T	5833474	2	4	9	1	0	0	0	0	0	0	0	1	14957	784	28	3		3	SOX11	2	5833474	Silent	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		5833474	237365899	11	698										
PPP1CB	5500	hgsc.bcm.edu	37	chr2	28975008	28975008	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	aagatggcggacggggagctGaacgtggacagcctcatcac	15	10	2	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr2:28975008G>T	ENST00000395366.2	+	1	290	c.18G>T	c.(16-18)ctG>ctT	p.L6L	PPP1CB_ENST00000358506.2_Silent_p.L6L|PPP1CB_ENST00000296122.6_Silent_p.L6L	NM_002709.2	NP_002700.1	P62140	PP1B_HUMAN	protein phosphatase 1, catalytic subunit, beta isozyme	6					cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|G2/M transition of mitotic cell cycle (GO:0000086)|glycogen metabolic process (GO:0005977)|mitotic cell cycle (GO:0000278)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of circadian rhythm (GO:0042752)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|glycogen granule (GO:0042587)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|myosin phosphatase activity (GO:0017018)|myosin-light-chain-phosphatase activity (GO:0050115)|phosphatase activity (GO:0016791)|protein kinase binding (GO:0019901)			cervix(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(172;0.155)					ACGGGGAGCTGAACGTGGACA	0.716																																					p.L6L		Atlas-SNP	.											.	PPP1CB	29	.	0			c.G18T						.						39	29	32					2																	28975008		1973	3768	5741	SO:0001819	synonymous_variant	5500	exon2			GGAGCTGAACGTG		CCDS33169.1	2p23	2013-01-18	2010-03-05		ENSG00000213639	ENSG00000213639	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9282	protein-coding gene	gene with protein product		600590	"protein phosphatase 1, catalytic subunit, beta isoform"			8312365	Standard	NM_002709		Approved	PP1B, PP-1B, PP1beta	uc002rmg.3	P62140	OTTHUMG00000152011	ENST00000395366.2:c.18G>T	chr2.hg19:g.28975008G>T		164.0	0.0		267.0	175.0	NM_206876	B2R5V4|D6W565|P37140|Q5U087|Q6FG45	Silent	SNP	ENST00000395366.2	hg19	CCDS33169.1																																																																																			.	.		0.716	PPP1CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324841.1			T	28975008	G	T	28975008	2	4	9	1	0	0	0	0	0	0	0	1	12362	1277	45	3		3	PPP1CB	2	28975008	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	23141534	28975008	214224365	12	699										
IWS1	55677	hgsc.bcm.edu	37	chr2	128244217	128244217	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	cccttgcacgggcacagaatCcaggatctccaggtctaaga	10	13	2	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr2:128244217C>A	ENST00000295321.4	-	13	2499	c.2240G>T	c.(2239-2241)gGa>gTa	p.G747V	AC010976.2_ENST00000595561.1_RNA|AC010976.2_ENST00000596439.1_RNA|AC010976.2_ENST00000599001.1_RNA|AC010976.2_ENST00000454503.2_RNA|AC010976.2_ENST00000598065.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	747	Interaction with SUPT6H and ALYREF.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		GGCACAGAATCCAGGATCTCC	0.522																																					p.G747V		Atlas-SNP	.											.	IWS1	61	.	0			c.G2240T						.						95	88	90					2																	128244217		2203	4300	6503	SO:0001583	missense	55677	exon13			CAGAATCCAGGAT	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.2240G>T	chr2.hg19:g.128244217C>A	ENSP00000295321:p.Gly747Val	87.0	0.0		77.0	23.0	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	hg19	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.841389	0.91197	.	.	ENSG00000163166	ENST00000295321;ENST00000433551	T	0.42131	0.98	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.69342	0.3100	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71407	-0.4602	9	.	.	.	-23.4974	19.4647	0.94932	0.0:1.0:0.0:0.0	.	747	Q96ST2	IWS1_HUMAN	V	747;700	ENSP00000295321:G747V	.	G	-	2	0	IWS1	127960687	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.770000	0.85390	2.592000	0.87571	0.655000	0.94253	GGA	.	.		0.522	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		A	128244217	C	A	128244217	3	1	9	1	0	0	0	0	1	0	0	0	7940	855	30	3	227	3	IWS1	2	128244217	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	99269209	128244217	114955156	13	700										
TTN	7273	hgsc.bcm.edu	37	chr2	179632561	179632561	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tttgcagttgacacgttgccTcctgccaccactgtgtactt	8	13	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr2:179632561T>C	ENST00000591111.1	-	40	9620	c.9396A>G	c.(9394-9396)ggA>ggG	p.G3132G	TTN_ENST00000360870.5_Silent_p.G3132G|TTN_ENST00000342175.6_Silent_p.G3086G|TTN_ENST00000359218.5_Silent_p.G3086G|TTN_ENST00000589042.1_Silent_p.G3132G|TTN_ENST00000342992.6_Silent_p.G3132G|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000460472.2_Silent_p.G3086G			Q8WZ42	TITIN_HUMAN	titin	13464	Ig-like 18.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACACGTTGCCTCCTGCCACCA	0.438																																					p.G3132G		Atlas-SNP	.											.	TTN	18412	.	0			c.A9396G						.						110	112	111					2																	179632561		2203	4300	6503	SO:0001819	synonymous_variant	7273	exon40			GTTGCCTCCTGCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.9396A>G	chr2.hg19:g.179632561T>C		82.0	0.0		75.0	20.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179632561	T	C	179632561	2	2	9	1	0	0	0	0	0	0	0	1	16750	1538	54	2		2	TTN	2	179632561	Silent	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10	51388344	179632561	63566812	14	701										
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226447694	226447694	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tgaccagcctcttctcctccGgccgcagcctgctgcgcaag	10	18	2	1	rs201097764	byFrequency	TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr2:226447694G>T	ENST00000272907.6	+	4	1974	c.1561G>T	c.(1561-1563)Ggc>Tgc	p.G521C	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	521					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CTTCTCCTCCGGCCGCAGCCT	0.701																																					p.G521C		Atlas-SNP	.											.	.	.	.	0			c.G1561T						.						11	14	13					2																	226447694		1871	4019	5890	SO:0001583	missense	57624	exon4			TCCTCCGGCCGCA	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1561G>T	chr2.hg19:g.226447694G>T	ENSP00000272907:p.Gly521Cys	118.0	0.0		102.0	33.0	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	hg19	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	G	16.05	3.013863	0.54468	.	.	ENSG00000144460	ENST00000272907	T	0.78003	-1.14	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.87430	0.6175	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87772	0.2606	10	0.72032	D	0.01	-26.4774	19.7096	0.96089	0.0:0.0:1.0:0.0	.	35;521	Q9P242-3;Q9P242	.;K1486_HUMAN	C	521	ENSP00000272907:G521C	ENSP00000272907:G521C	G	+	1	0	KIAA1486	226155938	1.000000	0.71417	0.201000	0.23476	0.053000	0.15095	9.476000	0.97823	2.652000	0.90054	0.655000	0.94253	GGC	.	G|0.999;A|0.001		0.701	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		T	226447694	G	T	226447694	3	4	9	1	0	0	0	0	1	0	0	0	8246	1116	39	1	1571	1	KIAA1486	2	226447694	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	46815133	226447694	16751679	15	702										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230672462	230672462	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	aatcctgttatatggatgccAgaggccccgatcatcacgcc	9	13	2	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr2:230672462A>T	ENST00000283943.5	-	16	2492	c.2314T>A	c.(2314-2316)Tgg>Agg	p.W772R	TRIP12_ENST00000389044.4_Missense_Mutation_p.W820R|TRIP12_ENST00000389045.3_Missense_Mutation_p.W475R|TRIP12_ENST00000543084.1_Intron	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	772	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TATGGATGCCAGAGGCCCCGA	0.458																																					p.W772R		Atlas-SNP	.											.	TRIP12	207	.	0			c.T2314A						.						168	139	149					2																	230672462		2203	4300	6503	SO:0001583	missense	9320	exon16			GATGCCAGAGGCC	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.2314T>A	chr2.hg19:g.230672462A>T	ENSP00000283943:p.Trp772Arg	77.0	0.0		81.0	25.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	hg19	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.525521	0.85600	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	T;T;T	0.68903	0.32;-0.36;0.32	5.23	5.23	0.72850	WWE domain (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80352	0.4607	M	0.67397	2.05	0.80722	D	1	D;D;D;D	0.76494	0.999;0.996;0.99;0.99	D;D;D;D	0.87578	0.998;0.992;0.969;0.969	T	0.82752	-0.0302	10	0.87932	D	0	.	15.424	0.75038	1.0:0.0:0.0:0.0	.	778;475;820;772	D4HL82;Q14CF1;Q14CA3;Q14669	.;.;.;TRIPC_HUMAN	R	772;475;820	ENSP00000283943:W772R;ENSP00000373697:W475R;ENSP00000373696:W820R	ENSP00000283943:W772R	W	-	1	0	TRIP12	230380706	1.000000	0.71417	0.993000	0.49108	0.991000	0.79684	9.135000	0.94478	2.103000	0.63969	0.383000	0.25322	TGG	.	.		0.458	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		T	230672462	A	T	230672462	3	4	9	1	0	0	0	0	1	0	0	0	16571	188	7	4	3768	4	TRIP12	2	230672462	Missense_Mutation	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	4224768	230672462	12526911	16	703										
FANCD2	2177	hgsc.bcm.edu	37	chr3	10083389	10083389	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gacttgacccaaacttcctaTtgaaggtagaaaagactcag	8	9	1	4			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr3:10083389T>C	ENST00000419585.1	+	10	939	c.778T>C	c.(778-780)Ttg>Ctg	p.L260L	FANCD2_ENST00000383807.1_Silent_p.L260L|FANCD2_ENST00000383806.1_Silent_p.L260L|FANCD2_ENST00000287647.3_Silent_p.L260L			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	260	Interaction with BRCA2.|Interaction with FANCE.				DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		AAACTTCCTATTGAAGGTAGA	0.438			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.L260L		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.T778C						.						84	81	82					3																	10083389		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon10	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TTCCTATTGAAGG	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.778T>C	chr3.hg19:g.10083389T>C		236.0	0.0		206.0	64.0	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	hg19	CCDS33696.1																																																																																			.	.		0.438	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			C	10083389	T	C	10083389	2	2	9	1	0	0	0	0	0	0	0	1	5673	1490	52	2		2	FANCD2	3	10083389	Silent	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10		10083389	187939041	17	704										
ARMC8	25852	hgsc.bcm.edu	37	chr3	138009428	138009428	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	aaattacgagacatgggcatCgtagatattctacacaaact	7	8	1	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr3:138009428C>A	ENST00000469044.1	+	21	2206	c.1935C>A	c.(1933-1935)atC>atA	p.I645I	NME9_ENST00000317876.4_Intron|ARMC8_ENST00000491704.1_Silent_p.I603I|ARMC8_ENST00000481646.1_Silent_p.I631I|ARMC8_ENST00000393058.3_Silent_p.I635I|ARMC8_ENST00000485396.1_Silent_p.I572I|NME9_ENST00000484930.1_Intron|NME9_ENST00000383180.2_Intron|ARMC8_ENST00000538260.1_Silent_p.I614I|ARMC8_ENST00000461822.1_Silent_p.I578I|NME9_ENST00000536478.1_Intron|NME9_ENST00000341790.5_Intron	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	645										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						ACATGGGCATCGTAGATATTC	0.428																																					p.I631I		Atlas-SNP	.											.	ARMC8	79	.	0			c.C1893A						.						79	75	77					3																	138009428		1916	4126	6042	SO:0001819	synonymous_variant	25852	exon22			GGGCATCGTAGAT		CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"Armadillo repeat containing"	24999	protein-coding gene	gene with protein product	"GID complex subunit 5, VID28 homolog (S. cerevisiae)"					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.1935C>A	chr3.hg19:g.138009428C>A		98.0	0.0		124.0	46.0	NM_015396	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Silent	SNP	ENST00000469044.1	hg19																																																																																				.	.		0.428	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396		A	138009428	C	A	138009428	2	1	9	1	0	0	0	0	0	0	0	1	957	874	31	1		1	ARMC8	3	138009428	Silent	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	127926039	138009428	60013002	18	705										
ZBBX	79740	hgsc.bcm.edu	37	chr3	167035353	167035353	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gtggatgtgggaacgtatctGgtagcattttaaaaagttgc	13	4	1	0	rs572404264		TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr3:167035353G>A	ENST00000392766.2	-	13	1356	c.1016C>T	c.(1015-1017)cCa>cTa	p.P339L	ZBBX_ENST00000392767.2_Missense_Mutation_p.P339L|ZBBX_ENST00000455345.2_Missense_Mutation_p.P339L|ZBBX_ENST00000307529.5_Missense_Mutation_p.P339L|ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000392764.1_Missense_Mutation_p.P310L	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	339				P -> S (in Ref. 2; BAB15532). {ECO:0000305}.		intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						GAACGTATCTGGTAGCATTTT	0.358													G|||	1	0.000199681	0	0	5008	,	,		17152	0		0	False		,,,				2504	0.001				p.P339L		Atlas-SNP	.											.	ZBBX	299	.	0			c.C1016T						.						173	156	161					3																	167035353		1834	4085	5919	SO:0001583	missense	79740	exon13			GTATCTGGTAGCA	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1016C>T	chr3.hg19:g.167035353G>A	ENSP00000376519:p.Pro339Leu	89.0	0.0		174.0	58.0	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	hg19	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	G	12.89	2.073929	0.36566	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.15603	2.59;2.59;2.57;2.57;2.41	4.78	0.915	0.19366	.	0.385688	0.25052	N	0.033512	T	0.11623	0.0283	L	0.39020	1.185	0.09310	N	1	B;B	0.20887	0.033;0.049	B;B	0.22601	0.04;0.026	T	0.19647	-1.0299	10	0.51188	T	0.08	-0.3935	5.3186	0.15870	0.1766:0.3181:0.5053:0.0	.	339;339	A8MT70-2;A8MT70	.;ZBBX_HUMAN	L	339;339;339;339;310	ENSP00000376519:P339L;ENSP00000376520:P339L;ENSP00000390232:P339L;ENSP00000305065:P339L;ENSP00000376517:P310L	ENSP00000305065:P339L	P	-	2	0	ZBBX	168518047	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.182000	0.16900	0.158000	0.19367	-0.181000	0.13052	CCA	.	.		0.358	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		A	167035353	G	A	167035353	3	1	9	1	0	0	0	0	1	0	0	0	17531	1348	47	3	1422	3	ZBBX	3	167035353	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	29025925	167035353	30987077	19	706										
DGKQ	1609	hgsc.bcm.edu	37	chr4	955623	955623	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	acacacccttgttgtgcagcCtgcaggacggggcaggtcac	13	13	1	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr4:955623C>T	ENST00000273814.3	-	20	2389		c.e20-1		DGKQ_ENST00000502309.1_5'Flank	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa						blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to ATP (GO:0033198)|thrombin receptor signaling pathway (GO:0070493)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|phospholipase binding (GO:0043274)			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GTTGTGCAGCCTGCAGGACGG	0.667																																					.	Esophageal Squamous(17;537 645 4447 26373)	Atlas-SNP	.											.	DGKQ	29	.	0			c.2316-1G>A						.						62	64	64					4																	955623		2202	4300	6502	SO:0001630	splice_region_variant	1609	exon21			TGCAGCCTGCAGG	L38707	CCDS3342.1	4p16.3	2008-08-29	2002-08-29		ENSG00000145214	ENSG00000145214			2856	protein-coding gene	gene with protein product		601207	"diacylglycerol kinase, theta (110kD)"	DAGK4		8617502, 9099683	Standard	NM_001347		Approved	DAGK, DAGK7	uc003gbw.4	P52824	OTTHUMG00000088629	ENST00000273814.3:c.2316-1G>A	chr4.hg19:g.955623C>T		37.0	0.0		31.0	10.0	NM_001347	Q6P3W4	Splice_Site	SNP	ENST00000273814.3	hg19	CCDS3342.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.777872	0.31502	.	.	ENSG00000145214	ENST00000273814;ENST00000509465	.	.	.	5.27	4.42	0.53409	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5968	0.50979	0.0:0.912:0.0:0.088	.	.	.	.	.	-1	.	.	.	-	.	.	DGKQ	945623	1.000000	0.71417	0.992000	0.48379	0.157000	0.22087	3.425000	0.52771	1.216000	0.43427	0.556000	0.70494	.	.	.		0.667	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1		Intron	T	955623	C	T	955623	5	4	9	1	0	0	0	0	0	0	1	0	4475	695	24	3	529	3	DGKQ	4	955623	Splice_Site	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		955623	190198653	20	707										
HTT	3064	hgsc.bcm.edu	37	chr4	3241612	3241612	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	aggatgggcaagctggagcaGgtggacgtgaaccttttctg	16	7	1	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr4:3241612G>C	ENST00000355072.5	+	67	9400	c.9255G>C	c.(9253-9255)caG>caC	p.Q3085H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	3085					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AGCTGGAGCAGGTGGACGTGA	0.577																																					p.Q3085H		Atlas-SNP	.											.	HTT	221	.	0			c.G9255C						.						32	34	34					4																	3241612		2156	4246	6402	SO:0001583	missense	3064	exon67			GGAGCAGGTGGAC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.9255G>C	chr4.hg19:g.3241612G>C	ENSP00000347184:p.Gln3085His	84.0	0.0		77.0	14.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	9.826	1.187014	0.21870	.	.	ENSG00000197386	ENST00000355072	T	0.05319	3.46	5.0	-4.71	0.03279	.	0.392033	0.27027	N	0.021291	T	0.02807	0.0084	L	0.29908	0.895	0.30878	N	0.731785	B	0.02656	0.0	B	0.04013	0.001	T	0.41070	-0.9529	10	0.15952	T	0.53	.	1.821	0.03110	0.3015:0.2371:0.3433:0.1181	.	3085	P42858	HD_HUMAN	H	3085	ENSP00000347184:Q3085H	ENSP00000347184:Q3085H	Q	+	3	2	HTT	3211410	0.001000	0.12720	0.932000	0.37286	0.997000	0.91878	-0.660000	0.05317	-0.986000	0.03498	0.655000	0.94253	CAG	.	.		0.577	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		C	3241612	G	C	3241612	3	2	9	1	0	0	0	0	1	0	0	0	7466	991	35	4	9521	4	HTT	4	3241612	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	2285989	3241612	187912664	21	708										
HOPX	84525	hgsc.bcm.edu	37	chr4	57522168	57522168	+	5'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tcgcggtctccgccgacatgGtccctgcgcgctgcggggca	15	16	1	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr4:57522168G>A	ENST00000337881.7	-	0	655				HOPX_ENST00000420433.1_Missense_Mutation_p.T18I|HOPX_ENST00000555760.2_5'UTR|HOPX_ENST00000317745.7_5'UTR|HOPX_ENST00000503639.3_5'UTR|HOPX_ENST00000381255.3_5'UTR|HOPX_ENST00000508121.1_Missense_Mutation_p.T18I|HOPX_ENST00000556376.2_5'UTR|HOPX_ENST00000556614.2_5'UTR|HOPX_ENST00000381260.3_5'UTR|HOPX_ENST00000553379.2_5'UTR|HOPX_ENST00000554144.1_Missense_Mutation_p.T18I	NM_139212.3	NP_631958.1	Q9BPY8	HOP_HUMAN	HOP homeobox						heart development (GO:0007507)|histone deacetylation (GO:0016575)|lung alveolus development (GO:0048286)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of heart contraction (GO:0008016)|regulation of protein binding (GO:0043393)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(2)|lung(5)|skin(1)	8	Glioma(25;0.08)|all_neural(26;0.101)					CGCCGACATGGTCCCTGCGCG	0.706																																					p.T18I		Atlas-SNP	.											.	HOPX	28	.	0			c.C53T						.						41	37	39					4																	57522168		2202	4300	6502	SO:0001623	5_prime_UTR_variant	84525	exon3			GACATGGTCCCTG		CCDS3507.1, CCDS47062.1, CCDS54767.1	4q12	2011-06-20			ENSG00000171476	ENSG00000171476		"Homeoboxes / PRD class"	24961	protein-coding gene	gene with protein product	"homeobox only domain"	607275				12297045	Standard	NM_032495		Approved	LAGY, HOP, OB1, NECC1, SMAP31	uc003hbz.2	Q9BPY8	OTTHUMG00000128768	ENST00000337881.7:c.-2C>T	chr4.hg19:g.57522168G>A		39.0	0.0		46.0	12.0	NM_032495	A8K0Z2|E9PB55|G3V294|Q8N0V6|Q96CI1	Missense_Mutation	SNP	ENST00000337881.7	hg19	CCDS3507.1	.	.	.	.	.	.	.	.	.	.	G	4.676	0.125718	0.08931	.	.	ENSG00000171476	ENST00000420433;ENST00000554144;ENST00000508121	T;T	0.58358	0.34;0.34	4.77	4.77	0.60923	.	0.418184	0.18554	U	0.137828	T	0.40247	0.1109	N	0.08118	0	0.29114	N	0.880681	P;P	0.45126	0.851;0.59	P;B	0.46629	0.522;0.112	T	0.41998	-0.9477	10	0.62326	D	0.03	-13.7595	13.313	0.60390	0.0:0.0:1.0:0.0	.	18;18	G3V294;E9PB55	.;.	I	18	ENSP00000396275:T18I;ENSP00000422175:T18I	ENSP00000370659:T18I	T	-	2	0	HOPX	57216925	1.000000	0.71417	0.992000	0.48379	0.018000	0.09664	3.325000	0.52030	2.187000	0.69744	0.491000	0.48974	ACC	.	.		0.706	HOPX-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250689.4			A	57522168	G	A	57522168	1	1	9	0	1	0	0	0	0	0	0	0	7294	1261	44	3		3	HOPX	4	57522168	5'UTR	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	54280556	57522168	133632108	22	709										
ALB	213	hgsc.bcm.edu	37	chr4	74283302	74283306	+	Frame_Shift_Del	DEL	AGAGG	AGAGG	-													0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gtgtcaactccaactcttgtAgaggtctcaagaaacctagg							TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	AGAGG	AGAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr4:74283302_74283306delAGAGG	ENST00000503124.1	+	9	1101_1105	c.894_898delAGAGG	c.(892-900)gtagaggtcfs	p.VEV298fs	ALB_ENST00000415165.2_Frame_Shift_Del_p.VEV256fs|ALB_ENST00000505649.1_Intron|ALB_ENST00000509063.1_Frame_Shift_Del_p.VEV448fs|ALB_ENST00000295897.4_Frame_Shift_Del_p.VEV448fs|ALB_ENST00000401494.3_Frame_Shift_Del_p.VEV333fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CAACTCTTGTAGAGGTCTCAAGAAA	0.39																																					p.448_449del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.1343_1347del						.																																			SO:0001589	frameshift_variant	213	exon11			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.894_898delAGAGG	chr4.hg19:g.74283302_74283306delAGAGG	ENSP00000421027:p.Val298fs	212.0	0.0		212.0	55.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.39	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74283306	AGAGG	-	74283302	7	5	9	1	0	1	0	1	0	0	0	0	486	407	15	0	1386	0	ALB	4	74283302	Frame_Shift_Del	DEL	AGAGG	TCGA-2Y-A9GZ-01A-11D-A38X-10	16761134	74283302	116870974	23	710										
ANXA5	308	hgsc.bcm.edu	37	chr4	122602881	122602881	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tcaggtgtccttgaagcaatAatttctgtcagtactttttc	7	8	3	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr4:122602881A>G	ENST00000296511.5	-	6	624	c.339T>C	c.(337-339)atT>atC	p.I113I	ANXA5_ENST00000515017.1_Intron|ANXA5_ENST00000501272.2_Silent_p.I53I|ANXA5_ENST00000509016.1_5'UTR	NM_001154.3	NP_001145.1	P08758	ANXA5_HUMAN	annexin A5	113					blood coagulation (GO:0007596)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of coagulation (GO:0050819)|response to organic substance (GO:0010033)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipase inhibitor activity (GO:0004859)|phospholipid binding (GO:0005543)			NS(1)|breast(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)	15						TTGAAGCAATAATTTCTGTCA	0.323																																					p.I113I	Pancreas(191;1279 2147 16046 17806 52646)|GBM(88;628 1285 16585 32846 50188)	Atlas-SNP	.											.	ANXA5	29	.	0			c.T339C						.						203	190	195					4																	122602881		2203	4300	6503	SO:0001819	synonymous_variant	308	exon6			AGCAATAATTTCT	U05770	CCDS3720.1	4q27	2008-02-05			ENSG00000164111	ENSG00000164111		"Annexins"	543	protein-coding gene	gene with protein product		131230		ENX2, ANX5		2960376	Standard	NM_001154		Approved		uc003idv.4	P08758	OTTHUMG00000133034	ENST00000296511.5:c.339T>C	chr4.hg19:g.122602881A>G		57.0	0.0		90.0	25.0	NM_001154	D3DNW7|Q6FHB3|Q6FI16|Q8WV69|Q9UDH9	Silent	SNP	ENST00000296511.5	hg19	CCDS3720.1																																																																																			.	.		0.323	ANXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256636.2	NM_001154		G	122602881	A	G	122602881	2	3	9	1	0	0	0	0	0	0	0	1	721	358	13	2		2	ANXA5	4	122602881	Silent	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	48319579	122602881	68551395	24	711										
NPY1R	4886	hgsc.bcm.edu	37	chr4	164246911	164246911	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ctttttaggcgtatatatatCtatggaagaaaaaagtttaa	7	3	1	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr4:164246911C>G	ENST00000296533.2	-	3	1231		c.e3-1		NPY1R_ENST00000509586.1_Splice_Site	NM_000909.5	NP_000900.1	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose metabolic process (GO:0006006)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|regulation of blood pressure (GO:0008217)|regulation of multicellular organism growth (GO:0040014)|sensory perception of pain (GO:0019233)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			breast(1)|cervix(1)|large_intestine(4)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)	30	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GTATATATATCTATGGAAGAA	0.318																																					.		Atlas-SNP	.											.	NPY1R	72	.	0			c.700-1G>C						.						46	45	45					4																	164246911		2202	4294	6496	SO:0001630	splice_region_variant	4886	exon4			ATATATCTATGGA		CCDS34089.1	4q31.3-q32	2012-08-08				ENSG00000164128		"GPCR / Class A : Neuropeptide receptors : Y"	7956	protein-coding gene	gene with protein product		162641		NPYR		8095935	Standard	NM_000909		Approved		uc003iqm.2	P25929		ENST00000296533.2:c.700-1G>C	chr4.hg19:g.164246911C>G		29.0	0.0		34.0	16.0	NM_000909	B2R6H5	Splice_Site	SNP	ENST00000296533.2	hg19	CCDS34089.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.841549	0.32513	.	.	ENSG00000164128	ENST00000296533;ENST00000512819	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1512	0.98086	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NPY1R	164466361	1.000000	0.71417	0.999000	0.59377	0.610000	0.37248	3.636000	0.54317	2.771000	0.95319	0.655000	0.94253	.	.	.		0.318	NPY1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364685.1		Intron	G	164246911	C	G	164246911	5	3	9	1	0	0	0	0	0	0	1	0	10617	927	32	4	459	4	NPY1R	4	164246911	Splice_Site	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	41644030	164246911	26907365	25	712										
AADAT	51166	hgsc.bcm.edu	37	chr4	170983132	170983140	+	In_Frame_Del	DEL	GGAGCATTA	GGAGCATTA	-													0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gacgtagaaagcatttccagGgagcattaatacctaagaga							TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	GGAGCATTA	GGAGCATTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr4:170983132_170983140delGGAGCATTA	ENST00000337664.4	-	12	1415_1423	c.1139_1147delTAATGCTCC	c.(1138-1149)ttaatgctccct>tct	p.380_383LMLP>S	AADAT_ENST00000509167.1_In_Frame_Del_p.384_387LMLP>S|AADAT_ENST00000353187.2_In_Frame_Del_p.380_383LMLP>S|AADAT_ENST00000515480.1_In_Frame_Del_p.380_383LMLP>S	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN	aminoadipate aminotransferase	380				L -> S (in Ref. 3; BAG51596). {ECO:0000305}.	2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	mitochondrial matrix (GO:0005759)	2-aminoadipate transaminase activity (GO:0047536)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)		GCATTTCCAGGGAGCATTAATACCTAAGA	0.402																																					p.380_383del		Pindel	.											.	AADAT	28	.	0			c.1140_1148del						.																																			SO:0001651	inframe_deletion	51166	exon13			.	AF097994	CCDS3814.1, CCDS75209.1	4q33	2010-12-09			ENSG00000109576	ENSG00000109576	2.6.1.39		17929	protein-coding gene	gene with protein product	"kynurenine aminotransferase II", "L kynurenine/alpha aminoadipate aminotransferase"	611754				12126930, 10441733	Standard	NM_182662		Approved	KATII, KAT2	uc003isr.3	Q8N5Z0	OTTHUMG00000160912	ENST00000337664.4:c.1139_1147delTAATGCTCC	chr4.hg19:g.170983132_170983140delGGAGCATTA	ENSP00000336808:p.Leu380_Pro383delinsSer	76.0	0.0		70.0	13.0	NM_182662	B3KP84|Q9UL02	In_Frame_Del	DEL	ENST00000337664.4	hg19	CCDS3814.1																																																																																			.	.		0.402	AADAT-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362952.1	NM_016228		-	170983140	GGAGCATTA	-	170983132	7	5	9	1	0	1	0	1	0	0	0	0	14	1232	43	0	138	0	AADAT	4	170983132	In_Frame_Del	DEL	GGAGCATTA	TCGA-2Y-A9GZ-01A-11D-A38X-10	6736221	170983132	20171144	26	713										
FRG1	2483	hgsc.bcm.edu	37	chr4	190878551	190878551	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ttttgttatttgtttcacttAggggaaaatggctttgttgg	11	3	1	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr4:190878551A>T	ENST00000226798.4	+	6	654		c.e6-1		FRG1_ENST00000514482.1_Splice_Site	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1						mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.?(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TGTTTCACTTAGGGGAAAATG	0.358																																					.		Atlas-SNP	.											FRG1,NS,malignant_melanoma,0,1	FRG1	76	.	1	Unknown(1)	NS(1)	c.433-2A>T						.						10	16	14					4																	190878551		2077	4234	6311	SO:0001630	splice_region_variant	2483	exon6			TCACTTAGGGGAA	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.433-1A>T	chr4.hg19:g.190878551A>T		83.0	0.0		84.0	4.0	NM_004477	A8K775	Splice_Site	SNP	ENST00000226798.4	hg19	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	N	13.55	2.270254	0.40194	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	.	.	.	3.8	3.8	0.43715	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8823	0.46946	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FRG1	191115545	1.000000	0.71417	1.000000	0.80357	0.407000	0.30961	9.035000	0.93752	1.517000	0.48917	0.373000	0.22412	.	.	.		0.358	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	Intron	T	190878551	A	T	190878551	5	4	9	1	0	0	0	0	0	0	1	0	6054	434	15	4	453	4	FRG1	4	190878551	Splice_Site	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	19895419	190878551	275725	27	714										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5463510	5463510	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	cccgttcagatgcaggcaggCaaaccgatggtggggaagaa	15	9	1	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr5:5463510C>G	ENST00000296564.7	+	13	4285	c.4063C>G	c.(4063-4065)Caa>Gaa	p.Q1355E		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1355					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						TGCAGGCAGGCAAACCGATGG	0.557																																					p.Q1355E		Atlas-SNP	.											.	KIAA0947	301	.	0			c.C4063G						.						32	34	33					5																	5463510		2018	4176	6194	SO:0001583	missense	23379	exon13			GGCAGGCAAACCG																												ENST00000296564.7:c.4063C>G	chr5.hg19:g.5463510C>G	ENSP00000296564:p.Gln1355Glu	86.0	0.0		98.0	16.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	C	5.188	0.220180	0.09863	.	.	ENSG00000164151	ENST00000296564	T	0.08896	3.04	4.49	-0.376	0.12505	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.44590	-0.9318	9	0.02654	T	1	3.2374	0.8985	0.01269	0.1764:0.367:0.2571:0.1995	.	1355	Q9Y2F5	K0947_HUMAN	E	1355	ENSP00000296564:Q1355E	ENSP00000296564:Q1355E	Q	+	1	0	KIAA0947	5516510	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.294000	0.19047	0.124000	0.18369	0.305000	0.20034	CAA	.	.		0.557	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			G	5463510	C	G	5463510	3	3	9	1	0	0	0	0	1	0	0	0	8211	711	25	4	4113	4	KIAA0947	5	5463510	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		5463510	175451750	28	715										
MARVELD2	153562	hgsc.bcm.edu	37	chr5	68728859	68728859	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	agaagttcaggctgtcctgaGgaagtttgatgagctggatg	15	5	1	4			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr5:68728859G>A	ENST00000325631.5	+	5	1516	c.1442G>A	c.(1441-1443)aGg>aAg	p.R481K	MARVELD2_ENST00000413223.2_Missense_Mutation_p.R365K	NM_001038603.2|NM_001244734.1	NP_001033692.2|NP_001231663.1	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	481					cell-cell junction organization (GO:0045216)|establishment of endothelial barrier (GO:0061028)|sensory perception of sound (GO:0007605)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(4)|skin(1)|urinary_tract(1)	15		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		GCTGTCCTGAGGAAGTTTGAT	0.478																																					p.R481K		Atlas-SNP	.											.	MARVELD2	49	.	0			c.G1442A						.						138	130	133					5																	68728859		2203	4300	6503	SO:0001583	missense	153562	exon5			TCCTGAGGAAGTT	AK055094	CCDS34175.1, CCDS58956.1	5q13.1	2007-05-01	2004-07-12	2004-07-14	ENSG00000152939	ENSG00000152939			26401	protein-coding gene	gene with protein product	"tricellulin"	610572	"MARVEL (membrane-associating) domain containing 2", "deafness, autosomal recessive 49"	MRVLDC2, DFNB49		17186462	Standard	NM_001038603		Approved	FLJ30532, TRIC	uc003jwq.3	Q8N4S9	OTTHUMG00000162512	ENST00000325631.5:c.1442G>A	chr5.hg19:g.68728859G>A	ENSP00000323264:p.Arg481Lys	80.0	0.0		150.0	57.0	NM_001038603	A1BQX0|A1BQX1|A8KA97|Q96NM9	Missense_Mutation	SNP	ENST00000325631.5	hg19	CCDS34175.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.331234	0.24167	.	.	ENSG00000152939	ENST00000325631;ENST00000454295;ENST00000512803;ENST00000436532;ENST00000413223	T;T;T;T;T	0.21031	2.03;2.03;2.03;2.03;2.03	5.74	4.87	0.63330	Occludin/RNA polymerase II elongation factor, ELL domain (1);	0.044737	0.85682	D	0.000000	T	0.09730	0.0239	N	0.13098	0.295	0.25626	N	0.986356	B;B	0.11235	0.001;0.004	B;B	0.11329	0.003;0.006	T	0.36407	-0.9749	10	0.02654	T	1	-28.9945	8.2015	0.31428	0.2349:0.0:0.7651:0.0	.	469;481	Q8N4S9-3;Q8N4S9	.;MALD2_HUMAN	K	481;469;481;365;365	ENSP00000323264:R481K;ENSP00000396244:R469K;ENSP00000423490:R481K;ENSP00000414776:R365K;ENSP00000398922:R365K	ENSP00000323264:R481K	R	+	2	0	MARVELD2	68764615	1.000000	0.71417	0.963000	0.40424	0.581000	0.36288	4.148000	0.58085	1.424000	0.47217	0.655000	0.94253	AGG	.	.		0.478	MARVELD2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369583.1	NM_144724		A	68728859	G	A	68728859	3	1	9	1	0	0	0	0	1	0	0	0	9327	1000	35	3	1456	3	MARVELD2	5	68728859	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	63265349	68728859	112186401	29	716										
APC	324	hgsc.bcm.edu	37	chr5	112179485	112179485	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ttattcaggtggatgcccctGaccaaaaaggaactgagata	10	8	1	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr5:112179485G>C	ENST00000457016.1	+	16	8574	c.8194G>C	c.(8194-8196)Gac>Cac	p.D2732H	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.D2732H|APC_ENST00000508376.2_Missense_Mutation_p.D2732H			P25054	APC_HUMAN	adenomatous polyposis coli	2732	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GGATGCCCCTGACCAAAAAGG	0.433		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.D2732H	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	1	Unknown(1)	skin(1)	c.G8194C						.						76	75	76					5																	112179485		2202	4300	6502	SO:0001583	missense	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	GCCCCTGACCAAA	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.8194G>C	chr5.hg19:g.112179485G>C	ENSP00000413133:p.Asp2732His	108.0	0.0		123.0	28.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	16.97	3.269261	0.59540	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.83335	-1.71;-1.71;-1.71	6.02	6.02	0.97574	EB-1 binding (1);	0.059777	0.64402	D	0.000002	D	0.86146	0.5863	L	0.29908	0.895	0.54753	D	0.999989	D;D	0.63880	0.993;0.993	D;D	0.64144	0.922;0.922	D	0.83520	0.0085	9	.	.	.	-10.9108	20.5407	0.99260	0.0:0.0:1.0:0.0	.	2734;2732	Q4LE70;P25054	.;APC_HUMAN	H	2732	ENSP00000413133:D2732H;ENSP00000257430:D2732H;ENSP00000427089:D2732H	.	D	+	1	0	APC	112207384	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.114000	0.89570	2.865000	0.98341	0.655000	0.94253	GAC	.	.		0.433	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112179485	G	C	112179485	3	2	9	1	0	0	0	0	1	0	0	0	763	1290	45	4	8252	4	APC	5	112179485	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	43450626	112179485	68735775	30	717										
FBN2	2201	hgsc.bcm.edu	37	chr5	127645697	127645697	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	atgcagttgtggcctccattGacctgcatgtactcaggtgg	12	10	1	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr5:127645697G>A	ENST00000508053.1	-	46	6152	c.5178C>T	c.(5176-5178)gtC>gtT	p.V1726V	FBN2_ENST00000262464.4_Silent_p.V1726V			P35556	FBN2_HUMAN	fibrillin 2	1726	EGF-like 28; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GGCCTCCATTGACCTGCATGT	0.458																																					p.V1726V		Atlas-SNP	.											.	FBN2	858	.	0			c.C5178T						.						104	95	98					5																	127645697		2203	4300	6503	SO:0001819	synonymous_variant	2201	exon40			TCCATTGACCTGC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.5178C>T	chr5.hg19:g.127645697G>A		228.0	0.0		248.0	111.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	.		0.458	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127645697	G	A	127645697	2	1	9	1	0	0	0	0	0	0	0	1	5711	1277	45	3		3	FBN2	5	127645697	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	15466212	127645697	53269563	31	718										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140264043	140264043	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tcggcaccgcccaccgagggCgcgtgcgcgccgggcaagcc	16	18	0	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr5:140264043C>A	ENST00000289272.2	+	1	2190	c.2190C>A	c.(2188-2190)ggC>ggA	p.G730G	PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000409494.1_Silent_p.G730G|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	730					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACCGAGGGCGCGTGCGCGC	0.662																																					p.G730G	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.C2190A						.						61	65	64					5																	140264043		2202	4298	6500	SO:0001819	synonymous_variant	56136	exon1			CGAGGGCGCGTGC	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.2190C>A	chr5.hg19:g.140264043C>A		156.0	0.0		207.0	42.0	NM_031865	O75277	Silent	SNP	ENST00000289272.2	hg19	CCDS4240.1																																																																																			.	.		0.662	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140264043	C	A	140264043	2	1	9	1	0	0	0	0	0	0	0	1	11532	755	27	1		1	PCDHA13	5	140264043	Silent	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	12618346	140264043	40651217	32	719										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160059337	160059337	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tattgggtccactcttcaccAtctgagtccagctcctttgg	8	13	3	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr5:160059337A>G	ENST00000327245.5	-	13	2265	c.1419T>C	c.(1417-1419)gaT>gaC	p.D473D	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	473					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACTCTTCACCATCTGAGTCCA	0.527																																					p.D473D		Atlas-SNP	.											.	ATP10B	201	.	0			c.T1419C						.						104	101	102					5																	160059337		1946	4133	6079	SO:0001819	synonymous_variant	23120	exon13			TTCACCATCTGAG	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.1419T>C	chr5.hg19:g.160059337A>G		65.0	0.0		89.0	18.0	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	hg19	CCDS43394.1																																																																																			.	.		0.527	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		G	160059337	A	G	160059337	2	3	9	1	0	0	0	0	0	0	0	1	1117	214	8	2		2	ATP10B	5	160059337	Silent	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	19795294	160059337	20855923	33	720										
CCNG1	900	hgsc.bcm.edu	37	chr5	162866373	162866373	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gtctgtggtttgagactaatTgagtctgcacacgataatgg	12	6	2	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr5:162866373T>C	ENST00000340828.2	+	2	335	c.111T>C	c.(109-111)atT>atC	p.I37I	CCNG1_ENST00000504553.1_5'Flank|RP11-541P9.3_ENST00000503504.1_RNA|CCNG1_ENST00000393929.1_Silent_p.I37I|CCNG1_ENST00000510664.1_Intron|RP11-541P9.3_ENST00000458002.2_RNA|CCNG1_ENST00000511683.2_Intron|CCNG1_ENST00000512163.1_Intron	NM_004060.3	NP_004051.1	P51959	CCNG1_HUMAN	cyclin G1	37					brain development (GO:0007420)|cell growth (GO:0016049)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to organonitrogen compound (GO:0010243)|syncytium formation (GO:0006949)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)		TGAGACTAATTGAGTCTGCAC	0.438																																					p.I37I		Atlas-SNP	.											.	CCNG1	28	.	0			c.T111C						.						138	128	131					5																	162866373		2203	4300	6503	SO:0001819	synonymous_variant	900	exon3			ACTAATTGAGTCT	D78341	CCDS4360.1	5q32-q34	2010-11-15			ENSG00000113328	ENSG00000113328			1592	protein-coding gene	gene with protein product		601578		CCNG		8954786, 8806701	Standard	NM_004060		Approved		uc003lzb.3	P51959	OTTHUMG00000130380	ENST00000340828.2:c.111T>C	chr5.hg19:g.162866373T>C		107.0	0.0		163.0	77.0	NM_199246	B2R7B2|B4DLW7|D3DQK7|Q15757|Q96L32	Silent	SNP	ENST00000340828.2	hg19	CCDS4360.1																																																																																			.	.		0.438	CCNG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252750.3	NM_004060		C	162866373	T	C	162866373	2	2	9	1	0	0	0	0	0	0	0	1	2925	1800	63	2		2	CCNG1	5	162866373	Silent	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10	2807036	162866373	18048887	34	721										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327864	16327864	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	agccccggagccctgctgagGtgctgctgctgctgctgctg	15	14	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr6:16327864G>C	ENST00000244769.4	-	8	1614	c.678C>G	c.(676-678)caC>caG	p.H226Q	ATXN1_ENST00000436367.1_Missense_Mutation_p.H226Q	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	226					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CCCTGCTGAGGtgctgctgct	0.652																																					p.H226Q		Atlas-SNP	.											.,1	ATXN1	117	.	0			c.C678G						.						11	15	13					6																	16327864		2150	4194	6344	SO:0001583	missense	6310	exon7			GCTGAGGTGCTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.678C>G	chr6.hg19:g.16327864G>C	ENSP00000244769:p.His226Gln	55.0	2.0		63.0	4.0	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	G	1.926	-0.447046	0.04572	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.27256	1.68;1.68	4.74	0.503	0.16940	.	0.308295	0.34291	N	0.004091	T	0.05686	0.0149	L	0.39397	1.21	0.09310	N	0.999995	B	0.32245	0.361	B	0.28638	0.092	T	0.23976	-1.0173	10	0.48119	T	0.1	-16.8942	3.2876	0.06937	0.3032:0.0:0.385:0.3119	.	226	P54253	ATX1_HUMAN	Q	226	ENSP00000244769:H226Q;ENSP00000416360:H226Q	ENSP00000244769:H226Q	H	-	3	2	ATXN1	16435843	0.437000	0.25593	0.006000	0.13384	0.009000	0.06853	0.925000	0.28791	0.191000	0.20236	0.563000	0.77884	CAC	.	.		0.652	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		C	16327864	G	C	16327864	3	2	9	1	0	0	0	0	1	0	0	0	1209	1252	44	4	1777	4	ATXN1	6	16327864	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10		16327864	154787203	35	722										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327924	16327924	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tgctgatgctgatgctgctgCtgctgctgctgctgctgctg	14	11	0	2	rs544512597	byFrequency	TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr6:16327924C>A	ENST00000244769.4	-	8	1554	c.618G>T	c.(616-618)caG>caT	p.Q206H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q206H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	206	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gatgctgctgctgctgctgct	0.662													c|||	7	0.00139776	0.0038	0.0014	5008	,	,		13096	0.001		0	False		,,,				2504	0				p.Q206H		Atlas-SNP	.											.	ATXN1	117	.	0			c.G618T						.																																			SO:0001583	missense	6310	exon7			CTGCTGCTGCTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.618G>T	chr6.hg19:g.16327924C>A	ENSP00000244769:p.Gln206His	32.0	0.0		51.0	6.0	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	c	5.966	0.362195	0.11296	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.46063	0.88;0.88	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.16727	0.0402	N	0.08118	0	0.09310	N	1	P	0.51240	0.943	P	0.55667	0.781	T	0.06338	-1.0832	8	0.56958	D	0.05	.	.	.	.	.	206	P54253	ATX1_HUMAN	H	206	ENSP00000244769:Q206H;ENSP00000416360:Q206H	ENSP00000244769:Q206H	Q	-	3	2	ATXN1	16435903	0.113000	0.22115	0.026000	0.17262	0.107000	0.19398	0.000000	0.12993	0.132000	0.18615	0.134000	0.15878	CAG	.	.		0.662	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		A	16327924	C	A	16327924	3	1	9	1	0	0	0	0	1	0	0	0	1209	796	28	3	1837	3	ATXN1	6	16327924	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	60	16327924	154787143	36	723										
ZNF391	346157	hgsc.bcm.edu	37	chr6	27368930	27368930	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gtggaaaagctttcagttggAtctcatcgcttactgaacat	9	8	2	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr6:27368930A>T	ENST00000244576.4	+	3	1326	c.781A>T	c.(781-783)Atc>Ttc	p.I261F	RP1-153G14.4_ENST00000607727.1_lincRNA	NM_001076781.1	NP_001070249.1	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(6)|lung(7)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	21						TTTCAGTTGGATCTCATCGCT	0.453																																					p.I261F		Atlas-SNP	.											.	ZNF391	90	.	0			c.A781T						.						67	72	70					6																	27368930		2201	4299	6500	SO:0001583	missense	346157	exon3			AGTTGGATCTCAT	BC132797	CCDS43429.1	6p21	2013-01-08			ENSG00000124613	ENSG00000124613		"Zinc fingers, C2H2-type"	18779	protein-coding gene	gene with protein product							Standard	NM_001076781		Approved	dJ153G14.3	uc003njf.1	Q9UJN7	OTTHUMG00000014477	ENST00000244576.4:c.781A>T	chr6.hg19:g.27368930A>T	ENSP00000244576:p.Ile261Phe	145.0	0.0		192.0	42.0	NM_001076781	B4DH77	Missense_Mutation	SNP	ENST00000244576.4	hg19	CCDS43429.1	.	.	.	.	.	.	.	.	.	.	A	4.570	0.105837	0.08780	.	.	ENSG00000124613	ENST00000244576	T	0.07567	3.18	4.0	2.8	0.32819	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01800	0.0057	N	0.25647	0.755	0.09310	N	1	P	0.43701	0.815	B	0.40677	0.337	T	0.44050	-0.9353	9	0.27785	T	0.31	.	4.6167	0.12430	0.6048:0.2011:0.0:0.1941	.	261	Q9UJN7	ZN391_HUMAN	F	261	ENSP00000244576:I261F	ENSP00000244576:I261F	I	+	1	0	ZNF391	27476909	0.000000	0.05858	0.762000	0.31397	0.942000	0.58702	-0.593000	0.05740	0.383000	0.24910	0.455000	0.32223	ATC	.	.		0.453	ZNF391-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040145.2	NM_001076781		T	27368930	A	T	27368930	3	4	9	1	0	0	0	0	1	0	0	0	17894	333	12	4	783	4	ZNF391	6	27368930	Missense_Mutation	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	11041006	27368930	143746137	37	724										
OR2J3	442186	hgsc.bcm.edu	37	chr6	29080176	29080176	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ctccttcaccttctgggtacCtctgtgtggacaccgccaag	9	15	3	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr6:29080176C>T	ENST00000377169.1	+	1	509	c.509C>T	c.(508-510)cCt>cTt	p.P170L		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	170						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						TTCTGGGTACCTCTGTGTGGA	0.502																																					p.P170L		Atlas-SNP	.											.	OR2J3	53	.	0			c.C509T						.						155	166	162					6																	29080176		1300	2570	3870	SO:0001583	missense	442186	exon1			GGGTACCTCTGTG		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"GPCR / Class A : Olfactory receptors"	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.509C>T	chr6.hg19:g.29080176C>T	ENSP00000366374:p.Pro170Leu	128.0	0.0		125.0	57.0	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	hg19	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.460920	0.26248	.	.	ENSG00000204701	ENST00000377169	T	0.00164	8.64	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00241	0.0007	M	0.87682	2.9	0.35033	D	0.758945	D	0.53885	0.963	P	0.58780	0.845	T	0.61063	-0.7138	9	0.87932	D	0	.	13.5409	0.61672	0.0:1.0:0.0:0.0	.	170	O76001	OR2J3_HUMAN	L	170	ENSP00000366374:P170L	ENSP00000366374:P170L	P	+	2	0	OR2J3	29188155	0.000000	0.05858	0.107000	0.21349	0.053000	0.15095	0.205000	0.17356	1.549000	0.49425	0.436000	0.28706	CCT	.	.		0.502	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			T	29080176	C	T	29080176	3	4	9	1	0	0	0	0	1	0	0	0	11013	681	24	3	511	3	OR2J3	6	29080176	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	1711246	29080176	142034891	38	725										
RXRB	6257	hgsc.bcm.edu	37	chr6	33164330	33164330	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ctcctcgggggctcccccagCcccctccccatccccatcct	6	25	0	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr6:33164330C>A	ENST00000374680.3	-	5	1085	c.874G>T	c.(874-876)Gct>Tct	p.A292S	RXRB_ENST00000374685.4_Missense_Mutation_p.A292S|RXRB_ENST00000544186.1_Missense_Mutation_p.A102S|RXRB_ENST00000413614.2_Missense_Mutation_p.A196S	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	292	Hinge.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	GCTCCCCCAGCCCCCTCCCCA	0.632																																					p.A292S		Atlas-SNP	.											.	RXRB	34	.	0			c.G874T						.						54	69	64					6																	33164330		1509	2706	4215	SO:0001583	missense	6257	exon5			CCCCAGCCCCCTC	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"Nuclear hormone receptors"	10478	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 2"	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.874G>T	chr6.hg19:g.33164330C>A	ENSP00000363812:p.Ala292Ser	137.0	0.0		130.0	60.0	NM_021976	P28703|Q59G65|Q5JP92|Q5STQ1	Missense_Mutation	SNP	ENST00000374680.3	hg19	CCDS4768.1	.	.	.	.	.	.	.	.	.	.	C	8.973	0.973361	0.18736	.	.	ENSG00000204231	ENST00000374685;ENST00000374680;ENST00000544186;ENST00000413614	T;T;T;D	0.91945	-0.34;-0.34;-0.34;-2.94	4.97	4.97	0.65823	Nuclear hormone receptor, ligand-binding (1);	0.311148	0.35708	N	0.003039	T	0.60766	0.2294	N	0.03917	-0.325	0.32124	N	0.587684	B;B;B;B;B;B;B;B	0.31077	0.307;0.032;0.029;0.0;0.012;0.016;0.032;0.016	B;B;B;B;B;B;B;B	0.20767	0.031;0.021;0.008;0.001;0.008;0.007;0.013;0.007	T	0.57365	-0.7824	10	0.07482	T	0.82	.	9.1972	0.37235	0.0:0.9042:0.0:0.0958	.	196;292;175;102;292;292;332;292	B7Z3E4;B7Z6J2;B7Z6X3;E9PK95;Q5STQ1;Q5STP9;Q59G65;P28702	.;.;.;.;.;.;.;RXRB_HUMAN	S	292;292;102;196	ENSP00000363817:A292S;ENSP00000363812:A292S;ENSP00000439222:A102S;ENSP00000415561:A196S	ENSP00000363812:A292S	A	-	1	0	RXRB	33272308	0.673000	0.27539	1.000000	0.80357	0.987000	0.75469	1.150000	0.31639	2.577000	0.86979	0.549000	0.68633	GCT	.	.		0.632	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		A	33164330	C	A	33164330	3	1	9	1	0	0	0	0	1	0	0	0	13779	739	26	3	751	3	RXRB	6	33164330	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	4084154	33164330	137950737	39	726										
MDGA1	266727	hgsc.bcm.edu	37	chr6	37614119	37614120	+	Frame_Shift_Ins	INS	-	-	A													0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tctccacacgccggaccgggINSatggccttgaccaccgcatt							TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr6:37614119_37614120insA	ENST00000434837.3	-	11	3256_3257	c.2078_2079insT	c.(2077-2079)atcfs	p.I693fs	MDGA1_ENST00000505425.1_Frame_Shift_Ins_p.I693fs|MDGA1_ENST00000510077.1_5'UTR|MDGA1_ENST00000297153.7_Frame_Shift_Ins_p.I696fs	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	693	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						GCCGGACCGGGATGGCCTTGAC	0.574																																					p.I693fs		Atlas-INDEL	.											.	MDGA1	104	.	0			c.2079_2080insT						.																																			SO:0001589	frameshift_variant	266727	exon11			.	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.2079dupT	chr6.hg19:g.37614120_37614120dupA	ENSP00000402584:p.Ile693fs	59.0	0.0		64.0	11.0	NM_153487	A6NHG0|Q8NBE3	Frame_Shift_Ins	INS	ENST00000434837.3	hg19	CCDS47417.1																																																																																			.	.		0.574	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			A	37614120	-	A	37614119	7	5	9	1	0	1	1	0	0	0	0	0	9415	1164	41	0	816	0	MDGA1	6	37614119	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GZ-01A-11D-A38X-10	4449789	37614119	133500948	40	727										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84317435	84317435	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	aacctgactgggacagccgcAgatgcagttgcaaataaatc	10	10	0	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr6:84317435A>T	ENST00000439399.2	-	13	1321	c.1005T>A	c.(1003-1005)tcT>tcA	p.S335S	SNAP91_ENST00000520302.1_Silent_p.S333S|SNAP91_ENST00000521485.1_Silent_p.S335S|SNAP91_ENST00000428679.2_Silent_p.S335S|SNAP91_ENST00000437520.1_Silent_p.S319S|SNAP91_ENST00000520213.1_Silent_p.S319S|SNAP91_ENST00000521743.1_Silent_p.S335S|SNAP91_ENST00000369694.2_Silent_p.S335S|SNAP91_ENST00000195649.6_Silent_p.S335S	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	335					clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		GGACAGCCGCAGATGCAGTTG	0.373																																					p.S335S		Atlas-SNP	.											.	SNAP91	199	.	0			c.T1005A						.						66	61	62					6																	84317435		1843	4085	5928	SO:0001819	synonymous_variant	9892	exon12			AGCCGCAGATGCA	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1005T>A	chr6.hg19:g.84317435A>T		125.0	0.0		85.0	65.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Silent	SNP	ENST00000439399.2	hg19	CCDS47455.1																																																																																			.	.		0.373	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			T	84317435	A	T	84317435	2	4	9	1	0	0	0	0	0	0	0	1	14848	175	7	4		4	SNAP91	6	84317435	Silent	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	46703316	84317435	86797632	41	728										
SLC16A10	117247	hgsc.bcm.edu	37	chr6	111543223	111543223	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	cagggttacttcgtgacaaaCtgggctcctatgatgtggca	12	9	0	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr6:111543223C>A	ENST00000368851.5	+	6	1508	c.1333C>A	c.(1333-1335)Ctg>Atg	p.L445M	SLC16A10_ENST00000368850.3_Missense_Mutation_p.L131M	NM_018593.4	NP_061063.2	Q8TF71	MOT10_HUMAN	solute carrier family 16 (aromatic amino acid transporter), member 10	445					amino acid transport (GO:0006865)|aromatic amino acid transport (GO:0015801)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)	12		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)	Droxidopa(DB06262)|Glycine(DB00145)|L-Alanine(DB00160)|L-Arginine(DB00125)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Cystine(DB00138)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Histidine(DB00117)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Lysine(DB00123)|L-Methionine(DB00134)|L-Phenylalanine(DB00120)|L-Proline(DB00172)|L-Serine(DB00133)|L-Threonine(DB00156)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|L-Valine(DB00161)|Liothyronine(DB00279)|Liotrix(DB01583)|Pyruvic acid(DB00119)	TCGTGACAAACTGGGCTCCTA	0.502																																					p.L445M		Atlas-SNP	.											.	SLC16A10	33	.	0			c.C1333A						.						129	123	125					6																	111543223		2203	4300	6503	SO:0001583	missense	117247	exon6			GACAAACTGGGCT	AF116652	CCDS5089.1	6q21-q22	2014-01-28	2013-07-18		ENSG00000112394	ENSG00000112394		"Solute carriers"	17027	protein-coding gene	gene with protein product		607550	"solute carrier family 16 (monocarboxylic acid transporters), member 10"			11278508, 11827462	Standard	NM_018593		Approved	TAT1, MCT10	uc003pus.3	Q8TF71	OTTHUMG00000015371	ENST00000368851.5:c.1333C>A	chr6.hg19:g.111543223C>A	ENSP00000357844:p.Leu445Met	129.0	0.0		105.0	12.0	NM_018593	B3KWY0|Q6ZMG0|Q8WVI5	Missense_Mutation	SNP	ENST00000368851.5	hg19	CCDS5089.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.026354	0.54683	.	.	ENSG00000112394	ENST00000368851;ENST00000368850	T;T	0.37235	1.21;1.21	5.52	2.61	0.31194	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.299915	0.32301	N	0.006282	T	0.27933	0.0688	L	0.54323	1.7	0.43793	D	0.996338	P	0.48640	0.913	P	0.52957	0.714	T	0.05733	-1.0867	10	0.54805	T	0.06	.	6.8449	0.23982	0.1327:0.6701:0.1279:0.0693	.	445	Q8TF71	MOT10_HUMAN	M	445;131	ENSP00000357844:L445M;ENSP00000357843:L131M	ENSP00000357843:L131M	L	+	1	2	SLC16A10	111649916	0.998000	0.40836	1.000000	0.80357	0.856000	0.48823	1.817000	0.39002	0.676000	0.31285	0.655000	0.94253	CTG	.	.		0.502	SLC16A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041822.2			A	111543223	C	A	111543223	3	1	9	1	0	0	0	0	1	0	0	0	14418	564	20	3	1355	3	SLC16A10	6	111543223	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	27225788	111543223	59571844	42	729										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119296226	119296226	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ttcacttcgtattctgagaaTttctttccccttaaattcca	3	11	3	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr6:119296226T>C	ENST00000338891.7	-	13	3174	c.2731A>G	c.(2731-2733)Att>Gtt	p.I911V	FAM184A_ENST00000368475.4_Missense_Mutation_p.I791V|FAM184A_ENST00000521531.1_Missense_Mutation_p.I911V|FAM184A_ENST00000352896.5_Missense_Mutation_p.I791V|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	911						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						ATTCTGAGAATTTCTTTCCCC	0.383																																					p.I911V		Atlas-SNP	.											.	FAM184A	109	.	0			c.A2731G						.						159	138	144					6																	119296226		1849	4096	5945	SO:0001583	missense	79632	exon13			TGAGAATTTCTTT	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2731A>G	chr6.hg19:g.119296226T>C	ENSP00000342604:p.Ile911Val	64.0	0.0		60.0	21.0	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	hg19	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	T	1.128	-0.653323	0.03480	.	.	ENSG00000111879	ENST00000521043;ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531	T;T;T;T	0.20200	2.63;2.62;2.1;2.09	5.4	3.03	0.35002	.	0.241182	0.38897	N	0.001537	T	0.01523	0.0049	N	0.01209	-0.955	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.12837	0.002;0.008;0.003	T	0.47005	-0.9150	10	0.02654	T	1	-5.3401	8.1897	0.31361	0.0:0.3147:0.0:0.6853	.	911;791;911	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	V	74;911;791;791;911	ENSP00000342604:I911V;ENSP00000326608:I791V;ENSP00000357460:I791V;ENSP00000430442:I911V	ENSP00000342604:I911V	I	-	1	0	FAM184A	119337925	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	3.097000	0.50251	0.451000	0.26802	0.528000	0.53228	ATT	.	.		0.383	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		C	119296226	T	C	119296226	3	2	9	1	0	0	0	0	1	0	0	0	5516	1493	52	2	715	2	FAM184A	6	119296226	Missense_Mutation	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10	7753003	119296226	51818841	43	730										
QKI	9444	hgsc.bcm.edu	37	chr6	163984603	163984603	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	agacaaatacagaccgctgtCatgccaaacggaactcctca	7	13	2	2	rs368366293		TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr6:163984603C>T	ENST00000361752.3	+	6	1337	c.786C>T	c.(784-786)gtC>gtT	p.V262V	QKI_ENST00000453779.2_Silent_p.V262V|QKI_ENST00000392127.2_Silent_p.V262V|QKI_ENST00000424802.3_Silent_p.V254V|QKI_ENST00000361195.2_Silent_p.V254V|QKI_ENST00000275262.7_Silent_p.V262V	NM_006775.2|NM_206853.2|NM_206854.2|NM_206855.2	NP_006766.1|NP_996735.1|NP_996736.1|NP_996737.1	Q96PU8	QKI_HUMAN	QKI, KH domain containing, RNA binding	262					long-chain fatty acid biosynthetic process (GO:0042759)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|muscle cell differentiation (GO:0042692)|myelination (GO:0042552)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|spermatid development (GO:0007286)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(5)|ovary(1)|prostate(3)|urinary_tract(2)	27		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)		AGACCGCTGTCATGCCAAACG	0.547																																					p.V262V		Atlas-SNP	.											.	QKI	80	.	0			c.C786T						.						99	92	94					6																	163984603		2203	4300	6503	SO:0001819	synonymous_variant	9444	exon6			CGCTGTCATGCCA	AB067798	CCDS5285.1, CCDS5286.1, CCDS5287.1, CCDS43525.1, CCDS75546.1	6q26	2011-09-12	2011-09-12		ENSG00000112531	ENSG00000112531			21100	protein-coding gene	gene with protein product		609590	"quaking homolog, KH domain RNA binding (mouse)"			10535969	Standard	NM_006775		Approved	QK3	uc003qui.3	Q96PU8	OTTHUMG00000015977	ENST00000361752.3:c.786C>T	chr6.hg19:g.163984603C>T		63.0	0.0		36.0	27.0	NM_206853	Q2I375|Q5MJQ1|Q969L9|Q96EJ3|Q96KA3|Q96PU6|Q96PU7|Q9P0X6|Q9P0X7|Q9P0X8|Q9P0X9|Q9P0Y0|Q9P0Y1	Silent	SNP	ENST00000361752.3	hg19	CCDS5285.1	.	.	.	.	.	.	.	.	.	.	C	7.475	0.647449	0.14516	.	.	ENSG00000112531	ENST00000537883;ENST00000544361	.	.	.	6.02	6.02	0.97574	.	.	.	.	.	T	0.72526	0.3471	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68554	-0.5378	4	.	.	.	-2.2742	20.5407	0.99260	0.0:1.0:0.0:0.0	.	.	.	.	Y	159;96	.	.	H	+	1	0	QKI	163904593	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.962000	0.49176	2.865000	0.98341	0.655000	0.94253	CAT	.	.		0.547	QKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043016.2	NM_006775		T	163984603	C	T	163984603	2	4	9	1	0	0	0	0	0	0	0	1	12888	813	29	3		3	QKI	6	163984603	Silent	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	44688377	163984603	7130464	44	731										
GRB10	2887	hgsc.bcm.edu	37	chr7	50680499	50680499	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gctcgtcctctgcacagagcAacctcagctctttagtttca	7	14	4	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr7:50680499A>T	ENST00000401949.1	-	13	1602	c.1133T>A	c.(1132-1134)tTg>tAg	p.L378*	GRB10_ENST00000439599.1_Nonsense_Mutation_p.L372*|GRB10_ENST00000403097.1_Nonsense_Mutation_p.L372*|GRB10_ENST00000402497.1_Nonsense_Mutation_p.L320*|GRB10_ENST00000406641.1_Nonsense_Mutation_p.L320*|GRB10_ENST00000402578.1_Nonsense_Mutation_p.L320*|GRB10_ENST00000335866.3_Nonsense_Mutation_p.L320*|GRB10_ENST00000357271.5_Nonsense_Mutation_p.L332*|GRB10_ENST00000407526.1_Nonsense_Mutation_p.L320*|GRB10_ENST00000398812.2_Nonsense_Mutation_p.L378*|GRB10_ENST00000398810.2_Nonsense_Mutation_p.L320*			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	378	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					TGCACAGAGCAACCTCAGCTC	0.473									Russell-Silver syndrome																												p.L378X		Atlas-SNP	.											.	GRB10	155	.	0			c.T1133A						.						122	127	125					7																	50680499		2133	4249	6382	SO:0001587	stop_gained	2887	exon10	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	CAGAGCAACCTCA		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.1133T>A	chr7.hg19:g.50680499A>T	ENSP00000385770:p.Leu378*	91.0	0.0		93.0	42.0	NM_005311	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Nonsense_Mutation	SNP	ENST00000401949.1	hg19	CCDS43582.1	.	.	.	.	.	.	.	.	.	.	A	41	8.648473	0.98899	.	.	ENSG00000106070	ENST00000398812;ENST00000439599;ENST00000335866;ENST00000398810;ENST00000402578;ENST00000403097;ENST00000406641;ENST00000357271;ENST00000407526;ENST00000401949;ENST00000402497	.	.	.	5.19	5.19	0.71726	.	0.108905	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.7824	15.0392	0.71774	1.0:0.0:0.0:0.0	.	.	.	.	X	378;372;320;320;320;372;320;332;320;378;320	.	ENSP00000338543:L320X	L	-	2	0	GRB10	50647993	1.000000	0.71417	0.967000	0.41034	0.549000	0.35272	9.334000	0.96470	1.955000	0.56771	0.533000	0.62120	TTG	.	.		0.473	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1			T	50680499	A	T	50680499	4	4	9	1	0	0	0	0	0	1	0	0	6765	131	5	4	679	4	GRB10	7	50680499	Nonsense_Mutation	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10		50680499	108458164	45	732										
PCLO	27445	hgsc.bcm.edu	37	chr7	82584100	82584100	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	agcatcagcatctagtagttTcctttcttcttctgtagaag	7	9	5	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr7:82584100T>A	ENST00000333891.9	-	5	6506	c.6169A>T	c.(6169-6171)Aaa>Taa	p.K2057*	PCLO_ENST00000423517.2_Nonsense_Mutation_p.K2057*	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCTAGTAGTTTCCTTTCTTCT	0.448																																					p.K2057X		Atlas-SNP	.											.	PCLO	1506	.	0			c.A6169T						.						89	84	86					7																	82584100		1905	4117	6022	SO:0001587	stop_gained	27445	exon5			GTAGTTTCCTTTC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.6169A>T	chr7.hg19:g.82584100T>A	ENSP00000334319:p.Lys2057*	67.0	0.0		98.0	15.0	NM_014510		Nonsense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	44	10.904087	0.99486	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	.	.	.	5.64	-1.55	0.08558	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.1613	0.65448	0.0:0.0736:0.7309:0.1954	.	.	.	.	X	1988;2057;2057	.	ENSP00000334319:K2057X	K	-	1	0	PCLO	82422036	0.002000	0.14202	0.001000	0.08648	0.056000	0.15407	0.474000	0.22148	-0.187000	0.10516	-0.375000	0.07067	AAA	.	.		0.448	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82584100	T	A	82584100	4	1	9	1	0	0	0	0	0	1	0	0	11592	1792	62	4	9360	4	PCLO	7	82584100	Nonsense_Mutation	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10	31903601	82584100	76554563	46	733										
MDFIC	29969	hgsc.bcm.edu	37	chr7	114563013	114563013	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tccctgcacccagcacctcaCagcccttcctccgtgcgccc	6	23	1	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr7:114563013C>G	ENST00000257724.3	+	2	515	c.252C>G	c.(250-252)caC>caG	p.H84Q	MDFIC_ENST00000393486.1_5'UTR|MDFIC_ENST00000448022.1_5'UTR|MDFIC_ENST00000423503.1_5'UTR					MyoD family inhibitor domain containing											breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						CAGCACCTCACAGCCCTTCCT	0.632																																					p.H84Q		Atlas-SNP	.											.	MDFIC	30	.	0			c.C252G						.						6	7	7					7																	114563013		1842	3758	5600	SO:0001583	missense	29969	exon2			ACCTCACAGCCCT	AF054589	CCDS34737.1, CCDS55155.1	7q31.1-q31.2	2006-01-11			ENSG00000135272	ENSG00000135272			28870	protein-coding gene	gene with protein product		614511				10671520	Standard	NM_199072		Approved	HIC	uc003vhf.3	Q9P1T7	OTTHUMG00000023647	ENST00000257724.3:c.252C>G	chr7.hg19:g.114563013C>G	ENSP00000257724:p.His84Gln	80.0	0.0		88.0	32.0	NM_001166346		Missense_Mutation	SNP	ENST00000257724.3	hg19	CCDS34737.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.604389	0.46423	.	.	ENSG00000135272	ENST00000257724	.	.	.	3.96	-0.767	0.11016	.	2.267060	0.02040	N	0.049187	T	0.22126	0.0533	.	.	.	0.20563	N	0.999883	.	.	.	.	.	.	T	0.11299	-1.0593	6	0.20519	T	0.43	.	5.7921	0.18367	0.3625:0.2963:0.3412:0.0	.	.	.	.	Q	84	.	ENSP00000257724:H84Q	H	+	3	2	MDFIC	114350249	0.000000	0.05858	0.000000	0.03702	0.828000	0.46876	-0.232000	0.09055	-0.003000	0.14444	0.305000	0.20034	CAC	.	.		0.632	MDFIC-007	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366397.1	NM_199072		G	114563013	C	G	114563013	3	3	9	1	0	0	0	0	1	0	0	0	9414	477	17	4	258	4	MDFIC	7	114563013	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	31978913	114563013	44575650	47	734										
WDR91	29062	hgsc.bcm.edu	37	chr7	134896232	134896232	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	actcccggaccagctcgtcaGtgcgctccacggcctccgcc	10	20	1	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr7:134896232G>A	ENST00000354475.4	-	1	54	c.23C>T	c.(22-24)aCt>aTt	p.T8I	WDR91_ENST00000423565.1_5'Flank|WDR91_ENST00000344400.5_Missense_Mutation_p.T8I	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	8										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						CAGCTCGTCAGTGCGCTCCAC	0.692																																					p.T8I		Atlas-SNP	.											.	WDR91	82	.	0			c.C23T						.						38	39	39					7																	134896232		2203	4300	6503	SO:0001583	missense	29062	exon1			TCGTCAGTGCGCT	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.23C>T	chr7.hg19:g.134896232G>A	ENSP00000346466:p.Thr8Ile	134.0	0.0		183.0	84.0	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	hg19	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	G	31	5.064593	0.93898	.	.	ENSG00000105875	ENST00000344400;ENST00000354475	T;T	0.64618	1.45;-0.11	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.68366	0.2993	L	0.43757	1.38	0.80722	D	1	D	0.54207	0.965	P	0.58130	0.833	T	0.62324	-0.6878	10	0.21014	T	0.42	-5.92	18.0315	0.89286	0.0:0.0:1.0:0.0	.	8	A4D1P6	WDR91_HUMAN	I	8	ENSP00000340877:T8I;ENSP00000346466:T8I	ENSP00000340877:T8I	T	-	2	0	WDR91	134546772	1.000000	0.71417	0.954000	0.39281	0.985000	0.73830	8.034000	0.88864	2.593000	0.87608	0.655000	0.94253	ACT	.	.		0.692	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		A	134896232	G	A	134896232	3	1	9	1	0	0	0	0	1	0	0	0	17353	1029	36	3	2280	3	WDR91	7	134896232	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	20333219	134896232	24242431	48	735										
FAM131B	9715	hgsc.bcm.edu	37	chr7	143053918	143053918	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ctccagagcagagtatcctgAagctggttgggaaggtccca	13	10	0	3			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr7:143053918A>C	ENST00000409408.1	-	6	2432	c.724T>G	c.(724-726)Tca>Gca	p.S242A	FAM131B_ENST00000409578.1_Missense_Mutation_p.S258A|FAM131B_ENST00000409346.1_Missense_Mutation_p.S242A|FAM131B_ENST00000409222.3_Missense_Mutation_p.S242A|FAM131B_ENST00000443739.2_Missense_Mutation_p.S270A			Q86XD5	F131B_HUMAN	family with sequence similarity 131, member B	242										breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24	Melanoma(164;0.205)					GAGTATCCTGAAGCTGGTTGG	0.597																																					p.S270A		Atlas-SNP	.											.	FAM131B	104	.	0			c.T808G						.						84	86	85					7																	143053918		2203	4300	6503	SO:0001583	missense	9715	exon7			ATCCTGAAGCTGG	BC045611	CCDS5882.1, CCDS47734.1	7q34	2007-03-20			ENSG00000159784	ENSG00000159784			22202	protein-coding gene	gene with protein product							Standard	NM_014690		Approved	KIAA0773	uc010lpa.3	Q86XD5	OTTHUMG00000152697	ENST00000409408.1:c.724T>G	chr7.hg19:g.143053918A>C	ENSP00000387017:p.Ser242Ala	71.0	0.0		72.0	19.0	NM_001031690	A4D2H6|A6NDW3|A8K605|B8ZZN2|D3DXE3|J3KQX2|Q7L0D6|Q86T97	Missense_Mutation	SNP	ENST00000409408.1	hg19	CCDS5882.1	.	.	.	.	.	.	.	.	.	.	A	2.752	-0.259893	0.05791	.	.	ENSG00000159784	ENST00000443739;ENST00000409578;ENST00000409346;ENST00000452076;ENST00000409408;ENST00000409222	T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96	5.46	4.1	0.47936	.	0.643562	0.16382	N	0.216865	T	0.12092	0.0294	N	0.14661	0.345	0.09310	N	1	B;B	0.19073	0.015;0.033	B;B	0.16289	0.015;0.015	T	0.13953	-1.0490	10	0.34782	T	0.22	-33.6518	9.3677	0.38234	0.8473:0.0:0.1527:0.0	.	258;242	Q86XD5-2;Q86XD5	.;F131B_HUMAN	A	270;258;242;246;242;242	ENSP00000410603:S270A;ENSP00000386568:S258A;ENSP00000386984:S242A;ENSP00000387017:S242A;ENSP00000387147:S242A	ENSP00000387147:S242A	S	-	1	0	FAM131B	142764040	0.000000	0.05858	0.355000	0.25773	0.799000	0.45148	0.289000	0.18957	2.072000	0.62099	0.533000	0.62120	TCA	.	.		0.597	FAM131B-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328057.1	NM_014690		C	143053918	A	C	143053918	3	2	9	1	0	0	0	0	1	0	0	0	5445	246	9	5	278	5	FAM131B	7	143053918	Missense_Mutation	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	8157686	143053918	16084745	49	736										
DPP6	1804	hgsc.bcm.edu	37	chr7	154561209	154561209	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gccgccatcaatgattcccgTgtccccatcatggagctccc	8	17	2	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr7:154561209T>C	ENST00000377770.3	+	9	1107	c.966T>C	c.(964-966)cgT>cgC	p.R322R	DPP6_ENST00000332007.3_Silent_p.R260R|DPP6_ENST00000427557.1_Silent_p.R215R|DPP6_ENST00000404039.1_Silent_p.R258R			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	322					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			ATGATTCCCGTGTCCCCATCA	0.547																																					p.R322R	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.T966C						.						66	67	67					7																	154561209		2005	4160	6165	SO:0001819	synonymous_variant	1804	exon9			TTCCCGTGTCCCC	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.966T>C	chr7.hg19:g.154561209T>C		100.0	0.0		104.0	18.0	NM_130797		Silent	SNP	ENST00000377770.3	hg19																																																																																				.	.		0.547	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		C	154561209	T	C	154561209	2	2	9	1	0	0	0	0	0	0	0	1	4732	1683	59	2		2	DPP6	7	154561209	Silent	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10	11507291	154561209	4577454	50	737										
MED30	90390	hgsc.bcm.edu	37	chr8	118533157	118533157	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gcgtcggggatggcgcccggGcccttcgccgggccccaggc	18	17	0	0	rs35108612		TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr8:118533157G>T	ENST00000297347.3	+	1	206	c.42G>T	c.(40-42)ggG>ggT	p.G14G	MED30_ENST00000522839.1_Silent_p.G14G	NM_080651.2	NP_542382.1	Q96HR3	MED30_HUMAN	mediator complex subunit 30	14					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.G14G(2)		kidney(1)|lung(3)|prostate(3)	7	all_cancers(13;3.41e-25)|Lung NSC(37;3.02e-05)|Ovarian(258;0.00163)		STAD - Stomach adenocarcinoma(47;0.0266)			TGGCGCCCGGGCCCTTCGCCG	0.721																																					p.G14G	Melanoma(81;817 1341 9674 26244 29255)	Atlas-SNP	.											MED30,NS,carcinoma,0,2	MED30	15	.	2	Substitution - coding silent(2)	prostate(2)	c.G42T						.						9	11	10					8																	118533157		2159	4232	6391	SO:0001819	synonymous_variant	90390	exon1			GCCCGGGCCCTTC	AY083305	CCDS6323.1, CCDS64959.1	8q24.11	2007-07-30	2007-07-30	2007-07-30	ENSG00000164758	ENSG00000164758			23032	protein-coding gene	gene with protein product		610237	"thyroid hormone receptor associated protein 6"	THRAP6			Standard	NM_080651		Approved	TRAP25	uc003yoj.3	Q96HR3	OTTHUMG00000164920	ENST00000297347.3:c.42G>T	chr8.hg19:g.118533157G>T		120.0	0.0		122.0	63.0	NM_080651	C6GKU9	Silent	SNP	ENST00000297347.3	hg19	CCDS6323.1																																																																																			.	.		0.721	MED30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380923.1	NM_080651		T	118533157	G	T	118533157	2	4	9	1	0	0	0	0	0	0	0	1	9457	1190	42	3		3	MED30	8	118533157	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10		118533157	27830865	51	738										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79244125	79244125	+	Frame_Shift_Del	DEL	A	A	-													0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tacttgatgatgctctctggAatgtggatgcaatccattgg							TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr9:79244125delA	ENST00000376718.3	-	16	9255	c.9132delT	c.(9130-9132)attfs	p.I3044fs	PRUNE2_ENST00000223609.6_Frame_Shift_Del_p.I309fs|PRUNE2_ENST00000443509.2_Frame_Shift_Del_p.I293fs|PRUNE2_ENST00000466266.2_Intron|PRUNE2_ENST00000428286.1_Frame_Shift_Del_p.I2686fs	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	3044	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TGCTCTCTGGAATGTGGATGC	0.383																																					p.P3045fs		Atlas-Indel,Pindel	.											.	PRUNE2	331	.	0			c.9133delC						.						93	83	86					9																	79244125		1568	3582	5150	SO:0001589	frameshift_variant	158471	exon16			.	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.9132delT	chr9.hg19:g.79244125delA	ENSP00000365908:p.Ile3044fs	42.0	0.0		27.0	15.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Frame_Shift_Del	DEL	ENST00000376718.3	hg19	CCDS47982.1																																																																																			.	.		0.383	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		-	79244125	A	-	79244125	7	5	9	1	0	1	0	1	0	0	0	0	12653	242	9	0	150	0	PRUNE2	9	79244125	Frame_Shift_Del	DEL	A	TCGA-2Y-A9GZ-01A-11D-A38X-10		79244125	61969306	52	739										
TTC16	158248	hgsc.bcm.edu	37	chr9	130482363	130482363	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ccctgtgtccccagggacaaTgcctttttgagcagtgtgcc	11	13	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr9:130482363T>C	ENST00000373289.3	+	5	513	c.433T>C	c.(433-435)Tgc>Cgc	p.C145R	PTRH1_ENST00000429848.1_Intron|PTRH1_ENST00000419060.1_Intron|TTC16_ENST00000393748.4_5'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	145										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						CCAGGGACAATGCCTTTTTGA	0.577																																					p.C145R		Atlas-SNP	.											.	TTC16	55	.	0			c.T433C						.						181	137	152					9																	130482363		2203	4300	6503	SO:0001583	missense	158248	exon5			GGACAATGCCTTT	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"Tetratricopeptide (TTC) repeat domain containing"	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.433T>C	chr9.hg19:g.130482363T>C	ENSP00000362386:p.Cys145Arg	42.0	0.0		45.0	5.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.526889	0.44969	.	.	ENSG00000167094	ENST00000373289;ENST00000316259	T	0.51574	0.7	4.84	4.84	0.62591	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.055189	0.64402	D	0.000001	T	0.64605	0.2613	M	0.74881	2.28	0.80722	D	1	D;D;D	0.76494	0.999;0.991;0.999	D;P;D	0.63033	0.91;0.83;0.91	T	0.66480	-0.5913	10	0.44086	T	0.13	-24.4916	13.384	0.60785	0.0:0.0:0.0:1.0	.	132;97;145	B4DZ42;B4DH05;Q8NEE8	.;.;TTC16_HUMAN	R	145;90	ENSP00000362386:C145R	ENSP00000319048:C90R	C	+	1	0	TTC16	129522184	1.000000	0.71417	0.998000	0.56505	0.572000	0.35998	3.850000	0.55918	2.045000	0.60652	0.164000	0.16699	TGC	.	.		0.577	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965		C	130482363	T	C	130482363	3	2	9	1	0	0	0	0	1	0	0	0	16698	1464	51	2	451	2	TTC16	9	130482363	Missense_Mutation	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10	51238238	130482363	10731068	53	740										
ZNF365	22891	hgsc.bcm.edu	37	chr10	64159446	64159446	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gagtcctcaagagacctctgCagacctccaaagaaagggga	11	11	2	3			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr10:64159446C>A	ENST00000395254.3	+	5	1402	c.1122C>A	c.(1120-1122)tgC>tgA	p.C374*	ZNF365_ENST00000395255.3_Intron|ZNF365_ENST00000410046.3_Intron|ZNF365_ENST00000466727.1_3'UTR	NM_014951.2	NP_055766.2	Q70YC4	TALAN_HUMAN	zinc finger protein 365	0										breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					GAGACCTCTGCAGACCTCCAA	0.522																																					p.C374X		Atlas-SNP	.											.	ZNF365	174	.	0			c.C1122A						.						85	85	85					10																	64159446		2203	4300	6503	SO:0001587	stop_gained	22891	exon5			CCTCTGCAGACCT	AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395254.3:c.1122C>A	chr10.hg19:g.64159446C>A	ENSP00000378674:p.Cys374*	111.0	0.0		133.0	27.0	NM_014951		Nonsense_Mutation	SNP	ENST00000395254.3	hg19	CCDS31209.1	.	.	.	.	.	.	.	.	.	.	C	38	7.149790	0.98096	.	.	ENSG00000138311	ENST00000395254	.	.	.	5.76	3.86	0.44501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	7.5414	0.27740	0.0:0.6128:0.2893:0.0979	.	.	.	.	X	374	.	ENSP00000378674:C374X	C	+	3	2	ZNF365	63829452	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	2.309000	0.43699	1.432000	0.47375	0.650000	0.86243	TGC	.	.		0.522	ZNF365-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048238.2	NM_014951		A	64159446	C	A	64159446	4	1	9	1	0	0	0	0	0	1	0	0	17884	718	25	3	1136	3	ZNF365	10	64159446	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		64159446	71375301	54	741										
C10orf119	79892	hgsc.bcm.edu	37	chr10	121616948	121616948	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gtttaaatcaagttcttgttGaggctgtgatatacataaaa	8	4	2	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr10:121616948G>A	ENST00000360003.3	-	5	500	c.331C>T	c.(331-333)Caa>Taa	p.Q111*	MCMBP_ENST00000466047.1_5'UTR|MCMBP_ENST00000369077.3_Nonsense_Mutation_p.Q111*	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	111					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.Q111E(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						AGTTCTTGTTGAGGCTGTGAT	0.318																																					p.Q111X		Atlas-SNP	.											MCMBP,NS,carcinoma,0,1	MCMBP	49	.	1	Substitution - Missense(1)	lung(1)	c.C331T						.						100	97	98					10																	121616948		2203	4300	6503	SO:0001587	stop_gained	79892	exon5			CTTGTTGAGGCTG	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"chromosome 10 open reading frame 119"	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.331C>T	chr10.hg19:g.121616948G>A	ENSP00000353098:p.Gln111*	102.0	0.0		108.0	62.0	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Nonsense_Mutation	SNP	ENST00000360003.3	hg19	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	G	34	5.297721	0.95574	.	.	ENSG00000197771	ENST00000360003;ENST00000369077	.	.	.	5.77	5.77	0.91146	.	0.164006	0.44483	D	0.000450	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-0.2118	20.0007	0.97408	0.0:0.0:1.0:0.0	.	.	.	.	X	111	.	ENSP00000353098:Q111X	Q	-	1	0	MCMBP	121606938	1.000000	0.71417	1.000000	0.80357	0.380000	0.30137	7.912000	0.87465	2.726000	0.93360	0.650000	0.86243	CAA	.	.		0.318	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		A	121616948	G	A	121616948	4	1	9	1	0	0	0	0	0	1	0	0	1590	1299	45	3	1645	3	C10orf119	10	121616948	Nonsense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	57457502	121616948	13917799	55	742										
OR4X2	119764	hgsc.bcm.edu	37	chr11	48266850	48266850	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tccttcatggagatctgctaCtcctccgctacagcccccaa	6	17	2	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr11:48266850C>A	ENST00000302329.3	+	1	243	c.195C>A	c.(193-195)taC>taA	p.Y65*		NM_001004727.1	NP_001004727.1	Q8NGF9	OR4X2_HUMAN	olfactory receptor, family 4, subfamily X, member 2	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(4)|lung(12)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	20						AGATCTGCTACTCCTCCGCTA	0.507																																					p.Y65X		Atlas-SNP	.											.	OR4X2	65	.	0			c.C195A						.						153	146	148					11																	48266850		2201	4298	6499	SO:0001587	stop_gained	119764	exon1			CTGCTACTCCTCC	AB065847	CCDS31486.1	11p11.2	2012-08-09			ENSG00000172208	ENSG00000172208		"GPCR / Class A : Olfactory receptors"	15184	protein-coding gene	gene with protein product							Standard	NM_001004727		Approved		uc001ngs.1	Q8NGF9	OTTHUMG00000165302	ENST00000302329.3:c.195C>A	chr11.hg19:g.48266850C>A	ENSP00000307751:p.Tyr65*	96.0	0.0		115.0	21.0	NM_001004727	B2RNK3|Q6IF73|Q96R63	Nonsense_Mutation	SNP	ENST00000302329.3	hg19	CCDS31486.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.558959	0.27827	.	.	ENSG00000172208	ENST00000302329	.	.	.	5.37	2.03	0.26663	.	0.000000	0.49305	D	0.000160	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9005	0.41344	0.0:0.7302:0.0:0.2698	.	.	.	.	X	65	.	ENSP00000307751:Y65X	Y	+	3	2	OR4X2	48223426	0.000000	0.05858	0.964000	0.40570	0.141000	0.21300	-0.219000	0.09228	0.643000	0.30638	-0.142000	0.14014	TAC	.	.		0.507	OR4X2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383376.2	NM_001004727		A	48266850	C	A	48266850	4	1	9	1	0	0	0	0	0	1	0	0	11094	576	20	3	197	3	OR4X2	11	48266850	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		48266850	86739666	56	743										
CREBZF	58487	hgsc.bcm.edu	37	chr11	85375448	85375448	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ttgcagcaggtcagagaagcGctgcatttcagcagccgcgg	14	11	2	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr11:85375448G>T	ENST00000527447.1	-	1	698	c.472C>A	c.(472-474)Cgc>Agc	p.R158S	CREBZF_ENST00000398294.2_Missense_Mutation_p.R76S|CREBZF_ENST00000531515.1_Intron|CREBZF_ENST00000534224.1_Intron	NM_001039618.2	NP_001034707.1	Q9NS37	ZHANG_HUMAN	CREB/ATF bZIP transcription factor	158					negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)				TCAGAGAAGCGCTGCATTTCA	0.637											OREG0021274	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R158S	NSCLC(172;674 2044 9050 18334 41735)	Atlas-SNP	.											.	CREBZF	26	.	0			c.C472A						.						24	28	27					11																	85375448		2036	4204	6240	SO:0001583	missense	58487	exon1			AGAAGCGCTGCAT	AF039942	CCDS41697.1	11q14.1	2013-01-10			ENSG00000137504	ENSG00000137504		"basic leucine zipper proteins"	24905	protein-coding gene	gene with protein product	"Zhangfei"	606444				10871379	Standard	NM_001039618		Approved	ZF	uc001pas.2	Q9NS37	OTTHUMG00000133648	ENST00000527447.1:c.472C>A	chr11.hg19:g.85375448G>T	ENSP00000433459:p.Arg158Ser	85.0	0.0	1236	119.0	5.0	NM_001039618	B2R8Q9|Q0P5U9|Q52LT3	Missense_Mutation	SNP	ENST00000527447.1	hg19	CCDS41697.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.408920	0.83340	.	.	ENSG00000137504	ENST00000398294;ENST00000527447	.	.	.	4.56	4.56	0.56223	.	0.000000	0.38381	N	0.001705	T	0.55800	0.1943	N	0.24115	0.695	0.36563	D	0.872539	D	0.63880	0.993	D	0.71184	0.972	T	0.59742	-0.7397	8	.	.	.	-32.0326	12.725	0.57166	0.0:0.0:1.0:0.0	.	158	Q9NS37	ZHANG_HUMAN	S	76;158	.	.	R	-	1	0	CREBZF	85053096	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.998000	0.57024	2.366000	0.80165	0.561000	0.74099	CGC	.	.		0.637	CREBZF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390191.2	NM_001039618		T	85375448	G	T	85375448	3	4	9	1	0	0	0	0	1	0	0	0	3865	1087	38	1	596	1	CREBZF	11	85375448	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	37108598	85375448	49631068	57	744										
SYTL2	54843	hgsc.bcm.edu	37	chr11	85411633	85411633	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tgcttcaagggcaactggtgCtgtctgaaaagtgaagaaat	12	6	2	3			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr11:85411633C>A	ENST00000528231.1	-	15	2555	c.2278G>T	c.(2278-2280)Gca>Tca	p.A760S	SYTL2_ENST00000527523.1_Missense_Mutation_p.A728S|SYTL2_ENST00000533892.1_Missense_Mutation_p.A162S|SYTL2_ENST00000359152.5_Missense_Mutation_p.A1606S|SYTL2_ENST00000389958.3_Missense_Mutation_p.A191S|SYTL2_ENST00000529581.1_Missense_Mutation_p.A202S|SYTL2_ENST00000354566.3_Missense_Mutation_p.A1098S|SYTL2_ENST00000524452.1_Missense_Mutation_p.A736S|SYTL2_ENST00000316356.4_Missense_Mutation_p.A761S|SYTL2_ENST00000389960.4_Missense_Mutation_p.A736S|SYTL2_ENST00000525702.1_Missense_Mutation_p.A202S|SYTL2_ENST00000525423.1_Missense_Mutation_p.A1082S	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	760					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		GCAACTGGTGCTGTCTGAAAA	0.433																																					p.A1098S		Atlas-SNP	.											.	SYTL2	231	.	0			c.G3292T						.						197	182	187					11																	85411633		2203	4299	6502	SO:0001583	missense	54843	exon10			CTGGTGCTGTCTG	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.2278G>T	chr11.hg19:g.85411633C>A	ENSP00000431701:p.Ala760Ser	58.0	0.0		69.0	33.0	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	hg19	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.510713	0.27036	.	.	ENSG00000137501	ENST00000389960;ENST00000359152;ENST00000354566;ENST00000316356;ENST00000525702;ENST00000525423;ENST00000529581;ENST00000389958;ENST00000530351;ENST00000528231;ENST00000533892;ENST00000527523;ENST00000524452	T;T;T;T;T;T;T;T;T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22	5.4	3.36	0.38483	.	0.611072	0.17980	N	0.155579	T	0.46171	0.1379	N	0.04880	-0.145	0.29799	N	0.832564	B;B;B;B;B;B;B;B;B;B	0.28026	0.049;0.097;0.059;0.049;0.097;0.198;0.198;0.198;0.001;0.004	B;B;B;B;B;B;B;B;B;B	0.36845	0.039;0.09;0.041;0.018;0.061;0.234;0.171;0.171;0.004;0.006	T	0.46261	-0.9204	9	.	.	.	-11.2216	10.0462	0.42188	0.1427:0.3957:0.4617:0.0	.	728;736;760;761;578;1058;1082;1098;191;162	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15;Q9HCH5-11;Q9HCH5-7;Q9HCH5-8;Q9HCH5-9;Q9HCH5-4	.;.;SYTL2_HUMAN;.;.;.;.;.;.;.	S	736;1606;1098;761;202;1082;202;191;477;760;162;728;736	ENSP00000374610:A736S;ENSP00000352065:A1606S;ENSP00000346576:A1098S;ENSP00000318803:A761S;ENSP00000432996:A202S;ENSP00000432694:A1082S;ENSP00000435855:A202S;ENSP00000374608:A191S;ENSP00000435009:A477S;ENSP00000431701:A760S;ENSP00000432144:A162S;ENSP00000434010:A728S;ENSP00000435238:A736S	.	A	-	1	0	SYTL2	85089281	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	1.571000	0.36450	1.207000	0.43291	0.563000	0.77884	GCA	.	.		0.433	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		A	85411633	C	A	85411633	3	1	9	1	0	0	0	0	1	0	0	0	15498	797	28	3	542	3	SYTL2	11	85411633	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	36185	85411633	49594883	58	745										
TMPRSS4	56649	hgsc.bcm.edu	37	chr11	117973865	117973865	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ctctgcgggcagcctctccaCttcatcccgaggaagcagct	10	16	3	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr11:117973865C>T	ENST00000437212.3	+	4	421	c.207C>T	c.(205-207)caC>caT	p.H69H	TMPRSS4_ENST00000522307.1_5'UTR|TMPRSS4_ENST00000523251.1_Silent_p.H29H|TMPRSS4_ENST00000522824.1_Silent_p.H69H|TMPRSS4_ENST00000534111.1_Silent_p.H67H			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	69	LDL-receptor class A.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		AGCCTCTCCACTTCATCCCGA	0.592																																					p.H69H		Atlas-SNP	.											.	TMPRSS4	46	.	0			c.C207T						.						143	140	141					11																	117973865		2200	4296	6496	SO:0001819	synonymous_variant	56649	exon4			TCTCCACTTCATC	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"Serine peptidases / Transmembrane"	11878	protein-coding gene	gene with protein product	"transmembrane serine protease 3", "membrane-type serine protease 2", "type II membrane serine protease"	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.207C>T	chr11.hg19:g.117973865C>T		76.0	0.0		101.0	19.0	NM_019894	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Silent	SNP	ENST00000437212.3	hg19	CCDS31684.1	.	.	.	.	.	.	.	.	.	.	C	1.741	-0.491691	0.04322	.	.	ENSG00000137648	ENST00000517544	.	.	.	5.16	4.21	0.49690	.	.	.	.	.	T	0.60157	0.2247	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57341	-0.7828	4	.	.	.	.	9.828	0.40923	0.1558:0.6935:0.1507:0.0	.	.	.	.	F	36	.	.	L	+	1	0	TMPRSS4	117479075	0.565000	0.26610	0.989000	0.46669	0.119000	0.20118	0.702000	0.25631	2.396000	0.81511	0.462000	0.41574	CTT	.	.		0.592	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894		T	117973865	C	T	117973865	2	4	9	1	0	0	0	0	0	0	0	1	16264	564	20	3		3	TMPRSS4	11	117973865	Silent	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	32562232	117973865	17032651	59	746										
GPR19	2842	hgsc.bcm.edu	37	chr12	12815252	12815252	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tcatccaactgtgctcctcaCttaattccatcaggtattgg	6	12	3	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr12:12815252C>T	ENST00000540510.1	-	2	323	c.131G>A	c.(130-132)aGt>aAt	p.S44N	GPR19_ENST00000332427.2_Missense_Mutation_p.S44N			P46093	GPR4_HUMAN	G protein-coupled receptor 19	0					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.048)		GTGCTCCTCACTTAATTCCAT	0.502																																					p.S44N		Atlas-SNP	.											.	GPR19	47	.	0			c.G131A						.						154	139	145					12																	12815252		2203	4300	6503	SO:0001583	missense	2842	exon4			TCCTCACTTAATT		CCDS8652.1	12p12.3	2014-01-30				ENSG00000183150		"GPCR / Class A : Orphans"	4473	protein-coding gene	gene with protein product		602927					Standard	NM_006143		Approved		uc001raq.2	Q15760		ENST00000540510.1:c.131G>A	chr12.hg19:g.12815252C>T	ENSP00000441832:p.Ser44Asn	159.0	0.0		149.0	46.0	NM_006143	A8K3T3|B0M0K1|Q6NWM4	Missense_Mutation	SNP	ENST00000540510.1	hg19	CCDS8652.1	.	.	.	.	.	.	.	.	.	.	C	0.167	-1.075678	0.01903	.	.	ENSG00000183150	ENST00000540510;ENST00000332427;ENST00000540796	T;T	0.68624	-0.34;-0.34	5.28	-5.54	0.02544	.	2.689110	0.01442	N	0.015129	T	0.42966	0.1226	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43097	-0.9412	10	0.10377	T	0.69	5.9676	11.4062	0.49900	0.0:0.2472:0.5973:0.1555	.	44	Q15760	GPR19_HUMAN	N	44	ENSP00000441832:S44N;ENSP00000333744:S44N	ENSP00000333744:S44N	S	-	2	0	GPR19	12706519	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.739000	0.04866	-1.230000	0.02561	-0.793000	0.03317	AGT	.	.		0.502	GPR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400662.1	NM_006143		T	12815252	C	T	12815252	3	4	9	1	0	0	0	0	1	0	0	0	6687	565	20	3	1120	3	GPR19	12	12815252	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		12815252	121036643	60	747										
PTPRO	5800	hgsc.bcm.edu	37	chr12	15747937	15747937	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	agaagaagcagcagttctgcAtcagtgatgtcatatacgag	11	7	3	3			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr12:15747937A>T	ENST00000281171.4	+	26	3943	c.3613A>T	c.(3613-3615)Atc>Ttc	p.I1205F	PTPRO_ENST00000542557.1_Missense_Mutation_p.I366F|PTPRO_ENST00000445537.2_Missense_Mutation_p.I394F|PTPRO_ENST00000544244.1_Missense_Mutation_p.I366F|PTPRO_ENST00000442921.2_Missense_Mutation_p.I394F|PTPRO_ENST00000348962.2_Missense_Mutation_p.I1177F	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	1205					axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				GCAGTTCTGCATCAGTGATGT	0.433																																					p.I1205F		Atlas-SNP	.											.	PTPRO	148	.	0			c.A3613T						.						149	128	135					12																	15747937		2203	4300	6503	SO:0001583	missense	5800	exon26			TTCTGCATCAGTG	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9678	protein-coding gene	gene with protein product	"osteoclastic transmembrane protein-tyrosine phosphatase"	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.3613A>T	chr12.hg19:g.15747937A>T	ENSP00000281171:p.Ile1205Phe	59.0	0.0		38.0	16.0	NM_030667	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	hg19	CCDS8675.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.798678	0.70567	.	.	ENSG00000151490	ENST00000281171;ENST00000348962;ENST00000442921;ENST00000542557;ENST00000445537;ENST00000544244	T;T;T;T;T;T	0.04119	3.73;3.82;3.7;3.73;3.7;3.73	4.83	3.65	0.41850	.	0.000000	0.44097	D	0.000498	T	0.10380	0.0254	M	0.62723	1.935	0.48762	D	0.999705	P;D;D	0.65815	0.609;0.995;0.991	B;P;B	0.50314	0.13;0.637;0.433	T	0.02596	-1.1136	10	0.52906	T	0.07	.	10.8243	0.46622	0.8584:0.0:0.0:0.1416	.	366;1177;1205	Q9UBT5;Q16827-2;Q16827	.;.;PTPRO_HUMAN	F	1205;1177;394;366;394;366	ENSP00000281171:I1205F;ENSP00000343434:I1177F;ENSP00000404188:I394F;ENSP00000437571:I366F;ENSP00000393449:I394F;ENSP00000439234:I366F	ENSP00000281171:I1205F	I	+	1	0	PTPRO	15639204	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.798000	0.62510	0.824000	0.34613	0.533000	0.62120	ATC	.	.		0.433	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			T	15747937	A	T	15747937	3	4	9	1	0	0	0	0	1	0	0	0	12824	217	8	4	3715	4	PTPRO	12	15747937	Missense_Mutation	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	2932685	15747937	118103958	61	748										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81719606	81719606	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tgagttccgagtttgcctaaCcccagggactcctgagctgc	11	13	0	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr12:81719606C>A	ENST00000549396.1	-	22	2752	c.2592G>T	c.(2590-2592)ggG>ggT	p.G864G	PPFIA2_ENST00000443686.3_Silent_p.G765G|PPFIA2_ENST00000550584.2_Silent_p.G864G|PPFIA2_ENST00000407050.4_Silent_p.G790G|PPFIA2_ENST00000549325.1_Silent_p.G846G|PPFIA2_ENST00000541017.1_Silent_p.G81G|PPFIA2_ENST00000541570.2_Silent_p.G431G|PPFIA2_ENST00000333447.7_Silent_p.G846G|PPFIA2_ENST00000552948.1_Silent_p.G864G|PPFIA2_ENST00000550359.2_Silent_p.G711G|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000548586.1_Silent_p.G864G	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	864					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						GTTTGCCTAACCCCAGGGACT	0.408																																					p.G864G		Atlas-SNP	.											.	PPFIA2	207	.	0			c.G2592T						.						78	77	78					12																	81719606		1846	4102	5948	SO:0001819	synonymous_variant	8499	exon21			GCCTAACCCCAGG	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.2592G>T	chr12.hg19:g.81719606C>A		51.0	0.0		85.0	34.0	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Silent	SNP	ENST00000549396.1	hg19	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	C	9.758	1.169424	0.21621	.	.	ENSG00000139220	ENST00000551147	.	.	.	5.83	-3.19	0.05171	.	.	.	.	.	T	0.50188	0.1601	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45600	-0.9250	4	.	.	.	-14.7526	6.8542	0.24032	0.3025:0.1603:0.4731:0.0641	.	.	.	.	F	27	.	.	V	-	1	0	PPFIA2	80243737	0.058000	0.20735	0.961000	0.40146	0.922000	0.55478	-1.153000	0.03169	-0.530000	0.06349	-0.283000	0.09986	GTT	.	.		0.408	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			A	81719606	C	A	81719606	2	1	9	1	0	0	0	0	0	0	0	1	12319	494	18	3		3	PPFIA2	12	81719606	Silent	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	65971669	81719606	52132289	62	749										
B3GNT4	79369	hgsc.bcm.edu	37	chr12	122691554	122691554	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gtcatccgccaagccctgccCaacaggaacactaaggtcaa	8	15	2	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr12:122691554C>T	ENST00000324189.4	+	3	1112	c.756C>T	c.(754-756)ccC>ccT	p.P252P	B3GNT4_ENST00000546192.1_Silent_p.P227P|B3GNT4_ENST00000535274.1_Silent_p.P227P|B3GNT4_ENST00000545141.1_Intron	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	252					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		AAGCCCTGCCCAACAGGAACA	0.567																																					p.P252P		Atlas-SNP	.											.	B3GNT4	35	.	0			c.C756T						.						97	81	86					12																	122691554		2203	4300	6503	SO:0001819	synonymous_variant	79369	exon3			CCTGCCCAACAGG	AB049586	CCDS9227.1	12q24	2013-02-19						"Beta 3-glycosyltransferases"	15683	protein-coding gene	gene with protein product		605864				11042166	Standard	NM_030765		Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000324189.4:c.756C>T	chr12.hg19:g.122691554C>T		55.0	0.0		51.0	21.0	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Silent	SNP	ENST00000324189.4	hg19	CCDS9227.1																																																																																			.	.		0.567	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765		T	122691554	C	T	122691554	2	4	9	1	0	0	0	0	0	0	0	1	1259	581	21	3		3	B3GNT4	12	122691554	Silent	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	40971948	122691554	11160341	63	750										
SOX21	11166	hgsc.bcm.edu	37	chr13	95363827	95363827	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gcggcggcggcggcggcggcAgcggcggcggcagcggccga	24	14	0	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr13:95363827A>G	ENST00000376945.2	-	1	562	c.477T>C	c.(475-477)gcT>gcC	p.A159A	SOX21-AS1_ENST00000438290.2_lincRNA	NM_007084.2	NP_009015.1	Q9Y651	SOX21_HUMAN	SRY (sex determining region Y)-box 21	159					hair follicle development (GO:0001942)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6	all_neural(89;0.0646)|Medulloblastoma(90;0.163)					cggcggcggcagcggcggcgg	0.751																																					p.A159A		Atlas-SNP	.											.	SOX21	21	.	0			c.T477C						.						1	2	2					13																	95363827		715	1520	2235	SO:0001819	synonymous_variant	11166	exon1			GGCGGCAGCGGCG	AF107044	CCDS9473.1	13q31-q32	2008-07-18			ENSG00000125285	ENSG00000125285		"SRY (sex determining region Y)-boxes"	11197	protein-coding gene	gene with protein product	"SRY-box 21"	604974				10441749	Standard	NM_007084		Approved	SOX25	uc001vma.3	Q9Y651	OTTHUMG00000017209	ENST00000376945.2:c.477T>C	chr13.hg19:g.95363827A>G		13.0	0.0		32.0	16.0	NM_007084	P35715|Q15504|Q5TBS1	Silent	SNP	ENST00000376945.2	hg19	CCDS9473.1																																																																																			.	.		0.751	SOX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045467.4	NM_007084		G	95363827	A	G	95363827	2	3	9	1	0	0	0	0	0	0	0	1	14965	175	7	2		2	SOX21	13	95363827	Silent	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10		95363827	19806051	64	751										
UGGT2	55757	hgsc.bcm.edu	37	chr13	96599334	96599334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ctgatatatcaaattcttctGcaatatagttgaaagctcgc	6	8	3	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr13:96599334G>A	ENST00000376747.3	-	15	1704	c.1634C>T	c.(1633-1635)gCa>gTa	p.A545V		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	545					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						AAATTCTTCTGCAATATAGTT	0.328																																					p.A545V		Atlas-SNP	.											.	UGGT2	127	.	0			c.C1634T						.						62	66	65					13																	96599334		2202	4299	6501	SO:0001583	missense	55757	exon15			TCTTCTGCAATAT	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.1634C>T	chr13.hg19:g.96599334G>A	ENSP00000365938:p.Ala545Val	242.0	0.0		321.0	148.0	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	hg19	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.680003	0.47886	.	.	ENSG00000102595	ENST00000376747	T	0.37058	1.22	5.82	3.06	0.35304	.	0.574837	0.19520	N	0.112318	T	0.27967	0.0689	L	0.50333	1.59	0.80722	D	1	B	0.12013	0.005	B	0.14023	0.01	T	0.05954	-1.0854	10	0.25106	T	0.35	-2.6196	6.0842	0.19958	0.2049:0.0:0.6638:0.1313	.	545	Q9NYU1	UGGG2_HUMAN	V	545	ENSP00000365938:A545V	ENSP00000365938:A545V	A	-	2	0	UGGT2	95397335	0.983000	0.35010	0.937000	0.37676	0.936000	0.57629	2.028000	0.41088	0.753000	0.32945	0.573000	0.79308	GCA	.	.		0.328	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		A	96599334	G	A	96599334	3	1	9	1	0	0	0	0	1	0	0	0	16957	1319	46	3	3016	3	UGGT2	13	96599334	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	1235507	96599334	18570544	65	752										
TEP1	7011	hgsc.bcm.edu	37	chr14	20841220	20841226	+	Frame_Shift_Del	DEL	CTTGATT	CTTGATT	-													0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ccacaagattagttccccagCttgatttccagatactgcca							TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	CTTGATT	CTTGATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr14:20841220_20841226delCTTGATT	ENST00000262715.5	-	48	6935_6941	c.6895_6901delAATCAAG	c.(6895-6903)aatcaagctfs	p.NQA2299fs	TEP1_ENST00000545983.1_Frame_Shift_Del_p.NQA637fs|TEP1_ENST00000556935.1_Frame_Shift_Del_p.NQA2191fs	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2299					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AGTTCCCCAGCTTGATTTCCAGATACT	0.522																																					p.2299_2301del		Atlas-Indel,Pindel	.											.	TEP1	224	.	0			c.6896_6902del						.																																			SO:0001589	frameshift_variant	7011	exon48			.		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.6895_6901delAATCAAG	chr14.hg19:g.20841220_20841226delCTTGATT	ENSP00000262715:p.Asn2299fs	58.0	0.0		80.0	27.0	NM_007110	A0AUV9	Frame_Shift_Del	DEL	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	.		0.522	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		-	20841226	CTTGATT	-	20841220	7	5	9	1	0	1	0	1	0	0	0	0	15774	797	28	0	1014	0	TEP1	14	20841220	Frame_Shift_Del	DEL	CTTGATT	TCGA-2Y-A9GZ-01A-11D-A38X-10		20841220	86508320	66	753										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33293348	33293348	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gctgagaaaaggggacttttAttcgtacttatctctctcat	8	8	2	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr14:33293348A>T	ENST00000280979.4	+	13	6499	c.6329A>T	c.(6328-6330)tAt>tTt	p.Y2110F	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2110					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GGGGACTTTTATTCGTACTTA	0.463																																					p.Y2110F	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.A6329T						.						96	95	96					14																	33293348		2203	4300	6503	SO:0001583	missense	9472	exon13			ACTTTTATTCGTA	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6329A>T	chr14.hg19:g.33293348A>T	ENSP00000280979:p.Tyr2110Phe	100.0	0.0		130.0	46.0	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.189135	0.78789	.	.	ENSG00000151320	ENST00000280979	T	0.58797	0.31	6.03	6.03	0.97812	.	0.140928	0.48767	D	0.000176	T	0.72922	0.3521	M	0.69823	2.125	0.80722	D	1	D	0.67145	0.996	D	0.70227	0.968	T	0.75886	-0.3159	10	0.72032	D	0.01	-14.8253	11.6145	0.51080	0.8673:0.0:0.0:0.1327	.	2110	Q13023	AKAP6_HUMAN	F	2110	ENSP00000280979:Y2110F	ENSP00000280979:Y2110F	Y	+	2	0	AKAP6	32363099	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.211000	0.77933	2.308000	0.77769	0.533000	0.62120	TAT	.	.		0.463	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33293348	A	T	33293348	3	4	9	1	0	0	0	0	1	0	0	0	455	449	16	4	6375	4	AKAP6	14	33293348	Missense_Mutation	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	12452128	33293348	74056192	67	754										
FERMT2	10979	hgsc.bcm.edu	37	chr14	53345391	53345391	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	cctgctcgtaaagctgattgAttctgattgcatcatactgc	8	10	2	3			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr14:53345391A>C	ENST00000395631.2	-	7	1088	c.872T>G	c.(871-873)aTc>aGc	p.I291S	FERMT2_ENST00000399304.3_Missense_Mutation_p.I291S|FERMT2_ENST00000343279.4_Missense_Mutation_p.I291S|FERMT2_ENST00000341590.3_Missense_Mutation_p.I291S|FERMT2_ENST00000553373.1_Missense_Mutation_p.I291S			Q96AC1	FERM2_HUMAN	fermitin family member 2	291	FERM.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					AAGCTGATTGATTCTGATTGC	0.363																																					p.I291S		Atlas-SNP	.											.	FERMT2	59	.	0			c.T872G						.						129	117	121					14																	53345391		2203	4300	6503	SO:0001583	missense	10979	exon7			TGATTGATTCTGA	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"Fermitins", "Pleckstrin homology (PH) domain containing"	15767	protein-coding gene	gene with protein product	"kindlin-2"	607746	"pleckstrin homology domain containing, family C (with FERM domain) member 1", "fermitin family homolog 2 (Drosophila)"	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.872T>G	chr14.hg19:g.53345391A>C	ENSP00000378993:p.Ile291Ser	56.0	0.0		81.0	39.0	NM_001135000	B5TJY2|Q14840|Q86TY7	Missense_Mutation	SNP	ENST00000395631.2	hg19	CCDS9713.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.321867	0.81580	.	.	ENSG00000073712	ENST00000395631;ENST00000341590;ENST00000554152;ENST00000343279;ENST00000553373;ENST00000399304	T;T;T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4;-1.4;-1.4	5.82	5.82	0.92795	Band 4.1 domain (1);FERM central domain (2);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.052499	0.85682	D	0.000000	D	0.89829	0.6828	M	0.80982	2.52	0.80722	D	1	P;P;P	0.50710	0.923;0.845;0.938	D;P;D	0.66979	0.913;0.882;0.948	D	0.91030	0.4863	10	0.87932	D	0	.	16.1777	0.81874	1.0:0.0:0.0:0.0	.	291;291;291	Q96AC1-2;Q96AC1;B5TJY2	.;FERM2_HUMAN;.	S	291;291;244;291;291;291	ENSP00000378993:I291S;ENSP00000340391:I291S;ENSP00000450741:I244S;ENSP00000342858:I291S;ENSP00000451084:I291S;ENSP00000382243:I291S	ENSP00000340391:I291S	I	-	2	0	FERMT2	52415141	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.287000	0.95975	2.222000	0.72286	0.383000	0.25322	ATC	.	.		0.363	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832		C	53345391	A	C	53345391	3	2	9	1	0	0	0	0	1	0	0	0	5826	333	12	5	1243	5	FERMT2	14	53345391	Missense_Mutation	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	20052043	53345391	54004149	68	755										
ADAM20	8748	hgsc.bcm.edu	37	chr14	70990870	70990870	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	caaaccgctgatgggtccacCagcccacaaaagaactttgc	8	14	0	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr14:70990870C>G	ENST00000256389.3	-	2	999	c.755G>C	c.(754-756)tGg>tCg	p.W252S	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	202	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		ATGGGTCCACCAGCCCACAAA	0.408																																					p.W252S		Atlas-SNP	.											.	ADAM20	59	.	0			c.G755C						.						59	56	57					14																	70990870		2203	4300	6503	SO:0001583	missense	8748	exon2			GTCCACCAGCCCA	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.755G>C	chr14.hg19:g.70990870C>G	ENSP00000256389:p.Trp252Ser	98.0	0.0		125.0	57.0	NM_003814	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	hg19	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.429048	0.43122	.	.	ENSG00000134007	ENST00000256389	T	0.00792	5.69	3.58	2.68	0.31781	Metallopeptidase, catalytic domain (1);	0.000000	0.37136	N	0.002236	T	0.01695	0.0054	M	0.82323	2.585	0.43394	D	0.995519	B	0.25904	0.137	B	0.26310	0.068	T	0.47548	-0.9109	10	0.54805	T	0.06	.	12.1339	0.53959	0.0:0.8263:0.1736:0.0	.	202	O43506	ADA20_HUMAN	S	252	ENSP00000256389:W252S	ENSP00000256389:W252S	W	-	2	0	ADAM20	70060623	0.809000	0.29036	0.693000	0.30195	0.000000	0.00434	0.975000	0.29449	1.060000	0.40578	-0.182000	0.12963	TGG	.	.		0.408	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			G	70990870	C	G	70990870	3	3	9	1	0	0	0	0	1	0	0	0	242	595	21	4	1579	4	ADAM20	14	70990870	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	17645479	70990870	36358670	69	756										
C14orf145	145508	hgsc.bcm.edu	37	chr14	81251871	81251871	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	atacagctgggttttcaattCatccttttcttttaaaatct	4	8	4	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr14:81251871C>A	ENST00000555265.1	-	15	1954	c.1579G>T	c.(1579-1581)Gaa>Taa	p.E527*	CEP128_ENST00000281129.3_Nonsense_Mutation_p.E527*			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	527						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						GTTTTCAATTCATCCTTTTCT	0.363																																					p.E527X		Atlas-SNP	.											.	CEP128	146	.	0			c.G1579T						.						21	21	21					14																	81251871		2195	4239	6434	SO:0001587	stop_gained	145508	exon14			TCAATTCATCCTT	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.1579G>T	chr14.hg19:g.81251871C>A	ENSP00000451162:p.Glu527*	72.0	0.0		114.0	19.0	NM_152446	B9EK52|Q86X97|Q96ML4	Nonsense_Mutation	SNP	ENST00000555265.1	hg19	CCDS32130.1	.	.	.	.	.	.	.	.	.	.	C	42	9.553027	0.99202	.	.	ENSG00000100629	ENST00000281129;ENST00000555265;ENST00000393619	.	.	.	5.75	5.75	0.90469	.	0.333709	0.31323	N	0.007846	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	20.3028	0.98618	0.0:1.0:0.0:0.0	.	.	.	.	X	527	.	ENSP00000281129:E527X	E	-	1	0	CEP128	80321624	1.000000	0.71417	0.997000	0.53966	0.910000	0.53928	3.056000	0.49923	2.876000	0.98609	0.643000	0.83706	GAA	.	.		0.363	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		A	81251871	C	A	81251871	4	1	9	1	0	0	0	0	0	1	0	0	1751	835	29	3	1749	3	C14orf145	14	81251871	Nonsense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	10261001	81251871	26097669	70	757										
FMN1	342184	hgsc.bcm.edu	37	chr15	33256458	33256458	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	aaggttggtgtagcattttgGcttaaaagagaaaatgacaa	11	3	0	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr15:33256458G>T	ENST00000559047.1	-	6	2987	c.2988C>A	c.(2986-2988)agC>agA	p.S996R	FMN1_ENST00000334528.9_Splice_Site_p.S773R|FMN1_ENST00000561249.1_Splice_Site_p.S898R			Q68DA7	FMN1_HUMAN	formin 1	996	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TAGCATTTTGGCTTAAAAGAG	0.343																																					p.S773R		Atlas-SNP	.											.	FMN1	174	.	0			c.C2319A						.						113	104	107					15																	33256458		1810	4079	5889	SO:0001630	splice_region_variant	342184	exon5			ATTTTGGCTTAAA	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2988-1C>A	chr15.hg19:g.33256458G>T		92.0	0.0		134.0	29.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.36	1.328584	0.24167	.	.	ENSG00000248905	ENST00000334528	T	0.16196	2.36	5.06	4.14	0.48551	.	0.222047	0.53938	D	0.000051	T	0.06234	0.0161	N	0.04116	-0.275	.	.	.	B	0.17465	0.022	B	0.23574	0.047	T	0.19192	-1.0313	9	0.15952	T	0.53	.	2.5443	0.04733	0.1664:0.1581:0.5318:0.1436	.	773	Q68DA7-5	.	R	773	ENSP00000333950:S773R	ENSP00000333950:S773R	S	-	3	2	FMN1	31043750	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	1.874000	0.39568	1.120000	0.41904	-0.251000	0.11542	AGC	.	.		0.343	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	Missense_Mutation	T	33256458	G	T	33256458	5	4	9	1	0	0	0	0	0	0	1	0	5957	1217	42	3	1323	3	FMN1	15	33256458	Splice_Site	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10		33256458	69274934	71	758										
RFX7	64864	hgsc.bcm.edu	37	chr15	56385627	56385627	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	atagaattcatggattcactGcaaatttgttgaaataatgg	8	4	2	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr15:56385627G>A	ENST00000559447.2	-	9	4279	c.4008C>T	c.(4006-4008)tgC>tgT	p.C1336C	RFX7_ENST00000422057.1_Intron|RFX7_ENST00000317318.6_Intron|RFX7_ENST00000423270.1_Silent_p.C1433C			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	1336					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TGGATTCACTGCAAATTTGTT	0.368																																					p.C1433C		Atlas-SNP	.											.	RFX7	170	.	0			c.C4299T						.						111	100	103					15																	56385627		1867	4103	5970	SO:0001819	synonymous_variant	64864	exon9			TTCACTGCAAATT			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.4008C>T	chr15.hg19:g.56385627G>A		64.0	0.0		69.0	9.0	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	hg19																																																																																				.	.		0.368	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		A	56385627	G	A	56385627	2	1	9	1	0	0	0	0	0	0	0	1	13283	1311	46	3		3	RFX7	15	56385627	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	23129169	56385627	46145765	72	759										
APH1B	83464	hgsc.bcm.edu	37	chr15	63571387	63571387	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ttctggttggtgtctctactGatttcgtcccttgtttggtt	10	8	2	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr15:63571387G>A	ENST00000261879.5	+	2	211	c.141G>A	c.(139-141)ctG>ctA	p.L47L	APH1B_ENST00000380343.4_Silent_p.L47L	NM_001145646.1|NM_031301.3	NP_001139118.1|NP_112591.2	Q8WW43	APH1B_HUMAN	APH1B gamma secretase subunit	47					apoptotic signaling pathway (GO:0097190)|membrane protein intracellular domain proteolysis (GO:0031293)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	peptidase activity (GO:0008233)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	12						TGTCTCTACTGATTTCGTCCC	0.373																																					p.L47L		Atlas-SNP	.											.	APH1B	27	.	0			c.G141A						.						185	172	176					15																	63571387		2203	4300	6503	SO:0001819	synonymous_variant	83464	exon2			TCTACTGATTTCG	AY358698	CCDS10184.1, CCDS45276.1	15q22.2	2013-05-01	2013-05-01		ENSG00000138613	ENSG00000138613			24080	protein-coding gene	gene with protein product		607630	"anterior pharynx defective 1 homolog B (C. elegans)"			12110170, 11230166	Standard	NM_031301		Approved	PSFL, APH-1B, DKFZp564D0372	uc002ama.3	Q8WW43	OTTHUMG00000132863	ENST00000261879.5:c.141G>A	chr15.hg19:g.63571387G>A		105.0	0.0		104.0	28.0	NM_001145646	A8K589|Q564N3|Q6UWQ1|Q9H0S0	Silent	SNP	ENST00000261879.5	hg19	CCDS10184.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.324917	0.60634	.	.	ENSG00000138613	ENST00000380340	.	.	.	4.64	0.149	0.14863	.	.	.	.	.	T	0.67832	0.2935	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67480	-0.5660	5	0.87932	D	0	-6.7644	10.0704	0.42330	0.0:0.4192:0.437:0.1438	.	.	.	.	N	69	.	ENSP00000369697:D69N	D	+	1	0	APH1B	61358440	0.987000	0.35691	0.022000	0.16811	0.764000	0.43329	1.486000	0.35530	-0.150000	0.11195	0.462000	0.41574	GAT	.	.		0.373	APH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256337.1	NM_031301		A	63571387	G	A	63571387	2	1	9	1	0	0	0	0	0	0	0	1	772	1277	45	3		3	APH1B	15	63571387	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	7185760	63571387	38960005	73	760										
HERC1	8925	hgsc.bcm.edu	37	chr15	63926085	63926086	+	Frame_Shift_Ins	INS	-	-	T													0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gtggaatttcctaagcctagINSttttccatagtctccatctc					rs371382538		TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr15:63926085_63926086insT	ENST00000443617.2	-	67	12741_12742	c.12654_12655insA	c.(12652-12657)aaactafs	p.L4219fs		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4219					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCTAAGCCTAGTTTTCCATAGT	0.426																																					p.L4219fs		Pindel	.											.	HERC1	624	.	0			c.12655_12656insA						.																																			SO:0001589	frameshift_variant	8925	exon67			.	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.12655dupA	chr15.hg19:g.63926089_63926089dupT	ENSP00000390158:p.Leu4219fs	231.0	0.0		173.0	34.0	NM_003922	Q8IW65	Frame_Shift_Ins	INS	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.		0.426	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63926086	-	T	63926085	7	5	9	1	0	1	1	0	0	0	0	0	7066	1020	36	0	1978	0	HERC1	15	63926085	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GZ-01A-11D-A38X-10	354698	63926085	38605307	74	761										
GOLGA6B	55889	hgsc.bcm.edu	37	chr15	72955008	72955008	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	aggctgtggaagaaggaggaGaggctacaaaagcaggagga	18	4	0	2	rs199550549	byFrequency	TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr15:72955008G>C	ENST00000421285.3	+	11	1263	c.1263G>C	c.(1261-1263)gaG>gaC	p.E421D	RN7SL853P_ENST00000477951.2_RNA	NM_018652.4	NP_061122.4	A6NDN3	GOG6B_HUMAN	golgin A6 family, member B	421						Golgi apparatus (GO:0005794)		p.E421D(1)		NS(1)|breast(1)|endometrium(1)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	16						AGAAGGAGGAGAGGCTACAAA	0.587																																					p.E421D		Atlas-SNP	.											GOLGA6B,NS,malignant_melanoma,0,1	GOLGA6B	30	.	1	Substitution - Missense(1)	NS(1)	c.G1263C						.						1	1	1					15																	72955008		108	305	413	SO:0001583	missense	55889	exon11			GGAGGAGAGGCTA		CCDS10245.2	15q24.1	2011-10-25	2010-02-12		ENSG00000215186	ENSG00000215186			32205	protein-coding gene	gene with protein product			"golgi autoantigen, golgin subfamily a, 6B"				Standard	XM_006720604		Approved		uc010uks.1	A6NDN3	OTTHUMG00000133511	ENST00000421285.3:c.1263G>C	chr15.hg19:g.72955008G>C	ENSP00000408132:p.Glu421Asp	68.0	0.0		44.0	3.0	NM_018652	A8MYY7	Missense_Mutation	SNP	ENST00000421285.3	hg19	CCDS10245.2	.	.	.	.	.	.	.	.	.	.	.	3.065	-0.192360	0.06259	.	.	ENSG00000215186	ENST00000421285	T	0.07444	3.19	.	.	.	.	.	.	.	.	T	0.06962	0.0177	L	0.47190	1.495	0.22888	N	0.99861	P	0.49961	0.93	B	0.40444	0.329	T	0.30208	-0.9986	8	0.62326	D	0.03	.	2.6645	0.05037	0.4931:0.0:0.5069:0.0	.	421	A6NDN3	GOG6B_HUMAN	D	421	ENSP00000408132:E421D	ENSP00000408132:E421D	E	+	3	2	GOLGA6B	70742062	0.998000	0.40836	0.134000	0.22075	0.265000	0.26407	0.636000	0.24644	0.088000	0.17205	0.089000	0.15464	GAG	.	G|1.000;|0.000		0.587	GOLGA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257474.4	NM_018652		C	72955008	G	C	72955008	3	2	9	1	0	0	0	0	1	0	0	0	6566	933	33	4	1305	4	GOLGA6B	15	72955008	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	9028923	72955008	29576384	75	762										
UBE2Q2	92912	hgsc.bcm.edu	37	chr15	76191767	76191767	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ttttttttcattctatttcaGgctggtacacccctccaaag	5	11	3	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr15:76191767G>A	ENST00000267938.4	+	13	1478		c.e13-1		UBE2Q2_ENST00000561851.1_Splice_Site|UBE2Q2_ENST00000569423.1_Splice_Site|UBE2Q2_ENST00000338677.4_Splice_Site	NM_173469.2	NP_775740.1	Q8WVN8	UB2Q2_HUMAN	ubiquitin-conjugating enzyme E2Q family member 2						protein K48-linked ubiquitination (GO:0070936)	cytoplasm (GO:0005737)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	12						TTCTATTTCAGGCTGGTACAC	0.308																																					.		Atlas-SNP	.											UBE2Q2,NS,carcinoma,0,1	UBE2Q2	26	.	0			c.1097-1G>A						.						90	83	85					15																	76191767		2197	4294	6491	SO:0001630	splice_region_variant	92912	exon13			ATTTCAGGCTGGT	BC017708	CCDS10286.1, CCDS45309.1, CCDS66839.1	15q24.2	2010-05-12	2008-05-02		ENSG00000140367	ENSG00000140367		"Ubiquitin-conjugating enzymes E2"	19248	protein-coding gene	gene with protein product		612501	"ubiquitin-conjugating enzyme E2Q (putative) 2"			16300736	Standard	NM_001145335		Approved	DKFZp762C143	uc002bbg.2	Q8WVN8	OTTHUMG00000142839	ENST00000267938.4:c.1097-1G>A	chr15.hg19:g.76191767G>A		41.0	0.0		15.0	11.0	NM_173469	B7Z3Q2|H3BRG2|Q8N4G6|Q96J08	Splice_Site	SNP	ENST00000267938.4	hg19	CCDS10286.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.909194	0.72868	.	.	ENSG00000140367	ENST00000338677;ENST00000267938;ENST00000426727	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.262	0.93971	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UBE2Q2	73978822	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.702000	0.91338	2.797000	0.96272	0.650000	0.86243	.	.	.		0.308	UBE2Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286475.1	NM_173469	Intron	A	76191767	G	A	76191767	5	1	9	1	0	0	0	0	0	0	1	0	16885	1014	35	3	1282	3	UBE2Q2	15	76191767	Splice_Site	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	3236759	76191767	26339625	76	763										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27549677	27549677	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	atgatcagtttcttcccccaCctgcaaatcggaaacaatcg	6	13	2	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr16:27549677C>A	ENST00000356183.4	-	3	447	c.432G>T	c.(430-432)agG>agT	p.R144S	GTF3C1_ENST00000561623.1_Splice_Site_p.R144S	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	144					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						TCTTCCCCCACCTGCAAATCG	0.478																																					p.R144S		Atlas-SNP	.											.	GTF3C1	210	.	0			c.G432T						.						57	54	55					16																	27549677		2197	4300	6497	SO:0001630	splice_region_variant	2975	exon3			CCCCCACCTGCAA	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.432-1G>T	chr16.hg19:g.27549677C>A		82.0	0.0		46.0	14.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.935060	0.52866	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.29655	1.56	5.38	3.4	0.38934	.	0.116290	0.56097	D	0.000021	T	0.30792	0.0776	M	0.68593	2.085	0.35990	D	0.836665	P;P	0.52577	0.954;0.825	B;B	0.41813	0.33;0.367	T	0.48790	-0.9004	10	0.62326	D	0.03	.	9.2211	0.37377	0.0:0.7167:0.0:0.2833	.	144;144	Q12789;Q12789-3	TF3C1_HUMAN;.	S	144	ENSP00000348510:R144S	ENSP00000348510:R144S	R	-	3	2	GTF3C1	27457178	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.066000	0.30604	1.410000	0.46936	0.563000	0.77884	AGG	.	.		0.478	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	Missense_Mutation	A	27549677	C	A	27549677	5	1	9	1	0	0	0	0	0	0	1	0	6881	521	18	3	6037	3	GTF3C1	16	27549677	Splice_Site	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		27549677	62805076	77	764										
CDH15	1013	hgsc.bcm.edu	37	chr16	89258218	89258218	+	Frame_Shift_Del	DEL	C	C	-													0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gcgccacggatgaggacctgCccccccacggggcccccttc							TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr16:89258218delC	ENST00000289746.2	+	10	1596	c.1531delC	c.(1531-1533)cccfs	p.P512fs		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	512	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		TGAGGACCTGCCCCCCCACGG	0.731																																					p.L510fs		Pindel	.											.	CDH15	54	.	0			c.1530delG						.						9	12	11					16																	89258218		2085	4090	6175	SO:0001589	frameshift_variant	1013	exon10			.	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"Cadherins / Major cadherins"	1754	protein-coding gene	gene with protein product		114019	"cadherin 15, M-cadherin (myotubule)"	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.1531delC	chr16.hg19:g.89258218delC	ENSP00000289746:p.Pro512fs	89.0	0.0		85.0	11.0	NM_004933		Frame_Shift_Del	DEL	ENST00000289746.2	hg19	CCDS10976.1																																																																																			.	.		0.731	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		-	89258218	C	-	89258218	7	5	9	1	0	1	0	1	0	0	0	0	3102	739	26	0	1569	0	CDH15	16	89258218	Frame_Shift_Del	DEL	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	61708541	89258218	1096535	78	765										
ALDOC	230	hgsc.bcm.edu	37	chr17	26900924	26900924	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ttgaatgatgcctcttcttcGctctgacccccagacaggaa	8	13	3	4	rs369962449		TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr17:26900924G>A	ENST00000226253.4	-	8	1303	c.828C>T	c.(826-828)agC>agT	p.S276S	ALDOC_ENST00000395321.2_Silent_p.S276S|RP11-192H23.5_ENST00000585189.1_RNA|PIGS_ENST00000308360.7_5'Flank|PIGS_ENST00000543734.1_5'Flank|ALDOC_ENST00000395319.3_Silent_p.S248S|PIGS_ENST00000395346.2_5'Flank	NM_005165.2	NP_005156.1	P09972	ALDOC_HUMAN	aldolase C, fructose-bisphosphate	276					aging (GO:0007568)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|epithelial cell differentiation (GO:0030855)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|organ regeneration (GO:0031100)|protein heterotetramerization (GO:0051290)|protein homotetramerization (GO:0051289)|response to hypoxia (GO:0001666)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	cytoskeletal protein binding (GO:0008092)|fructose-bisphosphate aldolase activity (GO:0004332)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Lung NSC(42;0.00431)					CCTCTTCTTCGCTCTGACCCC	0.572													G|||	1	0.000199681	0	0	5008	,	,		19892	0		0	False		,,,				2504	0.001				p.S276S		Atlas-SNP	.											.	ALDOC	22	.	0			c.C828T						.	G		1,4405	2.1+/-5.4	0,1,2202	107	107	107		828	4.4	1	17		107	0,8600		0,0,4300	no	coding-synonymous	ALDOC	NM_005165.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		276/365	26900924	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	230	exon8			TTCTTCGCTCTGA	AF054987	CCDS11236.1	17q11.2	2013-09-20			ENSG00000109107	ENSG00000109107	4.1.2.13		418	protein-coding gene	gene with protein product		103870					Standard	XM_005257947		Approved		uc002hbp.3	P09972	OTTHUMG00000132605	ENST00000226253.4:c.828C>T	chr17.hg19:g.26900924G>A		85.0	0.0		89.0	29.0	NM_005165	B2R5R3|Q3SYL3|Q6FH94|Q6P0L5	Silent	SNP	ENST00000226253.4	hg19	CCDS11236.1																																																																																			.	.		0.572	ALDOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255839.4			A	26900924	G	A	26900924	2	1	9	1	0	0	0	0	0	0	0	1	509	1078	38	1		1	ALDOC	17	26900924	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10		26900924	54294286	79	766										
ACACA	31	hgsc.bcm.edu	37	chr17	35454834	35454840	+	Frame_Shift_Del	DEL	ATGGTAA	ATGGTAA	-													0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gcaaactgcacggctacctgAtggtaaatgggaattaggaa							TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	ATGGTAA	ATGGTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr17:35454834_35454840delATGGTAA	ENST00000394406.2	-	53	6724_6730	c.6534_6540delTTACCAT	c.(6532-6540)atttaccatfs	p.IYH2178fs	ACACA_ENST00000353139.5_Frame_Shift_Del_p.IYH2215fs|ACACA_ENST00000335166.5_Frame_Shift_Del_p.IYH2100fs|ACACA_ENST00000360679.3_Frame_Shift_Del_p.IYH2120fs|ACACA_ENST00000361253.5_Frame_Shift_Del_p.IYH304fs	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	2178	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	CGGCTACCTGATGGTAAATGGGAATTA	0.502																																					p.2216_2218del	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-Indel,Pindel	.											.	ACACA	395	.	0			c.6646_6652del						.																																			SO:0001589	frameshift_variant	31	exon53			.	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.6534_6540delTTACCAT	chr17.hg19:g.35454834_35454840delATGGTAA	ENSP00000377928:p.Ile2178fs	124.0	0.0		127.0	22.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Frame_Shift_Del	DEL	ENST00000394406.2	hg19	CCDS11317.1																																																																																			.	.		0.502	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		-	35454840	ATGGTAA	-	35454834	7	5	9	1	0	1	0	1	0	0	0	0	106	330	12	0	516	0	ACACA	17	35454834	Frame_Shift_Del	DEL	ATGGTAA	TCGA-2Y-A9GZ-01A-11D-A38X-10	8553910	35454834	45740376	80	767										
TRIM37	4591	hgsc.bcm.edu	37	chr17	57181690	57181690	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	caacacagtttggagcaatgAggacacaggcgtgcatcccg	12	11	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr17:57181690A>T	ENST00000262294.7	-	2	346	c.87T>A	c.(85-87)ccT>ccA	p.P29P	TRIM37_ENST00000376149.3_5'UTR|TRIM37_ENST00000584889.1_Silent_p.P29P|AC099850.1_ENST00000451775.1_RNA|TRIM37_ENST00000393066.3_Silent_p.P29P|TRIM37_ENST00000393065.2_Intron	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	29					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					TGGAGCAATGAGGACACAGGC	0.368									Mulibrey Nanism																												p.P29P		Atlas-SNP	.											.	TRIM37	105	.	0			c.T87A						.						89	80	83					17																	57181690		2203	4300	6503	SO:0001819	synonymous_variant	4591	exon2	Familial Cancer Database	Perheentupa syndrome	GCAATGAGGACAC	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.87T>A	chr17.hg19:g.57181690A>T		253.0	1.0		547.0	278.0	NM_015294	Q7Z3E6|Q8IYF7|Q8WYF7	Silent	SNP	ENST00000262294.7	hg19	CCDS32694.1																																																																																			.	.		0.368	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		T	57181690	A	T	57181690	2	4	9	1	0	0	0	0	0	0	0	1	16526	291	11	4		4	TRIM37	17	57181690	Silent	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	21726856	57181690	24013520	81	768										
MED13	9969	hgsc.bcm.edu	37	chr17	60045496	60045496	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	aggctatatctctttgagatCcatagggttccagcataagt	9	8	1	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr17:60045496C>A	ENST00000397786.2	-	18	4167	c.4091G>T	c.(4090-4092)gGa>gTa	p.G1364V		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1364					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.G1364V(1)		breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TCTTTGAGATCCATAGGGTTC	0.383																																					p.G1364V		Atlas-SNP	.											MED13,NS,carcinoma,0,2	MED13	181	.	1	Substitution - Missense(1)	breast(1)	c.G4091T						.						140	125	130					17																	60045496		1835	4096	5931	SO:0001583	missense	9969	exon18			TGAGATCCATAGG	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.4091G>T	chr17.hg19:g.60045496C>A	ENSP00000380888:p.Gly1364Val	265.0	2.0		512.0	62.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.663911	0.88251	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.73258	-0.73	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.83285	0.5221	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	D	0.84332	0.0522	10	0.72032	D	0.01	-19.4547	19.5574	0.95357	0.0:1.0:0.0:0.0	.	1364	Q9UHV7	MED13_HUMAN	V	1364;1363	ENSP00000380888:G1364V	ENSP00000262436:G1363V	G	-	2	0	MED13	57400278	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.623000	0.88846	0.655000	0.94253	GGA	.	.		0.383	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		A	60045496	C	A	60045496	3	1	9	1	0	0	0	0	1	0	0	0	9439	855	30	3	2485	3	MED13	17	60045496	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	2863806	60045496	21149714	82	769										
RNF157	114804	hgsc.bcm.edu	37	chr17	74151751	74151751	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ccagacatggaggagacggtGtcagtgctgatctgggagga	17	7	2	3			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr17:74151751G>A	ENST00000269391.6	-	15	1722	c.1590C>T	c.(1588-1590)gaC>gaT	p.D530D	RNF157-AS1_ENST00000590137.1_RNA|RNF157_ENST00000319945.6_Silent_p.D530D|RNF157-AS1_ENST00000586661.1_RNA|RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000592748.1_RNA|RNF157-AS1_ENST00000585542.1_RNA	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	530	Ser-rich.						zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			AGGAGACGGTGTCAGTGCTGA	0.632																																					p.D530D	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.C1590T						.						48	36	40					17																	74151751		2203	4300	6503	SO:0001819	synonymous_variant	114804	exon15			GACGGTGTCAGTG	AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"RING-type (C3HC4) zinc fingers"	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.1590C>T	chr17.hg19:g.74151751G>A		108.0	0.0		220.0	69.0	NM_052916	Q8NB72|Q96N56	Silent	SNP	ENST00000269391.6	hg19	CCDS32740.1																																																																																			.	.		0.632	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732		A	74151751	G	A	74151751	2	1	9	1	0	0	0	0	0	0	0	1	13469	1368	48	3		3	RNF157	17	74151751	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	14106255	74151751	7043459	83	770										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22775123	22775123	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	aaggtttagagtgtcactcaCcaatcatgtgatttgcaaca	8	8	3	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr18:22775123C>A	ENST00000361524.3	-	5	3807		c.e5+1		ZNF521_ENST00000584787.1_Splice_Site|ZNF521_ENST00000538137.2_Splice_Site	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GTGTCACTCACCAATCATGTG	0.338			T	PAX5	ALL																																.		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.3658+1G>T						.						158	136	144					18																	22775123		2203	4300	6503	SO:0001630	splice_region_variant	25925	exon6			CACTCACCAATCA	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3658+1G>T	chr18.hg19:g.22775123C>A		27.0	0.0		47.0	7.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Splice_Site	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.095668	0.76870	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8984	0.96975	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF521	21029121	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.421000	0.80204	2.780000	0.95670	0.585000	0.79938	.	.	.		0.338	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	Intron	A	22775123	C	A	22775123	5	1	9	1	0	0	0	0	0	0	1	0	17980	521	18	3	292	3	ZNF521	18	22775123	Splice_Site	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		22775123	55302125	84	771										
MYO5B	4645	hgsc.bcm.edu	37	chr18	47566657	47566657	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	taagaagggcagctggttgcGttgtacatcaattgggtatt	13	5	1	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr18:47566657G>A	ENST00000285039.7	-	3	465	c.166C>T	c.(166-168)Cgc>Tgc	p.R56C		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	56					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		AGCTGGTTGCGTTGTACATCA	0.423																																					p.R56C		Atlas-SNP	.											.	MYO5B	178	.	0			c.C166T						.						285	276	279					18																	47566657		1969	4164	6133	SO:0001583	missense	4645	exon3			GGTTGCGTTGTAC	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.166C>T	chr18.hg19:g.47566657G>A	ENSP00000285039:p.Arg56Cys	188.0	0.0		137.0	34.0	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	hg19	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	g	11.47	1.648194	0.29336	.	.	ENSG00000167306	ENST00000285039;ENST00000356732	D	0.95342	-3.68	5.95	0.703	0.18116	.	0.983709	0.08333	N	0.962025	D	0.87414	0.6171	N	0.11560	0.145	0.09310	N	1	P;B	0.45715	0.865;0.002	P;B	0.46339	0.513;0.0	T	0.80261	-0.1456	10	0.54805	T	0.06	.	1.3274	0.02128	0.2283:0.1346:0.1268:0.5103	.	55;56	Q7Z7A5;Q9ULV0	.;MYO5B_HUMAN	C	56;55	ENSP00000285039:R56C	ENSP00000285039:R56C	R	-	1	0	MYO5B	45820655	0.000000	0.05858	0.046000	0.18839	0.074000	0.17049	-0.017000	0.12590	0.165000	0.19558	-1.480000	0.00990	CGC	.	.		0.423	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			A	47566657	G	A	47566657	3	1	9	1	0	0	0	0	1	0	0	0	10088	1145	40	1	5532	1	MYO5B	18	47566657	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	24791534	47566657	30510591	85	772										
MKNK2	2872	hgsc.bcm.edu	37	chr19	2042789	2042789	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gttatgcagaaagtccaaggCgctggccacgtcctgcacca	11	13	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr19:2042789C>T	ENST00000591601.1	-	7	609	c.574G>A	c.(574-576)Gcc>Acc	p.A192T	MKNK2_ENST00000591588.1_5'Flank|MKNK2_ENST00000541165.1_Missense_Mutation_p.A61T|MKNK2_ENST00000309340.7_Missense_Mutation_p.A192T|MKNK2_ENST00000588014.1_5'Flank|MKNK2_ENST00000591142.1_5'Flank|MKNK2_ENST00000250896.3_Missense_Mutation_p.A192T			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	192	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGTCCAAGGCGCTGGCCACG	0.657																																					p.A192T		Atlas-SNP	.											.	MKNK2	56	.	0			c.G574A						.						35	33	34					19																	2042789		2202	4295	6497	SO:0001583	missense	2872	exon8			CCAAGGCGCTGGC	AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"Putative map kinase interacting kinase"	605069	"G protein-coupled receptor kinase 7"	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.574G>A	chr19.hg19:g.2042789C>T	ENSP00000467811:p.Ala192Thr	44.0	0.0		41.0	20.0	NM_017572	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	hg19	CCDS12080.1	.	.	.	.	.	.	.	.	.	.	C	34	5.368462	0.95900	.	.	ENSG00000099875	ENST00000309340;ENST00000250896;ENST00000541165;ENST00000545627	T;T;T	0.57752	0.38;0.38;0.38	3.87	3.87	0.44632	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.115166	0.64402	D	0.000019	T	0.68366	0.2993	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.72338	0.977;0.79	T	0.69647	-0.5089	10	0.41790	T	0.15	-9.9485	14.5788	0.68271	0.0:1.0:0.0:0.0	.	192;192	Q9HBH9;Q9HBH9-2	MKNK2_HUMAN;.	T	192;192;61;132	ENSP00000309485:A192T;ENSP00000250896:A192T;ENSP00000438904:A61T	ENSP00000250896:A192T	A	-	1	0	MKNK2	1993789	1.000000	0.71417	0.994000	0.49952	0.722000	0.41435	7.465000	0.80898	2.007000	0.58848	0.556000	0.70494	GCC	.	.		0.657	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054		T	2042789	C	T	2042789	3	4	9	1	0	0	0	0	1	0	0	0	9614	768	27	1	946	1	MKNK2	19	2042789	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		2042789	57086194	86	773										
NR2F6	2063	hgsc.bcm.edu	37	chr19	17351535	17351535	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	agacggcagtactggcactgGttccggtggtgctggtcgat	16	9	0	1	rs2288539	byFrequency	TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr19:17351535G>C	ENST00000291442.3	-	2	1037	c.318C>G	c.(316-318)aaC>aaG	p.N106K	AC010646.3_ENST00000594059.1_5'UTR	NM_005234.3	NP_005225.2	P10588	NR2F6_HUMAN	nuclear receptor subfamily 2, group F, member 6	106					detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|entrainment of circadian clock by photoperiod (GO:0043153)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						ACTGGCACTGGTTCCGGTGGT	0.637																																					p.N106K		Atlas-SNP	.											.	NR2F6	18	.	0			c.C318G						.						169	125	140					19																	17351535		2203	4300	6503	SO:0001583	missense	2063	exon2			GCACTGGTTCCGG	X12794	CCDS12352.1	19p13.11	2013-09-20			ENSG00000160113	ENSG00000160113		"Nuclear hormone receptors"	7977	protein-coding gene	gene with protein product		132880		ERBAL2		2905047	Standard	NM_005234		Approved	EAR-2	uc002nfq.3	P10588	OTTHUMG00000182728	ENST00000291442.3:c.318C>G	chr19.hg19:g.17351535G>C	ENSP00000291442:p.Asn106Lys	96.0	0.0		86.0	22.0	NM_005234	B2RC68|Q5XGA0|Q6P586|Q9BUE8	Missense_Mutation	SNP	ENST00000291442.3	hg19	CCDS12352.1	.	.	.	.	.	.	.	.	.	.	G	19.44	3.828499	0.71258	.	.	ENSG00000160113	ENST00000291442;ENST00000536940	D	0.97161	-4.27	4.29	0.971	0.19698	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.85682	D	0.000000	D	0.97207	0.9087	M	0.63428	1.95	0.09310	P	0.99999999512266	D	0.76494	0.999	D	0.87578	0.998	D	0.96814	0.9599	9	0.87932	D	0	.	7.5691	0.27896	0.2956:0.0:0.7044:0.0	.	106	P10588	NR2F6_HUMAN	K	106;79	ENSP00000291442:N106K	ENSP00000291442:N106K	N	-	3	2	NR2F6	17212535	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.688000	0.46984	0.811000	0.34303	0.313000	0.20887	AAC	.	G|0.826;A|0.174		0.637	NR2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463325.1			C	17351535	G	C	17351535	3	2	9	1	0	0	0	0	1	0	0	0	10638	1252	44	4	908	4	NR2F6	19	17351535	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	15308746	17351535	41777448	87	774										
DDX49	54555	hgsc.bcm.edu	37	chr19	19032527	19032527	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tcctggggaagcctctagggCtgaaagactgcatcatcgtc	12	11	2	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr19:19032527C>A	ENST00000247003.4	+	3	362	c.295C>A	c.(295-297)Ctg>Atg	p.L99M	DDX49_ENST00000438170.2_5'UTR|COPE_ENST00000349893.4_5'Flank|COPE_ENST00000351079.4_5'Flank|AC002985.3_ENST00000596918.1_Intron|COPE_ENST00000262812.4_5'Flank|COPE_ENST00000600932.1_5'Flank	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	99	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	18			Epithelial(12;0.0289)			GCCTCTAGGGCTGAAAGACTG	0.647																																					p.L99M		Atlas-SNP	.											.	DDX49	37	.	0			c.C295A						.						115	100	105					19																	19032527		2203	4300	6503	SO:0001583	missense	54555	exon3			CTAGGGCTGAAAG		CCDS12390.1	19p12	2008-02-05				ENSG00000105671		"DEAD-boxes"	18684	protein-coding gene	gene with protein product							Standard	NM_019070		Approved	FLJ10432	uc002nkq.2	Q9Y6V7		ENST00000247003.4:c.295C>A	chr19.hg19:g.19032527C>A	ENSP00000247003:p.Leu99Met	122.0	0.0		86.0	23.0	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Missense_Mutation	SNP	ENST00000247003.4	hg19	CCDS12390.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.381942	0.61845	.	.	ENSG00000105671	ENST00000247003	T	0.20598	2.06	5.44	1.79	0.24919	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.37046	0.0989	M	0.63169	1.94	0.80722	D	1	D	0.63046	0.992	D	0.70227	0.968	T	0.04621	-1.0938	10	0.66056	D	0.02	-18.9413	7.9155	0.29816	0.0:0.6253:0.0:0.3747	.	99	Q9Y6V7	DDX49_HUMAN	M	99	ENSP00000247003:L99M	ENSP00000247003:L99M	L	+	1	2	DDX49	18893527	0.537000	0.26386	0.560000	0.28344	0.954000	0.61252	0.980000	0.29513	0.156000	0.19299	0.561000	0.74099	CTG	.	.		0.647	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070		A	19032527	C	A	19032527	3	1	9	1	0	0	0	0	1	0	0	0	4368	796	28	3	305	3	DDX49	19	19032527	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	1680992	19032527	40096456	88	775										
CIC	23152	hgsc.bcm.edu	37	chr19	42797243	42797243	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tgcctctgggcggcctggccCtgcaccccggcagcctctgg	14	18	2	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr19:42797243C>T	ENST00000575354.2	+	15	3645	c.3605C>T	c.(3604-3606)cCt>cTt	p.P1202L	CIC_ENST00000160740.3_Missense_Mutation_p.P1200L|CIC_ENST00000572681.2_Missense_Mutation_p.P2109L	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1202	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CGGCCTGGCCCTGCACCCCGG	0.706			"Mis, F, S"		oligodendroglioma																																p.P1202L		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.C3605T						.						10	12	11					19																	42797243		2168	4246	6414	SO:0001583	missense	23152	exon15			CTGGCCCTGCACC	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"capicua (Drosophila) homolog", "capicua homolog (Drosophila)"			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.3605C>T	chr19.hg19:g.42797243C>T	ENSP00000458663:p.Pro1202Leu	139.0	0.0		107.0	35.0	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	hg19	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.760871	0.31137	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	T	0.33000	0.0848	N	0.14661	0.345	0.36733	D	0.881839	P	0.36065	0.535	B	0.27887	0.084	T	0.50242	-0.8851	8	0.87932	D	0	-0.8271	12.9884	0.58604	0.0:1.0:0.0:0.0	.	1202	Q96RK0	CIC_HUMAN	L	1202	.	ENSP00000160740:P1202L	P	+	2	0	CIC	47489083	0.888000	0.30383	0.984000	0.44739	0.947000	0.59692	3.090000	0.50191	2.537000	0.85549	0.491000	0.48974	CCT	.	.		0.706	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			T	42797243	C	T	42797243	3	4	9	1	0	0	0	0	1	0	0	0	3426	681	24	3	3663	3	CIC	19	42797243	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	23764716	42797243	16331740	89	776										
SIGLEC8	27181	hgsc.bcm.edu	37	chr19	51960468	51960468	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tccttggaagacagtcatggTcaagttccaaggagggtctg	13	8	3	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr19:51960468T>C	ENST00000321424.3	-	3	817	c.751A>G	c.(751-753)Acc>Gcc	p.T251A	SIGLEC8_ENST00000430817.1_Intron|SIGLEC8_ENST00000597352.1_5'UTR|SIGLEC8_ENST00000340550.5_Missense_Mutation_p.T158A	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	251	Ig-like C2-type 2.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		ACAGTCATGGTCAAGTTCCAA	0.572																																					p.T251A		Atlas-SNP	.											.	SIGLEC8	130	.	0			c.A751G						.						100	95	96					19																	51960468		2203	4300	6503	SO:0001583	missense	27181	exon3			TCATGGTCAAGTT	AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.751A>G	chr19.hg19:g.51960468T>C	ENSP00000321077:p.Thr251Ala	61.0	0.0		46.0	10.0	NM_014442	Q7Z728	Missense_Mutation	SNP	ENST00000321424.3	hg19	CCDS33086.1	.	.	.	.	.	.	.	.	.	.	.	8.990	0.977436	0.18812	.	.	ENSG00000105366	ENST00000321424;ENST00000340550	T;T	0.64438	-0.1;1.1	2.14	-0.0501	0.13832	Immunoglobulin-like (1);	0.224693	0.23139	U	0.051485	T	0.56746	0.2006	L	0.60012	1.86	0.09310	N	1	B;B	0.31548	0.328;0.22	B;B	0.43251	0.413;0.109	T	0.48198	-0.9056	10	0.21540	T	0.41	.	4.4212	0.11481	0.0:0.3497:0.0:0.6503	.	158;251	Q9NYZ4-2;Q9NYZ4	.;SIGL8_HUMAN	A	251;158	ENSP00000321077:T251A;ENSP00000339448:T158A	ENSP00000321077:T251A	T	-	1	0	SIGLEC8	56652280	0.000000	0.05858	0.001000	0.08648	0.143000	0.21401	-0.019000	0.12546	-0.091000	0.12440	0.416000	0.27883	ACC	.	.		0.572	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442		C	51960468	T	C	51960468	3	2	9	1	0	0	0	0	1	0	0	0	14329	1667	58	2	768	2	SIGLEC8	19	51960468	Missense_Mutation	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10	9163225	51960468	7168515	90	777										
C19orf51	352909	hgsc.bcm.edu	37	chr19	55670499	55670499	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ccctgaggctgagccagaacCtctgagagtgaacctggaga	13	11	1	6			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr19:55670499C>A	ENST00000524407.2	-	12	1590	c.1557G>T	c.(1555-1557)gaG>gaT	p.E519D	CTD-2587H24.4_ENST00000587871.1_Intron|CTD-2587H24.5_ENST00000591665.1_RNA|DNAAF3_ENST00000455045.1_Missense_Mutation_p.E465D|TNNI3_ENST00000588882.1_5'Flank|TNNI3_ENST00000344887.5_5'Flank|DNAAF3_ENST00000527223.2_Missense_Mutation_p.E586D|DNAAF3_ENST00000587789.2_5'UTR|DNAAF3_ENST00000391720.4_Missense_Mutation_p.E566D|TNNI3_ENST00000590463.1_5'Flank			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	519					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											GAGCCAGAACCTCTGAGAGTG	0.617																																					p.E586D		Atlas-SNP	.											.	.	.	.	0			c.G1758T						.						25	27	27					19																	55670499		1857	4113	5970	SO:0001583	missense	352909	exon12			CAGAACCTCTGAG	AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"chromosome 19 open reading frame 51", "ciliary dyskinesia, primary 2"	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.1557G>T	chr19.hg19:g.55670499C>A	ENSP00000432046:p.Glu519Asp	129.0	0.0		93.0	28.0	NM_001256714	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Missense_Mutation	SNP	ENST00000524407.2	hg19	CCDS59422.1	.	.	.	.	.	.	.	.	.	.	c	12.04	1.817953	0.32145	.	.	ENSG00000167646	ENST00000301249;ENST00000455045;ENST00000391720	T;T	0.19669	2.15;2.13	3.77	-0.241	0.13043	.	0.416306	0.17608	N	0.168190	T	0.12092	0.0294	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.24963	0.115;0.009;0.015;0.005	B;B;B;B	0.20767	0.031;0.007;0.014;0.014	T	0.18967	-1.0320	10	0.37606	T	0.19	-6.6568	6.2192	0.20671	0.0:0.6633:0.1735:0.1632	.	586;465;539;519	E9PAX5;E3W9A1;Q8N9W5-3;Q8N9W5	.;.;.;CS051_HUMAN	D	586;465;566	ENSP00000394343:E465D;ENSP00000375600:E566D	ENSP00000301249:E586D	E	-	3	2	C19orf51	60362311	0.000000	0.05858	0.001000	0.08648	0.039000	0.13416	-0.603000	0.05674	0.030000	0.15379	0.556000	0.70494	GAG	.	.		0.617	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837		A	55670499	C	A	55670499	3	1	9	1	0	0	0	0	1	0	0	0	1935	680	24	3	72	3	C19orf51	19	55670499	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	3710031	55670499	3458484	91	778										
PEG3	5178	hgsc.bcm.edu	37	chr19	57328390	57328390	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	atagaggttctctctagtatGcatgatctggtgctcaacaa	9	8	4	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr19:57328390G>T	ENST00000326441.9	-	10	1783	c.1420C>A	c.(1420-1422)Cat>Aat	p.H474N	ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000599935.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.H474N|PEG3_ENST00000598410.1_Missense_Mutation_p.H350N|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.H348N	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	474					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TCTCTAGTATGCATGATCTGG	0.448																																					p.H474N		Atlas-SNP	.											.	PEG3	414	.	0			c.C1420A						.						197	171	180					19																	57328390		2203	4300	6503	SO:0001583	missense	5178	exon9			TAGTATGCATGAT	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.1420C>A	chr19.hg19:g.57328390G>T	ENSP00000326581:p.His474Asn	151.0	0.0		145.0	7.0	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	hg19	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.359120	0.82353	.	.	ENSG00000198300	ENST00000326441;ENST00000423103;ENST00000292074	T;T	0.47177	0.85;0.85	4.55	4.55	0.56014	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46442	D	0.000290	T	0.78710	0.4326	H	0.97103	3.94	.	.	.	D;D;D	0.89917	1.0;0.997;0.999	D;D;D	0.91635	0.999;0.994;0.998	D	0.87098	0.2177	9	0.87932	D	0	-34.4387	15.1826	0.72972	0.0:0.0:1.0:0.0	.	350;474;409	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	N	474;474;444	ENSP00000326581:H474N;ENSP00000403051:H474N	ENSP00000292074:H444N	H	-	1	0	ZIM2	62020202	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	6.451000	0.73481	2.515000	0.84797	0.650000	0.86243	CAT	.	.		0.448	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			T	57328390	G	T	57328390	3	4	9	1	0	0	0	0	1	0	0	0	11729	1319	46	3	3350	3	PEG3	19	57328390	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	1657891	57328390	1800593	92	779										
PSMF1	9491	hgsc.bcm.edu	37	chr20	1115886	1115886	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	ggagttcccccctgctaccgCcagagaggtggacccactcc	11	17	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr20:1115886C>G	ENST00000335877.6	+	4	664	c.488C>G	c.(487-489)gCc>gGc	p.A163G	PSMF1_ENST00000381898.4_Missense_Mutation_p.A75G|PSMF1_ENST00000438768.2_Intron|PSMF1_ENST00000484891.1_3'UTR|PSMF1_ENST00000246015.4_Missense_Mutation_p.A163G|PSMF1_ENST00000333082.3_Missense_Mutation_p.A163G	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	163	Pro-rich.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						CCTGCTACCGCCAGAGAGGTG	0.582																																					p.A163G		Atlas-SNP	.											.	PSMF1	27	.	0			c.C488G						.						81	73	76					20																	1115886		2203	4300	6503	SO:0001583	missense	9491	exon4			CTACCGCCAGAGA	D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"Proteasome (prosome, macropain) subunits"	9571	protein-coding gene	gene with protein product	"proteasome inhibitor hP131 subunit"					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.488C>G	chr20.hg19:g.1115886C>G	ENSP00000338039:p.Ala163Gly	91.0	0.0		129.0	34.0	NM_006814	A0AVQ9|D3DVW3|Q9H4I1	Missense_Mutation	SNP	ENST00000335877.6	hg19	CCDS13010.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.259794	0.39995	.	.	ENSG00000125818	ENST00000333082;ENST00000381898;ENST00000381899;ENST00000454500;ENST00000246015;ENST00000335877	T;T;T;T;T	0.44482	1.52;0.92;1.51;1.5;1.52	5.22	5.22	0.72569	.	0.356740	0.25256	N	0.031999	T	0.32675	0.0837	L	0.36672	1.1	0.30949	N	0.724997	P;P;B;B	0.42296	0.775;0.626;0.006;0.003	B;B;B;B	0.37550	0.225;0.253;0.007;0.002	T	0.26395	-1.0104	10	0.20519	T	0.43	-18.4618	15.8118	0.78571	0.0:1.0:0.0:0.0	.	75;75;163;163	F5H4Z3;B4DUJ0;Q5QPM7;Q92530	.;.;.;PSMF1_HUMAN	G	163;75;163;75;163;163	ENSP00000327704:A163G;ENSP00000371323:A75G;ENSP00000371324:A163G;ENSP00000246015:A163G;ENSP00000338039:A163G	ENSP00000246015:A163G	A	+	2	0	PSMF1	1063886	0.998000	0.40836	1.000000	0.80357	0.636000	0.38137	2.709000	0.47160	2.712000	0.92718	0.650000	0.86243	GCC	.	.		0.582	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578		G	1115886	C	G	1115886	3	3	9	1	0	0	0	0	1	0	0	0	12722	739	26	4	502	4	PSMF1	20	1115886	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		1115886	61909634	93	780										
TGM3	7053	hgsc.bcm.edu	37	chr20	2291690	2291690	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tatgggtaaccacgctgagaGagaagagtatgttcaggaag	14	5	1	3			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr20:2291690G>C	ENST00000381458.5	+	4	518	c.455G>C	c.(454-456)aGa>aCa	p.R152T		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	152					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	CACGCTGAGAGAGAAGAGTAT	0.468																																					p.R152T		Atlas-SNP	.											.	TGM3	105	.	0			c.G455C						.						159	150	153					20																	2291690		2203	4300	6503	SO:0001583	missense	7053	exon4			CTGAGAGAGAAGA	L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"Transglutaminases"	11779	protein-coding gene	gene with protein product	"E polypeptide, protein-glutamine-gamma-glutamyltransferase"	600238	"transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.455G>C	chr20.hg19:g.2291690G>C	ENSP00000370867:p.Arg152Thr	128.0	0.0		138.0	65.0	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	hg19	CCDS33435.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146920	0.77888	.	.	ENSG00000125780	ENST00000381458;ENST00000420960	D	0.91945	-2.94	5.58	5.58	0.84498	.	0.063428	0.85682	D	0.000000	D	0.97114	0.9057	H	0.94345	3.525	0.46542	D	0.999099	D	0.89917	1.0	D	0.70935	0.971	D	0.97470	1.0040	10	0.52906	T	0.07	.	17.0667	0.86561	0.0:0.0:1.0:0.0	.	152	Q08188	TGM3_HUMAN	T	152	ENSP00000370867:R152T	ENSP00000370867:R152T	R	+	2	0	TGM3	2239690	0.999000	0.42202	1.000000	0.80357	0.863000	0.49368	3.208000	0.51114	2.636000	0.89361	0.455000	0.32223	AGA	.	.		0.468	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245		C	2291690	G	C	2291690	3	2	9	1	0	0	0	0	1	0	0	0	15846	942	33	4	469	4	TGM3	20	2291690	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	1175804	2291690	60733830	94	781										
VPS16	64601	hgsc.bcm.edu	37	chr20	2843248	2843248	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gagagccagaaggcggacgaGtacctgcgggagatccagga	17	9	0	3			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr20:2843248G>C	ENST00000380445.3	+	12	1167	c.1095G>C	c.(1093-1095)gaG>gaC	p.E365D	VPS16_ENST00000481812.2_Splice_Site|VPS16_ENST00000380443.3_Missense_Mutation_p.E19D|VPS16_ENST00000380469.3_Intron|PTPRA_ENST00000380393.3_5'Flank	NM_022575.2	NP_072097.2	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 homolog (S. cerevisiae)	365					intracellular protein transport (GO:0006886)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|axon (GO:0030424)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	37						AGGCGGACGAGTACCTGCGGG	0.602																																					p.E365D		Atlas-SNP	.											.	VPS16	76	.	0			c.G1095C						.						45	49	48					20																	2843248		2203	4299	6502	SO:0001583	missense	64601	exon12			GGACGAGTACCTG	AF308801	CCDS13036.1, CCDS13037.1	20p13	2009-07-07	2009-07-07	2009-07-07	ENSG00000215305	ENSG00000215305			14584	protein-coding gene	gene with protein product		608550					Standard	NM_022575		Approved		uc002whe.3	Q9H269	OTTHUMG00000031714	ENST00000380445.3:c.1095G>C	chr20.hg19:g.2843248G>C	ENSP00000369810:p.Glu365Asp	52.0	0.0		48.0	25.0	NM_022575	Q5JUB1|Q8WU31|Q96EE7|Q96N92|Q9H1Q4|Q9H1Q5	Missense_Mutation	SNP	ENST00000380445.3	hg19	CCDS13036.1	.	.	.	.	.	.	.	.	.	.	G	13.96	2.392904	0.42410	.	.	ENSG00000215305	ENST00000380445;ENST00000380443	T;T	0.54675	0.67;0.56	5.08	0.868	0.19090	Vps16, N-terminal (1);	0.049806	0.85682	D	0.000000	T	0.36635	0.0974	L	0.41079	1.255	0.47584	D	0.999466	P;P	0.43633	0.813;0.604	B;B	0.38954	0.286;0.286	T	0.09271	-1.0682	10	0.59425	D	0.04	-27.4704	4.9337	0.13930	0.3324:0.1442:0.5234:0.0	.	19;365	Q5JUA8;Q9H269	.;VPS16_HUMAN	D	365;19	ENSP00000369810:E365D;ENSP00000369808:E19D	ENSP00000369808:E19D	E	+	3	2	VPS16	2791248	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	2.949000	0.49074	0.040000	0.15660	0.561000	0.74099	GAG	.	.		0.602	VPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077658.2	NM_022575		C	2843248	G	C	2843248	3	2	9	1	0	0	0	0	1	0	0	0	17208	1020	36	4	1141	4	VPS16	20	2843248	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	551558	2843248	60182272	95	782										
PAK7	57144	hgsc.bcm.edu	37	chr20	9560805	9560805	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	acgttacctttggaatgcacAttgtgggctcggacaagcga	12	9	0	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr20:9560805A>G	ENST00000378429.3	-	5	1523	c.977T>C	c.(976-978)aTg>aCg	p.M326T	RP5-986I17.2_ENST00000428769.1_RNA|PAK7_ENST00000353224.5_Missense_Mutation_p.M326T|PAK7_ENST00000378423.1_Missense_Mutation_p.M326T	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	326	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TGGAATGCACATTGTGGGCTC	0.502																																					p.M326T		Atlas-SNP	.											.	PAK7	194	.	0			c.T977C						.						292	238	256					20																	9560805		2203	4300	6503	SO:0001583	missense	57144	exon4			ATGCACATTGTGG	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.977T>C	chr20.hg19:g.9560805A>G	ENSP00000367686:p.Met326Thr	91.0	0.0		105.0	23.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	A	2.265	-0.368338	0.05069	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.71579	-0.58;-0.58;-0.58	5.93	4.89	0.63831	.	0.511356	0.25294	N	0.031711	T	0.45994	0.1370	N	0.14661	0.345	0.30989	N	0.721627	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.35968	-0.9767	9	.	.	.	.	2.1372	0.03765	0.3851:0.3355:0.2794:0.0	.	326;326	B0AZM9;Q9P286	.;PAK7_HUMAN	T	326;326;326;274	ENSP00000367686:M326T;ENSP00000322957:M326T;ENSP00000367679:M326T	.	M	-	2	0	PAK7	9508805	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	3.770000	0.55310	1.099000	0.41499	0.533000	0.62120	ATG	.	.		0.502	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			G	9560805	A	G	9560805	3	3	9	1	0	0	0	0	1	0	0	0	11414	217	8	2	1210	2	PAK7	20	9560805	Missense_Mutation	SNP	A	TCGA-2Y-A9GZ-01A-11D-A38X-10	6717557	9560805	53464715	96	783										
PABPC1L	80336	hgsc.bcm.edu	37	chr20	43550238	43550238	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	cctcctcctttccccaggccGtggtccatatgaacgggaag	10	15	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr20:43550238G>T	ENST00000217073.2	+	6	742	c.742G>T	c.(742-744)Gtg>Ttg	p.V248L	PABPC1L_ENST00000217074.4_Missense_Mutation_p.V248L|PABPC1L_ENST00000537323.1_Missense_Mutation_p.V248L|PABPC1L_ENST00000255136.3_Missense_Mutation_p.V248L			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	248	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						TCCCCAGGCCGTGGTCCATAT	0.617																																					p.V248L		Atlas-SNP	.											.	PABPC1L	59	.	0			c.G742T						.						102	101	102					20																	43550238		1568	3582	5150	SO:0001583	missense	80336	exon6			CAGGCCGTGGTCC	AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"RNA binding motif (RRM) containing"	15797	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 119"	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.742G>T	chr20.hg19:g.43550238G>T	ENSP00000217073:p.Val248Leu	94.0	0.0		84.0	40.0	NM_001124756	Q4VY17	Missense_Mutation	SNP	ENST00000217073.2	hg19	CCDS42878.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.660662	0.67586	.	.	ENSG00000101104	ENST00000217074;ENST00000255136;ENST00000537323;ENST00000217073	D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27	5.17	5.17	0.71159	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.116899	0.64402	D	0.000018	D	0.93311	0.7868	N	0.17379	0.485	0.80722	D	1	D	0.60575	0.988	D	0.64687	0.928	D	0.94877	0.8035	10	0.87932	D	0	.	18.2846	0.90110	0.0:0.0:1.0:0.0	.	248	Q4VXU2	PAP1L_HUMAN	L	248	ENSP00000217074:V248L;ENSP00000255136:V248L;ENSP00000445661:V248L;ENSP00000217073:V248L	ENSP00000217073:V248L	V	+	1	0	PABPC1L	42983652	1.000000	0.71417	0.766000	0.31476	0.021000	0.10359	9.835000	0.99442	2.421000	0.82119	0.563000	0.77884	GTG	.	.		0.617	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2			T	43550238	G	T	43550238	3	4	9	1	0	0	0	0	1	0	0	0	11373	1145	40	1	764	1	PABPC1L	20	43550238	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	33989433	43550238	19475282	97	784										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46262325	46262326	+	Frame_Shift_Ins	INS	-	-	T													0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tccgaaggtgtattcagagaINSttttttagtctaaatgatgg							TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr20:46262325_46262326insT	ENST00000371998.3	+	9	1100_1101	c.909_910insT	c.(910-912)tttfs	p.F304fs	NCOA3_ENST00000371997.3_Frame_Shift_Ins_p.F304fs|NCOA3_ENST00000341724.6_Frame_Shift_Ins_p.F304fs|NCOA3_ENST00000372004.3_Frame_Shift_Ins_p.F304fs			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	304					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GTATTCAGAGATTTTTTAGTCT	0.347																																					p.R303fs		Atlas-Indel,Pindel	.											.	NCOA3	156	.	0			c.909_910insT						.																																			SO:0001589	frameshift_variant	8202	exon9			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.915dupT	chr20.hg19:g.46262331_46262331dupT	ENSP00000361066:p.Phe304fs	234.0	0.0		301.0	63.0	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Frame_Shift_Ins	INS	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.		0.347	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		T	46262326	-	T	46262325	7	5	9	1	0	1	1	0	0	0	0	0	10239	330	12	0	935	0	NCOA3	20	46262325	Frame_Shift_Ins	INS	-	TCGA-2Y-A9GZ-01A-11D-A38X-10	2712087	46262325	16763195	98	785										
HRH3	11255	hgsc.bcm.edu	37	chr20	60791440	60791440	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gacggcttggagcccctcttGagtgagcgcggcctctcagt	14	13	2	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr20:60791440G>A	ENST00000340177.5	-	3	1244	c.960C>T	c.(958-960)ctC>ctT	p.L320L	HRH3_ENST00000317393.6_Silent_p.L320L	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	320					brain development (GO:0007420)|drinking behavior (GO:0042756)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of serotonin secretion (GO:0014063)|neurotransmitter secretion (GO:0007269)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of norepinephrine secretion (GO:0014061)|response to organic cyclic compound (GO:0014070)	integral component of plasma membrane (GO:0005887)|myelin sheath (GO:0043209)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|histamine receptor activity (GO:0004969)			breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Betahistine(DB06698)|Histamine Phosphate(DB00667)|Mirtazapine(DB00370)	AGCCCCTCTTGAGTGAGCGCG	0.697																																					p.L320L		Atlas-SNP	.											.	HRH3	25	.	0			c.C960T						.						8	8	8					20																	60791440		2174	4262	6436	SO:0001819	synonymous_variant	11255	exon3			CCTCTTGAGTGAG	AF140538	CCDS13493.1	20q13.33	2013-09-19			ENSG00000101180	ENSG00000101180		"GPCR / Class A : Histamine receptors"	5184	protein-coding gene	gene with protein product		604525				10347254	Standard	NM_007232		Approved	GPCR97	uc002ycf.2	Q9Y5N1	OTTHUMG00000032899	ENST00000340177.5:c.960C>T	chr20.hg19:g.60791440G>A		79.0	0.0		94.0	38.0	NM_007232	Q4QRI7|Q9GZX2|Q9H4K8	Silent	SNP	ENST00000340177.5	hg19	CCDS13493.1																																																																																			.	.		0.697	HRH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079994.1	NM_007232		A	60791440	G	A	60791440	2	1	9	1	0	0	0	0	0	0	0	1	7366	1277	45	3		3	HRH3	20	60791440	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	14529115	60791440	2234080	99	786										
USP16	10600	hgsc.bcm.edu	37	chr21	30409652	30409652	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	aaaaaattagaaaaagagagTaagaatgaacaagagagaga	10	1	0	6			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr21:30409652T>C	ENST00000334352.4	+	7	735	c.504T>C	c.(502-504)agT>agC	p.S168S	USP16_ENST00000535828.1_Intron|USP16_ENST00000399975.3_Silent_p.S167S|USP16_ENST00000399976.2_Silent_p.S168S	NM_001032410.1	NP_001027582.1			ubiquitin specific peptidase 16											breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(2)	34						AAAAAGAGAGTAAGAATGAAC	0.308																																					p.S168S	Melanoma(92;625 1444 27493 34101 44971)	Atlas-SNP	.											.	USP16	65	.	0			c.T504C						.						75	82	80					21																	30409652		2203	4300	6503	SO:0001819	synonymous_variant	10600	exon6			AGAGAGTAAGAAT	AF126736	CCDS13583.1, CCDS42912.1	21q21	2008-04-11	2005-08-08		ENSG00000156256	ENSG00000156256		"Ubiquitin-specific peptidases"	12614	protein-coding gene	gene with protein product		604735	"ubiquitin specific protease 16"			12838346	Standard	NM_006447		Approved	Ubp-M	uc002ymy.3	Q9Y5T5	OTTHUMG00000078802	ENST00000334352.4:c.504T>C	chr21.hg19:g.30409652T>C		158.0	0.0		214.0	41.0	NM_006447		Silent	SNP	ENST00000334352.4	hg19	CCDS13583.1																																																																																			.	.		0.308	USP16-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171847.1			C	30409652	T	C	30409652	2	2	9	1	0	0	0	0	0	0	0	1	17062	1635	57	2		2	USP16	21	30409652	Silent	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10		30409652	17720243	100	787										
MGAT3	4248	hgsc.bcm.edu	37	chr22	39884130	39884130	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tccgggagatgctgaccaatGgcaccttcgagtacatccgc	11	13	0	2	rs201303175		TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chr22:39884130G>A	ENST00000341184.6	+	2	993	c.778G>A	c.(778-780)Ggc>Agc	p.G260S		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase	260					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0003830)			endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|prostate(1)|skin(1)	24	Melanoma(58;0.04)					GCTGACCAATGGCACCTTCGA	0.647																																					p.G260S		Atlas-SNP	.											.	MGAT3	65	.	0			c.G778A						.						54	49	51					22																	39884130		2203	4300	6503	SO:0001583	missense	4248	exon2			ACCAATGGCACCT	D13789	CCDS13994.2	22q13.1	2013-02-25			ENSG00000128268	ENSG00000128268	2.4.1.144	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7046	protein-coding gene	gene with protein product		604621				8370666	Standard	NM_002409		Approved	GNT-III	uc010gxy.3	Q09327	OTTHUMG00000030185	ENST00000341184.6:c.778G>A	chr22.hg19:g.39884130G>A	ENSP00000345270:p.Gly260Ser	67.0	0.0		56.0	8.0	NM_002409	A6NGD0|Q14CK5|Q6IC49|Q9UH32	Missense_Mutation	SNP	ENST00000341184.6	hg19	CCDS13994.2	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004391	0.93287	.	.	ENSG00000128268	ENST00000341184	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.76644	0.4016	L	0.54908	1.71	0.58432	D	0.999995	D	0.89917	1.0	D	0.87578	0.998	T	0.75912	-0.3150	9	0.48119	T	0.1	.	19.2349	0.93855	0.0:0.0:1.0:0.0	.	260	Q09327	MGAT3_HUMAN	S	260	.	ENSP00000345270:G260S	G	+	1	0	MGAT3	38214076	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.289000	0.96061	2.571000	0.86741	0.561000	0.74099	GGC	.	G|0.999;A|0.001		0.647	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	NM_002409		A	39884130	G	A	39884130	3	1	9	1	0	0	0	0	1	0	0	0	9553	1348	47	3	780	3	MGAT3	22	39884130	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10		39884130	11420436	101	788										
ARSH	347527	hgsc.bcm.edu	37	chrX	2947346	2947346	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gaagggcgtcccactccgacCacgagttcctcttccactac	8	17	1	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chrX:2947346C>T	ENST00000381130.2	+	8	1258	c.1258C>T	c.(1258-1260)Cac>Tac	p.H420Y		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	420					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CCACTCCGACCACGAGTTCCT	0.547																																					p.H420Y		Atlas-SNP	.											.	ARSH	72	.	0			c.C1258T						.						147	111	123					X																	2947346		2203	4300	6503	SO:0001583	missense	347527	exon8			TCCGACCACGAGT	AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"Arylsulfatase family"	32488	protein-coding gene	gene with protein product		300586	"arylsulfatase H"			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.1258C>T	chrX.hg19:g.2947346C>T	ENSP00000370522:p.His420Tyr	165.0	0.0		175.0	75.0	NM_001011719		Missense_Mutation	SNP	ENST00000381130.2	hg19	CCDS35198.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.329060	0.41197	.	.	ENSG00000205667	ENST00000381130	D	0.91237	-2.81	3.5	3.5	0.40072	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	U	0.000000	D	0.96393	0.8823	H	0.94808	3.585	0.44380	D	0.997287	D	0.89917	1.0	D	0.85130	0.997	D	0.97493	1.0055	10	0.87932	D	0	.	14.4689	0.67501	0.0:1.0:0.0:0.0	.	420	Q5FYA8	ARSH_HUMAN	Y	420	ENSP00000370522:H420Y	ENSP00000370522:H420Y	H	+	1	0	ARSH	2957346	1.000000	0.71417	0.008000	0.14137	0.002000	0.02628	6.342000	0.72982	1.377000	0.46286	0.600000	0.82982	CAC	.	.		0.547	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719		T	2947346	C	T	2947346	3	4	9	1	0	0	0	0	1	0	0	0	993	594	21	3	1288	3	ARSH	23	2947346	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10		2947346	152323214	102	789										
CYBB	1536	hgsc.bcm.edu	37	chrX	37668941	37668941	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gacaattgcaagtcaacaccCtaagtaaggagtctgtcacc	8	11	3	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chrX:37668941C>G	ENST00000378588.4	+	12	1650	c.1583C>G	c.(1582-1584)cCt>cGt	p.P528R	CYBB_ENST00000536160.1_Missense_Mutation_p.P261R|CYBB_ENST00000545017.1_Missense_Mutation_p.P496R|TM4SF2_ENST00000465127.1_Intron	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	528					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|rough endoplasmic reticulum (GO:0005791)	flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|prostate(2)|skin(2)	32					Dextromethorphan(DB00514)	AGTCAACACCCTAAGTAAGGA	0.403																																					p.P528R		Atlas-SNP	.											.	CYBB	62	.	0			c.C1583G						.						85	69	75					X																	37668941		2202	4299	6501	SO:0001583	missense	1536	exon12			AACACCCTAAGTA	X04011	CCDS14242.1	Xp21.1	2014-09-17	2008-07-29		ENSG00000165168	ENSG00000165168		"Cytochrome b genes"	2578	protein-coding gene	gene with protein product		300481	"chronic granulomatous disease"	CGD			Standard	NM_000397		Approved	GP91-PHOX, NOX2	uc004ddr.2	P04839	OTTHUMG00000033175	ENST00000378588.4:c.1583C>G	chrX.hg19:g.37668941C>G	ENSP00000367851:p.Pro528Arg	168.0	0.0		245.0	43.0	NM_000397	A8K138|Q2PP16	Missense_Mutation	SNP	ENST00000378588.4	hg19	CCDS14242.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.342125	0.81911	.	.	ENSG00000165168	ENST00000378588;ENST00000545017;ENST00000536160	D;D;D	0.95069	-3.6;-3.6;-3.6	5.81	5.81	0.92471	Ferric reductase, NAD binding (1);	0.046961	0.85682	D	0.000000	D	0.95398	0.8506	M	0.65320	2	0.80722	D	1	B;P	0.45348	0.296;0.856	B;P	0.50754	0.183;0.649	D	0.94454	0.7670	10	0.37606	T	0.19	.	19.0421	0.93004	0.0:1.0:0.0:0.0	.	496;528	F5GWD2;P04839	.;CY24B_HUMAN	R	528;496;261	ENSP00000367851:P528R;ENSP00000441896:P496R;ENSP00000441958:P261R	ENSP00000367851:P528R	P	+	2	0	CYBB	37553885	1.000000	0.71417	0.996000	0.52242	0.986000	0.74619	7.362000	0.79507	2.446000	0.82766	0.600000	0.82982	CCT	.	.		0.403	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1			G	37668941	C	G	37668941	3	3	9	1	0	0	0	0	1	0	0	0	4135	681	24	4	1629	4	CYBB	23	37668941	Missense_Mutation	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	34721595	37668941	117601619	103	790										
RBM10	8241	hgsc.bcm.edu	37	chrX	47030585	47030585	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gaggaggaggaggaggaggaTgaggaggaggaggagaaggc	25	1	0	2	rs377667483		TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chrX:47030585T>G	ENST00000377604.3	+	4	1102	c.360T>G	c.(358-360)gaT>gaG	p.D120E	RBM10_ENST00000329236.7_Intron|RBM10_ENST00000345781.6_Intron	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	120	Poly-Glu.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						aggaggaggatgaggaggagg	0.667													T|||	2	0.000529801	0	0	3775	,	,		8316	0.002		0	False		,,,				2504	0				p.D185E	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.T555G						.						20	19	20					X																	47030585		2202	4297	6499	SO:0001583	missense	8241	exon4			GGAGGATGAGGAG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.360T>G	chrX.hg19:g.47030585T>G	ENSP00000366829:p.Asp120Glu	106.0	0.0		130.0	6.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	T	1.034	-0.680868	0.03353	.	.	ENSG00000182872	ENST00000377604	T	0.10960	2.82	2.89	-2.28	0.06826	Nucleotide-binding, alpha-beta plait (1);	0.397395	0.18197	N	0.148658	T	0.03783	0.0107	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.49153	-0.8969	10	0.02654	T	1	-3.1034	10.6013	0.45369	0.0:0.0:0.7699:0.2301	.	185;120;120	Q7Z3D7;P98175-2;P98175	.;.;RBM10_HUMAN	E	120	ENSP00000366829:D120E	ENSP00000366829:D120E	D	+	3	2	RBM10	46915529	0.996000	0.38824	0.881000	0.34555	0.930000	0.56654	-0.096000	0.11059	-0.655000	0.05387	-0.549000	0.04216	GAT	.	.		0.667	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		G	47030585	T	G	47030585	3	3	9	1	0	0	0	0	1	0	0	0	13126	1461	51	5	370	5	RBM10	23	47030585	Missense_Mutation	SNP	T	TCGA-2Y-A9GZ-01A-11D-A38X-10	9361644	47030585	108239975	104	791										
TRO	7216	hgsc.bcm.edu	37	chrX	54955556	54955556	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	tagctttggttgtgcacacaGcaccagcactagtttcagca	9	11	1	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chrX:54955556G>T	ENST00000173898.7	+	12	2511	c.2399G>T	c.(2398-2400)aGc>aTc	p.S800I	TRO_ENST00000375022.4_Intron|TRO_ENST00000399736.1_Intron|TRO_ENST00000375041.2_Missense_Mutation_p.S403I|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000420798.2_Missense_Mutation_p.S331I|TRO_ENST00000319167.8_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	800	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						TGTGCACACAGCACCAGCACT	0.522																																					p.S800I		Atlas-SNP	.											.	TRO	246	.	0			c.G2399T						.						64	63	64					X																	54955556		2176	4269	6445	SO:0001583	missense	7216	exon12			CACACAGCACCAG	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.2399G>T	chrX.hg19:g.54955556G>T	ENSP00000173898:p.Ser800Ile	109.0	0.0		127.0	45.0	NM_001039705	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	hg19	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	G	0.954	-0.705407	0.03255	.	.	ENSG00000067445	ENST00000173898;ENST00000420798;ENST00000375041	T;T;T	0.24151	1.87;1.87;1.87	3.15	0.304	0.15796	.	.	.	.	.	T	0.14874	0.0359	L	0.39898	1.24	0.09310	N	1	P;P	0.44578	0.838;0.718	B;B	0.32864	0.154;0.154	T	0.15521	-1.0434	9	0.87932	D	0	.	4.5843	0.12275	0.2392:0.1816:0.5792:0.0	.	403;800	B1AKE9;Q12816	.;TROP_HUMAN	I	800;331;403	ENSP00000173898:S800I;ENSP00000405126:S331I;ENSP00000364181:S403I	ENSP00000173898:S800I	S	+	2	0	TRO	54972281	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	0.981000	0.29526	-0.053000	0.13289	-0.217000	0.12591	AGC	.	.		0.522	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		T	54955556	G	T	54955556	3	4	9	1	0	0	0	0	1	0	0	0	16589	971	34	3	2441	3	TRO	23	54955556	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	7924971	54955556	100315004	105	792										
TBX22	50945	hgsc.bcm.edu	37	chrX	79282319	79282319	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gaaggtgttaaaacattctcCtttaaagaaactgagttcac	7	7	2	2			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chrX:79282319C>T	ENST00000373294.5	+	5	778	c.750C>T	c.(748-750)tcC>tcT	p.S250S	TBX22_ENST00000442340.1_Silent_p.S130S|TBX22_ENST00000373296.3_Silent_p.S250S|TBX22_ENST00000373291.1_Silent_p.S130S	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	250					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						AAACATTCTCCTTTAAAGAAA	0.478																																					p.S250S		Atlas-SNP	.											.	TBX22	118	.	0			c.C750T						.						115	88	97					X																	79282319		2203	4300	6503	SO:0001819	synonymous_variant	50945	exon5			ATTCTCCTTTAAA	AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"T-boxes"	11600	protein-coding gene	gene with protein product		300307	"cleft palate and/or ankyloglossia"	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.750C>T	chrX.hg19:g.79282319C>T		117.0	0.0		129.0	59.0	NM_016954	Q5JZ06|Q96LC0|Q9HBF1	Silent	SNP	ENST00000373294.5	hg19	CCDS14445.1																																																																																			.	.		0.478	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954		T	79282319	C	T	79282319	2	4	9	1	0	0	0	0	0	0	0	1	15673	668	24	3		3	TBX22	23	79282319	Silent	SNP	C	TCGA-2Y-A9GZ-01A-11D-A38X-10	24326763	79282319	75988241	106	793										
CD99L2	83692	hgsc.bcm.edu	37	chrX	150067008	150067008	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	gccttacctcgctggaccagGgtggccaaggagaaagcgag	15	11	0	1			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chrX:150067008G>T	ENST00000370377.3	-	1	171	c.54C>A	c.(52-54)acC>acA	p.T18T	CD99L2_ENST00000355149.3_Silent_p.T18T|CD99L2_ENST00000466436.1_Silent_p.T18T|CD99L2_ENST00000437787.2_Silent_p.T18T|CD99L2_ENST00000320893.6_Silent_p.T18T|CD99L2_ENST00000346693.4_5'UTR	NM_001242614.1|NM_031462.3	NP_001229543.1|NP_113650.2	Q8TCZ2	C99L2_HUMAN	CD99 molecule-like 2	18					cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GCTGGACCAGGGTGGCCAAGG	0.736																																					p.T18T		Atlas-SNP	.											.	CD99L2	47	.	0			c.C54A						.						3	2	2					X																	150067008		1338	2322	3660	SO:0001819	synonymous_variant	83692	exon1			GACCAGGGTGGCC	BC030536	CCDS14697.1, CCDS14698.1, CCDS35427.1, CCDS55527.1, CCDS76044.1	Xq28	2007-12-04	2006-03-28	2003-02-14	ENSG00000102181	ENSG00000102181			18237	protein-coding gene	gene with protein product		300846	"MIC2 like 1", "CD99 antigen-like 2"	MIC2L1			Standard	NM_001184808		Approved	CD99B	uc004fek.3	Q8TCZ2	OTTHUMG00000024247	ENST00000370377.3:c.54C>A	chrX.hg19:g.150067008G>T		65.0	0.0		110.0	55.0	NM_001242614	A8K2D5|A8K5R0|B3KWG2|B4DDL7|E7EMK5|E9PD27|Q8TAW2|Q8TCZ0|Q8TCZ1|Q9BQG9	Silent	SNP	ENST00000370377.3	hg19	CCDS35427.1																																																																																			.	.		0.736	CD99L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061199.1	NM_031462		T	150067008	G	T	150067008	2	4	9	1	0	0	0	0	0	0	0	1	3053	1219	43	3		3	CD99L2	23	150067008	Silent	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	70784689	150067008	5203552	107	794										
IRAK1	3654	hgsc.bcm.edu	37	chrX	153282005	153282005	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0925925925925926	10	1	1.84161119644991	2.37992831541219	1.60029662588061	0.680172297752053	1	0	cgggccaccatgctgctctgGctggggctggacccggcaaa	15	14	1	0			TCGA-2Y-A9GZ-01A-11D-A38X-10	TCGA-2Y-A9GZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305468d6-2f54-40f3-b39c-1b9adca1fe5d	4b702138-675a-4fe6-aacd-936c58da3d98	g.chrX:153282005G>T	ENST00000369980.3	-	9	1286	c.1119C>A	c.(1117-1119)agC>agA	p.S373R	IRAK1_ENST00000369974.2_Missense_Mutation_p.S373R|IRAK1_ENST00000429936.2_Missense_Mutation_p.S399R|IRAK1_ENST00000393682.1_Missense_Mutation_p.S399R|IRAK1_ENST00000477274.1_5'UTR|IRAK1_ENST00000393687.2_Missense_Mutation_p.S373R	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGCTGCTCTGGCTGGGGCTGG	0.642																																					p.S373R		Atlas-SNP	.											.	IRAK1	107	.	0			c.C1119A						.						41	40	40					X																	153282005		2203	4300	6503	SO:0001583	missense	3654	exon9			GCTCTGGCTGGGG	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.1119C>A	chrX.hg19:g.153282005G>T	ENSP00000358997:p.Ser373Arg	196.0	0.0		251.0	55.0	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Missense_Mutation	SNP	ENST00000369980.3	hg19	CCDS14740.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	14.19|14.19|14.19	2.462192|2.462192|2.462192	0.43736|0.43736|0.43736	.|.|.	.|.|.	ENSG00000184216|ENSG00000184216|ENSG00000184216	ENST00000437278|ENST00000443220|ENST00000369980;ENST00000369974;ENST00000393682;ENST00000393687;ENST00000429936	.|.|T;D;D;T;T	.|.|0.93307	.|.|1.37;-3.2;-3.2;1.37;1.37	4.85|4.85|4.85	-0.0032|-0.0032|-0.0032	0.14027|0.14027|0.14027	.|.|Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|.|0.477395	.|.|0.19313	.|.|N	.|.|0.117346	D|D|D	0.87767|0.87767|0.87767	0.6260|0.6260|0.6260	N|N|N	0.25647|0.25647|0.25647	0.755|0.755|0.755	0.22330|0.22330|0.22330	N|N|N	0.999194|0.999194|0.999194	.|.|D;P;P	.|.|0.54601	.|.|0.967;0.915;0.896	.|.|P;P;P	.|.|0.54965	.|.|0.663;0.765;0.653	T|T|T	0.79165|0.79165|0.79165	-0.1916|-0.1916|-0.1916	5|5|10	.|.|0.11485	.|.|T	.|.|0.65	-9.5279|-9.5279|-9.5279	1.5518|1.5518|1.5518	0.02576|0.02576|0.02576	0.2342:0.2613:0.3658:0.1388|0.2342:0.2613:0.3658:0.1388|0.2342:0.2613:0.3658:0.1388	.|.|.	.|.|373;373;373	.|.|P51617-4;P51617;P51617-2	.|.|.;IRAK1_HUMAN;.	D|T|R	46|144|373;373;399;373;399	.|.|ENSP00000358997:S373R;ENSP00000358991:S373R;ENSP00000377287:S399R;ENSP00000377291:S373R;ENSP00000392662:S399R	.|.|ENSP00000358991:S373R	A|P|S	-|-|-	2|1|3	0|0|2	IRAK1|IRAK1|IRAK1	152935199|152935199|152935199	0.041000|0.041000|0.041000	0.20044|0.20044|0.20044	0.862000|0.862000|0.862000	0.33874|0.33874|0.33874	0.813000|0.813000|0.813000	0.45954|0.45954|0.45954	-0.132000|-0.132000|-0.132000	0.10467|0.10467|0.10467	0.292000|0.292000|0.292000	0.22492|0.22492|0.22492	0.529000|0.529000|0.529000	0.55759|0.55759|0.55759	GCC|CCA|AGC	.	.		0.642	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3			T	153282005	G	T	153282005	3	4	9	1	0	0	0	0	1	0	0	0	7830	1194	42	3	1043	3	IRAK1	23	153282005	Missense_Mutation	SNP	G	TCGA-2Y-A9GZ-01A-11D-A38X-10	3214997	153282005	1988555	108	795										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7725058	7725058	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	cgggcccccttcacccaggcAgagatgtgcctcccctgctg	11	18	1	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr1:7725058A>G	ENST00000303635.7	+	9	2658	c.2451A>G	c.(2449-2451)gcA>gcG	p.A817A	CAMTA1_ENST00000439411.2_Silent_p.A817A	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	817					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TCACCCAGGCAGAGATGTGCC	0.697			T	WWTR1	epitheliod hemangioendothelioma																																p.A817A		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.A2451G						.						49	62	58					1																	7725058		2202	4296	6498	SO:0001819	synonymous_variant	23261	exon9			CCAGGCAGAGATG	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.2451A>G	chr1.hg19:g.7725058A>G		172.0	0.0		114.0	46.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	hg19	CCDS30576.1																																																																																			.	.		0.697	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		G	7725058	A	G	7725058	2	3	10	1	0	0	0	0	0	0	0	1	2615	175	7	2		2	CAMTA1	1	7725058	Silent	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10		7725058	241525563	1	796										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32162681	32162682	+	Frame_Shift_Ins	INS	-	-	G													0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ggcgggccttggaggtctctINSggggggcactgtttggtgga							TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr1:32162681_32162682insG	ENST00000373672.3	-	8	1262_1263	c.746_747insC	c.(745-747)ccafs	p.P249fs	COL16A1_ENST00000373668.3_Frame_Shift_Ins_p.P249fs|COL16A1_ENST00000271069.6_Frame_Shift_Ins_p.P249fs	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	249	Nonhelical region 10 (NC10).				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TGGAGGTCTCTGGGGGGCACTG	0.594																																					p.P249fs	Colon(143;498 1786 21362 25193 36625)	Atlas-Indel,Pindel	.											.	COL16A1	137	.	0			c.747_748insC						.																																			SO:0001589	frameshift_variant	1307	exon8			.	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.747dupC	chr1.hg19:g.32162687_32162687dupG	ENSP00000362776:p.Pro249fs	88.0	0.0		76.0	25.0	NM_001856	Q16593|Q59F89|Q71RG9	Frame_Shift_Ins	INS	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.		0.594	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		G	32162682	-	G	32162681	7	5	10	1	0	1	1	0	0	0	0	0	3675	1567	55	0	4323	0	COL16A1	1	32162681	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H0-01A-11D-A382-10	24437623	32162681	217087940	2	797										
SFPQ	6421	hgsc.bcm.edu	37	chr1	35653652	35653652	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tccatctcacgttgacgaatCatcatctcttcctctcttct	3	15	6	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr1:35653652C>T	ENST00000357214.5	-	7	1835	c.1737G>A	c.(1735-1737)atG>atA	p.M579I		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	579					alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)		SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				GTTGACGAATCATCATCTCTT	0.438			T	TFE3	papillary renal cell																																p.M579I		Atlas-SNP	.		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ	51	.	0			c.G1737A						.						388	334	352					1																	35653652		2203	4300	6503	SO:0001583	missense	6421	exon7			ACGAATCATCATC	X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"RNA binding motif (RRM) containing"	10774	protein-coding gene	gene with protein product	"polypyrimidine tract binding protein associated", "protein phosphatase 1, regulatory subunit 140"	605199	"splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.1737G>A	chr1.hg19:g.35653652C>T	ENSP00000349748:p.Met579Ile	48.0	0.0		63.0	29.0	NM_005066	P30808|Q5SZ71	Missense_Mutation	SNP	ENST00000357214.5	hg19	CCDS388.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181696	0.57800	.	.	ENSG00000116560	ENST00000357214	T	0.38722	1.12	5.81	5.81	0.92471	.	0.062008	0.64402	D	0.000003	T	0.33876	0.0878	L	0.27053	0.805	0.54753	D	0.999985	B	0.02656	0.0	B	0.04013	0.001	T	0.08932	-1.0698	9	.	.	.	-8.2257	20.0656	0.97703	0.0:1.0:0.0:0.0	.	579	P23246	SFPQ_HUMAN	I	579	ENSP00000349748:M579I	.	M	-	3	0	SFPQ	35426239	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.601000	0.61090	2.752000	0.94435	0.555000	0.69702	ATG	.	.		0.438	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		T	35653652	C	T	35653652	3	4	10	1	0	0	0	0	1	0	0	0	14175	826	29	3	402	3	SFPQ	1	35653652	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	3490971	35653652	213596969	3	798										
PSMB2	5690	hgsc.bcm.edu	37	chr1	36074978	36074978	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gcccttcatgctcatcatagCcagccaggaggaggttcaca	10	13	4	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr1:36074978C>T	ENST00000373237.3	-	4	728	c.317G>A	c.(316-318)gGc>gAc	p.G106D		NM_002794.4	NP_002785.1	P49721	PSB2_HUMAN	proteasome (prosome, macropain) subunit, beta type, 2	106					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|large_intestine(2)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)|Carfilzomib(DB08889)	CTCATCATAGCCAGCCAGGAG	0.507																																					p.G106D		Atlas-SNP	.											.	PSMB2	9	.	0			c.G317A						.						86	81	82					1																	36074978		2203	4300	6503	SO:0001583	missense	5690	exon4			TCATAGCCAGCCA	D26599	CCDS394.1, CCDS72755.1	1p34.2	2008-02-05			ENSG00000126067	ENSG00000126067		"Proteasome (prosome, macropain) subunits"	9539	protein-coding gene	gene with protein product		602175				7918633	Standard	NM_002794		Approved	HC7-I	uc001bzf.2	P49721	OTTHUMG00000004169	ENST00000373237.3:c.317G>A	chr1.hg19:g.36074978C>T	ENSP00000362334:p.Gly106Asp	164.0	0.0		191.0	13.0	NM_002794	D3DPS0|P31145|Q9BWZ9	Missense_Mutation	SNP	ENST00000373237.3	hg19	CCDS394.1	.	.	.	.	.	.	.	.	.	.	C	35	5.494386	0.96339	.	.	ENSG00000126067	ENST00000373237	T	0.35973	1.28	6.17	6.17	0.99709	.	0.095107	0.64402	D	0.000001	T	0.74245	0.3691	H	0.95365	3.66	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.995;0.995;0.999	T	0.80511	-0.1350	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	81;106;138	B7Z478;P49721;Q59FJ0	.;PSB2_HUMAN;.	D	106	ENSP00000362334:G106D	ENSP00000362334:G106D	G	-	2	0	PSMB2	35847565	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.681000	0.84073	2.941000	0.99782	0.655000	0.94253	GGC	.	.		0.507	PSMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012016.1	NM_002794		T	36074978	C	T	36074978	3	4	10	1	0	0	0	0	1	0	0	0	12689	739	26	3	300	3	PSMB2	1	36074978	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	421326	36074978	213175643	4	799										
PRCC	5546	hgsc.bcm.edu	37	chr1	156764567	156764567	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	caatggatgactaagtcattGacagaagagaaaaccatgaa	9	6	1	5			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr1:156764567G>T	ENST00000271526.4	+	5	1562	c.1290G>T	c.(1288-1290)ttG>ttT	p.L430F	PRCC_ENST00000353233.3_Missense_Mutation_p.L398F	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	430					mitotic cell cycle checkpoint (GO:0007093)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)			PRCC/TFE3(25)	breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(5)|upper_aerodigestive_tract(1)	15	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTAAGTCATTGACAGAAGAGA	0.468			T	TFE3	papillary renal																																p.L430F		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.G1290T						.						106	99	101					1																	156764567		2203	4300	6503	SO:0001583	missense	5546	exon5			GTCATTGACAGAA	X99720	CCDS1157.1	1q21.1	2008-02-05			ENSG00000143294	ENSG00000143294			9343	protein-coding gene	gene with protein product		179755				8872474	Standard	NM_005973		Approved	RCCP1	uc001fqa.3	Q92733	OTTHUMG00000041294	ENST00000271526.4:c.1290G>T	chr1.hg19:g.156764567G>T	ENSP00000271526:p.Leu430Phe	101.0	0.0		205.0	54.0	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Missense_Mutation	SNP	ENST00000271526.4	hg19	CCDS1157.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.2|22.2	4.261832|4.261832	0.80358|0.80358	.|.	.|.	ENSG00000143294|ENSG00000143294	ENST00000271526;ENST00000353233;ENST00000368201;ENST00000526188|ENST00000454659	T;T;T|.	0.52526|.	0.66;0.66;0.66|.	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	0.123548|.	0.53938|.	D|.	0.000058|.	T|.	0.26919|.	0.0659|.	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	D|D	0.999994|0.999994	D;P|.	0.54047|.	0.964;0.944|.	P;P|.	0.51806|.	0.68;0.497|.	T|.	0.06844|.	-1.0804|.	10|.	0.56958|.	D|.	0.05|.	-0.7622|-0.7622	11.5932|11.5932	0.50957|0.50957	0.0866:0.0:0.9134:0.0|0.0866:0.0:0.9134:0.0	.|.	398;430|.	A6NG79;Q92733|.	.;PRCC_HUMAN|.	F|L	430;398;406;137|196	ENSP00000271526:L430F;ENSP00000339300:L398F;ENSP00000434762:L137F|.	ENSP00000271526:L430F|.	L|X	+|+	3|2	2|2	PRCC|PRCC	155031191|155031191	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.998000|0.998000	0.95712|0.95712	1.716000|1.716000	0.37981|0.37981	2.728000|2.728000	0.93425|0.93425	0.655000|0.655000	0.94253|0.94253	TTG|TGA	.	.		0.468	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973		T	156764567	G	T	156764567	3	4	10	1	0	0	0	0	1	0	0	0	12459	1281	45	3	1308	3	PRCC	1	156764567	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	120689589	156764567	92486054	5	800										
PTPRC	5788	hgsc.bcm.edu	37	chr1	198700795	198700795	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ccaatccatgcagatattttGttggaaacttataagaggaa	8	6	0	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr1:198700795G>T	ENST00000367376.2	+	18	2079	c.1908G>T	c.(1906-1908)ttG>ttT	p.L636F	PTPRC_ENST00000442510.2_Missense_Mutation_p.L638F|PTPRC_ENST00000352140.3_Missense_Mutation_p.L588F|PTPRC_ENST00000348564.6_Missense_Mutation_p.L477F|PTPRC_ENST00000594404.1_Missense_Mutation_p.L475F	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	636					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						CAGATATTTTGTTGGAAACTT	0.353																																					p.L638F		Atlas-SNP	.											.	PTPRC	229	.	0			c.G1914T						.						140	138	138					1																	198700795		2203	4300	6503	SO:0001583	missense	5788	exon18			TATTTTGTTGGAA	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1908G>T	chr1.hg19:g.198700795G>T	ENSP00000356346:p.Leu636Phe	82.0	0.0		208.0	130.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	hg19		.	.	.	.	.	.	.	.	.	.	G	20.4	3.979451	0.74360	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.12147	2.71	5.66	3.76	0.43208	.	0.000000	0.39210	N	0.001427	T	0.40040	0.1101	M	0.85630	2.765	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.999;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.979;0.995;1.0;1.0;1.0	T	0.44772	-0.9306	10	0.87932	D	0	.	12.4264	0.55548	0.138:0.0:0.862:0.0	.	572;572;477;588;636	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	F	638;572;588;588;522;636;570;475	ENSP00000193532:L588F	ENSP00000306782:L475F	L	+	3	2	PTPRC	196967418	1.000000	0.71417	0.990000	0.47175	0.996000	0.88848	3.157000	0.50716	1.365000	0.46057	0.650000	0.86243	TTG	.	.		0.353	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198700795	G	T	198700795	3	4	10	1	0	0	0	0	1	0	0	0	12812	1368	48	3	1985	3	PTPRC	1	198700795	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	41936228	198700795	50549826	6	801										
CNTN2	6900	hgsc.bcm.edu	37	chr1	205027137	205027137	+	Frame_Shift_Del	DEL	G	G	-													0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ctattcccagaggagtccacGgaggagcaggtgttgctggc							TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr1:205027137delG	ENST00000331830.4	+	3	443	c.159delG	c.(157-159)acgfs	p.T53fs		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	53	Ig-like C2-type 1.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			AGGAGTCCACGGAGGAGCAGG	0.642																																					p.T53fs	Melanoma(183;2548 2817 37099 41192)	Atlas-Indel,Pindel	.											.	CNTN2	116	.	0			c.158delC						.						37	37	37					1																	205027137		2203	4300	6503	SO:0001589	frameshift_variant	6900	exon3			.	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.159delG	chr1.hg19:g.205027137delG	ENSP00000330633:p.Thr53fs	210.0	0.0		260.0	173.0	NM_005076	P78432|Q5T054	Frame_Shift_Del	DEL	ENST00000331830.4	hg19	CCDS1449.1																																																																																			.	.		0.642	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		-	205027137	G	-	205027137	7	5	10	1	0	1	0	1	0	0	0	0	3643	1103	39	0	165	0	CNTN2	1	205027137	Frame_Shift_Del	DEL	G	TCGA-2Y-A9H0-01A-11D-A382-10	6326342	205027137	44223484	7	802										
FAM177B	400823	hgsc.bcm.edu	37	chr1	222922851	222922851	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ttgctgtcttctttggtcttActcaacccaaatatcagtat	5	10	5	0	rs376128424		TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr1:222922851A>C	ENST00000445590.2	+	5	552	c.286A>C	c.(286-288)Act>Cct	p.T96P	FAM177B_ENST00000360827.2_Missense_Mutation_p.T96P	NM_207468.2	NP_997351.2	A6PVY3	F177B_HUMAN	family with sequence similarity 177, member B	96										breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	8						CTTTGGTCTTACTCAACCCAA	0.393																																					p.T96P		Atlas-SNP	.											.	FAM177B	19	.	0			c.A286C						.						116	105	109					1																	222922851		1873	4103	5976	SO:0001583	missense	400823	exon5			GGTCTTACTCAAC	AK125494	CCDS1535.2	1q41	2008-08-08			ENSG00000197520	ENSG00000197520			34395	protein-coding gene	gene with protein product							Standard	NM_207468		Approved	RP11-452F19.2, FLJ43505	uc001hnt.3	A6PVY3	OTTHUMG00000037766	ENST00000445590.2:c.286A>C	chr1.hg19:g.222922851A>C	ENSP00000414451:p.Thr96Pro	36.0	0.0		91.0	49.0	NM_207468	Q6ZUN8	Missense_Mutation	SNP	ENST00000445590.2	hg19	CCDS1535.2	.	.	.	.	.	.	.	.	.	.	a	12.93	2.085350	0.36758	.	.	ENSG00000197520	ENST00000434700;ENST00000445590;ENST00000360827;ENST00000456298	T;T;T;T	0.53857	0.6;1.14;1.14;0.6	5.01	0.229	0.15368	.	.	.	.	.	T	0.53206	0.1782	M	0.74467	2.265	0.09310	N	1	P	0.47677	0.899	P	0.44990	0.466	T	0.48139	-0.9061	9	0.66056	D	0.02	.	7.5642	0.27868	0.5436:0.0:0.4564:0.0	.	96	A6PVY3	F177B_HUMAN	P	96	ENSP00000391615:T96P;ENSP00000414451:T96P;ENSP00000354070:T96P;ENSP00000400233:T96P	ENSP00000354070:T96P	T	+	1	0	FAM177B	220989474	0.032000	0.19561	0.661000	0.29709	0.551000	0.35334	0.039000	0.13884	0.126000	0.18424	0.472000	0.43445	ACT	.	.		0.393	FAM177B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092151.2	NM_207468		C	222922851	A	C	222922851	3	2	10	1	0	0	0	0	1	0	0	0	5507	391	14	5	296	5	FAM177B	1	222922851	Missense_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	17895714	222922851	26327770	8	803										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71649966	71649966	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ctggcttgaaaaacagtccaAttgatgaaagtgaggtgcaa	11	6	0	4	rs61739715	byFrequency	TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr2:71649966A>C	ENST00000409544.1	+	22	3952	c.3322A>C	c.(3322-3324)Att>Ctt	p.I1108L	ZNF638_ENST00000264447.4_Missense_Mutation_p.I1108L|ZNF638_ENST00000355812.3_Intron|ZNF638_ENST00000409407.1_Missense_Mutation_p.I48L	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1108	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AAACAGTCCAATTGATGAAAG	0.348																																					p.I1108L		Atlas-SNP	.											.	ZNF638	179	.	0			c.A3322C						.						59	60	60					2																	71649966		2203	4300	6503	SO:0001583	missense	27332	exon22			AGTCCAATTGATG	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3322A>C	chr2.hg19:g.71649966A>C	ENSP00000386433:p.Ile1108Leu	91.0	0.0		139.0	62.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.474890	0.43942	.	.	ENSG00000075292	ENST00000394137;ENST00000264447;ENST00000409544;ENST00000409407;ENST00000462695	T;T;T	0.28454	1.61;1.61;1.86	5.32	4.44	0.53790	.	0.134805	0.33959	N	0.004388	T	0.14270	0.0345	N	0.08118	0	0.80722	D	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.09164	-1.0687	10	0.19590	T	0.45	-6.3233	8.2665	0.31817	0.1815:0.0:0.8185:0.0	.	1108;1108;1108	A8K583;Q14966-3;Q14966	.;.;ZN638_HUMAN	L	687;1108;1108;48;48	ENSP00000264447:I1108L;ENSP00000386433:I1108L;ENSP00000386813:I48L	ENSP00000264447:I1108L	I	+	1	0	ZNF638	71503474	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.475000	0.45162	0.751000	0.32900	-0.119000	0.15052	ATT	.	A|0.996;G|0.004		0.348	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		C	71649966	A	C	71649966	3	2	10	1	0	0	0	0	1	0	0	0	18070	101	4	5	3404	5	ZNF638	2	71649966	Missense_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10		71649966	171549407	9	804										
MTHFD2	10797	hgsc.bcm.edu	37	chr2	74438882	74438882	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ttccaggtattccaaatctgAtcacagcagatatgatcaag	7	9	3	3			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr2:74438882A>C	ENST00000394053.2	+	7	858	c.778A>C	c.(778-780)Atc>Ctc	p.I260L	MTHFD2_ENST00000409804.1_Missense_Mutation_p.I132L|MTHFD2_ENST00000394050.3_Missense_Mutation_p.I96L|MTHFD2_ENST00000409601.1_Intron|MTHFD2_ENST00000264090.4_Missense_Mutation_p.I158L|RP11-287D1.3_ENST00000451608.2_3'UTR	NM_006636.3	NP_006627.2	P13995	MTDC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase	260					folic acid-containing compound biosynthetic process (GO:0009396)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate metabolic process (GO:0046653)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	magnesium ion binding (GO:0000287)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NAD+) activity (GO:0004487)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|phosphate ion binding (GO:0042301)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6					Tetrahydrofolic acid(DB00116)	TCCAAATCTGATCACAGCAGA	0.408																																					p.I260L		Atlas-SNP	.											.	MTHFD2	43	.	0			c.A778C						.						80	74	76					2																	74438882		1915	4122	6037	SO:0001583	missense	10797	exon7			AATCTGATCACAG	X16396	CCDS1935.2	2p13.1	2008-05-02			ENSG00000065911	ENSG00000065911			7434	protein-coding gene	gene with protein product		604887				2587219, 8218174	Standard	NR_027405		Approved		uc002skk.3	P13995	OTTHUMG00000129814	ENST00000394053.2:c.778A>C	chr2.hg19:g.74438882A>C	ENSP00000377617:p.Ile260Leu	40.0	0.0		63.0	29.0	NM_006636	Q53G90|Q53GV5|Q53S36|Q7Z650	Missense_Mutation	SNP	ENST00000394053.2	hg19	CCDS1935.2	.	.	.	.	.	.	.	.	.	.	A	23.6	4.430197	0.83776	.	.	ENSG00000065911	ENST00000394053;ENST00000409804;ENST00000264090;ENST00000394050	T;T;T;T	0.61627	0.09;0.09;0.09;0.09	5.41	5.41	0.78517	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.71117	0.3302	M	0.64676	1.99	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.69665	-0.5084	10	0.33141	T	0.24	.	13.4509	0.61169	1.0:0.0:0.0:0.0	.	260	P13995	MTDC_HUMAN	L	260;132;158;96	ENSP00000377617:I260L;ENSP00000386536:I132L;ENSP00000264090:I158L;ENSP00000377614:I96L	ENSP00000264090:I158L	I	+	1	0	MTHFD2	74292390	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.883000	0.92426	2.041000	0.60428	0.456000	0.33151	ATC	.	.		0.408	MTHFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252045.2			C	74438882	A	C	74438882	3	2	10	1	0	0	0	0	1	0	0	0	9938	333	12	5	804	5	MTHFD2	2	74438882	Missense_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	2788916	74438882	168760491	10	805										
KIAA1310	55683	hgsc.bcm.edu	37	chr2	97302698	97302698	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ccggggagtgacaaagagcaTgcgggtggggcgggcactac	19	9	0	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr2:97302698T>C	ENST00000431828.1	-	2	251	c.175A>G	c.(175-177)Atg>Gtg	p.M59V	KANSL3_ENST00000441706.2_5'UTR|KANSL3_ENST00000599854.1_5'UTR|KANSL3_ENST00000487070.1_5'UTR|KANSL3_ENST00000440133.1_5'UTR|KANSL3_ENST00000435669.1_5'UTR			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	59					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											ACAAAGAGCATGCGGGTGGGG	0.567																																					p.M59V		Atlas-SNP	.											.	.	.	.	0			c.A175G						.						33	29	30					2																	97302698		692	1591	2283	SO:0001583	missense	55683	exon2			AGAGCATGCGGGT	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.175A>G	chr2.hg19:g.97302698T>C	ENSP00000396749:p.Met59Val	210.0	0.0		185.0	75.0	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	hg19	CCDS46361.1	.	.	.	.	.	.	.	.	.	.	T	9.679	1.148832	0.21288	.	.	ENSG00000114982	ENST00000431828	T	0.68181	-0.31	4.73	3.55	0.40652	.	.	.	.	.	T	0.50326	0.1609	N	0.22421	0.69	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.42599	-0.9442	9	0.46703	T	0.11	.	9.7095	0.40236	0.0:0.0:0.1751:0.8249	.	59	Q9P2N6-3	.	V	59	ENSP00000396749:M59V	ENSP00000410775:M59V	M	-	1	0	KIAA1310	96666425	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.689000	0.46993	0.816000	0.34421	0.460000	0.39030	ATG	.	.		0.567	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		C	97302698	T	C	97302698	3	2	10	1	0	0	0	0	1	0	0	0	8231	1464	51	2	2541	2	KIAA1310	2	97302698	Missense_Mutation	SNP	T	TCGA-2Y-A9H0-01A-11D-A382-10	22863816	97302698	145896675	11	806										
MARCH7	64844	hgsc.bcm.edu	37	chr2	160605311	160605311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ccgacaatgtcatgatcacaGtagatattattccttcaggt	7	9	3	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr2:160605311G>A	ENST00000259050.4	+	5	1632	c.1510G>A	c.(1510-1512)Gta>Ata	p.V504I	MARCH7_ENST00000409591.1_Missense_Mutation_p.V466I|MARCH7_ENST00000539065.1_Missense_Mutation_p.V448I|MARCH7_ENST00000409175.1_Missense_Mutation_p.V504I	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	504					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						CATGATCACAGTAGATATTAT	0.393																																					p.V504I		Atlas-SNP	.											.	MARCH7	48	.	0			c.G1510A						.						150	164	159					2																	160605311		2203	4300	6503	SO:0001583	missense	64844	exon5			ATCACAGTAGATA	AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	17393	protein-coding gene	gene with protein product		613334	"axotrophin", "membrane-associated ring finger (C3HC4) 7"	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.1510G>A	chr2.hg19:g.160605311G>A	ENSP00000259050:p.Val504Ile	69.0	0.0		90.0	37.0	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	hg19	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.386636	0.82902	.	.	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000409591	T;T;T;T	0.14640	2.49;2.52;2.49;2.49	5.88	5.88	0.94601	.	0.169262	0.51477	D	0.000084	T	0.38639	0.1048	M	0.66939	2.045	0.53688	D	0.999974	D;D;D	0.64830	0.994;0.994;0.994	D;D;D	0.70716	0.913;0.97;0.97	T	0.01508	-1.1337	10	0.51188	T	0.08	-16.0587	20.2441	0.98394	0.0:0.0:1.0:0.0	.	448;466;504	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	I	504;448;504;466	ENSP00000386830:V504I;ENSP00000442992:V448I;ENSP00000259050:V504I;ENSP00000387238:V466I	ENSP00000259050:V504I	V	+	1	0	MARCH7	160313557	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.562000	0.82300	2.774000	0.95407	0.655000	0.94253	GTA	.	.		0.393	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826		A	160605311	G	A	160605311	3	1	10	1	0	0	0	0	1	0	0	0	9315	1029	36	3	1524	3	MARCH7	2	160605311	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	63302613	160605311	82594062	12	807										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160862301	160862301	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	cttcatttttaccacactacTgatcaaactggtaataaaag	4	9	2	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr2:160862301T>G	ENST00000283243.7	-	11	1902	c.1696A>C	c.(1696-1698)Agt>Cgt	p.S566R	PLA2R1_ENST00000392771.1_Missense_Mutation_p.S566R	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	566	C-type lectin 3. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						ACCACACTACTGATCAAACTG	0.368																																					p.S566R		Atlas-SNP	.											.	PLA2R1	153	.	0			c.A1696C						.						99	104	102					2																	160862301		2203	4300	6503	SO:0001583	missense	22925	exon11			CACTACTGATCAA	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.1696A>C	chr2.hg19:g.160862301T>G	ENSP00000283243:p.Ser566Arg	105.0	0.0		117.0	58.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	hg19	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	T	13.95	2.389824	0.42410	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.18810	2.19;2.19	5.06	2.67	0.31697	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.148878	0.64402	D	0.000016	T	0.20333	0.0489	L	0.42245	1.32	0.43014	D	0.994557	D;B;P	0.54207	0.965;0.257;0.767	P;B;P	0.53912	0.737;0.166;0.465	T	0.33059	-0.9883	10	0.15952	T	0.53	.	1.6751	0.02820	0.1195:0.1635:0.1802:0.5367	.	566;566;566	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	R	566	ENSP00000283243:S566R;ENSP00000376524:S566R	ENSP00000283243:S566R	S	-	1	0	PLA2R1	160570547	0.687000	0.27671	1.000000	0.80357	0.932000	0.56968	0.749000	0.26320	0.356000	0.24157	-0.346000	0.07831	AGT	.	.		0.368	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			G	160862301	T	G	160862301	3	3	10	1	0	0	0	0	1	0	0	0	12019	1580	55	5	2783	5	PLA2R1	2	160862301	Missense_Mutation	SNP	T	TCGA-2Y-A9H0-01A-11D-A382-10	256990	160862301	82337072	13	808										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215838711	215838711	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ggagcaaacaccaaaattagTgatgggttctccactggtgt	11	8	1	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr2:215838711T>A	ENST00000272895.7	-	36	5743	c.5524A>T	c.(5524-5526)Act>Tct	p.T1842S	ABCA12_ENST00000389661.4_Missense_Mutation_p.T1524S	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1842					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CCAAAATTAGTGATGGGTTCT	0.383																																					p.T1842S	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.A5524T						.						194	178	183					2																	215838711		2203	4300	6503	SO:0001583	missense	26154	exon36			AATTAGTGATGGG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5524A>T	chr2.hg19:g.215838711T>A	ENSP00000272895:p.Thr1842Ser	47.0	0.0		93.0	41.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	9.616	1.132545	0.21041	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.87966	-2.32;-2.31	5.89	3.5	0.40072	.	1.217550	0.05679	N	0.589998	T	0.80819	0.4696	L	0.44542	1.39	0.40208	D	0.977592	B;B	0.09022	0.002;0.001	B;B	0.14578	0.011;0.003	T	0.62053	-0.6935	10	0.09338	T	0.73	.	5.3242	0.15896	0.0:0.1533:0.1502:0.6965	.	1842;1524	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	S	1842;1524	ENSP00000272895:T1842S;ENSP00000374312:T1524S	ENSP00000272895:T1842S	T	-	1	0	ABCA12	215546956	0.975000	0.34042	0.993000	0.49108	0.996000	0.88848	1.809000	0.38922	0.479000	0.27511	0.455000	0.32223	ACT	.	.		0.383	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		A	215838711	T	A	215838711	3	1	10	1	0	0	0	0	1	0	0	0	30	1696	59	4	2335	4	ABCA12	2	215838711	Missense_Mutation	SNP	T	TCGA-2Y-A9H0-01A-11D-A382-10	54976410	215838711	27360662	14	809										
ECEL1	9427	hgsc.bcm.edu	37	chr2	233346546	233346546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	aatgatggtgccgatgccccCgtagttgagagacctgggcc	14	11	0	3			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr2:233346546C>T	ENST00000304546.1	-	13	2020	c.1810G>A	c.(1810-1812)Ggg>Agg	p.G604R	ECEL1_ENST00000409941.1_Missense_Mutation_p.G602R	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	604					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		CCGATGCCCCCGTAGTTGAGA	0.682																																					p.G604R		Atlas-SNP	.											.	ECEL1	73	.	0			c.G1810A						.						81	72	75					2																	233346546		2203	4300	6503	SO:0001583	missense	9427	exon13			TGCCCCCGTAGTT	Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.1810G>A	chr2.hg19:g.233346546C>T	ENSP00000302051:p.Gly604Arg	252.0	0.0		177.0	64.0	NM_004826	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Missense_Mutation	SNP	ENST00000304546.1	hg19	CCDS2493.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.974381	0.92919	.	.	ENSG00000171551	ENST00000411860;ENST00000304546;ENST00000409941	D;D;D	0.89939	-2.59;-2.59;-2.59	5.54	5.54	0.83059	Peptidase M13, neprilysin, C-terminal (2);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97620	0.9220	H	0.99847	4.84	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99429	1.0935	10	0.87932	D	0	-38.1465	19.5428	0.95281	0.0:1.0:0.0:0.0	.	602;604	O95672-2;O95672	.;ECEL1_HUMAN	R	19;604;602	ENSP00000412683:G19R;ENSP00000302051:G604R;ENSP00000386333:G602R	ENSP00000302051:G604R	G	-	1	0	ECEL1	233054790	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.704000	0.84595	2.615000	0.88500	0.558000	0.71614	GGG	.	.		0.682	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		T	233346546	C	T	233346546	3	4	10	1	0	0	0	0	1	0	0	0	4893	652	23	1	541	1	ECEL1	2	233346546	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	17507835	233346546	9852827	15	810										
ING5	84289	hgsc.bcm.edu	37	chr2	242662639	242662639	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ttgcagtgtccaattgagtgGtttcactttgcctgcgtgga	12	8	1	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr2:242662639G>A	ENST00000313552.6	+	7	659	c.633G>A	c.(631-633)tgG>tgA	p.W211*	ING5_ENST00000406941.1_Nonsense_Mutation_p.W211*|AC114730.11_ENST00000435195.1_RNA	NM_032329.4	NP_115705.2	Q8WYH8	ING5_HUMAN	inhibitor of growth family, member 5	211					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|skin(1)	3		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.16e-33)|all cancers(36;4.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		CAATTGAGTGGTTTCACTTTG	0.517																																					p.W211X		Atlas-SNP	.											.	ING5	14	.	0			c.G633A						.						251	246	247					2																	242662639		2203	4300	6503	SO:0001587	stop_gained	84289	exon7			TGAGTGGTTTCAC	AF189286	CCDS33425.1	2q37.3	2013-01-28			ENSG00000168395	ENSG00000168395		"Zinc fingers, PHD-type"	19421	protein-coding gene	gene with protein product		608525				12750254	Standard	NM_032329		Approved	FLJ23842, p28ING5	uc002wcd.3	Q8WYH8	OTTHUMG00000151501	ENST00000313552.6:c.633G>A	chr2.hg19:g.242662639G>A	ENSP00000322142:p.Trp211*	181.0	0.0		140.0	56.0	NM_032329	A8K1P3|Q53NU6|Q57Z54|Q9BS30	Nonsense_Mutation	SNP	ENST00000313552.6	hg19	CCDS33425.1	.	.	.	.	.	.	.	.	.	.	G	36	5.760727	0.96906	.	.	ENSG00000168395	ENST00000313552;ENST00000406941	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.2098	19.7533	0.96277	0.0:0.0:1.0:0.0	.	.	.	.	X	211	.	ENSP00000322142:W211X	W	+	3	0	ING5	242311312	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.665000	0.91144	2.669000	0.90835	0.643000	0.83706	TGG	.	.		0.517	ING5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322901.3	NM_032329		A	242662639	G	A	242662639	4	1	10	1	0	0	0	0	0	1	0	0	7748	1270	44	3	659	3	ING5	2	242662639	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	9316093	242662639	536734	16	811										
DPPA4	55211	hgsc.bcm.edu	37	chr3	109049584	109049584	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ctcagaactttgcagggacgTttcccccttttccaccttta	6	14	1	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr3:109049584T>G	ENST00000335658.6	-	5	520	c.466A>C	c.(466-468)Acg>Ccg	p.T156P	DPPA4_ENST00000478791.1_5'UTR	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	156					lung-associated mesenchyme development (GO:0060484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(17)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						TGCAGGGACGTTTCCCCCTTT	0.463																																					p.T156P		Atlas-SNP	.											.	DPPA4	56	.	0			c.A466C						.						80	84	82					3																	109049584		2203	4300	6503	SO:0001583	missense	55211	exon5			GGGACGTTTCCCC	AK001575	CCDS33814.1	3q13.13	2014-01-28			ENSG00000121570	ENSG00000121570			19200	protein-coding gene	gene with protein product		614125					Standard	NM_018189		Approved	FLJ10713	uc003dxq.4	Q7L190	OTTHUMG00000159222	ENST00000335658.6:c.466A>C	chr3.hg19:g.109049584T>G	ENSP00000335306:p.Thr156Pro	217.0	0.0		202.0	93.0	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Missense_Mutation	SNP	ENST00000335658.6	hg19	CCDS33814.1	.	.	.	.	.	.	.	.	.	.	T	7.050	0.564363	0.13498	.	.	ENSG00000121570	ENST00000335658	T	0.23950	1.88	3.8	-5.44	0.02624	.	2.778230	0.00926	N	0.002652	T	0.09862	0.0242	N	0.08118	0	0.09310	N	1	P;P	0.45283	0.855;0.641	B;B	0.38327	0.271;0.154	T	0.12066	-1.0562	9	.	.	.	-0.0503	1.4213	0.02313	0.1282:0.3027:0.2885:0.2806	.	146;156	B7Z5Q7;Q7L190	.;DPPA4_HUMAN	P	156	ENSP00000335306:T156P	.	T	-	1	0	DPPA4	110532274	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.084000	0.03393	-1.147000	0.02851	-0.609000	0.04063	ACG	.	.		0.463	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189		G	109049584	T	G	109049584	3	3	10	1	0	0	0	0	1	0	0	0	4738	1725	60	5	460	5	DPPA4	3	109049584	Missense_Mutation	SNP	T	TCGA-2Y-A9H0-01A-11D-A382-10		109049584	88972846	17	812										
FAM131A	131408	hgsc.bcm.edu	37	chr3	184062581	184062581	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	caggactcactctacaactcGcccctcacagagtcctgcct	6	18	3	1	rs145026576	byFrequency	TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr3:184062581G>T	ENST00000310585.4	+	3	2195	c.831G>T	c.(829-831)tcG>tcT	p.S277S	FAM131A_ENST00000340957.5_Silent_p.S223S|FAM131A_ENST00000418281.1_Silent_p.S185S|EIF2B5_ENST00000444495.1_Intron|FAM131A_ENST00000453072.1_Silent_p.S223S|FAM131A_ENST00000383847.2_Silent_p.S308S|FAM131A_ENST00000450976.1_Silent_p.S223S			Q6UXB0	F131A_HUMAN	family with sequence similarity 131, member A	277						extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(2)|lung(9)|skin(1)	14	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCTACAACTCGCCCCTCACAG	0.672																																					p.S308S		Atlas-SNP	.											FAM131A_ENST00000383847,NS,carcinoma,0,2	FAM131A	37	.	0			c.G924T						.						41	48	45					3																	184062581		2203	4297	6500	SO:0001819	synonymous_variant	131408	exon6			CAACTCGCCCCTC	BC026221	CCDS3262.1, CCDS3262.2, CCDS54689.1	3q27.1	2007-03-20	2007-03-20	2007-03-20	ENSG00000175182	ENSG00000175182			28308	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 40"	C3orf40		12975309	Standard	NM_144635		Approved	MGC21688	uc003foe.3	Q6UXB0	OTTHUMG00000156206	ENST00000310585.4:c.831G>T	chr3.hg19:g.184062581G>T		115.0	0.0		80.0	36.0	NM_144635	D3DNT6|G5E9B1|Q8TA84	Silent	SNP	ENST00000310585.4	hg19																																																																																				.	G|1.000;A|0.000		0.672	FAM131A-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000343462.1	NM_144635		T	184062581	G	T	184062581	2	4	10	1	0	0	0	0	0	0	0	1	5444	1074	38	1		1	FAM131A	3	184062581	Silent	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	75012997	184062581	13959849	18	813										
LMLN	89782	hgsc.bcm.edu	37	chr3	197765494	197765494	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tctggcttctgctaggcaatCtgtttcctctgctggctgga	11	11	4	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr3:197765494C>G	ENST00000330198.4	+	16	1946	c.1924C>G	c.(1924-1926)Ctg>Gtg	p.L642V	LMLN_ENST00000420910.2_Missense_Mutation_p.L679V|LMLN-AS1_ENST00000423460.1_RNA|LMLN_ENST00000332636.5_Missense_Mutation_p.L590V|LMLN_ENST00000482695.1_Missense_Mutation_p.L627V	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	642					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		GCTAGGCAATCTGTTTCCTCT	0.398																																					p.L679V		Atlas-SNP	.											.	LMLN	53	.	0			c.C2035G						.						201	200	200					3																	197765494		2203	4300	6503	SO:0001583	missense	89782	exon17			GGCAATCTGTTTC	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.1924C>G	chr3.hg19:g.197765494C>G	ENSP00000328829:p.Leu642Val	73.0	0.0		157.0	71.0	NM_001136049	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	hg19	CCDS3332.1	.	.	.	.	.	.	.	.	.	.	C	14.07	2.425262	0.43020	.	.	ENSG00000185621	ENST00000482695;ENST00000330198;ENST00000420910;ENST00000332636	T;T;T;T	0.54279	0.64;0.58;0.6;0.6	5.31	3.52	0.40303	.	0.000000	0.64402	D	0.000012	T	0.55497	0.1924	L	0.27053	0.805	0.46725	D	0.999177	D;D;D;D;D	0.67145	0.993;0.996;0.996;0.993;0.996	D;D;D;D;D	0.75484	0.967;0.986;0.986;0.952;0.986	T	0.50224	-0.8853	10	0.33940	T	0.23	-10.4657	9.9321	0.41528	0.0:0.8324:0.0:0.1676	.	642;590;679;671;627	Q96KR4;F8WCE5;F8WB28;B4DR62;Q96KR4-2	LMLN_HUMAN;.;.;.;.	V	627;642;679;590	ENSP00000418324:L627V;ENSP00000328829:L642V;ENSP00000410926:L679V;ENSP00000328611:L590V	ENSP00000328829:L642V	L	+	1	2	LMLN	199249891	1.000000	0.71417	0.987000	0.45799	0.907000	0.53573	1.677000	0.37576	0.736000	0.32559	-0.145000	0.13849	CTG	.	.		0.398	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029		G	197765494	C	G	197765494	3	3	10	1	0	0	0	0	1	0	0	0	8856	912	32	4	2101	4	LMLN	3	197765494	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	13702913	197765494	256936	19	814										
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8220023	8220023	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ctcttaggatcccccaggacCccatcgacgatgccatgggt	10	15	1	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr4:8220023C>G	ENST00000245105.3	+	8	932	c.865C>G	c.(865-867)Ccc>Gcc	p.P289A	SH3TC1_ENST00000539824.1_Missense_Mutation_p.P213A	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	289										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						CCCCCAGGACCCCATCGACGA	0.577																																					p.P289A	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.C865G						.						62	61	61					4																	8220023		2203	4300	6503	SO:0001583	missense	54436	exon8			CAGGACCCCATCG	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"Tetratricopeptide (TTC) repeat domain containing"	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.865C>G	chr4.hg19:g.8220023C>G	ENSP00000245105:p.Pro289Ala	117.0	0.0		77.0	26.0	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	hg19	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	C	9.127	1.010382	0.19277	.	.	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265;ENST00000508641	T;T;T	0.17213	2.29;2.29;2.29	3.53	1.65	0.23941	.	0.502867	0.20790	N	0.085621	T	0.16128	0.0388	L	0.61218	1.895	0.29763	N	0.835407	B	0.31383	0.321	B	0.31946	0.138	T	0.09164	-1.0687	10	0.46703	T	0.11	-18.0482	5.7198	0.17980	0.0:0.6854:0.1997:0.1149	.	289	Q8TE82	S3TC1_HUMAN	A	27;289;213;118;98	ENSP00000245105:P289A;ENSP00000441045:P213A;ENSP00000426035:P98A	ENSP00000245105:P289A	P	+	1	0	SH3TC1	8270923	0.978000	0.34361	0.838000	0.33150	0.235000	0.25334	0.965000	0.29319	0.268000	0.21939	0.561000	0.74099	CCC	.	.		0.577	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		G	8220023	C	G	8220023	3	3	10	1	0	0	0	0	1	0	0	0	14276	623	22	4	891	4	SH3TC1	4	8220023	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10		8220023	182934253	20	815										
FAM114A1	92689	hgsc.bcm.edu	37	chr4	38933200	38933201	+	Frame_Shift_Ins	INS	-	-	A													0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ctcaagaccctcaagaagacINSaaaaaggaggaaaagaaaac					rs370882686		TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr4:38933200_38933201insA	ENST00000358869.2	+	11	1466_1467	c.1290_1291insA	c.(1291-1293)aaafs	p.K431fs	FAM114A1_ENST00000515037.1_Frame_Shift_Ins_p.K224fs	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	431						cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						CTCAAGAAGACAAAAAGGAGGA	0.371																																					p.D430fs		Atlas-Indel,Pindel	.											.	FAM114A1	42	.	0			c.1290_1291insA						.																																			SO:0001589	frameshift_variant	92689	exon11			.		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.1295dupA	chr4.hg19:g.38933205_38933205dupA	ENSP00000351740:p.Lys431fs	175.0	0.0		206.0	78.0	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Frame_Shift_Ins	INS	ENST00000358869.2	hg19	CCDS3447.1																																																																																			.	.		0.371	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389		A	38933201	-	A	38933200	7	5	10	1	0	1	1	0	0	0	0	0	5408	477	17	0	1324	0	FAM114A1	4	38933200	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H0-01A-11D-A382-10	30713177	38933200	152221076	21	816										
OR2V2	285659	hgsc.bcm.edu	37	chr5	180582886	180582886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ctgcaggatcggcagccagcActgaacccagggcatccagt	12	14	0	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr5:180582886A>G	ENST00000328275.1	+	1	944	c.944A>G	c.(943-945)cAc>cGc	p.H315R		NM_206880.1	NP_996763.1	Q96R30	OR2V2_HUMAN	olfactory receptor, family 2, subfamily V, member 2	315						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(89;8.26e-06)|all_epithelial(37;1.02e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.0103)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0652)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCAGCCAGCACTGAACCCAG	0.547																																					p.H315R		Atlas-SNP	.											.	OR2V2	56	.	0			c.A944G						.						19	22	21					5																	180582886		2181	4289	6470	SO:0001583	missense	285659	exon1			GCCAGCACTGAAC	AL161615	CCDS4461.1	5q35.3	2012-08-09			ENSG00000182613	ENSG00000182613		"GPCR / Class A : Olfactory receptors"	15341	protein-coding gene	gene with protein product				OR2V3			Standard	NM_206880		Approved	OST713	uc011dhj.2	Q96R30	OTTHUMG00000130933	ENST00000328275.1:c.944A>G	chr5.hg19:g.180582886A>G	ENSP00000332185:p.His315Arg	84.0	0.0		81.0	27.0	NM_206880	Q6IFL6|Q8NGV1	Missense_Mutation	SNP	ENST00000328275.1	hg19	CCDS4461.1	.	.	.	.	.	.	.	.	.	.	.	10.31	1.314534	0.23908	.	.	ENSG00000182613	ENST00000328275	T	0.00030	8.9	3.54	-7.08	0.01558	.	2.120730	0.02782	N	0.121081	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.38779	-0.9645	10	0.02654	T	1	.	7.1403	0.25552	0.1969:0.5375:0.0:0.2656	.	315	Q96R30	OR2V2_HUMAN	R	315	ENSP00000332185:H315R	ENSP00000332185:H315R	H	+	2	0	OR2V2	180515492	0.770000	0.28543	0.000000	0.03702	0.051000	0.14879	-0.239000	0.08965	-1.272000	0.02427	0.254000	0.18369	CAC	.	.		0.547	OR2V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253529.1			G	180582886	A	G	180582886	3	3	10	1	0	0	0	0	1	0	0	0	11040	159	6	2	946	2	OR2V2	5	180582886	Missense_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10		180582886	332374	22	817										
EYS	346007	hgsc.bcm.edu	37	chr6	64499079	64499079	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	actataaaccacactgccatTgagcaggcccacagccagga	8	14	0	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr6:64499079T>C	ENST00000370621.3	-	38	7976	c.7450A>G	c.(7450-7452)Aat>Gat	p.N2484D	EYS_ENST00000503581.1_Missense_Mutation_p.N2484D|EYS_ENST00000486069.1_5'UTR|EYS_ENST00000370616.2_Missense_Mutation_p.N2484D			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2484	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						ACACTGCCATTGAGCAGGCCC	0.522																																					p.N2484D		Atlas-SNP	.											.	EYS	527	.	0			c.A7450G						.						62	58	59					6																	64499079		692	1591	2283	SO:0001583	missense	346007	exon38			TGCCATTGAGCAG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.7450A>G	chr6.hg19:g.64499079T>C	ENSP00000359655:p.Asn2484Asp	51.0	0.0		76.0	31.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	t	15.64	2.894003	0.52121	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.68765	-0.35;-0.35;-0.35	4.95	-2.57	0.06248	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.527383	0.14190	N	0.335388	T	0.15132	0.0365	N	0.10760	0.04	0.09310	N	1	B;B	0.12013	0.004;0.005	B;B	0.12156	0.004;0.007	T	0.32375	-0.9909	10	0.13853	T	0.58	-0.1055	5.5419	0.17043	0.0:0.3278:0.2633:0.4089	.	2484;2484	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	D	2484	ENSP00000424243:N2484D;ENSP00000359655:N2484D;ENSP00000359650:N2484D	ENSP00000359650:N2484D	N	-	1	0	EYS	64557038	0.000000	0.05858	0.000000	0.03702	0.752000	0.42762	0.172000	0.16704	-0.329000	0.08527	0.524000	0.50904	AAT	.	.		0.522	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		C	64499079	T	C	64499079	3	2	10	1	0	0	0	0	1	0	0	0	5334	1812	63	2	2008	2	EYS	6	64499079	Missense_Mutation	SNP	T	TCGA-2Y-A9H0-01A-11D-A382-10		64499079	106615988	23	818										
HEATR2	54919	hgsc.bcm.edu	37	chr7	794224	794224	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ttctttccctttttcgttccAgagcgccgccctgtgctggg	10	14	1	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr7:794224A>G	ENST00000297440.6	+	5	1044		c.e5-1		HEATR2_ENST00000313147.5_Splice_Site	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2							cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		TTTTCGTTCCAGAGCGCCGCC	0.537																																					.		Atlas-SNP	.											.	HEATR2	62	.	0			c.1025-2A>G						.						121	134	130					7																	794224		2203	4300	6503	SO:0001630	splice_region_variant	54919	exon5			CGTTCCAGAGCGC	AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.1025-1A>G	chr7.hg19:g.794224A>G		238.0	0.0		184.0	71.0	NM_017802	Q69YL1|Q96FI9|Q9NX75	Splice_Site	SNP	ENST00000297440.6	hg19	CCDS34580.1	.	.	.	.	.	.	.	.	.	.	a	16.34	3.094448	0.56075	.	.	ENSG00000164818	ENST00000297440;ENST00000313147;ENST00000437419;ENST00000440747;ENST00000537862	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5709	0.76337	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HEATR2	760750	1.000000	0.71417	0.130000	0.21974	0.008000	0.06430	8.335000	0.90031	2.075000	0.62263	0.418000	0.28097	.	.	.		0.537	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802	Intron	G	794224	A	G	794224	5	3	10	1	0	0	0	0	0	0	1	0	7037	202	7	2	1041	2	HEATR2	7	794224	Splice_Site	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10		794224	158344439	24	819										
SDK1	221935	hgsc.bcm.edu	37	chr7	4014141	4014141	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ctgcgagattgtttctgaagGagggaatgactccaggatgg	15	6	1	3			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr7:4014141G>C	ENST00000404826.2	+	13	2097	c.1958G>C	c.(1957-1959)gGa>gCa	p.G653A	SDK1_ENST00000389531.3_Missense_Mutation_p.G653A	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	653	Ig-like C2-type 6.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GTTTCTGAAGGAGGGAATGAC	0.557																																					p.G653A		Atlas-SNP	.											.	SDK1	361	.	0			c.G1958C						.						150	111	124					7																	4014141		2203	4300	6503	SO:0001583	missense	221935	exon13			CTGAAGGAGGGAA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1958G>C	chr7.hg19:g.4014141G>C	ENSP00000385899:p.Gly653Ala	99.0	0.0		112.0	52.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.954552	0.34471	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.64438	-0.1;-0.1	5.35	5.35	0.76521	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.086976	0.47093	D	0.000249	T	0.50103	0.1596	N	0.13198	0.31	0.46317	D	0.99898	B	0.31077	0.307	B	0.35470	0.203	T	0.45804	-0.9236	10	0.25106	T	0.35	.	19.0581	0.93074	0.0:0.0:1.0:0.0	.	653	Q7Z5N4	SDK1_HUMAN	A	653	ENSP00000385899:G653A;ENSP00000374182:G653A	ENSP00000374182:G653A	G	+	2	0	SDK1	3980667	1.000000	0.71417	0.156000	0.22583	0.043000	0.13939	4.665000	0.61547	2.484000	0.83849	0.563000	0.77884	GGA	.	.		0.557	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		C	4014141	G	C	4014141	3	2	10	1	0	0	0	0	1	0	0	0	13983	1174	41	4	2008	4	SDK1	7	4014141	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	3219917	4014141	155124522	25	820										
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4825922	4825922	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	cggaagccgtctaccagcacCtgttcaccaggatcccggtg	11	15	2	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr7:4825922C>A	ENST00000348624.4	+	10	1268	c.1174C>A	c.(1174-1176)Ctg>Atg	p.L392M	MIR4656_ENST00000579503.1_RNA|AP5Z1_ENST00000401897.1_Missense_Mutation_p.L392M	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	392					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CTACCAGCACCTGTTCACCAG	0.627																																					p.L392M		Atlas-SNP	.											.	.	.	.	0			c.C1174A						.						56	64	61					7																	4825922		1995	4155	6150	SO:0001583	missense	9907	exon10			CAGCACCTGTTCA	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"KIAA0415"	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1174C>A	chr7.hg19:g.4825922C>A	ENSP00000297562:p.Leu392Met	131.0	0.0		91.0	45.0	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	hg19	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.911734	0.52439	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.52754	0.66;0.65	5.29	3.18	0.36537	.	0.188571	0.36303	N	0.002668	T	0.62865	0.2463	M	0.78637	2.42	0.19775	N	0.999952	D	0.76494	0.999	D	0.75484	0.986	T	0.52689	-0.8542	10	0.66056	D	0.02	.	5.4877	0.16759	0.0:0.6315:0.2011:0.1675	.	392	O43299	K0415_HUMAN	M	392	ENSP00000297562:L392M;ENSP00000384980:L392M	ENSP00000297562:L392M	L	+	1	2	KIAA0415	4792448	0.966000	0.33281	0.056000	0.19401	0.984000	0.73092	0.865000	0.27940	1.203000	0.43233	0.561000	0.74099	CTG	.	.		0.627	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			A	4825922	C	A	4825922	3	1	10	1	0	0	0	0	1	0	0	0	8184	680	24	3	1212	3	KIAA0415	7	4825922	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	811781	4825922	154312741	26	821										
COBL	23242	hgsc.bcm.edu	37	chr7	51096609	51096609	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tcgtcaatcttaatggctccGgtggagagggacacatctct	11	10	3	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr7:51096609G>A	ENST00000265136.7	-	10	2349	c.2184C>T	c.(2182-2184)acC>acT	p.T728T	COBL_ENST00000395542.2_Silent_p.T810T	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	728					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)	p.T728T(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TAATGGCTCCGGTGGAGAGGG	0.507																																					p.T728T	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											COBL,bladder,carcinoma,0,1	COBL	167	.	1	Substitution - coding silent(1)	urinary_tract(1)	c.C2184T						.						102	85	91					7																	51096609		2203	4300	6503	SO:0001819	synonymous_variant	23242	exon10			GGCTCCGGTGGAG	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.2184C>T	chr7.hg19:g.51096609G>A		125.0	0.0		110.0	45.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	hg19	CCDS34637.1																																																																																			.	.		0.507	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		A	51096609	G	A	51096609	2	1	10	1	0	0	0	0	0	0	0	1	3655	1103	39	1		1	COBL	7	51096609	Silent	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	46270687	51096609	108042054	27	822										
GNAT3	346562	hgsc.bcm.edu	37	chr7	80103624	80103624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tgattccagtcgttttcactCgagaatggagaacatcttgt	9	8	2	3			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr7:80103624C>T	ENST00000398291.3	-	5	626	c.533G>A	c.(532-534)cGa>cAa	p.R178Q	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	178					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						CGTTTTCACTCGAGAATGGAG	0.328																																					p.R178Q		Atlas-SNP	.											.	GNAT3	65	.	0			c.G533A						.						71	67	68					7																	80103624		1838	4106	5944	SO:0001583	missense	346562	exon5			TTCACTCGAGAAT		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.533G>A	chr7.hg19:g.80103624C>T	ENSP00000381339:p.Arg178Gln	44.0	0.0		60.0	16.0	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Missense_Mutation	SNP	ENST00000398291.3	hg19	CCDS47625.1	.	.	.	.	.	.	.	.	.	.	C	36	5.660119	0.96734	.	.	ENSG00000214415	ENST00000398291	D	0.91740	-2.9	5.99	5.99	0.97316	G protein alpha subunit, helical insertion (1);	0.000000	0.64402	U	0.000001	D	0.97782	0.9272	H	0.98407	4.225	0.80722	D	1	D	0.76494	0.999	P	0.62813	0.907	D	0.98556	1.0639	9	.	.	.	.	20.074	0.97736	0.0:1.0:0.0:0.0	.	178	A8MTJ3	GNAT3_HUMAN	Q	178	ENSP00000381339:R178Q	.	R	-	2	0	GNAT3	79941560	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.815000	0.69215	2.853000	0.98044	0.655000	0.94253	CGA	.	.		0.328	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370		T	80103624	C	T	80103624	3	4	10	1	0	0	0	0	1	0	0	0	6521	884	31	1	545	1	GNAT3	7	80103624	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	29007015	80103624	79035039	28	823										
DYNC1I1	1780	hgsc.bcm.edu	37	chr7	95665003	95665003	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tggctttcccaacgggagacGtcaataacttcgtggttggc	12	10	1	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr7:95665003G>A	ENST00000324972.6	+	13	1547	c.1354G>A	c.(1354-1356)Gtc>Atc	p.V452I	DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.V415I|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.V435I|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.V432I|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.V435I|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.V415I	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	452					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			AACGGGAGACGTCAATAACTT	0.468																																					p.V452I		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.G1354A						.						321	259	280					7																	95665003		2203	4300	6503	SO:0001583	missense	1780	exon13			GGAGACGTCAATA	AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"Cytoplasmic dyneins", "WD repeat domain containing"	2963	protein-coding gene	gene with protein product		603772	"dynein, cytoplasmic, intermediate polypeptide 1"	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.1354G>A	chr7.hg19:g.95665003G>A	ENSP00000320130:p.Val452Ile	64.0	0.0		149.0	61.0	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	hg19	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.112451	0.56398	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	5.1	5.1	0.69264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.76730	0.4028	L	0.31926	0.97	0.80722	D	1	P;D;D;P;P	0.54207	0.941;0.965;0.965;0.899;0.74	P;P;P;B;B	0.51135	0.459;0.66;0.66;0.275;0.163	T	0.72918	-0.4146	10	0.25751	T	0.34	0.0118	19.0933	0.93238	0.0:0.0:1.0:0.0	.	435;432;435;452;415	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	I	435;452;415;432;415;435	ENSP00000392337:V435I;ENSP00000320130:V452I;ENSP00000438377:V415I;ENSP00000398118:V432I;ENSP00000352348:V415I;ENSP00000412444:V435I	ENSP00000320130:V452I	V	+	1	0	DYNC1I1	95502939	1.000000	0.71417	0.995000	0.50966	0.083000	0.17756	9.657000	0.98554	2.830000	0.97506	0.585000	0.79938	GTC	.	.		0.468	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		A	95665003	G	A	95665003	3	1	10	1	0	0	0	0	1	0	0	0	4844	1145	40	1	1400	1	DYNC1I1	7	95665003	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	15561379	95665003	63473660	29	824										
CPA1	1357	hgsc.bcm.edu	37	chr7	130020953	130020953	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gcccaggcatcaggtgctccGaatctctgtagccgatgagg	13	12	2	1	rs547564304		TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr7:130020953G>C	ENST00000011292.3	+	2	230	c.80G>C	c.(79-81)cGa>cCa	p.R27P	CPA1_ENST00000484324.1_5'UTR	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	27					proteolysis (GO:0006508)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(18;0.0435)					CAGGTGCTCCGAATCTCTGTA	0.637													G|||	1	0.000199681	8e-04	0	5008	,	,		17788	0		0	False		,,,				2504	0				p.R27P		Atlas-SNP	.											.	CPA1	73	.	0			c.G80C						.						46	42	43					7																	130020953		2203	4300	6503	SO:0001583	missense	1357	exon2			TGCTCCGAATCTC		CCDS5820.1	7q32	2012-02-10			ENSG00000091704	ENSG00000091704	3.4.17.1		2296	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase A"	114850		CPA			Standard	NM_001868		Approved		uc003vpx.3	P15085	OTTHUMG00000157826	ENST00000011292.3:c.80G>C	chr7.hg19:g.130020953G>C	ENSP00000011292:p.Arg27Pro	356.0	0.0		266.0	96.0	NM_001868	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	Missense_Mutation	SNP	ENST00000011292.3	hg19	CCDS5820.1	.	.	.	.	.	.	.	.	.	.	G	18.68	3.676296	0.67928	.	.	ENSG00000091704	ENST00000011292	T	0.20463	2.07	4.54	4.54	0.55810	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.000000	0.85682	D	0.000000	T	0.53190	0.1781	M	0.91140	3.18	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63431	-0.6639	10	0.87932	D	0	.	12.6567	0.56791	0.0:0.0:1.0:0.0	.	27	P15085	CBPA1_HUMAN	P	27	ENSP00000011292:R27P	ENSP00000011292:R27P	R	+	2	0	CPA1	129808189	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	5.441000	0.66569	2.372000	0.80975	0.555000	0.69702	CGA	.	.		0.637	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868		C	130020953	G	C	130020953	3	2	10	1	0	0	0	0	1	0	0	0	3791	1058	37	4	86	4	CPA1	7	130020953	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	34355950	130020953	29117710	30	825										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3165891	3165891	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gtctccactcaaacaggtcaGggtgttgctgccatgcatgg	12	11	3	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr8:3165891G>A	ENST00000520002.1	-	25	4324	c.3769C>T	c.(3769-3771)Ctg>Ttg	p.L1257L	CSMD1_ENST00000602557.1_Silent_p.L1257L|CSMD1_ENST00000537824.1_Silent_p.L1256L|CSMD1_ENST00000539096.1_Silent_p.L1256L|CSMD1_ENST00000602723.1_Silent_p.L1257L|CSMD1_ENST00000400186.3_Silent_p.L1257L|CSMD1_ENST00000542608.1_Silent_p.L1256L			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1257	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		AAACAGGTCAGGGTGTTGCTG	0.527																																					p.L1256L		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C3766T						.						134	126	129					8																	3165891		2093	4223	6316	SO:0001819	synonymous_variant	64478	exon24			AGGTCAGGGTGTT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3769C>T	chr8.hg19:g.3165891G>A		61.0	0.0		39.0	23.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	G	4.645	0.119989	0.08881	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.22	-0.372	0.12520	.	.	.	.	.	T	0.39627	0.1085	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27571	-1.0070	4	.	.	.	.	0.6082	0.00756	0.3061:0.1082:0.2831:0.3026	.	.	.	.	L	736	.	.	P	-	2	0	CSMD1	3153298	0.960000	0.32886	0.064000	0.19789	0.637000	0.38172	1.532000	0.36029	0.163000	0.19507	0.561000	0.74099	CCT	.	.		0.527	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3165891	G	A	3165891	2	1	10	1	0	0	0	0	0	0	0	1	3946	991	35	3		3	CSMD1	8	3165891	Silent	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10		3165891	143198131	31	826										
ADAM7	8756	hgsc.bcm.edu	37	chr8	24349552	24349552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ttgcaagaactcagaaggctActgtttcatggggaaatgtc	11	7	2	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr8:24349552A>G	ENST00000175238.6	+	14	1576	c.1493A>G	c.(1492-1494)tAc>tGc	p.Y498C	ADAM7_ENST00000380789.1_Missense_Mutation_p.Y498C|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000520720.1_Missense_Mutation_p.Y270C|RP11-561E1.1_ENST00000519364.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	498	Cys-rich.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		TCAGAAGGCTACTGTTTCATG	0.468																																					p.Y498C		Atlas-SNP	.											.	ADAM7	165	.	0			c.A1493G						.						133	128	130					8																	24349552		2203	4299	6502	SO:0001583	missense	8756	exon14			AAGGCTACTGTTT	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"ADAM metallopeptidase domain containing"	214	protein-coding gene	gene with protein product		607310	"a disintegrin and metalloproteinase domain 7"				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.1493A>G	chr8.hg19:g.24349552A>G	ENSP00000175238:p.Tyr498Cys	58.0	0.0		107.0	43.0	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	hg19	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.163444	0.78226	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.26223	1.75;1.75;1.75	5.84	5.84	0.93424	ADAM, cysteine-rich (2);	0.000000	0.52532	D	0.000072	T	0.65344	0.2682	H	0.97158	3.95	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77645	-0.2510	10	0.87932	D	0	.	14.1687	0.65495	1.0:0.0:0.0:0.0	.	270;498	E5RK87;Q9H2U9	.;ADAM7_HUMAN	C	498;498;270;313	ENSP00000175238:Y498C;ENSP00000370166:Y498C;ENSP00000430400:Y270C	ENSP00000175238:Y498C	Y	+	2	0	ADAM7	24405442	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.438000	0.66550	2.231000	0.72958	0.533000	0.62120	TAC	.	.		0.468	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		G	24349552	A	G	24349552	3	3	10	1	0	0	0	0	1	0	0	0	251	391	14	2	1547	2	ADAM7	8	24349552	Missense_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	21183661	24349552	122014470	32	827										
AP3M2	10947	hgsc.bcm.edu	37	chr8	42015551	42015558	+	Frame_Shift_Del	DEL	ATTGGCTA	ATTGGCTA	-													0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	atgcttgacaatggttttccAttggctaccgagtcgaacat							TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	ATTGGCTA	ATTGGCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr8:42015551_42015558delATTGGCTA	ENST00000518421.1	+	4	657_664	c.366_373delATTGGCTA	c.(364-375)ccattggctaccfs	p.LAT123fs	AP3M2_ENST00000520685.1_Intron|AP3M2_ENST00000396926.3_Frame_Shift_Del_p.LAT123fs|AP3M2_ENST00000174653.3_Frame_Shift_Del_p.LAT123fs|AP3M2_ENST00000517922.1_Frame_Shift_Del_p.LAT123fs	NM_001134296.1	NP_001127768.1	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	123					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|stomach(1)	17	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)			ATGGTTTTCCATTGGCTACCGAGTCGAA	0.433																																					p.122_124del		Atlas-Indel,Pindel	.											.	AP3M2	41	.	0			c.365_372del						.																																			SO:0001589	frameshift_variant	10947	exon4			.	D38293	CCDS6125.1	8p11.2	2008-07-07			ENSG00000070718	ENSG00000070718			570	protein-coding gene	gene with protein product		610469				7601449	Standard	NM_006803		Approved	CLA20, AP47B	uc003xoo.3	P53677	OTTHUMG00000164060	ENST00000518421.1:c.366_373delATTGGCTA	chr8.hg19:g.42015551_42015558delATTGGCTA	ENSP00000428787:p.Leu123fs	105.0	0.0		91.0	32.0	NM_001134296	B2RCR0|D3DSY2|Q7Z472	Frame_Shift_Del	DEL	ENST00000518421.1	hg19	CCDS6125.1																																																																																			.	.		0.433	AP3M2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376996.1			-	42015558	ATTGGCTA	-	42015551	7	5	10	1	0	1	0	1	0	0	0	0	748	204	8	0	372	0	AP3M2	8	42015551	Frame_Shift_Del	DEL	ATTGGCTA	TCGA-2Y-A9H0-01A-11D-A382-10	17665999	42015551	104348471	33	828										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35295866	35295866	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tacttcaaggcagttcccggGactcttgtaatgactctatg	9	10	3	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr9:35295866G>A	ENST00000378495.3	+	8	922	c.700G>A	c.(700-702)Gac>Aac	p.D234N	UNC13B_ENST00000378496.4_Missense_Mutation_p.D234N|UNC13B_ENST00000396787.1_Missense_Mutation_p.D246N	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	234					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			CAGTTCCCGGGACTCTTGTAA	0.512																																					p.D234N		Atlas-SNP	.											.	UNC13B	153	.	0			c.G700A						.						78	68	72					9																	35295866		2203	4300	6503	SO:0001583	missense	10497	exon8			TCCCGGGACTCTT	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.700G>A	chr9.hg19:g.35295866G>A	ENSP00000367756:p.Asp234Asn	131.0	0.0		109.0	36.0	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	hg19	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.000172	0.74818	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496	D;T;T	0.83250	-1.7;0.99;0.99	5.8	5.8	0.92144	.	0.319160	0.32002	N	0.006739	T	0.75287	0.3829	L	0.34521	1.04	0.54753	D	0.999989	B;P;B	0.45715	0.007;0.865;0.319	B;B;B	0.36719	0.004;0.231;0.149	T	0.75079	-0.3444	10	0.30854	T	0.27	-2.5223	19.0598	0.93085	0.0:0.0:1.0:0.0	.	234;234;234	Q2NKJ5;F8W8M9;O14795	.;.;UN13B_HUMAN	N	246;234;234	ENSP00000380006:D246N;ENSP00000367756:D234N;ENSP00000367757:D234N	ENSP00000367756:D234N	D	+	1	0	UNC13B	35285866	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	9.476000	0.97823	2.741000	0.93983	0.585000	0.79938	GAC	.	.		0.512	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		A	35295866	G	A	35295866	3	1	10	1	0	0	0	0	1	0	0	0	17000	1174	41	3	730	3	UNC13B	9	35295866	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10		35295866	105917565	34	829										
NUP214	8021	hgsc.bcm.edu	37	chr9	134074363	134074363	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gtacctcagctgccaccacaAcagcagcaacctctgggttc	8	16	2	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr9:134074363A>G	ENST00000359428.5	+	29	5626	c.5482A>G	c.(5482-5484)Aca>Gca	p.T1828A	NUP214_ENST00000451030.1_Missense_Mutation_p.T1829A|NUP214_ENST00000411637.2_Missense_Mutation_p.T1818A|NUP214_ENST00000483497.2_Missense_Mutation_p.T654A			P35658	NU214_HUMAN	nucleoporin 214kDa	1828	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TGCCACCACAACAGCAGCAAC	0.502			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.T1828A	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.A5482G						.						52	58	56					9																	134074363		2203	4300	6503	SO:0001583	missense	8021	exon29			ACCACAACAGCAG	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.5482A>G	chr9.hg19:g.134074363A>G	ENSP00000352400:p.Thr1828Ala	106.0	0.0		86.0	35.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	A	8.691	0.907321	0.17833	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497	T;T;T;T	0.57907	0.85;0.88;0.86;0.37	6.07	3.71	0.42584	.	0.307454	0.23585	N	0.046617	T	0.30135	0.0755	N	0.08118	0	0.43287	D	0.995267	P;P;P;P;B	0.40970	0.734;0.734;0.734;0.734;0.394	B;B;B;B;B	0.42555	0.203;0.391;0.391;0.391;0.12	T	0.03829	-1.1000	10	0.22109	T	0.4	-16.5247	5.9935	0.19480	0.748:0.0:0.1018:0.1503	.	654;1257;1422;1818;1828	B7ZAV2;F5H131;Q5JUP9;P35658-4;P35658	.;.;.;.;NU214_HUMAN	A	1828;1818;1829;1807;1422;1257;654	ENSP00000352400:T1828A;ENSP00000396576:T1818A;ENSP00000405014:T1829A;ENSP00000436793:T654A	ENSP00000352400:T1828A	T	+	1	0	NUP214	133064184	0.994000	0.37717	0.318000	0.25279	0.016000	0.09150	3.294000	0.51787	1.089000	0.41292	0.533000	0.62120	ACA	.	.		0.502	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		G	134074363	A	G	134074363	3	3	10	1	0	0	0	0	1	0	0	0	10771	43	2	2	5596	2	NUP214	9	134074363	Missense_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	98778497	134074363	7139068	35	830										
CAMSAP1	157922	hgsc.bcm.edu	37	chr9	138774767	138774767	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gcctggatgacagactggtgTccctgtaaggcggccacctg	14	12	0	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr9:138774767T>C	ENST00000389532.4	-	2	382	c.318A>G	c.(316-318)ggA>ggG	p.G106G	CAMSAP1_ENST00000312405.6_5'Flank|CAMSAP1_ENST00000409386.3_Silent_p.G106G	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	106					cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		CAGACTGGTGTCCCTGTAAGG	0.577																																					p.G106G		Atlas-SNP	.											.	CAMSAP1	142	.	0			c.A318G						.						68	66	67					9																	138774767		692	1591	2283	SO:0001819	synonymous_variant	157922	exon2			CTGGTGTCCCTGT	AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.318A>G	chr9.hg19:g.138774767T>C		74.0	0.0		54.0	26.0	NM_015447	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Silent	SNP	ENST00000389532.4	hg19	CCDS35176.2																																																																																			.	.		0.577	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055024.2	XM_351857		C	138774767	T	C	138774767	2	2	10	1	0	0	0	0	0	0	0	1	2613	1654	58	2		2	CAMSAP1	9	138774767	Silent	SNP	T	TCGA-2Y-A9H0-01A-11D-A382-10	4700404	138774767	2438664	36	831										
C9orf172	389813	hgsc.bcm.edu	37	chr9	139741196	139741196	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ggaggggctgctgctatcccCcacctacctatcgctgcgtg	12	15	0	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr9:139741196C>G	ENST00000436881.1	+	1	2330	c.2330C>G	c.(2329-2331)cCc>cGc	p.P777R	PHPT1_ENST00000545326.1_5'Flank|PHPT1_ENST00000247665.10_5'Flank|PHPT1_ENST00000371661.1_5'Flank	NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	777										endometrium(2)|large_intestine(1)|lung(6)	9						CTGCTATCCCCCACCTACCTA	0.706																																					p.P777R		Atlas-SNP	.											.	C9orf172	23	.	0			c.C2330G						.						13	14	14					9																	139741196		1715	3722	5437	SO:0001583	missense	389813	exon1			TATCCCCCACCTA		CCDS48059.1	9q34.3	2012-04-03			ENSG00000232434	ENSG00000232434			37284	protein-coding gene	gene with protein product							Standard	NM_001080482		Approved		uc011meh.2	C9J069		ENST00000436881.1:c.2330C>G	chr9.hg19:g.139741196C>G	ENSP00000412388:p.Pro777Arg	85.0	0.0		75.0	17.0	NM_001080482		Missense_Mutation	SNP	ENST00000436881.1	hg19	CCDS48059.1	.	.	.	.	.	.	.	.	.	.	.	16.25	3.070957	0.55646	.	.	ENSG00000232434	ENST00000436881	.	.	.	3.63	3.63	0.41609	.	.	.	.	.	T	0.77032	0.4071	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80850	-0.1198	8	0.87932	D	0	-9.0615	14.3301	0.66550	0.0:1.0:0.0:0.0	.	777	C9J069	CI172_HUMAN	R	777	.	ENSP00000412388:P777R	P	+	2	0	C9orf172	138861017	1.000000	0.71417	1.000000	0.80357	0.545000	0.35147	5.368000	0.66133	1.573000	0.49748	0.165000	0.16767	CCC	.	.		0.706	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482		G	139741196	C	G	139741196	3	3	10	1	0	0	0	0	1	0	0	0	2473	623	22	4	2332	4	C9orf172	9	139741196	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	966429	139741196	1472235	37	832										
SLC39A12	221074	hgsc.bcm.edu	37	chr10	18250708	18250708	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tactgagcctcaggcaggatGaagattcctctttcctttca	8	11	3	3			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr10:18250708G>A	ENST00000377369.2	+	3	733	c.460G>A	c.(460-462)Gaa>Aaa	p.E154K	SLC39A12_ENST00000377374.4_Missense_Mutation_p.E154K|SLC39A12_ENST00000539911.1_Missense_Mutation_p.E20K|SLC39A12_ENST00000377371.3_Missense_Mutation_p.E154K	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	154					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						CAGGCAGGATGAAGATTCCTC	0.393																																					p.E154K		Atlas-SNP	.											.	SLC39A12	181	.	0			c.G460A						.						80	83	82					10																	18250708		2203	4300	6503	SO:0001583	missense	221074	exon3			CAGGATGAAGATT		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"Solute carriers"	20860	protein-coding gene	gene with protein product		608734	"solute carrier family 39 (metal ion transporter), member 12"			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.460G>A	chr10.hg19:g.18250708G>A	ENSP00000366586:p.Glu154Lys	126.0	0.0		192.0	83.0	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Missense_Mutation	SNP	ENST00000377369.2	hg19	CCDS44362.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.397757	0.83120	.	.	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219	T;T;T;T	0.64991	0.1;-0.05;0.1;-0.13	5.43	4.5	0.54988	.	0.057246	0.64402	D	0.000002	T	0.78502	0.4293	M	0.76002	2.32	0.49687	D	0.999814	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.81351	-0.0972	10	0.72032	D	0.01	-10.3986	14.9859	0.71348	0.0:0.1433:0.8567:0.0	.	154;154;154	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	K	154;154;154;20;74	ENSP00000366586:E154K;ENSP00000366591:E154K;ENSP00000366588:E154K;ENSP00000440445:E20K	ENSP00000366586:E154K	E	+	1	0	SLC39A12	18290714	1.000000	0.71417	0.993000	0.49108	0.976000	0.68499	6.537000	0.73847	1.230000	0.43646	0.650000	0.86243	GAA	.	.		0.393	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725		A	18250708	G	A	18250708	3	1	10	1	0	0	0	0	1	0	0	0	14630	1291	45	3	466	3	SLC39A12	10	18250708	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10		18250708	117284039	38	833										
SVIL	6840	hgsc.bcm.edu	37	chr10	29782297	29782297	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	agatttgccggtgacagtgaGcaccgtttcgtgcatcccgc	12	12	0	3			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr10:29782297G>A	ENST00000355867.4	-	21	4617	c.3865C>T	c.(3865-3867)Ctc>Ttc	p.L1289F	SVIL_ENST00000375400.3_Missense_Mutation_p.L863F|SVIL_ENST00000375398.2_Missense_Mutation_p.L1289F|SVIL_ENST00000535393.1_Missense_Mutation_p.L203F|SVIL_ENST00000538146.1_Missense_Mutation_p.L81F	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1289					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GTGACAGTGAGCACCGTTTCG	0.398																																					p.L1289F		Atlas-SNP	.											.	SVIL	226	.	0			c.C3865T						.						93	86	88					10																	29782297		2203	4300	6503	SO:0001583	missense	6840	exon21			CAGTGAGCACCGT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.3865C>T	chr10.hg19:g.29782297G>A	ENSP00000348128:p.Leu1289Phe	134.0	0.0		111.0	36.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.529773	0.64860	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;T	0.35236	2.58;2.58;2.58;2.43;1.32	4.28	4.28	0.50868	.	0.056922	0.64402	D	0.000002	T	0.54046	0.1834	M	0.72894	2.215	0.44500	D	0.997443	P;P;D;D	0.57899	0.906;0.906;0.981;0.967	P;P;P;P	0.61397	0.747;0.802;0.888;0.776	T	0.57785	-0.7751	10	0.59425	D	0.04	-19.1242	12.5627	0.56291	0.0843:0.0:0.9157:0.0	.	203;81;863;1289	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	F	863;1289;1289;203;243;81	ENSP00000364549:L863F;ENSP00000364547:L1289F;ENSP00000348128:L1289F;ENSP00000445472:L203F;ENSP00000440343:L81F	ENSP00000348128:L1289F	L	-	1	0	SVIL	29822303	0.992000	0.36948	0.403000	0.26384	0.981000	0.71138	2.013000	0.40942	2.217000	0.71921	0.485000	0.47835	CTC	.	.		0.398	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			A	29782297	G	A	29782297	3	1	10	1	0	0	0	0	1	0	0	0	15436	971	34	3	2851	3	SVIL	10	29782297	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	11531589	29782297	105752450	39	834										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37505130	37505130	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ttcaactagcctatcaaaaaTcttggatacagttcattctt	4	9	5	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr10:37505130T>A	ENST00000602533.1	+	32	2822	c.2723T>A	c.(2722-2724)aTc>aAc	p.I908N	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.I1027N|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.I908N			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	964					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CTATCAAAAATCTTGGATACA	0.323																																					p.I908N		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.T2723A						.						55	50	52					10																	37505130		1797	4066	5863	SO:0001583	missense	91074	exon32			CAAAAATCTTGGA	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.2723T>A	chr10.hg19:g.37505130T>A	ENSP00000473551:p.Ile908Asn	158.0	0.0		400.0	157.0	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	hg19		.	.	.	.	.	.	.	.	.	.	t	2.404	-0.336866	0.05278	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.25749	1.78;1.78	2.63	1.45	0.22620	.	.	.	.	.	T	0.26774	0.0655	L	0.61036	1.89	0.09310	N	1	D	0.54772	0.968	P	0.44518	0.452	T	0.12192	-1.0557	9	0.51188	T	0.08	.	6.8755	0.24145	0.0:0.0:0.2375:0.7625	.	964	Q9BXX3	AN30A_HUMAN	N	908;1027	ENSP00000354432:I908N;ENSP00000363792:I1027N	ENSP00000354432:I908N	I	+	2	0	ANKRD30A	37545136	0.988000	0.35896	0.005000	0.12908	0.003000	0.03518	2.736000	0.47385	0.145000	0.18977	-0.844000	0.03045	ATC	.	.		0.323	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		A	37505130	T	A	37505130	3	1	10	1	0	0	0	0	1	0	0	0	658	1435	50	4	2849	4	ANKRD30A	10	37505130	Missense_Mutation	SNP	T	TCGA-2Y-A9H0-01A-11D-A382-10	7722833	37505130	98029617	40	835										
RBP3	5949	hgsc.bcm.edu	37	chr10	48388858	48388858	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ctccaagtccacagctgtgcGgtaggcgccctgggccagct	13	15	0	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr10:48388858G>A	ENST00000224600.4	-	1	2133	c.2020C>T	c.(2020-2022)Cgc>Tgc	p.R674C	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	674	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	ACAGCTGTGCGGTAGGCGCCC	0.672																																					p.R674C		Atlas-SNP	.											.	RBP3	152	.	0			c.C2020T						.						26	30	29					10																	48388858		2196	4291	6487	SO:0001583	missense	5949	exon1			CTGTGCGGTAGGC	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.2020C>T	chr10.hg19:g.48388858G>A	ENSP00000224600:p.Arg674Cys	129.0	0.0		92.0	45.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	hg19	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.523988	0.44866	.	.	ENSG00000107618	ENST00000224600	T	0.52983	0.64	5.53	3.68	0.42216	.	0.180634	0.48286	N	0.000184	T	0.44603	0.1301	M	0.71036	2.16	0.80722	D	1	B	0.30179	0.271	B	0.20577	0.03	T	0.44360	-0.9333	10	0.72032	D	0.01	-15.3292	11.0	0.47600	0.1499:0.0:0.8501:0.0	.	674	P10745	RET3_HUMAN	C	674	ENSP00000224600:R674C	ENSP00000224600:R674C	R	-	1	0	RBP3	48008864	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.726000	0.61986	0.719000	0.32188	0.561000	0.74099	CGC	.	.		0.672	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		A	48388858	G	A	48388858	3	1	10	1	0	0	0	0	1	0	0	0	13172	1116	39	1	1739	1	RBP3	10	48388858	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	10883728	48388858	87145889	41	836										
VDAC2	7417	hgsc.bcm.edu	37	chr10	76980582	76980582	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gttgactttgattttgctggAcctgcaatccatggttcagc	10	9	1	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr10:76980582A>G	ENST00000332211.6	+	7	651	c.438A>G	c.(436-438)ggA>ggG	p.G146G	VDAC2_ENST00000535553.1_Silent_p.G107G|VDAC2_ENST00000313132.4_Silent_p.G161G|VDAC2_ENST00000472137.1_3'UTR|VDAC2_ENST00000543351.1_Silent_p.G146G	NM_003375.3	NP_003366.2	P45880	VDAC2_HUMAN	voltage-dependent anion channel 2	146					anion transport (GO:0006820)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein polymerization (GO:0032272)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	nucleotide binding (GO:0000166)|porin activity (GO:0015288)|voltage-gated anion channel activity (GO:0008308)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(2)|prostate(1)|urinary_tract(1)	10	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)	ATTTTGCTGGACCTGCAATCC	0.418																																					p.G161G		Atlas-SNP	.											.	VDAC2	27	.	0			c.A483G						.						99	97	98					10																	76980582		2203	4297	6500	SO:0001819	synonymous_variant	7417	exon8			TGCTGGACCTGCA	BC000165	CCDS7348.1, CCDS53544.1	10q22	2011-11-15			ENSG00000165637	ENSG00000165637		"Voltage-dependent anion channels"	12672	protein-coding gene	gene with protein product		193245				7517385, 10049775	Standard	NM_003375		Approved		uc021ptp.1	P45880	OTTHUMG00000018517	ENST00000332211.6:c.438A>G	chr10.hg19:g.76980582A>G		196.0	0.0		262.0	114.0	NM_001184783	Q5VWK1|Q5VWK3|Q6IB40|Q7L3J5|Q9BWK8|Q9Y5I6	Silent	SNP	ENST00000332211.6	hg19	CCDS7348.1																																																																																			.	.		0.418	VDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048792.1	NM_003375		G	76980582	A	G	76980582	2	3	10	1	0	0	0	0	0	0	0	1	17162	262	10	2		2	VDAC2	10	76980582	Silent	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	28591724	76980582	58554165	42	837										
PDZD8	118987	hgsc.bcm.edu	37	chr10	119133943	119133943	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gacgatgatggaggtgagctGgggcatgggccgcccttcaa	17	9	1	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr10:119133943G>A	ENST00000334464.5	-	1	1035	c.796C>T	c.(796-798)Cag>Tag	p.Q266*		NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	266					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		GAGGTGAGCTGGGGCATGGGC	0.587																																					p.Q266X		Atlas-SNP	.											.	PDZD8	85	.	0			c.C796T						.						64	70	68					10																	119133943		2203	4300	6503	SO:0001587	stop_gained	118987	exon1			TGAGCTGGGGCAT	AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.796C>T	chr10.hg19:g.119133943G>A	ENSP00000334642:p.Gln266*	143.0	0.0		117.0	53.0	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Nonsense_Mutation	SNP	ENST00000334464.5	hg19	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	G	39	7.443225	0.98286	.	.	ENSG00000165650	ENST00000334464	.	.	.	4.87	4.87	0.63330	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-9.7181	17.9979	0.89189	0.0:0.0:1.0:0.0	.	.	.	.	X	266	.	ENSP00000334642:Q266X	Q	-	1	0	PDZD8	119123933	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	9.247000	0.95444	2.230000	0.72887	0.655000	0.94253	CAG	.	.		0.587	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		A	119133943	G	A	119133943	4	1	10	1	0	0	0	0	0	1	0	0	11714	1357	47	3	2688	3	PDZD8	10	119133943	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	42153361	119133943	16400804	43	838										
EEF1G	1937	hgsc.bcm.edu	37	chr11	62334458	62334458	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tccgtggtgtgtcctttttaGgttgggtctctgcaaacttt	11	8	1	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr11:62334458G>A	ENST00000329251.4	-	7	807	c.677C>T	c.(676-678)cCt>cTt	p.P226L	MIR3654_ENST00000496634.2_3'UTR|EEF1G_ENST00000378019.3_Missense_Mutation_p.P276L	NM_001404.4	NP_001395.1	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1 gamma	226					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to virus (GO:0009615)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	translation elongation factor activity (GO:0003746)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GTCCTTTTTAGGTTGGGTCTC	0.537																																					p.P226L		Atlas-SNP	.											.	EEF1G	33	.	0			c.C677T						.						147	139	142					11																	62334458		1886	4107	5993	SO:0001583	missense	1937	exon7			TTTTTAGGTTGGG	X63526	CCDS44626.1	11q12.3	2008-02-05			ENSG00000254772	ENSG00000254772			3213	protein-coding gene	gene with protein product		130593				1598220, 1461723	Standard	NM_001404		Approved	EF1G	uc001ntm.1	P26641	OTTHUMG00000167567	ENST00000329251.4:c.677C>T	chr11.hg19:g.62334458G>A	ENSP00000331901:p.Pro226Leu	104.0	0.0		95.0	30.0	NM_001404	B4DTG2|Q6PJ62|Q6PK31|Q96CU2|Q9P196	Missense_Mutation	SNP	ENST00000329251.4	hg19	CCDS44626.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.550156	0.65311	.	.	ENSG00000254772	ENST00000329251;ENST00000378019	T;T	0.19938	2.11;2.11	4.8	4.8	0.61643	Glutathione S-transferase, C-terminal-like (1);	0.000000	0.85682	D	0.000000	T	0.38241	0.1033	M	0.67397	2.05	0.80722	D	1	D;B	0.62365	0.991;0.0	P;B	0.57101	0.813;0.003	T	0.08006	-1.0743	10	0.33141	T	0.24	.	15.7129	0.77644	0.0:0.0:1.0:0.0	.	276;226	B4DTG2;P26641	.;EF1G_HUMAN	L	226;276	ENSP00000331901:P226L;ENSP00000367258:P276L	ENSP00000331901:P226L	P	-	2	0	EEF1G	62091034	1.000000	0.71417	0.994000	0.49952	0.111000	0.19643	8.944000	0.92980	2.380000	0.81148	0.561000	0.74099	CCT	.	.		0.537	EEF1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395047.1	NM_001404		A	62334458	G	A	62334458	3	1	10	1	0	0	0	0	1	0	0	0	4930	1000	35	3	652	3	EEF1G	11	62334458	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10		62334458	72672058	44	839										
CTSC	1075	hgsc.bcm.edu	37	chr11	88061352	88061352	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	catgaacaaatgactgataaAatcagtgacatcctacaaag	6	8	1	4			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr11:88061352A>T	ENST00000227266.5	-	2	433				CTSC_ENST00000529974.1_Missense_Mutation_p.F111I|CTSC_ENST00000393301.4_5'UTR|CTSC_ENST00000524463.1_Missense_Mutation_p.F111I	NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C						aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)			large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGACTGATAAAATCAGTGACA	0.373																																					p.F111I		Atlas-SNP	.											.	CTSC	46	.	0			c.T331A						.						74	68	70					11																	88061352		2201	4299	6500	SO:0001627	intron_variant	1075	exon3			TGATAAAATCAGT	AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"Cathepsins"	2528	protein-coding gene	gene with protein product	"dipeptidyl peptidase 1"	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.318+6752T>A	chr11.hg19:g.88061352A>T		75.0	0.0		99.0	42.0	NM_148170	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	ENST00000227266.5	hg19	CCDS8282.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.372034	0.82573	.	.	ENSG00000109861	ENST00000524463;ENST00000529974	D;D	0.88046	-2.33;-2.33	5.76	4.64	0.57946	.	.	.	.	.	D	0.84329	0.5448	.	.	.	0.22880	N	0.998619	P;B	0.43750	0.816;0.419	P;B	0.44990	0.466;0.183	T	0.74109	-0.3771	7	.	.	.	.	8.5624	0.33518	0.913:0.0:0.087:0.0	.	111;111	Q2HIY8;P53634-2	.;.	I	111	ENSP00000432541:F111I;ENSP00000433539:F111I	.	F	-	1	0	CTSC	87701000	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.430000	0.52807	1.010000	0.39314	0.533000	0.62120	TTT	.	.		0.373	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814		T	88061352	A	T	88061352	1	4	10	0	1	0	0	0	0	0	0	0	4033	14	1	4		4	CTSC	11	88061352	Intron	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	25726894	88061352	46945164	45	840										
GRAMD1B	57476	hgsc.bcm.edu	37	chr11	123471213	123471213	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tggggcccgggataggacatAtatgatgatgttccggctct	14	8	1	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr11:123471213A>G	ENST00000529750.1	+	7	905	c.578A>G	c.(577-579)tAt>tGt	p.Y193C	GRAMD1B_ENST00000322282.7_Missense_Mutation_p.Y193C|GRAMD1B_ENST00000456860.2_Missense_Mutation_p.Y200C	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	193						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		GATAGGACATATATGATGATG	0.413																																					p.Y193C		Atlas-SNP	.											.	GRAMD1B	122	.	0			c.A578G						.						102	95	97					11																	123471213		1852	4093	5945	SO:0001583	missense	57476	exon7			GGACATATATGAT	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.578A>G	chr11.hg19:g.123471213A>G	ENSP00000436500:p.Tyr193Cys	38.0	0.0		69.0	18.0	NM_020716	Q6UW85|Q9ULL9	Missense_Mutation	SNP	ENST00000529750.1	hg19	CCDS53720.1	.	.	.	.	.	.	.	.	.	.	A	19.57	3.851960	0.71719	.	.	ENSG00000023171	ENST00000539133;ENST00000456860;ENST00000322282;ENST00000529750;ENST00000529432;ENST00000534764	T;T;T;T;T	0.41065	1.37;1.4;1.4;1.46;1.01	5.73	5.73	0.89815	.	0.124524	0.56097	D	0.000029	T	0.63212	0.2492	M	0.79475	2.455	0.80722	D	1	D;D;D;D	0.64830	0.994;0.992;0.975;0.987	P;P;P;P	0.60345	0.873;0.819;0.594;0.664	T	0.68405	-0.5417	10	0.87932	D	0	.	16.0093	0.80385	1.0:0.0:0.0:0.0	.	153;200;193;200	B7Z4N9;F5H572;Q3KR37;E7EPH8	.;.;GRM1B_HUMAN;.	C	200;200;193;193;153;189	ENSP00000402457:Y200C;ENSP00000325628:Y193C;ENSP00000436500:Y193C;ENSP00000432987:Y153C;ENSP00000434214:Y189C	ENSP00000325628:Y193C	Y	+	2	0	GRAMD1B	122976423	1.000000	0.71417	0.435000	0.26784	0.942000	0.58702	7.254000	0.78329	2.177000	0.69029	0.482000	0.46254	TAT	.	.		0.413	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		G	123471213	A	G	123471213	3	3	10	1	0	0	0	0	1	0	0	0	6757	449	16	2	604	2	GRAMD1B	11	123471213	Missense_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	35409861	123471213	11535303	46	841										
TNFRSF1A	7132	hgsc.bcm.edu	37	chr12	6438604	6438604	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	agcagctccagcgtggcctcGcgccgcggcgtgcgccgcct	15	18	0	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr12:6438604G>A	ENST00000162749.2	-	10	1541	c.1242C>T	c.(1240-1242)cgC>cgT	p.R414R	TNFRSF1A_ENST00000437813.3_5'Flank|TNFRSF1A_ENST00000540022.1_Silent_p.R371R	NM_001065.3	NP_001056.1	P19438	TNR1A_HUMAN	tumor necrosis factor receptor superfamily, member 1A	414	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|positive regulation of angiogenesis (GO:0045766)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|prostaglandin metabolic process (GO:0006693)|protein heterooligomerization (GO:0051291)|response to alkaloid (GO:0043279)|response to amino acid (GO:0043200)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|tetrapyrrole metabolic process (GO:0033013)|viral process (GO:0016032)	axon (GO:0030424)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	tumor necrosis factor-activated receptor activity (GO:0005031)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	19						GCGTGGCCTCGCGCCGCGGCG	0.726																																					p.R414R		Atlas-SNP	.											.	TNFRSF1A	39	.	0			c.C1242T						.						7	9	8					12																	6438604		2103	4099	6202	SO:0001819	synonymous_variant	7132	exon10			GGCCTCGCGCCGC	M75866	CCDS8542.1	12p13.2	2014-09-17			ENSG00000067182	ENSG00000067182		"Tumor necrosis factor receptor superfamily", "CD molecules"	11916	protein-coding gene	gene with protein product		191190		TNFR1		1655358, 2158863	Standard	NM_001065		Approved	TNF-R, TNFAR, TNFR60, TNF-R-I, CD120a, TNF-R55	uc001qnu.3	P19438	OTTHUMG00000168267	ENST00000162749.2:c.1242C>T	chr12.hg19:g.6438604G>A		489.0	1.0		299.0	126.0	NM_001065	A8K4X3|B2RDE4|B3KPQ1|B4DQB7|B4E309|B5M0B5|D3DUR1|Q9UCA4	Silent	SNP	ENST00000162749.2	hg19	CCDS8542.1																																																																																			.	.		0.726	TNFRSF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399038.1	NM_001065		A	6438604	G	A	6438604	2	1	10	1	0	0	0	0	0	0	0	1	16308	1074	38	1		1	TNFRSF1A	12	6438604	Silent	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10		6438604	127413291	47	842										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41421673	41421673	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tcacagctcctagccagcctCcaaggatcatcagttcagta	7	14	4	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr12:41421673C>G	ENST00000551295.2	+	22	2842	c.2725C>G	c.(2725-2727)Cca>Gca	p.P909A	CNTN1_ENST00000348761.2_Missense_Mutation_p.P898A|CNTN1_ENST00000550305.1_3'UTR|CNTN1_ENST00000347616.1_Missense_Mutation_p.P909A	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	909	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TAGCCAGCCTCCAAGGATCAT	0.408																																					p.P909A		Atlas-SNP	.											.	CNTN1	207	.	0			c.C2725G						.						126	110	116					12																	41421673		2203	4300	6503	SO:0001583	missense	1272	exon22			CAGCCTCCAAGGA	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.2725C>G	chr12.hg19:g.41421673C>G	ENSP00000447006:p.Pro909Ala	50.0	0.0		91.0	44.0	NM_001843	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.556673	0.86231	.	.	ENSG00000018236	ENST00000551295;ENST00000347616;ENST00000348761	T;T;T	0.53423	0.62;0.62;0.62	5.71	5.71	0.89125	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72716	0.3495	M	0.83603	2.65	0.80722	D	1	D;D	0.64830	0.994;0.989	D;D	0.68765	0.96;0.912	T	0.74685	-0.3582	10	0.66056	D	0.02	.	20.243	0.98386	0.0:1.0:0.0:0.0	.	898;909	Q12860-2;Q12860	.;CNTN1_HUMAN	A	909;909;898	ENSP00000447006:P909A;ENSP00000325660:P909A;ENSP00000261160:P898A	ENSP00000325660:P909A	P	+	1	0	CNTN1	39707940	1.000000	0.71417	0.721000	0.30653	0.997000	0.91878	6.543000	0.73874	2.868000	0.98415	0.557000	0.71058	CCA	.	.		0.408	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		G	41421673	C	G	41421673	3	3	10	1	0	0	0	0	1	0	0	0	3642	855	30	4	2807	4	CNTN1	12	41421673	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	34983069	41421673	92430222	48	843										
NAV3	89795	hgsc.bcm.edu	37	chr12	78579428	78579428	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	caactggacataaagatggcCgcagtgtgaaaattatagtc	10	7	0	2	rs201844408		TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr12:78579428C>A	ENST00000397909.2	+	31	5913	c.5740C>A	c.(5740-5742)Cgc>Agc	p.R1914S	NAV3_ENST00000228327.6_Missense_Mutation_p.R1892S|NAV3_ENST00000266692.7_Missense_Mutation_p.R1715S|NAV3_ENST00000552300.1_3'UTR|NAV3_ENST00000536525.2_Missense_Mutation_p.R1892S			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1914						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TAAAGATGGCCGCAGTGTGAA	0.343										HNSCC(70;0.22)																											p.R1892S		Atlas-SNP	.											.	NAV3	506	.	0			c.C5674A						.						136	124	128					12																	78579428		1877	4117	5994	SO:0001583	missense	89795	exon30			GATGGCCGCAGTG	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.5740C>A	chr12.hg19:g.78579428C>A	ENSP00000381007:p.Arg1914Ser	50.0	0.0		239.0	155.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.18|17.18	3.325145|3.325145	0.60634|0.60634	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000552895|ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788	.|T;T;T;T;T	.|0.27890	.|1.7;1.68;1.69;1.64;2.52	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	.|0.177347	.|0.26883	.|U	.|0.022003	T|T	0.31136|0.31136	0.0787|0.0787	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|B;B;B;P	.|0.36438	.|0.038;0.159;0.028;0.553	.|B;B;B;B	.|0.35114	.|0.02;0.142;0.003;0.196	T|T	0.02837|0.02837	-1.1104|-1.1104	5|10	.|0.21540	.|T	.|0.41	-13.5347|-13.5347	20.0782|20.0782	0.97758|0.97758	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1892;1715;1914;1892	.|E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2	.|.;.;NAV3_HUMAN;.	Q|S	786|1892;1914;1892;1715;506;514	.|ENSP00000446132:R1892S;ENSP00000381007:R1914S;ENSP00000228327:R1892S;ENSP00000266692:R1715S;ENSP00000448303:R514S	.|ENSP00000228327:R1892S	P|R	+|+	2|1	0|0	NAV3|NAV3	77103559|77103559	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.674000|5.674000	0.68117|0.68117	2.746000|2.746000	0.94184|0.94184	0.655000|0.655000	0.94253|0.94253	CCG|CGC	.	.		0.343	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78579428	C	A	78579428	3	1	10	1	0	0	0	0	1	0	0	0	10194	652	23	1	5792	1	NAV3	12	78579428	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	37157755	78579428	55272467	49	844										
PLEKHG7	440107	hgsc.bcm.edu	37	chr12	93147989	93147989	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ggaaaaggagcatggactctGctgagaaaatcatgatctac	11	7	3	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr12:93147989G>A	ENST00000344636.3	+	6	623	c.439G>A	c.(439-441)Gct>Act	p.A147T		NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	147	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						CATGGACTCTGCTGAGAAAAT	0.478																																					p.A147T		Atlas-SNP	.											.	PLEKHG7	38	.	0			c.G439A						.						101	90	93					12																	93147989		2203	4300	6503	SO:0001583	missense	440107	exon6			GACTCTGCTGAGA	AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"Pleckstrin homology (PH) domain containing"	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.439G>A	chr12.hg19:g.93147989G>A	ENSP00000344961:p.Ala147Thr	67.0	0.0		224.0	47.0	NM_001004330	B2RNR7	Missense_Mutation	SNP	ENST00000344636.3	hg19	CCDS31873.1	.	.	.	.	.	.	.	.	.	.	G	8.250	0.808888	0.16467	.	.	ENSG00000187510	ENST00000344636	T	0.62788	0.0	5.4	2.78	0.32641	Dbl homology (DH) domain (4);	0.434073	0.26418	N	0.024486	T	0.38692	0.1050	N	0.16790	0.44	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.19647	-1.0299	10	0.09843	T	0.71	-25.0696	8.4224	0.32710	0.7329:0.0:0.2671:0.0	.	147	Q6ZR37	PKHG7_HUMAN	T	147	ENSP00000344961:A147T	ENSP00000344961:A147T	A	+	1	0	PLEKHG7	91672120	0.000000	0.05858	0.027000	0.17364	0.928000	0.56348	0.447000	0.21710	0.248000	0.21435	0.491000	0.48974	GCT	.	.		0.478	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330		A	93147989	G	A	93147989	3	1	10	1	0	0	0	0	1	0	0	0	12084	1319	46	3	457	3	PLEKHG7	12	93147989	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	14568561	93147989	40703906	50	845										
MYO1H	283446	hgsc.bcm.edu	37	chr12	109853348	109853348	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tagccgtaagctggctggtcCaaagggccgaaagaggattg	15	8	0	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr12:109853348C>T	ENST00000431443.2	+	14	1502	c.1502C>T	c.(1501-1503)cCa>cTa	p.P501L	MYO1H_ENST00000310903.5_Missense_Mutation_p.P491L	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	501	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						CTGGCTGGTCCAAAGGGCCGA	0.517																																					p.P491L		Atlas-SNP	.											.	MYO1H	98	.	0			c.C1472T						.						47	48	48					12																	109853348		1938	4157	6095	SO:0001583	missense	283446	exon14			CTGGTCCAAAGGG		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.1502C>T	chr12.hg19:g.109853348C>T	ENSP00000444076:p.Pro501Leu	43.0	0.0		144.0	53.0	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	hg19		.	.	.	.	.	.	.	.	.	.	C	7.468	0.646053	0.14451	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	D;D	0.89123	-2.44;-2.47	5.5	5.5	0.81552	.	.	.	.	.	T	0.79173	0.4401	N	0.20328	0.56	0.40158	D	0.977031	P	0.38827	0.649	B	0.32624	0.149	T	0.78940	-0.2006	9	0.25106	T	0.35	.	13.7776	0.63064	0.1542:0.8458:0.0:0.0	.	491	F5H3C6	.	L	491;501	ENSP00000439182:P491L;ENSP00000444076:P501L	ENSP00000439182:P491L	P	+	2	0	MYO1H	108337731	0.890000	0.30428	0.178000	0.23040	0.815000	0.46073	2.697000	0.47060	2.568000	0.86640	0.655000	0.94253	CCA	.	.		0.517	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		T	109853348	C	T	109853348	3	4	10	1	0	0	0	0	1	0	0	0	10084	594	21	3	1526	3	MYO1H	12	109853348	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	16705359	109853348	23998547	51	846										
CSNK1A1L	122011	hgsc.bcm.edu	37	chr13	37679130	37679130	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ggtcccagaaggtccatgacTagcacattgttgtctttttc	9	10	1	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr13:37679130T>C	ENST00000379800.3	-	1	673	c.264A>G	c.(262-264)ctA>ctG	p.L88L		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	88	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		GGTCCATGACTAGCACATTGT	0.468																																					p.L88L		Atlas-SNP	.											.	CSNK1A1L	69	.	0			c.A264G						.						121	111	115					13																	37679130		2203	4300	6503	SO:0001819	synonymous_variant	122011	exon1			CATGACTAGCACA	BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.264A>G	chr13.hg19:g.37679130T>C		75.0	0.0		118.0	47.0	NM_145203	Q5T2N2	Silent	SNP	ENST00000379800.3	hg19	CCDS9363.1																																																																																			.	.		0.468	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203		C	37679130	T	C	37679130	2	2	10	1	0	0	0	0	0	0	0	1	3953	1509	53	2		2	CSNK1A1L	13	37679130	Silent	SNP	T	TCGA-2Y-A9H0-01A-11D-A382-10		37679130	77490748	52	847										
SLAIN1	122060	hgsc.bcm.edu	37	chr13	78320728	78320728	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tcattgagttcaggaaaaaaAgggacatgtagtgatcaaga	11	4	3	3			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr13:78320728A>G	ENST00000466548.1	+	5	956	c.930A>G	c.(928-930)aaA>aaG	p.K310K	SLAIN1_ENST00000351546.3_Silent_p.K47K|SLAIN1_ENST00000418532.1_Silent_p.K91K|SLAIN1_ENST00000488699.1_Silent_p.K168K|SLAIN1_ENST00000358679.3_Silent_p.K47K|SLAIN1_ENST00000314070.5_Intron|SLAIN1_ENST00000465831.1_3'UTR|SLAIN1_ENST00000267219.8_Silent_p.K91K	NM_001242868.1	NP_001229797.1	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1	310										breast(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)		CAGGAAAAAAAGGGACATGTA	0.403																																					p.K332K		Atlas-SNP	.											.	SLAIN1	43	.	0			c.A996G						.						133	121	125					13																	78320728		2203	4300	6503	SO:0001819	synonymous_variant	122060	exon4			AAAAAAAGGGACA	AK054608	CCDS9460.1, CCDS31995.1, CCDS31995.2, CCDS55901.1, CCDS73588.1, CCDS73589.1	13q22.3	2006-09-12	2006-09-12	2006-09-12	ENSG00000139737	ENSG00000139737			26387	protein-coding gene	gene with protein product		610491	"chromosome 13 open reading frame 32"	C13orf32		16546155	Standard	NM_001040153		Approved	FLJ30046	uc001vkk.3	Q8ND83	OTTHUMG00000017110	ENST00000466548.1:c.930A>G	chr13.hg19:g.78320728A>G		72.0	0.0		115.0	5.0	NM_001242868	A8K0Z9|B7Z209|Q5T6P4|Q5T6P7|Q8ND10|Q96NV0	Silent	SNP	ENST00000466548.1	hg19																																																																																				.	.		0.403	SLAIN1-009	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000355018.1	NM_144595		G	78320728	A	G	78320728	2	3	10	1	0	0	0	0	0	0	0	1	14380	69	3	2		2	SLAIN1	13	78320728	Silent	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	40641598	78320728	36849150	53	848										
MYO16	23026	hgsc.bcm.edu	37	chr13	109792761	109792761	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gggacgcgaggcccgcgggcGccccgggggcagcagcgcgc	21	16	0	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr13:109792761G>T	ENST00000357550.2	+	31	4176	c.4135G>T	c.(4135-4137)Gcc>Tcc	p.A1379S	MYO16_ENST00000356711.2_Missense_Mutation_p.A1379S	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			gcccgcgggcgccccgggggc	0.736																																					p.A1401S		Atlas-SNP	.											MYO16,lower_third,carcinoma,0,1	MYO16	285	.	0			c.G4201T						.						9	9	9					13																	109792761		2086	4051	6137	SO:0001583	missense	23026	exon32			GCGGGCGCCCCGG		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4135G>T	chr13.hg19:g.109792761G>T	ENSP00000350160:p.Ala1379Ser	79.0	0.0		50.0	17.0	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	hg19	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	G	9.766	1.171412	0.21621	.	.	ENSG00000041515	ENST00000356711;ENST00000357550	T;T	0.45276	0.9;0.9	4.84	2.08	0.27032	.	0.919043	0.08880	U	0.880173	T	0.18759	0.0450	N	0.02916	-0.46	0.34161	D	0.668651	B	0.27823	0.19	B	0.23716	0.048	T	0.29119	-1.0022	9	.	.	.	.	9.5435	0.39266	0.0756:0.2665:0.6578:0.0	.	1379	Q9Y6X6	MYO16_HUMAN	S	1379	ENSP00000349145:A1379S;ENSP00000350160:A1379S	.	A	+	1	0	MYO16	108590762	0.000000	0.05858	0.000000	0.03702	0.387000	0.30353	-0.071000	0.11505	0.091000	0.17302	0.305000	0.20034	GCC	.	.		0.736	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		T	109792761	G	T	109792761	3	4	10	1	0	0	0	0	1	0	0	0	10073	1087	38	1	4257	1	MYO16	13	109792761	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	31472033	109792761	5377117	54	849										
DAAM1	23002	hgsc.bcm.edu	37	chr14	59730340	59730340	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	aaccagcattgcccatgcccCctgtggaggagctggatgtc	12	13	0	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr14:59730340C>T	ENST00000395125.1	+	1	168	c.145C>T	c.(145-147)Cct>Tct	p.P49S	DAAM1_ENST00000360909.3_Missense_Mutation_p.P49S|DAAM1_ENST00000556135.1_Missense_Mutation_p.P49S|DAAM1_ENST00000351081.1_Missense_Mutation_p.P49S	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	49	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		GCCCATGCCCCCTGTGGAGGA	0.507																																					p.P49S		Atlas-SNP	.											.	DAAM1	95	.	0			c.C145T						.						110	96	101					14																	59730340		2203	4300	6503	SO:0001583	missense	23002	exon2			ATGCCCCCTGTGG	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.145C>T	chr14.hg19:g.59730340C>T	ENSP00000378557:p.Pro49Ser	135.0	0.0		123.0	56.0	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	hg19	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	C	8.294	0.818315	0.16607	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000358498;ENST00000556135;ENST00000395125	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	5.79	4.85	0.62838	GTPase-binding/formin homology 3 (1);Diaphanous GTPase-binding (1);	0.147991	0.45361	D	0.000376	T	0.81173	0.4767	N	0.13272	0.32	0.48975	D	0.999732	B;B;P	0.46859	0.122;0.149;0.885	B;B;P	0.51324	0.06;0.099;0.666	T	0.77024	-0.2741	10	0.02654	T	1	.	16.3348	0.83053	0.0:0.868:0.132:0.0	.	49;49;49	Q9Y4D1-2;Q9Y4D1;A8K6X5	.;DAAM1_HUMAN;.	S	49	ENSP00000354162:P49S;ENSP00000247170:P49S;ENSP00000450498:P49S;ENSP00000378557:P49S	ENSP00000247170:P49S	P	+	1	0	DAAM1	58800093	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	3.602000	0.54066	2.744000	0.94065	0.650000	0.86243	CCT	.	.		0.507	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		T	59730340	C	T	59730340	3	4	10	1	0	0	0	0	1	0	0	0	4217	623	22	3	147	3	DAAM1	14	59730340	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10		59730340	47619200	55	850										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63473124	63473124	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	acttcaaagcagtttgattcGtagttgtcaaaagtttgcct	8	7	2	1	rs373008977		TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr14:63473124G>A	ENST00000322893.7	-	3	532	c.264C>T	c.(262-264)taC>taT	p.Y88Y	KCNH5_ENST00000394968.1_Silent_p.Y30Y|KCNH5_ENST00000394964.2_Silent_p.Y30Y|KCNH5_ENST00000420622.2_Silent_p.Y88Y	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	88	PAS.				potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		AGTTTGATTCGTAGTTGTCAA	0.338																																					p.Y88Y		Atlas-SNP	.											.	KCNH5	320	.	0			c.C264T						.	G	,,	0,4404		0,0,2202	105	102	103		264,264,90	-1.1	1	14		103	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNH5	NM_139318.3,NM_172375.1,NM_172376.1	,,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,,	88/989,88/612,30/625	63473124	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	27133	exon3			TGATTCGTAGTTG	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.264C>T	chr14.hg19:g.63473124G>A		50.0	0.0		62.0	19.0	NM_172375	C9JP98	Silent	SNP	ENST00000322893.7	hg19	CCDS9756.1																																																																																			.	.		0.338	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63473124	G	A	63473124	2	1	10	1	0	0	0	0	0	0	0	1	8044	1140	40	1		1	KCNH5	14	63473124	Silent	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10	3742784	63473124	43876416	56	851										
LTK	4058	hgsc.bcm.edu	37	chr15	41796631	41796631	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	actgggtcatgatgcggtacCtggggagaggcaggagttca	17	7	2	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr15:41796631C>G	ENST00000263800.6	-	19	2352		c.e19-1		LTK_ENST00000453182.2_Splice_Site|LTK_ENST00000355166.5_Splice_Site|LTK_ENST00000561619.1_Splice_Site	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase						cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		GATGCGGTACCTGGGGAGAGG	0.627										TSP Lung(18;0.14)																											.		Atlas-SNP	.											.	LTK	117	.	0			c.2256-1G>C						.						84	73	77					15																	41796631		2203	4300	6503	SO:0001630	splice_region_variant	4058	exon20			CGGTACCTGGGGA	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.2256-1G>C	chr15.hg19:g.41796631C>G		82.0	0.0		72.0	26.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Splice_Site	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	C	19.84	3.902864	0.72754	.	.	ENSG00000062524	ENST00000355166;ENST00000263800;ENST00000453182	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1285	0.81410	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LTK	39583923	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	6.838000	0.75359	2.335000	0.79485	0.655000	0.94253	.	.	.		0.627	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		Intron	G	41796631	C	G	41796631	5	3	10	1	0	0	0	0	0	0	1	0	9089	695	24	4	347	4	LTK	15	41796631	Splice_Site	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10		41796631	60734761	57	852										
SLC24A5	283652	hgsc.bcm.edu	37	chr15	48429129	48429129	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ggctactctcagctctctatAagtttacatggccttagtca	7	11	3	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr15:48429129A>C	ENST00000341459.3	+	6	913	c.840A>C	c.(838-840)atA>atC	p.I280I	SLC24A5_ENST00000449382.2_Silent_p.I220I	NM_205850.2	NP_995322.1	Q71RS6	NCKX5_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 5	280					ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|negative regulation of melanin biosynthetic process (GO:0048022)|response to stimulus (GO:0050896)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|skin(1)|upper_aerodigestive_tract(1)	27		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		AGCTCTCTATAAGTTTACATG	0.363																																					p.I280I		Atlas-SNP	.											.	SLC24A5	64	.	0			c.A840C						.						80	81	81					15																	48429129		2198	4297	6495	SO:0001819	synonymous_variant	283652	exon6			CTCTATAAGTTTA	AF348468	CCDS10128.1	15q21.1	2014-01-28	2013-07-18		ENSG00000188467	ENSG00000188467		"Solute carriers"	20611	protein-coding gene	gene with protein product	"oculocutaneous albinism 6 (autosomal recessive)"	609802	"solute carrier family 24, member 5"			23364476	Standard	XM_005254308		Approved	JSX, OCA6	uc001zwe.3	Q71RS6	OTTHUMG00000131494	ENST00000341459.3:c.840A>C	chr15.hg19:g.48429129A>C		58.0	0.0		104.0	35.0	NM_205850	A5X8Z8|A5X8Z9|Q14CT4|Q6DKH3	Silent	SNP	ENST00000341459.3	hg19	CCDS10128.1																																																																																			.	.		0.363	SLC24A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254340.2	NM_205850		C	48429129	A	C	48429129	2	2	10	1	0	0	0	0	0	0	0	1	14484	352	13	5		5	SLC24A5	15	48429129	Silent	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	6632498	48429129	54102263	58	853										
FBN1	2200	hgsc.bcm.edu	37	chr15	48779389	48779389	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gtgtgcactcagctcacattCattgatgtctgtcgggaaaa	10	9	4	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr15:48779389C>A	ENST00000316623.5	-	29	3927	c.3472G>T	c.(3472-3474)Gaa>Taa	p.E1158*		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1158	EGF-like 18; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		AGCTCACATTCATTGATGTCT	0.468																																					p.E1158X		Atlas-SNP	.											.	FBN1	310	.	0			c.G3472T						.						84	78	80					15																	48779389		2198	4296	6494	SO:0001587	stop_gained	2200	exon29			CACATTCATTGAT	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.3472G>T	chr15.hg19:g.48779389C>A	ENSP00000325527:p.Glu1158*	65.0	0.0		76.0	30.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Nonsense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	46	12.843127	0.99700	.	.	ENSG00000166147	ENST00000316623	.	.	.	5.3	5.3	0.74995	.	0.046832	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.7483	0.91802	0.0:1.0:0.0:0.0	.	.	.	.	X	1158	.	ENSP00000325527:E1158X	E	-	1	0	FBN1	46566681	1.000000	0.71417	0.997000	0.53966	0.931000	0.56810	7.564000	0.82326	2.758000	0.94735	0.655000	0.94253	GAA	.	.		0.468	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48779389	C	A	48779389	4	1	10	1	0	0	0	0	0	1	0	0	5710	835	29	3	5295	3	FBN1	15	48779389	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	350260	48779389	53752003	59	854										
DPP8	54878	hgsc.bcm.edu	37	chr15	65759147	65759147	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	acttacttataaagaagtcaCagtgctagagaaaggagaaa	9	5	1	3			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr15:65759147C>G	ENST00000341861.5	-	14	3322	c.1742G>C	c.(1741-1743)tGt>tCt	p.C581S	DPP8_ENST00000321118.7_Missense_Mutation_p.C581S|DPP8_ENST00000559233.1_Missense_Mutation_p.C581S|DPP8_ENST00000321147.6_Missense_Mutation_p.C581S|DPP8_ENST00000358939.4_Missense_Mutation_p.C565S|DPP8_ENST00000339244.5_Missense_Mutation_p.C408S|DPP8_ENST00000300141.6_Missense_Mutation_p.C565S	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	581					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AAAGAAGTCACAGTGCTAGAG	0.358																																					p.C581S		Atlas-SNP	.											.	DPP8	78	.	0			c.G1742C						.						76	75	75					15																	65759147		2201	4299	6500	SO:0001583	missense	54878	exon15			AAGTCACAGTGCT	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"dipeptidyl peptidase VIII", "dipeptidyl peptidase IV-related protein-1", "prolyl dipeptidase DPP8"	606819	"dipeptidylpeptidase 8"			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.1742G>C	chr15.hg19:g.65759147C>G	ENSP00000339208:p.Cys581Ser	65.0	0.0		82.0	34.0	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Missense_Mutation	SNP	ENST00000341861.5	hg19	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.454142	0.43634	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000339244;ENST00000395652	T;T;T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68;1.68;1.68	5.61	5.61	0.85477	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.41581	0.1165	M	0.72894	2.215	0.54753	D	0.999988	B;B;D;P;P	0.56968	0.417;0.371;0.978;0.753;0.792	B;B;P;B;B	0.50659	0.356;0.141;0.647;0.406;0.3	T	0.11743	-1.0575	10	0.26408	T	0.33	-22.3355	19.718	0.96131	0.0:1.0:0.0:0.0	.	408;565;565;581;581	C9JSG1;Q6V1X1-3;Q6V1X1-4;Q6V1X1-2;Q6V1X1	.;.;.;.;DPP8_HUMAN	S	581;565;565;581;581;408;581	ENSP00000339208:C581S;ENSP00000351817:C565S;ENSP00000300141:C565S;ENSP00000318111:C581S;ENSP00000316373:C581S;ENSP00000341230:C408S;ENSP00000379013:C581S	ENSP00000300141:C565S	C	-	2	0	DPP8	63546200	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	5.661000	0.68025	2.663000	0.90544	0.454000	0.30748	TGT	.	.		0.358	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743		G	65759147	C	G	65759147	3	3	10	1	0	0	0	0	1	0	0	0	4734	478	17	4	982	4	DPP8	15	65759147	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	16979758	65759147	36772245	60	855										
HCN4	10021	hgsc.bcm.edu	37	chr15	73617688	73617688	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ggatgctctcctcgtcgaacAtcttgccctggtagcggtgc	12	13	2	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr15:73617688A>T	ENST00000261917.3	-	5	2681	c.1688T>A	c.(1687-1689)aTg>aAg	p.M563K		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	563					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		CTCGTCGAACATCTTGCCCTG	0.652																																					p.M563K		Atlas-SNP	.											.	HCN4	150	.	0			c.T1688A						.						95	96	96					15																	73617688		2198	4297	6495	SO:0001583	missense	10021	exon5			TCGAACATCTTGC	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1688T>A	chr15.hg19:g.73617688A>T	ENSP00000261917:p.Met563Lys	151.0	0.0		90.0	33.0	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	hg19	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	a	18.71	3.682281	0.68042	.	.	ENSG00000138622	ENST00000261917	D	0.96427	-4.01	3.28	3.28	0.37604	Cyclic nucleotide-binding-like (1);	.	.	.	.	D	0.97548	0.9197	M	0.82323	2.585	0.53005	D	0.999967	D	0.53885	0.963	D	0.63597	0.916	D	0.97148	0.9829	9	0.45353	T	0.12	.	12.1159	0.53866	1.0:0.0:0.0:0.0	.	563	Q9Y3Q4	HCN4_HUMAN	K	563	ENSP00000261917:M563K	ENSP00000261917:M563K	M	-	2	0	HCN4	71404741	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.956000	0.93066	1.504000	0.48704	0.449000	0.29647	ATG	.	.		0.652	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		T	73617688	A	T	73617688	3	4	10	1	0	0	0	0	1	0	0	0	7008	217	8	4	1939	4	HCN4	15	73617688	Missense_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	7858541	73617688	28913704	61	856										
APOB48R	55911	hgsc.bcm.edu	37	chr16	28506821	28506821	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ggggcttgccaagacaggagCggccaagcccaggagaggca	17	11	0	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr16:28506821C>A	ENST00000431282.1	+	2	469	c.459C>A	c.(457-459)agC>agA	p.S153R	APOBR_ENST00000328423.5_Missense_Mutation_p.S153R|CLN3_ENST00000569430.1_5'UTR|CLN3_ENST00000567160.1_5'UTR|APOBR_ENST00000564831.1_Missense_Mutation_p.S153R			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	153					cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						AAGACAGGAGCGGCCAAGCCC	0.617																																					p.S153R		Atlas-SNP	.											.	APOBR	89	.	0			c.C459A						.						9	12	11					16																	28506821		2013	4167	6180	SO:0001583	missense	55911	exon2			CAGGAGCGGCCAA	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"apolipoprotein B48 receptor", "apolipoprotein B100 receptor"	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.459C>A	chr16.hg19:g.28506821C>A	ENSP00000416094:p.Ser153Arg	399.0	0.0		266.0	106.0	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.90	1.481315	0.26598	.	.	ENSG00000184730	ENST00000328423;ENST00000431282	T;T	0.59502	0.26;0.26	4.88	-0.759	0.11045	.	.	.	.	.	T	0.41166	0.1147	N	0.20986	0.625	0.09310	N	1	P	0.44344	0.833	B	0.43386	0.418	T	0.28744	-1.0034	9	0.49607	T	0.09	-4.5254	5.6128	0.17414	0.0:0.5099:0.1398:0.3503	.	153	Q9NS13	.	R	153	ENSP00000327669:S153R;ENSP00000416094:S153R	ENSP00000327669:S153R	S	+	3	2	APOBR	28414322	0.000000	0.05858	0.014000	0.15608	0.030000	0.12068	-0.176000	0.09811	0.021000	0.15133	-0.245000	0.11935	AGC	.	.		0.617	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804		A	28506821	C	A	28506821	3	1	10	1	0	0	0	0	1	0	0	0	786	767	27	1	465	1	APOB48R	16	28506821	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10		28506821	61847932	62	857										
MYH2	4620	hgsc.bcm.edu	37	chr17	10443978	10443978	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tctccccttgactgacaaatGggtaatcatatgggttcgtg	10	9	2	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr17:10443978G>C	ENST00000245503.5	-	11	1325	c.941C>G	c.(940-942)cCa>cGa	p.P314R	MYH2_ENST00000397183.2_Missense_Mutation_p.P314R|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000532183.2_Missense_Mutation_p.P314R	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	314	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						ACTGACAAATGGGTAATCATA	0.363																																					p.P314R		Atlas-SNP	.											.	MYH2	390	.	0			c.C941G						.						103	94	97					17																	10443978		2203	4300	6503	SO:0001583	missense	4620	exon11			ACAAATGGGTAAT		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.941C>G	chr17.hg19:g.10443978G>C	ENSP00000245503:p.Pro314Arg	82.0	0.0		40.0	33.0	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	hg19	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.711468	0.48517	.	.	ENSG00000125414	ENST00000532183;ENST00000245503;ENST00000397183	D;D;D	0.86097	-2.07;-2.07;-2.07	5.25	5.25	0.73442	Myosin head, motor domain (2);	0.524332	0.14333	U	0.326202	D	0.82309	0.5009	N	0.17631	0.505	0.38045	D	0.935604	B;B	0.26512	0.04;0.151	B;B	0.43360	0.038;0.417	T	0.77194	-0.2677	10	0.26408	T	0.33	.	13.5171	0.61547	0.0:0.0:0.8339:0.1661	.	314;314	Q567P6;Q9UKX2	.;MYH2_HUMAN	R	314	ENSP00000433944:P314R;ENSP00000245503:P314R;ENSP00000380367:P314R	ENSP00000245503:P314R	P	-	2	0	MYH2	10384703	0.998000	0.40836	0.998000	0.56505	0.998000	0.95712	2.598000	0.46223	2.742000	0.94016	0.650000	0.86243	CCA	.	.		0.363	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		C	10443978	G	C	10443978	3	2	10	1	0	0	0	0	1	0	0	0	10044	1348	47	4	5004	4	MYH2	17	10443978	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10		10443978	70751232	63	858										
SLC13A2	9058	hgsc.bcm.edu	37	chr17	26822770	26822770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	cctctccctcctggtggccaCcttcaccgagtgcactagca	8	18	2	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr17:26822770C>T	ENST00000314669.5	+	10	1826	c.1406C>T	c.(1405-1407)aCc>aTc	p.T469I	SLC13A2_ENST00000537681.1_Missense_Mutation_p.T398I|SLC13A2_ENST00000444914.3_Missense_Mutation_p.T518I|SLC13A2_ENST00000545060.1_Missense_Mutation_p.T426I	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	469					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	CTGGTGGCCACCTTCACCGAG	0.612																																					p.T518I		Atlas-SNP	.											.	SLC13A2	125	.	0			c.C1553T						.						149	125	133					17																	26822770		2203	4300	6503	SO:0001583	missense	9058	exon10			TGGCCACCTTCAC	U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"Solute carriers"	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.1406C>T	chr17.hg19:g.26822770C>T	ENSP00000316202:p.Thr469Ile	39.0	0.0		34.0	8.0	NM_001145975	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	hg19	CCDS11231.1	.	.	.	.	.	.	.	.	.	.	C	0.027	-1.364550	0.01235	.	.	ENSG00000007216	ENST00000314669;ENST00000444914;ENST00000545060;ENST00000537681	T;T;T;T	0.02812	4.15;4.15;4.15;4.15	5.19	0.924	0.19418	.	0.517771	0.23666	N	0.045768	T	0.02494	0.0076	L	0.33710	1.025	0.43453	D	0.995649	B;B;B;B	0.22604	0.072;0.0;0.016;0.002	B;B;B;B	0.23275	0.045;0.014;0.018;0.02	T	0.53514	-0.8428	10	0.24483	T	0.36	-12.5262	9.0667	0.36467	0.0:0.6233:0.0:0.3767	.	426;518;398;469	F5GWV6;E7ETH5;G3V1L2;Q13183	.;.;.;S13A2_HUMAN	I	469;518;426;398	ENSP00000316202:T469I;ENSP00000392411:T518I;ENSP00000441935:T426I;ENSP00000440802:T398I	ENSP00000316202:T469I	T	+	2	0	SLC13A2	23846897	0.430000	0.25538	0.333000	0.25482	0.200000	0.23975	1.658000	0.37376	-0.030000	0.13804	-0.379000	0.06801	ACC	.	.		0.612	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984		T	26822770	C	T	26822770	3	4	10	1	0	0	0	0	1	0	0	0	14407	507	18	3	1591	3	SLC13A2	17	26822770	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	16378792	26822770	54372440	64	859										
ABCA9	10350	hgsc.bcm.edu	37	chr17	67023238	67023238	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ggatccaatccagcagtcggTtcatccaatagcaaaacctg	8	12	1	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr17:67023238T>A	ENST00000340001.4	-	15	2140	c.1929A>T	c.(1927-1929)gaA>gaT	p.E643D	ABCA9_ENST00000453985.2_Missense_Mutation_p.E643D|ABCA9_ENST00000370732.2_Missense_Mutation_p.E643D	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	643	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					CAGCAGTCGGTTCATCCAATA	0.408																																					p.E643D		Atlas-SNP	.											.	ABCA9	192	.	0			c.A1929T						.						71	72	71					17																	67023238		2203	4300	6503	SO:0001583	missense	10350	exon15			AGTCGGTTCATCC	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.1929A>T	chr17.hg19:g.67023238T>A	ENSP00000342216:p.Glu643Asp	41.0	0.0		96.0	12.0	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	hg19	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.724541	0.48728	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749	T;T	0.69435	-0.4;-0.4	5.31	1.88	0.25563	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.49305	D	0.000153	D	0.83105	0.5182	M	0.93462	3.42	0.47341	D	0.999394	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.988	T	0.82579	-0.0387	10	0.87932	D	0	.	8.0357	0.30491	0.0:0.3115:0.0:0.6885	.	643;643	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	D	643;626;643;638	ENSP00000342216:E643D;ENSP00000359767:E643D	ENSP00000342216:E643D	E	-	3	2	ABCA9	64534833	0.998000	0.40836	1.000000	0.80357	0.121000	0.20230	0.494000	0.22467	0.419000	0.25927	0.477000	0.44152	GAA	.	.		0.408	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		A	67023238	T	A	67023238	3	1	10	1	0	0	0	0	1	0	0	0	39	1722	60	4	3045	4	ABCA9	17	67023238	Missense_Mutation	SNP	T	TCGA-2Y-A9H0-01A-11D-A382-10	40200468	67023238	14171972	65	860										
PTPRM	5797	hgsc.bcm.edu	37	chr18	7955137	7955137	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	agaaccacccgttcctattgCcccacctcagctcgcctctg	6	19	2	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr18:7955137C>T	ENST00000332175.8	+	7	1894	c.857C>T	c.(856-858)gCc>gTc	p.A286V	PTPRM_ENST00000444013.1_Missense_Mutation_p.A73V|PTPRM_ENST00000400060.4_Missense_Mutation_p.A286V|PTPRM_ENST00000580170.1_Missense_Mutation_p.A286V|PTPRM_ENST00000400053.4_Missense_Mutation_p.A224V	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	286	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GTTCCTATTGCCCCACCTCAG	0.488																																					p.A286V		Atlas-SNP	.											.	PTPRM	185	.	0			c.C857T						.						66	64	65					18																	7955137		2203	4300	6503	SO:0001583	missense	5797	exon7			CTATTGCCCCACC	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.857C>T	chr18.hg19:g.7955137C>T	ENSP00000331418:p.Ala286Val	94.0	0.0		100.0	28.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.342388	0.61073	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	6.02	6.02	0.97574	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72700	0.3493	M	0.81802	2.56	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.76575	0.929;0.988;0.988	T	0.72431	-0.4296	10	0.54805	T	0.06	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	73;286;286	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	V	286;286;224;73	ENSP00000331418:A286V;ENSP00000382933:A286V;ENSP00000382927:A224V;ENSP00000387608:A73V	ENSP00000331418:A286V	A	+	2	0	PTPRM	7945137	1.000000	0.71417	0.661000	0.29709	0.986000	0.74619	7.818000	0.86416	2.865000	0.98341	0.655000	0.94253	GCC	.	.		0.488	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	7955137	C	T	7955137	3	4	10	1	0	0	0	0	1	0	0	0	12821	739	26	3	883	3	PTPRM	18	7955137	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10		7955137	70122111	66	861										
TWSG1	57045	hgsc.bcm.edu	37	chr18	9399524	9399524	+	Nonstop_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	atgtatgaactgcatgttttAaagaagacaaatgcaaacca	7	6	0	3			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr18:9399524A>T	ENST00000262120.5	+	5	862	c.671A>T	c.(670-672)tAa>tTa	p.*224L		NM_020648.5	NP_065699.1	Q9GZX9	TWSG1_HUMAN	twisted gastrulation BMP signaling modulator 1	0					BMP signaling pathway (GO:0030509)|camera-type eye development (GO:0043010)|cell differentiation (GO:0030154)|forebrain development (GO:0030900)|hemopoiesis (GO:0030097)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of BMP signaling pathway (GO:0030513)|salivary gland morphogenesis (GO:0007435)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|pancreas(2)	10						TGCATGTTTTAAAGAAGACAA	0.348																																					p.X224L		Atlas-SNP	.											.	TWSG1	23	.	0			c.A671T						.						68	67	67					18																	9399524		2203	4300	6503	SO:0001578	stop_lost	57045	exon5			TGTTTTAAAGAAG	AA486291	CCDS11844.1	18p11.3	2013-10-03	2013-10-03		ENSG00000128791	ENSG00000128791			12429	protein-coding gene	gene with protein product		605049	"twisted gastrulation homolog 1 (Drosophila)"			11260715	Standard	NM_020648		Approved	TSG	uc002knz.3	Q9GZX9	OTTHUMG00000131597	ENST00000262120.5:c.671A>T	chr18.hg19:g.9399524A>T	ENSP00000262120:p.*224Leuext*10	61.0	0.0		52.0	18.0	NM_020648	B2RE08|D3DUH9|Q8NBI7|Q96K46	Missense_Mutation	SNP	ENST00000262120.5	hg19	CCDS11844.1	.	.	.	.	.	.	.	.	.	.	A	13.53	2.264447	0.39995	.	.	ENSG00000128791	ENST00000262120	.	.	.	4.8	2.39	0.29439	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.2843	0.10848	0.5984:0.0:0.4016:0.0	.	.	.	.	L	224	.	.	X	+	2	2	TWSG1	9389524	1.000000	0.71417	0.958000	0.39756	0.777000	0.43975	3.958000	0.56737	0.686000	0.31488	0.374000	0.22700	TAA	.	.		0.348	TWSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254480.2			T	9399524	A	T	9399524	4	4	10	1	0	0	0	0	0	0	0	0	16800	369	13	4	685	4	TWSG1	18	9399524	Nonstop_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	1444387	9399524	68677724	67	862										
CHMP1B	57132	hgsc.bcm.edu	37	chr18	11851773	11851773	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	ggcggtgacgatgggcaaggTgaccaagtcgatggctggtg	19	7	0	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr18:11851773T>C	ENST00000526991.2	+	1	379	c.263T>C	c.(262-264)gTg>gCg	p.V88A	GNAL_ENST00000535121.1_Intron|GNAL_ENST00000334049.6_Intron|RP11-78A19.3_ENST00000586474.1_RNA|GNAL_ENST00000423027.3_Intron|GNAL_ENST00000269162.5_Intron	NM_020412.4	NP_065145.2	Q7LBR1	CHM1B_HUMAN	charged multivesicular body protein 1B	88					cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|protein transport (GO:0015031)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)			endometrium(1)|lung(1)|urinary_tract(1)	3						ATGGGCAAGGTGACCAAGTCG	0.537																																					p.V88A		Atlas-SNP	.											.	CHMP1B	16	.	0			c.T263C						.						138	150	146					18																	11851773		2159	4275	6434	SO:0001583	missense	57132	exon1			GCAAGGTGACCAA	AF306520	CCDS54180.1	18p11.21	2011-09-21	2011-09-21		ENSG00000255112	ENSG00000255112		"Charged multivesicular body proteins"	24287	protein-coding gene	gene with protein product		606486	"chromatin modifying protein 1B"			15537668	Standard	NM_020412		Approved	CHMP1.5, C18orf2, Vps46B	uc002kqe.3	Q7LBR1	OTTHUMG00000165820	ENST00000526991.2:c.263T>C	chr18.hg19:g.11851773T>C	ENSP00000432279:p.Val88Ala	63.0	0.0		40.0	23.0	NM_020412	Q96E89|Q9HD41	Missense_Mutation	SNP	ENST00000526991.2	hg19	CCDS54180.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.621079	0.87460	.	.	ENSG00000255112	ENST00000526991	T	0.76578	-1.03	5.08	5.08	0.68730	.	.	.	.	.	D	0.90597	0.7052	H	0.95745	3.715	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.92557	0.6055	9	0.87932	D	0	.	11.4276	0.50020	0.0:0.0:0.0:1.0	.	88	Q7LBR1	CHM1B_HUMAN	A	88	ENSP00000432279:V88A	ENSP00000432279:V88A	V	+	2	0	CHMP1B	11841773	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.263000	0.75096	0.533000	0.62120	GTG	.	.		0.537	CHMP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386375.2	NM_020412		C	11851773	T	C	11851773	3	2	10	1	0	0	0	0	1	0	0	0	3355	1696	59	2	265	2	CHMP1B	18	11851773	Missense_Mutation	SNP	T	TCGA-2Y-A9H0-01A-11D-A382-10	2452249	11851773	66225475	68	863										
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1429964	1429964	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	cctcttctgttctcttatctAggaatgtgggtgccggcagg	12	10	4	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr19:1429964A>C	ENST00000233078.4	+	9	861		c.e9-1		DAZAP1_ENST00000336761.6_Splice_Site	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1						cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCTCTTATCTAGGAATGTGGG	0.592																																					.		Atlas-SNP	.											.	DAZAP1	52	.	0			c.701-2A>C						.						56	45	49					19																	1429964		2195	4292	6487	SO:0001630	splice_region_variant	26528	exon9			TTATCTAGGAATG		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"RNA binding motif (RRM) containing"	2683	protein-coding gene	gene with protein product	"deleted in azoospermia associated protein 1"	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.701-1A>C	chr19.hg19:g.1429964A>C		120.0	0.0		79.0	25.0	NM_018959	Q96MJ3|Q9NRR9	Splice_Site	SNP	ENST00000233078.4	hg19	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	A	19.34	3.808395	0.70797	.	.	ENSG00000071626	ENST00000233078;ENST00000336761	.	.	.	4.89	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3044	0.60345	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DAZAP1	1380964	1.000000	0.71417	0.986000	0.45419	0.879000	0.50718	6.456000	0.73501	1.833000	0.53350	0.454000	0.30748	.	.	.		0.592	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711	Intron	C	1429964	A	C	1429964	5	2	10	1	0	0	0	0	0	0	1	0	4246	434	15	5	733	5	DAZAP1	19	1429964	Splice_Site	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10		1429964	57699019	69	864										
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606246	21606246	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	taagagaattcatactggacAgaaaccctacaaatgtgaag	8	7	1	3			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr19:21606246A>G	ENST00000355504.4	+	2	667	c.401A>G	c.(400-402)cAg>cGg	p.Q134R	ZNF493_ENST00000392288.2_Missense_Mutation_p.Q262R|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	134					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						CATACTGGACAGAAACCCTAC	0.363																																					p.Q262R		Atlas-SNP	.											.	ZNF493	178	.	0			c.A785G						.						40	43	42					19																	21606246		2203	4297	6500	SO:0001583	missense	284443	exon4			CTGGACAGAAACC	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.401A>G	chr19.hg19:g.21606246A>G	ENSP00000347691:p.Gln134Arg	108.0	0.0		211.0	80.0	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	hg19	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	8.227	0.803755	0.16467	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.19250	2.16;2.16	0.927	0.927	0.19437	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11452	0.0279	N	0.13003	0.285	0.80722	D	1	B;B	0.32467	0.046;0.372	B;B	0.33121	0.158;0.074	T	0.12889	-1.0530	9	0.72032	D	0.01	.	6.8319	0.23915	1.0:0.0:0.0:0.0	.	134;262	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	R	262;134	ENSP00000376110:Q262R;ENSP00000347691:Q134R	ENSP00000347691:Q134R	Q	+	2	0	ZNF493	21398086	0.709000	0.27886	0.317000	0.25265	0.305000	0.27757	2.645000	0.46621	0.321000	0.23259	0.315000	0.21342	CAG	.	.		0.363	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		G	21606246	A	G	21606246	3	3	10	1	0	0	0	0	1	0	0	0	17959	188	7	2	862	2	ZNF493	19	21606246	Missense_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	20176282	21606246	37522737	70	865										
RYR1	6261	hgsc.bcm.edu	37	chr19	38958307	38958307	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	catcttccgggcagagaaatCctatacagtgcagagcggcc	11	12	1	2			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr19:38958307C>A	ENST00000359596.3	+	25	3236	c.3236C>A	c.(3235-3237)tCc>tAc	p.S1079Y	RYR1_ENST00000355481.4_Missense_Mutation_p.S1079Y|RYR1_ENST00000360985.3_Missense_Mutation_p.S1079Y			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1079	6 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GCAGAGAAATCCTATACAGTG	0.587																																					p.S1079Y		Atlas-SNP	.											RYR1,acral,malignant_melanoma,0,1	RYR1	708	.	0			c.C3236A						.						99	93	95					19																	38958307		2203	4300	6503	SO:0001583	missense	6261	exon25			AGAAATCCTATAC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.3236C>A	chr19.hg19:g.38958307C>A	ENSP00000352608:p.Ser1079Tyr	131.0	0.0		89.0	39.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	c	7.897	0.733632	0.15574	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.74737	-0.87;-0.87;-0.87	2.77	2.77	0.32553	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.000000	0.64402	U	0.000020	D	0.83732	0.5318	M	0.81112	2.525	0.39065	D	0.960607	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.973	D	0.85766	0.1352	10	0.72032	D	0.01	.	9.5055	0.39044	0.0:0.8864:0.0:0.1136	.	1079;1079	P21817-2;P21817	.;RYR1_HUMAN	Y	1079	ENSP00000352608:S1079Y;ENSP00000347667:S1079Y;ENSP00000354254:S1079Y	ENSP00000347667:S1079Y	S	+	2	0	RYR1	43650147	0.862000	0.29867	0.999000	0.59377	0.683000	0.39861	1.061000	0.30542	1.883000	0.54544	0.154000	0.16183	TCC	.	.		0.587	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38958307	C	A	38958307	3	1	10	1	0	0	0	0	1	0	0	0	13783	855	30	3	3334	3	RYR1	19	38958307	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10	17352061	38958307	20170676	71	866										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33328358	33328358	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	cgccaggtaagctgggtcctGctgaggcagtgcccgggccc	16	14	0	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr20:33328358G>C	ENST00000374796.2	-	12	8272	c.5702C>G	c.(5701-5703)gCa>gGa	p.A1901G	NCOA6_ENST00000359003.2_Missense_Mutation_p.A1901G			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1901	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						GCTGGGTCCTGCTGAGGCAGT	0.592																																					p.A1901G		Atlas-SNP	.											.	NCOA6	219	.	0			c.C5702G						.						54	53	53					20																	33328358		2203	4300	6503	SO:0001583	missense	23054	exon11			GGTCCTGCTGAGG	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.5702C>G	chr20.hg19:g.33328358G>C	ENSP00000363929:p.Ala1901Gly	43.0	0.0		58.0	22.0	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	hg19	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.651618	0.47362	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.25579	1.79;1.79	5.65	4.64	0.57946	.	0.752314	0.12599	N	0.454854	T	0.14960	0.0361	N	0.08118	0	0.22081	N	0.999379	B	0.19200	0.034	B	0.14023	0.01	T	0.08411	-1.0723	10	0.36615	T	0.2	0.0536	13.2479	0.60033	0.0826:0.0:0.9174:0.0	.	1901	Q14686	NCOA6_HUMAN	G	1901	ENSP00000363929:A1901G;ENSP00000351894:A1901G	ENSP00000351894:A1901G	A	-	2	0	NCOA6	32792019	0.988000	0.35896	1.000000	0.80357	0.947000	0.59692	2.574000	0.46016	2.941000	0.99782	0.655000	0.94253	GCA	.	.		0.592	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		C	33328358	G	C	33328358	3	2	10	1	0	0	0	0	1	0	0	0	10242	1319	46	4	509	4	NCOA6	20	33328358	Missense_Mutation	SNP	G	TCGA-2Y-A9H0-01A-11D-A382-10		33328358	29697162	72	867										
SRMS	6725	hgsc.bcm.edu	37	chr20	62178723	62178724	+	Frame_Shift_Ins	INS	-	-	G													0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gtgttggggtccagggacccINSgggggtgccatggtccggct					rs572426427		TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr20:62178723_62178724insG	ENST00000217188.1	-	1	133_134	c.93_94insC	c.(91-96)cccgggfs	p.G32fs		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	32	N-terminal.				peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			TCCAGGGACCCGGGGGTGCCAT	0.693																																					p.G32fs		Atlas-INDEL	.											.	SRMS	48	.	0			c.94_95insC						.																																			SO:0001589	frameshift_variant	6725	exon1			.		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"SH2 domain containing"	11298	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 148"	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.94dupC	chr20.hg19:g.62178728_62178728dupG	ENSP00000217188:p.Gly32fs	202.0	0.0		160.0	10.0	NM_080823		Frame_Shift_Ins	INS	ENST00000217188.1	hg19	CCDS13525.1																																																																																			.	.		0.693	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823		G	62178724	-	G	62178723	7	5	10	1	0	1	1	0	0	0	0	0	15167	652	23	0	1404	0	SRMS	20	62178723	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H0-01A-11D-A382-10	28850365	62178723	846797	73	868										
SNRPD3	6634	hgsc.bcm.edu	37	chr22	24967931	24967931	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tgggacgtggaaacatctttCaaaagcgaagataattttct	9	6	3	1			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr22:24967931C>A	ENST00000215829.3	+	4	954	c.367C>A	c.(367-369)Caa>Aaa	p.Q123K	SNRPD3_ENST00000402849.1_Intron	NM_001278656.1|NM_004175.3	NP_001265585.1|NP_004166.1	P62318	SMD3_HUMAN	small nuclear ribonucleoprotein D3 polypeptide 18kDa	123	Arg/Lys-rich (basic).				gene expression (GO:0010467)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pICln-Sm protein complex (GO:0034715)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)|U7 snRNP (GO:0005683)	enzyme binding (GO:0019899)|histone pre-mRNA DCP binding (GO:0071208)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6						AAACATCTTTCAAAAGCGAAG	0.438																																					p.Q123K		Atlas-SNP	.											.	SNRPD3	12	.	0			c.C367A						.						99	88	92					22																	24967931		2203	4300	6503	SO:0001583	missense	6634	exon4			ATCTTTCAAAAGC	U15009	CCDS13828.1	22q11.23	2011-10-11	2002-08-29		ENSG00000100028	ENSG00000100028			11160	protein-coding gene	gene with protein product		601062	"small nuclear ribonucleoprotein D3 polypeptide (18kD)"			1701240, 7527560	Standard	NM_004175		Approved	SMD3, Sm-D3	uc003aam.1	P62318	OTTHUMG00000150727	ENST00000215829.3:c.367C>A	chr22.hg19:g.24967931C>A	ENSP00000215829:p.Gln123Lys	225.0	0.0		189.0	79.0	NM_004175	B4DJP7|B5BU13|P43331	Missense_Mutation	SNP	ENST00000215829.3	hg19	CCDS13828.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599794	0.46318	.	.	ENSG00000100028	ENST00000215829	.	.	.	5.99	5.99	0.97316	Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.053084	0.85682	D	0.000000	T	0.46870	0.1415	N	0.14661	0.345	0.80722	D	1	P	0.34587	0.458	B	0.39152	0.292	T	0.34625	-0.9821	9	0.20519	T	0.43	.	19.437	0.94799	0.0:1.0:0.0:0.0	.	123	P62318	SMD3_HUMAN	K	123	.	ENSP00000385994:Q123K	Q	+	1	0	SNRPD3	23297931	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	6.780000	0.75063	2.843000	0.97960	0.655000	0.94253	CAA	.	.		0.438	SNRPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319813.1	NM_004175		A	24967931	C	A	24967931	3	1	10	1	0	0	0	0	1	0	0	0	14881	827	29	3	377	3	SNRPD3	22	24967931	Missense_Mutation	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10		24967931	26336635	74	869										
KLHDC7B	113730	hgsc.bcm.edu	37	chr22	50987118	50987118	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	gcagcggggcgctcacggaaAagcaggaggaggcccggaag	19	10	1	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chr22:50987118A>T	ENST00000395676.2	+	1	657	c.523A>T	c.(523-525)Aag>Tag	p.K175*	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	175										central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	14		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GCTCACGGAAAAGCAGGAGGA	0.761																																					p.K175X		Atlas-SNP	.											.	KLHDC7B	39	.	0			c.A523T						.						2	3	3					22																	50987118		1643	3545	5188	SO:0001587	stop_gained	113730	exon1			ACGGAAAAGCAGG	BC009980	CCDS14097.2	22q13.33	2006-11-29		2005-12-13	ENSG00000130487	ENSG00000130487			25145	protein-coding gene	gene with protein product							Standard	NM_138433		Approved	MGC16635	uc003bmi.3	Q96G42	OTTHUMG00000150250	ENST00000395676.2:c.523A>T	chr22.hg19:g.50987118A>T	ENSP00000379034:p.Lys175*	103.0	0.0		55.0	45.0	NM_138433		Nonsense_Mutation	SNP	ENST00000395676.2	hg19	CCDS14097.2	.	.	.	.	.	.	.	.	.	.	A	17.97	3.519163	0.64634	.	.	ENSG00000130487	ENST00000395676	.	.	.	3.6	2.54	0.30619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.1696	0.31247	0.7962:0.2038:0.0:0.0	.	.	.	.	X	175	.	ENSP00000379034:K175X	K	+	1	0	KLHDC7B	49333984	0.000000	0.05858	0.115000	0.21578	0.077000	0.17291	0.115000	0.15540	0.449000	0.26747	0.165000	0.16767	AAG	.	.		0.761	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433		T	50987118	A	T	50987118	4	4	10	1	0	0	0	0	0	1	0	0	8370	15	1	4	525	4	KLHDC7B	22	50987118	Nonsense_Mutation	SNP	A	TCGA-2Y-A9H0-01A-11D-A382-10	26019187	50987118	317448	75	870										
ASMT	438	hgsc.bcm.edu	37	chrX	1742043	1742043	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.662896911700739	0.729186602870813	0.634075306844186	1	1	0	tgctccaaggttctcttcgcCgcctgcgagctgggcgtgtt	13	13	1	0			TCGA-2Y-A9H0-01A-11D-A382-10	TCGA-2Y-A9H0-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	87054fed-dd7d-4c27-af8f-4a559cca7800	d7df8ad9-70a5-4728-874c-8a1cf595ed35	g.chrX:1742043C>T	ENST00000381229.4	+	2	117	c.81C>T	c.(79-81)gcC>gcT	p.A27A	ASMT_ENST00000381233.3_Silent_p.A27A|ASMT_ENST00000381241.3_Silent_p.A27A			P46597	ASMT_HUMAN	acetylserotonin O-methyltransferase	27					cellular nitrogen compound metabolic process (GO:0034641)|indolalkylamine biosynthetic process (GO:0046219)|melatonin biosynthetic process (GO:0030187)|negative regulation of male gonad development (GO:2000019)|small molecule metabolic process (GO:0044281)|translation (GO:0006412)	cytosol (GO:0005829)	acetylserotonin O-methyltransferase activity (GO:0017096)|identical protein binding (GO:0042802)|O-methyltransferase activity (GO:0008171)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	16		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Melatonin(DB01065)	TTCTCTTCGCCGCCTGCGAGC	0.637																																					p.A27A		Atlas-SNP	.											.	ASMT	31	.	0			c.C81T						.						69	65	66					X																	1742043		2203	4296	6499	SO:0001819	synonymous_variant	438	exon2			CTTCGCCGCCTGC	M83779	CCDS14117.1, CCDS55364.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000196433	ENSG00000196433	2.1.1.4	"Pseudoautosomal regions / PAR1"	750	protein-coding gene	gene with protein product		300015, 402500				8397829, 7989373	Standard	NM_004043		Approved	HIOMT, ASMTY, HIOMTY	uc010ncy.3	P46597	OTTHUMG00000021065	ENST00000381229.4:c.81C>T	chrX.hg19:g.1742043C>T		213.0	0.0		129.0	112.0	NM_001171039	B2RC33|Q16598|Q5JQ72|Q5JQ73	Silent	SNP	ENST00000381229.4	hg19																																																																																				.	.		0.637	ASMT-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055612.1	NM_004043		T	1742043	C	T	1742043	2	4	10	1	0	0	0	0	0	0	0	1	1045	639	23	1		1	ASMT	23	1742043	Silent	SNP	C	TCGA-2Y-A9H0-01A-11D-A382-10		1742043	153528517	76	871										
MEGF6	1953	hgsc.bcm.edu	37	chr1	3407516	3407516	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gggttctcggggagccggagGggcccacctggaggggagag	22	9	1	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:3407516G>A	ENST00000356575.4	-	36	4750	c.4524C>T	c.(4522-4524)ccC>ccT	p.P1508P	MEGF6_ENST00000294599.4_Silent_p.P1196P	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1508						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GGAGCCGGAGGGGCCCACCTG	0.632																																					p.P1508P	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C4524T						.						35	45	42					1																	3407516		1950	4122	6072	SO:0001819	synonymous_variant	1953	exon36			CCGGAGGGGCCCA	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"EGF-like-domain, multiple 3"	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.4524C>T	chr1.hg19:g.3407516G>A		61.0	0.0		52.0	20.0	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	hg19	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	G	0.956	-0.704716	0.03255	.	.	ENSG00000162591	ENST00000491842	T	0.75260	-0.92	3.41	2.46	0.29980	.	0.420992	0.19241	U	0.119169	T	0.76176	0.3951	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	T	0.77032	-0.2738	7	0.72032	D	0.01	-0.2284	6.6805	0.23117	0.1385:0.0:0.8615:0.0	.	.	.	.	L	239	ENSP00000420386:P239L	ENSP00000420386:P239L	P	-	2	0	MEGF6	3397376	0.000000	0.05858	0.668000	0.29813	0.566000	0.35808	-0.183000	0.09712	1.759000	0.51996	0.655000	0.94253	CCC	.	.		0.632	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		A	3407516	G	A	3407516	2	1	11	1	0	0	0	0	0	0	0	1	9471	1219	43	3		3	MEGF6	1	3407516	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10		3407516	245843105	1	872										
MASP2	10747	hgsc.bcm.edu	37	chr1	11102990	11102990	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	cctgattcatctgtgacaaaGgtgatggtcaccgtgttgct	11	9	3	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:11102990G>C	ENST00000400897.3	-	6	846	c.831C>G	c.(829-831)acC>acG	p.T277T		NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	277	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		CTGTGACAAAGGTGATGGTCA	0.493																																					p.T277T	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											.	MASP2	71	.	0			c.C831G						.						226	194	205					1																	11102990		2203	4300	6503	SO:0001819	synonymous_variant	10747	exon6			GACAAAGGTGATG	X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"mannan-binding lectin serine protease 2", "mannan-binding lectin serine peptidase 1 pseudogene 1", "mannan-binding lectin serine protease 1 pseudogene 1"	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.831C>G	chr1.hg19:g.11102990G>C		98.0	0.0		88.0	24.0	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Silent	SNP	ENST00000400897.3	hg19	CCDS123.1																																																																																			.	.		0.493	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610		C	11102990	G	C	11102990	2	2	11	1	0	0	0	0	0	0	0	1	9332	987	35	4		4	MASP2	1	11102990	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	7695474	11102990	238147631	2	873										
PADI2	11240	hgsc.bcm.edu	37	chr1	17395676	17395676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gaggcccaggggctccaggaGgccacgcacgtgcatctcca	14	15	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:17395676G>A	ENST00000375486.4	-	16	1924	c.1861C>T	c.(1861-1863)Ctc>Ttc	p.L621F	PADI2_ENST00000466151.1_5'UTR|PADI2_ENST00000444885.2_Missense_Mutation_p.L505F	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	621					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	GGCTCCAGGAGGCCACGCACG	0.587																																					p.L621F		Atlas-SNP	.											.	PADI2	72	.	0			c.C1861T						.						112	100	104					1																	17395676		2203	4300	6503	SO:0001583	missense	11240	exon16			CCAGGAGGCCACG	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"Peptidyl arginine deiminases"	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.1861C>T	chr1.hg19:g.17395676G>A	ENSP00000364635:p.Leu621Phe	88.0	0.0		135.0	48.0	NM_007365	Q96DA7|Q9UPN2	Missense_Mutation	SNP	ENST00000375486.4	hg19	CCDS177.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803976	0.70682	.	.	ENSG00000117115	ENST00000375486;ENST00000444885	T;T	0.35973	1.28;1.28	5.46	4.52	0.55395	Protein-arginine deiminase, C-terminal (1);	0.068640	0.64402	D	0.000014	T	0.64864	0.2637	M	0.89214	3.015	0.80722	D	1	D;D	0.89917	1.0;0.99	D;D	0.76071	0.987;0.936	T	0.71570	-0.4553	10	0.66056	D	0.02	-21.9687	14.3329	0.66569	0.0:0.0:0.8513:0.1487	.	505;621	B4DIU3;Q9Y2J8	.;PADI2_HUMAN	F	621;505	ENSP00000364635:L621F;ENSP00000405894:L505F	ENSP00000364635:L621F	L	-	1	0	PADI2	17268263	1.000000	0.71417	0.978000	0.43139	0.653000	0.38743	4.601000	0.61090	2.582000	0.87167	0.655000	0.94253	CTC	.	.		0.587	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			A	17395676	G	A	17395676	3	1	11	1	0	0	0	0	1	0	0	0	11387	1000	35	3	140	3	PADI2	1	17395676	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	6292686	17395676	231854945	3	874										
ELOVL1	64834	hgsc.bcm.edu	37	chr1	43830911	43830911	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gagaagttgtagacaatcatGaagccacggagctggaaggg	15	6	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:43830911G>A	ENST00000372458.3	-	3	300	c.183C>T	c.(181-183)ttC>ttT	p.F61F	ELOVL1_ENST00000413844.2_Silent_p.F61F|ELOVL1_ENST00000470769.1_5'UTR	NM_001256399.1|NM_001256402.1|NM_022821.3	NP_001243328.1|NP_001243331.1|NP_073732.1	Q9BW60	ELOV1_HUMAN	ELOVL fatty acid elongase 1	61					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)			endometrium(1)|kidney(1)|large_intestine(1)|prostate(1)	4	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGACAATCATGAAGCCACGGA	0.522																																					p.F61F		Atlas-SNP	.											.	ELOVL1	18	.	0			c.C183T						.						71	66	67					1																	43830911		2203	4300	6503	SO:0001819	synonymous_variant	64834	exon3			AATCATGAAGCCA	AK001653	CCDS485.1, CCDS57987.1	1p34	2011-05-25	2011-05-25		ENSG00000066322	ENSG00000066322			14418	protein-coding gene	gene with protein product		611813	"elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1"				Standard	NM_022821		Approved	Ssc1	uc031pmf.1	Q9BW60	OTTHUMG00000007422	ENST00000372458.3:c.183C>T	chr1.hg19:g.43830911G>A		206.0	0.0		198.0	65.0	NM_001256399	B4DP24|Q53HT2|Q5JUY3|Q8WXU3|Q9NVD9|Q9Y396	Silent	SNP	ENST00000372458.3	hg19	CCDS485.1																																																																																			.	.		0.522	ELOVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019496.1	NM_022821		A	43830911	G	A	43830911	2	1	11	1	0	0	0	0	0	0	0	1	5075	1281	45	3		3	ELOVL1	1	43830911	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	26435235	43830911	205419710	4	875										
KDM4A	9682	hgsc.bcm.edu	37	chr1	44170005	44170005	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tcaagataccgggaagattaTattgagcctgcactataccg	9	9	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:44170005T>G	ENST00000372396.3	+	22	3293	c.3159T>G	c.(3157-3159)taT>taG	p.Y1053*	KDM4A-AS1_ENST00000418149.1_RNA|KDM4A-AS1_ENST00000398804.3_RNA|KDM4A-AS1_ENST00000453015.1_RNA|KDM4A-AS1_ENST00000434346.1_RNA|KDM4A-AS1_ENST00000439057.1_RNA	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	1053					cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						GGGAAGATTATATTGAGCCTG	0.483																																					p.Y1053X		Atlas-SNP	.											.	KDM4A	74	.	0			c.T3159G						.						141	145	143					1																	44170005		2203	4300	6503	SO:0001587	stop_gained	9682	exon22			AGATTATATTGAG	AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	22978	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 3A", "tudor domain containing 14A"	609764	"jumonji domain containing 2", "jumonji domain containing 2A"	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.3159T>G	chr1.hg19:g.44170005T>G	ENSP00000361473:p.Tyr1053*	80.0	0.0		96.0	26.0	NM_014663	Q5VVB1	Nonsense_Mutation	SNP	ENST00000372396.3	hg19	CCDS491.1	.	.	.	.	.	.	.	.	.	.	T	39	7.465155	0.98302	.	.	ENSG00000066135	ENST00000372396	.	.	.	5.8	-1.8	0.07907	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.8745	17.0927	0.86626	0.0:0.7677:0.0:0.2323	.	.	.	.	X	1053	.	ENSP00000361473:Y1053X	Y	+	3	2	KDM4A	43942592	1.000000	0.71417	0.866000	0.34008	0.992000	0.81027	1.408000	0.34668	-0.279000	0.09167	0.533000	0.62120	TAT	.	.		0.483	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663		G	44170005	T	G	44170005	4	3	11	1	0	0	0	0	0	1	0	0	8137	1413	49	5	3241	5	KDM4A	1	44170005	Nonsense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	339094	44170005	205080616	5	876										
C8B	732	hgsc.bcm.edu	37	chr1	57395082	57395082	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ctgctgtatcatctgctaggAgcagtcaagtgtttctgaag	11	8	4	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:57395082A>C	ENST00000371237.4	-	12	1837	c.1771T>G	c.(1771-1773)Tcc>Gcc	p.S591A	C8B_ENST00000543257.1_Missense_Mutation_p.S539A|C8B_ENST00000535057.1_Missense_Mutation_p.S529A	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	591	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						ATCTGCTAGGAGCAGTCAAGT	0.517																																					p.S591A		Atlas-SNP	.											.	C8B	107	.	0			c.T1771G						.						119	103	108					1																	57395082		2203	4300	6503	SO:0001583	missense	732	exon12			GCTAGGAGCAGTC	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"Complement system"	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.1771T>G	chr1.hg19:g.57395082A>C	ENSP00000360281:p.Ser591Ala	31.0	0.0		76.0	22.0	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	hg19	CCDS30730.1	.	.	.	.	.	.	.	.	.	.	A	18.24	3.579731	0.65992	.	.	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	T;T;T	0.27720	1.82;1.84;1.65	3.76	3.76	0.43208	.	1.501350	0.04137	N	0.318936	T	0.32406	0.0828	L	0.41492	1.28	0.24873	N	0.992274	B;B;B	0.15930	0.015;0.015;0.009	B;B;B	0.17098	0.017;0.011;0.005	T	0.25467	-1.0131	10	0.54805	T	0.06	24.0104	12.6727	0.56876	1.0:0.0:0.0:0.0	.	539;529;591	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	A	591;539;529	ENSP00000360281:S591A;ENSP00000442548:S539A;ENSP00000440113:S529A	ENSP00000360281:S591A	S	-	1	0	C8B	57167670	1.000000	0.71417	0.854000	0.33618	0.410000	0.31052	6.198000	0.72106	1.958000	0.56883	0.379000	0.24179	TCC	.	.		0.517	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2			C	57395082	A	C	57395082	3	2	11	1	0	0	0	0	1	0	0	0	2419	304	11	5	8	5	C8B	1	57395082	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	13225077	57395082	191855539	6	877										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70504820	70504820	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aacaggccagcaaaaacatcGccaaggatttgattagtcct	8	10	0	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:70504820G>C	ENST00000035383.5	+	19	3229	c.3199G>C	c.(3199-3201)Gcc>Ccc	p.A1067P	LRRC7_ENST00000310961.5_Missense_Mutation_p.A1072P|LRRC7_ENST00000415775.2_Missense_Mutation_p.A351P	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1067						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.A1067T(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CAAAAACATCGCCAAGGATTT	0.463																																					p.A1067P		Atlas-SNP	.											LRRC7,colon,carcinoma,0,1	LRRC7	400	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3199C						.						66	71	69					1																	70504820		2203	4300	6503	SO:0001583	missense	57554	exon19			AACATCGCCAAGG		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.3199G>C	chr1.hg19:g.70504820G>C	ENSP00000035383:p.Ala1067Pro	79.0	0.0		145.0	40.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	hg19	CCDS645.1	.	.	.	.	.	.	.	.	.	.	G	0.291	-0.979888	0.02197	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.36340	1.26;1.32;2.41	5.76	1.87	0.25490	.	0.189978	0.45867	D	0.000331	T	0.06962	0.0177	N	0.16130	0.375	0.28817	N	0.897917	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.10450	0.003;0.005;0.001	T	0.32903	-0.9889	10	0.36615	T	0.2	.	6.8269	0.23889	0.2764:0.1239:0.5996:0.0	.	351;1067;1067	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	P	1072;1067;351;890	ENSP00000309245:A1072P;ENSP00000035383:A1067P;ENSP00000394867:A351P	ENSP00000035383:A1067P	A	+	1	0	LRRC7	70277408	0.760000	0.28428	0.168000	0.22838	0.001000	0.01503	1.111000	0.31159	0.103000	0.17682	-0.122000	0.15005	GCC	.	.		0.463	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		C	70504820	G	C	70504820	3	2	11	1	0	0	0	0	1	0	0	0	9029	1087	38	4	3273	4	LRRC7	1	70504820	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	13109738	70504820	178745801	7	878										
PTGFR	5737	hgsc.bcm.edu	37	chr1	78958702	78958702	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gagccatagcagtatttgtaTatgcttctgataaagaatgg	10	5	1	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:78958702T>C	ENST00000370757.3	+	2	511	c.274T>C	c.(274-276)Tat>Cat	p.Y92H	PTGFR_ENST00000370758.1_Missense_Mutation_p.Y92H|PTGFR_ENST00000370756.3_Missense_Mutation_p.Y92H	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	92					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)			breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	AGTATTTGTATATGCTTCTGA	0.428																																					p.Y92H		Atlas-SNP	.											.	PTGFR	121	.	0			c.T274C						.						130	123	125					1																	78958702		2203	4300	6503	SO:0001583	missense	5737	exon2			TTTGTATATGCTT	AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"GPCR / Class A : Prostanoid receptors"	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.274T>C	chr1.hg19:g.78958702T>C	ENSP00000359793:p.Tyr92His	75.0	0.0		101.0	38.0	NM_000959	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Missense_Mutation	SNP	ENST00000370757.3	hg19	CCDS686.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.005698	0.35415	.	.	ENSG00000122420	ENST00000370758;ENST00000370757;ENST00000370756	T;T;T	0.38401	1.14;1.14;1.14	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.059523	0.64402	D	0.000001	T	0.41994	0.1183	L	0.37630	1.12	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.25641	-1.0126	10	0.42905	T	0.14	-22.8463	16.5479	0.84454	0.0:0.0:0.0:1.0	.	92;92	P43088;P43088-2	PF2R_HUMAN;.	H	92	ENSP00000359794:Y92H;ENSP00000359793:Y92H;ENSP00000359792:Y92H	ENSP00000359792:Y92H	Y	+	1	0	PTGFR	78731290	1.000000	0.71417	0.712000	0.30502	0.013000	0.08279	5.955000	0.70306	2.371000	0.80710	0.533000	0.62120	TAT	.	.		0.428	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		C	78958702	T	C	78958702	3	2	11	1	0	0	0	0	1	0	0	0	12762	1406	49	2	276	2	PTGFR	1	78958702	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	8453882	78958702	170291919	8	879										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103444972	103444972	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ctccattggcacctggaaacCcagggaatccagtggaaccc	10	14	0	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:103444972C>A	ENST00000370096.3	-	32	2888	c.2576G>T	c.(2575-2577)gGg>gTg	p.G859V	COL11A1_ENST00000358392.2_Missense_Mutation_p.G871V|COL11A1_ENST00000512756.1_Missense_Mutation_p.G743V|COL11A1_ENST00000353414.4_Missense_Mutation_p.G820V	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	859	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		ACCTGGAAACCCAGGGAATCC	0.353																																					p.G871V		Atlas-SNP	.											.	COL11A1	972	.	0			c.G2612T						.						42	46	44					1																	103444972		2203	4300	6503	SO:0001583	missense	1301	exon32			GGAAACCCAGGGA	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2576G>T	chr1.hg19:g.103444972C>A	ENSP00000359114:p.Gly859Val	109.0	0.0		220.0	62.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440828	0.83993	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.97941	-4.62;-4.62;-4.62;-4.62	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.99152	0.9707	M	0.94142	3.5	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;1.0;0.998;0.998	D	0.99360	1.0917	10	0.87932	D	0	.	18.5374	0.91015	0.0:1.0:0.0:0.0	.	743;820;871;859;79	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	V	859;871;820;79;743	ENSP00000359114:G859V;ENSP00000351163:G871V;ENSP00000302551:G820V;ENSP00000426533:G743V	ENSP00000302551:G820V	G	-	2	0	COL11A1	103217560	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.425000	0.66470	2.612000	0.88384	0.655000	0.94253	GGG	.	.		0.353	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103444972	C	A	103444972	3	1	11	1	0	0	0	0	1	0	0	0	3669	623	22	3	2988	3	COL11A1	1	103444972	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	24486270	103444972	145805649	9	880										
GABPB2	126626	hgsc.bcm.edu	37	chr1	151070417	151070417	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gctgctccattcatcttcacGtcgggtgaggttgttaacct	10	11	3	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:151070417G>A	ENST00000368918.3	+	5	892	c.561G>A	c.(559-561)acG>acA	p.T187T	GABPB2_ENST00000467551.1_3'UTR|GABPB2_ENST00000368916.1_Silent_p.T187T|GABPB2_ENST00000368917.1_Silent_p.T187T	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2	187					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(3)|liver(2)|lung(7)	15				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		TCATCTTCACGTCGGGTGAGG	0.418																																					p.T187T		Atlas-SNP	.											.	GABPB2	41	.	0			c.G561A						.						136	116	123					1																	151070417		2203	4300	6503	SO:0001819	synonymous_variant	126626	exon5			CTTCACGTCGGGT		CCDS983.1	1q21.2	2013-01-10			ENSG00000143458	ENSG00000143458		"Ankyrin repeat domain containing"	28441	protein-coding gene	gene with protein product						7958862	Standard	NM_144618		Approved	MGC29891	uc001ewr.2	Q8TAK5	OTTHUMG00000012193	ENST00000368918.3:c.561G>A	chr1.hg19:g.151070417G>A		155.0	0.0		194.0	48.0	NM_144618	B1AVJ8|D3DV14|Q8NAR5	Silent	SNP	ENST00000368918.3	hg19	CCDS983.1																																																																																			.	.		0.418	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033700.2	NM_144618		A	151070417	G	A	151070417	2	1	11	1	0	0	0	0	0	0	0	1	6167	1132	40	1		1	GABPB2	1	151070417	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	47625445	151070417	98180204	10	881										
FLG2	388698	hgsc.bcm.edu	37	chr1	152326933	152326933	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ggccaaagccagaggactgaCctgagcctggcctgtgttgt	14	11	0	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:152326933C>T	ENST00000388718.5	-	3	3401	c.3329G>A	c.(3328-3330)gGt>gAt	p.G1110D	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1110	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGAGGACTGACCTGAGCCTGG	0.517																																					p.G1110D		Atlas-SNP	.											.	FLG2	431	.	0			c.G3329A						.						253	258	257					1																	152326933		2203	4300	6503	SO:0001583	missense	388698	exon3			GACTGACCTGAGC	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.3329G>A	chr1.hg19:g.152326933C>T	ENSP00000373370:p.Gly1110Asp	55.0	0.0		197.0	44.0	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	hg19	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.167463	0.57476	.	.	ENSG00000143520	ENST00000388718	T	0.03745	3.82	4.78	4.78	0.61160	.	.	.	.	.	T	0.04907	0.0132	L	0.50333	1.59	0.20821	N	0.999844	D	0.60160	0.987	P	0.57548	0.823	T	0.34825	-0.9813	9	0.38643	T	0.18	-0.1739	13.3657	0.60682	0.0:1.0:0.0:0.0	.	1110	Q5D862	FILA2_HUMAN	D	1110	ENSP00000373370:G1110D	ENSP00000373370:G1110D	G	-	2	0	FLG2	150593557	0.000000	0.05858	0.006000	0.13384	0.190000	0.23558	0.546000	0.23284	2.210000	0.71456	0.558000	0.71614	GGT	.	.		0.517	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152326933	C	T	152326933	3	4	11	1	0	0	0	0	1	0	0	0	5931	507	18	3	3850	3	FLG2	1	152326933	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	1256516	152326933	96923688	11	882										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842253	154842253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gctgctgctgaagctgcggaGgctgaggctgcagcgagggt	19	9	0	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:154842253G>T	ENST00000271915.4	-	1	503	c.188C>A	c.(187-189)cCt>cAt	p.P63H	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	63	Gln-rich.|Pro-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	aagctgcggaggctgaggctg	0.697																																					p.P63H		Atlas-SNP	.											.	KCNN3	141	.	0			c.C188A						.						6	4	5					1																	154842253		1984	3925	5909	SO:0001583	missense	3782	exon1			TGCGGAGGCTGAG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.188C>A	chr1.hg19:g.154842253G>T	ENSP00000271915:p.Pro63His	70.0	0.0		109.0	15.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	g	11.14	1.552427	0.27739	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.56275	0.47	5.07	3.18	0.36537	.	1.727610	0.03258	N	0.182822	T	0.18551	0.0445	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.11372	-1.0590	8	0.33141	T	0.24	-4.1487	6.4327	0.21807	0.0918:0.0:0.7284:0.1798	.	.	.	.	H	63;158	ENSP00000271915:P63H	ENSP00000271915:P63H	P	-	2	0	KCNN3	153108877	0.863000	0.29885	1.000000	0.80357	0.998000	0.95712	1.873000	0.39558	0.823000	0.34589	0.563000	0.77884	CCT	.	.		0.697	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154842253	G	T	154842253	3	4	11	1	0	0	0	0	1	0	0	0	8089	1000	35	3	2061	3	KCNN3	1	154842253	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	2515320	154842253	94408368	12	883										
CD1B	910	hgsc.bcm.edu	37	chr1	158300831	158300831	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	acgaggtctggataacatgaAaggaggtcggcccctggaag	15	8	1	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:158300831A>T	ENST00000368168.3	-	2	190	c.83T>A	c.(82-84)tTt>tAt	p.F28Y		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	28					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					GATAACATGAAAGGAGGTCGG	0.473																																					p.F28Y		Atlas-SNP	.											.	CD1B	78	.	0			c.T83A						.						202	197	198					1																	158300831		2203	4300	6503	SO:0001583	missense	910	exon2			ACATGAAAGGAGG	M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1635	protein-coding gene	gene with protein product		188360	"CD1B antigen, b polypeptide", "CD1b antigen"	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.83T>A	chr1.hg19:g.158300831A>T	ENSP00000357150:p.Phe28Tyr	157.0	0.0		320.0	88.0	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Missense_Mutation	SNP	ENST00000368168.3	hg19	CCDS1176.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.605532	0.28623	.	.	ENSG00000158485	ENST00000368168	T	0.07688	3.17	4.15	-3.82	0.04281	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.741874	0.11633	N	0.544566	T	0.05731	0.0150	L	0.37897	1.145	0.09310	N	1	D;B	0.60575	0.988;0.389	P;B	0.61592	0.891;0.2	T	0.10660	-1.0620	10	0.49607	T	0.09	-2.9917	10.0175	0.42022	0.3325:0.0:0.0:0.6675	.	28;28	B4E0D2;P29016	.;CD1B_HUMAN	Y	28	ENSP00000357150:F28Y	ENSP00000357150:F28Y	F	-	2	0	CD1B	156567455	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.897000	0.04110	-0.846000	0.04174	-0.336000	0.08194	TTT	.	.		0.473	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764		T	158300831	A	T	158300831	3	4	11	1	0	0	0	0	1	0	0	0	2977	14	1	4	938	4	CD1B	1	158300831	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	3458578	158300831	90949790	13	884										
C1orf129	80133	hgsc.bcm.edu	37	chr1	171033398	171033399	+	Missense_Mutation	DNP	CC	CC	AA													0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tctacatcaaaaaattgaagCctctttacaattataactca					rs546065073		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:171033398_171033399CC>AA	ENST00000367759.4	+	22	2657_2658	c.2503_2504CC>AA	c.(2503-2505)CCt>AAt	p.P835N		NM_001163629.1	NP_001157101.1	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	439																	AAAATTGAAGCCTCTTTACAAT	0.332																																					p.P835T|p.P835H		Atlas-SNP	.											.	.	.	.	0			c.C2503A|c.C2504A						.																																			SO:0001583	missense	80133	exon22			TTGAAGCCTCTTT|TGAAGCCTCTTTA	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"maestro heat-like repeat containing"	26287	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 129"	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	Exception_encountered	chr1.hg19:g.171033398_171033399delinsAA	ENSP00000356733:p.Pro835Asn	250.0|249.0	0.0		491.0|488.0	246.0|243.0	NM_001163629	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367759.4	hg19	CCDS53429.1																																																																																			.	.		0.332	MROH9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_025063		AA	171033399	CC	AA	171033398	3	1	11	1	0	0	0	0	1	0	0	0	1998	739	26	3	2711	3	C1orf129	1	171033398	Missense_Mutation	DNP	CC	TCGA-2Y-A9H1-01A-11D-A382-10	12732567	171033398	78217223	14	885										
TNR	7143	hgsc.bcm.edu	37	chr1	175360435	175360435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ggcactcacctgtggagacgCtggccgaggtaggggggctg	19	10	1	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr1:175360435C>T	ENST00000367674.2	-	7	2204	c.1496G>A	c.(1495-1497)aGc>aAc	p.S499N	TNR_ENST00000263525.2_Missense_Mutation_p.S499N			Q92752	TENR_HUMAN	tenascin R	499	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TGTGGAGACGCTGGCCGAGGT	0.542																																					p.S499N		Atlas-SNP	.											.	TNR	399	.	0			c.G1496A						.						66	69	68					1																	175360435		2203	4300	6503	SO:0001583	missense	7143	exon7			GAGACGCTGGCCG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.1496G>A	chr1.hg19:g.175360435C>T	ENSP00000356646:p.Ser499Asn	54.0	0.0		106.0	33.0	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.018938	0.54576	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.55413	0.52;0.52	5.23	5.23	0.72850	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.050437	0.85682	D	0.000000	T	0.47948	0.1473	L	0.29908	0.895	0.49299	D	0.999774	D	0.54964	0.969	P	0.48654	0.585	T	0.32929	-0.9888	10	0.11794	T	0.64	.	18.3986	0.90507	0.0:1.0:0.0:0.0	.	499	Q92752	TENR_HUMAN	N	499	ENSP00000356646:S499N;ENSP00000263525:S499N	ENSP00000263525:S499N	S	-	2	0	TNR	173627058	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	6.050000	0.71063	2.429000	0.82318	0.655000	0.94253	AGC	.	.		0.542	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		T	175360435	C	T	175360435	3	4	11	1	0	0	0	0	1	0	0	0	16353	797	28	3	2648	3	TNR	1	175360435	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	4327037	175360435	73890186	15	886										
HADHB	3032	hgsc.bcm.edu	37	chr2	26477337	26477337	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ttcctcccagctacgagctgCcccaggtacagtaatttgta	8	13	0	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr2:26477337C>G	ENST00000317799.5	+	3	208	c.104C>G	c.(103-105)gCc>gGc	p.A35G	HADHB_ENST00000405867.3_Missense_Mutation_p.A35G|HADHB_ENST00000545822.1_5'UTR|HADHB_ENST00000537713.1_Missense_Mutation_p.A35G	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	35					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTACGAGCTGCCCCAGGTACA	0.353																																					p.A35G		Atlas-SNP	.											.	HADHB	50	.	0			c.C104G						.						50	47	48					2																	26477337		2203	4300	6503	SO:0001583	missense	3032	exon3			GAGCTGCCCCAGG		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"mitochondrial trifunctional protein, beta subunit"	143450	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.104C>G	chr2.hg19:g.26477337C>G	ENSP00000325136:p.Ala35Gly	132.0	0.0		199.0	72.0	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Missense_Mutation	SNP	ENST00000317799.5	hg19	CCDS1722.1	.	.	.	.	.	.	.	.	.	.	C	12.36	1.913903	0.33815	.	.	ENSG00000138029	ENST00000448743;ENST00000317799;ENST00000405867;ENST00000537713;ENST00000425035;ENST00000412805	D;D;D;D;D;D	0.97455	-3.89;-3.23;-3.34;-3.27;-4.39;-2.23	5.2	3.36	0.38483	.	0.609412	0.15497	N	0.259203	D	0.90734	0.7092	N	0.08118	0	0.58432	D	0.999998	B;B;B	0.26547	0.0;0.152;0.0	B;B;B	0.18263	0.0;0.021;0.0	D	0.86053	0.1527	10	0.59425	D	0.04	1.0E-4	8.9495	0.35781	0.0:0.7663:0.1499:0.0838	.	35;35;35	F5GZQ3;B5MD38;P55084	.;.;ECHB_HUMAN	G	35	ENSP00000415300:A35G;ENSP00000325136:A35G;ENSP00000385411:A35G;ENSP00000444295:A35G;ENSP00000404633:A35G;ENSP00000413103:A35G	ENSP00000325136:A35G	A	+	2	0	HADHB	26330841	0.533000	0.26354	0.952000	0.39060	0.974000	0.67602	1.580000	0.36547	0.669000	0.31146	0.650000	0.86243	GCC	.	.		0.353	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183		G	26477337	C	G	26477337	3	3	11	1	0	0	0	0	1	0	0	0	6953	739	26	4	110	4	HADHB	2	26477337	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10		26477337	216722036	16	887										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33359882	33359882	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	agtaaccacactggccgcatCaaggtggtctttactccgag	10	12	2	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr2:33359882C>A	ENST00000404816.2	+	5	1409	c.1056C>A	c.(1054-1056)atC>atA	p.I352I	LTBP1_ENST00000407925.1_Silent_p.I26I|LTBP1_ENST00000404525.1_Silent_p.I26I|LTBP1_ENST00000354476.3_Silent_p.I352I|LTBP1_ENST00000390003.4_Silent_p.I26I|LTBP1_ENST00000418533.2_Silent_p.I26I|LTBP1_ENST00000402934.1_Silent_p.I26I			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	352					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CTGGCCGCATCAAGGTGGTCT	0.488																																					p.I352I		Atlas-SNP	.											.	LTBP1	317	.	0			c.C1056A						.						107	93	98					2																	33359882		2203	4300	6503	SO:0001819	synonymous_variant	4052	exon5			CCGCATCAAGGTG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.1056C>A	chr2.hg19:g.33359882C>A		136.0	0.0		246.0	70.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	hg19	CCDS33177.2																																																																																			.	.		0.488	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		A	33359882	C	A	33359882	2	1	11	1	0	0	0	0	0	0	0	1	9082	816	29	3		3	LTBP1	2	33359882	Silent	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	6882545	33359882	209839491	17	888										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54858513	54858513	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gcacgagaacatcaagaacgAgatcgacaactacgaggagg	12	9	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr2:54858513A>T	ENST00000356805.4	+	16	3610	c.3329A>T	c.(3328-3330)gAg>gTg	p.E1110V	SPTBN1_ENST00000333896.5_Missense_Mutation_p.E1097V	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1110					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			ATCAAGAACGAGATCGACAAC	0.587																																					p.E1110V		Atlas-SNP	.											.	SPTBN1	378	.	0			c.A3329T						.						176	144	154					2																	54858513		2203	4300	6503	SO:0001583	missense	6711	exon16			AGAACGAGATCGA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3329A>T	chr2.hg19:g.54858513A>T	ENSP00000349259:p.Glu1110Val	162.0	0.0		189.0	77.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.586216	0.86851	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.50277	0.75;0.75	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.71609	0.3360	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	0.992;1.0	D;D	0.87578	0.982;0.998	T	0.76729	-0.2852	10	0.87932	D	0	.	15.727	0.77770	1.0:0.0:0.0:0.0	.	1097;1110	Q01082-3;Q01082	.;SPTB2_HUMAN	V	1110;1097	ENSP00000349259:E1110V;ENSP00000334156:E1097V	ENSP00000334156:E1097V	E	+	2	0	SPTBN1	54712017	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.281000	0.95811	2.118000	0.64928	0.533000	0.62120	GAG	.	.		0.587	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54858513	A	T	54858513	3	4	11	1	0	0	0	0	1	0	0	0	15134	304	11	4	3500	4	SPTBN1	2	54858513	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	21498631	54858513	188340860	18	889										
LCT	3938	hgsc.bcm.edu	37	chr2	136555611	136555611	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gcccttaccgagacttgttgAggcctgcagccaagctcctg	11	14	0	2	rs5834448		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr2:136555611A>G	ENST00000264162.2	-	13	4974	c.4964T>C	c.(4963-4965)cTc>cCc	p.L1655P		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1655	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	AGACTTGTTGAGGCCTGCAGC	0.552											OREG0014998	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1655P		Atlas-SNP	.											.	LCT	309	.	0			c.T4964C						.						98	90	93					2																	136555611		2203	4300	6503	SO:0001583	missense	3938	exon13			TTGTTGAGGCCTG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4964T>C	chr2.hg19:g.136555611A>G	ENSP00000264162:p.Leu1655Pro	38.0	0.0	1626	42.0	14.0	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	hg19	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.084469	0.76642	.	.	ENSG00000115850	ENST00000264162	T	0.33438	1.41	5.76	5.76	0.90799	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.064020	0.64402	D	0.000005	T	0.61751	0.2372	M	0.87180	2.865	0.80722	D	1	P	0.45569	0.861	D	0.64687	0.928	T	0.67530	-0.5647	10	0.87932	D	0	-22.6791	16.0843	0.81031	1.0:0.0:0.0:0.0	.	1655	P09848	LPH_HUMAN	P	1655	ENSP00000264162:L1655P	ENSP00000264162:L1655P	L	-	2	0	LCT	136272081	1.000000	0.71417	0.991000	0.47740	0.953000	0.61014	5.828000	0.69307	2.191000	0.70037	0.533000	0.62120	CTC	.	.		0.552	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		G	136555611	A	G	136555611	3	3	11	1	0	0	0	0	1	0	0	0	8702	304	11	2	839	2	LCT	2	136555611	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	81697098	136555611	106643762	19	890										
FMNL2	114793	hgsc.bcm.edu	37	chr2	153399308	153399308	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	cattcaaaagctcaaaggctAtctggatccagctgtaacca	7	11	3	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr2:153399308A>G	ENST00000288670.9	+	3	624	c.257A>G	c.(256-258)tAt>tGt	p.Y86C		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	86	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						CTCAAAGGCTATCTGGATCCA	0.433																																					p.Y86C		Atlas-SNP	.											.	FMNL2	75	.	0			c.A257G						.						152	142	145					2																	153399308		1921	4098	6019	SO:0001583	missense	114793	exon3			AAGGCTATCTGGA	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.257A>G	chr2.hg19:g.153399308A>G	ENSP00000288670:p.Tyr86Cys	69.0	0.0		124.0	38.0	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	hg19	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	A	18.43	3.621326	0.66787	.	.	ENSG00000157827	ENST00000288670	D	0.89123	-2.47	6.02	6.02	0.97574	.	0.054202	0.85682	D	0.000000	D	0.93148	0.7818	M	0.82056	2.57	0.80722	D	1	D	0.63046	0.992	P	0.55999	0.789	D	0.93836	0.7132	10	0.72032	D	0.01	.	15.5272	0.75919	1.0:0.0:0.0:0.0	.	86	Q96PY5-3	.	C	86	ENSP00000288670:Y86C	ENSP00000288670:Y86C	Y	+	2	0	FMNL2	153107554	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.501000	0.60393	2.311000	0.77944	0.533000	0.62120	TAT	.	.		0.433	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		G	153399308	A	G	153399308	3	3	11	1	0	0	0	0	1	0	0	0	5960	449	16	2	267	2	FMNL2	2	153399308	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	16843697	153399308	89800065	20	891										
CYTIP	9595	hgsc.bcm.edu	37	chr2	158272637	158272637	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	agtccatgttttccaaactgGggcaattagctgcatcacct	8	11	1	0	rs374851359		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr2:158272637G>C	ENST00000264192.3	-	8	753	c.632C>G	c.(631-633)cCc>cGc	p.P211R	CYTIP_ENST00000540637.1_Missense_Mutation_p.P105R	NM_004288.4	NP_004279.3	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein	211					regulation of cell adhesion (GO:0030155)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	15						TTCCAAACTGGGGCAATTAGC	0.453																																					p.P211R		Atlas-SNP	.											CYTIP,NS,carcinoma,0,1	CYTIP	45	.	0			c.C632G						.						48	41	43					2																	158272637		2203	4300	6503	SO:0001583	missense	9595	exon8			AAACTGGGGCAAT	L06633	CCDS2204.1	2q11.2	2011-09-08	2008-08-14	2008-08-19	ENSG00000115165	ENSG00000115165			9506	protein-coding gene	gene with protein product	"cytohesin binding protein HE", "cytohesin binder and regulator"	604448	"pleckstrin homology, Sec7 and coiled-coil domains, binding protein"	PSCDBP		18926288, 10343115, 11867758, 20530790, 21562043	Standard	NM_004288		Approved	B3-1, HE, CYBR, CASP, CYTHIP	uc002tzj.1	O60759	OTTHUMG00000154551	ENST00000264192.3:c.632C>G	chr2.hg19:g.158272637G>C	ENSP00000264192:p.Pro211Arg	52.0	0.0		86.0	33.0	NM_004288	B4DWH9|Q15630|Q8NE32	Missense_Mutation	SNP	ENST00000264192.3	hg19	CCDS2204.1	.	.	.	.	.	.	.	.	.	.	G	5.350	0.249932	0.10130	.	.	ENSG00000115165	ENST00000264192;ENST00000540637;ENST00000418920	T;T;T	0.54071	1.94;0.59;1.45	5.71	1.97	0.26223	.	0.520860	0.20892	N	0.083815	T	0.49474	0.1559	M	0.66939	2.045	0.09310	N	1	B	0.24092	0.097	B	0.29598	0.104	T	0.48692	-0.9013	10	0.62326	D	0.03	-0.7162	8.5093	0.33206	0.3091:0.0:0.6909:0.0	.	211	O60759	CYTIP_HUMAN	R	211;105;105	ENSP00000264192:P211R;ENSP00000440801:P105R;ENSP00000394308:P105R	ENSP00000264192:P211R	P	-	2	0	CYTIP	157980883	0.003000	0.15002	0.009000	0.14445	0.005000	0.04900	1.013000	0.29937	0.091000	0.17302	-0.150000	0.13652	CCC	.	.		0.453	CYTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254926.1	NM_004288		C	158272637	G	C	158272637	3	2	11	1	0	0	0	0	1	0	0	0	4209	1232	43	4	451	4	CYTIP	2	158272637	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	4873329	158272637	84926736	21	892										
STAT1	6772	hgsc.bcm.edu	37	chr2	191854348	191854348	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aaagatatcttacttatcaaAtaagactttgactttcaaat	3	6	3	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr2:191854348A>G	ENST00000361099.3	-	12	1477	c.1090T>C	c.(1090-1092)Ttt>Ctt	p.F364L	STAT1_ENST00000392323.2_Missense_Mutation_p.F366L|STAT1_ENST00000409465.1_Missense_Mutation_p.F364L|STAT1_ENST00000392322.3_Missense_Mutation_p.F364L|STAT1_ENST00000540176.1_3'UTR	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	364					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			TACTTATCAAATAAGACTTTG	0.269																																					p.F364L		Atlas-SNP	.											.	STAT1	93	.	0			c.T1090C						.																																			SO:0001583	missense	6772	exon12			TATCAAATAAGAC		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"SH2 domain containing"	11362	protein-coding gene	gene with protein product	"transcription factor ISGF-3 components p91/p84"	600555	"signal transducer and activator of transcription 1, 91kD"			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.1090T>C	chr2.hg19:g.191854348A>G	ENSP00000354394:p.Phe364Leu	398.0	0.0		512.0	184.0	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	hg19	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.017266	0.54576	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323	T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9	5.56	5.56	0.83823	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.147057	0.64402	D	0.000006	T	0.69842	0.3156	M	0.61703	1.905	0.80722	D	1	B;B	0.19073	0.033;0.009	B;B	0.21151	0.027;0.033	T	0.65323	-0.6196	10	0.29301	T	0.29	-24.8303	10.8909	0.46994	0.8597:0.0:0.0:0.1403	.	364;364	P42224-2;P42224	.;STAT1_HUMAN	L	364;364;364;366	ENSP00000354394:F364L;ENSP00000386244:F364L;ENSP00000376136:F364L;ENSP00000376137:F366L	ENSP00000354394:F364L	F	-	1	0	STAT1	191562593	0.998000	0.40836	1.000000	0.80357	0.989000	0.77384	3.798000	0.55522	2.120000	0.65058	0.454000	0.30748	TTT	.	.		0.269	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		G	191854348	A	G	191854348	3	3	11	1	0	0	0	0	1	0	0	0	15279	101	4	2	1222	2	STAT1	2	191854348	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	33581711	191854348	51345025	22	893										
AAMP	14	hgsc.bcm.edu	37	chr2	219134201	219134201	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aacccagccctcttcgttgcCctcttcctcctcttcttcct	3	20	4	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr2:219134201C>T	ENST00000248450.4	-	2	348	c.178G>A	c.(178-180)Ggc>Agc	p.G60S	AAMP_ENST00000444053.1_Missense_Mutation_p.G61S|PNKD_ENST00000273077.4_5'Flank|PNKD_ENST00000248451.3_5'Flank|AAMP_ENST00000420660.1_Missense_Mutation_p.G41S			Q13685	AAMP_HUMAN	angio-associated, migratory cell protein	60					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|positive regulation of endothelial cell migration (GO:0010595)|smooth muscle cell migration (GO:0014909)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(4)|ovary(2)|skin(1)	11		Renal(207;0.0474)		Epithelial(149;7.19e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCTTCGTTGCCCTCTTCCTCC	0.587																																					p.G60S		Atlas-SNP	.											.	AAMP	29	.	0			c.G178A						.						111	105	107					2																	219134201		2203	4300	6503	SO:0001583	missense	14	exon2			CGTTGCCCTCTTC	AB209790	CCDS33378.1	2q	2013-01-10			ENSG00000127837	ENSG00000127837		"WD repeat domain containing"	18	protein-coding gene	gene with protein product		603488				7743515	Standard	XM_005246325		Approved		uc002vhk.3	Q13685	OTTHUMG00000155202	ENST00000248450.4:c.178G>A	chr2.hg19:g.219134201C>T	ENSP00000248450:p.Gly60Ser	106.0	0.0		121.0	41.0	NM_001087	Q8WUJ9|Q96H92	Missense_Mutation	SNP	ENST00000248450.4	hg19	CCDS33378.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.473029	0.63737	.	.	ENSG00000127837	ENST00000248450;ENST00000444053;ENST00000420660;ENST00000447885	T;T;T;T	0.53640	0.62;0.63;0.61;0.87	4.56	4.56	0.56223	.	0.513245	0.20459	N	0.091937	T	0.37571	0.1008	L	0.34521	1.04	0.38698	D	0.952919	B;B;B	0.28378	0.127;0.127;0.209	B;B;B	0.29077	0.039;0.039;0.098	T	0.31586	-0.9938	10	0.33940	T	0.23	-8.7876	13.0252	0.58810	0.0:0.8242:0.1758:0.0	.	61;60;41	C9JEH3;Q13685;C9JG97	.;AAMP_HUMAN;.	S	60;61;41;14	ENSP00000248450:G60S;ENSP00000403343:G61S;ENSP00000416394:G41S;ENSP00000393818:G14S	ENSP00000248450:G60S	G	-	1	0	AAMP	218842445	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.430000	0.52807	2.378000	0.81104	0.655000	0.94253	GGC	.	.		0.587	AAMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338756.1	NM_001087		T	219134201	C	T	219134201	3	4	11	1	0	0	0	0	1	0	0	0	17	623	22	3	1166	3	AAMP	2	219134201	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	27279853	219134201	24065172	23	894										
ACCN4	55515	hgsc.bcm.edu	37	chr2	220396813	220396813	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gctggggttcggggtgtcccCaggcttccagacctttgtgt	15	11	0	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr2:220396813C>T	ENST00000347842.3	+	3	1213	c.1199C>T	c.(1198-1200)cCa>cTa	p.P400L	ASIC4_ENST00000358078.4_Missense_Mutation_p.P400L|ASIC4_ENST00000473709.1_3'UTR	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	400					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										GGGGTGTCCCCAGGCTTCCAG	0.622																																					p.P400L		Atlas-SNP	.											.	.	.	.	0			c.C1199T						.						65	70	69					2																	220396813		2203	4300	6503	SO:0001583	missense	55515	exon3			TGTCCCCAGGCTT	AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"Ion channels / Acid-sensing (proton-gated) ion channels"	21263	protein-coding gene	gene with protein product		606715	"amiloride-sensitive cation channel 4, pituitary", "amiloride-sensitive cation channel family member 4, pituitary"	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1199C>T	chr2.hg19:g.220396813C>T	ENSP00000326627:p.Pro400Leu	114.0	0.0		97.0	37.0	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Missense_Mutation	SNP	ENST00000347842.3	hg19	CCDS2442.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.685527	0.88639	.	.	ENSG00000072182	ENST00000347842;ENST00000358078	T;T	0.66280	-0.2;-0.2	3.8	3.8	0.43715	.	0.131097	0.51477	D	0.000098	D	0.82449	0.5039	M	0.92317	3.295	0.80722	D	1	D;D;D	0.76494	0.994;0.987;0.999	P;D;D	0.67382	0.863;0.94;0.951	D	0.87759	0.2597	10	0.72032	D	0.01	-2.9921	15.8578	0.78994	0.0:1.0:0.0:0.0	.	400;400;400	Q96FT7;Q96FT7-4;Q96FT7-2	ACCN4_HUMAN;.;.	L	400	ENSP00000326627:P400L;ENSP00000350786:P400L	ENSP00000326627:P400L	P	+	2	0	ACCN4	220105057	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	5.884000	0.69729	2.152000	0.67230	0.561000	0.74099	CCA	.	.		0.622	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674		T	220396813	C	T	220396813	3	4	11	1	0	0	0	0	1	0	0	0	131	594	21	3	1209	3	ACCN4	2	220396813	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	1262612	220396813	22802560	24	895										
C2orf85	285093	hgsc.bcm.edu	37	chr2	242814897	242814897	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ggaaggaggcggccagggccTcgtcccagtgggtcacgacg	18	12	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr2:242814897T>A	ENST00000343216.3	+	2	1218	c.1190T>A	c.(1189-1191)cTc>cAc	p.L397H		NM_173821.2	NP_776182.2																					GGCCAGGGCCTCGTCCCAGTG	0.617																																					p.L397H		Atlas-SNP	.											.	.	.	.	0			c.T1190A						.						27	32	31					2																	242814897		2008	4159	6167	SO:0001583	missense	285093	exon2			AGGGCCTCGTCCC																												ENST00000343216.3:c.1190T>A	chr2.hg19:g.242814897T>A	ENSP00000345374:p.Leu397His	96.0	0.0		53.0	15.0	NM_173821		Missense_Mutation	SNP	ENST00000343216.3	hg19	CCDS42843.1	.	.	.	.	.	.	.	.	.	.	.	10.02	1.234841	0.22626	.	.	ENSG00000188011	ENST00000343216	T	0.25579	1.79	2.41	-3.58	0.04597	.	.	.	.	.	T	0.10895	0.0266	N	0.08118	0	0.09310	N	1	D	0.56521	0.976	B	0.43728	0.429	T	0.12477	-1.0546	9	0.62326	D	0.03	-8.4013	2.7914	0.05389	0.1632:0.2019:0.4878:0.1471	.	397	Q14D33	CB085_HUMAN	H	397	ENSP00000345374:L397H	ENSP00000345374:L397H	L	+	2	0	C2orf85	242463570	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.575000	0.02131	-0.847000	0.04168	0.374000	0.22700	CTC	.	.		0.617	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1			A	242814897	T	A	242814897	3	1	11	1	0	0	0	0	1	0	0	0	2202	1551	54	4	1196	4	C2orf85	2	242814897	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	22418084	242814897	384476	25	896										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	55.0	0.0		150.0	54.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	11	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10		41266136	156756294	26	897										
CDCP1	64866	hgsc.bcm.edu	37	chr3	45132884	45132884	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gaccacgccgctccgctcctTaaagaaagtcaggcaggcca	10	15	1	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr3:45132884T>A	ENST00000296129.1	-	7	1908	c.1774A>T	c.(1774-1776)Aag>Tag	p.K592*		NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	592						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		CTCCGCTCCTTAAAGAAAGTC	0.632																																					p.K592X		Atlas-SNP	.											.	CDCP1	61	.	0			c.A1774T						.						34	33	33					3																	45132884		2203	4300	6503	SO:0001587	stop_gained	64866	exon7			GCTCCTTAAAGAA	AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"CD molecules"	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.1774A>T	chr3.hg19:g.45132884T>A	ENSP00000296129:p.Lys592*	87.0	0.0		75.0	19.0	NM_022842	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Nonsense_Mutation	SNP	ENST00000296129.1	hg19	CCDS2727.1	.	.	.	.	.	.	.	.	.	.	T	32	5.167200	0.94768	.	.	ENSG00000163814	ENST00000296129	.	.	.	5.84	3.35	0.38373	.	0.292843	0.36444	N	0.002594	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.4321	0.32764	0.0:0.0651:0.246:0.6889	.	.	.	.	X	592	.	ENSP00000296129:K592X	K	-	1	0	CDCP1	45107888	0.990000	0.36364	0.045000	0.18777	0.189000	0.23516	2.959000	0.49153	0.420000	0.25954	0.454000	0.30748	AAG	.	.		0.632	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842		A	45132884	T	A	45132884	4	1	11	1	0	0	0	0	0	1	0	0	3095	1763	61	4	748	4	CDCP1	3	45132884	Nonsense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	3866748	45132884	152889546	27	898										
ARIH2	10425	hgsc.bcm.edu	37	chr3	49006081	49006081	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gcgctacctcttcagggactAtgtggaggtatggccagcct	13	11	2	0	rs144088007		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr3:49006081A>G	ENST00000356401.4	+	7	992	c.653A>G	c.(652-654)tAt>tGt	p.Y218C	ARIH2_ENST00000490095.1_3'UTR|ARIH2_ENST00000449376.1_Missense_Mutation_p.Y218C	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	218					developmental cell growth (GO:0048588)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organismal development (GO:0007275)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		TTCAGGGACTATGTGGAGGTA	0.507																																					p.Y218C		Atlas-SNP	.											.	ARIH2	32	.	0			c.A653G						.	A	CYS/TYR	1,4405	2.1+/-5.4	0,1,2202	148	144	146		653	5.9	1	3	dbSNP_134	146	0,8600		0,0,4300	no	missense	ARIH2	NM_006321.2	194	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign	218/494	49006081	1,13005	2203	4300	6503	SO:0001583	missense	10425	exon7			GGGACTATGTGGA	AF099149	CCDS2780.1	3p21	2013-10-03	2013-10-03		ENSG00000177479	ENSG00000177479			690	protein-coding gene	gene with protein product	"all-trans retinoic acid inducible RING finger"	605615	"ariadne (Drosophila) homolog 2", "ariadne homolog 2 (Drosophila)"			10422847, 24058416	Standard	XM_005264798		Approved	TRIAD1	uc003cvb.3	O95376	OTTHUMG00000133547	ENST00000356401.4:c.653A>G	chr3.hg19:g.49006081A>G	ENSP00000348769:p.Tyr218Cys	54.0	0.0		41.0	16.0	NM_006321	Q9HBZ6|Q9UEM9	Missense_Mutation	SNP	ENST00000356401.4	hg19	CCDS2780.1	.	.	.	.	.	.	.	.	.	.	A	19.12	3.766000	0.69878	2.27E-4	0.0	ENSG00000177479	ENST00000356401;ENST00000449376;ENST00000444790;ENST00000395481	D;D	0.81579	-1.51;-1.51	5.95	5.95	0.96441	Zinc finger, C6HC-type (2);	0.000000	0.85682	D	0.000000	D	0.90403	0.6996	M	0.83774	2.66	0.80722	D	1	D;D;B	0.76494	0.999;0.999;0.212	D;D;B	0.85130	0.971;0.997;0.236	D	0.91349	0.5103	10	0.62326	D	0.03	.	16.4237	0.83790	1.0:0.0:0.0:0.0	.	225;218;218	B3KMG5;Q53ET9;O95376	.;.;ARI2_HUMAN	C	218;218;217;42	ENSP00000348769:Y218C;ENSP00000403222:Y218C	ENSP00000348769:Y218C	Y	+	2	0	ARIH2	48981085	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	8.932000	0.92897	2.279000	0.76181	0.533000	0.62120	TAT	.	A|1.000;G|0.000		0.507	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257525.1	NM_006321		G	49006081	A	G	49006081	3	3	11	1	0	0	0	0	1	0	0	0	924	449	16	2	671	2	ARIH2	3	49006081	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	3873197	49006081	149016349	28	899										
FLNB	2317	hgsc.bcm.edu	37	chr3	58067391	58067391	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gaaatcattcacccggatgtGgacgagcactcagttatgac	10	10	3	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr3:58067391G>A	ENST00000295956.4	+	4	840	c.675G>A	c.(673-675)gtG>gtA	p.V225V	FLNB_ENST00000358537.3_Silent_p.V225V|FLNB_ENST00000493452.1_Silent_p.V56V|FLNB_ENST00000490882.1_Silent_p.V225V|FLNB_ENST00000429972.2_Silent_p.V225V|FLNB_ENST00000419752.2_Silent_p.V56V|FLNB_ENST00000348383.5_Silent_p.V225V|FLNB_ENST00000357272.4_Silent_p.V225V	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	225	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		ACCCGGATGTGGACGAGCACT	0.498																																					p.V225V		Atlas-SNP	.											.	FLNB	430	.	0			c.G675A						.						148	138	141					3																	58067391		2203	4300	6503	SO:0001819	synonymous_variant	2317	exon4			GGATGTGGACGAG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.675G>A	chr3.hg19:g.58067391G>A		71.0	0.0		124.0	52.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	hg19	CCDS2885.1																																																																																			.	.		0.498	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		A	58067391	G	A	58067391	2	1	11	1	0	0	0	0	0	0	0	1	5942	1335	47	3		3	FLNB	3	58067391	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	9061310	58067391	139955039	29	900										
DCUN1D1	54165	hgsc.bcm.edu	37	chr3	182665421	182665421	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ggcaatggccatttctagatCtgaaatagtaaaaatgaatt	8	5	2	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr3:182665421C>A	ENST00000292782.4	-	5	674		c.e5-1		DCUN1D1_ENST00000469954.1_Splice_Site	NM_020640.2	NP_065691.2	Q96GG9	DCNL1_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 1							ubiquitin ligase complex (GO:0000151)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			ATTTCTAGATCTGAAATAGTA	0.279																																					.		Atlas-SNP	.											.	DCUN1D1	27	.	0			c.521-1G>T						.						42	44	43					3																	182665421		2194	4270	6464	SO:0001630	splice_region_variant	54165	exon6			CTAGATCTGAAAT	AF292100, AK056335	CCDS3240.1	3q26.3	2013-06-10	2013-06-10		ENSG00000043093	ENSG00000043093			18184	protein-coding gene	gene with protein product	"squamous cell carcinoma related oncogene"	605905	"DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)"			10777668, 15988528	Standard	NM_020640		Approved	RP42, SCRO, DCUN1L1, Tes3, SCCRO	uc003fld.1	Q96GG9	OTTHUMG00000158314	ENST00000292782.4:c.521-1G>T	chr3.hg19:g.182665421C>A		374.0	0.0		542.0	156.0	NM_020640	B2RB37|Q7L3G9|Q8TEX7|Q9H6M1|Q9HCT3	Splice_Site	SNP	ENST00000292782.4	hg19	CCDS3240.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153449	0.78114	.	.	ENSG00000043093	ENST00000292782;ENST00000458486;ENST00000469954	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0578	0.93072	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DCUN1D1	184148115	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.391000	0.79828	2.482000	0.83794	0.551000	0.68910	.	.	.		0.279	DCUN1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350658.1	NM_020640	Intron	A	182665421	C	A	182665421	5	1	11	1	0	0	0	0	0	0	1	0	4315	927	32	3	271	3	DCUN1D1	3	182665421	Splice_Site	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	124598030	182665421	15357009	30	901										
GPR78	27201	hgsc.bcm.edu	37	chr4	8589017	8589017	+	Frame_Shift_Del	DEL	C	C	-													0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gcaccagctgctgaagagaaCcccgcgcccagcgtccaccc							TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr4:8589017delC	ENST00000382487.4	+	3	1436	c.1019delC	c.(1018-1020)accfs	p.T340fs	GPR78_ENST00000509216.1_3'UTR	NM_080819.4	NP_543009.2	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	340					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(4)|kidney(4)|large_intestine(1)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	26						CTGAAGAGAACCCCGCGCCCA	0.647																																					p.T340fs		Atlas-Indel,Pindel	.											.	GPR78	58	.	0			c.1018delA						.						45	50	49					4																	8589017		2203	4300	6503	SO:0001589	frameshift_variant	27201	exon3			.	AF411107	CCDS3403.1	4p16.1	2012-08-21			ENSG00000155269	ENSG00000155269		"GPCR / Class A : Orphans"	4528	protein-coding gene	gene with protein product		606921				11574155	Standard	NM_080819		Approved		uc003glk.4	Q96P69	OTTHUMG00000128483	ENST00000382487.4:c.1019delC	chr4.hg19:g.8589017delC	ENSP00000371927:p.Thr340fs	275.0	0.0		239.0	69.0	NM_080819	Q8NGV3	Frame_Shift_Del	DEL	ENST00000382487.4	hg19	CCDS3403.1																																																																																			.	.		0.647	GPR78-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359201.1			-	8589017	C	-	8589017	7	5	11	1	0	1	0	1	0	0	0	0	6718	507	18	0	1029	0	GPR78	4	8589017	Frame_Shift_Del	DEL	C	TCGA-2Y-A9H1-01A-11D-A382-10		8589017	182565259	31	902										
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42457611	42457611	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aagccattaacaaaggcaaaCcagatctaggaaaaaaaacc	6	9	1	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr4:42457611C>A	ENST00000381668.5	-	28	2856	c.2625G>T	c.(2623-2625)tgG>tgT	p.W875C	ATP8A1_ENST00000264449.10_Missense_Mutation_p.W860C	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	875					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	CAAAGGCAAACCAGATCTAGG	0.358																																					p.W875C		Atlas-SNP	.											.	ATP8A1	206	.	0			c.G2625T						.						72	72	72					4																	42457611		2203	4300	6503	SO:0001583	missense	10396	exon28			GGCAAACCAGATC	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.2625G>T	chr4.hg19:g.42457611C>A	ENSP00000371084:p.Trp875Cys	174.0	0.0		245.0	79.0	NM_006095	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	hg19	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.120166	0.77323	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.74209	-0.82;-0.82	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000001	D	0.91385	0.7282	H	0.97103	3.94	0.80722	D	1	D;D;D	0.76494	0.994;0.999;0.999	D;D;D	0.76071	0.945;0.987;0.987	D	0.93860	0.7153	10	0.87932	D	0	.	19.5488	0.95310	0.0:1.0:0.0:0.0	.	860;875;867	Q32M35;Q9Y2Q0;E7EUK4	.;AT8A1_HUMAN;.	C	875;860	ENSP00000371084:W875C;ENSP00000264449:W860C	ENSP00000264449:W860C	W	-	3	0	ATP8A1	42152368	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.839000	0.62810	2.680000	0.91292	0.650000	0.86243	TGG	.	.		0.358	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		A	42457611	C	A	42457611	3	1	11	1	0	0	0	0	1	0	0	0	1192	508	18	3	909	3	ATP8A1	4	42457611	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	33868594	42457611	148696665	32	903										
OCIAD1	54940	hgsc.bcm.edu	37	chr4	48834685	48834685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	agagccgaatgcagaggttcCaagaccaattccccgtaact	9	12	0	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr4:48834685C>T	ENST00000381473.3	+	2	462	c.44C>T	c.(43-45)cCa>cTa	p.P15L	OCIAD1_ENST00000396448.2_Missense_Mutation_p.P15L|OCIAD1_ENST00000509122.1_Missense_Mutation_p.P15L|OCIAD1_ENST00000513391.2_Missense_Mutation_p.P15L|OCIAD1_ENST00000506801.1_Intron|OCIAD1_ENST00000508293.1_Missense_Mutation_p.P15L|OCIAD1_ENST00000264312.7_Missense_Mutation_p.P15L|OCIAD1_ENST00000512981.1_Intron|OCIAD1_ENST00000444354.2_Missense_Mutation_p.P15L|OCIAD1_ENST00000425583.2_Missense_Mutation_p.P15L	NM_001079839.2	NP_001073308.1	Q9NX40	OCAD1_HUMAN	OCIA domain containing 1	15	OCIA.					endosome (GO:0005768)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(2)|large_intestine(2)|lung(2)|prostate(1)|skin(2)	9						GCAGAGGTTCCAAGACCAATT	0.383																																					p.P20L		Atlas-SNP	.											.	OCIAD1	27	.	0			c.C59T						.						142	160	154					4																	48834685		2203	4300	6503	SO:0001583	missense	54940	exon2			AGGTTCCAAGACC	AF324350	CCDS3484.1, CCDS43228.1, CCDS47052.1	4p11	2010-03-19			ENSG00000109180	ENSG00000109180			16074	protein-coding gene	gene with protein product						11162530, 18328549	Standard	NM_017830		Approved	FLJ20455, TPA018, OCIA, Asrij	uc010igk.3	Q9NX40	OTTHUMG00000102095	ENST00000381473.3:c.44C>T	chr4.hg19:g.48834685C>T	ENSP00000370882:p.Pro15Leu	79.0	0.0		77.0	23.0	NM_001168254	C9K030|G8JLN7|Q9BZE8	Missense_Mutation	SNP	ENST00000381473.3	hg19	CCDS3484.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.541031	0.45280	.	.	ENSG00000109180	ENST00000504654;ENST00000509122;ENST00000509664;ENST00000505922;ENST00000514981;ENST00000511662;ENST00000508996;ENST00000507210;ENST00000264312;ENST00000396448;ENST00000512236;ENST00000509164;ENST00000511102;ENST00000381473;ENST00000444354;ENST00000509963;ENST00000425583;ENST00000508293;ENST00000513391	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.46819	0.92;0.95;0.92;0.95;0.95;0.86;0.88;0.93;0.95;0.93;0.86;0.89;0.95;0.89;0.86;0.86	4.13	3.26	0.37387	.	0.832273	0.10462	N	0.671809	T	0.27489	0.0675	N	0.08118	0	0.41011	D	0.985006	B;B;B;B	0.28713	0.22;0.082;0.082;0.213	B;B;B;B	0.25506	0.036;0.023;0.023;0.061	T	0.05484	-1.0882	10	0.36615	T	0.2	-0.9676	9.8208	0.40880	0.0:0.7903:0.2097:0.0	.	15;15;15;15	D6RBN5;Q9NX40-3;Q9NX40-2;Q9NX40	.;.;.;OCAD1_HUMAN	L	15	ENSP00000423381:P15L;ENSP00000422171:P15L;ENSP00000423845:P15L;ENSP00000424252:P15L;ENSP00000420917:P15L;ENSP00000264312:P15L;ENSP00000379725:P15L;ENSP00000426386:P15L;ENSP00000426902:P15L;ENSP00000427389:P15L;ENSP00000370882:P15L;ENSP00000399656:P15L;ENSP00000425633:P15L;ENSP00000416943:P15L;ENSP00000423002:P15L;ENSP00000423909:P15L	ENSP00000264312:P15L	P	+	2	0	OCIAD1	48529442	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.826000	0.39092	1.048000	0.40298	0.655000	0.94253	CCA	.	.		0.383	OCIAD1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361812.3	NM_017830		T	48834685	C	T	48834685	3	4	11	1	0	0	0	0	1	0	0	0	10826	594	21	3	65	3	OCIAD1	4	48834685	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	6377074	48834685	142319591	33	904										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62845399	62845399	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ctttttccgggggctccagaGtgaccgtaacaccatccaca	9	14	0	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr4:62845399G>A	ENST00000514591.1	+	17	3049	c.2720G>A	c.(2719-2721)aGt>aAt	p.S907N	LPHN3_ENST00000512091.2_Missense_Mutation_p.S907N|LPHN3_ENST00000514996.1_Missense_Mutation_p.S907N|LPHN3_ENST00000509896.1_Missense_Mutation_p.S975N|LPHN3_ENST00000506746.1_Missense_Mutation_p.S975N|LPHN3_ENST00000507625.1_Missense_Mutation_p.S975N|LPHN3_ENST00000514157.1_Missense_Mutation_p.S907N|LPHN3_ENST00000545650.1_Missense_Mutation_p.S907N|LPHN3_ENST00000507164.1_Missense_Mutation_p.S975N|LPHN3_ENST00000506700.1_Missense_Mutation_p.S907N|LPHN3_ENST00000504896.1_Missense_Mutation_p.S907N|LPHN3_ENST00000511324.1_Missense_Mutation_p.S975N|LPHN3_ENST00000508693.1_Missense_Mutation_p.S975N|LPHN3_ENST00000508946.1_Missense_Mutation_p.S907N|LPHN3_ENST00000506720.1_Missense_Mutation_p.S975N			Q9HAR2	LPHN3_HUMAN	latrophilin 3	894					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GGGCTCCAGAGTGACCGTAAC	0.488																																					p.S907N		Atlas-SNP	.											.	LPHN3	800	.	0			c.G2720A						.						204	206	205					4																	62845399		2063	4220	6283	SO:0001583	missense	23284	exon15			TCCAGAGTGACCG	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.2720G>A	chr4.hg19:g.62845399G>A	ENSP00000422533:p.Ser907Asn	61.0	0.0		115.0	41.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.718910	0.89205	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.5	5.5	0.81552	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.62417	0.2426	L	0.41710	1.295	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.996	D;D;D	0.79108	0.992;0.992;0.986	T	0.62431	-0.6856	10	0.54805	T	0.06	.	19.0068	0.92854	0.0:0.0:1.0:0.0	.	907;894;907	E9PE04;Q9HAR2;Q9HAR2-2	.;LPHN3_HUMAN;.	N	907;907;975;975;907;907;894;907;975;975;975;907;907;907;975;975;907	ENSP00000423388:S907N;ENSP00000422533:S907N;ENSP00000423787:S975N;ENSP00000425033:S975N;ENSP00000424120:S907N;ENSP00000439831:S907N;ENSP00000421476:S975N;ENSP00000424030:S975N;ENSP00000421372:S975N;ENSP00000425201:S907N;ENSP00000423434:S907N;ENSP00000421627:S907N;ENSP00000420931:S975N;ENSP00000425884:S975N;ENSP00000424258:S907N	ENSP00000280009:S907N	S	+	2	0	LPHN3	62527994	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.808000	0.99193	2.580000	0.87095	0.467000	0.42956	AGT	.	.		0.488	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			A	62845399	G	A	62845399	3	1	11	1	0	0	0	0	1	0	0	0	8926	1029	36	3	2778	3	LPHN3	4	62845399	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	14010714	62845399	128308877	34	905										
STAP1	26228	hgsc.bcm.edu	37	chr4	68442954	68442954	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aaagtggggaagaatggagaGgcttcattcttacagtaaca	12	5	2	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr4:68442954G>A	ENST00000265404.2	+	4	422	c.340G>A	c.(340-342)Ggc>Agc	p.G114S	STAP1_ENST00000396225.1_Missense_Mutation_p.G114S	NM_012108.2	NP_036240.1	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	114	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	12						AGAATGGAGAGGCTTCATTCT	0.363																																					p.G114S		Atlas-SNP	.											.	STAP1	46	.	0			c.G340A						.						85	78	80					4																	68442954		2203	4300	6503	SO:0001583	missense	26228	exon4			TGGAGAGGCTTCA	AB023483	CCDS3515.1	4q13.2	2013-02-14	2007-08-09		ENSG00000035720	ENSG00000035720		"SH2 domain containing"	24133	protein-coding gene	gene with protein product	"BCR downstream signaling 1"	604298				10518561, 10679268	Standard	NM_012108		Approved	STAP-1, BRDG1	uc003hde.4	Q9ULZ2	OTTHUMG00000129304	ENST00000265404.2:c.340G>A	chr4.hg19:g.68442954G>A	ENSP00000265404:p.Gly114Ser	188.0	0.0		339.0	115.0	NM_012108	B2R980	Missense_Mutation	SNP	ENST00000265404.2	hg19	CCDS3515.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.407790	0.83340	.	.	ENSG00000035720	ENST00000265404;ENST00000396225	T;T	0.73897	-0.79;-0.79	5.01	5.01	0.66863	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.85517	0.5715	M	0.77820	2.39	0.50632	D	0.999884	D	0.76494	0.999	D	0.91635	0.999	D	0.86629	0.1884	10	0.72032	D	0.01	-9.8908	14.0103	0.64493	0.0:0.0:1.0:0.0	.	114	Q9ULZ2	STAP1_HUMAN	S	114	ENSP00000265404:G114S;ENSP00000379527:G114S	ENSP00000265404:G114S	G	+	1	0	STAP1	68125549	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.389000	0.44407	2.764000	0.94973	0.655000	0.94253	GGC	.	.		0.363	STAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251434.1	NM_012108		A	68442954	G	A	68442954	3	1	11	1	0	0	0	0	1	0	0	0	15267	1000	35	3	354	3	STAP1	4	68442954	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	5597555	68442954	122711322	35	906										
PRSS12	8492	hgsc.bcm.edu	37	chr4	119204214	119204214	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ctcaaactcctctggtaccaGagtatgataatctccaaccc	5	14	3	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr4:119204214G>T	ENST00000296498.3	-	12	2374	c.2092C>A	c.(2092-2094)Ctg>Atg	p.L698M	PRSS12_ENST00000510903.1_5'UTR	NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	698	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						TCTGGTACCAGAGTATGATAA	0.453																																					p.L698M		Atlas-SNP	.											.	PRSS12	71	.	0			c.C2092A						.						147	155	152					4																	119204214		2203	4300	6503	SO:0001583	missense	8492	exon12			GTACCAGAGTATG	AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"Serine peptidases / Serine peptidases"	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.2092C>A	chr4.hg19:g.119204214G>T	ENSP00000296498:p.Leu698Met	38.0	0.0		71.0	22.0	NM_003619	Q9UP16	Missense_Mutation	SNP	ENST00000296498.3	hg19	CCDS3709.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.970656	0.53614	.	.	ENSG00000164099	ENST00000296498	D	0.89939	-2.59	5.88	1.22	0.21188	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.074425	0.56097	D	0.000039	D	0.88651	0.6494	L	0.34521	1.04	0.38363	D	0.944678	D	0.89917	1.0	D	0.79784	0.993	D	0.86179	0.1605	10	0.62326	D	0.03	.	6.5315	0.22330	0.3732:0.1156:0.5111:0.0	.	698	P56730	NETR_HUMAN	M	698	ENSP00000296498:L698M	ENSP00000296498:L698M	L	-	1	2	PRSS12	119423662	0.305000	0.24481	0.985000	0.45067	0.532000	0.34746	0.672000	0.25187	0.108000	0.17862	0.591000	0.81541	CTG	.	.		0.453	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2			T	119204214	G	T	119204214	3	4	11	1	0	0	0	0	1	0	0	0	12627	933	33	3	543	3	PRSS12	4	119204214	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	50761260	119204214	71950062	36	907										
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154525446	154525446	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gaaactgacattaaaacttcAgagaacacagccgagttcaa	7	9	2	2	rs17030219	byFrequency	TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr4:154525446A>G	ENST00000409663.3	+	25	3331	c.3279A>G	c.(3277-3279)tcA>tcG	p.S1093S	KIAA0922_ENST00000440693.1_Silent_p.S1010S|KIAA0922_ENST00000409959.3_Silent_p.S1094S	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1093						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TTAAAACTTCAGAGAACACAG	0.408																																					p.S1094S		Atlas-SNP	.											.	KIAA0922	214	.	0			c.A3282G						.						51	52	52					4																	154525446		2203	4300	6503	SO:0001819	synonymous_variant	23240	exon25			AACTTCAGAGAAC	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.3279A>G	chr4.hg19:g.154525446A>G		173.0	0.0		368.0	104.0	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	hg19	CCDS3783.2																																																																																			.	A|0.987;C|0.013		0.408	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		G	154525446	A	G	154525446	2	3	11	1	0	0	0	0	0	0	0	1	8210	175	7	2		2	KIAA0922	4	154525446	Silent	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	35321232	154525446	36628830	37	908										
FGB	2244	hgsc.bcm.edu	37	chr4	155487089	155487090	+	Frame_Shift_Ins	INS	-	-	A													0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	agccaaagcagctgccactcINSaaaagaaagtagaaagaaaa							TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr4:155487089_155487090insA	ENST00000302068.4	+	2	307_308	c.244_245insA	c.(244-246)caafs	p.Q82fs	FGB_ENST00000502545.1_3'UTR|FGB_ENST00000509493.1_Intron	NM_005141.4	NP_005132.2	P02675	FIBB_HUMAN	fibrinogen beta chain	82			Missing (in New York-1). {ECO:0000269|PubMed:3156856}.		blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|cellular response to interleukin-1 (GO:0071347)|cellular response to leptin stimulus (GO:0044320)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	chaperone binding (GO:0051087)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(22)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	AGCTGCCACTCAAAAGAAAGTA	0.574																																					p.Q82fs	NSCLC(106;1133 1613 21870 46110 52656)	Pindel	.											.	FGB	71	.	0			c.244_245insA						.																																			SO:0001589	frameshift_variant	2244	exon2			.		CCDS3786.1	4q28	2014-09-17			ENSG00000171564	ENSG00000171564		"Fibrinogen C domain containing", "Endogenous ligands"	3662	protein-coding gene	gene with protein product		134830	"fibrinogen, B beta polypeptide"				Standard	NM_005141		Approved		uc003ioa.4	P02675	OTTHUMG00000150331	ENST00000302068.4:c.248dupA	chr4.hg19:g.155487093_155487093dupA	ENSP00000306099:p.Gln82fs	126.0	0.0		205.0	43.0	NM_005141	A0JLR9|B2R7G3|Q32Q65|Q3KPF2	Frame_Shift_Ins	INS	ENST00000302068.4	hg19	CCDS3786.1																																																																																			.	.		0.574	FGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317595.1	NM_005141		A	155487090	-	A	155487089	7	5	11	1	0	1	1	0	0	0	0	0	5839	827	29	0	250	0	FGB	4	155487089	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H1-01A-11D-A382-10	961643	155487089	35667187	38	909										
NPY2R	4887	hgsc.bcm.edu	37	chr4	156135952	156135953	+	Nonsense_Mutation	DNP	CC	CC	AT													0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tggctgcctctccatgccttCcagcttgccgttgacattga							TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr4:156135952_156135953CC>AT	ENST00000329476.3	+	2	1350_1351	c.861_862CC>AT	c.(859-864)ttCCag>ttATag	p.287_288FQ>L*	NPY2R_ENST00000506608.1_Nonsense_Mutation_p.287_288FQ>L*	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	287					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	TCCATGCCTTCCAGCTTGCCGT	0.52																																					p.F287L|p.Q288X		Atlas-SNP	.											.|NPY2R,NS,carcinoma,0,1	NPY2R	87	.	0			c.C861A|c.C862T						.																																			SO:0001587	stop_gained	4887	exon2			TGCCTTCCAGCTT|GCCTTCCAGCTTG	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"GPCR / Class A : Neuropeptide receptors : Y"	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		Exception_encountered	chr4.hg19:g.156135952_156135953delinsAT	ENSP00000332591:p.F287_Q288delinsL*	49.0	0.0		132.0	37.0	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000329476.3	hg19	CCDS3791.1																																																																																			.	.		0.52	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910		AT	156135953	CC	AT	156135952	4	1	11	1	0	0	0	0	0	1	0	0	10618	854	30	3	863	3	NPY2R	4	156135952	Nonsense_Mutation	DNP	CC	TCGA-2Y-A9H1-01A-11D-A382-10	648863	156135952	35018324	39	910										
VCAN	1462	hgsc.bcm.edu	37	chr5	82837017	82837017	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gtctgatggtcaagctattgCagaccaaagtgaaataatac	9	7	2	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr5:82837017C>A	ENST00000265077.3	+	8	8760	c.8195C>A	c.(8194-8196)gCa>gAa	p.A2732E	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000343200.5_Missense_Mutation_p.A1745E|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2732	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CAAGCTATTGCAGACCAAAGT	0.408																																					p.A2732E		Atlas-SNP	.											.	VCAN	498	.	0			c.C8195A						.						41	39	39					5																	82837017		2203	4300	6503	SO:0001583	missense	1462	exon8			CTATTGCAGACCA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.8195C>A	chr5.hg19:g.82837017C>A	ENSP00000265077:p.Ala2732Glu	30.0	0.0		145.0	35.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.747501	0.89663	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.38401	1.14;1.14	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000005	T	0.60560	0.2278	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.50432	-0.8829	10	0.27785	T	0.31	.	18.6676	0.91497	0.0:1.0:0.0:0.0	.	1745;2732	P13611-2;P13611	.;CSPG2_HUMAN	E	2732;1745	ENSP00000265077:A2732E;ENSP00000340062:A1745E	ENSP00000265077:A2732E	A	+	2	0	VCAN	82872773	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.259000	0.51515	2.941000	0.99782	0.655000	0.94253	GCA	.	.		0.408	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82837017	C	A	82837017	3	1	11	1	0	0	0	0	1	0	0	0	17153	710	25	3	8221	3	VCAN	5	82837017	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10		82837017	98078243	40	911										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128864307	128864307	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	caaaaagaatgatatacattTagagatgtcaacaaactggg	8	5	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr5:128864307T>C	ENST00000274487.4	+	6	1392	c.1247T>C	c.(1246-1248)tTa>tCa	p.L416S	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	416	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.L416*(1)		NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GATATACATTTAGAGATGTCA	0.358																																					p.L416S		Atlas-SNP	.											ADAMTS19,NS,carcinoma,0,1	ADAMTS19	216	.	1	Substitution - Nonsense(1)	lung(1)	c.T1247C						.						95	99	98					5																	128864307		2203	4300	6503	SO:0001583	missense	171019	exon6			TACATTTAGAGAT	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1247T>C	chr5.hg19:g.128864307T>C	ENSP00000274487:p.Leu416Ser	127.0	0.0		352.0	172.0	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	T	5.134	0.210418	0.09757	.	.	ENSG00000145808	ENST00000274487	T	0.64260	-0.09	4.02	2.86	0.33363	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.405885	0.20588	N	0.089414	T	0.40372	0.1114	N	0.14661	0.345	0.36183	D	0.849586	B	0.16166	0.016	B	0.15052	0.012	T	0.33343	-0.9872	9	.	.	.	.	9.9033	0.41362	0.0:0.083:0.0:0.917	.	416	Q8TE59	ATS19_HUMAN	S	416	ENSP00000274487:L416S	.	L	+	2	0	ADAMTS19	128892206	1.000000	0.71417	0.982000	0.44146	0.967000	0.64934	3.795000	0.55499	0.891000	0.36235	0.529000	0.55759	TTA	.	.		0.358	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		C	128864307	T	C	128864307	3	2	11	1	0	0	0	0	1	0	0	0	264	1764	61	2	1269	2	ADAMTS19	5	128864307	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	46027290	128864307	52050953	41	912										
PPP2CA	5515	hgsc.bcm.edu	37	chr5	133541801	133541801	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aacctcttgcacgttggattCttttgtcaggatttctttag	8	8	4	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr5:133541801C>G	ENST00000481195.1	-	2	404	c.124G>C	c.(124-126)Gaa>Caa	p.E42Q	CDKL3_ENST00000609654.1_Missense_Mutation_p.E392Q|CDKL3_ENST00000609383.1_3'UTR|CTD-2410N18.4_ENST00000518409.1_RNA|PPP2CA_ENST00000231504.5_5'UTR|CTD-2410N18.5_ENST00000519718.1_Intron	NM_002715.2	NP_002706.1	P67775	PP2AA_HUMAN	protein phosphatase 2, catalytic subunit, alpha isozyme	42					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|meiotic nuclear division (GO:0007126)|mesoderm development (GO:0007498)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein dephosphorylation (GO:0006470)|protein heterotrimerization (GO:0070208)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of protein autophosphorylation (GO:0031952)|regulation of protein catabolic process (GO:0042176)|regulation of receptor activity (GO:0010469)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein phosphatase type 2A complex (GO:0000159)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|skin(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Vitamin E(DB00163)	ACGTTGGATTCTTTTGTCAGG	0.368																																					p.E42Q		Atlas-SNP	.											.	PPP2CA	29	.	0			c.G124C						.						130	116	121					5																	133541801		2203	4300	6503	SO:0001583	missense	5515	exon2			TGGATTCTTTTGT		CCDS4173.1	5q31.1	2013-01-24	2010-03-05		ENSG00000113575	ENSG00000113575	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9299	protein-coding gene	gene with protein product	"protein phosphatase 2A catalytic subunit, alpha isoform"	176915	"protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform"			8383590	Standard	NM_002715		Approved	PP2Calpha		P67775	OTTHUMG00000129119	ENST00000481195.1:c.124G>C	chr5.hg19:g.133541801C>G	ENSP00000418447:p.Glu42Gln	90.0	0.0		179.0	38.0	NM_002715	P05323|P13197	Missense_Mutation	SNP	ENST00000481195.1	hg19	CCDS4173.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.707532	0.89018	.	.	ENSG00000113575	ENST00000481195;ENST00000523082	T;T	0.08458	3.09;3.09	5.35	4.47	0.54385	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);	0.000000	0.85682	D	0.000000	T	0.26593	0.0650	M	0.65320	2	0.80722	D	1	D;P	0.76494	0.999;0.726	D;B	0.81914	0.995;0.313	T	0.01839	-1.1263	10	0.87932	D	0	-1.0918	15.6497	0.77081	0.1384:0.8616:0.0:0.0	.	392;42	B7Z2C5;P67775	.;PP2AA_HUMAN	Q	42;29	ENSP00000418447:E42Q;ENSP00000428816:E29Q	ENSP00000418447:E42Q	E	-	1	0	PPP2CA	133569700	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.776000	0.85560	1.373000	0.46208	0.591000	0.81541	GAA	.	.		0.368	PPP2CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251165.1	NM_002715		G	133541801	C	G	133541801	3	3	11	1	0	0	0	0	1	0	0	0	12392	922	32	4	829	4	PPP2CA	5	133541801	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	4677494	133541801	47373459	42	913										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140573599	140573599	+	Frame_Shift_Del	DEL	C	C	-													0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aggtcacctactcgctgctgCcgccccaagacccgcacctg							TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr5:140573599delC	ENST00000239446.4	+	1	1658	c.1474delC	c.(1474-1476)ccgfs	p.P493fs		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	493	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCGCTGCTGCCGCCCCAAGA	0.677																																					p.L491fs		Atlas-Indel,Pindel	.											.	PCDHB10	177	.	0			c.1473delG						.						94	108	103					5																	140573599		2203	4297	6500	SO:0001589	frameshift_variant	56126	exon1			.	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1474delC	chr5.hg19:g.140573599delC	ENSP00000239446:p.Pro493fs	135.0	0.0		176.0	36.0	NM_018930	Q96T99	Frame_Shift_Del	DEL	ENST00000239446.4	hg19	CCDS4252.1																																																																																			.	.		0.677	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		-	140573599	C	-	140573599	7	5	11	1	0	1	0	1	0	0	0	0	11544	739	26	0	1476	0	PCDHB10	5	140573599	Frame_Shift_Del	DEL	C	TCGA-2Y-A9H1-01A-11D-A382-10	7031798	140573599	40341661	43	914										
SLC36A3	285641	hgsc.bcm.edu	37	chr5	150678157	150678157	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ccacagatgcctcttaccaaCaagccggcattctttatggc	7	14	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr5:150678157C>A	ENST00000335230.3	-	2	627	c.216G>T	c.(214-216)ttG>ttT	p.L72F	SLC36A3_ENST00000377713.3_Missense_Mutation_p.L72F	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	72						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTCTTACCAACAAGCCGGCAT	0.507																																					p.L72F		Atlas-SNP	.											.	SLC36A3	54	.	0			c.G216T						.						86	73	77					5																	150678157		2203	4300	6503	SO:0001583	missense	285641	exon2			TACCAACAAGCCG	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"Solute carriers"	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.216G>T	chr5.hg19:g.150678157C>A	ENSP00000334750:p.Leu72Phe	62.0	0.0		80.0	37.0	NM_181774	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Missense_Mutation	SNP	ENST00000335230.3	hg19	CCDS4314.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243464	0.39697	.	.	ENSG00000186334	ENST00000335230;ENST00000377713	T;T	0.03152	4.03;4.03	4.62	-3.67	0.04476	.	0.251060	0.31495	N	0.007542	T	0.10937	0.0267	M	0.90369	3.11	0.21762	N	0.999558	P;P	0.48162	0.906;0.853	P;P	0.52823	0.611;0.71	T	0.02132	-1.1208	10	0.72032	D	0.01	.	6.9009	0.24283	0.0:0.5411:0.173:0.2859	.	72;72	Q495N2-3;Q495N2	.;S36A3_HUMAN	F	72	ENSP00000334750:L72F;ENSP00000366942:L72F	ENSP00000334750:L72F	L	-	3	2	SLC36A3	150658350	0.001000	0.12720	0.670000	0.29842	0.385000	0.30292	-1.408000	0.02485	-0.391000	0.07763	-1.152000	0.01820	TTG	.	.		0.507	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774		A	150678157	C	A	150678157	3	1	11	1	0	0	0	0	1	0	0	0	14610	477	17	3	1359	3	SLC36A3	5	150678157	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	10104558	150678157	30237103	44	915										
SOX30	11063	hgsc.bcm.edu	37	chr5	157078733	157078733	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aactcgggcctggaggtggcGccgtctgacgctgtcggcgg	18	12	1	1	rs577314769		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr5:157078733G>A	ENST00000265007.6	-	1	695	c.354C>T	c.(352-354)ggC>ggT	p.G118G	SOX30_ENST00000311371.5_Silent_p.G118G|SOX30_ENST00000519442.1_Intron	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	118					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGGAGGTGGCGCCGTCTGACG	0.701													.|||	1	0.000199681	8e-04	0	5008	,	,		12981	0		0	False		,,,				2504	0				p.G118G	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.C354T						.						4	5	5					5																	157078733		1990	4005	5995	SO:0001819	synonymous_variant	11063	exon1			GGTGGCGCCGTCT	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"SRY (sex determining region Y)-boxes"	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.354C>T	chr5.hg19:g.157078733G>A		62.0	0.0		97.0	12.0	NM_178424	O94995|Q8IYX6	Silent	SNP	ENST00000265007.6	hg19	CCDS4339.1																																																																																			.	.		0.701	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		A	157078733	G	A	157078733	2	1	11	1	0	0	0	0	0	0	0	1	14967	1074	38	1		1	SOX30	5	157078733	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	6400576	157078733	23836527	45	916										
NSD1	64324	hgsc.bcm.edu	37	chr5	176721059	176721059	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	cccccagtaccgctgcctccAgggccaagcactcacctggc	9	20	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr5:176721059A>G	ENST00000439151.2	+	23	6735	c.6690A>G	c.(6688-6690)ccA>ccG	p.P2230P	NSD1_ENST00000347982.4_Silent_p.P1961P|NSD1_ENST00000354179.4_Silent_p.P1961P|NSD1_ENST00000361032.4_Silent_p.P2127P	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2230	Pro-rich.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CGCTGCCTCCAGGGCCAAGCA	0.577			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.P2230P		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.A6690G						.						76	75	75					5																	176721059		2203	4300	6503	SO:0001819	synonymous_variant	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	GCCTCCAGGGCCA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6690A>G	chr5.hg19:g.176721059A>G		44.0	0.0		77.0	25.0	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.		0.577	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		G	176721059	A	G	176721059	2	3	11	1	0	0	0	0	0	0	0	1	10678	175	7	2		2	NSD1	5	176721059	Silent	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	19642326	176721059	4194201	46	917										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327286	16327286	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aggaccggtggccaggcttcCctaaatgcaggccacttttg	12	12	0	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr6:16327286C>G	ENST00000244769.4	-	8	2192	c.1256G>C	c.(1255-1257)gGg>gCg	p.G419A	ATXN1_ENST00000436367.1_Missense_Mutation_p.G419A	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	419					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				GCCAGGCTTCCCTAAATGCAG	0.622																																					p.G419A		Atlas-SNP	.											.	ATXN1	117	.	0			c.G1256C						.						148	160	156					6																	16327286		2203	4300	6503	SO:0001583	missense	6310	exon7			GGCTTCCCTAAAT	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1256G>C	chr6.hg19:g.16327286C>G	ENSP00000244769:p.Gly419Ala	49.0	0.0		53.0	16.0	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.328368	0.60743	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	D;D	0.85171	-1.95;-1.95	4.86	3.93	0.45458	.	0.000000	0.85682	D	0.000000	T	0.72503	0.3468	N	0.24115	0.695	0.58432	D	0.999998	P	0.41978	0.767	P	0.45138	0.471	T	0.75388	-0.3335	10	0.38643	T	0.18	-19.9113	14.5332	0.67942	0.0:0.8528:0.1472:0.0	.	419	P54253	ATX1_HUMAN	A	419	ENSP00000244769:G419A;ENSP00000416360:G419A	ENSP00000244769:G419A	G	-	2	0	ATXN1	16435265	1.000000	0.71417	0.996000	0.52242	0.919000	0.55068	4.302000	0.59092	2.241000	0.73720	0.561000	0.74099	GGG	.	.		0.622	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		G	16327286	C	G	16327286	3	3	11	1	0	0	0	0	1	0	0	0	1209	623	22	4	1199	4	ATXN1	6	16327286	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10		16327286	154787781	47	918										
GNL1	2794	hgsc.bcm.edu	37	chr6	30520392	30520392	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gagccattaccccaggtggcCccagccacatcccgagcaat	9	17	0	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr6:30520392C>T	ENST00000376621.3	-	8	1921	c.951G>A	c.(949-951)ggG>ggA	p.G317G		NM_005275.3	NP_005266.2	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	317	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				cellular response to DNA damage stimulus (GO:0006974)|GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)|signal transduction (GO:0007165)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			cervix(2)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						CCCAGGTGGCCCCAGCCACAT	0.587																																					p.G317G		Atlas-SNP	.											.	GNL1	47	.	0			c.G951A						.						66	66	66					6																	30520392		2203	4300	6503	SO:0001819	synonymous_variant	2794	exon8			GGTGGCCCCAGCC		CCDS4680.1	6p21.3	2010-02-17			ENSG00000204590	ENSG00000204590			4413	protein-coding gene	gene with protein product		143024				8180467	Standard	NM_005275		Approved	HSR1	uc003nqh.3	P36915	OTTHUMG00000031137	ENST00000376621.3:c.951G>A	chr6.hg19:g.30520392C>T		54.0	0.0		59.0	15.0	NM_005275	B0S838|Q96CT5	Silent	SNP	ENST00000376621.3	hg19	CCDS4680.1																																																																																			.	.		0.587	GNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076241.2			T	30520392	C	T	30520392	2	4	11	1	0	0	0	0	0	0	0	1	6543	610	22	3		3	GNL1	6	30520392	Silent	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	14193106	30520392	140594675	48	919										
ZBTB22	9278	hgsc.bcm.edu	37	chr6	33283384	33283384	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gttggccaggagcctgtgagGatgaggatgaagacgacgac	17	7	0	4			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr6:33283384G>A	ENST00000431845.2	-	2	1461	c.1310C>T	c.(1309-1311)tCc>tTc	p.S437F	TAPBP_ENST00000434618.2_5'Flank|ZBTB22_ENST00000418724.1_Missense_Mutation_p.S437F|TAPBP_ENST00000475304.1_5'Flank|TAPBP_ENST00000426633.2_5'Flank|TAPBP_ENST00000456592.2_5'Flank|TAPBP_ENST00000489157.1_5'Flank	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	437					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(3)	21						AGCCTGTGAGGATGAGGATGA	0.647																																					p.S437F		Atlas-SNP	.											.	ZBTB22	48	.	0			c.C1310T						.						112	124	120					6																	33283384		2203	4300	6503	SO:0001583	missense	9278	exon2			TGTGAGGATGAGG	Z97183	CCDS4775.1	6p21.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000236104	ENSG00000236104		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13085	protein-coding gene	gene with protein product		611439	"zinc finger protein 297"	ZNF297			Standard	NM_005453		Approved	BING1, ZNF297A, fruitless, fru, ZBTB22A	uc010juu.3	O15209	OTTHUMG00000031110	ENST00000431845.2:c.1310C>T	chr6.hg19:g.33283384G>A	ENSP00000407545:p.Ser437Phe	124.0	0.0		109.0	38.0	NM_001145338	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Missense_Mutation	SNP	ENST00000431845.2	hg19	CCDS4775.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.161734	0.38119	.	.	ENSG00000236104	ENST00000418724;ENST00000431845	T;T	0.05996	3.36;3.36	3.76	2.88	0.33553	.	.	.	.	.	T	0.06462	0.0166	L	0.40543	1.245	0.41788	D	0.989856	D	0.61080	0.989	D	0.65140	0.932	T	0.22765	-1.0207	9	0.52906	T	0.07	.	6.9586	0.24585	0.1291:0.0:0.8709:0.0	.	437	O15209	ZBT22_HUMAN	F	437	ENSP00000404403:S437F;ENSP00000407545:S437F	ENSP00000404403:S437F	S	-	2	0	ZBTB22	33391362	0.997000	0.39634	0.978000	0.43139	0.870000	0.49936	3.633000	0.54295	0.756000	0.33013	0.393000	0.25936	TCC	.	.		0.647	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2			A	33283384	G	A	33283384	3	1	11	1	0	0	0	0	1	0	0	0	17545	1174	41	3	598	3	ZBTB22	6	33283384	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	2762992	33283384	137831683	49	920										
PI16	221476	hgsc.bcm.edu	37	chr6	36926970	36926970	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	caaggcctacgcacggcagtGcgtgtggggccacaacaagg	15	12	0	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr6:36926970G>A	ENST00000373674.3	+	2	549	c.221G>A	c.(220-222)tGc>tAc	p.C74Y		NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	74	SCP.				negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCACGGCAGTGCGTGTGGGGC	0.667																																					p.C74Y		Atlas-SNP	.											.	PI16	50	.	0			c.G221A						.						23	21	21					6																	36926970		2201	4299	6500	SO:0001583	missense	221476	exon3			GGCAGTGCGTGTG		CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"microseminoprotein, beta-binding protein"		"protease inhibitor 16"				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.221G>A	chr6.hg19:g.36926970G>A	ENSP00000362778:p.Cys74Tyr	135.0	0.0		129.0	44.0	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	hg19	CCDS34440.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.629445	0.87660	.	.	ENSG00000164530	ENST00000536757;ENST00000373674	T	0.16597	2.33	5.29	5.29	0.74685	CAP domain (3);	0.000000	0.85682	D	0.000000	T	0.48537	0.1505	M	0.93241	3.395	0.53688	D	0.999976	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.63812	-0.6552	10	0.87932	D	0	.	18.5179	0.90942	0.0:0.0:1.0:0.0	.	74;74	Q6UXB8;Q6UXB8-2	PI16_HUMAN;.	Y	74	ENSP00000362778:C74Y	ENSP00000362778:C74Y	C	+	2	0	PI16	37034948	1.000000	0.71417	0.793000	0.32043	0.975000	0.68041	7.016000	0.76393	2.462000	0.83206	0.511000	0.50034	TGC	.	.		0.667	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370		A	36926970	G	A	36926970	3	1	11	1	0	0	0	0	1	0	0	0	11878	1319	46	3	227	3	PI16	6	36926970	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	3643586	36926970	134188097	50	921										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42227293	42227293	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gcgcggggagcgcagctggcTctggtacagggtggcgcccg	20	12	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr6:42227293T>C	ENST00000372922.4	-	9	2615	c.2053A>G	c.(2053-2055)Agc>Ggc	p.S685G	TRERF1_ENST00000354325.2_Missense_Mutation_p.S602G|TRERF1_ENST00000541110.1_Missense_Mutation_p.S705G|TRERF1_ENST00000340840.2_Missense_Mutation_p.S602G|TRERF1_ENST00000372917.4_Missense_Mutation_p.S602G	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	685	Interacts with CREBBP.|Pro-rich.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CGCAGCTGGCTCTGGTACAGG	0.706																																					p.S685G		Atlas-SNP	.											.	TRERF1	124	.	0			c.A2053G						.						25	35	31					6																	42227293		2199	4297	6496	SO:0001583	missense	55809	exon9			GCTGGCTCTGGTA	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.2053A>G	chr6.hg19:g.42227293T>C	ENSP00000362013:p.Ser685Gly	166.0	0.0		170.0	54.0	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	hg19	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.240207	0.79912	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.21543	2.01;2.0;2.13;2.0;2.01	5.32	5.32	0.75619	.	0.078338	0.53938	D	0.000042	T	0.26268	0.0641	M	0.80332	2.49	0.43368	D	0.995451	B;B;B;B;P	0.47604	0.421;0.297;0.297;0.421;0.898	B;B;B;B;P	0.47603	0.254;0.129;0.129;0.254;0.551	T	0.12630	-1.0540	10	0.72032	D	0.01	-12.703	15.2762	0.73742	0.0:0.0:0.0:1.0	.	602;705;685;441;441	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	G	705;602;685;602;602	ENSP00000439689:S705G;ENSP00000362008:S602G;ENSP00000362013:S685G;ENSP00000339438:S602G;ENSP00000346285:S602G	ENSP00000339438:S602G	S	-	1	0	TRERF1	42335271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.883000	0.87264	2.000000	0.58554	0.533000	0.62120	AGC	.	.		0.706	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		C	42227293	T	C	42227293	3	2	11	1	0	0	0	0	1	0	0	0	16490	1551	54	2	1589	2	TRERF1	6	42227293	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	5300323	42227293	128887774	51	922										
TIAM2	26230	hgsc.bcm.edu	37	chr6	155450964	155450964	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	agctgctgaggtactcacctAccttagcatcggaaacctcc	8	14	1	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr6:155450964A>C	ENST00000461783.3	+	6	1880	c.607A>C	c.(607-609)Acc>Ccc	p.T203P	TIAM2_ENST00000529824.2_Missense_Mutation_p.T203P|TIAM2_ENST00000318981.5_Missense_Mutation_p.T203P|TIAM2_ENST00000360366.4_Missense_Mutation_p.T203P|TIAM2_ENST00000456144.1_Missense_Mutation_p.T203P|TIAM2_ENST00000367174.2_5'UTR			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	203					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GTACTCACCTACCTTAGCATC	0.627																																					p.T203P		Atlas-SNP	.											.	TIAM2	161	.	0			c.A607C						.						40	38	38					6																	155450964		2203	4300	6503	SO:0001583	missense	26230	exon3			TCACCTACCTTAG		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.607A>C	chr6.hg19:g.155450964A>C	ENSP00000437188:p.Thr203Pro	63.0	0.0		66.0	15.0	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	hg19	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	A	9.247	1.039697	0.19669	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000360366;ENST00000529824	T;T;T;T;T;T	0.06768	3.38;3.26;3.33;3.38;3.4;3.33	4.64	0.821	0.18799	.	0.174023	0.50627	D	0.000107	T	0.02727	0.0082	L	0.60455	1.87	0.80722	D	1	P	0.43169	0.8	B	0.32289	0.143	T	0.48352	-0.9043	10	0.49607	T	0.09	.	8.5141	0.33235	0.6814:0.0:0.3186:0.0	.	203	Q8IVF5	TIAM2_HUMAN	P	203;449;203;203;203;203;203	ENSP00000437188:T203P;ENSP00000434901:T203P;ENSP00000407746:T203P;ENSP00000327315:T203P;ENSP00000353528:T203P;ENSP00000433348:T203P	ENSP00000327315:T203P	T	+	1	0	TIAM2	155492656	0.895000	0.30542	0.133000	0.22050	0.026000	0.11368	2.155000	0.42301	-0.027000	0.13873	0.402000	0.26972	ACC	.	.		0.627	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		C	155450964	A	C	155450964	3	2	11	1	0	0	0	0	1	0	0	0	15906	391	14	5	609	5	TIAM2	6	155450964	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	113223671	155450964	15664103	52	923										
C7orf28A	51622	hgsc.bcm.edu	37	chr7	5965278	5965278	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tgcagaagaggtcaagaaacTttgtgcaacgcagttcaaca	10	8	2	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr7:5965278T>G	ENST00000325974.6	+	15	1475	c.1409T>G	c.(1408-1410)cTt>cGt	p.L470R	CCZ1_ENST00000537980.1_Missense_Mutation_p.L327R|RSPH10B_ENST00000539903.1_3'UTR|CCZ1_ENST00000496860.1_3'UTR|RSPH10B_ENST00000535104.1_5'Flank	NM_015622.5	NP_056437.4	P86791	CCZ1_HUMAN	CCZ1 vacuolar protein trafficking and biogenesis associated homolog (S. cerevisiae)	470						lysosome (GO:0005764)|membrane (GO:0016020)				large_intestine(3)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	6						GTCAAGAAACTTTGTGCAACG	0.403																																					p.L470R		Atlas-SNP	.											.	CCZ1	21	.	0			c.T1409G						.						71	62	65					7																	5965278		2202	4296	6498	SO:0001583	missense	51622	exon15			AGAAACTTTGTGC	AF151801	CCDS34597.1	7p22.1	2014-02-13	2010-06-29	2010-06-29	ENSG00000122674	ENSG00000122674			21691	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 28A"	C7orf28A		10810093, 20305638	Standard	NM_015622		Approved	CGI-43, CCZ1A	uc003spf.3	P86791	OTTHUMG00000155502	ENST00000325974.6:c.1409T>G	chr7.hg19:g.5965278T>G	ENSP00000325681:p.Leu470Arg	851.0	2.0		852.0	247.0	NM_015622	A2RU45|O95766|Q9UG65|Q9Y359	Missense_Mutation	SNP	ENST00000325974.6	hg19	CCDS34597.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.045259	0.75846	.	.	ENSG00000122674	ENST00000325974;ENST00000537980	.	.	.	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.77198	0.4095	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80379	-0.1407	9	0.87932	D	0	-17.7306	13.6665	0.62398	0.0:0.0:0.0:1.0	.	470	P86790	CCZ1L_HUMAN	R	470;327	.	ENSP00000325681:L470R	L	+	2	0	CCZ1	5931804	1.000000	0.71417	0.993000	0.49108	0.872000	0.50106	7.635000	0.83286	1.890000	0.54733	0.450000	0.29827	CTT	.	.		0.403	CCZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340391.1	NM_015622		G	5965278	T	G	5965278	3	3	11	1	0	0	0	0	1	0	0	0	2385	1609	56	5	1467	5	C7orf28A	7	5965278	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10		5965278	153173385	53	924										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48411826	48411826	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ggcctggttcctggagaacaTggctgtgttgaccataagca	13	9	0	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr7:48411826T>C	ENST00000435803.1	+	33	10889	c.10865T>C	c.(10864-10866)aTg>aCg	p.M3622T		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3622					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTGGAGAACATGGCTGTGTTG	0.453																																					p.M3622T		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T10865C						.						179	176	177					7																	48411826		2049	4197	6246	SO:0001583	missense	154664	exon33			AGAACATGGCTGT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.10865T>C	chr7.hg19:g.48411826T>C	ENSP00000411096:p.Met3622Thr	45.0	0.0		122.0	31.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	1.321	-0.599506	0.03744	.	.	ENSG00000179869	ENST00000435803	D	0.83163	-1.69	5.77	-2.36	0.06663	.	1.028390	0.07712	N	0.942177	T	0.67524	0.2902	N	0.15975	0.35	0.09310	N	1	B;B	0.14438	0.002;0.01	B;B	0.15052	0.005;0.012	T	0.55140	-0.8187	10	0.56958	D	0.05	.	7.4768	0.27380	0.0:0.3991:0.123:0.4779	.	1324;3622	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	T	3622	ENSP00000411096:M3622T	ENSP00000411096:M3622T	M	+	2	0	ABCA13	48382372	0.788000	0.28762	0.036000	0.18154	0.312000	0.27988	1.075000	0.30716	-0.302000	0.08869	-0.290000	0.09829	ATG	.	.		0.453	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48411826	T	C	48411826	3	2	11	1	0	0	0	0	1	0	0	0	31	1464	51	2	10824	2	ABCA13	7	48411826	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	42446548	48411826	110726837	54	925										
RNF148	378925	hgsc.bcm.edu	37	chr7	122342165	122342165	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	agaattgggcactctaggtgTaagtctccagacgcaatcta	10	9	3	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr7:122342165T>C	ENST00000434824.1	-	1	856	c.640A>G	c.(640-642)Aca>Gca	p.T214A	CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000313070.7_Intron|RNF148_ENST00000447240.1_Intron|CADPS2_ENST00000334010.7_Intron|RNF133_ENST00000340112.2_5'Flank|CADPS2_ENST00000412584.2_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	214						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						ACTCTAGGTGTAAGTCTCCAG	0.443																																					p.T214A		Atlas-SNP	.											.	RNF148	71	.	0			c.A640G						.						92	88	89					7																	122342165		1962	4155	6117	SO:0001583	missense	378925	exon1			TAGGTGTAAGTCT	BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"RING-type (C3HC4) zinc fingers"	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.640A>G	chr7.hg19:g.122342165T>C	ENSP00000388207:p.Thr214Ala	22.0	0.0		51.0	16.0	NM_198085	A4D0X4|Q8N308	Missense_Mutation	SNP	ENST00000434824.1	hg19	CCDS47692.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.923573	0.00498	.	.	ENSG00000235631	ENST00000434824	T	0.04194	3.68	.	.	.	.	.	.	.	.	T	0.02012	0.0063	N	0.08118	0	0.33361	D	0.572291	B	0.02656	0.0	B	0.01281	0.0	T	0.43261	-0.9402	8	0.16896	T	0.51	.	2.6478	0.04990	0.0:0.4877:0.0:0.5123	.	214	Q8N7C7	RN148_HUMAN	A	214	ENSP00000388207:T214A	ENSP00000388207:T214A	T	-	1	0	RNF148	122129401	0.331000	0.24713	0.527000	0.27925	0.590000	0.36582	0.118000	0.15605	0.103000	0.17682	0.102000	0.15555	ACA	.	.		0.443	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085		C	122342165	T	C	122342165	3	2	11	1	0	0	0	0	1	0	0	0	13464	1638	57	2	281	2	RNF148	7	122342165	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	73930339	122342165	36796498	55	926										
HIPK2	28996	hgsc.bcm.edu	37	chr7	139316421	139316421	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	caataacacagcccagggacCacatgtcaattgcctcacaa	6	14	2	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr7:139316421C>T	ENST00000406875.3	-	3	1248	c.1154G>A	c.(1153-1155)tGg>tAg	p.W385*	HIPK2_ENST00000342645.6_Nonsense_Mutation_p.W385*|HIPK2_ENST00000428878.2_Nonsense_Mutation_p.W385*	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	385	Interaction with DAXX.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					GCCCAGGGACCACATGTCAAT	0.468																																					p.W385X		Atlas-SNP	.											.	HIPK2	192	.	0			c.G1154A						.						104	99	101					7																	139316421		1995	4200	6195	SO:0001587	stop_gained	28996	exon3			AGGGACCACATGT	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1154G>A	chr7.hg19:g.139316421C>T	ENSP00000385571:p.Trp385*	47.0	0.0		93.0	30.0	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Nonsense_Mutation	SNP	ENST00000406875.3	hg19		.	.	.	.	.	.	.	.	.	.	C	38	6.749965	0.97809	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8925	0.92410	0.0:1.0:0.0:0.0	.	.	.	.	X	385	.	ENSP00000343108:W385X	W	-	2	0	HIPK2	138966961	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.516000	0.81772	2.700000	0.92200	0.467000	0.42956	TGG	.	.		0.468	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		T	139316421	C	T	139316421	4	4	11	1	0	0	0	0	0	1	0	0	7126	595	21	3	2494	3	HIPK2	7	139316421	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	16974256	139316421	19822242	56	927										
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150765081	150765081	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	agactgagcgctgggggaagCcccacgtggcctccctctcc	13	16	1	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr7:150765081C>A	ENST00000485713.1	+	8	2127	c.1087C>A	c.(1087-1089)Ccc>Acc	p.P363T	SLC4A2_ENST00000461735.1_Missense_Mutation_p.P349T|SLC4A2_ENST00000392826.2_Missense_Mutation_p.P354T|SLC4A2_ENST00000413384.2_Missense_Mutation_p.P363T|SLC4A2_ENST00000310317.5_Missense_Mutation_p.P281T	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	363					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTGGGGGAAGCCCCACGTGGC	0.657																																					p.P363T		Atlas-SNP	.											.	SLC4A2	98	.	0			c.C1087A						.						32	35	34					7																	150765081		2203	4300	6503	SO:0001583	missense	6522	exon8			GGGAAGCCCCACG		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"Solute carriers"	11028	protein-coding gene	gene with protein product	"anion exchanger 2 type a", "anion exchanger 2 type b1", "anion exchanger 2 type b2"	109280	"erythrocyte membrane protein band 3-like 1", "solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.1087C>A	chr7.hg19:g.150765081C>A	ENSP00000419412:p.Pro363Thr	84.0	0.0		72.0	22.0	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	hg19	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316304	0.81469	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	D;D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22;-2.22	4.4	4.4	0.53042	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	D	0.95522	0.8545	H	0.95950	3.745	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.998	D	0.96998	0.9727	10	0.87932	D	0	.	15.7379	0.77859	0.0:1.0:0.0:0.0	.	354;349;363	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	T	363;363;281;354;349	ENSP00000419412:P363T;ENSP00000405600:P363T;ENSP00000311402:P281T;ENSP00000376571:P354T;ENSP00000419164:P349T	ENSP00000311402:P281T	P	+	1	0	SLC4A2	150396014	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	7.647000	0.83462	2.292000	0.77174	0.462000	0.41574	CCC	.	.		0.657	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		A	150765081	C	A	150765081	3	1	11	1	0	0	0	0	1	0	0	0	14669	739	26	3	1113	3	SLC4A2	7	150765081	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	11448660	150765081	8373582	57	928										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2976077	2976077	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	catgtacccattctgaaatgGgggtggatctggacagttct	12	8	3	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr8:2976077G>A	ENST00000520002.1	-	43	6832	c.6277C>T	c.(6277-6279)Cca>Tca	p.P2093S	CSMD1_ENST00000602723.1_Missense_Mutation_p.P2093S|CSMD1_ENST00000542608.1_Missense_Mutation_p.P2092S|CSMD1_ENST00000400186.3_Missense_Mutation_p.P2093S|CSMD1_ENST00000537824.1_Missense_Mutation_p.P2092S|CSMD1_ENST00000602557.1_Missense_Mutation_p.P2093S			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2093	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TTCTGAAATGGGGGTGGATCT	0.408																																					p.P2092S		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C6274T						.						125	121	122					8																	2976077		1957	4137	6094	SO:0001583	missense	64478	exon42			GAAATGGGGGTGG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.6277C>T	chr8.hg19:g.2976077G>A	ENSP00000430733:p.Pro2093Ser	128.0	0.0		79.0	39.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.95|19.95	3.921259|3.921259	0.73213|0.73213	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T|T;T;T;T	0.67865|0.63913	-0.29|-0.07;-0.07;-0.07;-0.07	5.03|5.03	3.19|3.19	0.36642|0.36642	.|Complement control module (2);Sushi/SCR/CCP (3);	0.142749|0.142749	0.47455|0.47455	D|N	0.000228|0.000228	T|T	0.69878|0.69878	0.3160|0.3160	L|L	0.47016|0.47016	1.485|1.485	0.80722|0.80722	D|D	1|1	.|B;P;P	.|0.38250	.|0.012;0.615;0.624	.|B;P;B	.|0.62014	.|0.037;0.897;0.341	T|T	0.62882|0.62882	-0.6760|-0.6760	8|10	0.33141|0.24483	T|T	0.24|0.36	.|.	10.1054|10.1054	0.42530|0.42530	0.0758:0.143:0.7811:0.0|0.0758:0.143:0.7811:0.0	.|.	.|2093;2093;2092	.|E5RIG2;Q96PZ7;F5H2I8	.|.;CSMD1_HUMAN;.	L|S	1572|2093;2093;1954;2092;2092	ENSP00000334828:P1572L|ENSP00000383047:P2093S;ENSP00000430733:P2093S;ENSP00000441462:P2092S;ENSP00000446243:P2092S	ENSP00000334828:P1572L|ENSP00000320445:P1954S	P|P	-|-	2|1	0|0	CSMD1|CSMD1	2963484|2963484	1.000000|1.000000	0.71417|0.71417	0.033000|0.033000	0.17914|0.17914	0.964000|0.964000	0.63967|0.63967	4.546000|4.546000	0.60705|0.60705	0.593000|0.593000	0.29745|0.29745	0.563000|0.563000	0.77884|0.77884	CCC|CCA	.	.		0.408	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2976077	G	A	2976077	3	1	11	1	0	0	0	0	1	0	0	0	3946	1232	43	3	4536	3	CSMD1	8	2976077	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10		2976077	143387945	58	929										
GFRA2	2675	hgsc.bcm.edu	37	chr8	21608422	21608422	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	agcatccaggcaatggttgcTcttggcgctgaccaccgggt	13	12	1	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr8:21608422T>C	ENST00000524240.1	-	4	1122	c.472A>G	c.(472-474)Agc>Ggc	p.S158G	GFRA2_ENST00000400782.4_Missense_Mutation_p.S53G|GFRA2_ENST00000518077.1_Missense_Mutation_p.S25G|GFRA2_ENST00000517328.1_Missense_Mutation_p.S158G	NM_001495.4	NP_001486.4	O00451	GFRA2_HUMAN	GDNF family receptor alpha 2	158					negative regulation of protein autophosphorylation (GO:0031953)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|prostate(1)|skin(1)	7				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		CAATGGTTGCTCTTGGCGCTG	0.602																																					p.S158G		Atlas-SNP	.											.	GFRA2	23	.	0			c.A472G						.						25	28	27					8																	21608422		2192	4284	6476	SO:0001583	missense	2675	exon4			GGTTGCTCTTGGC	AF002700	CCDS47816.1, CCDS55207.1	8p21.3	2008-05-02			ENSG00000168546	ENSG00000168546			4244	protein-coding gene	gene with protein product		601956				9177201	Standard	NM_001165038		Approved	RETL2, GDNFRB, NTNRA, TRNR2	uc003wzu.1	O00451	OTTHUMG00000163897	ENST00000524240.1:c.472A>G	chr8.hg19:g.21608422T>C	ENSP00000428518:p.Ser158Gly	111.0	0.0		81.0	50.0	NM_001495	E9PD47|O15316|O15328|Q58J92|Q6GTR9|Q7Z5C2	Missense_Mutation	SNP	ENST00000524240.1	hg19	CCDS47816.1	.	.	.	.	.	.	.	.	.	.	T	7.686	0.690104	0.15039	.	.	ENSG00000168546	ENST00000524240;ENST00000400782;ENST00000517328;ENST00000518077;ENST00000517892;ENST00000522071;ENST00000520826	T;T;T;T;T;T	0.44482	1.9;1.49;1.9;1.51;1.49;0.92	4.76	4.76	0.60689	.	0.252628	0.48286	D	0.000185	T	0.40040	0.1101	N	0.14661	0.345	0.32595	N	0.526654	D;D;B	0.62365	0.991;0.982;0.017	P;D;B	0.67548	0.64;0.952;0.007	T	0.38972	-0.9636	10	0.13470	T	0.59	-36.1787	10.173	0.42922	0.0:0.0:0.1674:0.8326	.	25;53;158	O00451-2;E9PD47;O00451	.;.;GFRA2_HUMAN	G	158;53;158;25;53;158;150	ENSP00000428518:S158G;ENSP00000383592:S53G;ENSP00000429445:S158G;ENSP00000429206:S25G;ENSP00000429979:S53G;ENSP00000428721:S158G	ENSP00000383592:S53G	S	-	1	0	GFRA2	21652702	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	2.972000	0.49256	1.784000	0.52394	0.260000	0.18958	AGC	.	.		0.602	GFRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376254.3	NM_001495		C	21608422	T	C	21608422	3	2	11	1	0	0	0	0	1	0	0	0	6356	1551	54	2	946	2	GFRA2	8	21608422	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	18632345	21608422	124755600	59	930										
DUSP26	78986	hgsc.bcm.edu	37	chr8	33449660	33449660	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	acgagggtaaggtggtggtaCagcatgaggtaggccagtac	17	6	0	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr8:33449660C>T	ENST00000256261.4	-	4	1024	c.507G>A	c.(505-507)ctG>ctA	p.L169L	DUSP26_ENST00000523956.1_Silent_p.L169L	NM_024025.1	NP_076930.1	Q9BV47	DUS26_HUMAN	dual specificity phosphatase 26 (putative)	169	Tyrosine-protein phosphatase.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell adhesion (GO:0045785)|positive regulation of peptidyl-serine dephosphorylation (GO:1902310)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	p53 binding (GO:0002039)|phosphoprotein phosphatase activity (GO:0004721)|phosphoserine phosphatase activity (GO:0004647)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA polymerase II activating transcription factor binding (GO:0001102)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)	15				KIRC - Kidney renal clear cell carcinoma(67;0.0918)|Kidney(114;0.111)		GGTGGTGGTACAGCATGAGGT	0.597																																					p.L169L		Atlas-SNP	.											.	DUSP26	42	.	0			c.G507A						.						110	87	95					8																	33449660		2203	4300	6503	SO:0001819	synonymous_variant	78986	exon4			GTGGTACAGCATG	AY902194	CCDS6092.1	8p12	2014-09-09			ENSG00000133878	ENSG00000133878		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	28161	protein-coding gene	gene with protein product							Standard	NM_024025		Approved	MGC1136, DUSP24	uc003xjp.3	Q9BV47	OTTHUMG00000163961	ENST00000256261.4:c.507G>A	chr8.hg19:g.33449660C>T		120.0	0.0		75.0	32.0	NM_024025	D3DSV8|Q9BTW0	Silent	SNP	ENST00000256261.4	hg19	CCDS6092.1																																																																																			.	.		0.597	DUSP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376564.1	NM_024025		T	33449660	C	T	33449660	2	4	11	1	0	0	0	0	0	0	0	1	4825	465	17	3		3	DUSP26	8	33449660	Silent	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	11841238	33449660	112914362	60	931										
PREX2	80243	hgsc.bcm.edu	37	chr8	69031729	69031729	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aggacaagatacatagttgcCttgagcatcttttcagccag	9	9	2	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr8:69031729C>A	ENST00000288368.4	+	28	3761	c.3484C>A	c.(3484-3486)Ctt>Att	p.L1162I		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1162					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						ACATAGTTGCCTTGAGCATCT	0.393																																					p.L1162I		Atlas-SNP	.											.	PREX2	614	.	0			c.C3484A						.						206	187	193					8																	69031729		2203	4300	6503	SO:0001583	missense	80243	exon28			AGTTGCCTTGAGC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3484C>A	chr8.hg19:g.69031729C>A	ENSP00000288368:p.Leu1162Ile	40.0	0.0		212.0	84.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190982	0.78789	.	.	ENSG00000046889	ENST00000288368;ENST00000396539	T	0.39592	1.07	5.39	3.21	0.36854	.	0.000000	0.64402	D	0.000004	T	0.46210	0.1381	M	0.62723	1.935	0.50171	D	0.999856	P	0.46142	0.873	P	0.51701	0.677	T	0.47446	-0.9117	10	0.72032	D	0.01	.	4.4749	0.11731	0.0:0.5573:0.0:0.4426	.	1162	Q70Z35	PREX2_HUMAN	I	1162;1168	ENSP00000288368:L1162I	ENSP00000288368:L1162I	L	+	1	0	PREX2	69194283	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	3.517000	0.53443	1.415000	0.47037	0.650000	0.86243	CTT	.	.		0.393	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		A	69031729	C	A	69031729	3	1	11	1	0	0	0	0	1	0	0	0	12489	681	24	3	3823	3	PREX2	8	69031729	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	35582069	69031729	77332293	61	932										
POP1	10940	hgsc.bcm.edu	37	chr8	99170330	99170330	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tctcctaggctttgtgactcAgggagatttttccatggctg	11	9	2	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr8:99170330A>T	ENST00000401707.2	+	16	2987	c.2906A>T	c.(2905-2907)cAg>cTg	p.Q969L	POP1_ENST00000349693.3_Missense_Mutation_p.Q969L	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	969					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			TTTGTGACTCAGGGAGATTTT	0.592																																					p.Q969L		Atlas-SNP	.											.	POP1	85	.	0			c.A2906T						.						95	99	98					8																	99170330		2203	4300	6503	SO:0001583	missense	10940	exon16			TGACTCAGGGAGA	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"processing of precursors 1"	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.2906A>T	chr8.hg19:g.99170330A>T	ENSP00000385787:p.Gln969Leu	37.0	0.0		115.0	43.0	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	hg19	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.844303	0.71488	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.15952	2.38;2.38	5.67	4.52	0.55395	.	0.259831	0.39274	N	0.001417	T	0.25865	0.0630	M	0.67953	2.075	0.38672	D	0.95233	D	0.54964	0.969	P	0.52159	0.691	T	0.09037	-1.0693	10	0.27082	T	0.32	-0.1377	8.1131	0.30926	0.8311:0.0:0.1689:0.0	.	969	Q99575	POP1_HUMAN	L	969	ENSP00000385787:Q969L;ENSP00000339529:Q969L	ENSP00000339529:Q969L	Q	+	2	0	POP1	99239506	1.000000	0.71417	0.993000	0.49108	0.957000	0.61999	4.859000	0.62954	0.979000	0.38497	0.455000	0.32223	CAG	.	.		0.592	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		T	99170330	A	T	99170330	3	4	11	1	0	0	0	0	1	0	0	0	12260	188	7	4	2964	4	POP1	8	99170330	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	30138601	99170330	47193692	62	933										
NIPAL2	79815	hgsc.bcm.edu	37	chr8	99224705	99224705	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tttatagaaatacaggagaaTgcagaaaattaatatttcta	6	3	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr8:99224705T>C	ENST00000341166.3	-	6	838	c.583A>G	c.(583-585)Att>Gtt	p.I195V	NIPAL2_ENST00000430223.2_Missense_Mutation_p.I195V|NIPAL2_ENST00000520545.1_5'UTR	NM_024759.1	NP_079035.1	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	195						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(3)|kidney(1)|large_intestine(2)|lung(5)|stomach(1)	12						TACAGGAGAATGCAGAAAATT	0.299																																					p.I195V		Atlas-SNP	.											.	NIPAL2	23	.	0			c.A583G						.						50	53	52					8																	99224705		2203	4297	6500	SO:0001583	missense	79815	exon6			GGAGAATGCAGAA	AK024017	CCDS6278.1	8q22.2	2009-03-24		2009-03-24	ENSG00000104361	ENSG00000104361			25854	protein-coding gene	gene with protein product				NPAL2		14702039	Standard	NM_024759		Approved	FLJ13955	uc003yil.1	Q9H841	OTTHUMG00000164668	ENST00000341166.3:c.583A>G	chr8.hg19:g.99224705T>C	ENSP00000339256:p.Ile195Val	21.0	0.0		185.0	23.0	NM_024759	A2RTY8	Missense_Mutation	SNP	ENST00000341166.3	hg19	CCDS6278.1	.	.	.	.	.	.	.	.	.	.	T	6.616	0.482133	0.12581	.	.	ENSG00000104361	ENST00000430223;ENST00000341166	D;D	0.90504	-2.68;-2.68	5.56	0.586	0.17434	.	0.289069	0.32703	N	0.005752	T	0.76814	0.4040	N	0.16130	0.375	0.37300	D	0.90866	B;B	0.06786	0.0;0.001	B;B	0.12156	0.006;0.007	T	0.63001	-0.6734	10	0.07813	T	0.8	-7.903	8.1431	0.31095	0.0:0.3175:0.0:0.6825	.	195;195	A2RTY8;Q9H841	.;NPAL2_HUMAN	V	195	ENSP00000407087:I195V;ENSP00000339256:I195V	ENSP00000339256:I195V	I	-	1	0	NIPAL2	99293881	0.996000	0.38824	0.951000	0.38953	0.992000	0.81027	0.419000	0.21247	0.078000	0.16900	0.533000	0.62120	ATT	.	.		0.299	NIPAL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379677.1	NM_024759		C	99224705	T	C	99224705	3	2	11	1	0	0	0	0	1	0	0	0	10434	1464	51	2	551	2	NIPAL2	8	99224705	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	54375	99224705	47139317	63	934										
ODF1	4956	hgsc.bcm.edu	37	chr8	103572893	103572893	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tgcaaagagttcagcttgccGccctgtgtggatgagaagga	14	8	1	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr8:103572893G>A	ENST00000285402.3	+	2	690	c.534G>A	c.(532-534)ccG>ccA	p.P178P	ODF1_ENST00000518835.1_Intron	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	178					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.P178P(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			TCAGCTTGCCGCCCTGTGTGG	0.517																																					p.P178P		Atlas-SNP	.											ODF1,NS,carcinoma,0,1	ODF1	55	.	1	Substitution - coding silent(1)	endometrium(1)	c.G534A						.						130	99	110					8																	103572893		2203	4300	6503	SO:0001819	synonymous_variant	4956	exon2			CTTGCCGCCCTGT	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"Heat shock proteins / HSPB"	8113	protein-coding gene	gene with protein product	"cancer/testis antigen 133"	182878	"outer dense fibre of sperm tails 1"			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.534G>A	chr8.hg19:g.103572893G>A		78.0	0.0		304.0	33.0	NM_024410	Q3SX72	Silent	SNP	ENST00000285402.3	hg19	CCDS6293.1																																																																																			.	.		0.517	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1			A	103572893	G	A	103572893	2	1	11	1	0	0	0	0	0	0	0	1	10835	1074	38	1		1	ODF1	8	103572893	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	4348188	103572893	42791129	64	935										
C8orf85	441376	hgsc.bcm.edu	37	chr8	117950586	117950586	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	cccacctcgtcccgcgtgcgActtcttcggggacggcagga	13	16	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr8:117950586A>G	ENST00000378279.3	+	1	149	c.104A>G	c.(103-105)gAc>gGc	p.D35G		NM_001025357.2	NP_001020528.1	Q4LEZ3	AARD_HUMAN	alanine and arginine rich domain containing protein	35					lung development (GO:0030324)												CCCGCGTGCGACTTCTTCGGG	0.692																																					p.D35G		Atlas-SNP	.											.	.	.	.	0			c.A104G						.						23	24	23					8																	117950586		2203	4300	6503	SO:0001583	missense	441376	exon1			CGTGCGACTTCTT	AB181519, BC140924	CCDS34935.1	8q24.11	2012-04-19	2012-04-19	2012-04-19	ENSG00000205002	ENSG00000205002			33842	protein-coding gene	gene with protein product	"Alanine and arginine-rich domain-containing protein"		"chromosome 8 open reading frame 85"	C8orf85			Standard	NM_001025357		Approved	LOC441376	uc003yof.3	Q4LEZ3	OTTHUMG00000164961	ENST00000378279.3:c.104A>G	chr8.hg19:g.117950586A>G	ENSP00000367528:p.Asp35Gly	130.0	0.0		586.0	219.0	NM_001025357	A5PKU8	Missense_Mutation	SNP	ENST00000378279.3	hg19	CCDS34935.1	.	.	.	.	.	.	.	.	.	.	A	0.171	-1.071249	0.01918	.	.	ENSG00000205002	ENST00000378279	T	0.28895	1.59	3.48	1.47	0.22746	.	0.863989	0.09657	N	0.772909	T	0.09158	0.0226	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37731	-0.9693	10	0.07482	T	0.82	0.0097	3.8652	0.09013	0.1301:0.0:0.6361:0.2338	.	35	Q4LEZ3	AARD_HUMAN	G	35	ENSP00000367528:D35G	ENSP00000367528:D35G	D	+	2	0	C8orf85	118019767	0.007000	0.16637	0.011000	0.14972	0.001000	0.01503	0.761000	0.26489	0.786000	0.33708	-0.251000	0.11542	GAC	.	.		0.692	AARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381195.1	NM_001025357		G	117950586	A	G	117950586	3	3	11	1	0	0	0	0	1	0	0	0	2443	275	10	2	106	2	C8orf85	8	117950586	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	14377693	117950586	28413436	65	936										
PIGO	84720	hgsc.bcm.edu	37	chr9	35092036	35092036	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ctcagggcatatgcaccattGtgccgtggggggtttgttgt	15	8	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr9:35092036G>A	ENST00000378617.3	-	7	2242	c.1848C>T	c.(1846-1848)caC>caT	p.H616H	PIGO_ENST00000341666.3_Silent_p.H616H|PIGO_ENST00000361778.2_Intron|PIGO_ENST00000298004.5_Intron	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	616					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			ATGCACCATTGTGCCGTGGGG	0.542																																					p.H616H		Atlas-SNP	.											.	PIGO	86	.	0			c.C1848T						.						61	52	55					9																	35092036		2203	4300	6503	SO:0001819	synonymous_variant	84720	exon7			ACCATTGTGCCGT	AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"Phosphatidylinositol glycan anchor biosynthesis"	23215	protein-coding gene	gene with protein product		614730	"phosphatidylinositol glycan, class O"			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.1848C>T	chr9.hg19:g.35092036G>A		91.0	0.0		109.0	35.0	NM_032634	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Silent	SNP	ENST00000378617.3	hg19	CCDS6575.1																																																																																			.	.		0.542	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	NM_032634		A	35092036	G	A	35092036	2	1	11	1	0	0	0	0	0	0	0	1	11903	1368	48	3		3	PIGO	9	35092036	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10		35092036	106121395	66	937										
ALDH1B1	219	hgsc.bcm.edu	37	chr9	38397141	38397141	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tcacccaggcactccaggccGggaccgtgtgggtaaacacc	12	15	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr9:38397141G>C	ENST00000377698.3	+	2	1549	c.1396G>C	c.(1396-1398)Ggg>Cgg	p.G466R		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	466					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)			NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		ACTCCAGGCCGGGACCGTGTG	0.592																																					p.G466R		Atlas-SNP	.											.	ALDH1B1	50	.	0			c.G1396C						.						65	63	64					9																	38397141		2203	4300	6503	SO:0001583	missense	219	exon2			CAGGCCGGGACCG	M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"Aldehyde dehydrogenases"	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.1396G>C	chr9.hg19:g.38397141G>C	ENSP00000366927:p.Gly466Arg	83.0	0.0		107.0	34.0	NM_000692	B2R8F0|Q8WX76|Q9BV45	Missense_Mutation	SNP	ENST00000377698.3	hg19	CCDS6615.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.843424	0.71488	.	.	ENSG00000137124	ENST00000377698;ENST00000540055	D	0.87029	-2.2	5.84	4.95	0.65309	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.64402	D	0.000004	D	0.96144	0.8743	H	0.98883	4.36	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97148	0.9829	10	0.87932	D	0	.	12.9396	0.58335	0.0785:0.0:0.9215:0.0	.	466	P30837	AL1B1_HUMAN	R	466;167	ENSP00000366927:G466R	ENSP00000366927:G466R	G	+	1	0	ALDH1B1	38387141	1.000000	0.71417	0.287000	0.24848	0.972000	0.66771	9.487000	0.97945	1.468000	0.48064	0.650000	0.86243	GGG	.	.		0.592	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1			C	38397141	G	C	38397141	3	2	11	1	0	0	0	0	1	0	0	0	493	1116	39	4	1398	4	ALDH1B1	9	38397141	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	3305105	38397141	102816290	67	938										
WNK2	65268	hgsc.bcm.edu	37	chr9	96018645	96018645	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gtccctccagcagcacttccCggatccggccatgagcttcg	10	17	0	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr9:96018645C>A	ENST00000297954.4	+	9	2099	c.2099C>A	c.(2098-2100)cCg>cAg	p.P700Q	WNK2_ENST00000395475.2_Intron|WNK2_ENST00000395477.2_Missense_Mutation_p.P700Q|WNK2_ENST00000427277.2_Missense_Mutation_p.P312Q|WNK2_ENST00000349097.3_Missense_Mutation_p.P312Q|WNK2_ENST00000356055.3_5'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	700					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CAGCACTTCCCGGATCCGGCC	0.736																																					p.P700Q		Atlas-SNP	.											.	WNK2	277	.	0			c.C2099A						.						8	9	9					9																	96018645		2171	4251	6422	SO:0001583	missense	65268	exon9			ACTTCCCGGATCC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.2099C>A	chr9.hg19:g.96018645C>A	ENSP00000297954:p.Pro700Gln	79.0	0.0		74.0	20.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	hg19		.	.	.	.	.	.	.	.	.	.	C	5.333	0.246830	0.10130	.	.	ENSG00000165238	ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277	T;T;T;T	0.68624	-0.34;-0.31;0.32;0.3	4.21	3.3	0.37823	.	0.426866	0.23139	N	0.051481	T	0.60599	0.2281	M	0.65975	2.015	0.80722	D	1	B;B;B;B	0.31153	0.31;0.207;0.31;0.207	B;B;B;B	0.31290	0.127;0.041;0.127;0.06	T	0.54268	-0.8319	10	0.11182	T	0.66	.	12.2786	0.54751	0.3239:0.6761:0.0:0.0	.	700;303;700;700	Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1	.;.;.;WNK2_HUMAN	Q	700;700;312;312	ENSP00000297954:P700Q;ENSP00000378860:P700Q;ENSP00000297876:P312Q;ENSP00000411181:P312Q	ENSP00000297954:P700Q	P	+	2	0	WNK2	95058466	0.941000	0.31946	0.729000	0.30791	0.002000	0.02628	1.830000	0.39131	0.979000	0.38497	-0.521000	0.04368	CCG	.	.		0.736	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		A	96018645	C	A	96018645	3	1	11	1	0	0	0	0	1	0	0	0	17393	652	23	1	2133	1	WNK2	9	96018645	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	57621504	96018645	45194786	68	939										
ERP44	23071	hgsc.bcm.edu	37	chr9	102782996	102782996	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ttttgctcaaaatatccaatGatatttcttttgctgcgctg	6	8	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr9:102782996G>T	ENST00000262455.6	-	6	688	c.489C>A	c.(487-489)atC>atA	p.I163I		NM_015051.1	NP_055866.1	Q9BS26	ERP44_HUMAN	endoplasmic reticulum protein 44	163					cell redox homeostasis (GO:0045454)|glycoprotein metabolic process (GO:0009100)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(2)	19						AATATCCAATGATATTTCTTT	0.328																																					p.I163I		Atlas-SNP	.											.	ERP44	38	.	0			c.C489A						.						80	73	75					9																	102782996		2202	4300	6502	SO:0001819	synonymous_variant	23071	exon6			TCCAATGATATTT	AB011145	CCDS35082.1	9q22.33	2011-10-19	2009-02-23	2009-02-23	ENSG00000023318	ENSG00000023318		"Protein disulfide isomerases"	18311	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 10"	609170	"thioredoxin domain containing 4 (endoplasmic reticulum)"	TXNDC4		11847130	Standard	NM_015051		Approved	KIAA0573, PDIA10	uc004bam.3	Q9BS26	OTTHUMG00000020363	ENST00000262455.6:c.489C>A	chr9.hg19:g.102782996G>T		35.0	0.0		78.0	19.0	NM_015051	O60319|Q4VXC1|Q5VWZ7|Q6UW14|Q8WX67	Silent	SNP	ENST00000262455.6	hg19	CCDS35082.1																																																																																			.	.		0.328	ERP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053402.1	XM_088476		T	102782996	G	T	102782996	2	4	11	1	0	0	0	0	0	0	0	1	5245	1280	45	3		3	ERP44	9	102782996	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	6764351	102782996	38430435	69	940										
ENG	2022	hgsc.bcm.edu	37	chr9	130588910	130588910	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aaggatggcagctctgtggtGttgacccccgggggctcttg	16	10	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr9:130588910G>T	ENST00000373203.4	-	4	802	c.402C>A	c.(400-402)aaC>aaA	p.N134K	ENG_ENST00000344849.3_Missense_Mutation_p.N134K|ENG_ENST00000480266.1_5'Flank	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	134	Required for interaction with EGL.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						GCTCTGTGGTGTTGACCCCCG	0.617									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia																												p.N134K		Atlas-SNP	.											.	ENG	44	.	0			c.C402A						.						62	60	61					9																	130588910		2203	4300	6503	SO:0001583	missense	2022	exon4	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	TGTGGTGTTGACC	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"CD molecules"	3349	protein-coding gene	gene with protein product		131195	"Osler-Rendu-Weber syndrome 1"	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.402C>A	chr9.hg19:g.130588910G>T	ENSP00000362299:p.Asn134Lys	104.0	0.0		87.0	5.0	NM_001114753	Q14248|Q14926|Q5T9C0	Missense_Mutation	SNP	ENST00000373203.4	hg19	CCDS48029.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.635369	0.47049	.	.	ENSG00000106991	ENST00000373203;ENST00000344849;ENST00000545345	T;T	0.40756	1.02;1.6	5.22	2.4	0.29515	.	0.286793	0.30193	N	0.010189	T	0.32585	0.0834	M	0.65975	2.015	0.09310	N	0.999997	P;P	0.43094	0.799;0.799	B;B	0.35931	0.214;0.214	T	0.20974	-1.0259	10	0.36615	T	0.2	-9.6678	5.093	0.14718	0.2547:0.1505:0.5948:0.0	.	134;134	Q5T9B9;P17813	.;EGLN_HUMAN	K	134	ENSP00000362299:N134K;ENSP00000341917:N134K	ENSP00000341917:N134K	N	-	3	2	ENG	129628731	0.000000	0.05858	0.007000	0.13788	0.501000	0.33797	0.084000	0.14891	0.306000	0.22856	-0.254000	0.11334	AAC	.	.		0.617	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1			T	130588910	G	T	130588910	3	4	11	1	0	0	0	0	1	0	0	0	5119	1368	48	3	1648	3	ENG	9	130588910	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	27805914	130588910	10624521	70	941										
NUP214	8021	hgsc.bcm.edu	37	chr9	134073496	134073496	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aaacttctgactctgttaaaAaagaacctgttcttgcccag	6	10	3	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr9:134073496A>T	ENST00000359428.5	+	29	4759	c.4615A>T	c.(4615-4617)Aaa>Taa	p.K1539*	NUP214_ENST00000411637.2_Nonsense_Mutation_p.K1529*|NUP214_ENST00000483497.2_Nonsense_Mutation_p.K365*|NUP214_ENST00000451030.1_Nonsense_Mutation_p.K1540*			P35658	NU214_HUMAN	nucleoporin 214kDa	1539	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		CTCTGTTAAAAAAGAACCTGT	0.537			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.K1539X	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.A4615T						.						46	48	47					9																	134073496		2203	4300	6503	SO:0001587	stop_gained	8021	exon29			GTTAAAAAAGAAC	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4615A>T	chr9.hg19:g.134073496A>T	ENSP00000352400:p.Lys1539*	101.0	0.0		113.0	42.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Nonsense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	A	45	11.278235	0.99540	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497;ENST00000531600;ENST00000541688	.	.	.	5.57	4.44	0.53790	.	0.000000	0.47093	D	0.000259	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.1444	9.9107	0.41403	0.9192:0.0:0.0808:0.0	.	.	.	.	X	1539;1529;1540;1518;1133;968;365;316;316	.	ENSP00000352400:K1539X	K	+	1	0	NUP214	133063317	0.065000	0.20965	0.226000	0.23910	0.572000	0.35998	1.033000	0.30191	2.119000	0.64992	0.459000	0.35465	AAA	.	.		0.537	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		T	134073496	A	T	134073496	4	4	11	1	0	0	0	0	0	1	0	0	10771	15	1	4	4729	4	NUP214	9	134073496	Nonsense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	3484586	134073496	7139935	71	942										
PNPLA7	375775	hgsc.bcm.edu	37	chr9	140361782	140361782	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tgcttacctcggcccactgcTtggcccggatccgcatctgg	11	16	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr9:140361782T>C	ENST00000277531.4	-	25	3137	c.2951A>G	c.(2950-2952)aAg>aGg	p.K984R	PNPLA7_ENST00000492278.1_5'UTR|PNPLA7_ENST00000406427.1_Missense_Mutation_p.K1009R|PNPLA7_ENST00000371457.1_Missense_Mutation_p.K590R	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	984	Patatin.				lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		GGCCCACTGCTTGGCCCGGAT	0.667																																					p.K1009R		Atlas-SNP	.											.	PNPLA7	124	.	0			c.A3026G						.						103	72	83					9																	140361782		2201	4298	6499	SO:0001583	missense	375775	exon26			CACTGCTTGGCCC	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"Patatin-like phospholipase domain containing"	24768	protein-coding gene	gene with protein product		612122	"chromosome 9 open reading frame 111"	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.2951A>G	chr9.hg19:g.140361782T>C	ENSP00000277531:p.Lys984Arg	68.0	0.0		80.0	30.0	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Missense_Mutation	SNP	ENST00000277531.4	hg19	CCDS7045.1	.	.	.	.	.	.	.	.	.	.	T	8.235	0.805591	0.16467	.	.	ENSG00000130653	ENST00000371457;ENST00000371446;ENST00000277531;ENST00000406427;ENST00000371451;ENST00000434090	T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1	5.41	4.13	0.48395	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.169680	0.48767	N	0.000175	T	0.49115	0.1538	N	0.04387	-0.21	0.28028	N	0.934251	B;B;B;B	0.18013	0.001;0.025;0.001;0.001	B;B;B;B	0.19946	0.009;0.027;0.013;0.009	T	0.43475	-0.9389	10	0.02654	T	1	-32.055	6.6828	0.23129	0.0:0.2909:0.0:0.7091	.	392;1009;984;250	E2QRF8;Q6ZV29-5;Q6ZV29;B3KXH5	.;.;PLPL7_HUMAN;.	R	590;392;984;1009;984;975	ENSP00000360512:K590R;ENSP00000360501:K392R;ENSP00000277531:K984R;ENSP00000384610:K1009R;ENSP00000400582:K975R	ENSP00000277531:K984R	K	-	2	0	PNPLA7	139481603	1.000000	0.71417	1.000000	0.80357	0.616000	0.37450	3.101000	0.50283	0.761000	0.33130	0.459000	0.35465	AAG	.	.		0.667	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286		C	140361782	T	C	140361782	3	2	11	1	0	0	0	0	1	0	0	0	12179	1609	56	2	1042	2	PNPLA7	9	140361782	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	6288286	140361782	851649	72	943										
PITX3	5309	hgsc.bcm.edu	37	chr10	103991819	103991819	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gctccgggcctctgcctcgcTgagcaggccgaactccatgg	13	16	1	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr10:103991819T>G	ENST00000370002.3	-	2	172	c.19A>C	c.(19-21)Agc>Cgc	p.S7R	PITX3_ENST00000539804.1_Missense_Mutation_p.S7R	NM_005029.3	NP_005020.1	O75364	PITX3_HUMAN	paired-like homeodomain 3	7					dopaminergic neuron differentiation (GO:0071542)|lens development in camera-type eye (GO:0002088)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|locomotory behavior (GO:0007626)|midbrain development (GO:0030901)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(1)|large_intestine(2)|lung(2)	5		Colorectal(252;0.00957)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		TCTGCCTCGCTGAGCAGGCCG	0.662																																					p.S7R		Atlas-SNP	.											.	PITX3	9	.	0			c.A19C						.						9	12	11					10																	103991819		2191	4283	6474	SO:0001583	missense	5309	exon2			CCTCGCTGAGCAG		CCDS7532.1	10q24.32	2013-11-14	2007-07-12		ENSG00000107859	ENSG00000107859		"Homeoboxes / PRD class"	9006	protein-coding gene	gene with protein product		602669	"paired-like homeodomain transcription factor 3", "anterior segment mesenchymal dysgenesis"	ASMD		9620774	Standard	NM_005029		Approved		uc001kuu.1	O75364	OTTHUMG00000018952	ENST00000370002.3:c.19A>C	chr10.hg19:g.103991819T>G	ENSP00000359019:p.Ser7Arg	77.0	0.0		76.0	22.0	NM_005029	Q5VZL2	Missense_Mutation	SNP	ENST00000370002.3	hg19	CCDS7532.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.240015	0.39598	.	.	ENSG00000107859	ENST00000370002;ENST00000539804	D;D	0.89196	-2.48;-2.48	5.58	1.93	0.25924	.	0.138414	0.64402	D	0.000007	T	0.71953	0.3401	N	0.14661	0.345	0.23468	N	0.997612	B	0.22604	0.072	B	0.20384	0.029	T	0.57590	-0.7785	10	0.02654	T	1	.	5.5871	0.17281	0.0:0.2243:0.1352:0.6405	.	7	O75364	PITX3_HUMAN	R	7	ENSP00000359019:S7R;ENSP00000439383:S7R	ENSP00000359019:S7R	S	-	1	0	PITX3	103981809	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	2.957000	0.49137	0.084000	0.17077	0.374000	0.22700	AGC	.	.		0.662	PITX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050031.1			G	103991819	T	G	103991819	3	3	11	1	0	0	0	0	1	0	0	0	11965	1580	55	5	901	5	PITX3	10	103991819	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10		103991819	31542928	73	944										
INA	9118	hgsc.bcm.edu	37	chr10	105048343	105048372	+	In_Frame_Del	DEL	ATATTAGAGGAGACAGTAATATCTACTAAG	ATATTAGAGGAGACAGTAATATCTACTAAG	-													0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	taggggaaagttttgaagaaAtattagaggagacagtaata					rs150252509		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	ATATTAGAGGAGACAGTAATATCTACTAAG	ATATTAGAGGAGACAGTAATATCTACTAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr10:105048343_105048372delATATTAGAGGAGACAGTAATATCTACTAAG	ENST00000369849.4	+	3	1466_1495	c.1417_1446delATATTAGAGGAGACAGTAATATCTACTAAG	c.(1417-1446)atattagaggagacagtaatatctactaagdel	p.ILEETVISTK473del		NM_032727.3	NP_116116.1	Q16352	AINX_HUMAN	internexin neuronal intermediate filament protein, alpha	473	Tail.				cell differentiation (GO:0030154)|neurofilament cytoskeleton organization (GO:0060052)|substantia nigra development (GO:0021762)	cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular space (GO:0005615)|neurofilament (GO:0005883)	structural constituent of cytoskeleton (GO:0005200)	p.S480Y(1)		breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)	13				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		TTTTGAAGAAATATTAGAGGAGACAGTAATATCTACTAAGAAAACCGAGA	0.374																																					p.472_482del		Atlas-Indel,Pindel	.											.	INA	34	.	1	Substitution - Missense(1)	large_intestine(1)	c.1416_1445del						.																																			SO:0001651	inframe_deletion	9118	exon3			.	S78296	CCDS7545.1	10q24	2013-01-16			ENSG00000148798	ENSG00000148798		"Intermediate filaments type IV"	6057	protein-coding gene	gene with protein product		605338		NEF5		7769995	Standard	NM_032727		Approved	NF-66	uc001kws.3	Q16352	OTTHUMG00000018986	ENST00000369849.4:c.1417_1446delATATTAGAGGAGACAGTAATATCTACTAAG	chr10.hg19:g.105048343_105048372delATATTAGAGGAGACAGTAATATCTACTAAG	ENSP00000358865:p.Ile473_Lys482del	149.0	0.0		183.0	34.0	NM_032727	B1AQK0|Q9BRC5	In_Frame_Del	DEL	ENST00000369849.4	hg19	CCDS7545.1																																																																																			.	.		0.374	INA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050145.1	NM_032727		-	105048372	ATATTAGAGGAGACAGTAATATCTACTAAG	-	105048343	7	5	11	1	0	1	0	1	0	0	0	0	7739	101	4	0	1427	0	INA	10	105048343	In_Frame_Del	DEL	ATATTAGAGGAGACAGTAATATCTACTAAG	TCGA-2Y-A9H1-01A-11D-A382-10	1056524	105048343	30486404	74	945										
ADAM12	8038	hgsc.bcm.edu	37	chr10	127806605	127806605	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	caaaatcaggtatcccccttAcccttcttgcccatgtctga	5	15	3	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr10:127806605A>G	ENST00000368679.4	-	6	922		c.e6+1		ADAM12_ENST00000368676.4_Splice_Site	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12						cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		TATCCCCCTTACCCTTCTTGC	0.493																																					.		Atlas-SNP	.											.	ADAM12	388	.	0			c.612+2T>C						.						183	165	171					10																	127806605		2203	4300	6503	SO:0001630	splice_region_variant	8038	exon7			CCCCTTACCCTTC	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.612+1T>C	chr10.hg19:g.127806605A>G		31.0	0.0		62.0	18.0	NM_003474	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Splice_Site	SNP	ENST00000368679.4	hg19	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	A	11.62	1.693361	0.30052	.	.	ENSG00000148848	ENST00000368679;ENST00000368676;ENST00000448723	.	.	.	4.89	3.74	0.42951	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2945	0.43616	0.8342:0.1658:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADAM12	127796595	1.000000	0.71417	0.987000	0.45799	0.240000	0.25518	1.895000	0.39778	0.866000	0.35629	0.533000	0.62120	.	.	.		0.493	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		Intron	G	127806605	A	G	127806605	5	3	11	1	0	0	0	0	0	0	1	0	236	405	14	2	2295	2	ADAM12	10	127806605	Splice_Site	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	22758262	127806605	7728142	75	946										
MUC2	4583	hgsc.bcm.edu	37	chr11	1093305	1093305	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	accaccaccactacggtgacCccaaccccaacacccaccgg	5	22	0	1	rs62637245		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr11:1093305C>G	ENST00000441003.2	+	30	5151	c.5124C>G	c.(5122-5124)acC>acG	p.T1708T	MUC2_ENST00000359061.5_Silent_p.T1675T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ctacggtgaccccaaccccaa	0.637																																					p.T1708T		Atlas-SNP	.											.	MUC2	614	.	0			c.C5124G						.						136	184	168					11																	1093305		1897	3515	5412	SO:0001819	synonymous_variant	4583	exon30			GGTGACCCCAACC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5124C>G	chr11.hg19:g.1093305C>G		20.0	0.0		19.0	7.0	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093305	C	G	1093305	2	3	11	1	0	0	0	0	0	0	0	1	9984	610	22	4		4	MUC2	11	1093305	Silent	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10		1093305	133913211	76	947										
OR51A7	119687	hgsc.bcm.edu	37	chr11	4928615	4928615	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tcattatgtctgttctcaatAactccgaagtcaagcttttc	5	10	4	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr11:4928615A>G	ENST00000359350.4	+	1	16	c.16A>G	c.(16-18)Aac>Gac	p.N6D	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGTTCTCAATAACTCCGAAGT	0.433																																					p.N6D		Atlas-SNP	.											.	OR51A7	86	.	0			c.A16G						.						85	80	81					11																	4928615		2201	4298	6499	SO:0001583	missense	119687	exon1			CTCAATAACTCCG	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"GPCR / Class A : Olfactory receptors"	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.16A>G	chr11.hg19:g.4928615A>G	ENSP00000352305:p.Asn6Asp	22.0	0.0		61.0	19.0	NM_001004749	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	hg19	CCDS31364.1	.	.	.	.	.	.	.	.	.	.	A	1.994	-0.431106	0.04669	.	.	ENSG00000176895	ENST00000359350;ENST00000545959	T	0.00505	6.93	5.02	-1.33	0.09172	.	0.557473	0.16229	N	0.223676	T	0.00328	0.0010	L	0.38175	1.15	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46219	-0.9207	10	0.35671	T	0.21	.	1.0455	0.01568	0.4545:0.1499:0.2511:0.1445	.	6	Q8NH64	O51A7_HUMAN	D	6	ENSP00000352305:N6D	ENSP00000352305:N6D	N	+	1	0	OR51A7	4885191	0.000000	0.05858	0.002000	0.10522	0.039000	0.13416	-1.319000	0.02702	-0.483000	0.06772	-1.587000	0.00848	AAC	.	.		0.433	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749		G	4928615	A	G	4928615	3	3	11	1	0	0	0	0	1	0	0	0	11097	362	13	2	18	2	OR51A7	11	4928615	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	3835310	4928615	130077901	77	948										
MED17	9440	hgsc.bcm.edu	37	chr11	93526996	93526996	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ctgtcctcttgatgtccaaaTtcctagtgatttagaggggt	10	8	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr11:93526996T>G	ENST00000251871.3	+	4	1027	c.740T>G	c.(739-741)aTt>aGt	p.I247S		NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	247					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			large_intestine(2)|lung(11)|ovary(1)	14		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GATGTCCAAATTCCTAGTGAT	0.318																																					p.I247S		Atlas-SNP	.											.	MED17	37	.	0			c.T740G						.						81	79	80					11																	93526996		2201	4298	6499	SO:0001583	missense	9440	exon4			TCCAAATTCCTAG	AF104254	CCDS8295.1	11q21	2007-07-30	2007-07-30	2007-07-30	ENSG00000042429	ENSG00000042429			2375	protein-coding gene	gene with protein product		603810	"cofactor required for Sp1 transcriptional activation, subunit 6 (77kD)", "cofactor required for Sp1 transcriptional activation, subunit 6, 77kDa"	CRSP6		9989412, 10198638	Standard	NM_004268		Approved	CRSP77, TRAP80, DRIP80	uc001pem.4	Q9NVC6	OTTHUMG00000167497	ENST00000251871.3:c.740T>G	chr11.hg19:g.93526996T>G	ENSP00000251871:p.Ile247Ser	96.0	0.0		132.0	43.0	NM_004268	B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Missense_Mutation	SNP	ENST00000251871.3	hg19	CCDS8295.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.147437	0.77888	.	.	ENSG00000042429	ENST00000251871;ENST00000427225;ENST00000528786	T;T	0.55413	0.52;0.52	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.65554	0.2702	M	0.61703	1.905	0.80722	D	1	D	0.63880	0.993	P	0.57620	0.824	T	0.68040	-0.5514	10	0.54805	T	0.06	-20.3107	15.554	0.76177	0.0:0.0:0.0:1.0	.	247	Q9NVC6	MED17_HUMAN	S	247;217;139	ENSP00000251871:I247S;ENSP00000433626:I139S	ENSP00000251871:I247S	I	+	2	0	MED17	93166644	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.941000	0.87700	2.095000	0.63458	0.533000	0.62120	ATT	.	.		0.318	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268		G	93526996	T	G	93526996	3	3	11	1	0	0	0	0	1	0	0	0	9444	1493	52	5	754	5	MED17	11	93526996	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	88598381	93526996	41479520	78	949										
PGR	5241	hgsc.bcm.edu	37	chr11	100933279	100933279	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aggtgtcaggttttgtgttgTcatgtcctgcatagatcaca	11	7	3	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr11:100933279T>C	ENST00000325455.5	-	4	3564	c.2111A>G	c.(2110-2112)gAc>gGc	p.D704G	PGR_ENST00000263463.5_Intron|PGR_ENST00000534013.1_Missense_Mutation_p.D110G	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	704	Steroid-binding.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	TTTTGTGTTGTCATGTCCTGC	0.423																																					p.D704G	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.A2111G						.						238	220	226					11																	100933279		2203	4300	6503	SO:0001583	missense	5241	exon4			GTGTTGTCATGTC	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"Nuclear hormone receptors"	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.2111A>G	chr11.hg19:g.100933279T>C	ENSP00000325120:p.Asp704Gly	72.0	0.0		168.0	50.0	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	hg19	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.534211	0.85812	.	.	ENSG00000082175	ENST00000325455;ENST00000534013	D;D	0.96685	-4.09;-4.09	5.86	5.86	0.93980	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.000000	0.85682	D	0.000000	D	0.98356	0.9454	M	0.88377	2.95	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.999	D	0.99368	1.0919	10	0.72032	D	0.01	.	16.254	0.82501	0.0:0.0:0.0:1.0	.	704;85	P06401;A7LQ08	PRGR_HUMAN;.	G	704;110	ENSP00000325120:D704G;ENSP00000436561:D110G	ENSP00000325120:D704G	D	-	2	0	PGR	100438489	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.685000	0.84117	2.232000	0.73038	0.533000	0.62120	GAC	.	.		0.423	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			C	100933279	T	C	100933279	3	2	11	1	0	0	0	0	1	0	0	0	11814	1667	58	2	710	2	PGR	11	100933279	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	7406283	100933279	34073237	79	950										
LMBR1L	55716	hgsc.bcm.edu	37	chr12	49496110	49496110	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tgtgtctgcagagccaggacCtgtctgtgtagcagctccat	12	11	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr12:49496110C>G	ENST00000267102.8	-	10	1161	c.819G>C	c.(817-819)caG>caC	p.Q273H	LMBR1L_ENST00000553204.1_5'Flank|LMBR1L_ENST00000395141.4_Missense_Mutation_p.Q268H|LMBR1L_ENST00000547382.1_Missense_Mutation_p.Q273H	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	273					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						GAGCCAGGACCTGTCTGTGTA	0.567																																					p.Q273H		Atlas-SNP	.											.	LMBR1L	61	.	0			c.G819C						.						144	134	137					12																	49496110		2203	4300	6503	SO:0001583	missense	55716	exon10			CAGGACCTGTCTG	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"limb region 1 homolog (mouse)-like"			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.819G>C	chr12.hg19:g.49496110C>G	ENSP00000267102:p.Gln273His	95.0	0.0		143.0	42.0	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Missense_Mutation	SNP	ENST00000267102.8	hg19	CCDS8780.2	.	.	.	.	.	.	.	.	.	.	C	17.55	3.418397	0.62622	.	.	ENSG00000139636	ENST00000267102;ENST00000547382;ENST00000395141	T;T;T	0.28454	1.61;1.61;1.61	5.65	4.73	0.59995	LMBR1-like membrane protein (1);	0.261816	0.45126	D	0.000393	T	0.20373	0.0490	N	0.08118	0	0.34175	D	0.670252	B;D;P;P;P	0.56035	0.115;0.974;0.799;0.832;0.731	B;P;B;P;B	0.47299	0.086;0.543;0.277;0.5;0.323	T	0.33954	-0.9848	10	0.72032	D	0.01	.	9.7867	0.40681	0.0:0.8308:0.0:0.1692	.	271;273;273;273;268	Q6UX01-2;Q6UX01-5;Q6UX01-3;Q6UX01;Q6UX01-4	.;.;.;LMBRL_HUMAN;.	H	273;273;268	ENSP00000267102:Q273H;ENSP00000447329:Q273H;ENSP00000378573:Q268H	ENSP00000267102:Q273H	Q	-	3	2	LMBR1L	47782377	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.264000	0.33015	1.561000	0.49584	0.655000	0.94253	CAG	.	.		0.567	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113		G	49496110	C	G	49496110	3	3	11	1	0	0	0	0	1	0	0	0	8850	680	24	4	682	4	LMBR1L	12	49496110	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10		49496110	84355785	80	951										
CCDC59	29080	hgsc.bcm.edu	37	chr12	82750988	82750988	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tttgagccttcttttccttcCgtagcaatttcttgtaactt	5	10	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr12:82750988C>T	ENST00000256151.7	-	2	626	c.215G>A	c.(214-216)cGg>cAg	p.R72Q	METTL25_ENST00000248306.3_5'Flank|CCDC59_ENST00000548126.1_5'UTR	NM_014167.4	NP_054886.2	Q9P031	TAP26_HUMAN	coiled-coil domain containing 59	72					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)	5						CTTTTCCTTCCGTAGCAATTT	0.368																																					p.R72Q		Atlas-SNP	.											.	CCDC59	17	.	0			c.G215A						.						125	119	121					12																	82750988		2203	4300	6503	SO:0001583	missense	29080	exon2			TCCTTCCGTAGCA	AF213377	CCDS9023.1	12q21.31	2007-10-17				ENSG00000133773			25005	protein-coding gene	gene with protein product						16630564, 12882447	Standard	NM_014167		Approved	HSPC128, TAP26, BR22	uc001szp.4	Q9P031		ENST00000256151.7:c.215G>A	chr12.hg19:g.82750988C>T	ENSP00000256151:p.Arg72Gln	82.0	0.0		91.0	35.0	NM_014167	Q9H2V5|Q9NW62	Missense_Mutation	SNP	ENST00000256151.7	hg19	CCDS9023.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.910181	0.33721	.	.	ENSG00000133773	ENST00000552377;ENST00000256151	.	.	.	5.43	5.43	0.79202	.	0.468033	0.23672	N	0.045701	T	0.26702	0.0653	L	0.39245	1.2	0.25735	N	0.985227	D	0.56521	0.976	B	0.39068	0.289	T	0.27331	-1.0077	9	0.33141	T	0.24	-3.652	10.7574	0.46245	0.0:0.88:0.0:0.12	.	72	Q9P031	TAP26_HUMAN	Q	72	.	ENSP00000256151:R72Q	R	-	2	0	CCDC59	81275119	0.112000	0.22096	0.128000	0.21923	0.008000	0.06430	1.265000	0.33027	2.546000	0.85860	0.655000	0.94253	CGG	.	.		0.368	CCDC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408186.1	NM_014167		T	82750988	C	T	82750988	3	4	11	1	0	0	0	0	1	0	0	0	2831	652	23	1	522	1	CCDC59	12	82750988	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	33254878	82750988	51100907	81	952										
GAS2L3	283431	hgsc.bcm.edu	37	chr12	101017580	101017580	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ttcagaaacaaaattcaaaaCccagcgtgccagttagtatt	6	9	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr12:101017580C>T	ENST00000539410.1	+	9	1383	c.997C>T	c.(997-999)Ccc>Tcc	p.P333S	GAS2L3_ENST00000547754.1_Missense_Mutation_p.P333S|GAS2L3_ENST00000266754.5_Missense_Mutation_p.P333S|GAS2L3_ENST00000537247.1_Missense_Mutation_p.P229S			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	333					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						AAATTCAAAACCCAGCGTGCC	0.448																																					p.P333S		Atlas-SNP	.											.	GAS2L3	76	.	0			c.C997T						.						57	57	57					12																	101017580		2203	4300	6503	SO:0001583	missense	283431	exon10			TCAAAACCCAGCG	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.997C>T	chr12.hg19:g.101017580C>T	ENSP00000439672:p.Pro333Ser	69.0	0.0		140.0	38.0	NM_174942	B2RCN2	Missense_Mutation	SNP	ENST00000539410.1	hg19	CCDS9079.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.519740	0.64634	.	.	ENSG00000139354	ENST00000266754;ENST00000547754;ENST00000537247;ENST00000539410	T;T;T;T	0.25579	1.81;1.81;1.79;1.81	5.71	5.71	0.89125	.	0.281738	0.35525	N	0.003152	T	0.30510	0.0767	L	0.49126	1.545	0.37945	D	0.932445	P	0.52577	0.954	P	0.47673	0.554	T	0.05767	-1.0865	10	0.20519	T	0.43	-14.6589	15.3495	0.74370	0.0:0.861:0.139:0.0	.	333	Q86XJ1	GA2L3_HUMAN	S	333;333;229;333	ENSP00000266754:P333S;ENSP00000448955:P333S;ENSP00000442406:P229S;ENSP00000439672:P333S	ENSP00000266754:P333S	P	+	1	0	GAS2L3	99541711	0.743000	0.28239	0.932000	0.37286	0.485000	0.33311	2.054000	0.41335	2.697000	0.92050	0.655000	0.94253	CCC	.	.		0.448	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942		T	101017580	C	T	101017580	3	4	11	1	0	0	0	0	1	0	0	0	6256	507	18	3	1027	3	GAS2L3	12	101017580	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	18266592	101017580	32834315	82	953										
UBE3B	89910	hgsc.bcm.edu	37	chr12	109959357	109959357	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tggggaaggctgtgtatgagGtaggaacgttaagaaacaga	16	3	0	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr12:109959357G>T	ENST00000342494.3	+	21	2959		c.e21+1		UBE3B_ENST00000434735.2_Splice_Site	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B						protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						TGTGTATGAGGTAGGAACGTT	0.453																																					.		Atlas-SNP	.											.	UBE3B	116	.	0			c.2364+1G>T						.						85	76	79					12																	109959357		2203	4300	6503	SO:0001630	splice_region_variant	89910	exon21			TATGAGGTAGGAA	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.2364+1G>T	chr12.hg19:g.109959357G>T		77.0	0.0		84.0	4.0	NM_183415	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Splice_Site	SNP	ENST00000342494.3	hg19	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.344620	0.82022	.	.	ENSG00000151148	ENST00000434735;ENST00000539599;ENST00000342494;ENST00000539584;ENST00000538070	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.86	0.88778	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UBE3B	108443740	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.842000	0.92136	2.684000	0.91462	0.655000	0.94253	.	.	.		0.453	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415	Intron	T	109959357	G	T	109959357	5	4	11	1	0	0	0	0	0	0	1	0	16895	1275	44	3	2439	3	UBE3B	12	109959357	Splice_Site	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	8941777	109959357	23892538	83	954										
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42179341	42179341	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tgattcggagggagtgcaccTgtcgccgaacagcacctgaa	13	11	0	2	rs544413664		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr13:42179341T>A	ENST00000379310.3	-	40	5017	c.4949A>T	c.(4948-4950)cAg>cTg	p.Q1650L		NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1650						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										GGAGTGCACCTGTCGCCGAAC	0.423													T|||	1	0.000199681	8e-04	0	5008	,	,		19877	0		0	False		,,,				2504	0				p.Q1650L		Atlas-SNP	.											.	.	.	.	0			c.A4949T						.						139	133	135					13																	42179341		1909	4120	6029	SO:0001583	missense	23078	exon40			TGCACCTGTCGCC	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.4949A>T	chr13.hg19:g.42179341T>A	ENSP00000368612:p.Gln1650Leu	29.0	0.0		68.0	29.0	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	hg19	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	T	32	5.121712	0.94385	.	.	ENSG00000102763	ENST00000251030;ENST00000379310	T	0.11930	2.73	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.42404	0.1201	M	0.82823	2.61	0.80722	D	1	D	0.63880	0.993	D	0.72338	0.977	T	0.36407	-0.9749	10	0.62326	D	0.03	.	16.4675	0.84087	0.0:0.0:0.0:1.0	.	1650	A3KMH1	K0564_HUMAN	L	1554;1650	ENSP00000368612:Q1650L	ENSP00000251030:Q1554L	Q	-	2	0	KIAA0564	41077341	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	7.930000	0.87610	2.367000	0.80283	0.528000	0.53228	CAG	.	.		0.423	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		A	42179341	T	A	42179341	3	1	11	1	0	0	0	0	1	0	0	0	8194	1580	55	4	792	4	KIAA0564	13	42179341	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10		42179341	72990537	84	955										
LMO7	4008	hgsc.bcm.edu	37	chr13	76381866	76381866	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	atgttctccgagcttttgaaGactttagaaagttctctgag	9	7	2	4			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr13:76381866G>A	ENST00000321797.8	+	8	1469	c.748G>A	c.(748-750)Gac>Aac	p.D250N	LMO7_ENST00000377534.3_Missense_Mutation_p.D535N|LMO7_ENST00000526202.1_Intron|LMO7_ENST00000341547.4_Intron|LMO7_ENST00000465261.2_Missense_Mutation_p.D250N|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Missense_Mutation_p.D535N			Q8WWI1	LMO7_HUMAN	LIM domain 7	535					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AGCTTTTGAAGACTTTAGAAA	0.408																																					p.D250N		Atlas-SNP	.											.	LMO7	334	.	0			c.G748A						.						84	81	82					13																	76381866		1568	3582	5150	SO:0001583	missense	4008	exon7			TTTGAAGACTTTA	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"F-box only protein 20"	604362	"LIM domain only 7"	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.748G>A	chr13.hg19:g.76381866G>A	ENSP00000317802:p.Asp250Asn	60.0	0.0		84.0	4.0	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.24|17.24	3.338365|3.338365	0.60963|0.60963	.|.	.|.	ENSG00000136153|ENSG00000136153	ENST00000357063;ENST00000377534;ENST00000321797;ENST00000465261|ENST00000447038	T;T;T;T|.	0.52754|.	0.65;0.65;0.65;0.65|.	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	0.376542|.	0.29544|.	N|.	0.011843|.	T|T	0.55114|0.55114	0.1900|0.1900	L|L	0.59436|0.59436	1.845|1.845	0.25346|0.25346	N|N	0.988907|0.988907	P;P|.	0.39480|.	0.675;0.675|.	B;B|.	0.35413|.	0.202;0.202|.	T|T	0.51521|0.51521	-0.8695|-0.8695	10|5	0.21540|.	T|.	0.41|.	-23.0716|-23.0716	13.0756|13.0756	0.59085|0.59085	0.0:0.0:0.7347:0.2653|0.0:0.0:0.7347:0.2653	.|.	535;250|.	Q8WWI1;E9PLH4|.	LMO7_HUMAN;.|.	N|K	535;535;250;250|158	ENSP00000349571:D535N;ENSP00000366757:D535N;ENSP00000317802:D250N;ENSP00000433352:D250N|.	ENSP00000317802:D250N|.	D|R	+|+	1|2	0|0	LMO7|LMO7	75279867|75279867	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	4.343000|4.343000	0.59348|0.59348	2.756000|2.756000	0.94617|0.94617	0.655000|0.655000	0.94253|0.94253	GAC|AGA	.	.		0.408	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		A	76381866	G	A	76381866	3	1	11	1	0	0	0	0	1	0	0	0	8864	942	33	3	1645	3	LMO7	13	76381866	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	34202525	76381866	38788012	85	956										
POTEG	404785	hgsc.bcm.edu	37	chr14	19566058	19566058	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aagaaaaacagatgctaaaaGtctcttctgaaaacagcaat	6	7	2	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr14:19566058G>A	ENST00000409832.3	+	6	1154	c.1102G>A	c.(1102-1104)Gtc>Atc	p.V368I	CTD-2311B13.5_ENST00000548748.1_lincRNA|RNU6-1239P_ENST00000391310.1_RNA	NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	368								p.V368F(1)		cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						GATGCTAAAAGTCTCTTCTGA	0.318																																					p.V368I		Atlas-SNP	.											POTEG,NS,malignant_melanoma,0,1	POTEG	118	.	1	Substitution - Missense(1)	lung(1)	c.G1102A						.						84	98	93					14																	19566058		1508	2699	4207	SO:0001583	missense	404785	exon6			CTAAAAGTCTCTT		CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33896	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 4"	608916	"ANKRD26-like family C, member 2"	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.1102G>A	chr14.hg19:g.19566058G>A	ENSP00000386971:p.Val368Ile	246.0	0.0		570.0	78.0	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	hg19	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	g	0.007	-1.960118	0.00465	.	.	ENSG00000222036	ENST00000409832	T	0.16897	2.31	2.2	-4.4	0.03600	Ankyrin repeat-containing domain (1);	.	.	.	.	T	0.05823	0.0152	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.40739	-0.9547	9	0.02654	T	1	.	3.6859	0.08328	0.2852:0.0:0.4944:0.2203	.	368	Q6S5H5	POTEG_HUMAN	I	368	ENSP00000386971:V368I	ENSP00000386971:V368I	V	+	1	0	POTEG	18636058	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.216000	0.09266	-0.934000	0.03733	-1.109000	0.02080	GTC	.	.		0.318	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356		A	19566058	G	A	19566058	3	1	11	1	0	0	0	0	1	0	0	0	12275	1029	36	3	1124	3	POTEG	14	19566058	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10		19566058	87783482	86	957										
KLHDC1	122773	hgsc.bcm.edu	37	chr14	50192421	50192421	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	taggaagagcagatattctgGggatggcataatgatgtcca	13	5	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr14:50192421G>A	ENST00000359332.2	+	6	591	c.501G>A	c.(499-501)tgG>tgA	p.W167*	KLHDC1_ENST00000554512.1_3'UTR	NM_172193.2	NP_751943.1	Q8N7A1	KLDC1_HUMAN	kelch domain containing 1	167						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|liver(2)|lung(5)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	12	all_epithelial(31;0.00244)|Breast(41;0.00964)					AGATATTCTGGGGATGGCATA	0.284																																					p.W167X		Atlas-SNP	.											.	KLHDC1	24	.	0			c.G501A						.						41	41	41					14																	50192421		2203	4296	6499	SO:0001587	stop_gained	122773	exon6			ATTCTGGGGATGG	AF111806	CCDS9692.1	14q21.3	2007-08-01			ENSG00000197776	ENSG00000197776			19836	protein-coding gene	gene with protein product		611281					Standard	NM_172193		Approved	MST025	uc001www.3	Q8N7A1	OTTHUMG00000140295	ENST00000359332.2:c.501G>A	chr14.hg19:g.50192421G>A	ENSP00000352282:p.Trp167*	562.0	0.0		830.0	302.0	NM_172193	B3KXD9|Q8WYI1	Nonsense_Mutation	SNP	ENST00000359332.2	hg19	CCDS9692.1	.	.	.	.	.	.	.	.	.	.	G	37	6.050918	0.97236	.	.	ENSG00000197776	ENST00000359332;ENST00000557128	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-6.656	19.8454	0.96706	0.0:0.0:1.0:0.0	.	.	.	.	X	167;38	.	ENSP00000352282:W167X	W	+	3	0	KLHDC1	49262171	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.864000	0.69575	2.850000	0.98022	0.650000	0.86243	TGG	.	.		0.284	KLHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276882.2	NM_172193		A	50192421	G	A	50192421	4	1	11	1	0	0	0	0	0	1	0	0	8363	1241	43	3	523	3	KLHDC1	14	50192421	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	30626363	50192421	57157119	87	958										
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493179	77493179	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	cccacgcccacctctgccacCgacgaagaggtcgaagacga	10	17	1	2	rs370738204		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr14:77493179C>A	ENST00000238647.3	-	1	1855	c.957G>T	c.(955-957)tcG>tcT	p.S319S		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	319					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						CCTCTGCCACCGACGAAGAGG	0.697																																					p.S319S		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.G957T						.						20	21	20					14																	77493179		2199	4298	6497	SO:0001819	synonymous_variant	64207	exon1			TGCCACCGACGAA	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.957G>T	chr14.hg19:g.77493179C>A		157.0	0.0		64.0	35.0	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	hg19	CCDS9854.1																																																																																			.	.		0.697	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		A	77493179	C	A	77493179	2	1	11	1	0	0	0	0	0	0	0	1	1775	639	23	1		1	C14orf4	14	77493179	Silent	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	27300758	77493179	29856361	88	959										
PTPN21	11099	hgsc.bcm.edu	37	chr14	88983540	88983540	+	Frame_Shift_Del	DEL	T	T	-													0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tccagctgcttcttcaaaggTttttccaaatctacccaccg							TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr14:88983540delT	ENST00000556564.1	-	3	530	c.246delA	c.(244-246)aaafs	p.K82fs	RP11-507K2.2_ENST00000555444.1_RNA|PTPN21_ENST00000328736.3_Frame_Shift_Del_p.K82fs|PTPN21_ENST00000554628.1_5'UTR	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	82	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TCTTCAAAGGTTTTTCCAAAT	0.438																																					p.P83fs		Atlas-Indel,Pindel	.											.	PTPN21	113	.	0			c.247delC						.						119	113	115					14																	88983540		2203	4300	6503	SO:0001589	frameshift_variant	11099	exon3			.	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.246delA	chr14.hg19:g.88983540delT	ENSP00000452414:p.Lys82fs	76.0	0.0		92.0	43.0	NM_007039		Frame_Shift_Del	DEL	ENST00000556564.1	hg19	CCDS9884.1																																																																																			.	.		0.438	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			-	88983540	T	-	88983540	7	5	11	1	0	1	0	1	0	0	0	0	12801	1722	60	0	3346	0	PTPN21	14	88983540	Frame_Shift_Del	DEL	T	TCGA-2Y-A9H1-01A-11D-A382-10	11490361	88983540	18366000	89	960										
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23890281	23890281	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	cgacggaggtcttggaggccTcttgagtggtggcagttgcc	17	9	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr15:23890281T>C	ENST00000532292.1	-	1	894	c.800A>G	c.(799-801)gAg>gGg	p.E267G		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	150					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		CTTGGAGGCCTCTTGAGTGGT	0.632																																					p.E870G		Atlas-SNP	.											MAGEL2_ENST00000532292,right_upper_lobe,carcinoma,0,1	MAGEL2	108	.	0			c.A2609G						.						34	43	40					15																	23890281		2175	4284	6459	SO:0001583	missense	54551	exon1			GAGGCCTCTTGAG	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.800A>G	chr15.hg19:g.23890281T>C	ENSP00000433433:p.Glu267Gly	100.0	0.0		139.0	47.0	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.89	1.478001	0.26511	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.22	0.501	0.16925	.	.	.	.	.	T	0.19248	0.0462	N	0.24115	0.695	0.09310	N	1	.	.	.	.	.	.	T	0.21552	-1.0242	5	.	.	.	.	0.7122	0.00926	0.169:0.1728:0.1743:0.4839	.	.	.	.	G	299	.	.	R	-	1	2	MAGEL2	21441374	0.783000	0.28701	0.017000	0.16124	0.139000	0.21198	0.209000	0.17435	0.064000	0.16427	0.533000	0.62120	AGG	.	.		0.632	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		C	23890281	T	C	23890281	3	2	11	1	0	0	0	0	1	0	0	0	9198	1551	54	2	1144	2	MAGEL2	15	23890281	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10		23890281	78641111	90	961										
HERC2	8924	hgsc.bcm.edu	37	chr15	28419679	28419679	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gcgtgtgatcttctggccttCtaagccttgcacgagtgtgg	13	10	3	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr15:28419679C>T	ENST00000261609.7	-	65	10027	c.9919G>A	c.(9919-9921)Gaa>Aaa	p.E3307K		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TTCTGGCCTTCTAAGCCTTGC	0.597																																					p.E3307K		Atlas-SNP	.											.	HERC2	501	.	0			c.G9919A						.						101	67	79					15																	28419679		2203	4300	6503	SO:0001583	missense	8924	exon65			GGCCTTCTAAGCC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9919G>A	chr15.hg19:g.28419679C>T	ENSP00000261609:p.Glu3307Lys	495.0	0.0		499.0	138.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409551	0.83340	.	.	ENSG00000128731	ENST00000261609	T	0.80480	-1.38	5.72	4.79	0.61399	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	T	0.81394	0.4813	N	0.11698	0.16	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.84236	0.0469	10	0.49607	T	0.09	.	16.5463	0.84446	0.0:0.8691:0.1309:0.0	.	3307	O95714	HERC2_HUMAN	K	3307	ENSP00000261609:E3307K	ENSP00000261609:E3307K	E	-	1	0	HERC2	26093274	1.000000	0.71417	0.656000	0.29637	0.398000	0.30690	6.079000	0.71291	1.380000	0.46344	0.591000	0.81541	GAA	.	.		0.597	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28419679	C	T	28419679	3	4	11	1	0	0	0	0	1	0	0	0	7067	922	32	3	4701	3	HERC2	15	28419679	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	4529398	28419679	74111713	91	962										
CHD2	1106	hgsc.bcm.edu	37	chr15	93496619	93496619	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aatccttgctgatgaaatggGcctaggaaagaccatccaga	10	9	0	4			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr15:93496619G>C	ENST00000394196.4	+	14	2603	c.1535G>C	c.(1534-1536)gGc>gCc	p.G512A	CHD2_ENST00000557381.1_Missense_Mutation_p.G512A	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	512	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GATGAAATGGGCCTAGGAAAG	0.388																																					p.G512A		Atlas-SNP	.											.	CHD2	280	.	0			c.G1535C						.						110	100	103					15																	93496619		2197	4298	6495	SO:0001583	missense	1106	exon14			AAATGGGCCTAGG	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.1535G>C	chr15.hg19:g.93496619G>C	ENSP00000377747:p.Gly512Ala	95.0	0.0		131.0	43.0	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	28.5	4.922732	0.92319	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.99811	-6.87;-6.87	5.41	5.41	0.78517	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.34853	U	0.003640	D	0.99912	0.9958	H	0.99820	4.81	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.95857	0.8880	10	0.87932	D	0	-14.9863	19.195	0.93684	0.0:0.0:1.0:0.0	.	512;512	O14647;O14647-2	CHD2_HUMAN;.	A	512	ENSP00000377747:G512A;ENSP00000451366:G512A	ENSP00000377747:G512A	G	+	2	0	CHD2	91297623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.864000	0.99589	2.537000	0.85549	0.563000	0.77884	GGC	.	.		0.388	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		C	93496619	G	C	93496619	3	2	11	1	0	0	0	0	1	0	0	0	3327	1203	42	4	1589	4	CHD2	15	93496619	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	65076940	93496619	9034773	92	963										
CHD2	1106	hgsc.bcm.edu	37	chr15	93567763	93567763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ccacacagataaactgggggAatataaacagcctctacccc	7	13	1	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr15:93567763A>G	ENST00000394196.4	+	39	6383	c.5315A>G	c.(5314-5316)gAa>gGa	p.E1772G		NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1772					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			AAACTGGGGGAATATAAACAG	0.542																																					p.E1772G		Atlas-SNP	.											.	CHD2	280	.	0			c.A5315G						.						91	95	94					15																	93567763		1916	4130	6046	SO:0001583	missense	1106	exon39			TGGGGGAATATAA	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.5315A>G	chr15.hg19:g.93567763A>G	ENSP00000377747:p.Glu1772Gly	135.0	0.0		165.0	8.0	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	A	17.36	3.370148	0.61624	.	.	ENSG00000173575	ENST00000394196	D	0.90004	-2.6	5.64	5.64	0.86602	.	.	.	.	.	T	0.79718	0.4494	N	0.08118	0	0.80722	D	1	B	0.14438	0.01	B	0.14023	0.01	T	0.74708	-0.3574	9	0.40728	T	0.16	-7.5698	16.1492	0.81602	1.0:0.0:0.0:0.0	.	1772	O14647	CHD2_HUMAN	G	1772	ENSP00000377747:E1772G	ENSP00000377747:E1772G	E	+	2	0	CHD2	91368767	1.000000	0.71417	0.935000	0.37517	0.930000	0.56654	6.361000	0.73070	2.272000	0.75746	0.460000	0.39030	GAA	.	.		0.542	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		G	93567763	A	G	93567763	3	3	11	1	0	0	0	0	1	0	0	0	3327	246	9	2	5469	2	CHD2	15	93567763	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	71144	93567763	8963629	93	964										
MRPL28	10573	hgsc.bcm.edu	37	chr16	419990	419990	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ctcgccgccccacaacccccGctgggattcggggggaaagt	13	16	0	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr16:419990G>A	ENST00000199706.8	-	2	264	c.229C>T	c.(229-231)Cgg>Tgg	p.R77W	MRPL28_ENST00000389675.2_Missense_Mutation_p.R77W|MRPL28_ENST00000429738.1_5'Flank	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	77					translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				CACAACCCCCGCTGGGATTCG	0.627																																					p.R77W		Atlas-SNP	.											.	MRPL28	15	.	0			c.C229T						.						63	64	63					16																	419990		2200	4300	6500	SO:0001583	missense	10573	exon2			ACCCCCGCTGGGA	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"Mitochondrial ribosomal proteins / large subunits"	14484	protein-coding gene	gene with protein product		604853	"melanoma-associated antigen recognised by cytotoxic T lymphocytes"	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.229C>T	chr16.hg19:g.419990G>A	ENSP00000199706:p.Arg77Trp	80.0	0.0		45.0	9.0	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Missense_Mutation	SNP	ENST00000199706.8	hg19	CCDS32349.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.570957	0.45798	.	.	ENSG00000086504	ENST00000397735;ENST00000199706;ENST00000397734;ENST00000389675;ENST00000441883;ENST00000447696;ENST00000450882	T;T;T;T;T	0.33216	1.83;1.83;1.83;1.42;1.42	4.85	-1.07	0.09968	.	1.314600	0.05174	N	0.500007	T	0.33876	0.0878	L	0.55213	1.73	0.18873	N	0.999985	D;D;D	0.56521	0.976;0.976;0.976	P;P;P	0.49047	0.599;0.599;0.599	T	0.33033	-0.9884	10	0.72032	D	0.01	-7.5072	3.873	0.09044	0.293:0.0:0.3371:0.3699	.	77;77;77	A2IDC6;Q13084;Q4TT38	.;RM28_HUMAN;.	W	77	ENSP00000199706:R77W;ENSP00000374326:R77W;ENSP00000398684:R77W;ENSP00000390399:R77W;ENSP00000395305:R77W	ENSP00000199706:R77W	R	-	1	2	MRPL28	359991	0.041000	0.20044	0.552000	0.28243	0.195000	0.23768	0.405000	0.21015	0.107000	0.17824	0.655000	0.94253	CGG	.	.		0.627	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2			A	419990	G	A	419990	3	1	11	1	0	0	0	0	1	0	0	0	9801	1086	38	1	561	1	MRPL28	16	419990	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10		419990	89934763	94	965										
C16orf71	146562	hgsc.bcm.edu	37	chr16	4794959	4794959	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aaggcctctgcttgtgcccgGaaggtgcctgccgacactcc	12	15	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr16:4794959G>T	ENST00000299320.5	+	6	1468	c.990G>T	c.(988-990)cgG>cgT	p.R330R	C16orf71_ENST00000590191.1_Silent_p.R344R|RP11-127I20.7_ENST00000588099.1_RNA	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	330										breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						CTTGTGCCCGGAAGGTGCCTG	0.632																																					p.R330R		Atlas-SNP	.											.	C16orf71	46	.	0			c.G990T						.						55	49	51					16																	4794959		2197	4300	6497	SO:0001819	synonymous_variant	146562	exon6			TGCCCGGAAGGTG	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.990G>T	chr16.hg19:g.4794959G>T		114.0	0.0		122.0	42.0	NM_139170	Q8NCV0	Silent	SNP	ENST00000299320.5	hg19	CCDS10521.1																																																																																			.	.		0.632	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170		T	4794959	G	T	4794959	2	4	11	1	0	0	0	0	0	0	0	1	1832	1161	41	3		3	C16orf71	16	4794959	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	4374969	4794959	85559794	95	966										
TGFB1I1	7041	hgsc.bcm.edu	37	chr16	31488866	31488866	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gcgcgccggcaagccctactGccagccctgcttcctgaagc	11	18	0	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr16:31488866G>A	ENST00000394863.3	+	11	1485	c.1355G>A	c.(1354-1356)tGc>tAc	p.C452Y	TGFB1I1_ENST00000567607.1_Missense_Mutation_p.C435Y|TGFB1I1_ENST00000394858.2_Missense_Mutation_p.C435Y|TGFB1I1_ENST00000361773.3_Missense_Mutation_p.C435Y	NM_001042454.2	NP_001035919.1	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced transcript 1	452	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|cell adhesion (GO:0007155)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|response to heat (GO:0009408)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|I-SMAD binding (GO:0070411)|Roundabout binding (GO:0048495)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(8)|upper_aerodigestive_tract(1)	9						AAGCCCTACTGCCAGCCCTGC	0.711																																					p.C452Y		Atlas-SNP	.											.	TGFB1I1	60	.	0			c.G1355A						.						17	17	17					16																	31488866		2194	4300	6494	SO:0001583	missense	7041	exon11			CCTACTGCCAGCC	AB007836	CCDS10713.1, CCDS42156.1	16p11	2008-02-05			ENSG00000140682	ENSG00000140682			11767	protein-coding gene	gene with protein product		602353				9422762, 10075738	Standard	NM_015927		Approved	Hic-5, TSC-5, ARA55, HIC-5	uc002ecd.2	O43294	OTTHUMG00000132467	ENST00000394863.3:c.1355G>A	chr16.hg19:g.31488866G>A	ENSP00000378332:p.Cys452Tyr	111.0	0.0		91.0	30.0	NM_001042454	B2R8D5|Q9BPW3|Q9Y2V5	Missense_Mutation	SNP	ENST00000394863.3	hg19	CCDS42156.1	.	.	.	.	.	.	.	.	.	.	G	33	5.221116	0.95139	.	.	ENSG00000140682	ENST00000394863;ENST00000361773;ENST00000394858	D;D;D	0.99319	-5.74;-5.74;-5.74	5.11	5.11	0.69529	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.99764	0.9904	H	0.99867	4.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96702	0.9519	10	0.87932	D	0	.	16.3886	0.83524	0.0:0.0:1.0:0.0	.	452	O43294	TGFI1_HUMAN	Y	452;435;435	ENSP00000378332:C452Y;ENSP00000355117:C435Y;ENSP00000378327:C435Y	ENSP00000355117:C435Y	C	+	2	0	TGFB1I1	31396367	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.908000	0.87438	2.539000	0.85634	0.491000	0.48974	TGC	.	.		0.711	TGFB1I1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255630.3			A	31488866	G	A	31488866	3	1	11	1	0	0	0	0	1	0	0	0	15832	1319	46	3	1397	3	TGFB1I1	16	31488866	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	26693907	31488866	58865887	96	967										
ZDHHC1	29800	hgsc.bcm.edu	37	chr16	67440191	67440191	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	agaagaggtacagcagccagGccacaatctggagcgggtga	15	9	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr16:67440191G>A	ENST00000348579.2	-	3	505	c.164C>T	c.(163-165)gCc>gTc	p.A55V		NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	55					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		CAGCAGCCAGGCCACAATCTG	0.657																																					p.A55V		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.C164T						.						49	35	40					16																	67440191		2196	4298	6494	SO:0001583	missense	29800	exon3			AGCCAGGCCACAA	U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"Zinc fingers, DHHC-type"	17916	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 1"	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.164C>T	chr16.hg19:g.67440191G>A	ENSP00000340299:p.Ala55Val	252.0	0.0		250.0	104.0	NM_013304	O15461	Missense_Mutation	SNP	ENST00000348579.2	hg19	CCDS10836.1	.	.	.	.	.	.	.	.	.	.	G	35	5.556830	0.96514	.	.	ENSG00000159714	ENST00000348579	T	0.40476	1.03	5.25	5.25	0.73442	.	0.089010	0.47852	D	0.000205	T	0.62171	0.2406	L	0.61218	1.895	0.58432	D	0.999992	D	0.67145	0.996	D	0.67725	0.953	T	0.65063	-0.6259	10	0.72032	D	0.01	.	17.8255	0.88664	0.0:0.0:1.0:0.0	.	55	Q8WTX9	ZDHC1_HUMAN	V	55	ENSP00000340299:A55V	ENSP00000340299:A55V	A	-	2	0	ZDHHC1	65997692	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.299000	0.72770	2.463000	0.83235	0.561000	0.74099	GCC	.	.		0.657	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304		A	67440191	G	A	67440191	3	1	11	1	0	0	0	0	1	0	0	0	17615	1203	42	3	1329	3	ZDHHC1	16	67440191	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	35951325	67440191	22914562	97	968										
DEF8	54849	hgsc.bcm.edu	37	chr16	90028418	90028495	+	Splice_Site	DEL	CTGGTTGGGTGTTGCCCGCTGCACGGGCCCTGGGTGGGTGTGAGAGGTGTCACCCGGCCGTGCCTGGCAGGTTTCTCG	CTGGTTGGGTGTTGCCCGCTGCACGGGCCCTGGGTGGGTGTGAGAGGTGTCACCCGGCCGTGCCTGGCAGGTTTCTCG	-													0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gtcacccggccgtgcctggcAggtttctcgctgcagcatgc					rs140137747|rs376017026|rs200795246|rs553966074|rs370039650|rs532929203|rs150893049|rs551718366	byFrequency	TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	CTGGTTGGGTGTTGCCCGCTGCACGGGCCCTGGGTGGGTGTGAGAGGTGTCACCCGGCCGTGCCTGGCAGGTTTCTCG	CTGGTTGGGTGTTGCCCGCTGCACGGGCCCTGGGTGGGTGTGAGAGGTGTCACCCGGCCGTGCCTGGCAGGTTTCTCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr16:90028418_90028495delCTGGTTGGGTGTTGCCCGCTGCACGGGCCCTGGGTGGGTGTGAGAGGTGTCACCCGGCCGTGCCTGGCAGGTTTCTCG	ENST00000268676.7	+	9	1079_1155	c.990_1066delCTGGTTGGGTGTTGCCCGCTGCACGGGCCCTGGGTGGGTGTGAGAGGTGTCACCCGGCCGTGCCTGGCAGGTTTCTCG	c.(988-1068)aactggttgggtgttgcccgctgcacgggccctgggtgggtgtgagaggtgtcacccggccgtgcctggcaggtttctcgt>aagt	p.330_356NWLGVARCTGPGWV*EVSPGRAWQVSR>K	DEF8_ENST00000570182.1_Splice_Site_p.259_285NWLGVARCTGPGWV*EVSPGRAWQVSR>K|DEF8_ENST00000563795.1_Splice_Site_p.269_295NWLGVARCTGPGWV*EVSPGRAWQVSR>K|DEF8_ENST00000567874.1_Splice_Site_p.209_235NWLGVARCTGPGWV*EVSPGRAWQVSR>K|DEF8_ENST00000569453.1_Splice_Site_p.269_295NWLGVARCTGPGWV*EVSPGRAWQVSR>K|DEF8_ENST00000563848.1_3'UTR|DEF8_ENST00000563594.1_Splice_Site_p.269_295NWLGVARCTGPGWV*EVSPGRAWQVSR>K	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	330					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)	p.S335C(1)		central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		CGTGCCTGGCAGGTTTCTCGCTGCAGCATGCGCTACCTGGCGCTGATGGTGTCTCGGCCCGTACTCAGGCTCCGGGAGATCAACCCTCTGCTGTTCAG	0.68																																					p.331_333del		Pindel	.											.	DEF8	28	.	1	Substitution - Missense(1)	lung(1)	c.991_997del						.																																			SO:0001630	splice_region_variant	54849	exon9			.	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.991-1CTGGTTGGGTGTTGCCCGCTGCACGGGCCCTGGGTGGGTGTGAGAGGTGTCACCCGGCCGTGCCTGGCAGGTTTCTCG>-	chr16.hg19:g.90028418_90028495delCTGGTTGGGTGTTGCCCGCTGCACGGGCCCTGGGTGGGTGTGAGAGGTGTCACCCGGCCGTGCCTGGCAGGTTTCTCG		44.0	0.0		38.0	13.0	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Frame_Shift_Del	DEL	ENST00000268676.7	hg19	CCDS10989.1																																																																																			.	.		0.68	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514	In_Frame_Del	-	90028495	CTGGTTGGGTGTTGCCCGCTGCACGGGCCCTGGGTGGGTGTGAGAGGTGTCACCCGGCCGTGCCTGGCAGGTTTCTCG	-	90028418	8	5	11	1	0	1	0	1	0	0	1	0	4389	202	7	0	1099	0	DEF8	16	90028418	Splice_Site	DEL	CTGGTTGGGTGTTGCCCGCTGCACGGGCCCTGGGTGGGTGTGAGAGGTGTCACCCGGCCGTGCCTGGCAGGTTTCTCG	TCGA-2Y-A9H1-01A-11D-A382-10	22588227	90028418	326335	98	969										
EIF5A	1984	hgsc.bcm.edu	37	chr17	7212975	7212975	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	atggcagatgacttggacttCgagacaggagatgcaggggc	16	7	0	4			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr17:7212975C>G	ENST00000336458.8	+	2	422	c.21C>G	c.(19-21)ttC>ttG	p.F7L	EIF5A_ENST00000571955.1_Missense_Mutation_p.F7L|EIF5A_ENST00000419711.2_Missense_Mutation_p.F7L|EIF5A_ENST00000416016.2_Missense_Mutation_p.F7L|EIF5A_ENST00000576930.1_Missense_Mutation_p.F7L|EIF5A_ENST00000336452.7_Missense_Mutation_p.F37L|EIF5A_ENST00000573542.1_Missense_Mutation_p.F7L|EIF5A_ENST00000572815.1_Missense_Mutation_p.F7L	NM_001970.4	NP_001961.1	P63241	IF5A1_HUMAN	eukaryotic translation initiation factor 5A	7					apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|mRNA export from nucleus (GO:0006406)|nucleocytoplasmic transport (GO:0006913)|peptidyl-lysine modification to peptidyl-hypusine (GO:0008612)|positive regulation of cell proliferation (GO:0008284)|positive regulation of translational elongation (GO:0045901)|positive regulation of translational termination (GO:0045905)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|translational frameshifting (GO:0006452)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation elongation factor activity (GO:0003746)|U6 snRNA binding (GO:0017070)			endometrium(2)|kidney(1)|large_intestine(2)|urinary_tract(1)	6						ACTTGGACTTCGAGACAGGAG	0.498																																					p.F37L		Atlas-SNP	.											EIF5A_ENST00000336452,NS,carcinoma,0,2	EIF5A	28	.	0			c.C111G						.						182	174	177					17																	7212975		2203	4300	6503	SO:0001583	missense	1984	exon2			GGACTTCGAGACA		CCDS11099.1, CCDS45601.1	17p13-p12	2009-05-01			ENSG00000132507	ENSG00000132507			3300	protein-coding gene	gene with protein product		600187				7759117	Standard	NM_001143760		Approved	EIF5A1, EIF-5A, MGC99547, MGC104255	uc002gfr.3	P63241	OTTHUMG00000102197	ENST00000336458.8:c.21C>G	chr17.hg19:g.7212975C>G	ENSP00000336776:p.Phe7Leu	65.0	0.0		66.0	14.0	NM_001143760	A8K9A0|D3DTP2|P10159|Q16182|Q7L7L3|Q7Z4L1|Q9D0G2	Missense_Mutation	SNP	ENST00000336458.8	hg19	CCDS11099.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.41|17.41	3.383433|3.383433	0.61845|0.61845	.|.	.|.	ENSG00000132507|ENSG00000132507	ENST00000336452;ENST00000336458;ENST00000419711;ENST00000416016|ENST00000355068	T;T;T;T|.	0.60797|.	0.16;0.24;0.24;0.24|.	4.13|4.13	4.13|4.13	0.48395|0.48395	.|.	0.074706|.	0.53938|.	D|.	0.000060|.	D|D	0.84593|0.84593	0.5506|0.5506	M|M	0.92219|0.92219	3.285|3.285	0.58432|0.58432	D|D	0.999999|0.999999	B;B|.	0.28082|.	0.048;0.2|.	B;B|.	0.35470|.	0.06;0.203|.	D|D	0.89063|0.89063	0.3464|0.3464	10|6	0.72032|0.87932	D|D	0.01|0	-13.7541|-13.7541	15.3285|15.3285	0.74186|0.74186	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	7;37|.	P63241;P63241-2|.	IF5A1_HUMAN;.|.	L|W	37;7;7;7|5	ENSP00000336702:F37L;ENSP00000336776:F7L;ENSP00000390677:F7L;ENSP00000396073:F7L|.	ENSP00000336702:F37L|ENSP00000347180:S5W	F|S	+|+	3|2	2|0	EIF5A|EIF5A	7153699|7153699	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	4.359000|4.359000	0.59449|0.59449	2.149000|2.149000	0.67028|0.67028	0.385000|0.385000	0.25706|0.25706	TTC|TCG	.	.		0.498	EIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220047.3	NM_001970		G	7212975	C	G	7212975	3	3	11	1	0	0	0	0	1	0	0	0	5043	883	31	4	117	4	EIF5A	17	7212975	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10		7212975	73982235	99	970										
MYH3	4621	hgsc.bcm.edu	37	chr17	10535931	10535931	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	atggcttcattcctgctccgCacctcggcgtccagggcgct	11	16	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr17:10535931C>T	ENST00000583535.1	-	34	4905	c.4818G>A	c.(4816-4818)gtG>gtA	p.V1606V	MYH3_ENST00000226209.7_Silent_p.V1606V	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1606					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TCCTGCTCCGCACCTCGGCGT	0.567																																					p.V1606V		Atlas-SNP	.											.	MYH3	227	.	0			c.G4818A						.						247	240	243					17																	10535931		2203	4300	6503	SO:0001819	synonymous_variant	4621	exon34			GCTCCGCACCTCG		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4818G>A	chr17.hg19:g.10535931C>T		69.0	0.0		58.0	20.0	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	hg19	CCDS11157.1																																																																																			.	.		0.567	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		T	10535931	C	T	10535931	2	4	11	1	0	0	0	0	0	0	0	1	10045	697	25	3		3	MYH3	17	10535931	Silent	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	3322956	10535931	70659279	100	971										
COG1	9382	hgsc.bcm.edu	37	chr17	71197399	71197399	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gtcgctcttcctctggtctgAgagtcctaatgacctgcctt	9	13	3	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr17:71197399A>T	ENST00000299886.4	+	7	1513	c.1433A>T	c.(1432-1434)gAg>gTg	p.E478V		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	478					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			CTCTGGTCTGAGAGTCCTAAT	0.532																																					p.E478V		Atlas-SNP	.											.	COG1	46	.	0			c.A1433T						.						166	149	154					17																	71197399		2203	4300	6503	SO:0001583	missense	9382	exon7			GGTCTGAGAGTCC		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"Components of oligomeric golgi complex"	6545	protein-coding gene	gene with protein product		606973	"low density lipoprotein receptor defect B complementing"	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1433A>T	chr17.hg19:g.71197399A>T	ENSP00000299886:p.Glu478Val	88.0	0.0		141.0	74.0	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	hg19	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.748012	0.49257	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.43688	0.94;0.96	5.28	5.28	0.74379	.	0.048522	0.85682	D	0.000000	T	0.65450	0.2692	M	0.77616	2.38	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.992;0.992	T	0.68659	-0.5350	10	0.52906	T	0.07	-30.2295	15.5073	0.75750	1.0:0.0:0.0:0.0	.	478;478;478	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	V	478	ENSP00000400111:E478V;ENSP00000299886:E478V	ENSP00000299886:E478V	E	+	2	0	COG1	68708994	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.718000	0.91430	2.120000	0.65058	0.533000	0.62120	GAG	.	.		0.532	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			T	71197399	A	T	71197399	3	4	11	1	0	0	0	0	1	0	0	0	3659	304	11	4	1459	4	COG1	17	71197399	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	60661468	71197399	9997811	101	972										
RECQL5	9400	hgsc.bcm.edu	37	chr17	73625530	73625530	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ggcaggagcctttggggaaaCcagctcccacccgcttgggt	14	13	0	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr17:73625530C>A	ENST00000317905.5	-	16	2132	c.1973G>T	c.(1972-1974)gGt>gTt	p.G658V	RECQL5_ENST00000423245.2_Missense_Mutation_p.G631V|RECQL5_ENST00000443199.2_5'UTR	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	658	Interaction with RAD51.				chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)			breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			TTTGGGGAAACCAGCTCCCAC	0.637								Other identified genes with known or suspected DNA repair function																													p.G658V		Atlas-SNP	.											.	RECQL5	77	.	0			c.G1973T						.						24	26	25					17																	73625530		1937	4097	6034	SO:0001583	missense	9400	exon16			GGGAAACCAGCTC	AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"RecQ protein 5"	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.1973G>T	chr17.hg19:g.73625530C>A	ENSP00000317636:p.Gly658Val	113.0	0.0		152.0	42.0	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Missense_Mutation	SNP	ENST00000317905.5	hg19	CCDS42380.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.737913	0.49045	.	.	ENSG00000108469	ENST00000443199;ENST00000423245;ENST00000317905	T	0.61980	0.06	4.96	4.96	0.65561	RecQ helicase-like 5 (2);	0.000000	0.85682	D	0.000000	T	0.77850	0.4192	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.78914	-0.2016	10	0.54805	T	0.06	-14.4253	17.3728	0.87383	0.0:1.0:0.0:0.0	.	658;631	O94762;Q6P4G0	RECQ5_HUMAN;.	V	253;658;658	ENSP00000317636:G658V	ENSP00000317636:G658V	G	-	2	0	RECQL5	71137125	0.998000	0.40836	1.000000	0.80357	0.950000	0.60333	3.825000	0.55730	2.564000	0.86499	0.561000	0.74099	GGT	.	.		0.637	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259		A	73625530	C	A	73625530	3	1	11	1	0	0	0	0	1	0	0	0	13218	507	18	3	1022	3	RECQL5	17	73625530	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	2428131	73625530	7569680	102	973										
UNC13D	201294	hgsc.bcm.edu	37	chr17	73831523	73831523	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	acagcgcgctgcacccgcgcCagggcctcgttgtacgtctt	12	16	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr17:73831523C>A	ENST00000207549.4	-	20	2194	c.1815G>T	c.(1813-1815)ctG>ctT	p.L605L	UNC13D_ENST00000412096.2_Silent_p.L605L	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	605	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCACCCGCGCCAGGGCCTCGT	0.687									Familial Hemophagocytic Lymphohistiocytosis																												p.L605L		Atlas-SNP	.											.	UNC13D	68	.	0			c.G1815T						.						28	30	30					17																	73831523		2202	4299	6501	SO:0001819	synonymous_variant	201294	exon20	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CCGCGCCAGGGCC	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.1815G>T	chr17.hg19:g.73831523C>A		97.0	0.0		117.0	52.0	NM_199242	B4DWG9|Q9H7K5	Silent	SNP	ENST00000207549.4	hg19	CCDS11730.1																																																																																			.	.		0.687	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		A	73831523	C	A	73831523	2	1	11	1	0	0	0	0	0	0	0	1	17002	581	21	3		3	UNC13D	17	73831523	Silent	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	205993	73831523	7363687	103	974										
MFSD11	79157	hgsc.bcm.edu	37	chr17	74737143	74737143	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gtttgccagtggtttattttAcaggtaagtagtgtaatctt	10	4	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr17:74737143A>T	ENST00000588460.1	+	3	2299	c.257A>T	c.(256-258)tAc>tTc	p.Y86F	MFSD11_ENST00000336509.4_Missense_Mutation_p.Y86F|MFSD11_ENST00000586622.1_Missense_Mutation_p.Y86F|MFSD11_ENST00000355954.3_Missense_Mutation_p.Y86F|MFSD11_ENST00000590514.1_Missense_Mutation_p.Y86F|MFSD11_ENST00000593181.1_Missense_Mutation_p.Y86F	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	86						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						GGTTTATTTTACAGGTAAGTA	0.358																																					p.Y86F		Atlas-SNP	.											.	MFSD11	47	.	0			c.A257T						.						182	169	173					17																	74737143		2203	4300	6503	SO:0001583	missense	79157	exon4			TATTTTACAGGTA	BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.257A>T	chr17.hg19:g.74737143A>T	ENSP00000464932:p.Tyr86Phe	76.0	0.0		82.0	18.0	NM_001242536	O43442|Q9NXI5	Missense_Mutation	SNP	ENST00000588460.1	hg19	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.322317	0.81580	.	.	ENSG00000092931	ENST00000336509;ENST00000355954	T;T	0.46451	0.87;0.87	5.8	5.8	0.92144	Major facilitator superfamily domain, general substrate transporter (1);	0.054484	0.85682	D	0.000000	T	0.59211	0.2177	M	0.84585	2.705	0.80722	D	1	B;B	0.34181	0.157;0.44	B;B	0.43575	0.079;0.424	T	0.64542	-0.6383	10	0.87932	D	0	-17.0347	16.1429	0.81539	1.0:0.0:0.0:0.0	.	86;86	O43934-2;O43934	.;MFS11_HUMAN	F	86	ENSP00000337240:Y86F;ENSP00000348225:Y86F	ENSP00000337240:Y86F	Y	+	2	0	MFSD11	72248738	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	8.952000	0.93031	2.209000	0.71365	0.460000	0.39030	TAC	.	.		0.358	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311		T	74737143	A	T	74737143	3	4	11	1	0	0	0	0	1	0	0	0	9538	391	14	4	267	4	MFSD11	17	74737143	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	905620	74737143	6458067	104	975										
AATK	9625	hgsc.bcm.edu	37	chr17	79093268	79093268	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	accgtgaagcgcgagaagggAgcgggcgtgggcgtgggcgc	22	9	0	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr17:79093268A>C	ENST00000326724.4	-	13	4020	c.3996T>G	c.(3994-3996)gcT>gcG	p.A1332A	AATK_ENST00000417379.1_Silent_p.A1229A	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1332			A -> T (in dbSNP:rs55713566). {ECO:0000269|PubMed:17344846}.		brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GCGAGAAGGGAGCGGGCGTGG	0.716																																					p.A1332A		Atlas-SNP	.											.	AATK	102	.	0			c.T3996G						.						16	21	19					17																	79093268		2003	4121	6124	SO:0001819	synonymous_variant	9625	exon13			GAAGGGAGCGGGC	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.3996T>G	chr17.hg19:g.79093268A>C		94.0	0.0		150.0	9.0	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	hg19	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	A	4.811	0.150783	0.09185	.	.	ENSG00000181409	ENST00000417379	.	.	.	3.45	-2.73	0.05950	.	.	.	.	.	T	0.51329	0.1668	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46034	-0.9220	4	.	.	.	.	7.6594	0.28394	0.4346:0.4849:0.0:0.0805	.	.	.	.	R	1285	.	.	L	-	2	0	AATK	76707863	0.000000	0.05858	0.023000	0.16930	0.123000	0.20343	-0.097000	0.11042	-0.530000	0.06349	-1.015000	0.02457	CTC	.	.		0.716	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		C	79093268	A	C	79093268	2	2	11	1	0	0	0	0	0	0	0	1	26	291	11	5		5	AATK	17	79093268	Silent	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	4356125	79093268	2101942	105	976										
TGIF1	7050	hgsc.bcm.edu	37	chr18	3447754	3447754	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ggatatgacttgctcgggcaAaagttgtgcattggcccgat	13	8	0	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr18:3447754A>G	ENST00000548489.2	+	1	148	c.17A>G	c.(16-18)aAa>aGa	p.K6R	TGIF1_ENST00000401449.1_Intron|TGIF1_ENST00000405385.3_5'Flank|TGIF1_ENST00000551402.1_5'Flank|TGIF1_ENST00000407501.2_5'Flank|TGIF1_ENST00000577543.1_5'Flank|TGIF1_ENST00000343820.5_5'Flank	NM_173207.1	NP_775299.1	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	0					determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				TGCTCGGGCAAAAGTTGTGCA	0.478																																					p.K6R		Atlas-SNP	.											.	TGIF1	41	.	0			c.A17G						.						132	123	126					18																	3447754		2203	4300	6503	SO:0001583	missense	7050	exon1			CGGGCAAAAGTTG	X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"Homeoboxes / TALE class"	11776	protein-coding gene	gene with protein product		602630	"TGFB-induced factor (TALE family homeobox)"	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000548489.2:c.17A>G	chr18.hg19:g.3447754A>G	ENSP00000447747:p.Lys6Arg	108.0	0.0		135.0	51.0	NM_173207	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Missense_Mutation	SNP	ENST00000548489.2	hg19	CCDS11832.1	.	.	.	.	.	.	.	.	.	.	A	1.121	-0.655391	0.03480	.	.	ENSG00000177426	ENST00000548489	T	0.51325	0.71	4.77	-0.678	0.11353	.	.	.	.	.	T	0.24736	0.0600	.	.	.	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.26052	-1.0114	8	0.12430	T	0.62	.	7.8993	0.29725	0.5129:0.0:0.4871:0.0	.	6	F8VZB6	.	R	6	ENSP00000447747:K6R	ENSP00000447747:K6R	K	+	2	0	TGIF1	3437754	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	0.284000	0.18864	-0.178000	0.10672	-0.874000	0.02982	AAA	.	.		0.478	TGIF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254366.4	NM_170695		G	3447754	A	G	3447754	3	3	11	1	0	0	0	0	1	0	0	0	15840	14	1	2	19	2	TGIF1	18	3447754	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10		3447754	74629494	106	977										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21441694	21441694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	acccaggcagcaacagtatgGtggcggatctccaggagctg	14	11	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr18:21441694G>A	ENST00000313654.9	+	35	4748	c.4507G>A	c.(4507-4509)Gtg>Atg	p.V1503M	LAMA3_ENST00000399516.3_Missense_Mutation_p.V1503M	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1503	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					CAACAGTATGGTGGCGGATCT	0.582																																					p.V1503M		Atlas-SNP	.											.	LAMA3	397	.	0			c.G4507A						.						45	48	47					18																	21441694		2022	4192	6214	SO:0001583	missense	3909	exon35			AGTATGGTGGCGG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.4507G>A	chr18.hg19:g.21441694G>A	ENSP00000324532:p.Val1503Met	63.0	0.0		85.0	33.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.471510	0.63737	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.20200	2.09;2.09	5.5	5.5	0.81552	Laminin B type IV (1);Growth factor, receptor (1);	.	.	.	.	T	0.45397	0.1340	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.67725	0.953;0.915	T	0.14587	-1.0467	9	0.34782	T	0.22	.	19.3976	0.94612	0.0:0.0:1.0:0.0	.	1503;1503	Q6VU67;Q16787	.;LAMA3_HUMAN	M	1503;1503;1501	ENSP00000324532:V1503M;ENSP00000382432:V1503M	ENSP00000324532:V1503M	V	+	1	0	LAMA3	19695692	1.000000	0.71417	0.820000	0.32676	0.356000	0.29392	9.125000	0.94402	2.580000	0.87095	0.555000	0.69702	GTG	.	.		0.582	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		A	21441694	G	A	21441694	3	1	11	1	0	0	0	0	1	0	0	0	8616	1261	44	3	4645	3	LAMA3	18	21441694	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	17993940	21441694	56635554	107	978										
PPAP2C	8612	hgsc.bcm.edu	37	chr19	287716	287716	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tccgagcgagaatagagccgGtctgtgtacaccaggtaggc	14	10	1	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr19:287716G>A	ENST00000269812.3	-	3	289	c.240C>T	c.(238-240)gaC>gaT	p.D80D	PPAP2C_ENST00000327790.3_Silent_p.D101D|PPAP2C_ENST00000434325.2_Silent_p.D24D	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	80					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AATAGAGCCGGTCTGTGTACA	0.627																																					p.D101D		Atlas-SNP	.											.	PPAP2C	38	.	0			c.C303T						.						158	178	171					19																	287716		2203	4300	6503	SO:0001819	synonymous_variant	8612	exon3			GAGCCGGTCTGTG	AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	3.1.3.4		9230	protein-coding gene	gene with protein product		607126				9570154, 9607309	Standard	NM_177543		Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.240C>T	chr19.hg19:g.287716G>A		113.0	0.0		82.0	22.0	NM_177543	A6NLV0|E9PAY8	Silent	SNP	ENST00000269812.3	hg19	CCDS12023.1																																																																																			.	.		0.627	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451777.2			A	287716	G	A	287716	2	1	11	1	0	0	0	0	0	0	0	1	12301	1252	44	3		3	PPAP2C	19	287716	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10		287716	58841267	108	979										
KIAA1543	57662	hgsc.bcm.edu	37	chr19	7670161	7670161	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ttctataccgaccagtacgcGcaggagcatgtgaagccccc	10	14	1	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr19:7670161G>T	ENST00000160298.4	+	2	299	c.198G>T	c.(196-198)gcG>gcT	p.A66A	CAMSAP3_ENST00000446248.2_Silent_p.A66A	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	66					epithelial cell-cell adhesion (GO:0090136)|microtubule anchoring (GO:0034453)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of organelle organization (GO:0033043)|zonula adherens maintenance (GO:0045218)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)|zonula adherens (GO:0005915)	microtubule minus-end binding (GO:0051011)			cervix(1)|endometrium(7)|kidney(3)|lung(6)|urinary_tract(2)	19						ACCAGTACGCGCAGGAGCATG	0.637																																					p.A66A		Atlas-SNP	.											.	CAMSAP3	131	.	0			c.G198T						.						105	114	111					19																	7670161		1998	4152	6150	SO:0001819	synonymous_variant	57662	exon2			GTACGCGCAGGAG	AB040976	CCDS42489.1, CCDS45947.1	19p13.3-p13.2	2014-06-12	2011-08-18	2011-08-18		ENSG00000076826			29307	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 80"	612685	"KIAA1543"	KIAA1543		11318610, 10819331, 19041755, 19508979	Standard	NM_001080429		Approved	Nezha, PPP1R80	uc002mgu.4	Q9P1Y5		ENST00000160298.4:c.198G>T	chr19.hg19:g.7670161G>T		173.0	0.0		138.0	50.0	NM_020902	Q8NDF1	Silent	SNP	ENST00000160298.4	hg19	CCDS42489.1																																																																																			.	.		0.637	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362		T	7670161	G	T	7670161	2	4	11	1	0	0	0	0	0	0	0	1	8252	1074	38	1		1	KIAA1543	19	7670161	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	7382445	7670161	51458822	109	980										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13409467	13409467	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ctcgcccccgtcggggccctCgccctcgccctcgccgcccc	10	26	0	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr19:13409467C>G	ENST00000360228.5	-	19	2979	c.2980G>C	c.(2980-2982)Gag>Cag	p.E994Q	CACNA1A_ENST00000573710.2_Missense_Mutation_p.E995Q	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	995					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	tcggggccctcgccctcgccc	0.791																																					p.E995Q		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G2983C						.						12	11	11					19																	13409467		1280	2619	3899	SO:0001583	missense	773	exon19			GGCCCTCGCCCTC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.2980G>C	chr19.hg19:g.13409467C>G	ENSP00000353362:p.Glu994Gln	110.0	0.0		158.0	7.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.600130	0.28534	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.95980	-3.87	1.91	1.91	0.25777	.	26.724300	0.00714	N	0.000849	D	0.95322	0.8482	L	0.54323	1.7	0.28666	N	0.905881	B;B;D	0.56521	0.199;0.3;0.976	B;B;P	0.51266	0.057;0.079;0.664	D	0.87459	0.2406	10	0.23302	T	0.38	.	9.8436	0.41013	0.0:1.0:0.0:0.0	.	995;998;994	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	Q	994;998;995;995	ENSP00000353362:E994Q	ENSP00000317661:E995Q	E	-	1	0	CACNA1A	13270467	0.000000	0.05858	0.977000	0.42913	0.760000	0.43138	0.548000	0.23314	1.389000	0.46526	0.407000	0.27541	GAG	.	.		0.791	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		G	13409467	C	G	13409467	3	3	11	1	0	0	0	0	1	0	0	0	2540	893	31	4	4758	4	CACNA1A	19	13409467	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	5739306	13409467	45719516	110	981										
NCAN	1463	hgsc.bcm.edu	37	chr19	19345806	19345806	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tgccagacattgatgactgcCtctgcagcccctgtgagaat	10	12	1	4	rs374113750		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr19:19345806C>G	ENST00000252575.6	+	10	3250	c.3151C>G	c.(3151-3153)Ctc>Gtc	p.L1051V	RNU6-1028P_ENST00000517164.1_RNA|NCAN_ENST00000538881.1_Missense_Mutation_p.L502V	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	1051	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	TGATGACTGCCTCTGCAGCCC	0.547																																					p.L1051V		Atlas-SNP	.											.	NCAN	277	.	0			c.C3151G						.						145	113	124					19																	19345806		2203	4300	6503	SO:0001583	missense	1463	exon10			GACTGCCTCTGCA	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans", "Endogenous ligands"	2465	protein-coding gene	gene with protein product	"neurocan proteoglycan"	600826	"chondroitin sulfate proteoglycan 3"	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.3151C>G	chr19.hg19:g.19345806C>G	ENSP00000252575:p.Leu1051Val	59.0	0.0		53.0	16.0	NM_004386	Q9UPK6	Missense_Mutation	SNP	ENST00000252575.6	hg19	CCDS12397.1	.	.	.	.	.	.	.	.	.	.	C	10.42	1.345916	0.24426	.	.	ENSG00000130287	ENST00000539499;ENST00000252575;ENST00000538881	D;D	0.98437	-4.93;-4.93	4.53	-9.07	0.00724	EGF-like calcium-binding, conserved site (1);EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	2.104420	0.02849	N	0.128956	D	0.93838	0.8029	L	0.43701	1.375	0.09310	N	1	B;B	0.15473	0.013;0.001	B;B	0.04013	0.001;0.001	D	0.87967	0.2734	10	0.12103	T	0.63	-0.8526	3.2716	0.06884	0.3516:0.3929:0.1576:0.0979	.	1065;1051	Q4LE67;O14594	.;NCAN_HUMAN	V	1065;1051;502	ENSP00000252575:L1051V;ENSP00000442202:L502V	ENSP00000252575:L1051V	L	+	1	0	NCAN	19206806	0.000000	0.05858	0.005000	0.12908	0.952000	0.60782	-0.070000	0.11523	-1.346000	0.02211	-0.340000	0.08031	CTC	.	.		0.547	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386		G	19345806	C	G	19345806	3	3	11	1	0	0	0	0	1	0	0	0	10213	681	24	4	3185	4	NCAN	19	19345806	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	5936339	19345806	39783177	111	982										
PLD3	23646	hgsc.bcm.edu	37	chr19	40875888	40875888	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ccgcatcgctgtgagcaagcCcagcgggccccagccacagg	13	17	0	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr19:40875888C>G	ENST00000409587.1	+	7	900	c.503C>G	c.(502-504)cCc>cGc	p.P168R	PLD3_ENST00000409281.1_Missense_Mutation_p.P168R|PLD3_ENST00000409735.4_Missense_Mutation_p.P168R|PLD3_ENST00000409419.1_Missense_Mutation_p.P168R|PLD3_ENST00000356508.5_Missense_Mutation_p.P168R			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	168					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			GTGAGCAAGCCCAGCGGGCCC	0.706																																					p.P168R		Atlas-SNP	.											.	PLD3	71	.	0			c.C503G						.						6	7	6					19																	40875888		2147	4205	6352	SO:0001583	missense	23646	exon7			GCAAGCCCAGCGG	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"phospholipase D3"			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.503C>G	chr19.hg19:g.40875888C>G	ENSP00000387050:p.Pro168Arg	97.0	0.0		95.0	34.0	NM_012268	Q92853|Q9BW87	Missense_Mutation	SNP	ENST00000409587.1	hg19	CCDS33027.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.303947	0.81136	.	.	ENSG00000105223	ENST00000409419;ENST00000409587;ENST00000356508;ENST00000536031;ENST00000409735;ENST00000409281;ENST00000359274	T;T;T;T;T;T	0.62639	0.75;0.75;0.75;0.75;0.75;0.01	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.72645	0.3486	M	0.67700	2.07	0.58432	D	0.999997	P	0.44816	0.844	P	0.53809	0.735	T	0.72537	-0.4263	10	0.49607	T	0.09	-24.985	15.5311	0.75964	0.0:1.0:0.0:0.0	.	168	Q8IV08	PLD3_HUMAN	R	168;168;168;149;168;168;168	ENSP00000386293:P168R;ENSP00000387050:P168R;ENSP00000348901:P168R;ENSP00000386938:P168R;ENSP00000387022:P168R;ENSP00000352220:P168R	ENSP00000348901:P168R	P	+	2	0	PLD3	45567728	0.995000	0.38212	0.985000	0.45067	0.951000	0.60555	3.361000	0.52306	2.728000	0.93425	0.561000	0.74099	CCC	.	.		0.706	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268		G	40875888	C	G	40875888	3	3	11	1	0	0	0	0	1	0	0	0	12056	623	22	4	521	4	PLD3	19	40875888	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	21530082	40875888	18253095	112	983										
SIGLEC8	27181	hgsc.bcm.edu	37	chr19	51958750	51958750	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ctgagctcggcaggtgaattCcccttcatccctcacgtgca	9	15	2	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr19:51958750C>A	ENST00000321424.3	-	4	1039	c.973G>T	c.(973-975)Gaa>Taa	p.E325*	SIGLEC8_ENST00000430817.1_Nonsense_Mutation_p.E216*|SIGLEC8_ENST00000597352.1_5'UTR|SIGLEC8_ENST00000340550.5_Nonsense_Mutation_p.E232*	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	325	Ig-like C2-type 2.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CAGGTGAATTCCCCTTCATCC	0.647																																					p.E325X		Atlas-SNP	.											.	SIGLEC8	130	.	0			c.G973T						.						56	54	55					19																	51958750		2203	4300	6503	SO:0001587	stop_gained	27181	exon4			TGAATTCCCCTTC	AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.973G>T	chr19.hg19:g.51958750C>A	ENSP00000321077:p.Glu325*	125.0	0.0		131.0	41.0	NM_014442	Q7Z728	Nonsense_Mutation	SNP	ENST00000321424.3	hg19	CCDS33086.1	.	.	.	.	.	.	.	.	.	.	.	16.84	3.232812	0.58777	.	.	ENSG00000105366	ENST00000430817;ENST00000321424;ENST00000340550	.	.	.	2.19	-0.738	0.11125	.	0.417856	0.17378	N	0.176395	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	5.1668	0.15090	0.0:0.648:0.0:0.352	.	.	.	.	X	216;325;232	.	ENSP00000321077:E325X	E	-	1	0	SIGLEC8	56650562	0.000000	0.05858	0.000000	0.03702	0.159000	0.22180	-0.585000	0.05794	-0.136000	0.11475	0.502000	0.49764	GAA	.	.		0.647	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442		A	51958750	C	A	51958750	4	1	11	1	0	0	0	0	0	1	0	0	14329	864	30	3	542	3	SIGLEC8	19	51958750	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	11082862	51958750	7170233	113	984										
ZNF468	90333	hgsc.bcm.edu	37	chr19	53344837	53344837	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tacattgtttctcttctaagTgaattatctgatgttttttt	5	5	3	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr19:53344837T>G	ENST00000595646.1	-	4	830	c.710A>C	c.(709-711)cAc>cCc	p.H237P	ZNF468_ENST00000390651.4_Missense_Mutation_p.H184P|ZNF468_ENST00000396409.4_Missense_Mutation_p.H184P|ZNF468_ENST00000243639.4_3'UTR|ZNF28_ENST00000594602.1_Intron			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	237					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		CTCTTCTAAGTGAATTATCTG	0.363																																					p.H237P		Atlas-SNP	.											.	ZNF468	46	.	0			c.A710C						.						88	78	82					19																	53344837		2203	4300	6503	SO:0001583	missense	90333	exon4			TCTAAGTGAATTA	AK023558	CCDS33094.1, CCDS62781.1	19q13.41	2013-01-08				ENSG00000204604		"Zinc fingers, C2H2-type", "-"	33105	protein-coding gene	gene with protein product						16144304	Standard	NM_001277120		Approved		uc002qaf.3	Q5VIY5		ENST00000595646.1:c.710A>C	chr19.hg19:g.53344837T>G	ENSP00000470381:p.His237Pro	52.0	0.0		91.0	33.0	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Missense_Mutation	SNP	ENST00000595646.1	hg19	CCDS33094.1	.	.	.	.	.	.	.	.	.	.	t	6.825	0.521427	0.13005	.	.	ENSG00000204604	ENST00000243639;ENST00000396409;ENST00000390651	T;T	0.67698	-0.28;-0.28	1.83	-0.595	0.11660	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.82949	0.5148	H	0.94808	3.585	0.09310	N	1	P	0.52577	0.954	D	0.74674	0.984	T	0.70766	-0.4783	9	0.87932	D	0	.	5.6836	0.17790	0.0:0.2901:0.0:0.7099	.	237	Q5VIY5	ZN468_HUMAN	P	237;184;184	ENSP00000379690:H184P;ENSP00000445669:H184P	ENSP00000243639:H237P	H	-	2	0	ZNF468	58036649	0.938000	0.31826	0.000000	0.03702	0.043000	0.13939	2.470000	0.45119	-0.423000	0.07394	0.341000	0.21757	CAC	.	.		0.363	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801		G	53344837	T	G	53344837	3	3	11	1	0	0	0	0	1	0	0	0	17943	1696	59	5	862	5	ZNF468	19	53344837	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	1386087	53344837	5784146	114	985										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53645787	53645787	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	cctttgtgtagtaaatctttCattacaaattcggaagagag	8	6	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr19:53645787C>T	ENST00000334197.7	-	5	362	c.294G>A	c.(292-294)atG>atA	p.M98I	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_Missense_Mutation_p.M99I|ZNF347_ENST00000452676.2_Missense_Mutation_p.M99I	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	98					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		GTAAATCTTTCATTACAAATT	0.338																																					p.M99I	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.G297A						.						41	38	39					19																	53645787		2203	4298	6501	SO:0001583	missense	84671	exon5			ATCTTTCATTACA	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.294G>A	chr19.hg19:g.53645787C>T	ENSP00000334146:p.Met98Ile	42.0	0.0		64.0	14.0	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	hg19	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.739872	0.00675	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.05925	3.37;3.37	3.05	-6.11	0.02131	.	.	.	.	.	T	0.02688	0.0081	N	0.12961	0.28	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.45175	-0.9279	9	0.27785	T	0.31	.	2.3291	0.04231	0.1129:0.4026:0.1984:0.286	.	99;98	G5E9N4;Q96SE7	.;ZN347_HUMAN	I	98;99	ENSP00000334146:M98I;ENSP00000405218:M99I	ENSP00000334146:M98I	M	-	3	0	ZNF347	58337599	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.635000	0.05471	-0.823000	0.04301	-1.058000	0.02302	ATG	.	.		0.338	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		T	53645787	C	T	53645787	3	4	11	1	0	0	0	0	1	0	0	0	17876	826	29	3	2229	3	ZNF347	19	53645787	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	300950	53645787	5483196	115	986										
SIRPG	55423	hgsc.bcm.edu	37	chr20	1629706	1629706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tgttgtactcaccacccaaaGccatctcagtgcctggtcca	7	15	2	0	rs370649250		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr20:1629706G>A	ENST00000303415.3	-	2	486	c.422C>T	c.(421-423)gCt>gTt	p.A141V	SIRPG_ENST00000381580.1_Missense_Mutation_p.A108V|SIRPG_ENST00000216927.4_Missense_Mutation_p.A141V|SIRPG_ENST00000381583.2_Missense_Mutation_p.A141V|RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000344103.4_Missense_Mutation_p.A141V	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	141					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						ACCACCCAAAGCCATCTCAGT	0.483																																					p.A141V		Atlas-SNP	.											.	SIRPG	61	.	0			c.C422T						.	G	VAL/ALA,VAL/ALA,VAL/ALA	1,4405		0,1,2202	193	173	180		422,422,422	1.9	0	20		180	0,8600		0,0,4300	no	missense,missense,missense	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	64,64,64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign	141/277,141/388,141/171	1629706	1,13005	2203	4300	6503	SO:0001583	missense	55423	exon2			CCCAAAGCCATCT	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.422C>T	chr20.hg19:g.1629706G>A	ENSP00000305529:p.Ala141Val	51.0	0.0		112.0	40.0	NM_001039508	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	hg19	CCDS13020.2	.	.	.	.	.	.	.	.	.	.	.	8.940	0.965641	0.18583	2.27E-4	0.0	ENSG00000089012	ENST00000381580;ENST00000344103;ENST00000303415;ENST00000381583;ENST00000216927	T;T;T;T;T	0.02140	4.43;4.52;4.43;4.43;4.43	1.93	1.93	0.25924	Immunoglobulin-like fold (1);	0.313450	0.27664	N	0.018373	T	0.01124	0.0037	N	0.14661	0.345	0.09310	N	1	P;B;B	0.42973	0.796;0.072;0.005	B;B;B	0.29942	0.109;0.011;0.008	T	0.55755	-0.8091	10	0.30854	T	0.27	.	7.3585	0.26733	0.0:0.0:1.0:0.0	.	141;141;141	Q9P1W8-3;Q9P1W8-4;Q9P1W8	.;.;SIRPG_HUMAN	V	108;141;141;141;141	ENSP00000370992:A108V;ENSP00000342759:A141V;ENSP00000305529:A141V;ENSP00000370995:A141V;ENSP00000216927:A141V	ENSP00000216927:A141V	A	-	2	0	SIRPG	1577706	0.002000	0.14202	0.027000	0.17364	0.160000	0.22226	0.181000	0.16880	1.392000	0.46585	0.195000	0.17529	GCT	.	.		0.483	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		A	1629706	G	A	1629706	3	1	11	1	0	0	0	0	1	0	0	0	14351	971	34	3	757	3	SIRPG	20	1629706	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10		1629706	61395814	116	987										
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51870043	51870043	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	cttcttctcttgcaggctacGcccaggaggaacagctgaaa	10	12	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr20:51870043G>A	ENST00000371497.5	+	2	933	c.46G>A	c.(46-48)Gcc>Acc	p.A16T	TSHZ2_ENST00000329613.6_Missense_Mutation_p.A13T|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000603338.2_Missense_Mutation_p.A13T	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	16					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			TGCAGGCTACGCCCaggagga	0.493																																					p.A16T		Atlas-SNP	.											.	TSHZ2	209	.	0			c.G46A						.						31	34	33					20																	51870043		2203	4299	6502	SO:0001583	missense	128553	exon2			GGCTACGCCCAGG	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.46G>A	chr20.hg19:g.51870043G>A	ENSP00000360552:p.Ala16Thr	23.0	0.0		44.0	16.0	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.768954	0.49680	.	.	ENSG00000182463	ENST00000371497;ENST00000329613	T;T	0.14022	2.54;2.54	5.7	5.7	0.88788	.	0.478642	0.23593	N	0.046538	T	0.09905	0.0243	N	0.22421	0.69	0.58432	D	0.999991	B	0.32382	0.368	B	0.17098	0.017	T	0.08534	-1.0717	10	0.72032	D	0.01	-18.5526	14.6446	0.68751	0.0:0.0:0.8545:0.1455	.	16	Q9NRE2	TSH2_HUMAN	T	16;13	ENSP00000360552:A16T;ENSP00000333114:A13T	ENSP00000333114:A13T	A	+	1	0	TSHZ2	51303450	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	4.076000	0.57591	2.685000	0.91497	0.643000	0.83706	GCC	.	.		0.493	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		A	51870043	G	A	51870043	3	1	11	1	0	0	0	0	1	0	0	0	16639	1087	38	1	52	1	TSHZ2	20	51870043	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10	50240337	51870043	11155477	117	988										
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62592718	62592718	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	actctcagaactgaactcctTcggacacagcagacagcggt	9	13	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr20:62592718T>G	ENST00000450537.1	-	16	2431	c.2371A>C	c.(2371-2373)Aag>Cag	p.K791Q	ZNF512B_ENST00000217130.3_Missense_Mutation_p.K791Q|ZNF512B_ENST00000369888.1_Missense_Mutation_p.K791Q			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	791					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTGAACTCCTTCGGACACAGC	0.622																																					p.K791Q		Atlas-SNP	.											.	ZNF512B	72	.	0			c.A2371C						.						109	96	101					20																	62592718		2202	4300	6502	SO:0001583	missense	57473	exon16			ACTCCTTCGGACA	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.2371A>C	chr20.hg19:g.62592718T>G	ENSP00000393795:p.Lys791Gln	33.0	0.0		32.0	12.0	NM_020713	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	hg19	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.616739	0.87359	.	.	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.26660	1.72;1.72;1.72	5.23	5.23	0.72850	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	T	0.46737	0.1408	L	0.55990	1.75	0.58432	D	0.999995	D	0.89917	1.0	D	0.91635	0.999	T	0.42666	-0.9438	10	0.56958	D	0.05	-25.2861	15.1094	0.72343	0.0:0.0:0.0:1.0	.	791	Q96KM6	Z512B_HUMAN	Q	791	ENSP00000358904:K791Q;ENSP00000393795:K791Q;ENSP00000217130:K791Q	ENSP00000217130:K791Q	K	-	1	0	ZNF512B	62063162	1.000000	0.71417	0.968000	0.41197	0.801000	0.45260	5.962000	0.70364	1.981000	0.57761	0.482000	0.46254	AAG	.	.		0.622	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		G	62592718	T	G	62592718	3	3	11	1	0	0	0	0	1	0	0	0	17972	1792	62	5	315	5	ZNF512B	20	62592718	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	10722675	62592718	432802	118	989										
CLDN14	23562	hgsc.bcm.edu	37	chr21	37833541	37833541	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aacttcatgccgctgggcagCagcgggttgtagaagttctg	14	9	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr21:37833541C>T	ENST00000399137.1	-	3	1319	c.453G>A	c.(451-453)ctG>ctA	p.L151L	AP000695.6_ENST00000429588.1_RNA|CLDN14_ENST00000399136.1_Silent_p.L151L|CLDN14_ENST00000342108.2_Silent_p.L151L|CLDN14_ENST00000399135.1_Silent_p.L151L|AP000695.4_ENST00000428667.1_RNA|CLDN14_ENST00000399139.1_Silent_p.L151L|AP000695.4_ENST00000454980.1_RNA	NM_144492.2	NP_652763.1	O95500	CLD14_HUMAN	claudin 14	151					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein complex assembly (GO:0006461)|tight junction assembly (GO:0070830)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|lung(5)|skin(1)	7						CGCTGGGCAGCAGCGGGTTGT	0.622																																					p.L151L		Atlas-SNP	.											.	CLDN14	25	.	0			c.G453A						.						84	78	80					21																	37833541		2203	4300	6503	SO:0001819	synonymous_variant	23562	exon3			GGGCAGCAGCGGG	AJ132445	CCDS13645.1	21q22.3	2008-07-31			ENSG00000159261	ENSG00000159261		"Claudins"	2035	protein-coding gene	gene with protein product		605608		DFNB29		11163249	Standard	NM_144492		Approved		uc002yvk.2	O95500	OTTHUMG00000086638	ENST00000399137.1:c.453G>A	chr21.hg19:g.37833541C>T		75.0	0.0		83.0	25.0	NM_144492		Silent	SNP	ENST00000399137.1	hg19	CCDS13645.1																																																																																			.	.		0.622	CLDN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194697.1	NM_144492		T	37833541	C	T	37833541	2	4	11	1	0	0	0	0	0	0	0	1	3477	697	25	3		3	CLDN14	21	37833541	Silent	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10		37833541	10296354	119	990										
TRAPPC10	7109	hgsc.bcm.edu	37	chr21	45451995	45451995	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ctggagatcagaatttatttAcctctgtttatccaacgctc	6	10	2	2			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr21:45451995A>C	ENST00000291574.4	+	2	266	c.91A>C	c.(91-93)Acc>Ccc	p.T31P	TRAPPC10_ENST00000380221.3_Missense_Mutation_p.T31P	NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	31					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						GAATTTATTTACCTCTGTTTA	0.378																																					p.T31P		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.A91C						.						170	169	169					21																	45451995		2203	4300	6503	SO:0001583	missense	7109	exon2			TTATTTACCTCTG	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"Trafficking protein particle complex"	11868	protein-coding gene	gene with protein product	"trafficking protein particle complex subunit 130", "TRAPP 130 kDa subunit"	602103	"transmembrane protein 1"	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.91A>C	chr21.hg19:g.45451995A>C	ENSP00000291574:p.Thr31Pro	66.0	0.0		104.0	29.0	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	hg19	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	A	17.77	3.471827	0.63737	.	.	ENSG00000160218	ENST00000380221;ENST00000291574	T;T	0.24538	1.85;1.85	5.5	4.15	0.48705	.	0.171408	0.49916	D	0.000125	T	0.27027	0.0662	L	0.56769	1.78	0.45307	D	0.998302	P;B	0.44478	0.836;0.277	P;B	0.44359	0.447;0.122	T	0.03221	-1.1059	10	0.54805	T	0.06	.	6.9416	0.24496	0.7804:0.0:0.0826:0.137	.	31;31	P48553;Q86SI7	TPC10_HUMAN;.	P	31	ENSP00000369570:T31P;ENSP00000291574:T31P	ENSP00000291574:T31P	T	+	1	0	TRAPPC10	44276423	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.432000	0.59922	2.089000	0.63090	0.528000	0.53228	ACC	.	.		0.378	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		C	45451995	A	C	45451995	3	2	11	1	0	0	0	0	1	0	0	0	16472	391	14	5	97	5	TRAPPC10	21	45451995	Missense_Mutation	SNP	A	TCGA-2Y-A9H1-01A-11D-A382-10	7618454	45451995	2677900	120	991										
GNAZ	2781	hgsc.bcm.edu	37	chr22	23437953	23437953	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	gagaattgaccgccacctgcGctcagagagccagcggcaac	12	14	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr22:23437953G>C	ENST00000248996.4	+	2	737	c.71G>C	c.(70-72)cGc>cCc	p.R24P	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	24					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		CGCCACCTGCGCTCAGAGAGC	0.602																																					p.R24P		Atlas-SNP	.											.	GNAZ	45	.	0			c.G71C						.						46	49	48					22																	23437953		2203	4300	6503	SO:0001583	missense	2781	exon2			ACCTGCGCTCAGA		CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.71G>C	chr22.hg19:g.23437953G>C	ENSP00000248996:p.Arg24Pro	146.0	0.0		96.0	30.0	NM_002073	B2R6C1|Q4QRJ6	Missense_Mutation	SNP	ENST00000248996.4	hg19	CCDS13804.1	.	.	.	.	.	.	.	.	.	.	G	32	5.167556	0.94768	.	.	ENSG00000128266	ENST00000248996	D	0.89415	-2.51	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	D	0.95004	0.8383	M	0.87097	2.86	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	D	0.95773	0.8810	10	0.87932	D	0	.	17.55	0.87873	0.0:0.0:1.0:0.0	.	24	P19086	GNAZ_HUMAN	P	24	ENSP00000248996:R24P	ENSP00000248996:R24P	R	+	2	0	GNAZ	21767953	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.531000	0.98054	2.456000	0.83038	0.655000	0.94253	CGC	.	.		0.602	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073		C	23437953	G	C	23437953	3	2	11	1	0	0	0	0	1	0	0	0	6522	1087	38	4	73	4	GNAZ	22	23437953	Missense_Mutation	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10		23437953	27866613	121	992										
APOBEC3A	200315	hgsc.bcm.edu	37	chr22	39357505	39357505	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tacagggtcacttggttcatCtcctggagcccctgcttctc	9	14	4	0	rs373904674		TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr22:39357505C>G	ENST00000402255.1	+	4	492	c.288C>G	c.(286-288)atC>atG	p.I96M	APOBEC3A_ENST00000249116.2_Missense_Mutation_p.I96M			P31941	ABC3A_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A	96	CMP/dCMP deaminase zinc-binding.				cellular response to xenobiotic stimulus (GO:0071466)|clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine (GO:0044356)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(2)|ovary(1)|skin(1)	5	Melanoma(58;0.04)					CTTGGTTCATCTCCTGGAGCC	0.597																																					p.I96M		Atlas-SNP	.											.	APOBEC3A	20	.	0			c.C288G						.						24	28	26					22																	39357505		2105	4013	6118	SO:0001583	missense	200315	exon3			GTTCATCTCCTGG	U03891	CCDS13981.1	22q13.1-q13.2	2014-01-28			ENSG00000128383	ENSG00000128383		"Apolipoprotein B mRNA editing enzymes"	17343	protein-coding gene	gene with protein product	"phorbolin I"	607109				11863358, 10469298	Standard	NM_145699		Approved	ARP3, PHRBN		P31941	OTTHUMG00000151004	ENST00000402255.1:c.288C>G	chr22.hg19:g.39357505C>G	ENSP00000384359:p.Ile96Met	111.0	0.0		106.0	30.0	NM_145699	A0AVM1|Q12807|Q5JZ93|Q9UH18	Missense_Mutation	SNP	ENST00000402255.1	hg19	CCDS13981.1	.	.	.	.	.	.	.	.	.	.	.	8.808	0.934451	0.18206	.	.	ENSG00000128383	ENST00000402255;ENST00000249116	T;T	0.67523	-0.27;-0.27	2.35	1.28	0.21552	APOBEC-like, N-terminal (1);APOBEC/CMP deaminase, zinc-binding (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.69106	0.3074	L	0.50993	1.605	0.20638	N	0.99987	B;D	0.55605	0.253;0.972	B;P	0.55871	0.133;0.786	T	0.57711	-0.7764	9	0.59425	D	0.04	.	8.1745	0.31275	0.2409:0.759:0.0:0.0	.	78;96	B7ZLZ1;P31941	.;ABC3A_HUMAN	M	96	ENSP00000384359:I96M;ENSP00000249116:I96M	ENSP00000249116:I96M	I	+	3	3	APOBEC3A	37687451	0.987000	0.35691	0.891000	0.34965	0.012000	0.07955	0.035000	0.13797	0.519000	0.28406	-0.302000	0.09304	ATC	.	.		0.597	APOBEC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320915.2	NM_145699		G	39357505	C	G	39357505	3	3	11	1	0	0	0	0	1	0	0	0	789	903	32	4	298	4	APOBEC3A	22	39357505	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	15919552	39357505	11947061	122	993										
SCO2	9997	hgsc.bcm.edu	37	chr22	50962567	50962567	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	agctgcctggcgcagggcttCtgttcgcttttgctgctgca	13	12	1	0			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chr22:50962567C>T	ENST00000543927.1	-	2	480	c.274G>A	c.(274-276)Gaa>Aaa	p.E92K	SCO2_ENST00000395693.3_Missense_Mutation_p.E92K|CTA-384D8.36_ENST00000608319.1_RNA|SCO2_ENST00000252785.3_Missense_Mutation_p.E92K|SCO2_ENST00000535425.1_Missense_Mutation_p.E92K	NM_001169109.1	NP_001162580.1	O43819	SCO2_HUMAN	SCO2 cytochrome c oxidase assembly protein	92	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|eye development (GO:0001654)|in utero embryonic development (GO:0001701)|muscle system process (GO:0003012)|oxidation-reduction process (GO:0055114)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			endometrium(1)|lung(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CGCAGGGCTTCTGTTCGCTTT	0.672																																					p.E92K		Atlas-SNP	.											.	SCO2	38	.	0			c.G274A						.						27	30	29					22																	50962567		2203	4298	6501	SO:0001583	missense	9997	exon2			GGGCTTCTGTTCG	AL021683	CCDS14095.1	22q13.33	2014-01-30	2012-10-15		ENSG00000130489	ENSG00000130489		"Mitochondrial respiratory chain complex assembly factors"	10604	protein-coding gene	gene with protein product		604272	"SCO (cytochrome oxidase deficient, yeast) homolog 2", "SCO cytochrome oxidase deficient homolog 2 (yeast)", "myopia 6"	MYP6		10218584, 16091356, 23643385	Standard	NM_005138		Approved	SCO1L	uc003bma.3	O43819	OTTHUMG00000150251	ENST00000543927.1:c.274G>A	chr22.hg19:g.50962567C>T	ENSP00000444433:p.Glu92Lys	57.0	0.0		58.0	20.0	NM_001169111	Q3T1B5|Q9UK87	Missense_Mutation	SNP	ENST00000543927.1	hg19	CCDS14095.1	.	.	.	.	.	.	.	.	.	.	C	5.086	0.201497	0.09652	.	.	ENSG00000130489	ENST00000395693;ENST00000543927;ENST00000535425;ENST00000252785;ENST00000439934;ENST00000423348	D;D;D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42;-3.42;-3.42	4.43	4.43	0.53597	Thioredoxin-like fold (2);	0.271361	0.29699	N	0.011439	D	0.85427	0.5694	N	0.05158	-0.105	0.43054	D	0.994669	B	0.23316	0.083	B	0.24701	0.055	T	0.81026	-0.1119	10	0.19590	T	0.45	-25.931	10.7393	0.46143	0.0:0.807:0.193:0.0	.	92	O43819	SCO2_HUMAN	K	92	ENSP00000379046:E92K;ENSP00000444433:E92K;ENSP00000444242:E92K;ENSP00000252785:E92K;ENSP00000415642:E92K;ENSP00000403570:E92K	ENSP00000252785:E92K	E	-	1	0	SCO2	49309433	0.895000	0.30542	0.974000	0.42286	0.092000	0.18411	1.996000	0.40776	2.473000	0.83533	0.563000	0.77884	GAA	.	.		0.672	SCO2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317091.1	NM_005138		T	50962567	C	T	50962567	3	4	11	1	0	0	0	0	1	0	0	0	13947	922	32	3	530	3	SCO2	22	50962567	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	11605062	50962567	341999	123	994										
WWC3	55841	hgsc.bcm.edu	37	chrX	10096096	10096096	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	cagctgcgctggcattccgtGcaggtgttcaccagctctga	12	13	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chrX:10096096G>A	ENST00000380861.4	+	16	2566	c.2175G>A	c.(2173-2175)gtG>gtA	p.V725V	WWC3_ENST00000454666.1_Silent_p.V725V	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	725					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.V725V(1)		NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						GGCATTCCGTGCAGGTGTTCA	0.572																																					p.V725V		Atlas-SNP	.											.	WWC3	142	.	1	Substitution - coding silent(1)	endometrium(1)	c.G2175A						.						96	86	89					X																	10096096		2203	4300	6503	SO:0001819	synonymous_variant	55841	exon16			TTCCGTGCAGGTG	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.2175G>A	chrX.hg19:g.10096096G>A		151.0	0.0		148.0	102.0	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	hg19	CCDS14136.1																																																																																			.	.		0.572	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		A	10096096	G	A	10096096	2	1	11	1	0	0	0	0	0	0	0	1	17428	1306	46	3		3	WWC3	23	10096096	Silent	SNP	G	TCGA-2Y-A9H1-01A-11D-A382-10		10096096	145174464	124	995										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91133725	91133725	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	aactgtcgttgtagttatttTcatcactgctgtagtaagat	8	6	2	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chrX:91133725T>C	ENST00000373094.1	+	2	3331	c.2486T>C	c.(2485-2487)tTc>tCc	p.F829S	PCDH11X_ENST00000504220.2_Missense_Mutation_p.F829S|PCDH11X_ENST00000373097.1_Missense_Mutation_p.F829S|PCDH11X_ENST00000373088.1_Missense_Mutation_p.F829S|PCDH11X_ENST00000361724.1_Missense_Mutation_p.F829S|PCDH11X_ENST00000361655.2_Missense_Mutation_p.F829S|PCDH11X_ENST00000395337.2_Missense_Mutation_p.F829S|PCDH11X_ENST00000298274.8_Missense_Mutation_p.F829S|PCDH11X_ENST00000406881.1_Missense_Mutation_p.F829S	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	829					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						GTAGTTATTTTCATCACTGCT	0.458																																					p.F829S	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.T2486C						.						57	51	53					X																	91133725		2203	4297	6500	SO:0001583	missense	27328	exon2			TTATTTTCATCAC	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.2486T>C	chrX.hg19:g.91133725T>C	ENSP00000362186:p.Phe829Ser	206.0	0.0		295.0	14.0	NM_001168363	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	hg19	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	T	0.575	-0.839325	0.02692	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43	5.15	3.98	0.46160	Protocadherin (1);	0.106561	0.64402	N	0.000004	T	0.34366	0.0895	M	0.74258	2.255	0.31032	N	0.717323	B;B;B;B;B;B;B;B	0.09022	0.002;0.001;0.002;0.002;0.002;0.002;0.001;0.001	B;B;B;B;B;B;B;B	0.20767	0.031;0.011;0.011;0.011;0.011;0.031;0.011;0.011	T	0.38993	-0.9635	10	0.87932	D	0	.	9.4868	0.38935	0.0:0.0845:0.0:0.9155	.	829;829;829;829;829;829;829;829	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	S	829	ENSP00000378746:F829S;ENSP00000362186:F829S;ENSP00000362189:F829S;ENSP00000355040:F829S;ENSP00000362180:F829S;ENSP00000423762:F829S;ENSP00000355105:F829S;ENSP00000384758:F829S;ENSP00000298274:F829S	ENSP00000298274:F829S	F	+	2	0	PCDH11X	91020381	1.000000	0.71417	0.858000	0.33744	0.002000	0.02628	4.929000	0.63455	0.618000	0.30179	-0.331000	0.08364	TTC	.	.		0.458	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		C	91133725	T	C	91133725	3	2	11	1	0	0	0	0	1	0	0	0	11517	1783	62	2	2492	2	PCDH11X	23	91133725	Missense_Mutation	SNP	T	TCGA-2Y-A9H1-01A-11D-A382-10	81037629	91133725	64136835	125	996										
GPR112	139378	hgsc.bcm.edu	37	chrX	135427542	135427542	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	tcctctaagaccttttctttCttaacatccttttcatttac	1	12	4	1			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chrX:135427542C>A	ENST00000394143.1	+	6	1968	c.1677C>A	c.(1675-1677)ttC>ttA	p.F559L	GPR112_ENST00000287534.4_Missense_Mutation_p.F496L|GPR112_ENST00000394141.1_Missense_Mutation_p.F354L|GPR112_ENST00000412101.1_Missense_Mutation_p.F354L|GPR112_ENST00000370652.1_Missense_Mutation_p.F559L	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	559					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CCTTTTCTTTCTTAACATCCT	0.403																																					p.F559L		Atlas-SNP	.											.	GPR112	459	.	0			c.C1677A						.						81	76	77					X																	135427542		2202	4298	6500	SO:0001583	missense	139378	exon6			TTCTTTCTTAACA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1677C>A	chrX.hg19:g.135427542C>A	ENSP00000377699:p.Phe559Leu	35.0	0.0		68.0	52.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	c	5.636	0.301957	0.10678	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.25579	1.82;1.82;1.79;1.93;1.79	3.42	-0.557	0.11800	.	.	.	.	.	T	0.15869	0.0382	L	0.27053	0.805	0.09310	N	1	B;B;B	0.15141	0.012;0.002;0.0	B;B;B	0.18263	0.021;0.002;0.001	T	0.26087	-1.0113	9	0.46703	T	0.11	.	6.0943	0.20010	0.0:0.4212:0.0:0.5787	.	496;354;559	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	L	559;559;354;496;354	ENSP00000377699:F559L;ENSP00000359686:F559L;ENSP00000416526:F354L;ENSP00000287534:F496L;ENSP00000377697:F354L	ENSP00000287534:F496L	F	+	3	2	GPR112	135255208	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.087000	0.14958	-0.142000	0.11354	0.411000	0.27672	TTC	.	.		0.403	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			A	135427542	C	A	135427542	3	1	11	1	0	0	0	0	1	0	0	0	6637	912	32	3	1687	3	GPR112	23	135427542	Missense_Mutation	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	44293817	135427542	19843018	126	997										
GABRE	2564	hgsc.bcm.edu	37	chrX	151123897	151123897	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0551181102362205	7	1	0.994283536585366	0.994283536585366	0.994283536585366	0.37070938215103	1	0	ttgtagatcaggaagttgagCacagcaaactccaacagagc	10	9	1	3			TCGA-2Y-A9H1-01A-11D-A382-10	TCGA-2Y-A9H1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	97b30224-993b-47df-ba5f-824fc6e21907	9f0f7a73-8f8c-40b4-a130-b04813913909	g.chrX:151123897C>T	ENST00000370328.3	-	8	1133	c.1080G>A	c.(1078-1080)gtG>gtA	p.V360V	GABRE_ENST00000370325.1_Silent_p.V360V|AF274855.1_ENST00000582865.1_RNA|GABRE_ENST00000483564.1_5'UTR	NM_004961.3	NP_004952.2	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor, epsilon	360					gamma-aminobutyric acid signaling pathway (GO:0007214)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|skin(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGAAGTTGAGCACAGCAAACT	0.493																																					p.V360V		Atlas-SNP	.											.	GABRE	141	.	0			c.G1080A						.						120	104	110					X																	151123897		2203	4300	6503	SO:0001819	synonymous_variant	2564	exon8			GTTGAGCACAGCA	Y09765	CCDS14703.1	Xq28	2012-06-22			ENSG00000102287	ENSG00000102287		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4085	protein-coding gene	gene with protein product	"GABA(A) receptor, epsilon"	300093				9039914, 9084408	Standard	NM_004961		Approved		uc004ffi.3	P78334	OTTHUMG00000024176	ENST00000370328.3:c.1080G>A	chrX.hg19:g.151123897C>T		73.0	0.0		26.0	7.0	NM_004961	E7ET93|O15345|O15346|Q6PCD2|Q99520	Silent	SNP	ENST00000370328.3	hg19	CCDS14703.1																																																																																			.	.		0.493	GABRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060903.1	NM_004961, NM_021990, NM_021984		T	151123897	C	T	151123897	2	4	11	1	0	0	0	0	0	0	0	1	6178	697	25	3		3	GABRE	23	151123897	Silent	SNP	C	TCGA-2Y-A9H1-01A-11D-A382-10	15696355	151123897	4146663	127	998										
GRIK3	2899	hgsc.bcm.edu	37	chr1	37356579	37356579	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ctctgtatgtcataggtcaaGgttgtgttgggcagcagagt	14	6	3	1			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr1:37356579G>T	ENST00000373091.3	-	2	250	c.234C>A	c.(232-234)acC>acA	p.T78T	GRIK3_ENST00000373093.4_Silent_p.T78T	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	78					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CATAGGTCAAGGTTGTGTTGG	0.547																																					p.T78T		Atlas-SNP	.											.	GRIK3	195	.	0			c.C234A						.						299	234	256					1																	37356579		2203	4300	6503	SO:0001819	synonymous_variant	2899	exon2			GGTCAAGGTTGTG	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.234C>A	chr1.hg19:g.37356579G>T		54.0	0.0		128.0	41.0	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	hg19	CCDS416.1																																																																																			.	.		0.547	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		T	37356579	G	T	37356579	2	4	12	1	0	0	0	0	0	0	0	1	6784	987	35	3		3	GRIK3	1	37356579	Silent	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10		37356579	211894042	1	999										
C8A	731	hgsc.bcm.edu	37	chr1	57378219	57378219	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	tgcttcaacaatggggtgccCatcctcgagggcaccagctg	12	13	1	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr1:57378219C>T	ENST00000361249.3	+	10	1620	c.1524C>T	c.(1522-1524)ccC>ccT	p.P508P		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	508	EGF-like.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						ATGGGGTGCCCATCCTCGAGG	0.612																																					p.P508P		Atlas-SNP	.											.	C8A	103	.	0			c.C1524T						.						83	85	84					1																	57378219		2203	4300	6503	SO:0001819	synonymous_variant	731	exon10			GGTGCCCATCCTC	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"Complement system"	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1524C>T	chr1.hg19:g.57378219C>T		229.0	0.0		490.0	122.0	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Silent	SNP	ENST00000361249.3	hg19	CCDS606.1																																																																																			.	.		0.612	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		T	57378219	C	T	57378219	2	4	12	1	0	0	0	0	0	0	0	1	2418	581	21	3		3	C8A	1	57378219	Silent	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	20021640	57378219	191872402	2	1000										
PYCR2	29920	hgsc.bcm.edu	37	chr1	226109910	226109910	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	gctgagatgggcaccttctcCacagagctgatggtgacacc	12	12	1	4			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr1:226109910C>T	ENST00000343818.6	-	3	460	c.312G>A	c.(310-312)gtG>gtA	p.V104V	PYCR2_ENST00000478402.1_5'UTR|RP4-559A3.7_ENST00000432920.2_Silent_p.V104V	NM_013328.2	NP_037460.2	Q96C36	P5CR2_HUMAN	pyrroline-5-carboxylate reductase family, member 2	104					L-proline biosynthetic process (GO:0055129)	cytoplasm (GO:0005737)	pyrroline-5-carboxylate reductase activity (GO:0004735)			kidney(1)|lung(3)	4	Breast(184;0.197)				L-Proline(DB00172)	GCACCTTCTCCACAGAGCTGA	0.607																																					p.V104V		Atlas-SNP	.											.	PYCR2	13	.	0			c.G312A						.						78	63	68					1																	226109910		2203	4300	6503	SO:0001819	synonymous_variant	29920	exon3			CTTCTCCACAGAG	AF151351	CCDS31043.1, CCDS73039.1	1q42.13	2008-02-05			ENSG00000143811	ENSG00000143811			30262	protein-coding gene	gene with protein product						12477932	Standard	NM_013328		Approved	P5CR2	uc001hpq.4	Q96C36	OTTHUMG00000037506	ENST00000343818.6:c.312G>A	chr1.hg19:g.226109910C>T		45.0	0.0		69.0	12.0	NM_013328	A8K798|Q7Z515|Q9Y5J4	Silent	SNP	ENST00000343818.6	hg19	CCDS31043.1																																																																																			.	.		0.607	PYCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091314.1	NM_013328		T	226109910	C	T	226109910	2	4	12	1	0	0	0	0	0	0	0	1	12871	581	21	3		3	PYCR2	1	226109910	Silent	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	168731691	226109910	23140711	3	1001										
TARBP1	6894	hgsc.bcm.edu	37	chr1	234534263	234534263	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ggtgatccattcatcttcaaTaaggcctgaaaggcgtggaa	11	8	3	2			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr1:234534263T>A	ENST00000040877.1	-	26	4107	c.4108A>T	c.(4108-4110)Att>Ttt	p.I1370F	TARBP1_ENST00000483404.1_Intron	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1370					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TCATCTTCAATAAGGCCTGAA	0.328																																					p.I1370F		Atlas-SNP	.											.	TARBP1	111	.	0			c.A4108T						.						76	78	77					1																	234534263		2203	4300	6503	SO:0001583	missense	6894	exon26			CTTCAATAAGGCC		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"tRNA methyltransferase 3 homolog (S. cerevisiae)"	605052	"Tar (HIV-1) RNA binding protein 1"			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.4108A>T	chr1.hg19:g.234534263T>A	ENSP00000040877:p.Ile1370Phe	50.0	0.0		93.0	12.0	NM_005646	Q9H581	Missense_Mutation	SNP	ENST00000040877.1	hg19	CCDS1601.1	.	.	.	.	.	.	.	.	.	.	T	15.19	2.760815	0.49468	.	.	ENSG00000059588	ENST00000040877	T	0.05996	3.36	5.85	-2.13	0.07144	.	1.014850	0.07850	N	0.964479	T	0.05640	0.0148	N	0.22421	0.69	0.18873	N	0.999986	B	0.26744	0.158	B	0.28232	0.087	T	0.42699	-0.9436	10	0.54805	T	0.06	-11.8186	11.4584	0.50195	0.0:0.515:0.0:0.485	.	1370	Q13395	TARB1_HUMAN	F	1370	ENSP00000040877:I1370F	ENSP00000040877:I1370F	I	-	1	0	TARBP1	232600886	0.014000	0.17966	0.013000	0.15412	0.976000	0.68499	0.287000	0.18920	-0.718000	0.04949	0.528000	0.53228	ATT	.	.		0.328	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646		A	234534263	T	A	234534263	3	1	12	1	0	0	0	0	1	0	0	0	15570	1406	49	4	777	4	TARBP1	1	234534263	Missense_Mutation	SNP	T	TCGA-2Y-A9H2-01A-12D-A382-10	8424353	234534263	14716358	4	1002										
PAPOLG	64895	hgsc.bcm.edu	37	chr2	61014655	61014655	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ttactttatagcaacaattaCgtatcaatgtggttccttgg	7	7	1	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:61014655C>T	ENST00000238714.3	+	15	1545	c.1296C>T	c.(1294-1296)taC>taT	p.Y432Y		NM_022894.3	NP_075045.2	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	432					mRNA polyadenylation (GO:0006378)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	35	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			GCAACAATTACGTATCAATGT	0.279																																					p.Y432Y	GBM(183;1497 2932 21839 46797)	Atlas-SNP	.											.	PAPOLG	66	.	0			c.C1296T						.						60	60	60					2																	61014655		2203	4300	6503	SO:0001819	synonymous_variant	64895	exon15			CAATTACGTATCA	AC012498	CCDS1863.1	2p16.1	2008-02-08			ENSG00000115421	ENSG00000115421	2.7.7.19		14982	protein-coding gene	gene with protein product							Standard	NM_022894		Approved	FLJ12972	uc002sai.3	Q9BWT3	OTTHUMG00000129419	ENST00000238714.3:c.1296C>T	chr2.hg19:g.61014655C>T		143.0	0.0		262.0	25.0	NM_022894	B2RBH4|Q59G05|Q969N1|Q9H8L2|Q9HAD0	Silent	SNP	ENST00000238714.3	hg19	CCDS1863.1																																																																																			.	.		0.279	PAPOLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251577.3	NM_022894		T	61014655	C	T	61014655	2	4	12	1	0	0	0	0	0	0	0	1	11440	547	19	1		1	PAPOLG	2	61014655	Silent	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10		61014655	182184718	5	1003										
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105892080	105892080	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	agttcctcgtctaagcagtaGgtaagaaaatccacgatgta	9	8	1	1			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:105892080G>C	ENST00000393359.2	-	8	2028	c.1602C>G	c.(1600-1602)acC>acG	p.T534T	TGFBRAP1_ENST00000258449.1_Silent_p.T534T			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	534					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						CTAAGCAGTAGGTAAGAAAAT	0.453																																					p.T534T	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C1602G						.						146	133	137					2																	105892080		2203	4300	6503	SO:0001819	synonymous_variant	9392	exon8			GCAGTAGGTAAGA	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.1602C>G	chr2.hg19:g.105892080G>C		138.0	0.0		174.0	26.0	NM_004257	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	hg19	CCDS2067.1																																																																																			.	.		0.453	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		C	105892080	G	C	105892080	2	2	12	1	0	0	0	0	0	0	0	1	15839	987	35	4		4	TGFBRAP1	2	105892080	Silent	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10	44877425	105892080	137307293	6	1004										
TMEM87B	84910	hgsc.bcm.edu	37	chr2	112813302	112813302	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ggctgtgcgcgcggtccctgAgctcgggctctggttagaga	17	11	1	2			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:112813302A>C	ENST00000283206.4	+	1	503	c.134A>C	c.(133-135)gAg>gCg	p.E45A		NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	45						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						GCGGTCCCTGAGCTCGGGCTC	0.726																																					p.E45A		Atlas-SNP	.											.	TMEM87B	52	.	0			c.A134C						.						13	15	15					2																	112813302		2180	4273	6453	SO:0001583	missense	84910	exon1			TCCCTGAGCTCGG	AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.134A>C	chr2.hg19:g.112813302A>C	ENSP00000283206:p.Glu45Ala	260.0	0.0		210.0	24.0	NM_032824	A8K2M9|Q1RLN2|Q53R54	Missense_Mutation	SNP	ENST00000283206.4	hg19	CCDS33275.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	16.99|16.99	3.275356|3.275356	0.59649|0.59649	.|.	.|.	ENSG00000153214|ENSG00000153214	ENST00000283206|ENST00000452614	.|.	.|.	.|.	3.81|3.81	2.51|2.51	0.30379|0.30379	.|.	0.073488|.	0.51477|.	D|.	0.000085|.	T|.	0.49508|.	0.1561|.	L|L	0.50333|0.50333	1.59|1.59	0.34714|0.34714	D|D	0.728045|0.728045	D;B|.	0.71674|.	0.998;0.11|.	D;B|.	0.78314|.	0.991;0.026|.	T|.	0.57694|.	-0.7767|.	9|.	0.66056|.	D|.	0.02|.	-12.6993|-12.6993	5.8903|5.8903	0.18909|0.18909	0.7658:0.0:0.0:0.2342|0.7658:0.0:0.0:0.2342	.|.	45;45|.	Q96K49-2;Q96K49|.	.;TM87B_HUMAN|.	A|C	45|2	.|.	ENSP00000283206:E45A|.	E|X	+|+	2|3	0|0	TMEM87B|TMEM87B	112529773|112529773	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.833000|0.833000	0.47200|0.47200	1.812000|1.812000	0.38952|0.38952	1.495000|1.495000	0.48549|0.48549	0.370000|0.370000	0.22315|0.22315	GAG|TGA	.	.		0.726	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824		C	112813302	A	C	112813302	3	2	12	1	0	0	0	0	1	0	0	0	16226	304	11	5	136	5	TMEM87B	2	112813302	Missense_Mutation	SNP	A	TCGA-2Y-A9H2-01A-12D-A382-10	6921222	112813302	130386071	7	1005										
PDE1A	5136	hgsc.bcm.edu	37	chr2	183129067	183129067	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ctgcttccagcacagatgccGcatattcaatattcttcttt	5	12	3	1			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:183129067G>A	ENST00000410103.1	-	3	259	c.176C>T	c.(175-177)gCg>gTg	p.A59V	PDE1A_ENST00000435564.1_Missense_Mutation_p.A59V|PDE1A_ENST00000536095.1_5'UTR|PDE1A_ENST00000351439.5_Missense_Mutation_p.A43V|PDE1A_ENST00000358139.2_Missense_Mutation_p.A59V|PDE1A_ENST00000409365.1_Missense_Mutation_p.A43V|PDE1A_ENST00000331935.6_Missense_Mutation_p.A59V|PDE1A_ENST00000456212.1_Missense_Mutation_p.A59V	NM_001003683.2	NP_001003683.1	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	59					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	CACAGATGCCGCATATTCAAT	0.373																																					p.A63V		Atlas-SNP	.											.	PDE1A	184	.	0			c.C188T						.						118	111	113					2																	183129067		2202	4300	6502	SO:0001583	missense	5136	exon3			GATGCCGCATATT		CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	3.1.4.17	"Phosphodiesterases"	8774	protein-coding gene	gene with protein product		171890				8557689, 11342109	Standard	NM_005019		Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000410103.1:c.176C>T	chr2.hg19:g.183129067G>A	ENSP00000387037:p.Ala59Val	78.0	0.0		198.0	36.0	NM_001258312	D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	Missense_Mutation	SNP	ENST00000410103.1	hg19	CCDS33344.1	.	.	.	.	.	.	.	.	.	.	G	34	5.336813	0.95758	.	.	ENSG00000115252	ENST00000435564;ENST00000409365;ENST00000331935;ENST00000351439;ENST00000410103;ENST00000358139;ENST00000456212	T;T;T;T;T;T;T	0.73575	-0.76;-0.72;-0.76;-0.72;-0.74;-0.74;-0.76	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.85265	0.5657	M	0.66297	2.02	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.91635	0.943;0.999;0.975	T	0.82866	-0.0245	10	0.37606	T	0.19	.	18.8374	0.92168	0.0:0.0:1.0:0.0	.	59;43;59	P54750;P54750-2;P54750-4	PDE1A_HUMAN;.;.	V	59;43;59;43;59;59;59	ENSP00000410309:A59V;ENSP00000386767:A43V;ENSP00000331574:A59V;ENSP00000309269:A43V;ENSP00000387037:A59V;ENSP00000350858:A59V;ENSP00000408874:A59V	ENSP00000331574:A59V	A	-	2	0	PDE1A	182837312	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.057000	0.93889	2.861000	0.98227	0.655000	0.94253	GCG	.	.		0.373	PDE1A-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334356.1			A	183129067	G	A	183129067	3	1	12	1	0	0	0	0	1	0	0	0	11642	1087	38	1	1561	1	PDE1A	2	183129067	Missense_Mutation	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10	70315765	183129067	60070306	8	1006										
USP37	57695	hgsc.bcm.edu	37	chr2	219374706	219374706	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	gaaagaattgacctacccctGcagttgctgctgttggtgag	12	9	0	3			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:219374706G>A	ENST00000258399.3	-	11	1433	c.1021C>T	c.(1021-1023)Cag>Tag	p.Q341*	USP37_ENST00000418019.1_Nonsense_Mutation_p.Q341*|USP37_ENST00000415516.1_Nonsense_Mutation_p.Q269*|USP37_ENST00000454775.1_Nonsense_Mutation_p.Q341*	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	341	USP.				G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		ACCTACCCCTGCAGTTGCTGC	0.383																																					p.Q341X		Atlas-SNP	.											.	USP37	76	.	0			c.C1021T						.						95	96	95					2																	219374706		2203	4300	6503	SO:0001587	stop_gained	57695	exon11			ACCCCTGCAGTTG	AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"Ubiquitin-specific peptidases"	20063	protein-coding gene	gene with protein product			"ubiquitin specific protease 37"			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.1021C>T	chr2.hg19:g.219374706G>A	ENSP00000258399:p.Gln341*	73.0	0.0		126.0	50.0	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Nonsense_Mutation	SNP	ENST00000258399.3	hg19	CCDS2418.1	.	.	.	.	.	.	.	.	.	.	G	37	6.056772	0.97241	.	.	ENSG00000135913	ENST00000258399;ENST00000454775;ENST00000415516;ENST00000418019	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	20.0951	0.97834	0.0:0.0:1.0:0.0	.	.	.	.	X	341;341;269;341	.	ENSP00000258399:Q341X	Q	-	1	0	USP37	219082950	1.000000	0.71417	0.989000	0.46669	0.433000	0.31745	6.419000	0.73345	2.753000	0.94483	0.467000	0.42956	CAG	.	.		0.383	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		A	219374706	G	A	219374706	4	1	12	1	0	0	0	0	0	1	0	0	17083	1328	46	3	1982	3	USP37	2	219374706	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10	36245639	219374706	23824667	9	1007										
GPC1	2817	hgsc.bcm.edu	37	chr2	241405663	241405663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	cgaccttcctcctgcccctcCtcctcttcctggcccttaca	4	22	1	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:241405663C>T	ENST00000264039.2	+	9	1881	c.1633C>T	c.(1633-1635)Ctc>Ttc	p.L545F	GPC1_ENST00000466624.1_3'UTR	NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	545					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		CCTGCCCCTCCTCCTCTTCCT	0.642																																					p.L545F		Atlas-SNP	.											.	GPC1	32	.	0			c.C1633T						.						44	56	52					2																	241405663		2203	4300	6503	SO:0001583	missense	2817	exon9			CCCCTCCTCCTCT	AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"Proteoglycans / Cell Surface : Glypicans"	4449	protein-coding gene	gene with protein product	"glypican proteoglycan 1"	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.1633C>T	chr2.hg19:g.241405663C>T	ENSP00000264039:p.Leu545Phe	162.0	0.0		188.0	90.0	NM_002081	B3KTD1|Q53QM4	Missense_Mutation	SNP	ENST00000264039.2	hg19	CCDS2534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	4.553|4.553	0.102749|0.102749	0.08731|0.08731	.|.	.|.	ENSG00000063660|ENSG00000063660	ENST00000264039|ENST00000420138	T|.	0.50277|.	0.75|.	4.05|4.05	-0.0157|-0.0157	0.13975|0.13975	.|.	26.672600|.	0.00550|.	U|.	0.000260|.	T|T	0.36496|0.36496	0.0969|0.0969	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	N|N	1|1	B|.	0.23377|.	0.084|.	B|.	0.27170|.	0.077|.	T|T	0.32534|0.32534	-0.9903|-0.9903	10|5	0.20519|.	T|.	0.43|.	-11.8264|-11.8264	2.7386|2.7386	0.05247|0.05247	0.3445:0.347:0.0:0.3084|0.3445:0.347:0.0:0.3084	.|.	545|.	P35052|.	GPC1_HUMAN|.	F|L	545|584	ENSP00000264039:L545F|.	ENSP00000264039:L545F|.	L|P	+|+	1|2	0|0	GPC1|GPC1	241054336|241054336	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.014000|0.014000	0.08584|0.08584	0.187000|0.187000	0.16998|0.16998	0.004000|0.004000	0.14682|0.14682	-0.345000|-0.345000	0.07892|0.07892	CTC|CCT	.	.		0.642	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081		T	241405663	C	T	241405663	3	4	12	1	0	0	0	0	1	0	0	0	6605	681	24	3	1667	3	GPC1	2	241405663	Missense_Mutation	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	22030957	241405663	1793710	10	1008										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4699862	4699862	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	tgcggaatgcccaagaaaagAtggtatactccctggtctct	10	10	1	2			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr3:4699862A>G	ENST00000443694.2	+	10	1006	c.1006A>G	c.(1006-1008)Atg>Gtg	p.M336V	ITPR1_ENST00000456211.2_Missense_Mutation_p.M336V|ITPR1_ENST00000423119.2_Missense_Mutation_p.M351V|ITPR1_ENST00000302640.8_Missense_Mutation_p.M336V|ITPR1_ENST00000354582.6_Missense_Mutation_p.M351V|ITPR1_ENST00000357086.4_Missense_Mutation_p.M351V|ITPR1_ENST00000544951.1_Intron			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	351	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	CCAAGAAAAGATGGTATACTC	0.527																																					p.M351V		Atlas-SNP	.											.	ITPR1	659	.	0			c.A1051G						.						167	167	167					3																	4699862		1987	4161	6148	SO:0001583	missense	3708	exon13			GAAAAGATGGTAT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.1006A>G	chr3.hg19:g.4699862A>G	ENSP00000401671:p.Met336Val	48.0	0.0		77.0	30.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.672447	0.29693	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13;-2.13;-2.13	5.19	5.19	0.71726	MIR motif (2);MIR (2);	0.092352	0.85682	D	0.000000	T	0.73148	0.3550	N	0.03608	-0.345	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.0;0.004;0.001	T	0.68454	-0.5404	10	0.30078	T	0.28	.	15.0661	0.71996	1.0:0.0:0.0:0.0	.	336;351;351	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	V	351;336;351;351;351;336;336	ENSP00000306253:M336V;ENSP00000346595:M351V;ENSP00000405934:M351V;ENSP00000349597:M351V;ENSP00000397885:M336V;ENSP00000401671:M336V	ENSP00000306253:M336V	M	+	1	0	ITPR1	4674862	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.751000	0.62169	1.959000	0.56917	0.533000	0.62120	ATG	.	.		0.527	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		G	4699862	A	G	4699862	3	3	12	1	0	0	0	0	1	0	0	0	7929	333	12	2	1093	2	ITPR1	3	4699862	Missense_Mutation	SNP	A	TCGA-2Y-A9H2-01A-12D-A382-10		4699862	193322568	11	1009										
BAP1	8314	hgsc.bcm.edu	37	chr3	52439158	52439167	+	Frame_Shift_Del	DEL	CTAGAAAGGC	CTAGAAAGGC	-													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	cttggcataattgtgattgtCtagaaaggccggcagccgct							TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	CTAGAAAGGC	CTAGAAAGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr3:52439158_52439167delCTAGAAAGGC	ENST00000460680.1	-	11	1546_1555	c.1075_1084delGCCTTTCTAG	c.(1075-1086)gcctttctagacfs	p.AFLD359fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.AFLD341fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F360L(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TTGTGATTGTCTAGAAAGGCCGGCAGCCGC	0.552			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.359_362del	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	1	Substitution - Missense(1)	kidney(1)	c.1076_1085del						.																																			SO:0001589	frameshift_variant	8314	exon11			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1075_1084delGCCTTTCTAG	chr3.hg19:g.52439158_52439167delCTAGAAAGGC	ENSP00000417132:p.Ala359fs	83.0	0.0		45.0	13.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.552	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52439167	CTAGAAAGGC	-	52439158	7	5	12	1	0	1	0	1	0	0	0	0	1311	913	32	0	1133	0	BAP1	3	52439158	Frame_Shift_Del	DEL	CTAGAAAGGC	TCGA-2Y-A9H2-01A-12D-A382-10	47739296	52439158	145583272	12	1010										
TACC3	10460	hgsc.bcm.edu	37	chr4	1746478	1746478	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	caggtccggagcaaggcccaGgcggaagcgttggccctcca	15	14	0	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr4:1746478G>A	ENST00000313288.4	+	15	2476	c.2370G>A	c.(2368-2370)caG>caA	p.Q790Q		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	790					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			GCAAGGCCCAGGCGGAAGCGT	0.672																																					p.Q790Q	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.G2370A						.						24	26	25					4																	1746478		2197	4298	6495	SO:0001819	synonymous_variant	10460	exon15			GGCCCAGGCGGAA	AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.2370G>A	chr4.hg19:g.1746478G>A		66.0	0.0		128.0	66.0	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Silent	SNP	ENST00000313288.4	hg19	CCDS3352.1																																																																																			.	.		0.672	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2			A	1746478	G	A	1746478	2	1	12	1	0	0	0	0	0	0	0	1	15518	991	35	3		3	TACC3	4	1746478	Silent	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10		1746478	189407798	13	1011										
KLF3	51274	hgsc.bcm.edu	37	chr4	38696400	38696400	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	gtcatcgtgcagcctgggaaGagacctttacctgtggaatc	12	10	1	1			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr4:38696400G>C	ENST00000261438.5	+	5	1034	c.729G>C	c.(727-729)aaG>aaC	p.K243N		NM_016531.5	NP_057615.3	P57682	KLF3_HUMAN	Kruppel-like factor 3 (basic)	243	Pro-rich.				cellular response to peptide (GO:1901653)|multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	18						AGCCTGGGAAGAGACCTTTAC	0.468																																					p.K243N		Atlas-SNP	.											KLF3,right_upper_lobe,carcinoma,0,1	KLF3	40	.	0			c.G729C						.						134	131	132					4																	38696400		2203	4300	6503	SO:0001583	missense	51274	exon5			TGGGAAGAGACCT	AF285837	CCDS3444.1	4p16.1-p15.2	2013-01-08			ENSG00000109787	ENSG00000109787		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	16516	protein-coding gene	gene with protein product	"basic Kruppel-like factor"	609392				18391014	Standard	NM_016531		Approved	BKLF	uc003gth.4	P57682	OTTHUMG00000097821	ENST00000261438.5:c.729G>C	chr4.hg19:g.38696400G>C	ENSP00000261438:p.Lys243Asn	64.0	0.0		105.0	8.0	NM_016531	Q6PIR1|Q86TN0|Q9P2X6	Missense_Mutation	SNP	ENST00000261438.5	hg19	CCDS3444.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.332441	0.60853	.	.	ENSG00000109787	ENST00000261438	T	0.57436	0.4	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.47266	0.1436	L	0.50333	1.59	0.80722	D	1	P	0.42827	0.791	B	0.34931	0.192	T	0.38908	-0.9639	10	0.18276	T	0.48	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	243	P57682	KLF3_HUMAN	N	243	ENSP00000261438:K243N	ENSP00000261438:K243N	K	+	3	2	KLF3	38372795	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.010000	0.40913	2.941000	0.99782	0.655000	0.94253	AAG	.	.		0.468	KLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215093.2			C	38696400	G	C	38696400	3	2	12	1	0	0	0	0	1	0	0	0	8356	933	33	4	743	4	KLF3	4	38696400	Missense_Mutation	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10	36949922	38696400	152457876	14	1012										
TLL1	7092	hgsc.bcm.edu	37	chr4	166986896	166986900	+	Frame_Shift_Del	DEL	GCAAA	GCAAA	-													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ctctgagtctaaactgcatgGcaaattctgtggcgctgaag					rs374208896|rs112517603	byFrequency	TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	GCAAA	GCAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr4:166986896_166986900delGCAAA	ENST00000061240.2	+	16	2716_2720	c.2069_2073delGCAAA	c.(2068-2073)ggcaaafs	p.GK690fs	TLL1_ENST00000507499.1_Frame_Shift_Del_p.GK713fs	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	690	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		AAACTGCATGGCAAATTCTGTGGCG	0.4																																					p.690_691del		Atlas-Indel,Pindel	.											.	TLL1	194	.	0			c.2068_2072del						.																																			SO:0001589	frameshift_variant	7092	exon16			.	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2069_2073delGCAAA	chr4.hg19:g.166986896_166986900delGCAAA	ENSP00000061240:p.Gly690fs	54.0	0.0		89.0	18.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Frame_Shift_Del	DEL	ENST00000061240.2	hg19	CCDS3811.1																																																																																			.	.		0.4	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			-	166986900	GCAAA	-	166986896	7	5	12	1	0	1	0	1	0	0	0	0	15960	1203	42	0	2131	0	TLL1	4	166986896	Frame_Shift_Del	DEL	GCAAA	TCGA-2Y-A9H2-01A-12D-A382-10	128290496	166986896	24167380	15	1013										
KIAA1712	80817	hgsc.bcm.edu	37	chr4	175224920	175224920	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	agtttatccaatgtgggtttGcagaatggaaaatccaaatt	9	5	0	1			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr4:175224920G>A	ENST00000503780.1	+	5	718	c.304G>A	c.(304-306)Gca>Aca	p.A102T	CEP44_ENST00000426172.1_Missense_Mutation_p.A102T|CEP44_ENST00000296519.4_Missense_Mutation_p.A102T|CEP44_ENST00000457424.2_Missense_Mutation_p.A102T	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	102						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)				endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						ATGTGGGTTTGCAGAATGGAA	0.313																																					p.A102T		Atlas-SNP	.											CEP44,NS,carcinoma,0,1	CEP44	35	.	0			c.G304A						.						74	77	76					4																	175224920		2201	4298	6499	SO:0001583	missense	80817	exon5			GGGTTTGCAGAAT	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"KIAA1712"	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.304G>A	chr4.hg19:g.175224920G>A	ENSP00000423153:p.Ala102Thr	184.0	0.0		239.0	35.0	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Missense_Mutation	SNP	ENST00000503780.1	hg19	CCDS34106.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.637284	0.87760	.	.	ENSG00000164118	ENST00000503780;ENST00000505124;ENST00000457424;ENST00000514712;ENST00000515299;ENST00000503053;ENST00000426172;ENST00000296519	T;T;T;T;T	0.58652	0.37;0.32;0.42;0.32;0.37	5.61	5.61	0.85477	.	0.122605	0.53938	D	0.000052	T	0.76033	0.3931	M	0.81942	2.565	0.42653	D	0.99345	D;D	0.76494	0.999;0.999	D;D	0.69479	0.964;0.964	T	0.78876	-0.2031	10	0.72032	D	0.01	.	14.8033	0.69932	0.0:0.0:0.8559:0.1441	.	102;102	Q9C0F1-2;Q9C0F1	.;CEP44_HUMAN	T	102	ENSP00000423153:A102T;ENSP00000389427:A102T;ENSP00000421128:A102T;ENSP00000408221:A102T;ENSP00000296519:A102T	ENSP00000296519:A102T	A	+	1	0	CEP44	175461495	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.531000	0.60602	2.804000	0.96469	0.650000	0.86243	GCA	.	.		0.313	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633		A	175224920	G	A	175224920	3	1	12	1	0	0	0	0	1	0	0	0	8262	1319	46	3	314	3	KIAA1712	4	175224920	Missense_Mutation	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10	8238024	175224920	15929356	16	1014										
TRIM23	373	hgsc.bcm.edu	37	chr5	64909990	64909990	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	aataggcccattctgcagtcGttccaaaagctccaataaag	7	11	1	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr5:64909990G>A	ENST00000231524.9	-	3	672	c.301C>T	c.(301-303)Cga>Tga	p.R101*	TRIM23_ENST00000274327.7_Nonsense_Mutation_p.R101*|TRIM23_ENST00000381018.3_Nonsense_Mutation_p.R101*	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	101					GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R101*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		TTCTGCAGTCGTTCCAAAAGC	0.363																																					p.R101X		Atlas-SNP	.											TRIM23,colon,carcinoma,+1,1	TRIM23	73	.	1	Substitution - Nonsense(1)	ovary(1)	c.C301T						.						117	123	121					5																	64909990		2203	4300	6503	SO:0001587	stop_gained	373	exon3			GCAGTCGTTCCAA	L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	660	protein-coding gene	gene with protein product		601747	"ADP-ribosylation factor domain protein 1, 64kDa", "tripartite motif-containing 23"	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.301C>T	chr5.hg19:g.64909990G>A	ENSP00000231524:p.Arg101*	211.0	1.0		449.0	201.0	NM_033228	Q9BZY4|Q9BZY5	Nonsense_Mutation	SNP	ENST00000231524.9	hg19	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.618182	0.87359	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	.	.	.	5.25	3.45	0.39498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9968	0.41905	0.0721:0.0:0.7895:0.1384	.	.	.	.	X	101	.	ENSP00000231524:R101X	R	-	1	2	TRIM23	64945746	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	4.087000	0.57671	0.589000	0.29677	0.585000	0.79938	CGA	.	.		0.363	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		A	64909990	G	A	64909990	4	1	12	1	0	0	0	0	0	1	0	0	16512	1153	40	1	1526	1	TRIM23	5	64909990	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10		64909990	116005270	17	1015										
GPR98	84059	hgsc.bcm.edu	37	chr5	90106981	90106981	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	aagaacaaactcttacccttAtattcctagatggagaaaga	6	8	1	4			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr5:90106981A>G	ENST00000405460.2	+	74	16000	c.15904A>G	c.(15904-15906)Ata>Gta	p.I5302V	GPR98_ENST00000425867.2_Missense_Mutation_p.I963V	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5302	Calx-beta 34. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TCTTACCCTTATATTCCTAGA	0.413																																					p.I5302V		Atlas-SNP	.											.	GPR98	605	.	0			c.A15904G						.						72	69	70					5																	90106981		1881	4116	5997	SO:0001583	missense	84059	exon74			ACCCTTATATTCC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.15904A>G	chr5.hg19:g.90106981A>G	ENSP00000384582:p.Ile5302Val	123.0	0.0		169.0	38.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	0.022	-1.411693	0.01145	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.26223	1.75;1.75	5.36	0.117	0.14652	Na-Ca exchanger/integrin-beta4 (1);	0.483045	0.23918	N	0.043270	T	0.07052	0.0179	N	0.01874	-0.695	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.002	T	0.34254	-0.9836	9	.	.	.	.	4.9113	0.13823	0.6515:0.0:0.2233:0.1252	.	963;5302;963	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	V	5302;5302;963	ENSP00000384582:I5302V;ENSP00000392618:I963V	.	I	+	1	0	GPR98	90142737	0.444000	0.25649	0.001000	0.08648	0.345000	0.29048	1.084000	0.30828	-0.212000	0.10109	-0.274000	0.10170	ATA	.	.		0.413	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	90106981	A	G	90106981	3	3	12	1	0	0	0	0	1	0	0	0	6730	449	16	2	16198	2	GPR98	5	90106981	Missense_Mutation	SNP	A	TCGA-2Y-A9H2-01A-12D-A382-10	25196991	90106981	90808279	18	1016										
PRR16	51334	hgsc.bcm.edu	37	chr5	120022106	120022106	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	agggcctcgagaacgagttcGgtttaatgaaaaagtacagt	12	6	0	2			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr5:120022106G>A	ENST00000407149.2	+	2	826	c.617G>A	c.(616-618)cGg>cAg	p.R206Q	PRR16_ENST00000379551.2_Missense_Mutation_p.R183Q|PRR16_ENST00000446965.1_Missense_Mutation_p.R136Q|PRR16_ENST00000505123.1_Missense_Mutation_p.R136Q			Q569H4	LARGN_HUMAN	proline rich 16	206	Pro-rich.				positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		GAACGAGTTCGGTTTAATGAA	0.473																																					p.R183Q		Atlas-SNP	.											PRR16,NS,carcinoma,+1,1	PRR16	71	.	0			c.G548A						.						70	71	71					5																	120022106		2203	4300	6503	SO:0001583	missense	51334	exon3			GAGTTCGGTTTAA	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.617G>A	chr5.hg19:g.120022106G>A	ENSP00000385118:p.Arg206Gln	105.0	0.0		183.0	31.0	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Missense_Mutation	SNP	ENST00000407149.2	hg19		.	.	.	.	.	.	.	.	.	.	G	29.5	5.014251	0.93404	.	.	ENSG00000184838	ENST00000407149;ENST00000379551;ENST00000509923;ENST00000505123;ENST00000446965	T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.83464	0.5260	M	0.69823	2.125	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.83343	-0.0007	9	.	.	.	-0.0429	17.8787	0.88833	0.0:0.0:1.0:0.0	.	206;183	Q569H4;Q569H4-3	PRR16_HUMAN;.	Q	206;183;136;136;136	ENSP00000385118:R206Q;ENSP00000368869:R183Q;ENSP00000421256:R136Q;ENSP00000423446:R136Q;ENSP00000405491:R136Q	.	R	+	2	0	PRR16	120050005	1.000000	0.71417	0.974000	0.42286	0.995000	0.86356	9.388000	0.97237	2.505000	0.84491	0.650000	0.86243	CGG	.	.		0.473	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644		A	120022106	G	A	120022106	3	1	12	1	0	0	0	0	1	0	0	0	12601	1116	39	1	554	1	PRR16	5	120022106	Missense_Mutation	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10	29915125	120022106	60893154	19	1017										
AFF4	27125	hgsc.bcm.edu	37	chr5	132270588	132270588	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	cttcatttcatcgtagtttcCaagcatactctgaatacgac	5	11	3	1			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr5:132270588C>T	ENST00000265343.5	-	3	548	c.169G>A	c.(169-171)Gga>Aga	p.G57R	AFF4_ENST00000378595.3_Missense_Mutation_p.G57R|AFF4_ENST00000491831.1_5'UTR	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	57					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCGTAGTTTCCAAGCATACTC	0.313																																					p.G57R	Ovarian(126;889 1733 2942 10745 11605)	Atlas-SNP	.											.	AFF4	120	.	0			c.G169A						.						95	100	98					5																	132270588		2202	4300	6502	SO:0001583	missense	27125	exon3			AGTTTCCAAGCAT	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.169G>A	chr5.hg19:g.132270588C>T	ENSP00000265343:p.Gly57Arg	53.0	0.0		62.0	23.0	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	hg19	CCDS4164.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.776460	0.90195	.	.	ENSG00000072364	ENST00000265343;ENST00000378595;ENST00000421773	D;D;D	0.83419	-1.72;-1.72;-1.72	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.92296	0.7556	M	0.82193	2.58	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.92511	0.6016	10	0.87932	D	0	-11.5109	20.1802	0.98196	0.0:1.0:0.0:0.0	.	57;57;57	Q9UHB7-3;Q9UHB7-2;Q9UHB7	.;.;AFF4_HUMAN	R	57	ENSP00000265343:G57R;ENSP00000367858:G57R;ENSP00000395268:G57R	ENSP00000265343:G57R	G	-	1	0	AFF4	132298487	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.786000	0.85741	2.777000	0.95525	0.655000	0.94253	GGA	.	.		0.313	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		T	132270588	C	T	132270588	3	4	12	1	0	0	0	0	1	0	0	0	359	603	21	3	3398	3	AFF4	5	132270588	Missense_Mutation	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	12248482	132270588	48644672	20	1018										
MDN1	23195	hgsc.bcm.edu	37	chr6	90513095	90513095	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	gtttgctcatcgacacacatAgccgttcatgcagatcatgg	9	11	3	1			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr6:90513095A>G	ENST00000369393.3	-	2	396	c.281T>C	c.(280-282)cTa>cCa	p.L94P	MDN1_ENST00000428876.1_Missense_Mutation_p.L94P			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	94					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.L94P(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CGACACACATAGCCGTTCATG	0.473																																					p.L94P		Atlas-SNP	.											MDN1,NS,carcinoma,0,1	MDN1	478	.	1	Substitution - Missense(1)	lung(1)	c.T281C						.						288	251	263					6																	90513095		2203	4300	6503	SO:0001583	missense	23195	exon2			ACACATAGCCGTT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.281T>C	chr6.hg19:g.90513095A>G	ENSP00000358400:p.Leu94Pro	83.0	0.0		49.0	2.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.995463	0.54147	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.30981	1.51;1.51;1.51	4.77	4.77	0.60923	.	0.000000	0.64402	D	0.000007	T	0.44850	0.1313	M	0.69823	2.125	0.80722	D	1	D;P	0.89917	1.0;0.604	D;B	0.91635	0.999;0.204	T	0.41662	-0.9496	10	0.42905	T	0.14	.	14.589	0.68351	1.0:0.0:0.0:0.0	.	94;94	Q6ZVV6;Q9NU22	.;MDN1_HUMAN	P	94	ENSP00000358400:L94P;ENSP00000413970:L94P;ENSP00000409664:L94P	ENSP00000358400:L94P	L	-	2	0	MDN1	90569816	1.000000	0.71417	0.998000	0.56505	0.897000	0.52465	8.727000	0.91480	1.917000	0.55516	0.254000	0.18369	CTA	.	.		0.473	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			G	90513095	A	G	90513095	3	3	12	1	0	0	0	0	1	0	0	0	9424	420	15	2	16913	2	MDN1	6	90513095	Missense_Mutation	SNP	A	TCGA-2Y-A9H2-01A-12D-A382-10		90513095	80601972	21	1019										
TMEM168	64418	hgsc.bcm.edu	37	chr7	112407741	112407741	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ataataagccgggaacaaaaGgaaccattcttttctctcca	6	10	2	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr7:112407741G>T	ENST00000312814.6	-	5	2165	c.1605C>A	c.(1603-1605)tcC>tcA	p.S535S	TMEM168_ENST00000454074.1_Silent_p.S535S	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	535						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						GGGAACAAAAGGAACCATTCT	0.403																																					p.S535S		Atlas-SNP	.											.	TMEM168	84	.	0			c.C1605A						.						64	64	64					7																	112407741		2203	4300	6503	SO:0001819	synonymous_variant	64418	exon5			ACAAAAGGAACCA		CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.1605C>A	chr7.hg19:g.112407741G>T		26.0	0.0		63.0	17.0	NM_022484	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Silent	SNP	ENST00000312814.6	hg19	CCDS5757.1																																																																																			.	.		0.403	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		T	112407741	G	T	112407741	2	4	12	1	0	0	0	0	0	0	0	1	16098	987	35	3		3	TMEM168	7	112407741	Silent	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10		112407741	46730922	22	1020										
HIPK2	28996	hgsc.bcm.edu	37	chr7	139311420	139311425	+	In_Frame_Del	DEL	TTCTCT	TTCTCT	-													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	cagggtttcgattggagtgaTtctcttgtcagcatcaatgg							TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	TTCTCT	TTCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr7:139311420_139311425delTTCTCT	ENST00000406875.3	-	6	1635_1640	c.1541_1546delAGAGAA	c.(1540-1548)aagagaatc>atc	p.KR514del	HIPK2_ENST00000428878.2_In_Frame_Del_p.KR514del|HIPK2_ENST00000342645.6_In_Frame_Del_p.KR514del	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	514	Interaction with DAXX.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					ATTGGAGTGATTCTCTTGTCAGCATC	0.49																																					p.514_516del		Atlas-Indel,Pindel	.											.	HIPK2	192	.	0			c.1542_1547del						.																																			SO:0001651	inframe_deletion	28996	exon6			.	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1541_1546delAGAGAA	chr7.hg19:g.139311420_139311425delTTCTCT	ENSP00000385571:p.Lys514_Arg515del	51.0	0.0		139.0	19.0	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	In_Frame_Del	DEL	ENST00000406875.3	hg19																																																																																				.	.		0.49	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		-	139311425	TTCTCT	-	139311420	7	5	12	1	0	1	0	1	0	0	0	0	7126	1493	52	0	2090	0	HIPK2	7	139311420	In_Frame_Del	DEL	TTCTCT	TCGA-2Y-A9H2-01A-12D-A382-10	26903679	139311420	19827243	23	1021										
NOS3	4846	hgsc.bcm.edu	37	chr7	150696315	150696315	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ccctgggcctgcgctggtacGccctcccggcagtgtccaac	12	18	0	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr7:150696315G>A	ENST00000484524.1	+	8	994	c.994G>A	c.(994-996)Gcc>Acc	p.A332T	NOS3_ENST00000461406.1_Missense_Mutation_p.A126T|NOS3_ENST00000467517.1_Missense_Mutation_p.A332T|NOS3_ENST00000297494.3_Missense_Mutation_p.A332T	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCGCTGGTACGCCCTCCCGGC	0.642																																					p.A332T		Atlas-SNP	.											.	NOS3	131	.	0			c.G994A						.						61	68	66					7																	150696315		2201	4295	6496	SO:0001583	missense	4846	exon8			TGGTACGCCCTCC		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.994G>A	chr7.hg19:g.150696315G>A	ENSP00000420215:p.Ala332Thr	42.0	0.0		61.0	9.0	NM_001160111	Q495E5	Missense_Mutation	SNP	ENST00000484524.1	hg19	CCDS55182.1	.	.	.	.	.	.	.	.	.	.	N	33	5.199781	0.94997	.	.	ENSG00000164867	ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517	T;T;T;T	0.35048	1.33;1.53;1.33;1.33	5.59	5.59	0.84812	Nitric oxide synthase, oxygenase domain (2);	0.000000	0.64402	D	0.000014	T	0.67078	0.2855	M	0.89353	3.025	0.54753	D	0.999985	D;D;D;D;D	0.89917	1.0;1.0;0.99;0.988;1.0	D;D;P;P;P	0.77004	0.989;0.989;0.812;0.699;0.868	T	0.73193	-0.4060	10	0.72032	D	0.01	-9.7199	17.0996	0.86645	0.0:0.0:1.0:0.0	.	332;332;332;126;332	A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474	.;.;.;.;NOS3_HUMAN	T	332;126;332;332	ENSP00000297494:A332T;ENSP00000417143:A126T;ENSP00000420215:A332T;ENSP00000420551:A332T	ENSP00000297494:A332T	A	+	1	0	NOS3	150327248	0.997000	0.39634	0.958000	0.39756	0.847000	0.48162	6.771000	0.74996	2.620000	0.88729	0.639000	0.83563	GCC	.	.		0.642	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		A	150696315	G	A	150696315	3	1	12	1	0	0	0	0	1	0	0	0	10553	1087	38	1	1024	1	NOS3	7	150696315	Missense_Mutation	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10	11384895	150696315	8442348	24	1022										
HGSNAT	138050	hgsc.bcm.edu	37	chr8	43054562	43054562	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	attctggtatatgtcggccaCgaggtgtttgagaactactt	11	7	1	1			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr8:43054562C>T	ENST00000458501.2	+	18	1842	c.1842C>T	c.(1840-1842)caC>caT	p.H614H	HGSNAT_ENST00000297798.7_Silent_p.H318H|HGSNAT_ENST00000521576.1_Silent_p.H303H|HGSNAT_ENST00000379644.4_Silent_p.H586H			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	614					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			ATGTCGGCCACGAGGTGTTTG	0.463																																					p.H586H		Atlas-SNP	.											.	HGSNAT	85	.	0			c.C1758T						.						58	59	59					8																	43054562		2194	4295	6489	SO:0001819	synonymous_variant	138050	exon18			CGGCCACGAGGTG		CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"transmembrane protein 76"	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.1842C>T	chr8.hg19:g.43054562C>T		60.0	0.0		99.0	16.0	NM_152419	B4E2V0	Silent	SNP	ENST00000458501.2	hg19																																																																																				.	.		0.463	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038		T	43054562	C	T	43054562	2	4	12	1	0	0	0	0	0	0	0	1	7097	535	19	1		1	HGSNAT	8	43054562	Silent	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10		43054562	103309460	25	1023										
PAG1	55824	hgsc.bcm.edu	37	chr8	81888977	81888977	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ggaagtgtgctgtttggagtTttttcgaagtctttaacagt	12	4	1	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr8:81888977T>G	ENST00000220597.4	-	9	1811	c.1101A>C	c.(1099-1101)aaA>aaC	p.K367N	PAG1_ENST00000523463.1_5'Flank	NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	367					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			TGTTTGGAGTTTTTTCGAAGT	0.507																																					p.K367N		Atlas-SNP	.											.	PAG1	39	.	0			c.A1101C						.						89	88	89					8																	81888977		2203	4300	6503	SO:0001583	missense	55824	exon9			TGGAGTTTTTTCG	AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"Csk-binding protein", "transmembrane adaptor protein PAG"	605767	"phosphoprotein associated with glycosphingolipid microdomains 1"			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.1101A>C	chr8.hg19:g.81888977T>G	ENSP00000220597:p.Lys367Asn	66.0	0.0		217.0	93.0	NM_018440	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Missense_Mutation	SNP	ENST00000220597.4	hg19	CCDS6227.1	.	.	.	.	.	.	.	.	.	.	T	1.653	-0.513401	0.04200	.	.	ENSG00000076641	ENST00000220597	.	.	.	5.05	-2.67	0.06059	.	0.407548	0.27048	N	0.021190	T	0.23846	0.0577	L	0.53249	1.67	0.24613	N	0.993714	B	0.06786	0.001	B	0.09377	0.004	T	0.26467	-1.0102	9	0.07482	T	0.82	-26.5581	2.2185	0.03966	0.1011:0.2411:0.309:0.3488	.	367	Q9NWQ8	PAG1_HUMAN	N	367	.	ENSP00000220597:K367N	K	-	3	2	PAG1	82051532	0.012000	0.17670	0.083000	0.20561	0.050000	0.14768	-0.098000	0.11024	-0.241000	0.09681	-0.331000	0.08364	AAA	.	.		0.507	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440		G	81888977	T	G	81888977	3	3	12	1	0	0	0	0	1	0	0	0	11397	1838	64	5	201	5	PAG1	8	81888977	Missense_Mutation	SNP	T	TCGA-2Y-A9H2-01A-12D-A382-10	38834415	81888977	64475045	26	1024										
C8orf33	65265	hgsc.bcm.edu	37	chr8	146278706	146278706	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	agcaggctattggagcaatcCgaaccctgcgcagcaaaaga	11	11	0	1	rs376887084		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr8:146278706C>T	ENST00000331434.6	+	4	541	c.427C>T	c.(427-429)Cga>Tga	p.R143*		NM_023080.2	NP_075568.1	Q9H7E9	CH033_HUMAN	chromosome 8 open reading frame 33	143										endometrium(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;9.1e-38)|all cancers(56;7.37e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.243)		TGGAGCAATCCGAACCCTGCG	0.527																																					p.R143X		Atlas-SNP	.											.	C8orf33	25	.	0			c.C427T						.	C	stop/ARG	1,4405		0,1,2202	91	104	100		427	1.6	0	8		100	0,8600		0,0,4300	no	stop-gained	C8orf33	NM_023080.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		143/230	146278706	1,13005	2203	4300	6503	SO:0001587	stop_gained	65265	exon4			GCAATCCGAACCC		CCDS34974.1	8q24.3	2012-04-11			ENSG00000182307	ENSG00000182307			26104	protein-coding gene	gene with protein product							Standard	NM_023080		Approved	FLJ20989	uc003zfc.4	Q9H7E9	OTTHUMG00000165256	ENST00000331434.6:c.427C>T	chr8.hg19:g.146278706C>T	ENSP00000330361:p.Arg143*	156.0	0.0		191.0	41.0	NM_023080	A6NGC0|Q96BT8	Nonsense_Mutation	SNP	ENST00000331434.6	hg19	CCDS34974.1	.	.	.	.	.	.	.	.	.	.	.	20.2	3.944224	0.73672	2.27E-4	0.0	ENSG00000182307	ENST00000331434	.	.	.	3.61	1.57	0.23409	.	0.229940	0.33610	N	0.004723	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.9088	3.7887	0.08710	0.2394:0.6277:0.0:0.1328	.	.	.	.	X	143	.	.	R	+	1	2	C8orf33	146249510	0.149000	0.22717	0.002000	0.10522	0.283000	0.27025	0.120000	0.15647	0.836000	0.34901	0.467000	0.42956	CGA	.	.		0.527	C8orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382995.1	NM_023080		T	146278706	C	T	146278706	4	4	12	1	0	0	0	0	0	1	0	0	2423	644	23	1	441	1	C8orf33	8	146278706	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	64389729	146278706	85316	27	1025										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27313397	27313397	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	cagttatctctctttctaatTcaacatttttcttcatttct	1	10	7	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr10:27313397T>G	ENST00000376087.4	-	28	4229	c.4064A>C	c.(4063-4065)gAa>gCa	p.E1355A	ANKRD26_ENST00000376070.3_Missense_Mutation_p.E912A|ANKRD26_ENST00000436985.2_Missense_Mutation_p.E1371A	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1354					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TCTTTCTAATTCAACATTTTT	0.249																																					p.E1355A		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A4064C						.						69	69	69					10																	27313397		1779	4044	5823	SO:0001583	missense	22852	exon28			TCTAATTCAACAT	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.4064A>C	chr10.hg19:g.27313397T>G	ENSP00000365255:p.Glu1355Ala	168.0	0.0		240.0	29.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	hg19	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	T	3.222	-0.159391	0.06544	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.77489	-1.1;-1.1;-1.1	4.89	3.73	0.42828	.	0.112806	0.36101	N	0.002799	T	0.57888	0.2084	N	0.17631	0.505	0.37940	D	0.932297	P;B;B	0.36144	0.539;0.404;0.004	B;B;B	0.30179	0.112;0.052;0.007	T	0.55418	-0.8144	10	0.21540	T	0.41	.	9.7359	0.40388	0.0:0.0:0.1824:0.8176	.	1355;1354;1371	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	A	912;1355;1371	ENSP00000365238:E912A;ENSP00000365255:E1355A;ENSP00000405112:E1371A	ENSP00000365238:E912A	E	-	2	0	ANKRD26	27353403	0.997000	0.39634	0.816000	0.32577	0.171000	0.22731	2.987000	0.49378	0.695000	0.31675	0.455000	0.32223	GAA	.	.		0.249	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			G	27313397	T	G	27313397	3	3	12	1	0	0	0	0	1	0	0	0	654	1783	62	5	1096	5	ANKRD26	10	27313397	Missense_Mutation	SNP	T	TCGA-2Y-A9H2-01A-12D-A382-10		27313397	108221350	28	1026										
EED	8726	hgsc.bcm.edu	37	chr11	85977167	85977167	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	aaataatgtcctgtggtatgGatcattctcttaaactttgg	8	6	2	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr11:85977167G>A	ENST00000263360.6	+	8	1455	c.769G>A	c.(769-771)Gat>Aat	p.D257N	EED_ENST00000528180.1_Intron|EED_ENST00000351625.6_Missense_Mutation_p.D257N|EED_ENST00000327320.4_Missense_Mutation_p.D257N	NM_003797.3	NP_003788.2	O75530	EED_HUMAN	embryonic ectoderm development	257	Interaction with EZH2. {ECO:0000250}.|Required for interaction with the matrix protein MA of HIV-1.				negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K27 methylation (GO:0061087)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	21		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				CTGTGGTATGGATCATTCTCT	0.284																																					p.D257N		Atlas-SNP	.											.	EED	50	.	0			c.G769A						.						91	101	98					11																	85977167		2201	4290	6491	SO:0001583	missense	8726	exon8			GGTATGGATCATT	AF078933	CCDS8273.1, CCDS8274.1	11q14.2-q22.3	2013-01-10			ENSG00000074266	ENSG00000074266		"WD repeat domain containing"	3188	protein-coding gene	gene with protein product	"WD protein associating with integrin cytoplasmic tails 1"	605984				9765275, 9806832	Standard	NM_003797		Approved	WAIT-1, HEED	uc001pbp.3	O75530	OTTHUMG00000167209	ENST00000263360.6:c.769G>A	chr11.hg19:g.85977167G>A	ENSP00000263360:p.Asp257Asn	106.0	0.0		140.0	21.0	NM_003797	A8K7V5|O00149|Q6NTH2|Q7LDA5|Q7LDG8|Q86VV2|Q9UNY7	Missense_Mutation	SNP	ENST00000263360.6	hg19	CCDS8273.1	.	.	.	.	.	.	.	.	.	.	G	35	5.521067	0.96416	.	.	ENSG00000074266	ENST00000263360;ENST00000351625;ENST00000327320;ENST00000533228;ENST00000534564	T;T;D	0.88975	0.89;0.89;-2.45	5.36	5.36	0.76844	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.95875	0.8657	M	0.91038	3.17	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96137	0.9097	9	.	.	.	-15.7044	19.4599	0.94912	0.0:0.0:1.0:0.0	.	257;257;257	O75530-3;O75530-2;O75530	.;.;EED_HUMAN	N	257;257;257;50;6	ENSP00000263360:D257N;ENSP00000338186:D257N;ENSP00000315587:D257N	.	D	+	1	0	EED	85654815	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.629000	0.98417	2.671000	0.90904	0.563000	0.77884	GAT	.	.		0.284	EED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393733.1	NM_003797		A	85977167	G	A	85977167	3	1	12	1	0	0	0	0	1	0	0	0	4924	1174	41	3	799	3	EED	11	85977167	Missense_Mutation	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10		85977167	49029349	29	1027										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19467760	19467760	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	tgaaatagatgaaagaaaatGaacctattatcaccatggtt	7	5	1	5			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr12:19467760G>T	ENST00000299275.6	+	13	1851				PLEKHA5_ENST00000355397.3_Intron|PLEKHA5_ENST00000317589.4_Intron|PLEKHA5_ENST00000538714.1_Intron|PLEKHA5_ENST00000543806.1_Nonsense_Mutation_p.E512*|PLEKHA5_ENST00000539256.1_Intron|PLEKHA5_ENST00000424268.1_Nonsense_Mutation_p.E512*|PLEKHA5_ENST00000359180.3_Intron|PLEKHA5_ENST00000429027.2_Nonsense_Mutation_p.E684*	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5						reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					GAAAGAAAATGAACCTATTAT	0.398																																					p.E684X	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.G2050T						.						131	110	117					12																	19467760		692	1591	2283	SO:0001627	intron_variant	54477	exon16			GAAAATGAACCTA	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.1846-5736G>T	chr12.hg19:g.19467760G>T		49.0	0.0		103.0	17.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Nonsense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	G	40	8.316369	0.98757	.	.	ENSG00000052126	ENST00000542828;ENST00000429027;ENST00000424268;ENST00000543806	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	18.9962	0.92813	0.0:0.0:1.0:0.0	.	.	.	.	X	685;684;512;512	.	ENSP00000400411:E512X	E	+	1	0	PLEKHA5	19359027	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.080000	0.94040	2.487000	0.83934	0.643000	0.83706	GAA	.	.		0.398	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		T	19467760	G	T	19467760	1	4	12	0	1	0	0	0	0	0	0	0	12068	1291	45	3		3	PLEKHA5	12	19467760	Intron	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10		19467760	114384135	30	1028										
C12orf41	54934	hgsc.bcm.edu	37	chr12	49075410	49075430	+	Start_Codon_Del	DEL	GTTCATAACCAAAACCTGCGG	GTTCATAACCAAAACCTGCGG	-													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	aagacgtgaatccgaatcctGttcataaccaaaacctgcgg					rs199711246		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	GTTCATAACCAAAACCTGCGG	GTTCATAACCAAAACCTGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr12:49075410_49075430delGTTCATAACCAAAACCTGCGG	ENST00000420613.2	-	0	39_53				KANSL2_ENST00000553086.1_Start_Codon_Del|KANSL2_ENST00000550347.1_In_Frame_Del_p.PQVLVMN179del|KANSL2_ENST00000357861.3_5'UTR	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2						chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)											TCCGAATCCTGTTCATAACCAAAACCTGCGGGGTCAAACGA	0.529																																					.		Atlas-Indel,Pindel	.											.	.	.	.	0			.						.																																			SO:0001582	initiator_codon_variant	54934	wholegene			.	AK094528	CCDS44869.1	12q13.11	2011-10-31	2011-10-31	2011-10-31	ENSG00000139620	ENSG00000139620			26024	protein-coding gene	gene with protein product		615488	"chromosome 12 open reading frame 41"	C12orf41		12477932	Standard	NM_017822		Approved	FLJ20436, NSL2	uc001rrz.2	Q9H9L4	OTTHUMG00000170392		chr12.hg19:g.49075410_49075430delGTTCATAACCAAAACCTGCGG		80.0	0.0		81.0	17.0	NM_017822	Q8N3B5|Q96CV0|Q9NX51	Frame_Shift_Del	DEL	ENST00000420613.2	hg19	CCDS44869.1																																																																																			.	.		0.529	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1	NM_017822		-	49075430	GTTCATAACCAAAACCTGCGG	-	49075410	7	5	12	1	0	1	0	1	0	0	0	0	1689	1368	48	0	1508	0	C12orf41	12	49075410	Start_Codon_Del	DEL	GTTCATAACCAAAACCTGCGG	TCGA-2Y-A9H2-01A-12D-A382-10	29607650	49075410	84776485	31	1029										
C12orf48	55010	hgsc.bcm.edu	37	chr12	102569312	102569312	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	aagatgcaactgattaaaggCcaaaacagcagggatccttt	9	8	0	2			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr12:102569312C>T	ENST00000358383.5	+	7	918	c.873C>T	c.(871-873)ggC>ggT	p.G291G	PARPBP_ENST00000541394.1_Silent_p.G368G|PARPBP_ENST00000392911.2_Silent_p.G210G|PARPBP_ENST00000543784.1_Intron|PARPBP_ENST00000378128.3_Intron|PARPBP_ENST00000327680.2_Silent_p.G210G|PARPBP_ENST00000535811.1_Intron			Q9NWS1	PARI_HUMAN	PARP1 binding protein	291					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(8)|urinary_tract(2)	11						TGATTAAAGGCCAAAACAGCA	0.353																																					p.G291G		Atlas-SNP	.											.	PARPBP	40	.	0			c.C873T						.						106	108	107					12																	102569312		2203	4300	6503	SO:0001819	synonymous_variant	55010	exon7			TAAAGGCCAAAAC	AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"PARP-1 binding protein"	613687	"chromosome 12 open reading frame 48"	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.873C>T	chr12.hg19:g.102569312C>T		105.0	0.0		166.0	52.0	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Silent	SNP	ENST00000358383.5	hg19	CCDS9090.2																																																																																			.	.		0.353	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915		T	102569312	C	T	102569312	2	4	12	1	0	0	0	0	0	0	0	1	1694	726	26	3		3	C12orf48	12	102569312	Silent	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	53493902	102569312	31282583	32	1030										
NBEA	26960	hgsc.bcm.edu	37	chr13	35883674	35883674	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	tctccttttaggaatggcaaAactctattcagaagaatgca	7	8	3	2			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr13:35883674A>T	ENST00000400445.3	+	36	6382	c.5848A>T	c.(5848-5850)Aac>Tac	p.N1950Y	NBEA_ENST00000310336.4_Missense_Mutation_p.N1950Y|NBEA_ENST00000379939.2_Missense_Mutation_p.N1947Y|NBEA_ENST00000540320.1_Missense_Mutation_p.N1950Y	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1950					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GGAATGGCAAAACTCTATTCA	0.313																																					p.N1950Y		Atlas-SNP	.											.	NBEA	340	.	0			c.A5848T						.						75	68	70					13																	35883674		1861	4120	5981	SO:0001583	missense	26960	exon36			TGGCAAAACTCTA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5848A>T	chr13.hg19:g.35883674A>T	ENSP00000383295:p.Asn1950Tyr	132.0	0.0		174.0	40.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.293074	0.80914	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.54479	0.57;0.58;0.58;0.57	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.71039	0.3293	M	0.71206	2.165	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.79784	0.978;0.993	T	0.73164	-0.4069	10	0.51188	T	0.08	.	15.3088	0.74014	1.0:0.0:0.0:0.0	.	1950;1947	Q8NFP9;Q5T321	NBEA_HUMAN;.	Y	1950;1950;1947;1950;577	ENSP00000440951:N1950Y;ENSP00000383295:N1950Y;ENSP00000369271:N1947Y;ENSP00000308534:N1950Y	ENSP00000308534:N1950Y	N	+	1	0	NBEA	34781674	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.730000	0.91510	2.029000	0.59856	0.533000	0.62120	AAC	.	.		0.313	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35883674	A	T	35883674	3	4	12	1	0	0	0	0	1	0	0	0	10196	14	1	4	5990	4	NBEA	13	35883674	Missense_Mutation	SNP	A	TCGA-2Y-A9H2-01A-12D-A382-10		35883674	79286204	33	1031										
TRIM13	10206	hgsc.bcm.edu	37	chr13	50586334	50586335	+	Frame_Shift_Ins	INS	-	-	A													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	aaaagtataacaagatcaagINSatctctcccaaaatgccagt							TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr13:50586334_50586335insA	ENST00000378182.3	+	2	996_997	c.258_259insA	c.(259-261)atcfs	p.I87fs	TRIM13_ENST00000478111.1_Intron|TRIM13_ENST00000457662.2_Frame_Shift_Ins_p.I87fs|TRIM13_ENST00000298772.5_Frame_Shift_Ins_p.I90fs|TRIM13_ENST00000356017.4_Frame_Shift_Ins_p.I90fs|TRIM13_ENST00000420995.2_Frame_Shift_Ins_p.I87fs	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13	87					anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		ACAAGATCAAGATCTCTCCCAA	0.446																																					p.K89fs		Atlas-Indel,Pindel	.											.	TRIM13	30	.	0			c.267_268insA						.																																			SO:0001589	frameshift_variant	10206	exon4			.	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9976	protein-coding gene	gene with protein product		605661	"ret finger protein 2", "tripartite motif-containing 13"	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.259dupA	chr13.hg19:g.50586335_50586335dupA	ENSP00000367424:p.Ile87fs	48.0	0.0		82.0	19.0	NM_001007278	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	Frame_Shift_Ins	INS	ENST00000378182.3	hg19	CCDS9423.1																																																																																			.	.		0.446	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278		A	50586335	-	A	50586334	7	5	12	1	0	1	1	0	0	0	0	0	16503	933	33	0	273	0	TRIM13	13	50586334	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H2-01A-12D-A382-10	14702660	50586334	64583544	34	1032										
COL4A1	1282	hgsc.bcm.edu	37	chr13	110835413	110835413	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ttctctcctggcaggcctggCcttcctggggttccgggaaa	13	13	1	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr13:110835413C>G	ENST00000375820.4	-	28	2143	c.2022G>C	c.(2020-2022)agG>agC	p.R674S		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	674	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			GCAGGCCTGGCCTTCCTGGGG	0.627																																					p.R674S		Atlas-SNP	.											.	COL4A1	372	.	0			c.G2022C						.																																			SO:0001583	missense	1282	exon28			GCCTGGCCTTCCT	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.2022G>C	chr13.hg19:g.110835413C>G	ENSP00000364979:p.Arg674Ser	88.0	0.0		71.0	16.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.289361	0.40494	.	.	ENSG00000187498	ENST00000375820	D	0.93307	-3.2	4.7	1.89	0.25635	.	0.290655	0.33691	N	0.004649	D	0.88149	0.6359	N	0.11064	0.09	0.80722	D	1	D	0.61697	0.99	P	0.62885	0.908	T	0.82194	-0.0578	10	0.09084	T	0.74	.	5.5931	0.17311	0.1543:0.5906:0.0:0.2551	.	674	P02462	CO4A1_HUMAN	S	674	ENSP00000364979:R674S	ENSP00000364979:R674S	R	-	3	2	COL4A1	109633414	0.651000	0.27340	0.997000	0.53966	0.954000	0.61252	0.201000	0.17276	0.484000	0.27630	0.561000	0.74099	AGG	.	.		0.627	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			G	110835413	C	G	110835413	3	3	12	1	0	0	0	0	1	0	0	0	3691	738	26	4	3087	4	COL4A1	13	110835413	Missense_Mutation	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	60249079	110835413	4334465	35	1033										
GMPR2	51292	hgsc.bcm.edu	37	chr14	24707793	24707798	+	Splice_Site	DEL	TTTAAG	TTTAAG	-													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ataaagtttttcctactttaAgagcctcagagggaaagaca							TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	TTTAAG	TTTAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr14:24707793_24707798delTTTAAG	ENST00000355299.4	+	10	1318_1322	c.857_861delTTTAAG	c.(856-861)atttaa>a	p.I*286del	GMPR2_ENST00000557854.1_In_Frame_Del_p.FK365del|GMPR2_ENST00000348719.7_In_Frame_Del_p.FK347del|GMPR2_ENST00000420554.2_Splice_Site_p.I*304del|GMPR2_ENST00000456667.3_Splice_Site_p.I*258del|GMPR2_ENST00000559836.1_Splice_Site_p.I*286del|GMPR2_ENST00000399440.2_Splice_Site_p.I*286del|GMPR2_ENST00000559910.1_Splice_Site_p.I*253del|GMPR2_ENST00000559104.1_Splice_Site_p.I*271del	NM_001002000.1	NP_001002000.1	Q9P2T1	GMPR2_HUMAN	guanosine monophosphate reductase 2	286	GMP binding.				GMP metabolic process (GO:0046037)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)	p.A287V(1)		large_intestine(4)|lung(3)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(265;0.0181)		TCCTACTTTAAGAGCCTCAGAGGGAA	0.476																																					.		Atlas-Indel,Pindel	.											.	GMPR2	37	.	1	Substitution - Missense(1)	large_intestine(1)	.						.																																			SO:0001630	splice_region_variant	51292	.			.		CCDS41935.1, CCDS45087.1, CCDS61419.1, CCDS73624.1	14q11.2	2006-11-24							4377	protein-coding gene	gene with protein product		610781					Standard	XM_005267742		Approved		uc001wnw.3	Q9P2T1		ENST00000355299.4:c.858-1TTTAAG>-	chr14.hg19:g.24707793_24707798delTTTAAG		99.0	0.0		148.0	41.0	.	D3DS66|Q567T0|Q6IAJ8|Q86T14	Splice_Site	DEL	ENST00000355299.4	hg19	CCDS41935.1																																																																																			.	.		0.476	GMPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415821.2	NM_016576	In_Frame_Del	-	24707798	TTTAAG	-	24707793	8	5	12	1	0	1	0	1	0	0	1	0	6505	86	3	0	944	0	GMPR2	14	24707793	Splice_Site	DEL	TTTAAG	TCGA-2Y-A9H2-01A-12D-A382-10		24707793	82641747	36	1034										
KIAA0831	22863	hgsc.bcm.edu	37	chr14	55878482	55878483	+	Frame_Shift_Ins	INS	-	-	G													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	caggtcccgggcgagcggccINSggggcccgcagccaggagcc					rs201727714		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr14:55878482_55878483insG	ENST00000247178.5	-	1	93_94	c.58_59insC	c.(58-60)cggfs	p.R20fs		NM_014924.4	NP_055739.2	Q6ZNE5	BAKOR_HUMAN	autophagy related 14	20					autophagic vacuole assembly (GO:0000045)|endosome to lysosome transport (GO:0008333)|positive regulation of autophagy (GO:0010508)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|pre-autophagosomal structure membrane (GO:0034045)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(2)	13						GGCGAGCGGCCGGGGCCCGCAG	0.693																																					p.R20fs		Atlas-Indel,Pindel	.											.	ATG14	36	.	0			c.59_60insC						.																																			SO:0001589	frameshift_variant	22863	exon1			.	AB020638	CCDS32087.1	14q22.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000126775	ENSG00000126775			19962	protein-coding gene	gene with protein product	"Barkor", "beclin 1-associated autophagy-related key regulator"	613515	"KIAA0831", "ATG14 autophagy related 14 homolog (S. cerevisiae)"	KIAA0831		18843052	Standard	NM_014924		Approved	ATG14L	uc001xbx.2	Q6ZNE5	OTTHUMG00000172129	ENST00000247178.5:c.59dupC	chr14.hg19:g.55878486_55878486dupG	ENSP00000247178:p.Arg20fs	204.0	0.0		99.0	44.0	NM_014924	A6NJE4|A8K9U5|B7ZWP5|O94920|Q32MK7|Q32MK8	Frame_Shift_Ins	INS	ENST00000247178.5	hg19	CCDS32087.1																																																																																			.	.		0.693	ATG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416992.1	NM_014924		G	55878483	-	G	55878482	7	5	12	1	0	1	1	0	0	0	0	0	8204	652	23	0	1459	0	KIAA0831	14	55878482	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H2-01A-12D-A382-10	31170689	55878482	51471058	37	1035										
SLC38A6	145389	hgsc.bcm.edu	37	chr14	61550366	61550378	+	Frame_Shift_Del	DEL	GGAGAACCAAACG	GGAGAACCAAACG	-													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	agccaagggaagaggcctcaGgagaaccaaacgtgtccaca					rs147438249	byFrequency	TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	GGAGAACCAAACG	GGAGAACCAAACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr14:61550366_61550378delGGAGAACCAAACG	ENST00000354886.2	+	17	1666_1678	c.1502_1514delGGAGAACCAAACG	c.(1501-1515)aggagaaccaaacgtfs	p.RRTKR501fs	SLC38A6_ENST00000456840.2_Frame_Shift_Del_p.GEPNV480fs	NM_001172702.1	NP_001166173.1	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	0					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		agaggcctcaggagaaccaaacgtgtccacacc	0.469																																					p.501_505del		Atlas-Indel,Pindel	.											.	SLC38A6	87	.	0			c.1501_1513del						.																																			SO:0001589	frameshift_variant	145389	exon17			.	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"Solute carriers"	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000354886.2:c.1502_1514delGGAGAACCAAACG	chr14.hg19:g.61550366_61550378delGGAGAACCAAACG	ENSP00000346959:p.Arg501fs	49.0	0.0		60.0	12.0	NM_001172702	C9JWA6|Q86SY5	Frame_Shift_Del	DEL	ENST00000354886.2	hg19	CCDS53900.1																																																																																			.	.		0.469	SLC38A6-201	KNOWN	basic|CCDS	protein_coding	protein_coding				-	61550378	GGAGAACCAAACG	-	61550366	7	5	12	1	0	1	0	1	0	0	0	0	14623	1000	35	0	1653	0	SLC38A6	14	61550366	Frame_Shift_Del	DEL	GGAGAACCAAACG	TCGA-2Y-A9H2-01A-12D-A382-10	5671884	61550366	45799174	38	1036										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102472421	102472421	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	tgagtacctgggtgttcaggAcaaactggtccagacccccc	11	13	1	2			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr14:102472421A>G	ENST00000360184.4	+	27	5794	c.5630A>G	c.(5629-5631)gAc>gGc	p.D1877G		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1877	AAA 1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GGTGTTCAGGACAAACTGGTC	0.473																																					p.D1877G		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A5630G						.						110	112	112					14																	102472421		2203	4300	6503	SO:0001583	missense	1778	exon27			TTCAGGACAAACT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.5630A>G	chr14.hg19:g.102472421A>G	ENSP00000348965:p.Asp1877Gly	65.0	0.0		43.0	18.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	a	23.7	4.445647	0.84101	.	.	ENSG00000197102	ENST00000360184	T	0.09163	3.01	6.06	6.06	0.98353	.	0.046426	0.85682	D	0.000000	T	0.15912	0.0383	N	0.20881	0.62	0.80722	D	1	P	0.50272	0.933	P	0.57679	0.825	T	0.16660	-1.0395	10	0.12103	T	0.63	.	16.6165	0.84917	1.0:0.0:0.0:0.0	.	1877	Q14204	DYHC1_HUMAN	G	1877	ENSP00000348965:D1877G	ENSP00000348965:D1877G	D	+	2	0	DYNC1H1	101542174	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.233000	0.72320	2.323000	0.78572	0.529000	0.55759	GAC	.	.		0.473	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		G	102472421	A	G	102472421	3	3	12	1	0	0	0	0	1	0	0	0	4843	275	10	2	5736	2	DYNC1H1	14	102472421	Missense_Mutation	SNP	A	TCGA-2Y-A9H2-01A-12D-A382-10	40922055	102472421	4877119	39	1037										
HCN4	10021	hgsc.bcm.edu	37	chr15	73635757	73635757	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ggtgaatatatcgaatgaggCgggagaggcgtaacaggcgt	17	5	0	3			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr15:73635757C>T	ENST00000261917.3	-	2	2171	c.1178G>A	c.(1177-1179)cGc>cAc	p.R393H	RP11-272D12.1_ENST00000557981.1_RNA|RP11-272D12.1_ENST00000558742.1_RNA	NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	393					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		TCGAATGAGGCGGGAGAGGCG	0.582																																					p.R393H		Atlas-SNP	.											HCN4,colon,carcinoma,0,1	HCN4	150	.	0			c.G1178A						.						63	51	55					15																	73635757		2198	4297	6495	SO:0001583	missense	10021	exon2			ATGAGGCGGGAGA	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1178G>A	chr15.hg19:g.73635757C>T	ENSP00000261917:p.Arg393His	78.0	0.0		148.0	66.0	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	hg19	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.587141	0.86851	.	.	ENSG00000138622	ENST00000261917	D	0.99591	-6.24	5.34	5.34	0.76211	Ion transport (1);	.	.	.	.	D	0.99746	0.9899	M	0.93420	3.415	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97434	1.0017	9	0.87932	D	0	.	19.4036	0.94640	0.0:1.0:0.0:0.0	.	393	Q9Y3Q4	HCN4_HUMAN	H	393	ENSP00000261917:R393H	ENSP00000261917:R393H	R	-	2	0	HCN4	71422810	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.671000	0.83941	2.657000	0.90304	0.655000	0.94253	CGC	.	.		0.582	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		T	73635757	C	T	73635757	3	4	12	1	0	0	0	0	1	0	0	0	7008	768	27	1	2461	1	HCN4	15	73635757	Missense_Mutation	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10		73635757	28895635	40	1038										
FAM86A	196483	hgsc.bcm.edu	37	chr16	5140112	5140112	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	aatgacaacatctggctggaAggcagagagctgatggaccg	14	8	1	3			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr16:5140112A>T	ENST00000427587.4	-	6	783	c.715T>A	c.(715-717)Ttc>Atc	p.F239I	FAM86A_ENST00000458008.4_Missense_Mutation_p.F205I|FAM86A_ENST00000587133.1_Missense_Mutation_p.F178I	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	239						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						TCTGGCTGGAAGGCAGAGAGC	0.597																																					p.F239I		Atlas-SNP	.											FAM86A,NS,neuroblastoma,0,1	FAM86A	32	.	0			c.T715A						.						33	38	36					16																	5140112		1413	2402	3815	SO:0001583	missense	196483	exon6			GCTGGAAGGCAGA	BC010084	CCDS10529.1, CCDS10530.1, CCDS73823.1	16p13.3	2012-11-07			ENSG00000118894	ENSG00000118894			32221	protein-coding gene	gene with protein product		615263					Standard	NM_201400		Approved	SB153, MGC19636	uc002cyo.2	Q96G04	OTTHUMG00000129527	ENST00000427587.4:c.715T>A	chr16.hg19:g.5140112A>T	ENSP00000398502:p.Phe239Ile	10.0	0.0		10.0	3.0	NM_201400	D3DUF0|Q96S85	Missense_Mutation	SNP	ENST00000427587.4	hg19	CCDS10529.1	.	.	.	.	.	.	.	.	.	.	a	7.916	0.737456	0.15574	.	.	ENSG00000118894	ENST00000458008;ENST00000427587	T;T	0.16457	2.34;2.34	5.02	1.62	0.23740	.	0.452369	0.23165	N	0.051195	T	0.09905	0.0243	L	0.27053	0.805	0.29093	N	0.881992	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.31943	-0.9925	10	0.18276	T	0.48	.	7.9111	0.29791	0.5683:0.0:0.4317:0.0	.	205;239	Q96G04-2;Q96G04	.;FA86A_HUMAN	I	205;239	ENSP00000389710:F205I;ENSP00000398502:F239I	ENSP00000398502:F239I	F	-	1	0	FAM86A	5080113	0.643000	0.27269	1.000000	0.80357	0.172000	0.22775	1.031000	0.30165	0.101000	0.17610	0.370000	0.22315	TTC	.	.		0.597	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400		T	5140112	A	T	5140112	3	4	12	1	0	0	0	0	1	0	0	0	5651	72	3	4	289	4	FAM86A	16	5140112	Missense_Mutation	SNP	A	TCGA-2Y-A9H2-01A-12D-A382-10		5140112	85214641	41	1039										
RLTPR	146206	hgsc.bcm.edu	37	chr16	67688114	67688114	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	cgcgtggacgagggcgtggaGgaattcttctccaaaaggct	15	9	2	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr16:67688114G>A	ENST00000334583.6	+	30	3511	c.3183G>A	c.(3181-3183)gaG>gaA	p.E1061E	RLTPR_ENST00000545661.1_Silent_p.E1025E	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	1061					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		AGGGCGTGGAGGAATTCTTCT	0.637																																					p.E1061E		Atlas-SNP	.											.	RLTPR	124	.	0			c.G3183A						.						30	33	32					16																	67688114		1949	4120	6069	SO:0001819	synonymous_variant	146206	exon30			CGTGGAGGAATTC	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.3183G>A	chr16.hg19:g.67688114G>A		67.0	0.0		43.0	15.0	NM_001013838	B8X2Z3	Silent	SNP	ENST00000334583.6	hg19	CCDS45513.1																																																																																			.	.		0.637	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		A	67688114	G	A	67688114	2	1	12	1	0	0	0	0	0	0	0	1	13409	991	35	3		3	RLTPR	16	67688114	Silent	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10	62548002	67688114	22666639	42	1040										
OR3A1	4994	hgsc.bcm.edu	37	chr17	3194961	3194961	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ccgcctccctgtgagcatccTccagatggcactctgcacat	8	17	1	2			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr17:3194961T>A	ENST00000323404.1	-	1	915	c.916A>T	c.(916-918)Agg>Tgg	p.R306W	RP11-64J4.2_ENST00000573491.1_RNA	NM_002550.2	NP_002541.2	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A, member 1	306					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	20						GTGAGCATCCTCCAGATGGCA	0.473																																					p.R306W	GBM(20;287 516 18743 28660 36594)	Atlas-SNP	.											.	OR3A1	46	.	0			c.A916T						.						84	81	82					17																	3194961		2203	4300	6503	SO:0001583	missense	4994	exon1			GCATCCTCCAGAT	X80391	CCDS11023.1	17p13.3	2012-08-09			ENSG00000180090	ENSG00000180090		"GPCR / Class A : Olfactory receptors"	8282	protein-coding gene	gene with protein product						8921386, 8647456	Standard	NM_002550		Approved	OLFRA03, OR40, OR17-40	uc002fvh.1	P47881	OTTHUMG00000090642	ENST00000323404.1:c.916A>T	chr17.hg19:g.3194961T>A	ENSP00000313803:p.Arg306Trp	42.0	0.0		57.0	12.0	NM_002550	Q4VB06|Q6IFM4	Missense_Mutation	SNP	ENST00000323404.1	hg19	CCDS11023.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.230450	0.39399	.	.	ENSG00000180090	ENST00000323404	T	0.41758	0.99	4.81	1.32	0.21799	.	0.546790	0.16683	N	0.203870	T	0.48241	0.1489	M	0.87180	2.865	0.09310	N	1	B	0.19331	0.035	B	0.15484	0.013	T	0.53725	-0.8398	10	0.87932	D	0	-4.3384	12.8912	0.58071	0.0:0.0:0.2034:0.7966	.	306	P47881	OR3A1_HUMAN	W	306	ENSP00000313803:R306W	ENSP00000313803:R306W	R	-	1	2	OR3A1	3141711	0.000000	0.05858	0.052000	0.19188	0.088000	0.18126	-1.926000	0.01562	0.561000	0.29186	0.533000	0.62120	AGG	.	.		0.473	OR3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207302.2			A	3194961	T	A	3194961	3	1	12	1	0	0	0	0	1	0	0	0	11046	1550	54	4	35	4	OR3A1	17	3194961	Missense_Mutation	SNP	T	TCGA-2Y-A9H2-01A-12D-A382-10		3194961	78000249	43	1041										
GRN	2896	hgsc.bcm.edu	37	chr17	42429084	42429086	+	In_Frame_Del	DEL	ATA	ATA	-													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	gaagagagatgtcccctgtgAtaatgtcagcagctgtccct							TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	ATA	ATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr17:42429084_42429086delATA	ENST00000053867.3	+	10	1162_1164	c.1100_1102delATA	c.(1099-1104)gataat>gat	p.N368del	GRN_ENST00000589265.1_In_Frame_Del_p.N211del|GRN_ENST00000589923.1_3'UTR	NM_002087.2	NP_002078.1	P28799	GRN_HUMAN	granulin	368					blastocyst hatching (GO:0001835)|cell death (GO:0008219)|embryo implantation (GO:0007566)|positive regulation of epithelial cell proliferation (GO:0050679)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	growth factor activity (GO:0008083)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GTCCCCTGTGATAATGTCAGCAG	0.601																																					p.367_367del		Atlas-Indel,Pindel	.											.	GRN	51	.	0			c.1099_1101del						.																																			SO:0001651	inframe_deletion	2896	exon10			.	M75161	CCDS11483.1	17q21.32	2014-09-17				ENSG00000030582			4601	protein-coding gene	gene with protein product	"progranulin"	138945				1417868, 9826678	Standard	XM_005257253		Approved	PCDGF, PGRN, CLN11	uc002igp.1	P28799		ENST00000053867.3:c.1100_1102delATA	chr17.hg19:g.42429084_42429086delATA	ENSP00000053867:p.Asn368del	43.0	0.0		74.0	12.0	NM_002087	D3DX55|P23781|P23782|P23783|P23784|Q53HQ8|Q53Y88|Q540U8|Q9BWE7|Q9H8S1|Q9UCH0	In_Frame_Del	DEL	ENST00000053867.3	hg19	CCDS11483.1																																																																																			.	.		0.601	GRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457766.1	NM_002087		-	42429086	ATA	-	42429084	7	5	12	1	0	1	0	1	0	0	0	0	6813	333	12	0	1134	0	GRN	17	42429084	In_Frame_Del	DEL	ATA	TCGA-2Y-A9H2-01A-12D-A382-10	39234123	42429084	38766126	44	1042										
HOXB6	3216	hgsc.bcm.edu	37	chr17	46675276	46675276	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	gactctttctcgcggtagaaGgccggcgccggcccgtagtc	14	14	2	1	rs577327660		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr17:46675276G>A	ENST00000484302.2	-	2	859	c.237C>T	c.(235-237)gcC>gcT	p.A79A	HOXB-AS3_ENST00000466037.2_RNA|HOXB6_ENST00000225648.3_Silent_p.A79A|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB6_ENST00000490419.1_5'Flank|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000492897.3_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000460041.1_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000480872.1_RNA			P17509	HXB6_HUMAN	homeobox B6	79					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte homeostasis (GO:0034101)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(1)|lung(4)	7						CGCGGTAGAAGGCCGGCGCCG	0.726													G|||	1	0.000199681	0	0.0014	5008	,	,		10490	0		0	False		,,,				2504	0				p.A79A		Atlas-SNP	.											.	HOXB6	13	.	0			c.C237T						.						5	6	5					17																	46675276		2129	4136	6265	SO:0001819	synonymous_variant	3216	exon3			GTAGAAGGCCGGC		CCDS11531.1	17q21.32	2011-06-20	2005-12-22		ENSG00000108511	ENSG00000108511		"Homeoboxes / ANTP class : HOXL subclass"	5117	protein-coding gene	gene with protein product		142961	"homeo box B6"	HOX2, HOX2B		1973146, 1358459	Standard	XM_005257284		Approved		uc002ins.1	P17509	OTTHUMG00000159912	ENST00000484302.2:c.237C>T	chr17.hg19:g.46675276G>A		148.0	0.0		122.0	70.0	NM_018952	A8K835|D3DTV5|P09068|Q9HB11|Q9UGH2	Silent	SNP	ENST00000484302.2	hg19	CCDS11531.1																																																																																			.	.		0.726	HOXB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358146.2			A	46675276	G	A	46675276	2	1	12	1	0	0	0	0	0	0	0	1	7314	987	35	3		3	HOXB6	17	46675276	Silent	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10	4246192	46675276	34519934	45	1043										
SIRT6	51548	hgsc.bcm.edu	37	chr19	4174810	4174811	+	Frame_Shift_Ins	INS	-	-	G													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	cagcttgggggtgggcgggcINSggggcaggggtggcagcgcc							TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:4174810_4174811insG	ENST00000337491.2	-	8	935_936	c.871_872insC	c.(871-873)cgcfs	p.R291fs	SIRT6_ENST00000601488.1_3'UTR|SIRT6_ENST00000381935.3_Frame_Shift_Ins_p.R219fs|SIRT6_ENST00000305232.6_Frame_Shift_Ins_p.R264fs|SIRT6_ENST00000594279.1_3'UTR	NM_016539.2	NP_057623.2	Q8N6T7	SIR6_HUMAN	sirtuin 6	291	Pro-rich.				histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|protein ADP-ribosylation (GO:0006471)|regulation of double-strand break repair via homologous recombination (GO:0010569)	nuclear telomeric heterochromatin (GO:0005724)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|lung(4)|ovary(1)|skin(1)	8		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.023)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTGGGCGGGCGGGGCAGGGGT	0.708																																					p.R291fs		Atlas-INDEL	.											.	SIRT6	16	.	0			c.872_873insC						.																																			SO:0001589	frameshift_variant	51548	exon8			.	AF233396	CCDS12122.1, CCDS54199.1	19p13.3	2010-06-25	2010-06-25			ENSG00000077463			14934	protein-coding gene	gene with protein product		606211	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 6", "sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae)"			10873683	Standard	NM_016539		Approved		uc002lzo.3	Q8N6T7		ENST00000337491.2:c.872dupC	chr19.hg19:g.4174814_4174814dupG	ENSP00000337332:p.Arg291fs	35.0	0.0		27.0	10.0	NM_016539	B2RCD0|O75291|Q6IAF5|Q6PK99|Q8NCD2|Q9BSI5|Q9BWP3|Q9NRC7|Q9UQD1	Frame_Shift_Ins	INS	ENST00000337491.2	hg19	CCDS12122.1																																																																																			.	.		0.708	SIRT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457931.2			G	4174811	-	G	4174810	7	5	12	1	0	1	1	0	0	0	0	0	14357	768	27	0	199	0	SIRT6	19	4174810	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H2-01A-12D-A382-10		4174810	54954173	46	1044										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17014374	17014374	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	gctccccaaaacctcacctgCatcaggcagcagccgtcccc	7	20	2	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:17014374C>A	ENST00000443236.1	-	34	4639	c.4608G>T	c.(4606-4608)atG>atT	p.M1536I		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1489						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						ACCTCACCTGCATCAGGCAGC	0.627																																					p.M1536I		Atlas-SNP	.											.	CPAMD8	192	.	0			c.G4608T						.						74	89	84					19																	17014374		2048	4193	6241	SO:0001583	missense	27151	exon34			CACCTGCATCAGG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.4608G>T	chr19.hg19:g.17014374C>A	ENSP00000402505:p.Met1536Ile	128.0	0.0		113.0	26.0	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	hg19	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.94|11.94	1.788366|1.788366	0.31593|0.31593	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440	.|.	.|.	.|.	3.32|3.32	2.26|2.26	0.28386|0.28386	.|.	.|7739.210000	.|0.00541	.|U	.|0.000222	T|T	0.56217|0.56217	0.1970|0.1970	L|L	0.50993|0.50993	1.605|1.605	0.80722|0.80722	D|D	1|1	.|B	.|0.32781	.|0.384	.|B	.|0.31290	.|0.127	T|T	0.33854|0.33854	-0.9852|-0.9852	5|9	.|0.56958	.|D	.|0.05	.|.	10.2643|10.2643	0.43445|0.43445	0.0:0.8995:0.0:0.1005|0.0:0.8995:0.0:0.1005	.|.	.|1489	.|Q8IZJ3	.|CPMD8_HUMAN	F|I	1547|1536	.|.	.|ENSP00000291440:M1536I	C|M	-|-	2|3	0|0	CPAMD8|CPAMD8	16875374|16875374	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	4.735000|4.735000	0.62051|0.62051	0.417000|0.417000	0.25871|0.25871	0.456000|0.456000	0.33151|0.33151	TGC|ATG	.	.		0.627	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		A	17014374	C	A	17014374	3	1	12	1	0	0	0	0	1	0	0	0	3797	710	25	3	1226	3	CPAMD8	19	17014374	Missense_Mutation	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	12839564	17014374	42114609	47	1045										
ZNF714	148206	hgsc.bcm.edu	37	chr19	21299919	21299921	+	Missense_Mutation	TNP	ATG	ATG	GCA													0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	tttcaaatgtaaaaaatgtgAtgaatcattttgcatgcttt							TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A|T|G	A|T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:21299919_21299921ATG>GCA	ENST00000596143.1	+	5	774_776	c.449_451ATG>GCA	c.(448-453)gATGaa>gGCAaa	p.150_151DE>GK	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	150					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AAAAAATGTGATGAATCATTTTG	0.291																																					p.D150G|p.D150D|p.E151K		Atlas-SNP	.											.	ZNF714	121	.	0			c.A449G|c.T450C|c.G451A						.																																			SO:0001583	missense	148206	exon5			AATGTGATGAATC|ATGTGATGAATCA|TGTGATGAATCAT	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.449_451ATG>GCA	chr19.hg19:g.21299919ATG>GCA	ENSP00000472368:p.D150_E151delinsGK	164.0|168.0|169.0	0.0		250.0|250.0|252.0	41.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation|Silent|Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1																																																																																			.	.		0.291	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		GCA	21299921	ATG	GCA	21299919	3	3	12	1	0	0	0	0	1	0	0	0	18133	333	12	2	459	2	ZNF714	19	21299919	Missense_Mutation	TNP	ATG	TCGA-2Y-A9H2-01A-12D-A382-10	4285545	21299919	37829064	48	1046										
MYH14	79784	hgsc.bcm.edu	37	chr19	50713649	50713649	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	gccgtgaccatgtcggtgccCgggcggaaggcgccccccag	16	16	0	1			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:50713649C>T	ENST00000596571.1	+	1	27	c.27C>T	c.(25-27)ccC>ccT	p.P9P	MYH14_ENST00000601313.1_Silent_p.P9P|MYH14_ENST00000440075.2_Silent_p.P9P|MYH14_ENST00000425460.1_Silent_p.P9P|MYH14_ENST00000598205.1_Silent_p.P9P|MYH14_ENST00000262269.8_Silent_p.P9P|MYH14_ENST00000376970.2_Silent_p.P9P			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	9					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		TGTCGGTGCCCGGGCGGAAGG	0.751																																					p.P9P		Atlas-SNP	.											.	MYH14	261	.	0			c.C27T						.						5	5	5					19																	50713649		1511	3440	4951	SO:0001819	synonymous_variant	79784	exon2			GGTGCCCGGGCGG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.27C>T	chr19.hg19:g.50713649C>T		154.0	0.0		56.0	11.0	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	hg19	CCDS59411.1																																																																																			.	.		0.751	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50713649	C	T	50713649	2	4	12	1	0	0	0	0	0	0	0	1	10042	639	23	1		1	MYH14	19	50713649	Silent	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	29413730	50713649	8415334	49	1047										
KLK1	3816	hgsc.bcm.edu	37	chr19	51322506	51322506	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	cacataagacagcactctgaCggcgacagaaggcttattgg	11	10	1	3	rs576085704		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:51322506C>T	ENST00000301420.2	-	5	768	c.733G>A	c.(733-735)Gtc>Atc	p.V245I	CTD-2568A17.5_ENST00000326989.5_lincRNA|KLK1_ENST00000448701.2_Missense_Mutation_p.V143I	NM_002257.2	NP_002248.1	P06870	KLK1_HUMAN	kallikrein 1	245	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			breast(1)|large_intestine(4)|lung(7)|urinary_tract(1)	13		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00399)	Aprotinin(DB06692)	AGCACTCTGACGGCGACAGAA	0.562													C|||	1	0.000199681	8e-04	0	5008	,	,		21306	0		0	False		,,,				2504	0				p.V245I		Atlas-SNP	.											.	KLK1	27	.	0			c.G733A						.						134	114	121					19																	51322506		2203	4300	6503	SO:0001583	missense	3816	exon5			CTCTGACGGCGAC	L10038	CCDS12804.1	19q13.3	2008-02-05	2006-10-27			ENSG00000167748	3.4.21.35	"Kallikreins"	6357	protein-coding gene	gene with protein product		147910	"kallikrein 1, renal/pancreas/salivary"			1684954, 16800724, 16800723	Standard	NM_002257		Approved	Klk6	uc002ptk.1	P06870		ENST00000301420.2:c.733G>A	chr19.hg19:g.51322506C>T	ENSP00000301420:p.Val245Ile	75.0	0.0		96.0	13.0	NM_002257	Q66US9|Q86U61|Q8TCV8|Q9BS53|Q9NQU4|Q9UD19|Q9UMJ1	Missense_Mutation	SNP	ENST00000301420.2	hg19	CCDS12804.1	.	.	.	.	.	.	.	.	.	.	c	12.22	1.872584	0.33069	.	.	ENSG00000167748	ENST00000301420;ENST00000448701	T;T	0.59364	3.3;0.27	3.53	0.196	0.15159	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.35307	0.0927	N	0.10916	0.065	0.09310	N	1	B	0.33379	0.41	B	0.37346	0.247	T	0.31110	-0.9955	9	0.87932	D	0	.	3.1007	0.06325	0.0:0.2592:0.2242:0.5166	.	245	P06870	KLK1_HUMAN	I	245;143	ENSP00000301420:V245I;ENSP00000400994:V143I	ENSP00000301420:V245I	V	-	1	0	KLK1	56014318	0.818000	0.29161	0.000000	0.03702	0.001000	0.01503	0.386000	0.20702	-0.036000	0.13669	-0.502000	0.04539	GTC	.	.		0.562	KLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464135.2	NM_002257		T	51322506	C	T	51322506	3	4	12	1	0	0	0	0	1	0	0	0	8406	536	19	1	59	1	KLK1	19	51322506	Missense_Mutation	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	608857	51322506	7806477	50	1048										
LILRA3	11026	hgsc.bcm.edu	37	chr19	54802575	54802575	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	tgtactggcccccgtaggagCggctcacagggcccagggtg	16	13	1	0	rs200980681	byFrequency	TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:54802575C>G	ENST00000251390.3	-	5	957	c.866G>C	c.(865-867)cGc>cCc	p.R289P	LILRA3_ENST00000391745.1_Missense_Mutation_p.R306P|LILRA3_ENST00000391744.3_Missense_Mutation_p.R225P	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	289	Ig-like C2-type 3.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCCGTAGGAGCGGCTCACAGG	0.662													.|||	8	0.00159744	0	0.0072	5008	,	,		10039	0.001		0.002	False		,,,				2504	0				p.R289P		Atlas-SNP	.											.	LILRA3	65	.	0			c.G866C						.																																			SO:0001583	missense	11026	exon5			TAGGAGCGGCTCA	U91926		19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.866G>C	chr19.hg19:g.54802575C>G	ENSP00000251390:p.Arg289Pro	8.0	0.0		10.0	5.0	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	hg19	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	C	1.908	-0.451501	0.04572	.	.	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.11277	2.79;2.79;2.79	2.03	-1.81	0.07882	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.569410	0.01087	N	0.005100	T	0.03608	0.0103	N	0.01081	-1.03	0.09310	N	1	B;B	0.19331	0.035;0.001	B;B	0.27170	0.077;0.025	T	0.30297	-0.9983	10	0.22109	T	0.4	.	2.9469	0.05849	0.4738:0.368:0.0:0.1583	.	289;289	E7EU74;Q8N6C8	.;LIRA3_HUMAN	P	289;225;306	ENSP00000251390:R289P;ENSP00000375624:R225P;ENSP00000375625:R306P	ENSP00000251390:R289P	R	-	2	0	LILRA3	59494387	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.120000	0.03273	-0.301000	0.08882	-0.238000	0.12139	CGC	.	C|0.999;G|0.001		0.662	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1			G	54802575	C	G	54802575	3	3	12	1	0	0	0	0	1	0	0	0	8795	768	27	4	465	4	LILRA3	19	54802575	Missense_Mutation	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	3480069	54802575	4326408	51	1049										
TFAP2C	7022	hgsc.bcm.edu	37	chr20	55209229	55209229	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	caaatcgaaaaatggaggccGgtccttgcgggagaagttgg	15	7	0	1			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr20:55209229G>T	ENST00000201031.2	+	5	1070	c.827G>T	c.(826-828)cGg>cTg	p.R276L	TFAP2C_ENST00000544508.1_Missense_Mutation_p.R107L	NM_003222.3	NP_003213.1	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma)	276					cell-cell signaling (GO:0007267)|cerebral cortex development (GO:0021987)|dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis (GO:0060598)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|forebrain neuron fate commitment (GO:0021877)|germ-line stem cell maintenance (GO:0030718)|hair follicle development (GO:0001942)|keratinocyte development (GO:0003334)|male gonad development (GO:0008584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermis development (GO:0045682)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sebaceous gland development (GO:0048733)|somatic stem cell maintenance (GO:0035019)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			Colorectal(105;0.229)			AATGGAGGCCGGTCCTTGCGG	0.448																																					p.R276L		Atlas-SNP	.											.	TFAP2C	51	.	0			c.G827T						.						74	79	78					20																	55209229		2203	4300	6503	SO:0001583	missense	7022	exon5			GAGGCCGGTCCTT		CCDS13454.1	20q13.2	2008-07-17	2001-11-28		ENSG00000087510	ENSG00000087510			11744	protein-coding gene	gene with protein product	"estrogen receptor factor 1"	601602	"transcription factor AP-2 gamma (activating enhancer-binding protein 2 gamma)"			8661133	Standard	NM_003222		Approved	AP2-GAMMA, ERF1, TFAP2G, hAP-2g	uc002xya.3	Q92754	OTTHUMG00000032805	ENST00000201031.2:c.827G>T	chr20.hg19:g.55209229G>T	ENSP00000201031:p.Arg276Leu	94.0	0.0		94.0	4.0	NM_003222	B4DWK3|O00685|O00730|Q86V30|Q8IVB6|Q9P1X2	Missense_Mutation	SNP	ENST00000201031.2	hg19	CCDS13454.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.307258	0.81247	.	.	ENSG00000087510	ENST00000201031;ENST00000544508	D;D	0.97186	-4.28;-4.28	5.3	5.3	0.74995	Transcription factor AP-2, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.98191	0.9402	M	0.89601	3.045	0.80722	D	1	P	0.50819	0.939	P	0.51777	0.679	D	0.99383	1.0923	10	0.87932	D	0	-23.6281	18.9667	0.92700	0.0:0.0:1.0:0.0	.	276	Q92754	AP2C_HUMAN	L	276;107	ENSP00000201031:R276L;ENSP00000442274:R107L	ENSP00000201031:R276L	R	+	2	0	TFAP2C	54642636	1.000000	0.71417	0.997000	0.53966	0.253000	0.25986	9.731000	0.98807	2.480000	0.83734	0.561000	0.74099	CGG	.	.		0.448	TFAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079823.2	NM_003222		T	55209229	G	T	55209229	3	4	12	1	0	0	0	0	1	0	0	0	15804	1116	39	1	845	1	TFAP2C	20	55209229	Missense_Mutation	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10		55209229	7816291	52	1050										
MORC2	22880	hgsc.bcm.edu	37	chr22	31342353	31342353	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	caatgccttcttcctcatgaAacgtgcgagacaggaagagg	11	10	2	3			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr22:31342353A>C	ENST00000397641.3	-	6	809	c.401T>G	c.(400-402)tTt>tGt	p.F134C	MORC2_ENST00000215862.4_Missense_Mutation_p.F72C			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	134						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						TTCCTCATGAAACGTGCGAGA	0.488																																					p.F72C		Atlas-SNP	.											.	MORC2	78	.	0			c.T215G						.						202	156	171					22																	31342353		2203	4300	6503	SO:0001583	missense	22880	exon7			TCATGAAACGTGC	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.401T>G	chr22.hg19:g.31342353A>C	ENSP00000380763:p.Phe134Cys	52.0	0.0		150.0	42.0	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	A	26.7	4.761248	0.89932	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	D;D	0.94931	-3.56;-3.56	5.15	5.15	0.70609	ATPase-like, ATP-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.97714	0.9250	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98745	1.0718	10	0.87932	D	0	.	15.1388	0.72595	1.0:0.0:0.0:0.0	.	134	Q9Y6X9	MORC2_HUMAN	C	134;72	ENSP00000380763:F134C;ENSP00000215862:F72C	ENSP00000215862:F72C	F	-	2	0	MORC2	29672353	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.761000	0.91691	2.160000	0.67779	0.454000	0.30748	TTT	.	.		0.488	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		C	31342353	A	C	31342353	3	2	12	1	0	0	0	0	1	0	0	0	9711	14	1	5	2781	5	MORC2	22	31342353	Missense_Mutation	SNP	A	TCGA-2Y-A9H2-01A-12D-A382-10		31342353	19962213	53	1051										
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50727540	50727540	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	ccagcgggtagggcaggtgcTccgagccacatgggaagctc	16	12	0	0			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr22:50727540T>C	ENST00000449103.1	-	4	1240	c.1100A>G	c.(1099-1101)gAg>gGg	p.E367G	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Missense_Mutation_p.E367G			O15031	PLXB2_HUMAN	plexin B2	367	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGGCAGGTGCTCCGAGCCACA	0.697																																					p.E367G		Atlas-SNP	.											.	PLXNB2	172	.	0			c.A1100G						.						9	11	11					22																	50727540		2052	4181	6233	SO:0001583	missense	23654	exon4			AGGTGCTCCGAGC		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.1100A>G	chr22.hg19:g.50727540T>C	ENSP00000409171:p.Glu367Gly	51.0	0.0		47.0	15.0	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	hg19	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.641799	0.87859	.	.	ENSG00000196576	ENST00000449103;ENST00000359337;ENST00000414275;ENST00000411680;ENST00000432455	T;T;T;T	0.04502	3.61;3.61;3.61;3.61	4.58	4.58	0.56647	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.235460	0.29218	N	0.012793	T	0.14141	0.0342	L	0.58354	1.805	0.80722	D	1	D	0.55385	0.971	P	0.60012	0.867	T	0.04268	-1.0964	10	0.29301	T	0.29	.	14.1091	0.65111	0.0:0.0:0.0:1.0	.	367	O15031	PLXB2_HUMAN	G	367;367;367;26;367	ENSP00000409171:E367G;ENSP00000352288:E367G;ENSP00000400679:E26G;ENSP00000392620:E367G	ENSP00000352288:E367G	E	-	2	0	PLXNB2	49069667	1.000000	0.71417	0.999000	0.59377	0.765000	0.43378	5.538000	0.67193	1.928000	0.55862	0.459000	0.35465	GAG	.	.		0.697	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		C	50727540	T	C	50727540	3	2	12	1	0	0	0	0	1	0	0	0	12133	1551	54	2	4552	2	PLXNB2	22	50727540	Missense_Mutation	SNP	T	TCGA-2Y-A9H2-01A-12D-A382-10	19385187	50727540	577026	54	1052										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5821285	5821285	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	gcccagctgggcttcatttcGctttggcagtgatgatagaa	12	9	1	3	rs398124364		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chrX:5821285G>T	ENST00000381095.3	-	5	2061	c.1434C>A	c.(1432-1434)agC>agA	p.S478R	NLGN4X_ENST00000538097.1_Missense_Mutation_p.S478R|NLGN4X_ENST00000275857.6_Missense_Mutation_p.S478R|NLGN4X_ENST00000381093.2_Missense_Mutation_p.S498R|NLGN4X_ENST00000381092.1_Missense_Mutation_p.S478R	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	478					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						GCTTCATTTCGCTTTGGCAGT	0.607																																					p.S478R		Atlas-SNP	.											.	NLGN4X	191	.	0			c.C1434A						.						67	59	62					X																	5821285		2203	4300	6503	SO:0001583	missense	57502	exon5			CATTTCGCTTTGG	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1434C>A	chrX.hg19:g.5821285G>T	ENSP00000370485:p.Ser478Arg	352.0	0.0		331.0	95.0	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.735781	0.30774	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	3.93	-1.39	0.08997	Carboxylesterase, type B (1);	.	.	.	.	T	0.65873	0.2733	L	0.51914	1.62	0.48452	D	0.999653	P;P;P	0.45428	0.75;0.858;0.456	P;P;B	0.50405	0.528;0.64;0.393	T	0.62632	-0.6813	9	0.51188	T	0.08	.	11.2547	0.49048	0.8693:0.0:0.1307:0.0	.	535;478;498	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	R	478;498;478;478;478	ENSP00000370485:S478R;ENSP00000370483:S498R;ENSP00000275857:S478R;ENSP00000370482:S478R;ENSP00000439203:S478R	ENSP00000275857:S478R	S	-	3	2	NLGN4X	5831285	0.962000	0.33011	0.734000	0.30879	0.799000	0.45148	0.146000	0.16180	-0.795000	0.04462	-0.881000	0.02953	AGC	.	.		0.607	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		T	5821285	G	T	5821285	3	4	12	1	0	0	0	0	1	0	0	0	10473	1078	38	1	1024	1	NLGN4X	23	5821285	Missense_Mutation	SNP	G	TCGA-2Y-A9H2-01A-12D-A382-10		5821285	149449275	55	1053										
RPS6KA6	27330	hgsc.bcm.edu	37	chrX	83359580	83359580	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.307366362451108	1.9978813559322	0	1	1	0	tagcctcccgttccgagaaaCatttttgtttgagaatacgg	9	9	0	2			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chrX:83359580C>T	ENST00000262752.2	-	17	1548	c.1541G>A	c.(1540-1542)tGt>tAt	p.C514Y	RPS6KA6_ENST00000543399.1_Missense_Mutation_p.C514Y|RPS6KA6_ENST00000495332.1_5'UTR	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	514	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						TTCCGAGAAACATTTTTGTTT	0.348																																					p.C514Y		Atlas-SNP	.											.	RPS6KA6	116	.	0			c.G1541A						.						87	76	80					X																	83359580		2202	4297	6499	SO:0001583	missense	27330	exon17			GAGAAACATTTTT	AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.1541G>A	chrX.hg19:g.83359580C>T	ENSP00000262752:p.Cys514Tyr	143.0	0.0		329.0	46.0	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	hg19	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	C	0.799	-0.756075	0.03019	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.38560	1.13;1.13	5.34	4.35	0.52113	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.162448	0.56097	D	0.000028	T	0.15739	0.0379	N	0.10733	0.035	0.32667	N	0.517343	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.29366	-1.0014	10	0.02654	T	1	.	4.045	0.09768	0.2276:0.555:0.0:0.2173	.	514;514	B7ZL90;Q9UK32	.;KS6A6_HUMAN	Y	514	ENSP00000262752:C514Y;ENSP00000440830:C514Y	ENSP00000262752:C514Y	C	-	2	0	RPS6KA6	83246236	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.091000	0.41691	2.205000	0.71048	0.600000	0.82982	TGT	.	.		0.348	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		T	83359580	C	T	83359580	3	4	12	1	0	0	0	0	1	0	0	0	13670	478	17	3	720	3	RPS6KA6	23	83359580	Missense_Mutation	SNP	C	TCGA-2Y-A9H2-01A-12D-A382-10	77538295	83359580	71910980	56	1054										
PANK4	55229	hgsc.bcm.edu	37	chr1	2441560	2441560	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggactcgctgtgggtcacgtCgttcagggcggggcctgagt	18	10	2	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:2441560C>T	ENST00000378466.3	-	17	1987	c.1975G>A	c.(1975-1977)Gac>Aac	p.D659N	PANK4_ENST00000435556.3_Missense_Mutation_p.D620N	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	659					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		TGGGTCACGTCGTTCAGGGCG	0.652																																					p.D659N		Atlas-SNP	.											.	PANK4	64	.	0			c.G1975A						.						65	53	57					1																	2441560		2193	4297	6490	SO:0001583	missense	55229	exon17			TCACGTCGTTCAG	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.1975G>A	chr1.hg19:g.2441560C>T	ENSP00000367727:p.Asp659Asn	231.0	0.0		119.0	24.0	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	hg19	CCDS42.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.420714	0.62622	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.72725	-0.68;-0.68	5.03	5.03	0.67393	Domain of unknown function DUF89 (2);	0.101757	0.64402	D	0.000004	D	0.86272	0.5893	M	0.89968	3.075	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89015	0.3431	10	0.87932	D	0	-33.8443	13.9394	0.64046	0.1523:0.8477:0.0:0.0	.	620;659	E9PHT6;Q9NVE7	.;PANK4_HUMAN	N	659;620	ENSP00000367727:D659N;ENSP00000421433:D620N	ENSP00000367727:D659N	D	-	1	0	PANK4	2431420	1.000000	0.71417	0.978000	0.43139	0.895000	0.52256	5.330000	0.65899	2.334000	0.79466	0.561000	0.74099	GAC	.	.		0.652	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1			T	2441560	C	T	2441560	3	4	13	1	0	0	0	0	1	0	0	0	11428	884	31	1	358	1	PANK4	1	2441560	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10		2441560	246809061	1	1055										
ESPN	83715	hgsc.bcm.edu	37	chr1	6488312	6488312	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gacaattctggtgccacagtCttgcatctggctgcccgctt	10	13	3	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:6488312C>T	ENST00000377828.1	+	2	489	c.321C>T	c.(319-321)gtC>gtT	p.V107V	MIR4252_ENST00000585139.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	107					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GTGCCACAGTCTTGCATCTGG	0.642																																					p.V107V		Atlas-SNP	.											.	ESPN	32	.	0			c.C321T						.						79	83	82					1																	6488312		2203	4300	6503	SO:0001819	synonymous_variant	83715	exon2			CACAGTCTTGCAT	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"Ankyrin repeat domain containing"	13281	protein-coding gene	gene with protein product		606351	"deafness, autosomal recessive 36"	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.321C>T	chr1.hg19:g.6488312C>T		201.0	0.0		104.0	25.0	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Silent	SNP	ENST00000377828.1	hg19	CCDS70.1																																																																																			.	.		0.642	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		T	6488312	C	T	6488312	2	4	13	1	0	0	0	0	0	0	0	1	5256	900	32	3		3	ESPN	1	6488312	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	4046752	6488312	242762309	2	1056										
DNAJC11	55735	hgsc.bcm.edu	37	chr1	6698364	6698364	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gcagcactcacagcggactcCgcctcttgcttcttctgcag	9	16	4	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:6698364C>T	ENST00000377577.5	-	12	1437	c.1314G>A	c.(1312-1314)gcG>gcA	p.A438A	DNAJC11_ENST00000542246.1_Silent_p.A400A|DNAJC11_ENST00000377573.5_Silent_p.A348A|DNAJC11_ENST00000294401.7_Silent_p.A386A|DNAJC11_ENST00000465508.1_5'UTR|DNAJC11_ENST00000349363.6_Intron	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	438						extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCGGACTCCGCCTCTTGCT	0.612																																					p.A438A		Atlas-SNP	.											.	DNAJC11	93	.	0			c.G1314A						.						86	74	78					1																	6698364		2203	4300	6503	SO:0001819	synonymous_variant	55735	exon12			GGACTCCGCCTCT	AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"Heat shock proteins / DNAJ (HSP40)"	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.1314G>A	chr1.hg19:g.6698364C>T		58.0	0.0		24.0	4.0	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Silent	SNP	ENST00000377577.5	hg19	CCDS87.1																																																																																			.	.		0.612	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198		T	6698364	C	T	6698364	2	4	13	1	0	0	0	0	0	0	0	1	4632	639	23	1		1	DNAJC11	1	6698364	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	210052	6698364	242552257	3	1057										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11561132	11561132	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	agaagcaacgggtgaaacctTtttaggggcccagaagccag	13	9	0	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:11561132T>A	ENST00000294484.6	+	2	221	c.83T>A	c.(82-84)tTt>tAt	p.F28Y	PTCHD2_ENST00000389575.3_Missense_Mutation_p.F28Y	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	28					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GGTGAAACCTTTTTAGGGGCC	0.637																																					p.F28Y		Atlas-SNP	.											.	PTCHD2	193	.	0			c.T83A						.						47	53	51					1																	11561132		1918	4113	6031	SO:0001583	missense	57540	exon2			AAACCTTTTTAGG	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.83T>A	chr1.hg19:g.11561132T>A	ENSP00000294484:p.Phe28Tyr	158.0	0.0		67.0	9.0	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	hg19	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	T	4.052	0.007321	0.07866	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	T;T	0.24908	1.83;1.83	5.78	-4.55	0.03441	.	3.256700	0.03411	U	0.204722	T	0.11452	0.0279	N	0.19112	0.55	0.09310	N	1	B	0.24533	0.105	B	0.16722	0.016	T	0.23190	-1.0195	10	0.02654	T	1	0.3108	4.6848	0.12752	0.1045:0.3852:0.3658:0.1445	.	28	Q9P2K9	PTHD2_HUMAN	Y	28	ENSP00000294484:F28Y;ENSP00000374226:F28Y	ENSP00000294484:F28Y	F	+	2	0	PTCHD2	11483719	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.639000	0.05446	-0.386000	0.07821	0.460000	0.39030	TTT	.	.		0.637	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		A	11561132	T	A	11561132	3	1	13	1	0	0	0	0	1	0	0	0	12745	1841	64	4	85	4	PTCHD2	1	11561132	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	4862768	11561132	237689489	4	1058										
EPHA2	1969	hgsc.bcm.edu	37	chr1	16464921	16464921	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aacttaaaaaatccaggcgaGcaggctggtggacacaggac	12	9	0	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:16464921G>T	ENST00000358432.5	-	4	982	c.828C>A	c.(826-828)tgC>tgA	p.C276*		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	276	Cys-rich.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	ATCCAGGCGAGCAGGCTGGTG	0.587																																					p.C276X		Atlas-SNP	.											.	EPHA2	102	.	0			c.C828A						.						45	46	45					1																	16464921		2203	4300	6503	SO:0001587	stop_gained	1969	exon4			AGGCGAGCAGGCT	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3386	protein-coding gene	gene with protein product		176946	"EphA2"	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.828C>A	chr1.hg19:g.16464921G>T	ENSP00000351209:p.Cys276*	84.0	0.0		53.0	9.0	NM_004431	B5A968|Q8N3Z2	Nonsense_Mutation	SNP	ENST00000358432.5	hg19	CCDS169.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.982965	0.93044	.	.	ENSG00000142627	ENST00000358432	.	.	.	5.12	3.06	0.35304	.	0.000000	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.5627	0.27860	0.2563:0.0:0.7437:0.0	.	.	.	.	X	276	.	ENSP00000351209:C276X	C	-	3	2	EPHA2	16337508	0.043000	0.20138	0.981000	0.43875	0.559000	0.35586	0.304000	0.19228	0.985000	0.38656	0.561000	0.74099	TGC	.	.		0.587	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431		T	16464921	G	T	16464921	4	4	13	1	0	0	0	0	0	1	0	0	5169	963	34	3	2158	3	EPHA2	1	16464921	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	4903789	16464921	232785700	5	1059										
PRPF38A	84950	hgsc.bcm.edu	37	chr1	52871471	52871471	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgcttcaaattcaacccgagAaggatatcattgtagagttt	8	7	3	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:52871471A>T	ENST00000257181.9	+	2	436	c.250A>T	c.(250-252)Aag>Tag	p.K84*	ORC1_ENST00000371568.3_5'Flank|PRPF38A_ENST00000474048.1_Intron|ORC1_ENST00000371566.1_5'Flank	NM_032864.3	NP_116253.2	Q8NAV1	PR38A_HUMAN	pre-mRNA processing factor 38A	84					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			cervix(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|stomach(1)	9						TCAACCCGAGAAGGATATCAT	0.388																																					p.K84X		Atlas-SNP	.											.	PRPF38A	36	.	0			c.A250T						.						87	86	87					1																	52871471		2203	4300	6503	SO:0001587	stop_gained	84950	exon2			CCCGAGAAGGATA	AK092038	CCDS567.1	1p32.3	2013-10-03	2013-10-03		ENSG00000134748	ENSG00000134748			25930	protein-coding gene	gene with protein product			"PRP38 pre-mRNA processing factor 38 (yeast) domain containing A"			12477932	Standard	NM_032864		Approved	FLJ14936, Prp38	uc001ctw.4	Q8NAV1	OTTHUMG00000008199	ENST00000257181.9:c.250A>T	chr1.hg19:g.52871471A>T	ENSP00000257181:p.Lys84*	132.0	0.0		106.0	8.0	NM_032864	Q96JW1|Q9BVZ8	Nonsense_Mutation	SNP	ENST00000257181.9	hg19	CCDS567.1	.	.	.	.	.	.	.	.	.	.	A	37	6.427268	0.97559	.	.	ENSG00000134748	ENST00000257181	.	.	.	5.72	5.72	0.89469	.	0.093222	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.0753	15.9967	0.80256	1.0:0.0:0.0:0.0	.	.	.	.	X	84	.	ENSP00000257181:K84X	K	+	1	0	PRPF38A	52644059	1.000000	0.71417	0.998000	0.56505	0.780000	0.44128	9.260000	0.95568	2.181000	0.69327	0.477000	0.44152	AAG	.	.		0.388	PRPF38A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022459.2	NM_032864		T	52871471	A	T	52871471	4	4	13	1	0	0	0	0	0	1	0	0	12579	247	9	4	256	4	PRPF38A	1	52871471	Nonsense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	36406550	52871471	196379150	6	1060										
DNAJC6	9829	hgsc.bcm.edu	37	chr1	65830467	65830467	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gagtgatacaatctgtgaccAggtacgcacattcttcccag	9	11	2	2	rs369490833		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:65830467A>T	ENST00000395325.3	+	2	329	c.172A>T	c.(172-174)Agc>Tgc	p.S58C	DNAJC6_ENST00000371069.4_Splice_Site_p.S115C|DNAJC6_ENST00000263441.7_Splice_Site_p.S45C	NM_014787.3	NP_055602.1	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	58	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell death (GO:0008219)|clathrin coat disassembly (GO:0072318)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytosol (GO:0005829)|synapse (GO:0045202)	protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(22)|ovary(1)|prostate(2)|skin(1)	39						ATCTGTGACCAGGTACGCACA	0.448																																					p.S115C		Atlas-SNP	.											.	DNAJC6	104	.	0			c.A343T						.						177	160	166					1																	65830467		2203	4300	6503	SO:0001630	splice_region_variant	9829	exon2			GTGACCAGGTACG	AB007942	CCDS30739.1, CCDS58004.1, CCDS58005.1	1p31.3	2011-09-02			ENSG00000116675	ENSG00000116675		"Heat shock proteins / DNAJ (HSP40)"	15469	protein-coding gene	gene with protein product	"auxilin"	608375				9455484, 11147971	Standard	NM_001256864		Approved	KIAA0473	uc001dce.2	O75061	OTTHUMG00000009066	ENST00000395325.3:c.173+1A>T	chr1.hg19:g.65830467A>T		44.0	0.0		93.0	16.0	NM_001256864	B7Z3V8|D3DQ65|D3DQ66|Q32M66|Q4G0K1|Q5T614|Q5T615	Missense_Mutation	SNP	ENST00000395325.3	hg19	CCDS30739.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.256889	0.80246	.	.	ENSG00000116675	ENST00000263441;ENST00000395325;ENST00000371069	D;D;D	0.94000	-3.3;-3.31;-3.33	5.07	5.07	0.68467	Phosphatase tensin type (1);	0.296394	0.36409	N	0.002616	D	0.94434	0.8209	M	0.61703	1.905	0.58432	D	0.999993	D;D;D	0.76494	0.999;0.996;0.996	P;P;P	0.61328	0.887;0.647;0.717	D	0.94990	0.8133	10	0.66056	D	0.02	.	15.0537	0.71894	1.0:0.0:0.0:0.0	.	115;58;45	O75061-2;O75061;D3DQ66	.;AUXI_HUMAN;.	C	45;58;115	ENSP00000263441:S45C;ENSP00000378735:S58C;ENSP00000360108:S115C	ENSP00000263441:S45C	S	+	1	0	DNAJC6	65603055	1.000000	0.71417	0.996000	0.52242	0.382000	0.30200	8.552000	0.90682	2.141000	0.66446	0.524000	0.50904	AGC	.	.		0.448	DNAJC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025134.1		Missense_Mutation	T	65830467	A	T	65830467	5	4	13	1	0	0	0	0	0	0	1	0	4655	202	7	4	178	4	DNAJC6	1	65830467	Splice_Site	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	12958996	65830467	183420154	7	1061										
RPE65	6121	hgsc.bcm.edu	37	chr1	68910485	68910485	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aatatattcttgcagggatcTgggaaagcacaggtgccaaa	11	7	2	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:68910485T>C	ENST00000262340.5	-	4	380	c.327A>G	c.(325-327)ccA>ccG	p.P109P		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	109					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						TGCAGGGATCTGGGAAAGCAC	0.403																																					p.P109P		Atlas-SNP	.											.	RPE65	87	.	0			c.A327G						.						92	91	91					1																	68910485		2203	4300	6503	SO:0001819	synonymous_variant	6121	exon4			GGGATCTGGGAAA	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.327A>G	chr1.hg19:g.68910485T>C		137.0	0.0		110.0	21.0	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	hg19	CCDS643.1																																																																																			.	.		0.403	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		C	68910485	T	C	68910485	2	2	13	1	0	0	0	0	0	0	0	1	13560	1567	55	2		2	RPE65	1	68910485	Silent	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	3080018	68910485	180340136	8	1062										
IFI44L	10964	hgsc.bcm.edu	37	chr1	79102796	79102796	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gaaggacaggattcactgtgTggcttatgtcttagacatca	11	7	3	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:79102796T>C	ENST00000370751.5	+	6	1135	c.956T>C	c.(955-957)gTg>gCg	p.V319A	IFI44L_ENST00000476521.1_3'UTR|IFI44L_ENST00000342282.3_Missense_Mutation_p.V61A	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	319					defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)				endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						ATTCACTGTGTGGCTTATGTC	0.363																																					p.V319A		Atlas-SNP	.											.	IFI44L	93	.	0			c.T956C						.						166	169	168					1																	79102796		2203	4300	6503	SO:0001583	missense	10964	exon6			ACTGTGTGGCTTA	AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"chromosome 1 open reading frame 29"	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.956T>C	chr1.hg19:g.79102796T>C	ENSP00000359787:p.Val319Ala	80.0	0.0		86.0	21.0	NM_006820	Q86TE1|Q96B64|Q99984	Missense_Mutation	SNP	ENST00000370751.5	hg19	CCDS687.2	.	.	.	.	.	.	.	.	.	.	T	19.24	3.788759	0.70337	.	.	ENSG00000137959	ENST00000370751;ENST00000342282	T;T	0.42513	2.62;0.97	4.08	4.08	0.47627	.	0.218465	0.30593	N	0.009281	T	0.47655	0.1457	M	0.63428	1.95	0.37145	D	0.901897	D	0.71674	0.998	D	0.68353	0.957	T	0.51490	-0.8699	10	0.49607	T	0.09	-14.041	11.2061	0.48771	0.0:0.0:0.0:1.0	.	319	Q53G44	IF44L_HUMAN	A	319;61	ENSP00000359787:V319A;ENSP00000342833:V61A	ENSP00000342833:V61A	V	+	2	0	IFI44L	78875384	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	5.130000	0.64745	1.790000	0.52503	0.377000	0.23210	GTG	.	.		0.363	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820		C	79102796	T	C	79102796	3	2	13	1	0	0	0	0	1	0	0	0	7527	1696	59	2	974	2	IFI44L	1	79102796	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	10192311	79102796	170147825	9	1063										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103444973	103444973	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tccattggcacctggaaaccCagggaatccagtggaaccct	10	13	0	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:103444973C>A	ENST00000370096.3	-	32	2887	c.2575G>T	c.(2575-2577)Ggg>Tgg	p.G859W	COL11A1_ENST00000353414.4_Missense_Mutation_p.G820W|COL11A1_ENST00000358392.2_Missense_Mutation_p.G871W|COL11A1_ENST00000512756.1_Missense_Mutation_p.G743W	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	859	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCTGGAAACCCAGGGAATCCA	0.348																																					p.G871W		Atlas-SNP	.											.	COL11A1	972	.	0			c.G2611T						.						42	45	44					1																	103444973		2203	4300	6503	SO:0001583	missense	1301	exon32			GAAACCCAGGGAA	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2575G>T	chr1.hg19:g.103444973C>A	ENSP00000359114:p.Gly859Trp	150.0	0.0		133.0	11.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.371545	0.82573	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.97994	-4.65;-4.65;-4.65;-4.65	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.99302	0.9756	H	0.97635	4.045	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999	D	0.98789	1.0735	10	0.87932	D	0	.	18.5374	0.91015	0.0:1.0:0.0:0.0	.	743;820;871;859;79	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	W	859;871;820;79;743	ENSP00000359114:G859W;ENSP00000351163:G871W;ENSP00000302551:G820W;ENSP00000426533:G743W	ENSP00000302551:G820W	G	-	1	0	COL11A1	103217561	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.133000	0.77259	2.612000	0.88384	0.655000	0.94253	GGG	.	.		0.348	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103444973	C	A	103444973	3	1	13	1	0	0	0	0	1	0	0	0	3669	594	21	3	2989	3	COL11A1	1	103444973	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	24342177	103444973	145805648	10	1064										
HIPK1	204851	hgsc.bcm.edu	37	chr1	114483828	114483828	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ttgaaatgttggagcagaacTtatatgattttctaaagcaa	8	4	1	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:114483828T>G	ENST00000369558.1	+	2	1055	c.823T>G	c.(823-825)Tta>Gta	p.L275V	HIPK1_ENST00000426820.2_Missense_Mutation_p.L275V|HIPK1_ENST00000369555.2_Missense_Mutation_p.L275V|HIPK1_ENST00000369559.4_Missense_Mutation_p.L275V|HIPK1_ENST00000369554.2_Missense_Mutation_p.L275V|HIPK1_ENST00000369561.4_Missense_Mutation_p.L275V			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	275	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGAGCAGAACTTATATGATTT	0.408																																					p.L275V		Atlas-SNP	.											.	HIPK1	195	.	0			c.T823G						.						82	81	82					1																	114483828		2203	4300	6503	SO:0001583	missense	204851	exon2			CAGAACTTATATG	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.823T>G	chr1.hg19:g.114483828T>G	ENSP00000358571:p.Leu275Val	103.0	0.0		78.0	12.0	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Missense_Mutation	SNP	ENST00000369558.1	hg19	CCDS867.1	.	.	.	.	.	.	.	.	.	.	T	16.97	3.267975	0.59540	.	.	ENSG00000163349	ENST00000426820;ENST00000369559;ENST00000443627;ENST00000369554;ENST00000369555;ENST00000369558;ENST00000369561	T;T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24;0.24	5.81	1.98	0.26296	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48767	D	0.000177	T	0.60379	0.2264	M	0.67700	2.07	0.80722	D	1	D;D	0.69078	0.997;0.974	D;D	0.76071	0.987;0.969	T	0.63620	-0.6596	10	0.87932	D	0	.	8.5641	0.33530	0.0:0.3049:0.0:0.6951	.	275;275	Q86Z02;Q86Z02-2	HIPK1_HUMAN;.	V	346;275;275;275;275;275;275	ENSP00000407442:L346V;ENSP00000358572:L275V;ENSP00000409673:L275V;ENSP00000358567:L275V;ENSP00000358568:L275V;ENSP00000358571:L275V;ENSP00000358574:L275V	ENSP00000358567:L275V	L	+	1	2	HIPK1	114285351	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	1.551000	0.36233	0.384000	0.24942	0.455000	0.32223	TTA	.	.		0.408	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		G	114483828	T	G	114483828	3	3	13	1	0	0	0	0	1	0	0	0	7125	1606	56	5	825	5	HIPK1	1	114483828	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	11038855	114483828	134766793	11	1065										
PDZK1	5174	hgsc.bcm.edu	37	chr1	145748506	145748506	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cccctgtgatgaatggaggtGtgcaaacttggacccagccc	12	12	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:145748506G>A	ENST00000344770.2	+	3	452	c.379G>A	c.(379-381)Gtg>Atg	p.V127M	PDZK1_ENST00000451928.2_Missense_Mutation_p.V127M|PDZK1_ENST00000417171.1_Missense_Mutation_p.V127M	NM_002614.4	NP_002605.2	Q5T2W1	NHRF3_HUMAN	PDZ domain containing 1	127					carnitine transport (GO:0015879)|cell proliferation (GO:0008283)|drug transport (GO:0015893)|establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of ion transmembrane transport (GO:0034767)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of anion transport (GO:0044070)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|transporter activity (GO:0005215)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	7	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			GAATGGAGGTGTGCAAACTTG	0.483																																					p.V127M		Atlas-SNP	.											.	PDZK1	15	.	0			c.G379A						.						34	40	38					1																	145748506		2203	4298	6501	SO:0001583	missense	5174	exon4			GGAGGTGTGCAAA	AF012281	CCDS72859.1, CCDS72860.1	1q21	2009-08-21			ENSG00000174827	ENSG00000174827			8821	protein-coding gene	gene with protein product		603831				9461128	Standard	NM_002614		Approved	PDZD1, NHERF3	uc001eoo.2	Q5T2W1	OTTHUMG00000013735	ENST00000344770.2:c.379G>A	chr1.hg19:g.145748506G>A	ENSP00000342143:p.Val127Met	383.0	0.0		378.0	120.0	NM_002614	B4DPB9|E7EU02|O60450|Q5T5P6|Q9BQ41	Missense_Mutation	SNP	ENST00000344770.2	hg19	CCDS924.1	.	.	.	.	.	.	.	.	.	.	G	9.823	1.186342	0.21870	.	.	ENSG00000174827	ENST00000443667;ENST00000417171;ENST00000451928;ENST00000344770	T;T;T;T	0.32753	1.44;1.52;1.57;1.52	5.84	3.98	0.46160	PDZ/DHR/GLGF (1);	1.045830	0.07476	N	0.902950	T	0.20901	0.0503	M	0.70275	2.135	0.09310	N	1	P;B	0.44090	0.826;0.375	B;B	0.42738	0.191;0.396	T	0.24870	-1.0148	10	0.48119	T	0.1	-13.7977	9.3114	0.37908	0.1663:0.0:0.8337:0.0	.	127;127	E7EU02;Q5T2W1	.;NHRF3_HUMAN	M	127	ENSP00000409291:V127M;ENSP00000394485:V127M;ENSP00000403422:V127M;ENSP00000342143:V127M	ENSP00000342143:V127M	V	+	1	0	PDZK1	144459863	0.000000	0.05858	0.001000	0.08648	0.034000	0.12701	0.762000	0.26503	0.817000	0.34445	0.591000	0.81541	GTG	.	.		0.483	PDZK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038502.2	NM_002614		A	145748506	G	A	145748506	3	1	13	1	0	0	0	0	1	0	0	0	11716	1377	48	3	385	3	PDZK1	1	145748506	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	31264678	145748506	103502115	12	1066										
FLG	2312	hgsc.bcm.edu	37	chr1	152282251	152282251	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ttccactgtctccgactacaGatgaatcttgtctgcgccca	7	14	3	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:152282251G>T	ENST00000368799.1	-	3	5146	c.5111C>A	c.(5110-5112)tCt>tAt	p.S1704Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1704	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCGACTACAGATGAATCTTG	0.572									Ichthyosis																												p.S1704Y		Atlas-SNP	.											.	FLG	900	.	0			c.C5111A						.						245	249	248					1																	152282251		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ACTACAGATGAAT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5111C>A	chr1.hg19:g.152282251G>T	ENSP00000357789:p.Ser1704Tyr	88.0	0.0		81.0	12.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	9.539	1.112979	0.20795	.	.	ENSG00000143631	ENST00000368799	T	0.04049	3.72	2.51	-0.85	0.10720	.	.	.	.	.	T	0.03651	0.0104	M	0.66939	2.045	0.09310	N	1	D	0.65815	0.995	D	0.76071	0.987	T	0.21314	-1.0249	9	0.02654	T	1	.	4.3855	0.11314	0.0:0.2424:0.4459:0.3116	.	1704	P20930	FILA_HUMAN	Y	1704	ENSP00000357789:S1704Y	ENSP00000357789:S1704Y	S	-	2	0	FLG	150548875	0.001000	0.12720	0.001000	0.08648	0.037000	0.13140	0.578000	0.23773	-0.154000	0.11118	0.306000	0.20318	TCT	.	.		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152282251	G	T	152282251	3	4	13	1	0	0	0	0	1	0	0	0	5930	942	33	3	7078	3	FLG	1	152282251	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	6533745	152282251	96968370	13	1067										
ASTN1	460	hgsc.bcm.edu	37	chr1	176992547	176992547	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgctcccgcctaccagtttcGgggtcacattggtgttcaca	10	13	2	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:176992547G>A	ENST00000367654.3	-	7	1642	c.1431C>T	c.(1429-1431)ccC>ccT	p.P477P	ASTN1_ENST00000424564.2_Silent_p.P477P|ASTN1_ENST00000367657.3_Silent_p.P477P|ASTN1_ENST00000361833.2_Silent_p.P477P|ASTN1_ENST00000281881.3_5'UTR	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	477	EGF-like 1.				locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TACCAGTTTCGGGGTCACATT	0.597																																					p.P477P		Atlas-SNP	.											.	ASTN1	314	.	0			c.C1431T						.						23	22	22					1																	176992547		2202	4300	6502	SO:0001819	synonymous_variant	460	exon7			AGTTTCGGGGTCA	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1431C>T	chr1.hg19:g.176992547G>A		203.0	0.0		166.0	14.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	hg19																																																																																				.	.		0.597	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		A	176992547	G	A	176992547	2	1	13	1	0	0	0	0	0	0	0	1	1064	1103	39	1		1	ASTN1	1	176992547	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	24710296	176992547	72258074	14	1068										
RALGPS2	55103	hgsc.bcm.edu	37	chr1	178871314	178871314	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggctgatgaccctgaacatcCtgatctcttcctgctgactg	9	13	1	5			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:178871314C>A	ENST00000367635.3	+	18	1936	c.1598C>A	c.(1597-1599)cCt>cAt	p.P533H	RALGPS2_ENST00000367634.2_Missense_Mutation_p.P507H	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	533	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.|Required for stimulation of nucleotide exchange by RALA. {ECO:0000250}.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						CCTGAACATCCTGATCTCTTC	0.393																																					p.P533H		Atlas-SNP	.											.	RALGPS2	69	.	0			c.C1598A						.						221	192	202					1																	178871314		2203	4300	6503	SO:0001583	missense	55103	exon18			AACATCCTGATCT	AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"Pleckstrin homology (PH) domain containing"	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.1598C>A	chr1.hg19:g.178871314C>A	ENSP00000356607:p.Pro533His	44.0	0.0		85.0	9.0	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Missense_Mutation	SNP	ENST00000367635.3	hg19	CCDS1325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.4|27.4	4.825067|4.825067	0.90955|0.90955	.|.	.|.	ENSG00000116191|ENSG00000116191	ENST00000367632|ENST00000367635;ENST00000367634;ENST00000324778;ENST00000535251	.|T;T;T	.|0.80994	.|-1.44;-1.44;-1.44	5.69|5.69	5.69|5.69	0.88448|0.88448	.|Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.89037|0.89037	0.6601|0.6601	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.69479	.|0.927;0.964	D|D	0.87911|0.87911	0.2697|0.2697	5|10	.|0.44086	.|T	.|0.13	.|.	19.4161|19.4161	0.94700|0.94700	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|507;533	.|B7Z7B1;Q86X27	.|.;RGPS2_HUMAN	M|H	124|533;507;498;182	.|ENSP00000356607:P533H;ENSP00000356606:P507H;ENSP00000313613:P498H	.|ENSP00000313613:P498H	L|P	+|+	1|2	2|0	RALGPS2|RALGPS2	177137937|177137937	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.962000|0.962000	0.63368|0.63368	7.452000|7.452000	0.80683|0.80683	2.683000|2.683000	0.91414|0.91414	0.655000|0.655000	0.94253|0.94253	CTG|CCT	.	.		0.393	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663		A	178871314	C	A	178871314	3	1	13	1	0	0	0	0	1	0	0	0	13033	681	24	3	1664	3	RALGPS2	1	178871314	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	1878767	178871314	70379307	15	1069										
ABL2	27	hgsc.bcm.edu	37	chr1	179077338	179077338	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gcccagagctgccttctttcCtccttcctgtgtttctgatg	8	14	2	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:179077338C>T	ENST00000502732.1	-	12	3267	c.3064G>A	c.(3064-3066)Gga>Aga	p.G1022R	ABL2_ENST00000344730.3_Missense_Mutation_p.G904R|ABL2_ENST00000512653.1_Missense_Mutation_p.G1007R|ABL2_ENST00000507173.1_Missense_Mutation_p.G898R|ABL2_ENST00000367623.4_Missense_Mutation_p.G1001R|ABL2_ENST00000511413.1_Missense_Mutation_p.G919R|ABL2_ENST00000504405.1_Missense_Mutation_p.G883R|ABL2_ENST00000408940.3_Missense_Mutation_p.G986R	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	1022	F-actin-binding. {ECO:0000250}.|Pro-rich.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	GCCTTCTTTCCTCCTTCCTGT	0.567			T	ETV6	AML																																p.G1022R		Atlas-SNP	.		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	ABL2	307	.	0			c.G3064A						.						108	104	106					1																	179077338		2203	4300	6503	SO:0001583	missense	27	exon12			TCTTTCCTCCTTC	M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.3064G>A	chr1.hg19:g.179077338C>T	ENSP00000427562:p.Gly1022Arg	81.0	0.0		71.0	13.0	NM_007314	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Missense_Mutation	SNP	ENST00000502732.1	hg19	CCDS30947.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.954531	0.34471	.	.	ENSG00000143322	ENST00000502732;ENST00000408940;ENST00000344730;ENST00000512653;ENST00000504405;ENST00000367623;ENST00000507173;ENST00000511413	T;T;T;T;T;T;T;T	0.74421	-0.82;-0.83;-0.84;-0.83;-0.83;-0.82;-0.83;-0.84	5.5	5.5	0.81552	F-actin binding (1);	0.128338	0.35615	N	0.003089	T	0.70281	0.3206	L	0.34521	1.04	0.32177	N	0.580821	P;B;B;P;P;P;P;P	0.50272	0.813;0.001;0.001;0.933;0.921;0.879;0.901;0.933	B;B;B;P;P;P;P;P	0.55577	0.373;0.007;0.007;0.646;0.779;0.595;0.607;0.646	T	0.68580	-0.5371	10	0.15066	T	0.55	.	7.7932	0.29133	0.0:0.7449:0.1662:0.0889	.	1001;898;919;883;1022;1007;986;904	P42684-6;P42684-7;P42684-5;P42684-4;P42684;P42684-3;D1MPS6;P42684-10	.;.;.;.;ABL2_HUMAN;.;.;.	R	1022;986;904;1007;883;1001;898;919	ENSP00000427562:G1022R;ENSP00000386152:G986R;ENSP00000339209:G904R;ENSP00000423578:G1007R;ENSP00000426831:G883R;ENSP00000356595:G1001R;ENSP00000423413:G898R;ENSP00000424697:G919R	ENSP00000339209:G904R	G	-	1	0	ABL2	177343961	0.424000	0.25490	1.000000	0.80357	0.882000	0.50991	0.646000	0.24797	2.735000	0.93741	0.655000	0.94253	GGA	.	.		0.567	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		T	179077338	C	T	179077338	3	4	13	1	0	0	0	0	1	0	0	0	93	690	24	3	488	3	ABL2	1	179077338	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	206024	179077338	70173283	16	1070										
CEP350	9857	hgsc.bcm.edu	37	chr1	179989802	179989802	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cttctagctctgatatgcaaGcctgttctcaagacaaagcc	7	12	3	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:179989802G>A	ENST00000367607.3	+	12	3311	c.2893G>A	c.(2893-2895)Gcc>Acc	p.A965T		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	965					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TGATATGCAAGCCTGTTCTCA	0.468																																					p.A965T		Atlas-SNP	.											.	CEP350	418	.	0			c.G2893A						.						122	126	124					1																	179989802		2203	4300	6503	SO:0001583	missense	9857	exon12			ATGCAAGCCTGTT	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.2893G>A	chr1.hg19:g.179989802G>A	ENSP00000356579:p.Ala965Thr	191.0	0.0		199.0	61.0	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	G	11.10	1.538635	0.27475	.	.	ENSG00000135837	ENST00000367607	T	0.13657	2.57	6.02	-0.966	0.10320	.	0.854746	0.09906	N	0.740485	T	0.05960	0.0155	N	0.19112	0.55	0.09310	N	1	B;B	0.28713	0.001;0.22	B;B	0.19148	0.001;0.024	T	0.38908	-0.9639	9	.	.	.	.	1.6551	0.02780	0.2391:0.2743:0.361:0.1257	.	965;965	E7EU22;Q5VT06	.;CE350_HUMAN	T	965	ENSP00000356579:A965T	.	A	+	1	0	CEP350	178256425	0.630000	0.27155	0.594000	0.28785	0.920000	0.55202	0.520000	0.22878	-0.117000	0.11872	-0.345000	0.07892	GCC	.	.		0.468	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		A	179989802	G	A	179989802	3	1	13	1	0	0	0	0	1	0	0	0	3256	971	34	3	2935	3	CEP350	1	179989802	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	912464	179989802	69260819	17	1071										
NVL	4931	hgsc.bcm.edu	37	chr1	224482050	224482050	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gtctcaaagcagggtctaacGagtctggtcgattagtagct	12	8	3	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:224482050G>A	ENST00000281701.6	-	12	1503	c.1244C>T	c.(1243-1245)tCg>tTg	p.S415L	NVL_ENST00000340871.4_Missense_Mutation_p.S226L|NVL_ENST00000391875.2_Missense_Mutation_p.S309L|NVL_ENST00000482491.1_Missense_Mutation_p.S139L|NVL_ENST00000361463.3_Missense_Mutation_p.S309L|NVL_ENST00000469075.1_Missense_Mutation_p.S324L	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	415						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		AGGGTCTAACGAGTCTGGTCG	0.458																																					p.S415L		Atlas-SNP	.											.	NVL	74	.	0			c.C1244T						.						90	84	86					1																	224482050		2203	4300	6503	SO:0001583	missense	4931	exon12			TCTAACGAGTCTG	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"ATPases / AAA-type"	8070	protein-coding gene	gene with protein product	"Nuclear valosin-containing protein-like", "nuclear VCP-like protein"	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.1244C>T	chr1.hg19:g.224482050G>A	ENSP00000281701:p.Ser415Leu	85.0	0.0		71.0	5.0	NM_002533	B4DMC4|B4DP98|Q96EM7	Missense_Mutation	SNP	ENST00000281701.6	hg19	CCDS1541.1	.	.	.	.	.	.	.	.	.	.	G	36	5.760521	0.96906	.	.	ENSG00000143748	ENST00000281701;ENST00000391875;ENST00000469075;ENST00000482491;ENST00000340871;ENST00000361463	D;D;D;D;D;D	0.92911	-3.13;-3.13;-3.13;-3.13;-3.13;-3.13	5.65	5.65	0.86999	ATPase, AAA-type, conserved site (1);ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.91838	0.7417	N	0.13327	0.33	0.80722	D	1	D;P;D	0.60160	0.987;0.948;0.975	P;P;P	0.60236	0.686;0.7;0.871	D	0.93190	0.6582	10	0.87932	D	0	-10.3576	20.0752	0.97739	0.0:0.0:1.0:0.0	.	226;324;415	B4DMC4;B4DP98;O15381	.;.;NVL_HUMAN	L	415;309;324;139;226;309	ENSP00000281701:S415L;ENSP00000375747:S309L;ENSP00000417826:S324L;ENSP00000417213:S139L;ENSP00000341362:S226L;ENSP00000354779:S309L	ENSP00000281701:S415L	S	-	2	0	NVL	222548673	1.000000	0.71417	0.955000	0.39395	0.894000	0.52154	9.582000	0.98214	2.826000	0.97356	0.491000	0.48974	TCG	.	.		0.458	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533		A	224482050	G	A	224482050	3	1	13	1	0	0	0	0	1	0	0	0	10789	1059	37	1	1374	1	NVL	1	224482050	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	44492248	224482050	24768571	18	1072										
DISC1	27185	hgsc.bcm.edu	37	chr1	231885681	231885681	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgggtttccagctgagacgtTacaacaaagattagaagacc	10	8	0	4			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:231885681T>C	ENST00000602281.1	+	4	1180	c.1127T>C	c.(1126-1128)tTa>tCa	p.L376S	DISC1_ENST00000439617.2_Missense_Mutation_p.L376S|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000535983.1_Missense_Mutation_p.L376S|DISC1_ENST00000537876.1_Missense_Mutation_p.L376S|DISC1_ENST00000539444.1_Missense_Mutation_p.L376S|DISC1_ENST00000602873.1_Missense_Mutation_p.L26S|DISC1_ENST00000366636.4_Missense_Mutation_p.L376S|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000366633.3_Missense_Mutation_p.L376S	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	376	Interaction with TRAF3IP1.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				GCTGAGACGTTACAACAAAGA	0.443																																					p.L408S		Atlas-SNP	.											.	DISC1	207	.	0			c.T1223C						.						90	91	91					1																	231885681		2203	4300	6503	SO:0001583	missense	27185	exon5			AGACGTTACAACA	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.1127T>C	chr1.hg19:g.231885681T>C	ENSP00000473425:p.Leu376Ser	129.0	0.0		235.0	25.0	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	hg19	CCDS59205.1	.	.	.	.	.	.	.	.	.	.	.	12.82	2.051985	0.36181	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944	T;T;T;T;T;T;T;T	0.18657	2.64;2.45;2.44;2.23;2.63;2.24;2.24;2.2	4.75	4.75	0.60458	.	0.376283	0.24983	N	0.034054	T	0.40932	0.1137	.	.	.	0.09310	N	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.76494	0.999;0.996;0.998;0.993;0.997;0.993;0.98;0.997;0.989;0.996;0.996;0.98;0.996;0.996;0.999;0.996;0.999;0.996;0.98	D;P;D;P;D;P;P;D;P;D;D;P;D;D;D;D;D;D;P	0.67231	0.95;0.893;0.95;0.827;0.911;0.857;0.773;0.911;0.839;0.931;0.931;0.731;0.931;0.931;0.95;0.918;0.95;0.918;0.731	T	0.22208	-1.0223	9	0.87932	D	0	-0.0869	10.5642	0.45163	0.0:0.0:0.0:1.0	.	408;376;408;376;376;376;376;376;26;376;376;376;376;376;376;376;376;376;376	C4P096;C4P094;E2QRA4;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0C1;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P0B1;A7E2W8;Q5T409;Q9NRI5-2;Q9NRI5;Q9NRI5-3	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.	S	376;376;376;408;376;376;376;376;376;376;376	ENSP00000403888:L376S;ENSP00000355596:L376S;ENSP00000443996:L376S;ENSP00000440909:L376S;ENSP00000355593:L376S;ENSP00000440953:L376S;ENSP00000295051:L376S;ENSP00000441193:L376S	ENSP00000295051:L376S	L	+	2	0	DISC1	229952304	0.048000	0.20356	0.002000	0.10522	0.367000	0.29736	3.707000	0.54838	1.977000	0.57605	0.533000	0.62120	TTA	.	.		0.443	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		C	231885681	T	C	231885681	3	2	13	1	0	0	0	0	1	0	0	0	4540	1764	61	2	1500	2	DISC1	1	231885681	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	7403631	231885681	17364940	19	1073										
ARID4B	51742	hgsc.bcm.edu	37	chr1	235345805	235345805	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ttgaagatttatctgttgtgTccttcttgacatcctttctc	6	9	3	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:235345805T>C	ENST00000264183.3	-	20	2926	c.2429A>G	c.(2428-2430)gAc>gGc	p.D810G	ARID4B_ENST00000366603.2_Missense_Mutation_p.D810G|ARID4B_ENST00000349213.3_Missense_Mutation_p.D724G|ARID4B_ENST00000494543.1_5'Flank	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	810					histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			ATCTGTTGTGTCCTTCTTGAC	0.333																																					p.D810G		Atlas-SNP	.											.	ARID4B	142	.	0			c.A2429G						.						184	165	171					1																	235345805		2203	4300	6503	SO:0001583	missense	51742	exon20			GTTGTGTCCTTCT	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"-"	15550	protein-coding gene	gene with protein product		609696	"retinoblastoma binding protein 1-like 1", "AT rich interactive domain 4B (RBP1- like)"	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.2429A>G	chr1.hg19:g.235345805T>C	ENSP00000264183:p.Asp810Gly	104.0	0.0		79.0	5.0	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Missense_Mutation	SNP	ENST00000264183.3	hg19	CCDS31061.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.09|14.09	2.432637|2.432637	0.43224|0.43224	.|.	.|.	ENSG00000054267|ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183|ENST00000444620	T;T;T|.	0.25085|.	1.87;1.82;1.82|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.387174|.	0.32473|.	N|.	0.006051|.	T|T	0.49592|0.49592	0.1566|0.1566	N|N	0.14661|0.14661	0.345|0.345	0.49915|0.49915	D|D	0.999838|0.999838	P;B;D;B|.	0.56521|.	0.873;0.001;0.976;0.002|.	B;B;P;B|.	0.44811|.	0.367;0.002;0.461;0.002|.	T|T	0.47222|0.47222	-0.9134|-0.9134	10|5	0.59425|.	D|.	0.04|.	-21.0593|-21.0593	16.4311|16.4311	0.83844|0.83844	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	491;810;724;810|.	Q4LE39-4;Q4LE39-3;Q4LE39-2;Q4LE39|.	.;.;.;ARI4B_HUMAN|.	G|A	810;724;810;810|210	ENSP00000264184:D724G;ENSP00000355562:D810G;ENSP00000264183:D810G|.	ENSP00000264183:D810G|.	D|T	-|-	2|1	0|0	ARID4B|ARID4B	233412428|233412428	1.000000|1.000000	0.71417|0.71417	0.940000|0.940000	0.37924|0.37924	0.991000|0.991000	0.79684|0.79684	4.010000|4.010000	0.57117|0.57117	2.277000|2.277000	0.76020|0.76020	0.528000|0.528000	0.53228|0.53228	GAC|ACA	.	.		0.333	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		C	235345805	T	C	235345805	3	2	13	1	0	0	0	0	1	0	0	0	920	1667	58	2	1529	2	ARID4B	1	235345805	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	3460124	235345805	13904816	20	1074										
HEATR1	55127	hgsc.bcm.edu	37	chr1	236757400	236757400	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gtagatttgaccatccattcCttcagtttcttctccttaat	4	11	3	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:236757400C>T	ENST00000366582.3	-	9	1219	c.1105G>A	c.(1105-1107)Gga>Aga	p.G369R	HEATR1_ENST00000366581.2_Missense_Mutation_p.G369R|HEATR1_ENST00000483073.1_5'Flank	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	369					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			CCATCCATTCCTTCAGTTTCT	0.294																																					p.G369R		Atlas-SNP	.											.	HEATR1	197	.	0			c.G1105A						.						140	138	139					1																	236757400		2203	4295	6498	SO:0001583	missense	55127	exon9			CCATTCCTTCAGT	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.1105G>A	chr1.hg19:g.236757400C>T	ENSP00000355541:p.Gly369Arg	69.0	0.0		84.0	10.0	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	hg19	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.871108	0.72065	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.66995	3.5;-0.24	5.54	5.54	0.83059	Armadillo-type fold (1);	0.558966	0.18889	N	0.128365	T	0.56352	0.1979	L	0.33485	1.01	0.80722	D	1	B	0.23735	0.09	B	0.24006	0.05	T	0.51655	-0.8678	10	0.09084	T	0.74	.	18.4263	0.90610	0.0:1.0:0.0:0.0	.	369	Q9H583	HEAT1_HUMAN	R	369	ENSP00000355541:G369R;ENSP00000355540:G369R	ENSP00000355540:G369R	G	-	1	0	HEATR1	234824023	0.993000	0.37304	0.960000	0.40013	0.836000	0.47400	4.691000	0.61738	2.777000	0.95525	0.591000	0.81541	GGA	.	.		0.294	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		T	236757400	C	T	236757400	3	4	13	1	0	0	0	0	1	0	0	0	7036	690	24	3	5477	3	HEATR1	1	236757400	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	1411595	236757400	12493221	21	1075										
ACTN2	88	hgsc.bcm.edu	37	chr1	236911058	236911058	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgggaacgcttactcagaagAggagagaagccctagaggtg	15	7	1	4			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:236911058A>G	ENST00000366578.4	+	13	1664	c.1498A>G	c.(1498-1500)Agg>Ggg	p.R500G	ACTN2_ENST00000546208.1_5'UTR|ACTN2_ENST00000542672.1_Missense_Mutation_p.R500G	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	500					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			TACTCAGAAGAGGAGAGAAGC	0.408																																					p.R500G		Atlas-SNP	.											.	ACTN2	191	.	0			c.A1498G						.						43	46	45					1																	236911058		2203	4300	6503	SO:0001583	missense	88	exon13			CAGAAGAGGAGAG	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.1498A>G	chr1.hg19:g.236911058A>G	ENSP00000355537:p.Arg500Gly	203.0	0.0		211.0	21.0	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	hg19	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	A	18.00	3.524628	0.64747	.	.	ENSG00000077522	ENST00000542672;ENST00000366578;ENST00000545611	T;T	0.61392	0.11;0.11	5.73	3.21	0.36854	.	0.000000	0.85682	D	0.000000	T	0.81588	0.4854	H	0.95365	3.66	0.80722	D	1	D;D;D;D	0.89917	0.989;1.0;0.999;0.992	D;D;D;D	0.97110	0.971;1.0;1.0;0.995	D	0.86445	0.1769	10	0.87932	D	0	.	12.9108	0.58179	0.627:0.373:0.0:0.0	.	285;500;270;500	B7Z4K1;B2RCS5;Q59FD9;P35609	.;.;.;ACTN2_HUMAN	G	500;500;269	ENSP00000443495:R500G;ENSP00000355537:R500G	ENSP00000355537:R500G	R	+	1	2	ACTN2	234977681	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	2.142000	0.42177	1.061000	0.40601	0.533000	0.62120	AGG	.	.		0.408	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		G	236911058	A	G	236911058	3	3	13	1	0	0	0	0	1	0	0	0	205	295	11	2	1548	2	ACTN2	1	236911058	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	153658	236911058	12339563	22	1076										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247016531	247016531	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acttcctggttaagcctgcgCtcagagacaataggaccttc	9	12	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:247016531C>T	ENST00000391829.2	-	32	4548	c.4425G>A	c.(4423-4425)gaG>gaA	p.E1475E	AHCTF1_ENST00000326225.3_Silent_p.E1484E|AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000366508.1_Silent_p.E1510E			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1475	Disordered. {ECO:0000250}.|Mediates transcriptional activity. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TAAGCCTGCGCTCAGAGACAA	0.408																																					p.E1484E	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.G4452A						.						45	42	43					1																	247016531		2203	4300	6503	SO:0001819	synonymous_variant	25909	exon32			CCTGCGCTCAGAG		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.4425G>A	chr1.hg19:g.247016531C>T		350.0	0.0		377.0	39.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	hg19																																																																																				.	.		0.408	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		T	247016531	C	T	247016531	2	4	13	1	0	0	0	0	0	0	0	1	408	796	28	3		3	AHCTF1	1	247016531	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	10105473	247016531	2234090	23	1077										
OR2T6	254879	hgsc.bcm.edu	37	chr1	248550917	248550917	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	caaactcagtaccatgaatgAaaacaatgaaaccttgacca	5	10	1	4			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr1:248550917A>G	ENST00000355728.2	+	1	8	c.8A>G	c.(7-9)gAa>gGa	p.E3G		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	3						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACCATGAATGAAAACAATGAA	0.388																																					p.E3G		Atlas-SNP	.											.	OR2T6	101	.	0			c.A8G						.						92	93	93					1																	248550917		2203	4300	6503	SO:0001583	missense	254879	exon1			TGAATGAAAACAA	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"GPCR / Class A : Olfactory receptors"	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.8A>G	chr1.hg19:g.248550917A>G	ENSP00000347965:p.Glu3Gly	51.0	0.0		96.0	6.0	NM_001005471	A6NE36	Missense_Mutation	SNP	ENST00000355728.2	hg19	CCDS31114.1	.	.	.	.	.	.	.	.	.	.	A	5.682	0.310393	0.10733	.	.	ENSG00000198104	ENST00000355728	T	0.20332	2.08	4.9	-3.04	0.05412	.	0.992297	0.08173	N	0.986694	T	0.10121	0.0248	N	0.10733	0.035	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38457	-0.9660	10	0.22706	T	0.39	.	11.371	0.49699	0.6188:0.0:0.3812:0.0	.	3	Q8NHC8	OR2T6_HUMAN	G	3	ENSP00000347965:E3G	ENSP00000347965:E3G	E	+	2	0	OR2T6	246617540	0.000000	0.05858	0.004000	0.12327	0.010000	0.07245	-0.042000	0.12063	-0.953000	0.03645	-0.288000	0.09946	GAA	.	.		0.388	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471		G	248550917	A	G	248550917	3	3	13	1	0	0	0	0	1	0	0	0	11038	246	9	2	10	2	OR2T6	1	248550917	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	1534386	248550917	699704	24	1078										
ADCY3	109	hgsc.bcm.edu	37	chr2	25045489	25045489	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgatcacccggaacttgggaTtgtccaggagctgaggccag	14	10	1	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:25045489T>A	ENST00000260600.5	-	18	3745	c.2894A>T	c.(2893-2895)aAt>aTt	p.N965I	RP11-443B20.1_ENST00000606114.1_RNA|ADCY3_ENST00000405392.1_Missense_Mutation_p.N552I	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	965					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					GAACTTGGGATTGTCCAGGAG	0.527																																					p.N965I		Atlas-SNP	.											.	ADCY3	114	.	0			c.A2894T						.						109	95	100					2																	25045489		2203	4300	6503	SO:0001583	missense	109	exon18			TTGGGATTGTCCA	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"Adenylate cyclases"	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.2894A>T	chr2.hg19:g.25045489T>A	ENSP00000260600:p.Asn965Ile	93.0	0.0		63.0	6.0	NM_004036	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	hg19	CCDS1715.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.900165	0.52227	.	.	ENSG00000138031	ENST00000260600;ENST00000405392;ENST00000415879	D;D	0.81499	-1.5;-1.5	5.55	5.55	0.83447	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.360765	0.32473	N	0.006060	T	0.67730	0.2924	N	0.11364	0.135	0.34767	D	0.733385	B;B;B	0.30146	0.27;0.27;0.077	B;B;B	0.33121	0.158;0.158;0.021	T	0.74990	-0.3475	10	0.44086	T	0.13	.	14.8147	0.70024	0.0:0.0:0.0:1.0	.	966;965;552	B7ZLX9;O60266;B3KT86	.;ADCY3_HUMAN;.	I	965;552;940	ENSP00000260600:N965I;ENSP00000384484:N552I	ENSP00000260600:N965I	N	-	2	0	ADCY3	24898993	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.962000	0.70364	2.333000	0.79357	0.533000	0.62120	AAT	.	.		0.527	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			A	25045489	T	A	25045489	3	1	13	1	0	0	0	0	1	0	0	0	295	1493	52	4	556	4	ADCY3	2	25045489	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10		25045489	218153884	25	1079										
PLB1	151056	hgsc.bcm.edu	37	chr2	28785968	28785968	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cctgggtgactctctcacggTaagtgaccctgatgcagaag	12	11	2	4			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:28785968T>G	ENST00000327757.5	+	18	1250		c.e18+2		PLB1_ENST00000329020.6_Splice_Site|PLB1_ENST00000422425.2_Splice_Site	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1						glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TCTCTCACGGTAAGTGACCCT	0.498																																					.		Atlas-SNP	.											.	PLB1	255	.	0			c.1206+2T>G						.						62	62	62					2																	28785968		2203	4300	6503	SO:0001630	splice_region_variant	151056	exon18			TCACGGTAAGTGA		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.1206+2T>G	chr2.hg19:g.28785968T>G		95.0	0.0		102.0	13.0	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Splice_Site	SNP	ENST00000327757.5	hg19	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	T	18.05	3.537514	0.65085	.	.	ENSG00000163803	ENST00000327757;ENST00000422425;ENST00000404858;ENST00000436544;ENST00000329020	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5302	0.50604	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PLB1	28639472	1.000000	0.71417	0.581000	0.28614	0.908000	0.53690	4.372000	0.59530	2.038000	0.60285	0.459000	0.35465	.	.	.		0.498	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		Intron	G	28785968	T	G	28785968	5	3	13	1	0	0	0	0	0	0	1	0	12033	1652	57	5	1311	5	PLB1	2	28785968	Splice_Site	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	3740479	28785968	214413405	26	1080										
KCNG3	170850	hgsc.bcm.edu	37	chr2	42671524	42671524	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	atcattctaagtaccctcaaGgtgactccagccctctggag	8	13	4	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:42671524G>C	ENST00000306078.1	-	2	1456	c.861C>G	c.(859-861)acC>acG	p.T287T	KCNG3_ENST00000394973.4_Silent_p.T276T	NM_133329.5|NM_172344.2	NP_579875.1|NP_758847.1	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G, member 3	287					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	6						GTACCCTCAAGGTGACTCCAG	0.453																																					p.T287T		Atlas-SNP	.											.	KCNG3	19	.	0			c.C861G						.						98	92	94					2																	42671524		2203	4300	6503	SO:0001819	synonymous_variant	170850	exon2			CCTCAAGGTGACT	AB070604	CCDS1809.1, CCDS42674.1	2p21	2011-07-05			ENSG00000171126	ENSG00000171126		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18306	protein-coding gene	gene with protein product		606767				11852086, 16382104	Standard	NM_133329		Approved	Kv6.3	uc002rsn.3	Q8TAE7	OTTHUMG00000128604	ENST00000306078.1:c.861C>G	chr2.hg19:g.42671524G>C		112.0	0.0		132.0	19.0	NM_133329	Q53SC1	Silent	SNP	ENST00000306078.1	hg19	CCDS1809.1																																																																																			.	.		0.453	KCNG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250464.2	NM_172344		C	42671524	G	C	42671524	2	2	13	1	0	0	0	0	0	0	0	1	8038	987	35	4		4	KCNG3	2	42671524	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	13885556	42671524	200527849	27	1081										
XPO1	7514	hgsc.bcm.edu	37	chr2	61726983	61726983	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tcctacttgctccaacaataTcactgataaaagttggccaa	5	11	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:61726983T>A	ENST00000401558.2	-	7	1182	c.455A>T	c.(454-456)gAt>gTt	p.D152V	XPO1_ENST00000404992.2_Missense_Mutation_p.D152V|XPO1_ENST00000406957.1_Missense_Mutation_p.D152V	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	152	Necessary for HTLV-1 Rex-mediated mRNA export.				gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			TCCAACAATATCACTGATAAA	0.353			Mis		CLL																																p.D152V		Atlas-SNP	.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1	108	.	0			c.A455T						.						83	84	84					2																	61726983		2203	4300	6503	SO:0001583	missense	7514	exon7			ACAATATCACTGA	Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.455A>T	chr2.hg19:g.61726983T>A	ENSP00000384863:p.Asp152Val	268.0	0.0		244.0	39.0	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	hg19	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.363474	0.82353	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957;ENST00000451765	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	5.84	5.84	0.93424	Exportin-1/Importin-beta-like (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.74574	0.3734	M	0.90759	3.145	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.80663	-0.1282	10	0.87932	D	0	-13.7935	16.2091	0.82146	0.0:0.0:0.0:1.0	.	152	O14980	XPO1_HUMAN	V	152	ENSP00000384863:D152V;ENSP00000385942:D152V;ENSP00000385559:D152V;ENSP00000413853:D152V	ENSP00000384863:D152V	D	-	2	0	XPO1	61580487	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.027000	0.88791	2.223000	0.72356	0.533000	0.62120	GAT	.	.		0.353	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		A	61726983	T	A	61726983	3	1	13	1	0	0	0	0	1	0	0	0	17460	1435	50	4	2836	4	XPO1	2	61726983	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	19055459	61726983	181472390	28	1082										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84822866	84822866	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aaaaaggcttgccacccaacAgtgtagtgccccagctcaaa	8	13	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:84822866A>C	ENST00000237449.6	+	17	2829	c.2821A>C	c.(2821-2823)Agt>Cgt	p.S941R	DNAH6_ENST00000398278.2_Missense_Mutation_p.S941R|DNAH6_ENST00000389394.3_Missense_Mutation_p.S941R			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	941	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GCCACCCAACAGTGTAGTGCC	0.383																																					p.S941R		Atlas-SNP	.											.	DNAH6	194	.	0			c.A2821C						.						100	94	95					2																	84822866		692	1591	2283	SO:0001583	missense	1768	exon18			CCCAACAGTGTAG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.2821A>C	chr2.hg19:g.84822866A>C	ENSP00000237449:p.Ser941Arg	102.0	0.0		68.0	10.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	14.53	2.562288	0.45694	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.60797	0.16;0.16;0.16	5.82	5.82	0.92795	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.40322	0.1112	N	0.11724	0.165	0.36169	D	0.848663	B	0.11235	0.004	B	0.16722	0.016	T	0.43327	-0.9398	9	0.18710	T	0.47	.	15.159	0.72767	1.0:0.0:0.0:0.0	.	941	Q9C0G6	DYH6_HUMAN	R	941	ENSP00000374045:S941R;ENSP00000381326:S941R;ENSP00000237449:S941R	ENSP00000237449:S941R	S	+	1	0	DNAH6	84676377	1.000000	0.71417	0.993000	0.49108	0.963000	0.63663	7.151000	0.77411	2.215000	0.71742	0.528000	0.53228	AGT	.	.		0.383	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		C	84822866	A	C	84822866	3	2	13	1	0	0	0	0	1	0	0	0	4607	188	7	5	2887	5	DNAH6	2	84822866	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	23095883	84822866	158376507	29	1083										
ACOXL	55289	hgsc.bcm.edu	37	chr2	111850452	111850452	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	caccccttagttttgtctgtTgtatggaaccaagctggtgt	10	9	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:111850452T>C	ENST00000389811.4	+	18	1765	c.1541T>C	c.(1540-1542)tTg>tCg	p.L514S	ACOXL_ENST00000439055.1_Missense_Mutation_p.L484S			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	514					fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						TTTTGTCTGTTGTATGGAACC	0.413																																					p.L484S		Atlas-SNP	.											.	ACOXL	93	.	0			c.T1451C						.						111	111	111					2																	111850452		2203	4300	6503	SO:0001583	missense	55289	exon17			GTCTGTTGTATGG		CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"acyl-Coenzyme A oxidase-like"				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.1541T>C	chr2.hg19:g.111850452T>C	ENSP00000374461:p.Leu514Ser	68.0	0.0		91.0	6.0	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	hg19		.	.	.	.	.	.	.	.	.	.	T	15.61	2.884952	0.51908	.	.	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000422487;ENST00000417074	T;T;T	0.70516	-0.49;-0.49;-0.49	5.87	5.87	0.94306	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.000000	0.47852	D	0.000204	D	0.84875	0.5569	M	0.82823	2.61	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.993;0.988;0.997	D	0.87073	0.2161	10	0.87932	D	0	-26.6067	14.2209	0.65826	0.0:0.0:0.0:1.0	.	484;484;514	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	S	514;484;335;322	ENSP00000374461:L514S;ENSP00000407761:L484S;ENSP00000387832:L322S	ENSP00000374461:L514S	L	+	2	0	ACOXL	111566923	0.996000	0.38824	0.116000	0.21606	0.515000	0.34225	4.519000	0.60517	2.244000	0.73946	0.533000	0.62120	TTG	.	.		0.413	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308		C	111850452	T	C	111850452	3	2	13	1	0	0	0	0	1	0	0	0	161	1821	63	2	1513	2	ACOXL	2	111850452	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	27027586	111850452	131348921	30	1084										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167266354	167266355	+	Frame_Shift_Ins	INS	-	-	T													0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aacatcagtgtctatcatcaINStggctattgcttggaaacat							TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:167266354_167266355insT	ENST00000409855.1	-	24	3928_3929	c.3802_3803insA	c.(3802-3804)atgfs	p.M1268fs		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1268					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	GTCTATCATCATGGCTATTGCT	0.356																																					p.M1268fs		Atlas-INDEL	.											.	SCN7A	410	.	0			c.3803_3804insA						.																																			SO:0001589	frameshift_variant	6332	exon24			.	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.3803dupA	chr2.hg19:g.167266355_167266355dupT	ENSP00000386796:p.Met1268fs	120.0	0.0		183.0	23.0	NM_002976		Frame_Shift_Ins	INS	ENST00000409855.1	hg19	CCDS46442.1																																																																																			.	.		0.356	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			T	167266355	-	T	167266354	7	5	13	1	0	1	1	0	0	0	0	0	13938	217	8	0	1253	0	SCN7A	2	167266354	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H3-01A-11D-A382-10	55415902	167266354	75933019	31	1085	3	2								
SCN7A	6332	hgsc.bcm.edu	37	chr2	167266356	167266357	+	Missense_Mutation	DNP	GG	GG	TA													0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acatcagtgtctatcatcatGgctattgcttggaaacatat					rs573169902		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:167266356_167266357GG>TA	ENST00000409855.1	-	24	3926_3927	c.3800_3801CC>TA	c.(3799-3801)gCC>gTA	p.A1267V		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1267					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	CTATCATCATGGCTATTGCTTG	0.351																																					p.A1267A|p.A1267V		Atlas-SNP	.											.	SCN7A	410	.	0			c.C3801A|c.C3800T						.																																			SO:0001583	missense	6332	exon24			CATCATGGCTATT|ATCATGGCTATTG	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.3800_3801delinsTA	chr2.hg19:g.167266356_167266357delinsTA	ENSP00000386796:p.Ala1267Val	118.0|116.0	0.0		178.0|179.0	22.0	NM_002976		Silent|Missense_Mutation	SNP	ENST00000409855.1	hg19	CCDS46442.1																																																																																			.	.		0.351	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			TA	167266357	GG	TA	167266356	3	4	13	1	0	0	0	0	1	0	0	0	13938	1335	47	3	1255	3	SCN7A	2	167266356	Missense_Mutation	DNP	GG	TCGA-2Y-A9H3-01A-11D-A382-10	2	167266356	75933017	32	1086	3	2								
TTN	7273	hgsc.bcm.edu	37	chr2	179417552	179417552	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gctggtacttcagcagccttCactggctctgtagtttcaca	9	12	4	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:179417552C>T	ENST00000591111.1	-	285	85376	c.85152G>A	c.(85150-85152)gtG>gtA	p.V28384V	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592600.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN_ENST00000460472.2_Silent_p.V20960V|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000589042.1_Silent_p.V30025V|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.V21152V|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.V27457V|TTN_ENST00000359218.5_Silent_p.V21085V			Q8WZ42	TITIN_HUMAN	titin	28384	Fibronectin type-III 106. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGCAGCCTTCACTGGCTCTG	0.438																																					p.V30025V		Atlas-SNP	.											.	TTN	18412	.	0			c.G90075A						.						61	57	58					2																	179417552		1907	4128	6035	SO:0001819	synonymous_variant	7273	exon335			AGCCTTCACTGGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.85152G>A	chr2.hg19:g.179417552C>T		76.0	0.0		175.0	13.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179417552	C	T	179417552	2	4	13	1	0	0	0	0	0	0	0	1	16750	813	29	3		3	TTN	2	179417552	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	12151196	179417552	63781821	33	1087										
CPS1	1373	hgsc.bcm.edu	37	chr2	211442191	211442191	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tagtaaagactacaaccactGgctggctaccaagagtttag	9	9	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:211442191G>A	ENST00000233072.5	+	4	624	c.428G>A	c.(427-429)tGg>tAg	p.W143*	CPS1_ENST00000430249.2_Nonsense_Mutation_p.W149*	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	143	Anthranilate phosphoribosyltransferase homolog.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TACAACCACTGGCTGGCTACC	0.418																																					p.W149X		Atlas-SNP	.											.	CPS1	485	.	0			c.G446A						.						154	154	154					2																	211442191		2203	4300	6503	SO:0001587	stop_gained	1373	exon5			ACCACTGGCTGGC	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.428G>A	chr2.hg19:g.211442191G>A	ENSP00000233072:p.Trp143*	89.0	0.0		106.0	9.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Nonsense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.038542	0.93630	.	.	ENSG00000021826	ENST00000523702;ENST00000430249;ENST00000539150;ENST00000233072;ENST00000536125	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.227	19.3439	0.94356	0.0:0.0:1.0:0.0	.	.	.	.	X	149;149;151;143;143	.	ENSP00000233072:W143X	W	+	2	0	CPS1	211150436	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.650000	0.91073	2.638000	0.89438	0.585000	0.79938	TGG	.	.		0.418	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			A	211442191	G	A	211442191	4	1	13	1	0	0	0	0	0	1	0	0	3825	1357	47	3	464	3	CPS1	2	211442191	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	32024639	211442191	31757182	34	1088										
CPS1	1373	hgsc.bcm.edu	37	chr2	211527868	211527868	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ctcccatgttttcctggcccCggttgagggatgctgacccc	11	15	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:211527868C>T	ENST00000233072.5	+	33	4145	c.3949C>T	c.(3949-3951)Cgg>Tgg	p.R1317W	CPS1_ENST00000430249.2_Missense_Mutation_p.R1323W|CPS1_ENST00000451903.2_Missense_Mutation_p.R866W	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1317					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TTCCTGGCCCCGGTTGAGGGA	0.383																																					p.R1323W		Atlas-SNP	.											CPS1_ENST00000430249,NS,carcinoma,0,4	CPS1	485	.	0			c.C3967T						.						47	51	50					2																	211527868		2203	4300	6503	SO:0001583	missense	1373	exon34			TGGCCCCGGTTGA	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3949C>T	chr2.hg19:g.211527868C>T	ENSP00000233072:p.Arg1317Trp	114.0	0.0		121.0	20.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.604266	0.66445	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	T;T;T	0.70749	-0.51;-0.51;-0.51	5.43	4.53	0.55603	ATP-grasp fold, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.88179	0.6367	H	0.96748	3.875	0.52099	D	0.999941	D;D	0.71674	0.998;0.994	P;P	0.62740	0.906;0.906	D	0.92127	0.5709	10	0.87932	D	0	-8.4052	14.7296	0.69372	0.2627:0.7373:0.0:0.0	.	1327;1317	Q59HF8;P31327	.;CPSM_HUMAN	W	1323;1325;1317;866	ENSP00000402608:R1323W;ENSP00000233072:R1317W;ENSP00000406136:R866W	ENSP00000233072:R1317W	R	+	1	2	CPS1	211236113	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	3.600000	0.54052	1.377000	0.46286	0.655000	0.94253	CGG	.	.		0.383	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211527868	C	T	211527868	3	4	13	1	0	0	0	0	1	0	0	0	3825	643	23	1	4101	1	CPS1	2	211527868	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	85677	211527868	31671505	35	1089										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212522515	212522515	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aagtggaatggcccgtccatGggtagtaaatgcagtcatga	13	7	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:212522515G>T	ENST00000342788.4	-	16	2220	c.1910C>A	c.(1909-1911)cCa>cAa	p.P637Q	ERBB4_ENST00000402597.1_Intron|ERBB4_ENST00000436443.1_Missense_Mutation_p.P637Q	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	637					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GCCCGTCCATGGGTAGTAAAT	0.433										TSP Lung(8;0.080)																											p.P637Q		Atlas-SNP	.											.	ERBB4	480	.	0			c.C1910A						.						276	214	235					2																	212522515		2203	4300	6503	SO:0001583	missense	2066	exon16			GTCCATGGGTAGT	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1910C>A	chr2.hg19:g.212522515G>T	ENSP00000342235:p.Pro637Gln	174.0	0.0		93.0	11.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.374971	0.24857	.	.	ENSG00000178568	ENST00000342788;ENST00000436443	T;T	0.75367	-0.93;-0.92	5.14	4.25	0.50352	.	0.267053	0.37761	N	0.001951	T	0.52741	0.1753	N	0.13098	0.295	0.80722	D	1	B;P;P	0.39116	0.004;0.66;0.529	B;B;B	0.35727	0.002;0.209;0.103	T	0.49862	-0.8894	10	0.12430	T	0.62	.	11.0488	0.47874	0.089:0.0:0.911:0.0	.	496;637;637	Q53QS8;Q15303-3;Q15303	.;.;ERBB4_HUMAN	Q	637	ENSP00000342235:P637Q;ENSP00000403204:P637Q	ENSP00000342235:P637Q	P	-	2	0	ERBB4	212230760	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.958000	0.63660	1.258000	0.44101	0.650000	0.86243	CCA	.	.		0.433	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212522515	G	T	212522515	3	4	13	1	0	0	0	0	1	0	0	0	5211	1348	47	3	2068	3	ERBB4	2	212522515	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	994647	212522515	30676858	36	1090										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222428899	222428899	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tcgttgtctgattcatagtaGtacaggttaaacgtctcctt	8	8	3	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:222428899G>T	ENST00000281821.2	-	3	416	c.375C>A	c.(373-375)taC>taA	p.Y125*	EPHA4_ENST00000409854.1_Nonsense_Mutation_p.Y125*|EPHA4_ENST00000392071.4_Nonsense_Mutation_p.Y74*|EPHA4_ENST00000409938.1_Nonsense_Mutation_p.Y125*	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	125	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		ATTCATAGTAGTACAGGTTAA	0.458																																					p.Y125X		Atlas-SNP	.											.	EPHA4	263	.	0			c.C375A						.						159	147	151					2																	222428899		2203	4300	6503	SO:0001587	stop_gained	2043	exon3			ATAGTAGTACAGG	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.375C>A	chr2.hg19:g.222428899G>T	ENSP00000281821:p.Tyr125*	98.0	0.0		99.0	17.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Nonsense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.116416	0.77323	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071;ENST00000419964;ENST00000541600	.	.	.	6.17	4.4	0.53042	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.4782	0.27390	0.3432:0.0:0.6568:0.0	.	.	.	.	X	125;125;125;74;66;125	.	ENSP00000281821:Y125X	Y	-	3	2	EPHA4	222137143	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.507000	0.45442	0.952000	0.37798	0.655000	0.94253	TAC	.	.		0.458	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222428899	G	T	222428899	4	4	13	1	0	0	0	0	0	1	0	0	5171	1024	36	3	2645	3	EPHA4	2	222428899	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	9906384	222428899	20770474	37	1091										
PAX3	5077	hgsc.bcm.edu	37	chr2	223066833	223066833	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tggtggtaggttccagacccCcggtgagaggggagagcgcg	19	9	0	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr2:223066833C>G	ENST00000350526.4	-	8	1386	c.1250G>C	c.(1249-1251)gGg>gCg	p.G417A	PAX3_ENST00000344493.4_Intron|PAX3_ENST00000392070.2_Missense_Mutation_p.G417A|PAX3_ENST00000409551.3_Missense_Mutation_p.G416A|PAX3_ENST00000464706.1_5'UTR|PAX3_ENST00000392069.2_Missense_Mutation_p.G417A|PAX3_ENST00000336840.6_Intron	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	417					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTCCAGACCCCCGGTGAGAGG	0.552			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.G417A		Atlas-SNP	.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	PAX3	106	.	0			c.G1250C						.						80	75	77					2																	223066833		2203	4300	6503	SO:0001583	missense	5077	exon8			AGACCCCCGGTGA		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.1250G>C	chr2.hg19:g.223066833C>G	ENSP00000343052:p.Gly417Ala	86.0	0.0		121.0	12.0	NM_181457	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Missense_Mutation	SNP	ENST00000350526.4	hg19	CCDS42826.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.278856	0.80692	.	.	ENSG00000135903	ENST00000392069;ENST00000350526;ENST00000392070;ENST00000409551;ENST00000464706	D;D;D;D	0.93906	-3.28;-3.28;-3.3;-3.31	5.81	5.81	0.92471	.	0.051938	0.85682	D	0.000000	D	0.94499	0.8229	L	0.54323	1.7	0.80722	D	1	D;P;P	0.60160	0.987;0.908;0.944	P;B;P	0.53360	0.724;0.344;0.545	D	0.93768	0.7072	10	0.46703	T	0.11	.	20.0784	0.97758	0.0:1.0:0.0:0.0	.	417;416;417	P23760;Q494Z4;G5E9C1	PAX3_HUMAN;.;.	A	417;417;417;416;134	ENSP00000375921:G417A;ENSP00000343052:G417A;ENSP00000375922:G417A;ENSP00000386750:G416A	ENSP00000343052:G417A	G	-	2	0	PAX3	222775077	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	7.294000	0.78760	2.736000	0.93811	0.655000	0.94253	GGG	.	.		0.552	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			G	223066833	C	G	223066833	3	3	13	1	0	0	0	0	1	0	0	0	11489	623	22	4	307	4	PAX3	2	223066833	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	637934	223066833	20132540	38	1092										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1444079	1444079	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tcagctgagcttctggttccAtttgaagaagactacttaat	8	8	2	4			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr3:1444079A>G	ENST00000446702.2	+	22	3522	c.2895A>G	c.(2893-2895)ccA>ccG	p.P965P	CNTN6_ENST00000539053.1_Silent_p.P893P|CNTN6_ENST00000350110.2_Silent_p.P965P			Q9UQ52	CNTN6_HUMAN	contactin 6	965	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TTCTGGTTCCATTTGAAGAAG	0.363																																					p.P965P		Atlas-SNP	.											.	CNTN6	245	.	0			c.A2895G						.						104	105	105					3																	1444079		2203	4299	6502	SO:0001819	synonymous_variant	27255	exon22			GGTTCCATTTGAA	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2895A>G	chr3.hg19:g.1444079A>G		209.0	0.0		241.0	30.0	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	hg19	CCDS2557.1																																																																																			.	.		0.363	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		G	1444079	A	G	1444079	2	3	13	1	0	0	0	0	0	0	0	1	3647	204	8	2		2	CNTN6	3	1444079	Silent	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10		1444079	196578351	39	1093										
BAP1	8314	hgsc.bcm.edu	37	chr3	52436677	52436708	+	Splice_Site	DEL	CTCTGGTCATCAATCTGTAGGAGAGAAGAAGA	CTCTGGTCATCAATCTGTAGGAGAGAAGAAGA	-													0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	catcgtagttgtgggtccttCtctggtcatcaatctgtagg							TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	CTCTGGTCATCAATCTGTAGGAGAGAAGAAGA	CTCTGGTCATCAATCTGTAGGAGAGAAGAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr3:52436677_52436708delCTCTGGTCATCAATCTGTAGGAGAGAAGAAGA	ENST00000460680.1	-	16	2455_2468	c.1984_1997delTCTTCTTCTCTCCTACAGATTGATGACCAGAG	c.(1984-1998)tcttcttctctccta>a	p.SSSLL662fs	BAP1_ENST00000296288.5_Splice_Site_p.SSSLL644fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R666_H669>N(1)|p.?(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GTGGGTCCTTCTCTGGTCATCAATCTGTAGGAGAGAAGAAGACTGAGAGCAC	0.534			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.662_666del	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	2	Unknown(1)|Complex - deletion inframe(1)	eye(2)	c.1984_1998del						.																																			SO:0001630	splice_region_variant	8314	exon16			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1984-1TCTTCTTCTCTCCTACAGATTGATGACCAGAG>-	chr3.hg19:g.52436677_52436708delCTCTGGTCATCAATCTGTAGGAGAGAAGAAGA		137.0	0.0		73.0	10.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	In_Frame_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.534	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		Frame_Shift_Del	-	52436708	CTCTGGTCATCAATCTGTAGGAGAGAAGAAGA	-	52436677	8	5	13	1	0	1	0	1	0	0	1	0	1311	913	32	0	200	0	BAP1	3	52436677	Splice_Site	DEL	CTCTGGTCATCAATCTGTAGGAGAGAAGAAGA	TCGA-2Y-A9H3-01A-11D-A382-10	50992598	52436677	145585753	40	1094										
IFT57	55081	hgsc.bcm.edu	37	chr3	107881360	107881360	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gctggttctggaataactgtGgcatgcatgttcctagtcat	11	8	2	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr3:107881360G>A	ENST00000264538.3	-	11	1501	c.1254C>T	c.(1252-1254)gcC>gcT	p.A418A	IFT57_ENST00000468021.1_5'Flank	NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	418	pDED.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			GAATAACTGTGGCATGCATGT	0.368																																					p.A418A		Atlas-SNP	.											.	IFT57	44	.	0			c.C1254T						.						219	184	196					3																	107881360		2203	4300	6503	SO:0001819	synonymous_variant	55081	exon11			AACTGTGGCATGC	AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"Intraflagellar transport homologs"	17367	protein-coding gene	gene with protein product		606621	"estrogen-related receptor beta like 1", "intraflagellar transport 57 homolog (Chlamydomonas)"	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.1254C>T	chr3.hg19:g.107881360G>A		68.0	0.0		109.0	19.0	NM_018010	Q96DA9	Silent	SNP	ENST00000264538.3	hg19	CCDS2951.1																																																																																			.	.		0.368	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010		A	107881360	G	A	107881360	2	1	13	1	0	0	0	0	0	0	0	1	7571	1335	47	3		3	IFT57	3	107881360	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	55444683	107881360	90141070	41	1095										
RHO	6010	hgsc.bcm.edu	37	chr3	129251433	129251433	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aggcagagaaggaggtcaccCgcatggtcatcatcatggtc	13	10	4	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr3:129251433C>A	ENST00000296271.3	+	4	848	c.754C>A	c.(754-756)Cgc>Agc	p.R252S		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	252					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)			breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	GGAGGTCACCCGCATGGTCAT	0.622																																					p.R252S	Esophageal Squamous(118;214 1623 30842 43234 46940)	Atlas-SNP	.											.	RHO	57	.	0			c.C754A						.						203	144	164					3																	129251433		2203	4300	6503	SO:0001583	missense	6010	exon4			GTCACCCGCATGG	AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"GPCR / Class A : Opsin receptors"	10012	protein-coding gene	gene with protein product	"opsin 2, rod pigment"	180380	"retinitis pigmentosa 4, autosomal dominant"	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.754C>A	chr3.hg19:g.129251433C>A	ENSP00000296271:p.Arg252Ser	95.0	0.0		58.0	10.0	NM_000539	Q16414|Q2M249	Missense_Mutation	SNP	ENST00000296271.3	hg19	CCDS3063.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.325952	0.81580	.	.	ENSG00000163914	ENST00000296271	T	0.37411	1.2	5.51	5.51	0.81932	GPCR, rhodopsin-like superfamily (1);	0.099731	0.64402	D	0.000002	T	0.70605	0.3243	H	0.95645	3.7	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79412	-0.1814	10	0.87932	D	0	.	13.9377	0.64034	0.152:0.848:0.0:0.0	.	252	P08100	OPSD_HUMAN	S	252	ENSP00000296271:R252S	ENSP00000296271:R252S	R	+	1	0	RHO	130734123	1.000000	0.71417	0.968000	0.41197	0.742000	0.42306	4.811000	0.62606	2.595000	0.87683	0.561000	0.74099	CGC	.	.		0.622	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539		A	129251433	C	A	129251433	3	1	13	1	0	0	0	0	1	0	0	0	13345	652	23	1	768	1	RHO	3	129251433	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	21370073	129251433	68770997	42	1096										
OTOP1	133060	hgsc.bcm.edu	37	chr4	4199209	4199209	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgtcctcagagagtttttcaGgctctcggtgaatggattca	11	8	4	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:4199209G>A	ENST00000296358.4	-	5	1376	c.1352C>T	c.(1351-1353)cCt>cTt	p.P451L		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	451					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GAGTTTTTCAGGCTCTCGGTG	0.542																																					p.P451L		Atlas-SNP	.											.	OTOP1	118	.	0			c.C1352T						.						56	60	58					4																	4199209		2203	4300	6503	SO:0001583	missense	133060	exon5			TTTTCAGGCTCTC	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1352C>T	chr4.hg19:g.4199209G>A	ENSP00000296358:p.Pro451Leu	85.0	0.0		116.0	15.0	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	hg19	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.837079	0.50951	.	.	ENSG00000163982	ENST00000296358	T	0.20332	2.08	4.66	4.66	0.58398	.	0.170162	0.52532	D	0.000076	T	0.36026	0.0952	M	0.73962	2.25	0.48288	D	0.999621	P	0.50528	0.936	P	0.52627	0.704	T	0.19679	-1.0298	10	0.72032	D	0.01	-0.1733	11.4055	0.49896	0.0:0.0:0.688:0.312	.	451	Q7RTM1	OTOP1_HUMAN	L	451	ENSP00000296358:P451L	ENSP00000296358:P451L	P	-	2	0	OTOP1	4250110	1.000000	0.71417	0.907000	0.35723	0.359000	0.29487	3.907000	0.56348	2.306000	0.77630	0.195000	0.17529	CCT	.	.		0.542	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		A	4199209	G	A	4199209	3	1	13	1	0	0	0	0	1	0	0	0	11314	1000	35	3	494	3	OTOP1	4	4199209	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10		4199209	186955067	43	1097										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13603610	13603610	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acgctatttacattggcttcGattttaactgcatgcacagc	7	10	0	0	rs561052858		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:13603610G>T	ENST00000040738.5	-	10	5049	c.4914C>A	c.(4912-4914)atC>atA	p.I1638I		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1638						nucleus (GO:0005634)	DNA binding (GO:0003677)										CATTGGCTTCGATTTTAACTG	0.473																																					p.I1638I		Atlas-SNP	.											BOD1L,NS,carcinoma,0,1	.	.	.	0			c.C4914A						.						162	166	165					4																	13603610		2203	4300	6503	SO:0001819	synonymous_variant	259282	exon10			GGCTTCGATTTTA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.4914C>A	chr4.hg19:g.13603610G>T		34.0	0.0		67.0	4.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Silent	SNP	ENST00000040738.5	hg19	CCDS3411.2																																																																																			.	.		0.473	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13603610	G	T	13603610	2	4	13	1	0	0	0	0	0	0	0	1	1483	1048	37	1		1	BOD1L	4	13603610	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	9404401	13603610	177550666	44	1098										
SEPSECS	51091	hgsc.bcm.edu	37	chr4	25160666	25160666	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gaaattgttgctgtccatgaTtgcaagttcatgtaaaaaga	9	5	1	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:25160666T>A	ENST00000382103.2	-	2	250	c.178A>T	c.(178-180)Atc>Ttc	p.I60F	SEPSECS_ENST00000302922.3_Intron|PI4K2B_ENST00000512921.1_5'Flank	NM_016955.3	NP_058651.3	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	60					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	pyridoxal phosphate binding (GO:0030170)|transferase activity, transferring selenium-containing groups (GO:0016785)|tRNA binding (GO:0000049)	p.I60F(1)		endometrium(1)|large_intestine(4)|lung(2)|stomach(1)	8		Breast(46;0.173)				CTGTCCATGATTGCAAGTTCA	0.388																																					p.I60F		Atlas-SNP	.											SEPSECS_ENST00000382103,NS,carcinoma,0,1	SEPSECS	55	.	1	Substitution - Missense(1)	lung(1)	c.A178T						.						147	148	148					4																	25160666		1904	4130	6034	SO:0001583	missense	51091	exon2			CCATGATTGCAAG	AJ238617	CCDS3432.1, CCDS3432.2	4p15.2	2008-10-27			ENSG00000109618	ENSG00000109618			30605	protein-coding gene	gene with protein product	"soluble liver antigen/liver pancreas antigen"	613009				16230358, 10931155, 17142313, 17194211	Standard	NM_016955		Approved	SLA/LP, SLA	uc003grg.3	Q9HD40	OTTHUMG00000128563	ENST00000382103.2:c.178A>T	chr4.hg19:g.25160666T>A	ENSP00000371535:p.Ile60Phe	208.0	1.0		151.0	15.0	NM_016955	A8K8W1|Q0D2P3|Q17RT1|Q9NXZ5|Q9UGM9|Q9Y353	Missense_Mutation	SNP	ENST00000382103.2	hg19	CCDS3432.2	.	.	.	.	.	.	.	.	.	.	T	16.33	3.092505	0.55968	.	.	ENSG00000109618	ENST00000382103;ENST00000513285	T;T	0.76709	-1.04;-1.04	5.71	0.466	0.16716	Pyridoxal phosphate-dependent transferase, major domain (1);	0.249250	0.39909	N	0.001227	T	0.59959	0.2232	N	0.22421	0.69	0.80722	D	1	B;B	0.26975	0.165;0.029	B;B	0.24974	0.057;0.003	T	0.42565	-0.9444	10	0.29301	T	0.29	-9.8897	9.4102	0.38487	0.0:0.3505:0.0:0.6495	.	59;60	Q9HD40-3;Q9HD40	.;SPCS_HUMAN	F	60;145	ENSP00000371535:I60F;ENSP00000423361:I145F	ENSP00000371535:I60F	I	-	1	0	SEPSECS	24769764	0.628000	0.27138	0.151000	0.22473	0.983000	0.72400	1.076000	0.30729	-0.148000	0.11234	0.528000	0.53228	ATC	.	.		0.388	SEPSECS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250414.2	NM_016955		A	25160666	T	A	25160666	3	1	13	1	0	0	0	0	1	0	0	0	14073	1493	52	4	1367	4	SEPSECS	4	25160666	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	11557056	25160666	165993610	45	1099										
KDR	3791	hgsc.bcm.edu	37	chr4	55974019	55974019	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggtgccgtactggtaggaatCcacaggagagattagagatt	14	6	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:55974019C>A	ENST00000263923.4	-	10	1592	c.1297G>T	c.(1297-1299)Gat>Tat	p.D433Y		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	433	Ig-like C2-type 5.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGGTAGGAATCCACAGGAGAG	0.473			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.D433Y		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.G1297T						.						198	171	180					4																	55974019		2203	4300	6503	SO:0001583	missense	3791	exon10			AGGAATCCACAGG	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.1297G>T	chr4.hg19:g.55974019C>A	ENSP00000263923:p.Asp433Tyr	70.0	0.0		137.0	18.0	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	hg19	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.595579	0.66219	.	.	ENSG00000128052	ENST00000263923	T	0.12569	2.67	4.89	4.89	0.63831	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.101606	0.64402	D	0.000003	T	0.37652	0.1011	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.983;0.995	T	0.15492	-1.0435	10	0.87932	D	0	.	18.2227	0.89906	0.0:1.0:0.0:0.0	.	433;433	P35968-2;P35968	.;VGFR2_HUMAN	Y	433	ENSP00000263923:D433Y	ENSP00000263923:D433Y	D	-	1	0	KDR	55668776	1.000000	0.71417	0.945000	0.38365	0.555000	0.35460	5.185000	0.65076	2.542000	0.85734	0.462000	0.41574	GAT	.	.		0.473	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55974019	C	A	55974019	3	1	13	1	0	0	0	0	1	0	0	0	8148	855	30	3	2857	3	KDR	4	55974019	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	30813353	55974019	135180257	46	1100										
PPAT	5471	hgsc.bcm.edu	37	chr4	57272854	57272854	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cttcagtaaagacgtgatttAcaagacccattcccttgaga	7	10	1	4			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:57272854A>G	ENST00000264220.2	-	3	346	c.209T>C	c.(208-210)gTa>gCa	p.V70A	PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	70	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	GACGTGATTTACAAGACCCAT	0.373																																					p.V70A		Atlas-SNP	.											.	PPAT	41	.	0			c.T209C						.						38	36	36					4																	57272854		2203	4300	6503	SO:0001583	missense	5471	exon3			TGATTTACAAGAC		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.209T>C	chr4.hg19:g.57272854A>G	ENSP00000264220:p.Val70Ala	57.0	0.0		57.0	5.0	NM_002703		Missense_Mutation	SNP	ENST00000264220.2	hg19	CCDS3505.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.728146	0.89390	.	.	ENSG00000128059	ENST00000264220	T	0.77358	-1.09	5.63	5.63	0.86233	Glutamine amidotransferase, type II (1);	0.052926	0.85682	D	0.000000	D	0.87063	0.6084	M	0.80847	2.515	0.80722	D	1	P	0.39831	0.69	P	0.54544	0.755	D	0.88276	0.2933	10	0.72032	D	0.01	-18.9665	15.8422	0.78857	1.0:0.0:0.0:0.0	.	70	Q06203	PUR1_HUMAN	A	70	ENSP00000264220:V70A	ENSP00000264220:V70A	V	-	2	0	PPAT	56967611	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.910000	0.92685	2.141000	0.66446	0.482000	0.46254	GTA	.	.		0.373	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		G	57272854	A	G	57272854	3	3	13	1	0	0	0	0	1	0	0	0	12311	391	14	2	1380	2	PPAT	4	57272854	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	1298835	57272854	133881422	47	1101										
ARHGAP24	83478	hgsc.bcm.edu	37	chr4	86898763	86898763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cctactcgggagttaacaaaAtgagtgtgcagaacttggca	11	8	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:86898763A>G	ENST00000395184.1	+	8	1313	c.847A>G	c.(847-849)Atg>Gtg	p.M283V	ARHGAP24_ENST00000395183.2_Missense_Mutation_p.M188V|ARHGAP24_ENST00000264343.4_Missense_Mutation_p.M190V	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	283	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		AGTTAACAAAATGAGTGTGCA	0.398																																					p.M283V		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.A847G						.						125	111	116					4																	86898763		2203	4300	6503	SO:0001583	missense	83478	exon8			AACAAAATGAGTG	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.847A>G	chr4.hg19:g.86898763A>G	ENSP00000378611:p.Met283Val	129.0	0.0		136.0	25.0	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	hg19	CCDS34025.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.554364	0.86231	.	.	ENSG00000138639	ENST00000395184;ENST00000395183;ENST00000514229;ENST00000264343	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.95	4.77	0.60923	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.075193	0.85682	N	0.000000	T	0.75250	0.3824	H	0.98786	4.33	0.80722	D	1	D;P;P	0.54047	0.964;0.929;0.858	P;P;B	0.60789	0.792;0.879;0.366	D	0.83475	0.0061	10	0.87932	D	0	.	11.9284	0.52833	0.9324:0.0:0.0676:0.0	.	188;190;283	Q8N264-3;Q8N264-2;Q8N264	.;.;RHG24_HUMAN	V	283;188;198;190	ENSP00000378611:M283V;ENSP00000378610:M188V;ENSP00000425589:M198V;ENSP00000264343:M190V	ENSP00000264343:M190V	M	+	1	0	ARHGAP24	87117787	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	1.081000	0.41110	0.460000	0.39030	ATG	.	.		0.398	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		G	86898763	A	G	86898763	3	3	13	1	0	0	0	0	1	0	0	0	873	101	4	2	989	2	ARHGAP24	4	86898763	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	29625909	86898763	104255513	48	1102										
DKK2	27123	hgsc.bcm.edu	37	chr4	107847000	107847022	+	Frame_Shift_Del	DEL	CAGCGCTTCTTTTTTCTCCGACA	CAGCGCTTCTTTTTTCTCCGACA	-													0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	agcacatgccatctcggtggCagcgcttcttttttctccga					rs373542751|rs541386879		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	CAGCGCTTCTTTTTTCTCCGACA	CAGCGCTTCTTTTTTCTCCGACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:107847000_107847022delCAGCGCTTCTTTTTTCTCCGACA	ENST00000285311.3	-	2	1012_1034	c.307_329delTGTCGGAGAAAAAAGAAGCGCTG	c.(307-330)tgtcggagaaaaaagaagcgctgcfs	p.CRRKKKRC103fs	DKK2_ENST00000510463.1_Frame_Shift_Del_p.CRRKKKRC57fs|DKK2_ENST00000513208.1_Frame_Shift_Del_p.CRRKKKRC3fs	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	103	DKK-type Cys-1.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		ATCTCGGTGGCAGCGCTTCTTTTTTCTCCGACACACCATGCAG	0.498																																					p.103_110del		Pindel	.											.	DKK2	96	.	0			c.308_330del						.																																			SO:0001589	frameshift_variant	27123	exon2			.	AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"dickkopf (Xenopus laevis) homolog 2", "dickkopf 2 homolog (Xenopus laevis)"			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.307_329delTGTCGGAGAAAAAAGAAGCGCTG	chr4.hg19:g.107847000_107847022delCAGCGCTTCTTTTTTCTCCGACA	ENSP00000285311:p.Cys103fs	58.0	0.0		76.0	12.0	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Frame_Shift_Del	DEL	ENST00000285311.3	hg19	CCDS3675.1																																																																																			.	.		0.498	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4			-	107847022	CAGCGCTTCTTTTTTCTCCGACA	-	107847000	7	5	13	1	0	1	0	1	0	0	0	0	4547	710	25	0	462	0	DKK2	4	107847000	Frame_Shift_Del	DEL	CAGCGCTTCTTTTTTCTCCGACA	TCGA-2Y-A9H3-01A-11D-A382-10	20948237	107847000	83307276	49	1103										
MAML3	55534	hgsc.bcm.edu	37	chr4	140811090	140811090	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgctgctgctgctgctgctgCtgctgctgctgctgctgctg	14	13	0	0	rs553194721|rs544518608|rs58287721	byFrequency	TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:140811090C>T	ENST00000509479.2	-	2	2356	c.1500G>A	c.(1498-1500)caG>caA	p.Q500Q	MAML3_ENST00000327122.5_Silent_p.Q344Q|MAML3_ENST00000398940.1_Intron	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.532													c|||	54	0.0107827	0.0363	0.0058	5008	,	,		15647	0		0	False		,,,				2504	0.002				p.Q500Q		Atlas-SNP	.											.	MAML3	192	.	0			c.G1500A						.						16	24	22					4																	140811090		2138	4277	6415	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1500G>A	chr4.hg19:g.140811090C>T		25.0	0.0		42.0	19.0	NM_018717		Silent	SNP	ENST00000509479.2	hg19	CCDS54805.1																																																																																			.	.		0.532	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811090	C	T	140811090	2	4	13	1	0	0	0	0	0	0	0	1	9216	796	28	3		3	MAML3	4	140811090	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	32964090	140811090	50343186	50	1104			1	5		3	2	15	N	G_C	7.959192e-05
MAML3	55534	hgsc.bcm.edu	37	chr4	140811102	140811102	+	Silent	SNP	C	C	T													0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgctgctgctgctgctgctgCtgctgctgctgctgctgctg							TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:140811102C>T	ENST00000509479.2	-	2	2344	c.1488G>A	c.(1486-1488)caG>caA	p.Q496Q	MAML3_ENST00000327122.5_Silent_p.Q340Q|MAML3_ENST00000398940.1_Silent_p.Q35Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.542																																					p.Q496Q		Atlas-SNP	.											.	MAML3	192	.	0			c.G1488A						.						13	19	17					4																	140811102		2124	4242	6366	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1488G>A	chr4.hg19:g.140811102C>T		73.0	0.0		43.0	11.0	NM_018717		Silent	SNP	ENST00000509479.2	hg19	CCDS54805.1																																																																																			.	.		0.542	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811102	C	T	140811102	2	4	13	1	0	0	0	0	0	0	0	1	9216	796	28	3		3	MAML3	4	140811102	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	12	140811102	50343174	51	1105	4	2	1	5		3	2	15	N	G_C	7.959192e-05
MAML3	55534	hgsc.bcm.edu	37	chr4	140811104	140811104	+	Missense_Mutation	SNP	G	G	T													0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ctgctgctgctgctgctgctGctgctgctgctgctgctgtt							TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:140811104G>T	ENST00000509479.2	-	2	2342	c.1486C>A	c.(1486-1488)Cag>Aag	p.Q496K	MAML3_ENST00000327122.5_Missense_Mutation_p.Q340K|MAML3_ENST00000398940.1_Missense_Mutation_p.Q35K	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					tgctgctgctgctgctgctgc	0.542																																					p.Q496K		Atlas-SNP	.											.	MAML3	192	.	0			c.C1486A						.						13	18	17					4																	140811104		2145	4254	6399	SO:0001583	missense	55534	exon2			GCTGCTGCTGCTG	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1486C>A	chr4.hg19:g.140811104G>T	ENSP00000421180:p.Gln496Lys	74.0	0.0		42.0	10.0	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	hg19	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	g	6.502	0.460780	0.12342	.	.	ENSG00000196782	ENST00000509479;ENST00000327122;ENST00000398940	T;T	0.64260	0.89;-0.09	4.53	4.53	0.55603	.	0.116387	0.37577	N	0.002035	T	0.39937	0.1097	N	0.08118	0	0.32507	N	0.538137	B	0.22276	0.067	B	0.19391	0.025	T	0.35025	-0.9805	10	0.06494	T	0.89	.	17.2683	0.87093	0.0:0.0:1.0:0.0	.	496	Q96JK9	MAML3_HUMAN	K	496;340;35	ENSP00000421180:Q496K;ENSP00000313316:Q340K	ENSP00000313316:Q340K	Q	-	1	0	MAML3	141030554	0.998000	0.40836	0.988000	0.46212	0.665000	0.39181	0.180000	0.16860	2.038000	0.60285	0.455000	0.32223	CAG	.	.		0.542	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811104	G	T	140811104	3	4	13	1	0	0	0	0	1	0	0	0	9216	1328	46	3	1938	3	MAML3	4	140811104	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	2	140811104	50343172	52	1106	4	2	1	5		3	2	15	N	G_C	7.959192e-05
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141590109	141590109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gctccccacgcatgctctccGggatgcccttcaacaccagc	8	19	2	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:141590109G>A	ENST00000442267.2	-	9	1624	c.1550C>T	c.(1549-1551)cCg>cTg	p.P517L		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	517	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				CATGCTCTCCGGGATGCCCTT	0.597																																					p.P517L		Atlas-SNP	.											.	TBC1D9	198	.	0			c.C1550T						.						43	51	49					4																	141590109		2181	4279	6460	SO:0001583	missense	23158	exon9			CTCTCCGGGATGC	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.1550C>T	chr4.hg19:g.141590109G>A	ENSP00000411197:p.Pro517Leu	66.0	0.0		57.0	8.0	NM_015130	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	hg19	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	G	35	5.549106	0.96488	.	.	ENSG00000109436	ENST00000442267	T	0.08984	3.03	5.61	5.61	0.85477	Rab-GAP/TBC domain (3);	0.000000	0.85682	D	0.000000	T	0.49626	0.1568	H	0.98664	4.295	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.69907	-0.5018	10	0.87932	D	0	-5.8246	20.0018	0.97417	0.0:0.0:1.0:0.0	.	517	Q6ZT07	TBCD9_HUMAN	L	517	ENSP00000411197:P517L	ENSP00000411197:P517L	P	-	2	0	TBC1D9	141809559	1.000000	0.71417	0.968000	0.41197	0.983000	0.72400	9.771000	0.98977	2.793000	0.96121	0.655000	0.94253	CCG	.	.		0.597	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		A	141590109	G	A	141590109	3	1	13	1	0	0	0	0	1	0	0	0	15642	1116	39	1	2302	1	TBC1D9	4	141590109	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	779005	141590109	49564167	53	1107										
LRBA	987	hgsc.bcm.edu	37	chr4	151656474	151656474	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tcaggataaattcagcttcaTttgctactcttactagatga	6	8	4	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:151656474T>A	ENST00000357115.3	-	36	5933	c.5690A>T	c.(5689-5691)aAt>aTt	p.N1897I	LRBA_ENST00000510413.1_Missense_Mutation_p.N1897I|LRBA_ENST00000507224.1_Missense_Mutation_p.N1897I|LRBA_ENST00000535741.1_Missense_Mutation_p.N1897I	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1897						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					TTCAGCTTCATTTGCTACTCT	0.378																																					p.N1897I		Atlas-SNP	.											.	LRBA	253	.	0			c.A5690T						.						300	262	275					4																	151656474		2203	4300	6503	SO:0001583	missense	987	exon36			GCTTCATTTGCTA	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.5690A>T	chr4.hg19:g.151656474T>A	ENSP00000349629:p.Asn1897Ile	66.0	0.0		108.0	15.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.4|24.4	4.529422|4.529422	0.85706|0.85706	.|.	.|.	ENSG00000198589|ENSG00000198589	ENST00000509835|ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	.|T;T;T;T	.|0.58652	.|0.32;0.32;0.32;0.32	5.06|5.06	5.06|5.06	0.68205|0.68205	.|Domain of unknown function DUF1088 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.76863|0.76863	0.4047|0.4047	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.997	.|D;D	.|0.91635	.|0.999;0.962	T|T	0.80865|0.80865	-0.1191|-0.1191	5|10	.|0.87932	.|D	.|0	.|.	14.7996|14.7996	0.69903|0.69903	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1897;1897	.|P50851;P50851-2	.|LRBA_HUMAN;.	L|I	550|1897	.|ENSP00000446299:N1897I;ENSP00000421552:N1897I;ENSP00000349629:N1897I;ENSP00000422180:N1897I	.|ENSP00000349629:N1897I	M|N	-|-	1|2	0|0	LRBA|LRBA	151875924|151875924	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	7.294000|7.294000	0.78760|0.78760	2.025000|2.025000	0.59659|0.59659	0.528000|0.528000	0.53228|0.53228	ATG|AAT	.	.		0.378	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			A	151656474	T	A	151656474	3	1	13	1	0	0	0	0	1	0	0	0	8940	1493	52	4	2993	4	LRBA	4	151656474	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	10066365	151656474	39497802	54	1108										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158257008	158257008	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acgaaaatttggaatgggatGgttggagaacttgtatatgg	14	2	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:158257008G>A	ENST00000264426.9	+	10	1731	c.1452G>A	c.(1450-1452)atG>atA	p.M484I	GRIA2_ENST00000296526.7_Missense_Mutation_p.M484I|GRIA2_ENST00000393815.2_Missense_Mutation_p.M437I|GRIA2_ENST00000507898.1_Missense_Mutation_p.M437I|GRIA2_ENST00000449365.1_Missense_Mutation_p.M437I	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	484					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GGAATGGGATGGTTGGAGAAC	0.418																																					p.M484I		Atlas-SNP	.											.	GRIA2	358	.	0			c.G1452A						.						172	154	160					4																	158257008		2203	4300	6503	SO:0001583	missense	2891	exon10			TGGGATGGTTGGA		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.1452G>A	chr4.hg19:g.158257008G>A	ENSP00000264426:p.Met484Ile	92.0	0.0		168.0	32.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.466383	0.63625	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	T;T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34;-1.34	5.86	5.86	0.93980	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.89291	0.6673	M	0.69358	2.11	0.80722	D	1	P;D;P	0.60575	0.86;0.988;0.86	P;D;P	0.73708	0.542;0.981;0.844	D	0.87880	0.2677	10	0.51188	T	0.08	.	20.5632	0.99335	0.0:0.0:1.0:0.0	.	484;484;437	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	I	437;437;484;484;437	ENSP00000426845:M437I;ENSP00000377403:M437I;ENSP00000296526:M484I;ENSP00000264426:M484I;ENSP00000389837:M437I	ENSP00000264426:M484I	M	+	3	0	GRIA2	158476458	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.937000	0.99478	0.650000	0.86243	ATG	.	.		0.418	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			A	158257008	G	A	158257008	3	1	13	1	0	0	0	0	1	0	0	0	6777	1348	47	3	1490	3	GRIA2	4	158257008	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	6600534	158257008	32897268	55	1109										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175897786	175897786	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	actaaatttagcaattgtagTtatggtgatttttgggaata	9	2	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:175897786T>C	ENST00000359240.3	+	5	1780	c.1110T>C	c.(1108-1110)agT>agC	p.S370S	ADAM29_ENST00000514159.1_Silent_p.S370S|ADAM29_ENST00000445694.1_Silent_p.S370S|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000404450.4_Silent_p.S370S	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	370	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		GCAATTGTAGTTATGGTGATT	0.393																																					p.S370S	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.T1110C						.						125	124	125					4																	175897786		2203	4300	6503	SO:0001819	synonymous_variant	11086	exon4			TTGTAGTTATGGT	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.1110T>C	chr4.hg19:g.175897786T>C		75.0	0.0		108.0	25.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Silent	SNP	ENST00000359240.3	hg19	CCDS3823.1																																																																																			.	.		0.393	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				C	175897786	T	C	175897786	2	2	13	1	0	0	0	0	0	0	0	1	247	1722	60	2		2	ADAM29	4	175897786	Silent	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	17640778	175897786	15256490	56	1110										
VEGFC	7424	hgsc.bcm.edu	37	chr4	177608548	177608548	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tacagacacactggcatgagTttctgtctagttctttgtgg	10	8	3	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr4:177608548T>C	ENST00000280193.2	-	6	1353	c.938A>G	c.(937-939)aAc>aGc	p.N313S	VEGFC_ENST00000507638.1_5'Flank|RP11-313E19.2_ENST00000504017.1_RNA|RP11-313E19.2_ENST00000509194.1_RNA	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	313	4 X 16 AA repeats of C-X(10)-C-X-C- X(1,3)-C.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)			biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		CTGGCATGAGTTTCTGTCTAG	0.502																																					p.N313S		Atlas-SNP	.											.	VEGFC	94	.	0			c.A938G						.						175	156	162					4																	177608548		1914	4142	6056	SO:0001583	missense	7424	exon6			CATGAGTTTCTGT	BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"vascular endothelial growth factor-related protein"	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.938A>G	chr4.hg19:g.177608548T>C	ENSP00000280193:p.Asn313Ser	62.0	0.0		78.0	7.0	NM_005429	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	hg19	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	T	13.77	2.336071	0.41398	.	.	ENSG00000150630	ENST00000280193	.	.	.	5.87	4.63	0.57726	.	0.322731	0.33670	N	0.004671	T	0.38134	0.1029	N	0.24115	0.695	0.33565	D	0.597894	B	0.23735	0.09	B	0.28385	0.089	T	0.48305	-0.9047	9	0.25751	T	0.34	-3.9507	11.36	0.49638	0.0:0.0:0.3247:0.6753	.	313	P49767	VEGFC_HUMAN	S	313	.	ENSP00000280193:N313S	N	-	2	0	VEGFC	177845542	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.444000	0.52914	2.242000	0.73789	0.528000	0.53228	AAC	.	.		0.502	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		C	177608548	T	C	177608548	3	2	13	1	0	0	0	0	1	0	0	0	17167	1725	60	2	332	2	VEGFC	4	177608548	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	1710762	177608548	13545728	57	1111										
C5orf38	153571	hgsc.bcm.edu	37	chr5	2752404	2752404	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggcgcccgcggctcgggtctTcctccgggcagtgcgcgcgg	18	16	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:2752404T>C	ENST00000334000.3	+	1	143	c.26T>C	c.(25-27)tTc>tCc	p.F9S	C5orf38_ENST00000457752.2_Missense_Mutation_p.F9S|IRX2_ENST00000502957.1_Intron|IRX2_ENST00000302057.5_5'Flank|IRX2_ENST00000382611.6_5'Flank|C5orf38_ENST00000397835.4_Missense_Mutation_p.F9S|C5orf38_ENST00000505778.1_Missense_Mutation_p.F9S|C5orf38_ENST00000515640.1_Missense_Mutation_p.F9S	NM_178569.2	NP_848664.1	Q86SI9	CEI_HUMAN	chromosome 5 open reading frame 38	9						extracellular region (GO:0005576)				endometrium(2)|large_intestine(1)|lung(1)	4				GBM - Glioblastoma multiforme(108;0.205)		GCTCGGGTCTTCCTCCGGGCA	0.731																																					p.F9S		Atlas-SNP	.											.	C5orf38	20	.	0			c.T26C						.						8	11	10					5																	2752404		2121	4175	6296	SO:0001583	missense	153571	exon1			GGGTCTTCCTCCG	AY249324	CCDS34131.1	5p15.33	2014-06-02			ENSG00000186493	ENSG00000186493			24226	protein-coding gene	gene with protein product	"coordinated expression to IRX2", "IRX2 neighbor"	610522				16515847, 16750006	Standard	XM_005248256		Approved	CEI, IRX2NB	uc003jdc.3	Q86SI9	OTTHUMG00000161741	ENST00000334000.3:c.26T>C	chr5.hg19:g.2752404T>C	ENSP00000334267:p.Phe9Ser	228.0	0.0		157.0	30.0	NM_178569		Missense_Mutation	SNP	ENST00000334000.3	hg19	CCDS34131.1	.	.	.	.	.	.	.	.	.	.	T	7.175	0.588333	0.13812	.	.	ENSG00000186493	ENST00000457752;ENST00000397835;ENST00000334000;ENST00000505778;ENST00000515640	.	.	.	1.57	0.28	0.15682	.	.	.	.	.	T	0.16557	0.0398	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20706	-1.0267	8	0.87932	D	0	.	3.5138	0.07717	0.4002:0.0:0.0:0.5998	.	9	Q86SI9	CEI_HUMAN	S	9	.	ENSP00000334267:F9S	F	+	2	0	C5orf38	2805404	0.000000	0.05858	0.041000	0.18516	0.034000	0.12701	0.022000	0.13511	0.074000	0.16767	0.379000	0.24179	TTC	.	.		0.731	C5orf38-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365956.2	NM_178569		C	2752404	T	C	2752404	3	2	13	1	0	0	0	0	1	0	0	0	2298	1783	62	2	28	2	C5orf38	5	2752404	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10		2752404	178162856	58	1112										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38431349	38431349	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gcacagcaaagaatggaatcTtacaggtggataagcagaag	12	6	1	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:38431349T>C	ENST00000354891.3	+	15	2471	c.2125T>C	c.(2125-2127)Tta>Cta	p.L709L	EGFLAM_ENST00000322350.5_Silent_p.L709L|EGFLAM_ENST00000397202.2_Silent_p.L75L|EGFLAM_ENST00000336740.6_Silent_p.L475L	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	709	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					GAATGGAATCTTACAGGTGGA	0.453																																					p.L709L	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.T2125C						.						150	128	135					5																	38431349		2203	4300	6503	SO:0001819	synonymous_variant	133584	exon15			GGAATCTTACAGG	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.2125T>C	chr5.hg19:g.38431349T>C		79.0	0.0		129.0	10.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	hg19	CCDS56363.1																																																																																			.	.		0.453	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		C	38431349	T	C	38431349	2	2	13	1	0	0	0	0	0	0	0	1	4968	1606	56	2		2	EGFLAM	5	38431349	Silent	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	35678945	38431349	142483911	59	1113										
GPR98	84059	hgsc.bcm.edu	37	chr5	90449149	90449149	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cgtcctctggaggatatggcCaggggtcactgatagccgat	14	10	2	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:90449149C>T	ENST00000405460.2	+	89	18832	c.18736C>T	c.(18736-18738)Cag>Tag	p.Q6246*	GPR98_ENST00000425867.2_Nonsense_Mutation_p.Q1907*	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	6246					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGGATATGGCCAGGGGTCACT	0.483																																					p.Q6246X		Atlas-SNP	.											.	GPR98	605	.	0			c.C18736T						.						65	65	65					5																	90449149		1891	4110	6001	SO:0001587	stop_gained	84059	exon89			TATGGCCAGGGGT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.18736C>T	chr5.hg19:g.90449149C>T	ENSP00000384582:p.Gln6246*	98.0	0.0		115.0	11.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Nonsense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	58	31.195922	0.99978	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	.	.	.	5.55	5.55	0.83447	.	0.215223	0.45361	D	0.000368	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.287	0.54797	0.2784:0.7215:0.0:0.0	.	.	.	.	X	6246;6246;1907	.	.	Q	+	1	0	GPR98	90484905	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	3.727000	0.54984	2.885000	0.99019	0.655000	0.94253	CAG	.	.		0.483	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90449149	C	T	90449149	4	4	13	1	0	0	0	0	0	1	0	0	6730	595	21	3	19090	3	GPR98	5	90449149	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	52017800	90449149	90466111	60	1114										
FAM81B	153643	hgsc.bcm.edu	37	chr5	94749835	94749835	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aatcgctcgccaggaagttaCtggaaagccacatccagacc	9	13	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:94749835C>T	ENST00000283357.5	+	4	524	c.478C>T	c.(478-480)Ctg>Ttg	p.L160L		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	160						nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		CAGGAAGTTACTGGAAAGCCA	0.433																																					p.L160L		Atlas-SNP	.											.	FAM81B	51	.	0			c.C478T						.						100	100	100					5																	94749835		1975	4163	6138	SO:0001819	synonymous_variant	153643	exon4			AAGTTACTGGAAA		CCDS43341.1	5q15	2008-02-05			ENSG00000153347	ENSG00000153347			26335	protein-coding gene	gene with protein product							Standard	NM_152548		Approved	FLJ25333	uc003kla.1	Q96LP2	OTTHUMG00000162837	ENST00000283357.5:c.478C>T	chr5.hg19:g.94749835C>T		95.0	0.0		140.0	7.0	NM_152548		Silent	SNP	ENST00000283357.5	hg19	CCDS43341.1																																																																																			.	.		0.433	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548		T	94749835	C	T	94749835	2	4	13	1	0	0	0	0	0	0	0	1	5637	564	20	3		3	FAM81B	5	94749835	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	4300686	94749835	86165425	61	1115										
FBN2	2201	hgsc.bcm.edu	37	chr5	127645693	127645693	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acccatgcagttgtggcctcCattgacctgcatgtactcag	9	13	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:127645693C>A	ENST00000508053.1	-	46	6156	c.5182G>T	c.(5182-5184)Gga>Tga	p.G1728*	FBN2_ENST00000262464.4_Nonsense_Mutation_p.G1728*			P35556	FBN2_HUMAN	fibrillin 2	1728	EGF-like 28; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TTGTGGCCTCCATTGACCTGC	0.458																																					p.G1728X		Atlas-SNP	.											.	FBN2	858	.	0			c.G5182T						.						105	95	98					5																	127645693		2203	4300	6503	SO:0001587	stop_gained	2201	exon40			GGCCTCCATTGAC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.5182G>T	chr5.hg19:g.127645693C>A	ENSP00000424571:p.Gly1728*	129.0	0.0		216.0	59.0	NM_001999	B4DU01|Q59ES6	Nonsense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	49	15.361092	0.99831	.	.	ENSG00000138829	ENST00000262464;ENST00000508053	.	.	.	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.1954	0.93686	0.0:1.0:0.0:0.0	.	.	.	.	X	1728	.	ENSP00000262464:G1728X	G	-	1	0	FBN2	127673592	1.000000	0.71417	0.981000	0.43875	0.993000	0.82548	4.804000	0.62554	2.772000	0.95346	0.650000	0.86243	GGA	.	.		0.458	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127645693	C	A	127645693	4	1	13	1	0	0	0	0	0	1	0	0	5711	603	21	3	3660	3	FBN2	5	127645693	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	32895858	127645693	53269567	62	1116										
FBN2	2201	hgsc.bcm.edu	37	chr5	127681186	127681186	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cccaagccgccccgacagcaCagcagcaggcatccatgcgg	11	18	0	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:127681186C>A	ENST00000508053.1	-	30	4054	c.3080G>T	c.(3079-3081)tGt>tTt	p.C1027F	FBN2_ENST00000508989.1_Missense_Mutation_p.C994F|FBN2_ENST00000262464.4_Missense_Mutation_p.C1027F			P35556	FBN2_HUMAN	fibrillin 2	1027	TB 5.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CCCGACAGCACAGCAGCAGGC	0.587																																					p.C1027F		Atlas-SNP	.											FBN2_ENST00000508053,NS,carcinoma,0,4	FBN2	858	.	0			c.G3080T						.						88	84	85					5																	127681186		2203	4300	6503	SO:0001583	missense	2201	exon24			ACAGCACAGCAGC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.3080G>T	chr5.hg19:g.127681186C>A	ENSP00000424571:p.Cys1027Phe	204.0	0.0		192.0	18.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.534334	0.85812	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.97404	-4.37;-4.37;-4.37	4.22	4.22	0.49857	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.64402	D	0.000001	D	0.98833	0.9606	M	0.93898	3.47	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.996	D	0.99289	1.0898	10	0.87932	D	0	.	17.9071	0.88921	0.0:1.0:0.0:0.0	.	994;1027	D6RJI3;P35556	.;FBN2_HUMAN	F	1027;1027;994	ENSP00000262464:C1027F;ENSP00000424571:C1027F;ENSP00000425596:C994F	ENSP00000262464:C1027F	C	-	2	0	FBN2	127709085	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.609000	0.82925	2.654000	0.90174	0.563000	0.77884	TGT	.	.		0.587	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127681186	C	A	127681186	3	1	13	1	0	0	0	0	1	0	0	0	5711	478	17	3	5826	3	FBN2	5	127681186	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	35493	127681186	53234074	63	1117										
RAD50	10111	hgsc.bcm.edu	37	chr5	131953889	131953889	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aacttcgagaaccacaatttCgggatgctgaggaaaagtat	10	7	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:131953889C>T	ENST00000265335.6	+	21	3679	c.3292C>T	c.(3292-3294)Cgg>Tgg	p.R1098W	RAD50_ENST00000378823.3_Missense_Mutation_p.R959W			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	1098					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACCACAATTTCGGGATGCTGA	0.328								Homologous recombination																													p.R1098W		Atlas-SNP	.											RAD50_ENST00000265335,NS,carcinoma,0,2	RAD50	246	.	0			c.C3292T						.						105	119	114					5																	131953889		2203	4299	6502	SO:0001583	missense	10111	exon21			CAATTTCGGGATG	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.3292C>T	chr5.hg19:g.131953889C>T	ENSP00000265335:p.Arg1098Trp	405.0	0.0		359.0	44.0	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	hg19	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.342217	0.61073	.	.	ENSG00000113522	ENST00000378823;ENST00000265335	T;T	0.05382	3.45;3.68	5.4	1.48	0.22813	.	0.604969	0.18076	N	0.152449	T	0.05914	0.0154	N	0.14661	0.345	0.09310	N	1	D	0.58620	0.983	P	0.50934	0.654	T	0.30736	-0.9968	10	0.87932	D	0	-1.4383	6.8185	0.23845	0.4855:0.3703:0.0:0.1442	.	1098	Q92878	RAD50_HUMAN	W	959;1098	ENSP00000368100:R959W;ENSP00000265335:R1098W	ENSP00000265335:R1098W	R	+	1	2	RAD50	131981788	0.997000	0.39634	0.994000	0.49952	0.995000	0.86356	1.163000	0.31798	0.316000	0.23135	0.655000	0.94253	CGG	.	.		0.328	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		T	131953889	C	T	131953889	3	4	13	1	0	0	0	0	1	0	0	0	12999	875	31	1	3374	1	RAD50	5	131953889	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	4272703	131953889	48961371	64	1118										
PHF15	23338	hgsc.bcm.edu	37	chr5	133902158	133902158	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gaggaaagccaatgccaaccAgccgctgctgacccccaaga	10	15	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:133902158A>T	ENST00000402835.1	+	9	1577	c.1322A>T	c.(1321-1323)cAg>cTg	p.Q441L	PHF15_ENST00000395003.1_Missense_Mutation_p.Q441L|PHF15_ENST00000361895.2_Missense_Mutation_p.Q441L|PHF15_ENST00000282605.4_Missense_Mutation_p.Q441L																NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AATGCCAACCAGCCGCTGCTG	0.632																																					p.Q441L		Atlas-SNP	.											.	PHF15	60	.	0			c.A1322T						.						50	45	47					5																	133902158		2203	4300	6503	SO:0001583	missense	23338	exon9			CCAACCAGCCGCT																												ENST00000402835.1:c.1322A>T	chr5.hg19:g.133902158A>T	ENSP00000384671:p.Gln441Leu	173.0	0.0		117.0	36.0	NM_015288		Missense_Mutation	SNP	ENST00000402835.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.36	3.100802	0.56183	.	.	ENSG00000043143	ENST00000413974;ENST00000448712;ENST00000282605;ENST00000361895;ENST00000432594;ENST00000402835;ENST00000395003	T;T;T;T	0.44083	0.93;0.95;0.95;0.96	5.63	5.63	0.86233	.	0.108387	0.64402	D	0.000008	T	0.37348	0.1000	L	0.35854	1.095	0.35177	D	0.77213	B;B;B;B;B;B	0.32051	0.354;0.133;0.04;0.133;0.064;0.133	B;B;B;B;B;B	0.31946	0.138;0.09;0.045;0.09;0.098;0.119	T	0.53337	-0.8453	10	0.87932	D	0	.	15.8202	0.78633	1.0:0.0:0.0:0.0	.	441;441;441;441;441;457	B4DFY8;Q9NQC1;B5MBX1;D3DQA3;Q9NQC1-3;B3KPL2	.;JADE2_HUMAN;.;.;.;.	L	441;457;441;441;441;441;441	ENSP00000282605:Q441L;ENSP00000354425:Q441L;ENSP00000384671:Q441L;ENSP00000378451:Q441L	ENSP00000282605:Q441L	Q	+	2	0	PHF15	133930057	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	4.053000	0.57427	2.146000	0.66826	0.482000	0.46254	CAG	.	.		0.632	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1			T	133902158	A	T	133902158	3	4	13	1	0	0	0	0	1	0	0	0	11835	188	7	4	1352	4	PHF15	5	133902158	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	1948269	133902158	47013102	65	1119										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140203048	140203048	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cgagaacgacaacgcgccggCgctgctggtgcctcgagtgg	16	13	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:140203048C>T	ENST00000529859.1	+	1	1688	c.1688C>T	c.(1687-1689)gCg>gTg	p.A563V	PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.A563V|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.A563V|PCDHA1_ENST00000504120.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	563	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A563V(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACGCGCCGGCGCTGCTGGTG	0.716																																					p.A563V		Atlas-SNP	.											PCDHA5_ENST00000529859,colon,carcinoma,0,2	PCDHA5	361	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1688T						.						49	55	53					5																	140203048		2202	4297	6499	SO:0001583	missense	56143	exon1			CGCCGGCGCTGCT	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.1688C>T	chr5.hg19:g.140203048C>T	ENSP00000436557:p.Ala563Val	121.0	0.0		91.0	27.0	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	hg19	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	C	0.453	-0.892821	0.02491	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.34667	1.35;1.35;1.35	4.0	0.435	0.16544	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.09774	0.0240	N	0.01086	-1.025	0.09310	N	1	B;B;B	0.17038	0.008;0.02;0.016	B;B;B	0.15484	0.005;0.013;0.013	T	0.35051	-0.9804	9	0.12103	T	0.63	.	4.1093	0.10052	0.0:0.3937:0.1791:0.4272	.	563;563;563	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	V	563	ENSP00000433416:A563V;ENSP00000436557:A563V;ENSP00000367366:A563V	ENSP00000367366:A563V	A	+	2	0	PCDHA5	140183232	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-1.911000	0.01583	0.268000	0.21939	0.461000	0.40582	GCG	.	.		0.716	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		T	140203048	C	T	140203048	3	4	13	1	0	0	0	0	1	0	0	0	11536	768	27	1	1690	1	PCDHA5	5	140203048	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	6300890	140203048	40712212	66	1120										
PCDHB4	56131	hgsc.bcm.edu	37	chr5	140501987	140501987	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tccaatattccctgaaagggAagtgctcttgaaaatactag	8	8	1	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:140501987A>T	ENST00000194152.1	+	1	407	c.407A>T	c.(406-408)gAa>gTa	p.E136V	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	136					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCTGAAAGGGAAGTGCTCTTG	0.413																																					p.E136V		Atlas-SNP	.											.	PCDHB4	177	.	0			c.A407T						.						53	59	57					5																	140501987		2203	4300	6503	SO:0001583	missense	56131	exon1			AAAGGGAAGTGCT	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"Cadherins / Protocadherins : Clustered"	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.407A>T	chr5.hg19:g.140501987A>T	ENSP00000194152:p.Glu136Val	156.0	0.0		163.0	53.0	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	hg19	CCDS4246.1	.	.	.	.	.	.	.	.	.	.	A	10.78	1.446108	0.25987	.	.	ENSG00000081818	ENST00000194152	T	0.19532	2.14	4.56	4.56	0.56223	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.38799	0.1054	M	0.73753	2.245	0.09310	N	1	B	0.33103	0.397	P	0.50825	0.651	T	0.41448	-0.9508	9	0.72032	D	0.01	.	5.9918	0.19470	0.7452:0.1677:0.087:0.0	.	136	Q9Y5E5	PCDB4_HUMAN	V	136	ENSP00000194152:E136V	ENSP00000194152:E136V	E	+	2	0	PCDHB4	140482171	0.000000	0.05858	0.557000	0.28306	0.747000	0.42532	0.156000	0.16382	2.033000	0.60031	0.533000	0.62120	GAA	.	.		0.413	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		T	140501987	A	T	140501987	3	4	13	1	0	0	0	0	1	0	0	0	11553	246	9	4	409	4	PCDHB4	5	140501987	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	298939	140501987	40413273	67	1121										
ZNF300	91975	hgsc.bcm.edu	37	chr5	150275988	150275988	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aaggcttttccacatgtaacAcatacacagcttttctcttt	4	11	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:150275988A>G	ENST00000274599.5	-	6	1233	c.813T>C	c.(811-813)tgT>tgC	p.C271C	ZNF300_ENST00000418587.2_Silent_p.C235C|ZNF300_ENST00000446148.2_Silent_p.C287C|ZNF300_ENST00000427179.1_3'UTR|ZNF300_ENST00000394226.2_Silent_p.C271C	NM_052860.2	NP_443092.1	Q96RE9	ZN300_HUMAN	zinc finger protein 300	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)	27		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CACATGTAACACATACACAGC	0.343																																					p.C287C		Atlas-SNP	.											.	ZNF300	69	.	0			c.T861C						.						133	132	133					5																	150275988		2203	4299	6502	SO:0001819	synonymous_variant	91975	exon7			TGTAACACATACA	AF395541	CCDS4311.2, CCDS54939.1, CCDS54940.1	5q33.1	2013-01-08			ENSG00000145908	ENSG00000145908		"Zinc fingers, C2H2-type", "-"	13091	protein-coding gene	gene with protein product		612429				14746915	Standard	NM_052860		Approved		uc021yfx.1	Q96RE9	OTTHUMG00000130076	ENST00000274599.5:c.813T>C	chr5.hg19:g.150275988A>G		53.0	0.0		110.0	28.0	NM_001172831	A8MY91|B3KU35|B4DU78|F5GWS1|Q06DQ3|Q17RP3|Q5H9N5	Silent	SNP	ENST00000274599.5	hg19	CCDS4311.2																																																																																			.	.		0.343	ZNF300-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_052860		G	150275988	A	G	150275988	2	3	13	1	0	0	0	0	0	0	0	1	17846	157	6	2		2	ZNF300	5	150275988	Silent	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	9774001	150275988	30639272	68	1122										
NMUR2	56923	hgsc.bcm.edu	37	chr5	151771949	151771949	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	caactgtgggtcatgctgggAgtgccactgtttgtggaaag	15	7	1	0	rs368060763		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:151771949A>T	ENST00000255262.3	-	4	1216	c.1051T>A	c.(1051-1053)Tcc>Acc	p.S351T		NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	351					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			TCATGCTGGGAGTGCCACTGT	0.522																																					p.S351T		Atlas-SNP	.											.	NMUR2	111	.	0			c.T1051A						.	A	THR/SER	0,4406		0,0,2203	147	135	139		1051	-8.4	0	5		139	1,8599	1.2+/-3.3	0,1,4299	no	missense	NMUR2	NM_020167.4	58	0,1,6502	TT,TA,AA		0.0116,0.0,0.0077	benign	351/416	151771949	1,13005	2203	4300	6503	SO:0001583	missense	56923	exon4			GCTGGGAGTGCCA	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.1051T>A	chr5.hg19:g.151771949A>T	ENSP00000255262:p.Ser351Thr	108.0	0.0		175.0	17.0	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	hg19	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	A	4.530	0.098363	0.08681	0.0	1.16E-4	ENSG00000132911	ENST00000255262	T	0.38077	1.16	4.57	-8.43	0.00953	.	0.764422	0.11426	N	0.565311	T	0.21022	0.0506	L	0.54323	1.7	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33240	-0.9876	10	0.10636	T	0.68	-7.6408	5.5988	0.17341	0.1832:0.0986:0.5222:0.196	.	351	Q9GZQ4	NMUR2_HUMAN	T	351	ENSP00000255262:S351T	ENSP00000255262:S351T	S	-	1	0	NMUR2	151752142	0.000000	0.05858	0.000000	0.03702	0.195000	0.23768	-0.300000	0.08243	-1.754000	0.01321	0.383000	0.25322	TCC	.	.		0.522	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		T	151771949	A	T	151771949	3	4	13	1	0	0	0	0	1	0	0	0	10516	304	11	4	200	4	NMUR2	5	151771949	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	1495961	151771949	29143311	69	1123										
NSD1	64324	hgsc.bcm.edu	37	chr5	176722371	176722371	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cttgctggtctcttggaagaGggcaagaccccaaaccagag	12	11	1	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:176722371G>A	ENST00000439151.2	+	23	8047	c.8002G>A	c.(8002-8004)Ggg>Agg	p.G2668R	NSD1_ENST00000347982.4_Missense_Mutation_p.G2399R|NSD1_ENST00000354179.4_Missense_Mutation_p.G2399R|NSD1_ENST00000361032.4_Missense_Mutation_p.G2565R	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2668					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TCTTGGAAGAGGGCAAGACCC	0.517			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.G2668R		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G8002A						.						65	68	67					5																	176722371		2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	GGAAGAGGGCAAG	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.8002G>A	chr5.hg19:g.176722371G>A	ENSP00000395929:p.Gly2668Arg	268.0	0.0		243.0	25.0	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.162393	0.57368	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.96041	-3.82;-3.83;-3.82;-3.89	5.04	4.15	0.48705	.	0.218016	0.32753	N	0.005700	D	0.92315	0.7562	N	0.19112	0.55	0.31791	N	0.629659	D;D	0.54047	0.961;0.964	P;P	0.48141	0.568;0.459	D	0.92994	0.6417	10	0.87932	D	0	.	13.4593	0.61219	0.0:0.0:0.8433:0.1567	.	2399;2668	Q96L73-2;Q96L73	.;NSD1_HUMAN	R	2399;2668;2399;2565	ENSP00000346111:G2399R;ENSP00000395929:G2668R;ENSP00000343209:G2399R;ENSP00000354310:G2565R	ENSP00000343209:G2399R	G	+	1	0	NSD1	176654977	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.108000	0.57817	1.456000	0.47831	0.655000	0.94253	GGG	.	.		0.517	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		A	176722371	G	A	176722371	3	1	13	1	0	0	0	0	1	0	0	0	10678	1000	35	3	8088	3	NSD1	5	176722371	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	24950422	176722371	4192889	70	1124										
MXD3	83463	hgsc.bcm.edu	37	chr5	176734612	176734612	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tagccaggcgccgccgccgtGcgagtagctgtgctcctggc	15	15	0	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:176734612G>A	ENST00000439742.2	-	6	1076	c.598C>T	c.(598-600)Cac>Tac	p.H200Y	MXD3_ENST00000427908.2_Intron|MXD3_ENST00000513063.1_Missense_Mutation_p.H200Y|MXD3_ENST00000423571.2_Silent_p.R225R	NM_031300.3	NP_112590.1	Q9BW11	MAD3_HUMAN	MAX dimerization protein 3	200					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCGCCGCCGTGCGAGTAGCTG	0.697																																					p.H200Y		Atlas-SNP	.											.	MXD3	13	.	0			c.C598T						.						22	25	24					5																	176734612		2201	4297	6498	SO:0001583	missense	83463	exon6			CGCCGTGCGAGTA	BC000745	CCDS4416.1, CCDS47347.1	5q35.3	2013-03-20			ENSG00000213347	ENSG00000213347		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	14008	protein-coding gene	gene with protein product		609450					Standard	NM_031300		Approved	MAD3, bHLHc13	uc003mgb.2	Q9BW11	OTTHUMG00000130854	ENST00000439742.2:c.598C>T	chr5.hg19:g.176734612G>A	ENSP00000401867:p.His200Tyr	177.0	0.0		105.0	10.0	NM_031300	B4E0J1|Q53HK1|Q7Z4Y0|Q8NDJ7|Q96ME3	Missense_Mutation	SNP	ENST00000439742.2	hg19	CCDS4416.1	.	.	.	.	.	.	.	.	.	.	G	8.824	0.938266	0.18206	.	.	ENSG00000213347	ENST00000439742;ENST00000303165;ENST00000513063	T;T	0.30182	1.54;1.54	5.11	2.1	0.27182	.	0.724938	0.13420	N	0.389241	T	0.16471	0.0396	L	0.36672	1.1	0.23624	N	0.997267	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.36114	-0.9761	10	0.02654	T	1	.	3.5288	0.07769	0.0877:0.1137:0.4668:0.3318	.	191;200	F8W9D2;Q9BW11	.;MAD3_HUMAN	Y	200;191;200	ENSP00000401867:H200Y;ENSP00000421463:H200Y	ENSP00000307720:H191Y	H	-	1	0	MXD3	176667218	0.061000	0.20836	0.125000	0.21846	0.001000	0.01503	0.861000	0.27885	0.525000	0.28522	-0.304000	0.09214	CAC	.	.		0.697	MXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253427.1			A	176734612	G	A	176734612	3	1	13	1	0	0	0	0	1	0	0	0	10009	1319	46	3	107	3	MXD3	5	176734612	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	12241	176734612	4180648	71	1125										
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178554970	178554970	+	Frame_Shift_Del	DEL	G	G	-													0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	accccctcacctccgccacaGggcttggagcacggagacca							TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:178554970delG	ENST00000251582.7	-	17	2708	c.2607delC	c.(2605-2607)cccfs	p.P869fs		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	869	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		CTCCGCCACAGGGCTTGGAGC	0.612																																					p.C870fs		Atlas-Indel,Pindel	.											.	ADAMTS2	190	.	0			c.2608delT						.						145	126	132					5																	178554970		2203	4300	6503	SO:0001589	frameshift_variant	9509	exon17			.	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.2607delC	chr5.hg19:g.178554970delG	ENSP00000251582:p.Pro869fs	68.0	0.0		42.0	10.0	NM_014244		Frame_Shift_Del	DEL	ENST00000251582.7	hg19	CCDS4444.1																																																																																			.	.		0.612	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		-	178554970	G	-	178554970	7	5	13	1	0	1	0	1	0	0	0	0	265	987	35	0	1052	0	ADAMTS2	5	178554970	Frame_Shift_Del	DEL	G	TCGA-2Y-A9H3-01A-11D-A382-10	1820358	178554970	2360290	72	1126										
CNOT6	57472	hgsc.bcm.edu	37	chr5	179980384	179980384	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cctggaatttttacatcaacAgggagctccatttaaataac	6	9	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:179980384A>G	ENST00000393356.1	+	6	723		c.e6-1		CNOT6_ENST00000502447.1_Intron|CNOT6_ENST00000261951.4_Splice_Site			Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	exoribonuclease activity (GO:0004532)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|skin(1)	23	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		TTACATCAACAGGGAGCTCCA	0.358																																					.		Atlas-SNP	.											.	CNOT6	47	.	0			c.300-2A>G						.						87	85	85					5																	179980384		2203	4300	6503	SO:0001630	splice_region_variant	57472	exon4			ATCAACAGGGAGC	AB033020	CCDS4455.1	5q35.3	2014-06-17			ENSG00000113300	ENSG00000113300			14099	protein-coding gene	gene with protein product		608951				11889047	Standard	XM_005265953		Approved	CCR4, KIAA1194, Ccr4a	uc003mlx.3	Q9ULM6	OTTHUMG00000130935	ENST00000393356.1:c.300-1A>G	chr5.hg19:g.179980384A>G		138.0	0.0		164.0	15.0	NM_015455	A7MD46|D3DWR0	Splice_Site	SNP	ENST00000393356.1	hg19	CCDS4455.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.421877	0.83559	.	.	ENSG00000113300	ENST00000261951;ENST00000393356	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2919	0.66284	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNOT6	179912990	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.157000	0.94714	2.181000	0.69327	0.460000	0.39030	.	.	.		0.358	CNOT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253532.1	NM_015455	Intron	G	179980384	A	G	179980384	5	3	13	1	0	0	0	0	0	0	1	0	3624	202	7	2	308	2	CNOT6	5	179980384	Splice_Site	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	1425414	179980384	934876	73	1127										
BTNL9	153579	hgsc.bcm.edu	37	chr5	180475133	180475133	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cgttccggaacaggaccaagTtggtcaaggacgacatcgcc	12	12	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr5:180475133T>A	ENST00000327705.9	+	3	547	c.316T>A	c.(316-318)Ttg>Atg	p.L106M	BTNL9_ENST00000376841.2_Missense_Mutation_p.L106M|BTNL9_ENST00000376842.3_Missense_Mutation_p.L106M|BTNL9_ENST00000515271.1_Missense_Mutation_p.L37M	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	106	Ig-like V-type.					integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGGACCAAGTTGGTCAAGGA	0.597																																					p.L106M		Atlas-SNP	.											.	BTNL9	58	.	0			c.T316A						.						69	57	61					5																	180475133		2203	4299	6502	SO:0001583	missense	153579	exon3			ACCAAGTTGGTCA	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.316T>A	chr5.hg19:g.180475133T>A	ENSP00000330200:p.Leu106Met	189.0	0.0		153.0	30.0	NM_152547	A6NL42|Q6P660|Q96DM5	Missense_Mutation	SNP	ENST00000327705.9	hg19	CCDS4460.2	.	.	.	.	.	.	.	.	.	.	T	15.81	2.943454	0.53079	.	.	ENSG00000165810	ENST00000376841;ENST00000327705;ENST00000376842;ENST00000376850;ENST00000515271	T;T;T;T	0.68765	-0.35;-0.35;-0.35;4.07	5.01	1.95	0.26073	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.235442	0.21467	N	0.074065	T	0.76912	0.4054	M	0.78344	2.41	0.09310	N	1	D;D	0.76494	0.999;0.985	D;D	0.74348	0.983;0.926	T	0.64351	-0.6428	10	0.66056	D	0.02	.	5.9993	0.19511	0.0:0.5363:0.0:0.4637	.	37;106	B7Z4Y8;Q6UXG8	.;BTNL9_HUMAN	M	106;106;106;106;37	ENSP00000366037:L106M;ENSP00000330200:L106M;ENSP00000366038:L106M;ENSP00000427345:L37M	ENSP00000330200:L106M	L	+	1	2	BTNL9	180407739	0.026000	0.19158	0.005000	0.12908	0.000000	0.00434	0.191000	0.17076	0.633000	0.30452	-0.417000	0.06048	TTG	.	.		0.597	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547		A	180475133	T	A	180475133	3	1	13	1	0	0	0	0	1	0	0	0	1570	1722	60	4	322	4	BTNL9	5	180475133	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	494749	180475133	440127	74	1128										
CPNE5	57699	hgsc.bcm.edu	37	chr6	36710255	36710255	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cggtccacgtagtcccggaaGggtacaaactggcaagtggg	15	10	0	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr6:36710255G>A	ENST00000244751.2	-	21	2196	c.1572C>T	c.(1570-1572)ccC>ccT	p.P524P	CPNE5_ENST00000459703.1_5'UTR|CPNE5_ENST00000393189.2_Silent_p.P232P	NM_020939.1	NP_065990.1	Q9HCH3	CPNE5_HUMAN	copine V	524	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(4)|liver(1)|lung(9)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						AGTCCCGGAAGGGTACAAACT	0.652																																					p.P524P		Atlas-SNP	.											.	CPNE5	56	.	0			c.C1572T						.						75	70	71					6																	36710255		2203	4300	6503	SO:0001819	synonymous_variant	57699	exon21			CCGGAAGGGTACA	H09181	CCDS4825.1	6p21.2	2010-05-28			ENSG00000124772	ENSG00000124772			2318	protein-coding gene	gene with protein product		604209				9430674	Standard	NM_020939		Approved	CPN5, COPN5, KIAA1599	uc003omr.1	Q9HCH3	OTTHUMG00000014602	ENST00000244751.2:c.1572C>T	chr6.hg19:g.36710255G>A		68.0	0.0		33.0	6.0	NM_020939	Q7Z6C8	Silent	SNP	ENST00000244751.2	hg19	CCDS4825.1																																																																																			.	.		0.652	CPNE5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040351.1	NM_020939		A	36710255	G	A	36710255	2	1	13	1	0	0	0	0	0	0	0	1	3817	987	35	3		3	CPNE5	6	36710255	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10		36710255	134404812	75	1129										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38840728	38840728	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggtcctgtggatgccatctgGattgagaacttaaattccgt	11	8	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr6:38840728G>T	ENST00000359357.3	+	49	6887	c.6633G>T	c.(6631-6633)tgG>tgT	p.W2211C	DNAH8_ENST00000441566.1_Missense_Mutation_p.W2175C|DNAH8_ENST00000449981.2_Missense_Mutation_p.W2428C			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2211	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ATGCCATCTGGATTGAGAACT	0.363																																					p.W2428C		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,0,2	DNAH8	1239	.	0			c.G7284T						.						73	74	73					6																	38840728		2203	4300	6503	SO:0001583	missense	1769	exon51			CATCTGGATTGAG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.6633G>T	chr6.hg19:g.38840728G>T	ENSP00000352312:p.Trp2211Cys	101.0	0.0		141.0	28.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	G	23.6	4.433592	0.83776	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	D;D;D	0.98747	-5.11;-5.11;-5.11	5.78	5.78	0.91487	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	D	0.99616	0.9860	H	0.98314	4.2	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97807	1.0248	10	0.87932	D	0	.	20.0114	0.97452	0.0:0.0:1.0:0.0	.	2211	Q96JB1	DYH8_HUMAN	C	2416;2416;2211;2175	ENSP00000333363:W2416C;ENSP00000352312:W2211C;ENSP00000402294:W2175C	ENSP00000333363:W2416C	W	+	3	0	DNAH8	38948706	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.843000	0.99491	2.745000	0.94114	0.655000	0.94253	TGG	.	.		0.363	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38840728	G	T	38840728	3	4	13	1	0	0	0	0	1	0	0	0	4609	1183	41	3	6819	3	DNAH8	6	38840728	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	2130473	38840728	132274339	76	1130										
COL21A1	81578	hgsc.bcm.edu	37	chr6	55924015	55924015	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tacccaaacccttggctcccTttttccccatttcttcctgg	4	17	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr6:55924015T>C	ENST00000244728.5	-	29	3031	c.2634A>G	c.(2632-2634)aaA>aaG	p.K878K	COL21A1_ENST00000535941.1_Silent_p.K878K|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000370808.2_Silent_p.K244K|COL21A1_ENST00000370819.1_Silent_p.K875K	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	878	Collagen-like 6.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			CTTGGCTCCCTTTTTCCCCAT	0.443																																					p.K878K		Atlas-SNP	.											.	COL21A1	201	.	0			c.A2634G						.						79	83	82					6																	55924015		1838	4087	5925	SO:0001819	synonymous_variant	81578	exon29			GCTCCCTTTTTCC	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"Collagens"	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.2634A>G	chr6.hg19:g.55924015T>C		53.0	0.0		110.0	5.0	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Silent	SNP	ENST00000244728.5	hg19	CCDS55025.1																																																																																			.	.		0.443	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			C	55924015	T	C	55924015	2	2	13	1	0	0	0	0	0	0	0	1	3682	1606	56	2		2	COL21A1	6	55924015	Silent	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	17083287	55924015	115191052	77	1131										
EYS	346007	hgsc.bcm.edu	37	chr6	65301778	65301778	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgaaagctctctagtgacaaTcagttcttggagtaagtagc	10	7	3	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr6:65301778T>A	ENST00000370621.3	-	26	4508	c.3982A>T	c.(3982-3984)Att>Ttt	p.I1328F	EYS_ENST00000503581.1_Missense_Mutation_p.I1328F|EYS_ENST00000370616.2_Missense_Mutation_p.I1328F			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1328					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CTAGTGACAATCAGTTCTTGG	0.428																																					p.I1328F		Atlas-SNP	.											.	EYS	527	.	0			c.A3982T						.						116	103	107					6																	65301778		692	1590	2282	SO:0001583	missense	346007	exon26			TGACAATCAGTTC		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.3982A>T	chr6.hg19:g.65301778T>A	ENSP00000359655:p.Ile1328Phe	56.0	0.0		98.0	11.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	T	14.10	2.433459	0.43224	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.82526	-1.62;-1.6;-1.6	5.62	5.62	0.85841	.	.	.	.	.	T	0.60064	0.2240	N	0.14661	0.345	0.26662	N	0.971899	P;P	0.50272	0.933;0.89	P;B	0.50049	0.629;0.286	T	0.52268	-0.8598	9	0.10111	T	0.7	.	10.2438	0.43328	0.1475:0.0:0.0:0.8525	.	1328;1328	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	F	1328	ENSP00000424243:I1328F;ENSP00000359655:I1328F;ENSP00000359650:I1328F	ENSP00000359650:I1328F	I	-	1	0	EYS	65358499	0.999000	0.42202	0.455000	0.27031	0.018000	0.09664	4.661000	0.61518	2.150000	0.67090	0.533000	0.62120	ATT	.	.		0.428	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	65301778	T	A	65301778	3	1	13	1	0	0	0	0	1	0	0	0	5334	1435	50	4	5369	4	EYS	6	65301778	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	9377763	65301778	105813289	78	1132										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75904566	75904566	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cccgttgtagggtccaccgtTattctgtaacccacaattgg	9	12	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr6:75904566T>A	ENST00000322507.8	-	3	480	c.171A>T	c.(169-171)atA>atT	p.I57I	COL12A1_ENST00000483888.2_Silent_p.I57I|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Silent_p.I57I	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	57	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						GGTCCACCGTTATTCTGTAAC	0.398																																					p.I57I		Atlas-SNP	.											.	COL12A1	385	.	0			c.A171T						.						117	114	115					6																	75904566		1837	4092	5929	SO:0001819	synonymous_variant	1303	exon3			CACCGTTATTCTG	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.171A>T	chr6.hg19:g.75904566T>A		65.0	0.0		97.0	16.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.398	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75904566	T	A	75904566	2	1	13	1	0	0	0	0	0	0	0	1	3671	1744	61	4		4	COL12A1	6	75904566	Silent	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	10602788	75904566	95210501	79	1133										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84269864	84269864	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	agctccaaaggggggcctcaTcatgggctgtgcaaacatga	13	10	2	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr6:84269864T>C	ENST00000439399.2	-	28	2906	c.2590A>G	c.(2590-2592)Atg>Gtg	p.M864V	SNAP91_ENST00000521485.1_Missense_Mutation_p.M859V|SNAP91_ENST00000437520.1_Missense_Mutation_p.M557V|SNAP91_ENST00000428679.2_Missense_Mutation_p.M864V|SNAP91_ENST00000369694.2_Missense_Mutation_p.M864V|SNAP91_ENST00000521743.1_Missense_Mutation_p.M864V|SNAP91_ENST00000520302.1_Missense_Mutation_p.M834V|SNAP91_ENST00000520213.1_Missense_Mutation_p.M557V|SNAP91_ENST00000195649.6_Missense_Mutation_p.M859V	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	864	Pro-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		GGGGGCCTCATCATGGGCTGT	0.522																																					p.M864V		Atlas-SNP	.											.	SNAP91	199	.	0			c.A2590G						.						71	72	71					6																	84269864		1964	4151	6115	SO:0001583	missense	9892	exon27			GCCTCATCATGGG	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.2590A>G	chr6.hg19:g.84269864T>C	ENSP00000400459:p.Met864Val	172.0	0.0		258.0	36.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.207561	0.58343	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000437520;ENST00000520302;ENST00000521743;ENST00000520213;ENST00000523448	T;T;T;T;T;T;T;T;T;T	0.26373	2.32;2.34;2.34;2.32;2.33;2.38;2.3;2.34;2.38;1.74	5.75	5.75	0.90469	.	0.114692	0.85682	D	0.000000	T	0.23410	0.0566	L	0.46157	1.445	0.23473	N	0.997601	B;B;P;P;P	0.36392	0.009;0.452;0.551;0.551;0.551	B;P;P;P;P	0.47786	0.004;0.557;0.448;0.448;0.448	T	0.13495	-1.0507	10	0.59425	D	0.04	-4.7975	16.0623	0.80847	0.0:0.0:0.0:1.0	.	740;557;834;864;862	B7Z2N2;O60641-3;E5RI02;O60641;E1P549	.;.;.;AP180_HUMAN;.	V	859;864;864;859;864;557;834;864;557;205	ENSP00000429776:M859V;ENSP00000358708:M864V;ENSP00000400459:M864V;ENSP00000195649:M859V;ENSP00000412492:M864V;ENSP00000413277:M557V;ENSP00000428511:M834V;ENSP00000428215:M864V;ENSP00000428026:M557V;ENSP00000430255:M205V	ENSP00000195649:M859V	M	-	1	0	SNAP91	84326583	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.454000	0.73493	2.195000	0.70347	0.533000	0.62120	ATG	.	.		0.522	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			C	84269864	T	C	84269864	3	2	13	1	0	0	0	0	1	0	0	0	14848	1435	50	2	141	2	SNAP91	6	84269864	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	8365298	84269864	86845203	80	1134										
PRDM13	59336	hgsc.bcm.edu	37	chr6	100057084	100057084	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tcttctaccgagcattgcgaGacgtccagccaggggaggag	14	11	2	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr6:100057084G>A	ENST00000369215.4	+	3	603	c.298G>A	c.(298-300)Gac>Aac	p.D100N		NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	100	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1)	17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		AGCATTGCGAGACGTCCAGCC	0.507																																					p.D100N		Atlas-SNP	.											.	PRDM13	65	.	0			c.G298A						.						57	63	61					6																	100057084		2099	4231	6330	SO:0001583	missense	59336	exon3			TTGCGAGACGTCC	AY004253	CCDS43487.1	6q16.2	2012-03-28			ENSG00000112238	ENSG00000112238			13998	protein-coding gene	gene with protein product							Standard	NM_021620		Approved		uc003pqg.1	Q9H4Q3	OTTHUMG00000015269	ENST00000369215.4:c.298G>A	chr6.hg19:g.100057084G>A	ENSP00000358217:p.Asp100Asn	135.0	0.0		119.0	18.0	NM_021620	Q5TGC1|Q5TGC2	Missense_Mutation	SNP	ENST00000369215.4	hg19	CCDS43487.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.451688	0.84209	.	.	ENSG00000112238	ENST00000369215;ENST00000369214	D;D	0.87729	-2.29;-2.29	5.51	5.51	0.81932	SET domain (2);	0.000000	0.40728	N	0.001034	D	0.90072	0.6899	L	0.50993	1.605	0.53005	D	0.999966	D	0.76494	0.999	D	0.64144	0.922	D	0.90634	0.4569	10	0.72032	D	0.01	-19.3072	19.0824	0.93187	0.0:0.0:1.0:0.0	.	100	Q9H4Q3	PRD13_HUMAN	N	100;110	ENSP00000358217:D100N;ENSP00000358216:D110N	ENSP00000358216:D110N	D	+	1	0	PRDM13	100163805	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.374000	0.97172	2.620000	0.88729	0.456000	0.33151	GAC	.	.		0.507	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2			A	100057084	G	A	100057084	3	1	13	1	0	0	0	0	1	0	0	0	12466	942	33	3	308	3	PRDM13	6	100057084	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	15787220	100057084	71057983	81	1135										
C6orf72	116254	hgsc.bcm.edu	37	chr6	149903658	149903658	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cccagtattctttcagttttTgaacatcatggtggttggaa	9	7	3	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr6:149903658T>G	ENST00000367419.5	+	7	921	c.800T>G	c.(799-801)tTg>tGg	p.L267W		NM_138785.3	NP_620140.1	Q9NU53	GINM1_HUMAN	glycoprotein integral membrane 1	267						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											TTTCAGTTTTTGAACATCATG	0.358																																					p.L267W		Atlas-SNP	.											.	.	.	.	0			c.T800G						.						165	165	165					6																	149903658		2203	4300	6503	SO:0001583	missense	116254	exon7			AGTTTTTGAACAT	BC014320	CCDS5216.1	6q24.3	2012-07-20	2012-07-20	2012-07-20	ENSG00000055211	ENSG00000055211			21074	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 72"	C6orf72			Standard	NM_138785		Approved	dJ12G14.2	uc003qmq.1	Q9NU53	OTTHUMG00000015789	ENST00000367419.5:c.800T>G	chr6.hg19:g.149903658T>G	ENSP00000356389:p.Leu267Trp	204.0	0.0		173.0	38.0	NM_138785	B2RDY7|E1P5A2	Missense_Mutation	SNP	ENST00000367419.5	hg19	CCDS5216.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.131893	0.77662	.	.	ENSG00000055211	ENST00000367419	.	.	.	5.59	5.59	0.84812	.	0.050426	0.85682	D	0.000000	T	0.63094	0.2482	L	0.57536	1.79	0.37037	D	0.896968	D	0.76494	0.999	D	0.65443	0.935	T	0.65232	-0.6218	8	.	.	.	-20.0881	14.6283	0.68638	0.0:0.0:0.0:1.0	.	267	Q9NU53	CF072_HUMAN	W	267	.	.	L	+	2	0	C6orf72	149945351	1.000000	0.71417	0.514000	0.27761	0.891000	0.51852	4.478000	0.60230	2.251000	0.74343	0.533000	0.62120	TTG	.	.		0.358	GINM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042644.1	NM_138785		G	149903658	T	G	149903658	3	3	13	1	0	0	0	0	1	0	0	0	2373	1821	63	5	826	5	C6orf72	6	149903658	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	49846574	149903658	21211409	82	1136										
KIF25	3834	hgsc.bcm.edu	37	chr6	168434666	168434666	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgttctgccgcttgacccacAgagtgacttaggaattatcc	9	11	1	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr6:168434666A>T	ENST00000443060.2	+	5	663	c.272A>T	c.(271-273)cAg>cTg	p.Q91L	KIF25_ENST00000351261.3_Missense_Mutation_p.Q91L|KIF25_ENST00000354419.2_Missense_Mutation_p.Q91L			Q9UIL4	KIF25_HUMAN	kinesin family member 25	91	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		CTTGACCCACAGAGTGACTTA	0.552																																					p.Q91L		Atlas-SNP	.											.	KIF25	75	.	0			c.A272T						.						92	82	85					6																	168434666		2203	4300	6503	SO:0001583	missense	3834	exon4			ACCCACAGAGTGA	AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"Kinesins"	6390	protein-coding gene	gene with protein product		603815	"kinesin-like 3"	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.272A>T	chr6.hg19:g.168434666A>T	ENSP00000388878:p.Gln91Leu	219.0	0.0		147.0	18.0	NM_030615	O94775|Q5SZU9	Missense_Mutation	SNP	ENST00000443060.2	hg19	CCDS5305.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.016275	0.35606	.	.	ENSG00000125337	ENST00000443060;ENST00000354419;ENST00000351261	T;T;T	0.75367	-0.93;-0.93;-0.93	4.11	-1.94	0.07571	Kinesin, motor domain (4);	0.974427	0.08388	N	0.953475	T	0.30665	0.0772	N	0.13272	0.32	0.09310	N	1	B;B	0.32918	0.39;0.091	B;B	0.35353	0.201;0.005	T	0.31943	-0.9925	10	0.52906	T	0.07	-7.8083	0.6664	0.00851	0.4451:0.1681:0.224:0.1628	.	91;91	Q9UIL4-2;Q9UIL4	.;KIF25_HUMAN	L	91	ENSP00000388878:Q91L;ENSP00000346401:Q91L;ENSP00000252688:Q91L	ENSP00000252688:Q91L	Q	+	2	0	KIF25	168177515	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.966000	0.29331	-0.550000	0.06183	0.459000	0.35465	CAG	.	.		0.552	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1			T	168434666	A	T	168434666	3	4	13	1	0	0	0	0	1	0	0	0	8302	188	7	4	282	4	KIF25	6	168434666	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	18531008	168434666	2680401	83	1137										
ISPD	729920	hgsc.bcm.edu	37	chr7	16460814	16460814	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gcaacacagctgccacggctTgcgggtggcgcccgggctcg	16	15	0	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr7:16460814T>G	ENST00000407010.2	-	1	133	c.134A>C	c.(133-135)cAa>cCa	p.Q45P	ISPD_ENST00000399310.3_Missense_Mutation_p.Q45P	NM_001101426.3	NP_001094896.1	A4D126	ISPD_HUMAN	isoprenoid synthase domain containing	45					axon guidance (GO:0007411)|isoprenoid biosynthetic process (GO:0008299)|protein O-linked mannosylation (GO:0035269)		nucleotidyltransferase activity (GO:0016779)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9						TGCCACGGCTTGCGGGTGGCG	0.731										Multiple Myeloma(15;0.18)																											p.Q45P		Atlas-SNP	.											.	ISPD	63	.	0			c.A134C						.						2	3	3					7																	16460814		1150	2487	3637	SO:0001583	missense	729920	exon1			ACGGCTTGCGGGT	AK124805		7p21.2	2010-03-19			ENSG00000214960	ENSG00000214960			37276	protein-coding gene	gene with protein product	"notch1-induced protein", "4-diphosphocytidyl-2C-methyl-D-erythritol synthase homolog (Arabidopsis)"	614631				11181995	Standard	NM_001101417		Approved	hCG_1745121, IspD, Nip	uc010ktx.2	A4D126	OTTHUMG00000152447	ENST00000407010.2:c.134A>C	chr7.hg19:g.16460814T>G	ENSP00000385478:p.Gln45Pro	964.0	0.0		536.0	67.0	NM_001101426	A8MU35|H9KVB2	Missense_Mutation	SNP	ENST00000407010.2	hg19		.	.	.	.	.	.	.	.	.	.	T	8.348	0.830249	0.16749	.	.	ENSG00000214960	ENST00000407010;ENST00000399310	D;D	0.86030	-2.06;-2.04	3.43	-5.93	0.02254	.	6.733810	0.01257	U	0.009067	T	0.65544	0.2701	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54715	-0.8252	10	0.30854	T	0.27	-11.129	1.788	0.03046	0.4958:0.201:0.1094:0.1938	.	45	A4D126	ISPD_HUMAN	P	45	ENSP00000385478:Q45P;ENSP00000382249:Q45P	ENSP00000382249:Q45P	Q	-	2	0	ISPD	16427339	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-1.607000	0.02070	-1.231000	0.02557	-0.958000	0.02645	CAA	.	.		0.731	ISPD-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000326252.4	NM_001101426		G	16460814	T	G	16460814	3	3	13	1	0	0	0	0	1	0	0	0	7873	1812	63	5	1261	5	ISPD	7	16460814	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10		16460814	142677849	84	1138										
NFE2L3	9603	hgsc.bcm.edu	37	chr7	26224237	26224237	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	attatcatgtaaacttcagcCaggctataagtcaggatgtg	9	7	3	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr7:26224237C>T	ENST00000056233.3	+	4	1178	c.919C>T	c.(919-921)Cag>Tag	p.Q307*		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	307					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						AAACTTCAGCCAGGCTATAAG	0.428																																					p.Q307X		Atlas-SNP	.											.	NFE2L3	77	.	0			c.C919T						.						122	115	118					7																	26224237		2203	4300	6503	SO:0001587	stop_gained	9603	exon4			TTCAGCCAGGCTA	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.919C>T	chr7.hg19:g.26224237C>T	ENSP00000056233:p.Gln307*	173.0	0.0		222.0	13.0	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Nonsense_Mutation	SNP	ENST00000056233.3	hg19	CCDS5396.1	.	.	.	.	.	.	.	.	.	.	C	35	5.520676	0.96416	.	.	ENSG00000050344	ENST00000056233;ENST00000398175	.	.	.	5.06	4.17	0.49024	.	0.584329	0.17952	N	0.156477	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-5.4925	14.3057	0.66384	0.0:0.717:0.283:0.0	.	.	.	.	X	307;13	.	ENSP00000056233:Q307X	Q	+	1	0	NFE2L3	26190762	0.799000	0.28903	0.989000	0.46669	0.764000	0.43329	2.441000	0.44864	1.258000	0.44101	0.467000	0.42956	CAG	.	.		0.428	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			T	26224237	C	T	26224237	4	4	13	1	0	0	0	0	0	1	0	0	10378	595	21	3	933	3	NFE2L3	7	26224237	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	9763423	26224237	132914426	85	1139										
HOXA2	3199	hgsc.bcm.edu	37	chr7	27142050	27142050	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	atcagcgacagggggaaaagAtgtcaggcactcagcgagcg	15	9	3	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr7:27142050A>T	ENST00000222718.5	-	1	380	c.70T>A	c.(70-72)Tct>Act	p.S24T	HOTAIRM1_ENST00000428939.3_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000593300.1_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	24					anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						GGGGGAAAAGATGTCAGGCAC	0.483																																					p.S24T		Atlas-SNP	.											.	HOXA2	56	.	0			c.T70A						.						117	124	122					7																	27142050		2203	4300	6503	SO:0001583	missense	3199	exon1			GAAAAGATGTCAG		CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996		"Homeoboxes / ANTP class : HOXL subclass"	5103	protein-coding gene	gene with protein product		604685	"homeo box A2"	HOX1K		1358459	Standard	NM_006735		Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.70T>A	chr7.hg19:g.27142050A>T	ENSP00000222718:p.Ser24Thr	985.0	0.0		516.0	64.0	NM_006735	A1L4K3|B2RMW3	Missense_Mutation	SNP	ENST00000222718.5	hg19	CCDS5403.1	.	.	.	.	.	.	.	.	.	.	A	16.51	3.144818	0.57044	.	.	ENSG00000105996	ENST00000222718	T	0.09255	3.0	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.36880	0.0983	M	0.84511	2.7	0.53688	D	0.999977	D	0.76494	0.999	D	0.68765	0.96	T	0.33752	-0.9856	10	0.66056	D	0.02	.	15.3211	0.74124	1.0:0.0:0.0:0.0	.	24	O43364	HXA2_HUMAN	T	24	ENSP00000222718:S24T	ENSP00000222718:S24T	S	-	1	0	HOXA2	27108575	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.873000	0.92357	2.019000	0.59389	0.482000	0.46254	TCT	.	.		0.483	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358508.2			T	27142050	A	T	27142050	3	4	13	1	0	0	0	0	1	0	0	0	7301	333	12	4	1068	4	HOXA2	7	27142050	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	917813	27142050	131996613	86	1140										
PDE1C	5137	hgsc.bcm.edu	37	chr7	31918662	31918662	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acgatgctcttgaaccggggCttctcgtcgctcctcctgag	11	14	2	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr7:31918662C>T	ENST00000396191.1	-	4	827	c.372G>A	c.(370-372)aaG>aaA	p.K124K	PDE1C_ENST00000396182.2_Silent_p.K124K|PDE1C_ENST00000396193.1_Silent_p.K184K|PDE1C_ENST00000396184.3_Silent_p.K124K|PDE1C_ENST00000321453.7_Silent_p.K124K	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	124					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	TGAACCGGGGCTTCTCGTCGC	0.532																																					p.K184K		Atlas-SNP	.											.	PDE1C	465	.	0			c.G552A						.						146	130	135					7																	31918662		2203	4300	6503	SO:0001819	synonymous_variant	5137	exon5			CCGGGGCTTCTCG	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.372G>A	chr7.hg19:g.31918662C>T		67.0	0.0		65.0	12.0	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Silent	SNP	ENST00000396191.1	hg19	CCDS55099.1																																																																																			.	.		0.532	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			T	31918662	C	T	31918662	2	4	13	1	0	0	0	0	0	0	0	1	11644	796	28	3		3	PDE1C	7	31918662	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	4776612	31918662	127220001	87	1141										
GLI3	2737	hgsc.bcm.edu	37	chr7	42011935	42011935	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gaaggagagtgaatgacataCcattggcttctctgccttga	11	8	1	4			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr7:42011935C>A	ENST00000395925.3	-	13	2188		c.e13+1		GLI3_ENST00000479210.1_Splice_Site	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3						anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GAATGACATACCATTGGCTTC	0.542									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												.		Atlas-SNP	.											.	GLI3	312	.	0			c.2103+1G>T						.						171	177	175					7																	42011935		2203	4300	6503	SO:0001630	splice_region_variant	2737	exon14	Familial Cancer Database	;	GACATACCATTGG		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.2103+1G>T	chr7.hg19:g.42011935C>A		83.0	0.0		116.0	6.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Splice_Site	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756699	0.89843	.	.	ENSG00000106571	ENST00000395925	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3214	0.98679	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GLI3	41978460	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.804000	0.96469	0.655000	0.94253	.	.	.		0.542	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	Intron	A	42011935	C	A	42011935	5	1	13	1	0	0	0	0	0	0	1	0	6447	521	18	3	2650	3	GLI3	7	42011935	Splice_Site	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	10093273	42011935	117126728	88	1142										
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138603038	138603038	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acagagtctcggcaccatccCctgatcccacgtctttctcc	6	18	3	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr7:138603038C>T	ENST00000422774.1	-	2	1382	c.1334G>A	c.(1333-1335)gGg>gAg	p.G445E	KIAA1549_ENST00000242365.4_Missense_Mutation_p.G395E|KIAA1549_ENST00000440172.1_Missense_Mutation_p.G445E			Q9HCM3	K1549_HUMAN	KIAA1549	445						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						GGCACCATCCCCTGATCCCAC	0.532			O	BRAF	pilocytic astrocytoma																																p.G445E	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.G1334A						.						76	75	75					7																	138603038		2092	4217	6309	SO:0001583	missense	57670	exon2			CCATCCCCTGATC		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1334G>A	chr7.hg19:g.138603038C>T	ENSP00000416040:p.Gly445Glu	101.0	0.0		94.0	13.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	hg19	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	C	14.74	2.625850	0.46840	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.61859	0.07;0.1;0.08	4.75	4.75	0.60458	.	0.000000	0.56097	D	0.000026	T	0.64080	0.2566	L	0.34521	1.04	0.32408	N	0.551066	D;D	0.71674	0.997;0.998	P;D	0.66979	0.888;0.948	T	0.67971	-0.5532	10	0.35671	T	0.21	.	15.0735	0.72059	0.0:1.0:0.0:0.0	.	445;445	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	E	445;395;445	ENSP00000406661:G445E;ENSP00000242365:G395E;ENSP00000416040:G445E	ENSP00000242365:G395E	G	-	2	0	KIAA1549	138253578	0.379000	0.25123	0.118000	0.21660	0.097000	0.18754	2.429000	0.44758	2.471000	0.83476	0.655000	0.94253	GGG	.	.		0.532	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			T	138603038	C	T	138603038	3	4	13	1	0	0	0	0	1	0	0	0	8253	623	22	3	4594	3	KIAA1549	7	138603038	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	96591103	138603038	20535625	89	1143										
ACTR3B	57180	hgsc.bcm.edu	37	chr7	152457013	152457013	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tggtggactgtggcaccgggTaagagcagctcggcgcccac	16	12	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr7:152457013T>A	ENST00000256001.8	+	1	178		c.e1+2		ACTR3B_ENST00000377776.3_Splice_Site|RN7SL845P_ENST00000484385.2_RNA|ACTR3B_ENST00000397282.2_Splice_Site|ACTR3B_ENST00000537264.1_Splice_Site	NM_020445.5	NP_065178.1	Q9P1U1	ARP3B_HUMAN	ARP3 actin-related protein 3 homolog B (yeast)							cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	13		all_hematologic(28;0.0592)|Prostate(32;0.191)	OV - Ovarian serous cystadenocarcinoma(82;0.0287)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0434)		TGGCACCGGGTAAGAGCAGCT	0.791																																					.		Atlas-SNP	.											.	ACTR3B	50	.	0			c.44+2T>A						.						2	4	3					7																	152457013		1712	3554	5266	SO:0001630	splice_region_variant	57180	exon1			ACCGGGTAAGAGC		CCDS5934.1, CCDS34782.1	7q36.1	2010-07-20			ENSG00000133627	ENSG00000133627			17256	protein-coding gene	gene with protein product						10806390	Standard	NM_001040135		Approved	ARP11, ARP3beta	uc003wle.2	Q9P1U1	OTTHUMG00000151463	ENST00000256001.8:c.44+2T>A	chr7.hg19:g.152457013T>A		50.0	0.0		44.0	14.0	NM_001040135	A8MTG1|B4DFW4|Q7Z526|Q96BT2	Splice_Site	SNP	ENST00000256001.8	hg19	CCDS5934.1	.	.	.	.	.	.	.	.	.	.	T	18.71	3.681758	0.68042	.	.	ENSG00000133627	ENST00000377776;ENST00000256001	.	.	.	3.31	3.31	0.37934	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.245	0.31682	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACTR3B	152087946	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	1.589000	0.36644	1.505000	0.48720	0.254000	0.18369	.	.	.		0.791	ACTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322803.1	NM_020445	Intron	A	152457013	T	A	152457013	5	1	13	1	0	0	0	0	0	0	1	0	213	1652	57	4	48	4	ACTR3B	7	152457013	Splice_Site	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	13853975	152457013	6681650	90	1144										
FABP4	2167	hgsc.bcm.edu	37	chr8	82391106	82391106	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	caacgtcccttggcttatgcTctctcataaactctcgtgga	7	13	3	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr8:82391106T>C	ENST00000256104.4	-	4	488	c.393A>G	c.(391-393)agA>agG	p.R131R	RP11-157I4.4_ENST00000524085.2_RNA|FABP4_ENST00000518669.1_5'UTR	NM_001442.2	NP_001433.1	P15090	FABP4_HUMAN	fatty acid binding protein 4, adipocyte	131					brown fat cell differentiation (GO:0050873)|cellular response to lithium ion (GO:0071285)|cholesterol homeostasis (GO:0042632)|cytokine production (GO:0001816)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of inflammatory response (GO:0050729)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|nucleus (GO:0005634)	fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|large_intestine(1)|ovary(1)|skin(1)	6			Epithelial(68;0.213)			TGGCTTATGCTCTCTCATAAA	0.383																																					p.R131R	NSCLC(35;550 1252 19644 48360)	Atlas-SNP	.											.	FABP4	17	.	0			c.A393G						.						189	158	168					8																	82391106		2203	4300	6503	SO:0001819	synonymous_variant	2167	exon4			TTATGCTCTCTCA	J02874	CCDS6230.1	8q21.13	2013-03-01			ENSG00000170323	ENSG00000170323		"Fatty acid binding protein family"	3559	protein-coding gene	gene with protein product		600434				2481498	Standard	NM_001442		Approved	A-FABP, aP2	uc003ycd.2	P15090	OTTHUMG00000164602	ENST00000256104.4:c.393A>G	chr8.hg19:g.82391106T>C		65.0	0.0		108.0	15.0	NM_001442	Q6IBA1	Silent	SNP	ENST00000256104.4	hg19	CCDS6230.1																																																																																			.	.		0.383	FABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379368.1	NM_001442		C	82391106	T	C	82391106	2	2	13	1	0	0	0	0	0	0	0	1	5364	1548	54	2		2	FABP4	8	82391106	Silent	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10		82391106	63972916	91	1145										
CPNE3	8895	hgsc.bcm.edu	37	chr8	87557040	87557040	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ttcagaccaccatgacaaaaCtgaaagaagcctccagaagc	7	12	1	5			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr8:87557040C>G	ENST00000521271.1	+	9	868	c.706C>G	c.(706-708)Ctg>Gtg	p.L236V	CPNE3_ENST00000198765.4_Missense_Mutation_p.L236V	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	236					lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						CATGACAAAACTGAAAGAAGC	0.318																																					p.L236V		Atlas-SNP	.											.	CPNE3	65	.	0			c.C706G						.						148	135	140					8																	87557040		2203	4300	6503	SO:0001583	missense	8895	exon9			ACAAAACTGAAAG	AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719			2316	protein-coding gene	gene with protein product		604207				9430674	Standard	NM_003909		Approved		uc003ydv.2	O75131		ENST00000521271.1:c.706C>G	chr8.hg19:g.87557040C>G	ENSP00000430934:p.Leu236Val	31.0	0.0		53.0	12.0	NM_003909	A8KA47|Q8IYA1	Missense_Mutation	SNP	ENST00000521271.1	hg19	CCDS6243.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.46|16.46	3.128810|3.128810	0.56721|0.56721	.|.	.|.	ENSG00000085719|ENSG00000085719	ENST00000198765;ENST00000521271|ENST00000517391	T;T|.	0.49139|.	0.79;0.79|.	5.8|5.8	5.8|5.8	0.92144|0.92144	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);|.	0.069915|.	0.64402|.	D|.	0.000016|.	T|T	0.76104|0.76104	0.3941|0.3941	M|M	0.77486|0.77486	2.375|2.375	0.58432|0.58432	D|D	0.999996|0.999996	P|.	0.38455|.	0.632|.	B|.	0.35899|.	0.213|.	T|T	0.75929|0.75929	-0.3144|-0.3144	10|5	0.56958|.	D|.	0.05|.	-0.0272|-0.0272	15.6367|15.6367	0.76961|0.76961	0.1379:0.8621:0.0:0.0|0.1379:0.8621:0.0:0.0	.|.	236|.	O75131|.	CPNE3_HUMAN|.	V|K	236|124	ENSP00000198765:L236V;ENSP00000430934:L236V|.	ENSP00000198765:L236V|.	L|N	+|+	1|3	2|2	CPNE3|CPNE3	87626156|87626156	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.222000|2.222000	0.42926|0.42926	2.737000|2.737000	0.93849|0.93849	0.650000|0.650000	0.86243|0.86243	CTG|AAC	.	.		0.318	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1			G	87557040	C	G	87557040	3	3	13	1	0	0	0	0	1	0	0	0	3815	564	20	4	732	4	CPNE3	8	87557040	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	5165934	87557040	58806982	92	1146										
AZIN1	51582	hgsc.bcm.edu	37	chr8	103851904	103851904	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggaacaagcaaatccggttcCaagagctgccaaaatctcaa	8	11	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr8:103851904C>G	ENST00000337198.5	-	4	1413	c.250G>C	c.(250-252)Gga>Cga	p.G84R	AZIN1_ENST00000522311.1_5'UTR|AZIN1_ENST00000347770.4_Missense_Mutation_p.G84R	NM_148174.2	NP_680479.1	O14977	AZIN1_HUMAN	antizyme inhibitor 1	84					cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|negative regulation of protein catabolic process (GO:0042177)|polyamine biosynthetic process (GO:0006596)|positive regulation of polyamine transmembrane transport (GO:1902269)|regulation of cellular amino acid metabolic process (GO:0006521)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|enzyme inhibitor activity (GO:0004857)|ornithine decarboxylase activator activity (GO:0042978)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	9	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)			AATCCGGTTCCAAGAGCTGCC	0.373																																					p.G84R		Atlas-SNP	.											.	AZIN1	26	.	0			c.G250C						.						117	101	106					8																	103851904		2203	4300	6503	SO:0001583	missense	51582	exon5			CGGTTCCAAGAGC	AAC25391	CCDS6295.1	8p22-q21.3	2005-03-21	2005-03-21	2005-03-21		ENSG00000155096			16432	protein-coding gene	gene with protein product	"ornithine decarboxylase 1-like"	607909	"ornithine decarboxylase antizyme inhibitor"	OAZIN		9349715, 9110174	Standard	XM_005250969		Approved	OAZI, ODC1L	uc003yky.3	O14977		ENST00000337198.5:c.250G>C	chr8.hg19:g.103851904C>G	ENSP00000337180:p.Gly84Arg	242.0	0.0		274.0	14.0	NM_015878	A6NCD5|Q6IBQ7|Q96D20	Missense_Mutation	SNP	ENST00000337198.5	hg19	CCDS6295.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.865186	0.91511	.	.	ENSG00000155096	ENST00000337198;ENST00000347770;ENST00000520402	T;T	0.64618	-0.11;-0.11	5.6	5.6	0.85130	Orn/DAP/Arg decarboxylase 2, N-terminal (1);	0.052031	0.85682	D	0.000000	D	0.82802	0.5116	M	0.93550	3.43	0.80722	D	1	D	0.76494	0.999	D	0.68483	0.958	D	0.86653	0.1899	10	0.87932	D	0	-10.0944	12.9068	0.58156	0.0:0.926:0.0:0.074	.	84	O14977	AZIN1_HUMAN	R	84	ENSP00000337180:G84R;ENSP00000321507:G84R	ENSP00000337180:G84R	G	-	1	0	AZIN1	103921080	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.048000	0.71046	2.642000	0.89623	0.650000	0.86243	GGA	.	.		0.373	AZIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380133.1			G	103851904	C	G	103851904	3	3	13	1	0	0	0	0	1	0	0	0	1242	603	21	4	1132	4	AZIN1	8	103851904	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	16294864	103851904	42512118	93	1147										
CDKN2B	1030	hgsc.bcm.edu	37	chr9	22008820	22008820	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gatcgcgcgcctcccgaaacGgttgactccgttgggatccg	13	14	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr9:22008820G>T	ENST00000276925.6	-	1	542	c.133C>A	c.(133-135)Cgt>Agt	p.R45S	CDKN2B-AS1_ENST00000582072.1_RNA|CDKN2B-AS1_ENST00000584020.1_RNA|CDKN2B-AS1_ENST00000577551.1_RNA|CDKN2B_ENST00000380142.4_Missense_Mutation_p.R45S|CDKN2B-AS1_ENST00000582301.1_RNA|CDKN2B_ENST00000539462.1_Missense_Mutation_p.R45S|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2B-AS1_ENST00000584816.1_RNA|CDKN2B-AS1_ENST00000580576.1_RNA|CDKN2B-AS1_ENST00000580467.1_RNA|CDKN2B-AS1_ENST00000583719.1_RNA|CDKN2B-AS1_ENST00000468603.2_RNA|CDKN2B-AS1_ENST00000584637.1_RNA|CDKN2B-AS1_ENST00000581051.1_RNA|CDKN2B-AS1_ENST00000455933.2_RNA|CDKN2B-AS1_ENST00000428597.1_RNA|CDKN2B-AS1_ENST00000585267.1_RNA|CDKN2B-AS1_ENST00000584351.1_RNA	NM_004936.3|NM_078487.2	NP_004927.2|NP_511042.1	P42772	CDN2B_HUMAN	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	45					aging (GO:0007568)|cell cycle arrest (GO:0007050)|cellular response to extracellular stimulus (GO:0031668)|cellular response to nutrient (GO:0031670)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|liver development (GO:0001889)|megakaryocyte differentiation (GO:0030219)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to cytokine (GO:0034097)|response to organic cyclic compound (GO:0014070)|spleen development (GO:0048536)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)	p.0(1)|p.0?(1)		lung(2)	2		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;1.31e-280)|Lung NSC(2;2.28e-131)|all_lung(2;2.11e-123)|Glioma(2;5.66e-57)|all_neural(2;3.05e-50)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;8.01e-33)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00369)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;3.29e-71)|Epithelial(2;9.08e-60)|LUSC - Lung squamous cell carcinoma(2;5.8e-46)|LUAD - Lung adenocarcinoma(2;1.43e-25)|BRCA - Breast invasive adenocarcinoma(2;5.37e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;6.92e-07)|KIRC - Kidney renal clear cell carcinoma(2;8.63e-07)|OV - Ovarian serous cystadenocarcinoma(39;0.014)|COAD - Colon adenocarcinoma(8;0.143)		CTCCCGAAACGGTTGACTCCG	0.751											OREG0019127	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R45S		Atlas-SNP	.											.	CDKN2B	12	.	2	Whole gene deletion(2)	lung(2)	c.C133A						.						8	10	9					9																	22008820		2177	4233	6410	SO:0001583	missense	1030	exon1			CGAAACGGTTGAC	AB060808	CCDS6512.1, CCDS6513.1	9p21	2008-07-21			ENSG00000147883	ENSG00000147883			1788	protein-coding gene	gene with protein product		600431				8078588	Standard	NM_004936		Approved	P15, MTS2, INK4B, TP15, CDK4I, p15INK4b	uc003zpo.3	P42772	OTTHUMG00000019691	ENST00000276925.6:c.133C>A	chr9.hg19:g.22008820G>T	ENSP00000276925:p.Arg45Ser	181.0	0.0	752	100.0	5.0	NM_078487	O15125|Q6FI09	Missense_Mutation	SNP	ENST00000276925.6	hg19	CCDS6512.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.571555	0.28003	.	.	ENSG00000147883	ENST00000276925;ENST00000380142;ENST00000539462	T;T;T	0.78816	-1.21;1.59;1.59	5.86	-1.71	0.08133	Ankyrin repeat-containing domain (3);	0.762297	0.13007	N	0.421239	T	0.47469	0.1447	N	0.10837	0.055	0.30740	N	0.746244	B;B	0.23735	0.006;0.09	B;B	0.23419	0.011;0.046	T	0.42799	-0.9430	10	0.07325	T	0.83	-0.8145	1.3886	0.02246	0.2845:0.234:0.3586:0.123	.	45;45	P42772;O15125	CDN2B_HUMAN;.	S	45	ENSP00000276925:R45S;ENSP00000369487:R45S;ENSP00000445136:R45S	ENSP00000276925:R45S	R	-	1	0	CDKN2B	21998820	0.010000	0.17322	0.918000	0.36340	0.905000	0.53344	-1.412000	0.02476	-0.656000	0.05380	0.650000	0.86243	CGT	.	.		0.751	CDKN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051932.2	NM_004936		T	22008820	G	T	22008820	3	4	13	1	0	0	0	0	1	0	0	0	3166	1116	39	1	372	1	CDKN2B	9	22008820	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10		22008820	119204611	94	1148										
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84606758	84606758	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acggaatatgttaacctcaaTtgctgttaagcatgacttgg	9	7	1	1	rs201640408		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr9:84606758T>C	ENST00000344803.2	+	4	1420	c.1373T>C	c.(1372-1374)aTt>aCt	p.I458T		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	458					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTAACCTCAATTGCTGTTAAG	0.423													T|||	1	0.000199681	8e-04	0	5008	,	,		21068	0		0	False		,,,				2504	0				p.I458T		Atlas-SNP	.											.	.	.	.	0			c.T1373C						.	T	THR/ILE	5,3897		0,5,1946	92	85	87		1373	-1.5	0	9		87	1,8275		0,1,4137	no	missense	FAM75D1	NM_001001670.2	89	0,6,6083	CC,CT,TT		0.0121,0.1281,0.0493	benign	458/1577	84606758	6,12172	1951	4138	6089	SO:0001583	missense	389763	exon4			CCTCAATTGCTGT		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.1373T>C	chr9.hg19:g.84606758T>C	ENSP00000341988:p.Ile458Thr	155.0	0.0		183.0	22.0	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	hg19	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	T	0.062	-1.221669	0.01530	0.001281	1.21E-4	ENSG00000214929	ENST00000344803	T	0.04706	3.57	2.41	-1.55	0.08558	.	2.368510	0.02041	N	0.049316	T	0.04588	0.0125	L	0.39633	1.23	0.09310	N	1	B	0.24882	0.113	B	0.26517	0.07	T	0.38067	-0.9678	10	0.18276	T	0.48	15.7014	2.1098	0.03700	0.2442:0.3116:0.0:0.4442	.	458	Q6ZQQ2	F75D1_HUMAN	T	458	ENSP00000341988:I458T	ENSP00000341988:I458T	I	+	2	0	FAM75D1	83796578	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.642000	0.02006	-0.344000	0.08338	0.416000	0.27883	ATT	.	.		0.423	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		C	84606758	T	C	84606758	3	2	13	1	0	0	0	0	1	0	0	0	5940	1493	52	2	1387	2	FLJ46321	9	84606758	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	62597938	84606758	56606673	95	1149										
NR5A1	2516	hgsc.bcm.edu	37	chr9	127265483	127265483	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	agtgcttgttgttctgcaccGtgcgcttgaagaagccctgc	12	11	1	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr9:127265483G>A	ENST00000373588.4	-	3	315	c.119C>T	c.(118-120)aCg>aTg	p.T40M		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	40					adrenal gland development (GO:0030325)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|hormone metabolic process (GO:0042445)|intracellular receptor signaling pathway (GO:0030522)|luteinization (GO:0001553)|maintenance of protein location in nucleus (GO:0051457)|male gonad development (GO:0008584)|multicellular organismal aging (GO:0010259)|negative regulation of female gonad development (GO:2000195)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|primary sex determination (GO:0007538)|regulation of steroid biosynthetic process (GO:0050810)|tissue development (GO:0009888)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)	2						GTTCTGCACCGTGCGCTTGAA	0.652																																					p.T40M		Atlas-SNP	.											.	NR5A1	32	.	0			c.C119T						.						59	51	53					9																	127265483		2197	4296	6493	SO:0001583	missense	2516	exon3			TGCACCGTGCGCT	D88155	CCDS6856.1	9q33	2013-01-16			ENSG00000136931	ENSG00000136931		"Nuclear hormone receptors"	7983	protein-coding gene	gene with protein product		184757		FTZF1		7789992	Standard	NM_004959		Approved	FTZ1, SF-1, ELP, AD4BP	uc004boo.1	Q13285	OTTHUMG00000020655	ENST00000373588.4:c.119C>T	chr9.hg19:g.127265483G>A	ENSP00000362690:p.Thr40Met	97.0	0.0		43.0	7.0	NM_004959	O15196|Q5T6F5	Missense_Mutation	SNP	ENST00000373588.4	hg19	CCDS6856.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267180	0.80469	.	.	ENSG00000136931	ENST00000373588;ENST00000455734	D;D	0.97731	-4.51;-4.51	4.57	3.68	0.42216	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.85682	D	0.000000	D	0.98495	0.9498	M	0.83118	2.625	0.53688	D	0.999975	D	0.89917	1.0	D	0.97110	1.0	D	0.99007	1.0813	10	0.87932	D	0	.	11.9196	0.52785	0.086:0.0:0.914:0.0	.	40	Q13285	STF1_HUMAN	M	40	ENSP00000362690:T40M;ENSP00000393245:T40M	ENSP00000362690:T40M	T	-	2	0	NR5A1	126305304	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	7.906000	0.87423	1.024000	0.39682	0.455000	0.32223	ACG	.	.		0.652	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959		A	127265483	G	A	127265483	3	1	13	1	0	0	0	0	1	0	0	0	10644	1145	40	1	1286	1	NR5A1	9	127265483	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	42658725	127265483	13947948	96	1150										
OLFML2A	169611	hgsc.bcm.edu	37	chr9	127570169	127570169	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aaggaccctgcagctcgagaCgacaggatctatgtcaccaa	10	12	2	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr9:127570169C>T	ENST00000373580.3	+	7	1278	c.1278C>T	c.(1276-1278)gaC>gaT	p.D426D	OLFML2A_ENST00000288815.5_Silent_p.D212D	NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	426	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						CAGCTCGAGACGACAGGATCT	0.607																																					p.D426D		Atlas-SNP	.											.	OLFML2A	61	.	0			c.C1278T						.						85	85	85					9																	127570169		2203	4300	6503	SO:0001819	synonymous_variant	169611	exon7			TCGAGACGACAGG	AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.1278C>T	chr9.hg19:g.127570169C>T		186.0	0.0		87.0	12.0	NM_182487	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Silent	SNP	ENST00000373580.3	hg19	CCDS6857.2																																																																																			.	.		0.607	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487		T	127570169	C	T	127570169	2	4	13	1	0	0	0	0	0	0	0	1	10866	535	19	1		1	OLFML2A	9	127570169	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	304686	127570169	13643262	97	1151										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131339545	131339545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gagagatcttgctgctctagAagacaaggtgggttttacaa	12	6	2	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr9:131339545A>G	ENST00000372731.4	+	7	1033	c.923A>G	c.(922-924)gAa>gGa	p.E308G	SPTAN1_ENST00000372739.3_Missense_Mutation_p.E308G|SPTAN1_ENST00000358161.5_Missense_Mutation_p.E308G	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	308					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GCTGCTCTAGAAGACAAGGTG	0.483																																					p.E308G	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.A923G						.						112	111	111					9																	131339545		2203	4300	6503	SO:0001583	missense	6709	exon7			CTCTAGAAGACAA	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.923A>G	chr9.hg19:g.131339545A>G	ENSP00000361816:p.Glu308Gly	74.0	0.0		102.0	10.0	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.829482	0.50845	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.53857	0.6;0.6;0.6	6.17	6.17	0.99709	.	0.202954	0.52532	D	0.000068	T	0.52869	0.1761	L	0.28504	0.86	0.80722	D	1	B;B;B;B;B	0.29862	0.01;0.173;0.259;0.126;0.005	B;B;B;B;B	0.42625	0.009;0.122;0.393;0.049;0.006	T	0.53837	-0.8382	10	0.51188	T	0.08	.	16.0034	0.80327	1.0:0.0:0.0:0.0	.	308;308;308;308;308	A6NG51;B4DTV8;Q13813-3;Q13813-2;Q13813	.;.;.;.;SPTA2_HUMAN	G	308	ENSP00000350882:E308G;ENSP00000361816:E308G;ENSP00000361824:E308G	ENSP00000350882:E308G	E	+	2	0	SPTAN1	130379366	1.000000	0.71417	0.998000	0.56505	0.503000	0.33858	8.962000	0.93254	2.371000	0.80710	0.533000	0.62120	GAA	.	.		0.483	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		G	131339545	A	G	131339545	3	3	13	1	0	0	0	0	1	0	0	0	15132	246	9	2	945	2	SPTAN1	9	131339545	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	3769376	131339545	9873886	98	1152										
TSC1	7248	hgsc.bcm.edu	37	chr9	135779815	135779815	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tacctccaaagtgggtccagTcgacagacttgctgggtaaa	11	10	0	1	rs118203620		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr9:135779815T>C	ENST00000298552.3	-	16	2245	c.2024A>G	c.(2023-2025)gAc>gGc	p.D675G	TSC1_ENST00000545250.1_Missense_Mutation_p.D624G|TSC1_ENST00000440111.2_Missense_Mutation_p.D675G	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	675					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		GTGGGTCCAGTCGACAGACTT	0.443			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.D675G		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.A2024G						.						68	64	65					9																	135779815		2203	4300	6503	SO:0001583	missense	7248	exon16	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GTCCAGTCGACAG	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.2024A>G	chr9.hg19:g.135779815T>C	ENSP00000298552:p.Asp675Gly	107.0	0.0		103.0	10.0	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	hg19	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.311024	0.81358	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	D;D;D	0.88741	-2.42;-2.42;-2.42	5.5	4.34	0.51931	.	0.088458	0.85682	D	0.000000	D	0.93197	0.7833	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77004	0.989;0.984	D	0.92618	0.6105	10	0.59425	D	0.04	-22.2566	11.0075	0.47644	0.1396:0.0:0.0:0.8604	.	624;675	B7Z897;Q92574	.;TSC1_HUMAN	G	675;675;624	ENSP00000298552:D675G;ENSP00000394524:D675G;ENSP00000444017:D624G	ENSP00000298552:D675G	D	-	2	0	TSC1	134769636	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	0.877000	0.35895	0.533000	0.62120	GAC	.	.		0.443	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			C	135779815	T	C	135779815	3	2	13	1	0	0	0	0	1	0	0	0	16620	1667	58	2	1502	2	TSC1	9	135779815	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	4440270	135779815	5433616	99	1153										
FAM13C	220965	hgsc.bcm.edu	37	chr10	61029804	61029804	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gagcagcctgctggtccccaCagagtggaggtcttctggtg	15	11	2	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr10:61029804C>G	ENST00000373868.2	-	7	745	c.658G>C	c.(658-660)Gtg>Ctg	p.V220L	FAM13C_ENST00000419214.2_Missense_Mutation_p.V220L|FAM13C_ENST00000422313.2_Missense_Mutation_p.V220L|FAM13C_ENST00000435852.2_Missense_Mutation_p.V220L|FAM13C_ENST00000468840.2_Missense_Mutation_p.V137L|FAM13C_ENST00000373867.3_Missense_Mutation_p.V137L|FAM13C_ENST00000442566.3_Missense_Mutation_p.V241L|FAM13C_ENST00000277705.6_Missense_Mutation_p.V241L	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	220										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CTGGTCCCCACAGAGTGGAGG	0.517																																					p.V220L		Atlas-SNP	.											.	FAM13C	124	.	0			c.G658C						.						106	96	100					10																	61029804		2203	4300	6503	SO:0001583	missense	220965	exon7			TCCCCACAGAGTG	U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"family with sequence similarity 13, member C1"	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.658G>C	chr10.hg19:g.61029804C>G	ENSP00000362975:p.Val220Leu	58.0	0.0		76.0	8.0	NM_198215	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	hg19	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	C	4.735	0.136632	0.09032	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000419214;ENST00000468840;ENST00000435852;ENST00000422313	T;T;T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;1.03;-1.13;-1.13;-1.13	5.53	-3.52	0.04682	.	0.727883	0.12602	N	0.454628	T	0.53514	0.1801	L	0.29908	0.895	0.09310	N	1	B;B;B;B;B	0.09022	0.0;0.0;0.002;0.0;0.0	B;B;B;B;B	0.08055	0.002;0.0;0.003;0.001;0.001	T	0.36114	-0.9761	10	0.13470	T	0.59	-0.1347	0.8453	0.01160	0.3254:0.1425:0.3086:0.2234	.	220;137;220;220;220	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31-3;Q8NE31	.;.;.;.;FA13C_HUMAN	L	137;220;241;241;220;137;220;220	ENSP00000362974:V137L;ENSP00000362975:V220L;ENSP00000395661:V241L;ENSP00000277705:V241L;ENSP00000391993:V220L;ENSP00000423896:V137L;ENSP00000392302:V220L;ENSP00000400241:V220L	ENSP00000277705:V241L	V	-	1	0	FAM13C	60699810	0.001000	0.12720	0.010000	0.14722	0.982000	0.71751	-0.490000	0.06482	-0.237000	0.09739	0.655000	0.94253	GTG	.	.		0.517	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			G	61029804	C	G	61029804	3	3	13	1	0	0	0	0	1	0	0	0	5459	478	17	4	1131	4	FAM13C	10	61029804	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10		61029804	74504943	100	1154										
ANK3	288	hgsc.bcm.edu	37	chr10	61847908	61847908	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ctttttgtgaacattacctgGaggcccactcgaattctttt	7	10	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr10:61847908G>T	ENST00000280772.2	-	29	3728	c.3537C>A	c.(3535-3537)ctC>ctA	p.L1179L	ANK3_ENST00000355288.2_Silent_p.L313L|ANK3_ENST00000503366.1_Silent_p.L1180L|ANK3_ENST00000373827.2_Silent_p.L1173L	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1179	ZU5 2. {ECO:0000255|PROSITE- ProRule:PRU00485}.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						ACATTACCTGGAGGCCCACTC	0.458																																					p.L1180L		Atlas-SNP	.											.	ANK3	703	.	0			c.C3540A						.						93	95	94					10																	61847908		2203	4300	6503	SO:0001819	synonymous_variant	288	exon30			TACCTGGAGGCCC	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.3537C>A	chr10.hg19:g.61847908G>T		73.0	0.0		60.0	8.0	NM_001204404	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.		0.458	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61847908	G	T	61847908	2	4	13	1	0	0	0	0	0	0	0	1	622	1161	41	3		3	ANK3	10	61847908	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	818104	61847908	73686839	101	1155										
CDH23	64072	hgsc.bcm.edu	37	chr10	73567129	73567129	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggcgcagtggatgcagatgaGggccccaacgcgatcgtgta	16	10	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr10:73567129G>T	ENST00000224721.6	+	57	8294	c.8289G>T	c.(8287-8289)gaG>gaT	p.E2763D	CDH23_ENST00000475158.1_3'UTR|CDH23_ENST00000398788.3_Missense_Mutation_p.E518D	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2758	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ATGCAGATGAGGGCCCCAACG	0.612																																					p.E2758D		Atlas-SNP	.											.	CDH23	365	.	0			c.G8274T						.						38	45	43					10																	73567129		2119	4231	6350	SO:0001583	missense	64072	exon56			AGATGAGGGCCCC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.8289G>T	chr10.hg19:g.73567129G>T	ENSP00000224721:p.Glu2763Asp	213.0	0.0		120.0	6.0	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	G	16.69	3.191983	0.58017	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.53206	0.63	4.77	1.87	0.25490	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.55178	0.1904	L	0.48935	1.535	0.53688	D	0.999974	D;D	0.89917	1.0;0.996	D;D	0.91635	0.999;0.953	T	0.45977	-0.9224	10	0.32370	T	0.25	.	8.4233	0.32714	0.309:0.0:0.691:0.0	.	2758;2758	E9PEX1;Q9H251	.;CAD23_HUMAN	D	2763;2758;2761;518	ENSP00000381768:E518D	ENSP00000224721:E2763D	E	+	3	2	CDH23	73237135	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	1.451000	0.35145	0.226000	0.20979	0.551000	0.68910	GAG	.	.		0.612	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73567129	G	T	73567129	3	4	13	1	0	0	0	0	1	0	0	0	3110	991	35	3	8845	3	CDH23	10	73567129	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	11719221	73567129	61967618	102	1156										
PNLIPRP3	119548	hgsc.bcm.edu	37	chr10	118202687	118202687	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggcagagagacatgtgcaatGtatgacatgaataagctcct	11	7	0	4			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr10:118202687G>C	ENST00000369230.3	+	3	470		c.e3+1			NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3						lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		CATGTGCAATGTATGACATGA	0.378																																					.		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.324+1G>C						.						130	114	119					10																	118202687		2203	4300	6503	SO:0001630	splice_region_variant	119548	exon3			TGCAATGTATGAC	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.324+1G>C	chr10.hg19:g.118202687G>C		67.0	0.0		91.0	7.0	NM_001011709		Splice_Site	SNP	ENST00000369230.3	hg19	CCDS31292.1	.	.	.	.	.	.	.	.	.	.	G	7.452	0.642850	0.14451	.	.	ENSG00000203837	ENST00000369230	.	.	.	4.64	2.71	0.32032	.	.	.	.	.	.	.	.	.	.	.	0.20821	N	0.999842	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.9681	0.24635	0.1022:0.1803:0.7175:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PNLIPRP3	118192677	1.000000	0.71417	0.003000	0.11579	0.019000	0.09904	3.807000	0.55591	1.050000	0.40346	0.650000	0.86243	.	.	.		0.378	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	Intron	C	118202687	G	C	118202687	5	2	13	1	0	0	0	0	0	0	1	0	12161	1391	48	4	335	4	PNLIPRP3	10	118202687	Splice_Site	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	44635558	118202687	17332060	103	1157										
OR51G1	79324	hgsc.bcm.edu	37	chr11	4944890	4944890	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggtgggaggcaatgctgagcAcggtgcgaaggatgagggcg	21	6	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr11:4944890A>G	ENST00000321961.2	-	1	747	c.680T>C	c.(679-681)gTg>gCg	p.V227A	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	227						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		AATGCTGAGCACGGTGCGAAG	0.537																																					p.V227A		Atlas-SNP	.											.	OR51G1	74	.	0			c.T680C						.						127	101	110					11																	4944890		2201	4298	6499	SO:0001583	missense	79324	exon1			CTGAGCACGGTGC	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"GPCR / Class A : Olfactory receptors"	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.680T>C	chr11.hg19:g.4944890A>G	ENSP00000322546:p.Val227Ala	71.0	0.0		90.0	19.0	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	hg19	CCDS31366.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.370337	0.42003	.	.	ENSG00000176879	ENST00000321961	T	0.00316	8.13	4.28	4.28	0.50868	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35525	U	0.003159	T	0.00754	0.0025	M	0.91972	3.26	0.18873	N	0.999988	P	0.49447	0.924	P	0.60415	0.874	T	0.11767	-1.0574	10	0.72032	D	0.01	.	12.3688	0.55244	1.0:0.0:0.0:0.0	.	227	Q8NGK1	O51G1_HUMAN	A	227	ENSP00000322546:V227A	ENSP00000322546:V227A	V	-	2	0	OR51G1	4901466	0.094000	0.21725	0.011000	0.14972	0.009000	0.06853	3.629000	0.54266	1.808000	0.52836	0.374000	0.22700	GTG	.	.		0.537	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237		G	4944890	A	G	4944890	3	3	13	1	0	0	0	0	1	0	0	0	11107	159	6	2	287	2	OR51G1	11	4944890	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10		4944890	130061626	104	1158										
NOX4	50507	hgsc.bcm.edu	37	chr11	89173873	89173873	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	taccagttgtgaagagaagtTttctaggatcctgagaaaaa	10	5	1	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr11:89173873T>A	ENST00000263317.4	-	6	696	c.458A>T	c.(457-459)aAa>aTa	p.K153I	NOX4_ENST00000343727.5_Missense_Mutation_p.K129I|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000375979.3_Intron|NOX4_ENST00000534731.1_Missense_Mutation_p.K153I|NOX4_ENST00000525196.1_Missense_Mutation_p.K153I|NOX4_ENST00000535633.1_Missense_Mutation_p.K129I|NOX4_ENST00000527626.1_Intron|NOX4_ENST00000542487.1_Missense_Mutation_p.K129I|NOX4_ENST00000532825.1_Missense_Mutation_p.K129I|NOX4_ENST00000527956.1_Missense_Mutation_p.K129I|NOX4_ENST00000528341.1_Missense_Mutation_p.K128I|NOX4_ENST00000413594.2_Missense_Mutation_p.K174I|NOX4_ENST00000424319.1_Missense_Mutation_p.K129I			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	153	Ferric oxidoreductase.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				GAAGAGAAGTTTTCTAGGATC	0.333																																					p.K153I		Atlas-SNP	.											NOX4,NS,carcinoma,0,1	NOX4	101	.	0			c.A458T						.						39	39	39					11																	89173873		2201	4299	6500	SO:0001583	missense	50507	exon6			AGAAGTTTTCTAG	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.458A>T	chr11.hg19:g.89173873T>A	ENSP00000263317:p.Lys153Ile	294.0	0.0		248.0	34.0	NM_001143836	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	hg19	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	T	13.22	2.172610	0.38413	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000528341;ENST00000413594	D;D;D;D;D;D;D;D;D;D;D	0.95622	-3.69;-3.69;-3.69;-3.67;-3.69;-3.62;-3.76;-3.69;-3.69;-3.67;-3.73	5.92	4.79	0.61399	Flavoprotein transmembrane component (1);	0.392618	0.28933	N	0.013670	D	0.94335	0.8179	L	0.39147	1.195	0.45161	D	0.998174	B;P;D;B;B	0.65815	0.04;0.8;0.995;0.074;0.091	B;P;P;B;B	0.54815	0.05;0.474;0.761;0.039;0.19	D	0.92367	0.5902	9	.	.	.	-17.5217	9.8969	0.41324	0.0:0.0784:0.0:0.9216	.	129;128;153;153;153	E9PMY6;E9PPP2;E9PI95;Q9NPH5-6;Q9NPH5	.;.;.;.;NOX4_HUMAN	I	129;129;129;153;153;153;129;129;129;128;174	ENSP00000412446:K129I;ENSP00000440172:K129I;ENSP00000344747:K129I;ENSP00000436892:K153I;ENSP00000436716:K153I;ENSP00000263317:K153I;ENSP00000434924:K129I;ENSP00000433797:K129I;ENSP00000439373:K129I;ENSP00000436970:K128I;ENSP00000405705:K174I	.	K	-	2	0	NOX4	88813521	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.125000	0.42016	1.060000	0.40578	-0.290000	0.09829	AAA	.	.		0.333	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		A	89173873	T	A	89173873	3	1	13	1	0	0	0	0	1	0	0	0	10567	1841	64	4	1330	4	NOX4	11	89173873	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	84228983	89173873	45832643	105	1159										
LAYN	143903	hgsc.bcm.edu	37	chr11	111431016	111431016	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aagccactcccgatgacatgTcttgtgactatgacaacatg	8	11	1	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr11:111431016T>C	ENST00000375615.3	+	8	1167	c.982T>C	c.(982-984)Tct>Cct	p.S328P	LAYN_ENST00000525126.1_3'UTR|LAYN_ENST00000436913.2_Missense_Mutation_p.S175P|LAYN_ENST00000533265.1_3'UTR|LAYN_ENST00000375614.2_Missense_Mutation_p.S320P	NM_001258390.1	NP_001245319.1	Q6UX15	LAYN_HUMAN	layilin	328						cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|ruffle (GO:0001726)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|skin(1)	14		all_cancers(61;9.06e-10)|all_epithelial(67;1.34e-05)|Melanoma(852;1.74e-05)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.086)		Epithelial(105;1.5e-06)|BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|all cancers(92;2.45e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0476)	Hyaluronan(DB08818)	CGATGACATGTCTTGTGACTA	0.468																																					p.S328P	Ovarian(17;551 586 12136 22082 22900)	Atlas-SNP	.											.	LAYN	35	.	0			c.T982C						.						140	120	126					11																	111431016		2201	4297	6498	SO:0001583	missense	143903	exon8			GACATGTCTTGTG		CCDS31676.1, CCDS58178.1, CCDS58179.1	11q23.1	2006-02-09			ENSG00000204381	ENSG00000204381			29471	protein-coding gene	gene with protein product						15913605	Standard	NM_001258390		Approved	FLJ30977, FLJ31092	uc001plr.2	Q6UX15	OTTHUMG00000166721	ENST00000375615.3:c.982T>C	chr11.hg19:g.111431016T>C	ENSP00000364765:p.Ser328Pro	162.0	0.0		167.0	33.0	NM_001258390	A6NJB0|B4DJU0|Q8TAY8|Q96NC5|Q96NF3	Missense_Mutation	SNP	ENST00000375615.3	hg19	CCDS58178.1	.	.	.	.	.	.	.	.	.	.	T	10.61	1.399070	0.25291	.	.	ENSG00000204381	ENST00000375614;ENST00000375615;ENST00000436913;ENST00000541011	T;T	0.05717	3.81;3.4	6.03	4.91	0.64330	.	0.142643	0.48286	D	0.000182	T	0.07818	0.0196	L	0.43701	1.375	0.37041	D	0.897144	B;B;B	0.21905	0.062;0.029;0.058	B;B;B	0.31101	0.124;0.023;0.022	T	0.25152	-1.0140	10	0.27785	T	0.31	-16.5524	11.3556	0.49613	0.0:0.0708:0.0:0.9292	.	175;328;320	B4DJU0;Q6UX15;Q6UX15-2	.;LAYN_HUMAN;.	P	320;328;175;283	ENSP00000364764:S320P;ENSP00000364765:S328P	ENSP00000364764:S320P	S	+	1	0	LAYN	110936226	0.981000	0.34729	0.933000	0.37362	0.257000	0.26127	1.498000	0.35660	2.308000	0.77769	0.533000	0.62120	TCT	.	.		0.468	LAYN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391187.1	NM_178834		C	111431016	T	C	111431016	3	2	13	1	0	0	0	0	1	0	0	0	8658	1667	58	2	984	2	LAYN	11	111431016	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	22257143	111431016	23575500	106	1160										
AMICA1	120425	hgsc.bcm.edu	37	chr11	118071326	118071326	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	agggctgccggggtcaccagTgcttgggaaagtagaaaagc	16	8	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr11:118071326T>C	ENST00000356289.5	-	7	947	c.774A>G	c.(772-774)acA>acG	p.T258T	AMICA1_ENST00000292067.7_Splice_Site_p.T248T|AMICA1_ENST00000526620.1_Splice_Site_p.T219T|AMICA1_ENST00000533261.1_Splice_Site_p.T247T	NM_001098526.1	NP_001091996.1	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen 1	258					blood coagulation (GO:0007596)|gamma-delta T cell activation (GO:0046629)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte migration (GO:0050900)|monocyte extravasation (GO:0035696)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|stomach(2)	20	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		GGGTCACCAGTGCTTGGGAAA	0.542																																					p.T258T		Atlas-SNP	.											.	AMICA1	49	.	0			c.A774G						.						66	69	68					11																	118071326		2200	4296	6496	SO:0001630	splice_region_variant	120425	exon7			CACCAGTGCTTGG	AY138965, AY358362	CCDS8391.1, CCDS41723.1, CCDS66240.1	11q23.3	2013-01-11				ENSG00000160593		"Immunoglobulin superfamily / V-set domain containing"	19084	protein-coding gene	gene with protein product		609770				12975309	Standard	NM_001098526		Approved	Gm638, AMICA	uc001psk.2	Q86YT9		ENST00000356289.5:c.773-1A>G	chr11.hg19:g.118071326T>C		89.0	0.0		76.0	12.0	NM_001098526	B0YIV1|B0YIV2|Q496M1|Q5DTC6|Q7Z499|Q8N9I7|Q8NF70	Silent	SNP	ENST00000356289.5	hg19	CCDS41723.1																																																																																			.	.		0.542	AMICA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392105.2	NM_153206	Silent	C	118071326	T	C	118071326	5	2	13	1	0	0	0	0	0	0	1	0	574	1710	59	2	426	2	AMICA1	11	118071326	Splice_Site	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	6640310	118071326	16935190	107	1161										
ITFG2	55846	hgsc.bcm.edu	37	chr12	2932026	2932026	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	catatatcattgatcacaacCgcaccgtcgtccgcttccaa	5	15	2	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:2932026C>T	ENST00000228799.2	+	10	1154	c.1015C>T	c.(1015-1017)Cgc>Tgc	p.R339C	ITFG2_ENST00000419778.2_Missense_Mutation_p.R162C|ITFG2_ENST00000542548.1_Missense_Mutation_p.R227C	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	339					germinal center B cell differentiation (GO:0002314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			TGATCACAACCGCACCGTCGT	0.512																																					p.R339C		Atlas-SNP	.											.	ITFG2	38	.	0			c.C1015T						.						145	111	123					12																	2932026		2203	4300	6503	SO:0001583	missense	55846	exon10			CACAACCGCACCG	AF220048	CCDS8513.1	12p13.33	2006-11-29		2006-07-25	ENSG00000111203	ENSG00000111203			30879	protein-coding gene	gene with protein product						12477932	Standard	NM_018463		Approved	MDS028	uc001qlb.2	Q969R8	OTTHUMG00000130617	ENST00000228799.2:c.1015C>T	chr12.hg19:g.2932026C>T	ENSP00000228799:p.Arg339Cys	150.0	0.0		85.0	5.0	NM_018463	A8K4Z5|D3DUQ2|Q6PKU5|Q96SX6	Missense_Mutation	SNP	ENST00000228799.2	hg19	CCDS8513.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.575724	0.86645	.	.	ENSG00000111203	ENST00000228799;ENST00000419778;ENST00000542548	T;T;T	0.70869	-0.52;2.26;2.26	5.08	5.08	0.68730	.	0.055569	0.64402	D	0.000001	D	0.83557	0.5280	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.64506	0.926	D	0.86116	0.1565	10	0.87932	D	0	-8.6533	17.476	0.87659	0.0:1.0:0.0:0.0	.	339	Q969R8	ITFG2_HUMAN	C	339;162;227	ENSP00000228799:R339C;ENSP00000401103:R162C;ENSP00000437870:R227C	ENSP00000228799:R339C	R	+	1	0	ITFG2	2802287	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	4.684000	0.61686	2.375000	0.81037	0.561000	0.74099	CGC	.	.		0.512	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	NM_018463		T	2932026	C	T	2932026	3	4	13	1	0	0	0	0	1	0	0	0	7879	652	23	1	1053	1	ITFG2	12	2932026	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10		2932026	130919869	108	1162										
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14578068	14578068	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	atgaaacttctgcagatcttGtagaaacgattaatgaaaat	7	5	2	4			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:14578068G>A	ENST00000540793.1	+	1	1374	c.1219G>A	c.(1219-1221)Gta>Ata	p.V407I	ATF7IP_ENST00000261168.4_Missense_Mutation_p.V407I|ATF7IP_ENST00000543189.1_Missense_Mutation_p.V407I|ATF7IP_ENST00000544627.1_Missense_Mutation_p.V415I|ATF7IP_ENST00000536444.1_Missense_Mutation_p.V407I|ATF7IP_ENST00000541654.1_3'UTR			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	407	Glu-rich.				DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						TGCAGATCTTGTAGAAACGAT	0.328																																					p.V407I		Atlas-SNP	.											.	ATF7IP	136	.	0			c.G1219A						.						56	59	58					12																	14578068		2203	4300	6503	SO:0001583	missense	55729	exon2			GATCTTGTAGAAA	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.1219G>A	chr12.hg19:g.14578068G>A	ENSP00000444589:p.Val407Ile	105.0	0.0		110.0	16.0	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	hg19	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	G	4.125	0.021496	0.08006	.	.	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000396279;ENST00000540793	T;T;T;T;T;T	0.24538	2.18;2.18;2.18;2.17;1.85;2.18	5.36	-4.75	0.03239	.	1.318910	0.05130	N	0.492347	T	0.17323	0.0416	L	0.44542	1.39	0.09310	N	1	B;B;B;B;B;B;B	0.16802	0.019;0.004;0.0;0.0;0.0;0.001;0.002	B;B;B;B;B;B;B	0.12837	0.008;0.003;0.0;0.001;0.001;0.002;0.002	T	0.27905	-1.0060	10	0.27785	T	0.31	0.5134	3.5649	0.07896	0.4759:0.2744:0.1556:0.0942	.	415;407;415;407;407;407;18	B4E2A2;B4DRL6;F5GX74;G3V1U0;Q6VMQ6;Q6VMQ6-2;B3KQF8	.;.;.;.;MCAF1_HUMAN;.;.	I	407;407;407;415;407;407	ENSP00000261168:V407I;ENSP00000443179:V407I;ENSP00000445955:V407I;ENSP00000440440:V415I;ENSP00000379575:V407I;ENSP00000444589:V407I	ENSP00000261168:V407I	V	+	1	0	ATF7IP	14469335	0.000000	0.05858	0.000000	0.03702	0.295000	0.27426	-0.961000	0.03845	-0.601000	0.05783	0.591000	0.81541	GTA	.	.		0.328	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		A	14578068	G	A	14578068	3	1	13	1	0	0	0	0	1	0	0	0	1087	1377	48	3	1221	3	ATF7IP	12	14578068	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	11646042	14578068	119273827	109	1163										
FGD4	121512	hgsc.bcm.edu	37	chr12	32729344	32729344	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgtctcaaaagaaaaacccaGtaaggtatcagatctcatca	6	9	4	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:32729344G>C	ENST00000427716.2	+	3	477	c.53G>C	c.(52-54)aGt>aCt	p.S18T	FGD4_ENST00000472289.1_Missense_Mutation_p.S18T|FGD4_ENST00000534526.2_Missense_Mutation_p.S155T|FGD4_ENST00000266482.3_5'UTR|FGD4_ENST00000546442.1_Intron|FGD4_ENST00000531134.1_Missense_Mutation_p.S103T|FGD4_ENST00000473513.1_3'UTR|FGD4_ENST00000525053.1_Missense_Mutation_p.S130T	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	18	Actin filament-binding. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					GAAAAACCCAGTAAGGTATCA	0.418																																					p.S18T		Atlas-SNP	.											.	FGD4	86	.	0			c.G53C						.						94	90	91					12																	32729344		2203	4300	6503	SO:0001583	missense	121512	exon3			AACCCAGTAAGGT	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.53G>C	chr12.hg19:g.32729344G>C	ENSP00000394487:p.Ser18Thr	181.0	0.0		121.0	19.0	NM_139241	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	hg19	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.664198	0.29604	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000472289;ENST00000427716;ENST00000525053	T;T;T;T	0.72942	-0.7;-0.65;-0.7;-0.66	5.51	4.62	0.57501	.	0.000000	0.64402	D	0.000018	T	0.71239	0.3316	N	0.19112	0.55	0.80722	D	1	B;B;B;D	0.89917	0.077;0.077;0.016;1.0	B;B;B;D	0.72982	0.015;0.015;0.015;0.979	T	0.73965	-0.3816	10	0.72032	D	0.01	-10.954	9.7655	0.40559	0.0735:0.1402:0.7863:0.0	.	130;103;18;18	E9PJX4;B7Z493;Q96M96;E9PQT1	.;.;FGD4_HUMAN;.	T	155;103;18;18;130	ENSP00000449273:S155T;ENSP00000431323:S103T;ENSP00000394487:S18T;ENSP00000433666:S130T	ENSP00000379089:S18T	S	+	2	0	FGD4	32620611	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.763000	0.38461	1.328000	0.45358	0.591000	0.81541	AGT	.	.		0.418	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		C	32729344	G	C	32729344	3	2	13	1	0	0	0	0	1	0	0	0	5843	1029	36	4	55	4	FGD4	12	32729344	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	18151276	32729344	101122551	110	1164										
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50189083	50189083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggactgggccgtggtactacCacagtctgcccagggagggc	16	12	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:50189083C>T	ENST00000335999.6	-	8	2761	c.2560G>A	c.(2560-2562)Ggt>Agt	p.G854S		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	850	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						GTGGTACTACCACAGTCTGCC	0.642																																					p.G854S		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.G2560A						.						89	93	92					12																	50189083		1934	4127	6061	SO:0001583	missense	57701	exon8			TACTACCACAGTC	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.2560G>A	chr12.hg19:g.50189083C>T	ENSP00000337998:p.Gly854Ser	76.0	0.0		46.0	4.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Missense_Mutation	SNP	ENST00000335999.6	hg19	CCDS41781.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.520|4.520	0.096470|0.096470	0.08681|0.08681	.|.	.|.	ENSG00000167566|ENSG00000167566	ENST00000335999;ENST00000354423|ENST00000433948	T|.	0.41758|.	0.99|.	4.5|4.5	1.6|1.6	0.23607|0.23607	.|.	0.161340|.	0.29814|.	N|.	0.011126|.	T|.	0.26412|.	0.0645|.	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	B;B;B|.	0.06786|.	0.0;0.0;0.001|.	B;B;B|.	0.13407|.	0.002;0.001;0.009|.	T|.	0.21999|.	-1.0229|.	10|.	0.15952|.	T|.	0.53|.	-2.1028|-2.1028	3.5867|3.5867	0.07973|0.07973	0.1747:0.5436:0.0:0.2817|0.1747:0.5436:0.0:0.2817	.|.	828;850;850|.	E2QRB5;Q9HCH0;Q9HCH0-2|.	.;NCK5L_HUMAN;.|.	S|X	854;828|568	ENSP00000337998:G854S|.	ENSP00000337998:G854S|.	G|W	-|-	1|2	0|0	NCKAP5L|NCKAP5L	48475350|48475350	0.001000|0.001000	0.12720|0.12720	0.155000|0.155000	0.22561|0.22561	0.780000|0.780000	0.44128|0.44128	0.225000|0.225000	0.17757|0.17757	0.225000|0.225000	0.20959|0.20959	0.561000|0.561000	0.74099|0.74099	GGT|TGG	.	.		0.642	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		T	50189083	C	T	50189083	3	4	13	1	0	0	0	0	1	0	0	0	10233	594	21	3	1468	3	NCKAP5L	12	50189083	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	17459739	50189083	83662812	111	1165										
TARBP2	7786	hgsc.bcm.edu	37	chr12	53895919	53895919	+	5'Flank	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aaagccgagggccaagcccaCcagcctaatttcaccttccg	8	16	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:53895919C>A	ENST00000267079.2	-	0	0				MAP3K12_ENST00000547488.1_5'Flank|TARBP2_ENST00000266987.2_Missense_Mutation_p.H58Q|RP11-793H13.11_ENST00000602306.1_RNA|TARBP2_ENST00000549028.1_3'UTR|TARBP2_ENST00000456234.2_Missense_Mutation_p.H37Q|TARBP2_ENST00000394357.2_Missense_Mutation_p.H37Q|TARBP2_ENST00000552857.1_Intron|MAP3K12_ENST00000547151.1_5'Flank	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12						histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						GCCAAGCCCACCAGCCTAATT	0.602																																					p.H58Q		Atlas-SNP	.											.	TARBP2	35	.	0			c.C174A						.						86	73	78					12																	53895919		2203	4300	6503	SO:0001631	upstream_gene_variant	6895	exon2			AGCCCACCAGCCT	U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854		chr12.hg19:g.53895919C>A	Exception_encountered	127.0	0.0		84.0	18.0	NM_134323	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Missense_Mutation	SNP	ENST00000267079.2	hg19	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278904	0.59758	.	.	ENSG00000139546	ENST00000266987;ENST00000456234;ENST00000549610;ENST00000394357	T;T;T	0.80033	-1.33;-1.33;-1.33	3.95	2.63	0.31362	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.053041	0.64402	D	0.000001	D	0.91277	0.7250	H	0.96576	3.845	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.81914	0.986;0.995;0.992	D	0.89643	0.3864	10	0.87932	D	0	-3.2345	6.7823	0.23652	0.0:0.7193:0.0:0.2807	.	58;58;58	F8VWR8;A8K3X2;Q15633	.;.;TRBP2_HUMAN	Q	58;37;58;37	ENSP00000266987:H58Q;ENSP00000416077:H37Q;ENSP00000377885:H37Q	ENSP00000266987:H58Q	H	+	3	2	TARBP2	52182186	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.796000	0.38794	0.634000	0.30469	0.467000	0.42956	CAC	.	.		0.602	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		A	53895919	C	A	53895919	1	1	13	0	1	0	0	0	0	0	0	0	15571	506	18	3		3	TARBP2	12	53895919	5'Flank	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	3706836	53895919	79955976	112	1166										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58131312	58131312	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ccctcccccggcggcggcggCggtggcggcggcagagaccg	19	17	0	1	rs561812307		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:58131312C>T	ENST00000547588.1	-	1	717	c.718G>A	c.(718-720)Gcc>Acc	p.A240T	AGAP2_ENST00000257897.3_Intron	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	240					axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						gcggcggcggcggtggcggcg	0.706																																					p.A240T		Atlas-SNP	.											AGAP2_ENST00000547588,NS,carcinoma,0,1	AGAP2	167	.	0			c.G718A						.						4	6	5					12																	58131312		1428	3301	4729	SO:0001583	missense	116986	exon1			CGGCGGCGGTGGC	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.718G>A	chr12.hg19:g.58131312C>T	ENSP00000449241:p.Ala240Thr	114.0	1.0		60.0	3.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	hg19	CCDS44932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.24|10.24	1.294811|1.294811	0.23564|0.23564	.|.	.|.	ENSG00000135439|ENSG00000135439	ENST00000547588|ENST00000328568	T|.	0.39997|.	1.05|.	3.81|3.81	-1.14|-1.14	0.09741|0.09741	.|.	1.354790|.	0.05448|.	N|.	0.548952|.	T|T	0.10508|0.10508	0.0257|0.0257	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.14012|.	0.009;0.005|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.24548|0.24548	-1.0157|-1.0157	10|5	0.56958|.	D|.	0.05|.	.|.	0.5619|0.5619	0.00680|0.00680	0.1874:0.3561:0.184:0.2724|0.1874:0.3561:0.184:0.2724	.|.	240;240|.	F8VVT9;Q99490|.	.;AGAP2_HUMAN|.	T|H	240|103	ENSP00000449241:A240T|.	ENSP00000449241:A240T|.	A|R	-|-	1|2	0|0	AGAP2|AGAP2	56417579|56417579	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	0.086000|0.086000	0.14935|0.14935	-0.555000|-0.555000	0.06142|0.06142	0.455000|0.455000	0.32223|0.32223	GCC|CGC	.	.		0.706	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		T	58131312	C	T	58131312	3	4	13	1	0	0	0	0	1	0	0	0	368	768	27	1	2936	1	AGAP2	12	58131312	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	4235393	58131312	75720583	113	1167										
SLC35E3	55508	hgsc.bcm.edu	37	chr12	69145812	69145812	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ttttatctcctaattttcagTgggtaggagccaaacagcat	8	8	2	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:69145812T>C	ENST00000398004.2	+	3	786	c.514T>C	c.(514-516)Tgg>Cgg	p.W172R		NM_018656.2	NP_061126.2	Q7Z769	S35E3_HUMAN	solute carrier family 35, member E3	172						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12	Breast(13;2.31e-06)|Renal(347;0.0684)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00372)			TAATTTTCAGTGGGTAGGAGC	0.433																																					p.W172R		Atlas-SNP	.											.	SLC35E3	23	.	0			c.T514C						.						146	133	137					12																	69145812		1931	4145	6076	SO:0001630	splice_region_variant	55508	exon3			TTTCAGTGGGTAG	AF148713, AY358943	CCDS41808.1	12q15	2014-09-04			ENSG00000175782	ENSG00000175782		"Solute carriers"	20864	protein-coding gene	gene with protein product						12975309	Standard	XM_005269006		Approved	BLOV1	uc001suh.3	Q7Z769	OTTHUMG00000169282	ENST00000398004.2:c.514-1T>C	chr12.hg19:g.69145812T>C		101.0	0.0		66.0	8.0	NM_018656	A8K0T0|Q0P5Y5|Q9P0V1	Missense_Mutation	SNP	ENST00000398004.2	hg19	CCDS41808.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.275390	0.80580	.	.	ENSG00000175782	ENST00000398004	T	0.62788	-0.0	5.59	5.59	0.84812	Domain of unknown function DUF250 (1);	0.114780	0.64402	D	0.000005	T	0.81688	0.4875	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.84423	0.0572	9	.	.	.	-1.6076	16.0729	0.80948	0.0:0.0:0.0:1.0	.	172	Q7Z769	S35E3_HUMAN	R	172	ENSP00000381089:W172R	.	W	+	1	0	SLC35E3	67432079	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	7.586000	0.82596	2.266000	0.75297	0.454000	0.30748	TGG	.	.		0.433	SLC35E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403241.1	NM_018656	Missense_Mutation	C	69145812	T	C	69145812	5	2	13	1	0	0	0	0	0	0	1	0	14601	1710	59	2	524	2	SLC35E3	12	69145812	Splice_Site	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	11014500	69145812	64706083	114	1168										
KCNC2	3747	hgsc.bcm.edu	37	chr12	75601611	75601611	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggcgacggctgcagcttgtcGcccgccgtggtcaagcagtc	15	14	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:75601611G>A	ENST00000549446.1	-	2	833	c.153C>T	c.(151-153)ggC>ggT	p.G51G	KCNC2_ENST00000341669.3_Silent_p.G51G|KCNC2_ENST00000540018.1_Silent_p.G51G|KCNC2_ENST00000393288.2_Silent_p.G51G|KCNC2_ENST00000350228.2_Silent_p.G51G|KCNC2_ENST00000298972.1_Silent_p.G51G|KCNC2_ENST00000550433.1_Silent_p.G51G|KCNC2_ENST00000548513.1_Silent_p.G51G	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	51					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	gcagcTTGTCGCCCGCCGTGG	0.731																																					p.G51G		Atlas-SNP	.											.	KCNC2	239	.	0			c.C153T						.						14	13	13					12																	75601611		1899	3767	5666	SO:0001819	synonymous_variant	3747	exon2			CTTGTCGCCCGCC	AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.153C>T	chr12.hg19:g.75601611G>A		96.0	0.0		47.0	9.0	NM_139137	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Silent	SNP	ENST00000549446.1	hg19	CCDS9007.1																																																																																			.	.		0.731	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		A	75601611	G	A	75601611	2	1	13	1	0	0	0	0	0	0	0	1	8024	1074	38	1		1	KCNC2	12	75601611	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	6455799	75601611	58250284	115	1169										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85546802	85546802	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tttactttttttgtgaaaagAttcctggaaacttaaaatgg	7	4	0	2	rs202153512		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:85546802A>T	ENST00000393217.2	+	21	4481	c.4420A>T	c.(4420-4422)Att>Ttt	p.I1474F		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1474										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		TTGTGAAAAGATTCCTGGAAA	0.294																																					p.I1474F		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A4420T						.						55	53	54					12																	85546802		1791	4046	5837	SO:0001630	splice_region_variant	84125	exon21			GAAAAGATTCCTG	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.4420-1A>T	chr12.hg19:g.85546802A>T		136.0	0.0		220.0	13.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	A	1.256	-0.617269	0.03663	.	.	ENSG00000133640	ENST00000393217	T	0.52526	0.66	5.47	0.239	0.15484	.	.	.	.	.	T	0.18882	0.0453	N	0.03608	-0.345	0.22552	N	0.998994	B	0.02656	0.0	B	0.01281	0.0	T	0.23226	-1.0194	8	.	.	.	.	4.0577	0.09824	0.4164:0.1872:0.0:0.3965	.	1474	Q96JM4	LRIQ1_HUMAN	F	1474	ENSP00000376910:I1474F	.	I	+	1	0	LRRIQ1	84070933	0.539000	0.26402	0.315000	0.25238	0.161000	0.22273	0.675000	0.25232	0.376000	0.24707	0.477000	0.44152	ATT	.	.		0.294	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	Missense_Mutation	T	85546802	A	T	85546802	5	4	13	1	0	0	0	0	0	0	1	0	9038	347	12	4	4502	4	LRRIQ1	12	85546802	Splice_Site	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	9945191	85546802	48305093	116	1170										
APAF1	317	hgsc.bcm.edu	37	chr12	99042536	99042536	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ctgcccttctccatgatggcAttcctgttgtctcttcttcc	6	15	3	1	rs139951279		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:99042536A>G	ENST00000551964.1	+	3	1007	c.271A>G	c.(271-273)Att>Gtt	p.I91V	APAF1_ENST00000550527.1_Missense_Mutation_p.I91V|APAF1_ENST00000359972.2_Missense_Mutation_p.I91V|APAF1_ENST00000357310.1_Missense_Mutation_p.I91V|APAF1_ENST00000547045.1_Missense_Mutation_p.I91V|APAF1_ENST00000547743.1_Missense_Mutation_p.I91V|APAF1_ENST00000333991.1_Missense_Mutation_p.I91V|APAF1_ENST00000552268.1_Missense_Mutation_p.I91V|APAF1_ENST00000339433.3_Missense_Mutation_p.I91V|APAF1_ENST00000549007.1_Missense_Mutation_p.I91V	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	91					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	CCATGATGGCATTCCTGTTGT	0.343																																					p.I91V		Atlas-SNP	.											.	APAF1	111	.	0			c.A271G						.						198	196	197					12																	99042536		2203	4300	6503	SO:0001583	missense	317	exon3			GATGGCATTCCTG	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.271A>G	chr12.hg19:g.99042536A>G	ENSP00000448165:p.Ile91Val	129.0	0.0		101.0	33.0	NM_001160	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.349366	0.41599	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000333991;ENST00000547743;ENST00000552268;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.59772	0.24;0.41;0.32;0.43;0.28;0.32;0.43	5.64	-5.07	0.02938	DEATH-like (2);	0.588283	0.19479	N	0.113265	T	0.35770	0.0943	L	0.29908	0.895	0.09310	N	0.999998	B;B;B;B;B	0.10296	0.0;0.003;0.0;0.0;0.0	B;B;B;B;B	0.19946	0.001;0.027;0.0;0.005;0.0	T	0.16988	-1.0384	10	0.28530	T	0.3	-4.3016	7.7624	0.28959	0.2537:0.4848:0.2616:0.0	.	91;91;91;91;91	O14727-6;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	V	91	ENSP00000448165:I91V;ENSP00000353059:I91V;ENSP00000349862:I91V;ENSP00000341830:I91V;ENSP00000448449:I91V;ENSP00000449791:I91V;ENSP00000448161:I91V	ENSP00000334558:I91V	I	+	1	0	APAF1	97566667	0.011000	0.17503	0.025000	0.17156	0.990000	0.78478	0.228000	0.17814	-0.711000	0.04995	0.533000	0.62120	ATT	.	A|1.000;T|0.000		0.343	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		G	99042536	A	G	99042536	3	3	13	1	0	0	0	0	1	0	0	0	755	217	8	2	277	2	APAF1	12	99042536	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	13495734	99042536	34809359	117	1171										
SLC5A8	160728	hgsc.bcm.edu	37	chr12	101577959	101577959	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acaaaaagtccaggaagtccTggataatcttgcagaatgtc	9	8	1	1	rs367557492		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:101577959T>C	ENST00000536262.2	-	8	1563	c.1005A>G	c.(1003-1005)ccA>ccG	p.P335P		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CAGGAAGTCCTGGATAATCTT	0.358																																					p.P335P	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.A1005G						.	T		0,4406		0,0,2203	79	77	78		1005	-6	0.6	12		78	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC5A8	NM_145913.3		0,1,6502	CC,CT,TT		0.0116,0.0,0.0077		335/611	101577959	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	160728	exon8			AAGTCCTGGATAA	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1005A>G	chr12.hg19:g.101577959T>C		190.0	0.0		203.0	16.0	NM_145913		Silent	SNP	ENST00000536262.2	hg19	CCDS9080.1																																																																																			.	.		0.358	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		C	101577959	T	C	101577959	2	2	13	1	0	0	0	0	0	0	0	1	14686	1567	55	2		2	SLC5A8	12	101577959	Silent	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	2535423	101577959	32273936	118	1172										
GPR109A	338442	hgsc.bcm.edu	37	chr12	123187336	123187336	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ccattctggatcggcatcttCttcttcaggaggtggactgt	11	10	5	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr12:123187336C>T	ENST00000328880.5	-	1	554	c.495G>A	c.(493-495)aaG>aaA	p.K165K	HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	165					negative regulation of lipid catabolic process (GO:0050995)|neutrophil apoptotic process (GO:0001781)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of neutrophil apoptotic process (GO:0033031)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nicotinic acid receptor activity (GO:0070553)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	15					Niacin(DB00627)	TCGGCATCTTCTTCTTCAGGA	0.542																																					p.K165K		Atlas-SNP	.											.	HCAR2	36	.	0			c.G495A						.						107	93	98					12																	123187336		2203	4300	6503	SO:0001819	synonymous_variant	338442	exon1			CATCTTCTTCTTC	AY148884	CCDS9235.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000182782	ENSG00000182782		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	24827	protein-coding gene	gene with protein product	"niacin receptor 1"	609163	"G protein-coupled receptor 109A"	GPR109A		21167710, 12522134, 12646212, 19141678, 18983141, 21454438	Standard	NM_177551		Approved	HCA2, HM74A, PUMAG, Puma-g, NIACR1	uc001ucx.1	Q8TDS4	OTTHUMG00000162722	ENST00000328880.5:c.495G>A	chr12.hg19:g.123187336C>T		66.0	0.0		79.0	7.0	NM_177551	A0PJL5|A7LGG3	Silent	SNP	ENST00000328880.5	hg19	CCDS9235.1																																																																																			.	.		0.542	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551		T	123187336	C	T	123187336	2	4	13	1	0	0	0	0	0	0	0	1	6633	912	32	3		3	GPR109A	12	123187336	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	21609377	123187336	10664559	119	1173										
CCNA1	8900	hgsc.bcm.edu	37	chr13	37011796	37011796	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gaatcaggtgttattctggaTcagaaaatgccttccctcca	8	10	3	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr13:37011796T>C	ENST00000255465.4	+	3	592	c.328T>C	c.(328-330)Tca>Cca	p.S110P	CCNA1_ENST00000463403.1_3'UTR|CCNA1_ENST00000418263.1_Missense_Mutation_p.S109P|CCNA1_ENST00000449823.1_Missense_Mutation_p.S66P|CCNA1_ENST00000440264.1_Missense_Mutation_p.S66P			P78396	CCNA1_HUMAN	cyclin A1	110					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		TTATTCTGGATCAGAAAATGC	0.468																																					p.S110P		Atlas-SNP	.											.	CCNA1	91	.	0			c.T328C						.						106	115	112					13																	37011796		2203	4300	6503	SO:0001583	missense	8900	exon3			TCTGGATCAGAAA	U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.328T>C	chr13.hg19:g.37011796T>C	ENSP00000255465:p.Ser110Pro	128.0	0.0		133.0	18.0	NM_003914	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Missense_Mutation	SNP	ENST00000255465.4	hg19	CCDS9357.1	.	.	.	.	.	.	.	.	.	.	T	12.76	2.035451	0.35893	.	.	ENSG00000133101	ENST00000440264;ENST00000449823;ENST00000418263;ENST00000255465	T;T;T;T	0.16196	2.4;2.4;2.36;2.36	5.47	3.07	0.35406	.	0.885835	0.10148	N	0.710001	T	0.16471	0.0396	M	0.62723	1.935	0.30723	N	0.748076	B;B	0.16166	0.003;0.016	B;B	0.11329	0.005;0.006	T	0.30504	-0.9976	10	0.45353	T	0.12	.	1.7545	0.02979	0.135:0.1476:0.1403:0.5772	.	109;110	P78396-2;P78396	.;CCNA1_HUMAN	P	66;66;109;110	ENSP00000400666:S66P;ENSP00000409873:S66P;ENSP00000396479:S109P;ENSP00000255465:S110P	ENSP00000255465:S110P	S	+	1	0	CCNA1	35909796	1.000000	0.71417	0.991000	0.47740	0.917000	0.54804	0.908000	0.28545	0.391000	0.25143	0.374000	0.22700	TCA	.	.		0.468	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914		C	37011796	T	C	37011796	3	2	13	1	0	0	0	0	1	0	0	0	2911	1435	50	2	338	2	CCNA1	13	37011796	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10		37011796	78158082	120	1174										
FREM2	341640	hgsc.bcm.edu	37	chr13	39261494	39261494	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ccgggaccatgcactcagccGggactcccgggttatcctcg	12	16	1	0	rs374997939		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr13:39261494G>C	ENST00000280481.7	+	1	229	c.13G>C	c.(13-15)Ggg>Cgg	p.G5R		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	5					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GCACTCAGCCGGGACTCCCGG	0.662																																					p.G5R		Atlas-SNP	.											.	FREM2	385	.	0			c.G13C						.						16	17	17					13																	39261494		2199	4298	6497	SO:0001583	missense	341640	exon1			TCAGCCGGGACTC	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.13G>C	chr13.hg19:g.39261494G>C	ENSP00000280481:p.Gly5Arg	341.0	0.0		234.0	24.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	5.293	0.239495	0.10023	.	.	ENSG00000150893	ENST00000280481	T	0.18016	2.24	5.29	-1.42	0.08913	.	0.510248	0.17723	N	0.164177	T	0.05960	0.0155	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.24548	-1.0157	10	0.34782	T	0.22	.	2.0579	0.03585	0.2874:0.3276:0.2742:0.1109	.	5	Q5SZK8	FREM2_HUMAN	R	5	ENSP00000280481:G5R	ENSP00000280481:G5R	G	+	1	0	FREM2	38159494	0.001000	0.12720	0.001000	0.08648	0.075000	0.17131	0.082000	0.14847	-0.405000	0.07599	0.655000	0.94253	GGG	.	.		0.662	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39261494	G	C	39261494	3	2	13	1	0	0	0	0	1	0	0	0	6053	1116	39	4	15	4	FREM2	13	39261494	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	2249698	39261494	75908384	121	1175										
COG6	57511	hgsc.bcm.edu	37	chr13	40256306	40256306	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tataatgttaattatttttcAggtgaatgcagaacattgac	7	4	1	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr13:40256306A>T	ENST00000455146.3	+	8	744		c.e8-1		COG6_ENST00000416691.1_Splice_Site|COG6_ENST00000465775.1_Splice_Site	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6						glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		ATTATTTTTCAGGTGAATGCA	0.368																																					.		Atlas-SNP	.											.	COG6	49	.	0			c.695-2A>T						.						61	63	62					13																	40256306		2203	4300	6503	SO:0001630	splice_region_variant	57511	exon8			TTTTTCAGGTGAA	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"Components of oligomeric golgi complex"	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.695-1A>T	chr13.hg19:g.40256306A>T		354.0	0.0		352.0	20.0	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Splice_Site	SNP	ENST00000455146.3	hg19	CCDS9370.1	.	.	.	.	.	.	.	.	.	.	A	18.75	3.690036	0.68271	.	.	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000455146	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0304	0.71701	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COG6	39154306	1.000000	0.71417	0.992000	0.48379	0.790000	0.44656	6.863000	0.75489	2.199000	0.70637	0.533000	0.62120	.	.	.		0.368	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3		Intron	T	40256306	A	T	40256306	5	4	13	1	0	0	0	0	0	0	1	0	3664	202	7	4	723	4	COG6	13	40256306	Splice_Site	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	994812	40256306	74913572	122	1176										
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42263626	42263626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gatcactggaaattttatgaGgtatgctgaactctgtttct	9	6	3	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr13:42263626G>A	ENST00000379310.3	-	34	4063	c.3995C>T	c.(3994-3996)cCt>cTt	p.P1332L	VWA8_ENST00000478987.1_5'UTR	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1332						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										AATTTTATGAGGTATGCTGAA	0.353																																					p.P1332L		Atlas-SNP	.											.	.	.	.	0			c.C3995T						.						89	81	83					13																	42263626		1822	4087	5909	SO:0001583	missense	23078	exon34			TTATGAGGTATGC	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.3995C>T	chr13.hg19:g.42263626G>A	ENSP00000368612:p.Pro1332Leu	22.0	0.0		61.0	5.0	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	hg19	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.031538	0.75504	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000478987	T	0.09350	2.99	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.12860	0.0312	L	0.56769	1.78	0.80722	D	1	P	0.42456	0.78	B	0.34138	0.176	T	0.03524	-1.1028	10	0.42905	T	0.14	.	17.2985	0.87175	0.0:0.0:1.0:0.0	.	1332	A3KMH1	K0564_HUMAN	L	1236;1332;103	ENSP00000368612:P1332L	ENSP00000251030:P1236L	P	-	2	0	KIAA0564	41161626	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.253000	0.78320	2.600000	0.87896	0.650000	0.86243	CCT	.	.		0.353	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		A	42263626	G	A	42263626	3	1	13	1	0	0	0	0	1	0	0	0	8194	1000	35	3	1770	3	KIAA0564	13	42263626	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	2007320	42263626	72906252	123	1177										
PHF11	51131	hgsc.bcm.edu	37	chr13	50097317	50097317	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	attttctctcctagccacccGaaacaatgaaatgtaataca	4	11	1	1	rs368988100		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr13:50097317G>A	ENST00000378319.3	+	7	618	c.577G>A	c.(577-579)Gaa>Aaa	p.E193K	PHF11_ENST00000488958.1_Missense_Mutation_p.E154K|PHF11_ENST00000357596.3_Missense_Mutation_p.E154K|PHF11_ENST00000460489.1_3'UTR	NM_001040443.1	NP_001035533.1	Q9UIL8	PHF11_HUMAN	PHD finger protein 11	193					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(3)|lung(1)	4		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		CTAGCCACCCGAAACAATGAA	0.353																																					p.E193K		Atlas-SNP	.											.	PHF11	20	.	0			c.G577A						.	G	LYS/GLU,LYS/GLU	0,4406		0,0,2203	78	71	74		460,577	0	0	13		74	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PHF11	NM_001040444.1,NM_001040443.1	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	154/293,193/332	50097317	1,13005	2203	4300	6503	SO:0001583	missense	51131	exon7			CCACCCGAAACAA	AB011031	CCDS31975.1, CCDS41887.1	13q14.11	2014-05-20			ENSG00000136147	ENSG00000136147		"Zinc fingers, PHD-type"	17024	protein-coding gene	gene with protein product	"IgE responsiveness (atopic)"	607796				10508479, 15057823	Standard	XM_005266417		Approved	NY-REN-34, BCAP, IGER	uc001vdb.3	Q9UIL8	OTTHUMG00000016916	ENST00000378319.3:c.577G>A	chr13.hg19:g.50097317G>A	ENSP00000367570:p.Glu193Lys	221.0	0.0		223.0	17.0	NM_001040443	Q5W0A4|Q5W0A6|Q9Y5A2	Missense_Mutation	SNP	ENST00000378319.3	hg19	CCDS31975.1	.	.	.	.	.	.	.	.	.	.	G	7.036	0.561595	0.13498	0.0	1.16E-4	ENSG00000136147	ENST00000378319;ENST00000496612;ENST00000357596;ENST00000442195;ENST00000488958	T;T;T;T;T	0.72835	-0.69;-0.27;-0.68;-0.67;-0.68	4.15	0.0112	0.14086	.	1.187720	0.06174	N	0.678183	T	0.52549	0.1741	L	0.28115	0.83	0.09310	N	1	B	0.17268	0.021	B	0.08055	0.003	T	0.25710	-1.0124	10	0.10902	T	0.67	-4.0635	6.6859	0.23144	0.4992:0.0:0.5008:0.0	.	193	Q9UIL8	PHF11_HUMAN	K	193;125;154;154;154	ENSP00000367570:E193K;ENSP00000419229:E125K;ENSP00000350209:E154K;ENSP00000405227:E154K;ENSP00000417539:E154K	ENSP00000350209:E154K	E	+	1	0	PHF11	48995318	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.279000	0.08479	-0.146000	0.11274	0.462000	0.41574	GAA	.	.		0.353	PHF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044915.1	NM_016119		A	50097317	G	A	50097317	3	1	13	1	0	0	0	0	1	0	0	0	11831	1059	37	1	603	1	PHF11	13	50097317	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	7833691	50097317	65072561	124	1178										
NALCN	259232	hgsc.bcm.edu	37	chr13	101755543	101755543	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	caaaaaaatttccttgaagcCgctgaaaagttctcgaacaa	6	9	1	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr13:101755543C>T	ENST00000251127.6	-	26	3118	c.3037G>A	c.(3037-3039)Ggc>Agc	p.G1013S		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1013					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.G1013C(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TCCTTGAAGCCGCTGAAAAGT	0.453																																					p.G1013S		Atlas-SNP	.											NALCN,NS,carcinoma,0,1	NALCN	431	.	1	Substitution - Missense(1)	lung(1)	c.G3037A						.						107	114	112					13																	101755543		2203	4300	6503	SO:0001583	missense	259232	exon26			TGAAGCCGCTGAA	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.3037G>A	chr13.hg19:g.101755543C>T	ENSP00000251127:p.Gly1013Ser	53.0	0.0		94.0	11.0	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.989463	0.93106	.	.	ENSG00000102452	ENST00000251127	D	0.97752	-4.52	5.03	5.03	0.67393	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97084	0.9047	N	0.16201	0.385	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	D	0.98750	1.0720	10	0.62326	D	0.03	.	18.7562	0.91833	0.0:1.0:0.0:0.0	.	1013	Q8IZF0	NALCN_HUMAN	S	1013	ENSP00000251127:G1013S	ENSP00000251127:G1013S	G	-	1	0	NALCN	100553544	1.000000	0.71417	0.978000	0.43139	0.924000	0.55760	7.345000	0.79337	2.488000	0.83962	0.650000	0.86243	GGC	.	.		0.453	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		T	101755543	C	T	101755543	3	4	13	1	0	0	0	0	1	0	0	0	10157	652	23	1	2255	1	NALCN	13	101755543	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	51658226	101755543	13414335	125	1179										
EFNB2	1948	hgsc.bcm.edu	37	chr13	107145464	107145464	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acaccgggtgcccgtagtcgCcgctgaccttctcgtagtga	12	14	1	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr13:107145464C>T	ENST00000245323.4	-	5	1075	c.926G>A	c.(925-927)gGc>gAc	p.G309D		NM_004093.3	NP_004084.1	P52799	EFNB2_HUMAN	ephrin-B2	309					anatomical structure morphogenesis (GO:0009653)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|lymph vessel development (GO:0001945)|negative regulation of keratinocyte proliferation (GO:0010839)|organ morphogenesis (GO:0009887)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|regulation of chemotaxis (GO:0050920)|viral process (GO:0016032)	focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					CCCGTAGTCGCCGCTGACCTT	0.602																																					p.G309D		Atlas-SNP	.											.	EFNB2	39	.	0			c.G926A						.						90	73	79					13																	107145464		2203	4300	6503	SO:0001583	missense	1948	exon5			TAGTCGCCGCTGA	L38734	CCDS9507.1	13q33	2011-03-09			ENSG00000125266	ENSG00000125266		"Ephrins"	3227	protein-coding gene	gene with protein product	"HTK ligand", "ligand of eph-related kinase 5", "eph-related receptor tyrosine kinase ligand 5"	600527		EPLG5		7833926	Standard	NM_004093		Approved	LERK5, Htk-L, HTKL, MGC126226, MGC126227, MGC126228	uc001vqi.3	P52799	OTTHUMG00000017324	ENST00000245323.4:c.926G>A	chr13.hg19:g.107145464C>T	ENSP00000245323:p.Gly309Asp	58.0	0.0		43.0	7.0	NM_004093	Q5JV56	Missense_Mutation	SNP	ENST00000245323.4	hg19	CCDS9507.1	.	.	.	.	.	.	.	.	.	.	C	35	5.465393	0.96257	.	.	ENSG00000125266	ENST00000245323	D	0.94092	-3.35	5.81	5.81	0.92471	.	0.044394	0.85682	D	0.000000	D	0.96574	0.8882	M	0.71206	2.165	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.96537	0.9397	10	0.87932	D	0	.	20.0826	0.97783	0.0:1.0:0.0:0.0	.	309	P52799	EFNB2_HUMAN	D	309	ENSP00000245323:G309D	ENSP00000245323:G309D	G	-	2	0	EFNB2	105943465	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.755000	0.85180	2.746000	0.94184	0.655000	0.94253	GGC	.	.		0.602	EFNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045733.4	NM_004093		T	107145464	C	T	107145464	3	4	13	1	0	0	0	0	1	0	0	0	4958	739	26	3	79	3	EFNB2	13	107145464	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	5389921	107145464	8024414	126	1180										
RIPK3	11035	hgsc.bcm.edu	37	chr14	24808688	24808688	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tacgatcttgaccgccacatCgtagccccacttcctatgtt	6	15	1	1	rs571257852		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr14:24808688C>T	ENST00000216274.5	-	2	354	c.136G>A	c.(136-138)Gat>Aat	p.D46N	RIPK3_ENST00000554338.1_5'UTR|RP11-934B9.3_ENST00000555591.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	46	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		ACCGCCACATCGTAGCCCCAC	0.612													C|||	1	0.000199681	0	0	5008	,	,		15851	0		0	False		,,,				2504	0.001				p.D46N	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											RIPK3,NS,carcinoma,0,1	RIPK3	43	.	0			c.G136A						.						124	125	125					14																	24808688		2203	4300	6503	SO:0001583	missense	11035	exon2			CCACATCGTAGCC	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.136G>A	chr14.hg19:g.24808688C>T	ENSP00000216274:p.Asp46Asn	122.0	0.0		80.0	21.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	hg19	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.321257	0.41096	.	.	ENSG00000129465	ENST00000216274	T	0.64618	-0.11	4.85	4.85	0.62838	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.433153	0.19700	N	0.108043	T	0.51432	0.1674	L	0.33093	0.98	0.23572	N	0.997389	P;P	0.49090	0.919;0.668	B;B	0.40825	0.341;0.082	T	0.53613	-0.8414	10	0.56958	D	0.05	-7.4261	13.339	0.60535	0.0:1.0:0.0:0.0	.	46;46	B4DJZ5;Q9Y572	.;RIPK3_HUMAN	N	46	ENSP00000216274:D46N	ENSP00000216274:D46N	D	-	1	0	RIPK3	23878528	0.009000	0.17119	0.381000	0.26106	0.233000	0.25261	0.888000	0.28268	2.518000	0.84900	0.561000	0.74099	GAT	.	.		0.612	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		T	24808688	C	T	24808688	3	4	13	1	0	0	0	0	1	0	0	0	13397	884	31	1	1456	1	RIPK3	14	24808688	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10		24808688	82540852	127	1181										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42355944	42355944	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tcttgcaaccctttgtgccaAgaaagggcttttatttgttc	8	9	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr14:42355944A>T	ENST00000298119.4	+	3	1305	c.116A>T	c.(115-117)aAg>aTg	p.K39M	LRFN5_ENST00000554171.1_Missense_Mutation_p.K39M|LRFN5_ENST00000554120.1_Missense_Mutation_p.K39M	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	39	LRRNT.					integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		CTTTGTGCCAAGAAAGGGCTT	0.393										HNSCC(30;0.082)																											p.K39M		Atlas-SNP	.											.	LRFN5	269	.	0			c.A116T						.						75	67	70					14																	42355944		2203	4300	6503	SO:0001583	missense	145581	exon3			GTGCCAAGAAAGG	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.116A>T	chr14.hg19:g.42355944A>T	ENSP00000298119:p.Lys39Met	163.0	0.0		151.0	22.0	NM_152447	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	hg19	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	A	17.26	3.344562	0.61073	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.53640	0.61;0.61;0.61	5.56	5.56	0.83823	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.64402	D	0.000013	T	0.66036	0.2749	M	0.71581	2.175	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.67382	0.951;0.94	T	0.69829	-0.5039	10	0.72032	D	0.01	.	13.6661	0.62396	1.0:0.0:0.0:0.0	.	39;39	G3V364;Q96NI6	.;LRFN5_HUMAN	M	39	ENSP00000298119:K39M;ENSP00000451897:K39M;ENSP00000451067:K39M	ENSP00000298119:K39M	K	+	2	0	LRFN5	41425694	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.098000	0.63641	0.528000	0.53228	AAG	.	.		0.393	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		T	42355944	A	T	42355944	3	4	13	1	0	0	0	0	1	0	0	0	8950	72	3	4	118	4	LRFN5	14	42355944	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	17547256	42355944	64993596	128	1182										
FAM179B	23116	hgsc.bcm.edu	37	chr14	45535866	45535866	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	agtaccttaaactcataactGgcttattaaatgcaaaagac	5	8	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr14:45535866G>T	ENST00000361577.3	+	16	4700	c.4486G>T	c.(4486-4488)Ggc>Tgc	p.G1496C	FAM179B_ENST00000361462.2_Missense_Mutation_p.G1549C|FAM179B_ENST00000382233.2_3'UTR	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1496										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						ACTCATAACTGGCTTATTAAA	0.353																																					p.G1496C		Atlas-SNP	.											.	FAM179B	115	.	0			c.G4486T						.						119	119	119					14																	45535866		2203	4300	6503	SO:0001583	missense	23116	exon16			ATAACTGGCTTAT	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.4486G>T	chr14.hg19:g.45535866G>T	ENSP00000355045:p.Gly1496Cys	82.0	0.0		87.0	8.0	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	G	17.96	3.517018	0.64634	.	.	ENSG00000198718	ENST00000361577;ENST00000361462	T;T	0.19250	2.16;2.16	5.59	1.79	0.24919	Armadillo-like helical (1);Armadillo-type fold (1);	0.402536	0.30401	N	0.009714	T	0.31263	0.0791	L	0.56769	1.78	0.80722	D	1	P;D	0.54207	0.877;0.965	P;P	0.55455	0.605;0.776	T	0.02075	-1.1218	10	0.72032	D	0.01	-2.9216	8.7175	0.34421	0.3721:0.0:0.6279:0.0	.	1549;1496	G3XAE9;Q9Y4F4	.;F179B_HUMAN	C	1496;1549	ENSP00000355045:G1496C;ENSP00000354917:G1549C	ENSP00000354917:G1549C	G	+	1	0	FAM179B	44605616	0.998000	0.40836	0.873000	0.34254	0.985000	0.73830	0.522000	0.22909	0.063000	0.16370	0.561000	0.74099	GGC	.	.		0.353	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		T	45535866	G	T	45535866	3	4	13	1	0	0	0	0	1	0	0	0	5511	1348	47	3	4548	3	FAM179B	14	45535866	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	3179922	45535866	61813674	129	1183										
SNURF	8926	hgsc.bcm.edu	37	chr15	25213176	25213176	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tcttagctgagacaccaagaGgtggttaaagccatattgga	11	7	1	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr15:25213176G>C	ENST00000577949.1	+	3	271	c.208G>C	c.(208-210)Ggt>Cgt	p.G70R	SNRPN_ENST00000554227.2_5'UTR|SNRPN_ENST00000400100.1_5'UTR|SNRPN_ENST00000400098.1_5'UTR|SNURF_ENST00000551312.2_Missense_Mutation_p.G70R|SNRPN_ENST00000577565.1_5'UTR|SNRPN_ENST00000553597.1_3'UTR|SNRPN_ENST00000400097.1_5'UTR|SNURF_ENST00000338094.6_Missense_Mutation_p.G70R|SNURF_ENST00000338327.4_Missense_Mutation_p.G70R|SNRPN_ENST00000390687.4_5'UTR|SNRPN_ENST00000346403.6_5'UTR			Q9Y675	SNURF_HUMAN	SNRPN upstream reading frame	70						nucleus (GO:0005634)				breast(2)|large_intestine(2)|lung(1)	5		all_cancers(20;1.4e-21)|Breast(32;0.000625)		all cancers(64;3.48e-07)|Epithelial(43;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0142)		GACACCAAGAGGTGGTTAAAG	0.453																																					p.G70R		Atlas-SNP	.											.	SNURF	17	.	0			c.G208C						.						105	93	97					15																	25213176		2203	4300	6503	SO:0001583	missense	8926	exon3			CCAAGAGGTGGTT		CCDS10016.1	15q11.2	2013-08-27			ENSG00000214265	ENSG00000214265			11171	protein-coding gene	gene with protein product						10318933	Standard	NM_022804		Approved		uc001ywu.3	Q9Y675	OTTHUMG00000129181	ENST00000577949.1:c.208G>C	chr15.hg19:g.25213176G>C	ENSP00000463201:p.Gly70Arg	67.0	0.0		78.0	22.0	NM_005678	A6NCW2	Missense_Mutation	SNP	ENST00000577949.1	hg19	CCDS10016.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476122	0.44044	.	.	ENSG00000214265	ENST00000338094;ENST00000338327	.	.	.	3.52	3.52	0.40303	.	.	.	.	.	T	0.68393	0.2996	.	.	.	0.32900	D	0.513065	D	0.76494	0.999	D	0.81914	0.995	T	0.74456	-0.3659	7	0.56958	D	0.05	-1.2974	10.871	0.46883	0.0:0.0:1.0:0.0	.	70	Q9Y675	SNURF_HUMAN	R	70	.	ENSP00000336543:G70R	G	+	1	0	SNURF	22764269	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.955000	0.49121	2.253000	0.74438	0.655000	0.94253	GGT	.	.		0.453	SNURF-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446300.1	NM_005678		C	25213176	G	C	25213176	3	2	13	1	0	0	0	0	1	0	0	0	14893	1000	35	4	218	4	SNURF	15	25213176	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10		25213176	77318216	130	1184										
BTBD1	53339	hgsc.bcm.edu	37	chr15	83686886	83686886	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgccattattattgccagggGaactaaaaaagaaaaaaaca	7	6	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr15:83686886G>C	ENST00000261721.4	-	8	1584	c.1382C>G	c.(1381-1383)tCc>tGc	p.S461C	RP11-382A20.5_ENST00000566841.1_RNA|RP11-382A20.7_ENST00000570202.1_RNA|BTBD1_ENST00000379403.2_3'UTR	NM_001011885.1|NM_025238.3	NP_001011885.1|NP_079514.1	Q9H0C5	BTBD1_HUMAN	BTB (POZ) domain containing 1	461					protein ubiquitination (GO:0016567)|regulation of protein binding (GO:0043393)	cytoplasmic mRNA processing body (GO:0000932)|protein complex (GO:0043234)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	10				all cancers(203;0.000186)		ATTGCCAGGGGAACTAAAAAA	0.343																																					p.S461C		Atlas-SNP	.											.	BTBD1	32	.	0			c.C1382G						.						58	63	61					15																	83686886		2203	4299	6502	SO:0001583	missense	53339	exon8			CCAGGGGAACTAA	AF355402	CCDS10322.1, CCDS32313.1	15q24	2013-01-08			ENSG00000064726	ENSG00000064726		"BTB/POZ domain containing"	1120	protein-coding gene	gene with protein product		608530					Standard	XM_006720573		Approved		uc002bjn.3	Q9H0C5	OTTHUMG00000147364	ENST00000261721.4:c.1382C>G	chr15.hg19:g.83686886G>C	ENSP00000261721:p.Ser461Cys	207.0	0.0		190.0	12.0	NM_025238	A6NMI8|Q9BX71|Q9NWN4	Missense_Mutation	SNP	ENST00000261721.4	hg19	CCDS10322.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.684081	0.68157	.	.	ENSG00000064726	ENST00000261721	T	0.80123	-1.34	5.95	5.95	0.96441	PHR (1);	0.121135	0.64402	D	0.000017	D	0.83078	0.5176	M	0.75884	2.315	0.80722	D	1	B	0.17038	0.02	B	0.21546	0.035	T	0.78937	-0.2007	10	0.87932	D	0	-20.0928	20.3931	0.98965	0.0:0.0:1.0:0.0	.	461	Q9H0C5	BTBD1_HUMAN	C	461	ENSP00000261721:S461C	ENSP00000261721:S461C	S	-	2	0	BTBD1	81477890	1.000000	0.71417	0.989000	0.46669	0.976000	0.68499	9.755000	0.98912	2.824000	0.97209	0.655000	0.94253	TCC	.	.		0.343	BTBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304008.1			C	83686886	G	C	83686886	3	2	13	1	0	0	0	0	1	0	0	0	1539	1174	41	4	70	4	BTBD1	15	83686886	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	58473710	83686886	18844506	131	1185										
POLG	5428	hgsc.bcm.edu	37	chr15	89867412	89867412	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ctcctggggcatcagctgctGcttcccctgttcgagacagt	11	14	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr15:89867412G>A	ENST00000268124.5	-	11	2329	c.1996C>T	c.(1996-1998)Cag>Tag	p.Q666*	POLG_ENST00000442287.2_Nonsense_Mutation_p.Q666*	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	666					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			ATCAGCTGCTGCTTCCCCTGT	0.597								DNA polymerases (catalytic subunits)																													p.Q666X	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.C1996T						.						67	60	62					15																	89867412		2200	4299	6499	SO:0001587	stop_gained	5428	exon11			GCTGCTGCTTCCC	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"DNA polymerases"	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.1996C>T	chr15.hg19:g.89867412G>A	ENSP00000268124:p.Gln666*	44.0	0.0		33.0	13.0	NM_002693	Q8NFM2|Q92515	Nonsense_Mutation	SNP	ENST00000268124.5	hg19	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	G	42	9.297219	0.99128	.	.	ENSG00000140521	ENST00000268124;ENST00000442287;ENST00000526314	.	.	.	5.13	4.15	0.48705	.	0.309685	0.33309	N	0.005044	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-9.133	14.0226	0.64565	0.0:0.2965:0.7035:0.0	.	.	.	.	X	666;666;122	.	ENSP00000268124:Q666X	Q	-	1	0	POLG	87668416	1.000000	0.71417	0.993000	0.49108	0.886000	0.51366	3.245000	0.51407	2.384000	0.81235	0.491000	0.48974	CAG	.	.		0.597	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		A	89867412	G	A	89867412	4	1	13	1	0	0	0	0	0	1	0	0	12209	1328	46	3	1775	3	POLG	15	89867412	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	6180526	89867412	12663980	132	1186										
IDH2	3418	hgsc.bcm.edu	37	chr15	90628312	90628313	+	Frame_Shift_Ins	INS	-	-	G													0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aagatgctggcgatggggttINSggtgctggtgggccggccct					rs202014285		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr15:90628312_90628313insG	ENST00000330062.3	-	9	1211_1212	c.1098_1099insC	c.(1096-1101)accaacfs	p.N367fs	IDH2_ENST00000539790.1_Frame_Shift_Ins_p.N237fs|IDH2_ENST00000540499.2_Frame_Shift_Ins_p.N315fs|IDH2_ENST00000559482.1_Frame_Shift_Ins_p.N258fs|RP11-617F23.1_ENST00000558334.1_RNA	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	367					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			GCGATGGGGTTGGTGCTGGTGG	0.663			M		GBM																																p.N367fs		Atlas-INDEL	.		Dom	yes		15	15q26.1	3418	"socitrate dehydrogenase 2 (NADP+), mitochondrial "		M	.	IDH2	1372	.	0			c.1099_1100insC						.																																			SO:0001589	frameshift_variant	3418	exon9			.		CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.1099dupC	chr15.hg19:g.90628314_90628314dupG	ENSP00000331897:p.Asn367fs	77.0	0.0		43.0	12.0	NM_002168	B2R6L6|B4DFL2|Q96GT3	Frame_Shift_Ins	INS	ENST00000330062.3	hg19	CCDS10359.1																																																																																			.	.		0.663	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			G	90628313	-	G	90628312	7	5	13	1	0	1	1	0	0	0	0	0	7504	1812	63	0	271	0	IDH2	15	90628312	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H3-01A-11D-A382-10	760900	90628312	11903080	133	1187										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	90986673	90986673	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gtttatgaggagctgctcacGcaagctgaaattcaaggcaa	11	8	2	2	rs375134287		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr15:90986673G>A	ENST00000268182.5	+	9	1000	c.876G>A	c.(874-876)acG>acA	p.T292T	IQGAP1_ENST00000560738.1_Intron	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	292					cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AGCTGCTCACGCAAGCTGAAA	0.358																																					p.T292T		Atlas-SNP	.											.	IQGAP1	140	.	0			c.G876A						.	G		0,4396		0,0,2198	87	84	85		876	-2.8	1	15		85	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	IQGAP1	NM_003870.3		0,1,6495	AA,AG,GG		0.0116,0.0,0.0077		292/1658	90986673	1,12991	2198	4298	6496	SO:0001819	synonymous_variant	8826	exon9			GCTCACGCAAGCT	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.876G>A	chr15.hg19:g.90986673G>A		177.0	0.0		244.0	53.0	NM_003870	A7MBM3	Silent	SNP	ENST00000268182.5	hg19	CCDS10362.1																																																																																			.	.		0.358	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		A	90986673	G	A	90986673	2	1	13	1	0	0	0	0	0	0	0	1	7823	1074	38	1		1	IQGAP1	15	90986673	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	358361	90986673	11544719	134	1188										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99434825	99434825	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	atccacgacggcgagtgcatGcaggagtgcccctcgggctt	14	13	0	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr15:99434825G>A	ENST00000268035.6	+	3	1523	c.912G>A	c.(910-912)atG>atA	p.M304I	IGF1R_ENST00000560432.1_3'UTR|RP11-654A16.1_ENST00000558736.1_RNA|IGF1R_ENST00000558762.1_Missense_Mutation_p.M304I	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	304					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GCGAGTGCATGCAGGAGTGCC	0.662																																					p.M304I		Atlas-SNP	.											.	IGF1R	147	.	0			c.G912A						.						44	41	42					15																	99434825		2197	4297	6494	SO:0001583	missense	3480	exon3			GTGCATGCAGGAG	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.912G>A	chr15.hg19:g.99434825G>A	ENSP00000268035:p.Met304Ile	1200.0	1.0		874.0	225.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.446814	0.63178	.	.	ENSG00000140443	ENST00000268035	D	0.97186	-4.28	5.01	5.01	0.66863	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.087654	0.49916	D	0.000128	D	0.92951	0.7757	L	0.35793	1.09	0.58432	D	0.999998	B;B	0.19935	0.04;0.002	B;B	0.20577	0.03;0.003	D	0.87913	0.2698	10	0.02654	T	1	.	13.638	0.62233	0.0:0.0:0.8451:0.1549	.	304;304	C9J5X1;P08069	.;IGF1R_HUMAN	I	304	ENSP00000268035:M304I	ENSP00000268035:M304I	M	+	3	0	IGF1R	97252348	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.440000	0.66563	2.477000	0.83638	0.555000	0.69702	ATG	.	.		0.662	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99434825	G	A	99434825	3	1	13	1	0	0	0	0	1	0	0	0	7580	1319	46	3	922	3	IGF1R	15	99434825	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	8448152	99434825	3096567	135	1189										
FBXL16	146330	hgsc.bcm.edu	37	chr16	744414	744414	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	acagcccggtggtggtgagcAgcgggcagcctgcggcgggg	21	11	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr16:744414A>C	ENST00000397621.1	-	6	1632	c.1301T>G	c.(1300-1302)cTg>cGg	p.L434R	FBXL16_ENST00000562585.1_5'Flank|LA16c-313D11.12_ENST00000566927.1_RNA|FBXL16_ENST00000562563.1_Missense_Mutation_p.L222R|FBXL16_ENST00000324361.5_Missense_Mutation_p.L434R	NM_153350.3	NP_699181.2	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	434										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)	10		Hepatocellular(780;0.0218)				GGTGGTGAGCAGCGGGCAGCC	0.751																																					p.L434R		Atlas-SNP	.											.	FBXL16	25	.	0			c.T1301G						.						5	7	7					16																	744414		2029	4051	6080	SO:0001583	missense	146330	exon6			GTGAGCAGCGGGC	BC036680	CCDS10421.1	16p13.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000127585	ENSG00000127585		"F-boxes / Leucine-rich repeats"	14150	protein-coding gene	gene with protein product		609082	"chromosome 16 open reading frame 22"	C16orf22		11157797	Standard	NM_153350		Approved	MGC33974, Fbl16	uc021taa.1	Q8N461	OTTHUMG00000090420	ENST00000397621.1:c.1301T>G	chr16.hg19:g.744414A>C	ENSP00000380746:p.Leu434Arg	198.0	0.0		113.0	16.0	NM_153350	B3KR59|D3DU60|Q2MHR2|Q96S14|Q9UJI0	Missense_Mutation	SNP	ENST00000397621.1	hg19	CCDS10421.1	.	.	.	.	.	.	.	.	.	.	a	8.900	0.956136	0.18507	.	.	ENSG00000127585	ENST00000397621;ENST00000324361	T;T	0.02323	4.34;4.34	4.49	4.49	0.54785	.	0.204953	0.35040	N	0.003487	T	0.02727	0.0082	N	0.13003	0.285	0.52099	D	0.999946	D	0.54772	0.968	P	0.47251	0.542	T	0.67825	-0.5570	10	0.15499	T	0.54	.	12.8013	0.57588	1.0:0.0:0.0:0.0	.	434	Q8N461	FXL16_HUMAN	R	434	ENSP00000380746:L434R;ENSP00000318674:L434R	ENSP00000318674:L434R	L	-	2	0	FBXL16	684415	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	8.279000	0.89901	1.897000	0.54924	0.450000	0.29827	CTG	.	.		0.751	FBXL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206851.2	NM_153350		C	744414	A	C	744414	3	2	13	1	0	0	0	0	1	0	0	0	5720	188	7	5	142	5	FBXL16	16	744414	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10		744414	89610339	136	1190										
PKD1	5310	hgsc.bcm.edu	37	chr16	2161188	2161188	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	agccatccccgaaggtccagTcgaagaggtagtgggccggg	16	11	0	1	rs559786831	byFrequency	TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr16:2161188T>G	ENST00000262304.4	-	15	4188	c.3980A>C	c.(3979-3981)gAc>gCc	p.D1327A	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.D1327A	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1327	PKD 8. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GAAGGTCCAGTCGAAGAGGTA	0.697																																					p.D1327A		Atlas-SNP	.											.	PKD1	184	.	0			c.A3980C						.						27	29	28					16																	2161188		2187	4295	6482	SO:0001583	missense	5310	exon15			GTCCAGTCGAAGA	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.3980A>C	chr16.hg19:g.2161188T>G	ENSP00000262304:p.Asp1327Ala	83.0	0.0		63.0	9.0	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	hg19	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	t	14.16	2.453112	0.43531	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.66280	-0.2;-0.2	5.72	5.72	0.89469	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (4);	0.434188	0.25954	N	0.027240	T	0.74764	0.3759	M	0.75447	2.3	0.34926	D	0.748896	P;P	0.48640	0.913;0.755	P;P	0.55055	0.767;0.61	T	0.82345	-0.0503	10	0.46703	T	0.11	.	16.0066	0.80367	0.0:0.0:0.0:1.0	.	1327;1327	P98161-3;P98161	.;PKD1_HUMAN	A	1327;1327;1008	ENSP00000262304:D1327A;ENSP00000399501:D1327A	ENSP00000262304:D1327A	D	-	2	0	PKD1	2101189	1.000000	0.71417	0.835000	0.33067	0.058000	0.15608	5.681000	0.68175	2.183000	0.69458	0.451000	0.29950	GAC	.	.		0.697	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			G	2161188	T	G	2161188	3	3	13	1	0	0	0	0	1	0	0	0	11972	1667	58	5	9059	5	PKD1	16	2161188	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	1416774	2161188	88193565	137	1191										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21139036	21139036	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aagagtctggtgtgcctccaGgcagtgtttctggatcacat	12	9	3	1	rs370177232		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr16:21139036G>A	ENST00000261383.3	-	8	1179	c.1180C>T	c.(1180-1182)Ctg>Ttg	p.L394L	CTC-508F8.1_ENST00000575612.1_RNA|DNAH3_ENST00000415178.1_Silent_p.L394L	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	394	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TGTGCCTCCAGGCAGTGTTTC	0.483																																					p.L394L		Atlas-SNP	.											.	DNAH3	1142	.	0			c.C1180T						.						136	126	130					16																	21139036		2201	4300	6501	SO:0001819	synonymous_variant	55567	exon8			CCTCCAGGCAGTG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1180C>T	chr16.hg19:g.21139036G>A		84.0	0.0		67.0	14.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	hg19	CCDS10594.1																																																																																			.	.		0.483	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21139036	G	A	21139036	2	1	13	1	0	0	0	0	0	0	0	1	4605	991	35	3		3	DNAH3	16	21139036	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	18977848	21139036	69215717	138	1192										
ERN2	10595	hgsc.bcm.edu	37	chr16	23706194	23706194	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	agagcaccactctgcccaggCcctggctgtcaggcccggtg	13	16	2	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr16:23706194C>G	ENST00000457008.2	-	16	1837	c.1799G>C	c.(1798-1800)gGc>gCc	p.G600A	ERN2_ENST00000256797.4_Missense_Mutation_p.G700A					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		TCTGCCCAGGCCCTGGCTGTC	0.632																																					p.G700A		Atlas-SNP	.											.	ERN2	131	.	0			c.G2099C						.						39	39	39					16																	23706194		2196	4300	6496	SO:0001583	missense	10595	exon17			CCCAGGCCCTGGC	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"ER to nucleus signalling 2"			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.1799G>C	chr16.hg19:g.23706194C>G	ENSP00000413812:p.Gly600Ala	130.0	0.0		71.0	8.0	NM_033266		Missense_Mutation	SNP	ENST00000457008.2	hg19		.	.	.	.	.	.	.	.	.	.	C	15.17	2.754856	0.49362	.	.	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.56275	0.47;0.47	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.69833	0.3155	L	0.58810	1.83	0.80722	D	1	D;P	0.89917	1.0;0.904	D;P	0.87578	0.998;0.68	T	0.71217	-0.4658	10	0.66056	D	0.02	.	16.9969	0.86370	0.0:1.0:0.0:0.0	.	600;652	E7ETG2;A5YM65	.;.	A	700;600	ENSP00000256797:G700A;ENSP00000413812:G600A	ENSP00000256797:G700A	G	-	2	0	ERN2	23613695	1.000000	0.71417	0.972000	0.41901	0.045000	0.14185	7.384000	0.79751	2.676000	0.91093	0.655000	0.94253	GGC	.	.		0.632	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1			G	23706194	C	G	23706194	3	3	13	1	0	0	0	0	1	0	0	0	5240	739	26	4	849	4	ERN2	16	23706194	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	2567158	23706194	66648559	139	1193										
PFAS	5198	hgsc.bcm.edu	37	chr17	8168227	8168227	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ccacaggtggaccgctctgtGggaggcctggtggcccagca	16	13	1	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr17:8168227G>T	ENST00000314666.6	+	18	2197	c.2064G>T	c.(2062-2064)gtG>gtT	p.V688V	PFAS_ENST00000545834.1_Silent_p.V264V	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	688					'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	ACCGCTCTGTGGGAGGCCTGG	0.642																																					p.V688V		Atlas-SNP	.											.	PFAS	91	.	0			c.G2064T						.						10	10	10					17																	8168227		2182	4287	6469	SO:0001819	synonymous_variant	5198	exon18			CTCTGTGGGAGGC	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"FGAR amidotransferase"	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.2064G>T	chr17.hg19:g.8168227G>T		116.0	0.0		100.0	10.0	NM_012393	A6H8V8	Silent	SNP	ENST00000314666.6	hg19	CCDS11136.1																																																																																			.	.		0.642	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2			T	8168227	G	T	8168227	2	4	13	1	0	0	0	0	0	0	0	1	11763	1335	47	3		3	PFAS	17	8168227	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10		8168227	73026983	140	1194										
SARM1	23098	hgsc.bcm.edu	37	chr17	26708300	26708318	+	Frame_Shift_Del	DEL	TGGGTCAGGCATCTTGGAG	TGGGTCAGGCATCTTGGAG	-													0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cccgtagagctggcgcggagTgggtcaggcatcttggagca					rs71373646|rs386796348|rs71373647|rs111956698|rs71373645	byFrequency	TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	TGGGTCAGGCATCTTGGAG	TGGGTCAGGCATCTTGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr17:26708300_26708318delTGGGTCAGGCATCTTGGAG	ENST00000457710.3	+	2	918_936	c.447_465delTGGGTCAGGCATCTTGGAG	c.(445-465)agtgggtcaggcatcttggagfs	p.SGSGILE149fs	TMEM199_ENST00000509083.1_Frame_Shift_Del_p.WVRHLGA204fs|SARM1_ENST00000379061.4_3'UTR|CTB-96E2.3_ENST00000591482.1_RNA	NM_015077.2	NP_055892.2	Q6SZW1	SARM1_HUMAN	sterile alpha and TIR motif containing 1	183					innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of apoptotic process (GO:0042981)|regulation of dendrite morphogenesis (GO:0048814)|regulation of neuron death (GO:1901214)|response to glucose (GO:0009749)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of mitochondrial outer membrane (GO:0031315)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|synapse (GO:0045202)				cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	12	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		TGGCGCGGAGTGGGTCAGGCATCTTGGAGCACATGTTCA	0.667																																					p.182_188del		Pindel	.											.	SARM1	40	.	0			c.545_563del						.																																			SO:0001589	frameshift_variant	23098	exon3			.	AB011096		17q11	2013-01-10			ENSG00000004139	ENSG00000004139		"Sterile alpha motif (SAM) domain containing"	17074	protein-coding gene	gene with protein product		607732				9628581	Standard	NM_015077		Approved	SARM, SAMD2, KIAA0524	uc010crl.1	Q6SZW1	OTTHUMG00000132499	ENST00000457710.3:c.447_465delTGGGTCAGGCATCTTGGAG	chr17.hg19:g.26708300_26708318delTGGGTCAGGCATCTTGGAG	ENSP00000406738:p.Ser149fs	303.0	0.0		173.0	13.0	NM_015077	O60277|Q7LGG3|Q9NXY5	Frame_Shift_Del	DEL	ENST00000457710.3	hg19																																																																																				.	.		0.667	SARM1-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000255679.3	NM_015077		-	26708318	TGGGTCAGGCATCTTGGAG	-	26708300	7	5	13	1	0	1	0	1	0	0	0	0	13857	1693	59	0	553	0	SARM1	17	26708300	Frame_Shift_Del	DEL	TGGGTCAGGCATCTTGGAG	TCGA-2Y-A9H3-01A-11D-A382-10	18540073	26708300	54486910	141	1195										
GPR179	440435	hgsc.bcm.edu	37	chr17	36491002	36491002	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggcctcggatcaccagaggtGcgtgctggatgcctcgctcc	14	14	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr17:36491002G>T	ENST00000342292.4	-	7	1579	c.1559C>A	c.(1558-1560)gCa>gAa	p.A520E		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	520					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CACCAGAGGTGCGTGCTGGAT	0.662																																					p.A520E		Atlas-SNP	.											.	GPR179	170	.	0			c.C1559A						.						18	22	21					17																	36491002		2144	4242	6386	SO:0001583	missense	440435	exon7			AGAGGTGCGTGCT		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.1559C>A	chr17.hg19:g.36491002G>T	ENSP00000345060:p.Ala520Glu	302.0	0.0		163.0	25.0	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.656990	0.47467	.	.	ENSG00000188888	ENST00000342292	D	0.87729	-2.29	4.24	2.24	0.28232	GPCR, family 3, C-terminal (2);	0.425014	0.21203	N	0.078422	T	0.76779	0.4035	L	0.29908	0.895	0.09310	N	1	B	0.33413	0.411	B	0.37015	0.239	T	0.63084	-0.6716	10	0.27082	T	0.32	0.1157	3.9058	0.09182	0.2952:0.1809:0.5239:0.0	.	520	Q6PRD1	GP179_HUMAN	E	520	ENSP00000345060:A520E	ENSP00000345060:A520E	A	-	2	0	GPR179	33744528	0.293000	0.24371	0.159000	0.22649	0.956000	0.61745	3.509000	0.53386	0.431000	0.26258	0.313000	0.20887	GCA	.	.		0.662	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			T	36491002	G	T	36491002	3	4	13	1	0	0	0	0	1	0	0	0	6682	1319	46	3	5564	3	GPR179	17	36491002	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	9782702	36491002	44704208	142	1196										
BRIP1	83990	hgsc.bcm.edu	37	chr17	59763365	59763365	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgaggtactgtactttaaagAggtcacttcaagtgtagact	10	6	2	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr17:59763365A>C	ENST00000259008.2	-	19	3004	c.2737T>G	c.(2737-2739)Tct>Gct	p.S913A	BRIP1_ENST00000577598.1_Missense_Mutation_p.S913A	NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	913	Interaction with BRCA1.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						TACTTTAAAGAGGTCACTTCA	0.368			"F, N, Mis"			"AML, leukemia, breast"		Involved in tolerance or repair of DNA crosslinks																													p.S913A		Atlas-SNP	.	yes	Rec		"Fanconi anaemia J, breast cancer susceptiblity"	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"L, E"	.	BRIP1	237	.	0			c.T2737G						.						184	183	183					17																	59763365		2203	4300	6503	SO:0001583	missense	83990	exon19			TTAAAGAGGTCAC	AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492		"Fanconi anemia, complementation groups"	20473	protein-coding gene	gene with protein product	"BRCA1/BRCA2-associated helicase 1"	605882				11595410, 11301010	Standard	NM_032043		Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.2737T>G	chr17.hg19:g.59763365A>C	ENSP00000259008:p.Ser913Ala	150.0	0.0		184.0	32.0	NM_032043	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000259008.2	hg19	CCDS11631.1	.	.	.	.	.	.	.	.	.	.	A	3.735	-0.054737	0.07362	.	.	ENSG00000136492	ENST00000259008	T	0.73363	-0.74	5.81	2.96	0.34315	.	0.951389	0.08798	N	0.892176	T	0.57770	0.2076	N	0.22421	0.69	0.09310	N	1	B;B	0.14438	0.002;0.01	B;B	0.09377	0.002;0.004	T	0.41574	-0.9501	9	.	.	.	-0.0019	5.6996	0.17875	0.7544:0.0:0.1052:0.1404	.	913;913	C9JGZ0;Q9BX63	.;FANCJ_HUMAN	A	913	ENSP00000259008:S913A	.	S	-	1	0	BRIP1	57118147	0.012000	0.17670	0.082000	0.20525	0.070000	0.16714	0.184000	0.16939	0.408000	0.25621	0.533000	0.62120	TCT	.	.		0.368	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043		C	59763365	A	C	59763365	3	2	13	1	0	0	0	0	1	0	0	0	1516	304	11	5	1020	5	BRIP1	17	59763365	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	23272363	59763365	21431845	143	1197										
EFCAB3	146779	hgsc.bcm.edu	37	chr17	60464701	60464701	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	attttcacatctttcctcagGgatagagacttaccaggatc	7	10	3	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr17:60464701G>A	ENST00000305286.3	+	3	153	c.75G>A	c.(73-75)agG>agA	p.R25R	EFCAB3_ENST00000450662.2_Splice_Site_p.R77R	NM_173503.3	NP_775774.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	25							calcium ion binding (GO:0005509)			cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			CTTTCCTCAGGGATAGAGACT	0.363																																					p.R77R		Atlas-SNP	.											.	EFCAB3	71	.	0			c.G231A						.						91	83	86					17																	60464701		2203	4300	6503	SO:0001630	splice_region_variant	146779	exon5			CCTCAGGGATAGA	AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"EF-hand domain containing"	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000305286.3:c.75-1G>A	chr17.hg19:g.60464701G>A		97.0	0.0		71.0	5.0	NM_001144933	J3KQM8	Silent	SNP	ENST00000305286.3	hg19	CCDS11632.1																																																																																			.	.		0.363	EFCAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379114.1	NM_173503	Silent	A	60464701	G	A	60464701	5	1	13	1	0	0	0	0	0	0	1	0	4937	1246	43	3	249	3	EFCAB3	17	60464701	Splice_Site	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	701336	60464701	20730509	144	1198										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6949123	6949123	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tccaattttcctggcctggtActgggagggcaggcctccta	12	12	0	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr18:6949123A>G	ENST00000389658.3	-	59	8626	c.8533T>C	c.(8533-8535)Tac>Cac	p.Y2845H		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2845	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CTGGCCTGGTACTGGGAGGGC	0.498																																					p.Y2845H		Atlas-SNP	.											.	LAMA1	458	.	0			c.T8533C						.						93	76	82					18																	6949123		2203	4300	6503	SO:0001583	missense	284217	exon59			CCTGGTACTGGGA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.8533T>C	chr18.hg19:g.6949123A>G	ENSP00000374309:p.Tyr2845His	150.0	0.0		117.0	17.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.409572	0.42715	.	.	ENSG00000101680	ENST00000389658	T	0.75704	-0.96	5.64	5.64	0.86602	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.070739	0.56097	D	0.000022	D	0.83908	0.5356	M	0.74881	2.28	0.47621	D	0.999474	P;P	0.47302	0.889;0.893	P;P	0.60012	0.536;0.867	T	0.82678	-0.0338	10	0.32370	T	0.25	.	15.5204	0.75862	1.0:0.0:0.0:0.0	.	2845;175	P25391;B3KSD8	LAMA1_HUMAN;.	H	2845	ENSP00000374309:Y2845H	ENSP00000374309:Y2845H	Y	-	1	0	LAMA1	6939123	1.000000	0.71417	0.921000	0.36526	0.090000	0.18270	5.962000	0.70364	2.140000	0.66376	0.454000	0.30748	TAC	.	.		0.498	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	6949123	A	G	6949123	3	3	13	1	0	0	0	0	1	0	0	0	8614	391	14	2	714	2	LAMA1	18	6949123	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10		6949123	71128125	145	1199										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31323005	31323005	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aggcccgggcccaacaagctCgggcccagcgagaggctgct	15	15	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr18:31323005C>G	ENST00000269197.5	+	12	3193	c.3193C>G	c.(3193-3195)Cgg>Ggg	p.R1065G		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1065	Ala-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						CCAACAAGCTCGGGCCCAGCG	0.612																																					p.R1065G		Atlas-SNP	.											.	ASXL3	405	.	0			c.C3193G						.						24	26	25					18																	31323005		1871	4084	5955	SO:0001583	missense	80816	exon12			CAAGCTCGGGCCC	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.3193C>G	chr18.hg19:g.31323005C>G	ENSP00000269197:p.Arg1065Gly	66.0	0.0		60.0	9.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.752247	0.49362	.	.	ENSG00000141431	ENST00000269197	T	0.53206	0.63	5.9	2.38	0.29361	.	0.560508	0.16050	N	0.232022	T	0.66025	0.2748	M	0.64404	1.975	0.30137	N	0.804248	D	0.89917	1.0	D	0.85130	0.997	T	0.68405	-0.5417	10	0.87932	D	0	.	16.0065	0.80367	0.4585:0.5415:0.0:0.0	.	1065	Q9C0F0	ASXL3_HUMAN	G	1065	ENSP00000269197:R1065G	ENSP00000269197:R1065G	R	+	1	2	ASXL3	29577003	0.912000	0.30974	0.815000	0.32552	0.991000	0.79684	1.923000	0.40055	0.638000	0.30545	0.650000	0.86243	CGG	.	.		0.612	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			G	31323005	C	G	31323005	3	3	13	1	0	0	0	0	1	0	0	0	1068	875	31	4	3239	4	ASXL3	18	31323005	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	24373882	31323005	46754243	146	1200										
SLC14A2	8170	hgsc.bcm.edu	37	chr18	43248313	43248313	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgaccctccctctcctgccaGgtcggccatcgctgcaggat	10	17	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr18:43248313G>C	ENST00000255226.6	+	15	2723		c.e15-1		SLC14A2_ENST00000589658.1_Splice_Site|SLC14A2_ENST00000586448.1_Splice_Site|RP11-116O18.3_ENST00000589510.1_RNA	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2						transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCTCCTGCCAGGTCGGCCATC	0.562																																					.		Atlas-SNP	.											.	SLC14A2	121	.	0			c.1908-1G>C						.						90	87	88					18																	43248313		2203	4300	6503	SO:0001630	splice_region_variant	8170	exon16			CTGCCAGGTCGGC	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"Solute carriers"	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.1908-1G>C	chr18.hg19:g.43248313G>C		71.0	0.0		66.0	15.0	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Splice_Site	SNP	ENST00000255226.6	hg19	CCDS11924.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.292428	0.40594	.	.	ENSG00000132874	ENST00000255226	.	.	.	4.83	4.83	0.62350	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1372	0.89623	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC14A2	41502311	1.000000	0.71417	0.935000	0.37517	0.129000	0.20672	8.890000	0.92477	2.503000	0.84419	0.563000	0.77884	.	.	.		0.562	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		Intron	C	43248313	G	C	43248313	5	2	13	1	0	0	0	0	0	0	1	0	14412	1014	35	4	1961	4	SLC14A2	18	43248313	Splice_Site	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	11925308	43248313	34828935	147	1201										
SERPINB7	8710	hgsc.bcm.edu	37	chr18	61460472	61460472	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gattatgatctcagcattgtGaatgggctttttgctgaaaa	10	5	1	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr18:61460472G>C	ENST00000398019.2	+	4	622	c.297G>C	c.(295-297)gtG>gtC	p.V99V	SERPINB7_ENST00000336429.2_Silent_p.V99V|SERPINB7_ENST00000540675.1_Silent_p.V82V|SERPINB7_ENST00000546027.1_Silent_p.V99V	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	99					negative regulation of endopeptidase activity (GO:0010951)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of transforming growth factor beta1 production (GO:0032914)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	27		Esophageal squamous(42;0.129)				TCAGCATTGTGAATGGGCTTT	0.348																																					p.V99V		Atlas-SNP	.											.	SERPINB7	66	.	0			c.G297C						.						117	106	110					18																	61460472		2203	4300	6503	SO:0001819	synonymous_variant	8710	exon4			CATTGTGAATGGG	AF027866	CCDS11988.1, CCDS58633.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166396	ENSG00000166396		"Serine (or cysteine) peptidase inhibitors"	13902	protein-coding gene	gene with protein product		603357	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 7"			24172014	Standard	NM_003784		Approved	MEGSIN	uc002ljl.4	O75635	OTTHUMG00000060591	ENST00000398019.2:c.297G>C	chr18.hg19:g.61460472G>C		122.0	0.0		94.0	12.0	NM_001261830	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Silent	SNP	ENST00000398019.2	hg19	CCDS11988.1																																																																																			.	.		0.348	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134007.1	NM_003784		C	61460472	G	C	61460472	2	2	13	1	0	0	0	0	0	0	0	1	14121	1277	45	4		4	SERPINB7	18	61460472	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	18212159	61460472	16616776	148	1202										
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1434870	1434870	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gcagcggctttggacgagggCagaaccacaacgtgcaaggg	16	10	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:1434870C>T	ENST00000233078.4	+	12	1344	c.1183C>T	c.(1183-1185)Cag>Tag	p.Q395*	DAZAP1_ENST00000336761.6_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	395					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGACGAGGGCAGAACCACAA	0.697																																					p.Q395X		Atlas-SNP	.											.	DAZAP1	52	.	0			c.C1183T						.						13	15	14					19																	1434870		2186	4270	6456	SO:0001587	stop_gained	26528	exon12			CGAGGGCAGAACC		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"RNA binding motif (RRM) containing"	2683	protein-coding gene	gene with protein product	"deleted in azoospermia associated protein 1"	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.1183C>T	chr19.hg19:g.1434870C>T	ENSP00000233078:p.Gln395*	129.0	0.0		75.0	13.0	NM_018959	Q96MJ3|Q9NRR9	Nonsense_Mutation	SNP	ENST00000233078.4	hg19	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	C	39	7.307424	0.98200	.	.	ENSG00000071626	ENST00000233078	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	17.8389	0.88709	0.0:1.0:0.0:0.0	.	.	.	.	X	395	.	ENSP00000233078:Q395X	Q	+	1	0	DAZAP1	1385870	1.000000	0.71417	0.985000	0.45067	0.971000	0.66376	7.493000	0.81493	2.454000	0.82982	0.561000	0.74099	CAG	.	.		0.697	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		T	1434870	C	T	1434870	4	4	13	1	0	0	0	0	0	1	0	0	4246	711	25	3	1322	3	DAZAP1	19	1434870	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10		1434870	57694113	149	1203										
ICAM5	7087	hgsc.bcm.edu	37	chr19	10403481	10403481	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cgcagcttcttctgcgacgcCaccctcgatgtggacgggga	13	14	2	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:10403481C>T	ENST00000221980.4	+	5	1218	c.1155C>T	c.(1153-1155)gcC>gcT	p.A385A		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	385	Ig-like C2-type 4.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			TCTGCGACGCCACCCTCGATG	0.622																																					p.A385A		Atlas-SNP	.											.	ICAM5	53	.	0			c.C1155T						.						51	55	54					19																	10403481		2203	4300	6503	SO:0001819	synonymous_variant	7087	exon5			CGACGCCACCCTC	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5348	protein-coding gene	gene with protein product	"telencephalin"	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1155C>T	chr19.hg19:g.10403481C>T		169.0	0.0		97.0	15.0	NM_003259	Q9Y6F3	Silent	SNP	ENST00000221980.4	hg19	CCDS12233.1																																																																																			.	.		0.622	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		T	10403481	C	T	10403481	2	4	13	1	0	0	0	0	0	0	0	1	7492	581	21	3		3	ICAM5	19	10403481	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	8968611	10403481	48725502	150	1204										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10597429	10597429	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tgtcattcgggtcacctcgcTccaggtgtctgtatctgggt	12	11	4	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:10597429T>C	ENST00000171111.5	-	6	2321	c.1774A>G	c.(1774-1776)Agc>Ggc	p.S592G	KEAP1_ENST00000393623.2_Missense_Mutation_p.S592G	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	592					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GTCACCTCGCTCCAGGTGTCT	0.587																																					p.S592G		Atlas-SNP	.											.	KEAP1	182	.	0			c.A1774G						.						110	99	102					19																	10597429		2203	4300	6503	SO:0001583	missense	9817	exon6			CCTCGCTCCAGGT	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1774A>G	chr19.hg19:g.10597429T>C	ENSP00000171111:p.Ser592Gly	99.0	0.0		70.0	11.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	T	9.096	1.002982	0.19121	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.79247	-1.25;-1.25	5.9	4.88	0.63580	Kelch-type beta propeller (1);	0.378221	0.30126	N	0.010347	T	0.79545	0.4464	M	0.87456	2.885	0.35613	D	0.808806	B	0.27971	0.196	B	0.29663	0.105	T	0.81309	-0.0991	10	0.51188	T	0.08	.	9.9583	0.41680	0.0:0.0796:0.0:0.9204	.	592	Q14145	KEAP1_HUMAN	G	592	ENSP00000171111:S592G;ENSP00000377245:S592G	ENSP00000171111:S592G	S	-	1	0	KEAP1	10458429	1.000000	0.71417	0.972000	0.41901	0.012000	0.07955	2.206000	0.42779	1.075000	0.40932	0.454000	0.30748	AGC	.	.		0.587	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		C	10597429	T	C	10597429	3	2	13	1	0	0	0	0	1	0	0	0	8150	1551	54	2	104	2	KEAP1	19	10597429	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	193948	10597429	48531554	151	1205										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17086047	17086047	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aaaggaatcagaaacatcatAatcttccagttcctggaaaa	6	8	3	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:17086047A>C	ENST00000443236.1	-	17	2102	c.2071T>G	c.(2071-2073)Tat>Gat	p.Y691D	CPAMD8_ENST00000388925.4_Missense_Mutation_p.Y430D	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	644						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GAAACATCATAATCTTCCAGT	0.552																																					p.Y691D		Atlas-SNP	.											.	CPAMD8	192	.	0			c.T2071G						.						38	39	39					19																	17086047		2038	4190	6228	SO:0001583	missense	27151	exon17			CATCATAATCTTC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.2071T>G	chr19.hg19:g.17086047A>C	ENSP00000402505:p.Tyr691Asp	206.0	0.0		105.0	12.0	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	hg19	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.40|15.40	2.822480|2.822480	0.50739|0.50739	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440;ENST00000388925	.|T	.|0.64438	.|-0.1	2.78|2.78	2.78|2.78	0.32641|0.32641	.|.	.|0.093976	.|0.45867	.|U	.|0.000322	T|T	0.70360|0.70360	0.3215|0.3215	L|L	0.59436|0.59436	1.845|1.845	0.35766|0.35766	D|D	0.820543|0.820543	.|D	.|0.71674	.|0.998	.|P	.|0.62014	.|0.897	T|T	0.77608|0.77608	-0.2524|-0.2524	5|10	.|0.59425	.|D	.|0.04	.|.	11.0433|11.0433	0.47844|0.47844	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|644	.|Q8IZJ3	.|CPMD8_HUMAN	M|D	701|691;430	.|ENSP00000373577:Y430D	.|ENSP00000291440:Y691D	I|Y	-|-	3|1	3|0	CPAMD8|CPAMD8	16947047|16947047	1.000000|1.000000	0.71417|0.71417	0.120000|0.120000	0.21714|0.21714	0.644000|0.644000	0.38419|0.38419	7.627000|7.627000	0.83176|0.83176	1.059000|1.059000	0.40554|0.40554	0.454000|0.454000	0.30748|0.30748	ATT|TAT	.	.		0.552	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		C	17086047	A	C	17086047	3	2	13	1	0	0	0	0	1	0	0	0	3797	362	13	5	3831	5	CPAMD8	19	17086047	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	6488618	17086047	42042936	152	1206										
SLC7A10	56301	hgsc.bcm.edu	37	chr19	33703796	33703796	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cacccgggaggctgtggtggGggggatgcagttggggaaca	21	7	0	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:33703796G>T	ENST00000253188.4	-	3	615	c.469C>A	c.(469-471)Ccc>Acc	p.P157T		NM_019849.2	NP_062823.1	Q9NS82	AAA1_HUMAN	solute carrier family 7 (neutral amino acid transporter light chain, asc system), member 10	157					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|D-alanine transport (GO:0042941)|D-serine transport (GO:0042942)|ion transport (GO:0006811)|L-serine transport (GO:0015825)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	18	Esophageal squamous(110;0.137)					GCTGTGGTGGGGGGGATGCAG	0.637																																					p.P157T		Atlas-SNP	.											.	SLC7A10	43	.	0			c.C469A						.						61	63	62					19																	33703796		2203	4300	6503	SO:0001583	missense	56301	exon3			TGGTGGGGGGGAT	AB037670	CCDS12431.1	19q13.11	2013-05-28	2011-07-12		ENSG00000130876	ENSG00000130876		"Solute carriers"	11058	protein-coding gene	gene with protein product		607959				10734121, 10863037	Standard	NM_019849		Approved	asc-1	uc002num.2	Q9NS82	OTTHUMG00000180344	ENST00000253188.4:c.469C>A	chr19.hg19:g.33703796G>T	ENSP00000253188:p.Pro157Thr	154.0	0.0		109.0	9.0	NM_019849	B2RE84	Missense_Mutation	SNP	ENST00000253188.4	hg19	CCDS12431.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.108997	0.56398	.	.	ENSG00000130876	ENST00000253188	D	0.88431	-2.38	4.34	4.34	0.51931	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.94719	0.8296	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95619	0.8679	10	0.72032	D	0.01	.	15.8308	0.78749	0.0:0.0:1.0:0.0	.	157	Q9NS82	AAA1_HUMAN	T	157	ENSP00000253188:P157T	ENSP00000253188:P157T	P	-	1	0	SLC7A10	38395636	1.000000	0.71417	0.973000	0.42090	0.152000	0.21847	6.657000	0.74402	1.963000	0.57068	0.462000	0.41574	CCC	.	.		0.637	SLC7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450846.2	NM_019849		T	33703796	G	T	33703796	3	4	13	1	0	0	0	0	1	0	0	0	14708	1232	43	3	1138	3	SLC7A10	19	33703796	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	16617749	33703796	25425187	153	1207										
PDCD2L	84306	hgsc.bcm.edu	37	chr19	34916924	34916924	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tggaatttggaacaattctaGtttacacatgtgagaagagt	10	4	1	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:34916924G>A	ENST00000246535.3	+	7	1023	c.976G>A	c.(976-978)Gtt>Att	p.V326I	UBA2_ENST00000246548.4_5'Flank|UBA2_ENST00000439527.2_5'Flank|PDCD2L_ENST00000587065.2_Missense_Mutation_p.V24I|CTD-2588C8.8_ENST00000592220.1_RNA	NM_032346.1	NP_115722.1	Q9BRP1	PDD2L_HUMAN	programmed cell death 2-like	326					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			AACAATTCTAGTTTACACATG	0.358																																					p.V326I		Atlas-SNP	.											.	PDCD2L	27	.	0			c.G976A						.						99	101	100					19																	34916924		2203	4300	6503	SO:0001583	missense	84306	exon7			ATTCTAGTTTACA	BC006146	CCDS12438.1	19q13.11	2008-02-05				ENSG00000126249			28194	protein-coding gene	gene with protein product		615661				16311922	Standard	NM_032346		Approved	MGC13096	uc002nvj.3	Q9BRP1		ENST00000246535.3:c.976G>A	chr19.hg19:g.34916924G>A	ENSP00000246535:p.Val326Ile	77.0	0.0		67.0	11.0	NM_032346		Missense_Mutation	SNP	ENST00000246535.3	hg19	CCDS12438.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.735870	0.30774	.	.	ENSG00000126249	ENST00000246535	.	.	.	5.56	3.47	0.39725	Programmed cell death protein 2, C-terminal (1);	0.118674	0.56097	N	0.000023	T	0.38348	0.1037	N	0.24115	0.695	0.45250	D	0.998252	B	0.20887	0.049	B	0.25405	0.06	T	0.11641	-1.0579	9	0.19590	T	0.45	-9.8948	7.0095	0.24855	0.2874:0.0:0.7126:0.0	.	326	Q9BRP1	PDD2L_HUMAN	I	326	.	ENSP00000246535:V326I	V	+	1	0	PDCD2L	39608764	0.902000	0.30710	0.997000	0.53966	0.963000	0.63663	1.389000	0.34453	1.160000	0.42584	0.650000	0.86243	GTT	.	.		0.358	PDCD2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459251.3	NM_032346		A	34916924	G	A	34916924	3	1	13	1	0	0	0	0	1	0	0	0	11629	1029	36	3	1002	3	PDCD2L	19	34916924	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	1213128	34916924	24212059	154	1208										
PSG11	5680	hgsc.bcm.edu	37	chr19	43522945	43522945	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggagattcagggtgactgggTcactgcggctggcactccct	15	11	2	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:43522945T>C	ENST00000401740.1	-	3	789	c.686A>G	c.(685-687)gAc>gGc	p.D229G	PSG11_ENST00000403486.1_Missense_Mutation_p.D107G|PSG11_ENST00000320078.7_Missense_Mutation_p.D229G|PSG11_ENST00000306322.7_Missense_Mutation_p.D107G|PSG11_ENST00000595312.1_5'UTR			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	229	Ig-like C2-type 1.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				GGTGACTGGGTCACTGCGGCT	0.522																																					p.D229G		Atlas-SNP	.											.	PSG11	57	.	0			c.A686G						.						198	207	204					19																	43522945		2201	4298	6499	SO:0001583	missense	5680	exon3			ACTGGGTCACTGC	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9516	protein-coding gene	gene with protein product	"pregnancy specific beta-1-glycoprotein 13"	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.686A>G	chr19.hg19:g.43522945T>C	ENSP00000384995:p.Asp229Gly	37.0	0.0		64.0	8.0	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	hg19	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	t	11.27	1.589418	0.28357	.	.	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.00986	5.47;5.47;5.47;5.47	1.13	1.13	0.20643	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.04543	0.0124	M	0.85710	2.77	0.09310	N	1	D;P	0.89917	1.0;0.929	D;P	0.97110	1.0;0.895	T	0.28902	-1.0029	9	0.72032	D	0.01	.	4.3746	0.11263	0.0:0.0:0.0:1.0	.	107;229	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	G	229;107;107;229	ENSP00000319140:D229G;ENSP00000385427:D107G;ENSP00000304913:D107G;ENSP00000384995:D229G	ENSP00000304913:D107G	D	-	2	0	PSG11	48214785	0.128000	0.22383	0.018000	0.16275	0.013000	0.08279	0.650000	0.24858	0.477000	0.27464	0.155000	0.16302	GAC	.	.		0.522	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		C	43522945	T	C	43522945	3	2	13	1	0	0	0	0	1	0	0	0	12666	1667	58	2	333	2	PSG11	19	43522945	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	8606021	43522945	15606038	155	1209										
EXOC3L2	90332	hgsc.bcm.edu	37	chr19	45721458	45721458	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ccctcaggcaggtgcacctgGtaaggctcgtcctgcattct	11	14	2	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:45721458G>A	ENST00000252482.3	-	6	687	c.660C>T	c.(658-660)taC>taT	p.Y220Y	EXOC3L2_ENST00000413988.1_Silent_p.Y220Y			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	220					exocytosis (GO:0006887)	exocyst (GO:0000145)				endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		GGTGCACCTGGTAAGGCTCGT	0.677																																					p.Y220Y		Atlas-SNP	.											.	EXOC3L2	30	.	0			c.C660T						.						11	9	9					19																	45721458		2160	4221	6381	SO:0001819	synonymous_variant	90332	exon7			CACCTGGTAAGGC	AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.660C>T	chr19.hg19:g.45721458G>A		141.0	0.0		107.0	12.0	NM_138568	Q8N9W2|Q96GV2	Silent	SNP	ENST00000252482.3	hg19	CCDS12657.1																																																																																			.	.		0.677	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568		A	45721458	G	A	45721458	2	1	13	1	0	0	0	0	0	0	0	1	5307	1256	44	3		3	EXOC3L2	19	45721458	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	2198513	45721458	13407525	156	1210										
PPP1R13L	10848	hgsc.bcm.edu	37	chr19	45895303	45895303	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggccccccatgacgatggaaGaggcggctgatgatctgctg	15	11	1	4			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:45895303G>A	ENST00000418234.2	-	8	1728	c.1650C>T	c.(1648-1650)ctC>ctT	p.L550L	PPP1R13L_ENST00000360957.5_Silent_p.L550L	NM_001142502.1	NP_001135974.1	Q8WUF5	IASPP_HUMAN	protein phosphatase 1, regulatory subunit 13 like	550	Pro-rich.				apoptotic process (GO:0006915)|cardiac muscle contraction (GO:0060048)|cardiac right ventricle morphogenesis (GO:0003215)|embryonic camera-type eye development (GO:0031076)|hair cycle (GO:0042633)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle tissue development (GO:0003229)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0182)		GACGATGGAAGAGGCGGCTGA	0.692																																					p.L550L	Pancreas(61;1447 1663 31419 50578)	Atlas-SNP	.											.	PPP1R13L	66	.	0			c.C1650T						.						38	46	43					19																	45895303		2203	4299	6502	SO:0001819	synonymous_variant	10848	exon8			ATGGAAGAGGCGG	AF078036	CCDS33050.1	19q13.32	2013-01-10	2011-10-04		ENSG00000104881	ENSG00000104881		"Ankyrin repeat domain containing"	18838	protein-coding gene	gene with protein product		607463	"protein phosphatase 1, regulatory (inhibitor) subunit 13 like"			10336463	Standard	NM_006663		Approved	RAI, IASPP	uc002pbo.3	Q8WUF5		ENST00000418234.2:c.1650C>T	chr19.hg19:g.45895303G>A		214.0	0.0		155.0	9.0	NM_001142502	Q2PNZ9|Q5DU71|Q5I1X4|Q6P1R7|Q6PKF8|Q9Y290	Silent	SNP	ENST00000418234.2	hg19	CCDS33050.1																																																																																			.	.		0.692	PPP1R13L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457586.1	NM_006663		A	45895303	G	A	45895303	2	1	13	1	0	0	0	0	0	0	0	1	12370	929	33	3		3	PPP1R13L	19	45895303	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	173845	45895303	13233680	157	1211										
OPA3	7408	hgsc.bcm.edu	37	chr19	46032653	46032653	+	IGR	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gcaccctcgttcagcggcttGatggcagcggcattgaaacc	12	13	1	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:46032653G>C	ENST00000245932.6	+	0	2305				OPA3_ENST00000323060.3_Missense_Mutation_p.I68M	NM_003370.3	NP_003361.1	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein						actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|neural tube closure (GO:0001843)|positive regulation of actin filament polymerization (GO:0030838)|protein homotetramerization (GO:0051289)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	profilin binding (GO:0005522)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)	18		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		TCAGCGGCTTGATGGCAGCGG	0.602																																					p.I68M		Atlas-SNP	.											.	OPA3	19	.	0			c.C204G						.						81	88	85					19																	46032653		2203	4300	6503	SO:0001628	intergenic_variant	80207	exon2			CGGCTTGATGGCA		CCDS33051.1	19q13.32	2012-02-22			ENSG00000125753	ENSG00000125753			12652	protein-coding gene	gene with protein product		601703				8812448	Standard	XM_005259199		Approved		uc002pcg.3	P50552			chr19.hg19:g.46032653G>C		339.0	0.0		229.0	14.0	NM_001017989	B2RBT9|Q6PIZ1|Q93035	Missense_Mutation	SNP	ENST00000245932.6	hg19	CCDS33051.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.666876	0.47677	.	.	ENSG00000125741	ENST00000323060	D	0.84660	-1.88	3.66	-7.15	0.01521	.	0.436137	0.21993	N	0.066130	D	0.85588	0.5731	.	.	.	0.80722	D	1	P	0.47962	0.903	P	0.55545	0.778	D	0.85229	0.1031	9	0.59425	D	0.04	-23.7572	10.4475	0.44503	0.1355:0.6938:0.1707:0.0	.	68	Q9H6K4-2	.	M	68	ENSP00000319817:I68M	ENSP00000319817:I68M	I	-	3	3	OPA3	50724493	0.804000	0.28969	0.078000	0.20375	0.402000	0.30811	-0.275000	0.08525	-0.879000	0.04002	0.555000	0.69702	ATC	.	.		0.602	VASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459589.1			C	46032653	G	C	46032653	1	2	13	0	1	0	0	0	0	0	0	0	10881	1280	45	4		4	OPA3	19	46032653	IGR	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	137350	46032653	13096330	158	1212										
PPP5C	5536	hgsc.bcm.edu	37	chr19	46893576	46893576	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aagcccatggcctatgccaaCacgctgctgcagctaggaat	10	13	0	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:46893576C>T	ENST00000012443.4	+	13	1576	c.1473C>T	c.(1471-1473)aaC>aaT	p.N491N	PPP5C_ENST00000391919.1_Silent_p.N363N|AC007193.8_ENST00000598616.1_RNA	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	491	Catalytic.				cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		CCTATGCCAACACGCTGCTGC	0.662																																					p.N491N		Atlas-SNP	.											.	PPP5C	44	.	0			c.C1473T						.						89	63	72					19																	46893576		2202	4298	6500	SO:0001819	synonymous_variant	5536	exon13			TGCCAACACGCTG		CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "Tetratricopeptide (TTC) repeat domain containing"	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.1473C>T	chr19.hg19:g.46893576C>T		113.0	0.0		107.0	28.0	NM_006247	Q16722|Q53XV2	Silent	SNP	ENST00000012443.4	hg19	CCDS12684.1																																																																																			.	.		0.662	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		T	46893576	C	T	46893576	2	4	13	1	0	0	0	0	0	0	0	1	12418	477	17	3		3	PPP5C	19	46893576	Silent	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	860923	46893576	12235407	159	1213										
CCDC155	147872	hgsc.bcm.edu	37	chr19	49920284	49920284	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ccttgcaggctgatctccctGtccctctaggagcccctcgc	9	18	2	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:49920284G>C	ENST00000447857.3	+	18	1592	c.1387G>C	c.(1387-1389)Gtc>Ctc	p.V463L		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	463						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						TGATCTCCCTGTCCCTCTAGG	0.587																																					p.V463L		Atlas-SNP	.											.	CCDC155	46	.	0			c.G1387C						.						28	29	29					19																	49920284		1984	4158	6142	SO:0001583	missense	147872	exon18			CTCCCTGTCCCTC		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.1387G>C	chr19.hg19:g.49920284G>C	ENSP00000404220:p.Val463Leu	107.0	0.0		74.0	5.0	NM_144688	Q96MC3	Missense_Mutation	SNP	ENST00000447857.3	hg19	CCDS46140.1	.	.	.	.	.	.	.	.	.	.	a	5.686	0.311173	0.10789	.	.	ENSG00000161609	ENST00000447857	T	0.30981	1.51	2.92	-0.569	0.11756	.	1.269890	0.05402	N	0.540950	T	0.10637	0.0260	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22103	-1.0226	10	0.15952	T	0.53	-22.8556	4.0118	0.09626	0.4385:0.1976:0.3639:0.0	.	463;463	C9JGW3;Q8N6L0	.;CC155_HUMAN	L	463	ENSP00000404220:V463L	ENSP00000404220:V463L	V	+	1	0	CCDC155	54612096	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	-0.047000	0.11963	-0.566000	0.06054	-0.420000	0.06012	GTC	.	.		0.587	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688		C	49920284	G	C	49920284	3	2	13	1	0	0	0	0	1	0	0	0	2790	1377	48	4	1453	4	CCDC155	19	49920284	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	3026708	49920284	9208699	160	1214										
ZNF577	84765	hgsc.bcm.edu	37	chr19	52375853	52375853	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tggggccacattcacttcatTtgtgaggcttattctctgtt	9	9	3	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:52375853T>C	ENST00000301399.5	-	7	1755	c.1390A>G	c.(1390-1392)Aat>Gat	p.N464D	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.N405D|ZNF577_ENST00000451628.2_Missense_Mutation_p.N405D	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	464					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TTCACTTCATTTGTGAGGCTT	0.363																																					p.N464D		Atlas-SNP	.											.	ZNF577	63	.	0			c.A1390G						.						59	57	58					19																	52375853		2203	4300	6503	SO:0001583	missense	84765	exon7			CTTCATTTGTGAG	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"Zinc fingers, C2H2-type", "-"	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1390A>G	chr19.hg19:g.52375853T>C	ENSP00000301399:p.Asn464Asp	52.0	0.0		57.0	15.0	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	hg19	CCDS12842.2	.	.	.	.	.	.	.	.	.	.	.	12.10	1.836364	0.32421	.	.	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.06528	3.29;3.34;3.34;3.29	3.04	3.04	0.35103	.	.	.	.	.	T	0.12603	0.0306	L	0.52573	1.65	0.21445	N	0.999688	D;D	0.76494	0.998;0.999	P;P	0.59948	0.739;0.866	T	0.12708	-1.0537	9	0.12430	T	0.62	.	9.1055	0.36696	0.0:0.0:0.0:1.0	.	464;405	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	D	464;405;405;464	ENSP00000301399:N464D;ENSP00000413476:N405D;ENSP00000389652:N405D;ENSP00000404509:N464D	ENSP00000301399:N464D	N	-	1	0	ZNF577	57067665	0.002000	0.14202	0.063000	0.19743	0.015000	0.08874	0.340000	0.19892	1.369000	0.46134	0.533000	0.62120	AAT	.	.		0.363	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		C	52375853	T	C	52375853	3	2	13	1	0	0	0	0	1	0	0	0	18024	1841	64	2	71	2	ZNF577	19	52375853	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	2455569	52375853	6753130	161	1215										
PPP2R1A	5518	hgsc.bcm.edu	37	chr19	52716305	52716305	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ggtgatgcccactctgcgccAggccgctgaagacaagtcct	12	14	1	3			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:52716305A>T	ENST00000322088.6	+	6	807	c.749A>T	c.(748-750)cAg>cTg	p.Q250L	PPP2R1A_ENST00000462990.1_Missense_Mutation_p.Q71L|PPP2R1A_ENST00000444322.2_Missense_Mutation_p.Q195L	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha	250	PP2A subunit B binding.|Polyoma small and medium T antigens Binding.				apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		ACTCTGCGCCAGGCCGCTGAA	0.632			Mis		clear cell ovarian carcinoma																																p.Q250L		Atlas-SNP	.		Dom?	yes		19	19q13.41	5518	"protein phosphatase 2, regulatory subunit A, alpha"		E	.	PPP2R1A	187	.	0			c.A749T						.						38	36	37					19																	52716305		2203	4300	6503	SO:0001583	missense	5518	exon6			TGCGCCAGGCCGC		CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9302	protein-coding gene	gene with protein product	"protein phosphatase 2A, regulatory subunit A, alpha isoform", "protein phosphatase 2, 65kDa regulatory subunit A"	605983	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform"				Standard	NR_033500		Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.749A>T	chr19.hg19:g.52716305A>T	ENSP00000324804:p.Gln250Leu	69.0	0.0		50.0	26.0	NM_014225	Q13773|Q6ICQ3|Q96DH3	Missense_Mutation	SNP	ENST00000322088.6	hg19	CCDS12849.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.265590	0.59431	.	.	ENSG00000105568	ENST00000423369;ENST00000391791;ENST00000322088;ENST00000444322	T;T	0.06449	3.3;3.3	4.48	4.48	0.54585	Armadillo-like helical (1);Armadillo-type fold (1);	0.106858	0.40302	N	0.001133	T	0.08758	0.0217	L	0.60455	1.87	0.58432	D	0.999999	B;B;B	0.11235	0.004;0.003;0.003	B;B;B	0.09377	0.004;0.001;0.001	T	0.05937	-1.0855	10	0.46703	T	0.11	-19.9349	12.0821	0.53677	1.0:0.0:0.0:0.0	.	195;250;250	F5H3X9;A8K7B7;P30153	.;.;2AAA_HUMAN	L	240;170;250;195	ENSP00000324804:Q250L;ENSP00000415067:Q195L	ENSP00000324804:Q250L	Q	+	2	0	PPP2R1A	57408117	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.949000	0.87791	2.017000	0.59298	0.533000	0.62120	CAG	.	.		0.632	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267967.2	NM_014225		T	52716305	A	T	52716305	3	4	13	1	0	0	0	0	1	0	0	0	12394	188	7	4	771	4	PPP2R1A	19	52716305	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	340452	52716305	6412678	162	1216										
ZNF766	90321	hgsc.bcm.edu	37	chr19	52793824	52793824	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cgaattgcataccttgcacgAcacgagaaagtgcatactgg	10	10	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:52793824A>C	ENST00000439461.1	+	4	823	c.780A>C	c.(778-780)cgA>cgC	p.R260R	CTD-2525I3.5_ENST00000594865.1_RNA|ZNF766_ENST00000359102.4_Silent_p.R275R|ZNF766_ENST00000593612.1_Silent_p.R275R|ZNF766_ENST00000599581.1_3'UTR	NM_001010851.2	NP_001010851.1	Q5HY98	ZN766_HUMAN	zinc finger protein 766	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	17				GBM - Glioblastoma multiforme(134;0.00236)|OV - Ovarian serous cystadenocarcinoma(262;0.00871)		ACCTTGCACGACACGAGAAAG	0.423																																					p.R260R		Atlas-SNP	.											.	ZNF766	45	.	0			c.A780C						.						41	43	42					19																	52793824		2190	4297	6487	SO:0001819	synonymous_variant	90321	exon4			TGCACGACACGAG	AK024074	CCDS46163.1	19q13.33	2013-01-08				ENSG00000196214		"Zinc fingers, C2H2-type", "-"	28063	protein-coding gene	gene with protein product							Standard	XM_006723458		Approved		uc002pyr.1	Q5HY98		ENST00000439461.1:c.780A>C	chr19.hg19:g.52793824A>C		140.0	0.0		113.0	27.0	NM_001010851	B2RNE0|Q7Z326	Silent	SNP	ENST00000439461.1	hg19	CCDS46163.1																																																																																			.	.		0.423	ZNF766-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462764.1	NM_001010851		C	52793824	A	C	52793824	2	2	13	1	0	0	0	0	0	0	0	1	18155	262	10	5		5	ZNF766	19	52793824	Silent	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	77519	52793824	6335159	163	1217										
ZNF611	81856	hgsc.bcm.edu	37	chr19	53217352	53217352	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gttcaggcatttccactctgCcaatgagaattctatagcca	7	11	3	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:53217352C>A	ENST00000319783.1	-	6	422	c.106G>T	c.(106-108)Gca>Tca	p.A36S	ZNF611_ENST00000600943.1_Intron|ZNF611_ENST00000543227.1_Missense_Mutation_p.A36S|ZNF611_ENST00000596702.1_Intron|ZNF611_ENST00000595798.1_Intron|ZNF611_ENST00000540744.1_Missense_Mutation_p.A36S|ZNF611_ENST00000453741.2_Intron|ZNF611_ENST00000602162.1_Intron	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	36	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TTCCACTCTGCCAATGAGAAT	0.453																																					p.A36S		Atlas-SNP	.											.	ZNF611	72	.	0			c.G106T						.						141	146	144					19																	53217352		2203	4300	6503	SO:0001583	missense	81856	exon6			ACTCTGCCAATGA	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"Zinc fingers, C2H2-type", "-"	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.106G>T	chr19.hg19:g.53217352C>A	ENSP00000322427:p.Ala36Ser	56.0	0.0		80.0	11.0	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	hg19	CCDS12855.1	.	.	.	.	.	.	.	.	.	.	.	5.314	0.243311	0.10077	.	.	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000319783	T;T;T	0.01665	4.7;4.7;4.7	3.03	3.03	0.35002	Krueppel-associated box (4);	.	.	.	.	T	0.02304	0.0071	L	0.45137	1.4	0.28593	N	0.909529	B	0.06786	0.001	B	0.21546	0.035	T	0.21518	-1.0243	9	0.87932	D	0	.	7.3157	0.26499	0.0:0.8691:0.0:0.1309	.	36	Q8N823	ZN611_HUMAN	S	36	ENSP00000437616:A36S;ENSP00000439211:A36S;ENSP00000322427:A36S	ENSP00000322427:A36S	A	-	1	0	ZNF611	57909164	0.034000	0.19679	0.159000	0.22649	0.010000	0.07245	0.772000	0.26647	1.534000	0.49203	0.298000	0.19748	GCA	.	.		0.453	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972		A	53217352	C	A	53217352	3	1	13	1	0	0	0	0	1	0	0	0	18052	739	26	3	2019	3	ZNF611	19	53217352	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	423528	53217352	5911631	164	1218										
ZNF677	342926	hgsc.bcm.edu	37	chr19	53740801	53740801	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tctccagtatggattctcttAtgttgggtaaggcttgaacg	11	7	2	1	rs566157588	byFrequency	TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:53740801A>G	ENST00000598513.1	-	5	1329	c.1179T>C	c.(1177-1179)caT>caC	p.H393H	ZNF677_ENST00000333952.4_Silent_p.H393H	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		GGATTCTCTTATGTTGGGTAA	0.408																																					p.H393H		Atlas-SNP	.											.	ZNF677	94	.	0			c.T1179C						.						99	87	91					19																	53740801		2203	4300	6503	SO:0001819	synonymous_variant	342926	exon5			TCTCTTATGTTGG	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1179T>C	chr19.hg19:g.53740801A>G		129.0	0.0		114.0	12.0	NM_182609		Silent	SNP	ENST00000598513.1	hg19	CCDS12861.1																																																																																			.	.		0.408	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		G	53740801	A	G	53740801	2	3	13	1	0	0	0	0	0	0	0	1	18099	446	16	2		2	ZNF677	19	53740801	Silent	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	523449	53740801	5388182	165	1219										
LENG9	94059	hgsc.bcm.edu	37	chr19	54974120	54974120	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ctggttcctggtgccctgtgCagagcggccttgtgctccct	13	14	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:54974120C>A	ENST00000333834.4	-	1	774	c.656G>T	c.(655-657)tGc>tTc	p.C219F		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	219							catalytic activity (GO:0003824)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)	11	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)		GTGCCCTGTGCAGAGCGGCCT	0.706																																					p.C219F		Atlas-SNP	.											.	LENG9	46	.	0			c.G656T						.						18	19	19					19																	54974120		2121	4161	6282	SO:0001583	missense	94059	exon1			CCTGTGCAGAGCG	AF211976		19q13.4	2014-05-06			ENSG00000182909	ENSG00000275183			16306	protein-coding gene	gene with protein product						10941842	Standard	NM_198988		Approved		uc010yez.2	Q96B70	OTTHUMG00000188273	ENST00000333834.4:c.656G>T	chr19.hg19:g.54974120C>A	ENSP00000331647:p.Cys219Phe	125.0	0.0		82.0	8.0	NM_198988	B2VAM3	Missense_Mutation	SNP	ENST00000333834.4	hg19	CCDS12895.2	.	.	.	.	.	.	.	.	.	.	C	0.694	-0.793242	0.02862	.	.	ENSG00000182909	ENST00000333834	T	0.29655	1.56	4.18	-1.03	0.10102	.	1.917040	0.03439	U	0.209091	T	0.18964	0.0455	N	0.19112	0.55	0.09310	N	1	B	0.14805	0.011	B	0.06405	0.002	T	0.19910	-1.0291	10	0.48119	T	0.1	6.0093	3.1507	0.06486	0.1662:0.4113:0.3241:0.0985	.	219	Q96B70	LENG9_HUMAN	F	219	ENSP00000331647:C219F	ENSP00000331647:C219F	C	-	2	0	LENG9	59665932	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.199000	0.03032	-0.279000	0.09167	-0.519000	0.04390	TGC	.	.		0.706	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140806.3	NM_198988		A	54974120	C	A	54974120	3	1	13	1	0	0	0	0	1	0	0	0	8734	710	25	3	853	3	LENG9	19	54974120	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	1233319	54974120	4154863	166	1220										
ZNF8	7554	hgsc.bcm.edu	37	chr19	58806125	58806125	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aagccctacaagtgtgccgaAtgtgggaagtctttctgcca	11	10	2	0			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr19:58806125A>G	ENST00000196548.5	+	4	1082	c.951A>G	c.(949-951)gaA>gaG	p.E317E	ZNF8_ENST00000608843.1_Silent_p.E317E|AC010642.1_ENST00000591325.1_3'UTR			P17098	ZNF8_HUMAN	zinc finger protein 8	317					BMP signaling pathway (GO:0030509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	19		all_cancers(17;6.46e-05)|Lung NSC(17;0.0233)|all_neural(62;0.0381)|all_epithelial(17;0.0427)|all_lung(17;0.057)|Ovarian(87;0.17)|Colorectal(82;0.227)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.00619)		AGTGTGCCGAATGTGGGAAGT	0.542																																					p.E317E		Atlas-SNP	.											.	ZNF8	60	.	0			c.A951G						.						98	101	100					19																	58806125		2203	4300	6503	SO:0001819	synonymous_variant	7554	exon4			TGCCGAATGTGGG	M29581	CCDS12974.1	19q13.43	2013-01-08	2006-05-09					"Zinc fingers, C2H2-type", "-"	13154	protein-coding gene	gene with protein product		194532	"zinc finger protein 8 (clone HF.18)"			2106481	Standard	NM_021089		Approved	HF.18, Zfp128	uc002qry.1	P17098		ENST00000196548.5:c.951A>G	chr19.hg19:g.58806125A>G		119.0	0.0		110.0	8.0	NM_021089	Q6PI99	Silent	SNP	ENST00000196548.5	hg19	CCDS12974.1																																																																																			.	.		0.542	ZNF8-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000459135.1	NM_021089		G	58806125	A	G	58806125	2	3	13	1	0	0	0	0	0	0	0	1	18182	98	4	2		2	ZNF8	19	58806125	Silent	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10	3832005	58806125	322858	167	1221										
C20orf103	24141	hgsc.bcm.edu	37	chr20	9496915	9496915	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ctcaacaggaaagccacaacAtgtccaagggacctgaggcg	11	12	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr20:9496915A>C	ENST00000246070.2	+	4	874	c.382A>C	c.(382-384)Atg>Ctg	p.M128L	RP5-1119D9.4_ENST00000443469.1_RNA|LAMP5_ENST00000427562.2_Missense_Mutation_p.M84L	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5	128						cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)											AAGCCACAACATGTCCAAGGG	0.582																																					p.M128L		Atlas-SNP	.											.	.	.	.	0			c.A382C						.						90	84	86					20																	9496915		2203	4300	6503	SO:0001583	missense	24141	exon4			CACAACATGTCCA	AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"brain and dendritic cell associated LAMP"	614641	"chromosome 20 open reading frame 103"	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.382A>C	chr20.hg19:g.9496915A>C	ENSP00000246070:p.Met128Leu	125.0	0.0		90.0	24.0	NM_012261	B4DHZ7|B7Z9Z9	Missense_Mutation	SNP	ENST00000246070.2	hg19	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	A	13.12	2.140808	0.37825	.	.	ENSG00000125869	ENST00000246070;ENST00000427562	T;T	0.39997	1.64;1.05	5.98	4.87	0.63330	.	0.412890	0.29152	N	0.012992	T	0.21186	0.0510	N	0.08118	0	0.19300	N	0.999977	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.17776	-1.0358	9	.	.	.	-3.1146	9.3835	0.38329	0.9164:0.0:0.0836:0.0	.	84;128	Q9UJQ1-2;Q9UJQ1	.;CT103_HUMAN	L	128;84	ENSP00000246070:M128L;ENSP00000406360:M84L	.	M	+	1	0	C20orf103	9444915	1.000000	0.71417	0.989000	0.46669	0.980000	0.70556	3.636000	0.54317	1.073000	0.40885	0.482000	0.46254	ATG	.	.		0.582	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261		C	9496915	A	C	9496915	3	2	13	1	0	0	0	0	1	0	0	0	2077	217	8	5	396	5	C20orf103	20	9496915	Missense_Mutation	SNP	A	TCGA-2Y-A9H3-01A-11D-A382-10		9496915	53528605	168	1222										
C20orf114	92747	hgsc.bcm.edu	37	chr20	31877770	31877770	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aggagctgctagtcaagatcCccctggacatggtggctgga	14	10	1	1	rs114635109	byFrequency	TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr20:31877770C>A	ENST00000253354.1	+	4	498	c.337C>A	c.(337-339)Ccc>Acc	p.P113T		NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	113					innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										AGTCAAGATCCCCCTGGACAT	0.582																																					p.P113T		Atlas-SNP	.											.	.	.	.	0			c.C337A						.						124	95	105					20																	31877770		2203	4300	6503	SO:0001583	missense	92747	exon4			AAGATCCCCCTGG	BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"BPI fold containing"	16108	protein-coding gene	gene with protein product	"von Ebner minor salivary gland protein"		"chromosome 20 open reading frame 114"	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.337C>A	chr20.hg19:g.31877770C>A	ENSP00000253354:p.Pro113Thr	121.0	0.0		93.0	7.0	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	hg19	CCDS13218.1	.	.	.	.	.	.	.	.	.	.	C	18.55	3.648141	0.67358	.	.	ENSG00000125999	ENST00000423645;ENST00000253354	T;T	0.06142	3.34;3.66	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000008	T	0.26919	0.0659	M	0.80847	2.515	0.39560	D	0.969115	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00842	-1.1544	10	0.56958	D	0.05	-35.2487	15.0609	0.71951	0.0:1.0:0.0:0.0	.	113;113	B2R7Z6;Q8TDL5	.;BPIB1_HUMAN	T	113	ENSP00000390471:P113T;ENSP00000253354:P113T	ENSP00000253354:P113T	P	+	1	0	BPIFB1	31341431	0.958000	0.32768	0.987000	0.45799	0.713000	0.41058	3.494000	0.53273	2.722000	0.93159	0.655000	0.94253	CCC	.	C|0.988;T|0.012		0.582	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197		A	31877770	C	A	31877770	3	1	13	1	0	0	0	0	1	0	0	0	2084	623	22	3	347	3	C20orf114	20	31877770	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	22380855	31877770	31147750	169	1223										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57769710	57769710	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tacttggcggtgcactttccTggtagcagcctccgagatga	12	11	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr20:57769710T>C	ENST00000371030.2	+	1	3636	c.3636T>C	c.(3634-3636)ccT>ccC	p.P1212P		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1212							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					TGCACTTTCCTGGTAGCAGCC	0.642																																					p.P1212P		Atlas-SNP	.											.	ZNF831	287	.	0			c.T3636C						.						29	34	33					20																	57769710		2090	4212	6302	SO:0001819	synonymous_variant	128611	exon1			CTTTCCTGGTAGC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.3636T>C	chr20.hg19:g.57769710T>C		160.0	0.0		104.0	23.0	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	hg19	CCDS42894.1																																																																																			.	.		0.642	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		C	57769710	T	C	57769710	2	2	13	1	0	0	0	0	0	0	0	1	18200	1567	55	2		2	ZNF831	20	57769710	Silent	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	25891940	57769710	5255810	170	1224										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19187289	19187289	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	cagctcatctgcatgaatgaCgatgtgaagaccacacagct	9	11	2	4	rs201881044		TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr22:19187289C>T	ENST00000263200.10	-	24	3901	c.3829G>A	c.(3829-3831)Gtc>Atc	p.V1277I	CLTCL1_ENST00000442042.2_5'UTR|CLTCL1_ENST00000427926.1_Missense_Mutation_p.V1277I|CLTCL1_ENST00000353891.5_Missense_Mutation_p.V1277I	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1277	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GCATGAATGACGATGTGAAGA	0.532			T	?	ALCL																																p.V1277I		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.G3829A						.	C	ILE/VAL,ILE/VAL	0,4308		0,0,2154	54	56	55		3829,3829	1.9	0.7	22		55	5,8509		0,5,4252	yes	missense,missense	CLTCL1	NM_001835.3,NM_007098.3	29,29	0,5,6406	TT,TC,CC		0.0587,0.0,0.039	possibly-damaging,possibly-damaging	1277/1584,1277/1641	19187289	5,12817	2154	4257	6411	SO:0001583	missense	8218	exon24			GAATGACGATGTG		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.3829G>A	chr22.hg19:g.19187289C>T	ENSP00000445677:p.Val1277Ile	81.0	0.0		42.0	10.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	C	5.123	0.208343	0.09757	0.0	5.87E-4	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.20200	2.09;2.09;2.09	3.99	1.88	0.25563	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.163547	0.39985	N	0.001207	T	0.18257	0.0438	L	0.33668	1.02	0.53005	D	0.999961	B;P;B;B	0.42961	0.143;0.795;0.303;0.303	B;P;B;B	0.50231	0.175;0.635;0.318;0.154	T	0.09378	-1.0677	10	0.02654	T	1	-14.0934	9.4942	0.38978	0.0:0.8254:0.0:0.1746	.	1277;100;100;1277	P53675-2;B7Z1Z7;B7Z2Y4;P53675	.;.;.;CLH2_HUMAN	I	1277	ENSP00000439662:V1277I;ENSP00000445677:V1277I;ENSP00000441158:V1277I	ENSP00000445677:V1277I	V	-	1	0	CLTCL1	17567289	0.999000	0.42202	0.708000	0.30435	0.703000	0.40648	4.215000	0.58534	0.345000	0.23873	0.591000	0.81541	GTC	.	.		0.532	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		T	19187289	C	T	19187289	3	4	13	1	0	0	0	0	1	0	0	0	3569	536	19	1	1129	1	CLTCL1	22	19187289	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10		19187289	32117277	171	1225										
PI4KA	5297	hgsc.bcm.edu	37	chr22	21098986	21098986	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	agtctttcttcacacaggccGggcgctcgctcagctgagtt	11	13	4	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr22:21098986G>A	ENST00000572273.1	-	30	3442	c.3212C>T	c.(3211-3213)cCg>cTg	p.P1071L	PI4KA_ENST00000255882.6_Missense_Mutation_p.P1129L			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1071					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			CACACAGGCCGGGCGCTCGCT	0.542																																					p.P1129L	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.C3386T						.						103	86	92					22																	21098986		2203	4300	6503	SO:0001583	missense	5297	exon30			CAGGCCGGGCGCT	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.3212C>T	chr22.hg19:g.21098986G>A	ENSP00000458238:p.Pro1071Leu	66.0	0.0		44.0	9.0	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.703062	0.96812	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.78227	0.4250	M	0.79926	2.475	0.80722	D	1	D	0.69078	0.997	P	0.56474	0.799	T	0.80344	-0.1422	9	0.72032	D	0.01	-24.274	20.1434	0.98067	0.0:0.0:1.0:0.0	.	1071	P42356	PI4KA_HUMAN	L	1071	.	ENSP00000255882:P1071L	P	-	2	0	PI4KA	19428986	1.000000	0.71417	0.973000	0.42090	0.968000	0.65278	9.863000	0.99569	2.769000	0.95229	0.563000	0.77884	CCG	.	.		0.542	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21098986	G	A	21098986	3	1	13	1	0	0	0	0	1	0	0	0	11882	1116	39	1	3026	1	PI4KA	22	21098986	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	1911697	21098986	30205580	172	1226										
SUSD2	56241	hgsc.bcm.edu	37	chr22	24583419	24583419	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	gttcctgtttggggccaactGtgagtgaccgtggagtatat	14	7	0	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr22:24583419G>C	ENST00000358321.3	+	11	2152		c.e11+1			NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2						immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						GGGGCCAACTGTGAGTGACCG	0.647																																					.		Atlas-SNP	.											.	SUSD2	68	.	0			c.1891+1G>C						.						60	60	60					22																	24583419		2203	4300	6503	SO:0001630	splice_region_variant	56241	exon11			CCAACTGTGAGTG	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.1891+1G>C	chr22.hg19:g.24583419G>C		51.0	0.0		33.0	5.0	NM_019601	Q9H5Y6	Splice_Site	SNP	ENST00000358321.3	hg19	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.946401	0.34377	.	.	ENSG00000099994	ENST00000358321	.	.	.	4.59	4.59	0.56863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3376	0.74269	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SUSD2	22913419	1.000000	0.71417	0.997000	0.53966	0.027000	0.11550	7.435000	0.80391	2.274000	0.75844	0.555000	0.69702	.	.	.		0.647	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601	Intron	C	24583419	G	C	24583419	5	2	13	1	0	0	0	0	0	0	1	0	15423	1391	48	4	1934	4	SUSD2	22	24583419	Splice_Site	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	3484433	24583419	26721147	173	1227										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38121679	38121679	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	tttgcagcacgaccccttccCcttcttcccagagccccgcg	7	20	1	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr22:38121679C>G	ENST00000406386.3	+	7	3371	c.3116C>G	c.(3115-3117)cCc>cGc	p.P1039R		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1039					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GACCCCTTCCCCTTCTTCCCA	0.652																																					p.P1039R		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C3116G						.						74	84	81					22																	38121679		1947	4122	6069	SO:0001583	missense	11078	exon7			CCTTCCCCTTCTT	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.3116C>G	chr22.hg19:g.38121679C>G	ENSP00000384312:p.Pro1039Arg	203.0	0.0		112.0	24.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.463200	0.63513	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.24151	1.87	4.86	4.86	0.63082	.	.	.	.	.	T	0.36771	0.0979	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	D	0.64237	0.923	T	0.08493	-1.0719	9	0.62326	D	0.03	.	13.4136	0.60956	0.0:1.0:0.0:0.0	.	1039	Q9H2D6	TARA_HUMAN	R	1039	ENSP00000384312:P1039R	ENSP00000384312:P1039R	P	+	2	0	TRIOBP	36451625	1.000000	0.71417	1.000000	0.80357	0.706000	0.40770	3.740000	0.55082	2.534000	0.85438	0.456000	0.33151	CCC	.	.		0.652	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			G	38121679	C	G	38121679	3	3	13	1	0	0	0	0	1	0	0	0	16568	623	22	4	3134	4	TRIOBP	22	38121679	Missense_Mutation	SNP	C	TCGA-2Y-A9H3-01A-11D-A382-10	13538260	38121679	13182887	174	1228										
DDX17	10521	hgsc.bcm.edu	37	chr22	38890726	38890726	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	attgcctacgttgatctgggTgtaatcacgaaggaaatcct	10	8	2	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chr22:38890726T>A	ENST00000396821.3	-	8	1222	c.1123A>T	c.(1123-1125)Acc>Tcc	p.T375S	DDX17_ENST00000381633.3_Missense_Mutation_p.T296S|DDX17_ENST00000432525.1_5'UTR	NM_001098504.1|NM_006386.4	NP_001091974|NP_006377.2	Q92841	DDX17_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 17	375	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of skeletal muscle cell differentiation (GO:2001014)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA helicase activity (GO:0003724)|RNA-dependent ATPase activity (GO:0008186)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	25	Melanoma(58;0.0286)					TTGATCTGGGTGTAATCACGA	0.458																																					p.T375S	Ovarian(55;1085 1454 6392 21425)	Atlas-SNP	.											.	DDX17	73	.	0			c.A1123T						.						187	160	169					22																	38890726		2203	4300	6503	SO:0001583	missense	10521	exon8			TCTGGGTGTAATC	U59321	CCDS33646.1, CCDS46706.1	22q13.1	2012-02-23	2012-02-23		ENSG00000100201	ENSG00000100201		"DEAD-boxes"	2740	protein-coding gene	gene with protein product		608469	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 17"			8871553, 17226766	Standard	NM_006386		Approved	P72	uc003avy.4	Q92841	OTTHUMG00000151136	ENST00000396821.3:c.1123A>T	chr22.hg19:g.38890726T>A	ENSP00000380033:p.Thr375Ser	159.0	0.0		111.0	10.0	NM_006386	B1AHM0|Q69YT1|Q6ICD6	Missense_Mutation	SNP	ENST00000396821.3	hg19	CCDS46706.1	.	.	.	.	.	.	.	.	.	.	T	16.88	3.243570	0.58995	.	.	ENSG00000100201	ENST00000396821;ENST00000381633;ENST00000403230;ENST00000404499	T;T;T	0.04454	3.62;3.62;3.62	5.83	5.83	0.93111	DEAD-like helicase (2);	0.222296	0.49305	D	0.000155	T	0.04952	0.0133	L	0.38692	1.165	0.80722	D	1	B;B;B	0.19583	0.001;0.037;0.022	B;B;B	0.23150	0.001;0.02;0.044	T	0.32268	-0.9913	10	0.72032	D	0.01	-13.0587	6.2361	0.20764	0.0:0.192:0.0:0.808	.	296;377;375	Q92841;Q59F66;Q92841-4	DDX17_HUMAN;.;.	S	375;296;375;377	ENSP00000380033:T375S;ENSP00000371046:T296S;ENSP00000385536:T375S	ENSP00000371046:T296S	T	-	1	0	DDX17	37220672	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.074000	0.50065	2.236000	0.73375	0.533000	0.62120	ACC	.	.		0.458	DDX17-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321476.2	NM_030881		A	38890726	T	A	38890726	3	1	13	1	0	0	0	0	1	0	0	0	4346	1696	59	4	1096	4	DDX17	22	38890726	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	769047	38890726	12413840	175	1229										
TAF1	6872	hgsc.bcm.edu	37	chrX	70617187	70617187	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	taactcttctgccactggacGctgtctcaagatttatcgca	7	12	3	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chrX:70617187G>A	ENST00000373790.4	+	23	3539	c.3488G>A	c.(3487-3489)cGc>cAc	p.R1163H	TAF1_ENST00000276072.3_Missense_Mutation_p.R1184H|TAF1_ENST00000449580.1_Missense_Mutation_p.R1163H|TAF1_ENST00000423759.1_Missense_Mutation_p.R1184H	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1163					cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.R1163H(1)|p.R1184H(1)		breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GCCACTGGACGCTGTCTCAAG	0.502																																					p.R1184H		Atlas-SNP	.											.	TAF1	439	.	2	Substitution - Missense(2)	endometrium(2)	c.G3551A						.						165	109	128					X																	70617187		2203	4300	6503	SO:0001583	missense	6872	exon23			CTGGACGCTGTCT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.3488G>A	chrX.hg19:g.70617187G>A	ENSP00000362895:p.Arg1163His	218.0	0.0		175.0	38.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	16.69|16.69	3.192034|3.192034	0.58017|0.58017	.|.	.|.	ENSG00000147133|ENSG00000147133	ENST00000483985|ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	.|T;T;T;T	.|0.18502	.|2.21;2.21;2.21;2.21	4.91|4.91	4.91|4.91	0.64330|0.64330	.|.	.|0.115711	.|0.64402	.|D	.|0.000015	T|T	0.24624|0.24624	0.0597|0.0597	M|M	0.67397|0.67397	2.05|2.05	0.51233|0.51233	D|D	0.99991|0.99991	.|B;B;B	.|0.18741	.|0.03;0.017;0.03	.|B;B;B	.|0.23419	.|0.046;0.016;0.035	T|T	0.04708|0.04708	-1.0932|-1.0932	5|10	.|0.54805	.|T	.|0.06	.|.	17.5217|17.5217	0.87789|0.87789	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1163;1163;1184	.|P21675-4;P21675;P21675-2	.|.;TAF1_HUMAN;.	T|H	74|1163;1163;1184;1184	.|ENSP00000362895:R1163H;ENSP00000389000:R1163H;ENSP00000406549:R1184H;ENSP00000276072:R1184H	.|ENSP00000276072:R1184H	A|R	+|+	1|2	0|0	TAF1|TAF1	70533912|70533912	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.336000|7.336000	0.79245|0.79245	2.322000|2.322000	0.78497|0.78497	0.449000|0.449000	0.29647|0.29647	GCT|CGC	.	.		0.502	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70617187	G	A	70617187	3	1	13	1	0	0	0	0	1	0	0	0	15528	1087	38	1	3641	1	TAF1	23	70617187	Missense_Mutation	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10		70617187	84653373	176	1230										
PGK1	5230	hgsc.bcm.edu	37	chrX	77359873	77359873	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	aagctgacgctggacaagctGgacgttaaagggaagcgggt	16	7	0	1			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chrX:77359873G>A	ENST00000373316.4	+	1	203	c.36G>A	c.(34-36)ctG>ctA	p.L12L	PGK1_ENST00000537456.1_5'Flank|PGK1_ENST00000442431.1_Silent_p.L12L	NM_000291.3	NP_000282.1	P00558	PGK1_HUMAN	phosphoglycerate kinase 1	12					carbohydrate metabolic process (GO:0005975)|epithelial cell differentiation (GO:0030855)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphoglycerate kinase activity (GO:0004618)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	24					Lamivudine(DB00709)	TGGACAAGCTGGACGTTAAAG	0.552																																					p.L12L		Atlas-SNP	.											.	PGK1	34	.	0			c.G36A						.						112	70	84					X																	77359873		2203	4296	6499	SO:0001819	synonymous_variant	5230	exon1			CAAGCTGGACGTT	L00159	CCDS14438.1	Xq13.3	2011-03-17			ENSG00000102144	ENSG00000102144	2.7.2.3		8896	protein-coding gene	gene with protein product		311800				6188151, 6099325	Standard	NM_000291		Approved		uc004ecz.4	P00558	OTTHUMG00000021888	ENST00000373316.4:c.36G>A	chrX.hg19:g.77359873G>A		51.0	0.0		39.0	21.0	NM_000291	A8K4W6|B7Z7A9|Q5J7W1|Q6IBT6|Q8NI87	Silent	SNP	ENST00000373316.4	hg19	CCDS14438.1																																																																																			.	.		0.552	PGK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057310.1			A	77359873	G	A	77359873	2	1	13	1	0	0	0	0	0	0	0	1	11799	1335	47	3		3	PGK1	23	77359873	Silent	SNP	G	TCGA-2Y-A9H3-01A-11D-A382-10	6742686	77359873	77910687	177	1231										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123526164	123526164	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0397727272727273	7	1	0.711914893617021	0.847517730496454	0.669092945128779	0.314685314685315	1	0	ttcctgtgcgggttatatgaTcaaaatctatggagagtagg	12	5	2	2			TCGA-2Y-A9H3-01A-11D-A382-10	TCGA-2Y-A9H3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4d274d44-da17-4591-ad59-a37a868e32d8	6e97c9c0-1710-4ff7-8fdc-180aaf2cfd90	g.chrX:123526164T>A	ENST00000371130.3	-	27	5468	c.5405A>T	c.(5404-5406)gAt>gTt	p.D1802V	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.D1809V	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1802					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GGTTATATGATCAAAATCTAT	0.423																																					p.D1809V		Atlas-SNP	.											.	.	.	.	0			c.A5426T						.						129	121	124					X																	123526164		2203	4299	6502	SO:0001583	missense	10178	exon28			ATATGATCAAAAT	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5405A>T	chrX.hg19:g.123526164T>A	ENSP00000360171:p.Asp1802Val	44.0	0.0		67.0	31.0	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	hg19	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.935625	0.73442	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.90900	-2.75;-2.71	5.54	5.54	0.83059	.	0.099413	0.64402	D	0.000001	D	0.93452	0.7911	M	0.79123	2.44	0.80722	D	1	D;D;D	0.59767	0.986;0.986;0.969	P;P;P	0.53954	0.617;0.738;0.643	D	0.94162	0.7415	10	0.87932	D	0	.	14.7475	0.69499	0.0:0.0:0.0:1.0	.	1808;1809;1802	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	V	1802;1809	ENSP00000360171:D1802V;ENSP00000403954:D1809V	ENSP00000360171:D1802V	D	-	2	0	ODZ1	123353845	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.258000	0.72487	1.863000	0.54032	0.486000	0.48141	GAT	.	.		0.423	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123526164	T	A	123526164	3	1	13	1	0	0	0	0	1	0	0	0	10843	1435	50	4	2792	4	ODZ1	23	123526164	Missense_Mutation	SNP	T	TCGA-2Y-A9H3-01A-11D-A382-10	46166291	123526164	31744396	178	1232										
PIAS3	10401	hgsc.bcm.edu	37	chr1	145578670	145578670	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ccagcggtttgaggaagcgcActttacctttgccctcacac	9	14	1	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr1:145578670A>G	ENST00000393045.2	+	3	566	c.476A>G	c.(475-477)cAc>cGc	p.H159R	PIAS3_ENST00000369298.1_Missense_Mutation_p.H124R|PIAS3_ENST00000369299.3_Missense_Mutation_p.H150R	NM_006099.3	NP_006090.2	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	159	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				positive regulation of gene expression (GO:0010628)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)|synapse (GO:0045202)	enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|SUMO ligase activity (GO:0019789)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)	28	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GAGGAAGCGCACTTTACCTTT	0.537																																					p.H159R		Atlas-SNP	.											.	PIAS3	96	.	0			c.A476G						.						217	189	199					1																	145578670		2203	4300	6503	SO:0001583	missense	10401	exon3			AAGCGCACTTTAC	AB021868	CCDS72866.1	1q21	2011-10-11			ENSG00000131788	ENSG00000131788		"Zinc fingers, MIZ-type"	16861	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 5"	605987				10319586	Standard	NM_006099		Approved	FLJ14651, ZMIZ5	uc001eoc.1	Q9Y6X2	OTTHUMG00000013750	ENST00000393045.2:c.476A>G	chr1.hg19:g.145578670A>G	ENSP00000376765:p.His159Arg	142.0	0.0		123.0	13.0	NM_006099	Q9UFI3	Missense_Mutation	SNP	ENST00000393045.2	hg19	CCDS920.2	.	.	.	.	.	.	.	.	.	.	A	14.07	2.425798	0.43020	.	.	ENSG00000131788	ENST00000393046;ENST00000369299;ENST00000393045;ENST00000369298	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	4.22	3.1	0.35709	PINIT domain (1);	0.000000	0.51477	D	0.000099	T	0.18551	0.0445	L	0.29908	0.895	0.37603	D	0.920659	P;D	0.53619	0.6;0.961	B;P	0.48552	0.429;0.581	T	0.02444	-1.1158	10	0.25106	T	0.35	-10.0179	7.6914	0.28569	0.898:0.0:0.102:0.0	.	150;159	F8WA94;Q9Y6X2	.;PIAS3_HUMAN	R	150;150;159;124	ENSP00000376766:H150R;ENSP00000358305:H150R;ENSP00000376765:H159R;ENSP00000358304:H124R	ENSP00000358304:H124R	H	+	2	0	PIAS3	144290027	0.307000	0.24500	0.995000	0.50966	0.996000	0.88848	1.374000	0.34283	0.668000	0.31126	0.533000	0.62120	CAC	.	.		0.537	PIAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038533.4	NM_006099		G	145578670	A	G	145578670	3	3	14	1	0	0	0	0	1	0	0	0	11886	159	6	2	486	2	PIAS3	1	145578670	Missense_Mutation	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10		145578670	103671951	1	1233										
OR2L3	391192	hgsc.bcm.edu	37	chr1	248224048	248224048	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	attcttcccaccatcaagaaTtggccttttcctcttcatcc	3	15	4	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr1:248224048T>C	ENST00000359959.3	+	1	65	c.65T>C	c.(64-66)aTt>aCt	p.I22T	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	22						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			CCATCAAGAATTGGCCTTTTC	0.403																																					p.I22T		Atlas-SNP	.											.	OR2L3	97	.	0			c.T65C						.						246	243	244					1																	248224048		2203	4300	6503	SO:0001583	missense	391192	exon1			CAAGAATTGGCCT	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"GPCR / Class A : Olfactory receptors"	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.65T>C	chr1.hg19:g.248224048T>C	ENSP00000353044:p.Ile22Thr	145.0	0.0		124.0	50.0	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	hg19	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.674830	0.00104	.	.	ENSG00000198128	ENST00000359959	T	0.09073	3.02	2.05	2.05	0.26809	.	.	.	.	.	T	0.05090	0.0136	N	0.25789	0.76	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.44298	-0.9337	9	0.16896	T	0.51	.	3.8172	0.08821	0.0:0.1971:0.0:0.8029	.	22	Q8NG85	OR2L3_HUMAN	T	22	ENSP00000353044:I22T	ENSP00000353044:I22T	I	+	2	0	OR2L3	246290671	0.000000	0.05858	0.160000	0.22671	0.425000	0.31504	-1.732000	0.01851	0.928000	0.37168	0.379000	0.24179	ATT	.	.		0.403	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		C	248224048	T	C	248224048	3	2	14	1	0	0	0	0	1	0	0	0	11017	1493	52	2	67	2	OR2L3	1	248224048	Missense_Mutation	SNP	T	TCGA-2Y-A9H4-01A-11D-A382-10	102645378	248224048	1026573	2	1234										
NTSR2	23620	hgsc.bcm.edu	37	chr2	11798629	11798629	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gtccgggtttctgggggatcCccaaagcctgaagctgtatc	13	11	1	1	rs150650740		TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr2:11798629C>T	ENST00000306928.5	-	4	1243	c.1209G>A	c.(1207-1209)ggG>ggA	p.G403G		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	403					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	CTGGGGGATCCCCAAAGCCTG	0.547																																					p.G403G		Atlas-SNP	.											.	NTSR2	36	.	0			c.G1209A						.	C		0,4406		0,0,2203	87	93	91		1209	4.3	1	2	dbSNP_134	91	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NTSR2	NM_012344.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		403/411	11798629	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23620	exon4			GGGATCCCCAAAG	Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"GPCR / Class A : Neurotensin receptors"	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.1209G>A	chr2.hg19:g.11798629C>T		96.0	0.0		125.0	37.0	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Silent	SNP	ENST00000306928.5	hg19	CCDS1681.1																																																																																			.	C|1.000;T|0.000		0.547	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1			T	11798629	C	T	11798629	2	4	14	1	0	0	0	0	0	0	0	1	10720	610	22	3		3	NTSR2	2	11798629	Silent	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10		11798629	231400744	3	1235										
NTSR2	23620	hgsc.bcm.edu	37	chr2	11810006	11810006	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ctccaccggcacgccgaccaGcagcagcagcaggcccgcga	12	19	0	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr2:11810006G>C	ENST00000306928.5	-	1	284	c.250C>G	c.(250-252)Ctg>Gtg	p.L84V		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	84					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	ACGCCGACCAGCAGCAGCAGC	0.721																																					p.L84V		Atlas-SNP	.											.	NTSR2	36	.	0			c.C250G						.						5	7	7					2																	11810006		2033	4077	6110	SO:0001583	missense	23620	exon1			CGACCAGCAGCAG	Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"GPCR / Class A : Neurotensin receptors"	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.250C>G	chr2.hg19:g.11810006G>C	ENSP00000303686:p.Leu84Val	66.0	0.0		70.0	4.0	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Missense_Mutation	SNP	ENST00000306928.5	hg19	CCDS1681.1	.	.	.	.	.	.	.	.	.	.	G	0.370	-0.934435	0.02340	.	.	ENSG00000169006	ENST00000306928	T	0.41065	1.01	3.42	1.57	0.23409	GPCR, rhodopsin-like superfamily (1);	1.351940	0.05480	N	0.554731	T	0.37210	0.0995	L	0.39514	1.22	0.23095	N	0.998303	B	0.02656	0.0	B	0.10450	0.005	T	0.33445	-0.9868	10	0.16896	T	0.51	-2.428	13.7547	0.62928	0.0:0.2905:0.7095:0.0	.	84	O95665	NTR2_HUMAN	V	84	ENSP00000303686:L84V	ENSP00000303686:L84V	L	-	1	2	NTSR2	11727457	0.824000	0.29247	0.925000	0.36789	0.098000	0.18820	0.039000	0.13884	0.107000	0.17824	-2.840000	0.00105	CTG	.	.		0.721	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1			C	11810006	G	C	11810006	3	2	14	1	0	0	0	0	1	0	0	0	10720	962	34	4	998	4	NTSR2	2	11810006	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	11377	11810006	231389367	4	1236										
USP34	9736	hgsc.bcm.edu	37	chr2	61597513	61597514	+	Frame_Shift_Ins	INS	-	-	A													0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tcagtcgcccttctgctgccINSaaaaaattcaaaatcacttg							TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr2:61597513_61597514insA	ENST00000398571.2	-	10	1269_1270	c.1193_1194insT	c.(1192-1194)ttgfs	p.L398fs		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	398					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			CTTCTGCTGCCAAAAAATTCAA	0.332																																					p.L398fs		Atlas-Indel,Pindel	.											.	USP34	334	.	0			c.1194_1195insT						.																																			SO:0001589	frameshift_variant	9736	exon10			.	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.1194dupT	chr2.hg19:g.61597519_61597519dupA	ENSP00000381577:p.Leu398fs	333.0	0.0		354.0	118.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Frame_Shift_Ins	INS	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.		0.332	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			A	61597514	-	A	61597513	7	5	14	1	0	1	1	0	0	0	0	0	17080	593	21	0	9730	0	USP34	2	61597513	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H4-01A-11D-A382-10	49787507	61597513	181601860	5	1237										
RGPD4	285190	hgsc.bcm.edu	37	chr2	108488174	108488174	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tcagacacaacaataaaaccCaatcctgaaaacactgggcc	5	13	1	2			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr2:108488174C>A	ENST00000408999.3	+	20	3791	c.3714C>A	c.(3712-3714)ccC>ccA	p.P1238P	RGPD4_ENST00000354986.4_Silent_p.P1238P	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1238					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						CAATAAAACCCAATCCTGAAA	0.418																																					p.P1238P		Atlas-SNP	.											.	RGPD4	112	.	0			c.C3714A						.						28	24	25					2																	108488174		691	1590	2281	SO:0001819	synonymous_variant	285190	exon20			AAAACCCAATCCT	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.3714C>A	chr2.hg19:g.108488174C>A		233.0	0.0		158.0	104.0	NM_182588	B9A029	Silent	SNP	ENST00000408999.3	hg19	CCDS46381.1																																																																																			.	.		0.418	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		A	108488174	C	A	108488174	2	1	14	1	0	0	0	0	0	0	0	1	13303	581	21	3		3	RGPD4	2	108488174	Silent	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	46890661	108488174	134711199	6	1238										
KBTBD5	131377	hgsc.bcm.edu	37	chr3	42727774	42727774	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gcgcgctgcccaccgtcttcGagagcgtgcgctgccgcttg	14	16	1	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr3:42727774G>A	ENST00000287777.4	+	1	764	c.664G>A	c.(664-666)Gag>Aag	p.E222K		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	222	BACK.				multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)											CACCGTCTTCGAGAGCGTGCG	0.716																																					p.E222K		Atlas-SNP	.											KBTBD5,NS,carcinoma,0,1	.	.	.	0			c.G664A						.						12	12	12					3																	42727774		2171	4249	6420	SO:0001583	missense	131377	exon1			GTCTTCGAGAGCG	AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119		"Kelch-like", "BTB/POZ domain containing"	30372	protein-coding gene	gene with protein product	"sarcosynapsin", "nemaline myopathy type 8"	615340	"kelch repeat and BTB (POZ) domain containing 5", "kelch-like 40 (Drosophila)"	KBTBD5		23746549	Standard	NM_152393		Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.664G>A	chr3.hg19:g.42727774G>A	ENSP00000287777:p.Glu222Lys	78.0	0.0		64.0	32.0	NM_152393	Q86SI1|Q96MR2	Missense_Mutation	SNP	ENST00000287777.4	hg19	CCDS2703.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.230177	0.58777	.	.	ENSG00000157119	ENST00000287777	T	0.68479	-0.33	4.56	3.68	0.42216	BTB/Kelch-associated (2);	0.164086	0.53938	N	0.000060	T	0.59542	0.2201	L	0.41961	1.31	0.45272	D	0.998278	B	0.30021	0.265	B	0.33750	0.169	T	0.58825	-0.7568	10	0.41790	T	0.15	.	12.5689	0.56326	0.0808:0.0:0.9192:0.0	.	222	Q2TBA0	KBTB5_HUMAN	K	222	ENSP00000287777:E222K	ENSP00000287777:E222K	E	+	1	0	KBTBD5	42702778	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.308000	0.59129	1.154000	0.42482	0.655000	0.94253	GAG	.	.		0.716	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256651.1	NM_152393		A	42727774	G	A	42727774	3	1	14	1	0	0	0	0	1	0	0	0	8005	1059	37	1	666	1	KBTBD5	3	42727774	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10		42727774	155294656	7	1239										
CISH	1154	hgsc.bcm.edu	37	chr3	50649061	50649061	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ggggcagagagccgcgcttaCccctgaacgcagaggaccat	14	13	0	3			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr3:50649061C>T	ENST00000348721.3	-	1	201		c.e1+1		MAPKAPK3_ENST00000446044.1_5'Flank|CISH_ENST00000443053.2_Splice_Site	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein						intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of signal transduction (GO:0009968)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				breast(2)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		GCCGCGCTTACCCCTGAACGC	0.731											OREG0015590	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	CISH	27	.	0			c.20+1G>A						.						7	8	8					3																	50649061		2035	3978	6013	SO:0001630	splice_region_variant	1154	exon2			CGCTTACCCCTGA	Z77852	CCDS2831.1, CCDS46834.1	3p21.3	2013-02-14			ENSG00000114737	ENSG00000114737		"Suppressors of cytokine signaling", "SH2 domain containing"	1984	protein-coding gene	gene with protein product		602441				9465889, 7796808	Standard	NM_013324		Approved	CIS, G18, CIS-1, SOCS	uc003dax.3	Q9NSE2	OTTHUMG00000156853	ENST00000348721.3:c.20+1G>A	chr3.hg19:g.50649061C>T		275.0	0.0	971	190.0	60.0	NM_145071	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Splice_Site	SNP	ENST00000348721.3	hg19	CCDS2831.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.645694	0.87958	.	.	ENSG00000114737	ENST00000348721	.	.	.	5.63	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7112	0.77629	0.1377:0.8623:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CISH	50624065	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.257000	0.51500	1.380000	0.46344	0.561000	0.74099	.	.	.		0.731	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071	Intron	T	50649061	C	T	50649061	5	4	14	1	0	0	0	0	0	0	1	0	3439	521	18	3	842	3	CISH	3	50649061	Splice_Site	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	7921287	50649061	147373369	8	1240										
HPS3	84343	hgsc.bcm.edu	37	chr3	148858010	148858010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ttcctgttgccctgtgaaagGagaccttctcgttggctgca	11	11	1	2			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr3:148858010G>A	ENST00000296051.2	+	2	577	c.437G>A	c.(436-438)gGa>gAa	p.G146E	HPS3_ENST00000460120.1_Intron	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	146					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CCTGTGAAAGGAGACCTTCTC	0.428									Hermansky-Pudlak syndrome																												p.G146E		Atlas-SNP	.											.	HPS3	104	.	0			c.G437A						.						134	131	132					3																	148858010		2203	4300	6503	SO:0001583	missense	84343	exon2	Familial Cancer Database	HPS, HPS1-8	TGAAAGGAGACCT	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.437G>A	chr3.hg19:g.148858010G>A	ENSP00000296051:p.Gly146Glu	159.0	0.0		213.0	94.0	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	hg19	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.887920	0.91814	.	.	ENSG00000163755	ENST00000296051	D	0.92099	-2.97	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.96093	0.8727	M	0.75264	2.295	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96066	0.9042	10	0.87932	D	0	-24.0005	19.8692	0.96843	0.0:0.0:1.0:0.0	.	146	Q969F9	HPS3_HUMAN	E	146	ENSP00000296051:G146E	ENSP00000296051:G146E	G	+	2	0	HPS3	150340700	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.554000	0.90689	2.762000	0.94881	0.585000	0.79938	GGA	.	.		0.428	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		A	148858010	G	A	148858010	3	1	14	1	0	0	0	0	1	0	0	0	7349	1174	41	3	443	3	HPS3	3	148858010	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	98208949	148858010	49164420	9	1241										
LIPH	200879	hgsc.bcm.edu	37	chr3	185234915	185234915	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	cgtcattggaggatctttccCccttagatggtctttccaat	8	11	3	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr3:185234915C>A	ENST00000296252.4	-	7	1063	c.922G>T	c.(922-924)Ggg>Tgg	p.G308W	LIPH_ENST00000424591.2_Missense_Mutation_p.G274W	NM_139248.2	NP_640341.1	Q8WWY8	LIPH_HUMAN	lipase, member H	308					lipid catabolic process (GO:0016042)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(2)	20	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			GGATCTTTCCCCCTTAGATGG	0.388																																					p.G308W		Atlas-SNP	.											.	LIPH	56	.	0			c.G922T						.						249	224	233					3																	185234915		2203	4300	6503	SO:0001583	missense	200879	exon7			CTTTCCCCCTTAG	AY093498	CCDS3272.1	3q27	2012-07-31			ENSG00000163898	ENSG00000163898			18483	protein-coding gene	gene with protein product		607365				12213196, 12063250	Standard	XM_006713529		Approved	mPA-PLA1, PLA1B, mPA-PLA1alpha, LPDLR	uc003fpm.3	Q8WWY8	OTTHUMG00000156657	ENST00000296252.4:c.922G>T	chr3.hg19:g.185234915C>A	ENSP00000296252:p.Gly308Trp	129.0	0.0		104.0	40.0	NM_139248	A2IBA7|Q8TEC7	Missense_Mutation	SNP	ENST00000296252.4	hg19	CCDS3272.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.090192	0.36855	.	.	ENSG00000163898	ENST00000296252;ENST00000424591	D;D	0.89552	-2.53;-2.39	5.7	-1.13	0.09775	Lipase, N-terminal (1);	1.193380	0.05899	N	0.629665	D	0.90676	0.7075	L	0.55990	1.75	0.09310	N	1	D;P	0.59767	0.986;0.837	P;P	0.58520	0.799;0.84	T	0.80571	-0.1323	10	0.72032	D	0.01	-3.5428	8.4521	0.32877	0.0:0.2996:0.483:0.2174	.	274;308	A2IBA6;Q8WWY8	.;LIPH_HUMAN	W	308;274	ENSP00000296252:G308W;ENSP00000396384:G274W	ENSP00000296252:G308W	G	-	1	0	LIPH	186717609	0.000000	0.05858	0.000000	0.03702	0.415000	0.31203	-0.191000	0.09601	0.055000	0.16094	0.563000	0.77884	GGG	.	.		0.388	LIPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345153.1			A	185234915	C	A	185234915	3	1	14	1	0	0	0	0	1	0	0	0	8833	623	22	3	449	3	LIPH	3	185234915	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	36376905	185234915	12787515	10	1242										
HS3ST1	9957	hgsc.bcm.edu	37	chr4	11401383	11401383	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gaagtggacctcgttctccgCggccgccacgtcggggtgca	15	14	1	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr4:11401383C>A	ENST00000002596.5	-	2	1421	c.247G>T	c.(247-249)Gcg>Tcg	p.A83S		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	83					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						TCGTTCTCCGCGGCCGCCACG	0.657																																					p.A83S		Atlas-SNP	.											.	HS3ST1	41	.	0			c.G247T						.						64	55	58					4																	11401383		2203	4300	6503	SO:0001583	missense	9957	exon2			TCTCCGCGGCCGC	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"Sulfotransferases, membrane-bound"	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.247G>T	chr4.hg19:g.11401383C>A	ENSP00000002596:p.Ala83Ser	79.0	0.0		67.0	25.0	NM_005114	B3KUA6|Q6PEY8	Missense_Mutation	SNP	ENST00000002596.5	hg19	CCDS3408.1	.	.	.	.	.	.	.	.	.	.	C	35	5.451715	0.96205	.	.	ENSG00000002587	ENST00000002596	T	0.51817	0.69	5.81	5.81	0.92471	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.66157	0.2761	L	0.58302	1.8	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.59016	-0.7533	10	0.29301	T	0.29	.	19.0707	0.93134	0.0:1.0:0.0:0.0	.	83	O14792	HS3S1_HUMAN	S	83	ENSP00000002596:A83S	ENSP00000002596:A83S	A	-	1	0	HS3ST1	11010481	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	7.818000	0.86416	2.746000	0.94184	0.655000	0.94253	GCG	.	.		0.657	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114		A	11401383	C	A	11401383	3	1	14	1	0	0	0	0	1	0	0	0	7372	768	27	1	680	1	HS3ST1	4	11401383	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10		11401383	179752893	11	1243										
NFXL1	152518	hgsc.bcm.edu	37	chr4	47907301	47907301	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	acaaattaggcatgtcatagCccctgcttgaaaagcttcat	7	10	2	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr4:47907301C>G	ENST00000507489.1	-	4	645	c.469G>C	c.(469-471)Gct>Cct	p.A157P	NFXL1_ENST00000381538.3_Missense_Mutation_p.A157P|NFXL1_ENST00000329043.3_Missense_Mutation_p.A157P	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	157						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						CATGTCATAGCCCCTGCTTGA	0.343																																					p.A157P		Atlas-SNP	.											.	NFXL1	79	.	0			c.G469C						.						158	165	163					4																	47907301		2203	4300	6503	SO:0001583	missense	152518	exon4			TCATAGCCCCTGC	AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"ovarian zinc finger protein"						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.469G>C	chr4.hg19:g.47907301C>G	ENSP00000422037:p.Ala157Pro	88.0	0.0		88.0	4.0	NM_152995	B1Q2K1|Q86VG1|Q8WVH1	Missense_Mutation	SNP	ENST00000507489.1	hg19	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	C	28.3	4.911594	0.92178	.	.	ENSG00000170448	ENST00000381538;ENST00000507489;ENST00000329043	T;T;T	0.67523	-0.27;-0.27;-0.27	5.84	5.84	0.93424	.	0.072469	0.51477	D	0.000081	T	0.80592	0.4652	M	0.69248	2.105	0.58432	D	0.999998	D	0.76494	0.999	D	0.67103	0.949	T	0.77259	-0.2654	10	0.36615	T	0.2	-15.1185	20.1295	0.97995	0.0:1.0:0.0:0.0	.	157	Q6ZNB6	NFXL1_HUMAN	P	157	ENSP00000370949:A157P;ENSP00000422037:A157P;ENSP00000333113:A157P	ENSP00000333113:A157P	A	-	1	0	NFXL1	47602058	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.587000	0.74071	2.758000	0.94735	0.591000	0.81541	GCT	.	.		0.343	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995		G	47907301	C	G	47907301	3	3	14	1	0	0	0	0	1	0	0	0	10397	739	26	4	2346	4	NFXL1	4	47907301	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	36505918	47907301	143246975	12	1244										
INTU	27152	hgsc.bcm.edu	37	chr4	128625436	128625436	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	acaattttggggtcttctctAttttacaaggtaagttgaag	9	5	2	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr4:128625436A>G	ENST00000335251.6	+	10	1660	c.1557A>G	c.(1555-1557)ctA>ctG	p.L519L	INTU_ENST00000512995.1_3'UTR	NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	519					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						GGTCTTCTCTATTTTACAAGG	0.318																																					p.L519L		Atlas-SNP	.											.	INTU	92	.	0			c.A1557G						.						111	117	115					4																	128625436		2203	4300	6503	SO:0001819	synonymous_variant	27152	exon10			TTCTCTATTTTAC	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.1557A>G	chr4.hg19:g.128625436A>G		89.0	0.0		128.0	8.0	NM_015693	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Silent	SNP	ENST00000335251.6	hg19	CCDS34061.1																																																																																			.	.		0.318	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		G	128625436	A	G	128625436	2	3	14	1	0	0	0	0	0	0	0	1	7795	436	16	2		2	INTU	4	128625436	Silent	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10	80718135	128625436	62528840	13	1245										
FGA	2243	hgsc.bcm.edu	37	chr4	155507053	155507053	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ttcatcagggtgcctatggcGgaacccatccagagtaccta	10	12	2	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr4:155507053G>A	ENST00000302053.3	-	5	1606	c.1528C>T	c.(1528-1530)Cgc>Tgc	p.R510C	FGA_ENST00000403106.3_Missense_Mutation_p.R510C	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	510					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	TGCCTATGGCGGAACCCATCC	0.488																																					p.R510C	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.C1528T						.						107	104	105					4																	155507053		2203	4300	6503	SO:0001583	missense	2243	exon5			TATGGCGGAACCC		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1528C>T	chr4.hg19:g.155507053G>A	ENSP00000306361:p.Arg510Cys	70.0	0.0		76.0	31.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.514680	0.44763	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.57107	0.42;0.42	5.56	-0.177	0.13307	Fibrinogen alpha C domain (1);	.	.	.	.	T	0.45316	0.1336	N	0.14661	0.345	0.09310	N	1	D;D	0.76494	0.998;0.999	P;P	0.60541	0.731;0.876	T	0.33854	-0.9852	9	0.36615	T	0.2	.	5.7513	0.18148	0.3491:0.437:0.2139:0.0	.	510;510	P02671-2;P02671	.;FIBA_HUMAN	C	510	ENSP00000306361:R510C;ENSP00000385981:R510C	ENSP00000306361:R510C	R	-	1	0	FGA	155726503	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.158000	0.10070	-0.260000	0.09418	0.655000	0.94253	CGC	.	.		0.488	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		A	155507053	G	A	155507053	3	1	14	1	0	0	0	0	1	0	0	0	5838	1116	39	1	1124	1	FGA	4	155507053	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	26881617	155507053	35647223	14	1246										
PLCXD3	345557	hgsc.bcm.edu	37	chr5	41382054	41382054	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tctcagtgatggatgcttgaAgaaactggatcagtttctcg	11	7	3	3			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr5:41382054A>G	ENST00000377801.3	-	2	760	c.686T>C	c.(685-687)cTt>cCt	p.L229P	PLCXD3_ENST00000328457.3_Missense_Mutation_p.L229P			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	229					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GGATGCTTGAAGAAACTGGAT	0.527																																					p.L229P		Atlas-SNP	.											.	PLCXD3	86	.	0			c.T686C						.						63	68	66					5																	41382054		2203	4300	6503	SO:0001583	missense	345557	exon2			GCTTGAAGAAACT		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.686T>C	chr5.hg19:g.41382054A>G	ENSP00000367032:p.Leu229Pro	82.0	0.0		132.0	42.0	NM_001005473	A6NL04	Missense_Mutation	SNP	ENST00000377801.3	hg19	CCDS34150.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.149324	0.78001	.	.	ENSG00000182836	ENST00000377801;ENST00000328457	.	.	.	6.07	6.07	0.98685	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.000000	0.85682	D	0.000000	T	0.80555	0.4645	M	0.81942	2.565	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.82993	-0.0181	9	0.87932	D	0	-13.1939	16.6406	0.85098	1.0:0.0:0.0:0.0	.	229	Q63HM9	PLCX3_HUMAN	P	229	.	ENSP00000333751:L229P	L	-	2	0	PLCXD3	41417811	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.852000	0.92215	2.326000	0.78906	0.533000	0.62120	CTT	.	.		0.527	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875		G	41382054	A	G	41382054	3	3	14	1	0	0	0	0	1	0	0	0	12052	72	3	2	287	2	PLCXD3	5	41382054	Missense_Mutation	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10		41382054	139533206	15	1247										
CHSY3	337876	hgsc.bcm.edu	37	chr5	129240619	129240619	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tcatcgcccccagggtggcgGagctgagcgagaggaagaga	17	10	1	3			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr5:129240619G>A	ENST00000305031.4	+	1	455	c.97G>A	c.(97-99)Gag>Aag	p.E33K	CTC-575N7.1_ENST00000503616.1_RNA|CTC-575N7.1_ENST00000515569.1_RNA	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	33					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		CAGGGTGGCGGAGCTGAGCGA	0.716																																					p.E33K		Atlas-SNP	.											.	CHSY3	92	.	0			c.G97A						.						7	8	8					5																	129240619		2129	4185	6314	SO:0001583	missense	337876	exon1			GTGGCGGAGCTGA	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.97G>A	chr5.hg19:g.129240619G>A	ENSP00000302629:p.Glu33Lys	57.0	0.0		39.0	11.0	NM_175856	B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	hg19	CCDS34223.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903842	0.72754	.	.	ENSG00000198108	ENST00000305031	T	0.72835	-0.69	2.69	2.69	0.31865	.	.	.	.	.	T	0.65112	0.2660	L	0.32530	0.975	0.52099	D	0.999945	D	0.55172	0.97	P	0.48704	0.587	T	0.64901	-0.6298	8	.	.	.	.	14.1047	0.65080	0.0:0.0:1.0:0.0	.	33	Q70JA7	CHSS3_HUMAN	K	33	ENSP00000302629:E33K	.	E	+	1	0	CHSY3	129268518	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.411000	0.73298	1.814000	0.52955	0.460000	0.39030	GAG	.	.		0.716	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856		A	129240619	G	A	129240619	3	1	14	1	0	0	0	0	1	0	0	0	3415	1175	41	3	99	3	CHSY3	5	129240619	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	87858565	129240619	51674641	16	1248										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130769233	130769233	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gaggaacaccgttcatcctgTagagctgcagacatggagtc	12	10	1	2	rs373104489		TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr5:130769233T>C	ENST00000509018.1	-	25	4069	c.3864A>G	c.(3862-3864)ctA>ctG	p.L1288L	RAPGEF6_ENST00000507093.1_Silent_p.L1296L|RAPGEF6_ENST00000307984.5_Silent_p.L1301L|CTC-432M15.3_ENST00000514667.1_Silent_p.L1338L|RAPGEF6_ENST00000296859.6_Silent_p.L1296L	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1288	Ser-rich.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		GTTCATCCTGTAGAGCTGCAG	0.502																																					p.L1301L	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.A3903G						.	T	,,,	1,4405	2.1+/-5.4	0,1,2202	180	147	158		3888,3903,3888,3864	-11.5	0.4	5		158	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAPGEF6	NM_001164386.1,NM_001164387.1,NM_001164388.1,NM_016340.5	,,,	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	,,,	1296/1610,1301/1510,1296/1505,1288/1602	130769233	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51735	exon27			ATCCTGTAGAGCT	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3864A>G	chr5.hg19:g.130769233T>C		134.0	0.0		137.0	69.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Silent	SNP	ENST00000509018.1	hg19	CCDS34225.1																																																																																			.	.		0.502	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		C	130769233	T	C	130769233	2	2	14	1	0	0	0	0	0	0	0	1	13063	1625	57	2		2	RAPGEF6	5	130769233	Silent	SNP	T	TCGA-2Y-A9H4-01A-11D-A382-10	1528614	130769233	50146027	17	1249										
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140257029	140257029	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tgaaggaccacggtgagcccGcgctgacgtccacggccacg	14	15	0	3			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr5:140257029G>A	ENST00000398631.2	+	1	1972	c.1972G>A	c.(1972-1974)Gcg>Acg	p.A658T	PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	658	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGTGAGCCCGCGCTGACGTC	0.692																																					p.A658T	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.G1972A						.						75	78	77					5																	140257029		2203	4299	6502	SO:0001583	missense	56137	exon1			GAGCCCGCGCTGA	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1972G>A	chr5.hg19:g.140257029G>A	ENSP00000381628:p.Ala658Thr	185.0	0.0		195.0	102.0	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	hg19	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	5.629	0.300800	0.10678	.	.	ENSG00000251664	ENST00000398631	T	0.52295	0.67	4.81	-0.584	0.11702	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.34454	0.0898	L	0.39147	1.195	0.09310	N	1	B;B	0.26318	0.035;0.146	B;B	0.28232	0.013;0.087	T	0.30001	-0.9993	9	0.56958	D	0.05	.	4.2249	0.10575	0.1494:0.4071:0.332:0.1115	.	658;658	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	T	658	ENSP00000381628:A658T	ENSP00000381628:A658T	A	+	1	0	PCDHA12	140237213	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.325000	0.07976	-0.510000	0.06523	0.561000	0.74099	GCG	.	.		0.692	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140257029	G	A	140257029	3	1	14	1	0	0	0	0	1	0	0	0	11531	1087	38	1	1974	1	PCDHA12	5	140257029	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	9487796	140257029	40658231	18	1250										
CLK4	57396	hgsc.bcm.edu	37	chr5	178040819	178040819	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	acggcctacattttttacgaTtttcactgctacatgcatgc	6	11	1	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr5:178040819T>G	ENST00000316308.4	-	6	736	c.568A>C	c.(568-570)Atc>Ctc	p.I190L		NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	190	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		TTTTTTACGATTTTCACTGCT	0.353																																					p.I190L		Atlas-SNP	.											CLK4_ENST00000316308,NS,carcinoma,0,2	CLK4	103	.	0			c.A568C						.						116	111	113					5																	178040819		2203	4299	6502	SO:0001583	missense	57396	exon6			TTACGATTTTCAC	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.568A>C	chr5.hg19:g.178040819T>G	ENSP00000316948:p.Ile190Leu	129.0	0.0		129.0	81.0	NM_020666		Missense_Mutation	SNP	ENST00000316308.4	hg19	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.773026	0.90108	.	.	ENSG00000113240	ENST00000316308;ENST00000536763	T	0.20738	2.05	5.17	5.17	0.71159	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.40448	0.1117	L	0.52266	1.64	0.80722	D	1	D;P;P	0.63046	0.992;0.937;0.937	D;D;D	0.85130	0.997;0.997;0.997	T	0.22626	-1.0211	10	0.87932	D	0	.	13.24	0.59992	0.0:0.0:0.0:1.0	.	190;190;190	B7ZL31;B9EG64;Q9HAZ1	.;.;CLK4_HUMAN	L	190	ENSP00000316948:I190L	ENSP00000316948:I190L	I	-	1	0	CLK4	177973425	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.930000	0.87610	2.074000	0.62210	0.482000	0.46254	ATC	.	.		0.353	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			G	178040819	T	G	178040819	3	3	14	1	0	0	0	0	1	0	0	0	3541	1493	52	5	909	5	CLK4	5	178040819	Missense_Mutation	SNP	T	TCGA-2Y-A9H4-01A-11D-A382-10	37783790	178040819	2874441	19	1251										
FLT4	2324	hgsc.bcm.edu	37	chr5	180041181	180041214	+	Splice_Site	DEL	TGGGGAGACAGAGGGAAGCTTGTCCCGTGGTGGA	TGGGGAGACAGAGGGAAGCTTGTCCCGTGGTGGA	-													0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	acttcaggggcagccgggccTggggagacagagggaagctt					rs659268|rs2934602|rs373004354|rs2934601|rs369575233|rs368887610|rs201584222	byFrequency	TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	TGGGGAGACAGAGGGAAGCTTGTCCCGTGGTGGA	TGGGGAGACAGAGGGAAGCTTGTCCCGTGGTGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr5:180041181_180041214delTGGGGAGACAGAGGGAAGCTTGTCCCGTGGTGGA	ENST00000261937.6	-	24	3298		c.e24-2		FLT4_ENST00000393347.3_Splice_Site|FLT4_ENST00000502649.1_Splice_Site	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4						blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGCCGGGCCTGGGGAGACAGAGGGAAGCTTGTCCCGTGGTGGATGGGGAGACG	0.641																																					.	Colon(97;1075 1466 27033 27547 35871)	Pindel	.											.	FLT4	356	.	0			.						.																																			SO:0001630	splice_region_variant	2324	.			.	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3220-2TCCACCACGGGACAAGCTTCCCTCTGTCTCCCCA>-	chr5.hg19:g.180041181_180041214delTGGGGAGACAGAGGGAAGCTTGTCCCGTGGTGGA		93.0	0.0		96.0	14.0	.	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Splice_Site	DEL	ENST00000261937.6	hg19	CCDS4457.1																																																																																			.	.		0.641	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		Intron	-	180041214	TGGGGAGACAGAGGGAAGCTTGTCCCGTGGTGGA	-	180041181	8	5	14	1	0	1	0	1	0	0	1	0	5952	1594	55	0	909	0	FLT4	5	180041181	Splice_Site	DEL	TGGGGAGACAGAGGGAAGCTTGTCCCGTGGTGGA	TCGA-2Y-A9H4-01A-11D-A382-10	2000362	180041181	874079	20	1252										
TRIM7	81786	hgsc.bcm.edu	37	chr5	180622567	180622567	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gcgggtgttggtgtcgaagcGgcaggggtggttgggcaggt	23	5	0	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr5:180622567G>A	ENST00000274773.7	-	7	1196	c.1135C>T	c.(1135-1137)Cgc>Tgc	p.R379C	CTC-338M12.6_ENST00000512508.1_RNA|TRIM7_ENST00000393315.1_Missense_Mutation_p.R171C|CTC-338M12.5_ENST00000508877.1_RNA|TRIM7_ENST00000504241.1_5'UTR|CTC-338M12.5_ENST00000514487.1_RNA|CTC-338M12.6_ENST00000502812.2_RNA|TRIM7_ENST00000422067.2_Missense_Mutation_p.R171C|CTC-338M12.6_ENST00000509080.1_RNA|TRIM7_ENST00000361809.3_Missense_Mutation_p.R171C|TRIM7_ENST00000393319.3_Missense_Mutation_p.R197C	NM_203293.1	NP_976038.1	Q9C029	TRIM7_HUMAN	tripartite motif containing 7	379	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|stomach(1)	17	all_cancers(89;6.03e-06)|all_epithelial(37;7.1e-07)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000172)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;2e-06)|Epithelial(171;1.35e-05)|OV - Ovarian serous cystadenocarcinoma(192;0.000128)|Kidney(146;0.0674)|GBM - Glioblastoma multiforme(465;0.0802)		GTGTCGAAGCGGCAGGGGTGG	0.687																																					p.R379C	Esophageal Squamous(128;2258 2308 35507 48647)	Atlas-SNP	.											.	TRIM7	56	.	0			c.C1135T						.						36	38	37					5																	180622567		2196	4271	6467	SO:0001583	missense	81786	exon7			CGAAGCGGCAGGG	AF220032	CCDS4462.1, CCDS4463.1, CCDS4464.1, CCDS43414.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146054	ENSG00000146054		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16278	protein-coding gene	gene with protein product	"glycogenin-interacting protein", "tripartite motif protein TRIM7"	609315	"tripartite motif-containing 7"			11331580	Standard	NM_203294		Approved	RNF90, GNIP	uc003mmz.1	Q9C029	OTTHUMG00000130963	ENST00000274773.7:c.1135C>T	chr5.hg19:g.180622567G>A	ENSP00000274773:p.Arg379Cys	166.0	0.0		160.0	7.0	NM_203293	A2RUE4|D3DWR7|Q969F5|Q96F67|Q96J89|Q96J90	Missense_Mutation	SNP	ENST00000274773.7	hg19	CCDS4462.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.943644	0.53079	.	.	ENSG00000146054	ENST00000274773;ENST00000393315;ENST00000361809;ENST00000393319;ENST00000422067	T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24	4.74	4.74	0.60224	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.000000	0.51477	D	0.000084	D	0.82664	0.5086	H	0.95224	3.64	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.88272	0.2930	10	0.87932	D	0	.	15.2392	0.73455	0.0:0.0:1.0:0.0	.	379;197	Q9C029;Q9C029-4	TRIM7_HUMAN;.	C	379;171;171;197;171	ENSP00000274773:R379C;ENSP00000376991:R171C;ENSP00000355059:R171C;ENSP00000376994:R197C;ENSP00000391458:R171C	ENSP00000274773:R379C	R	-	1	0	TRIM7	180555173	0.997000	0.39634	0.664000	0.29753	0.104000	0.19210	2.598000	0.46223	2.166000	0.68216	0.549000	0.68633	CGC	.	.		0.687	TRIM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253569.3	NM_203296		A	180622567	G	A	180622567	3	1	14	1	0	0	0	0	1	0	0	0	16558	1116	39	1	404	1	TRIM7	5	180622567	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	581386	180622567	292693	21	1253										
C6orf27	80737	hgsc.bcm.edu	37	chr6	31736935	31736935	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ggacaagatctcacgccgagCtcgaccctgaacccttgatg	10	14	1	3			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr6:31736935C>T	ENST00000375688.4	-	10	1563	c.1363G>A	c.(1363-1365)Gct>Act	p.A455T	VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000375686.3_Missense_Mutation_p.A455T|VWA7_ENST00000447450.1_Missense_Mutation_p.A455T			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	455	VWFA.					extracellular region (GO:0005576)											TCACGCCGAGCTCGACCCTGA	0.522																																					p.A455T		Atlas-SNP	.											.	.	.	.	0			c.G1363A						.						158	111	128					6																	31736935		1511	2709	4220	SO:0001583	missense	80737	exon10			GCCGAGCTCGACC		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"chromosome 6 open reading frame 27"	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.1363G>A	chr6.hg19:g.31736935C>T	ENSP00000364840:p.Ala455Thr	74.0	0.0		54.0	19.0	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	hg19	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	C	7.206	0.594503	0.13875	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	T;T;T	0.30182	2.75;2.54;1.54	5.65	-1.68	0.08212	von Willebrand factor, type A (1);	1.131360	0.06463	N	0.729808	T	0.03520	0.0101	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.39761	-0.9598	10	0.23891	T	0.37	0.2041	5.7011	0.17883	0.0:0.3373:0.3064:0.3563	.	455	Q9Y334	G7C_HUMAN	T	455	ENSP00000364840:A455T;ENSP00000364838:A455T;ENSP00000390554:A455T	ENSP00000364838:A455T	A	-	1	0	C6orf27	31844914	0.000000	0.05858	0.001000	0.08648	0.135000	0.20990	-0.336000	0.07863	-0.422000	0.07405	0.462000	0.41574	GCT	.	.		0.522	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		T	31736935	C	T	31736935	3	4	14	1	0	0	0	0	1	0	0	0	2364	797	28	3	1343	3	C6orf27	6	31736935	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10		31736935	139378132	22	1254										
TDRD6	221400	hgsc.bcm.edu	37	chr6	46658262	46658262	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	aggaacatacaaggacttaaAactctaatgtctgatattca	6	7	3	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr6:46658262A>C	ENST00000316081.6	+	1	2397	c.2397A>C	c.(2395-2397)aaA>aaC	p.K799N	RP11-446F17.3_ENST00000422284.2_RNA|TDRD6_ENST00000544460.1_Missense_Mutation_p.K799N|RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000434329.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	799					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			AAGGACTTAAAACTCTAATGT	0.423																																					p.K799N		Atlas-SNP	.											.	TDRD6	205	.	0			c.A2397C						.						91	94	93					6																	46658262		2203	4300	6503	SO:0001583	missense	221400	exon1			ACTTAAAACTCTA	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.2397A>C	chr6.hg19:g.46658262A>C	ENSP00000346065:p.Lys799Asn	149.0	0.0		140.0	65.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	hg19	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	A	11.51	1.661681	0.29515	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.09163	3.01;3.01	5.75	3.34	0.38264	Maternal tudor protein (1);	0.578652	0.20572	N	0.089702	T	0.01870	0.0059	N	0.25890	0.77	0.09310	N	1	B;B	0.17852	0.02;0.024	B;B	0.22152	0.022;0.038	T	0.46048	-0.9219	10	0.18276	T	0.48	-17.4949	4.1992	0.10458	0.615:0.0:0.2405:0.1445	.	799;799	F5H5M3;O60522	.;TDRD6_HUMAN	N	799	ENSP00000443299:K799N;ENSP00000346065:K799N	ENSP00000346065:K799N	K	+	3	2	TDRD6	46766221	0.003000	0.15002	0.162000	0.22713	0.869000	0.49853	1.379000	0.34340	0.968000	0.38212	0.533000	0.62120	AAA	.	.		0.423	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		C	46658262	A	C	46658262	3	2	14	1	0	0	0	0	1	0	0	0	15749	11	1	5	2399	5	TDRD6	6	46658262	Missense_Mutation	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10	14921327	46658262	124456805	23	1255										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128320011	128320012	+	Frame_Shift_Ins	INS	-	-	A													0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	aggtagcgaggtacgtctagINSaaggcgactggactctgctg							TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr6:128320011_128320012insA	ENST00000368215.3	-	16	2528_2529	c.2529_2530insT	c.(2527-2532)cttctafs	p.L844fs	PTPRK_ENST00000368210.3_Frame_Shift_Ins_p.L857fs|PTPRK_ENST00000524481.1_5'Flank|PTPRK_ENST00000368207.3_Frame_Shift_Ins_p.L871fs|PTPRK_ENST00000368226.4_Frame_Shift_Ins_p.L845fs|PTPRK_ENST00000532331.1_Frame_Shift_Ins_p.L861fs|PTPRK_ENST00000368213.5_Frame_Shift_Ins_p.L845fs|PTPRK_ENST00000368227.3_Frame_Shift_Ins_p.L857fs			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	844					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		GGTACGTCTAGAAGGCGACTGG	0.446																																					p.L845fs		Atlas-Indel,Pindel	.											.	PTPRK	330	.	0			c.2533_2534insT						.																																			SO:0001589	frameshift_variant	5796	exon16			.	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2530dupT	chr6.hg19:g.128320013_128320013dupA	ENSP00000357198:p.Leu844fs	65.0	0.0		106.0	36.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Frame_Shift_Ins	INS	ENST00000368215.3	hg19																																																																																				.	.		0.446	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			A	128320012	-	A	128320011	7	5	14	1	0	1	1	0	0	0	0	0	12820	933	33	0	1871	0	PTPRK	6	128320011	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H4-01A-11D-A382-10	81661749	128320011	42795056	24	1256										
MUC17	140453	hgsc.bcm.edu	37	chr7	100685401	100685401	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	caggtcaccactatgcgtatGtctactccaagtgaaggaag	10	10	2	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr7:100685401G>T	ENST00000306151.4	+	3	10768	c.10704G>T	c.(10702-10704)atG>atT	p.M3568I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3568	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CTATGCGTATGTCTACTCCAA	0.468																																					p.M3568I		Atlas-SNP	.											.	MUC17	804	.	0			c.G10704T						.						208	207	208					7																	100685401		2203	4300	6503	SO:0001583	missense	140453	exon3			GCGTATGTCTACT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.10704G>T	chr7.hg19:g.100685401G>T	ENSP00000302716:p.Met3568Ile	89.0	0.0		81.0	40.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	0.025	-1.380485	0.01204	.	.	ENSG00000169876	ENST00000306151	T	0.01838	4.61	1.34	-2.68	0.06041	.	.	.	.	.	T	0.01156	0.0038	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.21546	0.035	T	0.46303	-0.9201	9	0.37606	T	0.19	.	0.8373	0.01142	0.1665:0.3307:0.1729:0.3299	.	3568	Q685J3	MUC17_HUMAN	I	3568	ENSP00000302716:M3568I	ENSP00000302716:M3568I	M	+	3	0	MUC17	100472121	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.229000	0.00549	-2.030000	0.00929	-1.038000	0.02383	ATG	.	.		0.468	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100685401	G	T	100685401	3	4	14	1	0	0	0	0	1	0	0	0	9983	1377	48	3	10714	3	MUC17	7	100685401	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10		100685401	58453262	25	1257										
SNX16	64089	hgsc.bcm.edu	37	chr8	82752214	82752214	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	taggaactgggacataaggaGttgccatcttcttttggctt	11	7	2	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr8:82752214G>T	ENST00000345957.4	-	2	286	c.8C>A	c.(7-9)aCt>aAt	p.T3N	SNX16_ENST00000353788.4_Missense_Mutation_p.T3N|SNX16_ENST00000396330.2_Missense_Mutation_p.T3N	NM_152836.2	NP_690049.1	P57768	SNX16_HUMAN	sorting nexin 16	3					early endosome to late endosome transport (GO:0045022)|endosome to lysosome transport (GO:0008333)|protein targeting to lysosome (GO:0006622)	early endosome (GO:0005769)|extrinsic component of endosome membrane (GO:0031313)|late endosome (GO:0005770)|lysosome (GO:0005764)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			large_intestine(1)|ovary(1)|pancreas(1)|skin(2)	5						GACATAAGGAGTTGCCATCTT	0.393																																					p.T3N		Atlas-SNP	.											.	SNX16	21	.	0			c.C8A						.						138	136	137					8																	82752214		2203	4300	6503	SO:0001583	missense	64089	exon2			TAAGGAGTTGCCA	AF305779	CCDS6234.1, CCDS6235.1	8q21.13	2011-05-03			ENSG00000104497	ENSG00000104497		"Sorting nexins"	14980	protein-coding gene	gene with protein product		614903				12461558, 12813048	Standard	NM_152837		Approved		uc003ycn.3	P57768	OTTHUMG00000164727	ENST00000345957.4:c.8C>A	chr8.hg19:g.82752214G>T	ENSP00000322652:p.Thr3Asn	50.0	0.0		37.0	11.0	NM_152836	A8K4D8|Q658L0|Q8N4U3	Missense_Mutation	SNP	ENST00000345957.4	hg19	CCDS6234.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.298349	0.81025	.	.	ENSG00000104497	ENST00000353788;ENST00000396330;ENST00000345957;ENST00000520618;ENST00000523757;ENST00000521810;ENST00000519119;ENST00000519817;ENST00000518183;ENST00000521773	T;T;T;T;T;T;T	0.56611	0.67;0.59;0.59;0.72;0.68;0.74;0.45	5.64	5.64	0.86602	.	0.103190	0.64402	D	0.000002	T	0.67785	0.2930	M	0.68317	2.08	0.42183	D	0.991694	D;D	0.58970	0.984;0.984	P;P	0.56612	0.802;0.802	T	0.70699	-0.4800	10	0.72032	D	0.01	-7.4989	18.7004	0.91618	0.0:0.0:1.0:0.0	.	3;3	Q658L0;P57768	.;SNX16_HUMAN	N	3	ENSP00000322631:T3N;ENSP00000379621:T3N;ENSP00000322652:T3N;ENSP00000428699:T3N;ENSP00000430038:T3N;ENSP00000428734:T3N;ENSP00000427876:T3N	ENSP00000322652:T3N	T	-	2	0	SNX16	82914769	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.891000	0.87319	2.681000	0.91329	0.561000	0.74099	ACT	.	.		0.393	SNX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379929.1	NM_022133		T	82752214	G	T	82752214	3	4	14	1	0	0	0	0	1	0	0	0	14902	1029	36	3	1054	3	SNX16	8	82752214	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10		82752214	63611808	26	1258										
GPIHBP1	338328	hgsc.bcm.edu	37	chr8	144297217	144297217	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	cggtggaggggacccaggtgAccatgacctgctgccagtcc	15	13	0	2	rs369222108		TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr8:144297217A>T	ENST00000330824.2	+	4	454	c.379A>T	c.(379-381)Acc>Tcc	p.T127S		NM_178172.3	NP_835466.1	Q8IV16	HDBP1_HUMAN	glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1	127	UPAR/Ly6.				cholesterol homeostasis (GO:0042632)|intracellular protein transport (GO:0006886)|positive regulation of chylomicron remnant clearance (GO:0090321)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein import (GO:0017038)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|protein transmembrane transport (GO:0071806)|response to heparin (GO:0071503)|transcytosis (GO:0045056)|triglyceride homeostasis (GO:0070328)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|external side of plasma membrane (GO:0009897)|high-density lipoprotein particle (GO:0034364)	chylomicron binding (GO:0035478)|lipase binding (GO:0035473)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|protein transmembrane transporter activity (GO:0008320)			lung(2)	2	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GACCCAGGTGACCATGACCTG	0.672																																					p.T127S		Atlas-SNP	.											.	GPIHBP1	12	.	0			c.A379T						.						74	74	74					8																	144297217		2203	4298	6501	SO:0001583	missense	338328	exon4			CAGGTGACCATGA	AF088057	CCDS34954.1	8q24.3	2014-07-14	2008-02-07						24945	protein-coding gene	gene with protein product	"endothelial cell LPL transporter"	612757	"GPI anchored high density lipoprotein binding protein 1"			12496272, 17883852, 17620854, 17403372	Standard	NM_178172		Approved	LOC338328, GPI-HBP1	uc003yxu.2	Q8IV16		ENST00000330824.2:c.379A>T	chr8.hg19:g.144297217A>T	ENSP00000329266:p.Thr127Ser	104.0	0.0		114.0	61.0	NM_178172	Q6P3T2|Q86W15	Missense_Mutation	SNP	ENST00000330824.2	hg19	CCDS34954.1	.	.	.	.	.	.	.	.	.	.	A	11.87	1.768697	0.31320	.	.	ENSG00000182851	ENST00000330824	T	0.69306	-0.39	4.39	3.23	0.37069	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	0.139481	0.33572	N	0.004777	T	0.69251	0.3090	M	0.70595	2.14	0.09310	N	1	D	0.55605	0.972	P	0.51701	0.677	T	0.61178	-0.7115	10	0.49607	T	0.09	-10.3827	6.7826	0.23654	0.8892:0.0:0.1108:0.0	.	127	Q8IV16	HDBP1_HUMAN	S	127	ENSP00000329266:T127S	ENSP00000329266:T127S	T	+	1	0	GPIHBP1	144368592	0.803000	0.28956	0.015000	0.15790	0.053000	0.15095	2.561000	0.45905	0.648000	0.30732	0.374000	0.22700	ACC	.	.		0.672	GPIHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381113.1	NM_178172		T	144297217	A	T	144297217	3	4	14	1	0	0	0	0	1	0	0	0	6620	275	10	4	393	4	GPIHBP1	8	144297217	Missense_Mutation	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10	61545003	144297217	2066805	27	1259										
GNA14	9630	hgsc.bcm.edu	37	chr9	80144021	80144021	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	acatactgtatccttagcgtGtccatcgctctgatcatggc	8	12	2	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr9:80144021G>A	ENST00000341700.6	-	2	786	c.273C>T	c.(271-273)gaC>gaT	p.D91D	RP11-466A17.1_ENST00000439145.1_RNA	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	91					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						TCCTTAGCGTGTCCATCGCTC	0.483																																					p.D91D		Atlas-SNP	.											.	GNA14	50	.	0			c.C273T						.						387	307	334					9																	80144021		2203	4300	6503	SO:0001819	synonymous_variant	9630	exon2			TAGCGTGTCCATC	AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.273C>T	chr9.hg19:g.80144021G>A		128.0	0.0		117.0	34.0	NM_004297	B1ALW3	Silent	SNP	ENST00000341700.6	hg19	CCDS6657.1																																																																																			.	.		0.483	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1			A	80144021	G	A	80144021	2	1	14	1	0	0	0	0	0	0	0	1	6510	1368	48	3		3	GNA14	9	80144021	Silent	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10		80144021	61069410	28	1260										
TMEFF1	8577	hgsc.bcm.edu	37	chr9	103278965	103278965	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ctttttaaacagaagaggaaGggtcaggggcagaagttcac	13	6	2	3			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr9:103278965G>A	ENST00000374879.4	+	5	904	c.472G>A	c.(472-474)Ggg>Agg	p.G158R	TMEFF1_ENST00000334943.6_Missense_Mutation_p.G119R|MSANTD3-TMEFF1_ENST00000502978.1_Missense_Mutation_p.R121K	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	158					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				AGAAGAGGAAGGGTCAGGGGC	0.398																																					p.G232R		Atlas-SNP	.											.	.	.	.	0			c.G694A						.						90	85	87					9																	103278965		2203	4300	6503	SO:0001583	missense	100526694	exon5			GAGGAAGGGTCAG	U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"tomoregulin-1", "cancer/testis antigen family 120, member 1"	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.472G>A	chr9.hg19:g.103278965G>A	ENSP00000364013:p.Gly158Arg	133.0	0.0		101.0	32.0	NM_001198812	Q13086|Q8N3T8	Missense_Mutation	SNP	ENST00000374879.4	hg19	CCDS6750.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.3|26.3	4.723128|4.723128	0.89298|0.89298	.|.	.|.	ENSG00000241697|ENSG00000251349	ENST00000334943;ENST00000374879|ENST00000502978	T;T|.	0.59502|.	0.27;0.26|.	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59418|0.59418	0.2192|0.2192	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.79108|.	0.986;0.992|.	T|T	0.50725|0.50725	-0.8794|-0.8794	10|5	0.23891|.	T|.	0.37|.	-10.9338|-10.9338	18.0718|18.0718	0.89410|0.89410	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	158;119|.	Q8IYR6;Q8IYR6-2|.	TEFF1_HUMAN;.|.	R|K	119;158|121	ENSP00000334447:G119R;ENSP00000364013:G158R|.	ENSP00000334447:G119R|.	G|R	+|+	1|2	0|0	TMEFF1|C9orf30-TMEFF1	102318786|102318786	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.998000|7.998000	0.88491|0.88491	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GGG|AGG	.	.		0.398	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692		A	103278965	G	A	103278965	3	1	14	1	0	0	0	0	1	0	0	0	16028	1000	35	3	490	3	TMEFF1	9	103278965	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	23134944	103278965	37934466	29	1261										
PAPPA	5069	hgsc.bcm.edu	37	chr9	119097256	119097256	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gcttcagttcgcccctggtcGccatctcgggggtggccctc	13	16	2	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr9:119097256G>A	ENST00000328252.3	+	13	3883	c.3514G>A	c.(3514-3516)Gcc>Acc	p.A1172T	PAPPA_ENST00000534838.1_Missense_Mutation_p.A210T	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1172					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						GCCCCTGGTCGCCATCTCGGG	0.617																																					p.A1172T		Atlas-SNP	.											.	PAPPA	243	.	0			c.G3514A						.						113	95	101					9																	119097256		2203	4300	6503	SO:0001583	missense	5069	exon13			CTGGTCGCCATCT		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.3514G>A	chr9.hg19:g.119097256G>A	ENSP00000330658:p.Ala1172Thr	98.0	0.0		72.0	24.0	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	hg19	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	G	36	5.637047	0.96693	.	.	ENSG00000182752	ENST00000328252;ENST00000534838	T;T	0.05319	4.24;3.46	5.86	5.86	0.93980	.	0.045243	0.85682	D	0.000000	T	0.29491	0.0735	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	0.983;1.0	P;D	0.87578	0.45;0.998	T	0.00436	-1.1740	10	0.72032	D	0.01	-25.892	20.1865	0.98220	0.0:0.0:1.0:0.0	.	210;1172	F5GZ19;Q13219	.;PAPP1_HUMAN	T	1172;210	ENSP00000330658:A1172T;ENSP00000441461:A210T	ENSP00000330658:A1172T	A	+	1	0	PAPPA	118137077	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.434000	0.97515	2.775000	0.95449	0.655000	0.94253	GCC	.	.		0.617	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		A	119097256	G	A	119097256	3	1	14	1	0	0	0	0	1	0	0	0	11441	1087	38	1	3564	1	PAPPA	9	119097256	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	15818291	119097256	22116175	30	1262										
ST8SIA6	338596	hgsc.bcm.edu	37	chr10	17363249	17363249	+	Frame_Shift_Del	DEL	G	G	-													0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ttgaaagaggtacccgtgttGgccctgaaggaaaatgctgg							TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr10:17363249delG	ENST00000377602.4	-	8	899	c.825delC	c.(823-825)gccfs	p.A275fs		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	275					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						TACCCGTGTTGGCCCTGAAGG	0.428																																					p.N276fs		Atlas-Indel,Pindel	.											.	ST8SIA6	85	.	0			c.826delA						.						94	103	100					10																	17363249		2203	4300	6503	SO:0001589	frameshift_variant	338596	exon8			.		CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.825delC	chr10.hg19:g.17363249delG	ENSP00000366827:p.Ala275fs	220.0	0.0		206.0	30.0	NM_001004470	B0YJ97|B9EH72|Q5VZH4	Frame_Shift_Del	DEL	ENST00000377602.4	hg19	CCDS31158.1																																																																																			.	.		0.428	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		-	17363249	G	-	17363249	7	5	14	1	0	1	0	1	0	0	0	0	15251	1335	47	0	375	0	ST8SIA6	10	17363249	Frame_Shift_Del	DEL	G	TCGA-2Y-A9H4-01A-11D-A382-10		17363249	118171498	31	1263										
PRRG4	79056	hgsc.bcm.edu	37	chr11	32875007	32875007	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	cacagtgtttcaccaccaccAccatatcctgggcacacaaa	5	16	1	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr11:32875007A>G	ENST00000257836.3	+	6	868	c.615A>G	c.(613-615)ccA>ccG	p.P205P		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	205	Poly-Pro.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	7	Breast(20;0.206)					CACCACCACCACCATATCCTG	0.443																																					p.P205P		Atlas-SNP	.											.	PRRG4	15	.	0			c.A615G						.						124	123	123					11																	32875007		2202	4299	6501	SO:0001819	synonymous_variant	79056	exon6			ACCACCACCATAT	AF326351	CCDS7881.1	11p13	2008-02-05			ENSG00000135378	ENSG00000135378			30799	protein-coding gene	gene with protein product		611690				11171957	Standard	NM_024081		Approved	TMG4	uc001mtx.3	Q9BZD6	OTTHUMG00000166219	ENST00000257836.3:c.615A>G	chr11.hg19:g.32875007A>G		122.0	0.0		97.0	41.0	NM_024081		Silent	SNP	ENST00000257836.3	hg19	CCDS7881.1																																																																																			.	.		0.443	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081		G	32875007	A	G	32875007	2	3	14	1	0	0	0	0	0	0	0	1	12620	146	6	2		2	PRRG4	11	32875007	Silent	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10		32875007	102131509	32	1264										
OR4S2	219431	hgsc.bcm.edu	37	chr11	55419121	55419121	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	acattgccatggtcgttatcTttttcggcccctgtactttt	7	11	1	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr11:55419121T>C	ENST00000312422.2	+	1	742	c.742T>C	c.(742-744)Ttt>Ctt	p.F248L		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				GGTCGTTATCTTTTTCGGCCC	0.483																																					p.F248L		Atlas-SNP	.											.	OR4S2	89	.	0			c.T742C						.						169	138	149					11																	55419121		2179	4027	6206	SO:0001583	missense	219431	exon1			GTTATCTTTTTCG	BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"GPCR / Class A : Olfactory receptors"	15183	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily S, member 2 pseudogene"	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.742T>C	chr11.hg19:g.55419121T>C	ENSP00000310337:p.Phe248Leu	81.0	0.0		124.0	43.0	NM_001004059	Q6IF72	Missense_Mutation	SNP	ENST00000312422.2	hg19	CCDS31505.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.380776	0.42207	.	.	ENSG00000174982	ENST00000312422	T	0.00285	8.3	5.35	5.35	0.76521	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000040	T	0.00300	0.0009	M	0.78223	2.4	0.32788	N	0.501534	B	0.30326	0.276	B	0.31614	0.133	T	0.18555	-1.0333	10	0.72032	D	0.01	.	9.509	0.39065	0.0:0.0842:0.0:0.9158	.	248	Q8NH73	OR4S2_HUMAN	L	248	ENSP00000310337:F248L	ENSP00000310337:F248L	F	+	1	0	OR4S2	55175697	0.002000	0.14202	1.000000	0.80357	0.591000	0.36615	1.170000	0.31883	2.028000	0.59812	0.443000	0.29094	TTT	.	.		0.483	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059		C	55419121	T	C	55419121	3	2	14	1	0	0	0	0	1	0	0	0	11092	1609	56	2	744	2	OR4S2	11	55419121	Missense_Mutation	SNP	T	TCGA-2Y-A9H4-01A-11D-A382-10	22544114	55419121	79587395	33	1265										
RELA	5970	hgsc.bcm.edu	37	chr11	65422301	65422301	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ggctggggcctgggccagagCtgataccatggctggagcag	18	10	0	2			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr11:65422301C>A	ENST00000406246.3	-	11	1465	c.1204G>T	c.(1204-1206)Gct>Tct	p.A402S	RELA_ENST00000308639.9_Missense_Mutation_p.A399S|RELA_ENST00000525693.1_3'UTR	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	402					acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						tgggccagagctgataccatg	0.716																																					p.A402S		Atlas-SNP	.											.	RELA	44	.	0			c.G1204T						.						6	8	7					11																	65422301		2156	4233	6389	SO:0001583	missense	5970	exon11			CCAGAGCTGATAC	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1204G>T	chr11.hg19:g.65422301C>A	ENSP00000384273:p.Ala402Ser	153.0	0.0		108.0	41.0	NM_021975	Q6GTV1|Q6SLK1	Missense_Mutation	SNP	ENST00000406246.3	hg19	CCDS31609.1	.	.	.	.	.	.	.	.	.	.	C	1.361	-0.588830	0.03799	.	.	ENSG00000173039	ENST00000406246;ENST00000308639;ENST00000545816;ENST00000532999	T;T;T	0.49432	0.78;0.78;0.78	3.82	0.804	0.18697	.	2.226600	0.01700	N	0.027155	T	0.27241	0.0668	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.002;0.002;0.001;0.0	T	0.22034	-1.0228	10	0.02654	T	1	0.4006	5.6637	0.17682	0.0:0.495:0.3917:0.1133	.	392;389;399;402;413	Q04206-3;Q04206-2;Q04206-4;Q04206;B4E082	.;.;.;TF65_HUMAN;.	S	402;399;413;413	ENSP00000384273:A402S;ENSP00000311508:A399S;ENSP00000433526:A413S	ENSP00000311508:A399S	A	-	1	0	RELA	65178877	0.008000	0.16893	0.001000	0.08648	0.771000	0.43674	-0.111000	0.10807	-0.000000	0.14550	-0.287000	0.09952	GCT	.	.		0.716	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		A	65422301	C	A	65422301	3	1	14	1	0	0	0	0	1	0	0	0	13231	797	28	3	455	3	RELA	11	65422301	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	10003180	65422301	69584215	34	1266										
OAF	220323	hgsc.bcm.edu	37	chr11	120082155	120082155	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gcggacagcgacgcggacagCatcagcctcgagctgcgcaa	14	14	1	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr11:120082155C>T	ENST00000328965.4	+	1	681	c.168C>T	c.(166-168)agC>agT	p.S56S	OAF_ENST00000531220.1_5'UTR	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	56						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(5)	6		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		ACGCGGACAGCATCAGCCTCG	0.711																																					p.S56S		Atlas-SNP	.											.	OAF	12	.	0			c.C168T						.						18	18	18					11																	120082155		2192	4283	6475	SO:0001819	synonymous_variant	220323	exon1			GGACAGCATCAGC	BC047726	CCDS8430.1	11q23.3	2010-11-23			ENSG00000184232	ENSG00000184232			28752	protein-coding gene	gene with protein product						12477932	Standard	NM_178507		Approved	MGC52117	uc001pxb.3	Q86UD1	OTTHUMG00000166139	ENST00000328965.4:c.168C>T	chr11.hg19:g.120082155C>T		155.0	0.0		106.0	41.0	NM_178507		Silent	SNP	ENST00000328965.4	hg19	CCDS8430.1																																																																																			.	.		0.711	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507		T	120082155	C	T	120082155	2	4	14	1	0	0	0	0	0	0	0	1	10807	709	25	3		3	OAF	11	120082155	Silent	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	54659854	120082155	14924361	35	1267										
OR6X1	390260	hgsc.bcm.edu	37	chr11	123624701	123624701	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	actgggcccaacatcacagtAgaaatgactgataacattat	7	9	1	3			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr11:123624701A>G	ENST00000327930.2	-	1	552	c.526T>C	c.(526-528)Tac>Cac	p.Y176H		NM_001005188.1	NP_001005188.1	Q8NH79	OR6X1_HUMAN	olfactory receptor, family 6, subfamily X, member 1	176						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)	23		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		ACATCACAGTAGAAATGACTG	0.512																																					p.Y176H		Atlas-SNP	.											OR6X1,NS,malignant_melanoma,0,1	OR6X1	54	.	0			c.T526C						.						89	91	90					11																	123624701		2202	4299	6501	SO:0001583	missense	390260	exon1			CACAGTAGAAATG	AB065510	CCDS31695.1	11q24.1	2012-08-09			ENSG00000221931	ENSG00000221931		"GPCR / Class A : Olfactory receptors"	14737	protein-coding gene	gene with protein product							Standard	NM_001005188		Approved		uc010rzy.2	Q8NH79	OTTHUMG00000166011	ENST00000327930.2:c.526T>C	chr11.hg19:g.123624701A>G	ENSP00000333724:p.Tyr176His	79.0	0.0		70.0	25.0	NM_001005188	B9EGW9|Q6IFA0	Missense_Mutation	SNP	ENST00000327930.2	hg19	CCDS31695.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.919282	0.73098	.	.	ENSG00000221931	ENST00000327930	T	0.00130	8.69	4.37	4.37	0.52481	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00300	0.0009	L	0.58810	1.83	0.37683	D	0.923574	P	0.41188	0.741	P	0.52957	0.714	D	0.86616	0.1876	9	0.44086	T	0.13	-9.2246	11.6004	0.50999	1.0:0.0:0.0:0.0	.	176	Q8NH79	OR6X1_HUMAN	H	176	ENSP00000333724:Y176H	ENSP00000333724:Y176H	Y	-	1	0	OR6X1	123129911	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	8.765000	0.91724	1.845000	0.53610	0.528000	0.53228	TAC	.	.		0.512	OR6X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387436.1	NM_001005188		G	123624701	A	G	123624701	3	3	14	1	0	0	0	0	1	0	0	0	11221	420	15	2	414	2	OR6X1	11	123624701	Missense_Mutation	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10	3542546	123624701	11381815	36	1268										
OR8D4	338662	hgsc.bcm.edu	37	chr11	123777184	123777184	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tgactgagtttcttctttcaGgattaactgaacaagcagag	9	7	3	4			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr11:123777184G>A	ENST00000321355.2	+	1	76	c.46G>A	c.(46-48)Gga>Aga	p.G16R		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	16						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		TCTTCTTTCAGGATTAACTGA	0.408																																					p.G16R		Atlas-SNP	.											.	OR8D4	62	.	0			c.G46A						.						91	86	88					11																	123777184		2202	4299	6501	SO:0001583	missense	338662	exon1			CTTTCAGGATTAA	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"GPCR / Class A : Olfactory receptors"	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.46G>A	chr11.hg19:g.123777184G>A	ENSP00000325381:p.Gly16Arg	55.0	0.0		56.0	22.0	NM_001005197	Q6IFE9	Missense_Mutation	SNP	ENST00000321355.2	hg19	CCDS31698.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.306476	0.60305	.	.	ENSG00000181518	ENST00000321355	T	0.00659	5.94	5.58	4.67	0.58626	.	0.000000	0.45361	D	0.000365	T	0.06325	0.0163	M	0.92122	3.275	0.32385	N	0.554106	D	0.89917	1.0	D	0.79784	0.993	T	0.03473	-1.1033	10	0.87932	D	0	.	13.3545	0.60621	0.0776:0.0:0.9224:0.0	.	16	Q8NGM9	OR8D4_HUMAN	R	16	ENSP00000325381:G16R	ENSP00000325381:G16R	G	+	1	0	OR8D4	123282394	1.000000	0.71417	0.174000	0.22961	0.948000	0.59901	5.220000	0.65267	1.344000	0.45657	-0.136000	0.14681	GGA	.	.		0.408	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197		A	123777184	G	A	123777184	3	1	14	1	0	0	0	0	1	0	0	0	11242	1001	35	3	48	3	OR8D4	11	123777184	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	152483	123777184	11229332	37	1269										
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14839106	14839106	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	attacttactacatctggaaGgtggagtatgtacatgaggg	12	5	1	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr12:14839106G>A	ENST00000261170.3	-	3	520	c.384C>T	c.(382-384)acC>acT	p.T128T	RP11-174G6.1_ENST00000501178.2_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	128					intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	ACATCTGGAAGGTGGAGTATG	0.403																																					p.T128T		Atlas-SNP	.											.	GUCY2C	126	.	0			c.C384T						.						100	84	89					12																	14839106		2203	4300	6503	SO:0001819	synonymous_variant	2984	exon3			CTGGAAGGTGGAG		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.384C>T	chr12.hg19:g.14839106G>A		83.0	0.0		67.0	28.0	NM_004963	B2RMY6	Silent	SNP	ENST00000261170.3	hg19	CCDS8664.1																																																																																			.	.		0.403	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			A	14839106	G	A	14839106	2	1	14	1	0	0	0	0	0	0	0	1	6905	987	35	3		3	GUCY2C	12	14839106	Silent	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10		14839106	119012789	38	1270										
C12orf11	55726	hgsc.bcm.edu	37	chr12	27059306	27059306	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ttcaaacgtccagcaaattcCtgatgttttctggaattggc	8	9	2	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr12:27059306C>T	ENST00000261191.7	-	16	2546	c.2010G>A	c.(2008-2010)caG>caA	p.Q670Q	ASUN_ENST00000539625.1_Silent_p.Q569Q	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	670					centrosome localization (GO:0051642)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|protein localization to nuclear envelope (GO:0090435)|regulation of fertilization (GO:0080154)|regulation of mitotic cell cycle (GO:0007346)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CAGCAAATTCCTGATGTTTTC	0.338																																					p.Q670Q		Atlas-SNP	.											.	.	.	.	0			c.G2010A						.						112	119	116					12																	27059306		2203	4298	6501	SO:0001819	synonymous_variant	55726	exon16			AAATTCCTGATGT	AK001222	CCDS8708.1	12p12.3	2013-05-08	2013-05-08	2011-12-09	ENSG00000064102	ENSG00000064102			20174	protein-coding gene	gene with protein product	"spermatogenesis associated 30"	615079	"chromosome 12 open reading frame 11", "asunder, spermatogenesis regulator homolog (Drosphila)"	C12orf11		12414650, 19357193, 23097494	Standard	NM_018164		Approved	FLJ10637, NET48, Mat89Bb, SPATA30	uc001rhk.4	Q9NVM9	OTTHUMG00000169193	ENST00000261191.7:c.2010G>A	chr12.hg19:g.27059306C>T		98.0	0.0		93.0	10.0	NM_018164	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Silent	SNP	ENST00000261191.7	hg19	CCDS8708.1																																																																																			.	.		0.338	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164		T	27059306	C	T	27059306	2	4	14	1	0	0	0	0	0	0	0	1	1677	680	24	3		3	C12orf11	12	27059306	Silent	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	12220200	27059306	106792589	39	1271										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43858526	43858526	+	Nonsense_Mutation	SNP	G	G	T													0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ttgtcaagaagacattccccGtaaccagtactgtaacagtg							TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr12:43858526G>T	ENST00000389420.3	-	10	1376	c.1377C>A	c.(1375-1377)taC>taA	p.Y459*	ADAMTS20_ENST00000553158.1_Nonsense_Mutation_p.Y459*	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	459	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		GACATTCCCCGTAACCAGTAC	0.358																																					p.Y459X		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.C1377A						.						67	63	64					12																	43858526		2203	4300	6503	SO:0001587	stop_gained	80070	exon10			TTCCCCGTAACCA	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1377C>A	chr12.hg19:g.43858526G>T	ENSP00000374071:p.Tyr459*	56.0	0.0		58.0	29.0	NM_025003	A6NNC9|J3QT00	Nonsense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	g	15.52	2.857468	0.51376	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	.	.	.	4.74	-1.11	0.09840	.	0.445102	0.18955	N	0.126576	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.541	0.17038	0.5745:0.0:0.3076:0.118	.	.	.	.	X	459	.	ENSP00000374068:Y459X	Y	-	3	2	ADAMTS20	42144793	0.999000	0.42202	0.803000	0.32268	0.076000	0.17211	0.886000	0.28241	-0.209000	0.10156	-0.435000	0.05868	TAC	.	.		0.358	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43858526	G	T	43858526	4	4	14	1	0	0	0	0	0	1	0	0	266	1140	40	1	4474	1	ADAMTS20	12	43858526	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	16799220	43858526	89993369	40	1272	5	2								
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43858528	43858528	+	Missense_Mutation	SNP	A	A	T													0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gtcaagaagacattccccgtAaccagtactgtaacagtgac							TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr12:43858528A>T	ENST00000389420.3	-	10	1374	c.1375T>A	c.(1375-1377)Tac>Aac	p.Y459N	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.Y459N	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	459	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		CATTCCCCGTAACCAGTACTG	0.358																																					p.Y459N		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T1375A						.						65	61	63					12																	43858528		2203	4300	6503	SO:0001583	missense	80070	exon10			CCCCGTAACCAGT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1375T>A	chr12.hg19:g.43858528A>T	ENSP00000374071:p.Tyr459Asn	57.0	0.0		57.0	28.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	A	1.119	-0.655929	0.03480	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.03524	3.9;3.9	4.74	0.821	0.18799	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.445102	0.18955	N	0.126576	T	0.02156	0.0067	N	0.16201	0.385	0.80722	D	1	B	0.15719	0.014	B	0.25614	0.062	T	0.51140	-0.8743	10	0.37606	T	0.19	.	2.8819	0.05649	0.4805:0.0:0.3141:0.2054	.	459	P59510	ATS20_HUMAN	N	459	ENSP00000374071:Y459N;ENSP00000448341:Y459N	ENSP00000374068:Y459N	Y	-	1	0	ADAMTS20	42144795	1.000000	0.71417	0.666000	0.29783	0.009000	0.06853	3.621000	0.54210	0.279000	0.22186	-1.335000	0.01260	TAC	.	.		0.358	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43858528	A	T	43858528	3	4	14	1	0	0	0	0	1	0	0	0	266	362	13	4	4476	4	ADAMTS20	12	43858528	Missense_Mutation	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10	2	43858528	89993367	41	1273	5	2								
HNRNPA1	3178	hgsc.bcm.edu	37	chr12	54675175	54675176	+	Frame_Shift_Ins	INS	-	-	A													0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tccccccactctagtctcctINSaaagagcccgaacagctgag							TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr12:54675175_54675176insA	ENST00000340913.6	+	2	74_75	c.21_22insA	c.(22-24)aaafs	p.K8fs	HNRNPA1_ENST00000330752.8_Frame_Shift_Ins_p.K8fs|HNRNPA1_ENST00000546500.1_Frame_Shift_Ins_p.K8fs|CBX5_ENST00000209875.4_5'Flank|RP11-968A15.8_ENST00000553061.1_RNA|HNRNPA1_ENST00000547276.1_Frame_Shift_Ins_p.K8fs|RP11-968A15.2_ENST00000547177.1_RNA	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1	8	Globular A domain.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|nuclear export (GO:0051168)|nuclear import (GO:0051170)|RNA export from nucleus (GO:0006405)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20						TCTAGTCTCCTAAAGAGCCCGA	0.485																																					p.P7fs	Colon(83;502 1289 8436 16406 24870)	Pindel	.											.	HNRNPA1	72	.	0			c.21_22insA						.																																			SO:0001589	frameshift_variant	3178	exon2			.	BC009600	CCDS41793.1, CCDS44909.1	12q13.1	2013-10-11		2007-08-16	ENSG00000135486	ENSG00000135486		"RNA binding motif (RRM) containing"	5031	protein-coding gene	gene with protein product		164017		HNRPA1		1733858	Standard	XR_245923		Approved	hnRNPA1, hnRNP-A1	uc001sfl.3	P09651		ENST00000340913.6:c.24dupA	chr12.hg19:g.54675178_54675178dupA	ENSP00000341826:p.Lys8fs	94.0	0.0		77.0	21.0	NM_002136	A8K4Z8|Q3MIB7|Q6PJZ7	Frame_Shift_Ins	INS	ENST00000340913.6	hg19	CCDS44909.1																																																																																			.	.		0.485	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157		A	54675176	-	A	54675175	7	5	14	1	0	1	1	0	0	0	0	0	7266	1509	53	0	27	0	HNRNPA1	12	54675175	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H4-01A-11D-A382-10	10816647	54675175	79176720	42	1274										
DNAJC14	85406	hgsc.bcm.edu	37	chr12	56222310	56222310	+	Frame_Shift_Del	DEL	T	T	-													0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gcgggtaccattaggagcagTccctgctgagtccctgagtc							TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr12:56222310delT	ENST00000357606.3	-	3	422	c.133delA	c.(133-135)actfs	p.T45fs	DNAJC14_ENST00000317269.3_Frame_Shift_Del_p.T45fs|DNAJC14_ENST00000317287.5_Frame_Shift_Del_p.T45fs|RP11-762I7.5_ENST00000546837.1_5'Flank|TMEM198B_ENST00000478241.1_RNA			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14	45					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						TTAGGAGCAGTCCCTGCTGAG	0.592																																					p.T45fs		Atlas-Indel,Pindel	.											.	DNAJC14	52	.	0			c.134delC						.						152	132	139					12																	56222310		2203	4300	6503	SO:0001589	frameshift_variant	85406	exon2			.	AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"Heat shock proteins / DNAJ (HSP40)"	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3		ENST00000357606.3:c.133delA	chr12.hg19:g.56222310delT	ENSP00000350223:p.Thr45fs	163.0	0.0		142.0	51.0	NM_032364	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	Frame_Shift_Del	DEL	ENST00000357606.3	hg19	CCDS8894.1																																																																																			.	.		0.592	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409095.1	NM_032364		-	56222310	T	-	56222310	7	5	14	1	0	1	0	1	0	0	0	0	4635	1667	58	0	1999	0	DNAJC14	12	56222310	Frame_Shift_Del	DEL	T	TCGA-2Y-A9H4-01A-11D-A382-10	1547135	56222310	77629585	43	1275										
SELPLG	6404	hgsc.bcm.edu	37	chr12	109017847	109017847	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gcaggctccacagtggtagaCtcaggggttccaggcccagt	14	12	1	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr12:109017847C>T	ENST00000550948.1	-	2	461	c.237G>A	c.(235-237)gaG>gaA	p.E79E	SELPLG_ENST00000228463.6_Silent_p.E95E|SELPLG_ENST00000388962.3_Silent_p.E79E			Q14242	SELPL_HUMAN	selectin P ligand	79					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						CAGTGGTAGACTCAGGGGTTC	0.567																																					p.E95E		Atlas-SNP	.											.	SELPLG	138	.	0			c.G285A						.						76	65	69					12																	109017847		2203	4300	6503	SO:0001819	synonymous_variant	6404	exon2			GGTAGACTCAGGG		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"CD molecules", "Endogenous ligands"	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.237G>A	chr12.hg19:g.109017847C>T		133.0	0.0		83.0	29.0	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Silent	SNP	ENST00000550948.1	hg19	CCDS31895.2																																																																																			.	.		0.567	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1			T	109017847	C	T	109017847	2	4	14	1	0	0	0	0	0	0	0	1	14035	564	20	3		3	SELPLG	12	109017847	Silent	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	52795537	109017847	24834048	44	1276										
SACS	26278	hgsc.bcm.edu	37	chr13	23910913	23910913	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	caactgataaaggtatggtgCcgcctcaaaatttaaatgaa	8	7	1	2			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr13:23910913C>A	ENST00000382292.3	-	9	7375	c.7102G>T	c.(7102-7104)Gca>Tca	p.A2368S	SACS_ENST00000402364.1_Missense_Mutation_p.A1618S|SACS_ENST00000382298.3_Missense_Mutation_p.A2368S			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2368					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AGGTATGGTGCCGCCTCAAAA	0.353																																					p.A2368S		Atlas-SNP	.											.	SACS	871	.	0			c.G7102T						.						48	50	49					13																	23910913		2202	4299	6501	SO:0001583	missense	26278	exon10			ATGGTGCCGCCTC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.7102G>T	chr13.hg19:g.23910913C>A	ENSP00000371729:p.Ala2368Ser	82.0	0.0		93.0	42.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	7.570	0.666480	0.14710	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.92048	-2.96;-2.96;-2.96	5.84	5.84	0.93424	.	0.054520	0.64402	D	0.000001	D	0.88793	0.6533	L	0.38838	1.175	0.42463	D	0.992792	B	0.14438	0.01	B	0.08055	0.003	T	0.83113	-0.0122	10	0.25106	T	0.35	.	20.1379	0.98040	0.0:1.0:0.0:0.0	.	2368	Q9NZJ4	SACS_HUMAN	S	2368;1618;2368	ENSP00000371729:A2368S;ENSP00000385844:A1618S;ENSP00000371735:A2368S	ENSP00000371729:A2368S	A	-	1	0	SACS	22808913	1.000000	0.71417	1.000000	0.80357	0.050000	0.14768	4.643000	0.61390	2.779000	0.95612	0.655000	0.94253	GCA	.	.		0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23910913	C	A	23910913	3	1	14	1	0	0	0	0	1	0	0	0	13819	739	26	3	6641	3	SACS	13	23910913	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10		23910913	91258965	45	1277										
NBEA	26960	hgsc.bcm.edu	37	chr13	35632969	35632969	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	actcaacccagcacagatatTtgcaattcatcagttaggac	6	11	3	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr13:35632969T>G	ENST00000400445.3	+	8	1742	c.1208T>G	c.(1207-1209)tTt>tGt	p.F403C	NBEA_ENST00000540320.1_Missense_Mutation_p.F403C|NBEA_ENST00000310336.4_Missense_Mutation_p.F403C|NBEA_ENST00000379939.2_Missense_Mutation_p.F403C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	403					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GCACAGATATTTGCAATTCAT	0.358																																					p.F403C		Atlas-SNP	.											.	NBEA	340	.	0			c.T1208G						.						38	34	35					13																	35632969		1814	4070	5884	SO:0001583	missense	26960	exon8			AGATATTTGCAAT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.1208T>G	chr13.hg19:g.35632969T>G	ENSP00000383295:p.Phe403Cys	295.0	1.0		345.0	134.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.197130	0.58126	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.62490	0.2432	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.68941	-0.5276	10	0.45353	T	0.12	.	15.4109	0.74917	0.0:0.0:0.0:1.0	.	403	Q5T321	.	C	403	ENSP00000440951:F403C;ENSP00000383295:F403C;ENSP00000369271:F403C;ENSP00000308534:F403C	ENSP00000308534:F403C	F	+	2	0	NBEA	34530969	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.188000	0.72045	2.111000	0.64477	0.528000	0.53228	TTT	.	.		0.358	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35632969	T	G	35632969	3	3	14	1	0	0	0	0	1	0	0	0	10196	1841	64	5	1238	5	NBEA	13	35632969	Missense_Mutation	SNP	T	TCGA-2Y-A9H4-01A-11D-A382-10	11722056	35632969	79536909	46	1278										
NBEA	26960	hgsc.bcm.edu	37	chr13	36180583	36180583	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gaactaattccagagttctaCtacctaccagagatgtttgt	7	9	1	2			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr13:36180583C>T	ENST00000400445.3	+	48	7851	c.7317C>T	c.(7315-7317)taC>taT	p.Y2439Y	NBEA_ENST00000379922.3_5'UTR|NBEA_ENST00000537702.1_Silent_p.Y232Y|NBEA_ENST00000540320.1_Silent_p.Y2439Y|NBEA_ENST00000310336.4_Silent_p.Y2439Y|NBEA_ENST00000379939.2_Silent_p.Y2436Y	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2439	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026, ECO:0000305}.				protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CAGAGTTCTACTACCTACCAG	0.313																																					p.Y2439Y		Atlas-SNP	.											.	NBEA	340	.	0			c.C7317T						.						94	87	89					13																	36180583		1842	4105	5947	SO:0001819	synonymous_variant	26960	exon48			GTTCTACTACCTA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.7317C>T	chr13.hg19:g.36180583C>T		107.0	0.0		108.0	41.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.313	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	36180583	C	T	36180583	2	4	14	1	0	0	0	0	0	0	0	1	10196	576	20	3		3	NBEA	13	36180583	Silent	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	547614	36180583	78989295	47	1279										
SAMD4A	23034	hgsc.bcm.edu	37	chr14	55034783	55034783	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ctgcctggagcactcgctggCcgactgcgccgagctgcacg	14	16	0	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr14:55034783C>G	ENST00000554335.1	+	2	812	c.149C>G	c.(148-150)gCc>gGc	p.A50G	SAMD4A_ENST00000251091.5_Missense_Mutation_p.A50G|SAMD4A_ENST00000357634.3_Missense_Mutation_p.A49G|SAMD4A_ENST00000392067.3_Missense_Mutation_p.A50G|SAMD4A_ENST00000555112.1_3'UTR			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	50					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						CACTCGCTGGCCGACTGCGCC	0.711																																					p.A50G		Atlas-SNP	.											.	SAMD4A	68	.	0			c.C149G						.						21	21	21					14																	55034783		2199	4299	6498	SO:0001583	missense	23034	exon1			CGCTGGCCGACTG	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"Sterile alpha motif (SAM) domain containing"	23023	protein-coding gene	gene with protein product	"smaug homolog (Drosophila)"	610747	"sterile alpha motif domain containing 4"	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.149C>G	chr14.hg19:g.55034783C>G	ENSP00000452535:p.Ala50Gly	23.0	0.0		13.0	5.0	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	hg19	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	C	24.3	4.517723	0.85495	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634	T;T;T	0.74421	-0.84;-0.84;-0.84	5.4	4.45	0.53987	.	0.072472	0.52532	D	0.000071	T	0.78923	0.4360	L	0.52759	1.655	0.27234	N	0.959326	D;P	0.62365	0.991;0.759	D;B	0.67103	0.949;0.186	T	0.69573	-0.5109	10	0.45353	T	0.12	-12.012	8.4758	0.33012	0.1543:0.7688:0.0:0.0768	.	50;50	Q9UPU9-3;Q9UPU9	.;SMAG1_HUMAN	G	50;50;50;49;49	ENSP00000452535:A50G;ENSP00000375919:A50G;ENSP00000350261:A49G	ENSP00000306381:A50G	A	+	2	0	SAMD4A	54104533	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.720000	0.61944	2.531000	0.85337	0.542000	0.68232	GCC	.	.		0.711	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		G	55034783	C	G	55034783	3	3	14	1	0	0	0	0	1	0	0	0	13836	739	26	4	148	4	SAMD4A	14	55034783	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10		55034783	52314757	48	1280										
DAAM1	23002	hgsc.bcm.edu	37	chr14	59835462	59835462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tgaccttgtttcagctttacGctcaggagaagtgtttgaca	10	8	2	3			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr14:59835462G>A	ENST00000395125.1	+	25	3145	c.3122G>A	c.(3121-3123)cGc>cAc	p.R1041H	DAAM1_ENST00000360909.3_Missense_Mutation_p.R1031H|DAAM1_ENST00000553966.1_3'UTR|DAAM1_ENST00000351081.1_Missense_Mutation_p.R1041H	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	1041	DAD. {ECO:0000255|PROSITE- ProRule:PRU00577}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		TCAGCTTTACGCTCAGGAGAA	0.413																																					p.R1041H		Atlas-SNP	.											.	DAAM1	95	.	0			c.G3122A						.						125	118	120					14																	59835462		2203	4300	6503	SO:0001583	missense	23002	exon25			CTTTACGCTCAGG	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.3122G>A	chr14.hg19:g.59835462G>A	ENSP00000378557:p.Arg1041His	146.0	0.0		166.0	65.0	NM_014992	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	hg19	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.882217	0.91740	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000395125	D;D;D	0.82433	-1.61;-1.61;-1.61	5.64	5.64	0.86602	Actin-binding FH2/DRF autoregulatory (1);Diaphanous autoregulatory (1);	0.050738	0.85682	N	0.000000	D	0.91382	0.7281	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	D	0.91773	0.5429	10	0.87932	D	0	.	19.7154	0.96115	0.0:0.0:1.0:0.0	.	1031;1041	Q9Y4D1-2;Q9Y4D1	.;DAAM1_HUMAN	H	1031;1041;1041	ENSP00000354162:R1031H;ENSP00000247170:R1041H;ENSP00000378557:R1041H	ENSP00000247170:R1041H	R	+	2	0	DAAM1	58905215	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.807000	0.99171	2.664000	0.90586	0.655000	0.94253	CGC	.	.		0.413	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		A	59835462	G	A	59835462	3	1	14	1	0	0	0	0	1	0	0	0	4217	1087	38	1	3220	1	DAAM1	14	59835462	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	4800679	59835462	47514078	49	1281										
C14orf115	55237	hgsc.bcm.edu	37	chr14	74823991	74823991	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	aggcctcctgtttccccagcAgcttctccaacgtgtggcac	9	16	1	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr14:74823991A>T	ENST00000256362.4	+	2	746	c.505A>T	c.(505-507)Agc>Tgc	p.S169C		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	169					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						TTTCCCCAGCAGCTTCTCCAA	0.597																																					p.S169C		Atlas-SNP	.											.	VRTN	79	.	0			c.A505T						.						117	110	113					14																	74823991		2203	4300	6503	SO:0001583	missense	55237	exon2			CCCAGCAGCTTCT	AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 115", "vertebrae development homolog (pig)"	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.505A>T	chr14.hg19:g.74823991A>T	ENSP00000256362:p.Ser169Cys	39.0	0.0		23.0	15.0	NM_018228	Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	hg19	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	A	14.18	2.459296	0.43634	.	.	ENSG00000133980	ENST00000256362	T	0.47177	0.85	5.05	5.05	0.67936	.	0.138925	0.50627	D	0.000107	T	0.54013	0.1832	L	0.27053	0.805	0.45250	D	0.998253	D	0.89917	1.0	D	0.67231	0.95	T	0.58994	-0.7537	10	0.87932	D	0	-0.5668	13.4994	0.61445	1.0:0.0:0.0:0.0	.	169	Q9H8Y1	VRTN_HUMAN	C	169	ENSP00000256362:S169C	ENSP00000256362:S169C	S	+	1	0	VRTN	73893744	1.000000	0.71417	0.975000	0.42487	0.099000	0.18886	4.098000	0.57748	2.123000	0.65237	0.459000	0.35465	AGC	.	.		0.597	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228		T	74823991	A	T	74823991	3	4	14	1	0	0	0	0	1	0	0	0	1742	188	7	4	507	4	C14orf115	14	74823991	Missense_Mutation	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10	14988529	74823991	32525549	50	1282										
RYR3	6263	hgsc.bcm.edu	37	chr15	33765670	33765670	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	accattcataaggagcagagGaagttctgcctggcagccga	12	10	2	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr15:33765670G>T	ENST00000389232.4	+	2	172	c.102G>T	c.(100-102)agG>agT	p.R34S	RYR3_ENST00000415757.3_Missense_Mutation_p.R34S	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	34					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AGGAGCAGAGGAAGTTCTGCC	0.547																																					p.R34S		Atlas-SNP	.											.	RYR3	760	.	0			c.G102T						.						102	106	104					15																	33765670		2091	4211	6302	SO:0001583	missense	6263	exon2			GCAGAGGAAGTTC		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.102G>T	chr15.hg19:g.33765670G>T	ENSP00000373884:p.Arg34Ser	47.0	0.0		56.0	16.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.375900	0.24857	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.96334	-3.98;-3.98	4.86	0.365	0.16131	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);	0.000000	0.85682	D	0.000000	D	0.95478	0.8531	L	0.46157	1.445	0.45087	D	0.998101	D;D	0.63880	0.981;0.993	D;P	0.69142	0.962;0.874	D	0.91887	0.5520	10	0.46703	T	0.11	.	3.7773	0.08665	0.3096:0.3915:0.2989:0.0	.	34;34	Q15413-2;Q15413	.;RYR3_HUMAN	S	34	ENSP00000373884:R34S;ENSP00000399610:R34S	ENSP00000354735:R34S	R	+	3	2	RYR3	31552962	1.000000	0.71417	0.963000	0.40424	0.953000	0.61014	1.441000	0.35035	0.210000	0.20664	0.650000	0.86243	AGG	.	.		0.547	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33765670	G	T	33765670	3	4	14	1	0	0	0	0	1	0	0	0	13785	1165	41	3	108	3	RYR3	15	33765670	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10		33765670	68765722	51	1283										
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40259627	40259627	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ctaccttgcaatgaatctcaAagagcaagacgactccatcg	7	12	1	3			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr15:40259627A>G	ENST00000263791.5	+	9	1143	c.1100A>G	c.(1099-1101)aAa>aGa	p.K367R	EIF2AK4_ENST00000559624.1_Missense_Mutation_p.K367R|EIF2AK4_ENST00000382727.2_Missense_Mutation_p.K367R	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	367	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		ATGAATCTCAAAGAGCAAGAC	0.443																																					p.K367R		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.A1100G						.						84	82	83					15																	40259627		1951	4148	6099	SO:0001583	missense	440275	exon9			ATCTCAAAGAGCA	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.1100A>G	chr15.hg19:g.40259627A>G	ENSP00000263791:p.Lys367Arg	177.0	0.0		170.0	36.0	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	hg19	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	A	5.638	0.302373	0.10678	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.64803	-0.12;-0.12	5.36	-2.23	0.06930	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.725269	0.13509	N	0.382622	T	0.39118	0.1066	N	0.12920	0.275	0.20563	N	0.999887	B;B	0.06786	0.0;0.001	B;B	0.11329	0.006;0.001	T	0.24548	-1.0157	10	0.17369	T	0.5	-5.5525	11.8436	0.52368	0.5416:0.0:0.4584:0.0	.	367;367	Q9P2K8;Q9P2K8-3	E2AK4_HUMAN;.	R	367	ENSP00000263791:K367R;ENSP00000372174:K367R	ENSP00000263791:K367R	K	+	2	0	EIF2AK4	38046919	0.041000	0.20044	0.872000	0.34217	0.870000	0.49936	-0.040000	0.12104	-0.230000	0.09840	-0.274000	0.10170	AAA	.	.		0.443	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			G	40259627	A	G	40259627	3	3	14	1	0	0	0	0	1	0	0	0	5001	14	1	2	1134	2	EIF2AK4	15	40259627	Missense_Mutation	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10	6493957	40259627	62271765	52	1284										
SPESP1	246777	hgsc.bcm.edu	37	chr15	69238044	69238044	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gagccaggtcgtgagaaaaaAtctaactctccaaaacatgt	8	9	2	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr15:69238044A>G	ENST00000310673.3	+	2	325	c.171A>G	c.(169-171)aaA>aaG	p.K57K	NOX5_ENST00000260364.5_Intron|RP11-809H16.2_ENST00000557966.1_RNA|SPESP1_ENST00000560188.1_3'UTR|NOX5_ENST00000455873.3_Intron|NOX5_ENST00000448182.3_Intron	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1	57					acrosome reaction (GO:0007340)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19						GTGAGAAAAAATCTAACTCTC	0.378																																					p.K57K		Atlas-SNP	.											.	SPESP1	39	.	0			c.A171G						.						105	108	107					15																	69238044		2200	4298	6498	SO:0001819	synonymous_variant	246777	exon2			GAAAAAATCTAAC	AF275321	CCDS10230.1	15q22.31	2011-04-15				ENSG00000258484			15570	protein-coding gene	gene with protein product		609399				12773409	Standard	NM_145658		Approved	SP-ESP	uc002arn.2	Q6UW49		ENST00000310673.3:c.171A>G	chr15.hg19:g.69238044A>G		213.0	0.0		212.0	84.0	NM_145658	Q8NG22|Q8WVH8	Silent	SNP	ENST00000310673.3	hg19	CCDS10230.1																																																																																			.	.		0.378	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257125.1	NM_145658		G	69238044	A	G	69238044	2	3	14	1	0	0	0	0	0	0	0	1	15055	98	4	2		2	SPESP1	15	69238044	Silent	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10	28978417	69238044	33293348	53	1285										
RHBDL1	9028	hgsc.bcm.edu	37	chr16	727559	727559	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	cacctggccaacgttgtcatGgtaacgggcctgcccggtgg	14	13	1	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr16:727559G>T	ENST00000219551.2	+	5	1011	c.984G>T	c.(982-984)atG>atT	p.M328I	LA16c-313D11.9_ENST00000571933.1_RNA|STUB1_ENST00000219548.4_5'Flank|LA16c-313D11.9_ENST00000567091.1_RNA|RHBDL1_ENST00000352681.3_Splice_Site_p.M263I|STUB1_ENST00000565677.1_5'Flank			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	328					signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(1)|lung(4)|urinary_tract(3)	9		Hepatocellular(780;0.0218)				ACGTTGTCATGGTAACGGGCC	0.672																																					p.M328I		Atlas-SNP	.											.	RHBDL1	14	.	0			c.G984T						.						27	29	29					16																	727559		2190	4294	6484	SO:0001630	splice_region_variant	9028	exon5			TGTCATGGTAACG	Y17108	CCDS61779.1	16p13.3	2008-02-05	2001-11-28	2003-04-11	ENSG00000103269	ENSG00000103269			10007	protein-coding gene	gene with protein product		603264	"rhomboid (veinlet, Drosophila)-like"	RHBDL		9662444	Standard	NM_001278720		Approved	RRP	uc002cis.1	O75783	OTTHUMG00000121141	ENST00000219551.2:c.984+1G>T	chr16.hg19:g.727559G>T		46.0	0.0		40.0	16.0	NM_003961	A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Missense_Mutation	SNP	ENST00000219551.2	hg19	CCDS10418.1	.	.	.	.	.	.	.	.	.	.	G	16.61	3.172607	0.57584	.	.	ENSG00000103269	ENST00000352681;ENST00000450775;ENST00000219551	T;T	0.11063	2.81;2.81	4.16	4.16	0.48862	Peptidase S54, rhomboid domain (1);	0.000000	0.85682	D	0.000000	T	0.23926	0.0579	L	0.39147	1.195	0.80722	D	1	D;P;D	0.57571	0.98;0.943;0.961	D;D;P	0.75020	0.985;0.93;0.794	T	0.01252	-1.1405	10	0.51188	T	0.08	-28.0367	15.0314	0.71710	0.0:0.0:1.0:0.0	.	263;328;263	B4DFK3;O75783;O75783-2	.;RHBL1_HUMAN;.	I	263;263;328	ENSP00000344206:M263I;ENSP00000219551:M328I	ENSP00000219551:M328I	M	+	3	0	RHBDL1	667560	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	8.935000	0.92923	1.875000	0.54330	0.561000	0.74099	ATG	.	.		0.672	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1	NM_003961	Missense_Mutation	T	727559	G	T	727559	5	4	14	1	0	0	0	0	0	0	1	0	13336	1362	47	3	1002	3	RHBDL1	16	727559	Splice_Site	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10		727559	89627194	54	1286										
OTOA	146183	hgsc.bcm.edu	37	chr16	21739616	21739616	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tcatggggaacctgctgtgtCacttgccggcagccatcatc	11	13	3	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr16:21739616C>T	ENST00000286149.4	+	19	2114	c.2113C>T	c.(2113-2115)Cac>Tac	p.H705Y	OTOA_ENST00000388957.3_Missense_Mutation_p.H367Y|OTOA_ENST00000388956.4_Missense_Mutation_p.H612Y|OTOA_ENST00000388958.3_Missense_Mutation_p.H691Y			Q7RTW8	OTOAN_HUMAN	otoancorin	705					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CCTGCTGTGTCACTTGCCGGC	0.562																																					p.H691Y		Atlas-SNP	.											.	OTOA	144	.	0			c.C2071T						.						107	90	95					16																	21739616		2198	4300	6498	SO:0001583	missense	146183	exon19			CTGTGTCACTTGC	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.2113C>T	chr16.hg19:g.21739616C>T	ENSP00000286149:p.His705Tyr	97.0	0.0		72.0	23.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	hg19		.	.	.	.	.	.	.	.	.	.	C	15.98	2.993706	0.54041	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956;ENST00000388957;ENST00000338456	T;T;T;T	0.66099	-0.19;-0.19;-0.18;-0.17	5.29	5.29	0.74685	.	0.062767	0.64402	D	0.000007	T	0.75729	0.3889	M	0.68952	2.095	0.43683	D	0.996122	D;D;D;D	0.89917	1.0;1.0;0.998;1.0	D;D;D;D	0.91635	0.999;0.999;0.978;0.999	T	0.72855	-0.4166	10	0.28530	T	0.3	-15.9596	14.4211	0.67183	0.0:1.0:0.0:0.0	.	705;612;367;691	Q7RTW8;B3KWU3;Q7RTW8-2;E9PF51	OTOAN_HUMAN;.;.;.	Y	691;705;612;367;100	ENSP00000373610:H691Y;ENSP00000286149:H705Y;ENSP00000373608:H612Y;ENSP00000373609:H367Y	ENSP00000286149:H705Y	H	+	1	0	OTOA	21647117	1.000000	0.71417	0.998000	0.56505	0.324000	0.28378	4.184000	0.58323	2.457000	0.83068	0.655000	0.94253	CAC	.	.		0.562	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			T	21739616	C	T	21739616	3	4	14	1	0	0	0	0	1	0	0	0	11311	826	29	3	2191	3	OTOA	16	21739616	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	21012057	21739616	68615137	55	1287										
TP53	7157	hgsc.bcm.edu	37	chr17	7579420	7579420	+	Frame_Shift_Del	DEL	G	G	-													0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gaagatgacaggggccaggaGggggctggtgcaggggccgc					rs587783062		TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr17:7579420delG	ENST00000269305.4	-	4	456	c.267delC	c.(265-267)cccfs	p.P89fs	TP53_ENST00000359597.4_Frame_Shift_Del_p.P89fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.P89fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.P89fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.P89fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Del_p.P89fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	89	Interaction with WWOX.		P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.S90fs*59(6)|p.A76_S90del15(3)|p.A88fs*32(3)|p.G59fs*23(3)|p.V73fs*9(1)|p.D48fs*55(1)|p.P85fs*58(1)|p.S33fs*23(1)|p.A86fs*33(1)|p.A86fs*32(1)|p.P87fs*54(1)|p.P13fs*18(1)|p.A88fs*52(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGGGCCAGGAGGGGGCTGGTG	0.627		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.S90fs	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,0,1	TP53	33396	.	32	Deletion - Frameshift(15)|Whole gene deletion(8)|Insertion - Frameshift(6)|Deletion - In frame(3)	liver(6)|upper_aerodigestive_tract(4)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|prostate(4)|bone(4)|central_nervous_system(2)|breast(2)|stomach(1)|urinary_tract(1)	c.268delT						.						45	52	50					17																	7579420		2202	4299	6501	SO:0001589	frameshift_variant	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.267delC	chr17.hg19:g.7579420delG	ENSP00000269305:p.Pro89fs	168.0	0.0		105.0	62.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.627	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7579420	G	-	7579420	7	5	14	1	0	1	0	1	0	0	0	0	16396	987	35	0	1035	0	TP53	17	7579420	Frame_Shift_Del	DEL	G	TCGA-2Y-A9H4-01A-11D-A382-10		7579420	73615790	56	1288										
MED24	9862	hgsc.bcm.edu	37	chr17	38186019	38186019	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	accttgaggatgtttgtgacAgtgggctccgcccggaggat	15	9	0	2			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr17:38186019A>G	ENST00000394128.2	-	13	1329	c.1248T>C	c.(1246-1248)acT>acC	p.T416T	MED24_ENST00000394126.1_Silent_p.T441T|MED24_ENST00000394127.2_Silent_p.T403T|MED24_ENST00000501516.3_Silent_p.T435T|SNORD124_ENST00000459577.1_RNA|MED24_ENST00000356271.3_Silent_p.T403T	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	416					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					TGTTTGTGACAGTGGGCTCCG	0.547																																					p.T416T		Atlas-SNP	.											.	MED24	89	.	0			c.T1248C						.						203	161	175					17																	38186019		2203	4300	6503	SO:0001819	synonymous_variant	9862	exon13			TGTGACAGTGGGC	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1248T>C	chr17.hg19:g.38186019A>G		86.0	0.0		66.0	30.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	hg19	CCDS11359.1																																																																																			.	.		0.547	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		G	38186019	A	G	38186019	2	3	14	1	0	0	0	0	0	0	0	1	9451	175	7	2		2	MED24	17	38186019	Silent	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10	30606599	38186019	43009191	57	1289										
RNMT	8731	hgsc.bcm.edu	37	chr18	13741655	13741655	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	agacttagccctgggggctaTtttattggtactactcccaa	9	10	0	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr18:13741655T>A	ENST00000383314.2	+	7	1179	c.939T>A	c.(937-939)taT>taA	p.Y313*	RNMT_ENST00000535051.1_Nonsense_Mutation_p.Y71*|RNMT_ENST00000592764.1_Nonsense_Mutation_p.Y313*|RNMT_ENST00000589866.1_Nonsense_Mutation_p.Y313*|RNMT_ENST00000543302.2_Nonsense_Mutation_p.Y313*|RNMT_ENST00000262173.3_Nonsense_Mutation_p.Y313*			O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	313	mRNA cap 0 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00895}.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA (guanine-N7)-methylation (GO:0036265)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|receptor complex (GO:0043235)	mRNA (guanine-N7-)-methyltransferase activity (GO:0004482)|RNA binding (GO:0003723)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						CTGGGGGCTATTTTATTGGTA	0.363																																					p.Y313X	GBM(29;474 594 19092 36647 41529)	Atlas-SNP	.											.	RNMT	42	.	0			c.T939A						.						97	98	98					18																	13741655		2203	4300	6503	SO:0001587	stop_gained	8731	exon7			GGGCTATTTTATT	AF067791	CCDS11867.1	18p11.21	2008-05-14			ENSG00000101654	ENSG00000101654	2.1.1.56		10075	protein-coding gene	gene with protein product		603514				9828141, 9705270	Standard	NM_003799		Approved	RG7MT1	uc002ksl.1	O43148	OTTHUMG00000131718	ENST00000383314.2:c.939T>A	chr18.hg19:g.13741655T>A	ENSP00000372804:p.Tyr313*	104.0	0.0		82.0	30.0	NM_003799	B0YJ90|D3DUJ5|O94996|Q9UIJ9	Nonsense_Mutation	SNP	ENST00000383314.2	hg19	CCDS11867.1	.	.	.	.	.	.	.	.	.	.	T	39	7.882852	0.98542	.	.	ENSG00000101654	ENST00000383314;ENST00000535051;ENST00000543302;ENST00000262173	.	.	.	5.61	4.46	0.54185	.	0.050900	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.8991	11.2654	0.49108	0.0:0.0714:0.0:0.9286	.	.	.	.	X	313;71;313;313	.	ENSP00000262173:Y313X	Y	+	3	2	RNMT	13731655	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.516000	0.60496	0.972000	0.38314	0.482000	0.46254	TAT	.	.		0.363	RNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254636.1	NM_003799		A	13741655	T	A	13741655	4	1	14	1	0	0	0	0	0	1	0	0	13521	1500	52	4	957	4	RNMT	18	13741655	Nonsense_Mutation	SNP	T	TCGA-2Y-A9H4-01A-11D-A382-10		13741655	64335593	58	1290										
NETO1	81832	hgsc.bcm.edu	37	chr18	70461395	70461395	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tgtaccacttgcaatcaacaGcctcgctagcagtagctttg	8	12	1	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr18:70461395G>T	ENST00000327305.6	-	6	1253	c.596C>A	c.(595-597)gCt>gAt	p.A199D	NETO1_ENST00000299430.2_Missense_Mutation_p.A198D|NETO1_ENST00000583169.1_Missense_Mutation_p.A199D	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	199	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		GCAATCAACAGCCTCGCTAGC	0.458																																					p.A199D		Atlas-SNP	.											.	NETO1	178	.	0			c.C596A						.						202	173	183					18																	70461395		2203	4300	6503	SO:0001583	missense	81832	exon6			TCAACAGCCTCGC	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.596C>A	chr18.hg19:g.70461395G>T	ENSP00000313088:p.Ala199Asp	158.0	0.0		200.0	38.0	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	hg19	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	G	17.22	3.335085	0.60853	.	.	ENSG00000166342	ENST00000327305;ENST00000299430	T;T	0.17691	2.26;2.26	5.29	5.29	0.74685	CUB (5);	0.000000	0.64402	D	0.000014	T	0.45994	0.1370	M	0.78916	2.43	0.80722	D	1	D;D	0.76494	0.999;0.987	D;D	0.85130	0.997;0.95	T	0.43621	-0.9380	10	0.54805	T	0.06	-18.7142	18.9328	0.92572	0.0:0.0:1.0:0.0	.	198;199	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	D	199;198	ENSP00000313088:A199D;ENSP00000299430:A198D	ENSP00000299430:A198D	A	-	2	0	NETO1	68612375	1.000000	0.71417	0.996000	0.52242	0.396000	0.30629	9.476000	0.97823	2.462000	0.83206	0.655000	0.94253	GCT	.	.		0.458	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		T	70461395	G	T	70461395	3	4	14	1	0	0	0	0	1	0	0	0	10348	971	34	3	1025	3	NETO1	18	70461395	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	56719740	70461395	7615853	59	1291										
TJP3	27134	hgsc.bcm.edu	37	chr19	3728689	3728689	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tatctgacgtggtacctggaGggccggcggagggcaggcta	18	9	1	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr19:3728689G>A	ENST00000541714.2	+	3	598	c.136G>A	c.(136-138)Ggg>Agg	p.G46R	TJP3_ENST00000539908.2_Missense_Mutation_p.G10R|TJP3_ENST00000382008.3_Missense_Mutation_p.G46R|TJP3_ENST00000589378.1_Missense_Mutation_p.G55R|TJP3_ENST00000262968.9_Missense_Mutation_p.G65R|TJP3_ENST00000587686.1_Missense_Mutation_p.G65R	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	46	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTACCTGGAGGGCCGGCGGA	0.647																																					p.G55R		Atlas-SNP	.											.	TJP3	79	.	0			c.G163A						.						35	38	37					19																	3728689		2203	4300	6503	SO:0001583	missense	27134	exon3			CCTGGAGGGCCGG	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"zona occludens 3"	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.136G>A	chr19.hg19:g.3728689G>A	ENSP00000439278:p.Gly46Arg	93.0	0.0		81.0	34.0	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	hg19	CCDS32873.2	.	.	.	.	.	.	.	.	.	.	G	16.22	3.060555	0.55432	.	.	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.56275	1.02;0.47;1.02;1.72	4.02	4.02	0.46733	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	D	0.82637	0.5080	H	0.98577	4.27	0.80722	D	1	D;D;D;D	0.76494	0.999;0.981;0.998;0.998	D;D;D;D	0.77557	0.99;0.916;0.987;0.986	D	0.89944	0.4075	10	0.87932	D	0	.	15.7177	0.77681	0.0:0.0:1.0:0.0	.	65;65;46;46	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	R	46;10;46;65	ENSP00000439278:G46R;ENSP00000439991:G10R;ENSP00000371438:G46R;ENSP00000262968:G65R	ENSP00000262968:G65R	G	+	1	0	TJP3	3679689	1.000000	0.71417	0.237000	0.24090	0.015000	0.08874	8.821000	0.92009	2.253000	0.74438	0.456000	0.33151	GGG	.	.		0.647	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1			A	3728689	G	A	3728689	3	1	14	1	0	0	0	0	1	0	0	0	15946	1000	35	3	199	3	TJP3	19	3728689	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10		3728689	55400294	60	1292										
OR7A5	26659	hgsc.bcm.edu	37	chr19	14938215	14938215	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ggttcagcatgggggtgaccAcagtgtacatcactgaggct	14	9	2	2			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr19:14938215A>T	ENST00000322301.3	-	2	926	c.839T>A	c.(838-840)gTg>gAg	p.V280E	OR7A5_ENST00000594432.1_Missense_Mutation_p.V280E|OR7A5_ENST00000601611.1_Intron			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	280					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						GGGGGTGACCACAGTGTACAT	0.468																																					p.V280E		Atlas-SNP	.											.	OR7A5	43	.	0			c.T839A						.						85	78	80					19																	14938215		2203	4300	6503	SO:0001583	missense	26659	exon1			GTGACCACAGTGT	X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"GPCR / Class A : Olfactory receptors"	8368	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily A, member 5 pseudogene"				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.839T>A	chr19.hg19:g.14938215A>T	ENSP00000316955:p.Val280Glu	91.0	0.0		58.0	29.0	NM_017506	B2R682|Q6IFP1|Q96R96	Missense_Mutation	SNP	ENST00000322301.3	hg19	CCDS12318.1	.	.	.	.	.	.	.	.	.	.	a	12.24	1.879670	0.33162	.	.	ENSG00000188269	ENST00000322301	T	0.00316	8.13	3.12	0.873	0.19118	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00998	0.0033	H	0.98701	4.305	0.09310	N	1	D	0.76494	0.999	D	0.79784	0.993	T	0.45977	-0.9224	9	0.87932	D	0	.	3.212	0.06686	0.5407:0.2157:0.2436:0.0	.	280	Q15622	OR7A5_HUMAN	E	280	ENSP00000316955:V280E	ENSP00000316955:V280E	V	-	2	0	OR7A5	14799215	0.007000	0.16637	0.172000	0.22920	0.556000	0.35491	2.383000	0.44354	0.013000	0.14918	0.102000	0.15555	GTG	.	.		0.468	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506		T	14938215	A	T	14938215	3	4	14	1	0	0	0	0	1	0	0	0	11225	159	6	4	124	4	OR7A5	19	14938215	Missense_Mutation	SNP	A	TCGA-2Y-A9H4-01A-11D-A382-10	11209526	14938215	44190768	61	1293										
SIRPG	55423	hgsc.bcm.edu	37	chr20	1616060	1616060	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tatgttcaccaggaaccagcTtgtccagttgtaggtaccat	9	10	1	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr20:1616060T>A	ENST00000303415.3	-	4	998	c.934A>T	c.(934-936)Agc>Tgc	p.S312C	RP11-77C3.3_ENST00000456177.1_RNA|RP11-77C3.3_ENST00000437384.1_RNA|SIRPG_ENST00000381583.2_Intron|SIRPG_ENST00000216927.4_Intron|SIRPG_ENST00000344103.4_Intron|SIRPG_ENST00000381580.1_Missense_Mutation_p.S279C	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	312	Ig-like C1-type 2.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						AGGAACCAGCTTGTCCAGTTG	0.547																																					p.S312C		Atlas-SNP	.											.	SIRPG	61	.	0			c.A934T						.						227	178	194					20																	1616060		2203	4300	6503	SO:0001583	missense	55423	exon4			ACCAGCTTGTCCA	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.934A>T	chr20.hg19:g.1616060T>A	ENSP00000305529:p.Ser312Cys	206.0	0.0		155.0	54.0	NM_018556	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	hg19	CCDS13020.2	.	.	.	.	.	.	.	.	.	.	.	14.29	2.491278	0.44249	.	.	ENSG00000089012	ENST00000381580;ENST00000303415	T;T	0.00892	5.57;5.57	1.6	1.6	0.23607	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.342187	0.28566	N	0.014892	T	0.06234	0.0161	H	0.95151	3.63	0.44067	D	0.996818	D	0.61080	0.989	D	0.71870	0.975	T	0.01004	-1.1484	10	0.59425	D	0.04	.	5.2806	0.15673	0.0:0.0:0.0:1.0	.	312	Q9P1W8	SIRPG_HUMAN	C	279;312	ENSP00000370992:S279C;ENSP00000305529:S312C	ENSP00000305529:S312C	S	-	1	0	SIRPG	1564060	0.926000	0.31397	0.512000	0.27736	0.260000	0.26232	3.102000	0.50291	0.977000	0.38444	0.164000	0.16699	AGC	.	.		0.547	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		A	1616060	T	A	1616060	3	1	14	1	0	0	0	0	1	0	0	0	14351	1609	56	4	237	4	SIRPG	20	1616060	Missense_Mutation	SNP	T	TCGA-2Y-A9H4-01A-11D-A382-10		1616060	61409460	62	1294										
TAF4	6874	hgsc.bcm.edu	37	chr20	60639513	60639513	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gtgcggccactcacctggggGcagctggaagttctggatgt	16	10	2	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr20:60639513G>A	ENST00000252996.4	-	1	1353	c.1354C>T	c.(1354-1356)Ccc>Tcc	p.P452S	hsa-mir-3195_ENST00000585001.1_RNA	NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	452					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			TCACCTGGGGGCAGCTGGAAG	0.687																																					p.P452S		Atlas-SNP	.											.	TAF4	84	.	0			c.C1354T						.						6	8	7					20																	60639513		2115	4196	6311	SO:0001583	missense	6874	exon1			CTGGGGGCAGCTG	Y11354	CCDS33500.1	20q13.33	2010-02-26	2002-08-29	2002-01-18	ENSG00000130699	ENSG00000130699			11537	protein-coding gene	gene with protein product		601796	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1, 130kD"	TAF4A, TAF2C1, TAF2C		8942982, 9192867	Standard	NM_003185		Approved	TAFII130, TAFII135	uc002ybs.3	O00268	OTTHUMG00000032893	ENST00000252996.4:c.1354C>T	chr20.hg19:g.60639513G>A	ENSP00000252996:p.Pro452Ser	71.0	0.0		68.0	16.0	NM_003185	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Missense_Mutation	SNP	ENST00000252996.4	hg19	CCDS33500.1	.	.	.	.	.	.	.	.	.	.	g	21.2	4.112596	0.77210	.	.	ENSG00000130699	ENST00000252996;ENST00000436129	T;T	0.30182	1.54;1.54	2.75	2.75	0.32379	.	0.233720	0.36167	N	0.002744	T	0.30039	0.0752	L	0.49455	1.56	0.58432	D	0.999999	B	0.32781	0.384	B	0.37144	0.242	T	0.08617	-1.0713	10	0.27785	T	0.31	.	13.4609	0.61227	0.0:0.0:1.0:0.0	.	452	O00268	TAF4_HUMAN	S	452;316	ENSP00000252996:P452S;ENSP00000399091:P316S	ENSP00000252996:P452S	P	-	1	0	TAF4	60072908	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	6.497000	0.73674	1.104000	0.41587	0.177000	0.17058	CCC	.	.		0.687	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185		A	60639513	G	A	60639513	3	1	14	1	0	0	0	0	1	0	0	0	15541	1203	42	3	1963	3	TAF4	20	60639513	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10	59023453	60639513	2386007	63	1295										
TTC3	7267	hgsc.bcm.edu	37	chr21	38538061	38538061	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	atcacggctcaagaaaaaaaGgaagaagaaaaacattaaaa	7	5	2	3			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chr21:38538061G>A	ENST00000399017.2	+	33	6292	c.3545G>A	c.(3544-3546)aGg>aAg	p.R1182K	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Missense_Mutation_p.R1182K|TTC3_ENST00000355666.1_Missense_Mutation_p.R1182K	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1182	Arg/Lys-rich (basic).				negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AAGAAAAAAAGGAAGAAGAAA	0.378																																					p.R1182K	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.G3545A						.						111	122	118					21																	38538061		2196	4298	6494	SO:0001583	missense	7267	exon33			AAAAAAGGAAGAA	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.3545G>A	chr21.hg19:g.38538061G>A	ENSP00000381981:p.Arg1182Lys	62.0	0.0		70.0	31.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	G	7.270	0.606887	0.14002	.	.	ENSG00000182670	ENST00000438055;ENST00000355666;ENST00000399017;ENST00000354749	T;T;T;T	0.14022	2.54;3.1;3.1;3.1	4.69	3.78	0.43462	.	0.314194	0.27866	N	0.017534	T	0.24044	0.0582	L	0.46157	1.445	0.37162	D	0.902635	D;D	0.67145	0.996;0.994	D;D	0.76071	0.987;0.97	T	0.04017	-1.0984	9	.	.	.	-15.7093	6.1288	0.20194	0.1643:0.263:0.5727:0.0	.	240;1182	Q5GIT6;P53804	.;TTC3_HUMAN	K	1164;1182;1182;1182	ENSP00000391891:R1164K;ENSP00000347889:R1182K;ENSP00000381981:R1182K;ENSP00000346791:R1182K	.	R	+	2	0	TTC3	37459931	1.000000	0.71417	0.998000	0.56505	0.845000	0.48019	1.521000	0.35910	2.318000	0.78349	0.655000	0.94253	AGG	.	.		0.378	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			A	38538061	G	A	38538061	3	1	14	1	0	0	0	0	1	0	0	0	16712	1000	35	3	3671	3	TTC3	21	38538061	Missense_Mutation	SNP	G	TCGA-2Y-A9H4-01A-11D-A382-10		38538061	9591834	64	1296										
TNMD	64102	hgsc.bcm.edu	37	chrX	99854661	99854661	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	aaggaggacgagtcatctgtCgtgtcatcatgccttgtaac	11	9	4	0			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chrX:99854661C>T	ENST00000373031.4	+	7	1118	c.901C>T	c.(901-903)Cgt>Tgt	p.R301C		NM_022144.2	NP_071427.2	Q9H2S6	TNMD_HUMAN	tenomodulin	301					cellular response to BMP stimulus (GO:0071773)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|tendon cell differentiation (GO:0035990)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(7)|skin(1)	16						AGTCATCTGTCGTGTCATCAT	0.507																																					p.R301C		Atlas-SNP	.											.	TNMD	40	.	0			c.C901T						.						98	60	73					X																	99854661		2203	4300	6503	SO:0001583	missense	64102	exon7			ATCTGTCGTGTCA	AF191770	CCDS14469.1	Xq21.33-q23	2012-10-10			ENSG00000000005	ENSG00000000005		"BRICHOS domain containing"	17757	protein-coding gene	gene with protein product	"BRICHOS domain containing 4"	300459					Standard	NM_022144		Approved	myodulin, ChM1L, tendin, TEM, BRICD4	uc004efy.4	Q9H2S6	OTTHUMG00000022001	ENST00000373031.4:c.901C>T	chrX.hg19:g.99854661C>T	ENSP00000362122:p.Arg301Cys	72.0	0.0		99.0	87.0	NM_022144	Q9HBX0|Q9UJG0	Missense_Mutation	SNP	ENST00000373031.4	hg19	CCDS14469.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.428152	0.83667	.	.	ENSG00000000005	ENST00000373031	T	0.37584	1.19	5.87	5.87	0.94306	.	0.064498	0.64402	D	0.000004	T	0.34193	0.0889	L	0.39898	1.24	0.58432	D	0.999999	D	0.61697	0.99	B	0.43809	0.432	T	0.17745	-1.0359	10	0.87932	D	0	-30.575	14.0258	0.64584	0.1508:0.8492:0.0:0.0	.	301	Q9H2S6	TNMD_HUMAN	C	301	ENSP00000362122:R301C	ENSP00000362122:R301C	R	+	1	0	TNMD	99741317	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.920000	0.48844	2.469000	0.83416	0.594000	0.82650	CGT	.	.		0.507	TNMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057481.1	NM_022144		T	99854661	C	T	99854661	3	4	14	1	0	0	0	0	1	0	0	0	16337	884	31	1	927	1	TNMD	23	99854661	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10		99854661	55415899	65	1297										
GPRASP1	9737	hgsc.bcm.edu	37	chrX	101909785	101909785	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	gtttggggctggaaaggaggCcaaattcaggtccaaaatga	14	6	1	1	rs17339512	byFrequency	TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chrX:101909785C>T	ENST00000361600.5	+	5	1745	c.944C>T	c.(943-945)gCc>gTc	p.A315V	GPRASP1_ENST00000415986.1_Missense_Mutation_p.A315V|RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000537097.1_Missense_Mutation_p.A315V|GPRASP1_ENST00000444152.1_Missense_Mutation_p.A315V	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	315			A -> G (in dbSNP:rs17339512). {ECO:0000269|PubMed:9455477}.		endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						GGAAAGGAGGCCAAATTCAGG	0.488																																					p.A315V		Atlas-SNP	.											.	GPRASP1	140	.	0			c.C944T						.						94	93	93					X																	101909785		2203	4300	6503	SO:0001583	missense	9737	exon3			AGGAGGCCAAATT	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"Armadillo repeat containing"	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.944C>T	chrX.hg19:g.101909785C>T	ENSP00000355146:p.Ala315Val	57.0	0.0		86.0	4.0	NM_001099411	O43168|Q96LA1	Missense_Mutation	SNP	ENST00000361600.5	hg19	CCDS35352.1	.	.	.	.	.	.	.	.	.	.	C	7.503	0.653137	0.14580	.	.	ENSG00000198932	ENST00000415986;ENST00000444152;ENST00000361600;ENST00000537097	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	1.94	-0.0574	0.13801	.	.	.	.	.	T	0.08403	0.0209	L	0.46614	1.455	0.20196	N	0.999927	B	0.24132	0.098	B	0.12837	0.008	T	0.34179	-0.9839	9	0.34782	T	0.22	-0.001	4.2854	0.10853	0.0:0.5984:0.2349:0.1667	.	315	Q5JY77	GASP1_HUMAN	V	315	ENSP00000393691:A315V;ENSP00000409420:A315V;ENSP00000355146:A315V;ENSP00000445683:A315V	ENSP00000355146:A315V	A	+	2	0	GPRASP1	101796441	0.000000	0.05858	0.023000	0.16930	0.103000	0.19146	-0.198000	0.09505	-0.107000	0.12088	0.279000	0.19357	GCC	.	C|0.962;G|0.038		0.488	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		T	101909785	C	T	101909785	3	4	14	1	0	0	0	0	1	0	0	0	6731	739	26	3	946	3	GPRASP1	23	101909785	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	2055124	101909785	53360775	66	1298										
IRS4	8471	hgsc.bcm.edu	37	chrX	107978096	107978096	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	ccccggccatttcctgagccCcaattgttcataggcatgta	8	14	1	1			TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chrX:107978096C>A	ENST00000372129.2	-	1	1555	c.1479G>T	c.(1477-1479)tgG>tgT	p.W493C	RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	493					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						TTCCTGAGCCCCAATTGTTCA	0.577																																					p.W493C		Atlas-SNP	.											.	IRS4	253	.	0			c.G1479T						.						129	121	124					X																	107978096		2203	4300	6503	SO:0001583	missense	8471	exon1			TGAGCCCCAATTG	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1479G>T	chrX.hg19:g.107978096C>A	ENSP00000361202:p.Trp493Cys	70.0	0.0		116.0	55.0	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	hg19	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.383719	0.25031	.	.	ENSG00000133124	ENST00000372129	T	0.35605	1.3	4.2	4.2	0.49525	.	0.549745	0.18258	N	0.146724	T	0.30198	0.0757	L	0.27053	0.805	0.45899	D	0.998741	D	0.54047	0.964	P	0.46975	0.533	T	0.02581	-1.1138	10	0.44086	T	0.13	-2.7108	10.7654	0.46291	0.0:0.9026:0.0:0.0974	.	493	O14654	IRS4_HUMAN	C	493	ENSP00000361202:W493C	ENSP00000361202:W493C	W	-	3	0	IRS4	107864752	0.999000	0.42202	1.000000	0.80357	0.915000	0.54546	1.780000	0.38634	2.355000	0.79922	0.596000	0.82720	TGG	.	.		0.577	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107978096	C	A	107978096	3	1	14	1	0	0	0	0	1	0	0	0	7851	624	22	3	2298	3	IRS4	23	107978096	Missense_Mutation	SNP	C	TCGA-2Y-A9H4-01A-11D-A382-10	6068311	107978096	47292464	67	1299										
UPF3B	65109	hgsc.bcm.edu	37	chrX	118975219	118975222	+	Splice_Site	DEL	TCTC	TCTC	-													0.0149253731343284	1	1	0.289170506912442	0	0.323870967741935	1	1	0	tctctcttttcttctctcatTctctagaaagaaacatcaac							TCGA-2Y-A9H4-01A-11D-A382-10	TCGA-2Y-A9H4-10A-01D-A385-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a12a5c70-7c82-4f2b-972f-81a029234685	cc2a8833-5e36-487f-bcb8-1fcb198152ff	g.chrX:118975219_118975222delTCTC	ENST00000276201.2	-	7	694_696	c.625_627delGAGA	c.(625-627)gagdel	p.E209fs	UPF3B_ENST00000345865.2_Splice_Site_p.E209fs|UPF3B_ENST00000478840.1_5'UTR	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	209	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						cttctCTCATTCTCTAGAAAGAAA	0.363																																					p.209_210del		Atlas-Indel,Pindel	.											.	UPF3B	74	.	0			c.625_628del						.																																			SO:0001630	splice_region_variant	65109	exon7			.	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.625-1GAGA>-	chrX.hg19:g.118975219_118975222delTCTC		26.0	0.0		38.0	30.0	NM_023010	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Frame_Shift_Del	DEL	ENST00000276201.2	hg19	CCDS14588.1																																																																																			.	.		0.363	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1		Frame_Shift_Del	-	118975222	TCTC	-	118975219	8	5	14	1	0	1	0	1	0	0	1	0	17021	1780	62	0	844	0	UPF3B	23	118975219	Splice_Site	DEL	TCTC	TCGA-2Y-A9H4-01A-11D-A382-10	10997123	118975219	36295341	68	1300										
SPEN	23013	hgsc.bcm.edu	37	chr1	16257447	16257447	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gacatctgagggagcaaacaGcacaactgattccattcaag	9	10	2	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr1:16257447G>T	ENST00000375759.3	+	11	4916	c.4712G>T	c.(4711-4713)aGc>aTc	p.S1571I		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1571					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GGAGCAAACAGCACAACTGAT	0.428																																					p.S1571I		Atlas-SNP	.											.	SPEN	374	.	0			c.G4712T						.						76	79	78					1																	16257447		2203	4300	6503	SO:0001583	missense	23013	exon11			CAAACAGCACAAC		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.4712G>T	chr1.hg19:g.16257447G>T	ENSP00000364912:p.Ser1571Ile	197.0	0.0		109.0	5.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	10.54	1.379420	0.24944	.	.	ENSG00000065526	ENST00000375759	T	0.10668	2.85	5.03	2.1	0.27182	.	.	.	.	.	T	0.06962	0.0177	L	0.27053	0.805	0.40985	D	0.9848	P	0.34780	0.468	B	0.29942	0.109	T	0.34502	-0.9826	9	0.52906	T	0.07	-4.2988	8.0954	0.30824	0.1442:0.131:0.7248:0.0	.	1571	Q96T58	MINT_HUMAN	I	1571	ENSP00000364912:S1571I	ENSP00000364912:S1571I	S	+	2	0	SPEN	16130034	1.000000	0.71417	0.106000	0.21319	0.012000	0.07955	2.845000	0.48254	0.284000	0.22305	0.563000	0.77884	AGC	.	.		0.428	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16257447	G	T	16257447	3	4	15	1	0	0	0	0	1	0	0	0	15053	971	34	3	4754	3	SPEN	1	16257447	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10		16257447	232993174	1	1301										
KLHDC7A	127707	hgsc.bcm.edu	37	chr1	18807799	18807799	+	Frame_Shift_Del	DEL	G	G	-													0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ggcccctatgtcctggtcacGggggccacttccacagacag							TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr1:18807799delG	ENST00000400664.1	+	1	376	c.324delG	c.(322-324)acgfs	p.T108fs		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	108						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TCCTGGTCACGGGGGCCACTT	0.652																																					p.T108fs		Atlas-Indel,Pindel	.											.	KLHDC7A	60	.	0			c.323delC						.						19	23	21					1																	18807799		1963	4150	6113	SO:0001589	frameshift_variant	127707	exon1			.	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.324delG	chr1.hg19:g.18807799delG	ENSP00000383505:p.Thr108fs	308.0	0.0		155.0	16.0	NM_152375	Q8N8W6	Frame_Shift_Del	DEL	ENST00000400664.1	hg19	CCDS185.2																																																																																			.	.		0.652	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375		-	18807799	G	-	18807799	7	5	15	1	0	1	0	1	0	0	0	0	8369	1103	39	0	326	0	KLHDC7A	1	18807799	Frame_Shift_Del	DEL	G	TCGA-2Y-A9H5-01A-11D-A382-10	2550352	18807799	230442822	2	1302										
CSMD2	114784	hgsc.bcm.edu	37	chr1	33999415	33999415	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cggacacagtcaggtggggtTccactccaggtcaggtttgg	15	10	2	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr1:33999415T>C	ENST00000373381.4	-	63	10148	c.9972A>G	c.(9970-9972)ggA>ggG	p.G3324G		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3180						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CAGGTGGGGTTCCACTCCAGG	0.557																																					p.G3180G		Atlas-SNP	.											.	CSMD2	946	.	0			c.A9540G						.						137	115	122					1																	33999415		2203	4300	6503	SO:0001819	synonymous_variant	114784	exon62			TGGGGTTCCACTC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.9972A>G	chr1.hg19:g.33999415T>C		125.0	0.0		78.0	43.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	hg19																																																																																				.	.		0.557	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		C	33999415	T	C	33999415	2	2	15	1	0	0	0	0	0	0	0	1	3947	1770	62	2		2	CSMD2	1	33999415	Silent	SNP	T	TCGA-2Y-A9H5-01A-11D-A382-10	15191616	33999415	215251206	3	1303										
CYP4B1	1580	hgsc.bcm.edu	37	chr1	47276518	47276518	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ctggacaaagtggtgtcctgGgcccaccagttcccgtatgc	12	13	0	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr1:47276518G>T	ENST00000271153.4	+	2	255	c.219G>T	c.(217-219)tgG>tgT	p.W73C	CYP4B1_ENST00000371919.4_Missense_Mutation_p.W73C|CYP4B1_ENST00000546128.1_3'UTR|CYP4B1_ENST00000371923.4_Missense_Mutation_p.W73C|CYP4B1_ENST00000452782.2_5'Flank			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	73					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	TGGTGTCCTGGGCCCACCAGT	0.552																																					p.W73C		Atlas-SNP	.											.	CYP4B1	81	.	0			c.G219T						.						99	84	89					1																	47276518		2203	4300	6503	SO:0001583	missense	1580	exon2			GTCCTGGGCCCAC	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"Cytochrome P450s"	2644	protein-coding gene	gene with protein product		124075	"cytochrome P450, subfamily IVB, polypeptide 1"				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.219G>T	chr1.hg19:g.47276518G>T	ENSP00000271153:p.Trp73Cys	63.0	0.0		57.0	32.0	NM_000779	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Missense_Mutation	SNP	ENST00000271153.4	hg19	CCDS542.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.940218	0.34283	.	.	ENSG00000142973	ENST00000371923;ENST00000271153;ENST00000371919	T;T;T	0.79940	-1.32;-1.32;-0.36	5.35	4.44	0.53790	.	0.332477	0.34853	N	0.003624	D	0.86117	0.5856	L	0.54908	1.71	0.80722	D	1	D;B;B	0.89917	1.0;0.039;0.049	D;B;B	0.77004	0.989;0.067;0.111	D	0.85542	0.1216	10	0.44086	T	0.13	.	12.9384	0.58329	0.0796:0.0:0.9204:0.0	.	73;73;73	Q8IZB0;P13584-2;P13584	.;.;CP4B1_HUMAN	C	73	ENSP00000360991:W73C;ENSP00000271153:W73C;ENSP00000360987:W73C	ENSP00000271153:W73C	W	+	3	0	CYP4B1	47049105	1.000000	0.71417	0.850000	0.33497	0.670000	0.39368	4.439000	0.59968	1.278000	0.44430	-0.299000	0.09455	TGG	.	.		0.552	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779		T	47276518	G	T	47276518	3	4	15	1	0	0	0	0	1	0	0	0	4187	1241	43	3	225	3	CYP4B1	1	47276518	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	13277103	47276518	201974103	4	1304										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157504613	157504613	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tctggacttcacagtgaagtGtcacagtggctccttcaaaa	9	10	4	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr1:157504613G>A	ENST00000361835.3	-	8	1629	c.1472C>T	c.(1471-1473)aCa>aTa	p.T491I	FCRL5_ENST00000368191.3_Missense_Mutation_p.T406I|FCRL5_ENST00000356953.4_Missense_Mutation_p.T491I|FCRL5_ENST00000368189.3_Missense_Mutation_p.T491I|FCRL5_ENST00000368190.3_Missense_Mutation_p.T491I	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	491	Ig-like C2-type 5.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				ACAGTGAAGTGTCACAGTGGC	0.507																																					p.T491I		Atlas-SNP	.											.	FCRL5	177	.	0			c.C1472T						.						52	51	51					1																	157504613		2203	4300	6503	SO:0001583	missense	83416	exon8			TGAAGTGTCACAG	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.1472C>T	chr1.hg19:g.157504613G>A	ENSP00000354691:p.Thr491Ile	93.0	0.0		223.0	125.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	hg19	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	G	11.70	1.716459	0.30413	.	.	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191;ENST00000368189	T;T;T;T;T	0.16743	2.32;2.32;2.32;2.32;2.32	3.34	1.18	0.20946	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19967	0.0480	M	0.75777	2.31	0.09310	N	1	D;D;D;D;D;P	0.71674	0.997;0.998;0.997;0.973;0.991;0.91	D;D;D;P;P;P	0.72075	0.976;0.953;0.921;0.744;0.706;0.475	T	0.03662	-1.1015	9	0.41790	T	0.15	.	5.1908	0.15209	0.0:0.2524:0.5196:0.228	.	522;406;491;491;491;491	B4DW39;F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9-4;Q96RD9	.;.;.;.;.;FCRL5_HUMAN	I	491;491;491;406;491	ENSP00000354691:T491I;ENSP00000349434:T491I;ENSP00000357173:T491I;ENSP00000357174:T406I;ENSP00000357172:T491I	ENSP00000349434:T491I	T	-	2	0	FCRL5	155771237	0.001000	0.12720	0.019000	0.16419	0.012000	0.07955	0.330000	0.19715	0.729000	0.32403	0.313000	0.20887	ACA	.	.		0.507	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		A	157504613	G	A	157504613	3	1	15	1	0	0	0	0	1	0	0	0	5806	1377	48	3	1501	3	FCRL5	1	157504613	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	110228095	157504613	91746008	5	1305										
POGK	57645	hgsc.bcm.edu	37	chr1	166818813	166818813	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ccgtgccccagcacctgccgGaagacctgactgagaaactc	10	16	0	3			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr1:166818813G>A	ENST00000367875.1	+	5	1357	c.997G>A	c.(997-999)Gaa>Aaa	p.E333K	POGK_ENST00000367876.4_Missense_Mutation_p.E333K|POGK_ENST00000537173.1_Missense_Mutation_p.E215K|POGK_ENST00000536514.1_Missense_Mutation_p.E248K			Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	333					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	22						GCACCTGCCGGAAGACCTGAC	0.547																																					p.E333K	GBM(76;192 1530 30153 48742)	Atlas-SNP	.											.	POGK	54	.	0			c.G997A						.						77	80	79					1																	166818813		2203	4300	6503	SO:0001583	missense	57645	exon5			CTGCCGGAAGACC	AB040946	CCDS1254.1	1q23.2	2013-01-08			ENSG00000143157	ENSG00000143157		"-"	18800	protein-coding gene	gene with protein product	"KRAB box domain containing 2"						Standard	NM_017542		Approved	KIAA15131, LST003, BASS2, KRBOX2	uc001gdt.1	Q9P215	OTTHUMG00000034325	ENST00000367875.1:c.997G>A	chr1.hg19:g.166818813G>A	ENSP00000356849:p.Glu333Lys	95.0	0.0		111.0	55.0	NM_017542	Q5TIJ1|Q8TE07	Missense_Mutation	SNP	ENST00000367875.1	hg19	CCDS1254.1	.	.	.	.	.	.	.	.	.	.	G	14.06	2.423340	0.43020	.	.	ENSG00000143157	ENST00000537173;ENST00000536514;ENST00000367876;ENST00000367875	T;T;T;T	0.33654	1.41;1.4;4.66;4.66	5.5	4.59	0.56863	.	0.000000	0.52532	D	0.000077	T	0.08223	0.0205	N	0.14661	0.345	0.32819	D	0.502434	B;B;B	0.31837	0.175;0.342;0.068	B;B;B	0.31751	0.135;0.092;0.012	T	0.17077	-1.0381	8	.	.	.	-25.3765	7.5282	0.27668	0.0863:0.1672:0.7465:0.0	.	215;248;333	G3V1P0;B4DS22;Q9P215	.;.;POGK_HUMAN	K	215;248;333;333	ENSP00000442763:E215K;ENSP00000441187:E248K;ENSP00000356850:E333K;ENSP00000356849:E333K	.	E	+	1	0	POGK	165085437	0.041000	0.20044	0.612000	0.29024	0.909000	0.53808	0.867000	0.27968	1.551000	0.49450	0.655000	0.94253	GAA	.	.		0.547	POGK-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082888.1	NM_017542		A	166818813	G	A	166818813	3	1	15	1	0	0	0	0	1	0	0	0	12194	1175	41	3	1011	3	POGK	1	166818813	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	9314200	166818813	82431808	6	1306										
ELF3	1999	hgsc.bcm.edu	37	chr1	201981100	201981101	+	Frame_Shift_Ins	INS	-	-	G													0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gcagagaaggccagctggttINSgggggaacagccccagttct							TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr1:201981100_201981101insG	ENST00000359651.3	+	2	3371_3372	c.179_180insG	c.(178-183)ttggggfs	p.LG60fs	RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Frame_Shift_Ins_p.LG60fs|ELF3_ENST00000495848.1_3'UTR|ELF3_ENST00000367284.5_Frame_Shift_Ins_p.LG60fs|RP11-465N4.4_ENST00000419190.1_RNA					E74-like factor 3 (ets domain transcription factor, epithelial-specific )											breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						GCCAGCTGGTTGGGGGAACAGC	0.535																																					p.L60fs		Atlas-Indel,Pindel	.											.	ELF3	92	.	0			c.179_180insG						.																																			SO:0001589	frameshift_variant	1999	exon3			.	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.184dupG	chr1.hg19:g.201981105_201981105dupG	ENSP00000352673:p.Leu60fs	189.0	0.0		200.0	92.0	NM_004433		Frame_Shift_Ins	INS	ENST00000359651.3	hg19	CCDS1419.1																																																																																			.	.		0.535	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		G	201981101	-	G	201981100	7	5	15	1	0	1	1	0	0	0	0	0	5057	1821	63	0	185	0	ELF3	1	201981100	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H5-01A-11D-A382-10	35162287	201981100	47269521	7	1307										
RYR2	6262	hgsc.bcm.edu	37	chr1	237532889	237532889	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cggacatgccatattgctgcGccattcctatagtggcatgg	11	11	0	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr1:237532889G>A	ENST00000366574.2	+	6	682	c.365G>A	c.(364-366)cGc>cAc	p.R122H	RYR2_ENST00000542537.1_Missense_Mutation_p.R106H|RYR2_ENST00000360064.6_Missense_Mutation_p.R120H	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	122	MIR 1. {ECO:0000255|PROSITE- ProRule:PRU00131}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.R120H(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATATTGCTGCGCCATTCCTAT	0.463																																					p.R122H		Atlas-SNP	.											RYR2,colon,carcinoma,+1,1	RYR2	1273	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G365A						.						151	125	133					1																	237532889		1967	4162	6129	SO:0001583	missense	6262	exon6			TGCTGCGCCATTC	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.365G>A	chr1.hg19:g.237532889G>A	ENSP00000355533:p.Arg122His	70.0	0.0		141.0	13.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	34	5.316181	0.95655	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.93659	-3.26;-3.26;-3.26	5.55	5.55	0.83447	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);MIR motif (2);	0.000000	0.64402	D	0.000004	D	0.96738	0.8935	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	D	0.96962	0.9702	10	0.87932	D	0	.	18.6233	0.91328	0.0:0.0:1.0:0.0	.	122	Q92736	RYR2_HUMAN	H	122;120;106	ENSP00000355533:R122H;ENSP00000353174:R120H;ENSP00000443798:R106H	ENSP00000353174:R120H	R	+	2	0	RYR2	235599512	1.000000	0.71417	0.952000	0.39060	0.919000	0.55068	9.386000	0.97228	2.755000	0.94549	0.655000	0.94253	CGC	.	.		0.463	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237532889	G	A	237532889	3	1	15	1	0	0	0	0	1	0	0	0	13784	1087	38	1	387	1	RYR2	1	237532889	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	35551789	237532889	11717732	8	1308										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247007207	247007207	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cgaaactaattctttcagctGtgcaggaacctctatttttt	6	9	3	0	rs542305190		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr1:247007207G>A	ENST00000391829.2	-	34	6538	c.6415C>T	c.(6415-6417)Cag>Tag	p.Q2139*	AHCTF1_ENST00000326225.3_Nonsense_Mutation_p.Q2148*|AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000366508.1_Nonsense_Mutation_p.Q2174*			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	2139	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TCTTTCAGCTGTGCAGGAACC	0.318																																					p.Q2148X	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.C6442T						.						61	60	60					1																	247007207		2202	4299	6501	SO:0001587	stop_gained	25909	exon34			TCAGCTGTGCAGG		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.6415C>T	chr1.hg19:g.247007207G>A	ENSP00000375705:p.Gln2139*	434.0	0.0		689.0	161.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Nonsense_Mutation	SNP	ENST00000391829.2	hg19		.	.	.	.	.	.	.	.	.	.	G	45	11.579505	0.99578	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	.	.	.	4.86	3.89	0.44902	.	0.196774	0.36234	N	0.002712	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	-4.3443	10.2343	0.43273	0.0:0.1432:0.71:0.1468	.	.	.	.	X	2174;2148;2139	.	ENSP00000355465:Q2148X	Q	-	1	0	AHCTF1	245073830	1.000000	0.71417	0.950000	0.38849	0.386000	0.30323	3.158000	0.50723	2.386000	0.81285	0.467000	0.42956	CAG	.	.		0.318	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		A	247007207	G	A	247007207	4	1	15	1	0	0	0	0	0	1	0	0	408	1386	48	3	397	3	AHCTF1	1	247007207	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	9474318	247007207	2243414	9	1309										
SLC1A4	6509	hgsc.bcm.edu	37	chr2	65248223	65248223	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cccctggtgacacaccagaaCcccgctggccccgtggccag	11	19	0	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr2:65248223C>T	ENST00000234256.3	+	8	1785	c.1542C>T	c.(1540-1542)aaC>aaT	p.N514N	SLC1A4_ENST00000531327.1_Silent_p.N216N	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	514					amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	CACACCAGAACCCCGCTGGCC	0.597																																					p.N514N		Atlas-SNP	.											.	SLC1A4	33	.	0			c.C1542T						.						77	75	75					2																	65248223		2203	4300	6503	SO:0001819	synonymous_variant	6509	exon8			CCAGAACCCCGCT		CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"Solute carriers"	10942	protein-coding gene	gene with protein product	"alanine/serine/cysteine/threonine transporter"	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.1542C>T	chr2.hg19:g.65248223C>T		205.0	0.0		187.0	11.0	NM_003038	B7Z3C0|D6W5F0	Silent	SNP	ENST00000234256.3	hg19	CCDS1879.1																																																																																			.	.		0.597	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038		T	65248223	C	T	65248223	2	4	15	1	0	0	0	0	0	0	0	1	14449	506	18	3		3	SLC1A4	2	65248223	Silent	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10		65248223	177951150	10	1310										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141457818	141457818	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	aaattgaattactgtacttaCtttcaacaattacttgtctg	4	7	2	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr2:141457818C>T	ENST00000389484.3	-	41	7771		c.e41+1			NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B						protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACTGTACTTACTTTCAACAAT	0.313										TSP Lung(27;0.18)																											.	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.6799+1G>A						.						70	73	72					2																	141457818		2203	4297	6500	SO:0001630	splice_region_variant	53353	exon42			TACTTACTTTCAA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.6799+1G>A	chr2.hg19:g.141457818C>T		46.0	0.0		73.0	37.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Splice_Site	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072492	0.76415	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	.	.	.	3.95	3.95	0.45737	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5232	0.84322	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRP1B	141174288	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.710000	0.84655	2.176000	0.68965	0.585000	0.79938	.	.	.		0.313	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Intron	T	141457818	C	T	141457818	5	4	15	1	0	0	0	0	0	0	1	0	8964	579	20	3	7203	3	LRP1B	2	141457818	Splice_Site	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	76209595	141457818	101741555	11	1311										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148672850	148672853	+	Frame_Shift_Del	DEL	TGGA	TGGA	-													0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ggggaagatttggttgtgtcTggaaagcccagttgcttaac							TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	TGGA	TGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr2:148672850_148672853delTGGA	ENST00000241416.7	+	5	1255_1258	c.619_622delTGGA	c.(619-624)tggaaafs	p.WK207fs	ACVR2A_ENST00000404590.1_Frame_Shift_Del_p.WK207fs|ACVR2A_ENST00000535787.1_Frame_Shift_Del_p.WK99fs	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	207	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TGGTTGTGTCTGGAAAGCCCAGTT	0.407																																					p.206_207del		Atlas-Indel,Pindel	.											.	ACVR2A	125	.	0			c.618_621del						.																																			SO:0001589	frameshift_variant	92	exon5			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.619_622delTGGA	chr2.hg19:g.148672850_148672853delTGGA	ENSP00000241416:p.Trp207fs	102.0	0.0		160.0	72.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Frame_Shift_Del	DEL	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.407	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		-	148672853	TGGA	-	148672850	7	5	15	1	0	1	0	1	0	0	0	0	223	1580	55	0	637	0	ACVR2A	2	148672850	Frame_Shift_Del	DEL	TGGA	TCGA-2Y-A9H5-01A-11D-A382-10	7215032	148672850	94526523	12	1312										
NEUROD1	4760	hgsc.bcm.edu	37	chr2	182543445	182543445	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tcctcagtgagtcctcctctGcgttcatggtttcgaggtcg	11	12	3	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr2:182543445G>A	ENST00000295108.3	-	2	600	c.143C>T	c.(142-144)gCa>gTa	p.A48V	NEUROD1_ENST00000496876.1_Intron|CERKL_ENST00000479558.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	48					amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			GTCCTCCTCTGCGTTCATGGT	0.572																																					p.A48V		Atlas-SNP	.											.	NEUROD1	67	.	0			c.C143T						.						128	100	109					2																	182543445		2203	4300	6503	SO:0001583	missense	4760	exon2			TCCTCTGCGTTCA	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"Basic helix-loop-helix proteins"	7762	protein-coding gene	gene with protein product	"beta-cell E-box transactivator 2", "neurogenic helix-loop-helix protein NEUROD"	601724	"neurogenic differentiation 1"	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.143C>T	chr2.hg19:g.182543445G>A	ENSP00000295108:p.Ala48Val	75.0	0.0		67.0	31.0	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Missense_Mutation	SNP	ENST00000295108.3	hg19	CCDS2283.1	.	.	.	.	.	.	.	.	.	.	G	14.41	2.527217	0.44969	.	.	ENSG00000162992	ENST00000295108	D	0.95238	-3.65	5.9	4.97	0.65823	.	0.924596	0.09179	N	0.837729	D	0.87533	0.6201	N	0.08118	0	0.09310	N	1	B	0.20671	0.047	B	0.10450	0.005	T	0.75800	-0.3190	10	0.34782	T	0.22	-0.1502	11.3896	0.49806	0.0:0.0:0.7135:0.2865	.	48	Q13562	NDF1_HUMAN	V	48	ENSP00000295108:A48V	ENSP00000295108:A48V	A	-	2	0	NEUROD1	182251690	0.055000	0.20627	0.812000	0.32479	0.927000	0.56198	1.051000	0.30417	2.788000	0.95919	0.650000	0.86243	GCA	.	.		0.572	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		A	182543445	G	A	182543445	3	1	15	1	0	0	0	0	1	0	0	0	10357	1319	46	3	931	3	NEUROD1	2	182543445	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	33870595	182543445	60655928	13	1313										
DIS3L2	129563	hgsc.bcm.edu	37	chr2	232880381	232880381	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	aagagaggaacactcatccaGgtgcttaaaatctactggaa	9	8	2	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr2:232880381G>A	ENST00000409307.1	+	2	210	c.210G>A	c.(208-210)caG>caA	p.Q70Q	DIS3L2_ENST00000325385.7_Splice_Site_p.Q70Q|DIS3L2_ENST00000409401.3_Splice_Site_p.Q70Q|AC105461.1_ENST00000413841.1_RNA|DIS3L2_ENST00000273009.6_Splice_Site_p.Q70Q|DIS3L2_ENST00000360410.4_Splice_Site_p.Q70Q					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CACTCATCCAGGTGCTTAAAA	0.398																																					p.Q70Q		Atlas-SNP	.											.	DIS3L2	77	.	0			c.G210A						.						100	88	92					2																	232880381		1869	4109	5978	SO:0001630	splice_region_variant	129563	exon3			CATCCAGGTGCTT	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.210+1G>A	chr2.hg19:g.232880381G>A		25.0	0.0		68.0	31.0	NM_001257282		Silent	SNP	ENST00000409307.1	hg19	CCDS42834.1																																																																																			.	.		0.398	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383	Silent	A	232880381	G	A	232880381	5	1	15	1	0	0	0	0	0	0	1	0	4539	1014	35	3	216	3	DIS3L2	2	232880381	Splice_Site	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	50336936	232880381	10318992	14	1314										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78706267	78706267	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cccagctggatgaactgaggCtcactctttaccccagaccc	8	16	2	3			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr3:78706267C>T	ENST00000464233.1	-	18	2708	c.2595G>A	c.(2593-2595)gaG>gaA	p.E865E	ROBO1_ENST00000467549.1_Silent_p.E829E|ROBO1_ENST00000495273.1_Silent_p.E829E|ROBO1_ENST00000436010.2_Silent_p.E826E	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	865	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TGAACTGAGGCTCACTCTTTA	0.522																																					p.E865E		Atlas-SNP	.											.	ROBO1	833	.	0			c.G2595A						.						54	58	57					3																	78706267		2018	4182	6200	SO:0001819	synonymous_variant	6091	exon18			CTGAGGCTCACTC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2595G>A	chr3.hg19:g.78706267C>T		65.0	0.0		61.0	25.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.		0.522	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78706267	C	T	78706267	2	4	15	1	0	0	0	0	0	0	0	1	13528	796	28	3		3	ROBO1	3	78706267	Silent	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10		78706267	119316163	15	1315										
LRRC66	339977	hgsc.bcm.edu	37	chr4	52861214	52861214	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cctgtgtctcttgggtcaccGtatggaacctcgctgtagtg	12	11	2	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr4:52861214G>A	ENST00000343457.3	-	4	1980	c.1974C>T	c.(1972-1974)taC>taT	p.Y658Y		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	658						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(8)|lung(34)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	58						TTGGGTCACCGTATGGAACCT	0.542																																					p.Y658Y		Atlas-SNP	.											.	LRRC66	128	.	0			c.C1974T						.						81	79	80					4																	52861214		2002	4162	6164	SO:0001819	synonymous_variant	339977	exon4			GTCACCGTATGGA	BC040414	CCDS43229.1	4q12	2008-08-08			ENSG00000188993	ENSG00000188993			34299	protein-coding gene	gene with protein product							Standard	XM_005265739		Approved		uc003gzi.3	Q68CR7	OTTHUMG00000160623	ENST00000343457.3:c.1974C>T	chr4.hg19:g.52861214G>A		35.0	0.0		44.0	21.0	NM_001024611		Silent	SNP	ENST00000343457.3	hg19	CCDS43229.1																																																																																			.	.		0.542	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		A	52861214	G	A	52861214	2	1	15	1	0	0	0	0	0	0	0	1	9027	1140	40	1		1	LRRC66	4	52861214	Silent	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10		52861214	138293062	16	1316										
PAQR3	152559	hgsc.bcm.edu	37	chr4	79851430	79851430	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	atcttcgacatgttttttctGaccgatggcaggaaaaaaga	9	7	2	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr4:79851430G>A	ENST00000512733.1	-	3	611	c.398C>T	c.(397-399)tCa>tTa	p.S133L	PAQR3_ENST00000295462.3_Nonsense_Mutation_p.Q79*|PAQR3_ENST00000380645.4_Missense_Mutation_p.S133L	NM_001040202.1	NP_001035292.1	Q6TCH7	PAQR3_HUMAN	progestin and adipoQ receptor family member III	133					negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein phosphorylation (GO:0001933)|protein localization to Golgi apparatus (GO:0034067)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	8						TGTTTTTTCTGACCGATGGCA	0.363																																					p.S133L		Atlas-SNP	.											.	PAQR3	28	.	0			c.C398T						.						77	79	78					4																	79851430		2203	4300	6503	SO:0001583	missense	152559	exon3			TTTTCTGACCGAT	AK055774	CCDS34020.1	4q21	2008-02-05				ENSG00000163291			30130	protein-coding gene	gene with protein product		614577				16044242	Standard	XM_006714104		Approved		uc003hlp.1	Q6TCH7		ENST00000512733.1:c.398C>T	chr4.hg19:g.79851430G>A	ENSP00000421981:p.Ser133Leu	57.0	0.0		114.0	42.0	NM_001040202	A8K5B7|B3KP59|Q6PIQ1|Q86X05|Q8NCP9	Missense_Mutation	SNP	ENST00000512733.1	hg19	CCDS34020.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.756666|6.756666	0.97817|0.97817	.|.	.|.	ENSG00000163291|ENSG00000163291	ENST00000295462|ENST00000512733;ENST00000380645	.|T;T	.|0.29655	.|1.56;1.56	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.67382	.|0.2887	M|M	0.91818|0.91818	3.245|3.245	0.80722|0.80722	A|A	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.83275	.|0.996	.|T	.|0.72887	.|-0.4156	.|9	0.87932|0.87932	D|D	0|0	-5.6583|-5.6583	20.6439|20.6439	0.99570|0.99570	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|133	.|Q6TCH7	.|PAQR3_HUMAN	X|L	79|133	.|ENSP00000421981:S133L;ENSP00000370019:S133L	ENSP00000295462:Q79X|ENSP00000344203:S133L	Q|S	-|-	1|2	0|0	PAQR3|PAQR3	80070454|80070454	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	9.835000|9.835000	0.99442|0.99442	2.884000|2.884000	0.98904|0.98904	0.655000|0.655000	0.94253|0.94253	CAG|TCA	.	.		0.363	PAQR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363442.1	NM_177453		A	79851430	G	A	79851430	3	1	15	1	0	0	0	0	1	0	0	0	11445	1294	45	3	553	3	PAQR3	4	79851430	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	26990216	79851430	111302846	17	1317										
SEC31A	22872	hgsc.bcm.edu	37	chr4	83800020	83800020	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	attttcaccacctgcaatcaGaactccagagacatctcctt	4	14	3	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr4:83800020G>A	ENST00000395310.2	-	4	447	c.265C>T	c.(265-267)Ctg>Ttg	p.L89L	SEC31A_ENST00000513858.1_Silent_p.L89L|SEC31A_ENST00000326950.5_Silent_p.L89L|SEC31A_ENST00000508479.1_Silent_p.L89L|SEC31A_ENST00000509142.1_Silent_p.L89L|SEC31A_ENST00000436790.2_5'UTR|SEC31A_ENST00000505984.1_Silent_p.L89L|SEC31A_ENST00000348405.4_Silent_p.L89L|SEC31A_ENST00000443462.2_Silent_p.L84L|SEC31A_ENST00000505472.1_Silent_p.L89L|SEC31A_ENST00000311785.7_Silent_p.L89L|SEC31A_ENST00000500777.2_Silent_p.L89L|SEC31A_ENST00000432794.1_Silent_p.L89L|SEC31A_ENST00000448323.1_Silent_p.L89L|SEC31A_ENST00000508502.1_Silent_p.L89L|SEC31A_ENST00000355196.2_Silent_p.L89L	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	89					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				CCTGCAATCAGAACTCCAGAG	0.368																																					p.L89L		Atlas-SNP	.											SEC31A_ENST00000432794,right_upper_lobe,carcinoma,0,2	SEC31A	227	.	0			c.C265T						.						69	68	68					4																	83800020		2203	4300	6503	SO:0001819	synonymous_variant	22872	exon4			CAATCAGAACTCC	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.265C>T	chr4.hg19:g.83800020G>A		285.0	1.0		341.0	127.0	NM_001077206	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Silent	SNP	ENST00000395310.2	hg19	CCDS3596.1																																																																																			.	.		0.368	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		A	83800020	G	A	83800020	2	1	15	1	0	0	0	0	0	0	0	1	14013	933	33	3		3	SEC31A	4	83800020	Silent	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	3948590	83800020	107354256	18	1318										
AGPAT9	84803	hgsc.bcm.edu	37	chr4	84502954	84502954	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tggtgtgggtgctgggcgtcAtagtgcgctattgtgtccta	16	7	1	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr4:84502954A>T	ENST00000395226.2	+	4	666	c.448A>T	c.(448-450)Ata>Tta	p.I150L	AGPAT9_ENST00000264409.4_Missense_Mutation_p.I150L	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	150					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				GCTGGGCGTCATAGTGCGCTA	0.448																																					p.I150L		Atlas-SNP	.											.	AGPAT9	41	.	0			c.A448T						.						239	225	230					4																	84502954		2203	4300	6503	SO:0001583	missense	84803	exon4			GGCGTCATAGTGC	AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	28157	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, theta"	610958	"1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.448A>T	chr4.hg19:g.84502954A>T	ENSP00000378651:p.Ile150Leu	89.0	0.0		118.0	42.0	NM_001256421	Q68CJ4|Q6GPI6|Q96NA3	Missense_Mutation	SNP	ENST00000395226.2	hg19	CCDS3606.1	.	.	.	.	.	.	.	.	.	.	A	2.573	-0.299238	0.05532	.	.	ENSG00000138678	ENST00000395226;ENST00000264409	T;T	0.39997	1.05;1.05	5.66	-7.66	0.01277	.	0.536654	0.21293	N	0.076927	T	0.11707	0.0285	N	0.12443	0.215	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39035	-0.9633	10	0.02654	T	1	-0.0015	1.9387	0.03342	0.1604:0.3611:0.2368:0.2416	.	150	Q53EU6	GPAT3_HUMAN	L	150	ENSP00000378651:I150L;ENSP00000264409:I150L	ENSP00000264409:I150L	I	+	1	0	AGPAT9	84721978	0.000000	0.05858	0.034000	0.17996	0.963000	0.63663	-2.026000	0.01434	-1.373000	0.02134	-0.328000	0.08392	ATA	.	.		0.448	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717		T	84502954	A	T	84502954	3	4	15	1	0	0	0	0	1	0	0	0	392	217	8	4	458	4	AGPAT9	4	84502954	Missense_Mutation	SNP	A	TCGA-2Y-A9H5-01A-11D-A382-10	702934	84502954	106651322	19	1319										
NDST3	9348	hgsc.bcm.edu	37	chr4	119161760	119161760	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cagggccccgtgcaccctcgGagctcagagccttgcagaag	13	15	1	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr4:119161760G>A	ENST00000296499.5	+	11	2603	c.2200G>A	c.(2200-2202)Gag>Aag	p.E734K		NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	734	Heparan sulfate N-sulfotransferase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						TGCACCCTCGGAGCTCAGAGC	0.517																																					p.E734K		Atlas-SNP	.											.	NDST3	107	.	0			c.G2200A						.						78	75	76					4																	119161760		2203	4300	6503	SO:0001583	missense	9348	exon11			CCCTCGGAGCTCA	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.2200G>A	chr4.hg19:g.119161760G>A	ENSP00000296499:p.Glu734Lys	65.0	0.0		122.0	46.0	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Missense_Mutation	SNP	ENST00000296499.5	hg19	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	G	0.050	-1.252808	0.01469	.	.	ENSG00000164100	ENST00000296499	T	0.54479	0.57	5.49	3.78	0.43462	Sulfotransferase domain (1);	0.331420	0.30890	N	0.008673	T	0.37348	0.1000	L	0.32530	0.975	0.80722	D	1	B	0.06786	0.001	B	0.13407	0.009	T	0.13098	-1.0522	10	0.07482	T	0.82	.	12.3309	0.55039	0.1373:0.0:0.8627:0.0	.	734	O95803	NDST3_HUMAN	K	734	ENSP00000296499:E734K	ENSP00000296499:E734K	E	+	1	0	NDST3	119381208	1.000000	0.71417	0.035000	0.18076	0.012000	0.07955	2.943000	0.49026	0.808000	0.34231	-0.150000	0.13652	GAG	.	.		0.517	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		A	119161760	G	A	119161760	3	1	15	1	0	0	0	0	1	0	0	0	10266	1175	41	3	2238	3	NDST3	4	119161760	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	34658806	119161760	71992516	20	1320										
LARP1B	55132	hgsc.bcm.edu	37	chr4	128999019	128999019	+	Frame_Shift_Del	DEL	G	G	-													0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	agagaaggttgaaaagagaaGtaacagtgacagcaaagaaa							TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr4:128999019delG	ENST00000326639.6	+	4	330	c.119delG	c.(118-120)agtfs	p.S40fs	LARP1B_ENST00000441387.1_Frame_Shift_Del_p.S40fs|LARP1B_ENST00000354456.3_5'UTR|LARP1B_ENST00000427266.1_Frame_Shift_Del_p.S40fs|LARP1B_ENST00000264584.5_Frame_Shift_Del_p.S40fs|LARP1B_ENST00000512292.1_Frame_Shift_Del_p.S40fs|LARP1B_ENST00000432347.2_Frame_Shift_Del_p.S40fs|LARP1B_ENST00000394288.3_Frame_Shift_Del_p.S40fs	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	40						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						GAAAAGAGAAGTAACAGTGAC	0.388																																					p.S40fs		Atlas-Indel,Pindel	.											.	LARP1B	120	.	0			c.118delA						.						87	88	88					4																	128999019		2203	4300	6503	SO:0001589	frameshift_variant	55132	exon4			.		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.119delG	chr4.hg19:g.128999019delG	ENSP00000321997:p.Ser40fs	399.0	0.0		406.0	59.0	NM_032239	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Frame_Shift_Del	DEL	ENST00000326639.6	hg19	CCDS3738.1																																																																																			.	.		0.388	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		-	128999019	G	-	128999019	7	5	15	1	0	1	0	1	0	0	0	0	8638	1029	36	0	125	0	LARP1B	4	128999019	Frame_Shift_Del	DEL	G	TCGA-2Y-A9H5-01A-11D-A382-10	9837259	128999019	62155257	21	1321										
SLC10A7	84068	hgsc.bcm.edu	37	chr4	147431063	147431063	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	acttttaaagatttaaacatAcccttttaaaagccattcgt	3	8	0	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr4:147431063A>T	ENST00000507030.1	-	3	320		c.e3+1		SLC10A7_ENST00000264986.3_Intron|SLC10A7_ENST00000335472.7_Splice_Site|SLC10A7_ENST00000394059.4_Splice_Site|SLC10A7_ENST00000511315.1_Splice_Site|SLC10A7_ENST00000432059.2_Splice_Site|SLC10A7_ENST00000511374.1_Intron|SLC10A7_ENST00000394062.3_Splice_Site			Q0GE19	NTCP7_HUMAN	solute carrier family 10, member 7						sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|skin(1)	16	all_hematologic(180;0.151)					ATTTAAACATACCCTTTTAAA	0.348																																					.		Atlas-SNP	.											.	SLC10A7	32	.	0			c.320+2T>A						.						61	64	63					4																	147431063		2203	4300	6503	SO:0001630	splice_region_variant	84068	exon4			AAACATACCCTTT	AY346324	CCDS3768.1, CCDS34073.1, CCDS75198.1	4q31.2	2013-07-18	2013-07-18	2006-12-19	ENSG00000120519	ENSG00000120519		"Solute carriers"	23088	protein-coding gene	gene with protein product		611459	"chromosome 4 open reading frame 13"	C4orf13		15932064	Standard	NM_032128		Approved	MGC25043, DKFZp566M114, DKFZp313H0531, DKFZp779O2438	uc003ikr.2	Q0GE19	OTTHUMG00000161437	ENST00000507030.1:c.320+1T>A	chr4.hg19:g.147431063A>T		113.0	0.0		128.0	51.0	NM_001029998	A7E2E6|A7MAX9|Q0VAP9|Q45NG1|Q45NG2|Q5H9S6|Q6P4E6|Q8IZ62|Q8NBP8|Q9H0M9	Splice_Site	SNP	ENST00000507030.1	hg19	CCDS34073.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.198209	0.79015	.	.	ENSG00000120519	ENST00000432059;ENST00000335472;ENST00000507030;ENST00000394062;ENST00000394059	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.737	0.62824	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC10A7	147650513	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.207000	0.72159	2.049000	0.60858	0.533000	0.62120	.	.	.		0.348	SLC10A7-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366932.1	NM_032128	Intron	T	147431063	A	T	147431063	5	4	15	1	0	0	0	0	0	0	1	0	14394	405	14	4	785	4	SLC10A7	4	147431063	Splice_Site	SNP	A	TCGA-2Y-A9H5-01A-11D-A382-10	18432044	147431063	43723213	22	1322										
BRD9	65980	hgsc.bcm.edu	37	chr5	887508	887508	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cttaaagcctgcgtgaaggaTcttcttcgccaacttgtagt	9	10	2	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr5:887508T>A	ENST00000467963.1	-	6	851	c.685A>T	c.(685-687)Atc>Ttc	p.I229F	BRD9_ENST00000323510.4_Missense_Mutation_p.I113F|BRD9_ENST00000494422.1_5'Flank|BRD9_ENST00000388890.4_Missense_Mutation_p.I113F|BRD9_ENST00000483173.1_Missense_Mutation_p.I176F|BRD9_ENST00000435709.2_Missense_Mutation_p.I113F	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	229					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			GCGTGAAGGATCTTCTTCGCC	0.488																																					p.I229F		Atlas-SNP	.											.	BRD9	113	.	0			c.A685T						.						207	193	198					5																	887508		2203	4300	6503	SO:0001583	missense	65980	exon6			GAAGGATCTTCTT	AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310			25818	protein-coding gene	gene with protein product						12477932	Standard	NM_023924		Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.685A>T	chr5.hg19:g.887508T>A	ENSP00000419765:p.Ile229Phe	72.0	0.0		73.0	17.0	NM_023924	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	Missense_Mutation	SNP	ENST00000467963.1	hg19	CCDS34127.2	.	.	.	.	.	.	.	.	.	.	t	12.76	2.034037	0.35893	.	.	ENSG00000028310	ENST00000323510;ENST00000388890;ENST00000483173;ENST00000467963;ENST00000435709;ENST00000489093	T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13	5.35	4.17	0.49024	Bromodomain (3);	0.169713	0.51477	D	0.000089	T	0.15262	0.0368	N	0.08118	0	0.47374	D	0.999409	P;P;P;P	0.51791	0.948;0.723;0.724;0.942	B;B;B;P	0.48189	0.408;0.256;0.345;0.57	T	0.06427	-1.0827	10	0.87932	D	0	.	11.0832	0.48072	0.0:0.0:0.2968:0.7032	.	176;229;113;113	B4DMQ2;Q9H8M2;Q9H8M2-1;Q9H8M2-3	.;BRD9_HUMAN;.;.	F	113;113;176;229;113;113	ENSP00000323557:I113F;ENSP00000373542:I113F;ENSP00000419845:I176F;ENSP00000419765:I229F;ENSP00000402984:I113F;ENSP00000420722:I113F	ENSP00000323557:I113F	I	-	1	0	BRD9	940508	1.000000	0.71417	1.000000	0.80357	0.073000	0.16967	3.248000	0.51430	0.845000	0.35118	0.533000	0.62120	ATC	.	.		0.488	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354113.1	NM_023924		A	887508	T	A	887508	3	1	15	1	0	0	0	0	1	0	0	0	1509	1435	50	4	1152	4	BRD9	5	887508	Missense_Mutation	SNP	T	TCGA-2Y-A9H5-01A-11D-A382-10		887508	180027752	23	1323										
EMB	133418	hgsc.bcm.edu	37	chr5	49695712	49695712	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cattttttctatgcctggggAcattattttctataccattg	6	8	2	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr5:49695712A>G	ENST00000303221.5	-	8	1162	c.947T>C	c.(946-948)gTc>gCc	p.V316A	EMB_ENST00000514111.1_Missense_Mutation_p.V266A|EMB_ENST00000508934.1_Missense_Mutation_p.V262A	NM_198449.2	NP_940851.1	Q6PCB8	EMB_HUMAN	embigin	316					cell adhesion (GO:0007155)|plasma membrane lactate transport (GO:0035879)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	organic cyclic compound binding (GO:0097159)			breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	15	Lung SC(58;0.218)	Lung NSC(810;0.0795)				ATGCCTGGGGACATTATTTTC	0.269																																					p.V316A		Atlas-SNP	.											.	EMB	42	.	0			c.T947C						.						71	75	74					5																	49695712		2197	4284	6481	SO:0001583	missense	133418	exon8			CTGGGGACATTAT	BC059398	CCDS3953.1	5q11.1	2013-01-29	2010-06-24		ENSG00000170571	ENSG00000170571		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30465	protein-coding gene	gene with protein product		615669	"embigin homolog (mouse)"			9438341	Standard	NM_198449		Approved	MGC71745	uc003jom.3	Q6PCB8	OTTHUMG00000131161	ENST00000303221.5:c.947T>C	chr5.hg19:g.49695712A>G	ENSP00000302289:p.Val316Ala	227.0	0.0		416.0	129.0	NM_198449	B7Z6S3|B7Z902	Missense_Mutation	SNP	ENST00000303221.5	hg19	CCDS3953.1	.	.	.	.	.	.	.	.	.	.	A	0.015	-1.540046	0.00934	.	.	ENSG00000170571	ENST00000303221;ENST00000510295;ENST00000508934;ENST00000514111	T;T;T	0.42513	0.97;0.99;1.0	4.33	-7.35	0.01422	.	1.418890	0.04651	N	0.407153	T	0.16085	0.0387	N	0.08118	0	0.09310	N	0.999999	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.001	T	0.10730	-1.0617	9	.	.	.	0.0166	1.9822	0.03429	0.4347:0.2233:0.2296:0.1125	.	262;316	D6RDX7;Q6PCB8	.;EMB_HUMAN	A	316;288;262;266	ENSP00000302289:V316A;ENSP00000425215:V262A;ENSP00000426404:V266A	.	V	-	2	0	EMB	49731469	0.017000	0.18338	0.005000	0.12908	0.588000	0.36517	-0.390000	0.07332	-1.442000	0.01955	-0.425000	0.05940	GTC	.	.		0.269	EMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253853.1	NM_198449		G	49695712	A	G	49695712	3	3	15	1	0	0	0	0	1	0	0	0	5087	275	10	2	44	2	EMB	5	49695712	Missense_Mutation	SNP	A	TCGA-2Y-A9H5-01A-11D-A382-10	48808204	49695712	131219548	24	1324										
SRFBP1	153443	hgsc.bcm.edu	37	chr5	121355923	121355923	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tacagcgtgaagcaactgtcAtcagtgagcaaaaagtcaaa	9	8	3	2	rs374380607		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr5:121355923A>G	ENST00000339397.4	+	6	565	c.493A>G	c.(493-495)Atc>Gtc	p.I165V		NM_152546.2	NP_689759.2			serum response factor binding protein 1											central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		AGCAACTGTCATCAGTGAGCA	0.343																																					p.I165V		Atlas-SNP	.											.	SRFBP1	47	.	0			c.A493G						.	A	VAL/ILE	0,3744		0,0,1872	109	99	102		493	-5.1	0	5		102	1,8189		0,1,4094	no	missense	SRFBP1	NM_152546.2	29	0,1,5966	GG,GA,AA		0.0122,0.0,0.0084	benign	165/430	121355923	1,11933	1872	4095	5967	SO:0001583	missense	153443	exon6			ACTGTCATCAGTG	AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"BUD22 homolog (S. cerevisiae)"	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.493A>G	chr5.hg19:g.121355923A>G	ENSP00000341324:p.Ile165Val	132.0	0.0		181.0	56.0	NM_152546		Missense_Mutation	SNP	ENST00000339397.4	hg19	CCDS43354.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.895756	0.00522	0.0	1.22E-4	ENSG00000151304	ENST00000339397	.	.	.	5.2	-5.13	0.02884	.	1.855570	0.01872	N	0.037266	T	0.15478	0.0373	N	0.10664	0.02	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.14035	-1.0487	9	0.11485	T	0.65	8.3821	4.878	0.13665	0.4647:0.0:0.3207:0.2146	.	165	Q8NEF9	SRFB1_HUMAN	V	165	.	ENSP00000341324:I165V	I	+	1	0	SRFBP1	121383822	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.166000	0.16583	-1.012000	0.03387	-0.468000	0.05107	ATC	.	.		0.343	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546		G	121355923	A	G	121355923	3	3	15	1	0	0	0	0	1	0	0	0	15159	217	8	2	515	2	SRFBP1	5	121355923	Missense_Mutation	SNP	A	TCGA-2Y-A9H5-01A-11D-A382-10	71660211	121355923	59559337	25	1325										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135692906	135692906	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ccagcattttccggaccaccGggatgttgccatactcagcc	9	15	1	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr5:135692906G>A	ENST00000513104.1	-	2	452	c.170C>T	c.(169-171)cCg>cTg	p.P57L	TRPC7_ENST00000426057.2_Missense_Mutation_p.P57L|TRPC7_ENST00000355180.3_Missense_Mutation_p.P57L	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	57					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCGGACCACCGGGATGTTGCC	0.607																																					p.P57L		Atlas-SNP	.											.	TRPC7	126	.	0			c.C170T						.						95	108	103					5																	135692906		2158	4275	6433	SO:0001583	missense	57113	exon2			ACCACCGGGATGT	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.170C>T	chr5.hg19:g.135692906G>A	ENSP00000426070:p.Pro57Leu	67.0	0.0		79.0	24.0	NM_001167576	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	hg19	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	G	26.2	4.713245	0.89112	.	.	ENSG00000069018	ENST00000355180;ENST00000426057;ENST00000513104;ENST00000265193	T;T;T	0.70749	-0.51;-0.51;-0.51	5.2	5.2	0.72013	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.80507	0.4636	L	0.42744	1.35	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;0.995;1.0;1.0	D;P;D;D	0.91635	0.999;0.798;0.992;0.992	T	0.81516	-0.0897	10	0.66056	D	0.02	-18.1038	18.9316	0.92568	0.0:0.0:1.0:0.0	.	57;57;57;57	Q8IWP7;F5H5U9;Q70T25;Q9HCX4	.;.;.;TRPC7_HUMAN	L	57	ENSP00000347312:P57L;ENSP00000441628:P57L;ENSP00000426070:P57L	ENSP00000265193:P57L	P	-	2	0	TRPC7	135720805	1.000000	0.71417	0.967000	0.41034	0.997000	0.91878	9.657000	0.98554	2.691000	0.91804	0.655000	0.94253	CCG	.	.		0.607	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135692906	G	A	135692906	3	1	15	1	0	0	0	0	1	0	0	0	16599	1116	39	1	2462	1	TRPC7	5	135692906	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	14336983	135692906	45222354	26	1326										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141324975	141324976	+	Missense_Mutation	DNP	CT	CT	TG													0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cctgctgctgctgctgctgcCtctgctcttgccctcagtcc					rs13188049|rs3833449		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr5:141324975_141324976CT>TG	ENST00000231484.3	-	4	4735_4736	c.3525_3526AG>CA	c.(3523-3528)agAGgc>agCAgc	p.1175_1176RG>SS		NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1175					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ctgctgctgcctctgctCTTGC	0.584																																					p.G1176S|p.R1175S		Atlas-SNP	.											.	PCDH12	133	.	0			c.G3526A|c.A3525C						.																																			SO:0001583	missense	51294	exon4			TGCTGCCTCTGCT|GCTGCCTCTGCTC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.3525_3526delinsTG	chr5.hg19:g.141324975_141324976delinsTG	ENSP00000231484:p.R1175_G1176delinsSS	95.0|100.0	0.0		72.0	10.0|9.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1																																																																																			.	.		0.584	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		TG	141324976	CT	TG	141324975	3	4	15	1	0	0	0	0	1	0	0	0	11519	681	24	3	32	3	PCDH12	5	141324975	Missense_Mutation	DNP	CT	TCGA-2Y-A9H5-01A-11D-A382-10	5632069	141324975	39590285	27	1327										
DSP	1832	hgsc.bcm.edu	37	chr6	7585481	7585481	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tgcacaggtggcatcatccaCccaaccacgggccagaagct	10	15	1	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr6:7585481C>T	ENST00000379802.3	+	24	8327	c.7986C>T	c.(7984-7986)caC>caT	p.H2662H	DSP_ENST00000418664.2_Silent_p.H2063H	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2662	4.5 X 38 AA tandem repeats (Domain C).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GCATCATCCACCCAACCACGG	0.562																																					p.H2662H		Atlas-SNP	.											.	DSP	306	.	0			c.C7986T						.						93	90	91					6																	7585481		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon24			CATCCACCCAACC	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.7986C>T	chr6.hg19:g.7585481C>T		144.0	0.0		249.0	65.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.562	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7585481	C	T	7585481	2	4	15	1	0	0	0	0	0	0	0	1	4783	506	18	3		3	DSP	6	7585481	Silent	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10		7585481	163529586	28	1328										
HIST1H3F	8968	hgsc.bcm.edu	37	chr6	26250518	26250518	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	agcacacaggttggtgtcctCaaagagccccaccaggtaag	11	12	1	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr6:26250518C>T	ENST00000446824.2	-	1	317	c.316G>A	c.(316-318)Gag>Aag	p.E106K	HIST1H2BH_ENST00000356350.2_5'Flank	NM_021018.2	NP_066298.1	P68431	H31_HUMAN	histone cluster 1, H3f	106					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			lung(6)|urinary_tract(1)	7						TTGGTGTCCTCAAAGAGCCCC	0.602											OREG0017241	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E106K		Atlas-SNP	.											.	HIST1H3F	16	.	0			c.G316A						.						103	100	101					6																	26250518		2203	4300	6503	SO:0001583	missense	8968	exon1			TGTCCTCAAAGAG	Z80786	CCDS4600.1	6p22.1	2011-01-27	2006-10-11	2003-03-14	ENSG00000256316	ENSG00000277775		"Histones / Replication-dependent"	4773	protein-coding gene	gene with protein product		602816	"H3 histone family, member I", "histone 1, H3f"	H3FI		9119399, 12408966	Standard	NM_021018		Approved	H3/i	uc003nhg.1	P68431	OTTHUMG00000014435	ENST00000446824.2:c.316G>A	chr6.hg19:g.26250518C>T	ENSP00000444823:p.Glu106Lys	125.0	0.0	785	149.0	7.0	NM_021018	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000446824.2	hg19	CCDS4600.1	.	.	.	.	.	.	.	.	.	.	.	14.31	2.497506	0.44455	.	.	ENSG00000256316	ENST00000446824	T	0.71341	-0.56	4.82	4.82	0.62117	.	.	.	.	.	T	0.79305	0.4423	.	.	.	0.46901	D	0.999242	.	.	.	.	.	.	T	0.81895	-0.0723	6	0.87932	D	0	.	17.7536	0.88442	0.0:1.0:0.0:0.0	.	.	.	.	K	106	ENSP00000444823:E106K	ENSP00000444823:E106K	E	-	1	0	HIST1H3F	26358497	1.000000	0.71417	1.000000	0.80357	0.247000	0.25773	7.666000	0.83877	2.602000	0.87976	0.561000	0.74099	GAG	.	.		0.602	HIST1H3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040098.1	NM_021018		T	26250518	C	T	26250518	3	4	15	1	0	0	0	0	1	0	0	0	7169	835	29	3	98	3	HIST1H3F	6	26250518	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	18665037	26250518	144864549	29	1329										
OR11A1	26531	hgsc.bcm.edu	37	chr6	29394996	29394996	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gtgaccaccagccccatgtaCcgtctgggccccatcaggag	11	16	2	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr6:29394996C>A	ENST00000377149.1	-	5	895	c.423G>T	c.(421-423)cgG>cgT	p.R141R	OR11A1_ENST00000377148.1_Silent_p.R141R|OR11A1_ENST00000377147.2_Silent_p.R141R|OR5V1_ENST00000377154.1_Intron			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	141						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						GCCCCATGTACCGTCTGGGCC	0.577																																					p.R141R		Atlas-SNP	.											.	OR11A1	30	.	0			c.G423T						.						73	81	78					6																	29394996		1507	2708	4215	SO:0001819	synonymous_variant	26531	exon1			CATGTACCGTCTG		CCDS34363.1	6p22.2-p21.31	2014-02-19	2002-02-28		ENSG00000204694	ENSG00000204694		"GPCR / Class A : Olfactory receptors"	8176	protein-coding gene	gene with protein product			"olfactory receptor, family 11, subfamily A, member 2"	OR11A2			Standard	XM_005249001		Approved	hs6M1-18	uc003nmg.3	Q9GZK7	OTTHUMG00000031225	ENST00000377149.1:c.423G>T	chr6.hg19:g.29394996C>A		66.0	0.0		120.0	35.0	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Silent	SNP	ENST00000377149.1	hg19	CCDS34363.1																																																																																			.	.		0.577	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1			A	29394996	C	A	29394996	2	1	15	1	0	0	0	0	0	0	0	1	10933	494	18	3		3	OR11A1	6	29394996	Silent	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	3144478	29394996	141720071	30	1330										
DAAM2	23500	hgsc.bcm.edu	37	chr6	39824089	39824089	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tgcagtgaccatggccccccGcaagaggagccaccatggcc	12	16	0	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr6:39824089G>A	ENST00000398904.2	+	2	193	c.11G>A	c.(10-12)cGc>cAc	p.R4H	DAAM2_ENST00000274867.4_Missense_Mutation_p.R4H|DAAM2_ENST00000405961.3_Missense_Mutation_p.R4H|DAAM2_ENST00000494405.1_3'UTR|DAAM2_ENST00000538976.1_Missense_Mutation_p.R4H			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	4					actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					ATGGCCCCCCGCAAGAGGAGC	0.617																																					p.R4H		Atlas-SNP	.											DAAM2,rectum,NS,0,1	DAAM2	101	.	0			c.G11A						.						20	23	22					6																	39824089		1992	4156	6148	SO:0001583	missense	23500	exon2			CCCCCCGCAAGAG	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.11G>A	chr6.hg19:g.39824089G>A	ENSP00000381876:p.Arg4His	88.0	0.0		114.0	5.0	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.623445	0.87460	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976;ENST00000405961	D;D;D	0.81499	-1.5;-1.5;-1.5	5.92	5.05	0.67936	.	0.106857	0.64402	N	0.000012	T	0.80003	0.4544	M	0.66939	2.045	0.47737	D	0.999501	B;B;D	0.69078	0.003;0.002;0.997	B;B;P	0.52481	0.005;0.002;0.7	T	0.83021	-0.0167	10	0.66056	D	0.02	.	13.9184	0.63916	0.074:0.0:0.926:0.0	.	4;4;4	G5EA45;Q86T65;F2Z2Q2	.;DAAM2_HUMAN;.	H	4	ENSP00000274867:R4H;ENSP00000381876:R4H;ENSP00000437808:R4H	ENSP00000274867:R4H	R	+	2	0	DAAM2	39932067	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	6.243000	0.72384	1.499000	0.48617	0.655000	0.94253	CGC	.	.		0.617	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			A	39824089	G	A	39824089	3	1	15	1	0	0	0	0	1	0	0	0	4218	1087	38	1	13	1	DAAM2	6	39824089	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	10429093	39824089	131290978	31	1331										
GFRAL	389400	hgsc.bcm.edu	37	chr6	55264182	55264182	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tctaggagaagtaatctatgCtgccatgtgcatgacagtca	10	8	3	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr6:55264182C>T	ENST00000340465.2	+	8	1150	c.1064C>T	c.(1063-1065)gCt>gTt	p.A355V		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	355					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			GTAATCTATGCTGCCATGTGC	0.323																																					p.A355V		Atlas-SNP	.											.	GFRAL	91	.	0			c.C1064T						.						80	80	80					6																	55264182		2203	4300	6503	SO:0001583	missense	389400	exon8			TCTATGCTGCCAT	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.1064C>T	chr6.hg19:g.55264182C>T	ENSP00000343636:p.Ala355Val	167.0	0.0		316.0	91.0	NM_207410	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	hg19	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.469728	0.26423	.	.	ENSG00000187871	ENST00000340465	T	0.35236	1.32	5.79	0.807	0.18714	.	0.936787	0.08873	N	0.881279	T	0.05181	0.0138	N	0.14661	0.345	0.09310	N	1	B	0.17852	0.024	B	0.12837	0.008	T	0.42137	-0.9469	10	0.10111	T	0.7	-1.0493	4.3899	0.11335	0.0:0.4131:0.3197:0.2672	.	355	Q6UXV0	GFRAL_HUMAN	V	355	ENSP00000343636:A355V	ENSP00000343636:A355V	A	+	2	0	GFRAL	55372141	0.000000	0.05858	0.000000	0.03702	0.960000	0.62799	-0.372000	0.07504	0.063000	0.16370	0.655000	0.94253	GCT	.	.		0.323	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		T	55264182	C	T	55264182	3	4	15	1	0	0	0	0	1	0	0	0	6359	797	28	3	1094	3	GFRAL	6	55264182	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	15440093	55264182	115850885	32	1332										
C7orf30	115416	hgsc.bcm.edu	37	chr7	23338995	23338995	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gggccgggcggccgtgtggcGcggctgctcgccccactaat	17	15	0	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr7:23338995G>A	ENST00000466681.1	+	1	177	c.24G>A	c.(22-24)gcG>gcA	p.A8A	MALSU1_ENST00000479974.1_Intron	NM_138446.1	NP_612455.1	Q96EH3	MASU1_HUMAN	mitochondrial assembly of ribosomal large subunit 1	8					negative regulation of mitochondrial translation (GO:0070130)|ribosomal large subunit biogenesis (GO:0042273)	mitochondrion (GO:0005739)											GCCGTGTGGCGCGGCTGCTCG	0.721																																					p.A8A		Atlas-SNP	.											.	.	.	.	0			c.G24A						.						6	8	7					7																	23338995		1921	4002	5923	SO:0001819	synonymous_variant	115416	exon1			TGTGGCGCGGCTG	BC012331	CCDS5381.1	7p15.3	2013-05-24	2012-02-20	2012-02-20	ENSG00000156928	ENSG00000156928			21721	protein-coding gene	gene with protein product		614624	"chromosome 7 open reading frame 30"	C7orf30		22238376, 22238375	Standard	NM_138446		Approved	mtRsfA	uc003swd.1	Q96EH3	OTTHUMG00000128443	ENST00000466681.1:c.24G>A	chr7.hg19:g.23338995G>A		89.0	0.0		104.0	9.0	NM_138446	A4D154	Silent	SNP	ENST00000466681.1	hg19	CCDS5381.1																																																																																			.	.		0.721	MALSU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250241.2	NM_138446		A	23338995	G	A	23338995	2	1	15	1	0	0	0	0	0	0	0	1	2388	1074	38	1		1	C7orf30	7	23338995	Silent	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10		23338995	135799668	33	1333										
PEG10	23089	hgsc.bcm.edu	37	chr7	94293724	94293727	+	Frame_Shift_Del	DEL	AAAG	AAAG	-													0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tgcgcctgacgcaggaagaaAaagaaagacgcagaaagctg							TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr7:94293724_94293727delAAAG	ENST00000482108.1	+	2	1335_1338	c.856_859delAAAG	c.(856-861)aaagaafs	p.KE286fs	PEG10_ENST00000488574.1_Frame_Shift_Del_p.KE286fs	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	286					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GCAGGAAGAAAAAGAAAGACGCAG	0.593																																					p.361_362del		Pindel	.											.	PEG10	36	.	0			c.1083_1086del						.																																			SO:0001589	frameshift_variant	23089	exon2			.	AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.856_859delAAAG	chr7.hg19:g.94293728_94293731delAAAG	ENSP00000417587:p.Lys286fs	163.0	0.0		142.0	29.0	NM_001172438	Q96A68|Q9UPV1	Frame_Shift_Del	DEL	ENST00000482108.1	hg19	CCDS55126.1																																																																																			.	.		0.593	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340751.1	NM_015068		-	94293727	AAAG	-	94293724	7	5	15	1	0	1	0	1	0	0	0	0	11728	15	1	0	1090	0	PEG10	7	94293724	Frame_Shift_Del	DEL	AAAG	TCGA-2Y-A9H5-01A-11D-A382-10	70954729	94293724	64844939	34	1334										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107875102	107875102	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	caataatgtaatcttttggaGactgttgggtgatggttgga	13	3	1	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr7:107875102G>T	ENST00000425651.2	-	3	154	c.155C>A	c.(154-156)tCt>tAt	p.S52Y	NRCAM_ENST00000413765.2_Missense_Mutation_p.S52Y|NRCAM_ENST00000379028.3_Missense_Mutation_p.S52Y|NRCAM_ENST00000379024.4_Missense_Mutation_p.S52Y|NRCAM_ENST00000351718.4_Missense_Mutation_p.S46Y|NRCAM_ENST00000379022.4_Missense_Mutation_p.S52Y	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	52	Ig-like 1.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						ATCTTTTGGAGACTGTTGGGT	0.363																																					p.S52Y		Atlas-SNP	.											.	NRCAM	267	.	0			c.C155A						.						107	115	112					7																	107875102		2203	4300	6503	SO:0001583	missense	4897	exon3			TTTGGAGACTGTT		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.155C>A	chr7.hg19:g.107875102G>T	ENSP00000401244:p.Ser52Tyr	62.0	0.0		97.0	25.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	G	33	5.256128	0.95336	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022;ENST00000445979;ENST00000417701;ENST00000442580;ENST00000419936;ENST00000456431;ENST00000418239	T;T;T;T;T;T;T;T;T;T	0.68903	2.49;2.49;2.49;2.49;2.49;2.49;2.49;-0.36;-0.36;-0.36	5.61	5.61	0.85477	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.84741	0.5539	M	0.84433	2.695	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.86207	0.1622	10	0.87932	D	0	.	19.9997	0.97405	0.0:0.0:1.0:0.0	.	52;52;52;46;52	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	Y	52;52;52;52;46;52;52;52;46;46;52;46;46;52	ENSP00000368314:S52Y;ENSP00000407858:S52Y;ENSP00000325269:S46Y;ENSP00000368310:S52Y;ENSP00000401244:S52Y;ENSP00000368308:S52Y;ENSP00000390421:S46Y;ENSP00000390868:S52Y;ENSP00000397544:S46Y;ENSP00000408203:S46Y	ENSP00000325269:S46Y	S	-	2	0	NRCAM	107662338	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.813000	0.99286	2.813000	0.96785	0.655000	0.94253	TCT	.	.		0.363	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		T	107875102	G	T	107875102	3	4	15	1	0	0	0	0	1	0	0	0	10653	942	33	3	3901	3	NRCAM	7	107875102	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	13581378	107875102	51263561	35	1335										
ZNF800	168850	hgsc.bcm.edu	37	chr7	127014128	127014128	+	Frame_Shift_Del	DEL	G	G	-													0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gtggagaatgggtaatggaaGggggtgaagattctacagaa							TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr7:127014128delG	ENST00000393313.1	-	5	1853	c.1262delC	c.(1261-1263)cctfs	p.P421fs	ZNF800_ENST00000393312.1_Frame_Shift_Del_p.P421fs|ZNF800_ENST00000265827.3_Frame_Shift_Del_p.P421fs|ZNF800_ENST00000485577.1_5'Flank			Q2TB10	ZN800_HUMAN	zinc finger protein 800	421					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						GGTAATGGAAGGGGGTGAAGA	0.358																																					p.P421fs		Pindel	.											.	ZNF800	78	.	0			c.1263delT						.						84	90	88					7																	127014128		2203	4298	6501	SO:0001589	frameshift_variant	168850	exon5			.	AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"Zinc fingers, C2H2-type"	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.1262delC	chr7.hg19:g.127014128delG	ENSP00000376989:p.Pro421fs	99.0	0.0		173.0	42.0	NM_176814	Q9HBN0	Frame_Shift_Del	DEL	ENST00000393313.1	hg19	CCDS5795.1																																																																																			.	.		0.358	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814		-	127014128	G	-	127014128	7	5	15	1	0	1	0	1	0	0	0	0	18184	1000	35	0	740	0	ZNF800	7	127014128	Frame_Shift_Del	DEL	G	TCGA-2Y-A9H5-01A-11D-A382-10	19139026	127014128	32124535	36	1336										
AGPAT5	55326	hgsc.bcm.edu	37	chr8	6566226	6566226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tgctccacacgtactccatgCgctacctgctgcccagcgtc	8	18	0	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr8:6566226C>T	ENST00000285518.6	+	1	349	c.37C>T	c.(37-39)Cgc>Tgc	p.R13C	CTD-2541M15.1_ENST00000522897.1_RNA|CTD-2541M15.1_ENST00000527490.1_RNA|CTD-2541M15.1_ENST00000525186.1_RNA	NM_018361.3	NP_060831.2	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	13					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		AGPAT5/MCPH1(2)	endometrium(2)|kidney(2)|large_intestine(4)|lung(3)	11			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		GTACTCCATGCGCTACCTGCT	0.721																																					p.R13C		Atlas-SNP	.											.	AGPAT5	31	.	0			c.C37T						.						28	27	27					8																	6566226		2202	4299	6501	SO:0001583	missense	55326	exon1			TCCATGCGCTACC	AF375789	CCDS34796.1	8p23.1	2013-02-05	2013-02-05		ENSG00000155189	ENSG00000155189	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20886	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, epsilon"	614796	"1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"				Standard	NM_018361		Approved	FLJ11210, LPAAT-e, LPAAT-epsilon	uc003wqo.3	Q9NUQ2	OTTHUMG00000163656	ENST00000285518.6:c.37C>T	chr8.hg19:g.6566226C>T	ENSP00000285518:p.Arg13Cys	39.0	0.0		22.0	7.0	NM_018361	Q8IZ47|Q9BQG4	Missense_Mutation	SNP	ENST00000285518.6	hg19	CCDS34796.1	.	.	.	.	.	.	.	.	.	.	c	13.61	2.289508	0.40494	.	.	ENSG00000155189	ENST00000285518;ENST00000518327	T	0.33865	1.39	3.86	2.96	0.34315	.	0.119093	0.64402	U	0.000017	T	0.53642	0.1809	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	1.0;1.0	P;D	0.66602	0.88;0.945	T	0.50320	-0.8842	10	0.36615	T	0.2	-5.8326	10.4172	0.44329	0.197:0.803:0.0:0.0	.	13;13	E5RH21;Q9NUQ2	.;PLCE_HUMAN	C	13;5	ENSP00000285518:R13C	ENSP00000285518:R13C	R	+	1	0	AGPAT5	6553634	1.000000	0.71417	0.788000	0.31933	0.684000	0.39900	5.431000	0.66507	0.577000	0.29470	0.297000	0.19635	CGC	.	.		0.721	AGPAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374684.1	NM_018361		T	6566226	C	T	6566226	3	4	15	1	0	0	0	0	1	0	0	0	390	768	27	1	39	1	AGPAT5	8	6566226	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10		6566226	139797796	37	1337										
NRG1	3084	hgsc.bcm.edu	37	chr8	32600258	32600258	+	Intron	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ggccagcttctacagtacgtCcactccctttctgtctctgc	7	16	3	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr8:32600258C>A	ENST00000405005.3	+	7	700				NRG1_ENST00000287845.5_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000520502.2_Missense_Mutation_p.S288Y|NRG1_ENST00000520407.1_Missense_Mutation_p.S414Y|NRG1_ENST00000539990.1_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000287842.3_Intron|NRG1_ENST00000523079.1_Intron			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TACAGTACGTCCACTCCCTTT	0.463																																					p.S414Y		Atlas-SNP	.											.	NRG1	260	.	0			c.C1241A						.						289	240	257					8																	32600258		2203	4300	6503	SO:0001627	intron_variant	3084	exon5			GTACGTCCACTCC	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.700+665C>A	chr8.hg19:g.32600258C>A		44.0	0.0		50.0	22.0	NM_013962	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	hg19	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304664	0.81136	.	.	ENSG00000157168	ENST00000520407;ENST00000520502	T	0.77098	-1.07	6.03	6.03	0.97812	.	.	.	.	.	T	0.78470	0.4288	N	0.08118	0	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.998;0.999	T	0.77656	-0.2506	8	.	.	.	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	198;288;233;414	B0FWZ3;Q02297-10;Q02297-8;Q02297-9	.;.;.;.	Y	414;288	ENSP00000434640:S414Y	.	S	+	2	0	NRG1	32719800	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.794000	0.85869	2.861000	0.98227	0.655000	0.94253	TCC	.	.		0.463	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			A	32600258	C	A	32600258	1	1	15	0	1	0	0	0	0	0	0	0	10656	855	30	3		3	NRG1	8	32600258	Intron	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	26034032	32600258	113763764	38	1338										
PREX2	80243	hgsc.bcm.edu	37	chr8	68965476	68965476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tttgaaagaaagagaacggcGgaaaggtgggtgtatgaatt	15	2	0	4			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr8:68965476G>A	ENST00000288368.4	+	9	1365	c.1088G>A	c.(1087-1089)cGg>cAg	p.R363Q	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	363					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.R363Q(2)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AGAGAACGGCGGAAAGGTGGG	0.373																																					p.R363Q		Atlas-SNP	.											PREX2_ENST00000354677,NS,carcinoma,0,6	PREX2	614	.	2	Substitution - Missense(2)	lung(2)	c.G1088A						.						107	104	105					8																	68965476		2203	4300	6503	SO:0001583	missense	80243	exon9			AACGGCGGAAAGG	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1088G>A	chr8.hg19:g.68965476G>A	ENSP00000288368:p.Arg363Gln	112.0	0.0		246.0	62.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	36	5.643888	0.96704	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.61040	0.14	5.74	5.74	0.90152	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.74114	0.3674	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.74197	-0.3743	10	0.62326	D	0.03	.	19.9189	0.97077	0.0:0.0:1.0:0.0	.	363;363;363	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	Q	363	ENSP00000288368:R363Q	ENSP00000288368:R363Q	R	+	2	0	PREX2	69128030	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.707000	0.92482	0.655000	0.94253	CGG	.	.		0.373	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		A	68965476	G	A	68965476	3	1	15	1	0	0	0	0	1	0	0	0	12489	1116	39	1	1122	1	PREX2	8	68965476	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	36365218	68965476	77398546	39	1339										
TM7SF4	81501	hgsc.bcm.edu	37	chr8	105360974	105360974	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	catagcggccgctgcctcctGgattatcacgtgtgttctgc	11	13	2	0	rs149253106		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr8:105360974G>T	ENST00000297581.2	+	2	243	c.194G>T	c.(193-195)tGg>tTg	p.W65L	DPYS_ENST00000521601.1_Intron|DCSTAMP_ENST00000517991.1_Missense_Mutation_p.W65L	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	65					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											GCTGCCTCCTGGATTATCACG	0.507																																					p.W65L		Atlas-SNP	.											.	.	.	.	0			c.G194T						.						134	121	125					8																	105360974		2203	4300	6503	SO:0001583	missense	81501	exon2			CCTCCTGGATTAT	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"Dendritic cells (DC)-specific transmembrane protein", "IL-Four INDuced"	605933	"transmembrane 7 superfamily member 4"	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.194G>T	chr8.hg19:g.105360974G>T	ENSP00000297581:p.Trp65Leu	65.0	0.0		128.0	18.0	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	hg19	CCDS6301.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.587901	0.86851	.	.	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.27890	1.64	5.84	4.93	0.64822	.	0.372666	0.28279	N	0.015924	T	0.50154	0.1599	M	0.69823	2.125	0.48236	D	0.999617	D	0.65815	0.995	P	0.59703	0.862	T	0.44436	-0.9328	9	.	.	.	-11.3121	15.3565	0.74431	0.0:0.1382:0.8618:0.0	.	65	Q9H295	TM7S4_HUMAN	L	65	ENSP00000297581:W65L	.	W	+	2	0	TM7SF4	105430150	1.000000	0.71417	0.931000	0.37212	0.019000	0.09904	3.852000	0.55934	2.779000	0.95612	0.655000	0.94253	TGG	.	G|1.000;A|0.000		0.507	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		T	105360974	G	T	105360974	3	4	15	1	0	0	0	0	1	0	0	0	15991	1357	47	3	196	3	TM7SF4	8	105360974	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	36395498	105360974	41003048	40	1340										
KLHL38	340359	hgsc.bcm.edu	37	chr8	124659239	124659239	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cattttgaaccacgagtttcTggaaatgtgataaacctgag	9	7	1	3			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr8:124659239T>C	ENST00000325995.7	-	2	1389	c.1366A>G	c.(1366-1368)Aga>Gga	p.R456G	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	456								p.R456G(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						CACGAGTTTCTGGAAATGTGA	0.438																																					p.R456G		Atlas-SNP	.											KLHL38,NS,carcinoma,0,1	KLHL38	81	.	1	Substitution - Missense(1)	lung(1)	c.A1366G						.						173	166	169					8																	124659239		1946	4139	6085	SO:0001583	missense	340359	exon2			AGTTTCTGGAAAT		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"Kelch-like", "BTB/POZ domain containing"	34435	protein-coding gene	gene with protein product			"kelch-like 38 (Drosophila)"				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1366A>G	chr8.hg19:g.124659239T>C	ENSP00000321475:p.Arg456Gly	115.0	0.0		167.0	75.0	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	hg19	CCDS43766.1	.	.	.	.	.	.	.	.	.	.	t	13.15	2.151622	0.38021	.	.	ENSG00000175946	ENST00000325995	T	0.66280	-0.2	5.04	5.04	0.67666	Kelch-type beta propeller (1);	0.093858	0.64402	D	0.000002	T	0.55940	0.1952	L	0.47716	1.5	0.44555	D	0.997517	B	0.11235	0.004	B	0.09377	0.004	T	0.52815	-0.8525	10	0.37606	T	0.19	.	14.8202	0.70068	0.0:0.0:0.0:1.0	.	456	Q2WGJ6	KLH38_HUMAN	G	456	ENSP00000321475:R456G	ENSP00000321475:R456G	R	-	1	2	KLHL38	124728420	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	4.090000	0.57693	1.916000	0.55485	0.370000	0.22315	AGA	.	.		0.438	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1			C	124659239	T	C	124659239	3	2	15	1	0	0	0	0	1	0	0	0	8399	1588	55	2	387	2	KLHL38	8	124659239	Missense_Mutation	SNP	T	TCGA-2Y-A9H5-01A-11D-A382-10	19298265	124659239	21704783	41	1341										
TMEM2	23670	hgsc.bcm.edu	37	chr9	74327050	74327050	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ttcctgggggttatctgccaGgaattcttcatgaggaagcc	12	9	3	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr9:74327050G>C	ENST00000377044.4	-	16	3257	c.2718C>G	c.(2716-2718)tcC>tcG	p.S906S	TMEM2_ENST00000377066.5_Silent_p.S843S	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	906					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		TTATCTGCCAGGAATTCTTCA	0.423																																					p.S906S		Atlas-SNP	.											.	TMEM2	112	.	0			c.C2718G						.						123	116	119					9																	74327050		2203	4300	6503	SO:0001819	synonymous_variant	23670	exon16			CTGCCAGGAATTC		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.2718C>G	chr9.hg19:g.74327050G>C		99.0	0.0		105.0	36.0	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	hg19	CCDS6638.1																																																																																			.	.		0.423	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		C	74327050	G	C	74327050	2	2	15	1	0	0	0	0	0	0	0	1	16136	987	35	4		4	TMEM2	9	74327050	Silent	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10		74327050	66886381	42	1342										
TLE1	7088	hgsc.bcm.edu	37	chr9	84202721	84202721	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	aatgtcaatacagctggctcCgtctgtgtggccctggaatt	11	10	2	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr9:84202721C>A	ENST00000376499.3	-	17	2916	c.1852G>T	c.(1852-1854)Gga>Tga	p.G618*		NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	618					multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)	p.G618R(2)|p.G618*(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						CAGCTGGCTCCGTCTGTGTGG	0.502																																					p.G618X	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	Atlas-SNP	.											TLE1,NS,carcinoma,0,2	TLE1	81	.	3	Substitution - Missense(2)|Substitution - Nonsense(1)	lung(2)|endometrium(1)	c.G1852T						.						79	78	78					9																	84202721		2203	4300	6503	SO:0001587	stop_gained	7088	exon17			TGGCTCCGTCTGT		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"WD repeat domain containing"	11837	protein-coding gene	gene with protein product	"enhancer of split groucho 1"	600189	"transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.1852G>T	chr9.hg19:g.84202721C>A	ENSP00000365682:p.Gly618*	72.0	0.0		61.0	29.0	NM_005077	A8K495|Q5T3G4|Q969V9	Nonsense_Mutation	SNP	ENST00000376499.3	hg19	CCDS6661.1	.	.	.	.	.	.	.	.	.	.	c	49	15.075900	0.99821	.	.	ENSG00000196781	ENST00000376499	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-12.0128	19.9738	0.97296	0.0:1.0:0.0:0.0	.	.	.	.	X	618	.	ENSP00000365682:G618X	G	-	1	0	TLE1	83392541	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.818000	0.86416	2.732000	0.93576	0.655000	0.94253	GGA	.	.		0.502	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077		A	84202721	C	A	84202721	4	1	15	1	0	0	0	0	0	1	0	0	15953	661	23	1	476	1	TLE1	9	84202721	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	9875671	84202721	57010710	43	1343										
FGD3	89846	hgsc.bcm.edu	37	chr9	95797700	95797700	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gaggagaggctggactcgggGcatgtgtggaagctgcagtg	20	6	0	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr9:95797700G>T	ENST00000375482.3	+	18	2503	c.2007G>T	c.(2005-2007)ggG>ggT	p.G669G	FGD3_ENST00000337352.6_Silent_p.G669G|FGD3_ENST00000538555.1_Silent_p.G272G|FGD3_ENST00000416701.2_Silent_p.G668G	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	669	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						TGGACTCGGGGCATGTGTGGA	0.657																																					p.G669G		Atlas-SNP	.											.	FGD3	116	.	0			c.G2007T						.						31	40	37					9																	95797700		2157	4270	6427	SO:0001819	synonymous_variant	89846	exon18			CTCGGGGCATGTG	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16027	protein-coding gene	gene with protein product			"FGD1 family, member 3"			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.2007G>T	chr9.hg19:g.95797700G>T		168.0	0.0		81.0	37.0	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Silent	SNP	ENST00000375482.3	hg19	CCDS43849.1																																																																																			.	.		0.657	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086		T	95797700	G	T	95797700	2	4	15	1	0	0	0	0	0	0	0	1	5842	1190	42	3		3	FGD3	9	95797700	Silent	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	11594979	95797700	45415731	44	1344										
NEK6	10783	hgsc.bcm.edu	37	chr9	127074820	127074820	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	acgctgtcttttcgctgctcGctggcggacttccagatcga	11	13	1	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr9:127074820G>A	ENST00000320246.5	+	3	268	c.123G>A	c.(121-123)tcG>tcA	p.S41S	NEK6_ENST00000394199.2_Silent_p.S75S|NEK6_ENST00000540326.1_Silent_p.S59S|NEK6_ENST00000539416.1_Silent_p.S66S|NEK6_ENST00000546191.1_Silent_p.S41S|NEK6_ENST00000373603.1_Silent_p.S41S|NEK6_ENST00000545174.1_Silent_p.S41S|NEK6_ENST00000373600.3_Silent_p.S75S	NM_014397.5	NP_055212.2	Q9HC98	NEK6_HUMAN	NIMA-related kinase 6	41	Interaction with ARHGAP33, ANKRA2, CDC42, PRDX3, RAD26L, RBBP6, RPS7 and TRIP4.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cellular senescence (GO:2000772)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinesin binding (GO:0019894)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15						TTCGCTGCTCGCTGGCGGACT	0.612																																					p.S75S	NSCLC(122;934 1785 18647 44295 45571)	Atlas-SNP	.											.	NEK6	47	.	0			c.G225A						.						53	49	50					9																	127074820		2203	4300	6503	SO:0001819	synonymous_variant	10783	exon4			CTGCTCGCTGGCG	AF087909	CCDS6854.1, CCDS48015.1, CCDS55338.1, CCDS55339.1	9q33.3-q34.11	2012-11-15	2012-11-15		ENSG00000119408	ENSG00000119408			7749	protein-coding gene	gene with protein product	"putative serine-threonine protein kinase"	604884	"NIMA (never in mitosis gene a)-related kinase 6"			10702691	Standard	NM_001145001		Approved	SID6-1512	uc004boh.3	Q9HC98	OTTHUMG00000020650	ENST00000320246.5:c.123G>A	chr9.hg19:g.127074820G>A		92.0	0.0		43.0	10.0	NM_001166171	B7Z2D9|Q5TBG3|Q5TBG9|Q6FG86|Q6IAR3|Q96E83|Q9ULX2	Silent	SNP	ENST00000320246.5	hg19	CCDS6854.1																																																																																			.	.		0.612	NEK6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054016.1	NM_014397		A	127074820	G	A	127074820	2	1	15	1	0	0	0	0	0	0	0	1	10337	1074	38	1		1	NEK6	9	127074820	Silent	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	31277120	127074820	14138611	45	1345										
CACNA1B	774	hgsc.bcm.edu	37	chr9	141016411	141016411	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cagctcgggtggccgagcacGgcacagctaccaccaccctg	12	17	0	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr9:141016411G>A	ENST00000371372.1	+	47	7125	c.6980G>A	c.(6979-6981)cGg>cAg	p.R2327Q	CACNA1B_ENST00000371363.1_Missense_Mutation_p.R2325Q|CACNA1B_ENST00000371355.4_Missense_Mutation_p.R2328Q|CACNA1B_ENST00000371357.1_Missense_Mutation_p.R2326Q|CACNA1B_ENST00000277549.5_Missense_Mutation_p.R1521Q|CACNA1B_ENST00000277551.2_3'UTR	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	2327					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GGCCGAGCACGGCACAGCTAC	0.632																																					p.R2327Q		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G6980A						.						24	26	26					9																	141016411		2099	4214	6313	SO:0001583	missense	774	exon46			GAGCACGGCACAG	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.6980G>A	chr9.hg19:g.141016411G>A	ENSP00000360423:p.Arg2327Gln	42.0	0.0		19.0	10.0	NM_000718	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.504795	0.64410	.	.	ENSG00000148408	ENST00000371372;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.96913	-3.95;-4.17;-3.95;-3.94;-3.94	5.22	5.22	0.72569	.	0.575551	0.16297	N	0.220603	D	0.94076	0.8101	N	0.21373	0.66	0.49130	D	0.999753	D;D	0.63880	0.993;0.993	P;P	0.47470	0.548;0.548	D	0.93142	0.6542	10	0.30854	T	0.27	.	18.7817	0.91934	0.0:0.0:1.0:0.0	.	2326;2325	B1AQK7;B1AQK6	.;.	Q	2327;1521;2325;2326;2328	ENSP00000360423:R2327Q;ENSP00000277549:R1521Q;ENSP00000360414:R2325Q;ENSP00000360408:R2326Q;ENSP00000360406:R2328Q	ENSP00000277549:R1521Q	R	+	2	0	CACNA1B	140136232	1.000000	0.71417	0.993000	0.49108	0.827000	0.46813	2.754000	0.47532	2.443000	0.82685	0.561000	0.74099	CGG	.	.		0.632	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		A	141016411	G	A	141016411	3	1	15	1	0	0	0	0	1	0	0	0	2541	1116	39	1	7162	1	CACNA1B	9	141016411	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	13941591	141016411	197020	46	1346										
CUL2	8453	hgsc.bcm.edu	37	chr10	35320492	35320492	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tgagcctgtcttccacttcaTtctctgtcatccctttcgct	5	15	4	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr10:35320492T>C	ENST00000374748.1	-	14	1539	c.1226A>G	c.(1225-1227)aAt>aGt	p.N409S	CUL2_ENST00000602371.1_Missense_Mutation_p.N352S|CUL2_ENST00000374742.1_Missense_Mutation_p.N409S|CUL2_ENST00000374749.3_Missense_Mutation_p.N409S|CUL2_ENST00000374751.3_Missense_Mutation_p.N409S|CUL2_ENST00000537177.1_Missense_Mutation_p.N428S|CUL2_ENST00000374746.1_Missense_Mutation_p.N409S			Q13617	CUL2_HUMAN	cullin 2	409					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						TTCCACTTCATTCTCTGTCAT	0.383																																					p.N428S		Atlas-SNP	.											.	CUL2	63	.	0			c.A1283G						.						187	157	167					10																	35320492		2203	4300	6503	SO:0001583	missense	8453	exon13			ACTTCATTCTCTG	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.1226A>G	chr10.hg19:g.35320492T>C	ENSP00000363880:p.Asn409Ser	103.0	0.0		107.0	33.0	NM_001198778	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Missense_Mutation	SNP	ENST00000374748.1	hg19	CCDS7179.1	.	.	.	.	.	.	.	.	.	.	T	7.220	0.597130	0.13875	.	.	ENSG00000108094	ENST00000374751;ENST00000374748;ENST00000374746;ENST00000374749;ENST00000374754;ENST00000374742;ENST00000537177	T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	5.87	4.71	0.59529	Cullin, N-terminal (1);Cullin homology (2);	0.040038	0.85682	N	0.000000	T	0.37517	0.1006	N	0.01188	-0.97	0.58432	D	0.999999	B;B;B	0.12013	0.005;0.004;0.005	B;B;B	0.15052	0.009;0.007;0.012	T	0.41963	-0.9479	10	0.02654	T	1	-17.8391	12.0765	0.53647	0.0:0.068:0.0:0.932	.	409;428;409	Q5T2B5;G3V1S2;Q13617	.;.;CUL2_HUMAN	S	409;409;409;409;352;409;428	ENSP00000363883:N409S;ENSP00000363880:N409S;ENSP00000363878:N409S;ENSP00000363881:N409S;ENSP00000363874:N409S;ENSP00000444856:N428S	ENSP00000363874:N409S	N	-	2	0	CUL2	35360498	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.267000	0.72546	1.004000	0.39156	0.482000	0.46254	AAT	.	.		0.383	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591		C	35320492	T	C	35320492	3	2	15	1	0	0	0	0	1	0	0	0	4057	1493	52	2	1047	2	CUL2	10	35320492	Missense_Mutation	SNP	T	TCGA-2Y-A9H5-01A-11D-A382-10		35320492	100214255	47	1347										
NODAL	4838	hgsc.bcm.edu	37	chr10	72195410	72195410	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ccagcactctccagctacccTggacatctgcttctccaggg	8	17	3	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr10:72195410T>C	ENST00000287139.3	-	2	522	c.523A>G	c.(523-525)Agg>Ggg	p.R175G	AC022532.1_ENST00000420338.2_Silent_p.P119P	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN	nodal growth differentiation factor	175					axial mesodermal cell fate specification (GO:0048327)|brain development (GO:0007420)|cell migration involved in gastrulation (GO:0042074)|digestive tract morphogenesis (GO:0048546)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic pattern specification (GO:0009880)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endodermal cell differentiation (GO:0035987)|epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification (GO:0060802)|floor plate morphogenesis (GO:0033505)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|heart looping (GO:0001947)|inhibition of neuroepithelial cell differentiation (GO:0002085)|left lung morphogenesis (GO:0060460)|liver development (GO:0001889)|maternal placenta development (GO:0001893)|maternal process involved in parturition (GO:0060137)|mesendoderm development (GO:0048382)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of chorionic trophoblast cell proliferation (GO:1901383)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of trophoblast cell migration (GO:1901164)|neural fold formation (GO:0001842)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|placenta development (GO:0001890)|polarity specification of proximal/distal axis (GO:0010085)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gastrulation (GO:0010470)|regulation of stem cell maintenance (GO:2000036)|SMAD protein signal transduction (GO:0060395)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway involved in primitive streak formation (GO:0090010)|trophectodermal cellular morphogenesis (GO:0001831)|vasculature development (GO:0001944)	extracellular space (GO:0005615)	morphogen activity (GO:0016015)|type I activin receptor binding (GO:0070698)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						CCAGCTACCCTGGACATCTGC	0.627																																					p.R175G		Atlas-SNP	.											.	NODAL	32	.	0			c.A523G						.						35	36	36					10																	72195410		2203	4300	6503	SO:0001583	missense	4838	exon2			CTACCCTGGACAT	BC033585	CCDS7304.1	10q22.1	2012-12-07	2012-12-07		ENSG00000156574	ENSG00000156574			7865	protein-coding gene	gene with protein product		601265	"nodal, mouse, homolog", "nodal homolog (mouse)"			9354794	Standard	NM_018055		Approved		uc001jrc.2	Q96S42	OTTHUMG00000018408	ENST00000287139.3:c.523A>G	chr10.hg19:g.72195410T>C	ENSP00000287139:p.Arg175Gly	140.0	0.0		133.0	39.0	NM_018055	Q2M3A5|Q8N4V3	Missense_Mutation	SNP	ENST00000287139.3	hg19	CCDS7304.1	.	.	.	.	.	.	.	.	.	.	T	4.847	0.157546	0.09236	.	.	ENSG00000156574	ENST00000287139;ENST00000414871	D;D	0.84589	-1.87;-1.86	5.99	3.66	0.41972	.	0.534934	0.21679	N	0.070760	T	0.67581	0.2908	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.53143	-0.8480	10	0.21540	T	0.41	.	8.4465	0.32845	0.0:0.2077:0.0:0.7923	.	175	Q96S42	NODAL_HUMAN	G	175;120	ENSP00000287139:R175G;ENSP00000394468:R120G	ENSP00000287139:R175G	R	-	1	2	NODAL	71865416	0.000000	0.05858	0.816000	0.32577	0.180000	0.23129	-0.410000	0.07151	1.065000	0.40693	0.533000	0.62120	AGG	.	.		0.627	NODAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048511.1	NM_018055		C	72195410	T	C	72195410	3	2	15	1	0	0	0	0	1	0	0	0	10527	1579	55	2	528	2	NODAL	10	72195410	Missense_Mutation	SNP	T	TCGA-2Y-A9H5-01A-11D-A382-10	36874918	72195410	63339337	48	1348										
NKX2-3	159296	hgsc.bcm.edu	37	chr10	101295220	101295220	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gccgccgccgccgccgccgcCgccgccgcagcagcggcggc	16	23	0	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr10:101295220C>A	ENST00000344586.7	+	2	1036	c.837C>A	c.(835-837)gcC>gcA	p.A279A		NM_145285.2	NP_660328.2	Q8TAU0	NKX23_HUMAN	NK2 homeobox 3	279	Poly-Ala.				CD4-positive, alpha-beta T cell differentiation (GO:0043367)|gland morphogenesis (GO:0022612)|leukocyte homeostasis (GO:0001776)|leukocyte migration (GO:0050900)|lymph node development (GO:0048535)|macrophage differentiation (GO:0030225)|odontogenesis of dentin-containing tooth (GO:0042475)|Peyer's patch development (GO:0048541)|plasma cell differentiation (GO:0002317)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic digestive tract morphogenesis (GO:0048621)|regulation of cell proliferation (GO:0042127)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)|triglyceride metabolic process (GO:0006641)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.45e-08)		ccgccgccgccgccgccgcAG	0.781																																					p.A279A	Pancreas(173;2021 2035 19403 19989 27291)	Atlas-SNP	.											.	NKX2-3	11	.	0			c.C837A						.						1	1	1					10																	101295220		45	145	190	SO:0001819	synonymous_variant	159296	exon2			CGCCGCCGCCGCC		CCDS41558.1	10q24.2	2013-09-20	2011-06-01	2002-10-04	ENSG00000119919	ENSG00000119919		"Homeoboxes / ANTP class : NKL subclass"	7836	protein-coding gene	gene with protein product		606727	"NK-2 (Drosophila) homolog C", "NK2 transcription factor related, locus 3 (Drosophila)"	NKX2C		1346742, 9142493	Standard	NM_145285		Approved	NKX2.3, CSX3, NKX4-3	uc009xwj.3	Q8TAU0	OTTHUMG00000018887	ENST00000344586.7:c.837C>A	chr10.hg19:g.101295220C>A		32.0	0.0		34.0	5.0	NM_145285	B4DUZ4|Q9NYS6	Silent	SNP	ENST00000344586.7	hg19	CCDS41558.1																																																																																			.	.		0.781	NKX2-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049808.2			A	101295220	C	A	101295220	2	1	15	1	0	0	0	0	0	0	0	1	10460	639	23	1		1	NKX2-3	10	101295220	Silent	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	29099810	101295220	34239527	49	1349										
OR51F2	119694	hgsc.bcm.edu	37	chr11	4842843	4842843	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cataagcctatgtactatttCctctctatgctttcagccac	4	13	2	0	rs557130556		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr11:4842843C>G	ENST00000322110.5	+	1	293	c.228C>G	c.(226-228)ttC>ttG	p.F76L	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004753.1	NP_001004753.1	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F, member 2	76						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGTACTATTTCCTCTCTATGC	0.458																																					p.F76L		Atlas-SNP	.											.	OR51F2	72	.	0			c.C228G						.						207	200	203					11																	4842843		2201	4298	6499	SO:0001583	missense	119694	exon1			CTATTTCCTCTCT	BK004281	CCDS31361.1	11p15.4	2012-08-09			ENSG00000176925	ENSG00000176925		"GPCR / Class A : Olfactory receptors"	15197	protein-coding gene	gene with protein product							Standard	NM_001004753		Approved		uc010qyn.2	Q8NH61	OTTHUMG00000066508	ENST00000322110.5:c.228C>G	chr11.hg19:g.4842843C>G	ENSP00000323952:p.Phe76Leu	58.0	0.0		129.0	41.0	NM_001004753	Q6IFI1	Missense_Mutation	SNP	ENST00000322110.5	hg19	CCDS31361.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.964784	0.34659	.	.	ENSG00000176925	ENST00000322110	T	0.13778	2.56	4.43	-0.248	0.13015	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	U	0.000640	T	0.12944	0.0314	M	0.64997	1.995	0.29237	N	0.872899	B	0.29115	0.233	B	0.31946	0.138	T	0.10314	-1.0635	10	0.66056	D	0.02	.	4.8058	0.13319	0.0:0.3468:0.1609:0.4923	.	76	Q8NH61	O51F2_HUMAN	L	76	ENSP00000323952:F76L	ENSP00000323952:F76L	F	+	3	2	OR51F2	4799419	0.228000	0.23718	0.999000	0.59377	0.695000	0.40330	-0.421000	0.07053	0.158000	0.19367	0.561000	0.74099	TTC	.	.		0.458	OR51F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142181.1	NM_001004753		G	4842843	C	G	4842843	3	3	15	1	0	0	0	0	1	0	0	0	11106	854	30	4	230	4	OR51F2	11	4842843	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10		4842843	130163673	50	1350										
LDHC	3948	hgsc.bcm.edu	37	chr11	18467772	18467772	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tgtagtgcctatgaaattatCaagctgaaggggtatacctc	10	7	1	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr11:18467772C>T	ENST00000541669.1	+	7	837	c.726C>T	c.(724-726)atC>atT	p.I242I	LDHC_ENST00000536880.1_Silent_p.I228I|LDHC_ENST00000544105.1_Intron|LDHC_ENST00000535809.1_Intron|LDHC_ENST00000537486.1_Intron|LDHC_ENST00000280704.4_Silent_p.I242I|LDHC_ENST00000546146.1_Intron			P07864	LDHC_HUMAN	lactate dehydrogenase C	242					ATP biosynthetic process (GO:0006754)|cellular carbohydrate metabolic process (GO:0044262)|lactate biosynthetic process from pyruvate (GO:0019244)|lactate oxidation (GO:0019516)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|motile cilium (GO:0031514)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ATGAAATTATCAAGCTGAAGG	0.368																																					p.I242I		Atlas-SNP	.											.	LDHC	37	.	0			c.C726T						.						159	158	158					11																	18467772		2199	4293	6492	SO:0001819	synonymous_variant	3948	exon7			AATTATCAAGCTG	AY286300	CCDS7840.1	11p15.1	2012-10-02			ENSG00000166796	ENSG00000166796	1.1.1.27		6544	protein-coding gene	gene with protein product	"cancer/testis antigen 32"	150150					Standard	NM_002301		Approved	CT32	uc001mom.4	P07864	OTTHUMG00000167722	ENST00000541669.1:c.726C>T	chr11.hg19:g.18467772C>T		103.0	0.0		92.0	35.0	NM_002301	D3DQY4|Q6GSG8|Q7Z7J4	Silent	SNP	ENST00000541669.1	hg19	CCDS7840.1																																																																																			.	.		0.368	LDHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395892.1	NM_017448		T	18467772	C	T	18467772	2	4	15	1	0	0	0	0	0	0	0	1	8711	816	29	3		3	LDHC	11	18467772	Silent	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	13624929	18467772	116538744	51	1351										
PAMR1	25891	hgsc.bcm.edu	37	chr11	35456179	35456179	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	caggtcagtaacacagtgggCagccaccaccacagtgcgct	11	14	1	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr11:35456179C>T	ENST00000378880.2	-	10	1952	c.1507G>A	c.(1507-1509)Gcc>Acc	p.A503T	PAMR1_ENST00000378878.3_Missense_Mutation_p.A392T|PAMR1_ENST00000532848.1_Missense_Mutation_p.A463T|PAMR1_ENST00000278360.3_Missense_Mutation_p.A520T	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	503	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						ACACAGTGGGCAGCCACCACC	0.572																																					p.A520T		Atlas-SNP	.											.	PAMR1	85	.	0			c.G1558A						.						100	87	91					11																	35456179		2202	4298	6500	SO:0001583	missense	25891	exon11			AGTGGGCAGCCAC		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"regeneration-associated muscle protease"					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.1507G>A	chr11.hg19:g.35456179C>T	ENSP00000368158:p.Ala503Thr	96.0	0.0		119.0	45.0	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	hg19	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	C	35	5.534571	0.96460	.	.	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605	D;D;D;D;D	0.96940	-4.18;-4.18;-4.18;-4.18;-4.18	5.36	5.36	0.76844	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.98378	0.9461	M	0.87900	2.915	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.998	D	0.99349	1.0914	10	0.87932	D	0	.	19.0909	0.93227	0.0:1.0:0.0:0.0	.	392;503;520	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	T	520;503;392;463;480	ENSP00000278360:A520T;ENSP00000368158:A503T;ENSP00000368156:A392T;ENSP00000433868:A463T;ENSP00000432591:A480T	ENSP00000278360:A520T	A	-	1	0	PAMR1	35412755	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.818000	0.86416	2.526000	0.85167	0.555000	0.69702	GCC	.	.		0.572	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430		T	35456179	C	T	35456179	3	4	15	1	0	0	0	0	1	0	0	0	11422	710	25	3	663	3	PAMR1	11	35456179	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	16988407	35456179	99550337	52	1352										
KCNA1	3736	hgsc.bcm.edu	37	chr12	5021467	5021467	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	aatcttcaagctctcccgccActctaagggcctccagatcc	6	17	4	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr12:5021467A>T	ENST00000382545.3	+	2	2030	c.923A>T	c.(922-924)cAc>cTc	p.H308L	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	308					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	CTCTCCCGCCACTCTAAGGGC	0.547																																					p.H308L		Atlas-SNP	.											.	KCNA1	112	.	0			c.A923T						.						65	72	70					12																	5021467		2203	4300	6503	SO:0001583	missense	3736	exon2			CCCGCCACTCTAA	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.923A>T	chr12.hg19:g.5021467A>T	ENSP00000371985:p.His308Leu	85.0	0.0		81.0	15.0	NM_000217	A6NM83|Q3MIQ9	Missense_Mutation	SNP	ENST00000382545.3	hg19	CCDS8535.1	.	.	.	.	.	.	.	.	.	.	A	19.49	3.837405	0.71373	.	.	ENSG00000111262	ENST00000382545;ENST00000228858	D	0.97404	-4.37	5.08	5.08	0.68730	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98391	0.9465	M	0.84433	2.695	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.99421	1.0933	10	0.87932	D	0	.	14.4841	0.67603	1.0:0.0:0.0:0.0	.	308	Q09470	KCNA1_HUMAN	L	308	ENSP00000371985:H308L	ENSP00000228858:H308L	H	+	2	0	KCNA1	4891728	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.073000	0.93992	2.254000	0.74563	0.533000	0.62120	CAC	.	.		0.547	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217		T	5021467	A	T	5021467	3	4	15	1	0	0	0	0	1	0	0	0	8010	159	6	4	925	4	KCNA1	12	5021467	Missense_Mutation	SNP	A	TCGA-2Y-A9H5-01A-11D-A382-10		5021467	128830428	53	1353										
CLEC7A	64581	hgsc.bcm.edu	37	chr12	10279240	10279240	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tgtgtgggttgactgtggttCtctttatttcttgatagaaa	11	4	2	3			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr12:10279240C>A	ENST00000304084.8	-	3	424	c.270G>T	c.(268-270)gaG>gaT	p.E90D	CLEC7A_ENST00000533022.1_Missense_Mutation_p.E90D|CLEC7A_ENST00000298523.5_Intron|CLEC7A_ENST00000396484.2_Intron|CLEC7A_ENST00000353231.5_Intron	NM_197947.2	NP_922938.1	Q9BXN2	CLC7A_HUMAN	C-type lectin domain family 7, member A	90					carbohydrate mediated signaling (GO:0009756)|cell recognition (GO:0008037)|defense response to protozoan (GO:0042832)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|MHC protein binding (GO:0042287)|signaling pattern recognition receptor activity (GO:0008329)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	7						GACTGTGGTTCTCTTTATTTC	0.398																																					p.E90D		Atlas-SNP	.											.	CLEC7A	55	.	0			c.G270T						.						177	161	166					12																	10279240		1864	4104	5968	SO:0001583	missense	64581	exon3			GTGGTTCTCTTTA	AY009090	CCDS8613.1, CCDS8614.1, CCDS8617.1, CCDS41753.1, CCDS41754.1, CCDS53744.1	12p13.2-p12.3	2014-09-17		2005-02-09	ENSG00000172243	ENSG00000172243		"C-type lectin domain containing"	14558	protein-coding gene	gene with protein product		606264	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 12"	CLECSF12			Standard	XM_005253468		Approved	dectin-1, hDectin-1	uc001qxg.2	Q9BXN2	OTTHUMG00000133597	ENST00000304084.8:c.270G>T	chr12.hg19:g.10279240C>A	ENSP00000302569:p.Glu90Asp	110.0	0.0		105.0	30.0	NM_197947	B2R861|B7Z494|B7Z5A9|B7Z5B9|Q6IPS7|Q96D32|Q96DR9|Q96LD3|Q96PA4|Q96PA5|Q96PA6|Q96PA7|Q96PA8|Q9H1K3	Missense_Mutation	SNP	ENST00000304084.8	hg19	CCDS41753.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.217541	0.58560	.	.	ENSG00000172243	ENST00000304084;ENST00000533022	T;T	0.08370	3.1;3.1	3.96	2.11	0.27256	C-type lectin-like (1);	0.575853	0.15772	N	0.245370	T	0.07683	0.0193	L	0.59436	1.845	0.52501	D	0.999959	B;B;B	0.18461	0.028;0.028;0.006	B;B;B	0.18561	0.022;0.013;0.006	T	0.14783	-1.0460	10	0.12766	T	0.61	.	5.354	0.16051	0.0:0.6804:0.2079:0.1117	.	90;90;90	Q9BXN2-4;Q9BXN2-3;Q9BXN2	.;.;CLC7A_HUMAN	D	90	ENSP00000302569:E90D;ENSP00000431461:E90D	ENSP00000302569:E90D	E	-	3	2	CLEC7A	10170507	0.040000	0.19996	0.717000	0.30585	0.988000	0.76386	0.158000	0.16422	0.614000	0.30107	0.655000	0.94253	GAG	.	.		0.398	CLEC7A-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390772.1	NM_197954		A	10279240	C	A	10279240	3	1	15	1	0	0	0	0	1	0	0	0	3523	912	32	3	489	3	CLEC7A	12	10279240	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	5257773	10279240	123572655	54	1354										
DERA	51071	hgsc.bcm.edu	37	chr12	16109926	16109926	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cggcagttctgaggcgtgcgGaacaaatccaggctcgcaga	14	11	1	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr12:16109926G>A	ENST00000428559.2	+	2	300	c.88G>A	c.(88-90)Gaa>Aaa	p.E30K	DERA_ENST00000532964.1_Missense_Mutation_p.E30K|DERA_ENST00000526530.1_5'UTR	NM_015954.2	NP_057038.2	Q9Y315	DEOC_HUMAN	deoxyribose-phosphate aldolase (putative)	30					deoxyribonucleoside catabolic process (GO:0046121)|deoxyribonucleotide catabolic process (GO:0009264)|deoxyribose phosphate catabolic process (GO:0046386)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	deoxyribose-phosphate aldolase activity (GO:0004139)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		Hepatocellular(102;0.121)				GAGGCGTGCGGAACAAATCCA	0.448																																					p.E30K		Atlas-SNP	.											.	DERA	20	.	0			c.G88A						.						67	69	68					12																	16109926		1894	4101	5995	SO:0001583	missense	51071	exon2			CGTGCGGAACAAA	AF132960	CCDS44838.1, CCDS73451.1	12p12.3	2010-06-24	2010-06-24		ENSG00000023697	ENSG00000023697	4.1.2.4		24269	protein-coding gene	gene with protein product			"2-deoxyribose-5-phosphate aldolase homolog (C. elegans)"			12546782	Standard	XM_006719083		Approved	CGI-26, DEOC	uc001rde.3	Q9Y315	OTTHUMG00000165537	ENST00000428559.2:c.88G>A	chr12.hg19:g.16109926G>A	ENSP00000416583:p.Glu30Lys	94.0	0.0		134.0	48.0	NM_015954	Q53HN9|Q6PHW2	Missense_Mutation	SNP	ENST00000428559.2	hg19	CCDS44838.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.301793	0.23736	.	.	ENSG00000023697	ENST00000428559;ENST00000531803;ENST00000532964	.	.	.	5.14	-0.44	0.12261	.	0.537012	0.20780	N	0.085801	T	0.36138	0.0956	L	0.32530	0.975	0.23661	N	0.997176	B	0.24258	0.1	B	0.15870	0.014	T	0.12016	-1.0564	9	0.25106	T	0.35	-6.6666	19.0954	0.93248	0.0:0.6579:0.3421:0.0	.	30	Q9Y315	DEOC_HUMAN	K	30;51;30	.	ENSP00000416583:E30K	E	+	1	0	DERA	16001193	0.947000	0.32204	0.003000	0.11579	0.993000	0.82548	1.626000	0.37039	-0.279000	0.09167	0.655000	0.94253	GAA	.	.		0.448	DERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384731.1	NM_015954		A	16109926	G	A	16109926	3	1	15	1	0	0	0	0	1	0	0	0	4447	1175	41	3	94	3	DERA	12	16109926	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	5830686	16109926	117741969	55	1355										
RACGAP1	29127	hgsc.bcm.edu	37	chr12	50386074	50386074	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	acattgtcactgggtctggaTtgggcacagcatgggccact	13	10	2	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr12:50386074T>C	ENST00000548961.1	-	1	67	c.62A>G	c.(61-63)aAt>aGt	p.N21S	RACGAP1_ENST00000454520.2_Missense_Mutation_p.N511S|RACGAP1_ENST00000434422.1_Missense_Mutation_p.N511S|RACGAP1_ENST00000547905.1_Missense_Mutation_p.N511S|RACGAP1_ENST00000427314.2_Missense_Mutation_p.N511S|RACGAP1_ENST00000312377.5_Missense_Mutation_p.N511S|RACGAP1_ENST00000551016.1_Missense_Mutation_p.N511S					Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						TGGGTCTGGATTGGGCACAGC	0.458																																					p.N511S		Atlas-SNP	.											.	RACGAP1	36	.	0			c.A1532G						.						135	123	127					12																	50386074		2203	4300	6503	SO:0001583	missense	29127	exon16			TCTGGATTGGGCA		CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000548961.1:c.62A>G	chr12.hg19:g.50386074T>C	ENSP00000446889:p.Asn21Ser	65.0	0.0		100.0	32.0	NM_013277		Missense_Mutation	SNP	ENST00000548961.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.56	3.649766	0.67358	.	.	ENSG00000161800	ENST00000548961;ENST00000427314;ENST00000312377;ENST00000434422;ENST00000454520;ENST00000551016;ENST00000547905;ENST00000549342	T;T;T;T;T;T;T	0.25749	1.78;1.78;1.78;1.78;1.78;1.78;3.0	6.06	6.06	0.98353	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.164261	0.64402	D	0.000003	T	0.26195	0.0639	L	0.54323	1.7	0.80722	D	1	B	0.28378	0.209	B	0.22601	0.04	T	0.03597	-1.1021	10	0.21014	T	0.42	-23.5346	16.6127	0.84892	0.0:0.0:0.0:1.0	.	511	Q9H0H5	RGAP1_HUMAN	S	21;511;511;511;511;511;511;247	ENSP00000404190:N511S;ENSP00000309871:N511S;ENSP00000413241:N511S;ENSP00000404808:N511S;ENSP00000449374:N511S;ENSP00000449370:N511S;ENSP00000449565:N247S	ENSP00000309871:N511S	N	-	2	0	RACGAP1	48672341	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.015000	0.88690	2.322000	0.78497	0.528000	0.53228	AAT	.	.		0.458	RACGAP1-017	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000406031.2	NM_013277		C	50386074	T	C	50386074	3	2	15	1	0	0	0	0	1	0	0	0	12992	1493	52	2	382	2	RACGAP1	12	50386074	Missense_Mutation	SNP	T	TCGA-2Y-A9H5-01A-11D-A382-10	34276148	50386074	83465821	56	1356										
LRP1	4035	hgsc.bcm.edu	37	chr12	57605033	57605033	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gctcccgacaatgccgctgcActgcctactttgagggatcg	11	14	0	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr12:57605033A>T	ENST00000243077.3	+	84	13457	c.12991A>T	c.(12991-12993)Act>Tct	p.T4331S		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4331	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	ATGCCGCTGCACTGCCTACTT	0.582																																					p.T4331S		Atlas-SNP	.											.	LRP1	428	.	0			c.A12991T						.						101	81	88					12																	57605033		2203	4300	6503	SO:0001583	missense	4035	exon84			CGCTGCACTGCCT	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.12991A>T	chr12.hg19:g.57605033A>T	ENSP00000243077:p.Thr4331Ser	76.0	0.0		81.0	26.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	A	8.923	0.961476	0.18583	.	.	ENSG00000123384	ENST00000243077	T	0.09723	2.95	4.39	1.92	0.25849	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.568939	0.15146	N	0.278009	T	0.04363	0.0120	N	0.04508	-0.205	0.45852	D	0.998713	B	0.02656	0.0	B	0.01281	0.0	T	0.40421	-0.9564	10	0.30854	T	0.27	.	5.5265	0.16960	0.548:0.1542:0.0:0.2978	.	4331	Q07954	LRP1_HUMAN	S	4331	ENSP00000243077:T4331S	ENSP00000243077:T4331S	T	+	1	0	LRP1	55891300	0.051000	0.20477	0.965000	0.40720	0.088000	0.18126	1.288000	0.33296	0.209000	0.20645	-0.695000	0.03696	ACT	.	.		0.582	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57605033	A	T	57605033	3	4	15	1	0	0	0	0	1	0	0	0	8960	159	6	4	13325	4	LRP1	12	57605033	Missense_Mutation	SNP	A	TCGA-2Y-A9H5-01A-11D-A382-10	7218959	57605033	76246862	57	1357										
VPS37B	79720	hgsc.bcm.edu	37	chr12	123380577	123380585	+	In_Frame_Del	DEL	GGCGAACCG	GGCGAACCG	-													0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	agctgcaccagcgacagcccGgcgaaccgggcttcgctccc					rs574348056		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	GGCGAACCG	GGCGAACCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr12:123380577_123380585delGGCGAACCG	ENST00000267202.2	-	1	406_414	c.25_33delCGGTTCGCC	c.(25-33)cggttcgccdel	p.RFA9del		NM_024667.2	NP_078943.1	Q9H9H4	VP37B_HUMAN	vacuolar protein sorting 37 homolog B (S. cerevisiae)	9					endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)				breast(1)|central_nervous_system(1)|large_intestine(1)|skin(1)|urinary_tract(1)	5	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.08e-05)|Epithelial(86;0.000197)|BRCA - Breast invasive adenocarcinoma(302;0.205)		GCGACAGCCCGGCGAACCGGGCTTCGCTC	0.718																																					p.9_12del		Atlas-Indel,Pindel	.											.	VPS37B	26	.	0			c.26_34del						.																																			SO:0001651	inframe_deletion	79720	exon1			.	AK022812	CCDS9239.1	12q24.31	2008-02-05	2006-04-04		ENSG00000139722	ENSG00000139722			25754	protein-coding gene	gene with protein product		610037	"vacuolar protein sorting 37B (yeast)"			15218037	Standard	NM_024667		Approved	FLJ12750	uc001udl.3	Q9H9H4	OTTHUMG00000168767	ENST00000267202.2:c.25_33delCGGTTCGCC	chr12.hg19:g.123380577_123380585delGGCGAACCG	ENSP00000267202:p.Arg9_Ala11del	67.0	0.0		60.0	16.0	NM_024667		In_Frame_Del	DEL	ENST00000267202.2	hg19	CCDS9239.1																																																																																			.	.		0.718	VPS37B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400946.1	NM_024667		-	123380585	GGCGAACCG	-	123380577	7	5	15	1	0	1	0	1	0	0	0	0	17221	1103	39	0	840	0	VPS37B	12	123380577	In_Frame_Del	DEL	GGCGAACCG	TCGA-2Y-A9H5-01A-11D-A382-10	65775544	123380577	10471318	58	1358										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130184653	130184653	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cacggtgtagtagagctccaCgggggtcccctccggctggt	15	13	0	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr12:130184653C>T	ENST00000422113.2	-	2	996	c.670G>A	c.(670-672)Gtg>Atg	p.V224M	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	224					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.V224M(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TAGAGCTCCACGGGGGTCCCC	0.667																																					p.V224M		Atlas-SNP	.											TMEM132D,NS,carcinoma,0,1	TMEM132D	299	.	1	Substitution - Missense(1)	breast(1)	c.G670A						.						50	51	51					12																	130184653		2203	4300	6503	SO:0001583	missense	121256	exon2			GCTCCACGGGGGT	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.670G>A	chr12.hg19:g.130184653C>T	ENSP00000408581:p.Val224Met	73.0	0.0		89.0	28.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.693085	0.48202	.	.	ENSG00000151952	ENST00000422113	T	0.15017	2.46	5.35	5.35	0.76521	.	0.000000	0.56097	D	0.000021	T	0.39384	0.1076	L	0.55103	1.725	0.50171	D	0.999854	D	0.89917	1.0	D	0.91635	0.999	T	0.03315	-1.1049	9	.	.	.	-32.7882	19.0705	0.93134	0.0:1.0:0.0:0.0	.	224	Q14C87	T132D_HUMAN	M	224	ENSP00000408581:V224M	.	V	-	1	0	TMEM132D	128750606	1.000000	0.71417	0.946000	0.38457	0.055000	0.15305	7.590000	0.82653	2.482000	0.83794	0.650000	0.86243	GTG	.	.		0.667	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	130184653	C	T	130184653	3	4	15	1	0	0	0	0	1	0	0	0	16062	536	19	1	2661	1	TMEM132D	12	130184653	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	6804076	130184653	3667242	59	1359										
C13orf23	80209	hgsc.bcm.edu	37	chr13	39587824	39587824	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tctgtggggtagggatggctGatggggcatagcacttgtta	17	5	1	1	rs546645213		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr13:39587824G>A	ENST00000352251.3	-	11	2398	c.1565C>T	c.(1564-1566)tCa>tTa	p.S522L	PROSER1_ENST00000350125.3_Missense_Mutation_p.S500L|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	522	Ser-rich.																AGGGATGGCTGATGGGGCATA	0.547													G|||	1	0.000199681	0	0	5008	,	,		19675	0.001		0	False		,,,				2504	0				p.S522L		Atlas-SNP	.											.	.	.	.	0			c.C1565T						.						72	74	73					13																	39587824		2203	4300	6503	SO:0001583	missense	80209	exon11			ATGGCTGATGGGG	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.1565C>T	chr13.hg19:g.39587824G>A	ENSP00000332034:p.Ser522Leu	110.0	0.0		93.0	34.0	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	hg19	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	G	12.98	2.099943	0.37048	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.33654	1.41;1.4	4.85	3.98	0.46160	.	.	.	.	.	T	0.28300	0.0699	L	0.29908	0.895	0.09310	N	1	B;B	0.28933	0.228;0.228	B;B	0.30855	0.121;0.085	T	0.15150	-1.0447	8	.	.	.	-0.1145	12.7869	0.57512	0.0:0.3154:0.6846:0.0	.	500;522	A6NJ97;Q86XN7	.;PRSR1_HUMAN	L	522;500	ENSP00000332034:S522L;ENSP00000339123:S500L	.	S	-	2	0	PROSER1	38485824	0.991000	0.36638	0.001000	0.08648	0.028000	0.11728	8.085000	0.89518	0.992000	0.38840	0.561000	0.74099	TCA	.	.		0.547	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		A	39587824	G	A	39587824	3	1	15	1	0	0	0	0	1	0	0	0	1723	1294	45	3	1281	3	C13orf23	13	39587824	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10		39587824	75582054	60	1360										
LHFP	10186	hgsc.bcm.edu	37	chr13	39952662	39952662	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cagccagcaccaatcaacaaGcctgcaaagagataagacaa	7	12	1	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr13:39952662G>C	ENST00000379589.3	-	3	849	c.387C>G	c.(385-387)ggC>ggG	p.G129G		NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	129						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)		HMGA2/LHFP(2)	breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		CAATCAACAAGCCTGCAAAGA	0.498			T	HMGA2	lipoma																																p.G129G		Atlas-SNP	.		Dom	yes		13	13q12	10186	lipoma HMGIC fusion partner		M	.	LHFP	31	.	0			c.C387G						.						60	57	58					13																	39952662		2203	4300	6503	SO:0001630	splice_region_variant	10186	exon3			CAACAAGCCTGCA	AF098807	CCDS9369.1	13q12	2008-07-18			ENSG00000183722	ENSG00000183722			6586	protein-coding gene	gene with protein product		606710				10329012	Standard	NM_005780		Approved	MGC22429	uc001uxf.3	Q9Y693	OTTHUMG00000016767	ENST00000379589.3:c.386-1C>G	chr13.hg19:g.39952662G>C		51.0	0.0		58.0	28.0	NM_005780	B2R7M2|Q53FC0|Q96SH5	Silent	SNP	ENST00000379589.3	hg19	CCDS9369.1																																																																																			.	.		0.498	LHFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044619.1	NM_005780	Silent	C	39952662	G	C	39952662	5	2	15	1	0	0	0	0	0	0	1	0	8772	985	34	4	223	4	LHFP	13	39952662	Splice_Site	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	364838	39952662	75217216	61	1361										
GZMB	3002	hgsc.bcm.edu	37	chr14	25102229	25102229	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	taagataagccatgtaggggCgggagtggggcttggcctca	17	7	1	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr14:25102229C>T	ENST00000216341.4	-	2	201	c.95G>A	c.(94-96)cGc>cAc	p.R32H	RP11-104E19.1_ENST00000555300.1_RNA|GZMB_ENST00000382542.1_Missense_Mutation_p.R66H|GZMB_ENST00000415355.3_Missense_Mutation_p.R20H|RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000382540.1_Missense_Mutation_p.R32H|GZMB_ENST00000526004.1_Missense_Mutation_p.R32H			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	32	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.			RP -> PR (in Ref. 12; AA sequence). {ECO:0000305}.	apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		CATGTAGGGGCGGGAGTGGGG	0.562																																					p.R32H		Atlas-SNP	.											.	GZMB	73	.	0			c.G95A						.						112	114	113					14																	25102229		2203	4300	6503	SO:0001583	missense	3002	exon2			TAGGGGCGGGAGT	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"fragmentin 2", "cytotoxic serine protease B", "cathepsin G-like 1", "T-cell serine protease 1-3E"	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.95G>A	chr14.hg19:g.25102229C>T	ENSP00000216341:p.Arg32His	63.0	0.0		82.0	32.0	NM_004131	Q8N1D2|Q9UCC1	Missense_Mutation	SNP	ENST00000216341.4	hg19	CCDS9633.1	.	.	.	.	.	.	.	.	.	.	c	13.49	2.252849	0.39797	.	.	ENSG00000100453	ENST00000415355;ENST00000216341;ENST00000382542;ENST00000382540;ENST00000526004	T;D;D;T;T	0.92752	0.31;-3.1;-3.1;1.58;-1.48	5.04	1.23	0.21249	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.33290	N	0.005070	D	0.82346	0.5017	N	0.13098	0.295	0.22911	N	0.998572	P;B	0.39535	0.677;0.371	B;B	0.39119	0.291;0.118	T	0.74630	-0.3601	10	0.49607	T	0.09	.	7.4777	0.27387	0.0:0.656:0.0:0.344	.	20;32	Q6XGZ4;P10144	.;GRAB_HUMAN	H	20;32;66;32;32	ENSP00000387385:R20H;ENSP00000216341:R32H;ENSP00000371982:R66H;ENSP00000371980:R32H;ENSP00000434213:R32H	ENSP00000216341:R32H	R	-	2	0	GZMB	24172069	0.208000	0.23494	0.159000	0.22649	0.976000	0.68499	0.541000	0.23207	0.123000	0.18342	-0.137000	0.14449	CGC	.	.		0.562	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131		T	25102229	C	T	25102229	3	4	15	1	0	0	0	0	1	0	0	0	6925	768	27	1	664	1	GZMB	14	25102229	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10		25102229	82247311	62	1362										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94046579	94046579	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ctattataaacaatgtcttcCaagccccctgggggggatcc	9	12	1	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr14:94046579C>A	ENST00000393151.2	+	19	2518	c.2518C>A	c.(2518-2520)Caa>Aaa	p.Q840K	UNC79_ENST00000256339.4_Missense_Mutation_p.Q663K|UNC79_ENST00000555664.1_Missense_Mutation_p.Q840K|UNC79_ENST00000553484.1_Missense_Mutation_p.Q840K			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	840					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.I654_H670del(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CAATGTCTTCCAAGCCCCCTG	0.433																																					p.Q663K		Atlas-SNP	.											.	UNC79	366	.	1	Deletion - In frame(1)	ovary(1)	c.C1987A						.						74	85	81					14																	94046579		2203	4300	6503	SO:0001583	missense	57578	exon19			GTCTTCCAAGCCC	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.2518C>A	chr14.hg19:g.94046579C>A	ENSP00000376858:p.Gln840Lys	103.0	0.0		117.0	6.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	C	12.95	2.091445	0.36952	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	5.01	4.1	0.47936	.	0.056983	0.64402	N	0.000001	T	0.28167	0.0695	L	0.29908	0.895	0.44227	D	0.997061	P	0.48911	0.917	D	0.63488	0.915	T	0.01791	-1.1273	10	0.48119	T	0.1	-5.4024	14.4764	0.67548	0.1483:0.8517:0.0:0.0	.	840	C9JQL1	.	K	663;840;840;840;840	ENSP00000256339:Q663K;ENSP00000450868:Q840K;ENSP00000451360:Q840K;ENSP00000376858:Q840K	ENSP00000256339:Q663K	Q	+	1	0	KIAA1409	93116332	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	1.067000	0.40740	0.561000	0.74099	CAA	.	.		0.433	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94046579	C	A	94046579	3	1	15	1	0	0	0	0	1	0	0	0	8239	595	21	3	2049	3	KIAA1409	14	94046579	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	68944350	94046579	13302961	63	1363										
CYFIP1	23191	hgsc.bcm.edu	37	chr15	22940832	22940832	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	catttcggagctggcgcgctAcagcaacagcgaggtgcgcc	14	13	0	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr15:22940832A>G	ENST00000313077.7	+	11	1222	c.1097A>G	c.(1096-1098)tAc>tGc	p.Y366C	CYFIP1_ENST00000560848.1_Missense_Mutation_p.Y366C	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		CTGGCGCGCTACAGCAACAGC	0.582																																					p.Y366C		Atlas-SNP	.											.	CYFIP1	159	.	0			c.A1097G						.						47	37	40					15																	22940832		2203	4300	6503	SO:0001583	missense	23191	exon11			CGCGCTACAGCAA	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"selective hybridizing clone", "cytoplasmic FMRP interacting protein 1"	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.1097A>G	chr15.hg19:g.22940832A>G	ENSP00000324549:p.Tyr366Cys	210.0	0.0		192.0	56.0	NM_014608		Missense_Mutation	SNP	ENST00000313077.7	hg19	CCDS10009.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.632944	0.87660	.	.	ENSG00000068793	ENST00000313077;ENST00000412127	T	0.18960	2.18	5.63	5.63	0.86233	.	0.000000	0.64402	D	0.000006	T	0.32496	0.0831	L	0.43152	1.355	0.80722	D	1	D;D	0.64830	0.994;0.991	P;P	0.54759	0.707;0.76	T	0.02075	-1.1218	10	0.52906	T	0.07	-27.4278	15.8446	0.78876	1.0:0.0:0.0:0.0	.	394;366	E7EQ04;Q7L576	.;CYFP1_HUMAN	C	366;394	ENSP00000324549:Y366C	ENSP00000324549:Y366C	Y	+	2	0	CYFIP1	20492273	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	9.104000	0.94239	2.152000	0.67230	0.482000	0.46254	TAC	.	.		0.582	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608		G	22940832	A	G	22940832	3	3	15	1	0	0	0	0	1	0	0	0	4139	391	14	2	1135	2	CYFIP1	15	22940832	Missense_Mutation	SNP	A	TCGA-2Y-A9H5-01A-11D-A382-10		22940832	79590560	64	1364										
FBN1	2200	hgsc.bcm.edu	37	chr15	48736756	48736756	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	accttcacacttctcattttGaagactgtatccaggtgggc	8	11	2	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr15:48736756G>A	ENST00000316623.5	-	49	6474	c.6019C>T	c.(6019-6021)Caa>Taa	p.Q2007*		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2007	EGF-like 34; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TTCTCATTTTGAAGACTGTAT	0.428																																					p.Q2007X		Atlas-SNP	.											.	FBN1	310	.	0			c.C6019T						.						150	137	141					15																	48736756		2198	4296	6494	SO:0001587	stop_gained	2200	exon49			CATTTTGAAGACT	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.6019C>T	chr15.hg19:g.48736756G>A	ENSP00000325527:p.Gln2007*	33.0	0.0		95.0	12.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Nonsense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	37	6.288066	0.97444	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	.	.	.	6.07	6.07	0.98685	.	0.208189	0.51477	D	0.000087	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	.	11.5352	0.50633	0.0:0.1341:0.7269:0.1389	.	.	.	.	X	2007;575;897	.	ENSP00000325527:Q2007X	Q	-	1	0	FBN1	46524048	0.999000	0.42202	0.965000	0.40720	0.907000	0.53573	2.874000	0.48483	2.885000	0.99019	0.655000	0.94253	CAA	.	.		0.428	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48736756	G	A	48736756	4	1	15	1	0	0	0	0	0	1	0	0	5710	1299	45	3	2668	3	FBN1	15	48736756	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	25795924	48736756	53794636	65	1365										
FANCI	55215	hgsc.bcm.edu	37	chr15	89826381	89826381	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	agctagccagcttgatgcccGaaaatctgcagttgctgggt	12	10	1	1	rs368127142		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr15:89826381G>A	ENST00000310775.7	+	17	1684	c.1598G>A	c.(1597-1599)cGa>cAa	p.R533Q	FANCI_ENST00000300027.8_Missense_Mutation_p.R533Q	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	533					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CTTGATGCCCGAAAATCTGCA	0.438								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R533Q		Atlas-SNP	.											.	FANCI	129	.	0			c.G1598A						.	G	GLN/ARG,GLN/ARG	0,4400		0,0,2200	133	128	130		1598,1598	6	1	15		130	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	FANCI	NM_001113378.1,NM_018193.2	43,43	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	533/1329,533/1269	89826381	1,12997	2200	4299	6499	SO:0001583	missense	55215	exon17	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ATGCCCGAAAATC	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.1598G>A	chr15.hg19:g.89826381G>A	ENSP00000310842:p.Arg533Gln	63.0	0.0		68.0	27.0	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	hg19	CCDS45346.1	.	.	.	.	.	.	.	.	.	.	G	36	5.670481	0.96754	0.0	1.16E-4	ENSG00000140525	ENST00000300027;ENST00000310775;ENST00000447611	D;D;D	0.94650	-3.48;-3.48;-3.48	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.97377	0.9142	M	0.78049	2.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96998	0.9727	10	0.59425	D	0.04	-11.9968	20.5666	0.99351	0.0:0.0:1.0:0.0	.	533;533;533	Q9NVI1;Q9NVI1-2;Q9NVI1-1	FANCI_HUMAN;.;.	Q	533	ENSP00000300027:R533Q;ENSP00000310842:R533Q;ENSP00000413249:R533Q	ENSP00000300027:R533Q	R	+	2	0	FANCI	87627385	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.609000	0.98334	2.854000	0.98071	0.655000	0.94253	CGA	.	.		0.438	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		A	89826381	G	A	89826381	3	1	15	1	0	0	0	0	1	0	0	0	5677	1058	37	1	1660	1	FANCI	15	89826381	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	41089625	89826381	12705011	66	1366										
CDH1	999	hgsc.bcm.edu	37	chr16	68867249	68867250	+	Frame_Shift_Ins	INS	-	-	T													0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cttatgattctctgctcgtgINStttgactatgaaggaagcgg							TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr16:68867249_68867250insT	ENST00000261769.5	+	16	2687_2688	c.2496_2497insT	c.(2497-2499)tttfs	p.F833fs	CDH1_ENST00000422392.2_Frame_Shift_Ins_p.F772fs|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	833	Required for binding alpha, beta and gamma catenins.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CTCTGCTCGTGTTTGACTATGA	0.49			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												p.V832fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	.	CDH1	535	.	0			c.2496_2497insT						.																																			SO:0001589	frameshift_variant	999	exon16	Familial Cancer Database	HDGC	.	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.2499dupT	chr16.hg19:g.68867252_68867252dupT	ENSP00000261769:p.Phe833fs	84.0	0.0		80.0	29.0	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Frame_Shift_Ins	INS	ENST00000261769.5	hg19	CCDS10869.1																																																																																			.	.		0.49	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		T	68867250	-	T	68867249	7	5	15	1	0	1	1	0	0	0	0	0	3097	1364	48	0	2558	0	CDH1	16	68867249	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H5-01A-11D-A382-10		68867249	21487504	67	1367										
ZNF18	7566	hgsc.bcm.edu	37	chr17	11881727	11881727	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ttctgggccatgggggctctTggctgccccttctgggaggt	16	11	3	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr17:11881727T>G	ENST00000322748.3	-	9	1801	c.1197A>C	c.(1195-1197)ccA>ccC	p.P399P	ZNF18_ENST00000580306.2_Silent_p.P399P|ZNF18_ENST00000454073.3_Silent_p.P398P|RP11-1096G20.5_ENST00000580270.1_RNA	NM_144680.2	NP_653281.2	P17022	ZNF18_HUMAN	zinc finger protein 18	399					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	14				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		TGGGGGCTCTTGGCTGCCCCT	0.512																																					p.P399P		Atlas-SNP	.											.	ZNF18	42	.	0			c.A1197C						.						58	64	62					17																	11881727		2203	4300	6503	SO:0001819	synonymous_variant	7566	exon9			GGCTCTTGGCTGC	X52342	CCDS32568.1	17p12	2013-01-09	2006-05-10		ENSG00000154957	ENSG00000154957		"Zinc fingers, C2H2-type", "-", "-", "-"	12969	protein-coding gene	gene with protein product		194524	"zinc finger protein 18 (KOX 11)"			15702252	Standard	XM_005256786		Approved	ZKSCAN6, KOX11, HDSG1, Zfp535, ZNF535, ZSCAN38	uc002gng.1	P17022	OTTHUMG00000178307	ENST00000322748.3:c.1197A>C	chr17.hg19:g.11881727T>G		61.0	0.0		100.0	27.0	NM_144680	Q5QHQ3|Q8IYC4|Q8NAH6	Silent	SNP	ENST00000322748.3	hg19	CCDS32568.1																																																																																			.	.		0.512	ZNF18-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441450.2	XM_085596		G	11881727	T	G	11881727	2	3	15	1	0	0	0	0	0	0	0	1	17762	1799	63	5		5	ZNF18	17	11881727	Silent	SNP	T	TCGA-2Y-A9H5-01A-11D-A382-10		11881727	69313483	68	1368										
GIT1	28964	hgsc.bcm.edu	37	chr17	27903137	27903137	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gtgcactgaatagatggcgtCgtcctctagctcctggggat	13	10	1	2	rs374985717		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr17:27903137C>T	ENST00000225394.3	-	15	1872	c.1624G>A	c.(1624-1626)Gac>Aac	p.D542N	GIT1_ENST00000581348.1_Missense_Mutation_p.D551N|GIT1_ENST00000579937.1_Missense_Mutation_p.D542N|RP11-68I3.2_ENST00000581474.1_RNA|GIT1_ENST00000394869.3_Missense_Mutation_p.D551N	NM_014030.3	NP_054749.2	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 1	542					regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				READ - Rectum adenocarcinoma(3;0.0419)|Colorectal(3;0.069)		TAGATGGCGTCGTCCTCTAGC	0.607																																					p.D551N	Colon(81;41 1719 20078 35068)	Atlas-SNP	.											.	GIT1	84	.	0			c.G1651A						.	C	ASN/ASP,ASN/ASP	0,4406		0,0,2203	98	96	97		1651,1624	4.2	1	17		97	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GIT1	NM_001085454.1,NM_014030.3	23,23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	551/771,542/762	27903137	1,13005	2203	4300	6503	SO:0001583	missense	28964	exon16			TGGCGTCGTCCTC	AF124490	CCDS11250.1, CCDS42290.1	17p11.2	2013-01-10	2008-09-05		ENSG00000108262	ENSG00000108262		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4272	protein-coding gene	gene with protein product		608434	"G protein-coupled receptor kinase interactor 1"			9826657, 10896954	Standard	NM_014030		Approved		uc002heg.2	Q9Y2X7	OTTHUMG00000132730	ENST00000225394.3:c.1624G>A	chr17.hg19:g.27903137C>T	ENSP00000225394:p.Asp542Asn	127.0	0.0		65.0	25.0	NM_001085454	B4DGU9|B4DSV3|Q86SS0|Q9BRJ4	Missense_Mutation	SNP	ENST00000225394.3	hg19	CCDS11250.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.142745	0.57044	0.0	1.16E-4	ENSG00000108262	ENST00000225394;ENST00000394869	T;T	0.69926	-0.38;-0.44	5.21	4.17	0.49024	.	0.344692	0.31484	N	0.007570	T	0.46190	0.1380	N	0.08118	0	0.33729	D	0.617985	D;P;B;D	0.61080	0.98;0.564;0.429;0.989	B;B;B;P	0.44394	0.368;0.026;0.012;0.448	T	0.54450	-0.8292	10	0.19147	T	0.46	.	13.2569	0.60083	0.1582:0.8418:0.0:0.0	.	555;551;551;542	Q59FC3;Q9Y2X7-3;B4DGU9;Q9Y2X7	.;.;.;GIT1_HUMAN	N	542;551	ENSP00000225394:D542N;ENSP00000378338:D551N	ENSP00000225394:D542N	D	-	1	0	GIT1	24927263	0.988000	0.35896	0.976000	0.42696	0.826000	0.46750	3.386000	0.52492	2.598000	0.87819	0.462000	0.41574	GAC	.	.		0.607	GIT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256073.1	NM_014030		T	27903137	C	T	27903137	3	4	15	1	0	0	0	0	1	0	0	0	6404	884	31	1	685	1	GIT1	17	27903137	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	16021410	27903137	53292073	69	1369										
HOXB4	3214	hgsc.bcm.edu	37	chr17	46655285	46655285	+	Frame_Shift_Del	DEL	G	G	-													0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gggctctttgcacgcggagtGggacgggctggggtgcaggg							TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr17:46655285delG	ENST00000332503.5	-	1	2188	c.397delC	c.(397-399)cacfs	p.H133fs	HOXB3_ENST00000460160.1_Intron|HOXB3_ENST00000476342.1_Intron|HOXB3_ENST00000472863.1_Intron|HOXB3_ENST00000489475.1_Intron|HOXB3_ENST00000498678.1_Intron|MIR10A_ENST00000385043.1_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000465120.3_Intron|HOXB3_ENST00000485909.2_5'Flank|HOXB3_ENST00000552000.2_Intron	NM_024015.4	NP_076920.1	P17483	HXB4_HUMAN	homeobox B4	133	Pro-rich (part of the transcriptional activation domain).				anterior/posterior pattern specification (GO:0009952)|bone marrow development (GO:0048539)|cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|hematopoietic stem cell differentiation (GO:0060218)|morphogenesis of an epithelial sheet (GO:0002011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell division (GO:0048103)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	9						CACGCGGAGTGGGACGGGCTG	0.736																																					p.H133fs		Atlas-Indel,Pindel	.											.	HOXB4	16	.	0			c.398delA						.						22	26	25					17																	46655285		2148	4183	6331	SO:0001589	frameshift_variant	3214	exon1			.		CCDS11529.1	17q21.32	2011-06-20	2005-12-22		ENSG00000182742	ENSG00000182742		"Homeoboxes / ANTP class : HOXL subclass"	5115	protein-coding gene	gene with protein product		142965	"homeo box B4"	HOX2, HOX2F		1973146, 1358459	Standard	NM_024015		Approved		uc002inp.3	P17483	OTTHUMG00000159920	ENST00000332503.5:c.397delC	chr17.hg19:g.46655285delG	ENSP00000328928:p.His133fs	84.0	0.0		71.0	22.0	NM_024015	Q9NTA0	Frame_Shift_Del	DEL	ENST00000332503.5	hg19	CCDS11529.1																																																																																			.	.		0.736	HOXB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358259.2			-	46655285	G	-	46655285	7	5	15	1	0	1	0	1	0	0	0	0	7312	1348	47	0	366	0	HOXB4	17	46655285	Frame_Shift_Del	DEL	G	TCGA-2Y-A9H5-01A-11D-A382-10	18752148	46655285	34539925	70	1370										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48703836	48703836	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	caaccccacctgggcacagaCccctctaaccttgggggcca	9	18	1	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr17:48703836C>T	ENST00000359106.5	+	38	6858	c.6858C>T	c.(6856-6858)gaC>gaT	p.D2286D	CACNA1G_ENST00000515165.1_Silent_p.D2193D|CACNA1G_ENST00000354983.4_Silent_p.D2252D|CACNA1G_ENST00000515765.1_Silent_p.D2230D|CACNA1G_ENST00000505165.1_Silent_p.D2114D|CACNA1G_ENST00000507510.2_Silent_p.D2241D|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000507336.1_Silent_p.D2275D|CACNA1G_ENST00000503485.1_Silent_p.D2159D|CACNA1G_ENST00000502264.1_Silent_p.D2215D|CACNA1G_ENST00000510115.1_Silent_p.D2207D|CACNA1G_ENST00000507896.1_Silent_p.D2103D|CACNA1G_ENST00000358244.5_Silent_p.D2080D|CACNA1G_ENST00000510366.1_Silent_p.D2141D|CACNA1G_ENST00000515411.1_Silent_p.D2223D|CACNA1G_ENST00000514717.1_Silent_p.D2136D|CACNA1G_ENST00000352832.5_Silent_p.D2159D|CACNA1G_ENST00000514181.1_Silent_p.D2168D|CACNA1G_ENST00000514079.1_Silent_p.D2200D|CACNA1G_ENST00000512389.1_Silent_p.D2182D|CACNA1G_ENST00000442258.2_Silent_p.D2152D|CACNA1G_ENST00000429973.2_Silent_p.D2175D|CACNA1G_ENST00000513964.1_Silent_p.D2148D|CACNA1G_ENST00000507609.1_Silent_p.D2186D|CACNA1G_ENST00000360761.4_Silent_p.D2170D|CACNA1G_ENST00000513689.2_Silent_p.D2196D	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2286					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	TGGGCACAGACCCCTCTAACC	0.657											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D2286D		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C6858T						.						10	14	13					17																	48703836		1888	4079	5967	SO:0001819	synonymous_variant	8913	exon38			CACAGACCCCTCT	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.6858C>T	chr17.hg19:g.48703836C>T		216.0	0.0	956	144.0	29.0	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	hg19	CCDS45730.1																																																																																			.	.		0.657	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		T	48703836	C	T	48703836	2	4	15	1	0	0	0	0	0	0	0	1	2546	506	18	3		3	CACNA1G	17	48703836	Silent	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	2048551	48703836	32491374	71	1371										
TBX2	6909	hgsc.bcm.edu	37	chr17	59482827	59482827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ggacgaggggcgcaaggaggCggccgagggcaaggagcagg	23	8	0	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr17:59482827C>T	ENST00000240328.3	+	6	1597	c.1316C>T	c.(1315-1317)gCg>gTg	p.A439V	RP11-332H18.4_ENST00000592009.1_RNA	NM_005994.3	NP_005985.3	Q13207	TBX2_HUMAN	T-box 2	439					aorta morphogenesis (GO:0035909)|atrioventricular canal development (GO:0036302)|cardiac muscle tissue development (GO:0048738)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|developmental growth involved in morphogenesis (GO:0060560)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|endocardial cushion morphogenesis (GO:0003203)|mammary placode formation (GO:0060596)|muscle cell fate determination (GO:0007521)|negative regulation of cardiac chamber formation (GO:1901211)|negative regulation of heart looping (GO:1901208)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|palate development (GO:0060021)|pharynx development (GO:0060465)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(7)|ovary(1)	9						CGCAAGGAGGCGGCCGAGGGC	0.736																																					p.A439V	GBM(3;187 253 11467 14965 23079)	Atlas-SNP	.											.	TBX2	30	.	0			c.C1316T						.						7	9	8					17																	59482827		2121	4175	6296	SO:0001583	missense	6909	exon6			AGGAGGCGGCCGA	AB209378	CCDS11627.2	17q23.2	2012-01-23			ENSG00000121068	ENSG00000121068		"T-boxes"	11597	protein-coding gene	gene with protein product		600747				8530034	Standard	NM_005994		Approved		uc010wox.2	Q13207	OTTHUMG00000156986	ENST00000240328.3:c.1316C>T	chr17.hg19:g.59482827C>T	ENSP00000240328:p.Ala439Val	123.0	0.0		93.0	12.0	NM_005994	Q16424|Q7Z647	Missense_Mutation	SNP	ENST00000240328.3	hg19	CCDS11627.2	.	.	.	.	.	.	.	.	.	.	C	6.804	0.517355	0.13005	.	.	ENSG00000121068	ENST00000240328	D	0.86432	-2.12	4.34	-2.1	0.07210	.	1.044700	0.07574	N	0.919000	T	0.67933	0.2946	N	0.08118	0	0.09310	N	0.999996	B	0.28026	0.198	B	0.25884	0.064	T	0.56414	-0.7983	10	0.29301	T	0.29	.	1.8212	0.03111	0.1219:0.2259:0.3655:0.2867	.	439	Q13207	TBX2_HUMAN	V	439	ENSP00000240328:A439V	ENSP00000240328:A439V	A	+	2	0	TBX2	56837609	0.090000	0.21635	0.018000	0.16275	0.087000	0.18053	0.592000	0.23984	-0.141000	0.11374	0.561000	0.74099	GCG	.	.		0.736	TBX2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346977.2	NM_005994		T	59482827	C	T	59482827	3	4	15	1	0	0	0	0	1	0	0	0	15670	768	27	1	1338	1	TBX2	17	59482827	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	10778991	59482827	21712383	72	1372										
ATP8B1	5205	hgsc.bcm.edu	37	chr18	55315840	55315840	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tccgcgtagccccgctggtgCgagaaggcgtaggccgagcg	17	13	0	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr18:55315840C>T	ENST00000283684.4	-	27	3635	c.3636G>A	c.(3634-3636)tcG>tcA	p.S1212S	RP11-35G9.3_ENST00000591854.1_RNA|RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|ATP8B1_ENST00000536015.1_Silent_p.S1212S|RP11-35G9.3_ENST00000599199.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	1212					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				CCCGCTGGTGCGAGAAGGCGT	0.682																																					p.S1212S		Atlas-SNP	.											.	ATP8B1	126	.	0			c.G3636A						.						21	22	21					18																	55315840		2202	4298	6500	SO:0001819	synonymous_variant	5205	exon28			CTGGTGCGAGAAG	AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"ATPases / P-type"	3706	protein-coding gene	gene with protein product		602397	"ATPase, Class I, type 8B, member 1", "ATPase, class I, type 8B, member 1"	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.3636G>A	chr18.hg19:g.55315840C>T		144.0	0.0		93.0	4.0	NM_005603	Q9BTP8	Silent	SNP	ENST00000283684.4	hg19	CCDS11965.1																																																																																			.	.		0.682	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603		T	55315840	C	T	55315840	2	4	15	1	0	0	0	0	0	0	0	1	1194	755	27	1		1	ATP8B1	18	55315840	Silent	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10		55315840	22761408	73	1373										
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19757110	19757110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	cggtgaggatggtgtacaggTtgaagatgttgggcaggggc	20	4	0	3			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr19:19757110T>C	ENST00000357324.6	-	23	3178	c.3152A>G	c.(3151-3153)aAc>aGc	p.N1051S	GMIP_ENST00000445806.2_5'Flank|GMIP_ENST00000587238.1_5'Flank|GMIP_ENST00000203556.4_5'Flank|ATP13A1_ENST00000291503.5_Missense_Mutation_p.N933S	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	1051						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GGTGTACAGGTTGAAGATGTT	0.617																																					p.N1051S	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.A3152G						.						195	190	192					19																	19757110		2203	4300	6503	SO:0001583	missense	57130	exon23			TACAGGTTGAAGA	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"ATPases / P-type"	24215	protein-coding gene	gene with protein product	"cation transporting ATPase"		"ATPase type 13A"	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.3152A>G	chr19.hg19:g.19757110T>C	ENSP00000349877:p.Asn1051Ser	162.0	0.0		120.0	36.0	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Missense_Mutation	SNP	ENST00000357324.6	hg19	CCDS32970.2	.	.	.	.	.	.	.	.	.	.	T	18.78	3.696860	0.68386	.	.	ENSG00000105726	ENST00000291503;ENST00000357324	T;T	0.54675	0.56;0.56	4.61	4.61	0.57282	.	0.087332	0.85682	D	0.000000	T	0.34832	0.0911	N	0.25890	0.77	0.80722	D	1	B;P	0.36110	0.22;0.537	B;B	0.36378	0.223;0.219	T	0.18053	-1.0349	10	0.05959	T	0.93	-31.0281	11.9699	0.53058	0.0:0.0:0.0:1.0	.	1051;933	Q9HD20;Q9HD20-2	AT131_HUMAN;.	S	933;1051	ENSP00000291503:N933S;ENSP00000349877:N1051S	ENSP00000291503:N933S	N	-	2	0	ATP13A1	19618110	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	7.583000	0.82559	1.714000	0.51371	0.402000	0.26972	AAC	.	.		0.617	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		C	19757110	T	C	19757110	3	2	15	1	0	0	0	0	1	0	0	0	1123	1725	60	2	478	2	ATP13A1	19	19757110	Missense_Mutation	SNP	T	TCGA-2Y-A9H5-01A-11D-A382-10		19757110	39371873	74	1374										
SFRS16	11129	hgsc.bcm.edu	37	chr19	45570624	45570624	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ccactcaggggaccgctacaGgcggggcggccggggcctca	17	15	2	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr19:45570624G>A	ENST00000221455.3	+	14	1537	c.1439G>A	c.(1438-1440)aGg>aAg	p.R480K	CLASRP_ENST00000544944.2_Missense_Mutation_p.R480K|CLASRP_ENST00000391953.4_Missense_Mutation_p.R418K	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	480	Arg-rich.|Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						GACCGCTACAGGCGGGGCGGC	0.736																																					p.R480K		Atlas-SNP	.											.	CLASRP	44	.	0			c.G1439A						.						2	2	2					19																	45570624		1062	2309	3371	SO:0001583	missense	11129	exon14			GCTACAGGCGGGG	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"Clk4 associating SR-related protein"		"splicing factor, arginine/serine-rich 16"	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.1439G>A	chr19.hg19:g.45570624G>A	ENSP00000221455:p.Arg480Lys	98.0	0.0		78.0	37.0	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Missense_Mutation	SNP	ENST00000221455.3	hg19	CCDS12652.2	.	.	.	.	.	.	.	.	.	.	G	10.17	1.276405	0.23307	.	.	ENSG00000104859	ENST00000221455;ENST00000391952;ENST00000391953;ENST00000544944	T;T;T;T	0.36520	1.39;1.25;1.39;1.25	4.26	3.21	0.36854	.	0.275476	0.17624	N	0.167621	T	0.17704	0.0425	N	0.12182	0.205	0.26478	N	0.975155	B;B;B	0.28667	0.0;0.219;0.14	B;B;B	0.32090	0.0;0.14;0.067	T	0.26710	-1.0095	10	0.09084	T	0.74	-5.6513	7.0685	0.25165	0.1274:0.0:0.8726:0.0	.	418;480;480	F8WAG9;F5H0Q6;Q8N2M8	.;.;CLASR_HUMAN	K	480;480;418;480	ENSP00000221455:R480K;ENSP00000375814:R480K;ENSP00000375815:R418K;ENSP00000438702:R480K	ENSP00000221455:R480K	R	+	2	0	CLASRP	50262464	0.242000	0.23868	0.826000	0.32828	0.992000	0.81027	2.536000	0.45693	0.975000	0.38392	0.455000	0.32223	AGG	.	.		0.736	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056		A	45570624	G	A	45570624	3	1	15	1	0	0	0	0	1	0	0	0	14187	1000	35	3	1489	3	SFRS16	19	45570624	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	25813514	45570624	13558359	75	1375										
LRRC4B	94030	hgsc.bcm.edu	37	chr19	51021449	51021449	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ggcggttccttctccgtcccCcgcggctgcagggcctcctc	12	19	1	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr19:51021449C>A	ENST00000599957.1	-	3	1718	c.1521G>T	c.(1519-1521)cgG>cgT	p.R507R	LRRC4B_ENST00000389201.3_Silent_p.R507R			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	507	Gly-rich.				positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		TCTCCGTCCCCCGCGGCTGCA	0.716																																					p.R507R		Atlas-SNP	.											.	LRRC4B	89	.	0			c.G1521T						.						8	10	9					19																	51021449		1812	3927	5739	SO:0001819	synonymous_variant	94030	exon3			CGTCCCCCGCGGC	BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"Immunoglobulin superfamily / I-set domain containing", "Endogenous ligands"	25042	protein-coding gene	gene with protein product	"netrin-G3 ligand"		"leucine-rich repeats and immunoglobulin-like domains 4"	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.1521G>T	chr19.hg19:g.51021449C>A		50.0	0.0		35.0	12.0	NM_001080457	Q3ZCQ4|Q58F20	Silent	SNP	ENST00000599957.1	hg19	CCDS42595.1																																																																																			.	.		0.716	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457		A	51021449	C	A	51021449	2	1	15	1	0	0	0	0	0	0	0	1	9016	610	22	3		3	LRRC4B	19	51021449	Silent	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	5450825	51021449	8107534	76	1376										
NFATC2	4773	hgsc.bcm.edu	37	chr20	50139906	50139906	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	agccacaggggggtacccagCcggggagccgtggtcctggg	19	12	0	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr20:50139906C>A	ENST00000396009.3	-	2	1093	c.874G>T	c.(874-876)Gct>Tct	p.A292S	NFATC2_ENST00000609507.1_Missense_Mutation_p.A73S|NFATC2_ENST00000414705.1_Missense_Mutation_p.A272S|NFATC2_ENST00000609943.1_Missense_Mutation_p.A272S|NFATC2_ENST00000371564.3_Missense_Mutation_p.A292S|NFATC2_ENST00000610033.1_Missense_Mutation_p.A73S	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	292					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GGGTACCCAGCCGGGGAGCCG	0.701																																					p.A292S		Atlas-SNP	.											.	NFATC2	112	.	0			c.G874T						.						8	10	9					20																	50139906		2124	4179	6303	SO:0001583	missense	4773	exon2			ACCCAGCCGGGGA	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.874G>T	chr20.hg19:g.50139906C>A	ENSP00000379330:p.Ala292Ser	141.0	0.0		114.0	39.0	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	hg19	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	C	0.100	-1.153650	0.01700	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000371567;ENST00000414705	T;T;T	0.78924	-1.22;-1.22;-1.22	5.24	4.29	0.51040	.	0.571341	0.18477	N	0.140058	T	0.57666	0.2069	N	0.14661	0.345	0.09310	N	0.999994	B;P;P;P	0.48640	0.085;0.828;0.913;0.828	B;B;B;B	0.38378	0.02;0.272;0.145;0.107	T	0.48364	-0.9042	10	0.29301	T	0.29	-5.8432	9.3834	0.38327	0.0:0.7792:0.1443:0.0766	.	272;272;292;292	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	S	292;292;73;272	ENSP00000360619:A292S;ENSP00000379330:A292S;ENSP00000396471:A272S	ENSP00000360619:A292S	A	-	1	0	NFATC2	49573313	0.001000	0.12720	0.094000	0.20943	0.106000	0.19336	0.235000	0.17948	1.189000	0.43028	0.305000	0.20034	GCT	.	.		0.701	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		A	50139906	C	A	50139906	3	1	15	1	0	0	0	0	1	0	0	0	10371	739	26	3	1987	3	NFATC2	20	50139906	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10		50139906	12885614	77	1377										
DGCR14	8220	hgsc.bcm.edu	37	chr22	19126717	19126717	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	tggagctggcacctgctcagGgcttggctgaaggggtccct	16	11	1	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chr22:19126717G>C	ENST00000252137.6	-	6	820	c.777C>G	c.(775-777)gcC>gcG	p.A259A		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	259					mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					ACCTGCTCAGGGCTTGGCTGA	0.647																																					p.A259A		Atlas-SNP	.											.	DGCR14	43	.	0			c.C777G						.						45	44	44					22																	19126717		2203	4300	6503	SO:0001819	synonymous_variant	8220	exon6			GCTCAGGGCTTGG	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"DiGeorge syndrome critical region gene 13"	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.777C>G	chr22.hg19:g.19126717G>C		74.0	0.0		69.0	20.0	NM_022719	Q49AH7|Q9BTZ4	Silent	SNP	ENST00000252137.6	hg19	CCDS13756.1																																																																																			.	.		0.647	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2			C	19126717	G	C	19126717	2	2	15	1	0	0	0	0	0	0	0	1	4462	1219	43	4		4	DGCR14	22	19126717	Silent	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10		19126717	32177849	78	1378										
HCCS	3052	hgsc.bcm.edu	37	chrX	11132958	11132958	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	atacttgattatttcaggctGtccagtgaatacagagccat	8	8	1	3			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chrX:11132958G>T	ENST00000321143.4	+	3	306	c.104G>T	c.(103-105)tGt>tTt	p.C35F	Y_RNA_ENST00000384422.1_RNA|HCCS_ENST00000380763.3_Missense_Mutation_p.C35F|HCCS_ENST00000380762.4_Missense_Mutation_p.C35F	NM_001122608.2|NM_001171991.2|NM_005333.4	NP_001116080.1|NP_001165462.1|NP_005324.3	P53701	CCHL_HUMAN	holocytochrome c synthase	35					organ morphogenesis (GO:0009887)|oxidation-reduction process (GO:0055114)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	holocytochrome-c synthase activity (GO:0004408)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(3)	7						ATTTCAGGCTGTCCAGTGAAT	0.458																																					p.C35F	Ovarian(86;1338 1347 1462 10340 37882)	Atlas-SNP	.											.	HCCS	17	.	0			c.G104T						.						108	88	95					X																	11132958		2203	4300	6503	SO:0001583	missense	3052	exon3			CAGGCTGTCCAGT		CCDS14139.1	Xp22	2014-01-31	2010-05-11		ENSG00000004961	ENSG00000004961	4.4.1.17		4837	protein-coding gene	gene with protein product	"cytochrome c heme-lyase"	300056	"holocytochrome c synthase (cytochrome c heme-lyase)", "microphthalamia with linear skin defects"	MLS		8364577, 12444108	Standard	NM_001122608		Approved	CCHL	uc004cuj.3	P53701	OTTHUMG00000021128	ENST00000321143.4:c.104G>T	chrX.hg19:g.11132958G>T	ENSP00000326579:p.Cys35Phe	47.0	0.0		82.0	15.0	NM_001122608	B3KUS1|Q502X8	Missense_Mutation	SNP	ENST00000321143.4	hg19	CCDS14139.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.653635	0.29425	.	.	ENSG00000004961	ENST00000321143;ENST00000380763;ENST00000380762	D;D;D	0.94537	-3.45;-3.45;-3.45	5.08	4.21	0.49690	.	0.153570	0.64402	D	0.000013	D	0.96700	0.8923	M	0.80508	2.5	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.96217	0.9157	10	0.59425	D	0.04	-13.8235	10.5123	0.44868	0.0976:0.0:0.9024:0.0	.	35	P53701	CCHL_HUMAN	F	35	ENSP00000326579:C35F;ENSP00000370140:C35F;ENSP00000370139:C35F	ENSP00000326579:C35F	C	+	2	0	HCCS	11042879	1.000000	0.71417	0.966000	0.40874	0.028000	0.11728	4.214000	0.58527	1.053000	0.40415	0.600000	0.82982	TGT	.	.		0.458	HCCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055742.1			T	11132958	G	T	11132958	3	4	15	1	0	0	0	0	1	0	0	0	6999	1377	48	3	110	3	HCCS	23	11132958	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10		11132958	144137602	79	1379										
DMD	1756	hgsc.bcm.edu	37	chrX	32235037	32235037	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	caaatcaaagacttaccttaAgataccatttgtatttagca	4	8	1	2			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chrX:32235037A>T	ENST00000357033.4	-	44	6640	c.6434T>A	c.(6433-6435)cTt>cAt	p.L2145H	DMD_ENST00000378677.2_Missense_Mutation_p.L2141H	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2145					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				ACTTACCTTAAGATACCATTT	0.333																																					p.L2145H		Atlas-SNP	.											.	DMD	2127	.	0			c.T6434A						.						65	53	57					X																	32235037		2202	4297	6499	SO:0001583	missense	1756	exon44			ACCTTAAGATACC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.6434T>A	chrX.hg19:g.32235037A>T	ENSP00000354923:p.Leu2145His	227.0	0.0		427.0	37.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.51|18.51	3.639674|3.639674	0.67244|0.67244	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000542849;ENST00000535280|ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033	.|T;T	.|0.36699	.|1.24;1.24	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|0.000000	.|0.33712	.|U	.|0.004637	.|T	.|0.56001	.|0.1956	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.76494	.|0.997;0.999;0.999;0.999;0.998;0.999	.|P;D;D;D;D;D	.|0.69824	.|0.891;0.943;0.934;0.966;0.947;0.95	.|T	.|0.55560	.|-0.8122	.|10	.|0.39692	.|T	.|0.17	.|.	13.0598|13.0598	0.59000|0.59000	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|804;2137;2145;2141;804;801	.|P11532-2;P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.|.;.;DMD_HUMAN;.;.;.	.|H	-1|2137;804;801;2141;2145	.|ENSP00000367948:L2141H;ENSP00000354923:L2145H	.|ENSP00000354923:L2145H	.|L	-|-	.|2	.|0	DMD|DMD	32144958|32144958	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.873000|0.873000	0.50193|0.50193	5.589000|5.589000	0.67523|0.67523	1.879000|1.879000	0.54435|0.54435	0.345000|0.345000	0.21793|0.21793	.|CTT	.	.		0.333	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32235037	A	T	32235037	3	4	15	1	0	0	0	0	1	0	0	0	4582	72	3	4	4915	4	DMD	23	32235037	Missense_Mutation	SNP	A	TCGA-2Y-A9H5-01A-11D-A382-10	21102079	32235037	123035523	80	1380										
HDAC6	10013	hgsc.bcm.edu	37	chrX	48678643	48678643	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gatgggccttgccagtggccGcattatccttatcctagagg	12	11	0	1	rs186499554		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chrX:48678643G>T	ENST00000334136.5	+	23	2496	c.2318G>T	c.(2317-2319)cGc>cTc	p.R773L	HDAC6_ENST00000444343.2_Missense_Mutation_p.R787L|HDAC6_ENST00000376619.2_Missense_Mutation_p.R773L			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	773	Histone deacetylase 2.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	GCCAGTGGCCGCATTATCCTT	0.572																																					p.R773L	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.G2318T						.						70	55	60					X																	48678643		2203	4300	6503	SO:0001583	missense	10013	exon23			GTGGCCGCATTAT	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.2318G>T	chrX.hg19:g.48678643G>T	ENSP00000334061:p.Arg773Leu	105.0	0.0		93.0	25.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	hg19	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	g	18.55	3.648599	0.67358	.	.	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619	T;T;T	0.72167	-0.63;-0.63;-0.63	5.25	0.59	0.17458	Histone deacetylase domain (2);	0.331642	0.30979	N	0.008485	D	0.82737	0.5102	M	0.88377	2.95	0.80722	D	1	D;D;D;D	0.69078	0.991;0.997;0.992;0.991	D;D;D;D	0.71870	0.945;0.975;0.971;0.945	T	0.80876	-0.1186	10	0.87932	D	0	-8.2783	8.741	0.34558	0.4142:0.0:0.5858:0.0	.	763;136;421;773	B4DZN1;B3KY98;B3KVK5;Q9UBN7	.;.;.;HDAC6_HUMAN	L	787;773;773	ENSP00000398566:R787L;ENSP00000334061:R773L;ENSP00000365804:R773L	ENSP00000334061:R773L	R	+	2	0	HDAC6	48563587	0.727000	0.28069	0.464000	0.27143	0.975000	0.68041	0.989000	0.29629	-0.218000	0.10018	-0.180000	0.13094	CGC	.	G|0.999;A|0.001		0.572	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		T	48678643	G	T	48678643	3	4	15	1	0	0	0	0	1	0	0	0	7020	1087	38	1	2404	1	HDAC6	23	48678643	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	16443606	48678643	106591917	81	1381										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73963443	73963443	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	gtctcgaacattgtcctgaaAggattcatatcgaattttca	7	8	3	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chrX:73963443A>C	ENST00000055682.6	-	3	1560	c.949T>G	c.(949-951)Ttt>Gtt	p.F317V		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	317					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						TTGTCCTGAAAGGATTCATAT	0.423																																					p.F317V		Atlas-SNP	.											.	KIAA2022	262	.	0			c.T949G						.						97	83	88					X																	73963443		2203	4300	6503	SO:0001583	missense	340533	exon3			CCTGAAAGGATTC		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.949T>G	chrX.hg19:g.73963443A>C	ENSP00000055682:p.Phe317Val	105.0	0.0		206.0	75.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.499667	0.64298	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.54479	0.57;0.57	5.83	5.83	0.93111	.	0.062190	0.64402	D	0.000004	T	0.69504	0.3118	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.72564	-0.4255	10	0.87932	D	0	-10.5577	15.144	0.72633	1.0:0.0:0.0:0.0	.	317	Q5QGS0	K2022_HUMAN	V	317	ENSP00000362567:F317V;ENSP00000055682:F317V	ENSP00000055682:F317V	F	-	1	0	KIAA2022	73880168	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.962000	0.93254	1.959000	0.56917	0.486000	0.48141	TTT	.	.		0.423	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		C	73963443	A	C	73963443	3	2	15	1	0	0	0	0	1	0	0	0	8278	72	3	5	3609	5	KIAA2022	23	73963443	Missense_Mutation	SNP	A	TCGA-2Y-A9H5-01A-11D-A382-10	25284800	73963443	81307117	82	1382										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123517915	123517915	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	agcttgtgtggttgtacaaaTgagtaactcttatggggttg	13	4	1	1			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chrX:123517915T>G	ENST00000371130.3	-	29	6908	c.6845A>C	c.(6844-6846)cAt>cCt	p.H2282P	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.H2289P	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2282					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTTGTACAAATGAGTAACTCT	0.448																																					p.H2289P		Atlas-SNP	.											.	.	.	.	0			c.A6866C						.						133	131	132					X																	123517915		2203	4299	6502	SO:0001583	missense	10178	exon30			TACAAATGAGTAA	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.6845A>C	chrX.hg19:g.123517915T>G	ENSP00000360171:p.His2282Pro	74.0	0.0		140.0	64.0	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	hg19	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	17.57	3.422305	0.62622	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.87256	-2.23;-2.2	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.94042	0.8091	M	0.87180	2.865	0.80722	D	1	D;D;D	0.89917	0.998;0.999;1.0	D;D;D	0.80764	0.991;0.994;0.981	D	0.94934	0.8085	10	0.87932	D	0	.	14.8334	0.70164	0.0:0.0:0.0:1.0	.	2288;2289;2282	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	P	2282;2289	ENSP00000360171:H2282P;ENSP00000403954:H2289P	ENSP00000360171:H2282P	H	-	2	0	ODZ1	123345596	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	1.884000	0.54569	0.486000	0.48141	CAT	.	.		0.448	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		G	123517915	T	G	123517915	3	3	15	1	0	0	0	0	1	0	0	0	10843	1464	51	5	1344	5	ODZ1	23	123517915	Missense_Mutation	SNP	T	TCGA-2Y-A9H5-01A-11D-A382-10	49554472	123517915	31752645	83	1383										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718857	142718857	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	acacattgcaaatttccaccGatatgtcagaatctgcattt	5	10	2	1	rs376093373		TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chrX:142718857G>A	ENST00000381779.4	-	2	293	c.68C>T	c.(67-69)tCg>tTg	p.S23L	SLITRK4_ENST00000356928.1_Missense_Mutation_p.S23L|SLITRK4_ENST00000338017.4_Missense_Mutation_p.S23L	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	23						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					AATTTCCACCGATATGTCAGA	0.418																																					p.S23L		Atlas-SNP	.											.	SLITRK4	162	.	0			c.C68T						.	G	LEU/SER,LEU/SER,LEU/SER	1,3834		0,1,1631,571	65	59	61		68,68,68	5.6	1	X		61	0,6728		0,0,2428,1872	no	missense,missense,missense	SLITRK4	NM_001184749.1,NM_001184750.1,NM_173078.3	145,145,145	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	benign,benign,benign	23/838,23/838,23/838	142718857	1,10562	2203	4300	6503	SO:0001583	missense	139065	exon2			TCCACCGATATGT	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.68C>T	chrX.hg19:g.142718857G>A	ENSP00000371198:p.Ser23Leu	317.0	0.0		392.0	128.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	G	4.184	0.032694	0.08101	2.61E-4	0.0	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.54866	0.55;0.55;0.55	5.6	5.6	0.85130	.	0.356473	0.29565	N	0.011797	T	0.51210	0.1661	M	0.78049	2.395	0.37739	D	0.925542	B	0.31837	0.342	B	0.24155	0.051	T	0.56372	-0.7990	10	0.10111	T	0.7	-3.2942	17.0278	0.86452	0.0:0.0:1.0:0.0	.	23	Q8IW52	SLIK4_HUMAN	L	23	ENSP00000371198:S23L;ENSP00000349400:S23L;ENSP00000336627:S23L	ENSP00000336627:S23L	S	-	2	0	SLITRK4	142546523	0.998000	0.40836	0.984000	0.44739	0.983000	0.72400	5.887000	0.69751	2.340000	0.79590	0.594000	0.82650	TCG	.	.		0.418	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		A	142718857	G	A	142718857	3	1	15	1	0	0	0	0	1	0	0	0	14760	1059	37	1	2449	1	SLITRK4	23	142718857	Missense_Mutation	SNP	G	TCGA-2Y-A9H5-01A-11D-A382-10	19200942	142718857	12551703	84	1384										
SRPK3	26576	hgsc.bcm.edu	37	chrX	153049751	153049751	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0705882352941176	6	1	1.33968253968254	0	1.52072072072072	0.00699300699300699	0.217365967365967	0	ctgctctgccttccccagcaCcattcggtgcctcgaacctc	7	19	1	0			TCGA-2Y-A9H5-01A-11D-A382-10	TCGA-2Y-A9H5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10106872-3169-465f-900a-b6e74debfc51	978cf657-0928-40db-9f1c-888305de2cbb	g.chrX:153049751C>G	ENST00000370101.3	+	11	1196	c.1150C>G	c.(1150-1152)Cca>Gca	p.P384A	SRPK3_ENST00000489426.1_Missense_Mutation_p.P451A|SRPK3_ENST00000370104.1_Missense_Mutation_p.P383A|SRPK3_ENST00000370108.3_Missense_Mutation_p.P351A|SRPK3_ENST00000393786.3_Missense_Mutation_p.P350A|IDH3G_ENST00000497043.1_5'Flank|SRPK3_ENST00000370100.1_Missense_Mutation_p.P309A	NM_001170760.1|NM_014370.3	NP_001164231.1|NP_055185.2	Q9UPE1	SRPK3_HUMAN	SRSF protein kinase 3	384	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|muscle tissue development (GO:0060537)|skeletal muscle tissue development (GO:0007519)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(2)|pancreas(2)|urinary_tract(1)	13	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					TTCCCCAGCACCATTCGGTGC	0.602																																					p.P384A	Esophageal Squamous(167;766 3400 32156)	Atlas-SNP	.											.	SRPK3	63	.	0			c.C1150G						.						59	53	55					X																	153049751		2203	4300	6503	SO:0001583	missense	26576	exon11			CCAGCACCATTCG	AF027406	CCDS35441.1, CCDS55537.1, CCDS55538.1	Xq28	2010-06-23	2010-06-23	2006-08-17	ENSG00000184343	ENSG00000184343			11402	protein-coding gene	gene with protein product			"serine/threonine kinase 23", "SFRS protein kinase 3"	STK23		16140986	Standard	NM_014370		Approved	MSSK1	uc004fil.3	Q9UPE1	OTTHUMG00000024207	ENST00000370101.3:c.1150C>G	chrX.hg19:g.153049751C>G	ENSP00000359119:p.Pro384Ala	280.0	0.0		213.0	69.0	NM_014370	Q13583|Q4F970|Q562F5|Q9UM62	Missense_Mutation	SNP	ENST00000370101.3	hg19	CCDS35441.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.506484	0.26949	.	.	ENSG00000184343	ENST00000489426;ENST00000393786;ENST00000370104;ENST00000370108;ENST00000370101;ENST00000370100	T;T;T;T;T;T	0.54479	0.57;0.63;0.59;0.62;0.59;0.58	4.92	3.02	0.34903	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.150969	0.30277	N	0.009987	T	0.25457	0.0619	N	0.12961	0.28	0.09310	N	0.999994	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.0;0.001	T	0.11155	-1.0599	10	0.09843	T	0.71	-8.2074	2.7423	0.05257	0.3255:0.4254:0.1559:0.0932	.	308;383;350;384;451	Q9UPE1-2;Q9UPE1-4;Q9UPE1-3;Q9UPE1;E7ETV6	.;.;.;SRPK3_HUMAN;.	A	451;350;383;351;384;309	ENSP00000420058:P451A;ENSP00000377376:P350A;ENSP00000359122:P383A;ENSP00000359126:P351A;ENSP00000359119:P384A;ENSP00000359118:P309A	ENSP00000359118:P309A	P	+	1	0	SRPK3	152702945	0.996000	0.38824	0.228000	0.23943	0.440000	0.31957	2.271000	0.43364	1.038000	0.40049	0.529000	0.55759	CCA	.	.		0.602	SRPK3-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354501.1	NM_014370		G	153049751	C	G	153049751	3	3	15	1	0	0	0	0	1	0	0	0	15176	507	18	4	1192	4	SRPK3	23	153049751	Missense_Mutation	SNP	C	TCGA-2Y-A9H5-01A-11D-A382-10	10330894	153049751	2220809	85	1385										
TNNI3K	100526835	hgsc.bcm.edu	37	chr1	74819702	74819702	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	accacggtcacattcgcctgGttcagttcttactggataat	8	11	3	0			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr1:74819702G>A	ENST00000370899.3	+	13	1406	c.1369G>A	c.(1369-1371)Gtt>Att	p.V457I	FPGT-TNNI3K_ENST00000370895.1_Missense_Mutation_p.V457I|TNNI3K_ENST00000370891.2_Missense_Mutation_p.V457I|RP11-439H8.4_ENST00000415549.2_RNA|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.V470I|TNNI3K_ENST00000326637.3_Missense_Mutation_p.V356I	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		CATTCGCCTGGTTCAGTTCTT	0.418																																					p.V457I		Atlas-SNP	.											.	.	.	.	0			c.G1369A						.						161	141	148					1																	74819702		2203	4300	6503	SO:0001583	missense	100526835	exon13			CGCCTGGTTCAGT			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.1369G>A	chr1.hg19:g.74819702G>A	ENSP00000359936:p.Val457Ile	79.0	0.0		68.0	33.0	NM_001112808		Missense_Mutation	SNP	ENST00000370899.3	hg19		.	.	.	.	.	.	.	.	.	.	G	21.8	4.205257	0.79127	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000557284;ENST00000370891;ENST00000326637	T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42	5.22	2.33	0.28932	Ankyrin repeat-containing domain (4);	0.122893	0.53938	N	0.000042	T	0.69115	0.3075	M	0.73430	2.235	0.44454	D	0.997387	P;D;D;D	0.67145	0.831;0.983;0.983;0.996	P;P;P;D	0.76071	0.596;0.876;0.826;0.987	T	0.68017	-0.5520	10	0.39692	T	0.17	.	8.4223	0.32707	0.1393:0.1279:0.7328:0.0	.	356;457;457;457	Q59H18;Q59H18-1;Q59H18-4;Q59H18-3	TNI3K_HUMAN;.;.;.	I	457;457;457;457;356	ENSP00000359936:V457I;ENSP00000359932:V457I;ENSP00000450895:V457I;ENSP00000359928:V457I;ENSP00000322251:V356I	ENSP00000322251:V356I	V	+	1	0	RP11-653A5.2;AC093158.1	74592290	1.000000	0.71417	0.999000	0.59377	0.963000	0.63663	6.180000	0.71981	0.356000	0.24157	-0.175000	0.13238	GTT	.	.		0.418	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			A	74819702	G	A	74819702	3	1	16	1	0	0	0	0	1	0	0	0	16344	1261	44	3	1463	3	TNNI3K	1	74819702	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10		74819702	174430919	1	1386										
IVL	3713	hgsc.bcm.edu	37	chr1	152883099	152883099	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	aggaggggcagctggaggtcCcagaggagcagatggggcag	21	7	0	2	rs541702541	byFrequency	TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr1:152883099C>T	ENST00000368764.3	+	2	890	c.826C>T	c.(826-828)Cca>Tca	p.P276S	IVL_ENST00000392667.2_Missense_Mutation_p.P130S			P07476	INVO_HUMAN	involucrin	276	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gcTGGAGGTCCCAGAGGAGCA	0.637													C|||	2	0.000399361	0	0.0029	5008	,	,		19342	0		0	False		,,,				2504	0				p.P276S		Atlas-SNP	.											.	IVL	100	.	0			c.C826T						.						16	15	15					1																	152883099		2039	3988	6027	SO:0001583	missense	3713	exon2			GAGGTCCCAGAGG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.826C>T	chr1.hg19:g.152883099C>T	ENSP00000357753:p.Pro276Ser	184.0	0.0		287.0	63.0	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	hg19	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	C	8.482	0.859906	0.17178	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.09445	3.19;2.98	3.62	-1.67	0.08238	.	.	.	.	.	T	0.02494	0.0076	L	0.58101	1.795	0.09310	N	1	P	0.42123	0.771	B	0.42282	0.382	T	0.31586	-0.9938	9	0.09590	T	0.72	.	0.4282	0.00467	0.334:0.2865:0.1642:0.2153	.	276	P07476	INVO_HUMAN	S	276;130	ENSP00000357753:P276S;ENSP00000376435:P130S	ENSP00000357753:P276S	P	+	1	0	IVL	151149723	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.090000	0.11163	-0.154000	0.11118	0.194000	0.17425	CCA	.	.		0.637	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		T	152883099	C	T	152883099	3	4	16	1	0	0	0	0	1	0	0	0	7938	623	22	3	828	3	IVL	1	152883099	Missense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	78063397	152883099	96367522	2	1387										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190067855	190067855	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	cttcaaggtgaggagcatccGcttacgccaggagggatcaa	13	10	2	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr1:190067855G>T	ENST00000367462.3	-	8	1825	c.1594C>A	c.(1594-1596)Cgg>Agg	p.R532R	BRINP3_ENST00000534846.1_Silent_p.R430R	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	532					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											AGGAGCATCCGCTTACGCCAG	0.433																																					p.R532R		Atlas-SNP	.											.	FAM5C	343	.	0			c.C1594A						.						119	116	117					1																	190067855		2203	4300	6503	SO:0001819	synonymous_variant	339479	exon8			GCATCCGCTTACG	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1594C>A	chr1.hg19:g.190067855G>T		82.0	0.0		151.0	37.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Silent	SNP	ENST00000367462.3	hg19	CCDS1373.1																																																																																			.	.		0.433	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190067855	G	T	190067855	2	4	16	1	0	0	0	0	0	0	0	1	5602	1086	38	1		1	FAM5C	1	190067855	Silent	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	37184756	190067855	59182766	3	1388										
CR2	1380	hgsc.bcm.edu	37	chr1	207649630	207649630	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ccctaacgggaaccatactgGtggaaacatagctcgatttt	9	10	0	0			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr1:207649630G>A	ENST00000367058.3	+	14	2780	c.2591G>A	c.(2590-2592)gGt>gAt	p.G864D	CR2_ENST00000367057.3_Missense_Mutation_p.G923D|CR2_ENST00000367059.3_Intron|CR2_ENST00000458541.2_Missense_Mutation_p.G837D	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	864	Sushi 14. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						AACCATACTGGTGGAAACATA	0.498																																					p.G923D		Atlas-SNP	.											.	CR2	164	.	0			c.G2768A						.						153	139	144					1																	207649630		2203	4300	6503	SO:0001583	missense	1380	exon15			ATACTGGTGGAAA	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.2591G>A	chr1.hg19:g.207649630G>A	ENSP00000356025:p.Gly864Asp	46.0	0.0		195.0	47.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.573726	0.45902	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000458541	T;T;T	0.50277	0.75;0.75;0.75	4.87	3.95	0.45737	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.54775	0.1879	L	0.35723	1.085	0.43084	D	0.994749	D;D	0.71674	0.998;0.997	D;D	0.71414	0.961;0.973	T	0.52434	-0.8576	9	0.35671	T	0.21	.	11.8047	0.52147	0.0:0.1781:0.8219:0.0	.	864;923	P20023;P20023-3	CR2_HUMAN;.	D	864;923;837	ENSP00000356025:G864D;ENSP00000356024:G923D;ENSP00000404222:G837D	ENSP00000356024:G923D	G	+	2	0	CR2	205716253	0.284000	0.24287	0.688000	0.30117	0.319000	0.28217	1.238000	0.32707	1.360000	0.45960	0.655000	0.94253	GGT	.	.		0.498	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		A	207649630	G	A	207649630	3	1	16	1	0	0	0	0	1	0	0	0	3844	1261	44	3	2826	3	CR2	1	207649630	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	17581775	207649630	41600991	4	1389										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227223280	227223280	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	gtggttggagctttgtttacAcaagttatatggcatgagaa	12	4	0	1	rs371390192		TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr1:227223280A>G	ENST00000366769.3	-	24	4414	c.3123T>C	c.(3121-3123)tgT>tgC	p.C1041C	CDC42BPA_ENST00000366764.2_Silent_p.C1013C|CDC42BPA_ENST00000366767.3_Silent_p.C960C|CDC42BPA_ENST00000535525.1_Silent_p.C1021C|CDC42BPA_ENST00000334218.5_Silent_p.C1041C|CDC42BPA_ENST00000366765.3_Silent_p.C1054C|CDC42BPA_ENST00000366766.2_Silent_p.C1076C	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				CTTTGTTTACACAAGTTATAT	0.383																																					p.C1041C		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.T3123C						.	A	,	0,4406		0,0,2203	89	90	90		3123,2880	4.7	1	1		90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CDC42BPA	NM_003607.3,NM_014826.4	,	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,	1041/1720,960/1639	227223280	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8476	exon24			GTTTACACAAGTT	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.3123T>C	chr1.hg19:g.227223280A>G		67.0	0.0		136.0	33.0	NM_003607		Silent	SNP	ENST00000366769.3	hg19	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.388599	0.25118	0.0	1.16E-4	ENSG00000143776	ENST00000448940;ENST00000442054;ENST00000441725	D;D;D	0.99898	-7.61;-7.61;-7.61	5.8	4.67	0.58626	.	0.000000	0.85682	D	0.000000	D	0.99802	0.9915	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.96290	0.9213	7	0.87932	D	0	.	11.7355	0.51763	0.9313:0.0:0.0687:0.0	.	.	.	.	R	244;370;266	ENSP00000415388:C244R;ENSP00000401051:C370R;ENSP00000408165:C266R	ENSP00000408165:C266R	C	-	1	0	CDC42BPA	225289903	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.058000	0.49939	1.024000	0.39682	0.528000	0.53228	TGT	.	.		0.383	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		G	227223280	A	G	227223280	2	3	16	1	0	0	0	0	0	0	0	1	3074	157	6	2		2	CDC42BPA	1	227223280	Silent	SNP	A	TCGA-2Y-A9H6-01A-11D-A38X-10	19573650	227223280	22027341	5	1390										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245809435	245809435	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	tgtggtagtgtctggaggtcGcagccgcctgcatctcattg	14	10	2	0			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr1:245809435G>A	ENST00000407071.2	+	10	2551	c.2111G>A	c.(2110-2112)cGc>cAc	p.R704H	KIF26B_ENST00000366518.4_Missense_Mutation_p.R323H	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	704	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TCTGGAGGTCGCAGCCGCCTG	0.502																																					p.R704H		Atlas-SNP	.											KIF26B_ENST00000407071,colon,carcinoma,0,2	KIF26B	343	.	0			c.G2111A						.						55	56	55					1																	245809435		1936	4140	6076	SO:0001583	missense	55083	exon10			GAGGTCGCAGCCG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2111G>A	chr1.hg19:g.245809435G>A	ENSP00000385545:p.Arg704His	31.0	0.0		96.0	43.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.423362	0.83559	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.17528	2.27;2.27	5.78	5.78	0.91487	Kinesin, motor domain (4);	.	.	.	.	T	0.42314	0.1197	L	0.56396	1.775	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.13098	-1.0522	9	0.87932	D	0	.	20.0114	0.97452	0.0:0.0:1.0:0.0	.	323;704	B7WPD9;Q2KJY2	.;KI26B_HUMAN	H	704;323;320	ENSP00000385545:R704H;ENSP00000355475:R323H	ENSP00000355475:R323H	R	+	2	0	KIF26B	243876058	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.476000	0.97823	2.724000	0.93272	0.555000	0.69702	CGC	.	.		0.502	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245809435	G	A	245809435	3	1	16	1	0	0	0	0	1	0	0	0	8304	1087	38	1	2149	1	KIF26B	1	245809435	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	18586155	245809435	3441186	6	1391										
CMPK2	129607	hgsc.bcm.edu	37	chr2	6991720	6991720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	aggtttgagcaggtcctctgGccactggtacacagggtgat	14	9	1	2	rs372816766		TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr2:6991720G>A	ENST00000256722.5	-	4	1086	c.1087C>T	c.(1087-1089)Cca>Tca	p.P363S	CMPK2_ENST00000458098.1_Intron|CMPK2_ENST00000478738.1_5'UTR|CMPK2_ENST00000404168.1_Missense_Mutation_p.P363S	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	363					cellular response to lipopolysaccharide (GO:0071222)|dTDP biosynthetic process (GO:0006233)|dUDP biosynthetic process (GO:0006227)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)|thymidylate kinase activity (GO:0004798)|UMP kinase activity (GO:0033862)			large_intestine(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AGGTCCTCTGGCCACTGGTAC	0.617																																					p.P363S		Atlas-SNP	.											.	CMPK2	30	.	0			c.C1087T						.	G	SER/PRO	0,4104		0,0,2052	96	101	100		1087	5.2	1	2		100	1,8423		0,1,4211	no	missense	CMPK2	NM_207315.2	74	0,1,6263	AA,AG,GG		0.0119,0.0,0.0080	probably-damaging	363/450	6991720	1,12527	2052	4212	6264	SO:0001583	missense	129607	exon4			CCTCTGGCCACTG		CCDS42648.1, CCDS58695.1, CCDS58696.1	2p25.2	2008-01-25			ENSG00000134326	ENSG00000134326	2.7.4.14		27015	protein-coding gene	gene with protein product	"cytidylate kinase 2"	611787				17999954	Standard	NM_207315		Approved	TYKi, UMP-CMPK2	uc002qyo.4	Q5EBM0	OTTHUMG00000151629	ENST00000256722.5:c.1087C>T	chr2.hg19:g.6991720G>A	ENSP00000256722:p.Pro363Ser	80.0	0.0		137.0	44.0	NM_001256477	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Missense_Mutation	SNP	ENST00000256722.5	hg19	CCDS42648.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.494398	0.64186	0.0	1.19E-4	ENSG00000134326	ENST00000256722;ENST00000404168	T;T	0.39787	1.06;1.06	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.66056	0.2751	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68739	-0.5329	10	0.72032	D	0.01	-13.7264	19.1591	0.93524	0.0:0.0:1.0:0.0	.	363	Q5EBM0	CMPK2_HUMAN	S	363	ENSP00000256722:P363S;ENSP00000384915:P363S	ENSP00000256722:P363S	P	-	1	0	CMPK2	6909171	1.000000	0.71417	0.998000	0.56505	0.038000	0.13279	9.525000	0.98039	2.596000	0.87737	0.561000	0.74099	CCA	.	.		0.617	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315		A	6991720	G	A	6991720	3	1	16	1	0	0	0	0	1	0	0	0	3583	1203	42	3	270	3	CMPK2	2	6991720	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10		6991720	236207653	7	1392										
ASB3	100302652	hgsc.bcm.edu	37	chr2	53977937	53977937	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	tacctaaaaacaatggtgtcGtttcttctaaagtagttgca	7	7	2	0	rs540542893		TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr2:53977937G>A	ENST00000263634.3	-	3	472	c.338C>T	c.(337-339)aCg>aTg	p.T113M	ASB3_ENST00000406625.2_Missense_Mutation_p.T148M|GPR75-ASB3_ENST00000482829.1_5'UTR|GPR75-ASB3_ENST00000406687.1_Missense_Mutation_p.T40M|GPR75-ASB3_ENST00000352846.3_Missense_Mutation_p.T151M|ASB3_ENST00000498475.2_Intron|GPR75-ASB3_ENST00000394717.2_Missense_Mutation_p.T40M	NM_016115.4	NP_057199.1			GPR75-ASB3 readthrough																		CAATGGTGTCGTTTCTTCTAA	0.353																																					p.T151M		Atlas-SNP	.											ASB3,caecum,carcinoma,0,1	.	.	.	0			c.C452T						.						115	116	116					2																	53977937		2203	4300	6503	SO:0001583	missense	100302652	exon3			GGTGTCGTTTCTT		CCDS54361.1	2p16	2013-01-23			ENSG00000115239	ENSG00000115239			40043	other	readthrough							Standard	NM_001164165		Approved				OTTHUMG00000129279	ENST00000263634.3:c.338C>T	chr2.hg19:g.53977937G>A	ENSP00000263634:p.Thr113Met	60.0	0.0		84.0	5.0	NM_001164165		Missense_Mutation	SNP	ENST00000263634.3	hg19	CCDS1846.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.493614	0.64186	.	.	ENSG00000115239	ENST00000263634;ENST00000406625;ENST00000406687;ENST00000394717;ENST00000352846;ENST00000446049	T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13	5.54	4.65	0.58169	Ankyrin repeat-containing domain (4);	0.174333	0.49916	D	0.000140	T	0.64294	0.2585	N	0.16478	0.41	0.28771	N	0.9003909999999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.991;0.976;0.964	T	0.69128	-0.5227	9	0.31617	T	0.26	-15.9352	14.2721	0.66157	0.0:0.0:0.7299:0.2701	.	113;148;113	B4DZX6;Q2TAI4;Q9Y575	.;.;ASB3_HUMAN	M	113;148;40;40;151;113	ENSP00000263634:T113M;ENSP00000385085:T148M;ENSP00000384728:T40M;ENSP00000378206:T40M;ENSP00000313756:T151M	ENSP00000263634:T113M	T	-	2	0	ASB3	53831441	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.037000	0.57311	1.451000	0.47736	0.591000	0.81541	ACG	.	.		0.353	GPR75-ASB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251402.3			A	53977937	G	A	53977937	3	1	16	1	0	0	0	0	1	0	0	0	1024	1145	40	1	1250	1	ASB3	2	53977937	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	46986217	53977937	189221436	8	1393										
MTHFD2	10797	hgsc.bcm.edu	37	chr2	74435849	74435849	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ggaaataatcaagcgaactgGtaggtatatcccagaattgc	10	7	1	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr2:74435849G>T	ENST00000394053.2	+	4	642		c.e4+1		MTHFD2_ENST00000409804.1_Intron|MTHFD2_ENST00000264090.4_Splice_Site|MTHFD2_ENST00000394050.3_Splice_Site|MTHFD2_ENST00000409601.1_Splice_Site	NM_006636.3	NP_006627.2	P13995	MTDC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase						folic acid-containing compound biosynthetic process (GO:0009396)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate metabolic process (GO:0046653)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	magnesium ion binding (GO:0000287)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NAD+) activity (GO:0004487)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|phosphate ion binding (GO:0042301)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6					Tetrahydrofolic acid(DB00116)	AAGCGAACTGGTAGGTATATC	0.403																																					.		Atlas-SNP	.											.	MTHFD2	43	.	0			c.562+1G>T						.						205	184	191					2																	74435849		1874	4103	5977	SO:0001630	splice_region_variant	10797	exon4			GAACTGGTAGGTA	X16396	CCDS1935.2	2p13.1	2008-05-02			ENSG00000065911	ENSG00000065911			7434	protein-coding gene	gene with protein product		604887				2587219, 8218174	Standard	NR_027405		Approved		uc002skk.3	P13995	OTTHUMG00000129814	ENST00000394053.2:c.562+1G>T	chr2.hg19:g.74435849G>T		64.0	0.0		114.0	5.0	NM_006636	Q53G90|Q53GV5|Q53S36|Q7Z650	Splice_Site	SNP	ENST00000394053.2	hg19	CCDS1935.2	.	.	.	.	.	.	.	.	.	.	G	20.9	4.061533	0.76187	.	.	ENSG00000065911	ENST00000394053;ENST00000264090;ENST00000394050;ENST00000409601	.	.	.	4.4	4.4	0.53042	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3381	0.74273	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MTHFD2	74289357	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.010000	0.93611	2.409000	0.81822	0.650000	0.86243	.	.	.		0.403	MTHFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252045.2		Intron	T	74435849	G	T	74435849	5	4	16	1	0	0	0	0	0	0	1	0	9938	1275	44	3	577	3	MTHFD2	2	74435849	Splice_Site	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	20457912	74435849	168763524	9	1394										
ATOH8	84913	hgsc.bcm.edu	37	chr2	85981810	85981810	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	cccgcgcgccccgcgccgtcAgcacccccagcaccgccagc	10	25	1	0			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr2:85981810A>G	ENST00000306279.3	+	1	794	c.498A>G	c.(496-498)tcA>tcG	p.S166S	ATOH8_ENST00000463422.1_3'UTR	NM_032827.6	NP_116216.2	Q96SQ7	ATOH8_HUMAN	atonal homolog 8 (Drosophila)	166	Pro-rich.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(1)|lung(2)	5						ccgcgccgTCAGCACCCCCAG	0.706																																					p.S166S		Atlas-SNP	.											.	ATOH8	15	.	0			c.A498G						.						8	10	10					2																	85981810		2020	4087	6107	SO:0001819	synonymous_variant	84913	exon1			GCCGTCAGCACCC	AK074681	CCDS1985.1	2p11.2	2013-05-21			ENSG00000168874	ENSG00000168874		"Basic helix-loop-helix proteins"	24126	protein-coding gene	gene with protein product	"basic helix loop helix transcription factor 6"					12419857	Standard	NM_032827		Approved	HATH6, FLJ14708, bHLHa21	uc002sqn.3	Q96SQ7	OTTHUMG00000130178	ENST00000306279.3:c.498A>G	chr2.hg19:g.85981810A>G		143.0	0.0		124.0	38.0	NM_032827	Q504S2|Q659B0	Silent	SNP	ENST00000306279.3	hg19	CCDS1985.1																																																																																			.	.		0.706	ATOH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252496.1	NM_032827		G	85981810	A	G	85981810	2	3	16	1	0	0	0	0	0	0	0	1	1114	175	7	2		2	ATOH8	2	85981810	Silent	SNP	A	TCGA-2Y-A9H6-01A-11D-A38X-10	11545961	85981810	157217563	10	1395										
KIAA1310	55683	hgsc.bcm.edu	37	chr2	97274706	97274708	+	In_Frame_Del	DEL	CTT	CTT	-													0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ctgcgggccacatcgcggggCttcttcttcttctcagcatc							TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr2:97274706_97274708delCTT	ENST00000431828.1	-	13	1553_1555	c.1477_1479delAAG	c.(1477-1479)aagdel	p.K493del	KANSL3_ENST00000440133.1_In_Frame_Del_p.K287del|KANSL3_ENST00000441706.2_In_Frame_Del_p.K406del|KANSL3_ENST00000599854.1_In_Frame_Del_p.K406del|KANSL3_ENST00000487070.1_5'UTR			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	493					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CATCGCGGGGCTTCTTCTTCTTC	0.601																																					p.493_494del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1478_1480del						.																																			SO:0001651	inframe_deletion	55683	exon13			.	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.1477_1479delAAG	chr2.hg19:g.97274715_97274717delCTT	ENSP00000396749:p.Lys493del	123.0	0.0		148.0	38.0	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	In_Frame_Del	DEL	ENST00000431828.1	hg19	CCDS46361.1																																																																																			.	.		0.601	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		-	97274708	CTT	-	97274706	7	5	16	1	0	1	0	1	0	0	0	0	8231	796	28	0	1193	0	KIAA1310	2	97274706	In_Frame_Del	DEL	CTT	TCGA-2Y-A9H6-01A-11D-A38X-10	11292896	97274706	145924667	11	1396										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228881378	228881378	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ttcttttttagaatctaaagGgctgtggtttgtaagagaag	11	3	2	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr2:228881378G>T	ENST00000392056.3	-	7	4238	c.4192C>A	c.(4192-4194)Cct>Act	p.P1398T	SPHKAP_ENST00000344657.5_Missense_Mutation_p.P1398T	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1398						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GAATCTAAAGGGCTGTGGTTT	0.458																																					p.P1398T		Atlas-SNP	.											.	SPHKAP	750	.	0			c.C4192A						.						90	96	94					2																	228881378		2203	4300	6503	SO:0001583	missense	80309	exon7			CTAAAGGGCTGTG		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4192C>A	chr2.hg19:g.228881378G>T	ENSP00000375909:p.Pro1398Thr	76.0	0.0		100.0	29.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	hg19	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	G	3.048	-0.196108	0.06259	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.11385	2.78;2.78	5.52	-0.811	0.10857	.	1.268580	0.05103	N	0.487452	T	0.06142	0.0159	N	0.14661	0.345	0.09310	N	1	B;B;B	0.15473	0.003;0.013;0.013	B;B;B	0.17979	0.005;0.006;0.02	T	0.42189	-0.9466	10	0.14252	T	0.57	.	6.0883	0.19980	0.0:0.2987:0.3239:0.3773	.	429;1398;1398	B3KR30;Q2M3C7;Q2M3C7-2	.;SPKAP_HUMAN;.	T	1398	ENSP00000375909:P1398T;ENSP00000339886:P1398T	ENSP00000339886:P1398T	P	-	1	0	SPHKAP	228589622	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.393000	0.07305	-0.117000	0.11872	-0.262000	0.10625	CCT	.	.		0.458	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228881378	G	T	228881378	3	4	16	1	0	0	0	0	1	0	0	0	15063	1232	43	3	934	3	SPHKAP	2	228881378	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	131606672	228881378	14317995	12	1397										
CCR4	1233	hgsc.bcm.edu	37	chr3	32995552	32995552	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	caacattctcggattggtgaTccccttagggatcatgctgt	10	10	2	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr3:32995552T>A	ENST00000330953.5	+	2	806	c.638T>A	c.(637-639)aTc>aAc	p.I213N		NM_005508.4	NP_005499.1	P51679	CCR4_HUMAN	chemokine (C-C motif) receptor 4	213					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuron migration (GO:0001764)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of positive chemotaxis (GO:0050927)|response to antibiotic (GO:0046677)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)|tolerance induction (GO:0002507)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			NS(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)|stomach(1)	16						GGATTGGTGATCCCCTTAGGG	0.468																																					p.I213N		Atlas-SNP	.											.	CCR4	36	.	0			c.T638A						.						146	130	135					3																	32995552		2203	4300	6503	SO:0001583	missense	1233	exon2			TGGTGATCCCCTT	X85740	CCDS2656.1	3p24-p21.3	2012-08-08			ENSG00000183813	ENSG00000183813		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1605	protein-coding gene	gene with protein product		604836				7642634, 8884276	Standard	NM_005508		Approved	CC-CKR-4, CMKBR4, CKR4, k5-5, ChemR13, CD194	uc003cfg.1	P51679	OTTHUMG00000130752	ENST00000330953.5:c.638T>A	chr3.hg19:g.32995552T>A	ENSP00000332659:p.Ile213Asn	118.0	0.0		187.0	102.0	NM_005508	Q9ULY6|Q9ULY7	Missense_Mutation	SNP	ENST00000330953.5	hg19	CCDS2656.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.632813	0.47049	.	.	ENSG00000183813	ENST00000330953	T	0.44083	0.93	5.95	5.95	0.96441	GPCR, rhodopsin-like superfamily (1);	0.348334	0.24745	N	0.035948	T	0.67287	0.2877	M	0.90309	3.105	0.21416	N	0.999693	D	0.56287	0.975	P	0.57057	0.812	T	0.67753	-0.5589	10	0.87932	D	0	.	16.0852	0.81042	0.0:0.0:0.0:1.0	.	213	P51679	CCR4_HUMAN	N	213	ENSP00000332659:I213N	ENSP00000332659:I213N	I	+	2	0	CCR4	32970556	0.991000	0.36638	0.009000	0.14445	0.079000	0.17450	8.040000	0.89188	2.279000	0.76181	0.533000	0.62120	ATC	.	.		0.468	CCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253252.2			A	32995552	T	A	32995552	3	1	16	1	0	0	0	0	1	0	0	0	2945	1435	50	4	640	4	CCR4	3	32995552	Missense_Mutation	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10		32995552	165026878	13	1398										
BAP1	51533	hgsc.bcm.edu	37	chr3	52442001	52442005	+	5'Flank	DEL	CTTCA	CTTCA	-													0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ctgaaacccttggtgaagtcCttcatgcgactcagggtggg							TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	CTTCA	CTTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr3:52442001_52442005delCTTCA	ENST00000327906.3	+	0	0				BAP1_ENST00000296288.5_Frame_Shift_Del_p.MK115fs|BAP1_ENST00000460680.1_Frame_Shift_Del_p.MK115fs	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		TGGTGAAGTCCTTCATGCGACTCAG	0.576																																					p.115_117del		Atlas-Indel,Pindel	.											.	BAP1	371	.	0			c.345_349del						.																																			SO:0001631	upstream_gene_variant	8314	exon5			.	AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"Zinc fingers, PHD-type"	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		chr3.hg19:g.52442001_52442005delCTTCA	Exception_encountered	271.0	0.0		151.0	67.0	NM_004656	K4DI82	Frame_Shift_Del	DEL	ENST00000327906.3	hg19	CCDS2854.1																																																																																			.	.		0.576	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1	NM_016483		-	52442005	CTTCA	-	52442001	6	5	16	0	1	1	0	1	0	0	0	0	1311	680	24	0		0	BAP1	3	52442001	5'Flank	DEL	CTTCA	TCGA-2Y-A9H6-01A-11D-A38X-10	19446449	52442001	145580429	14	1399										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57496652	57496652	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	gtgatccagccattcctgctGaataggtactaaaggactac	9	10	0	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr3:57496652G>A	ENST00000351747.2	-	5	514	c.334C>T	c.(334-336)Cag>Tag	p.Q112*	DNAH12_ENST00000311202.6_Nonsense_Mutation_p.Q112*|DNAH12_ENST00000389536.4_Nonsense_Mutation_p.Q112*|RNU6-1181P_ENST00000384191.1_RNA	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	112	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						CATTCCTGCTGAATAGGTACT	0.348																																					p.Q112X		Atlas-SNP	.											.	DNAH12	182	.	0			c.C334T						.						100	95	97					3																	57496652		2203	4300	6503	SO:0001587	stop_gained	201625	exon5			CCTGCTGAATAGG	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.334C>T	chr3.hg19:g.57496652G>A	ENSP00000295937:p.Gln112*	84.0	0.0		75.0	4.0	NM_198564	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Nonsense_Mutation	SNP	ENST00000351747.2	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.600504	0.96614	.	.	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536;ENST00000311202	.	.	.	4.95	4.02	0.46733	.	0.184221	0.35466	N	0.003187	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	14.0533	0.64751	0.0:0.0:0.8486:0.1514	.	.	.	.	X	112	.	ENSP00000312554:Q112X	Q	-	1	0	DNAH12	57471692	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.003000	0.76310	2.293000	0.77203	0.563000	0.77884	CAG	.	.		0.348	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		A	57496652	G	A	57496652	4	1	16	1	0	0	0	0	0	1	0	0	4602	1299	45	3	9207	3	DNAH12	3	57496652	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	5054651	57496652	140525778	15	1400										
YEATS2	55689	hgsc.bcm.edu	37	chr3	183446490	183446490	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ttctctaggtatatacctccGgataagagggaagaaaatga	10	6	1	3			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr3:183446490G>A	ENST00000305135.5	+	7	858	c.663G>A	c.(661-663)ccG>ccA	p.P221P		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	221	YEATS. {ECO:0000255|PROSITE- ProRule:PRU00376}.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ATATACCTCCGGATAAGAGGG	0.358																																					p.P221P		Atlas-SNP	.											.	YEATS2	111	.	0			c.G663A						.						92	89	90					3																	183446490		1812	4084	5896	SO:0001819	synonymous_variant	55689	exon7			ACCTCCGGATAAG	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.663G>A	chr3.hg19:g.183446490G>A		90.0	0.0		116.0	36.0	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Silent	SNP	ENST00000305135.5	hg19	CCDS43175.1																																																																																			.	.		0.358	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023		A	183446490	G	A	183446490	2	1	16	1	0	0	0	0	0	0	0	1	17487	1103	39	1		1	YEATS2	3	183446490	Silent	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	125949838	183446490	14575940	16	1401										
MASP1	5648	hgsc.bcm.edu	37	chr3	186980462	186980462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	gagtctgctctgtgtctgtgGtctccctgccacagaaggtt	12	11	4	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr3:186980462G>A	ENST00000337774.5	-	3	673	c.284C>T	c.(283-285)aCc>aTc	p.T95I	MASP1_ENST00000296280.6_Missense_Mutation_p.T95I|MASP1_ENST00000495249.1_Intron|MASP1_ENST00000392470.2_Missense_Mutation_p.T69I|MASP1_ENST00000392472.2_5'UTR|MASP1_ENST00000169293.6_Missense_Mutation_p.T95I	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	95	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.|Homodimerization. {ECO:0000250}.|Interaction with FCN2.|Interaction with MBL2.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		TGTGTCTGTGGTCTCCCTGCC	0.542																																					p.T95I		Atlas-SNP	.											.	MASP1	240	.	0			c.C284T						.						71	67	68					3																	186980462		2203	4300	6503	SO:0001583	missense	5648	exon3			TCTGTGGTCTCCC	D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"Serine peptidases / Serine peptidases"	6901	protein-coding gene	gene with protein product		600521	"mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.284C>T	chr3.hg19:g.186980462G>A	ENSP00000336792:p.Thr95Ile	134.0	0.0		311.0	20.0	NM_139125	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Missense_Mutation	SNP	ENST00000337774.5	hg19	CCDS33907.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.823962	0.50739	.	.	ENSG00000127241	ENST00000337774;ENST00000296280;ENST00000169293;ENST00000392470;ENST00000392475	T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64	5.63	4.75	0.60458	CUB (5);	0.308262	0.38164	N	0.001783	T	0.17323	0.0416	N	0.12527	0.23	0.39073	D	0.960758	B;B;B;P	0.34562	0.052;0.023;0.434;0.457	B;B;B;B	0.32465	0.066;0.014;0.127;0.146	T	0.11743	-1.0575	10	0.40728	T	0.16	.	11.016	0.47689	0.0:0.1399:0.7146:0.1454	.	69;95;95;95	F8W876;P48740-3;P48740-2;P48740	.;.;.;MASP1_HUMAN	I	95;95;95;69;102	ENSP00000336792:T95I;ENSP00000296280:T95I;ENSP00000169293:T95I;ENSP00000376262:T69I;ENSP00000376267:T102I	ENSP00000169293:T95I	T	-	2	0	MASP1	188463156	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.326000	0.52037	1.497000	0.48584	0.655000	0.94253	ACC	.	.		0.542	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879		A	186980462	G	A	186980462	3	1	16	1	0	0	0	0	1	0	0	0	9331	1261	44	3	2816	3	MASP1	3	186980462	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	3533972	186980462	11041968	17	1402										
CORIN	10699	hgsc.bcm.edu	37	chr4	47685816	47685816	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	acacaaggctgtaattaaggCacttgcctgtgtgacagtga	11	8	0	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr4:47685816C>A	ENST00000273857.4	-	7	952	c.953G>T	c.(952-954)tGc>tTc	p.C318F	CORIN_ENST00000505909.1_Missense_Mutation_p.C318F|CORIN_ENST00000502252.1_Missense_Mutation_p.C251F|CORIN_ENST00000504584.1_Missense_Mutation_p.C318F|CORIN_ENST00000508498.1_Missense_Mutation_p.C179F	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	318	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						GTAATTAAGGCACTTGCCTGT	0.428																																					p.C318F		Atlas-SNP	.											.	CORIN	154	.	0			c.G953T						.						126	117	120					4																	47685816		2203	4300	6503	SO:0001583	missense	10699	exon7			TTAAGGCACTTGC	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"Serine peptidases / Transmembrane"	19012	protein-coding gene	gene with protein product		605236	"corin, serine protease"			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.953G>T	chr4.hg19:g.47685816C>A	ENSP00000273857:p.Cys318Phe	31.0	0.0		49.0	21.0	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	hg19	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692392	0.88735	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252;ENST00000505909;ENST00000504584	D;D;D;D;D	0.99919	-8.0;-8.0;-8.0;-8.0;-8.0	5.83	5.83	0.93111	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99947	0.9977	H	0.96048	3.76	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;1.0	D	0.96309	0.9227	10	0.87932	D	0	.	20.1133	0.97917	0.0:1.0:0.0:0.0	.	318;318;251;179;318	B7Z4R1;B4E2W9;B4E1Y7;B4DZA3;Q9Y5Q5	.;.;.;.;CORIN_HUMAN	F	318;179;251;318;318	ENSP00000273857:C318F;ENSP00000425597:C179F;ENSP00000424212:C251F;ENSP00000425401:C318F;ENSP00000423216:C318F	ENSP00000273857:C318F	C	-	2	0	CORIN	47380573	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.163000	0.77524	2.762000	0.94881	0.591000	0.81541	TGC	.	.		0.428	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2			A	47685816	C	A	47685816	3	1	16	1	0	0	0	0	1	0	0	0	3754	710	25	3	2239	3	CORIN	4	47685816	Missense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10		47685816	143468460	18	1403										
TIFA	92610	hgsc.bcm.edu	37	chr4	113199372	113199372	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	agctgcagagaaaactgaacTcgggaaacctgtttgtcctg	11	9	0	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr4:113199372T>A	ENST00000361717.3	-	2	482	c.201A>T	c.(199-201)cgA>cgT	p.R67R	TIFA_ENST00000500655.2_Silent_p.R67R	NM_052864.2	NP_443096.1	Q96CG3	TIFA_HUMAN	TRAF-interacting protein with forkhead-associated domain	67	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.				I-kappaB kinase/NF-kappaB signaling (GO:0007249)					breast(2)|endometrium(1)|large_intestine(1)|lung(1)|skin(1)	6		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00172)		AAAACTGAACTCGGGAAACCT	0.378																																					p.R67R		Atlas-SNP	.											.	TIFA	15	.	0			c.A201T						.						66	76	73					4																	113199372		2190	4296	6486	SO:0001819	synonymous_variant	92610	exon2			CTGAACTCGGGAA	BC008294	CCDS34051.1	4q25	2008-03-17				ENSG00000145365			19075	protein-coding gene	gene with protein product	"TRAF2 binding protein", "TRAF6 binding protein"	609028				1179819	Standard	NM_052864		Approved	MGC20791, T2BP, T6BP, TIFAA	uc003ial.3	Q96CG3		ENST00000361717.3:c.201A>T	chr4.hg19:g.113199372T>A		47.0	0.0		90.0	40.0	NM_052864		Silent	SNP	ENST00000361717.3	hg19	CCDS34051.1																																																																																			.	.		0.378	TIFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363647.2	NM_052864		A	113199372	T	A	113199372	2	1	16	1	0	0	0	0	0	0	0	1	15909	1538	54	4		4	TIFA	4	113199372	Silent	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10	65513556	113199372	77954904	19	1404										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155156796	155156796	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	agatgagtatcagaaacactAaaaaggagaccaccaggctg	10	8	1	4			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr4:155156796A>G	ENST00000357232.4	-	25	7642	c.7643T>C	c.(7642-7644)tTa>tCa	p.L2548S		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2548					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CAGAAACACTAAAAAGGAGAC	0.378																																					p.L2548S		Atlas-SNP	.											.	DCHS2	594	.	0			c.T7643C						.						58	60	60					4																	155156796		2202	4300	6502	SO:0001583	missense	54798	exon25			AACACTAAAAAGG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.7643T>C	chr4.hg19:g.155156796A>G	ENSP00000349768:p.Leu2548Ser	67.0	0.0		186.0	64.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	A	9.614	1.132078	0.21041	.	.	ENSG00000197410	ENST00000357232	T	0.58797	0.31	5.53	5.53	0.82687	.	0.652243	0.12944	N	0.426388	T	0.54532	0.1864	L	0.51422	1.61	0.80722	D	1	P	0.38922	0.651	B	0.35240	0.198	T	0.58989	-0.7538	10	0.72032	D	0.01	.	15.6563	0.77136	1.0:0.0:0.0:0.0	.	2548	Q6V1P9	PCD23_HUMAN	S	2548	ENSP00000349768:L2548S	ENSP00000349768:L2548S	L	-	2	0	DCHS2	155376246	0.013000	0.17824	0.144000	0.22314	0.325000	0.28411	2.114000	0.41911	2.096000	0.63516	0.383000	0.25322	TTA	.	.		0.378	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155156796	A	G	155156796	3	3	16	1	0	0	0	0	1	0	0	0	4290	372	13	2	1111	2	DCHS2	4	155156796	Missense_Mutation	SNP	A	TCGA-2Y-A9H6-01A-11D-A38X-10	41957424	155156796	35997480	20	1405										
PDCD6	10016	hgsc.bcm.edu	37	chr5	311465	311465	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	tcgaaagtttgacaggcaggGacgggggcagattgccttcg	16	8	0	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr5:311465G>A	ENST00000264933.4	+	5	525	c.425G>A	c.(424-426)gGa>gAa	p.G142E	PDCD6_ENST00000507528.1_Missense_Mutation_p.G140E|AHRR_ENST00000512529.1_Intron|PDCD6_ENST00000505221.1_Intron|AHRR_ENST00000316418.5_Intron|PDCD6_ENST00000511482.1_3'UTR|AHRR_ENST00000505113.1_Intron	NM_001267556.1|NM_001267558.1|NM_013232.3	NP_001254485.1|NP_001254487.1|NP_037364.1	O75340	PDCD6_HUMAN	programmed cell death 6	142	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)			breast(2)|endometrium(1)|large_intestine(4)|lung(1)	8			Epithelial(17;0.00193)|OV - Ovarian serous cystadenocarcinoma(19;0.00489)|all cancers(22;0.00511)|Lung(60;0.113)			GACAGGCAGGGACGGGGGCAG	0.577																																					p.G142E		Atlas-SNP	.											.	PDCD6	24	.	0			c.G425A						.						104	86	92					5																	311465		2203	4299	6502	SO:0001583	missense	10016	exon5			GGCAGGGACGGGG	AF035606	CCDS3854.1, CCDS58940.1, CCDS58941.1, CCDS75222.1, CCDS75223.1	5p15.33	2013-01-10			ENSG00000249915	ENSG00000249915		"EF-hand domain containing"	8765	protein-coding gene	gene with protein product	"apoptosis-linked gene-2"	601057				8560270	Standard	NM_013232		Approved	ALG-2, PEF1B	uc003jat.1	O75340	OTTHUMG00000090283	ENST00000264933.4:c.425G>A	chr5.hg19:g.311465G>A	ENSP00000264933:p.Gly142Glu	125.0	0.0		102.0	32.0	NM_013232	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Missense_Mutation	SNP	ENST00000264933.4	hg19	CCDS3854.1	.	.	.	.	.	.	.	.	.	.	g	14.07	2.426116	0.43020	.	.	ENSG00000249915	ENST00000264933;ENST00000507528;ENST00000507473	T;T;T	0.80909	-0.85;-0.85;-1.43	5.83	5.83	0.93111	EF-hand-like domain (1);	.	.	.	.	D	0.85885	0.5801	M	0.89904	3.07	0.80722	D	1	B;B	0.31040	0.305;0.176	B;B	0.35510	0.145;0.204	D	0.84821	0.0796	9	0.42905	T	0.14	.	17.6162	0.88068	0.0:0.0:1.0:0.0	.	140;142	Q2YDC2;O75340	.;PDCD6_HUMAN	E	142;140;55	ENSP00000264933:G142E;ENSP00000423815:G140E;ENSP00000425370:G55E	ENSP00000264933:G142E	G	+	2	0	PDCD6	364465	1.000000	0.71417	0.980000	0.43619	0.255000	0.26057	7.489000	0.81451	2.763000	0.94921	0.655000	0.94253	GGA	.	.		0.577	PDCD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206609.2	NM_013232		A	311465	G	A	311465	3	1	16	1	0	0	0	0	1	0	0	0	11632	1174	41	3	443	3	PDCD6	5	311465	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10		311465	180603795	21	1406										
FBXL7	23194	hgsc.bcm.edu	37	chr5	15936876	15936876	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ccaagctggagtcccgcctgCggtacctgagcatcgcgcac	12	16	0	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr5:15936876C>A	ENST00000504595.1	+	4	1538	c.1057C>A	c.(1057-1059)Cgg>Agg	p.R353R	FBXL7_ENST00000329673.7_Silent_p.R341R|MIR887_ENST00000401258.1_RNA|FBXL7_ENST00000510662.1_Silent_p.R306R	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	353					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						GTCCCGCCTGCGGTACCTGAG	0.662																																					p.R353R		Atlas-SNP	.											FBXL7,colon,carcinoma,0,1	FBXL7	138	.	0			c.C1057A						.						26	29	28					5																	15936876		2179	4269	6448	SO:0001819	synonymous_variant	23194	exon4			CGCCTGCGGTACC	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.1057C>A	chr5.hg19:g.15936876C>A		79.0	0.0		77.0	18.0	NM_012304	B9EGF1|D6RDY7|O94926	Silent	SNP	ENST00000504595.1	hg19	CCDS54833.1																																																																																			.	.		0.662	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		A	15936876	C	A	15936876	2	1	16	1	0	0	0	0	0	0	0	1	5732	759	27	1		1	FBXL7	5	15936876	Silent	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	15625411	15936876	164978384	22	1407										
RASA1	5921	hgsc.bcm.edu	37	chr5	86672234	86672234	+	Frame_Shift_Del	DEL	G	G	-													0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	tatgcgctgccagttgagccGattacagaaagggcatgcca							TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr5:86672234delG	ENST00000274376.6	+	16	2600	c.2036delG	c.(2035-2037)cgafs	p.R679fs	CTC-428H11.2_ENST00000607486.1_RNA|RASA1_ENST00000456692.2_Frame_Shift_Del_p.R502fs|RASA1_ENST00000506290.1_Frame_Shift_Del_p.R513fs|RASA1_ENST00000512763.1_Frame_Shift_Del_p.R512fs	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	679					blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		CAGTTGAGCCGATTACAGAAA	0.418																																					p.R679fs		Atlas-Indel,Pindel	.											.	RASA1	213	.	0			c.2035delC						.						90	86	87					5																	86672234		2203	4300	6503	SO:0001589	frameshift_variant	5921	exon16			.		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.2036delG	chr5.hg19:g.86672234delG	ENSP00000274376:p.Arg679fs	59.0	0.0		148.0	52.0	NM_002890	B2R6W3|Q9UDI1	Frame_Shift_Del	DEL	ENST00000274376.6	hg19	CCDS34200.1																																																																																			.	.		0.418	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		-	86672234	G	-	86672234	7	5	16	1	0	1	0	1	0	0	0	0	13075	1058	37	0	2110	0	RASA1	5	86672234	Frame_Shift_Del	DEL	G	TCGA-2Y-A9H6-01A-11D-A38X-10	70735358	86672234	94243026	23	1408										
CFB	629	hgsc.bcm.edu	37	chr6	31914168	31914168	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	aggtgtgaccaccactccatGgtctttggcccggccccagg	12	15	1	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr6:31914168G>T	ENST00000425368.2	+	2	596	c.83G>T	c.(82-84)tGg>tTg	p.W28L	CFB_ENST00000556679.1_Missense_Mutation_p.W530L|CFB_ENST00000456570.1_Missense_Mutation_p.W530L|CFB_ENST00000477310.1_Intron	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	28			W -> Q (in allele FA; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:2249879}.|W -> R (in allele S). {ECO:0000269|PubMed:2249879, ECO:0000269|PubMed:8181962, ECO:0000269|PubMed:8225386, ECO:0000269|PubMed:8247029}.		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						ACCACTCCATGGTCTTTGGCC	0.602																																					p.W28L		Atlas-SNP	.											.	CFB	33	.	0			c.G83T						.						76	77	77					6																	31914168		1511	2709	4220	SO:0001583	missense	629	exon2			CTCCATGGTCTTT	L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"Complement system"	1037	protein-coding gene	gene with protein product		138470	"B-factor, properdin"	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.83G>T	chr6.hg19:g.31914168G>T	ENSP00000416561:p.Trp28Leu	115.0	0.0		148.0	56.0	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	hg19	CCDS4729.1	.	.	.	.	.	.	.	.	.	.	G	0.384	-0.927020	0.02377	.	.	ENSG00000243649;ENSG00000243649;ENSG00000243649;ENSG00000244255	ENST00000556679;ENST00000475617;ENST00000425368;ENST00000456570	T;T;T;T	0.79749	-1.3;2.62;-1.21;-1.3	5.31	-1.91	0.07641	.	2.179520	0.02368	N	0.077582	T	0.31857	0.0810	N	0.08118	0	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.18429	-1.0337	10	0.16420	T	0.52	-0.0381	0.0697	0.00021	0.3185:0.1961:0.1662:0.3192	.	28;530;28;28	B4E1Z1;B4E1Z4;P00751;P00751-2	.;.;CFAB_HUMAN;.	L	530;28;28;530	ENSP00000451848:W530L;ENSP00000420090:W28L;ENSP00000416561:W28L;ENSP00000410815:W530L	ENSP00000416561:W28L	W	+	2	0	CFB;XXbac-BPG116M5.17	32022147	0.055000	0.20627	0.000000	0.03702	0.085000	0.17905	0.782000	0.26788	0.018000	0.15052	-0.541000	0.04245	TGG	.	.		0.602	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		T	31914168	G	T	31914168	3	4	16	1	0	0	0	0	1	0	0	0	3280	1357	47	3	89	3	CFB	6	31914168	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10		31914168	139200899	24	1409										
KIAA0895	23366	hgsc.bcm.edu	37	chr7	36373513	36373513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	cttggcccgtacacaataatCccatcttgtattggggtcct	8	12	1	0			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr7:36373513C>T	ENST00000297063.6	-	5	1308	c.1258G>A	c.(1258-1260)Gat>Aat	p.D420N	KIAA0895_ENST00000440378.1_Missense_Mutation_p.D417N|KIAA0895_ENST00000317020.6_Missense_Mutation_p.D369N|KIAA0895_ENST00000338533.5_Missense_Mutation_p.D407N|KIAA0895_ENST00000453212.1_Missense_Mutation_p.D175N|KIAA0895_ENST00000436884.1_Missense_Mutation_p.D317N|KIAA0895_ENST00000480192.1_5'UTR	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	420										breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						ACACAATAATCCCATCTTGTA	0.448																																					p.D420N		Atlas-SNP	.											.	KIAA0895	89	.	0			c.G1258A						.						94	93	93					7																	36373513		1865	4088	5953	SO:0001583	missense	23366	exon5			AATAATCCCATCT	BC028678	CCDS43570.1, CCDS47573.1, CCDS56482.1, CCDS56483.1, CCDS56484.1, CCDS75583.1	7p14.2	2008-11-27			ENSG00000164542	ENSG00000164542			22206	protein-coding gene	gene with protein product							Standard	NM_015314		Approved		uc003tfd.2	Q8NCT3	OTTHUMG00000154939	ENST00000297063.6:c.1258G>A	chr7.hg19:g.36373513C>T	ENSP00000297063:p.Asp420Asn	101.0	0.0		162.0	54.0	NM_001100425	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Missense_Mutation	SNP	ENST00000297063.6	hg19	CCDS43570.1	.	.	.	.	.	.	.	.	.	.	C	35	5.435945	0.96168	.	.	ENSG00000164542	ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000436884;ENST00000453212	.	.	.	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.77458	0.4133	M	0.62723	1.935	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.999;0.998;0.998	T	0.76421	-0.2965	9	0.41790	T	0.15	-18.4965	18.7786	0.91922	0.0:1.0:0.0:0.0	.	417;317;420;407;369	B7ZLT4;B4DF35;Q8NCT3;Q8NCT3-2;Q8NCT3-3	.;.;K0895_HUMAN;.;.	N	420;407;369;417;317;175	.	ENSP00000297063:D420N	D	-	1	0	KIAA0895	36340038	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.357000	0.79456	2.515000	0.84797	0.655000	0.94253	GAT	.	.		0.448	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314		T	36373513	C	T	36373513	3	4	16	1	0	0	0	0	1	0	0	0	8206	855	30	3	316	3	KIAA0895	7	36373513	Missense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10		36373513	122765150	25	1410										
LRGUK	136332	hgsc.bcm.edu	37	chr7	133821880	133821880	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	gtctacctcaatctaactttAtcagtgagtatgacaaaatc	5	9	4	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr7:133821880A>G	ENST00000285928.2	+	2	471	c.402A>G	c.(400-402)ttA>ttG	p.L134L	LRGUK_ENST00000473068.1_3'UTR	NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	134						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						ATCTAACTTTATCAGTGAGTA	0.473																																					p.L134L		Atlas-SNP	.											.	LRGUK	113	.	0			c.A402G						.						69	63	65					7																	133821880		2203	4300	6503	SO:0001819	synonymous_variant	136332	exon2			AACTTTATCAGTG	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.402A>G	chr7.hg19:g.133821880A>G		42.0	0.0		74.0	21.0	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	hg19	CCDS5830.1																																																																																			.	.		0.473	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		G	133821880	A	G	133821880	2	3	16	1	0	0	0	0	0	0	0	1	8952	446	16	2		2	LRGUK	7	133821880	Silent	SNP	A	TCGA-2Y-A9H6-01A-11D-A38X-10	97448367	133821880	25316783	26	1411										
TAS2R41	259287	hgsc.bcm.edu	37	chr7	143175617	143175617	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ctcagagaatgcagcacaacGggcacagcctgcaggacccc	11	15	1	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr7:143175617G>T	ENST00000408916.1	+	1	652	c.652G>T	c.(652-654)Ggg>Tgg	p.G218W	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	218					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.G218R(1)		endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					GCAGCACAACGGGCACAGCCT	0.478																																					p.G218W		Atlas-SNP	.											TAS2R41,caecum,carcinoma,0,1	TAS2R41	43	.	1	Substitution - Missense(1)	large_intestine(1)	c.G652T						.						70	77	75					7																	143175617		2047	4195	6242	SO:0001583	missense	259287	exon1			CACAACGGGCACA	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.652G>T	chr7.hg19:g.143175617G>T	ENSP00000386201:p.Gly218Trp	50.0	0.0		120.0	5.0	NM_176883	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Missense_Mutation	SNP	ENST00000408916.1	hg19	CCDS43663.1	.	.	.	.	.	.	.	.	.	.	G	8.203	0.798688	0.16397	.	.	ENSG00000221855	ENST00000408916	T	0.00768	5.72	6.0	-2.08	0.07254	.	1.076560	0.07393	U	0.889477	T	0.01454	0.0047	M	0.78344	2.41	0.09310	N	1	B	0.30526	0.283	B	0.29267	0.1	T	0.29427	-1.0012	10	0.72032	D	0.01	.	8.3065	0.32045	0.3903:0.0:0.5148:0.0949	.	218	P59536	T2R41_HUMAN	W	218	ENSP00000386201:G218W	ENSP00000386201:G218W	G	+	1	0	TAS2R41	142885739	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.176000	0.09811	-1.107000	0.03004	-1.814000	0.00607	GGG	.	.		0.478	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1			T	143175617	G	T	143175617	3	4	16	1	0	0	0	0	1	0	0	0	15594	1116	39	1	654	1	TAS2R41	7	143175617	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	9353737	143175617	15963046	27	1412										
C8orf45	157777	hgsc.bcm.edu	37	chr8	67789682	67789682	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	tatacatctcagagattttaTatgatgcaaggaattgtgat	8	4	1	3			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr8:67789682T>C	ENST00000422365.2	+	5	555	c.384T>C	c.(382-384)taT>taC	p.Y128Y	MCMDC2_ENST00000313616.5_Silent_p.Y128Y|MCMDC2_ENST00000492775.1_Silent_p.Y128Y|MCMDC2_ENST00000541540.1_Silent_p.Y65Y|MCMDC2_ENST00000469823.1_3'UTR|MCMDC2_ENST00000396592.3_Silent_p.Y128Y	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	128					DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						AGAGATTTTATATGATGCAAG	0.358																																					p.Y128Y		Atlas-SNP	.											.	MCMDC2	84	.	0			c.T384C						.						94	87	90					8																	67789682		2203	4300	6503	SO:0001819	synonymous_variant	157777	exon5			ATTTTATATGATG	BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460			26368	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 45"	C8orf45			Standard	NM_173518		Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068	ENST00000422365.2:c.384T>C	chr8.hg19:g.67789682T>C		114.0	0.0		131.0	35.0	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Silent	SNP	ENST00000422365.2	hg19	CCDS6197.2																																																																																			.	.		0.358	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518		C	67789682	T	C	67789682	2	2	16	1	0	0	0	0	0	0	0	1	2432	1413	49	2		2	C8orf45	8	67789682	Silent	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10		67789682	78574340	28	1413										
UBAP2	55833	hgsc.bcm.edu	37	chr9	33932569	33932569	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	cagacacttactgtgtgtgaCgtgctcgaggagagggctgc	15	9	0	3			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr9:33932569C>T	ENST00000379238.1	-	19	2283	c.2166G>A	c.(2164-2166)acG>acA	p.T722T	UBAP2_ENST00000449054.1_Silent_p.T722T|SNORD121B_ENST00000458838.1_RNA|UBAP2_ENST00000360802.1_Silent_p.T722T|UBAP2_ENST00000418786.2_Intron|UBAP2_ENST00000379239.4_Silent_p.T455T|UBAP2_ENST00000539807.1_Silent_p.T477T					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		CTGTGTGTGACGTGCTCGAGG	0.562																																					p.T722T		Atlas-SNP	.											.	UBAP2	82	.	0			c.G2166A						.						112	99	103					9																	33932569		2203	4300	6503	SO:0001819	synonymous_variant	55833	exon19			GTGTGACGTGCTC	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.2166G>A	chr9.hg19:g.33932569C>T		74.0	0.0		55.0	30.0	NM_018449		Silent	SNP	ENST00000379238.1	hg19	CCDS6547.1																																																																																			.	.		0.562	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		T	33932569	C	T	33932569	2	4	16	1	0	0	0	0	0	0	0	1	16852	523	19	1		1	UBAP2	9	33932569	Silent	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10		33932569	107280862	29	1414										
SARDH	1757	hgsc.bcm.edu	37	chr9	136595229	136595229	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	gtctggatggaaccatgctgAgtctccacacccgcgacccg	11	15	2	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr9:136595229A>C	ENST00000371872.4	-	5	1028	c.771T>G	c.(769-771)acT>acG	p.T257T	SARDH_ENST00000422262.2_Silent_p.T89T|SARDH_ENST00000298628.5_Silent_p.T257T|SARDH_ENST00000439388.1_Silent_p.T257T|SARDH_ENST00000371867.1_Silent_p.T168T	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	257					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		AACCATGCTGAGTCTCCACAC	0.582																																					p.T257T		Atlas-SNP	.											.	SARDH	112	.	0			c.T771G						.						113	100	104					9																	136595229		2203	4300	6503	SO:0001819	synonymous_variant	1757	exon5			ATGCTGAGTCTCC		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.771T>G	chr9.hg19:g.136595229A>C		102.0	0.0		76.0	6.0	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	hg19	CCDS6978.1																																																																																			.	.		0.582	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			C	136595229	A	C	136595229	2	2	16	1	0	0	0	0	0	0	0	1	13856	291	11	5		5	SARDH	9	136595229	Silent	SNP	A	TCGA-2Y-A9H6-01A-11D-A38X-10	102662660	136595229	4618202	30	1415										
OPTN	10133	hgsc.bcm.edu	37	chr10	13154620	13154620	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	tcctcagaagattcctttgtTgaaattaggatggctgtgag	11	6	1	4			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr10:13154620T>G	ENST00000378748.3	+	6	899	c.537T>G	c.(535-537)gtT>gtG	p.V179V	OPTN_ENST00000378752.3_Silent_p.V179V|OPTN_ENST00000378764.2_Silent_p.V179V|OPTN_ENST00000482140.1_3'UTR|OPTN_ENST00000378757.2_Silent_p.V179V|OPTN_ENST00000263036.5_Silent_p.V179V|OPTN_ENST00000378747.3_Silent_p.V179V	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	179	Interaction with Rab8.				cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						ATTCCTTTGTTGAAATTAGGA	0.438																																					p.V179V		Atlas-SNP	.											.	OPTN	57	.	0			c.T537G						.						105	110	109					10																	13154620		2203	4300	6503	SO:0001819	synonymous_variant	10133	exon5			CTTTGTTGAAATT	AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"glaucoma 1, open angle, E (adult-onset)"	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.537T>G	chr10.hg19:g.13154620T>G		115.0	0.0		103.0	10.0	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Silent	SNP	ENST00000378748.3	hg19	CCDS7094.1																																																																																			.	.		0.438	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980		G	13154620	T	G	13154620	2	3	16	1	0	0	0	0	0	0	0	1	10898	1799	63	5		5	OPTN	10	13154620	Silent	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10		13154620	122380127	31	1416										
EPS8L2	64787	hgsc.bcm.edu	37	chr11	720644	720644	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	acggtgcagcgcagccagacGgtcctcaaccagctgcgcta	12	15	1	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr11:720644G>C	ENST00000533256.1	+	7	750	c.375G>C	c.(373-375)acG>acC	p.T125T	EPS8L2_ENST00000530636.1_Silent_p.T125T|AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000318562.8_Silent_p.T125T|EPS8L2_ENST00000526198.1_Silent_p.T141T			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	125	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCAGCCAGACGGTCCTCAACC	0.662																																					p.T125T		Atlas-SNP	.											.	EPS8L2	42	.	0			c.G375C						.						23	22	22					11																	720644		2195	4294	6489	SO:0001819	synonymous_variant	64787	exon6			CCAGACGGTCCTC	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.375G>C	chr11.hg19:g.720644G>C		142.0	0.0		68.0	35.0	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	hg19	CCDS31328.1																																																																																			.	.		0.662	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		C	720644	G	C	720644	2	2	16	1	0	0	0	0	0	0	0	1	5198	1103	39	4		4	EPS8L2	11	720644	Silent	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10		720644	134285872	32	1417										
HIPK3	10114	hgsc.bcm.edu	37	chr11	33308510	33308510	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ctggagaaggtgactatcagTtagtacagcatgaagtctta	11	6	2	3			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr11:33308510T>A	ENST00000303296.4	+	2	855	c.550T>A	c.(550-552)Tta>Ata	p.L184I	HIPK3_ENST00000379016.3_Missense_Mutation_p.L184I|HIPK3_ENST00000456517.1_Missense_Mutation_p.L184I|HIPK3_ENST00000525975.1_Missense_Mutation_p.L184I	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	184					apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						TGACTATCAGTTAGTACAGCA	0.428																																					p.L184I		Atlas-SNP	.											.	HIPK3	92	.	0			c.T550A						.						85	78	81					11																	33308510		2202	4298	6500	SO:0001583	missense	10114	exon2			TATCAGTTAGTAC	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.550T>A	chr11.hg19:g.33308510T>A	ENSP00000304226:p.Leu184Ile	92.0	0.0		88.0	37.0	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	T	15.19	2.760749	0.49468	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.27256	1.68;1.68;1.68;1.68	5.65	4.53	0.55603	Protein kinase-like domain (1);	0.000000	0.49916	D	0.000135	T	0.27313	0.0670	M	0.62723	1.935	0.50313	D	0.999861	P;P	0.38078	0.545;0.617	B;B	0.37833	0.259;0.132	T	0.04752	-1.0929	10	0.87932	D	0	.	9.2193	0.37366	0.0:0.1568:0.0:0.8432	.	184;184	Q9H422-2;Q9H422	.;HIPK3_HUMAN	I	184	ENSP00000431710:L184I;ENSP00000304226:L184I;ENSP00000368301:L184I;ENSP00000398241:L184I	ENSP00000304226:L184I	L	+	1	2	HIPK3	33265086	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	1.858000	0.39408	0.987000	0.38709	-0.361000	0.07541	TTA	.	.		0.428	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		A	33308510	T	A	33308510	3	1	16	1	0	0	0	0	1	0	0	0	7127	1722	60	4	552	4	HIPK3	11	33308510	Missense_Mutation	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10	32587866	33308510	101698006	33	1418										
KDELC2	143888	hgsc.bcm.edu	37	chr11	108369075	108369075	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	gcgcagctgcagcagcagggCccgcgggaggcggcgcatgg	20	13	0	0			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr11:108369075C>A	ENST00000323468.5	-	1	84	c.19G>T	c.(19-21)Gcc>Tcc	p.A7S		NM_153705.4	NP_714916.3	Q7Z4H8	KDEL2_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 2	7						endoplasmic reticulum (GO:0005783)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;6.93e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;0.00016)|OV - Ovarian serous cystadenocarcinoma(223;0.132)|Colorectal(284;0.14)		AGCAGCAGGGCCCGCGGGAGG	0.816																																					p.A7S		Atlas-SNP	.											.	KDELC2	37	.	0			c.G19T						.						1	1	1					11																	108369075		449	962	1411	SO:0001583	missense	143888	exon1			GCAGGGCCCGCGG	AF533708	CCDS41711.1	11q32	2010-11-18			ENSG00000178202	ENSG00000178202			28496	protein-coding gene	gene with protein product						12975309	Standard	NM_153705		Approved	MGC33424	uc001pkj.2	Q7Z4H8	OTTHUMG00000166535	ENST00000323468.5:c.19G>T	chr11.hg19:g.108369075C>A	ENSP00000315386:p.Ala7Ser	45.0	0.0		24.0	7.0	NM_153705	Q6UWW2|Q6ZUM9|Q8N7L8|Q8NE24	Missense_Mutation	SNP	ENST00000323468.5	hg19	CCDS41711.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633310	0.47049	.	.	ENSG00000178202	ENST00000323468	T	0.17691	2.26	3.03	1.07	0.20283	.	3.165320	0.01740	N	0.029361	T	0.09423	0.0232	N	0.08118	0	0.44976	D	0.997998	B	0.12630	0.006	B	0.08055	0.003	T	0.28004	-1.0057	10	0.17832	T	0.49	-0.2676	6.3994	0.21630	0.1822:0.7108:0.0:0.107	.	7	Q7Z4H8	KDEL2_HUMAN	S	7	ENSP00000315386:A7S	ENSP00000315386:A7S	A	-	1	0	KDELC2	107874285	0.001000	0.12720	0.005000	0.12908	0.299000	0.27559	1.109000	0.31135	0.297000	0.22615	0.313000	0.20887	GCC	.	.		0.816	KDELC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390273.1	NM_153705		A	108369075	C	A	108369075	3	1	16	1	0	0	0	0	1	0	0	0	8127	739	26	3	1536	3	KDELC2	11	108369075	Missense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	75060565	108369075	26637441	34	1419										
CHD4	1108	hgsc.bcm.edu	37	chr12	6710863	6710863	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ggtgagggttcgataatcctCctctgagaacacgtggtcaa	12	9	2	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr12:6710863C>A	ENST00000357008.2	-	5	671	c.508G>T	c.(508-510)Gag>Tag	p.E170*	CHD4_ENST00000544040.1_Nonsense_Mutation_p.E163*|CHD4_ENST00000544484.1_Nonsense_Mutation_p.E167*|CHD4_ENST00000309577.6_Nonsense_Mutation_p.E170*	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	170					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						CGATAATCCTCCTCTGAGAAC	0.493																																					p.E170X	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.G508T						.						271	275	274					12																	6710863		2203	4300	6503	SO:0001587	stop_gained	1108	exon5			AATCCTCCTCTGA	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.508G>T	chr12.hg19:g.6710863C>A	ENSP00000349508:p.Glu170*	111.0	0.0		110.0	39.0	NM_001273	Q8IXZ5	Nonsense_Mutation	SNP	ENST00000357008.2	hg19	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	37	6.262264	0.97421	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464;ENST00000545942	.	.	.	5.87	5.87	0.94306	.	0.060254	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-2.4517	16.49	0.84198	0.1314:0.8686:0.0:0.0	.	.	.	.	X	167;163;170;170;144;170	.	ENSP00000312419:E170X	E	-	1	0	CHD4	6581124	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.776000	0.85560	2.774000	0.95407	0.650000	0.86243	GAG	.	.		0.493	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6710863	C	A	6710863	4	1	16	1	0	0	0	0	0	1	0	0	3329	864	30	3	5374	3	CHD4	12	6710863	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10		6710863	127141032	35	1420										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81769684	81769684	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ggtaacgcttttcaagggttGtaattctttcttccatatct	7	8	4	0			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr12:81769684G>T	ENST00000549396.1	-	10	1182	c.1022C>A	c.(1021-1023)aCa>aAa	p.T341K	PPFIA2_ENST00000548586.1_Missense_Mutation_p.T341K|PPFIA2_ENST00000333447.7_Missense_Mutation_p.T323K|RP11-315E17.1_ENST00000546936.1_RNA|PPFIA2_ENST00000550584.2_Missense_Mutation_p.T341K|PPFIA2_ENST00000443686.3_Missense_Mutation_p.T242K|PPFIA2_ENST00000552948.1_Missense_Mutation_p.T341K|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000549325.1_Missense_Mutation_p.T323K|PPFIA2_ENST00000550359.2_Missense_Mutation_p.T188K|PPFIA2_ENST00000407050.4_Missense_Mutation_p.T267K	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	341	Glu-rich.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						TTCAAGGGTTGTAATTCTTTC	0.328																																					p.T341K		Atlas-SNP	.											.	PPFIA2	207	.	0			c.C1022A						.						221	201	207					12																	81769684		1877	4139	6016	SO:0001583	missense	8499	exon9			AGGGTTGTAATTC	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.1022C>A	chr12.hg19:g.81769684G>T	ENSP00000450337:p.Thr341Lys	53.0	0.0		95.0	25.0	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	hg19	CCDS55857.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.5|21.5	4.154820|4.154820	0.78114|0.78114	.|.	.|.	ENSG00000139220|ENSG00000139220	ENST00000548790|ENST00000549396;ENST00000549325;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948	.|T;T;T;T;T;T;T	.|0.77750	.|1.22;1.22;1.22;-1.12;1.22;1.22;1.22	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	.|0.129904	.|0.52532	.|D	.|0.000067	D|D	0.83013|0.83013	0.5162|0.5162	M|M	0.87038|0.87038	2.855|2.855	0.80722|0.80722	D|D	1|1	.|P;P	.|0.41673	.|0.578;0.759	.|B;B	.|0.41332	.|0.354;0.248	D|D	0.86476|0.86476	0.1788|0.1788	5|10	.|0.62326	.|D	.|0.03	-13.4936|-13.4936	19.0352|19.0352	0.92974|0.92974	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|241;341	.|B7Z4H8;O75334	.|.;LIPA2_HUMAN	K|K	159|341;323;267;352;323;341;242;341	.|ENSP00000450337:T341K;ENSP00000450298:T323K;ENSP00000385093:T267K;ENSP00000327416:T323K;ENSP00000449338:T341K;ENSP00000388373:T242K;ENSP00000447868:T341K	.|ENSP00000327416:T323K	Q|T	-|-	1|2	0|0	PPFIA2|PPFIA2	80293815|80293815	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.986000|0.986000	0.74619|0.74619	4.506000|4.506000	0.60428|0.60428	2.567000|2.567000	0.86603|0.86603	0.650000|0.650000	0.86243|0.86243	CAA|ACA	.	.		0.328	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			T	81769684	G	T	81769684	3	4	16	1	0	0	0	0	1	0	0	0	12319	1377	48	3	2843	3	PPFIA2	12	81769684	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	75058821	81769684	52082211	36	1421										
TGM1	7051	hgsc.bcm.edu	37	chr14	24729790	24729790	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	cgttgggggaagtgtggaccCgcaggttcagattctgccca	15	10	2	1	rs369636498		TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr14:24729790C>T	ENST00000206765.6	-	4	746	c.623G>A	c.(622-624)cGg>cAg	p.R208Q	TGM1_ENST00000544573.1_Intron	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	208					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	AGTGTGGACCCGCAGGTTCAG	0.607													C|||	1	0.000199681	0	0	5008	,	,		19613	0		0	False		,,,				2504	0.001				p.R208Q		Atlas-SNP	.											.	TGM1	73	.	0			c.G623A						.	C	GLN/ARG	0,4406		0,0,2203	202	167	178		623	3.8	0.6	14		178	1,8599	1.2+/-3.3	0,1,4299	no	missense	TGM1	NM_000359.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	208/818	24729790	1,13005	2203	4300	6503	SO:0001583	missense	7051	exon4			TGGACCCGCAGGT	D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"Transglutaminases"	11777	protein-coding gene	gene with protein product	"K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"	190195	"transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.623G>A	chr14.hg19:g.24729790C>T	ENSP00000206765:p.Arg208Gln	161.0	0.0		126.0	6.0	NM_000359	B4DWR7|Q197M4	Missense_Mutation	SNP	ENST00000206765.6	hg19	CCDS9622.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.293991	0.23564	0.0	1.16E-4	ENSG00000092295	ENST00000206765	D	0.83992	-1.79	5.89	3.76	0.43208	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	0.195706	0.46442	D	0.000296	T	0.65668	0.2713	N	0.05487	-0.04	0.23440	N	0.997677	B	0.27316	0.175	B	0.16722	0.016	T	0.56854	-0.7910	10	0.33940	T	0.23	-17.2242	13.0381	0.58882	0.0:0.8426:0.0:0.1574	.	208	P22735	TGM1_HUMAN	Q	208	ENSP00000206765:R208Q	ENSP00000206765:R208Q	R	-	2	0	TGM1	23799630	0.187000	0.23238	0.643000	0.29450	0.572000	0.35998	2.043000	0.41231	1.507000	0.48752	0.563000	0.77884	CGG	.	.		0.607	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359		T	24729790	C	T	24729790	3	4	16	1	0	0	0	0	1	0	0	0	15844	652	23	1	1878	1	TGM1	14	24729790	Missense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10		24729790	82619750	37	1422										
RAD51L1	5890	hgsc.bcm.edu	37	chr14	68331792	68331802	+	Frame_Shift_Del	DEL	AACATGGGAGG	AACATGGGAGG	-													0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ttttggctacattacccaccAacatgggaggattagaagga							TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	AACATGGGAGG	AACATGGGAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr14:68331792_68331802delAACATGGGAGG	ENST00000487270.1	+	5	436_446	c.388_398delAACATGGGAGG	c.(388-399)aacatgggaggafs	p.NMGG130fs	RAD51B_ENST00000390683.3_Frame_Shift_Del_p.NMGG130fs|RAD51B_ENST00000471583.1_Frame_Shift_Del_p.NMGG130fs|RAD51B_ENST00000487861.1_Frame_Shift_Del_p.NMGG130fs|RAD51B_ENST00000488612.1_Frame_Shift_Del_p.NMGG130fs	NM_133509.3	NP_598193.2	O15315	RA51B_HUMAN	RAD51 paralog B	130					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)		HMGA2/RAD51B(11)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11						ATTACCCACCAACATGGGAGGATTAGAAGGA	0.318								Direct reversal of damage																													p.129_133del		Atlas-INDEL	.											.	RAD51B	80	.	0			c.387_397del						.																																			SO:0001589	frameshift_variant	5890	exon5			.	U84138	CCDS9789.1, CCDS9790.1	14q23-q24.2	2013-07-02	2013-07-02	2011-07-01	ENSG00000182185	ENSG00000182185			9822	protein-coding gene	gene with protein product		602948	"RAD51 (S. cerevisiae)-like 1", "RAD51-like 1 (S. cerevisiae)", "RAD51 homolog B (S. cerevisiae)"	RAD51L1		6261043, 9207106	Standard	NM_002877		Approved	REC2, hREC2, R51H2	uc001xkf.2	O15315	OTTHUMG00000157530	ENST00000487270.1:c.388_398delAACATGGGAGG	chr14.hg19:g.68331792_68331802delAACATGGGAGG	ENSP00000419471:p.Asn130fs	66.0	0.0		62.0	10.0	NM_002877	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	Frame_Shift_Del	DEL	ENST00000487270.1	hg19	CCDS9789.1																																																																																			.	.		0.318	RAD51B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349063.1			-	68331802	AACATGGGAGG	-	68331792	7	5	16	1	0	1	0	1	0	0	0	0	13004	130	5	0	402	0	RAD51L1	14	68331792	Frame_Shift_Del	DEL	AACATGGGAGG	TCGA-2Y-A9H6-01A-11D-A38X-10	43602002	68331792	39017748	38	1423										
TRPM7	54822	hgsc.bcm.edu	37	chr15	50903454	50903454	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ttcataagtgagcaatttcaTagccatggtttcatcttgtc	7	8	4	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr15:50903454T>C	ENST00000313478.7	-	17	2397	c.2116A>G	c.(2116-2118)Atg>Gtg	p.M706V	TRPM7_ENST00000560955.1_Missense_Mutation_p.M706V	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	706					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		AGCAATTTCATAGCCATGGTT	0.363																																					p.M706V		Atlas-SNP	.											.	TRPM7	145	.	0			c.A2116G						.						110	99	102					15																	50903454		1831	4087	5918	SO:0001583	missense	54822	exon17			ATTTCATAGCCAT	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.2116A>G	chr15.hg19:g.50903454T>C	ENSP00000320239:p.Met706Val	79.0	0.0		107.0	29.0	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	hg19	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.592645	0.86953	.	.	ENSG00000092439	ENST00000313478	D	0.81908	-1.55	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.88381	0.6421	M	0.84846	2.72	0.58432	D	0.999999	P	0.50943	0.94	P	0.49561	0.615	D	0.90488	0.4465	10	0.87932	D	0	-16.7725	15.6872	0.77421	0.0:0.0:0.0:1.0	.	706	Q96QT4	TRPM7_HUMAN	V	706	ENSP00000320239:M706V	ENSP00000320239:M706V	M	-	1	0	TRPM7	48690746	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.100000	0.63781	0.533000	0.62120	ATG	.	.		0.363	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		C	50903454	T	C	50903454	3	2	16	1	0	0	0	0	1	0	0	0	16606	1406	49	2	3573	2	TRPM7	15	50903454	Missense_Mutation	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10		50903454	51627938	39	1424										
LMF1	64788	hgsc.bcm.edu	37	chr16	1020930	1020930	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	tccgagtacccagtcttccgCctcctcagcgactccgcggg	10	18	2	0			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr16:1020930C>T	ENST00000262301.11	-	1	69	c.51G>A	c.(49-51)agG>agA	p.R17R	LMF1_ENST00000543238.1_5'UTR|LMF1_ENST00000568897.1_5'Flank|LMF1_ENST00000399843.2_Silent_p.R17R|LMF1_ENST00000539379.1_Silent_p.R10R	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	17					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				CAGTCTTCCGCCTCCTCAGCG	0.746																																					p.R17R		Atlas-SNP	.											.	LMF1	42	.	0			c.G51A						.						6	9	8					16																	1020930		1820	4008	5828	SO:0001819	synonymous_variant	64788	exon1			CTTCCGCCTCCTC	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"chromosome 16 open reading frame 26", "transmembrane protein 112"	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.51G>A	chr16.hg19:g.1020930C>T		141.0	0.0		122.0	32.0	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	hg19	CCDS45373.1																																																																																			.	.		0.746	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773		T	1020930	C	T	1020930	2	4	16	1	0	0	0	0	0	0	0	1	8854	738	26	3		3	LMF1	16	1020930	Silent	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10		1020930	89333823	40	1425										
MAPK8IP3	23162	hgsc.bcm.edu	37	chr16	1808157	1808157	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	tggactcgccaggggagttcTcaggtgagtatctcactctc	12	11	3	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr16:1808157T>C	ENST00000250894.4	+	9	1379	c.1222T>C	c.(1222-1224)Tca>Cca	p.S408P	MAPK8IP3_ENST00000356010.5_Missense_Mutation_p.S408P	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	408					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						AGGGGAGTTCTCAGGTGAGTA	0.567																																					p.S408P		Atlas-SNP	.											.	MAPK8IP3	164	.	0			c.T1222C						.						107	111	109					16																	1808157		2026	4170	6196	SO:0001583	missense	23162	exon9			GAGTTCTCAGGTG	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"homolog of Drosophila Sunday driver 2"	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.1222T>C	chr16.hg19:g.1808157T>C	ENSP00000250894:p.Ser408Pro	91.0	0.0		67.0	22.0	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Missense_Mutation	SNP	ENST00000250894.4	hg19	CCDS10442.2	.	.	.	.	.	.	.	.	.	.	T	16.35	3.097415	0.56075	.	.	ENSG00000138834	ENST00000250894;ENST00000356010	T;T	0.34472	1.38;1.36	5.21	5.21	0.72293	.	.	.	.	.	T	0.28101	0.0693	L	0.29908	0.895	0.23150	N	0.998211	P;B	0.35944	0.529;0.405	B;B	0.34180	0.158;0.177	T	0.22173	-1.0224	9	0.72032	D	0.01	0.7974	10.8577	0.46808	0.0:0.0:0.1579:0.8421	.	409;408	B7ZMF3;Q9UPT6	.;JIP3_HUMAN	P	408	ENSP00000250894:S408P;ENSP00000348290:S408P	ENSP00000250894:S408P	S	+	1	0	MAPK8IP3	1748158	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	6.213000	0.72194	1.985000	0.57927	0.459000	0.35465	TCA	.	.		0.567	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439		C	1808157	T	C	1808157	3	2	16	1	0	0	0	0	1	0	0	0	9295	1551	54	2	1268	2	MAPK8IP3	16	1808157	Missense_Mutation	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10	787227	1808157	88546596	41	1426										
CAMKK1	84254	hgsc.bcm.edu	37	chr17	3788636	3788636	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	accaacctctgcatctgagaTggccacgtggtgggactcga	12	12	2	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr17:3788636T>C	ENST00000348335.2	-	2	494	c.346A>G	c.(346-348)Atc>Gtc	p.I116V	CAMKK1_ENST00000381769.2_Missense_Mutation_p.I143V|CAMKK1_ENST00000158166.5_Missense_Mutation_p.I116V|CAMKK1_ENST00000381771.2_Missense_Mutation_p.I116V	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	116					synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	11				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		GCATCTGAGATGGCCACGTGG	0.637																																					p.I116V		Atlas-SNP	.											.	CAMKK1	70	.	0			c.A346G						.						14	17	16					17																	3788636		2184	4263	6447	SO:0001583	missense	84254	exon2			CTGAGATGGCCAC	AL136576	CCDS11038.1, CCDS11039.1	17p13.3	2004-02-18			ENSG00000004660	ENSG00000004660			1469	protein-coding gene	gene with protein product		611411				11230166	Standard	NM_172207		Approved	DKFZp761M0423, CAMKKA, MGC34095	uc002fwt.3	Q8N5S9	OTTHUMG00000090725	ENST00000348335.2:c.346A>G	chr17.hg19:g.3788636T>C	ENSP00000323118:p.Ile116Val	68.0	0.0		75.0	7.0	NM_032294	Q9BQH3	Missense_Mutation	SNP	ENST00000348335.2	hg19	CCDS11038.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.220470	0.58560	.	.	ENSG00000004660	ENST00000381769;ENST00000348335;ENST00000381771;ENST00000158166	T;T;T;T	0.48836	0.8;0.8;0.8;0.8	5.05	5.05	0.67936	Protein kinase-like domain (1);	0.053765	0.64402	D	0.000001	T	0.49541	0.1563	L	0.50333	1.59	0.58432	D	0.999996	P;P	0.40302	0.712;0.589	P;B	0.46718	0.525;0.222	T	0.42632	-0.9440	10	0.30078	T	0.28	-21.0111	12.7728	0.57432	0.0:0.0:0.0:1.0	.	116;116	F8W9H1;Q8N5S9	.;KKCC1_HUMAN	V	143;116;116;116	ENSP00000371188:I143V;ENSP00000323118:I116V;ENSP00000371190:I116V;ENSP00000158166:I116V	ENSP00000158166:I116V	I	-	1	0	CAMKK1	3735385	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	6.926000	0.75835	2.126000	0.65437	0.402000	0.26972	ATC	.	.		0.637	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207		C	3788636	T	C	3788636	3	2	16	1	0	0	0	0	1	0	0	0	2608	1464	51	2	1353	2	CAMKK1	17	3788636	Missense_Mutation	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10		3788636	77406574	42	1427										
USP6	9098	hgsc.bcm.edu	37	chr17	5041019	5041019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	acaggtgttgatgccaataaCcagcattgctcttaaggttc	9	9	1	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr17:5041019C>T	ENST00000574788.1	+	20	3129	c.899C>T	c.(898-900)aCc>aTc	p.T300I	USP6_ENST00000332776.4_Missense_Mutation_p.T300I|USP6_ENST00000304328.5_5'UTR|USP6_ENST00000250066.6_Missense_Mutation_p.T300I			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	300					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						ATGCCAATAACCAGCATTGCT	0.577			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																p.T300I		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C899T						.						249	218	228					17																	5041019		2203	4300	6503	SO:0001583	missense	9098	exon12			CAATAACCAGCAT	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.899C>T	chr17.hg19:g.5041019C>T	ENSP00000460380:p.Thr300Ile	33.0	0.0		42.0	13.0	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	hg19	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	C	14.69	2.611401	0.46631	.	.	ENSG00000129204	ENST00000332776;ENST00000250066	T;T	0.21191	2.02;2.02	.	.	.	Rab-GAP/TBC domain (3);	0.392224	0.33110	N	0.005270	T	0.13543	0.0328	L	0.40543	1.245	0.80722	D	1	P	0.41008	0.735	B	0.32980	0.156	T	0.04870	-1.0921	8	0.87932	D	0	.	.	.	.	.	300	P35125	UBP6_HUMAN	I	300	ENSP00000328010:T300I;ENSP00000250066:T300I	ENSP00000250066:T300I	T	+	2	0	USP6	4981743	0.997000	0.39634	0.023000	0.16930	0.023000	0.10783	4.523000	0.60545	0.119000	0.18210	0.121000	0.15741	ACC	.	.		0.577	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		T	5041019	C	T	5041019	3	4	16	1	0	0	0	0	1	0	0	0	17101	507	18	3	941	3	USP6	17	5041019	Missense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	1252383	5041019	76154191	43	1428										
ACAP1	9744	hgsc.bcm.edu	37	chr17	7247901	7247901	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	accaagcttaagagaggggcCtggtggcctggtgatggaag	17	7	0	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr17:7247901C>A	ENST00000158762.3	+	10	994	c.788C>A	c.(787-789)cCt>cAt	p.P263H		NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	263	Required for formation of endosomal tubules when overexpressed with PIP5K1C.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						AGAGAGGGGCCTGGTGGCCTG	0.592																																					p.P263H		Atlas-SNP	.											.	ACAP1	66	.	0			c.C788A						.						56	46	49					17																	7247901		2011	3869	5880	SO:0001583	missense	9744	exon10			AGGGGCCTGGTGG	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.788C>A	chr17.hg19:g.7247901C>A	ENSP00000158762:p.Pro263His	71.0	0.0		85.0	32.0	NM_014716	Q53XN9	Missense_Mutation	SNP	ENST00000158762.3	hg19	CCDS11101.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.738068	0.30774	.	.	ENSG00000072818	ENST00000158762	T	0.04551	3.6	5.24	4.27	0.50696	.	0.328645	0.32106	N	0.006564	T	0.06234	0.0161	L	0.57536	1.79	0.80722	D	1	P	0.45348	0.856	B	0.36186	0.219	T	0.23119	-1.0197	10	0.62326	D	0.03	.	11.8561	0.52437	0.0:0.9139:0.0:0.0861	.	263	Q15027	ACAP1_HUMAN	H	263	ENSP00000158762:P263H	ENSP00000158762:P263H	P	+	2	0	ACAP1	7188625	0.995000	0.38212	0.111000	0.21465	0.180000	0.23129	3.855000	0.55957	1.354000	0.45846	0.563000	0.77884	CCT	.	.		0.592	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		A	7247901	C	A	7247901	3	1	16	1	0	0	0	0	1	0	0	0	118	681	24	3	826	3	ACAP1	17	7247901	Missense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	2206882	7247901	73947309	44	1429										
FXR2	9513	hgsc.bcm.edu	37	chr17	7504837	7504837	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	tcgcttcacaggggcttctgTggttgactgggaggaaacca	14	9	2	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr17:7504837T>C	ENST00000250113.7	-	7	884	c.550A>G	c.(550-552)Aca>Gca	p.T184A		NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	184						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.?(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		GGGGCTTCTGTGGTTGACTGG	0.502																																					p.T184A		Atlas-SNP	.											.	FXR2	44	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.A550G						.						141	138	139					17																	7504837		1910	4122	6032	SO:0001583	missense	9513	exon7			CTTCTGTGGTTGA	U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.550A>G	chr17.hg19:g.7504837T>C	ENSP00000250113:p.Thr184Ala	104.0	0.0		87.0	32.0	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Missense_Mutation	SNP	ENST00000250113.7	hg19	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.706631	0.48412	.	.	ENSG00000129245	ENST00000250113	T	0.35605	1.3	5.44	4.34	0.51931	.	0.107908	0.64402	D	0.000006	T	0.22781	0.0550	N	0.19112	0.55	0.31668	N	0.644681	B;B	0.22851	0.076;0.076	B;B	0.23716	0.048;0.048	T	0.15925	-1.0420	10	0.39692	T	0.17	0.0495	8.2772	0.31879	0.3181:0.0:0.0:0.6818	.	184;184	Q86V09;P51116	.;FXR2_HUMAN	A	184	ENSP00000250113:T184A	ENSP00000250113:T184A	T	-	1	0	FXR2	7445562	0.997000	0.39634	1.000000	0.80357	0.991000	0.79684	3.947000	0.56652	0.865000	0.35603	0.523000	0.50628	ACA	.	.		0.502	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1			C	7504837	T	C	7504837	3	2	16	1	0	0	0	0	1	0	0	0	6124	1696	59	2	1415	2	FXR2	17	7504837	Missense_Mutation	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10	256936	7504837	73690373	45	1430										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48684344	48684344	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ctggatgctgtgggcgtggaCcagcaggtagggctgaggtg	20	7	0	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr17:48684344C>T	ENST00000359106.5	+	24	4506	c.4506C>T	c.(4504-4506)gaC>gaT	p.D1502D	CACNA1G_ENST00000507336.1_Silent_p.D1502D|CACNA1G_ENST00000514717.1_Silent_p.D1479D|CACNA1G_ENST00000507609.1_Silent_p.D1502D|CACNA1G_ENST00000514079.1_Silent_p.D1502D|CACNA1G_ENST00000512389.1_Silent_p.D1502D|CACNA1G_ENST00000515411.1_Silent_p.D1502D|CACNA1G_ENST00000515165.1_Silent_p.D1502D|CACNA1G_ENST00000429973.2_Silent_p.D1502D|CACNA1G_ENST00000513689.2_Silent_p.D1502D|CACNA1G_ENST00000503485.1_Silent_p.D1502D|CACNA1G_ENST00000502264.1_Silent_p.D1479D|CACNA1G_ENST00000513964.1_Silent_p.D1502D|CACNA1G_ENST00000515765.1_Silent_p.D1502D|CACNA1G_ENST00000354983.4_Silent_p.D1479D|CACNA1G_ENST00000505165.1_Silent_p.D1502D|CACNA1G_ENST00000360761.4_Silent_p.D1479D|CACNA1G_ENST00000510115.1_Silent_p.D1479D|CACNA1G_ENST00000352832.5_Silent_p.D1479D|CACNA1G_ENST00000358244.5_Silent_p.D1479D|CACNA1G_ENST00000507896.1_Silent_p.D1502D|CACNA1G_ENST00000442258.2_Silent_p.D1479D|CACNA1G_ENST00000507510.2_Silent_p.D1502D|CACNA1G_ENST00000510366.1_Silent_p.D1502D|CACNA1G_ENST00000514181.1_Silent_p.D1502D	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1502					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	TGGGCGTGGACCAGCAGGTAG	0.587																																					p.D1502D		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C4506T						.						102	97	99					17																	48684344		2130	4228	6358	SO:0001819	synonymous_variant	8913	exon24			CGTGGACCAGCAG	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.4506C>T	chr17.hg19:g.48684344C>T		76.0	0.0		65.0	16.0	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	hg19	CCDS45730.1																																																																																			.	.		0.587	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		T	48684344	C	T	48684344	2	4	16	1	0	0	0	0	0	0	0	1	2546	506	18	3		3	CACNA1G	17	48684344	Silent	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	41179507	48684344	32510866	46	1431										
CACNG4	27092	hgsc.bcm.edu	37	chr17	65026622	65026622	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	atcatcgtctacatttccagCaacacaggtgacccgagtga	8	12	2	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr17:65026622C>T	ENST00000262138.3	+	4	488	c.486C>T	c.(484-486)agC>agT	p.S162S	AC005544.1_ENST00000375684.1_5'Flank|RP11-74H8.1_ENST00000579138.1_RNA	NM_014405.3	NP_055220.1	Q9UBN1	CCG4_HUMAN	calcium channel, voltage-dependent, gamma subunit 4	162					membrane depolarization (GO:0051899)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(3)	19	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			ACATTTCCAGCAACACAGGTG	0.532																																					p.S162S		Atlas-SNP	.											.	CACNG4	44	.	0			c.C486T						.						138	136	136					17																	65026622		2203	4300	6503	SO:0001819	synonymous_variant	27092	exon4			TTCCAGCAACACA	AH008289	CCDS11667.1	17q24	2006-01-23				ENSG00000075461		"Calcium channel subunits"	1408	protein-coding gene	gene with protein product		606404				10613843	Standard	NM_014405		Approved	MGC11138, MGC24983	uc002jft.2	Q9UBN1		ENST00000262138.3:c.486C>T	chr17.hg19:g.65026622C>T		230.0	0.0		188.0	15.0	NM_014405	B2RCK0	Silent	SNP	ENST00000262138.3	hg19	CCDS11667.1																																																																																			.	.		0.532	CACNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447036.1	NM_014405		T	65026622	C	T	65026622	2	4	16	1	0	0	0	0	0	0	0	1	2561	709	25	3		3	CACNG4	17	65026622	Silent	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	16342278	65026622	16168588	47	1432										
BPTF	2186	hgsc.bcm.edu	37	chr17	65920661	65920661	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	gtttctcctttttttcctgcAgagtggagaaagaaaaggca	10	7	1	3			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr17:65920661A>G	ENST00000321892.4	+	17	6147		c.e17-1		BPTF_ENST00000424123.3_Splice_Site|BPTF_ENST00000335221.5_Splice_Site|BPTF_ENST00000306378.6_Splice_Site			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor						anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTTTTCCTGCAGAGTGGAGAA	0.418																																					.		Atlas-SNP	.											.	BPTF	415	.	0			c.6087-2A>G						.						77	74	75					17																	65920661		2203	4300	6503	SO:0001630	splice_region_variant	2186	exon17			TCCTGCAGAGTGG	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.6087-1A>G	chr17.hg19:g.65920661A>G		195.0	0.0		274.0	82.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Splice_Site	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	A	22.2	4.259431	0.80246	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2325	0.73401	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BPTF	63351123	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	8.867000	0.92314	2.054000	0.61138	0.528000	0.53228	.	.	.		0.418	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	Intron	G	65920661	A	G	65920661	5	3	16	1	0	0	0	0	0	0	1	0	1497	202	7	2	6151	2	BPTF	17	65920661	Splice_Site	SNP	A	TCGA-2Y-A9H6-01A-11D-A38X-10	894039	65920661	15274549	48	1433										
FASN	2194	hgsc.bcm.edu	37	chr17	80045255	80045255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	cctgtgggtggcagggtcgaTgtggatggcggtgacacggg	21	7	0	1	rs141517558		TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr17:80045255T>C	ENST00000306749.2	-	20	3387	c.3169A>G	c.(3169-3171)Atc>Gtc	p.I1057V		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1057					acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GCAGGGTCGATGTGGATGGCG	0.642																																					p.I1057V	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.A3169G						.	T	VAL/ILE	0,4406		0,0,2203	117	88	97		3169	3.8	0.9	17	dbSNP_134	97	1,8595	1.2+/-3.3	0,1,4297	no	missense	FASN	NM_004104.4	29	0,1,6500	CC,CT,TT		0.0116,0.0,0.0077	benign	1057/2512	80045255	1,13001	2203	4298	6501	SO:0001583	missense	2194	exon20			GGTCGATGTGGAT	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.3169A>G	chr17.hg19:g.80045255T>C	ENSP00000304592:p.Ile1057Val	57.0	0.0		63.0	18.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.301515	0.23736	0.0	1.16E-4	ENSG00000169710	ENST00000306749;ENST00000545909	T	0.34667	1.35	3.85	3.85	0.44370	.	0.136306	0.49305	D	0.000143	T	0.37892	0.1020	M	0.77406	2.37	0.44006	D	0.996719	B	0.32829	0.386	B	0.27170	0.077	T	0.40979	-0.9534	10	0.46703	T	0.11	-36.3329	12.7742	0.57437	0.0:0.0:0.0:1.0	.	1057	P49327	FAS_HUMAN	V	1057;22	ENSP00000304592:I1057V	ENSP00000304592:I1057V	I	-	1	0	FASN	77638544	0.992000	0.36948	0.903000	0.35520	0.628000	0.37860	2.072000	0.41510	1.617000	0.50277	0.402000	0.26972	ATC	.	T|1.000;C|0.000		0.642	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		C	80045255	T	C	80045255	3	2	16	1	0	0	0	0	1	0	0	0	5691	1464	51	2	4462	2	FASN	17	80045255	Missense_Mutation	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10	14124594	80045255	1149955	49	1434										
DLGAP1	9229	hgsc.bcm.edu	37	chr18	3729263	3729263	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	catagctgtggctccgcatgCggaagcagccgggcatgggc	16	12	0	0			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr18:3729263C>T	ENST00000315677.3	-	7	2058	c.1463G>A	c.(1462-1464)cGc>cAc	p.R488H	DLGAP1_ENST00000400149.3_Missense_Mutation_p.R196H|DLGAP1_ENST00000581527.1_Missense_Mutation_p.R488H|DLGAP1_ENST00000515196.2_Missense_Mutation_p.R488H|DLGAP1_ENST00000400150.3_Missense_Mutation_p.R194H|DLGAP1_ENST00000581699.1_Missense_Mutation_p.R194H|DLGAP1_ENST00000534970.1_Missense_Mutation_p.R200H|DLGAP1_ENST00000478161.1_5'UTR|DLGAP1_ENST00000400155.1_Missense_Mutation_p.R194H|DLGAP1_ENST00000400145.2_Missense_Mutation_p.R186H|DLGAP1_ENST00000539435.1_Missense_Mutation_p.R186H|DLGAP1_ENST00000584874.1_Missense_Mutation_p.R488H|DLGAP1_ENST00000400147.2_Missense_Mutation_p.R186H	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	488					synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				GCTCCGCATGCGGAAGCAGCC	0.667																																					p.R488H		Atlas-SNP	.											.	DLGAP1	201	.	0			c.G1463A						.						45	37	39					18																	3729263		2203	4299	6502	SO:0001583	missense	9229	exon7			CGCATGCGGAAGC	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"discs, large (Drosophila) homolog-associated protein 1"			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.1463G>A	chr18.hg19:g.3729263C>T	ENSP00000316377:p.Arg488His	158.0	0.0		177.0	46.0	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	hg19	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	C	36	5.719610	0.96839	.	.	ENSG00000170579	ENST00000315677;ENST00000400147;ENST00000400150;ENST00000400149;ENST00000400155;ENST00000534970;ENST00000539435;ENST00000400145;ENST00000515196	D;D;D;D;D;D;D;D;D	0.92099	-2.97;-2.97;-2.97;-2.97;-2.97;-2.97;-2.97;-2.97;-2.97	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.96827	0.8964	M	0.87269	2.87	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	0.996;0.996;0.999;0.996;0.999;0.999;0.998;0.999;1.0	D	0.96809	0.9595	10	0.87932	D	0	-23.9211	20.2821	0.98520	0.0:1.0:0.0:0.0	.	488;200;174;194;186;488;186;488;186	B7Z9Y4;B7Z2H2;B7Z2J5;A8MWN8;B7Z2I2;Q6IS01;O14490-3;O14490;O14490-2	.;.;.;.;.;.;.;DLGP1_HUMAN;.	H	488;186;194;196;194;200;186;186;488	ENSP00000316377:R488H;ENSP00000383011:R186H;ENSP00000383014:R194H;ENSP00000383013:R196H;ENSP00000383019:R194H;ENSP00000437817:R200H;ENSP00000446312:R186H;ENSP00000383010:R186H;ENSP00000445973:R488H	ENSP00000316377:R488H	R	-	2	0	DLGAP1	3719263	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.811000	0.86092	2.786000	0.95864	0.563000	0.77884	CGC	.	.		0.667	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4			T	3729263	C	T	3729263	3	4	16	1	0	0	0	0	1	0	0	0	4561	768	27	1	1498	1	DLGAP1	18	3729263	Missense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10		3729263	74347985	50	1435										
MBD1	4152	hgsc.bcm.edu	37	chr18	47800628	47800639	+	In_Frame_Del	DEL	GTCGCAGCAGAA	GTCGCAGCAGAA	-													0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ctgcccccgaatttgggcttGtcgcagcagaagtcgcagcg					rs115570375		TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	GTCGCAGCAGAA	GTCGCAGCAGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr18:47800628_47800639delGTCGCAGCAGAA	ENST00000591416.1	-	11	1494_1505	c.1063_1074delTTCTGCTGCGAC	c.(1063-1074)ttctgctgcgacdel	p.FCCD355del	MBD1_ENST00000269468.5_In_Frame_Del_p.FCCD355del|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000382948.5_In_Frame_Del_p.FCCD355del|MBD1_ENST00000588937.1_In_Frame_Del_p.FCCD332del|MBD1_ENST00000457839.2_In_Frame_Del_p.FCCD380del|MBD1_ENST00000347968.3_Intron|MBD1_ENST00000269471.5_In_Frame_Del_p.FCCD332del|MBD1_ENST00000590208.1_In_Frame_Del_p.FCCD355del|MBD1_ENST00000585672.1_In_Frame_Del_p.FCCD305del|MBD1_ENST00000339998.6_In_Frame_Del_p.FCCD355del|MBD1_ENST00000591535.1_In_Frame_Del_p.FCCD332del|MBD1_ENST00000398495.2_Intron|MBD1_ENST00000398488.1_Intron|MBD1_ENST00000424334.2_In_Frame_Del_p.FCCD406del|MBD1_ENST00000436910.1_In_Frame_Del_p.FCCD332del|MBD1_ENST00000349085.2_Intron|MBD1_ENST00000398493.1_Intron|MBD1_ENST00000585595.1_In_Frame_Del_p.FCCD380del|MBD1_ENST00000353909.3_In_Frame_Del_p.FCCD306del			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	355					negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						ATTTGGGCTTGTCGCAGCAGAAGTCGCAGCGG	0.651																																					p.380_384del		Atlas-Indel,Pindel	.											MBD1_ENST00000457839,colon,carcinoma,0,4	MBD1	228	.	0			c.1139_1150del						.																																			SO:0001651	inframe_deletion	4152	exon12			.	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.1063_1074delTTCTGCTGCGAC	chr18.hg19:g.47800628_47800639delGTCGCAGCAGAA	ENSP00000467017:p.Phe355_Asp358del	169.0	0.0		108.0	15.0	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	In_Frame_Del	DEL	ENST00000591416.1	hg19	CCDS11943.1																																																																																			.	.		0.651	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846		-	47800639	GTCGCAGCAGAA	-	47800628	7	5	16	1	0	1	0	1	0	0	0	0	9351	1368	48	0	961	0	MBD1	18	47800628	In_Frame_Del	DEL	GTCGCAGCAGAA	TCGA-2Y-A9H6-01A-11D-A38X-10	44071365	47800628	30276620	51	1436										
DSEL	92126	hgsc.bcm.edu	37	chr18	65181841	65181841	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	aatgtcctgtaaacattaacGccatgatccatgggggagct	10	9	0	1			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr18:65181841G>A	ENST00000310045.7	-	2	1508	c.35C>T	c.(34-36)gCg>gTg	p.A12V	RP11-638L3.1_ENST00000583687.1_lincRNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	2					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				AAACATTAACGCCATGATCCA	0.393																																					p.A12V		Atlas-SNP	.											.	DSEL	196	.	0			c.C35T						.						70	66	67					18																	65181841		2203	4299	6502	SO:0001583	missense	92126	exon2			ATTAACGCCATGA	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.35C>T	chr18.hg19:g.65181841G>A	ENSP00000310565:p.Ala12Val	168.0	0.0		160.0	9.0	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	hg19	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.030696	0.93575	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.24538	1.85	5.01	5.01	0.66863	.	0.305004	0.30320	U	0.009881	T	0.44456	0.1294	L	0.41236	1.265	0.51012	D	0.999906	D	0.89917	1.0	D	0.78314	0.991	T	0.42548	-0.9445	10	0.87932	D	0	-0.1329	18.3235	0.90246	0.0:0.0:1.0:0.0	.	2	Q8IZU8	DSEL_HUMAN	V	12;2	ENSP00000310565:A12V	ENSP00000310565:A12V	A	-	2	0	DSEL	63332821	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.134000	0.89606	2.332000	0.79248	0.561000	0.74099	GCG	.	.		0.393	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		A	65181841	G	A	65181841	3	1	16	1	0	0	0	0	1	0	0	0	4777	1087	38	1	3637	1	DSEL	18	65181841	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10	17381213	65181841	12895407	52	1437										
C19orf6	91304	hgsc.bcm.edu	37	chr19	1011186	1011186	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	agaaggcgaagtggtagagaTagaagaacctgcggggcggg	19	5	0	4	rs369432576		TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr19:1011186T>C	ENST00000356663.3	-	10	1347	c.1226A>G	c.(1225-1227)tAt>tGt	p.Y409C	TMEM259_ENST00000333175.5_Intron	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	409						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GTGGTAGAGATAGAAGAACCT	0.662																																					p.Y409C		Atlas-SNP	.											.	.	.	.	0			c.A1226G						.		CYS/TYR,	2,4388		0,2,2193	35	32	33		1226,	4.2	1	19		33	0,8592		0,0,4296	no	missense,intron	C19orf6	NM_001033026.1,NM_033420.3	194,	0,2,6489	CC,CT,TT		0.0,0.0456,0.0154	probably-damaging,	409/621,	1011186	2,12980	2195	4296	6491	SO:0001583	missense	91304	exon10			TAGAGATAGAAGA	BC008957	CCDS12052.1, CCDS32862.1	19p13.3	2013-02-06	2013-02-06	2013-02-06	ENSG00000182087	ENSG00000182087			17039	protein-coding gene	gene with protein product	"membralin", "aspecific BCL2 ARE-binding protein 1"	611011	"chromosome 19 open reading frame 6"	C19orf6		12638133, 16084606	Standard	XM_005259675		Approved	MGC4022, ASBABP1, MBRL	uc002lqr.1	Q4ZIN3		ENST00000356663.3:c.1226A>G	chr19.hg19:g.1011186T>C	ENSP00000349087:p.Tyr409Cys	102.0	0.0		58.0	11.0	NM_001033026	O60392|Q8NF79|Q96H30	Missense_Mutation	SNP	ENST00000356663.3	hg19	CCDS32862.1	.	.	.	.	.	.	.	.	.	.	t	17.50	3.404275	0.62288	4.56E-4	0.0	ENSG00000182087	ENST00000356663	.	.	.	4.17	4.17	0.49024	.	0.000000	0.85682	U	0.000000	T	0.74997	0.3790	L	0.61036	1.89	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77593	-0.2530	9	0.72032	D	0.01	-12.1875	12.4368	0.55604	0.0:0.0:0.0:1.0	.	409	Q4ZIN3	MBRL_HUMAN	C	409	.	ENSP00000349087:Y409C	Y	-	2	0	C19orf6	962186	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	3.650000	0.54424	1.531000	0.49152	0.319000	0.21371	TAT	.	.		0.662	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420		C	1011186	T	C	1011186	3	2	16	1	0	0	0	0	1	0	0	0	1943	1406	49	2	644	2	C19orf6	19	1011186	Missense_Mutation	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10		1011186	58117797	53	1438										
PRR19	284338	hgsc.bcm.edu	37	chr19	42814219	42814219	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ctgagtttgccacaggccttCccccggaggaacctgattca	10	14	1	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr19:42814219C>G	ENST00000499536.2	+	1	1294	c.483C>G	c.(481-483)ttC>ttG	p.F161L	PRR19_ENST00000598490.1_Missense_Mutation_p.F161L|PRR19_ENST00000341747.3_Missense_Mutation_p.F161L			A6NJB7	PRR19_HUMAN	proline rich 19	161										NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	10		Prostate(69;0.00682)				CACAGGCCTTCCCCCGGAGGA	0.637																																					p.F161L		Atlas-SNP	.											.	PRR19	30	.	0			c.C483G						.						50	50	50					19																	42814219		2203	4300	6503	SO:0001583	missense	284338	exon2			GGCCTTCCCCCGG	AK124116	CCDS33036.1	19q13.2	2007-12-17				ENSG00000188368			33728	protein-coding gene	gene with protein product							Standard	NM_199285		Approved	MGC70924	uc002oti.3	A6NJB7		ENST00000499536.2:c.483C>G	chr19.hg19:g.42814219C>G	ENSP00000445247:p.Phe161Leu	67.0	0.0		61.0	14.0	NM_199285	A8K663|B3KW48|Q6P584	Missense_Mutation	SNP	ENST00000499536.2	hg19	CCDS33036.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.269207	0.59540	.	.	ENSG00000188368	ENST00000341747;ENST00000499536	.	.	.	4.86	1.47	0.22746	.	0.000000	0.48767	D	0.000179	T	0.47192	0.1432	L	0.34521	1.04	0.30497	N	0.770786	D;D	0.76494	0.996;0.999	D;D	0.83275	0.99;0.996	T	0.46925	-0.9156	9	0.87932	D	0	-14.1294	7.2696	0.26250	0.0:0.7177:0.0:0.2823	.	161;161	A6NJB7;A6NJB7-2	PRR19_HUMAN;.	L	161	.	ENSP00000342709:F161L	F	+	3	2	PRR19	47506059	0.996000	0.38824	1.000000	0.80357	0.756000	0.42949	0.048000	0.14078	0.325000	0.23359	-0.150000	0.13652	TTC	.	.		0.637	PRR19-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463735.1	NM_199285		G	42814219	C	G	42814219	3	3	16	1	0	0	0	0	1	0	0	0	12603	854	30	4	485	4	PRR19	19	42814219	Missense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	41803033	42814219	16314764	54	1439										
PPFIA3	8541	hgsc.bcm.edu	37	chr19	49651354	49651354	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	ccccagatcctggcatatggCgacatgaaccacgagtgggt	12	12	0	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr19:49651354C>T	ENST00000334186.4	+	24	3199	c.2850C>T	c.(2848-2850)ggC>ggT	p.G950G	PPFIA3_ENST00000602351.1_Silent_p.G941G	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	950					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		TGGCATATGGCGACATGAACC	0.617																																					p.G950G		Atlas-SNP	.											.	PPFIA3	71	.	0			c.C2850T						.						63	63	63					19																	49651354		2203	4300	6503	SO:0001819	synonymous_variant	8541	exon24			ATATGGCGACATG	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"Sterile alpha motif (SAM) domain containing"	9247	protein-coding gene	gene with protein product	"protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3", "liprin-alpha 3", "liprin"	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.2850C>T	chr19.hg19:g.49651354C>T		149.0	0.0		165.0	43.0	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Silent	SNP	ENST00000334186.4	hg19	CCDS12758.1																																																																																			.	.		0.617	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660		T	49651354	C	T	49651354	2	4	16	1	0	0	0	0	0	0	0	1	12320	755	27	1		1	PPFIA3	19	49651354	Silent	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	6837135	49651354	9477629	55	1440										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54313990	54313990	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	cccagcagaggcaccagggtCcctgaggatcgtggaaagaa	14	11	0	3			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr19:54313990C>T	ENST00000324134.6	-	3	1091	c.923G>A	c.(922-924)gGa>gAa	p.G308E	NLRP12_ENST00000351894.4_Missense_Mutation_p.G308E|NLRP12_ENST00000391773.1_Missense_Mutation_p.G308E|NLRP12_ENST00000391775.3_Missense_Mutation_p.G308E|NLRP12_ENST00000345770.5_Missense_Mutation_p.G308E|NLRP12_ENST00000391772.1_Missense_Mutation_p.G308E|NLRP12_ENST00000354278.3_Missense_Mutation_p.G308E|NLRP12_ENST00000535162.1_Missense_Mutation_p.G308E	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	308	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)	p.G308V(1)		NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		GCACCAGGGTCCCTGAGGATC	0.577																																					p.C308Y		Atlas-SNP	.											NLRP12_ENST00000345770,NS,carcinoma,0,2	NLRP12	236	.	1	Substitution - Missense(1)	lung(1)	c.G923A						.						46	48	47					19																	54313990		2203	4300	6503	SO:0001583	missense	91662	exon3			CAGGGTCCCTGAG	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.923G>A	chr19.hg19:g.54313990C>T	ENSP00000319377:p.Gly308Glu	100.0	0.0		99.0	14.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	hg19	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	C	6.165	0.398558	0.11696	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.74106	-0.75;-0.78;-0.81;-0.81;-0.79;-0.75;-0.78	4.47	2.28	0.28536	NACHT nucleoside triphosphatase (1);	0.158996	0.29692	N	0.011453	T	0.47469	0.1447	N	0.02420	-0.555	0.09310	N	0.999999	P;P;P;P	0.49559	0.925;0.811;0.811;0.846	P;P;P;P	0.46389	0.489;0.489;0.489;0.515	T	0.46925	-0.9156	10	0.12103	T	0.63	.	7.5178	0.27610	0.0:0.7813:0.0:0.2187	.	308;308;308;308	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	E	308	ENSP00000319377:G308E;ENSP00000438030:G308E;ENSP00000340473:G308E;ENSP00000346231:G308E;ENSP00000375655:G308E;ENSP00000375653:G308E;ENSP00000375652:G308E	ENSP00000319377:G308E	G	-	2	0	NLRP12	59005802	0.000000	0.05858	0.452000	0.26994	0.850000	0.48378	-0.914000	0.04038	1.025000	0.39708	0.306000	0.20318	GGA	.	.		0.577	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		T	54313990	C	T	54313990	3	4	16	1	0	0	0	0	1	0	0	0	10483	855	30	3	2390	3	NLRP12	19	54313990	Missense_Mutation	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	4662636	54313990	4814993	56	1441										
RPN2	6185	hgsc.bcm.edu	37	chr20	35866808	35866808	+	Intron	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	cctctttcctttggcaggatCgctgcagagcagagcagtag	12	11	1	2			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chr20:35866808C>A	ENST00000237530.6	+	16	2194				RPN2_ENST00000470352.1_Intron|RPN2_ENST00000373622.5_Silent_p.I597I	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II						aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				TTGGCAGGATCGCTGCAGAGC	0.502																																					p.I597I		Atlas-SNP	.											.	RPN2	45	.	0			c.C1791A						.						59	49	52					20																	35866808		1568	3582	5150	SO:0001627	intron_variant	6185	exon16			CAGGATCGCTGCA	Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"oligosaccharyltransferase complex subunit (non-catalytic)"	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.1883+1696C>A	chr20.hg19:g.35866808C>A		76.0	0.0		127.0	40.0	NM_001135771	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Silent	SNP	ENST00000237530.6	hg19	CCDS13291.1																																																																																			.	.		0.502	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079076.2	NM_002951		A	35866808	C	A	35866808	1	1	16	0	1	0	0	0	0	0	0	0	13623	874	31	1		1	RPN2	20	35866808	Intron	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10		35866808	27158712	57	1442										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140995873	140995873	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	gtgattccttgacagacagcGagtccttgatagagagcgag	13	8	0	5			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chrX:140995873G>A	ENST00000285879.4	+	4	2969	c.2683G>A	c.(2683-2685)Gag>Aag	p.E895K	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	895										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					GACAGACAGCGAGTCCTTGAT	0.478										HNSCC(15;0.026)																											p.E895K		Atlas-SNP	.											.	MAGEC1	317	.	0			c.G2683A						.						167	170	169					X																	140995873		2203	4300	6503	SO:0001583	missense	9947	exon4			GACAGCGAGTCCT	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.2683G>A	chrX.hg19:g.140995873G>A	ENSP00000285879:p.Glu895Lys	99.0	0.0		206.0	70.0	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	hg19	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	g	8.301	0.819868	0.16678	.	.	ENSG00000155495	ENST00000285879	T	0.02085	4.46	0.724	-1.45	0.08828	.	.	.	.	.	T	0.01320	0.0043	N	0.19112	0.55	0.19300	N	0.999974	P	0.52463	0.953	B	0.37346	0.247	T	0.44590	-0.9318	8	0.59425	D	0.04	.	.	.	.	.	895	O60732	MAGC1_HUMAN	K	895	ENSP00000285879:E895K	ENSP00000285879:E895K	E	+	1	0	MAGEC1	140823539	0.003000	0.15002	0.000000	0.03702	0.011000	0.07611	-0.290000	0.08354	-0.970000	0.03569	0.279000	0.19357	GAG	.	.		0.478	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		A	140995873	G	A	140995873	3	1	16	1	0	0	0	0	1	0	0	0	9189	1059	37	1	2689	1	MAGEC1	23	140995873	Missense_Mutation	SNP	G	TCGA-2Y-A9H6-01A-11D-A38X-10		140995873	14274687	58	1443										
MAGEA5	4104	hgsc.bcm.edu	37	chrX	151283912	151283912	+	RNA	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	aggacacagcctcctgctccTcagtagtggcagcctgcaca	10	15	1	0			TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chrX:151283912T>A	ENST00000509345.2	-	0	424																											CTCCTGCTCCTCAGTAGTGGC	0.622																																					p.E34V		Atlas-SNP	.											.	.	.	.	0			c.A101T						.						45	47	46					X																	151283912		2203	4300	6503			0	exon4			TGCTCCTCAGTAG																													chrX.hg19:g.151283912T>A		164.0	0.0		291.0	111.0	NM_001204811		Missense_Mutation	SNP	ENST00000509345.2	hg19																																																																																				.	.		0.622	RP11-1007I13.4-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000445981.1			A	151283912	T	A	151283912	1	1	16	0	1	0	0	0	0	0	0	0	9178	1551	54	4		4	MAGEA5	23	151283912	RNA	SNP	T	TCGA-2Y-A9H6-01A-11D-A38X-10	10288039	151283912	3986648	59	1444										
ZNF275	10838	hgsc.bcm.edu	37	chrX	152612617	152612617	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.332602739726027	0	0.361524717093508	1	1	0	gtagctgcggagccccagccCggccccagtagggccctgga	15	16	0	0	rs370281502		TCGA-2Y-A9H6-01A-11D-A38X-10	TCGA-2Y-A9H6-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ee12965-26aa-443a-b8de-f4a79dc3e857	b27b338e-86e5-4131-83cf-206c52b809b7	g.chrX:152612617C>T	ENST00000421401.3	+	4	651	c.474C>T	c.(472-474)ccC>ccT	p.P158P	ZNF275_ENST00000370249.2_Silent_p.P105P|ZNF275_ENST00000370251.3_Silent_p.P158P|ZNF275_ENST00000440091.1_Silent_p.P188P			Q9NSD4	ZN275_HUMAN	zinc finger protein 275	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGCCCCAGCCCGGCCCCAGTA	0.612																																					p.P158P		Atlas-SNP	.											.	ZNF275	44	.	0			c.C474T						.	C		1,3497		0,1,1463,570	31	34	33		474	-9.7	0	X		33	0,6512		0,0,2358,1796	no	coding-synonymous	ZNF275	NM_001080485.3		0,1,3821,2366	TT,TC,CC,C		0.0,0.0286,0.01		158/330	152612617	1,10009	2034	4154	6188	SO:0001819	synonymous_variant	10838	exon4			CCAGCCCGGCCCC	BC041602		Xq28	2013-01-08			ENSG00000063587	ENSG00000063587		"Zinc fingers, C2H2-type", "-"	13069	protein-coding gene	gene with protein product							Standard	NM_001080485		Approved		uc004fhg.2	Q9NSD4	OTTHUMG00000067450	ENST00000421401.3:c.474C>T	chrX.hg19:g.152612617C>T		203.0	0.0		237.0	74.0	NM_001080485	A6NE92	Silent	SNP	ENST00000421401.3	hg19																																																																																				.	.		0.612	ZNF275-201	KNOWN	basic	protein_coding	protein_coding		NM_001080485		T	152612617	C	T	152612617	2	4	16	1	0	0	0	0	0	0	0	1	17825	639	23	1		1	ZNF275	23	152612617	Silent	SNP	C	TCGA-2Y-A9H6-01A-11D-A38X-10	1328705	152612617	2657943	60	1445										
SPEN	23013	hgsc.bcm.edu	37	chr1	16263693	16263693	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ggtgagcccctgcagcctccTcagcctgtgcagtccacaca	10	17	1	1	rs549209393	byFrequency	TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr1:16263693T>G	ENST00000375759.3	+	12	10266	c.10062T>G	c.(10060-10062)ccT>ccG	p.P3354P		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	3354	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TGCAGCCTCCTCAGCCTGTGC	0.647																																					p.P3354P		Atlas-SNP	.											.	SPEN	374	.	0			c.T10062G						.						46	52	50					1																	16263693		2203	4298	6501	SO:0001819	synonymous_variant	23013	exon12			GCCTCCTCAGCCT		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.10062T>G	chr1.hg19:g.16263693T>G		79.0	0.0		40.0	19.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	hg19	CCDS164.1																																																																																			.	.		0.647	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16263693	T	G	16263693	2	3	17	1	0	0	0	0	0	0	0	1	15053	1538	54	5		5	SPEN	1	16263693	Silent	SNP	T	TCGA-2Y-A9H7-01A-11D-A38X-10		16263693	232986928	1	1446										
MAST2	23139	hgsc.bcm.edu	37	chr1	46499912	46499912	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	atctcccactcaaggctaccGggtgacccccgatgctgtgc	10	16	2	1	rs368958391		TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr1:46499912G>A	ENST00000361297.2	+	28	4125	c.3842G>A	c.(3841-3843)cGg>cAg	p.R1281Q	MAST2_ENST00000372009.2_Missense_Mutation_p.R1188Q	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CAAGGCTACCGGGTGACCCCC	0.582																																					p.R1281Q		Atlas-SNP	.											.	MAST2	136	.	0			c.G3842A						.		GLN/ARG	0,3910		0,0,1955	58	62	60		3842	4.8	1	1		60	1,8309		0,1,4154	no	missense	MAST2	NM_015112.2	43	0,1,6109	AA,AG,GG		0.012,0.0,0.0082	probably-damaging	1281/1799	46499912	1,12219	1955	4155	6110	SO:0001583	missense	23139	exon28			GCTACCGGGTGAC	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.3842G>A	chr1.hg19:g.46499912G>A	ENSP00000354671:p.Arg1281Gln	66.0	0.0		46.0	31.0	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	hg19	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	g	28.7	4.945700	0.92593	0.0	1.2E-4	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.39056	1.1;1.1	4.84	4.84	0.62591	.	0.170176	0.48767	D	0.000168	T	0.68128	0.2967	M	0.83118	2.625	0.42403	D	0.992574	D;D	0.89917	1.0;1.0	D;D	0.87578	0.92;0.998	T	0.72388	-0.4309	10	0.46703	T	0.11	-1.3506	17.9868	0.89158	0.0:0.0:1.0:0.0	.	1188;1281	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	Q	1281;1188	ENSP00000354671:R1281Q;ENSP00000361079:R1188Q	ENSP00000354671:R1281Q	R	+	2	0	MAST2	46272499	1.000000	0.71417	0.979000	0.43373	0.870000	0.49936	7.883000	0.87264	2.221000	0.72209	0.552000	0.68991	CGG	.	.		0.582	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		A	46499912	G	A	46499912	3	1	17	1	0	0	0	0	1	0	0	0	9334	1116	39	1	3952	1	MAST2	1	46499912	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	30236219	46499912	202750709	2	1447										
SELENBP1	8991	hgsc.bcm.edu	37	chr1	151337513	151337513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tctgagggcctccagccaccCgttttcccttgggaaaacca	9	15	1	1	rs544356174		TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr1:151337513C>T	ENST00000368868.5	-	11	1236	c.1145G>A	c.(1144-1146)cGg>cAg	p.R382Q	SELENBP1_ENST00000435071.1_Missense_Mutation_p.R318Q|SELENBP1_ENST00000426705.2_Missense_Mutation_p.R424Q|SELENBP1_ENST00000473693.1_5'Flank|SELENBP1_ENST00000447402.3_Missense_Mutation_p.R320Q	NM_003944.3	NP_003935.2	Q13228	SBP1_HUMAN	selenium binding protein 1	382					protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	selenium binding (GO:0008430)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|urinary_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TCCAGCCACCCGTTTTCCCTT	0.577													C|||	1	0.000199681	0	0	5008	,	,		19581	0.001		0	False		,,,				2504	0				p.R424Q		Atlas-SNP	.											.	SELENBP1	44	.	0			c.G1271A						.						39	34	36					1																	151337513		2203	4300	6503	SO:0001583	missense	8991	exon11			GCCACCCGTTTTC	U29091	CCDS995.1, CCDS58027.1, CCDS60266.1	1q21.3	2014-05-19			ENSG00000143416	ENSG00000143416			10719	protein-coding gene	gene with protein product		604188				9027582	Standard	NM_003944		Approved	hSP56, hSBP, LPSB	uc010pcy.3	Q13228	OTTHUMG00000012498	ENST00000368868.5:c.1145G>A	chr1.hg19:g.151337513C>T	ENSP00000357861:p.Arg382Gln	73.0	0.0		99.0	25.0	NM_001258289	A6NML9|A6PVW9|B2RDR3|B4DKP6|B4E1F3|Q49AQ8|Q96GX7	Missense_Mutation	SNP	ENST00000368868.5	hg19	CCDS995.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.992901	0.54041	.	.	ENSG00000143416	ENST00000368868;ENST00000447402;ENST00000435071	.	.	.	4.52	1.55	0.23275	WD40/YVTN repeat-like-containing domain (1);	0.340561	0.26742	N	0.022731	T	0.46386	0.1390	M	0.85630	2.765	0.47441	D	0.999424	B;B;B;B	0.22276	0.016;0.067;0.007;0.014	B;B;B;B	0.24541	0.003;0.054;0.015;0.015	T	0.49504	-0.8933	9	0.45353	T	0.12	-9.4969	7.0869	0.25261	0.0:0.6317:0.0:0.3683	.	320;235;318;382	B4E1F3;B4DPI7;Q13228-2;Q13228	.;.;.;SBP1_HUMAN	Q	382;320;318	.	ENSP00000357861:R382Q	R	-	2	0	SELENBP1	149604137	0.000000	0.05858	0.872000	0.34217	0.984000	0.73092	-0.181000	0.09740	0.534000	0.28695	0.655000	0.94253	CGG	.	.		0.577	SELENBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034904.4			T	151337513	C	T	151337513	3	4	17	1	0	0	0	0	1	0	0	0	14029	652	23	1	281	1	SELENBP1	1	151337513	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	104837601	151337513	97913108	3	1448										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158648224	158648224	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gtaagtttgcagcattggacAgagctttctgtctctggaga	12	7	2	2	rs121918634		TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr1:158648224A>G	ENST00000368147.4	-	6	959	c.779T>C	c.(778-780)cTg>cCg	p.L260P		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	260			L -> P (in EL2; Nigerian). {ECO:0000269|PubMed:2794061}.		actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGCATTGGACAGAGCTTTCTG	0.428																																					p.L260P		Atlas-SNP	.											.	SPTA1	720	.	0			c.T779C	GRCh37	CM890108	SPTA1	M	rs121918634	.						120	111	114					1																	158648224		1870	4115	5985	SO:0001583	missense	6708	exon6			TTGGACAGAGCTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.779T>C	chr1.hg19:g.158648224A>G	ENSP00000357129:p.Leu260Pro	55.0	0.0		109.0	36.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.859325	0.51376	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.80909	-1.43;-1.43	4.66	4.66	0.58398	.	0.000000	0.26439	N	0.024363	D	0.90421	0.7001	M	0.93462	3.42	0.80722	A	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93002	0.6424	9	0.87932	D	0	.	13.3542	0.60619	1.0:0.0:0.0:0.0	.	260	P02549	SPTA1_HUMAN	P	260	ENSP00000357130:L260P;ENSP00000357129:L260P	ENSP00000357129:L260P	L	-	2	0	SPTA1	156914848	1.000000	0.71417	0.203000	0.23512	0.130000	0.20726	8.035000	0.88872	2.080000	0.62538	0.528000	0.53228	CTG	.	.		0.428	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		G	158648224	A	G	158648224	3	3	17	1	0	0	0	0	1	0	0	0	15131	188	7	2	6668	2	SPTA1	1	158648224	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10	7310711	158648224	90602397	4	1449										
DNM3	26052	hgsc.bcm.edu	37	chr1	172356496	172356496	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ctcctggatacagcactctcGcaggtaagaagatggccccg	11	13	1	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr1:172356496G>T	ENST00000355305.5	+	19	2457	c.2300G>T	c.(2299-2301)cGc>cTc	p.R767L	DNM3_ENST00000358155.4_Missense_Mutation_p.R761L|DNM3_ENST00000367731.1_Missense_Mutation_p.R757L			Q9UQ16	DYN3_HUMAN	dynamin 3	767					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CAGCACTCTCGCAGGTAAGAA	0.617																																					p.R761L		Atlas-SNP	.											.	DNM3	85	.	0			c.G2282T						.						21	22	22					1																	172356496		2006	4160	6166	SO:0001583	missense	26052	exon19			ACTCTCGCAGGTA	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.2300G>T	chr1.hg19:g.172356496G>T	ENSP00000347457:p.Arg767Leu	80.0	0.0		148.0	45.0	NM_015569	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	hg19		.	.	.	.	.	.	.	.	.	.	G	14.13	2.442639	0.43326	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000355305;ENST00000367731;ENST00000485254	D;D;D;T	0.92595	-3.07;-3.07;-3.07;-0.66	5.04	5.04	0.67666	.	0.227351	0.31949	N	0.006809	D	0.83050	0.5170	L	0.61218	1.895	0.80722	D	1	P;B;B	0.38110	0.618;0.235;0.235	B;B;B	0.32864	0.145;0.067;0.154	T	0.81504	-0.0903	10	0.19590	T	0.45	.	10.9111	0.47110	0.0881:0.0:0.9119:0.0	.	767;757;761	Q9UQ16;Q9UQ16-2;Q9UQ16-3	DYN3_HUMAN;.;.	L	771;761;767;757;130	ENSP00000350876:R761L;ENSP00000347457:R767L;ENSP00000356705:R757L;ENSP00000429165:R130L	ENSP00000347457:R767L	R	+	2	0	DNM3	170623119	0.997000	0.39634	1.000000	0.80357	0.886000	0.51366	-0.229000	0.09098	2.507000	0.84556	0.585000	0.79938	CGC	.	.		0.617	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		T	172356496	G	T	172356496	3	4	17	1	0	0	0	0	1	0	0	0	4675	1087	38	1	2356	1	DNM3	1	172356496	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	13708272	172356496	76894125	5	1450										
NFASC	23114	hgsc.bcm.edu	37	chr1	204913476	204913476	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ccaccgccgccctgggtccaTgcagccttcctcctctgcct	8	21	1	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr1:204913476T>G	ENST00000401399.1	+	2	232	c.33T>G	c.(31-33)caT>caG	p.H11Q	NFASC_ENST00000367170.4_Missense_Mutation_p.H11Q|NFASC_ENST00000338515.6_Missense_Mutation_p.H11Q|NFASC_ENST00000338586.6_Missense_Mutation_p.H11Q|NFASC_ENST00000403080.1_Missense_Mutation_p.H11Q|NFASC_ENST00000367169.4_Missense_Mutation_p.H11Q|NFASC_ENST00000367171.4_Missense_Mutation_p.H11Q|NFASC_ENST00000404907.1_Missense_Mutation_p.H11Q|NFASC_ENST00000360049.4_Missense_Mutation_p.H11Q|NFASC_ENST00000404076.1_Missense_Mutation_p.H11Q|NFASC_ENST00000339876.6_Missense_Mutation_p.H11Q|NFASC_ENST00000367172.4_Missense_Mutation_p.H11Q|NFASC_ENST00000539706.1_Missense_Mutation_p.H11Q|NFASC_ENST00000513543.1_Missense_Mutation_p.H11Q			O94856	NFASC_HUMAN	neurofascin	11					axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CCTGGGTCCATGCAGCCTTCC	0.592																																					p.H11Q		Atlas-SNP	.											.	NFASC	396	.	0			c.T33G						.						47	43	44					1																	204913476		2203	4300	6503	SO:0001583	missense	23114	exon3			GGTCCATGCAGCC	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.33T>G	chr1.hg19:g.204913476T>G	ENSP00000385637:p.His11Gln	63.0	0.0		83.0	49.0	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	hg19	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	T	9.470	1.095264	0.20471	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000505079;ENST00000404907;ENST00000513543	T;T;T;T;T;T;T;T;T;T;T;T;T;D;T;T	0.84660	0.0;-0.06;0.0;0.01;-0.0;-0.0;0.06;0.08;0.03;-0.48;-0.47;-0.04;-0.0;-1.88;0.06;0.08	5.33	-4.8	0.03190	.	0.393107	0.18882	N	0.128542	T	0.69984	0.3172	N	0.08118	0	0.09310	N	1	B;B;B;P;B;B	0.37573	0.002;0.0;0.003;0.6;0.0;0.068	B;B;B;B;B;B	0.43728	0.006;0.001;0.001;0.429;0.0;0.017	T	0.65837	-0.6071	10	0.21540	T	0.41	.	12.4975	0.55937	0.0:0.3576:0.0:0.6424	.	11;11;113;11;11;11	O94856-11;O94856-8;B4DRH7;O94856-9;O94856-3;O94856-2	.;.;.;.;.;.	Q	11	ENSP00000356140:H11Q;ENSP00000356139:H11Q;ENSP00000356138:H11Q;ENSP00000342128:H11Q;ENSP00000344786:H11Q;ENSP00000343509:H11Q;ENSP00000438614:H11Q;ENSP00000353154:H11Q;ENSP00000356137:H11Q;ENSP00000412161:H11Q;ENSP00000384875:H11Q;ENSP00000385676:H11Q;ENSP00000385637:H11Q;ENSP00000427586:H11Q;ENSP00000384061:H11Q;ENSP00000425908:H11Q	ENSP00000295776:H11Q	H	+	3	2	NFASC	203180099	0.000000	0.05858	0.023000	0.16930	0.769000	0.43574	-2.069000	0.01381	-0.788000	0.04504	-0.337000	0.08149	CAT	.	.		0.592	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		G	204913476	T	G	204913476	3	3	17	1	0	0	0	0	1	0	0	0	10368	1461	51	5	35	5	NFASC	1	204913476	Missense_Mutation	SNP	T	TCGA-2Y-A9H7-01A-11D-A38X-10	32556980	204913476	44337145	6	1451										
CNIH4	29097	hgsc.bcm.edu	37	chr1	224559054	224559054	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	atacacaatcgagggcagctGaagtcacacatgaaagaagc	10	9	1	3	rs143487399		TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr1:224559054G>A	ENST00000465271.1	+	4	396	c.321G>A	c.(319-321)ctG>ctA	p.L107L	CNIH4_ENST00000366858.3_Intron|CNIH4_ENST00000366857.5_Intron|CNIH4_ENST00000468318.1_3'UTR|CNIH4_ENST00000366856.3_Silent_p.L107L	NM_014184.3	NP_054903.1	Q9P003	CNIH4_HUMAN	cornichon family AMPA receptor auxiliary protein 4	107					intracellular signal transduction (GO:0035556)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(3)|lung(2)|ovary(2)	7				GBM - Glioblastoma multiforme(131;0.00341)		GAGGGCAGCTGAAGTCACACA	0.398																																					p.L107L		Atlas-SNP	.											.	CNIH4	17	.	0			c.G321A						.						209	187	195					1																	224559054		2203	4300	6503	SO:0001819	synonymous_variant	29097	exon4			GCAGCTGAAGTCA		CCDS1543.1, CCDS60429.1, CCDS60430.1	1q42.12	2013-08-28	2013-08-28		ENSG00000143771	ENSG00000143771			25013	protein-coding gene	gene with protein product			"cornichon homolog 4 (Drosophila)"			11042152	Standard	NM_014184		Approved	HSPC163	uc001hom.2	Q9P003	OTTHUMG00000037635	ENST00000465271.1:c.321G>A	chr1.hg19:g.224559054G>A		107.0	0.0		171.0	46.0	NM_014184	A8K1Q8|B2R553|Q9H0X8	Silent	SNP	ENST00000465271.1	hg19	CCDS1543.1																																																																																			.	G|1.000;C|0.000		0.398	CNIH4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091754.1	NM_014184		A	224559054	G	A	224559054	2	1	17	1	0	0	0	0	0	0	0	1	3607	1277	45	3		3	CNIH4	1	224559054	Silent	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	19645578	224559054	24691567	7	1452										
RYR2	6262	hgsc.bcm.edu	37	chr1	237947690	237947690	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gaaagcgagaaggagaggccGgaagagcaggggccgaggat	20	6	0	3			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr1:237947690G>A	ENST00000366574.2	+	90	12995	c.12678G>A	c.(12676-12678)ccG>ccA	p.P4226P	RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Silent_p.P4210P|RYR2_ENST00000360064.6_Silent_p.P4232P	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4226					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.P4224P(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGGAGAGGCCGGAAGAGCAGG	0.547																																					p.P4226P		Atlas-SNP	.											RYR2,NS,carcinoma,+1,1	RYR2	1273	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G12678A						.						59	66	64					1																	237947690		1978	4163	6141	SO:0001819	synonymous_variant	6262	exon90			GAGGCCGGAAGAG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.12678G>A	chr1.hg19:g.237947690G>A		100.0	0.0		181.0	98.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.547	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237947690	G	A	237947690	2	1	17	1	0	0	0	0	0	0	0	1	13784	1103	39	1		1	RYR2	1	237947690	Silent	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	13388636	237947690	11302931	8	1453										
EIF2B4	8890	hgsc.bcm.edu	37	chr2	27587708	27587708	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	taactgtgctgtccctacccGtgacatcacagacccgttgg	9	14	1	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr2:27587708G>A	ENST00000347454.4	-	12	1420	c.1249C>T	c.(1249-1251)Cgg>Tgg	p.R417W	EIF2B4_ENST00000451130.2_Missense_Mutation_p.R437W|EIF2B4_ENST00000493344.2_Missense_Mutation_p.R438W|AC074117.10_ENST00000412749.1_RNA|EIF2B4_ENST00000445933.2_Missense_Mutation_p.R416W	NM_001034116.1|NM_015636.3	NP_001029288.1|NP_056451.3	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B, subunit 4 delta, 67kDa	417					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation (GO:0045947)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translation (GO:0006417)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(5)|skin(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTCCCTACCCGTGACATCACA	0.493																																					p.R437W		Atlas-SNP	.											.	EIF2B4	48	.	0			c.C1309T						.						76	68	70					2																	27587708		2203	4300	6503	SO:0001583	missense	8890	exon11			CTACCCGTGACAT	AJ011306	CCDS33164.1, CCDS46244.1, CCDS46245.1	2p23.3	2008-02-05	2002-08-29		ENSG00000115211	ENSG00000115211			3260	protein-coding gene	gene with protein product		606687	"eukaryotic translation initiation factor 2B, subunit 4 (delta, 67kD)"			8929216, 7982969	Standard	NM_172195		Approved	EIF2Bdelta, EIF-2B, DKFZP586J0119, EIF2B	uc002rjz.3	Q9UI10	OTTHUMG00000151927	ENST00000347454.4:c.1249C>T	chr2.hg19:g.27587708G>A	ENSP00000233552:p.Arg417Trp	107.0	0.0		145.0	8.0	NM_172195	Q53RY7|Q5BJF4|Q9BUV9|Q9UBG4|Q9UIQ9|Q9UJ95	Missense_Mutation	SNP	ENST00000347454.4	hg19	CCDS33164.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.798255	0.70567	.	.	ENSG00000115211	ENST00000347454;ENST00000414437;ENST00000445933;ENST00000451130;ENST00000493344	D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23	4.9	1.9	0.25705	.	0.052587	0.85682	D	0.000000	D	0.97139	0.9065	M	0.94021	3.485	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.998;0.998	D	0.97373	0.9977	10	0.87932	D	0	-9.7662	13.0216	0.58791	0.0:0.0:0.5844:0.4156	.	414;416;417;437	F5H6W1;Q9UI10-3;Q9UI10;Q9UI10-2	.;.;EI2BD_HUMAN;.	W	417;414;416;437;438	ENSP00000233552:R417W;ENSP00000394397:R416W;ENSP00000394869:R437W;ENSP00000429323:R438W	ENSP00000233552:R417W	R	-	1	2	EIF2B4	27441212	1.000000	0.71417	0.921000	0.36526	0.988000	0.76386	5.486000	0.66856	0.625000	0.30304	-0.182000	0.12963	CGG	.	.		0.493	EIF2B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324448.1			A	27587708	G	A	27587708	3	1	17	1	0	0	0	0	1	0	0	0	5005	1144	40	1	330	1	EIF2B4	2	27587708	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10		27587708	215611665	9	1454										
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40387905	40387905	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	atgcagagaaaggcactcacCagcactgacagtgatagctt	10	10	1	3			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr2:40387905C>A	ENST00000403092.1	-	9	2302	c.2269G>T	c.(2269-2271)Ggg>Tgg	p.G757W	SLC8A1-AS1_ENST00000444629.1_RNA|SLC8A1-AS1_ENST00000599268.1_RNA|SLC8A1-AS1_ENST00000597385.1_RNA|SLC8A1_ENST00000542756.1_Splice_Site_p.G752W|SLC8A1_ENST00000405901.3_Splice_Site_p.G752W|SLC8A1-AS1_ENST00000599740.1_RNA|SLC8A1-AS1_ENST00000593878.1_RNA|SLC8A1-AS1_ENST00000593848.1_RNA|SLC8A1_ENST00000402441.1_Splice_Site_p.G721W|SLC8A1_ENST00000542024.1_Splice_Site_p.G721W|SLC8A1_ENST00000406391.2_Splice_Site_p.G721W|SLC8A1-AS1_ENST00000596532.1_RNA|SLC8A1-AS1_ENST00000435515.1_RNA|SLC8A1_ENST00000405269.1_Splice_Site_p.G721W|SLC8A1_ENST00000332839.4_Splice_Site_p.G757W|SLC8A1-AS1_ENST00000599956.1_RNA|SLC8A1_ENST00000406785.2_Splice_Site_p.G721W|SLC8A1_ENST00000408028.2_Splice_Site_p.G749W|SLC8A1-AS1_ENST00000598247.1_RNA|SLC8A1-AS1_ENST00000597170.1_RNA|SLC8A1-AS1_ENST00000601679.1_RNA			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	757					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	AGGCACTCACCAGCACTGACA	0.443																																					p.G757W		Atlas-SNP	.											.	SLC8A1	221	.	0			c.G2269T						.						136	127	130					2																	40387905		2203	4300	6503	SO:0001630	splice_region_variant	6546	exon8			ACTCACCAGCACT		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.2269+1G>T	chr2.hg19:g.40387905C>A		49.0	0.0		74.0	25.0	NM_021097	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	hg19	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507187	0.85282	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.34472	1.39;1.4;1.4;1.4;1.39;1.39;1.4;1.36;1.39;1.39	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.62588	0.2440	M	0.78637	2.42	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	0.997;1.0;0.97;1.0	T	0.61978	-0.6951	9	.	.	.	.	17.4714	0.87647	0.0:1.0:0.0:0.0	.	721;744;752;757	P32418-2;P32418-3;F6VPY9;P32418	.;.;.;NAC1_HUMAN	W	721;757;752;757;752;721;721;757;749;744;721;721	ENSP00000383886:G721W;ENSP00000440727:G752W;ENSP00000384763:G757W;ENSP00000385678:G752W;ENSP00000385188:G721W;ENSP00000385535:G721W;ENSP00000332931:G757W;ENSP00000384908:G749W;ENSP00000385811:G721W;ENSP00000443515:G721W	.	G	-	1	0	SLC8A1	40241409	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.534000	0.82004	2.788000	0.95919	0.650000	0.86243	GGG	.	.		0.443	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097	Missense_Mutation	A	40387905	C	A	40387905	5	1	17	1	0	0	0	0	0	0	1	0	14721	608	21	3	664	3	SLC8A1	2	40387905	Splice_Site	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	12800197	40387905	202811468	10	1455										
ELMOD3	84173	hgsc.bcm.edu	37	chr2	85590252	85590252	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	aagaaccatggcattctccaGgctctgaccacagaagctta	8	12	2	3			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr2:85590252G>A	ENST00000409890.2	+	6	829	c.162G>A	c.(160-162)caG>caA	p.Q54Q	ELMOD3_ENST00000315658.7_Silent_p.Q54Q|ELMOD3_ENST00000490508.1_3'UTR|ELMOD3_ENST00000409344.3_Silent_p.Q54Q|ELMOD3_ENST00000393852.4_Silent_p.Q54Q|ELMOD3_ENST00000409013.3_Silent_p.Q54Q|ELMOD3_ENST00000428955.2_Silent_p.Q54Q			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3	54					phagocytosis (GO:0006909)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	12						GCATTCTCCAGGCTCTGACCA	0.522																																					p.Q54Q		Atlas-SNP	.											.	ELMOD3	53	.	0			c.G162A						.						76	73	74					2																	85590252		2203	4300	6503	SO:0001819	synonymous_variant	84173	exon6			TCTCCAGGCTCTG	AF258573	CCDS1973.1, CCDS46352.1	2p11.2	2014-01-28	2008-08-14	2008-08-14	ENSG00000115459	ENSG00000115459		"RNA binding motif (RRM) containing"	26158	protein-coding gene	gene with protein product		615427	"RNA binding motif protein 29", "RNA binding motif and ELMO/CED-12 domain 1", "deafness, autosomal recessive 88"	RBM29, RBED1, DFNB88		24039609	Standard	NM_032213		Approved	FLJ21977	uc010ysn.2	Q96FG2	OTTHUMG00000130170	ENST00000409890.2:c.162G>A	chr2.hg19:g.85590252G>A		68.0	0.0		75.0	37.0	NM_001135022	B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Silent	SNP	ENST00000409890.2	hg19	CCDS46352.1																																																																																			.	.		0.522	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213		A	85590252	G	A	85590252	2	1	17	1	0	0	0	0	0	0	0	1	5072	991	35	3		3	ELMOD3	2	85590252	Silent	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	45202347	85590252	157609121	11	1456										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160289825	160289825	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	taaccttcttcaggctcttcGatgactcttgtttctttaac	5	11	5	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr2:160289825G>C	ENST00000392783.2	-	9	1838	c.1343C>G	c.(1342-1344)tCg>tGg	p.S448W	BAZ2B_ENST00000355831.2_Missense_Mutation_p.S448W|BAZ2B_ENST00000343439.5_Missense_Mutation_p.S446W|BAZ2B_ENST00000392782.1_Missense_Mutation_p.S446W	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	448					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CAGGCTCTTCGATGACTCTTG	0.358																																					p.S448W		Atlas-SNP	.											.	BAZ2B	196	.	0			c.C1343G						.						158	148	151					2																	160289825		1885	4112	5997	SO:0001583	missense	29994	exon9			CTCTTCGATGACT	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.1343C>G	chr2.hg19:g.160289825G>C	ENSP00000376534:p.Ser448Trp	64.0	0.0		54.0	17.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	G	12.92	2.082413	0.36758	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000546335	D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43	5.87	4.98	0.66077	.	0.482216	0.15223	U	0.273830	D	0.92990	0.7769	L	0.51422	1.61	0.53688	D	0.999978	D;D;D;D;D	0.89917	1.0;0.997;0.995;0.988;0.992	D;P;P;P;P	0.79108	0.992;0.83;0.747;0.747;0.563	D	0.92865	0.6309	10	0.87932	D	0	-2.5662	16.6818	0.85294	0.0:0.1338:0.8662:0.0	.	448;252;446;446;448	Q9UIF8-3;Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;.;BAZ2B_HUMAN	W	446;448;448;446;385	ENSP00000376533:S446W;ENSP00000376534:S448W;ENSP00000348087:S448W;ENSP00000339670:S446W	ENSP00000339670:S446W	S	-	2	0	BAZ2B	159998071	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	3.703000	0.54808	1.452000	0.47756	0.655000	0.94253	TCG	.	.		0.358	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			C	160289825	G	C	160289825	3	2	17	1	0	0	0	0	1	0	0	0	1332	1059	37	4	5279	4	BAZ2B	2	160289825	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	74699573	160289825	82909548	12	1457										
LRP2	4036	hgsc.bcm.edu	37	chr2	170058284	170058284	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ggcaccctgcctcatcactgCcatcaccacagtcattgtag	7	16	4	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr2:170058284C>G	ENST00000263816.3	-	44	8591	c.8306G>C	c.(8305-8307)gGc>gCc	p.G2769A		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2769	LDL-receptor class A 17. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CTCATCACTGCCATCACCACA	0.502																																					p.G2769A		Atlas-SNP	.											.	LRP2	751	.	0			c.G8306C						.						164	137	146					2																	170058284		2203	4300	6503	SO:0001583	missense	4036	exon44			TCACTGCCATCAC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.8306G>C	chr2.hg19:g.170058284C>G	ENSP00000263816:p.Gly2769Ala	44.0	0.0		46.0	19.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815182	0.50527	.	.	ENSG00000081479	ENST00000263816	D	0.96396	-4.0	5.7	4.58	0.56647	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.229367	0.49916	D	0.000137	D	0.94225	0.8146	L	0.54908	1.71	0.80722	D	1	B	0.22541	0.071	B	0.29353	0.101	D	0.91135	0.4941	10	0.54805	T	0.06	.	9.5885	0.39532	0.0:0.0858:0.0:0.9142	.	2769	P98164	LRP2_HUMAN	A	2769	ENSP00000263816:G2769A	ENSP00000263816:G2769A	G	-	2	0	LRP2	169766530	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.202000	0.42743	1.026000	0.39733	0.650000	0.86243	GGC	.	.		0.502	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170058284	C	G	170058284	3	3	17	1	0	0	0	0	1	0	0	0	8965	739	26	4	5805	4	LRP2	2	170058284	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	9768459	170058284	73141089	13	1458										
CCDC141	285025	hgsc.bcm.edu	37	chr2	179718305	179718305	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tgcactctgtggaatattttCcaactcttacaactgtggca	7	10	2	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr2:179718305C>T	ENST00000420890.2	-	20	3224	c.3107G>A	c.(3106-3108)gGa>gAa	p.G1036E	CCDC141_ENST00000295723.5_Missense_Mutation_p.G461E	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	1036										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			GGAATATTTTCCAACTCTTAC	0.388																																					p.G1036E		Atlas-SNP	.											CCDC141_ENST00000420890,mucosal,malignant_melanoma,0,4	CCDC141	362	.	0			c.G3107A						.						111	111	111					2																	179718305		2203	4300	6503	SO:0001583	missense	285025	exon20			TATTTTCCAACTC	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.3107G>A	chr2.hg19:g.179718305C>T	ENSP00000395995:p.Gly1036Glu	55.0	0.0		104.0	37.0	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	hg19		.	.	.	.	.	.	.	.	.	.	C	17.39	3.377901	0.61735	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723	T;T;T	0.31247	1.5;1.5;1.5	5.85	5.85	0.93711	.	0.000000	0.51477	D	0.000090	T	0.29976	0.0750	L	0.34521	1.04	0.37079	D	0.898886	P	0.49358	0.923	P	0.47470	0.548	T	0.06972	-1.0797	10	0.22109	T	0.4	-12.8104	14.34	0.66619	0.0:0.9295:0.0:0.0704	.	461	Q6ZP82	CC141_HUMAN	E	1036;480;461	ENSP00000395995:G1036E;ENSP00000344627:G480E;ENSP00000295723:G461E	ENSP00000295723:G461E	G	-	2	0	CCDC141	179426550	0.998000	0.40836	0.998000	0.56505	0.960000	0.62799	3.951000	0.56684	2.768000	0.95171	0.655000	0.94253	GGA	.	.		0.388	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		T	179718305	C	T	179718305	3	4	17	1	0	0	0	0	1	0	0	0	2777	855	30	3	1261	3	CCDC141	2	179718305	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	9660021	179718305	63481068	14	1459										
THUMPD3	25917	hgsc.bcm.edu	37	chr3	9412987	9412987	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tagattattatgaaaatccaGccatcaaagaggatgtatca	7	6	2	3			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr3:9412987G>A	ENST00000345094.3	+	4	908	c.574G>A	c.(574-576)Gcc>Acc	p.A192T	THUMPD3_ENST00000515662.2_Missense_Mutation_p.A192T|THUMPD3_ENST00000452837.2_Missense_Mutation_p.A192T|SETD5-AS1_ENST00000468186.1_RNA	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	192	THUMP. {ECO:0000255|PROSITE- ProRule:PRU00529}.					cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		TGAAAATCCAGCCATCAAAGA	0.343																																					p.A192T		Atlas-SNP	.											.	THUMPD3	46	.	0			c.G574A						.						72	77	75					3																	9412987		2203	4300	6503	SO:0001583	missense	25917	exon4			AATCCAGCCATCA	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.574G>A	chr3.hg19:g.9412987G>A	ENSP00000339532:p.Ala192Thr	186.0	0.0		222.0	75.0	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Missense_Mutation	SNP	ENST00000345094.3	hg19	CCDS2573.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.01|15.01	2.707154|2.707154	0.48412|0.48412	.|.	.|.	ENSG00000134077|ENSG00000134077	ENST00000452837;ENST00000345094;ENST00000515662|ENST00000416603	T;T;T|.	0.43294|.	0.95;0.95;0.95|.	5.94|5.94	5.06|5.06	0.68205|0.68205	THUMP (2);|.	0.480071|.	0.23766|.	N|.	0.044768|.	T|T	0.62036|0.62036	0.2395|0.2395	L|L	0.57536|0.57536	1.79|1.79	0.41436|0.41436	D|D	0.98789|0.98789	B|.	0.14012|.	0.009|.	B|.	0.15484|.	0.013|.	T|T	0.59456|0.59456	-0.7451|-0.7451	10|5	0.24483|.	T|.	0.36|.	-10.5002|-10.5002	9.6357|9.6357	0.39806|0.39806	0.0771:0.1447:0.7782:0.0|0.0771:0.1447:0.7782:0.0	.|.	192|.	Q9BV44|.	THUM3_HUMAN|.	T|N	192|24	ENSP00000395893:A192T;ENSP00000339532:A192T;ENSP00000424064:A192T|.	ENSP00000339532:A192T|.	A|S	+|+	1|2	0|0	THUMPD3|THUMPD3	9387987|9387987	0.481000|0.481000	0.25941|0.25941	1.000000|1.000000	0.80357|0.80357	0.923000|0.923000	0.55619|0.55619	1.687000|1.687000	0.37680|0.37680	2.826000|2.826000	0.97356|0.97356	0.561000|0.561000	0.74099|0.74099	GCC|AGC	.	.		0.343	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453		A	9412987	G	A	9412987	3	1	17	1	0	0	0	0	1	0	0	0	15899	971	34	3	584	3	THUMPD3	3	9412987	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10		9412987	188609443	15	1460										
CAMK1	8536	hgsc.bcm.edu	37	chr3	9807539	9807539	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ccaccagcttctgcgtcctcTtatcttctgccaggatcacc	6	17	5	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr3:9807539T>A	ENST00000256460.3	-	3	296	c.119A>T	c.(118-120)aAg>aTg	p.K40M	OGG1_ENST00000302036.7_Missense_Mutation_p.L332H|OGG1_ENST00000349503.5_Missense_Mutation_p.L265H|OGG1_ENST00000449570.2_3'UTR|OGG1_ENST00000302008.8_3'UTR|OGG1_ENST00000383826.5_3'UTR	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	40	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|nucleocytoplasmic transport (GO:0006913)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of synapse structural plasticity (GO:0051835)|protein phosphorylation (GO:0006468)|regulation of muscle cell differentiation (GO:0051147)|regulation of protein binding (GO:0043393)|regulation of protein localization (GO:0032880)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	12	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		CTGCGTCCTCTTATCTTCTGC	0.577																																					p.L332H		Atlas-SNP	.											.	OGG1	57	.	0			c.T995A						.						81	75	77					3																	9807539		2203	4300	6503	SO:0001583	missense	4968	exon7			GTCCTCTTATCTT	L41816	CCDS2582.1	3p25.3	2004-02-27			ENSG00000134072	ENSG00000134072			1459	protein-coding gene	gene with protein product		604998				7641687	Standard	NM_003656		Approved	CaMKI	uc003bst.3	Q14012	OTTHUMG00000128419	ENST00000256460.3:c.119A>T	chr3.hg19:g.9807539T>A	ENSP00000256460:p.Lys40Met	63.0	0.0		78.0	34.0	NM_016821	Q3KPF6	Missense_Mutation	SNP	ENST00000256460.3	hg19	CCDS2582.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.50|19.50	3.838995|3.838995	0.71373|0.71373	.|.	.|.	ENSG00000134072|ENSG00000114026	ENST00000256460|ENST00000302036;ENST00000349503	T|T;T	0.68025|0.62941	-0.3|-0.01;0.79	4.87|4.87	4.87|4.87	0.63330|0.63330	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.051090|.	0.85682|.	D|.	0.000000|.	T|T	0.75391|0.75391	0.3843|0.3843	M|M	0.75264|0.75264	2.295|2.295	0.80722|0.80722	D|D	1|1	P|D;D	0.41978|0.76494	0.767|0.999;0.998	P|D;P	0.50490|0.69479	0.642|0.964;0.819	T|T	0.76299|0.76299	-0.3010|-0.3010	10|9	0.72032|0.45353	D|T	0.01|0.12	0.356|0.356	10.8818|10.8818	0.46944|0.46944	0.0:0.0775:0.0:0.9225|0.0:0.0775:0.0:0.9225	.|.	40|265;332	Q14012|E5KPM6;E5KPM5	KCC1A_HUMAN|.;.	M|H	40|332;265	ENSP00000256460:K40M|ENSP00000306561:L332H;ENSP00000303132:L265H	ENSP00000256460:K40M|ENSP00000306561:L332H	K|L	-|+	2|2	0|0	CAMK1|OGG1	9782539|9782539	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.706000|0.706000	0.40770|0.40770	3.427000|3.427000	0.52785|0.52785	1.952000|1.952000	0.56665|0.56665	0.374000|0.374000	0.22700|0.22700	AAG|CTT	.	.		0.577	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656		A	9807539	T	A	9807539	3	1	17	1	0	0	0	0	1	0	0	0	2598	1609	56	4	1033	4	CAMK1	3	9807539	Missense_Mutation	SNP	T	TCGA-2Y-A9H7-01A-11D-A38X-10	394552	9807539	188214891	16	1461										
HDAC11	79885	hgsc.bcm.edu	37	chr3	13546008	13546008	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gctggtgttccggatggtccGtggccgccgggtgcccatcc	16	14	0	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr3:13546008G>A	ENST00000295757.3	+	10	1052	c.869G>A	c.(868-870)cGt>cAt	p.R290H	HDAC11_ENST00000402271.1_Missense_Mutation_p.R211H|HDAC11_ENST00000402259.1_Missense_Mutation_p.R124H|HDAC11_ENST00000522202.1_Missense_Mutation_p.R239H|HDAC11_ENST00000405025.1_3'UTR|HDAC11_ENST00000404040.1_Missense_Mutation_p.R190H|HDAC11_ENST00000446613.2_Missense_Mutation_p.R98H|HDAC11_ENST00000433119.1_3'UTR|HDAC11_ENST00000404548.1_3'UTR|HDAC11_ENST00000437379.2_Missense_Mutation_p.R262H	NM_024827.3	NP_079103.2	Q96DB2	HDA11_HUMAN	histone deacetylase 11	290	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|oligodendrocyte development (GO:0014003)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(4)|prostate(3)	13						CGGATGGTCCGTGGCCGCCGG	0.612																																					p.R290H		Atlas-SNP	.											.	HDAC11	39	.	0			c.G869A						.						86	72	77					3																	13546008		2203	4300	6503	SO:0001583	missense	79885	exon10			TGGTCCGTGGCCG	AK025426	CCDS2615.1, CCDS46760.1	3p25.1	2008-07-18			ENSG00000163517	ENSG00000163517	3.5.1.98		19086	protein-coding gene	gene with protein product		607226				11948178	Standard	NM_001136041		Approved		uc003bxy.3	Q96DB2	OTTHUMG00000129800	ENST00000295757.3:c.869G>A	chr3.hg19:g.13546008G>A	ENSP00000295757:p.Arg290His	71.0	0.0		51.0	22.0	NM_024827	B4DDK1|Q9H6I7|Q9H6X3|Q9NTC9	Missense_Mutation	SNP	ENST00000295757.3	hg19	CCDS2615.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.157660	0.78114	.	.	ENSG00000163517	ENST00000295757;ENST00000402259;ENST00000402271;ENST00000446613;ENST00000404040;ENST00000522202;ENST00000437379	T;T;T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49;-0.49;-0.49	5.38	5.38	0.77491	Histone deacetylase domain (2);	0.179190	0.45867	D	0.000325	D	0.83640	0.5298	M	0.75447	2.3	0.51767	D	0.999934	D;D	0.89917	1.0;1.0	D;D	0.72338	0.967;0.977	D	0.85555	0.1224	10	0.87932	D	0	-13.9604	16.6271	0.84974	0.0:0.0:1.0:0.0	.	239;290	B4DDK1;Q96DB2	.;HDA11_HUMAN	H	290;124;211;98;190;239;262	ENSP00000295757:R290H;ENSP00000384706:R124H;ENSP00000384123:R211H;ENSP00000401487:R98H;ENSP00000385475:R190H;ENSP00000429794:R239H;ENSP00000395188:R262H	ENSP00000295757:R290H	R	+	2	0	HDAC11	13521008	1.000000	0.71417	0.918000	0.36340	0.436000	0.31835	5.150000	0.64869	2.516000	0.84829	0.561000	0.74099	CGT	.	.		0.612	HDAC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252028.5	NM_024827		A	13546008	G	A	13546008	3	1	17	1	0	0	0	0	1	0	0	0	7015	1145	40	1	907	1	HDAC11	3	13546008	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	3738469	13546008	184476422	17	1462										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51297607	51297607	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gccttggagtaccttttcaaGttcattgtacagtcacggat	9	9	3	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr3:51297607G>A	ENST00000266037.9	+	23	2228	c.2205G>A	c.(2203-2205)aaG>aaA	p.K735K		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	735					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ACCTTTTCAAGTTCATTGTAC	0.458																																					p.K735K		Atlas-SNP	.											.	DOCK3	397	.	0			c.G2205A						.						89	87	88					3																	51297607		1937	4148	6085	SO:0001819	synonymous_variant	1795	exon23			TTTCAAGTTCATT	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.2205G>A	chr3.hg19:g.51297607G>A		68.0	0.0		87.0	36.0	NM_004947	O15017	Silent	SNP	ENST00000266037.9	hg19	CCDS46835.1																																																																																			.	.		0.458	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		A	51297607	G	A	51297607	2	1	17	1	0	0	0	0	0	0	0	1	4690	1020	36	3		3	DOCK3	3	51297607	Silent	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	37751599	51297607	146724823	18	1463										
ZDHHC23	254887	hgsc.bcm.edu	37	chr3	113672983	113672983	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gctacctcagcaatccagcaAgcggtgacagatctctaagc	9	13	2	2	rs370935137		TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr3:113672983A>T	ENST00000330212.3	+	3	897	c.598A>T	c.(598-600)Agc>Tgc	p.S200C	ZDHHC23_ENST00000498275.1_Missense_Mutation_p.S194C	NM_173570.3	NP_775841.2	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC-type containing 23	200					protein localization to plasma membrane (GO:0072659)|protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|urinary_tract(2)	16						CAATCCAGCAAGCGGTGACAG	0.557																																					p.S200C		Atlas-SNP	.											.	ZDHHC23	38	.	0			c.A598T						.						110	116	114					3																	113672983		2203	4300	6503	SO:0001583	missense	254887	exon3			CCAGCAAGCGGTG	AK127025	CCDS33827.1	3q13.31	2008-05-02			ENSG00000184307	ENSG00000184307		"Zinc fingers, DHHC-type"	28654	protein-coding gene	gene with protein product						12477932	Standard	NM_173570		Approved	MGC42530	uc003eau.3	Q8IYP9	OTTHUMG00000159335	ENST00000330212.3:c.598A>T	chr3.hg19:g.113672983A>T	ENSP00000330485:p.Ser200Cys	145.0	0.0		164.0	56.0	NM_173570	D3DN76	Missense_Mutation	SNP	ENST00000330212.3	hg19	CCDS33827.1	.	.	.	.	.	.	.	.	.	.	A	7.063	0.566726	0.13560	.	.	ENSG00000184307	ENST00000330212;ENST00000498275	T;T	0.47177	0.85;0.85	5.7	-7.1	0.01547	.	1.044020	0.07344	N	0.881239	T	0.26085	0.0636	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.14023	0.01	T	0.29761	-1.0001	10	0.49607	T	0.09	-1.1867	4.2589	0.10732	0.3561:0.1858:0.3739:0.0843	.	200	Q8IYP9	ZDH23_HUMAN	C	200;194	ENSP00000330485:S200C;ENSP00000417840:S194C	ENSP00000330485:S200C	S	+	1	0	ZDHHC23	115155673	0.000000	0.05858	0.001000	0.08648	0.195000	0.23768	0.013000	0.13310	-0.777000	0.04572	0.459000	0.35465	AGC	.	.		0.557	ZDHHC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354702.1	NM_173570		T	113672983	A	T	113672983	3	4	17	1	0	0	0	0	1	0	0	0	17629	72	3	4	604	4	ZDHHC23	3	113672983	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10	62375376	113672983	84349447	19	1464										
FXR1	8087	hgsc.bcm.edu	37	chr3	180666144	180666144	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	atgtcttttagttttatgtcAttgaatatgctgcttgtgac	8	5	2	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr3:180666144A>G	ENST00000357559.4	+	5	664	c.280A>G	c.(280-282)Att>Gtt	p.I94V	FXR1_ENST00000480918.1_Missense_Mutation_p.I81V|FXR1_ENST00000445140.2_Missense_Mutation_p.I94V|FXR1_ENST00000491062.1_Missense_Mutation_p.I45V|FXR1_ENST00000305586.7_Missense_Mutation_p.I9V|FXR1_ENST00000468861.1_Missense_Mutation_p.I9V	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	94	Agenet-like 2.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			GTTTTATGTCATTGAATATGC	0.303																																					p.I94V		Atlas-SNP	.											.	FXR1	75	.	0			c.A280G						.						37	38	38					3																	180666144		2201	4300	6501	SO:0001583	missense	8087	exon5			TATGTCATTGAAT	M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.280A>G	chr3.hg19:g.180666144A>G	ENSP00000350170:p.Ile94Val	80.0	0.0		99.0	40.0	NM_001013438	A8K9B8|Q7Z450|Q8N6R8	Missense_Mutation	SNP	ENST00000357559.4	hg19	CCDS3238.1	.	.	.	.	.	.	.	.	.	.	A	17.93	3.508970	0.64410	.	.	ENSG00000114416	ENST00000469882;ENST00000484790;ENST00000465551;ENST00000357559;ENST00000305586;ENST00000491062;ENST00000468861;ENST00000445140;ENST00000484958;ENST00000480918;ENST00000484042	T;T;T;T;T;T;T;T;T;T;T	0.44881	0.96;0.93;0.91;2.09;1.76;1.18;1.27;1.4;1.01;1.96;0.97	5.83	5.83	0.93111	Agenet (1);	0.000000	0.85682	D	0.000000	T	0.54415	0.1857	L	0.33189	0.99	0.80722	D	1	P;D;D;D;B;B	0.63046	0.894;0.992;0.983;0.967;0.022;0.288	D;D;D;D;B;P	0.83275	0.979;0.996;0.977;0.946;0.158;0.848	T	0.51942	-0.8641	10	0.39692	T	0.17	-21.9532	16.2005	0.82071	1.0:0.0:0.0:0.0	.	81;45;9;9;94;94	B4DXZ6;E9PFF5;E7EU85;E7ERF5;P51114-2;P51114	.;.;.;.;.;FXR1_HUMAN	V	9;9;9;94;9;45;9;94;9;81;98	ENSP00000419793:I9V;ENSP00000417125:I9V;ENSP00000418724:I9V;ENSP00000350170:I94V;ENSP00000307633:I9V;ENSP00000420643:I45V;ENSP00000420515:I9V;ENSP00000388828:I94V;ENSP00000419933:I9V;ENSP00000418097:I81V;ENSP00000417513:I98V	ENSP00000307633:I9V	I	+	1	0	FXR1	182148838	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.227000	0.72691	0.528000	0.53228	ATT	.	.		0.303	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5			G	180666144	A	G	180666144	3	3	17	1	0	0	0	0	1	0	0	0	6123	217	8	2	298	2	FXR1	3	180666144	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10	66993161	180666144	17356286	20	1465										
NPFFR2	10886	hgsc.bcm.edu	37	chr4	72994622	72994622	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	catgcctataacactgctggAcaatattatagcaggtatgt	8	8	0	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr4:72994622A>G	ENST00000308744.6	+	2	718	c.620A>G	c.(619-621)gAc>gGc	p.D207G	NPFFR2_ENST00000358749.3_Missense_Mutation_p.D105G|NPFFR2_ENST00000344413.5_Intron|NPFFR2_ENST00000395999.1_Missense_Mutation_p.D108G	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	207					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			ACACTGCTGGACAATATTATA	0.383																																					p.D207G		Atlas-SNP	.											.	NPFFR2	98	.	0			c.A620G						.						106	102	104					4																	72994622		2203	4300	6503	SO:0001583	missense	10886	exon2			TGCTGGACAATAT	AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"GPCR / Class A :  Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors"	4525	protein-coding gene	gene with protein product	"neuropeptide FF 2"	607449	"G protein-coupled receptor 74"	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.620A>G	chr4.hg19:g.72994622A>G	ENSP00000307822:p.Asp207Gly	70.0	0.0		70.0	27.0	NM_004885	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	hg19	CCDS3551.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.979105	0.74360	.	.	ENSG00000056291	ENST00000308744;ENST00000395999;ENST00000358749	T;T;T	0.38240	1.15;1.15;1.15	5.75	5.75	0.90469	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000057	T	0.55016	0.1894	M	0.66297	2.02	0.80722	D	1	P;P	0.48407	0.819;0.91	P;P	0.61132	0.616;0.884	T	0.49542	-0.8929	10	0.27082	T	0.32	.	15.7296	0.77790	1.0:0.0:0.0:0.0	.	108;207	Q9Y5X5-3;Q9Y5X5	.;NPFF2_HUMAN	G	207;108;105	ENSP00000307822:D207G;ENSP00000379321:D108G;ENSP00000351599:D105G	ENSP00000307822:D207G	D	+	2	0	NPFFR2	73213486	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	9.136000	0.94489	2.188000	0.69820	0.528000	0.53228	GAC	.	.		0.383	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		G	72994622	A	G	72994622	3	3	17	1	0	0	0	0	1	0	0	0	10587	275	10	2	632	2	NPFFR2	4	72994622	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10		72994622	118159654	21	1466										
COQ2	27235	hgsc.bcm.edu	37	chr4	84205844	84205844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ccagggcgaaggagcggcccCgccagcccggcagccacgcc	15	19	0	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr4:84205844C>T	ENST00000311469.4	-	1	223	c.224G>A	c.(223-225)cGg>cAg	p.R75Q	COQ2_ENST00000439031.2_Missense_Mutation_p.R38Q|COQ2_ENST00000311461.7_Missense_Mutation_p.R25Q	NM_015697.7	NP_056512.5	Q96H96	COQ2_HUMAN	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	25					cell death (GO:0008219)|glycerol metabolic process (GO:0006071)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	4-hydroxybenzoate decaprenyltransferase activity (GO:0002083)|4-hydroxybenzoate nonaprenyltransferase activity (GO:0047293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)	8		Hepatocellular(203;0.114)				GGAGCGGCCCCGCCAGCCCGG	0.786																																					p.R75Q		Atlas-SNP	.											.	COQ2	22	.	0			c.G224A						.						2	2	2					4																	84205844		878	2038	2916	SO:0001583	missense	27235	exon1			CGGCCCCGCCAGC		CCDS47090.1, CCDS47090.2	4q21.23	2013-05-23	2013-05-23				2.5.1.39		25223	protein-coding gene	gene with protein product	"4-hydroxybenzoate polyprenyltransferase"	609825	"coenzyme Q2 homolog, prenyltransferase (yeast)"			15153069, 17332895	Standard	NM_015697		Approved	CL640, FLJ26072	uc003hog.3	Q96H96		ENST00000311469.4:c.224G>A	chr4.hg19:g.84205844C>T	ENSP00000310873:p.Arg75Gln	502.0	0.0		550.0	249.0	NM_015697	O95331|Q1JQ78|Q684R2	Missense_Mutation	SNP	ENST00000311469.4	hg19	CCDS47090.2	.	.	.	.	.	.	.	.	.	.	C	13.43	2.234729	0.39498	.	.	ENSG00000173085	ENST00000311469;ENST00000439031;ENST00000311461	T;T;T	0.79554	-1.26;-1.21;-1.28	3.33	0.579	0.17397	.	1.239200	0.05804	N	0.612818	T	0.68604	0.3019	L	0.40543	1.245	0.09310	N	1	B;B	0.19583	0.037;0.037	B;B	0.04013	0.001;0.001	T	0.45818	-0.9235	10	0.19590	T	0.45	-20.464	3.4231	0.07401	0.0:0.5306:0.2181:0.2513	.	25;25	E2QRG7;Q96H96	.;COQ2_HUMAN	Q	75;38;25	ENSP00000310873:R75Q;ENSP00000409275:R38Q;ENSP00000311835:R25Q	ENSP00000311835:R25Q	R	-	2	0	COQ2	84424868	0.000000	0.05858	0.000000	0.03702	0.152000	0.21847	-0.315000	0.08081	0.072000	0.16694	-0.499000	0.04595	CGG	.	.		0.786	COQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363027.3	NM_015697		T	84205844	C	T	84205844	3	4	17	1	0	0	0	0	1	0	0	0	3747	652	23	1	1069	1	COQ2	4	84205844	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	11211222	84205844	106948432	22	1467										
TET2	54790	hgsc.bcm.edu	37	chr4	106164733	106164733	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ggtgatccacgcaggtggttCgcagaagcagcagtgaagag	16	8	0	4			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr4:106164733C>T	ENST00000540549.1	+	6	4461	c.3601C>T	c.(3601-3603)Cgc>Tgc	p.R1201C	TET2_ENST00000380013.4_Missense_Mutation_p.R1201C|TET2_ENST00000513237.1_Missense_Mutation_p.R1222C|TET2_ENST00000545826.1_Silent_p.F1170F			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1201					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		GCAGGTGGTTCGCAGAAGCAG	0.527			"Mis N, F"		MDS																																p.R1201C		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.C3601T						.						186	175	178					4																	106164733		692	1591	2283	SO:0001583	missense	54790	exon6			GTGGTTCGCAGAA	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.3601C>T	chr4.hg19:g.106164733C>T	ENSP00000442788:p.Arg1201Cys	73.0	0.0		64.0	20.0	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	hg19	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.423447	0.83559	.	.	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.42513	0.97;0.97;0.97	5.64	4.77	0.60923	TET cysteine-rich domain (1);	.	.	.	.	T	0.69106	0.3074	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.75178	-0.3409	9	0.87932	D	0	.	16.0104	0.80399	0.1348:0.8651:0.0:0.0	.	1222;1201	E7EQS8;Q6N021	.;TET2_HUMAN	C	1201;1222;1201	ENSP00000442788:R1201C;ENSP00000425443:R1222C;ENSP00000369351:R1201C	ENSP00000369351:R1201C	R	+	1	0	TET2	106384182	1.000000	0.71417	0.884000	0.34674	0.514000	0.34195	7.684000	0.84104	2.664000	0.90586	0.655000	0.94253	CGC	.	.		0.527	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106164733	C	T	106164733	3	4	17	1	0	0	0	0	1	0	0	0	15785	884	31	1	3704	1	TET2	4	106164733	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	21958889	106164733	84989543	23	1468										
FAT1	2195	hgsc.bcm.edu	37	chr4	187630712	187630712	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cttagaaagcaaaagtctccGagaatgtactcttcagcttt	7	9	3	2	rs373265178		TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr4:187630712G>A	ENST00000441802.2	-	2	479	c.270C>T	c.(268-270)ctC>ctT	p.L90L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	90	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L90L(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AAAAGTCTCCGAGAATGTACT	0.393										HNSCC(5;0.00058)																											p.L90L	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,colon,carcinoma,0,1	FAT1	500	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C270T						.	G		1,3767		0,1,1883	90	83	85		270	-4.1	0.7	4		85	0,8226		0,0,4113	no	coding-synonymous	FAT1	NM_005245.3		0,1,5996	AA,AG,GG		0.0,0.0265,0.0083		90/4589	187630712	1,11993	1884	4113	5997	SO:0001819	synonymous_variant	2195	exon2			GTCTCCGAGAATG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.270C>T	chr4.hg19:g.187630712G>A		81.0	0.0		96.0	38.0	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.393	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187630712	G	A	187630712	2	1	17	1	0	0	0	0	0	0	0	1	5697	1045	37	1		1	FAT1	4	187630712	Silent	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	81465979	187630712	3523564	24	1469										
SNCB	6620	hgsc.bcm.edu	37	chr5	176056620	176056620	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gcggctgccacaacgccctcCttggccatggacaggccctt	11	17	0	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr5:176056620C>T	ENST00000310112.3	-	3	286	c.36G>A	c.(34-36)aaG>aaA	p.K12K	SNCB_ENST00000393693.2_Silent_p.K12K|MIR4281_ENST00000580852.1_RNA|SNCB_ENST00000506696.1_Silent_p.K12K|EIF4E1B_ENST00000318682.6_5'Flank|SNCB_ENST00000510387.1_Silent_p.K12K	NM_001001502.1	NP_001001502.1	Q16143	SYUB_HUMAN	synuclein, beta	12					dopamine metabolic process (GO:0042417)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|inclusion body (GO:0016234)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|terminal bouton (GO:0043195)	calcium ion binding (GO:0005509)|phospholipase inhibitor activity (GO:0004859)			breast(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	10	all_cancers(89;0.00222)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAACGCCCTCCTTGGCCATGG	0.682																																					p.K12K		Atlas-SNP	.											.	SNCB	20	.	0			c.G36A						.						47	37	40					5																	176056620		2203	4300	6503	SO:0001819	synonymous_variant	6620	exon3			GCCCTCCTTGGCC	AF053134	CCDS4406.1	5q35	2008-07-18			ENSG00000074317	ENSG00000074317			11140	protein-coding gene	gene with protein product		602569				7558013, 9806846	Standard	NM_003085		Approved		uc003meq.3	Q16143	OTTHUMG00000130661	ENST00000310112.3:c.36G>A	chr5.hg19:g.176056620C>T		147.0	0.0		147.0	63.0	NM_001001502	Q6IAX7	Silent	SNP	ENST00000310112.3	hg19	CCDS4406.1																																																																																			.	.		0.682	SNCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253152.2	NM_001001502		T	176056620	C	T	176056620	2	4	17	1	0	0	0	0	0	0	0	1	14857	680	24	3		3	SNCB	5	176056620	Silent	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10		176056620	4858640	25	1470										
ZFP2	80108	hgsc.bcm.edu	37	chr5	178358992	178358992	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ggtaaagcttttacccaaagCatgaatttgacagttcatca	7	8	2	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr5:178358992C>T	ENST00000361362.2	+	5	1208	c.678C>T	c.(676-678)agC>agT	p.S226S	ZFP2_ENST00000520301.1_Silent_p.S226S|ZFP2_ENST00000503510.2_Silent_p.S226S|ZFP2_ENST00000523286.1_Silent_p.S226S	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	226					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		TTACCCAAAGCATGAATTTGA	0.363																																					p.S226S		Atlas-SNP	.											.	ZFP2	70	.	0			c.C678T						.						48	51	50					5																	178358992		2203	4300	6503	SO:0001819	synonymous_variant	80108	exon5			CCAAAGCATGAAT	AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"Zinc fingers, C2H2-type"	26138	protein-coding gene	gene with protein product			"zinc finger protein 2 homolog (mouse)"				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.678C>T	chr5.hg19:g.178358992C>T		70.0	0.0		98.0	42.0	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Silent	SNP	ENST00000361362.2	hg19	CCDS4440.1																																																																																			.	.		0.363	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613		T	178358992	C	T	178358992	2	4	17	1	0	0	0	0	0	0	0	1	17656	709	25	3		3	ZFP2	5	178358992	Silent	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	2302372	178358992	2556268	26	1471										
SFRS3	6428	hgsc.bcm.edu	37	chr6	36564715	36564715	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	atttgaagatccccgagatgCagctgatgcagtccgagagc	12	10	0	5			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr6:36564715C>A	ENST00000373715.6	+	2	292	c.176C>A	c.(175-177)gCa>gAa	p.A59E	SRSF3_ENST00000339436.7_Missense_Mutation_p.A59E	NM_003017.4	NP_003008.1	P84103	SRSF3_HUMAN	serine/arginine-rich splicing factor 3	59	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.|Sufficiernt for interaction with NXF1.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(2)	7						CCCCGAGATGCAGCTGATGCA	0.428																																					p.A59E		Atlas-SNP	.											.	SRSF3	28	.	0			c.C176A						.						62	65	64					6																	36564715		2203	4300	6503	SO:0001583	missense	6428	exon2			GAGATGCAGCTGA	L10838	CCDS4823.1	6p21	2013-02-12	2010-06-22	2010-06-22	ENSG00000112081	ENSG00000112081		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10785	protein-coding gene	gene with protein product		603364	"splicing factor, arginine/serine-rich 3"	SFRS3		1577277, 20516191	Standard	NM_003017		Approved	SRp20	uc003omj.3	P84103	OTTHUMG00000014599	ENST00000373715.6:c.176C>A	chr6.hg19:g.36564715C>A	ENSP00000362820:p.Ala59Glu	87.0	0.0		96.0	35.0	NM_003017	B4E241|O08831|P23152|Q5R3K0	Missense_Mutation	SNP	ENST00000373715.6	hg19	CCDS4823.1	.	.	.	.	.	.	.	.	.	.	C	36	5.632616	0.96682	.	.	ENSG00000112081	ENST00000373715;ENST00000339436	T;D	0.84660	1.47;-1.88	5.47	5.47	0.80525	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.94837	0.8332	H	0.95402	3.665	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.87578	0.997;0.998	D	0.95687	0.8737	10	0.87932	D	0	.	19.7017	0.96057	0.0:1.0:0.0:0.0	.	59;59	B4E241;P84103	.;SRSF3_HUMAN	E	59	ENSP00000362820:A59E;ENSP00000344762:A59E	ENSP00000344762:A59E	A	+	2	0	SRSF3	36672693	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.776000	0.85560	2.724000	0.93272	0.561000	0.74099	GCA	.	.		0.428	SRSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040347.2	NM_003017		A	36564715	C	A	36564715	3	1	17	1	0	0	0	0	1	0	0	0	14193	710	25	3	178	3	SFRS3	6	36564715	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10		36564715	134550352	27	1472										
TREML1	340205	hgsc.bcm.edu	37	chr6	41121748	41121748	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ctgagctttgacatcctggaGcctgtagtggcactgcacca	11	12	0	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr6:41121748G>C	ENST00000426005.2	-	2	167	c.124C>G	c.(124-126)Ctc>Gtc	p.L42V	TREML1_ENST00000437044.2_Intron|TREML1_ENST00000373127.4_Missense_Mutation_p.L42V	NM_178174.2	NP_835468.1	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid cells-like 1	42	Ig-like V-type.				calcium-mediated signaling (GO:0019722)|innate immune response (GO:0045087)|platelet activation (GO:0030168)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)				breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					ACATCCTGGAGCCTGTAGTGG	0.632																																					p.L42V		Atlas-SNP	.											.	TREML1	20	.	0			c.C124G						.						36	38	37					6																	41121748		2203	4300	6503	SO:0001583	missense	340205	exon2			CCTGGAGCCTGTA	AF534822	CCDS4851.1, CCDS64420.1, CCDS64421.1	6p21.1	2013-01-11			ENSG00000161911	ENSG00000161911		"Immunoglobulin superfamily / V-set domain containing"	20434	protein-coding gene	gene with protein product	"TREM-like transcript 1"	609714				12393607, 12645956	Standard	NM_178174		Approved	TLT1, dJ238O23.3	uc011duc.3	Q86YW5	OTTHUMG00000016231	ENST00000426005.2:c.124C>G	chr6.hg19:g.41121748G>C	ENSP00000402855:p.Leu42Val	81.0	0.0		93.0	41.0	NM_178174	Q496B3|Q8IWY1|Q8IWY2	Missense_Mutation	SNP	ENST00000426005.2	hg19	CCDS4851.1	.	.	.	.	.	.	.	.	.	.	G	7.986	0.752245	0.15778	.	.	ENSG00000161911	ENST00000373127;ENST00000426005	T;T	0.21734	1.99;1.99	5.97	5.97	0.96955	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.514439	0.18110	N	0.151384	T	0.13157	0.0319	L	0.58669	1.825	0.80722	D	1	B;B	0.34161	0.397;0.439	B;B	0.31442	0.13;0.066	T	0.02417	-1.1162	10	0.29301	T	0.29	.	15.9281	0.79635	0.0:0.0:1.0:0.0	.	42;42	Q86YW5;Q86YW5-2	TRML1_HUMAN;.	V	42	ENSP00000362219:L42V;ENSP00000402855:L42V	ENSP00000362219:L42V	L	-	1	0	TREML1	41229726	0.462000	0.25791	0.207000	0.23584	0.032000	0.12392	4.697000	0.61782	2.837000	0.97791	0.655000	0.94253	CTC	.	.		0.632	TREML1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043538.2	NM_178174		C	41121748	G	C	41121748	3	2	17	1	0	0	0	0	1	0	0	0	16487	971	34	4	829	4	TREML1	6	41121748	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	4557033	41121748	129993319	28	1473										
FOXP4	116113	hgsc.bcm.edu	37	chr6	41558024	41558024	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cccagagctggcccagaatcAtgagttctacaagaacgccg	10	13	2	4			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr6:41558024A>G	ENST00000307972.4	+	11	1385	c.1373A>G	c.(1372-1374)cAt>cGt	p.H458R	FOXP4_ENST00000373063.3_Missense_Mutation_p.H445R|FOXP4_ENST00000373057.3_Missense_Mutation_p.H456R|FOXP4_ENST00000409208.1_Missense_Mutation_p.H446R|FOXP4_ENST00000373060.1_Missense_Mutation_p.H458R			Q8IVH2	FOXP4_HUMAN	forkhead box P4	458					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GCCCAGAATCATGAGTTCTAC	0.622																																					p.H458R		Atlas-SNP	.											.	FOXP4	83	.	0			c.A1373G						.						108	116	113					6																	41558024		2203	4300	6503	SO:0001583	missense	116113	exon12			AGAATCATGAGTT	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"Forkhead boxes"	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.1373A>G	chr6.hg19:g.41558024A>G	ENSP00000309823:p.His458Arg	102.0	0.0		108.0	36.0	NM_001012426	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	hg19	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.074509	0.36566	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	D;D;D;D;D	0.89617	-2.5;-2.54;-2.53;-2.5;-2.5	3.95	3.95	0.45737	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.128751	0.53938	D	0.000058	T	0.73536	0.3599	L	0.36672	1.1	0.41306	D	0.987076	B;B;B	0.17465	0.022;0.012;0.011	B;B;B	0.14578	0.009;0.011;0.002	T	0.69986	-0.4996	10	0.20519	T	0.43	.	13.147	0.59467	1.0:0.0:0.0:0.0	.	445;456;458	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	R	458;445;446;456;458	ENSP00000362151:H458R;ENSP00000362154:H445R;ENSP00000386958:H446R;ENSP00000362148:H456R;ENSP00000309823:H458R	ENSP00000309823:H458R	H	+	2	0	FOXP4	41666002	1.000000	0.71417	0.987000	0.45799	0.958000	0.62258	6.296000	0.72751	1.576000	0.49790	0.374000	0.22700	CAT	.	.		0.622	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		G	41558024	A	G	41558024	3	3	17	1	0	0	0	0	1	0	0	0	6037	217	8	2	1415	2	FOXP4	6	41558024	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10	436276	41558024	129557043	29	1474										
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	10	12	0	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000230354.6_Silent_p.Q60Q|TBP_ENST00000540980.1_Silent_p.Q40Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		54.0	0.0		30.0	5.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	17	1	0	0	0	0	0	0	0	1	15659	962	34	3		3	TBP	6	170871004	Silent	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	129312980	170871004	244063	30	1475										
AMPH	273	hgsc.bcm.edu	37	chr7	38543259	38543259	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	atacacattacctttgattgCtgctaaatatcctcggagtt	6	9	0	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr7:38543259C>A	ENST00000356264.2	-	3	411	c.196G>T	c.(196-198)Gca>Tca	p.A66S	AMPH_ENST00000428293.2_Missense_Mutation_p.A66S|AMPH_ENST00000325590.5_Missense_Mutation_p.A66S	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	66	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						CCTTTGATTGCTGCTAAATAT	0.388																																					p.A66S		Atlas-SNP	.											.	AMPH	157	.	0			c.G196T						.						232	193	206					7																	38543259		2203	4300	6503	SO:0001583	missense	273	exon3			TGATTGCTGCTAA		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.196G>T	chr7.hg19:g.38543259C>A	ENSP00000348602:p.Ala66Ser	53.0	0.0		89.0	35.0	NM_139316	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	hg19	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	C	16.28	3.077713	0.55753	.	.	ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000544070	T;T;T	0.60548	0.18;0.18;0.18	5.92	5.92	0.95590	BAR (3);	0.000000	0.85682	D	0.000000	T	0.67078	0.2855	L	0.39633	1.23	0.58432	D	0.999997	D;D	0.76494	0.991;0.999	D;D	0.80764	0.962;0.994	T	0.58205	-0.7677	10	0.15952	T	0.53	-20.0998	17.2374	0.87002	0.0:1.0:0.0:0.0	.	66;66	P49418-2;P49418	.;AMPH_HUMAN	S	66	ENSP00000317441:A66S;ENSP00000348602:A66S;ENSP00000390734:A66S	ENSP00000317441:A66S	A	-	1	0	AMPH	38509784	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.642000	0.61383	2.809000	0.96659	0.655000	0.94253	GCA	.	.		0.388	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		A	38543259	C	A	38543259	3	1	17	1	0	0	0	0	1	0	0	0	588	797	28	3	1967	3	AMPH	7	38543259	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10		38543259	120595404	31	1476										
ZNF394	84124	hgsc.bcm.edu	37	chr7	99097503	99097503	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cggtccagccacctcctggtAacgcagctgcctaaagtgca	10	15	0	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr7:99097503A>C	ENST00000337673.6	-	1	417	c.214T>G	c.(214-216)Tac>Gac	p.Y72D	ZNF394_ENST00000394177.3_Intron|ZNF394_ENST00000426306.2_Missense_Mutation_p.Y72D|ZNF789_ENST00000494186.1_Intron|ZNF789_ENST00000493485.1_Intron	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	72	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					ACCTCCTGGTAACGCAGCTGC	0.622																																					p.Y72D	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											.	ZNF394	48	.	0			c.T214G						.						49	50	50					7																	99097503		2203	4300	6503	SO:0001583	missense	84124	exon1			CCTGGTAACGCAG	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"Zinc fingers, C2H2-type", "-", "-", "-"	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.214T>G	chr7.hg19:g.99097503A>C	ENSP00000337363:p.Tyr72Asp	57.0	0.0		37.0	13.0	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Missense_Mutation	SNP	ENST00000337673.6	hg19	CCDS5666.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.993101	0.74703	.	.	ENSG00000160908	ENST00000337673;ENST00000426306	T;T	0.07114	3.22;3.22	3.98	3.98	0.46160	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.000000	0.43260	D	0.000588	T	0.35711	0.0941	H	0.94503	3.545	0.34367	D	0.691645	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.993	T	0.59590	-0.7426	10	0.87932	D	0	.	9.5527	0.39319	1.0:0.0:0.0:0.0	.	72;72	Q05DA6;Q53GI3	.;ZN394_HUMAN	D	72	ENSP00000337363:Y72D;ENSP00000409565:Y72D	ENSP00000337363:Y72D	Y	-	1	0	ZNF394	98935439	0.965000	0.33210	0.986000	0.45419	0.731000	0.41821	3.287000	0.51732	2.035000	0.60131	0.459000	0.35465	TAC	.	.		0.622	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164		C	99097503	A	C	99097503	3	2	17	1	0	0	0	0	1	0	0	0	17895	362	13	5	1483	5	ZNF394	7	99097503	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10	60554244	99097503	60041160	32	1477										
ALKBH4	54784	hgsc.bcm.edu	37	chr7	102105175	102105175	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ccttaccgctgggggcagctCccagggcgggtcactgccgc	15	16	1	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr7:102105175C>T	ENST00000292566.3	-	1	148	c.109G>A	c.(109-111)Gag>Aag	p.E37K	MIR5090_ENST00000582533.1_RNA|LRWD1_ENST00000292616.5_5'Flank	NM_017621.3	NP_060091.1	Q9NXW9	ALKB4_HUMAN	alkB, alkylation repair homolog 4 (E. coli)	37					actomyosin structure organization (GO:0031032)|cleavage furrow ingression (GO:0036090)|protein demethylation (GO:0006482)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	contractile ring (GO:0070938)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)	actin binding (GO:0003779)|demethylase activity (GO:0032451)|metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			kidney(1)|lung(5)|skin(2)	8						GGGGGCAGCTCCCAGGGCGGG	0.687																																					p.E37K		Atlas-SNP	.											.	ALKBH4	21	.	0			c.G109A						.						14	19	17					7																	102105175		2149	4237	6386	SO:0001583	missense	54784	exon1			GCAGCTCCCAGGG	BC017096	CCDS5723.1	7q22.1	2006-02-09			ENSG00000160993	ENSG00000160993		"Alkylation repair homologs"	21900	protein-coding gene	gene with protein product		613302					Standard	NM_017621		Approved	FLJ20013	uc003uzl.3	Q9NXW9	OTTHUMG00000157720	ENST00000292566.3:c.109G>A	chr7.hg19:g.102105175C>T	ENSP00000292566:p.Glu37Lys	125.0	0.0		144.0	58.0	NM_017621	Q53H92|Q9H6A4	Missense_Mutation	SNP	ENST00000292566.3	hg19	CCDS5723.1	.	.	.	.	.	.	.	.	.	.	C	0.296	-0.976719	0.02215	.	.	ENSG00000160993	ENST00000292566	T	0.49139	0.79	5.18	-2.04	0.07343	.	1.188620	0.05847	N	0.620516	T	0.25044	0.0608	N	0.10972	0.075	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22277	-1.0221	10	0.09590	T	0.72	-1.8695	9.5419	0.39257	0.0:0.3959:0.3103:0.2937	.	37	Q9NXW9	ALKB4_HUMAN	K	37	ENSP00000292566:E37K	ENSP00000292566:E37K	E	-	1	0	ALKBH4	101892180	0.677000	0.27577	0.719000	0.30619	0.049000	0.14656	-0.095000	0.11077	-0.059000	0.13154	-0.657000	0.03884	GAG	.	.		0.687	ALKBH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349503.1	NM_017621		T	102105175	C	T	102105175	3	4	17	1	0	0	0	0	1	0	0	0	529	864	30	3	811	3	ALKBH4	7	102105175	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	3007672	102105175	57033488	33	1478										
TRPV5	56302	hgsc.bcm.edu	37	chr7	142626585	142626585	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ctgtggctctggcagagacaCtggccctgcgggtgagcagg	17	11	1	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr7:142626585C>T	ENST00000265310.1	-	4	773	c.425G>A	c.(424-426)aGt>aAt	p.S142N	TRPV5_ENST00000442623.1_Missense_Mutation_p.S142N	NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	142					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					GGCAGAGACACTGGCCCTGCG	0.597																																					p.S142N		Atlas-SNP	.											.	TRPV5	164	.	0			c.G425A						.						87	78	81					7																	142626585		2203	4300	6503	SO:0001583	missense	56302	exon4			GAGACACTGGCCC	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.425G>A	chr7.hg19:g.142626585C>T	ENSP00000265310:p.Ser142Asn	88.0	0.0		85.0	36.0	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	hg19	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	C	11.33	1.606211	0.28623	.	.	ENSG00000127412	ENST00000265310;ENST00000439304;ENST00000442623	T;T;T	0.49720	0.77;0.77;0.77	4.85	3.95	0.45737	Ankyrin repeat-containing domain (4);	0.209114	0.51477	D	0.000099	T	0.19327	0.0464	N	0.02865	-0.47	0.25441	N	0.98809	B;B	0.11235	0.0;0.004	B;B	0.09377	0.004;0.004	T	0.06285	-1.0835	10	0.27785	T	0.31	-0.0019	5.4082	0.16332	0.0:0.7323:0.0:0.2677	.	142;142	E9PBZ6;Q9NQA5	.;TRPV5_HUMAN	N	142;136;142	ENSP00000265310:S142N;ENSP00000406361:S136N;ENSP00000406572:S142N	ENSP00000265310:S142N	S	-	2	0	TRPV5	142336707	0.987000	0.35691	0.977000	0.42913	0.929000	0.56500	2.442000	0.44873	2.396000	0.81511	0.563000	0.77884	AGT	.	.		0.597	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		T	142626585	C	T	142626585	3	4	17	1	0	0	0	0	1	0	0	0	16614	565	20	3	1812	3	TRPV5	7	142626585	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	40521410	142626585	16512078	34	1479										
AMAC1L2	83650	hgsc.bcm.edu	37	chr8	11189172	11189172	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	actacaggaggggaccacagGtgtctacaccaccctgggct	12	13	1	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr8:11189172G>T	ENST00000382435.4	+	1	776	c.557G>T	c.(556-558)gGt>gTt	p.G186V		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	186						integral component of membrane (GO:0016021)											GGGACCACAGGTGTCTACACC	0.592																																					p.G186V		Atlas-SNP	.											.	.	.	.	0			c.G557T						.						159	155	156					8																	11189172		2203	4300	6503	SO:0001583	missense	83650	exon1			CCACAGGTGTCTA	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"Solute carriers"	15546	protein-coding gene	gene with protein product		615199	"acyl-malonyl condensing enzyme 1-like 2"	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.557G>T	chr8.hg19:g.11189172G>T	ENSP00000371872:p.Gly186Val	50.0	0.0		30.0	19.0	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	hg19	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	G	9.298	1.052472	0.19907	.	.	ENSG00000177710	ENST00000382435	T	0.28895	1.59	.	.	.	.	0.000000	0.48767	D	0.000169	T	0.32971	0.0847	L	0.29908	0.895	0.34262	D	0.68	D	0.69078	0.997	D	0.63597	0.916	T	0.37056	-0.9722	8	0.27082	T	0.32	-5.8052	.	.	.	.	186	Q96KT7	S35G5_HUMAN	V	186	ENSP00000371872:G186V	ENSP00000371872:G186V	G	+	2	0	SLC35G5	11226582	0.001000	0.12720	0.053000	0.19242	0.042000	0.13812	0.240000	0.18042	0.088000	0.17205	0.089000	0.15464	GGT	.	.		0.592	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028		T	11189172	G	T	11189172	3	4	17	1	0	0	0	0	1	0	0	0	560	1261	44	3	559	3	AMAC1L2	8	11189172	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10		11189172	135174850	35	1480										
NKX3-1	4824	hgsc.bcm.edu	37	chr8	23538754	23538754	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ttaccaaaaagctgggctccAgctgcccacgcagtacaggt	10	13	0	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr8:23538754A>T	ENST00000380871.4	-	2	722	c.685T>A	c.(685-687)Tgg>Agg	p.W229R	NKX3-1_ENST00000523261.1_Missense_Mutation_p.W154R	NM_006167.3	NP_006158.2	Q99801	NKX31_HUMAN	NK3 homeobox 1	229					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|androgen receptor signaling pathway (GO:0030521)|branching involved in prostate gland morphogenesis (GO:0060442)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to steroid hormone stimulus (GO:0071383)|cellular response to tumor necrosis factor (GO:0071356)|dorsal aorta development (GO:0035907)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|heart development (GO:0007507)|male gonad development (GO:0008584)|metanephros development (GO:0001656)|mitotic cell cycle arrest (GO:0071850)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of transcription, DNA-templated (GO:0045892)|pharyngeal system development (GO:0060037)|positive regulation of androgen secretion (GO:2000836)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell death (GO:0010942)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein kinase B signaling (GO:0043491)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|salivary gland development (GO:0007431)|somitogenesis (GO:0001756)|steroid hormone mediated signaling pathway (GO:0043401)	intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|core promoter binding (GO:0001047)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|histone deacetylase binding (GO:0042826)|protein kinase activator activity (GO:0030295)|protein self-association (GO:0043621)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			large_intestine(3)|lung(4)|prostate(5)|skin(2)	14		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)		GCTGGGCTCCAGCTGCCCACG	0.542																																					p.W229R		Atlas-SNP	.											.	NKX3-1	25	.	0			c.T685A						.						52	53	53					8																	23538754		2203	4300	6503	SO:0001583	missense	4824	exon2			GGCTCCAGCTGCC		CCDS6042.1, CCDS59095.1	8p21.2	2012-03-09	2007-07-09	2002-10-04	ENSG00000167034	ENSG00000167034		"Homeoboxes / ANTP class : NKL subclass"	7838	protein-coding gene	gene with protein product		602041	"NK homeobox (Drosophila), family 3, A", "NK3 transcription factor related, locus 1 (Drosophila)"	NKX3A		9226374	Standard	NM_006167		Approved	NKX3.1, BAPX2	uc011kzx.2	Q99801	OTTHUMG00000097851	ENST00000380871.4:c.685T>A	chr8.hg19:g.23538754A>T	ENSP00000370253:p.Trp229Arg	94.0	0.0		41.0	29.0	NM_006167	O15465|Q9H2P4|Q9H2P5|Q9H2P6|Q9H2P7|Q9HBG0	Missense_Mutation	SNP	ENST00000380871.4	hg19	CCDS6042.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.024483	0.75390	.	.	ENSG00000167034	ENST00000380871;ENST00000300332;ENST00000523261	D;D	0.94758	-3.51;-3.33	5.97	5.97	0.96955	.	0.228552	0.31734	N	0.007150	D	0.96901	0.8988	M	0.79475	2.455	0.58432	D	0.999999	D	0.76494	0.999	D	0.71184	0.972	D	0.97350	0.9963	10	0.87932	D	0	.	14.4129	0.67128	1.0:0.0:0.0:0.0	.	229	Q99801	NKX31_HUMAN	R	229;185;154	ENSP00000370253:W229R;ENSP00000429729:W154R	ENSP00000300332:W185R	W	-	1	0	NKX3-1	23594699	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.809000	0.91944	2.288000	0.76882	0.533000	0.62120	TGG	.	.		0.542	NKX3-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215141.2			T	23538754	A	T	23538754	3	4	17	1	0	0	0	0	1	0	0	0	10464	188	7	4	23	4	NKX3-1	8	23538754	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10	12349582	23538754	122825268	36	1481										
WDYHV1	55093	hgsc.bcm.edu	37	chr8	124449502	124449502	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tgaagaactttgcttctgacCgatctcacatgaaagactcc	7	11	2	5			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr8:124449502C>A	ENST00000287387.2	+	5	561	c.436C>A	c.(436-438)Cga>Aga	p.R146R	WDYHV1_ENST00000518125.1_5'UTR|WDYHV1_ENST00000517609.1_3'UTR|WDYHV1_ENST00000523356.1_Silent_p.R146R|WDYHV1_ENST00000523984.1_Silent_p.R86R	NM_018024.1	NP_060494.1	Q96HA8	NTAQ1_HUMAN	WDYHV motif containing 1	146					cellular protein modification process (GO:0006464)	cytosol (GO:0005829)|nucleus (GO:0005634)	protein-N-terminal glutamine amidohydrolase activity (GO:0070773)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(3)	17						TGCTTCTGACCGATCTCACAT	0.458																																					p.R146R		Atlas-SNP	.											.	WDYHV1	30	.	0			c.C436A						.						76	75	75					8																	124449502		2203	4300	6503	SO:0001819	synonymous_variant	55093	exon5			TCTGACCGATCTC	AK001066	CCDS6344.1, CCDS64965.1	8q24.13	2008-10-01	2008-10-01	2008-10-01		ENSG00000156795			25490	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 32"	C8orf32		12477932	Standard	NM_018024		Approved	FLJ10204	uc003yqn.1	Q96HA8		ENST00000287387.2:c.436C>A	chr8.hg19:g.124449502C>A		57.0	0.0		73.0	31.0	NM_018024	B4DE68|Q9NW95	Silent	SNP	ENST00000287387.2	hg19	CCDS6344.1																																																																																			.	.		0.458	WDYHV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381772.1	NM_018024		A	124449502	C	A	124449502	2	1	17	1	0	0	0	0	0	0	0	1	17358	644	23	1		1	WDYHV1	8	124449502	Silent	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	100910748	124449502	21914520	37	1482										
HSDL2	84263	hgsc.bcm.edu	37	chr9	115179158	115179158	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cttatttgaaaaagagcaaaGttgctcatatcctcaatatc	5	8	2	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr9:115179158G>T	ENST00000398805.3	+	5	660	c.433G>T	c.(433-435)Gtt>Ttt	p.V145F	HSDL2_ENST00000262542.7_Missense_Mutation_p.V25F|HSDL2_ENST00000398803.1_Intron|HSDL2_ENST00000539114.1_Intron|HSDL2_ENST00000488101.1_3'UTR	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	145						membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|cervix(2)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	13						AAAGAGCAAAGTTGCTCATAT	0.373																																					p.V145F		Atlas-SNP	.											.	HSDL2	24	.	0			c.G433T						.						97	91	93					9																	115179158		1836	4093	5929	SO:0001583	missense	84263	exon5			AGCAAAGTTGCTC	AY093428	CCDS43864.1, CCDS56582.1	9q32	2011-09-14			ENSG00000119471	ENSG00000119471		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18572	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 13C, member 1"		"chromosome 9 open reading frame 99"	C9orf99		12834046, 19027726	Standard	NM_032303		Approved	SDR13C1	uc004bga.2	Q6YN16	OTTHUMG00000020504	ENST00000398805.3:c.433G>T	chr9.hg19:g.115179158G>T	ENSP00000381785:p.Val145Phe	44.0	0.0		83.0	39.0	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	hg19	CCDS43864.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.293201	0.40594	.	.	ENSG00000119471	ENST00000398805;ENST00000262542	D;T	0.87887	-2.31;1.98	6.17	-4.94	0.03057	NAD(P)-binding domain (1);	0.652152	0.16698	N	0.203256	T	0.68778	0.3038	N	0.03154	-0.405	0.58432	D	0.999999	P	0.38677	0.642	B	0.35688	0.208	T	0.59043	-0.7528	10	0.39692	T	0.17	.	16.1353	0.81481	0.4063:0.0:0.5937:0.0	.	145	Q6YN16	HSDL2_HUMAN	F	145;25	ENSP00000381785:V145F;ENSP00000262542:V25F	ENSP00000262542:V25F	V	+	1	0	HSDL2	114218979	1.000000	0.71417	0.711000	0.30485	0.750000	0.42670	1.418000	0.34782	-1.258000	0.02471	-0.768000	0.03414	GTT	.	.		0.373	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303		T	115179158	G	T	115179158	3	4	17	1	0	0	0	0	1	0	0	0	7403	1029	36	3	451	3	HSDL2	9	115179158	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10		115179158	26034273	38	1483										
CIZ1	25792	hgsc.bcm.edu	37	chr9	130943066	130943066	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tggggggtctgacttgtcttCcacaggcattgtctgagaag	14	8	3	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr9:130943066C>A	ENST00000393608.1	-	6	818	c.616G>T	c.(616-618)Gaa>Taa	p.E206*	CIZ1_ENST00000357558.5_Nonsense_Mutation_p.E206*|CIZ1_ENST00000538431.1_Nonsense_Mutation_p.E206*|CIZ1_ENST00000372948.3_Nonsense_Mutation_p.E206*|CIZ1_ENST00000277465.4_Nonsense_Mutation_p.E206*|CIZ1_ENST00000325721.8_Nonsense_Mutation_p.E177*|CIZ1_ENST00000372954.1_Nonsense_Mutation_p.E182*|CIZ1_ENST00000541172.1_Nonsense_Mutation_p.E105*|CIZ1_ENST00000372938.5_Nonsense_Mutation_p.E206*|CIZ1_ENST00000476727.2_5'UTR	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	206					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						GACTTGTCTTCCACAGGCATT	0.567																																					p.E236X		Atlas-SNP	.											.	CIZ1	75	.	0			c.G706T						.						48	52	51					9																	130943066		2203	4300	6503	SO:0001587	stop_gained	25792	exon6			TGTCTTCCACAGG	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.616G>T	chr9.hg19:g.130943066C>A	ENSP00000377232:p.Glu206*	35.0	0.0		25.0	10.0	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Nonsense_Mutation	SNP	ENST00000393608.1	hg19	CCDS6894.1	.	.	.	.	.	.	.	.	.	.	C	36	5.950745	0.97139	.	.	ENSG00000148337	ENST00000372954;ENST00000393608;ENST00000538431;ENST00000357558;ENST00000325721;ENST00000537314;ENST00000541172;ENST00000277465;ENST00000372941;ENST00000372948;ENST00000372938;ENST00000415526;ENST00000324544	.	.	.	4.52	4.52	0.55395	.	0.313408	0.23079	N	0.052173	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-3.5089	12.938	0.58327	0.0:1.0:0.0:0.0	.	.	.	.	X	182;206;206;206;177;173;105;206;182;206;206;128;206	.	ENSP00000277465:E206X	E	-	1	0	CIZ1	129982887	0.553000	0.26513	0.985000	0.45067	0.962000	0.63368	3.303000	0.51858	2.497000	0.84241	0.655000	0.94253	GAA	.	.		0.567	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		A	130943066	C	A	130943066	4	1	17	1	0	0	0	0	0	1	0	0	3443	864	30	3	2128	3	CIZ1	9	130943066	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	15763908	130943066	10270365	39	1484										
SLC39A12	221074	hgsc.bcm.edu	37	chr10	18270325	18270325	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	aggaggactttaagcaaatgAgtccagggatcatccagcag	12	8	1	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr10:18270325A>T	ENST00000377369.2	+	6	1282	c.1009A>T	c.(1009-1011)Agt>Tgt	p.S337C	SLC39A12_ENST00000377371.3_Missense_Mutation_p.S337C|SLC39A12_ENST00000539911.1_Missense_Mutation_p.S203C|SLC39A12_ENST00000377374.4_Missense_Mutation_p.S337C	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	337					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						TAAGCAAATGAGTCCAGGGAT	0.502																																					p.S337C		Atlas-SNP	.											.	SLC39A12	181	.	0			c.A1009T						.						77	71	73					10																	18270325		2203	4300	6503	SO:0001583	missense	221074	exon6			CAAATGAGTCCAG		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"Solute carriers"	20860	protein-coding gene	gene with protein product		608734	"solute carrier family 39 (metal ion transporter), member 12"			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.1009A>T	chr10.hg19:g.18270325A>T	ENSP00000366586:p.Ser337Cys	130.0	0.0		135.0	44.0	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Missense_Mutation	SNP	ENST00000377369.2	hg19	CCDS44362.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.954772	0.53293	.	.	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219	T;T;T;T	0.55588	0.73;0.51;0.69;0.59	5.8	5.8	0.92144	.	0.119688	0.85682	D	0.000000	T	0.44685	0.1305	L	0.49699	1.58	0.54753	D	0.999982	B;B;P	0.37233	0.445;0.317;0.588	B;B;B	0.36418	0.224;0.159;0.224	T	0.43065	-0.9414	10	0.05620	T	0.96	-16.1981	16.1499	0.81605	1.0:0.0:0.0:0.0	.	337;337;337	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	C	337;337;337;203;257	ENSP00000366586:S337C;ENSP00000366591:S337C;ENSP00000366588:S337C;ENSP00000440445:S203C	ENSP00000366586:S337C	S	+	1	0	SLC39A12	18310331	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.162000	0.64942	2.220000	0.72140	0.533000	0.62120	AGT	.	.		0.502	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725		T	18270325	A	T	18270325	3	4	17	1	0	0	0	0	1	0	0	0	14630	304	11	4	1027	4	SLC39A12	10	18270325	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10		18270325	117264422	40	1485										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49658574	49658574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gggcagacgagtcgctggcgCggcaggccgtgcagctgctg	19	12	0	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr10:49658574C>T	ENST00000249601.4	-	9	1894	c.1598G>A	c.(1597-1599)cGc>cAc	p.R533H	ARHGAP22_ENST00000417912.2_Missense_Mutation_p.R549H|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.R374H|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.R424H|ARHGAP22_ENST00000477708.2_Missense_Mutation_p.R366H|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.R443H|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.R539H	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	533	Ser-rich.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GTCGCTGGCGCGGCAGGCCGT	0.721																																					p.R549H		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.G1646A						.						9	10	10					10																	49658574		2099	4140	6239	SO:0001583	missense	58504	exon9			CTGGCGCGGCAGG	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.1598G>A	chr10.hg19:g.49658574C>T	ENSP00000249601:p.Arg533His	53.0	0.0		47.0	21.0	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	hg19	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.232279	0.39498	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000477708;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T;T	0.28255	2.73;2.41;1.62;2.05;2.39;2.69;2.74	5.24	3.03	0.35002	.	0.722220	0.14384	N	0.322976	T	0.22589	0.0545	L	0.50333	1.59	0.21627	N	0.999613	B;B;B;B;B;P	0.46656	0.033;0.033;0.055;0.033;0.055;0.882	B;B;B;B;B;B	0.31614	0.007;0.007;0.016;0.007;0.016;0.133	T	0.09207	-1.0685	10	0.34782	T	0.22	.	11.9395	0.52892	0.0:0.8314:0.0:0.1686	.	539;533;549;533;443;366	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3;D6R9V6	.;.;.;RHG22_HUMAN;.;.	H	533;424;374;366;443;539;549	ENSP00000249601:R533H;ENSP00000363287:R424H;ENSP00000363285:R374H;ENSP00000422868:R366H;ENSP00000410054:R443H;ENSP00000416701:R539H;ENSP00000412461:R549H	ENSP00000249601:R533H	R	-	2	0	ARHGAP22	49328580	0.997000	0.39634	0.989000	0.46669	0.905000	0.53344	2.376000	0.44292	1.211000	0.43351	0.591000	0.81541	CGC	.	.		0.721	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		T	49658574	C	T	49658574	3	4	17	1	0	0	0	0	1	0	0	0	872	768	27	1	506	1	ARHGAP22	10	49658574	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	31388249	49658574	85876173	41	1486										
CHAT	1103	hgsc.bcm.edu	37	chr10	50872913	50872913	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	acccccagccagagaccatcCttttctgcatctctagcttt	5	16	2	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr10:50872913C>A	ENST00000337653.2	+	15	2221	c.2068C>A	c.(2068-2070)Ctt>Att	p.L690I	CHAT_ENST00000395562.2_Missense_Mutation_p.L608I|CHAT_ENST00000455728.2_Intron|CHAT_ENST00000395559.2_Missense_Mutation_p.L572I|CHAT_ENST00000339797.1_Missense_Mutation_p.L572I|CHAT_ENST00000351556.3_Missense_Mutation_p.L572I	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	690					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	AGAGACCATCCTTTTCTGCAT	0.512																																					p.L690I		Atlas-SNP	.											.	CHAT	162	.	0			c.C2068A						.						224	207	212					10																	50872913		2203	4300	6503	SO:0001583	missense	1103	exon15			ACCATCCTTTTCT	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.2068C>A	chr10.hg19:g.50872913C>A	ENSP00000337103:p.Leu690Ile	99.0	0.0		95.0	31.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	hg19	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	C	4.855	0.158863	0.09236	.	.	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562	D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43	5.76	3.51	0.40186	.	0.187520	0.45606	D	0.000356	T	0.76069	0.3936	N	0.11651	0.15	0.35028	D	0.758538	B	0.18741	0.03	B	0.28849	0.095	T	0.70992	-0.4721	10	0.19147	T	0.46	-11.6538	6.9467	0.24522	0.1865:0.6799:0.0:0.1337	.	690	P28329	CLAT_HUMAN	I	572;572;572;690;608	ENSP00000343486:L572I;ENSP00000345878:L572I;ENSP00000378926:L572I;ENSP00000337103:L690I;ENSP00000378929:L608I	ENSP00000337103:L690I	L	+	1	0	CHAT	50542919	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	0.483000	0.22292	1.388000	0.46506	0.655000	0.94253	CTT	.	.		0.512	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		A	50872913	C	A	50872913	3	1	17	1	0	0	0	0	1	0	0	0	3315	681	24	3	2170	3	CHAT	10	50872913	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	1214339	50872913	84661834	42	1487										
PLEKHA1	59338	hgsc.bcm.edu	37	chr10	124189324	124189324	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cttcaaggtccagactgtctCtccaagagaaccagcttcca	7	14	2	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr10:124189324C>T	ENST00000368990.3	+	12	1216	c.1085C>T	c.(1084-1086)tCt>tTt	p.S362F	PLEKHA1_ENST00000368988.1_Missense_Mutation_p.L376F|PLEKHA1_ENST00000368989.2_Missense_Mutation_p.L376F|PLEKHA1_ENST00000433307.1_Missense_Mutation_p.S362F|PLEKHA1_ENST00000538022.1_3'UTR	NM_001001974.2	NP_001001974.1	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	362					androgen metabolic process (GO:0008209)|B cell receptor signaling pathway (GO:0050853)|cellular response to hydrogen peroxide (GO:0070301)|establishment of protein localization (GO:0045184)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|multicellular organism growth (GO:0035264)|negative regulation of protein kinase B signaling (GO:0051898)|palate development (GO:0060021)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|ruffle organization (GO:0031529)|skeletal system morphogenesis (GO:0048705)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CAGACTGTCTCTCCAAGAGAA	0.468																																					p.S362F		Atlas-SNP	.											.	PLEKHA1	33	.	0			c.C1085T						.						97	91	93					10																	124189324		2203	4300	6503	SO:0001583	missense	59338	exon12			CTGTCTCTCCAAG	AF286160	CCDS7629.1, CCDS55730.1	10q26.3	2013-01-10	2002-01-14		ENSG00000107679	ENSG00000107679		"Pleckstrin homology (PH) domain containing"	14335	protein-coding gene	gene with protein product	"tandem PH domain containing protein-1"	607772	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 1"			11001876, 15485858	Standard	NM_001001974		Approved	TAPP1	uc001lge.2	Q9HB21	OTTHUMG00000019184	ENST00000368990.3:c.1085C>T	chr10.hg19:g.124189324C>T	ENSP00000357986:p.Ser362Phe	67.0	0.0		104.0	40.0	NM_021622	B3KQ55|D3DRE2|Q9BVK0	Missense_Mutation	SNP	ENST00000368990.3	hg19	CCDS7629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.3|20.3	3.967131|3.967131	0.74131|0.74131	.|.	.|.	ENSG00000107679|ENSG00000107679	ENST00000368989;ENST00000368988|ENST00000368990;ENST00000409427;ENST00000433307	T;T|T;T	0.11277|0.06218	2.79;2.79|3.33;3.33	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|1.118330	.|0.06320	.|N	.|0.704226	T|T	0.09113|0.09113	0.0225|0.0225	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|B	.|0.29805	.|0.257	.|B	.|0.35353	.|0.201	T|T	0.51795|0.51795	-0.8660|-0.8660	7|9	0.29301|.	T|.	0.29|.	-4.4286|-4.4286	20.0793|20.0793	0.97766|0.97766	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|362	.|Q9HB21	.|PKHA1_HUMAN	F|F	376|362	ENSP00000357985:L376F;ENSP00000357984:L376F|ENSP00000357986:S362F;ENSP00000394416:S362F	ENSP00000357984:L376F|.	L|S	+|+	1|2	0|0	PLEKHA1|PLEKHA1	124179314|124179314	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.585000|3.585000	0.53943|0.53943	2.826000|2.826000	0.97356|0.97356	0.650000|0.650000	0.86243|0.86243	CTC|TCT	.	.		0.468	PLEKHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050783.1	NM_001001974		T	124189324	C	T	124189324	3	4	17	1	0	0	0	0	1	0	0	0	12064	913	32	3	1127	3	PLEKHA1	10	124189324	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	73316411	124189324	11345423	43	1488										
IRF7	3665	hgsc.bcm.edu	37	chr11	613275	613275	+	Frame_Shift_Del	DEL	A	A	-													0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cagcaggcaggctggggtggAggggctggcggagcctgggg							TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr11:613275delA	ENST00000397574.2	-	9	1537	c.1168delT	c.(1168-1170)tccfs	p.S390fs	IRF7_ENST00000525445.1_Frame_Shift_Del_p.S284fs|IRF7_ENST00000397562.3_Frame_Shift_Del_p.S97fs|IRF7_ENST00000397570.1_Frame_Shift_Del_p.S361fs|IRF7_ENST00000330243.5_Frame_Shift_Del_p.S403fs|IRF7_ENST00000397566.1_Frame_Shift_Del_p.S403fs|IRF7_ENST00000348655.6_Frame_Shift_Del_p.S361fs	NM_001572.3	NP_001563.2	Q92985	IRF7_HUMAN	interferon regulatory factor 7	390					cellular response to DNA damage stimulus (GO:0006974)|cytokine-mediated signaling pathway (GO:0019221)|establishment of viral latency (GO:0019043)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-alpha production (GO:0032607)|interferon-beta production (GO:0032608)|interferon-gamma-mediated signaling pathway (GO:0060333)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of adaptive immune response (GO:0002819)|regulation of immune response (GO:0050776)|regulation of monocyte differentiation (GO:0045655)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|regulation of MyD88-independent toll-like receptor signaling pathway (GO:0034127)|regulation of type I interferon production (GO:0032479)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;7.68e-28)|Epithelial(43;7.44e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;6.96e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCTGGGGTGGAGGGGCTGGCG	0.667																																					p.S403fs		Atlas-Indel,Pindel	.											.	IRF7	23	.	0			c.1208delC						.						13	19	17					11																	613275		2181	4291	6472	SO:0001589	frameshift_variant	3665	exon7			.	U53830	CCDS7703.1, CCDS7704.1, CCDS7705.1	11p15.5	2005-10-10			ENSG00000185507	ENSG00000185507			6122	protein-coding gene	gene with protein product		605047					Standard	XM_005252906		Approved		uc001lqh.3	Q92985	OTTHUMG00000132019	ENST00000397574.2:c.1168delT	chr11.hg19:g.613275delA	ENSP00000380704:p.Ser390fs	95.0	0.0		97.0	31.0	NM_004031	B9EGL3|O00331|O00332|O00333|O75924|Q9UE79	Frame_Shift_Del	DEL	ENST00000397574.2	hg19	CCDS7703.1																																																																																			.	.		0.667	IRF7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255026.1	NM_001572		-	613275	A	-	613275	7	5	17	1	0	1	0	1	0	0	0	0	7844	304	11	0	355	0	IRF7	11	613275	Frame_Shift_Del	DEL	A	TCGA-2Y-A9H7-01A-11D-A38X-10		613275	134393241	44	1489										
ZNF214	7761	hgsc.bcm.edu	37	chr11	7022371	7022371	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tgctgaactatgagcttctgTtctttttccatggagaggtt	10	7	2	3			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr11:7022371T>C	ENST00000278314.4	-	3	858	c.543A>G	c.(541-543)gaA>gaG	p.E181E	ZNF214_ENST00000536068.1_Silent_p.E181E|ZNF214_ENST00000531083.1_5'Flank	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	181					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		TGAGCTTCTGTTCTTTTTCCA	0.438																																					p.E181E	Ovarian(22;251 657 736 21522 46864)	Atlas-SNP	.											.	ZNF214	65	.	0			c.A543G						.						110	111	110					11																	7022371		2200	4294	6494	SO:0001819	synonymous_variant	7761	exon3			CTTCTGTTCTTTT	AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"Zinc fingers, C2H2-type", "-"	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.543A>G	chr11.hg19:g.7022371T>C		53.0	0.0		80.0	29.0	NM_013249	B2R8Q1	Silent	SNP	ENST00000278314.4	hg19	CCDS31418.1																																																																																			.	.		0.438	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1			C	7022371	T	C	7022371	2	2	17	1	0	0	0	0	0	0	0	1	17785	1722	60	2		2	ZNF214	11	7022371	Silent	SNP	T	TCGA-2Y-A9H7-01A-11D-A38X-10	6409096	7022371	127984145	45	1490										
UEVLD	55293	hgsc.bcm.edu	37	chr11	18553955	18553955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tatcttctttcagtgtggttTtgataacttcagatactcca	6	8	4	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr11:18553955T>C	ENST00000396197.3	-	12	1356	c.1328A>G	c.(1327-1329)aAa>aGa	p.K443R	UEVLD_ENST00000379387.4_Missense_Mutation_p.K421R|UEVLD_ENST00000535484.1_3'UTR|UEVLD_ENST00000540666.1_5'UTR|UEVLD_ENST00000541984.1_3'UTR|UEVLD_ENST00000320750.6_3'UTR|UEVLD_ENST00000543987.1_3'UTR	NM_001040697.2|NM_001261384.1	NP_001035787.1|NP_001248313.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						CAGTGTGGTTTTGATAACTTC	0.358																																					p.K443R		Atlas-SNP	.											.	UEVLD	58	.	0			c.A1328G						.						143	135	138					11																	18553955		2199	4293	6492	SO:0001583	missense	55293	exon12			GTGGTTTTGATAA	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000396197.3:c.1328A>G	chr11.hg19:g.18553955T>C	ENSP00000379500:p.Lys443Arg	71.0	0.0		108.0	40.0	NM_001040697		Missense_Mutation	SNP	ENST00000396197.3	hg19	CCDS41624.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.652799	0.29336	.	.	ENSG00000151116	ENST00000396197;ENST00000379387;ENST00000540110	T;T	0.67523	-0.27;-0.27	5.31	4.17	0.49024	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.254323	0.32640	U	0.005822	T	0.53417	0.1795	L	0.39566	1.225	0.23107	N	0.998289	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.46978	-0.9152	10	0.46703	T	0.11	-1.3138	6.7105	0.23274	0.0:0.0807:0.1519:0.7674	.	421;443	B4DL43;Q8IX04	.;UEVLD_HUMAN	R	443;421;220	ENSP00000379500:K443R;ENSP00000368697:K421R	ENSP00000368697:K421R	K	-	2	0	UEVLD	18510531	0.021000	0.18746	0.896000	0.35187	0.635000	0.38103	0.030000	0.13688	0.854000	0.35336	0.459000	0.35465	AAA	.	.		0.358	UEVLD-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395923.2	NM_018314		C	18553955	T	C	18553955	3	2	17	1	0	0	0	0	1	0	0	0	16948	1841	64	2	91	2	UEVLD	11	18553955	Missense_Mutation	SNP	T	TCGA-2Y-A9H7-01A-11D-A38X-10	11531584	18553955	116452561	46	1491										
LGR4	55366	hgsc.bcm.edu	37	chr11	27389741	27389741	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tgtgagtacatgccacagtcGtagtagaaatcctgttccag	10	9	0	2	rs145204350|rs375970924		TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr11:27389741G>A	ENST00000379214.4	-	18	2972	c.2529C>T	c.(2527-2529)taC>taT	p.Y843Y	LGR4_ENST00000389858.4_Silent_p.Y819Y	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	843					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						TGCCACAGTCGTAGTAGAAAT	0.438																																					p.Y843Y		Atlas-SNP	.											.	LGR4	87	.	0			c.C2529T						.	G		1,4403	2.1+/-5.4	0,1,2201	163	156	159		2529	-10.8	0.2	11	dbSNP_134	159	0,8598		0,0,4299	no	coding-synonymous	LGR4	NM_018490.2		0,1,6500	AA,AG,GG		0.0,0.0227,0.0077		843/952	27389741	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	55366	exon18			ACAGTCGTAGTAG	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.2529C>T	chr11.hg19:g.27389741G>A		58.0	0.0		76.0	30.0	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Silent	SNP	ENST00000379214.4	hg19	CCDS31449.1																																																																																			.	G|1.000;A|0.000		0.438	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		A	27389741	G	A	27389741	2	1	17	1	0	0	0	0	0	0	0	1	8765	1140	40	1		1	LGR4	11	27389741	Silent	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	8835786	27389741	107616775	47	1492										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398285	25398285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ggcactcttgcctacgccacCagctccaactaccacaagtt	6	17	1	0	rs121913530		TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr12:25398285C>A	ENST00000256078.4	-	2	97	c.34G>T	c.(34-36)Ggt>Tgt	p.G12C	KRAS_ENST00000557334.1_Missense_Mutation_p.G12C|KRAS_ENST00000556131.1_Missense_Mutation_p.G12C|KRAS_ENST00000311936.3_Missense_Mutation_p.G12C	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12C	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	KRAS_ENST00000256078,NS,adenocarcinoma,+1,3	KRAS	30930	.	5144	Substitution - Missense(5142)|Insertion - In frame(2)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	c.G34T	GRCh37	CM076251	KRAS	M	rs121913530	.						93	83	86					12																	25398285		2203	4300	6503	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	CGCCACCAGCTCC	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>T	chr12.hg19:g.25398285C>A	ENSP00000256078:p.Gly12Cys	137.0	0.0		150.0	53.0	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676185	0.88445	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90466	0.7014	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	D	0.91833	0.5477	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	C	12	ENSP00000308495:G12C;ENSP00000452512:G12C;ENSP00000256078:G12C;ENSP00000451856:G12C	ENSP00000256078:G12C	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.	.		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398285	C	A	25398285	3	1	17	1	0	0	0	0	1	0	0	0	8447	594	21	3	672	3	KRAS	12	25398285	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10		25398285	108453610	48	1493										
ASCL1	429	hgsc.bcm.edu	37	chr12	103352142	103352170	+	Frame_Shift_Del	DEL	CGCAGCCGCCGCAGCGGCAGCGCAGAGCG	CGCAGCCGCCGCAGCGGCAGCGCAGAGCG	-													0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	acggccgcagccgcggcggcCgcagccgccgcagcggcagc					rs558732328|rs552552603|rs554829144|rs545982257|rs139008516|rs568951072	byFrequency	TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	CGCAGCCGCCGCAGCGGCAGCGCAGAGCG	CGCAGCCGCCGCAGCGGCAGCGCAGAGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr12:103352142_103352170delCGCAGCCGCCGCAGCGGCAGCGCAGAGCG	ENST00000266744.3	+	1	679_707	c.120_148delCGCAGCCGCCGCAGCGGCAGCGCAGAGCG	c.(118-150)gccgcagccgccgcagcggcagcgcagagcgcgfs	p.AAAAAAAAQSA40fs		NM_004316.3	NP_004307.2	P50553	ASCL1_HUMAN	achaete-scute family bHLH transcription factor 1	40	Poly-Ala.				adrenal chromaffin cell differentiation (GO:0061104)|carotid body glomus cell differentiation (GO:0061103)|cell maturation (GO:0048469)|cellular response to magnetism (GO:0071259)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|lung epithelial cell differentiation (GO:0060487)|lung neuroendocrine cell differentiation (GO:0061100)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroblast fate determination (GO:0007400)|neuroblast proliferation (GO:0007405)|neurogenesis (GO:0022008)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron fate commitment (GO:0003359)|Notch signaling pathway (GO:0007219)|olfactory pit development (GO:0060166)|oligodendrocyte development (GO:0014003)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial cell differentiation (GO:0030856)|regulation of gene expression (GO:0010468)|regulation of mitotic cell cycle (GO:0007346)|regulation of timing of subpallium neuron differentiation (GO:0060165)|response to epidermal growth factor (GO:0070849)|response to folic acid (GO:0051593)|response to lithium ion (GO:0010226)|response to retinoic acid (GO:0032526)|spinal cord association neuron differentiation (GO:0021527)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|stomach neuroendocrine cell differentiation (GO:0061102)|subpallium neuron fate commitment (GO:0060163)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)|vestibular nucleus development (GO:0021750)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)			NS(3)|large_intestine(1)|lung(1)	5						ccgcggcggccgcagccgccgcagcggcagcgcagagcgcgcagcagca	0.769																																					p.40_49del		Atlas-INDEL	.											.	ASCL1	16	.	0			c.119_147del						.																																			SO:0001589	frameshift_variant	429	exon1			.	L08424	CCDS31886.1	12q22-q23	2013-10-17	2013-10-17			ENSG00000139352		"Basic helix-loop-helix proteins"	738	protein-coding gene	gene with protein product		100790	"achaete-scute complex (Drosophila) homolog-like 1", "achaete-scute complex-like 1 (Drosophila)", "achaete-scute complex homolog 1 (Drosophila)"			8390674	Standard	NM_004316		Approved	ASH1, HASH1, bHLHa46	uc001tjr.4	P50553		ENST00000266744.3:c.120_148delCGCAGCCGCCGCAGCGGCAGCGCAGAGCG	chr12.hg19:g.103352142_103352170delCGCAGCCGCCGCAGCGGCAGCGCAGAGCG	ENSP00000266744:p.Ala40fs	46.0	0.0		40.0	18.0	NM_004316	A8K3C4|Q9BQ30	Frame_Shift_Del	DEL	ENST00000266744.3	hg19	CCDS31886.1																																																																																			.	.		0.769	ASCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406707.1			-	103352170	CGCAGCCGCCGCAGCGGCAGCGCAGAGCG	-	103352142	7	5	17	1	0	1	0	1	0	0	0	0	1034	639	23	0	122	0	ASCL1	12	103352142	Frame_Shift_Del	DEL	CGCAGCCGCCGCAGCGGCAGCGCAGAGCG	TCGA-2Y-A9H7-01A-11D-A38X-10	77953857	103352142	30499753	49	1494										
ATP2A2	488	hgsc.bcm.edu	37	chr12	110719613	110719613	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ccatggagaacgcgcacaccAagacggtggaggaggtgctg	16	10	0	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr12:110719613A>C	ENST00000539276.2	+	1	128	c.19A>C	c.(19-21)Aag>Cag	p.K7Q	ATP2A2_ENST00000308664.6_Missense_Mutation_p.K7Q|ATP2A2_ENST00000395494.2_Missense_Mutation_p.K7Q|ATP2A2_ENST00000552636.1_Intron			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	7					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						CGCGCACACCAAGACGGTGGA	0.701																																					p.K7Q		Atlas-SNP	.											.	ATP2A2	78	.	0			c.A19C						.						60	48	52					12																	110719613		2167	4279	6446	SO:0001583	missense	488	exon1			CACACCAAGACGG		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.19A>C	chr12.hg19:g.110719613A>C	ENSP00000440045:p.Lys7Gln	50.0	0.0		30.0	12.0	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Missense_Mutation	SNP	ENST00000539276.2	hg19	CCDS9144.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.214457	0.79352	.	.	ENSG00000174437	ENST00000308664;ENST00000395494;ENST00000539276	T;T;T	0.78246	-1.16;-1.16;-1.16	5.21	5.21	0.72293	ATPase, P-type cation-transporter, N-terminal (2);	0.101923	0.64402	D	0.000003	T	0.73745	0.3626	L	0.55834	1.745	0.80722	D	1	B;B;B	0.18610	0.029;0.005;0.012	B;B;B	0.21151	0.033;0.004;0.011	T	0.69355	-0.5167	10	0.30854	T	0.27	.	15.0866	0.72158	1.0:0.0:0.0:0.0	.	7;7;7	P16615-4;P16615-2;P16615	.;.;AT2A2_HUMAN	Q	7	ENSP00000311186:K7Q;ENSP00000378872:K7Q;ENSP00000440045:K7Q	ENSP00000311186:K7Q	K	+	1	0	ATP2A2	109203996	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	6.972000	0.76110	1.970000	0.57323	0.454000	0.30748	AAG	.	.		0.701	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		C	110719613	A	C	110719613	3	2	17	1	0	0	0	0	1	0	0	0	1137	131	5	5	21	5	ATP2A2	12	110719613	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10	7367471	110719613	23132282	50	1495										
BRAP	8315	hgsc.bcm.edu	37	chr12	112119568	112119568	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gtttatgcattccttactgtGatctttacttctttgcgcag	7	9	2	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr12:112119568G>A	ENST00000327551.6	-	3	366	c.226C>T	c.(226-228)Cac>Tac	p.H76Y	BRAP_ENST00000539060.1_5'Flank|BRAP_ENST00000419234.4_Missense_Mutation_p.H106Y			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	0					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						TCCTTACTGTGATCTTTACTT	0.408																																					p.H106Y	Pancreas(146;846 1904 7830 25130 26065)	Atlas-SNP	.											.	BRAP	42	.	0			c.C316T						.						174	159	164					12																	112119568		2203	4300	6503	SO:0001583	missense	8315	exon3			TACTGTGATCTTT	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"RING-type (C3HC4) zinc fingers"	1099	protein-coding gene	gene with protein product	"impedes mitogenic signal propagation", "galectin-2-binding protein"	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.226C>T	chr12.hg19:g.112119568G>A	ENSP00000330813:p.His76Tyr	173.0	0.0		211.0	91.0	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000327551.6	hg19		.	.	.	.	.	.	.	.	.	.	G	9.876	1.200176	0.22121	.	.	ENSG00000089234	ENST00000419234;ENST00000327551	T;T	0.42131	0.98;0.98	6.08	4.23	0.50019	.	1.161590	0.05993	N	0.646308	T	0.31544	0.0800	N	0.22421	0.69	0.09310	N	0.999999	B	0.14012	0.009	B	0.14578	0.011	T	0.27191	-1.0081	10	0.62326	D	0.03	-0.7492	5.8425	0.18641	0.0654:0.1208:0.5643:0.2496	.	106	Q7Z569	BRAP_HUMAN	Y	106;76	ENSP00000403524:H106Y;ENSP00000330813:H76Y	ENSP00000330813:H76Y	H	-	1	0	BRAP	110603951	0.510000	0.26171	0.869000	0.34112	0.427000	0.31564	1.597000	0.36729	0.871000	0.35750	0.655000	0.94253	CAC	.	.		0.408	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			A	112119568	G	A	112119568	3	1	17	1	0	0	0	0	1	0	0	0	1499	1290	45	3	1502	3	BRAP	12	112119568	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	1399955	112119568	21732327	51	1496										
CCDC122	160857	hgsc.bcm.edu	37	chr13	44411471	44411471	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ctgcagttttttccaattgtTgaatgttccattgccactgt	7	9	0	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr13:44411471T>A	ENST00000444614.3	-	7	1025	c.767A>T	c.(766-768)cAa>cTa	p.Q256L		NM_144974.3	NP_659411.2	Q5T0U0	CC122_HUMAN	coiled-coil domain containing 122	256										endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9		Lung NSC(96;7.5e-06)|Breast(139;0.00765)|Hepatocellular(98;0.00826)|Prostate(109;0.0143)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000767)|BRCA - Breast invasive adenocarcinoma(63;0.128)		TTCCAATTGTTGAATGTTCCA	0.388																																					p.Q256L		Atlas-SNP	.											.	CCDC122	21	.	0			c.A767T						.						158	141	146					13																	44411471		1877	4103	5980	SO:0001583	missense	160857	exon7			AATTGTTGAATGT	AK056408	CCDS9390.2	13q14.11	2008-10-30			ENSG00000151773	ENSG00000151773			26478	protein-coding gene	gene with protein product		613408					Standard	NM_144974		Approved	FLJ31846	uc010acf.3	Q5T0U0	OTTHUMG00000017413	ENST00000444614.3:c.767A>T	chr13.hg19:g.44411471T>A	ENSP00000407763:p.Gln256Leu	50.0	0.0		67.0	27.0	NM_144974	B2RP70|B7ZMI9|Q96MV0	Missense_Mutation	SNP	ENST00000444614.3	hg19	CCDS9390.2	.	.	.	.	.	.	.	.	.	.	T	15.48	2.845539	0.51164	.	.	ENSG00000151773	ENST00000444614	T	0.41758	0.99	5.2	4.02	0.46733	.	.	.	.	.	T	0.40347	0.1113	L	0.53249	1.67	0.80722	D	1	B	0.25609	0.13	B	0.32624	0.149	T	0.34502	-0.9826	9	0.87932	D	0	.	8.6548	0.34058	0.0:0.0881:0.0:0.9119	.	256	Q5T0U0	CC122_HUMAN	L	256	ENSP00000407763:Q256L	ENSP00000407763:Q256L	Q	-	2	0	CCDC122	43309471	1.000000	0.71417	0.982000	0.44146	0.952000	0.60782	1.835000	0.39181	0.926000	0.37118	0.477000	0.44152	CAA	.	.		0.388	CCDC122-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276172.4	NM_144974		A	44411471	T	A	44411471	3	1	17	1	0	0	0	0	1	0	0	0	2760	1812	63	4	58	4	CCDC122	13	44411471	Missense_Mutation	SNP	T	TCGA-2Y-A9H7-01A-11D-A38X-10		44411471	70758407	52	1497										
VPS36	51028	hgsc.bcm.edu	37	chr13	53010479	53010479	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	atgtaggagttcttactactCtggaatgggccaggttcttt	11	7	3	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr13:53010479C>A	ENST00000378060.4	-	4	324	c.297G>T	c.(295-297)caG>caT	p.Q99H	VPS36_ENST00000480923.1_5'UTR	NM_001282168.1|NM_001282169.1|NM_016075.2	NP_001269097.1|NP_001269098.1|NP_057159.2	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36 homolog (S. cerevisiae)	99					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	17		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		TCTTACTACTCTGGAATGGGC	0.388																																					p.Q99H		Atlas-SNP	.											.	VPS36	38	.	0			c.G297T						.						106	100	102					13																	53010479		2203	4300	6503	SO:0001583	missense	51028	exon4			ACTACTCTGGAAT	AF151903	CCDS9434.1, CCDS73577.1	13q14.13	2008-02-05	2007-01-12	2005-08-02	ENSG00000136100	ENSG00000136100			20312	protein-coding gene	gene with protein product		610903	"chromosome 13 open reading frame 9", "vacuolar protein sorting 36 homolog (yeast)"	C13orf9		11278625, 15755741	Standard	NM_016075		Approved	CGI-145, Eap45	uc001vgs.3	Q86VN1	OTTHUMG00000016964	ENST00000378060.4:c.297G>T	chr13.hg19:g.53010479C>A	ENSP00000367299:p.Gln99His	154.0	0.0		161.0	67.0	NM_016075	A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3	Missense_Mutation	SNP	ENST00000378060.4	hg19	CCDS9434.1	.	.	.	.	.	.	.	.	.	.	.	16.61	3.172212	0.57584	.	.	ENSG00000136100	ENST00000378060	.	.	.	5.93	3.82	0.43975	.	0.000000	0.85682	D	0.000000	T	0.44244	0.1284	L	0.57536	1.79	0.58432	D	0.999997	D	0.61080	0.989	B	0.43838	0.433	T	0.35943	-0.9768	9	0.16896	T	0.51	.	7.0428	0.25029	0.0:0.6681:0.0:0.3319	.	99	Q86VN1	VPS36_HUMAN	H	99	.	ENSP00000367299:Q99H	Q	-	3	2	VPS36	51908480	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.986000	0.29590	1.438000	0.47492	0.655000	0.94253	CAG	.	.		0.388	VPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045059.3			A	53010479	C	A	53010479	3	1	17	1	0	0	0	0	1	0	0	0	17219	912	32	3	907	3	VPS36	13	53010479	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	8599008	53010479	62159399	53	1498										
SEC23A	10484	hgsc.bcm.edu	37	chr14	39560758	39560758	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gccttcacatccaagttcatGaacctgaaccattctcccaa	4	15	3	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr14:39560758G>A	ENST00000307712.6	-	5	1043	c.526C>T	c.(526-528)Cat>Tat	p.H176Y	SEC23A_ENST00000536508.1_Missense_Mutation_p.H50Y|SEC23A_ENST00000537403.1_5'Flank|SEC23A_ENST00000545328.2_Missense_Mutation_p.H147Y	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	176					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		CCAAGTTCATGAACCTGAACC	0.383																																					p.H176Y		Atlas-SNP	.											.	SEC23A	73	.	0			c.C526T						.						119	109	112					14																	39560758		2203	4300	6503	SO:0001583	missense	10484	exon5			GTTCATGAACCTG	X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"Sec23 (S. cerevisiae) homolog A"			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.526C>T	chr14.hg19:g.39560758G>A	ENSP00000306881:p.His176Tyr	83.0	0.0		102.0	44.0	NM_006364	B2R5P4|B3KXI2|Q8NE16	Missense_Mutation	SNP	ENST00000307712.6	hg19	CCDS9668.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.659353	0.88154	.	.	ENSG00000100934	ENST00000307712;ENST00000536508;ENST00000545328;ENST00000554645	T;T;T	0.71579	-0.58;-0.58;-0.58	5.46	5.46	0.80206	Sec23/Sec24, trunk domain (1);	0.000000	0.85682	D	0.000000	T	0.81517	0.4839	M	0.80746	2.51	0.80722	D	1	P;P;P;B	0.46457	0.878;0.603;0.603;0.173	P;B;B;B	0.52309	0.695;0.399;0.283;0.105	T	0.82202	-0.0574	10	0.46703	T	0.11	-25.565	19.2992	0.94136	0.0:0.0:1.0:0.0	.	64;147;50;176	G3V531;F5H365;F5H6C4;Q15436	.;.;.;SC23A_HUMAN	Y	176;50;147;64	ENSP00000306881:H176Y;ENSP00000437715:H50Y;ENSP00000445393:H147Y	ENSP00000306881:H176Y	H	-	1	0	SEC23A	38630509	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.772000	0.98984	2.544000	0.85801	0.563000	0.77884	CAT	.	.		0.383	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2			A	39560758	G	A	39560758	3	1	17	1	0	0	0	0	1	0	0	0	14006	1290	45	3	1835	3	SEC23A	14	39560758	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10		39560758	67788782	54	1499										
C14orf50	145376	hgsc.bcm.edu	37	chr14	65054887	65054887	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gcgttctccagtcatgtctaCtctgctgccatctctcagag	8	14	6	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr14:65054887C>T	ENST00000298705.1	+	11	1052	c.956C>T	c.(955-957)aCt>aTt	p.T319I	RP11-973N13.3_ENST00000556634.1_RNA|RP11-973N13.3_ENST00000554454.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	319					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GTCATGTCTACTCTGCTGCCA	0.443																																					p.T319I		Atlas-SNP	.											.	.	.	.	0			c.C956T						.						111	109	110					14																	65054887		2203	4300	6503	SO:0001583	missense	145376	exon11			TGTCTACTCTGCT		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20097	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 50"	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.956C>T	chr14.hg19:g.65054887C>T	ENSP00000298705:p.Thr319Ile	65.0	0.0		78.0	41.0	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	hg19	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.954092	0.73902	.	.	ENSG00000165807	ENST00000298705	T	0.32515	1.45	5.55	5.55	0.83447	.	0.092039	0.47455	D	0.000224	T	0.52025	0.1709	M	0.63428	1.95	0.38144	D	0.938536	D	0.76494	0.999	D	0.68943	0.961	T	0.57201	-0.7852	10	0.72032	D	0.01	-17.6391	15.0284	0.71687	0.0:1.0:0.0:0.0	.	319	Q96LQ0	PPR36_HUMAN	I	319	ENSP00000298705:T319I	ENSP00000298705:T319I	T	+	2	0	C14orf50	64124640	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	3.737000	0.55060	2.596000	0.87737	0.655000	0.94253	ACT	.	.		0.443	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		T	65054887	C	T	65054887	3	4	17	1	0	0	0	0	1	0	0	0	1779	565	20	3	998	3	C14orf50	14	65054887	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	25494129	65054887	42294653	55	1500										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68265207	68265207	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cctcaggcaagtgaggctctGggtgaagatcagcagaggtg	16	8	3	4			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr14:68265207G>C	ENST00000347230.4	-	11	1910	c.1772C>G	c.(1771-1773)cCa>cGa	p.P591R	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.P591R	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	591					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		GTGAGGCTCTGGGTGAAGATC	0.512																																					p.P591R		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.C1772G						.						84	75	78					14																	68265207		2203	4300	6503	SO:0001583	missense	23503	exon11			GGCTCTGGGTGAA	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.1772C>G	chr14.hg19:g.68265207G>C	ENSP00000251119:p.Pro591Arg	81.0	0.0		107.0	42.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.213479	0.39102	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.25912	1.91;1.77	5.56	4.67	0.58626	.	0.598474	0.17249	N	0.181242	T	0.30008	0.0751	L	0.44542	1.39	0.29869	N	0.826968	D;P;B	0.59357	0.985;0.631;0.294	P;B;B	0.49708	0.62;0.246;0.057	T	0.15607	-1.0431	10	0.59425	D	0.04	-12.4627	10.4876	0.44731	0.0:0.1175:0.5253:0.3572	.	591;591;591	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	R	591;570;591	ENSP00000251119:P591R;ENSP00000450603:P591R	ENSP00000251119:P591R	P	-	2	0	ZFYVE26	67334960	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	1.143000	0.31553	1.344000	0.45657	0.655000	0.94253	CCA	.	.		0.512	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		C	68265207	G	C	68265207	3	2	17	1	0	0	0	0	1	0	0	0	17683	1348	47	4	5975	4	ZFYVE26	14	68265207	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	3210320	68265207	39084333	56	1501										
ZC3H14	79882	hgsc.bcm.edu	37	chr14	89038562	89038562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cgcaggagtcaaaaaccacaAatgtcaggtaagagtctggt	11	8	3	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr14:89038562A>G	ENST00000251038.5	+	5	649	c.424A>G	c.(424-426)Aat>Gat	p.N142D	ZC3H14_ENST00000557607.1_5'UTR|ZC3H14_ENST00000302216.8_Missense_Mutation_p.N142D|ZC3H14_ENST00000336693.4_Missense_Mutation_p.N108D|ZC3H14_ENST00000359301.3_Missense_Mutation_p.N108D|ZC3H14_ENST00000555755.1_Missense_Mutation_p.N142D|ZC3H14_ENST00000393514.5_Missense_Mutation_p.N142D|ZC3H14_ENST00000556945.1_Missense_Mutation_p.N142D	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	142						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						AAAAACCACAAATGTCAGGTA	0.453																																					p.N142D		Atlas-SNP	.											.	ZC3H14	71	.	0			c.A424G						.						58	58	58					14																	89038562		2203	4300	6503	SO:0001583	missense	79882	exon5			ACCACAAATGTCA	AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"Zinc fingers, CCCH-type domain containing"	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.424A>G	chr14.hg19:g.89038562A>G	ENSP00000251038:p.Asn142Asp	186.0	0.0		231.0	95.0	NM_001160104	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Missense_Mutation	SNP	ENST00000251038.5	hg19	CCDS32133.1	.	.	.	.	.	.	.	.	.	.	A	8.085	0.773296	0.16051	.	.	ENSG00000100722	ENST00000251038;ENST00000393530;ENST00000353091;ENST00000359301;ENST00000302216;ENST00000380684;ENST00000556945;ENST00000556158;ENST00000555799;ENST00000555755;ENST00000393514;ENST00000336693;ENST00000557693	.	.	.	5.43	1.59	0.23543	.	0.702444	0.14348	N	0.325255	T	0.25232	0.0613	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.28128	0.066;0.066;0.201;0.066	B;B;B;B	0.23275	0.022;0.022;0.045;0.022	T	0.14337	-1.0476	9	0.12103	T	0.63	-3.146	4.5407	0.12056	0.5825:0.0:0.2753:0.1422	.	142;142;142;142	G3V5R4;Q6PJT7-2;Q6PJT7-3;Q6PJT7	.;.;.;ZC3HE_HUMAN	D	142;142;142;108;142;123;142;129;108;142;142;108;108	.	ENSP00000251038:N142D	N	+	1	0	ZC3H14	88108315	0.002000	0.14202	0.004000	0.12327	0.072000	0.16883	0.619000	0.24388	0.903000	0.36546	0.455000	0.32223	AAT	.	.		0.453	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824		G	89038562	A	G	89038562	3	3	17	1	0	0	0	0	1	0	0	0	17581	14	1	2	442	2	ZC3H14	14	89038562	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10	20773355	89038562	18310978	57	1502										
MTMR15	22909	hgsc.bcm.edu	37	chr15	31197246	31197246	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	agtaaagcagaagatcagtcCctactttaaaagtaatgatg	8	6	1	3			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr15:31197246C>A	ENST00000362065.4	+	2	671	c.380C>A	c.(379-381)cCc>cAc	p.P127H	FAN1_ENST00000561607.1_Missense_Mutation_p.P127H|FAN1_ENST00000565466.1_Missense_Mutation_p.P127H|FAN1_ENST00000561594.1_Missense_Mutation_p.P127H	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	127					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						AAGATCAGTCCCTACTTTAAA	0.393								Direct reversal of damage																													p.P127H		Atlas-SNP	.											.	FAN1	77	.	0			c.C380A						.						78	71	74					15																	31197246		2202	4300	6502	SO:0001583	missense	22909	exon2			TCAGTCCCTACTT		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"KIAA1018", "myotubularin related protein 15"	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.380C>A	chr15.hg19:g.31197246C>A	ENSP00000354497:p.Pro127His	110.0	0.0		124.0	49.0	NM_001146095	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	hg19	CCDS32186.1	.	.	.	.	.	.	.	.	.	.	C	19.11	3.764185	0.69878	.	.	ENSG00000198690	ENST00000362065	D	0.90133	-2.62	5.33	5.33	0.75918	.	0.104769	0.64402	D	0.000003	D	0.94394	0.8197	L	0.57536	1.79	0.54753	D	0.999989	D;D	0.89917	1.0;1.0	D;D	0.74348	0.962;0.983	D	0.94674	0.7859	10	0.87932	D	0	-15.5681	18.9753	0.92733	0.0:1.0:0.0:0.0	.	127;127	Q9Y2M0;Q9Y2M0-2	FAN1_HUMAN;.	H	127	ENSP00000354497:P127H	ENSP00000354497:P127H	P	+	2	0	FAN1	28984538	1.000000	0.71417	1.000000	0.80357	0.375000	0.29983	4.170000	0.58229	2.655000	0.90218	0.462000	0.41574	CCC	.	.		0.393	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967		A	31197246	C	A	31197246	3	1	17	1	0	0	0	0	1	0	0	0	9952	623	22	3	382	3	MTMR15	15	31197246	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10		31197246	71334146	58	1503										
C15orf39	56905	hgsc.bcm.edu	37	chr15	75501057	75501057	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cactgcgggagctcgccctgCcaggctgcacctcacgcatg	12	17	1	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr15:75501057C>T	ENST00000360639.2	+	2	2988	c.2668C>T	c.(2668-2670)Cca>Tca	p.P890S	RP11-69H7.3_ENST00000563568.1_RNA|C15orf39_ENST00000567617.1_Missense_Mutation_p.P890S|C15orf39_ENST00000394987.4_Missense_Mutation_p.P890S			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	890						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						GCTCGCCCTGCCAGGCTGCAC	0.677																																					p.P890S		Atlas-SNP	.											.	C15orf39	64	.	0			c.C2668T						.						24	21	22					15																	75501057		2197	4292	6489	SO:0001583	missense	56905	exon2			GCCCTGCCAGGCT	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 38~Name Same As HGNC:28782"				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.2668C>T	chr15.hg19:g.75501057C>T	ENSP00000353854:p.Pro890Ser	23.0	0.0		40.0	20.0	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	hg19	CCDS10276.1	.	.	.	.	.	.	.	.	.	.	C	4.258	0.046891	0.08243	.	.	ENSG00000167173	ENST00000360639;ENST00000394987;ENST00000446981	T;T	0.16073	2.37;2.37	5.44	4.47	0.54385	.	0.568298	0.19135	N	0.121827	T	0.08537	0.0212	N	0.08118	0	0.09310	N	1	B;B	0.25719	0.021;0.132	B;B	0.18561	0.022;0.008	T	0.16247	-1.0409	10	0.46703	T	0.11	-6.7891	9.2834	0.37742	0.2247:0.6384:0.1369:0.0	.	452;890	Q2VPA3;Q6ZRI6	.;CO039_HUMAN	S	890;890;288	ENSP00000353854:P890S;ENSP00000378438:P890S	ENSP00000353854:P890S	P	+	1	0	C15orf39	73288110	0.954000	0.32549	0.463000	0.27130	0.012000	0.07955	2.068000	0.41471	2.556000	0.86216	0.561000	0.74099	CCA	.	.		0.677	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		T	75501057	C	T	75501057	3	4	17	1	0	0	0	0	1	0	0	0	1795	739	26	3	2670	3	C15orf39	15	75501057	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	44303811	75501057	27030335	59	1504										
ZNF592	9640	hgsc.bcm.edu	37	chr15	85326095	85326095	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tcaggatcagcccccgatgtGccggccgtgagtgtcattgt	13	12	3	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr15:85326095G>T	ENST00000560079.2	+	4	477	c.189G>T	c.(187-189)gtG>gtT	p.V63V	ZNF592_ENST00000299927.3_Silent_p.V63V	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	63					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CCCCCGATGTGCCGGCCGTGA	0.532																																					p.V63V		Atlas-SNP	.											.	ZNF592	95	.	0			c.G189T						.						100	90	93					15																	85326095		2203	4299	6502	SO:0001819	synonymous_variant	9640	exon4			CGATGTGCCGGCC	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"Zinc fingers, C2H2-type"	28986	protein-coding gene	gene with protein product		613624	"spinocerebellar ataxia, autosomal recessive 5"	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.189G>T	chr15.hg19:g.85326095G>T		77.0	0.0		86.0	31.0	NM_014630	Q2M1T2|Q504Y9	Silent	SNP	ENST00000560079.2	hg19	CCDS32317.1																																																																																			.	.		0.532	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		T	85326095	G	T	85326095	2	4	17	1	0	0	0	0	0	0	0	1	18037	1306	46	3		3	ZNF592	15	85326095	Silent	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	9825038	85326095	17205297	60	1505										
AXIN1	8312	hgsc.bcm.edu	37	chr16	396147	396147	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gacgcctggcgtcggactcaCctgaactctctgccttcgct	10	16	2	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr16:396147C>G	ENST00000262320.3	-	2	1250		c.e2+1		AXIN1_ENST00000354866.3_Splice_Site|AXIN1_ENST00000481769.1_Intron	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1						activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GTCGGACTCACCTGAACTCTC	0.617																																					.		Atlas-SNP	.											.	AXIN1	290	.	0			c.878+1G>C						.						30	32	31					16																	396147		2203	4299	6502	SO:0001630	splice_region_variant	8312	exon3			GACTCACCTGAAC	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.878+1G>C	chr16.hg19:g.396147C>G		49.0	0.0		18.0	17.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Splice_Site	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	C	15.08	2.727611	0.48833	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.173	0.93588	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AXIN1	336148	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.710000	0.84655	2.516000	0.84829	0.655000	0.94253	.	.	.		0.617	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		Intron	G	396147	C	G	396147	5	3	17	1	0	0	0	0	0	0	1	0	1236	521	18	4	1749	4	AXIN1	16	396147	Splice_Site	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10		396147	89958606	61	1506										
STUB1	339123	hgsc.bcm.edu	37	chr16	731813	731813	+	3'UTR	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ggagctggaagagtgccagcGaaaccacgagggtgatgagg	18	7	0	3	rs145094142		TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr16:731813G>A	ENST00000293882.4	-	0	1985				STUB1_ENST00000564370.1_Missense_Mutation_p.R110Q|STUB1_ENST00000566181.2_3'UTR|JMJD8_ENST00000454700.1_3'UTR|STUB1_ENST00000219548.4_Missense_Mutation_p.R182Q|LA16c-313D11.9_ENST00000567091.1_RNA|STUB1_ENST00000565677.1_Missense_Mutation_p.R110Q|LA16c-313D11.9_ENST00000571933.1_RNA|JMJD8_ENST00000412368.2_3'UTR|JMJD8_ENST00000609261.1_3'UTR			Q96S16	JMJD8_HUMAN	jumonji domain containing 8							extracellular vesicular exosome (GO:0070062)				breast(1)	1						GAGTGCCAGCGAAACCACGAG	0.627																																					p.R182Q		Atlas-SNP	.											.	STUB1	26	.	0			c.G545A						.	G	,GLN/ARG	0,4398		0,0,2199	38	39	39		,545	3.2	1	16	dbSNP_134	39	1,8599	1.2+/-3.3	0,1,4299	no	utr-3,missense	STUB1,JMJD8	NM_001005920.2,NM_005861.2	,43	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	,benign	,182/304	731813	1,12997	2199	4300	6499	SO:0001624	3_prime_UTR_variant	10273	exon4			GCCAGCGAAACCA		CCDS45369.1	16p13.3	2008-07-28	2008-07-28	2008-07-28		ENSG00000161999			14148	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 20"	C16orf20			Standard	NM_001005920		Approved		uc002ciw.1	Q96S16		ENST00000293882.4:c.*981C>T	chr16.hg19:g.731813G>A		155.0	0.0		91.0	69.0	NM_005861	B2RNS7|D3DU58|Q4PKE3|Q4VBY1|Q6GMW5|Q71RB8	Missense_Mutation	SNP	ENST00000293882.4	hg19		.	.	.	.	.	.	.	.	.	.	G	5.715	0.316461	0.10789	0.0	1.16E-4	ENSG00000103266	ENST00000219548	T	0.14516	2.5	4.15	3.19	0.36642	.	0.157867	0.44688	D	0.000427	T	0.06188	0.0160	N	0.11427	0.14	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.29458	-1.0011	10	0.12766	T	0.61	-28.6077	8.7441	0.34575	0.1906:0.0:0.8094:0.0	.	182	Q9UNE7	CHIP_HUMAN	Q	182	ENSP00000219548:R182Q	ENSP00000219548:R182Q	R	+	2	0	STUB1	671814	1.000000	0.71417	0.996000	0.52242	0.710000	0.40934	1.768000	0.38511	1.092000	0.41356	-0.273000	0.10243	CGA	.	G|1.000;A|0.000		0.627	JMJD8-201	KNOWN	basic	protein_coding	protein_coding		NM_001005920		A	731813	G	A	731813	1	1	17	0	1	0	0	0	0	0	0	0	15350	1058	37	1		1	STUB1	16	731813	3'UTR	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	335666	731813	89622940	62	1507										
PKD1	5310	hgsc.bcm.edu	37	chr16	2141435	2141435	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cgggcgtaccgaggtgagcaGaggcagcgagaggcccgcgc	19	12	0	3			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr16:2141435G>A	ENST00000262304.4	-	42	11909	c.11701C>T	c.(11701-11703)Ctg>Ttg	p.L3901L	MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA|PKD1_ENST00000423118.1_Silent_p.L3900L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3901					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GAGGTGAGCAGAGGCAGCGAG	0.806																																					p.L3901L		Atlas-SNP	.											.	PKD1	184	.	0			c.C11701T	GRCh37	CI062279	PKD1	I		.						1	1	1					16																	2141435		417	744	1161	SO:0001819	synonymous_variant	5310	exon42			TGAGCAGAGGCAG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.11701C>T	chr16.hg19:g.2141435G>A		55.0	0.0		21.0	13.0	NM_001009944	Q15140|Q15141	Silent	SNP	ENST00000262304.4	hg19	CCDS32369.1																																																																																			.	.		0.806	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2141435	G	A	2141435	2	1	17	1	0	0	0	0	0	0	0	1	11972	933	33	3		3	PKD1	16	2141435	Silent	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	1409622	2141435	88213318	63	1508										
C16orf86	388284	hgsc.bcm.edu	37	chr16	67702330	67702330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gtccactagtgacccccaccCatgccctggctcccctcgga	8	20	0	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr16:67702330C>T	ENST00000403458.4	+	4	936	c.781C>T	c.(781-783)Cat>Tat	p.H261Y	ENKD1_ENST00000602409.1_5'Flank|ENKD1_ENST00000243878.4_5'Flank|ENKD1_ENST00000602644.1_5'Flank	NM_001012984.2	NP_001013002.2	Q6ZW13	CP086_HUMAN	chromosome 16 open reading frame 86	261										endometrium(2)|lung(4)	6		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		GACCCCCACCCATGCCCTGGC	0.662											OREG0023886	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H261Y		Atlas-SNP	.											.	C16orf86	20	.	0			c.C781T						.						22	27	25					16																	67702330		1987	4156	6143	SO:0001583	missense	388284	exon4			CCCACCCATGCCC		CCDS32468.2	16q22.1	2008-10-30			ENSG00000159761	ENSG00000159761			33755	protein-coding gene	gene with protein product							Standard	NM_001012984		Approved	FLJ41802	uc002ety.3	Q6ZW13	OTTHUMG00000150527	ENST00000403458.4:c.781C>T	chr16.hg19:g.67702330C>T	ENSP00000384117:p.His261Tyr	53.0	0.0	1101	35.0	23.0	NM_001012984	B5MCW6	Missense_Mutation	SNP	ENST00000403458.4	hg19	CCDS32468.2	.	.	.	.	.	.	.	.	.	.	C	11.46	1.644261	0.29246	.	.	ENSG00000159761	ENST00000403458	.	.	.	5.95	3.99	0.46301	.	.	.	.	.	T	0.31071	0.0785	L	0.32530	0.975	0.09310	N	1	B	0.20261	0.043	B	0.17433	0.018	T	0.14448	-1.0472	8	0.27785	T	0.31	-0.6268	9.6959	0.40156	0.0:0.8363:0.0:0.1637	.	261	Q6ZW13	CP086_HUMAN	Y	261	.	ENSP00000384117:H261Y	H	+	1	0	C16orf86	66259831	0.001000	0.12720	0.042000	0.18584	0.013000	0.08279	1.133000	0.31430	1.532000	0.49169	0.563000	0.77884	CAT	.	.		0.662	C16orf86-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318767.2	NM_001012984		T	67702330	C	T	67702330	3	4	17	1	0	0	0	0	1	0	0	0	1841	594	21	3	795	3	C16orf86	16	67702330	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	65560895	67702330	22652423	64	1509										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7722313	7722313	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tgcatacctccaagatcacaGccacagaggtgactgagcag	10	12	1	4			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr17:7722313G>A	ENST00000572933.1	+	71	12207	c.10747G>A	c.(10747-10749)Gcc>Acc	p.A3583T	DNAH2_ENST00000389173.2_Missense_Mutation_p.A3583T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3583	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CAAGATCACAGCCACAGAGGT	0.612																																					p.A3583T		Atlas-SNP	.											.	DNAH2	498	.	0			c.G10747A						.						66	58	60					17																	7722313		2203	4300	6503	SO:0001583	missense	146754	exon70			ATCACAGCCACAG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.10747G>A	chr17.hg19:g.7722313G>A	ENSP00000458355:p.Ala3583Thr	47.0	0.0		52.0	24.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.549886	0.45383	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.68624	-0.34	4.31	4.31	0.51392	.	0.223986	0.36854	N	0.002370	T	0.74230	0.3689	M	0.69823	2.125	0.80722	D	1	P;P	0.47910	0.881;0.902	P;P	0.51945	0.614;0.685	T	0.78773	-0.2073	10	0.87932	D	0	.	13.8355	0.63406	0.0:0.0:1.0:0.0	.	3544;3583	Q9P225-2;Q9P225	.;DYH2_HUMAN	T	3544;3583	ENSP00000373825:A3583T	ENSP00000353818:A3544T	A	+	1	0	DNAH2	7663038	0.998000	0.40836	0.107000	0.21349	0.112000	0.19704	5.291000	0.65667	2.228000	0.72767	0.462000	0.41574	GCC	.	.		0.612	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7722313	G	A	7722313	3	1	17	1	0	0	0	0	1	0	0	0	4604	971	34	3	11025	3	DNAH2	17	7722313	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10		7722313	73472897	65	1510										
TAOK1	57551	hgsc.bcm.edu	37	chr17	27778638	27778638	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ctcttcttcaaagaagatccAgagaagctcttcacagatct	6	11	6	4			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr17:27778638A>C	ENST00000261716.3	+	2	591	c.72A>C	c.(70-72)ccA>ccC	p.P24P	TAOK1_ENST00000536202.1_Silent_p.P24P	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	24					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|execution phase of apoptosis (GO:0097194)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of cytoskeleton organization (GO:0051493)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28			Colorectal(6;0.198)			AAGAAGATCCAGAGAAGCTCT	0.443																																					p.P24P		Atlas-SNP	.											.	TAOK1	151	.	0			c.A72C						.						111	108	109					17																	27778638		2203	4300	6503	SO:0001819	synonymous_variant	57551	exon2			AGATCCAGAGAAG	AB037782	CCDS32601.1, CCDS56024.1	17q11.2	2014-01-28				ENSG00000160551			29259	protein-coding gene	gene with protein product		610266				10718198, 14517247	Standard	NM_020791		Approved	KIAA1361, MARKK, PSK2, MAP3K16, FLJ14314, TAO1	uc002hdz.2	Q7L7X3		ENST00000261716.3:c.72A>C	chr17.hg19:g.27778638A>C		32.0	0.0		50.0	22.0	NM_025142	A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Silent	SNP	ENST00000261716.3	hg19	CCDS32601.1																																																																																			.	.		0.443	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791		C	27778638	A	C	27778638	2	2	17	1	0	0	0	0	0	0	0	1	15562	175	7	5		5	TAOK1	17	27778638	Silent	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10	20056325	27778638	53416572	66	1511										
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28380584	28380584	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	agccaactgcagagcaagaaCtgtacatagaatcagtaata	8	8	1	3			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr17:28380584C>G	ENST00000394835.3	+	10	1804	c.1612C>G	c.(1612-1614)Ctg>Gtg	p.L538V	EFCAB5_ENST00000394832.2_Missense_Mutation_p.L538V|EFCAB5_ENST00000320856.5_Missense_Mutation_p.L538V|EFCAB5_ENST00000536908.2_Missense_Mutation_p.L482V|EFCAB5_ENST00000541045.1_Missense_Mutation_p.L195V|EFCAB5_ENST00000378738.3_Missense_Mutation_p.L538V	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	538							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						AGAGCAAGAACTGTACATAGA	0.428																																					p.L538V		Atlas-SNP	.											.	EFCAB5	122	.	0			c.C1612G						.						86	80	82					17																	28380584		1965	4154	6119	SO:0001583	missense	374786	exon10			CAAGAACTGTACA	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.1612C>G	chr17.hg19:g.28380584C>G	ENSP00000378312:p.Leu538Val	98.0	0.0		148.0	58.0	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	hg19	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	C	7.000	0.554665	0.13436	.	.	ENSG00000176927	ENST00000536908;ENST00000534836;ENST00000541045;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598;ENST00000419434	T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.71	0.635	0.17723	.	3.096610	0.01357	N	0.012083	T	0.38188	0.1031	L	0.50333	1.59	0.09310	N	1	P;P;P;P;B;B	0.51933	0.728;0.822;0.949;0.655;0.228;0.228	B;B;B;B;B;B	0.42593	0.095;0.121;0.392;0.194;0.083;0.121	T	0.24154	-1.0168	10	0.30078	T	0.28	5.7694	5.1239	0.14875	0.133:0.6436:0.1299:0.0935	.	482;482;538;538;538;538	B4DS75;F5GYL2;A8MSY9;B5MEA3;E7EVS9;A4FU69	.;.;.;.;.;EFCB5_HUMAN	V	482;281;195;538;538;538;538;482;344	ENSP00000440619:L482V;ENSP00000445575:L195V;ENSP00000378312:L538V;ENSP00000322003:L538V;ENSP00000378309:L538V;ENSP00000368012:L538V;ENSP00000417009:L344V	ENSP00000322003:L538V	L	+	1	2	EFCAB5	25404710	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.005000	0.13129	0.163000	0.19507	-0.176000	0.13171	CTG	.	.		0.428	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		G	28380584	C	G	28380584	3	3	17	1	0	0	0	0	1	0	0	0	4940	564	20	4	1650	4	EFCAB5	17	28380584	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	601946	28380584	52814626	67	1512										
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40620078	40620078	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	acattccgattatggacaccGgtgaaaacccagaggttccc	9	12	0	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr17:40620078G>C	ENST00000343619.4	+	4	370	c.247G>C	c.(247-249)Ggt>Cgt	p.G83R	ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.G83R|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.G83R|ATP6V0A1_ENST00000544137.1_Intron|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.G83R|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.G83R|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.G83R	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	83					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		TATGGACACCGGTGAAAACCC	0.398																																					p.G83R		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.G247C						.						89	88	88					17																	40620078		2203	4300	6503	SO:0001583	missense	535	exon4			GACACCGGTGAAA	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"ATPases / V-type"	865	protein-coding gene	gene with protein product		192130	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 1", "ATPase, H+ transporting, lysosomal V0 subunit A1"	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.247G>C	chr17.hg19:g.40620078G>C	ENSP00000342951:p.Gly83Arg	277.0	0.0		331.0	120.0	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	hg19	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650195	0.87958	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728	D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05;-2.05	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	D	0.89431	0.6713	L	0.38733	1.17	0.80722	D	1	D;D;P;D;D;D	0.89917	1.0;1.0;0.946;1.0;0.993;0.985	D;D;P;D;P;D	0.97110	0.999;1.0;0.836;1.0;0.904;0.95	D	0.86699	0.1928	10	0.31617	T	0.26	-13.9006	20.4777	0.99188	0.0:0.0:1.0:0.0	.	83;83;83;83;83;83	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1;F5H569	.;.;.;VPP1_HUMAN;.;.	R	83	ENSP00000342951:G83R;ENSP00000444676:G83R;ENSP00000377415:G83R;ENSP00000264649:G83R;ENSP00000443991:G83R	ENSP00000264649:G83R	G	+	1	0	ATP6V0A1	37873604	1.000000	0.71417	0.973000	0.42090	0.902000	0.53008	9.837000	0.99465	2.840000	0.97914	0.655000	0.94253	GGT	.	.		0.398	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020		C	40620078	G	C	40620078	3	2	17	1	0	0	0	0	1	0	0	0	1168	1116	39	4	257	4	ATP6V0A1	17	40620078	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	12239494	40620078	40575132	68	1513										
KCNH6	81033	hgsc.bcm.edu	37	chr17	61615955	61615955	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gcacctcggcgacgtgctctCcaccctctacttcatctccc	6	20	4	0	rs560791257		TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr17:61615955C>T	ENST00000583023.1	+	8	1897	c.1886C>T	c.(1885-1887)tCc>tTc	p.S629F	KCNH6_ENST00000314672.5_Missense_Mutation_p.S629F|KCNH6_ENST00000456941.2_Missense_Mutation_p.S576F|KCNH6_ENST00000581784.1_Missense_Mutation_p.S576F	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	629					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GACGTGCTCTCCACCCTCTAC	0.682													C|||	1	0.000199681	0	0	5008	,	,		15390	0		0	False		,,,				2504	0.001				p.S629F		Atlas-SNP	.											.	KCNH6	122	.	0			c.C1886T						.						43	37	39					17																	61615955		2203	4300	6503	SO:0001583	missense	81033	exon8			TGCTCTCCACCCT	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.1886C>T	chr17.hg19:g.61615955C>T	ENSP00000463533:p.Ser629Phe	134.0	0.0		140.0	59.0	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	hg19	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.617776	0.87359	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D;D	0.96940	-4.18;-4.18	3.97	3.97	0.46021	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.340703	0.29486	N	0.012004	D	0.97272	0.9108	M	0.84846	2.72	0.50467	D	0.999874	B;P;P;P	0.50272	0.182;0.755;0.933;0.755	B;P;P;P	0.51415	0.264;0.637;0.669;0.637	D	0.98233	1.0484	10	0.72032	D	0.01	.	16.2244	0.82284	0.0:1.0:0.0:0.0	.	506;629;576;629	B4DPJ3;B4DKC0;Q9H252-2;Q9H252	.;.;.;KCNH6_HUMAN	F	629;576	ENSP00000318212:S629F;ENSP00000396900:S576F	ENSP00000318212:S629F	S	+	2	0	KCNH6	58969687	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.807000	0.69157	2.040000	0.60383	0.491000	0.48974	TCC	.	.		0.682	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		T	61615955	C	T	61615955	3	4	17	1	0	0	0	0	1	0	0	0	8045	855	30	3	1916	3	KCNH6	17	61615955	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10	20995877	61615955	19579255	69	1514										
NETO1	81832	hgsc.bcm.edu	37	chr18	70417298	70417298	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	aaaatctattgatactgaccGctggacggctttatcgtgtc	9	9	1	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr18:70417298G>A	ENST00000327305.6	-	9	2197	c.1540C>T	c.(1540-1542)Cgg>Tgg	p.R514W	NETO1_ENST00000583169.1_Splice_Site_p.R514W|NETO1_ENST00000299430.2_Splice_Site_p.R513W|RNA5SP460_ENST00000516789.1_RNA	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	514					memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		GATACTGACCGCTGGACGGCT	0.433																																					p.R514W		Atlas-SNP	.											.	NETO1	178	.	0			c.C1540T						.						79	69	72					18																	70417298		2203	4300	6503	SO:0001630	splice_region_variant	81832	exon9			CTGACCGCTGGAC	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.1541+1C>T	chr18.hg19:g.70417298G>A		25.0	0.0		26.0	11.0	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	hg19	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	G	30	5.049745	0.93740	.	.	ENSG00000166342	ENST00000327305;ENST00000299430	T;T	0.33438	1.41;1.41	5.76	5.76	0.90799	.	0.000000	0.52532	D	0.000079	T	0.54498	0.1862	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	T	0.53187	-0.8474	10	0.87932	D	0	-8.9025	19.973	0.97292	0.0:0.0:1.0:0.0	.	513;514	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	W	514;513	ENSP00000313088:R514W;ENSP00000299430:R513W	ENSP00000299430:R513W	R	-	1	2	NETO1	68568278	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.429000	0.97481	2.725000	0.93324	0.460000	0.39030	CGG	.	.		0.433	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999	Missense_Mutation	A	70417298	G	A	70417298	5	1	17	1	0	0	0	0	0	0	1	0	10348	1101	38	1	69	1	NETO1	18	70417298	Splice_Site	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10		70417298	7659950	70	1515										
CTDP1	9150	hgsc.bcm.edu	37	chr18	77474841	77474841	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	tatccagcgacagcgagagcAgcagtgagtccgagggcacg	15	11	0	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr18:77474841A>T	ENST00000299543.7	+	8	1528	c.1381A>T	c.(1381-1383)Agc>Tgc	p.S461C	CTDP1_ENST00000075430.7_Missense_Mutation_p.S461C	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	461	Ser-rich.				exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		CAGCGAGAGCAGCAGTGAGTC	0.667																																					p.S461C		Atlas-SNP	.											.	CTDP1	67	.	0			c.A1381T						.						13	14	13					18																	77474841		2189	4276	6465	SO:0001583	missense	9150	exon8			GAGAGCAGCAGTG	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.1381A>T	chr18.hg19:g.77474841A>T	ENSP00000299543:p.Ser461Cys	119.0	0.0		127.0	44.0	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	hg19	CCDS12017.1	.	.	.	.	.	.	.	.	.	.	A	13.63	2.295974	0.40594	.	.	ENSG00000060069	ENST00000299543;ENST00000075430	T;T	0.11385	2.81;2.78	3.64	2.47	0.30058	.	0.579692	0.19134	N	0.121860	T	0.15869	0.0382	L	0.46157	1.445	0.32894	D	0.512227	D;D;D	0.67145	0.996;0.992;0.985	P;P;P	0.56216	0.794;0.794;0.628	T	0.17228	-1.0376	10	0.56958	D	0.05	-15.7834	5.1306	0.14907	0.583:0.0:0.417:0.0	.	342;461;461	Q9Y5B0-3;Q9Y5B0-4;Q9Y5B0	.;.;CTDP1_HUMAN	C	461	ENSP00000299543:S461C;ENSP00000075430:S461C	ENSP00000075430:S461C	S	+	1	0	CTDP1	75575829	0.998000	0.40836	0.997000	0.53966	0.212000	0.24457	3.484000	0.53201	0.580000	0.29522	-0.376000	0.06991	AGC	.	.		0.667	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715		T	77474841	A	T	77474841	3	4	17	1	0	0	0	0	1	0	0	0	4004	188	7	4	1411	4	CTDP1	18	77474841	Missense_Mutation	SNP	A	TCGA-2Y-A9H7-01A-11D-A38X-10	7057543	77474841	602407	71	1516										
FBN3	84467	hgsc.bcm.edu	37	chr19	8160952	8160952	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ttccacaaggctgccggtcaCactcgtcaatgtctgcagaa	9	13	3	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr19:8160952C>G	ENST00000600128.1	-	45	5966	c.5552G>C	c.(5551-5553)tGt>tCt	p.C1851S	FBN3_ENST00000270509.2_Missense_Mutation_p.C1851S|FBN3_ENST00000601739.1_Missense_Mutation_p.C1851S			Q75N90	FBN3_HUMAN	fibrillin 3	1851	EGF-like 29; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CTGCCGGTCACACTCGTCAAT	0.567																																					p.C1851S		Atlas-SNP	.											.	FBN3	300	.	0			c.G5552C						.						117	91	100					19																	8160952		2203	4300	6503	SO:0001583	missense	84467	exon44			CGGTCACACTCGT		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5552G>C	chr19.hg19:g.8160952C>G	ENSP00000470498:p.Cys1851Ser	72.0	0.0		104.0	40.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.452401	0.43531	.	.	ENSG00000142449	ENST00000270509	D	0.99429	-5.89	3.91	3.91	0.45181	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.99510	0.9825	M	0.91090	3.175	0.80722	D	1	D	0.57257	0.979	P	0.60173	0.87	D	0.98113	1.0421	10	0.56958	D	0.05	.	16.2735	0.82632	0.0:1.0:0.0:0.0	.	1851	Q75N90	FBN3_HUMAN	S	1851	ENSP00000270509:C1851S	ENSP00000270509:C1851S	C	-	2	0	FBN3	8066952	1.000000	0.71417	0.126000	0.21872	0.007000	0.05969	7.075000	0.76798	1.859000	0.53934	0.655000	0.94253	TGT	.	.		0.567	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		G	8160952	C	G	8160952	3	3	17	1	0	0	0	0	1	0	0	0	5712	478	17	4	2957	4	FBN3	19	8160952	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10		8160952	50968031	72	1517										
EPOR	2057	hgsc.bcm.edu	37	chr19	11491864	11491864	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gttgctcagcacacactcggTgcggccctccaggatctcca	10	16	2	0			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr19:11491864T>A	ENST00000222139.6	-	5	711	c.607A>T	c.(607-609)Acc>Tcc	p.T203S	EPOR_ENST00000592375.2_Missense_Mutation_p.T203S	NM_000121.3	NP_000112.1	P19235	EPOR_HUMAN	erythropoietin receptor	203	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brain development (GO:0007420)|decidualization (GO:0046697)|erythropoietin-mediated signaling pathway (GO:0038162)|heart development (GO:0007507)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	erythropoietin receptor activity (GO:0004900)|identical protein binding (GO:0042802)			endometrium(1)|lung(2)|ovary(1)|urinary_tract(1)	5					Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)|Epoetin Zeta(DB08923)|Peginesatide(DB08894)	ACACACTCGGTGCGGCCCTCC	0.682											OREG0025255	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T203S		Atlas-SNP	.											.	EPOR	26	.	0			c.A607T						.						3	4	4					19																	11491864		1941	3850	5791	SO:0001583	missense	2057	exon5			ACTCGGTGCGGCC	M34986	CCDS12260.1	19p13.3-p13.2	2013-02-11				ENSG00000187266		"Fibronectin type III domain containing"	3416	protein-coding gene	gene with protein product		133171					Standard	NM_000121		Approved		uc002mrj.2	P19235		ENST00000222139.6:c.607A>T	chr19.hg19:g.11491864T>A	ENSP00000222139:p.Thr203Ser	101.0	0.0	672	109.0	44.0	NM_000121	B2RCG4|Q15443|Q2M205	Missense_Mutation	SNP	ENST00000222139.6	hg19	CCDS12260.1	.	.	.	.	.	.	.	.	.	.	t	13.58	2.279033	0.40294	.	.	ENSG00000187266	ENST00000222139	D	0.86956	-2.19	5.64	5.64	0.86602	Fibronectin, type III (4);Long hematopoietin receptor, single chain, conserved site (1);Immunoglobulin-like fold (1);	0.222215	0.46758	D	0.000265	T	0.80221	0.4583	L	0.29908	0.895	0.34350	D	0.689792	B	0.32968	0.392	B	0.32677	0.15	T	0.83324	-0.0016	10	0.29301	T	0.29	-26.5643	13.3961	0.60853	0.0:0.0:0.0:1.0	.	203	P19235	EPOR_HUMAN	S	203	ENSP00000222139:T203S	ENSP00000222139:T203S	T	-	1	0	EPOR	11352864	1.000000	0.71417	0.997000	0.53966	0.301000	0.27625	2.305000	0.43664	2.164000	0.68074	0.449000	0.29647	ACC	.	.		0.682	EPOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458791.1			A	11491864	T	A	11491864	3	1	17	1	0	0	0	0	1	0	0	0	5191	1696	59	4	935	4	EPOR	19	11491864	Missense_Mutation	SNP	T	TCGA-2Y-A9H7-01A-11D-A38X-10	3330912	11491864	47637119	73	1518										
ISYNA1	51477	hgsc.bcm.edu	37	chr19	18547823	18547824	+	Frame_Shift_Del	DEL	CG	CG	-													0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ggcgccaccatgggcagcacCgcgctgaagggtacgaacac							TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr19:18547823_18547824delCG	ENST00000338128.8	-	4	591_592	c.374_375delCG	c.(373-375)gcgfs	p.A125fs	ISYNA1_ENST00000578963.1_5'UTR|ISYNA1_ENST00000457269.4_Frame_Shift_Del_p.A71fs|ISYNA1_ENST00000317018.6_5'UTR|ISYNA1_ENST00000545187.1_Intron	NM_001170938.1|NM_016368.4	NP_001164409.1|NP_057452.1	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	125					inositol biosynthetic process (GO:0006021)|inositol phosphate metabolic process (GO:0043647)|phospholipid biosynthetic process (GO:0008654)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-3-phosphate synthase activity (GO:0004512)			breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	12						TGGGCAGCACCGCGCTGAAGGG	0.713																																					p.125_126del		Atlas-Indel,Pindel	.											.	ISYNA1	31	.	0			c.375_376del						.																																			SO:0001589	frameshift_variant	51477	exon4			.		CCDS12379.1, CCDS54234.1, CCDS62603.1	19p13.11	2014-09-04			ENSG00000105655	ENSG00000105655	5.5.1.4		29821	protein-coding gene	gene with protein product	"myo-inositol 1-phosphate synthase"	611670				15024000, 12941308	Standard	NM_016368		Approved	Ino1, INOS, IPS	uc002njd.2	Q9NPH2	OTTHUMG00000179027	ENST00000338128.8:c.374_375delCG	chr19.hg19:g.18547825_18547826delCG	ENSP00000337746:p.Ala125fs	106.0	0.0		128.0	54.0	NM_016368	B3KRT1|G5E9U0|Q6NXT5|Q7Z525|Q9BT65|Q9H2Y2|Q9NSU0|Q9NVW7	Frame_Shift_Del	DEL	ENST00000338128.8	hg19	CCDS12379.1																																																																																			.	.		0.713	ISYNA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444469.2	NM_016368		-	18547824	CG	-	18547823	7	5	17	1	0	1	0	1	0	0	0	0	7876	639	23	0	1333	0	ISYNA1	19	18547823	Frame_Shift_Del	DEL	CG	TCGA-2Y-A9H7-01A-11D-A38X-10	7055959	18547823	40581160	74	1519										
TIMM50	92609	hgsc.bcm.edu	37	chr19	39972548	39972548	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	agagatcgggagccgcgggaGcactaaggcgcaagggccac	17	11	0	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr19:39972548G>A	ENST00000607714.1	+	2	156	c.134G>A	c.(133-135)aGc>aAc	p.S45N	TIMM50_ENST00000314349.4_Missense_Mutation_p.S148N|TIMM50_ENST00000599794.1_Intron|TIMM50_ENST00000544017.1_5'UTR			Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)	45					cellular protein metabolic process (GO:0044267)|mitochondrial membrane organization (GO:0007006)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein targeting to mitochondrion (GO:0006626)|release of cytochrome c from mitochondria (GO:0001836)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)	interleukin-2 receptor binding (GO:0005134)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)			NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGCCGCGGGAGCACTAAGGCG	0.627																																					p.S148N		Atlas-SNP	.											.	TIMM50	37	.	0			c.G443A						.						72	82	79					19																	39972548		2203	4300	6503	SO:0001583	missense	92609	exon2			GCGGGAGCACTAA	BC009072	CCDS33023.1	19q13.2	2010-06-21	2006-04-04		ENSG00000105197	ENSG00000105197		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	23656	protein-coding gene	gene with protein product		607381	"translocase of inner mitochondrial membrane 50 homolog (yeast)"			12437925	Standard	NM_001001563		Approved	TIM50L	uc002olu.1	Q3ZCQ8		ENST00000607714.1:c.134G>A	chr19.hg19:g.39972548G>A	ENSP00000475531:p.Ser45Asn	55.0	0.0		49.0	17.0	NM_001001563	Q330K1|Q6QA00|Q96FJ5|Q96GY2|Q9H370	Missense_Mutation	SNP	ENST00000607714.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.83	2.653638	0.47362	.	.	ENSG00000105197	ENST00000314349	.	.	.	4.24	3.2	0.36748	.	0.664310	0.14279	N	0.329649	T	0.21145	0.0509	N	0.08118	0	0.21933	N	0.999462	B	0.02656	0.0	B	0.09377	0.004	T	0.17745	-1.0359	8	.	.	.	-8.512	9.5116	0.39080	0.1016:0.0:0.8984:0.0	.	148	Q3ZCQ8-2	.	N	148	.	.	S	+	2	0	TIMM50	44664388	0.039000	0.19947	0.005000	0.12908	0.548000	0.35241	1.854000	0.39368	1.120000	0.41904	0.561000	0.74099	AGC	.	.		0.627	TIMM50-021	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470728.1	NM_001001563		A	39972548	G	A	39972548	3	1	17	1	0	0	0	0	1	0	0	0	15928	971	34	3	449	3	TIMM50	19	39972548	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	21424725	39972548	19156435	75	1520										
PSG1	5669	hgsc.bcm.edu	37	chr19	43382260	43382260	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	gtctactacatatgatgtaaTgtaatggtagaggtccctca	9	7	2	2			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr19:43382260T>A	ENST00000436291.2	-	2	351	c.235A>T	c.(235-237)Att>Ttt	p.I79F	PSG1_ENST00000312439.6_Missense_Mutation_p.I79F|PSG1_ENST00000595356.1_Missense_Mutation_p.I79F|PSG1_ENST00000244296.2_Missense_Mutation_p.I79F|PSG1_ENST00000595124.1_Missense_Mutation_p.I79F|PSG1_ENST00000403380.3_Missense_Mutation_p.I79F|PSG1_ENST00000601073.1_5'UTR	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	79	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TATGATGTAATGTAATGGTAG	0.433																																					p.I79F		Atlas-SNP	.											.	PSG1	196	.	0			c.A235T						.						234	228	230					19																	43382260		2202	4299	6501	SO:0001583	missense	5669	exon2			ATGTAATGTAATG		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.235A>T	chr19.hg19:g.43382260T>A	ENSP00000413041:p.Ile79Phe	69.0	0.0		83.0	40.0	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	hg19	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	12.25	1.881571	0.33255	.	.	ENSG00000231924	ENST00000270059;ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56	1.64	1.64	0.23874	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.87148	0.6105	H	0.97340	3.985	0.09310	N	1	D;P;D;P;D;P;D;D;P	0.89917	0.973;0.907;0.99;0.729;0.999;0.914;1.0;0.997;0.907	D;P;D;P;D;D;D;D;P	0.85130	0.94;0.873;0.92;0.755;0.987;0.938;0.994;0.997;0.873	T	0.73733	-0.3890	9	0.87932	D	0	.	5.4006	0.16293	0.0:0.0:0.0:1.0	.	79;79;79;79;79;79;79;79;79	O75238;P11464-4;G5E9F7;P11464;Q8NBY8;P11464-3;Q9UPK8;O75237;P11464-2	.;.;.;PSG1_HUMAN;.;.;.;.;.	F	79	ENSP00000413041:I79F;ENSP00000385386:I79F;ENSP00000308970:I79F;ENSP00000244296:I79F	ENSP00000244296:I79F	I	-	1	0	PSG1	48074100	0.027000	0.19231	0.003000	0.11579	0.015000	0.08874	1.883000	0.39658	1.029000	0.39812	0.155000	0.16302	ATT	.	.		0.433	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1			A	43382260	T	A	43382260	3	1	17	1	0	0	0	0	1	0	0	0	12665	1464	51	4	1097	4	PSG1	19	43382260	Missense_Mutation	SNP	T	TCGA-2Y-A9H7-01A-11D-A38X-10	3409712	43382260	15746723	76	1521										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31021697	31021697	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	agccacagcccactaaagagGagcccaaagtcccgcccatc	8	17	0	1			TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr20:31021697G>T	ENST00000375687.4	+	12	2120	c.1696G>T	c.(1696-1698)Gag>Tag	p.E566*	ASXL1_ENST00000306058.5_Nonsense_Mutation_p.E561*	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	566	Interaction with NCOA1. {ECO:0000250}.				bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CACTAAAGAGGAGCCCAAAGT	0.507			"F, N, Mis"		"MDS, CMML"																																p.E566X		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.G1696T						.						54	60	58					20																	31021697		2203	4300	6503	SO:0001587	stop_gained	171023	exon11			AAAGAGGAGCCCA	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.1696G>T	chr20.hg19:g.31021697G>T	ENSP00000364839:p.Glu566*	94.0	0.0		89.0	33.0	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Nonsense_Mutation	SNP	ENST00000375687.4	hg19	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	G	41	8.691263	0.98916	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	.	.	.	5.02	5.02	0.67125	.	0.050239	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-10.7937	18.905	0.92456	0.0:0.0:1.0:0.0	.	.	.	.	X	566;566;566;505;561	.	ENSP00000305119:E561X	E	+	1	0	ASXL1	30485358	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.350000	0.79385	2.780000	0.95670	0.655000	0.94253	GAG	.	.		0.507	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		T	31021697	G	T	31021697	4	4	17	1	0	0	0	0	0	1	0	0	1066	1175	41	3	1748	3	ASXL1	20	31021697	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10		31021697	32003823	77	1522										
FAM65C	140876	hgsc.bcm.edu	37	chr20	49232571	49232571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	cctcctggtgtctttgtggcGtccagacaggtggtccagct	13	12	1	1	rs147229572	byFrequency	TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr20:49232571G>A	ENST00000327979.2	-	4	715	c.304C>T	c.(304-306)Cgc>Tgc	p.R102C	MIR1302-5_ENST00000408164.1_RNA|FAM65C_ENST00000535356.1_Missense_Mutation_p.R106C|FAM65C_ENST00000045083.2_Missense_Mutation_p.R102C			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	102								p.R102C(2)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCTTTGTGGCGTCCAGACAGG	0.542													G|||	2	0.000399361	0	0	5008	,	,		19561	0		0	False		,,,				2504	0.002				p.R102C		Atlas-SNP	.											FAM65C,NS,carcinoma,0,3	FAM65C	87	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C304T						.	G	CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	105	91	96		304	-0.7	0.1	20	dbSNP_134	96	0,8600		0,0,4300	no	missense	FAM65C	NM_080829.2	180	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	benign	102/947	49232571	4,13002	2203	4300	6503	SO:0001583	missense	140876	exon4			TGTGGCGTCCAGA	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.304C>T	chr20.hg19:g.49232571G>A	ENSP00000332663:p.Arg102Cys	61.0	0.0		51.0	23.0	NM_080829	Q5QPB6|Q9NQQ2	Missense_Mutation	SNP	ENST00000327979.2	hg19	CCDS13431.2	.	.	.	.	.	.	.	.	.	.	G	10.88	1.474409	0.26423	9.08E-4	0.0	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	T;T;T	0.02216	4.39;4.39;4.39	5.07	-0.7	0.11273	.	0.321942	0.34700	N	0.003757	T	0.01627	0.0052	L	0.27053	0.805	0.22693	N	0.998845	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.002	T	0.43310	-0.9399	10	0.49607	T	0.09	-14.0537	5.2312	0.15422	0.3895:0.0:0.4795:0.131	.	106;102	F5H0X2;Q96MK2	.;FA65C_HUMAN	C	102;102;106	ENSP00000332663:R102C;ENSP00000045083:R102C;ENSP00000439802:R106C	ENSP00000045083:R102C	R	-	1	0	FAM65C	48665978	0.983000	0.35010	0.123000	0.21794	0.734000	0.41952	2.692000	0.47018	-0.057000	0.13199	-0.263000	0.10527	CGC	.	G|1.000;A|0.000		0.542	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			A	49232571	G	A	49232571	3	1	17	1	0	0	0	0	1	0	0	0	5609	1145	40	1	2612	1	FAM65C	20	49232571	Missense_Mutation	SNP	G	TCGA-2Y-A9H7-01A-11D-A38X-10	18210874	49232571	13792949	78	1523										
TPTE	7179	hgsc.bcm.edu	37	chr21	10906915	10906915	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0632911392405063	5	1	0.843465045592705	0	1.07350096711799	0.0151515151515152	0.256887052341599	0	ggagctatacttaatcggatCcagctacaacatcactggaa	8	10	1	0	rs169758	byFrequency	TCGA-2Y-A9H7-01A-11D-A38X-10	TCGA-2Y-A9H7-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e447e430-664c-4a56-9017-620aef1f0ffb	b2219bf0-50ab-4c4d-a22d-6b2a5c4bb365	g.chr21:10906915C>G	ENST00000361285.4	-	24	1975	c.1646G>C	c.(1645-1647)gGa>gCa	p.G549A	TPTE_ENST00000342420.5_Missense_Mutation_p.G511A|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Missense_Mutation_p.G531A	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	549			G -> E (in dbSNP:rs169758).		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TTAATCGGATCCAGCTACAAC	0.393																																					p.G549A		Atlas-SNP	.											.	TPTE	513	.	0			c.G1646C						.						135	119	124					21																	10906915		2203	4300	6503	SO:0001583	missense	7179	exon24			TCGGATCCAGCTA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1646G>C	chr21.hg19:g.10906915C>G	ENSP00000355208:p.Gly549Ala	124.0	0.0		168.0	38.0	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	11.87	1.768066	0.31320	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.95103	-3.35;-3.61;-3.43	1.79	-3.58	0.04597	.	.	.	.	.	D	0.82834	0.5123	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.31655	0.334;0.334;0.225	B;B;B	0.20767	0.031;0.031;0.014	T	0.73522	-0.3956	8	0.29301	T	0.29	.	3.6687	0.08265	0.3648:0.4609:0.1743:0.0	.	511;531;549	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	A	531;549;511	ENSP00000298232:G531A;ENSP00000355208:G549A;ENSP00000344441:G511A	ENSP00000298232:G531A	G	-	2	0	TPTE	9928786	0.003000	0.15002	0.000000	0.03702	0.030000	0.12068	0.139000	0.16036	-0.821000	0.04312	0.184000	0.17185	GGA	.	C|0.947;T|0.053		0.393	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			G	10906915	C	G	10906915	3	3	17	1	0	0	0	0	1	0	0	0	16445	855	30	4	13	4	TPTE	21	10906915	Missense_Mutation	SNP	C	TCGA-2Y-A9H7-01A-11D-A38X-10		10906915	37222980	79	1524										
PRKCZ	5590	hgsc.bcm.edu	37	chr1	2106687	2106687	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ccaaagagaggctcggctgcCggccacagactggattttct	12	12	1	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:2106687C>T	ENST00000400921.2	+	13	1644	c.961C>T	c.(961-963)Cgg>Tgg	p.R321W	PRKCZ_ENST00000400920.1_Missense_Mutation_p.R321W|PRKCZ_ENST00000479263.1_3'UTR	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta	504	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	GCTCGGCTGCCGGCCACAGAC	0.572																																					p.R504W		Atlas-SNP	.											.	PRKCZ	84	.	0			c.C1510T						.						46	53	51					1																	2106687		2203	4300	6503	SO:0001583	missense	5590	exon16			GGCTGCCGGCCAC	BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.961C>T	chr1.hg19:g.2106687C>T	ENSP00000383712:p.Arg321Trp	108.0	0.0		88.0	41.0	NM_002744	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Missense_Mutation	SNP	ENST00000400921.2	hg19	CCDS41229.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.896240	0.72639	.	.	ENSG00000067606	ENST00000378567;ENST00000400921;ENST00000461106;ENST00000400920	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	4.97	4.06	0.47325	Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.116916	0.64402	D	0.000018	T	0.65333	0.2681	M	0.78344	2.41	0.35043	D	0.75989	D;D;D;D	0.61080	0.962;0.962;0.962;0.989	P;P;P;P	0.55303	0.67;0.67;0.67;0.773	T	0.76852	-0.2806	10	0.49607	T	0.09	.	12.6853	0.56944	0.0:0.9193:0.0:0.0807	.	400;328;400;504	E9PCW2;B3KUN5;B7Z2J7;Q05513	.;.;.;KPCZ_HUMAN	W	504;321;400;321	ENSP00000367830:R504W;ENSP00000383712:R321W;ENSP00000426412:R400W;ENSP00000383711:R321W	ENSP00000367830:R504W	R	+	1	2	PRKCZ	2096547	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	5.523000	0.67099	1.221000	0.43506	0.638000	0.83543	CGG	.	.		0.572	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		T	2106687	C	T	2106687	3	4	18	1	0	0	0	0	1	0	0	0	12529	643	23	1	1572	1	PRKCZ	1	2106687	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10		2106687	247143934	1	1525										
H6PD	9563	hgsc.bcm.edu	37	chr1	9323715	9323737	+	Frame_Shift_Del	DEL	CGGCGCAGAGCCAGTGCCTGCCC	CGGCGCAGAGCCAGTGCCTGCCC	-													0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gagcgaaaagcactgggccgCggcgcagagccagtgcctgc					rs199663762|rs139280233|rs149231638|rs147080717	byFrequency	TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	CGGCGCAGAGCCAGTGCCTGCCC	CGGCGCAGAGCCAGTGCCTGCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:9323715_9323737delCGGCGCAGAGCCAGTGCCTGCCC	ENST00000377403.2	+	5	1465_1487	c.1163_1185delCGGCGCAGAGCCAGTGCCTGCCC	c.(1162-1185)gcggcgcagagccagtgcctgcccfs	p.AAQSQCLP388fs	H6PD_ENST00000602477.1_Frame_Shift_Del_p.AAQSQCLP399fs	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	388	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)	p.A389A(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		CACTGGGCCGCGGCGCAGAGCCAGTGCCTGCCCCGGCAGCTCG	0.641																																					p.388_395del		Atlas-Indel,Pindel	.											.	H6PD	71	.	1	Substitution - coding silent(1)	endometrium(1)	c.1162_1184del						.																																			SO:0001589	frameshift_variant	9563	exon5			.	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"glucose dehyrogenase"	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.1163_1185delCGGCGCAGAGCCAGTGCCTGCCC	chr1.hg19:g.9323715_9323737delCGGCGCAGAGCCAGTGCCTGCCC	ENSP00000366620:p.Ala388fs	150.0	0.0		153.0	46.0	NM_004285	Q4TT33|Q66I35|Q68DT3	Frame_Shift_Del	DEL	ENST00000377403.2	hg19	CCDS101.1																																																																																			.	.		0.641	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		-	9323737	CGGCGCAGAGCCAGTGCCTGCCC	-	9323715	7	5	18	1	0	1	0	1	0	0	0	0	6945	768	27	0	1177	0	H6PD	1	9323715	Frame_Shift_Del	DEL	CGGCGCAGAGCCAGTGCCTGCCC	TCGA-2Y-A9H8-01A-11D-A38X-10	7217028	9323715	239926906	2	1526										
TMEM39B	55116	hgsc.bcm.edu	37	chr1	32557607	32557607	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	cctttgtgcctgtctggttcGtgaaggtgcgtacctcaagc	12	11	2	1	rs202154275		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:32557607G>A	ENST00000336294.5	+	6	1068	c.922G>A	c.(922-924)Gtg>Atg	p.V308M	TMEM39B_ENST00000373634.4_Missense_Mutation_p.V109M|TMEM39B_ENST00000487305.1_3'UTR|TMEM39B_ENST00000456834.2_3'UTR|TMEM39B_ENST00000427288.1_Missense_Mutation_p.V193M	NM_018056.2	NP_060526.2	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	308						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(5)|ovary(1)|prostate(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TGTCTGGTTCGTGAAGGTGCG	0.562																																					p.V308M		Atlas-SNP	.											.	TMEM39B	66	.	0			c.G922A						.	G	MET/VAL	0,4406		0,0,2203	66	59	61		922	4.9	1	1		61	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMEM39B	NM_018056.2	21	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	308/493	32557607	2,13004	2203	4300	6503	SO:0001583	missense	55116	exon6			TGGTTCGTGAAGG	AL136695	CCDS351.2	1p35.1	2008-02-05			ENSG00000121775	ENSG00000121775			25510	protein-coding gene	gene with protein product						12477932	Standard	NM_018056		Approved	FLJ10315	uc010ogv.2	Q9GZU3	OTTHUMG00000004020	ENST00000336294.5:c.922G>A	chr1.hg19:g.32557607G>A	ENSP00000338165:p.Val308Met	52.0	0.0		33.0	5.0	NM_018056	B4DKN8|B4DQE6|B4DTN8|D3DPP4|Q6IA44	Missense_Mutation	SNP	ENST00000336294.5	hg19	CCDS351.2	.	.	.	.	.	.	.	.	.	.	G	30	5.056509	0.93793	0.0	2.33E-4	ENSG00000121775	ENST00000336294;ENST00000373634;ENST00000427288	.	.	.	4.95	4.95	0.65309	.	0.115829	0.64402	D	0.000017	T	0.79811	0.4510	M	0.74881	2.28	0.58432	D	0.999998	D;D;D	0.89917	0.997;1.0;0.995	P;D;P	0.91635	0.866;0.999;0.866	T	0.82293	-0.0529	9	0.72032	D	0.01	-13.4165	18.5641	0.91111	0.0:0.0:1.0:0.0	.	308;193;181	Q9GZU3;B4DTN8;Q9NW51	TM39B_HUMAN;.;.	M	308;109;193	.	ENSP00000338165:V308M	V	+	1	0	TMEM39B	32330194	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	9.329000	0.96413	2.462000	0.83206	0.462000	0.41574	GTG	.	.		0.562	TMEM39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011489.2	NM_018056		A	32557607	G	A	32557607	3	1	18	1	0	0	0	0	1	0	0	0	16177	1145	40	1	944	1	TMEM39B	1	32557607	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	23233892	32557607	216693014	3	1527										
INADL	10207	hgsc.bcm.edu	37	chr1	62579830	62579830	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tgtatagagatgaggcacacTaccgggatgaggagaacttg	14	6	0	4			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:62579830T>G	ENST00000371158.2	+	35	4681	c.4567T>G	c.(4567-4569)Tac>Gac	p.Y1523D	INADL_ENST00000316485.6_Missense_Mutation_p.Y1553D|INADL_ENST00000545929.1_Missense_Mutation_p.Y168D|INADL_ENST00000543708.1_Missense_Mutation_p.Y337D	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1523					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TGAGGCACACTACCGGGATGA	0.582																																					p.Y1523D		Atlas-SNP	.											.	INADL	179	.	0			c.T4567G						.						84	81	82					1																	62579830		2203	4300	6503	SO:0001583	missense	10207	exon35			GCACACTACCGGG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4567T>G	chr1.hg19:g.62579830T>G	ENSP00000360200:p.Tyr1523Asp	158.0	0.0		147.0	59.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	T	15.89	2.967048	0.53507	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000543708;ENST00000545929	T;T;T;T	0.31510	2.28;2.71;2.28;1.49	5.5	4.37	0.52481	PDZ/DHR/GLGF (1);	0.299519	0.27270	N	0.020139	T	0.51736	0.1692	M	0.67953	2.075	0.47153	D	0.999334	P;P;D;D;B;P	0.89917	0.547;0.609;0.999;1.0;0.051;0.698	B;B;D;D;B;P	0.91635	0.374;0.168;0.995;0.999;0.061;0.804	T	0.52426	-0.8577	10	0.72032	D	0.01	.	11.2962	0.49280	0.0:0.071:0.0:0.9289	.	168;337;982;1553;1523;1495	F5GY89;B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;.;INADL_HUMAN;.	D	1523;1553;1553;1495;337;168	ENSP00000360200:Y1523D;ENSP00000326199:Y1553D;ENSP00000445790:Y337D;ENSP00000440094:Y168D	ENSP00000326199:Y1553D	Y	+	1	0	INADL	62352418	1.000000	0.71417	0.980000	0.43619	0.988000	0.76386	4.073000	0.57570	0.926000	0.37118	0.460000	0.39030	TAC	.	.		0.582	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62579830	T	G	62579830	3	3	18	1	0	0	0	0	1	0	0	0	7740	1522	53	5	4701	5	INADL	1	62579830	Missense_Mutation	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10	30022223	62579830	186670791	4	1528										
MSH4	4438	hgsc.bcm.edu	37	chr1	76349304	76349304	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ccattctattttttttcttaAgttcgaccagaatttactga	4	8	2	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:76349304A>C	ENST00000263187.3	+	15	2010		c.e15-1			NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4						ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						TTTTTTCTTAAGTTCGACCAG	0.303								Mismatch excision repair (MMR)																													.		Atlas-SNP	.											.	MSH4	147	.	0			c.1907-2A>C						.						37	39	38					1																	76349304		2199	4299	6498	SO:0001630	splice_region_variant	4438	exon15			TTCTTAAGTTCGA	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.1907-1A>C	chr1.hg19:g.76349304A>C		90.0	0.0		126.0	28.0	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Splice_Site	SNP	ENST00000263187.3	hg19	CCDS670.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.010945	0.75046	.	.	ENSG00000057468	ENST00000263187	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.74	0.77887	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MSH4	76121892	1.000000	0.71417	0.979000	0.43373	0.865000	0.49528	8.654000	0.91092	2.107000	0.64212	0.491000	0.48974	.	.	.		0.303	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	Intron	C	76349304	A	C	76349304	5	2	18	1	0	0	0	0	0	0	1	0	9881	86	3	5	1963	5	MSH4	1	76349304	Splice_Site	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10	13769474	76349304	172901317	5	1529										
APCS	325	hgsc.bcm.edu	37	chr1	159558023	159558023	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tagtgatctctctcgtgcctAcagcctcttctcctacaata	5	14	4	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:159558023A>G	ENST00000255040.2	+	2	294	c.197A>G	c.(196-198)tAc>tGc	p.Y66C		NM_001639.3	NP_001630.1	P02743	SAMP_HUMAN	amyloid P component, serum	66	Pentaxin.				acute-phase response (GO:0006953)|chaperone-mediated protein complex assembly (GO:0051131)|innate immune response (GO:0045087)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of exo-alpha-sialidase activity (GO:1903016)|negative regulation of glycoprotein metabolic process (GO:1903019)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral process (GO:0048525)|negative regulation of wound healing (GO:0061045)|protein folding (GO:0006457)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|unfolded protein binding (GO:0051082)|virion binding (GO:0046790)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_hematologic(112;0.0429)					TCTCGTGCCTACAGCCTCTTC	0.413																																					p.Y66C		Atlas-SNP	.											.	APCS	48	.	0			c.A197G						.						116	115	115					1																	159558023		2203	4300	6503	SO:0001583	missense	325	exon2			GTGCCTACAGCCT		CCDS1186.1	1q21-q23	2012-10-02			ENSG00000132703	ENSG00000132703			584	protein-coding gene	gene with protein product	"pentaxin-related", "9.5S alpha-1-glycoprotein"	104770				2987268	Standard	NM_001639		Approved	SAP, PTX2, MGC88159	uc001ftv.3	P02743	OTTHUMG00000022741	ENST00000255040.2:c.197A>G	chr1.hg19:g.159558023A>G	ENSP00000255040:p.Tyr66Cys	51.0	0.0		170.0	54.0	NM_001639		Missense_Mutation	SNP	ENST00000255040.2	hg19	CCDS1186.1	.	.	.	.	.	.	.	.	.	.	A	10.98	1.503199	0.26949	.	.	ENSG00000132703	ENST00000255040	T	0.63580	-0.05	4.45	4.45	0.53987	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.255216	0.36932	N	0.002326	T	0.72203	0.3431	M	0.86268	2.805	0.09310	N	0.999996	D	0.89917	1.0	D	0.80764	0.994	T	0.65849	-0.6068	10	0.51188	T	0.08	-2.7363	12.0095	0.53278	1.0:0.0:0.0:0.0	.	66	P02743	SAMP_HUMAN	C	66	ENSP00000255040:Y66C	ENSP00000255040:Y66C	Y	+	2	0	APCS	157824647	0.054000	0.20591	0.102000	0.21198	0.006000	0.05464	2.603000	0.46266	1.984000	0.57885	0.533000	0.62120	TAC	.	.		0.413	APCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059024.2	NM_001639		G	159558023	A	G	159558023	3	3	18	1	0	0	0	0	1	0	0	0	767	391	14	2	203	2	APCS	1	159558023	Missense_Mutation	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10	83208719	159558023	89692598	6	1530										
CCDC19	25790	hgsc.bcm.edu	37	chr1	159854288	159854288	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ctgctccttctcctgctcccGctgctcagcaagcagcgatc	8	18	2	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:159854288G>A	ENST00000368099.4	-	7	899	c.835C>T	c.(835-837)Cgg>Tgg	p.R279W	CCDC19_ENST00000426543.2_Missense_Mutation_p.R194W|CCDC19_ENST00000476696.1_5'UTR	NM_012337.2	NP_036469.2														endometrium(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	26	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			TCCTGCTCCCGCTGCTCAGCA	0.507																																					p.R279W		Atlas-SNP	.											.	CCDC19	79	.	0			c.C835T						.						242	225	231					1																	159854288		2203	4300	6503	SO:0001583	missense	25790	exon7			GCTCCCGCTGCTC																												ENST00000368099.4:c.835C>T	chr1.hg19:g.159854288G>A	ENSP00000357079:p.Arg279Trp	45.0	0.0		56.0	6.0	NM_012337		Missense_Mutation	SNP	ENST00000368099.4	hg19	CCDS30914.1	.	.	.	.	.	.	.	.	.	.	G	17.37	3.371577	0.61624	.	.	ENSG00000213085	ENST00000368099;ENST00000426543	T;T	0.11063	2.81;2.81	4.81	2.88	0.33553	.	0.200040	0.41194	D	0.000930	T	0.13372	0.0324	M	0.62723	1.935	0.32801	D	0.500154	D;D	0.89917	1.0;1.0	D;D	0.63033	0.91;0.91	T	0.02424	-1.1161	9	.	.	.	-17.0808	11.035	0.47795	0.0:0.0:0.5102:0.4897	.	279;279	A8K884;Q9UL16	.;CCD19_HUMAN	W	279;194	ENSP00000357079:R279W;ENSP00000403044:R194W	.	R	-	1	2	CCDC19	158120912	0.998000	0.40836	0.999000	0.59377	0.933000	0.57130	2.357000	0.44125	0.514000	0.28300	-0.169000	0.13324	CGG	.	.		0.507	CCDC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085979.1			A	159854288	G	A	159854288	3	1	18	1	0	0	0	0	1	0	0	0	2797	1086	38	1	844	1	CCDC19	1	159854288	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	296265	159854288	89396333	7	1531										
NCSTN	23385	hgsc.bcm.edu	37	chr1	160321028	160321028	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tcagtgctatcaagatcacaAcctgagtcagaatggctcag	9	10	5	3			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:160321028A>G	ENST00000294785.5	+	6	724	c.599A>G	c.(598-600)aAc>aGc	p.N200S	NCSTN_ENST00000459963.1_Intron|NCSTN_ENST00000535857.1_Intron|NCSTN_ENST00000392212.4_Missense_Mutation_p.N180S|NCSTN_ENST00000368063.1_Missense_Mutation_p.N180S|NCSTN_ENST00000368065.4_Intron	NM_015331.2	NP_056146.1	Q92542	NICA_HUMAN	nicastrin	200					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2)	34	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CAAGATCACAACCTGAGTCAG	0.552																																					p.N200S		Atlas-SNP	.											.	NCSTN	64	.	0			c.A599G						.						161	116	131					1																	160321028		2203	4300	6503	SO:0001583	missense	23385	exon6			ATCACAACCTGAG	AF240468	CCDS1203.1	1q22-q23	2014-09-17			ENSG00000162736	ENSG00000162736			17091	protein-coding gene	gene with protein product		605254				9039502, 10993067	Standard	XM_005245053		Approved	KIAA0253, APH2	uc001fvx.3	Q92542	OTTHUMG00000033110	ENST00000294785.5:c.599A>G	chr1.hg19:g.160321028A>G	ENSP00000294785:p.Asn200Ser	183.0	0.0		283.0	79.0	NM_015331	Q5T207|Q5T208|Q86VV5	Missense_Mutation	SNP	ENST00000294785.5	hg19	CCDS1203.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.629907	0.67015	.	.	ENSG00000162736	ENST00000294785;ENST00000368063;ENST00000392212	T;T;T	0.72505	-0.66;-0.66;-0.66	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.81384	0.4811	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.84486	0.0608	10	0.66056	D	0.02	-26.4305	12.0472	0.53487	1.0:0.0:0.0:0.0	.	180;200	Q92542-2;Q92542	.;NICA_HUMAN	S	200;180;180	ENSP00000294785:N200S;ENSP00000357042:N180S;ENSP00000376047:N180S	ENSP00000294785:N200S	N	+	2	0	NCSTN	158587652	1.000000	0.71417	1.000000	0.80357	0.585000	0.36419	7.795000	0.85887	2.068000	0.61886	0.533000	0.62120	AAC	.	.		0.552	NCSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080622.1	NM_015331		G	160321028	A	G	160321028	3	3	18	1	0	0	0	0	1	0	0	0	10250	43	2	2	621	2	NCSTN	1	160321028	Missense_Mutation	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10	466740	160321028	88929593	8	1532										
LMOD1	25802	hgsc.bcm.edu	37	chr1	201868843	201868843	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gcttggcgatctccatctccGtcttgcctccacagatgtgt	9	14	3	1	rs368400320		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:201868843G>A	ENST00000367288.4	-	2	1544	c.1298C>T	c.(1297-1299)aCg>aTg	p.T433M	RP11-307B6.3_ENST00000458139.1_RNA|RP11-307B6.3_ENST00000414927.1_RNA	NM_012134.2	NP_036266.2	P29536	LMOD1_HUMAN	leiomodin 1 (smooth muscle)	433					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						CTCCATCTCCGTCTTGCCTCC	0.582																																					p.T433M		Atlas-SNP	.											.	LMOD1	59	.	0			c.C1298T						.	G	MET/THR	0,4252		0,0,2126	79	80	80		1298	4.5	0.9	1		80	1,8495		0,1,4247	no	missense	LMOD1	NM_012134.2	81	0,1,6373	AA,AG,GG		0.0118,0.0,0.0078	probably-damaging	433/601	201868843	1,12747	2126	4248	6374	SO:0001583	missense	25802	exon2			ATCTCCGTCTTGC	X54162	CCDS53457.1	1q32.1	2008-05-22			ENSG00000163431	ENSG00000163431			6647	protein-coding gene	gene with protein product		602715					Standard	NM_012134		Approved	64kD, D1, 1D	uc021phl.1	P29536	OTTHUMG00000035802	ENST00000367288.4:c.1298C>T	chr1.hg19:g.201868843G>A	ENSP00000356257:p.Thr433Met	110.0	0.0		195.0	32.0	NM_012134	B1APV6|C4AMB1|Q68EN2	Missense_Mutation	SNP	ENST00000367288.4	hg19	CCDS53457.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029613	0.75504	0.0	1.18E-4	ENSG00000163431	ENST00000367288;ENST00000400965;ENST00000412469	D	0.92149	-2.98	4.53	4.53	0.55603	.	0.000000	0.41194	D	0.000925	D	0.94188	0.8135	L	0.47716	1.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.995;0.996	D	0.94802	0.7971	10	0.72032	D	0.01	-25.5685	14.7808	0.69766	0.0:0.0:1.0:0.0	.	382;433	B4E3S9;P29536	.;LMOD1_HUMAN	M	433;433;382	ENSP00000356257:T433M	ENSP00000356257:T433M	T	-	2	0	LMOD1	200135466	1.000000	0.71417	0.878000	0.34440	0.769000	0.43574	7.848000	0.86902	2.033000	0.60031	0.650000	0.86243	ACG	.	.		0.582	LMOD1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087085.2			A	201868843	G	A	201868843	3	1	18	1	0	0	0	0	1	0	0	0	8865	1145	40	1	512	1	LMOD1	1	201868843	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	41547815	201868843	47381778	9	1533										
MIA3	375056	hgsc.bcm.edu	37	chr1	222791466	222791466	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ccacaacatggctgcggcgcCtgggctgctcgtctggctgc	14	15	1	0	rs560508185		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:222791466C>G	ENST00000344922.5	+	1	39	c.14C>G	c.(13-15)cCt>cGt	p.P5R	MIA3_ENST00000344507.1_Missense_Mutation_p.P5R|MIA3_ENST00000344441.6_Missense_Mutation_p.P5R|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	5					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		GCTGCGGCGCCTGGGCTGCTC	0.766																																					p.P5R		Atlas-SNP	.											.	MIA3	167	.	0			c.C14G						.						2	4	3					1																	222791466		1559	3511	5070	SO:0001583	missense	375056	exon1			CGGCGCCTGGGCT		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.14C>G	chr1.hg19:g.222791466C>G	ENSP00000340900:p.Pro5Arg	81.0	0.0		135.0	37.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	hg19	CCDS41470.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.240026	0.39598	.	.	ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000344507	T;T;T	0.33216	3.46;3.46;1.42	4.25	-8.5	0.00927	.	.	.	.	.	T	0.14098	0.0341	L	0.27053	0.805	0.09310	N	0.999995	B	0.09022	0.002	B	0.04013	0.001	T	0.17349	-1.0372	9	0.31617	T	0.26	.	2.9138	0.05745	0.2917:0.191:0.3837:0.1336	.	5	Q5JRA6	MIA3_HUMAN	R	5	ENSP00000340900:P5R;ENSP00000340587:P5R;ENSP00000341348:P5R	ENSP00000325973:P5R	P	+	2	0	MIA3	220858089	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.880000	0.04183	-2.270000	0.00683	-0.365000	0.07479	CCT	.	.		0.766	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		G	222791466	C	G	222791466	3	3	18	1	0	0	0	0	1	0	0	0	9574	681	24	4	16	4	MIA3	1	222791466	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	20922623	222791466	26459155	10	1534										
FMN2	56776	hgsc.bcm.edu	37	chr1	240256479	240256479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ggaggatgcttttgaggatgCgccccggggctctccggggg	19	10	1	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr1:240256479C>T	ENST00000319653.9	+	1	1300	c.1070C>T	c.(1069-1071)gCg>gTg	p.A357V		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	357					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TTTGAGGATGCGCCCCGGGGC	0.731																																					p.A357V		Atlas-SNP	.											.	FMN2	451	.	0			c.C1070T						.						6	9	8					1																	240256479		1867	3810	5677	SO:0001583	missense	56776	exon1			AGGATGCGCCCCG	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1070C>T	chr1.hg19:g.240256479C>T	ENSP00000318884:p.Ala357Val	43.0	0.0		76.0	12.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	C	11.96	1.795641	0.31777	.	.	ENSG00000155816	ENST00000319653	T	0.30714	1.52	3.9	3.9	0.45041	.	0.420177	0.22296	N	0.061926	T	0.47507	0.1449	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.43491	-0.9388	10	0.56958	D	0.05	.	11.0905	0.48113	0.0:0.8114:0.1886:0.0	.	357	Q9NZ56	FMN2_HUMAN	V	357	ENSP00000318884:A357V	ENSP00000318884:A357V	A	+	2	0	FMN2	238323102	0.987000	0.35691	0.882000	0.34594	0.786000	0.44442	3.068000	0.50018	2.155000	0.67459	0.407000	0.27541	GCG	.	.		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240256479	C	T	240256479	3	4	18	1	0	0	0	0	1	0	0	0	5958	768	27	1	1072	1	FMN2	1	240256479	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	17465013	240256479	8994142	11	1535										
ROCK2	9475	hgsc.bcm.edu	37	chr2	11341101	11341101	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	acagaagcaattgtagcatcTttttccgtaagttcctgttt	7	8	1	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr2:11341101T>C	ENST00000315872.6	-	23	3340	c.2892A>G	c.(2890-2892)aaA>aaG	p.K964K	ROCK2_ENST00000401753.1_Silent_p.K721K	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	964					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TTGTAGCATCTTTTTCCGTAA	0.333																																					p.K964K		Atlas-SNP	.											.	ROCK2	224	.	0			c.A2892G						.						213	195	201					2																	11341101		1853	4085	5938	SO:0001819	synonymous_variant	9475	exon23			AGCATCTTTTTCC	D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.2892A>G	chr2.hg19:g.11341101T>C		108.0	0.0		90.0	5.0	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Silent	SNP	ENST00000315872.6	hg19	CCDS42654.1																																																																																			.	.		0.333	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			C	11341101	T	C	11341101	2	2	18	1	0	0	0	0	0	0	0	1	13533	1606	56	2		2	ROCK2	2	11341101	Silent	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10		11341101	231858272	12	1536										
TTC30A	92104	hgsc.bcm.edu	37	chr2	178482808	178482808	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	aatctcagcgatatgcttcaGtgctgaggcatactgtcggc	11	10	2	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr2:178482808G>C	ENST00000355689.5	-	1	886	c.622C>G	c.(622-624)Ctg>Gtg	p.L208V	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	208					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				autonomic_ganglia(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			ATATGCTTCAGTGCTGAGGCA	0.552																																					p.L208V		Atlas-SNP	.											TTC30A,colon,carcinoma,0,1	TTC30A	60	.	0			c.C622G						.						68	67	67					2																	178482808		2203	4300	6503	SO:0001583	missense	92104	exon1			GCTTCAGTGCTGA	AK024008	CCDS2276.1	2q31.2	2013-01-11			ENSG00000197557	ENSG00000197557		"Tetratricopeptide (TTC) repeat domain containing"	25853	protein-coding gene	gene with protein product						12477932	Standard	NM_152275		Approved	FLJ13946	uc002ulo.3	Q86WT1	OTTHUMG00000132528	ENST00000355689.5:c.622C>G	chr2.hg19:g.178482808G>C	ENSP00000347915:p.Leu208Val	84.0	0.0		120.0	29.0	NM_152275	A8K8N0|Q8IVP2	Missense_Mutation	SNP	ENST00000355689.5	hg19	CCDS2276.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.884810	0.33255	.	.	ENSG00000197557	ENST00000355689	T	0.75938	-0.98	5.78	2.99	0.34606	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.061993	0.64402	D	0.000005	D	0.85102	0.5620	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84800	0.0784	10	0.59425	D	0.04	.	9.3125	0.37915	0.2808:0.0:0.7192:0.0	.	208	Q86WT1	TT30A_HUMAN	V	208	ENSP00000347915:L208V	ENSP00000347915:L208V	L	-	1	2	TTC30A	178191054	0.948000	0.32251	0.295000	0.24960	0.660000	0.38997	1.525000	0.35953	0.808000	0.34231	0.549000	0.68633	CTG	.	.		0.552	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275		C	178482808	G	C	178482808	3	2	18	1	0	0	0	0	1	0	0	0	16713	1020	36	4	1379	4	TTC30A	2	178482808	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	167141707	178482808	64716565	13	1537										
TTN	7273	hgsc.bcm.edu	37	chr2	179567285	179567285	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gttctgttggtcctttgtacCatgttacaatggcatcatca	8	9	3	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr2:179567285C>T	ENST00000591111.1	-	105	29602	c.29378G>A	c.(29377-29379)tGg>tAg	p.W9793*	TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.W8866*|TTN_ENST00000589042.1_Nonsense_Mutation_p.W10110*|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	13871	Ig-like 79.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCTTTGTACCATGTTACAAT	0.458																																					p.W10110X		Atlas-SNP	.											.	TTN	18412	.	0			c.G30329A						.						216	215	215					2																	179567285		2013	4181	6194	SO:0001587	stop_gained	7273	exon107			TTGTACCATGTTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.29378G>A	chr2.hg19:g.179567285C>T	ENSP00000465570:p.Trp9793*	87.0	0.0		118.0	29.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	60	45.622505	0.99987	.	.	ENSG00000155657	ENST00000342992	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.8805	0.96895	0.0:1.0:0.0:0.0	.	.	.	.	X	8866	.	ENSP00000343764:W8866X	W	-	2	0	TTN	179275530	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	7.818000	0.86416	2.704000	0.92352	0.655000	0.94253	TGG	.	.		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179567285	C	T	179567285	4	4	18	1	0	0	0	0	0	1	0	0	16750	595	21	3	74224	3	TTN	2	179567285	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	1084477	179567285	63632088	14	1538										
ITGA4	3676	hgsc.bcm.edu	37	chr2	182358128	182358128	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	aatggccgtgcagatgggatCtcgtcaaccttctcacaggt	11	11	3	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr2:182358128C>T	ENST00000397033.2	+	11	1660	c.1230C>T	c.(1228-1230)atC>atT	p.I410I		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	410					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	CAGATGGGATCTCGTCAACCT	0.373																																					p.I410I		Atlas-SNP	.											.	ITGA4	142	.	0			c.C1230T						.						106	100	102					2																	182358128		1877	4100	5977	SO:0001819	synonymous_variant	3676	exon11			TGGGATCTCGTCA		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.1230C>T	chr2.hg19:g.182358128C>T		65.0	0.0		98.0	20.0	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	hg19	CCDS42788.1																																																																																			.	.		0.373	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			T	182358128	C	T	182358128	2	4	18	1	0	0	0	0	0	0	0	1	7887	903	32	3		3	ITGA4	2	182358128	Silent	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	2790843	182358128	60841245	15	1539										
RUFY4	285180	hgsc.bcm.edu	37	chr2	218939997	218939997	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	aagttccaggaaacataggtAcccccagagcatgtgggagc	12	10	0	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr2:218939997A>G	ENST00000344321.7	+	9	1300	c.782A>G	c.(781-783)tAc>tGc	p.Y261C	RUFY4_ENST00000463872.1_3'UTR|RUFY4_ENST00000441828.2_3'UTR|RUFY4_ENST00000374155.3_Missense_Mutation_p.Y281C	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	261							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		AAACATAGGTACCCCCAGAGC	0.547																																					p.Y261C		Atlas-SNP	.											.	RUFY4	59	.	0			c.A782G						.						23	24	24					2																	218939997		1917	4132	6049	SO:0001583	missense	285180	exon9			ATAGGTACCCCCA	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"Zinc fingers, FYVE domain containing"	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.782A>G	chr2.hg19:g.218939997A>G	ENSP00000345900:p.Tyr261Cys	259.0	1.0		253.0	116.0	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	hg19		.	.	.	.	.	.	.	.	.	.	A	8.611	0.889205	0.17540	.	.	ENSG00000188282	ENST00000344321;ENST00000374155	T;T	0.41065	1.6;1.01	4.64	-3.97	0.04094	.	2.497390	0.01419	N	0.014315	T	0.21427	0.0516	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05146	-1.0903	10	0.35671	T	0.21	0.3247	1.5201	0.02514	0.2703:0.1967:0.361:0.172	.	261	Q6ZNE9	RUFY4_HUMAN	C	261;281	ENSP00000345900:Y261C;ENSP00000363270:Y281C	ENSP00000345900:Y261C	Y	+	2	0	RUFY4	218648242	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-3.932000	0.00331	-1.226000	0.02574	0.383000	0.25322	TAC	.	.		0.547	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483		G	218939997	A	G	218939997	3	3	18	1	0	0	0	0	1	0	0	0	13756	391	14	2	808	2	RUFY4	2	218939997	Missense_Mutation	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10	36581869	218939997	24259376	16	1540										
SPEG	10290	hgsc.bcm.edu	37	chr2	220348089	220348089	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	accccagagactggggctgcCacccccatggactggcagga	13	15	0	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr2:220348089C>A	ENST00000312358.7	+	30	6036	c.5904C>A	c.(5902-5904)gcC>gcA	p.A1968A	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1968					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CTGGGGCTGCCACCCCCATGG	0.701																																					p.A1968A		Atlas-SNP	.											.	SPEG	272	.	0			c.C5904A						.						9	11	11					2																	220348089		1812	4014	5826	SO:0001819	synonymous_variant	10290	exon30			GGCTGCCACCCCC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.5904C>A	chr2.hg19:g.220348089C>A		65.0	0.0		78.0	38.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.701	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220348089	C	A	220348089	2	1	18	1	0	0	0	0	0	0	0	1	15051	581	21	3		3	SPEG	2	220348089	Silent	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	1408092	220348089	22851284	17	1541										
RBMS3	27303	hgsc.bcm.edu	37	chr3	29476348	29476348	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	agttgagtaaaaccaacctgTacattcgaggcctcccacca	7	13	0	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr3:29476348T>A	ENST00000383767.2	+	2	526	c.190T>A	c.(190-192)Tac>Aac	p.Y64N	RBMS3_ENST00000445033.1_Missense_Mutation_p.Y64N|RBMS3_ENST00000452462.1_Missense_Mutation_p.Y64N|RBMS3_ENST00000434693.2_Missense_Mutation_p.Y63N|RBMS3_ENST00000456853.1_Missense_Mutation_p.Y64N|RBMS3_ENST00000383766.2_Missense_Mutation_p.Y63N|RBMS3_ENST00000273139.9_Missense_Mutation_p.Y64N|RBMS3_ENST00000396583.3_Missense_Mutation_p.Y64N			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	64	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				AACCAACCTGTACATTCGAGG	0.567																																					p.Y64N		Atlas-SNP	.											.	RBMS3	62	.	0			c.T190A						.						245	186	206					3																	29476348		2203	4300	6503	SO:0001583	missense	27303	exon2			AACCTGTACATTC	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"RNA binding motif (RRM) containing"	13427	protein-coding gene	gene with protein product	"RNA-binding protein"	605786	"RNA binding motif, single stranded interacting protein"			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.190T>A	chr3.hg19:g.29476348T>A	ENSP00000373277:p.Tyr64Asn	278.0	1.0		329.0	139.0	NM_001003793	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Missense_Mutation	SNP	ENST00000383767.2	hg19	CCDS33724.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.900007	0.92035	.	.	ENSG00000144642	ENST00000434693;ENST00000396583;ENST00000383767;ENST00000445033;ENST00000273139;ENST00000383766;ENST00000452462;ENST00000456853	T;T;T;T;T;T;T;T	0.20332	2.08;2.08;2.08;2.08;2.08;2.08;2.08;2.08	5.63	5.63	0.86233	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.53867	0.1823	M	0.88377	2.95	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.62253	-0.6893	9	.	.	.	.	15.8275	0.78725	0.0:0.0:0.0:1.0	.	64;64;63;64	G5E9J9;Q6XE24-2;Q6XE24-3;Q6XE24	.;.;.;RBMS3_HUMAN	N	63;64;64;64;64;63;64;64	ENSP00000395592:Y63N;ENSP00000379828:Y64N;ENSP00000373277:Y64N;ENSP00000391934:Y64N;ENSP00000273139:Y64N;ENSP00000373276:Y63N;ENSP00000397926:Y64N;ENSP00000400519:Y64N	.	Y	+	1	0	RBMS3	29451352	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.036000	0.88901	2.142000	0.66516	0.533000	0.62120	TAC	.	.		0.567	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792		A	29476348	T	A	29476348	3	1	18	1	0	0	0	0	1	0	0	0	13165	1638	57	4	196	4	RBMS3	3	29476348	Missense_Mutation	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10		29476348	168546082	18	1542										
ULK4	54986	hgsc.bcm.edu	37	chr3	41607592	41607592	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	aatgcaatcacactttgcatGgtattacccagaatgctctc	6	11	2	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr3:41607592G>A	ENST00000301831.4	-	32	3612	c.3150C>T	c.(3148-3150)acC>acT	p.T1050T		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	1050					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CACTTTGCATGGTATTACCCA	0.353																																					p.T1050T		Atlas-SNP	.											.	ULK4	150	.	0			c.C3150T						.						148	136	140					3																	41607592		1900	4127	6027	SO:0001819	synonymous_variant	54986	exon32			TTGCATGGTATTA	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.3150C>T	chr3.hg19:g.41607592G>A		85.0	0.0		104.0	28.0	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Silent	SNP	ENST00000301831.4	hg19	CCDS43071.1																																																																																			.	.		0.353	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		A	41607592	G	A	41607592	2	1	18	1	0	0	0	0	0	0	0	1	16993	1335	47	3		3	ULK4	3	41607592	Silent	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	12131244	41607592	156414838	19	1543										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52419370	52419370	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tagctgctgcgcacttctgaGgatgtagccaagatgcagga	13	9	1	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr3:52419370G>A	ENST00000420323.2	+	54	8793	c.8532G>A	c.(8530-8532)gaG>gaA	p.E2844E		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2844	Stalk. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GCACTTCTGAGGATGTAGCCA	0.602											OREG0015612	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E2844E		Atlas-SNP	.											.	DNAH1	534	.	0			c.G8532A						.						52	60	58					3																	52419370		2052	4036	6088	SO:0001819	synonymous_variant	25981	exon54			TTCTGAGGATGTA	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.8532G>A	chr3.hg19:g.52419370G>A		111.0	0.0	984	99.0	54.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	hg19	CCDS46842.1																																																																																			.	.		0.602	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52419370	G	A	52419370	2	1	18	1	0	0	0	0	0	0	0	1	4599	991	35	3		3	DNAH1	3	52419370	Silent	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	10811778	52419370	145603060	20	1544										
ABI3BP	25890	hgsc.bcm.edu	37	chr3	100508351	100508351	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gcctcacagtagtataaaatCtgtgtggcgctgaaacagag	11	8	2	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr3:100508351C>G	ENST00000284322.5	-	24	2085	c.1976G>C	c.(1975-1977)aGa>aCa	p.R659T	ABI3BP_ENST00000383691.4_Missense_Mutation_p.R613T|ABI3BP_ENST00000471714.1_Missense_Mutation_p.R1336T	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	659	Pro-rich.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						AGTATAAAATCTGTGTGGCGC	0.428																																					p.R659T		Atlas-SNP	.											.	ABI3BP	305	.	0			c.G1976C						.						71	65	67					3																	100508351		1838	4094	5932	SO:0001583	missense	25890	exon24			TAAAATCTGTGTG	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"Fibronectin type III domain containing"	17265	protein-coding gene	gene with protein product	"target of Nesh-SH3"	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.1976G>C	chr3.hg19:g.100508351C>G	ENSP00000284322:p.Arg659Thr	53.0	0.0		93.0	29.0	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	hg19	CCDS46880.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	13.53|13.53|13.53	2.263853|2.263853|2.263853	0.39995|0.39995|0.39995	.|.|.	.|.|.	ENSG00000154175|ENSG00000154175|ENSG00000154175	ENST00000495591;ENST00000471901|ENST00000497395|ENST00000471714;ENST00000284322;ENST00000383692;ENST00000429331;ENST00000383691;ENST00000486770	.|.|T;T;T	.|.|0.52295	.|.|2.2;0.67;1.62	5.7|5.7|5.7	4.6|4.6|4.6	0.57074|0.57074|0.57074	.|.|.	.|.|0.317635	.|.|0.33591	.|.|N	.|.|0.004746	T|T|T	0.49201|0.49201|0.49201	0.1543|0.1543|0.1543	L|L|L	0.51422|0.51422|0.51422	1.61|1.61|1.61	0.24137|0.24137|0.24137	N|N|N	0.995746|0.995746|0.995746	.|.|D;P;D;D	.|.|0.65815	.|.|0.995;0.893;0.995;0.986	.|.|P;P;P;P	.|.|0.56278	.|.|0.795;0.504;0.791;0.784	T|T|T	0.38735|0.38735|0.38735	-0.9647|-0.9647|-0.9647	5|5|10	.|.|0.17832	.|.|T	.|.|0.49	-24.5682|-24.5682|-24.5682	7.3993|7.3993|7.3993	0.26954|0.26954|0.26954	0.0:0.8592:0.0:0.1408|0.0:0.8592:0.0:0.1408|0.0:0.8592:0.0:0.1408	.|.|.	.|.|613;659;1336;343	.|.|B4DSV9;Q7Z7G0;D3YTG3;D3YTD6	.|.|.;TARSH_HUMAN;.;.	H|H|T	715;239|74|1336;659;343;45;613;71	.|.|ENSP00000420524:R1336T;ENSP00000284322:R659T;ENSP00000373189:R613T	.|.|ENSP00000284322:R659T	D|Q|R	-|-|-	1|3|2	0|2|0	ABI3BP|ABI3BP|ABI3BP	101991041|101991041|101991041	0.208000|0.208000|0.208000	0.23494|0.23494|0.23494	0.924000|0.924000|0.924000	0.36721|0.36721|0.36721	0.098000|0.098000|0.098000	0.18820|0.18820|0.18820	1.846000|1.846000|1.846000	0.39289|0.39289|0.39289	2.852000|2.852000|2.852000	0.98041|0.98041|0.98041	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GAT|CAG|AGA	.	.		0.428	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			G	100508351	C	G	100508351	3	3	18	1	0	0	0	0	1	0	0	0	91	913	32	4	1299	4	ABI3BP	3	100508351	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	48088981	100508351	97514079	21	1545										
RETNLB	84666	hgsc.bcm.edu	37	chr3	108474658	108474658	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	cagcagcgggcagtggtccaGtccaccacactgcactggca	12	15	0	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr3:108474658G>T	ENST00000295755.6	-	3	501	c.303C>A	c.(301-303)gaC>gaA	p.D101E	RETNLB_ENST00000482939.1_Intron	NM_032579.2	NP_115968.1	Q9BQ08	RETNB_HUMAN	resistin like beta	101					cell proliferation (GO:0008283)	extracellular region (GO:0005576)				endometrium(1)|kidney(3)|lung(10)|prostate(1)|skin(1)	16						CAGTGGTCCAGTCCACCACAC	0.567																																					p.D101E		Atlas-SNP	.											.	RETNLB	38	.	0			c.C303A						.						101	95	97					3																	108474658		2203	4300	6503	SO:0001583	missense	84666	exon3			GGTCCAGTCCACC	AF290873	CCDS2953.1	3q13.1	2008-02-05			ENSG00000163515	ENSG00000163515			20388	protein-coding gene	gene with protein product		605645				10921885, 12574343	Standard	NM_032579		Approved	HXCP2, FIZZ2, RELMb	uc003dxh.2	Q9BQ08	OTTHUMG00000159393	ENST00000295755.6:c.303C>A	chr3.hg19:g.108474658G>T	ENSP00000295755:p.Asp101Glu	330.0	2.0		278.0	175.0	NM_032579	Q14D27	Missense_Mutation	SNP	ENST00000295755.6	hg19	CCDS2953.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.739584	0.49045	.	.	ENSG00000163515	ENST00000295755	T	0.61742	0.08	4.14	-1.09	0.09904	.	0.130837	0.33772	N	0.004572	T	0.49355	0.1552	M	0.75085	2.285	0.28303	N	0.923033	P	0.51240	0.943	B	0.41332	0.354	T	0.52215	-0.8605	10	0.87932	D	0	-13.6635	4.9206	0.13867	0.3737:0.1487:0.4776:0.0	.	101	Q9BQ08	RETNB_HUMAN	E	101	ENSP00000295755:D101E	ENSP00000295755:D101E	D	-	3	2	RETNLB	109957348	1.000000	0.71417	0.557000	0.28306	0.404000	0.30871	0.754000	0.26390	-0.510000	0.06523	0.655000	0.94253	GAC	.	.		0.567	RETNLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355093.1			T	108474658	G	T	108474658	3	4	18	1	0	0	0	0	1	0	0	0	13252	1020	36	3	36	3	RETNLB	3	108474658	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	7966307	108474658	89547772	22	1546										
MCCC1	56922	hgsc.bcm.edu	37	chr3	182756812	182756832	+	Splice_Site	DEL	GATCACTCACATTGTACTGAC	GATCACTCACATTGTACTGAC	-													0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ggcacggtctcagatcactcAcattgtactgacgaaggctg					rs369847846|rs146689034		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	GATCACTCACATTGTACTGAC	GATCACTCACATTGTACTGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr3:182756812_182756832delGATCACTCACATTGTACTGAC	ENST00000265594.4	-	12	1505_1524	c.1359_1378delGTCAGTACAATGTGAGTGATC	c.(1357-1380)tagtcagtacaatgtgagtgatct>tact	p.453_460*SVQCE*S>Y	MCCC1_ENST00000539926.1_Splice_Site_p.318_325*SVQCE*S>Y|MCCC1_ENST00000492597.1_Splice_Site_p.344_351*SVQCE*S>Y|MCCC1_ENST00000489909.1_5'Flank	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	453	Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	CAGATCACTCACATTGTACTGACGAAGGCTGTACCTCAGTT	0.516																																					p.456_459del		Atlas-Indel,Pindel	.											.	MCCC1	87	.	0			c.1368_1377del						.																																			SO:0001630	splice_region_variant	56922	exon12			.	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1377+1GTCAGTACAATGTGAGTGATC>-	chr3.hg19:g.182756812_182756832delGATCACTCACATTGTACTGAC		116.0	0.0		158.0	32.0	NM_020166	Q59ES4|Q9H959|Q9NS97	Frame_Shift_Del	DEL	ENST00000265594.4	hg19	CCDS3241.1																																																																																			.	.		0.516	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	In_Frame_Del	-	182756832	GATCACTCACATTGTACTGAC	-	182756812	8	5	18	1	0	1	0	1	0	0	1	0	9383	173	6	0	830	0	MCCC1	3	182756812	Splice_Site	DEL	GATCACTCACATTGTACTGAC	TCGA-2Y-A9H8-01A-11D-A38X-10	74282154	182756812	15265618	23	1547										
EPHB3	2049	hgsc.bcm.edu	37	chr3	184295691	184295691	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	cttctctatctccaggctctGgggcccagcagctccaggag	11	15	3	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr3:184295691G>T	ENST00000330394.2	+	8	2097	c.1645G>T	c.(1645-1647)Ggg>Tgg	p.G549W	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	549					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TCCAGGCTCTGGGGCCCAGCA	0.632																																					p.G549W		Atlas-SNP	.											.	EPHB3	114	.	0			c.G1645T						.						78	79	79					3																	184295691		2203	4300	6503	SO:0001583	missense	2049	exon8			GGCTCTGGGGCCC	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3394	protein-coding gene	gene with protein product		601839	"EphB3"	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.1645G>T	chr3.hg19:g.184295691G>T	ENSP00000332118:p.Gly549Trp	74.0	0.0		67.0	20.0	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.249200	0.39797	.	.	ENSG00000182580	ENST00000330394	T	0.74737	-0.87	5.04	3.22	0.36961	.	0.625953	0.14572	N	0.311408	T	0.66036	0.2749	L	0.39898	1.24	0.09310	N	1	D	0.53885	0.963	P	0.47044	0.535	T	0.55585	-0.8118	10	0.40728	T	0.16	.	4.2542	0.10708	0.2705:0.1763:0.5532:0.0	.	549	P54753	EPHB3_HUMAN	W	549	ENSP00000332118:G549W	ENSP00000332118:G549W	G	+	1	0	EPHB3	185778385	0.907000	0.30839	0.125000	0.21846	0.790000	0.44656	1.286000	0.33273	0.510000	0.28216	0.448000	0.29417	GGG	.	.		0.632	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		T	184295691	G	T	184295691	3	4	18	1	0	0	0	0	1	0	0	0	5178	1348	47	3	1675	3	EPHB3	3	184295691	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	1538879	184295691	13726739	24	1548										
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193120567	193120567	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gggtcatttgccaagtccctCtgccatatccgatactggct	9	13	2	0	rs200859894		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr3:193120567C>A	ENST00000342695.4	-	30	3787	c.3465G>T	c.(3463-3465)caG>caT	p.Q1155H	ATP13A4_ENST00000482964.1_5'UTR|ATP13A4_ENST00000400270.2_Missense_Mutation_p.Q171H|ATP13A4_ENST00000392443.3_Missense_Mutation_p.Q1136H	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1155						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.Q1155H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		CCAAGTCCCTCTGCCATATCC	0.468																																					p.Q1155H		Atlas-SNP	.											ATP13A4,colon,carcinoma,0,1	ATP13A4	154	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3465T						.						88	86	87					3																	193120567		2203	4300	6503	SO:0001583	missense	84239	exon30			GTCCCTCTGCCAT	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"ATPases / P-type"	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.3465G>T	chr3.hg19:g.193120567C>A	ENSP00000339182:p.Gln1155His	45.0	0.0		72.0	22.0	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	hg19	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	C	16.69	3.193252	0.58017	.	.	ENSG00000127249	ENST00000400270;ENST00000392443;ENST00000342695	T;T;T	0.63417	-0.04;-0.04;-0.04	5.0	3.17	0.36434	.	0.094778	0.45606	N	0.000345	T	0.68997	0.3062	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.66340	-0.5948	10	0.51188	T	0.08	-10.8733	5.6238	0.17470	0.0:0.6601:0.1633:0.1765	.	1155	Q4VNC1	AT134_HUMAN	H	171;1136;1155	ENSP00000383129:Q171H;ENSP00000376238:Q1136H;ENSP00000339182:Q1155H	ENSP00000339182:Q1155H	Q	-	3	2	ATP13A4	194603261	0.980000	0.34600	0.980000	0.43619	0.919000	0.55068	0.715000	0.25822	0.602000	0.29896	-0.223000	0.12442	CAG	.	C|1.000;T|0.000		0.468	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		A	193120567	C	A	193120567	3	1	18	1	0	0	0	0	1	0	0	0	1126	912	32	3	129	3	ATP13A4	3	193120567	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	8824876	193120567	4901863	25	1549										
C4orf21	55345	hgsc.bcm.edu	37	chr4	113527240	113527240	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tctcttctttacttcccgagGaagagaactaggataaaata	7	8	2	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr4:113527240G>A	ENST00000505019.1	-	9	2851	c.2726C>T	c.(2725-2727)tCc>tTc	p.S909F	C4orf21_ENST00000309071.5_Missense_Mutation_p.S909F	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		909						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.S909Y(2)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		ACTTCCCGAGGAAGAGAACTA	0.323																																					p.S909F		Atlas-SNP	.											C4orf21_ENST00000505019,rectum,carcinoma,0,2	C4orf21	223	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2726T						.						66	75	72					4																	113527240		2203	4299	6502	SO:0001583	missense	55345	exon9			CCCGAGGAAGAGA																												ENST00000505019.1:c.2726C>T	chr4.hg19:g.113527240G>A	ENSP00000424737:p.Ser909Phe	78.0	0.0		85.0	26.0	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.92	2.680284	0.47886	.	.	ENSG00000138658	ENST00000505019;ENST00000309071	D;T	0.84070	-1.8;1.69	5.03	5.03	0.67393	.	1.159930	0.06414	N	0.721095	D	0.86887	0.6041	L	0.47716	1.5	0.80722	D	1	D;P	0.55385	0.971;0.95	P;P	0.54401	0.751;0.735	T	0.79815	-0.1644	10	0.72032	D	0.01	5.5705	13.8469	0.63472	0.0:0.0:1.0:0.0	.	909;909	Q86YA3;G5EA02	CD021_HUMAN;.	F	909	ENSP00000424737:S909F;ENSP00000309095:S909F	ENSP00000309095:S909F	S	-	2	0	C4orf21	113746689	0.997000	0.39634	0.457000	0.27056	0.840000	0.47671	3.421000	0.52742	2.315000	0.78130	0.650000	0.86243	TCC	.	.		0.323	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1			A	113527240	G	A	113527240	3	1	18	1	0	0	0	0	1	0	0	0	2256	1174	41	3	3668	3	C4orf21	4	113527240	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10		113527240	77627036	26	1550										
ANP32C	55016	hgsc.bcm.edu	37	chr4	165118848	165118848	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ccgcagctctgaatgaatccGtctgcccatctccatctctc	6	17	4	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr4:165118848G>A	ENST00000503008.1	-	2	864				MARCH1_ENST00000514618.1_Intron|MARCH1_ENST00000508725.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GAATGAATCCGTCTGCCCATC	0.552																																					p.R6W		Atlas-SNP	.											ANP32C,bladder,carcinoma,0,2	ANP32C	59	.	0			c.C16T						.						97	100	99					4																	165118848		2203	4300	6503	SO:0001627	intron_variant	23520	exon1			GAATCCGTCTGCC	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	26077	protein-coding gene	gene with protein product		613331	"membrane-associated ring finger (C3HC4) 1"			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-86034C>T	chr4.hg19:g.165118848G>A		66.0	0.0		71.0	22.0	NM_012403	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	hg19	CCDS54814.1																																																																																			.	.		0.552	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923		A	165118848	G	A	165118848	1	1	18	0	1	0	0	0	0	0	0	0	707	1144	40	1		1	ANP32C	4	165118848	Intron	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	51591608	165118848	26035428	27	1551										
HELT	391723	hgsc.bcm.edu	37	chr4	185940140	185940140	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tgagcccaaatggcacttgcGccctggtggtggaggcatct	14	11	1	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr4:185940140G>A	ENST00000515777.1	+	1	115				HELT_ENST00000505610.1_Intron|HELT_ENST00000338875.4_Missense_Mutation_p.A20T			A6NFD8	HELT_HUMAN	helt bHLH transcription factor						central nervous system development (GO:0007417)|GABAergic neuron differentiation in basal ganglia (GO:0021858)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	14		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;8.92e-26)|Epithelial(43;3.02e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-11)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		TGGCACTTGCGCCCTGGTGGT	0.632																																					p.A20T		Atlas-SNP	.											.	HELT	34	.	0			c.G58A						.						87	71	76					4																	185940140		2203	4300	6503	SO:0001627	intron_variant	391723	exon1			ACTTGCGCCCTGG	BC144567	CCDS75214.1, CCDS75215.1	4q35.1	2014-07-17	2011-09-12		ENSG00000187821	ENSG00000187821		"Basic helix-loop-helix proteins"	33783	protein-coding gene	gene with protein product	"megane bHLH factor", "HES-like"		"Hey-like transcription factor (zebrafish)", "HES/HEY-like transcription factor"			14764602, 17611227	Standard	XM_005262989		Approved	HESL, HCM1228, Mgn, bHLHb44, MEGANE	uc011ckq.2	A6NFD8	OTTHUMG00000160484	ENST00000515777.1:c.27+31G>A	chr4.hg19:g.185940140G>A		167.0	0.0		138.0	86.0	NM_001029887	B2RTS5|B7ZMI7|B7ZMI8	Missense_Mutation	SNP	ENST00000515777.1	hg19		.	.	.	.	.	.	.	.	.	.	G	8.592	0.884735	0.17540	.	.	ENSG00000187821	ENST00000338875	T	0.31769	1.48	4.73	4.73	0.59995	.	0.118798	0.30003	N	0.010643	T	0.14830	0.0358	N	0.08118	0	0.23731	N	0.996996	P	0.47545	0.897	B	0.37692	0.256	T	0.10941	-1.0608	10	0.42905	T	0.14	.	11.4233	0.49996	0.0:0.2382:0.7618:0.0	.	20	A6NFD8	HELT_HUMAN	T	20	ENSP00000343464:A20T	ENSP00000343464:A20T	A	+	1	0	HELT	186177134	1.000000	0.71417	0.996000	0.52242	0.224000	0.24922	2.353000	0.44089	2.473000	0.83533	0.561000	0.74099	GCC	.	.		0.632	HELT-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000360792.1	NM_001300781		A	185940140	G	A	185940140	1	1	18	0	1	0	0	0	0	0	0	0	7057	1087	38	1		1	HELT	4	185940140	Intron	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	20821292	185940140	5214136	28	1552										
BDP1	55814	hgsc.bcm.edu	37	chr5	70782327	70782327	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	acagaggaaaagcgccctttTgacttcgatttttttgctca	8	9	1	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr5:70782327T>C	ENST00000358731.4	+	9	1349	c.1086T>C	c.(1084-1086)ttT>ttC	p.F362F	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	362	Required for phosphorylation by CSNK2A1.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		AGCGCCCTTTTGACTTCGATT	0.294																																					p.F362F		Atlas-SNP	.											.	BDP1	204	.	0			c.T1086C						.						64	62	63					5																	70782327		1793	4061	5854	SO:0001819	synonymous_variant	55814	exon9			CCCTTTTGACTTC	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.1086T>C	chr5.hg19:g.70782327T>C		239.0	0.0		321.0	79.0	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Silent	SNP	ENST00000358731.4	hg19	CCDS43328.1																																																																																			.	.		0.294	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		C	70782327	T	C	70782327	2	2	18	1	0	0	0	0	0	0	0	1	1395	1809	63	2		2	BDP1	5	70782327	Silent	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10		70782327	110132933	29	1553										
IER3	8870	hgsc.bcm.edu	37	chr6	30712143	30712143	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tgcccgcgagaggcgctgggGcgcccggcaggggccgctgc	20	15	0	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr6:30712143G>A	ENST00000259874.5	-	1	188	c.153C>T	c.(151-153)cgC>cgT	p.R51R	FLOT1_ENST00000456573.2_5'Flank|XXbac-BPG252P9.10_ENST00000607333.1_RNA|FLOT1_ENST00000470643.1_5'Flank|FLOT1_ENST00000376389.3_5'Flank|IER3_ENST00000376377.2_Silent_p.R51R	NM_003897.3	NP_003888.2	P46695	IEX1_HUMAN	immediate early response 3	51					anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glycolytic process (GO:0045820)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|negative regulation of systemic arterial blood pressure (GO:0003085)|positive regulation of protein catabolic process (GO:0045732)|regulation of DNA repair (GO:0006282)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of response to DNA damage stimulus (GO:2001020)|response to protozoan (GO:0001562)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)	1						AGGCGCTGGGGCGCCCGGCAG	0.736																																					p.R51R		Atlas-SNP	.											.	IER3	5	.	0			c.C153T						.						9	13	12					6																	30712143		1214	2513	3727	SO:0001819	synonymous_variant	8870	exon1			GCTGGGGCGCCCG	AF083421	CCDS4689.1	6p21.3	2010-02-17			ENSG00000137331	ENSG00000137331			5392	protein-coding gene	gene with protein product		602996				8603392, 9703517	Standard	NM_003897		Approved	IEX-1, DIF-2, PRG1, IEX-1L	uc003nrn.3	P46695	OTTHUMG00000031265	ENST00000259874.5:c.153C>T	chr6.hg19:g.30712143G>A		143.0	0.0		224.0	53.0	NM_003897	Q5SU30|Q92691|Q93044	Silent	SNP	ENST00000259874.5	hg19	CCDS4689.1																																																																																			.	.		0.736	IER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076578.2			A	30712143	G	A	30712143	2	1	18	1	0	0	0	0	0	0	0	1	7515	1190	42	3		3	IER3	6	30712143	Silent	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10		30712143	140402924	30	1554										
NOX3	50508	hgsc.bcm.edu	37	chr6	155776002	155776002	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ctgacaggtattagaattagCatgcagttaaaattcaggca	9	6	1	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr6:155776002C>T	ENST00000159060.2	-	3	300	c.198G>A	c.(196-198)atG>atA	p.M66I		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	66	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		TTAGAATTAGCATGCAGTTAA	0.373																																					p.M66I		Atlas-SNP	.											.	NOX3	93	.	0			c.G198A						.						68	68	68					6																	155776002		2203	4300	6503	SO:0001583	missense	50508	exon3			AATTAGCATGCAG	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.198G>A	chr6.hg19:g.155776002C>T	ENSP00000159060:p.Met66Ile	120.0	0.0		124.0	80.0	NM_015718	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	hg19	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.022955	0.54683	.	.	ENSG00000074771	ENST00000159060	D	0.90504	-2.68	5.91	5.04	0.67666	Flavoprotein transmembrane component (1);	0.000000	0.85682	D	0.000000	D	0.84911	0.5577	L	0.54965	1.715	0.40084	D	0.976174	P	0.34462	0.454	B	0.34931	0.192	D	0.86393	0.1737	10	0.56958	D	0.05	-35.2106	14.5068	0.67758	0.0:0.9302:0.0:0.0698	.	66	Q9HBY0	NOX3_HUMAN	I	66	ENSP00000159060:M66I	ENSP00000159060:M66I	M	-	3	0	NOX3	155817694	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.674000	0.61612	2.804000	0.96469	0.650000	0.86243	ATG	.	.		0.373	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			T	155776002	C	T	155776002	3	4	18	1	0	0	0	0	1	0	0	0	10566	710	25	3	1552	3	NOX3	6	155776002	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	125063859	155776002	15339065	31	1555										
USP42	84132	hgsc.bcm.edu	37	chr7	6150812	6150812	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tcttcagacccatcagcctaTcagaatcagcctggcagctc	7	15	5	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr7:6150812T>C	ENST00000306177.5	+	2	206	c.48T>C	c.(46-48)taT>taC	p.Y16Y		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	16					cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		CATCAGCCTATCAGAATCAGC	0.453																																					p.Y16Y		Atlas-SNP	.											.	USP42	138	.	0			c.T48C						.						73	69	70					7																	6150812		1957	4146	6103	SO:0001819	synonymous_variant	84132	exon2			AGCCTATCAGAAT	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"Ubiquitin-specific peptidases"	20068	protein-coding gene	gene with protein product			"ubiquitin specific protease 42"			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.48T>C	chr7.hg19:g.6150812T>C		106.0	0.0		173.0	66.0	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Silent	SNP	ENST00000306177.5	hg19	CCDS47535.1																																																																																			.	.		0.453	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526		C	6150812	T	C	6150812	2	2	18	1	0	0	0	0	0	0	0	1	17088	1442	50	2		2	USP42	7	6150812	Silent	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10		6150812	152987851	32	1556										
HOXA2	3199	hgsc.bcm.edu	37	chr7	27141906	27141906	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	cgcggggctcggcttggggcGgccgccagcgccgtggcgag	21	14	0	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr7:27141906G>A	ENST00000222718.5	-	1	524	c.214C>T	c.(214-216)Cgc>Tgc	p.R72C	HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000593300.1_RNA|HOTAIRM1_ENST00000428939.3_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000434063.3_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	72					anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						GGCTTGGGGCGGCCGCCAGCG	0.701																																					p.R72C		Atlas-SNP	.											.	HOXA2	56	.	0			c.C214T						.						15	19	18					7																	27141906		2123	4271	6394	SO:0001583	missense	3199	exon1			TGGGGCGGCCGCC		CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996		"Homeoboxes / ANTP class : HOXL subclass"	5103	protein-coding gene	gene with protein product		604685	"homeo box A2"	HOX1K		1358459	Standard	NM_006735		Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.214C>T	chr7.hg19:g.27141906G>A	ENSP00000222718:p.Arg72Cys	828.0	0.0		764.0	41.0	NM_006735	A1L4K3|B2RMW3	Missense_Mutation	SNP	ENST00000222718.5	hg19	CCDS5403.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.280938	0.40394	.	.	ENSG00000105996	ENST00000222718	D	0.93189	-3.18	5.49	4.6	0.57074	.	0.109676	0.64402	D	0.000006	D	0.93481	0.7920	M	0.86343	2.81	0.80722	D	1	B	0.20261	0.043	B	0.18263	0.021	D	0.92244	0.5803	10	0.72032	D	0.01	.	13.3753	0.60734	0.0765:0.0:0.9235:0.0	.	72	O43364	HXA2_HUMAN	C	72	ENSP00000222718:R72C	ENSP00000222718:R72C	R	-	1	0	HOXA2	27108431	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.894000	0.63206	2.584000	0.87258	0.591000	0.81541	CGC	.	.		0.701	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358508.2			A	27141906	G	A	27141906	3	1	18	1	0	0	0	0	1	0	0	0	7301	1116	39	1	924	1	HOXA2	7	27141906	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	20991094	27141906	131996757	33	1557										
GLI3	2737	hgsc.bcm.edu	37	chr7	42065983	42065983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	catgtggagagagacgggcgCggaagagtaggtgaagctca	18	6	1	4	rs375277249		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr7:42065983C>T	ENST00000395925.3	-	8	1141	c.1057G>A	c.(1057-1059)Gcg>Acg	p.A353T	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	353					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GAGACGGGCGCGGAAGAGTAG	0.537									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.A353T		Atlas-SNP	.											.	GLI3	312	.	0			c.G1057A						.						92	88	90					7																	42065983		2203	4300	6503	SO:0001583	missense	2737	exon8	Familial Cancer Database	;	CGGGCGCGGAAGA		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.1057G>A	chr7.hg19:g.42065983C>T	ENSP00000379258:p.Ala353Thr	94.0	0.0		136.0	36.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	C	0.081	-1.184119	0.01620	.	.	ENSG00000106571	ENST00000395925	T	0.12774	2.65	5.9	4.92	0.64577	.	0.044427	0.85682	D	0.000000	T	0.03263	0.0095	N	0.01576	-0.805	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.42832	-0.9428	10	0.02654	T	1	.	3.8897	0.09113	0.0:0.682:0.0:0.3179	.	353	P10071	GLI3_HUMAN	T	353	ENSP00000379258:A353T	ENSP00000379258:A353T	A	-	1	0	GLI3	42032508	1.000000	0.71417	0.472000	0.27241	0.132000	0.20833	5.675000	0.68123	2.788000	0.95919	0.650000	0.86243	GCG	.	.		0.537	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42065983	C	T	42065983	3	4	18	1	0	0	0	0	1	0	0	0	6447	768	27	1	3717	1	GLI3	7	42065983	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	14924077	42065983	117072680	34	1558										
AEBP1	165	hgsc.bcm.edu	37	chr7	44153377	44153377	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gagatcatggccatgaacggGaaccggcctatcccacacat	10	13	1	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr7:44153377G>A	ENST00000223357.3	+	21	3299	c.2994G>A	c.(2992-2994)ggG>ggA	p.G998G	MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_Silent_p.G573G	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	998	Required for transcriptional repression. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						CCATGAACGGGAACCGGCCTA	0.612																																					p.G998G		Atlas-SNP	.											.	AEBP1	102	.	0			c.G2994A						.						131	127	128					7																	44153377		2203	4300	6503	SO:0001819	synonymous_variant	165	exon21			GAACGGGAACCGG	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"aortic carboxypeptidase-like protein", "adipocyte enhancer binding protein 1"	602981	"AE-binding protein 1"			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.2994G>A	chr7.hg19:g.44153377G>A		114.0	0.0		150.0	60.0	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Silent	SNP	ENST00000223357.3	hg19	CCDS5476.1																																																																																			.	.		0.612	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		A	44153377	G	A	44153377	2	1	18	1	0	0	0	0	0	0	0	1	349	1161	41	3		3	AEBP1	7	44153377	Silent	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	2087394	44153377	114985286	35	1559										
POM121L12	285877	hgsc.bcm.edu	37	chr7	53103524	53103524	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	agggtcgccagagtccctggCccctgaggtccctgactcag	13	15	1	3			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr7:53103524C>T	ENST00000408890.4	+	1	176	c.160C>T	c.(160-162)Ccc>Tcc	p.P54S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	54										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GAGTCCCTGGCCCCTGAGGTC	0.701																																					p.P54S		Atlas-SNP	.											.	POM121L12	146	.	0			c.C160T						.						28	34	32					7																	53103524		1992	4162	6154	SO:0001583	missense	285877	exon1			CCCTGGCCCCTGA		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.160C>T	chr7.hg19:g.53103524C>T	ENSP00000386133:p.Pro54Ser	229.0	0.0		299.0	50.0	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	hg19	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	C	1.909	-0.451167	0.04572	.	.	ENSG00000221900	ENST00000408890	T	0.36520	1.25	1.49	0.545	0.17190	.	.	.	.	.	T	0.25531	0.0621	L	0.42245	1.32	0.09310	N	1	B	0.26318	0.146	B	0.18561	0.022	T	0.17379	-1.0371	9	0.30078	T	0.28	.	6.7225	0.23338	0.0:0.8119:0.0:0.1881	.	54	Q8N7R1	P1L12_HUMAN	S	54	ENSP00000386133:P54S	ENSP00000386133:P54S	P	+	1	0	POM121L12	53071018	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	-1.482000	0.02320	-0.150000	0.11195	-1.786000	0.00637	CCC	.	.		0.701	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		T	53103524	C	T	53103524	3	4	18	1	0	0	0	0	1	0	0	0	12250	739	26	3	162	3	POM121L12	7	53103524	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	8950147	53103524	106035139	36	1560										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87160674	87160674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	cagacaacattttcatttcaAcaactcctgctattgcaatg	4	11	2	1	rs565619660		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr7:87160674A>G	ENST00000265724.3	-	22	3038	c.2621T>C	c.(2620-2622)gTt>gCt	p.V874A	ABCB1_ENST00000543898.1_Missense_Mutation_p.V810A|ABCB1_ENST00000488737.2_5'UTR	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	874	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	TTTCATTTCAACAACTCCTGC	0.358													A|||	1	0.000199681	8e-04	0	5008	,	,		17993	0		0	False		,,,				2504	0				p.V874A		Atlas-SNP	.											.	ABCB1	263	.	0			c.T2621C						.						146	144	145					7																	87160674		2203	4300	6503	SO:0001583	missense	5243	exon22			ATTTCAACAACTC	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.2621T>C	chr7.hg19:g.87160674A>G	ENSP00000265724:p.Val874Ala	85.0	0.0		182.0	79.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	hg19	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	A	15.80	2.941101	0.53079	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.90197	-2.63;-2.63	5.67	5.67	0.87782	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.569557	0.19168	N	0.121019	D	0.90263	0.6955	L	0.39633	1.23	0.34052	D	0.656306	B;B	0.31026	0.003;0.304	B;B	0.43082	0.032;0.407	D	0.91908	0.5537	10	0.36615	T	0.2	-5.9364	16.1924	0.82000	1.0:0.0:0.0:0.0	.	810;874	B5AK60;P08183	.;MDR1_HUMAN	A	655;874;810	ENSP00000265724:V874A;ENSP00000444095:V810A	ENSP00000265724:V874A	V	-	2	0	ABCB1	86998610	1.000000	0.71417	0.954000	0.39281	0.996000	0.88848	6.517000	0.73759	2.287000	0.76781	0.482000	0.46254	GTT	.	.		0.358	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		G	87160674	A	G	87160674	3	3	18	1	0	0	0	0	1	0	0	0	40	43	2	2	1253	2	ABCB1	7	87160674	Missense_Mutation	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10	34057150	87160674	71977989	37	1561										
FLNC	2318	hgsc.bcm.edu	37	chr7	128492798	128492798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gctgaagcgcctgcccaaccGgcacattggtgagcgtgggg	16	12	0	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr7:128492798G>A	ENST00000325888.8	+	36	6257	c.5996G>A	c.(5995-5997)cGg>cAg	p.R1999Q	FLNC_ENST00000346177.6_Missense_Mutation_p.R1966Q|RP11-309L24.2_ENST00000469965.1_RNA	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1999					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CTGCCCAACCGGCACATTGGT	0.652																																					p.R1999Q		Atlas-SNP	.											FLNC,NS,carcinoma,0,2	FLNC	339	.	0			c.G5996A						.						42	47	45					7																	128492798		2013	4184	6197	SO:0001583	missense	2318	exon36			CCAACCGGCACAT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.5996G>A	chr7.hg19:g.128492798G>A	ENSP00000327145:p.Arg1999Gln	162.0	0.0		157.0	118.0	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	hg19	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.173938	0.78452	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	T;T	0.41758	0.99;0.99	5.97	5.97	0.96955	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.129340	0.50627	D	0.000112	T	0.51500	0.1678	L	0.44542	1.39	0.38909	D	0.957482	D;P	0.71674	0.998;0.818	P;B	0.58172	0.834;0.193	T	0.53143	-0.8480	10	0.62326	D	0.03	.	14.023	0.64568	0.0774:0.0:0.9226:0.0	.	1966;1999	Q14315-2;Q14315	.;FLNC_HUMAN	Q	1999;1966	ENSP00000327145:R1999Q;ENSP00000344002:R1966Q	ENSP00000327145:R1999Q	R	+	2	0	FLNC	128280034	0.998000	0.40836	1.000000	0.80357	0.950000	0.60333	3.390000	0.52523	2.837000	0.97791	0.655000	0.94253	CGG	.	.		0.652	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128492798	G	A	128492798	3	1	18	1	0	0	0	0	1	0	0	0	5943	1116	39	1	6138	1	FLNC	7	128492798	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	41332124	128492798	30645865	38	1562										
ARHGEF10	9639	hgsc.bcm.edu	37	chr8	1830810	1830810	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ctccgtcgcagatgcagaagCtcgtgaaggccgcgaaggac	14	12	0	3			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr8:1830810C>T	ENST00000398564.1	+	10	1045	c.1045C>T	c.(1045-1047)Ctc>Ttc	p.L349F	ARHGEF10_ENST00000262112.6_Missense_Mutation_p.L349F|ARHGEF10_ENST00000398560.1_Missense_Mutation_p.L310F|ARHGEF10_ENST00000520359.1_Missense_Mutation_p.L286F|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.L349F|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.L324F			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	349					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		GATGCAGAAGCTCGTGAAGGC	0.582																																					p.L324F		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.C970T						.						28	28	28					8																	1830810		2151	4212	6363	SO:0001583	missense	9639	exon10			CAGAAGCTCGTGA	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"Rho guanine nucleotide exchange factors"	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.1045C>T	chr8.hg19:g.1830810C>T	ENSP00000381571:p.Leu349Phe	262.0	1.0		247.0	128.0	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.32	1.901717	0.33535	.	.	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398560;ENST00000398564;ENST00000262112	T;T;T;T;T;T	0.64991	0.03;0.22;0.02;-0.13;0.02;0.02	5.31	4.43	0.53597	.	0.000000	0.64402	D	0.000001	T	0.60379	0.2264	L	0.55103	1.725	0.46798	D	0.999204	B;B;B;P	0.45212	0.089;0.185;0.144;0.853	B;B;B;B	0.43508	0.039;0.109;0.085;0.422	T	0.62267	-0.6890	10	0.46703	T	0.11	-32.6965	13.58	0.61896	0.0:0.9249:0.0:0.0751	.	349;310;286;324	O15013;E9PB39;O15013-7;O15013-5	ARHGA_HUMAN;.;.;.	F	324;286;349;310;349;349	ENSP00000340297:L324F;ENSP00000427909:L286F;ENSP00000431012:L349F;ENSP00000381568:L310F;ENSP00000381571:L349F;ENSP00000262112:L349F	ENSP00000262112:L349F	L	+	1	0	ARHGEF10	1818217	1.000000	0.71417	0.362000	0.25862	0.334000	0.28698	2.169000	0.42434	1.226000	0.43582	0.561000	0.74099	CTC	.	.		0.582	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding				T	1830810	C	T	1830810	3	4	18	1	0	0	0	0	1	0	0	0	894	797	28	3	1004	3	ARHGEF10	8	1830810	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10		1830810	144533212	39	1563										
CPEB3	22849	hgsc.bcm.edu	37	chr10	93811980	93811980	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gcccgtggctcagctccagcGgaacgggacgtgacgagggc	17	13	1	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr10:93811980G>A	ENST00000265997.4	-	10	2258	c.2086C>T	c.(2086-2088)Cgc>Tgc	p.R696C	CPEB3_ENST00000412050.4_Missense_Mutation_p.R682C	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	696					3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				CAGCTCCAGCGGAACGGGACG	0.607																																					p.R696C		Atlas-SNP	.											.	CPEB3	43	.	0			c.C2086T						.						28	28	28					10																	93811980		2203	4300	6503	SO:0001583	missense	22849	exon10			TCCAGCGGAACGG	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.2086C>T	chr10.hg19:g.93811980G>A	ENSP00000265997:p.Arg696Cys	112.0	0.0		96.0	55.0	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	hg19	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.068177	0.76301	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.60040	0.28;0.22	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.71558	0.3354	L	0.54323	1.7	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	P;P;P	0.61275	0.886;0.719;0.855	T	0.73272	-0.4035	10	0.87932	D	0	-10.1112	19.7072	0.96079	0.0:0.0:1.0:0.0	.	696;682;682	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	C	682;682;696	ENSP00000398310:R682C;ENSP00000265997:R696C	ENSP00000265997:R696C	R	-	1	0	CPEB3	93801960	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.662000	0.90505	0.591000	0.81541	CGC	.	.		0.607	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		A	93811980	G	A	93811980	3	1	18	1	0	0	0	0	1	0	0	0	3804	1116	39	1	14	1	CPEB3	10	93811980	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10		93811980	41722767	40	1564										
SMC3	9126	hgsc.bcm.edu	37	chr10	112349410	112349410	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	aaagctcgagtagaagaactGgacagaaaatattacgaagt	10	5	0	3			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr10:112349410G>A	ENST00000361804.4	+	14	1479	c.1353G>A	c.(1351-1353)ctG>ctA	p.L451L		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	451					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		TAGAAGAACTGGACAGAAAAT	0.279																																					p.L451L		Atlas-SNP	.											.	SMC3	103	.	0			c.G1353A						.						30	31	31					10																	112349410		2202	4298	6500	SO:0001819	synonymous_variant	9126	exon14			AGAACTGGACAGA	AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.1353G>A	chr10.hg19:g.112349410G>A		718.0	0.0		720.0	176.0	NM_005445	A8K156|O60464|Q5T482	Silent	SNP	ENST00000361804.4	hg19	CCDS31285.1																																																																																			.	.		0.279	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		A	112349410	G	A	112349410	2	1	18	1	0	0	0	0	0	0	0	1	14799	1335	47	3		3	SMC3	10	112349410	Silent	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	18537430	112349410	23185337	41	1565										
TACC2	10579	hgsc.bcm.edu	37	chr10	123845998	123845998	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	accagtggactccatgccatGcctggaccggatgccacttc	10	15	0	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr10:123845998G>T	ENST00000369005.1	+	4	4323	c.3983G>T	c.(3982-3984)tGc>tTc	p.C1328F	TACC2_ENST00000515603.1_Missense_Mutation_p.C1328F|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Missense_Mutation_p.C1328F|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000334433.3_Missense_Mutation_p.C1328F|TACC2_ENST00000453444.2_Missense_Mutation_p.C1328F	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1328					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TCCATGCCATGCCTGGACCGG	0.612																																					p.C1328F		Atlas-SNP	.											.	TACC2	271	.	0			c.G3983T						.						68	56	60					10																	123845998		2203	4300	6503	SO:0001583	missense	10579	exon4			TGCCATGCCTGGA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.3983G>T	chr10.hg19:g.123845998G>T	ENSP00000358001:p.Cys1328Phe	80.0	0.0		74.0	14.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	hg19	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.165033	0.00318	.	.	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.03242	4.03;4.1;4.0;4.03;4.1	4.11	1.84	0.25277	.	0.271361	0.19922	N	0.103077	T	0.01835	0.0058	N	0.14661	0.345	0.25968	N	0.982536	B;B;B	0.18461	0.028;0.028;0.028	B;B;B	0.11329	0.006;0.006;0.006	T	0.47674	-0.9099	10	0.06891	T	0.86	-2.826	5.909	0.19016	0.7668:0.0:0.2332:0.0	.	1328;1328;1328	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	F	1328;1328;1328;1328;1328;1318	ENSP00000358001:C1328F;ENSP00000424467:C1328F;ENSP00000427618:C1328F;ENSP00000334280:C1328F;ENSP00000395048:C1328F	ENSP00000334280:C1328F	C	+	2	0	TACC2	123835988	0.439000	0.25610	1.000000	0.80357	0.123000	0.20343	0.184000	0.16939	0.705000	0.31890	-0.390000	0.06520	TGC	.	.		0.612	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123845998	G	T	123845998	3	4	18	1	0	0	0	0	1	0	0	0	15517	1319	46	3	3993	3	TACC2	10	123845998	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	11496588	123845998	11688749	42	1566										
SWAP70	23075	hgsc.bcm.edu	37	chr11	9754136	9754136	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tccaccacacaaagaagcccGccagcgtcggaaagaactcc	8	16	0	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr11:9754136G>A	ENST00000318950.6	+	7	1062	c.959G>A	c.(958-960)cGc>cAc	p.R320H	SWAP70_ENST00000447399.2_Missense_Mutation_p.R262H	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	320					isotype switching (GO:0045190)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	11				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		AAAGAAGCCCGCCAGCGTCGG	0.502																																					p.R320H		Atlas-SNP	.											SWAP70,NS,carcinoma,0,1	SWAP70	40	.	0			c.G959A						.						27	28	28					11																	9754136		2199	4292	6491	SO:0001583	missense	23075	exon7			AAGCCCGCCAGCG	AB014540	CCDS31426.1, CCDS73257.1	11p15	2013-01-10			ENSG00000133789	ENSG00000133789		"Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	17070	protein-coding gene	gene with protein product		604762				9734811, 10681448	Standard	XM_005252829		Approved	KIAA0640, SWAP-70	uc001mhw.3	Q9UH65	OTTHUMG00000165865	ENST00000318950.6:c.959G>A	chr11.hg19:g.9754136G>A	ENSP00000315630:p.Arg320His	262.0	0.0		311.0	148.0	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	hg19	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.039675	0.93630	.	.	ENSG00000133789	ENST00000447399;ENST00000318950;ENST00000534662	T;T;T	0.31510	1.88;1.49;3.1	5.26	5.26	0.73747	.	0.051447	0.85682	D	0.000000	T	0.53417	0.1795	L	0.54323	1.7	0.53688	D	0.999974	D;D;D	0.89917	1.0;1.0;1.0	P;P;D	0.83275	0.902;0.886;0.996	T	0.54523	-0.8281	10	0.66056	D	0.02	-7.7113	18.8921	0.92408	0.0:0.0:1.0:0.0	.	262;320;262	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	H	262;320;171	ENSP00000399056:R262H;ENSP00000315630:R320H;ENSP00000435587:R171H	ENSP00000315630:R320H	R	+	2	0	SWAP70	9710712	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	9.455000	0.97625	2.439000	0.82584	0.563000	0.77884	CGC	.	.		0.502	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055		A	9754136	G	A	9754136	3	1	18	1	0	0	0	0	1	0	0	0	15440	1087	38	1	985	1	SWAP70	11	9754136	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10		9754136	125252380	43	1567										
ACRBP	57121	hgsc.bcm.edu	37	chr12	6747504	6747504	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ctggctccatcgaagcacaaCgtcctcacttttgccagggc	9	15	1	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr12:6747504C>T	ENST00000329858.4	-	0	0				ACRBP_ENST00000542357.1_5'Flank|ACRBP_ENST00000414226.2_Missense_Mutation_p.V493I|ACRBP_ENST00000229243.2_Missense_Mutation_p.V526I|LPAR5_ENST00000540335.1_5'Flank	NM_020400.5	NP_065133.1	Q9H1C0	LPAR5_HUMAN	lysophosphatidic acid receptor 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V526I(1)		endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7						CGAAGCACAACGTCCTCACTT	0.557																																					p.V526I	NSCLC(74;891 2312 37538)	Atlas-SNP	.											ACRBP,caecum,carcinoma,0,1	ACRBP	52	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1576A						.						135	109	118					12																	6747504		2203	4300	6503	SO:0001631	upstream_gene_variant	84519	exon10			GCACAACGTCCTC	AJ272207	CCDS8553.1	12p13.31	2012-08-08	2008-04-11	2008-04-11		ENSG00000184574		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	13307	protein-coding gene	gene with protein product		606926	"G protein-coupled receptor 92"	GPR93, GPR92		11062477, 11574155, 16774927, 16651401	Standard	NM_020400		Approved	KPG_010, LPA5	uc009zer.2	Q9H1C0			chr12.hg19:g.6747504C>T	Exception_encountered	78.0	0.0		75.0	16.0	NM_032489		Missense_Mutation	SNP	ENST00000329858.4	hg19	CCDS8553.1	.	.	.	.	.	.	.	.	.	.	C	0.686	-0.796423	0.02862	.	.	ENSG00000111644	ENST00000229243;ENST00000414226	T;T	0.44083	0.93;0.93	4.7	-9.4	0.00616	.	2.277090	0.01801	N	0.032918	T	0.19005	0.0456	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09707	-1.0662	10	0.18710	T	0.47	-10.7213	3.7466	0.08551	0.0807:0.1952:0.3506:0.3736	.	493;526	E7EP66;Q8NEB7	.;ACRBP_HUMAN	I	526;493	ENSP00000229243:V526I;ENSP00000402725:V493I	ENSP00000229243:V526I	V	-	1	0	ACRBP	6617765	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-1.600000	0.02083	-2.147000	0.00799	-2.075000	0.00382	GTT	.	.		0.557	LPAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400699.1	NM_020400		T	6747504	C	T	6747504	1	4	18	0	1	0	0	0	0	0	0	0	170	536	19	1		1	ACRBP	12	6747504	5'Flank	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10		6747504	127104391	44	1568										
SYT10	341359	hgsc.bcm.edu	37	chr12	33560128	33560128	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gattttgacatcttcgttttGgttgccctcagagtcaactg	9	9	3	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr12:33560128G>C	ENST00000228567.3	-	3	969	c.673C>G	c.(673-675)Caa>Gaa	p.Q225E	SYT10_ENST00000535526.1_Missense_Mutation_p.Q44E|RP11-438D14.2_ENST00000561632.1_lincRNA|SYT10_ENST00000567656.1_5'Flank	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	225					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					TCTTCGTTTTGGTTGCCCTCA	0.383																																					p.Q225E		Atlas-SNP	.											.	SYT10	109	.	0			c.C673G						.						131	117	122					12																	33560128		2203	4300	6503	SO:0001583	missense	341359	exon3			CGTTTTGGTTGCC	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"Synaptotagmins"	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.673C>G	chr12.hg19:g.33560128G>C	ENSP00000228567:p.Gln225Glu	103.0	0.0		129.0	31.0	NM_198992	Q495U2	Missense_Mutation	SNP	ENST00000228567.3	hg19	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	G	0.568	-0.842346	0.02671	.	.	ENSG00000110975	ENST00000228567;ENST00000535526	T;T	0.49139	0.89;0.79	4.94	1.14	0.20703	.	0.714878	0.11459	U	0.561978	T	0.23014	0.0556	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27938	-1.0059	10	0.02654	T	1	.	6.6268	0.22835	0.0:0.0834:0.3088:0.6078	.	225	Q6XYQ8	SYT10_HUMAN	E	225;44	ENSP00000228567:Q225E;ENSP00000438691:Q44E	ENSP00000228567:Q225E	Q	-	1	0	SYT10	33451395	0.693000	0.27728	0.003000	0.11579	0.663000	0.39108	1.557000	0.36299	0.085000	0.17107	-0.457000	0.05445	CAA	.	.		0.383	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992		C	33560128	G	C	33560128	3	2	18	1	0	0	0	0	1	0	0	0	15481	1357	47	4	918	4	SYT10	12	33560128	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	26812624	33560128	100291767	45	1569										
POLE	5426	hgsc.bcm.edu	37	chr12	133254296	133254296	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tcagtaatgacaccgcccctCtgcagaacactaggaattaa	7	12	2	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr12:133254296C>T	ENST00000320574.5	-	7	631	c.588G>A	c.(586-588)caG>caA	p.Q196Q	POLE_ENST00000535270.1_Silent_p.Q169Q	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	196					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	CACCGCCCCTCTGCAGAACAC	0.498								DNA polymerases (catalytic subunits)																													p.Q196Q		Atlas-SNP	.											.	POLE	416	.	0			c.G588A						.						83	79	80					12																	133254296		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon7			GCCCCTCTGCAGA		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.588G>A	chr12.hg19:g.133254296C>T		162.0	0.0		108.0	77.0	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	hg19	CCDS9278.1																																																																																			.	.		0.498	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		T	133254296	C	T	133254296	2	4	18	1	0	0	0	0	0	0	0	1	12205	912	32	3		3	POLE	12	133254296	Silent	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	99694168	133254296	597599	46	1570										
RASL11A	387496	hgsc.bcm.edu	37	chr13	27847361	27847361	+	Frame_Shift_Del	DEL	T	T	-													0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	aacaagggggaccttttgcaTgcccggcaggtgcagacaca							TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr13:27847361delT	ENST00000241463.4	+	4	1077	c.459delT	c.(457-459)catfs	p.H153fs	RASL11A_ENST00000480803.1_3'UTR	NM_206827.1	NP_996563.1			RAS-like, family 11, member A											breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	10		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0173)|GBM - Glioblastoma multiforme(144;0.0557)|OV - Ovarian serous cystadenocarcinoma(117;0.152)|Epithelial(112;0.164)		ACCTTTTGCATGCCCGGCAGG	0.537																																					p.H153fs		Atlas-Indel,Pindel	.											.	RASL11A	26	.	0			c.458delA						.						73	61	65					13																	27847361		2203	4300	6503	SO:0001589	frameshift_variant	387496	exon4			.	AY439004	CCDS9321.1	13q12.2	2014-05-09			ENSG00000122035	ENSG00000122035			23802	protein-coding gene	gene with protein product		612403				15033445	Standard	NM_206827		Approved		uc001urd.1	Q6T310	OTTHUMG00000016627	ENST00000241463.4:c.459delT	chr13.hg19:g.27847361delT	ENSP00000241463:p.His153fs	264.0	0.0		168.0	122.0	NM_206827		Frame_Shift_Del	DEL	ENST00000241463.4	hg19	CCDS9321.1																																																																																			.	.		0.537	RASL11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044265.2	NM_206827		-	27847361	T	-	27847361	7	5	18	1	0	1	0	1	0	0	0	0	13096	1461	51	0	473	0	RASL11A	13	27847361	Frame_Shift_Del	DEL	T	TCGA-2Y-A9H8-01A-11D-A38X-10		27847361	87322517	47	1571										
OR4K17	390436	hgsc.bcm.edu	37	chr14	20586326	20586326	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ctcctacagtctgatcctcaTaaccattaagaaccactctc	3	15	3	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr14:20586326T>A	ENST00000315543.4	+	1	761	c.761T>A	c.(760-762)aTa>aAa	p.I254K		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		CTGATCCTCATAACCATTAAG	0.418																																					p.I254K		Atlas-SNP	.											.	OR4K17	58	.	0			c.T761A						.						148	143	145					14																	20586326		2203	4300	6503	SO:0001583	missense	390436	exon1			TCCTCATAACCAT		CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"GPCR / Class A : Olfactory receptors"	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.761T>A	chr14.hg19:g.20586326T>A	ENSP00000319197:p.Ile254Lys	64.0	0.0		159.0	7.0	NM_001004715	Q6IF12	Missense_Mutation	SNP	ENST00000315543.4	hg19	CCDS32030.1	.	.	.	.	.	.	.	.	.	.	.	7.168	0.587126	0.13812	.	.	ENSG00000176230	ENST00000315543	T	0.36878	1.23	2.86	-1.85	0.07784	GPCR, rhodopsin-like superfamily (1);	0.285191	0.18470	U	0.140259	T	0.26159	0.0638	L	0.46567	1.45	0.09310	N	1	B	0.28055	0.199	B	0.32342	0.144	T	0.22103	-1.0226	10	0.62326	D	0.03	.	4.2351	0.10621	0.0:0.2304:0.3373:0.4323	.	226	Q8NGC6	OR4KH_HUMAN	K	254	ENSP00000319197:I254K	ENSP00000319197:I254K	I	+	2	0	OR4K17	19656166	0.000000	0.05858	0.007000	0.13788	0.375000	0.29983	-2.093000	0.01353	-0.085000	0.12573	0.332000	0.21555	ATA	.	.		0.418	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1			A	20586326	T	A	20586326	3	1	18	1	0	0	0	0	1	0	0	0	11080	1406	49	4	763	4	OR4K17	14	20586326	Missense_Mutation	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10		20586326	86763214	48	1572										
KIAA1370	56204	hgsc.bcm.edu	37	chr15	52879386	52879386	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	aggaggtactcgataaccccTtttaccaagggactctaaag	9	10	1	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr15:52879386T>C	ENST00000261844.7	-	11	2991	c.2839A>G	c.(2839-2841)Agg>Ggg	p.R947G	RP11-23N2.4_ENST00000566344.1_RNA|FAM214A_ENST00000546305.2_Missense_Mutation_p.R954G|RP11-23N2.4_ENST00000562062.1_RNA	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	947																	CGATAACCCCTTTTACCAAGG	0.333																																					p.R947G		Atlas-SNP	.											.	.	.	.	0			c.A2839G						.						132	123	126					15																	52879386		1833	4080	5913	SO:0001583	missense	56204	exon11			AACCCCTTTTACC	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"KIAA1370"	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.2839A>G	chr15.hg19:g.52879386T>C	ENSP00000261844:p.Arg947Gly	143.0	0.0		132.0	6.0	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	hg19	CCDS45263.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.339121	0.81911	.	.	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T	0.33654	1.4;1.4	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.51126	0.1656	L	0.39898	1.24	0.80722	D	1	D;D	0.65815	0.995;0.991	D;D	0.73380	0.98;0.955	T	0.53330	-0.8454	10	0.66056	D	0.02	.	15.0489	0.71850	0.0:0.0:0.0:1.0	.	954;947	F5H8G0;Q32MH5	.;K1370_HUMAN	G	947;947;946;954	ENSP00000261844:R947G;ENSP00000443598:R954G	ENSP00000261844:R947G	R	-	1	2	KIAA1370	50666678	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.846000	0.69444	1.949000	0.56562	0.528000	0.53228	AGG	.	.		0.333	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		C	52879386	T	C	52879386	3	2	18	1	0	0	0	0	1	0	0	0	8235	1608	56	2	403	2	KIAA1370	15	52879386	Missense_Mutation	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10		52879386	49652006	49	1573										
PDE8A	5151	hgsc.bcm.edu	37	chr15	85652345	85652345	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ctagacgtcaaagctgttgcCtcccgtgcaactgaaggtga	11	11	1	3			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr15:85652345C>T	ENST00000310298.4	+	13	1350	c.1098C>T	c.(1096-1098)gcC>gcT	p.A366A	PDE8A_ENST00000557957.1_Silent_p.A294A|PDE8A_ENST00000339708.5_Silent_p.A320A|PDE8A_ENST00000557819.2_3'UTR|PDE8A_ENST00000394553.1_Silent_p.A366A			O60658	PDE8A_HUMAN	phosphodiesterase 8A	366					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	AAGCTGTTGCCTCCCGTGCAA	0.433																																					p.A366A		Atlas-SNP	.											.	PDE8A	50	.	0			c.C1098T						.						99	93	95					15																	85652345		2203	4299	6502	SO:0001819	synonymous_variant	5151	exon12			TGTTGCCTCCCGT	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"Phosphodiesterases"	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.1098C>T	chr15.hg19:g.85652345C>T		333.0	0.0		342.0	240.0	NM_002605	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Silent	SNP	ENST00000310298.4	hg19	CCDS10336.1																																																																																			.	.		0.433	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		T	85652345	C	T	85652345	2	4	18	1	0	0	0	0	0	0	0	1	11662	668	24	3		3	PDE8A	15	85652345	Silent	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	32772959	85652345	16879047	50	1574										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94901809	94901809	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gacattgaagtgtggggaaaGgacaacaaaaagcatgagga	14	4	0	2	rs534609623		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr15:94901809G>T	ENST00000357742.4	+	9	1269	c.1269G>T	c.(1267-1269)aaG>aaT	p.K423N	MCTP2_ENST00000331706.4_Missense_Mutation_p.K11N|MCTP2_ENST00000451018.3_Missense_Mutation_p.K423N|MCTP2_ENST00000557742.1_Missense_Mutation_p.K11N|MCTP2_ENST00000543482.1_3'UTR	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	423	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			TGTGGGGAAAGGACAACAAAA	0.507																																					p.K423N		Atlas-SNP	.											.	MCTP2	122	.	0			c.G1269T						.						126	109	115					15																	94901809		2197	4298	6495	SO:0001583	missense	55784	exon9			GGGAAAGGACAAC	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.1269G>T	chr15.hg19:g.94901809G>T	ENSP00000350377:p.Lys423Asn	170.0	0.0		142.0	86.0	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	hg19	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.334768	0.81801	.	.	ENSG00000140563	ENST00000451018;ENST00000331706;ENST00000357742	T;T;T	0.72282	-0.4;-0.64;-0.4	5.78	3.91	0.45181	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.044071	0.85682	D	0.000000	T	0.81602	0.4857	M	0.76170	2.325	0.52501	D	0.999953	D;D;D	0.89917	0.961;1.0;1.0	P;D;D	0.97110	0.882;0.999;1.0	T	0.81611	-0.0854	10	0.72032	D	0.01	.	9.7826	0.40658	0.2025:0.0:0.7975:0.0	.	423;11;423	Q6DN12-2;Q6DN12-4;Q6DN12	.;.;MCTP2_HUMAN	N	423;11;423	ENSP00000395109:K423N;ENSP00000329646:K11N;ENSP00000350377:K423N	ENSP00000329646:K11N	K	+	3	2	MCTP2	92702813	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.433000	0.44793	0.790000	0.33803	0.650000	0.86243	AAG	.	.		0.507	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		T	94901809	G	T	94901809	3	4	18	1	0	0	0	0	1	0	0	0	9410	991	35	3	1303	3	MCTP2	15	94901809	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	9249464	94901809	7629583	51	1575										
WDR90	197335	hgsc.bcm.edu	37	chr16	706396	706396	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	cacctgggcttcctggacacGctgtcccgggtgtaccacat	11	15	0	0	rs577796944		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr16:706396G>A	ENST00000293879.4	+	18	2061	c.2061G>A	c.(2059-2061)acG>acA	p.T687T	WDR90_ENST00000549091.1_Silent_p.T687T|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	687										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				TCCTGGACACGCTGTCCCGGG	0.697																																					p.T687T		Atlas-SNP	.											.	WDR90	107	.	0			c.G2061A						.						13	17	16					16																	706396		2119	4223	6342	SO:0001819	synonymous_variant	197335	exon18			GGACACGCTGTCC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.2061G>A	chr16.hg19:g.706396G>A		90.0	0.0		76.0	26.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	hg19	CCDS42092.1																																																																																			.	.		0.697	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		A	706396	G	A	706396	2	1	18	1	0	0	0	0	0	0	0	1	17352	1074	38	1		1	WDR90	16	706396	Silent	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10		706396	89648357	52	1576										
GGA2	23062	hgsc.bcm.edu	37	chr16	23486224	23486224	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ggggagtgaaattgtacttaCtgggcttaacagactccaaa	11	7	0	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr16:23486224C>G	ENST00000309859.4	-	14	1533		c.e14+1		GGA2_ENST00000569182.1_5'Flank|GGA2_ENST00000567468.1_Intron	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2						intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		ATTGTACTTACTGGGCTTAAC	0.478																																					.		Atlas-SNP	.											.	GGA2	49	.	0			c.1450+1G>C						.						57	64	62					16																	23486224		2197	4300	6497	SO:0001630	splice_region_variant	23062	exon15			TACTTACTGGGCT	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.1450+1G>C	chr16.hg19:g.23486224C>G		410.0	1.0		307.0	199.0	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Splice_Site	SNP	ENST00000309859.4	hg19	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	C	18.18	3.566366	0.65651	.	.	ENSG00000103365	ENST00000309859	.	.	.	5.02	5.02	0.67125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2485	0.66004	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GGA2	23393725	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	5.050000	0.64251	2.509000	0.84616	0.549000	0.68633	.	.	.		0.478	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1		Intron	G	23486224	C	G	23486224	5	3	18	1	0	0	0	0	0	0	1	0	6361	579	20	4	406	4	GGA2	16	23486224	Splice_Site	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	22779828	23486224	66868529	53	1577										
SF3B3	23450	hgsc.bcm.edu	37	chr16	70601427	70601427	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	aagaagaagttactccgaaaAtgtgagaataaggtaagtgt	11	3	0	3			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr16:70601427A>T	ENST00000302516.5	+	21	3151	c.2940A>T	c.(2938-2940)aaA>aaT	p.K980N		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	980					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				TACTCCGAAAATGTGAGAATA	0.507																																					p.K980N		Atlas-SNP	.											.	SF3B3	99	.	0			c.A2940T						.						148	138	142					16																	70601427		2198	4300	6498	SO:0001583	missense	23450	exon21			CCGAAAATGTGAG	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.2940A>T	chr16.hg19:g.70601427A>T	ENSP00000305790:p.Lys980Asn	162.0	0.0		118.0	79.0	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	hg19	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.444983	0.83993	.	.	ENSG00000189091	ENST00000302516	T	0.50548	0.74	6.17	-5.99	0.02213	WD40/YVTN repeat-like-containing domain (1);Cleavage/polyadenylation specificity factor, A subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.72534	0.3472	H	0.94222	3.51	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	T	0.81239	-0.1023	10	0.72032	D	0.01	.	17.3479	0.87314	0.5672:0.0:0.4328:0.0	.	980	Q15393	SF3B3_HUMAN	N	980	ENSP00000305790:K980N	ENSP00000305790:K980N	K	+	3	2	SF3B3	69158928	0.995000	0.38212	0.864000	0.33941	0.901000	0.52897	0.346000	0.19997	-0.911000	0.03843	-0.854000	0.03029	AAA	.	.		0.507	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		T	70601427	A	T	70601427	3	4	18	1	0	0	0	0	1	0	0	0	14167	98	4	4	3018	4	SF3B3	16	70601427	Missense_Mutation	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10	47115203	70601427	19753326	54	1578										
ZNF286B	729288	hgsc.bcm.edu	37	chr17	18565670	18565670	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ttcccacattcttgacatttAtaaggtttctctccagtatg	5	10	2	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr17:18565670A>G	ENST00000545289.1	-	5	1399	c.1149T>C	c.(1147-1149)taT>taC	p.Y383Y	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	383					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						CTTGACATTTATAAGGTTTCT	0.378																																					p.Y383Y		Atlas-SNP	.											.	ZNF286B	75	.	0			c.T1149C						.						9	10	9					17																	18565670		688	1572	2260	SO:0001819	synonymous_variant	729288	exon5			ACATTTATAAGGT		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"Zinc fingers, C2H2-type"	33241	protein-coding gene	gene with protein product	"zinc finger protein 590"		"zinc finger protein 286-like", "zinc finger 286C pseudogene"	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.1149T>C	chr17.hg19:g.18565670A>G		233.0	0.0		235.0	100.0	NM_001145045		Silent	SNP	ENST00000545289.1	hg19	CCDS58523.1																																																																																			.	.		0.378	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047		G	18565670	A	G	18565670	2	3	18	1	0	0	0	0	0	0	0	1	17839	456	16	2		2	ZNF286B	17	18565670	Silent	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10		18565670	62629540	55	1579										
KRT38	8687	hgsc.bcm.edu	37	chr17	39597054	39597054	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gccaaaaggcacatgggggcAatgttggcctctgccccagg	14	12	1	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr17:39597054A>G	ENST00000246646.3	-	1	119	c.120T>C	c.(118-120)atT>atC	p.I40I		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	40	Head.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				ACATGGGGGCAATGTTGGCCT	0.637																																					p.I40I		Atlas-SNP	.											.	KRT38	63	.	0			c.T120C						.						50	52	52					17																	39597054		2203	4300	6503	SO:0001819	synonymous_variant	8687	exon1			GGGGGCAATGTTG	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"-", "Intermediate filaments type I, keratins (acidic)"	6456	protein-coding gene	gene with protein product		604542	"keratin, hair, acidic, 8"	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.120T>C	chr17.hg19:g.39597054A>G		126.0	0.0		146.0	38.0	NM_006771	A2RRM5|Q6A164	Silent	SNP	ENST00000246646.3	hg19	CCDS11392.1																																																																																			.	.		0.637	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		G	39597054	A	G	39597054	2	3	18	1	0	0	0	0	0	0	0	1	8484	126	5	2		2	KRT38	17	39597054	Silent	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10	21031384	39597054	41598156	56	1580										
KLHL11	55175	hgsc.bcm.edu	37	chr17	40021606	40021606	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gccgccgccgccgccgccgcCactgccgcagccgccatctt	11	23	1	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr17:40021606C>T	ENST00000319121.3	-	1	78	c.18G>A	c.(16-18)gtG>gtA	p.V6V	ACLY_ENST00000588779.1_5'Flank	NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	6										NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				ccgccgccgccactgccgcag	0.692																																					p.V6V		Atlas-SNP	.											.	KLHL11	44	.	0			c.G18A						.						2	2	2					17																	40021606		624	1581	2205	SO:0001819	synonymous_variant	55175	exon1			CGCCGCCACTGCC		CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"Kelch-like", "BTB/POZ domain containing"	19008	protein-coding gene	gene with protein product			"kelch-like 11 (Drosophila)"				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.18G>A	chr17.hg19:g.40021606C>T		17.0	0.0		24.0	5.0	NM_018143		Silent	SNP	ENST00000319121.3	hg19	CCDS11411.1																																																																																			.	.		0.692	KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143		T	40021606	C	T	40021606	2	4	18	1	0	0	0	0	0	0	0	1	8376	581	21	3		3	KLHL11	17	40021606	Silent	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	424552	40021606	41173604	57	1581										
HDAC5	10014	hgsc.bcm.edu	37	chr17	42157529	42157529	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	cagatgtccttcaacagcatCaaacccggcggagactagga	10	12	2	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr17:42157529C>G	ENST00000393622.2	-	23	3221	c.2890G>C	c.(2890-2892)Gat>Cat	p.D964H	HDAC5_ENST00000336057.5_Missense_Mutation_p.D879H|HDAC5_ENST00000586802.1_Missense_Mutation_p.D964H|HDAC5_ENST00000225983.6_Missense_Mutation_p.D965H	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	964	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		TCAACAGCATCAAACCCGGCG	0.562																																					p.D965H		Atlas-SNP	.											.	HDAC5	67	.	0			c.G2893C						.						153	120	131					17																	42157529		2203	4300	6503	SO:0001583	missense	10014	exon23			CAGCATCAAACCC	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.2890G>C	chr17.hg19:g.42157529C>G	ENSP00000377244:p.Asp964His	63.0	0.0		67.0	18.0	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	hg19	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.559032	0.86335	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	D;D;D	0.91843	-2.92;-2.92;-2.92	4.92	4.92	0.64577	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	D	0.98204	0.9406	H	0.99874	4.875	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99585	1.0974	10	0.87932	D	0	-13.6106	17.0541	0.86529	0.0:1.0:0.0:0.0	.	879;965;964	Q9UQL6-2;Q9UQL6-3;Q9UQL6	.;.;HDAC5_HUMAN	H	965;964;879	ENSP00000225983:D965H;ENSP00000377244:D964H;ENSP00000337290:D879H	ENSP00000225983:D965H	D	-	1	0	HDAC5	39513055	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.609000	0.82925	2.560000	0.86352	0.655000	0.94253	GAT	.	.		0.562	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		G	42157529	C	G	42157529	3	3	18	1	0	0	0	0	1	0	0	0	7019	826	29	4	498	4	HDAC5	17	42157529	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	2135923	42157529	39037681	58	1582										
ACE	1636	hgsc.bcm.edu	37	chr17	61568652	61568652	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gcccgtgcctcctgagttctGgaacaagtcgatgctggaga	13	11	1	2			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr17:61568652G>A	ENST00000290866.4	+	19	2846	c.2822G>A	c.(2821-2823)tGg>tAg	p.W941*	ACE_ENST00000577647.1_Nonsense_Mutation_p.W367*|ACE_ENST00000290863.6_Nonsense_Mutation_p.W367*|ACE_ENST00000490216.2_Nonsense_Mutation_p.W367*|ACE_ENST00000421982.2_Nonsense_Mutation_p.W187*|ACE_ENST00000413513.3_Nonsense_Mutation_p.W367*|ACE_ENST00000428043.1_Nonsense_Mutation_p.W941*	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	941	Peptidase M2 2.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	CCTGAGTTCTGGAACAAGTCG	0.607																																					p.W941X		Atlas-SNP	.											.	ACE	187	.	0			c.G2822A						.						64	65	65					17																	61568652		2203	4300	6503	SO:0001587	stop_gained	1636	exon19			AGTTCTGGAACAA	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.2822G>A	chr17.hg19:g.61568652G>A	ENSP00000290866:p.Trp941*	62.0	0.0		84.0	17.0	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Nonsense_Mutation	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	G	38	6.911983	0.97928	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863;ENST00000413513;ENST00000421982	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.5004	19.1504	0.93485	0.0:0.0:1.0:0.0	.	.	.	.	X	941;941;367;367;187	.	ENSP00000290863:W367X	W	+	2	0	ACE	58922384	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.864000	0.99589	2.498000	0.84270	0.561000	0.74099	TGG	.	.		0.607	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			A	61568652	G	A	61568652	4	1	18	1	0	0	0	0	0	1	0	0	136	1357	47	3	3099	3	ACE	17	61568652	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	19411123	61568652	19626558	59	1583										
ERN1	2081	hgsc.bcm.edu	37	chr17	62135324	62135324	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gacacggtggtaggtgcgttTtctgaagtctggtcaaccag	14	8	3	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr17:62135324T>G	ENST00000433197.3	-	12	1331	c.1236A>C	c.(1234-1236)gaA>gaC	p.E412D		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						TAGGTGCGTTTTCTGAAGTCT	0.557																																					p.E412D		Atlas-SNP	.											.	ERN1	102	.	0			c.A1236C						.						45	48	47					17																	62135324		2014	4164	6178	SO:0001583	missense	2081	exon12			TGCGTTTTCTGAA	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"inositol-requiring enzyme 1"	604033	"ER to nucleus signalling 1"			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.1236A>C	chr17.hg19:g.62135324T>G	ENSP00000401445:p.Glu412Asp	99.0	0.0		72.0	28.0	NM_001433		Missense_Mutation	SNP	ENST00000433197.3	hg19	CCDS45762.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.769114	0.31320	.	.	ENSG00000178607	ENST00000433197	T	0.59906	0.23	5.37	-1.2	0.09554	.	0.733470	0.13846	N	0.358718	T	0.35128	0.0921	N	0.22421	0.69	0.19300	N	0.999977	B	0.02656	0.0	B	0.01281	0.0	T	0.16778	-1.0391	10	0.20519	T	0.43	-2.3521	6.6717	0.23072	0.0:0.4218:0.1389:0.4394	.	412	O75460	ERN1_HUMAN	D	412	ENSP00000401445:E412D	ENSP00000401445:E412D	E	-	3	2	ERN1	59489056	0.851000	0.29673	0.122000	0.21767	0.800000	0.45204	0.123000	0.15708	-0.260000	0.09418	0.459000	0.35465	GAA	.	.		0.557	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		G	62135324	T	G	62135324	3	3	18	1	0	0	0	0	1	0	0	0	5239	1838	64	5	1741	5	ERN1	17	62135324	Missense_Mutation	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10	566672	62135324	19059886	60	1584										
CANT1	124583	hgsc.bcm.edu	37	chr17	76993228	76993228	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tccatgcctctccccttctcCgccaggtgggactccaggac	9	18	2	0	rs149367726		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr17:76993228C>T	ENST00000302345.2	-	2	971	c.477G>A	c.(475-477)gcG>gcA	p.A159A	CANT1_ENST00000591732.1_5'Flank|CANT1_ENST00000591773.1_Silent_p.A159A|CANT1_ENST00000392446.5_Silent_p.A159A	NM_001159773.1|NM_138793.3	NP_001153245.1|NP_620148.1	Q8WVQ1	CANT1_HUMAN	calcium activated nucleotidase 1	159					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|proteoglycan biosynthetic process (GO:0030166)|signal transduction (GO:0007165)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|signal transducer activity (GO:0004871)|uridine-diphosphatase activity (GO:0045134)		CANT1/ETV4(3)	cervix(1)|endometrium(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)	16			BRCA - Breast invasive adenocarcinoma(99;0.0362)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			TCCCCTTCTCCGCCAGGTGGG	0.567			T	ETV4	prostate																																p.A159A		Atlas-SNP	.		Dom	yes		17	17q25	124583	calcium activated nucleotidase 1		E	.	CANT1	39	.	0			c.G477A						.	C	,,	1,4405	2.1+/-5.4	0,1,2202	120	121	121		477,477,477	-10.5	0.2	17	dbSNP_134	121	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CANT1	NM_001159772.1,NM_001159773.1,NM_138793.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	159/402,159/402,159/402	76993228	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	124583	exon4			CTTCTCCGCCAGG	AJ312208	CCDS11760.1	17q25.3	2008-02-05	2004-10-12	2004-10-15		ENSG00000171302			19721	protein-coding gene	gene with protein product	"Soluble Ca-Activated Nucleotidase, isozyme 1"	613165				12167635	Standard	NM_138793		Approved	SHAPY, SCAN-1	uc002jwk.3	Q8WVQ1		ENST00000302345.2:c.477G>A	chr17.hg19:g.76993228C>T		116.0	0.0		113.0	31.0	NM_001159772	B4DJ54|Q7Z2J7|Q8NG05|Q8NHP0|Q9BSD5	Silent	SNP	ENST00000302345.2	hg19	CCDS11760.1																																																																																			.	C|1.000;T|0.000		0.567	CANT1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437723.2	NM_138793		T	76993228	C	T	76993228	2	4	18	1	0	0	0	0	0	0	0	1	2619	639	23	1		1	CANT1	17	76993228	Silent	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	14857904	76993228	4201982	61	1585										
MEX3C	51320	hgsc.bcm.edu	37	chr18	48703513	48703513	+	5'UTR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tcattgagctctatatagttTcctgtacgcatggcaatatg	8	8	2	1	rs140545981		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr18:48703513T>A	ENST00000591040.1	-	0	476							Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		CTATATAGTTTCCTGTACGCA	0.453																																					p.G396G		Atlas-SNP	.											.	MEX3C	77	.	0			c.A1188T						.	T		0,4406		0,0,2203	131	123	126		1188	3.5	1	18	dbSNP_134	126	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MEX3C	NM_016626.4		0,1,6502	AA,AT,TT		0.0116,0.0,0.0077		396/660	48703513	1,13005	2203	4300	6503	SO:0001623	5_prime_UTR_variant	51320	exon2			ATAGTTTCCTGTA	BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	28040	protein-coding gene	gene with protein product		611005	"ring finger and KH domain containing 2", "mex-3 homolog C (C. elegans)"	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693	ENST00000591040.1:c.-323A>T	chr18.hg19:g.48703513T>A		42.0	0.0		74.0	36.0	NM_016626	A1L022|Q9NZE3	Silent	SNP	ENST00000591040.1	hg19																																																																																				.	T|1.000;A|0.000		0.453	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000449559.1	NM_016626		A	48703513	T	A	48703513	1	1	18	0	1	0	0	0	0	0	0	0	9520	1770	62	4		4	MEX3C	18	48703513	5'UTR	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10		48703513	29373735	62	1586										
PTBP1	5725	hgsc.bcm.edu	37	chr19	806459	806459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ggcccccctggccatcccctCggcggcggcggcagctgcgg	16	19	0	0	rs375905582		TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr19:806459C>T	ENST00000349038.4	+	9	1017	c.944C>T	c.(943-945)tCg>tTg	p.S315L	PTBP1_ENST00000356948.6_Missense_Mutation_p.S341L|MIR4745_ENST00000577608.1_RNA|PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000394601.4_Missense_Mutation_p.S334L	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	315					alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCATCCCCTCGGCGGCGGCG	0.697																																					p.S341L		Atlas-SNP	.											.	PTBP1	43	.	0			c.C1022T						.						14	16	15					19																	806459		2188	4269	6457	SO:0001583	missense	5725	exon10			TCCCCTCGGCGGC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"RNA binding motif (RRM) containing"	9583	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein I"	600693	"polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.944C>T	chr19.hg19:g.806459C>T	ENSP00000014112:p.Ser315Leu	196.0	0.0		205.0	58.0	NM_002819	Q9BUQ0	Missense_Mutation	SNP	ENST00000349038.4	hg19	CCDS32859.1	.	.	.	.	.	.	.	.	.	.	C	6.549	0.469532	0.12461	.	.	ENSG00000011304	ENST00000356948;ENST00000394601;ENST00000349038	T;T;T	0.47528	0.84;0.86;1.13	4.2	3.16	0.36331	.	0.506824	0.20455	N	0.092014	T	0.30978	0.0782	L	0.43152	1.355	0.22266	N	0.999248	B;B;B	0.34399	0.003;0.039;0.452	B;B;B	0.23716	0.002;0.008;0.048	T	0.13282	-1.0515	10	0.10902	T	0.67	-3.3526	9.5598	0.39362	0.0:0.8929:0.0:0.1071	.	315;334;341	P26599;P26599-2;Q9BUQ0	PTBP1_HUMAN;.;.	L	341;334;315	ENSP00000349428:S341L;ENSP00000408096:S334L;ENSP00000014112:S315L	ENSP00000014112:S315L	S	+	2	0	PTBP1	757459	0.997000	0.39634	0.024000	0.17045	0.015000	0.08874	3.978000	0.56881	0.747000	0.32809	0.563000	0.77884	TCG	.	.		0.697	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1			T	806459	C	T	806459	3	4	18	1	0	0	0	0	1	0	0	0	12737	893	31	1	1060	1	PTBP1	19	806459	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10		806459	58322524	63	1587										
APBA3	9546	hgsc.bcm.edu	37	chr19	3759745	3759745	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	gcaccgtctccagccagggtTccggggaactgcttgagctc	13	14	1	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr19:3759745T>G	ENST00000316757.3	-	2	718	c.518A>C	c.(517-519)gAa>gCa	p.E173A	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	173					in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCCAGGGTTCCGGGGAACT	0.662																																					p.E173A		Atlas-SNP	.											.	APBA3	28	.	0			c.A518C						.						27	32	30					19																	3759745		2203	4297	6500	SO:0001583	missense	9546	exon2			CAGGGTTCCGGGG	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"X11-like 2"	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.518A>C	chr19.hg19:g.3759745T>G	ENSP00000315136:p.Glu173Ala	109.0	0.0		89.0	35.0	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	hg19	CCDS12110.1	.	.	.	.	.	.	.	.	.	.	T	14.98	2.695838	0.48202	.	.	ENSG00000011132	ENST00000316757	T	0.08102	3.13	4.69	4.69	0.59074	.	0.135912	0.28635	N	0.014652	T	0.17577	0.0422	L	0.34521	1.04	0.39725	D	0.971525	D	0.63880	0.993	D	0.74674	0.984	T	0.01743	-1.1283	10	0.62326	D	0.03	.	11.5285	0.50595	0.0:0.0:0.0:1.0	.	173	O96018	APBA3_HUMAN	A	173	ENSP00000315136:E173A	ENSP00000315136:E173A	E	-	2	0	APBA3	3710745	0.787000	0.28750	0.495000	0.27527	0.506000	0.33950	1.603000	0.36794	1.761000	0.52028	0.459000	0.35465	GAA	.	.		0.662	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2			G	3759745	T	G	3759745	3	3	18	1	0	0	0	0	1	0	0	0	758	1783	62	5	1249	5	APBA3	19	3759745	Missense_Mutation	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10	2953286	3759745	55369238	64	1588										
MUC16	94025	hgsc.bcm.edu	37	chr19	9074291	9074291	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	cctgtttgggtggtgatggtCactcctgaagattctgtcat	12	8	3	3			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr19:9074291C>A	ENST00000397910.4	-	3	13358	c.13155G>T	c.(13153-13155)gtG>gtT	p.V4385V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4387	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGTGATGGTCACTCCTGAAG	0.473																																					p.V4385V		Atlas-SNP	.											.	MUC16	4315	.	0			c.G13155T						.						134	132	132					19																	9074291		2053	4182	6235	SO:0001819	synonymous_variant	94025	exon3			GATGGTCACTCCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.13155G>T	chr19.hg19:g.9074291C>A		105.0	0.0		160.0	13.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9074291	C	A	9074291	2	1	18	1	0	0	0	0	0	0	0	1	9982	813	29	3		3	MUC16	19	9074291	Silent	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	5314546	9074291	50054692	65	1589										
CRTC1	23373	hgsc.bcm.edu	37	chr19	18870874	18870874	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	cctgatccccgccacccacaAcacaggggggtccctgcccg	10	20	0	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr19:18870874A>T	ENST00000321949.8	+	8	748	c.722A>T	c.(721-723)aAc>aTc	p.N241I	CRTC1_ENST00000594658.1_Missense_Mutation_p.N200I|CRTC1_ENST00000338797.6_Missense_Mutation_p.N257I|CRTC1_ENST00000601916.1_Missense_Mutation_p.N166I	NM_015321.2	NP_056136.2			CREB regulated transcription coactivator 1										CRTC1/MAML2(516)	NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	19						GCCACCCACAACACAGGGGGG	0.667																																					p.N257I		Atlas-SNP	.											.	CRTC1	88	.	0			c.A770T						.						99	113	108					19																	18870874		2203	4300	6503	SO:0001583	missense	23373	exon9			CCCACAACACAGG	AY040323	CCDS32963.1, CCDS42525.1	19p13	2012-07-31	2005-11-24	2005-11-24					16062	protein-coding gene	gene with protein product	"transducer of regulated cAMP response element-binding protein"	607536	"mucoepidermoid carcinoma translocated 1"	MECT1		12539049, 14536081, 14506290	Standard	NM_015321		Approved	KIAA0616, FLJ14027, TORC1	uc010ebv.3	Q6UUV9		ENST00000321949.8:c.722A>T	chr19.hg19:g.18870874A>T	ENSP00000323332:p.Asn241Ile	245.0	0.0		231.0	52.0	NM_001098482		Missense_Mutation	SNP	ENST00000321949.8	hg19	CCDS32963.1	.	.	.	.	.	.	.	.	.	.	a	16.44	3.124550	0.56613	.	.	ENSG00000105662	ENST00000262813;ENST00000338797;ENST00000321949	T;T	0.55588	0.51;0.51	4.59	4.59	0.56863	Transducer of regulated CREB activity, middle domain (1);	0.091344	0.85682	N	0.000000	T	0.51210	0.1661	M	0.64997	1.995	0.51012	D	0.999908	P;B;P	0.42785	0.79;0.427;0.63	B;B;B	0.42625	0.377;0.331;0.393	T	0.57429	-0.7813	10	0.87932	D	0	-21.4334	9.4489	0.38714	0.9124:0.0:0.0876:0.0	.	241;257;241	Q6UUV9-3;Q6UUV9-2;Q6UUV9	.;.;CRTC1_HUMAN	I	241;257;241	ENSP00000345001:N257I;ENSP00000323332:N241I	ENSP00000262813:N241I	N	+	2	0	CRTC1	18731874	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.961000	0.63681	1.719000	0.51432	0.375000	0.23000	AAC	.	.		0.667	CRTC1-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465151.3	NM_025021		T	18870874	A	T	18870874	3	4	18	1	0	0	0	0	1	0	0	0	3901	43	2	4	804	4	CRTC1	19	18870874	Missense_Mutation	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10	9796583	18870874	40258109	66	1590										
PPP5C	5536	hgsc.bcm.edu	37	chr19	46893387	46893387	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	agttccaccagttcacagcaGtggtgagtcacccctcaggg	11	13	3	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr19:46893387G>C	ENST00000012443.4	+	12	1538	c.1435G>C	c.(1435-1437)Gtg>Ctg	p.V479L	AC007193.8_ENST00000598616.1_RNA|PPP5C_ENST00000391919.1_Missense_Mutation_p.V351L	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	479	Catalytic.				cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		GTTCACAGCAGTGGTGAGTCA	0.637																																					p.V479L		Atlas-SNP	.											.	PPP5C	44	.	0			c.G1435C						.						121	96	105					19																	46893387		2203	4300	6503	SO:0001583	missense	5536	exon12			ACAGCAGTGGTGA		CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "Tetratricopeptide (TTC) repeat domain containing"	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.1435G>C	chr19.hg19:g.46893387G>C	ENSP00000012443:p.Val479Leu	112.0	0.0		131.0	34.0	NM_006247	Q16722|Q53XV2	Missense_Mutation	SNP	ENST00000012443.4	hg19	CCDS12684.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.915482	0.92178	.	.	ENSG00000011485	ENST00000012443;ENST00000451918;ENST00000391919	T;T	0.05319	3.46;3.46	5.46	5.46	0.80206	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);	0.000000	0.85682	D	0.000000	T	0.13884	0.0336	M	0.85542	2.76	0.80722	D	1	P;P	0.47841	0.899;0.901	B;B	0.39419	0.132;0.299	T	0.03103	-1.1072	10	0.59425	D	0.04	-21.0563	16.7989	0.85609	0.0:0.0:1.0:0.0	.	479;479	B2R6R6;P53041	.;PPP5_HUMAN	L	479;466;351	ENSP00000012443:V479L;ENSP00000375786:V351L	ENSP00000012443:V479L	V	+	1	0	PPP5C	51585227	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	9.107000	0.94261	2.566000	0.86566	0.563000	0.77884	GTG	.	.		0.637	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		C	46893387	G	C	46893387	3	2	18	1	0	0	0	0	1	0	0	0	12418	1029	36	4	1481	4	PPP5C	19	46893387	Missense_Mutation	SNP	G	TCGA-2Y-A9H8-01A-11D-A38X-10	28022513	46893387	12235596	67	1591										
SLC8A2	6543	hgsc.bcm.edu	37	chr19	47960453	47960453	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ccggcgccggtcatcagccgCgtggcctggatgcggtagaa	16	13	2	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr19:47960453C>T	ENST00000236877.6	-	3	1469	c.1074G>A	c.(1072-1074)acG>acA	p.T358T	SLC8A2_ENST00000542837.1_Silent_p.T114T|SLC8A2_ENST00000539381.1_Intron	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	358					blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		TCATCAGCCGCGTGGCCTGGA	0.716																																					p.T358T		Atlas-SNP	.											SLC8A2,colon,carcinoma,0,1	SLC8A2	77	.	0			c.G1074A						.						5	4	5					19																	47960453		2029	3878	5907	SO:0001819	synonymous_variant	6543	exon3			CAGCCGCGTGGCC	AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"Solute carriers"	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.1074G>A	chr19.hg19:g.47960453C>T		92.0	1.0		68.0	7.0	NM_015063	B4DYQ9	Silent	SNP	ENST00000236877.6	hg19	CCDS33065.1																																																																																			.	.		0.716	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1			T	47960453	C	T	47960453	2	4	18	1	0	0	0	0	0	0	0	1	14722	755	27	1		1	SLC8A2	19	47960453	Silent	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10	1067066	47960453	11168530	68	1592										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20150059	20150059	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ggtccctttcaacacctgcaCcctcgagcaggacctctacg	8	17	2	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr20:20150059C>A	ENST00000245957.5	+	13	1416	c.1340C>A	c.(1339-1341)aCc>aAc	p.T447N	C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000451767.2_Missense_Mutation_p.T447N|C20orf26_ENST00000377306.1_Missense_Mutation_p.T447N	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		447										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		AACACCTGCACCCTCGAGCAG	0.483																																					p.T447N		Atlas-SNP	.											.	C20orf26	188	.	0			c.C1340A						.						112	99	104					20																	20150059		2203	4300	6503	SO:0001583	missense	26074	exon13			CCTGCACCCTCGA																												ENST00000245957.5:c.1340C>A	chr20.hg19:g.20150059C>A	ENSP00000245957:p.Thr447Asn	121.0	0.0		188.0	34.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	hg19	CCDS33447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.06|13.06	2.124910|2.124910	0.37533|0.37533	.|.	.|.	ENSG00000089101|ENSG00000089101	ENST00000431753|ENST00000343997;ENST00000339482;ENST00000389655;ENST00000245957;ENST00000377306;ENST00000451767	.|T;T;T	.|0.12879	.|2.64;2.64;2.64	5.87|5.87	1.65|1.65	0.23941|0.23941	.|.	.|0.639077	.|0.16063	.|N	.|0.231362	T|T	0.23410|0.23410	0.0566|0.0566	L|L	0.49126|0.49126	1.545|1.545	0.80722|0.80722	D|D	1|1	.|D;B;P	.|0.76494	.|0.999;0.264;0.919	.|D;B;P	.|0.64877	.|0.93;0.149;0.504	T|T	0.02728|0.02728	-1.1118|-1.1118	5|10	.|0.29301	.|T	.|0.29	.|.	7.6774|7.6774	0.28494|0.28494	0.0:0.5999:0.2546:0.1455|0.0:0.5999:0.2546:0.1455	.|.	.|447;427;447	.|Q8NHU2-3;F8W6K4;Q8NHU2	.|.;.;CT026_HUMAN	T|N	13|387;41;427;447;447;447	.|ENSP00000245957:T447N;ENSP00000366521:T447N;ENSP00000414537:T447N	.|ENSP00000245957:T447N	P|T	+|+	1|2	0|0	C20orf26|C20orf26	20098059|20098059	0.474000|0.474000	0.25886|0.25886	0.964000|0.964000	0.40570|0.40570	0.014000|0.014000	0.08584|0.08584	0.709000|0.709000	0.25734|0.25734	0.456000|0.456000	0.26937|0.26937	-0.176000|-0.176000	0.13171|0.13171	CCC|ACC	.	.		0.483	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			A	20150059	C	A	20150059	3	1	18	1	0	0	0	0	1	0	0	0	2108	507	18	3	1386	3	C20orf26	20	20150059	Missense_Mutation	SNP	C	TCGA-2Y-A9H8-01A-11D-A38X-10		20150059	42875461	69	1593										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44650434	44650435	+	Frame_Shift_Ins	INS	-	-	C													0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	ggttcacggtcacctcgctgINSccccccgcagggcccgccag							TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chr20:44650434_44650435insC	ENST00000454036.2	+	1	79_80	c.30_31insC	c.(31-33)cccfs	p.P11fs	RP11-465L10.10_ENST00000535913.1_RNA|RP11-465L10.10_ENST00000419897.1_RNA	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	11					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	TCACCTCGCTGCCCCCCGCAGG	0.703																																					p.L10fs		Atlas-INDEL	.											.	SLC12A5	181	.	0			c.30_31insC						.																																			SO:0001589	frameshift_variant	57468	exon1			.	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.36dupC	chr20.hg19:g.44650440_44650440dupC	ENSP00000387694:p.Pro11fs	39.0	0.0		60.0	10.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Frame_Shift_Ins	INS	ENST00000454036.2	hg19	CCDS46610.1																																																																																			.	.		0.703	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			C	44650435	-	C	44650434	7	5	18	1	0	1	1	0	0	0	0	0	14401	1306	46	0	32	0	SLC12A5	20	44650434	Frame_Shift_Ins	INS	-	TCGA-2Y-A9H8-01A-11D-A38X-10	24500375	44650434	18375086	70	1594										
ZDHHC15	158866	hgsc.bcm.edu	37	chrX	74644581	74644581	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	caggccacaaagagaagaaaAaggacatggaacttagagcg	12	7	0	3			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chrX:74644581A>T	ENST00000373367.3	-	8	872	c.642T>A	c.(640-642)ctT>ctA	p.L214L	ZDHHC15_ENST00000373361.3_Missense_Mutation_p.F174Y|ZDHHC15_ENST00000541184.1_Silent_p.L205L	NM_144969.2	NP_659406.1	Q96MV8	ZDH15_HUMAN	zinc finger, DHHC-type containing 15	214					establishment of protein localization (GO:0045184)|protein palmitoylation (GO:0018345)|synaptic vesicle maturation (GO:0016188)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(1)|lung(11)|ovary(2)|skin(2)	26						AGAGAAGAAAAAGGACATGGA	0.388																																					p.L214L		Atlas-SNP	.											.	ZDHHC15	65	.	0			c.T642A						.						85	62	70					X																	74644581		2203	4300	6503	SO:0001819	synonymous_variant	158866	exon8			AAGAAAAAGGACA	AK056374	CCDS14430.1, CCDS55454.1	Xq13.3	2008-05-02			ENSG00000102383	ENSG00000102383		"Zinc fingers, DHHC-type"	20342	protein-coding gene	gene with protein product		300576					Standard	NM_144969		Approved	FLJ31812, MRX91	uc004ecg.3	Q96MV8	OTTHUMG00000021866	ENST00000373367.3:c.642T>A	chrX.hg19:g.74644581A>T		580.0	0.0		677.0	441.0	NM_144969	B3KVG7|Q3SY30|Q6UWH3	Silent	SNP	ENST00000373367.3	hg19	CCDS14430.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.817808	0.50633	.	.	ENSG00000102383	ENST00000373361	T	0.47528	0.84	5.58	0.0606	0.14336	.	.	.	.	.	T	0.49864	0.1582	.	.	.	0.46185	D	0.99891	.	.	.	.	.	.	T	0.49263	-0.8958	6	0.72032	D	0.01	-3.893	5.6294	0.17501	0.5658:0.1378:0.2964:0.0	.	.	.	.	Y	174	ENSP00000362459:F174Y	ENSP00000362459:F174Y	F	-	2	0	ZDHHC15	74561306	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	1.125000	0.31332	0.025000	0.15241	0.486000	0.48141	TTT	.	.		0.388	ZDHHC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057283.1	NM_144969		T	74644581	A	T	74644581	2	4	18	1	0	0	0	0	0	0	0	1	17620	1	1	4		4	ZDHHC15	23	74644581	Silent	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10		74644581	80625979	71	1595										
TAF9B	51616	hgsc.bcm.edu	37	chrX	77393577	77393577	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	aataaatttttgcatcatccAgaattgtagtcacataacct	4	8	2	1			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chrX:77393577A>C	ENST00000341864.5	-	3	246	c.152T>G	c.(151-153)cTg>cGg	p.L51R		NM_015975.4	NP_057059.2	Q9HBM6	TAF9B_HUMAN	TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa	51					DNA-templated transcription, initiation (GO:0006352)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell growth (GO:0030307)|programmed cell death (GO:0012501)|protein stabilization (GO:0050821)|response to organic cyclic compound (GO:0014070)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	14						TGCATCATCCAGAATTGTAGT	0.348																																					p.L51R		Atlas-SNP	.											.	TAF9B	30	.	0			c.T152G						.						96	83	88					X																	77393577		2203	4296	6499	SO:0001583	missense	51616	exon3			TCATCCAGAATTG	AF220509	CCDS35340.1	Xq13.1-q21.1	2010-08-16	2006-01-04	2006-01-04	ENSG00000187325	ENSG00000187325			17306	protein-coding gene	gene with protein product		300754	"TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa"	TAF9L		15899866	Standard	XM_005262142		Approved	TAFII31L, DN-7, DN7, TFIID-31	uc004eda.3	Q9HBM6	OTTHUMG00000021887	ENST00000341864.5:c.152T>G	chrX.hg19:g.77393577A>C	ENSP00000339917:p.Leu51Arg	365.0	1.0		282.0	182.0	NM_015975	B2RUZ9|Q9Y2S3	Missense_Mutation	SNP	ENST00000341864.5	hg19	CCDS35340.1	.	.	.	.	.	.	.	.	.	.	A	18.07	3.542286	0.65198	.	.	ENSG00000187325	ENST00000341864	T	0.60171	0.21	4.42	4.42	0.53409	Histone-fold (2);	0.075878	0.56097	D	0.000038	T	0.76407	0.3983	M	0.90650	3.135	0.52099	D	0.999947	D	0.63046	0.992	P	0.62089	0.898	T	0.81075	-0.1097	10	0.87932	D	0	-4.6992	10.9279	0.47201	1.0:0.0:0.0:0.0	.	51	Q9HBM6	TAF9B_HUMAN	R	51	ENSP00000339917:L51R	ENSP00000339917:L51R	L	-	2	0	TAF9B	77280233	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.635000	0.91006	1.544000	0.49359	0.417000	0.27973	CTG	.	.		0.348	TAF9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057308.1	NM_015975		C	77393577	A	C	77393577	3	2	18	1	0	0	0	0	1	0	0	0	15551	188	7	5	623	5	TAF9B	23	77393577	Missense_Mutation	SNP	A	TCGA-2Y-A9H8-01A-11D-A38X-10	2748996	77393577	77876983	72	1596										
NKAP	79576	hgsc.bcm.edu	37	chrX	119077493	119077493	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	0.829594017094017	2.3110119047619	0.505533854166667	1	1	0	tttgctgggcttcggactctTcgacgaactgcgacgtcttc	11	12	2	0			TCGA-2Y-A9H8-01A-11D-A38X-10	TCGA-2Y-A9H8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8ce4db3-59d7-41a4-bd0d-d6dc39a003e4	ea9d6487-fc5c-429d-9870-af174a03bd4d	g.chrX:119077493T>C	ENST00000371410.3	-	1	242	c.76A>G	c.(76-78)Aag>Gag	p.K26E		NM_024528.3	NP_078804.2	Q8N5F7	NKAP_HUMAN	NFKB activating protein	26	Ser-rich.				granulocyte differentiation (GO:0030851)|hematopoietic stem cell proliferation (GO:0071425)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|stem cell maintenance (GO:0019827)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)	20						TTCGGACTCTTCGACGAACTG	0.701																																					p.K26E		Atlas-SNP	.											.	NKAP	53	.	0			c.A76G						.						23	26	25					X																	119077493		2202	4297	6499	SO:0001583	missense	79576	exon1			GACTCTTCGACGA	BC012770	CCDS14592.1	Xq24	2010-07-20			ENSG00000101882	ENSG00000101882			29873	protein-coding gene	gene with protein product	"NF kappaB activating protein"	300766				14550261	Standard	NM_024528		Approved	FLJ22626	uc004esh.3	Q8N5F7	OTTHUMG00000022284	ENST00000371410.3:c.76A>G	chrX.hg19:g.119077493T>C	ENSP00000360464:p.Lys26Glu	229.0	0.0		156.0	109.0	NM_024528	Q6IPW6|Q96BQ2|Q9H638	Missense_Mutation	SNP	ENST00000371410.3	hg19	CCDS14592.1	.	.	.	.	.	.	.	.	.	.	t	9.027	0.986418	0.18889	.	.	ENSG00000101882	ENST00000371410	T	0.14144	2.53	4.23	-0.205	0.13196	.	0.898886	0.09692	N	0.768202	T	0.11324	0.0276	L	0.40543	1.245	0.09310	N	1	B	0.12013	0.005	B	0.14023	0.01	T	0.34950	-0.9808	10	0.31617	T	0.26	-0.344	9.1299	0.36839	0.0:0.0:0.5836:0.4164	.	26	Q8N5F7	NKAP_HUMAN	E	26	ENSP00000360464:K26E	ENSP00000360464:K26E	K	-	1	0	NKAP	118961521	0.000000	0.05858	0.003000	0.11579	0.018000	0.09664	0.151000	0.16283	0.108000	0.17862	0.438000	0.28831	AAG	.	.		0.701	NKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058072.1	NM_024528		C	119077493	T	C	119077493	3	2	18	1	0	0	0	0	1	0	0	0	10448	1792	62	2	1207	2	NKAP	23	119077493	Missense_Mutation	SNP	T	TCGA-2Y-A9H8-01A-11D-A38X-10	41683916	119077493	36193067	73	1597										
EPHA8	2046	hgsc.bcm.edu	37	chr1	22902961	22902961	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cgcgacctgggggccagcacAcaagaaagccagttcctcaa	11	14	1	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr1:22902961A>T	ENST00000166244.3	+	3	483	c.411A>T	c.(409-411)acA>acT	p.T137T	EPHA8_ENST00000538803.1_Silent_p.T137T|EPHA8_ENST00000374644.4_Silent_p.T137T	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	137	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGGCCAGCACACAAGAAAGCC	0.612																																					p.T137T		Atlas-SNP	.											.	EPHA8	221	.	0			c.A411T						.						79	70	73					1																	22902961		2203	4300	6503	SO:0001819	synonymous_variant	2046	exon3			CAGCACACAAGAA	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.411A>T	chr1.hg19:g.22902961A>T		212.0	0.0		219.0	98.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.		0.612	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		T	22902961	A	T	22902961	2	4	19	1	0	0	0	0	0	0	0	1	5175	146	6	4		4	EPHA8	1	22902961	Silent	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10		22902961	226347660	1	1598										
RNPC3	55599	hgsc.bcm.edu	37	chr1	104068797	104068797	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cttctggtcaggcacctgccGgctgagcttactgctgagga	13	12	2	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr1:104068797G>T	ENST00000533099.1	+	2	341	c.105G>T	c.(103-105)ccG>ccT	p.P35P	RP11-153F1.1_ENST00000444810.1_RNA|RP11-153F1.1_ENST00000447322.2_RNA|RNPC3_ENST00000524631.1_Silent_p.P35P|RNPC3_ENST00000423855.2_Silent_p.P35P|RN7SKP285_ENST00000410137.1_RNA			Q96LT9	RBM40_HUMAN	RNA-binding region (RNP1, RRM) containing 3	35	Necessary for interaction with PDCD7.|RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Lung(183;0.111)|Epithelial(280;0.122)|all cancers(265;0.125)|Colorectal(144;0.163)		GGCACCTGCCGGCTGAGCTTA	0.632																																					p.P35P		Atlas-SNP	.											.	RNPC3	20	.	0			c.G105T						.						43	41	42					1																	104068797		692	1591	2283	SO:0001819	synonymous_variant	55599	exon1			CCTGCCGGCTGAG	AB058742, AY099329	CCDS781.1	1p21.1	2013-07-16			ENSG00000185946	ENSG00000185946		"RNA binding motif (RRM) containing"	18666	protein-coding gene	gene with protein product	"U11/U12 snRNP 65K"					14974681, 15146077	Standard	NM_017619		Approved	KIAA1839, FLJ20008, RBM40, SNRNP65	uc010oun.2	Q96LT9	OTTHUMG00000166613	ENST00000533099.1:c.105G>T	chr1.hg19:g.104068797G>T		170.0	0.0		144.0	64.0	NM_017619	A8K1C9|D3DT74|Q5TZ87|Q96FK7|Q96JI8|Q9NSU7|Q9NXX2	Silent	SNP	ENST00000533099.1	hg19	CCDS781.1																																																																																			.	.		0.632	RNPC3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390812.1	NM_017619		T	104068797	G	T	104068797	2	4	19	1	0	0	0	0	0	0	0	1	13523	1103	39	1		1	RNPC3	1	104068797	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	81165836	104068797	145181824	2	1599										
LASS2	29956	hgsc.bcm.edu	37	chr1	150941409	150941409	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cttacagctcaaagaagtatCgaacgatgaggaagagcaag	11	7	1	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr1:150941409C>T	ENST00000271688.6	-	2	544	c.158G>A	c.(157-159)cGa>cAa	p.R53Q	CERS2_ENST00000345896.4_Intron|RP11-316M1.12_ENST00000560481.1_RNA|RP11-316M1.12_ENST00000561111.1_RNA|CERS2_ENST00000561294.1_Missense_Mutation_p.R53Q|CERS2_ENST00000368954.5_Missense_Mutation_p.R53Q	NM_181746.3	NP_859530.1	Q96G23	CERS2_HUMAN	ceramide synthase 2	53					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AAAGAAGTATCGAACGATGAG	0.502																																					p.R53Q		Atlas-SNP	.											LASS2,colon,carcinoma,0,1	.	.	.	0			c.G158A						.						148	121	130					1																	150941409		2203	4300	6503	SO:0001583	missense	29956	exon2			AAGTATCGAACGA	AF189062	CCDS973.1	1q21.3	2012-09-20	2011-07-08	2011-07-08	ENSG00000143418	ENSG00000143418		"Homeoboxes / CERS class"	14076	protein-coding gene	gene with protein product		606920	"longevity assurance (LAG1, S. cerevisiae) homolog 2", "LAG1 longevity assurance homolog 2 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 2"	LASS2		11543633	Standard	NM_181746		Approved	SP260, FLJ10243	uc001evz.3	Q96G23	OTTHUMG00000035064	ENST00000271688.6:c.158G>A	chr1.hg19:g.150941409C>T	ENSP00000271688:p.Arg53Gln	88.0	0.0		170.0	39.0	NM_022075	D3DV06|Q5SZE5|Q9HD96|Q9NW79	Missense_Mutation	SNP	ENST00000271688.6	hg19	CCDS973.1	.	.	.	.	.	.	.	.	.	.	C	32	5.132742	0.94517	.	.	ENSG00000143418	ENST00000368954;ENST00000271688;ENST00000368949;ENST00000361419;ENST00000421609;ENST00000457392	T;T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92;-0.92	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.88433	0.6435	M	0.93241	3.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91206	0.4995	10	0.87932	D	0	-5.1005	16.6517	0.85218	0.0:1.0:0.0:0.0	.	53	Q96G23	CERS2_HUMAN	Q	53;53;73;53;53;53	ENSP00000357950:R53Q;ENSP00000271688:R53Q;ENSP00000357945:R73Q;ENSP00000355020:R53Q;ENSP00000393239:R53Q;ENSP00000394012:R53Q	ENSP00000271688:R53Q	R	-	2	0	CERS2	149208033	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	7.005000	0.76323	2.496000	0.84212	0.650000	0.86243	CGA	.	.		0.502	CERS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084897.2	NM_022075		T	150941409	C	T	150941409	3	4	19	1	0	0	0	0	1	0	0	0	8648	884	31	1	1024	1	LASS2	1	150941409	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	46872612	150941409	98309212	3	1600										
FLG	2312	hgsc.bcm.edu	37	chr1	152280892	152280892	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	agtgtccagacctatctaccGattgctcttggtgggacccc	10	13	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr1:152280892G>A	ENST00000368799.1	-	3	6505	c.6470C>T	c.(6469-6471)tCg>tTg	p.S2157L	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2157	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTATCTACCGATTGCTCTTG	0.597									Ichthyosis																												p.S2157L		Atlas-SNP	.											FLG,NS,carcinoma,+1,2	FLG	900	.	0			c.C6470T						.						386	328	348					1																	152280892		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCTACCGATTGCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6470C>T	chr1.hg19:g.152280892G>A	ENSP00000357789:p.Ser2157Leu	139.0	0.0		209.0	76.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	5.683	0.310525	0.10733	.	.	ENSG00000143631	ENST00000368799	T	0.03745	3.82	2.59	-1.71	0.08133	.	.	.	.	.	T	0.01061	0.0035	L	0.55103	1.725	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.45483	-0.9258	9	0.26408	T	0.33	.	4.0063	0.09603	0.1329:0.0:0.3602:0.5069	.	2157	P20930	FILA_HUMAN	L	2157	ENSP00000357789:S2157L	ENSP00000357789:S2157L	S	-	2	0	FLG	150547516	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.268000	0.18571	-0.390000	0.07774	-0.663000	0.03849	TCG	.	.		0.597	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152280892	G	A	152280892	3	1	19	1	0	0	0	0	1	0	0	0	5930	1059	37	1	5719	1	FLG	1	152280892	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	1339483	152280892	96969729	4	1601										
OR6N2	81442	hgsc.bcm.edu	37	chr1	158746473	158746473	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aaaggacatgggaagaaagtCaaagatgagcaagactagct	12	5	1	4			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr1:158746473C>G	ENST00000339258.1	-	1	952	c.953G>C	c.(952-954)tGa>tCa	p.*318S		NM_001005278.1	NP_001005278.1	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N, member 2	0						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(6)|lung(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(112;0.0378)					GGAAGAAAGTCAAAGATGAGC	0.378																																					p.X318S		Atlas-SNP	.											.	OR6N2	78	.	0			c.G953C						.						128	124	125					1																	158746473		2203	4300	6503	SO:0001630	splice_region_variant	81442	exon1			GAAAGTCAAAGAT	BK004200	CCDS30906.1	1q23.1	2012-08-09			ENSG00000188340	ENSG00000188340		"GPCR / Class A : Olfactory receptors"	15035	protein-coding gene	gene with protein product							Standard	NM_001005278		Approved		uc010pir.2	Q8NGY6	OTTHUMG00000022775	ENST00000339258.1:c.951+1G>C	chr1.hg19:g.158746473C>G		35.0	0.0		87.0	29.0	NM_001005278	Q6IFR2	Missense_Mutation	SNP	ENST00000339258.1	hg19	CCDS30906.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.033822	0.35893	.	.	ENSG00000188340	ENST00000339258	.	.	.	4.24	2.12	0.27331	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.0105	0.30351	0.0:0.769:0.0:0.231	.	.	.	.	S	318	.	.	X	-	2	2	OR6N2	157013097	0.000000	0.05858	0.111000	0.21465	0.212000	0.24457	-0.052000	0.11865	0.955000	0.37878	0.650000	0.86243	TGA	.	.		0.378	OR6N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059068.1		Nonstop_Mutation	G	158746473	C	G	158746473	5	3	19	1	0	0	0	0	0	0	1	0	11216	840	29	4	3	4	OR6N2	1	158746473	Splice_Site	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	6465581	158746473	90504148	5	1602										
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222716922	222716922	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gttaggatcagcccgagaaaCcttcatctcactaattcgga	8	11	3	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr1:222716922C>T	ENST00000343410.6	-	2	989	c.931G>A	c.(931-933)Gtt>Att	p.V311I		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	311					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		GCCCGAGAAACCTTCATCTCA	0.443																																					p.V311I		Atlas-SNP	.											.	HHIPL2	122	.	0			c.G931A						.						281	308	299					1																	222716922		2203	4300	6503	SO:0001583	missense	79802	exon2			GAGAAACCTTCAT	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"KIAA1822-like"	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.931G>A	chr1.hg19:g.222716922C>T	ENSP00000342118:p.Val311Ile	110.0	0.0		100.0	44.0	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	hg19	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	C	19.48	3.835620	0.71373	.	.	ENSG00000143512	ENST00000343410	T	0.10960	2.82	5.57	4.66	0.58398	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.121221	0.53938	D	0.000050	T	0.21550	0.0519	L	0.55103	1.725	0.45580	D	0.998527	P	0.39551	0.678	P	0.49387	0.609	T	0.00770	-1.1573	10	0.41790	T	0.15	-11.6888	16.3171	0.82932	0.0:0.8676:0.1324:0.0	.	311	Q6UWX4	HIPL2_HUMAN	I	311	ENSP00000342118:V311I	ENSP00000342118:V311I	V	-	1	0	HHIPL2	220783545	0.967000	0.33354	0.998000	0.56505	0.991000	0.79684	2.349000	0.44054	1.325000	0.45301	0.591000	0.81541	GTT	.	.		0.443	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		T	222716922	C	T	222716922	3	4	19	1	0	0	0	0	1	0	0	0	7103	507	18	3	1275	3	HHIPL2	1	222716922	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	63970449	222716922	26533699	6	1603										
HADHB	3032	hgsc.bcm.edu	37	chr2	26501661	26501661	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aattccgatttaatttcctaGcacctgaggtaaggcttgtg	9	8	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:26501661G>T	ENST00000317799.5	+	8	726	c.622G>T	c.(622-624)Gca>Tca	p.A208S	HADHB_ENST00000405867.3_Intron|HADHB_ENST00000545822.1_Missense_Mutation_p.A186S|HADHB_ENST00000494615.1_3'UTR|HADHB_ENST00000537713.1_Missense_Mutation_p.A193S	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	208					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAATTTCCTAGCACCTGAGGT	0.423																																					p.A208S		Atlas-SNP	.											.	HADHB	50	.	0			c.G622T						.						123	123	123					2																	26501661		2203	4300	6503	SO:0001583	missense	3032	exon8			TTCCTAGCACCTG		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"mitochondrial trifunctional protein, beta subunit"	143450	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.622G>T	chr2.hg19:g.26501661G>T	ENSP00000325136:p.Ala208Ser	94.0	0.0		108.0	55.0	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Missense_Mutation	SNP	ENST00000317799.5	hg19	CCDS1722.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312602	0.23908	.	.	ENSG00000138029	ENST00000317799;ENST00000537713;ENST00000545822	D;D;D	0.93189	-3.17;-3.18;-3.16	5.58	-8.39	0.00969	Thiolase, N-terminal (1);Thiolase-like (1);	0.497156	0.22113	N	0.064455	T	0.79747	0.4499	N	0.12831	0.26	0.09310	N	0.999996	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.15052	0.004;0.012;0.007	T	0.68292	-0.5447	9	.	.	.	-0.0618	9.8181	0.40865	0.34:0.0:0.5287:0.1314	.	193;186;208	F5GZQ3;B4E2W0;P55084	.;.;ECHB_HUMAN	S	208;193;186	ENSP00000325136:A208S;ENSP00000444295:A193S;ENSP00000442665:A186S	.	A	+	1	0	HADHB	26355165	0.327000	0.24678	0.004000	0.12327	0.965000	0.64279	0.647000	0.24812	-0.852000	0.04141	-0.271000	0.10264	GCA	.	.		0.423	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183		T	26501661	G	T	26501661	3	4	19	1	0	0	0	0	1	0	0	0	6953	971	34	3	648	3	HADHB	2	26501661	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10		26501661	216697712	7	1604										
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40655983	40655983	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ctcaaagatatcatcatctaTgatacccactctgatttcct	3	12	5	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:40655983T>A	ENST00000403092.1	-	2	1471	c.1438A>T	c.(1438-1440)Ata>Tta	p.I480L	SLC8A1_ENST00000542756.1_Missense_Mutation_p.I480L|SLC8A1_ENST00000406391.2_Missense_Mutation_p.I480L|SLC8A1_ENST00000402441.1_Missense_Mutation_p.I480L|SLC8A1_ENST00000542024.1_Missense_Mutation_p.I480L|SLC8A1_ENST00000332839.4_Missense_Mutation_p.I480L|SLC8A1_ENST00000408028.2_Missense_Mutation_p.I480L|SLC8A1_ENST00000405269.1_Missense_Mutation_p.I480L|SLC8A1_ENST00000405901.3_Missense_Mutation_p.I480L|SLC8A1_ENST00000406785.2_Missense_Mutation_p.I480L			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	480	Calx-beta 1.				blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	TCATCATCTATGATACCCACT	0.418																																					p.I480L		Atlas-SNP	.											.	SLC8A1	221	.	0			c.A1438T						.						75	70	72					2																	40655983		2203	4300	6503	SO:0001583	missense	6546	exon1			CATCTATGATACC		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.1438A>T	chr2.hg19:g.40655983T>A	ENSP00000384763:p.Ile480Leu	67.0	0.0		83.0	31.0	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	hg19	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	T	16.26	3.073855	0.55646	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55	6.17	6.17	0.99709	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.42720	0.1215	L	0.46567	1.45	0.80722	D	1	P;B;P;B;P	0.42357	0.736;0.075;0.736;0.055;0.777	P;B;P;B;P	0.51833	0.552;0.33;0.552;0.091;0.681	T	0.27673	-1.0067	10	0.87932	D	0	.	14.7743	0.69713	0.0:0.0:0.0:1.0	.	480;480;480;480;480	P32418-4;P32418-2;P32418-3;F6VPY9;P32418	.;.;.;.;NAC1_HUMAN	L	480	ENSP00000383886:I480L;ENSP00000440727:I480L;ENSP00000384763:I480L;ENSP00000385678:I480L;ENSP00000385188:I480L;ENSP00000385535:I480L;ENSP00000332931:I480L;ENSP00000384908:I480L;ENSP00000385811:I480L;ENSP00000443515:I480L	ENSP00000332931:I480L	I	-	1	0	SLC8A1	40509487	1.000000	0.71417	0.996000	0.52242	0.696000	0.40369	7.881000	0.87252	2.371000	0.80710	0.533000	0.62120	ATA	.	.		0.418	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		A	40655983	T	A	40655983	3	1	19	1	0	0	0	0	1	0	0	0	14721	1464	51	4	1631	4	SLC8A1	2	40655983	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	14154322	40655983	202543390	8	1605										
MSH6	2956	hgsc.bcm.edu	37	chr2	48018238	48018238	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	caacaaggggctgggttagcAaaaggcttttaaagccatat	11	7	0	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:48018238A>T	ENST00000234420.5	+	2	585	c.433A>T	c.(433-435)Aaa>Taa	p.K145*	MSH6_ENST00000540021.1_Intron|MSH6_ENST00000538136.1_5'UTR|FBXO11_ENST00000405808.1_Intron	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	145	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTGGGTTAGCAAAAGGCTTTT	0.463			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.K145X		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.A433T						.						79	82	81					2																	48018238		2203	4300	6503	SO:0001587	stop_gained	2956	exon2	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	GTTAGCAAAAGGC	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.433A>T	chr2.hg19:g.48018238A>T	ENSP00000234420:p.Lys145*	152.0	0.0		166.0	71.0	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Nonsense_Mutation	SNP	ENST00000234420.5	hg19	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.844280	0.91197	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000446255;ENST00000455383;ENST00000420813;ENST00000411819	.	.	.	5.63	5.63	0.86233	.	0.284105	0.38548	N	0.001652	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.8151	5.7735	0.18267	0.712:0.1462:0.1418:0.0	.	.	.	.	X	145;143;145;46;46;46	.	ENSP00000234420:K145X	K	+	1	0	MSH6	47871742	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	2.171000	0.42453	2.128000	0.65567	0.455000	0.32223	AAA	.	.		0.463	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		T	48018238	A	T	48018238	4	4	19	1	0	0	0	0	0	1	0	0	9883	131	5	4	439	4	MSH6	2	48018238	Nonsense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	7362255	48018238	195181135	9	1606										
PDCL3	79031	hgsc.bcm.edu	37	chr2	101186107	101186107	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tcggagaagttttggagatcTcagggaaggattatgttcaa	13	4	2	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:101186107T>A	ENST00000264254.6	+	4	670	c.292T>A	c.(292-294)Tca>Aca	p.S98T		NM_024065.4	NP_076970.1	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	98	Thioredoxin fold. {ECO:0000250}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|protein folding (GO:0006457)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|viral process (GO:0016032)	cytoplasm (GO:0005737)	protein binding involved in protein folding (GO:0044183)			endometrium(3)|large_intestine(2)|liver(1)|lung(6)	12						TTTGGAGATCTCAGGGAAGGA	0.458																																					p.S98T		Atlas-SNP	.											.	PDCL3	27	.	0			c.T292A						.						84	86	85					2																	101186107		2203	4298	6501	SO:0001583	missense	79031	exon4			GAGATCTCAGGGA	AF267853	CCDS33261.1	2q12	2008-02-05			ENSG00000115539	ENSG00000115539			28860	protein-coding gene	gene with protein product		611678					Standard	NM_024065		Approved	VIAF1	uc002tao.2	Q9H2J4	OTTHUMG00000153141	ENST00000264254.6:c.292T>A	chr2.hg19:g.101186107T>A	ENSP00000264254:p.Ser98Thr	140.0	0.0		194.0	85.0	NM_024065	B2RA00|Q53S68	Missense_Mutation	SNP	ENST00000264254.6	hg19	CCDS33261.1	.	.	.	.	.	.	.	.	.	.	.	16.15	3.040997	0.55003	.	.	ENSG00000115539	ENST00000264254;ENST00000416255	T;T	0.15952	2.38;2.38	4.59	4.59	0.56863	Phosducin, thioredoxin-like domain (1);Thioredoxin-like fold (2);	0.069308	0.64402	D	0.000012	T	0.22044	0.0531	M	0.62266	1.93	0.50632	D	0.999884	B	0.15473	0.013	B	0.28638	0.092	T	0.03354	-1.1045	10	0.30078	T	0.28	-25.0944	14.2704	0.66149	0.0:0.0:0.0:1.0	.	98	Q9H2J4	PDCL3_HUMAN	T	98;48	ENSP00000264254:S98T;ENSP00000413936:S48T	ENSP00000264254:S98T	S	+	1	0	PDCL3	100552539	1.000000	0.71417	0.999000	0.59377	0.927000	0.56198	7.680000	0.84062	1.816000	0.52996	0.454000	0.30748	TCA	.	.		0.458	PDCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329734.1	NM_024065		A	101186107	T	A	101186107	3	1	19	1	0	0	0	0	1	0	0	0	11637	1551	54	4	306	4	PDCL3	2	101186107	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	53167869	101186107	142013266	10	1607										
MRPS9	64965	hgsc.bcm.edu	37	chr2	105696507	105696507	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tactggcaaacagtcatactAttcattaatgcatgtaagta	6	7	2	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:105696507A>G	ENST00000258455.3	+	5	586	c.476A>G	c.(475-477)tAt>tGt	p.Y159C		NM_182640.2	NP_872578.1	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9	159					DNA damage response, detection of DNA damage (GO:0042769)|peptide biosynthetic process (GO:0043043)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						CAGTCATACTATTCATTAATG	0.333																																					p.Y159C		Atlas-SNP	.											.	MRPS9	32	.	0			c.A476G						.						134	121	125					2																	105696507		2203	4300	6503	SO:0001583	missense	64965	exon5			CATACTATTCATT		CCDS2065.1	2q12.1	2012-09-13			ENSG00000135972	ENSG00000135972		"Mitochondrial ribosomal proteins / small subunits"	14501	protein-coding gene	gene with protein product	"28S ribosomal protein S9, mitochondrial"	611975				11279123	Standard	NM_182640		Approved	RPMS9, MRP-S9, S9mt	uc002tcn.4	P82933	OTTHUMG00000130807	ENST00000258455.3:c.476A>G	chr2.hg19:g.105696507A>G	ENSP00000258455:p.Tyr159Cys	42.0	0.0		53.0	10.0	NM_182640	Q6PG40	Missense_Mutation	SNP	ENST00000258455.3	hg19	CCDS2065.1	.	.	.	.	.	.	.	.	.	.	A	19.63	3.863744	0.71949	.	.	ENSG00000135972	ENST00000258455	D	0.92199	-2.99	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.96367	0.8815	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96975	0.9711	10	0.87932	D	0	-16.6605	15.9892	0.80188	1.0:0.0:0.0:0.0	.	159	P82933	RT09_HUMAN	C	159	ENSP00000258455:Y159C	ENSP00000258455:Y159C	Y	+	2	0	MRPS9	105062939	1.000000	0.71417	0.634000	0.29324	0.876000	0.50452	8.165000	0.89663	2.180000	0.69256	0.533000	0.62120	TAT	.	.		0.333	MRPS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253352.1	NM_182640		G	105696507	A	G	105696507	3	3	19	1	0	0	0	0	1	0	0	0	9858	449	16	2	494	2	MRPS9	2	105696507	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	4510400	105696507	137502866	11	1608										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167262815	167262815	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ccatttactgttgaaaattgCatcaagcatcccatcccaac	4	13	1	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:167262815C>A	ENST00000409855.1	-	25	4450	c.4324G>T	c.(4324-4326)Gca>Tca	p.A1442S		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1442					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TTGAAAATTGCATCAAGCATC	0.393																																					p.A1442S		Atlas-SNP	.											.	SCN7A	410	.	0			c.G4324T						.						149	142	144					2																	167262815		1882	4139	6021	SO:0001583	missense	6332	exon25			AAATTGCATCAAG	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.4324G>T	chr2.hg19:g.167262815C>A	ENSP00000386796:p.Ala1442Ser	202.0	0.0		389.0	162.0	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	hg19	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.040357	0.55003	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.98455	-4.94	5.14	3.22	0.36961	Ion transport (1);	0.209915	0.33875	N	0.004474	D	0.97576	0.9206	L	0.41573	1.285	0.39571	D	0.969285	D	0.71674	0.998	D	0.67103	0.949	D	0.97456	1.0031	10	0.87932	D	0	.	8.7256	0.34467	0.0:0.7588:0.1542:0.087	.	1442	Q01118	SCN7A_HUMAN	S	1442	ENSP00000386796:A1442S	ENSP00000259060:A1442S	A	-	1	0	SCN7A	166971061	0.999000	0.42202	0.911000	0.35937	0.521000	0.34408	3.082000	0.50128	1.539000	0.49286	0.591000	0.81541	GCA	.	.		0.393	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			A	167262815	C	A	167262815	3	1	19	1	0	0	0	0	1	0	0	0	13938	710	25	3	728	3	SCN7A	2	167262815	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	61566308	167262815	75936558	12	1609										
TTN	7273	hgsc.bcm.edu	37	chr2	179424152	179424152	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	taaattggtaactttgtaggAgaggcggttacagttgttgg	14	3	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:179424152A>C	ENST00000591111.1	-	276	82008	c.81784T>G	c.(81784-81786)Tcc>Gcc	p.S27262A	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S20030A|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S19963A|TTN_ENST00000460472.2_Missense_Mutation_p.S19838A|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S28903A|TTN_ENST00000342992.6_Missense_Mutation_p.S26335A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27262	Fibronectin type-III 98. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTTTGTAGGAGAGGCGGTTA	0.433																																					p.S28903A		Atlas-SNP	.											.	TTN	18412	.	0			c.T86707G						.						106	109	108					2																	179424152		1848	4095	5943	SO:0001583	missense	7273	exon326			TGTAGGAGAGGCG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.81784T>G	chr2.hg19:g.179424152A>C	ENSP00000465570:p.Ser27262Ala	135.0	0.0		167.0	32.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	11.27	1.589867	0.28357	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59638	0.25;0.25;0.25;0.25	5.31	4.07	0.47477	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50497	0.1619	L	0.52823	1.66	0.31512	N	0.66342	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.57406	-0.7817	9	0.87932	D	0	.	7.576	0.27937	0.7149:0.1455:0.0:0.1396	.	19838;19963;20030;27262	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	26335;19838;20030;19963;19835	ENSP00000343764:S26335A;ENSP00000434586:S19838A;ENSP00000340554:S20030A;ENSP00000352154:S19963A	ENSP00000340554:S20030A	S	-	1	0	TTN	179132398	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.656000	0.61483	2.129000	0.65627	0.533000	0.62120	TCC	.	.		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179424152	A	C	179424152	3	2	19	1	0	0	0	0	1	0	0	0	16750	304	11	5	21420	5	TTN	2	179424152	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	12161337	179424152	63775221	13	1610										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196741411	196741411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gatttccttatttagttgatTtaaaagaaaattctatataa	4	3	1	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:196741411T>C	ENST00000312428.6	-	37	6074	c.5974A>G	c.(5974-5976)Aat>Gat	p.N1992D		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1992	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TTTAGTTGATTTAAAAGAAAA	0.294																																					p.N1992D		Atlas-SNP	.											.	DNAH7	512	.	0			c.A5974G						.						77	68	71					2																	196741411		1792	4063	5855	SO:0001583	missense	56171	exon37			GTTGATTTAAAAG	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.5974A>G	chr2.hg19:g.196741411T>C	ENSP00000311273:p.Asn1992Asp	43.0	0.0		76.0	31.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	T	14.70	2.614965	0.46631	.	.	ENSG00000118997	ENST00000312428	T	0.39997	1.05	5.64	5.64	0.86602	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.45558	0.1348	L	0.55481	1.735	0.80722	D	1	B	0.26602	0.154	B	0.35655	0.207	T	0.34825	-0.9813	10	0.35671	T	0.21	.	15.6824	0.77381	0.0:0.0:0.0:1.0	.	1992	Q8WXX0	DYH7_HUMAN	D	1992	ENSP00000311273:N1992D	ENSP00000311273:N1992D	N	-	1	0	DNAH7	196449656	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.400000	0.59709	2.367000	0.80283	0.528000	0.53228	AAT	.	.		0.294	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196741411	T	C	196741411	3	2	19	1	0	0	0	0	1	0	0	0	4608	1841	64	2	6216	2	DNAH7	2	196741411	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	17317259	196741411	46457962	14	1611										
HECW2	57520	hgsc.bcm.edu	37	chr2	197185161	197185161	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ggttgtagctgagcatttgaTcactgcaagaagagaaatgc	12	6	1	4			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:197185161T>C	ENST00000260983.3	-	8	1069	c.887A>G	c.(886-888)gAt>gGt	p.D296G	HECW2_ENST00000409111.1_Intron	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	296					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						GAGCATTTGATCACTGCAAGA	0.502																																					p.D296G		Atlas-SNP	.											.	HECW2	239	.	0			c.A887G						.						75	72	73					2																	197185161		2203	4300	6503	SO:0001583	missense	57520	exon8			ATTTGATCACTGC	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.887A>G	chr2.hg19:g.197185161T>C	ENSP00000260983:p.Asp296Gly	140.0	0.0		171.0	23.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754737	0.69648	.	.	ENSG00000138411	ENST00000260983	T	0.36520	1.25	5.1	5.1	0.69264	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.48466	0.1501	L	0.32530	0.975	0.54753	D	0.999981	D	0.69078	0.997	D	0.77004	0.989	T	0.50474	-0.8824	9	0.72032	D	0.01	.	13.6242	0.62155	0.0:0.0:0.0:1.0	.	296	Q9P2P5	HECW2_HUMAN	G	296	ENSP00000260983:D296G	ENSP00000260983:D296G	D	-	2	0	HECW2	196893406	1.000000	0.71417	0.531000	0.27976	0.506000	0.33950	4.625000	0.61262	2.131000	0.65755	0.459000	0.35465	GAT	.	.		0.502	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		C	197185161	T	C	197185161	3	2	19	1	0	0	0	0	1	0	0	0	7052	1435	50	2	3919	2	HECW2	2	197185161	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	443750	197185161	46014212	15	1612										
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197878357	197878357	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cagccagatccagagcagtgCggcctttctcatccctgatg	10	14	1	3	rs374386037		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:197878357C>T	ENST00000328737.2	-	18	1803	c.1727G>A	c.(1726-1728)cGc>cAc	p.R576H	ANKRD44_ENST00000337207.5_Missense_Mutation_p.R576H|ANKRD44_ENST00000282272.8_Missense_Mutation_p.R593H|ANKRD44_ENST00000450567.1_Missense_Mutation_p.R576H			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	601										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CAGAGCAGTGCGGCCTTTCTC	0.498																																					p.R601H		Atlas-SNP	.											.	ANKRD44	281	.	0			c.G1802A						.	C	HIS/ARG	0,4406		0,0,2203	226	215	219		1802	4.4	1	2		219	1,8599	1.2+/-3.3	0,1,4299	no	missense	ANKRD44	NM_001195144.1	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	601/994	197878357	1,13005	2203	4300	6503	SO:0001583	missense	91526	exon18			GCAGTGCGGCCTT	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1727G>A	chr2.hg19:g.197878357C>T	ENSP00000331516:p.Arg576His	113.0	0.0		135.0	63.0	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	hg19		.	.	.	.	.	.	.	.	.	.	C	19.13	3.767764	0.69878	0.0	1.16E-4	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000422886	T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.78547	0.4300	M	0.64170	1.965	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.75096	-0.3438	10	0.22109	T	0.4	.	17.2648	0.87083	0.0:1.0:0.0:0.0	.	619	Q8N8A2-2	.	H	416;593;576;576;576;276	ENSP00000403415:R416H;ENSP00000282272:R593H;ENSP00000331516:R576H;ENSP00000402420:R576H;ENSP00000338794:R576H;ENSP00000416319:R276H	ENSP00000282272:R593H	R	-	2	0	ANKRD44	197586602	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.795000	0.62489	2.294000	0.77228	0.655000	0.94253	CGC	.	.		0.498	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		T	197878357	C	T	197878357	3	4	19	1	0	0	0	0	1	0	0	0	672	768	27	1	1068	1	ANKRD44	2	197878357	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	693196	197878357	45321016	16	1613										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207171124	207171124	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aaacccagtagtgctaaagcAcatcttgattgtgatgtctc	8	9	2	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr2:207171124A>G	ENST00000374423.3	+	5	2258	c.1872A>G	c.(1870-1872)gcA>gcG	p.A624A		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	624							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GTGCTAAAGCACATCTTGATT	0.428																																					p.A624A		Atlas-SNP	.											.	ZDBF2	531	.	0			c.A1872G						.						126	116	120					2																	207171124		1900	4136	6036	SO:0001819	synonymous_variant	57683	exon5			TAAAGCACATCTT	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.1872A>G	chr2.hg19:g.207171124A>G		26.0	0.0		74.0	29.0	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	hg19	CCDS46501.1																																																																																			.	.		0.428	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		G	207171124	A	G	207171124	2	3	19	1	0	0	0	0	0	0	0	1	17614	146	6	2		2	ZDBF2	2	207171124	Silent	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	9292767	207171124	36028249	17	1614										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19389280	19389280	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ctgatgcaaaaaagtccaaaTtcatacttctgcattttagc	5	9	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr3:19389280T>C	ENST00000328405.2	+	5	900	c.634T>C	c.(634-636)Ttc>Ctc	p.F212L	KCNH8_ENST00000475063.1_3'UTR	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	212					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						AAAGTCCAAATTCATACTTCT	0.373																																					p.F212L	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.T634C						.						149	138	142					3																	19389280		2203	4299	6502	SO:0001583	missense	131096	exon5			TCCAAATTCATAC	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.634T>C	chr3.hg19:g.19389280T>C	ENSP00000328813:p.Phe212Leu	72.0	0.0		126.0	52.0	NM_144633	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	hg19	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.477707	0.84640	.	.	ENSG00000183960	ENST00000328405	D	0.98901	-5.22	5.89	5.89	0.94794	.	0.000000	0.33382	U	0.004976	D	0.97964	0.9330	L	0.55743	1.74	0.80722	D	1	B;P	0.43973	0.034;0.823	B;P	0.48089	0.049;0.566	D	0.98047	1.0385	9	.	.	.	.	16.3109	0.82869	0.0:0.0:0.0:1.0	.	212;212	B7Z398;Q96L42	.;KCNH8_HUMAN	L	212	ENSP00000328813:F212L	.	F	+	1	0	KCNH8	19364284	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.251000	0.72441	2.257000	0.74773	0.460000	0.39030	TTC	.	.		0.373	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		C	19389280	T	C	19389280	3	2	19	1	0	0	0	0	1	0	0	0	8047	1493	52	2	652	2	KCNH8	3	19389280	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10		19389280	178633150	18	1615										
MAP4	4134	hgsc.bcm.edu	37	chr3	47910778	47910778	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tgcattagattcaggctttcGggttgtagcagctgcctctg	12	9	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr3:47910778G>A	ENST00000360240.6	-	14	3417	c.2899C>T	c.(2899-2901)Cga>Tga	p.R967*	MAP4_ENST00000420772.2_Intron|MAP4_ENST00000264724.11_Nonsense_Mutation_p.R702*|MAP4_ENST00000462206.1_5'Flank|MAP4_ENST00000426837.2_Nonsense_Mutation_p.R2112*|MAP4_ENST00000441748.2_Intron|MAP4_ENST00000395734.3_Nonsense_Mutation_p.R967*|MAP4_ENST00000383737.4_Intron	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	967					cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	TCAGGCTTTCGGGTTGTAGCA	0.463																																					p.R967X		Atlas-SNP	.											.	MAP4	176	.	0			c.C2899T						.						144	138	140					3																	47910778		2203	4300	6503	SO:0001587	stop_gained	4134	exon14			GCTTTCGGGTTGT		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.2899C>T	chr3.hg19:g.47910778G>A	ENSP00000353375:p.Arg967*	106.0	0.0		129.0	58.0	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Nonsense_Mutation	SNP	ENST00000360240.6	hg19	CCDS33750.1	.	.	.	.	.	.	.	.	.	.	G	46	12.165166	0.99642	.	.	ENSG00000047849	ENST00000264724;ENST00000395734;ENST00000426837;ENST00000360240;ENST00000383736	.	.	.	5.82	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.0553	10.3329	0.43833	0.0:0.1979:0.6643:0.1377	.	.	.	.	X	702;967;2112;967;687	.	ENSP00000264724:R702X	R	-	1	2	MAP4	47885782	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	2.079000	0.41577	1.330000	0.45394	0.563000	0.77884	CGA	.	.		0.463	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375		A	47910778	G	A	47910778	4	1	19	1	0	0	0	0	0	1	0	0	9267	1124	39	1	734	1	MAP4	3	47910778	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	28521498	47910778	150111652	19	1616										
MST1R	4486	hgsc.bcm.edu	37	chr3	49933256	49933256	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gagcgtgctctgtgggacccCatctggccctggccgcacca	13	16	2	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr3:49933256C>T	ENST00000296474.3	-	12	2881	c.2854G>A	c.(2854-2856)Ggg>Agg	p.G952R	MST1R_ENST00000344206.4_Missense_Mutation_p.G903R	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	952					cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		TGTGGGACCCCATCTGGCCCT	0.617																																					p.G952R		Atlas-SNP	.											.	MST1R	205	.	0			c.G2854A						.						64	63	64					3																	49933256		2203	4300	6503	SO:0001583	missense	4486	exon12			GGACCCCATCTGG	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.2854G>A	chr3.hg19:g.49933256C>T	ENSP00000296474:p.Gly952Arg	36.0	0.0		44.0	6.0	NM_002447	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	hg19	CCDS2807.1	.	.	.	.	.	.	.	.	.	.	C	6.580	0.475439	0.12521	.	.	ENSG00000164078	ENST00000296474;ENST00000344206	T;T	0.73897	-0.79;-0.67	4.54	-0.859	0.10685	.	0.595335	0.18888	N	0.128389	T	0.41236	0.1150	N	0.04043	-0.29	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.24764	-1.0151	10	0.10636	T	0.68	-5.8864	4.0998	0.10009	0.0:0.3536:0.338:0.3084	.	952	Q04912	RON_HUMAN	R	952;903	ENSP00000296474:G952R;ENSP00000341325:G903R	ENSP00000296474:G952R	G	-	1	0	MST1R	49908260	0.000000	0.05858	0.001000	0.08648	0.098000	0.18820	-0.538000	0.06120	-0.000000	0.14550	0.491000	0.48974	GGG	.	.		0.617	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			T	49933256	C	T	49933256	3	4	19	1	0	0	0	0	1	0	0	0	9900	594	21	3	1384	3	MST1R	3	49933256	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	2022478	49933256	148089174	20	1617										
RNF168	165918	hgsc.bcm.edu	37	chr3	196199175	196199175	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	atctggggaagattcgggggAcacttttcttctttttgcag	12	7	3	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr3:196199175A>G	ENST00000318037.3	-	6	1825	c.1231T>C	c.(1231-1233)Tcc>Ccc	p.S411P	CTD-2002J20.1_ENST00000610042.1_RNA	NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	411					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		GATTCGGGGGACACTTTTCTT	0.383																																					p.S411P		Atlas-SNP	.											.	RNF168	49	.	0			c.T1231C						.						123	119	120					3																	196199175		2203	4300	6503	SO:0001583	missense	165918	exon6			CGGGGGACACTTT	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.1231T>C	chr3.hg19:g.196199175A>G	ENSP00000320898:p.Ser411Pro	74.0	0.0		99.0	8.0	NM_152617	Q8NA67|Q96NS4	Missense_Mutation	SNP	ENST00000318037.3	hg19	CCDS3317.1	.	.	.	.	.	.	.	.	.	.	A	8.737	0.917952	0.17982	.	.	ENSG00000163961	ENST00000318037	T	0.08008	3.14	5.81	3.35	0.38373	.	0.753892	0.12445	N	0.468260	T	0.05823	0.0152	N	0.22421	0.69	0.09310	N	1	P	0.34934	0.476	B	0.28553	0.091	T	0.34030	-0.9845	10	0.59425	D	0.04	0.1595	8.7077	0.34365	0.8031:0.1292:0.0677:0.0	.	411	Q8IYW5	RN168_HUMAN	P	411	ENSP00000320898:S411P	ENSP00000320898:S411P	S	-	1	0	RNF168	197683572	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.995000	0.29706	0.420000	0.25954	0.482000	0.46254	TCC	.	.		0.383	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		G	196199175	A	G	196199175	3	3	19	1	0	0	0	0	1	0	0	0	13474	275	10	2	488	2	RNF168	3	196199175	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	146265919	196199175	1823255	21	1618										
ZNF732	654254	hgsc.bcm.edu	37	chr4	266039	266039	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gattaaataccatttaaagtCtttgccacattcttcacatg	4	9	3	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr4:266039C>A	ENST00000419098.1	-	4	617	c.607G>T	c.(607-609)Gac>Tac	p.D203Y		NM_001137608.1	NP_001131080.1	B4DXR9	ZN732_HUMAN	zinc finger protein 732	203					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)	3						CATTTAAAGTCTTTGCCACAT	0.368																																					p.D202Y		Atlas-SNP	.											ZNF732_ENST00000419098,NS,carcinoma,0,4	ZNF732	117	.	0			c.G604T						.						77	64	68					4																	266039		692	1591	2283	SO:0001583	missense	654254	exon3			TAAAGTCTTTGCC	AK302099	CCDS46990.1	4p16.3	2014-02-12	2009-07-22		ENSG00000186777	ENSG00000186777		"Zinc fingers, C2H2-type", "-"	37138	protein-coding gene	gene with protein product							Standard	NM_001137608		Approved	FLJ59067	uc011buu.1	B4DXR9	OTTHUMG00000159883	ENST00000419098.1:c.607G>T	chr4.hg19:g.266039C>A	ENSP00000415774:p.Asp203Tyr	81.0	0.0		117.0	24.0	NM_001137608		Missense_Mutation	SNP	ENST00000419098.1	hg19	CCDS46990.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.495962	0.26774	.	.	ENSG00000186777	ENST00000419098	T	0.17054	2.3	0.937	0.937	0.19494	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17109	0.0411	L	0.31578	0.945	0.09310	N	0.999998	P	0.48589	0.912	P	0.52454	0.699	T	0.13602	-1.0503	9	0.87932	D	0	.	3.3245	0.07062	0.0:0.6837:0.0:0.3163	.	203	B4DXR9	ZN732_HUMAN	Y	203	ENSP00000415774:D203Y	ENSP00000415774:D203Y	D	-	1	0	ZNF732	256039	0.000000	0.05858	0.301000	0.25044	0.279000	0.26890	-0.185000	0.09684	0.392000	0.25172	0.393000	0.25936	GAC	.	.		0.368	ZNF732-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357937.2	NM_001137608		A	266039	C	A	266039	3	1	19	1	0	0	0	0	1	0	0	0	18138	913	32	3	1154	3	ZNF732	4	266039	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10		266039	190888237	22	1619										
D4S234E	27065	hgsc.bcm.edu	37	chr4	4411339	4411339	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tcgccctggccttcctcaccTgcgtcgtcttcctggttgtc	9	17	2	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr4:4411339T>A	ENST00000421177.2	+	8	2277	c.286T>A	c.(286-288)Tgc>Agc	p.C96S	NSG1_ENST00000505246.1_Missense_Mutation_p.C96S|NSG1_ENST00000513555.1_Missense_Mutation_p.C96S|NSG1_ENST00000433139.2_Missense_Mutation_p.C96S|NSG1_ENST00000504171.1_Missense_Mutation_p.C57S|NSG1_ENST00000397958.1_Missense_Mutation_p.C96S|NSG1_ENST00000506380.1_Missense_Mutation_p.C96S			P42857	NSG1_HUMAN		96					clathrin coat assembly (GO:0048268)|dopamine receptor signaling pathway (GO:0007212)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)											CTTCCTCACCTGCGTCGTCTT	0.602																																					p.C96S		Atlas-SNP	.											.	.	.	.	0			c.T286A						.						191	147	162					4																	4411339		2203	4300	6503	SO:0001583	missense	0	exon4			CTCACCTGCGTCG																												ENST00000421177.2:c.286T>A	chr4.hg19:g.4411339T>A	ENSP00000388823:p.Cys96Ser	88.0	0.0		82.0	34.0	NM_014392	B4DXC5|Q49AQ1	Missense_Mutation	SNP	ENST00000421177.2	hg19	CCDS3376.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.274754	0.80580	.	.	ENSG00000168824	ENST00000421177;ENST00000513555;ENST00000505246;ENST00000506380;ENST00000397958;ENST00000433139;ENST00000504171	.	.	.	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.77558	0.4148	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	0.991;1.0	D;D	0.91635	0.987;0.999	T	0.80942	-0.1157	9	0.87932	D	0	-18.7562	13.3663	0.60687	0.0:0.0:0.0:1.0	.	57;96	B4DXC5;P42857	.;NSG1_HUMAN	S	96;96;96;96;96;96;57	.	ENSP00000381049:C96S	C	+	1	0	AC110814.1	4462240	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.195000	0.77798	1.728000	0.51552	0.459000	0.35465	TGC	.	.		0.602	NSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246799.1			A	4411339	T	A	4411339	3	1	19	1	0	0	0	0	1	0	0	0	4216	1580	55	4	296	4	D4S234E	4	4411339	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	4145300	4411339	186742937	23	1620										
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25767058	25767058	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gtctcccatcttcaaatatgCtgcaggaaataaagcacaga	7	10	3	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr4:25767058C>T	ENST00000399878.3	-	20	2968		c.e20-1		SEL1L3_ENST00000264868.5_Splice_Site|SEL1L3_ENST00000502949.1_Splice_Site	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)							integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						TTCAAATATGCTGCAGGAAAT	0.418																																					.		Atlas-SNP	.											.	SEL1L3	62	.	0			c.2846-1G>A						.						103	100	101					4																	25767058		1890	4115	6005	SO:0001630	splice_region_variant	23231	exon21			AATATGCTGCAGG	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.2846-1G>A	chr4.hg19:g.25767058C>T		81.0	0.0		72.0	28.0	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Splice_Site	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201008	0.79015	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949;ENST00000507618	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8251	0.92115	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEL1L3	25376156	1.000000	0.71417	0.923000	0.36655	0.724000	0.41520	5.561000	0.67339	2.439000	0.82584	0.543000	0.68304	.	.	.		0.418	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	Intron	T	25767058	C	T	25767058	5	4	19	1	0	0	0	0	0	0	1	0	14027	811	28	3	573	3	SEL1L3	4	25767058	Splice_Site	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	21355719	25767058	165387218	24	1621										
CLOCK	9575	hgsc.bcm.edu	37	chr4	56308736	56308736	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ttatacagtggggctgtaagAgtgctctgtgtctgactggg	15	6	2	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr4:56308736A>C	ENST00000309964.4	-	20	2218	c.1968T>G	c.(1966-1968)acT>acG	p.T656T	CLOCK_ENST00000381322.1_Silent_p.T656T|CLOCK_ENST00000513440.1_Silent_p.T656T	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	656	Interaction with NR3C1. {ECO:0000250|UniProtKB:O08785}.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			GGGCTGTAAGAGTGCTCTGTG	0.438																																					p.T656T		Atlas-SNP	.											.	CLOCK	81	.	0			c.T1968G						.						170	170	170					4																	56308736		2203	4300	6503	SO:0001819	synonymous_variant	9575	exon21			TGTAAGAGTGCTC	AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	2082	protein-coding gene	gene with protein product		601851	"clock (mouse) homolog", "clock homolog (mouse)"			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.1968T>G	chr4.hg19:g.56308736A>C		112.0	0.0		128.0	54.0	NM_004898	A0AV01|A2I2N9|O14516|Q9UIT8	Silent	SNP	ENST00000309964.4	hg19	CCDS3500.1																																																																																			.	.		0.438	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		C	56308736	A	C	56308736	2	2	19	1	0	0	0	0	0	0	0	1	3551	291	11	5		5	CLOCK	4	56308736	Silent	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	30541678	56308736	134845540	25	1622										
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69188594	69188594	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aatactttcatcggggggaaAcagaagacaaagctgggttc	12	7	1	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr4:69188594A>G	ENST00000344157.4	-	11	1809	c.1474T>C	c.(1474-1476)Ttt>Ctt	p.F492L	YTHDC1_ENST00000355665.3_Missense_Mutation_p.F474L|YTHDC1_ENST00000579690.1_Missense_Mutation_p.F492L	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	492	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						TCGGGGGGAAACAGAAGACAA	0.413																																					p.F492L		Atlas-SNP	.											.	YTHDC1	81	.	0			c.T1474C						.						87	91	90					4																	69188594		2203	4300	6503	SO:0001583	missense	91746	exon11			GGGGAAACAGAAG	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.1474T>C	chr4.hg19:g.69188594A>G	ENSP00000339245:p.Phe492Leu	180.0	0.0		257.0	119.0	NM_001031732	Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	hg19	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.781351	0.49891	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.35421	1.31;1.31	6.06	6.06	0.98353	YTH domain (2);	0.093907	0.85682	D	0.000000	T	0.59101	0.2169	M	0.62266	1.93	0.80722	D	1	D;D	0.89917	0.97;1.0	D;D	0.85130	0.984;0.997	T	0.59841	-0.7378	10	0.59425	D	0.04	.	16.6245	0.84952	1.0:0.0:0.0:0.0	.	474;492	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	L	492;474	ENSP00000339245:F492L;ENSP00000347888:F474L	ENSP00000339245:F492L	F	-	1	0	YTHDC1	68871189	1.000000	0.71417	0.987000	0.45799	0.987000	0.75469	8.536000	0.90627	2.323000	0.78572	0.528000	0.53228	TTT	.	.		0.413	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		G	69188594	A	G	69188594	3	3	19	1	0	0	0	0	1	0	0	0	17511	43	2	2	737	2	YTHDC1	4	69188594	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	12879858	69188594	121965682	26	1623										
INPP4B	8821	hgsc.bcm.edu	37	chr4	143226623	143226623	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	agacccacctcaggctcaggAccagcaattgctcctttgac	8	15	2	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr4:143226623A>G	ENST00000513000.1	-	10	924	c.491T>C	c.(490-492)gTc>gCc	p.V164A	INPP4B_ENST00000308502.4_Missense_Mutation_p.V164A|INPP4B_ENST00000508116.1_Missense_Mutation_p.V164A|INPP4B_ENST00000509777.1_Missense_Mutation_p.V164A|INPP4B_ENST00000262992.4_Missense_Mutation_p.V164A	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	164					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CAGGCTCAGGACCAGCAATTG	0.383																																					p.V164A		Atlas-SNP	.											.	INPP4B	132	.	0			c.T491C						.						200	216	211					4																	143226623		2203	4300	6503	SO:0001583	missense	8821	exon10			CTCAGGACCAGCA	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.491T>C	chr4.hg19:g.143226623A>G	ENSP00000425487:p.Val164Ala	291.0	0.0		345.0	149.0	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	hg19	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	A	8.262	0.811404	0.16537	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64;1.64;1.64	5.74	4.03	0.46877	C2 calcium/lipid-binding domain, CaLB (1);	0.485095	0.21380	N	0.075494	T	0.15435	0.0372	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28427	-1.0044	10	0.08179	T	0.78	.	9.7886	0.40692	0.1612:0.0:0.8388:0.0	.	35;164	B7Z6T2;O15327	.;INP4B_HUMAN	A	164;164;164;35;164;164;164;35	ENSP00000425487:V164A;ENSP00000262992:V164A;ENSP00000308441:V164A;ENSP00000423954:V164A;ENSP00000422793:V164A;ENSP00000427250:V164A;ENSP00000421065:V35A	ENSP00000262992:V164A	V	-	2	0	INPP4B	143446073	1.000000	0.71417	0.412000	0.26496	0.957000	0.61999	2.806000	0.47947	0.787000	0.33731	-0.239000	0.12128	GTC	.	.		0.383	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		G	143226623	A	G	143226623	3	3	19	1	0	0	0	0	1	0	0	0	7762	275	10	2	2355	2	INPP4B	4	143226623	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	74038029	143226623	47927653	27	1624										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155410658	155410658	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ctcggtctagagtccggataGtgctgatcgcaccgctttcg	12	12	1	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr4:155410658G>A	ENST00000339452.1	-	1	2210	c.1850C>T	c.(1849-1851)aCt>aTt	p.T617I	DCHS2_ENST00000456341.2_Missense_Mutation_p.T610I|DCHS2_ENST00000443500.1_Missense_Mutation_p.T617I	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1742	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AGTCCGGATAGTGCTGATCGC	0.602																																					p.T617I		Atlas-SNP	.											.	DCHS2	594	.	0			c.C1850T						.						47	48	48					4																	155410658		692	1591	2283	SO:0001583	missense	54798	exon1			CGGATAGTGCTGA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.1850C>T	chr4.hg19:g.155410658G>A	ENSP00000345062:p.Thr617Ile	129.0	0.0		175.0	31.0	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000339452.1	hg19	CCDS47150.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305510	0.60305	.	.	ENSG00000197410	ENST00000339452;ENST00000544161;ENST00000456341;ENST00000443500	T;T;T	0.55760	0.5;0.5;0.5	5.17	5.17	0.71159	.	.	.	.	.	T	0.60818	0.2298	L	0.43701	1.375	0.39861	D	0.973372	D;D	0.71674	0.998;0.965	D;P	0.70016	0.967;0.896	T	0.57608	-0.7782	9	0.31617	T	0.26	.	10.9228	0.47174	0.0857:0.0:0.9143:0.0	.	617;617	E9PG03;E9PC11	.;.	I	617;617;610;617	ENSP00000345062:T617I;ENSP00000408543:T610I;ENSP00000395539:T617I	ENSP00000345062:T617I	T	-	2	0	DCHS2	155630108	1.000000	0.71417	0.962000	0.40283	0.608000	0.37181	6.354000	0.73036	2.692000	0.91855	0.557000	0.71058	ACT	.	.		0.602	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552		A	155410658	G	A	155410658	3	1	19	1	0	0	0	0	1	0	0	0	4290	1029	36	3	9234	3	DCHS2	4	155410658	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	12184035	155410658	35743618	28	1625										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155412105	155412105	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gaagctgtagtggtcccgccGctcgcggtccaggcgccgcg	16	15	0	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr4:155412105G>A	ENST00000339452.1	-	1	763	c.403C>T	c.(403-405)Cgg>Tgg	p.R135W	DCHS2_ENST00000456341.2_Missense_Mutation_p.R128W|DCHS2_ENST00000443500.1_Missense_Mutation_p.R135W	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1336	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TGGTCCCGCCGCTCGCGGTCC	0.672																																					p.R135W		Atlas-SNP	.											.	DCHS2	594	.	0			c.C403T						.						8	13	11					4																	155412105		685	1574	2259	SO:0001583	missense	54798	exon1			CCCGCCGCTCGCG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.403C>T	chr4.hg19:g.155412105G>A	ENSP00000345062:p.Arg135Trp	263.0	0.0		434.0	253.0	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000339452.1	hg19	CCDS47150.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.784462	0.70222	.	.	ENSG00000197410	ENST00000339452;ENST00000544161;ENST00000456341;ENST00000443500	T;T;T	0.66995	-0.24;-0.24;-0.24	4.51	4.51	0.55191	.	.	.	.	.	T	0.81123	0.4757	M	0.86805	2.84	0.21386	N	0.999707	D;D	0.89917	0.994;1.0	P;P	0.61592	0.696;0.891	T	0.72789	-0.4187	9	0.72032	D	0.01	.	11.07	0.47997	0.0:0.0:0.68:0.32	.	135;135	E9PG03;E9PC11	.;.	W	135;135;128;135	ENSP00000345062:R135W;ENSP00000408543:R128W;ENSP00000395539:R135W	ENSP00000345062:R135W	R	-	1	2	DCHS2	155631555	0.958000	0.32768	0.983000	0.44433	0.988000	0.76386	1.011000	0.29911	2.049000	0.60858	0.462000	0.41574	CGG	.	.		0.672	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552		A	155412105	G	A	155412105	3	1	19	1	0	0	0	0	1	0	0	0	4290	1086	38	1	10681	1	DCHS2	4	155412105	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	1447	155412105	35742171	29	1626										
HCN1	348980	hgsc.bcm.edu	37	chr5	45695977	45695977	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ccccccgccggctcctcgccGccgccgccgccgccgccacc	10	28	0	0	rs56063136|rs56060059		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr5:45695977G>A	ENST00000303230.4	-	1	276	c.219C>T	c.(217-219)ggC>ggT	p.G73G		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	73	Gly-rich.				apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						GCTCCTcgccgccgccgccgc	0.771																																					p.G73G		Atlas-SNP	.											.	HCN1	298	.	0			c.C219T						.						4	5	5					5																	45695977		1679	3595	5274	SO:0001819	synonymous_variant	348980	exon1			CTCGCCGCCGCCG	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.219C>T	chr5.hg19:g.45695977G>A		22.0	0.0		58.0	18.0	NM_021072		Silent	SNP	ENST00000303230.4	hg19	CCDS3952.1																																																																																			.	.		0.771	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		A	45695977	G	A	45695977	2	1	19	1	0	0	0	0	0	0	0	1	7005	1074	38	1		1	HCN1	5	45695977	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10		45695977	135219283	30	1627										
ITGA1	3672	hgsc.bcm.edu	37	chr5	52229759	52229759	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ccacatttcaattgctgccaAtgagacagtccctgaagtta	7	11	1	2	rs539547486		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr5:52229759A>G	ENST00000282588.6	+	23	3355	c.2897A>G	c.(2896-2898)aAt>aGt	p.N966S	CTD-2175A23.1_ENST00000505701.1_RNA|CTD-2175A23.1_ENST00000503559.1_RNA	NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	966					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				ATTGCTGCCAATGAGACAGTC	0.284																																					p.N966S		Atlas-SNP	.											.	ITGA1	112	.	0			c.A2897G						.						45	49	47					5																	52229759		2197	4280	6477	SO:0001583	missense	3672	exon23			CTGCCAATGAGAC	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.2897A>G	chr5.hg19:g.52229759A>G	ENSP00000282588:p.Asn966Ser	379.0	0.0		517.0	191.0	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	hg19	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.043823	0.55110	.	.	ENSG00000213949	ENST00000282588	T	0.49720	0.77	5.77	5.77	0.91146	Integrin alpha-2 (1);	0.269411	0.41938	D	0.000789	T	0.35248	0.0925	L	0.34521	1.04	0.42538	D	0.993063	B	0.21821	0.061	B	0.25759	0.063	T	0.17048	-1.0382	10	0.09084	T	0.74	.	12.482	0.55850	1.0:0.0:0.0:0.0	.	966	P56199	ITA1_HUMAN	S	966	ENSP00000282588:N966S	ENSP00000282588:N966S	N	+	2	0	ITGA1	52265516	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.041000	0.57339	2.194000	0.70268	0.528000	0.53228	AAT	.	.		0.284	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		G	52229759	A	G	52229759	3	3	19	1	0	0	0	0	1	0	0	0	7881	101	4	2	2987	2	ITGA1	5	52229759	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	6533782	52229759	128685501	31	1628										
SLCO4C1	353189	hgsc.bcm.edu	37	chr5	101627074	101627074	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aagagaccccaatttatattCtccactgaaaaattgtggca	6	9	1	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr5:101627074C>A	ENST00000310954.6	-	2	878	c.592G>T	c.(592-594)Gaa>Taa	p.E198*		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		AATTTATATTCTCCACTGAAA	0.358																																					p.E198X		Atlas-SNP	.											SLCO4C1,NS,carcinoma,0,1	SLCO4C1	113	.	0			c.G592T						.						75	74	75					5																	101627074		2203	4300	6503	SO:0001587	stop_gained	353189	exon2			TATATTCTCCACT	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"Solute carriers"	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.592G>T	chr5.hg19:g.101627074C>A	ENSP00000309741:p.Glu198*	196.0	0.0		245.0	14.0	NM_180991		Nonsense_Mutation	SNP	ENST00000310954.6	hg19	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.296652	0.81025	.	.	ENSG00000173930	ENST00000310954	.	.	.	5.43	-5.92	0.02261	.	2.242970	0.01637	N	0.023842	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	9.8536	0.41073	0.0:0.4518:0.1658:0.3824	.	.	.	.	X	198	.	ENSP00000309741:E198X	E	-	1	0	SLCO4C1	101654973	0.000000	0.05858	0.001000	0.08648	0.280000	0.26924	-0.636000	0.05465	-2.033000	0.00925	-1.094000	0.02160	GAA	.	.		0.358	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991		A	101627074	C	A	101627074	4	1	19	1	0	0	0	0	0	1	0	0	14745	922	32	3	1630	3	SLCO4C1	5	101627074	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	49397315	101627074	79288186	32	1629										
PKD2L2	27039	hgsc.bcm.edu	37	chr5	137241951	137241951	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tacttcatggcagttttactCtgtgaagctcctcagatatg	8	9	3	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr5:137241951C>A	ENST00000508883.1	+	6	829	c.803C>A	c.(802-804)tCt>tAt	p.S268Y	PKD2L2_ENST00000508638.1_Missense_Mutation_p.S268Y|PKD2L2_ENST00000290431.5_Missense_Mutation_p.S268Y|PKD2L2_ENST00000350250.4_Missense_Mutation_p.S234Y|PKD2L2_ENST00000502810.1_Missense_Mutation_p.S268Y			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	268					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CAGTTTTACTCTGTGAAGCTC	0.368																																					p.S268Y		Atlas-SNP	.											.	PKD2L2	68	.	0			c.C803A						.						127	119	121					5																	137241951		1830	4089	5919	SO:0001583	missense	27039	exon6			TTTACTCTGTGAA	AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"Voltage-gated ion channels / Transient receptor potential cation channels"	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.803C>A	chr5.hg19:g.137241951C>A	ENSP00000424725:p.Ser268Tyr	131.0	0.0		171.0	79.0	NM_001258448	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	hg19		.	.	.	.	.	.	.	.	.	.	C	26.3	4.729213	0.89390	.	.	ENSG00000078795	ENST00000503015;ENST00000350250;ENST00000508638;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T;T;T	0.73681	-0.77;-0.77;-0.77;-0.77;-0.77;-0.77	5.12	5.12	0.69794	Polycystin cation channel, PKD1/PKD2 (1);	0.000000	0.64402	D	0.000017	D	0.85004	0.5598	M	0.62723	1.935	0.49582	D	0.999801	D;D;D	0.89917	0.992;1.0;1.0	D;D;D	0.91635	0.958;0.999;0.999	D	0.86604	0.1868	10	0.87932	D	0	-10.9603	18.1552	0.89688	0.0:1.0:0.0:0.0	.	268;268;268	Q9NZM6;E9PC91;Q9NZM6-5	PK2L2_HUMAN;.;.	Y	178;234;268;268;268;268	ENSP00000424885:S178Y;ENSP00000344177:S234Y;ENSP00000423382:S268Y;ENSP00000425513:S268Y;ENSP00000424725:S268Y;ENSP00000290431:S268Y	ENSP00000290431:S268Y	S	+	2	0	PKD2L2	137269850	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.786000	0.85741	2.396000	0.81511	0.467000	0.42956	TCT	.	.		0.368	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		A	137241951	C	A	137241951	3	1	19	1	0	0	0	0	1	0	0	0	11977	913	32	3	825	3	PKD2L2	5	137241951	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	35614877	137241951	43673309	33	1630										
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140228373	140228373	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ccgcgaggagctgtgcgggcGgagcgcggagtgcagcatcc	19	12	0	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr5:140228373G>A	ENST00000532602.1	+	1	1326	c.293G>A	c.(292-294)cGg>cAg	p.R98Q	PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.R98Q|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	98	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGTGCGGGCGGAGCGCGGAG	0.567																																					p.R98Q	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G293A						.						100	90	93					5																	140228373		2197	4261	6458	SO:0001583	missense	9752	exon1			GCGGGCGGAGCGC	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.293G>A	chr5.hg19:g.140228373G>A	ENSP00000436042:p.Arg98Gln	187.0	0.0		245.0	36.0	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	hg19	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	G	10.54	1.377557	0.24944	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.26373	1.74;1.74	3.91	3.02	0.34903	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.296211	0.17413	U	0.175101	T	0.10809	0.0264	N	0.13198	0.31	0.09310	N	1	B;P	0.49090	0.067;0.919	B;B	0.38428	0.021;0.273	T	0.12553	-1.0543	10	0.46703	T	0.11	.	2.3719	0.04332	0.2068:0.0:0.5001:0.293	.	98;98	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	Q	98	ENSP00000436042:R98Q;ENSP00000367362:R98Q	ENSP00000367362:R98Q	R	+	2	0	PCDHA9	140208557	0.000000	0.05858	0.998000	0.56505	0.685000	0.39939	0.165000	0.16564	2.155000	0.67459	0.586000	0.80456	CGG	.	.		0.567	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140228373	G	A	140228373	3	1	19	1	0	0	0	0	1	0	0	0	11540	1116	39	1	295	1	PCDHA9	5	140228373	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	2986422	140228373	40686887	34	1631										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141335204	141335204	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tcttttctgtccggcagatgGacatgaacaaagccaggatc	10	10	2	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr5:141335204G>T	ENST00000231484.3	-	1	3423	c.2213C>A	c.(2212-2214)tCc>tAc	p.S738Y	AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	738					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGGCAGATGGACATGAACAA	0.582																																					p.S738Y		Atlas-SNP	.											.	PCDH12	133	.	0			c.C2213A						.						66	58	61					5																	141335204		2203	4300	6503	SO:0001583	missense	51294	exon1			CAGATGGACATGA	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2213C>A	chr5.hg19:g.141335204G>T	ENSP00000231484:p.Ser738Tyr	86.0	0.0		94.0	36.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	G	17.12	3.307565	0.60305	.	.	ENSG00000113555	ENST00000231484	T	0.53423	0.62	5.01	4.14	0.48551	.	0.062533	0.64402	D	0.000003	T	0.61009	0.2313	M	0.62723	1.935	0.43250	D	0.995179	D	0.71674	0.998	D	0.63488	0.915	T	0.63629	-0.6594	10	0.62326	D	0.03	.	11.0435	0.47844	0.0898:0.0:0.9102:0.0	.	738	Q9NPG4	PCD12_HUMAN	Y	738	ENSP00000231484:S738Y	ENSP00000231484:S738Y	S	-	2	0	PCDH12	141315388	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.233000	0.72320	1.360000	0.45960	0.561000	0.74099	TCC	.	.		0.582	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		T	141335204	G	T	141335204	3	4	19	1	0	0	0	0	1	0	0	0	11519	1174	41	3	1357	3	PCDH12	5	141335204	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	1106831	141335204	39580056	35	1632										
FAT2	2196	hgsc.bcm.edu	37	chr5	150945848	150945848	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	accgaggctctgattcgcggTccaggtgtcctgtaacaacc	11	13	1	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr5:150945848T>C	ENST00000261800.5	-	1	2657	c.2645A>G	c.(2644-2646)gAc>gGc	p.D882G		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	882	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGATTCGCGGTCCAGGTGTCC	0.552																																					p.D882G		Atlas-SNP	.											.	FAT2	465	.	0			c.A2645G						.						94	90	91					5																	150945848		2203	4300	6503	SO:0001583	missense	2196	exon1			TCGCGGTCCAGGT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2645A>G	chr5.hg19:g.150945848T>C	ENSP00000261800:p.Asp882Gly	151.0	0.0		202.0	99.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.756354	0.69648	.	.	ENSG00000086570	ENST00000261800	T	0.65178	-0.14	5.67	5.67	0.87782	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000001	D	0.84848	0.5563	H	0.94503	3.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89114	0.3498	10	0.72032	D	0.01	.	15.924	0.79597	0.0:0.0:0.0:1.0	.	882	Q9NYQ8	FAT2_HUMAN	G	882	ENSP00000261800:D882G	ENSP00000261800:D882G	D	-	2	0	FAT2	150926041	1.000000	0.71417	0.971000	0.41717	0.782000	0.44232	7.975000	0.88055	2.163000	0.67991	0.459000	0.35465	GAC	.	.		0.552	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		C	150945848	T	C	150945848	3	2	19	1	0	0	0	0	1	0	0	0	5698	1667	58	2	10496	2	FAT2	5	150945848	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	9610644	150945848	29969412	36	1633										
CAGE1	285782	hgsc.bcm.edu	37	chr6	7378874	7378874	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cataagaagcttggaggttgGctagggttgagggcagattc	16	5	0	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:7378874G>A	ENST00000512086.1	-	4	865	c.663C>T	c.(661-663)agC>agT	p.S221S	CAGE1_ENST00000338150.4_Silent_p.S221S|CAGE1_ENST00000379918.4_Silent_p.S221S|CAGE1_ENST00000509324.1_Intron|CAGE1_ENST00000502583.1_Silent_p.S221S|CAGE1_ENST00000296742.7_Silent_p.S85S			Q8TC20	CAGE1_HUMAN	cancer antigen 1	221										breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					TTGGAGGTTGGCTAGGGTTGA	0.393																																					p.S221S		Atlas-SNP	.											.	CAGE1	165	.	0			c.C663T						.						175	170	172					6																	7378874		1840	4089	5929	SO:0001819	synonymous_variant	285782	exon4			AGGTTGGCTAGGG	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"cancer/testis antigen 95"	608304	"cancer/testis antigen 3"	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.663C>T	chr6.hg19:g.7378874G>A		189.0	0.0		212.0	96.0	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Silent	SNP	ENST00000512086.1	hg19																																																																																				.	.		0.393	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745		A	7378874	G	A	7378874	2	1	19	1	0	0	0	0	0	0	0	1	2574	1194	42	3		3	CAGE1	6	7378874	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10		7378874	163736193	37	1634										
MRS2	57380	hgsc.bcm.edu	37	chr6	24403393	24403393	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tcctcccgttgctgcctgcgGccgccgagccaacctgattg	11	17	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:24403393G>T	ENST00000378386.3	+	1	212	c.119G>T	c.(118-120)gGc>gTc	p.G40V	MRS2_ENST00000378353.1_Missense_Mutation_p.G40V|MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000535061.1_Missense_Mutation_p.G40V|MRS2_ENST00000543597.1_5'UTR|MRS2_ENST00000443868.2_Missense_Mutation_p.G40V|MRS2_ENST00000274747.7_Missense_Mutation_p.G40V	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	40						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12						GCTGCCTGCGGCCGCCGAGCC	0.701																																					p.G40V		Atlas-SNP	.											.	MRS2	31	.	0			c.G119T						.						26	27	27					6																	24403393		2202	4295	6497	SO:0001583	missense	57380	exon1			CCTGCGGCCGCCG	AF288288	CCDS4552.1, CCDS69055.1, CCDS69056.1, CCDS75408.1	6p22.3-p22.1	2013-05-03	2013-05-03	2008-01-18	ENSG00000124532	ENSG00000124532			13785	protein-coding gene	gene with protein product			"MRS2-like, magnesium homeostasis factor (S. cerevisiae)", "MRS2 magnesium homeostasis factor homolog (S. cerevisiae)"	MRS2L			Standard	XM_005249242		Approved		uc003neb.3	Q9HD23	OTTHUMG00000014355	ENST00000378386.3:c.119G>T	chr6.hg19:g.24403393G>T	ENSP00000367637:p.Gly40Val	41.0	0.0		44.0	12.0	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Missense_Mutation	SNP	ENST00000378386.3	hg19	CCDS4552.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935352	0.52866	.	.	ENSG00000124532	ENST00000274747;ENST00000535061;ENST00000378386;ENST00000378353;ENST00000443868	T;T;T;T;T	0.53857	0.6;0.99;1.3;0.73;1.29	5.01	5.01	0.66863	.	0.973329	0.08365	N	0.957109	T	0.36082	0.0954	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.28552	0.215;0.032;0.215;0.078	B;B;B;B	0.38755	0.24;0.055;0.281;0.037	T	0.16100	-1.0414	10	0.66056	D	0.02	-7.0205	13.6908	0.62544	0.0:0.0:1.0:0.0	.	40;40;40;40	F5GWH3;B4DQL2;Q9HD23;Q9HD23-2	.;.;MRS2_HUMAN;.	V	40	ENSP00000274747:G40V;ENSP00000441839:G40V;ENSP00000367637:G40V;ENSP00000367604:G40V;ENSP00000399585:G40V	ENSP00000274747:G40V	G	+	2	0	MRS2	24511372	0.006000	0.16342	0.916000	0.36221	0.014000	0.08584	0.513000	0.22770	2.585000	0.87301	0.655000	0.94253	GGC	.	.		0.701	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1			T	24403393	G	T	24403393	3	4	19	1	0	0	0	0	1	0	0	0	9860	1203	42	3	121	3	MRS2	6	24403393	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	17024519	24403393	146711674	38	1635										
TDP2	51567	hgsc.bcm.edu	37	chr6	24651152	24651152	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ctgctgctgctctgaaaaatAttcgatcaaaacgaagttta	7	8	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:24651152A>T	ENST00000378198.4	-	7	1123	c.953T>A	c.(952-954)aTa>aAa	p.I318K	TDP2_ENST00000545995.1_Missense_Mutation_p.I348K|TDP2_ENST00000341060.3_Missense_Mutation_p.I260K			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	318					cell surface receptor signaling pathway (GO:0007166)|double-strand break repair (GO:0006302)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|PML body (GO:0016605)	5'-tyrosyl-DNA phosphodiesterase activity (GO:0070260)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)|tyrosyl-RNA phosphodiesterase activity (GO:0036317)			kidney(2)|large_intestine(1)|lung(5)|ovary(1)	9						TCTGAAAAATATTCGATCAAA	0.398								Direct reversal of damage																													p.I318K		Atlas-SNP	.											.	TDP2	29	.	0			c.T953A						.						98	96	97					6																	24651152		2203	4300	6503	SO:0001583	missense	51567	exon7			AAAAATATTCGAT	AJ269473	CCDS4557.1	6p22.3-p22.1	2010-05-07	2010-05-07	2010-05-07	ENSG00000111802	ENSG00000111802	3.1.4.-		17768	protein-coding gene	gene with protein product		605764	"TRAF and TNF receptor associated protein"	TTRAP		11478795	Standard	NM_016614		Approved		uc003nej.3	O95551	OTTHUMG00000014360	ENST00000378198.4:c.953T>A	chr6.hg19:g.24651152A>T	ENSP00000367440:p.Ile318Lys	127.0	0.0		226.0	146.0	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Missense_Mutation	SNP	ENST00000378198.4	hg19	CCDS4557.1	.	.	.	.	.	.	.	.	.	.	A	34	5.378913	0.95945	.	.	ENSG00000111802	ENST00000378198;ENST00000545995;ENST00000545780;ENST00000341060	D;D;D	0.85861	-2.04;-2.04;-2.04	6.07	6.07	0.98685	Endonuclease/exonuclease/phosphatase (2);	0.182021	0.56097	D	0.000040	D	0.90031	0.6887	M	0.70275	2.135	0.80722	D	1	D	0.59767	0.986	D	0.66497	0.944	D	0.91230	0.5013	10	0.87932	D	0	-18.1364	16.6288	0.85011	1.0:0.0:0.0:0.0	.	318	O95551	TYDP2_HUMAN	K	318;348;240;260	ENSP00000367440:I318K;ENSP00000437637:I348K;ENSP00000345345:I260K	ENSP00000345345:I260K	I	-	2	0	TDP2	24759131	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	8.809000	0.91944	2.326000	0.78906	0.533000	0.62120	ATA	.	.		0.398	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1			T	24651152	A	T	24651152	3	4	19	1	0	0	0	0	1	0	0	0	15744	449	16	4	139	4	TDP2	6	24651152	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	247759	24651152	146463915	39	1636										
SLC17A2	10246	hgsc.bcm.edu	37	chr6	25917052	25917052	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tgaccatcgcctttatggggAcagctcgtccaggagaactg	12	11	0	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:25917052A>T	ENST00000265425.3	-	7	811	c.791T>A	c.(790-792)gTc>gAc	p.V264D	SLC17A2_ENST00000377850.3_Missense_Mutation_p.V264D|SLC17A2_ENST00000360488.3_Missense_Mutation_p.V264D			O00624	NPT3_HUMAN	solute carrier family 17, member 2	264					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	31						CTTTATGGGGACAGCTCGTCC	0.498																																					p.V264D		Atlas-SNP	.											.	SLC17A2	70	.	0			c.T791A						.						92	85	88					6																	25917052		2203	4300	6503	SO:0001583	missense	10246	exon8			ATGGGGACAGCTC	U90544	CCDS4567.1, CCDS69060.1	6p22.2	2013-07-18	2013-07-18		ENSG00000112337	ENSG00000112337		"Solute carriers"	10930	protein-coding gene	gene with protein product		611049	"solute carrier family 17 (sodium phosphate), member 2"			9149941	Standard	NM_001286123		Approved	NPT3	uc003nfl.3	O00624	OTTHUMG00000014413	ENST00000265425.3:c.791T>A	chr6.hg19:g.25917052A>T	ENSP00000265425:p.Val264Asp	95.0	0.0		121.0	53.0	NM_005835	A6NK81|A6NLD6|Q5TB84|Q76P85	Missense_Mutation	SNP	ENST00000265425.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.86	3.712393	0.68730	.	.	ENSG00000112337	ENST00000360488;ENST00000377850;ENST00000265425	T;T;T	0.60299	0.2;0.2;0.2	4.65	4.65	0.58169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.311671	0.23569	N	0.046769	T	0.56934	0.2019	L	0.49126	1.545	0.58432	D	0.999999	P;P;D	0.57571	0.949;0.949;0.98	P;P;P	0.59948	0.866;0.633;0.844	T	0.63157	-0.6700	10	0.87932	D	0	.	10.6641	0.45719	1.0:0.0:0.0:0.0	.	264;264;264	O00624;A6NK81;O00624-2	NPT3_HUMAN;.;.	D	264	ENSP00000353677:V264D;ENSP00000367081:V264D;ENSP00000265425:V264D	ENSP00000265425:V264D	V	-	2	0	SLC17A2	26025031	0.994000	0.37717	1.000000	0.80357	0.620000	0.37586	6.228000	0.72288	2.067000	0.61834	0.460000	0.39030	GTC	.	.		0.498	SLC17A2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040075.1			T	25917052	A	T	25917052	3	4	19	1	0	0	0	0	1	0	0	0	14432	275	10	4	535	4	SLC17A2	6	25917052	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	1265900	25917052	145198015	40	1637										
HIST1H4G	8369	hgsc.bcm.edu	37	chr6	26247145	26247145	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aatattatcgctcagtacctTgcgatggcacttggcaccgc	9	12	1	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:26247145T>C	ENST00000244537.4	-	1	114	c.61A>G	c.(61-63)Aag>Gag	p.K21E		NM_003547.2	NP_003538.1	Q99525	H4G_HUMAN	histone cluster 1, H4g	21						nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				CTCAGTACCTTGCGATGGCAC	0.512																																					p.K21E		Atlas-SNP	.											.	HIST1H4G	18	.	0			c.A61G						.						54	50	51					6																	26247145		2203	4300	6503	SO:0001583	missense	8369	exon1			GTACCTTGCGATG	Z80788	CCDS4599.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124578	ENSG00000275663		"Histones / Replication-dependent"	4792	protein-coding gene	gene with protein product		602832	"H4 histone family, member L", "histone 1, H4g"	H4FL		9119399, 12408966	Standard	NM_003547		Approved	H4/l	uc003nhf.3	Q99525	OTTHUMG00000014444	ENST00000244537.4:c.61A>G	chr6.hg19:g.26247145T>C	ENSP00000244537:p.Lys21Glu	60.0	0.0		75.0	34.0	NM_003547		Missense_Mutation	SNP	ENST00000244537.4	hg19	CCDS4599.1	.	.	.	.	.	.	.	.	.	.	.	12.19	1.864828	0.32977	.	.	ENSG00000124578	ENST00000244537	.	.	.	3.34	3.34	0.38264	Histone-fold (2);	.	.	.	.	T	0.47691	0.1459	.	.	.	0.41624	D	0.988984	P	0.41748	0.761	P	0.45660	0.489	T	0.56926	-0.7898	7	0.87932	D	0	.	11.7312	0.51737	0.0:0.0:0.0:1.0	.	21	Q99525	H4G_HUMAN	E	21	.	ENSP00000244537:K21E	K	-	1	0	HIST1H4G	26355124	1.000000	0.71417	0.316000	0.25252	0.003000	0.03518	5.573000	0.67417	1.502000	0.48669	0.410000	0.27636	AAG	.	.		0.512	HIST1H4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040107.1	NM_003547		C	26247145	T	C	26247145	3	2	19	1	0	0	0	0	1	0	0	0	7180	1821	63	2	239	2	HIST1H4G	6	26247145	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	330093	26247145	144867922	41	1638										
MRPS18B	28973	hgsc.bcm.edu	37	chr6	30587275	30587275	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tcttctcctttgtaggttccCctccagactctttgcaccaa	5	15	3	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:30587275C>T	ENST00000259873.4	+	2	241	c.84C>T	c.(82-84)ccC>ccT	p.P28P	PPP1R10_ENST00000484449.1_5'Flank|PPP1R10_ENST00000376511.2_5'Flank|MRPS18B_ENST00000472229.1_3'UTR|MRPS18B_ENST00000506373.2_Silent_p.P28P	NM_014046.3	NP_054765.1	Q9Y676	RT18B_HUMAN	mitochondrial ribosomal protein S18B	28					translation (GO:0006412)	cell junction (GO:0030054)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(2)	13						TGTAGGTTCCCCTCCAGACTC	0.403																																					p.P28P		Atlas-SNP	.											.	MRPS18B	22	.	0			c.C84T						.						71	87	82					6																	30587275		1507	2707	4214	SO:0001819	synonymous_variant	28973	exon2			GGTTCCCCTCCAG	AF100761	CCDS4682.1	6p21	2012-09-13			ENSG00000204568	ENSG00000204568		"Mitochondrial ribosomal proteins / small subunits"	14516	protein-coding gene	gene with protein product		611982				11279123	Standard	NM_014046		Approved	MRPS18-2, PTD017, C6orf14, HSPC183	uc003nqo.2	Q9Y676	OTTHUMG00000031268	ENST00000259873.4:c.84C>T	chr6.hg19:g.30587275C>T		64.0	0.0		79.0	33.0	NM_014046	A6NDQ0|Q659G4|Q9BS27	Silent	SNP	ENST00000259873.4	hg19	CCDS4682.1																																																																																			.	.		0.403	MRPS18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076584.2			T	30587275	C	T	30587275	2	4	19	1	0	0	0	0	0	0	0	1	9838	610	22	3		3	MRPS18B	6	30587275	Silent	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	4340130	30587275	140527792	42	1639										
ZBTB9	221504	hgsc.bcm.edu	37	chr6	33424037	33424038	+	Frame_Shift_Del	DEL	TG	TG	-													0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tggaaaacgctttggttgccTgtgtgggaagcggtttgcag							TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:33424037_33424038delTG	ENST00000395064.2	+	2	1428_1429	c.1160_1161delTG	c.(1159-1161)ctgfs	p.L387fs		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	387	Gly-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						TTTGGTTGCCTGTGTGGGAAGC	0.609																																					p.387_387del		Atlas-Indel,Pindel	.											.	ZBTB9	23	.	0			c.1159_1160del						.																																			SO:0001589	frameshift_variant	221504	exon2			.	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.1160_1161delTG	chr6.hg19:g.33424041_33424042delTG	ENSP00000378503:p.Leu387fs	106.0	0.0		104.0	37.0	NM_152735	A2AB19	Frame_Shift_Del	DEL	ENST00000395064.2	hg19	CCDS4780.1																																																																																			.	.		0.609	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735		-	33424038	TG	-	33424037	7	5	19	1	0	1	0	1	0	0	0	0	17573	1580	55	0	1162	0	ZBTB9	6	33424037	Frame_Shift_Del	DEL	TG	TCGA-2Y-A9H9-01A-21D-A38X-10	2836762	33424037	137691030	43	1640										
MDN1	23195	hgsc.bcm.edu	37	chr6	90377748	90377748	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cgtacctgttcttcatttccGatctggtcactcacatcctt	5	14	5	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:90377748G>T	ENST00000369393.3	-	84	14194	c.14079C>A	c.(14077-14079)atC>atA	p.I4693I	MDN1_ENST00000468568.1_5'Flank|MDN1_ENST00000428876.1_Silent_p.I4693I			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4693					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTTCATTTCCGATCTGGTCAC	0.418																																					p.I4693I		Atlas-SNP	.											.	MDN1	478	.	0			c.C14079A						.						260	199	220					6																	90377748		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon84			ATTTCCGATCTGG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14079C>A	chr6.hg19:g.90377748G>T		81.0	0.0		107.0	5.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.418	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90377748	G	T	90377748	2	4	19	1	0	0	0	0	0	0	0	1	9424	1048	37	1		1	MDN1	6	90377748	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	56953711	90377748	80737319	44	1641										
MDN1	23195	hgsc.bcm.edu	37	chr6	90410473	90410473	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cacttggagacggttaatgtCttcctgccatccactctccc	7	15	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:90410473C>G	ENST00000369393.3	-	56	8645	c.8530G>C	c.(8530-8532)Gac>Cac	p.D2844H	MDN1_ENST00000428876.1_Missense_Mutation_p.D2844H			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2844					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CGGTTAATGTCTTCCTGCCAT	0.483																																					p.D2844H		Atlas-SNP	.											.	MDN1	478	.	0			c.G8530C						.						96	91	93					6																	90410473		2203	4300	6503	SO:0001583	missense	23195	exon56			TAATGTCTTCCTG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.8530G>C	chr6.hg19:g.90410473C>G	ENSP00000358400:p.Asp2844His	123.0	0.0		175.0	69.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.931679	0.34096	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03689	3.84;3.84	5.64	5.64	0.86602	.	0.118700	0.56097	D	0.000036	T	0.01835	0.0058	N	0.24115	0.695	0.32743	N	0.507442	P	0.51351	0.944	P	0.45881	0.496	T	0.46091	-0.9216	10	0.62326	D	0.03	.	9.8913	0.41292	0.0:0.8435:0.0:0.1565	.	2844	Q9NU22	MDN1_HUMAN	H	2844	ENSP00000358400:D2844H;ENSP00000413970:D2844H	ENSP00000358400:D2844H	D	-	1	0	MDN1	90467194	1.000000	0.71417	0.996000	0.52242	0.560000	0.35617	1.907000	0.39897	2.660000	0.90430	0.655000	0.94253	GAC	.	.		0.483	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			G	90410473	C	G	90410473	3	3	19	1	0	0	0	0	1	0	0	0	9424	913	32	4	8448	4	MDN1	6	90410473	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	32725	90410473	80704594	45	1642										
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117116996	117116996	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ttggagcatttagattgaatTtgctatattaaaagtgaaaa	8	2	0	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:117116996T>C	ENST00000310357.3	-	5	1572	c.1551A>G	c.(1549-1551)caA>caG	p.Q517Q	GPRC6A_ENST00000368549.3_Silent_p.Q446Q|GPRC6A_ENST00000530250.1_Silent_p.Q342Q	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	517					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TAGATTGAATTTGCTATATTA	0.299																																					p.Q517Q		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A1551G						.						68	65	66					6																	117116996		2203	4300	6503	SO:0001819	synonymous_variant	222545	exon5			TTGAATTTGCTAT	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1551A>G	chr6.hg19:g.117116996T>C		69.0	0.0		63.0	34.0	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	hg19	CCDS5112.1																																																																																			.	.		0.299	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			C	117116996	T	C	117116996	2	2	19	1	0	0	0	0	0	0	0	1	6737	1838	64	2		2	GPRC6A	6	117116996	Silent	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	26706523	117116996	53998071	46	1643										
NCOA7	135112	hgsc.bcm.edu	37	chr6	126210902	126210902	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gtagttctctttcccaggcgGgtgatcccataactgagggc	12	11	1	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr6:126210902G>T	ENST00000368357.3	+	10	2054	c.1702G>T	c.(1702-1704)Ggt>Tgt	p.G568C	NCOA7_ENST00000229634.9_Missense_Mutation_p.G453C|NCOA7_ENST00000392477.2_Missense_Mutation_p.G568C	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	568					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		TTCCCAGGCGGGTGATCCCAT	0.433																																					p.G568C		Atlas-SNP	.											.	NCOA7	92	.	0			c.G1702T						.						52	56	54					6																	126210902		2203	4299	6502	SO:0001583	missense	135112	exon10			CAGGCGGGTGATC	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 4"	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.1702G>T	chr6.hg19:g.126210902G>T	ENSP00000357341:p.Gly568Cys	102.0	0.0		128.0	34.0	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	hg19	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	G	2.055	-0.416693	0.04766	.	.	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000413085	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.8	-1.88	0.07713	.	0.679402	0.15062	N	0.282709	T	0.05547	0.0146	L	0.27053	0.805	0.09310	N	1	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.10450	0.005;0.004;0.002	T	0.29882	-0.9997	10	0.52906	T	0.07	-1.3197	1.3744	0.02217	0.3571:0.103:0.3301:0.2098	.	557;557;568	B3KXK4;Q8NI08-2;Q8NI08	.;.;NCOA7_HUMAN	C	568;568;453;366	ENSP00000357341:G568C;ENSP00000376269:G568C;ENSP00000229634:G453C;ENSP00000389186:G366C	ENSP00000229634:G453C	G	+	1	0	NCOA7	126252595	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.287000	0.08388	-0.101000	0.12219	0.655000	0.94253	GGT	.	.		0.433	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748		T	126210902	G	T	126210902	3	4	19	1	0	0	0	0	1	0	0	0	10243	1232	43	3	1732	3	NCOA7	6	126210902	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	9093906	126210902	44904165	47	1644										
C7orf25	79020	hgsc.bcm.edu	37	chr7	42949271	42949271	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ttgtgtagtcttttggtaagGgggtggctagagcctcttta	14	5	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr7:42949271G>C	ENST00000350427.4	-	2	1504	c.1229C>G	c.(1228-1230)cCc>cGc	p.P410R	C7orf25_ENST00000431882.2_Missense_Mutation_p.P468R|C7orf25_ENST00000438029.1_Missense_Mutation_p.P410R|PSMA2_ENST00000442788.1_3'UTR|C7orf25_ENST00000447342.1_Missense_Mutation_p.P410R			Q9BPX7	CG025_HUMAN	chromosome 7 open reading frame 25	410										endometrium(6)|kidney(1)|large_intestine(7)|lung(2)|skin(1)	17						TTTTGGTAAGGGGGTGGCTAG	0.413																																					p.P468R		Atlas-SNP	.											.	C7orf25	36	.	0			c.C1403G						.						99	100	100					7																	42949271		2203	4300	6503	SO:0001583	missense	79020	exon2			GGTAAGGGGGTGG	BC001845	CCDS5466.1, CCDS47576.1	7p14.1	2011-11-24			ENSG00000136197	ENSG00000136197			21703	protein-coding gene	gene with protein product							Standard	NM_024054		Approved	MGC2821	uc003thx.4	Q9BPX7	OTTHUMG00000128869	ENST00000350427.4:c.1229C>G	chr7.hg19:g.42949271G>C	ENSP00000343364:p.Pro410Arg	137.0	0.0		198.0	71.0	NM_001099858	A4D1V2|J3KR36|Q9H779	Missense_Mutation	SNP	ENST00000350427.4	hg19	CCDS5466.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.722966	0.68959	.	.	ENSG00000136197	ENST00000350427;ENST00000447342;ENST00000431882;ENST00000438029	T;T;T;T	0.48522	0.86;0.86;0.81;0.86	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.69984	0.3172	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.68784	-0.5317	10	0.62326	D	0.03	-0.8237	20.6282	0.99521	0.0:0.0:1.0:0.0	.	468;410	B4DQM3;Q9BPX7	.;CG025_HUMAN	R	410;410;468;410	ENSP00000343364:P410R;ENSP00000413029:P410R;ENSP00000416290:P468R;ENSP00000396597:P410R	ENSP00000343364:P410R	P	-	2	0	C7orf25	42915796	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	9.224000	0.95209	2.871000	0.98454	0.655000	0.94253	CCC	.	.		0.413	C7orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250814.2	NM_024054		C	42949271	G	C	42949271	3	2	19	1	0	0	0	0	1	0	0	0	2382	1232	43	4	40	4	C7orf25	7	42949271	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10		42949271	116189392	48	1645										
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80378240	80378240	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cctcctgtctttgtctttctGtaacagccacttgatagatg	7	11	3	2	rs557931063		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr7:80378240G>A	ENST00000265361.3	-	17	2377	c.1816C>T	c.(1816-1818)Cag>Tag	p.Q606*	SEMA3C_ENST00000544525.1_Nonsense_Mutation_p.Q624*|SEMA3C_ENST00000419255.2_Nonsense_Mutation_p.Q606*	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	606	Ig-like C2-type.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TTGTCTTTCTGTAACAGCCAC	0.468													G|||	1	0.000199681	8e-04	0	5008	,	,		17269	0		0	False		,,,				2504	0				p.Q606X		Atlas-SNP	.											.	SEMA3C	106	.	0			c.C1816T						.						148	134	139					7																	80378240		2203	4300	6503	SO:0001587	stop_gained	10512	exon17			CTTTCTGTAACAG	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"Semaphorins", "Immunoglobulin superfamily / I-set domain containing"	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1816C>T	chr7.hg19:g.80378240G>A	ENSP00000265361:p.Gln606*	36.0	0.0		75.0	37.0	NM_006379	B4DRL8	Nonsense_Mutation	SNP	ENST00000265361.3	hg19	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	G	44	10.795397	0.99469	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	.	.	.	5.38	5.38	0.77491	.	0.051716	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.1326	0.93413	0.0:0.0:1.0:0.0	.	.	.	.	X	606;606;624	.	ENSP00000265361:Q606X	Q	-	1	0	SEMA3C	80216176	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.837000	0.99465	2.511000	0.84671	0.563000	0.77884	CAG	.	.		0.468	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		A	80378240	G	A	80378240	4	1	19	1	0	0	0	0	0	1	0	0	14041	1386	48	3	447	3	SEMA3C	7	80378240	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	37428969	80378240	78760423	49	1646										
RNF148	378925	hgsc.bcm.edu	37	chr7	122342140	122342140	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ttatttgacttcgcctcctgGtgaaagaattgggcactcta	9	9	1	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr7:122342140G>T	ENST00000434824.1	-	1	881	c.665C>A	c.(664-666)aCc>aAc	p.T222N	CADPS2_ENST00000334010.7_Intron|RNF148_ENST00000447240.1_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000449022.2_Intron|RNF133_ENST00000340112.2_5'Flank|CADPS2_ENST00000412584.2_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	222						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						TCGCCTCCTGGTGAAAGAATT	0.418																																					p.T222N		Atlas-SNP	.											.	RNF148	71	.	0			c.C665A						.						83	77	79					7																	122342140		1921	4138	6059	SO:0001583	missense	378925	exon1			CTCCTGGTGAAAG	BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"RING-type (C3HC4) zinc fingers"	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.665C>A	chr7.hg19:g.122342140G>T	ENSP00000388207:p.Thr222Asn	34.0	0.0		107.0	26.0	NM_198085	A4D0X4|Q8N308	Missense_Mutation	SNP	ENST00000434824.1	hg19	CCDS47692.1	.	.	.	.	.	.	.	.	.	.	G	5.564	0.288948	0.10513	.	.	ENSG00000235631	ENST00000434824	T	0.04275	3.66	5.37	-0.286	0.12862	.	.	.	.	.	T	0.02230	0.0069	N	0.10874	0.06	0.28891	N	0.893848	B	0.02656	0.0	B	0.06405	0.002	T	0.46748	-0.9169	9	0.19147	T	0.46	.	3.7165	0.08439	0.0799:0.3417:0.3305:0.2479	.	222	Q8N7C7	RN148_HUMAN	N	222	ENSP00000388207:T222N	ENSP00000388207:T222N	T	-	2	0	RNF148	122129376	0.000000	0.05858	0.945000	0.38365	0.683000	0.39861	0.073000	0.14640	0.245000	0.21373	-0.310000	0.09108	ACC	.	.		0.418	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085		T	122342140	G	T	122342140	3	4	19	1	0	0	0	0	1	0	0	0	13464	1261	44	3	256	3	RNF148	7	122342140	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	41963900	122342140	36796523	50	1647										
ZNF467	168544	hgsc.bcm.edu	37	chr7	149463194	149463194	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ccctggctccagtttgtacgCggcagccagatgccccaggt	12	15	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr7:149463194C>T	ENST00000302017.3	-	5	810	c.397G>A	c.(397-399)Gcg>Acg	p.A133T	ZNF467_ENST00000484747.1_Intron	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	133					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|urinary_tract(1)	13	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AGTTTGTACGCGGCAGCCAGA	0.662																																					p.A133T		Atlas-SNP	.											.	ZNF467	50	.	0			c.G397A						.						34	34	34					7																	149463194		2203	4300	6503	SO:0001583	missense	168544	exon5			TGTACGCGGCAGC	BC029296	CCDS5899.1	7q36.1	2013-01-08			ENSG00000181444	ENSG00000181444		"Zinc fingers, C2H2-type"	23154	protein-coding gene	gene with protein product		614040				12426389	Standard	NM_207336		Approved	EZI, Zfp467	uc003wgd.2	Q7Z7K2	OTTHUMG00000157883	ENST00000302017.3:c.397G>A	chr7.hg19:g.149463194C>T	ENSP00000304769:p.Ala133Thr	87.0	0.0		101.0	7.0	NM_207336		Missense_Mutation	SNP	ENST00000302017.3	hg19	CCDS5899.1	.	.	.	.	.	.	.	.	.	.	c	6.296	0.422643	0.11928	.	.	ENSG00000181444	ENST00000302017	T	0.07327	3.2	4.16	-2.73	0.05950	.	0.652197	0.11569	N	0.550983	T	0.03564	0.0102	N	0.17082	0.46	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.46707	-0.9172	10	0.08599	T	0.76	-3.4854	5.0458	0.14483	0.1339:0.443:0.0:0.4231	.	133	Q7Z7K2	ZN467_HUMAN	T	133	ENSP00000304769:A133T	ENSP00000304769:A133T	A	-	1	0	ZNF467	149094127	0.000000	0.05858	0.000000	0.03702	0.582000	0.36321	-2.572000	0.00912	-0.816000	0.04340	0.298000	0.19748	GCG	.	.		0.662	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349833.1	NM_207336		T	149463194	C	T	149463194	3	4	19	1	0	0	0	0	1	0	0	0	17942	768	27	1	1394	1	ZNF467	7	149463194	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	27121054	149463194	9675469	51	1648										
ADAM28	10863	hgsc.bcm.edu	37	chr8	24201031	24201031	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tcccctaggtgtgtgaccatGagctccagtgtcaatgtgag	12	10	1	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr8:24201031G>T	ENST00000265769.4	+	18	2034	c.1924G>T	c.(1924-1926)Gag>Tag	p.E642*	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000397649.3_Nonsense_Mutation_p.E389*|RP11-624C23.1_ENST00000523578.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	642	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		GTGTGACCATGAGCTCCAGTG	0.483																																					p.E642X	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.G1924T						.						189	147	161					8																	24201031		2203	4300	6503	SO:0001587	stop_gained	10863	exon18			GACCATGAGCTCC	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.1924G>T	chr8.hg19:g.24201031G>T	ENSP00000265769:p.Glu642*	57.0	0.0		58.0	42.0	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Nonsense_Mutation	SNP	ENST00000265769.4	hg19	CCDS34865.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.949562|5.949562	0.97134|0.97134	.|.	.|.	ENSG00000042980|ENSG00000042980	ENST00000265769;ENST00000397649|ENST00000521629;ENST00000518326	.|.	.|.	.|.	5.37|5.37	3.55|3.55	0.40652|0.40652	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.02654|.	T|.	1|.	.|.	9.3849|9.3849	0.38336|0.38336	0.1736:0.0:0.8264:0.0|0.1736:0.0:0.8264:0.0	.|.	.|.	.|.	.|.	X|L	642;389|274;67	.|.	ENSP00000265769:E642X|.	E|X	+|+	1|2	0|2	ADAM28|ADAM28	24256976|24256976	0.994000|0.994000	0.37717|0.37717	0.965000|0.965000	0.40720|0.40720	0.916000|0.916000	0.54674|0.54674	2.214000|2.214000	0.42853|0.42853	1.418000|1.418000	0.47098|0.47098	0.655000|0.655000	0.94253|0.94253	GAG|TGA	.	.		0.483	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		T	24201031	G	T	24201031	4	4	19	1	0	0	0	0	0	1	0	0	246	1291	45	3	2050	3	ADAM28	8	24201031	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10		24201031	122162991	52	1649										
NRG1	3084	hgsc.bcm.edu	37	chr8	32616839	32616839	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tccagcaatacgtatctaaaAacgtcatctccagtgagcat	6	11	3	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr8:32616839A>C	ENST00000405005.3	+	10	946	c.946A>C	c.(946-948)Aac>Cac	p.N316H	NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000521670.1_Missense_Mutation_p.N316H|NRG1_ENST00000287842.3_Missense_Mutation_p.N313H|NRG1_ENST00000539990.1_Missense_Mutation_p.N159H|NRG1_ENST00000356819.4_Missense_Mutation_p.N321H|NRG1_ENST00000519301.1_Missense_Mutation_p.N266H|NRG1_ENST00000523079.1_Missense_Mutation_p.N313H|NRG1_ENST00000287845.5_Missense_Mutation_p.N287H|NRG1_ENST00000338921.4_Missense_Mutation_p.N324H			Q02297	NRG1_HUMAN	neuregulin 1	316					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CGTATCTAAAAACGTCATCTC	0.393																																					p.N321H		Atlas-SNP	.											.	NRG1	260	.	0			c.A961C						.						179	152	161					8																	32616839		2203	4300	6503	SO:0001583	missense	3084	exon11			TCTAAAAACGTCA	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.946A>C	chr8.hg19:g.32616839A>C	ENSP00000384620:p.Asn316His	74.0	0.0		57.0	21.0	NM_013956	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	hg19	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.565394	0.86439	.	.	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T	0.61392	0.11;0.11;0.11;0.11;0.11;0.11;0.11;0.11;0.11;0.11;0.11;0.11	6.16	6.16	0.99307	Neuregulin 1-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.76118	0.3943	M	0.69823	2.125	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;0.999;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.995;0.999;0.998;0.999;0.998;0.996;0.998;1.0;0.998;0.997	T	0.78303	-0.2256	10	0.87932	D	0	2.832	16.8061	0.85666	1.0:0.0:0.0:0.0	.	159;162;313;287;321;312;324;313;316;321;316	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	H	283;266;389;313;324;321;316;287;313;316;316;159	ENSP00000430053:N283H;ENSP00000429582:N266H;ENSP00000429067:N389H;ENSP00000430120:N313H;ENSP00000343395:N324H;ENSP00000349275:N321H;ENSP00000287840:N316H;ENSP00000287845:N287H;ENSP00000287842:N313H;ENSP00000384620:N316H;ENSP00000428828:N316H;ENSP00000439276:N159H	ENSP00000287840:N316H	N	+	1	0	NRG1	32736381	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	8.594000	0.90836	2.367000	0.80283	0.528000	0.53228	AAC	.	.		0.393	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			C	32616839	A	C	32616839	3	2	19	1	0	0	0	0	1	0	0	0	10656	14	1	5	2580	5	NRG1	8	32616839	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	8415808	32616839	113747183	53	1650										
MOS	4342	hgsc.bcm.edu	37	chr8	57025864	57025864	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tggaagcacagcagatcttcCaacttctcagagcaaccgaa	8	12	2	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr8:57025864C>A	ENST00000311923.1	-	1	677	c.678G>T	c.(676-678)ttG>ttT	p.L226F		NM_005372.1	NP_005363.1	P00540	MOS_HUMAN	v-mos Moloney murine sarcoma viral oncogene homolog	226	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|chromatin organization (GO:0006325)|establishment of meiotic spindle orientation (GO:0051296)|MAPK cascade (GO:0000165)|meiotic spindle organization (GO:0000212)|negative regulation of metaphase/anaphase transition of meiotic cell cycle (GO:1902103)|protein autophosphorylation (GO:0046777)|regulation of meiosis (GO:0040020)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(12)|ovary(1)|urinary_tract(2)	22			Epithelial(17;0.00117)|all cancers(17;0.00879)			GCAGATCTTCCAACTTCTCAG	0.537																																					p.L226F	Esophageal Squamous(124;373 2870 4778)	Atlas-SNP	.											.	MOS	63	.	0			c.G678T						.						70	75	73					8																	57025864		2203	4300	6503	SO:0001583	missense	4342	exon1			ATCTTCCAACTTC		CCDS6164.1	8q11	2012-10-02			ENSG00000172680	ENSG00000172680			7199	protein-coding gene	gene with protein product		190060				9552420	Standard	NM_005372		Approved		uc011leb.2	P00540	OTTHUMG00000164299	ENST00000311923.1:c.678G>T	chr8.hg19:g.57025864C>A	ENSP00000310722:p.Leu226Phe	97.0	0.0		96.0	45.0	NM_005372	Q3KPG9|Q3KPH0	Missense_Mutation	SNP	ENST00000311923.1	hg19	CCDS6164.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.797781	0.31777	.	.	ENSG00000172680	ENST00000311923	T	0.66815	-0.23	5.8	-1.31	0.09230	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.086238	0.47852	D	0.000202	T	0.66925	0.2839	L	0.45285	1.41	0.32530	N	0.535079	D	0.76494	0.999	D	0.81914	0.995	T	0.67325	-0.5699	10	0.87932	D	0	.	3.1329	0.06429	0.1108:0.4293:0.1093:0.3506	.	226	P00540	MOS_HUMAN	F	226	ENSP00000310722:L226F	ENSP00000310722:L226F	L	-	3	2	MOS	57188418	0.686000	0.27661	0.006000	0.13384	0.204000	0.24138	0.205000	0.17356	-0.124000	0.11724	0.561000	0.74099	TTG	.	.		0.537	MOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378174.1	NM_005372		A	57025864	C	A	57025864	3	1	19	1	0	0	0	0	1	0	0	0	9721	593	21	3	365	3	MOS	8	57025864	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	24409025	57025864	89338158	54	1651										
NCOA2	10499	hgsc.bcm.edu	37	chr8	71037078	71037078	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gtcgtagccccagtaaagccTggatcaggttgctgacttat	11	10	1	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr8:71037078T>C	ENST00000452400.2	-	20	4120	c.3939A>G	c.(3937-3939)ccA>ccG	p.P1313P	NCOA2_ENST00000267974.4_Silent_p.P401P	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	1313					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CAGTAAAGCCTGGATCAGGTT	0.468			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.P1313P		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.A3939G						.						94	97	96					8																	71037078		1894	4145	6039	SO:0001819	synonymous_variant	10499	exon20			AAAGCCTGGATCA	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.3939A>G	chr8.hg19:g.71037078T>C		54.0	0.0		135.0	87.0	NM_006540	Q14CD2	Silent	SNP	ENST00000452400.2	hg19	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	T	10.30	1.312159	0.23821	.	.	ENSG00000140396	ENST00000518363	.	.	.	5.82	-2.18	0.07037	.	.	.	.	.	T	0.40119	0.1104	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30119	-0.9989	4	.	.	.	.	2.3671	0.04322	0.2834:0.0643:0.2227:0.4295	.	.	.	.	R	414	.	.	Q	-	2	0	NCOA2	71199632	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	0.559000	0.23485	-0.236000	0.09753	0.533000	0.62120	CAG	.	.		0.468	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			C	71037078	T	C	71037078	2	2	19	1	0	0	0	0	0	0	0	1	10238	1567	55	2		2	NCOA2	8	71037078	Silent	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	14011214	71037078	75326944	55	1652										
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885352	88885352	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tgtctgatgacaccaggaatTggccatcttggaggatttgc	12	8	2	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr8:88885352T>A	ENST00000319675.3	-	1	944	c.848A>T	c.(847-849)cAa>cTa	p.Q283L		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	283										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						CACCAGGAATTGGCCATCTTG	0.502																																					p.Q283L		Atlas-SNP	.											.	DCAF4L2	187	.	0			c.A848T						.						97	88	91					8																	88885352		2203	4300	6503	SO:0001583	missense	138009	exon1			AGGAATTGGCCAT	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.848A>T	chr8.hg19:g.88885352T>A	ENSP00000316496:p.Gln283Leu	100.0	0.0		120.0	40.0	NM_152418		Missense_Mutation	SNP	ENST00000319675.3	hg19	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	T	11.75	1.731188	0.30684	.	.	ENSG00000176566	ENST00000319675	T	0.24350	1.86	1.39	1.39	0.22231	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.352041	0.33005	N	0.005384	T	0.18173	0.0436	L	0.33710	1.025	0.33177	D	0.549095	B	0.31256	0.316	B	0.35655	0.207	T	0.16512	-1.0400	10	0.45353	T	0.12	.	6.5295	0.22320	0.0:0.0:0.0:1.0	.	283	Q8NA75	DC4L2_HUMAN	L	283	ENSP00000316496:Q283L	ENSP00000316496:Q283L	Q	-	2	0	DCAF4L2	88954468	1.000000	0.71417	0.007000	0.13788	0.007000	0.05969	3.481000	0.53179	0.627000	0.30340	0.383000	0.25322	CAA	.	.		0.502	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		A	88885352	T	A	88885352	3	1	19	1	0	0	0	0	1	0	0	0	4274	1812	63	4	343	4	DCAF4L2	8	88885352	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	17848274	88885352	57478670	56	1653										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113301671	113301671	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	actggcctaaaagggaacgcTttcctgtgcaggaatagtga	12	8	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr8:113301671T>C	ENST00000297405.5	-	57	9315	c.9071A>G	c.(9070-9072)aAg>aGg	p.K3024R	CSMD3_ENST00000455883.2_Missense_Mutation_p.K2855R|CSMD3_ENST00000352409.3_Missense_Mutation_p.K2954R|CSMD3_ENST00000343508.3_Missense_Mutation_p.K2984R	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3024	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAGGGAACGCTTTCCTGTGCA	0.473										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.K3024R		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A9071G						.						117	105	109					8																	113301671		2203	4300	6503	SO:0001583	missense	114788	exon57			GAACGCTTTCCTG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9071A>G	chr8.hg19:g.113301671T>C	ENSP00000297405:p.Lys3024Arg	62.0	0.0		102.0	40.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.156250	0.38021	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08	6.17	3.83	0.44106	Complement control module (2);Sushi/SCR/CCP (3);	0.417853	0.24525	N	0.037775	T	0.37320	0.0999	N	0.10760	0.04	0.29226	N	0.873632	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.25433	-1.0132	10	0.54805	T	0.06	.	5.5656	0.17168	0.0:0.3437:0.0:0.6563	.	2855;3024;2984	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	R	2984;3024;2294;2855;2954	ENSP00000345799:K2984R;ENSP00000297405:K3024R;ENSP00000341558:K2294R;ENSP00000412263:K2855R;ENSP00000343124:K2954R	ENSP00000297405:K3024R	K	-	2	0	CSMD3	113370847	0.984000	0.35163	1.000000	0.80357	0.994000	0.84299	2.589000	0.46145	1.149000	0.42402	0.533000	0.62120	AAG	.	.		0.473	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113301671	T	C	113301671	3	2	19	1	0	0	0	0	1	0	0	0	3948	1609	56	2	2112	2	CSMD3	8	113301671	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	24416319	113301671	33062351	57	1654										
BAI1	575	hgsc.bcm.edu	37	chr8	143546087	143546087	+	Frame_Shift_Del	DEL	G	G	-													0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tccgtggagtacctggtggtGgggaaccgcaaccccagccg							TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr8:143546087delG	ENST00000517894.1	+	2	1422	c.528delG	c.(526-528)gtgfs	p.V176fs	BAI1_ENST00000323289.5_Frame_Shift_Del_p.V176fs			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	176					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					ACCTGGTGGTGGGGAACCGCA	0.741																																					p.V176fs		Atlas-Indel,Pindel	.											.	BAI1	146	.	0			c.527delT						.						10	16	14					8																	143546087		1321	2618	3939	SO:0001589	frameshift_variant	575	exon1			.	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.528delG	chr8.hg19:g.143546087delG	ENSP00000430945:p.Val176fs	47.0	0.0		62.0	23.0	NM_001702		Frame_Shift_Del	DEL	ENST00000517894.1	hg19																																																																																				.	.		0.741	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		-	143546087	G	-	143546087	7	5	19	1	0	1	0	1	0	0	0	0	1298	1335	47	0	530	0	BAI1	8	143546087	Frame_Shift_Del	DEL	G	TCGA-2Y-A9H9-01A-21D-A38X-10	30244416	143546087	2817935	58	1655										
CNTLN	54875	hgsc.bcm.edu	37	chr9	17394651	17394651	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tccctcttaaaacagcaacaAgaagatacagagaccagaga	7	10	1	4			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr9:17394651A>G	ENST00000380647.3	+	15	2283	c.2199A>G	c.(2197-2199)caA>caG	p.Q733Q	CNTLN_ENST00000262360.5_Silent_p.Q733Q|CNTLN_ENST00000425824.1_Silent_p.Q733Q			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	733					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AACAGCAACAAGAAGATACAG	0.313																																					p.Q733Q		Atlas-SNP	.											.	CNTLN	128	.	0			c.A2199G						.						66	61	63					9																	17394651		1798	4071	5869	SO:0001819	synonymous_variant	54875	exon15			GCAACAAGAAGAT	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.2199A>G	chr9.hg19:g.17394651A>G		244.0	0.0		392.0	163.0	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Silent	SNP	ENST00000380647.3	hg19	CCDS43789.1																																																																																			.	.		0.313	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		G	17394651	A	G	17394651	2	3	19	1	0	0	0	0	0	0	0	1	3641	69	3	2		2	CNTLN	9	17394651	Silent	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10		17394651	123818780	59	1656										
SPAG8	4882	hgsc.bcm.edu	37	chr9	35811469	35811469	+	IGR	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cccagaggcaggaccaggatGagagccagagccatgaccag	14	12	0	4	rs571991371		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr9:35811469G>A	ENST00000342694.2	+	0	3686				SPAG8_ENST00000484764.1_Missense_Mutation_p.H190Y|HINT2_ENST00000474908.1_5'Flank|SPAG8_ENST00000340291.2_Missense_Mutation_p.H192Y|TMEM8B_ENST00000377996.1_5'Flank|SPAG8_ENST00000479751.1_5'Flank|SPAG8_ENST00000396638.2_Missense_Mutation_p.H192Y|AL133410.1_ENST00000582432.1_RNA	NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2						bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	GGACCAGGATGagagccagag	0.632																																					p.H192Y		Atlas-SNP	.											.	SPAG8	67	.	0			c.C574T						.						50	47	48					9																	35811469		2203	4300	6503	SO:0001628	intergenic_variant	26206	exon2			CAGGATGAGAGCC	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871		chr9.hg19:g.35811469G>A		30.0	0.0		44.0	20.0	NM_001039592	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	hg19	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	G	8.669	0.902302	0.17760	.	.	ENSG00000137098	ENST00000340291;ENST00000484764;ENST00000396638	T;T;T	0.41758	0.99;0.99;0.99	4.21	1.29	0.21616	.	1.201680	0.05881	N	0.626454	T	0.23806	0.0576	N	0.08118	0	0.09310	N	1	B;B	0.30455	0.28;0.28	B;B	0.31495	0.131;0.131	T	0.27088	-1.0084	10	0.51188	T	0.08	0.133	4.7488	0.13050	0.0:0.5941:0.1915:0.2144	.	192;192	E9PDV6;Q99932-2	.;.	Y	192;190;192	ENSP00000340982:H192Y;ENSP00000418072:H190Y;ENSP00000379878:H192Y	ENSP00000340982:H192Y	H	-	1	0	SPAG8	35801469	0.096000	0.21769	0.000000	0.03702	0.021000	0.10359	0.744000	0.26245	0.134000	0.18681	-0.165000	0.13383	CAT	.	.		0.632	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			A	35811469	G	A	35811469	1	1	19	0	1	0	0	0	0	0	0	0	14999	1290	45	3		3	SPAG8	9	35811469	IGR	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	18416818	35811469	105401962	60	1657										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79324435	79324435	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	attctcctcaaaaaggttccAggaatctaccttttcatata	4	10	4	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr9:79324435A>G	ENST00000376718.3	-	8	2878	c.2755T>C	c.(2755-2757)Tgg>Cgg	p.W919R	PRUNE2_ENST00000428286.1_Missense_Mutation_p.W560R	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	919					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AAAAGGTTCCAGGAATCTACC	0.398																																					p.W919R		Atlas-SNP	.											.	PRUNE2	331	.	0			c.T2755C						.						229	215	219					9																	79324435		1568	3582	5150	SO:0001583	missense	158471	exon8			GGTTCCAGGAATC	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.2755T>C	chr9.hg19:g.79324435A>G	ENSP00000365908:p.Trp919Arg	117.0	0.0		80.0	20.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.07|14.07	2.425229|2.425229	0.43020|0.43020	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376718;ENST00000428286;ENST00000422033	.|T;T	.|0.74526	.|-0.82;-0.85	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	.|0.000000	.|0.47852	.|D	.|0.000204	T|T	0.80803|0.80803	0.4693|0.4693	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	T|T	0.82991|0.82991	-0.0182|-0.0182	5|10	.|0.87932	.|D	.|0	-6.1607|-6.1607	16.1922|16.1922	0.82000|0.82000	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|919	.|Q8WUY3	.|PRUN2_HUMAN	P|R	240|919;560;918	.|ENSP00000365908:W919R;ENSP00000397425:W560R	.|ENSP00000365908:W919R	L|W	-|-	2|1	0|0	PRUNE2|PRUNE2	78514255|78514255	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.526000|0.526000	0.34562|0.34562	6.414000|6.414000	0.73318|0.73318	2.226000|2.226000	0.72624|0.72624	0.459000|0.459000	0.35465|0.35465	CTG|TGG	.	.		0.398	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		G	79324435	A	G	79324435	3	3	19	1	0	0	0	0	1	0	0	0	12653	188	7	2	6559	2	PRUNE2	9	79324435	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	43512966	79324435	61888996	61	1658										
TLE1	7088	hgsc.bcm.edu	37	chr9	84235385	84235385	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ggagtccttatcatccacctTccttttcttgatgtcattgg	7	11	3	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr9:84235385T>C	ENST00000376499.3	-	9	1746	c.682A>G	c.(682-684)Aag>Gag	p.K228E	TLE1_ENST00000464999.1_5'UTR|TLE1_ENST00000376472.1_5'UTR	NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	228	CCN domain.				multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						TCATCCACCTTCCTTTTCTTG	0.388																																					p.K228E	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	Atlas-SNP	.											.	TLE1	81	.	0			c.A682G						.						185	161	170					9																	84235385		2203	4300	6503	SO:0001583	missense	7088	exon9			CCACCTTCCTTTT		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"WD repeat domain containing"	11837	protein-coding gene	gene with protein product	"enhancer of split groucho 1"	600189	"transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.682A>G	chr9.hg19:g.84235385T>C	ENSP00000365682:p.Lys228Glu	105.0	0.0		97.0	5.0	NM_005077	A8K495|Q5T3G4|Q969V9	Missense_Mutation	SNP	ENST00000376499.3	hg19	CCDS6661.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.830039	0.91036	.	.	ENSG00000196781	ENST00000376499;ENST00000355002;ENST00000418319	T;T	0.59224	0.28;0.92	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.75466	0.3853	M	0.86420	2.815	0.80722	D	1	P;P;P;B;P	0.43885	0.713;0.745;0.82;0.39;0.745	P;P;P;B;B	0.54815	0.761;0.493;0.576;0.054;0.41	T	0.76075	-0.3092	10	0.35671	T	0.21	-20.0721	16.3514	0.83213	0.0:0.0:0.0:1.0	.	154;228;255;238;228	B4E345;B4DEF9;Q59EF7;Q5T3G3;Q04724	.;.;.;.;TLE1_HUMAN	E	228;238;238	ENSP00000365682:K228E;ENSP00000391347:K238E	ENSP00000347102:K238E	K	-	1	0	TLE1	83425205	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.004000	0.88535	2.252000	0.74401	0.533000	0.62120	AAG	.	.		0.388	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077		C	84235385	T	C	84235385	3	2	19	1	0	0	0	0	1	0	0	0	15953	1792	62	2	1678	2	TLE1	9	84235385	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	4910950	84235385	56978046	62	1659										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767525	105767525	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aaaggcaaagactcggcaacAgaatctgaaggtgaaaaagg	12	6	1	4			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr9:105767525A>T	ENST00000374798.3	+	5	682	c.612A>T	c.(610-612)acA>acT	p.T204T	CYLC2_ENST00000487798.1_Silent_p.T204T	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	204	3 X approximate tandem repeats.|31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				ACTCGGCAACAGAATCTGAAG	0.368																																					p.T204T		Atlas-SNP	.											.	CYLC2	109	.	0			c.A612T						.						80	78	79					9																	105767525		2203	4300	6503	SO:0001819	synonymous_variant	1539	exon5			GGCAACAGAATCT	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.612A>T	chr9.hg19:g.105767525A>T		298.0	0.0		190.0	141.0	NM_001340	B2R8F4|Q5VVJ9	Silent	SNP	ENST00000374798.3	hg19	CCDS35085.1																																																																																			.	.		0.368	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		T	105767525	A	T	105767525	2	4	19	1	0	0	0	0	0	0	0	1	4144	175	7	4		4	CYLC2	9	105767525	Silent	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	21532140	105767525	35445906	63	1660										
RBM18	92400	hgsc.bcm.edu	37	chr9	125007619	125007619	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cattcttgttatgatcatatCtctgaaaatgagaaatagag	7	5	3	4	rs149650476		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr9:125007619C>A	ENST00000417201.3	-	5	469	c.329G>T	c.(328-330)aGa>aTa	p.R110I	RBM18_ENST00000483428.1_5'UTR	NM_033117.3	NP_149108.1	Q96H35	RBM18_HUMAN	RNA binding motif protein 18	110							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7						ATGATCATATCTCTGAAAATG	0.388																																					p.R110I		Atlas-SNP	.											.	RBM18	15	.	0			c.G329T						.						119	117	118					9																	125007619		2203	4300	6503	SO:0001630	splice_region_variant	92400	exon5			TCATATCTCTGAA	AK057676	CCDS6839.1	9q34.11	2013-02-12			ENSG00000119446	ENSG00000119446		"RNA binding motif (RRM) containing"	28413	protein-coding gene	gene with protein product						12477932	Standard	NM_033117		Approved	MGC2734	uc004bma.2	Q96H35	OTTHUMG00000020602	ENST00000417201.3:c.328-1G>T	chr9.hg19:g.125007619C>A		31.0	0.0		22.0	13.0	NM_033117	B3KQ89	Missense_Mutation	SNP	ENST00000417201.3	hg19	CCDS6839.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.037796	0.75617	.	.	ENSG00000119446	ENST00000417201	T	0.36878	1.23	5.57	5.57	0.84162	Nucleotide-binding, alpha-beta plait (1);	0.040141	0.85682	D	0.000000	T	0.36717	0.0977	L	0.51422	1.61	0.80722	D	1	P	0.39551	0.678	B	0.36335	0.222	T	0.26985	-1.0087	10	0.59425	D	0.04	-13.9192	18.5452	0.91043	0.0:1.0:0.0:0.0	.	110	Q96H35	RBM18_HUMAN	I	110	ENSP00000409315:R110I	ENSP00000409315:R110I	R	-	2	0	RBM18	124047440	1.000000	0.71417	0.991000	0.47740	0.961000	0.63080	6.161000	0.71868	2.630000	0.89119	0.655000	0.94253	AGA	.	C|1.000;T|0.000		0.388	RBM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053928.2	NM_033117	Missense_Mutation	A	125007619	C	A	125007619	5	1	19	1	0	0	0	0	0	0	1	0	13135	927	32	3	251	3	RBM18	9	125007619	Splice_Site	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	19240094	125007619	16205812	64	1661										
NEK6	10783	hgsc.bcm.edu	37	chr9	127089633	127089633	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gcagacatcaagcctgccaaCgtgttcatcacagccacggg	10	14	3	1	rs553709380		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr9:127089633C>T	ENST00000320246.5	+	7	676	c.531C>T	c.(529-531)aaC>aaT	p.N177N	NEK6_ENST00000394199.2_Silent_p.N211N|NEK6_ENST00000539416.1_Silent_p.N202N|NEK6_ENST00000373603.1_Silent_p.N177N|NEK6_ENST00000373600.3_Silent_p.N211N|NEK6_ENST00000540326.1_Silent_p.N195N|NEK6_ENST00000546191.1_Silent_p.N177N|NEK6_ENST00000545174.1_Silent_p.N177N	NM_014397.5	NP_055212.2	Q9HC98	NEK6_HUMAN	NIMA-related kinase 6	177	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cellular senescence (GO:2000772)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinesin binding (GO:0019894)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15						AGCCTGCCAACGTGTTCATCA	0.627																																					p.N211N	NSCLC(122;934 1785 18647 44295 45571)	Atlas-SNP	.											.	NEK6	47	.	0			c.C633T						.						260	231	241					9																	127089633		2203	4300	6503	SO:0001819	synonymous_variant	10783	exon8			TGCCAACGTGTTC	AF087909	CCDS6854.1, CCDS48015.1, CCDS55338.1, CCDS55339.1	9q33.3-q34.11	2012-11-15	2012-11-15		ENSG00000119408	ENSG00000119408			7749	protein-coding gene	gene with protein product	"putative serine-threonine protein kinase"	604884	"NIMA (never in mitosis gene a)-related kinase 6"			10702691	Standard	NM_001145001		Approved	SID6-1512	uc004boh.3	Q9HC98	OTTHUMG00000020650	ENST00000320246.5:c.531C>T	chr9.hg19:g.127089633C>T		59.0	0.0		28.0	24.0	NM_001166171	B7Z2D9|Q5TBG3|Q5TBG9|Q6FG86|Q6IAR3|Q96E83|Q9ULX2	Silent	SNP	ENST00000320246.5	hg19	CCDS6854.1																																																																																			.	.		0.627	NEK6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054016.1	NM_014397		T	127089633	C	T	127089633	2	4	19	1	0	0	0	0	0	0	0	1	10337	535	19	1		1	NEK6	9	127089633	Silent	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	2082014	127089633	14123798	65	1662										
TYSND1	219743	hgsc.bcm.edu	37	chr10	71905794	71905794	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	acgcccagcagcgcaaaccaGcccagcgctctcagttgatc	9	17	1	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr10:71905794G>C	ENST00000287078.6	-	1	548	c.549C>G	c.(547-549)ggC>ggG	p.G183G	TYSND1_ENST00000335494.5_Silent_p.G183G|TYSND1_ENST00000494143.1_5'Flank	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	183					protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						GCGCAAACCAGCCCAGCGCTC	0.701																																					p.G183G		Atlas-SNP	.											.	TYSND1	20	.	0			c.C549G						.						25	26	25					10																	71905794		2197	4289	6486	SO:0001819	synonymous_variant	219743	exon1			AAACCAGCCCAGC	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.549C>G	chr10.hg19:g.71905794G>C		112.0	0.0		118.0	54.0	NM_173555	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	Silent	SNP	ENST00000287078.6	hg19	CCDS31213.1																																																																																			.	.		0.701	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555		C	71905794	G	C	71905794	2	2	19	1	0	0	0	0	0	0	0	1	16832	958	34	4		4	TYSND1	10	71905794	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10		71905794	63628953	66	1663										
INPP5F	22876	hgsc.bcm.edu	37	chr10	121571371	121571371	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aaatcagagaagccaccaggAactaattagccagctcttac	7	11	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr10:121571371A>C	ENST00000361976.2	+	15	1956	c.1790A>C	c.(1789-1791)gAa>gCa	p.E597A		NM_014937.3	NP_055752.1	Q01968	OCRL_HUMAN	inositol polyphosphate-5-phosphatase F	0	ASH.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(9)|lung(5)|ovary(5)|pancreas(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		AGCCACCAGGAACTAATTAGC	0.433																																					p.E597A		Atlas-SNP	.											.	INPP5F	112	.	0			c.A1790C						.						119	129	125					10																	121571371		2203	4300	6503	SO:0001583	missense	22876	exon15			ACCAGGAACTAAT	AB023183	CCDS7616.1, CCDS58098.1	10q26.13	2009-02-03			ENSG00000198825	ENSG00000198825			17054	protein-coding gene	gene with protein product		609389				10231032, 11274189	Standard	NM_014937		Approved	SAC2, KIAA0966, hSac2	uc001leo.3	Q9Y2H2	OTTHUMG00000019158	ENST00000361976.2:c.1790A>C	chr10.hg19:g.121571371A>C	ENSP00000354519:p.Glu597Ala	89.0	0.0		91.0	25.0	NM_014937	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000361976.2	hg19	CCDS7616.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.499255	0.85069	.	.	ENSG00000198825	ENST00000361976	T	0.41065	1.01	5.68	5.68	0.88126	.	0.052878	0.85682	D	0.000000	T	0.62575	0.2439	M	0.61703	1.905	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.63659	-0.6587	10	0.52906	T	0.07	-27.6394	15.9323	0.79672	1.0:0.0:0.0:0.0	.	597	Q9Y2H2	SAC2_HUMAN	A	597	ENSP00000354519:E597A	ENSP00000354519:E597A	E	+	2	0	INPP5F	121561361	1.000000	0.71417	0.985000	0.45067	0.983000	0.72400	9.270000	0.95690	2.175000	0.68902	0.533000	0.62120	GAA	.	.		0.433	INPP5F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050679.1	NM_014937		C	121571371	A	C	121571371	3	2	19	1	0	0	0	0	1	0	0	0	7767	246	9	5	1848	5	INPP5F	10	121571371	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	49665577	121571371	13963376	67	1664										
OR4C3	256144	hgsc.bcm.edu	37	chr11	48346805	48346805	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	attcttcttctatggctcctAaactcattgctgactcattg	5	11	5	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr11:48346805A>T	ENST00000319856.4	+	1	334	c.313A>T	c.(313-315)Aaa>Taa	p.K105*		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	78						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						TATGGCTCCTAAACTCATTGC	0.463																																					p.K105X		Atlas-SNP	.											.	OR4C3	75	.	0			c.A313T						.						194	183	187					11																	48346805		2201	4298	6499	SO:0001587	stop_gained	256144	exon1			GCTCCTAAACTCA	AB065567	CCDS31489.1	11p11.2	2012-08-09				ENSG00000176547		"GPCR / Class A : Olfactory receptors"	14697	protein-coding gene	gene with protein product							Standard	NM_001004702		Approved		uc010rhv.2	Q8NH37	OTTHUMG00000166579	ENST00000319856.4:c.313A>T	chr11.hg19:g.48346805A>T	ENSP00000321419:p.Lys105*	72.0	0.0		105.0	7.0	NM_001004702	B2RNF2|Q6IFB3	Nonsense_Mutation	SNP	ENST00000319856.4	hg19	CCDS31489.1	.	.	.	.	.	.	.	.	.	.	A	15.12	2.740389	0.49045	.	.	ENSG00000176547	ENST00000319856	.	.	.	5.78	5.78	0.91487	.	0.118890	0.37857	N	0.001915	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.2031	0.65716	1.0:0.0:0.0:0.0	.	.	.	.	X	105	.	ENSP00000321419:K105X	K	+	1	0	OR4C3	48303381	0.441000	0.25626	0.982000	0.44146	0.426000	0.31534	2.853000	0.48317	2.245000	0.73994	0.391000	0.25812	AAA	.	.		0.463	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702		T	48346805	A	T	48346805	4	4	19	1	0	0	0	0	0	1	0	0	11059	363	13	4	315	4	OR4C3	11	48346805	Nonsense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10		48346805	86659711	68	1665										
DDB1	1642	hgsc.bcm.edu	37	chr11	61097043	61097043	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	taatgccggtctctgaggggCggccaatgcggtcctgagaa	15	10	1	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr11:61097043C>A	ENST00000301764.7	-	4	738	c.341G>T	c.(340-342)cGc>cTc	p.R114L	DDB1_ENST00000545930.1_5'Flank|DDB1_ENST00000450997.2_Intron	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	114	Interaction with CDT1.|WD repeat beta-propeller A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						CTCTGAGGGGCGGCCAATGCG	0.507								Nucleotide excision repair (NER)																													p.R114L		Atlas-SNP	.											.	DDB1	100	.	0			c.G341T						.						27	25	26					11																	61097043		2203	4299	6502	SO:0001583	missense	1642	exon4			GAGGGGCGGCCAA	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.341G>T	chr11.hg19:g.61097043C>A	ENSP00000301764:p.Arg114Leu	71.0	0.0		107.0	54.0	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Missense_Mutation	SNP	ENST00000301764.7	hg19	CCDS31576.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.900919	0.92035	.	.	ENSG00000167986	ENST00000301764;ENST00000539426;ENST00000535283;ENST00000542337	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	5.09	4.17	0.49024	.	0.049992	0.85682	D	0.000000	T	0.69637	0.3133	M	0.85373	2.75	0.80722	D	1	D;D	0.57257	0.979;0.961	P;P	0.61940	0.896;0.896	T	0.76895	-0.2790	10	0.72032	D	0.01	-12.0855	15.9702	0.80008	0.0:0.8649:0.1351:0.0	.	114;114	B7Z2A1;Q16531	.;DDB1_HUMAN	L	114;58;58;114	ENSP00000301764:R114L;ENSP00000445554:R58L;ENSP00000441825:R58L;ENSP00000444105:R114L	ENSP00000301764:R114L	R	-	2	0	DDB1	60853619	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	7.474000	0.81024	1.263000	0.44181	0.563000	0.77884	CGC	.	.		0.507	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		A	61097043	C	A	61097043	3	1	19	1	0	0	0	0	1	0	0	0	4325	768	27	1	3177	1	DDB1	11	61097043	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	12750238	61097043	73909473	69	1666										
PRSS23	11098	hgsc.bcm.edu	37	chr11	86519158	86519158	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aacatcagtgaagttatccaCgggctgcaccggcaccctgg	11	13	1	1	rs200816081		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr11:86519158C>T	ENST00000280258.5	+	2	898	c.473C>T	c.(472-474)aCg>aTg	p.T158M	PRSS23_ENST00000533902.2_Intron|PRSS23_ENST00000441050.1_Missense_Mutation_p.T126M	NM_007173.4	NP_009104.1	O95084	PRS23_HUMAN	protease, serine, 23	158						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(9)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AAGTTATCCACGGGCTGCACC	0.512																																					p.T158M		Atlas-SNP	.											.	PRSS23	49	.	0			c.C473T						.						68	68	68					11																	86519158		2201	4299	6500	SO:0001583	missense	11098	exon2			TATCCACGGGCTG	AF015287	CCDS8278.1	11q14.2	2010-05-12			ENSG00000150687	ENSG00000150687		"Serine peptidases / Serine peptidases"	14370	protein-coding gene	gene with protein product							Standard	XM_005273727		Approved	SPUVE, SIG13	uc001pcb.3	O95084		ENST00000280258.5:c.473C>T	chr11.hg19:g.86519158C>T	ENSP00000280258:p.Thr158Met	170.0	0.0		187.0	72.0	NM_007173	B2RDJ1|B4E2J3|Q6IBI0	Missense_Mutation	SNP	ENST00000280258.5	hg19	CCDS8278.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.404741	0.83230	.	.	ENSG00000150687	ENST00000280258;ENST00000441050	D;D	0.89343	-2.5;-2.5	6.17	6.17	0.99709	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (2);	0.000000	0.85682	D	0.000000	D	0.93491	0.7923	L	0.52905	1.665	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91504	0.5221	9	.	.	.	-10.9442	20.8794	0.99867	0.0:1.0:0.0:0.0	.	126;158	B4E2J3;O95084	.;PRS23_HUMAN	M	158;126	ENSP00000280258:T158M;ENSP00000393015:T126M	.	T	+	2	0	PRSS23	86196806	1.000000	0.71417	0.478000	0.27316	0.958000	0.62258	7.395000	0.79876	2.941000	0.99782	0.655000	0.94253	ACG	.	C|0.999;T|0.001		0.512	PRSS23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393805.2	NM_007173		T	86519158	C	T	86519158	3	4	19	1	0	0	0	0	1	0	0	0	12632	536	19	1	475	1	PRSS23	11	86519158	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	25422115	86519158	48487358	70	1667										
FAT3	120114	hgsc.bcm.edu	37	chr11	92531256	92531256	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ttggaacatcagtcattctaAtctctgccatcagtcaatct	5	11	7	0	rs71473491		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr11:92531256A>C	ENST00000298047.6	+	9	5094	c.5077A>C	c.(5077-5079)Atc>Ctc	p.I1693L	FAT3_ENST00000409404.2_Missense_Mutation_p.I1693L|FAT3_ENST00000525166.1_Missense_Mutation_p.I1543L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1693	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AGTCATTCTAATCTCTGCCAT	0.388										TCGA Ovarian(4;0.039)																											p.I1693L		Atlas-SNP	.											.	FAT3	1822	.	0			c.A5077C						.						114	114	114					11																	92531256		1951	4139	6090	SO:0001583	missense	120114	exon9			ATTCTAATCTCTG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.5077A>C	chr11.hg19:g.92531256A>C	ENSP00000298047:p.Ile1693Leu	107.0	0.0		145.0	61.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	A	15.20	2.762544	0.49574	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.47177	0.85;0.85;0.85	5.93	5.93	0.95920	.	.	.	.	.	T	0.20170	0.0485	N	0.03238	-0.38	0.80722	D	1	B	0.11235	0.004	B	0.06405	0.002	T	0.22906	-1.0203	9	0.13108	T	0.6	.	5.3182	0.15866	0.6863:0.1689:0.1448:0.0	.	1693	Q8TDW7-3	.	L	1693;1693;1543	ENSP00000298047:I1693L;ENSP00000387040:I1693L;ENSP00000432586:I1543L	ENSP00000298047:I1693L	I	+	1	0	FAT3	92170904	0.964000	0.33143	0.953000	0.39169	0.988000	0.76386	2.094000	0.41719	2.273000	0.75805	0.482000	0.46254	ATC	.	A|0.500;G|0.500		0.388	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		C	92531256	A	C	92531256	3	2	19	1	0	0	0	0	1	0	0	0	5699	101	4	5	5111	5	FAT3	11	92531256	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	6012098	92531256	42475260	71	1668										
TAF1D	79101	hgsc.bcm.edu	37	chr11	93471289	93471289	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	actcacctcaaacgttaaaaTttttctccaaggtgcgtttt	5	10	3	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr11:93471289T>C	ENST00000448108.2	-	3	1095	c.445A>G	c.(445-447)Att>Gtt	p.I149V	TAF1D_ENST00000546088.1_5'Flank|SNORA40_ENST00000388090.1_RNA	NM_024116.3	NP_077021.1	Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa	149					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(3)|prostate(1)|skin(2)	7						AACGTTAAAATTTTTCTCCAA	0.338																																					p.I149V		Atlas-SNP	.											.	TAF1D	18	.	0			c.A445G						.						75	82	79					11																	93471289		2200	4297	6497	SO:0001583	missense	79101	exon3			TTAAAATTTTTCT		CCDS8293.1	11q21	2012-05-30	2008-09-30	2008-09-30	ENSG00000166012	ENSG00000166012			28759	protein-coding gene	gene with protein product		612823	"Josephin domain containing 3"	JOSD3		15520167, 17318177	Standard	NM_024116		Approved	MGC5306, TAF(I)41	uc001pec.3	Q9H5J8	OTTHUMG00000167451	ENST00000448108.2:c.445A>G	chr11.hg19:g.93471289T>C	ENSP00000410409:p.Ile149Val	75.0	0.0		86.0	34.0	NM_024116	Q6I9Y6	Missense_Mutation	SNP	ENST00000448108.2	hg19	CCDS8293.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.557087	0.27827	.	.	ENSG00000166012	ENST00000448108	.	.	.	5.45	4.31	0.51392	.	0.351548	0.27636	N	0.018486	T	0.47563	0.1452	L	0.50333	1.59	0.28449	N	0.916438	D	0.58620	0.983	P	0.57720	0.826	T	0.35895	-0.9770	9	0.19147	T	0.46	-18.2288	8.985	0.35988	0.1647:0.0:0.0:0.8353	.	149	Q9H5J8	TAF1D_HUMAN	V	149	.	ENSP00000314971:I149V	I	-	1	0	TAF1D	93110937	1.000000	0.71417	0.997000	0.53966	0.061000	0.15899	2.263000	0.43293	0.989000	0.38761	-0.327000	0.08410	ATT	.	.		0.338	TAF1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394662.2	NM_024116		C	93471289	T	C	93471289	3	2	19	1	0	0	0	0	1	0	0	0	15537	1493	52	2	407	2	TAF1D	11	93471289	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	940033	93471289	41535227	72	1669										
PDZD3	79849	hgsc.bcm.edu	37	chr11	119059807	119059807	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ctgttgggggacagaatgacCtggagaggcttcagcagctg	16	8	1	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr11:119059807C>T	ENST00000531114.1	+	8	2128	c.1579C>T	c.(1579-1581)Ctg>Ttg	p.L527L	PDZD3_ENST00000392817.2_Silent_p.L527L|PDZD3_ENST00000322712.4_Silent_p.L447L|PDZD3_ENST00000525131.1_Silent_p.L448L|PDZD3_ENST00000355547.5_Silent_p.L461L			Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	527	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cGMP-mediated signaling (GO:0019934)|ion transport (GO:0006811)|negative regulation of cGMP biosynthetic process (GO:0030827)|negative regulation of guanylate cyclase activity (GO:0031283)|receptor guanylyl cyclase signaling pathway (GO:0007168)|response to toxic substance (GO:0009636)|water transport (GO:0006833)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|subapical complex (GO:0035003)	guanylate cyclase inhibitor activity (GO:0030251)|ion channel inhibitor activity (GO:0008200)|protein C-terminus binding (GO:0008022)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	14	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)		ACAGAATGACCTGGAGAGGCT	0.637																																					p.L461L		Atlas-SNP	.											.	PDZD3	42	.	0			c.C1381T						.						46	46	46					11																	119059807		2200	4295	6495	SO:0001819	synonymous_variant	79849	exon10			AATGACCTGGAGA	AK091966	CCDS8417.1, CCDS53719.1	11q23.3	2008-02-05	2006-01-24	2006-01-24	ENSG00000172367	ENSG00000172367			19891	protein-coding gene	gene with protein product		607146	"PDZ domain containing 2"	PDZK2		11950846	Standard	NM_024791		Approved	FLJ22756, IKEPP	uc001pvz.3	Q86UT5	OTTHUMG00000166224	ENST00000531114.1:c.1579C>T	chr11.hg19:g.119059807C>T		31.0	0.0		37.0	16.0	NM_001168468	Q8N6R4|Q8NAW7|Q8NEX7|Q9H5Z3	Silent	SNP	ENST00000531114.1	hg19																																																																																				.	.		0.637	PDZD3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388471.1	NM_024791		T	119059807	C	T	119059807	2	4	19	1	0	0	0	0	0	0	0	1	11711	680	24	3		3	PDZD3	11	119059807	Silent	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	25588518	119059807	15946709	73	1670										
CLEC1B	51266	hgsc.bcm.edu	37	chr12	10149501	10149501	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	attcatgtcagtgcagtactGcttactctcttcccatgtta	6	11	3	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr12:10149501G>C	ENST00000298527.6	-	4	561	c.382C>G	c.(382-384)Cag>Gag	p.Q128E	CLEC1B_ENST00000428126.2_Missense_Mutation_p.Q95E|CLEC1B_ENST00000348658.4_Missense_Mutation_p.Q95E	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	128	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.Q32*(1)|p.Q128*(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						GTGCAGTACTGCTTACTCTCT	0.423																																					p.Q128E		Atlas-SNP	.											CLEC1B_ENST00000398939,bladder,carcinoma,0,2	CLEC1B	39	.	2	Substitution - Nonsense(2)	urinary_tract(2)	c.C382G						.						186	165	172					12																	10149501		1893	4139	6032	SO:0001583	missense	51266	exon4			AGTACTGCTTACT	AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"C-type lectin domain containing"	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.382C>G	chr12.hg19:g.10149501G>C	ENSP00000298527:p.Gln128Glu	60.0	0.0		68.0	21.0	NM_016509	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	hg19	CCDS41752.1	.	.	.	.	.	.	.	.	.	.	G	3.125	-0.179754	0.06380	.	.	ENSG00000165682	ENST00000398937;ENST00000428126;ENST00000298527;ENST00000348658;ENST00000398939	T;T;T;T	0.16457	2.34;2.34;2.34;2.34	4.05	-2.33	0.06724	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.927767	0.09066	N	0.853623	T	0.07728	0.0194	L	0.27053	0.805	0.09310	N	1	B;B	0.19935	0.015;0.04	B;B	0.14023	0.004;0.01	T	0.41070	-0.9529	10	0.07030	T	0.85	.	2.6442	0.04979	0.0988:0.1443:0.2839:0.4731	.	95;128	Q9P126-2;Q9P126	.;CLC1B_HUMAN	E	35;95;128;95;32	ENSP00000381910:Q35E;ENSP00000406338:Q95E;ENSP00000298527:Q128E;ENSP00000327169:Q95E	ENSP00000298527:Q128E	Q	-	1	0	CLEC1B	10040768	0.063000	0.20901	0.014000	0.15608	0.422000	0.31414	0.205000	0.17356	-0.297000	0.08934	0.491000	0.48974	CAG	.	.		0.423	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509		C	10149501	G	C	10149501	3	2	19	1	0	0	0	0	1	0	0	0	3508	1328	46	4	319	4	CLEC1B	12	10149501	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10		10149501	123702394	74	1671										
H2AFJ	55766	hgsc.bcm.edu	37	chr12	14927760	14927760	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ccaggccgtgctgctgcccaAgaagacggagagtcagaaga	14	11	1	5	rs371368734		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr12:14927760A>G	ENST00000544848.1	+	1	491	c.356A>G	c.(355-357)aAg>aGg	p.K119R		NM_177925.2	NP_808760.1	Q9BTM1	H2AJ_HUMAN	H2A histone family, member J	119						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|kidney(1)|ovary(1)|skin(1)	5						CTGCTGCCCAAGAAGACGGAG	0.612																																					p.K119R		Atlas-SNP	.											.	H2AFJ	14	.	0			c.A356G						.	A	ARG/LYS	1,4405		0,1,2202	56	56	56		356	3.5	1	12		56	0,8600		0,0,4300	no	missense	H2AFJ	NM_177925.2	26	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign	119/130	14927760	1,13005	2203	4300	6503	SO:0001583	missense	55766	exon1			TGCCCAAGAAGAC	AK001765	CCDS31752.1	12p12.3	2012-09-11			ENSG00000246705	ENSG00000246705		"Histones / Replication-independent"	14456	protein-coding gene	gene with protein product							Standard	NM_177925		Approved	FLJ10903, MGC921	uc009zia.3	Q9BTM1	OTTHUMG00000168736	ENST00000544848.1:c.356A>G	chr12.hg19:g.14927760A>G	ENSP00000438553:p.Lys119Arg	159.0	0.0		160.0	76.0	NM_177925	Q9NV63	Missense_Mutation	SNP	ENST00000544848.1	hg19	CCDS31752.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.23|13.23	2.174360|2.174360	0.38413|0.38413	2.27E-4|2.27E-4	0.0|0.0	ENSG00000246705|ENSG00000246705	ENST00000228929|ENST00000544848	.|D	.|0.86097	.|-2.07	4.64|4.64	3.5|3.5	0.40072|0.40072	.|Histone-fold (2);Histone H2A (1);	.|.	.|.	.|.	.|.	.|D	.|0.87884	.|0.6290	M|M	0.86805|0.86805	2.84|2.84	0.40764|0.40764	D|D	0.983032|0.983032	.|B	.|0.21821	.|0.061	.|B	.|0.36418	.|0.224	.|D	.|0.86763	.|0.1968	.|9	.|0.72032	.|D	.|0.01	.|.	8.9898|8.9898	0.36017|0.36017	0.9112:0.0:0.0888:0.0|0.9112:0.0:0.0888:0.0	.|.	.|119	.|Q9BTM1	.|H2AJ_HUMAN	.|R	-1|119	.|ENSP00000438553:K119R	.|ENSP00000373730:K119R	.|K	+|+	.|2	.|0	H2AFJ|H2AFJ	14819027|14819027	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.183000|7.183000	0.77697|0.77697	1.090000|1.090000	0.41315|0.41315	-0.280000|-0.280000	0.10049|0.10049	.|AAG	.	.		0.612	H2AFJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400845.1	NM_177925		G	14927760	A	G	14927760	3	3	19	1	0	0	0	0	1	0	0	0	6935	72	3	2	358	2	H2AFJ	12	14927760	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	4778259	14927760	118924135	75	1672										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43846185	43846185	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ttggttccagcaacctgacaAtagagtttacaacgatcctt	7	10	0	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr12:43846185A>G	ENST00000389420.3	-	14	1970	c.1971T>C	c.(1969-1971)taT>taC	p.Y657Y	ADAMTS20_ENST00000553158.1_Silent_p.Y657Y	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	657	Cys-rich.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		CAACCTGACAATAGAGTTTAC	0.348																																					p.Y657Y		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T1971C						.						89	85	87					12																	43846185		2203	4300	6503	SO:0001819	synonymous_variant	80070	exon14			CTGACAATAGAGT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1971T>C	chr12.hg19:g.43846185A>G		68.0	0.0		125.0	47.0	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.		0.348	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43846185	A	G	43846185	2	3	19	1	0	0	0	0	0	0	0	1	266	108	4	2		2	ADAMTS20	12	43846185	Silent	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	28918425	43846185	90005710	76	1673										
PUS7L	83448	hgsc.bcm.edu	37	chr12	44148379	44148379	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tttggaattttctttctttgCatccaaatatttaaaaaagt	4	5	2	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr12:44148379C>A	ENST00000416848.2	-	2	1158	c.670G>T	c.(670-672)Gca>Tca	p.A224S	PUS7L_ENST00000553166.1_Missense_Mutation_p.A224S|PUS7L_ENST00000344862.5_Missense_Mutation_p.A224S|PUS7L_ENST00000431332.3_Intron|PUS7L_ENST00000551923.1_Missense_Mutation_p.A224S	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	224					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		TCTTTCTTTGCATCCAAATAT	0.299																																					p.A224S		Atlas-SNP	.											.	PUS7L	73	.	0			c.G670T						.						69	68	69					12																	44148379		2203	4298	6501	SO:0001583	missense	83448	exon2			TCTTTGCATCCAA	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.670G>T	chr12.hg19:g.44148379C>A	ENSP00000415899:p.Ala224Ser	149.0	0.0		216.0	17.0	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Missense_Mutation	SNP	ENST00000416848.2	hg19	CCDS8743.1	.	.	.	.	.	.	.	.	.	.	C	33	5.248839	0.95305	.	.	ENSG00000129317	ENST00000416848;ENST00000344862;ENST00000551923;ENST00000553166	T;T;T;T	0.24350	1.91;1.91;1.91;1.86	5.35	5.35	0.76521	Pseudouridine synthase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.03148	-1.1067	10	0.21540	T	0.41	-22.8576	19.9585	0.97232	0.0:1.0:0.0:0.0	.	224	Q9H0K6	PUS7L_HUMAN	S	224	ENSP00000415899:A224S;ENSP00000343081:A224S;ENSP00000447706:A224S;ENSP00000446865:A224S	ENSP00000343081:A224S	A	-	1	0	PUS7L	42434646	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.210000	0.77924	2.894000	0.99253	0.655000	0.94253	GCA	.	.		0.299	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		A	44148379	C	A	44148379	3	1	19	1	0	0	0	0	1	0	0	0	12849	710	25	3	1467	3	PUS7L	12	44148379	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	302194	44148379	89703516	77	1674										
POLR3B	55703	hgsc.bcm.edu	37	chr12	106903268	106903268	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	atgcctgcaagctgctcttcCaggaactacagtctatgaac	8	12	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr12:106903268C>G	ENST00000228347.4	+	28	3565	c.3343C>G	c.(3343-3345)Cag>Gag	p.Q1115E	POLR3B_ENST00000539066.1_Missense_Mutation_p.Q1057E|RP11-144F15.1_ENST00000551505.1_Intron	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	1115					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GCTGCTCTTCCAGGAACTACA	0.443																																					p.Q1115E		Atlas-SNP	.											.	POLR3B	123	.	0			c.C3343G						.						160	133	142					12																	106903268		2203	4300	6503	SO:0001583	missense	55703	exon28			CTCTTCCAGGAAC	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.3343C>G	chr12.hg19:g.106903268C>G	ENSP00000228347:p.Gln1115Glu	82.0	0.0		98.0	40.0	NM_018082	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	hg19	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.923286	0.92319	.	.	ENSG00000013503	ENST00000228347;ENST00000539066	T;T	0.78003	-1.14;-1.14	5.57	5.57	0.84162	RNA polymerase Rpb2, domain 7 (1);	0.000000	0.85682	D	0.000000	D	0.92844	0.7724	H	0.97240	3.965	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.94982	0.8126	10	0.87932	D	0	-16.5766	19.557	0.95354	0.0:1.0:0.0:0.0	.	1115	Q9NW08	RPC2_HUMAN	E	1115;1057	ENSP00000228347:Q1115E;ENSP00000445721:Q1057E	ENSP00000228347:Q1115E	Q	+	1	0	POLR3B	105427398	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.818000	0.86416	2.630000	0.89119	0.655000	0.94253	CAG	.	.		0.443	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		G	106903268	C	G	106903268	3	3	19	1	0	0	0	0	1	0	0	0	12238	595	21	4	3453	4	POLR3B	12	106903268	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	62754889	106903268	26948627	78	1675										
RHOF	54509	hgsc.bcm.edu	37	chr12	122218862	122218862	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ctcaggtctgtcttgcagccGatgagcaccatggggatccc	12	13	3	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr12:122218862G>A	ENST00000267205.2	-	4	1015	c.387C>T	c.(385-387)atC>atT	p.I129I	TMEM120B_ENST00000449592.2_3'UTR|TMEM120B_ENST00000538055.1_3'UTR|RHOF_ENST00000537265.1_Silent_p.I29I|RHOF_ENST00000537171.1_Silent_p.I129I	NM_019034.2	NP_061907.2	Q9HBH0	RHOF_HUMAN	ras homolog family member F (in filopodia)	129					actin filament organization (GO:0007015)|GTP catabolic process (GO:0006184)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(1)|ovary(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;4.38e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.223)		TCTTGCAGCCGATGAGCACCA	0.672																																					p.I129I		Atlas-SNP	.											.	RHOF	6	.	0			c.C387T						.						34	33	34					12																	122218862		2203	4300	6503	SO:0001819	synonymous_variant	54509	exon4			GCAGCCGATGAGC	AK000254	CCDS9222.1	12q24.31	2013-09-23	2012-02-27	2004-03-24	ENSG00000139725	ENSG00000139725			15703	protein-coding gene	gene with protein product			"ras homolog gene family, member F (in filopodia)"	ARHF		11084341	Standard	NM_019034		Approved	FLJ20247, RIF	uc001ubb.3	Q9HBH0	OTTHUMG00000169077	ENST00000267205.2:c.387C>T	chr12.hg19:g.122218862G>A		119.0	0.0		116.0	45.0	NM_019034	Q8WVB1|Q9NXH6	Silent	SNP	ENST00000267205.2	hg19	CCDS9222.1																																																																																			.	.		0.672	RHOF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402165.1			A	122218862	G	A	122218862	2	1	19	1	0	0	0	0	0	0	0	1	13353	1048	37	1		1	RHOF	12	122218862	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	15315594	122218862	11633033	79	1676										
AACS	65985	hgsc.bcm.edu	37	chr12	125621327	125621327	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	acgccttccagcctgacttgGttaagaggatccgtgacgcc	11	13	0	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr12:125621327G>T	ENST00000316519.6	+	17	2004	c.1798G>T	c.(1798-1800)Gtt>Ttt	p.V600F	AACS_ENST00000261686.6_Intron|AACS_ENST00000543665.1_Intron|AACS_ENST00000316543.10_Missense_Mutation_p.V198F|AACS_ENST00000545511.1_Intron	NM_023928.3	NP_076417.2	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	600					adipose tissue development (GO:0060612)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cellular response to testosterone stimulus (GO:0071394)|fatty acid metabolic process (GO:0006631)|liver development (GO:0001889)|positive regulation of insulin secretion (GO:0032024)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to purine-containing compound (GO:0014074)|response to starvation (GO:0042594)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)	acetoacetate-CoA ligase activity (GO:0030729)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|liver(1)|lung(16)|ovary(1)|stomach(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		GCCTGACTTGGTTAAGAGGAT	0.607																																					p.V600F		Atlas-SNP	.											.	AACS	59	.	0			c.G1798T						.						126	106	113					12																	125621327		2203	4300	6503	SO:0001583	missense	65985	exon17			GACTTGGTTAAGA	AK022451	CCDS9263.1	12q24.31	2010-09-29			ENSG00000081760	ENSG00000081760	6.2.1.16	"Acyl-CoA synthetase family"	21298	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 1"	614364				12623130, 17762044	Standard	NM_023928		Approved	FLJ12389, SUR-5, ACSF1	uc001uhc.3	Q86V21	OTTHUMG00000168550	ENST00000316519.6:c.1798G>T	chr12.hg19:g.125621327G>T	ENSP00000324842:p.Val600Phe	76.0	0.0		97.0	43.0	NM_023928	Q49AB9|Q49AC3|Q658Q8|Q8IWD2|Q8NEW5|Q9BSJ9|Q9H829|Q9HA19	Missense_Mutation	SNP	ENST00000316519.6	hg19	CCDS9263.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.925067	0.52759	.	.	ENSG00000081760	ENST00000316519;ENST00000316543;ENST00000539251;ENST00000536118	T;T;T;T	0.11063	2.81;2.81;2.81;2.81	5.3	4.4	0.53042	.	0.058805	0.64402	D	0.000002	T	0.24586	0.0596	M	0.82517	2.595	0.80722	D	1	P	0.52842	0.956	P	0.48795	0.59	T	0.11084	-1.0602	10	0.56958	D	0.05	.	14.6054	0.68475	0.0:0.2775:0.7225:0.0	.	600	Q86V21	AACS_HUMAN	F	600;198;65;155	ENSP00000324842:V600F;ENSP00000324929:V198F;ENSP00000439151:V65F;ENSP00000441331:V155F	ENSP00000324842:V600F	V	+	1	0	AACS	124187280	1.000000	0.71417	0.952000	0.39060	0.085000	0.17905	5.888000	0.69758	1.339000	0.45563	0.561000	0.74099	GTT	.	.		0.607	AACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400202.1	NM_023928		T	125621327	G	T	125621327	3	4	19	1	0	0	0	0	1	0	0	0	9	1261	44	3	1864	3	AACS	12	125621327	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	3402465	125621327	8230568	80	1677										
ZNF10	7556	hgsc.bcm.edu	37	chr12	133728487	133728487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aaattcaccaagagacccatCctggtgaggaccagtcaaga	9	11	2	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr12:133728487C>T	ENST00000248211.6	+	4	475	c.253C>T	c.(253-255)Cct>Tct	p.P85S	ZNF10_ENST00000426665.2_Missense_Mutation_p.P85S|ZNF10_ENST00000402932.2_Missense_Mutation_p.P85S|ZNF268_ENST00000416488.1_Missense_Mutation_p.P85S|CTD-2140B24.4_ENST00000540096.2_Missense_Mutation_p.P85S	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	85	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		AGAGACCCATCCTGGTGAGGA	0.542																																					p.P85S		Atlas-SNP	.											.	ZNF10	58	.	0			c.C253T						.						62	58	59					12																	133728487		2203	4300	6503	SO:0001583	missense	7556	exon4			ACCCATCCTGGTG	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"Zinc fingers, C2H2-type", "-"	12879	protein-coding gene	gene with protein product		194538	"zinc finger protein 10 (KOX 1)"			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.253C>T	chr12.hg19:g.133728487C>T	ENSP00000248211:p.Pro85Ser	91.0	0.0		74.0	36.0	NM_015394	B2RBS1|Q8TC91	Missense_Mutation	SNP	ENST00000248211.6	hg19	CCDS9283.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.755363	0.31046	.	.	ENSG00000256223;ENSG00000256223;ENSG00000256223;ENSG00000256223;ENSG00000090612	ENST00000248211;ENST00000426665;ENST00000402932;ENST00000537119;ENST00000416488	T;T;T;T;T	0.05717	3.4;3.4;3.57;4.62;5.69	3.82	2.87	0.33458	Krueppel-associated box (1);	0.432093	0.17278	N	0.180109	T	0.06050	0.0157	L	0.52573	1.65	0.58432	D	0.999997	B	0.29862	0.259	B	0.26614	0.071	T	0.33369	-0.9871	9	.	.	.	.	6.2098	0.20623	0.0:0.846:0.0:0.154	.	85	P21506	ZNF10_HUMAN	S	85;85;85;43;85	ENSP00000248211:P85S;ENSP00000393814:P85S;ENSP00000384893:P85S;ENSP00000437397:P43S;ENSP00000409295:P85S	.	P	+	1	0	ZNF10;ZNF268	132238560	0.003000	0.15002	0.710000	0.30468	0.019000	0.09904	-0.440000	0.06888	0.871000	0.35750	0.563000	0.77884	CCT	.	.		0.542	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394		T	133728487	C	T	133728487	3	4	19	1	0	0	0	0	1	0	0	0	17727	855	30	3	263	3	ZNF10	12	133728487	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	8107160	133728487	123408	81	1678										
EFNB2	1948	hgsc.bcm.edu	37	chr13	107187266	107187266	+	Frame_Shift_Del	DEL	A	A	-													0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cagttctgcataaaaccatcAaaacaccccagcagtacttc							TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr13:107187266delA	ENST00000245323.4	-	1	196	c.47delT	c.(46-48)ttgfs	p.L16fs		NM_004093.3	NP_004084.1	P52799	EFNB2_HUMAN	ephrin-B2	16					anatomical structure morphogenesis (GO:0009653)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|lymph vessel development (GO:0001945)|negative regulation of keratinocyte proliferation (GO:0010839)|organ morphogenesis (GO:0009887)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|regulation of chemotaxis (GO:0050920)|viral process (GO:0016032)	focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					TAAAACCATCAAAACACCCCA	0.537																																					p.L16fs		Atlas-Indel,Pindel	.											.	EFNB2	39	.	0			c.48delG						.						95	102	99					13																	107187266		2202	4300	6502	SO:0001589	frameshift_variant	1948	exon1			.	L38734	CCDS9507.1	13q33	2011-03-09			ENSG00000125266	ENSG00000125266		"Ephrins"	3227	protein-coding gene	gene with protein product	"HTK ligand", "ligand of eph-related kinase 5", "eph-related receptor tyrosine kinase ligand 5"	600527		EPLG5		7833926	Standard	NM_004093		Approved	LERK5, Htk-L, HTKL, MGC126226, MGC126227, MGC126228	uc001vqi.3	P52799	OTTHUMG00000017324	ENST00000245323.4:c.47delT	chr13.hg19:g.107187266delA	ENSP00000245323:p.Leu16fs	97.0	0.0		111.0	51.0	NM_004093	Q5JV56	Frame_Shift_Del	DEL	ENST00000245323.4	hg19	CCDS9507.1																																																																																			.	.		0.537	EFNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045733.4	NM_004093		-	107187266	A	-	107187266	7	5	19	1	0	1	0	1	0	0	0	0	4958	131	5	0	974	0	EFNB2	13	107187266	Frame_Shift_Del	DEL	A	TCGA-2Y-A9H9-01A-21D-A38X-10		107187266	7982612	82	1679										
SOX1	6656	hgsc.bcm.edu	37	chr13	112723111	112723111	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gcactaccagggcgcgggcgCgggcgtgaacggcacggtgc	19	13	0	1	rs199891204|rs137969745	byFrequency	TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr13:112723111C>T	ENST00000330949.1	+	1	1199	c.1139C>T	c.(1138-1140)gCg>gTg	p.A380V		NM_005986.2	NP_005977.2	O00570	SOX1_HUMAN	SRY (sex determining region Y)-box 1	380					chromatin organization (GO:0006325)|forebrain neuron development (GO:0021884)|lens morphogenesis in camera-type eye (GO:0002089)|neuron migration (GO:0001764)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(4)	4	all_lung(23;0.000652)|Lung NSC(43;0.017)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	all_cancers(25;0.000331)|Lung NSC(25;0.0496)|all_lung(25;0.0831)|all_epithelial(44;0.0868)|Breast(118;0.231)		OV - Ovarian serous cystadenocarcinoma(48;0.132)		GGCGCGGGCGCGGGCGTGAAC	0.791																																					p.A380V		Atlas-SNP	.											SOX1,spinal_cord,glioma,0,1	SOX1	14	.	0			c.C1139T						.						1	1	1					13																	112723111		785	1888	2673	SO:0001583	missense	6656	exon1			CGGGCGCGGGCGT		CCDS9523.1	13q34	2008-07-18			ENSG00000182968	ENSG00000182968		"SRY (sex determining region Y)-boxes"	11189	protein-coding gene	gene with protein product	"SRY-related HMG-box gene 1"	602148				9337405	Standard	NM_005986		Approved		uc001vsb.1	O00570	OTTHUMG00000017362	ENST00000330949.1:c.1139C>T	chr13.hg19:g.112723111C>T	ENSP00000330218:p.Ala380Val	21.0	0.0		10.0	4.0	NM_005986	Q5W0Q1	Missense_Mutation	SNP	ENST00000330949.1	hg19	CCDS9523.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.301562	0.60195	.	.	ENSG00000182968	ENST00000330949	D	0.83075	-1.68	3.44	3.44	0.39384	.	0.178100	0.37577	U	0.002031	T	0.65015	0.2651	N	0.04880	-0.145	0.33320	D	0.567251	B	0.27971	0.196	B	0.14578	0.011	T	0.70077	-0.4971	10	0.32370	T	0.25	.	15.1474	0.72667	0.0:1.0:0.0:0.0	.	380	O00570	SOX1_HUMAN	V	380	ENSP00000330218:A380V	ENSP00000330218:A380V	A	+	2	0	SOX1	111771112	0.987000	0.35691	1.000000	0.80357	0.983000	0.72400	4.048000	0.57390	1.754000	0.51921	0.555000	0.69702	GCG	.	.		0.791	SOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045817.3	NM_005986		T	112723111	C	T	112723111	3	4	19	1	0	0	0	0	1	0	0	0	14955	768	27	1	1141	1	SOX1	13	112723111	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	5535845	112723111	2446767	83	1680										
OR11H6	122748	hgsc.bcm.edu	37	chr14	20692318	20692318	+	Frame_Shift_Del	DEL	C	C	-													0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	atctgtcgtccattacactaCccctccatcatgactgggaa							TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr14:20692318delC	ENST00000315519.2	+	1	528	c.450delC	c.(448-450)tacfs	p.Y150fs		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		CATTACACTACCCCTCCATCA	0.428																																					p.Y150fs		Atlas-Indel,Pindel	.											.	OR11H6	60	.	0			c.449delA						.						134	132	133					14																	20692318		2203	4300	6503	SO:0001589	frameshift_variant	122748	exon1			.		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"GPCR / Class A : Olfactory receptors"	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.450delC	chr14.hg19:g.20692318delC	ENSP00000319071:p.Tyr150fs	48.0	0.0		80.0	35.0	NM_001004480	Q6IF08	Frame_Shift_Del	DEL	ENST00000315519.2	hg19	CCDS32033.1																																																																																			.	.		0.428	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1			-	20692318	C	-	20692318	7	5	19	1	0	1	0	1	0	0	0	0	10938	518	18	0	452	0	OR11H6	14	20692318	Frame_Shift_Del	DEL	C	TCGA-2Y-A9H9-01A-21D-A38X-10		20692318	86657222	84	1681										
CDKN3	1033	hgsc.bcm.edu	37	chr14	54866651	54866651	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gtgagtttgactcatcagatGaagagcctattgaagatgaa	11	5	2	8			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr14:54866651G>A	ENST00000541304.1	+	2	89	c.49G>A	c.(49-51)Gaa>Aaa	p.E17K	CDKN3_ENST00000556102.2_Missense_Mutation_p.E17K|CDKN3_ENST00000458126.2_Missense_Mutation_p.E17K|CDKN3_ENST00000543789.2_Missense_Mutation_p.E17K|CDKN3_ENST00000556305.1_3'UTR|CDKN3_ENST00000442975.2_Intron|CDKN3_ENST00000335183.6_Missense_Mutation_p.E17K			Q00526	CDK3_HUMAN	cyclin-dependent kinase inhibitor 3	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|G0 to G1 transition (GO:0045023)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|stomach(1)	3						CTCATCAGATGAAGAGCCTAT	0.308																																					p.E17K	Pancreas(40;634 1012 9382 49950 52462)	Atlas-SNP	.											.	CDKN3	9	.	0			c.G49A						.						97	94	95					14																	54866651		2203	4295	6498	SO:0001583	missense	1033	exon2			TCAGATGAAGAGC	U02681	CCDS9716.1, CCDS45109.1	14q22	2011-08-25	2008-08-01		ENSG00000100526	ENSG00000100526		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1791	protein-coding gene	gene with protein product	"kinase associated phosphatase", "cyclin-dependent kinase inhibitor", "CDK2-associated dual specificity phosphatase"	123832				8242750, 7698009	Standard	NM_005192		Approved	KAP, CDI1	uc001xap.3	Q16667	OTTHUMG00000140302	ENST00000541304.1:c.49G>A	chr14.hg19:g.54866651G>A	ENSP00000445572:p.Glu17Lys	356.0	1.0		370.0	157.0	NM_005192		Missense_Mutation	SNP	ENST00000541304.1	hg19		.	.	.	.	.	.	.	.	.	.	G	22.9	4.344253	0.82022	.	.	ENSG00000100526	ENST00000335183;ENST00000543789;ENST00000458126;ENST00000556102;ENST00000541304;ENST00000439312;ENST00000434252	T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56	5.17	5.17	0.71159	Cyclin-dependent kinase inhibitor 3, bac/eukaryotic (1);	0.047098	0.85682	D	0.000000	T	0.60881	0.2303	M	0.73962	2.25	0.80722	D	1	P;P	0.50819	0.925;0.939	B;P	0.48368	0.439;0.575	T	0.67098	-0.5756	10	0.87932	D	0	-22.7559	14.0296	0.64606	0.0:0.0:1.0:0.0	.	17;17	F8WDR6;Q16667	.;CDKN3_HUMAN	K	17	ENSP00000335357:E17K;ENSP00000440404:E17K;ENSP00000396451:E17K;ENSP00000450711:E17K;ENSP00000445572:E17K	ENSP00000216414:E16K	E	+	1	0	CDKN3	53936401	1.000000	0.71417	0.979000	0.43373	0.896000	0.52359	4.497000	0.60367	2.687000	0.91594	0.561000	0.74099	GAA	.	.		0.308	CDKN3-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000411158.1			A	54866651	G	A	54866651	3	1	19	1	0	0	0	0	1	0	0	0	3169	1291	45	3	55	3	CDKN3	14	54866651	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	34174333	54866651	52482889	85	1682										
MKRN3	7681	hgsc.bcm.edu	37	chr15	23812175	23812175	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	actgcccatttggagacacaTgcttttacaagcatgaatac	7	10	0	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr15:23812175T>C	ENST00000314520.3	+	1	1722	c.1246T>C	c.(1246-1248)Tgc>Cgc	p.C416R	MKRN3_ENST00000568252.1_Intron|MKRN3_ENST00000564592.1_Intron|RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000568945.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	416					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		TGGAGACACATGCTTTTACAA	0.517																																					p.C416R		Atlas-SNP	.											.	MKRN3	155	.	0			c.T1246C						.						96	94	95					15																	23812175		2203	4300	6503	SO:0001583	missense	7681	exon1			GACACATGCTTTT	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"RING-type (C3HC4) zinc fingers"	7114	protein-coding gene	gene with protein product	"zinc finger protein 127"	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.1246T>C	chr15.hg19:g.23812175T>C	ENSP00000313881:p.Cys416Arg	110.0	0.0		105.0	43.0	NM_005664		Missense_Mutation	SNP	ENST00000314520.3	hg19	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	T	14.08	2.427546	0.43122	.	.	ENSG00000179455	ENST00000314520	D	0.87571	-2.27	4.01	4.01	0.46588	Zinc finger, CCCH-type (2);	0.000000	0.85682	D	0.000000	D	0.93585	0.7952	M	0.89287	3.02	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94256	0.7498	10	0.87932	D	0	.	11.5517	0.50725	0.0:0.0:0.0:1.0	.	416	Q13064	MKRN3_HUMAN	R	416	ENSP00000313881:C416R	ENSP00000313881:C416R	C	+	1	0	MKRN3	21363268	1.000000	0.71417	0.550000	0.28217	0.160000	0.22226	4.404000	0.59735	2.049000	0.60858	0.533000	0.62120	TGC	.	.		0.517	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664		C	23812175	T	C	23812175	3	2	19	1	0	0	0	0	1	0	0	0	9617	1464	51	2	1248	2	MKRN3	15	23812175	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10		23812175	78719217	86	1683										
USP8	9101	hgsc.bcm.edu	37	chr15	50789394	50789394	+	Missense_Mutation	SNP	A	A	C													0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	taaaaaagatagaaatctggAagttaccacctgtgctttta							TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr15:50789394A>C	ENST00000396444.3	+	18	3342	c.3004A>C	c.(3004-3006)Aag>Cag	p.K1002Q	RP11-562A8.4_ENST00000560380.1_RNA|USP8_ENST00000307179.4_Missense_Mutation_p.K1002Q|USP8_ENST00000433963.1_Missense_Mutation_p.K1002Q|USP8_ENST00000425032.3_Missense_Mutation_p.K896Q|RP11-562A8.5_ENST00000560159.1_lincRNA	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	1002	USP.				cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		AGAAATCTGGAAGTTACCACC	0.363																																					p.K1002Q		Atlas-SNP	.											.	USP8	90	.	0			c.A3004C						.						87	88	88					15																	50789394		2196	4294	6490	SO:0001583	missense	9101	exon18			ATCTGGAAGTTAC	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"Ubiquitin-specific peptidases"	12631	protein-coding gene	gene with protein product		603158	"ubiquitin specific protease 8"			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.3004A>C	chr15.hg19:g.50789394A>C	ENSP00000379721:p.Lys1002Gln	98.0	0.0		114.0	27.0	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	hg19	CCDS10137.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.007400	0.93287	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032;ENST00000419830;ENST00000396440	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	5.32	5.32	0.75619	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.43743	0.1261	M	0.66939	2.045	0.80722	D	1	P;P	0.41624	0.757;0.574	B;B	0.42995	0.404;0.312	T	0.48364	-0.9042	10	0.66056	D	0.02	-19.4425	15.5747	0.76368	1.0:0.0:0.0:0.0	.	896;1002	B4DKA8;P40818	.;UBP8_HUMAN	Q	1002;1002;1002;896;220;215	ENSP00000379721:K1002Q;ENSP00000405537:K1002Q;ENSP00000302239:K1002Q;ENSP00000412682:K896Q	ENSP00000302239:K1002Q	K	+	1	0	USP8	48576686	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.870000	0.92336	2.139000	0.66308	0.528000	0.53228	AAG	.	.		0.363	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		C	50789394	A	C	50789394	3	2	19	1	0	0	0	0	1	0	0	0	17104	247	9	5	3070	5	USP8	15	50789394	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	26977219	50789394	51741998	87	1684	6	2								
USP8	9101	hgsc.bcm.edu	37	chr15	50789399	50789401	+	In_Frame_Del	DEL	ACC	ACC	-													0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aagatagaaatctggaagttAccacctgtgcttttagtgca							TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	ACC	ACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr15:50789399_50789401delACC	ENST00000396444.3	+	18	3347_3349	c.3009_3011delACC	c.(3007-3012)ttacca>tta	p.P1005del	RP11-562A8.4_ENST00000560380.1_RNA|USP8_ENST00000307179.4_In_Frame_Del_p.P1005del|USP8_ENST00000433963.1_In_Frame_Del_p.P1005del|USP8_ENST00000425032.3_In_Frame_Del_p.P899del|RP11-562A8.5_ENST00000560159.1_lincRNA	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	1005	USP.				cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		TCTGGAAGTTACCACCTGTGCTT	0.36																																					p.1003_1004del		Atlas-Indel,Pindel	.											.	USP8	90	.	0			c.3008_3010del						.																																			SO:0001651	inframe_deletion	9101	exon18			.	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"Ubiquitin-specific peptidases"	12631	protein-coding gene	gene with protein product		603158	"ubiquitin specific protease 8"			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.3009_3011delACC	chr15.hg19:g.50789402_50789404delACC	ENSP00000379721:p.Pro1005del	95.0	0.0		110.0	29.0	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	In_Frame_Del	DEL	ENST00000396444.3	hg19	CCDS10137.1																																																																																			.	.		0.36	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		-	50789401	ACC	-	50789399	7	5	19	1	0	1	0	1	0	0	0	0	17104	388	14	0	3075	0	USP8	15	50789399	In_Frame_Del	DEL	ACC	TCGA-2Y-A9H9-01A-21D-A38X-10	5	50789399	51741993	88	1685	6	2								
MEGF11	84465	hgsc.bcm.edu	37	chr15	66274611	66274611	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gtagccaggtgcgcagaggcActcgccggcgcgggggtcgc	19	13	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr15:66274611A>T	ENST00000409699.2	-	6	782	c.610T>A	c.(610-612)Tgc>Agc	p.C204S	MEGF11_ENST00000395625.2_Missense_Mutation_p.C129S|MEGF11_ENST00000288745.3_Missense_Mutation_p.C129S|MEGF11_ENST00000360698.4_Missense_Mutation_p.C204S|MEGF11_ENST00000395614.1_5'UTR|MEGF11_ENST00000422354.1_Missense_Mutation_p.C204S			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	204	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						GCGCAGAGGCACTCGCCGGCG	0.731																																					p.C204S		Atlas-SNP	.											.	MEGF11	70	.	0			c.T610A						.						2	2	2					15																	66274611		1580	3107	4687	SO:0001583	missense	84465	exon6			AGAGGCACTCGCC	AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.610T>A	chr15.hg19:g.66274611A>T	ENSP00000386908:p.Cys204Ser	60.0	0.0		55.0	19.0	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	hg19	CCDS10213.2	.	.	.	.	.	.	.	.	.	.	A	17.51	3.406569	0.62399	.	.	ENSG00000157890	ENST00000409699;ENST00000288745;ENST00000422354;ENST00000395625;ENST00000360698	T;T;T;T;D	0.99984	-1.33;-1.33;-1.33;-1.33;-11.36	3.73	2.57	0.30868	EGF-like, laminin (2);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.148379	0.31188	U	0.008099	D	0.99986	0.9997	H	0.98721	4.31	0.58432	D	0.999997	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.999	D	0.96597	0.9442	10	0.87932	D	0	.	9.1404	0.36899	0.8153:0.1847:0.0:0.0	.	204;129	A6BM72;A6BM72-2	MEG11_HUMAN;.	S	204;129;204;129;204	ENSP00000386908:C204S;ENSP00000288745:C129S;ENSP00000414475:C204S;ENSP00000378987:C129S;ENSP00000353919:C204S	ENSP00000288745:C129S	C	-	1	0	MEGF11	64061665	1.000000	0.71417	0.971000	0.41717	0.357000	0.29423	8.879000	0.92398	0.490000	0.27771	-0.488000	0.04728	TGC	.	.		0.731	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445		T	66274611	A	T	66274611	3	4	19	1	0	0	0	0	1	0	0	0	9470	159	6	4	2596	4	MEGF11	15	66274611	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	15485212	66274611	36256781	89	1686										
SMAD3	4088	hgsc.bcm.edu	37	chr15	67457388	67457388	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tatgaagaaggacgaggtctGcgtgaatccctaccactacc	10	11	1	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr15:67457388G>T	ENST00000327367.4	+	2	672	c.362G>T	c.(361-363)tGc>tTc	p.C121F	SMAD3_ENST00000540846.2_Missense_Mutation_p.C16F|SMAD3_ENST00000537194.2_5'Flank|SMAD3_ENST00000439724.3_Missense_Mutation_p.C77F	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	121	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		GACGAGGTCTGCGTGAATCCC	0.607																																					p.C121F		Atlas-SNP	.											.	SMAD3	119	.	0			c.G362T						.						94	91	92					15																	67457388		2201	4299	6500	SO:0001583	missense	4088	exon2			AGGTCTGCGTGAA	BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"SMADs"	6769	protein-coding gene	gene with protein product		603109	"MAD, mothers against decapentaplegic homolog 3 (Drosophila)", "SMAD, mothers against DPP homolog 3 (Drosophila)"	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.362G>T	chr15.hg19:g.67457388G>T	ENSP00000332973:p.Cys121Phe	57.0	0.0		53.0	18.0	NM_005902	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Missense_Mutation	SNP	ENST00000327367.4	hg19	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.361582	0.82353	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000540846;ENST00000439724	D;D;D	0.97994	-4.65;-4.65;-4.65	4.39	4.39	0.52855	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.99223	0.9730	H	0.97682	4.055	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.87578	0.998;0.968	D	0.98766	1.0726	10	0.87932	D	0	.	17.1514	0.86779	0.0:0.0:1.0:0.0	.	77;121	B7Z4Z5;P84022	.;SMAD3_HUMAN	F	121;121;16;77	ENSP00000332973:C121F;ENSP00000437757:C16F;ENSP00000401133:C77F	ENSP00000332973:C121F	C	+	2	0	SMAD3	65244442	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.428000	0.97476	2.270000	0.75569	0.561000	0.74099	TGC	.	.		0.607	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902		T	67457388	G	T	67457388	3	4	19	1	0	0	0	0	1	0	0	0	14774	1319	46	3	446	3	SMAD3	15	67457388	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	1182777	67457388	35074004	90	1687										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72231259	72231259	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gaggtgttctgggatttttcCgggttatacctagcaaaatt	11	6	1	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr15:72231259C>T	ENST00000356056.5	-	16	2784	c.2312G>A	c.(2311-2313)cGg>cAg	p.R771Q	MYO9A_ENST00000424560.1_Missense_Mutation_p.R771Q|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000564571.1_Missense_Mutation_p.R771Q|MYO9A_ENST00000566885.1_Missense_Mutation_p.R391Q|MYO9A_ENST00000444904.1_Missense_Mutation_p.R752Q	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	771	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GGGATTTTTCCGGGTTATACC	0.318																																					p.R771Q		Atlas-SNP	.											.	MYO9A	203	.	0			c.G2312A						.						62	64	64					15																	72231259		2199	4296	6495	SO:0001583	missense	4649	exon16			TTTTTCCGGGTTA	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.2312G>A	chr15.hg19:g.72231259C>T	ENSP00000348349:p.Arg771Gln	36.0	0.0		77.0	26.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.022035	0.93462	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	D;D;D	0.86366	-2.11;-2.11;-2.11	5.45	5.45	0.79879	Myosin head, motor domain (1);	.	.	.	.	D	0.90786	0.7107	M	0.61703	1.905	0.52501	D	0.99995	D;P;D	0.89917	1.0;0.89;0.997	P;B;P	0.62740	0.906;0.171;0.736	D	0.88532	0.3103	9	0.25751	T	0.34	.	14.7606	0.69604	0.0:1.0:0.0:0.0	.	752;752;771	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	Q	771;771;752;752	ENSP00000348349:R771Q;ENSP00000399162:R771Q;ENSP00000398250:R752Q	ENSP00000261864:R752Q	R	-	2	0	MYO9A	70018313	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	5.609000	0.67661	2.573000	0.86826	0.585000	0.79938	CGG	.	.		0.318	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		T	72231259	C	T	72231259	3	4	19	1	0	0	0	0	1	0	0	0	10093	652	23	1	5442	1	MYO9A	15	72231259	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	4773871	72231259	30300133	91	1688										
C15orf42	90381	hgsc.bcm.edu	37	chr15	90168109	90168109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ctctcctctgatgccttcccGtgacgtgcactgtaccacag	8	16	2	2	rs149974689		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr15:90168109G>A	ENST00000268138.7	+	20	4673	c.4568G>A	c.(4567-4569)cGt>cAt	p.R1523H	TICRR_ENST00000560985.1_Missense_Mutation_p.R1522H|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1523			R -> C (in dbSNP:rs894157). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										ATGCCTTCCCGTGACGTGCAC	0.582																																					p.R1523H		Atlas-SNP	.											.	.	.	.	0			c.G4568A						.	G	HIS/ARG	0,4400		0,0,2200	106	113	111		4568	-3.8	0	15	dbSNP_134	111	1,8597	1.2+/-3.3	0,1,4298	yes	missense	C15orf42	NM_152259.3	29	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	benign	1523/1911	90168109	1,12997	2200	4299	6499	SO:0001583	missense	90381	exon20			CTTCCCGTGACGT	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.4568G>A	chr15.hg19:g.90168109G>A	ENSP00000268138:p.Arg1523His	85.0	0.0		111.0	54.0	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	hg19	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	G	11.51	1.659346	0.29515	0.0	1.16E-4	ENSG00000140534	ENST00000268138	T	0.08193	3.12	5.12	-3.77	0.04346	.	0.815093	0.11014	N	0.609103	T	0.02807	0.0084	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44065	-0.9352	10	0.16896	T	0.51	1.6738	2.561	0.04771	0.3969:0.3531:0.1357:0.1142	.	1523	Q7Z2Z1	TICRR_HUMAN	H	1523	ENSP00000268138:R1523H	ENSP00000268138:R1523H	R	+	2	0	C15orf42	87969113	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.017000	0.12590	-0.956000	0.03631	-0.302000	0.09304	CGT	.	G|1.000;A|0.000		0.582	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		A	90168109	G	A	90168109	3	1	19	1	0	0	0	0	1	0	0	0	1798	1145	40	1	4646	1	C15orf42	15	90168109	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	17936850	90168109	12363283	92	1689										
C15orf32	145858	hgsc.bcm.edu	37	chr15	93015518	93015518	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aacggctccccctttctcggCgaggccatgtgtctggaccc	11	16	2	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr15:93015518C>T	ENST00000333334.2	+	1	635	c.140C>T	c.(139-141)gCg>gTg	p.A47V	RP11-763K15.1_ENST00000554440.1_lincRNA|C15orf32_ENST00000556865.1_Missense_Mutation_p.A47V	NM_153040.2	NP_694585.1	Q32M92	CO032_HUMAN	chromosome 15 open reading frame 32	47										endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	12	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0493)|OV - Ovarian serous cystadenocarcinoma(32;0.125)			CCTTTCTCGGCGAGGCCATGT	0.527																																					p.A47V		Atlas-SNP	.											.	C15orf32	22	.	0			c.C140T						.						102	105	104					15																	93015518		2198	4298	6496	SO:0001583	missense	145858	exon1			TCTCGGCGAGGCC		CCDS10373.1, CCDS73784.1	15q26.1	2014-09-10			ENSG00000183643	ENSG00000183643			26549	protein-coding gene	gene with protein product							Standard	NM_153040		Approved	FLJ32831	uc002brc.1	Q32M92	OTTHUMG00000149844	ENST00000333334.2:c.140C>T	chr15.hg19:g.93015518C>T	ENSP00000330267:p.Ala47Val	188.0	0.0		192.0	91.0	NM_153040	C5HTZ8|Q96M45	Missense_Mutation	SNP	ENST00000333334.2	hg19	CCDS10373.1	.	.	.	.	.	.	.	.	.	.	C	2.546	-0.305101	0.05495	.	.	ENSG00000183643	ENST00000333334	T	0.54866	0.55	1.8	-1.45	0.08828	.	.	.	.	.	T	0.22975	0.0555	N	0.03608	-0.345	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.16070	-1.0415	9	0.87932	D	0	.	1.0073	0.01489	0.2283:0.3942:0.2242:0.1533	.	47	Q32M92	CO032_HUMAN	V	47	ENSP00000330267:A47V	ENSP00000330267:A47V	A	+	2	0	C15orf32	90816522	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.193000	0.03049	-0.397000	0.07691	-1.298000	0.01336	GCG	.	.		0.527	C15orf32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313527.2	NM_153040		T	93015518	C	T	93015518	3	4	19	1	0	0	0	0	1	0	0	0	1792	768	27	1	142	1	C15orf32	15	93015518	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	2847409	93015518	9515874	93	1690										
GSPT1	2935	hgsc.bcm.edu	37	chr16	11991733	11991750	+	5'UTR	DEL	TTGAACCTAGACAAGAGA	TTGAACCTAGACAAGAGA	-													0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ttccatgctaacagctgaatTtgaacctagacaagagattg							TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	TTGAACCTAGACAAGAGA	TTGAACCTAGACAAGAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr16:11991733_11991750delTTGAACCTAGACAAGAGA	ENST00000563468.1	-	0	0_12				GSPT1_ENST00000420576.2_5'UTR|GSPT1_ENST00000439887.2_Splice_Site_p.132_134VSC>G|RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000434724.2_Splice_Site_p.132_134VSC>G			P15170	ERF3A_HUMAN	G1 to S phase transition 1						G1/S transition of mitotic cell cycle (GO:0000082)|GTP catabolic process (GO:0006184)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|translational termination (GO:0006415)	intracellular (GO:0005622)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation release factor activity (GO:0003747)			breast(1)|central_nervous_system(1)|kidney(4)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	14						ACAGCTGAATTTGAACCTAGACAAGAGATTGAAATATA	0.307																																					p.132_134del		Atlas-Indel,Pindel	.											.	GSPT1	71	.	0			c.395_401del						.																																			SO:0001623	5_prime_UTR_variant	2935	exon3			.	BC008391	CCDS45412.1, CCDS45413.1, CCDS45414.1	16p13.1	2008-08-01							4621	protein-coding gene	gene with protein product		139259				2511002, 17700517	Standard	NM_002094		Approved	GST1, ETF3A, eRF3a	uc002dbt.3	P15170		ENST00000563468.1:c.-27TCTCTTGTCTAGGTTCAA>-	chr16.hg19:g.11991733_11991750delTTGAACCTAGACAAGAGA		180.0	0.0		195.0	41.0	NM_001130006	J3KQG6|Q96GF2	Frame_Shift_Del	DEL	ENST00000563468.1	hg19	CCDS45414.1																																																																																			.	.		0.307	GSPT1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421513.1	NM_002094		-	11991750	TTGAACCTAGACAAGAGA	-	11991733	6	5	19	0	1	1	0	1	0	0	0	0	6835	1841	64	0		0	GSPT1	16	11991733	5'UTR	DEL	TTGAACCTAGACAAGAGA	TCGA-2Y-A9H9-01A-21D-A38X-10		11991733	78363020	94	1691										
GPR139	124274	hgsc.bcm.edu	37	chr16	20043728	20043728	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gtggtacttgagcgggtggcAgacagcgatatacctgtcaa	14	8	1	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr16:20043728A>G	ENST00000570682.1	-	2	691	c.391T>C	c.(391-393)Tgc>Cgc	p.C131R		NM_001002911.2	NP_001002911.1	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	131					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	30						AGCGGGTGGCAGACAGCGATA	0.498																																					p.C131R		Atlas-SNP	.											.	GPR139	75	.	0			c.T391C						.						175	138	150					16																	20043728		2203	4300	6503	SO:0001583	missense	124274	exon2			GGTGGCAGACAGC	AY255545	CCDS32398.1	16p13.11	2012-08-21						"GPCR / Class A : Orphans"	19995	protein-coding gene	gene with protein product						12679517	Standard	XM_005255114		Approved	PGR3	uc002dgu.1	Q6DWJ6		ENST00000570682.1:c.391T>C	chr16.hg19:g.20043728A>G	ENSP00000458791:p.Cys131Arg	114.0	0.0		149.0	73.0	NM_001002911	A8K5R9|Q86SP2|Q8TDU8	Missense_Mutation	SNP	ENST00000570682.1	hg19	CCDS32398.1	.	.	.	.	.	.	.	.	.	.	A	18.00	3.525661	0.64860	.	.	ENSG00000180269	ENST00000326571	.	.	.	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.75184	0.3815	L	0.55103	1.725	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.75906	-0.3152	9	0.51188	T	0.08	-49.3405	15.1985	0.73116	1.0:0.0:0.0:0.0	.	131	Q6DWJ6	GP139_HUMAN	R	131	.	ENSP00000370779:C131R	C	-	1	0	GPR139	19951229	1.000000	0.71417	0.997000	0.53966	0.860000	0.49131	8.730000	0.91510	2.186000	0.69663	0.533000	0.62120	TGC	.	.		0.498	GPR139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438522.1	NM_001002911		G	20043728	A	G	20043728	3	3	19	1	0	0	0	0	1	0	0	0	6656	188	7	2	674	2	GPR139	16	20043728	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	8051995	20043728	70311025	95	1692										
CDH11	1009	hgsc.bcm.edu	37	chr16	65026819	65026819	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cagtgacattccacagtaccTgtctgtgcttccaccgaaaa	7	13	1	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr16:65026819T>C	ENST00000268603.4	-	5	1257	c.642A>G	c.(640-642)acA>acG	p.T214T	CDH11_ENST00000566827.1_Splice_Site_p.T88T|CDH11_ENST00000394156.3_Splice_Site_p.T214T	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	214	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CCACAGTACCTGTCTGTGCTT	0.423			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.T214T		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	.	CDH11	260	.	0			c.A642G						.						145	112	123					16																	65026819		2203	4300	6503	SO:0001630	splice_region_variant	1009	exon5			AGTACCTGTCTGT	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.643+1A>G	chr16.hg19:g.65026819T>C		27.0	0.0		55.0	24.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	hg19	CCDS10803.1																																																																																			.	.		0.423	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	Silent	C	65026819	T	C	65026819	5	2	19	1	0	0	0	0	0	0	1	0	3099	1594	55	2	1784	2	CDH11	16	65026819	Splice_Site	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	44983091	65026819	25327934	96	1693										
GPR172B	55065	hgsc.bcm.edu	37	chr17	4937150	4937150	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	caacagcaacaggagaccccGgaaggcggcagctgaagtga	14	11	0	3	rs370188723		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr17:4937150G>A	ENST00000424747.1	-	3	1346	c.634C>T	c.(634-636)Cgg>Tgg	p.R212W	SLC52A1_ENST00000254853.5_Missense_Mutation_p.R212W|SLC52A1_ENST00000512825.2_Missense_Mutation_p.R212W	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	212					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										AGGAGACCCCGGAAGGCGGCA	0.602																																					p.R212W		Atlas-SNP	.											.	.	.	.	0			c.C634T						.	G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	66	68	68		634,634	1.1	0.9	17		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GPR172B	NM_001104577.1,NM_017986.3	101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	212/449,212/449	4937150	1,13005	2203	4300	6503	SO:0001583	missense	55065	exon3			GACCCCGGAAGGC	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"Solute carriers"	30225	protein-coding gene	gene with protein product	"riboflavin transporter 1"	607883	"G protein-coupled receptor 172B"	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.634C>T	chr17.hg19:g.4937150G>A	ENSP00000399979:p.Arg212Trp	126.0	0.0		77.0	55.0	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Missense_Mutation	SNP	ENST00000424747.1	hg19	CCDS11066.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.151509	0.38021	0.0	1.16E-4	ENSG00000132517	ENST00000254853;ENST00000512825;ENST00000424747	T;T;T	0.74315	-0.83;-0.68;-0.83	1.11	1.11	0.20524	.	0.687859	0.14531	N	0.313864	T	0.45875	0.1364	N	0.08118	0	0.20074	N	0.999938	P;B	0.34615	0.459;0.33	B;B	0.18871	0.023;0.006	T	0.31916	-0.9926	10	0.34782	T	0.22	.	8.0807	0.30744	0.0:0.0:1.0:0.0	.	212;212	F5H5Y1;Q9NWF4	.;RFT_HUMAN	W	212	ENSP00000254853:R212W;ENSP00000443026:R212W;ENSP00000399979:R212W	ENSP00000254853:R212W	R	-	1	2	GPR172B	4877874	.	.	0.908000	0.35775	0.673000	0.39480	.	.	0.910000	0.36722	0.563000	0.77884	CGG	.	.		0.602	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986		A	4937150	G	A	4937150	3	1	19	1	0	0	0	0	1	0	0	0	6678	1115	39	1	724	1	GPR172B	17	4937150	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10		4937150	76258060	97	1694										
C17orf68	80169	hgsc.bcm.edu	37	chr17	8140795	8140795	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	accagagcactcaatcgaacTagactcccagccaggtttcg	8	14	1	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr17:8140795T>G	ENST00000315684.8	-	5	697	c.690A>C	c.(688-690)ctA>ctC	p.L230L	CTC1_ENST00000581671.1_5'UTR	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	230					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						TCAATCGAACTAGACTCCCAG	0.498																																					p.L230L		Atlas-SNP	.											.	CTC1	75	.	0			c.A690C						.						98	97	97					17																	8140795		2009	4166	6175	SO:0001819	synonymous_variant	80169	exon5			TCGAACTAGACTC	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"conserved telomere maintenance component 1", "alpha accessory factor 132", "conserved telomere capping protein 1"	613129	"tmp494178", "chromosome 17 open reading frame 68"	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.690A>C	chr17.hg19:g.8140795T>G		100.0	0.0		53.0	36.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	hg19	CCDS42259.1																																																																																			.	.		0.498	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		G	8140795	T	G	8140795	2	3	19	1	0	0	0	0	0	0	0	1	1878	1509	53	5		5	C17orf68	17	8140795	Silent	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	3203645	8140795	73054415	98	1695										
TLK2	11011	hgsc.bcm.edu	37	chr17	60685417	60685417	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gacagccttttggccataacCagtctcagcaagacatccta	7	13	1	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr17:60685417C>T	ENST00000326270.9	+	22	2321	c.2053C>T	c.(2053-2055)Cag>Tag	p.Q685*	TLK2_ENST00000582809.1_Nonsense_Mutation_p.Q514*|TLK2_ENST00000343388.7_Nonsense_Mutation_p.Q631*|TLK2_ENST00000346027.5_Nonsense_Mutation_p.Q663*|TLK2_ENST00000542523.1_Nonsense_Mutation_p.Q631*	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	685	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						TGGCCATAACCAGTCTCAGCA	0.398																																					p.Q663X		Atlas-SNP	.											.	TLK2	223	.	0			c.C1987T						.						64	66	66					17																	60685417		2203	4300	6503	SO:0001587	stop_gained	11011	exon21			CATAACCAGTCTC	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.2053C>T	chr17.hg19:g.60685417C>T	ENSP00000316512:p.Gln685*	229.0	0.0		338.0	95.0	NM_006852	D3DU07|Q9UKI7|Q9Y4F7	Nonsense_Mutation	SNP	ENST00000326270.9	hg19		.	.	.	.	.	.	.	.	.	.	C	41	8.548131	0.98859	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	.	.	.	5.78	5.78	0.91487	.	0.052921	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.0021	0.92838	0.0:1.0:0.0:0.0	.	.	.	.	X	663;631;685;631	.	ENSP00000316512:Q685X	Q	+	1	0	TLK2	58039149	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.794000	0.85869	2.724000	0.93272	0.563000	0.77884	CAG	.	.		0.398	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852		T	60685417	C	T	60685417	4	4	19	1	0	0	0	0	0	1	0	0	15959	595	21	3	2065	3	TLK2	17	60685417	Nonsense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	52544622	60685417	20509793	99	1696										
MARCH10	162333	hgsc.bcm.edu	37	chr17	60814012	60814012	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cctcttgtctgggctcggatTtggtgtcccacgaaagaggg	14	10	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr17:60814012T>A	ENST00000311269.5	-	6	1491	c.1217A>T	c.(1216-1218)aAa>aTa	p.K406I	RP11-156L14.1_ENST00000579201.1_RNA|RP11-156L14.1_ENST00000584597.1_RNA|MARCH10_ENST00000583600.1_Missense_Mutation_p.K444I|RP11-156L14.1_ENST00000577270.1_RNA|RP11-156L14.1_ENST00000582564.1_RNA|MARCH10_ENST00000544856.2_Missense_Mutation_p.K405I|MARCH10_ENST00000456609.2_Missense_Mutation_p.K406I	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	406					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						GGGCTCGGATTTGGTGTCCCA	0.498																																					p.K406I		Atlas-SNP	.											.	MARCH10	102	.	0			c.A1217T						.						85	72	76					17																	60814012		2203	4300	6503	SO:0001583	missense	162333	exon6			TCGGATTTGGTGT	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"RING-type (C3HC4) zinc fingers", "MARCH membrane-associated ring fingers"	26655	protein-coding gene	gene with protein product		613337	"ring finger protein 190", "membrane-associated ring finger (C3HC4) 10"	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.1217A>T	chr17.hg19:g.60814012T>A	ENSP00000311496:p.Lys406Ile	80.0	0.0		130.0	76.0	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Missense_Mutation	SNP	ENST00000311269.5	hg19	CCDS11635.1	.	.	.	.	.	.	.	.	.	.	T	8.240	0.806576	0.16467	.	.	ENSG00000173838	ENST00000456609;ENST00000311269;ENST00000544856	T;T;T	0.36878	1.23;1.23;1.23	5.49	0.604	0.17547	.	0.722811	0.13001	N	0.421669	T	0.39384	0.1076	M	0.66939	2.045	0.09310	N	1	P;P;P	0.49783	0.883;0.928;0.883	B;P;B	0.50708	0.445;0.648;0.445	T	0.32241	-0.9914	10	0.72032	D	0.01	-3.7253	1.5562	0.02585	0.2938:0.0824:0.1528:0.4711	.	405;405;406	B3KVK0;G3V1Q5;Q8NA82	.;.;MARHA_HUMAN	I	406;406;405	ENSP00000416177:K406I;ENSP00000311496:K406I;ENSP00000443746:K405I	ENSP00000311496:K406I	K	-	2	0	MARCH10	58167744	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.254000	0.08781	-0.192000	0.10432	-1.969000	0.00466	AAA	.	.		0.498	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598		A	60814012	T	A	60814012	3	1	19	1	0	0	0	0	1	0	0	0	9308	1841	64	4	1233	4	MARCH10	17	60814012	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	128595	60814012	20381198	100	1697										
MFSD11	79157	hgsc.bcm.edu	37	chr17	74772613	74772613	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cccagcatttgccatcttcaAgtttgttcaggtaacctctt	6	12	4	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr17:74772613A>T	ENST00000588460.1	+	12	3217	c.1175A>T	c.(1174-1176)aAg>aTg	p.K392M	MFSD11_ENST00000355954.3_Missense_Mutation_p.K340M|MFSD11_ENST00000586622.1_Missense_Mutation_p.K392M|MFSD11_ENST00000590514.1_Missense_Mutation_p.K392M|MFSD11_ENST00000336509.4_Missense_Mutation_p.K392M|MFSD11_ENST00000593181.1_Missense_Mutation_p.K340M|MFSD11_ENST00000590070.1_3'UTR	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	392						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						GCCATCTTCAAGTTTGTTCAG	0.433																																					p.K392M		Atlas-SNP	.											MFSD11,NS,lymphoid_neoplasm,0,1	MFSD11	47	.	0			c.A1175T						.						167	160	162					17																	74772613		2203	4300	6503	SO:0001583	missense	79157	exon12			TCTTCAAGTTTGT	BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.1175A>T	chr17.hg19:g.74772613A>T	ENSP00000464932:p.Lys392Met	46.0	0.0		60.0	36.0	NM_001242532	O43442|Q9NXI5	Missense_Mutation	SNP	ENST00000588460.1	hg19	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.912704	0.72983	.	.	ENSG00000092931	ENST00000336509;ENST00000355954	T;T	0.80393	-1.37;-1.37	5.43	5.43	0.79202	Major facilitator superfamily domain, general substrate transporter (1);	0.044496	0.85682	D	0.000000	D	0.90926	0.7148	M	0.89478	3.035	0.80722	D	1	D;D	0.89917	1.0;0.96	D;P	0.77004	0.989;0.802	D	0.92324	0.5868	10	0.59425	D	0.04	-15.4372	15.4756	0.75478	1.0:0.0:0.0:0.0	.	340;392	O43934-2;O43934	.;MFS11_HUMAN	M	392;340	ENSP00000337240:K392M;ENSP00000348225:K340M	ENSP00000337240:K392M	K	+	2	0	MFSD11	72284208	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	6.088000	0.71371	2.046000	0.60703	0.460000	0.39030	AAG	.	.		0.433	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311		T	74772613	A	T	74772613	3	4	19	1	0	0	0	0	1	0	0	0	9538	72	3	4	1221	4	MFSD11	17	74772613	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	13958601	74772613	6422597	101	1698										
FASN	2194	hgsc.bcm.edu	37	chr17	80044945	80044945	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cccttgcacagttgcagctcCtcctgcagggcagcgcgctc	11	17	0	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr17:80044945C>A	ENST00000306749.2	-	21	3626	c.3408G>T	c.(3406-3408)gaG>gaT	p.E1136D		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1136					acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GTTGCAGCTCCTCCTGCAGGG	0.657																																					p.E1136D	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G3408T						.						31	33	32					17																	80044945		2198	4293	6491	SO:0001583	missense	2194	exon21			CAGCTCCTCCTGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.3408G>T	chr17.hg19:g.80044945C>A	ENSP00000304592:p.Glu1136Asp	115.0	0.0		176.0	51.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	3.109	-0.183054	0.06340	.	.	ENSG00000169710	ENST00000306749;ENST00000545909	T	0.47177	0.85	4.08	2.94	0.34122	.	0.787182	0.11807	N	0.527514	T	0.25644	0.0624	N	0.24115	0.695	0.09310	N	0.999994	B	0.02656	0.0	B	0.06405	0.002	T	0.20405	-1.0276	10	0.14252	T	0.57	-10.6052	0.8161	0.01103	0.1832:0.3361:0.2757:0.205	.	1136	P49327	FAS_HUMAN	D	1136;101	ENSP00000304592:E1136D	ENSP00000304592:E1136D	E	-	3	2	FASN	77638234	0.000000	0.05858	0.995000	0.50966	0.114000	0.19823	-0.596000	0.05720	0.814000	0.34374	0.478000	0.44815	GAG	.	.		0.657	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80044945	C	A	80044945	3	1	19	1	0	0	0	0	1	0	0	0	5691	680	24	3	4219	3	FASN	17	80044945	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	5272332	80044945	1150265	102	1699										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8777845	8777845	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tttcagagttccctaaaaagAagaagcactcgggaaatgta	9	7	1	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr18:8777845A>G	ENST00000306329.11	+	4	1452	c.1452A>G	c.(1450-1452)agA>agG	p.R484R	SOGA2_ENST00000517570.1_Silent_p.R124R|SOGA2_ENST00000359865.3_Silent_p.R124R|SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000400050.3_Silent_p.R124R																							CCCTAAAAAGAAGAAGCACTC	0.433																																					p.R124R		Atlas-SNP	.											.	.	.	.	0			c.A372G						.						130	123	125					18																	8777845		2203	4300	6503	SO:0001819	synonymous_variant	23255	exon5			AAAAAGAAGAAGC																												ENST00000306329.11:c.1452A>G	chr18.hg19:g.8777845A>G		99.0	0.0		100.0	34.0	NM_015210		Silent	SNP	ENST00000306329.11	hg19																																																																																				.	.		0.433	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			G	8777845	A	G	8777845	2	3	19	1	0	0	0	0	0	0	0	1	8203	243	9	2		2	KIAA0802	18	8777845	Silent	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10		8777845	69299403	103	1700										
NOL4	8715	hgsc.bcm.edu	37	chr18	31599308	31599308	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tccattttctctcgcctctcGttccatcttgaggtcagaaa	6	13	4	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr18:31599308G>A	ENST00000261592.5	-	6	1327	c.1030C>T	c.(1030-1032)Cga>Tga	p.R344*	NOL4_ENST00000589544.1_Nonsense_Mutation_p.R344*|NOL4_ENST00000535475.1_Nonsense_Mutation_p.R189*|NOL4_ENST00000535384.1_Nonsense_Mutation_p.R59*|NOL4_ENST00000538587.1_Nonsense_Mutation_p.R270*|NOL4_ENST00000269185.4_Nonsense_Mutation_p.R230*	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	344						nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						CTCGCCTCTCGTTCCATCTTG	0.378																																					p.R344X		Atlas-SNP	.											NOL4,colon,carcinoma,0,1	NOL4	139	.	0			c.C1030T						.						128	112	117					18																	31599308		2203	4300	6503	SO:0001587	stop_gained	8715	exon6			CCTCTCGTTCCAT	AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.1030C>T	chr18.hg19:g.31599308G>A	ENSP00000261592:p.Arg344*	42.0	0.0		69.0	27.0	NM_003787	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Nonsense_Mutation	SNP	ENST00000261592.5	hg19	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	G	42	9.537866	0.99199	.	.	ENSG00000101746	ENST00000261592;ENST00000269185;ENST00000399171;ENST00000535384;ENST00000535475;ENST00000538587	.	.	.	5.75	3.9	0.45041	.	0.189837	0.35349	N	0.003278	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.5001	13.8409	0.63437	0.0:0.0:0.601:0.399	.	.	.	.	X	344;230;93;59;189;270	.	ENSP00000261592:R344X	R	-	1	2	NOL4	29853306	1.000000	0.71417	0.983000	0.44433	0.995000	0.86356	1.503000	0.35715	0.718000	0.32166	0.542000	0.68232	CGA	.	.		0.378	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		A	31599308	G	A	31599308	4	1	19	1	0	0	0	0	0	1	0	0	10533	1153	40	1	910	1	NOL4	18	31599308	Nonsense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	22821463	31599308	46477940	104	1701										
ABCA7	10347	hgsc.bcm.edu	37	chr19	1046943	1046943	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gcgccatggggctcagccgcGcggtgctctggctaggctgg	18	13	2	0	rs142076058|rs375206158	byFrequency	TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr19:1046943G>A	ENST00000263094.6	+	14	1996	c.1765G>A	c.(1765-1767)Gcg>Acg	p.A589T	ABCA7_ENST00000435683.2_Missense_Mutation_p.A451T|ABCA7_ENST00000533574.1_Intron|ABCA7_ENST00000433129.1_Missense_Mutation_p.A589T	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	589					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTCAGCCGCGCGGTGCTCTG	0.692																																					p.A589T		Atlas-SNP	.											.	ABCA7	174	.	0			c.G1765A						.						17	17	17					19																	1046943		2168	4264	6432	SO:0001583	missense	10347	exon14			AGCCGCGCGGTGC	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.1765G>A	chr19.hg19:g.1046943G>A	ENSP00000263094:p.Ala589Thr	66.0	0.0		89.0	44.0	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	g	9.217	1.032304	0.19590	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.82984	-1.67;-1.67	4.68	1.23	0.21249	.	.	.	.	.	T	0.75774	0.3895	L	0.41961	1.31	0.09310	N	1	B;B	0.25351	0.102;0.124	B;B	0.26693	0.031;0.072	T	0.65030	-0.6267	9	0.49607	T	0.09	.	8.8132	0.34981	0.2683:0.0:0.7317:0.0	.	451;589	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	T	589	ENSP00000263094:A589T;ENSP00000414062:A589T	ENSP00000263094:A589T	A	+	1	0	ABCA7	997943	0.884000	0.30299	0.000000	0.03702	0.024000	0.10985	3.405000	0.52630	0.419000	0.25927	-0.299000	0.09455	GCG	.	.		0.692	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1046943	G	A	1046943	3	1	19	1	0	0	0	0	1	0	0	0	37	1087	38	1	1815	1	ABCA7	19	1046943	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10		1046943	58082040	105	1702										
SBNO2	22904	hgsc.bcm.edu	37	chr19	1116910	1116910	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cgcctcgcccgtggactgcaGcccgatgaccacgcactgtg	12	17	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr19:1116910G>A	ENST00000361757.3	-	16	1957	c.1720C>T	c.(1720-1722)Ctg>Ttg	p.L574L	SBNO2_ENST00000438103.2_Silent_p.L517L|SBNO2_ENST00000587024.1_Silent_p.L564L	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	574					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGGACTGCAGCCCGATGACC	0.687																																					p.L574L		Atlas-SNP	.											.	SBNO2	112	.	0			c.C1720T						.						23	28	26					19																	1116910		2137	4211	6348	SO:0001819	synonymous_variant	22904	exon16			ACTGCAGCCCGAT	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.1720C>T	chr19.hg19:g.1116910G>A		19.0	0.0		26.0	7.0	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	hg19	CCDS45894.1																																																																																			.	.		0.687	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		A	1116910	G	A	1116910	2	1	19	1	0	0	0	0	0	0	0	1	13878	962	34	3		3	SBNO2	19	1116910	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	69967	1116910	58012073	106	1703										
ZNF799	90576	hgsc.bcm.edu	37	chr19	12502454	12502454	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tagaacactgtttacattcaTacagtttctccccagtatgt	5	10	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr19:12502454T>C	ENST00000430385.3	-	4	958	c.758A>G	c.(757-759)tAt>tGt	p.Y253C	ZNF799_ENST00000419318.1_Missense_Mutation_p.Y221C|CTD-3105H18.14_ENST00000435033.1_Intron	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						TTTACATTCATACAGTTTCTC	0.363																																					p.Y253C		Atlas-SNP	.											.	ZNF799	111	.	0			c.A758G						.						82	93	89					19																	12502454		2203	4298	6501	SO:0001583	missense	90576	exon4			CATTCATACAGTT	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"Zinc fingers, C2H2-type", "-"	28071	protein-coding gene	gene with protein product			"zinc finger protein 842"	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.758A>G	chr19.hg19:g.12502454T>C	ENSP00000411084:p.Tyr253Cys	54.0	0.0		113.0	50.0	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	hg19	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	T	10.60	1.396845	0.25205	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.25414	1.8;1.8	1.31	1.31	0.21738	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.51702	0.1690	M	0.91406	3.205	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.34279	-0.9835	9	0.87932	D	0	.	3.4352	0.07442	0.3607:0.0:0.0:0.6393	.	253	Q96GE5	ZN799_HUMAN	C	221;253	ENSP00000415278:Y221C;ENSP00000411084:Y253C	ENSP00000415278:Y221C	Y	-	2	0	ZNF799	12363454	0.000000	0.05858	0.009000	0.14445	0.146000	0.21551	-0.618000	0.05578	0.846000	0.35142	0.352000	0.21897	TAT	.	.		0.363	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		C	12502454	T	C	12502454	3	2	19	1	0	0	0	0	1	0	0	0	18181	1406	49	2	1177	2	ZNF799	19	12502454	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	11385544	12502454	46626529	107	1704										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23543878	23543878	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	atggctaaaagctttgccacAttcttcacatttgtagggtt	8	8	2	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr19:23543878A>G	ENST00000300619.7	-	4	2108	c.1903T>C	c.(1903-1905)Tgt>Cgt	p.C635R	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Missense_Mutation_p.C603R|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	635					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				GCTTTGCCACATTCTTCACAT	0.393																																					p.C635R		Atlas-SNP	.											.	ZNF91	349	.	0			c.T1903C						.						63	67	66					19																	23543878		2165	4277	6442	SO:0001583	missense	7644	exon4			TGCCACATTCTTC	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1903T>C	chr19.hg19:g.23543878A>G	ENSP00000300619:p.Cys635Arg	112.0	0.0		164.0	77.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	A	13.70	2.314341	0.40996	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	D;D	0.85955	-2.05;-2.05	1.71	1.71	0.24356	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93910	0.8051	H	0.97635	4.045	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.92717	0.6188	9	0.87932	D	0	.	8.2031	0.31436	1.0:0.0:0.0:0.0	.	603;635	Q05481-2;Q05481	.;ZNF91_HUMAN	R	635;603	ENSP00000300619:C635R;ENSP00000380272:C603R	ENSP00000300619:C635R	C	-	1	0	ZNF91	23335718	0.996000	0.38824	0.036000	0.18154	0.022000	0.10575	4.518000	0.60510	0.765000	0.33221	0.172000	0.16884	TGT	.	.		0.393	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		G	23543878	A	G	23543878	3	3	19	1	0	0	0	0	1	0	0	0	18215	217	8	2	1676	2	ZNF91	19	23543878	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	11041424	23543878	35585105	108	1705										
LSR	51599	hgsc.bcm.edu	37	chr19	35758051	35758051	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cctccacgaggacgactggcGatctcggccttcccggggcc	13	17	1	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr19:35758051G>T	ENST00000361790.3	+	9	1487	c.1328G>T	c.(1327-1329)cGa>cTa	p.R443L	USF2_ENST00000222305.3_5'Flank|LSR_ENST00000360798.3_Missense_Mutation_p.R375L|LSR_ENST00000347609.4_Missense_Mutation_p.R385L|LSR_ENST00000602122.1_Missense_Mutation_p.R423L|USF2_ENST00000594064.1_5'Flank|LSR_ENST00000354900.3_Missense_Mutation_p.R424L|USF2_ENST00000379134.3_5'Flank|USF2_ENST00000343550.5_5'Flank|LSR_ENST00000427250.1_Missense_Mutation_p.R287L|USF2_ENST00000595068.1_5'Flank|AD000684.2_ENST00000602262.1_RNA	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	443					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GACGACTGGCGATCTCGGCCT	0.692																																					p.R443L		Atlas-SNP	.											.	LSR	60	.	0			c.G1328T						.						29	37	34					19																	35758051		2106	4230	6336	SO:0001583	missense	51599	exon9			ACTGGCGATCTCG	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1328G>T	chr19.hg19:g.35758051G>T	ENSP00000354575:p.Arg443Leu	178.0	0.0		147.0	67.0	NM_205834	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Missense_Mutation	SNP	ENST00000361790.3	hg19	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.309538	0.81247	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000360798;ENST00000347609;ENST00000427250	T;T;T;T;T	0.71103	0.28;0.46;-0.07;0.19;-0.54	4.88	3.84	0.44239	.	0.399200	0.24111	N	0.041452	T	0.77778	0.4181	L	0.53249	1.67	0.09310	N	0.999995	B;D;B;B;P;D	0.71674	0.289;0.998;0.412;0.412;0.569;0.975	B;D;B;B;B;P	0.69654	0.09;0.965;0.205;0.251;0.101;0.762	T	0.67352	-0.5692	10	0.72032	D	0.01	-7.1397	10.2419	0.43316	0.0972:0.0:0.9028:0.0	.	381;385;423;375;424;443	Q9BT33;Q86X29-2;Q86X29-3;A6NDW3;E9PHD4;Q86X29	.;.;.;.;.;LSR_HUMAN	L	443;424;375;385;287	ENSP00000354575:R443L;ENSP00000346976:R424L;ENSP00000354034:R375L;ENSP00000262627:R385L;ENSP00000394479:R287L	ENSP00000262627:R385L	R	+	2	0	LSR	40449891	0.896000	0.30565	0.983000	0.44433	0.757000	0.42996	2.338000	0.43957	2.245000	0.73994	0.555000	0.69702	CGA	.	.		0.692	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		T	35758051	G	T	35758051	3	4	19	1	0	0	0	0	1	0	0	0	9073	1058	37	1	1362	1	LSR	19	35758051	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	12214173	35758051	23370932	109	1706										
ZNF780B	163131	hgsc.bcm.edu	37	chr19	40540678	40540678	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ctacactccttacatacaaaGggtttcgcactggaatgagt	8	10	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr19:40540678G>C	ENST00000434248.1	-	5	2153	c.2088C>G	c.(2086-2088)ccC>ccG	p.P696P	ZNF780B_ENST00000221355.6_Silent_p.P548P	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	696					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TACATACAAAGGGTTTCGCAC	0.383																																					p.P696P		Atlas-SNP	.											.	ZNF780B	143	.	0			c.C2088G						.						75	82	80					19																	40540678		2186	4294	6480	SO:0001819	synonymous_variant	163131	exon5			TACAAAGGGTTTC	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"Zinc fingers, C2H2-type", "-"	33109	protein-coding gene	gene with protein product			"zinc finger protein 779"	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.2088C>G	chr19.hg19:g.40540678G>C		84.0	0.0		124.0	52.0	NM_001005851	B9EH00	Silent	SNP	ENST00000434248.1	hg19	CCDS46077.1																																																																																			.	.		0.383	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		C	40540678	G	C	40540678	2	2	19	1	0	0	0	0	0	0	0	1	18168	987	35	4		4	ZNF780B	19	40540678	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	4782627	40540678	18588305	110	1707										
ZNF808	388558	hgsc.bcm.edu	37	chr19	53057402	53057402	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ggtaaggcttttaatcatcaAtcaagccttgcacgtcatca	7	10	5	0	rs375755660		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr19:53057402A>G	ENST00000359798.4	+	5	1413	c.1233A>G	c.(1231-1233)caA>caG	p.Q411Q		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	411					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		TTAATCATCAATCAAGCCTTG	0.383													A|||	1	0.000199681	0	0	5008	,	,		22364	0		0.001	False		,,,				2504	0				p.Q411Q		Atlas-SNP	.											.	ZNF808	81	.	0			c.A1233G						.	A		1,4395		0,1,2197	72	77	75		1233	0.4	0	19		75	4,8586		0,4,4291	no	coding-synonymous	ZNF808	NM_001039886.3		0,5,6488	GG,GA,AA		0.0466,0.0227,0.0385		411/904	53057402	5,12981	2198	4295	6493	SO:0001819	synonymous_variant	388558	exon5			TCATCAATCAAGC	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.1233A>G	chr19.hg19:g.53057402A>G		115.0	0.0		122.0	61.0	NM_001039886	Q68CN7	Silent	SNP	ENST00000359798.4	hg19	CCDS46167.1																																																																																			.	.		0.383	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		G	53057402	A	G	53057402	2	3	19	1	0	0	0	0	0	0	0	1	18188	98	4	2		2	ZNF808	19	53057402	Silent	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	12516724	53057402	6071581	111	1708										
DPRX	503834	hgsc.bcm.edu	37	chr19	54140215	54140215	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cattctggctctcctgcctgTtcatctaaccaaagtcgaga	7	13	4	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr19:54140215T>C	ENST00000376650.1	+	3	600	c.549T>C	c.(547-549)tgT>tgC	p.C183C		NM_001012728.1	NP_001012746.1	A6NFQ7	DPRX_HUMAN	divergent-paired related homeobox	183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(4)|large_intestine(1)|lung(7)	12	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.013)		CTCCTGCCTGTTCATCTAACC	0.448																																					p.C183C		Atlas-SNP	.											.	DPRX	34	.	0			c.T549C						.						109	106	107					19																	54140215		2203	4300	6503	SO:0001819	synonymous_variant	503834	exon3			TGCCTGTTCATCT		CCDS33103.1	19q13.42	2011-06-20			ENSG00000204595	ENSG00000204595		"Homeoboxes / PRD class"	32166	protein-coding gene	gene with protein product		611165					Standard	NM_001012728		Approved		uc002qcf.1	A6NFQ7		ENST00000376650.1:c.549T>C	chr19.hg19:g.54140215T>C		95.0	0.0		107.0	44.0	NM_001012728		Silent	SNP	ENST00000376650.1	hg19	CCDS33103.1																																																																																			.	.		0.448	DPRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409880.1	NM_001012728		C	54140215	T	C	54140215	2	2	19	1	0	0	0	0	0	0	0	1	4740	1731	60	2		2	DPRX	19	54140215	Silent	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	1082813	54140215	4988768	112	1709										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54314219	54314219	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cttcccgtccgcccagtccaGcatcaccttgtgtgccagca	8	18	1	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr19:54314219G>A	ENST00000324134.6	-	3	862	c.694C>T	c.(694-696)Ctg>Ttg	p.L232L	NLRP12_ENST00000351894.4_Silent_p.L232L|NLRP12_ENST00000391773.1_Silent_p.L232L|NLRP12_ENST00000391775.3_Silent_p.L232L|NLRP12_ENST00000535162.1_Silent_p.L232L|NLRP12_ENST00000354278.3_Silent_p.L232L|NLRP12_ENST00000345770.5_Silent_p.L232L|NLRP12_ENST00000391772.1_Silent_p.L232L	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	232	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		GCCCAGTCCAGCATCACCTTG	0.587																																					p.A232S		Atlas-SNP	.											.	NLRP12	236	.	0			c.G694T						.						86	64	71					19																	54314219		2203	4300	6503	SO:0001819	synonymous_variant	91662	exon3			AGTCCAGCATCAC	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.694C>T	chr19.hg19:g.54314219G>A		79.0	0.0		76.0	18.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	hg19	CCDS12864.1																																																																																			.	.		0.587	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		A	54314219	G	A	54314219	2	1	19	1	0	0	0	0	0	0	0	1	10483	962	34	3		3	NLRP12	19	54314219	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	174004	54314219	4814764	113	1710										
SIRPD	128646	hgsc.bcm.edu	37	chr20	1515074	1515074	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ttccttccctgtttggattaTtttgacagcaagcctgaaat	7	9	0	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr20:1515074T>G	ENST00000381623.3	-	4	1780	c.591A>C	c.(589-591)aaA>aaC	p.K197N	SIRPD_ENST00000381621.1_Missense_Mutation_p.K198N			Q9H106	SIRPD_HUMAN	signal-regulatory protein delta	197						extracellular region (GO:0005576)				breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)	15						GTTTGGATTATTTTGACAGCA	0.358																																					p.K197N		Atlas-SNP	.											.	SIRPD	34	.	0			c.A591C						.						148	141	143					20																	1515074		2203	4300	6503	SO:0001583	missense	128646	exon4			GGATTATTTTGAC	AL049634	CCDS13018.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000125900	ENSG00000125900		"Signal-regulatory proteins", "Immunoglobulin superfamily / V-set domain containing"	16248	protein-coding gene	gene with protein product			"protein tyrosine phosphatase, non-receptor type substrate 1-like 2"	PTPNS1L2		16339511	Standard	NM_178460		Approved	dJ576H24.4	uc002wfi.3	Q9H106	OTTHUMG00000031674	ENST00000381623.3:c.591A>C	chr20.hg19:g.1515074T>G	ENSP00000371036:p.Lys197Asn	47.0	0.0		62.0	27.0	NM_178460	B3KS88|Q5TFQ6	Missense_Mutation	SNP	ENST00000381623.3	hg19	CCDS13018.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.839|6.839	0.524001|0.524001	0.13066|0.13066	.|.	.|.	ENSG00000125900|ENSG00000125900	ENST00000381623;ENST00000381621|ENST00000429387	T;T|.	0.02258|.	4.37;4.42|.	1.52|1.52	1.52|1.52	0.23074|0.23074	.|.	.|.	.|.	.|.	.|.	T|T	0.16041|0.16041	0.0386|0.0386	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	D|.	0.56287|.	0.975|.	B|.	0.42522|.	0.39|.	T|T	0.23048|0.23048	-1.0199|-1.0199	9|5	0.87932|.	D|.	0|.	.|.	5.1562|5.1562	0.15036|0.15036	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	197|.	Q9H106|.	SIRPD_HUMAN|.	N|T	197;198|80	ENSP00000371036:K197N;ENSP00000371034:K198N|.	ENSP00000371034:K198N|.	K|N	-|-	3|2	2|0	SIRPD|SIRPD	1463074|1463074	0.004000|0.004000	0.15560|0.15560	0.015000|0.015000	0.15790|0.15790	0.483000|0.483000	0.33249|0.33249	0.353000|0.353000	0.20130|0.20130	0.943000|0.943000	0.37553|0.37553	0.459000|0.459000	0.35465|0.35465	AAA|AAT	.	.		0.358	SIRPD-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077552.1	NM_178460		G	1515074	T	G	1515074	3	3	19	1	0	0	0	0	1	0	0	0	14350	1490	52	5	6	5	SIRPD	20	1515074	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10		1515074	61510446	114	1711										
NAA20	51126	hgsc.bcm.edu	37	chr20	20013187	20013187	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tgtggatctctttgtaagagTatctaaccaagttgcagtta	9	6	2	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr20:20013187T>C	ENST00000334982.4	+	5	622	c.341T>C	c.(340-342)gTa>gCa	p.V114A	NAA20_ENST00000484480.1_3'UTR|NAA20_ENST00000398602.2_Missense_Mutation_p.V102A|NAA20_ENST00000310450.4_Intron	NM_016100.4	NP_057184.1	P61599	NAA20_HUMAN	N(alpha)-acetyltransferase 20, NatB catalytic subunit	114	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.					cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	peptide alpha-N-acetyltransferase activity (GO:0004596)			endometrium(3)|lung(2)|prostate(1)	6						TTTGTAAGAGTATCTAACCAA	0.383																																					p.V114A		Atlas-SNP	.											.	NAA20	15	.	0			c.T341C						.						81	78	79					20																	20013187		2203	4300	6503	SO:0001583	missense	51126	exon5			TAAGAGTATCTAA	AF085355	CCDS13141.1, CCDS13142.1, CCDS42854.1	20p11.23	2010-05-07	2010-01-14	2010-01-14	ENSG00000173418	ENSG00000173418	2.3.1.88	"N(alpha)-acetyltransferase subunits"	15908	protein-coding gene	gene with protein product	"N-acetyltransferase 3 homolog (S. cerevisiae)"	610833	"N-acetyltransferase 5, ARD1 subunit (arrest-defective 1, S. cerevisiae, homolog)", "N-acetyltransferase 5 (ARD1 homolog, S. cerevisiae)", "N-acetyltransferase 5", "N-acetyltransferase 5 (GCN5-related, putative)"	NAT5		12888564, 19660095	Standard	NM_016100		Approved	dJ1002M8.1, NAT3	uc002wrp.3	P61599	OTTHUMG00000031998	ENST00000334982.4:c.341T>C	chr20.hg19:g.20013187T>C	ENSP00000335636:p.Val114Ala	94.0	0.0		154.0	7.0	NM_016100	A6NHA3|B2R4G4|Q5TFT7|Q9D7H8|Q9H0Y4|Q9NQH6|Q9Y6D2	Missense_Mutation	SNP	ENST00000334982.4	hg19	CCDS13141.1	.	.	.	.	.	.	.	.	.	.	T	11.49	1.653013	0.29336	.	.	ENSG00000173418	ENST00000334982;ENST00000398602	T;T	0.22336	1.96;1.96	5.72	5.72	0.89469	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.126159	0.53938	D	0.000054	T	0.15478	0.0373	N	0.20357	0.565	0.80722	D	1	B;B	0.16166	0.016;0.008	B;B	0.24006	0.01;0.05	T	0.10917	-1.0609	9	.	.	.	-40.4821	14.9842	0.71332	0.0:0.0:0.0:1.0	.	102;114	A8MZB2;P61599	.;NAA20_HUMAN	A	114;102	ENSP00000335636:V114A;ENSP00000381603:V102A	.	V	+	2	0	NAA20	19961187	1.000000	0.71417	0.978000	0.43139	0.997000	0.91878	7.907000	0.87430	2.183000	0.69458	0.533000	0.62120	GTA	.	.		0.383	NAA20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078217.2	NM_016100		C	20013187	T	C	20013187	3	2	19	1	0	0	0	0	1	0	0	0	10129	1638	57	2	380	2	NAA20	20	20013187	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	18498113	20013187	43012333	115	1712										
WFDC6	57119	hgsc.bcm.edu	37	chr20	44168001	44168001	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aggttcctggatgtcccccaAaaggatgaatggtaccagga	12	9	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr20:44168001A>G	ENST00000354280.4	-	0	1987				WFDC6_ENST00000600168.1_Silent_p.L16L|EPPIN-WFDC6_ENST00000504988.1_Intron|WFDC6_ENST00000372670.3_Silent_p.L16L|EPPIN_ENST00000555685.1_Intron	NM_020398.3	NP_065131.1	O95925	EPPI_HUMAN	epididymal peptidase inhibitor						defense response to bacterium (GO:0042742)|negative regulation of peptidase activity (GO:0010466)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										ATGTCCCCCAAAAGGATGAAT	0.517																																					p.L16L		Atlas-SNP	.											.	WFDC6	13	.	0			c.T46C						.						126	112	116					20																	44168001		2203	4300	6503	SO:0001628	intergenic_variant	140870	exon1			CCCCCAAAAGGAT	AF286370	CCDS13359.1	20q13.12	2014-01-21	2012-08-22	2012-08-22	ENSG00000101448	ENSG00000101448		"WAP four-disulfide core domain containing"	15932	protein-coding gene	gene with protein product	"epididymal protease inhibitor", "cancer/testis antigen 72"	609031	"serine protease inhibitor-like, with Kunitz and WAP domains 1 (eppin)", "serine peptidase inhibitor-like, with Kunitz and WAP domains 1 (eppin)"	SPINLW1		11404006, 12206714	Standard	NM_020398		Approved	EPPIN1, EPPIN2, EPPIN3, dJ461P17.2, WAP7, WFDC7, CT71		O95925	OTTHUMG00000032588		chr20.hg19:g.44168001A>G		87.0	0.0		139.0	53.0	NM_080827	A6PVD6|Q86TP9|Q96SD7|Q9HD30	Silent	SNP	ENST00000354280.4	hg19	CCDS13359.1																																																																																			.	.		0.517	EPPIN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079467.4			G	44168001	A	G	44168001	1	3	19	0	1	0	0	0	0	0	0	0	17370	11	1	2		2	WFDC6	20	44168001	IGR	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	24154814	44168001	18857519	116	1713										
WFDC6	57119	hgsc.bcm.edu	37	chr20	44168025	44168025	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	gatgaatggtaccaggattgGcagaagtcctgagagtccca	13	8	0	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr20:44168025G>A	ENST00000354280.4	-	0	1987				WFDC6_ENST00000600168.1_Missense_Mutation_p.P8S|EPPIN-WFDC6_ENST00000504988.1_Intron|WFDC6_ENST00000372670.3_Missense_Mutation_p.P8S|EPPIN_ENST00000555685.1_Intron	NM_020398.3	NP_065131.1	O95925	EPPI_HUMAN	epididymal peptidase inhibitor						defense response to bacterium (GO:0042742)|negative regulation of peptidase activity (GO:0010466)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										ACCAGGATTGGCAGAAGTCCT	0.517																																					p.P8S		Atlas-SNP	.											.	WFDC6	13	.	0			c.C22T						.						124	110	115					20																	44168025		2203	4300	6503	SO:0001628	intergenic_variant	140870	exon1			GGATTGGCAGAAG	AF286370	CCDS13359.1	20q13.12	2014-01-21	2012-08-22	2012-08-22	ENSG00000101448	ENSG00000101448		"WAP four-disulfide core domain containing"	15932	protein-coding gene	gene with protein product	"epididymal protease inhibitor", "cancer/testis antigen 72"	609031	"serine protease inhibitor-like, with Kunitz and WAP domains 1 (eppin)", "serine peptidase inhibitor-like, with Kunitz and WAP domains 1 (eppin)"	SPINLW1		11404006, 12206714	Standard	NM_020398		Approved	EPPIN1, EPPIN2, EPPIN3, dJ461P17.2, WAP7, WFDC7, CT71		O95925	OTTHUMG00000032588		chr20.hg19:g.44168025G>A		92.0	0.0		142.0	54.0	NM_080827	A6PVD6|Q86TP9|Q96SD7|Q9HD30	Missense_Mutation	SNP	ENST00000354280.4	hg19	CCDS13359.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.805465	0.31961	.	.	ENSG00000243543	ENST00000372670;ENST00000372665	T	0.33654	1.4	3.42	1.45	0.22620	.	.	.	.	.	T	0.20292	0.0488	.	.	.	0.46499	D	0.999073	P	0.42203	0.773	B	0.35312	0.2	T	0.03695	-1.1012	8	0.30078	T	0.28	.	5.6084	0.17392	0.2556:0.0:0.7444:0.0	.	8	Q9BQY6-2	.	S	8	ENSP00000361750:P8S	ENSP00000361750:P8S	P	-	1	0	WFDC6	43601439	0.974000	0.33945	0.648000	0.29521	0.221000	0.24807	0.513000	0.22770	0.447000	0.26695	0.455000	0.32223	CCA	.	.		0.517	EPPIN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079467.4			A	44168025	G	A	44168025	1	1	19	0	1	0	0	0	0	0	0	0	17370	1203	42	3		3	WFDC6	20	44168025	IGR	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	24	44168025	18857495	117	1714										
ZNF334	55713	hgsc.bcm.edu	37	chr20	45131451	45131451	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	atctgtattttttcattcccAaatgacttttctcatgcttc	3	10	3	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr20:45131451A>C	ENST00000347606.4	-	5	709	c.527T>G	c.(526-528)tTg>tGg	p.L176W	ZNF334_ENST00000593880.1_Missense_Mutation_p.L199W|ZNF334_ENST00000457685.2_Missense_Mutation_p.L138W	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	176					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				TTTCATTCCCAAATGACTTTT	0.338																																					p.L176W		Atlas-SNP	.											.	ZNF334	101	.	0			c.T527G						.						94	90	91					20																	45131451		2203	4300	6503	SO:0001583	missense	55713	exon5			ATTCCCAAATGAC	AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"Zinc fingers, C2H2-type", "-"	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.527T>G	chr20.hg19:g.45131451A>C	ENSP00000255129:p.Leu176Trp	63.0	0.0		97.0	40.0	NM_018102	Q5T6U2|Q9NVW4	Missense_Mutation	SNP	ENST00000347606.4	hg19	CCDS33480.1	.	.	.	.	.	.	.	.	.	.	A	7.988	0.752741	0.15778	.	.	ENSG00000198185	ENST00000457685;ENST00000347606	T;T	0.16196	2.36;2.36	3.3	0.21	0.15231	.	.	.	.	.	T	0.11537	0.0281	N	0.19112	0.55	0.09310	N	1	P;P;P	0.50369	0.934;0.934;0.934	B;B;B	0.43680	0.427;0.427;0.427	T	0.21143	-1.0254	9	0.72032	D	0.01	.	7.2764	0.26288	0.3397:0.0:0.6603:0.0	.	138;176;199	B3KQ93;Q9HCZ1;Q8N3P8	.;ZN334_HUMAN;.	W	138;176	ENSP00000402582:L138W;ENSP00000255129:L176W	ENSP00000255129:L176W	L	-	2	0	ZNF334	44564858	0.030000	0.19436	0.001000	0.08648	0.099000	0.18886	1.311000	0.33562	0.225000	0.20959	-1.055000	0.02315	TTG	.	.		0.338	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			C	45131451	A	C	45131451	3	2	19	1	0	0	0	0	1	0	0	0	17866	131	5	5	1519	5	ZNF334	20	45131451	Missense_Mutation	SNP	A	TCGA-2Y-A9H9-01A-21D-A38X-10	963426	45131451	17894069	118	1715										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57766716	57766716	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ggcgccgggggcggcctcctGgaggaaggggacaaggccgg	22	11	0	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr20:57766716G>T	ENST00000371030.2	+	1	642	c.642G>T	c.(640-642)ctG>ctT	p.L214L		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	214							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GCGGCCTCCTGGAGGAAGGGG	0.667																																					p.L214L		Atlas-SNP	.											.	ZNF831	287	.	0			c.G642T						.						26	32	30					20																	57766716		1874	4094	5968	SO:0001819	synonymous_variant	128611	exon1			CCTCCTGGAGGAA	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.642G>T	chr20.hg19:g.57766716G>T		69.0	0.0		100.0	41.0	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	hg19	CCDS42894.1																																																																																			.	.		0.667	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57766716	G	T	57766716	2	4	19	1	0	0	0	0	0	0	0	1	18200	1335	47	3		3	ZNF831	20	57766716	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	12635265	57766716	5258804	119	1716										
KRTAP21-2	337978	hgsc.bcm.edu	37	chr21	32119370	32119393	+	In_Frame_Del	DEL	AGCCATAGCCACAGCCAGTTCCAT	AGCCATAGCCACAGCCAGTTCCAT	-													0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	acagccagagccgtatccacAgccatagccacagccagttc					rs561745493|rs141027580		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	AGCCATAGCCACAGCCAGTTCCAT	AGCCATAGCCACAGCCAGTTCCAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr21:32119370_32119393delAGCCATAGCCACAGCCAGTTCCAT	ENST00000333892.2	-	1	158_181	c.128_151delATGGAACTGGCTGTGGCTATGGCT	c.(127-153)tatggaactggctgtggctatggctgt>tgt	p.YGTGCGYG43del		NM_181617.1	NP_853648.1	Q3LI59	KR212_HUMAN	keratin associated protein 21-2	43						intermediate filament (GO:0005882)	structural constituent of cutaneous appendage (GO:0030281)	p.G46V(1)		lung(4)|skin(2)|upper_aerodigestive_tract(1)	7						ccgtatccacagccatagccacagccagttccatagccagagcc	0.54																																					p.43_51del		Atlas-INDEL	.											.	KRTAP21-2	16	.	1	Substitution - Missense(1)	lung(1)	c.129_152del						.																																			SO:0001651	inframe_deletion	337978	exon1			.	AP001709	CCDS13605.1	21q22.1	2006-03-13			ENSG00000187026	ENSG00000187026		"Keratin associated proteins"	18946	protein-coding gene	gene with protein product						12359730	Standard	NM_181617		Approved	KAP21.2	uc011adh.2	Q3LI59	OTTHUMG00000057769	ENST00000333892.2:c.128_151delATGGAACTGGCTGTGGCTATGGCT	chr21.hg19:g.32119370_32119393delAGCCATAGCCACAGCCAGTTCCAT	ENSP00000334287:p.Tyr43_Gly50del	62.0	0.0		67.0	26.0	NM_181617		In_Frame_Del	DEL	ENST00000333892.2	hg19	CCDS13605.1																																																																																			.	.		0.54	KRTAP21-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128221.2			-	32119393	AGCCATAGCCACAGCCAGTTCCAT	-	32119370	7	5	19	1	0	1	0	1	0	0	0	0	8548	188	7	0	102	0	KRTAP21-2	21	32119370	In_Frame_Del	DEL	AGCCATAGCCACAGCCAGTTCCAT	TCGA-2Y-A9H9-01A-21D-A38X-10		32119370	16010525	120	1717										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47656824	47656824	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	agagtctgaggaagatagagGggaagggaagttaaatccgt	16	3	1	4			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr21:47656824G>C	ENST00000397708.1	-	28	5957	c.5703C>G	c.(5701-5703)ccC>ccG	p.P1901P	MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000420074.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA|MCM3AP_ENST00000291688.1_Silent_p.P1901P|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP_ENST00000467026.1_5'UTR			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1901					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					GAAGATAGAGGGGAAGGGAAG	0.383																																					p.P1901P		Atlas-SNP	.											.	MCM3AP	146	.	0			c.C5703G						.						119	115	117					21																	47656824		2203	4300	6503	SO:0001819	synonymous_variant	8888	exon27			ATAGAGGGGAAGG	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.5703C>G	chr21.hg19:g.47656824G>C		69.0	0.0		66.0	30.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	hg19	CCDS13734.1																																																																																			.	.		0.383	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		C	47656824	G	C	47656824	2	2	19	1	0	0	0	0	0	0	0	1	9397	1219	43	4		4	MCM3AP	21	47656824	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	15537454	47656824	473071	121	1718										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26243585	26243585	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	agggtccagcttgctgggttCcacatcctggaggctctgcg	14	12	1	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr22:26243585C>T	ENST00000407587.2	+	20	3913	c.3744C>T	c.(3742-3744)ttC>ttT	p.F1248F	MYO18B_ENST00000536101.1_Silent_p.F1247F|MYO18B_ENST00000335473.7_Silent_p.F1247F			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1247	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TTGCTGGGTTCCACATCCTGG	0.597																																					p.F1247F		Atlas-SNP	.											.	MYO18B	322	.	0			c.C3741T						.						22	27	25					22																	26243585		2102	4220	6322	SO:0001819	synonymous_variant	84700	exon20			TGGGTTCCACATC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.3744C>T	chr22.hg19:g.26243585C>T		56.0	0.0		59.0	24.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26243585	C	T	26243585	2	4	19	1	0	0	0	0	0	0	0	1	10075	854	30	3		3	MYO18B	22	26243585	Silent	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10		26243585	25060981	122	1719										
OSM	5008	hgsc.bcm.edu	37	chr22	30659920	30659920	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	agtctcttgcctttcctggaGggtctggtcctgcgcacccc	11	15	2	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chr22:30659920G>A	ENST00000215781.2	-	3	751	c.711C>T	c.(709-711)ccC>ccT	p.P237P	OSM_ENST00000403389.1_Silent_p.P216P	NM_020530.4	NP_065391.1	P13725	ONCM_HUMAN	oncostatin M	237					behavioral response to pain (GO:0048266)|cell proliferation (GO:0008283)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hormone secretion (GO:0046888)|negative regulation of meiosis (GO:0045835)|peripheral nervous system development (GO:0007422)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of growth (GO:0040008)|response to heat (GO:0009408)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	extracellular space (GO:0005615)|oncostatin-M receptor complex (GO:0005900)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|oncostatin-M receptor binding (GO:0005147)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|skin(3)	11			Epithelial(10;0.206)			CTTTCCTGGAGGGTCTGGTCC	0.667																																					p.P237P		Atlas-SNP	.											.	OSM	23	.	0			c.C711T						.						93	93	93					22																	30659920		2203	4300	6503	SO:0001819	synonymous_variant	5008	exon3			CCTGGAGGGTCTG	AF129855	CCDS13873.1	22q12.2	2011-07-21			ENSG00000099985	ENSG00000099985			8506	protein-coding gene	gene with protein product		165095				1717982	Standard	NM_020530		Approved	MGC20461	uc003ahb.3	P13725	OTTHUMG00000150913	ENST00000215781.2:c.711C>T	chr22.hg19:g.30659920G>A		46.0	0.0		41.0	20.0	NM_020530	Q6FHP8|Q9UCP6	Silent	SNP	ENST00000215781.2	hg19	CCDS13873.1																																																																																			.	.		0.667	OSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320512.1	NM_020530		A	30659920	G	A	30659920	2	1	19	1	0	0	0	0	0	0	0	1	11300	987	35	3		3	OSM	22	30659920	Silent	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	4416335	30659920	20644646	123	1720										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34148402	34148402	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	cctgtgagaagaatttgtccTcatccttttcatctagctcc	6	12	3	2			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chrX:34148402T>A	ENST00000346193.3	-	1	2045	c.1994A>T	c.(1993-1995)gAg>gTg	p.E665V		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	665										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						GAATTTGTCCTCATCCTTTTC	0.453																																					p.E665V		Atlas-SNP	.											.	FAM47A	249	.	0			c.A1994T						.						90	91	91					X																	34148402		2196	4294	6490	SO:0001583	missense	158724	exon1			TTGTCCTCATCCT	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1994A>T	chrX.hg19:g.34148402T>A	ENSP00000345029:p.Glu665Val	73.0	0.0		79.0	68.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.686588	0.29962	.	.	ENSG00000185448	ENST00000346193	T	0.63580	-0.05	1.49	1.49	0.22878	.	.	.	.	.	T	0.72795	0.3505	M	0.81497	2.545	0.09310	N	1	D	0.69078	0.997	P	0.62089	0.898	T	0.59573	-0.7429	9	0.87932	D	0	.	4.6966	0.12806	0.0:0.0:0.0:1.0	.	665	Q5JRC9	FA47A_HUMAN	V	665	ENSP00000345029:E665V	ENSP00000345029:E665V	E	-	2	0	FAM47A	34058323	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.853000	0.27777	0.859000	0.35456	0.441000	0.28932	GAG	.	.		0.453	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		A	34148402	T	A	34148402	3	1	19	1	0	0	0	0	1	0	0	0	5577	1551	54	4	385	4	FAM47A	23	34148402	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10		34148402	121122158	124	1721										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107869539	107869539	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	aggcgacaaaggtgatcctgGtatttcaagcattggtcttc	11	8	2	1	rs281874712		TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chrX:107869539G>T	ENST00000361603.2	+	36	3450	c.3206G>T	c.(3205-3207)gGt>gTt	p.G1069V	COL4A5_ENST00000328300.6_Missense_Mutation_p.G1069V	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1069	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GGTGATCCTGGTATTTCAAGC	0.478									Alport syndrome with Diffuse Leiomyomatosis																												p.G1069V		Atlas-SNP	.											.	COL4A5	262	.	0			c.G3206T						.						128	111	117					X																	107869539		2203	4300	6503	SO:0001583	missense	1287	exon36	Familial Cancer Database		ATCCTGGTATTTC	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.3206G>T	chrX.hg19:g.107869539G>T	ENSP00000354505:p.Gly1069Val	42.0	0.0		71.0	16.0	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	hg19	CCDS14543.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.45|19.45	3.829467|3.829467	0.71258|0.71258	.|.	.|.	ENSG00000188153|ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186|ENST00000505728	D;D|.	0.99429|.	-5.89;-5.89|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87962|0.87962	0.6310|0.6310	H|H	0.95151|0.95151	3.63|3.63	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.83275|.	0.996;0.996;0.996|.	D|D	0.91351|0.91351	0.5104|0.5104	10|5	0.87932|.	D|.	0|.	.|.	18.9086|18.9086	0.92474|0.92474	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1069;677;1069|.	E7EVY4;Q49AM6;P29400|.	.;.;CO4A5_HUMAN|.	V|L	1069|147	ENSP00000331902:G1069V;ENSP00000354505:G1069V|.	ENSP00000331902:G1069V|.	G|V	+|+	2|1	0|0	COL4A5|COL4A5	107756195|107756195	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.760000|0.760000	0.43138|0.43138	6.896000|6.896000	0.75665|0.75665	2.412000|2.412000	0.81896|0.81896	0.600000|0.600000	0.82982|0.82982	GGT|GTA	.	.		0.478	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			T	107869539	G	T	107869539	3	4	19	1	0	0	0	0	1	0	0	0	3696	1261	44	3	3348	3	COL4A5	23	107869539	Missense_Mutation	SNP	G	TCGA-2Y-A9H9-01A-21D-A38X-10	73721137	107869539	47401021	125	1722										
UPF3B	65109	hgsc.bcm.edu	37	chrX	118975169	118975172	+	Frame_Shift_Del	DEL	TTTC	TTTC	-													0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tctcttcttctctttgtcttTttctttctatttctctcctc							TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	TTTC	TTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chrX:118975169_118975172delTTTC	ENST00000276201.2	-	7	743_746	c.674_677delGAAA	c.(673-678)agaaaafs	p.RK225fs	UPF3B_ENST00000345865.2_Frame_Shift_Del_p.RK225fs|UPF3B_ENST00000478840.1_5'UTR	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	225	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						tctttgtctttttctttctatttc	0.338																																					p.225_226del		Atlas-Indel,Pindel	.											.	UPF3B	74	.	0			c.675_678del	GRCh37	CD075577	UPF3B	D		.																																			SO:0001589	frameshift_variant	65109	exon7			.	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.674_677delGAAA	chrX.hg19:g.118975173_118975176delTTTC	ENSP00000276201:p.Arg225fs	39.0	0.0		80.0	64.0	NM_023010	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Frame_Shift_Del	DEL	ENST00000276201.2	hg19	CCDS14588.1																																																																																			.	.		0.338	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			-	118975172	TTTC	-	118975169	7	5	19	1	0	1	0	1	0	0	0	0	17021	1841	64	0	794	0	UPF3B	23	118975169	Frame_Shift_Del	DEL	TTTC	TCGA-2Y-A9H9-01A-21D-A38X-10	11105630	118975169	36295391	126	1723										
DCAF12L2	340578	hgsc.bcm.edu	37	chrX	125299403	125299403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	ggccaggctgttggggttttCgccgccggtggccagaagcg	18	11	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chrX:125299403C>T	ENST00000360028.2	-	1	531	c.505G>A	c.(505-507)Gaa>Aaa	p.E169K	DCAF12L2_ENST00000538699.1_Missense_Mutation_p.E169K			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	169										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						TTGGGGTTTTCGCCGCCGGTG	0.677																																					p.E169K		Atlas-SNP	.											.	DCAF12L2	157	.	0			c.G505A						.						60	67	65					X																	125299403		2203	4300	6503	SO:0001583	missense	340578	exon1			GGTTTTCGCCGCC	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"WD repeat domain containing"	32950	protein-coding gene	gene with protein product			"WD repeat domain 40C"	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.505G>A	chrX.hg19:g.125299403C>T	ENSP00000353128:p.Glu169Lys	99.0	0.0		101.0	81.0	NM_001013628	B2RN42	Missense_Mutation	SNP	ENST00000360028.2	hg19	CCDS43991.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.947202	0.34377	.	.	ENSG00000198354	ENST00000538699;ENST00000360028	T;T	0.35048	1.33;1.33	4.09	2.24	0.28232	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.34178	N	0.004186	T	0.30885	0.0779	M	0.64997	1.995	0.33674	D	0.611292	D	0.58620	0.983	P	0.44597	0.454	T	0.41963	-0.9479	10	0.23891	T	0.37	.	4.6519	0.12599	0.0:0.6534:0.2207:0.1259	.	169	Q5VW00	DC122_HUMAN	K	169	ENSP00000441489:E169K;ENSP00000353128:E169K	ENSP00000353128:E169K	E	-	1	0	DCAF12L2	125127084	1.000000	0.71417	0.047000	0.18901	0.005000	0.04900	6.736000	0.74811	0.461000	0.27071	0.544000	0.68410	GAA	.	.		0.677	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		T	125299403	C	T	125299403	3	4	19	1	0	0	0	0	1	0	0	0	4267	893	31	1	890	1	DCAF12L2	23	125299403	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	6324234	125299403	29971157	127	1724										
VGLL1	51442	hgsc.bcm.edu	37	chrX	135631014	135631014	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	acctggttccagagccccagCctgatgggaaacgtgagcct	12	13	0	3			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chrX:135631014C>G	ENST00000370634.3	+	3	651	c.481C>G	c.(481-483)Cct>Gct	p.P161A	MIR934_ENST00000401241.1_RNA	NM_016267.3	NP_057351.1	Q99990	VGLL1_HUMAN	vestigial-like family member 1	161					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(192;0.000127)					AGAGCCCCAGCCTGATGGGAA	0.622																																					p.P161A		Atlas-SNP	.											.	VGLL1	41	.	0			c.C481G						.						94	88	90					X																	135631014		2203	4300	6503	SO:0001583	missense	51442	exon3			CCCCAGCCTGATG	AF137387	CCDS14658.1	Xq26.3	2014-03-03	2014-03-03		ENSG00000102243	ENSG00000102243			20985	protein-coding gene	gene with protein product		300583	"vestigial like 1 (Drosophila)"			10518497	Standard	NM_016267		Approved	TONDU, TDU	uc004ezy.3	Q99990	OTTHUMG00000022509	ENST00000370634.3:c.481C>G	chrX.hg19:g.135631014C>G	ENSP00000359668:p.Pro161Ala	59.0	0.0		84.0	7.0	NM_016267	Q5H915	Missense_Mutation	SNP	ENST00000370634.3	hg19	CCDS14658.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.38|14.38	2.518971|2.518971	0.44866|0.44866	.|.	.|.	ENSG00000102243|ENSG00000102243	ENST00000440515|ENST00000370634	.|T	.|0.47528	.|0.84	5.81|5.81	4.04|4.04	0.47022|0.47022	.|.	.|0.423027	.|0.28388	.|N	.|0.015522	T|T	0.29190|0.29190	0.0726|0.0726	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	.|P	.|0.47762	.|0.9	.|B	.|0.39419	.|0.299	T|T	0.10567|0.10567	-1.0624|-1.0624	5|10	.|0.11182	.|T	.|0.66	-3.6397|-3.6397	7.0765|7.0765	0.25207|0.25207	0.0:0.7991:0.0:0.2009|0.0:0.7991:0.0:0.2009	.|.	.|161	.|Q99990	.|VGLL1_HUMAN	G|A	125|161	.|ENSP00000359668:P161A	.|ENSP00000359668:P161A	A|P	+|+	2|1	0|0	VGLL1|VGLL1	135458680|135458680	0.001000|0.001000	0.12720|0.12720	0.003000|0.003000	0.11579|0.11579	0.911000|0.911000	0.54048|0.54048	0.905000|0.905000	0.28504|0.28504	1.214000|1.214000	0.43395|0.43395	0.600000|0.600000	0.82982|0.82982	GCC|CCT	.	.		0.622	VGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058493.1	NM_016267		G	135631014	C	G	135631014	3	3	19	1	0	0	0	0	1	0	0	0	17173	739	26	4	487	4	VGLL1	23	135631014	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	10331611	135631014	19639546	128	1725										
MAGEC2	51438	hgsc.bcm.edu	37	chrX	141290940	141290940	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	tccaggtaatgtccctgcacCcaaactttagtgaggagctc	9	12	0	1			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chrX:141290940C>A	ENST00000247452.3	-	3	1181	c.834G>T	c.(832-834)tgG>tgT	p.W278C		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	278	Interaction with TRIM28.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					GTCCCTGCACCCAAACTTTAG	0.532										HNSCC(46;0.14)																											p.W278C		Atlas-SNP	.											.	MAGEC2	102	.	0			c.G834T						.						91	92	91					X																	141290940		2203	4300	6503	SO:0001583	missense	51438	exon3			CTGCACCCAAACT	AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"cancer/testis antigen 10"	300468	"melanoma antigen, family E, 1, cancer/testis specific"	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.834G>T	chrX.hg19:g.141290940C>A	ENSP00000354660:p.Trp278Cys	47.0	0.0		50.0	25.0	NM_016249	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Missense_Mutation	SNP	ENST00000247452.3	hg19	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	11.35	1.612412	0.28712	.	.	ENSG00000046774	ENST00000247452	T	0.04809	3.55	0.988	0.988	0.19796	.	0.216956	0.39020	U	0.001481	T	0.08223	0.0205	M	0.74881	2.28	0.09310	N	0.999998	P	0.41784	0.762	P	0.44897	0.463	T	0.10636	-1.0621	10	0.87932	D	0	.	4.9988	0.14253	0.0:1.0:0.0:0.0	.	278	Q9UBF1	MAGC2_HUMAN	C	278	ENSP00000354660:W278C	ENSP00000354660:W278C	W	-	3	0	MAGEC2	141118606	0.029000	0.19370	0.031000	0.17742	0.423000	0.31445	-0.397000	0.07269	0.770000	0.33336	0.284000	0.19432	TGG	.	.		0.532	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		A	141290940	C	A	141290940	3	1	19	1	0	0	0	0	1	0	0	0	9190	624	22	3	291	3	MAGEC2	23	141290940	Missense_Mutation	SNP	C	TCGA-2Y-A9H9-01A-21D-A38X-10	5659926	141290940	13979620	129	1726										
F8	2157	hgsc.bcm.edu	37	chrX	154194337	154194337	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0310077519379845	4	1	0.597371565113501	1.49342891278375	0.373357228195938	1	1	0	agtcttaaaggtttcatctgTgtatgccataaatcggactt	8	7	3	0			TCGA-2Y-A9H9-01A-21D-A38X-10	TCGA-2Y-A9H9-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5586a43-bdc1-4030-93f8-cfb7bfa6a4b1	5ab2f233-e5fe-41df-9cef-56c0fdd900d3	g.chrX:154194337T>C	ENST00000360256.4	-	9	1551	c.1351A>G	c.(1351-1353)Aca>Gca	p.T451A	F8_ENST00000483822.1_5'UTR	NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	451	F5/8 type A 2.|Plastocyanin-like 3.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	GTTTCATCTGTGTATGCCATA	0.378																																					p.T451A		Atlas-SNP	.											.	F8	646	.	0			c.A1351G						.						150	131	137					X																	154194337		2203	4300	6503	SO:0001583	missense	2157	exon9			CATCTGTGTATGC	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.1351A>G	chrX.hg19:g.154194337T>C	ENSP00000353393:p.Thr451Ala	50.0	0.0		76.0	66.0	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	hg19	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.552954	0.65425	.	.	ENSG00000185010	ENST00000360256	D	0.99150	-5.49	5.24	4.03	0.46877	Cupredoxin (2);	0.155438	0.56097	D	0.000034	D	0.99080	0.9684	M	0.89095	3.005	0.28399	N	0.918741	D	0.89917	1.0	D	0.87578	0.998	D	0.96480	0.9355	10	0.54805	T	0.06	-15.3364	3.9807	0.09493	0.1875:0.1:0.0:0.7124	.	451	P00451	FA8_HUMAN	A	451	ENSP00000353393:T451A	ENSP00000353393:T451A	T	-	1	0	F8	153847531	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.689000	0.46993	0.607000	0.29982	0.381000	0.24937	ACA	.	.		0.378	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			C	154194337	T	C	154194337	3	2	19	1	0	0	0	0	1	0	0	0	5352	1696	59	2	5804	2	F8	23	154194337	Missense_Mutation	SNP	T	TCGA-2Y-A9H9-01A-21D-A38X-10	12903397	154194337	1076223	130	1727										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27023908	27023908	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	atggcctcgcagtgttggggGgctgcggcggcggcagctgc	20	11	0	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:27023908G>A	ENST00000324856.7	+	1	1385	c.1014G>A	c.(1012-1014)ggG>ggA	p.G338G	ARID1A_ENST00000457599.2_Silent_p.G338G	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	338					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.A339fs*24(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGTGTTGGGGggctgcggcgg	0.801			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.G338G		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.,1	ARID1A	842	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.G1014A						.						1	1	1					1																	27023908		519	1451	1970	SO:0001819	synonymous_variant	8289	exon1			TTGGGGGGCTGCG	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1014G>A	chr1.hg19:g.27023908G>A		10.0	0.0		11.0	5.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Silent	SNP	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.801	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27023908	G	A	27023908	2	1	20	1	0	0	0	0	0	0	0	1	913	1219	43	3		3	ARID1A	1	27023908	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10		27023908	222226713	1	1728										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34089022	34089022	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tctgcaccatcaaatacttcCagcgagtcccagttctgctc	6	15	3	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:34089022C>T	ENST00000373380.1	-	15	2509	c.2289G>A	c.(2287-2289)ctG>ctA	p.L763L	CSMD2_ENST00000373377.1_5'UTR|CSMD2_ENST00000373381.4_Silent_p.L1890L|CSMD2_ENST00000373388.2_5'UTR			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1850	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CAAATACTTCCAGCGAGTCCC	0.502																																					p.L1850L		Atlas-SNP	.											.	CSMD2	946	.	0			c.G5550A						.						127	111	117					1																	34089022		2203	4300	6503	SO:0001819	synonymous_variant	114784	exon36			TACTTCCAGCGAG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2289G>A	chr1.hg19:g.34089022C>T		117.0	0.0		121.0	43.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373380.1	hg19																																																																																				.	.		0.502	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		T	34089022	C	T	34089022	2	4	20	1	0	0	0	0	0	0	0	1	3947	581	21	3		3	CSMD2	1	34089022	Silent	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	7065114	34089022	215161599	2	1729										
NRD1	4898	hgsc.bcm.edu	37	chr1	52303276	52303276	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tcagctttgaccacagcaaaAacaggctctgcaattgctag	8	11	2	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:52303276A>C	ENST00000354831.7	-	3	836	c.647T>G	c.(646-648)tTt>tGt	p.F216C	NRD1_ENST00000544028.1_Intron|NRD1_ENST00000352171.7_Intron|MIR761_ENST00000390787.1_RNA|NRD1_ENST00000539524.1_Missense_Mutation_p.F84C|NRD1_ENST00000485608.1_Intron	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						CCACAGCAAAAACAGGCTCTG	0.353																																					p.F216C		Atlas-SNP	.											.	NRD1	89	.	0			c.T647G						.						78	79	79					1																	52303276		2203	4300	6503	SO:0001583	missense	4898	exon3			AGCAAAAACAGGC	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.647T>G	chr1.hg19:g.52303276A>C	ENSP00000346890:p.Phe216Cys	59.0	0.0		90.0	33.0	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	A	12.26	1.884446	0.33255	.	.	ENSG00000078618	ENST00000354831;ENST00000539524	T;T	0.38077	1.16;1.28	4.76	2.18	0.27775	.	0.614781	0.16279	N	0.221447	T	0.15219	0.0367	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07673	-1.0760	10	0.20519	T	0.43	-6.5935	4.9061	0.13799	0.6169:0.1954:0.0:0.1877	.	216	B1AKJ5	.	C	216;84	ENSP00000346890:F216C;ENSP00000444416:F84C	ENSP00000346890:F216C	F	-	2	0	NRD1	52075864	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.903000	0.28475	0.901000	0.36495	0.533000	0.62120	TTT	.	.		0.353	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		C	52303276	A	C	52303276	3	2	20	1	0	0	0	0	1	0	0	0	10654	14	1	5	3136	5	NRD1	1	52303276	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	18214254	52303276	196947345	3	1730										
WDR78	79819	hgsc.bcm.edu	37	chr1	67371059	67371059	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ttggttgtgtggcattgttcCtatataagaaaaataaaata	8	3	0	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:67371059C>T	ENST00000371026.3	-	2	226		c.e2-1		WDR78_ENST00000431318.1_Splice_Site|WDR78_ENST00000371022.3_Splice_Site|WDR78_ENST00000371023.3_Splice_Site|WDR78_ENST00000488333.1_Splice_Site	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78						hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						GGCATTGTTCCTATATAAGAA	0.303																																					.		Atlas-SNP	.											.	WDR78	102	.	0			c.171-1G>A						.						65	64	64					1																	67371059		2203	4300	6503	SO:0001630	splice_region_variant	79819	exon3			TTGTTCCTATATA	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"WD repeat domain containing"	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.171-1G>A	chr1.hg19:g.67371059C>T		77.0	0.0		62.0	26.0	NM_024763	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Splice_Site	SNP	ENST00000371026.3	hg19	CCDS635.1	.	.	.	.	.	.	.	.	.	.	C	4.447	0.082795	0.08533	.	.	ENSG00000152763	ENST00000371026;ENST00000371023;ENST00000371022	.	.	.	4.1	3.19	0.36642	.	.	.	.	.	.	.	.	.	.	.	0.24560	N	0.993973	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.9488	0.30001	0.0:0.8907:0.0:0.1093	.	.	.	.	.	-1	.	.	.	-	.	.	WDR78	67143647	0.228000	0.23718	0.003000	0.11579	0.001000	0.01503	0.911000	0.28584	1.324000	0.45282	-0.266000	0.10368	.	.	.		0.303	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	Intron	T	67371059	C	T	67371059	5	4	20	1	0	0	0	0	0	0	1	0	17343	695	24	3	2497	3	WDR78	1	67371059	Splice_Site	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	15067783	67371059	181879562	4	1731										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103491838	103491838	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	acactttcagcctctttataCtctgcttccccatactcata	2	15	4	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:103491838C>A	ENST00000370096.3	-	6	1143	c.831G>T	c.(829-831)gaG>gaT	p.E277D	COL11A1_ENST00000353414.4_Intron|COL11A1_ENST00000512756.1_Missense_Mutation_p.E277D|COL11A1_ENST00000358392.2_Intron	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	277	Nonhelical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCTCTTTATACTCTGCTTCCC	0.418																																					p.E277D		Atlas-SNP	.											.	COL11A1	972	.	0			c.G831T						.						238	208	218					1																	103491838		2203	4300	6503	SO:0001583	missense	1301	exon6			TTTATACTCTGCT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.831G>T	chr1.hg19:g.103491838C>A	ENSP00000359114:p.Glu277Asp	124.0	0.0		116.0	35.0	NM_001854	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.586806	0.28268	.	.	ENSG00000060718	ENST00000370096;ENST00000512756	D;D	0.88124	-2.32;-2.34	5.39	-9.67	0.00531	.	.	.	.	.	T	0.32010	0.0815	N	0.01168	-0.975	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09335	-1.0679	9	0.12766	T	0.61	.	1.7358	0.02941	0.203:0.3332:0.2874:0.1765	.	277;277	E9PCU0;P12107	.;COBA1_HUMAN	D	277	ENSP00000359114:E277D;ENSP00000426533:E277D	ENSP00000359114:E277D	E	-	3	2	COL11A1	103264426	0.042000	0.20092	0.958000	0.39756	0.990000	0.78478	-1.177000	0.03096	-1.032000	0.03304	-0.311000	0.09066	GAG	.	.		0.418	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103491838	C	A	103491838	3	1	20	1	0	0	0	0	1	0	0	0	3669	564	20	3	4994	3	COL11A1	1	103491838	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	36120779	103491838	145758783	5	1732										
MAGI3	260425	hgsc.bcm.edu	37	chr1	114225757	114225757	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	catcagtctcttctccagaaAaatgtgagtaagagggatcc	9	9	3	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:114225757A>C	ENST00000307546.9	+	21	3642	c.3567A>C	c.(3565-3567)aaA>aaC	p.K1189N	MAGI3_ENST00000369615.1_3'UTR	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	1214					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCTCCAGAAAAATGTGAGTA	0.378																																					p.K1189N		Atlas-SNP	.											.	MAGI3	181	.	0			c.A3567C						.						74	70	71					1																	114225757		1568	3582	5150	SO:0001583	missense	260425	exon21			CCAGAAAAATGTG	AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.3567A>C	chr1.hg19:g.114225757A>C	ENSP00000304604:p.Lys1189Asn	192.0	0.0		229.0	85.0	NM_001142782	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Missense_Mutation	SNP	ENST00000307546.9	hg19	CCDS44196.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.664503	0.47572	.	.	ENSG00000081026	ENST00000307546;ENST00000546156	T	0.53206	0.63	5.54	5.54	0.83059	.	0.074069	0.56097	D	0.000038	T	0.17874	0.0429	L	0.27053	0.805	0.80722	D	1	B	0.10296	0.003	B	0.09377	0.004	T	0.11348	-1.0591	10	0.46703	T	0.11	.	6.9564	0.24574	0.7723:0.1514:0.0764:0.0	.	1189	Q5TCQ9-4	.	N	1189;229	ENSP00000304604:K1189N	ENSP00000304604:K1189N	K	+	3	2	MAGI3	114027280	0.995000	0.38212	0.938000	0.37757	0.975000	0.68041	1.134000	0.31442	2.230000	0.72887	0.455000	0.32223	AAA	.	.		0.378	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		C	114225757	A	C	114225757	3	2	20	1	0	0	0	0	1	0	0	0	9201	11	1	5	3703	5	MAGI3	1	114225757	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	10733919	114225757	135024864	6	1733										
S100A7A	338324	hgsc.bcm.edu	37	chr1	153390690	153390690	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gagaacttccccaatttcctCagtgcctgtgtgagttgggg	12	10	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:153390690C>T	ENST00000368729.4	+	2	189	c.132C>T	c.(130-132)ctC>ctT	p.L44L	S100A7A_ENST00000329256.2_Silent_p.L44L|S100A7A_ENST00000368728.2_Silent_p.L44L	NM_176823.3	NP_789793.1	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7A	44	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein self-association (GO:0043621)	p.L44L(1)		cervix(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	12	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCAATTTCCTCAGTGCCTGTG	0.498																																					p.L44L		Atlas-SNP	.											S100A7A,NS,carcinoma,0,1	S100A7A	24	.	1	Substitution - coding silent(1)	endometrium(1)	c.C132T						.						163	144	150					1																	153390690		2203	4300	6503	SO:0001819	synonymous_variant	338324	exon2			TTTCCTCAGTGCC	AY189118	CCDS30872.1	1q22	2013-01-10	2006-09-11	2006-09-11	ENSG00000184330	ENSG00000184330		"S100 calcium binding proteins", "EF-hand domain containing"	21657	protein-coding gene	gene with protein product			"S100 calcium binding protein A15", "S100 calcium binding protein A7-like 1"	S100A15, S100A7L1		11230159	Standard	NM_176823		Approved	S100A7f	uc001fbt.1	Q86SG5	OTTHUMG00000013122	ENST00000368729.4:c.132C>T	chr1.hg19:g.153390690C>T		76.0	1.0		144.0	14.0	NM_176823	D3DV38|Q5SY69	Silent	SNP	ENST00000368729.4	hg19	CCDS30872.1																																																																																			.	.		0.498	S100A7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036786.2	NM_176823		T	153390690	C	T	153390690	2	4	20	1	0	0	0	0	0	0	0	1	13799	813	29	3		3	S100A7A	1	153390690	Silent	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	39164933	153390690	95859931	7	1734										
TNR	7143	hgsc.bcm.edu	37	chr1	175365900	175365900	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tcccattccagctcaatggaCctgtcgctgataccagccac	7	16	1	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:175365900C>G	ENST00000367674.2	-	5	1728	c.1020G>C	c.(1018-1020)agG>agC	p.R340S	TNR_ENST00000263525.2_Missense_Mutation_p.R340S			Q92752	TENR_HUMAN	tenascin R	340	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					GCTCAATGGACCTGTCGCTGA	0.607																																					p.R340S		Atlas-SNP	.											.	TNR	399	.	0			c.G1020C						.						75	79	78					1																	175365900		2203	4300	6503	SO:0001583	missense	7143	exon5			AATGGACCTGTCG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.1020G>C	chr1.hg19:g.175365900C>G	ENSP00000356646:p.Arg340Ser	97.0	0.0		62.0	40.0	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.622|6.622	0.483121|0.483121	0.12581|0.12581	.|.	.|.	ENSG00000116147|ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673|ENST00000422274	T;T|.	0.54479|.	0.57;0.57|.	5.95|5.95	5.02|5.02	0.67125|0.67125	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.539436|.	0.22022|.	N|.	0.065706|.	T|T	0.24005|0.24005	0.0581|0.0581	N|N	0.05230|0.05230	-0.09|-0.09	0.31839|0.31839	N|N	0.623663|0.623663	B|.	0.12013|.	0.005|.	B|.	0.14578|.	0.011|.	T|T	0.29274|0.29274	-1.0017|-1.0017	10|5	0.13853|.	T|.	0.58|.	.|.	10.4668|10.4668	0.44614|0.44614	0.2655:0.606:0.1286:0.0|0.2655:0.606:0.1286:0.0	.|.	340|.	Q92752|.	TENR_HUMAN|.	S|L	340|65	ENSP00000356646:R340S;ENSP00000263525:R340S|.	ENSP00000263525:R340S|.	R|V	-|-	3|1	2|0	TNR|TNR	173632523|173632523	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.750000|0.750000	0.26334|0.26334	1.468000|1.468000	0.48064|0.48064	0.563000|0.563000	0.77884|0.77884	AGG|GTC	.	.		0.607	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		G	175365900	C	G	175365900	3	3	20	1	0	0	0	0	1	0	0	0	16353	506	18	4	3132	4	TNR	1	175365900	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	21975210	175365900	73884721	8	1735										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179631330	179631330	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gttacctctacaggctaagaTgggaaaaggaggtgatgctg	14	6	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:179631330T>C	ENST00000367614.1	+	14	2611	c.2252T>C	c.(2251-2253)aTg>aCg	p.M751T	TDRD5_ENST00000294848.8_Missense_Mutation_p.M751T|TDRD5_ENST00000444136.1_Missense_Mutation_p.M805T	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	751					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						CAGGCTAAGATGGGAAAAGGA	0.448																																					p.M805T		Atlas-SNP	.											.	TDRD5	149	.	0			c.T2414C						.						147	126	133					1																	179631330		2203	4300	6503	SO:0001583	missense	163589	exon15			CTAAGATGGGAAA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2252T>C	chr1.hg19:g.179631330T>C	ENSP00000356586:p.Met751Thr	83.0	0.0		88.0	27.0	NM_001199085	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	T	10.83	1.461819	0.26248	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.32988	2.61;2.61;2.81;1.43	5.41	3.02	0.34903	.	0.919717	0.09338	N	0.815961	T	0.17365	0.0417	L	0.47716	1.5	0.09310	N	1	B;P	0.42827	0.01;0.791	B;B	0.29598	0.027;0.104	T	0.07966	-1.0745	10	0.10377	T	0.69	-23.7189	4.6966	0.12806	0.0:0.0974:0.1945:0.7082	.	805;751	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	T	751;751;805;261	ENSP00000356586:M751T;ENSP00000294848:M751T;ENSP00000406052:M805T;ENSP00000410744:M261T	ENSP00000294848:M751T	M	+	2	0	TDRD5	177897953	0.998000	0.40836	0.540000	0.28089	0.925000	0.55904	1.364000	0.34171	2.179000	0.69175	0.528000	0.53228	ATG	.	.		0.448	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		C	179631330	T	C	179631330	3	2	20	1	0	0	0	0	1	0	0	0	15748	1464	51	2	2302	2	TDRD5	1	179631330	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	4265430	179631330	69619291	9	1736										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186050420	186050420	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	caagagtgcactgatagagtGtttatccagtggcagcccag	12	9	0	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:186050420G>A	ENST00000271588.4	+	56	8910	c.8681G>A	c.(8680-8682)tGt>tAt	p.C2894Y	HMCN1_ENST00000367492.2_Missense_Mutation_p.C2894Y	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2894	Ig-like C2-type 27.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTGATAGAGTGTTTATCCAGT	0.458																																					p.C2894Y		Atlas-SNP	.											.	HMCN1	797	.	0			c.G8681A						.						157	151	153					1																	186050420		2203	4300	6503	SO:0001583	missense	83872	exon56			TAGAGTGTTTATC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8681G>A	chr1.hg19:g.186050420G>A	ENSP00000271588:p.Cys2894Tyr	83.0	0.0		56.0	33.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.804114	0.90623	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.73789	-0.78;-0.78	5.86	5.86	0.93980	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93406	0.7897	H	0.99697	4.71	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.95891	0.8907	10	0.87932	D	0	.	20.1772	0.98182	0.0:0.0:1.0:0.0	.	2894	Q96RW7	HMCN1_HUMAN	Y	2894	ENSP00000271588:C2894Y;ENSP00000356462:C2894Y	ENSP00000271588:C2894Y	C	+	2	0	HMCN1	184317043	1.000000	0.71417	0.944000	0.38274	0.897000	0.52465	9.414000	0.97362	2.778000	0.95560	0.655000	0.94253	TGT	.	.		0.458	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186050420	G	A	186050420	3	1	20	1	0	0	0	0	1	0	0	0	7229	1377	48	3	8903	3	HMCN1	1	186050420	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	6419090	186050420	63200201	10	1737										
FLVCR1	28982	hgsc.bcm.edu	37	chr1	213068556	213068556	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	aatcttctgattgtttttatAgataccagctgacagtccca	6	9	2	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:213068556A>G	ENST00000366971.4	+	10	1791		c.e10-1		FLVCR1_ENST00000483790.1_Splice_Site	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1						blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	heme transporter activity (GO:0015232)|transporter activity (GO:0005215)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2)	12				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		TTGTTTTTATAGATACCAGCT	0.353																																					.	Esophageal Squamous(199;2235 2952 19233 26256)	Atlas-SNP	.											.	FLVCR1	31	.	0			c.1594-2A>G						.						92	88	90					1																	213068556		2203	4300	6503	SO:0001630	splice_region_variant	28982	exon10			TTTTATAGATACC	AF118637	CCDS1510.1	1q32.3	2014-05-30			ENSG00000162769	ENSG00000162769		"Solute carriers"	24682	protein-coding gene	gene with protein product		609144	"ataxia, posterior column 1, with retinitis pigmentosa"	AXPC1		10400745, 10648427, 21070897	Standard	NM_014053		Approved	FLVCR, MFSD7B, PCA	uc001hjt.3	Q9Y5Y0	OTTHUMG00000036924	ENST00000366971.4:c.1594-1A>G	chr1.hg19:g.213068556A>G		174.0	0.0		279.0	75.0	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Splice_Site	SNP	ENST00000366971.4	hg19	CCDS1510.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.159079	0.38119	.	.	ENSG00000162769	ENST00000366971;ENST00000419102	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8184	0.52224	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FLVCR1	211135179	0.998000	0.40836	0.997000	0.53966	0.362000	0.29581	4.223000	0.58587	2.039000	0.60335	0.533000	0.62120	.	.	.		0.353	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053	Intron	G	213068556	A	G	213068556	5	3	20	1	0	0	0	0	0	0	1	0	5953	434	15	2	1630	2	FLVCR1	1	213068556	Splice_Site	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	27018136	213068556	36182065	11	1738										
NUP133	55746	hgsc.bcm.edu	37	chr1	229631723	229631723	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tctgaagaatcatctaattcCcatttactgatgtttgaact	5	8	3	4			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr1:229631723C>T	ENST00000261396.3	-	7	982	c.891G>A	c.(889-891)tgG>tgA	p.W297*	NUP133_ENST00000537506.1_Nonsense_Mutation_p.W281*	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	297					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				CATCTAATTCCCATTTACTGA	0.353																																					p.W297X		Atlas-SNP	.											.	NUP133	111	.	0			c.G891A						.						110	107	108					1																	229631723		2203	4300	6503	SO:0001587	stop_gained	55746	exon7			TAATTCCCATTTA		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.891G>A	chr1.hg19:g.229631723C>T	ENSP00000261396:p.Trp297*	28.0	0.0		49.0	26.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Nonsense_Mutation	SNP	ENST00000261396.3	hg19	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	C	38	7.118482	0.98074	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.7656	19.5382	0.95264	0.0:1.0:0.0:0.0	.	.	.	.	X	297;297;297;281	.	ENSP00000261396:W297X	W	-	3	0	NUP133	227698346	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.445000	0.73456	2.621000	0.88768	0.650000	0.86243	TGG	.	.		0.353	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		T	229631723	C	T	229631723	4	4	20	1	0	0	0	0	0	1	0	0	10763	624	22	3	2659	3	NUP133	1	229631723	Nonsense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	16563167	229631723	19618898	12	1739										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25469632	25469632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ccgggaacagcttccccgcgCggctgctggccacctggagg	15	16	0	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:25469632C>T	ENST00000264709.3	-	10	1473	c.1136G>A	c.(1135-1137)cGc>cAc	p.R379H	DNMT3A_ENST00000402667.1_Missense_Mutation_p.R156H|DNMT3A_ENST00000380746.4_Missense_Mutation_p.R190H|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000321117.5_Missense_Mutation_p.R379H	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	379	Interaction with DNMT1 and DNMT3B.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCCCCGCGCGGCTGCTGGC	0.632			"Mis, F, N, S"		AML																																p.R379H		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.G1136A						.						63	65	65					2																	25469632		2201	4299	6500	SO:0001583	missense	1788	exon10			CCCGCGCGGCTGC		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1136G>A	chr2.hg19:g.25469632C>T	ENSP00000264709:p.Arg379His	59.0	0.0		52.0	5.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	ENST00000264709.3	hg19	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.528548	0.64860	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	4.87	3.97	0.46021	.	0.000000	0.85682	D	0.000000	T	0.68458	0.3003	M	0.63843	1.955	0.80722	D	1	D;P	0.63880	0.993;0.534	P;B	0.44946	0.465;0.012	T	0.73291	-0.4029	10	0.62326	D	0.03	-4.7029	11.3924	0.49822	0.0:0.9088:0.0:0.0912	.	379;190	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	H	190;379;379;156	ENSP00000370122:R190H;ENSP00000324375:R379H;ENSP00000264709:R379H;ENSP00000384237:R156H	ENSP00000264709:R379H	R	-	2	0	DNMT3A	25323136	1.000000	0.71417	0.953000	0.39169	0.543000	0.35085	7.472000	0.80996	2.535000	0.85469	0.655000	0.94253	CGC	.	.		0.632	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		T	25469632	C	T	25469632	3	4	20	1	0	0	0	0	1	0	0	0	4678	768	27	1	1658	1	DNMT3A	2	25469632	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10		25469632	217729741	13	1740										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25497874	25497874	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tgatgtagtaggggtcccccGcctggaaggtgagcctcggc	16	11	0	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:25497874G>T	ENST00000264709.3	-	6	912	c.575C>A	c.(574-576)gCg>gAg	p.A192E	DNMT3A_ENST00000321117.5_Missense_Mutation_p.A192E	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	192					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGGTCCCCCGCCTGGAAGGT	0.697			"Mis, F, N, S"		AML																																p.A192E		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	DNMT3A,colon,carcinoma,0,1	DNMT3A	1807	.	0			c.C575A						.						35	33	34					2																	25497874		2203	4300	6503	SO:0001583	missense	1788	exon6			TCCCCCGCCTGGA		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.575C>A	chr2.hg19:g.25497874G>T	ENSP00000264709:p.Ala192Glu	137.0	0.0		118.0	40.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	ENST00000264709.3	hg19	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	G	33	5.271735	0.95429	.	.	ENSG00000119772	ENST00000321117;ENST00000264709	D;D	0.95518	-3.73;-3.73	5.24	5.24	0.73138	.	0.000000	0.64402	D	0.000002	D	0.95497	0.8537	N	0.24115	0.695	0.80722	D	1	D	0.69078	0.997	D	0.74348	0.983	D	0.96106	0.9073	10	0.56958	D	0.05	-9.9332	16.3295	0.83004	0.0:0.0:1.0:0.0	.	192	Q9Y6K1	DNM3A_HUMAN	E	192	ENSP00000324375:A192E;ENSP00000264709:A192E	ENSP00000264709:A192E	A	-	2	0	DNMT3A	25351378	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	9.004000	0.93583	2.448000	0.82819	0.561000	0.74099	GCG	.	.		0.697	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		T	25497874	G	T	25497874	3	4	20	1	0	0	0	0	1	0	0	0	4678	1087	38	1	2315	1	DNMT3A	2	25497874	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	28242	25497874	217701499	14	1741										
EFEMP1	2202	hgsc.bcm.edu	37	chr2	56103824	56103824	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ctgacagatgaatgaaccaaGaatgttgtagcactgctgag	11	7	0	6			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:56103824G>A	ENST00000394555.2	-	7	1249	c.814C>T	c.(814-816)Ctt>Ttt	p.L272F	EFEMP1_ENST00000355426.3_Missense_Mutation_p.L272F|EFEMP1_ENST00000424836.2_Intron|EFEMP1_ENST00000394554.1_Missense_Mutation_p.L272F	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	272	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.|Mediates interaction with TIMP3.				epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AATGAACCAAGAATGTTGTAG	0.338																																					p.L272F	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.C814T						.						126	111	116					2																	56103824		2203	4300	6503	SO:0001583	missense	2202	exon7			AACCAAGAATGTT	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"Fibulins"	3218	protein-coding gene	gene with protein product	"fibulin 3"	601548	"fibrillin-like", "EGF-containing fibulin-like extracellular matrix protein 1"	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.814C>T	chr2.hg19:g.56103824G>A	ENSP00000378058:p.Leu272Phe	280.0	0.0		416.0	149.0	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Missense_Mutation	SNP	ENST00000394555.2	hg19	CCDS1857.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.871614	0.33069	.	.	ENSG00000115380	ENST00000394555;ENST00000394554;ENST00000405693;ENST00000355426	D;D;D	0.87887	-2.31;-2.31;-2.31	5.73	5.73	0.89815	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.56097	D	0.000032	T	0.77837	0.4190	N	0.24115	0.695	0.80722	D	1	P	0.43826	0.818	B	0.39299	0.296	T	0.75883	-0.3160	10	0.11794	T	0.64	.	14.7367	0.69422	0.0:0.2642:0.7358:0.0	.	272	Q12805	FBLN3_HUMAN	F	272;272;128;272	ENSP00000378058:L272F;ENSP00000378057:L272F;ENSP00000347596:L272F	ENSP00000347596:L272F	L	-	1	0	EFEMP1	55957328	0.991000	0.36638	1.000000	0.80357	0.999000	0.98932	1.886000	0.39688	2.679000	0.91253	0.650000	0.86243	CTT	.	.		0.338	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2			A	56103824	G	A	56103824	3	1	20	1	0	0	0	0	1	0	0	0	4943	942	33	3	687	3	EFEMP1	2	56103824	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	30605950	56103824	187095549	15	1742										
ELMOD3	84173	hgsc.bcm.edu	37	chr2	85604561	85604561	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tcaaagaccttgccgatggcGcaggagattttccgcctgtc	11	12	1	2	rs371072018		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:85604561G>A	ENST00000409890.2	+	11	1369	c.702G>A	c.(700-702)gcG>gcA	p.A234A	ELMOD3_ENST00000315658.7_Silent_p.A234A|ELMOD3_ENST00000409344.3_Silent_p.A234A|ELMOD3_ENST00000409013.3_Silent_p.A234A|ELMOD3_ENST00000490508.1_3'UTR|ELMOD3_ENST00000393852.4_Silent_p.A234A|ELMOD3_ENST00000428955.2_Silent_p.A234A			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3	234	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				phagocytosis (GO:0006909)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	12						TGCCGATGGCGCAGGAGATTT	0.582																																					p.A234A		Atlas-SNP	.											.	ELMOD3	53	.	0			c.G702A						.	G	,,,	0,4406		0,0,2203	102	81	88		702,702,702,702	-11.5	0.7	2		88	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ELMOD3	NM_001135021.1,NM_001135022.1,NM_001135023.1,NM_032213.4	,,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,,	234/382,234/382,234/382,234/392	85604561	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	84173	exon11			GATGGCGCAGGAG	AF258573	CCDS1973.1, CCDS46352.1	2p11.2	2014-01-28	2008-08-14	2008-08-14	ENSG00000115459	ENSG00000115459		"RNA binding motif (RRM) containing"	26158	protein-coding gene	gene with protein product		615427	"RNA binding motif protein 29", "RNA binding motif and ELMO/CED-12 domain 1", "deafness, autosomal recessive 88"	RBM29, RBED1, DFNB88		24039609	Standard	NM_032213		Approved	FLJ21977	uc010ysn.2	Q96FG2	OTTHUMG00000130170	ENST00000409890.2:c.702G>A	chr2.hg19:g.85604561G>A		43.0	0.0		39.0	9.0	NM_001135022	B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Silent	SNP	ENST00000409890.2	hg19	CCDS46352.1																																																																																			.	.		0.582	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213		A	85604561	G	A	85604561	2	1	20	1	0	0	0	0	0	0	0	1	5072	1074	38	1		1	ELMOD3	2	85604561	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	29500737	85604561	157594812	16	1743										
RNF103	7844	hgsc.bcm.edu	37	chr2	86849812	86849812	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tccaccagctcccggacatcCttcttctcgggcaaccctga	7	18	2	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:86849812C>T	ENST00000237455.4	-	1	1166	c.198G>A	c.(196-198)aaG>aaA	p.K66K	RNF103_ENST00000477307.1_5'UTR|RNF103-CHMP3_ENST00000604011.1_Intron|CHMP3_ENST00000439940.2_Intron	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	66					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K66delK(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						CCCGGACATCCTTCTTCTCGG	0.617																																					p.K66K		Atlas-SNP	.											.,1	RNF103	58	.	1	Deletion - In frame(1)	large_intestine(1)	c.G198A						.						73	81	79					2																	86849812		2203	4300	6503	SO:0001819	synonymous_variant	7844	exon1			GACATCCTTCTTC	D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"RING-type (C3HC4) zinc fingers"	12859	protein-coding gene	gene with protein product		602507	"zinc finger protein 103 homolog (mouse)"	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.198G>A	chr2.hg19:g.86849812C>T		152.0	0.0		164.0	73.0	NM_005667	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Silent	SNP	ENST00000237455.4	hg19	CCDS33237.1																																																																																			.	.		0.617	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667		T	86849812	C	T	86849812	2	4	20	1	0	0	0	0	0	0	0	1	13438	680	24	3		3	RNF103	2	86849812	Silent	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	1245251	86849812	156349561	17	1744										
KCNH7	90134	hgsc.bcm.edu	37	chr2	163291972	163291973	+	Missense_Mutation	DNP	GA	GA	TT													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ccaaatgcaagccagccagtGagcaatcagggcaaagatgc							TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:163291972_163291973GA>TT	ENST00000332142.5	-	8	1788_1789	c.1689_1690TC>AA	c.(1687-1692)gcTCac>gcAAac	p.H564N	KCNH7_ENST00000328032.4_Missense_Mutation_p.H557N	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	564					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GCCAGCCAGTGAGCAATCAGGG	0.48																																					p.H564N|p.A563A	GBM(196;1492 2208 17507 24132 45496)	Atlas-SNP	.											.	KCNH7	378	.	0			c.C1690A|c.T1689A						.																																			SO:0001583	missense	90134	exon8			GCCAGTGAGCAAT|CCAGTGAGCAATC	AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.1689_1690delinsTT	chr2.hg19:g.163291972_163291973delinsTT	ENSP00000331727:p.His564Asn	120.0|119.0	0.0		145.0|140.0	58.0|56.0	NM_033272	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation|Silent	SNP	ENST00000332142.5	hg19	CCDS2219.1																																																																																			.	.		0.48	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		TT	163291973	GA	TT	163291972	3	4	20	1	0	0	0	0	1	0	0	0	8046	1290	45	3	2002	3	KCNH7	2	163291972	Missense_Mutation	DNP	GA	TCGA-2Y-A9HA-01A-11D-A38X-10	76442160	163291972	79907401	18	1745										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178562092	178562092	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gtgaggtctgttgccaatatTgactgcttcaaaagctgcat	10	8	2	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:178562092T>G	ENST00000286063.6	-	15	2630	c.2313A>C	c.(2311-2313)tcA>tcC	p.S771S	PDE11A_ENST00000389683.3_Silent_p.S327S|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000409504.1_Silent_p.S413S|AC012499.1_ENST00000412133.1_RNA|PDE11A_ENST00000449286.2_Silent_p.S413S|AC012499.1_ENST00000450227.1_RNA|PDE11A_ENST00000358450.4_Silent_p.S521S	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	771	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	TTGCCAATATTGACTGCTTCA	0.398									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.S771S		Atlas-SNP	.											.	PDE11A	283	.	0			c.A2313C						.						162	135	144					2																	178562092		2203	4300	6503	SO:0001819	synonymous_variant	50940	exon15	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	CAATATTGACTGC	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2313A>C	chr2.hg19:g.178562092T>G		49.0	0.0		61.0	27.0	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Silent	SNP	ENST00000286063.6	hg19	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	T	9.810	1.182806	0.21870	.	.	ENSG00000128655	ENST00000433879	.	.	.	5.57	1.39	0.22231	.	.	.	.	.	T	0.44519	0.1297	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23976	-1.0173	4	.	.	.	.	3.2999	0.06979	0.0972:0.1311:0.2174:0.5543	.	.	.	.	P	379	.	.	Q	-	2	0	PDE11A	178270338	0.614000	0.27017	1.000000	0.80357	0.998000	0.95712	-0.370000	0.07523	0.360000	0.24265	0.528000	0.53228	CAA	.	.		0.398	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			G	178562092	T	G	178562092	2	3	20	1	0	0	0	0	0	0	0	1	11640	1799	63	5		5	PDE11A	2	178562092	Silent	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	15270120	178562092	64637281	19	1746										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196709853	196709853	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	atctgagcaggggatatctcTtcctttgcacaaagttgtcc	9	10	2	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:196709853T>C	ENST00000312428.6	-	47	8918	c.8818A>G	c.(8818-8820)Aga>Gga	p.R2940G		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2940					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GGGATATCTCTTCCTTTGCAC	0.393																																					p.R2940G		Atlas-SNP	.											.	DNAH7	512	.	0			c.A8818G						.						139	124	129					2																	196709853		1854	4102	5956	SO:0001583	missense	56171	exon47			TATCTCTTCCTTT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.8818A>G	chr2.hg19:g.196709853T>C	ENSP00000311273:p.Arg2940Gly	109.0	0.0		111.0	39.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	T	12.19	1.864216	0.32977	.	.	ENSG00000118997	ENST00000312428	T	0.23348	1.91	5.8	4.66	0.58398	.	0.219924	0.46145	N	0.000303	T	0.27731	0.0682	M	0.70275	2.135	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.04885	-1.0920	10	0.24483	T	0.36	.	11.2587	0.49069	0.0:0.0718:0.0:0.9282	.	2940	Q8WXX0	DYH7_HUMAN	G	2940	ENSP00000311273:R2940G	ENSP00000311273:R2940G	R	-	1	2	DNAH7	196418098	0.279000	0.24239	0.114000	0.21550	0.953000	0.61014	3.575000	0.53870	1.034000	0.39945	0.528000	0.53228	AGA	.	.		0.393	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196709853	T	C	196709853	3	2	20	1	0	0	0	0	1	0	0	0	4608	1617	56	2	3332	2	DNAH7	2	196709853	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	18147761	196709853	46489520	20	1747										
FAM117B	150864	hgsc.bcm.edu	37	chr2	203630440	203630440	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	caagtacagtcatgccatcaGcttctctactcccaccacca	4	17	3	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:203630440G>A	ENST00000392238.2	+	8	1723	c.1723G>A	c.(1723-1725)Gct>Act	p.A575T	FAM117B_ENST00000303116.6_Missense_Mutation_p.A331T			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	575										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						CATGCCATCAGCTTCTCTACT	0.512																																					p.A575T		Atlas-SNP	.											FAM117B_ENST00000392238,colon,carcinoma,0,2	FAM117B	73	.	0			c.G1723A						.						106	99	101					2																	203630440		2203	4300	6503	SO:0001583	missense	150864	exon8			CCATCAGCTTCTC	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.1723G>A	chr2.hg19:g.203630440G>A	ENSP00000376071:p.Ala575Thr	95.0	0.0		122.0	52.0	NM_173511	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Missense_Mutation	SNP	ENST00000392238.2	hg19	CCDS33362.2	.	.	.	.	.	.	.	.	.	.	G	10.05	1.244235	0.22796	.	.	ENSG00000138439	ENST00000303116;ENST00000392238	.	.	.	5.75	2.95	0.34219	.	0.659654	0.14918	N	0.290835	T	0.12987	0.0315	N	0.03115	-0.41	0.23095	N	0.998305	B	0.16802	0.019	B	0.12156	0.007	T	0.21177	-1.0253	9	0.19147	T	0.46	-4.0791	2.4797	0.04584	0.1249:0.3727:0.3338:0.1686	.	575	Q6P1L5	F117B_HUMAN	T	331;575	.	ENSP00000306299:A331T	A	+	1	0	FAM117B	203338685	0.853000	0.29707	0.482000	0.27366	0.826000	0.46750	1.311000	0.33562	0.756000	0.33013	-0.311000	0.09066	GCT	.	.		0.512	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511		A	203630440	G	A	203630440	3	1	20	1	0	0	0	0	1	0	0	0	5415	971	34	3	1753	3	FAM117B	2	203630440	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	6920587	203630440	39568933	21	1748										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220427162	220427162	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	aggaggccgactcatcgtcaAtttcacacaagtactcgccg	9	13	3	0	rs535601955		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:220427162A>G	ENST00000404537.1	-	8	2971	c.2915T>C	c.(2914-2916)aTt>aCt	p.I972T	OBSL1_ENST00000373873.4_Missense_Mutation_p.I972T|OBSL1_ENST00000603926.1_Missense_Mutation_p.I972T|OBSL1_ENST00000289656.3_Missense_Mutation_p.I559T|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000265318.4_Missense_Mutation_p.I972T|OBSL1_ENST00000373876.1_Missense_Mutation_p.I972T	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	972	Ig-like 7.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CTCATCGTCAATTTCACACAA	0.657													A|||	1	0.000199681	0	0.0014	5008	,	,		20147	0		0	False		,,,				2504	0				p.I972T		Atlas-SNP	.											.	OBSL1	120	.	0			c.T2915C						.						72	82	79					2																	220427162		2203	4299	6502	SO:0001583	missense	23363	exon8			TCGTCAATTTCAC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.2915T>C	chr2.hg19:g.220427162A>G	ENSP00000385636:p.Ile972Thr	103.0	0.0		72.0	25.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	hg19	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	A	7.575	0.667437	0.14710	.	.	ENSG00000124006	ENST00000265318;ENST00000404537;ENST00000373876;ENST00000373873;ENST00000289656	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	4.72	3.38	0.38709	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.40570	0.1122	N	0.01048	-1.04	0.36032	D	0.8395	B;B;B;B	0.30281	0.275;0.133;0.013;0.041	P;B;B;B	0.44447	0.45;0.401;0.005;0.032	T	0.46569	-0.9182	9	0.27082	T	0.32	.	3.239	0.06774	0.6076:0.0:0.3924:0.0	.	973;972;559;972	A4KVA4;O75147;A8MSZ8;O75147-2	.;OBSL1_HUMAN;.;.	T	972;972;972;972;559	ENSP00000265318:I972T;ENSP00000385636:I972T;ENSP00000362983:I972T;ENSP00000362980:I972T;ENSP00000289656:I559T	ENSP00000265318:I972T	I	-	2	0	OBSL1	220135406	0.951000	0.32395	0.999000	0.59377	0.942000	0.58702	5.731000	0.68554	1.898000	0.54952	0.533000	0.62120	ATT	.	.		0.657	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			G	220427162	A	G	220427162	3	3	20	1	0	0	0	0	1	0	0	0	10822	101	4	2	2983	2	OBSL1	2	220427162	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	16796722	220427162	22772211	22	1749										
FAM124B	79843	hgsc.bcm.edu	37	chr2	225244883	225244883	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	caggggaagcatgccagctcCcaagatgccattcttaacac	9	13	1	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:225244883C>A	ENST00000409685.3	-	2	1040	c.775G>T	c.(775-777)Gga>Tga	p.G259*	FAM124B_ENST00000389874.3_3'UTR	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	259										endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		ATGCCAGCTCCCAAGATGCCA	0.507																																					p.G259X		Atlas-SNP	.											.	FAM124B	71	.	0			c.G775T						.						43	45	44					2																	225244883		692	1591	2283	SO:0001587	stop_gained	79843	exon2			CAGCTCCCAAGAT	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.775G>T	chr2.hg19:g.225244883C>A	ENSP00000386895:p.Gly259*	101.0	0.0		94.0	37.0	NM_001122779	A6NNC7|Q8NBZ4|Q8TAV7	Nonsense_Mutation	SNP	ENST00000409685.3	hg19	CCDS46527.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.023859	0.93462	.	.	ENSG00000124019	ENST00000409685	.	.	.	5.71	3.88	0.44766	.	.	.	.	.	.	.	.	.	.	.	0.19575	N	0.999964	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-0.4856	9.0671	0.36469	0.0:0.8273:0.0:0.1727	.	.	.	.	X	259	.	ENSP00000386895:G259X	G	-	1	0	FAM124B	224953127	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	0.578000	0.23773	0.720000	0.32209	0.655000	0.94253	GGA	.	.		0.507	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		A	225244883	C	A	225244883	4	1	20	1	0	0	0	0	0	1	0	0	5431	632	22	3	596	3	FAM124B	2	225244883	Nonsense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	4817721	225244883	17954490	23	1750										
UGT1A1	54578	hgsc.bcm.edu	37	chr2	234681067	234681087	+	In_Frame_Del	DEL	CTTGGACGTGATTGGTTTCCT	CTTGGACGTGATTGGTTTCCT	-													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	acctggtaccagtaccattcCttggacgtgattggtttcct					rs114123636	byFrequency	TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	CTTGGACGTGATTGGTTTCCT	CTTGGACGTGATTGGTTTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr2:234681067_234681087delCTTGGACGTGATTGGTTTCCT	ENST00000305139.6	+	5	1600_1620	c.1461_1481delCTTGGACGTGATTGGTTTCCT	c.(1459-1482)tccttggacgtgattggtttcctc>tcc	p.LDVIGFL488del	UGT1A9_ENST00000354728.4_In_Frame_Del_p.LDVIGFL486del|UGT1A1_ENST00000608381.1_In_Frame_Del_p.LDVIGFL490del|UGT1A5_ENST00000373414.3_In_Frame_Del_p.LDVIGFL490del|UGT1A1_ENST00000609637.1_In_Frame_Del_p.LDVIGFL486del|UGT1A1_ENST00000609767.1_In_Frame_Del_p.LDVIGFL490del|UGT1A8_ENST00000305208.5_In_Frame_Del_p.LDVIGFL489del|UGT1A1_ENST00000608383.1_In_Frame_Del_p.LDVIGFL489del|UGT1A10_ENST00000344644.5_In_Frame_Del_p.LDVIGFL486del|UGT1A4_ENST00000373409.3_In_Frame_Del_p.LDVIGFL490del|UGT1A3_ENST00000482026.1_In_Frame_Del_p.LDVIGFL490del|UGT1A1_ENST00000373450.4_In_Frame_Del_p.LDVIGFL486del|UGT1A7_ENST00000373426.3_In_Frame_Del_p.LDVIGFL486del|UGT1A6_ENST00000373424.1_In_Frame_Del_p.LDVIGFL221del	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	488					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	AGTACCATTCCTTGGACGTGATTGGTTTCCTCTTGGCCGTC	0.561																																					p.489_496del		Atlas-Indel,Pindel	.											.	UGT1A5	66	.	0			c.1466_1486del	GRCh37	CM066253	UGT1A1	M		.																																			SO:0001651	inframe_deletion	54579	exon5			.	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"UDP glucuronosyltransferases"	12538	other	complex locus constituent		606431	"UDP glycosyltransferase 1 family, polypeptide A6"			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.1461_1481delCTTGGACGTGATTGGTTTCCT	chr2.hg19:g.234681067_234681087delCTTGGACGTGATTGGTTTCCT	ENSP00000303174:p.Leu488_Leu494del	143.0	0.0		126.0	10.0	NM_019078	A6NKK6|B8K289|Q96TE7	In_Frame_Del	DEL	ENST00000305139.6	hg19	CCDS2507.1																																																																																			.	.		0.561	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862		-	234681087	CTTGGACGTGATTGGTTTCCT	-	234681067	7	5	20	1	0	1	0	1	0	0	0	0	16959	668	24	0	1482	0	UGT1A1	2	234681067	In_Frame_Del	DEL	CTTGGACGTGATTGGTTTCCT	TCGA-2Y-A9HA-01A-11D-A38X-10	9436184	234681067	8518306	24	1751										
C3orf35	339883	hgsc.bcm.edu	37	chr3	37476365	37476365	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tgaagttcagaaaagggaggGgactgactcaatcccagctg	13	8	2	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr3:37476365G>T	ENST00000328376.5	+	6	1236	c.257G>T	c.(256-258)gGg>gTg	p.G86V	C3orf35_ENST00000481400.1_3'UTR	NM_178339.2	NP_848029.2	Q8IVJ8	APRG1_HUMAN	chromosome 3 open reading frame 35	86						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	11						aaaagggaggggactgactca	0.458																																					p.G86V		Atlas-SNP	.											.	C3orf35	21	.	0			c.G257T						.						30	30	30					3																	37476365		1882	4096	5978	SO:0001583	missense	339883	exon6			GGGAGGGGACTGA	AJ493599	CCDS43065.1, CCDS46792.1	3p22.3	2014-05-22			ENSG00000198590	ENSG00000198590			24082	protein-coding gene	gene with protein product	"AP20 region protein", "APRG1 tumor suppressor candidate"	611429				12543795	Standard	NM_178342		Approved	APRG1	uc003cha.4	Q8IVJ8	OTTHUMG00000155923	ENST00000328376.5:c.257G>T	chr3.hg19:g.37476365G>T	ENSP00000331625:p.Gly86Val	228.0	0.0		268.0	115.0	NM_178339	B7ZMA0|Q8IVJ5|Q8IVJ9	Missense_Mutation	SNP	ENST00000328376.5	hg19	CCDS43065.1	.	.	.	.	.	.	.	.	.	.	G	3.250	-0.153496	0.06585	.	.	ENSG00000198590	ENST00000328376	T	0.59083	0.29	0.565	-0.605	0.11623	.	.	.	.	.	T	0.31513	0.0799	N	0.08118	0	0.09310	N	1	B	0.21520	0.057	B	0.14023	0.01	T	0.18147	-1.0346	8	0.87932	D	0	.	.	.	.	.	86	Q8IVJ8	APRG1_HUMAN	V	86	ENSP00000331625:G86V	ENSP00000331625:G86V	G	+	2	0	C3orf35	37451369	0.037000	0.19845	0.010000	0.14722	0.010000	0.07245	0.364000	0.20325	-0.311000	0.08754	-0.311000	0.09066	GGG	.	.		0.458	C3orf35-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342344.2	NM_178338		T	37476365	G	T	37476365	3	4	20	1	0	0	0	0	1	0	0	0	2227	1232	43	3	397	3	C3orf35	3	37476365	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10		37476365	160546065	25	1752										
SLC25A38	54977	hgsc.bcm.edu	37	chr3	39433406	39433406	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	agcatctatcacagtgagggGcaccggggcctcttcagtgg	14	11	4	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr3:39433406G>T	ENST00000273158.4	+	5	896	c.519G>T	c.(517-519)ggG>ggT	p.G173G		NM_017875.2	NP_060345.2			solute carrier family 25, member 38											breast(1)|endometrium(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		ACAGTGAGGGGCACCGGGGCC	0.517																																					p.G173G		Atlas-SNP	.											.	SLC25A38	25	.	0			c.G519T						.						80	78	78					3																	39433406		2203	4300	6503	SO:0001819	synonymous_variant	54977	exon5			TGAGGGGCACCGG	BC013194	CCDS2685.1	3p22.1	2013-05-22			ENSG00000144659	ENSG00000144659		"Solute carriers"	26054	protein-coding gene	gene with protein product		610819				16949250	Standard	NM_017875		Approved	FLJ20551	uc003cjo.2	Q96DW6	OTTHUMG00000131289	ENST00000273158.4:c.519G>T	chr3.hg19:g.39433406G>T		108.0	0.0		124.0	52.0	NM_017875		Silent	SNP	ENST00000273158.4	hg19	CCDS2685.1																																																																																			.	.		0.517	SLC25A38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254057.3	NM_017875		T	39433406	G	T	39433406	2	4	20	1	0	0	0	0	0	0	0	1	14517	1190	42	3		3	SLC25A38	3	39433406	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	1957041	39433406	158589024	26	1753										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266125	41266125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	aatccattctggtgccactaCcacagctccttctctgagtg	7	14	2	1	rs121913413		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr3:41266125C>T	ENST00000349496.5	+	3	402	c.122C>T	c.(121-123)aCc>aTc	p.T41I	CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41I|CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41I|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41I|CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	41			T -> A (in hepatoblastoma and hepatocellular carcinoma; also in a desmoid tumor; strongly reduces phosphorylation and degradation; abolishes phosphorylation on Ser-33 and Ser-37 and enhances transactivation of target genes). {ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10398436, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10655994, ECO:0000269|PubMed:9927029}.|T -> I (in PTR, hepatocellular carcinoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T41I(74)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41N(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A39_T42del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGTGCCACTACCACAGCTCCT	0.507		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.T41I	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,98	CTNNB1	4904	.	204	Deletion - In frame(95)|Substitution - Missense(83)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)	liver(105)|large_intestine(24)|pituitary(20)|endometrium(14)|stomach(8)|skin(6)|biliary_tract(5)|haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|pancreas(3)|thyroid(2)|small_intestine(2)|prostate(2)|ovary(2)|bone(2)|adrenal_gland(1)|cervix(1)	c.C122T						.						90	77	81					3																	41266125		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CCACTACCACAGC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.122C>T	chr3.hg19:g.41266125C>T	ENSP00000344456:p.Thr41Ile	94.0	0.0		141.0	56.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568904	0.86439	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.71082	0.3298	M	0.79258	2.445	0.80722	D	1	D	0.67145	0.996	D	0.68039	0.955	T	0.72893	-0.4154	10	0.87932	D	0	-8.9189	20.2983	0.98569	0.0:1.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	I	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34I;ENSP00000385604:T41I;ENSP00000412219:T41I;ENSP00000379486:T41I;ENSP00000344456:T41I;ENSP00000411226:T34I;ENSP00000379488:T41I;ENSP00000409302:T41I;ENSP00000401599:T41I	ENSP00000344456:T41I	T	+	2	0	CTNNB1	41241129	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	ACC	.	.		0.507	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266125	C	T	41266125	3	4	20	1	0	0	0	0	1	0	0	0	4018	507	18	3	128	3	CTNNB1	3	41266125	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	1832719	41266125	156756305	27	1754										
MAP4	4134	hgsc.bcm.edu	37	chr3	47957487	47957487	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gctgactgccccacatcctgCagagattctaaatgggaatc	9	12	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr3:47957487C>A	ENST00000360240.6	-	7	2348	c.1830G>T	c.(1828-1830)ctG>ctT	p.L610L	MAP4_ENST00000383737.4_Intron|MAP4_ENST00000395734.3_Silent_p.L610L|MAP4_ENST00000426837.2_Silent_p.L627L	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	610					cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	CCACATCCTGCAGAGATTCTA	0.438																																					p.L610L		Atlas-SNP	.											.	MAP4	176	.	0			c.G1830T						.						181	184	183					3																	47957487		2203	4300	6503	SO:0001819	synonymous_variant	4134	exon7			ATCCTGCAGAGAT		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1830G>T	chr3.hg19:g.47957487C>A		31.0	0.0		47.0	18.0	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Silent	SNP	ENST00000360240.6	hg19	CCDS33750.1																																																																																			.	.		0.438	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375		A	47957487	C	A	47957487	2	1	20	1	0	0	0	0	0	0	0	1	9267	697	25	3		3	MAP4	3	47957487	Silent	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	6691362	47957487	150064943	28	1755										
CD47	961	hgsc.bcm.edu	37	chr3	107798844	107798844	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	catagaagtcttaccaacacGatattttagctcgatgatcg	7	9	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr3:107798844G>A	ENST00000361309.5	-	2	499	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	CD47_ENST00000355354.7_Missense_Mutation_p.R132C	NM_001777.3	NP_001768.1	Q08722	CD47_HUMAN	CD47 molecule	132					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|opsonization (GO:0008228)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of inflammatory response (GO:0050729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T cell activation (GO:0050870)|response to bacterium (GO:0009617)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(3;0.0191)|Epithelial(53;0.118)			TTACCAACACGATATTTTAGC	0.413																																					p.R132C		Atlas-SNP	.											.	CD47	37	.	0			c.C394T						.						202	175	184					3																	107798844		1870	4111	5981	SO:0001583	missense	961	exon2			CAACACGATATTT		CCDS43125.1, CCDS43126.1	3q13.1-q13.2	2013-01-11	2006-03-28		ENSG00000196776	ENSG00000196776		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1682	protein-coding gene	gene with protein product	"antigen identified by monoclonal antibody 1D8", "antigenic surface determinant protein OA3", "integrin associated protein", "Rh-related antigen", "leukocyte surface antigen CD47", "CD47 glycoprotein"	601028	"CD47 antigen (Rh-related antigen, integrin-associated signal transducer)"	MER6		8294396, 2277087	Standard	XM_005247908		Approved	IAP, OA3	uc003dwt.1	Q08722	OTTHUMG00000044216	ENST00000361309.5:c.394C>T	chr3.hg19:g.107798844G>A	ENSP00000355361:p.Arg132Cys	80.0	0.0		117.0	36.0	NM_198793	A8K198|D3DN59|Q53Y71|Q96A60	Missense_Mutation	SNP	ENST00000361309.5	hg19	CCDS43126.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.652276	0.47362	.	.	ENSG00000196776	ENST00000355354;ENST00000361309	.	.	.	6.04	6.04	0.98038	CD47 immunoglobulin-like (1);	0.075364	0.56097	D	0.000027	T	0.62648	0.2445	L	0.57536	1.79	0.09310	N	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	P;P;D;D	0.65573	0.894;0.894;0.936;0.936	T	0.59182	-0.7502	9	0.72032	D	0.01	.	12.9803	0.58559	0.0:0.0:0.8388:0.1612	.	132;132;132;132	Q08722-2;Q08722-3;E9PB22;Q08722	.;.;.;CD47_HUMAN	C	132	.	ENSP00000347512:R132C	R	-	1	0	CD47	109281534	0.009000	0.17119	0.557000	0.28306	0.310000	0.27922	1.742000	0.38248	2.873000	0.98535	0.561000	0.74099	CGT	.	.		0.413	CD47-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000102793.1	NM_001777		A	107798844	G	A	107798844	3	1	20	1	0	0	0	0	1	0	0	0	3021	1058	37	1	621	1	CD47	3	107798844	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	59841357	107798844	90223586	29	1756										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113377134	113377134	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ctcttgctgcaagagctactAtatcagtttgctctacaaag	7	10	3	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr3:113377134A>G	ENST00000478658.1	-	5	3412	c.3395T>C	c.(3394-3396)aTa>aCa	p.I1132T	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.I1132T			Q68DE3	K2018_HUMAN	KIAA2018	1132						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						AAGAGCTACTATATCAGTTTG	0.443																																					p.I1132T		Atlas-SNP	.											.	KIAA2018	180	.	0			c.T3395C						.						126	119	122					3																	113377134		1935	4145	6080	SO:0001583	missense	205717	exon7			GCTACTATATCAG	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.3395T>C	chr3.hg19:g.113377134A>G	ENSP00000420721:p.Ile1132Thr	57.0	0.0		92.0	29.0	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	hg19	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	A	18.23	3.578056	0.65878	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.20069	2.1;2.1	5.43	5.43	0.79202	.	0.048192	0.85682	D	0.000000	T	0.34395	0.0896	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.66084	0.941	T	0.05321	-1.0892	10	0.51188	T	0.08	-13.1732	15.4858	0.75564	1.0:0.0:0.0:0.0	.	1132	Q68DE3	K2018_HUMAN	T	1132	ENSP00000320794:I1132T;ENSP00000420721:I1132T	ENSP00000320794:I1132T	I	-	2	0	KIAA2018	114859824	1.000000	0.71417	0.991000	0.47740	0.981000	0.71138	8.785000	0.91822	2.070000	0.61991	0.459000	0.35465	ATA	.	.		0.443	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		G	113377134	A	G	113377134	3	3	20	1	0	0	0	0	1	0	0	0	8277	449	16	2	3346	2	KIAA2018	3	113377134	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	5578290	113377134	84645296	30	1757										
TF	7018	hgsc.bcm.edu	37	chr3	133483097	133483120	+	Splice_Site	DEL	TGTCTTGGCAGAAAACTACAATAG	TGTCTTGGCAGAAAACTACAATAG	-													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ggcaagtgtggtctggtgccTgtcttggcagaaaactacaa					rs113133048		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	TGTCTTGGCAGAAAACTACAATAG	TGTCTTGGCAGAAAACTACAATAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr3:133483097_133483120delTGTCTTGGCAGAAAACTACAATAG	ENST00000402696.3	+	10	1760_1782	c.1275_1297delTGTCTTGGCAGAAAACTACAATAG	c.(1273-1299)cctgtcttggcagaaaactacaataga>ccga	p.VLAENYNR426del	TF_ENST00000264998.3_Splice_Site_p.VLAENYNR299del	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	426	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	GTCTGGTGCCTGTCTTGGCAGAAAACTACAATAGTAAGTGGTGG	0.487																																					p.425_433del		Pindel	.											.	TF	116	.	0			c.1274_1297del						.																																			SO:0001630	splice_region_variant	7018	exon10			.		CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.1297+1TGTCTTGGCAGAAAACTACAATAG>-	chr3.hg19:g.133483097_133483120delTGTCTTGGCAGAAAACTACAATAG		85.0	0.0		79.0	18.0	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	In_Frame_Del	DEL	ENST00000402696.3	hg19	CCDS3080.1																																																																																			.	.		0.487	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	In_Frame_Del	-	133483120	TGTCTTGGCAGAAAACTACAATAG	-	133483097	8	5	20	1	0	1	0	1	0	0	1	0	15800	1567	55	0	1313	0	TF	3	133483097	Splice_Site	DEL	TGTCTTGGCAGAAAACTACAATAG	TCGA-2Y-A9HA-01A-11D-A38X-10	20105963	133483097	64539333	31	1758										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140123535	140123535	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gaggccattgacgaggactgCtccccacagtacagccagat	11	13	0	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr3:140123535C>A	ENST00000458420.3	+	4	754	c.564C>A	c.(562-564)tgC>tgA	p.C188*	AC092988.1_ENST00000580582.1_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	188	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						ACGAGGACTGCTCCCCACAGT	0.532										HNSCC(16;0.037)																											p.C188X	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.C564A						.						147	122	130					3																	140123535		2203	4300	6503	SO:0001587	stop_gained	64084	exon4			GGACTGCTCCCCA	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.564C>A	chr3.hg19:g.140123535C>A	ENSP00000402460:p.Cys188*	131.0	0.0		136.0	54.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Nonsense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	C	35	5.560943	0.96527	.	.	ENSG00000158258	ENST00000458420	.	.	.	5.66	0.182	0.15077	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.6237	8.7125	0.34393	0.0:0.5135:0.0:0.4865	.	.	.	.	X	188	.	ENSP00000402460:C188X	C	+	3	2	CLSTN2	141606225	0.996000	0.38824	0.997000	0.53966	0.595000	0.36748	0.471000	0.22100	0.083000	0.17047	0.563000	0.77884	TGC	.	.		0.532	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		A	140123535	C	A	140123535	4	1	20	1	0	0	0	0	0	1	0	0	3564	805	28	3	578	3	CLSTN2	3	140123535	Nonsense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	6640438	140123535	57898895	32	1759										
TNFSF10	8743	hgsc.bcm.edu	37	chr3	172241126	172241126	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tgtgaagatcacgatcagcaCgcaggtctgtcccaggctgg	13	11	3	2	rs11545817		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr3:172241126C>T	ENST00000241261.2	-	1	171	c.49G>A	c.(49-51)Gtg>Atg	p.V17M	TNFSF10_ENST00000420541.2_Missense_Mutation_p.V17M	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	17					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			ACGATCAGCACGCAGGTCTGT	0.557																																					p.V17M		Atlas-SNP	.											.	TNFSF10	30	.	0			c.G49A						.						132	112	119					3																	172241126		2203	4300	6503	SO:0001583	missense	8743	exon1			TCAGCACGCAGGT	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.49G>A	chr3.hg19:g.172241126C>T	ENSP00000241261:p.Val17Met	99.0	0.0		108.0	36.0	NM_001190943	A1Y9B3	Missense_Mutation	SNP	ENST00000241261.2	hg19	CCDS3219.1	.	.	.	.	.	.	.	.	.	.	C	4.451	0.083501	0.08533	.	.	ENSG00000121858	ENST00000241261;ENST00000420541	T;T	0.31510	1.49;1.49	5.53	0.449	0.16619	.	0.479411	0.24762	N	0.035803	T	0.13286	0.0322	N	0.22421	0.69	0.09310	N	1	P;B	0.38745	0.645;0.297	B;B	0.30401	0.115;0.015	T	0.13980	-1.0489	10	0.44086	T	0.13	-1.4204	3.3367	0.07103	0.2872:0.3872:0.0:0.3256	rs11545817	17;17	A1Y9B3;P50591	.;TNF10_HUMAN	M	17	ENSP00000241261:V17M;ENSP00000389931:V17M	ENSP00000241261:V17M	V	-	1	0	TNFSF10	173723820	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	-0.900000	0.04097	-0.212000	0.10109	-0.150000	0.13652	GTG	.	.		0.557	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1			T	172241126	C	T	172241126	3	4	20	1	0	0	0	0	1	0	0	0	16316	536	19	1	816	1	TNFSF10	3	172241126	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	32117591	172241126	25781304	33	1760										
EVC2	132884	hgsc.bcm.edu	37	chr4	5630306	5630306	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ctctcgtgcttctgaatgagGtgagtcagctgggctgcagc	14	10	3	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr4:5630306G>C	ENST00000344408.5	-	12	1919	c.1866C>G	c.(1864-1866)caC>caG	p.H622Q	EVC2_ENST00000310917.2_Missense_Mutation_p.H542Q|EVC2_ENST00000344938.1_Missense_Mutation_p.H622Q	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	622					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TCTGAATGAGGTGAGTCAGCT	0.522																																					p.H622Q		Atlas-SNP	.											.	EVC2	202	.	0			c.C1866G						.						118	98	105					4																	5630306		2203	4300	6503	SO:0001583	missense	132884	exon12			AATGAGGTGAGTC	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1866C>G	chr4.hg19:g.5630306G>C	ENSP00000342144:p.His622Gln	82.0	0.0		68.0	19.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	G	8.804	0.933676	0.18206	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.76186	-1.0;-1.0;-1.0	4.8	-0.939	0.10408	.	0.192353	0.46758	D	0.000262	T	0.55081	0.1898	N	0.22421	0.69	0.09310	N	0.999999	B	0.12630	0.006	B	0.12837	0.008	T	0.36720	-0.9736	10	0.13108	T	0.6	-0.6203	13.1892	0.59700	0.0768:0.642:0.2812:0.0	.	622	Q86UK5	LBN_HUMAN	Q	622;542;622	ENSP00000339954:H622Q;ENSP00000311683:H542Q;ENSP00000342144:H622Q	ENSP00000311683:H542Q	H	-	3	2	EVC2	5681207	0.000000	0.05858	0.498000	0.27564	0.870000	0.49936	-1.093000	0.03362	-0.130000	0.11599	0.484000	0.47621	CAC	.	.		0.522	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		C	5630306	G	C	5630306	3	2	20	1	0	0	0	0	1	0	0	0	5288	1252	44	4	2104	4	EVC2	4	5630306	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10		5630306	185523970	34	1761										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62903534	62903534	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cattggttcagggaaaacatCtggttctcgaactcctggac	10	10	3	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr4:62903534C>A	ENST00000514591.1	+	23	3802	c.3473C>A	c.(3472-3474)tCt>tAt	p.S1158Y	LPHN3_ENST00000506720.1_Missense_Mutation_p.S1226Y|LPHN3_ENST00000514996.1_Missense_Mutation_p.S1149Y|LPHN3_ENST00000506746.1_Missense_Mutation_p.S1217Y|LPHN3_ENST00000545650.1_Missense_Mutation_p.S1158Y|LPHN3_ENST00000507625.1_Missense_Mutation_p.S1217Y|LPHN3_ENST00000514157.1_Missense_Mutation_p.S1149Y|LPHN3_ENST00000507164.1_Missense_Mutation_p.S1217Y|LPHN3_ENST00000509896.1_Missense_Mutation_p.S1226Y|LPHN3_ENST00000508693.1_Missense_Mutation_p.S1226Y|LPHN3_ENST00000506700.1_Missense_Mutation_p.S1149Y|LPHN3_ENST00000504896.1_Missense_Mutation_p.S1158Y|LPHN3_ENST00000508946.1_Missense_Mutation_p.S1158Y|LPHN3_ENST00000511324.1_Missense_Mutation_p.S1217Y|LPHN3_ENST00000512091.2_Missense_Mutation_p.S1158Y			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1136					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GGGAAAACATCTGGTTCTCGA	0.413																																					p.S1158Y		Atlas-SNP	.											LPHN3_ENST00000514591,NS,carcinoma,0,3	LPHN3	800	.	0			c.C3473A						.						131	132	132					4																	62903534		1991	4183	6174	SO:0001583	missense	23284	exon21			AAACATCTGGTTC	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.3473C>A	chr4.hg19:g.62903534C>A	ENSP00000422533:p.Ser1158Tyr	141.0	0.0		183.0	11.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.339503	0.81911	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03	5.33	5.33	0.75918	GPCR, family 2, latrophilin, C-terminal (1);	0.282499	0.35466	N	0.003182	T	0.56775	0.2008	L	0.52573	1.65	0.50039	D	0.999848	D;D;D	0.61080	0.989;0.989;0.974	P;P;P	0.58077	0.832;0.832;0.66	T	0.58951	-0.7545	10	0.87932	D	0	.	19.3821	0.94542	0.0:1.0:0.0:0.0	.	1158;1136;1158	E9PE04;Q9HAR2;Q9HAR2-2	.;LPHN3_HUMAN;.	Y	1158;1158;1226;1217;1149;1158;1136;1158;1217;1226;1217;1149;1158;1158;1226;1217;1149	ENSP00000423388:S1158Y;ENSP00000422533:S1158Y;ENSP00000423787:S1226Y;ENSP00000425033:S1217Y;ENSP00000424120:S1149Y;ENSP00000439831:S1158Y;ENSP00000421476:S1217Y;ENSP00000424030:S1226Y;ENSP00000421372:S1217Y;ENSP00000425201:S1149Y;ENSP00000423434:S1158Y;ENSP00000421627:S1158Y;ENSP00000420931:S1226Y;ENSP00000425884:S1217Y;ENSP00000424258:S1149Y	ENSP00000280009:S1158Y	S	+	2	0	LPHN3	62586129	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.438000	0.80431	2.653000	0.90120	0.650000	0.86243	TCT	.	.		0.413	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			A	62903534	C	A	62903534	3	1	20	1	0	0	0	0	1	0	0	0	8926	913	32	3	3555	3	LPHN3	4	62903534	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	57273228	62903534	128250742	35	1762										
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72423536	72423536	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cacctgttcactttcctgcaGgtgttgtgtctggccctgct	10	13	2	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr4:72423536G>T	ENST00000264485.5	+	22	2988	c.2871G>T	c.(2869-2871)caG>caT	p.Q957H	SLC4A4_ENST00000351898.6_Missense_Mutation_p.Q873H|SLC4A4_ENST00000425175.1_Missense_Mutation_p.Q957H|SLC4A4_ENST00000340595.3_Missense_Mutation_p.Q913H	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	957					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	CTTTCCTGCAGGTGTTGTGTC	0.493																																					p.Q957H		Atlas-SNP	.											.	SLC4A4	269	.	0			c.G2871T						.						156	123	134					4																	72423536		2203	4300	6503	SO:0001583	missense	8671	exon22			CCTGCAGGTGTTG	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.2871G>T	chr4.hg19:g.72423536G>T	ENSP00000264485:p.Gln957His	60.0	0.0		105.0	40.0	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.375272	0.82682	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000340595	D;D;D;D	0.86562	-2.13;-2.12;-1.68;-2.14	5.95	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.95079	0.8406	H	0.95043	3.615	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.95790	0.8824	10	0.87932	D	0	.	11.9044	0.52703	0.139:0.0:0.861:0.0	.	957;873;913;957	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1	.;.;.;S4A4_HUMAN	H	957;957;873;913	ENSP00000264485:Q957H;ENSP00000393557:Q957H;ENSP00000307349:Q873H;ENSP00000344272:Q913H	ENSP00000264485:Q957H	Q	+	3	2	SLC4A4	72642400	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.606000	0.54095	1.520000	0.48965	0.563000	0.77884	CAG	.	.		0.493	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		T	72423536	G	T	72423536	3	4	20	1	0	0	0	0	1	0	0	0	14671	991	35	3	3074	3	SLC4A4	4	72423536	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	9520002	72423536	118730740	36	1763										
GRID2	2895	hgsc.bcm.edu	37	chr4	94145811	94145811	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ggtgcttctgcttgctaatgCttttcataagaagctggagg	12	7	2	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr4:94145811C>A	ENST00000282020.4	+	7	1268	c.1010C>A	c.(1009-1011)gCt>gAt	p.A337D	GRID2_ENST00000510992.1_Missense_Mutation_p.A242D	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	337					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		CTTGCTAATGCTTTTCATAAG	0.443																																					p.A337D		Atlas-SNP	.											.	GRID2	233	.	0			c.C1010A						.						86	82	83					4																	94145811		2203	4300	6503	SO:0001583	missense	2895	exon7			CTAATGCTTTTCA	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.1010C>A	chr4.hg19:g.94145811C>A	ENSP00000282020:p.Ala337Asp	95.0	0.0		106.0	40.0	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	hg19	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.567908	0.86439	.	.	ENSG00000152208	ENST00000282020;ENST00000510992;ENST00000512631	D;D;D	0.95035	-3.59;-3.59;-3.59	5.53	5.53	0.82687	Extracellular ligand-binding receptor (1);	0.180348	0.49305	D	0.000158	D	0.94761	0.8309	L	0.32530	0.975	0.49299	D	0.999777	P;P;D	0.62365	0.77;0.77;0.991	B;B;P	0.56960	0.409;0.409;0.81	D	0.95371	0.8464	10	0.87932	D	0	.	19.4895	0.95044	0.0:1.0:0.0:0.0	.	242;337;242	E9PH24;O43424;Q4KKU8	.;GRID2_HUMAN;.	D	337;242;18	ENSP00000282020:A337D;ENSP00000421257:A242D;ENSP00000423331:A18D	ENSP00000282020:A337D	A	+	2	0	GRID2	94364834	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.040000	0.70980	2.596000	0.87737	0.655000	0.94253	GCT	.	.		0.443	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			A	94145811	C	A	94145811	3	1	20	1	0	0	0	0	1	0	0	0	6781	797	28	3	1036	3	GRID2	4	94145811	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	21722275	94145811	97008465	37	1764										
LRIT3	345193	hgsc.bcm.edu	37	chr4	110772897	110772897	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ttggatgggaattctctggcTgctttcccttgggcatctct	11	10	2	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr4:110772897T>A	ENST00000594814.1	+	2	354	c.354T>A	c.(352-354)gcT>gcA	p.A118A	LRIT3_ENST00000379920.3_Silent_p.A73A|LRIT3_ENST00000327908.3_5'UTR	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	118					regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		ATTCTCTGGCTGCTTTCCCTT	0.512																																					p.A118A		Atlas-SNP	.											.	LRIT3	107	.	0			c.T354A						.						124	103	109					4																	110772897		692	1591	2283	SO:0001819	synonymous_variant	345193	exon2			TCTGGCTGCTTTC	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"Immunoglobulin superfamily / I-set domain containing"	24783	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 4"	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.354T>A	chr4.hg19:g.110772897T>A		73.0	0.0		93.0	9.0	NM_198506	C9J1C2|Q6ZTG1	Silent	SNP	ENST00000594814.1	hg19	CCDS3688.3																																																																																			.	.		0.512	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506		A	110772897	T	A	110772897	2	1	20	1	0	0	0	0	0	0	0	1	8958	1567	55	4		4	LRIT3	4	110772897	Silent	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	16627086	110772897	80381379	38	1765										
IRX1	79192	hgsc.bcm.edu	37	chr5	3601148	3601148	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	atcctagcagccctcccgtcCgcctgattaagggtcttctt	8	15	2	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr5:3601148C>A	ENST00000302006.3	+	4	1489	c.1437C>A	c.(1435-1437)tcC>tcA	p.S479S	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	479					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CCCTCCCGTCCGCCTGATTAA	0.582																																					p.S479S		Atlas-SNP	.											.	IRX1	106	.	0			c.C1437A						.						43	48	46					5																	3601148		2203	4299	6502	SO:0001819	synonymous_variant	79192	exon4			CCCGTCCGCCTGA	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.1437C>A	chr5.hg19:g.3601148C>A		159.0	0.0		141.0	37.0	NM_024337	Q7Z2F8|Q8N312	Silent	SNP	ENST00000302006.3	hg19	CCDS34132.1																																																																																			.	.		0.582	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		A	3601148	C	A	3601148	2	1	20	1	0	0	0	0	0	0	0	1	7852	639	23	1		1	IRX1	5	3601148	Silent	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10		3601148	177314112	39	1766										
RAB3C	115827	hgsc.bcm.edu	37	chr5	57913469	57913469	+	Splice_Site	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tttgttttgtttttatcacaGatggcctctgcccaagatgc	8	9	2	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr5:57913469G>A	ENST00000282878.4	+	2	193		c.e2-1			NM_138453.2	NP_612462.1	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family						antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)	21		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		TTTTATCACAGATGGCCTCTG	0.413																																					.		Atlas-SNP	.											.	RAB3C	47	.	0			c.25-1G>A						.						54	53	53					5																	57913469		2203	4300	6503	SO:0001630	splice_region_variant	115827	exon2			ATCACAGATGGCC	AY026936	CCDS3976.1	5q13	2008-02-05			ENSG00000152932	ENSG00000152932		"RAB, member RAS oncogene"	30269	protein-coding gene	gene with protein product		612829				12296628	Standard	NM_138453		Approved		uc003jrp.3	Q96E17	OTTHUMG00000097053	ENST00000282878.4:c.25-1G>A	chr5.hg19:g.57913469G>A		118.0	0.0		218.0	96.0	NM_138453		Splice_Site	SNP	ENST00000282878.4	hg19	CCDS3976.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.343801	0.82022	.	.	ENSG00000152932	ENST00000282878	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8247	0.96612	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RAB3C	57949226	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.476000	0.97823	2.696000	0.92011	0.655000	0.94253	.	.	.		0.413	RAB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214156.2	NM_138453	Intron	A	57913469	G	A	57913469	5	1	20	1	0	0	0	0	0	0	1	0	12948	956	33	3	30	3	RAB3C	5	57913469	Splice_Site	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	54312321	57913469	123001791	40	1767										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140432309	140432309	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cgggaggaggtctcaggctaTaatatcaccattgttgccat	11	9	2	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr5:140432309T>C	ENST00000306549.3	+	1	1331	c.1254T>C	c.(1252-1254)taT>taC	p.Y418Y		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	418	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCTCAGGCTATAATATCACCA	0.448																																					p.Y418Y		Atlas-SNP	.											.	PCDHB1	148	.	0			c.T1254C						.						102	100	100					5																	140432309		2203	4300	6503	SO:0001819	synonymous_variant	29930	exon1			AGGCTATAATATC	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1254T>C	chr5.hg19:g.140432309T>C		121.0	0.0		147.0	51.0	NM_013340	Q2M257	Silent	SNP	ENST00000306549.3	hg19	CCDS4243.1																																																																																			.	.		0.448	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		C	140432309	T	C	140432309	2	2	20	1	0	0	0	0	0	0	0	1	11543	1413	49	2		2	PCDHB1	5	140432309	Silent	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	82518840	140432309	40482951	41	1768										
SPINK5	11005	hgsc.bcm.edu	37	chr5	147505382	147505382	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gtgctgatggaaagttctatAcaaacaagtgctacatgtgc	10	7	1	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr5:147505382A>G	ENST00000256084.7	+	29	2878	c.2836A>G	c.(2836-2838)Aca>Gca	p.T946A	SPINK5_ENST00000359874.3_Missense_Mutation_p.T976A	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	946	Kazal-like 14. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAAGTTCTATACAAACAAGTG	0.448																																					p.T976A		Atlas-SNP	.											.	SPINK5	245	.	0			c.A2926G						.						256	249	251					5																	147505382		1924	4155	6079	SO:0001583	missense	11005	exon30			TTCTATACAAACA	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.2836A>G	chr5.hg19:g.147505382A>G	ENSP00000256084:p.Thr946Ala	111.0	0.0		161.0	77.0	NM_001127698	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	hg19	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	A	0.018	-1.473297	0.01044	.	.	ENSG00000133710	ENST00000359874;ENST00000256084	T;T	0.04156	3.69;3.69	5.37	2.68	0.31781	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.816530	0.10857	N	0.626518	T	0.01730	0.0055	N	0.01779	-0.725	0.09310	N	1	B;B	0.20988	0.05;0.018	B;B	0.26614	0.026;0.071	T	0.48768	-0.9006	10	0.07990	T	0.79	-7.4038	3.6044	0.08037	0.6191:0.2389:0.142:0.0	.	976;946	Q9NQ38-3;Q9NQ38	.;ISK5_HUMAN	A	976;946	ENSP00000352936:T976A;ENSP00000256084:T946A	ENSP00000256084:T946A	T	+	1	0	SPINK5	147485575	0.000000	0.05858	0.065000	0.19835	0.023000	0.10783	0.351000	0.20096	0.969000	0.38237	0.459000	0.35465	ACA	.	.		0.448	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		G	147505382	A	G	147505382	3	3	20	1	0	0	0	0	1	0	0	0	15077	391	14	2	3056	2	SPINK5	5	147505382	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	7073073	147505382	33409878	42	1769										
NMUR2	56923	hgsc.bcm.edu	37	chr5	151771871	151771871	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tgggaattggggacctatatCttcggtcagctccacaaagt	11	9	2	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr5:151771871C>G	ENST00000255262.3	-	4	1294	c.1129G>C	c.(1129-1131)Gat>Cat	p.D377H		NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	377					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			GGACCTATATCTTCGGTCAGC	0.502																																					p.D377H		Atlas-SNP	.											.	NMUR2	111	.	0			c.G1129C						.						160	151	154					5																	151771871		2203	4300	6503	SO:0001583	missense	56923	exon4			CTATATCTTCGGT	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.1129G>C	chr5.hg19:g.151771871C>G	ENSP00000255262:p.Asp377His	109.0	0.0		172.0	79.0	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	hg19	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.577213	0.28092	.	.	ENSG00000132911	ENST00000255262	T	0.71103	-0.54	4.37	4.37	0.52481	.	0.363145	0.19974	N	0.101914	T	0.78304	0.4262	M	0.62723	1.935	0.42957	D	0.99439	D	0.62365	0.991	P	0.55112	0.769	T	0.81593	-0.0862	10	0.66056	D	0.02	-13.8738	16.3623	0.83273	0.0:1.0:0.0:0.0	.	377	Q9GZQ4	NMUR2_HUMAN	H	377	ENSP00000255262:D377H	ENSP00000255262:D377H	D	-	1	0	NMUR2	151752064	0.995000	0.38212	0.865000	0.33974	0.033000	0.12548	0.797000	0.26999	2.376000	0.81061	0.467000	0.42956	GAT	.	.		0.502	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		G	151771871	C	G	151771871	3	3	20	1	0	0	0	0	1	0	0	0	10516	913	32	4	122	4	NMUR2	5	151771871	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	4266489	151771871	29143389	43	1770										
GABRA1	2554	hgsc.bcm.edu	37	chr5	161324165	161324166	+	Missense_Mutation	DNP	CC	CC	AA													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	agaaaaacaacacttacgctCcaacagcaaccagctacacc							TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr5:161324165_161324166CC>AA	ENST00000428797.2	+	11	1463_1464	c.1108_1109CC>AA	c.(1108-1110)CCa>AAa	p.P370K	GABRA1_ENST00000444819.1_Missense_Mutation_p.P370K|GABRA1_ENST00000023897.6_Missense_Mutation_p.P370K|GABRA1_ENST00000393943.4_Missense_Mutation_p.P370K|GABRA1_ENST00000420560.1_Missense_Mutation_p.P370K|GABRA1_ENST00000437025.2_Missense_Mutation_p.P370K	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	370					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	CACTTACGCTCCAACAGCAACC	0.436																																					p.P370T|p.P370Q		Atlas-SNP	.											.	GABRA1	132	.	0			c.C1108A|c.C1109A						.																																			SO:0001583	missense	2554	exon11			TACGCTCCAACAG|ACGCTCCAACAGC		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	Exception_encountered	chr5.hg19:g.161324165_161324166delinsAA	ENSP00000393097:p.Pro370Lys	181.0|184.0	0.0		234.0|238.0	116.0	NM_001127643	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	hg19	CCDS4357.1																																																																																			.	.		0.436	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		AA	161324166	CC	AA	161324165	3	1	20	1	0	0	0	0	1	0	0	0	6168	855	30	3	1142	3	GABRA1	5	161324165	Missense_Mutation	DNP	CC	TCGA-2Y-A9HA-01A-11D-A38X-10	9552294	161324165	19591095	44	1771										
ZNF354B	117608	hgsc.bcm.edu	37	chr5	178310514	178310514	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tcatctcagaaagaagtcctActtatgtaatgaatgtggca	8	7	2	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr5:178310514A>G	ENST00000322434.3	+	5	1287	c.1061A>G	c.(1060-1062)tAc>tGc	p.Y354C	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	354					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGAAGTCCTACTTATGTAAT	0.403																																					p.Y354C		Atlas-SNP	.											.	ZNF354B	67	.	0			c.A1061G						.						89	94	92					5																	178310514		2203	4300	6503	SO:0001583	missense	117608	exon5			AGTCCTACTTATG	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"Zinc fingers, C2H2-type", "-"	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.1061A>G	chr5.hg19:g.178310514A>G	ENSP00000327143:p.Tyr354Cys	241.0	1.0		347.0	152.0	NM_058230	A8K0V2|Q5U5Z4	Missense_Mutation	SNP	ENST00000322434.3	hg19	CCDS4439.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.031280	0.35797	.	.	ENSG00000178338	ENST00000322434	T	0.19938	2.11	3.62	0.984	0.19773	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15782	0.0380	L	0.51914	1.62	0.21386	N	0.9997	B	0.27229	0.172	B	0.14578	0.011	T	0.28267	-1.0049	9	0.87932	D	0	-2.1273	3.0338	0.06114	0.5323:0.0:0.1151:0.3525	.	354	Q96LW1	Z354B_HUMAN	C	354	ENSP00000327143:Y354C	ENSP00000327143:Y354C	Y	+	2	0	ZNF354B	178243120	0.035000	0.19736	0.996000	0.52242	0.985000	0.73830	1.168000	0.31859	0.479000	0.27511	0.459000	0.35465	TAC	.	.		0.403	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230		G	178310514	A	G	178310514	3	3	20	1	0	0	0	0	1	0	0	0	17880	391	14	2	1075	2	ZNF354B	5	178310514	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	16986349	178310514	2604746	45	1772										
C6orf145	221749	hgsc.bcm.edu	37	chr6	3751739	3751739	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	acgaacatgttcacgagcgaCgtgccctcaaacaccgccga	9	15	2	0	rs369797402		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr6:3751739C>A	ENST00000380283.4	-	1	521	c.27G>T	c.(25-27)acG>acT	p.T9T	RP11-420L9.5_ENST00000603791.1_RNA|PXDC1_ENST00000477592.2_5'UTR	NM_183373.3	NP_899229.2	Q5TGL8	PXDC1_HUMAN	PX domain containing 1	9	PX.						phosphatidylinositol binding (GO:0035091)										TCACGAGCGACGTGCCCTCAA	0.726																																					p.T9T		Atlas-SNP	.											.	.	.	.	0			c.G27T						.						14	13	14					6																	3751739		2186	4277	6463	SO:0001819	synonymous_variant	221749	exon1			GAGCGACGTGCCC	AJ420534	CCDS4486.1	6p25.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000168994	ENSG00000168994			21361	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 145"	C6orf145			Standard	NM_183373		Approved		uc003mvt.2	Q5TGL8	OTTHUMG00000014146	ENST00000380283.4:c.27G>T	chr6.hg19:g.3751739C>A		126.0	0.0		108.0	43.0	NM_183373	A8K0N3|Q6PGP0|Q86XB7	Silent	SNP	ENST00000380283.4	hg19	CCDS4486.1																																																																																			.	.		0.726	PXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039688.1	NM_183373		A	3751739	C	A	3751739	2	1	20	1	0	0	0	0	0	0	0	1	2336	523	19	1		1	C6orf145	6	3751739	Silent	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10		3751739	167363328	46	1773										
BMP6	654	hgsc.bcm.edu	37	chr6	7845445	7845445	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gttcaacttatcccagattcCtgagggtgaggtggtgacgg	14	8	1	4			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr6:7845445C>T	ENST00000283147.6	+	2	896	c.737C>T	c.(736-738)cCt>cTt	p.P246L		NM_001718.4	NP_001709.1	P22004	BMP6_HUMAN	bone morphogenetic protein 6	246					BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular response to mechanical stimulus (GO:0071260)|endochondral ossification (GO:0001958)|eye development (GO:0001654)|growth (GO:0040007)|immune response (GO:0006955)|inflammatory response (GO:0006954)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|osteoblast differentiation (GO:0001649)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of bone mineralization (GO:0030501)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to activity (GO:0014823)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to retinoic acid (GO:0032526)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|type B pancreatic cell development (GO:0003323)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)|protein heterodimerization activity (GO:0046982)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	23	Ovarian(93;0.0721)					TCCCAGATTCCTGAGGGTGAG	0.438																																					p.P246L		Atlas-SNP	.											.	BMP6	67	.	0			c.C737T						.						125	124	124					6																	7845445		2203	4300	6503	SO:0001583	missense	654	exon2			AGATTCCTGAGGG	AF083030	CCDS4503.1	6p24-p23	2014-01-30	2003-10-06		ENSG00000153162	ENSG00000153162		"Bone morphogenetic proteins", "Endogenous ligands"	1073	protein-coding gene	gene with protein product		112266	"vegetal related growth factor (TGFB-related)"	VGR		1427904, 1453478	Standard	NM_001718		Approved	VGR1	uc003mxu.4	P22004	OTTHUMG00000014217	ENST00000283147.6:c.737C>T	chr6.hg19:g.7845445C>T	ENSP00000283147:p.Pro246Leu	130.0	0.0		189.0	8.0	NM_001718	Q5TCP3	Missense_Mutation	SNP	ENST00000283147.6	hg19	CCDS4503.1	.	.	.	.	.	.	.	.	.	.	C	31	5.071294	0.93950	.	.	ENSG00000153162	ENST00000537240;ENST00000283147;ENST00000540959	T	0.70516	-0.49	5.41	5.41	0.78517	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83514	0.5271	M	0.80028	2.48	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85507	0.1195	10	0.87932	D	0	.	19.1986	0.93699	0.0:1.0:0.0:0.0	.	246	P22004	BMP6_HUMAN	L	168;246;209	ENSP00000283147:P246L	ENSP00000283147:P246L	P	+	2	0	BMP6	7790444	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.302000	0.78861	2.528000	0.85240	0.557000	0.71058	CCT	.	.		0.438	BMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039794.1	NM_001718		T	7845445	C	T	7845445	3	4	20	1	0	0	0	0	1	0	0	0	1464	681	24	3	743	3	BMP6	6	7845445	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	4093706	7845445	163269622	47	1774										
EEF1E1	9521	hgsc.bcm.edu	37	chr6	8090503	8090503	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tagactttatcttcaagataTgaattaagatcctagaaaaa	5	5	2	5			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr6:8090503T>C	ENST00000379715.5	-	3	356	c.300A>G	c.(298-300)tcA>tcG	p.S100S	EEF1E1_ENST00000507463.1_Silent_p.S100S|EEF1E1-BLOC1S5_ENST00000397456.2_Silent_p.S100S|EEF1E1_ENST00000429723.2_Silent_p.S100S	NM_004280.4	NP_004271.1	O43324	MCA3_HUMAN	eukaryotic translation elongation factor 1 epsilon 1	100	C-terminal.|GST C-terminal.				gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				endometrium(1)|prostate(1)	2	Ovarian(93;0.0398)					CTTCAAGATATGAATTAAGAT	0.249																																					p.S100S		Atlas-SNP	.											.	EEF1E1	11	.	0			c.A300G						.						46	46	46					6																	8090503		2192	4284	6476	SO:0001819	synonymous_variant	9521	exon3			AAGATATGAATTA	AF054186	CCDS4507.1, CCDS47370.1	6p24.3	2009-05-20			ENSG00000124802	ENSG00000124802			3212	protein-coding gene	gene with protein product	"aminoacyl tRNA synthetase complex-interacting multifunctional protein 3"	609206		P18		9653160	Standard	NM_004280		Approved	AIMP3	uc003mxz.3	O43324	OTTHUMG00000014221	ENST00000379715.5:c.300A>G	chr6.hg19:g.8090503T>C		145.0	0.0		222.0	92.0	NM_001135650	C9JLK5|Q5THS2	Silent	SNP	ENST00000379715.5	hg19	CCDS4507.1	.	.	.	.	.	.	.	.	.	.	T	8.223	0.802981	0.16397	.	.	ENSG00000124802	ENST00000502429	.	.	.	4.82	-9.65	0.00537	.	.	.	.	.	T	0.09555	0.0235	.	.	.	0.33570	D	0.598482	.	.	.	.	.	.	T	0.05920	-1.0856	4	.	.	.	-3.2086	0.7347	0.00963	0.3725:0.2543:0.1968:0.1763	.	.	.	.	R	87	.	.	H	-	2	0	EEF1E1	8035502	0.000000	0.05858	0.818000	0.32626	0.945000	0.59286	-2.866000	0.00723	-1.935000	0.01049	0.379000	0.24179	CAT	.	.		0.249	EEF1E1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039799.2	NM_004280		C	8090503	T	C	8090503	2	2	20	1	0	0	0	0	0	0	0	1	4929	1451	51	2		2	EEF1E1	6	8090503	Silent	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	245058	8090503	163024564	48	1775										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32166815	32166815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gagagctccatgctctcggcGtcgacgccggatgagctgga	15	12	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr6:32166815G>A	ENST00000375023.3	-	24	4561	c.4423C>T	c.(4423-4425)Cgc>Tgc	p.R1475C	NOTCH4_ENST00000443903.2_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1475	Poly-Arg.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TGCTCTCGGCGTCGACGCCGG	0.677																																					p.R1475C		Atlas-SNP	.											.	NOTCH4	201	.	0			c.C4423T						.						52	66	61					6																	32166815		1508	2707	4215	SO:0001583	missense	4855	exon24			CTCGGCGTCGACG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.4423C>T	chr6.hg19:g.32166815G>A	ENSP00000364163:p.Arg1475Cys	168.0	0.0		178.0	68.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.651320	0.47362	.	.	ENSG00000204301	ENST00000375023	D	0.84070	-1.8	4.9	4.02	0.46733	.	0.000000	0.44097	D	0.000483	D	0.88115	0.6350	M	0.77486	2.375	0.80722	D	1	P;D	0.89917	0.553;1.0	B;D	0.83275	0.069;0.996	D	0.89834	0.3998	10	0.87932	D	0	.	12.6217	0.56607	0.0:0.0:0.833:0.167	.	1475;1474	Q99466;B0S882	NOTC4_HUMAN;.	C	1475	ENSP00000364163:R1475C	ENSP00000364163:R1475C	R	-	1	0	NOTCH4	32274793	0.847000	0.29606	0.144000	0.22314	0.130000	0.20726	2.251000	0.43187	1.405000	0.46838	-0.324000	0.08512	CGC	.	.		0.677	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32166815	G	A	32166815	3	1	20	1	0	0	0	0	1	0	0	0	10560	1145	40	1	1616	1	NOTCH4	6	32166815	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	24076312	32166815	138948252	49	1776										
TBCC	6903	hgsc.bcm.edu	37	chr6	42713787	42713787	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gtctccggtcctgacagcagCagcggagcaactgacggact	13	13	1	2	rs555582056		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr6:42713787C>A	ENST00000372876.1	-	1	47	c.25G>T	c.(25-27)Gct>Tct	p.A9S	TBCC_ENST00000244625.2_Missense_Mutation_p.A9S	NM_003192.2	NP_003183	Q15814	TBCC_HUMAN	tubulin folding cofactor C	9					'de novo' posttranslational protein folding (GO:0051084)|cell morphogenesis (GO:0000902)|cellular protein metabolic process (GO:0044267)|GTP catabolic process (GO:0006184)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)	chaperone binding (GO:0051087)|GTPase activity (GO:0003924)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(3)	14	Colorectal(47;0.196)		all cancers(41;0.00122)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.125)			CTGACAGCAGCAGCGGAGCAA	0.612																																					p.A9S		Atlas-SNP	.											.	TBCC	31	.	0			c.G25T						.						48	49	48					6																	42713787		2203	4300	6503	SO:0001583	missense	6903	exon1			CAGCAGCAGCGGA	U61234	CCDS4872.1	6p21.1	2008-02-05	2006-11-21		ENSG00000124659	ENSG00000124659			11580	protein-coding gene	gene with protein product		602971	"tubulin-specific chaperone c"			8706133, 11847227	Standard	NM_003192		Approved	CFC	uc003osl.3	Q15814	OTTHUMG00000014704	ENST00000372876.1:c.25G>T	chr6.hg19:g.42713787C>A	ENSP00000361967:p.Ala9Ser	108.0	0.0		85.0	20.0	NM_003192	Q53Y43|Q5T787	Missense_Mutation	SNP	ENST00000372876.1	hg19	CCDS4872.1	.	.	.	.	.	.	.	.	.	.	C	6.498	0.460051	0.12342	.	.	ENSG00000124659	ENST00000372876;ENST00000244625	T;T	0.15139	2.45;2.45	5.04	3.26	0.37387	.	1.119980	0.06952	U	0.814750	T	0.07638	0.0192	L	0.57536	1.79	0.09310	N	1	B	0.27823	0.19	B	0.27608	0.081	T	0.42396	-0.9454	10	0.25106	T	0.35	-2.0378	10.9818	0.47499	0.0:0.8433:0.0:0.1567	.	9	Q15814	TBCC_HUMAN	S	9	ENSP00000361967:A9S;ENSP00000244625:A9S	ENSP00000244625:A9S	A	-	1	0	TBCC	42821765	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.058000	0.14301	0.641000	0.30601	0.563000	0.77884	GCT	.	.		0.612	TBCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040559.1	NM_003192		A	42713787	C	A	42713787	3	1	20	1	0	0	0	0	1	0	0	0	15646	710	25	3	1019	3	TBCC	6	42713787	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	10546972	42713787	128401280	50	1777										
HSP90AB1	3326	hgsc.bcm.edu	37	chr6	44218166	44218166	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	atgaggaggatgacagcggtAaggataagaagaagaaaact	14	3	0	5			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr6:44218166A>G	ENST00000371554.1	+	6	1001	c.787A>G	c.(787-789)Aag>Gag	p.K263E	HSP90AB1_ENST00000353801.3_Missense_Mutation_p.K263E|HSP90AB1_ENST00000371646.5_Missense_Mutation_p.K263E			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	263					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			tgacagcggtaaggataagaa	0.403																																					p.K263E		Atlas-SNP	.											.	HSP90AB1	83	.	0			c.A787G						.						61	58	59					6																	44218166		2203	4300	6503	SO:0001583	missense	3326	exon6			AGCGGTAAGGATA	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"Heat shock proteins / HSPC"	5258	protein-coding gene	gene with protein product		140572	"heat shock 90kD protein 1, beta", "heat shock 90kDa protein 1, beta"	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.787A>G	chr6.hg19:g.44218166A>G	ENSP00000360609:p.Lys263Glu	263.0	0.0		255.0	84.0	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Missense_Mutation	SNP	ENST00000371554.1	hg19	CCDS4909.1	.	.	.	.	.	.	.	.	.	.	A	11.46	1.644627	0.29246	.	.	ENSG00000096384	ENST00000371646;ENST00000353801;ENST00000371554	T;T;T	0.07908	3.15;3.15;3.15	4.41	4.41	0.53225	.	0.395534	0.21317	U	0.076531	T	0.08447	0.0210	L	0.35288	1.05	0.80722	D	1	B;D;B	0.57257	0.0;0.979;0.0	B;D;B	0.71414	0.003;0.973;0.001	T	0.37337	-0.9710	10	0.15066	T	0.55	-16.4717	13.3386	0.60533	1.0:0.0:0.0:0.0	.	225;253;263	B4DMA2;B4DGL0;P08238	.;.;HS90B_HUMAN	E	263	ENSP00000360709:K263E;ENSP00000325875:K263E;ENSP00000360609:K263E	ENSP00000325875:K263E	K	+	1	0	HSP90AB1	44326144	1.000000	0.71417	0.352000	0.25734	0.523000	0.34469	5.694000	0.68272	1.643000	0.50594	0.377000	0.23210	AAG	.	.		0.403	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355		G	44218166	A	G	44218166	3	3	20	1	0	0	0	0	1	0	0	0	7411	363	13	2	805	2	HSP90AB1	6	44218166	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	1504379	44218166	126896901	51	1778										
TDRD6	221400	hgsc.bcm.edu	37	chr6	46656123	46656123	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ttgtggcaccgctgccgcgtGgtcagccggcaggcacagga	16	13	1	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr6:46656123G>T	ENST00000316081.6	+	1	258	c.258G>T	c.(256-258)gtG>gtT	p.V86V	TDRD6_ENST00000544460.1_Silent_p.V86V|RP11-446F17.3_ENST00000434329.2_RNA|RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000422284.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	86	Tudor 1. {ECO:0000255|PROSITE- ProRule:PRU00211}.				germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			GCTGCCGCGTGGTCAGCCGGC	0.741																																					p.V86V		Atlas-SNP	.											.	TDRD6	205	.	0			c.G258T						.						5	7	6					6																	46656123		1961	3850	5811	SO:0001819	synonymous_variant	221400	exon1			CCGCGTGGTCAGC	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.258G>T	chr6.hg19:g.46656123G>T		54.0	0.0		76.0	30.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Silent	SNP	ENST00000316081.6	hg19	CCDS34470.1																																																																																			.	.		0.741	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		T	46656123	G	T	46656123	2	4	20	1	0	0	0	0	0	0	0	1	15749	1335	47	3		3	TDRD6	6	46656123	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	2437957	46656123	124458944	52	1779										
DEFB113	245927	hgsc.bcm.edu	37	chr6	49936539	49936539	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	accacgaacaagctgacattCtctttttctctctgcaactt	4	13	3	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr6:49936539C>A	ENST00000398718.1	-	2	99	c.100G>T	c.(100-102)Gaa>Taa	p.E34*		NM_001037729.1	NP_001032818.1	Q30KQ7	DB113_HUMAN	defensin, beta 113	34					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Lung NSC(77;0.042)					AGCTGACATTCTCTTTTTCTC	0.398																																					p.E34X		Atlas-SNP	.											.	DEFB113	18	.	0			c.G100T						.						108	104	106					6																	49936539		1883	4100	5983	SO:0001587	stop_gained	245927	exon2			GACATTCTCTTTT	DQ012017	CCDS43472.1	6p12.3	2010-03-30			ENSG00000214642	ENSG00000214642		"Defensins, beta"	18094	protein-coding gene	gene with protein product						11854508, 16033865	Standard	NM_001037729		Approved	DEFB-13	uc011dwq.2	Q30KQ7	OTTHUMG00000160210	ENST00000398718.1:c.100G>T	chr6.hg19:g.49936539C>A	ENSP00000381703:p.Glu34*	39.0	0.0		88.0	34.0	NM_001037729		Nonsense_Mutation	SNP	ENST00000398718.1	hg19	CCDS43472.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.412861	0.25465	.	.	ENSG00000214642	ENST00000398718	.	.	.	4.15	0.0686	0.14370	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-9.5634	4.9287	0.13907	0.0:0.4178:0.3875:0.1947	.	.	.	.	X	34	.	.	E	-	1	0	DEFB113	50044498	0.074000	0.21230	0.369000	0.25952	0.287000	0.27160	-0.023000	0.12456	-0.109000	0.12044	0.557000	0.71058	GAA	.	.		0.398	DEFB113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359666.1			A	49936539	C	A	49936539	4	1	20	1	0	0	0	0	0	1	0	0	4404	922	32	3	144	3	DEFB113	6	49936539	Nonsense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	3280416	49936539	121178528	53	1780										
AKD1	221264	hgsc.bcm.edu	37	chr6	109867191	109867191	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	attcaggtcccactttctttTcagttttgagtagtagtttt	7	7	3	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr6:109867191T>A	ENST00000424296.2	-	26	3180	c.3104A>T	c.(3103-3105)gAa>gTa	p.E1035V	AK9_ENST00000355283.1_Missense_Mutation_p.E114V|AK9_ENST00000341338.6_Missense_Mutation_p.E114V	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1035	Adenylate kinase 2.|NMPbind 2. {ECO:0000250}.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										CACTTTCTTTTCAGTTTTGAG	0.378																																					p.E1035V		Atlas-SNP	.											.	AKD1	223	.	0			c.A3104T						.						98	98	98					6																	109867191		2203	4300	6503	SO:0001583	missense	221264	exon26			TTCTTTTCAGTTT	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"chromosome 6 open reading frame 224", "adenylate kinase domain containing 2", "chromosome 6 open reading frame 199", "adenylate kinase domain containing 1"	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.3104A>T	chr6.hg19:g.109867191T>A	ENSP00000410186:p.Glu1035Val	171.0	0.0		259.0	122.0	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	hg19	CCDS55048.1	.	.	.	.	.	.	.	.	.	.	T	13.64	2.296198	0.40594	.	.	ENSG00000155085	ENST00000424296;ENST00000355283;ENST00000341338	T;T;T	0.66815	-0.23;0.87;0.87	5.32	2.94	0.34122	ATPase, AAA+ type, core (1);	0.196192	0.46758	D	0.000276	T	0.55513	0.1925	M	0.74389	2.26	0.25945	N	0.982822	P;D	0.54397	0.589;0.966	B;P	0.49012	0.229;0.598	T	0.52328	-0.8590	9	.	.	.	.	8.7351	0.34523	0.0:0.2175:0.0:0.7825	.	114;1035	Q5TCS8-5;Q5TCS8	.;AKD1_HUMAN	V	1035;114;114	ENSP00000410186:E1035V;ENSP00000347431:E114V;ENSP00000344637:E114V	.	E	-	2	0	AKD1	109973884	0.991000	0.36638	0.543000	0.28128	0.821000	0.46438	2.004000	0.40854	0.433000	0.26313	-0.379000	0.06801	GAA	.	.		0.378	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		A	109867191	T	A	109867191	3	1	20	1	0	0	0	0	1	0	0	0	460	1783	62	4	2695	4	AKD1	6	109867191	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	59930652	109867191	61247876	54	1781										
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117113979	117113979	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gaagataataaggatcggtcTatagaggcacttcagaaatt	10	5	2	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr6:117113979T>C	ENST00000310357.3	-	6	2128	c.2107A>G	c.(2107-2109)Aga>Gga	p.R703G	GPRC6A_ENST00000368549.3_Missense_Mutation_p.R632G|GPRC6A_ENST00000530250.1_Missense_Mutation_p.R528G	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	703					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		AGGATCGGTCTATAGAGGCAC	0.423																																					p.R703G		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A2107G						.						76	73	74					6																	117113979		2203	4300	6503	SO:0001583	missense	222545	exon6			TCGGTCTATAGAG	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2107A>G	chr6.hg19:g.117113979T>C	ENSP00000309493:p.Arg703Gly	120.0	0.0		225.0	119.0	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	hg19	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	T	5.391	0.257404	0.10239	.	.	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.87491	-2.26;-2.26;-2.26	4.61	4.61	0.57282	GPCR, family 3, C-terminal (2);	0.203142	0.34002	N	0.004347	T	0.55940	0.1952	N	0.04116	-0.275	0.24901	N	0.992108	B;B;B	0.19200	0.0;0.027;0.034	B;B;B	0.20577	0.004;0.018;0.03	T	0.42155	-0.9468	10	0.15952	T	0.53	.	14.16	0.65441	0.0:0.0:0.0:1.0	.	632;528;703	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	G	703;632;528	ENSP00000309493:R703G;ENSP00000357537:R632G;ENSP00000433465:R528G	ENSP00000309493:R703G	R	-	1	2	GPRC6A	117220672	1.000000	0.71417	0.937000	0.37676	0.040000	0.13550	2.355000	0.44107	1.933000	0.56026	0.482000	0.46254	AGA	.	.		0.423	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			C	117113979	T	C	117113979	3	2	20	1	0	0	0	0	1	0	0	0	6737	1530	53	2	677	2	GPRC6A	6	117113979	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	7246788	117113979	54001088	55	1782										
MAD1L1	8379	hgsc.bcm.edu	37	chr7	1997344	1997344	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ccgctcgccttccagctcctCgaccttcaacctgcaaggac	7	19	1	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr7:1997344C>T	ENST00000406869.1	-	16	2073	c.1516G>A	c.(1516-1518)Gag>Aag	p.E506K	MAD1L1_ENST00000265854.7_Missense_Mutation_p.E506K|MAD1L1_ENST00000399654.2_Missense_Mutation_p.E506K|MAD1L1_ENST00000402746.1_Missense_Mutation_p.E414K			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	506	Necessary for interaction with NEK2.				mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		TCCAGCTCCTCGACCTTCAAC	0.627																																					p.E506K		Atlas-SNP	.											.	MAD1L1	81	.	0			c.G1516A						.						50	57	55					7																	1997344		2132	4233	6365	SO:0001583	missense	8379	exon16			GCTCCTCGACCTT	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.1516G>A	chr7.hg19:g.1997344C>T	ENSP00000385334:p.Glu506Lys	132.0	0.0		95.0	40.0	NM_003550	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	hg19	CCDS43539.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.629487	0.67015	.	.	ENSG00000002822	ENST00000402746;ENST00000399654;ENST00000406869;ENST00000442131;ENST00000265854;ENST00000450235;ENST00000438959	T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.42471	0.1204	M	0.64260	1.97	0.52099	D	0.999945	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.988;0.988	T	0.15549	-1.0433	10	0.21014	T	0.42	-34.5149	16.9161	0.86152	0.0:1.0:0.0:0.0	.	505;414;506	A4D218;B3KR41;Q9Y6D9	.;.;MD1L1_HUMAN	K	414;506;506;57;506;57;173	ENSP00000384155:E414K;ENSP00000382562:E506K;ENSP00000385334:E506K;ENSP00000265854:E506K;ENSP00000394886:E57K;ENSP00000414877:E173K	ENSP00000265854:E506K	E	-	1	0	MAD1L1	1963870	1.000000	0.71417	0.921000	0.36526	0.031000	0.12232	5.065000	0.64344	2.209000	0.71365	0.462000	0.41574	GAG	.	.		0.627	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		T	1997344	C	T	1997344	3	4	20	1	0	0	0	0	1	0	0	0	9156	893	31	1	656	1	MAD1L1	7	1997344	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10		1997344	157141319	56	1783										
NFE2L3	9603	hgsc.bcm.edu	37	chr7	26224374	26224374	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	aattctcataccaccaatccTgagcaaacccttcctggaac	4	15	1	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr7:26224374T>G	ENST00000056233.3	+	4	1315	c.1056T>G	c.(1054-1056)ccT>ccG	p.P352P		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	352					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						CCACCAATCCTGAGCAAACCC	0.408																																					p.P352P		Atlas-SNP	.											.	NFE2L3	77	.	0			c.T1056G						.						93	87	89					7																	26224374		2203	4300	6503	SO:0001819	synonymous_variant	9603	exon4			CAATCCTGAGCAA	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1056T>G	chr7.hg19:g.26224374T>G		164.0	0.0		230.0	104.0	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Silent	SNP	ENST00000056233.3	hg19	CCDS5396.1																																																																																			.	.		0.408	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			G	26224374	T	G	26224374	2	3	20	1	0	0	0	0	0	0	0	1	10378	1567	55	5		5	NFE2L3	7	26224374	Silent	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	24227030	26224374	132914289	57	1784										
PCLO	27445	hgsc.bcm.edu	37	chr7	82764194	82764194	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gctttggggactgttgaggtGtggggacagtttggccagcg	19	6	0	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr7:82764194G>T	ENST00000333891.9	-	3	3009	c.2672C>A	c.(2671-2673)aCa>aAa	p.T891K	PCLO_ENST00000423517.2_Missense_Mutation_p.T891K	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTGTTGAGGTGTGGGGACAGT	0.532																																					p.T891K		Atlas-SNP	.											.	PCLO	1506	.	0			c.C2672A						.						197	196	196					7																	82764194		1988	4162	6150	SO:0001583	missense	27445	exon3			TGAGGTGTGGGGA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.2672C>A	chr7.hg19:g.82764194G>T	ENSP00000334319:p.Thr891Lys	126.0	0.0		134.0	54.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	8.810	0.934925	0.18206	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.15017	2.46;2.46	6.07	-2.2	0.06994	.	.	.	.	.	T	0.08935	0.0221	N	0.22421	0.69	0.09310	N	1	B;B	0.20988	0.05;0.05	B;B	0.18871	0.023;0.023	T	0.36237	-0.9756	9	0.87932	D	0	.	1.5701	0.02613	0.3412:0.0892:0.3372:0.2324	.	891;891	Q9Y6V0-5;Q9Y6V0-6	.;.	K	837;891;891	ENSP00000334319:T891K;ENSP00000388393:T891K	ENSP00000334319:T891K	T	-	2	0	PCLO	82602130	0.000000	0.05858	0.001000	0.08648	0.845000	0.48019	-0.282000	0.08445	-0.082000	0.12640	0.655000	0.94253	ACA	.	.		0.532	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82764194	G	T	82764194	3	4	20	1	0	0	0	0	1	0	0	0	11592	1377	48	3	12865	3	PCLO	7	82764194	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	56539820	82764194	76374469	58	1785										
STEAP2	261729	hgsc.bcm.edu	37	chr7	89856657	89856657	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tttattacggcaccaagtatAggagatttccaccttggttg	9	8	0	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr7:89856657A>T	ENST00000287908.3	+	3	1258	c.865A>T	c.(865-867)Agg>Tgg	p.R289W	STEAP2_ENST00000394621.2_Missense_Mutation_p.R289W|STEAP2_ENST00000394626.1_Missense_Mutation_p.R289W|STEAP2_ENST00000394622.2_Missense_Mutation_p.R289W|STEAP2_ENST00000402625.2_Missense_Mutation_p.R289W|STEAP2_ENST00000394629.2_Missense_Mutation_p.R289W|STEAP2_ENST00000394632.1_Missense_Mutation_p.R289W	NM_001244944.1|NM_152999.3	NP_001231873.1|NP_694544.2	Q8NFT2	STEA2_HUMAN	STEAP family member 2, metalloreductase	289	Ferric oxidoreductase.				copper ion import (GO:0015677)|endocytosis (GO:0006897)|ferric iron import into cell (GO:0097461)|Golgi to plasma membrane transport (GO:0006893)|iron ion homeostasis (GO:0055072)|regulated secretory pathway (GO:0045055)|response to hormone (GO:0009725)	cytosol (GO:0005829)|early endosome (GO:0005769)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15	all_hematologic(106;0.112)					CACCAAGTATAGGAGATTTCC	0.428																																					p.R289W		Atlas-SNP	.											.	STEAP2	78	.	0			c.A865T						.						87	86	87					7																	89856657		2203	4300	6503	SO:0001583	missense	261729	exon4			AAGTATAGGAGAT	AF455138	CCDS5615.1, CCDS43612.1, CCDS59064.1	7q21.13	2011-09-30	2011-09-30		ENSG00000157214	ENSG00000157214			17885	protein-coding gene	gene with protein product		605094	"prostate cancer associated protein 1", "six transmembrane epithelial antigen of the prostate 2"	PCANAP1		10613842, 12095985	Standard	NM_001040665		Approved	IPCA-1, STAMP1, STMP	uc003ujz.3	Q8NFT2	OTTHUMG00000023341	ENST00000287908.3:c.865A>T	chr7.hg19:g.89856657A>T	ENSP00000287908:p.Arg289Trp	107.0	0.0		154.0	56.0	NM_001244946	A4D1F1|G5E9C6|Q6UXN6|Q6YPB1|Q8IUE7	Missense_Mutation	SNP	ENST00000287908.3	hg19	CCDS5615.1	.	.	.	.	.	.	.	.	.	.	A	19.63	3.864351	0.71949	.	.	ENSG00000157214	ENST00000287908;ENST00000394626;ENST00000394622;ENST00000394632;ENST00000394624;ENST00000394621;ENST00000402625;ENST00000394629	D;D;D;D;D;D;D	0.91180	-2.8;-2.8;-2.8;-2.8;-2.8;-2.8;-2.8	6.04	3.47	0.39725	Flavoprotein transmembrane component (1);	0.043679	0.85682	D	0.000000	D	0.93861	0.8036	M	0.72118	2.19	0.44547	D	0.997508	D;D;D;D	0.67145	0.996;0.994;0.986;0.986	D;D;D;P	0.68039	0.925;0.955;0.928;0.895	D	0.93354	0.6721	9	.	.	.	-12.1991	13.9666	0.64213	0.5677:0.4323:0.0:0.0	.	289;289;289;289	G5E9C6;Q6YPB2;Q8NFT2;B5MC02	.;.;STEA2_HUMAN;.	W	289	ENSP00000287908:R289W;ENSP00000378123:R289W;ENSP00000378120:R289W;ENSP00000378128:R289W;ENSP00000378119:R289W;ENSP00000384191:R289W;ENSP00000378125:R289W	.	R	+	1	2	STEAP2	89694593	0.999000	0.42202	1.000000	0.80357	0.945000	0.59286	2.588000	0.46137	1.021000	0.39600	0.460000	0.39030	AGG	.	.		0.428	STEAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059662.4	NM_152999		T	89856657	A	T	89856657	3	4	20	1	0	0	0	0	1	0	0	0	15293	411	15	4	871	4	STEAP2	7	89856657	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	7092463	89856657	69282006	59	1786										
PEX1	5189	hgsc.bcm.edu	37	chr7	92134134	92134134	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gcaatgaggtcaaggtcatcCagcaggacaacagatggctg	13	9	2	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr7:92134134C>G	ENST00000248633.4	-	12	2078	c.1983G>C	c.(1981-1983)ctG>ctC	p.L661L	PEX1_ENST00000541751.1_Silent_p.L78L|PEX1_ENST00000428214.1_Intron|PEX1_ENST00000438045.1_Silent_p.L339L	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	661			Missing (in PBD1A and PBD1B). {ECO:0000269|PubMed:9539740}.		ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			CAAGGTCATCCAGCAGGACAA	0.502																																					p.L661L		Atlas-SNP	.											.	PEX1	102	.	0			c.G1983C						.						180	166	171					7																	92134134		2203	4300	6503	SO:0001819	synonymous_variant	5189	exon12			GTCATCCAGCAGG	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.1983G>C	chr7.hg19:g.92134134C>G		66.0	0.0		65.0	27.0	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	hg19	CCDS5627.1																																																																																			.	.		0.502	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		G	92134134	C	G	92134134	2	3	20	1	0	0	0	0	0	0	0	1	11744	581	21	4		4	PEX1	7	92134134	Silent	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	2277477	92134134	67004529	60	1787										
ZNF394	84124	hgsc.bcm.edu	37	chr7	99096409	99096409	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tccctccgtgctgggtccagGcgctcccactcctcccaggt	10	19	0	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr7:99096409G>A	ENST00000337673.6	-	2	716	c.513C>T	c.(511-513)cgC>cgT	p.R171R	ZNF394_ENST00000426306.2_Intron|ZNF789_ENST00000493485.1_Intron|ZNF394_ENST00000394177.3_5'UTR|ZNF789_ENST00000494186.1_Intron	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	171	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					CTGGGTCCAGGCGCTCCCACT	0.582																																					p.R171R	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											.	ZNF394	48	.	0			c.C513T						.						116	90	98					7																	99096409		2203	4300	6503	SO:0001819	synonymous_variant	84124	exon2			GTCCAGGCGCTCC	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"Zinc fingers, C2H2-type", "-", "-", "-"	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.513C>T	chr7.hg19:g.99096409G>A		76.0	0.0		86.0	38.0	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Silent	SNP	ENST00000337673.6	hg19	CCDS5666.1																																																																																			.	.		0.582	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164		A	99096409	G	A	99096409	2	1	20	1	0	0	0	0	0	0	0	1	17895	1190	42	3		3	ZNF394	7	99096409	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	6962275	99096409	60042254	61	1788										
RELN	5649	hgsc.bcm.edu	37	chr7	103363632	103363632	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tgttgttgtattaaggcctgTggtaatctaaagaaaaaaga	10	3	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr7:103363632T>C	ENST00000428762.1	-	8	919	c.760A>G	c.(760-762)Aca>Gca	p.T254A	RELN_ENST00000424685.2_Missense_Mutation_p.T254A|RELN_ENST00000343529.5_Missense_Mutation_p.T254A	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	254					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TTAAGGCCTGTGGTAATCTAA	0.363																																					p.T254A	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A760G						.						74	74	74					7																	103363632		2203	4300	6503	SO:0001583	missense	5649	exon8			GGCCTGTGGTAAT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.760A>G	chr7.hg19:g.103363632T>C	ENSP00000392423:p.Thr254Ala	208.0	0.0		218.0	68.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	T	9.169	1.020621	0.19433	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.21734	1.99;1.99;1.99	5.38	4.21	0.49690	.	0.246949	0.41938	D	0.000795	T	0.14141	0.0342	L	0.29908	0.895	0.23282	N	0.997989	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.11842	-1.0571	10	0.30854	T	0.27	.	8.9933	0.36037	0.0:0.149:0.0:0.851	.	254;254	P78509-2;P78509	.;RELN_HUMAN	A	254	ENSP00000392423:T254A;ENSP00000345694:T254A;ENSP00000388446:T254A	ENSP00000345694:T254A	T	-	1	0	RELN	103150868	0.995000	0.38212	0.997000	0.53966	0.981000	0.71138	1.097000	0.30988	2.155000	0.67459	0.482000	0.46254	ACA	.	.		0.363	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103363632	T	C	103363632	3	2	20	1	0	0	0	0	1	0	0	0	13235	1696	59	2	9854	2	RELN	7	103363632	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	4267223	103363632	55775031	62	1789										
HBP1	26959	hgsc.bcm.edu	37	chr7	106822886	106822886	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gcatgtaccagctgagttcaGatgtttcacatcaagaatac	8	9	3	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr7:106822886G>A	ENST00000222574.4	+	3	424	c.238G>A	c.(238-240)Gat>Aat	p.D80N	HBP1_ENST00000485846.1_Missense_Mutation_p.D80N|HBP1_ENST00000468410.1_Missense_Mutation_p.D80N	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	80					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						GCTGAGTTCAGATGTTTCACA	0.413																																					p.D90N		Atlas-SNP	.											.	HBP1	31	.	0			c.G268A						.						106	93	98					7																	106822886		2203	4300	6503	SO:0001583	missense	26959	exon3			AGTTCAGATGTTT	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.238G>A	chr7.hg19:g.106822886G>A	ENSP00000222574:p.Asp80Asn	113.0	0.0		118.0	12.0	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Missense_Mutation	SNP	ENST00000222574.4	hg19	CCDS5741.1	.	.	.	.	.	.	.	.	.	.	G	19.53	3.845485	0.71603	.	.	ENSG00000105856	ENST00000468410;ENST00000464009;ENST00000222574;ENST00000497535;ENST00000485846;ENST00000479011;ENST00000498408	D;D;D	0.99167	-5.51;-5.51;-5.51	5.85	5.85	0.93711	.	0.093671	0.85682	D	0.000000	D	0.96580	0.8884	N	0.24115	0.695	0.43408	D	0.995548	B;P;P	0.38504	0.281;0.634;0.501	B;B;B	0.34242	0.027;0.178;0.086	D	0.96833	0.9612	10	0.66056	D	0.02	-5.9031	16.4237	0.83790	0.0:0.1313:0.8687:0.0	.	90;80;80	B4DJ36;O60381-3;O60381	.;.;HBP1_HUMAN	N	80;80;80;80;80;80;72	ENSP00000420500:D80N;ENSP00000222574:D80N;ENSP00000418738:D80N	ENSP00000222574:D80N	D	+	1	0	HBP1	106610122	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.000000	0.76290	2.774000	0.95407	0.563000	0.77884	GAT	.	.		0.413	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		A	106822886	G	A	106822886	3	1	20	1	0	0	0	0	1	0	0	0	6994	942	33	3	244	3	HBP1	7	106822886	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	3459254	106822886	52315777	63	1790										
LMOD2	442721	hgsc.bcm.edu	37	chr7	123302963	123302963	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tcccaaaggctgccaccaccTcctcctcctccccctcctcc	3	25	0	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr7:123302963T>A	ENST00000458573.2	+	2	1480	c.1323T>A	c.(1321-1323)ccT>ccA	p.P441P	LMOD2_ENST00000456238.2_Intron	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	441	Pro-rich.					cytoskeleton (GO:0005856)		p.P441P(1)									tgccaccacctcctcctcctc	0.572																																					p.P441P		Atlas-SNP	.											LMOD2_ENST00000458573,NS,carcinoma,0,1	LMOD2	62	.	1	Substitution - coding silent(1)	endometrium(1)	c.T1323A						.						19	18	19					7																	123302963		1881	4064	5945	SO:0001819	synonymous_variant	442721	exon2			ACCACCTCCTCCT	AC006333	CCDS47693.1	7q31.32	2008-08-08			ENSG00000170807	ENSG00000170807			6648	protein-coding gene	gene with protein product		608006					Standard	NM_207163		Approved		uc003vky.2	Q6P5Q4	OTTHUMG00000157149	ENST00000458573.2:c.1323T>A	chr7.hg19:g.123302963T>A		73.0	0.0		77.0	4.0	NM_207163	A4D0W9|A4D0Y2|Q8WVJ8	Silent	SNP	ENST00000458573.2	hg19	CCDS47693.1																																																																																			.	.		0.572	LMOD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348525.1			A	123302963	T	A	123302963	2	1	20	1	0	0	0	0	0	0	0	1	8866	1538	54	4		4	LMOD2	7	123302963	Silent	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	16480077	123302963	35835700	64	1791										
ZYX	7791	hgsc.bcm.edu	37	chr7	143080168	143080168	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ccgagggcccccagcctcatCtccggctccagcccctaagt	9	20	2	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr7:143080168C>A	ENST00000322764.5	+	5	1121	c.776C>A	c.(775-777)tCt>tAt	p.S259Y	ZYX_ENST00000392910.2_Missense_Mutation_p.S102Y|ZYX_ENST00000477373.1_3'UTR|AC093673.5_ENST00000429630.1_RNA|ZYX_ENST00000449423.2_Missense_Mutation_p.S172Y	NM_001010972.1|NM_003461.4	NP_001010972.1|NP_003452.1	Q15942	ZYX_HUMAN	zyxin	259					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|integrin-mediated signaling pathway (GO:0007229)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)	17	Melanoma(164;0.205)					CCAGCCTCATCTCCGGCTCCA	0.607																																					p.S259Y		Atlas-SNP	.											.	ZYX	46	.	0			c.C776A						.						116	145	135					7																	143080168		2203	4300	6503	SO:0001583	missense	7791	exon5			CCTCATCTCCGGC	X95735	CCDS5883.1	7q32	2010-02-26			ENSG00000159840	ENSG00000159840			13200	protein-coding gene	gene with protein product		602002				8917469, 8940160	Standard	XM_005250052		Approved		uc003wcx.3	Q15942	OTTHUMG00000023822	ENST00000322764.5:c.776C>A	chr7.hg19:g.143080168C>A	ENSP00000324422:p.Ser259Tyr	164.0	0.0		125.0	70.0	NM_003461	A4D2G6|Q6I9S4	Missense_Mutation	SNP	ENST00000322764.5	hg19	CCDS5883.1	.	.	.	.	.	.	.	.	.	.	C	0.097	-1.157397	0.01686	.	.	ENSG00000159840	ENST00000322764;ENST00000354434;ENST00000449423;ENST00000392910	T;T;T;T	0.54071	0.67;0.64;0.63;0.59	4.02	3.12	0.35913	.	1.134650	0.06812	U	0.790514	T	0.44477	0.1295	L	0.36672	1.1	0.09310	N	1	P;P	0.39576	0.679;0.454	B;B	0.37833	0.259;0.259	T	0.36553	-0.9743	10	0.49607	T	0.09	.	9.2961	0.37815	0.0:0.8983:0.0:0.1017	.	172;259	B4DQR8;Q15942	.;ZYX_HUMAN	Y	259;227;172;102	ENSP00000324422:S259Y;ENSP00000346417:S227Y;ENSP00000394158:S172Y;ENSP00000376642:S102Y	ENSP00000324422:S259Y	S	+	2	0	ZYX	142790290	0.163000	0.22920	0.004000	0.12327	0.283000	0.27025	4.938000	0.63519	1.795000	0.52594	0.655000	0.94253	TCT	.	.		0.607	ZYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156296.2	NM_003461		A	143080168	C	A	143080168	3	1	20	1	0	0	0	0	1	0	0	0	18269	913	32	3	790	3	ZYX	7	143080168	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	19777205	143080168	16058495	65	1792										
ADAM28	10863	hgsc.bcm.edu	37	chr8	24181394	24181394	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gccttagttggtatggaaatCtggactgacaaggataagat	12	5	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr8:24181394C>A	ENST00000265769.4	+	9	878	c.768C>A	c.(766-768)atC>atA	p.I256I	ADAM28_ENST00000540823.1_Silent_p.I23I|ADAM28_ENST00000437154.2_Silent_p.I256I|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000397649.3_Silent_p.I3I|ADAM28_ENST00000518516.1_3'UTR	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	256	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		GTATGGAAATCTGGACTGACA	0.363																																					p.I256I	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.C768A						.						93	93	93					8																	24181394		2203	4299	6502	SO:0001819	synonymous_variant	10863	exon9			GGAAATCTGGACT	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.768C>A	chr8.hg19:g.24181394C>A		86.0	0.0		88.0	8.0	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	hg19	CCDS34865.1																																																																																			.	.		0.363	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		A	24181394	C	A	24181394	2	1	20	1	0	0	0	0	0	0	0	1	246	903	32	3		3	ADAM28	8	24181394	Silent	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10		24181394	122182628	66	1793										
IMPA1	3612	hgsc.bcm.edu	37	chr8	82583199	82583199	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	aacaggaatgcaaaaaagctTttccatattagaaagaacca	6	7	0	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr8:82583199T>G	ENST00000256108.5	-	7	1006	c.541A>C	c.(541-543)Aag>Cag	p.K181Q	IMPA1_ENST00000523710.1_5'UTR|IMPA1_ENST00000449740.2_Missense_Mutation_p.K240Q|IMPA1_ENST00000311489.4_Intron	NM_005536.3	NP_005527.1	P29218	IMPA1_HUMAN	inositol(myo)-1(or 4)-monophosphatase 1	181					inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|inositol monophosphate phosphatase activity (GO:0052834)|lithium ion binding (GO:0031403)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|stomach(1)	18					Lithium(DB01356)	CAAAAAAGCTTTTCCATATTA	0.373																																					p.K240Q		Atlas-SNP	.											.	IMPA1	46	.	0			c.A718C						.						74	68	70					8																	82583199		2203	4300	6503	SO:0001583	missense	3612	exon8			AAAGCTTTTCCAT		CCDS6231.1, CCDS47883.1, CCDS47884.1	8q21.1-q21.3	2008-01-28			ENSG00000133731	ENSG00000133731	3.1.3.25		6050	protein-coding gene	gene with protein product		602064		IMPA		1377913	Standard	NM_005536		Approved		uc011lfq.1	P29218	OTTHUMG00000164682	ENST00000256108.5:c.541A>C	chr8.hg19:g.82583199T>G	ENSP00000256108:p.Lys181Gln	263.0	0.0		513.0	95.0	NM_001144878	B2R733|B4DLN3|B7Z6Q4|J3KQT7|Q9UK71	Missense_Mutation	SNP	ENST00000256108.5	hg19	CCDS6231.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.26|11.26	1.586328|1.586328	0.28268|0.28268	.|.	.|.	ENSG00000133731|ENSG00000133731	ENST00000256108;ENST00000449740;ENST00000519964;ENST00000521360|ENST00000523942	T;T;T;T|.	0.53206|.	0.63;0.63;0.63;0.63|.	4.16|4.16	4.16|4.16	0.48862|0.48862	.|.	0.584488|0.584488	0.19380|0.19380	N|N	0.115699|0.115699	T|T	0.60261|0.60261	0.2255|0.2255	L|L	0.47716|0.47716	1.5|1.5	0.41322|0.41322	D|D	0.987185|0.987185	P;B|.	0.34977|.	0.478;0.098|.	B;B|.	0.36534|.	0.227;0.079|.	T|T	0.58255|0.58255	-0.7668|-0.7668	10|6	0.46703|.	T|.	0.11|.	-14.8569|-14.8569	13.155|13.155	0.59511|0.59511	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	240;181|.	B7Z6Q4;P29218|.	.;IMPA1_HUMAN|.	Q|T	181;240;173;146|205	ENSP00000256108:K181Q;ENSP00000408526:K240Q;ENSP00000429322:K173Q;ENSP00000430283:K146Q|.	ENSP00000256108:K181Q|.	K|K	-|-	1|2	0|0	IMPA1|IMPA1	82745754|82745754	1.000000|1.000000	0.71417|0.71417	0.803000|0.803000	0.32268|0.32268	0.268000|0.268000	0.26511|0.26511	5.486000|5.486000	0.66856|0.66856	1.632000|1.632000	0.50472|0.50472	0.443000|0.443000	0.29094|0.29094	AAG|AAA	.	.		0.373	IMPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379723.1			G	82583199	T	G	82583199	3	3	20	1	0	0	0	0	1	0	0	0	7731	1850	64	5	304	5	IMPA1	8	82583199	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	58401805	82583199	63780823	67	1794										
SPAG1	6674	hgsc.bcm.edu	37	chr8	101206459	101206459	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tccgaagatgaagaaggaaaAagcggaagaaaacatgaaga	12	4	0	6	rs56246127	byFrequency	TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr8:101206459A>C	ENST00000388798.2	+	10	1250	c.1059A>C	c.(1057-1059)aaA>aaC	p.K353N	SPAG1_ENST00000520643.1_Missense_Mutation_p.K353N|SPAG1_ENST00000520508.1_Missense_Mutation_p.K353N|SPAG1_ENST00000251809.3_Missense_Mutation_p.K353N	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	353					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		AAGAAGGAAAAAGCGGAAGAA	0.358																																					p.K353N		Atlas-SNP	.											.	SPAG1	80	.	0			c.A1059C						.						64	64	64					8																	101206459		2203	4300	6503	SO:0001583	missense	6674	exon10			AGGAAAAAGCGGA	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.1059A>C	chr8.hg19:g.101206459A>C	ENSP00000373450:p.Lys353Asn	592.0	0.0		1241.0	56.0	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	hg19	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	A	0.762	-0.768896	0.02974	.	.	ENSG00000104450	ENST00000520643;ENST00000251809;ENST00000520508;ENST00000388798	T;T;T;T	0.63417	2.83;-0.04;2.83;-0.04	5.39	0.943	0.19531	.	0.615169	0.15977	N	0.235509	T	0.48370	0.1496	L	0.41824	1.3	0.09310	N	1	P;P	0.44195	0.828;0.804	B;B	0.41764	0.366;0.16	T	0.32188	-0.9916	10	0.32370	T	0.25	-15.8264	6.443	0.21861	0.5813:0.0:0.4187:0.0	.	353;353	Q07617;G3XAM3	SPAG1_HUMAN;.	N	353	ENSP00000427716:K353N;ENSP00000251809:K353N;ENSP00000428070:K353N;ENSP00000373450:K353N	ENSP00000251809:K353N	K	+	3	2	SPAG1	101275635	0.154000	0.22792	0.011000	0.14972	0.025000	0.11179	1.135000	0.31454	0.261000	0.21753	-0.425000	0.05940	AAA	.	.		0.358	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		C	101206459	A	C	101206459	3	2	20	1	0	0	0	0	1	0	0	0	14990	11	1	5	1093	5	SPAG1	8	101206459	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	18623260	101206459	45157563	68	1795										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113694807	113694807	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cttcctaattgaaagttgtcCccaaaccgccgtgcattgat	7	12	0	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr8:113694807C>A	ENST00000297405.5	-	16	2785	c.2541G>T	c.(2539-2541)ggG>ggT	p.G847G	CSMD3_ENST00000352409.3_Silent_p.G847G|CSMD3_ENST00000455883.2_Silent_p.G743G|CSMD3_ENST00000343508.3_Silent_p.G807G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	847	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GAAAGTTGTCCCCAAACCGCC	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G847G		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G2541T						.						107	107	107					8																	113694807		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon16			GTTGTCCCCAAAC	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2541G>T	chr8.hg19:g.113694807C>A		109.0	0.0		195.0	122.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113694807	C	A	113694807	2	1	20	1	0	0	0	0	0	0	0	1	3948	610	22	3		3	CSMD3	8	113694807	Silent	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	12488348	113694807	32669215	69	1796										
COLEC10	10584	hgsc.bcm.edu	37	chr8	120103443	120103443	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ggcaatattggcaagactggGcccattgggaagaagggtaa	15	6	0	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr8:120103443G>T	ENST00000332843.2	+	3	317	c.276G>T	c.(274-276)ggG>ggT	p.G92G	COLEC10_ENST00000521788.1_3'UTR	NM_006438.3	NP_006429.2	Q9Y6Z7	COL10_HUMAN	collectin sub-family member 10 (C-type lectin)	92	Collagen-like.					collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21	all_cancers(13;4.13e-26)|Lung NSC(37;1.36e-07)|Ovarian(258;0.018)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00113)			GCAAGACTGGGCCCATTGGGA	0.423																																					p.G92G		Atlas-SNP	.											.	COLEC10	46	.	0			c.G276T						.						143	135	138					8																	120103443		2203	4300	6503	SO:0001819	synonymous_variant	10584	exon3			GACTGGGCCCATT	AB002631	CCDS6327.1	8q23-q24.1	2007-12-19				ENSG00000184374		"Collectins"	2220	protein-coding gene	gene with protein product		607620				10224141	Standard	NM_006438		Approved	CL-L1	uc003yoo.3	Q9Y6Z7		ENST00000332843.2:c.276G>T	chr8.hg19:g.120103443G>T		180.0	0.0		393.0	82.0	NM_006438	Q3SYH6|Q6UW19	Silent	SNP	ENST00000332843.2	hg19	CCDS6327.1																																																																																			.	.		0.423	COLEC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381225.1			T	120103443	G	T	120103443	2	4	20	1	0	0	0	0	0	0	0	1	3712	1190	42	3		3	COLEC10	8	120103443	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	6408636	120103443	26260579	70	1797										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125083748	125083748	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ttgcgttttgtggttccaggGctccttctgcatctacaaaa	9	10	2	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr8:125083748G>T	ENST00000522917.1	+	31	4174	c.3968G>T	c.(3967-3969)gGc>gTc	p.G1323V	FER1L6_ENST00000399018.1_Splice_Site_p.G1323V|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1323						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TGGTTCCAGGGCTCCTTCTGC	0.532																																					p.G1323V		Atlas-SNP	.											.	FER1L6	268	.	0			c.G3968T						.						78	80	79					8																	125083748		1911	4121	6032	SO:0001630	splice_region_variant	654463	exon31			TCCAGGGCTCCTT	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.3967-1G>T	chr8.hg19:g.125083748G>T		46.0	0.0		126.0	9.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.476025	0.84640	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.89343	-2.5;-2.5	5.96	5.96	0.96718	.	0.059893	0.64402	U	0.000003	D	0.94974	0.8374	M	0.90977	3.165	0.80722	D	1	D	0.69078	0.997	P	0.55965	0.788	D	0.95140	0.8263	10	0.66056	D	0.02	-20.9261	20.422	0.99049	0.0:0.0:1.0:0.0	.	1323	Q2WGJ9	FR1L6_HUMAN	V	1323	ENSP00000428280:G1323V;ENSP00000381982:G1323V	ENSP00000381982:G1323V	G	+	2	0	FER1L6	125152929	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.233000	0.78125	2.832000	0.97577	0.655000	0.94253	GGC	.	.		0.532	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	Missense_Mutation	T	125083748	G	T	125083748	5	4	20	1	0	0	0	0	0	0	1	0	5823	1217	42	3	4086	3	FER1L6	8	125083748	Splice_Site	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	4980305	125083748	21280274	71	1798										
SCRIB	23513	hgsc.bcm.edu	37	chr8	144895116	144895116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gtccaggcacaccaggcgccGcaggttcccgagctcctgca	12	17	0	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr8:144895116G>A	ENST00000320476.3	-	8	664	c.658C>T	c.(658-660)Cgg>Tgg	p.R220W	SCRIB_ENST00000356994.2_Missense_Mutation_p.R220W|SCRIB_ENST00000377533.3_Missense_Mutation_p.R139W|MIR937_ENST00000401271.1_RNA	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	220	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			ACCAGGCGCCGCAGGTTCCCG	0.682																																					p.R220W	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C658T						.						28	30	29					8																	144895116		2195	4298	6493	SO:0001583	missense	23513	exon8			GGCGCCGCAGGTT	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.658C>T	chr8.hg19:g.144895116G>A	ENSP00000322938:p.Arg220Trp	128.0	0.0		197.0	8.0	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411500	0.83340	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533	T;T;T	0.10477	2.87;2.87;2.87	4.52	3.63	0.41609	.	.	.	.	.	T	0.27205	0.0667	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	T	0.01143	-1.1438	9	0.72032	D	0.01	.	13.1256	0.59354	0.0:0.0:0.8383:0.1617	.	220;220	Q14160;Q14160-3	SCRIB_HUMAN;.	W	220;220;139	ENSP00000349486:R220W;ENSP00000322938:R220W;ENSP00000366756:R139W	ENSP00000322938:R220W	R	-	1	2	SCRIB	144967104	1.000000	0.71417	1.000000	0.80357	0.637000	0.38172	5.438000	0.66550	0.966000	0.38159	0.563000	0.77884	CGG	.	.		0.682	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		A	144895116	G	A	144895116	3	1	20	1	0	0	0	0	1	0	0	0	13952	1086	38	1	4429	1	SCRIB	8	144895116	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	19811368	144895116	1468906	72	1799										
SPINK4	27290	hgsc.bcm.edu	37	chr9	33246666	33246666	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ctgttcccagatgtccaaccTggtctgcggcactgatgggc	12	13	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr9:33246666T>C	ENST00000379721.3	+	3	200	c.155T>C	c.(154-156)cTg>cCg	p.L52P	SPINK4_ENST00000379725.1_Missense_Mutation_p.L75P|SPINK4_ENST00000379723.1_Missense_Mutation_p.L75P	NM_014471.1	NP_055286.1	O60575	ISK4_HUMAN	serine peptidase inhibitor, Kazal type 4	52	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				response to drug (GO:0042493)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			lung(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)			ATGTCCAACCTGGTCTGCGGC	0.572																																					p.L52P		Atlas-SNP	.											.	SPINK4	7	.	0			c.T155C						.						177	151	160					9																	33246666		2203	4300	6503	SO:0001583	missense	27290	exon3			CCAACCTGGTCTG	AF048700	CCDS6536.1	9p13.3	2011-08-31	2005-08-17		ENSG00000122711	ENSG00000122711		"Serine peptidase inhibitors, Kazal type"	16646	protein-coding gene	gene with protein product		613929	"serine protease inhibitor, Kazal type 4"			1400298, 17333166	Standard	NM_014471		Approved	PEC-60, MGC133107	uc003zsh.3	O60575	OTTHUMG00000019762	ENST00000379721.3:c.155T>C	chr9.hg19:g.33246666T>C	ENSP00000369045:p.Leu52Pro	53.0	0.0		45.0	12.0	NM_014471	Q2YDT7	Missense_Mutation	SNP	ENST00000379721.3	hg19	CCDS6536.1	.	.	.	.	.	.	.	.	.	.	T	4.026	0.002320	0.07819	.	.	ENSG00000122711	ENST00000379725;ENST00000379723;ENST00000379721	T;T;T	0.59638	0.25;0.25;0.25	4.7	-6.05	0.02172	Proteinase inhibitor I1, Kazal (3);	0.343628	0.25532	N	0.030021	T	0.23289	0.0563	.	.	.	0.09310	N	0.999993	B	0.06786	0.001	B	0.06405	0.002	T	0.37934	-0.9684	9	0.02654	T	1	-0.6536	8.9833	0.35979	0.1295:0.6869:0.0:0.1836	.	52	O60575	ISK4_HUMAN	P	75;75;52	ENSP00000369048:L75P;ENSP00000369046:L75P;ENSP00000369045:L52P	ENSP00000369045:L52P	L	+	2	0	SPINK4	33236666	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	-1.118000	0.03280	-1.232000	0.02554	0.379000	0.24179	CTG	.	.		0.572	SPINK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052035.1	NM_014471		C	33246666	T	C	33246666	3	2	20	1	0	0	0	0	1	0	0	0	15076	1580	55	2	165	2	SPINK4	9	33246666	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10		33246666	107966765	73	1800										
NPR2	4882	hgsc.bcm.edu	37	chr9	35792605	35792605	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gcccgtggacctgcggtttgTcagctccgaactggaaggcg	15	12	1	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr9:35792605T>C	ENST00000342694.2	+	1	455	c.200T>C	c.(199-201)gTc>gCc	p.V67A		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	67					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	CTGCGGTTTGTCAGCTCCGAA	0.657																																					p.V67A		Atlas-SNP	.											.	NPR2	162	.	0			c.T200C						.						71	66	68					9																	35792605		2203	4300	6503	SO:0001583	missense	4882	exon1			GGTTTGTCAGCTC	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.200T>C	chr9.hg19:g.35792605T>C	ENSP00000341083:p.Val67Ala	75.0	0.0		55.0	6.0	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	hg19	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	T	9.938	1.216743	0.22373	.	.	ENSG00000159899	ENST00000342694	D	0.82526	-1.62	4.09	4.09	0.47781	Extracellular ligand-binding receptor (1);	0.000000	0.39834	N	0.001252	T	0.63896	0.2550	N	0.08118	0	0.39311	D	0.965079	B;B	0.16802	0.001;0.019	B;B	0.18871	0.006;0.023	T	0.59225	-0.7494	10	0.11182	T	0.66	.	10.8585	0.46812	0.0:0.0:0.0:1.0	.	67;67	P20594-2;P20594	.;ANPRB_HUMAN	A	67	ENSP00000341083:V67A	ENSP00000341083:V67A	V	+	2	0	NPR2	35782605	0.022000	0.18835	1.000000	0.80357	0.995000	0.86356	0.428000	0.21395	1.835000	0.53391	0.460000	0.39030	GTC	.	.		0.657	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			C	35792605	T	C	35792605	3	2	20	1	0	0	0	0	1	0	0	0	10604	1667	58	2	202	2	NPR2	9	35792605	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	2545939	35792605	105420826	74	1801										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73461375	73461375	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tttcccaaagacttgcttgaGttttggctggagttcaaagt	10	7	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr9:73461375G>T	ENST00000377111.2	-	4	838	c.595C>A	c.(595-597)Ctc>Atc	p.L199I	TRPM3_ENST00000358082.3_Missense_Mutation_p.L46I|TRPM3_ENST00000377110.3_Missense_Mutation_p.L199I|TRPM3_ENST00000396292.4_Missense_Mutation_p.L46I|TRPM3_ENST00000361823.5_Missense_Mutation_p.L46I|TRPM3_ENST00000377097.3_Missense_Mutation_p.L46I|TRPM3_ENST00000423814.3_Missense_Mutation_p.L201I|TRPM3_ENST00000377106.1_Missense_Mutation_p.L46I|TRPM3_ENST00000396280.5_Missense_Mutation_p.L46I|TRPM3_ENST00000360823.2_Missense_Mutation_p.L46I|TRPM3_ENST00000396285.1_Missense_Mutation_p.L46I|TRPM3_ENST00000377101.1_Missense_Mutation_p.L46I|TRPM3_ENST00000357533.2_Missense_Mutation_p.L201I|TRPM3_ENST00000408909.2_Missense_Mutation_p.L46I|TRPM3_ENST00000396283.1_Missense_Mutation_p.L46I|TRPM3_ENST00000377105.1_Missense_Mutation_p.L46I	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	199					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						ACTTGCTTGAGTTTTGGCTGG	0.493																																					p.L199I		Atlas-SNP	.											.	TRPM3	700	.	0			c.C595A						.						178	178	178					9																	73461375		2203	4300	6503	SO:0001583	missense	80036	exon4			GCTTGAGTTTTGG	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.595C>A	chr9.hg19:g.73461375G>T	ENSP00000366315:p.Leu199Ile	118.0	0.0		90.0	4.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	16.94|16.94|16.94	3.261854|3.261854|3.261854	0.59431|0.59431|0.59431	.|.|.	.|.|.	ENSG00000083067|ENSG00000083067|ENSG00000083067	ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814;ENST00000377101;ENST00000396283;ENST00000361823;ENST00000455451|ENST00000377097|ENST00000396280	T;T;T;T;T;T;T;T;T;T;T;T;T;T|.|.	0.10382|.|.	2.88;2.88;2.88;2.88;2.88;2.88;2.88;2.88;2.88;2.88;2.88;2.88;2.88;2.88|.|.	5.86|5.86|5.86	5.86|5.86|5.86	0.93980|0.93980|0.93980	.|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.72803|0.72803|0.72803	0.3506|0.3506|0.3506	M|M|M	0.71920|0.71920|0.71920	2.185|2.185|2.185	0.52501|0.52501|0.52501	D|D|D	0.999951|0.999951|0.999951	P;D;P;B;P;D;B;P;D;P;D|.|.	0.76494|.|.	0.568;0.999;0.63;0.099;0.534;0.996;0.102;0.584;0.996;0.634;0.986|.|.	B;D;B;B;B;D;B;B;D;B;D|.|.	0.72625|.|.	0.234;0.963;0.347;0.119;0.382;0.978;0.025;0.263;0.978;0.202;0.966|.|.	T|T|T	0.71807|0.71807|0.71807	-0.4481|-0.4481|-0.4481	10|5|5	0.34782|.|.	T|.|.	0.22|.|.	-8.7036|-8.7036|-8.7036	13.4018|13.4018|13.4018	0.60887|0.60887|0.60887	0.0715:0.0:0.9285:0.0|0.0715:0.0:0.9285:0.0|0.0715:0.0:0.9285:0.0	.|.|.	199;201;46;199;199;199;201;46;46;199;46|.|.	Q9HCF6;Q4VXD2;Q504Y1;Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3|.|.	TRPM3_HUMAN;.;.;.;.;.;.;.;.;.;.|.|.	I|K|N	199;199;46;46;46;201;46;46;46;46;201;46;46;46;46|88|45	ENSP00000366315:L199I;ENSP00000366314:L199I;ENSP00000366310:L46I;ENSP00000354066:L46I;ENSP00000366309:L46I;ENSP00000350140:L201I;ENSP00000386127:L46I;ENSP00000379581:L46I;ENSP00000379587:L46I;ENSP00000350791:L46I;ENSP00000389542:L201I;ENSP00000366305:L46I;ENSP00000379579:L46I;ENSP00000355395:L46I|.|.	ENSP00000350140:L201I|.|.	L|N|T	-|-|-	1|3|2	0|2|0	TRPM3|TRPM3|TRPM3	72651195|72651195|72651195	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.989000|0.989000|0.989000	0.77384|0.77384|0.77384	7.952000|7.952000|7.952000	0.87827|0.87827|0.87827	2.781000|2.781000|2.781000	0.95711|0.95711|0.95711	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	CTC|AAC|ACT	.	.		0.493	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		T	73461375	G	T	73461375	3	4	20	1	0	0	0	0	1	0	0	0	16602	1029	36	3	4739	3	TRPM3	9	73461375	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	37668770	73461375	67752056	75	1802										
RBM18	92400	hgsc.bcm.edu	37	chr9	125023740	125023740	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ctgaaaggatggatgcattcTccaggggaagagttttggtt	14	5	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr9:125023740T>C	ENST00000417201.3	-	2	172	c.32A>G	c.(31-33)gAg>gGg	p.E11G	RBM18_ENST00000483428.1_5'UTR	NM_033117.3	NP_149108.1	Q96H35	RBM18_HUMAN	RNA binding motif protein 18	11							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7						GGATGCATTCTCCAGGGGAAG	0.443																																					p.E11G		Atlas-SNP	.											.	RBM18	15	.	0			c.A32G						.						153	143	147					9																	125023740		2203	4300	6503	SO:0001583	missense	92400	exon2			GCATTCTCCAGGG	AK057676	CCDS6839.1	9q34.11	2013-02-12			ENSG00000119446	ENSG00000119446		"RNA binding motif (RRM) containing"	28413	protein-coding gene	gene with protein product						12477932	Standard	NM_033117		Approved	MGC2734	uc004bma.2	Q96H35	OTTHUMG00000020602	ENST00000417201.3:c.32A>G	chr9.hg19:g.125023740T>C	ENSP00000409315:p.Glu11Gly	118.0	0.0		78.0	53.0	NM_033117	B3KQ89	Missense_Mutation	SNP	ENST00000417201.3	hg19	CCDS6839.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.358302	0.61403	.	.	ENSG00000119446	ENST00000417201	T	0.13307	2.6	5.69	4.55	0.56014	.	0.145674	0.64402	D	0.000013	T	0.13157	0.0319	L	0.36672	1.1	0.51767	D	0.999938	P	0.46987	0.888	B	0.43889	0.435	T	0.03545	-1.1026	10	0.39692	T	0.17	-21.5232	10.7134	0.45997	0.0:0.0753:0.0:0.9247	.	11	Q96H35	RBM18_HUMAN	G	11	ENSP00000409315:E11G	ENSP00000409315:E11G	E	-	2	0	RBM18	124063561	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.523000	0.73787	1.111000	0.41721	0.533000	0.62120	GAG	.	.		0.443	RBM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053928.2	NM_033117		C	125023740	T	C	125023740	3	2	20	1	0	0	0	0	1	0	0	0	13135	1551	54	2	560	2	RBM18	9	125023740	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	51562365	125023740	16189691	76	1803										
FBXO18	84893	hgsc.bcm.edu	37	chr10	5948067	5948067	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cagccgtgcaccaatgacatGgccaaaagcaattctgttgg	10	11	1	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr10:5948067G>T	ENST00000362091.4	+	3	340	c.225G>T	c.(223-225)atG>atT	p.M75I	FBXO18_ENST00000397269.3_5'UTR|FBXO18_ENST00000470089.1_3'UTR|FBXO18_ENST00000379999.5_Missense_Mutation_p.M126I	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	75					DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						CCAATGACATGGCCAAAAGCA	0.527																																					p.M126I		Atlas-SNP	.											.	FBXO18	108	.	0			c.G378T						.						79	71	74					10																	5948067		2203	4300	6503	SO:0001583	missense	84893	exon4			TGACATGGCCAAA	AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"F-boxes /  "other""	13620	protein-coding gene	gene with protein product		607222	"F-box only protein 18"			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.225G>T	chr10.hg19:g.5948067G>T	ENSP00000355415:p.Met75Ile	173.0	0.0		205.0	107.0	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Missense_Mutation	SNP	ENST00000362091.4	hg19	CCDS7072.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.016233	0.54468	.	.	ENSG00000134452	ENST00000362091;ENST00000379999	.	.	.	5.76	5.76	0.90799	.	0.196924	0.50627	D	0.000106	T	0.72763	0.3501	L	0.56769	1.78	0.80722	D	1	P;P;P	0.50528	0.631;0.498;0.936	B;B;P	0.61201	0.229;0.115;0.885	T	0.67522	-0.5649	9	0.25751	T	0.34	-39.3798	15.4761	0.75481	0.0:0.0:1.0:0.0	.	126;75;1	Q8NFZ0-2;Q8NFZ0;Q2TAK1	.;FBX18_HUMAN;.	I	75;126	.	ENSP00000355415:M75I	M	+	3	0	FBXO18	5988073	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.501000	0.53325	2.713000	0.92767	0.655000	0.94253	ATG	.	.		0.527	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807		T	5948067	G	T	5948067	3	4	20	1	0	0	0	0	1	0	0	0	5739	1348	47	3	397	3	FBXO18	10	5948067	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10		5948067	129586680	77	1804										
ENKUR	219670	hgsc.bcm.edu	37	chr10	25284594	25284594	+	Frame_Shift_Del	DEL	G	G	-													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cctttttattgatgtactttGgaactagtcctgaaggctca							TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr10:25284594delG	ENST00000331161.4	-	3	647	c.428delC	c.(427-429)ccafs	p.P143fs	ENKUR_ENST00000376363.1_Frame_Shift_Del_p.P143fs	NM_145010.3	NP_659447.1	Q8TC29	ENKUR_HUMAN	enkurin, TRPC channel interacting protein	143						motile cilium (GO:0031514)		p.P143Q(1)		endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						GATGTACTTTGGAACTAGTCC	0.348																																					p.P143fs		Atlas-Indel,Pindel	.											.	ENKUR	30	.	1	Substitution - Missense(1)	lung(1)	c.429delA						.						149	145	146					10																	25284594		2203	4300	6503	SO:0001589	frameshift_variant	219670	exon3			.	AK095021	CCDS7146.1, CCDS73075.1	10p12.31	2014-08-13	2009-04-28	2009-04-28	ENSG00000151023	ENSG00000151023			28388	protein-coding gene	gene with protein product		611025	"chromosome 10 open reading frame 63"	C10orf63		17217053, 15385169	Standard	NM_145010		Approved	MGC26778, enkurin, CFAP106	uc001isg.2	Q8TC29	OTTHUMG00000017827	ENST00000331161.4:c.428delC	chr10.hg19:g.25284594delG	ENSP00000331044:p.Pro143fs	68.0	0.0		111.0	44.0	NM_145010	A8K8Y0|D3DRV2	Frame_Shift_Del	DEL	ENST00000331161.4	hg19	CCDS7146.1																																																																																			.	.		0.348	ENKUR-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047239.2	NM_145010		-	25284594	G	-	25284594	7	5	20	1	0	1	0	1	0	0	0	0	5122	1348	47	0	358	0	ENKUR	10	25284594	Frame_Shift_Del	DEL	G	TCGA-2Y-A9HA-01A-11D-A38X-10	19336527	25284594	110250153	78	1805										
MARCH8	220972	hgsc.bcm.edu	37	chr10	45954609	45954609	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tctcctcagcagtacggtcaAtgagcacatacaaggaccag	9	12	3	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr10:45954609A>G	ENST00000319836.3	-	6	1279	c.530T>C	c.(529-531)aTt>aCt	p.I177T	MARCH8_ENST00000476962.1_5'UTR|MARCH8_ENST00000395769.2_Missense_Mutation_p.I177T|MARCH8_ENST00000453424.2_Missense_Mutation_p.I459T|MARCH8_ENST00000395771.3_Missense_Mutation_p.I177T	NM_145021.4	NP_659458.2	Q5T0T0	MARH8_HUMAN	membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase	177					immune system process (GO:0002376)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	12						AGTACGGTCAATGAGCACATA	0.552																																					p.I177T	NSCLC(102;658 1594 2173 16344 34808)	Atlas-SNP	.											.	MARCH8	29	.	0			c.T530C						.						182	140	154					10																	45954609		2203	4300	6503	SO:0001583	missense	220972	exon6			CGGTCAATGAGCA	AL833316	CCDS7213.1, CCDS60519.1	10q11.22	2013-01-09	2012-02-23	2005-01-27	ENSG00000165406	ENSG00000165406		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	23356	protein-coding gene	gene with protein product		613335	"c-mir, cellular modulator of immune recognition", "membrane-associated ring finger (C3HC4) 8"	MIR		12582153, 14722266	Standard	XM_005271804		Approved	c-MIR, MARCH-VIII, RNF178	uc001jch.2	Q5T0T0	OTTHUMG00000019345	ENST00000319836.3:c.530T>C	chr10.hg19:g.45954609A>G	ENSP00000317087:p.Ile177Thr	70.0	0.0		101.0	28.0	NM_001002266	B2R8E7|H0Y7C6|Q5T0S8|Q8TC72	Missense_Mutation	SNP	ENST00000319836.3	hg19	CCDS7213.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.327070	0.81690	.	.	ENSG00000165406	ENST00000395771;ENST00000319836;ENST00000395769	T;T;T	0.13657	2.57;2.57;2.57	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.35008	0.0917	M	0.71206	2.165	0.80722	D	1	D;D	0.67145	0.996;0.981	D;D	0.65684	0.937;0.914	T	0.06303	-1.0834	10	0.62326	D	0.03	-22.4289	13.9558	0.64147	1.0:0.0:0.0:0.0	.	177;341	Q5T0T0;Q5JQ16	MARH8_HUMAN;.	T	177	ENSP00000379118:I177T;ENSP00000317087:I177T;ENSP00000379116:I177T	ENSP00000317087:I177T	I	-	2	0	MARCH8	45274615	1.000000	0.71417	0.941000	0.38009	0.802000	0.45316	9.339000	0.96797	2.184000	0.69523	0.533000	0.62120	ATT	.	.		0.552	MARCH8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051217.1	NM_145021		G	45954609	A	G	45954609	3	3	20	1	0	0	0	0	1	0	0	0	9316	101	4	2	353	2	MARCH8	10	45954609	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	20670015	45954609	89580138	79	1806										
KIAA0913	23053	hgsc.bcm.edu	37	chr10	75552318	75552318	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tgaagaagatggtggtgtgtActtctcggaagggcctgagc	16	6	1	4			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr10:75552318A>G	ENST00000605216.1	+	10	2238	c.2021A>G	c.(2020-2022)tAc>tGc	p.Y674C	ZSWIM8_ENST00000604524.1_Missense_Mutation_p.Y674C|ZSWIM8_ENST00000431225.1_3'UTR|ZSWIM8_ENST00000398706.2_Missense_Mutation_p.Y674C|ZSWIM8_ENST00000604729.1_Missense_Mutation_p.Y674C|ZSWIM8_ENST00000603114.1_Intron	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	674							zinc ion binding (GO:0008270)										GGTGGTGTGTACTTCTCGGAA	0.607																																					p.Y674C		Atlas-SNP	.											.	.	.	.	0			c.A2021G						.						50	54	53					10																	75552318		1942	4127	6069	SO:0001583	missense	23053	exon10			GTGTGTACTTCTC	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"Zinc fingers, SWIM-type"	23528	protein-coding gene	gene with protein product			"KIAA0913"	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.2021A>G	chr10.hg19:g.75552318A>G	ENSP00000474748:p.Tyr674Cys	109.0	0.0		110.0	21.0	NM_001242488	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Missense_Mutation	SNP	ENST00000605216.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.50|12.50	1.957183|1.957183	0.34565|0.34565	.|.	.|.	ENSG00000214655|ENSG00000214655	ENST00000431225|ENST00000398706	.|T	.|0.43688	.|0.94	5.4|5.4	4.25|4.25	0.50352|0.50352	.|.	.|0.715004	.|0.11731	.|U	.|0.534986	T|T	0.33177|0.33177	0.0854|0.0854	L|L	0.29908|0.29908	0.895|0.895	0.34874|0.34874	D|D	0.7439|0.7439	.|B;B;B;B	.|0.09022	.|0.002;0.0;0.002;0.002	.|B;B;B;B	.|0.06405	.|0.002;0.0;0.002;0.002	T|T	0.30119|0.30119	-0.9989|-0.9989	5|10	.|0.42905	.|T	.|0.14	-5.9973|-5.9973	11.7821|11.7821	0.52021|0.52021	0.8683:0.0:0.0:0.1317|0.8683:0.0:0.0:0.1317	.|.	.|674;674;674;674	.|A7E2V4;A7E2V4-3;A7E2V4-5;A7E2V4-4	.|K0913_HUMAN;.;.;.	A|C	171|674	.|ENSP00000381693:Y674C	.|ENSP00000381693:Y674C	T|Y	+|+	1|2	0|0	KIAA0913|KIAA0913	75222324|75222324	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.764000|4.764000	0.62264|0.62264	1.043000|1.043000	0.40175|0.40175	0.533000|0.533000	0.62120|0.62120	ACT|TAC	.	.		0.607	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		G	75552318	A	G	75552318	3	3	20	1	0	0	0	0	1	0	0	0	8209	391	14	2	2059	2	KIAA0913	10	75552318	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	29597709	75552318	59982429	80	1807										
CYP2C18	1562	hgsc.bcm.edu	37	chr10	96480254	96480254	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	acaacgagcaccactctgagAtatggactcctgctcctgct	8	14	1	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr10:96480254A>G	ENST00000285979.6	+	6	1120	c.921A>G	c.(919-921)agA>agG	p.R307R	CYP2C19_ENST00000464755.1_3'UTR|CYP2C18_ENST00000339022.5_Silent_p.R248R	NM_000772.2	NP_000763.1	P33260	CP2CI_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 18	307					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	26		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Aminophenazone(DB01424)|Antipyrine(DB01435)|Buprenorphine(DB00921)|Clobazam(DB00349)|Clotiazepam(DB01559)|Cyclophosphamide(DB00531)|Dapsone(DB00250)|Desipramine(DB01151)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Ifosfamide(DB01181)|Imipramine(DB00458)|Lansoprazole(DB00448)|Lidocaine(DB00281)|Methadone(DB00333)|Omeprazole(DB00338)|Pegvisomant(DB00082)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Propofol(DB00818)|Tolbutamide(DB01124)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vilazodone(DB06684)|Warfarin(DB00682)	CCACTCTGAGATATGGACTCC	0.453																																					p.R307R		Atlas-SNP	.											.	CYP2C18	79	.	0			c.A921G						.						145	135	138					10																	96480254		2203	4300	6503	SO:0001819	synonymous_variant	1562	exon6			TCTGAGATATGGA	M61853	CCDS7435.1, CCDS44460.1	10q24	2003-11-12	2003-01-14		ENSG00000108242	ENSG00000108242		"Cytochrome P450s"	2620	protein-coding gene	gene with protein product		601131	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18"	CYP2C17		1896026, 2009263	Standard	NM_000772		Approved	P450IIC17, CPCI, CYP2C		P33260	OTTHUMG00000018796	ENST00000285979.6:c.921A>G	chr10.hg19:g.96480254A>G		49.0	0.0		84.0	47.0	NM_000772	B2R8K2|Q16703|Q16751|Q4VAT5|Q6GRG1	Silent	SNP	ENST00000285979.6	hg19	CCDS7435.1																																																																																			.	.		0.453	CYP2C18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049486.1	NM_000772		G	96480254	A	G	96480254	2	3	20	1	0	0	0	0	0	0	0	1	4167	330	12	2		2	CYP2C18	10	96480254	Silent	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	20927936	96480254	39054493	81	1808										
C10orf84	63877	hgsc.bcm.edu	37	chr10	120070724	120070724	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cttaagtaaactcacccccaTgcaagtttcttcttttttcg	4	12	3	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr10:120070724T>C	ENST00000369183.4	-	8	904	c.645A>G	c.(643-645)gcA>gcG	p.A215A	FAM204A_ENST00000469758.1_5'UTR|FAM204A_ENST00000369172.4_Silent_p.A215A	NM_022063.2	NP_071346.1	Q9H8W3	F204A_HUMAN	family with sequence similarity 204, member A	215										kidney(1)|large_intestine(5)|lung(4)|ovary(1)	11						CTCACCCCCATGCAAGTTTCT	0.363																																					p.A215A		Atlas-SNP	.											.	FAM204A	20	.	0			c.A645G						.						77	79	78					10																	120070724		2203	4300	6503	SO:0001819	synonymous_variant	63877	exon7			CCCCCATGCAAGT	AK023250	CCDS7605.1	10q26.12	2011-06-01	2011-06-01	2011-06-01	ENSG00000165669	ENSG00000165669			25794	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 84"	C10orf84		12477932	Standard	NM_022063		Approved	FLJ13188, bA319I23.1	uc010qss.1	Q9H8W3	OTTHUMG00000019131	ENST00000369183.4:c.645A>G	chr10.hg19:g.120070724T>C		92.0	0.0		152.0	71.0	NM_001134672	D3DRC6|Q5T373|Q9H5V5	Silent	SNP	ENST00000369183.4	hg19	CCDS7605.1																																																																																			.	.		0.363	FAM204A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050596.2	NM_022063		C	120070724	T	C	120070724	2	2	20	1	0	0	0	0	0	0	0	1	1623	1451	51	2		2	C10orf84	10	120070724	Silent	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	23590470	120070724	15464023	82	1809										
ADAM12	8038	hgsc.bcm.edu	37	chr10	127824210	127824210	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cagaatatccccgtacatgtCcatggtagtaacagtgaccc	8	12	0	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr10:127824210C>T	ENST00000368679.4	-	5	677	c.368G>A	c.(367-369)gGa>gAa	p.G123E	ADAM12_ENST00000368676.4_Missense_Mutation_p.G123E	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	123					cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CCGTACATGTCCATGGTAGTA	0.453																																					p.G123E		Atlas-SNP	.											.	ADAM12	388	.	0			c.G368A						.						148	113	125					10																	127824210		2203	4300	6503	SO:0001583	missense	8038	exon5			ACATGTCCATGGT	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.368G>A	chr10.hg19:g.127824210C>T	ENSP00000357668:p.Gly123Glu	103.0	0.0		122.0	74.0	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	hg19	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.931097	0.73327	.	.	ENSG00000148848	ENST00000368679;ENST00000368676;ENST00000448723	T;T;T	0.51817	0.69;0.69;0.69	4.17	4.17	0.49024	Peptidase M12B, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.76212	0.3956	H	0.95402	3.665	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.72075	0.976;0.959;0.959;0.959;0.976	D	0.84007	0.0346	10	0.87932	D	0	.	13.7996	0.63192	0.0:1.0:0.0:0.0	.	120;120;123;120;123	A8K6G4;O43184-3;O43184-2;O43184-4;O43184	.;.;.;.;ADA12_HUMAN	E	123;123;120	ENSP00000357668:G123E;ENSP00000357665:G123E;ENSP00000391268:G120E	ENSP00000357665:G123E	G	-	2	0	ADAM12	127814200	0.964000	0.33143	0.525000	0.27900	0.274000	0.26718	4.666000	0.61554	2.158000	0.67659	0.491000	0.48974	GGA	.	.		0.453	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			T	127824210	C	T	127824210	3	4	20	1	0	0	0	0	1	0	0	0	236	855	30	3	2545	3	ADAM12	10	127824210	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	7753486	127824210	7710537	83	1810										
ST5	6764	hgsc.bcm.edu	37	chr11	8752073	8752073	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ggcccagccgtttctccagcCggtagaaagagtcccggaca	12	14	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:8752073C>T	ENST00000534127.1	-	6	1149	c.764G>A	c.(763-765)cGg>cAg	p.R255Q	ST5_ENST00000526757.1_Intron|ST5_ENST00000530438.1_Intron|ST5_ENST00000313726.6_Missense_Mutation_p.R255Q|ST5_ENST00000357665.1_Missense_Mutation_p.R255Q	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	255					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		TTTCTCCAGCCGGTAGAAAGA	0.622																																					p.R255Q		Atlas-SNP	.											.	ST5	85	.	0			c.G764A						.						37	45	43					11																	8752073		2196	4292	6488	SO:0001583	missense	6764	exon6			TCCAGCCGGTAGA	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"DENN/MADD domain containing"	11350	protein-coding gene	gene with protein product	"DENN/MADD domain containing 2B"	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.764G>A	chr11.hg19:g.8752073C>T	ENSP00000433528:p.Arg255Gln	73.0	0.0		76.0	28.0	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	hg19	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	C	32	5.186385	0.94885	.	.	ENSG00000166444	ENST00000534127;ENST00000313726;ENST00000357665	T;T;T	0.21932	1.98;1.98;1.98	6.17	6.17	0.99709	.	0.405962	0.25555	N	0.029868	T	0.46698	0.1406	L	0.58101	1.795	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.06807	-1.0806	10	0.48119	T	0.1	-14.0429	20.8794	0.99867	0.0:1.0:0.0:0.0	.	255	P78524	ST5_HUMAN	Q	255	ENSP00000433528:R255Q;ENSP00000319678:R255Q;ENSP00000350294:R255Q	ENSP00000319678:R255Q	R	-	2	0	ST5	8708649	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.627000	0.67784	2.941000	0.99782	0.655000	0.94253	CGG	.	.		0.622	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		T	8752073	C	T	8752073	3	4	20	1	0	0	0	0	1	0	0	0	15235	652	23	1	2721	1	ST5	11	8752073	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10		8752073	126254443	84	1811										
INSC	387755	hgsc.bcm.edu	37	chr11	15134030	15134030	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ggagccatgagacggcccccTggcaatggagaggcggccag	17	12	0	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:15134030T>C	ENST00000379554.3	+	1	61	c.15T>C	c.(13-15)ccT>ccC	p.P5P	INSC_ENST00000379556.3_5'Flank|INSC_ENST00000424273.1_5'Flank	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	5					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						GACGGCCCCCTGGCAATGGAG	0.622																																					p.P5P		Atlas-SNP	.											INSC,colon,carcinoma,0,1	INSC	104	.	0			c.T15C						.						49	60	57					11																	15134030		1951	4125	6076	SO:0001819	synonymous_variant	387755	exon1			GCCCCCTGGCAAT	AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"inscuteable spindle orientation adaptor protein"	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.15T>C	chr11.hg19:g.15134030T>C		89.0	0.0		96.0	7.0	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Silent	SNP	ENST00000379554.3	hg19	CCDS41621.1																																																																																			.	.		0.622	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853		C	15134030	T	C	15134030	2	2	20	1	0	0	0	0	0	0	0	1	7773	1567	55	2		2	INSC	11	15134030	Silent	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	6381957	15134030	119872486	85	1812										
SPTY2D1	144108	hgsc.bcm.edu	37	chr11	18636742	18636742	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ctggactcttagccttattgTgtggggtgaccatgggccca	13	10	1	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:18636742T>C	ENST00000336349.5	-	3	1314	c.1079A>G	c.(1078-1080)cAc>cGc	p.H360R	SPTY2D1_ENST00000543776.1_5'Flank	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	360	Ser-rich.									breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						AGCCTTATTGTGTGGGGTGAC	0.562																																					p.H360R		Atlas-SNP	.											.	SPTY2D1	72	.	0			c.A1079G						.						109	118	115					11																	18636742		2199	4293	6492	SO:0001583	missense	144108	exon3			TTATTGTGTGGGG	BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.1079A>G	chr11.hg19:g.18636742T>C	ENSP00000337991:p.His360Arg	123.0	0.0		114.0	31.0	NM_194285	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Missense_Mutation	SNP	ENST00000336349.5	hg19	CCDS31441.1	.	.	.	.	.	.	.	.	.	.	T	4.825	0.153335	0.09185	.	.	ENSG00000179119	ENST00000336349	T	0.20738	2.05	5.84	1.96	0.26148	.	0.852389	0.10952	N	0.615985	T	0.16769	0.0403	L	0.36672	1.1	0.09310	N	1	B	0.24823	0.112	B	0.16722	0.016	T	0.28396	-1.0045	10	0.15066	T	0.55	1.2857	13.6712	0.62427	0.0:0.0:0.4321:0.5679	.	360	Q68D10	SPT2_HUMAN	R	360	ENSP00000337991:H360R	ENSP00000337991:H360R	H	-	2	0	SPTY2D1	18593318	0.210000	0.23517	0.007000	0.13788	0.155000	0.21991	0.619000	0.24388	0.050000	0.15949	0.460000	0.39030	CAC	.	.		0.562	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285		C	18636742	T	C	18636742	3	2	20	1	0	0	0	0	1	0	0	0	15141	1696	59	2	994	2	SPTY2D1	11	18636742	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	3502712	18636742	116369774	86	1813										
ANO3	63982	hgsc.bcm.edu	37	chr11	26563568	26563568	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	catctattatatgagcgctgGgcacgctggggaatgtggta	14	7	1	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:26563568G>T	ENST00000256737.3	+	11	1959	c.1107G>T	c.(1105-1107)tgG>tgT	p.W369C	ANO3_ENST00000529242.1_3'UTR|ANO3_ENST00000537978.1_Missense_Mutation_p.W353C|ANO3_ENST00000531568.1_Missense_Mutation_p.W223C|ANO3_ENST00000525139.1_Missense_Mutation_p.W353C	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	369					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						ATGAGCGCTGGGCACGCTGGG	0.408																																					p.W369C		Atlas-SNP	.											.	ANO3	145	.	0			c.G1107T						.						73	68	70					11																	26563568		2203	4299	6502	SO:0001583	missense	63982	exon11			GCGCTGGGCACGC	AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	14004	protein-coding gene	gene with protein product	"transmembrane protein 16C (eight membrane-spanning domains)"	610110	"chromosome 11 open reading frame 25", "transmembrane protein 16C"	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.1107G>T	chr11.hg19:g.26563568G>T	ENSP00000256737:p.Trp369Cys	76.0	0.0		102.0	28.0	NM_031418	B7Z3F5	Missense_Mutation	SNP	ENST00000256737.3	hg19	CCDS31447.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.476853	0.84640	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.87458	0.6182	H	0.94306	3.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.99	D	0.90660	0.4589	10	0.87932	D	0	.	19.3706	0.94481	0.0:0.0:1.0:0.0	.	271;369	B7Z7Y6;Q9BYT9	.;ANO3_HUMAN	C	353;353;369;271;223	ENSP00000440737:W353C;ENSP00000432576:W353C;ENSP00000256737:W369C;ENSP00000432394:W223C	ENSP00000256737:W369C	W	+	3	0	ANO3	26520144	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.785000	0.99042	2.584000	0.87258	0.655000	0.94253	TGG	.	.		0.408	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		T	26563568	G	T	26563568	3	4	20	1	0	0	0	0	1	0	0	0	698	1241	43	3	1149	3	ANO3	11	26563568	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	7926826	26563568	108442948	87	1814										
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57070061	57070061	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ccaggtgccatccacgtcttCtgtctggctggcctcaccat	9	16	4	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:57070061C>T	ENST00000532437.1	-	6	4866	c.4555G>A	c.(4555-4557)Gaa>Aaa	p.E1519K	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.E1519K			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1519	Acidic.|Tankyrase-binding.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TCCACGTCTTCTGTCTGGCTG	0.672																																					p.E1519K		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4555A						.						29	29	29					11																	57070061		2201	4296	6497	SO:0001583	missense	85456	exon7			CGTCTTCTGTCTG	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.4555G>A	chr11.hg19:g.57070061C>T	ENSP00000437271:p.Glu1519Lys	84.0	0.0		81.0	27.0	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	hg19	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.135251	0.56828	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.37058	1.22;1.22	4.68	4.68	0.58851	.	0.576304	0.15639	N	0.252007	T	0.41096	0.1144	L	0.51422	1.61	0.23510	N	0.997522	P;P	0.49961	0.93;0.799	P;B	0.47299	0.543;0.289	T	0.33929	-0.9849	10	0.72032	D	0.01	-5.9322	13.4519	0.61176	0.0:1.0:0.0:0.0	.	1519;100	Q9C0C2;Q86TK2	TB182_HUMAN;.	K	1519	ENSP00000350990:E1519K;ENSP00000437271:E1519K	ENSP00000350990:E1519K	E	-	1	0	TNKS1BP1	56826637	0.006000	0.16342	0.129000	0.21949	0.061000	0.15899	0.868000	0.27982	2.315000	0.78130	0.561000	0.74099	GAA	.	.		0.672	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		T	57070061	C	T	57070061	3	4	20	1	0	0	0	0	1	0	0	0	16335	922	32	3	654	3	TNKS1BP1	11	57070061	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	30506493	57070061	77936455	88	1815										
C11orf9	745	hgsc.bcm.edu	37	chr11	61537823	61537823	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	agcccacttgccaggcccccCgccacccccaccacccccac	5	27	0	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:61537823C>T	ENST00000278836.5	+	5	662	c.566C>T	c.(565-567)cCg>cTg	p.P189L	TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000265460.5_Missense_Mutation_p.P180L	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	189	Pro-rich.				central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CCAGGCCCCCCGCCACCCCCA	0.697																																					p.P189L		Atlas-SNP	.											.	.	.	.	0			c.C566T						.						3	3	3					11																	61537823		1914	3793	5707	SO:0001583	missense	745	exon5			GCCCCCCGCCACC		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"myelin gene regulatory factor"	608329	"chromosome 11 open reading frame 9"	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.566C>T	chr11.hg19:g.61537823C>T	ENSP00000278836:p.Pro189Leu	160.0	0.0		146.0	51.0	NM_001127392	O43582|Q9P1Q6	Missense_Mutation	SNP	ENST00000278836.5	hg19	CCDS44622.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.768455	0.69878	.	.	ENSG00000124920	ENST00000278836;ENST00000265460	T;T	0.32272	1.46;1.48	4.04	4.04	0.47022	.	0.106814	0.41938	D	0.000800	T	0.15132	0.0365	N	0.12182	0.205	0.80722	D	1	B;B	0.31519	0.327;0.22	B;B	0.24541	0.054;0.042	T	0.09314	-1.0680	10	0.29301	T	0.29	-20.9772	10.7765	0.46353	0.0:0.9095:0.0:0.0905	.	180;189	Q9Y2G1-2;Q9Y2G1	.;MRF_HUMAN	L	189;180	ENSP00000278836:P189L;ENSP00000265460:P180L	ENSP00000265460:P180L	P	+	2	0	C11orf9	61294399	0.987000	0.35691	0.478000	0.27316	0.632000	0.37999	5.292000	0.65673	2.184000	0.69523	0.491000	0.48974	CCG	.	.		0.697	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		T	61537823	C	T	61537823	3	4	20	1	0	0	0	0	1	0	0	0	1673	652	23	1	607	1	C11orf9	11	61537823	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	4467762	61537823	73468693	89	1816										
DLG2	1740	hgsc.bcm.edu	37	chr11	84996278	84996278	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gtatacctctgaagatttttGaagtctgtcatggcacggag	11	7	3	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:84996278G>A	ENST00000376104.2	-	4	483	c.172C>T	c.(172-174)Caa>Taa	p.Q58*	DLG2_ENST00000543673.1_Nonsense_Mutation_p.Q58*	NM_001142699.1	NP_001136171.1	Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0	L27 1. {ECO:0000255|PROSITE- ProRule:PRU00365}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				GAAGATTTTTGAAGTCTGTCA	0.368																																					p.Q58X		Atlas-SNP	.											.	DLG2	448	.	0			c.C172T						.						200	180	186					11																	84996278		1568	3581	5149	SO:0001587	stop_gained	1740	exon4			ATTTTTGAAGTCT	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000376104.2:c.172C>T	chr11.hg19:g.84996278G>A	ENSP00000365272:p.Gln58*	69.0	0.0		69.0	24.0	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Nonsense_Mutation	SNP	ENST00000376104.2	hg19	CCDS44690.1	.	.	.	.	.	.	.	.	.	.	G	16.07	3.019643	0.54576	.	.	ENSG00000150672	ENST00000376104;ENST00000543673;ENST00000546021	.	.	.	5.89	4.98	0.66077	.	0.229512	0.26428	N	0.024422	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4393	0.67303	0.071:0.0:0.929:0.0	.	.	.	.	X	58	.	.	Q	-	1	0	DLG2	84673926	1.000000	0.71417	0.134000	0.22075	0.187000	0.23431	6.323000	0.72891	1.484000	0.48361	0.655000	0.94253	CAA	.	.		0.368	DLG2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259245.3	NM_001364		A	84996278	G	A	84996278	4	1	20	1	0	0	0	0	0	1	0	0	4557	1299	45	3	3060	3	DLG2	11	84996278	Nonsense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	23458455	84996278	50010238	90	1817										
FAT3	120114	hgsc.bcm.edu	37	chr11	92495069	92495069	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ccaaaacagtcaaccatttgGgtggtggttcaggttctaga	11	8	3	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:92495069G>T	ENST00000298047.6	+	4	3734	c.3717G>T	c.(3715-3717)tgG>tgT	p.W1239C	RP11-203F8.1_ENST00000529884.1_RNA|FAT3_ENST00000409404.2_Missense_Mutation_p.W1239C|FAT3_ENST00000525166.1_Missense_Mutation_p.W1089C			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1239	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CAACCATTTGGGTGGTGGTTC	0.448										TCGA Ovarian(4;0.039)																											p.W1239C		Atlas-SNP	.											.	FAT3	1822	.	0			c.G3717T						.						194	185	188					11																	92495069		1904	4121	6025	SO:0001583	missense	120114	exon4			CATTTGGGTGGTG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.3717G>T	chr11.hg19:g.92495069G>T	ENSP00000298047:p.Trp1239Cys	98.0	0.0		126.0	45.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	18.45	3.626742	0.66901	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.51071	0.72;0.72;0.72	5.44	5.44	0.79542	.	.	.	.	.	T	0.52041	0.1710	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63060	-0.6721	9	0.59425	D	0.04	.	19.2605	0.93966	0.0:0.0:1.0:0.0	.	1239	Q8TDW7-3	.	C	1239;1239;1089	ENSP00000298047:W1239C;ENSP00000387040:W1239C;ENSP00000432586:W1089C	ENSP00000298047:W1239C	W	+	3	0	FAT3	92134717	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.797000	0.85911	2.531000	0.85337	0.563000	0.77884	TGG	.	.		0.448	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92495069	G	T	92495069	3	4	20	1	0	0	0	0	1	0	0	0	5699	1241	43	3	3731	3	FAT3	11	92495069	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	7498791	92495069	42511447	91	1818										
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118498741	118498741	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gattggcacactccaggaccGccctcccagccctttccgtg	9	18	0	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:118498741G>A	ENST00000361417.2	+	7	1613	c.1202G>A	c.(1201-1203)cGc>cAc	p.R401H	PHLDB1_ENST00000356063.5_Missense_Mutation_p.R401H	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	401										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CTCCAGGACCGCCCTCCCAGC	0.607																																					p.R401H		Atlas-SNP	.											.	PHLDB1	103	.	0			c.G1202A						.						88	87	87					11																	118498741		2200	4295	6495	SO:0001583	missense	23187	exon6			AGGACCGCCCTCC		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.1202G>A	chr11.hg19:g.118498741G>A	ENSP00000354498:p.Arg401His	68.0	0.0		75.0	21.0	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	hg19	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.070860	0.76301	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000356063	T;T	0.39056	1.11;1.1	5.32	5.32	0.75619	.	0.232964	0.41396	D	0.000882	T	0.52008	0.1708	L	0.46157	1.445	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.989	P;P;P	0.62014	0.897;0.881;0.474	T	0.44159	-0.9346	10	0.41790	T	0.15	-22.2486	11.7262	0.51710	0.0805:0.0:0.9195:0.0	.	401;401;401	Q86UU1-3;Q86UU1-2;Q86UU1	.;.;PHLB1_HUMAN	H	401;160;401	ENSP00000354498:R401H;ENSP00000348359:R401H	ENSP00000348359:R401H	R	+	2	0	PHLDB1	118003951	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.227000	0.89787	2.769000	0.95229	0.563000	0.77884	CGC	.	.		0.607	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		A	118498741	G	A	118498741	3	1	20	1	0	0	0	0	1	0	0	0	11860	1087	38	1	1220	1	PHLDB1	11	118498741	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	26003672	118498741	16507775	92	1819										
ROBO4	54538	hgsc.bcm.edu	37	chr11	124767647	124767656	+	Frame_Shift_Del	DEL	CAGGGAACCC	CAGGGAACCC	-													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	atgagcaggagcagcagaggCagggaacccctgccccccag							TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	CAGGGAACCC	CAGGGAACCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:124767647_124767656delCAGGGAACCC	ENST00000306534.3	-	1	521_530	c.36_45delGGGTTCCCTG	c.(34-45)aggggttccctgfs	p.RGSL12fs	ROBO4_ENST00000533054.1_5'UTR|ROBO4_ENST00000526899.1_Intron	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	12					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GCAGCAGAGGCAGGGAACCCCTGCCCCCCA	0.619																																					p.13_16del		Atlas-INDEL	.											.	ROBO4	130	.	0			c.37_46del						.																																			SO:0001589	frameshift_variant	54538	exon1			.	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.36_45delGGGTTCCCTG	chr11.hg19:g.124767647_124767656delCAGGGAACCC	ENSP00000304945:p.Arg12fs	304.0	0.0		235.0	42.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Frame_Shift_Del	DEL	ENST00000306534.3	hg19	CCDS8455.1																																																																																			.	.		0.619	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		-	124767656	CAGGGAACCC	-	124767647	7	5	20	1	0	1	0	1	0	0	0	0	13531	697	25	0	3050	0	ROBO4	11	124767647	Frame_Shift_Del	DEL	CAGGGAACCC	TCGA-2Y-A9HA-01A-11D-A38X-10	6268906	124767647	10238869	93	1820	7	2	1	6		3	2	13	N	GC_CAGGGAACCC_AGGGAACCCCTGC	5.232978e-05
ROBO4	54538	hgsc.bcm.edu	37	chr11	124767648	124767660	+	Frame_Shift_Del	DEL	AGGGAACCCCTGC	AGGGAACCCCTGC	-													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tgagcaggagcagcagaggcAgggaacccctgccccccagg					rs79793746	byFrequency	TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	AGGGAACCCCTGC	AGGGAACCCCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:124767648_124767660delAGGGAACCCCTGC	ENST00000306534.3	-	1	517_529	c.32_44delGCAGGGGTTCCCT	c.(31-45)ggcaggggttccctgfs	p.GRGSL11fs	ROBO4_ENST00000533054.1_5'UTR|ROBO4_ENST00000526899.1_Intron	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	11					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		CAGCAGAGGCAGGGAACCCCTGCCCCCCAGGAG	0.62																																					p.11_15del		Pindel	.											.	ROBO4	130	.	0			c.33_45del						.																																			SO:0001589	frameshift_variant	54538	exon1			.	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.32_44delGCAGGGGTTCCCT	chr11.hg19:g.124767648_124767660delAGGGAACCCCTGC	ENSP00000304945:p.Gly11fs	290.0	0.0		229.0	44.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Frame_Shift_Del	DEL	ENST00000306534.3	hg19	CCDS8455.1																																																																																			.	.		0.62	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		-	124767660	AGGGAACCCCTGC	-	124767648	7	5	20	1	0	1	0	1	0	0	0	0	13531	188	7	0	3051	0	ROBO4	11	124767648	Frame_Shift_Del	DEL	AGGGAACCCCTGC	TCGA-2Y-A9HA-01A-11D-A38X-10	1	124767648	10238868	94	1821	7	2	1	6		3	2	13	N	GC_CAGGGAACCC_AGGGAACCCCTGC	5.232978e-05
ROBO4	54538	hgsc.bcm.edu	37	chr11	124767659	124767660	+	Frame_Shift_Del	DEL	GC	GC	-													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	agcagaggcagggaacccctGccccccaggaggctgtctcc							TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr11:124767659_124767660delGC	ENST00000306534.3	-	1	517_518	c.32_33delGC	c.(31-33)ggcfs	p.G11fs	ROBO4_ENST00000533054.1_5'UTR|ROBO4_ENST00000526899.1_Intron	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	11					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GGGAACCCCTGCCCCCCAGGAG	0.619																																					p.11_12del		Atlas-INDEL	.											.	ROBO4	130	.	0			c.33_34del						.																																			SO:0001589	frameshift_variant	54538	exon1			.	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.32_33delGC	chr11.hg19:g.124767659_124767660delGC	ENSP00000304945:p.Gly11fs	272.0	0.0		217.0	42.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Frame_Shift_Del	DEL	ENST00000306534.3	hg19	CCDS8455.1																																																																																			.	.		0.619	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		-	124767660	GC	-	124767659	7	5	20	1	0	1	0	1	0	0	0	0	13531	1306	46	0	3062	0	ROBO4	11	124767659	Frame_Shift_Del	DEL	GC	TCGA-2Y-A9HA-01A-11D-A38X-10	11	124767659	10238857	95	1822			1	6		3	2	13	N	GC_CAGGGAACCC_AGGGAACCCCTGC	5.232978e-05
C12orf35	55196	hgsc.bcm.edu	37	chr12	32137127	32137127	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	aaggttctgtgggccagcaaActacataccagacctcagaa	9	11	2	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr12:32137127A>G	ENST00000312561.4	+	4	3652	c.3238A>G	c.(3238-3240)Act>Gct	p.T1080A	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1080																	GGGCCAGCAAACTACATACCA	0.418																																					p.T1080A		Atlas-SNP	.											.	.	.	.	0			c.A3238G						.						101	97	98					12																	32137127		2203	4299	6502	SO:0001583	missense	55196	exon4			CAGCAAACTACAT	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3238A>G	chr12.hg19:g.32137127A>G	ENSP00000310338:p.Thr1080Ala	119.0	0.0		145.0	44.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	A	2.802	-0.248988	0.05867	.	.	ENSG00000174718	ENST00000312561	T	0.11495	2.77	5.37	-4.63	0.03359	.	2.607030	0.01366	N	0.012407	T	0.07863	0.0197	L	0.29908	0.895	0.09310	N	1	B	0.21225	0.053	B	0.15484	0.013	T	0.27806	-1.0063	9	.	.	.	.	6.8637	0.24082	0.4508:0.0:0.4275:0.1217	.	1080	Q9HCM1	CL035_HUMAN	A	1080	ENSP00000310338:T1080A	.	T	+	1	0	C12orf35	32028394	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.171000	0.16685	-1.259000	0.02468	0.460000	0.39030	ACT	.	.		0.418	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		G	32137127	A	G	32137127	3	3	20	1	0	0	0	0	1	0	0	0	1684	43	2	2	3240	2	C12orf35	12	32137127	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10		32137127	101714768	96	1823										
TFCP2	7024	hgsc.bcm.edu	37	chr12	51489814	51489814	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	acatgcttcttcctgaaagtTctgtatcatctgaaaaatgc	6	9	4	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr12:51489814T>C	ENST00000257915.5	-	14	1887	c.1429A>G	c.(1429-1431)Aac>Gac	p.N477D	TFCP2_ENST00000307660.4_Missense_Mutation_p.N426D|TFCP2_ENST00000548115.1_Missense_Mutation_p.N426D|TFCP2_ENST00000549867.1_Missense_Mutation_p.N399D	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	477					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						TCCTGAAAGTTCTGTATCATC	0.358																																					p.N477D		Atlas-SNP	.											.	TFCP2	49	.	0			c.A1429G						.						124	118	120					12																	51489814		2203	4297	6500	SO:0001583	missense	7024	exon14			GAAAGTTCTGTAT	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.1429A>G	chr12.hg19:g.51489814T>C	ENSP00000257915:p.Asn477Asp	74.0	0.0		74.0	28.0	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	hg19	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.953162	0.92660	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000549867;ENST00000548115;ENST00000548108	T;T;T;T;T	0.51325	2.11;0.72;2.16;0.71;1.94	5.75	5.75	0.90469	.	0.154798	0.56097	D	0.000033	T	0.68174	0.2972	M	0.73598	2.24	0.54753	D	0.99998	D;P;D;D	0.71674	0.994;0.701;0.972;0.998	D;B;P;D	0.71184	0.955;0.201;0.901;0.972	T	0.71251	-0.4648	10	0.62326	D	0.03	-21.1478	15.3417	0.74303	0.0:0.0:0.0:1.0	.	426;399;477;477	Q12800-2;F8VX55;Q12800;Q12800-4	.;.;TFCP2_HUMAN;.	D	477;426;399;426;379	ENSP00000257915:N477D;ENSP00000304411:N426D;ENSP00000449742:N399D;ENSP00000447991:N426D;ENSP00000449280:N379D	ENSP00000257915:N477D	N	-	1	0	TFCP2	49776081	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.281000	0.78621	2.330000	0.79161	0.477000	0.44152	AAC	.	.		0.358	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653		C	51489814	T	C	51489814	3	2	20	1	0	0	0	0	1	0	0	0	15810	1783	62	2	87	2	TFCP2	12	51489814	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	19352687	51489814	82362081	97	1824										
TAOK3	51347	hgsc.bcm.edu	37	chr12	118599689	118599689	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tccagctggttttccagttcCgtctggtgctgtaaacggat	11	10	1	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr12:118599689C>A	ENST00000392533.3	-	18	2533	c.2043G>T	c.(2041-2043)acG>acT	p.T681T	TAOK3_ENST00000543709.1_5'Flank|TAOK3_ENST00000419821.2_Silent_p.T681T|TAOK3_ENST00000537952.1_Silent_p.T221T	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	681					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TTTCCAGTTCCGTCTGGTGCT	0.493																																					p.T681T		Atlas-SNP	.											.	TAOK3	151	.	0			c.G2043T						.						228	195	206					12																	118599689		2203	4300	6503	SO:0001819	synonymous_variant	51347	exon18			CAGTTCCGTCTGG	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.2043G>T	chr12.hg19:g.118599689C>A		61.0	0.0		78.0	25.0	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Silent	SNP	ENST00000392533.3	hg19	CCDS9188.1	.	.	.	.	.	.	.	.	.	.	A	10.07	1.248839	0.22880	.	.	ENSG00000135090	ENST00000359811	.	.	.	5.55	-1.67	0.08238	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	4.358	0.11188	0.4223:0.3753:0.1101:0.0923	.	.	.	.	X	299	.	ENSP00000352863:G299X	G	-	1	0	TAOK3	117084072	0.015000	0.18098	0.995000	0.50966	0.994000	0.84299	-0.635000	0.05471	-0.149000	0.11215	-0.256000	0.11100	GGA	.	.		0.493	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281		A	118599689	C	A	118599689	2	1	20	1	0	0	0	0	0	0	0	1	15564	639	23	1		1	TAOK3	12	118599689	Silent	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	67109875	118599689	15252206	98	1825										
TDRD3	81550	hgsc.bcm.edu	37	chr13	61103006	61103006	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cctgattatttttatgacagGaaatcacaaacaataaataa	4	6	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr13:61103006G>C	ENST00000196169.3	+	11	2156	c.1368G>C	c.(1366-1368)agG>agC	p.R456S	TDRD3_ENST00000377881.2_Missense_Mutation_p.R456S|TDRD3_ENST00000535286.1_Missense_Mutation_p.R549S|TDRD3_ENST00000377894.2_Missense_Mutation_p.R456S	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	456					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		TTTATGACAGGAAATCACAAA	0.279																																					p.R549S	Colon(36;164 906 35820 50723)	Atlas-SNP	.											.	TDRD3	123	.	0			c.G1647C						.						36	41	40					13																	61103006		2194	4296	6490	SO:0001583	missense	81550	exon11			TGACAGGAAATCA	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.1368G>C	chr13.hg19:g.61103006G>C	ENSP00000196169:p.Arg456Ser	362.0	0.0		306.0	42.0	NM_001146070	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	hg19	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.721810	0.48728	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286	D;D;D;D	0.94497	-3.44;-3.44;-3.44;-3.44	5.74	2.99	0.34606	.	0.214739	0.53938	D	0.000045	D	0.95771	0.8624	M	0.64997	1.995	0.53688	D	0.999978	D;D;D	0.89917	0.962;1.0;0.999	P;D;D	0.83275	0.604;0.996;0.991	D	0.93871	0.7162	9	.	.	.	-16.074	9.7929	0.40717	0.2314:0.0:0.7686:0.0	.	549;455;456	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	S	456;456;456;549	ENSP00000196169:R456S;ENSP00000367113:R456S;ENSP00000367126:R456S;ENSP00000440190:R549S	.	R	+	3	2	TDRD3	60001007	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.170000	0.42443	0.406000	0.25560	-0.142000	0.14014	AGG	.	.		0.279	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		C	61103006	G	C	61103006	3	2	20	1	0	0	0	0	1	0	0	0	15747	1165	41	4	1689	4	TDRD3	13	61103006	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10		61103006	54066872	99	1826										
OR11H6	122748	hgsc.bcm.edu	37	chr14	20692717	20692717	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tatgtgagcccaacatcaggGaacccagcaggaatgcagaa	11	10	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr14:20692717G>A	ENST00000315519.2	+	1	927	c.849G>A	c.(847-849)ggG>ggA	p.G283G		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		CAACATCAGGGAACCCAGCAG	0.443																																					p.G283G		Atlas-SNP	.											.	OR11H6	60	.	0			c.G849A						.						117	108	111					14																	20692717		2203	4300	6503	SO:0001819	synonymous_variant	122748	exon1			ATCAGGGAACCCA		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"GPCR / Class A : Olfactory receptors"	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.849G>A	chr14.hg19:g.20692717G>A		79.0	0.0		72.0	27.0	NM_001004480	Q6IF08	Silent	SNP	ENST00000315519.2	hg19	CCDS32033.1																																																																																			.	.		0.443	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1			A	20692717	G	A	20692717	2	1	20	1	0	0	0	0	0	0	0	1	10938	1161	41	3		3	OR11H6	14	20692717	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10		20692717	86656823	100	1827										
SALL2	6297	hgsc.bcm.edu	37	chr14	21992917	21992917	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gggaatgccagatgaggcgaGgcaatcagctgatctgtgct	15	8	2	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr14:21992917G>T	ENST00000327430.3	-	2	1239	c.945C>A	c.(943-945)gcC>gcA	p.A315A	SALL2_ENST00000450879.2_Silent_p.A178A|SALL2_ENST00000538754.1_Intron|AE000658.22_ENST00000535893.1_RNA|SALL2_ENST00000317492.5_Intron	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		GATGAGGCGAGGCAATCAGCT	0.637																																					p.A315A		Atlas-SNP	.											.	SALL2	95	.	0			c.C945A						.						36	39	38					14																	21992917		2201	4300	6501	SO:0001819	synonymous_variant	6297	exon2			AGGCGAGGCAATC	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"Zinc fingers, C2H2-type"	10526	protein-coding gene	gene with protein product		602219	"sal (Drosophila)-like 2", "sal-like 2 (Drosophila)"			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.945C>A	chr14.hg19:g.21992917G>T		37.0	0.0		51.0	18.0	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Silent	SNP	ENST00000327430.3	hg19	CCDS32045.1	.	.	.	.	.	.	.	.	.	.	G	3.434	-0.115530	0.06881	.	.	ENSG00000165821	ENST00000546363	.	.	.	4.3	-1.03	0.10102	.	.	.	.	.	T	0.22513	0.0543	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.25813	-1.0121	4	.	.	.	-29.0434	3.7987	0.08750	0.3807:0.0:0.4563:0.163	.	.	.	.	H	174	.	.	P	-	2	0	SALL2	21062757	1.000000	0.71417	0.154000	0.22540	0.930000	0.56654	2.455000	0.44988	-0.452000	0.07087	0.655000	0.94253	CCT	.	.		0.637	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407		T	21992917	G	T	21992917	2	4	20	1	0	0	0	0	0	0	0	1	13826	987	35	3		3	SALL2	14	21992917	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	1300200	21992917	85356623	101	1828										
CPSF2	53981	hgsc.bcm.edu	37	chr14	92625383	92625414	+	Frame_Shift_Del	DEL	TGAATTAGCTTGGATAGATGGTGTCTTAGATA	TGAATTAGCTTGGATAGATGGTGTCTTAGATA	-													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ttttgtaaggcaaaagatgcTgaattagcttggatagatgg					rs369230200		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	TGAATTAGCTTGGATAGATGGTGTCTTAGATA	TGAATTAGCTTGGATAGATGGTGTCTTAGATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr14:92625383_92625414delTGAATTAGCTTGGATAGATGGTGTCTTAGATA	ENST00000298875.4	+	14	2163_2194	c.1878_1909delTGAATTAGCTTGGATAGATGGTGTCTTAGATA	c.(1876-1911)gctgaattagcttggatagatggtgtcttagatatgfs	p.ELAWIDGVLDM627fs		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	627					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		CAAAAGATGCTGAATTAGCTTGGATAGATGGTGTCTTAGATATGAGAGTTTC	0.418																																					p.626_636del	Ovarian(78;28 1788 18702 44111)	Atlas-Indel,Pindel	.											CPSF2,NS,carcinoma,0,1	CPSF2	63	.	0			c.1877_1908del						.																																			SO:0001589	frameshift_variant	53981	exon14			.	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"cleavage and polyadenylation specific factor 2, 100kD subunit"			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.1878_1909delTGAATTAGCTTGGATAGATGGTGTCTTAGATA	chr14.hg19:g.92625383_92625414delTGAATTAGCTTGGATAGATGGTGTCTTAGATA	ENSP00000298875:p.Glu627fs	222.0	0.0		190.0	32.0	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Frame_Shift_Del	DEL	ENST00000298875.4	hg19	CCDS9902.1																																																																																			.	.		0.418	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1			-	92625414	TGAATTAGCTTGGATAGATGGTGTCTTAGATA	-	92625383	7	5	20	1	0	1	0	1	0	0	0	0	3827	1567	55	0	1924	0	CPSF2	14	92625383	Frame_Shift_Del	DEL	TGAATTAGCTTGGATAGATGGTGTCTTAGATA	TCGA-2Y-A9HA-01A-11D-A38X-10	70632466	92625383	14724157	102	1829										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94173087	94173087	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ccagcttcgcctccaggctaTtcagaaccacgtgaaccacc	7	17	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr14:94173087T>A	ENST00000393151.2	+	50	7745	c.7745T>A	c.(7744-7746)aTt>aAt	p.I2582N	UNC79_ENST00000553484.1_Missense_Mutation_p.I2604N|UNC79_ENST00000555664.1_Missense_Mutation_p.I2543N|UNC79_ENST00000256339.4_Missense_Mutation_p.I2405N			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2582					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CTCCAGGCTATTCAGAACCAC	0.572																																					p.I2405N		Atlas-SNP	.											.	UNC79	366	.	0			c.T7214A						.						71	76	74					14																	94173087		2203	4300	6503	SO:0001583	missense	57578	exon50			AGGCTATTCAGAA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7745T>A	chr14.hg19:g.94173087T>A	ENSP00000376858:p.Ile2582Asn	130.0	0.0		115.0	50.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	T	21.1	4.102135	0.76983	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.21191	2.02;2.05;2.02;2.02	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.39517	0.1081	L	0.44542	1.39	0.80722	D	1	D	0.67145	0.996	D	0.71414	0.973	T	0.14392	-1.0474	10	0.72032	D	0.01	-19.0661	16.1338	0.81465	0.0:0.0:0.0:1.0	.	2604	C9JQL1	.	N	2405;2543;2604;2582;2604	ENSP00000256339:I2405N;ENSP00000450868:I2543N;ENSP00000451360:I2604N;ENSP00000376858:I2582N	ENSP00000256339:I2405N	I	+	2	0	KIAA1409	93242840	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.040000	0.89188	2.216000	0.71823	0.459000	0.35465	ATT	.	.		0.572	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94173087	T	A	94173087	3	1	20	1	0	0	0	0	1	0	0	0	8239	1493	52	4	7400	4	KIAA1409	14	94173087	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	1547704	94173087	13176453	103	1830										
AK7	122481	hgsc.bcm.edu	37	chr14	96953300	96953300	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gaggctcagtcaattcccctGagaaactatttaatgaccta	7	10	2	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr14:96953300G>A	ENST00000267584.4	+	17	2084	c.2040G>A	c.(2038-2040)ctG>ctA	p.L680L		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	680	DPY-30.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		CAATTCCCCTGAGAAACTATT	0.393																																					p.L680L		Atlas-SNP	.											.	AK7	69	.	0			c.G2040A						.						88	87	87					14																	96953300		2203	4300	6503	SO:0001819	synonymous_variant	122481	exon17			TCCCCTGAGAAAC	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.2040G>A	chr14.hg19:g.96953300G>A		68.0	0.0		67.0	22.0	NM_152327	Q8IYP6	Silent	SNP	ENST00000267584.4	hg19	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	G	6.905	0.536470	0.13188	.	.	ENSG00000140057	ENST00000554706	.	.	.	5.45	2.41	0.29592	.	.	.	.	.	T	0.46014	0.1371	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32322	-0.9911	4	.	.	.	-21.3558	3.2749	0.06894	0.1854:0.1356:0.5405:0.1385	.	.	.	.	K	102	.	.	E	+	1	0	AK7	96023053	1.000000	0.71417	0.998000	0.56505	0.765000	0.43378	3.352000	0.52239	0.766000	0.33244	0.591000	0.81541	GAG	.	.		0.393	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			A	96953300	G	A	96953300	2	1	20	1	0	0	0	0	0	0	0	1	444	1277	45	3		3	AK7	14	96953300	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	2780213	96953300	10396240	104	1831										
RYR3	6263	hgsc.bcm.edu	37	chr15	33961610	33961610	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ctgcccctgcccagaggagaTtcgggaggagctgtatgatt	14	10	0	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr15:33961610T>C	ENST00000389232.4	+	37	5745	c.5675T>C	c.(5674-5676)aTt>aCt	p.I1892T	RYR3_ENST00000415757.3_Missense_Mutation_p.I1892T	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1892	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CCAGAGGAGATTCGGGAGGAG	0.458																																					p.I1892T		Atlas-SNP	.											.	RYR3	760	.	0			c.T5675C						.						101	100	100					15																	33961610		1879	4106	5985	SO:0001583	missense	6263	exon37			AGGAGATTCGGGA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.5675T>C	chr15.hg19:g.33961610T>C	ENSP00000373884:p.Ile1892Thr	106.0	0.0		99.0	34.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.383338	0.61845	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.73469	-0.75;-0.34	5.29	5.29	0.74685	.	0.064498	0.64402	D	0.000007	T	0.82153	0.4975	L	0.60455	1.87	0.38780	D	0.954731	D;P	0.59357	0.985;0.94	P;P	0.60789	0.879;0.497	D	0.85571	0.1234	10	0.87932	D	0	.	15.4016	0.74845	0.0:0.0:0.0:1.0	.	1892;1892	Q15413-2;Q15413	.;RYR3_HUMAN	T	1892	ENSP00000373884:I1892T;ENSP00000399610:I1892T	ENSP00000354735:I1892T	I	+	2	0	RYR3	31748902	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.081000	0.71309	2.222000	0.72286	0.533000	0.62120	ATT	.	.		0.458	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			C	33961610	T	C	33961610	3	2	20	1	0	0	0	0	1	0	0	0	13785	1493	52	2	5821	2	RYR3	15	33961610	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10		33961610	68569782	105	1832										
C15orf55	256646	hgsc.bcm.edu	37	chr15	34640395	34640395	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ggatgggggcccttgcctcaGtggggctggggctggcaagg	21	9	1	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr15:34640395G>A	ENST00000333756.4	+	2	397	c.242G>A	c.(241-243)aGt>aAt	p.S81N	NUTM1_ENST00000537011.1_Missense_Mutation_p.S109N|NUTM1_ENST00000438749.3_Missense_Mutation_p.S99N	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	81	Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCTTGCCTCAGTGGGGCTGGG	0.557																																					p.S81N		Atlas-SNP	.											.	C15orf55	110	.	0			c.G242A						.						78	77	78					15																	34640395		2201	4298	6499	SO:0001583	missense	256646	exon2			GCCTCAGTGGGGC	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"nuclear protein in testis"	608963	"chromosome 15 open reading frame 55"	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.242G>A	chr15.hg19:g.34640395G>A	ENSP00000329448:p.Ser81Asn	86.0	0.0		110.0	40.0	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	hg19	CCDS32190.1	.	.	.	.	.	.	.	.	.	.	G	11.46	1.645101	0.29246	.	.	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000354999;ENST00000333756	T;T;T	0.35789	1.29;1.29;1.29	5.49	1.38	0.22167	Nuclear Testis  protein, N-terminal (1);	0.413136	0.23777	N	0.044677	T	0.36663	0.0975	L	0.52364	1.645	0.09310	N	0.999998	P;P;B	0.43938	0.822;0.787;0.011	P;B;B	0.48598	0.583;0.372;0.018	T	0.16335	-1.0406	10	0.33141	T	0.24	.	8.9065	0.35526	0.0831:0.4666:0.4503:0.0	.	99;109;81	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	N	109;99;81;81	ENSP00000444896:S109N;ENSP00000407031:S99N;ENSP00000329448:S81N	ENSP00000329448:S81N	S	+	2	0	C15orf55	32427687	0.993000	0.37304	0.704000	0.30370	0.234000	0.25298	0.417000	0.21214	0.006000	0.14734	-0.175000	0.13238	AGT	.	.		0.557	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		A	34640395	G	A	34640395	3	1	20	1	0	0	0	0	1	0	0	0	1805	1029	36	3	248	3	C15orf55	15	34640395	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	678785	34640395	67890997	106	1833										
GABPB1	2553	hgsc.bcm.edu	37	chr15	50595257	50595257	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	caccacctcttgatgattgtGttctgtggcccaatggagag	11	10	2	3	rs376724985		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr15:50595257G>T	ENST00000220429.8	-	4	508	c.340C>A	c.(340-342)Cac>Aac	p.H114N	GABPB1_ENST00000560825.1_Missense_Mutation_p.H114N|GABPB1_ENST00000543881.1_Missense_Mutation_p.H38N|GABPB1_ENST00000396464.3_Missense_Mutation_p.H114N|GABPB1_ENST00000380877.3_Missense_Mutation_p.H114N|GABPB1_ENST00000429662.2_Missense_Mutation_p.H114N|GABPB1_ENST00000359031.4_Missense_Mutation_p.H114N			Q06547	GABP1_HUMAN	GA binding protein transcription factor, beta subunit 1	114					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(1)|large_intestine(7)|lung(5)	14						TGATGATTGTGTTCTGTGGCC	0.343																																					p.H114N		Atlas-SNP	.											.	GABPB1	33	.	0			c.C340A						.						140	126	131					15																	50595257		2196	4295	6491	SO:0001583	missense	2553	exon4			GATTGTGTTCTGT	D13316	CCDS10135.1, CCDS10136.1, CCDS32239.1, CCDS45258.1	15q21.2	2013-01-10	2008-02-25	2008-02-25	ENSG00000104064	ENSG00000104064		"Ankyrin repeat domain containing"	4074	protein-coding gene	gene with protein product		600610	"GA binding protein transcription factor, beta subunit 2"	GABPB2		7958862	Standard	NM_016655		Approved	E4TF1-47, GABPB	uc001zyb.3	Q06547	OTTHUMG00000131642	ENST00000220429.8:c.340C>A	chr15.hg19:g.50595257G>T	ENSP00000220429:p.His114Asn	30.0	0.0		44.0	18.0	NM_016654	A8IE52|Q06545|Q12940|Q12941|Q12942|Q8IYD0	Missense_Mutation	SNP	ENST00000220429.8	hg19	CCDS32239.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.655514	0.67586	.	.	ENSG00000104064	ENST00000220429;ENST00000380877;ENST00000543881;ENST00000396464;ENST00000429662;ENST00000359031	T;T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07;0.07	6.17	6.17	0.99709	Ankyrin repeat-containing domain (3);	0.053984	0.64402	D	0.000001	T	0.48484	0.1502	N	0.17838	0.53	0.80722	D	1	B;B;P;B;B	0.35433	0.273;0.028;0.501;0.33;0.283	B;B;B;B;B	0.39706	0.211;0.026;0.297;0.307;0.204	T	0.33240	-0.9876	10	0.10636	T	0.68	-4.1401	20.8794	0.99867	0.0:0.0:1.0:0.0	.	114;114;114;114;114	B7Z726;Q06547-3;Q06547-4;Q06547;Q06547-2	.;.;.;GABP1_HUMAN;.	N	114;114;38;114;114;114	ENSP00000220429:H114N;ENSP00000370259:H114N;ENSP00000442500:H38N;ENSP00000379728:H114N;ENSP00000395771:H114N;ENSP00000351923:H114N	ENSP00000220429:H114N	H	-	1	0	GABPB1	48382549	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.769000	0.85360	2.941000	0.99782	0.655000	0.94253	CAC	.	.		0.343	GABPB1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000418294.1			T	50595257	G	T	50595257	3	4	20	1	0	0	0	0	1	0	0	0	6166	1377	48	3	919	3	GABPB1	15	50595257	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	15954862	50595257	51936135	107	1834										
SLCO3A1	28232	hgsc.bcm.edu	37	chr15	92459362	92459362	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ggcacgcgggcaccggccgcGcctgatcggctgcggcggca	18	16	0	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr15:92459362G>T	ENST00000318445.6	+	2	534	c.320G>T	c.(319-321)cGc>cTc	p.R107L	SLCO3A1_ENST00000424469.2_Missense_Mutation_p.R107L	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	107					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	CACCGGCCGCGCCTGATCGGC	0.677																																					p.R107L		Atlas-SNP	.											.	SLCO3A1	84	.	0			c.G320T						.						21	18	19					15																	92459362		2084	4064	6148	SO:0001583	missense	28232	exon2			GGCCGCGCCTGAT	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"Solute carriers"	10952	protein-coding gene	gene with protein product		612435	"solute carrier family 21 (organic anion transporter), member 11"	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.320G>T	chr15.hg19:g.92459362G>T	ENSP00000320634:p.Arg107Leu	57.0	0.0		49.0	18.0	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Missense_Mutation	SNP	ENST00000318445.6	hg19	CCDS10371.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.010901	0.75046	.	.	ENSG00000176463	ENST00000318445;ENST00000424469;ENST00000553304	T;T;T	0.49720	0.77;0.77;0.77	5.22	3.32	0.38043	Major facilitator superfamily domain, general substrate transporter (1);	0.051348	0.85682	D	0.000000	T	0.61009	0.2313	M	0.64080	1.96	0.80722	D	1	P;D;D	0.89917	0.648;0.998;1.0	B;D;D	0.91635	0.107;0.994;0.999	T	0.56829	-0.7914	10	0.35671	T	0.21	.	9.4833	0.38913	0.0747:0.0:0.7824:0.1428	.	49;107;107	Q9UIG8-3;Q9UIG8-2;Q9UIG8	.;.;SO3A1_HUMAN	L	107;107;49	ENSP00000320634:R107L;ENSP00000387846:R107L;ENSP00000450559:R49L	ENSP00000320634:R107L	R	+	2	0	SLCO3A1	90260366	1.000000	0.71417	0.994000	0.49952	0.906000	0.53458	9.199000	0.95003	0.691000	0.31592	0.655000	0.94253	CGC	.	.		0.677	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272		T	92459362	G	T	92459362	3	4	20	1	0	0	0	0	1	0	0	0	14743	1087	38	1	326	1	SLCO3A1	15	92459362	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	41864105	92459362	10072030	108	1835										
HAGHL	84264	hgsc.bcm.edu	37	chr16	778845	778845	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gcaacctggagtttgcccagAaagtggagccctgcaacgac	12	12	0	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr16:778845A>G	ENST00000341413.4	+	7	831	c.550A>G	c.(550-552)Aaa>Gaa	p.K184E	HAGHL_ENST00000549114.1_3'UTR|HAGHL_ENST00000564545.1_3'UTR|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000389703.3_Missense_Mutation_p.K184E|CCDC78_ENST00000293889.6_5'Flank|HAGHL_ENST00000561546.1_Missense_Mutation_p.K184E|HAGHL_ENST00000564537.1_3'UTR			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	184							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				GTTTGCCCAGAAAGTGGAGCC	0.662																																					p.K184E	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											.	HAGHL	18	.	0			c.A550G						.						27	27	27					16																	778845		2186	4293	6479	SO:0001583	missense	84264	exon6			GCCCAGAAAGTGG	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"hydroxyacyl glutathione hydrolase-like"			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.550A>G	chr16.hg19:g.778845A>G	ENSP00000341952:p.Lys184Glu	171.0	0.0		129.0	51.0	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Missense_Mutation	SNP	ENST00000341413.4	hg19		.	.	.	.	.	.	.	.	.	.	A	13.01	2.107910	0.37242	.	.	ENSG00000103253	ENST00000341413;ENST00000389703	D;D	0.95554	-3.74;-3.74	4.68	-0.551	0.11822	.	0.318671	0.29410	N	0.012225	D	0.92103	0.7497	N	0.22421	0.69	0.09310	N	1	D;D;D	0.65815	0.978;0.995;0.967	P;P;B	0.59115	0.588;0.852;0.437	D	0.85408	0.1135	10	0.27785	T	0.31	-6.8329	5.2321	0.15428	0.5008:0.3257:0.1734:0.0	.	184;184;184	B4DED4;Q6PII5-2;Q6PII5	.;.;HAGHL_HUMAN	E	184	ENSP00000341952:K184E;ENSP00000374353:K184E	ENSP00000341952:K184E	K	+	1	0	HAGHL	718846	0.000000	0.05858	0.005000	0.12908	0.278000	0.26855	0.804000	0.27098	-0.120000	0.11809	0.459000	0.35465	AAA	.	.		0.662	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304		G	778845	A	G	778845	3	3	20	1	0	0	0	0	1	0	0	0	6955	247	9	2	572	2	HAGHL	16	778845	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10		778845	89575908	109	1836										
IGFALS	3483	hgsc.bcm.edu	37	chr16	1841152	1841152	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gctctgctcctcaatgcccaCgaggccgttgtccttgagga	11	14	2	1	rs200564045		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr16:1841152C>G	ENST00000215539.3	-	2	1377	c.1267G>C	c.(1267-1269)Gtg>Ctg	p.V423L	IGFALS_ENST00000415638.3_Missense_Mutation_p.V461L			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit	423					cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						TCAATGCCCACGAGGCCGTTG	0.692																																					p.V461L		Atlas-SNP	.											.	IGFALS	29	.	0			c.G1381C						.						18	22	21					16																	1841152		2186	4285	6471	SO:0001583	missense	3483	exon2			TGCCCACGAGGCC	M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638	ENST00000215539.3:c.1267G>C	chr16.hg19:g.1841152C>G	ENSP00000215539:p.Val423Leu	74.0	0.0		51.0	22.0	NM_001146006	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	hg19	CCDS10446.1	.	.	.	.	.	.	.	.	.	.	C	3.077	-0.189835	0.06299	.	.	ENSG00000099769	ENST00000215539;ENST00000415638	T;T	0.24151	1.87;1.87	4.68	-9.35	0.00633	.	0.965904	0.08571	N	0.926114	T	0.13286	0.0322	L	0.31926	0.97	0.09310	N	1	B;B	0.26081	0.141;0.024	B;B	0.22880	0.04;0.042	T	0.15037	-1.0451	10	0.34782	T	0.22	.	6.5128	0.22232	0.3895:0.3294:0.0:0.2811	.	461;423	E9PGU3;P35858	.;ALS_HUMAN	L	423;461	ENSP00000215539:V423L;ENSP00000416683:V461L	ENSP00000215539:V423L	V	-	1	0	IGFALS	1781153	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.109000	0.03309	-2.028000	0.00931	-0.397000	0.06425	GTG	.	.		0.692	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2			G	1841152	C	G	1841152	3	3	20	1	0	0	0	0	1	0	0	0	7586	536	19	4	554	4	IGFALS	16	1841152	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	1062307	1841152	88513601	110	1837										
ANKS3	124401	hgsc.bcm.edu	37	chr16	4780104	4780104	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cgtgccacatggacaagctgCggttcaggagttccggctcg	14	12	1	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr16:4780104C>T	ENST00000304283.4	-	3	341	c.47G>A	c.(46-48)cGc>cAc	p.R16H	RP11-127I20.7_ENST00000588099.1_RNA|ANKS3_ENST00000592711.1_Missense_Mutation_p.R16H|ANKS3_ENST00000450067.2_5'UTR|ANKS3_ENST00000446014.2_5'UTR|ANKS3_ENST00000585773.1_Intron	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	16										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						GGACAAGCTGCGGTTCAGGAG	0.597																																					p.R16H		Atlas-SNP	.											.	ANKS3	44	.	0			c.G47A						.						75	62	67					16																	4780104		2197	4300	6497	SO:0001583	missense	124401	exon3			AAGCTGCGGTTCA	AK057329	CCDS10520.1, CCDS73820.1	16p13.3	2013-01-10			ENSG00000168096	ENSG00000168096		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	29422	protein-coding gene	gene with protein product						11853319	Standard	NM_133450		Approved	KIAA1977, FLJ32345, FLJ32767	uc002cxj.2	Q6ZW76	OTTHUMG00000129478	ENST00000304283.4:c.47G>A	chr16.hg19:g.4780104C>T	ENSP00000304586:p.Arg16His	61.0	0.0		69.0	28.0	NM_133450	B4DWU4|D3DUE2|Q8TF25	Missense_Mutation	SNP	ENST00000304283.4	hg19	CCDS10520.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.418416	0.62622	.	.	ENSG00000168096	ENST00000304283	T	0.36699	1.24	5.82	4.87	0.63330	.	0.427454	0.27896	N	0.017413	T	0.16981	0.0408	N	0.03608	-0.345	0.80722	D	1	B	0.23735	0.09	B	0.16289	0.015	T	0.07597	-1.0764	10	0.17369	T	0.5	-4.3007	14.0612	0.64802	0.0:0.9281:0.0:0.0719	.	16	Q6ZW76	ANKS3_HUMAN	H	16	ENSP00000304586:R16H	ENSP00000304586:R16H	R	-	2	0	ANKS3	4720105	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.320000	0.51991	1.477000	0.48234	0.561000	0.74099	CGC	.	.		0.597	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450		T	4780104	C	T	4780104	3	4	20	1	0	0	0	0	1	0	0	0	690	768	27	1	1983	1	ANKS3	16	4780104	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	2938952	4780104	85574649	111	1838										
NFAT5	10725	hgsc.bcm.edu	37	chr16	69724937	69724937	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	agcagtatgattaagagtgaAgatgttactccaatggaagt	11	4	0	4			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr16:69724937A>C	ENST00000354436.2	+	11	2133	c.1815A>C	c.(1813-1815)gaA>gaC	p.E605D	NFAT5_ENST00000567239.1_Missense_Mutation_p.E622D|NFAT5_ENST00000432919.1_Missense_Mutation_p.E623D|NFAT5_ENST00000393742.2_Missense_Mutation_p.E529D|NFAT5_ENST00000349945.1_Missense_Mutation_p.E529D|NFAT5_ENST00000566899.1_Missense_Mutation_p.E529D	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	605					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TTAAGAGTGAAGATGTTACTC	0.348																																					p.E623D		Atlas-SNP	.											.	NFAT5	184	.	0			c.A1869C						.						103	101	101					16																	69724937		2198	4297	6495	SO:0001583	missense	10725	exon12			GAGTGAAGATGTT	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.1815A>C	chr16.hg19:g.69724937A>C	ENSP00000346420:p.Glu605Asp	196.0	0.0		131.0	78.0	NM_138713	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Missense_Mutation	SNP	ENST00000354436.2	hg19	CCDS10881.1	.	.	.	.	.	.	.	.	.	.	A	32	5.134342	0.94517	.	.	ENSG00000102908	ENST00000432919;ENST00000426654;ENST00000349945;ENST00000354436;ENST00000393742	T;T;T;T	0.52295	0.69;0.67;0.68;0.67	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.62829	0.2460	L	0.56769	1.78	0.58432	D	0.999998	D;D;D	0.63880	0.993;0.993;0.984	P;P;D	0.68192	0.864;0.864;0.956	T	0.59252	-0.7489	10	0.26408	T	0.33	-3.2161	15.3914	0.74747	1.0:0.0:0.0:0.0	.	622;605;623	A2RRB4;O94916;E9PHR7	.;NFAT5_HUMAN;.	D	623;622;529;605;529	ENSP00000396538:E623D;ENSP00000338806:E529D;ENSP00000346420:E605D;ENSP00000377343:E529D	ENSP00000338806:E529D	E	+	3	2	NFAT5	68282438	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.394000	0.66285	2.042000	0.60477	0.533000	0.62120	GAA	.	.		0.348	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		C	69724937	A	C	69724937	3	2	20	1	0	0	0	0	1	0	0	0	10369	69	3	5	1915	5	NFAT5	16	69724937	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	64944833	69724937	20629816	112	1839										
TP53	7157	hgsc.bcm.edu	37	chr17	7577572	7577572	+	Frame_Shift_Del	DEL	T	T	-													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	catgcaggaactgttacacaTgtagttgtagtggatggtgg							TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr17:7577572delT	ENST00000269305.4	-	7	898	c.709delA	c.(709-711)atgfs	p.M237fs	TP53_ENST00000455263.2_Frame_Shift_Del_p.M237fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.M237fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.M237fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.M237fs|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000359597.4_Frame_Shift_Del_p.M237fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	237	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		M -> I (in LFS; germline mutation and in sporadic cancers; somatic mutation).|M -> K (in sporadic cancers; somatic mutation).|M -> L (in sporadic cancers; somatic mutation).|M -> R (in sporadic cancers; somatic mutation).|M -> T (in sporadic cancers; somatic mutation).|M -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.M237V(6)|p.?(5)|p.M237L(5)|p.M237fs*10(2)|p.Y236_M237delYM(1)|p.Y236_M237insXX(1)|p.H233fs*6(1)|p.M144L(1)|p.M237_N239delMCN(1)|p.Y236_M243delYMCNSSCM(1)|p.V225fs*23(1)|p.Y236_M237>*L(1)|p.H233_C242del10(1)|p.M237fs*1(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGTTACACATGTAGTTGTAG	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.M237fs	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,+1,30	TP53	33396	.	36	Substitution - Missense(12)|Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(5)|Deletion - In frame(4)|Insertion - In frame(1)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(6)|breast(6)|biliary_tract(5)|upper_aerodigestive_tract(4)|bone(4)|central_nervous_system(2)|urinary_tract(2)|ovary(2)|cervix(1)|stomach(1)|large_intestine(1)|lung(1)|pancreas(1)	c.710delT						.						128	101	110					17																	7577572		2203	4300	6503	SO:0001589	frameshift_variant	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.709delA	chr17.hg19:g.7577572delT	ENSP00000269305:p.Met237fs	81.0	0.0		44.0	28.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7577572	T	-	7577572	7	5	20	1	0	1	0	1	0	0	0	0	16396	1464	51	0	581	0	TP53	17	7577572	Frame_Shift_Del	DEL	T	TCGA-2Y-A9HA-01A-11D-A38X-10		7577572	73617638	113	1840										
EZH1	2145	hgsc.bcm.edu	37	chr17	40854591	40854591	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ctcgatccccacgtacttgaGagcatcagcttggctgtacc	9	14	1	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr17:40854591G>A	ENST00000428826.2	-	21	2324	c.2203C>T	c.(2203-2205)Ctc>Ttc	p.L735F	EZH1_ENST00000592743.1_Missense_Mutation_p.L735F|EZH1_ENST00000435174.1_Missense_Mutation_p.L596F|EZH1_ENST00000415827.2_Missense_Mutation_p.L726F|EZH1_ENST00000590078.1_Missense_Mutation_p.L665F|EZH1_ENST00000585893.1_Missense_Mutation_p.L695F|EZH1_ENST00000590783.1_5'Flank			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	735				VVMVNGDHRIGIFAKRAIQAGEELFFDYRYSQADALKYVGI ERETDVL -> GESQ (in Ref. 2; BAA25019). {ECO:0000305}.	anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)			breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		ACGTACTTGAGAGCATCAGCT	0.562																																					p.L735F		Atlas-SNP	.											.	EZH1	62	.	0			c.C2203T						.						123	85	98					17																	40854591		2199	4296	6495	SO:0001583	missense	2145	exon21			ACTTGAGAGCATC		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.2203C>T	chr17.hg19:g.40854591G>A	ENSP00000404658:p.Leu735Phe	94.0	0.0		113.0	12.0	NM_001991	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Missense_Mutation	SNP	ENST00000428826.2	hg19	CCDS32659.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.997112	0.93167	.	.	ENSG00000108799	ENST00000264646;ENST00000428826;ENST00000415827;ENST00000435174	D;D	0.82526	-1.62;-1.62	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	D	0.90693	0.7080	M	0.70903	2.155	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.998;0.997	D;D;D;D	0.72625	0.978;0.978;0.978;0.973	D	0.91106	0.4918	10	0.72032	D	0.01	.	19.1135	0.93328	0.0:0.0:1.0:0.0	.	596;695;741;735	Q92800-5;Q92800-3;Q92800-2;Q92800	.;.;.;EZH1_HUMAN	F	738;735;695;596	ENSP00000404658:L735F;ENSP00000404071:L596F	ENSP00000264646:L738F	L	-	1	0	EZH1	38108117	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.619000	0.61218	2.757000	0.94681	0.462000	0.41574	CTC	.	.		0.562	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		A	40854591	G	A	40854591	3	1	20	1	0	0	0	0	1	0	0	0	5335	942	33	3	44	3	EZH1	17	40854591	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	33277019	40854591	40340619	114	1841										
SFRS1	6426	hgsc.bcm.edu	37	chr17	56082880	56082880	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tctgctacggcttctgctacGactacggcttcgagatcgag	11	12	2	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr17:56082880G>T	ENST00000258962.4	-	4	842	c.634C>A	c.(634-636)Cgt>Agt	p.R212S	RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000581497.1_5'Flank|SRSF1_ENST00000585096.1_Intron|SRSF1_ENST00000582730.2_3'UTR|SRSF1_ENST00000584773.1_Missense_Mutation_p.R212S	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	212	Arg/Ser-rich (RS domain).|Interacts with SAFB1.				cardiac muscle contraction (GO:0060048)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA 3'-end processing (GO:0031124)|mRNA 5'-splice site recognition (GO:0000395)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CTTCTGCTACGACTACGGCTT	0.512																																					p.R212S		Atlas-SNP	.											.	SRSF1	41	.	0			c.C634A						.						158	146	150					17																	56082880		2203	4300	6503	SO:0001583	missense	6426	exon4			TGCTACGACTACG		CCDS11600.1, CCDS58580.1	17q22	2013-02-12	2010-06-22	2010-06-22	ENSG00000136450	ENSG00000136450		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10780	protein-coding gene	gene with protein product	"splicing factor 2", "pre-mRNA-splicing factor SF2, P33 subunit", "alternate splicing factor", "SR splicing factor 1"	600812	"splicing factor, arginine/serine-rich 1"	SFRS1		8530103, 20516191	Standard	NM_006924		Approved	ASF, SF2, SRp30a, SF2p33, MGC5228	uc002ivi.3	Q07955		ENST00000258962.4:c.634C>A	chr17.hg19:g.56082880G>T	ENSP00000258962:p.Arg212Ser	119.0	0.0		106.0	47.0	NM_006924	B2R6Z7|D3DTZ3|Q13809	Missense_Mutation	SNP	ENST00000258962.4	hg19	CCDS11600.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.328364	0.24080	.	.	ENSG00000136450	ENST00000258962	T	0.19394	2.15	5.65	4.67	0.58626	.	0.825711	0.11230	N	0.585740	T	0.23133	0.0559	L	0.46157	1.445	0.80722	D	1	B	0.12013	0.005	B	0.06405	0.002	T	0.04281	-1.0963	10	0.24483	T	0.36	.	16.8491	0.85989	0.0:0.1285:0.8715:0.0	.	212	Q07955	SRSF1_HUMAN	S	212	ENSP00000258962:R212S	ENSP00000258962:R212S	R	-	1	0	SRSF1	53437879	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.581000	0.74045	1.488000	0.48433	0.650000	0.86243	CGT	.	.		0.512	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924		T	56082880	G	T	56082880	3	4	20	1	0	0	0	0	1	0	0	0	14180	1058	37	1	116	1	SFRS1	17	56082880	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	15228289	56082880	25112330	115	1842										
CCDC45	90799	hgsc.bcm.edu	37	chr17	62506387	62506387	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ctacttgcaggtcagcttgtCtcacataacaggttggtata	9	9	2	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr17:62506387C>G	ENST00000556440.2	+	3	755	c.245C>G	c.(244-246)tCt>tGt	p.S82C	CEP95_ENST00000581056.1_Missense_Mutation_p.S82C|CEP95_ENST00000553412.1_5'UTR	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	82						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						GTCAGCTTGTCTCACATAACA	0.353																																					p.S82C		Atlas-SNP	.											.	CEP95	103	.	0			c.C245G						.						111	101	104					17																	62506387		1920	4143	6063	SO:0001583	missense	90799	exon3			GCTTGTCTCACAT	AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.245C>G	chr17.hg19:g.62506387C>G	ENSP00000450461:p.Ser82Cys	103.0	0.0		120.0	43.0	NM_138363	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	hg19	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.402941	0.42613	.	.	ENSG00000258890	ENST00000553956;ENST00000556440	T;T	0.35236	1.32;1.32	5.76	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.61035	0.2315	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.65697	-0.6105	10	0.52906	T	0.07	-11.9883	16.1905	0.81986	0.1343:0.8657:0.0:0.0	.	82	Q96GE4	CEP95_HUMAN	C	82	ENSP00000452317:S82C;ENSP00000450461:S82C	ENSP00000438458:S82C	S	+	2	0	CEP95	59936849	1.000000	0.71417	1.000000	0.80357	0.002000	0.02628	6.761000	0.74945	1.433000	0.47394	-0.324000	0.08512	TCT	.	.		0.353	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		G	62506387	C	G	62506387	3	3	20	1	0	0	0	0	1	0	0	0	2818	913	32	4	255	4	CCDC45	17	62506387	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	6423507	62506387	18688823	116	1843										
UTS2R	2837	hgsc.bcm.edu	37	chr17	80332945	80332945	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	agcgcgcctccttcaagcggGcccggcggccgggggcgcgc	18	17	1	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr17:80332945G>C	ENST00000313135.2	+	1	793	c.745G>C	c.(745-747)Gcc>Ccc	p.A249P		NM_018949.1	NP_061822.1	Q9UKP6	UR2R_HUMAN	urotensin 2 receptor	249					blood circulation (GO:0008015)|negative regulation of blood pressure (GO:0045776)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cell growth (GO:0030307)|positive regulation of circadian sleep/wake cycle, REM sleep (GO:0046005)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of vasoconstriction (GO:0045907)|regulation of vasodilation (GO:0042312)|response to drug (GO:0042493)|signal transduction (GO:0007165)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)|urotensin II receptor activity (GO:0001604)			breast(1)|endometrium(4)|kidney(1)|lung(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.00928)|BRCA - Breast invasive adenocarcinoma(99;0.0833)			CTTCAAgcgggcccggcggcc	0.756																																					p.A249P		Atlas-SNP	.											.	UTS2R	25	.	0			c.G745C						.						2	3	2					17																	80332945		1489	3167	4656	SO:0001583	missense	2837	exon1			AAGCGGGCCCGGC	AF140631	CCDS11810.1	17q25.3	2013-04-30	2004-07-13	2004-07-13		ENSG00000181408			4468	protein-coding gene	gene with protein product		600896	"G protein-coupled receptor 14"	GPR14		8666380, 10499587	Standard	NM_018949		Approved		uc010wvl.2	Q9UKP6		ENST00000313135.2:c.745G>C	chr17.hg19:g.80332945G>C	ENSP00000323516:p.Ala249Pro	31.0	0.0		21.0	11.0	NM_018949	B2RMV8	Missense_Mutation	SNP	ENST00000313135.2	hg19	CCDS11810.1	.	.	.	.	.	.	.	.	.	.	G	6.912	0.537893	0.13188	.	.	ENSG00000181408	ENST00000313135	T	0.37584	1.19	4.86	-6.49	0.01890	GPCR, rhodopsin-like superfamily (1);	0.067292	0.64402	U	0.000015	T	0.16599	0.0399	L	0.31420	0.93	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.05305	-1.0893	10	0.66056	D	0.02	.	2.0181	0.03502	0.3206:0.3512:0.2141:0.1141	.	249	Q9UKP6	UR2R_HUMAN	P	249	ENSP00000323516:A249P	ENSP00000323516:A249P	A	+	1	0	UTS2R	77926234	0.121000	0.22262	0.000000	0.03702	0.002000	0.02628	0.778000	0.26732	-1.088000	0.03077	-1.130000	0.01982	GCC	.	.		0.756	UTS2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443506.1	NM_018949		C	80332945	G	C	80332945	3	2	20	1	0	0	0	0	1	0	0	0	17121	1203	42	4	747	4	UTS2R	17	80332945	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	17826558	80332945	862265	117	1844										
FOXK2	3607	hgsc.bcm.edu	37	chr17	80477826	80477826	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	acccgcgggcggcggggccgGgggcggcggggccgggggcg	27	13	0	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr17:80477826G>C	ENST00000335255.5	+	1	236	c.62G>C	c.(61-63)gGg>gCg	p.G21A		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	21	Gly-rich.			AAAAALSGAGTPPAGGGAGGGGAGGGGSPPGGWAVARLEGR EFEYLMKKRSVTIGRNSSQGSVDVSMGHSSFISRRHLEIFT PPGGGGHGGAAPELPPAQPRPDAGGDFYLRCLGKNG -> Q (in Ref. 1; CAA43200). {ECO:0000305}.	positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ggcggggccgggggcggcggg	0.846																																					p.G21A		Atlas-SNP	.											FOXK2,NS,carcinoma,0,1	FOXK2	46	.	0			c.G62C						.						1	1	1					17																	80477826		122	223	345	SO:0001583	missense	3607	exon1			GGGCCGGGGGCGG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.62G>C	chr17.hg19:g.80477826G>C	ENSP00000335677:p.Gly21Ala	2.0	0.0		3.0	2.0	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	hg19	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	.	2.177	-0.388435	0.04932	.	.	ENSG00000141568	ENST00000335255;ENST00000335241	D	0.93076	-3.16	1.8	1.8	0.24995	.	.	.	.	.	D	0.89375	0.6697	N	0.08118	0	0.25222	N	0.98989	D;D;D	0.71674	0.998;0.996;0.998	D;D;D	0.68621	0.959;0.91;0.959	T	0.80350	-0.1419	9	0.14252	T	0.57	.	6.724	0.23346	0.0:0.0:1.0:0.0	.	21;21;21	Q01167-3;Q01167;Q01167-2	.;FOXK2_HUMAN;.	A	21	ENSP00000335677:G21A	ENSP00000334321:G21A	G	+	2	0	FOXK2	78071115	0.917000	0.31117	0.403000	0.26384	0.773000	0.43773	0.923000	0.28757	0.820000	0.34516	0.486000	0.48141	GGG	.	.		0.846	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		C	80477826	G	C	80477826	3	2	20	1	0	0	0	0	1	0	0	0	6023	1232	43	4	64	4	FOXK2	17	80477826	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	144881	80477826	717384	118	1845										
LPIN2	9663	hgsc.bcm.edu	37	chr18	2920307	2920307	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cgcctcaagacaggtcatccAggtccacttcagggatcggg	12	13	3	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr18:2920307A>T	ENST00000261596.4	-	20	2913	c.2675T>A	c.(2674-2676)cTg>cAg	p.L892Q	RP11-737O24.5_ENST00000608032.1_RNA	NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	892					cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		CAGGTCATCCAGGTCCACTTC	0.597																																					p.L892Q		Atlas-SNP	.											.	LPIN2	75	.	0			c.T2675A						.						54	51	52					18																	2920307		2203	4300	6503	SO:0001583	missense	9663	exon20			TCATCCAGGTCCA	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.2675T>A	chr18.hg19:g.2920307A>T	ENSP00000261596:p.Leu892Gln	116.0	0.0		134.0	43.0	NM_014646	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	hg19	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	A	18.90	3.721232	0.68959	.	.	ENSG00000101577	ENST00000261596	D	0.81908	-1.55	5.92	5.92	0.95590	.	0.289862	0.37623	N	0.002010	D	0.84379	0.5459	M	0.71036	2.16	0.39025	D	0.959823	P	0.45634	0.863	P	0.44561	0.453	D	0.85259	0.1049	10	0.36615	T	0.2	.	16.3648	0.83312	1.0:0.0:0.0:0.0	.	892	Q92539	LPIN2_HUMAN	Q	892	ENSP00000261596:L892Q	ENSP00000261596:L892Q	L	-	2	0	LPIN2	2910307	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	4.521000	0.60532	2.263000	0.75096	0.533000	0.62120	CTG	.	.		0.597	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		T	2920307	A	T	2920307	3	4	20	1	0	0	0	0	1	0	0	0	8928	188	7	4	19	4	LPIN2	18	2920307	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10		2920307	75156941	119	1846										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7026082	7026082	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	aagcactgctcacagtggacGccggtggtgttgtgcgcaca	14	11	1	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr18:7026082G>T	ENST00000389658.3	-	17	2391	c.2298C>A	c.(2296-2298)ggC>ggA	p.G766G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	766	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CACAGTGGACGCCGGTGGTGT	0.562																																					p.G766G		Atlas-SNP	.											.	LAMA1	458	.	0			c.C2298A						.						42	32	35					18																	7026082		2203	4299	6502	SO:0001819	synonymous_variant	284217	exon17			GTGGACGCCGGTG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2298C>A	chr18.hg19:g.7026082G>T		161.0	0.0		155.0	51.0	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.562	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	7026082	G	T	7026082	2	4	20	1	0	0	0	0	0	0	0	1	8614	1074	38	1		1	LAMA1	18	7026082	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	4105775	7026082	71051166	120	1847										
DCC	1630	hgsc.bcm.edu	37	chr18	50734122	50734122	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cgaatatagtcttcgattctTagcttataatcgctatggtc	7	8	2	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr18:50734122T>A	ENST00000442544.2	+	11	2412	c.1796T>A	c.(1795-1797)tTa>tAa	p.L599*	DCC_ENST00000412726.1_Nonsense_Mutation_p.L447*|DCC_ENST00000581580.1_Nonsense_Mutation_p.L254*	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	599	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CTTCGATTCTTAGCTTATAAT	0.363																																					p.L599X		Atlas-SNP	.											.	DCC	360	.	0			c.T1796A						.						148	153	151					18																	50734122		2203	4300	6503	SO:0001587	stop_gained	1630	exon11			GATTCTTAGCTTA	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.1796T>A	chr18.hg19:g.50734122T>A	ENSP00000389140:p.Leu599*	75.0	0.0		96.0	15.0	NM_005215		Nonsense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	T	40	8.202669	0.98704	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	.	.	.	5.83	5.83	0.93111	.	0.097761	0.40818	N	0.001005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	15.1823	0.72968	0.0:0.0:0.0:1.0	.	.	.	.	X	599;532;447	.	ENSP00000304146:L532X	L	+	2	0	DCC	48988120	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.587000	0.74071	2.240000	0.73641	0.528000	0.53228	TTA	.	.		0.363	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		A	50734122	T	A	50734122	4	1	20	1	0	0	0	0	0	1	0	0	4284	1764	61	4	1838	4	DCC	18	50734122	Nonsense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	43708040	50734122	27343126	121	1848										
CCDC68	80323	hgsc.bcm.edu	37	chr18	52604189	52604189	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tgcttctctggaggcttgcaGctagaaaaaaggtcactatg	11	8	2	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr18:52604189G>T	ENST00000591504.1	-	6	620	c.346C>A	c.(346-348)Ctg>Atg	p.L116M	CCDC68_ENST00000432185.1_Splice_Site_p.L116M|CCDC68_ENST00000337363.4_Splice_Site_p.L116M	NM_025214.2	NP_079490.1	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68	116										breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|stomach(1)	14				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)		GAGGCTTGCAGCTAGAAAAAA	0.408																																					p.L116M		Atlas-SNP	.											.	CCDC68	38	.	0			c.C346A						.						96	86	89					18																	52604189		2203	4300	6503	SO:0001630	splice_region_variant	80323	exon6			CTTGCAGCTAGAA		CCDS11959.1	18q21	2006-02-07			ENSG00000166510	ENSG00000166510			24350	protein-coding gene	gene with protein product	"cutaneous T-cell lymphoma associated antigen"					11149944, 15142679	Standard	NM_025214		Approved	SE57-1	uc002lft.3	Q9H2F9	OTTHUMG00000132708	ENST00000591504.1:c.346-1C>A	chr18.hg19:g.52604189G>T		48.0	0.0		72.0	30.0	NM_025214	B2R9I3	Missense_Mutation	SNP	ENST00000591504.1	hg19	CCDS11959.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.357158	0.61293	.	.	ENSG00000166510	ENST00000337363;ENST00000432185	T;T	0.48201	0.82;0.82	5.53	2.25	0.28309	.	0.000000	0.48767	D	0.000169	T	0.63212	0.2492	M	0.73598	2.24	0.32562	N	0.53092	D	0.89917	1.0	D	0.91635	0.999	T	0.69397	-0.5156	10	0.56958	D	0.05	-7.9276	8.3355	0.32213	0.3055:0.0:0.6945:0.0	.	116	Q9H2F9	CCD68_HUMAN	M	116	ENSP00000337209:L116M;ENSP00000413406:L116M	ENSP00000337209:L116M	L	-	1	2	CCDC68	50755187	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.004000	0.29822	0.813000	0.34350	0.650000	0.86243	CTG	.	.		0.408	CCDC68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256006.1	NM_025214	Missense_Mutation	T	52604189	G	T	52604189	5	4	20	1	0	0	0	0	0	0	1	0	2842	985	34	3	689	3	CCDC68	18	52604189	Splice_Site	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	1870067	52604189	25473059	122	1849										
ZNF236	7776	hgsc.bcm.edu	37	chr18	74672680	74672680	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ttgtgagaaagccttcaaccAgaagagtgcgctgcaggtgc	13	9	1	3			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr18:74672680A>G	ENST00000253159.8	+	30	5480	c.5282A>G	c.(5281-5283)cAg>cGg	p.Q1761R	ZNF236_ENST00000320610.9_Missense_Mutation_p.Q1763R	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1761					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		GCCTTCAACCAGAAGAGTGCG	0.522																																					p.Q1761R		Atlas-SNP	.											.	ZNF236	325	.	0			c.A5282G						.						112	118	116					18																	74672680		2011	4191	6202	SO:0001583	missense	7776	exon30			TCAACCAGAAGAG	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"Zinc fingers, C2H2-type"	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.5282A>G	chr18.hg19:g.74672680A>G	ENSP00000253159:p.Gln1761Arg	71.0	0.0		111.0	39.0	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	hg19	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.523993	0.44866	.	.	ENSG00000130856	ENST00000253159	T	0.07444	3.19	5.29	4.13	0.48395	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.05547	0.0146	N	0.10837	0.055	0.51012	D	0.999907	P	0.40578	0.722	B	0.40825	0.341	T	0.50466	-0.8825	10	0.36615	T	0.2	.	11.0637	0.47964	0.9273:0.0:0.0727:0.0	.	1761	Q9UL36	ZN236_HUMAN	R	1761	ENSP00000253159:Q1761R	ENSP00000253159:Q1761R	Q	+	2	0	ZNF236	72801668	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.924000	0.92827	0.857000	0.35407	0.533000	0.62120	CAG	.	.		0.522	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			G	74672680	A	G	74672680	3	3	20	1	0	0	0	0	1	0	0	0	17804	188	7	2	5400	2	ZNF236	18	74672680	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	22068491	74672680	3404568	123	1850										
ZNF99	7652	hgsc.bcm.edu	37	chr19	22940974	22940974	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	attgctttatgtctagtaagAtgtgaagattgcttaaaagc	9	4	1	3	rs531461646		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr19:22940974A>T	ENST00000596209.1	-	4	1827	c.1737T>A	c.(1735-1737)caT>caA	p.H579Q	ZNF99_ENST00000397104.3_Missense_Mutation_p.H488Q	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	579					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GTCTAGTAAGATGTGAAGATT	0.358													G|||	1	0.000199681	0	0	5008	,	,		20367	0		0.001	False		,,,				2504	0				p.H579Q		Atlas-SNP	.											.	ZNF99	273	.	0			c.T1737A						.						52	55	54					19																	22940974		2088	4234	6322	SO:0001583	missense	7652	exon4			AGTAAGATGTGAA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1737T>A	chr19.hg19:g.22940974A>T	ENSP00000472969:p.His579Gln	205.0	0.0		248.0	86.0	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	-	0.004	-2.261918	0.00262	.	.	ENSG00000213973	ENST00000397104	T	0.13196	2.61	1.44	-2.88	0.05682	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06005	0.0156	N	0.20530	0.585	0.09310	N	1	B	0.26445	0.149	B	0.28232	0.087	T	0.36212	-0.9757	9	0.12766	T	0.61	.	1.0921	0.01665	0.3595:0.3386:0.1339:0.168	.	488	A8MXY4	ZNF99_HUMAN	Q	488	ENSP00000380293:H488Q	ENSP00000380293:H488Q	H	-	3	2	ZNF99	22732814	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.546000	0.00932	-2.705000	0.00396	-1.395000	0.01148	CAT	.	.		0.358	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		T	22940974	A	T	22940974	3	4	20	1	0	0	0	0	1	0	0	0	18219	330	12	4	1660	4	ZNF99	19	22940974	Missense_Mutation	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10		22940974	36188009	124	1851										
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48598746	48598746	+	Silent	SNP	A	A	C													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	aggaaagtcaggtctctctcAgggtgagttctgaccagtct							TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr19:48598746A>C	ENST00000599921.1	-	7	1041	c.684T>G	c.(682-684)ccT>ccG	p.P228P	PLA2G4C_ENST00000413144.2_Silent_p.P228P|PLA2G4C_ENST00000354276.3_Silent_p.P228P|PLA2G4C_ENST00000599111.1_Silent_p.P238P			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	228	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		GGTCTCTCTCAGGGTGAGTTC	0.542																																					p.P238P		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.T714G						.						117	132	127					19																	48598746		2203	4300	6503	SO:0001819	synonymous_variant	8605	exon7			TCTCTCAGGGTGA	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.684T>G	chr19.hg19:g.48598746A>C		74.0	0.0		94.0	21.0	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Silent	SNP	ENST00000599921.1	hg19	CCDS12710.1																																																																																			.	.		0.542	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			C	48598746	A	C	48598746	2	2	20	1	0	0	0	0	0	0	0	1	12012	175	7	5		5	PLA2G4C	19	48598746	Silent	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	25657772	48598746	10530237	125	1852	8	2								
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48598748	48598748	+	Missense_Mutation	SNP	G	G	A													0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gaaagtcaggtctctctcagGgtgagttctgaccagtcttc							TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr19:48598748G>A	ENST00000599921.1	-	7	1039	c.682C>T	c.(682-684)Cct>Tct	p.P228S	PLA2G4C_ENST00000413144.2_Missense_Mutation_p.P228S|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.P228S|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.P238S			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	228	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		TCTCTCTCAGGGTGAGTTCTG	0.542																																					p.P238S		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.C712T						.						118	133	128					19																	48598748		2203	4300	6503	SO:0001583	missense	8605	exon7			TCTCAGGGTGAGT	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.682C>T	chr19.hg19:g.48598748G>A	ENSP00000469473:p.Pro228Ser	73.0	0.0		94.0	21.0	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	hg19	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434007	0.62955	.	.	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.06068	3.35;3.35	3.31	0.941	0.19519	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.163986	0.40144	U	0.001176	T	0.22166	0.0534	M	0.88512	2.96	0.24709	N	0.993217	D;D	0.89917	1.0;0.997	D;D	0.73708	0.981;0.955	T	0.05225	-1.0898	10	0.72032	D	0.01	-4.3176	4.6451	0.12568	0.1367:0.2252:0.6381:0.0	.	238;228	B4DI40;Q9UP65	.;PA24C_HUMAN	S	228	ENSP00000346228:P228S;ENSP00000400036:P228S	ENSP00000346228:P228S	P	-	1	0	PLA2G4C	53290560	0.959000	0.32827	0.111000	0.21465	0.831000	0.47069	1.301000	0.33447	0.031000	0.15407	0.205000	0.17691	CCT	.	.		0.542	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			A	48598748	G	A	48598748	3	1	20	1	0	0	0	0	1	0	0	0	12012	1232	43	3	991	3	PLA2G4C	19	48598748	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	2	48598748	10530235	126	1853	8	2								
HSPA12B	116835	hgsc.bcm.edu	37	chr20	3730781	3730781	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cactgctggcccacaccgtgCaggggcgctcaacatctcgc	11	17	2	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr20:3730781C>T	ENST00000254963.2	+	11	1353	c.1208C>T	c.(1207-1209)gCa>gTa	p.A403V	HSPA12B_ENST00000542646.1_Missense_Mutation_p.A237V	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	403							ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						CCACACCGTGCAGGGGCGCTC	0.632																																					p.A403V		Atlas-SNP	.											.	HSPA12B	43	.	0			c.C1208T						.						21	21	21					20																	3730781		2201	4299	6500	SO:0001583	missense	116835	exon11			ACCGTGCAGGGGC	AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"Heat shock proteins / HSP70"	16193	protein-coding gene	gene with protein product		610702	"chromosome 20 open reading frame 60"	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.1208C>T	chr20.hg19:g.3730781C>T	ENSP00000254963:p.Ala403Val	98.0	0.0		126.0	43.0	NM_052970	D3DVX7|Q2TAK3|Q9BR52	Missense_Mutation	SNP	ENST00000254963.2	hg19	CCDS13061.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372665	0.61624	.	.	ENSG00000132622	ENST00000254963;ENST00000542646;ENST00000399701	T;T;T	0.09817	2.94;2.94;2.94	5.31	5.31	0.75309	.	0.515319	0.21821	N	0.068615	T	0.07234	0.0183	N	0.08118	0	0.46396	D	0.999023	B;B	0.12630	0.006;0.006	B;B	0.13407	0.009;0.009	T	0.39354	-0.9618	10	0.31617	T	0.26	.	16.8598	0.86014	0.0:1.0:0.0:0.0	.	402;403	B7ZLP2;Q96MM6	.;HS12B_HUMAN	V	403;237;317	ENSP00000254963:A403V;ENSP00000441506:A237V;ENSP00000382608:A317V	ENSP00000254963:A403V	A	+	2	0	HSPA12B	3678781	0.357000	0.24938	0.011000	0.14972	0.613000	0.37349	4.680000	0.61656	2.650000	0.89964	0.551000	0.68910	GCA	.	.		0.632	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970		T	3730781	C	T	3730781	3	4	20	1	0	0	0	0	1	0	0	0	7414	710	25	3	1246	3	HSPA12B	20	3730781	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10		3730781	59294739	127	1854										
PTPRT	11122	hgsc.bcm.edu	37	chr20	41306596	41306596	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gagcactcggatctcatactCaacatcggggtccagatgcc	10	13	2	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr20:41306596C>A	ENST00000373187.1	-	7	1062	c.1063G>T	c.(1063-1065)Gag>Tag	p.E355*	PTPRT_ENST00000373198.4_Nonsense_Mutation_p.E355*|PTPRT_ENST00000373190.1_Nonsense_Mutation_p.E355*|PTPRT_ENST00000356100.2_Nonsense_Mutation_p.E355*|PTPRT_ENST00000373201.1_Nonsense_Mutation_p.E355*|PTPRT_ENST00000373193.3_Nonsense_Mutation_p.E355*|PTPRT_ENST00000373184.1_Nonsense_Mutation_p.E355*			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	355	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				ATCTCATACTCAACATCGGGG	0.577																																					p.E355X		Atlas-SNP	.											.	PTPRT	372	.	0			c.G1063T						.						125	127	127					20																	41306596		1981	4171	6152	SO:0001587	stop_gained	11122	exon7			CATACTCAACATC	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1063G>T	chr20.hg19:g.41306596C>A	ENSP00000362283:p.Glu355*	96.0	0.0		121.0	46.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Nonsense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	C	39	7.798242	0.98495	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.1814	0.93625	0.0:1.0:0.0:0.0	.	.	.	.	X	355	.	ENSP00000348408:E355X	E	-	1	0	PTPRT	40740010	1.000000	0.71417	1.000000	0.80357	0.616000	0.37450	5.959000	0.70339	2.705000	0.92388	0.655000	0.94253	GAG	.	.		0.577	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	41306596	C	A	41306596	4	1	20	1	0	0	0	0	0	1	0	0	12827	835	29	3	3423	3	PTPRT	20	41306596	Nonsense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	37575815	41306596	21718924	128	1855										
PPP1R3D	5509	hgsc.bcm.edu	37	chr20	58514513	58514513	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	gcctcgacgggcggcgggaaAtcgggcaccaggcaatgcag	17	12	0	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr20:58514513A>G	ENST00000370996.3	-	1	839	c.474T>C	c.(472-474)gaT>gaC	p.D158D	FAM217B_ENST00000358293.3_Intron|FAM217B_ENST00000360816.3_5'Flank	NM_006242.3	NP_006233.1	O95685	PPR3D_HUMAN	protein phosphatase 1, regulatory subunit 3D	158					dephosphorylation (GO:0016311)|glycogen metabolic process (GO:0005977)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)	glycogen granule (GO:0042587)|intracellular membrane-bounded organelle (GO:0043231)	protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|urinary_tract(1)	13	all_lung(29;0.00391)		BRCA - Breast invasive adenocarcinoma(7;5.12e-09)			GCGGCGGGAAATCGGGCACCA	0.672																																					p.D158D		Atlas-SNP	.											.	PPP1R3D	23	.	0			c.T474C						.						17	20	19					20																	58514513		2175	4248	6423	SO:0001819	synonymous_variant	5509	exon1			CGGGAAATCGGGC	Y18206	CCDS13483.1	20q13.3	2012-04-17	2011-10-04	2001-08-01	ENSG00000132825	ENSG00000132825		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9294	protein-coding gene	gene with protein product		603326	"protein phosphatase 1, regulatory (inhibitor) subunit 3D"	PPP1R6		9414128, 9275233	Standard	NM_006242		Approved		uc002ybb.3	O95685	OTTHUMG00000032876	ENST00000370996.3:c.474T>C	chr20.hg19:g.58514513A>G		165.0	0.0		147.0	27.0	NM_006242	Q6DK02	Silent	SNP	ENST00000370996.3	hg19	CCDS13483.1																																																																																			.	.		0.672	PPP1R3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079940.2	NM_006242		G	58514513	A	G	58514513	2	3	20	1	0	0	0	0	0	0	0	1	12386	98	4	2		2	PPP1R3D	20	58514513	Silent	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	17207917	58514513	4511007	129	1856										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60890252	60890252	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cttggcatgtgcgatcttctTgcttgtctcgtctgtggtgg	13	9	4	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr20:60890252T>G	ENST00000252999.3	-	59	7945	c.7879A>C	c.(7879-7881)Aag>Cag	p.K2627Q		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2627	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCGATCTTCTTGCTTGTCTCG	0.627																																					p.K2627Q		Atlas-SNP	.											.	LAMA5	268	.	0			c.A7879C						.						35	36	36					20																	60890252		2197	4288	6485	SO:0001583	missense	3911	exon59			TCTTCTTGCTTGT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7879A>C	chr20.hg19:g.60890252T>G	ENSP00000252999:p.Lys2627Gln	25.0	0.0		20.0	7.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	t	7.421	0.636824	0.14386	.	.	ENSG00000130702	ENST00000252999	T	0.18960	2.18	4.02	-1.56	0.08532	.	0.559587	0.19189	N	0.120468	T	0.12433	0.0302	L	0.40543	1.245	0.22591	N	0.998957	B	0.12013	0.005	B	0.06405	0.002	T	0.36237	-0.9756	10	0.13853	T	0.58	.	7.2242	0.26005	0.0:0.6545:0.1746:0.1709	.	2627	O15230	LAMA5_HUMAN	Q	2627	ENSP00000252999:K2627Q	ENSP00000252999:K2627Q	K	-	1	0	LAMA5	60323647	0.039000	0.19947	0.601000	0.28877	0.593000	0.36681	-0.003000	0.12901	-0.463000	0.06973	0.375000	0.23000	AAG	.	.		0.627	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		G	60890252	T	G	60890252	3	3	20	1	0	0	0	0	1	0	0	0	8618	1821	63	5	3296	5	LAMA5	20	60890252	Missense_Mutation	SNP	T	TCGA-2Y-A9HA-01A-11D-A38X-10	2375739	60890252	2135268	130	1857										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41385098	41385098	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ccgctgaggtaatgtggccaCggcccccggctgccacgact	13	16	0	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr21:41385098C>T	ENST00000400454.1	-	33	6379	c.5902G>A	c.(5902-5904)Gtg>Atg	p.V1968M		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1968				HRPGDLIHLPPYLRMDFLLNRGGPGTSRDLSLGQACLEPQK SRTLKRPTVLEPIPMEAASSASSTREGQSWQPGAVATLPQR EGAELGQAAKMSSSQESLLDSRGHLKGNNPYAKSYTLV -> IGQVTSYICLHTLEWTFC (in Ref. 1; AAC17966). {ECO:0000305}.	cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AATGTGGCCACGGCCCCCGGC	0.652																																					p.V1968M	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											DSCAM,colon,carcinoma,0,1	DSCAM	347	.	0			c.G5902A						.						27	30	29					21																	41385098		1934	4142	6076	SO:0001583	missense	1826	exon33			TGGCCACGGCCCC	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.5902G>A	chr21.hg19:g.41385098C>T	ENSP00000383303:p.Val1968Met	90.0	0.0		107.0	48.0	NM_001389	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	.	16.97	3.267763	0.59540	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.60171	0.21;0.32	5.39	5.39	0.77823	.	0.121903	0.56097	D	0.000031	T	0.39600	0.1084	N	0.08118	0	0.44194	D	0.997015	P	0.36660	0.564	B	0.31337	0.128	T	0.47394	-0.9121	10	0.56958	D	0.05	.	19.17	0.93574	0.0:1.0:0.0:0.0	.	1968	O60469	DSCAM_HUMAN	M	1968;1702	ENSP00000383303:V1968M;ENSP00000385342:V1702M	ENSP00000383303:V1968M	V	-	1	0	DSCAM	40306968	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	5.562000	0.67346	2.521000	0.84997	0.557000	0.71058	GTG	.	.		0.652	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		T	41385098	C	T	41385098	3	4	20	1	0	0	0	0	1	0	0	0	4770	536	19	1	140	1	DSCAM	21	41385098	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10		41385098	6744797	131	1858										
PWP2	5822	hgsc.bcm.edu	37	chr21	45545890	45545890	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	tccactgcttttgctgttctAggaatttttgaaccgaagaa	8	8	1	2			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr21:45545890A>T	ENST00000291576.7	+	16	2092		c.e16-1			NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)						signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		TTGCTGTTCTAGGAATTTTTG	0.542																																					.		Atlas-SNP	.											.	PWP2	64	.	0			c.1966-2A>T						.						83	83	83					21																	45545890		2203	4300	6503	SO:0001630	splice_region_variant	5822	exon16			TGTTCTAGGAATT		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"WD repeat domain containing"	9711	protein-coding gene	gene with protein product		601475	"PWP2 (periodic tryptophan protein, yeast) homolog"	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.1966-1A>T	chr21.hg19:g.45545890A>T		63.0	0.0		56.0	21.0	NM_005049	B2RAG8|Q96A77	Splice_Site	SNP	ENST00000291576.7	hg19	CCDS33579.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.236941	0.58886	.	.	ENSG00000241945	ENST00000291576	.	.	.	4.55	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4484	0.55664	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PWP2	44370318	1.000000	0.71417	0.986000	0.45419	0.860000	0.49131	7.576000	0.82467	1.813000	0.52934	0.482000	0.46254	.	.	.		0.542	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049	Intron	T	45545890	A	T	45545890	5	4	20	1	0	0	0	0	0	0	1	0	12859	434	15	4	2026	4	PWP2	21	45545890	Splice_Site	SNP	A	TCGA-2Y-A9HA-01A-11D-A38X-10	4160792	45545890	2584005	132	1859										
IL17RA	23765	hgsc.bcm.edu	37	chr22	17589625	17589625	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	acgtagtctgctacttcagcGaggtcagctgtgacggcgac	13	11	3	1	rs561912993		TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr22:17589625G>C	ENST00000319363.6	+	13	1649	c.1516G>C	c.(1516-1518)Gag>Cag	p.E506Q		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	506	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)	p.E506*(1)		endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		CTACTTCAGCGAGGTCAGCTG	0.627																																					p.E506Q		Atlas-SNP	.											IL17RA,NS,carcinoma,0,1	IL17RA	62	.	1	Substitution - Nonsense(1)	lung(1)	c.G1516C						.						30	30	30					22																	17589625		2203	4300	6503	SO:0001583	missense	23765	exon13			TTCAGCGAGGTCA	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"Interleukins and interleukin receptors", "CD molecules"	5985	protein-coding gene	gene with protein product		605461	"interleukin 17 receptor"	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.1516G>C	chr22.hg19:g.17589625G>C	ENSP00000320936:p.Glu506Gln	71.0	0.0		71.0	3.0	NM_014339	O43844|Q20WK1	Missense_Mutation	SNP	ENST00000319363.6	hg19	CCDS13739.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.826944	0.50739	.	.	ENSG00000177663	ENST00000425985;ENST00000319363	T	0.30182	1.54	5.2	5.2	0.72013	SEFIR (1);	0.314770	0.33650	N	0.004693	T	0.28896	0.0717	N	0.19112	0.55	0.36559	D	0.872317	P;P	0.49307	0.922;0.902	P;P	0.47346	0.506;0.544	T	0.14896	-1.0456	10	0.30854	T	0.27	-12.7135	18.732	0.91738	0.0:0.0:1.0:0.0	.	454;506	D3YTB4;Q96F46	.;I17RA_HUMAN	Q	454;506	ENSP00000320936:E506Q	ENSP00000320936:E506Q	E	+	1	0	IL17RA	15969625	1.000000	0.71417	0.167000	0.22817	0.009000	0.06853	7.897000	0.87356	2.425000	0.82216	0.462000	0.41574	GAG	.	.		0.627	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339		C	17589625	G	C	17589625	3	2	20	1	0	0	0	0	1	0	0	0	7648	1059	37	4	1566	4	IL17RA	22	17589625	Missense_Mutation	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10		17589625	33714941	133	1860										
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50656996	50656996	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	agcaggaaggagaagacgccGctgtacttgctcacgcagcc	13	12	1	2	rs373718907	byFrequency	TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chr22:50656996G>A	ENST00000248846.5	-	22	4979	c.4875C>T	c.(4873-4875)agC>agT	p.S1625S	TUBGCP6_ENST00000439308.2_3'UTR|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1625					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)	p.S1625S(1)		breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		AGAAGACGCCGCTGTACTTGC	0.642													G|||	2	0.000399361	0.0015	0	5008	,	,		17239	0		0	False		,,,				2504	0				p.S1625S		Atlas-SNP	.											TUBGCP6,NS,carcinoma,0,1	TUBGCP6	132	.	1	Substitution - coding silent(1)	kidney(1)	c.C4875T						.	G		0,4406		0,0,2203	52	48	49		4875	1.2	1	22		49	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TUBGCP6	NM_020461.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		1625/1820	50656996	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	85378	exon22			GACGCCGCTGTAC	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.4875C>T	chr22.hg19:g.50656996G>A		196.0	0.0		141.0	55.0	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	hg19	CCDS14087.1																																																																																			.	.		0.642	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		A	50656996	G	A	50656996	2	1	20	1	0	0	0	0	0	0	0	1	16785	1078	38	1		1	TUBGCP6	22	50656996	Silent	SNP	G	TCGA-2Y-A9HA-01A-11D-A38X-10	33067371	50656996	647570	134	1861										
ARX	170302	hgsc.bcm.edu	37	chrX	25022795	25022795	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	ggagggcagcctttagcacaCctccttgcccgtgctggtgc	13	14	0	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chrX:25022795C>A	ENST00000379044.4	-	5	1891	c.1681G>T	c.(1681-1683)Gtg>Ttg	p.V561L		NM_139058.2	NP_620689.1	Q96QS3	ARX_HUMAN	aristaless related homeobox	561					axon guidance (GO:0007411)|cell proliferation in forebrain (GO:0021846)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex tangential migration (GO:0021800)|embryonic olfactory bulb interneuron precursor migration (GO:0021831)|epithelial cell fate commitment (GO:0072148)|globus pallidus development (GO:0021759)|lipid digestion (GO:0044241)|positive regulation of organ growth (GO:0046622)|regulation of cell proliferation (GO:0042127)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			kidney(1)|large_intestine(2)|lung(1)	4						CTTTAGCACACCTCCTTGCCC	0.657																																					p.V561L		Atlas-SNP	.											.	ARX	19	.	0			c.G1681T						.						7	8	8					X																	25022795		1842	3405	5247	SO:0001583	missense	170302	exon5			AGCACACCTCCTT	AY038071	CCDS14215.1	Xp21.3	2011-06-20			ENSG00000004848	ENSG00000004848		"Homeoboxes / PRD class"	18060	protein-coding gene	gene with protein product	"cancer/testis antigen 121"	300382	"mental retardation, X-linked 54", "mental retardation, X-linked 43", "mental retardation, X-linked 36", "mental retardation, X-linked 29", "mental retardation, X-linked 32", "mental retardation, X-linked 33", "mental retardation, X-linked 38", "mental retardation, X-linked 87", "mental retardation, X-linked 76"	MRXS1, PRTS, MRX76, MRX54, MRX43, MRX36, MRX29, MRX32, MRX33, MRX38, MRX87		11889467, 15850492, 17480217	Standard	NM_139058		Approved	ISSX, CT121, EIEE1	uc004dbp.4	Q96QS3	OTTHUMG00000021275	ENST00000379044.4:c.1681G>T	chrX.hg19:g.25022795C>A	ENSP00000368332:p.Val561Leu	85.0	0.0		68.0	56.0	NM_139058		Missense_Mutation	SNP	ENST00000379044.4	hg19	CCDS14215.1	.	.	.	.	.	.	.	.	.	.	c	25.0	4.597087	0.87055	.	.	ENSG00000004848	ENST00000379044	D	0.92965	-3.14	3.93	3.93	0.45458	.	0.000000	0.64402	D	0.000002	D	0.89801	0.6820	L	0.38531	1.155	0.53688	D	0.999979	D	0.54207	0.965	P	0.47044	0.535	D	0.90977	0.4824	10	0.62326	D	0.03	.	15.0075	0.71524	0.0:1.0:0.0:0.0	.	561	Q96QS3	ARX_HUMAN	L	561	ENSP00000368332:V561L	ENSP00000368332:V561L	V	-	1	0	ARX	24932716	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.218000	0.65257	1.793000	0.52555	0.431000	0.28591	GTG	.	.		0.657	ARX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056109.1			A	25022795	C	A	25022795	3	1	20	1	0	0	0	0	1	0	0	0	1004	507	18	3	11	3	ARX	23	25022795	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10		25022795	130247765	135	1862										
NR0B1	190	hgsc.bcm.edu	37	chrX	30327147	30327147	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	cgctctgcccaccccgggatCagagccgcacgaacagcccc	10	20	2	1			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chrX:30327147C>T	ENST00000378970.4	-	1	568	c.334G>A	c.(334-336)Gat>Aat	p.D112N	NR0B1_ENST00000378963.1_5'Flank|NR0B1_ENST00000453287.1_Missense_Mutation_p.D112N	NM_000475.4	NP_000466.2	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1	112	4 X 67 AA tandem repeats.				adrenal gland development (GO:0030325)|gene expression (GO:0010467)|gonad development (GO:0008406)|hypothalamus development (GO:0021854)|intracellular receptor signaling pathway (GO:0030522)|Leydig cell differentiation (GO:0033327)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of cell differentiation (GO:0045596)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|protein localization (GO:0008104)|response to immobilization stress (GO:0035902)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)|steroid biosynthetic process (GO:0006694)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	AF-2 domain binding (GO:0050682)|DNA binding (GO:0003677)|DNA hairpin binding (GO:0032448)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|steroid hormone receptor binding (GO:0035258)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	24					Dexamethasone(DB01234)|Tretinoin(DB00755)	ACCCCGGGATCAGAGCCGCAC	0.682											OREG0019719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D112N		Atlas-SNP	.											.	NR0B1	61	.	0			c.G334A						.						21	24	23					X																	30327147		2196	4285	6481	SO:0001583	missense	190	exon1			CGGGATCAGAGCC	S74720	CCDS14223.1	Xp21.3	2014-06-28			ENSG00000169297	ENSG00000169297		"Nuclear hormone receptors"	7960	protein-coding gene	gene with protein product		300473	"dosage-sensitive sex reversal"	AHC, DSS		1301166, 10412368	Standard	NM_000475		Approved	DAX1, AHCH	uc004dcf.4	P51843	OTTHUMG00000021323	ENST00000378970.4:c.334G>A	chrX.hg19:g.30327147C>T	ENSP00000368253:p.Asp112Asn	131.0	0.0	816	117.0	11.0	NM_000475	Q96F69	Missense_Mutation	SNP	ENST00000378970.4	hg19	CCDS14223.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.444103	0.25987	.	.	ENSG00000169297	ENST00000378970;ENST00000453287	D;D	0.97772	-3.69;-4.53	4.42	3.48	0.39840	.	0.347180	0.21084	N	0.080433	D	0.91821	0.7412	N	0.08118	0	0.09310	N	1	B	0.33777	0.425	B	0.31495	0.131	D	0.87560	0.2471	10	0.87932	D	0	-4.4626	9.2072	0.37296	0.0:0.6808:0.3192:0.0	.	112	P51843	NR0B1_HUMAN	N	112	ENSP00000368253:D112N;ENSP00000396403:D112N	ENSP00000368253:D112N	D	-	1	0	NR0B1	30237068	0.002000	0.14202	0.241000	0.24154	0.215000	0.24574	0.960000	0.29253	2.167000	0.68274	0.513000	0.50165	GAT	.	.		0.682	NR0B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056161.1	NM_000475		T	30327147	C	T	30327147	3	4	20	1	0	0	0	0	1	0	0	0	10622	826	29	3	1086	3	NR0B1	23	30327147	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	5304352	30327147	124943413	136	1863										
WDR45	11152	hgsc.bcm.edu	37	chrX	48932926	48932926	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0814814814814815	11	1	1.81886082098615	1.52122905027933	1.90153631284916	0.0233334945430511	0.304738562091504	0	caatcataggccccaccttgCccacgcgagccagcctgcag	9	18	1	0			TCGA-2Y-A9HA-01A-11D-A38X-10	TCGA-2Y-A9HA-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	606c736e-1be8-44fc-b474-9dea8b63538f	c6d9a5a6-64e5-45ab-8251-ed6d2f3514aa	g.chrX:48932926C>A	ENST00000376372.3	-	10	1023	c.842G>T	c.(841-843)gGc>gTc	p.G281V	WDR45_ENST00000553851.1_Intron|WDR45_ENST00000322995.8_Missense_Mutation_p.G292V|WDR45_ENST00000473974.1_Intron|WDR45_ENST00000396681.4_Missense_Mutation_p.G267V|PRAF2_ENST00000376386.3_5'Flank|WDR45_ENST00000376368.2_Missense_Mutation_p.G282V|WDR45_ENST00000465431.1_5'Flank|PRAF2_ENST00000376390.4_5'Flank|WDR45_ENST00000485908.1_Missense_Mutation_p.G246V|AF196779.12_ENST00000376358.3_Intron|PRAF2_ENST00000491199.1_5'Flank|WDR45_ENST00000356463.3_Missense_Mutation_p.G282V	NM_001029896.1	NP_001025067.1	Q9Y484	WIPI4_HUMAN	WD repeat domain 45	281					autophagy (GO:0006914)|cell death (GO:0008219)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	19						CCCCACCTTGCCCACGCGAGC	0.642																																					p.G282V		Atlas-SNP	.											.	WDR45	40	.	0			c.G845T						.						25	23	24					X																	48932926		2203	4300	6503	SO:0001583	missense	11152	exon11			ACCTTGCCCACGC	BC003037	CCDS14318.1, CCDS35250.1	Xp11.23	2013-06-06	2004-09-02	2004-09-03	ENSG00000196998	ENSG00000196998		"WD repeat domain containing"	28912	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 5"	300526	"WD repeat domain, X-linked 1"	WDRX1		12477932	Standard	NM_007075		Approved	JM5, WIPI4, NBIA5	uc004dmk.1	Q9Y484	OTTHUMG00000034500	ENST00000376372.3:c.842G>T	chrX.hg19:g.48932926C>A	ENSP00000365551:p.Gly281Val	146.0	0.0		103.0	69.0	NM_007075	A6NGH5|B7WPI2|Q5MNZ5|Q6IBS7|Q6NT94|Q96H03	Missense_Mutation	SNP	ENST00000376372.3	hg19	CCDS35250.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.252555	0.59212	.	.	ENSG00000196998	ENST00000376372;ENST00000322995;ENST00000356463;ENST00000485908;ENST00000376368;ENST00000396681	T;T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22;-1.22	4.09	2.05	0.26809	.	0.000000	0.85682	D	0.000000	D	0.84252	0.5431	M	0.64170	1.965	0.80722	D	1	P;D;D;D	0.89917	0.937;1.0;0.999;0.996	P;D;D;D	0.76575	0.672;0.979;0.988;0.924	D	0.84560	0.0649	10	0.62326	D	0.03	-21.2042	12.0233	0.53356	0.0:0.6757:0.3243:0.0	.	292;246;282;281	Q9Y484-2;C9JYH8;Q9Y484-3;Q9Y484	.;.;.;WIPI4_HUMAN	V	281;292;282;246;282;267	ENSP00000365551:G281V;ENSP00000365543:G292V;ENSP00000348848:G282V;ENSP00000419897:G246V;ENSP00000365546:G282V;ENSP00000379913:G267V	ENSP00000365543:G292V	G	-	2	0	WDR45	48819870	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.080000	0.76837	0.797000	0.33971	0.409000	0.27619	GGC	.	.		0.642	WDR45-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083418.2	NM_007075		A	48932926	C	A	48932926	3	1	20	1	0	0	0	0	1	0	0	0	17312	739	26	3	248	3	WDR45	23	48932926	Missense_Mutation	SNP	C	TCGA-2Y-A9HA-01A-11D-A38X-10	18605779	48932926	106337634	137	1864										
ARHGEF10L	55160	hgsc.bcm.edu	37	chr1	18014160	18014160	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	atggccttctcctccggcacCtccatccgcctcttccacac	5	21	2	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr1:18014160C>G	ENST00000361221.3	+	27	3261	c.3102C>G	c.(3100-3102)acC>acG	p.T1034T	ARHGEF10L_ENST00000375415.1_Silent_p.T995T|ARHGEF10L_ENST00000434513.1_Silent_p.T1029T|ARHGEF10L_ENST00000375408.3_Silent_p.T807T|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000167825.4_Silent_p.T737T|ARHGEF10L_ENST00000452522.1_Silent_p.T995T	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	1034						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		CCTCCGGCACCTCCATCCGCC	0.632																																					p.T1034T		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.C3102G						.						82	72	76					1																	18014160		2202	4299	6501	SO:0001819	synonymous_variant	55160	exon27			CGGCACCTCCATC	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.3102C>G	chr1.hg19:g.18014160C>G		146.0	0.0		69.0	18.0	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Silent	SNP	ENST00000361221.3	hg19	CCDS182.1																																																																																			.	.		0.632	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		G	18014160	C	G	18014160	2	3	21	1	0	0	0	0	0	0	0	1	895	668	24	4		4	ARHGEF10L	1	18014160	Silent	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		18014160	231236461	1	1865										
DOCK7	85440	hgsc.bcm.edu	37	chr1	63021551	63021551	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	cggaaaacataatgaatataTgatgcaagaaggctgtttct	9	5	1	3			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr1:63021551T>C	ENST00000340370.5	-	21	2558	c.2541A>G	c.(2539-2541)tcA>tcG	p.S847S	DOCK7_ENST00000251157.5_Silent_p.S847S	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	847					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						AATGAATATATGATGCAAGAA	0.343																																					p.S847S		Atlas-SNP	.											.	DOCK7	184	.	0			c.A2541G						.						176	168	171					1																	63021551		2203	4300	6503	SO:0001819	synonymous_variant	85440	exon21			AATATATGATGCA		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.2541A>G	chr1.hg19:g.63021551T>C		30.0	0.0		58.0	18.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	hg19	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	T	7.301	0.613127	0.14066	.	.	ENSG00000116641	ENST00000454575	.	.	.	5.45	-10.9	0.00192	.	.	.	.	.	T	0.44159	0.1280	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55147	-0.8186	4	.	.	.	.	7.816	0.29260	0.0668:0.2764:0.4676:0.1892	.	.	.	.	V	19	.	.	I	-	1	0	DOCK7	62794139	0.005000	0.15991	0.433000	0.26760	0.852000	0.48524	-1.505000	0.02273	-2.265000	0.00688	-0.316000	0.08728	ATA	.	.		0.343	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		C	63021551	T	C	63021551	2	2	21	1	0	0	0	0	0	0	0	1	4694	1451	51	2		2	DOCK7	1	63021551	Silent	SNP	T	TCGA-2Y-A9HB-01A-11D-A38X-10	45007391	63021551	186229070	2	1866										
DOCK7	85440	hgsc.bcm.edu	37	chr1	63091000	63091000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	agttacaagcatcatctccaCttgttgtcctttcaagtgat	6	10	3	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr1:63091000C>T	ENST00000340370.5	-	12	1372	c.1355G>A	c.(1354-1356)aGt>aAt	p.S452N	DOCK7_ENST00000251157.5_Missense_Mutation_p.S452N|DOCK7_ENST00000404627.2_Missense_Mutation_p.S452N	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	452					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						ATCATCTCCACTTGTTGTCCT	0.383																																					p.S452N		Atlas-SNP	.											.	DOCK7	184	.	0			c.G1355A						.						188	191	190					1																	63091000		2203	4300	6503	SO:0001583	missense	85440	exon12			TCTCCACTTGTTG		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.1355G>A	chr1.hg19:g.63091000C>T	ENSP00000340742:p.Ser452Asn	104.0	0.0		155.0	52.0	NM_001272002	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	hg19	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.413664	0.83449	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.39229	1.09;1.09;1.09	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.38401	0.1039	L	0.48642	1.525	0.80722	D	1	P;P;P;P;B	0.40332	0.67;0.551;0.713;0.713;0.138	P;B;B;B;B	0.47626	0.552;0.32;0.446;0.446;0.071	T	0.34825	-0.9813	10	0.56958	D	0.05	.	17.6705	0.88216	0.0:1.0:0.0:0.0	.	452;452;452;452;452	Q96NI0;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3	.;.;.;.;.	N	452	ENSP00000251157:S452N;ENSP00000340742:S452N;ENSP00000384446:S452N	ENSP00000251157:S452N	S	-	2	0	DOCK7	62863588	1.000000	0.71417	0.998000	0.56505	0.875000	0.50365	7.184000	0.77705	2.386000	0.81285	0.467000	0.42956	AGT	.	.		0.383	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		T	63091000	C	T	63091000	3	4	21	1	0	0	0	0	1	0	0	0	4694	565	20	3	5126	3	DOCK7	1	63091000	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	69449	63091000	186159621	3	1867										
ZNF644	84146	hgsc.bcm.edu	37	chr1	91406004	91406004	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	actaaagcaatcctcggtatAacgagttatcttgcttacat	6	9	1	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr1:91406004A>G	ENST00000370440.1	-	3	1124	c.907T>C	c.(907-909)Tat>Cat	p.Y303H	ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000337393.5_Missense_Mutation_p.Y303H			Q9H582	ZN644_HUMAN	zinc finger protein 644	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TCCTCGGTATAACGAGTTATC	0.333																																					p.Y303H		Atlas-SNP	.											.	ZNF644	120	.	0			c.T907C						.						90	87	88					1																	91406004		2203	4299	6502	SO:0001583	missense	84146	exon3			CGGTATAACGAGT	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.907T>C	chr1.hg19:g.91406004A>G	ENSP00000359469:p.Tyr303His	44.0	0.0		59.0	22.0	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	hg19	CCDS731.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.42|16.42	3.118885|3.118885	0.56505|0.56505	.|.	.|.	ENSG00000122482|ENSG00000122482	ENST00000541557|ENST00000370440;ENST00000337393	.|T;T	.|0.00626	.|6.13;6.13	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	.|0.122258	.|0.64402	.|D	.|0.000019	T|T	0.01029|0.01029	0.0034|0.0034	L|L	0.32530|0.32530	0.975|0.975	0.54753|0.54753	D|D	0.999984|0.999984	.|D	.|0.71674	.|0.998	.|D	.|0.75484	.|0.986	T|T	0.80327|0.80327	-0.1429|-0.1429	6|10	0.87932|0.48119	D|T	0|0.1	-11.6017|-11.6017	15.756|15.756	0.78025|0.78025	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|303	.|Q9H582	.|ZN644_HUMAN	S|H	302|303	.|ENSP00000359469:Y303H;ENSP00000337008:Y303H	ENSP00000442287:L302S|ENSP00000337008:Y303H	L|Y	-|-	2|1	0|0	ZNF644|ZNF644	91178592|91178592	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	4.588000|4.588000	0.60999|0.60999	2.131000|2.131000	0.65755|0.65755	0.533000|0.533000	0.62120|0.62120	TTA|TAT	.	.		0.333	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		G	91406004	A	G	91406004	3	3	21	1	0	0	0	0	1	0	0	0	18075	362	13	2	3092	2	ZNF644	1	91406004	Missense_Mutation	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10	28315004	91406004	157844617	4	1868										
FAM20B	9917	hgsc.bcm.edu	37	chr1	179041061	179041061	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ctcccagcattcgggtgtccAcctggaacagactgaactac	9	14	0	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr1:179041061A>T	ENST00000263733.4	+	8	1348	c.1012A>T	c.(1012-1014)Acc>Tcc	p.T338S		NM_014864.3	NP_055679.1	O75063	XYLK_HUMAN	family with sequence similarity 20, member B	338						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(3)	14						TCGGGTGTCCACCTGGAACAG	0.448																																					p.T338S		Atlas-SNP	.											.	FAM20B	38	.	0			c.A1012T						.						117	121	119					1																	179041061		2203	4300	6503	SO:0001583	missense	9917	exon8			GTGTCCACCTGGA	AB007944	CCDS1328.1	1q25.2	2013-04-29			ENSG00000116199	ENSG00000116199			23017	protein-coding gene	gene with protein product	"glycosaminoglycan xylosylkinase"	611063				9455484, 19473117	Standard	NM_014864		Approved	KIAA0475, GXK1	uc001gmc.3	O75063	OTTHUMG00000035073	ENST00000263733.4:c.1012A>T	chr1.hg19:g.179041061A>T	ENSP00000263733:p.Thr338Ser	228.0	0.0		342.0	145.0	NM_014864	Q5W0C3|Q5W0C4	Missense_Mutation	SNP	ENST00000263733.4	hg19	CCDS1328.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.638596	0.87760	.	.	ENSG00000116199	ENST00000263733	D	0.81821	-1.54	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.90484	0.7019	M	0.87900	2.915	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.92100	0.5687	10	0.87932	D	0	-26.9284	13.9203	0.63928	1.0:0.0:0.0:0.0	.	338	O75063	XYLK_HUMAN	S	338	ENSP00000263733:T338S	ENSP00000263733:T338S	T	+	1	0	FAM20B	177307684	1.000000	0.71417	0.371000	0.25978	0.940000	0.58332	9.339000	0.96797	2.012000	0.59069	0.533000	0.62120	ACC	.	.		0.448	FAM20B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084922.1	NM_014864		T	179041061	A	T	179041061	3	4	21	1	0	0	0	0	1	0	0	0	5543	159	6	4	1038	4	FAM20B	1	179041061	Missense_Mutation	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10	87635057	179041061	70209560	5	1869										
SMG7	9887	hgsc.bcm.edu	37	chr1	183519889	183519889	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ttgctattatttaatagatcAttcaacaccagccagccagt	5	10	2	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr1:183519889A>G	ENST00000347615.2	+	20	3106	c.2987A>G	c.(2986-2988)cAt>cGt	p.H996R	SMG7_ENST00000507469.1_Missense_Mutation_p.H1000R|SMG7_ENST00000367537.3_Missense_Mutation_p.H1029R|SMG7_ENST00000456731.2_Missense_Mutation_p.H908R|SMG7_ENST00000515829.2_Missense_Mutation_p.H950R|SMG7_ENST00000508461.1_Missense_Mutation_p.H1004R	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	996	Ser-rich.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						TTAATAGATCATTCAACACCA	0.388																																					p.H1004R		Atlas-SNP	.											.	SMG7	165	.	0			c.A3011G						.						95	92	93					1																	183519889		2203	4300	6503	SO:0001583	missense	9887	exon20			TAGATCATTCAAC	D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.2987A>G	chr1.hg19:g.183519889A>G	ENSP00000340766:p.His996Arg	137.0	0.0		437.0	97.0	NM_001174061	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	hg19	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284373	0.80803	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T	0.20881	2.05;2.07;2.05;2.06;2.05;2.04	5.45	5.45	0.79879	.	0.180930	0.52532	D	0.000076	T	0.33294	0.0858	L	0.29908	0.895	0.80722	D	1	D;D;D;D;P	0.71674	0.998;0.998;0.997;0.998;0.915	D;D;D;D;B	0.71184	0.958;0.958;0.972;0.958;0.297	T	0.03157	-1.1066	10	0.30078	T	0.28	-8.5781	15.8223	0.78667	1.0:0.0:0.0:0.0	.	1004;908;950;996;1000	E9PCI0;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;SMG7_HUMAN;.	R	908;1029;1004;996;1000;950	ENSP00000407629:H908R;ENSP00000356507:H1029R;ENSP00000426915:H1004R;ENSP00000340766:H996R;ENSP00000425133:H1000R;ENSP00000421358:H950R	ENSP00000340766:H996R	H	+	2	0	SMG7	181786512	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.451000	0.90343	2.188000	0.69820	0.528000	0.53228	CAT	.	.		0.388	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		G	183519889	A	G	183519889	3	3	21	1	0	0	0	0	1	0	0	0	14813	217	8	2	3219	2	SMG7	1	183519889	Missense_Mutation	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10	4478828	183519889	65730732	6	1870										
PGBD5	79605	hgsc.bcm.edu	37	chr1	230492978	230492978	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	cttggcatacatgtttgtctGcaccaccatgttcttgagga	9	10	2	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr1:230492978G>A	ENST00000525115.1	-	2	237	c.214C>T	c.(214-216)Cag>Tag	p.Q72*	PGBD5_ENST00000391860.1_Nonsense_Mutation_p.Q26*|PGBD5_ENST00000321327.2_Nonsense_Mutation_p.Q171*			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	72						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		ATGTTTGTCTGCACCACCATG	0.577																																					p.Q141X		Atlas-SNP	.											.	PGBD5	73	.	0			c.C421T						.						79	74	76					1																	230492978		2203	4300	6503	SO:0001587	stop_gained	79605	exon2			TTGTCTGCACCAC	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.214C>T	chr1.hg19:g.230492978G>A	ENSP00000431404:p.Gln72*	134.0	0.0		154.0	94.0	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Nonsense_Mutation	SNP	ENST00000525115.1	hg19		.	.	.	.	.	.	.	.	.	.	G	37	6.486591	0.97607	.	.	ENSG00000177614	ENST00000391860;ENST00000321327;ENST00000525115	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-44.5156	20.0313	0.97540	0.0:0.0:1.0:0.0	.	.	.	.	X	26;171;72	.	ENSP00000322530:Q171X	Q	-	1	0	PGBD5	228559601	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.848000	0.99507	2.746000	0.94184	0.655000	0.94253	CAG	.	.		0.577	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		A	230492978	G	A	230492978	4	1	21	1	0	0	0	0	0	1	0	0	11793	1328	46	3	1177	3	PGBD5	1	230492978	Nonsense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	46973089	230492978	18757643	7	1871										
RYR2	6262	hgsc.bcm.edu	37	chr1	237824155	237824155	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tcaaagaatctttaaaaactAtgctggcttggggctggaga	11	6	2	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr1:237824155A>G	ENST00000366574.2	+	56	8661	c.8344A>G	c.(8344-8346)Atg>Gtg	p.M2782V	RYR2_ENST00000360064.6_Missense_Mutation_p.M2780V|RYR2_ENST00000542537.1_Missense_Mutation_p.M2766V	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2782	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTTAAAAACTATGCTGGCTTG	0.383																																					p.M2782V		Atlas-SNP	.											.	RYR2	1273	.	0			c.A8344G						.						42	43	42					1																	237824155		1488	3344	4832	SO:0001583	missense	6262	exon56			AAAACTATGCTGG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.8344A>G	chr1.hg19:g.237824155A>G	ENSP00000355533:p.Met2782Val	259.0	0.0		439.0	249.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.485689	0.84854	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.91686	-2.89;-2.89;-2.89	5.46	5.46	0.80206	Ryanodine receptor Ryr (1);	0.000000	0.85682	D	0.000000	D	0.93644	0.7970	L	0.58925	1.835	0.80722	D	1	D	0.61697	0.99	P	0.55345	0.774	D	0.94324	0.7556	10	0.87932	D	0	-18.0478	15.8331	0.78773	1.0:0.0:0.0:0.0	.	2782	Q92736	RYR2_HUMAN	V	2782;2780;2766	ENSP00000355533:M2782V;ENSP00000353174:M2780V;ENSP00000443798:M2766V	ENSP00000353174:M2780V	M	+	1	0	RYR2	235890778	1.000000	0.71417	0.927000	0.36925	0.937000	0.57800	8.844000	0.92147	2.192000	0.70111	0.460000	0.39030	ATG	.	.		0.383	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237824155	A	G	237824155	3	3	21	1	0	0	0	0	1	0	0	0	13784	449	16	2	8566	2	RYR2	1	237824155	Missense_Mutation	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10	7331177	237824155	11426466	8	1872										
WDR64	128025	hgsc.bcm.edu	37	chr1	241875158	241875158	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	aacactttttgctactgtgtTaaggcaaatgtgattgtcac	8	7	1	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr1:241875158T>G	ENST00000366552.2	+	8	1206	c.999T>G	c.(997-999)gtT>gtG	p.V333V	WDR64_ENST00000437684.2_Silent_p.V333V	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	333										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GCTACTGTGTTAAGGCAAATG	0.408																																					p.V333V		Atlas-SNP	.											.	WDR64	234	.	0			c.T999G						.						118	110	113					1																	241875158		2203	4300	6503	SO:0001819	synonymous_variant	128025	exon8			CTGTGTTAAGGCA	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.999T>G	chr1.hg19:g.241875158T>G		63.0	0.0		157.0	28.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Silent	SNP	ENST00000366552.2	hg19																																																																																				.	.		0.408	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		G	241875158	T	G	241875158	2	3	21	1	0	0	0	0	0	0	0	1	17330	1741	61	5		5	WDR64	1	241875158	Silent	SNP	T	TCGA-2Y-A9HB-01A-11D-A38X-10	4051003	241875158	7375463	9	1873										
SNX17	9784	hgsc.bcm.edu	37	chr2	27596783	27596783	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ggaagtgctgctcagcaacgGgcagaaagttctggtcaacg	14	9	3	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr2:27596783G>A	ENST00000233575.2	+	5	599	c.377G>A	c.(376-378)gGg>gAg	p.G126E	SNX17_ENST00000537606.1_Missense_Mutation_p.G101E|SNX17_ENST00000542478.1_5'UTR|SNX17_ENST00000543024.1_5'UTR	NM_001267059.1|NM_001267061.1|NM_014748.3	NP_001253988.1|NP_001253990.1|NP_055563.1	Q15036	SNX17_HUMAN	sorting nexin 17	126	FERM-like.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				cholesterol catabolic process (GO:0006707)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|receptor-mediated endocytosis (GO:0006898)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)	low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol binding (GO:0035091)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCAGCAACGGGCAGAAAGTT	0.557																																					p.G126E		Atlas-SNP	.											SNX17,NS,carcinoma,0,1	SNX17	40	.	0			c.G377A						.						125	106	113					2																	27596783		2203	4300	6503	SO:0001583	missense	9784	exon5			GCAACGGGCAGAA	D31764	CCDS1750.1, CCDS58704.1	2p23-p22	2008-05-21			ENSG00000115234	ENSG00000115234		"Sorting nexins"	14979	protein-coding gene	gene with protein product		605963				12169628, 15769472	Standard	NM_014748		Approved	KIAA0064	uc002rkg.2	Q15036	OTTHUMG00000097781	ENST00000233575.2:c.377G>A	chr2.hg19:g.27596783G>A	ENSP00000233575:p.Gly126Glu	190.0	0.0		116.0	38.0	NM_014748	B4DQM7|Q53HN7|Q6IAS3	Missense_Mutation	SNP	ENST00000233575.2	hg19	CCDS1750.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.111183	0.56398	.	.	ENSG00000115234	ENST00000233575;ENST00000537606	T;T	0.78707	-1.2;-1.2	5.2	5.2	0.72013	Ras-association (1);	0.096917	0.64402	D	0.000001	D	0.86585	0.5968	M	0.64997	1.995	0.80722	D	1	P;D;D;D	0.89917	0.858;1.0;1.0;1.0	B;D;D;D	0.76575	0.172;0.988;0.988;0.976	D	0.87378	0.2355	10	0.72032	D	0.01	-16.8695	17.4469	0.87580	0.0:0.0:1.0:0.0	.	101;114;106;126	B4DQM7;B4DTB8;B4DQ37;Q15036	.;.;.;SNX17_HUMAN	E	126;101	ENSP00000233575:G126E;ENSP00000439208:G101E	ENSP00000233575:G126E	G	+	2	0	SNX17	27450287	1.000000	0.71417	0.996000	0.52242	0.947000	0.59692	6.700000	0.74619	2.705000	0.92388	0.561000	0.74099	GGG	.	.		0.557	SNX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215024.1	NM_014748		A	27596783	G	A	27596783	3	1	21	1	0	0	0	0	1	0	0	0	14903	1232	43	3	395	3	SNX17	2	27596783	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10		27596783	215602590	10	1874										
MEMO1	51072	hgsc.bcm.edu	37	chr2	32157198	32157198	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gacccacagtacgtatatccTgcatggctacaaaacaaaat	6	11	0	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr2:32157198T>C	ENST00000295065.5	-	3	459	c.150A>G	c.(148-150)gcA>gcG	p.A50A	DPY30_ENST00000446765.1_5'UTR|MEMO1_ENST00000490459.1_5'UTR|MEMO1_ENST00000379383.3_Silent_p.A53A|MEMO1_ENST00000426310.2_Intron|MEMO1_ENST00000404530.1_Silent_p.A50A|MEMO1_ENST00000407893.3_Silent_p.A50A	NM_015955.2	NP_057039.1	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1	50					regulation of microtubule-based process (GO:0032886)	cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|breast(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	17	Acute lymphoblastic leukemia(172;0.155)					ACGTATATCCTGCATGGCTAC	0.333																																					p.A50A		Atlas-SNP	.											.	MEMO1	36	.	0			c.A150G						.						80	79	80					2																	32157198		2203	4300	6503	SO:0001819	synonymous_variant	51072	exon3			ATATCCTGCATGG	AF132961	CCDS1776.1, CCDS46255.1	2p22-p21	2010-05-24	2007-02-12	2007-02-12	ENSG00000162959	ENSG00000162959			14014	protein-coding gene	gene with protein product		611786	"chromosome 2 open reading frame 4"	C2orf4		15156151	Standard	NM_015955		Approved	CGI-27, MEMO	uc002rnx.3	Q9Y316	OTTHUMG00000128453	ENST00000295065.5:c.150A>G	chr2.hg19:g.32157198T>C		244.0	0.0		368.0	141.0	NM_015955	B4DLS0|D6W575|Q5R2V8|Q5R2V9|Q6NSL5	Silent	SNP	ENST00000295065.5	hg19	CCDS1776.1																																																																																			.	.		0.333	MEMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250251.2	NM_015955		C	32157198	T	C	32157198	2	2	21	1	0	0	0	0	0	0	0	1	9480	1567	55	2		2	MEMO1	2	32157198	Silent	SNP	T	TCGA-2Y-A9HB-01A-11D-A38X-10	4560415	32157198	211042175	11	1875										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32822997	32822997	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tgtcttcatcctctagtgtgTttgtacgctgtgatgaggag	12	7	3	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr2:32822997T>G	ENST00000421745.2	+	69	13926	c.13792T>G	c.(13792-13794)Ttt>Gtt	p.F4598V		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4598	Ubiquitin-conjugating.				apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CTCTAGTGTGTTTGTACGCTG	0.448																																					p.F4598V	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T13792G						.						112	91	98					2																	32822997		2203	4300	6503	SO:0001583	missense	57448	exon69			AGTGTGTTTGTAC	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.13792T>G	chr2.hg19:g.32822997T>G	ENSP00000393596:p.Phe4598Val	29.0	0.0		40.0	8.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	28.0	4.879279	0.91740	.	.	ENSG00000115760	ENST00000421745	T	0.71817	-0.6	5.15	5.15	0.70609	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.80904	0.4713	L	0.54323	1.7	0.80722	D	1	D	0.67145	0.996	D	0.81914	0.995	T	0.83050	-0.0153	10	0.87932	D	0	.	15.2722	0.73712	0.0:0.0:0.0:1.0	.	4598	Q9NR09	BIRC6_HUMAN	V	4598	ENSP00000393596:F4598V	ENSP00000393596:F4598V	F	+	1	0	BIRC6	32676501	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.997000	0.88414	2.078000	0.62432	0.477000	0.44152	TTT	.	.		0.448	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		G	32822997	T	G	32822997	3	3	21	1	0	0	0	0	1	0	0	0	1438	1725	60	5	14066	5	BIRC6	2	32822997	Missense_Mutation	SNP	T	TCGA-2Y-A9HB-01A-11D-A38X-10	665799	32822997	210376376	12	1876										
EGR4	1961	hgsc.bcm.edu	37	chr2	73519846	73519846	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gcgcaggcccctccaggaagCaggagtcggctaagtcccca	13	15	0	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr2:73519846C>G	ENST00000545030.1	-	2	583	c.509G>C	c.(508-510)tGc>tCc	p.C170S	EGR4_ENST00000436467.2_Missense_Mutation_p.C67S	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	170					cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CTCCAGGAAGCAGGAGTCGGC	0.637																																					p.C170S		Atlas-SNP	.											.	EGR4	52	.	0			c.G509C						.						19	22	21					2																	73519846		2200	4297	6497	SO:0001583	missense	1961	exon2			AGGAAGCAGGAGT		CCDS1925.2	2p13	2013-01-08			ENSG00000135625	ENSG00000135625		"Zinc fingers, C2H2-type"	3241	protein-coding gene	gene with protein product		128992				1584812	Standard	NM_001965		Approved	NGFI-C, PAT133	uc010yrj.2	Q05215	OTTHUMG00000129774	ENST00000545030.1:c.509G>C	chr2.hg19:g.73519846C>G	ENSP00000445626:p.Cys170Ser	268.0	0.0		125.0	28.0	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Missense_Mutation	SNP	ENST00000545030.1	hg19	CCDS1925.2	.	.	.	.	.	.	.	.	.	.	C	13.91	2.378407	0.42207	.	.	ENSG00000135625	ENST00000545030;ENST00000436467	T;T	0.14391	2.51;2.89	4.2	3.24	0.37175	.	0.277795	0.31134	N	0.008193	T	0.09905	0.0243	N	0.24115	0.695	0.31017	N	0.718565	B;B	0.18013	0.015;0.025	B;B	0.19666	0.011;0.026	T	0.05468	-1.0883	10	0.72032	D	0.01	-18.3002	10.9551	0.47354	0.2772:0.7228:0.0:0.0	.	67;170	Q05215;G3V1T5	EGR4_HUMAN;.	S	170;67	ENSP00000445626:C170S;ENSP00000419687:C67S	ENSP00000419687:C67S	C	-	2	0	EGR4	73373354	0.997000	0.39634	1.000000	0.80357	0.981000	0.71138	0.317000	0.19487	2.182000	0.69389	0.555000	0.69702	TGC	.	.		0.637	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965		G	73519846	C	G	73519846	3	3	21	1	0	0	0	0	1	0	0	0	4976	710	25	4	1264	4	EGR4	2	73519846	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	40696849	73519846	169679527	13	1877										
LRP2	4036	hgsc.bcm.edu	37	chr2	170099496	170099496	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ttcatccgagttgtcactgcAatcaaaaacaccatcacaac	4	13	4	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr2:170099496A>C	ENST00000263816.3	-	24	3922	c.3637T>G	c.(3637-3639)Tgc>Ggc	p.C1213G	LRP2_ENST00000443831.1_Missense_Mutation_p.C1076G	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1213	LDL-receptor class A 12. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TTGTCACTGCAATCAAAAACA	0.388																																					p.C1213G		Atlas-SNP	.											.	LRP2	751	.	0			c.T3637G						.						164	158	160					2																	170099496		2203	4300	6503	SO:0001583	missense	4036	exon24			CACTGCAATCAAA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.3637T>G	chr2.hg19:g.170099496A>C	ENSP00000263816:p.Cys1213Gly	105.0	0.0		100.0	22.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.824658	0.90955	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.99919	-8.0;-8.0	5.76	5.76	0.90799	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99953	0.9980	H	0.99074	4.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.96092	0.9062	10	0.72032	D	0.01	.	16.0843	0.81031	1.0:0.0:0.0:0.0	.	1076;1213	E9PC35;P98164	.;LRP2_HUMAN	G	1213;1076	ENSP00000263816:C1213G;ENSP00000409813:C1076G	ENSP00000263816:C1213G	C	-	1	0	LRP2	169807742	1.000000	0.71417	0.995000	0.50966	0.954000	0.61252	9.281000	0.95811	2.191000	0.70037	0.533000	0.62120	TGC	.	.		0.388	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		C	170099496	A	C	170099496	3	2	21	1	0	0	0	0	1	0	0	0	8965	130	5	5	10554	5	LRP2	2	170099496	Missense_Mutation	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10	96579650	170099496	73099877	14	1878										
CCDC108	255101	hgsc.bcm.edu	37	chr2	219886575	219886575	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	taatagagggtgcagttgccGtcattcaggaggacaaggaa	14	6	2	1	rs552052317		TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr2:219886575G>A	ENST00000341552.5	-	18	3140	c.3057C>T	c.(3055-3057)gaC>gaT	p.D1019D	CCDC108_ENST00000453220.1_Silent_p.D1019D|CCDC108_ENST00000441968.1_Silent_p.D1019D	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	1019						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGCAGTTGCCGTCATTCAGGA	0.607													G|||	1	0.000199681	8e-04	0	5008	,	,		17916	0		0	False		,,,				2504	0				p.D1019D		Atlas-SNP	.											.	CCDC108	208	.	0			c.C3057T						.						149	150	150					2																	219886575		2203	4300	6503	SO:0001819	synonymous_variant	255101	exon18			GTTGCCGTCATTC	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.3057C>T	chr2.hg19:g.219886575G>A		239.0	0.0		221.0	10.0	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	hg19	CCDS2430.2																																																																																			.	.		0.607	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		A	219886575	G	A	219886575	2	1	21	1	0	0	0	0	0	0	0	1	2745	1136	40	1		1	CCDC108	2	219886575	Silent	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	49787079	219886575	23312798	15	1879										
SERPINE2	5270	hgsc.bcm.edu	37	chr2	224866386	224866386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gccgtatctcatcaccatggCgagctgcttcttggtcctgc	10	14	3	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr2:224866386C>T	ENST00000258405.4	-	2	474	c.232G>A	c.(232-234)Gcc>Acc	p.A78T	SERPINE2_ENST00000447280.2_Missense_Mutation_p.A90T|SERPINE2_ENST00000409840.3_Missense_Mutation_p.A78T|SERPINE2_ENST00000409304.1_Missense_Mutation_p.A78T	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	78					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		ATCACCATGGCGAGCTGCTTC	0.577																																					p.A90T		Atlas-SNP	.											.	SERPINE2	103	.	0			c.G268A						.						78	68	71					2																	224866386		2203	4300	6503	SO:0001583	missense	5270	exon2			CCATGGCGAGCTG	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"Serine (or cysteine) peptidase inhibitors"	8951	protein-coding gene	gene with protein product	"glial-derived nexin 1"	177010	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.232G>A	chr2.hg19:g.224866386C>T	ENSP00000258405:p.Ala78Thr	54.0	0.0		46.0	7.0	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Missense_Mutation	SNP	ENST00000258405.4	hg19	CCDS2460.1	.	.	.	.	.	.	.	.	.	.	C	0.036	-1.306444	0.01353	.	.	ENSG00000135919	ENST00000409304;ENST00000258405;ENST00000409840;ENST00000447280;ENST00000432738;ENST00000454956	D;D;D;D;D;D	0.84660	-1.88;-1.88;-1.88;-1.88;-1.88;-1.88	5.67	0.476	0.16779	Serpin domain (3);	0.408702	0.28921	N	0.013718	T	0.65428	0.2690	N	0.11724	0.165	0.19300	N	0.999979	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.48703	-0.9012	10	0.18276	T	0.48	.	5.3815	0.16194	0.1216:0.2:0.0:0.6784	.	90;78	B4DIF2;P07093	.;GDN_HUMAN	T	78;78;78;90;78;78	ENSP00000386412:A78T;ENSP00000258405:A78T;ENSP00000386969:A78T;ENSP00000415786:A90T;ENSP00000408452:A78T;ENSP00000399655:A78T	ENSP00000258405:A78T	A	-	1	0	SERPINE2	224574630	1.000000	0.71417	0.133000	0.22050	0.054000	0.15201	1.150000	0.31639	-0.138000	0.11434	-1.004000	0.02495	GCC	.	.		0.577	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216		T	224866386	C	T	224866386	3	4	21	1	0	0	0	0	1	0	0	0	14127	768	27	1	996	1	SERPINE2	2	224866386	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	4979811	224866386	18332987	16	1880										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266124	41266124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gaatccattctggtgccactAccacagctccttctctgagt	7	14	2	1	rs121913412		TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr3:41266124A>G	ENST00000349496.5	+	3	401	c.121A>G	c.(121-123)Acc>Gcc	p.T41A	CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41A|CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41A|CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	41			T -> A (in hepatoblastoma and hepatocellular carcinoma; also in a desmoid tumor; strongly reduces phosphorylation and degradation; abolishes phosphorylation on Ser-33 and Ser-37 and enhances transactivation of target genes). {ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10398436, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10655994, ECO:0000269|PubMed:9927029}.|T -> I (in PTR, hepatocellular carcinoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T41A(550)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41P(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.A39_T42del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGTGCCACTACCACAGCTCC	0.507	T41A(CCK81_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.T41A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	681	Substitution - Missense(559)|Deletion - In frame(96)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)	soft_tissue(387)|liver(158)|large_intestine(61)|endometrium(17)|kidney(11)|stomach(8)|biliary_tract(7)|ovary(6)|small_intestine(4)|lung(4)|prostate(4)|adrenal_gland(3)|haematopoietic_and_lymphoid_tissue(3)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|salivary_gland(1)|pituitary(1)|pancreas(1)	c.A121G						.						89	77	81					3																	41266124		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCCACTACCACAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.121A>G	chr3.hg19:g.41266124A>G	ENSP00000344456:p.Thr41Ala	69.0	1.0		135.0	29.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449381	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.63117	0.2484	M	0.79258	2.445	0.80722	D	1	P	0.50943	0.94	P	0.52267	0.694	T	0.68561	-0.5376	10	0.87932	D	0	-8.9189	16.3453	0.83126	1.0:0.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	A	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34A;ENSP00000385604:T41A;ENSP00000412219:T41A;ENSP00000379486:T41A;ENSP00000344456:T41A;ENSP00000411226:T34A;ENSP00000379488:T41A;ENSP00000409302:T41A;ENSP00000401599:T41A	ENSP00000344456:T41A	T	+	1	0	CTNNB1	41241128	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	ACC	.	.		0.507	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266124	A	G	41266124	3	3	21	1	0	0	0	0	1	0	0	0	4018	391	14	2	127	2	CTNNB1	3	41266124	Missense_Mutation	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10		41266124	156756306	17	1881										
LARS2	23395	hgsc.bcm.edu	37	chr3	45517966	45517966	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tttcctatcaccaggttcatGggcaagccacgggcgaaaag	11	11	2	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr3:45517966G>C	ENST00000415258.1	+	9	1006	c.865G>C	c.(865-867)Ggg>Cgg	p.G289R	LARS2_ENST00000265537.3_Missense_Mutation_p.G289R|LARS2_ENST00000414984.1_Missense_Mutation_p.G246R			Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	289					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	CCAGGTTCATGGGCAAGCCAC	0.552																																					p.G289R		Atlas-SNP	.											.	LARS2	48	.	0			c.G865C						.						126	128	127					3																	45517966		2203	4300	6503	SO:0001583	missense	23395	exon10			GTTCATGGGCAAG	AJ312685	CCDS2728.1	3p21.3	2012-10-26			ENSG00000011376	ENSG00000011376	6.1.1.4	"Aminoacyl tRNA synthetases / Class I"	17095	protein-coding gene	gene with protein product	"leucine tRNA ligase 2, mitochondrial"	604544				20194621, 15123417	Standard	NM_015340		Approved	KIAA0028, LEURS, MGC26121	uc003cop.1	Q15031	OTTHUMG00000133177	ENST00000415258.1:c.865G>C	chr3.hg19:g.45517966G>C	ENSP00000408576:p.Gly289Arg	139.0	0.0		257.0	76.0	NM_015340		Missense_Mutation	SNP	ENST00000415258.1	hg19	CCDS2728.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.461265	0.43736	.	.	ENSG00000011376	ENST00000265537;ENST00000415258;ENST00000414984	T;T;T	0.36157	1.27;1.27;1.27	5.45	5.45	0.79879	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.050710	0.85682	D	0.000000	T	0.62183	0.2407	M	0.85859	2.78	0.58432	D	0.999999	D;D	0.76494	0.999;0.995	D;D	0.75020	0.985;0.975	T	0.67055	-0.5767	10	0.66056	D	0.02	-24.0841	12.2187	0.54420	0.0822:0.0:0.9178:0.0	.	246;289	E9PHM2;Q15031	.;SYLM_HUMAN	R	289;289;246	ENSP00000265537:G289R;ENSP00000408576:G289R;ENSP00000412893:G246R	ENSP00000265537:G289R	G	+	1	0	LARS2	45492970	1.000000	0.71417	0.357000	0.25798	0.053000	0.15095	6.419000	0.73345	2.555000	0.86185	0.563000	0.77884	GGG	.	.		0.552	LARS2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345001.1	NM_015340		C	45517966	G	C	45517966	3	2	21	1	0	0	0	0	1	0	0	0	8644	1348	47	4	895	4	LARS2	3	45517966	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	4251842	45517966	152504464	18	1882										
EIF4A2	1974	hgsc.bcm.edu	37	chr3	186502787	186502787	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tcaagctcagtcaggtactgGcaagacagccacatttgcta	9	11	3	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr3:186502787G>C	ENST00000323963.5	+	4	309	c.245G>C	c.(244-246)gGc>gCc	p.G82A	SNORA81_ENST00000408493.2_RNA|EIF4A2_ENST00000356531.5_Intron|SNORA4_ENST00000584302.1_RNA|SNORD2_ENST00000459163.1_RNA|EIF4A2_ENST00000440191.2_Missense_Mutation_p.G83A|SNORA63_ENST00000363548.1_RNA|SNORA63_ENST00000363450.1_RNA|RP11-573D15.9_ENST00000577781.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	82	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		TCAGGTACTGGCAAGACAGCC	0.448			T	BCL6	NHL																																p.G82A		Atlas-SNP	.		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	.	EIF4A2	55	.	0			c.G245C						.						174	156	162					3																	186502787		2203	4300	6503	SO:0001583	missense	1974	exon4			GTACTGGCAAGAC	D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"DEAD-boxes"	3284	protein-coding gene	gene with protein product		601102	"eukaryotic translation initiation factor 4A, isoform 2"	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.245G>C	chr3.hg19:g.186502787G>C	ENSP00000326381:p.Gly82Ala	120.0	0.0		86.0	28.0	NM_001967	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	hg19	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.985235	0.74474	.	.	ENSG00000156976	ENST00000445596;ENST00000323963;ENST00000440191	D;D;D	0.85411	-1.98;-1.98;-1.98	4.7	4.7	0.59300	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96027	0.8706	H	0.99752	4.75	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79784	0.956;0.993	D	0.97673	1.0168	10	0.87932	D	0	-16.8913	15.5195	0.75854	0.0:0.0:1.0:0.0	.	83;82	Q14240-2;Q14240	.;IF4A2_HUMAN	A	82;82;83	ENSP00000415878:G82A;ENSP00000326381:G82A;ENSP00000398370:G83A	ENSP00000326381:G82A	G	+	2	0	EIF4A2	187985481	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.045000	0.93812	2.592000	0.87571	0.585000	0.79938	GGC	.	.		0.448	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		C	186502787	G	C	186502787	3	2	21	1	0	0	0	0	1	0	0	0	5027	1203	42	4	259	4	EIF4A2	3	186502787	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	140984821	186502787	11519643	19	1883										
TMEM207	131920	hgsc.bcm.edu	37	chr3	190167544	190167544	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ctggaatagcggcaaacacaAgatccctatcgttgagatcg	10	10	0	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr3:190167544A>C	ENST00000354905.2	-	1	121	c.55T>G	c.(55-57)Ttg>Gtg	p.L19V		NM_207316.1	NP_997199.1	Q6UWW9	TM207_HUMAN	transmembrane protein 207	19						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(4)	7	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)		GGCAAACACAAGATCCCTATC	0.413																																					p.L19V		Atlas-SNP	.											.	TMEM207	19	.	0			c.T55G						.						165	139	147					3																	190167544		2203	4300	6503	SO:0001583	missense	131920	exon1			AACACAAGATCCC	BC071780	CCDS3297.1	3q28	2008-02-18			ENSG00000198398	ENSG00000198398			33705	protein-coding gene	gene with protein product		614786					Standard	NM_207316		Approved		uc003fsj.2	Q6UWW9	OTTHUMG00000156213	ENST00000354905.2:c.55T>G	chr3.hg19:g.190167544A>C	ENSP00000346981:p.Leu19Val	52.0	0.0		75.0	23.0	NM_207316		Missense_Mutation	SNP	ENST00000354905.2	hg19	CCDS3297.1	.	.	.	.	.	.	.	.	.	.	A	2.718	-0.267240	0.05754	.	.	ENSG00000198398	ENST00000354905	T	0.06068	3.35	5.29	2.76	0.32466	.	0.865799	0.09511	N	0.792276	T	0.06508	0.0167	L	0.47716	1.5	0.09310	N	1	P	0.40731	0.728	B	0.36666	0.23	T	0.36286	-0.9754	10	0.87932	D	0	.	4.5123	0.11917	0.7277:0.0:0.1002:0.172	.	19	Q6UWW9	TM207_HUMAN	V	19	ENSP00000346981:L19V	ENSP00000346981:L19V	L	-	1	2	TMEM207	191650238	0.078000	0.21339	0.002000	0.10522	0.008000	0.06430	-0.026000	0.12392	0.961000	0.38030	0.477000	0.44152	TTG	.	.		0.413	TMEM207-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343515.1	NM_207316		C	190167544	A	C	190167544	3	2	21	1	0	0	0	0	1	0	0	0	16147	69	3	5	405	5	TMEM207	3	190167544	Missense_Mutation	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10	3664757	190167544	7854886	20	1884										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6107374	6107374	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tccaggatctcctgctgcagCcgcaggcgctctccatcgaa	10	16	2	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr4:6107374C>T	ENST00000282924.5	-	3	935	c.450G>A	c.(448-450)cgG>cgA	p.R150R	JAKMIP1_ENST00000409371.3_Intron|JAKMIP1_ENST00000409831.1_Silent_p.R150R|JAKMIP1_ENST00000409021.3_Silent_p.R150R|JAKMIP1_ENST00000410077.2_Intron|JAKMIP1_ENST00000457227.2_Intron	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	150	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCTGCTGCAGCCGCAGGCGCT	0.682																																					p.R150R		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.G450A						.						17	15	16					4																	6107374		2198	4292	6490	SO:0001819	synonymous_variant	152789	exon3			CTGCAGCCGCAGG	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.450G>A	chr4.hg19:g.6107374C>T		76.0	0.0		50.0	18.0	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Silent	SNP	ENST00000282924.5	hg19	CCDS3385.1																																																																																			.	.		0.682	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		T	6107374	C	T	6107374	2	4	21	1	0	0	0	0	0	0	0	1	7949	726	26	3		3	JAKMIP1	4	6107374	Silent	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		6107374	185046902	21	1885										
ANK2	287	hgsc.bcm.edu	37	chr4	114276704	114276704	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	actgagagttttcagaaagaGgccactctaggctctcccaa	9	11	3	3			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr4:114276704G>T	ENST00000357077.4	+	38	6983	c.6930G>T	c.(6928-6930)gaG>gaT	p.E2310D	ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.E2277D|ANK2_ENST00000394537.3_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2310					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TTCAGAAAGAGGCCACTCTAG	0.493																																					p.E2310D		Atlas-SNP	.											.	ANK2	576	.	0			c.G6930T						.						43	44	44					4																	114276704		2203	4300	6503	SO:0001583	missense	287	exon38			GAAAGAGGCCACT	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.6930G>T	chr4.hg19:g.114276704G>T	ENSP00000349588:p.Glu2310Asp	60.0	0.0		93.0	33.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	G	3.119	-0.180958	0.06380	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.71461	-0.57;-0.57	5.79	3.1	0.35709	.	0.464019	0.19603	N	0.110349	T	0.62221	0.2410	M	0.64997	1.995	0.09310	N	0.999993	B;B	0.14805	0.004;0.011	B;B	0.14023	0.002;0.01	T	0.51244	-0.8730	9	.	.	.	.	5.6225	0.17465	0.1648:0.0:0.6783:0.1569	.	2277;2310	Q01484;Q01484-4	ANK2_HUMAN;.	D	2310;2277	ENSP00000349588:E2310D;ENSP00000264366:E2277D	.	E	+	3	2	ANK2	114496153	0.364000	0.24997	0.001000	0.08648	0.016000	0.09150	0.478000	0.22212	0.350000	0.24002	0.655000	0.94253	GAG	.	.		0.493	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114276704	G	T	114276704	3	4	21	1	0	0	0	0	1	0	0	0	621	991	35	3	7145	3	ANK2	4	114276704	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	108169330	114276704	76877572	22	1886										
APC	324	hgsc.bcm.edu	37	chr5	112173329	112173329	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gtttgacaatagtcagtaatGcatgtggaactttgtggaat	11	4	1	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr5:112173329G>T	ENST00000457016.1	+	16	2418	c.2038G>T	c.(2038-2040)Gca>Tca	p.A680S	APC_ENST00000508376.2_Missense_Mutation_p.A680S|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.A680S			P25054	APC_HUMAN	adenomatous polyposis coli	680	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGTCAGTAATGCATGTGGAAC	0.378		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.A680S	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	1	Unknown(1)	skin(1)	c.G2038T						.						89	90	90					5																	112173329		2202	4300	6502	SO:0001583	missense	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AGTAATGCATGTG	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2038G>T	chr5.hg19:g.112173329G>T	ENSP00000413133:p.Ala680Ser	76.0	0.0		123.0	61.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	18.36	3.607475	0.66558	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.83335	-1.71;-1.71;-1.71;-1.71;-1.71	5.99	5.99	0.97316	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88905	0.6564	L	0.39898	1.24	0.80722	D	1	P;P	0.49358	0.923;0.923	D;D	0.72625	0.978;0.978	D	0.88757	0.3254	10	0.87932	D	0	-17.9049	20.4777	0.99188	0.0:0.0:1.0:0.0	.	682;680	Q4LE70;P25054	.;APC_HUMAN	S	680;662;680;680;680	ENSP00000413133:A680S;ENSP00000423224:A662S;ENSP00000257430:A680S;ENSP00000427089:A680S;ENSP00000423828:A680S	ENSP00000257430:A680S	A	+	1	0	APC	112201228	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.476000	0.97823	2.840000	0.97914	0.655000	0.94253	GCA	.	.		0.378	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112173329	G	T	112173329	3	4	21	1	0	0	0	0	1	0	0	0	763	1319	46	3	2096	3	APC	5	112173329	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10		112173329	68741931	23	1887										
MEGF10	84466	hgsc.bcm.edu	37	chr5	126791174	126791174	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	atatgccactattaaagaccCacctgtacttatcccgaaaa	4	12	0	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr5:126791174C>T	ENST00000274473.6	+	25	3374	c.3107C>T	c.(3106-3108)cCa>cTa	p.P1036L	MEGF10_ENST00000510828.1_3'UTR|MEGF10_ENST00000503335.2_Missense_Mutation_p.P1036L	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	1036	Necessary for formation of large intracellular vacuoles.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.P1036L(1)		breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		ATTAAAGACCCACCTGTACTT	0.423																																					p.P1036L		Atlas-SNP	.											MEGF10,NS,carcinoma,0,1	MEGF10	152	.	1	Substitution - Missense(1)	lung(1)	c.C3107T						.						120	132	128					5																	126791174		2203	4300	6503	SO:0001583	missense	84466	exon25			AAGACCCACCTGT	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.3107C>T	chr5.hg19:g.126791174C>T	ENSP00000274473:p.Pro1036Leu	123.0	1.0		319.0	142.0	NM_032446	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	hg19	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.549343	0.45383	.	.	ENSG00000145794	ENST00000503335;ENST00000274473	T;T	0.74947	-0.89;-0.89	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000001	T	0.79470	0.4451	L	0.41492	1.28	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.71041	-0.4707	10	0.02654	T	1	-9.3156	19.843	0.96697	0.0:1.0:0.0:0.0	.	1036	Q96KG7	MEG10_HUMAN	L	1036	ENSP00000423354:P1036L;ENSP00000274473:P1036L	ENSP00000274473:P1036L	P	+	2	0	MEGF10	126819073	1.000000	0.71417	0.998000	0.56505	0.965000	0.64279	7.487000	0.81328	2.679000	0.91253	0.655000	0.94253	CCA	.	.		0.423	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		T	126791174	C	T	126791174	3	4	21	1	0	0	0	0	1	0	0	0	9469	594	21	3	3197	3	MEGF10	5	126791174	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	14617845	126791174	54124086	24	1888										
RAD50	10111	hgsc.bcm.edu	37	chr5	131939116	131939116	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	aagaaacactcttgggtacaAtaatgcctgaagaagaaagt	9	6	1	4			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr5:131939116A>G	ENST00000265335.6	+	14	2719	c.2332A>G	c.(2332-2334)Ata>Gta	p.I778V	RAD50_ENST00000378823.3_Missense_Mutation_p.I639V			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	778					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTTGGGTACAATAATGCCTGA	0.368								Homologous recombination																													p.I778V		Atlas-SNP	.											.	RAD50	246	.	0			c.A2332G						.						124	114	117					5																	131939116		2203	4300	6503	SO:0001583	missense	10111	exon14			GGTACAATAATGC	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.2332A>G	chr5.hg19:g.131939116A>G	ENSP00000265335:p.Ile778Val	177.0	0.0		337.0	93.0	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	hg19	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	A	7.958	0.746245	0.15710	.	.	ENSG00000113522	ENST00000378823;ENST00000265335	T;T	0.04603	3.59;3.82	5.16	1.37	0.22104	.	0.313588	0.32430	N	0.006120	T	0.01870	0.0059	N	0.04508	-0.205	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.47156	-0.9139	10	0.18710	T	0.47	-9.0847	4.529	0.11995	0.5516:0.0:0.3075:0.1409	.	778	Q92878	RAD50_HUMAN	V	639;778	ENSP00000368100:I639V;ENSP00000265335:I778V	ENSP00000265335:I778V	I	+	1	0	RAD50	131967015	0.050000	0.20438	0.988000	0.46212	0.957000	0.61999	0.362000	0.20284	0.348000	0.23949	-0.256000	0.11100	ATA	.	.		0.368	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		G	131939116	A	G	131939116	3	3	21	1	0	0	0	0	1	0	0	0	12999	101	4	2	2386	2	RAD50	5	131939116	Missense_Mutation	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10	5147942	131939116	48976144	25	1889										
BTNL9	153579	hgsc.bcm.edu	37	chr5	180486695	180486695	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tccacgacaccttctcgggcGcgctctgtgcgtacttcagg	11	15	3	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr5:180486695G>A	ENST00000327705.9	+	11	1672	c.1441G>A	c.(1441-1443)Gcg>Acg	p.A481T	BTNL9_ENST00000376842.3_Missense_Mutation_p.A482T	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	481	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTTCTCGGGCGCGCTCTGTGC	0.667																																					p.A481T		Atlas-SNP	.											.	BTNL9	58	.	0			c.G1441A						.						37	35	36					5																	180486695		2203	4300	6503	SO:0001583	missense	153579	exon11			TCGGGCGCGCTCT	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.1441G>A	chr5.hg19:g.180486695G>A	ENSP00000330200:p.Ala481Thr	172.0	0.0		94.0	16.0	NM_152547	A6NL42|Q6P660|Q96DM5	Missense_Mutation	SNP	ENST00000327705.9	hg19	CCDS4460.2	.	.	.	.	.	.	.	.	.	.	g	5.406	0.260076	0.10239	.	.	ENSG00000165810	ENST00000327705;ENST00000376842	T;T	0.60548	0.18;0.18	4.22	-7.0	0.01599	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	1.157270	0.06801	N	0.788764	T	0.18964	0.0455	N	0.01656	-0.775	0.09310	N	0.999998	B	0.11235	0.004	B	0.14023	0.01	T	0.23868	-1.0176	10	0.05721	T	0.95	.	4.5035	0.11876	0.2159:0.4869:0.2028:0.0945	.	481	Q6UXG8	BTNL9_HUMAN	T	481;482	ENSP00000330200:A481T;ENSP00000366038:A482T	ENSP00000330200:A481T	A	+	1	0	BTNL9	180419301	0.000000	0.05858	0.011000	0.14972	0.021000	0.10359	-0.392000	0.07314	-1.343000	0.02219	0.449000	0.29647	GCG	.	.		0.667	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547		A	180486695	G	A	180486695	3	1	21	1	0	0	0	0	1	0	0	0	1570	1087	38	1	1479	1	BTNL9	5	180486695	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	48547579	180486695	428565	26	1890										
FANCE	2178	hgsc.bcm.edu	37	chr6	35434031	35434031	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ttctccccagatcactgagaCccagaggctgggcctggcta	11	14	2	3			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr6:35434031C>G	ENST00000229769.2	+	10	1705	c.1520C>G	c.(1519-1521)aCc>aGc	p.T507S	RPL10A_ENST00000322203.6_5'Flank	NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	507					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						ATCACTGAGACCCAGAGGCTG	0.577			"N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.T507S		Atlas-SNP	.	yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	"Fanconi anemia, complementation group E"		L	.	FANCE	45	.	0			c.C1520G						.						92	90	91					6																	35434031		2203	4300	6503	SO:0001583	missense	2178	exon10	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTGAGACCCAGAG	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039		"Fanconi anemia, complementation groups"	3586	protein-coding gene	gene with protein product		613976		FACE		7662964, 11001585	Standard	XM_005248885		Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.1520C>G	chr6.hg19:g.35434031C>G	ENSP00000229769:p.Thr507Ser	97.0	0.0		78.0	28.0	NM_021922	A8K907|Q4ZGH2	Missense_Mutation	SNP	ENST00000229769.2	hg19	CCDS4805.1	.	.	.	.	.	.	.	.	.	.	C	8.762	0.923820	0.18056	.	.	ENSG00000112039	ENST00000229769	T	0.47177	0.85	5.77	1.85	0.25348	Fanconi Anaemia group E protein, C-terminal (1);	0.825347	0.11256	N	0.583076	T	0.08626	0.0214	N	0.19112	0.55	0.09310	N	1	B	0.16166	0.016	B	0.17979	0.02	T	0.39143	-0.9628	10	0.07990	T	0.79	-17.3398	4.1775	0.10358	0.1642:0.5669:0.0:0.2689	.	507	Q9HB96	FANCE_HUMAN	S	507	ENSP00000229769:T507S	ENSP00000229769:T507S	T	+	2	0	FANCE	35542009	0.070000	0.21116	0.505000	0.27651	0.829000	0.46940	0.653000	0.24902	0.042000	0.15717	-0.258000	0.10820	ACC	.	.		0.577	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040282.1			G	35434031	C	G	35434031	3	3	21	1	0	0	0	0	1	0	0	0	5674	507	18	4	1558	4	FANCE	6	35434031	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		35434031	135681036	27	1891										
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83863710	83863710	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	cttggaaaaaagaagcttttGacctctttatggatcccagt	8	8	1	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr6:83863710G>T	ENST00000349129.2	+	32	6597	c.6337G>T	c.(6337-6339)Gac>Tac	p.D2113Y	DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Missense_Mutation_p.D2104Y|DOPEY1_ENST00000237163.5_Missense_Mutation_p.D2043Y	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2113					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		AGAAGCTTTTGACCTCTTTAT	0.443																																					p.D2113Y		Atlas-SNP	.											.	DOPEY1	190	.	0			c.G6337T						.						219	217	217					6																	83863710		2203	4300	6503	SO:0001583	missense	23033	exon32			GCTTTTGACCTCT	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.6337G>T	chr6.hg19:g.83863710G>T	ENSP00000195654:p.Asp2113Tyr	68.0	0.0		75.0	4.0	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	hg19	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.636113	0.87760	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.53857	0.6;1.29	4.94	4.94	0.65067	.	0.091396	0.64402	D	0.000001	T	0.65595	0.2706	M	0.61703	1.905	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.75020	0.985;0.97;0.978	T	0.68911	-0.5284	10	0.87932	D	0	.	18.3686	0.90399	0.0:0.0:1.0:0.0	.	2004;2104;2113	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	Y	2113;2043;2043	ENSP00000195654:D2113Y;ENSP00000237163:D2043Y	ENSP00000237163:D2043Y	D	+	1	0	DOPEY1	83920429	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.229000	0.95273	2.584000	0.87258	0.557000	0.71058	GAC	.	.		0.443	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		T	83863710	G	T	83863710	3	4	21	1	0	0	0	0	1	0	0	0	4709	1290	45	3	6455	3	DOPEY1	6	83863710	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	48429679	83863710	87251357	28	1892										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102134116	102134116	+	Frame_Shift_Del	DEL	G	G	-													0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tgttaacatgacagggttcaGaatattaaatacagaaaata							TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr6:102134116delG	ENST00000421544.1	+	6	1329	c.839delG	c.(838-840)agafs	p.R280fs	GRIK2_ENST00000369137.3_Frame_Shift_Del_p.R280fs|GRIK2_ENST00000369134.4_Frame_Shift_Del_p.R231fs|GRIK2_ENST00000369138.1_Frame_Shift_Del_p.R280fs|GRIK2_ENST00000413795.1_Frame_Shift_Del_p.R280fs|GRIK2_ENST00000358361.3_Frame_Shift_Del_p.R280fs|GRIK2_ENST00000318991.6_Frame_Shift_Del_p.R280fs	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	280					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	ACAGGGTTCAGAATATTAAAT	0.423																																					p.R280fs		Atlas-Indel,Pindel	.											.	GRIK2	487	.	0			c.838delA						.						90	88	89					6																	102134116		2203	4300	6503	SO:0001589	frameshift_variant	2898	exon6			.		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.839delG	chr6.hg19:g.102134116delG	ENSP00000397026:p.Arg280fs	59.0	0.0		136.0	46.0	NM_001166247	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Frame_Shift_Del	DEL	ENST00000421544.1	hg19	CCDS5048.1																																																																																			.	.		0.423	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			-	102134116	G	-	102134116	7	5	21	1	0	1	0	1	0	0	0	0	6783	942	33	0	861	0	GRIK2	6	102134116	Frame_Shift_Del	DEL	G	TCGA-2Y-A9HB-01A-11D-A38X-10	18270406	102134116	68980951	29	1893										
REV3L	5980	hgsc.bcm.edu	37	chr6	111695908	111695908	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tatgctttctcgatgtacctTtctcatttgttttttgtttt	5	7	2	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr6:111695908T>G	ENST00000358835.3	-	14	4104	c.3650A>C	c.(3649-3651)aAa>aCa	p.K1217T	REV3L_ENST00000435970.1_Missense_Mutation_p.K1139T|REV3L_ENST00000368805.1_Missense_Mutation_p.K1217T|REV3L_ENST00000368802.3_Missense_Mutation_p.K1217T			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1217					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CGATGTACCTTTCTCATTTGT	0.338								DNA polymerases (catalytic subunits)																													p.K1217T		Atlas-SNP	.											.	REV3L	386	.	0			c.A3650C						.						85	84	84					6																	111695908		2203	4300	6503	SO:0001583	missense	5980	exon13			GTACCTTTCTCAT	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.3650A>C	chr6.hg19:g.111695908T>G	ENSP00000351697:p.Lys1217Thr	20.0	0.0		46.0	15.0	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	T	23.0	4.357682	0.82243	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.02787	4.25;4.25;4.25;4.16	5.32	5.32	0.75619	Ribonuclease H-like (1);	0.571312	0.18173	N	0.149400	T	0.07818	0.0196	L	0.59436	1.845	0.40602	D	0.981594	D	0.76494	0.999	D	0.78314	0.991	T	0.05099	-1.0906	10	0.72032	D	0.01	.	15.5723	0.76349	0.0:0.0:0.0:1.0	.	1217	O60673	DPOLZ_HUMAN	T	1217;1217;1217;1139	ENSP00000357792:K1217T;ENSP00000357795:K1217T;ENSP00000351697:K1217T;ENSP00000402003:K1139T	ENSP00000351697:K1217T	K	-	2	0	REV3L	111802601	1.000000	0.71417	0.968000	0.41197	0.827000	0.46813	5.412000	0.66392	2.139000	0.66308	0.533000	0.62120	AAA	.	.		0.338	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		G	111695908	T	G	111695908	3	3	21	1	0	0	0	0	1	0	0	0	13255	1841	64	5	5822	5	REV3L	6	111695908	Missense_Mutation	SNP	T	TCGA-2Y-A9HB-01A-11D-A38X-10	9561792	111695908	59419159	30	1894										
OSBPL3	26031	hgsc.bcm.edu	37	chr7	24911674	24911674	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tcccccctcagtccttccacCacttcccagctgtcctgttc	4	21	1	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr7:24911674C>T	ENST00000313367.2	-	3	562	c.111G>A	c.(109-111)gtG>gtA	p.V37V	OSBPL3_ENST00000353930.1_Silent_p.V37V|OSBPL3_ENST00000396431.1_Silent_p.V37V|OSBPL3_ENST00000409069.1_Silent_p.V37V|OSBPL3_ENST00000431825.2_Silent_p.V37V|OSBPL3_ENST00000352860.1_Silent_p.V37V|OSBPL3_ENST00000396429.1_Silent_p.V37V	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	37					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						GTCCTTCCACCACTTCCCAGC	0.413																																					p.V37V		Atlas-SNP	.											.	OSBPL3	100	.	0			c.G111A						.						97	89	92					7																	24911674		2203	4300	6503	SO:0001819	synonymous_variant	26031	exon3			TTCCACCACTTCC	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.111G>A	chr7.hg19:g.24911674C>T		88.0	0.0		94.0	39.0	NM_145321	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Silent	SNP	ENST00000313367.2	hg19	CCDS5390.1																																																																																			.	.		0.413	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2			T	24911674	C	T	24911674	2	4	21	1	0	0	0	0	0	0	0	1	11288	581	21	3		3	OSBPL3	7	24911674	Silent	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		24911674	134226989	31	1895										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44575496	44575496	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	agagagatgtacaggaatatGacaatgtagctggtggcaaa	13	4	0	3	rs200986707		TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr7:44575496G>A	ENST00000289547.4	-	5	1981	c.1926C>T	c.(1924-1926)gtC>gtT	p.V642V	NPC1L1_ENST00000546276.1_Silent_p.V642V|NPC1L1_ENST00000381160.3_Silent_p.V642V|NPC1L1_ENST00000423141.1_Silent_p.V642V	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	642	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	ACAGGAATATGACAATGTAGC	0.582																																					p.V642V		Atlas-SNP	.											.	NPC1L1	141	.	0			c.C1926T						.						117	103	108					7																	44575496		2203	4300	6503	SO:0001819	synonymous_variant	29881	exon5			GAATATGACAATG		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.1926C>T	chr7.hg19:g.44575496G>A		101.0	0.0		72.0	22.0	NM_001101648	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	hg19	CCDS5491.1																																																																																			.	G|0.999;T|0.001		0.582	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		A	44575496	G	A	44575496	2	1	21	1	0	0	0	0	0	0	0	1	10580	1277	45	3		3	NPC1L1	7	44575496	Silent	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	19663822	44575496	114563167	32	1896										
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150761796	150761796	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tgaggatgaggccagcgaggCtgagggggcccgggctctca	19	10	1	3			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr7:150761796C>T	ENST00000485713.1	+	4	1441	c.401C>T	c.(400-402)gCt>gTt	p.A134V	SLC4A2_ENST00000392826.2_Missense_Mutation_p.A125V|SLC4A2_ENST00000413384.2_Missense_Mutation_p.A134V|SLC4A2_ENST00000461735.1_Missense_Mutation_p.A120V|SLC4A2_ENST00000310317.5_Missense_Mutation_p.A52V	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	134	Pro-rich.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCCAGCGAGGCTGAGGGGGCC	0.701																																					p.A134V		Atlas-SNP	.											.	SLC4A2	98	.	0			c.C401T						.						26	32	30					7																	150761796		2203	4300	6503	SO:0001583	missense	6522	exon4			GCGAGGCTGAGGG		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"Solute carriers"	11028	protein-coding gene	gene with protein product	"anion exchanger 2 type a", "anion exchanger 2 type b1", "anion exchanger 2 type b2"	109280	"erythrocyte membrane protein band 3-like 1", "solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.401C>T	chr7.hg19:g.150761796C>T	ENSP00000419412:p.Ala134Val	245.0	0.0		119.0	43.0	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	hg19	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	C	9.404	1.078781	0.20227	.	.	ENSG00000164889	ENST00000483786;ENST00000485713;ENST00000413384;ENST00000490898;ENST00000463414;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T;T;T;T	0.75367	0.95;-0.9;-0.9;1.51;0.93;-0.93;-0.9;-0.9	5.3	4.41	0.53225	.	0.821622	0.10565	N	0.659854	T	0.57125	0.2032	N	0.22421	0.69	0.24271	N	0.995245	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.40979	-0.9534	10	0.10111	T	0.7	.	8.5651	0.33534	0.0:0.8247:0.0:0.1753	.	125;120;134	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	V	134;134;134;134;134;52;125;120	ENSP00000417808:A134V;ENSP00000419412:A134V;ENSP00000405600:A134V;ENSP00000418114:A134V;ENSP00000418584:A134V;ENSP00000311402:A52V;ENSP00000376571:A125V;ENSP00000419164:A120V	ENSP00000311402:A52V	A	+	2	0	SLC4A2	150392729	0.365000	0.25006	0.935000	0.37517	0.012000	0.07955	0.996000	0.29719	2.478000	0.83669	0.563000	0.77884	GCT	.	.		0.701	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		T	150761796	C	T	150761796	3	4	21	1	0	0	0	0	1	0	0	0	14669	797	28	3	411	3	SLC4A2	7	150761796	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	106186300	150761796	8376867	33	1897										
TNFRSF10B	8795	hgsc.bcm.edu	37	chr8	22885267	22885267	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ctcagggtccccaccaccacCtaaaaaagaagcagtctcct	6	16	2	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr8:22885267C>T	ENST00000276431.4	-	6	1033		c.e6-1		TNFRSF10B_ENST00000542226.1_Splice_Site|TNFRSF10B_ENST00000519910.1_5'Flank|TNFRSF10B_ENST00000347739.3_Splice_Site	NM_003842.4|NM_147187.2	NP_003833.4|NP_671716.2	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily, member 10b						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to endoplasmic reticulum stress (GO:0034976)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|TRAIL binding (GO:0045569)			NS(1)|endometrium(2)|large_intestine(7)|liver(1)|lung(3)|skin(1)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		CCACCACCACCTAAAAAAGAA	0.622																																					.	GBM(94;1064 1342 1839 21060 42553)	Atlas-SNP	.											.	TNFRSF10B	34	.	0			c.749-1G>A						.						63	56	58					8																	22885267		2203	4300	6503	SO:0001630	splice_region_variant	8795	exon7			CACCACCTAAAAA	AF012628	CCDS6035.1, CCDS6036.1	8p22-p21	2006-02-22			ENSG00000120889	ENSG00000120889		"Tumor necrosis factor receptor superfamily", "CD molecules"	11905	protein-coding gene	gene with protein product		603612				9285725, 9311998	Standard	NM_003842		Approved	DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262	uc003xcu.2	O14763	OTTHUMG00000097826	ENST00000276431.4:c.749-1G>A	chr8.hg19:g.22885267C>T		77.0	0.0		35.0	17.0	NM_003842	O14720|O15508|O15517|O15531|Q6UXM8|Q7Z360|Q9BVE0	Splice_Site	SNP	ENST00000276431.4	hg19	CCDS6035.1	.	.	.	.	.	.	.	.	.	.	c	6.217	0.408112	0.11754	.	.	ENSG00000120889	ENST00000276431;ENST00000347739;ENST00000542226	.	.	.	2.44	2.44	0.29823	.	.	.	.	.	.	.	.	.	.	.	0.41469	D	0.988092	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4828	0.33054	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TNFRSF10B	22941212	0.328000	0.24687	0.109000	0.21407	0.017000	0.09413	2.253000	0.43205	1.665000	0.50811	0.655000	0.94253	.	.	.		0.622	TNFRSF10B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215099.2	NM_147187	Intron	T	22885267	C	T	22885267	5	4	21	1	0	0	0	0	0	0	1	0	16296	695	24	3	590	3	TNFRSF10B	8	22885267	Splice_Site	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		22885267	123478755	34	1898										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321471	52321471	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tctgagagcctgggattcccGctccgagctcccgtaaacgt	11	14	1	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr8:52321471G>A	ENST00000356297.4	-	17	2813	c.2713C>T	c.(2713-2715)Cgg>Tgg	p.R905W	PXDNL_ENST00000543296.1_Missense_Mutation_p.R905W	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	905					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TGGGATTCCCGCTCCGAGCTC	0.587																																					p.R905W		Atlas-SNP	.											PXDNL_ENST00000356297,right_upper_lobe,carcinoma,+1,4	PXDNL	414	.	0			c.C2713T						.						38	43	41					8																	52321471		1990	4153	6143	SO:0001583	missense	137902	exon17			ATTCCCGCTCCGA		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2713C>T	chr8.hg19:g.52321471G>A	ENSP00000348645:p.Arg905Trp	217.0	0.0		117.0	30.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	7.352	0.623064	0.14193	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.69806	-0.43;-0.43	4.03	-1.77	0.07982	.	0.817539	0.10469	N	0.671059	T	0.61048	0.2316	M	0.76328	2.33	0.21861	N	0.999501	B	0.18863	0.031	B	0.20955	0.032	T	0.54057	-0.8350	10	0.66056	D	0.02	.	4.7256	0.12939	0.1743:0.0:0.4214:0.4044	.	905	A1KZ92	PXDNL_HUMAN	W	905	ENSP00000348645:R905W;ENSP00000444865:R905W	ENSP00000348645:R905W	R	-	1	2	PXDNL	52484024	0.000000	0.05858	0.000000	0.03702	0.134000	0.20937	0.394000	0.20834	-0.970000	0.03569	-0.258000	0.10820	CGG	.	.		0.587	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52321471	G	A	52321471	3	1	21	1	0	0	0	0	1	0	0	0	12863	1086	38	1	1706	1	PXDNL	8	52321471	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	29436204	52321471	94042551	35	1899										
JPH1	56704	hgsc.bcm.edu	37	chr8	75157022	75157022	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ttcacgtagtagccgtgataCtgagaatgcagctccccgtt	10	11	1	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr8:75157022C>T	ENST00000342232.4	-	4	1687	c.1647G>A	c.(1645-1647)caG>caA	p.Q549Q	JPH1_ENST00000518195.1_5'UTR	NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	549					calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			AGCCGTGATACTGAGAATGCA	0.612																																					p.Q549Q		Atlas-SNP	.											.	JPH1	77	.	0			c.G1647A						.						71	62	65					8																	75157022		2203	4300	6503	SO:0001819	synonymous_variant	56704	exon4			GTGATACTGAGAA	AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.1647G>A	chr8.hg19:g.75157022C>T		50.0	0.0		56.0	17.0	NM_020647	B2RTZ0	Silent	SNP	ENST00000342232.4	hg19	CCDS6217.1																																																																																			.	.		0.612	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1			T	75157022	C	T	75157022	2	4	21	1	0	0	0	0	0	0	0	1	7969	564	20	3		3	JPH1	8	75157022	Silent	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	22835551	75157022	71207000	36	1900										
C8orf85	441376	hgsc.bcm.edu	37	chr8	117950650	117950650	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ctcgccgccagcccgctgctGgaggacctcagacgacggct	13	17	1	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr8:117950650G>A	ENST00000378279.3	+	1	213	c.168G>A	c.(166-168)ctG>ctA	p.L56L		NM_001025357.2	NP_001020528.1	Q4LEZ3	AARD_HUMAN	alanine and arginine rich domain containing protein	56					lung development (GO:0030324)												GCCCGCTGCTGGAGGACCTCA	0.746																																					p.L56L		Atlas-SNP	.											C8orf85,NS,carcinoma,0,1	.	.	.	0			c.G168A						.						12	13	13					8																	117950650		2166	4253	6419	SO:0001819	synonymous_variant	441376	exon1			GCTGCTGGAGGAC	AB181519, BC140924	CCDS34935.1	8q24.11	2012-04-19	2012-04-19	2012-04-19	ENSG00000205002	ENSG00000205002			33842	protein-coding gene	gene with protein product	"Alanine and arginine-rich domain-containing protein"		"chromosome 8 open reading frame 85"	C8orf85			Standard	NM_001025357		Approved	LOC441376	uc003yof.3	Q4LEZ3	OTTHUMG00000164961	ENST00000378279.3:c.168G>A	chr8.hg19:g.117950650G>A		151.0	0.0		91.0	33.0	NM_001025357	A5PKU8	Silent	SNP	ENST00000378279.3	hg19	CCDS34935.1																																																																																			.	.		0.746	AARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381195.1	NM_001025357		A	117950650	G	A	117950650	2	1	21	1	0	0	0	0	0	0	0	1	2443	1335	47	3		3	C8orf85	8	117950650	Silent	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	42793628	117950650	28413372	37	1901										
TG	7038	hgsc.bcm.edu	37	chr8	133911108	133911108	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gttggaaacaggctagatccCaagaaaacccatctccaaaa	7	11	1	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr8:133911108C>T	ENST00000220616.4	+	14	3323	c.3283C>T	c.(3283-3285)Caa>Taa	p.Q1095*	TG_ENST00000377869.1_Nonsense_Mutation_p.Q1095*	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1095	Thyroglobulin type-1 9. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.Q1095K(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GGCTAGATCCCAAGAAAACCC	0.552																																					p.Q1095X		Atlas-SNP	.											TG,NS,carcinoma,0,1	TG	416	.	1	Substitution - Missense(1)	ovary(1)	c.C3283T						.						79	66	70					8																	133911108		2203	4300	6503	SO:0001587	stop_gained	7038	exon14			AGATCCCAAGAAA	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.3283C>T	chr8.hg19:g.133911108C>T	ENSP00000220616:p.Gln1095*	142.0	0.0		111.0	38.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Nonsense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.242778|6.242778	0.97408|0.97408	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000543313|ENST00000377869;ENST00000220616	.|.	.|.	.|.	5.74|5.74	4.85|4.85	0.62838|0.62838	.|.	.|0.333863	.|0.25848	.|N	.|0.027910	T|.	0.32406|.	0.0828|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34850|.	-0.9812|.	3|.	.|0.11182	.|T	.|0.66	.|.	8.0944|8.0944	0.30820|0.30820	0.1517:0.626:0.2223:0.0|0.1517:0.626:0.2223:0.0	.|.	.|.	.|.	.|.	L|X	2|1095	.|.	.|ENSP00000220616:Q1095X	P|Q	+|+	2|1	0|0	TG|TG	133980290|133980290	0.011000|0.011000	0.17503|0.17503	0.039000|0.039000	0.18376|0.18376	0.351000|0.351000	0.29236|0.29236	1.418000|1.418000	0.34782|0.34782	2.702000|2.702000	0.92279|0.92279	0.655000|0.655000	0.94253|0.94253	CCA|CAA	.	.		0.552	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133911108	C	T	133911108	4	4	21	1	0	0	0	0	0	1	0	0	15828	595	21	3	3337	3	TG	8	133911108	Nonsense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	15960458	133911108	12452914	38	1902										
TOP1MT	116447	hgsc.bcm.edu	37	chr8	144406772	144406772	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	acctccttccactggtgcccCgccggcggctcggggatctt	12	17	1	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr8:144406772C>A	ENST00000329245.4	-	6	733	c.699G>T	c.(697-699)gcG>gcT	p.A233A	TOP1MT_ENST00000521193.1_Silent_p.A135A|TOP1MT_ENST00000523676.1_Silent_p.A135A|TOP1MT_ENST00000519148.1_Silent_p.A135A	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	233					DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	ACTGGTGCCCCGCCGGCGGCT	0.562																																					p.A233A		Atlas-SNP	.											.	TOP1MT	63	.	0			c.G699T						.						93	94	94					8																	144406772		2203	4300	6503	SO:0001819	synonymous_variant	116447	exon6			GTGCCCCGCCGGC	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.699G>T	chr8.hg19:g.144406772C>A		94.0	0.0		39.0	7.0	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Silent	SNP	ENST00000329245.4	hg19	CCDS6400.1																																																																																			.	.		0.562	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963		A	144406772	C	A	144406772	2	1	21	1	0	0	0	0	0	0	0	1	16379	639	23	1		1	TOP1MT	8	144406772	Silent	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	10495664	144406772	1957250	39	1903										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144940679	144940679	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gcagcacgcccttccacatgGcctggtagatgctcatcttc	9	15	2	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr8:144940679G>T	ENST00000525985.1	-	2	6814	c.6743C>A	c.(6742-6744)gCc>gAc	p.A2248D				P58107	EPIPL_HUMAN	epiplakin 1	2248						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTTCCACATGGCCTGGTAGAT	0.711																																					p.A2248D		Atlas-SNP	.											.	EPPK1	199	.	0			c.C6743A						.						60	57	58					8																	144940679		2185	4252	6437	SO:0001583	missense	83481	exon1			CACATGGCCTGGT	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6743C>A	chr8.hg19:g.144940679G>T	ENSP00000436337:p.Ala2248Asp	91.0	0.0		54.0	13.0	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	G	32	5.129311	0.94473	.	.	ENSG00000227184	ENST00000525985	D	0.97598	-4.45	4.67	4.67	0.58626	.	.	.	.	.	D	0.98413	0.9472	M	0.84433	2.695	0.53688	D	0.999977	D	0.89917	1.0	D	0.97110	1.0	D	0.99274	1.0894	9	0.87932	D	0	.	15.1226	0.72457	0.0:0.0:1.0:0.0	.	2248	E9PPU0	.	D	2248	ENSP00000436337:A2248D	ENSP00000436337:A2248D	A	-	2	0	EPPK1	145012667	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.795000	0.99099	2.420000	0.82092	0.591000	0.81541	GCC	.	.		0.711	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144940679	G	T	144940679	3	4	21	1	0	0	0	0	1	0	0	0	5192	1203	42	3	523	3	EPPK1	8	144940679	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	533907	144940679	1423343	40	1904										
IFNA8	3445	hgsc.bcm.edu	37	chr9	21409340	21409340	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	cctttctcctgcctgaaggaCagacatgactttgaattccc	7	13	1	4			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr9:21409340C>A	ENST00000380205.1	+	1	195	c.165C>A	c.(163-165)gaC>gaA	p.D55E		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	55					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		GCCTGAAGGACAGACATGACT	0.507																																					p.D55E		Atlas-SNP	.											.	IFNA8	19	.	0			c.C165A						.						109	107	108					9																	21409340		2203	4300	6503	SO:0001583	missense	3445	exon1			GAAGGACAGACAT		CCDS6507.1	9p22	2010-08-24			ENSG00000120242	ENSG00000120242		"Interferons"	5429	protein-coding gene	gene with protein product	"interferon alpha-B''", "interferon alpha type 201"	147568				1385305	Standard	NM_002170		Approved	IFN-alphaB	uc003zpc.1	P32881	OTTHUMG00000019677	ENST00000380205.1:c.165C>A	chr9.hg19:g.21409340C>A	ENSP00000369553:p.Asp55Glu	59.0	0.0		69.0	17.0	NM_002170	P01565|P09236|Q5VWV7|Q5VYQ3	Missense_Mutation	SNP	ENST00000380205.1	hg19	CCDS6507.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.359335	0.24598	.	.	ENSG00000120242	ENST00000380205	T	0.06608	3.28	3.43	2.51	0.30379	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.507012	0.20203	N	0.097050	T	0.14013	0.0339	M	0.73753	2.245	0.25727	N	0.985314	P	0.35894	0.526	P	0.49192	0.602	T	0.04191	-1.0970	10	0.66056	D	0.02	.	4.692	0.12785	0.0:0.7621:0.0:0.2379	.	55	P32881	IFNA8_HUMAN	E	55	ENSP00000369553:D55E	ENSP00000369553:D55E	D	+	3	2	IFNA8	21399340	0.149000	0.22717	0.562000	0.28370	0.264000	0.26372	0.489000	0.22387	1.914000	0.55421	0.561000	0.74099	GAC	.	.		0.507	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1	NM_002170		A	21409340	C	A	21409340	3	1	21	1	0	0	0	0	1	0	0	0	7552	477	17	3	167	3	IFNA8	9	21409340	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		21409340	119804091	41	1905										
ABL1	25	hgsc.bcm.edu	37	chr9	133759735	133759735	+	Silent	SNP	G	G	C													0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ggcttccggtctccccacctGtggaagaagtccagcacgct							TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr9:133759735G>C	ENST00000318560.5	+	11	2439	c.2058G>C	c.(2056-2058)ctG>ctC	p.L686L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	686					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CTCCCCACCTGTGGAAGAAGT	0.687			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.L705L		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.G2115C						.						14	17	16					9																	133759735		2184	4252	6436	SO:0001819	synonymous_variant	25	exon11			CCACCTGTGGAAG	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2058G>C	chr9.hg19:g.133759735G>C		114.0	0.0		58.0	24.0	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	hg19	CCDS35166.1																																																																																			.	.		0.687	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		C	133759735	G	C	133759735	2	2	21	1	0	0	0	0	0	0	0	1	92	1364	48	4		4	ABL1	9	133759735	Silent	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	112350395	133759735	7453696	42	1906	9	2								
ABL1	25	hgsc.bcm.edu	37	chr9	133759741	133759741	+	Missense_Mutation	SNP	G	G	T													0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	cggtctccccacctgtggaaGaagtccagcacgctgaccag							TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr9:133759741G>T	ENST00000318560.5	+	11	2445	c.2064G>T	c.(2062-2064)aaG>aaT	p.K688N		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	688					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	ACCTGTGGAAGAAGTCCAGCA	0.692			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.K707N		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.G2121T						.						14	17	16					9																	133759741		2184	4263	6447	SO:0001583	missense	25	exon11			GTGGAAGAAGTCC	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2064G>T	chr9.hg19:g.133759741G>T	ENSP00000323315:p.Lys688Asn	111.0	0.0		58.0	26.0	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	hg19	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.457431	0.63401	.	.	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.13196	2.61;2.61	5.42	-5.24	0.02789	.	0.044485	0.85682	D	0.000000	T	0.21718	0.0523	L	0.61218	1.895	0.80722	D	1	D;D	0.58620	0.971;0.983	P;P	0.52267	0.58;0.694	T	0.07385	-1.0775	10	0.52906	T	0.07	.	18.0736	0.89421	0.2097:0.0:0.7903:0.0	.	688;725	P00519;Q59FK4	ABL1_HUMAN;.	N	503;707;688	ENSP00000361423:K707N;ENSP00000323315:K688N	ENSP00000323315:K688N	K	+	3	2	ABL1	132749562	0.058000	0.20735	0.959000	0.39883	0.917000	0.54804	-0.375000	0.07475	-1.014000	0.03379	-0.367000	0.07326	AAG	.	.		0.692	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		T	133759741	G	T	133759741	3	4	21	1	0	0	0	0	1	0	0	0	92	933	33	3	2246	3	ABL1	9	133759741	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	6	133759741	7453690	43	1907	9	2								
CAMSAP1	157922	hgsc.bcm.edu	37	chr9	138714941	138714941	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	aggctcttcccgtggctcttCgtggccgtggggtgtggctg	17	11	2	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr9:138714941C>T	ENST00000389532.4	-	11	1630	c.1566G>A	c.(1564-1566)acG>acA	p.T522T	CAMSAP1_ENST00000312405.6_Silent_p.T244T|CAMSAP1_ENST00000409386.3_Silent_p.T533T|CAMSAP1_ENST00000483991.1_5'UTR	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	522					cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		CGTGGCTCTTCGTGGCCGTGG	0.557																																					p.T522T		Atlas-SNP	.											CAMSAP1,NS,carcinoma,0,1	CAMSAP1	142	.	0			c.G1566A						.						187	185	186					9																	138714941		2203	4300	6503	SO:0001819	synonymous_variant	157922	exon11			GCTCTTCGTGGCC	AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.1566G>A	chr9.hg19:g.138714941C>T		192.0	0.0		88.0	29.0	NM_015447	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Silent	SNP	ENST00000389532.4	hg19	CCDS35176.2																																																																																			.	.		0.557	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055024.2	XM_351857		T	138714941	C	T	138714941	2	4	21	1	0	0	0	0	0	0	0	1	2613	871	31	1		1	CAMSAP1	9	138714941	Silent	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	4955200	138714941	2498490	44	1908										
C9orf140	89958	hgsc.bcm.edu	37	chr9	139959358	139959358	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ccttcagcatgaggatggtcTgctgctgccagaccgggggt	15	11	2	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr9:139959358T>A	ENST00000409687.3	-	5	1140	c.1013A>T	c.(1012-1014)cAg>cTg	p.Q338L	RP11-229P13.23_ENST00000456356.2_RNA|RP11-229P13.22_ENST00000435463.2_RNA	NM_178448.3	NP_848543.2	Q86UD0	SAPC2_HUMAN	suppressor APC domain containing 2	338						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)											GAGGATGGTCTGCTGCTGCCA	0.721																																					p.Q338L		Atlas-SNP	.											.	.	.	.	0			c.A1013T						.						15	14	14					9																	139959358		2158	4248	6406	SO:0001583	missense	89958	exon5			ATGGTCTGCTGCT	BC024299	CCDS7027.2	9q34.3	2012-02-08	2012-02-08	2012-02-08	ENSG00000186193	ENSG00000186193			28055	protein-coding gene	gene with protein product		612057	"chromosome 9 open reading frame 140"	C9orf140		12477932	Standard	NM_178448		Approved	p42.3	uc011men.2	Q86UD0	OTTHUMG00000020961	ENST00000409687.3:c.1013A>T	chr9.hg19:g.139959358T>A	ENSP00000386348:p.Gln338Leu	102.0	0.0		54.0	18.0	NM_178448		Missense_Mutation	SNP	ENST00000409687.3	hg19	CCDS7027.2	.	.	.	.	.	.	.	.	.	.	T	14.76	2.631329	0.46944	.	.	ENSG00000186193	ENST00000409687	T	0.48836	0.8	4.19	4.19	0.49359	.	1.190600	0.06363	N	0.712143	T	0.59622	0.2207	M	0.67953	2.075	0.34878	D	0.7443	P	0.51791	0.948	P	0.51324	0.666	T	0.59873	-0.7372	10	0.59425	D	0.04	-1.0488	10.7252	0.46064	0.0:0.0:0.0:1.0	.	338	Q86UD0	CI140_HUMAN	L	338	ENSP00000386348:Q338L	ENSP00000386348:Q338L	Q	-	2	0	C9orf140	139079179	1.000000	0.71417	1.000000	0.80357	0.263000	0.26337	3.106000	0.50322	1.762000	0.52044	0.260000	0.18958	CAG	.	.		0.721	SAPCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055215.2	NM_178448		A	139959358	T	A	139959358	3	1	21	1	0	0	0	0	1	0	0	0	2462	1580	55	4	179	4	C9orf140	9	139959358	Missense_Mutation	SNP	T	TCGA-2Y-A9HB-01A-11D-A38X-10	1244417	139959358	1254073	45	1909										
PITX3	5309	hgsc.bcm.edu	37	chr10	103991828	103991828	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ctctgcctcgctgagcaggcCgaactccatggagggagggc	15	13	1	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr10:103991828C>A	ENST00000370002.3	-	2	163	c.10G>T	c.(10-12)Ggc>Tgc	p.G4C	PITX3_ENST00000539804.1_Missense_Mutation_p.G4C	NM_005029.3	NP_005020.1	O75364	PITX3_HUMAN	paired-like homeodomain 3	4					dopaminergic neuron differentiation (GO:0071542)|lens development in camera-type eye (GO:0002088)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|locomotory behavior (GO:0007626)|midbrain development (GO:0030901)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(1)|large_intestine(2)|lung(2)	5		Colorectal(252;0.00957)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		CTGAGCAGGCCGAACTCCATG	0.652																																					p.G4C		Atlas-SNP	.											.	PITX3	9	.	0			c.G10T						.						9	11	10					10																	103991828		2191	4282	6473	SO:0001583	missense	5309	exon2			GCAGGCCGAACTC		CCDS7532.1	10q24.32	2013-11-14	2007-07-12		ENSG00000107859	ENSG00000107859		"Homeoboxes / PRD class"	9006	protein-coding gene	gene with protein product		602669	"paired-like homeodomain transcription factor 3", "anterior segment mesenchymal dysgenesis"	ASMD		9620774	Standard	NM_005029		Approved		uc001kuu.1	O75364	OTTHUMG00000018952	ENST00000370002.3:c.10G>T	chr10.hg19:g.103991828C>A	ENSP00000359019:p.Gly4Cys	128.0	0.0		58.0	20.0	NM_005029	Q5VZL2	Missense_Mutation	SNP	ENST00000370002.3	hg19	CCDS7532.1	.	.	.	.	.	.	.	.	.	.	C	16.32	3.090921	0.55968	.	.	ENSG00000107859	ENST00000370002;ENST00000539804	D;D	0.89343	-2.5;-2.5	5.58	3.67	0.42095	.	0.156761	0.53938	D	0.000046	T	0.72771	0.3502	N	0.08118	0	0.29602	N	0.847578	P	0.40619	0.724	B	0.34779	0.189	T	0.71748	-0.4499	10	0.62326	D	0.03	.	5.5485	0.17078	0.0:0.6014:0.0:0.3986	.	4	O75364	PITX3_HUMAN	C	4	ENSP00000359019:G4C;ENSP00000439383:G4C	ENSP00000359019:G4C	G	-	1	0	PITX3	103981818	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	1.666000	0.37460	1.298000	0.44778	0.455000	0.32223	GGC	.	.		0.652	PITX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050031.1			A	103991828	C	A	103991828	3	1	21	1	0	0	0	0	1	0	0	0	11965	652	23	1	910	1	PITX3	10	103991828	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		103991828	31542919	46	1910										
FAM160A2	84067	hgsc.bcm.edu	37	chr11	6244964	6244964	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tgccctctcgatgcacaaaaGggacaaggcgagaaaagaga	12	9	1	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr11:6244964G>A	ENST00000449352.2	-	3	916	c.653C>T	c.(652-654)cCt>cTt	p.P218L	FAM160A2_ENST00000265978.4_Missense_Mutation_p.P218L|FAM160A2_ENST00000524416.1_Missense_Mutation_p.P218L			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	218					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						ATGCACAAAAGGGACAAGGCG	0.602																																					p.P218L		Atlas-SNP	.											.	FAM160A2	100	.	0			c.C653T						.						96	112	107					11																	6244964		2201	4296	6497	SO:0001583	missense	84067	exon3			ACAAAAGGGACAA		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 56"	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.653C>T	chr11.hg19:g.6244964G>A	ENSP00000416918:p.Pro218Leu	265.0	0.0		226.0	69.0	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	hg19	CCDS44530.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.660666	0.67586	.	.	ENSG00000051009	ENST00000449352;ENST00000442917;ENST00000265978;ENST00000524416	T;T;T	0.31247	1.5;1.5;1.5	5.1	5.1	0.69264	.	0.056991	0.64402	D	0.000001	T	0.60625	0.2283	M	0.87180	2.865	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.75020	0.985;0.982;0.964	T	0.61724	-0.7004	10	0.33940	T	0.23	2.261	17.6783	0.88236	0.0:0.0:1.0:0.0	.	218;218;218	E9PJK5;Q8N612;Q8N612-2	.;F16A2_HUMAN;.	L	218;143;218;218	ENSP00000416918:P218L;ENSP00000265978:P218L;ENSP00000431773:P218L	ENSP00000265978:P218L	P	-	2	0	FAM160A2	6201540	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	6.340000	0.72973	2.671000	0.90904	0.655000	0.94253	CCT	.	.		0.602	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127		A	6244964	G	A	6244964	3	1	21	1	0	0	0	0	1	0	0	0	5474	1000	35	3	2347	3	FAM160A2	11	6244964	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10		6244964	128761552	47	1911										
SUV420H1	51111	hgsc.bcm.edu	37	chr11	67934456	67934457	+	Frame_Shift_Ins	INS	-	-	T													0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tcccttacttacttgcattgINStttttttcctgagtggtatc							TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr11:67934456_67934457insT	ENST00000304363.4	-	10	1519_1520	c.1166_1167insA	c.(1165-1167)aacfs	p.N389fs	SUV420H1_ENST00000405515.1_Frame_Shift_Ins_p.N389fs|SUV420H1_ENST00000402789.1_Frame_Shift_Ins_p.N389fs|SUV420H1_ENST00000402185.2_Frame_Shift_Ins_p.N366fs|SUV420H1_ENST00000401547.2_Frame_Shift_Ins_p.N389fs	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	389					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TACTTGCATTGTTTTTTTCCTG	0.317																																					p.N389fs		Atlas-Indel,Pindel	.											.	SUV420H1	125	.	0			c.1167_1168insA						.																																			SO:0001589	frameshift_variant	51111	exon10			.	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.1167dupA	chr11.hg19:g.67934463_67934463dupT	ENSP00000305899:p.Asn389fs	55.0	0.0		74.0	24.0	NM_016028	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Frame_Shift_Ins	INS	ENST00000304363.4	hg19	CCDS31623.1																																																																																			.	.		0.317	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		T	67934457	-	T	67934456	7	5	21	1	0	1	1	0	0	0	0	0	15429	1368	48	0	1506	0	SUV420H1	11	67934456	Frame_Shift_Ins	INS	-	TCGA-2Y-A9HB-01A-11D-A38X-10	61689492	67934456	67072060	48	1912										
FAT3	120114	hgsc.bcm.edu	37	chr11	92533685	92533685	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ttttcacaaagcacatacgtAgctgaggtgagagagaacgt	11	7	1	3			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr11:92533685A>T	ENST00000298047.6	+	9	7523	c.7506A>T	c.(7504-7506)gtA>gtT	p.V2502V	FAT3_ENST00000525166.1_Silent_p.V2352V|FAT3_ENST00000409404.2_Silent_p.V2502V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2502	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GCACATACGTAGCTGAGGTGA	0.498										TCGA Ovarian(4;0.039)																											p.V2502V		Atlas-SNP	.											.	FAT3	1822	.	0			c.A7506T						.						84	81	82					11																	92533685		2051	4195	6246	SO:0001819	synonymous_variant	120114	exon9			ATACGTAGCTGAG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.7506A>T	chr11.hg19:g.92533685A>T		59.0	0.0		101.0	31.0	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	hg19																																																																																				.	.		0.498	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92533685	A	T	92533685	2	4	21	1	0	0	0	0	0	0	0	1	5699	407	15	4		4	FAT3	11	92533685	Silent	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10	24599229	92533685	42472831	49	1913										
SORL1	6653	hgsc.bcm.edu	37	chr11	121393351	121393351	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ctcagtcagctcctcaacctCcagctccggagaatgcccat	7	17	3	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr11:121393351C>T	ENST00000260197.7	+	10	1590	c.1461C>T	c.(1459-1461)ctC>ctT	p.L487L	SORL1_ENST00000532451.1_3'UTR	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	487					cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		TCCTCAACCTCCAGCTCCGGA	0.547																																					p.L487L		Atlas-SNP	.											.	SORL1	218	.	0			c.C1461T						.						168	154	159					11																	121393351		2203	4299	6502	SO:0001819	synonymous_variant	6653	exon10			CAACCTCCAGCTC	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.1461C>T	chr11.hg19:g.121393351C>T		50.0	0.0		74.0	16.0	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	hg19	CCDS8436.1																																																																																			.	.		0.547	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		T	121393351	C	T	121393351	2	4	21	1	0	0	0	0	0	0	0	1	14949	842	30	3		3	SORL1	11	121393351	Silent	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	28859666	121393351	13613165	50	1914										
CSDA	8531	hgsc.bcm.edu	37	chr12	10865872	10865872	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gtaacggcgccgatctgcagCgtaacgactcccttccacag	10	15	1	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr12:10865872C>T	ENST00000228251.4	-	5	711	c.511G>A	c.(511-513)Gct>Act	p.A171T	YBX3_ENST00000279550.7_Missense_Mutation_p.A171T	NM_003651.4	NP_003642.3	P16989	YBOX3_HUMAN	Y box binding protein 3	171					3'-UTR-mediated mRNA stabilization (GO:0070935)|cellular hyperosmotic response (GO:0071474)|cellular response to tumor necrosis factor (GO:0071356)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of necroptotic process (GO:0060546)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoplasmic translation (GO:2000767)|positive regulation of organ growth (GO:0046622)|response to cold (GO:0009409)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|tight junction (GO:0005923)	double-stranded DNA binding (GO:0003690)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|Rho GTPase binding (GO:0017048)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)										CGATCTGCAGCGTAACGACTC	0.502																																					p.A171T		Atlas-SNP	.											.	CSDA	35	.	0			c.G511A						.						92	99	97					12																	10865872		2203	4300	6503	SO:0001583	missense	8531	exon5			CTGCAGCGTAACG	L29064	CCDS8630.1, CCDS44831.1	12p13.1	2013-03-13	2013-03-13	2013-03-13	ENSG00000060138	ENSG00000060138			2428	protein-coding gene	gene with protein product	"cold-shock domain containing A1"	603437	"cold shock domain protein A"	CSDA		2977358, 8710501	Standard	NM_003651		Approved	dbpA, ZONAB, CSDA1	uc001qyt.3	P16989	OTTHUMG00000168409	ENST00000228251.4:c.511G>A	chr12.hg19:g.10865872C>T	ENSP00000228251:p.Ala171Thr	52.0	0.0		28.0	13.0	NM_003651	B2RBW6|Q14121|Q969N6|Q96B76	Missense_Mutation	SNP	ENST00000228251.4	hg19	CCDS8630.1	.	.	.	.	.	.	.	.	.	.	C	34	5.324672	0.95708	.	.	ENSG00000060138	ENST00000279550;ENST00000228251	T;T	0.34472	1.4;1.36	5.49	4.58	0.56647	.	0.000000	0.64402	D	0.000003	T	0.61553	0.2356	M	0.80028	2.48	0.51233	D	0.999914	D;D	0.89917	1.0;1.0	D;D	0.91635	0.984;0.999	T	0.66160	-0.5993	10	0.56958	D	0.05	.	13.9601	0.64172	0.0:0.8467:0.1533:0.0	.	171;171	P16989-2;P16989	.;DBPA_HUMAN	T	171	ENSP00000279550:A171T;ENSP00000228251:A171T	ENSP00000228251:A171T	A	-	1	0	CSDA	10757139	1.000000	0.71417	0.936000	0.37596	0.985000	0.73830	6.605000	0.74155	1.268000	0.44264	0.491000	0.48974	GCT	.	.		0.502	YBX3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399628.1	NM_003651		T	10865872	C	T	10865872	3	4	21	1	0	0	0	0	1	0	0	0	3929	768	27	1	627	1	CSDA	12	10865872	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		10865872	122986023	51	1915										
MCRS1	10445	hgsc.bcm.edu	37	chr12	49960179	49960179	+	Intron	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	catctgggctcagacctggcCcagaccttccacgctgggca	11	16	2	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr12:49960179C>G	ENST00000550165.1	-	4	277				MCRS1_ENST00000343810.4_Intron|MCRS1_ENST00000357123.4_Missense_Mutation_p.G15A|MCRS1_ENST00000546244.1_Intron			Q96EZ8	MCRS1_HUMAN	microspherule protein 1						cellular protein modification process (GO:0006464)|chromatin organization (GO:0006325)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|Ino80 complex (GO:0031011)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)	23						CAGACCTGGCCCAGACCTTCC	0.622																																					p.G15A		Atlas-SNP	.											.	MCRS1	40	.	0			c.G44C						.						33	29	30					12																	49960179		2201	4296	6497	SO:0001627	intron_variant	10445	exon1			CCTGGCCCAGACC	BC011794	CCDS8787.1, CCDS31795.1, CCDS61118.1	12q13.12	2011-07-06				ENSG00000187778		"INO80 complex subunits"	6960	protein-coding gene	gene with protein product	"INO80 complex subunit Q"	609504				9765390, 9654073	Standard	NM_006337		Approved	ICP22BP, MSP58, P78, MCRS2, INO80Q	uc001rui.1	Q96EZ8		ENST00000550165.1:c.11-181G>C	chr12.hg19:g.49960179C>G		99.0	0.0		63.0	25.0	NM_001012300	O14742|O75497|Q6VN53|Q7Z372	Missense_Mutation	SNP	ENST00000550165.1	hg19	CCDS8787.1	.	.	.	.	.	.	.	.	.	.	C	1.232	-0.623867	0.03636	.	.	ENSG00000187778	ENST00000357123	.	.	.	3.63	3.63	0.41609	.	1.145640	0.06318	N	0.703861	T	0.56307	0.1976	.	.	.	0.80722	D	1	B	0.19706	0.038	B	0.14578	0.011	T	0.50659	-0.8802	8	0.87932	D	0	-1.3425	10.6615	0.45704	0.0:1.0:0.0:0.0	.	15	Q96EZ8-2	.	A	15	.	ENSP00000349640:G15A	G	-	2	0	MCRS1	48246446	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.073000	0.50057	1.849000	0.53698	0.563000	0.77884	GGG	.	.		0.622	MCRS1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405102.1	NM_006337		G	49960179	C	G	49960179	1	3	21	0	1	0	0	0	0	0	0	0	9408	623	22	4		4	MCRS1	12	49960179	Intron	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	39094307	49960179	83891716	52	1916										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58120766	58120766	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	agctcacgtacccacagcagCagttgcgtgatgacgacgtg	12	12	1	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr12:58120766C>T	ENST00000547588.1	-	18	3326	c.3327G>A	c.(3325-3327)ctG>ctA	p.L1109L	AGAP2-AS1_ENST00000542466.2_5'UTR|AGAP2_ENST00000257897.3_Silent_p.L753L|RP11-571M6.8_ENST00000548410.2_RNA	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	1109					axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						CCCACAGCAGCAGTTGCGTGA	0.657											OREG0021951	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1109L		Atlas-SNP	.											.	AGAP2	167	.	0			c.G3327A						.						17	20	19					12																	58120766		2202	4298	6500	SO:0001819	synonymous_variant	116986	exon18			CAGCAGCAGTTGC	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.3327G>A	chr12.hg19:g.58120766C>T		109.0	0.0	1028	64.0	24.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Silent	SNP	ENST00000547588.1	hg19	CCDS44932.1	.	.	.	.	.	.	.	.	.	.	C	8.233	0.805079	0.16467	.	.	ENSG00000135439	ENST00000328568	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	T	0.63931	0.2553	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62567	-0.6827	4	.	.	.	.	12.4071	0.55445	0.169:0.831:0.0:0.0	.	.	.	.	T	953	.	.	A	-	1	0	AGAP2	56407033	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	0.909000	0.28558	2.276000	0.75962	0.455000	0.32223	GCT	.	.		0.657	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		T	58120766	C	T	58120766	2	4	21	1	0	0	0	0	0	0	0	1	368	697	25	3		3	AGAP2	12	58120766	Silent	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	8160587	58120766	75731129	53	1917										
SOS2	6655	hgsc.bcm.edu	37	chr14	50649189	50649189	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ttgtaaacttacttctgccaAatcttcaaaacagctgccag	5	11	3	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr14:50649189A>T	ENST00000216373.5	-	6	1124	c.850T>A	c.(850-852)Ttg>Atg	p.L284M	SOS2_ENST00000555794.1_5'Flank|SOS2_ENST00000543680.1_Missense_Mutation_p.L284M	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	284	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					ACTTCTGCCAAATCTTCAAAA	0.378																																					p.L284M		Atlas-SNP	.											.	SOS2	195	.	0			c.T850A						.						73	69	70					14																	50649189		2203	4300	6503	SO:0001583	missense	6655	exon6			CTGCCAAATCTTC	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11188	protein-coding gene	gene with protein product		601247	"son of sevenless (Drosophilia) homolog 2"			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.850T>A	chr14.hg19:g.50649189A>T	ENSP00000216373:p.Leu284Met	55.0	0.0		77.0	27.0	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	hg19	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	A	16.99	3.274935	0.59649	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.68903	-0.36;-0.36	5.54	1.89	0.25635	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.61198	0.2328	L	0.49513	1.565	0.51482	D	0.999928	P;P	0.45240	0.78;0.854	B;P	0.47603	0.377;0.551	T	0.54741	-0.8248	10	0.34782	T	0.22	.	6.779	0.23636	0.5725:0.0:0.4275:0.0	.	284;284	B7ZKT6;Q07890	.;SOS2_HUMAN	M	284	ENSP00000216373:L284M;ENSP00000445328:L284M	ENSP00000216373:L284M	L	-	1	2	SOS2	49718939	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.342000	0.43992	0.395000	0.25257	-0.263000	0.10527	TTG	.	.		0.378	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2			T	50649189	A	T	50649189	3	4	21	1	0	0	0	0	1	0	0	0	14952	11	1	4	3220	4	SOS2	14	50649189	Missense_Mutation	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10		50649189	56700351	54	1918										
TDP1	55775	hgsc.bcm.edu	37	chr14	90446920	90446920	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ctctatgaagaaggcctccgGgttgtcatacacacctccaa	8	13	2	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr14:90446920G>T	ENST00000335725.4	+	8	1078	c.828G>T	c.(826-828)cgG>cgT	p.R276R	TDP1_ENST00000393454.2_Silent_p.R276R|TDP1_ENST00000393452.3_Silent_p.R276R|TDP1_ENST00000555565.1_3'UTR|TDP1_ENST00000555880.1_Silent_p.R276R|TDP1_ENST00000357382.3_Silent_p.R37R	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	276					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		AAGGCCTCCGGGTTGTCATAC	0.438								Repair of DNA-protein crosslinks																													p.R276R		Atlas-SNP	.											.	TDP1	47	.	0			c.G828T						.						117	110	112					14																	90446920		2203	4300	6503	SO:0001819	synonymous_variant	55775	exon8			CCTCCGGGTTGTC	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.828G>T	chr14.hg19:g.90446920G>T		55.0	0.0		94.0	29.0	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Silent	SNP	ENST00000335725.4	hg19	CCDS9888.1																																																																																			.	.		0.438	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		T	90446920	G	T	90446920	2	4	21	1	0	0	0	0	0	0	0	1	15743	1219	43	3		3	TDP1	14	90446920	Silent	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	39797731	90446920	16902620	55	1919										
SERPINA1	5265	hgsc.bcm.edu	37	chr14	94848963	94848964	+	Frame_Shift_Del	DEL	TG	TG	-													0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	taattcaccagagcaaaaacTgtgtctctgtcaagctcctt							TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr14:94848963_94848964delTG	ENST00000448921.1	-	4	1183_1184	c.611_612delCA	c.(610-612)acafs	p.T204fs	SERPINA1_ENST00000393088.4_Frame_Shift_Del_p.T204fs|SERPINA1_ENST00000437397.1_Frame_Shift_Del_p.T204fs|SERPINA1_ENST00000393087.4_Frame_Shift_Del_p.T204fs|SERPINA1_ENST00000402629.1_Frame_Shift_Del_p.T204fs|SERPINA1_ENST00000555289.1_5'Flank|SERPINA1_ENST00000355814.4_Frame_Shift_Del_p.T204fs|SERPINA1_ENST00000440909.1_Frame_Shift_Del_p.T204fs|SERPINA1_ENST00000449399.3_Frame_Shift_Del_p.T204fs|SERPINA1_ENST00000404814.4_Frame_Shift_Del_p.T204fs	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	204					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		GAGCAAAAACTGTGTCTCTGTC	0.436																																					p.204_205del		Atlas-Indel,Pindel	.											.,1	SERPINA1	51	.	0			c.612_613del						.																																			SO:0001589	frameshift_variant	5265	exon4			.	X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"Serine (or cysteine) peptidase inhibitors"	8941	protein-coding gene	gene with protein product	"protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"	107400	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.611_612delCA	chr14.hg19:g.94848965_94848966delTG	ENSP00000416066:p.Thr204fs	105.0	0.0		123.0	51.0	NM_001127701	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Frame_Shift_Del	DEL	ENST00000448921.1	hg19	CCDS9925.1																																																																																			.	.		0.436	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235		-	94848964	TG	-	94848963	7	5	21	1	0	1	0	1	0	0	0	0	14101	1567	55	0	660	0	SERPINA1	14	94848963	Frame_Shift_Del	DEL	TG	TCGA-2Y-A9HB-01A-11D-A38X-10	4402043	94848963	12500577	56	1920										
DLK1	8788	hgsc.bcm.edu	37	chr14	101201153	101201153	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ttcagtacaacagcggggagGacctggccgtcaacatcatc	11	12	3	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr14:101201153G>A	ENST00000341267.4	+	5	1314	c.1072G>A	c.(1072-1074)Gac>Aac	p.D358N	RP11-566J3.4_ENST00000608876.1_lincRNA|DLK1_ENST00000331224.6_Missense_Mutation_p.D285N	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	358					cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				CAGCGGGGAGGACCTGGCCGT	0.582																																					p.D358N		Atlas-SNP	.											.	DLK1	57	.	0			c.G1072A						.						102	96	98					14																	101201153		2203	4300	6503	SO:0001583	missense	8788	exon5			GGGGAGGACCTGG	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"delta-like homolog (Drosophila)"			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.1072G>A	chr14.hg19:g.101201153G>A	ENSP00000340292:p.Asp358Asn	91.0	0.0		46.0	21.0	NM_003836	P15803|Q96DW5	Missense_Mutation	SNP	ENST00000341267.4	hg19	CCDS9963.1	.	.	.	.	.	.	.	.	.	.	G	7.900	0.734183	0.15574	.	.	ENSG00000185559	ENST00000341267;ENST00000331224	D;D	0.87179	-2.22;-2.2	4.61	3.71	0.42584	.	0.530450	0.17800	N	0.161613	T	0.75824	0.3902	N	0.08118	0	0.80722	D	1	P;P	0.42692	0.787;0.546	B;B	0.44163	0.443;0.156	T	0.76721	-0.2855	10	0.56958	D	0.05	.	7.8965	0.29710	0.1809:0.0:0.8191:0.0	.	285;358	P80370-2;P80370	.;DLK1_HUMAN	N	358;285	ENSP00000340292:D358N;ENSP00000331081:D285N	ENSP00000331081:D285N	D	+	1	0	DLK1	100270906	1.000000	0.71417	0.103000	0.21229	0.006000	0.05464	5.923000	0.70045	2.113000	0.64589	0.491000	0.48974	GAC	.	.		0.582	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1			A	101201153	G	A	101201153	3	1	21	1	0	0	0	0	1	0	0	0	4566	1174	41	3	1090	3	DLK1	14	101201153	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	6352190	101201153	6148387	57	1921										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48058110	48058110	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	caaaaaggtcatctcattacAgttggataaagatcaccacg	7	9	3	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr15:48058110A>T	ENST00000316364.5	+	14	1911	c.1472A>T	c.(1471-1473)cAg>cTg	p.Q491L	SEMA6D_ENST00000355997.3_Missense_Mutation_p.Q491L|SEMA6D_ENST00000537942.1_Missense_Mutation_p.Q491L|SEMA6D_ENST00000389428.3_Missense_Mutation_p.Q491L|SEMA6D_ENST00000354744.4_Missense_Mutation_p.Q491L|SEMA6D_ENST00000558014.1_Missense_Mutation_p.Q491L|SEMA6D_ENST00000389433.2_Missense_Mutation_p.Q491L|SEMA6D_ENST00000558816.1_Missense_Mutation_p.Q491L|SEMA6D_ENST00000536845.2_Missense_Mutation_p.Q491L|SEMA6D_ENST00000358066.4_Missense_Mutation_p.Q491L|SEMA6D_ENST00000389432.2_Missense_Mutation_p.Q491L	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	491	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		ATCTCATTACAGTTGGATAAA	0.423																																					p.Q491L		Atlas-SNP	.											.	SEMA6D	322	.	0			c.A1472T						.						219	191	200					15																	48058110		2198	4297	6495	SO:0001583	missense	80031	exon14			CATTACAGTTGGA	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1472A>T	chr15.hg19:g.48058110A>T	ENSP00000324857:p.Gln491Leu	53.0	0.0		126.0	7.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	A	17.01	3.280456	0.59758	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997	T;T;T;T;T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12;2.12;2.12;2.12;2.12	5.68	5.68	0.88126	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	0.050581	0.85682	D	0.000000	T	0.21550	0.0519	L	0.47078	1.49	0.80722	D	1	P;B;P;P;B	0.40302	0.621;0.322;0.621;0.712;0.359	B;B;B;B;B	0.35727	0.077;0.056;0.119;0.209;0.077	T	0.02190	-1.1198	10	0.87932	D	0	.	15.926	0.79618	1.0:0.0:0.0:0.0	.	491;491;491;491;491	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	L	491	ENSP00000442040:Q491L;ENSP00000446152:Q491L;ENSP00000324857:Q491L;ENSP00000374084:Q491L;ENSP00000374083:Q491L;ENSP00000346786:Q491L;ENSP00000350770:Q491L;ENSP00000374079:Q491L;ENSP00000348276:Q491L	ENSP00000324857:Q491L	Q	+	2	0	SEMA6D	45845402	1.000000	0.71417	0.889000	0.34880	0.951000	0.60555	9.339000	0.96797	2.164000	0.68074	0.528000	0.53228	CAG	.	.		0.423	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		T	48058110	A	T	48058110	3	4	21	1	0	0	0	0	1	0	0	0	14057	188	7	4	1526	4	SEMA6D	15	48058110	Missense_Mutation	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10		48058110	54473282	58	1922										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88690596	88690596	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gactcagcgtctggaagagcTgccacgagagtgtggtgagc	16	9	2	3			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr15:88690596T>C	ENST00000360948.2	-	5	595	c.434A>G	c.(433-435)cAg>cGg	p.Q145R	NTRK3_ENST00000542733.2_Missense_Mutation_p.Q47R|NTRK3_ENST00000357724.2_Missense_Mutation_p.Q145R|NTRK3_ENST00000540489.2_Missense_Mutation_p.Q145R|NTRK3_ENST00000355254.2_Missense_Mutation_p.Q145R|NTRK3_ENST00000394480.2_Missense_Mutation_p.Q145R|NTRK3_ENST00000317501.3_Missense_Mutation_p.Q145R|NTRK3_ENST00000558676.1_Missense_Mutation_p.Q145R|NTRK3_ENST00000557856.1_Missense_Mutation_p.Q145R	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	145					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CTGGAAGAGCTGCCACGAGAG	0.458			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.Q145R		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.A434G						.						74	64	67					15																	88690596		2201	4299	6500	SO:0001583	missense	4916	exon6			AAGAGCTGCCACG	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.434A>G	chr15.hg19:g.88690596T>C	ENSP00000354207:p.Gln145Arg	96.0	0.0		172.0	89.0	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.927686	0.34002	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42;0.42;0.42	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.34629	0.0904	N	0.02202	-0.64	0.45439	D	0.998411	P;P;B;P;P;B	0.49185	0.801;0.92;0.004;0.891;0.804;0.004	B;P;B;P;B;B	0.48952	0.339;0.551;0.007;0.596;0.415;0.007	T	0.35599	-0.9782	10	0.22109	T	0.4	.	13.3964	0.60856	0.0:0.0:0.0:1.0	.	47;145;145;145;145;145	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	R	145;145;145;145;47;145;145	ENSP00000377990:Q145R;ENSP00000354207:Q145R;ENSP00000350356:Q145R;ENSP00000347397:Q145R;ENSP00000437773:Q47R;ENSP00000444673:Q145R;ENSP00000318328:Q145R	ENSP00000318328:Q145R	Q	-	2	0	NTRK3	86491600	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.114000	0.64648	2.095000	0.63458	0.460000	0.39030	CAG	.	.		0.458	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				C	88690596	T	C	88690596	3	2	21	1	0	0	0	0	1	0	0	0	10717	1580	55	2	2407	2	NTRK3	15	88690596	Missense_Mutation	SNP	T	TCGA-2Y-A9HB-01A-11D-A38X-10	40632486	88690596	13840796	59	1923										
NR2F2	7026	hgsc.bcm.edu	37	chr15	96877632	96877632	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	cgagctgtttgtgttgaatgCggcgcagtgctccatgcccc	13	12	0	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr15:96877632C>G	ENST00000394166.3	+	2	2159	c.770C>G	c.(769-771)gCg>gGg	p.A257G	MIR1469_ENST00000410719.1_RNA|NR2F2_ENST00000394171.2_Missense_Mutation_p.A104G|NR2F2_ENST00000421109.2_Missense_Mutation_p.A124G|NR2F2_ENST00000453270.2_Missense_Mutation_p.A104G	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	257	Interaction with ZFPM2. {ECO:0000250}.|Ligand-binding. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.A257V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			GTGTTGAATGCGGCGCAGTGC	0.677																																					p.A257G		Atlas-SNP	.											NR2F2,NS,carcinoma,0,1	NR2F2	35	.	1	Substitution - Missense(1)	endometrium(1)	c.C770G						.						86	76	80					15																	96877632		2197	4298	6495	SO:0001583	missense	7026	exon2			TGAATGCGGCGCA	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"Nuclear hormone receptors"	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.770C>G	chr15.hg19:g.96877632C>G	ENSP00000377721:p.Ala257Gly	134.0	1.0		98.0	22.0	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	hg19	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	C	35	5.504944	0.96371	.	.	ENSG00000185551	ENST00000421109;ENST00000394166;ENST00000394171;ENST00000453270	T;T;D;D	0.96885	0.65;0.65;-4.16;-4.16	5.09	5.09	0.68999	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.98523	0.9507	M	0.91510	3.215	0.80722	D	1	D;P	0.89917	1.0;0.946	D;P	0.97110	1.0;0.849	D	0.99346	1.0913	10	0.59425	D	0.04	.	18.4813	0.90812	0.0:1.0:0.0:0.0	.	257;124	P24468;Q3KQR7	COT2_HUMAN;.	G	124;257;104;104	ENSP00000401674:A124G;ENSP00000377721:A257G;ENSP00000377726:A104G;ENSP00000389853:A104G	ENSP00000377721:A257G	A	+	2	0	NR2F2	94678636	1.000000	0.71417	0.987000	0.45799	0.981000	0.71138	7.818000	0.86416	2.376000	0.81061	0.655000	0.94253	GCG	.	.		0.677	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			G	96877632	C	G	96877632	3	3	21	1	0	0	0	0	1	0	0	0	10637	768	27	4	823	4	NR2F2	15	96877632	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	8187036	96877632	5653760	60	1924										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24826592	24826592	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ggctggccacgtgccaaatcGcctaacggctctagcagtgt	12	13	1	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr16:24826592G>A	ENST00000395799.3	+	19	4926	c.4797G>A	c.(4795-4797)tcG>tcA	p.S1599S	CTD-2515A14.1_ENST00000568895.1_RNA|TNRC6A_ENST00000432286.2_Silent_p.S77S|TNRC6A_ENST00000315183.7_Silent_p.S1550S	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1599					cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		GTGCCAAATCGCCTAACGGCT	0.438																																					p.S1599S		Atlas-SNP	.											.	TNRC6A	171	.	0			c.G4797A						.						77	73	74					16																	24826592		2197	4300	6497	SO:0001819	synonymous_variant	27327	exon19			CAAATCGCCTAAC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.4797G>A	chr16.hg19:g.24826592G>A		82.0	0.0		70.0	31.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	G	9.931	1.214738	0.22289	.	.	ENSG00000090905	ENST00000450465	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	T	0.71204	0.3312	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68674	-0.5346	4	.	.	.	-5.317	14.4704	0.67512	0.0699:0.0:0.9301:0.0	.	.	.	.	T	490	.	.	A	+	1	0	TNRC6A	24734093	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.951000	0.56684	2.809000	0.96659	0.655000	0.94253	GCC	.	.		0.438	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24826592	G	A	24826592	2	1	21	1	0	0	0	0	0	0	0	1	16355	1074	38	1		1	TNRC6A	16	24826592	Silent	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10		24826592	65528161	61	1925										
RNF40	9810	hgsc.bcm.edu	37	chr16	30774809	30774809	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gctgtcttcagcgcctgaggCacctgggacccaggaggggc	16	13	2	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr16:30774809C>G	ENST00000324685.6	+	4	806	c.371C>G	c.(370-372)gCa>gGa	p.A124G	RNF40_ENST00000357890.5_Missense_Mutation_p.A124G|RNF40_ENST00000402121.3_Intron|C16orf93_ENST00000545825.1_5'Flank|C16orf93_ENST00000543610.1_5'Flank|C16orf93_ENST00000541260.1_5'Flank|RNF40_ENST00000563683.1_Missense_Mutation_p.A124G	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	124					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			GCGCCTGAGGCACCTGGGACC	0.577																																					p.A124G		Atlas-SNP	.											.	RNF40	83	.	0			c.C371G						.						56	57	57					16																	30774809		2197	4300	6497	SO:0001583	missense	9810	exon4			CTGAGGCACCTGG	AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"RING-type (C3HC4) zinc fingers"	16867	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"	607700	"ring finger protein 40"			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.371C>G	chr16.hg19:g.30774809C>G	ENSP00000325677:p.Ala124Gly	179.0	0.0		96.0	46.0	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	hg19	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	C	6.101	0.386969	0.11581	.	.	ENSG00000103549	ENST00000324685;ENST00000357890	T;T	0.30714	1.52;1.52	5.84	0.0452	0.14229	.	0.702903	0.14066	N	0.343745	T	0.11879	0.0289	N	0.08118	0	0.19575	N	0.999963	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.24905	-1.0147	10	0.23302	T	0.38	-3.0577	3.7695	0.08636	0.2584:0.3624:0.0:0.3792	.	124;124;124	O75150-4;A8K6K1;O75150	.;.;BRE1B_HUMAN	G	124	ENSP00000325677:A124G;ENSP00000350563:A124G	ENSP00000325677:A124G	A	+	2	0	RNF40	30682310	0.001000	0.12720	0.083000	0.20561	0.732000	0.41865	-0.046000	0.11983	0.098000	0.17522	0.563000	0.77884	GCA	.	.		0.577	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771		G	30774809	C	G	30774809	3	3	21	1	0	0	0	0	1	0	0	0	13508	710	25	4	381	4	RNF40	16	30774809	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	5948217	30774809	59579944	62	1926										
PDPR	55066	hgsc.bcm.edu	37	chr16	70161189	70161189	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tgctggctctaccaggttctGtgctggcatcctgagcactg	12	12	2	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr16:70161189G>T	ENST00000288050.4	+	4	1211	c.254G>T	c.(253-255)tGt>tTt	p.C85F	PDPR_ENST00000568530.1_Missense_Mutation_p.C85F|PDPR_ENST00000398122.3_5'UTR	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	85					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		ACCAGGTTCTGTGCTGGCATC	0.478																																					p.C85F		Atlas-SNP	.											.	PDPR	66	.	0			c.G254T						.						34	31	32					16																	70161189		1825	4065	5890	SO:0001583	missense	55066	exon4			GGTTCTGTGCTGG		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.254G>T	chr16.hg19:g.70161189G>T	ENSP00000288050:p.Cys85Phe	187.0	0.0		176.0	59.0	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	hg19	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.895545	0.52121	.	.	ENSG00000090857	ENST00000288050	T	0.81078	-1.45	4.7	4.7	0.59300	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	T	0.65228	0.2671	N	0.03608	-0.345	0.80722	D	1	B	0.21520	0.057	B	0.26094	0.066	T	0.65689	-0.6107	10	0.62326	D	0.03	.	17.0035	0.86386	0.0:0.0:1.0:0.0	.	85	Q8NCN5	PDPR_HUMAN	F	85	ENSP00000288050:C85F	ENSP00000288050:C85F	C	+	2	0	PDPR	68718690	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.777000	0.85628	2.312000	0.78011	0.645000	0.84053	TGT	.	.		0.478	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990		T	70161189	G	T	70161189	3	4	21	1	0	0	0	0	1	0	0	0	11698	1377	48	3	260	3	PDPR	16	70161189	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	39386380	70161189	20193564	63	1927										
TOP2A	7153	hgsc.bcm.edu	37	chr17	38569014	38569014	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tccaggaaaatactcactggCagtttatttccattaagaaa	6	8	1	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr17:38569014C>T	ENST00000423485.1	-	7	944	c.786G>A	c.(784-786)ctG>ctA	p.L262L		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	262					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	TACTCACTGGCAGTTTATTTC	0.348																																					p.L262L		Atlas-SNP	.											.	TOP2A	124	.	0			c.G786A						.						60	54	56					17																	38569014		1841	4091	5932	SO:0001819	synonymous_variant	7153	exon7			CACTGGCAGTTTA		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.786G>A	chr17.hg19:g.38569014C>T		170.0	0.0		115.0	6.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	hg19	CCDS45672.1																																																																																			.	.		0.348	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			T	38569014	C	T	38569014	2	4	21	1	0	0	0	0	0	0	0	1	16380	697	25	3		3	TOP2A	17	38569014	Silent	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		38569014	42626196	64	1928										
STAT5A	6776	hgsc.bcm.edu	37	chr17	40453352	40453352	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gacccagaccaagtttgcagCcaccgtacgcctgctggtgg	12	14	0	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr17:40453352C>G	ENST00000345506.4	+	10	1691	c.1049C>G	c.(1048-1050)gCc>gGc	p.A350G	STAT5A_ENST00000588868.1_Missense_Mutation_p.A350G|STAT5A_ENST00000546010.2_Missense_Mutation_p.A320G|STAT5A_ENST00000452307.2_Missense_Mutation_p.A350G|STAT5A_ENST00000590949.1_Missense_Mutation_p.A350G	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	350					2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		AAGTTTGCAGCCACCGTACGC	0.582																																					p.A350G		Atlas-SNP	.											.	STAT5A	49	.	0			c.C1049G						.						157	136	143					17																	40453352		2203	4300	6503	SO:0001583	missense	6776	exon10			TTGCAGCCACCGT	U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"SH2 domain containing"	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.1049C>G	chr17.hg19:g.40453352C>G	ENSP00000341208:p.Ala350Gly	125.0	0.0		77.0	24.0	NM_003152	Q1KLZ6	Missense_Mutation	SNP	ENST00000345506.4	hg19	CCDS11424.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.540950	0.65085	.	.	ENSG00000126561	ENST00000345506;ENST00000546010;ENST00000540577;ENST00000452307	D;D;D	0.89617	-2.54;-2.54;-2.54	4.87	4.87	0.63330	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.92760	0.7698	L	0.60957	1.885	0.80722	D	1	B;P;B	0.50617	0.028;0.937;0.074	B;P;B	0.61722	0.104;0.893;0.158	D	0.93663	0.6983	10	0.87932	D	0	-9.6895	18.0732	0.89417	0.0:1.0:0.0:0.0	.	320;352;350	Q1KLZ6;Q59GY7;P42229	.;.;STA5A_HUMAN	G	350;320;352;350	ENSP00000341208:A350G;ENSP00000443107:A320G;ENSP00000400320:A350G	ENSP00000341208:A350G	A	+	2	0	STAT5A	37706878	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	7.689000	0.84165	2.274000	0.75844	0.306000	0.20318	GCC	.	.		0.582	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152		G	40453352	C	G	40453352	3	3	21	1	0	0	0	0	1	0	0	0	15283	739	26	4	1079	4	STAT5A	17	40453352	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10	1884338	40453352	40741858	65	1929										
FASN	2194	hgsc.bcm.edu	37	chr17	80041427	80041427	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	tgagaaaggtcgaatttgccAatttccaggaagcgaccgtg	12	8	0	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr17:80041427A>G	ENST00000306749.2	-	31	5525	c.5307T>C	c.(5305-5307)atT>atC	p.I1769I	FASN_ENST00000579758.1_5'Flank	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1769	Enoyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CGAATTTGCCAATTTCCAGGA	0.637																																					p.I1769I	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.T5307C						.						54	52	53					17																	80041427		2198	4297	6495	SO:0001819	synonymous_variant	2194	exon31			TTTGCCAATTTCC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.5307T>C	chr17.hg19:g.80041427A>G		148.0	0.0		87.0	28.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.637	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		G	80041427	A	G	80041427	2	3	21	1	0	0	0	0	0	0	0	1	5691	126	5	2		2	FASN	17	80041427	Silent	SNP	A	TCGA-2Y-A9HB-01A-11D-A38X-10	39588075	80041427	1153783	66	1930										
SIGLEC15	284266	hgsc.bcm.edu	37	chr18	43418834	43418836	+	In_Frame_Del	DEL	GGG	GGG	-													0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gccgtgcggagcccgcgtgaGggtcacggccacctagtgac					rs180893016		TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	GGG	GGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr18:43418834_43418836delGGG	ENST00000389474.3	+	4	865_867	c.648_650delGGG	c.(646-651)gagggt>gat	p.216_217EG>D	SIGLEC15_ENST00000587418.1_5'UTR|SIGLEC15_ENST00000602118.2_3'UTR|SIGLEC15_ENST00000546268.1_In_Frame_Del_p.62_63EG>D	NM_213602.2	NP_998767.1	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	216	Ig-like C2-type.				cellular response to lipoprotein particle stimulus (GO:0071402)|innate immune response (GO:0045087)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of bone resorption (GO:0045124)|regulation of osteoclast development (GO:2001204)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)		p.G217D(1)		endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						GCCCGCGTGAGGGTCACGGCCAC	0.744																																					p.216_217del		Atlas-Indel,Pindel	.											.	SIGLEC15	10	.	1	Substitution - Missense(1)	lung(1)	c.647_649del						.																																			SO:0001651	inframe_deletion	284266	exon4			.	AK095432	CCDS32819.1	18q21.1	2014-01-28	2007-05-31	2007-05-31	ENSG00000197046	ENSG00000197046		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	27596	protein-coding gene	gene with protein product			"CD33 antigen-like 3", "CD33 molecule-like 3"	CD33L3		17483134	Standard	NM_213602		Approved	HsT1361	uc002lbl.1	Q6ZMC9		ENST00000389474.3:c.648_650delGGG	chr18.hg19:g.43418834_43418836delGGG	ENSP00000374125:p.Glu216_Gly217delinsAsp	172.0	0.0		91.0	32.0	NM_213602	A8K2Y5|B4DVQ9	In_Frame_Del	DEL	ENST00000389474.3	hg19	CCDS32819.1																																																																																			.	.		0.744	SIGLEC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410768.2	NM_213602		-	43418836	GGG	-	43418834	7	5	21	1	0	1	0	1	0	0	0	0	14325	991	35	0	662	0	SIGLEC15	18	43418834	In_Frame_Del	DEL	GGG	TCGA-2Y-A9HB-01A-11D-A38X-10		43418834	34658414	67	1931										
NFIC	4782	hgsc.bcm.edu	37	chr19	3452573	3452573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	cacctacttcccccacacggCcatccgctacccacctcatc	3	23	1	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr19:3452573C>T	ENST00000443272.2	+	8	1229	c.1178C>T	c.(1177-1179)gCc>gTc	p.A393V	NFIC_ENST00000586919.1_Missense_Mutation_p.A360V|NFIC_ENST00000589123.1_Missense_Mutation_p.A384V|NFIC_ENST00000346156.5_Missense_Mutation_p.A360V|NFIC_ENST00000395111.3_Missense_Mutation_p.A384V|NFIC_ENST00000590282.1_Missense_Mutation_p.A393V|NFIC_ENST00000341919.3_Missense_Mutation_p.A393V	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	393					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		CCCCACACGGCCATCCGCTAC	0.652																																					p.A393V		Atlas-SNP	.											NFIC,colon,carcinoma,0,1	NFIC	36	.	0			c.C1178T						.						187	159	168					19																	3452573		2203	4300	6503	SO:0001583	missense	4782	exon8			ACACGGCCATCCG	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.1178C>T	chr19.hg19:g.3452573C>T	ENSP00000396843:p.Ala393Val	129.0	0.0		40.0	16.0	NM_001245004	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	hg19	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890863	0.91889	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T	0.53640	0.61;0.61;0.61	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.66117	0.2757	M	0.65498	2.005	0.52501	D	0.999953	D;D;D;D;D	0.76494	0.999;0.999;0.998;0.972;0.998	D;D;D;P;D	0.83275	0.996;0.996;0.994;0.592;0.994	T	0.69614	-0.5098	10	0.54805	T	0.06	.	15.0657	0.71992	0.0:1.0:0.0:0.0	.	393;393;384;393;384	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	V	384;384;360;393;393;393	ENSP00000378543:A384V;ENSP00000301935:A360V;ENSP00000342194:A393V	ENSP00000269778:A393V	A	+	2	0	NFIC	3403573	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.240000	0.78192	1.874000	0.54306	0.555000	0.69702	GCC	.	.		0.652	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597		T	3452573	C	T	3452573	3	4	21	1	0	0	0	0	1	0	0	0	10381	739	26	3	1215	3	NFIC	19	3452573	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		3452573	55676410	68	1932										
MATK	4145	hgsc.bcm.edu	37	chr19	3778345	3778345	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gcagctgctcatgaggacgtGcacggggcctggacagccct	15	13	1	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr19:3778345G>T	ENST00000310132.6	-	14	1758	c.1360C>A	c.(1360-1362)Cac>Aac	p.H454N	MATK_ENST00000395040.2_Missense_Mutation_p.H413N|MATK_ENST00000395045.2_Missense_Mutation_p.H455N|MATK_ENST00000585778.1_Missense_Mutation_p.H453N	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	454	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGAGGACGTGCACGGGGCCT	0.697																																					p.H455N		Atlas-SNP	.											.	MATK	108	.	0			c.C1363A						.						27	32	30					19																	3778345		2203	4293	6496	SO:0001583	missense	4145	exon14			GGACGTGCACGGG	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"SH2 domain containing"	6906	protein-coding gene	gene with protein product	"Csk-homologous kinase", "tyrosine-protein kinase CTK", "protein kinase HYL", "hematopoietic consensus tyrosine-lacking kinase", "tyrosylprotein kinase", "hydroxyaryl-protein kinase", "Csk-type protein tyrosine kinase", "HYL tyrosine kinase", "tyrosine kinase MATK", "leukocyte carboxyl-terminal src kinase related"	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.1360C>A	chr19.hg19:g.3778345G>T	ENSP00000308734:p.His454Asn	165.0	0.0		83.0	32.0	NM_002378	B3KNZ9|Q9NST8	Missense_Mutation	SNP	ENST00000310132.6	hg19	CCDS12114.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.485877	0.26686	.	.	ENSG00000007264	ENST00000395045;ENST00000310132;ENST00000395040	D;D;D	0.82255	-1.59;-1.59;-1.59	3.68	0.123	0.14709	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.078323	0.52532	D	0.000064	T	0.71230	0.3315	L	0.31476	0.935	0.09310	N	1	P;P;P	0.35821	0.523;0.523;0.523	B;B;B	0.39562	0.303;0.303;0.303	T	0.64067	-0.6494	10	0.87932	D	0	-22.8259	5.4811	0.16723	0.6168:0.0:0.3832:0.0	.	454;455;454	F1T0G6;B3KNZ9;P42679	.;.;MATK_HUMAN	N	455;454;413	ENSP00000378485:H455N;ENSP00000308734:H454N;ENSP00000378481:H413N	ENSP00000308734:H454N	H	-	1	0	MATK	3729345	1.000000	0.71417	0.000000	0.03702	0.573000	0.36030	5.962000	0.70364	0.254000	0.21573	-0.219000	0.12488	CAC	.	.		0.697	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355		T	3778345	G	T	3778345	3	4	21	1	0	0	0	0	1	0	0	0	9341	1319	46	3	167	3	MATK	19	3778345	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	325772	3778345	55350638	69	1933										
C21orf45	54069	hgsc.bcm.edu	37	chr21	33641405	33641405	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	gcctcccacagcttcatttgTaatgctttcaagacatcttc	5	13	3	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chr21:33641405T>C	ENST00000290130.3	-	5	699	c.645A>G	c.(643-645)ttA>ttG	p.L215L	MIS18A_ENST00000486363.1_5'Flank	NM_018944.2	NP_061817.1	Q9NYP9	MS18A_HUMAN	MIS18 kinetochore protein A	215					CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of DNA methylation (GO:0044030)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	7						GCTTCATTTGTAATGCTTTCA	0.353																																					p.L215L		Atlas-SNP	.											.	MIS18A	11	.	0			c.A645G						.						102	92	95					21																	33641405		2203	4300	6503	SO:0001819	synonymous_variant	54069	exon5			CATTTGTAATGCT	AF231921	CCDS13611.1	21q22.11	2013-10-21	2013-10-21	2011-02-23	ENSG00000159055	ENSG00000159055			1286	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 46", "chromosome 21 open reading frame 45", "MIS18 kinetochore protein homolog A (S. pombe)"	C21orf46, C21orf45		17199038	Standard	NM_018944		Approved	B28, FASP1, hMis18alpha	uc002ypi.3	Q9NYP9	OTTHUMG00000085308	ENST00000290130.3:c.645A>G	chr21.hg19:g.33641405T>C		524.0	1.0		243.0	124.0	NM_018944	B2R562|Q542Z0	Silent	SNP	ENST00000290130.3	hg19	CCDS13611.1																																																																																			.	.		0.353	MIS18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193090.1	NM_018944		C	33641405	T	C	33641405	2	2	21	1	0	0	0	0	0	0	0	1	2128	1635	57	2		2	C21orf45	21	33641405	Silent	SNP	T	TCGA-2Y-A9HB-01A-11D-A38X-10		33641405	14488490	70	1934										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5811119	5811119	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	agctgcttcatctgcagagaCatgatctcttcgttctggat	9	10	4	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chrX:5811119C>A	ENST00000381095.3	-	6	2817	c.2190G>T	c.(2188-2190)atG>atT	p.M730I	NLGN4X_ENST00000381093.2_Missense_Mutation_p.M750I|NLGN4X_ENST00000538097.1_Missense_Mutation_p.M730I|NLGN4X_ENST00000381092.1_Missense_Mutation_p.M730I|NLGN4X_ENST00000275857.6_Missense_Mutation_p.M730I	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	730					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						TCTGCAGAGACATGATCTCTT	0.552																																					p.M730I		Atlas-SNP	.											.	NLGN4X	191	.	0			c.G2190T						.						162	121	135					X																	5811119		2203	4300	6503	SO:0001583	missense	57502	exon6			CAGAGACATGATC	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.2190G>T	chrX.hg19:g.5811119C>A	ENSP00000370485:p.Met730Ile	68.0	0.0		57.0	39.0	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	C	9.648	1.140726	0.21205	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.16597	2.33;2.33;2.33;2.33;2.33	3.82	3.82	0.43975	.	0.599350	0.13950	N	0.351623	T	0.22126	0.0533	M	0.72894	2.215	0.44816	D	0.997821	B;B;B	0.31274	0.212;0.212;0.317	B;B;B	0.31547	0.062;0.062;0.132	T	0.03922	-1.0992	10	0.25106	T	0.35	.	14.222	0.65833	0.0:1.0:0.0:0.0	.	787;730;750	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	I	730;750;730;730;730	ENSP00000370485:M730I;ENSP00000370483:M750I;ENSP00000275857:M730I;ENSP00000370482:M730I;ENSP00000439203:M730I	ENSP00000275857:M730I	M	-	3	0	NLGN4X	5821119	1.000000	0.71417	0.982000	0.44146	0.266000	0.26442	3.945000	0.56637	1.508000	0.48769	0.513000	0.50165	ATG	.	.		0.552	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		A	5811119	C	A	5811119	3	1	21	1	0	0	0	0	1	0	0	0	10473	478	17	3	264	3	NLGN4X	23	5811119	Missense_Mutation	SNP	C	TCGA-2Y-A9HB-01A-11D-A38X-10		5811119	149459441	71	1935										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20206619	20206619	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	aggattttttttttacctgtTaacttgatgtgaccttcttc	6	7	1	2			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chrX:20206619T>A	ENST00000379565.3	-	8	834	c.627A>T	c.(625-627)ttA>ttT	p.L209F	RPS6KA3_ENST00000544447.1_Missense_Mutation_p.L181F|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.L180F|RPS6KA3_ENST00000540702.1_Missense_Mutation_p.L181F	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	209	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TTTTACCTGTTAACTTGATGT	0.264																																					p.L209F		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.A627T						.						20	19	19					X																	20206619		2171	4264	6435	SO:0001583	missense	6197	exon8			ACCTGTTAACTTG	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.627A>T	chrX.hg19:g.20206619T>A	ENSP00000368884:p.Leu209Phe	271.0	1.0		388.0	177.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	T	13.53	2.263264	0.39995	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702;ENST00000457145	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	5.11	1.55	0.23275	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000005	T	0.65883	0.2734	M	0.90650	3.135	0.58432	D	0.999998	D;D;D;D	0.89917	0.999;1.0;0.997;1.0	D;D;D;D	0.85130	0.986;0.996;0.971;0.997	T	0.69150	-0.5221	10	0.87932	D	0	.	9.2431	0.37509	0.0:0.2936:0.0:0.7064	.	181;180;181;209	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	F	209;181;180;181;180	ENSP00000368884:L209F;ENSP00000440220:L181F;ENSP00000368865:L180F;ENSP00000444837:L181F;ENSP00000407655:L180F	ENSP00000368865:L180F	L	-	3	2	RPS6KA3	20116540	0.630000	0.27155	1.000000	0.80357	0.157000	0.22087	-0.261000	0.08694	0.615000	0.30124	0.412000	0.27726	TTA	.	.		0.264	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		A	20206619	T	A	20206619	3	1	21	1	0	0	0	0	1	0	0	0	13667	1751	61	4	1655	4	RPS6KA3	23	20206619	Missense_Mutation	SNP	T	TCGA-2Y-A9HB-01A-11D-A38X-10	14395500	20206619	135063941	72	1936										
NR0B1	190	hgsc.bcm.edu	37	chrX	30327260	30327260	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	agaggatgctgccctgccgtGggtggtctttaccgcaaaag	14	10	1	1			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chrX:30327260G>T	ENST00000378970.4	-	1	455	c.221C>A	c.(220-222)cCa>cAa	p.P74Q	NR0B1_ENST00000378963.1_5'Flank|NR0B1_ENST00000453287.1_Missense_Mutation_p.P74Q	NM_000475.4	NP_000466.2	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1	74	4 X 67 AA tandem repeats.				adrenal gland development (GO:0030325)|gene expression (GO:0010467)|gonad development (GO:0008406)|hypothalamus development (GO:0021854)|intracellular receptor signaling pathway (GO:0030522)|Leydig cell differentiation (GO:0033327)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of cell differentiation (GO:0045596)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|protein localization (GO:0008104)|response to immobilization stress (GO:0035902)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)|steroid biosynthetic process (GO:0006694)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	AF-2 domain binding (GO:0050682)|DNA binding (GO:0003677)|DNA hairpin binding (GO:0032448)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|steroid hormone receptor binding (GO:0035258)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	24					Dexamethasone(DB01234)|Tretinoin(DB00755)	GCCCTGCCGTGGGTGGTCTTT	0.677																																					p.P74Q		Atlas-SNP	.											.	NR0B1	61	.	0			c.C221A						.						25	21	22					X																	30327260		2194	4285	6479	SO:0001583	missense	190	exon1			TGCCGTGGGTGGT	S74720	CCDS14223.1	Xp21.3	2014-06-28			ENSG00000169297	ENSG00000169297		"Nuclear hormone receptors"	7960	protein-coding gene	gene with protein product		300473	"dosage-sensitive sex reversal"	AHC, DSS		1301166, 10412368	Standard	NM_000475		Approved	DAX1, AHCH	uc004dcf.4	P51843	OTTHUMG00000021323	ENST00000378970.4:c.221C>A	chrX.hg19:g.30327260G>T	ENSP00000368253:p.Pro74Gln	135.0	0.0		76.0	51.0	NM_000475	Q96F69	Missense_Mutation	SNP	ENST00000378970.4	hg19	CCDS14223.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.169015	0.57584	.	.	ENSG00000169297	ENST00000378970;ENST00000453287	D;D	0.97553	-3.56;-4.43	4.27	3.33	0.38152	.	0.334229	0.28036	N	0.016850	D	0.96291	0.8790	L	0.39397	1.21	0.31003	N	0.720125	D	0.58620	0.983	P	0.61201	0.885	D	0.93643	0.6966	10	0.59425	D	0.04	-3.9043	8.3741	0.32432	0.0:0.236:0.764:0.0	.	74	P51843	NR0B1_HUMAN	Q	74	ENSP00000368253:P74Q;ENSP00000396403:P74Q	ENSP00000368253:P74Q	P	-	2	0	NR0B1	30237181	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	1.805000	0.38883	2.102000	0.63906	0.513000	0.50165	CCA	.	.		0.677	NR0B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056161.1	NM_000475		T	30327260	G	T	30327260	3	4	21	1	0	0	0	0	1	0	0	0	10622	1348	47	3	1199	3	NR0B1	23	30327260	Missense_Mutation	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	10120641	30327260	124943300	73	1937										
STAG2	10735	hgsc.bcm.edu	37	chrX	123196845	123196845	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0136986301369863	1	1	0.214211695040711	0	0.299896373056995	1	1	0	ttcctcagttattagcaaaaGtaagtttgtgtcaatatcat	6	6	3	0			TCGA-2Y-A9HB-01A-11D-A38X-10	TCGA-2Y-A9HB-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bb715136-b745-4c73-a3d5-e7a63b10fba2	53b59194-cc58-4bbf-a05d-c627c7485018	g.chrX:123196845G>C	ENST00000371160.1	+	18	2021		c.e18+1		STAG2_ENST00000371157.3_Splice_Site|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371145.3_Splice_Site|STAG2_ENST00000218089.9_Splice_Site|STAG2_ENST00000371144.3_Splice_Site|STAG2_ENST00000354548.5_Splice_Site	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2						meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						ATTAGCAAAAGTAAGTTTGTG	0.348																																					.		Atlas-SNP	.											.	STAG2	309	.	0			c.1731+1G>C						.						87	78	81					X																	123196845		2203	4300	6503	SO:0001630	splice_region_variant	10735	exon18			GCAAAAGTAAGTT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1731+1G>C	chrX.hg19:g.123196845G>C		124.0	0.0		162.0	101.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Splice_Site	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.677576	0.88445	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9779	0.92745	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	STAG2	123024526	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.809000	0.99208	2.430000	0.82344	0.544000	0.68410	.	.	.		0.348	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	Intron	C	123196845	G	C	123196845	5	2	21	1	0	0	0	0	0	0	1	0	15258	1043	36	4	1794	4	STAG2	23	123196845	Splice_Site	SNP	G	TCGA-2Y-A9HB-01A-11D-A38X-10	92869585	123196845	32073715	74	1938										
PLCH2	9651	hgsc.bcm.edu	37	chr1	2436408	2436408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	agggggccctggttttgtgcGgcgctcctcctcccgcagcc	14	16	0	0	rs374511532		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:2436408G>A	ENST00000419816.2	+	22	4281	c.4007G>A	c.(4006-4008)cGg>cAg	p.R1336Q	PLCH2_ENST00000378486.3_Missense_Mutation_p.R1336Q|PLCH2_ENST00000449969.1_3'UTR|PLCH2_ENST00000378488.3_Missense_Mutation_p.R1300Q			O75038	PLCH2_HUMAN	phospholipase C, eta 2	1336					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		GGTTTTGTGCGGCGCTCCTCC	0.731																																					p.R1336Q		Atlas-SNP	.											.	PLCH2	131	.	0			c.G4007A						.	G	GLN/ARG	0,3172		0,0,1586	3	4	4		4007	2.5	0.8	1		4	5,7217		0,5,3606	no	missense	PLCH2	NM_014638.2	43	0,5,5192	AA,AG,GG		0.0692,0.0,0.0481	possibly-damaging	1336/1417	2436408	5,10389	1586	3611	5197	SO:0001583	missense	9651	exon22			TTGTGCGGCGCTC	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"EF-hand domain containing"	29037	protein-coding gene	gene with protein product		612836	"phospholipase C-like 4"	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.4007G>A	chr1.hg19:g.2436408G>A	ENSP00000389803:p.Arg1336Gln	62.0	0.0		56.0	23.0	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Missense_Mutation	SNP	ENST00000419816.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.82|16.82	3.229367|3.229367	0.58777|0.58777	0.0|0.0	6.92E-4|6.92E-4	ENSG00000149527|ENSG00000149527	ENST00000419816|ENST00000378486;ENST00000378488;ENST00000278878	.|T;T	.|0.64618	.|0.17;-0.11	4.41|4.41	2.52|2.52	0.30459|0.30459	.|.	.|1.454070	.|0.04326	.|N	.|0.351512	T|T	0.57359|0.57359	0.2048|0.2048	M|M	0.73217|0.73217	2.22|2.22	0.80722|0.80722	D|D	1|1	.|D;P	.|0.53745	.|0.962;0.584	.|B;B	.|0.32677	.|0.15;0.058	T|T	0.55522|0.55522	-0.8128|-0.8128	5|9	.|.	.|.	.|.	.|.	9.0964|9.0964	0.36642|0.36642	0.1805:0.0:0.8195:0.0|0.1805:0.0:0.8195:0.0	.|.	.|1088;1336	.|B9DI82;O75038	.|.;PLCH2_HUMAN	S|Q	631|1336;1300;1088	.|ENSP00000367747:R1336Q;ENSP00000367749:R1300Q	.|.	G|R	+|+	1|2	0|0	PLCH2|PLCH2	2426268|2426268	1.000000|1.000000	0.71417|0.71417	0.832000|0.832000	0.32986|0.32986	0.251000|0.251000	0.25915|0.25915	7.139000|7.139000	0.77314|0.77314	0.320000|0.320000	0.23234|0.23234	0.491000|0.491000	0.48974|0.48974	GGC|CGG	.	.		0.731	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		A	2436408	G	A	2436408	3	1	22	1	0	0	0	0	1	0	0	0	12047	1116	39	1	4093	1	PLCH2	1	2436408	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10		2436408	246814213	1	1939										
PRDM16	63976	hgsc.bcm.edu	37	chr1	3329297	3329297	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tgccccaggtgtgcccggcgCggatgccccagcagcccccg	14	19	0	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:3329297C>T	ENST00000270722.5	+	9	2585	c.2536C>T	c.(2536-2538)Cgg>Tgg	p.R846W	PRDM16_ENST00000378398.3_Missense_Mutation_p.R847W|PRDM16_ENST00000378391.2_Missense_Mutation_p.R846W|PRDM16_ENST00000511072.1_Missense_Mutation_p.R847W|PRDM16_ENST00000514189.1_Missense_Mutation_p.R847W|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000441472.2_Missense_Mutation_p.R846W|PRDM16_ENST00000442529.2_Missense_Mutation_p.R846W			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	846	Interaction with CTBP1 and CTBP2. {ECO:0000250}.|Mediates interaction with SKI and regulation of TGF-beta signaling.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GTGCCCGGCGCGGATGCCCCA	0.692			T	EVI1	"MDS, AML"																																p.R846W		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C2536T						.						7	8	8					1																	3329297		1795	3908	5703	SO:0001583	missense	63976	exon9			CCGGCGCGGATGC	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.2536C>T	chr1.hg19:g.3329297C>T	ENSP00000270722:p.Arg846Trp	88.0	0.0		65.0	34.0	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	hg19	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	C	8.280	0.815354	0.16607	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.06608	3.3;3.32;3.33;3.34;3.32;3.31;3.33;3.28;3.29	4.05	3.11	0.35812	.	0.268828	0.25628	U	0.029366	T	0.10208	0.0250	L	0.43152	1.355	0.26118	N	0.980596	B;B;D;B	0.55385	0.001;0.001;0.971;0.001	B;B;P;B	0.49047	0.0;0.002;0.599;0.001	T	0.05084	-1.0907	10	0.56958	D	0.05	.	13.1324	0.59391	0.1617:0.8382:0.0:0.0	.	846;846;846;846	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	W	847;847;846;846;846;847;846;662;662;655	ENSP00000426975:R847W;ENSP00000367651:R847W;ENSP00000407968:R846W;ENSP00000405253:R846W;ENSP00000367643:R846W;ENSP00000421400:R847W;ENSP00000270722:R846W;ENSP00000422504:R662W;ENSP00000425796:R655W	ENSP00000270722:R846W	R	+	1	2	PRDM16	3319157	1.000000	0.71417	0.117000	0.21633	0.033000	0.12548	5.440000	0.66563	0.803000	0.34113	-0.332000	0.08345	CGG	.	.		0.692	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		T	3329297	C	T	3329297	3	4	22	1	0	0	0	0	1	0	0	0	12469	759	27	1	2570	1	PRDM16	1	3329297	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	892889	3329297	245921324	2	1940										
NMNAT1	64802	hgsc.bcm.edu	37	chr1	10042386	10042386	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aaaggtcaagctgctgtgtgGggcagatttattggagtcct	14	6	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:10042386G>T	ENST00000377205.1	+	5	611	c.467G>T	c.(466-468)gGg>gTg	p.G156V	RP11-807G9.2_ENST00000413148.1_RNA	NM_022787.3	NP_073624.2	Q9HAN9	NMNA1_HUMAN	nicotinamide nucleotide adenylyltransferase 1	156			G -> R (in LCA9). {ECO:0000269|PubMed:22842227}.		NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)			large_intestine(2)|lung(2)|stomach(1)	5		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.31e-08)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(185;0.00028)|BRCA - Breast invasive adenocarcinoma(304;0.00032)|KIRC - Kidney renal clear cell carcinoma(229;0.00101)|STAD - Stomach adenocarcinoma(132;0.00908)|READ - Rectum adenocarcinoma(331;0.0419)		CTGCTGTGTGGGGCAGATTTA	0.483																																					p.G156V		Atlas-SNP	.											.	NMNAT1	18	.	0			c.G467T						.						104	101	102					1																	10042386		2203	4300	6503	SO:0001583	missense	64802	exon5			TGTGTGGGGCAGA	AF312734	CCDS108.1, CCDS72698.1	1p36.22	2014-01-28	2003-04-30	2003-05-02	ENSG00000173614	ENSG00000173614	2.7.7.1		17877	protein-coding gene	gene with protein product		608700	"nicotinamide nucleotide adenylyltransferase", "Leber congenital amaurosis 9", "Leber's congenital amaurosis 9"	LCA9		11248244, 11027696, 22842227	Standard	XR_244792		Approved	NMNAT, PNAT1	uc001aqp.3	Q9HAN9	OTTHUMG00000001799	ENST00000377205.1:c.467G>T	chr1.hg19:g.10042386G>T	ENSP00000366410:p.Gly156Val	92.0	0.0		84.0	27.0	NM_022787	B1AN63|Q8TAE9|Q9H247|Q9H6B6	Missense_Mutation	SNP	ENST00000377205.1	hg19	CCDS108.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.712659	0.89112	.	.	ENSG00000173614	ENST00000377205	D	0.99915	-7.99	5.12	5.12	0.69794	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.99945	0.9976	H	0.95982	3.75	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95988	0.8983	10	0.87932	D	0	-1.8287	18.9958	0.92812	0.0:0.0:1.0:0.0	.	156	Q9HAN9	NMNA1_HUMAN	V	156	ENSP00000366410:G156V	ENSP00000366410:G156V	G	+	2	0	NMNAT1	9964973	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.449000	0.97603	2.549000	0.85964	0.456000	0.33151	GGG	.	.		0.483	NMNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005029.1			T	10042386	G	T	10042386	3	4	22	1	0	0	0	0	1	0	0	0	10507	1232	43	3	481	3	NMNAT1	1	10042386	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	6713089	10042386	239208235	3	1941										
KIAA0090	23065	hgsc.bcm.edu	37	chr1	19568962	19568962	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ggccaaccagcccaagtgccTggaaactgaacacaagtaca	9	13	0	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:19568962T>A	ENST00000477853.1	-	5	428	c.386A>T	c.(385-387)cAg>cTg	p.Q129L	RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375208.3_Missense_Mutation_p.Q107L|EMC1_ENST00000375199.3_Missense_Mutation_p.Q129L	NM_001271427.1|NM_001271428.1|NM_015047.2	NP_001258356.1|NP_001258357.1|NP_055862.1	Q8N766	EMC1_HUMAN	ER membrane protein complex subunit 1	129						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											CCCAAGTGCCTGGAAACTGAA	0.552																																					p.Q129L		Atlas-SNP	.											.	.	.	.	0			c.A386T						.						94	83	86					1																	19568962		2203	4300	6503	SO:0001583	missense	23065	exon5			AGTGCCTGGAAAC		CCDS190.1, CCDS59190.1, CCDS59191.1	1p36.13	2012-05-23	2012-05-23	2012-05-23	ENSG00000127463	ENSG00000127463			28957	protein-coding gene	gene with protein product			"KIAA0090"	KIAA0090		22119785	Standard	NM_015047		Approved		uc001bbo.4	Q8N766	OTTHUMG00000002497	ENST00000477853.1:c.386A>T	chr1.hg19:g.19568962T>A	ENSP00000420608:p.Gln129Leu	72.0	0.0		53.0	31.0	NM_001271427	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	hg19	CCDS190.1	.	.	.	.	.	.	.	.	.	.	T	33	5.268798	0.95429	.	.	ENSG00000127463	ENST00000477853;ENST00000375199;ENST00000375208	T;T;T	0.41400	1.0;1.0;1.91	6.08	6.08	0.98989	Quinonprotein alcohol dehydrogenase-like (2);	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	L	0.56769	1.78	0.80722	D	1	D;D;D;D	0.69078	0.991;0.991;0.996;0.997	P;P;D;D	0.66602	0.852;0.889;0.909;0.945	T	0.52866	-0.8518	10	0.25751	T	0.34	.	15.4678	0.75416	0.0:0.0:0.0:1.0	.	107;129;129;129	Q8N766-4;Q8N766-2;Q8N766-3;Q8N766	.;.;.;K0090_HUMAN	L	129;129;107	ENSP00000420608:Q129L;ENSP00000364345:Q129L;ENSP00000364354:Q107L	ENSP00000364345:Q129L	Q	-	2	0	KIAA0090	19441549	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.883000	0.69721	2.333000	0.79357	0.533000	0.62120	CAG	.	.		0.552	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047		A	19568962	T	A	19568962	3	1	22	1	0	0	0	0	1	0	0	0	8162	1580	55	4	2671	4	KIAA0090	1	19568962	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	9526576	19568962	229681659	4	1942										
PTPRU	10076	hgsc.bcm.edu	37	chr1	29602163	29602163	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aaggtgtcagccgctacaccAtcaagaacctgctgccctat	8	14	2	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:29602163A>T	ENST00000345512.3	+	8	1477	c.1348A>T	c.(1348-1350)Atc>Ttc	p.I450F	PTPRU_ENST00000323874.8_Missense_Mutation_p.I450F|PTPRU_ENST00000428026.2_Missense_Mutation_p.I450F|PTPRU_ENST00000356870.3_Missense_Mutation_p.I450F|PTPRU_ENST00000460170.2_Missense_Mutation_p.I450F|PTPRU_ENST00000373779.3_Missense_Mutation_p.I450F	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	450	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		CCGCTACACCATCAAGAACCT	0.557																																					p.I450F		Atlas-SNP	.											.	PTPRU	374	.	0			c.A1348T						.						185	144	158					1																	29602163		2203	4300	6503	SO:0001583	missense	10076	exon8			TACACCATCAAGA	U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.1348A>T	chr1.hg19:g.29602163A>T	ENSP00000334941:p.Ile450Phe	422.0	0.0		306.0	146.0	NM_001195001	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	hg19	CCDS334.1	.	.	.	.	.	.	.	.	.	.	A	16.74	3.206762	0.58343	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;0.4;0.4	5.4	5.4	0.78164	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.150917	0.45126	D	0.000398	T	0.40040	0.1101	L	0.52573	1.65	0.44762	D	0.997762	P;B;P;P;P	0.42409	0.705;0.233;0.705;0.779;0.581	B;B;B;B;B	0.30029	0.11;0.069;0.11;0.051;0.051	T	0.37430	-0.9706	9	.	.	.	.	10.9844	0.47514	0.8439:0.1561:0.0:0.0	.	450;450;450;450;450	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	F	450	ENSP00000334941:I450F;ENSP00000362884:I450F;ENSP00000349333:I450F;ENSP00000314987:I450F;ENSP00000392332:I450F;ENSP00000432906:I450F	.	I	+	1	0	PTPRU	29474750	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.775000	0.55349	2.177000	0.69029	0.523000	0.50628	ATC	.	.		0.557	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			T	29602163	A	T	29602163	3	4	22	1	0	0	0	0	1	0	0	0	12828	217	8	4	1378	4	PTPRU	1	29602163	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	10033201	29602163	219648458	5	1943										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34035031	34035031	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ggccatgcactcacgcacccTggagcccaccagtgtgtatc	10	16	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:34035031T>A	ENST00000373381.4	-	52	8250	c.8074A>T	c.(8074-8076)Agg>Tgg	p.R2692W		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2694	Sushi 17. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCACGCACCCTGGAGCCCACC	0.587																																					p.R2694W		Atlas-SNP	.											.	CSMD2	946	.	0			c.A8080T						.						92	82	85					1																	34035031		2203	4300	6503	SO:0001583	missense	114784	exon53			GCACCCTGGAGCC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.8074A>T	chr1.hg19:g.34035031T>A	ENSP00000362479:p.Arg2692Trp	101.0	0.0		67.0	21.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	T	14.76	2.630863	0.46944	.	.	ENSG00000121904	ENST00000373381	T	0.66099	-0.19	5.47	-3.92	0.04155	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.80132	0.4567	M	0.86343	2.81	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.949	D	0.83907	0.0293	10	0.72032	D	0.01	.	21.0284	0.99944	0.0:0.0:0.8124:0.1876	.	2694;2692	Q7Z408;E7EUA6	CSMD2_HUMAN;.	W	2692	ENSP00000362479:R2692W	ENSP00000241312:R2694W	R	-	1	2	CSMD2	33807618	1.000000	0.71417	0.985000	0.45067	0.009000	0.06853	1.213000	0.32407	-0.590000	0.05866	-1.444000	0.01066	AGG	.	.		0.587	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	34035031	T	A	34035031	3	1	22	1	0	0	0	0	1	0	0	0	3947	1579	55	4	2451	4	CSMD2	1	34035031	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	4432868	34035031	215215590	6	1944										
OMA1	115209	hgsc.bcm.edu	37	chr1	58971782	58971782	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tcgattgccatgagaagggtGtgtagataaccattctggca	12	7	1	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:58971782G>A	ENST00000371226.3	-	8	1428	c.1315C>T	c.(1315-1317)Cac>Tac	p.H439Y	OMA1_ENST00000358603.2_Missense_Mutation_p.H439Y|DAB1_ENST00000485760.1_5'UTR	NM_145243.3	NP_660286.1	Q96E52	OMA1_HUMAN	OMA1 zinc metallopeptidase	439					cristae formation (GO:0042407)|diet induced thermogenesis (GO:0002024)|energy homeostasis (GO:0097009)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrial protein processing (GO:0034982)|negative regulation of mitochondrial fusion (GO:0010637)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(1)|large_intestine(6)|liver(2)|lung(6)|prostate(1)|skin(1)	18	all_cancers(7;6.54e-05)					TGAGAAGGGTGTGTAGATAAC	0.453																																					p.H439Y		Atlas-SNP	.											.	OMA1	50	.	0			c.C1315T						.						144	127	133					1																	58971782		2203	4300	6503	SO:0001583	missense	115209	exon8			AAGGGTGTGTAGA	AK091101	CCDS608.1	1p32.2-p32.1	2013-05-03	2013-05-03		ENSG00000162600	ENSG00000162600			29661	protein-coding gene	gene with protein product	"overlapping activity with M-AAA protease", "zinc metallopeptidase OMA1"		"OMA1 zinc metallopeptidase homolog (S. cerevisiae)"			12477932	Standard	NM_145243		Approved	MPRP-1, YKR087C, ZMPOMA1, FLJ33782	uc001cyy.3	Q96E52	OTTHUMG00000010068	ENST00000371226.3:c.1315C>T	chr1.hg19:g.58971782G>A	ENSP00000360270:p.His439Tyr	96.0	0.0		78.0	18.0	NM_145243	D3DQ54|Q5T3G6|Q5T3G7|Q5T3G8|Q5T3G9|Q5T3H0|Q8NBB3	Missense_Mutation	SNP	ENST00000371226.3	hg19	CCDS608.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.2|26.2	4.716958|4.716958	0.89205|0.89205	.|.	.|.	ENSG00000162600|ENSG00000162600	ENST00000358603;ENST00000371226|ENST00000421528	D;D|D	0.91407|0.84516	-2.84;-2.84|-1.86	5.34|5.34	5.34|5.34	0.76211|0.76211	.|.	0.049804|.	0.85682|.	D|.	0.000000|.	D|D	0.95433|0.95433	0.8517|0.8517	H|H	0.97390|0.97390	3.995|3.995	0.54753|0.54753	D|D	0.999981|0.999981	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.96709|0.96709	0.9524|0.9524	10|7	0.87932|0.87932	D|D	0|0	-7.6031|-7.6031	17.9783|17.9783	0.89133|0.89133	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	439;439|.	Q96E52;Q96E52-2|.	OMA1_HUMAN;.|.	Y|I	439|280	ENSP00000351417:H439Y;ENSP00000360270:H439Y|ENSP00000391941:T280I	ENSP00000351417:H439Y|ENSP00000391941:T280I	H|T	-|-	1|2	0|0	OMA1|OMA1	58744370|58744370	1.000000|1.000000	0.71417|0.71417	0.975000|0.975000	0.42487|0.42487	0.918000|0.918000	0.54935|0.54935	8.712000|8.712000	0.91403|0.91403	2.785000|2.785000	0.95823|0.95823	0.650000|0.650000	0.86243|0.86243	CAC|ACA	.	.		0.453	OMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027819.1	NM_145243		A	58971782	G	A	58971782	3	1	22	1	0	0	0	0	1	0	0	0	10873	1377	48	3	267	3	OMA1	1	58971782	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	24936751	58971782	190278839	7	1945										
IL23R	149233	hgsc.bcm.edu	37	chr1	67648612	67648612	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tgctgggaagctcacctacaTagacacaaaatacgtggtac	9	10	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:67648612T>A	ENST00000347310.5	+	4	632	c.461T>A	c.(460-462)aTa>aAa	p.I154K	C1orf141_ENST00000371007.2_Intron|IL23R_ENST00000371002.1_Missense_Mutation_p.I154K	NM_144701.2	NP_653302.2	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor	154	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|interleukin-23-mediated signaling pathway (GO:0038155)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)	interleukin-23 receptor complex (GO:0072536)|receptor complex (GO:0043235)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	21						CTCACCTACATAGACACAAAA	0.478																																					p.I154K		Atlas-SNP	.											.	IL23R	52	.	0			c.T461A						.						127	116	120					1																	67648612		2203	4300	6503	SO:0001583	missense	149233	exon4			CCTACATAGACAC	AF461422	CCDS637.1	1p31.2	2008-02-05			ENSG00000162594	ENSG00000162594			19100	protein-coding gene	gene with protein product		607562				12023369	Standard	NM_144701		Approved	IL-23R	uc001ddo.3	Q5VWK5	OTTHUMG00000009092	ENST00000347310.5:c.461T>A	chr1.hg19:g.67648612T>A	ENSP00000321345:p.Ile154Lys	128.0	0.0		112.0	22.0	NM_144701	C9JGX4|Q4VGP1|Q4VGP2|Q4VGP3|Q4VGP4|Q4VGP5|Q4VGP6|Q5VWK7|Q8IW84|Q8NFQ9|Q96AS1	Missense_Mutation	SNP	ENST00000347310.5	hg19	CCDS637.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.469966	0.43839	.	.	ENSG00000162594	ENST00000347310;ENST00000431791;ENST00000441823;ENST00000416525;ENST00000540911;ENST00000371002;ENST00000540775;ENST00000543799	T;T	0.23552	1.9;1.9	5.24	5.24	0.73138	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.621107	0.16267	N	0.221996	T	0.23965	0.0580	L	0.53249	1.67	0.80722	D	1	P;P;P;P;P;D	0.53151	0.925;0.95;0.925;0.874;0.925;0.958	B;P;P;P;P;P	0.50708	0.387;0.648;0.466;0.571;0.466;0.466	T	0.03394	-1.1041	10	0.87932	D	0	-31.2694	11.5495	0.50713	0.0:0.0:0.0:1.0	.	8;13;13;8;154;154	B6HY71;E9PHX4;E9PG12;B6HY79;Q5VWK5-3;Q5VWK5	.;.;.;.;.;IL23R_HUMAN	K	154;13;13;13;13;154;109;109	ENSP00000321345:I154K;ENSP00000360041:I154K	ENSP00000321345:I154K	I	+	2	0	IL23R	67421200	0.332000	0.24722	0.969000	0.41365	0.505000	0.33919	4.204000	0.58460	1.987000	0.57996	0.460000	0.39030	ATA	.	.		0.478	IL23R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025199.2	NM_144701		A	67648612	T	A	67648612	3	1	22	1	0	0	0	0	1	0	0	0	7685	1406	49	4	471	4	IL23R	1	67648612	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	8676830	67648612	181602009	8	1946										
CHIA	27159	hgsc.bcm.edu	37	chr1	111861228	111861228	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aacccctccaacactggaatTggtgcccccacctctggtgc	8	17	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:111861228T>A	ENST00000369740.1	+	9	946	c.843T>A	c.(841-843)atT>atA	p.I281I	RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000483391.1_Silent_p.I120I|CHIA_ENST00000430615.1_Silent_p.I173I|CHIA_ENST00000353665.6_Silent_p.I120I|CHIA_ENST00000343320.6_Silent_p.I281I|CHIA_ENST00000451398.2_Silent_p.I120I	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	281					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		ACACTGGAATTGGTGCCCCCA	0.532																																					p.I281I		Atlas-SNP	.											.	CHIA	115	.	0			c.T843A						.						153	147	149					1																	111861228		2203	4300	6503	SO:0001819	synonymous_variant	27159	exon9			TGGAATTGGTGCC	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.843T>A	chr1.hg19:g.111861228T>A		146.0	0.0		89.0	30.0	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	hg19	CCDS41368.1																																																																																			.	.		0.532	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			A	111861228	T	A	111861228	2	1	22	1	0	0	0	0	0	0	0	1	3344	1800	63	4		4	CHIA	1	111861228	Silent	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	44212616	111861228	137389393	9	1947										
HAX1	10456	hgsc.bcm.edu	37	chr1	154245239	154245239	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tccggggctttttcggctttCctggacctcggaggtgagag	15	10	0	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:154245239C>A	ENST00000328703.7	+	1	253	c.40C>A	c.(40-42)Cct>Act	p.P14T	HAX1_ENST00000483970.2_Missense_Mutation_p.P14T|HAX1_ENST00000457918.2_Missense_Mutation_p.P14T|HAX1_ENST00000532105.1_De_novo_Start_InFrame	NM_006118.3	NP_006109.2	O00165	HAX1_HUMAN	HCLS1 associated protein X-1	14	Required for localization in mitochondria. {ECO:0000250}.				cellular response to cytokine stimulus (GO:0071345)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin filament polymerization (GO:0030833)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein targeting to mitochondrion (GO:1903214)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|lamellipodium (GO:0030027)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|sarcoplasmic reticulum (GO:0016529)|transcription factor complex (GO:0005667)	interleukin-1 binding (GO:0019966)|protein N-terminus binding (GO:0047485)			cervix(1)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	15	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TTTCGGCTTTCCTGGACCTCG	0.567									Kostmann syndrome																												p.P14T		Atlas-SNP	.											.	HAX1	25	.	0			c.C40A						.						55	54	54					1																	154245239		2203	4300	6503	SO:0001583	missense	10456	exon1	Familial Cancer Database	Kostmann Infantile Agranulocytosis, Severe Congenital Neutropenia, Congenital Agranulocytosis	GGCTTTCCTGGAC	U68566	CCDS1064.1, CCDS44230.1	1q21.3	2014-09-17			ENSG00000143575	ENSG00000143575			16915	protein-coding gene	gene with protein product	"HCLS1 (and PKD2) associated protein"	605998				9058808, 10760273	Standard	NM_006118		Approved	HS1BP1, HCLSBP1	uc001fes.3	O00165	OTTHUMG00000035978	ENST00000328703.7:c.40C>A	chr1.hg19:g.154245239C>A	ENSP00000329002:p.Pro14Thr	115.0	0.0		131.0	28.0	NM_006118	A8W4W9|A8W4X0|B4DUJ7|Q5VYD5|Q5VYD7|Q96AU4|Q9BS80	Missense_Mutation	SNP	ENST00000328703.7	hg19	CCDS1064.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.976550	0.74360	.	.	ENSG00000143575	ENST00000328703;ENST00000457918;ENST00000483970;ENST00000435087	T;T;T;T	0.66280	0.97;-0.2;0.97;0.97	4.53	-0.145	0.13436	.	0.199329	0.42964	D	0.000623	T	0.39200	0.1069	M	0.71581	2.175	0.80722	D	1	B;B;P	0.35575	0.167;0.03;0.51	B;B;B	0.32864	0.085;0.055;0.154	T	0.38478	-0.9659	10	0.72032	D	0.01	-6.9549	7.363	0.26758	0.0:0.5613:0.0:0.4387	.	14;14;14	O00165-2;O00165-5;O00165	.;.;HAX1_HUMAN	T	14	ENSP00000329002:P14T;ENSP00000411448:P14T;ENSP00000435088:P14T;ENSP00000394920:P14T	ENSP00000329002:P14T	P	+	1	0	HAX1	152511863	0.999000	0.42202	0.999000	0.59377	0.986000	0.74619	0.922000	0.28734	0.080000	0.16959	0.655000	0.94253	CCT	.	.		0.567	HAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087650.1	NM_006118		A	154245239	C	A	154245239	3	1	22	1	0	0	0	0	1	0	0	0	6984	855	30	3	42	3	HAX1	1	154245239	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	42384011	154245239	95005382	10	1948										
PYGO2	90780	hgsc.bcm.edu	37	chr1	154931785	154931785	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	caggctggggagcccctgacCaggtctctggagaggagaag	17	10	1	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:154931785C>T	ENST00000368457.2	-	3	862	c.691G>A	c.(691-693)Ggt>Agt	p.G231S	RP11-307C12.12_ENST00000605085.1_RNA|PYGO2_ENST00000368456.1_Missense_Mutation_p.G194S|PYGO2_ENST00000483463.1_5'Flank	NM_138300.3	NP_612157.1	Q9BRQ0	PYGO2_HUMAN	pygopus family PHD finger 2	231	Pro-rich.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|developmental growth (GO:0048589)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mammary gland development (GO:0030879)|palate development (GO:0060021)|positive regulation of chromatin binding (GO:0035563)|post-embryonic development (GO:0009791)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|spermatid nucleus differentiation (GO:0007289)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase regulator activity (GO:0035034)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)|skin(2)|urinary_tract(1)	10	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			AGCCCCTGACCAGGTCTCTGG	0.632																																					p.G231S	NSCLC(87;357 1460 1955 21029 23522)	Atlas-SNP	.											.	PYGO2	32	.	0			c.G691A						.						27	32	30					1																	154931785		2203	4300	6503	SO:0001583	missense	90780	exon3			CCTGACCAGGTCT	BC006132	CCDS1075.1	1q22	2013-10-09	2013-10-09		ENSG00000163348	ENSG00000163348		"Zinc fingers, PHD-type"	30257	protein-coding gene	gene with protein product		606903	"pygopus homolog 2 (Drosophila)"			11988739	Standard	NM_138300		Approved		uc001fft.3	Q9BRQ0	OTTHUMG00000037370	ENST00000368457.2:c.691G>A	chr1.hg19:g.154931785C>T	ENSP00000357442:p.Gly231Ser	144.0	0.0		157.0	14.0	NM_138300	Q8WYZ4|Q96CY2	Missense_Mutation	SNP	ENST00000368457.2	hg19	CCDS1075.1	.	.	.	.	.	.	.	.	.	.	C	11.94	1.788679	0.31685	.	.	ENSG00000163348	ENST00000368457;ENST00000368456	T;T	0.42513	0.97;0.98	4.72	4.72	0.59763	.	0.153445	0.41396	D	0.000881	T	0.06462	0.0166	N	0.08118	0	0.31468	N	0.66873	B	0.23058	0.079	B	0.15870	0.014	T	0.19943	-1.0290	10	0.05525	T	0.97	-5.8889	8.7651	0.34698	0.0:0.9001:0.0:0.0999	.	231	Q9BRQ0	PYGO2_HUMAN	S	231;194	ENSP00000357442:G231S;ENSP00000357441:G194S	ENSP00000357441:G194S	G	-	1	0	PYGO2	153198409	0.124000	0.22315	1.000000	0.80357	0.989000	0.77384	0.232000	0.17891	2.454000	0.82982	0.462000	0.41574	GGT	.	.		0.632	PYGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090949.1	NM_138300		T	154931785	C	T	154931785	3	4	22	1	0	0	0	0	1	0	0	0	12879	594	21	3	533	3	PYGO2	1	154931785	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	686546	154931785	94318836	11	1949										
OR10K2	391107	hgsc.bcm.edu	37	chr1	158390373	158390373	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	acatttggatggcacagcccAggaaagaaatggtcttcttc	10	9	2	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:158390373A>T	ENST00000314902.2	-	1	283	c.284T>A	c.(283-285)cTg>cAg	p.L95Q		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	95						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					GGCACAGCCCAGGAAAGAAAT	0.478																																					p.L95Q		Atlas-SNP	.											.	OR10K2	69	.	0			c.T284A						.						178	174	175					1																	158390373		2203	4300	6503	SO:0001583	missense	391107	exon1			CAGCCCAGGAAAG	AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"GPCR / Class A : Olfactory receptors"	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.284T>A	chr1.hg19:g.158390373A>T	ENSP00000324251:p.Leu95Gln	112.0	0.0		139.0	41.0	NM_001004476		Missense_Mutation	SNP	ENST00000314902.2	hg19	CCDS30896.1	.	.	.	.	.	.	.	.	.	.	A	1.710	-0.499247	0.04291	.	.	ENSG00000180708	ENST00000314902	T	0.00397	7.57	4.1	1.66	0.24008	GPCR, rhodopsin-like superfamily (1);	0.798993	0.10278	N	0.693841	T	0.00039	0.0001	N	0.25031	0.7	0.09310	N	1	P	0.39717	0.684	B	0.29267	0.1	T	0.00001	-1.2757	10	0.19147	T	0.46	.	3.7156	0.08437	0.6486:0.0:0.1881:0.1633	.	95	Q6IF99	O10K2_HUMAN	Q	95	ENSP00000324251:L95Q	ENSP00000324251:L95Q	L	-	2	0	OR10K2	156656997	0.000000	0.05858	0.482000	0.27366	0.398000	0.30690	-0.297000	0.08276	0.214000	0.20742	0.383000	0.25322	CTG	.	.		0.478	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476		T	158390373	A	T	158390373	3	4	22	1	0	0	0	0	1	0	0	0	10923	188	7	4	656	4	OR10K2	1	158390373	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	3458588	158390373	90860248	12	1950										
TNFSF18	8995	hgsc.bcm.edu	37	chr1	173010529	173010529	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aggagatgaattggggatttGctagtaaaatgataccccag	12	5	0	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:173010529G>A	ENST00000404377.3	-	3	578	c.578C>T	c.(577-579)gCa>gTa	p.A193V	RP1-15D23.2_ENST00000432694.2_lincRNA|TNFSF18_ENST00000239468.2_Missense_Mutation_p.A171V	NM_005092.3	NP_005083.2	Q9UNG2	TNF18_HUMAN	tumor necrosis factor (ligand) superfamily, member 18	193					cell-cell signaling (GO:0007267)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of T cell proliferation (GO:0042129)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|tumor necrosis factor receptor superfamily binding (GO:0032813)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)	9						TTGGGGATTTGCTAGTAAAAT	0.413																																					p.A193V		Atlas-SNP	.											.	TNFSF18	24	.	0			c.C578T						.						86	83	84					1																	173010529		2203	4300	6503	SO:0001583	missense	8995	exon3			GGATTTGCTAGTA	AF117713	CCDS1305.2	1q23	2008-02-05			ENSG00000120337	ENSG00000120337		"Tumor necrosis factor (ligand) superfamily"	11932	protein-coding gene	gene with protein product		603898				10037686, 10074428	Standard	NM_005092		Approved	AITRL, TL6, hGITRL	uc001giu.2	Q9UNG2	OTTHUMG00000034835	ENST00000404377.3:c.578C>T	chr1.hg19:g.173010529G>A	ENSP00000385470:p.Ala193Val	121.0	0.0		148.0	91.0	NM_005092	A9IQG8|O95852|Q6ISV1	Missense_Mutation	SNP	ENST00000404377.3	hg19	CCDS1305.2	.	.	.	.	.	.	.	.	.	.	G	15.92	2.976194	0.53720	.	.	ENSG00000120337	ENST00000404377;ENST00000239468	.	.	.	5.66	1.98	0.26296	Tumour necrosis factor-like (2);	0.734354	0.12572	N	0.457166	T	0.10337	0.0253	L	0.27053	0.805	0.09310	N	1	B	0.15719	0.014	B	0.10450	0.005	T	0.22452	-1.0216	9	0.41790	T	0.15	-2.1274	3.2248	0.06728	0.2377:0.0:0.5088:0.2535	.	193	Q9UNG2	TNF18_HUMAN	V	193;171	.	ENSP00000239468:A171V	A	-	2	0	TNFSF18	171277152	0.009000	0.17119	0.001000	0.08648	0.759000	0.43091	0.990000	0.29642	0.698000	0.31739	0.655000	0.94253	GCA	.	.		0.413	TNFSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084268.2	NM_005092		A	173010529	G	A	173010529	3	1	22	1	0	0	0	0	1	0	0	0	16324	1319	46	3	25	3	TNFSF18	1	173010529	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	14620156	173010529	76240092	13	1951										
TRIM11	81559	hgsc.bcm.edu	37	chr1	228588704	228588704	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ggcagctggcagcggccctcGagctcggcgatgagctcagc	16	14	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:228588704G>A	ENST00000284551.6	-	3	974	c.696C>T	c.(694-696)ctC>ctT	p.L232L	TRIM11_ENST00000460651.1_5'UTR|TRIM11_ENST00000366699.3_Silent_p.L232L|TRIM11_ENST00000493030.2_Silent_p.L107L	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	232					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of neurogenesis (GO:0050768)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of viral entry into host cell (GO:0046598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	18		Prostate(94;0.0724)				AGCGGCCCTCGAGCTCGGCGA	0.726																																					p.L232L		Atlas-SNP	.											.	TRIM11	38	.	0			c.C696T						.						8	10	9					1																	228588704		2161	4243	6404	SO:0001819	synonymous_variant	81559	exon3			GCCCTCGAGCTCG	AF220125	CCDS31048.1	1q42.13	2013-01-09	2011-01-25		ENSG00000154370	ENSG00000154370		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16281	protein-coding gene	gene with protein product		607868	"tripartite motif-containing 11"			11331580	Standard	NM_145214		Approved	RNF92, BIA1	uc001hss.3	Q96F44	OTTHUMG00000039773	ENST00000284551.6:c.696C>T	chr1.hg19:g.228588704G>A		80.0	0.0		82.0	45.0	NM_145214	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Silent	SNP	ENST00000284551.6	hg19	CCDS31048.1																																																																																			.	.		0.726	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095995.3	NM_145214		A	228588704	G	A	228588704	2	1	22	1	0	0	0	0	0	0	0	1	16502	1045	37	1		1	TRIM11	1	228588704	Silent	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	55578175	228588704	20661917	14	1952										
WDR64	128025	hgsc.bcm.edu	37	chr1	241920625	241920625	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cctcatggtgatctgggagcTgcctgatgttgtgcctttcc	12	11	2	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:241920625T>C	ENST00000366552.2	+	14	1988	c.1781T>C	c.(1780-1782)cTg>cCg	p.L594P	WDR64_ENST00000437684.2_Missense_Mutation_p.L594P	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	594										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			ATCTGGGAGCTGCCTGATGTT	0.408																																					p.L594P		Atlas-SNP	.											.	WDR64	234	.	0			c.T1781C						.						127	107	114					1																	241920625		2203	4300	6503	SO:0001583	missense	128025	exon14			GGGAGCTGCCTGA	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1781T>C	chr1.hg19:g.241920625T>C	ENSP00000355510:p.Leu594Pro	93.0	0.0		107.0	71.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.52|12.52	1.963589|1.963589	0.34659|0.34659	.|.	.|.	ENSG00000162843|ENSG00000162843	ENST00000425826|ENST00000366552;ENST00000437684;ENST00000414635	.|T;T;T	.|0.61627	.|0.09;0.09;0.09	5.54|5.54	5.54|5.54	0.83059|0.83059	.|WD40 repeat-like-containing domain (1);	.|0.000000	.|0.43579	.|D	.|0.000554	T|T	0.72374|0.72374	0.3452|0.3452	M|M	0.68952|0.68952	2.095|2.095	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.85130	.|0.991;0.997	T|T	0.71255|0.71255	-0.4647|-0.4647	5|10	.|0.33940	.|T	.|0.23	-8.8387|-8.8387	13.205|13.205	0.59790|0.59790	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|594;314	.|B1ANS9;D1MPS4	.|WDR64_HUMAN;.	R|P	73|594;594;365	.|ENSP00000355510:L594P;ENSP00000402446:L594P;ENSP00000406656:L365P	.|ENSP00000355510:L594P	C|L	+|+	1|2	0|0	WDR64|WDR64	239987248|239987248	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.030000|0.030000	0.12068|0.12068	4.049000|4.049000	0.57397|0.57397	2.099000|2.099000	0.63709|0.63709	0.528000|0.528000	0.53228|0.53228	TGC|CTG	.	.		0.408	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		C	241920625	T	C	241920625	3	2	22	1	0	0	0	0	1	0	0	0	17330	1580	55	2	1835	2	WDR64	1	241920625	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	13331921	241920625	7329996	15	1953										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247593020	247593020	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ggatgagagtgttgtgtgaaAcgctccagcatcctggctgt	14	8	0	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr1:247593020A>G	ENST00000336119.3	+	4	3036	c.2290A>G	c.(2290-2292)Acg>Gcg	p.T764A	NLRP3_ENST00000366496.2_Missense_Mutation_p.T764A|NLRP3_ENST00000348069.2_Intron|NLRP3_ENST00000391827.2_Intron|NLRP3_ENST00000366497.2_Missense_Mutation_p.T764A|NLRP3_ENST00000391828.3_Missense_Mutation_p.T764A	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	764					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			GTTGTGTGAAACGCTCCAGCA	0.512																																					p.T764A		Atlas-SNP	.											.	NLRP3	286	.	0			c.A2290G						.						99	92	94					1																	247593020		2203	4300	6503	SO:0001583	missense	114548	exon4			TGTGAAACGCTCC	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.2290A>G	chr1.hg19:g.247593020A>G	ENSP00000337383:p.Thr764Ala	96.0	0.0		146.0	56.0	NM_004895	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	A	0.018	-1.470333	0.01044	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000366496	D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31	4.21	-2.3	0.06785	.	0.886354	0.09463	N	0.798745	T	0.65407	0.2688	N	0.02765	-0.5	0.09310	N	1	B;B;B	0.15473	0.0;0.013;0.0	B;B;B	0.23018	0.0;0.043;0.002	T	0.56715	-0.7933	10	0.02654	T	1	.	9.6047	0.39626	0.3475:0.0:0.6525:0.0	.	764;764;764	B7ZKS9;Q96P20-5;Q96P20	.;.;NALP3_HUMAN	A	764	ENSP00000375704:T764A;ENSP00000355453:T764A;ENSP00000337383:T764A;ENSP00000355452:T764A	ENSP00000337383:T764A	T	+	1	0	NLRP3	245659643	0.008000	0.16893	0.000000	0.03702	0.074000	0.17049	1.550000	0.36223	-0.277000	0.09193	-0.403000	0.06358	ACG	.	.		0.512	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		G	247593020	A	G	247593020	3	3	22	1	0	0	0	0	1	0	0	0	10487	43	2	2	2304	2	NLRP3	1	247593020	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	5672395	247593020	1657601	16	1954										
REG1A	5967	hgsc.bcm.edu	37	chr2	79349980	79349980	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	catctagaaccgccgctggcActggagcagtgggtccctgg	14	13	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:79349980A>G	ENST00000233735.1	+	5	438	c.335A>G	c.(334-336)cAc>cGc	p.H112R		NM_002909.4	NP_002900.2	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha	112	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|growth factor activity (GO:0008083)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(26)|prostate(1)|upper_aerodigestive_tract(1)	39						CGCCGCTGGCACTGGAGCAGT	0.557																																					p.H112R		Atlas-SNP	.											.	REG1A	74	.	0			c.A335G						.						112	111	111					2																	79349980		2203	4300	6503	SO:0001583	missense	5967	exon5			GCTGGCACTGGAG		CCDS1964.1	2p12	2008-09-04	2008-06-04		ENSG00000115386	ENSG00000115386			9951	protein-coding gene	gene with protein product	"pancreatic stone protein", "pancreatic thread protein"	167770	"regenerating islet-derived 1 alpha (pancreatic stone protein, pancreatic thread protein)"	REG		2332435, 8333731	Standard	NM_002909		Approved	PSP, PTP, PSPS, PSPS1	uc002snz.3	P05451	OTTHUMG00000130016	ENST00000233735.1:c.335A>G	chr2.hg19:g.79349980A>G	ENSP00000233735:p.His112Arg	133.0	0.0		98.0	19.0	NM_002909	P11379|Q4ZG28	Missense_Mutation	SNP	ENST00000233735.1	hg19	CCDS1964.1	.	.	.	.	.	.	.	.	.	.	a	9.271	1.045592	0.19748	.	.	ENSG00000115386	ENST00000233735	T	0.07114	3.22	2.92	0.459	0.16678	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.580363	0.14402	N	0.321842	T	0.07548	0.0190	N	0.13235	0.315	0.23309	N	0.997936	D	0.71674	0.998	P	0.61477	0.889	T	0.21895	-1.0232	10	0.08179	T	0.78	.	4.3454	0.11131	0.596:0.0:0.404:0.0	.	112	P05451	REG1A_HUMAN	R	112	ENSP00000233735:H112R	ENSP00000233735:H112R	H	+	2	0	REG1A	79203488	0.159000	0.22864	0.988000	0.46212	0.900000	0.52787	0.088000	0.14979	0.325000	0.23359	0.455000	0.32223	CAC	.	.		0.557	REG1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252289.1	NM_002909		G	79349980	A	G	79349980	3	3	22	1	0	0	0	0	1	0	0	0	13225	159	6	2	349	2	REG1A	2	79349980	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10		79349980	163849393	17	1955										
SFTPB	6439	hgsc.bcm.edu	37	chr2	85888601	85888602	+	Missense_Mutation	DNP	GG	GG	AT													0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	acagctgagttctcatcaaaGgtcggggctgtggatacact							TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:85888601_85888602GG>AT	ENST00000519937.2	-	10	1159_1160	c.1140_1141CC>AT	c.(1138-1143)gaCCtt>gaATtt	p.380_381DL>EF	SFTPB_ENST00000342375.3_Missense_Mutation_p.380_381DL>EF|SFTPB_ENST00000393822.3_Missense_Mutation_p.392_393DL>EF|SFTPB_ENST00000409383.1_Missense_Mutation_p.392_393DL>EF			P07988	PSPB_HUMAN	surfactant protein B	380					organ morphogenesis (GO:0009887)|respiratory gaseous exchange (GO:0007585)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)	16						TCTCATCAAAGGTCGGGGCTGT	0.653																																					p.L393F|p.D392E		Atlas-SNP	.											.	SFTPB	49	.	0			c.C1177T|c.C1176A						.																																			SO:0001583	missense	6439	exon11			ATCAAAGGTCGGG|TCAAAGGTCGGGG	J02761	CCDS1983.1, CCDS1983.2	2p12-p11.2	2008-08-26	2008-08-26		ENSG00000168878	ENSG00000168878			10801	protein-coding gene	gene with protein product		178640	"surfactant, pulmonary-associated protein B"	SFTP3		2924687, 1346779	Standard	NM_198843		Approved	SP-B	uc002sqh.3	P07988	OTTHUMG00000130181	ENST00000519937.2:c.1140_1141delinsAT	chr2.hg19:g.85888601_85888602delinsAT	ENSP00000428719:p.D380_L381delinsEF	46.0	0.0		38.0	7.0	NM_198843	Q96R04	Missense_Mutation	SNP	ENST00000519937.2	hg19																																																																																				.	.		0.653	SFTPB-001	KNOWN	alternative_3_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252499.3	NM_198843		AT	85888602	GG	AT	85888601	3	1	22	1	0	0	0	0	1	0	0	0	14206	1000	35	3	8	3	SFTPB	2	85888601	Missense_Mutation	DNP	GG	TCGA-3K-AAZ8-01A-12D-A38X-10	6538621	85888601	157310772	18	1956										
ZAP70	7535	hgsc.bcm.edu	37	chr2	98349640	98349640	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gctcatctactgcctgaaggAggcctgccccaacagcagtg	11	14	2	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:98349640A>T	ENST00000264972.5	+	6	970	c.755A>T	c.(754-756)gAg>gTg	p.E252V	ZAP70_ENST00000451498.2_5'Flank|ZAP70_ENST00000463643.1_3'UTR|ZAP70_ENST00000442208.1_Missense_Mutation_p.E126V	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	252	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						TGCCTGAAGGAGGCCTGCCCC	0.687																																					p.E252V		Atlas-SNP	.											.	ZAP70	77	.	0			c.A755T						.						36	37	37					2																	98349640		2203	4299	6502	SO:0001583	missense	7535	exon6			TGAAGGAGGCCTG	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"SH2 domain containing"	12858	protein-coding gene	gene with protein product		176947	"zeta-chain (TCR) associated protein kinase (70 kD)"	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.755A>T	chr2.hg19:g.98349640A>T	ENSP00000264972:p.Glu252Val	165.0	0.0		133.0	65.0	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Missense_Mutation	SNP	ENST00000264972.5	hg19	CCDS33254.1	.	.	.	.	.	.	.	.	.	.	A	18.40	3.615729	0.66672	.	.	ENSG00000115085	ENST00000264972;ENST00000442208	D;D	0.92299	-3.01;-3.01	5.41	4.24	0.50183	SH2 motif (2);	0.123452	0.35646	N	0.003079	D	0.91264	0.7246	L	0.39020	1.185	0.58432	D	0.999999	D;P	0.56287	0.975;0.913	P;P	0.61328	0.887;0.592	D	0.87103	0.2180	10	0.13853	T	0.58	.	10.3545	0.43956	0.8531:0.0:0.0:0.1469	.	126;252	P43403-3;P43403	.;ZAP70_HUMAN	V	252;126	ENSP00000264972:E252V;ENSP00000411141:E126V	ENSP00000264972:E252V	E	+	2	0	ZAP70	97716072	1.000000	0.71417	0.996000	0.52242	0.701000	0.40568	8.605000	0.90883	0.970000	0.38263	0.533000	0.62120	GAG	.	.		0.687	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1			T	98349640	A	T	98349640	3	4	22	1	0	0	0	0	1	0	0	0	17529	304	11	4	769	4	ZAP70	2	98349640	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	12461039	98349640	144849733	19	1957										
TSN	7247	hgsc.bcm.edu	37	chr2	122522838	122522838	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aatgactccctgaggaagcgCtacgacggattgaaatatga	11	8	0	4			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:122522838C>T	ENST00000389682.3	+	6	829	c.582C>T	c.(580-582)cgC>cgT	p.R194R	TSN_ENST00000536142.1_3'UTR|TSN_ENST00000498545.1_3'UTR|TSN_ENST00000409193.1_Silent_p.R189R	NM_001261401.1|NM_004622.2	NP_001248330.1|NP_004613.1	Q15631	TSN_HUMAN	translin	194	Leucine-zipper. {ECO:0000255}.				DNA recombination (GO:0006310)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|mRNA binding (GO:0003729)|sequence-specific DNA binding (GO:0043565)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)|skin(1)	12		Ovarian(717;0.0563)|Prostate(154;0.116)				TGAGGAAGCGCTACGACGGAT	0.493																																					p.R194R		Atlas-SNP	.											.	TSN	31	.	0			c.C582T						.						173	174	174					2																	122522838		2203	4300	6503	SO:0001819	synonymous_variant	7247	exon6			GAAGCGCTACGAC	X78627	CCDS33284.1, CCDS58723.1	2q21.1	2008-05-23			ENSG00000211460	ENSG00000211460			12379	protein-coding gene	gene with protein product	"recombination hotspot associated factor"	600575				7947454, 9244443	Standard	NM_004622		Approved	TRSLN, BCLF-1, REHF-1	uc002tnl.3	Q15631	OTTHUMG00000153334	ENST00000389682.3:c.582C>T	chr2.hg19:g.122522838C>T		108.0	0.0		82.0	38.0	NM_004622	B7Z3X8|Q5U0K7	Silent	SNP	ENST00000389682.3	hg19	CCDS33284.1																																																																																			.	.		0.493	TSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330767.1	NM_004622		T	122522838	C	T	122522838	2	4	22	1	0	0	0	0	0	0	0	1	16644	784	28	3		3	TSN	2	122522838	Silent	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	24173198	122522838	120676535	20	1958										
METTL5	29081	hgsc.bcm.edu	37	chr2	170672031	170672031	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tccattctgcagctttctttTgaacatgctgaacataaata	5	9	2	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:170672031T>C	ENST00000260953.5	-	5	813	c.497A>G	c.(496-498)cAa>cGa	p.Q166R	METTL5_ENST00000409965.1_Missense_Mutation_p.Q166R|METTL5_ENST00000409837.1_Missense_Mutation_p.Q166R|METTL5_ENST00000308099.3_Intron|METTL5_ENST00000392640.2_Missense_Mutation_p.Q166R|METTL5_ENST00000409340.1_Missense_Mutation_p.Q67R|U3_ENST00000517172.1_RNA|METTL5_ENST00000410097.1_Missense_Mutation_p.Q166R	NM_014168.2	NP_054887.2	Q9NRN9	METL5_HUMAN	methyltransferase like 5	166							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|large_intestine(5)|lung(1)|prostate(1)	10						AGCTTTCTTTTGAACATGCTG	0.299																																					p.Q166R		Atlas-SNP	.											.	METTL5	24	.	0			c.A497G						.						95	89	91					2																	170672031		2202	4300	6502	SO:0001583	missense	29081	exon5			TTCTTTTGAACAT	AF201938	CCDS33320.1	2q31.1	2011-01-28			ENSG00000138382	ENSG00000138382			25006	protein-coding gene	gene with protein product						11042152	Standard	XM_005246478		Approved	HSPC133	uc002ufn.3	Q9NRN9	OTTHUMG00000154117	ENST00000260953.5:c.497A>G	chr2.hg19:g.170672031T>C	ENSP00000260953:p.Gln166Arg	101.0	0.0		67.0	12.0	NM_014168	D3DPC9|Q9NVX1	Missense_Mutation	SNP	ENST00000260953.5	hg19	CCDS33320.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.862|7.862	0.726351|0.726351	0.15439|0.15439	.|.	.|.	ENSG00000138382|ENSG00000138382	ENST00000442181|ENST00000409837;ENST00000409340;ENST00000260953;ENST00000409965;ENST00000392640;ENST00000410097	.|T;T;T;T	.|0.41400	.|1.01;1.0;1.0;1.0	5.42|5.42	4.24|4.24	0.50183|0.50183	.|.	.|0.226290	.|0.46442	.|D	.|0.000291	T|T	0.28101|0.28101	0.0693|0.0693	N|N	0.26130|0.26130	0.795|0.795	0.52501|0.52501	D|D	0.999959|0.999959	.|B;B	.|0.09022	.|0.002;0.001	.|B;B	.|0.15052	.|0.012;0.005	T|T	0.05338|0.05338	-1.0891|-1.0891	5|10	.|0.15499	.|T	.|0.54	-15.4463|-15.4463	11.4073|11.4073	0.49904|0.49904	0.1448:0.0:0.0:0.8552|0.1448:0.0:0.0:0.8552	.|.	.|166;166	.|B8ZZC8;Q9NRN9	.|.;METL5_HUMAN	E|R	77|166;67;166;166;166;166	.|ENSP00000387106:Q67R;ENSP00000260953:Q166R;ENSP00000386582:Q166R;ENSP00000376415:Q166R	.|ENSP00000260953:Q166R	K|Q	-|-	1|2	0|0	METTL5|METTL5	170380277|170380277	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.753000|0.753000	0.42808|0.42808	2.987000|2.987000	0.49378|0.49378	0.957000|0.957000	0.37930|0.37930	-0.527000|-0.527000	0.04329|0.04329	AAA|CAA	.	.		0.299	METTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333957.1	NM_014168		C	170672031	T	C	170672031	3	2	22	1	0	0	0	0	1	0	0	0	9512	1812	63	2	144	2	METTL5	2	170672031	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	48149193	170672031	72527342	21	1959										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171239700	171239700	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	taagcatatactctccacagGtaagggatgttttaagagca	9	7	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:171239700G>A	ENST00000408978.4	+	11	1328		c.e11+1		MYO3B_ENST00000602629.1_Splice_Site|MYO3B_ENST00000409044.3_Splice_Site|MYO3B_ENST00000334231.6_Splice_Site	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB						peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						CTCTCCACAGGTAAGGGATGT	0.358																																					.		Atlas-SNP	.											.	MYO3B	320	.	0			c.1185+1G>A						.						117	109	112					2																	171239700		1813	4082	5895	SO:0001630	splice_region_variant	140469	exon11			CCACAGGTAAGGG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1185+1G>A	chr2.hg19:g.171239700G>A		95.0	0.0		81.0	7.0	NM_138995	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Splice_Site	SNP	ENST00000408978.4	hg19	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	G	31	5.078752	0.94050	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2191	0.98319	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MYO3B	170947946	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.585000	0.98223	2.780000	0.95670	0.655000	0.94253	.	.	.		0.358	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		Intron	A	171239700	G	A	171239700	5	1	22	1	0	0	0	0	0	0	1	0	10086	1275	44	3	1228	3	MYO3B	2	171239700	Splice_Site	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	567669	171239700	71959673	22	1960										
TTN	7273	hgsc.bcm.edu	37	chr2	179424990	179424990	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gcattttctgcataaacacgAtattcatattcacatccttc	3	11	3	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:179424990A>G	ENST00000591111.1	-	276	81170	c.80946T>C	c.(80944-80946)taT>taC	p.Y26982Y	TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Silent_p.Y28623Y|TTN_ENST00000342992.6_Silent_p.Y26055Y|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.Y19750Y|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Silent_p.Y19683Y|TTN_ENST00000460472.2_Silent_p.Y19558Y|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26982	Fibronectin type-III 96. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATAAACACGATATTCATATT	0.418																																					p.Y28623Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T85869C						.						105	104	104					2																	179424990		1920	4129	6049	SO:0001819	synonymous_variant	7273	exon326			AACACGATATTCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.80946T>C	chr2.hg19:g.179424990A>G		157.0	0.0		103.0	53.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179424990	A	G	179424990	2	3	22	1	0	0	0	0	0	0	0	1	16750	340	12	2		2	TTN	2	179424990	Silent	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	8185290	179424990	63774383	23	1961										
TTN	7273	hgsc.bcm.edu	37	chr2	179489281	179489281	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gggtacagtcatgtataacaAgttttctgaccctgccatca	8	10	3	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:179489281A>T	ENST00000591111.1	-	192	40027	c.39803T>A	c.(39802-39804)cTt>cAt	p.L13268H	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L14909H|TTN_ENST00000342992.6_Missense_Mutation_p.L12341H|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L6036H|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L5969H|TTN_ENST00000460472.2_Missense_Mutation_p.L5844H			Q8WZ42	TITIN_HUMAN	titin	13268	Ig-like 88.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGTATAACAAGTTTTCTGAC	0.383																																					p.L14909H		Atlas-SNP	.											.	TTN	18412	.	0			c.T44726A						.						122	120	121					2																	179489281		1891	4095	5986	SO:0001583	missense	7273	exon242			ATAACAAGTTTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.39803T>A	chr2.hg19:g.179489281A>T	ENSP00000465570:p.Leu13268His	209.0	0.0		167.0	16.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.51	2.854982	0.51376	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.25250	1.81;1.81;1.81;1.81	6.06	6.06	0.98353	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.70824	0.3268	H	0.99325	4.515	0.58432	D	0.999997	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.84217	0.0459	9	0.87932	D	0	.	16.6245	0.84952	1.0:0.0:0.0:0.0	.	5844;5969;6036;13268	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	12341;5844;6036;5969;5844	ENSP00000343764:L12341H;ENSP00000434586:L5844H;ENSP00000340554:L6036H;ENSP00000352154:L5969H	ENSP00000340554:L6036H	L	-	2	0	TTN	179197526	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.281000	0.95811	2.323000	0.78572	0.528000	0.53228	CTT	.	.		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179489281	A	T	179489281	3	4	22	1	0	0	0	0	1	0	0	0	16750	72	3	4	63451	4	TTN	2	179489281	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	64291	179489281	63710092	24	1962										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198267481	198267481	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aaaagctctagctgttgtgtTacggacatactcatccatgt	8	9	2	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:198267481T>G	ENST00000335508.6	-	14	1967	c.1876A>C	c.(1876-1878)Aac>Cac	p.N626H	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	626					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.N626Y(2)|p.N626D(1)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GCTGTTGTGTTACGGACATAC	0.438			Mis		myelodysplastic syndrome																																p.N626H		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	SF3B1,NS,carcinoma,0,10	SF3B1	1038	.	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.A1876C						.						96	93	94					2																	198267481		2203	4300	6503	SO:0001583	missense	23451	exon14			TTGTGTTACGGAC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1876A>C	chr2.hg19:g.198267481T>G	ENSP00000335321:p.Asn626His	102.0	0.0		118.0	13.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.711895	0.89112	.	.	ENSG00000115524	ENST00000335508	T	0.65732	-0.17	5.82	5.82	0.92795	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85894	0.5803	H	0.96015	3.755	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90396	0.4399	10	0.87932	D	0	.	16.1839	0.81934	0.0:0.0:0.0:1.0	.	626	O75533	SF3B1_HUMAN	H	626	ENSP00000335321:N626H	ENSP00000335321:N626H	N	-	1	0	SF3B1	197975726	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.948000	0.87774	2.222000	0.72286	0.533000	0.62120	AAC	.	.		0.438	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			G	198267481	T	G	198267481	3	3	22	1	0	0	0	0	1	0	0	0	14164	1754	61	5	2086	5	SF3B1	2	198267481	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	18778200	198267481	44931892	25	1963										
CCDC108	255101	hgsc.bcm.edu	37	chr2	219875570	219875570	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gtgagaagatccacaagaccCgggcagtgctgcctggctgg	15	11	0	3	rs564721573		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:219875570C>T	ENST00000341552.5	-	25	4189	c.4106G>A	c.(4105-4107)cGg>cAg	p.R1369Q	AC097468.4_ENST00000441450.1_RNA|CCDC108_ENST00000441968.1_Missense_Mutation_p.R1369Q|CCDC108_ENST00000453220.1_Missense_Mutation_p.R1369Q	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	1369						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCACAAGACCCGGGCAGTGCT	0.567													C|||	1	0.000199681	0	0	5008	,	,		21069	0		0	False		,,,				2504	0.001				p.R1369Q		Atlas-SNP	.											.	CCDC108	208	.	0			c.G4106A						.						56	50	52					2																	219875570		2203	4300	6503	SO:0001583	missense	255101	exon25			AAGACCCGGGCAG	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.4106G>A	chr2.hg19:g.219875570C>T	ENSP00000340776:p.Arg1369Gln	150.0	0.0		86.0	44.0	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	hg19	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	C	5.170	0.216994	0.09810	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.04502	3.61;3.61;3.61	5.44	-5.48	0.02592	.	1.050440	0.07548	N	0.914865	T	0.01800	0.0057	N	0.05124	-0.11	0.09310	N	1	B	0.14805	0.011	B	0.11329	0.006	T	0.47837	-0.9086	10	0.09843	T	0.71	-3.1705	4.0874	0.09953	0.0975:0.307:0.0976:0.498	.	1369	Q6ZU64	CC108_HUMAN	Q	1369	ENSP00000340776:R1369Q;ENSP00000413377:R1369Q;ENSP00000409117:R1369Q	ENSP00000340776:R1369Q	R	-	2	0	CCDC108	219583814	0.000000	0.05858	0.000000	0.03702	0.259000	0.26198	-1.017000	0.03630	-1.139000	0.02881	0.650000	0.86243	CGG	.	.		0.567	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		T	219875570	C	T	219875570	3	4	22	1	0	0	0	0	1	0	0	0	2745	652	23	1	1715	1	CCDC108	2	219875570	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	21608089	219875570	23323803	26	1964										
SCG2	7857	hgsc.bcm.edu	37	chr2	224462660	224462660	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ggaaaatacgacgttttctgAtttgctgcactctccatccc	7	12	2	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr2:224462660A>G	ENST00000305409.2	-	2	1573	c.1341T>C	c.(1339-1341)aaT>aaC	p.N447N		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		ACGTTTTCTGATTTGCTGCAC	0.478																																					p.N447N		Atlas-SNP	.											.	SCG2	99	.	0			c.T1341C						.						102	103	102					2																	224462660		2203	4300	6503	SO:0001819	synonymous_variant	7857	exon2			TTTCTGATTTGCT	M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"secretoneurin", "chromogranin C"	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.1341T>C	chr2.hg19:g.224462660A>G		55.0	0.0		45.0	23.0	NM_003469	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Silent	SNP	ENST00000305409.2	hg19	CCDS2457.1																																																																																			.	.		0.478	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		G	224462660	A	G	224462660	2	3	22	1	0	0	0	0	0	0	0	1	13906	330	12	2		2	SCG2	2	224462660	Silent	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	4587090	224462660	18736713	27	1965										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19384192	19384192	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aaagaagagaaaagaacaaaTtgaaaataaataacgtaggt	8	2	0	4	rs150723210		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr3:19384192T>C	ENST00000328405.2	+	4	822	c.556T>C	c.(556-558)Ttg>Ctg	p.L186L		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	186					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						AAAGAACAAATTGAAAATAAA	0.458																																					p.L186L	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.T556C						.	T		1,4405	2.1+/-5.4	0,1,2202	78	81	80		556	-0.7	1	3	dbSNP_134	80	0,8600		0,0,4300	no	coding-synonymous	KCNH8	NM_144633.2		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		186/1108	19384192	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	131096	exon4			AACAAATTGAAAA	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.556T>C	chr3.hg19:g.19384192T>C		178.0	0.0		146.0	39.0	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	hg19	CCDS2632.1																																																																																			.	T|1.000;C|0.000		0.458	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		C	19384192	T	C	19384192	2	2	22	1	0	0	0	0	0	0	0	1	8047	1490	52	2		2	KCNH8	3	19384192	Silent	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10		19384192	178638238	28	1966										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266137	41266137	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tgccactaccacagctccttCtctgagtggtaaaggcaatc	8	13	1	1	rs121913409		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr3:41266137C>T	ENST00000349496.5	+	3	414	c.134C>T	c.(133-135)tCt>tTt	p.S45F	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45F(384)|p.S45del(53)|p.A5_A80del(53)|p.S45C(19)|p.S45Y(17)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.S45fs*2(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACAGCTCCTTCTCTGAGTGGT	0.498	S45F(HCC15_LUNG)|S45F(LS180_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+1,2	CTNNB1	4904	.	601	Substitution - Missense(421)|Deletion - In frame(152)|Complex - deletion inframe(20)|Unknown(7)|Deletion - Frameshift(1)	soft_tissue(233)|liver(141)|large_intestine(85)|kidney(74)|endometrium(16)|skin(11)|adrenal_gland(9)|stomach(7)|biliary_tract(5)|ovary(4)|lung(3)|central_nervous_system(2)|cervix(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(1)|pituitary(1)|prostate(1)|bone(1)|pancreas(1)	c.C134T						.						84	74	77					3																	41266137		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTCCTTCTCTGAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.134C>T	chr3.hg19:g.41266137C>T	ENSP00000344456:p.Ser45Phe	135.0	0.0		121.0	60.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569754	0.86439	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.68165	0.2971	M	0.65677	2.01	0.80722	D	1	D	0.67145	0.996	D	0.64687	0.928	T	0.68895	-0.5288	10	0.87932	D	0	-13.6823	20.2983	0.98569	0.0:1.0:0.0:0.0	.	45	P35222	CTNB1_HUMAN	F	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38F;ENSP00000385604:S45F;ENSP00000412219:S45F;ENSP00000379486:S45F;ENSP00000344456:S45F;ENSP00000411226:S38F;ENSP00000379488:S45F;ENSP00000409302:S45F;ENSP00000401599:S45F	ENSP00000344456:S45F	S	+	2	0	CTNNB1	41241141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266137	C	T	41266137	3	4	22	1	0	0	0	0	1	0	0	0	4018	913	32	3	140	3	CTNNB1	3	41266137	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	21881945	41266137	156756293	29	1967										
KIF15	56992	hgsc.bcm.edu	37	chr3	44841897	44841897	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	actggcggagcttgcttcagGacagacaccaccagaaagct	11	12	1	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr3:44841897G>T	ENST00000326047.4	+	11	1339	c.1190G>T	c.(1189-1191)gGa>gTa	p.G397V	KIF15_ENST00000425755.1_Missense_Mutation_p.G32V	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	397					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		CTTGCTTCAGGACAGACACCA	0.483																																					p.G397V		Atlas-SNP	.											.	KIF15	103	.	0			c.G1190T						.						93	85	88					3																	44841897		2203	4300	6503	SO:0001583	missense	56992	exon11			CTTCAGGACAGAC	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.1190G>T	chr3.hg19:g.44841897G>T	ENSP00000324020:p.Gly397Val	385.0	0.0		311.0	80.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	hg19	CCDS33744.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.250989	0.39797	.	.	ENSG00000163808	ENST00000326047;ENST00000481166;ENST00000396031;ENST00000425755	T;D;T	0.81659	-0.64;-1.52;1.83	5.35	5.35	0.76521	.	0.150342	0.31257	N	0.007968	T	0.76321	0.3971	L	0.50333	1.59	0.54753	D	0.999989	B;B	0.28880	0.226;0.039	B;B	0.26614	0.071;0.011	T	0.75651	-0.3244	10	0.56958	D	0.05	.	14.995	0.71425	0.0:0.0:0.857:0.143	.	32;397	C9JKA9;Q9NS87	.;KIF15_HUMAN	V	397;169;396;32	ENSP00000324020:G397V;ENSP00000425499:G169V;ENSP00000389982:G32V	ENSP00000324020:G397V	G	+	2	0	KIF15	44816901	1.000000	0.71417	0.368000	0.25939	0.039000	0.13416	3.137000	0.50562	2.659000	0.90383	0.655000	0.94253	GGA	.	.		0.483	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			T	44841897	G	T	44841897	3	4	22	1	0	0	0	0	1	0	0	0	8286	1174	41	3	1232	3	KIF15	3	44841897	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	3575760	44841897	153180533	30	1968										
SEMA3F	6405	hgsc.bcm.edu	37	chr3	50225206	50225206	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cgtgcactgcagctcagcgaTcgtggcctctactcctgcac	10	16	2	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr3:50225206T>C	ENST00000002829.3	+	19	2500	c.2016T>C	c.(2014-2016)gaT>gaC	p.D672D	SEMA3F_ENST00000413852.1_Silent_p.D573D|SEMA3F_ENST00000434342.1_Silent_p.D641D	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	672	Ig-like C2-type.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		AGCTCAGCGATCGTGGCCTCT	0.617																																					p.D672D		Atlas-SNP	.											.	SEMA3F	62	.	0			c.T2016C						.						64	50	55					3																	50225206		2203	4300	6503	SO:0001819	synonymous_variant	6405	exon19			CAGCGATCGTGGC	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10728	protein-coding gene	gene with protein product	"sema IV"	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.2016T>C	chr3.hg19:g.50225206T>C		76.0	0.0		69.0	37.0	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Silent	SNP	ENST00000002829.3	hg19	CCDS2811.1																																																																																			.	.		0.617	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186		C	50225206	T	C	50225206	2	2	22	1	0	0	0	0	0	0	0	1	14044	1432	50	2		2	SEMA3F	3	50225206	Silent	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	5383309	50225206	147797224	31	1969										
GRM2	2912	hgsc.bcm.edu	37	chr3	51749599	51749599	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tggtcaaggcctcaggtcggGagctctgctacatcctgctg	13	12	3	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr3:51749599G>T	ENST00000395052.3	+	4	2044	c.1810G>T	c.(1810-1812)Gag>Tag	p.E604*	GRM2_ENST00000475478.1_3'UTR|GRM2_ENST00000442933.2_Intron	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	604					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CTCAGGTCGGGAGCTCTGCTA	0.587																																					p.E604X		Atlas-SNP	.											.	GRM2	91	.	0			c.G1810T						.						125	115	118					3																	51749599		2203	4300	6503	SO:0001587	stop_gained	2912	exon4			GGTCGGGAGCTCT	L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.1810G>T	chr3.hg19:g.51749599G>T	ENSP00000378492:p.Glu604*	45.0	0.0		51.0	13.0	NM_000839	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Nonsense_Mutation	SNP	ENST00000395052.3	hg19	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	G	39	7.671535	0.98425	.	.	ENSG00000164082	ENST00000395052	.	.	.	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.3413	0.94342	0.0:0.0:1.0:0.0	.	.	.	.	X	604	.	ENSP00000378492:E604X	E	+	1	0	GRM2	51724639	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.855000	0.99526	2.664000	0.90586	0.561000	0.74099	GAG	.	.		0.587	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			T	51749599	G	T	51749599	4	4	22	1	0	0	0	0	0	1	0	0	6806	1175	41	3	1820	3	GRM2	3	51749599	Nonsense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	1524393	51749599	146272831	32	1970										
OR5H2	79310	hgsc.bcm.edu	37	chr3	98001887	98001887	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tggaaccttggtctgattgcTcttatctggaatgacccaca	9	10	3	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr3:98001887T>C	ENST00000355273.2	+	1	156	c.156T>C	c.(154-156)gcT>gcC	p.A52A	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						GTCTGATTGCTCTTATCTGGA	0.428																																					p.A52A		Atlas-SNP	.											.	OR5H2	63	.	0			c.T156C						.						353	327	336					3																	98001887		2203	4300	6503	SO:0001819	synonymous_variant	79310	exon1			GATTGCTCTTATC		CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"GPCR / Class A : Olfactory receptors"	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.156T>C	chr3.hg19:g.98001887T>C		124.0	0.0		103.0	49.0	NM_001005482	Q6IF87	Silent	SNP	ENST00000355273.2	hg19	CCDS33801.1																																																																																			.	.		0.428	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2			C	98001887	T	C	98001887	2	2	22	1	0	0	0	0	0	0	0	1	11171	1538	54	2		2	OR5H2	3	98001887	Silent	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	46252288	98001887	100020543	33	1971										
OR5K4	403278	hgsc.bcm.edu	37	chr3	98072899	98072899	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tctttctgggcaacctggctCtgatggattcctgctgttcc	10	12	3	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr3:98072899C>T	ENST00000354924.2	+	1	202	c.202C>T	c.(202-204)Ctg>Ttg	p.L68L	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005517.1	NP_001005517.1	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K, member 4	68						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	21						CAACCTGGCTCTGATGGATTC	0.438																																					p.L68L		Atlas-SNP	.											.	OR5K4	75	.	0			c.C202T						.						296	294	295					3																	98072899		2203	4300	6503	SO:0001819	synonymous_variant	403278	exon1			CTGGCTCTGATGG		CCDS33802.1	3q11.2	2013-09-23			ENSG00000196098	ENSG00000196098		"GPCR / Class A : Olfactory receptors"	31291	protein-coding gene	gene with protein product							Standard	NM_001005517		Approved		uc011bgv.2	A6NMS3	OTTHUMG00000160081	ENST00000354924.2:c.202C>T	chr3.hg19:g.98072899C>T		108.0	0.0		61.0	18.0	NM_001005517		Silent	SNP	ENST00000354924.2	hg19	CCDS33802.1																																																																																			.	.		0.438	OR5K4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359114.1			T	98072899	C	T	98072899	2	4	22	1	0	0	0	0	0	0	0	1	11178	912	32	3		3	OR5K4	3	98072899	Silent	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	71012	98072899	99949531	34	1972										
GNB4	59345	hgsc.bcm.edu	37	chr3	179131380	179131380	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aatgtggtggtctgctgggcAgtttcgatgtcccataaagc	13	8	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr3:179131380A>C	ENST00000232564.3	-	8	805	c.519T>G	c.(517-519)acT>acG	p.T173T	GNB4_ENST00000468623.1_Silent_p.T173T|GNB4_ENST00000465153.1_5'UTR	NM_021629.3	NP_067642.1	Q9HAV0	GBB4_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 4	173					cell death (GO:0008219)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	16	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			TCTGCTGGGCAGTTTCGATGT	0.423																																					p.T173T	Melanoma(105;1405 1491 7265 20440 33721)	Atlas-SNP	.											.	GNB4	37	.	0			c.T519G						.						122	119	120					3																	179131380		2203	4300	6503	SO:0001819	synonymous_variant	59345	exon8			CTGGGCAGTTTCG	AF300648	CCDS3230.1	3q27.1	2013-01-10			ENSG00000114450	ENSG00000114450		"WD repeat domain containing"	20731	protein-coding gene	gene with protein product		610863				10644457, 11842130	Standard	NM_021629		Approved		uc003fjv.4	Q9HAV0	OTTHUMG00000157440	ENST00000232564.3:c.519T>G	chr3.hg19:g.179131380A>C		166.0	0.0		236.0	35.0	NM_021629	B3KMH5|D3DNR8	Silent	SNP	ENST00000232564.3	hg19	CCDS3230.1	.	.	.	.	.	.	.	.	.	.	A	9.962	1.223046	0.22457	.	.	ENSG00000114450	ENST00000466899	.	.	.	5.66	-5.14	0.02875	.	.	.	.	.	T	0.49047	0.1534	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47420	-0.9119	4	.	.	.	-18.4996	6.9939	0.24772	0.3626:0.3225:0.3149:0.0	.	.	.	.	G	96	.	.	C	-	1	0	GNB4	180614074	0.000000	0.05858	0.895000	0.35142	0.998000	0.95712	-2.069000	0.01381	-1.266000	0.02446	0.528000	0.53228	TGC	.	.		0.423	GNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258218.1	NM_021629		C	179131380	A	C	179131380	2	2	22	1	0	0	0	0	0	0	0	1	6528	175	7	5		5	GNB4	3	179131380	Silent	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	81058481	179131380	18891050	35	1973										
MASP1	5648	hgsc.bcm.edu	37	chr3	186978538	186978538	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gtaggctctacctcggcaggTcctgttgtctgtgtggagga	15	9	2	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr3:186978538T>C	ENST00000337774.5	-	4	927	c.538A>G	c.(538-540)Acc>Gcc	p.T180A	MASP1_ENST00000392472.2_Missense_Mutation_p.T67A|MASP1_ENST00000495249.1_Intron|MASP1_ENST00000169293.6_Missense_Mutation_p.T180A|MASP1_ENST00000392470.2_Missense_Mutation_p.T154A|MASP1_ENST00000296280.6_Missense_Mutation_p.T180A	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	180	EGF-like; calcium-binding.|Homodimerization. {ECO:0000250}.|Interaction with FCN2.|Interaction with MBL2.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		CCTCGGCAGGTCCTGTTGTCT	0.507																																					p.T180A		Atlas-SNP	.											.	MASP1	240	.	0			c.A538G						.						160	122	135					3																	186978538		2203	4300	6503	SO:0001583	missense	5648	exon4			GGCAGGTCCTGTT	D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"Serine peptidases / Serine peptidases"	6901	protein-coding gene	gene with protein product		600521	"mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.538A>G	chr3.hg19:g.186978538T>C	ENSP00000336792:p.Thr180Ala	115.0	0.0		133.0	37.0	NM_139125	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Missense_Mutation	SNP	ENST00000337774.5	hg19	CCDS33907.1	.	.	.	.	.	.	.	.	.	.	T	30	5.050255	0.93740	.	.	ENSG00000127241	ENST00000337774;ENST00000296280;ENST00000392472;ENST00000541896;ENST00000169293;ENST00000392470;ENST00000392475	D;D;D;D;D;D	0.97378	-2.94;-2.94;-2.94;-2.94;-2.94;-4.36	5.57	5.57	0.84162	EGF-like region, conserved site (1);EGF-like calcium-binding (2);	0.047224	0.85682	D	0.000000	D	0.98012	0.9345	M	0.71206	2.165	0.80722	D	1	D;D;D;D;D	0.76494	0.995;0.996;0.999;0.998;0.998	D;P;D;D;D	0.70227	0.946;0.888;0.968;0.928;0.957	D	0.98503	1.0615	10	0.54805	T	0.06	.	15.2194	0.73299	0.0:0.0:0.0:1.0	.	154;180;67;180;180	F8W876;P48740-3;P48740-4;P48740-2;P48740	.;.;.;.;MASP1_HUMAN	A	180;180;67;67;180;154;187	ENSP00000336792:T180A;ENSP00000296280:T180A;ENSP00000376264:T67A;ENSP00000169293:T180A;ENSP00000376262:T154A;ENSP00000376267:T187A	ENSP00000169293:T180A	T	-	1	0	MASP1	188461232	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.062000	0.71155	2.242000	0.73789	0.528000	0.53228	ACC	.	.		0.507	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879		C	186978538	T	C	186978538	3	2	22	1	0	0	0	0	1	0	0	0	9331	1667	58	2	2558	2	MASP1	3	186978538	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	7847158	186978538	11043892	36	1974										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13578590	13578590	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ggatcagaaactgatttctgGcgttttctttctggctctga	10	8	5	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr4:13578590G>A	ENST00000040738.5	-	25	9045	c.8910C>T	c.(8908-8910)cgC>cgT	p.R2970R		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2970						nucleus (GO:0005634)	DNA binding (GO:0003677)										CTGATTTCTGGCGTTTTCTTT	0.453																																					p.R2970R		Atlas-SNP	.											.	.	.	.	0			c.C8910T						.						116	113	114					4																	13578590		2203	4300	6503	SO:0001819	synonymous_variant	259282	exon25			TTTCTGGCGTTTT	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.8910C>T	chr4.hg19:g.13578590G>A		74.0	0.0		78.0	43.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Silent	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	9.654	1.142264	0.21205	.	.	ENSG00000038219	ENST00000507943	.	.	.	5.67	1.49	0.22878	.	.	.	.	.	T	0.51278	0.1665	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37888	-0.9686	4	.	.	.	-3.3794	4.7732	0.13166	0.3496:0.1633:0.487:0.0	.	.	.	.	V	79	.	.	A	-	2	0	BOD1L	13187688	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	0.740000	0.26188	0.342000	0.23796	0.655000	0.94253	GCC	.	.		0.453	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13578590	G	A	13578590	2	1	22	1	0	0	0	0	0	0	0	1	1483	1190	42	3		3	BOD1L	4	13578590	Silent	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10		13578590	177575686	37	1975										
ALB	213	hgsc.bcm.edu	37	chr4	74279213	74279215	+	In_Frame_Del	DEL	TGT	TGT	-													0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ggaatgctgtgaaaaacctcTgttggaaaaatcccactgca							TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr4:74279213_74279215delTGT	ENST00000503124.1	+	6	677_679	c.470_472delTGT	c.(469-474)ctgttg>ctg	p.157_158LL>L	ALB_ENST00000415165.2_In_Frame_Del_p.115_116LL>L|ALB_ENST00000509063.1_In_Frame_Del_p.307_308LL>L|ALB_ENST00000401494.3_In_Frame_Del_p.192_193LL>L|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000295897.4_In_Frame_Del_p.307_308LL>L			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GAAAAACCTCTGTTGGAAAAATC	0.409																																					p.307_307del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.919_921del						.																																			SO:0001651	inframe_deletion	213	exon8			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.470_472delTGT	chr4.hg19:g.74279213_74279215delTGT	ENSP00000421027:p.Leu158del	154.0	0.0		128.0	30.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	In_Frame_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.409	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74279215	TGT	-	74279213	7	5	22	1	0	1	0	1	0	0	0	0	486	1580	55	0	950	0	ALB	4	74279213	In_Frame_Del	DEL	TGT	TCGA-3K-AAZ8-01A-12D-A38X-10	60700623	74279213	116875063	38	1976										
ALB	213	hgsc.bcm.edu	37	chr4	74283862	74283863	+	Frame_Shift_Del	DEL	AG	AG	-													0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	agaaaacgccagtaagtgacAgagtcaccaaatgctgcaca							TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr4:74283862_74283863delAG	ENST00000503124.1	+	10	1243_1244	c.1036_1037delAG	c.(1036-1038)agafs	p.R346fs	ALB_ENST00000415165.2_Frame_Shift_Del_p.R304fs|ALB_ENST00000509063.1_Frame_Shift_Del_p.R496fs|ALB_ENST00000401494.3_Frame_Shift_Del_p.R381fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000295897.4_Frame_Shift_Del_p.R496fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGTAAGTGACAGAGTCACCAAA	0.455																																					p.495_496del		Pindel	.											.	ALB	132	.	0			c.1485_1486del						.																																			SO:0001589	frameshift_variant	213	exon12			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1036_1037delAG	chr4.hg19:g.74283864_74283865delAG	ENSP00000421027:p.Arg346fs	98.0	0.0		67.0	13.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.455	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74283863	AG	-	74283862	7	5	22	1	0	1	0	1	0	0	0	0	486	180	7	0	1532	0	ALB	4	74283862	Frame_Shift_Del	DEL	AG	TCGA-3K-AAZ8-01A-12D-A38X-10	4649	74283862	116870414	39	1977										
DSPP	1834	hgsc.bcm.edu	37	chr4	88536436	88536436	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	agcgatagcagtgacagcagCaacagcagtgacagcagtga	13	9	0	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr4:88536436C>T	ENST00000282478.7	+	4	2655	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	DSPP_ENST00000399271.1_Silent_p.S874S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	874	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagcaacagcagtg	0.502																																					p.S874S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2622T						.						70	85	79					4																	88536436		1641	2936	4577	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCAACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2622C>T	chr4.hg19:g.88536436C>T		293.0	0.0		245.0	19.0	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.502	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88536436	C	T	88536436	2	4	22	1	0	0	0	0	0	0	0	1	4784	709	25	3		3	DSPP	4	88536436	Silent	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	14252574	88536436	102617840	40	1978										
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154519794	154519794	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tggaaggatttggagcaagaGagttattaaaagtgggtgga	16	1	0	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr4:154519794G>A	ENST00000409663.3	+	21	2225	c.2173G>A	c.(2173-2175)Gag>Aag	p.E725K	KIAA0922_ENST00000409959.3_Missense_Mutation_p.E726K|KIAA0922_ENST00000440693.1_Missense_Mutation_p.E642K	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	725						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TGGAGCAAGAGAGTTATTAAA	0.448																																					p.E726K		Atlas-SNP	.											.	KIAA0922	214	.	0			c.G2176A						.						144	145	144					4																	154519794		2203	4300	6503	SO:0001583	missense	23240	exon21			GCAAGAGAGTTAT	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.2173G>A	chr4.hg19:g.154519794G>A	ENSP00000386574:p.Glu725Lys	144.0	0.0		125.0	64.0	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	hg19	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	G	27.5	4.838923	0.91117	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.20881	2.32;2.04;2.32;2.05	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.53029	0.1771	M	0.82630	2.6	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.997	D;D;D	0.91635	0.996;0.999;0.989	T	0.56637	-0.7946	10	0.62326	D	0.03	-23.5905	19.574	0.95434	0.0:0.0:1.0:0.0	.	642;726;725	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	K	725;642;726;503	ENSP00000386574:E725K;ENSP00000409663:E642K;ENSP00000386787:E726K;ENSP00000240487:E503K	ENSP00000240487:E503K	E	+	1	0	KIAA0922	154739244	1.000000	0.71417	0.116000	0.21606	0.634000	0.38068	9.276000	0.95745	2.607000	0.88179	0.655000	0.94253	GAG	.	.		0.448	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		A	154519794	G	A	154519794	3	1	22	1	0	0	0	0	1	0	0	0	8210	943	33	3	2258	3	KIAA0922	4	154519794	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	65983358	154519794	36634482	41	1979										
RGS7BP	401190	hgsc.bcm.edu	37	chr5	63802553	63802553	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ctgcagagcggagattgggaGcgcaggggcagcggctccga	19	10	0	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr5:63802553G>A	ENST00000334025.2	+	1	428	c.102G>A	c.(100-102)gaG>gaA	p.E34E	RGS7BP_ENST00000508162.1_3'UTR	NM_001029875.1|NM_001271890.1|NM_001271891.1	NP_001025046.1|NP_001258819.1|NP_001258820.1	Q6MZT1	R7BP_HUMAN	regulator of G-protein signaling 7 binding protein	34					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|stomach(1)	11		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)		GAGATTGGGAGCGCAGGGGCA	0.587																																					p.E34E		Atlas-SNP	.											.	RGS7BP	32	.	0			c.G102A						.						32	44	40					5																	63802553		2203	4300	6503	SO:0001819	synonymous_variant	401190	exon1			TTGGGAGCGCAGG	BX640900	CCDS34170.1	5q12.3	2008-02-05	2007-08-14		ENSG00000186479	ENSG00000186479			23271	protein-coding gene	gene with protein product		610890	"regulator of G-protein signalling 7 binding protein"			15632198	Standard	NM_001271890		Approved	R7BP	uc003jtj.4	Q6MZT1	OTTHUMG00000162293	ENST00000334025.2:c.102G>A	chr5.hg19:g.63802553G>A		318.0	1.0		295.0	126.0	NM_001029875	B7Z3X1	Silent	SNP	ENST00000334025.2	hg19	CCDS34170.1																																																																																			.	.		0.587	RGS7BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368464.1	NM_001029875		A	63802553	G	A	63802553	2	1	22	1	0	0	0	0	0	0	0	1	13326	962	34	3		3	RGS7BP	5	63802553	Silent	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10		63802553	117112707	42	1980										
FBN2	2201	hgsc.bcm.edu	37	chr5	127666336	127666336	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	atgagcccggggtatttacaCactgagcattgatgctacac	10	10	0	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr5:127666336C>A	ENST00000508053.1	-	39	5248	c.4274G>T	c.(4273-4275)tGt>tTt	p.C1425F	FBN2_ENST00000507835.1_Missense_Mutation_p.C275F|FBN2_ENST00000262464.4_Missense_Mutation_p.C1425F|FBN2_ENST00000508989.1_Missense_Mutation_p.C1392F			P35556	FBN2_HUMAN	fibrillin 2	1425	EGF-like 23; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		C -> R (in DA9). {ECO:0000269|PubMed:19006240}.		anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GGTATTTACACACTGAGCATT	0.483																																					p.C1425F		Atlas-SNP	.											.	FBN2	858	.	0			c.G4274T	GRCh37	CM090536	FBN2	M		.						148	132	138					5																	127666336		2203	4300	6503	SO:0001583	missense	2201	exon33			TTTACACACTGAG	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.4274G>T	chr5.hg19:g.127666336C>A	ENSP00000424571:p.Cys1425Phe	126.0	0.0		143.0	64.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.753645	0.89753	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000507835;ENST00000508989	D;D;D;D	0.99445	-5.91;-5.91;-5.91;-5.91	5.14	5.14	0.70334	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000003	D	0.99816	0.9919	H	0.99444	4.57	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.996	D	0.96664	0.9491	10	0.87932	D	0	.	19.1483	0.93477	0.0:1.0:0.0:0.0	.	1392;1425	D6RJI3;P35556	.;FBN2_HUMAN	F	1425;1425;275;1392	ENSP00000262464:C1425F;ENSP00000424571:C1425F;ENSP00000426839:C275F;ENSP00000425596:C1392F	ENSP00000262464:C1425F	C	-	2	0	FBN2	127694235	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.585000	0.82584	2.835000	0.97688	0.591000	0.81541	TGT	.	.		0.483	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127666336	C	A	127666336	3	1	22	1	0	0	0	0	1	0	0	0	5711	478	17	3	4596	3	FBN2	5	127666336	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	63863783	127666336	53248924	43	1981										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140563472	140563472	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cagatatcagatgtcaatgaTaacgcccccactttcaccca	5	14	3	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr5:140563472T>A	ENST00000361016.2	+	1	2493	c.1338T>A	c.(1336-1338)gaT>gaA	p.D446E		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	446	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATGTCAATGATAACGCCCCCA	0.527																																					p.D446E		Atlas-SNP	.											.	PCDHB16	159	.	0			c.T1338A						.						138	129	132					5																	140563472		2203	4300	6503	SO:0001583	missense	57717	exon1			CAATGATAACGCC	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1338T>A	chr5.hg19:g.140563472T>A	ENSP00000354293:p.Asp446Glu	128.0	0.0		108.0	43.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.932596	0.52866	.	.	ENSG00000196963	ENST00000361016	T	0.67171	-0.25	4.3	1.47	0.22746	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.36268	N	0.002684	D	0.85898	0.5804	H	0.97758	4.07	0.32255	N	0.570899	D	0.89917	1.0	D	0.91635	0.999	D	0.87110	0.2184	10	0.87932	D	0	.	10.0661	0.42303	0.0:0.8261:0.0:0.1739	.	446	Q9NRJ7	PCDBG_HUMAN	E	446	ENSP00000354293:D446E	ENSP00000354293:D446E	D	+	3	2	PCDHB16	140543656	0.995000	0.38212	0.984000	0.44739	0.057000	0.15508	0.614000	0.24314	0.230000	0.21059	-0.400000	0.06385	GAT	.	.		0.527	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140563472	T	A	140563472	3	1	22	1	0	0	0	0	1	0	0	0	11550	1403	49	4	1340	4	PCDHB16	5	140563472	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	12897136	140563472	40351788	44	1982										
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140735666	140735666	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gttgaattctctgagtggggAtataacaatattggggggtc	14	4	1	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr5:140735666A>G	ENST00000571252.1	+	1	899	c.899A>G	c.(898-900)gAt>gGt	p.D300G	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	300	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGAGTGGGGATATAACAATA	0.438																																					p.D300G		Atlas-SNP	.											PCDHGA4_ENST00000571252,NS,carcinoma,0,2	PCDHGA4	150	.	0			c.A899G						.						49	49	49					5																	140735666		1851	4091	5942	SO:0001583	missense	56111	exon1			GTGGGGATATAAC	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.899A>G	chr5.hg19:g.140735666A>G	ENSP00000458570:p.Asp300Gly	101.0	2.0		106.0	9.0	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.		0.438	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		G	140735666	A	G	140735666	3	3	22	1	0	0	0	0	1	0	0	0	11565	333	12	2	901	2	PCDHGA4	5	140735666	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	172194	140735666	40179594	45	1983										
MAPK9	5601	hgsc.bcm.edu	37	chr5	179666988	179666988	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tcataaatttgaggtggtggCtaaaaattaaatcatatgta	8	3	2	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr5:179666988C>T	ENST00000452135.2	-	10	1295		c.e10-1		MAPK9_ENST00000343111.6_Splice_Site|MAPK9_ENST00000397072.3_Splice_Site|MAPK9_ENST00000393360.3_Splice_Site|MAPK9_ENST00000524170.1_5'Flank|MAPK9_ENST00000455781.1_Splice_Site|MAPK9_ENST00000347470.4_Splice_Site			P45984	MK09_HUMAN	mitogen-activated protein kinase 9						cellular response to growth factor stimulus (GO:0071363)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV (GO:0034644)|central nervous system development (GO:0007417)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neuron projection development (GO:0031175)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell morphogenesis involved in differentiation (GO:0010770)|positive regulation of chemokine production (GO:0032722)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|protein targeting to mitochondrion (GO:0006626)|regulation of JNK cascade (GO:0046328)|regulation of protein ubiquitination (GO:0031396)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to amine (GO:0014075)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|JUN kinase activity (GO:0004705)|transcription factor binding (GO:0008134)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGGTGGTGGCTAAAAATTAA	0.333																																					.		Atlas-SNP	.											.	MAPK9	173	.	0			c.997-1G>A						.						140	133	135					5																	179666988		2203	4300	6503	SO:0001630	splice_region_variant	5601	exon11			TGGTGGCTAAAAA	U09759	CCDS4453.1, CCDS4454.1, CCDS43409.1, CCDS43410.1, CCDS47356.1	5q35	2011-06-09			ENSG00000050748	ENSG00000050748	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6886	protein-coding gene	gene with protein product	"Jun kinase"	602896		PRKM9		8001819	Standard	NM_002752		Approved	JNK2, p54a, SAPK	uc003mls.4	P45984	OTTHUMG00000130934	ENST00000452135.2:c.997-1G>A	chr5.hg19:g.179666988C>T		35.0	0.0		29.0	9.0	NM_002752	A8K0S3|B5BU66|B5M0B4|D3DWQ8|D3DWQ9|Q15708|Q15710|Q15711|Q8N5C5	Splice_Site	SNP	ENST00000452135.2	hg19	CCDS4453.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.311057	0.81358	.	.	ENSG00000050748	ENST00000452135;ENST00000393360;ENST00000455781;ENST00000343111;ENST00000347470	.	.	.	5.15	5.15	0.70609	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1831	0.86859	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MAPK9	179599594	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.711000	0.84669	2.555000	0.86185	0.655000	0.94253	.	.	.		0.333	MAPK9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253530.3		Intron	T	179666988	C	T	179666988	5	4	22	1	0	0	0	0	0	0	1	0	9296	811	28	3	295	3	MAPK9	5	179666988	Splice_Site	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	38931322	179666988	1248272	46	1984										
DTNBP1	84062	hgsc.bcm.edu	37	chr6	15663083	15663083	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tgcacgctcagcagccgctcGcgaagggtctccagcattgc	12	15	2	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr6:15663083G>A	ENST00000344537.5	-	1	190	c.18C>T	c.(16-18)cgC>cgT	p.R6R	DTNBP1_ENST00000338950.5_Silent_p.R6R|DTNBP1_ENST00000355917.3_Silent_p.R6R	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	6					actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			GCAGCCGCTCGCGAAGGGTCT	0.721									Hermansky-Pudlak syndrome																												p.R6R		Atlas-SNP	.											.	DTNBP1	56	.	0			c.C18T						.						30	43	39					6																	15663083		2071	4103	6174	SO:0001819	synonymous_variant	84062	exon1	Familial Cancer Database	HPS, HPS1-8	CCGCTCGCGAAGG	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"Biogenesis of lysosomal organelles complex-1 subunits"	17328	protein-coding gene	gene with protein product	"dysbindin-1", "biogenesis of lysosomal organelles complex-1, subunit 8"	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.18C>T	chr6.hg19:g.15663083G>A		97.0	0.0		132.0	35.0	NM_183040	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Silent	SNP	ENST00000344537.5	hg19	CCDS4534.1																																																																																			.	.		0.721	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122		A	15663083	G	A	15663083	2	1	22	1	0	0	0	0	0	0	0	1	4792	1074	38	1		1	DTNBP1	6	15663083	Silent	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10		15663083	155451984	47	1985										
FAM65B	9750	hgsc.bcm.edu	37	chr6	24874014	24874014	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gagagcggaggaattttcaaTgaaggagttacacctatgga	13	5	1	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr6:24874014T>A	ENST00000259698.4	-	3	290	c.115A>T	c.(115-117)Att>Ttt	p.I39F	FAM65B_ENST00000510784.2_Missense_Mutation_p.I73F|FAM65B_ENST00000540914.1_Missense_Mutation_p.I39F|FAM65B_ENST00000538035.1_Missense_Mutation_p.I68F|FAM65B_ENST00000378023.4_Missense_Mutation_p.I39F	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	39					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						GAATTTTCAATGAAGGAGTTA	0.398																																					p.I39F		Atlas-SNP	.											.	FAM65B	134	.	0			c.A115T						.						83	74	77					6																	24874014		1835	4095	5930	SO:0001583	missense	9750	exon3			TTTCAATGAAGGA	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.115A>T	chr6.hg19:g.24874014T>A	ENSP00000259698:p.Ile39Phe	88.0	0.0		127.0	75.0	NM_015864	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	hg19	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.549093	0.45383	.	.	ENSG00000111913	ENST00000259698;ENST00000538035;ENST00000378023;ENST00000540914;ENST00000510784	T;T;T;T;T	0.02369	4.32;4.32;4.32;4.32;4.32	5.53	5.53	0.82687	.	0.089331	0.85682	D	0.000000	T	0.01421	0.0046	N	0.03154	-0.405	0.50813	D	0.999894	D;D;P;D	0.69078	0.962;0.995;0.9;0.997	P;P;P;P	0.59171	0.704;0.845;0.49;0.853	T	0.71632	-0.4534	10	0.19147	T	0.46	-23.4493	11.6593	0.51337	0.0:0.0:0.148:0.852	.	73;68;39;39	B7Z6U4;F5GX51;Q9Y4F9-2;Q9Y4F9	.;.;.;FA65B_HUMAN	F	39;68;39;39;73	ENSP00000259698:I39F;ENSP00000441138:I68F;ENSP00000367262:I39F;ENSP00000438425:I39F;ENSP00000441305:I73F	ENSP00000259698:I39F	I	-	1	0	FAM65B	24981993	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.876000	0.56115	2.107000	0.64212	0.533000	0.62120	ATT	.	.		0.398	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			A	24874014	T	A	24874014	3	1	22	1	0	0	0	0	1	0	0	0	5608	1464	51	4	3185	4	FAM65B	6	24874014	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	9210931	24874014	146241053	48	1986										
TNFRSF21	27242	hgsc.bcm.edu	37	chr6	47253741	47253741	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	atgtgctcagggcgtggaaaGatggctgtgccaggggaagg	19	6	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr6:47253741G>A	ENST00000296861.2	-	2	1080	c.687C>T	c.(685-687)atC>atT	p.I229I		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	229					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			GGCGTGGAAAGATGGCTGTGC	0.522																																					p.I229I		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.C687T						.						121	93	102					6																	47253741		2203	4300	6503	SO:0001819	synonymous_variant	27242	exon2			TGGAAAGATGGCT	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"Tumor necrosis factor receptor superfamily", "CD molecules"	13469	protein-coding gene	gene with protein product	"death receptor 6"	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.687C>T	chr6.hg19:g.47253741G>A		114.0	0.0		157.0	43.0	NM_014452	B2RDI9|Q0D2P5|Q96D86	Silent	SNP	ENST00000296861.2	hg19	CCDS4921.1																																																																																			.	.		0.522	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		A	47253741	G	A	47253741	2	1	22	1	0	0	0	0	0	0	0	1	16310	932	33	3		3	TNFRSF21	6	47253741	Silent	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	22379727	47253741	123861326	49	1987										
DST	667	hgsc.bcm.edu	37	chr6	56484410	56484410	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cctttttcatgattaagagaTtctaattctaactgataatt	4	6	3	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr6:56484410T>G	ENST00000370765.6	-	23	4529	c.4422A>C	c.(4420-4422)gaA>gaC	p.E1474D	DST_ENST00000361203.3_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	6325					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GATTAAGAGATTCTAATTCTA	0.358																																					p.E1474D		Atlas-SNP	.											.	DST	1427	.	0			c.A4422C						.						99	100	100					6																	56484410		2203	4300	6503	SO:0001583	missense	667	exon23			AAGAGATTCTAAT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.4422A>C	chr6.hg19:g.56484410T>G	ENSP00000359801:p.Glu1474Asp	74.0	0.0		110.0	27.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	hg19	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	T	14.47	2.544264	0.45280	.	.	ENSG00000151914	ENST00000370765	T	0.31510	1.49	5.23	-2.51	0.06365	.	.	.	.	.	T	0.11024	0.0269	.	.	.	0.19575	N	0.999969	P	0.37276	0.589	B	0.35770	0.21	T	0.05386	-1.0888	7	0.44086	T	0.13	.	13.77	0.63019	0.0:0.5186:0.0:0.4814	.	1474	Q03001-3	.	D	1474	ENSP00000359801:E1474D	ENSP00000359801:E1474D	E	-	3	2	DST	56592369	0.977000	0.34250	0.965000	0.40720	0.952000	0.60782	0.092000	0.15066	-0.733000	0.04850	-0.280000	0.10049	GAA	.	.		0.358	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		G	56484410	T	G	56484410	3	3	22	1	0	0	0	0	1	0	0	0	4785	1490	52	5	15981	5	DST	6	56484410	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	9230669	56484410	114630657	50	1988										
LGSN	51557	hgsc.bcm.edu	37	chr6	63995538	63995538	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tagacctggacacgccgtggAggtctgttgcttcaaatcgt	12	10	2	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr6:63995538A>C	ENST00000370657.4	-	3	317	c.284T>G	c.(283-285)cTc>cGc	p.L95R	LGSN_ENST00000370658.5_Missense_Mutation_p.L95R			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	95					glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)			NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CACGCCGTGGAGGTCTGTTGC	0.418																																					p.L95R		Atlas-SNP	.											.	LGSN	82	.	0			c.T284G						.						117	98	104					6																	63995538		2203	4300	6503	SO:0001583	missense	51557	exon3			CCGTGGAGGTCTG	AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"glutamate-ammonia ligase (glutamine synthetase) domain containing 1"	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.284T>G	chr6.hg19:g.63995538A>C	ENSP00000359691:p.Leu95Arg	122.0	0.0		143.0	45.0	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	hg19	CCDS4964.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.134947	0.77662	.	.	ENSG00000146166	ENST00000370658;ENST00000370657	T;T	0.48836	0.8;0.8	5.61	5.61	0.85477	Glutamine synthetase, beta-Grasp (3);	0.057207	0.64402	D	0.000001	T	0.67739	0.2925	M	0.86502	2.82	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.996	T	0.74925	-0.3498	10	0.87932	D	0	-12.0797	15.2783	0.73760	1.0:0.0:0.0:0.0	.	95;95	Q5TDP6-2;Q5TDP6	.;LGSN_HUMAN	R	95	ENSP00000359692:L95R;ENSP00000359691:L95R	ENSP00000359691:L95R	L	-	2	0	LGSN	64053497	1.000000	0.71417	0.366000	0.25914	0.918000	0.54935	8.252000	0.89840	2.269000	0.75478	0.533000	0.62120	CTC	.	.		0.418	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571		C	63995538	A	C	63995538	3	2	22	1	0	0	0	0	1	0	0	0	8768	304	11	5	1253	5	LGSN	6	63995538	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	7511128	63995538	107119529	51	1989										
LCA5	167691	hgsc.bcm.edu	37	chr6	80223048	80223048	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tttcagtttctgtaaggaaaAttttgtcctaaatagttcac	6	6	3	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr6:80223048A>G	ENST00000392959.1	-	4	1212	c.601T>C	c.(601-603)Ttt>Ctt	p.F201L	LCA5_ENST00000369846.4_Missense_Mutation_p.F201L|LCA5_ENST00000467898.3_Missense_Mutation_p.F201L	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	201					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		TGTAAGGAAAATTTTGTCCTA	0.368																																					p.F201L		Atlas-SNP	.											.	LCA5	71	.	0			c.T601C						.						163	158	160					6																	80223048		2203	4300	6503	SO:0001583	missense	167691	exon3			AGGAAAATTTTGT		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.601T>C	chr6.hg19:g.80223048A>G	ENSP00000376686:p.Phe201Leu	133.0	0.0		121.0	50.0	NM_001122769	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	hg19	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	A	8.893	0.954434	0.18431	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.76316	-1.01;-1.01	6.07	2.41	0.29592	.	0.474766	0.22705	N	0.056656	T	0.42108	0.1188	L	0.51422	1.61	0.24980	N	0.991608	B;B	0.22480	0.01;0.07	B;B	0.17098	0.017;0.013	T	0.23440	-1.0188	10	0.10902	T	0.67	-4.303	3.8199	0.08832	0.465:0.0:0.1498:0.3853	.	201;201	B4DRL2;Q86VQ0	.;LCA5_HUMAN	L	201	ENSP00000358861:F201L;ENSP00000376686:F201L	ENSP00000358861:F201L	F	-	1	0	LCA5	80279767	0.991000	0.36638	0.999000	0.59377	0.996000	0.88848	0.753000	0.26376	0.516000	0.28340	0.533000	0.62120	TTT	.	.		0.368	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		G	80223048	A	G	80223048	3	3	22	1	0	0	0	0	1	0	0	0	8665	101	4	2	1516	2	LCA5	6	80223048	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	16227510	80223048	90892019	52	1990										
FRMD1	79981	hgsc.bcm.edu	37	chr6	168462619	168462619	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cgtgtagtaaaccagcttctGtgctgcgggcagcccatcca	11	13	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr6:168462619G>T	ENST00000283309.6	-	8	977	c.913C>A	c.(913-915)Cag>Aag	p.Q305K	FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000440994.2_Missense_Mutation_p.Q237K|FRMD1_ENST00000537786.1_Missense_Mutation_p.Q76K	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	305	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		ACCAGCTTCTGTGCTGCGGGC	0.632																																					p.Q305K	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.C913A						.						27	28	28					6																	168462619		2202	4300	6502	SO:0001583	missense	79981	exon8			GCTTCTGTGCTGC		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.913C>A	chr6.hg19:g.168462619G>T	ENSP00000283309:p.Gln305Lys	132.0	0.0		150.0	56.0	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	hg19	CCDS5306.1	.	.	.	.	.	.	.	.	.	.	G	4.442	0.081857	0.08533	.	.	ENSG00000153303	ENST00000283309;ENST00000440994;ENST00000537786	T;T;T	0.81247	-1.47;-1.47;-1.47	2.37	1.46	0.22682	FERM domain (1);	0.219292	0.27491	N	0.019123	T	0.38480	0.1042	N	0.08118	0	0.23665	N	0.997162	B;B;B;B	0.14012	0.009;0.004;0.004;0.009	B;B;B;B	0.20384	0.012;0.003;0.007;0.029	T	0.38351	-0.9665	10	0.25751	T	0.34	.	8.6375	0.33957	0.0:0.0:0.7704:0.2296	.	240;305;237;200	B7Z8G9;Q8N878;Q8N878-2;Q5SZU5	.;FRMD1_HUMAN;.;.	K	305;237;76	ENSP00000283309:Q305K;ENSP00000414115:Q237K;ENSP00000440078:Q76K	ENSP00000283309:Q305K	Q	-	1	0	FRMD1	168205468	0.993000	0.37304	0.007000	0.13788	0.031000	0.12232	1.398000	0.34554	0.328000	0.23435	0.313000	0.20887	CAG	.	.		0.632	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919		T	168462619	G	T	168462619	3	4	22	1	0	0	0	0	1	0	0	0	6057	1386	48	3	752	3	FRMD1	6	168462619	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	88239571	168462619	2652448	53	1991										
CDK13	8621	hgsc.bcm.edu	37	chr7	40133764	40133764	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tccagcatcaagatatgaggAtcttggagctaacgccagaa	10	9	2	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr7:40133764A>C	ENST00000181839.4	+	14	4329	c.3724A>C	c.(3724-3726)Atc>Ctc	p.I1242L	CDK13_ENST00000340829.5_Missense_Mutation_p.I1182L	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	1242					alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						AGATATGAGGATCTTGGAGCT	0.468																																					p.I1242L		Atlas-SNP	.											.	CDK13	114	.	0			c.A3724C						.						102	94	97					7																	40133764		2203	4300	6503	SO:0001583	missense	8621	exon14			ATGAGGATCTTGG	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.3724A>C	chr7.hg19:g.40133764A>C	ENSP00000181839:p.Ile1242Leu	150.0	0.0		117.0	44.0	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Missense_Mutation	SNP	ENST00000181839.4	hg19	CCDS5461.1	.	.	.	.	.	.	.	.	.	.	A	1.084	-0.666159	0.03428	.	.	ENSG00000065883	ENST00000181839;ENST00000340829	T;T	0.46819	0.86;0.86	5.26	2.88	0.33553	.	.	.	.	.	T	0.19366	0.0465	N	0.03608	-0.345	0.18873	N	0.999981	B;B	0.10296	0.003;0.0	B;B	0.09377	0.004;0.0	T	0.19224	-1.0312	8	.	.	.	0.7849	2.8832	0.05654	0.415:0.3731:0.0833:0.1287	.	1182;1242	Q14004-2;Q14004	.;CDK13_HUMAN	L	1242;1182	ENSP00000181839:I1242L;ENSP00000340557:I1182L	.	I	+	1	0	CDK13	40100289	0.924000	0.31332	0.839000	0.33178	0.957000	0.61999	1.196000	0.32198	0.816000	0.34421	0.459000	0.35465	ATC	.	.		0.468	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		C	40133764	A	C	40133764	3	2	22	1	0	0	0	0	1	0	0	0	3131	333	12	5	3778	5	CDK13	7	40133764	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10		40133764	119004899	54	1992										
GIGYF1	64599	hgsc.bcm.edu	37	chr7	100284298	100284298	+	Frame_Shift_Del	DEL	C	C	-													0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tggcggagcgccagcggtcgCcgtctcgccggggccctgct							TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr7:100284298delC	ENST00000275732.5	-	7	1877	c.668delG	c.(667-669)ggcfs	p.G223fs	GIGYF1_ENST00000471340.2_Intron	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	223					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					CCAGCGGTCGCCGTCTCGCCG	0.687																																					p.G223fs		Atlas-Indel,Pindel	.											.	GIGYF1	113	.	0			c.669delC						.						27	33	31					7																	100284298		2199	4288	6487	SO:0001589	frameshift_variant	64599	exon7			.	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"GYF domain containing 1"	612064	"PERQ amino acid rich, with GYF domain 1"	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.668delG	chr7.hg19:g.100284298delC	ENSP00000275732:p.Gly223fs	57.0	0.0		63.0	34.0	NM_022574	Q6Y7W7|Q8WZ38	Frame_Shift_Del	DEL	ENST00000275732.5	hg19	CCDS34708.1																																																																																			.	.		0.687	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		-	100284298	C	-	100284298	7	5	22	1	0	1	0	1	0	0	0	0	6385	739	26	0	2511	0	GIGYF1	7	100284298	Frame_Shift_Del	DEL	C	TCGA-3K-AAZ8-01A-12D-A38X-10	60150534	100284298	58854365	55	1993										
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138794071	138794071	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gaagcagcacacctccgggtCcgccatggcgcgctggctgt	14	15	0	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr7:138794071C>A	ENST00000242351.5	-	1	323	c.7G>T	c.(7-9)Gac>Tac	p.D3Y	ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.D3Y|ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.D3Y	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	3	N-terminal domain.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						ACCTCCGGGTCCGCCATGGCG	0.682																																					p.D3Y		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.G7T						.						9	11	11					7																	138794071		2036	4192	6228	SO:0001583	missense	56829	exon1			CCGGGTCCGCCAT	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.7G>T	chr7.hg19:g.138794071C>A	ENSP00000242351:p.Asp3Tyr	73.0	0.0		67.0	6.0	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	hg19	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.482207	0.84747	.	.	ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652	T;T;T	0.37235	1.21;1.21;1.21	4.74	4.74	0.60224	.	0.133103	0.35124	N	0.003425	T	0.59059	0.2166	M	0.74881	2.28	0.52099	D	0.999941	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.982	T	0.63198	-0.6691	10	0.87932	D	0	.	13.0949	0.59187	0.0:1.0:0.0:0.0	.	3;3	Q7Z2W4-2;Q7Z2W4	.;ZCCHV_HUMAN	Y	3	ENSP00000242351:D3Y;ENSP00000418385:D3Y;ENSP00000419855:D3Y	ENSP00000242351:D3Y	D	-	1	0	ZC3HAV1	138444611	0.996000	0.38824	0.992000	0.48379	0.956000	0.61745	4.205000	0.58466	2.461000	0.83175	0.491000	0.48974	GAC	.	.		0.682	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		A	138794071	C	A	138794071	3	1	22	1	0	0	0	0	1	0	0	0	17590	855	30	3	2757	3	ZC3HAV1	7	138794071	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	38509773	138794071	20344592	56	1994										
FASTK	10922	hgsc.bcm.edu	37	chr7	150776949	150776949	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tcagcagcaggccagacagcCgagcaggggaggtctgagca	16	11	2	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr7:150776949C>T	ENST00000297532.6	-	2	220	c.143G>A	c.(142-144)cGg>cAg	p.R48Q	FASTK_ENST00000540185.1_Missense_Mutation_p.R14Q|FASTK_ENST00000353841.2_Intron|FASTK_ENST00000482571.1_Missense_Mutation_p.R48Q|FASTK_ENST00000489884.1_Intron	NM_006712.4	NP_006703.1	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase	48					apoptotic signaling pathway (GO:0097190)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|Fas-activated serine/threonine kinase activity (GO:0033867)|protein serine/threonine kinase activity (GO:0004674)			lung(4)|stomach(2)	6			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)		GCCAGACAGCCGAGCAGGGGA	0.622																																					p.R48Q		Atlas-SNP	.											FASTK,NS,carcinoma,0,1	FASTK	29	.	0			c.G143A						.						33	21	25					7																	150776949		2196	4298	6494	SO:0001583	missense	10922	exon2			GACAGCCGAGCAG		CCDS5918.1, CCDS5919.1, CCDS59088.1	7q35	2006-07-06			ENSG00000164896	ENSG00000164896			24676	protein-coding gene	gene with protein product		606965				7544399, 15572676	Standard	NM_006712		Approved	FAST	uc003wix.2	Q14296	OTTHUMG00000158694	ENST00000297532.6:c.143G>A	chr7.hg19:g.150776949C>T	ENSP00000297532:p.Arg48Gln	225.0	0.0		222.0	22.0	NM_006712	A8K867|F8VTW9|Q59EM8|Q8IVA0	Missense_Mutation	SNP	ENST00000297532.6	hg19	CCDS5918.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.003204	0.35320	.	.	ENSG00000164896	ENST00000483105;ENST00000297530;ENST00000297532;ENST00000482571;ENST00000540185	T;T;T	0.52057	0.68;0.68;0.68	4.64	2.77	0.32553	.	0.221198	0.29537	N	0.011861	T	0.34250	0.0891	N	0.24115	0.695	0.29591	N	0.848441	B;B;D	0.54601	0.098;0.032;0.967	B;B;B	0.42282	0.011;0.005;0.382	T	0.32824	-0.9892	10	0.87932	D	0	-35.999	12.6106	0.56547	0.0:0.6799:0.3201:0.0	.	14;48;48	G3V1R6;F8VTW9;Q14296	.;.;FASTK_HUMAN	Q	48;48;48;48;14	ENSP00000297532:R48Q;ENSP00000418516:R48Q;ENSP00000444498:R14Q	ENSP00000297530:R48Q	R	-	2	0	FASTK	150407882	1.000000	0.71417	0.988000	0.46212	0.897000	0.52465	0.905000	0.28504	0.608000	0.30000	0.655000	0.94253	CGG	.	.		0.622	FASTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351832.2	NM_006712		T	150776949	C	T	150776949	3	4	22	1	0	0	0	0	1	0	0	0	5692	652	23	1	1542	1	FASTK	7	150776949	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	11982878	150776949	8361714	57	1995										
STAR	6770	hgsc.bcm.edu	37	chr8	38006210	38006210	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aatccacgtgctaggggtggGgccccccagggccctccggt	15	15	0	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr8:38006210G>A	ENST00000276449.4	-	2	573	c.127C>T	c.(127-129)Ccc>Tcc	p.P43S	RP11-90P5.2_ENST00000520598.1_RNA	NM_000349.2	NP_000340.2	P49675	STAR_HUMAN	steroidogenic acute regulatory protein	43					bile acid biosynthetic process (GO:0006699)|biphenyl metabolic process (GO:0018879)|brain development (GO:0007420)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth hormone stimulus (GO:0071378)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-alpha (GO:0035457)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to luteinizing hormone stimulus (GO:0071373)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cholesterol metabolic process (GO:0008203)|circadian sleep/wake cycle, REM sleep (GO:0042747)|dibenzo-p-dioxin metabolic process (GO:0018894)|diterpenoid metabolic process (GO:0016101)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|glucocorticoid metabolic process (GO:0008211)|insecticide metabolic process (GO:0017143)|intracellular cholesterol transport (GO:0032367)|male gonad development (GO:0008584)|negative regulation of neuron apoptotic process (GO:0043524)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of gene expression (GO:0010628)|positive regulation of neurogenesis (GO:0050769)|progesterone biosynthetic process (GO:0006701)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of steroid biosynthetic process (GO:0050810)|response to activity (GO:0014823)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to hydrogen peroxide (GO:0042542)|response to ionizing radiation (GO:0010212)|response to lead ion (GO:0010288)|response to leptin (GO:0044321)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytosol (GO:0005829)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	cholesterol binding (GO:0015485)			breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11	Colorectal(12;0.000442)	all_lung(54;0.0151)|Lung NSC(58;0.0295)		READ - Rectum adenocarcinoma(644;0.188)		CTAGGGGTGGGGCCCCCCAGG	0.627																																					p.P43S		Atlas-SNP	.											.	STAR	29	.	0			c.C127T						.						41	46	44					8																	38006210		2203	4300	6503	SO:0001583	missense	6770	exon2			GGGTGGGGCCCCC	BC010550	CCDS6102.1	8p11.2	2011-09-13	2007-05-15		ENSG00000147465	ENSG00000147465		"StAR-related lipid transfer (START) domain containing"	11359	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 1"	600617	"steroidogenic acute regulator"			7761400	Standard	NM_000349		Approved	StAR, STARD1	uc003xkv.1	P49675	OTTHUMG00000164058	ENST00000276449.4:c.127C>T	chr8.hg19:g.38006210G>A	ENSP00000276449:p.Pro43Ser	46.0	0.0		19.0	8.0	NM_000349	Q16396	Missense_Mutation	SNP	ENST00000276449.4	hg19	CCDS6102.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.135866	0.37728	.	.	ENSG00000147465	ENST00000276449	D	0.86030	-2.06	5.28	4.39	0.52855	.	0.148333	0.64402	N	0.000008	T	0.79094	0.4388	L	0.45285	1.41	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	T	0.74219	-0.3736	10	0.44086	T	0.13	-18.5292	10.2032	0.43097	0.0738:0.0:0.7913:0.1349	.	43	P49675	STAR_HUMAN	S	43	ENSP00000276449:P43S	ENSP00000276449:P43S	P	-	1	0	STAR	38125367	0.984000	0.35163	0.866000	0.34008	0.312000	0.27988	1.280000	0.33202	1.329000	0.45376	0.462000	0.41574	CCC	.	.		0.627	STAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376990.2	NM_000349		A	38006210	G	A	38006210	3	1	22	1	0	0	0	0	1	0	0	0	15269	1232	43	3	754	3	STAR	8	38006210	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10		38006210	108357812	58	1996										
POLB	5423	hgsc.bcm.edu	37	chr8	42218856	42218856	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gatgttctcctgacccatccCagcttcacttcagaatcaac	5	15	4	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr8:42218856C>A	ENST00000265421.4	+	10	764	c.594C>A	c.(592-594)ccC>ccA	p.P198P	POLB_ENST00000538005.1_Silent_p.P44P	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	198					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	TGACCCATCCCAGCTTCACTT	0.413								DNA polymerases (catalytic subunits)																													p.P198P		Atlas-SNP	.											.	POLB	60	.	0			c.C594A						.						153	130	138					8																	42218856		2203	4300	6503	SO:0001819	synonymous_variant	5423	exon10			CCATCCCAGCTTC		CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	2.7.7.7	"DNA polymerases"	9174	protein-coding gene	gene with protein product		174760					Standard	NM_002690		Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.594C>A	chr8.hg19:g.42218856C>A		76.0	0.0		40.0	20.0	NM_002690	B2RC78|Q3KP48|Q6FI34	Silent	SNP	ENST00000265421.4	hg19	CCDS6129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.119|1.119	-0.655987|-0.655987	0.03480|0.03480	.|.	.|.	ENSG00000070501|ENSG00000070501	ENST00000518579;ENST00000517393|ENST00000521290	T;T|.	0.49432|.	0.78;0.78|.	5.58|5.58	0.27|0.27	0.15635|0.15635	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.43122|0.43122	0.1233|0.1233	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.27226|0.27226	-1.0080|-1.0080	7|4	0.87932|.	D|.	0|.	-1.8742|-1.8742	2.7484|2.7484	0.05273|0.05273	0.5288:0.2554:0.0826:0.1332|0.5288:0.2554:0.0826:0.1332	.|.	.|.	.|.	.|.	Q|K	56;14|129	ENSP00000430478:P56Q;ENSP00000428144:P14Q|.	ENSP00000428144:P14Q|.	P|Q	+|+	2|1	0|0	POLB|POLB	42338013|42338013	0.100000|0.100000	0.21855|0.21855	1.000000|1.000000	0.80357|0.80357	0.005000|0.005000	0.04900|0.04900	-0.194000|-0.194000	0.09559|0.09559	0.408000|0.408000	0.25621|0.25621	-0.388000|-0.388000	0.06559|0.06559	CCA|CAG	.	.		0.413	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377242.1	NM_002690		A	42218856	C	A	42218856	2	1	22	1	0	0	0	0	0	0	0	1	12198	581	21	3		3	POLB	8	42218856	Silent	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	4212646	42218856	104145166	59	1997										
CRISPLD1	83690	hgsc.bcm.edu	37	chr8	75929313	75929313	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ctgctggctgtttggatagtAaagctaaagttattggcagt	12	5	0	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr8:75929313A>G	ENST00000262207.4	+	9	1429	c.961A>G	c.(961-963)Aaa>Gaa	p.K321E	CRISPLD1_ENST00000517786.1_Missense_Mutation_p.K135E|CRISPLD1_ENST00000523524.1_Missense_Mutation_p.K133E	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	321	LCCL 1. {ECO:0000255|PROSITE- ProRule:PRU00123}.				face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			TTTGGATAGTAAAGCTAAAGT	0.279																																					p.K321E		Atlas-SNP	.											.	CRISPLD1	94	.	0			c.A961G						.						88	92	91					8																	75929313		2203	4294	6497	SO:0001583	missense	83690	exon9			GATAGTAAAGCTA	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.961A>G	chr8.hg19:g.75929313A>G	ENSP00000262207:p.Lys321Glu	211.0	0.0		301.0	48.0	NM_031461	B2RA60|B7Z929	Missense_Mutation	SNP	ENST00000262207.4	hg19	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	A	16.40	3.113744	0.56398	.	.	ENSG00000121005	ENST00000262207;ENST00000523524;ENST00000517786	D;D;D	0.89552	-2.53;-2.53;-2.53	5.12	5.12	0.69794	LCCL (5);	0.215343	0.48286	D	0.000186	D	0.86719	0.6000	L	0.58101	1.795	0.33246	D	0.55793	B;B	0.23185	0.081;0.067	B;B	0.25506	0.061;0.049	D	0.88675	0.3198	10	0.66056	D	0.02	.	11.982	0.53125	0.8555:0.1445:0.0:0.0	.	135;321	B7Z929;Q9H336	.;CRLD1_HUMAN	E	321;133;135	ENSP00000262207:K321E;ENSP00000430105:K133E;ENSP00000429746:K135E	ENSP00000262207:K321E	K	+	1	0	CRISPLD1	76091868	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.565000	0.60836	2.276000	0.75962	0.528000	0.53228	AAA	.	.		0.279	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		G	75929313	A	G	75929313	3	3	22	1	0	0	0	0	1	0	0	0	3884	363	13	2	991	2	CRISPLD1	8	75929313	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	33710457	75929313	70434709	60	1998										
CDH17	1015	hgsc.bcm.edu	37	chr8	95164135	95164135	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gatccttggcagtcacattgCccactttagtgcctatagct	8	12	1	0	rs189236130		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr8:95164135C>T	ENST00000027335.3	-	13	1881	c.1757G>A	c.(1756-1758)gGc>gAc	p.G586D	CDH17_ENST00000441892.2_Missense_Mutation_p.G372D|CDH17_ENST00000450165.2_Missense_Mutation_p.G586D	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	586	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			AGTCACATTGCCCACTTTAGT	0.502																																					p.G586D		Atlas-SNP	.											.	CDH17	119	.	0			c.G1757A						.						175	128	144					8																	95164135		2203	4300	6503	SO:0001583	missense	1015	exon13			ACATTGCCCACTT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1757G>A	chr8.hg19:g.95164135C>T	ENSP00000027335:p.Gly586Asp	89.0	0.0		109.0	79.0	NM_004063	Q15336|Q2M2E0	Missense_Mutation	SNP	ENST00000027335.3	hg19	CCDS6260.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.665485	0.67700	.	.	ENSG00000079112	ENST00000027335;ENST00000441892;ENST00000450165	T;T;T	0.54071	0.59;0.59;0.59	5.72	0.351	0.16042	Cadherin (3);Cadherin-like (1);	0.345734	0.25280	N	0.031801	T	0.55657	0.1934	M	0.83774	2.66	0.09310	N	0.999996	P;P	0.43662	0.814;0.728	P;B	0.48334	0.574;0.328	T	0.51490	-0.8699	10	0.66056	D	0.02	-1.3322	3.0135	0.06052	0.3679:0.3077:0.2426:0.0817	.	372;586	E7EN24;Q12864	.;CAD17_HUMAN	D	586;372;586	ENSP00000027335:G586D;ENSP00000392811:G372D;ENSP00000401468:G586D	ENSP00000027335:G586D	G	-	2	0	CDH17	95233311	0.997000	0.39634	0.267000	0.24556	0.572000	0.35998	1.189000	0.32114	0.389000	0.25086	0.655000	0.94253	GGC	.	C|1.000;A|0.000		0.502	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		T	95164135	C	T	95164135	3	4	22	1	0	0	0	0	1	0	0	0	3104	739	26	3	765	3	CDH17	8	95164135	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	19234822	95164135	51199887	61	1999										
DOCK8	81704	hgsc.bcm.edu	37	chr9	376287	376287	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aatattgaagtgcaagctgtTtcttctgtacacacccaggt	8	9	2	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr9:376287T>C	ENST00000453981.1	+	19	2299	c.2187T>C	c.(2185-2187)gtT>gtC	p.V729V	DOCK8_ENST00000469391.1_Silent_p.V661V|DOCK8_ENST00000432829.2_Silent_p.V661V|DOCK8_ENST00000382331.1_Silent_p.V31V|DOCK8_ENST00000382329.1_Silent_p.V196V			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	729	DHR-1.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TGCAAGCTGTTTCTTCTGTAC	0.403																																					p.V729V		Atlas-SNP	.											.	DOCK8	401	.	0			c.T2187C						.						131	127	128					9																	376287		2203	4300	6503	SO:0001819	synonymous_variant	81704	exon19			AGCTGTTTCTTCT	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.2187T>C	chr9.hg19:g.376287T>C		106.0	0.0		91.0	45.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	hg19	CCDS6440.2																																																																																			.	.		0.403	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		C	376287	T	C	376287	2	2	22	1	0	0	0	0	0	0	0	1	4695	1828	64	2		2	DOCK8	9	376287	Silent	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10		376287	140837144	62	2000										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5921657	5921657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ccttgtaacagggtaactttTtgtgatataatctacttgtt	7	6	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr9:5921657T>C	ENST00000399933.3	-	8	4338	c.4339A>G	c.(4339-4341)Aaa>Gaa	p.K1447E	KIAA2026_ENST00000381461.2_Missense_Mutation_p.K1417E	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1447										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		GGGTAACTTTTTGTGATATAA	0.373																																					p.K1447E		Atlas-SNP	.											.	KIAA2026	231	.	0			c.A4339G						.						171	160	163					9																	5921657		1923	4146	6069	SO:0001583	missense	158358	exon8			AACTTTTTGTGAT	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.4339A>G	chr9.hg19:g.5921657T>C	ENSP00000382815:p.Lys1447Glu	122.0	0.0		91.0	19.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	hg19		.	.	.	.	.	.	.	.	.	.	T	12.82	2.051833	0.36181	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	4.53	4.53	0.55603	.	0.000000	0.64402	D	0.000006	T	0.25975	0.0633	L	0.27053	0.805	0.22873	N	0.998623	B	0.28998	0.23	B	0.23574	0.047	T	0.11518	-1.0584	9	0.24483	T	0.36	-8.6695	8.7102	0.34378	0.0:0.0857:0.0:0.9143	.	1447	Q5HYC2	K2026_HUMAN	E	1447;1417	.	ENSP00000370870:K1417E	K	-	1	0	KIAA2026	5911657	0.998000	0.40836	0.998000	0.56505	0.954000	0.61252	3.468000	0.53086	1.919000	0.55581	0.392000	0.25879	AAA	.	.		0.373	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		C	5921657	T	C	5921657	3	2	22	1	0	0	0	0	1	0	0	0	8279	1850	64	2	1976	2	KIAA2026	9	5921657	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	5545370	5921657	135291774	63	2001										
GADD45G	10912	hgsc.bcm.edu	37	chr9	92220779	92220779	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gggtgcgccgggcgacctgcActgcatcctcatttcggtga	14	13	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr9:92220779A>C	ENST00000252506.6	+	3	462	c.353A>C	c.(352-354)cAc>cCc	p.H118P	GADD45G_ENST00000494726.1_3'UTR|GADD45G_ENST00000375769.1_Missense_Mutation_p.H100P	NM_006705.3	NP_006696.1	O95257	GA45G_HUMAN	growth arrest and DNA-damage-inducible, gamma	118					activation of MAPKK activity (GO:0000186)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of cell cycle (GO:0051726)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				lung(2)	2						GGCGACCTGCACTGCATCCTC	0.697																																					p.H118P	Colon(131;320 2336 18973 23919)	Atlas-SNP	.											.	GADD45G	12	.	0			c.A353C						.						30	27	28					9																	92220779		2202	4297	6499	SO:0001583	missense	10912	exon3			ACCTGCACTGCAT	D83023	CCDS6686.1	9q22.1-q22.2	2008-07-21			ENSG00000130222	ENSG00000130222			4097	protein-coding gene	gene with protein product	"gadd-related protein, 17 kD", "growth arrest and DNA-damage-inducible gamma"	604949				9827804, 10496071	Standard	NM_006705		Approved	DDIT2, GADD45gamma, GRP17, CR6	uc004aqq.3	O95257	OTTHUMG00000020187	ENST00000252506.6:c.353A>C	chr9.hg19:g.92220779A>C	ENSP00000252506:p.His118Pro	86.0	0.0		74.0	36.0	NM_006705	Q5VZ87|Q9C076	Missense_Mutation	SNP	ENST00000252506.6	hg19	CCDS6686.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.115465	0.77323	.	.	ENSG00000130222	ENST00000252506;ENST00000375769	T;T	0.41400	1.0;1.0	4.45	3.26	0.37387	.	0.103298	0.64402	D	0.000003	T	0.52141	0.1716	M	0.85373	2.75	0.58432	D	0.999999	P	0.52842	0.956	P	0.47786	0.557	T	0.59156	-0.7507	10	0.66056	D	0.02	-5.8375	10.1809	0.42968	0.832:0.168:0.0:0.0	.	118	O95257	GA45G_HUMAN	P	118;100	ENSP00000252506:H118P;ENSP00000364924:H100P	ENSP00000252506:H118P	H	+	2	0	GADD45G	91410599	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.475000	0.90417	0.814000	0.34374	0.459000	0.35465	CAC	.	.		0.697	GADD45G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053000.1	NM_006705		C	92220779	A	C	92220779	3	2	22	1	0	0	0	0	1	0	0	0	6191	159	6	5	363	5	GADD45G	9	92220779	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	86299122	92220779	48992652	64	2002										
ZNF483	158399	hgsc.bcm.edu	37	chr9	114304529	114304529	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aatgagagtggagaaaaaacTcataaatgtagtaagtgtgg	12	2	1	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr9:114304529T>C	ENST00000309235.5	+	6	1472	c.1314T>C	c.(1312-1314)acT>acC	p.T438T	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	438					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						GAGAAAAAACTCATAAATGTA	0.388																																					p.T438T		Atlas-SNP	.											.	ZNF483	78	.	0			c.T1314C						.						59	64	62					9																	114304529		2203	4300	6503	SO:0001819	synonymous_variant	158399	exon6			AAAAACTCATAAA	AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"Zinc fingers, C2H2-type", "-", "-", "-"	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.1314T>C	chr9.hg19:g.114304529T>C		99.0	0.0		78.0	15.0	NM_133464	Q5VZN2|Q8NAE1	Silent	SNP	ENST00000309235.5	hg19	CCDS35106.1																																																																																			.	.		0.388	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567		C	114304529	T	C	114304529	2	2	22	1	0	0	0	0	0	0	0	1	17951	1538	54	2		2	ZNF483	9	114304529	Silent	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	22083750	114304529	26908902	65	2003										
RAB14	51552	hgsc.bcm.edu	37	chr9	123943729	123943729	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cactggttagccggcctcccTgcggggctgaaggtttgtgt	15	11	0	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr9:123943729T>C	ENST00000373840.4	-	8	830	c.593A>G	c.(592-594)cAg>cGg	p.Q198R		NM_016322.3	NP_057406.2	P61106	RAB14_HUMAN	RAB14, member RAS oncogene family	198					embryo development (GO:0009790)|endocytic recycling (GO:0032456)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi to endosome transport (GO:0006895)|GTP catabolic process (GO:0006184)|intracellular transport (GO:0046907)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|rough endoplasmic reticulum (GO:0005791)|trans-Golgi network transport vesicle (GO:0030140)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						CCGGCCTCCCTGCGGGGCTGA	0.527																																					p.Q198R		Atlas-SNP	.											.	RAB14	14	.	0			c.A593G						.						98	96	97					9																	123943729		2203	4300	6503	SO:0001583	missense	51552	exon8			CCTCCCTGCGGGG	AF152463	CCDS6827.1	9q32-q34.11	2008-07-21			ENSG00000119396	ENSG00000119396		"RAB, member RAS oncogene"	16524	protein-coding gene	gene with protein product	"F protein-binding protein 1", "bA165P4.3 (member RAS oncogene family)", "small GTP binding protein RAB14"	612673				9792283, 15004230	Standard	NM_016322		Approved	FBP, RAB-14	uc004blc.3	P61106	OTTHUMG00000020582	ENST00000373840.4:c.593A>G	chr9.hg19:g.123943729T>C	ENSP00000362946:p.Gln198Arg	177.0	0.0		134.0	51.0	NM_016322	B3KR31|P35287|Q5JVD4|Q6Q7K5|Q969L0|Q9UI11	Missense_Mutation	SNP	ENST00000373840.4	hg19	CCDS6827.1	.	.	.	.	.	.	.	.	.	.	T	0.699	-0.791664	0.02884	.	.	ENSG00000119396	ENST00000373840	T	0.61392	0.11	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.42131	0.1189	N	0.19112	0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33954	-0.9848	10	0.11794	T	0.64	.	15.8056	0.78506	0.0:0.0:0.0:1.0	.	198	P61106	RAB14_HUMAN	R	198	ENSP00000362946:Q198R	ENSP00000362946:Q198R	Q	-	2	0	RAB14	122983550	1.000000	0.71417	1.000000	0.80357	0.491000	0.33493	7.891000	0.87319	2.323000	0.78572	0.528000	0.53228	CAG	.	.		0.527	RAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053857.1	NM_016322		C	123943729	T	C	123943729	3	2	22	1	0	0	0	0	1	0	0	0	12915	1580	55	2	58	2	RAB14	9	123943729	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	9639200	123943729	17269702	66	2004										
ANGPTL2	23452	hgsc.bcm.edu	37	chr9	129854065	129854065	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gcagcttataatactcgctcTcaggttccaggcggaaactg	10	11	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr9:129854065T>G	ENST00000373425.3	-	4	1783	c.1166A>C	c.(1165-1167)gAg>gCg	p.E389A	RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000424082.2_Intron|RALGPS1_ENST00000259351.5_Intron|RALGPS1_ENST00000394022.3_Intron|ANGPTL2_ENST00000373417.1_Missense_Mutation_p.E87A|RALGPS1_ENST00000373436.1_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	389	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						ATACTCGCTCTCAGGTTCCAG	0.557																																					p.E389A		Atlas-SNP	.											.	ANGPTL2	46	.	0			c.A1166C						.						176	176	176					9																	129854065		2203	4300	6503	SO:0001583	missense	23452	exon4			TCGCTCTCAGGTT	AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"Fibrinogen C domain containing"	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.1166A>C	chr9.hg19:g.129854065T>G	ENSP00000362524:p.Glu389Ala	114.0	0.0		97.0	7.0	NM_012098	Q5JT58|Q8NCH7	Missense_Mutation	SNP	ENST00000373425.3	hg19	CCDS6868.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.984327	0.93044	.	.	ENSG00000136859	ENST00000373425;ENST00000373417	D;D	0.84589	-1.87;-1.87	5.2	5.2	0.72013	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.85682	D	0.000000	D	0.92515	0.7623	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93155	0.6553	10	0.54805	T	0.06	.	15.3682	0.74541	0.0:0.0:0.0:1.0	.	389	Q9UKU9	ANGL2_HUMAN	A	389;87	ENSP00000362524:E389A;ENSP00000362516:E87A	ENSP00000362516:E87A	E	-	2	0	ANGPTL2	128893886	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	7.997000	0.88414	2.082000	0.62665	0.533000	0.62120	GAG	.	.		0.557	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098		G	129854065	T	G	129854065	3	3	22	1	0	0	0	0	1	0	0	0	614	1551	54	5	323	5	ANGPTL2	9	129854065	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	5910336	129854065	11359366	67	2005										
C9orf163	158055	hgsc.bcm.edu	37	chr9	139379108	139379108	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gccggcggctggtgagggagGgggtgatatccgtgccacgc	20	10	0	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr9:139379108G>C	ENST00000354376.1	+	1	1162	c.208G>C	c.(208-210)Ggg>Cgg	p.G70R		NM_152571.2	NP_689784.1	Q8N9P6	CI163_HUMAN	chromosome 9 open reading frame 163	70										kidney(1)|lung(1)	2		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.36e-06)|Epithelial(140;5.65e-06)		GGTGAGGGAGGGGGTGATATC	0.687																																					p.G70R		Atlas-SNP	.											.	C9orf163	9	.	0			c.G208C						.						20	22	22					9																	139379108		2200	4297	6497	SO:0001583	missense	158055	exon1			AGGGAGGGGGTGA	AK055336	CCDS7001.1	9q34.3	2006-03-21			ENSG00000196366	ENSG00000196366			26718	protein-coding gene	gene with protein product							Standard	NM_152571		Approved	FLJ36779	uc004chy.3	Q8N9P6	OTTHUMG00000131725	ENST00000354376.1:c.208G>C	chr9.hg19:g.139379108G>C	ENSP00000346345:p.Gly70Arg	117.0	0.0		87.0	44.0	NM_152571		Missense_Mutation	SNP	ENST00000354376.1	hg19	CCDS7001.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.321036	0.23994	.	.	ENSG00000196366	ENST00000354376	T	0.58797	0.31	3.49	3.49	0.39957	.	.	.	.	.	T	0.54854	0.1884	N	0.08118	0	0.09310	N	1	D	0.71674	0.998	D	0.66979	0.948	T	0.49588	-0.8924	9	0.87932	D	0	.	11.1833	0.48642	0.0:0.0:1.0:0.0	.	70	Q8N9P6	CI163_HUMAN	R	70	ENSP00000346345:G70R	ENSP00000346345:G70R	G	+	1	0	C9orf163	138498929	1.000000	0.71417	0.006000	0.13384	0.103000	0.19146	2.215000	0.42862	1.901000	0.55032	0.511000	0.50034	GGG	.	.		0.687	C9orf163-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254644.1	NM_152571		C	139379108	G	C	139379108	3	2	22	1	0	0	0	0	1	0	0	0	2469	1232	43	4	210	4	C9orf163	9	139379108	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	9525043	139379108	1834323	68	2006										
ARMC3	219681	hgsc.bcm.edu	37	chr10	23292182	23292182	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cttttattgacagggctttaGatatccttgaagaagttaac	8	6	0	4			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr10:23292182G>C	ENST00000298032.5	+	13	1654	c.1570G>C	c.(1570-1572)Gat>Cat	p.D524H	ARMC3_ENST00000376528.4_Missense_Mutation_p.D261H|ARMC3_ENST00000409983.3_Missense_Mutation_p.D524H|ARMC3_ENST00000409049.3_Missense_Mutation_p.D524H	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	524						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CAGGGCTTTAGATATCCTTGA	0.358																																					p.D524H		Atlas-SNP	.											.	ARMC3	102	.	0			c.G1570C						.						70	71	71					10																	23292182		2203	4300	6503	SO:0001583	missense	219681	exon13			GCTTTAGATATCC	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"Armadillo repeat containing"	30964	protein-coding gene	gene with protein product	"cancer/testis antigen 81"	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1570G>C	chr10.hg19:g.23292182G>C	ENSP00000298032:p.Asp524His	163.0	0.0		144.0	56.0	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Missense_Mutation	SNP	ENST00000298032.5	hg19	CCDS7142.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.687452	0.68157	.	.	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000376523;ENST00000409049;ENST00000376528	T;T;T;T	0.66280	-0.2;-0.2;1.03;0.61	5.53	3.66	0.41972	Armadillo-like helical (1);	0.724237	0.14280	N	0.329594	T	0.71392	0.3334	M	0.65975	2.015	0.44454	D	0.997388	P;D	0.60160	0.842;0.987	P;P	0.55222	0.626;0.771	T	0.71185	-0.4667	10	0.66056	D	0.02	-9.1706	12.4944	0.55918	0.1385:0.0:0.8615:0.0	.	524;524	Q5W041-4;Q5W041	.;ARMC3_HUMAN	H	524;524;460;524;261	ENSP00000298032:D524H;ENSP00000386943:D524H;ENSP00000387288:D524H;ENSP00000365711:D261H	ENSP00000298032:D524H	D	+	1	0	ARMC3	23332188	1.000000	0.71417	0.978000	0.43139	0.993000	0.82548	4.386000	0.59620	0.677000	0.31305	0.563000	0.77884	GAT	.	.		0.358	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		C	23292182	G	C	23292182	3	2	22	1	0	0	0	0	1	0	0	0	952	942	33	4	1616	4	ARMC3	10	23292182	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10		23292182	112242565	69	2007										
CNNM1	26507	hgsc.bcm.edu	37	chr10	101120654	101120654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	agcggcatgacttctccttgTttaagctttcggacacggag	11	10	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr10:101120654T>C	ENST00000356713.4	+	3	2069	c.1780T>C	c.(1780-1782)Ttt>Ctt	p.F594L	CNNM1_ENST00000370528.3_Missense_Mutation_p.F523L|CNNM1_ENST00000446890.1_Missense_Mutation_p.F523L|CNNM1_ENST00000370534.4_Missense_Mutation_p.F229L	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	594					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		CTTCTCCTTGTTTAAGCTTTC	0.547																																					p.F594L		Atlas-SNP	.											.	CNNM1	101	.	0			c.T1780C						.						136	134	134					10																	101120654		2203	4300	6503	SO:0001583	missense	26507	exon3			TCCTTGTTTAAGC	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"cyclin M1"	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.1780T>C	chr10.hg19:g.101120654T>C	ENSP00000349147:p.Phe594Leu	55.0	0.0		75.0	34.0	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Missense_Mutation	SNP	ENST00000356713.4	hg19	CCDS7478.2	.	.	.	.	.	.	.	.	.	.	T	33	5.233422	0.95207	.	.	ENSG00000119946	ENST00000356713;ENST00000446890;ENST00000370528;ENST00000370534;ENST00000545665	D;D;D;T	0.85629	-2.01;-1.97;-1.92;-0.87	5.74	4.59	0.56863	.	0.000000	0.85682	D	0.000000	D	0.92678	0.7673	M	0.87682	2.9	0.80722	D	1	P;D;D;B	0.89917	0.842;1.0;0.989;0.125	B;D;D;B	0.91635	0.265;0.999;0.956;0.168	D	0.92957	0.6385	10	0.62326	D	0.03	-19.0144	12.9964	0.58648	0.0:0.0:0.1351:0.8649	.	229;594;229;594	F5H5J0;Q9NRU3-2;B7Z5S3;Q9NRU3	.;.;.;CNNM1_HUMAN	L	594;523;523;229;47	ENSP00000349147:F594L;ENSP00000406492:F523L;ENSP00000359559:F523L;ENSP00000359565:F229L	ENSP00000349147:F594L	F	+	1	0	CNNM1	101110644	1.000000	0.71417	0.982000	0.44146	0.973000	0.67179	8.040000	0.89188	0.981000	0.38548	-0.313000	0.08912	TTT	.	.		0.547	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348		C	101120654	T	C	101120654	3	2	22	1	0	0	0	0	1	0	0	0	3614	1725	60	2	1790	2	CNNM1	10	101120654	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	77828472	101120654	34414093	70	2008										
PCGF6	84108	hgsc.bcm.edu	37	chr10	105110554	105110554	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tcctcctcttcttcctcctcCagctcctcttcttcttccaa	1	20	5	0	rs375327410		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr10:105110554C>T	ENST00000369847.3	-	1	337	c.270G>A	c.(268-270)ctG>ctA	p.L90L	PCGF6_ENST00000490296.1_5'UTR|PCGF6_ENST00000337211.4_Silent_p.L90L	NM_001011663.1	NP_001011663.1	Q9BYE7	PCGF6_HUMAN	polycomb group ring finger 6	90	Glu-rich.				negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(3)	8		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)		cttcctcctccagctcctctt	0.642																																					p.L90L		Atlas-SNP	.											RNF134,right_lower_lobe,carcinoma,0,2	PCGF6	23	.	0			c.G270A						.	C	,	2,4382		0,2,2190	14	13	13		270,270	2.5	1	10		13	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	PCGF6	NM_001011663.1,NM_032154.3	,	0,2,6488	TT,TC,CC		0.0,0.0456,0.0154	,	90/351,90/276	105110554	2,12978	2192	4298	6490	SO:0001819	synonymous_variant	84108	exon1			CTCCTCCAGCTCC	AB047006	CCDS7546.1, CCDS31275.1	10q24.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000156374	ENSG00000156374		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	21156	protein-coding gene	gene with protein product		607816	"ring finger protein 134"	RNF134		12167161	Standard	NM_032154		Approved	MBLR	uc001kwt.3	Q9BYE7	OTTHUMG00000018982	ENST00000369847.3:c.270G>A	chr10.hg19:g.105110554C>T		76.0	0.0		74.0	8.0	NM_001011663	A8K3R4|Q5SYD1|Q5SYD6|Q96ID9|Q96SJ1	Silent	SNP	ENST00000369847.3	hg19	CCDS31275.1																																																																																			.	.		0.642	PCGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050132.1	NM_032154		T	105110554	C	T	105110554	2	4	22	1	0	0	0	0	0	0	0	1	11587	581	21	3		3	PCGF6	10	105110554	Silent	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	3989900	105110554	30424193	71	2009										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6643123	6643123	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gacaacgggtgagcgagcagCcagaggagacagagagggtg	19	7	0	4			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr11:6643123C>G	ENST00000299441.3	-	21	10195	c.9784G>C	c.(9784-9786)Gct>Cct	p.A3262P	RP11-732A19.5_ENST00000526456.1_RNA|TPP1_ENST00000534644.1_5'Flank|TPP1_ENST00000299427.6_5'Flank|TPP1_ENST00000533371.1_5'Flank|TPP1_ENST00000528657.1_5'Flank|RP11-732A19.9_ENST00000545572.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	3262					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGCGAGCAGCCAGAGGAGAC	0.627																																					p.A3262P		Atlas-SNP	.											.	DCHS1	277	.	0			c.G9784C						.						58	52	54					11																	6643123		2201	4296	6497	SO:0001583	missense	8642	exon21			GAGCAGCCAGAGG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.9784G>C	chr11.hg19:g.6643123C>G	ENSP00000299441:p.Ala3262Pro	59.0	0.0		69.0	12.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.45|17.45	3.393418|3.393418	0.62066|0.62066	.|.	.|.	ENSG00000166341|ENSG00000166341	ENST00000299441|ENST00000442153	T|.	0.70282|.	-0.47|.	5.01|5.01	5.01|5.01	0.66863|0.66863	.|.	0.000000|.	0.42053|.	D|.	0.000772|.	T|T	0.79399|0.79399	0.4439|0.4439	M|M	0.83483|0.83483	2.645|2.645	0.58432|0.58432	D|D	0.999999|0.999999	P|.	0.42409|.	0.779|.	B|.	0.32149|.	0.141|.	T|T	0.82829|0.82829	-0.0264|-0.0264	10|6	0.66056|0.87932	D|D	0.02|0	.|.	17.0523|17.0523	0.86523|0.86523	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	3262|.	Q96JQ0|.	PCD16_HUMAN|.	P|C	3262|21	ENSP00000299441:A3262P|.	ENSP00000299441:A3262P|ENSP00000390601:W21C	A|W	-|-	1|3	0|0	DCHS1|DCHS1	6599699|6599699	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	7.611000|7.611000	0.82962|0.82962	2.595000|2.595000	0.87683|0.87683	0.462000|0.462000	0.41574|0.41574	GCT|TGG	.	.		0.627	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		G	6643123	C	G	6643123	3	3	22	1	0	0	0	0	1	0	0	0	4289	739	26	4	116	4	DCHS1	11	6643123	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10		6643123	128363393	72	2010										
OR2AG1	144125	hgsc.bcm.edu	37	chr11	6806964	6806964	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ctccatatgccatcaaatgaGgggaggaagaaagcccttgt	11	9	1	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr11:6806964G>A	ENST00000307401.4	+	1	717	c.696G>A	c.(694-696)gaG>gaA	p.E232E		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATCAAATGAGGGGAGGAAGA	0.488																																					p.E232E		Atlas-SNP	.											.	OR2AG1	57	.	0			c.G696A						.						192	168	176					11																	6806964		2201	4296	6497	SO:0001819	synonymous_variant	144125	exon1			AAATGAGGGGAGG	AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"GPCR / Class A : Olfactory receptors"	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.696G>A	chr11.hg19:g.6806964G>A		84.0	0.0		67.0	31.0	NM_001004489	B9EKV7|Q6IFG7|Q96R26	Silent	SNP	ENST00000307401.4	hg19	CCDS31414.1																																																																																			.	.		0.488	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385980.1	NM_001004489		A	6806964	G	A	6806964	2	1	22	1	0	0	0	0	0	0	0	1	10993	991	35	3		3	OR2AG1	11	6806964	Silent	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	163841	6806964	128199552	73	2011										
ROM1	6094	hgsc.bcm.edu	37	chr11	62381849	62381849	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ttcagactcctacgcccaccCcctgttcgatccccgacaac	5	20	1	1	rs374111556		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr11:62381849C>G	ENST00000278833.3	+	2	1251	c.710C>G	c.(709-711)cCc>cGc	p.P237R	ROM1_ENST00000534093.1_Missense_Mutation_p.P28A|EML3_ENST00000394773.2_5'Flank|EML3_ENST00000278845.4_5'Flank|EML3_ENST00000494176.2_5'Flank|EML3_ENST00000529309.1_5'Flank	NM_000327.3	NP_000318	Q03395	ROM1_HUMAN	retinal outer segment membrane protein 1	237					camera-type eye photoreceptor cell differentiation (GO:0060219)|cell adhesion (GO:0007155)|regulation of gene expression (GO:0010468)|retina vasculature development in camera-type eye (GO:0061298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	8						TACGCCCACCCCCTGTTCGAT	0.602																																					p.P237R		Atlas-SNP	.											.	ROM1	32	.	0			c.C710G						.	C	ARG/PRO	1,4403	2.1+/-5.4	0,1,2201	102	99	100		710	5.1	1	11		100	0,8598		0,0,4299	no	missense	ROM1	NM_000327.3	103	0,1,6500	GG,GC,CC		0.0,0.0227,0.0077	probably-damaging	237/352	62381849	1,13001	2202	4299	6501	SO:0001583	missense	6094	exon2			CCCACCCCCTGTT	L07894	CCDS8024.1	11q13	2013-02-14				ENSG00000149489		"Tetraspanins"	10254	protein-coding gene	gene with protein product		180721				8504299	Standard	NM_000327		Approved	TSPAN23, ROM	uc001ntv.3	Q03395		ENST00000278833.3:c.710C>G	chr11.hg19:g.62381849C>G	ENSP00000278833:p.Pro237Arg	84.0	0.0		53.0	15.0	NM_000327	B2R978	Missense_Mutation	SNP	ENST00000278833.3	hg19	CCDS8024.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.83|16.83	3.232563|3.232563	0.58777|0.58777	2.27E-4|2.27E-4	0.0|0.0	ENSG00000149489|ENSG00000149489	ENST00000525801;ENST00000534093;ENST00000525947|ENST00000278833	.|T	.|0.78816	.|-1.21	5.05|5.05	5.05|5.05	0.67936|0.67936	.|Tetraspanin, EC2 domain (1);	0.224693|0.224693	0.39341|0.39341	N|N	0.001393|0.001393	T|T	0.81456|0.81456	0.4826|0.4826	L|L	0.44542|0.44542	1.39|1.39	0.35660|0.35660	D|D	0.812427|0.812427	.|D	.|0.65815	.|0.995	.|D	.|0.66497	.|0.944	D|D	0.84417|0.84417	0.0569|0.0569	7|10	0.87932|0.44086	D|T	0|0.13	-28.2708|-28.2708	11.3965|11.3965	0.49845|0.49845	0.1808:0.8191:0.0:0.0|0.1808:0.8191:0.0:0.0	.|.	.|237	.|Q03395	.|ROM1_HUMAN	A|R	28|237	.|ENSP00000278833:P237R	ENSP00000433566:P28A|ENSP00000278833:P237R	P|P	+|+	1|2	0|0	ROM1|ROM1	62138425|62138425	0.998000|0.998000	0.40836|0.40836	0.997000|0.997000	0.53966|0.53966	0.829000|0.829000	0.46940|0.46940	1.729000|1.729000	0.38115|0.38115	2.514000|2.514000	0.84764|0.84764	0.462000|0.462000	0.41574|0.41574	CCC|CCC	.	.		0.602	ROM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394929.1	NM_000327		G	62381849	C	G	62381849	3	3	22	1	0	0	0	0	1	0	0	0	13536	623	22	4	716	4	ROM1	11	62381849	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	55574885	62381849	72624667	74	2012										
B3GAT3	26229	hgsc.bcm.edu	37	chr11	62389402	62389402	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aagtaggcgagaaacacgttCttcagcttcagcttcatggc	10	10	4	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr11:62389402C>T	ENST00000265471.5	-	1	245	c.18G>A	c.(16-18)aaG>aaA	p.K6K	B3GAT3_ENST00000534026.1_Silent_p.K6K|B3GAT3_ENST00000531383.1_Silent_p.K6K	NM_012200.3	NP_036332.2	O94766	B3GA3_HUMAN	beta-1,3-glucuronyltransferase 3	6					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|glucuronosyltransferase activity (GO:0015020)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)|urinary_tract(1)	12						GAAACACGTTCTTCAGCTTCA	0.726																																					p.K6K		Atlas-SNP	.											.	B3GAT3	24	.	0			c.G18A						.						48	43	45					11																	62389402		2202	4296	6498	SO:0001819	synonymous_variant	26229	exon1			CACGTTCTTCAGC	AB009598	CCDS8025.1	11q12	2014-07-08	2014-07-08		ENSG00000149541	ENSG00000149541	2.4.1.135	"Beta-1,3-glucuronyltransferases"	923	protein-coding gene	gene with protein product	"glucuronosyltransferase I", "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3"	606374	"beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)"			9506957	Standard	NM_012200		Approved	GlcAT-I	uc001ntw.3	O94766	OTTHUMG00000167685	ENST00000265471.5:c.18G>A	chr11.hg19:g.62389402C>T		216.0	0.0		177.0	9.0	NM_012200	B7ZAB3|Q96I06|Q9UEP0	Silent	SNP	ENST00000265471.5	hg19	CCDS8025.1																																																																																			.	.		0.726	B3GAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395588.1	NM_012200		T	62389402	C	T	62389402	2	4	22	1	0	0	0	0	0	0	0	1	1255	912	32	3		3	B3GAT3	11	62389402	Silent	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	7553	62389402	72617114	75	2013										
MRGPRF	116535	hgsc.bcm.edu	37	chr11	68772841	68772841	+	Frame_Shift_Del	DEL	C	C	-													0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ctcagcgccgtcccgcagggCccgctggaagaccaccctga							TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr11:68772841delC	ENST00000309099.6	-	3	1319	c.937delG	c.(937-939)gccfs	p.A313fs	RP11-554A11.5_ENST00000562506.1_RNA|MRGPRF_ENST00000441623.1_Frame_Shift_Del_p.A313fs	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	313						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TCCCGCAGGGCCCGCTGGAAG	0.682																																					p.A313fs		Atlas-INDEL	.											.	MRGPRF	22	.	0			c.938delC						.						13	11	11					11																	68772841		2175	4265	6440	SO:0001589	frameshift_variant	116535	exon3			.	AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"GPCR / Class A : Orphans"	24828	protein-coding gene	gene with protein product		607233	"G protein-coupled receptor 168", "G protein-coupled receptor 140"	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.937delG	chr11.hg19:g.68772841delC	ENSP00000309782:p.Ala313fs	48.0	0.0		28.0	13.0	NM_001098515	B3KV43|Q8NBK8	Frame_Shift_Del	DEL	ENST00000309099.6	hg19	CCDS8188.1																																																																																			.	.		0.682	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015		-	68772841	C	-	68772841	7	5	22	1	0	1	0	1	0	0	0	0	9774	739	26	0	98	0	MRGPRF	11	68772841	Frame_Shift_Del	DEL	C	TCGA-3K-AAZ8-01A-12D-A38X-10	6383439	68772841	66233675	76	2014										
ACER3	55331	hgsc.bcm.edu	37	chr11	76727823	76727823	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ctatcttcacatccttttcaGgtaggaaatagagacttttt	6	8	3	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr11:76727823G>C	ENST00000532485.1	+	9	808	c.704G>C	c.(703-705)aGt>aCt	p.S235T	ACER3_ENST00000526597.1_Splice_Site_p.S140T|ACER3_ENST00000533873.1_Splice_Site_p.S198T|ACER3_ENST00000544113.1_Splice_Site_p.S102T|ACER3_ENST00000538157.1_Splice_Site_p.S193T	NM_018367.5	NP_060837.3	Q9NUN7	ACER3_HUMAN	alkaline ceramidase 3	235					ceramide metabolic process (GO:0006672)|phytosphingosine biosynthetic process (GO:0071602)|positive regulation of cell proliferation (GO:0008284)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of Golgi membrane (GO:0030173)	phytoceramidase activity (GO:0070774)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	9						ATCCTTTTCAGGTAGGAAATA	0.323																																					p.S235T		Atlas-SNP	.											.	ACER3	19	.	0			c.G704C						.						134	113	120					11																	76727823		2200	4292	6492	SO:0001630	splice_region_variant	55331	exon9			TTTTCAGGTAGGA	AF214454	CCDS8247.1, CCDS73352.1	11q13.5	2013-01-25	2008-12-19	2008-12-19	ENSG00000078124	ENSG00000078124	3.5.1.23	"Alkaline ceramidase"	16066	protein-coding gene	gene with protein product	"alkaline phytoceramidase"		"phytoceramidase, alkaline"	PHCA		11356846, 18619555	Standard	XM_005274090		Approved	FLJ11238, APHC	uc009yum.1	Q9NUN7	OTTHUMG00000165225	ENST00000532485.1:c.704+1G>C	chr11.hg19:g.76727823G>C		82.0	0.0		66.0	19.0	NM_018367	B2RC99	Missense_Mutation	SNP	ENST00000532485.1	hg19	CCDS8247.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.985215	0.53934	.	.	ENSG00000078124	ENST00000534206;ENST00000532485;ENST00000526597;ENST00000533873;ENST00000538157;ENST00000544113	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.41073	0.1143	L	0.55834	1.745	0.80722	D	1	B;B	0.29612	0.136;0.251	B;B	0.28709	0.054;0.093	T	0.27088	-1.0084	10	0.39692	T	0.17	-3.2967	16.3566	0.83237	0.0:0.0:1.0:0.0	.	198;235	B7Z2Q2;Q9NUN7	.;ACER3_HUMAN	T	193;235;140;198;193;102	ENSP00000435733:S193T;ENSP00000434480:S235T;ENSP00000431149:S140T;ENSP00000436252:S198T;ENSP00000440916:S193T;ENSP00000440663:S102T	ENSP00000431149:S140T	S	+	2	0	ACER3	76405471	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.737000	0.84957	2.446000	0.82766	0.555000	0.69702	AGT	.	.		0.323	ACER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382770.2	NM_018367	Missense_Mutation	C	76727823	G	C	76727823	5	2	22	1	0	0	0	0	0	0	1	0	140	1014	35	4	738	4	ACER3	11	76727823	Splice_Site	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	7954982	76727823	58278693	77	2015										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117374731	117374731	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gtggtactgctgggggttccCgctccctggaaggaggcagc	17	11	0	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr11:117374731C>T	ENST00000321322.6	-	11	2369	c.2368G>A	c.(2368-2370)Ggg>Agg	p.G790R	DSCAML1_ENST00000527706.1_Missense_Mutation_p.G520R	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	730	Ig-like C2-type 9.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		TGGGGGTTCCCGCTCCCTGGA	0.632																																					p.G790R		Atlas-SNP	.											.	DSCAML1	286	.	0			c.G2368A						.						71	69	70					11																	117374731		2201	4296	6497	SO:0001583	missense	57453	exon11			GGTTCCCGCTCCC		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2368G>A	chr11.hg19:g.117374731C>T	ENSP00000315465:p.Gly790Arg	72.0	0.0		56.0	13.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689871	0.88735	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.66638	-0.22;-0.22	4.29	4.29	0.51040	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65196	0.2668	N	0.05554	-0.025	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65721	-0.6099	9	0.22109	T	0.4	.	16.9369	0.86205	0.0:1.0:0.0:0.0	.	730	Q8TD84	DSCL1_HUMAN	R	520;790;497	ENSP00000434335:G520R;ENSP00000315465:G790R	ENSP00000315465:G790R	G	-	1	0	DSCAML1	116879941	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.605000	0.82844	2.237000	0.73441	0.462000	0.41574	GGG	.	.		0.632	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117374731	C	T	117374731	3	4	22	1	0	0	0	0	1	0	0	0	4771	652	23	1	4065	1	DSCAML1	11	117374731	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	40646908	117374731	17631785	78	2016										
OR8B4	283162	hgsc.bcm.edu	37	chr11	124294237	124294237	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aagagggggagaacgtcacaCagataatggtcaatgacgtt	13	6	2	4			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr11:124294237C>A	ENST00000356130.3	-	1	552	c.531G>T	c.(529-531)ctG>ctT	p.L177L		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GAACGTCACACAGATAATGGT	0.507																																					p.L177L		Atlas-SNP	.											.	OR8B4	60	.	0			c.G531T						.						92	63	73					11																	124294237		2201	4299	6500	SO:0001819	synonymous_variant	283162	exon1			GTCACACAGATAA	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"GPCR / Class A : Olfactory receptors"	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.531G>T	chr11.hg19:g.124294237C>A		138.0	0.0		90.0	52.0	NM_001005196	B2RNF8|Q6IFQ7	Silent	SNP	ENST00000356130.3	hg19	CCDS31710.1																																																																																			.	.		0.507	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196		A	124294237	C	A	124294237	2	1	22	1	0	0	0	0	0	0	0	1	11238	465	17	3		3	OR8B4	11	124294237	Silent	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	6919506	124294237	10712279	79	2017										
CHEK1	1111	hgsc.bcm.edu	37	chr11	125496682	125496683	+	Frame_Shift_Ins	INS	-	-	A													0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	catggcagtgccctttgtggINSaagactgggacttggtgcaa							TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr11:125496682_125496683insA	ENST00000534070.1	+	2	274_275	c.19_20insA	c.(19-21)gaafs	p.E7fs	CHEK1_ENST00000428830.2_Frame_Shift_Ins_p.E7fs|CHEK1_ENST00000438015.1_Frame_Shift_Ins_p.E7fs|CHEK1_ENST00000532449.1_3'UTR|CHEK1_ENST00000278916.3_Frame_Shift_Ins_p.E7fs|CHEK1_ENST00000524737.1_Frame_Shift_Ins_p.E7fs|CHEK1_ENST00000544373.1_Frame_Shift_Ins_p.E7fs|CHEK1_ENST00000427383.2_Frame_Shift_Ins_p.K98fs	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	7	Interaction with CLSPN. {ECO:0000250}.				cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		GCCCTTTGTGGAAGACTGGGAC	0.49								Other conserved DNA damage response genes			OREG0021478	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E7fs		Atlas-Indel,Pindel	.											.	CHEK1	44	.	0			c.19_20insA						.																																			SO:0001589	frameshift_variant	1111	exon2			.	AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"CHK1 (checkpoint, S.pombe) homolog", "CHK1 checkpoint homolog (S. pombe)"			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.21dupA	chr11.hg19:g.125496684_125496684dupA	ENSP00000435371:p.Glu7fs	155.0	0.0	1542	159.0	26.0	NM_001114122	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Frame_Shift_Ins	INS	ENST00000534070.1	hg19	CCDS8459.1																																																																																			.	.		0.49	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274		A	125496683	-	A	125496682	7	5	22	1	0	1	1	0	0	0	0	0	3336	1175	41	0	21	0	CHEK1	11	125496682	Frame_Shift_Ins	INS	-	TCGA-3K-AAZ8-01A-12D-A38X-10	1202445	125496682	9509834	80	2018										
LEPREL2	10536	hgsc.bcm.edu	37	chr12	6946251	6946251	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cggtgcttaaggctgcgcagGtgagcacaggaggcacccgg	17	11	0	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr12:6946251G>A	ENST00000538102.1	+	0	710				LEPREL2_ENST00000396725.2_RNA|LEPREL2_ENST00000606935.1_RNA|LEPREL2_ENST00000251761.8_RNA			Q8IVL6	P3H3_HUMAN	leprecan-like 2						extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)	endoplasmic reticulum lumen (GO:0005788)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)			breast(1)|cervix(1)|endometrium(2)|lung(6)	10					L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	GGCTGCGCAGGTGAGCACAGG	0.667																																					.		Atlas-SNP	.											.	LEPREL2	87	.	0			c.1559+1G>A						.						26	28	28					12																	6946251		1967	4153	6120			10536	exon10			GCGCAGGTGAGCA	U47926	CCDS61027.1	12p13.31	2014-03-25			ENSG00000110811	ENSG00000110811			19318	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 3"	610342				15063763	Standard	NM_014262		Approved	GRCB, HSU47926, P3H3		Q8IVL6	OTTHUMG00000168516		chr12.hg19:g.6946251G>A		23.0	0.0		15.0	12.0	NM_014262	Q13512|Q15740|Q66K32|Q6NX61|Q7L2T1	Splice_Site	SNP	ENST00000538102.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.82	3.229547	0.58777	.	.	ENSG00000110811	ENST00000396725;ENST00000290510	.	.	.	4.35	4.35	0.52113	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0709	0.86573	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LEPREL2	6816512	1.000000	0.71417	1.000000	0.80357	0.492000	0.33523	8.374000	0.90133	2.253000	0.74438	0.462000	0.41574	.	.	.		0.667	LEPREL2-006	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000399998.1	NM_014262		A	6946251	G	A	6946251	1	1	22	0	1	0	0	0	0	0	0	0	8740	1275	44	3		3	LEPREL2	12	6946251	RNA	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10		6946251	126905644	81	2019										
C12orf77	196415	hgsc.bcm.edu	37	chr12	25148920	25148920	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	acaggagttgcaggcatccaTcgtatgctgtccagcgtctg	12	11	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr12:25148920T>A	ENST00000549828.1	-	3	432	c.228A>T	c.(226-228)cgA>cgT	p.R76R	C12orf77_ENST00000434912.3_Silent_p.R21R|C12orf77_ENST00000549262.1_Silent_p.R21R	NM_001101339.1	NP_001094809.1	C9JDV5	CL097_HUMAN	chromosome 12 open reading frame 77	76										endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7						CAGGCATCCATCGTATGCTGT	0.502																																					p.R76R		Atlas-SNP	.											.	C12orf77	18	.	0			c.A228T						.						85	90	88					12																	25148920		1991	4157	6148	SO:0001819	synonymous_variant	196415	exon3			CATCCATCGTATG	BC046192	CCDS44846.1	12p12.1	2009-09-30			ENSG00000226397	ENSG00000226397			27282	protein-coding gene	gene with protein product						12477932	Standard	NM_001101339		Approved		uc001rgf.3	C9JDV5	OTTHUMG00000170185	ENST00000549828.1:c.228A>T	chr12.hg19:g.25148920T>A		134.0	0.0		143.0	75.0	NM_001101339		Silent	SNP	ENST00000549828.1	hg19	CCDS44846.1																																																																																			.	.		0.502	C12orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407827.1	NM_001101339		A	25148920	T	A	25148920	2	1	22	1	0	0	0	0	0	0	0	1	1718	1422	50	4		4	C12orf77	12	25148920	Silent	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	18202669	25148920	108702975	82	2020										
DENND5B	160518	hgsc.bcm.edu	37	chr12	31633069	31633069	+	Frame_Shift_Del	DEL	A	A	-													0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cttacttgtaacttcttcatAaaaagtgagaacaaaaccat							TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr12:31633069delA	ENST00000389082.5	-	3	622	c.358delT	c.(358-360)tatfs	p.Y120fs	DENND5B_ENST00000354285.4_Frame_Shift_Del_p.Y142fs|DENND5B_ENST00000545147.1_Intron|DENND5B_ENST00000306833.6_Frame_Shift_Del_p.Y155fs|DENND5B_ENST00000536562.1_Frame_Shift_Del_p.Y155fs	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	120	UDENN.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						ACTTCTTCATAAAAAGTGAGA	0.413																																					p.Y120fs		Atlas-Indel,Pindel	.											.	DENND5B	114	.	0			c.359delA						.						61	58	59					12																	31633069		1959	4165	6124	SO:0001589	frameshift_variant	160518	exon3			.	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.358delT	chr12.hg19:g.31633069delA	ENSP00000373734:p.Tyr120fs	104.0	0.0		80.0	36.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Frame_Shift_Del	DEL	ENST00000389082.5	hg19	CCDS44857.1																																																																																			.	.		0.413	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		-	31633069	A	-	31633069	7	5	22	1	0	1	0	1	0	0	0	0	4439	362	13	0	3542	0	DENND5B	12	31633069	Frame_Shift_Del	DEL	A	TCGA-3K-AAZ8-01A-12D-A38X-10	6484149	31633069	102218826	83	2021										
ARID2	196528	hgsc.bcm.edu	37	chr12	46231189	46231189	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aatgtcaagggatagattttTaaagatgagaggtgagtttt	12	1	1	4			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr12:46231189T>G	ENST00000334344.6	+	9	1281	c.1109T>G	c.(1108-1110)tTa>tGa	p.L370*	ARID2_ENST00000444670.1_5'UTR|ARID2_ENST00000422737.1_Nonsense_Mutation_p.L221*|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	370					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GATAGATTTTTAAAGATGAGA	0.303			"N, S, F"		hepatocellular carcinoma																																p.L370X		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.T1109G						.						68	75	73					12																	46231189		2201	4297	6498	SO:0001587	stop_gained	196528	exon9			GATTTTTAAAGAT		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1109T>G	chr12.hg19:g.46231189T>G	ENSP00000335044:p.Leu370*	131.0	0.0		105.0	53.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Nonsense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	T	39	7.866150	0.98534	.	.	ENSG00000189079	ENST00000334344;ENST00000422737	.	.	.	5.33	5.33	0.75918	.	0.072848	0.53938	D	0.000041	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-0.1393	15.3006	0.73949	0.0:0.0:0.0:1.0	.	.	.	.	X	370;221	.	ENSP00000335044:L370X	L	+	2	0	ARID2	44517456	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.698000	0.84413	2.011000	0.59026	0.260000	0.18958	TTA	.	.		0.303	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		G	46231189	T	G	46231189	4	3	22	1	0	0	0	0	0	1	0	0	915	1764	61	5	1143	5	ARID2	12	46231189	Nonsense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	14598120	46231189	87620706	84	2022										
MLL2	8085	hgsc.bcm.edu	37	chr12	49445845	49445845	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tggggacaggggcgatgcttCaggtggtggggatagaggcg	22	5	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr12:49445845C>T	ENST00000301067.7	-	10	1620	c.1621G>A	c.(1621-1623)Gaa>Aaa	p.E541K		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	541	15 X 5 AA repeats of S/P-P-P-E/P-E/A.|Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GGCGATGCTTCAGGTGGTGGG	0.577																																					p.E541K		Atlas-SNP	.											.	MLL2	1173	.	0			c.G1621A						.						76	83	81					12																	49445845		2088	4209	6297	SO:0001583	missense	8085	exon10			ATGCTTCAGGTGG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.1621G>A	chr12.hg19:g.49445845C>T	ENSP00000301067:p.Glu541Lys	135.0	0.0		120.0	23.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	9.111	1.006505	0.19199	.	.	ENSG00000167548	ENST00000301067	T	0.80393	-1.37	3.69	2.8	0.32819	.	.	.	.	.	T	0.64000	0.2559	N	0.14661	0.345	0.21762	N	0.999559	B	0.02656	0.0	B	0.01281	0.0	T	0.56396	-0.7986	9	0.87932	D	0	.	5.8266	0.18556	0.0:0.7639:0.0:0.2361	.	541	O14686	MLL2_HUMAN	K	541	ENSP00000301067:E541K	ENSP00000301067:E541K	E	-	1	0	MLL2	47732112	0.000000	0.05858	0.986000	0.45419	0.844000	0.47949	-0.211000	0.09332	1.142000	0.42291	0.313000	0.20887	GAA	.	.		0.577	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49445845	C	T	49445845	3	4	22	1	0	0	0	0	1	0	0	0	9630	835	29	3	15172	3	MLL2	12	49445845	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	3214656	49445845	84406050	85	2023										
LRP1	4035	hgsc.bcm.edu	37	chr12	57562953	57562953	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tggggacaacagtgacgaagCcggctgcagccactcctgtt	13	12	0	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr12:57562953C>A	ENST00000243077.3	+	20	3492	c.3026C>A	c.(3025-3027)gCc>gAc	p.A1009D	LRP1_ENST00000553446.1_3'UTR	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1009	LDL-receptor class A 6. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	AGTGACGAAGCCGGCTGCAGC	0.607																																					p.A1009D		Atlas-SNP	.											.	LRP1	428	.	0			c.C3026A						.						71	66	68					12																	57562953		2203	4300	6503	SO:0001583	missense	4035	exon20			ACGAAGCCGGCTG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.3026C>A	chr12.hg19:g.57562953C>A	ENSP00000243077:p.Ala1009Asp	57.0	0.0		65.0	41.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.936664	0.73442	.	.	ENSG00000123384	ENST00000243077	D	0.95482	-3.72	4.97	4.08	0.47627	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.161263	0.39544	N	0.001332	D	0.88908	0.6565	N	0.25789	0.76	0.80722	D	1	B	0.15719	0.014	B	0.16289	0.015	T	0.81477	-0.0915	10	0.12103	T	0.63	.	7.4899	0.27456	0.1647:0.7496:0.0:0.0857	.	1009	Q07954	LRP1_HUMAN	D	1009	ENSP00000243077:A1009D	ENSP00000243077:A1009D	A	+	2	0	LRP1	55849220	0.670000	0.27512	0.950000	0.38849	0.991000	0.79684	1.145000	0.31577	1.336000	0.45506	0.561000	0.74099	GCC	.	.		0.607	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57562953	C	A	57562953	3	1	22	1	0	0	0	0	1	0	0	0	8960	739	26	3	3104	3	LRP1	12	57562953	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	8117108	57562953	76288942	86	2024										
P2RX7	5027	hgsc.bcm.edu	37	chr12	121622253	121622253	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tagccccgtctggtgccagtGtggaagctgcctcccatctc	11	15	2	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr12:121622253G>A	ENST00000546057.1	+	13	1579	c.1436G>A	c.(1435-1437)tGt>tAt	p.C479Y	P2RX7_ENST00000328963.5_Missense_Mutation_p.C309Y|P2RX7_ENST00000541446.1_Missense_Mutation_p.C190Y|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000535250.1_Missense_Mutation_p.C389Y	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	479					apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGGTGCCAGTGTGGAAGCTGC	0.602																																					p.C479Y		Atlas-SNP	.											.	P2RX7	53	.	0			c.G1436A						.						60	56	57					12																	121622253		2203	4300	6503	SO:0001583	missense	5027	exon13			GCCAGTGTGGAAG	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.1436G>A	chr12.hg19:g.121622253G>A	ENSP00000442349:p.Cys479Tyr	52.0	0.0		70.0	11.0	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	hg19	CCDS9213.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.478629	0.63849	.	.	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.37411	2.48;1.84;2.21;1.2	5.21	5.21	0.72293	.	0.000000	0.49305	D	0.000151	T	0.64616	0.2614	M	0.85197	2.74	0.50171	D	0.999858	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.999;0.999	T	0.70813	-0.4770	10	0.87932	D	0	.	15.4642	0.75387	0.0:0.0:1.0:0.0	.	309;190;389;479	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	Y	479;309;389;190	ENSP00000442349:C479Y;ENSP00000330696:C309Y;ENSP00000442572:C389Y;ENSP00000437471:C190Y	ENSP00000330696:C309Y	C	+	2	0	P2RX7	120106636	1.000000	0.71417	0.976000	0.42696	0.539000	0.34962	6.856000	0.75450	2.429000	0.82318	0.591000	0.81541	TGT	.	.		0.602	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562		A	121622253	G	A	121622253	3	1	22	1	0	0	0	0	1	0	0	0	11354	1377	48	3	1486	3	P2RX7	12	121622253	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	64059300	121622253	12229642	87	2025										
KNTC1	9735	hgsc.bcm.edu	37	chr12	123057714	123057714	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tacaaccaccatagtgttccGaatgtttgataaagtgctgg	9	8	0	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr12:123057714G>C	ENST00000333479.7	+	26	2342	c.2165G>C	c.(2164-2166)cGa>cCa	p.R722P	KNTC1_ENST00000450485.2_Missense_Mutation_p.R685P	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	722					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		ATAGTGTTCCGAATGTTTGAT	0.378																																					p.R722P		Atlas-SNP	.											KNTC1,NS,carcinoma,0,1	KNTC1	182	.	0			c.G2165C						.						122	119	120					12																	123057714		1844	4085	5929	SO:0001583	missense	9735	exon26			TGTTCCGAATGTT		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.2165G>C	chr12.hg19:g.123057714G>C	ENSP00000328236:p.Arg722Pro	155.0	0.0		143.0	34.0	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	hg19	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.925374	0.52759	.	.	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.25749	1.78;2.3	5.45	5.45	0.79879	.	0.132610	0.53938	D	0.000056	T	0.48943	0.1528	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77557	0.99;0.957	T	0.27331	-1.0077	10	0.35671	T	0.21	-9.528	19.2801	0.94050	0.0:0.0:1.0:0.0	.	685;722	E7ES84;P50748	.;KNTC1_HUMAN	P	685;722	ENSP00000397992:R685P;ENSP00000328236:R722P	ENSP00000328236:R722P	R	+	2	0	KNTC1	121623667	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.320000	0.65841	2.570000	0.86706	0.655000	0.94253	CGA	.	.		0.378	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			C	123057714	G	C	123057714	3	2	22	1	0	0	0	0	1	0	0	0	8437	1058	37	4	2263	4	KNTC1	12	123057714	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	1435461	123057714	10794181	88	2026										
FOXO1	2308	hgsc.bcm.edu	37	chr13	41134803	41134803	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tcctggccagactggagagaTgctttcttcttggcagctcg	12	11	2	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr13:41134803T>C	ENST00000379561.5	-	2	1209	c.825A>G	c.(823-825)gcA>gcG	p.A275A	FOXO1_ENST00000473775.1_5'Flank	NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	275					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		ACTGGAGAGATGCTTTCTTCT	0.527																																					p.A275A		Atlas-SNP	.											.	FOXO1	110	.	0			c.A825G						.						88	81	84					13																	41134803		2203	4300	6503	SO:0001819	synonymous_variant	2308	exon2			GAGAGATGCTTTC		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"Forkhead boxes"	3819	protein-coding gene	gene with protein product		136533	"forkhead homolog in rhabdomyosarcoma"	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.825A>G	chr13.hg19:g.41134803T>C		129.0	0.0		101.0	25.0	NM_002015	O43523|Q5VYC7|Q6NSK6	Silent	SNP	ENST00000379561.5	hg19	CCDS9371.1																																																																																			.	.		0.527	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015		C	41134803	T	C	41134803	2	2	22	1	0	0	0	0	0	0	0	1	6031	1451	51	2		2	FOXO1	13	41134803	Silent	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10		41134803	74035075	89	2027										
PCDH20	64881	hgsc.bcm.edu	37	chr13	61985776	61985776	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cactcactttcaccagtaagCgatggagcccataatctgtc	7	13	3	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr13:61985776C>T	ENST00000409186.1	-	5	4561	c.2456G>A	c.(2455-2457)cGc>cAc	p.R819H	PCDH20_ENST00000409204.4_Missense_Mutation_p.R819H			Q8N6Y1	PCD20_HUMAN	protocadherin 20	819	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		CACCAGTAAGCGATGGAGCCC	0.478																																					p.R819H		Atlas-SNP	.											.	PCDH20	265	.	0			c.G2456A						.						132	123	126					13																	61985776		2203	4300	6503	SO:0001583	missense	64881	exon2			AGTAAGCGATGGA	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.2456G>A	chr13.hg19:g.61985776C>T	ENSP00000386653:p.Arg819His	98.0	0.0		85.0	14.0	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	hg19	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	C	20.9	4.067874	0.76301	.	.	ENSG00000197991	ENST00000409204;ENST00000409186;ENST00000358674	T;T	0.51817	0.69;0.69	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000006	T	0.48466	0.1501	L	0.58101	1.795	0.58432	D	0.999998	B	0.31383	0.321	B	0.25405	0.06	T	0.50065	-0.8871	10	0.87932	D	0	.	20.1338	0.98010	0.0:1.0:0.0:0.0	.	819	A8K1K9	.	H	819;819;565	ENSP00000387250:R819H;ENSP00000386653:R819H	ENSP00000351500:R565H	R	-	2	0	PCDH20	60883777	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.745000	0.85046	2.770000	0.95276	0.655000	0.94253	CGC	.	.		0.478	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		T	61985776	C	T	61985776	3	4	22	1	0	0	0	0	1	0	0	0	11524	768	27	1	403	1	PCDH20	13	61985776	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	20850973	61985776	53184102	90	2028										
PRKCH	5583	hgsc.bcm.edu	37	chr14	61924300	61924300	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gaaggacgtgattctgcaggAtgatgatgtggaatgcacca	14	6	1	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr14:61924300A>T	ENST00000332981.5	+	9	1566	c.1181A>T	c.(1180-1182)gAt>gTt	p.D394V	PRKCH_ENST00000555082.1_Missense_Mutation_p.D233V	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	394	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		ATTCTGCAGGATGATGATGTG	0.502																																					p.D394V	Melanoma(135;863 1779 8064 14443 26348)	Atlas-SNP	.											.	PRKCH	89	.	0			c.A1181T						.						266	247	253					14																	61924300		2203	4300	6503	SO:0001583	missense	5583	exon9			TGCAGGATGATGA	M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.1181A>T	chr14.hg19:g.61924300A>T	ENSP00000329127:p.Asp394Val	98.0	0.0		109.0	44.0	NM_006255	B4DJN5|Q16246|Q8NE03	Missense_Mutation	SNP	ENST00000332981.5	hg19	CCDS9752.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.701013	0.88924	.	.	ENSG00000027075	ENST00000332981;ENST00000555082	T;T	0.65549	-0.16;-0.16	5.74	5.74	0.90152	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	T	0.70334	0.3212	L	0.31526	0.94	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.74112	-0.3770	10	0.87932	D	0	.	16.0499	0.80749	1.0:0.0:0.0:0.0	.	394	P24723	KPCL_HUMAN	V	394;233	ENSP00000329127:D394V;ENSP00000450981:D233V	ENSP00000329127:D394V	D	+	2	0	PRKCH	60994053	1.000000	0.71417	0.942000	0.38095	0.890000	0.51754	9.339000	0.96797	2.193000	0.70182	0.533000	0.62120	GAT	.	.		0.502	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255		T	61924300	A	T	61924300	3	4	22	1	0	0	0	0	1	0	0	0	12525	333	12	4	1215	4	PRKCH	14	61924300	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10		61924300	45425240	91	2029										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63246590	63246590	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gcccggacgttcgcacatgcAtgggcaagggtggtttcctt	14	11	0	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr14:63246590A>G	ENST00000322893.7	-	10	2143	c.1875T>C	c.(1873-1875)caT>caC	p.H625H	KCNH5_ENST00000394968.1_Silent_p.H567H|KCNH5_ENST00000420622.2_Intron	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	625					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TCGCACATGCATGGGCAAGGG	0.443																																					p.H625H		Atlas-SNP	.											.	KCNH5	320	.	0			c.T1875C						.						102	89	94					14																	63246590		2203	4300	6503	SO:0001819	synonymous_variant	27133	exon10			ACATGCATGGGCA	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.1875T>C	chr14.hg19:g.63246590A>G		155.0	0.0		152.0	74.0	NM_139318	C9JP98	Silent	SNP	ENST00000322893.7	hg19	CCDS9756.1																																																																																			.	.		0.443	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		G	63246590	A	G	63246590	2	3	22	1	0	0	0	0	0	0	0	1	8044	214	8	2		2	KCNH5	14	63246590	Silent	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	1322290	63246590	44102950	92	2030										
MLH3	27030	hgsc.bcm.edu	37	chr14	75514207	75514207	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ggaaacgtgtctataccaggGgaaagagggggatgtatcag	16	5	2	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr14:75514207G>C	ENST00000556740.1	-	1	2187	c.2152C>G	c.(2152-2154)Ccc>Gcc	p.P718A	MLH3_ENST00000355774.2_Missense_Mutation_p.P718A|MLH3_ENST00000556257.1_Missense_Mutation_p.P718A|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000238662.7_Missense_Mutation_p.P718A|MLH3_ENST00000380968.2_5'UTR			Q9UHC1	MLH3_HUMAN	mutL homolog 3	718					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		CTATACCAGGGGAAAGAGGGG	0.378								Mismatch excision repair (MMR)																													p.P718A		Atlas-SNP	.											.	MLH3	200	.	0			c.C2152G						.						84	86	85					14																	75514207		2203	4300	6503	SO:0001583	missense	27030	exon2			ACCAGGGGAAAGA	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.2152C>G	chr14.hg19:g.75514207G>C	ENSP00000452316:p.Pro718Ala	108.0	0.0		119.0	31.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	hg19	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	G	6.981	0.551106	0.13374	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	3.56	2.62	0.31277	.	0.403671	0.24145	N	0.041125	T	0.30103	0.0754	L	0.59436	1.845	0.09310	N	1	P;P	0.47841	0.901;0.657	B;B	0.42030	0.373;0.197	T	0.12734	-1.0536	10	0.56958	D	0.05	-0.4652	10.7352	0.46120	0.0:0.3741:0.6259:0.0	.	718;718	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	A	718	ENSP00000348020:P718A;ENSP00000238662:P718A;ENSP00000451540:P718A;ENSP00000452316:P718A	ENSP00000238662:P718A	P	-	1	0	MLH3	74583960	0.523000	0.26274	0.018000	0.16275	0.122000	0.20287	0.848000	0.27710	0.419000	0.25927	0.655000	0.94253	CCC	.	.		0.378	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		C	75514207	G	C	75514207	3	2	22	1	0	0	0	0	1	0	0	0	9627	1232	43	4	2257	4	MLH3	14	75514207	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	12267617	75514207	31835333	93	2031										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105416987	105416987	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gcctttcaggtccagcttggGgcccttaacatctatctggg	11	12	3	0	rs547264247	byFrequency	TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr14:105416987G>C	ENST00000333244.5	-	7	4920	c.4801C>G	c.(4801-4803)Ccc>Gcc	p.P1601A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1601						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TCCAGCTTGGGGCCCTTAACA	0.597													.|||	9	0.00179712	0.0045	0	5008	,	,		15394	0		0	False		,,,				2504	0.0031				p.P1601A		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	.	0			c.C4801G						.						102	114	110					14																	105416987		1802	4024	5826	SO:0001583	missense	113146	exon7			GCTTGGGGCCCTT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4801C>G	chr14.hg19:g.105416987G>C	ENSP00000353114:p.Pro1601Ala	102.0	2.0		103.0	7.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	10.98	1.503413	0.26949	.	.	ENSG00000185567	ENST00000333244	T	0.02812	4.15	3.41	2.49	0.30216	.	.	.	.	.	T	0.14830	0.0358	M	0.90082	3.085	0.24426	N	0.994593	D	0.63880	0.993	P	0.62491	0.903	T	0.06162	-1.0842	9	0.33141	T	0.24	-8.4935	10.9913	0.47551	0.095:0.0:0.905:0.0	.	1601	Q8IVF2	AHNK2_HUMAN	A	1601	ENSP00000353114:P1601A	ENSP00000353114:P1601A	P	-	1	0	AHNAK2	104488032	0.008000	0.16893	0.124000	0.21820	0.109000	0.19521	0.698000	0.25571	0.622000	0.30249	0.485000	0.47835	CCC	.	.		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105416987	G	C	105416987	3	2	22	1	0	0	0	0	1	0	0	0	415	1232	43	4	12590	4	AHNAK2	14	105416987	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	29902780	105416987	1932553	94	2032										
ZFP106	64397	hgsc.bcm.edu	37	chr15	42743691	42743691	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	atttgtctccagggccactgTaattccaattatttgtacta	6	9	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr15:42743691T>A	ENST00000263805.4	-	2	1036	c.710A>T	c.(709-711)tAc>tTc	p.Y237F	ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	237					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										AGGGCCACTGTAATTCCAATT	0.393																																					p.Y237F		Atlas-SNP	.											.	ZFP106	117	.	0			c.A710T						.						107	105	106					15																	42743691		2203	4299	6502	SO:0001583	missense	64397	exon2			CCACTGTAATTCC	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"Zinc fingers, C2H2-type"	12886	protein-coding gene	gene with protein product	"SH3-domain binding protein 3"		"zinc finger protein 106 homolog (mouse)"	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.710A>T	chr15.hg19:g.42743691T>A	ENSP00000263805:p.Tyr237Phe	118.0	0.0		95.0	24.0	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	hg19	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	T	9.969	1.225074	0.22457	.	.	ENSG00000103994	ENST00000263805	T	0.55588	0.51	5.74	5.74	0.90152	.	0.265322	0.32836	N	0.005581	T	0.28797	0.0714	N	0.16743	0.435	0.80722	D	1	P;B	0.35155	0.487;0.034	B;B	0.30943	0.122;0.01	T	0.17018	-1.0383	10	0.12430	T	0.62	-13.2159	6.5	0.22164	0.2396:0.0:0.1274:0.633	.	20;237	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	F	237	ENSP00000263805:Y237F	ENSP00000263805:Y237F	Y	-	2	0	ZFP106	40530983	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.297000	0.43593	2.186000	0.69663	0.524000	0.50904	TAC	.	.		0.393	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		A	42743691	T	A	42743691	3	1	22	1	0	0	0	0	1	0	0	0	17652	1638	57	4	5013	4	ZFP106	15	42743691	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10		42743691	59787701	95	2033										
ZNF609	23060	hgsc.bcm.edu	37	chr15	64967423	64967423	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cgactggctagcatcaaggcTgaagccgacaagatctacag	11	11	2	2	rs368660859		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr15:64967423T>C	ENST00000326648.3	+	4	2498	c.2370T>C	c.(2368-2370)gcT>gcC	p.A790A		NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	790						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GCATCAAGGCTGAAGCCGACA	0.542																																					p.A790A		Atlas-SNP	.											.	ZNF609	106	.	0			c.T2370C						.	T		1,4403		0,1,2201	56	59	58		2370	-3.8	1	15		58	0,8582		0,0,4291	no	coding-synonymous	ZNF609	NM_015042.1		0,1,6492	CC,CT,TT		0.0,0.0227,0.0077		790/1412	64967423	1,12985	2202	4291	6493	SO:0001819	synonymous_variant	23060	exon4			CAAGGCTGAAGCC	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"Zinc fingers, C2H2-type"	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.2370T>C	chr15.hg19:g.64967423T>C		92.0	0.0		80.0	44.0	NM_015042	Q0D2I2	Silent	SNP	ENST00000326648.3	hg19	CCDS32270.1																																																																																			.	.		0.542	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833		C	64967423	T	C	64967423	2	2	22	1	0	0	0	0	0	0	0	1	18050	1567	55	2		2	ZNF609	15	64967423	Silent	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	22223732	64967423	37563969	96	2034										
CHRNA5	1138	hgsc.bcm.edu	37	chr15	78873234	78873234	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	agactacgaaagatgggttcGtcctgtggaacacctgaatg	12	8	0	3	rs202057419		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr15:78873234G>A	ENST00000299565.5	+	2	388	c.188G>A	c.(187-189)cGt>cAt	p.R63H	CHRNA5_ENST00000559554.1_Missense_Mutation_p.R63H	NM_000745.3	NP_000736.2	P30532	ACHA5_HUMAN	cholinergic receptor, nicotinic, alpha 5 (neuronal)	63					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|skin(3)	15					Galantamine(DB00674)|Nicotine(DB00184)	AGATGGGTTCGTCCTGTGGAA	0.328																																					p.R63H		Atlas-SNP	.											.	CHRNA5	48	.	0			c.G188A						.						92	94	93					15																	78873234		2196	4293	6489	SO:0001583	missense	1138	exon2			GGGTTCGTCCTGT		CCDS10304.1	15q24	2012-02-11	2012-02-07		ENSG00000169684	ENSG00000169684		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1959	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 5 (neuronal)"	118505	"cholinergic receptor, nicotinic, alpha polypeptide 5"			2004777	Standard	NM_000745		Approved		uc002bdy.3	P30532	OTTHUMG00000143858	ENST00000299565.5:c.188G>A	chr15.hg19:g.78873234G>A	ENSP00000299565:p.Arg63His	100.0	0.0		65.0	25.0	NM_000745	Q15824|Q99554	Missense_Mutation	SNP	ENST00000299565.5	hg19	CCDS10304.1	.	.	.	.	.	.	.	.	.	.	G	33	5.202410	0.94997	.	.	ENSG00000169684	ENST00000299565;ENST00000394802	D	0.83250	-1.7	5.52	5.52	0.82312	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.94228	0.8147	H	0.95043	3.615	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95534	0.8606	10	0.87932	D	0	.	19.4388	0.94809	0.0:0.0:1.0:0.0	.	63	P30532	ACHA5_HUMAN	H	63;14	ENSP00000299565:R63H	ENSP00000299565:R63H	R	+	2	0	CHRNA5	76660289	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.848000	0.99507	2.590000	0.87494	0.655000	0.94253	CGT	.	.		0.328	CHRNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290106.1			A	78873234	G	A	78873234	3	1	22	1	0	0	0	0	1	0	0	0	3388	1145	40	1	194	1	CHRNA5	15	78873234	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	13905811	78873234	23658158	97	2035										
MPV17L	255027	hgsc.bcm.edu	37	chr16	15501839	15501839	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	atggagaacagcttacgctgGagtctgtggttttctctggg	14	7	2	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr16:15501839G>A	ENST00000396385.3	+	4	580	c.461G>A	c.(460-462)gGa>gAa	p.G154E	MPV17L_ENST00000287594.7_Nonsense_Mutation_p.W130*|RP11-1021N1.1_ENST00000568222.1_Intron	NM_001128423.1	NP_001121895.1	Q2QL34	MP17L_HUMAN	MPV17 mitochondrial membrane protein-like	154					negative regulation of hydrogen peroxide biosynthetic process (GO:0010730)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|reactive oxygen species metabolic process (GO:0072593)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	receptor binding (GO:0005102)			kidney(2)|large_intestine(1)|skin(1)	4						GCTTACGCTGGAGTCTGTGGT	0.498																																					p.W130X		Atlas-SNP	.											.	MPV17L	21	.	0			c.G390A						.						66	59	61					16																	15501839		2197	4298	6495	SO:0001583	missense	255027	exon3			ACGCTGGAGTCTG	DQ004255	CCDS10560.1, CCDS45421.1	16p13.11	2009-04-06			ENSG00000156968	ENSG00000156968			26827	protein-coding gene	gene with protein product						16631601	Standard	NM_001128423		Approved	FLJ39599, MLPH1, MLPH2, MPV17L1	uc002ddn.2	Q2QL34	OTTHUMG00000129882	ENST00000396385.3:c.461G>A	chr16.hg19:g.15501839G>A	ENSP00000379669:p.Gly154Glu	90.0	0.0		118.0	48.0	NM_173803	B4DDY1|Q6P7T6|Q8N8E9	Nonsense_Mutation	SNP	ENST00000396385.3	hg19	CCDS45421.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	14.73|14.73	2.621863|2.621863	0.46840|0.46840	.|.	.|.	ENSG00000156968|ENSG00000156968	ENST00000396385|ENST00000287594	D|.	0.85556|.	-2.0|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	0.000000|.	0.64402|.	U|.	0.000005|.	T|.	0.43055|.	0.1230|.	.|.	.|.	.|.	0.46222|0.46222	D|D	0.998932|0.998932	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|.	0.32402|.	-0.9908|.	9|.	0.66056|0.02654	D|T	0.02|1	-3.7697|-3.7697	15.6672|15.6672	0.77238|0.77238	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	154|.	Q2QL34|.	MP17L_HUMAN|.	E|X	154|130	ENSP00000379669:G154E|.	ENSP00000379669:G154E|ENSP00000287594:W130X	G|W	+|+	2|3	0|0	MPV17L|MPV17L	15409340|15409340	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.017000|0.017000	0.09413|0.09413	6.145000|6.145000	0.71769|0.71769	2.486000|2.486000	0.83907|0.83907	0.471000|0.471000	0.43371|0.43371	GGA|TGG	.	.		0.498	MPV17L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422450.1	NM_173803		A	15501839	G	A	15501839	3	1	22	1	0	0	0	0	1	0	0	0	9755	1183	41	3	475	3	MPV17L	16	15501839	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10		15501839	74852914	98	2036										
ABCC1	4363	hgsc.bcm.edu	37	chr16	16177302	16177302	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	catcctttttggatgtcagcTggaggaaccatattacaggt	10	8	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr16:16177302T>A	ENST00000399410.3	+	17	2370	c.2195T>A	c.(2194-2196)cTg>cAg	p.L732Q	ABCC1_ENST00000399408.2_Missense_Mutation_p.L732Q|ABCC1_ENST00000351154.5_Intron|ABCC1_ENST00000345148.5_Missense_Mutation_p.L732Q|ABCC1_ENST00000349029.5_Intron|ABCC1_ENST00000346370.5_Missense_Mutation_p.L732Q	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	732	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	GGATGTCAGCTGGAGGAACCA	0.537																																					p.L732Q		Atlas-SNP	.											.	ABCC1	156	.	0			c.T2195A						.						78	81	80					16																	16177302		2024	4214	6238	SO:0001583	missense	4363	exon17			GTCAGCTGGAGGA	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.2195T>A	chr16.hg19:g.16177302T>A	ENSP00000382342:p.Leu732Gln	141.0	0.0		134.0	40.0	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	hg19	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	T	6.272	0.418367	0.11870	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000345148;ENST00000536381	D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76	5.27	4.15	0.48705	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.818608	0.11011	N	0.609513	D	0.86606	0.5973	L	0.54323	1.7	0.09310	N	1	B;P;B;B	0.34837	0.196;0.472;0.375;0.324	B;B;B;B	0.34180	0.032;0.158;0.177;0.111	T	0.79642	-0.1718	10	0.56958	D	0.05	-14.0027	5.0393	0.14451	0.0:0.121:0.1851:0.6938	.	732;732;732;732	P33527-4;P33527-3;P33527;P33527-9	.;.;MRP1_HUMAN;.	Q	732;732;732;732;406	ENSP00000382342:L732Q;ENSP00000382340:L732Q;ENSP00000263019:L732Q;ENSP00000263014:L732Q	ENSP00000263014:L732Q	L	+	2	0	ABCC1	16084803	0.000000	0.05858	0.589000	0.28718	0.124000	0.20399	-0.327000	0.07955	2.006000	0.58801	0.460000	0.39030	CTG	.	.		0.537	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		A	16177302	T	A	16177302	3	1	22	1	0	0	0	0	1	0	0	0	49	1580	55	4	2261	4	ABCC1	16	16177302	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	675463	16177302	74177451	99	2037										
GPT2	84706	hgsc.bcm.edu	37	chr16	46956209	46956209	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	acctgcaccctgagatcaagGgccagctggtgaagctgctg	13	12	1	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr16:46956209G>T	ENST00000340124.4	+	9	1205	c.1093G>T	c.(1093-1095)Ggc>Tgc	p.G365C	GPT2_ENST00000440783.2_Missense_Mutation_p.G265C	NM_133443.2	NP_597700.1	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase (alanine aminotransferase) 2	365					2-oxoglutarate metabolic process (GO:0006103)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|L-alanine metabolic process (GO:0042851)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|Phenelzine(DB00780)	TGAGATCAAGGGCCAGCTGGT	0.607																																					p.G365C		Atlas-SNP	.											.	GPT2	40	.	0			c.G1093T						.						97	81	86					16																	46956209		2203	4300	6503	SO:0001583	missense	84706	exon9			ATCAAGGGCCAGC		CCDS10725.1, CCDS45478.1	16q12.1	2008-02-05			ENSG00000166123	ENSG00000166123	2.6.1.2		18062	protein-coding gene	gene with protein product		138210					Standard	NM_133443		Approved	ALT2	uc002eel.3	Q8TD30	OTTHUMG00000132541	ENST00000340124.4:c.1093G>T	chr16.hg19:g.46956209G>T	ENSP00000345282:p.Gly365Cys	59.0	0.0		50.0	17.0	NM_133443	Q8N9E2	Missense_Mutation	SNP	ENST00000340124.4	hg19	CCDS10725.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.854771	0.91355	.	.	ENSG00000166123	ENST00000340124;ENST00000440783	D;T	0.90620	-2.7;1.92	4.84	4.84	0.62591	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.114312	0.56097	D	0.000023	D	0.91016	0.7174	L	0.32530	0.975	0.80722	D	1	P	0.40431	0.717	P	0.51866	0.682	D	0.91817	0.5464	10	0.59425	D	0.04	.	18.3066	0.90184	0.0:0.0:1.0:0.0	.	365	Q8TD30	ALAT2_HUMAN	C	365;265	ENSP00000345282:G365C;ENSP00000413804:G265C	ENSP00000345282:G365C	G	+	1	0	GPT2	45513710	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.697000	0.98697	2.407000	0.81776	0.462000	0.41574	GGC	.	.		0.607	GPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255741.2			T	46956209	G	T	46956209	3	4	22	1	0	0	0	0	1	0	0	0	6747	1232	43	3	1123	3	GPT2	16	46956209	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	30778907	46956209	43398544	100	2038										
CYLD	1540	hgsc.bcm.edu	37	chr16	50816274	50816274	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gtgaagtagtagaagaaaatActccaccaaaaatggaaaaa	8	5	0	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr16:50816274A>C	ENST00000427738.3	+	10	1928	c.1723A>C	c.(1723-1725)Act>Cct	p.T575P	RP11-327F22.4_ENST00000564510.1_RNA|CYLD_ENST00000311559.9_Missense_Mutation_p.T575P|CYLD_ENST00000564326.1_Missense_Mutation_p.T572P|RP11-327F22.4_ENST00000575917.1_RNA|CYLD_ENST00000568704.2_Missense_Mutation_p.T390P|CYLD_ENST00000398568.2_Missense_Mutation_p.T572P|CYLD_ENST00000540145.1_Missense_Mutation_p.T575P|CYLD_ENST00000566206.1_Missense_Mutation_p.T572P|CYLD_ENST00000569418.1_Missense_Mutation_p.T572P			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	575	Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				AGAAGAAAATACTCCACCAAA	0.303			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.T575P		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.A1723C						.						93	84	87					16																	50816274		1809	4076	5885	SO:0001583	missense	1540	exon12	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	GAAAATACTCCAC	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1723A>C	chr16.hg19:g.50816274A>C	ENSP00000392025:p.Thr575Pro	141.0	0.0		146.0	63.0	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	hg19	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.473870	0.84640	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T	0.74315	-0.83;-0.83;-0.83	5.61	5.61	0.85477	Cytoskeleton-associated protein, Gly-rich domain (1);	0.044311	0.85682	D	0.000000	T	0.78685	0.4322	N	0.24115	0.695	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.83275	0.991;0.996;0.996;0.991	T	0.81475	-0.0916	10	0.62326	D	0.03	-21.2581	15.8025	0.78463	1.0:0.0:0.0:0.0	.	572;575;572;575	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	P	575;575;572;572	ENSP00000445447:T575P;ENSP00000308928:T575P;ENSP00000381574:T572P	ENSP00000308928:T575P	T	+	1	0	CYLD	49373775	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.861000	0.92277	2.127000	0.65507	0.482000	0.46254	ACT	.	.		0.303	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			C	50816274	A	C	50816274	3	2	22	1	0	0	0	0	1	0	0	0	4145	391	14	5	1757	5	CYLD	16	50816274	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	3860065	50816274	39538479	101	2039										
CHST5	23563	hgsc.bcm.edu	37	chr16	75563641	75563641	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tgcacgatgcgcaggttgagCgcggggtcgctgagcagcgg	19	10	0	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr16:75563641C>T	ENST00000336257.3	-	3	2036	c.642G>A	c.(640-642)gcG>gcA	p.A214A	CHST5_ENST00000541075.1_Silent_p.A220A|RP11-77K12.7_ENST00000460606.1_3'UTR	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	214					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)	24						GCAGGTTGAGCGCGGGGTCGC	0.716																																					p.A214A		Atlas-SNP	.											.	CHST5	47	.	0			c.G642A						.						50	55	54					16																	75563641		2197	4299	6496	SO:0001819	synonymous_variant	23563	exon3			GTTGAGCGCGGGG	AF176839	CCDS10919.1	16q23.1	2008-02-05			ENSG00000135702	ENSG00000135702		"Sulfotransferases, membrane-bound"	1973	protein-coding gene	gene with protein product		604817				10491328, 11017086	Standard	NM_024533		Approved	I-GLCNAC-6-ST, FLJ22167	uc002fei.3	Q9GZS9	OTTHUMG00000137610	ENST00000336257.3:c.642G>A	chr16.hg19:g.75563641C>T		67.0	0.0		59.0	21.0	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Silent	SNP	ENST00000336257.3	hg19	CCDS10919.1																																																																																			.	.		0.716	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126		T	75563641	C	T	75563641	2	4	22	1	0	0	0	0	0	0	0	1	3409	755	27	1		1	CHST5	16	75563641	Silent	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	24747367	75563641	14791112	102	2040										
C17orf68	80169	hgsc.bcm.edu	37	chr17	8141726	8141726	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ttacctcacagctcaggacgCcagtgttatctctcacatag	7	13	4	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr17:8141726C>A	ENST00000315684.8	-	3	426	c.419G>T	c.(418-420)gGc>gTc	p.G140V	CTC1_ENST00000581671.1_5'UTR	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	140					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						GCTCAGGACGCCAGTGTTATC	0.498																																					p.G140V		Atlas-SNP	.											.	CTC1	75	.	0			c.G419T						.						146	145	146					17																	8141726		2033	4199	6232	SO:0001583	missense	80169	exon3			AGGACGCCAGTGT	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"conserved telomere maintenance component 1", "alpha accessory factor 132", "conserved telomere capping protein 1"	613129	"tmp494178", "chromosome 17 open reading frame 68"	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.419G>T	chr17.hg19:g.8141726C>A	ENSP00000313759:p.Gly140Val	111.0	0.0		104.0	50.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Missense_Mutation	SNP	ENST00000315684.8	hg19	CCDS42259.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.539257	0.65085	.	.	ENSG00000178971	ENST00000315684;ENST00000449476	D;D	0.94613	-3.47;-3.47	5.94	5.94	0.96194	.	0.065120	0.64402	D	0.000014	D	0.96852	0.8972	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96924	0.9676	10	0.87932	D	0	-13.3161	15.8634	0.79043	0.0:1.0:0.0:0.0	.	140	Q2NKJ3	CTC1_HUMAN	V	140	ENSP00000313759:G140V;ENSP00000396018:G140V	ENSP00000313759:G140V	G	-	2	0	CTC1	8082451	0.998000	0.40836	0.966000	0.40874	0.532000	0.34746	4.899000	0.63245	2.826000	0.97356	0.561000	0.74099	GGC	.	.		0.498	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		A	8141726	C	A	8141726	3	1	22	1	0	0	0	0	1	0	0	0	1878	739	26	3	3318	3	C17orf68	17	8141726	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10		8141726	73053484	103	2041										
STX8	9482	hgsc.bcm.edu	37	chr17	9460750	9460750	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tggaaatgtttacatggataCatctgatgtgttgacacagc	10	6	1	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr17:9460750C>T	ENST00000306357.4	-	3	640		c.e3+1		STX8_ENST00000574431.1_Splice_Site|STX8_ENST00000573373.1_Splice_Site|RP11-565F19.2_ENST00000607496.1_RNA	NM_004853.2	NP_004844.1	Q9UNK0	STX8_HUMAN	syntaxin 8						endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|transport (GO:0006810)|vesicle fusion (GO:0006906)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(1)	12						TACATGGATACATCTGATGTG	0.433																																					.		Atlas-SNP	.											.	STX8	28	.	0			c.212+1G>A						.						102	87	92					17																	9460750		2203	4300	6503	SO:0001630	splice_region_variant	9482	exon4			TGGATACATCTGA	AF115323	CCDS32565.1	17p13.1	2012-05-25			ENSG00000170310	ENSG00000170310			11443	protein-coding gene	gene with protein product		604203				9852078, 10198254	Standard	NM_004853		Approved	CARB	uc002glx.3	Q9UNK0	OTTHUMG00000177844	ENST00000306357.4:c.212+1G>A	chr17.hg19:g.9460750C>T		92.0	0.0		72.0	32.0	NM_004853	O60712|Q53XT8	Splice_Site	SNP	ENST00000306357.4	hg19	CCDS32565.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.125926	0.56721	.	.	ENSG00000170310	ENST00000306357	.	.	.	5.84	4.86	0.63082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.267	0.54684	0.1699:0.8301:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	STX8	9401475	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.420000	0.59841	1.448000	0.47680	0.557000	0.71058	.	.	.		0.433	STX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439206.3	NM_004853	Intron	T	9460750	C	T	9460750	5	4	22	1	0	0	0	0	0	0	1	0	15366	492	17	3	521	3	STX8	17	9460750	Splice_Site	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	1319024	9460750	71734460	104	2042										
ULK2	9706	hgsc.bcm.edu	37	chr17	19699421	19699421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cttttacctgccaaacactgCcttgctctgctgctcggccc	7	17	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr17:19699421C>T	ENST00000395544.4	-	19	2483	c.1984G>A	c.(1984-1986)Gca>Aca	p.A662T	ULK2_ENST00000580130.1_5'Flank|ULK2_ENST00000361658.2_Missense_Mutation_p.A662T	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	662			A -> V (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					CCAAACACTGCCTTGCTCTGC	0.443																																					p.A662T		Atlas-SNP	.											.	ULK2	142	.	0			c.G1984A						.						104	99	100					17																	19699421		2203	4300	6503	SO:0001583	missense	9706	exon19			ACACTGCCTTGCT	AB014523	CCDS11213.1	17p11.2	2014-02-12	2013-07-02		ENSG00000083290	ENSG00000083290	2.7.11.1		13480	protein-coding gene	gene with protein product		608650	"unc-51 (C. elegans)-like kinase 2", "unc-51-like kinase 2 (C. elegans)"			10557072	Standard	NM_014683		Approved	KIAA0623, Unc51.2, ATG1B	uc002gwn.3	Q8IYT8	OTTHUMG00000059511	ENST00000395544.4:c.1984G>A	chr17.hg19:g.19699421C>T	ENSP00000378914:p.Ala662Thr	100.0	0.0		104.0	15.0	NM_001142610	A8MY69|O75119	Missense_Mutation	SNP	ENST00000395544.4	hg19	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.058505	0.36277	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	T;T	0.43688	0.94;0.94	6.02	2.82	0.32997	.	0.145914	0.64402	N	0.000006	T	0.35278	0.0926	L	0.57536	1.79	0.38186	D	0.939757	B	0.06786	0.001	B	0.04013	0.001	T	0.20538	-1.0272	10	0.23891	T	0.37	-5.0641	9.4888	0.38946	0.0:0.6895:0.0:0.3105	.	662	Q8IYT8	ULK2_HUMAN	T	662	ENSP00000354877:A662T;ENSP00000378914:A662T	ENSP00000354877:A662T	A	-	1	0	ULK2	19640013	0.998000	0.40836	0.918000	0.36340	0.862000	0.49288	1.036000	0.30228	0.778000	0.33520	-0.136000	0.14681	GCA	.	.		0.443	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683		T	19699421	C	T	19699421	3	4	22	1	0	0	0	0	1	0	0	0	16991	739	26	3	1162	3	ULK2	17	19699421	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	10238671	19699421	61495789	105	2043										
AKAP1	8165	hgsc.bcm.edu	37	chr17	55183730	55183730	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ccaggatagaggtgtcgaggGagaactgggcaatgaggaga	18	5	0	4	rs538528140		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr17:55183730G>A	ENST00000337714.3	+	2	1138	c.905G>A	c.(904-906)gGa>gAa	p.G302E	AKAP1_ENST00000571629.1_Missense_Mutation_p.G302E|AKAP1_ENST00000314126.3_Missense_Mutation_p.G302E|AKAP1_ENST00000539273.1_Missense_Mutation_p.G302E|AKAP1_ENST00000572557.1_Missense_Mutation_p.G302E	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	302					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					GGTGTCGAGGGAGAACTGGGC	0.542																																					p.G302E		Atlas-SNP	.											.	AKAP1	73	.	0			c.G905A						.						81	88	86					17																	55183730		2203	4300	6503	SO:0001583	missense	8165	exon3			TCGAGGGAGAACT	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Tudor domain containing"	367	protein-coding gene	gene with protein product	"protein kinase anchoring protein 1", "dual specificity A-kinase-anchoring protein 1", "protein phosphatase 1, regulatory subunit 43", "tudor domain containing 17"	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.905G>A	chr17.hg19:g.55183730G>A	ENSP00000337736:p.Gly302Glu	102.0	0.0		98.0	41.0	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	hg19	CCDS11594.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774798	0.49786	.	.	ENSG00000121057	ENST00000337714;ENST00000314126;ENST00000427138;ENST00000539273	T;T;T	0.19806	2.44;2.12;2.44	4.74	2.71	0.32032	.	0.777035	0.13077	N	0.415602	T	0.15825	0.0381	L	0.45581	1.43	0.09310	N	1	P	0.35077	0.483	B	0.30943	0.122	T	0.15983	-1.0418	10	0.30854	T	0.27	-0.9566	6.4953	0.22138	0.0984:0.1823:0.7193:0.0	.	302	Q92667	AKAP1_HUMAN	E	302;302;344;302	ENSP00000337736:G302E;ENSP00000314075:G302E;ENSP00000443139:G302E	ENSP00000314075:G302E	G	+	2	0	AKAP1	52538729	0.036000	0.19791	0.010000	0.14722	0.337000	0.28794	0.293000	0.19029	0.569000	0.29329	0.561000	0.74099	GGA	.	.		0.542	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1			A	55183730	G	A	55183730	3	1	22	1	0	0	0	0	1	0	0	0	445	1174	41	3	907	3	AKAP1	17	55183730	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	35484309	55183730	26011480	106	2044										
MARCH10	162333	hgsc.bcm.edu	37	chr17	60821843	60821843	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gggctgactgtaaatctcctCaggtttggcttcctctttct	9	11	4	1	rs199898215		TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr17:60821843C>A	ENST00000311269.5	-	5	703	c.429G>T	c.(427-429)ctG>ctT	p.L143L	MARCH10_ENST00000583600.1_Silent_p.L181L|MARCH10_ENST00000544856.2_Silent_p.L142L|MARCH10_ENST00000456609.2_Silent_p.L143L	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	143					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						TAAATCTCCTCAGGTTTGGCT	0.463																																					p.L143L		Atlas-SNP	.											MARCH10,NS,carcinoma,0,1	MARCH10	102	.	0			c.G429T						.						119	109	112					17																	60821843		2203	4300	6503	SO:0001819	synonymous_variant	162333	exon5			TCTCCTCAGGTTT	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"RING-type (C3HC4) zinc fingers", "MARCH membrane-associated ring fingers"	26655	protein-coding gene	gene with protein product		613337	"ring finger protein 190", "membrane-associated ring finger (C3HC4) 10"	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.429G>T	chr17.hg19:g.60821843C>A		83.0	0.0		73.0	25.0	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Silent	SNP	ENST00000311269.5	hg19	CCDS11635.1																																																																																			.	C|1.000;G|0.000		0.463	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598		A	60821843	C	A	60821843	2	1	22	1	0	0	0	0	0	0	0	1	9308	813	29	3		3	MARCH10	17	60821843	Silent	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	5638113	60821843	20373367	107	2045										
MFSD11	79157	hgsc.bcm.edu	37	chr17	74737074	74737074	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tggagtgttctctgcttcaaAtttgattacaccgtcagtgg	10	8	3	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr17:74737074A>G	ENST00000588460.1	+	3	2230	c.188A>G	c.(187-189)aAt>aGt	p.N63S	MFSD11_ENST00000355954.3_Missense_Mutation_p.N63S|MFSD11_ENST00000590514.1_Missense_Mutation_p.N63S|MFSD11_ENST00000593181.1_Missense_Mutation_p.N63S|MFSD11_ENST00000586622.1_Missense_Mutation_p.N63S|MFSD11_ENST00000336509.4_Missense_Mutation_p.N63S	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	63						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						TCTGCTTCAAATTTGATTACA	0.363																																					p.N63S		Atlas-SNP	.											.	MFSD11	47	.	0			c.A188G						.						247	229	235					17																	74737074		2203	4300	6503	SO:0001583	missense	79157	exon4			CTTCAAATTTGAT	BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.188A>G	chr17.hg19:g.74737074A>G	ENSP00000464932:p.Asn63Ser	73.0	0.0		77.0	27.0	NM_001242536	O43442|Q9NXI5	Missense_Mutation	SNP	ENST00000588460.1	hg19	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.480426	0.84747	.	.	ENSG00000092931	ENST00000336509;ENST00000355954	T;T	0.43294	0.95;0.95	5.8	5.8	0.92144	Major facilitator superfamily domain, general substrate transporter (1);	0.039732	0.85682	D	0.000000	T	0.58409	0.2120	M	0.66560	2.04	0.80722	D	1	D;P	0.67145	0.996;0.88	P;P	0.59546	0.821;0.859	T	0.55604	-0.8115	10	0.30078	T	0.28	-24.0367	16.1429	0.81539	1.0:0.0:0.0:0.0	.	63;63	O43934-2;O43934	.;MFS11_HUMAN	S	63	ENSP00000337240:N63S;ENSP00000348225:N63S	ENSP00000337240:N63S	N	+	2	0	MFSD11	72248669	1.000000	0.71417	0.966000	0.40874	0.960000	0.62799	5.908000	0.69916	2.209000	0.71365	0.460000	0.39030	AAT	.	.		0.363	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311		G	74737074	A	G	74737074	3	3	22	1	0	0	0	0	1	0	0	0	9538	101	4	2	198	2	MFSD11	17	74737074	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	13915231	74737074	6458136	108	2046										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22805711	22805711	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	aaacttcctggcagagggtgCagcgaaagaagacaaaggtg	14	7	0	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr18:22805711C>A	ENST00000361524.3	-	4	2319	c.2171G>T	c.(2170-2172)tGc>tTc	p.C724F	ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Missense_Mutation_p.C724F|ZNF521_ENST00000584787.1_Missense_Mutation_p.C504F	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	724					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GCAGAGGGTGCAGCGAAAGAA	0.453			T	PAX5	ALL																																p.C724F		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.G2171T						.						83	84	84					18																	22805711		2203	4300	6503	SO:0001583	missense	25925	exon4			AGGGTGCAGCGAA	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2171G>T	chr18.hg19:g.22805711C>A	ENSP00000354794:p.Cys724Phe	136.0	0.0		156.0	61.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.281195	0.23392	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.58940	0.3;0.3	6.17	6.17	0.99709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	D	0.85204	0.5643	H	0.96430	3.82	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88351	0.2981	10	0.87932	D	0	-23.4339	20.8794	0.99867	0.0:1.0:0.0:0.0	.	724	Q96K83	ZN521_HUMAN	F	724;758;724	ENSP00000354794:C724F;ENSP00000382352:C724F	ENSP00000354794:C724F	C	-	2	0	ZNF521	21059709	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	TGC	.	.		0.453	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		A	22805711	C	A	22805711	3	1	22	1	0	0	0	0	1	0	0	0	17980	710	25	3	1784	3	ZNF521	18	22805711	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10		22805711	55271537	109	2047										
NEDD4L	23327	hgsc.bcm.edu	37	chr18	55833084	55833084	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tctcgccaaaaaggacatctTtggagccaggtatgttggct	11	9	2	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr18:55833084T>A	ENST00000400345.3	+	2	396	c.113T>A	c.(112-114)tTt>tAt	p.F38Y	NEDD4L_ENST00000256830.9_Missense_Mutation_p.F38Y|NEDD4L_ENST00000435432.2_5'UTR|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000357895.5_Missense_Mutation_p.F30Y|NEDD4L_ENST00000588516.1_3'UTR|NEDD4L_ENST00000356462.6_Missense_Mutation_p.F38Y|NEDD4L_ENST00000382850.4_Missense_Mutation_p.F38Y|NEDD4L_ENST00000586263.1_Missense_Mutation_p.F30Y|NEDD4L_ENST00000256832.7_5'UTR|NEDD4L_ENST00000456986.1_5'UTR	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	38	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						AAGGACATCTTTGGAGCCAGG	0.408																																					p.F38Y		Atlas-SNP	.											.	NEDD4L	126	.	0			c.T113A						.						156	141	146					18																	55833084		1832	4087	5919	SO:0001583	missense	23327	exon2			ACATCTTTGGAGC	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.113T>A	chr18.hg19:g.55833084T>A	ENSP00000383199:p.Phe38Tyr	116.0	0.0		88.0	11.0	NM_015277	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	hg19	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.960136	0.74016	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000357895	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	5.92	5.92	0.95590	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.75110	0.3805	M	0.73217	2.22	0.80722	D	1	P;P;P;P;P	0.44946	0.628;0.846;0.578;0.845;0.755	P;P;B;P;P	0.50231	0.533;0.45;0.146;0.483;0.635	T	0.78132	-0.2323	9	0.72032	D	0.01	.	15.3488	0.74368	0.0:0.0:0.0:1.0	.	30;30;38;38;38	Q96PU5-6;Q96PU5-7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;NED4L_HUMAN;.	Y	38;38;38;38;30	ENSP00000383199:F38Y;ENSP00000372301:F38Y;ENSP00000348847:F38Y;ENSP00000256830:F38Y;ENSP00000350569:F30Y	ENSP00000256830:F38Y	F	+	2	0	NEDD4L	53984082	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.686000	0.68211	2.269000	0.75478	0.460000	0.39030	TTT	.	.		0.408	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			A	55833084	T	A	55833084	3	1	22	1	0	0	0	0	1	0	0	0	10320	1841	64	4	147	4	NEDD4L	18	55833084	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	33027373	55833084	22244164	110	2048										
SERPINB13	5275	hgsc.bcm.edu	37	chr18	61260116	61260116	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	agattatgttgaaaaatattAtcatgcatctctggaacctg	7	6	2	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr18:61260116A>G	ENST00000344731.5	+	5	485	c.383A>G	c.(382-384)tAt>tGt	p.Y128C	SERPINB13_ENST00000269489.5_Missense_Mutation_p.Y128C	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	128					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						GAAAAATATTATCATGCATCT	0.318																																					p.Y128C		Atlas-SNP	.											.	SERPINB13	51	.	0			c.A383G						.						85	93	90					18																	61260116		2203	4300	6503	SO:0001583	missense	5275	exon5			AATATTATCATGC	AF169949, BC101821	CCDS11985.1	18q21.33	2014-02-18	2005-08-18		ENSG00000197641	ENSG00000197641		"Serine (or cysteine) peptidase inhibitors"	8944	protein-coding gene	gene with protein product		604445	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13"	PI13		9297979, 10512713, 24172014	Standard	NM_012397		Approved	HUR7, hurpin, headpin	uc002ljc.3	Q9UIV8	OTTHUMG00000060406	ENST00000344731.5:c.383A>G	chr18.hg19:g.61260116A>G	ENSP00000341584:p.Tyr128Cys	88.0	0.0		97.0	37.0	NM_012397	A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Missense_Mutation	SNP	ENST00000344731.5	hg19	CCDS11985.1	.	.	.	.	.	.	.	.	.	.	A	19.57	3.853167	0.71719	.	.	ENSG00000197641	ENST00000431153;ENST00000269489;ENST00000344731	D;D;D	0.87334	-2.24;-2.24;-2.24	5.63	4.43	0.53597	Serpin domain (3);	0.133198	0.34879	N	0.003612	D	0.94771	0.8312	H	0.94503	3.545	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94978	0.8123	10	0.87932	D	0	.	11.3852	0.49780	0.8644:0.0:0.0:0.1356	.	137;128	B7ZKV6;Q9UIV8	.;SPB13_HUMAN	C	158;128;128	ENSP00000388300:Y158C;ENSP00000269489:Y128C;ENSP00000341584:Y128C	ENSP00000269489:Y128C	Y	+	2	0	SERPINB13	59411096	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.376000	0.73141	1.012000	0.39366	0.454000	0.30748	TAT	.	.		0.318	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397		G	61260116	A	G	61260116	3	3	22	1	0	0	0	0	1	0	0	0	14115	449	16	2	397	2	SERPINB13	18	61260116	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	5427032	61260116	16817132	111	2049										
CDC37	11140	hgsc.bcm.edu	37	chr19	10514108	10514108	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	atgttggggtgcgtctcgtcTtcatcatcagacacctcaat	9	11	6	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr19:10514108T>G	ENST00000222005.2	-	1	101	c.48A>C	c.(46-48)gaA>gaC	p.E16D	MIR1181_ENST00000408639.1_RNA	NM_007065.3	NP_008996.1	Q16543	CDC37_HUMAN	cell division cycle 37	16					protein targeting (GO:0006605)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	16			OV - Ovarian serous cystadenocarcinoma(20;4.65e-10)|Epithelial(33;6.48e-07)|all cancers(31;2.31e-06)	GBM - Glioblastoma multiforme(1328;0.0318)		GCGTCTCGTCTTCATCATCAG	0.672																																					p.E16D		Atlas-SNP	.											.	CDC37	32	.	0			c.A48C						.						87	68	75					19																	10514108		2203	4300	6503	SO:0001583	missense	11140	exon1			CTCGTCTTCATCA	U63131	CCDS12237.1	19p13.2	2013-01-17	2013-01-17		ENSG00000105401	ENSG00000105401			1735	protein-coding gene	gene with protein product	"CDC37 cell division cycle 37 homolog", "Hsp90 co-chaperone Cdc37", "CDC37 (cell division cycle 37, S. cerevisiae, homolog)"	605065	"CDC37 (cell division cycle 37, S. cerevisiae, homolog)", "CDC37 cell division cycle 37 homolog (S. cerevisiae)", "cell division cycle 37 homolog (S. cerevisiae)"			8703009, 8666233	Standard	NM_007065		Approved	P50CDC37	uc002mof.1	Q16543		ENST00000222005.2:c.48A>C	chr19.hg19:g.10514108T>G	ENSP00000222005:p.Glu16Asp	46.0	0.0		43.0	19.0	NM_007065	Q53YA2	Missense_Mutation	SNP	ENST00000222005.2	hg19	CCDS12237.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.801104	0.90538	.	.	ENSG00000105401	ENST00000222005	T	0.59083	0.29	4.76	-0.551	0.11822	Cdc37, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71221	0.3314	M	0.80616	2.505	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.69525	-0.5122	10	0.87932	D	0	.	8.3422	0.32249	0.0:0.471:0.0:0.529	.	16;16	Q6FG59;Q16543	.;CDC37_HUMAN	D	16	ENSP00000222005:E16D	ENSP00000222005:E16D	E	-	3	2	CDC37	10375108	0.980000	0.34600	0.994000	0.49952	0.990000	0.78478	0.135000	0.15952	-0.218000	0.10018	-0.366000	0.07423	GAA	.	.		0.672	CDC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451987.1	NM_007065		G	10514108	T	G	10514108	3	3	22	1	0	0	0	0	1	0	0	0	3070	1606	56	5	1120	5	CDC37	19	10514108	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10		10514108	48614875	112	2050										
CPAMD8	9002	hgsc.bcm.edu	37	chr19	17004084	17004084	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tggccccatctgtggaacggGctggcgctctgggtgctgct	16	12	2	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr19:17004084G>A	ENST00000248076.3	+	0	3473				CPAMD8_ENST00000443236.1_Silent_p.S1878S|CPAMD8_ENST00000597335.1_5'Flank	NM_003950.2	NP_003941.2	Q96RI0	PAR4_HUMAN	coagulation factor II (thrombin) receptor-like 3						blood coagulation (GO:0007596)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			cervix(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						TGTGGAACGGGCTGGCGCTCT	0.627																																					p.S1878S		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C5634T						.						16	17	17					19																	17004084		1918	4102	6020	SO:0001628	intergenic_variant	27151	exon42			GAACGGGCTGGCG	AF055917	CCDS12350.1	19p12	2012-08-08						"GPCR / Class A : Protease activated receptors"	3540	protein-coding gene	gene with protein product	"proteinase-activated receptor-4"	602779				9618465	Standard	XM_005260139		Approved	PAR4	uc002nfa.3	Q96RI0			chr19.hg19:g.17004084G>A		64.0	0.0		57.0	11.0	NM_015692	O76067|Q6DK42	Silent	SNP	ENST00000248076.3	hg19	CCDS12350.1	.	.	.	.	.	.	.	.	.	.	G	3.087	-0.187828	0.06299	.	.	ENSG00000160111	ENST00000443236	.	.	.	1.81	-1.89	0.07689	.	.	.	.	.	T	0.21761	0.0524	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.28554	-1.0040	4	.	.	.	.	4.1779	0.10360	0.0:0.2223:0.327:0.4507	.	.	.	.	V	1889	.	.	A	-	2	0	CPAMD8	16865084	0.118000	0.22208	0.001000	0.08648	0.077000	0.17291	0.346000	0.19997	-0.411000	0.07530	-0.489000	0.04712	GCC	.	.		0.627	F2RL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462875.1			A	17004084	G	A	17004084	1	1	22	0	1	0	0	0	0	0	0	0	3797	1194	42	3		3	CPAMD8	19	17004084	IGR	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	6489976	17004084	42124899	113	2051										
GATAD2A	54815	hgsc.bcm.edu	37	chr19	19612126	19612126	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gcctttgtgaaggcgctgcaGcaggaacaggagattgagca	15	8	0	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr19:19612126G>A	ENST00000360315.3	+	9	1713	c.1401G>A	c.(1399-1401)caG>caA	p.Q467Q	GATAD2A_ENST00000537887.1_Silent_p.Q96Q|GATAD2A_ENST00000404158.1_Silent_p.Q468Q|GATAD2A_ENST00000358713.3_Silent_p.Q467Q|GATAD2A_ENST00000429563.2_Silent_p.Q295Q|GATAD2A_ENST00000252577.5_Silent_p.Q467Q	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	467	CR2; histone tail-binding.				anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						AGGCGCTGCAGCAGGAACAGG	0.647																																					p.Q467Q		Atlas-SNP	.											.	GATAD2A	81	.	0			c.G1401A						.						27	23	24					19																	19612126		2203	4299	6502	SO:0001819	synonymous_variant	54815	exon9			GCTGCAGCAGGAA	AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"GATA zinc finger domain containing"	29989	protein-coding gene	gene with protein product	"p66 alpha"	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.1401G>A	chr19.hg19:g.19612126G>A		159.0	0.0		146.0	58.0	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Silent	SNP	ENST00000360315.3	hg19	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	G	9.661	1.144026	0.21205	.	.	ENSG00000167491	ENST00000418032	.	.	.	5.18	0.532	0.17114	.	.	.	.	.	T	0.58119	0.2100	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53479	-0.8433	4	.	.	.	-22.6318	10.2073	0.43120	0.299:0.0:0.701:0.0	.	.	.	.	T	94	.	.	A	+	1	0	GATAD2A	19473126	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.591000	0.46163	0.286000	0.22352	0.645000	0.84053	GCA	.	.		0.647	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660		A	19612126	G	A	19612126	2	1	22	1	0	0	0	0	0	0	0	1	6268	962	34	3		3	GATAD2A	19	19612126	Silent	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	2608042	19612126	39516857	114	2052										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31767550	31767550	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	taacagcgtgcttgctggcaAaggtccgattgcaaagtttg	12	8	0	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr19:31767550A>G	ENST00000240587.4	-	2	3476	c.3149T>C	c.(3148-3150)tTt>tCt	p.F1050S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	1050					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CTTGCTGGCAAAGGTCCGATT	0.488																																					p.F1050S		Atlas-SNP	.											TSHZ3_ENST00000240587,right_upper_lobe,carcinoma,0,2	TSHZ3	549	.	0			c.T3149C						.						155	139	145					19																	31767550		2203	4300	6503	SO:0001583	missense	57616	exon2			CTGGCAAAGGTCC	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.3149T>C	chr19.hg19:g.31767550A>G	ENSP00000240587:p.Phe1050Ser	228.0	0.0		185.0	78.0	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	hg19	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	A	17.65	3.442907	0.63067	.	.	ENSG00000121297	ENST00000240587	T	0.20598	2.06	5.93	5.93	0.95920	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	T	0.49695	0.1572	M	0.78049	2.395	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.53063	-0.8491	10	0.87932	D	0	-8.4156	16.3871	0.83514	1.0:0.0:0.0:0.0	.	1050	Q63HK5	TSH3_HUMAN	S	1050	ENSP00000240587:F1050S	ENSP00000240587:F1050S	F	-	2	0	TSHZ3	36459390	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.930000	0.92872	2.265000	0.75225	0.533000	0.62120	TTT	.	.		0.488	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		G	31767550	A	G	31767550	3	3	22	1	0	0	0	0	1	0	0	0	16640	14	1	2	100	2	TSHZ3	19	31767550	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	12155424	31767550	27361433	115	2053										
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39961060	39961060	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gcagctctgctcagagacagCatcaggtgtggatgttgggg	16	8	3	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr19:39961060C>T	ENST00000599117.1	+	19	1941	c.1574C>T	c.(1573-1575)gCa>gTa	p.A525V	SUPT5H_ENST00000402194.2_Missense_Mutation_p.A521V|SUPT5H_ENST00000359191.6_Missense_Mutation_p.A521V|SUPT5H_ENST00000598725.1_Missense_Mutation_p.A525V|SUPT5H_ENST00000432763.2_Missense_Mutation_p.A525V			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	525					7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TCAGAGACAGCATCAGGTGTG	0.632																																					p.A525V		Atlas-SNP	.											.	SUPT5H	119	.	0			c.C1574T						.						118	113	115					19																	39961060		2203	4300	6503	SO:0001583	missense	6829	exon17			AGACAGCATCAGG	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"suppressor of Ty (S.cerevisiae) 5 homolog"			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.1574C>T	chr19.hg19:g.39961060C>T	ENSP00000470252:p.Ala525Val	119.0	0.0		105.0	38.0	NM_003169	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	hg19	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	C	36	5.866255	0.97043	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.84197	0.5419	M	0.86651	2.83	0.80722	D	1	P;D;D	0.62365	0.955;0.991;0.984	P;D;P	0.66979	0.776;0.948;0.889	D	0.85149	0.0985	8	.	.	.	-19.2641	19.0242	0.92926	0.0:1.0:0.0:0.0	.	317;521;525	B4DJK4;O00267-2;O00267	.;.;SPT5H_HUMAN	V	525;521;503;525	.	.	A	+	2	0	SUPT5H	44652900	1.000000	0.71417	0.891000	0.34965	0.992000	0.81027	7.585000	0.82584	2.788000	0.95919	0.557000	0.71058	GCA	.	.		0.632	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		T	39961060	C	T	39961060	3	4	22	1	0	0	0	0	1	0	0	0	15414	710	25	3	1640	3	SUPT5H	19	39961060	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	8193510	39961060	19167923	116	2054										
LENG8	114823	hgsc.bcm.edu	37	chr19	54964820	54964820	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ccatccgcaccccaacaccaAgggactctgaaccaggtaac	7	17	1	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr19:54964820A>G	ENST00000326764.5	+	5	890	c.411A>G	c.(409-411)caA>caG	p.Q137Q	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	0										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		CCCAACACCAAGGGACTCTGA	0.552																																					p.Q137Q		Atlas-SNP	.											.	LENG8	73	.	0			c.A411G						.						96	79	85					19																	54964820		2203	4300	6503	SO:0001819	synonymous_variant	114823	exon5			ACACCAAGGGACT	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.411A>G	chr19.hg19:g.54964820A>G		21.0	0.0		23.0	4.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Silent	SNP	ENST00000326764.5	hg19	CCDS12894.1																																																																																			.	.		0.552	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		G	54964820	A	G	54964820	2	3	22	1	0	0	0	0	0	0	0	1	8733	69	3	2		2	LENG8	19	54964820	Silent	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	15003760	54964820	4164163	117	2055										
BTBD3	22903	hgsc.bcm.edu	37	chr20	11899220	11899220	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cttatcccggccccaaactgGcagggtctttatcccaccat	7	16	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr20:11899220G>A	ENST00000405977.1	+	2	922	c.297G>A	c.(295-297)tgG>tgA	p.W99*	BTBD3_ENST00000378226.2_Nonsense_Mutation_p.W99*|RP4-742J24.2_ENST00000439529.1_RNA|BTBD3_ENST00000254977.3_Nonsense_Mutation_p.W38*|BTBD3_ENST00000399006.2_Nonsense_Mutation_p.W38*	NM_001282550.1|NM_001282552.1|NM_001282554.1	NP_001269479.1|NP_001269481.1|NP_001269483.1	Q9Y2F9	BTBD3_HUMAN	BTB (POZ) domain containing 3	99					cerebral cortex development (GO:0021987)|dendrite morphogenesis (GO:0048813)	cytosol (GO:0005829)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(18)|ovary(3)|skin(2)	34						CCCCAAACTGGCAGGGTCTTT	0.478																																					p.W99X		Atlas-SNP	.											.	BTBD3	92	.	0			c.G297A						.						83	96	91					20																	11899220		2203	4300	6503	SO:0001587	stop_gained	22903	exon1			AAACTGGCAGGGT	AB023169	CCDS13113.1, CCDS13114.1	20p12.2	2013-01-08			ENSG00000132640	ENSG00000132640		"BTB/POZ domain containing"	15854	protein-coding gene	gene with protein product		615566					Standard	NM_001282551		Approved	KIAA0952, dJ742J24.1	uc002wnz.3	Q9Y2F9	OTTHUMG00000031889	ENST00000405977.1:c.297G>A	chr20.hg19:g.11899220G>A	ENSP00000384545:p.Trp99*	213.0	0.0		182.0	88.0	NM_014962	D3DW19|Q5JY73	Nonsense_Mutation	SNP	ENST00000405977.1	hg19	CCDS13113.1	.	.	.	.	.	.	.	.	.	.	G	38	6.904433	0.97924	.	.	ENSG00000132640	ENST00000254977;ENST00000399006;ENST00000405977;ENST00000422390;ENST00000378226	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	.	.	.	X	38;38;99;38;99	.	ENSP00000254977:W38X	W	+	3	0	BTBD3	11847220	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	TGG	.	.		0.478	BTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078021.3			A	11899220	G	A	11899220	4	1	22	1	0	0	0	0	0	1	0	0	1546	1212	42	3	299	3	BTBD3	20	11899220	Nonsense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10		11899220	51126300	118	2056										
E2F1	1869	hgsc.bcm.edu	37	chr20	32265105	32265105	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	acaggaaaacatcgatcgggCcttgtttgctcttaagggag	12	8	1	0			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr20:32265105C>A	ENST00000343380.5	-	6	1011	c.872G>T	c.(871-873)gGc>gTc	p.G291V	NECAB3_ENST00000375238.4_5'Flank|RP1-63M2.5_ENST00000606866.1_RNA|NECAB3_ENST00000246190.6_5'Flank	NM_005225.2	NP_005216.1	Q01094	E2F1_HUMAN	E2F transcription factor 1	291	Required for interaction with TRIM28.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|DNA damage checkpoint (GO:0000077)|forebrain development (GO:0030900)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|mRNA stabilization (GO:0048255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(2)|breast(1)|endometrium(3)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	16						ATCGATCGGGCCTTGTTTGCT	0.602																																					p.G291V		Atlas-SNP	.											.	E2F1	41	.	0			c.G872T						.						73	74	74					20																	32265105		2203	4300	6503	SO:0001583	missense	1869	exon6			ATCGGGCCTTGTT		CCDS13224.1	20q11	2008-05-14			ENSG00000101412	ENSG00000101412			3113	protein-coding gene	gene with protein product		189971		RBBP3		8964493	Standard	NM_005225		Approved	RBP3	uc002wzu.4	Q01094	OTTHUMG00000032265	ENST00000343380.5:c.872G>T	chr20.hg19:g.32265105C>A	ENSP00000345571:p.Gly291Val	112.0	0.0		104.0	19.0	NM_005225	Q13143|Q92768	Missense_Mutation	SNP	ENST00000343380.5	hg19	CCDS13224.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.327054	0.60743	.	.	ENSG00000101412	ENST00000343380	D	0.99727	-6.55	4.85	4.85	0.62838	.	0.171106	0.50627	D	0.000101	D	0.99616	0.9860	M	0.81614	2.55	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.97650	1.0154	10	0.66056	D	0.02	-31.4745	13.5067	0.61486	0.0:0.8433:0.1567:0.0	.	291	Q01094	E2F1_HUMAN	V	291	ENSP00000345571:G291V	ENSP00000345571:G291V	G	-	2	0	E2F1	31728766	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.590000	0.82653	2.526000	0.85167	0.462000	0.41574	GGC	.	.		0.602	E2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078731.2			A	32265105	C	A	32265105	3	1	22	1	0	0	0	0	1	0	0	0	4868	739	26	3	449	3	E2F1	20	32265105	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	20365885	32265105	30760415	119	2057										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35422173	35422173	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gagctttggtgagccatactTgggggagcagcagggccgct	17	9	0	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr20:35422173T>C	ENST00000357779.3	-	14	3924	c.3598A>G	c.(3598-3600)Aag>Gag	p.K1200E	SOGA1_ENST00000456801.2_Missense_Mutation_p.K1041E|SOGA1_ENST00000279034.6_Intron|SOGA1_ENST00000237536.4_Missense_Mutation_p.K1438E			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	1200					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						GAGCCATACTTGGGGGAGCAG	0.632																																					p.K1438E		Atlas-SNP	.											.	SOGA1	136	.	0			c.A4312G						.						9	10	10					20																	35422173		691	1586	2277	SO:0001583	missense	140710	exon14			CATACTTGGGGGA	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.3598A>G	chr20.hg19:g.35422173T>C	ENSP00000350424:p.Lys1200Glu	27.0	0.0		22.0	10.0	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	hg19		.	.	.	.	.	.	.	.	.	.	T	23.1	4.369192	0.82463	.	.	ENSG00000149639	ENST00000237536;ENST00000456801;ENST00000357779	T;T;T	0.33865	1.39;1.5;1.44	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.53318	0.1789	M	0.72894	2.215	0.58432	D	0.999996	.	.	.	.	.	.	T	0.58521	-0.7622	8	0.87932	D	0	-46.5654	13.3518	0.60605	0.0:0.0:0.0:1.0	.	.	.	.	E	1438;1041;1200	ENSP00000237536:K1438E;ENSP00000413886:K1041E;ENSP00000350424:K1200E	ENSP00000237536:K1438E	K	-	1	0	KIAA0889	34855587	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.980000	0.70516	2.000000	0.58554	0.459000	0.35465	AAG	.	.		0.632	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		C	35422173	T	C	35422173	3	2	22	1	0	0	0	0	1	0	0	0	2085	1821	63	2	743	2	C20orf117	20	35422173	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	3157068	35422173	27603347	120	2058										
BMP7	655	hgsc.bcm.edu	37	chr20	55746127	55746127	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tgagctgcgtgggcgcacagCagggcttgggcaccgtttcc	16	12	0	1			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr20:55746127C>A	ENST00000395863.3	-	7	1689	c.1184G>T	c.(1183-1185)tGc>tTc	p.C395F	BMP7_ENST00000395864.3_Missense_Mutation_p.C329F|BMP7_ENST00000460817.1_5'UTR	NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	395					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of an epithelial tube (GO:0048754)|cartilage development (GO:0051216)|cellular response to hypoxia (GO:0071456)|dendrite development (GO:0016358)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint morphogenesis (GO:0060272)|epithelial cell differentiation (GO:0030855)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|mesenchymal cell differentiation (GO:0048762)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|mesonephros development (GO:0001823)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephros development (GO:0001656)|monocyte aggregation (GO:0070487)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis (GO:0072040)|negative regulation of mitosis (GO:0045839)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of dendrite development (GO:1900006)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of removal of superoxide radicals (GO:2000121)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|steroid hormone mediated signaling pathway (GO:0043401)|ureteric bud development (GO:0001657)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	heparin binding (GO:0008201)			endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			GGGCGCACAGCAGGGCTTGGG	0.552																																					p.C395F		Atlas-SNP	.											.	BMP7	60	.	0			c.G1184T						.						110	90	97					20																	55746127		2203	4300	6503	SO:0001583	missense	655	exon7			GCACAGCAGGGCT		CCDS13455.1	20q13	2014-01-30	2008-05-22		ENSG00000101144	ENSG00000101144		"Bone morphogenetic proteins", "Endogenous ligands"	1074	protein-coding gene	gene with protein product	"osteogenic protein 1"	112267				1427904	Standard	NM_001719		Approved	OP-1	uc010gip.1	P18075	OTTHUMG00000032812	ENST00000395863.3:c.1184G>T	chr20.hg19:g.55746127C>A	ENSP00000379204:p.Cys395Phe	124.0	0.0		99.0	32.0	NM_001719	Q9H512|Q9NTQ7	Missense_Mutation	SNP	ENST00000395863.3	hg19	CCDS13455.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.009264	0.93346	.	.	ENSG00000101144	ENST00000395863;ENST00000395864	D;D	0.95069	-3.6;-3.6	5.47	5.47	0.80525	Transforming growth factor-beta, C-terminal (3);	0.084839	0.85682	D	0.000000	D	0.98704	0.9565	H	0.99143	4.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.99;0.999	D	0.99548	1.0965	10	0.87932	D	0	.	19.3422	0.94347	0.0:1.0:0.0:0.0	.	329;395	B1AKZ9;P18075	.;BMP7_HUMAN	F	395;329	ENSP00000379204:C395F;ENSP00000379205:C329F	ENSP00000379204:C395F	C	-	2	0	BMP7	55179534	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.711000	0.84669	2.567000	0.86603	0.655000	0.94253	TGC	.	.		0.552	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079831.2			A	55746127	C	A	55746127	3	1	22	1	0	0	0	0	1	0	0	0	1465	710	25	3	115	3	BMP7	20	55746127	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	20323954	55746127	7279393	121	2059										
UMODL1	89766	hgsc.bcm.edu	37	chr21	43531290	43531364	+	Intron	DEL	CCAGCCAGGGGAGCCCCAGCCAGGGGAGCCTCAGACAGGAGAGTACCAGCCAGGCGAGCCCCAGCCAGAGGAGCA	CCAGCCAGGGGAGCCCCAGCCAGGGGAGCCTCAGACAGGAGAGTACCAGCCAGGCGAGCCCCAGCCAGAGGAGCA	-													0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	gagccccagccaggtgaaccCcagccaggggagccccagcc					rs535263851|rs200737746|rs201758093|rs76618631|rs566694501|rs114358105|rs539769558	byFrequency	TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	CCAGCCAGGGGAGCCCCAGCCAGGGGAGCCTCAGACAGGAGAGTACCAGCCAGGCGAGCCCCAGCCAGAGGAGCA	CCAGCCAGGGGAGCCCCAGCCAGGGGAGCCTCAGACAGGAGAGTACCAGCCAGGCGAGCCCCAGCCAGAGGAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr21:43531290_43531364delCCAGCCAGGGGAGCCCCAGCCAGGGGAGCCTCAGACAGGAGAGTACCAGCCAGGCGAGCCCCAGCCAGAGGAGCA	ENST00000408910.2	+	11	1899				UMODL1_ENST00000400424.2_Intron|UMODL1_ENST00000400427.1_In_Frame_Del_p.SQGSPSQGSLRQESTSQASPSQRST582del|UMODL1_ENST00000408989.2_In_Frame_Del_p.SQGSPSQGSLRQESTSQASPSQRST654del|C21orf128_ENST00000329015.2_5'Flank	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1						adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CAGGTGAACCCCAGCCAGGGGAGCCCCAGCCAGGGGAGCCTCAGACAGGAGAGTACCAGCCAGGCGAGCCCCAGCCAGAGGAGCACCAGCCAGGG	0.698																																					p.653_677del	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Pindel	.											.	UMODL1	186	.	0			c.1957_2031del						.																																			SO:0001627	intron_variant	89766	exon11			.		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1899+59CCAGCCAGGGGAGCCCCAGCCAGGGGAGCCTCAGACAGGAGAGTACCAGCCAGGCGAGCCCCAGCCAGAGGAGCA>-	chr21.hg19:g.43531290_43531364delCCAGCCAGGGGAGCCCCAGCCAGGGGAGCCTCAGACAGGAGAGTACCAGCCAGGCGAGCCCCAGCCAGAGGAGCA		66.0	0.0		76.0	16.0	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	In_Frame_Del	DEL	ENST00000408910.2	hg19	CCDS42936.1																																																																																			.	.		0.698	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			-	43531364	CCAGCCAGGGGAGCCCCAGCCAGGGGAGCCTCAGACAGGAGAGTACCAGCCAGGCGAGCCCCAGCCAGAGGAGCA	-	43531290	6	5	22	0	1	1	0	1	0	0	0	0	16995	623	22	0		0	UMODL1	21	43531290	Intron	DEL	CCAGCCAGGGGAGCCCCAGCCAGGGGAGCCTCAGACAGGAGAGTACCAGCCAGGCGAGCCCCAGCCAGAGGAGCA	TCGA-3K-AAZ8-01A-12D-A38X-10		43531290	4598605	122	2060										
GAB4	128954	hgsc.bcm.edu	37	chr22	17446135	17446135	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	attgatgaccctgttgtttcTcaggttgggcggtgttgggt	15	6	1	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr22:17446135T>G	ENST00000400588.1	-	7	1419	c.1312A>C	c.(1312-1314)Aga>Cga	p.R438R	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	438										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				CTGTTGTTTCTCAGGTTGGGC	0.552																																					p.R438R		Atlas-SNP	.											.	GAB4	95	.	0			c.A1312C						.						174	180	178					22																	17446135		2013	4215	6228	SO:0001819	synonymous_variant	128954	exon7			TGTTTCTCAGGTT	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"Pleckstrin homology (PH) domain containing"	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.1312A>C	chr22.hg19:g.17446135T>G		121.0	0.0		116.0	52.0	NM_001037814		Silent	SNP	ENST00000400588.1	hg19	CCDS42976.1																																																																																			.	.		0.552	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		G	17446135	T	G	17446135	2	3	22	1	0	0	0	0	0	0	0	1	6159	1559	54	5		5	GAB4	22	17446135	Silent	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10		17446135	33858431	123	2061										
BPIL2	254240	hgsc.bcm.edu	37	chr22	32833794	32833794	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	agtaatttctggagaactgaTtagggagtaatccagcagag	12	5	1	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr22:32833794T>A	ENST00000397452.1	-	8	810	c.700A>T	c.(700-702)Atc>Ttc	p.I234F	BPIFC_ENST00000300399.3_Missense_Mutation_p.I234F|BPIFC_ENST00000534972.1_5'UTR|BPIFC_ENST00000432451.2_Missense_Mutation_p.I48F			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	234						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										GGAGAACTGATTAGGGAGTAA	0.348																																					p.I234F		Atlas-SNP	.											.	.	.	.	0			c.A700T						.						101	93	96					22																	32833794		2203	4300	6503	SO:0001583	missense	254240	exon7			AACTGATTAGGGA	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.700A>T	chr22.hg19:g.32833794T>A	ENSP00000380594:p.Ile234Phe	64.0	0.0		58.0	17.0	NM_174932	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	hg19	CCDS13906.1	.	.	.	.	.	.	.	.	.	.	T	13.77	2.335994	0.41398	.	.	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000432451	T;T;T	0.04809	3.55;3.55;3.55	5.68	-2.33	0.06724	.	0.536174	0.21330	N	0.076310	T	0.04724	0.0128	M	0.81802	2.56	0.09310	N	0.999996	P;P	0.39216	0.664;0.664	B;B	0.31191	0.08;0.125	T	0.25779	-1.0122	10	0.72032	D	0.01	-3.846	1.2887	0.02056	0.1224:0.2264:0.2513:0.3999	.	48;234	A2RRF1;Q8NFQ6	.;BPIFC_HUMAN	F	234;234;48	ENSP00000380594:I234F;ENSP00000300399:I234F;ENSP00000408920:I48F	ENSP00000300399:I234F	I	-	1	0	BPIFC	31163794	0.000000	0.05858	0.024000	0.17045	0.991000	0.79684	-0.967000	0.03821	-0.346000	0.08312	0.533000	0.62120	ATC	.	.		0.348	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		A	32833794	T	A	32833794	3	1	22	1	0	0	0	0	1	0	0	0	1494	1493	52	4	859	4	BPIL2	22	32833794	Missense_Mutation	SNP	T	TCGA-3K-AAZ8-01A-12D-A38X-10	15387659	32833794	18470772	124	2062										
MPST	4357	hgsc.bcm.edu	37	chr22	37425290	37425290	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	ccacatcccaggtaccgtgaAcatccccttcacagacttcc	5	18	1	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr22:37425290A>G	ENST00000397225.2	+	3	1544	c.629A>G	c.(628-630)aAc>aGc	p.N210S	MPST_ENST00000404393.1_3'UTR|MPST_ENST00000341116.3_Missense_Mutation_p.N210S|MPST_ENST00000401419.3_Missense_Mutation_p.N210S|MPST_ENST00000397129.1_Missense_Mutation_p.N230S|MPST_ENST00000404802.3_Missense_Mutation_p.N210S|MPST_ENST00000429360.2_Missense_Mutation_p.N210S			P25325	THTM_HUMAN	mercaptopyruvate sulfurtransferase	210	Rhodanese 2. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cyanate catabolic process (GO:0009440)|hydrogen sulfide biosynthetic process (GO:0070814)|response to toxic substance (GO:0009636)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|neuron projection (GO:0043005)|synapse (GO:0045202)	3-mercaptopyruvate sulfurtransferase activity (GO:0016784)|thiosulfate sulfurtransferase activity (GO:0004792)			central_nervous_system(2)|kidney(1)|lung(2)|prostate(1)|skin(1)	7						GGTACCGTGAACATCCCCTTC	0.547																																					p.N230S		Atlas-SNP	.											.	MPST	14	.	0			c.A689G						.						49	43	45					22																	37425290		2203	4300	6503	SO:0001583	missense	4357	exon3			CCGTGAACATCCC	X59434	CCDS13939.1	22q13.1	2010-04-27			ENSG00000128309	ENSG00000128309	2.8.1.2		7223	protein-coding gene	gene with protein product	"human liver rhodanese"	602496				1953758	Standard	NM_021126		Approved	MST, TST2	uc011amu.3	P25325	OTTHUMG00000150543	ENST00000397225.2:c.629A>G	chr22.hg19:g.37425290A>G	ENSP00000380402:p.Asn210Ser	111.0	0.0		128.0	56.0	NM_021126	A8MZ34|B3KP52|J3KPV7|O75750|Q6FHN9	Missense_Mutation	SNP	ENST00000397225.2	hg19	CCDS13939.1	.	.	.	.	.	.	.	.	.	.	A	11.79	1.744594	0.30865	.	.	ENSG00000128309	ENST00000401419;ENST00000397129;ENST00000404802;ENST00000341116;ENST00000429360;ENST00000397225;ENST00000446076	T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54	5.35	5.35	0.76521	Rhodanese-like (5);	0.040345	0.85682	D	0.000000	T	0.29190	0.0726	L	0.56280	1.765	0.80722	D	1	P;P	0.42375	0.778;0.778	B;B	0.39258	0.295;0.295	T	0.05582	-1.0876	10	0.39692	T	0.17	-13.9949	11.3057	0.49334	0.9267:0.0:0.0733:0.0	.	210;210	Q6FHN9;P25325	.;THTM_HUMAN	S	210;230;210;210;210;210;211	ENSP00000384812:N210S;ENSP00000380318:N230S;ENSP00000383950:N210S;ENSP00000342333:N210S;ENSP00000411719:N210S;ENSP00000380402:N210S	ENSP00000342333:N210S	N	+	2	0	MPST	35755236	1.000000	0.71417	0.997000	0.53966	0.679000	0.39708	3.982000	0.56909	2.013000	0.59113	0.528000	0.53228	AAC	.	.		0.547	MPST-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318832.1	NM_001013440		G	37425290	A	G	37425290	3	3	22	1	0	0	0	0	1	0	0	0	9753	43	2	2	699	2	MPST	22	37425290	Missense_Mutation	SNP	A	TCGA-3K-AAZ8-01A-12D-A38X-10	4591496	37425290	13879276	125	2063										
ENTHD1	150350	hgsc.bcm.edu	37	chr22	40140015	40140015	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	tattctttttagcagaatcaGagttatttggaagaattccc	7	6	2	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chr22:40140015G>C	ENST00000325157.6	-	7	1743	c.1493C>G	c.(1492-1494)tCt>tGt	p.S498C		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	498										breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					AGCAGAATCAGAGTTATTTGG	0.438																																					p.S498C		Atlas-SNP	.											.	ENTHD1	83	.	0			c.C1493G						.						55	58	57					22																	40140015		2203	4300	6503	SO:0001583	missense	150350	exon7			GAATCAGAGTTAT	AK093154	CCDS13998.1	22q13.1	2006-06-26			ENSG00000176177	ENSG00000176177			26352	protein-coding gene	gene with protein product						12477932	Standard	NM_152512		Approved	FLJ25421	uc003ayg.3	Q8IYW4	OTTHUMG00000151098	ENST00000325157.6:c.1493C>G	chr22.hg19:g.40140015G>C	ENSP00000317431:p.Ser498Cys	134.0	0.0		118.0	52.0	NM_152512	B0QYD5|Q5H9F7|Q96LK3	Missense_Mutation	SNP	ENST00000325157.6	hg19	CCDS13998.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.436111	0.25813	.	.	ENSG00000176177	ENST00000325157	T	0.34472	1.36	5.63	4.61	0.57282	.	1.023730	0.07785	N	0.954025	T	0.55878	0.1948	M	0.66939	2.045	0.09310	N	1	D	0.71674	0.998	P	0.60173	0.87	T	0.40251	-0.9573	10	0.87932	D	0	-0.252	10.7061	0.45956	0.088:0.0:0.912:0.0	.	498	Q8IYW4	ENTD1_HUMAN	C	498	ENSP00000317431:S498C	ENSP00000317431:S498C	S	-	2	0	ENTHD1	38469961	0.959000	0.32827	0.003000	0.11579	0.051000	0.14879	4.746000	0.62133	1.363000	0.46019	0.557000	0.71058	TCT	.	.		0.438	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512		C	40140015	G	C	40140015	3	2	22	1	0	0	0	0	1	0	0	0	5139	942	33	4	334	4	ENTHD1	22	40140015	Missense_Mutation	SNP	G	TCGA-3K-AAZ8-01A-12D-A38X-10	2714725	40140015	11164551	126	2064										
CXorf38	159013	hgsc.bcm.edu	37	chrX	40506585	40506585	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	cgcgagggctgcaccgtgagCcgccgcggcagacggcgcgg	19	15	0	2			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chrX:40506585C>T	ENST00000327877.5	-	1	214	c.188G>A	c.(187-189)gGc>gAc	p.G63D	CXorf38_ENST00000378421.1_5'UTR|CXorf38_ENST00000378426.1_5'UTR|CXorf38_ENST00000440784.2_Missense_Mutation_p.G63D|CXorf38_ENST00000378418.2_Missense_Mutation_p.G63D	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	63										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						GCACCGTGAGCCGCCGCGGCA	0.756																																					p.G63D		Atlas-SNP	.											.	CXorf38	29	.	0			c.G188A						.						2	3	3					X																	40506585		1413	2900	4313	SO:0001583	missense	159013	exon1			CGTGAGCCGCCGC	AL832829	CCDS14253.1	Xp11	2008-02-05			ENSG00000185753	ENSG00000185753			28589	protein-coding gene	gene with protein product							Standard	NM_144970		Approved	MGC39350	uc004dew.3	Q8TB03	OTTHUMG00000024104	ENST00000327877.5:c.188G>A	chrX.hg19:g.40506585C>T	ENSP00000330488:p.Gly63Asp	23.0	0.0		10.0	6.0	NM_144970	B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	hg19	CCDS14253.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.679496	0.47886	.	.	ENSG00000185753	ENST00000327877;ENST00000440784;ENST00000378418	T;T	0.45276	0.95;0.9	4.65	3.78	0.43462	.	0.620260	0.17251	N	0.181162	T	0.31544	0.0800	L	0.40543	1.245	0.09310	N	1	P;B	0.36909	0.573;0.253	B;B	0.36244	0.22;0.128	T	0.10870	-1.0611	10	0.31617	T	0.26	-1.7911	8.1768	0.31287	0.0:0.8003:0.0:0.1997	.	63;63	E7EN46;Q8TB03	.;CX038_HUMAN	D	63	ENSP00000330488:G63D;ENSP00000400019:G63D	ENSP00000330488:G63D	G	-	2	0	CXorf38	40391529	0.006000	0.16342	0.819000	0.32651	0.698000	0.40448	0.440000	0.21592	1.075000	0.40932	0.506000	0.49869	GGC	.	.		0.756	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3	NM_144970		T	40506585	C	T	40506585	3	4	22	1	0	0	0	0	1	0	0	0	4109	739	26	3	795	3	CXorf38	23	40506585	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10		40506585	114763975	127	2065										
PDZD4	57595	hgsc.bcm.edu	37	chrX	153068845	153068845	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	8	1	1.27111111111111	1.76543209876543	1.16260162601626	0.153434800493624	0.751940625889747	0	agagaagagggttgtagaccCgcttgccatcggcggagcgc	16	10	0	3			TCGA-3K-AAZ8-01A-12D-A38X-10	TCGA-3K-AAZ8-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca7f5e36-bbb3-44aa-b0c7-3f170a2bbc0f	c70e868a-ba0a-4b90-ad4d-d61ed7b34ecf	g.chrX:153068845C>T	ENST00000164640.4	-	8	2464	c.2273G>A	c.(2272-2274)cGg>cAg	p.R758Q	PDZD4_ENST00000544474.1_Missense_Mutation_p.R649Q|PDZD4_ENST00000475140.1_5'Flank|PDZD4_ENST00000393758.2_Missense_Mutation_p.R683Q	NM_032512.2	NP_115901.2	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	758						cytoplasm (GO:0005737)		p.R758L(1)		breast(3)|cervix(1)|endometrium(5)|lung(13)|skin(1)	23	all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GTTGTAGACCCGCTTGCCATC	0.652																																					p.R758Q		Atlas-SNP	.											.	PDZD4	67	.	1	Substitution - Missense(1)	lung(1)	c.G2273A						.						61	48	52					X																	153068845		2199	4299	6498	SO:0001583	missense	57595	exon8			TAGACCCGCTTGC	AK091444	CCDS14732.1	Xq28	2008-02-05		2006-01-24	ENSG00000067840	ENSG00000067840			21167	protein-coding gene	gene with protein product		300634		PDZK4		10819331, 15077175	Standard	NM_032512		Approved	KIAA1444, LU1, FLJ34125, PDZRN4L	uc004fiz.1	Q76G19	OTTHUMG00000024209	ENST00000164640.4:c.2273G>A	chrX.hg19:g.153068845C>T	ENSP00000164640:p.Arg758Gln	32.0	0.0		21.0	15.0	NM_032512	B3KXB1|B7ZKY3|Q8NB75|Q9BUH9|Q9P284	Missense_Mutation	SNP	ENST00000164640.4	hg19	CCDS14732.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.128136	0.56721	.	.	ENSG00000067840	ENST00000164640;ENST00000393758;ENST00000537633;ENST00000544474	T;T;T	0.74842	-0.88;-0.88;-0.88	5.64	4.78	0.61160	.	0.052317	0.64402	D	0.000001	T	0.76572	0.4006	M	0.67953	2.075	0.37954	D	0.932731	P;D;D;D;P	0.60160	0.796;0.98;0.975;0.987;0.658	B;P;B;P;B	0.48114	0.124;0.567;0.314;0.566;0.071	T	0.81187	-0.1047	10	0.66056	D	0.02	-31.7173	12.6483	0.56748	0.0:0.9169:0.0:0.0831	.	649;764;758;683;662	B7ZKY3;Q17RL8;Q76G19;D3DWW0;B3KVR9	.;.;PDZD4_HUMAN;.;.	Q	758;683;662;649	ENSP00000164640:R758Q;ENSP00000377355:R683Q;ENSP00000442033:R649Q	ENSP00000164640:R758Q	R	-	2	0	PDZD4	152722039	0.190000	0.23276	0.986000	0.45419	0.374000	0.29953	3.162000	0.50755	1.153000	0.42468	-0.297000	0.09499	CGG	.	.		0.652	PDZD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061013.3	NM_032512		T	153068845	C	T	153068845	3	4	22	1	0	0	0	0	1	0	0	0	11712	652	23	1	40	1	PDZD4	23	153068845	Missense_Mutation	SNP	C	TCGA-3K-AAZ8-01A-12D-A38X-10	112562260	153068845	2201715	128	2066										
DVL1	1855	hgsc.bcm.edu	37	chr1	1273715	1273715	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatcttgttgaccgtgtgccGcaggaagccgtgcttcagca	13	11	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:1273715G>A	ENST00000378888.5	-	13	1725	c.1441C>T	c.(1441-1443)Cgg>Tgg	p.R481W	DVL1_ENST00000378891.5_Missense_Mutation_p.R456W			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	481	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|collateral sprouting (GO:0048668)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|cytoplasmic microtubule organization (GO:0031122)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|negative regulation of protein binding (GO:0032091)|negative regulation of protein kinase activity (GO:0006469)|neural tube development (GO:0021915)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prepulse inhibition (GO:0060134)|protein localization to microtubule (GO:0035372)|protein localization to nucleus (GO:0034504)|receptor clustering (GO:0043113)|regulation of neurotransmitter levels (GO:0001505)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|social behavior (GO:0035176)|synapse organization (GO:0050808)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	axon (GO:0030424)|cell cortex (GO:0005938)|clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|growth cone (GO:0030426)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	enzyme binding (GO:0019899)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|Rac GTPase binding (GO:0048365)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		ACCGTGTGCCGCAGGAAGCCG	0.647																																					p.R456W		Atlas-SNP	.											.	DVL1	36	.	0			c.C1366T						.						61	55	57					1																	1273715		2203	4298	6501	SO:0001583	missense	1855	exon13			TGTGCCGCAGGAA	AF006011	CCDS22.1	1p36	2013-05-22	2013-05-22		ENSG00000107404	ENSG00000107404		"Dishevelled homologs"	3084	protein-coding gene	gene with protein product		601365	"dishevelled 1 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 1 (Drosophila)"			8817329	Standard	NM_004421		Approved		uc001aer.4	O14640	OTTHUMG00000003069	ENST00000378888.5:c.1441C>T	chr1.hg19:g.1273715G>A	ENSP00000368166:p.Arg481Trp	88.0	0.0		67.0	27.0	NM_004421	Q5TA33|Q5TA35	Missense_Mutation	SNP	ENST00000378888.5	hg19		.	.	.	.	.	.	.	.	.	.	G	17.12	3.308401	0.60305	.	.	ENSG00000107404	ENST00000378891;ENST00000378888;ENST00000345100;ENST00000263743	T;T	0.23552	1.9;1.9	3.48	0.306	0.15806	DEP domain (6);Winged helix-turn-helix transcription repressor DNA-binding (2);	0.065039	0.64402	D	0.000013	T	0.54679	0.1873	M	0.90595	3.13	0.58432	D	0.999997	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.997;0.989;0.981	T	0.63453	-0.6634	10	0.87932	D	0	.	13.219	0.59877	0.0:0.0:0.2627:0.7373	.	139;481;456;456	G3XA93;O14640;P54792;O14640-2	.;DVL1_HUMAN;DVL1L_HUMAN;.	W	456;481;230;139	ENSP00000368169:R456W;ENSP00000368166:R481W	ENSP00000263743:R139W	R	-	1	2	DVL1	1263578	0.963000	0.33076	0.998000	0.56505	0.987000	0.75469	0.169000	0.16641	-0.032000	0.13758	-0.513000	0.04457	CGG	.	.		0.647	DVL1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008490.1	NM_004421		A	1273715	G	A	1273715	3	1	23	1	0	0	0	0	1	0	0	0	4837	1086	38	1	658	1	DVL1	1	1273715	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10		1273715	247976906	1	2067										
MMEL1	79258	hgsc.bcm.edu	37	chr1	2560839	2560840	+	Frame_Shift_Ins	INS	-	-	C													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcagcagcagcagcagcagINSccccccctccaggaaccccg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:2560839_2560840insC	ENST00000378412.3	-	2	245_246	c.84_85insG	c.(82-87)gggctgfs	p.L29fs	MMEL1_ENST00000511099.1_5'Flank|MMEL1_ENST00000288709.6_Frame_Shift_Ins_p.L20fs|MMEL1_ENST00000502556.1_Frame_Shift_Ins_p.L29fs			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	29						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		agcagcagcagcCCCCCCTCCA	0.723																																					p.L29fs		Pindel	.											.	MMEL1	64	.	0			c.85_86insG						.																																			SO:0001589	frameshift_variant	79258	exon2			.	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"membrane metallo-endopeptidase-like 2"	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.85dupG	chr1.hg19:g.2560846_2560846dupC	ENSP00000367668:p.Leu29fs	258.0	0.0		246.0	63.0	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Frame_Shift_Ins	INS	ENST00000378412.3	hg19	CCDS30569.2																																																																																			.	.		0.723	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467		C	2560840	-	C	2560839	7	5	23	1	0	1	1	0	0	0	0	0	9655	962	34	0	2346	0	MMEL1	1	2560839	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	1287124	2560839	246689782	2	2068										
C1orf174	339448	hgsc.bcm.edu	37	chr1	3807306	3807306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctgttggattcttctgctcCggacccggcactgtgttttg	12	11	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:3807306C>T	ENST00000361605.3	-	3	543	c.445G>A	c.(445-447)Gga>Aga	p.G149R	C1orf174_ENST00000486765.1_5'UTR	NM_207356.2	NP_997239.2	Q8IYL3	CA174_HUMAN	chromosome 1 open reading frame 174	149						nucleus (GO:0005634)				endometrium(1)|large_intestine(5)|lung(4)|prostate(1)	11	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)		TCTTCTGCTCCGGACCCGGCA	0.552																																					p.G149R		Atlas-SNP	.											.	C1orf174	20	.	0			c.G445A						.						98	89	92					1																	3807306		2203	4300	6503	SO:0001583	missense	339448	exon3			CTGCTCCGGACCC	BC035643	CCDS53.1	1p36.32	2012-07-25			ENSG00000198912	ENSG00000198912			27915	protein-coding gene	gene with protein product						12477932	Standard	NM_207356		Approved	RP13-531C17.2	uc001alf.3	Q8IYL3	OTTHUMG00000003739	ENST00000361605.3:c.445G>A	chr1.hg19:g.3807306C>T	ENSP00000355306:p.Gly149Arg	123.0	0.0		93.0	38.0	NM_207356	A8K0C8|A8MUG9|Q5SR20|Q6NX36	Missense_Mutation	SNP	ENST00000361605.3	hg19	CCDS53.1	.	.	.	.	.	.	.	.	.	.	C	7.306	0.614107	0.14129	.	.	ENSG00000198912	ENST00000361605	T	0.06218	3.33	5.56	3.67	0.42095	.	0.776019	0.11796	N	0.528623	T	0.08537	0.0212	L	0.43152	1.355	0.09310	N	1	D	0.53619	0.961	P	0.46885	0.53	T	0.21759	-1.0236	10	0.14656	T	0.56	-5.474	11.4202	0.49976	0.0:0.8484:0.0:0.1516	.	149	Q8IYL3	CA174_HUMAN	R	149	ENSP00000355306:G149R	ENSP00000355306:G149R	G	-	1	0	C1orf174	3797166	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-2.141000	0.01300	1.337000	0.45525	0.563000	0.77884	GGA	.	.		0.552	C1orf174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010539.1	NM_207356		T	3807306	C	T	3807306	3	4	23	1	0	0	0	0	1	0	0	0	2017	661	23	1	294	1	C1orf174	1	3807306	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1246467	3807306	245443315	3	2069										
CHD5	26038	hgsc.bcm.edu	37	chr1	6202186	6202186	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccaaggatagcgagccctcAccttcatacggaataccttc	7	14	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:6202186A>G	ENST00000262450.3	-	15	2536		c.e15+1		CHD5_ENST00000378021.1_Splice_Site	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5						tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GCGAGCCCTCACCTTCATACG	0.597																																					.		Atlas-SNP	.											.	CHD5	267	.	0			c.2436+2T>C						.						143	136	138					1																	6202186		2203	4300	6503	SO:0001630	splice_region_variant	26038	exon16			GCCCTCACCTTCA	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2436+1T>C	chr1.hg19:g.6202186A>G		122.0	0.0		120.0	43.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Splice_Site	SNP	ENST00000262450.3	hg19	CCDS57.1	.	.	.	.	.	.	.	.	.	.	A	15.10	2.734198	0.48939	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279	.	.	.	4.07	4.07	0.47477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3346	0.60509	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CHD5	6124773	1.000000	0.71417	0.980000	0.43619	0.512000	0.34134	6.186000	0.72026	1.609000	0.50190	0.459000	0.35465	.	.	.		0.597	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	Intron	G	6202186	A	G	6202186	5	3	23	1	0	0	0	0	0	0	1	0	3330	173	6	2	3534	2	CHD5	1	6202186	Splice_Site	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2394880	6202186	243048435	4	2070										
PLEKHG5	57449	hgsc.bcm.edu	37	chr1	6531575	6531575	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagcctttgaggaagtccccGggctgtagcagcgctcgcgt	14	12	0	1	rs139904931	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:6531575G>A	ENST00000400915.3	-	13	1488	c.1422C>T	c.(1420-1422)ccC>ccT	p.P474P	PLEKHG5_ENST00000340850.5_Silent_p.P418P|PLEKHG5_ENST00000400913.1_Silent_p.P418P|PLEKHG5_ENST00000537245.1_Silent_p.P497P|PLEKHG5_ENST00000535355.1_Silent_p.P487P|PLEKHG5_ENST00000377732.1_Silent_p.P455P|PLEKHG5_ENST00000377728.3_Silent_p.P418P|PLEKHG5_ENST00000377737.2_Silent_p.P418P|PLEKHG5_ENST00000377748.1_Silent_p.P495P|PLEKHG5_ENST00000544978.1_Silent_p.P418P|PLEKHG5_ENST00000377725.1_Silent_p.P418P|PLEKHG5_ENST00000377740.3_Silent_p.P495P	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	474	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)	p.P495P(1)		liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		GGAAGTCCCCGGGCTGTAGCA	0.711																																					p.P497P		Atlas-SNP	.											PLEKHG5_ENST00000377748,NS,carcinoma,0,1	PLEKHG5	66	.	1	Substitution - coding silent(1)	prostate(1)	c.C1491T						.						14	18	17					1																	6531575		2198	4283	6481	SO:0001819	synonymous_variant	57449	exon13			GTCCCCGGGCTGT	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"Pleckstrin homology (PH) domain containing"	29105	protein-coding gene	gene with protein product	"synectin-binding guanine exchange factor"	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.1422C>T	chr1.hg19:g.6531575G>A		181.0	0.0		140.0	55.0	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Silent	SNP	ENST00000400915.3	hg19	CCDS41241.1																																																																																			.	G|0.997;C|0.003		0.711	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631		A	6531575	G	A	6531575	2	1	23	1	0	0	0	0	0	0	0	1	12082	1103	39	1		1	PLEKHG5	1	6531575	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	329389	6531575	242719046	5	2071										
ZBTB48	3104	hgsc.bcm.edu	37	chr1	6642238	6642238	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgtgcagctgagccagccCtgagcgcgggctccctagca	13	16	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:6642238C>T	ENST00000377674.4	+	3	969	c.811C>T	c.(811-813)Ctg>Ttg	p.L271L		NM_001278647.1|NM_001278648.1|NM_005341.2	NP_001265576.1|NP_001265577.1|NP_005332.1	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	271					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		TGAGCCAGCCCTGAGCGCGGG	0.552																																					p.L271L	Esophageal Squamous(125;1449 1657 4031 29866 49542)	Atlas-SNP	.											.	ZBTB48	33	.	0			c.C811T						.						69	68	68					1																	6642238		2203	4300	6503	SO:0001819	synonymous_variant	3104	exon3			CCAGCCCTGAGCG	BC013573	CCDS84.1	1p36.3	2013-01-08	2006-09-20	2006-09-20	ENSG00000204859	ENSG00000204859		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	4930	protein-coding gene	gene with protein product		165270	"GLI-Kruppel family member HKR3"	HKR3		2850480, 8661141	Standard	NM_001278647		Approved	ZNF855	uc001anx.3	P10074	OTTHUMG00000001438	ENST00000377674.4:c.811C>T	chr1.hg19:g.6642238C>T		200.0	0.0		164.0	59.0	NM_005341	Q5SY19	Silent	SNP	ENST00000377674.4	hg19	CCDS84.1																																																																																			.	.		0.552	ZBTB48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004193.1	NM_005341		T	6642238	C	T	6642238	2	4	23	1	0	0	0	0	0	0	0	1	17564	680	24	3		3	ZBTB48	1	6642238	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	110663	6642238	242608383	6	2072										
DNAJC11	55735	hgsc.bcm.edu	37	chr1	6697322	6697322	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actgcaggggcacagtcacgTcaatcaccttcaccttctcg	8	15	5	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:6697322T>C	ENST00000377577.5	-	14	1583	c.1460A>G	c.(1459-1461)gAc>gGc	p.D487G	DNAJC11_ENST00000542246.1_Missense_Mutation_p.D449G|DNAJC11_ENST00000377573.5_Missense_Mutation_p.D397G|DNAJC11_ENST00000349363.6_Intron|DNAJC11_ENST00000465508.1_5'UTR|DNAJC11_ENST00000294401.7_Missense_Mutation_p.D435G	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	487						extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		CACAGTCACGTCAATCACCTT	0.547																																					p.D487G		Atlas-SNP	.											.	DNAJC11	93	.	0			c.A1460G						.						271	203	226					1																	6697322		2203	4300	6503	SO:0001583	missense	55735	exon14			GTCACGTCAATCA	AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"Heat shock proteins / DNAJ (HSP40)"	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.1460A>G	chr1.hg19:g.6697322T>C	ENSP00000366800:p.Asp487Gly	126.0	0.0		107.0	40.0	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Missense_Mutation	SNP	ENST00000377577.5	hg19	CCDS87.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.837986	0.91117	.	.	ENSG00000007923	ENST00000377577;ENST00000294401;ENST00000542246;ENST00000377573	T;T;T;T	0.63096	0.82;0.72;0.44;-0.02	5.54	5.54	0.83059	DnaJ-like protein C11, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84534	0.5493	H	0.94886	3.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.986;0.999;0.999	D	0.88947	0.3384	10	0.87932	D	0	-8.1167	14.8693	0.70444	0.0:0.0:0.0:1.0	.	397;435;487	B4DGD5;Q9NVH1-3;Q9NVH1	.;.;DJC11_HUMAN	G	487;435;449;397	ENSP00000366800:D487G;ENSP00000294401:D435G;ENSP00000444020:D449G;ENSP00000366796:D397G	ENSP00000294401:D435G	D	-	2	0	DNAJC11	6619909	1.000000	0.71417	0.918000	0.36340	0.991000	0.79684	7.502000	0.81614	2.107000	0.64212	0.533000	0.62120	GAC	.	.		0.547	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198		C	6697322	T	C	6697322	3	2	23	1	0	0	0	0	1	0	0	0	4632	1667	58	2	231	2	DNAJC11	1	6697322	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	55084	6697322	242553299	7	2073										
PER3	8863	hgsc.bcm.edu	37	chr1	7854025	7854025	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctttctttctagcagctgcaCggtatgaatgtgctccggtg	11	10	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:7854025C>T	ENST00000361923.2	+	5	773	c.598C>T	c.(598-600)Cgg>Tgg	p.R200W	PER3_ENST00000377541.1_Missense_Mutation_p.R200W|PER3_ENST00000377532.3_Missense_Mutation_p.R201W	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	200					circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		AGCAGCTGCACGGTATGAATG	0.428																																					p.R200W		Atlas-SNP	.											.	PER3	95	.	0			c.C598T						.						158	154	155					1																	7854025		2203	4300	6503	SO:0001583	missense	8863	exon5			GCTGCACGGTATG	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.598C>T	chr1.hg19:g.7854025C>T	ENSP00000355031:p.Arg200Trp	111.0	0.0		134.0	64.0	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	hg19	CCDS89.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.212237	0.79240	.	.	ENSG00000049246	ENST00000377541;ENST00000377532;ENST00000361923	T;T;T	0.31510	1.49;2.92;2.92	4.41	4.41	0.53225	.	0.616314	0.15113	N	0.279841	T	0.34629	0.0904	N	0.08118	0	0.29974	N	0.818265	D;D;D;D	0.76494	0.999;0.992;0.995;0.999	P;P;D;P	0.65233	0.82;0.859;0.933;0.82	T	0.39121	-0.9629	10	0.52906	T	0.07	.	16.1524	0.81632	0.0:1.0:0.0:0.0	.	200;201;201;200	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	W	200;201;200	ENSP00000366764:R200W;ENSP00000366755:R201W;ENSP00000355031:R200W	ENSP00000355031:R200W	R	+	1	2	PER3	7776612	0.077000	0.21312	0.006000	0.13384	0.002000	0.02628	3.621000	0.54210	2.273000	0.75805	0.591000	0.81541	CGG	.	.		0.428	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		T	7854025	C	T	7854025	3	4	23	1	0	0	0	0	1	0	0	0	11740	527	19	1	616	1	PER3	1	7854025	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1156703	7854025	241396596	8	2074										
PER3	8863	hgsc.bcm.edu	37	chr1	7887318	7887318	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcgcatcagaacgcacagCcctgctgcccctccgcggcc	11	19	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:7887318C>T	ENST00000361923.2	+	17	2480	c.2305C>T	c.(2305-2307)Ccc>Tcc	p.P769S	PER3_ENST00000377532.3_Missense_Mutation_p.P777S|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	769	Pro-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GAACGCACAGCCCTGCTGCCC	0.682																																					p.P769S		Atlas-SNP	.											.	PER3	95	.	0			c.C2305T						.						38	44	42					1																	7887318		2203	4299	6502	SO:0001583	missense	8863	exon17			GCACAGCCCTGCT	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2305C>T	chr1.hg19:g.7887318C>T	ENSP00000355031:p.Pro769Ser	150.0	0.0		160.0	68.0	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	hg19	CCDS89.1	.	.	.	.	.	.	.	.	.	.	C	10.49	1.366043	0.24684	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.09723	2.95;2.95	4.33	1.33	0.21861	.	2.473990	0.01395	N	0.013374	T	0.17365	0.0417	L	0.37507	1.11	0.09310	N	1	D;P;P;D	0.76494	0.999;0.473;0.607;0.999	D;B;B;D	0.64144	0.922;0.145;0.28;0.922	T	0.44605	-0.9317	10	0.07030	T	0.85	.	4.4648	0.11684	0.0:0.4257:0.3652:0.209	.	769;777;777;769	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	S	777;769	ENSP00000366755:P777S;ENSP00000355031:P769S	ENSP00000355031:P769S	P	+	1	0	PER3	7809905	0.037000	0.19845	0.015000	0.15790	0.025000	0.11179	1.031000	0.30165	0.105000	0.17753	0.561000	0.74099	CCC	.	.		0.682	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		T	7887318	C	T	7887318	3	4	23	1	0	0	0	0	1	0	0	0	11740	739	26	3	2371	3	PER3	1	7887318	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	33293	7887318	241363303	9	2075										
CLSTN1	22883	hgsc.bcm.edu	37	chr1	9795966	9795966	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacgcctctgccactgtcttCgaggacctgcaggtccagcc	10	17	2	0	rs201640412		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:9795966C>T	ENST00000377298.4	-	12	2503	c.1711G>A	c.(1711-1713)Gaa>Aaa	p.E571K	CLSTN1_ENST00000361311.4_Missense_Mutation_p.E561K|CLSTN1_ENST00000377288.3_Missense_Mutation_p.E552K|CLSTN1_ENST00000477264.1_5'Flank	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	571					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)	p.E571K(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		CCACTGTCTTCGAGGACCTGC	0.597																																					p.E571K		Atlas-SNP	.											CLSTN1,colon,carcinoma,0,1	CLSTN1	88	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1711A						.	C	LYS/GLU,LYS/GLU	0,4406		0,0,2203	65	65	65		1711,1681	5.8	0.1	1		65	4,8596	3.7+/-12.6	0,4,4296	no	missense,missense	CLSTN1	NM_001009566.1,NM_014944.3	56,56	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	possibly-damaging,possibly-damaging	571/982,561/972	9795966	4,13002	2203	4300	6503	SO:0001583	missense	22883	exon12			TGTCTTCGAGGAC	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"Cadherins / Cadherin-related"	17447	protein-coding gene	gene with protein product	"cadherin-related family member 12"	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.1711G>A	chr1.hg19:g.9795966C>T	ENSP00000366513:p.Glu571Lys	83.0	0.0		96.0	31.0	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	hg19	CCDS30580.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.085223	0.55861	0.0	4.65E-4	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.34072	1.38;1.38;1.38;1.38	5.77	5.77	0.91146	.	0.152343	0.64402	D	0.000017	T	0.45034	0.1322	L	0.55481	1.735	0.58432	D	0.99999	P;D;D	0.58620	0.95;0.983;0.971	B;P;B	0.47981	0.164;0.563;0.359	T	0.23833	-1.0177	10	0.39692	T	0.17	-13.2539	19.9983	0.97395	0.0:1.0:0.0:0.0	.	552;561;571	B4E3Q1;O94985-2;O94985	.;.;CSTN1_HUMAN	K	571;561;372;552;552	ENSP00000366513:E571K;ENSP00000354997:E561K;ENSP00000401934:E372K;ENSP00000366502:E552K	ENSP00000354997:E561K	E	-	1	0	CLSTN1	9718553	1.000000	0.71417	0.057000	0.19452	0.313000	0.28021	4.859000	0.62954	2.724000	0.93272	0.561000	0.74099	GAA	.	C|0.999;T|0.001		0.597	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1			T	9795966	C	T	9795966	3	4	23	1	0	0	0	0	1	0	0	0	3563	893	31	1	1266	1	CLSTN1	1	9795966	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1908648	9795966	239454655	10	2076										
CASZ1	54897	hgsc.bcm.edu	37	chr1	10713986	10713986	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctccgtgtccttggcgcccaGcagcgagggcggcagcccca	14	17	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:10713986G>T	ENST00000377022.3	-	11	2445	c.2128C>A	c.(2128-2130)Ctg>Atg	p.L710M	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Missense_Mutation_p.L710M	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	710					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		TTGGCGCCCAGCAGCGAGGGC	0.657																																					p.L710M		Atlas-SNP	.											.	CASZ1	150	.	0			c.C2128A						.						47	49	48					1																	10713986		2203	4300	6503	SO:0001583	missense	54897	exon11			CGCCCAGCAGCGA	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.2128C>A	chr1.hg19:g.10713986G>T	ENSP00000366221:p.Leu710Met	108.0	0.0		112.0	46.0	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	hg19	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170630	0.78452	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.84	4.84	0.62591	.	0.366421	0.27495	N	0.019106	T	0.63651	0.2529	L	0.29908	0.895	0.38147	D	0.938617	D;D;D	0.76494	0.999;0.996;0.98	D;P;P	0.68192	0.956;0.9;0.788	T	0.67526	-0.5648	9	0.54805	T	0.06	-6.3503	13.7821	0.63089	0.0:0.0:0.8462:0.1537	.	734;710;710	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	M	710	.	ENSP00000339445:L710M	L	-	1	2	CASZ1	10636573	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.391000	0.59652	2.619000	0.88677	0.561000	0.74099	CTG	.	.		0.657	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		T	10713986	G	T	10713986	3	4	23	1	0	0	0	0	1	0	0	0	2687	962	34	3	3199	3	CASZ1	1	10713986	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	918020	10713986	238536635	11	2077										
C1orf127	148345	hgsc.bcm.edu	37	chr1	11007833	11007833	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagctcctgctggagtgaggCcccccggccagcctggaagg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:11007833delC	ENST00000377008.4	-	11	2304	c.1858delG	c.(1858-1860)gccfs	p.A620fs	C1orf127_ENST00000377004.4_Frame_Shift_Del_p.A787fs			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	620										NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TGGAGTGAGGCCCCCCGGCCA	0.627																																					p.A787fs		Atlas-Indel,Pindel	.											.	C1orf127	134	.	0			c.2360delC						.						24	24	24					1																	11007833		2203	4300	6503	SO:0001589	frameshift_variant	148345	exon12			.	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1858delG	chr1.hg19:g.11007833delC	ENSP00000366207:p.Ala620fs	87.0	0.0		97.0	37.0	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Frame_Shift_Del	DEL	ENST00000377008.4	hg19																																																																																				.	.		0.627	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		-	11007833	C	-	11007833	7	5	23	1	0	1	0	1	0	0	0	0	1996	739	26	0	116	0	C1orf127	1	11007833	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	293847	11007833	238242788	12	2078										
C1orf127	148345	hgsc.bcm.edu	37	chr1	11009719	11009719	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggccggtgcaggaggtcccGagaaagccattcctgggcag	16	11	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:11009719G>A	ENST00000377008.4	-	10	1197	c.751C>T	c.(751-753)Cgg>Tgg	p.R251W	C1orf127_ENST00000377004.4_Missense_Mutation_p.R418W			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	251	Pro-rich.									NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		AGGAGGTCCCGAGAAAGCCAT	0.632																																					p.R418W		Atlas-SNP	.											.	C1orf127	134	.	0			c.C1252T						.						42	36	38					1																	11009719		2199	4300	6499	SO:0001583	missense	148345	exon11			GGTCCCGAGAAAG	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.751C>T	chr1.hg19:g.11009719G>A	ENSP00000366207:p.Arg251Trp	132.0	0.0		118.0	45.0	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	hg19		.	.	.	.	.	.	.	.	.	.	G	6.613	0.481543	0.12581	.	.	ENSG00000175262	ENST00000377004;ENST00000377008	T;T	0.30981	1.51;1.51	3.16	-0.889	0.10580	.	2.454000	0.01735	N	0.029072	T	0.18718	0.0449	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.31806	-0.9930	10	0.59425	D	0.04	1.1221	8.5329	0.33346	0.3534:0.0:0.6466:0.0	.	269;251	B7ZLG7;Q8N9H9	.;CA127_HUMAN	W	418;251	ENSP00000366203:R418W;ENSP00000366207:R251W	ENSP00000366203:R418W	R	-	1	2	C1orf127	10932306	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	0.229000	0.17833	-0.441000	0.07201	-1.583000	0.00853	CGG	.	.		0.632	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		A	11009719	G	A	11009719	3	1	23	1	0	0	0	0	1	0	0	0	1996	1057	37	1	1227	1	C1orf127	1	11009719	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1886	11009719	238240902	13	2079										
EXOSC10	5394	hgsc.bcm.edu	37	chr1	11151567	11151567	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caccttacggttccagctggAcactaccgttttggggacct	10	13	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:11151567A>G	ENST00000376936.4	-	4	509	c.460T>C	c.(460-462)Tcc>Ccc	p.S154P	EXOSC10_ENST00000544779.1_Missense_Mutation_p.S154P|EXOSC10_ENST00000304457.7_Missense_Mutation_p.S154P	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	154					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		TTCCAGCTGGACACTACCGTT	0.458																																					p.S154P	Colon(179;105 1987 14326 27364 29542)	Atlas-SNP	.											.	EXOSC10	59	.	0			c.T460C						.						72	71	71					1																	11151567		2203	4300	6503	SO:0001583	missense	5394	exon4			AGCTGGACACTAC	BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 2 (100kD)"	605960	"polymyositis/scleroderma autoantigen 2, 100kDa"	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.460T>C	chr1.hg19:g.11151567A>G	ENSP00000366135:p.Ser154Pro	123.0	0.0		132.0	38.0	NM_001001998	B1AKQ0|B1AKQ1|Q15158	Missense_Mutation	SNP	ENST00000376936.4	hg19	CCDS30584.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.216668	0.79352	.	.	ENSG00000171824	ENST00000376936;ENST00000304457;ENST00000544779	.	.	.	6.03	4.9	0.64082	.	0.050617	0.85682	N	0.000000	T	0.76535	0.4001	M	0.77616	2.38	0.58432	D	0.999999	D;D	0.69078	0.997;0.995	D;D	0.68192	0.956;0.929	T	0.76846	-0.2808	9	0.46703	T	0.11	-19.1249	11.155	0.48482	0.9288:0.0:0.0712:0.0	.	154;154	Q01780-2;Q01780	.;EXOSX_HUMAN	P	154	.	ENSP00000307307:S154P	S	-	1	0	EXOSC10	11074154	1.000000	0.71417	0.994000	0.49952	0.629000	0.37895	8.534000	0.90620	1.113000	0.41760	0.454000	0.30748	TCC	.	.		0.458	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998		G	11151567	A	G	11151567	3	3	23	1	0	0	0	0	1	0	0	0	5316	275	10	2	2285	2	EXOSC10	1	11151567	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	141848	11151567	238099054	14	2080										
MIIP	60672	hgsc.bcm.edu	37	chr1	12082888	12082888	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccctctgtgcttccttcctcAgcccagggtgaccttctctg	8	17	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:12082888A>G	ENST00000235332.4	+	4	631		c.e4-1		MIIP_ENST00000466860.1_Splice_Site|Y_RNA_ENST00000365591.1_RNA|MIIP_ENST00000436478.2_Splice_Site	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein											autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						TTCCTTCCTCAGCCCAGGGTG	0.567																																					.		Atlas-SNP	.											.	MIIP	34	.	0			c.463-2A>G						.						57	48	51					1																	12082888		2203	4300	6503	SO:0001630	splice_region_variant	60672	exon4			TTCCTCAGCCCAG	AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"invasion inhibitory protein 45"	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.463-1A>G	chr1.hg19:g.12082888A>G		77.0	0.0		57.0	19.0	NM_021933	C0KL22|Q96HU6|Q9H839|Q9HA00	Splice_Site	SNP	ENST00000235332.4	hg19	CCDS143.1	.	.	.	.	.	.	.	.	.	.	A	9.245	1.039384	0.19669	.	.	ENSG00000116691	ENST00000235332;ENST00000436478	.	.	.	3.54	3.54	0.40534	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.776	0.34762	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MIIP	12005475	0.988000	0.35896	0.947000	0.38551	0.340000	0.28889	2.501000	0.45389	1.831000	0.53308	0.254000	0.18369	.	.	.		0.567	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933	Intron	G	12082888	A	G	12082888	5	3	23	1	0	0	0	0	0	0	1	0	9594	202	7	2	471	2	MIIP	1	12082888	Splice_Site	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	931321	12082888	237167733	15	2081										
TMEM51	55092	hgsc.bcm.edu	37	chr1	15541641	15541641	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgctgaccgccatcggcctgGggatgctggtccttggggtg	17	12	0	1	rs147062114		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:15541641G>T	ENST00000428417.1	+	2	504	c.58G>T	c.(58-60)Ggg>Tgg	p.G20W	TMEM51_ENST00000434578.2_Missense_Mutation_p.G20W|TMEM51_ENST00000376008.2_Missense_Mutation_p.G20W|TMEM51_ENST00000376014.3_Missense_Mutation_p.G20W|TMEM51_ENST00000400796.3_Missense_Mutation_p.G20W	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	20						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		CATCGGCCTGGGGATGCTGGT	0.607																																					p.G20W		Atlas-SNP	.											.	TMEM51	28	.	0			c.G58T						.	G	TRP/GLY,TRP/GLY,TRP/GLY,TRP/GLY	1,4405	2.1+/-5.4	0,1,2202	95	98	97		58,58,58,58	5.5	1	1	dbSNP_134	97	0,8600		0,0,4300	no	missense,missense,missense,missense	TMEM51	NM_001136216.1,NM_001136217.1,NM_001136218.1,NM_018022.2	184,184,184,184	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	20/254,20/254,20/254,20/254	15541641	1,13005	2203	4300	6503	SO:0001583	missense	55092	exon2			GGCCTGGGGATGC	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 72"	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.58G>T	chr1.hg19:g.15541641G>T	ENSP00000394899:p.Gly20Trp	44.0	0.0		65.0	29.0	NM_018022	A8K819	Missense_Mutation	SNP	ENST00000428417.1	hg19	CCDS154.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.891637	0.91889	2.27E-4	0.0	ENSG00000171729	ENST00000428417;ENST00000376014;ENST00000451326;ENST00000434578;ENST00000400796;ENST00000376008;ENST00000303840	T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.81866	0.4913	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83408	0.0026	10	0.87932	D	0	11.5582	18.4425	0.90671	0.0:0.0:1.0:0.0	.	20;20	Q9BSA0;Q9NW97	.;TMM51_HUMAN	W	20	ENSP00000394899:G20W;ENSP00000365182:G20W;ENSP00000412298:G20W;ENSP00000409665:G20W;ENSP00000383600:G20W;ENSP00000365176:G20W	ENSP00000303666:G20W	G	+	1	0	TMEM51	15414228	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.744000	0.91596	2.612000	0.88384	0.655000	0.94253	GGG	.	G|1.000;T|0.000		0.607	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022		T	15541641	G	T	15541641	3	4	23	1	0	0	0	0	1	0	0	0	16192	1232	43	3	60	3	TMEM51	1	15541641	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3458753	15541641	233708980	16	2082										
CLCNKB	1188	hgsc.bcm.edu	37	chr1	16377520	16377520	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggttcaccatctttgggaccCttgccttcttcctggttatg	9	12	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:16377520C>A	ENST00000375679.4	+	12	1315	c.1204C>A	c.(1204-1206)Ctt>Att	p.L402I	CLCNKB_ENST00000375667.3_Missense_Mutation_p.L233I	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	402					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CTTTGGGACCCTTGCCTTCTT	0.642																																					p.L402I		Atlas-SNP	.											.	CLCNKB	50	.	0			c.C1204A						.						77	84	82					1																	16377520		2203	4300	6503	SO:0001583	missense	1188	exon12			GGGACCCTTGCCT	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"Ion channels / Chloride channels : Voltage-sensitive"	2027	protein-coding gene	gene with protein product		602023	"chloride channel Kb"				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1204C>A	chr1.hg19:g.16377520C>A	ENSP00000364831:p.Leu402Ile	142.0	0.0		132.0	59.0	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Missense_Mutation	SNP	ENST00000375679.4	hg19	CCDS168.1	.	.	.	.	.	.	.	.	.	.	c	17.44	3.390206	0.62066	.	.	ENSG00000184908	ENST00000375679;ENST00000331579;ENST00000375667	D;D	0.96136	-3.92;-3.92	4.59	4.59	0.56863	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.96849	0.8971	M	0.81497	2.545	0.49582	D	0.999808	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95358	0.8453	10	0.27082	T	0.32	.	8.1502	0.31137	0.0:0.8827:0.0:0.1173	.	233;402	Q5T5Q7;P51801	.;CLCKB_HUMAN	I	402;274;233	ENSP00000364831:L402I;ENSP00000364819:L233I	ENSP00000332055:L274I	L	+	1	0	CLCNKB	16250107	0.996000	0.38824	0.993000	0.49108	0.989000	0.77384	3.671000	0.54576	2.090000	0.63153	0.561000	0.74099	CTT	.	.		0.642	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085		A	16377520	C	A	16377520	3	1	23	1	0	0	0	0	1	0	0	0	3472	681	24	3	1394	3	CLCNKB	1	16377520	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	835879	16377520	232873101	17	2083										
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17328825	17328825	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctggaggctgaggccatggcGggagcggtggacgtcgtcac	19	10	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:17328825G>A	ENST00000326735.8	-	7	634	c.601C>T	c.(601-603)Cgc>Tgc	p.R201C	ATP13A2_ENST00000341676.5_Missense_Mutation_p.R196C|ATP13A2_ENST00000452699.1_Missense_Mutation_p.R196C|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000502860.1_5'Flank			Q9NQ11	AT132_HUMAN	ATPase type 13A2	201					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGGCCATGGCGGGAGCGGTGG	0.672																																					p.R201C		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C601T						.						40	34	36					1																	17328825		2203	4299	6502	SO:0001583	missense	23400	exon7			CATGGCGGGAGCG	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.601C>T	chr1.hg19:g.17328825G>A	ENSP00000327214:p.Arg201Cys	334.0	0.0		342.0	156.0	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	hg19	CCDS175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.344|6.344	0.431639|0.431639	0.12045|0.12045	.|.	.|.	ENSG00000159363|ENSG00000159363	ENST00000510069;ENST00000508222;ENST00000509619|ENST00000326735;ENST00000341676;ENST00000452699;ENST00000511957	.|D;D;D;D	.|0.89123	.|-2.47;-2.47;-2.47;-2.47	4.89|4.89	-3.19|-3.19	0.05171|0.05171	.|ATPase, P-type cation-transporter, N-terminal (1);	.|0.418143	.|0.28718	.|N	.|0.014368	T|T	0.77811|0.77811	0.4186|0.4186	L|L	0.33624|0.33624	1.015|1.015	0.09310|0.09310	N|N	0.999999|0.999999	.|B;B;B	.|0.17268	.|0.021;0.005;0.002	.|B;B;B	.|0.10450	.|0.005;0.002;0.003	T|T	0.64622|0.64622	-0.6364|-0.6364	5|10	.|0.48119	.|T	.|0.1	-2.4527|-2.4527	6.0407|6.0407	0.19732|0.19732	0.1704:0.0:0.3217:0.508|0.1704:0.0:0.3217:0.508	.|.	.|196;196;201	.|Q5JXY1;Q6S9Z9;Q9NQ11	.|.;.;AT132_HUMAN	L|C	175;107;187|201;196;196;105	.|ENSP00000327214:R201C;ENSP00000341115:R196C;ENSP00000413307:R196C;ENSP00000427241:R105C	.|ENSP00000327214:R201C	P|R	-|-	2|1	0|0	ATP13A2|ATP13A2	17201412|17201412	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.037000|0.037000	0.13140|0.13140	0.090000|0.090000	0.15025|0.15025	-0.312000|-0.312000	0.08741|0.08741	0.561000|0.561000	0.74099|0.74099	CCG|CGC	.	.		0.672	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		A	17328825	G	A	17328825	3	1	23	1	0	0	0	0	1	0	0	0	1124	1116	39	1	3269	1	ATP13A2	1	17328825	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	951305	17328825	231921796	18	2084										
PADI2	11240	hgsc.bcm.edu	37	chr1	17418998	17418998	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcggtcggggcctttggtcCgcaggatcatctgggacatg	17	10	2	0	rs372515836		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:17418998C>A	ENST00000375486.4	-	6	623	c.560G>T	c.(559-561)cGg>cTg	p.R187L	PADI2_ENST00000444885.2_Intron|PADI2_ENST00000375481.1_Missense_Mutation_p.R187L	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	187					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	GCCTTTGGTCCGCAGGATCAT	0.527																																					p.R187L		Atlas-SNP	.											.	PADI2	72	.	0			c.G560T						.						76	70	72					1																	17418998		2203	4300	6503	SO:0001583	missense	11240	exon6			TTGGTCCGCAGGA	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"Peptidyl arginine deiminases"	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.560G>T	chr1.hg19:g.17418998C>A	ENSP00000364635:p.Arg187Leu	119.0	0.0		111.0	14.0	NM_007365	Q96DA7|Q9UPN2	Missense_Mutation	SNP	ENST00000375486.4	hg19	CCDS177.1	.	.	.	.	.	.	.	.	.	.	C	35	5.452748	0.96223	.	.	ENSG00000117115	ENST00000375486;ENST00000375481	T;T	0.19669	2.13;2.13	5.59	5.59	0.84812	Protein-arginine deiminase (PAD), central domain (2);	0.000000	0.85682	D	0.000000	T	0.45696	0.1355	M	0.79011	2.435	0.80722	D	1	P	0.50943	0.94	P	0.57776	0.827	T	0.37596	-0.9699	10	0.54805	T	0.06	-32.5878	18.1583	0.89701	0.0:1.0:0.0:0.0	.	187	Q9Y2J8	PADI2_HUMAN	L	187	ENSP00000364635:R187L;ENSP00000364630:R187L	ENSP00000364630:R187L	R	-	2	0	PADI2	17291585	1.000000	0.71417	0.990000	0.47175	0.997000	0.91878	5.239000	0.65371	2.642000	0.89623	0.561000	0.74099	CGG	.	.		0.527	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			A	17418998	C	A	17418998	3	1	23	1	0	0	0	0	1	0	0	0	11387	652	23	1	1481	1	PADI2	1	17418998	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	90173	17418998	231831623	19	2085										
PADI1	29943	hgsc.bcm.edu	37	chr1	17555492	17555492	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cactgtgggcttccgcatggCcccctggatcatgacgccca							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:17555492delC	ENST00000375471.4	+	8	967	c.875delC	c.(874-876)gccfs	p.A292fs		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	292					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	TTCCGCATGGCCCCCTGGATC	0.637																																					p.A292fs	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-Indel,Pindel	.											.	PADI1	77	.	0			c.874delG						.						44	33	37					1																	17555492		2202	4300	6502	SO:0001589	frameshift_variant	29943	exon8			.	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"Peptidyl arginine deiminases"	18367	protein-coding gene	gene with protein product	"peptidylarginine deiminase type I", "protein-arginine deiminase type-1", "hPAD-colony 10"	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.875delC	chr1.hg19:g.17555492delC	ENSP00000364620:p.Ala292fs	56.0	0.0		52.0	23.0	NM_013358	A1L4K6|Q70SX6	Frame_Shift_Del	DEL	ENST00000375471.4	hg19	CCDS178.1																																																																																			.	.		0.637	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		-	17555492	C	-	17555492	7	5	23	1	0	1	0	1	0	0	0	0	11386	739	26	0	905	0	PADI1	1	17555492	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	136494	17555492	231695129	20	2086										
ARHGEF10L	55160	hgsc.bcm.edu	37	chr1	17983183	17983183	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgcaggatgggacccttgCtgcttaccctcggaccagcg	12	15	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:17983183C>A	ENST00000361221.3	+	25	2999	c.2840C>A	c.(2839-2841)gCt>gAt	p.A947D	ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.A720D|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.A650D|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.A908D|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.A908D|ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.A942D|ARHGEF10L_ENST00000469726.1_3'UTR	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	947						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GGGACCCTTGCTGCTTACCCT	0.647																																					p.A947D		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.C2840A						.						45	45	45					1																	17983183		2203	4300	6503	SO:0001583	missense	55160	exon25			CCCTTGCTGCTTA	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.2840C>A	chr1.hg19:g.17983183C>A	ENSP00000355060:p.Ala947Asp	161.0	0.0		151.0	38.0	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	hg19	CCDS182.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.924970	0.73213	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415;ENST00000375408;ENST00000457829;ENST00000167825	T;T;T;T;T;T	0.63580	3.33;3.33;-0.05;3.33;3.33;3.33	4.72	4.72	0.59763	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.311872	0.34676	N	0.003775	T	0.80513	0.4637	M	0.85462	2.755	0.44570	D	0.99753	D;D;D;D;D;D;D	0.76494	0.984;0.998;0.995;0.992;0.995;0.999;0.996	P;D;D;P;D;D;D	0.74023	0.811;0.979;0.933;0.899;0.948;0.982;0.959	D	0.84243	0.0473	10	0.72032	D	0.01	-26.1294	15.1562	0.72743	0.0:1.0:0.0:0.0	.	720;942;650;708;903;908;947	Q5VXI4;Q9HCE6-5;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;.;ARGAL_HUMAN	D	947;908;942;908;720;720;650	ENSP00000355060:A947D;ENSP00000399401:A908D;ENSP00000394621:A942D;ENSP00000364564:A908D;ENSP00000364557:A720D;ENSP00000167825:A650D	ENSP00000167825:A650D	A	+	2	0	ARHGEF10L	17855770	0.960000	0.32886	1.000000	0.80357	0.913000	0.54294	2.350000	0.44063	2.161000	0.67846	0.555000	0.69702	GCT	.	.		0.647	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		A	17983183	C	A	17983183	3	1	23	1	0	0	0	0	1	0	0	0	895	797	28	3	2934	3	ARHGEF10L	1	17983183	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	427691	17983183	231267438	21	2087										
CDA	978	hgsc.bcm.edu	37	chr1	20931423	20931423	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actctgctctcttctcagggTgcaacatagaaaatgcctgc	8	12	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:20931423T>C	ENST00000375071.3	+	2	339	c.157T>C	c.(157-159)Tgc>Cgc	p.C53R	CDA_ENST00000461985.1_3'UTR	NM_001785.2	NP_001776.1	P32320	CDD_HUMAN	cytidine deaminase	53	CMP/dCMP deaminase zinc-binding.				cell surface receptor signaling pathway (GO:0007166)|cytidine deamination (GO:0009972)|cytosine metabolic process (GO:0019858)|negative regulation of cell growth (GO:0030308)|negative regulation of nucleotide metabolic process (GO:0045980)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine-containing compound salvage (GO:0008655)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	cytidine deaminase activity (GO:0004126)|nucleoside binding (GO:0001882)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)	CTTCTCAGGGTGCAACATAGA	0.522																																					p.C53R	Pancreas(74;49 1356 2772 27818 40529)	Atlas-SNP	.											.	CDA	19	.	0			c.T157C						.						90	78	82					1																	20931423		2203	4300	6503	SO:0001583	missense	978	exon2			TCAGGGTGCAACA	BC054036	CCDS210.1	1p36.2-p35	2008-02-05			ENSG00000158825	ENSG00000158825	3.5.4.5		1712	protein-coding gene	gene with protein product		123920				8422236, 9878810	Standard	NM_001785		Approved	CDD	uc001bdk.3	P32320	OTTHUMG00000002845	ENST00000375071.3:c.157T>C	chr1.hg19:g.20931423T>C	ENSP00000364212:p.Cys53Arg	142.0	0.0		124.0	39.0	NM_001785		Missense_Mutation	SNP	ENST00000375071.3	hg19	CCDS210.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.297091	0.81025	.	.	ENSG00000158825	ENST00000375071	T	0.42131	0.98	5.75	5.75	0.90469	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.000000	0.85682	D	0.000000	T	0.78641	0.4315	H	0.99286	4.5	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86682	0.1917	10	0.87932	D	0	.	12.4468	0.55654	0.0:0.0:0.0:1.0	.	53	P32320	CDD_HUMAN	R	53	ENSP00000364212:C53R	ENSP00000364212:C53R	C	+	1	0	CDA	20804010	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.790000	0.75115	2.192000	0.70111	0.459000	0.35465	TGC	.	.		0.522	CDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007965.1	NM_001785		C	20931423	T	C	20931423	3	2	23	1	0	0	0	0	1	0	0	0	3054	1696	59	2	163	2	CDA	1	20931423	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2948240	20931423	228319198	22	2088										
EPHA8	2046	hgsc.bcm.edu	37	chr1	22928128	22928128	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttccttcacagggacgtgcGcgccctgggcatcaccctca	10	17	3	0	rs139543017		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:22928128G>A	ENST00000166244.3	+	17	2984	c.2912G>A	c.(2911-2913)cGc>cAc	p.R971H		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	971	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGGGACGTGCGCGCCCTGGGC	0.697																																					p.R971H		Atlas-SNP	.											.	EPHA8	221	.	0			c.G2912A						.	G	HIS/ARG	0,4380		0,0,2190	17	19	18		2912	5.2	1	1	dbSNP_134	18	1,8575		0,1,4287	no	missense	EPHA8	NM_020526.3	29	0,1,6477	AA,AG,GG		0.0117,0.0,0.0077	probably-damaging	971/1006	22928128	1,12955	2190	4288	6478	SO:0001583	missense	2046	exon17			ACGTGCGCGCCCT	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.2912G>A	chr1.hg19:g.22928128G>A	ENSP00000166244:p.Arg971His	213.0	0.0		168.0	66.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	hg19	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.137159	0.37728	0.0	1.17E-4	ENSG00000070886	ENST00000166244	T	0.51574	0.7	5.23	5.23	0.72850	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.071675	0.56097	D	0.000030	T	0.60894	0.2304	L	0.59436	1.845	0.80722	D	1	D	0.64830	0.994	P	0.58780	0.845	T	0.60073	-0.7334	10	0.48119	T	0.1	.	16.319	0.82939	0.0:0.0:1.0:0.0	.	971	P29322	EPHA8_HUMAN	H	971	ENSP00000166244:R971H	ENSP00000166244:R971H	R	+	2	0	EPHA8	22800715	0.953000	0.32496	0.960000	0.40013	0.004000	0.04260	2.257000	0.43240	2.722000	0.93159	0.491000	0.48974	CGC	.	G|1.000;A|0.000		0.697	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		A	22928128	G	A	22928128	3	1	23	1	0	0	0	0	1	0	0	0	5175	1087	38	1	3151	1	EPHA8	1	22928128	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1996705	22928128	226322493	23	2089										
C1QA	712	hgsc.bcm.edu	37	chr1	22965607	22965607	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaccgtaccagaaccactccGgccgattcgtctgcactgta	8	15	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:22965607G>A	ENST00000374642.3	+	3	649	c.445G>A	c.(445-447)Ggc>Agc	p.G149S	C1QA_ENST00000402322.1_Missense_Mutation_p.G149S	NM_015991.2	NP_057075.1	P02745	C1QA_HUMAN	complement component 1, q subcomponent, A chain	149	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				cell-cell signaling (GO:0007267)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	collagen trimer (GO:0005581)|complement component C1 complex (GO:0005602)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|liver(1)|lung(3)|skin(1)	6		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.41e-27)|Colorectal(126;1.52e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.63e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000541)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GAACCACTCCGGCCGATTCGT	0.592																																					p.G149S		Atlas-SNP	.											.	C1QA	31	.	0			c.G445A						.						84	75	78					1																	22965607		2203	4300	6503	SO:0001583	missense	712	exon3			CACTCCGGCCGAT	AF135157	CCDS226.1	1p36.3-p34.1	2014-09-17	2006-02-09		ENSG00000173372	ENSG00000173372		"Complement system"	1241	protein-coding gene	gene with protein product		120550	"complement component 1, q subcomponent, alpha polypeptide"			1537612	Standard	NM_015991		Approved		uc001bfy.3	P02745	OTTHUMG00000002893	ENST00000374642.3:c.445G>A	chr1.hg19:g.22965607G>A	ENSP00000363773:p.Gly149Ser	232.0	0.0		201.0	82.0	NM_015991	B2R4X2|Q5T963	Missense_Mutation	SNP	ENST00000374642.3	hg19	CCDS226.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.907539	0.52333	.	.	ENSG00000173372	ENST00000374642;ENST00000438241;ENST00000402322	T;T;T	0.66995	-0.24;-0.24;-0.24	5.67	4.76	0.60689	Tumour necrosis factor-like (2);Complement C1q protein (4);	.	.	.	.	T	0.78830	0.4345	M	0.73598	2.24	0.47547	D	0.999458	D	0.71674	0.998	D	0.63113	0.911	T	0.80495	-0.1357	9	0.52906	T	0.07	0.1645	13.3906	0.60823	0.0763:0.0:0.9237:0.0	.	149	P02745	C1QA_HUMAN	S	149	ENSP00000363773:G149S;ENSP00000416841:G149S;ENSP00000385564:G149S	ENSP00000363773:G149S	G	+	1	0	C1QA	22838194	1.000000	0.71417	0.132000	0.22025	0.022000	0.10575	5.948000	0.70249	1.419000	0.47118	0.561000	0.74099	GGC	.	.		0.592	C1QA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008087.2	NM_015991		A	22965607	G	A	22965607	3	1	23	1	0	0	0	0	1	0	0	0	1956	1116	39	1	451	1	C1QA	1	22965607	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	37479	22965607	226285014	24	2090										
EPHB2	2048	hgsc.bcm.edu	37	chr1	23191427	23191427	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caatgagacctccctcatgcTggagtggacccctccccgcg	10	17	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:23191427T>A	ENST00000400191.3	+	5	1043	c.1025T>A	c.(1024-1026)cTg>cAg	p.L342Q	EPHB2_ENST00000465676.1_3'UTR|EPHB2_ENST00000374630.3_Missense_Mutation_p.L342Q|EPHB2_ENST00000374632.3_Missense_Mutation_p.L342Q|EPHB2_ENST00000374627.1_Missense_Mutation_p.L336Q|MIR4253_ENST00000581187.1_RNA|EPHB2_ENST00000544305.1_Missense_Mutation_p.L342Q	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	342	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		TCCCTCATGCTGGAGTGGACC	0.677																																					p.L342Q		Atlas-SNP	.											.	EPHB2	257	.	0			c.T1025A						.						58	65	63					1																	23191427		2203	4300	6503	SO:0001583	missense	2048	exon5			TCATGCTGGAGTG	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3393	protein-coding gene	gene with protein product		600997	"EphB2"	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1025T>A	chr1.hg19:g.23191427T>A	ENSP00000383053:p.Leu342Gln	174.0	0.0		214.0	84.0	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	hg19		.	.	.	.	.	.	.	.	.	.	T	24.1	4.492364	0.84962	.	.	ENSG00000133216	ENST00000374625;ENST00000544305;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.26	5.26	0.73747	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000008	D	0.87063	0.6084	H	0.96239	3.79	0.54753	D	0.999989	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.984;0.998;0.996;0.994	D	0.90943	0.4799	10	0.87932	D	0	.	14.1516	0.65389	0.0:0.0:0.0:1.0	.	342;342;360;342	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	Q	342;342;342;342;342;336	ENSP00000444174:L342Q;ENSP00000363761:L342Q;ENSP00000383053:L342Q;ENSP00000363763:L342Q;ENSP00000363758:L336Q	ENSP00000363755:L342Q	L	+	2	0	EPHB2	23064014	1.000000	0.71417	0.957000	0.39632	0.987000	0.75469	7.868000	0.87116	2.208000	0.71279	0.460000	0.39030	CTG	.	.		0.677	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		A	23191427	T	A	23191427	3	1	23	1	0	0	0	0	1	0	0	0	5177	1580	55	4	1043	4	EPHB2	1	23191427	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	225820	23191427	226059194	25	2091										
ASAP3	55616	hgsc.bcm.edu	37	chr1	23763464	23763464	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgcatgcgcgaaaagcgcacGcccagttcgcggtggacgcc	14	14	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:23763464G>A	ENST00000336689.3	-	15	1460	c.1416C>T	c.(1414-1416)ggC>ggT	p.G472G	ASAP3_ENST00000437606.2_Silent_p.G463G|ASAP3_ENST00000495646.1_5'Flank	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	472	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						AAAAGCGCACGCCCAGTTCGC	0.677																																					p.G472G		Atlas-SNP	.											.	ASAP3	65	.	0			c.C1416T						.						23	23	23					1																	23763464		2202	4298	6500	SO:0001819	synonymous_variant	55616	exon15			GCGCACGCCCAGT	AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	14987	protein-coding gene	gene with protein product	"centaurin, beta 6"		"development and differentiation enhancing factor-like 1"	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.1416C>T	chr1.hg19:g.23763464G>A		116.0	0.0		129.0	52.0	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Silent	SNP	ENST00000336689.3	hg19	CCDS235.1																																																																																			.	.		0.677	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		A	23763464	G	A	23763464	2	1	23	1	0	0	0	0	0	0	0	1	1012	1074	38	1		1	ASAP3	1	23763464	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	572037	23763464	225487157	26	2092										
SRRM1	10250	hgsc.bcm.edu	37	chr1	24995828	24995828	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctccccagtcaccaagagaCgttcaccttcattatcatcc	5	16	4	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:24995828C>T	ENST00000323848.9	+	14	2269	c.1954C>T	c.(1954-1956)Cgt>Tgt	p.R652C	SRRM1_ENST00000447431.2_Missense_Mutation_p.R664C|SRRM1_ENST00000479034.1_3'UTR|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000374389.4_Missense_Mutation_p.R661C	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	652	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CACCAAGAGACGTTCACCTTC	0.557																																					p.R652C	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											SRRM1,NS,carcinoma,0,1	SRRM1	81	.	0			c.C1954T						.						79	77	78					1																	24995828		2203	4300	6503	SO:0001583	missense	10250	exon14			AAGAGACGTTCAC	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1954C>T	chr1.hg19:g.24995828C>T	ENSP00000326261:p.Arg652Cys	222.0	0.0		222.0	84.0	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	hg19	CCDS255.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165145	0.78339	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.34275	1.37;1.37;1.37	5.85	5.85	0.93711	.	0.000000	0.64402	D	0.000007	T	0.58192	0.2105	L	0.50333	1.59	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.83275	0.996;0.535	T	0.57236	-0.7846	10	0.87932	D	0	-1.3183	20.1542	0.98100	0.0:1.0:0.0:0.0	.	664;652	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	C	652;664;661	ENSP00000326261:R652C;ENSP00000391430:R664C;ENSP00000363510:R661C	ENSP00000326261:R652C	R	+	1	0	SRRM1	24868415	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	6.904000	0.75708	2.767000	0.95098	0.563000	0.77884	CGT	.	.		0.557	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		T	24995828	C	T	24995828	3	4	23	1	0	0	0	0	1	0	0	0	15183	536	19	1	2008	1	SRRM1	1	24995828	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1232364	24995828	224254793	27	2093										
CCDC21	64793	hgsc.bcm.edu	37	chr1	26586251	26586251	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agagagtcgctcaaagtggcGttgcagaagcattctgagga	14	7	2	3	rs534974823		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:26586251G>A	ENST00000252992.4	+	7	1430	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	CEP85_ENST00000451429.2_Silent_p.A382A	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	433						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						TCAAAGTGGCGTTGCAGAAGC	0.463													G|||	1	0.000199681	0	0.0014	5008	,	,		21547	0		0	False		,,,				2504	0				p.A433A		Atlas-SNP	.											.	CEP85	61	.	0			c.G1299A						.						119	118	118					1																	26586251		2203	4300	6503	SO:0001819	synonymous_variant	64793	exon7			AGTGGCGTTGCAG	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"coiled-coil domain containing 21"	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.1299G>A	chr1.hg19:g.26586251G>A		218.0	0.0		223.0	69.0	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Silent	SNP	ENST00000252992.4	hg19	CCDS277.1	.	.	.	.	.	.	.	.	.	.	G	8.413	0.844673	0.16963	.	.	ENSG00000130695	ENST00000453146	.	.	.	6.07	-5.35	0.02697	.	.	.	.	.	T	0.40423	0.1116	.	.	.	0.37854	D	0.929493	.	.	.	.	.	.	T	0.46857	-0.9161	4	.	.	.	-5.7386	4.8867	0.13706	0.2822:0.0792:0.4595:0.1791	.	.	.	.	H	107	.	.	R	+	2	0	CEP85	26458838	0.000000	0.05858	0.053000	0.19242	0.858000	0.48976	-2.122000	0.01321	-0.445000	0.07159	-0.290000	0.09829	CGT	.	.		0.463	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778		A	26586251	G	A	26586251	2	1	23	1	0	0	0	0	0	0	0	1	2798	1132	40	1		1	CCDC21	1	26586251	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1590423	26586251	222664370	28	2094										
UBXN11	91544	hgsc.bcm.edu	37	chr1	26609381	26609381	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgctcagcggccaaggtgggCgtctccaccacaatctcctg	11	16	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:26609381C>T	ENST00000374222.1	-	14	1589	c.1125G>A	c.(1123-1125)acG>acA	p.T375T	UBXN11_ENST00000374221.3_Silent_p.T375T|UBXN11_ENST00000314675.7_Silent_p.T255T|UBXN11_ENST00000374223.1_Silent_p.T132T|UBXN11_ENST00000357089.4_Silent_p.T342T|UBXN11_ENST00000374217.2_Silent_p.T342T			Q5T124	UBX11_HUMAN	UBX domain protein 11	375						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						CCAAGGTGGGCGTCTCCACCA	0.642																																					p.T375T		Atlas-SNP	.											.	UBXN11	54	.	0			c.G1125A						.						67	78	75					1																	26609381		2102	4237	6339	SO:0001819	synonymous_variant	91544	exon14			GGTGGGCGTCTCC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"UBX domain containing"	30600	protein-coding gene	gene with protein product	"socius"	609151	"UBX domain containing 5"	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1125G>A	chr1.hg19:g.26609381C>T		99.0	0.0		96.0	23.0	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	hg19	CCDS41288.1																																																																																			.	.		0.642	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		T	26609381	C	T	26609381	2	4	23	1	0	0	0	0	0	0	0	1	16928	755	27	1		1	UBXN11	1	26609381	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	23130	26609381	222641240	29	2095										
FCN3	8547	hgsc.bcm.edu	37	chr1	27697179	27697179	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catagtgggcgaaagtacggTtaccattaaagtcttccagc	10	9	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:27697179T>A	ENST00000270879.4	-	7	571	c.566A>T	c.(565-567)aAc>aTc	p.N189I	FCN3_ENST00000354982.2_Missense_Mutation_p.N178I	NM_003665.2	NP_003656.2	O75636	FCN3_HUMAN	ficolin (collagen/fibrinogen domain containing) 3	189	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	7		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GAAAGTACGGTTACCATTAAA	0.582																																					p.N189I		Atlas-SNP	.											.	FCN3	30	.	0			c.A566T						.						153	157	155					1																	27697179		2203	4300	6503	SO:0001583	missense	8547	exon7			GTACGGTTACCAT	D88587	CCDS300.1, CCDS301.1	1p36.11	2014-09-17	2013-09-12		ENSG00000142748	ENSG00000142748		"Fibrinogen C domain containing"	3625	protein-coding gene	gene with protein product	"Hakata antigen"	604973	"ficolin (collagen/fibrinogen domain-containing) 3 (Hakata antigen)"			9694814, 10330454	Standard	NM_003665		Approved	FCNH, HAKA1	uc001boa.3	O75636	OTTHUMG00000005722	ENST00000270879.4:c.566A>T	chr1.hg19:g.27697179T>A	ENSP00000270879:p.Asn189Ile	168.0	0.0		106.0	48.0	NM_003665	Q6IBJ5|Q8WW86	Missense_Mutation	SNP	ENST00000270879.4	hg19	CCDS300.1	.	.	.	.	.	.	.	.	.	.	T	15.68	2.903872	0.52333	.	.	ENSG00000142748	ENST00000270879;ENST00000354982;ENST00000498393	T;T	0.23552	1.9;1.9	4.62	-4.0	0.04057	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.938058	0.08880	N	0.880214	T	0.18964	0.0455	L	0.41961	1.31	0.09310	N	1	B;B	0.21606	0.015;0.058	B;B	0.26202	0.045;0.067	T	0.36792	-0.9733	10	0.51188	T	0.08	.	5.4862	0.16751	0.0:0.3113:0.2594:0.4293	.	178;189	Q6UXM4;O75636	.;FCN3_HUMAN	I	189;178;67	ENSP00000270879:N189I;ENSP00000347077:N178I	ENSP00000270879:N189I	N	-	2	0	FCN3	27569766	0.000000	0.05858	0.000000	0.03702	0.823000	0.46562	-0.277000	0.08502	-0.855000	0.04125	0.456000	0.33151	AAC	.	.		0.582	FCN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000015667.1			A	27697179	T	A	27697179	3	1	23	1	0	0	0	0	1	0	0	0	5801	1725	60	4	341	4	FCN3	1	27697179	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1087798	27697179	221553442	30	2096										
AHDC1	27245	hgsc.bcm.edu	37	chr1	27876444	27876444	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcacagcgtctacctcccccCggccccgtttgcgtgggtgc	11	18	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:27876444C>T	ENST00000247087.5	-	5	2779	c.2183G>A	c.(2182-2184)cGg>cAg	p.R728Q	AHDC1_ENST00000374011.2_Missense_Mutation_p.R728Q			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	728	Gly-rich.						DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		TACCTCCCCCCGGCCCCGTTT	0.647																																					p.R728Q		Atlas-SNP	.											.	AHDC1	98	.	0			c.G2183A						.						33	31	32					1																	27876444		2203	4300	6503	SO:0001583	missense	27245	exon6			TCCCCCCGGCCCC	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.2183G>A	chr1.hg19:g.27876444C>T	ENSP00000247087:p.Arg728Gln	250.0	0.0		174.0	65.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	hg19	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.342280	0.81911	.	.	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.52983	0.64;0.64	5.38	5.38	0.77491	.	0.244715	0.27846	U	0.017619	T	0.52773	0.1755	N	0.24115	0.695	0.37859	D	0.929645	D	0.71674	0.998	P	0.59012	0.85	T	0.60870	-0.7177	10	0.66056	D	0.02	-9.3255	17.8971	0.88892	0.0:1.0:0.0:0.0	.	728	Q5TGY3	AHDC1_HUMAN	Q	728	ENSP00000247087:R728Q;ENSP00000363123:R728Q	ENSP00000247087:R728Q	R	-	2	0	AHDC1	27749031	0.987000	0.35691	1.000000	0.80357	0.988000	0.76386	3.961000	0.56759	2.512000	0.84698	0.555000	0.69702	CGG	.	.		0.647	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			T	27876444	C	T	27876444	3	4	23	1	0	0	0	0	1	0	0	0	412	652	23	1	2632	1	AHDC1	1	27876444	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	179265	27876444	221374177	31	2097										
SESN2	83667	hgsc.bcm.edu	37	chr1	28598852	28598852	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccacatggccgagtttctgCagactggtggtgaccctgag	13	12	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:28598852C>A	ENST00000253063.3	+	4	733	c.412C>A	c.(412-414)Cag>Aag	p.Q138K		NM_031459.4	NP_113647.1	P58004	SESN2_HUMAN	sestrin 2	138					autophagy (GO:0006914)|fatty acid beta-oxidation (GO:0006635)|glucose import (GO:0046323)|mitochondrial DNA metabolic process (GO:0032042)|protein kinase B signaling (GO:0043491)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of response to reactive oxygen species (GO:1901031)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	27		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)		CGAGTTTCTGCAGACTGGTGG	0.622																																					p.Q138K		Atlas-SNP	.											.	SESN2	51	.	0			c.C412A						.						67	71	69					1																	28598852		2203	4300	6503	SO:0001583	missense	83667	exon4			TTTCTGCAGACTG	AY123223	CCDS321.1	1p35.2	2008-02-05			ENSG00000130766	ENSG00000130766			20746	protein-coding gene	gene with protein product		607767				12607115, 12203114	Standard	NM_031459		Approved	SES2, DKFZp761M0212, HI95, SEST2	uc001bps.3	P58004	OTTHUMG00000003532	ENST00000253063.3:c.412C>A	chr1.hg19:g.28598852C>A	ENSP00000253063:p.Gln138Lys	73.0	0.0		83.0	33.0	NM_031459	Q5T7D0|Q96SI5	Missense_Mutation	SNP	ENST00000253063.3	hg19	CCDS321.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530154	0.27387	.	.	ENSG00000130766	ENST00000253063	T	0.21932	1.98	5.46	5.46	0.80206	.	0.277061	0.36167	N	0.002744	T	0.21267	0.0512	L	0.37630	1.12	0.58432	D	0.999992	B	0.29481	0.245	B	0.37550	0.253	T	0.02208	-1.1195	10	0.06099	T	0.92	-32.1059	18.9052	0.92458	0.0:1.0:0.0:0.0	.	138	P58004	SESN2_HUMAN	K	138	ENSP00000253063:Q138K	ENSP00000253063:Q138K	Q	+	1	0	SESN2	28471439	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	5.723000	0.68492	2.568000	0.86640	0.591000	0.81541	CAG	.	.		0.622	SESN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009840.1			A	28598852	C	A	28598852	3	1	23	1	0	0	0	0	1	0	0	0	14140	711	25	3	426	3	SESN2	1	28598852	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	722408	28598852	220651769	32	2098										
RAB42	115273	hgsc.bcm.edu	37	chr1	28920546	28920547	+	Frame_Shift_Ins	INS	-	-	G													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catcaagctagaagagggctINSgggggggtgtccggctcatc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:28920546_28920547insG	ENST00000373826.3	+	2	541_542	c.235_236insG	c.(235-237)tggfs	p.W79fs	TAF12_ENST00000471683.1_Intron|RAB42_ENST00000465518.1_3'UTR	NM_152304.1	NP_689517.1	Q8N4Z0	RAB42_HUMAN	RAB42, member RAS oncogene family	79					small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00618)|all_lung(284;0.00909)|Breast(348;0.0249)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0577)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00298)|KIRC - Kidney renal clear cell carcinoma(1967;0.00948)|BRCA - Breast invasive adenocarcinoma(304;0.0213)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAGAGGGCTGGGGGGGTGTC	0.584																																					p.W192fs		Atlas-Indel,Pindel	.											.,1	RAB42	10	.	0			c.574_575insG						.																																			SO:0001589	frameshift_variant	115273	exon2			.	BC033175	CCDS325.1	1p35.3	2014-02-12	2006-04-28		ENSG00000188060	ENSG00000188060		"RAB, member RAS oncogene"	28702	protein-coding gene	gene with protein product			"RAB42, member RAS homolog family"				Standard	NM_152304		Approved	MGC45806	uc001bqv.3	Q8N4Z0	OTTHUMG00000003656	ENST00000373826.3:c.242dupG	chr1.hg19:g.28920553_28920553dupG	ENSP00000362932:p.Trp79fs	137.0	0.0		92.0	31.0	NM_001193532	B2R5G2	Frame_Shift_Ins	INS	ENST00000373826.3	hg19	CCDS325.1																																																																																			.	.		0.584	RAB42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010371.1	NM_152304		G	28920547	-	G	28920546	7	5	23	1	0	1	1	0	0	0	0	0	12959	1580	55	0	237	0	RAB42	1	28920546	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	321694	28920546	220330075	33	2099										
GMEB1	10691	hgsc.bcm.edu	37	chr1	29010172	29010172	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgggggatgtggttgtggtAcctactgaaggaaatgaagg	18	3	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:29010172A>G	ENST00000294409.2	+	2	138	c.48A>G	c.(46-48)gtA>gtG	p.V16V	GMEB1_ENST00000480454.1_3'UTR|GMEB1_ENST00000361872.4_Silent_p.V16V|GMEB1_ENST00000373816.1_Silent_p.V16V	NM_006582.3	NP_006573.2	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding protein 1	16					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)	11		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		TGGTTGTGGTACCTACTGAAG	0.478																																					p.V16V		Atlas-SNP	.											.	GMEB1	28	.	0			c.A48G						.						193	172	179					1																	29010172		2203	4300	6503	SO:0001819	synonymous_variant	10691	exon2			TGTGGTACCTACT	AF099013	CCDS327.1, CCDS328.1	1p35	2008-02-05			ENSG00000162419	ENSG00000162419			4370	protein-coding gene	gene with protein product		604409				10386584, 10523663	Standard	NM_006582		Approved	P96PIF, PIF96	uc001bra.3	Q9Y692	OTTHUMG00000003647	ENST00000294409.2:c.48A>G	chr1.hg19:g.29010172A>G		154.0	0.0		131.0	38.0	NM_006582	B1AT48|Q9NWH1|Q9UKD0	Silent	SNP	ENST00000294409.2	hg19	CCDS327.1																																																																																			.	.		0.478	GMEB1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000010333.1	NM_006582		G	29010172	A	G	29010172	2	3	23	1	0	0	0	0	0	0	0	1	6495	378	14	2		2	GMEB1	1	29010172	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	89626	29010172	220240449	34	2100										
IQCC	55721	hgsc.bcm.edu	37	chr1	32673443	32673443	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atcatctgggatggtaccttGggggggccagagcatagtgt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:32673443delG	ENST00000291358.6	+	5	1182	c.1161delG	c.(1159-1161)ttgfs	p.L387fs	IQCC_ENST00000537469.1_Frame_Shift_Del_p.L467fs|RP4-622L5.7_ENST00000421616.1_RNA|RP4-622L5.7_ENST00000373604.4_RNA|DCDC2B_ENST00000409358.1_5'Flank	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	387										endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ATGGTACCTTGGGGGGGCCAG	0.552																																					p.L467fs		Pindel	.											.,1	IQCC	46	.	0			c.1400delT						.						82	89	87					1																	32673443		2203	4300	6503	SO:0001589	frameshift_variant	55721	exon5			.	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.1161delG	chr1.hg19:g.32673443delG	ENSP00000291358:p.Leu387fs	361.0	0.0		314.0	83.0	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Frame_Shift_Del	DEL	ENST00000291358.6	hg19	CCDS355.1																																																																																			.	.		0.552	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134		-	32673443	G	-	32673443	7	5	23	1	0	1	0	1	0	0	0	0	7813	1339	47	0	1419	0	IQCC	1	32673443	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	3663271	32673443	216577178	35	2101										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34083155	34083155	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacatcattcaccaagtagcGctcgccagtcttcaccccgt	6	17	4	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:34083155G>A	ENST00000373380.1	-	17	2729	c.2509C>T	c.(2509-2511)Cgc>Tgc	p.R837C	CSMD2_ENST00000373388.2_Missense_Mutation_p.R63C|CSMD2_ENST00000373377.1_Missense_Mutation_p.R63C|CSMD2_ENST00000373381.4_Missense_Mutation_p.R1964C			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1924	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				ACCAAGTAGCGCTCGCCAGTC	0.567																																					p.R1924C		Atlas-SNP	.											.	CSMD2	946	.	0			c.C5770T						.						112	86	95					1																	34083155		2203	4300	6503	SO:0001583	missense	114784	exon38			AGTAGCGCTCGCC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2509C>T	chr1.hg19:g.34083155G>A	ENSP00000362478:p.Arg837Cys	97.0	0.0		81.0	46.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	G	23.8	4.457652	0.84317	.	.	ENSG00000121904	ENST00000373381;ENST00000373380;ENST00000373377;ENST00000373388	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	5.67	5.67	0.87782	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	M	0.83603	2.65	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.57470	-0.7806	10	0.66056	D	0.02	.	13.3258	0.60459	0.0:0.0:0.842:0.158	.	837;1924;1964	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	C	1964;837;63;63	ENSP00000362479:R1964C;ENSP00000362478:R837C;ENSP00000362475:R63C;ENSP00000362486:R63C	ENSP00000241312:R1924C	R	-	1	0	CSMD2	33855742	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	2.739000	0.47409	2.676000	0.91093	0.655000	0.94253	CGC	.	.		0.567	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		A	34083155	G	A	34083155	3	1	23	1	0	0	0	0	1	0	0	0	3947	1087	38	1	4821	1	CSMD2	1	34083155	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1409712	34083155	215167466	36	2102										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34090759	34090759	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccggagttgcattcgaagcGgacgatggcccccaccgaga	14	13	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:34090759G>A	ENST00000373380.1	-	13	2231	c.2011C>T	c.(2011-2013)Cgc>Tgc	p.R671C	CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373377.1_5'UTR|CSMD2_ENST00000373381.4_Missense_Mutation_p.R1798C			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1758	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CATTCGAAGCGGACGATGGCC	0.652																																					p.R1758C		Atlas-SNP	.											.	CSMD2	946	.	0			c.C5272T						.						76	67	70					1																	34090759		2203	4300	6503	SO:0001583	missense	114784	exon34			CGAAGCGGACGAT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2011C>T	chr1.hg19:g.34090759G>A	ENSP00000362478:p.Arg671Cys	200.0	0.0		168.0	70.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	G	25.8	4.674746	0.88445	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.66815	-0.23;-0.23	6.17	6.17	0.99709	Complement control module (2);Sushi/SCR/CCP (3);	0.117450	0.64402	D	0.000014	D	0.86104	0.5853	M	0.92367	3.3	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	P;D;D	0.70016	0.828;0.932;0.967	D	0.85728	0.1329	10	0.38643	T	0.18	.	19.4432	0.94831	0.0:0.0:1.0:0.0	.	671;1758;1798	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	C	1798;671	ENSP00000362479:R1798C;ENSP00000362478:R671C	ENSP00000241312:R1758C	R	-	1	0	CSMD2	33863346	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	4.566000	0.60843	2.941000	0.99782	0.655000	0.94253	CGC	.	.		0.652	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		A	34090759	G	A	34090759	3	1	23	1	0	0	0	0	1	0	0	0	3947	1116	39	1	5335	1	CSMD2	1	34090759	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	7604	34090759	215159862	37	2103										
GJB4	127534	hgsc.bcm.edu	37	chr1	35227148	35227148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtcatgcacgtggcctaccGcgaggaacgcgagcgcaagc	15	13	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:35227148G>A	ENST00000339480.1	+	2	663	c.293G>A	c.(292-294)cGc>cAc	p.R98H	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	98					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				GTGGCCTACCGCGAGGAACGC	0.637																																					p.R98H		Atlas-SNP	.											GJB4,NS,haematopoietic_neoplasm,0,1	GJB4	51	.	0			c.G293A						.						86	65	72					1																	35227148		2203	4300	6503	SO:0001583	missense	127534	exon2			CCTACCGCGAGGA		CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"Ion channels / Gap junction proteins (connexins)"	4286	protein-coding gene	gene with protein product	"connexin 30.3"	605425	"gap junction protein, beta 4 (connexin 30.3)", "gap junction protein, beta 4"				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.293G>A	chr1.hg19:g.35227148G>A	ENSP00000345868:p.Arg98His	90.0	1.0		75.0	28.0	NM_153212	B3KQ82	Missense_Mutation	SNP	ENST00000339480.1	hg19	CCDS383.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.423700	0.83559	.	.	ENSG00000189433	ENST00000339480	D	0.99129	-5.46	5.73	4.82	0.62117	Connexin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98902	0.9628	M	0.77103	2.36	0.42241	D	0.991933	D	0.76494	0.999	P	0.57204	0.815	D	0.99100	1.0843	10	0.52906	T	0.07	.	14.3259	0.66521	0.0717:0.0:0.9283:0.0	.	98	Q9NTQ9	CXB4_HUMAN	H	98	ENSP00000345868:R98H	ENSP00000345868:R98H	R	+	2	0	GJB4	34999735	0.868000	0.29978	0.878000	0.34440	0.479000	0.33129	4.164000	0.58190	1.445000	0.47624	0.655000	0.94253	CGC	.	.		0.637	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212		A	35227148	G	A	35227148	3	1	23	1	0	0	0	0	1	0	0	0	6418	1087	38	1	295	1	GJB4	1	35227148	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1136389	35227148	214023473	38	2104										
GJA4	2701	hgsc.bcm.edu	37	chr1	35260244	35260244	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctcggtggcagaagatggtCgcctgcgcatccgcggagca	15	12	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:35260244C>T	ENST00000342280.4	+	2	518	c.430C>T	c.(430-432)Cgc>Tgc	p.R144C		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	144					blood vessel development (GO:0001568)|calcium ion transport (GO:0006816)|cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|endothelium development (GO:0003158)|response to pain (GO:0048265)|transport (GO:0006810)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(4)|stomach(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				AGAAGATGGTCGCCTGCGCAT	0.657																																					p.R144C		Atlas-SNP	.											.	GJA4	25	.	0			c.C430T						.						33	36	35					1																	35260244		2203	4300	6503	SO:0001583	missense	2701	exon2			GATGGTCGCCTGC	M96789	CCDS30669.1	1p35.1	2008-02-05	2007-01-16		ENSG00000187513	ENSG00000187513		"Ion channels / Gap junction proteins (connexins)"	4278	protein-coding gene	gene with protein product	"connexin 37"	121012	"gap junction protein, alpha 4, 37kD (connexin 37)", "gap junction protein, alpha 4, 37kDa (connexin 37)"			9843209, 7680674	Standard	XM_005270750		Approved	CX37	uc001bya.3	P35212	OTTHUMG00000004050	ENST00000342280.4:c.430C>T	chr1.hg19:g.35260244C>T	ENSP00000343676:p.Arg144Cys	43.0	0.0		45.0	13.0	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Missense_Mutation	SNP	ENST00000342280.4	hg19	CCDS30669.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.191990	0.38707	.	.	ENSG00000187513	ENST00000342280;ENST00000450137;ENST00000543143	D;D	0.97870	-4.56;-4.58	5.48	4.57	0.56435	.	0.754074	0.12461	N	0.466846	D	0.96975	0.9012	L	0.50333	1.59	0.52501	D	0.999951	D;D	0.65815	0.995;0.994	P;P	0.52343	0.696;0.451	D	0.95143	0.8265	10	0.87932	D	0	.	9.2276	0.37416	0.1443:0.7827:0.0:0.073	.	144;144	Q5JW71;P35212	.;CXA4_HUMAN	C	144	ENSP00000343676:R144C;ENSP00000409186:R144C	ENSP00000343676:R144C	R	+	1	0	GJA4	35032831	0.033000	0.19621	0.064000	0.19789	0.072000	0.16883	2.660000	0.46749	1.295000	0.44724	-0.140000	0.14226	CGC	.	.		0.657	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060		T	35260244	C	T	35260244	3	4	23	1	0	0	0	0	1	0	0	0	6411	884	31	1	432	1	GJA4	1	35260244	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	33096	35260244	213990377	39	2105										
EIF2C3	192669	hgsc.bcm.edu	37	chr1	36521336	36521336	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agataccttacgcacaatgtActtcgcttaaatagtccaag	6	10	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:36521336A>G	ENST00000373191.4	+	19	2922	c.2573A>G	c.(2572-2574)tAc>tGc	p.Y858C	AGO3_ENST00000246314.6_Missense_Mutation_p.Y624C	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	858					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										CGCACAATGTACTTCGCTTAA	0.423																																					p.Y858C		Atlas-SNP	.											.	.	.	.	0			c.A2573G						.						149	123	132					1																	36521336		2203	4300	6503	SO:0001583	missense	192669	exon19			CAATGTACTTCGC	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"Argonaute/PIWI family"	18421	protein-coding gene	gene with protein product	"argonaute 3"	607355	"eukaryotic translation initiation factor 2C, 3"	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.2573A>G	chr1.hg19:g.36521336A>G	ENSP00000362287:p.Tyr858Cys	74.0	0.0		100.0	6.0	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	hg19	CCDS399.1	.	.	.	.	.	.	.	.	.	.	A	19.66	3.869021	0.72065	.	.	ENSG00000126070	ENST00000373191;ENST00000246314	T;T	0.15718	2.41;2.4	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.41373	0.1156	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.29792	-1.0000	10	0.87932	D	0	-58.0065	15.4359	0.75146	1.0:0.0:0.0:0.0	.	858	Q9H9G7	AGO3_HUMAN	C	858;624	ENSP00000362287:Y858C;ENSP00000246314:Y624C	ENSP00000246314:Y624C	Y	+	2	0	EIF2C3	36293923	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.287000	0.95975	2.194000	0.70268	0.533000	0.62120	TAC	.	.		0.423	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852		G	36521336	A	G	36521336	3	3	23	1	0	0	0	0	1	0	0	0	5009	391	14	2	2647	2	EIF2C3	1	36521336	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1261092	36521336	212729285	40	2106										
OSCP1	127700	hgsc.bcm.edu	37	chr1	36915910	36915910	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcccgcagccgttggtcgaGgatgtaaagcatctccccgc	13	14	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:36915910G>T	ENST00000356637.5	-	1	124	c.61C>A	c.(61-63)Ctc>Atc	p.L21I	OSCP1_ENST00000235532.5_Missense_Mutation_p.L21I|OSCP1_ENST00000354267.3_Missense_Mutation_p.L21I|OSCP1_ENST00000315643.9_Missense_Mutation_p.L21I			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	21					transport (GO:0006810)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						CGTTGGTCGAGGATGTAAAGC	0.667											OREG0013369	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L21I		Atlas-SNP	.											.	OSCP1	48	.	0			c.C61A						.						45	46	46					1																	36915910		2203	4300	6503	SO:0001583	missense	127700	exon1			GGTCGAGGATGTA		CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"oxidored nitro domain containing protein"	608854	"chromosome 1 open reading frame 102"	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.61C>A	chr1.hg19:g.36915910G>T	ENSP00000349052:p.Leu21Ile	296.0	0.0	866	327.0	105.0	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Missense_Mutation	SNP	ENST00000356637.5	hg19		.	.	.	.	.	.	.	.	.	.	G	22.1	4.238260	0.79800	.	.	ENSG00000116885	ENST00000235532;ENST00000356637;ENST00000315643;ENST00000354267	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	4.56	3.64	0.41730	.	0.000000	0.64402	D	0.000003	T	0.45074	0.1324	L	0.45744	1.44	0.52099	D	0.999946	P;P;P	0.51147	0.932;0.706;0.942	P;P;P	0.55824	0.523;0.589;0.785	T	0.38112	-0.9676	10	0.54805	T	0.06	.	11.8718	0.52525	0.086:0.0:0.914:0.0	.	21;21;21	Q8WVF1-4;Q8WVF1-3;Q8WVF1	.;.;OSCP1_HUMAN	I	21	ENSP00000235532:L21I;ENSP00000349052:L21I;ENSP00000314541:L21I;ENSP00000346216:L21I	ENSP00000235532:L21I	L	-	1	0	OSCP1	36688497	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.097000	0.50251	1.033000	0.39918	0.655000	0.94253	CTC	.	.		0.667	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047		T	36915910	G	T	36915910	3	4	23	1	0	0	0	0	1	0	0	0	11295	1000	35	3	1278	3	OSCP1	1	36915910	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	394574	36915910	212334711	41	2107										
RHBDL2	54933	hgsc.bcm.edu	37	chr1	39352294	39352294	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgctttatcaaagcagctaAacaccgtgtagccaatggac	9	10	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:39352294A>G	ENST00000289248.2	-	8	1802	c.794T>C	c.(793-795)tTt>tCt	p.F265S	RHBDL2_ENST00000372990.1_Missense_Mutation_p.F265S|RP5-864K19.4_ENST00000433671.2_RNA|RHBDL2_ENST00000538156.1_Missense_Mutation_p.F332S|RHBDL2_ENST00000372985.3_Missense_Mutation_p.F345S			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			AAAGCAGCTAAACACCGTGTA	0.408																																					p.F265S		Atlas-SNP	.											.	RHBDL2	28	.	0			c.T794C						.						124	118	120					1																	39352294		2203	4300	6503	SO:0001583	missense	54933	exon8			CAGCTAAACACCG	AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315			16083	protein-coding gene	gene with protein product		608962	"rhomboid (veinlet, Drosophila)-like 2"				Standard	NM_017821		Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.794T>C	chr1.hg19:g.39352294A>G	ENSP00000289248:p.Phe265Ser	108.0	0.0		99.0	37.0	NM_017821	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	Missense_Mutation	SNP	ENST00000289248.2	hg19	CCDS30680.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.823707	0.90873	.	.	ENSG00000158315	ENST00000372990;ENST00000289248;ENST00000538156;ENST00000372985	T;T;T;T	0.13196	2.61;2.61;2.61;2.61	6.03	6.03	0.97812	Peptidase S54, rhomboid domain (1);	0.000000	0.85682	D	0.000000	T	0.39759	0.1090	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72338	0.977;0.977	T	0.24977	-1.0145	10	0.87932	D	0	-20.5891	15.5407	0.76043	1.0:0.0:0.0:0.0	.	345;265	B7Z1Y9;Q9NX52	.;RHBL2_HUMAN	S	265;265;332;345	ENSP00000362081:F265S;ENSP00000289248:F265S;ENSP00000439227:F332S;ENSP00000362076:F345S	ENSP00000289248:F265S	F	-	2	0	RHBDL2	39124881	1.000000	0.71417	0.995000	0.50966	0.950000	0.60333	7.907000	0.87430	2.308000	0.77769	0.533000	0.62120	TTT	.	.		0.408	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001216.1	NM_017821		G	39352294	A	G	39352294	3	3	23	1	0	0	0	0	1	0	0	0	13337	14	1	2	121	2	RHBDL2	1	39352294	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2436384	39352294	209898327	42	2108										
MACF1	23499	hgsc.bcm.edu	37	chr1	39827077	39827077	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaaagagcagcttggaggccAcccgtgagatggtgacccga	14	10	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:39827077A>G	ENST00000372915.3	+	48	12601	c.12514A>G	c.(12514-12516)Acc>Gcc	p.T4172A	MACF1_ENST00000545844.1_Missense_Mutation_p.T2105A|MACF1_ENST00000564288.1_Missense_Mutation_p.T4167A|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000289893.4_Missense_Mutation_p.T2607A|MACF1_ENST00000539005.1_Missense_Mutation_p.T2105A|MACF1_ENST00000567887.1_Missense_Mutation_p.T4204A|MACF1_ENST00000361689.2_Missense_Mutation_p.T2105A|MACF1_ENST00000317713.7_Missense_Mutation_p.T2105A			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4172					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CTTGGAGGCCACCCGTGAGAT	0.532																																					p.T2105A		Atlas-SNP	.											.	MACF1	909	.	0			c.A6313G						.						76	73	74					1																	39827077		2203	4300	6503	SO:0001583	missense	23499	exon45			GAGGCCACCCGTG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.12514A>G	chr1.hg19:g.39827077A>G	ENSP00000362006:p.Thr4172Ala	249.0	0.0		242.0	68.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.5|28.5	4.923491|4.923491	0.92319|0.92319	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	.|T;T;T;T;T;T	.|0.34072	.|1.38;1.43;1.38;1.38;1.38;1.38	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	.|0.000000	.|0.64402	.|D	.|0.000004	T|T	0.57784|0.57784	0.2077|0.2077	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	.|D;B;D;P	.|0.89917	.|1.0;0.198;0.997;0.841	.|D;B;D;P	.|0.85130	.|0.997;0.155;0.969;0.62	T|T	0.52997|0.52997	-0.8500|-0.8500	5|10	.|0.32370	.|T	.|0.25	.|.	16.5885|16.5885	0.84745|0.84745	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|4172;2105;2105;2070	.|Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3	.|MACF1_HUMAN;.;.;.	R|A	1238|2105;4172;2105;2105;2105;2607	.|ENSP00000439537:T2105A;ENSP00000362006:T4172A;ENSP00000354573:T2105A;ENSP00000313438:T2105A;ENSP00000444364:T2105A;ENSP00000289893:T2607A	.|ENSP00000289893:T2607A	H|T	+|+	2|1	0|0	MACF1|MACF1	39599664|39599664	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	8.962000|8.962000	0.93254|0.93254	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	CAC|ACC	.	.		0.532	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39827077	A	G	39827077	3	3	23	1	0	0	0	0	1	0	0	0	9153	159	6	2	12638	2	MACF1	1	39827077	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	474783	39827077	209423544	43	2109										
COL9A2	1298	hgsc.bcm.edu	37	chr1	40771858	40771858	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcccaggctggcctggcacaCcctgcagaaagaagttgaag	12	12	0	3	rs199502479		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:40771858C>G	ENST00000372748.3	-	20	1106	c.1010G>C	c.(1009-1011)gGt>gCt	p.G337A	COL9A2_ENST00000466267.1_5'Flank	NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	337	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			GCCTGGCACACCCTGCAGAAA	0.587																																					p.G337A		Atlas-SNP	.											.	COL9A2	63	.	0			c.G1010C						.						62	57	58					1																	40771858		2203	4300	6503	SO:0001630	splice_region_variant	1298	exon20			GGCACACCCTGCA	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.1009-1G>C	chr1.hg19:g.40771858C>G		60.0	0.0		68.0	34.0	NM_001852	B2RMP9	Missense_Mutation	SNP	ENST00000372748.3	hg19	CCDS450.1	.	.	.	.	.	.	.	.	.	.	.	19.16	3.774406	0.70107	.	.	ENSG00000049089	ENST00000372748	D	0.99329	-5.75	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.99515	0.9827	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98249	1.0492	10	0.87932	D	0	.	14.4487	0.67370	0.0:1.0:0.0:0.0	.	337	Q14055	CO9A2_HUMAN	A	337	ENSP00000361834:G337A	ENSP00000361834:G337A	G	-	2	0	COL9A2	40544445	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.269000	0.72558	2.479000	0.83701	0.655000	0.94253	GGT	.	C|0.999;G|0.001		0.587	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852	Missense_Mutation	G	40771858	C	G	40771858	5	3	23	1	0	0	0	0	0	0	1	0	3710	521	18	4	1111	4	COL9A2	1	40771858	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	944781	40771858	208478763	44	2110										
TMEM125	128218	hgsc.bcm.edu	37	chr1	43738760	43738760	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggtgctgctcagtggcctcGtgctgctggtcaccggcctg	15	13	2	0	rs143350378	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:43738760G>C	ENST00000432792.2	+	4	937	c.367G>C	c.(367-369)Gtg>Ctg	p.V123L	TMEM125_ENST00000439858.1_Missense_Mutation_p.V123L			Q96AQ2	TM125_HUMAN	transmembrane protein 125	123						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(1)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CAGTGGCCTCGTGCTGCTGGT	0.721																																					p.V123L		Atlas-SNP	.											.	TMEM125	18	.	0			c.G367C						.						22	24	23					1																	43738760		2198	4293	6491	SO:0001583	missense	128218	exon4			GGCCTCGTGCTGC	BC016858	CCDS480.1	1p34.2	2006-02-16			ENSG00000179178	ENSG00000179178			28275	protein-coding gene	gene with protein product							Standard	NM_144626		Approved	MGC17299	uc021oml.1	Q96AQ2	OTTHUMG00000007288	ENST00000432792.2:c.367G>C	chr1.hg19:g.43738760G>C	ENSP00000429275:p.Val123Leu	81.0	0.0		81.0	32.0	NM_144626	D3DPX1	Missense_Mutation	SNP	ENST00000432792.2	hg19	CCDS480.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.366544	0.61513	.	.	ENSG00000179178	ENST00000439858;ENST00000432792	T;T	0.43294	0.95;0.95	5.24	5.24	0.73138	.	0.350030	0.29059	N	0.013275	T	0.25791	0.0628	N	0.17082	0.46	0.30566	N	0.764038	B	0.29253	0.239	B	0.21360	0.034	T	0.17592	-1.0364	10	0.35671	T	0.21	.	12.2066	0.54355	0.0783:0.0:0.9217:0.0	.	123	Q96AQ2	TM125_HUMAN	L	123	ENSP00000429775:V123L;ENSP00000429275:V123L	ENSP00000429275:V123L	V	+	1	0	TMEM125	43511347	0.980000	0.34600	0.929000	0.37066	0.676000	0.39594	2.566000	0.45948	2.446000	0.82766	0.455000	0.32223	GTG	.	G|0.997;A|0.003		0.721	TMEM125-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019032.2	NM_144626		C	43738760	G	C	43738760	3	2	23	1	0	0	0	0	1	0	0	0	16052	1145	40	4	369	4	TMEM125	1	43738760	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2966902	43738760	205511861	45	2111										
TIE1	7075	hgsc.bcm.edu	37	chr1	43772515	43772515	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cattcatgtcccccaggatcCtacttctacaccctggactg	6	16	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:43772515C>A	ENST00000372476.3	+	4	568	c.489C>A	c.(487-489)tcC>tcA	p.S163S	TIE1_ENST00000538015.1_Silent_p.S163S|TIE1_ENST00000441333.2_Silent_p.S163S|TIE1_ENST00000433781.2_5'Flank	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	163					angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CCCCAGGATCCTACTTCTACA	0.577																																					p.S163S		Atlas-SNP	.											.	TIE1	132	.	0			c.C489A						.						94	90	91					1																	43772515		2203	4300	6503	SO:0001819	synonymous_variant	7075	exon4			AGGATCCTACTTC	BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11809	protein-coding gene	gene with protein product		600222	"tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.489C>A	chr1.hg19:g.43772515C>A		57.0	0.0		35.0	16.0	NM_005424	B5A949|B5A950	Silent	SNP	ENST00000372476.3	hg19	CCDS482.1																																																																																			.	.		0.577	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424		A	43772515	C	A	43772515	2	1	23	1	0	0	0	0	0	0	0	1	15908	668	24	3		3	TIE1	1	43772515	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	33755	43772515	205478106	46	2112										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43895374	43895374	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccttaccccaaccattcagCatagagaccgaggacctaag	7	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:43895374C>T	ENST00000562955.1	+	28	3996	c.3996C>T	c.(3994-3996)agC>agT	p.S1332S	SZT2_ENST00000372442.1_Splice_Site_p.S490S	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1389					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						AACCATTCAGCATAGAGACCG	0.537																																					p.S1332S		Atlas-SNP	.											.	SZT2	383	.	0			c.C3996T						.						88	86	87					1																	43895374		2203	4300	6503	SO:0001630	splice_region_variant	23334	exon28			ATTCAGCATAGAG	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.3996-1C>T	chr1.hg19:g.43895374C>T		81.0	0.0		91.0	36.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	hg19	CCDS30694.2																																																																																			.	.		0.537	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	Silent	T	43895374	C	T	43895374	5	4	23	1	0	0	0	0	0	0	1	0	8187	724	25	3	1516	3	KIAA0467	1	43895374	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	122859	43895374	205355247	47	2113										
TOE1	114034	hgsc.bcm.edu	37	chr1	45806886	45806886	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	taatttcgtggctgtggacaCggtgagagttgggaaacaag	15	5	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:45806886C>T	ENST00000372090.5	+	2	777	c.194C>T	c.(193-195)aCg>aTg	p.T65M	TOE1_ENST00000539779.1_Intron|MUTYH_ENST00000529984.1_5'Flank|MUTYH_ENST00000528332.2_5'Flank|MUTYH_ENST00000528013.2_5'Flank|MUTYH_ENST00000355498.2_5'Flank|MUTYH_ENST00000354383.6_5'Flank|MUTYH_ENST00000372098.3_5'Flank|MUTYH_ENST00000488731.2_5'Flank|MUTYH_ENST00000450313.1_5'Flank|MUTYH_ENST00000372100.5_5'Flank|TESK2_ENST00000486676.1_5'Flank|MUTYH_ENST00000448481.1_5'Flank|TOE1_ENST00000495703.1_3'UTR|MUTYH_ENST00000372110.3_5'Flank|MUTYH_ENST00000372104.1_5'Flank|MUTYH_ENST00000456914.2_5'Flank|MUTYH_ENST00000531105.1_5'Flank|MUTYH_ENST00000372115.3_5'Flank	NM_025077.3	NP_079353.3	Q96GM8	TOE1_HUMAN	target of EGR1, member 1 (nuclear)	65						nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	11	Acute lymphoblastic leukemia(166;0.155)					GCTGTGGACACGGTGAGAGTT	0.547																																					p.T65M		Atlas-SNP	.											.	TOE1	27	.	0			c.C194T						.						114	102	106					1																	45806886		2203	4300	6503	SO:0001630	splice_region_variant	114034	exon2			TGGACACGGTGAG		CCDS521.1	1p33	2011-02-03			ENSG00000132773	ENSG00000132773			15954	protein-coding gene	gene with protein product		613931				12562764	Standard	NM_025077		Approved		uc009vxq.3	Q96GM8	OTTHUMG00000007678	ENST00000372090.5:c.195+1C>T	chr1.hg19:g.45806886C>T		113.0	0.0		118.0	8.0	NM_025077	B4DEM6|Q6IA35|Q8IWN5|Q9H846	Missense_Mutation	SNP	ENST00000372090.5	hg19	CCDS521.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.819469	0.90873	.	.	ENSG00000132773	ENST00000372090	T	0.25579	1.79	5.61	5.61	0.85477	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.52191	0.1719	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.951;0.995	T	0.46148	-0.9212	10	0.52906	T	0.07	-10.9192	20.0018	0.97417	0.0:1.0:0.0:0.0	.	71;65	B4DP23;Q96GM8	.;TOE1_HUMAN	M	65	ENSP00000361162:T65M	ENSP00000361162:T65M	T	+	2	0	TOE1	45579473	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.706000	0.74649	2.793000	0.96121	0.655000	0.94253	ACG	.	.		0.547	TOE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020517.1	NM_025077	Missense_Mutation	T	45806886	C	T	45806886	5	4	23	1	0	0	0	0	0	0	1	0	16364	550	19	1	200	1	TOE1	1	45806886	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1911512	45806886	203443735	48	2114										
MMACHC	25974	hgsc.bcm.edu	37	chr1	45974679	45974679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgctgtgacaccccaggagcGctactcagaagagcagaagg	13	11	1	4	rs202189863		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:45974679G>A	ENST00000401061.4	+	4	921	c.641G>A	c.(640-642)cGc>cAc	p.R214H		NM_015506.2	NP_056321.2	Q9Y4U1	MMAC_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblC type, with homocystinuria	214					cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8	Acute lymphoblastic leukemia(166;0.155)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CCCCAGGAGCGCTACTCAGAA	0.562																																					p.R214H		Atlas-SNP	.											.	MMACHC	22	.	0			c.G641A						.						102	110	107					1																	45974679		2020	4181	6201	SO:0001583	missense	25974	exon4			AGGAGCGCTACTC		CCDS41324.1	1p34.1	2011-05-12			ENSG00000132763	ENSG00000132763			24525	protein-coding gene	gene with protein product		609831				16311595	Standard	NM_015506		Approved	DKFZP564I122, cblC	uc009vxv.3	Q9Y4U1	OTTHUMG00000007742	ENST00000401061.4:c.641G>A	chr1.hg19:g.45974679G>A	ENSP00000383840:p.Arg214His	112.0	0.0		111.0	45.0	NM_015506	Q5T157|Q9BRQ7	Missense_Mutation	SNP	ENST00000401061.4	hg19	CCDS41324.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.040292	0.75732	.	.	ENSG00000132763	ENST00000401061	D	0.97455	-4.39	5.8	5.8	0.92144	.	0.506686	0.21686	N	0.070650	D	0.97932	0.9320	M	0.77820	2.39	0.25042	N	0.991199	D	0.89917	1.0	D	0.69654	0.965	D	0.94221	0.7467	10	0.72032	D	0.01	-19.6562	10.1719	0.42915	0.1479:0.0:0.8521:0.0	.	214	Q9Y4U1	MMAC_HUMAN	H	214	ENSP00000383840:R214H	ENSP00000383840:R214H	R	+	2	0	MMACHC	45747266	0.964000	0.33143	0.998000	0.56505	0.982000	0.71751	2.431000	0.44775	2.758000	0.94735	0.563000	0.77884	CGC	.	G|0.999;A|0.001		0.562	MMACHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020864.2	NM_015506		A	45974679	G	A	45974679	3	1	23	1	0	0	0	0	1	0	0	0	9650	1087	38	1	655	1	MMACHC	1	45974679	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	167793	45974679	203275942	49	2115										
SLC5A9	200010	hgsc.bcm.edu	37	chr1	48696305	48696305	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctggagccctcttcatccagAtggcattgggctggaacctg	12	12	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:48696305A>T	ENST00000438567.2	+	5	590	c.538A>T	c.(538-540)Atg>Ttg	p.M180L	RP5-1024N4.4_ENST00000606809.1_RNA|SLC5A9_ENST00000533824.1_Missense_Mutation_p.M201L|SLC5A9_ENST00000236495.5_Missense_Mutation_p.M205L|SLC5A9_ENST00000420136.2_Intron	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	180					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						CTTCATCCAGATGGCATTGGG	0.577																																					p.M205L		Atlas-SNP	.											.	SLC5A9	82	.	0			c.A613T						.						134	104	114					1																	48696305		2203	4300	6503	SO:0001583	missense	200010	exon6			ATCCAGATGGCAT	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"Solute carriers"	22146	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 9"				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.538A>T	chr1.hg19:g.48696305A>T	ENSP00000401730:p.Met180Leu	81.0	0.0		73.0	32.0	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	hg19	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	A	6.081	0.383290	0.11524	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	D;D;D	0.86432	-2.12;-2.12;-2.12	5.3	2.89	0.33648	.	0.547984	0.22109	N	0.064514	T	0.48187	0.1486	N	0.00104	-2.125	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.003;0.004;0.004	T	0.56938	-0.7896	10	0.02654	T	1	.	4.2483	0.10682	0.6841:0.0:0.1534:0.1625	.	201;180;205	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	L	201;180;205	ENSP00000431900:M201L;ENSP00000401730:M180L;ENSP00000236495:M205L	ENSP00000236495:M205L	M	+	1	0	SLC5A9	48468892	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.936000	0.40183	0.993000	0.38866	0.533000	0.62120	ATG	.	.		0.577	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		T	48696305	A	T	48696305	3	4	23	1	0	0	0	0	1	0	0	0	14687	333	12	4	635	4	SLC5A9	1	48696305	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2721626	48696305	200554316	50	2116										
CDKN2C	1031	hgsc.bcm.edu	37	chr1	51439649	51439649	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgaaagaccgaactggtttcGctgtcattcatgatgcggcc	11	10	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:51439649G>A	ENST00000262662.1	+	4	2248	c.214G>A	c.(214-216)Gct>Act	p.A72T	CDKN2C_ENST00000396148.1_Missense_Mutation_p.A72T|CDKN2C_ENST00000371761.3_Missense_Mutation_p.A72T			P42773	CDN2C_HUMAN	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	72			A -> P (in breast cancer; loss of CDK6 interaction). {ECO:0000269|PubMed:8840966, ECO:0000269|PubMed:9636670}.		cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|oligodendrocyte differentiation (GO:0048709)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)	p.0?(11)|p.?(1)		central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|thyroid(1)	23				GBM - Glioblastoma multiforme(3;3.61e-13)|all cancers(3;0.00151)		AACTGGTTTCGCTGTCATTCA	0.453			D		"glioma, MM"																																p.A72T	Melanoma(47;50 1155 4767 22863 47597)	Atlas-SNP	.		Rec	yes		1	1p32	1031	"cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)"		"O, L"	CDKN2C,NS,carcinoma,0,1	CDKN2C	24	.	12	Whole gene deletion(11)|Unknown(1)	central_nervous_system(6)|haematopoietic_and_lymphoid_tissue(5)|thyroid(1)	c.G214A						.						99	96	97					1																	51439649		2203	4300	6503	SO:0001583	missense	1031	exon3			GGTTTCGCTGTCA	BC000598	CCDS555.1	1p32.3	2013-01-10			ENSG00000123080	ENSG00000123080		"Ankyrin repeat domain containing"	1789	protein-coding gene	gene with protein product		603369				8001816, 9636670	Standard	NM_001262		Approved	INK4C, p18	uc001csg.3	P42773	OTTHUMG00000008046	ENST00000262662.1:c.214G>A	chr1.hg19:g.51439649G>A	ENSP00000262662:p.Ala72Thr	97.0	0.0		126.0	41.0	NM_001262	Q8TB83	Missense_Mutation	SNP	ENST00000262662.1	hg19	CCDS555.1	.	.	.	.	.	.	.	.	.	.	G	7.071	0.568271	0.13560	.	.	ENSG00000123080	ENST00000262662;ENST00000396148;ENST00000371761	T;T;T	0.57107	0.42;0.42;0.42	5.31	5.31	0.75309	Ankyrin repeat-containing domain (3);	0.052316	0.85682	D	0.000000	T	0.13970	0.0338	N	0.00125	-2.05	0.42527	D	0.993023	B	0.15930	0.015	B	0.11329	0.006	T	0.45086	-0.9285	10	0.02654	T	1	-7.1292	12.8511	0.57858	0.0:0.0:0.7209:0.2791	.	72	P42773	CDN2C_HUMAN	T	72	ENSP00000262662:A72T;ENSP00000379452:A72T;ENSP00000360826:A72T	ENSP00000262662:A72T	A	+	1	0	CDKN2C	51212237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.497000	0.45354	2.770000	0.95276	0.655000	0.94253	GCT	.	.		0.453	CDKN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022058.1	NM_001262		A	51439649	G	A	51439649	3	1	23	1	0	0	0	0	1	0	0	0	3167	1087	38	1	220	1	CDKN2C	1	51439649	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2743344	51439649	197810972	51	2117										
CPT2	1376	hgsc.bcm.edu	37	chr1	53679110	53679110	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggctttgcccctgtggtctCtgatggctttggtgttgggt	16	8	1	1	rs201913567		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:53679110C>T	ENST00000371486.3	+	5	2335	c.1820C>T	c.(1819-1821)tCt>tTt	p.S607F	C1orf123_ENST00000470385.1_5'Flank|RP5-1024G6.2_ENST00000452466.1_RNA	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	607					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	CCTGTGGTCTCTGATGGCTTT	0.552																																					p.S607F		Atlas-SNP	.											.	CPT2	34	.	0			c.C1820T						.						173	154	160					1																	53679110		2203	4300	6503	SO:0001583	missense	1376	exon5			TGGTCTCTGATGG	BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"carnitine palmitoyltransferase II"	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.1820C>T	chr1.hg19:g.53679110C>T	ENSP00000360541:p.Ser607Phe	156.0	0.0		151.0	64.0	NM_000098	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	hg19	CCDS575.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.420844	0.83559	.	.	ENSG00000157184	ENST00000371486	D	0.96745	-4.11	5.9	5.9	0.94986	.	0.272836	0.42964	D	0.000640	D	0.95326	0.8483	L	0.29908	0.895	0.41806	D	0.989945	P	0.40000	0.698	P	0.46419	0.516	D	0.95385	0.8476	10	0.66056	D	0.02	-0.6538	20.2789	0.98501	0.0:1.0:0.0:0.0	.	607	P23786	CPT2_HUMAN	F	607	ENSP00000360541:S607F	ENSP00000360541:S607F	S	+	2	0	CPT2	53451698	0.984000	0.35163	0.998000	0.56505	0.979000	0.70002	5.984000	0.70548	2.788000	0.95919	0.650000	0.86243	TCT	.	C|1.000;G|0.000		0.552	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098		T	53679110	C	T	53679110	3	4	23	1	0	0	0	0	1	0	0	0	3836	913	32	3	1838	3	CPT2	1	53679110	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2239461	53679110	195571511	52	2118										
DIRAS3	9077	hgsc.bcm.edu	37	chr1	68512696	68512696	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgcagagcgcggttgccgtcGccactcttgctgtcggtgat	14	12	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:68512696G>A	ENST00000370981.1	-	4	921	c.285C>T	c.(283-285)ggC>ggT	p.G95G	GNG12-AS1_ENST00000413628.1_RNA|GNG12-AS1_ENST00000420587.1_RNA|DIRAS3_ENST00000395201.1_Silent_p.G95G			O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	95					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of gene expression by genetic imprinting (GO:0006349)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GGTTGCCGTCGCCACTCTTGC	0.592																																					p.G95G		Atlas-SNP	.											.	DIRAS3	31	.	0			c.C285T						.						111	115	114					1																	68512696		2203	4300	6503	SO:0001819	synonymous_variant	9077	exon2			GCCGTCGCCACTC	U96750	CCDS641.1	1p31	2014-05-09		2005-01-27	ENSG00000162595	ENSG00000162595			687	protein-coding gene	gene with protein product		605193	"ras homolog gene family, member I"	ARHI		9874798	Standard	XM_006711027		Approved	NOEY2	uc001ded.3	O95661	OTTHUMG00000009544	ENST00000370981.1:c.285C>T	chr1.hg19:g.68512696G>A		110.0	0.0		137.0	70.0	NM_004675	B3KMP3	Silent	SNP	ENST00000370981.1	hg19	CCDS641.1																																																																																			.	.		0.592	DIRAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026354.2	NM_004675		A	68512696	G	A	68512696	2	1	23	1	0	0	0	0	0	0	0	1	4534	1074	38	1		1	DIRAS3	1	68512696	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	14833586	68512696	180737925	53	2119										
RPE65	6121	hgsc.bcm.edu	37	chr1	68905283	68905283	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgaatcggtcactgcaggggAattgtacaacgatctctgac	11	9	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:68905283A>G	ENST00000262340.5	-	7	739	c.686T>C	c.(685-687)tTc>tCc	p.F229S		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	229					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						ACTGCAGGGGAATTGTACAAC	0.373																																					p.F229S		Atlas-SNP	.											.	RPE65	87	.	0			c.T686C						.						190	182	185					1																	68905283		2203	4300	6503	SO:0001583	missense	6121	exon7			CAGGGGAATTGTA	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.686T>C	chr1.hg19:g.68905283A>G	ENSP00000262340:p.Phe229Ser	84.0	0.0		75.0	36.0	NM_000329	A8K1L0|Q5T9U3	Missense_Mutation	SNP	ENST00000262340.5	hg19	CCDS643.1	.	.	.	.	.	.	.	.	.	.	a	22.8	4.338621	0.81911	.	.	ENSG00000116745	ENST00000262340	D	0.94613	-3.47	5.56	5.56	0.83823	.	0.043773	0.85682	D	0.000000	D	0.96725	0.8931	M	0.81239	2.535	0.58432	D	0.999999	D	0.89917	1.0	D	0.75020	0.985	D	0.97199	0.9863	10	0.62326	D	0.03	-9.4536	15.7331	0.77822	1.0:0.0:0.0:0.0	.	229	Q16518	RPE65_HUMAN	S	229	ENSP00000262340:F229S	ENSP00000262340:F229S	F	-	2	0	RPE65	68677871	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.771000	0.91751	2.112000	0.64535	0.524000	0.50904	TTC	.	.		0.373	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		G	68905283	A	G	68905283	3	3	23	1	0	0	0	0	1	0	0	0	13560	246	9	2	947	2	RPE65	1	68905283	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	392587	68905283	180345338	54	2120										
LRRC40	55631	hgsc.bcm.edu	37	chr1	70614318	70614318	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aatcagaattgtttcaagtgTgaagatacgatatagaactt	8	4	2	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:70614318T>A	ENST00000370952.3	-	14	1634	c.1555A>T	c.(1555-1557)Aca>Tca	p.T519S		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	519						membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						GTTTCAAGTGTGAAGATACGA	0.338																																					p.T519S		Atlas-SNP	.											.	LRRC40	66	.	0			c.A1555T						.						98	97	97					1																	70614318		2203	4300	6503	SO:0001583	missense	55631	exon14			CAAGTGTGAAGAT		CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1555A>T	chr1.hg19:g.70614318T>A	ENSP00000359990:p.Thr519Ser	111.0	0.0		86.0	32.0	NM_017768	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	hg19	CCDS646.1	.	.	.	.	.	.	.	.	.	.	T	5.492	0.275784	0.10403	.	.	ENSG00000066557	ENST00000370952	T	0.44482	0.92	5.73	2.14	0.27477	.	0.264710	0.44097	N	0.000500	T	0.03477	0.0100	N	0.02830	-0.485	0.26957	N	0.965892	B	0.09022	0.002	B	0.06405	0.002	T	0.43310	-0.9399	10	0.02654	T	1	.	5.0628	0.14566	0.1259:0.2213:0.0:0.6528	.	519	Q9H9A6	LRC40_HUMAN	S	519	ENSP00000359990:T519S	ENSP00000359990:T519S	T	-	1	0	LRRC40	70386906	0.072000	0.21174	0.487000	0.27428	0.950000	0.60333	0.282000	0.18829	0.108000	0.17862	-0.336000	0.08194	ACA	.	.		0.338	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		A	70614318	T	A	70614318	3	1	23	1	0	0	0	0	1	0	0	0	9007	1696	59	4	261	4	LRRC40	1	70614318	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1709035	70614318	178636303	55	2121										
PTGER3	5733	hgsc.bcm.edu	37	chr1	71437417	71437417	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caactccgttctttcattatCtgttagaatagagagagaaa	7	7	3	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:71437417C>T	ENST00000306666.5	-	4	1380		c.e4-1		PTGER3_ENST00000356595.4_Intron|PTGER3_ENST00000354608.5_Intron|PTGER3_ENST00000414819.1_Intron|PTGER3_ENST00000460330.1_Intron|PTGER3_ENST00000370931.3_Intron|PTGER3_ENST00000351052.5_Intron|PTGER3_ENST00000370932.2_Intron	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)						cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	CTTTCATTATCTGTTAGAATA	0.303																																					.		Atlas-SNP	.											.	PTGER3	246	.	0			c.1170-1G>A						.						102	110	107					1																	71437417		2203	4297	6500	SO:0001630	splice_region_variant	5733	exon5			CATTATCTGTTAG	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.1170-1G>A	chr1.hg19:g.71437417C>T		606.0	0.0		566.0	213.0	NM_198719	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Splice_Site	SNP	ENST00000306666.5	hg19	CCDS657.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.260033	0.59321	.	.	ENSG00000050628	ENST00000306666	.	.	.	4.19	4.19	0.49359	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3246	0.55003	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PTGER3	71210005	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	2.904000	0.48719	2.605000	0.88082	0.650000	0.86243	.	.	.		0.303	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957	Intron	T	71437417	C	T	71437417	5	4	23	1	0	0	0	0	0	0	1	0	12757	927	32	3	220	3	PTGER3	1	71437417	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	823099	71437417	177813204	56	2122										
ST6GALNAC3	256435	hgsc.bcm.edu	37	chr1	77094388	77094388	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atattttcttcatgaacatgCcccatatgggggtcataggt	9	8	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:77094388C>T	ENST00000328299.3	+	5	963	c.815C>T	c.(814-816)gCc>gTc	p.A272V		NM_152996.2	NP_694541.2	Q8NDV1	SIA7C_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	272					glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sialyltransferase activity (GO:0008373)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|ovary(3)|prostate(1)|skin(2)	36						CATGAACATGCCCCATATGGG	0.368																																					p.A272V		Atlas-SNP	.											.	ST6GALNAC3	71	.	0			c.C815T						.						116	119	118					1																	77094388		2203	4299	6502	SO:0001583	missense	256435	exon5			AACATGCCCCATA		CCDS672.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000184005	ENSG00000184005		"Sialyltransferases"	19343	protein-coding gene	gene with protein product	"ST6GALNAC III"	610133	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) C"	SIAT7C			Standard	NM_152996		Approved		uc001dhh.2	Q8NDV1	OTTHUMG00000009615	ENST00000328299.3:c.815C>T	chr1.hg19:g.77094388C>T	ENSP00000329214:p.Ala272Val	77.0	0.0		87.0	39.0	NM_152996	Q6PCE0|Q6UX29|Q8N259	Missense_Mutation	SNP	ENST00000328299.3	hg19	CCDS672.1	.	.	.	.	.	.	.	.	.	.	c	20.6	4.015689	0.75161	.	.	ENSG00000184005	ENST00000328299;ENST00000394993;ENST00000415813	T	0.32753	1.44	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.38161	0.1030	L	0.61387	1.9	0.51233	D	0.999916	P;P	0.43701	0.752;0.815	P;P	0.50537	0.459;0.643	T	0.11060	-1.0603	10	0.56958	D	0.05	-9.2724	19.8598	0.96779	0.0:1.0:0.0:0.0	.	171;272	B4DM98;Q8NDV1	.;SIA7C_HUMAN	V	272;271;170	ENSP00000329214:A272V	ENSP00000329214:A272V	A	+	2	0	ST6GALNAC3	76866976	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	5.685000	0.68204	2.761000	0.94854	0.645000	0.84053	GCC	.	.		0.368	ST6GALNAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026501.1	NM_152996		T	77094388	C	T	77094388	3	4	23	1	0	0	0	0	1	0	0	0	15240	739	26	3	847	3	ST6GALNAC3	1	77094388	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5656971	77094388	172156233	57	2123										
RBMXL1	494115	hgsc.bcm.edu	37	chr1	89449438	89449438	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tatttgccaaatactgtttcAagagctttctcatttgtttc	5	8	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:89449438A>G	ENST00000321792.5	-	2	499	c.72T>C	c.(70-72)ctT>ctC	p.L24L	CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000260508.4_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000413769.1_5'UTR|RBMXL1_ENST00000399794.2_Silent_p.L24L|CCBL2_ENST00000446900.2_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	24	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										ATACTGTTTCAAGAGCTTTCT	0.408											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L24L		Atlas-SNP	.											.	.	.	.	0			c.T72C						.						185	184	184					1																	89449438		2203	4300	6503	SO:0001819	synonymous_variant	494115	exon3			TGTTTCAAGAGCT	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"RNA binding motif (RRM) containing"	25073	protein-coding gene	gene with protein product	"kynurenine aminotransferase III"					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.72T>C	chr1.hg19:g.89449438A>G		337.0	0.0	1267	291.0	35.0	NM_001162536		Silent	SNP	ENST00000321792.5	hg19	CCDS716.1																																																																																			.	.		0.408	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610		G	89449438	A	G	89449438	2	3	23	1	0	0	0	0	0	0	0	1	13168	117	5	2		2	RBMXL1	1	89449438	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	12355050	89449438	159801183	58	2124										
CCBL2	56267	hgsc.bcm.edu	37	chr1	89453938	89453940	+	In_Frame_Del	DEL	AGA	AGA	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagtaagcaatacctacagcAgaagtagagaatccgaggat					rs146441129		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:89453938_89453940delAGA	ENST00000260508.4	-	2	431_433	c.94_96delTCT	c.(94-96)tctdel	p.S32del	CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000370485.2_In_Frame_Del_p.S32del|RBMXL1_ENST00000413769.1_5'UTR|RBMXL1_ENST00000321792.5_Intron|RBMXL1_ENST00000399794.2_5'UTR|CCBL2_ENST00000446900.2_5'UTR	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	32					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	mitochondrion (GO:0005739)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|kynurenine-glyoxylate transaminase activity (GO:0047315)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|ovary(2)|skin(2)|soft_tissue(1)	18		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)		TACCTACAGCAGAAGTAGAGAAT	0.35																																					p.32_33del		Atlas-Indel,Pindel	.											.	CCBL2	138	.	0			c.95_97del						.																																			SO:0001651	inframe_deletion	56267	exon2			.	AF091090	CCDS30766.1, CCDS30767.1	1p22.2	2009-06-23			ENSG00000137944	ENSG00000137944			33238	protein-coding gene	gene with protein product		610656				16376499	Standard	NM_001008662		Approved	RBM1, RP11-82K18.3, KAT3	uc001dmp.2	Q6YP21	OTTHUMG00000010617	ENST00000260508.4:c.94_96delTCT	chr1.hg19:g.89453938_89453940delAGA	ENSP00000260508:p.Ser32del	594.0	0.0		552.0	104.0	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	In_Frame_Del	DEL	ENST00000260508.4	hg19	CCDS30766.1																																																																																			.	.		0.35	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661		-	89453940	AGA	-	89453938	7	5	23	1	0	1	0	1	0	0	0	0	2735	175	7	0	1320	0	CCBL2	1	89453938	In_Frame_Del	DEL	AGA	TCGA-4R-AA8I-01A-11D-A382-10	4500	89453938	159796683	59	2125										
CDC7	8317	hgsc.bcm.edu	37	chr1	91977470	91977470	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcaattttttatataataggCgcctgaaaaagtaagtatga	8	4	0	2	rs539320135		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:91977470C>T	ENST00000428239.1	+	6	821	c.562C>T	c.(562-564)Cgc>Tgc	p.R188C	CDC7_ENST00000234626.6_Missense_Mutation_p.R188C|CDC7_ENST00000430031.2_Missense_Mutation_p.R160C	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	188	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		ATATAATAGGCGCCTGAAAAA	0.294																																					p.R188C		Atlas-SNP	.											.	CDC7	74	.	0			c.C562T						.						58	60	60					1																	91977470		2203	4298	6501	SO:0001583	missense	8317	exon6			AATAGGCGCCTGA	AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1", "CDC7 cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 homolog (S. cerevisiae)"	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.562C>T	chr1.hg19:g.91977470C>T	ENSP00000393139:p.Arg188Cys	391.0	0.0		433.0	24.0	NM_001134419	D3DT31|O00558|Q5T5U5	Missense_Mutation	SNP	ENST00000428239.1	hg19	CCDS734.1	.	.	.	.	.	.	.	.	.	.	C	14.74	2.625080	0.46840	.	.	ENSG00000097046	ENST00000430031;ENST00000234626;ENST00000428239	T;T;T	0.06933	3.24;3.24;3.24	5.72	3.86	0.44501	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.914960	0.09617	N	0.778113	T	0.14098	0.0341	M	0.81942	2.565	0.19300	N	0.999974	D;D	0.89917	1.0;1.0	D;D	0.69479	0.964;0.939	T	0.19679	-1.0298	10	0.59425	D	0.04	0.0174	6.1234	0.20165	0.1316:0.6623:0.0:0.2061	.	160;188	B7Z5H7;O00311	.;CDC7_HUMAN	C	160;188;188	ENSP00000407477:R160C;ENSP00000234626:R188C;ENSP00000393139:R188C	ENSP00000234626:R188C	R	+	1	0	CDC7	91750058	0.129000	0.22400	0.093000	0.20910	0.893000	0.52053	1.443000	0.35057	0.784000	0.33661	0.467000	0.42956	CGC	.	.		0.294	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027928.1	NM_003503		T	91977470	C	T	91977470	3	4	23	1	0	0	0	0	1	0	0	0	3086	768	27	1	580	1	CDC7	1	91977470	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2523532	91977470	157273151	60	2126										
SLC30A7	148867	hgsc.bcm.edu	37	chr1	101379226	101379226	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctttgttttctaggccacggAcacagtcattccctctttaa	6	12	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:101379226A>T	ENST00000370112.4	+	6	706	c.519A>T	c.(517-519)ggA>ggT	p.G173G	SLC30A7_ENST00000357650.4_Silent_p.G173G	NM_001144884.1|NM_133496.4	NP_001138356.1|NP_598003.2	Q8NEW0	ZNT7_HUMAN	solute carrier family 30 (zinc transporter), member 7	173	His-rich loop.				cellular protein metabolic process (GO:0044267)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	cation transmembrane transporter activity (GO:0008324)			endometrium(3)|large_intestine(2)|lung(10)	15		all_epithelial(167;0.000445)|all_lung(203;0.00645)|Lung NSC(277;0.0119)		Epithelial(280;0.0437)|all cancers(265;0.0498)|COAD - Colon adenocarcinoma(174;0.162)|Colorectal(144;0.19)|Lung(183;0.201)		TAGGCCACGGACACAGTCATT	0.408																																					p.G173G	NSCLC(91;473 1491 3102 16827 21633)	Atlas-SNP	.											.	SLC30A7	33	.	0			c.A519T						.						152	124	134					1																	101379226		2203	4300	6503	SO:0001819	synonymous_variant	148867	exon6			CCACGGACACAGT	AF233345	CCDS776.1	1p21.1	2013-05-22			ENSG00000162695	ENSG00000162695		"Solute carriers"	19306	protein-coding gene	gene with protein product		611149				12446736	Standard	NM_133496		Approved	ZnTL2, ZNT7	uc001dto.2	Q8NEW0	OTTHUMG00000011815	ENST00000370112.4:c.519A>T	chr1.hg19:g.101379226A>T		188.0	0.0		197.0	90.0	NM_133496	B2R949|D3DT61|Q8TCH2	Silent	SNP	ENST00000370112.4	hg19	CCDS776.1																																																																																			.	.		0.408	SLC30A7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032711.1	NM_133496		T	101379226	A	T	101379226	2	4	23	1	0	0	0	0	0	0	0	1	14575	262	10	4		4	SLC30A7	1	101379226	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	9401756	101379226	147871395	61	2127										
NTNG1	22854	hgsc.bcm.edu	37	chr1	108023282	108023282	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgccagaacggagggacgtgCcacaacaacgtgcgctgcct	13	13	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:108023282C>T	ENST00000370068.1	+	8	2286	c.1440C>T	c.(1438-1440)tgC>tgT	p.C480C	NTNG1_ENST00000370061.3_Silent_p.C446C|NTNG1_ENST00000370067.1_Silent_p.C401C|NTNG1_ENST00000370070.2_Silent_p.C401C|NTNG1_ENST00000542803.1_Silent_p.C480C|NTNG1_ENST00000370066.1_Silent_p.C421C|NTNG1_ENST00000370072.3_Silent_p.C435C|NTNG1_ENST00000370073.2_Silent_p.C480C|NTNG1_ENST00000370071.2_Silent_p.C421C|NTNG1_ENST00000370065.1_Silent_p.C435C|NTNG1_ENST00000370074.4_Silent_p.C379C			Q9Y2I2	NTNG1_HUMAN	netrin G1	480					axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		GAGGGACGTGCCACAACAACG	0.667																																					p.C480C		Atlas-SNP	.											.	NTNG1	274	.	0			c.C1440T						.						28	31	30					1																	108023282		2203	4300	6503	SO:0001819	synonymous_variant	22854	exon8			GACGTGCCACAAC	AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"Netrins"	23319	protein-coding gene	gene with protein product	"netrin G1f", "Netrin-G1"	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.1440C>T	chr1.hg19:g.108023282C>T		100.0	0.0		99.0	42.0	NM_001113226	Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Silent	SNP	ENST00000370068.1	hg19	CCDS44180.1																																																																																			.	.		0.667	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917		T	108023282	C	T	108023282	2	4	23	1	0	0	0	0	0	0	0	1	10713	747	26	3		3	NTNG1	1	108023282	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	6644056	108023282	141227339	62	2128										
FAM102B	284611	hgsc.bcm.edu	37	chr1	109171126	109171126	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaaagtattctagagccatgTgatgaaattgagcagaaaat	10	4	1	5			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:109171126T>C	ENST00000370035.3	+	8	1102	c.762T>C	c.(760-762)tgT>tgC	p.C254C	FAM102B_ENST00000405454.1_Silent_p.C254C	NM_001010883.2	NP_001010883.2	Q5T8I3	F102B_HUMAN	family with sequence similarity 102, member B	254										autonomic_ganglia(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	5		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		TAGAGCCATGTGATGAAATTG	0.423																																					p.C254C		Atlas-SNP	.											.	FAM102B	49	.	0			c.T762C						.						79	87	84					1																	109171126		2203	4300	6503	SO:0001819	synonymous_variant	284611	exon8			GCCATGTGATGAA	CR749397	CCDS30786.2	1p13.3	2012-11-05			ENSG00000162636	ENSG00000162636			27637	protein-coding gene	gene with protein product	"sym-3 homolog B (C. elegans)"						Standard	NM_001010883		Approved	DKFZp779B126, SYM-3B	uc010ouy.2	Q5T8I3	OTTHUMG00000010967	ENST00000370035.3:c.762T>C	chr1.hg19:g.109171126T>C		139.0	0.0		167.0	68.0	NM_001010883	A1L1A1|B0QZ46|B0QZ47|Q68DH7	Silent	SNP	ENST00000370035.3	hg19	CCDS30786.2																																																																																			.	.		0.423	FAM102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030188.3	NM_001010883		C	109171126	T	C	109171126	2	2	23	1	0	0	0	0	0	0	0	1	5388	1702	59	2		2	FAM102B	1	109171126	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1147844	109171126	140079495	63	2129										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109801459	109801459	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgcgggagccctgcgagaActacatgcgctgcgtgtcgg	15	13	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:109801459A>G	ENST00000271332.3	+	2	3777	c.3716A>G	c.(3715-3717)aAc>aGc	p.N1239S		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1239	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CCCTGCGAGAACTACATGCGC	0.672																																					p.N1239S	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.A3716G						.						41	35	37					1																	109801459		2203	4300	6503	SO:0001583	missense	1952	exon2			GCGAGAACTACAT	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.3716A>G	chr1.hg19:g.109801459A>G	ENSP00000271332:p.Asn1239Ser	128.0	0.0		149.0	36.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.194416	0.78902	.	.	ENSG00000143126	ENST00000271332	T	0.69561	-0.41	4.54	4.54	0.55810	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.77226	0.4099	M	0.84511	2.7	0.49130	D	0.999754	D	0.76494	0.999	D	0.63703	0.917	T	0.80690	-0.1270	9	0.52906	T	0.07	.	13.991	0.64367	1.0:0.0:0.0:0.0	.	1239	Q9HCU4	CELR2_HUMAN	S	1239	ENSP00000271332:N1239S	ENSP00000271332:N1239S	N	+	2	0	CELSR2	109602982	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.066000	0.76734	2.039000	0.60335	0.379000	0.24179	AAC	.	.		0.672	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		G	109801459	A	G	109801459	3	3	23	1	0	0	0	0	1	0	0	0	3224	43	2	2	3722	2	CELSR2	1	109801459	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	630333	109801459	139449162	64	2130										
EPS8L3	79574	hgsc.bcm.edu	37	chr1	110300674	110300674	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcccttaggacatggttcaGcacttcctgggccccaaaca	9	14	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:110300674G>A	ENST00000361965.4	-	9	830	c.724C>T	c.(724-726)Ctg>Ttg	p.L242L	EPS8L3_ENST00000494151.1_5'Flank|EPS8L3_ENST00000361852.4_Silent_p.L242L|RP4-735C1.4_ENST00000431955.1_RNA|EPS8L3_ENST00000369805.3_Silent_p.L243L	NM_133181.3	NP_573444.2	Q8TE67	ES8L3_HUMAN	EPS8-like 3	242						cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	32		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		ACATGGTTCAGCACTTCCTGG	0.572																																					p.L243L		Atlas-SNP	.											.	EPS8L3	73	.	0			c.C727T						.						113	118	117					1																	110300674		2203	4300	6503	SO:0001819	synonymous_variant	79574	exon9			GGTTCAGCACTTC	AK025175	CCDS813.1, CCDS814.1, CCDS815.1	1p13.2	2008-02-05			ENSG00000198758	ENSG00000198758			21297	protein-coding gene	gene with protein product		614989				12620401	Standard	NM_139053		Approved	FLJ21522, MGC16817	uc001dyq.2	Q8TE67	OTTHUMG00000011651	ENST00000361965.4:c.724C>T	chr1.hg19:g.110300674G>A		55.0	0.0		59.0	22.0	NM_139053	A8K833|Q5T8Q6|Q5T8Q7|Q5T8Q8|Q96E47|Q9H719	Silent	SNP	ENST00000361965.4	hg19	CCDS814.1																																																																																			.	.		0.572	EPS8L3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032234.1	NM_024526		A	110300674	G	A	110300674	2	1	23	1	0	0	0	0	0	0	0	1	5199	962	34	3		3	EPS8L3	1	110300674	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	499215	110300674	138949947	65	2131										
VANGL1	81839	hgsc.bcm.edu	37	chr1	116226598	116226598	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgccactggccagtcccgggCcatgattgctgcagctgctc	12	15	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:116226598C>T	ENST00000355485.2	+	6	1251	c.980C>T	c.(979-981)gCc>gTc	p.A327V	VANGL1_ENST00000369510.4_Missense_Mutation_p.A325V|VANGL1_ENST00000474344.1_3'UTR|VANGL1_ENST00000369509.1_Missense_Mutation_p.A327V|VANGL1_ENST00000310260.3_Missense_Mutation_p.A327V	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	327					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		CAGTCCCGGGCCATGATTGCT	0.522																																					p.A327V		Atlas-SNP	.											.	VANGL1	65	.	0			c.C980T						.						61	60	61					1																	116226598		2203	4300	6503	SO:0001583	missense	81839	exon6			CCCGGGCCATGAT	AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)", "vang-like 1 (van gogh, Drosophila)"			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.980C>T	chr1.hg19:g.116226598C>T	ENSP00000347672:p.Ala327Val	501.0	1.0		503.0	219.0	NM_138959	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	hg19	CCDS883.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.023933	0.75390	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	4.76	4.76	0.60689	.	0.052282	0.85682	D	0.000000	T	0.81978	0.4937	M	0.87456	2.885	0.80722	D	1	B;B	0.18968	0.026;0.032	B;B	0.20184	0.017;0.028	T	0.82408	-0.0472	10	0.62326	D	0.03	-14.8885	17.9983	0.89191	0.0:1.0:0.0:0.0	.	325;327	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	V	327;325;327;327	ENSP00000347672:A327V;ENSP00000358523:A325V;ENSP00000310800:A327V;ENSP00000358522:A327V	ENSP00000310800:A327V	A	+	2	0	VANGL1	116028121	1.000000	0.71417	0.998000	0.56505	0.798000	0.45092	7.313000	0.78978	2.474000	0.83562	0.551000	0.68910	GCC	.	.		0.522	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			T	116226598	C	T	116226598	3	4	23	1	0	0	0	0	1	0	0	0	17134	739	26	3	998	3	VANGL1	1	116226598	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5925924	116226598	133024023	66	2132										
ZNF697	90874	hgsc.bcm.edu	37	chr1	120166363	120166363	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggtgctgcaggaaggcggcGccaggactgaagctctcccc	15	13	1	1	rs587712785	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:120166363G>A	ENST00000421812.2	-	3	722	c.603C>T	c.(601-603)ggC>ggT	p.G201G		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	201					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		GGAAGGCGGCGCCAGGACTGA	0.716													G|||	2	0.000399361	0	0	5008	,	,		10022	0		0	False		,,,				2504	0.002				p.G201G		Atlas-SNP	.											.	ZNF697	26	.	0			c.C603T						.						3	5	4					1																	120166363		1736	3553	5289	SO:0001819	synonymous_variant	90874	exon3			GGCGGCGCCAGGA	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"Zinc fingers, C2H2-type"	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.603C>T	chr1.hg19:g.120166363G>A		79.0	0.0		59.0	24.0	NM_001080470	Q96IT2	Silent	SNP	ENST00000421812.2	hg19	CCDS44202.1																																																																																			.	.		0.716	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286		A	120166363	G	A	120166363	2	1	23	1	0	0	0	0	0	0	0	1	18115	1074	38	1		1	ZNF697	1	120166363	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3939765	120166363	129084258	67	2133										
ZNF697	90874	hgsc.bcm.edu	37	chr1	120166521	120166521	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acctcggtgccgactccccaGggagagatgtcgcctccagg	13	15	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:120166521G>T	ENST00000421812.2	-	3	564	c.445C>A	c.(445-447)Ctg>Atg	p.L149M		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	149					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		CGACTCCCCAGGGAGAGATGT	0.701																																					p.L149M		Atlas-SNP	.											.	ZNF697	26	.	0			c.C445A						.						13	17	16					1																	120166521		1989	4132	6121	SO:0001583	missense	90874	exon3			TCCCCAGGGAGAG	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"Zinc fingers, C2H2-type"	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.445C>A	chr1.hg19:g.120166521G>T	ENSP00000396857:p.Leu149Met	190.0	0.0		193.0	77.0	NM_001080470	Q96IT2	Missense_Mutation	SNP	ENST00000421812.2	hg19	CCDS44202.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.299814	0.23650	.	.	ENSG00000143067	ENST00000421812	T	0.12672	2.66	4.34	2.31	0.28768	.	.	.	.	.	T	0.06690	0.0171	L	0.27053	0.805	0.23320	N	0.997911	D	0.54964	0.969	P	0.53490	0.727	T	0.23404	-1.0189	9	0.46703	T	0.11	.	7.1493	0.25601	0.1036:0.2801:0.6163:0.0	.	149	Q5TEC3	ZN697_HUMAN	M	149	ENSP00000396857:L149M	ENSP00000396857:L149M	L	-	1	2	ZNF697	119968044	0.000000	0.05858	0.983000	0.44433	0.007000	0.05969	-0.080000	0.11339	0.959000	0.37980	0.561000	0.74099	CTG	.	.		0.701	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286		T	120166521	G	T	120166521	3	4	23	1	0	0	0	0	1	0	0	0	18115	991	35	3	1196	3	ZNF697	1	120166521	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	158	120166521	129084100	68	2134										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120468048	120468048	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaagtggggaggagcagttgGcccaggggttctccatggtg	19	7	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:120468048G>A	ENST00000256646.2	-	25	4610	c.4391C>T	c.(4390-4392)gCc>gTc	p.A1464V	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1464	Negative regulatory region (NRR).				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGAGCAGTTGGCCCAGGGGTT	0.567			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.A1464V		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C4391T						.						95	91	93					1																	120468048		2203	4300	6503	SO:0001583	missense	4853	exon25	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CAGTTGGCCCAGG	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.4391C>T	chr1.hg19:g.120468048G>A	ENSP00000256646:p.Ala1464Val	175.0	0.0		138.0	51.0	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	hg19	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.478314	0.26511	.	.	ENSG00000134250	ENST00000256646	D	0.82344	-1.6	5.86	4.94	0.65067	Notch domain (3);	0.000000	0.37577	U	0.002029	T	0.67942	0.2947	L	0.43923	1.385	0.47819	D	0.999525	B	0.15141	0.012	B	0.14578	0.011	T	0.65063	-0.6259	10	0.36615	T	0.2	.	13.4972	0.61432	0.0742:0.0:0.9258:0.0	.	1464	Q04721	NOTC2_HUMAN	V	1464	ENSP00000256646:A1464V	ENSP00000256646:A1464V	A	-	2	0	NOTCH2	120269571	0.999000	0.42202	1.000000	0.80357	0.343000	0.28985	1.182000	0.32029	2.775000	0.95449	0.655000	0.94253	GCC	.	.		0.567	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		A	120468048	G	A	120468048	3	1	23	1	0	0	0	0	1	0	0	0	10557	1203	42	3	3064	3	NOTCH2	1	120468048	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	301527	120468048	128782573	69	2135										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	145075655	145075655	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagggtgtggccgccgcagCtgcttcttcctcctcggccg	13	17	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:145075655C>A	ENST00000530740.1	-	1	246	c.208G>T	c.(208-210)Gct>Tct	p.A70S	PDE4DIP_ENST00000369348.3_Missense_Mutation_p.A70S|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.A70S|PDE4DIP_ENST00000369345.4_Missense_Mutation_p.A70S			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GCCGCCGCAGCTGCTTCTTCC	0.716			T	PDGFRB	MPD																																p.A70S		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G208T						.						42	52	49					1																	145075655		2195	4287	6482	SO:0001583	missense	9659	exon1			CCGCAGCTGCTTC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.208G>T	chr1.hg19:g.145075655C>A	ENSP00000435654:p.Ala70Ser	224.0	0.0		184.0	31.0	NM_022359	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000530740.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.59	2.282591	0.40394	.	.	ENSG00000178104	ENST00000530740;ENST00000369359;ENST00000369348;ENST00000369345	T;T;T	0.15017	3.82;3.8;2.46	3.54	3.54	0.40534	.	.	.	.	.	T	0.10809	0.0264	N	0.19112	0.55	0.22693	N	0.998847	D;P	0.60160	0.987;0.598	P;B	0.56398	0.797;0.175	T	0.10847	-1.0612	9	0.87932	D	0	.	10.7869	0.46411	0.0:1.0:0.0:0.0	.	70;70	Q5TB27;E9PJ64	.;.	S	70	ENSP00000435654:A70S;ENSP00000358366:A70S;ENSP00000358354:A70S	ENSP00000358351:A70S	A	-	1	0	PDE4DIP	143787012	0.919000	0.31177	0.482000	0.27366	0.419000	0.31324	1.871000	0.39539	1.960000	0.56953	0.511000	0.50034	GCT	.	.		0.716	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359		A	145075655	C	A	145075655	3	1	23	1	0	0	0	0	1	0	0	0	11652	797	28	3	8604	3	PDE4DIP	1	145075655	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	24607607	145075655	104174966	70	2136										
NUDT17	200035	hgsc.bcm.edu	37	chr1	145589355	145589355	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggtccggctcccaggaggcCacacacactccgtgcgaagc	12	16	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:145589355C>G	ENST00000334513.5	-	1	84	c.73G>C	c.(73-75)Ggc>Cgc	p.G25R	NUDT17_ENST00000444015.2_5'Flank	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	25							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(2)	9	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCCAGGAGGCCACACACACTC	0.692											OREG0013751	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G25R		Atlas-SNP	.											.	NUDT17	25	.	0			c.G73C						.						12	12	12					1																	145589355		2163	4229	6392	SO:0001583	missense	200035	exon1			GGAGGCCACACAC	BC046352	CCDS72865.1	1q21.1	2008-02-05			ENSG00000186364	ENSG00000186364		"Nudix motif containing"	26618	protein-coding gene	gene with protein product						12477932	Standard	NM_001012758		Approved	FLJ34433	uc001eoe.3	P0C025	OTTHUMG00000013752	ENST00000334513.5:c.73G>C	chr1.hg19:g.145589355C>G	ENSP00000334437:p.Gly25Arg	151.0	0.0	1695	163.0	17.0	NM_001012758		Missense_Mutation	SNP	ENST00000334513.5	hg19	CCDS30830.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.562678	0.45694	.	.	ENSG00000186364	ENST00000334513	.	.	.	4.26	2.33	0.28932	.	0.192024	0.43747	N	0.000529	T	0.16257	0.0391	L	0.43152	1.355	0.36385	D	0.862148	P;B	0.46784	0.884;0.024	B;B	0.35240	0.198;0.013	T	0.02774	-1.1112	9	0.44086	T	0.13	-2.582	6.0627	0.19846	0.0:0.7042:0.1899:0.1059	.	25;25	B4DNV8;P0C025	.;NUD17_HUMAN	R	25	.	ENSP00000334437:G25R	G	-	1	0	NUDT17	144300712	0.018000	0.18449	0.997000	0.53966	0.971000	0.66376	0.604000	0.24164	0.406000	0.25560	0.585000	0.79938	GGC	.	.		0.692	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395		G	145589355	C	G	145589355	3	3	23	1	0	0	0	0	1	0	0	0	10743	594	21	4	945	4	NUDT17	1	145589355	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	513700	145589355	103661266	71	2137										
GJA5	2702	hgsc.bcm.edu	37	chr1	147230336	147230336	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agacgtcgcttgtcactatgAtagccatggggaaggcggtg	15	8	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:147230336A>T	ENST00000271348.2	-	2	1172	c.1011T>A	c.(1009-1011)taT>taA	p.Y337*	RP11-433J22.2_ENST00000428911.1_RNA|GJA5_ENST00000369237.1_Nonsense_Mutation_p.Y337*	NM_005266.5	NP_005257.2	P36382	CXA5_HUMAN	gap junction protein, alpha 5, 40kDa	337					angiogenesis (GO:0001525)|artery morphogenesis (GO:0048844)|atrial cardiac muscle cell action potential (GO:0086014)|atrial septum development (GO:0003283)|AV node cell to bundle of His cell communication by electrical coupling (GO:0086053)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|gap junction assembly (GO:0016264)|mitral valve development (GO:0003174)|outflow tract morphogenesis (GO:0003151)|pulmonary valve formation (GO:0003193)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|transmembrane transport (GO:0055085)|ventricular septum development (GO:0003281)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)	gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling (GO:0086077)|gap junction channel activity involved in cardiac conduction electrical coupling (GO:0086075)|gap junction hemi-channel activity (GO:0055077)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	20	all_hematologic(923;0.0276)		LUSC - Lung squamous cell carcinoma(543;0.202)			TGTCACTATGATAGCCATGGG	0.552																																					p.Y337X		Atlas-SNP	.											.	GJA5	64	.	0			c.T1011A						.						126	116	119					1																	147230336		2203	4300	6503	SO:0001587	stop_gained	2702	exon2			ACTATGATAGCCA		CCDS929.1	1q21.1	2008-02-05	2007-01-16		ENSG00000143140	ENSG00000265107		"Ion channels / Gap junction proteins (connexins)"	4279	protein-coding gene	gene with protein product	"connexin 40"	121013	"gap junction protein, alpha 5, 40kD (connexin 40)", "gap junction protein, alpha 5, 40kDa (connexin 40)"				Standard	NM_005266		Approved	CX40	uc001eps.1	P36382	OTTHUMG00000014020	ENST00000271348.2:c.1011T>A	chr1.hg19:g.147230336A>T	ENSP00000271348:p.Tyr337*	92.0	0.0		112.0	36.0	NM_005266	Q5T3B6|Q5U0N6	Nonsense_Mutation	SNP	ENST00000271348.2	hg19	CCDS929.1	.	.	.	.	.	.	.	.	.	.	A	37	6.130235	0.97310	.	.	ENSG00000143140	ENST00000271348;ENST00000369237	.	.	.	5.38	3.45	0.39498	.	1.050290	0.07374	N	0.886237	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.9372	0.52880	0.1412:0.0:0.8588:0.0	.	.	.	.	X	337	.	ENSP00000271348:Y337X	Y	-	3	2	GJA5	145696960	0.995000	0.38212	0.974000	0.42286	0.878000	0.50629	2.438000	0.44837	0.828000	0.34709	-0.177000	0.13119	TAT	.	.		0.552	GJA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039422.2	NM_181703		T	147230336	A	T	147230336	4	4	23	1	0	0	0	0	0	1	0	0	6412	340	12	4	69	4	GJA5	1	147230336	Nonsense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1640981	147230336	102020285	72	2138										
GJA8	2703	hgsc.bcm.edu	37	chr1	147380385	147380385	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacgcggtgcactacgtccgCatggaggagaagcgcaaaag	14	11	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:147380385C>T	ENST00000369235.1	+	1	303	c.303C>T	c.(301-303)cgC>cgT	p.R101R	GJA8_ENST00000240986.4_Silent_p.R101R			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	101					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					ACTACGTCCGCATGGAGGAGA	0.657																																					p.R101R	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											.	GJA8	108	.	0			c.C303T						.						79	71	73					1																	147380385		2203	4300	6503	SO:0001819	synonymous_variant	2703	exon2			CGTCCGCATGGAG	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.303C>T	chr1.hg19:g.147380385C>T		47.0	0.0		89.0	39.0	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Silent	SNP	ENST00000369235.1	hg19	CCDS30834.1																																																																																			.	.		0.657	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		T	147380385	C	T	147380385	2	4	23	1	0	0	0	0	0	0	0	1	6413	697	25	3		3	GJA8	1	147380385	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	150049	147380385	101870236	73	2139										
TARS2	80222	hgsc.bcm.edu	37	chr1	150470091	150470091	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaacagtcagggcactgggAgcattatcaggaagacatgt	14	7	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:150470091A>G	ENST00000369064.3	+	10	1140	c.1106A>G	c.(1105-1107)gAg>gGg	p.E369G	TARS2_ENST00000369054.2_Missense_Mutation_p.E239G|TARS2_ENST00000606933.1_Missense_Mutation_p.E287G|TARS2_ENST00000463555.1_3'UTR|TARS2_ENST00000438568.2_3'UTR	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	369					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	GGGCACTGGGAGCATTATCAG	0.547																																					p.E369G		Atlas-SNP	.											.	TARS2	91	.	0			c.A1106G						.						81	72	75					1																	150470091		2203	4300	6503	SO:0001583	missense	80222	exon10			ACTGGGAGCATTA	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	30740	protein-coding gene	gene with protein product	"threonine tRNA ligase 2, mitochondrial"	612805	"threonyl-tRNA synthetase-like 1"	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.1106A>G	chr1.hg19:g.150470091A>G	ENSP00000358060:p.Glu369Gly	79.0	0.0		78.0	16.0	NM_025150	Q53GW7|Q96I50|Q9H9V2	Missense_Mutation	SNP	ENST00000369064.3	hg19	CCDS952.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.191271	0.58017	.	.	ENSG00000143374	ENST00000369054;ENST00000369064;ENST00000369051;ENST00000369052	T;T;T	0.70045	-0.45;-0.45;-0.45	5.53	4.38	0.52667	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.126361	0.53938	D	0.000057	T	0.43678	0.1258	L	0.43598	1.365	0.80722	D	1	B;B;B	0.27140	0.169;0.07;0.039	B;B;B	0.29524	0.103;0.046;0.032	T	0.42498	-0.9448	10	0.37606	T	0.19	-20.8973	12.4379	0.55610	0.8597:0.1403:0.0:0.0	.	239;94;369	Q9H9V2;E7EVR9;Q9BW92	.;.;SYTM_HUMAN	G	239;369;94;94	ENSP00000358050:E239G;ENSP00000358060:E369G;ENSP00000358047:E94G	ENSP00000358047:E94G	E	+	2	0	TARS2	148736715	1.000000	0.71417	0.995000	0.50966	0.757000	0.42996	5.488000	0.66869	1.071000	0.40834	0.533000	0.62120	GAG	.	.		0.547	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150		G	150470091	A	G	150470091	3	3	23	1	0	0	0	0	1	0	0	0	15575	304	11	2	1144	2	TARS2	1	150470091	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3089706	150470091	98780530	74	2140										
ANXA9	8416	hgsc.bcm.edu	37	chr1	150958820	150958820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	accccaccccagatttccagGtggaggctgtggatgacatc	11	13	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:150958820G>A	ENST00000368947.4	+	8	957	c.481G>A	c.(481-483)Gtg>Atg	p.V161M		NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	161					single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGATTTCCAGGTGGAGGCTGT	0.562																																					p.V161M		Atlas-SNP	.											.	ANXA9	28	.	0			c.G481A						.						71	64	66					1																	150958820		2203	4300	6503	SO:0001583	missense	8416	exon8			TTCCAGGTGGAGG	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"Annexins"	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.481G>A	chr1.hg19:g.150958820G>A	ENSP00000357943:p.Val161Met	102.0	0.0		97.0	32.0	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Missense_Mutation	SNP	ENST00000368947.4	hg19	CCDS975.2	.	.	.	.	.	.	.	.	.	.	G	11.99	1.802630	0.31869	.	.	ENSG00000143412	ENST00000368947	T	0.03496	3.91	5.1	3.21	0.36854	.	0.398477	0.25704	N	0.028842	T	0.01523	0.0049	L	0.42245	1.32	0.24730	N	0.993099	B	0.22276	0.067	B	0.30716	0.119	T	0.42865	-0.9426	10	0.72032	D	0.01	.	6.7983	0.23736	0.0914:0.0:0.7347:0.1739	.	161	O76027	ANXA9_HUMAN	M	161	ENSP00000357943:V161M	ENSP00000357943:V161M	V	+	1	0	ANXA9	149225444	1.000000	0.71417	1.000000	0.80357	0.666000	0.39218	1.395000	0.34520	0.651000	0.30788	0.462000	0.41574	GTG	.	.		0.562	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568		A	150958820	G	A	150958820	3	1	23	1	0	0	0	0	1	0	0	0	725	1261	44	3	503	3	ANXA9	1	150958820	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	488729	150958820	98291801	75	2141										
LCE1A	353131	hgsc.bcm.edu	37	chr1	152799972	152799972	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcctgccagcagagccagcaGcagtgccagccccctcccaa	9	19	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:152799972G>A	ENST00000335123.2	+	1	24	c.24G>A	c.(22-24)caG>caA	p.Q8Q		NM_178348.2	NP_848125.1	Q5T7P2	LCE1A_HUMAN	late cornified envelope 1A	8	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	8	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGAGCCAGCAGCAGTGCCAGC	0.612																																					p.Q8Q		Atlas-SNP	.											.	LCE1A	23	.	0			c.G24A						.						51	61	58					1																	152799972		2203	4300	6503	SO:0001819	synonymous_variant	353131	exon1			CCAGCAGCAGTGC		CCDS1028.1	1q21.3	2011-01-28			ENSG00000186844	ENSG00000186844		"Late cornified envelopes"	29459	protein-coding gene	gene with protein product		612603				11698679	Standard	NM_178348		Approved	LEP1	uc010pdw.2	Q5T7P2	OTTHUMG00000012447	ENST00000335123.2:c.24G>A	chr1.hg19:g.152799972G>A		352.0	0.0		366.0	20.0	NM_178348		Silent	SNP	ENST00000335123.2	hg19	CCDS1028.1																																																																																			.	.		0.612	LCE1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034660.2	NM_178348		A	152799972	G	A	152799972	2	1	23	1	0	0	0	0	0	0	0	1	8668	962	34	3		3	LCE1A	1	152799972	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1841152	152799972	96450649	76	2142										
GATAD2B	57459	hgsc.bcm.edu	37	chr1	153784289	153784289	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atggagcgggcagatgtgggTatgccacgctggaggctgct	18	8	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:153784289T>C	ENST00000368655.4	-	10	1809	c.1566A>G	c.(1564-1566)atA>atG	p.I522M		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	522					ATP-dependent chromatin remodeling (GO:0043044)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	38	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CAGATGTGGGTATGCCACGCT	0.522																																					p.I522M		Atlas-SNP	.											.	GATAD2B	62	.	0			c.A1566G						.						60	59	59					1																	153784289		2203	4300	6503	SO:0001583	missense	57459	exon10			TGTGGGTATGCCA	AF411836	CCDS1054.1	1q21.3	2013-01-25			ENSG00000143614	ENSG00000143614		"GATA zinc finger domain containing"	30778	protein-coding gene	gene with protein product	"transcription repressor p66 beta component of the MeCP1 complex"	614998				10574461, 11756549	Standard	NM_020699		Approved	P66beta	uc001fdb.4	Q8WXI9	OTTHUMG00000037162	ENST00000368655.4:c.1566A>G	chr1.hg19:g.153784289T>C	ENSP00000357644:p.Ile522Met	99.0	0.0		112.0	44.0	NM_020699	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Missense_Mutation	SNP	ENST00000368655.4	hg19	CCDS1054.1	.	.	.	.	.	.	.	.	.	.	t	15.87	2.961229	0.53400	.	.	ENSG00000143614	ENST00000368655	T	0.32515	1.45	5.52	-5.57	0.02521	.	0.172208	0.51477	N	0.000084	T	0.03827	0.0108	N	0.22421	0.69	0.26593	N	0.973165	B	0.18461	0.028	B	0.09377	0.004	T	0.23332	-1.0191	10	0.35671	T	0.21	-16.6883	0.536	0.00636	0.3899:0.1497:0.2224:0.238	.	522	Q8WXI9	P66B_HUMAN	M	522	ENSP00000357644:I522M	ENSP00000357644:I522M	I	-	3	3	GATAD2B	152050913	0.828000	0.29307	0.965000	0.40720	0.994000	0.84299	-0.193000	0.09573	-0.721000	0.04929	-0.359000	0.07587	ATA	.	.		0.522	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699		C	153784289	T	C	153784289	3	2	23	1	0	0	0	0	1	0	0	0	6269	1628	57	2	223	2	GATAD2B	1	153784289	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	984317	153784289	95466332	77	2143										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153912225	153912225	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccctgcggccacacactgcCtcgtagtctgtcagtaggaa	11	14	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:153912225C>A	ENST00000361217.4	-	12	2077	c.1659G>T	c.(1657-1659)gaG>gaT	p.E553D		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	553					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CACACACTGCCTCGTAGTCTG	0.632																																					p.E553D		Atlas-SNP	.											.	DENND4B	210	.	0			c.G1659T						.						50	60	57					1																	153912225		2084	4208	6292	SO:0001583	missense	9909	exon12			CACTGCCTCGTAG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.1659G>T	chr1.hg19:g.153912225C>A	ENSP00000354597:p.Glu553Asp	94.0	0.0		64.0	26.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	C	3.956	-0.011375	0.07727	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06142	3.34;3.34	5.14	4.21	0.49690	.	0.260438	0.38111	N	0.001816	T	0.00580	0.0019	N	0.01352	-0.895	0.31911	N	0.614708	B	0.06786	0.001	B	0.04013	0.001	T	0.49570	-0.8926	10	0.02654	T	1	-23.6371	7.8022	0.29180	0.0:0.6486:0.2643:0.087	.	553	O75064	DEN4B_HUMAN	D	553;564	ENSP00000354597:E553D;ENSP00000357635:E564D	ENSP00000354597:E553D	E	-	3	2	DENND4B	152178849	0.925000	0.31364	1.000000	0.80357	0.992000	0.81027	0.345000	0.19979	2.689000	0.91719	0.462000	0.41574	GAG	.	.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		A	153912225	C	A	153912225	3	1	23	1	0	0	0	0	1	0	0	0	4436	680	24	3	2899	3	DENND4B	1	153912225	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	127936	153912225	95338396	78	2144										
UBE2Q1	55585	hgsc.bcm.edu	37	chr1	154527247	154527247	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcttcatcttctgaagacacGtcttcctgtgtgcactgcag	8	12	5	2	rs372396696		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:154527247G>A	ENST00000292211.4	-	4	631	c.552C>T	c.(550-552)gaC>gaT	p.D184D	UBE2Q1_ENST00000497453.1_5'UTR|UBE2Q1-AS1_ENST00000441613.1_RNA	NM_017582.6	NP_060052.3	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q family member 1	184					embryo implantation (GO:0007566)|fertilization (GO:0009566)|mating behavior (GO:0007617)|prolactin secretion (GO:0070459)|protein ubiquitination (GO:0016567)|reproductive system development (GO:0061458)|suckling behavior (GO:0001967)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			CTGAAGACACGTCTTCCTGTG	0.557																																					p.D184D		Atlas-SNP	.											UBE2Q1,NS,carcinoma,0,1	UBE2Q1	35	.	0			c.C552T						.	G		0,4406		0,0,2203	67	59	62		552	-8.5	0.7	1		62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	UBE2Q1	NM_017582.6		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		184/423	154527247	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55585	exon4			AGACACGTCTTCC	AJ243666	CCDS1069.1	1q22	2008-05-02	2008-05-02	2005-08-05	ENSG00000160714	ENSG00000160714		"Ubiquitin-conjugating enzymes E2"	15698	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2Q (putative)"	UBE2Q			Standard	NM_017582		Approved	PRO3094, NICE-5	uc001fff.1	Q7Z7E8	OTTHUMG00000037265	ENST00000292211.4:c.552C>T	chr1.hg19:g.154527247G>A		268.0	0.0		270.0	98.0	NM_017582	B4DF92|Q3B841|Q5I0X2|Q6IS04|Q6P7P2|Q96MV4|Q9BVX5|Q9UGL6	Silent	SNP	ENST00000292211.4	hg19	CCDS1069.1																																																																																			.	.		0.557	UBE2Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090704.1	NM_017582		A	154527247	G	A	154527247	2	1	23	1	0	0	0	0	0	0	0	1	16884	1136	40	1		1	UBE2Q1	1	154527247	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	615022	154527247	94723374	79	2145										
CHRNB2	1141	hgsc.bcm.edu	37	chr1	154542783	154542783	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctgaagagtttgacaacaTgaagaaagttcggctccctt	10	9	0	5			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:154542783T>C	ENST00000368476.3	+	4	569	c.305T>C	c.(304-306)aTg>aCg	p.M102T		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	102					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	TTTGACAACATGAAGAAAGTT	0.542																																					p.M102T		Atlas-SNP	.											.	CHRNB2	74	.	0			c.T305C						.						77	65	69					1																	154542783		2203	4300	6503	SO:0001583	missense	1141	exon4			ACAACATGAAGAA	U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1962	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 2 (neuronal)"	118507	"cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.305T>C	chr1.hg19:g.154542783T>C	ENSP00000357461:p.Met102Thr	127.0	0.0		123.0	48.0	NM_000748	Q9UEH9	Missense_Mutation	SNP	ENST00000368476.3	hg19	CCDS1070.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.321818	0.60634	.	.	ENSG00000160716	ENST00000368476	T	0.78816	-1.21	5.03	5.03	0.67393	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.54759	0.1878	N	0.17631	0.505	0.58432	D	0.999997	P	0.42161	0.772	B	0.38755	0.281	T	0.67787	-0.5580	10	0.87932	D	0	.	14.6012	0.68443	0.0:0.0:0.0:1.0	.	102	P17787	ACHB2_HUMAN	T	102	ENSP00000357461:M102T	ENSP00000357461:M102T	M	+	2	0	CHRNB2	152809407	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.868000	0.87116	2.114000	0.64651	0.460000	0.39030	ATG	.	.		0.542	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748		C	154542783	T	C	154542783	3	2	23	1	0	0	0	0	1	0	0	0	3393	1464	51	2	319	2	CHRNB2	1	154542783	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	15536	154542783	94707838	80	2146										
PKLR	5313	hgsc.bcm.edu	37	chr1	155261612	155261612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agatggcttctggaggttcaCggtaaagcaaggggaagact	15	6	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:155261612C>T	ENST00000342741.4	-	10	1591	c.1553G>A	c.(1552-1554)cGt>cAt	p.R518H	PKLR_ENST00000392414.3_Missense_Mutation_p.R487H	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	518					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	TGGAGGTTCACGGTAAAGCAA	0.582																																					p.R518H		Atlas-SNP	.											.	PKLR	70	.	0			c.G1553A						.						94	92	93					1																	155261612		2203	4300	6503	SO:0001583	missense	5313	exon10			GGTTCACGGTAAA	BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.1553G>A	chr1.hg19:g.155261612C>T	ENSP00000339933:p.Arg518His	273.0	0.0		267.0	99.0	NM_000298	O75758|P11973	Missense_Mutation	SNP	ENST00000342741.4	hg19	CCDS1109.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.700978	0.48307	.	.	ENSG00000143627	ENST00000423816;ENST00000392414;ENST00000342741;ENST00000271946	D;D	0.99042	-5.36;-5.36	4.85	2.99	0.34606	Pyruvate kinase, C-terminal (2);Pyruvate kinase, alpha/beta (1);	0.179887	0.46145	N	0.000302	D	0.93890	0.8045	N	0.25957	0.775	0.38695	D	0.952866	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	D	0.91033	0.4865	10	0.45353	T	0.12	-0.5084	9.2448	0.37518	0.0:0.8232:0.0:0.1768	.	518;509	P30613;B1AVT1	KPYR_HUMAN;.	H	543;487;518;432	ENSP00000376214:R487H;ENSP00000339933:R518H	ENSP00000271946:R432H	R	-	2	0	PKLR	153528236	0.924000	0.31332	0.968000	0.41197	0.990000	0.78478	0.758000	0.26447	0.766000	0.33244	0.563000	0.77884	CGT	.	.		0.582	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298		T	155261612	C	T	155261612	3	4	23	1	0	0	0	0	1	0	0	0	11985	536	19	1	179	1	PKLR	1	155261612	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	718829	155261612	93989009	81	2147										
FDPS	2224	hgsc.bcm.edu	37	chr1	155282158	155282158	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgctgatagtctccagcgggCctggactgtgggctggtgtg	17	9	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:155282158C>T	ENST00000356657.6	+	4	614	c.452C>T	c.(451-453)gCc>gTc	p.A151V	FDPS_ENST00000487002.1_3'UTR|FDPS_ENST00000368356.4_Missense_Mutation_p.A151V|FDPS_ENST00000447866.1_Missense_Mutation_p.A85V	NM_001135821.1	NP_001129293.1	P14324	FPPS_HUMAN	farnesyl diphosphate synthase	151					cholesterol biosynthetic process (GO:0006695)|farnesyl diphosphate biosynthetic process (GO:0045337)|geranyl diphosphate biosynthetic process (GO:0033384)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dimethylallyltranstransferase activity (GO:0004161)|geranyltranstransferase activity (GO:0004337)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)	CTCCAGCGGGCCTGGACTGTG	0.572																																					p.A151V		Atlas-SNP	.											.	FDPS	41	.	0			c.C452T						.						61	51	54					1																	155282158		2203	4300	6503	SO:0001583	missense	2224	exon4			AGCGGGCCTGGAC	J05262	CCDS1110.1, CCDS44241.1, CCDS72940.1	1q22	2012-07-13	2010-06-24		ENSG00000160752	ENSG00000160752	2.5.1.1, 2.5.1.10		3631	protein-coding gene	gene with protein product	"farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase"	134629				1968462	Standard	NM_002004		Approved		uc001fkc.2	P14324	OTTHUMG00000013909	ENST00000356657.6:c.452C>T	chr1.hg19:g.155282158C>T	ENSP00000349078:p.Ala151Val	61.0	0.0		65.0	6.0	NM_001135821	D3DV91|E9PCI9|Q96G29	Missense_Mutation	SNP	ENST00000356657.6	hg19	CCDS1110.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.959479	0.74016	.	.	ENSG00000160752	ENST00000447866;ENST00000368356;ENST00000356657	T;T;T	0.64803	-0.12;-0.12;-0.12	4.66	4.66	0.58398	Terpenoid synthase (2);	0.136032	0.34088	N	0.004275	T	0.49966	0.1588	M	0.62016	1.91	0.80722	D	1	B	0.30033	0.266	B	0.32342	0.144	T	0.57831	-0.7743	10	0.52906	T	0.07	-17.0909	14.9164	0.70801	0.0:1.0:0.0:0.0	.	151	P14324	FPPS_HUMAN	V	85;151;151	ENSP00000391755:A85V;ENSP00000357340:A151V;ENSP00000349078:A151V	ENSP00000349078:A151V	A	+	2	0	FDPS	153548782	1.000000	0.71417	0.964000	0.40570	0.884000	0.51177	4.480000	0.60243	2.582000	0.87167	0.462000	0.41574	GCC	.	.		0.572	FDPS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039053.1	NM_002004		T	155282158	C	T	155282158	3	4	23	1	0	0	0	0	1	0	0	0	5811	739	26	3	462	3	FDPS	1	155282158	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	20546	155282158	93968463	82	2148										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155450461	155450461	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctctgatctttctaattctaGcccttttggagaccggcatg	8	11	4	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:155450461G>T	ENST00000368346.3	-	3	2839	c.2200C>A	c.(2200-2202)Cta>Ata	p.L734I	ASH1L_ENST00000392403.3_Missense_Mutation_p.L734I			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	734					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TCTAATTCTAGCCCTTTTGGA	0.393																																					p.L734I		Atlas-SNP	.											.	ASH1L	279	.	0			c.C2200A						.						68	72	70					1																	155450461		2203	4300	6503	SO:0001583	missense	55870	exon3			ATTCTAGCCCTTT	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.2200C>A	chr1.hg19:g.155450461G>T	ENSP00000357330:p.Leu734Ile	73.0	0.0		75.0	34.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	G	16.83	3.230756	0.58777	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.91631	-2.88;-2.88	5.38	5.38	0.77491	.	0.000000	0.47852	D	0.000206	D	0.82449	0.5039	N	0.14661	0.345	0.80722	D	1	P;P	0.41784	0.649;0.762	B;B	0.42555	0.219;0.391	T	0.82635	-0.0360	10	0.23302	T	0.38	.	18.916	0.92506	0.0:0.0:1.0:0.0	.	734;734	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	I	734	ENSP00000357330:L734I;ENSP00000376204:L734I	ENSP00000357330:L734I	L	-	1	2	ASH1L	153717085	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.445000	0.44899	2.791000	0.96007	0.650000	0.86243	CTA	.	.		0.393	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		T	155450461	G	T	155450461	3	4	23	1	0	0	0	0	1	0	0	0	1041	962	34	3	6798	3	ASH1L	1	155450461	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	168303	155450461	93800160	83	2149										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155452064	155452064	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcctttaaatcaggatcccgGctaccaagaagagtagatgg	10	9	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:155452064G>A	ENST00000368346.3	-	3	1236	c.597C>T	c.(595-597)agC>agT	p.S199S	ASH1L_ENST00000392403.3_Silent_p.S199S|ASH1L_ENST00000548830.1_3'UTR			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	199					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CAGGATCCCGGCTACCAAGAA	0.423																																					p.S199S		Atlas-SNP	.											.	ASH1L	279	.	0			c.C597T						.						131	131	131					1																	155452064		2203	4300	6503	SO:0001819	synonymous_variant	55870	exon3			ATCCCGGCTACCA	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.597C>T	chr1.hg19:g.155452064G>A		117.0	0.0		117.0	5.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.		0.423	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155452064	G	A	155452064	2	1	23	1	0	0	0	0	0	0	0	1	1041	1194	42	3		3	ASH1L	1	155452064	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1603	155452064	93798557	84	2150										
LMNA	4000	hgsc.bcm.edu	37	chr1	156106161	156106161	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagcacgcacgcactagcggGcgcgtggccgtggaggaggt	18	12	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:156106161G>T	ENST00000368300.4	+	7	1526	c.1314G>T	c.(1312-1314)ggG>ggT	p.G438G	LMNA_ENST00000368297.1_Silent_p.G357G|LMNA_ENST00000368299.3_Silent_p.G438G|LMNA_ENST00000368301.2_Silent_p.G438G|LMNA_ENST00000361308.4_Silent_p.G438G|LMNA_ENST00000473598.2_Silent_p.G339G|LMNA_ENST00000392353.3_Silent_p.G357G|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000347559.2_Silent_p.G438G|LMNA_ENST00000448611.2_Silent_p.G326G	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	438	LTD.|Tail.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					GCACTAGCGGGCGCGTGGCCG	0.612									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												p.G438G		Atlas-SNP	.											.	LMNA	31	.	0			c.G1314T						.						40	45	43					1																	156106161		2203	4299	6502	SO:0001819	synonymous_variant	4000	exon7	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	TAGCGGGCGCGTG	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1314G>T	chr1.hg19:g.156106161G>T		94.0	0.0		77.0	18.0	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	hg19	CCDS1129.1	.	.	.	.	.	.	.	.	.	.	G	7.183	0.589956	0.13812	.	.	ENSG00000160789	ENST00000392355	.	.	.	5.74	-3.71	0.04424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7858	0.40675	0.0683:0.5407:0.2967:0.0943	.	.	.	.	.	-1	.	.	.	+	.	.	LMNA	154372785	0.014000	0.17966	0.989000	0.46669	0.649000	0.38597	-0.910000	0.04054	-0.203000	0.10251	0.655000	0.94253	.	.	.		0.612	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707		T	156106161	G	T	156106161	2	4	23	1	0	0	0	0	0	0	0	1	8857	1190	42	3		3	LMNA	1	156106161	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	654097	156106161	93144460	85	2151										
INSRR	3645	hgsc.bcm.edu	37	chr1	156814001	156814001	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaagaaaccaagggcagcaaGaacgatgagcagcgtgagcc	14	9	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:156814001G>T	ENST00000368195.3	-	15	3205	c.2809C>A	c.(2809-2811)Ctt>Att	p.L937I	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	937					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AGGGCAGCAAGAACGATGAGC	0.582																																					p.L937I		Atlas-SNP	.											.	INSRR	309	.	0			c.C2809A						.						90	87	88					1																	156814001		2203	4300	6503	SO:0001583	missense	3645	exon15			CAGCAAGAACGAT	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2809C>A	chr1.hg19:g.156814001G>T	ENSP00000357178:p.Leu937Ile	75.0	0.0		75.0	42.0	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.250541	0.39797	.	.	ENSG00000027644	ENST00000368195	T	0.75477	-0.94	5.18	5.18	0.71444	.	0.000000	0.38058	N	0.001829	T	0.79598	0.4473	.	.	.	0.45791	D	0.998679	D	0.69078	0.997	D	0.72625	0.978	T	0.76479	-0.2944	9	0.25106	T	0.35	.	15.4079	0.74893	0.0:0.0:1.0:0.0	.	937	P14616	INSRR_HUMAN	I	937	ENSP00000357178:L937I	ENSP00000357178:L937I	L	-	1	0	INSRR	155080625	1.000000	0.71417	0.999000	0.59377	0.964000	0.63967	4.948000	0.63590	2.398000	0.81561	0.462000	0.41574	CTT	.	.		0.582	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		T	156814001	G	T	156814001	3	4	23	1	0	0	0	0	1	0	0	0	7783	942	33	3	1115	3	INSRR	1	156814001	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	707840	156814001	92436620	86	2152										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156914894	156914894	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtagccctctaaacggtggcGgttctctgtttgttttaccg	11	10	2	0	rs140673049		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:156914894G>A	ENST00000361409.2	-	29	3530	c.2788C>T	c.(2788-2790)Cgc>Tgc	p.R930C	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.R970C|ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000315174.8_Missense_Mutation_p.R346C	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	930					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AAACGGTGGCGGTTCTCTGTT	0.597																																					p.R970C		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.C2908T						.	G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	109	112	111		2788,2908	5.3	1	1	dbSNP_134	111	0,8600		0,0,4300	no	missense,missense	ARHGEF11	NM_014784.2,NM_198236.1	180,180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	930/1523,970/1563	156914894	1,13005	2203	4300	6503	SO:0001583	missense	9826	exon30			GGTGGCGGTTCTC	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.2788C>T	chr1.hg19:g.156914894G>A	ENSP00000354644:p.Arg930Cys	108.0	0.0		99.0	6.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	hg19	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	G	16.02	3.005245	0.54254	2.27E-4	0.0	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.69435	-0.4;-0.4;-0.4	5.28	5.28	0.74379	Dbl homology (DH) domain (1);	0.242198	0.28853	N	0.013938	T	0.44891	0.1315	L	0.42245	1.32	0.58432	D	0.999999	B;B;B	0.23735	0.08;0.09;0.035	B;B;B	0.19148	0.024;0.016;0.015	T	0.53265	-0.8463	10	0.87932	D	0	-11.8718	10.5742	0.45217	0.0:0.142:0.7113:0.1467	.	346;930;970	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	C	970;930;346	ENSP00000357177:R970C;ENSP00000354644:R930C;ENSP00000313470:R346C	ENSP00000313470:R346C	R	-	1	0	ARHGEF11	155181518	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.412000	0.52679	2.756000	0.94617	0.650000	0.86243	CGC	.	G|1.000;A|0.000		0.597	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		A	156914894	G	A	156914894	3	1	23	1	0	0	0	0	1	0	0	0	896	1116	39	1	1828	1	ARHGEF11	1	156914894	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	100893	156914894	92335727	87	2153										
FCRL1	115350	hgsc.bcm.edu	37	chr1	157772454	157772454	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcacatcagcgacagggaccCctgtgtggacacaagatgac	11	12	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:157772454C>A	ENST00000368176.3	-	4	387	c.320G>T	c.(319-321)aGg>aTg	p.R107M	FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000358292.3_Splice_Site_p.R107M|FCRL1_ENST00000491942.1_Splice_Site_p.R107M	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GACAGGGACCCCTGTGTGGAC	0.532																																					p.R107M	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.G320T						.						32	32	32					1																	157772454		2203	4300	6503	SO:0001630	splice_region_variant	115350	exon4			GGGACCCCTGTGT	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.320-1G>T	chr1.hg19:g.157772454C>A		68.0	0.0		72.0	31.0	NM_001159397	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Missense_Mutation	SNP	ENST00000368176.3	hg19	CCDS1170.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.994161	0.35226	.	.	ENSG00000163534	ENST00000358292;ENST00000368176;ENST00000491942	T;T;T	0.46451	0.87;1.03;1.04	5.41	4.48	0.54585	Immunoglobulin-like fold (1);	1.789910	0.03248	N	0.181392	T	0.59770	0.2218	M	0.86420	2.815	0.31474	N	0.667962	D;D;D	0.89917	1.0;1.0;0.994	D;D;P	0.76071	0.976;0.987;0.753	T	0.14896	-1.0456	10	0.34782	T	0.22	.	11.7722	0.51965	0.1762:0.8238:0.0:0.0	.	107;107;107	Q96LA6-3;Q96LA6-2;Q96LA6	.;.;FCRL1_HUMAN	M	107	ENSP00000351039:R107M;ENSP00000357158:R107M;ENSP00000418130:R107M	ENSP00000351039:R107M	R	-	2	0	FCRL1	156039078	0.991000	0.36638	0.800000	0.32199	0.032000	0.12392	3.843000	0.55865	1.398000	0.46701	-0.181000	0.13052	AGG	.	.		0.532	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938	Missense_Mutation	A	157772454	C	A	157772454	5	1	23	1	0	0	0	0	0	0	1	0	5802	637	22	3	1067	3	FCRL1	1	157772454	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	857560	157772454	91478167	88	2154										
OR10R2	343406	hgsc.bcm.edu	37	chr1	158449993	158449993	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catcaatctactttctgtggCcaggacaatctccttcaact	5	13	5	0	rs200874337		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:158449993C>T	ENST00000368152.1	+	1	326	c.326C>T	c.(325-327)gCc>gTc	p.A109V	RP11-144L1.4_ENST00000419738.1_RNA|RP11-144L1.4_ENST00000426251.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A109G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					CTTTCTGTGGCCAGGACAATC	0.443																																					p.A109V		Atlas-SNP	.											OR10R2,NS,NS,0,1	OR10R2	81	.	1	Substitution - Missense(1)	pancreas(1)	c.C326T						.	C	VAL/ALA	0,4406		0,0,2203	360	304	323		326	1.1	1	1		323	1,8599	1.2+/-3.3	0,1,4299	no	missense	OR10R2	NM_001004472.1	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	109/336	158449993	1,13005	2203	4300	6503	SO:0001583	missense	343406	exon1			CTGTGGCCAGGAC	AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"GPCR / Class A : Olfactory receptors"	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.326C>T	chr1.hg19:g.158449993C>T	ENSP00000357134:p.Ala109Val	96.0	0.0		99.0	34.0	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	hg19	CCDS30898.1	.	.	.	.	.	.	.	.	.	.	c	9.721	1.159721	0.21454	0.0	1.16E-4	ENSG00000198965	ENST00000368152	T	0.03035	4.07	4.28	1.11	0.20524	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00724	0.0024	N	0.12637	0.245	0.09310	N	1	B	0.22211	0.066	B	0.19391	0.025	T	0.47736	-0.9094	9	0.45353	T	0.12	.	4.4412	0.11575	0.1614:0.5368:0.0:0.3018	.	109	Q8NGX6	O10R2_HUMAN	V	109	ENSP00000357134:A109V	ENSP00000357134:A109V	A	+	2	0	OR10R2	156716617	0.000000	0.05858	0.985000	0.45067	0.962000	0.63368	-2.129000	0.01313	0.425000	0.26087	0.655000	0.94253	GCC	.	C|0.999;T|0.001		0.443	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472		T	158449993	C	T	158449993	3	4	23	1	0	0	0	0	1	0	0	0	10926	739	26	3	328	3	OR10R2	1	158449993	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	677539	158449993	90800628	89	2155										
IGSF9	57549	hgsc.bcm.edu	37	chr1	159897228	159897228	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cggcggcggcggaaggccagGaattcctcccgaagggcagc	17	13	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:159897228G>T	ENST00000368094.1	-	21	3644	c.3447C>A	c.(3445-3447)ttC>ttA	p.F1149L	IGSF9_ENST00000493195.1_5'UTR|IGSF9_ENST00000361509.3_Missense_Mutation_p.F1133L|TAGLN2_ENST00000478033.1_5'Flank|TAGLN2_ENST00000320307.4_5'Flank|TAGLN2_ENST00000368097.4_5'Flank	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	1149					dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GGAAGGCCAGGAATTCCTCCC	0.642																																					p.F1149L		Atlas-SNP	.											.	IGSF9	123	.	0			c.C3447A						.						47	52	50					1																	159897228		2203	4299	6502	SO:0001583	missense	57549	exon21			GGCCAGGAATTCC	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.3447C>A	chr1.hg19:g.159897228G>T	ENSP00000357073:p.Phe1149Leu	332.0	0.0		324.0	111.0	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	hg19	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	G	34	5.372148	0.95923	.	.	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.77229	-1.08;-1.02	5.52	5.52	0.82312	.	0.000000	0.43747	D	0.000522	T	0.73697	0.3620	L	0.29908	0.895	0.36065	D	0.841694	P;B	0.49447	0.924;0.064	P;B	0.60682	0.878;0.028	T	0.73833	-0.3858	9	.	.	.	-17.7567	14.9501	0.71067	0.0:0.0:1.0:0.0	.	1149;687	Q9P2J2;C9JI81	TUTLA_HUMAN;.	L	1133;1149;687	ENSP00000355049:F1133L;ENSP00000357073:F1149L	.	F	-	3	2	IGSF9	158163852	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.466000	0.53071	2.608000	0.88229	0.563000	0.77884	TTC	.	.		0.642	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		T	159897228	G	T	159897228	3	4	23	1	0	0	0	0	1	0	0	0	7614	1165	41	3	96	3	IGSF9	1	159897228	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1447235	159897228	89353393	90	2156										
ATP1A2	477	hgsc.bcm.edu	37	chr1	160109518	160109518	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcatgggtgtagccctccgcAtgtacccgctcaagtgagtg	13	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:160109518A>T	ENST00000361216.3	+	21	3018	c.2929A>T	c.(2929-2931)Atg>Ttg	p.M977L	ATP1A2_ENST00000392233.3_Missense_Mutation_p.M977L	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	977					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			AGCCCTCCGCATGTACCCGCT	0.562																																					p.M977L		Atlas-SNP	.											.	ATP1A2	167	.	0			c.A2929T						.						90	80	84					1																	160109518		2203	4300	6503	SO:0001583	missense	477	exon21			CTCCGCATGTACC	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.2929A>T	chr1.hg19:g.160109518A>T	ENSP00000354490:p.Met977Leu	84.0	0.0		88.0	37.0	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	hg19	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.514058	0.64522	.	.	ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000435866	D;D	0.95272	-3.66;-3.66	4.37	4.37	0.52481	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.93566	0.7946	L	0.52573	1.65	0.58432	D	0.999998	P;P	0.40398	0.521;0.716	P;P	0.55508	0.668;0.777	D	0.93040	0.6456	10	0.40728	T	0.16	.	11.8574	0.52446	1.0:0.0:0.0:0.0	.	877;977	F5GXJ7;P50993	.;AT1A2_HUMAN	L	977;977;680	ENSP00000354490:M977L;ENSP00000376066:M977L	ENSP00000354490:M977L	M	+	1	0	ATP1A2	158376142	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.270000	0.78493	1.960000	0.56953	0.533000	0.62120	ATG	.	.		0.562	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		T	160109518	A	T	160109518	3	4	23	1	0	0	0	0	1	0	0	0	1129	217	8	4	3011	4	ATP1A2	1	160109518	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	212290	160109518	89141103	91	2157										
SLAMF1	6504	hgsc.bcm.edu	37	chr1	160604472	160604472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gttgctgatagggttgctcaCggtgcagatgtagatattgt	14	5	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:160604472C>T	ENST00000302035.6	-	3	980	c.631G>A	c.(631-633)Gtg>Atg	p.V211M	SLAMF1_ENST00000235739.5_Missense_Mutation_p.V211M|SLAMF1_ENST00000538290.1_Missense_Mutation_p.V211M|SLAMF1_ENST00000355199.3_Missense_Mutation_p.V211M	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	211	Ig-like C2-type.				lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GGGTTGCTCACGGTGCAGATG	0.607																																					p.V211M		Atlas-SNP	.											SLAMF1,NS,carcinoma,0,1	SLAMF1	74	.	0			c.G631A						.						164	148	154					1																	160604472		2203	4300	6503	SO:0001583	missense	6504	exon3			TGCTCACGGTGCA	U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10903	protein-coding gene	gene with protein product		603492	"signaling lymphocytic activation molecule"	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.631G>A	chr1.hg19:g.160604472C>T	ENSP00000306190:p.Val211Met	168.0	1.0		146.0	73.0	NM_003037	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	hg19	CCDS1207.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.585236	0.28268	.	.	ENSG00000117090	ENST00000302035;ENST00000235739;ENST00000538290;ENST00000355199	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	4.3	4.3	0.51218	Immunoglobulin-like (1);	0.508912	0.20685	N	0.087577	T	0.57961	0.2089	M	0.88450	2.955	0.09310	N	1	D	0.69078	0.997	P	0.56823	0.807	T	0.53961	-0.8364	10	0.72032	D	0.01	-22.4655	12.5815	0.56393	0.0:1.0:0.0:0.0	.	211	Q13291	SLAF1_HUMAN	M	211	ENSP00000306190:V211M;ENSP00000235739:V211M;ENSP00000438406:V211M;ENSP00000347333:V211M	ENSP00000235739:V211M	V	-	1	0	SLAMF1	158871096	0.008000	0.16893	0.020000	0.16555	0.016000	0.09150	2.513000	0.45494	2.680000	0.91292	0.650000	0.86243	GTG	.	.		0.607	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1			T	160604472	C	T	160604472	3	4	23	1	0	0	0	0	1	0	0	0	14382	536	19	1	396	1	SLAMF1	1	160604472	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	494954	160604472	88646149	92	2158										
MPZ	4359	hgsc.bcm.edu	37	chr1	161276499	161276499	+	Splice_Site	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccccatcccttctcacaccTttttcaaagacatacagcgt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:161276499delT	ENST00000533357.1	-	3	513	c.447delA	c.(445-447)aaa>aa	p.K149fs	MPZ_ENST00000336559.4_Splice_Site_p.K149fs|MPZ_ENST00000360451.6_Splice_Site_p.K159fs|MPZ_ENST00000491222.2_5'UTR|MPZ_ENST00000526189.1_Intron	NM_000530.6	NP_000521.2	P25189	MYP0_HUMAN	myelin protein zero	149					cell death (GO:0008219)|cell-cell junction maintenance (GO:0045217)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	10	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)	Breast(1374;0.181)	BRCA - Breast invasive adenocarcinoma(70;0.00376)			TTCTCACACCTTTTTCAAAGA	0.522																																					p.V150fs		Atlas-INDEL	.											.	MPZ	29	.	0			c.448delG						.						150	128	136					1																	161276499		2203	4300	6503	SO:0001630	splice_region_variant	4359	exon3			.	BC006491	CCDS1229.1, CCDS1229.2	1q22	2014-09-17	2008-08-01		ENSG00000158887	ENSG00000158887		"Immunoglobulin superfamily / V-set domain containing"	7225	protein-coding gene	gene with protein product		159440	"Charcot-Marie-Tooth neuropathy 1B"	CMT1, CMT1B		7693129	Standard	NM_000530		Approved	HMSNIB	uc001gaf.4	P25189	OTTHUMG00000034341	ENST00000533357.1:c.448+1A>-	chr1.hg19:g.161276499delT		173.0	0.0		145.0	11.0	NM_000530	Q16072|Q5VTH4|Q92677|Q9BR67	Frame_Shift_Del	DEL	ENST00000533357.1	hg19	CCDS1229.2																																																																																			.	.		0.522	MPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082987.2	NM_000530	Frame_Shift_Del	-	161276499	T	-	161276499	8	5	23	1	0	1	0	1	0	0	1	0	9757	1623	56	0	315	0	MPZ	1	161276499	Splice_Site	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	672027	161276499	87974122	93	2159										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171501935	171501935	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagaaaaagaaaaagaactaGaacggcagaaagaaaaggaa	10	3	0	6			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:171501935G>C	ENST00000338920.4	+	12	1939	c.1702G>C	c.(1702-1704)Gaa>Caa	p.E568Q	PRRC2C_ENST00000426496.2_Missense_Mutation_p.E568Q|PRRC2C_ENST00000367742.3_Missense_Mutation_p.E570Q|PRRC2C_ENST00000392078.3_Missense_Mutation_p.E570Q	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	568	Glu-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										aaaagaactagaacggcagaa	0.373																																					p.E568Q		Atlas-SNP	.											.	.	.	.	0			c.G1702C						.						33	36	35					1																	171501935		2190	4279	6469	SO:0001583	missense	23215	exon12			GAACTAGAACGGC	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.1702G>C	chr1.hg19:g.171501935G>C	ENSP00000343629:p.Glu568Gln	286.0	0.0		282.0	104.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	G	12.69	2.013741	0.35511	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080;ENST00000483654	T;T;T;T	0.06449	3.3;3.3;3.3;3.3	6.02	5.11	0.69529	.	0.181808	0.26959	N	0.021630	T	0.04363	0.0120	L	0.47716	1.5	0.30105	N	0.807104	P;P	0.49559	0.925;0.598	P;B	0.47075	0.536;0.188	T	0.24728	-1.0152	9	.	.	.	.	13.0212	0.58789	0.0745:0.0:0.9255:0.0	.	568;570	Q9Y520-4;E7EPN9	.;.	Q	570;568;568;570;568;324;326	ENSP00000375928:E570Q;ENSP00000410219:E568Q;ENSP00000356716:E570Q;ENSP00000343629:E568Q	.	E	+	1	0	PRRC2C	169768559	1.000000	0.71417	0.976000	0.42696	0.847000	0.48162	6.234000	0.72326	1.558000	0.49541	0.650000	0.86243	GAA	.	.		0.373	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		C	171501935	G	C	171501935	3	2	23	1	0	0	0	0	1	0	0	0	1321	943	33	4	1744	4	BAT2L2	1	171501935	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	10225436	171501935	77748686	94	2160										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171514805	171514805	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagtggatgctctatcacagTttgatctcaacaattatgca	7	8	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:171514805T>C	ENST00000338920.4	+	17	5182	c.4945T>C	c.(4945-4947)Ttt>Ctt	p.F1649L	PRRC2C_ENST00000426496.2_Missense_Mutation_p.F1649L|PRRC2C_ENST00000367742.3_Missense_Mutation_p.F1651L|PRRC2C_ENST00000392078.3_Missense_Mutation_p.F1651L	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1649					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TCTATCACAGTTTGATCTCAA	0.289																																					p.F1649L		Atlas-SNP	.											.	.	.	.	0			c.T4945C						.						68	66	66					1																	171514805		2203	4300	6503	SO:0001583	missense	23215	exon17			TCACAGTTTGATC	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4945T>C	chr1.hg19:g.171514805T>C	ENSP00000343629:p.Phe1649Leu	691.0	1.0		727.0	259.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	T	16.26	3.073650	0.55646	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.02446	4.29;4.29;4.29;4.29	5.5	5.5	0.81552	.	0.000000	0.45126	D	0.000382	T	0.09555	0.0235	M	0.75777	2.31	0.58432	D	0.999999	D	0.71674	0.998	D	0.80764	0.994	T	0.01030	-1.1475	10	0.87932	D	0	.	15.6564	0.77140	0.0:0.0:0.0:1.0	.	1649	Q9Y520-4	.	L	1651;1650;1649;1651;1649;1406	ENSP00000375928:F1651L;ENSP00000410219:F1649L;ENSP00000356716:F1651L;ENSP00000343629:F1649L	ENSP00000343629:F1649L	F	+	1	0	PRRC2C	169781429	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.695000	0.84257	2.103000	0.63969	0.524000	0.50904	TTT	.	.		0.289	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		C	171514805	T	C	171514805	3	2	23	1	0	0	0	0	1	0	0	0	1321	1725	60	2	5007	2	BAT2L2	1	171514805	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	12870	171514805	77735816	95	2161										
RABGAP1L	9910	hgsc.bcm.edu	37	chr1	174606551	174606551	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gttattactcgagatattcaTcgtacatttcccgcacatga	6	10	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:174606551T>C	ENST00000251507.4	+	14	1923	c.1749T>C	c.(1747-1749)caT>caC	p.H583H		NM_014857.4	NP_055672.3	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	0										NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						GAGATATTCATCGTACATTTC	0.358																																					p.H583H		Atlas-SNP	.											.	RABGAP1L	103	.	0			c.T1749C						.						114	103	107					1																	174606551		2203	4300	6503	SO:0001819	synonymous_variant	9910	exon14			TATTCATCGTACA	AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061			24663	protein-coding gene	gene with protein product		609238				10585558	Standard	NM_014857		Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000251507.4:c.1749T>C	chr1.hg19:g.174606551T>C		388.0	1.0		422.0	175.0	NM_014857	B7ZAA4	Silent	SNP	ENST00000251507.4	hg19	CCDS1314.1																																																																																			.	.		0.358	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084497.1	NM_001243765		C	174606551	T	C	174606551	2	2	23	1	0	0	0	0	0	0	0	1	12980	1432	50	2		2	RABGAP1L	1	174606551	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3091746	174606551	74644070	96	2162										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181680167	181680167	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcgccagcagcagattgagcGtgagctgaatggctaccgtg	15	10	0	4	rs575157426		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:181680167G>A	ENST00000367573.2	+	8	1133	c.1133G>A	c.(1132-1134)cGt>cAt	p.R378H	CACNA1E_ENST00000358338.5_Missense_Mutation_p.R329H|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R329H|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R378H|CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R378H|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R378H	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	378	Binding to the beta subunit. {ECO:0000250}.				calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CAGATTGAGCGTGAGCTGAAT	0.577													G|||	1	0.000199681	8e-04	0	5008	,	,		20107	0		0	False		,,,				2504	0				p.R378H		Atlas-SNP	.											CACNA1E_ENST00000367573,colon,carcinoma,0,2	CACNA1E	778	.	0			c.G1133A						.						66	72	70					1																	181680167		1986	4158	6144	SO:0001583	missense	777	exon8			TTGAGCGTGAGCT	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1133G>A	chr1.hg19:g.181680167G>A	ENSP00000356545:p.Arg378His	96.0	0.0		73.0	33.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.870022	0.91587	.	.	ENSG00000198216	ENST00000524607;ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.93906	-3.31;-3.31;-3.31;-3.31;-3.31;-3.31;-3.31	5.29	4.37	0.52481	.	0.109385	0.56097	D	0.000032	D	0.94640	0.8272	M	0.70595	2.14	0.80722	D	1	D;D	0.56287	0.975;0.975	P;P	0.52710	0.707;0.59	D	0.94675	0.7860	10	0.66056	D	0.02	.	14.8817	0.70537	0.0:0.0:0.8551:0.1449	.	378;378	Q15878-2;Q15878-3	.;.	H	378;378;378;329;329;378;378	ENSP00000432038:R378H;ENSP00000356542:R378H;ENSP00000434814:R378H;ENSP00000350183:R329H;ENSP00000351101:R329H;ENSP00000353222:R378H;ENSP00000356545:R378H	ENSP00000350183:R329H	R	+	2	0	CACNA1E	179946790	1.000000	0.71417	0.806000	0.32338	0.911000	0.54048	9.717000	0.98755	1.209000	0.43321	0.655000	0.94253	CGT	.	.		0.577	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181680167	G	A	181680167	3	1	23	1	0	0	0	0	1	0	0	0	2544	1145	40	1	1163	1	CACNA1E	1	181680167	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	7073616	181680167	67570454	97	2163										
DHX9	1660	hgsc.bcm.edu	37	chr1	182812563	182812563	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagagtgaagaagttccagcTtttggggtaagtacctatgg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:182812563delT	ENST00000367549.3	+	3	356	c.246delT	c.(244-246)gctfs	p.A82fs		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	82	Interaction with CREBBP.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						AAGTTCCAGCTTTTGGGGTAA	0.353																																					p.A82fs	Colon(69;210 1162 3697 13559 39565)	Atlas-Indel,Pindel	.											.	DHX9	114	.	0			c.245delC						.						122	116	118					1																	182812563		1837	4099	5936	SO:0001589	frameshift_variant	1660	exon3			.	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.246delT	chr1.hg19:g.182812563delT	ENSP00000356520:p.Ala82fs	70.0	0.0		82.0	32.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Frame_Shift_Del	DEL	ENST00000367549.3	hg19	CCDS41444.1																																																																																			.	.		0.353	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		-	182812563	T	-	182812563	7	5	23	1	0	1	0	1	0	0	0	0	4518	1596	56	0	252	0	DHX9	1	182812563	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	1132396	182812563	66438058	98	2164										
LAMC2	3918	hgsc.bcm.edu	37	chr1	183204833	183204833	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaagcggaagcggtagcccGgacggtgctgtggtgcaagg	20	8	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:183204833G>A	ENST00000264144.4	+	16	2489	c.2424G>A	c.(2422-2424)ccG>ccA	p.P808P	LAMC2_ENST00000493293.1_Silent_p.P808P	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	808	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						GCGGTAGCCCGGACGGTGCTG	0.557											OREG0014042	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P808P		Atlas-SNP	.											.	LAMC2	113	.	0			c.G2424A						.						88	82	84					1																	183204833		2203	4300	6503	SO:0001819	synonymous_variant	3918	exon16			TAGCCCGGACGGT	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.2424G>A	chr1.hg19:g.183204833G>A		171.0	0.0	1982	196.0	96.0	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Silent	SNP	ENST00000264144.4	hg19	CCDS1352.1																																																																																			.	.		0.557	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		A	183204833	G	A	183204833	2	1	23	1	0	0	0	0	0	0	0	1	8624	1103	39	1		1	LAMC2	1	183204833	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	392270	183204833	66045788	99	2165										
EDEM3	80267	hgsc.bcm.edu	37	chr1	184688333	184688333	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gttttttaatcacctgatatAacatttcatgagtttcaata	4	6	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:184688333A>G	ENST00000318130.8	-	11	1390	c.1124T>C	c.(1123-1125)tTa>tCa	p.L375S	EDEM3_ENST00000367512.3_Missense_Mutation_p.L332S	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	375					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CACCTGATATAACATTTCATG	0.313																																					p.L375S		Atlas-SNP	.											.	EDEM3	63	.	0			c.T1124C						.						85	92	90					1																	184688333		2203	4295	6498	SO:0001583	missense	80267	exon11			TGATATAACATTT	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"chromosome 1 open reading frame 22"	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.1124T>C	chr1.hg19:g.184688333A>G	ENSP00000318147:p.Leu375Ser	110.0	0.0		103.0	40.0	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Missense_Mutation	SNP	ENST00000318130.8	hg19	CCDS1363.2	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107954	0.77096	.	.	ENSG00000116406	ENST00000318130;ENST00000367512	T;T	0.72835	-0.69;-0.69	4.83	4.83	0.62350	.	0.000000	0.64402	D	0.000004	D	0.82504	0.5051	M	0.72624	2.21	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.84659	0.0705	10	0.66056	D	0.02	.	14.421	0.67183	1.0:0.0:0.0:0.0	.	375	Q9BZQ6	EDEM3_HUMAN	S	375;332	ENSP00000318147:L375S;ENSP00000356482:L332S	ENSP00000318147:L375S	L	-	2	0	EDEM3	182954956	1.000000	0.71417	0.893000	0.35052	0.993000	0.82548	9.154000	0.94694	1.816000	0.52996	0.379000	0.24179	TTA	.	.		0.313	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191		G	184688333	A	G	184688333	3	3	23	1	0	0	0	0	1	0	0	0	4915	372	13	2	1714	2	EDEM3	1	184688333	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1483500	184688333	64562288	100	2166										
PRG4	10216	hgsc.bcm.edu	37	chr1	186276994	186276994	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccctaaagggactgctccaActaccctcaaggaacctgca	7	16	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:186276994A>G	ENST00000445192.2	+	7	2188	c.2143A>G	c.(2143-2145)Act>Gct	p.T715A	PRG4_ENST00000367483.4_Missense_Mutation_p.T674A|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Missense_Mutation_p.T672A|PRG4_ENST00000367485.4_Missense_Mutation_p.T622A	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	715	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GACTGCTCCAACTACCCTCAA	0.577																																					p.T715A		Atlas-SNP	.											.	PRG4	259	.	0			c.A2143G						.						165	177	173					1																	186276994		2203	4300	6503	SO:0001583	missense	10216	exon7			GCTCCAACTACCC	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2143A>G	chr1.hg19:g.186276994A>G	ENSP00000399679:p.Thr715Ala	99.0	0.0		114.0	8.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	hg19	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	-	6.484	0.457467	0.12342	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05258	3.47;3.59;3.48;3.59	2.52	-2.0	0.07433	.	0.170014	0.27577	U	0.018760	T	0.04092	0.0114	L	0.39147	1.195	0.09310	N	1	B;B;B;B	0.18013	0.025;0.025;0.015;0.025	B;B;B;B	0.12837	0.008;0.008;0.003;0.008	T	0.38394	-0.9663	9	.	.	.	.	4.6698	0.12683	0.2507:0.4692:0.2801:0.0	.	581;622;715;674	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	A	672;581;674;622;715	ENSP00000356456:T672A;ENSP00000356453:T674A;ENSP00000356455:T622A;ENSP00000399679:T715A	.	T	+	1	0	PRG4	184543617	0.000000	0.05858	0.001000	0.08648	0.176000	0.22953	-0.805000	0.04530	0.026000	0.15269	0.138000	0.15974	ACT	.	.		0.577	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		G	186276994	A	G	186276994	3	3	23	1	0	0	0	0	1	0	0	0	12493	43	2	2	2165	2	PRG4	1	186276994	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1588661	186276994	62973627	101	2167										
F13B	2165	hgsc.bcm.edu	37	chr1	197026474	197026474	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caacgtatttctgctgacccAtggatctcaaaattaagttc	6	10	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:197026474A>G	ENST00000367412.1	-	6	970	c.927T>C	c.(925-927)caT>caC	p.H309H		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	309	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						CTGCTGACCCATGGATCTCAA	0.373																																					p.H309H		Atlas-SNP	.											.	F13B	137	.	0			c.T927C						.						204	189	194					1																	197026474		2203	4300	6503	SO:0001819	synonymous_variant	2165	exon6			TGACCCATGGATC	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.927T>C	chr1.hg19:g.197026474A>G		176.0	0.0		196.0	11.0	NM_001994	A8K3E5|Q5VYL5	Silent	SNP	ENST00000367412.1	hg19	CCDS1388.1																																																																																			.	.		0.373	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994		G	197026474	A	G	197026474	2	3	23	1	0	0	0	0	0	0	0	1	5343	214	8	2		2	F13B	1	197026474	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	10749480	197026474	52224147	102	2168										
ASPM	259266	hgsc.bcm.edu	37	chr1	197070523	197070524	+	Frame_Shift_Ins	INS	-	-	T													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggtgctgttcctgaatctgINStttttttatgttcatgtcct					rs587783274		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:197070523_197070524insT	ENST00000367409.4	-	18	8113_8114	c.7857_7858insA	c.(7855-7860)aaacagfs	p.Q2620fs	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2620			Q -> H (in dbSNP:rs12138336).		developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TCCTGAATCTGTTTTTTTATGT	0.347																																					p.Q2620fs		Atlas-Indel,Pindel	.											.,1	ASPM	444	.	0			c.7858_7859insA						.																																			SO:0001589	frameshift_variant	259266	exon18			.	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.7858dupA	chr1.hg19:g.197070530_197070530dupT	ENSP00000356379:p.Gln2620fs	36.0	0.0		35.0	10.0	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Frame_Shift_Ins	INS	ENST00000367409.4	hg19	CCDS1389.1																																																																																			.	.		0.347	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		T	197070524	-	T	197070523	7	5	23	1	0	1	1	0	0	0	0	0	1056	1386	48	0	2619	0	ASPM	1	197070523	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	44049	197070523	52180098	103	2169										
ASPM	259266	hgsc.bcm.edu	37	chr1	197113197	197113197	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcggccttctttgagtggtgTccagttaacagaaataacaa	9	8	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:197113197T>C	ENST00000367409.4	-	2	587	c.331A>G	c.(331-333)Aca>Gca	p.T111A	ASPM_ENST00000294732.7_Missense_Mutation_p.T111A	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	111					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTGAGTGGTGTCCAGTTAACA	0.299																																					p.T111A		Atlas-SNP	.											.	ASPM	444	.	0			c.A331G						.						63	64	64					1																	197113197		2202	4287	6489	SO:0001583	missense	259266	exon2			GTGGTGTCCAGTT	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.331A>G	chr1.hg19:g.197113197T>C	ENSP00000356379:p.Thr111Ala	160.0	0.0		180.0	56.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.218993	0.79464	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367406	T;T	0.72942	-0.7;1.08	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	T	0.82015	0.4945	M	0.61703	1.905	0.58432	D	0.99999	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	D	0.83890	0.0284	10	0.72032	D	0.01	.	15.4173	0.74980	0.0:0.0:0.0:1.0	.	111;111	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	A	111	ENSP00000356379:T111A;ENSP00000294732:T111A	ENSP00000294732:T111A	T	-	1	0	ASPM	195379820	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.587000	0.67510	2.180000	0.69256	0.519000	0.50382	ACA	.	.		0.299	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		C	197113197	T	C	197113197	3	2	23	1	0	0	0	0	1	0	0	0	1056	1667	58	2	10210	2	ASPM	1	197113197	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	42674	197113197	52137424	104	2170										
NAV1	89796	hgsc.bcm.edu	37	chr1	201752586	201752586	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cactagccaatcttgacaagGtcaactccaacagtctggat	7	12	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:201752586G>A	ENST00000367296.4	+	7	2830	c.2410G>A	c.(2410-2412)Gtc>Atc	p.V804I	IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000469130.1_3'UTR|NAV1_ENST00000367300.3_Missense_Mutation_p.V804I|NAV1_ENST00000295624.6_Missense_Mutation_p.V804I|NAV1_ENST00000367302.1_Missense_Mutation_p.V817I|NAV1_ENST00000367295.1_Missense_Mutation_p.V413I|NAV1_ENST00000367297.4_Missense_Mutation_p.V804I	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	804					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						TCTTGACAAGGTCAACTCCAA	0.468																																					p.V804I		Atlas-SNP	.											.	NAV1	143	.	0			c.G2410A						.						288	288	288					1																	201752586		2203	4300	6503	SO:0001583	missense	89796	exon7			GACAAGGTCAACT	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"neuron navigator-1", "pore membrane and/or filament interacting like protein 3"	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.2410G>A	chr1.hg19:g.201752586G>A	ENSP00000356265:p.Val804Ile	115.0	0.0		108.0	42.0	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	hg19	CCDS1414.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.51|17.51	3.408346|3.408346	0.62399|0.62399	.|.	.|.	ENSG00000134369|ENSG00000134369	ENST00000430015|ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000391966;ENST00000367295	.|T;T;T;T;T;T	.|0.08008	.|3.14;3.17;3.17;3.17;3.14;3.17	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.19846|0.19846	0.0477|0.0477	L|L	0.31752|0.31752	0.955|0.955	0.41019|0.41019	D|D	0.985068|0.985068	.|B;B;P;D;B	.|0.53312	.|0.347;0.208;0.488;0.959;0.208	.|B;B;B;D;B	.|0.67103	.|0.146;0.047;0.126;0.949;0.038	T|T	0.00981|0.00981	-1.1492|-1.1492	5|10	.|0.59425	.|D	.|0.04	-37.7154|-37.7154	18.7862|18.7862	0.91955|0.91955	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|804;413;804;312;804	.|Q8NEY1-6;Q8NEY1-5;Q8NEY1;A8MYI2;Q8NEY1-3	.|.;.;NAV1_HUMAN;.;.	D|I	361|817;804;804;804;804;312;413	.|ENSP00000356271:V817I;ENSP00000356265:V804I;ENSP00000295624:V804I;ENSP00000356266:V804I;ENSP00000356269:V804I;ENSP00000356264:V413I	.|ENSP00000295624:V804I	G|V	+|+	2|1	0|0	NAV1|NAV1	200019209|200019209	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.565000|3.565000	0.53798|0.53798	2.524000|2.524000	0.85096|0.85096	0.585000|0.585000	0.79938|0.79938	GGT|GTC	.	.		0.468	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		A	201752586	G	A	201752586	3	1	23	1	0	0	0	0	1	0	0	0	10192	1261	44	3	2493	3	NAV1	1	201752586	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	4639389	201752586	47498035	105	2171										
SYT2	127833	hgsc.bcm.edu	37	chr1	202568405	202568407	+	In_Frame_Del	DEL	TCT	TCT	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gttgaagtatgggttcagggTcttcttcttcacggttgtct							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:202568405_202568407delTCT	ENST00000367267.1	-	8	1184_1186	c.992_994delAGA	c.(991-996)aagacc>acc	p.K331del	SYT2_ENST00000367268.4_In_Frame_Del_p.K331del	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	331	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000250}.				neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	GGGTTCAGGGTCTTCTTCTTCAC	0.542																																					p.331_332del		Atlas-Indel,Pindel	.											.	SYT2	51	.	0			c.993_995del						.																																			SO:0001651	inframe_deletion	127833	exon8			.	AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"Synaptotagmins"	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.992_994delAGA	chr1.hg19:g.202568411_202568413delTCT	ENSP00000356236:p.Lys331del	114.0	0.0		122.0	43.0	NM_001136504	Q496K5|Q8NBE5	In_Frame_Del	DEL	ENST00000367267.1	hg19	CCDS1427.1																																																																																			.	.		0.542	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402		-	202568407	TCT	-	202568405	7	5	23	1	0	1	0	1	0	0	0	0	15489	1667	58	0	273	0	SYT2	1	202568405	In_Frame_Del	DEL	TCT	TCGA-4R-AA8I-01A-11D-A382-10	815819	202568405	46682216	106	2172										
CR2	1380	hgsc.bcm.edu	37	chr1	207648316	207648316	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaaattgcagtgcagaagtgAttctaaaggacatggatctt	10	5	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:207648316A>T	ENST00000367058.3	+	13	2483	c.2294A>T	c.(2293-2295)gAt>gTt	p.D765V	CR2_ENST00000367059.3_Missense_Mutation_p.D765V|CR2_ENST00000458541.2_Missense_Mutation_p.D738V|CR2_ENST00000367057.3_Missense_Mutation_p.D824V	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	765	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						TGCAGAAGTGATTCTAAAGGA	0.458																																					p.D824V		Atlas-SNP	.											.	CR2	164	.	0			c.A2471T						.						120	127	125					1																	207648316		2203	4300	6503	SO:0001583	missense	1380	exon14			GAAGTGATTCTAA	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.2294A>T	chr1.hg19:g.207648316A>T	ENSP00000356025:p.Asp765Val	97.0	0.0		106.0	47.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	A	13.76	2.332655	0.41297	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	4.65	4.65	0.58169	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.49440	0.1557	M	0.75150	2.29	0.21697	N	0.999586	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.78314	0.991;0.975;0.984	T	0.36890	-0.9729	9	0.62326	D	0.03	.	11.0163	0.47691	1.0:0.0:0.0:0.0	.	765;765;824	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	V	765;824;765;738	ENSP00000356025:D765V;ENSP00000356024:D824V;ENSP00000356026:D765V;ENSP00000404222:D738V	ENSP00000356024:D824V	D	+	2	0	CR2	205714939	0.844000	0.29557	0.012000	0.15200	0.777000	0.43975	2.659000	0.46741	2.038000	0.60285	0.496000	0.49642	GAT	.	.		0.458	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		T	207648316	A	T	207648316	3	4	23	1	0	0	0	0	1	0	0	0	3844	333	12	4	2525	4	CR2	1	207648316	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	5079911	207648316	41602305	107	2173										
KCNH1	3756	hgsc.bcm.edu	37	chr1	210857113	210857113	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcttggcacaatcgcccccgCcccccttggggcccaggcac							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:210857113delC	ENST00000271751.4	-	11	2507	c.2480delG	c.(2479-2481)ggcfs	p.G829fs	KCNH1_ENST00000367007.4_Frame_Shift_Del_p.G802fs			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	829					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		ATCGCCCCCGCCCCCCTTGGG	0.652																																					p.G827fs		Pindel	.											.	KCNH1	199	.	0			c.2481delC						.						43	51	48					1																	210857113		2203	4300	6503	SO:0001589	frameshift_variant	3756	exon11			.	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.2480delG	chr1.hg19:g.210857113delC	ENSP00000271751:p.Gly829fs	50.0	0.0		43.0	11.0	NM_172362	B1AQ26|O76035|Q14CL3	Frame_Shift_Del	DEL	ENST00000271751.4	hg19	CCDS1496.1																																																																																			.	.		0.652	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		-	210857113	C	-	210857113	7	5	23	1	0	1	0	1	0	0	0	0	8040	739	26	0	493	0	KCNH1	1	210857113	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	3208797	210857113	38393508	108	2174										
ANGEL2	90806	hgsc.bcm.edu	37	chr1	213178563	213178563	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagcttaatatcacctcgccTtggattatacaacagatgcg	7	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:213178563T>G	ENST00000366962.3	-	5	1100	c.946A>C	c.(946-948)Agg>Cgg	p.R316R	ANGEL2_ENST00000360506.2_Silent_p.R147R|ANGEL2_ENST00000535388.1_Silent_p.R147R|ANGEL2_ENST00000540642.1_Silent_p.R190R|ANGEL2_ENST00000544555.1_Silent_p.R147R|ANGEL2_ENST00000473303.1_5'Flank	NM_144567.3	NP_653168.2	Q5VTE6	ANGE2_HUMAN	angel homolog 2 (Drosophila)	316										central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(1)	24				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		TCACCTCGCCTTGGATTATAC	0.453																																					p.R316R		Atlas-SNP	.											.	ANGEL2	45	.	0			c.A946C						.						125	111	116					1																	213178563		2203	4300	6503	SO:0001819	synonymous_variant	90806	exon5			CTCGCCTTGGATT	AL079275	CCDS1512.1, CCDS73027.1	1q32.3	2014-06-17			ENSG00000174606	ENSG00000174606			30534	protein-coding gene	gene with protein product						11943475	Standard	XM_005273344		Approved	KIAA0759L, FLJ12793, Ccr4d	uc001hjz.3	Q5VTE6	OTTHUMG00000036927	ENST00000366962.3:c.946A>C	chr1.hg19:g.213178563T>G		84.0	0.0		87.0	40.0	NM_144567	B7Z2U4|D3DTA3|Q86X13|Q8NHH3	Silent	SNP	ENST00000366962.3	hg19	CCDS1512.1																																																																																			.	.		0.453	ANGEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089693.1	NM_144567		G	213178563	T	G	213178563	2	3	23	1	0	0	0	0	0	0	0	1	609	1608	56	5		5	ANGEL2	1	213178563	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2321450	213178563	36072058	109	2175										
GPATCH2	55105	hgsc.bcm.edu	37	chr1	217688182	217688182	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actcatggtgatgagaatccGgggaaaaatgaaccattctc	10	8	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:217688182G>A	ENST00000366935.3	-	6	1258	c.1148C>T	c.(1147-1149)cCg>cTg	p.P383L		NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	383					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		ATGAGAATCCGGGGAAAAATG	0.348																																					p.P383L		Atlas-SNP	.											.	GPATCH2	53	.	0			c.C1148T						.						46	46	46					1																	217688182		2203	4300	6503	SO:0001583	missense	55105	exon6			GAATCCGGGGAAA	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "G patch domain containing"	25499	protein-coding gene	gene with protein product	"cancer/testis antigen 110", "protein phosphatase 1, regulatory subunit 30"			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.1148C>T	chr1.hg19:g.217688182G>A	ENSP00000355902:p.Pro383Leu	399.0	0.0		435.0	177.0	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Missense_Mutation	SNP	ENST00000366935.3	hg19	CCDS1518.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964408	0.53507	.	.	ENSG00000092978	ENST00000366935	T	0.31247	1.5	5.95	5.95	0.96441	.	0.106321	0.64402	D	0.000003	T	0.27629	0.0679	L	0.51422	1.61	0.80722	D	1	D	0.52996	0.957	B	0.39068	0.289	T	0.02933	-1.1092	10	0.25106	T	0.35	-25.4565	15.0324	0.71717	0.0:0.0:0.8247:0.1753	.	383	Q9NW75	GPTC2_HUMAN	L	383	ENSP00000355902:P383L	ENSP00000355902:P383L	P	-	2	0	GPATCH2	215754805	1.000000	0.71417	0.992000	0.48379	0.932000	0.56968	3.689000	0.54706	2.827000	0.97445	0.650000	0.86243	CCG	.	.		0.348	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040		A	217688182	G	A	217688182	3	1	23	1	0	0	0	0	1	0	0	0	6599	1116	39	1	458	1	GPATCH2	1	217688182	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	4509619	217688182	31562439	110	2176										
GPATCH2	55105	hgsc.bcm.edu	37	chr1	217793392	217793392	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agatgtcctgtgggagatctActgccatgcgttttaccttt	10	9	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:217793392A>T	ENST00000366935.3	-	2	616	c.506T>A	c.(505-507)gTa>gAa	p.V169E	GPATCH2_ENST00000366934.3_Missense_Mutation_p.V169E	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	169					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		TGGGAGATCTACTGCCATGCG	0.483																																					p.V169E		Atlas-SNP	.											.	GPATCH2	53	.	0			c.T506A						.						222	200	207					1																	217793392		2203	4300	6503	SO:0001583	missense	55105	exon2			AGATCTACTGCCA	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "G patch domain containing"	25499	protein-coding gene	gene with protein product	"cancer/testis antigen 110", "protein phosphatase 1, regulatory subunit 30"			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.506T>A	chr1.hg19:g.217793392A>T	ENSP00000355902:p.Val169Glu	53.0	0.0		56.0	25.0	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Missense_Mutation	SNP	ENST00000366935.3	hg19	CCDS1518.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.325385	0.60743	.	.	ENSG00000092978	ENST00000366935;ENST00000366934	T;T	0.40225	1.04;1.04	5.66	5.66	0.87406	.	0.105548	0.64402	D	0.000006	T	0.51839	0.1698	L	0.42245	1.32	0.47511	D	0.999444	D;D	0.67145	0.976;0.996	P;P	0.56474	0.799;0.719	T	0.54029	-0.8354	10	0.66056	D	0.02	-9.1519	15.8881	0.79269	1.0:0.0:0.0:0.0	.	169;169	Q9NW75-2;Q9NW75	.;GPTC2_HUMAN	E	169	ENSP00000355902:V169E;ENSP00000355901:V169E	ENSP00000355901:V169E	V	-	2	0	GPATCH2	215860015	0.997000	0.39634	0.023000	0.16930	0.256000	0.26092	8.561000	0.90715	2.147000	0.66899	0.482000	0.46254	GTA	.	.		0.483	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040		T	217793392	A	T	217793392	3	4	23	1	0	0	0	0	1	0	0	0	6599	391	14	4	1116	4	GPATCH2	1	217793392	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	105210	217793392	31457229	111	2177										
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220387265	220387265	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttggttggagataaggataaAacacaatcttggagccagga	12	5	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:220387265A>G	ENST00000358951.2	-	3	353	c.237T>C	c.(235-237)gtT>gtC	p.V79V		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	79					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		ATAAGGATAAAACACAATCTT	0.363																																					p.V79V		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.T237C						.						118	113	115					1																	220387265		2203	4300	6503	SO:0001819	synonymous_variant	25782	exon3			GGATAAAACACAA	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.237T>C	chr1.hg19:g.220387265A>G		79.0	0.0		88.0	6.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Silent	SNP	ENST00000358951.2	hg19	CCDS31028.1																																																																																			.	.		0.363	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		G	220387265	A	G	220387265	2	3	23	1	0	0	0	0	0	0	0	1	12951	1	1	2		2	RAB3GAP2	1	220387265	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2593873	220387265	28863356	112	2178										
C1orf58	148362	hgsc.bcm.edu	37	chr1	222902172	222902172	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgtttctacacagcttatgTaagtattcacaacgctaaaa	6	8	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:222902172T>C	ENST00000340934.5	+	9	1162		c.e9+2		BROX_ENST00000537020.1_Splice_Site|BROX_ENST00000539697.1_Splice_Site	NM_144695.2	NP_653296.2	Q5VW32	BROX_HUMAN	BRO1 domain and CAAX motif containing							extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|stomach(1)	14						ACAGCTTATGTAAGTATTCAC	0.363																																					.		Atlas-SNP	.											.	BROX	45	.	0			c.756+2T>C						.						75	74	74					1																	222902172		2203	4300	6503	SO:0001630	splice_region_variant	148362	exon9			CTTATGTAAGTAT		CCDS1534.1, CCDS73036.1, CCDS73037.1	1q41	2010-11-30	2010-11-30	2010-11-30	ENSG00000162819	ENSG00000162819			26512	protein-coding gene	gene with protein product	"BRO1 domain containing protein"		"chromosome 1 open reading frame 58"	C1orf58		18190528	Standard	XM_005273065		Approved	FLJ32421	uc001hnq.1	Q5VW32	OTTHUMG00000037650	ENST00000340934.5:c.756+2T>C	chr1.hg19:g.222902172T>C		57.0	0.0		72.0	34.0	NM_144695	B7Z9G5|Q96MG1	Splice_Site	SNP	ENST00000340934.5	hg19	CCDS1534.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.154572	0.78114	.	.	ENSG00000162819	ENST00000340934;ENST00000537020;ENST00000539697	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9967	0.80256	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	BROX	220968795	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	7.579000	0.82511	2.181000	0.69327	0.477000	0.44152	.	.	.		0.363	BROX-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091815.2	NM_144695	Intron	C	222902172	T	C	222902172	5	2	23	1	0	0	0	0	0	0	1	0	2052	1652	57	2	788	2	C1orf58	1	222902172	Splice_Site	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2514907	222902172	26348449	113	2179										
PARP1	142	hgsc.bcm.edu	37	chr1	226556018	226556018	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtcgctgctgccctgagacAccgcctggagaggaggggac	16	12	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:226556018A>T	ENST00000366794.5	-	16	2302	c.2159T>A	c.(2158-2160)gTg>gAg	p.V720E	PARP1_ENST00000490921.1_5'UTR	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	720	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		GCCCTGAGACACCGCCTGGAG	0.582								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.V720E		Atlas-SNP	.											.	PARP1	100	.	0			c.T2159A						.						51	54	53					1																	226556018		2203	4300	6503	SO:0001583	missense	142	exon16			TGAGACACCGCCT	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"Poly (ADP-ribose) polymerases"	270	protein-coding gene	gene with protein product		173870	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)", "poly (ADP-ribose) polymerase family, member 1"	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.2159T>A	chr1.hg19:g.226556018A>T	ENSP00000355759:p.Val720Glu	90.0	0.0		72.0	21.0	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	hg19	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.514751	0.85389	.	.	ENSG00000143799	ENST00000366794	T	0.14516	2.5	5.59	5.59	0.84812	Poly(ADP-ribose) polymerase, regulatory domain (4);	0.185224	0.47852	D	0.000218	T	0.29652	0.0740	M	0.72894	2.215	0.80722	D	1	P	0.38565	0.637	P	0.48454	0.578	T	0.02009	-1.1230	10	0.87932	D	0	.	15.7618	0.78087	1.0:0.0:0.0:0.0	.	720	P09874	PARP1_HUMAN	E	720	ENSP00000355759:V720E	ENSP00000355759:V720E	V	-	2	0	PARP1	224622641	1.000000	0.71417	0.910000	0.35882	0.676000	0.39594	8.957000	0.93082	2.123000	0.65237	0.533000	0.62120	GTG	.	.		0.582	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		T	226556018	A	T	226556018	3	4	23	1	0	0	0	0	1	0	0	0	11463	159	6	4	917	4	PARP1	1	226556018	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3653846	226556018	22694603	114	2180										
GJC2	57165	hgsc.bcm.edu	37	chr1	228345912	228345913	+	In_Frame_Ins	INS	-	-	GAG													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcccatgctgggcctgggcINSgaggaggaggaggaggagga							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:228345912_228345913insGAG	ENST00000366714.2	+	2	628_629	c.453_454insGAG	c.(454-456)gag>GAGgag	p.152_152E>EE		NM_020435.3	NP_065168.2	Q5T442	CXG2_HUMAN	gap junction protein, gamma 2, 47kDa	152	Glu-rich.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|response to toxic substance (GO:0009636)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)	gap junction channel activity (GO:0005243)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7		Prostate(94;0.0405)				TGGGCCTGGGCgaggaggagga	0.787																																					p.G151delinsGE		Atlas-Indel,Pindel	.											.	GJC2	20	.	0			c.453_454insGAG						.																																			SO:0001652	inframe_insertion	57165	exon2			.	AF014643	CCDS1569.1	1q41-q42	2009-01-02	2007-12-14	2007-11-06	ENSG00000198835	ENSG00000198835		"Ion channels / Gap junction proteins (connexins)"	17494	protein-coding gene	gene with protein product	"connexin 47"	608803	"gap junction protein, alpha 12, 47kDa"	GJA12		19056803	Standard	NM_020435		Approved	CX47, CX46.6, SPG44	uc001hsk.3	Q5T442	OTTHUMG00000039771	ENST00000366714.2:c.472_474dupGAG	chr1.hg19:g.228345919_228345921dupGAG	ENSP00000355675:p.Glu158dup	349.0	0.0		364.0	88.0	NM_020435	O43440|Q7Z7J2|Q8IWJ9	In_Frame_Ins	INS	ENST00000366714.2	hg19	CCDS1569.1																																																																																			.	.		0.787	GJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095985.1	NM_020435		GAG	228345913	-	GAG	228345912	7	5	23	1	0	1	1	0	0	0	0	0	6423	755	27	0	455	0	GJC2	1	228345912	In_Frame_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	1789894	228345912	20904709	115	2181										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228399645	228399645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcagccggtggcggccggcgCgcgcttccgtctggcccagg	18	16	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:228399645C>T	ENST00000422127.1	+	2	205	c.161C>T	c.(160-162)gCg>gTg	p.A54V	OBSCN_ENST00000570156.2_Missense_Mutation_p.A54V|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A54V|C1orf145_ENST00000295012.5_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	54	Ig-like 1.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCGGCCGGCGCGCGCTTCCGT	0.692																																					p.A54V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C161T						.						7	9	9					1																	228399645		1969	4077	6046	SO:0001583	missense	84033	exon2			CCGGCGCGCGCTT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.161C>T	chr1.hg19:g.228399645C>T	ENSP00000409493:p.Ala54Val	176.0	0.0		136.0	60.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.613199	0.46631	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.40476	1.03;1.03	4.66	1.53	0.23141	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.259107	0.29752	N	0.011296	T	0.29620	0.0739	L	0.41906	1.305	0.80722	D	1	B;B	0.25169	0.119;0.098	B;B	0.18561	0.022;0.013	T	0.06679	-1.0813	10	0.33940	T	0.23	.	9.251	0.37555	0.0:0.31:0.588:0.1021	.	54;54	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	V	54	ENSP00000284548:A54V;ENSP00000409493:A54V	ENSP00000284548:A54V	A	+	2	0	OBSCN	226466268	1.000000	0.71417	0.060000	0.19600	0.479000	0.33129	4.036000	0.57304	0.388000	0.25054	0.555000	0.69702	GCG	.	.		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228399645	C	T	228399645	3	4	23	1	0	0	0	0	1	0	0	0	10821	768	27	1	163	1	OBSCN	1	228399645	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	53733	228399645	20850976	116	2182										
URB2	9816	hgsc.bcm.edu	37	chr1	229786983	229786983	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgttatctgtcattacaggTaatgctgaaagccatccctt	7	10	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:229786983T>C	ENST00000258243.2	+	8	4287	c.4151T>C	c.(4150-4152)gTa>gCa	p.V1384A		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1384						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						TCATTACAGGTAATGCTGAAA	0.358																																					p.V1384A		Atlas-SNP	.											.	URB2	152	.	0			c.T4151C						.						87	82	84					1																	229786983		2203	4300	6503	SO:0001630	splice_region_variant	9816	exon8			TACAGGTAATGCT	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"nucleolar preribosomal-associated protein 1"		"KIAA0133"	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.4150-1T>C	chr1.hg19:g.229786983T>C		137.0	0.0		140.0	6.0	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	hg19	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.738248	0.69304	.	.	ENSG00000135763	ENST00000258243	T	0.42900	0.96	5.78	5.78	0.91487	Nucleolar 27S pre-rRNA processing, Urb2/Npa2, C-terminal (1);	0.054294	0.64402	D	0.000001	T	0.49525	0.1562	L	0.56769	1.78	0.50313	D	0.999864	D	0.52996	0.957	P	0.52823	0.71	T	0.48603	-0.9021	9	.	.	.	-15.1399	10.4436	0.44479	0.0:0.0725:0.0:0.9275	.	1384	Q14146	URB2_HUMAN	A	1384	ENSP00000258243:V1384A	.	V	+	2	0	URB2	227853606	1.000000	0.71417	0.968000	0.41197	0.820000	0.46376	4.991000	0.63883	2.199000	0.70637	0.533000	0.62120	GTA	.	.		0.358	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	Missense_Mutation	C	229786983	T	C	229786983	5	2	23	1	0	0	0	0	0	0	1	0	17040	1652	57	2	4177	2	URB2	1	229786983	Splice_Site	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1387338	229786983	19463638	117	2183										
CAPN9	10753	hgsc.bcm.edu	37	chr1	230916293	230916293	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaagacttcttcagataccaCgcttctcgggccagaagcaa	8	12	3	3	rs200514450		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:230916293C>T	ENST00000271971.2	+	11	1433	c.1320C>T	c.(1318-1320)caC>caT	p.H440H	RP11-99J16__A.2_ENST00000452640.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000412344.1_RNA|CAPN9_ENST00000366666.2_Silent_p.H377H|CAPN9_ENST00000354537.1_Silent_p.H414H	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	440	Domain III.				digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				TCAGATACCACGCTTCTCGGG	0.522																																					p.H440H		Atlas-SNP	.											.	CAPN9	116	.	0			c.C1320T						.						102	98	100					1																	230916293		2203	4300	6503	SO:0001819	synonymous_variant	10753	exon11			ATACCACGCTTCT	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"EF-hand domain containing"	1486	protein-coding gene	gene with protein product	"novel calpain large subunit-4"	606401	"calpain 9 (nCL-4)"			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1320C>T	chr1.hg19:g.230916293C>T		123.0	0.0		125.0	50.0	NM_006615	B1APS1|B1AQI0|Q9NS74	Silent	SNP	ENST00000271971.2	hg19	CCDS1586.1																																																																																			.	C|0.999;T|0.001		0.522	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615		T	230916293	C	T	230916293	2	4	23	1	0	0	0	0	0	0	0	1	2634	535	19	1		1	CAPN9	1	230916293	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1129310	230916293	18334328	118	2184										
C1orf124	83932	hgsc.bcm.edu	37	chr1	231488843	231488843	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatgtgagtgggtctgaagaTacattcccaaataaacgacc	10	8	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:231488843T>A	ENST00000295050.7	+	5	1542	c.1206T>A	c.(1204-1206)gaT>gaA	p.D402E	SPRTN_ENST00000391858.4_3'UTR	NM_001010984.2|NM_032018.5	NP_001010984.1|NP_114407.3	Q9H040	SPRTN_HUMAN	SprT-like N-terminal domain	402					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of protein ubiquitination (GO:0031398)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|ubiquitin binding (GO:0043130)										GGTCTGAAGATACATTCCCAA	0.368																																					p.D402E		Atlas-SNP	.											.	.	.	.	0			c.T1206A						.						72	72	72					1																	231488843		2203	4300	6503	SO:0001583	missense	83932	exon5			TGAAGATACATTC	AL512744	CCDS1594.1, CCDS31054.1, CCDS58066.1	1q42.12-q43	2013-01-30	2012-06-18	2012-06-18	ENSG00000010072	ENSG00000010072			25356	protein-coding gene	gene with protein product	"SprT-like domain at the N terminus", "DNA damage-targeting VCP (p97) adaptor"		"chromosome 1 open reading frame 124"	C1orf124		22681887	Standard	NM_032018		Approved	DKFZP547N043, Spartan, DVC1	uc001hur.4	Q9H040	OTTHUMG00000038022	ENST00000295050.7:c.1206T>A	chr1.hg19:g.231488843T>A	ENSP00000295050:p.Asp402Glu	320.0	1.0		294.0	134.0	NM_032018	B1AKT0|B5MEF7|Q5TE78|Q6UWW6|Q96BC5|Q96KA0	Missense_Mutation	SNP	ENST00000295050.7	hg19	CCDS1594.1	.	.	.	.	.	.	.	.	.	.	T	11.95	1.792729	0.31685	.	.	ENSG00000010072	ENST00000295050	T	0.41758	0.99	5.55	-1.27	0.09347	.	0.689033	0.14116	N	0.340365	T	0.16557	0.0398	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.21965	-1.0230	10	0.08599	T	0.76	-8.3951	2.3029	0.04167	0.1252:0.1668:0.4162:0.2918	.	402	Q9H040	CA124_HUMAN	E	402	ENSP00000295050:D402E	ENSP00000295050:D402E	D	+	3	2	C1orf124	229555466	0.000000	0.05858	0.001000	0.08648	0.080000	0.17528	-0.685000	0.05167	-0.198000	0.10333	0.523000	0.50628	GAT	.	.		0.368	SPRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092858.1	NM_032018		A	231488843	T	A	231488843	3	1	23	1	0	0	0	0	1	0	0	0	1994	1403	49	4	1259	4	C1orf124	1	231488843	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	572550	231488843	17761778	119	2185										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232600968	232600968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cggttgtgacaaagttctccGccagatctttcaagtactcc	8	12	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:232600968G>A	ENST00000366630.1	-	8	2796	c.2438C>T	c.(2437-2439)gCg>gTg	p.A813V	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.A813V|SIPA1L2_ENST00000308942.4_5'Flank			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	813					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				AAAGTTCTCCGCCAGATCTTT	0.463																																					p.A813V		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.C2438T						.						112	110	111					1																	232600968		1963	4162	6125	SO:0001583	missense	57568	exon7			TTCTCCGCCAGAT	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.2438C>T	chr1.hg19:g.232600968G>A	ENSP00000355589:p.Ala813Val	135.0	0.0		151.0	62.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.490593	0.64074	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.57752	0.38;0.38	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.51991	0.1707	L	0.41824	1.3	0.80722	D	1	D	0.56035	0.974	P	0.45506	0.483	T	0.49062	-0.8978	10	0.39692	T	0.17	-24.3291	20.053	0.97634	0.0:0.0:1.0:0.0	.	813	Q9P2F8	SI1L2_HUMAN	V	813	ENSP00000355589:A813V;ENSP00000262861:A813V	ENSP00000262861:A813V	A	-	2	0	SIPA1L2	230667591	1.000000	0.71417	0.968000	0.41197	0.959000	0.62525	7.984000	0.88150	2.733000	0.93635	0.650000	0.86243	GCG	.	.		0.463	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232600968	G	A	232600968	3	1	23	1	0	0	0	0	1	0	0	0	14345	1087	38	1	2790	1	SIPA1L2	1	232600968	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1112125	232600968	16649653	120	2186										
LYST	1130	hgsc.bcm.edu	37	chr1	235860518	235860519	+	Frame_Shift_Ins	INS	-	-	G													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	accacaggtactggagcactINSgggggaacccacgtattccc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:235860518_235860519insG	ENST00000389794.3	-	46	10602_10603	c.10428_10429insC	c.(10426-10431)cccagtfs	p.S3477fs	LYST_ENST00000473037.1_5'UTR|LYST_ENST00000389793.2_Frame_Shift_Ins_p.S3477fs			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3477					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ACTGGAGCACTGGGGGAACCCA	0.475																																					p.S3477fs		Atlas-Indel,Pindel	.											.	LYST	370	.	0			c.10429_10430insC						.																																			SO:0001589	frameshift_variant	1130	exon46			.	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.10429dupC	chr1.hg19:g.235860523_235860523dupG	ENSP00000374444:p.Ser3477fs	469.0	0.0		483.0	147.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Frame_Shift_Ins	INS	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.475	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			G	235860519	-	G	235860518	7	5	23	1	0	1	1	0	0	0	0	0	9137	1580	55	0	1008	0	LYST	1	235860518	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	3259550	235860518	13390103	121	2187										
ERO1LB	56605	hgsc.bcm.edu	37	chr1	236445027	236445027	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagctcagggtgaccagcagCtgcaccgcggccgctacccc	12	17	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:236445027C>G	ENST00000354619.5	-	1	258	c.57G>C	c.(55-57)caG>caC	p.Q19H	ERO1LB_ENST00000327333.8_Missense_Mutation_p.Q19H	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	19					4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	TGACCAGCAGCTGCACCGCGG	0.741																																					p.Q19H		Atlas-SNP	.											.	ERO1LB	48	.	0			c.G57C						.						6	7	7					1																	236445027		2042	4045	6087	SO:0001583	missense	56605	exon1			CAGCAGCTGCACC	AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.57G>C	chr1.hg19:g.236445027C>G	ENSP00000346635:p.Gln19His	113.0	0.0		108.0	6.0	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	hg19	CCDS31064.1	.	.	.	.	.	.	.	.	.	.	c	3.312	-0.140533	0.06669	.	.	ENSG00000086619	ENST00000354619;ENST00000327333	T;T	0.45276	1.52;0.9	4.17	-0.0922	0.13658	.	0.767685	0.11822	N	0.526099	T	0.21267	0.0512	N	0.22421	0.69	0.21527	N	0.999655	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22521	-1.0214	10	0.15499	T	0.54	-0.059	2.9591	0.05887	0.1952:0.4612:0.0:0.3435	.	19;19	B4DF57;Q86YB8	.;ERO1B_HUMAN	H	19	ENSP00000346635:Q19H;ENSP00000377574:Q19H	ENSP00000377574:Q19H	Q	-	3	2	ERO1LB	234511650	0.999000	0.42202	0.979000	0.43373	0.008000	0.06430	0.710000	0.25748	0.010000	0.14839	-0.679000	0.03777	CAG	.	.		0.741	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891		G	236445027	C	G	236445027	3	3	23	1	0	0	0	0	1	0	0	0	5242	796	28	4	1410	4	ERO1LB	1	236445027	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	584509	236445027	12805594	122	2188										
MTR	4548	hgsc.bcm.edu	37	chr1	236959039	236959039	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caagacctgtcgcaacccggTaacgctgcgaccccgtctgc	10	17	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:236959039T>C	ENST00000366577.5	+	1	428		c.e1+2		MTR_ENST00000535889.1_Splice_Site|MTR_ENST00000418145.2_Splice_Site	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase						cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	CGCAACCCGGTAACGCTGCGA	0.632																																					.		Atlas-SNP	.											.	MTR	127	.	0			c.34+2T>C						.						98	74	82					1																	236959039		2203	4300	6503	SO:0001630	splice_region_variant	4548	exon1			ACCCGGTAACGCT	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.34+2T>C	chr1.hg19:g.236959039T>C		67.0	0.0		65.0	27.0	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Splice_Site	SNP	ENST00000366577.5	hg19	CCDS1614.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.824365	0.90955	.	.	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000418145;ENST00000535889	.	.	.	3.79	3.79	0.43588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2732	0.37684	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	MTR	235025662	1.000000	0.71417	0.983000	0.44433	0.930000	0.56654	2.736000	0.47385	1.931000	0.55961	0.519000	0.50382	.	.	.		0.632	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	Intron	C	236959039	T	C	236959039	5	2	23	1	0	0	0	0	0	0	1	0	9967	1652	57	2	38	2	MTR	1	236959039	Splice_Site	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	514012	236959039	12291582	123	2189										
RYR2	6262	hgsc.bcm.edu	37	chr1	237951398	237951398	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agaagtgccagagtcagcatTctggaagaaaatcatagcat	10	7	3	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:237951398T>A	ENST00000366574.2	+	92	13756	c.13439T>A	c.(13438-13440)tTc>tAc	p.F4480Y	RYR2_ENST00000542537.1_Missense_Mutation_p.F4464Y|RYR2_ENST00000360064.6_Missense_Mutation_p.F4486Y	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4480					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAGTCAGCATTCTGGAAGAAA	0.383																																					p.F4480Y		Atlas-SNP	.											.	RYR2	1273	.	0			c.T13439A						.						97	106	103					1																	237951398		2098	4248	6346	SO:0001583	missense	6262	exon92			CAGCATTCTGGAA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.13439T>A	chr1.hg19:g.237951398T>A	ENSP00000355533:p.Phe4480Tyr	827.0	1.0		813.0	341.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.786066	0.70337	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.94417	-3.42;-3.42;-3.42	4.55	4.55	0.56014	Ryanodine Receptor TM 4-6 (1);	0.000000	0.64402	U	0.000006	D	0.89795	0.6818	L	0.41492	1.28	0.80722	D	1	D	0.54207	0.965	B	0.39339	0.297	D	0.88248	0.2914	10	0.27082	T	0.32	.	12.7682	0.57403	0.0:0.0:0.0:1.0	.	4480	Q92736	RYR2_HUMAN	Y	4480;4486;4464	ENSP00000355533:F4480Y;ENSP00000353174:F4486Y;ENSP00000443798:F4464Y	ENSP00000353174:F4486Y	F	+	2	0	RYR2	236018021	1.000000	0.71417	0.999000	0.59377	0.519000	0.34347	7.388000	0.79795	1.816000	0.52996	0.477000	0.44152	TTC	.	.		0.383	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237951398	T	A	237951398	3	1	23	1	0	0	0	0	1	0	0	0	13784	1783	62	4	13805	4	RYR2	1	237951398	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	992359	237951398	11299223	124	2190										
FH	2271	hgsc.bcm.edu	37	chr1	241680550	241680550	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacggtctgggcgccataatActtatcatttggcaccttta	8	11	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:241680550A>G	ENST00000366560.3	-	2	237	c.199T>C	c.(199-201)Tat>Cat	p.Y67H	FH_ENST00000493477.1_5'UTR	NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	67					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		GCGCCATAATACTTATCATTT	0.403			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												p.Y67H	Melanoma(148;1573 2486 7381 46575)	Atlas-SNP	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	.	FH	64	.	0			c.T199C						.						137	123	128					1																	241680550		2203	4300	6503	SO:0001583	missense	2271	exon2	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	CATAATACTTATC	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.199T>C	chr1.hg19:g.241680550A>G	ENSP00000355518:p.Tyr67His	102.0	0.0		112.0	45.0	NM_000143	B1ANK7	Missense_Mutation	SNP	ENST00000366560.3	hg19	CCDS1617.1	.	.	.	.	.	.	.	.	.	.	A	18.30	3.592783	0.66219	.	.	ENSG00000091483	ENST00000366560	D	0.99458	-5.93	5.75	4.63	0.57726	Lyase 1, N-terminal (1);L-Aspartase-like (1);L-Aspartase-like, N-terminal (1);	0.114903	0.64402	D	0.000008	D	0.99677	0.9879	H	0.97896	4.1	0.80722	D	1	D	0.65815	0.995	D	0.76071	0.987	D	0.97864	1.0282	10	0.87932	D	0	-7.926	10.1351	0.42701	0.9209:0.0:0.0791:0.0	.	67	P07954	FUMH_HUMAN	H	67	ENSP00000355518:Y67H	ENSP00000355518:Y67H	Y	-	1	0	FH	239747173	1.000000	0.71417	1.000000	0.80357	0.423000	0.31445	8.852000	0.92215	1.118000	0.41863	0.528000	0.53228	TAT	.	.		0.403	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		G	241680550	A	G	241680550	3	3	23	1	0	0	0	0	1	0	0	0	5883	391	14	2	1369	2	FH	1	241680550	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3729152	241680550	7570071	125	2191										
ZNF695	57116	hgsc.bcm.edu	37	chr1	247150429	247150429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacattcttcacatttgtagGgtttctctccagtatgaatt	6	9	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:247150429G>A	ENST00000339986.7	-	4	1535	c.1388C>T	c.(1387-1389)cCc>cTc	p.P463L	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	463					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ACATTTGTAGGGTTTCTCTCC	0.383																																					p.P463L		Atlas-SNP	.											.	ZNF695	55	.	0			c.C1388T						.						67	71	70					1																	247150429		2116	4249	6365	SO:0001583	missense	57116	exon4			TTGTAGGGTTTCT		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"Zinc fingers, C2H2-type", "-"	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.1388C>T	chr1.hg19:g.247150429G>A	ENSP00000341236:p.Pro463Leu	67.0	0.0		80.0	40.0	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	hg19	CCDS44344.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.489160	0.44249	.	.	ENSG00000197472	ENST00000339986	T	0.17054	2.3	0.642	-0.87	0.10646	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27629	0.0679	L	0.58101	1.795	0.44247	D	0.997091	D	0.76494	0.999	D	0.63703	0.917	T	0.08932	-1.0698	9	0.62326	D	0.03	.	5.3174	0.15862	0.0:0.0:0.6708:0.3292	.	463	Q8IW36	ZN695_HUMAN	L	463	ENSP00000341236:P463L	ENSP00000341236:P463L	P	-	2	0	ZNF695	245217052	1.000000	0.71417	0.127000	0.21898	0.858000	0.48976	4.808000	0.62583	-0.308000	0.08792	0.205000	0.17691	CCC	.	.		0.383	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394		A	247150429	G	A	247150429	3	1	23	1	0	0	0	0	1	0	0	0	18113	1232	43	3	163	3	ZNF695	1	247150429	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	5469879	247150429	2100192	126	2192										
ZNF496	84838	hgsc.bcm.edu	37	chr1	247464566	247464566	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggctgttctctagagatcgcGggttgccgccagctacagga	14	11	1	1	rs551292960		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:247464566G>A	ENST00000294753.4	-	9	1483	c.1019C>T	c.(1018-1020)cCg>cTg	p.P340L	ZNF496_ENST00000462139.1_5'UTR|ZNF496_ENST00000366498.2_Missense_Mutation_p.P376L	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	340					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			TAGAGATCGCGGGTTGCCGCC	0.602													G|||	1	0.000199681	0	0	5008	,	,		16776	0		0	False		,,,				2504	0.001				p.P340L		Atlas-SNP	.											.	ZNF496	80	.	0			c.C1019T						.						60	67	65					1																	247464566		2137	4161	6298	SO:0001583	missense	84838	exon9			GATCGCGGGTTGC	BC007263	CCDS1631.1	1q44	2013-01-09			ENSG00000162714	ENSG00000162714		"Zinc fingers, C2H2-type", "-", "-", "-"	23713	protein-coding gene	gene with protein product		613911				12477932	Standard	NM_032752		Approved	ZKSCAN17, MGC15548, ZSCAN49	uc001ico.3	Q96IT1	OTTHUMG00000041164	ENST00000294753.4:c.1019C>T	chr1.hg19:g.247464566G>A	ENSP00000294753:p.Pro340Leu	34.0	0.0		38.0	13.0	NM_032752	Q8TBS2	Missense_Mutation	SNP	ENST00000294753.4	hg19	CCDS1631.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.488895	0.26686	.	.	ENSG00000162714	ENST00000294753;ENST00000366498	T;T	0.07908	3.16;3.15	4.12	2.08	0.27032	.	1.265160	0.05423	N	0.544600	T	0.04092	0.0114	N	0.14661	0.345	0.09310	N	0.999995	P;B	0.38280	0.625;0.016	B;B	0.21917	0.037;0.002	T	0.37009	-0.9724	10	0.30854	T	0.27	-0.8852	4.979	0.14155	0.3226:0.0:0.6774:0.0	.	376;340	Q96IT1-2;Q96IT1	.;ZN496_HUMAN	L	340;376	ENSP00000294753:P340L;ENSP00000355454:P376L	ENSP00000294753:P340L	P	-	2	0	ZNF496	245531189	0.968000	0.33430	0.001000	0.08648	0.032000	0.12392	0.000000	0.12993	0.578000	0.29487	0.655000	0.94253	CCG	.	.		0.602	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752		A	247464566	G	A	247464566	3	1	23	1	0	0	0	0	1	0	0	0	17960	1116	39	1	748	1	ZNF496	1	247464566	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	314137	247464566	1786055	127	2193										
OR2T1	26696	hgsc.bcm.edu	37	chr1	248569984	248569984	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gattaaccacttcttctgtgAggcaccagcagtcctgaagt	9	11	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:248569984A>G	ENST00000366474.1	+	1	689	c.689A>G	c.(688-690)gAg>gGg	p.E230G		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTCTTCTGTGAGGCACCAGCA	0.512																																					p.E230G		Atlas-SNP	.											.	OR2T1	89	.	0			c.A689G						.						165	147	153					1																	248569984		2203	4300	6503	SO:0001583	missense	26696	exon1			TCTGTGAGGCACC	U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"GPCR / Class A : Olfactory receptors"	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.689A>G	chr1.hg19:g.248569984A>G	ENSP00000355430:p.Glu230Gly	93.0	0.0		109.0	32.0	NM_030904	Q6IEZ9	Missense_Mutation	SNP	ENST00000366474.1	hg19	CCDS31115.1	.	.	.	.	.	.	.	.	.	.	a	18.27	3.587845	0.66105	.	.	ENSG00000175143	ENST00000366474	T	0.00227	8.5	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37012	U	0.002281	T	0.00815	0.0027	M	0.93375	3.41	0.39267	D	0.964328	D	0.89917	1.0	D	0.97110	1.0	T	0.57808	-0.7747	10	0.87932	D	0	.	13.3845	0.60789	1.0:0.0:0.0:0.0	.	230	O43869	OR2T1_HUMAN	G	230	ENSP00000355430:E230G	ENSP00000355430:E230G	E	+	2	0	OR2T1	246636607	1.000000	0.71417	0.993000	0.49108	0.704000	0.40688	4.920000	0.63390	1.993000	0.58246	0.528000	0.53228	GAG	.	.		0.512	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2			G	248569984	A	G	248569984	3	3	23	1	0	0	0	0	1	0	0	0	11025	304	11	2	691	2	OR2T1	1	248569984	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1105418	248569984	680637	128	2194										
OR2T2	401992	hgsc.bcm.edu	37	chr1	248616797	248616797	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacaggatgaactctgctgaGggccggcgcaaagcctttgc	13	12	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:248616797G>T	ENST00000342927.3	+	1	721	c.699G>T	c.(697-699)gaG>gaT	p.E233D		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACTCTGCTGAGGGCCGGCGCA	0.557																																					p.E233D		Atlas-SNP	.											.	OR2T2	73	.	0			c.G699T						.						65	48	54					1																	248616797		2187	4262	6449	SO:0001583	missense	401992	exon1			TGCTGAGGGCCGG	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"GPCR / Class A : Olfactory receptors"	14725	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily T, member 2 pseudogene"	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.699G>T	chr1.hg19:g.248616797G>T	ENSP00000343062:p.Glu233Asp	248.0	0.0		245.0	11.0	NM_001004136	B2RNM1|B9EH01	Missense_Mutation	SNP	ENST00000342927.3	hg19	CCDS31116.1	.	.	.	.	.	.	.	.	.	.	g	5.467	0.271212	0.10349	.	.	ENSG00000196240	ENST00000342927	T	0.00193	8.58	3.61	1.47	0.22746	GPCR, rhodopsin-like superfamily (1);	0.283792	0.24876	N	0.034884	T	0.00210	0.0006	M	0.73962	2.25	0.09310	N	1	B	0.16603	0.018	B	0.22152	0.038	T	0.43605	-0.9381	10	0.72032	D	0.01	.	4.4295	0.11520	0.5104:0.0:0.4896:0.0	.	233	Q6IF00	OR2T2_HUMAN	D	233	ENSP00000343062:E233D	ENSP00000343062:E233D	E	+	3	2	OR2T2	246683420	0.000000	0.05858	0.145000	0.22337	0.010000	0.07245	-0.302000	0.08221	0.711000	0.32018	0.449000	0.29647	GAG	.	.		0.557	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136		T	248616797	G	T	248616797	3	4	23	1	0	0	0	0	1	0	0	0	11029	991	35	3	701	3	OR2T2	1	248616797	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	46813	248616797	633824	129	2195										
ZNF672	79894	hgsc.bcm.edu	37	chr1	249142190	249142190	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcaagggcttcctggagagCgccacgctggtgcgccacca	15	14	0	1	rs373331980		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:249142190C>T	ENST00000306562.3	+	4	1463	c.717C>T	c.(715-717)agC>agT	p.S239S		NM_024836.1	NP_079112.1	Q499Z4	ZN672_HUMAN	zinc finger protein 672	239					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(1)	5	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TCCTGGAGAGCGCCACGCTGG	0.652																																					p.S239S		Atlas-SNP	.											.	ZNF672	32	.	0			c.C717T						.	C		1,4363		0,1,2181	9	9	9		717	-7.9	0.6	1		9	0,8506		0,0,4253	no	coding-synonymous	ZNF672	NM_024836.1		0,1,6434	TT,TC,CC		0.0,0.0229,0.0078		239/453	249142190	1,12869	2182	4253	6435	SO:0001819	synonymous_variant	79894	exon4			GGAGAGCGCCACG	AK027476	CCDS1638.1	1q44	2013-01-08			ENSG00000171161	ENSG00000171161		"Zinc fingers, C2H2-type"	26179	protein-coding gene	gene with protein product	"hypothetical protein FLJ22301"					12477932	Standard	NM_024836		Approved	FLJ22301	uc001iex.3	Q499Z4	OTTHUMG00000040377	ENST00000306562.3:c.717C>T	chr1.hg19:g.249142190C>T		81.0	0.0		61.0	25.0	NM_024836	Q96H65|Q96IM3|Q9H6G5	Silent	SNP	ENST00000306562.3	hg19	CCDS1638.1																																																																																			.	.		0.652	ZNF672-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097125.2	NM_024836		T	249142190	C	T	249142190	2	4	23	1	0	0	0	0	0	0	0	1	18094	767	27	1		1	ZNF672	1	249142190	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	525393	249142190	108431	130	2196										
PXDN	7837	hgsc.bcm.edu	37	chr2	1670259	1670259	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gattacaaaagtgggtcgagCtgtcacaattaaacagaaat	9	6	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:1670259C>T	ENST00000252804.4	-	10	1069		c.e10-1		PXDN_ENST00000483018.1_Splice_Site	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)						extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GTGGGTCGAGCTGTCACAATT	0.483																																					.		Atlas-SNP	.											.	PXDN	255	.	0			c.1019-1G>A						.						24	25	25					2																	1670259		1947	4139	6086	SO:0001630	splice_region_variant	7837	exon11			GTCGAGCTGTCAC	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1019-1G>A	chr2.hg19:g.1670259C>T		190.0	0.0		167.0	73.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Splice_Site	SNP	ENST00000252804.4	hg19	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.450884	0.84209	.	.	ENSG00000130508	ENST00000252804;ENST00000433670	.	.	.	5.09	5.09	0.68999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6763	0.85280	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PXDN	1649266	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.744000	0.85034	2.369000	0.80426	0.655000	0.94253	.	.	.		0.483	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	Intron	T	1670259	C	T	1670259	5	4	23	1	0	0	0	0	0	0	1	0	12862	811	28	3	3477	3	PXDN	2	1670259	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10		1670259	241529114	131	2197										
TTC15	51112	hgsc.bcm.edu	37	chr2	3469411	3469411	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtatcattcggttatcaagtAttacccagagcaagagcccc	8	11	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:3469411A>G	ENST00000324266.5	+	9	1916	c.1721A>G	c.(1720-1722)tAt>tGt	p.Y574C	TRAPPC12_ENST00000469147.1_3'UTR|TRAPPC12_ENST00000382110.2_Missense_Mutation_p.Y574C	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	574					vesicle-mediated transport (GO:0016192)												GTTATCAAGTATTACCCAGAG	0.527																																					p.Y574C		Atlas-SNP	.											.	.	.	.	0			c.A1721G						.						121	117	119					2																	3469411		2203	4300	6503	SO:0001583	missense	51112	exon9			TCAAGTATTACCC	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"Trafficking protein particle complex", "Tetratricopeptide (TTC) repeat domain containing"	24284	protein-coding gene	gene with protein product		614139	"tetratricopeptide repeat domain 15"	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1721A>G	chr2.hg19:g.3469411A>G	ENSP00000324318:p.Tyr574Cys	101.0	0.0		82.0	15.0	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	hg19	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	A	10.58	1.389474	0.25118	.	.	ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266;ENST00000415624	T;T;T	0.62941	-0.01;-0.01;-0.01	5.65	-3.1	0.05315	.	0.311783	0.36101	N	0.002794	T	0.45175	0.1329	L	0.47716	1.5	0.34164	D	0.669015	B;B	0.24675	0.109;0.035	B;B	0.26693	0.072;0.023	T	0.11842	-1.0571	10	0.40728	T	0.16	.	4.1305	0.10148	0.4903:0.0:0.2797:0.23	.	563;574	E7ENL7;Q8WVT3	.;TPC12_HUMAN	C	574;563;574;72	ENSP00000371544:Y574C;ENSP00000324318:Y574C;ENSP00000396592:Y72C	ENSP00000303612:Y563C	Y	+	2	0	TTC15	3448418	0.978000	0.34361	0.000000	0.03702	0.001000	0.01503	2.607000	0.46300	-0.842000	0.04195	-0.290000	0.09829	TAT	.	.		0.527	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		G	3469411	A	G	3469411	3	3	23	1	0	0	0	0	1	0	0	0	16697	449	16	2	1751	2	TTC15	2	3469411	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1799152	3469411	239729962	132	2198										
NBAS	51594	hgsc.bcm.edu	37	chr2	15359052	15359052	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcatcagcacagaaaggccGcagccactccagcaggtcct	10	15	2	1	rs200331420		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:15359052G>A	ENST00000281513.5	-	48	6302	c.6277C>T	c.(6277-6279)Cgg>Tgg	p.R2093W	NBAS_ENST00000441750.1_Missense_Mutation_p.R1973W	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2093					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CAGAAAGGCCGCAGCCACTCC	0.557																																					p.R2093W		Atlas-SNP	.											.	NBAS	246	.	0			c.C6277T						.						37	41	40					2																	15359052		2203	4300	6503	SO:0001583	missense	51594	exon48			AAGGCCGCAGCCA	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.6277C>T	chr2.hg19:g.15359052G>A	ENSP00000281513:p.Arg2093Trp	293.0	0.0		291.0	113.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.295724	0.60086	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.32515	1.45;1.45	5.57	4.69	0.59074	.	0.056518	0.64402	D	0.000002	T	0.34716	0.0907	M	0.63843	1.955	0.53688	D	0.999979	P;P	0.51791	0.948;0.498	B;B	0.43728	0.429;0.064	T	0.27938	-1.0059	10	0.87932	D	0	.	12.4462	0.55651	0.0:0.0:0.5767:0.4233	.	1973;2093	A2RRP1-2;A2RRP1	.;NBAS_HUMAN	W	1973;2093	ENSP00000413201:R1973W;ENSP00000281513:R2093W	ENSP00000281513:R2093W	R	-	1	2	NBAS	15276503	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.600000	0.46240	1.334000	0.45468	0.591000	0.81541	CGG	.	G|0.999;C|0.001		0.557	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		A	15359052	G	A	15359052	3	1	23	1	0	0	0	0	1	0	0	0	10195	1086	38	1	858	1	NBAS	2	15359052	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	11889641	15359052	227840321	133	2199										
NBAS	51594	hgsc.bcm.edu	37	chr2	15607895	15607895	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaaagctcttcataggagatActgtcaatgtctatttcacc	7	9	5	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:15607895A>G	ENST00000281513.5	-	18	1936	c.1911T>C	c.(1909-1911)agT>agC	p.S637S	NBAS_ENST00000441750.1_Silent_p.S637S	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	637					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CATAGGAGATACTGTCAATGT	0.338																																					p.S637S		Atlas-SNP	.											.	NBAS	246	.	0			c.T1911C						.						100	94	96					2																	15607895		2202	4300	6502	SO:0001819	synonymous_variant	51594	exon18			GGAGATACTGTCA	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1911T>C	chr2.hg19:g.15607895A>G		322.0	0.0		338.0	127.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	hg19	CCDS1685.1																																																																																			.	.		0.338	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		G	15607895	A	G	15607895	2	3	23	1	0	0	0	0	0	0	0	1	10195	388	14	2		2	NBAS	2	15607895	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	248843	15607895	227591478	134	2200										
DDX1	1653	hgsc.bcm.edu	37	chr2	15768807	15768807	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaagcaaaactacgtacatcGaattggcagagtaggaagag	11	6	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:15768807G>A	ENST00000381341.2	+	23	2194	c.1805G>A	c.(1804-1806)cGa>cAa	p.R602Q	DDX1_ENST00000233084.3_Missense_Mutation_p.R602Q			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	602	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Necessary for interaction with HNRNPK.|Necessary for interaction with replicase polyprotein 1ab nsp14 of IBV.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		TACGTACATCGAATTGGCAGA	0.323																																					p.R602Q		Atlas-SNP	.											.	DDX1	70	.	0			c.G1805A						.						62	63	63					2																	15768807		2203	4300	6503	SO:0001583	missense	1653	exon22			TACATCGAATTGG	X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"DEAD-boxes"	2734	protein-coding gene	gene with protein product		601257	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.1805G>A	chr2.hg19:g.15768807G>A	ENSP00000370745:p.Arg602Gln	166.0	0.0		147.0	61.0	NM_004939	B4DME8|B4DPN6	Missense_Mutation	SNP	ENST00000381341.2	hg19	CCDS1686.1	.	.	.	.	.	.	.	.	.	.	G	37	6.066328	0.97251	.	.	ENSG00000079785	ENST00000381341;ENST00000233084;ENST00000543614	D;D	0.82344	-1.6;-1.6	6.17	6.17	0.99709	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.93174	0.7826	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93112	0.6517	10	0.87932	D	0	-14.4893	20.8794	0.99867	0.0:0.0:1.0:0.0	.	602	Q92499	DDX1_HUMAN	Q	602;602;586	ENSP00000370745:R602Q;ENSP00000233084:R602Q	ENSP00000233084:R602Q	R	+	2	0	DDX1	15686258	1.000000	0.71417	0.870000	0.34147	0.987000	0.75469	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	CGA	.	.		0.323	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939		A	15768807	G	A	15768807	3	1	23	1	0	0	0	0	1	0	0	0	4343	1058	37	1	1891	1	DDX1	2	15768807	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	160912	15768807	227430566	135	2201										
MYCN	4613	hgsc.bcm.edu	37	chr2	16082705	16082705	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggagccggccgcgccggggcCgccctgcccgccgagctcgc	17	20	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:16082705C>T	ENST00000281043.3	+	2	816	c.519C>T	c.(517-519)gcC>gcT	p.A173A	MYCNOS_ENST00000419083.1_RNA|MYCNOS_ENST00000439180.1_RNA|MYCNOS_ENST00000453400.1_RNA|MYCNOS_ENST00000448719.1_RNA|MYCNOS_ENST00000420452.1_RNA	NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	173					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			gcgccggggccgccctgcccg	0.811			A		neuroblastoma																																p.A173A		Atlas-SNP	.		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	.	MYCN	63	.	0			c.C519T						.						1	2	1					2																	16082705		736	1843	2579	SO:0001819	synonymous_variant	4613	exon2			CGGGGCCGCCCTG	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.519C>T	chr2.hg19:g.16082705C>T		102.0	0.0		92.0	35.0	NM_005378	Q53XS5|Q6LDT9	Silent	SNP	ENST00000281043.3	hg19	CCDS1687.1																																																																																			.	.		0.811	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		T	16082705	C	T	16082705	2	4	23	1	0	0	0	0	0	0	0	1	10030	639	23	1		1	MYCN	2	16082705	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	313898	16082705	227116668	136	2202										
APOB	338	hgsc.bcm.edu	37	chr2	21225513	21225514	+	Frame_Shift_Del	DEL	TA	TA	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgagattacatctattagttTatgtttccttaactcgaaag							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:21225513_21225514delTA	ENST00000233242.1	-	29	12907_12908	c.12780_12781delTA	c.(12778-12783)cataaafs	p.HK4260fs	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4260					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTATTAGTTTATGTTTCCTTA	0.361																																					p.4261_4261del		Atlas-Indel,Pindel	.											.	APOB	761	.	0			c.12781_12782del						.																																			SO:0001589	frameshift_variant	338	exon29			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.12780_12781delTA	chr2.hg19:g.21225513_21225514delTA	ENSP00000233242:p.His4260fs	138.0	0.0		123.0	48.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.361	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21225514	TA	-	21225513	7	5	23	1	0	1	0	1	0	0	0	0	785	1763	61	0	914	0	APOB	2	21225513	Frame_Shift_Del	DEL	TA	TCGA-4R-AA8I-01A-11D-A382-10	5142808	21225513	221973860	137	2203										
APOB	338	hgsc.bcm.edu	37	chr2	21265319	21265319	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcatagttgtatgtgtactTccggaggtgcttgaatcggg	13	7	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:21265319T>C	ENST00000233242.1	-	3	278	c.151A>G	c.(151-153)Aag>Gag	p.K51E	APOB_ENST00000399256.4_Missense_Mutation_p.K51E	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	51	Heparin-binding.|Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATGTGTACTTCCGGAGGTGC	0.512																																					p.K51E		Atlas-SNP	.											.	APOB	761	.	0			c.A151G						.						159	142	148					2																	21265319		2203	4300	6503	SO:0001583	missense	338	exon3			TGTACTTCCGGAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.151A>G	chr2.hg19:g.21265319T>C	ENSP00000233242:p.Lys51Glu	159.0	0.0		139.0	59.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	17.76	3.469715	0.63625	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.36520	1.25;1.25	5.58	5.58	0.84498	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.000000	0.64402	D	0.000008	T	0.62514	0.2434	M	0.80183	2.485	0.39872	D	0.973521	D	0.89917	1.0	D	0.79784	0.993	T	0.69187	-0.5211	10	0.72032	D	0.01	.	15.055	0.71908	0.0:0.0:0.0:1.0	.	51	P04114	APOB_HUMAN	E	51	ENSP00000233242:K51E;ENSP00000382200:K51E	ENSP00000233242:K51E	K	-	1	0	APOB	21118824	1.000000	0.71417	0.991000	0.47740	0.360000	0.29518	3.325000	0.52030	2.254000	0.74563	0.533000	0.62120	AAG	.	.		0.512	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21265319	T	C	21265319	3	2	23	1	0	0	0	0	1	0	0	0	785	1792	62	2	13648	2	APOB	2	21265319	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	39806	21265319	221934054	138	2204										
NCOA1	8648	hgsc.bcm.edu	37	chr2	24952369	24952369	+	Splice_Site	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttctggcttcttttctaacaGgggggtggattagatgtatt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:24952369delG	ENST00000406961.1	+	17	3538		c.e17-1		NCOA1_ENST00000348332.3_Splice_Site|NCOA1_ENST00000407230.1_Splice_Site|NCOA1_ENST00000395856.3_Splice_Site|NCOA1_ENST00000405141.1_Splice_Site|NCOA1_ENST00000288599.5_Splice_Site|NCOA1_ENST00000538539.1_Splice_Site			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1						androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTTCTAACAGGGGGGTGGAT	0.373			T	PAX3	alveolar rhadomyosarcoma																																.		Atlas-INDEL	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.2887-2G>-						.						72	72	72					2																	24952369		2203	4300	6503	SO:0001630	splice_region_variant	8648	exon15			.	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.2887-1G>-	chr2.hg19:g.24952369delG		129.0	0.0		125.0	11.0	NM_147233	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Splice_Site	DEL	ENST00000406961.1	hg19	CCDS1712.1																																																																																			.	.		0.373	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	Intron	-	24952369	G	-	24952369	8	5	23	1	0	1	0	1	0	0	1	0	10237	1014	35	0	2936	0	NCOA1	2	24952369	Splice_Site	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	3687050	24952369	218247004	139	2205										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25497864	25497864	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgcgcttgctgatgtagtaGgggtcccccgcctggaaggt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:25497864delG	ENST00000264709.3	-	6	922	c.585delC	c.(583-585)cccfs	p.P195fs	DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.P195fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	195					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGATGTAGTAGGGGTCCCCCG	0.701			"Mis, F, N, S"		AML																																p.Y196fs		Atlas-Indel,Pindel	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.586delT						.						39	37	38					2																	25497864		2203	4300	6503	SO:0001589	frameshift_variant	1788	exon6			.		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.585delC	chr2.hg19:g.25497864delG	ENSP00000264709:p.Pro195fs	126.0	0.0		136.0	53.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.		0.701	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		-	25497864	G	-	25497864	7	5	23	1	0	1	0	1	0	0	0	0	4678	987	35	0	2305	0	DNMT3A	2	25497864	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	545495	25497864	217701509	140	2206										
C2orf39	92749	hgsc.bcm.edu	37	chr2	26676396	26676396	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caagattctggaggccttcgTcatgggtctgaagaagccta	12	9	3	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:26676396T>C	ENST00000288710.2	+	14	1972	c.1898T>C	c.(1897-1899)gTc>gCc	p.V633A		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	633			V -> F (in dbSNP:rs12623642).		axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											GAGGCCTTCGTCATGGGTCTG	0.617																																					p.V633A		Atlas-SNP	.											.	CCDC164	84	.	0			c.T1898C						.						52	55	54					2																	26676396		2203	4300	6503	SO:0001583	missense	92749	exon14			CCTTCGTCATGGG	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"chromosome 2 open reading frame 39", "coiled-coil domain containing 164", "dynein regulatory complex subunit 1 homolog (Chlamydomonas)"	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.1898T>C	chr2.hg19:g.26676396T>C	ENSP00000288710:p.Val633Ala	156.0	0.0		143.0	57.0	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	hg19	CCDS1723.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.054675	0.75960	.	.	ENSG00000157856	ENST00000288710	T	0.20069	2.1	5.03	5.03	0.67393	.	0.302633	0.31747	N	0.007127	T	0.27697	0.0681	M	0.67953	2.075	0.36542	D	0.871378	P	0.40534	0.72	B	0.40506	0.331	T	0.39742	-0.9599	10	0.72032	D	0.01	-28.8909	14.0395	0.64665	0.0:0.0:0.0:1.0	.	633	Q96MC2	CC164_HUMAN	A	633	ENSP00000288710:V633A	ENSP00000288710:V633A	V	+	2	0	CCDC164	26529900	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	3.595000	0.54016	2.028000	0.59812	0.496000	0.49642	GTC	.	.		0.617	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038		C	26676396	T	C	26676396	3	2	23	1	0	0	0	0	1	0	0	0	2166	1667	58	2	1952	2	C2orf39	2	26676396	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1178532	26676396	216522977	141	2207										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32696085	32696085	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgtcatctctctccaggagTactagatattcccatgatca	6	12	4	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:32696085T>C	ENST00000421745.2	+	32	6619	c.6485T>C	c.(6484-6486)gTa>gCa	p.V2162A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2162					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TCTCCAGGAGTACTAGATATT	0.393																																					p.V2162A	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T6485C						.						139	112	121					2																	32696085		2202	4299	6501	SO:0001583	missense	57448	exon32			CAGGAGTACTAGA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.6485T>C	chr2.hg19:g.32696085T>C	ENSP00000393596:p.Val2162Ala	121.0	0.0		126.0	55.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	18.72	3.684730	0.68157	.	.	ENSG00000115760	ENST00000421745	T	0.73789	-0.78	5.3	5.3	0.74995	.	0.070053	0.56097	D	0.000029	T	0.80336	0.4604	L	0.44542	1.39	0.58432	D	0.999996	D	0.58970	0.984	D	0.65443	0.935	T	0.78785	-0.2068	10	0.33940	T	0.23	.	15.2916	0.73870	0.0:0.0:0.0:1.0	.	2162	Q9NR09	BIRC6_HUMAN	A	2162	ENSP00000393596:V2162A	ENSP00000393596:V2162A	V	+	2	0	BIRC6	32549589	1.000000	0.71417	0.999000	0.59377	0.678000	0.39670	8.036000	0.88901	1.999000	0.58509	0.524000	0.50904	GTA	.	.		0.393	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32696085	T	C	32696085	3	2	23	1	0	0	0	0	1	0	0	0	1438	1638	57	2	6611	2	BIRC6	2	32696085	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	6019689	32696085	210503288	142	2208										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32696135	32696135	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttatgctggtgtccaggttgCtggattatgtggcaactgtt	13	6	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:32696135C>T	ENST00000421745.2	+	32	6669	c.6535C>T	c.(6535-6537)Ctg>Ttg	p.L2179L		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2179					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					GTCCAGGTTGCTGGATTATGT	0.428																																					p.L2179L	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C6535T						.						148	119	129					2																	32696135		2202	4299	6501	SO:0001819	synonymous_variant	57448	exon32			AGGTTGCTGGATT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.6535C>T	chr2.hg19:g.32696135C>T		134.0	0.0		165.0	75.0	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.		0.428	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32696135	C	T	32696135	2	4	23	1	0	0	0	0	0	0	0	1	1438	796	28	3		3	BIRC6	2	32696135	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	50	32696135	210503238	143	2209										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33500964	33500964	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atactgtgacagcgggtaccGcatgactcagagaggccgtt	13	10	1	3	rs142262862		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:33500964G>A	ENST00000404816.2	+	18	3319	c.2966G>A	c.(2965-2967)cGc>cAc	p.R989H	LTBP1_ENST00000354476.3_Missense_Mutation_p.R990H|LTBP1_ENST00000407925.1_Missense_Mutation_p.R663H|LTBP1_ENST00000402934.1_Missense_Mutation_p.R610H|LTBP1_ENST00000390003.4_Missense_Mutation_p.R664H|LTBP1_ENST00000418533.2_Missense_Mutation_p.R663H|LTBP1_ENST00000404525.1_Missense_Mutation_p.R610H			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	989	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AGCGGGTACCGCATGACTCAG	0.572																																					p.R989H		Atlas-SNP	.											.	LTBP1	317	.	0			c.G2966A						.						119	107	111					2																	33500964		2203	4300	6503	SO:0001583	missense	4052	exon18			GGTACCGCATGAC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.2966G>A	chr2.hg19:g.33500964G>A	ENSP00000386043:p.Arg989His	85.0	0.0		65.0	17.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	G	10.12	1.261759	0.23051	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925	D;D;D;D;D;D;D	0.92299	-2.26;-2.26;-2.26;-2.26;-3.01;-2.26;-2.26	4.73	2.8	0.32819	EGF-like calcium-binding (2);	.	.	.	.	D	0.85358	0.5678	L	0.33792	1.035	0.80722	D	1	B;B;B;B;B;B	0.12630	0.006;0.005;0.003;0.005;0.005;0.005	B;B;B;B;B;B	0.14578	0.011;0.004;0.003;0.006;0.01;0.006	T	0.80013	-0.1560	9	0.44086	T	0.13	.	7.1534	0.25624	0.1695:0.0:0.6905:0.1399	.	989;663;610;663;664;990	Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	LTBP1_HUMAN;.;.;.;.;.	H	989;990;664;663;610;610;663	ENSP00000386043:R989H;ENSP00000346467:R990H;ENSP00000374653:R664H;ENSP00000393057:R663H;ENSP00000384373:R610H;ENSP00000385359:R610H;ENSP00000384091:R663H	ENSP00000346467:R990H	R	+	2	0	LTBP1	33354468	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.344000	0.52174	1.134000	0.42165	0.655000	0.94253	CGC	.	G|1.000;T|0.000		0.572	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		A	33500964	G	A	33500964	3	1	23	1	0	0	0	0	1	0	0	0	9082	1087	38	1	3091	1	LTBP1	2	33500964	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	804829	33500964	209698409	144	2210										
FAM98A	25940	hgsc.bcm.edu	37	chr2	33810066	33810066	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgccatcttggtatctattgTcctgctggtagccaccaccc	8	15	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:33810066T>C	ENST00000238823.8	-	8	1474	c.1334A>G	c.(1333-1335)gAc>gGc	p.D445G	FAM98A_ENST00000441530.2_Missense_Mutation_p.D250G|FAM98A_ENST00000498340.1_5'Flank|FAM98A_ENST00000403368.1_3'UTR			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	446	Gly-rich.						poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					GTATCTATTGTCCTGCTGGTA	0.587																																					p.D445G		Atlas-SNP	.											.	FAM98A	42	.	0			c.A1334G						.						153	133	140					2																	33810066		2203	4300	6503	SO:0001583	missense	25940	exon8			CTATTGTCCTGCT		CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.1334A>G	chr2.hg19:g.33810066T>C	ENSP00000238823:p.Asp445Gly	76.0	0.0		102.0	34.0	NM_015475	B2RNA2|Q9Y3Y6	Missense_Mutation	SNP	ENST00000238823.8	hg19	CCDS33179.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.434634	0.43224	.	.	ENSG00000119812	ENST00000238823;ENST00000395190;ENST00000441530	T;T	0.48522	0.81;0.84	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.30978	0.0782	N	0.08118	0	0.50171	D	0.999859	B;B;B;B	0.17852	0.024;0.024;0.015;0.024	B;B;B;B	0.15052	0.012;0.012;0.011;0.007	T	0.08086	-1.0739	10	0.39692	T	0.17	-12.4697	16.1354	0.81481	0.0:0.0:0.0:1.0	.	446;276;445;283	Q8NCA5;B4DY25;Q8NCA5-2;B3KTW4	FA98A_HUMAN;.;.;.	G	445;446;250	ENSP00000238823:D445G;ENSP00000408716:D250G	ENSP00000238823:D445G	D	-	2	0	FAM98A	33663570	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.125000	0.77193	2.207000	0.71202	0.533000	0.62120	GAC	.	.		0.587	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475		C	33810066	T	C	33810066	3	2	23	1	0	0	0	0	1	0	0	0	5664	1667	58	2	226	2	FAM98A	2	33810066	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	309102	33810066	209389307	145	2211										
SOCS5	9655	hgsc.bcm.edu	37	chr2	46986966	46986966	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgcatgcccgaattgagcagTggaatcacaactttagtttc	9	9	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:46986966T>C	ENST00000306503.5	+	2	1469	c.1297T>C	c.(1297-1299)Tgg>Cgg	p.W433R	SOCS5_ENST00000394861.2_Missense_Mutation_p.W433R	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	433	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell growth (GO:0016049)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|JAK-STAT cascade (GO:0007259)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of signal transduction (GO:0009968)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)		receptor tyrosine kinase binding (GO:0030971)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(9)|ovary(2)	22		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			AATTGAGCAGTGGAATCACAA	0.493																																					p.W433R		Atlas-SNP	.											.	SOCS5	62	.	0			c.T1297C						.						112	110	111					2																	46986966		2203	4300	6503	SO:0001583	missense	9655	exon2			GAGCAGTGGAATC	AB014571	CCDS1830.1	2p21	2013-02-14			ENSG00000171150	ENSG00000171150		"Suppressors of cytokine signaling", "SH2 domain containing"	16852	protein-coding gene	gene with protein product		607094				9734811, 11230166	Standard	NM_014011		Approved	KIAA0671, SOCS-5, CIS6, CISH6, Cish5	uc002rvf.3	O75159	OTTHUMG00000128852	ENST00000306503.5:c.1297T>C	chr2.hg19:g.46986966T>C	ENSP00000305133:p.Trp433Arg	173.0	0.0		83.0	4.0	NM_144949	Q53SD4|Q8IYZ4	Missense_Mutation	SNP	ENST00000306503.5	hg19	CCDS1830.1	.	.	.	.	.	.	.	.	.	.	T	18.05	3.538077	0.65085	.	.	ENSG00000171150	ENST00000306503;ENST00000394861	D;D	0.87571	-2.27;-2.27	5.43	5.43	0.79202	SH2 motif (4);	0.131240	0.64402	D	0.000014	D	0.87645	0.6229	N	0.17674	0.51	0.80722	D	1	D	0.55172	0.97	P	0.62885	0.908	D	0.89211	0.3564	10	0.59425	D	0.04	-15.4853	15.3001	0.73940	0.0:0.0:0.0:1.0	.	433	O75159	SOCS5_HUMAN	R	433	ENSP00000305133:W433R;ENSP00000378330:W433R	ENSP00000305133:W433R	W	+	1	0	SOCS5	46840470	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.121000	0.71602	2.279000	0.76181	0.533000	0.62120	TGG	.	.		0.493	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250791.2			C	46986966	T	C	46986966	3	2	23	1	0	0	0	0	1	0	0	0	14932	1696	59	2	1299	2	SOCS5	2	46986966	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	13176900	46986966	196212407	146	2212										
USP34	9736	hgsc.bcm.edu	37	chr2	61633160	61633160	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acaatgtttacaaagctggtCccggagcacttgaacttggg	11	9	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:61633160C>A	ENST00000398571.2	-	3	311	c.235G>T	c.(235-237)Gac>Tac	p.D79Y		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	79					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			CAAAGCTGGTCCCGGAGCACT	0.378																																					p.D79Y		Atlas-SNP	.											.	USP34	334	.	0			c.G235T						.						139	124	129					2																	61633160		1870	4110	5980	SO:0001583	missense	9736	exon3			GCTGGTCCCGGAG	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.235G>T	chr2.hg19:g.61633160C>A	ENSP00000381577:p.Asp79Tyr	146.0	0.0		65.0	46.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.967301	0.74131	.	.	ENSG00000115464	ENST00000398571	T	0.14144	2.53	6.07	6.07	0.98685	.	.	.	.	.	T	0.34687	0.0906	L	0.47716	1.5	0.54753	D	0.999987	D	0.76494	0.999	D	0.80764	0.994	T	0.00406	-1.1759	9	0.62326	D	0.03	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	79	Q70CQ2	UBP34_HUMAN	Y	79	ENSP00000381577:D79Y	ENSP00000381577:D79Y	D	-	1	0	USP34	61486664	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.591000	0.67536	2.885000	0.99019	0.655000	0.94253	GAC	.	.		0.378	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			A	61633160	C	A	61633160	3	1	23	1	0	0	0	0	1	0	0	0	17080	855	30	3	10717	3	USP34	2	61633160	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	14646194	61633160	181566213	147	2213										
TMEM17	200728	hgsc.bcm.edu	37	chr2	62733210	62733210	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtccgattggaatcactgaAcacggcccggctgaagtttc	12	11	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:62733210A>G	ENST00000335390.5	-	1	266	c.55T>C	c.(55-57)Ttc>Ctc	p.F19L		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	19					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GAATCACTGAACACGGCCCGG	0.667																																					p.F19L		Atlas-SNP	.											.	TMEM17	19	.	0			c.T55C						.						31	33	32					2																	62733210		2203	4300	6503	SO:0001583	missense	200728	exon1			CACTGAACACGGC		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.55T>C	chr2.hg19:g.62733210A>G	ENSP00000335094:p.Phe19Leu	195.0	0.0		113.0	74.0	NM_198276	Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	hg19	CCDS1871.1	.	.	.	.	.	.	.	.	.	.	A	14.80	2.643489	0.47258	.	.	ENSG00000186889	ENST00000335390	T	0.51817	0.69	4.82	4.82	0.62117	.	0.093568	0.64402	D	0.000002	T	0.37517	0.1006	L	0.32530	0.975	0.45899	D	0.998746	B	0.20780	0.048	B	0.18263	0.021	T	0.29119	-1.0022	10	0.66056	D	0.02	-15.613	11.9159	0.52765	1.0:0.0:0.0:0.0	.	19	Q86X19	TMM17_HUMAN	L	19	ENSP00000335094:F19L	ENSP00000335094:F19L	F	-	1	0	TMEM17	62586714	1.000000	0.71417	1.000000	0.80357	0.323000	0.28346	4.391000	0.59652	2.043000	0.60533	0.374000	0.22700	TTC	.	.		0.667	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276		G	62733210	A	G	62733210	3	3	23	1	0	0	0	0	1	0	0	0	16100	43	2	2	557	2	TMEM17	2	62733210	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1100050	62733210	180466163	148	2214										
ADD2	119	hgsc.bcm.edu	37	chr2	70900405	70900405	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagatgtggagggcaacgcTgaagaactcgcacacggccg	14	12	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:70900405T>A	ENST00000264436.4	-	15	2186				ADD2_ENST00000355733.3_Missense_Mutation_p.S599C|ADD2_ENST00000407644.2_Intron	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)						actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						AGGGCAACGCTGAAGAACTCG	0.542																																					p.S599C		Atlas-SNP	.											.	ADD2	261	.	0			c.A1795T						.						86	81	82					2																	70900405		2203	4300	6503	SO:0001627	intron_variant	119	exon15			CAACGCTGAAGAA	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.1742-267A>T	chr2.hg19:g.70900405T>A		151.0	0.0		77.0	60.0	NM_017488	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	hg19	CCDS1906.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.455236	0.43634	.	.	ENSG00000075340	ENST00000355733	T	0.08370	3.1	3.21	-2.93	0.05598	.	.	.	.	.	T	0.04952	0.0133	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.42766	-0.9432	8	0.87932	D	0	.	0.6394	0.00808	0.2385:0.1292:0.3475:0.2848	.	599	P35612-3	.	C	599	ENSP00000347972:S599C	ENSP00000347972:S599C	S	-	1	0	ADD2	70753913	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.777000	0.04669	-0.689000	0.05149	0.377000	0.23210	AGC	.	.		0.542	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		A	70900405	T	A	70900405	1	1	23	0	1	0	0	0	0	0	0	0	305	1580	55	4		4	ADD2	2	70900405	Intron	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	8167195	70900405	172298968	149	2215										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71650049	71650049	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaagaaagtactcccagcatTcaaacagaaactttggtaca	7	9	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:71650049T>G	ENST00000409544.1	+	22	4035	c.3405T>G	c.(3403-3405)atT>atG	p.I1135M	ZNF638_ENST00000409407.1_Missense_Mutation_p.I75M|ZNF638_ENST00000264447.4_Missense_Mutation_p.I1135M|ZNF638_ENST00000355812.3_Intron	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1135	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						CTCCCAGCATTCAAACAGAAA	0.408																																					p.I1135M		Atlas-SNP	.											.	ZNF638	179	.	0			c.T3405G						.						96	94	95					2																	71650049		2203	4300	6503	SO:0001583	missense	27332	exon22			CAGCATTCAAACA	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3405T>G	chr2.hg19:g.71650049T>G	ENSP00000386433:p.Ile1135Met	210.0	0.0		122.0	89.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	T	4.379	0.069935	0.08436	.	.	ENSG00000075292	ENST00000394137;ENST00000264447;ENST00000409544;ENST00000409407;ENST00000462695	T;T;T	0.34667	1.35;1.35;1.49	5.54	-0.259	0.12971	.	0.665977	0.14043	N	0.345301	T	0.16854	0.0405	N	0.17082	0.46	0.40676	D	0.982268	B;B;B	0.10296	0.003;0.001;0.0	B;B;B	0.09377	0.004;0.004;0.002	T	0.12426	-1.0548	10	0.45353	T	0.12	-0.7711	1.1287	0.01740	0.1947:0.1154:0.3386:0.3513	.	1135;1135;1135	A8K583;Q14966-3;Q14966	.;.;ZN638_HUMAN	M	714;1135;1135;75;75	ENSP00000264447:I1135M;ENSP00000386433:I1135M;ENSP00000386813:I75M	ENSP00000264447:I1135M	I	+	3	3	ZNF638	71503557	0.254000	0.23992	0.197000	0.23402	0.329000	0.28539	0.712000	0.25779	0.090000	0.17273	-1.333000	0.01266	ATT	.	.		0.408	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		G	71650049	T	G	71650049	3	3	23	1	0	0	0	0	1	0	0	0	18070	1771	62	5	3487	5	ZNF638	2	71650049	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	749644	71650049	171549324	150	2216										
DYSF	8291	hgsc.bcm.edu	37	chr2	71740432	71740432	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acagcaccatggacacgagaTactctggaaagaagtggccg	12	10	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:71740432T>C	ENST00000258104.3	+	6	734				DYSF_ENST00000413539.2_Missense_Mutation_p.Y174H|DYSF_ENST00000429174.2_Intron|DYSF_ENST00000410020.3_Missense_Mutation_p.Y175H|DYSF_ENST00000409582.3_Missense_Mutation_p.Y174H|DYSF_ENST00000409762.1_Missense_Mutation_p.Y174H|DYSF_ENST00000409366.1_Intron|DYSF_ENST00000409651.1_Missense_Mutation_p.Y175H|DYSF_ENST00000410041.1_Missense_Mutation_p.Y175H|DYSF_ENST00000394120.2_Intron|DYSF_ENST00000409744.1_Intron	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin						plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GGACACGAGATACTCTGGAAA	0.637																																					p.Y175H		Atlas-SNP	.											.	DYSF	536	.	0			c.T523C						.						31	39	37					2																	71740432		692	1591	2283	SO:0001627	intron_variant	8291	exon6			ACGAGATACTCTG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.458-414T>C	chr2.hg19:g.71740432T>C		249.0	0.0		131.0	94.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.361528	0.41801	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000409651;ENST00000410020;ENST00000410041	D;D;D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59;-1.59;-1.59	5.31	2.93	0.34026	.	.	.	.	.	T	0.76535	0.4001	.	.	.	0.21802	N	0.999536	D;D;P;P;D;D	0.59357	0.985;0.985;0.814;0.814;0.985;0.967	P;P;P;B;P;P	0.49085	0.563;0.563;0.532;0.408;0.563;0.6	T	0.62714	-0.6796	8	0.15499	T	0.54	-8.3227	6.9853	0.24725	0.0:0.182:0.0:0.818	.	175;175;175;174;174;174	O75923-8;O75923-13;O75923-11;O75923-5;O75923-2;O75923-7	.;.;.;.;.;.	H	174;174;174;175;175;175	ENSP00000407046:Y174H;ENSP00000387137:Y174H;ENSP00000386547:Y174H;ENSP00000386683:Y175H;ENSP00000386881:Y175H;ENSP00000386617:Y175H	ENSP00000386547:Y174H	Y	+	1	0	DYSF	71593940	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	0.843000	0.27640	0.344000	0.23847	0.443000	0.29094	TAC	.	.		0.637	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		C	71740432	T	C	71740432	1	2	23	0	1	0	0	0	0	0	0	0	4861	1406	49	2		2	DYSF	2	71740432	Intron	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	90383	71740432	171458941	151	2217										
DYSF	8291	hgsc.bcm.edu	37	chr2	71755509	71755509	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttggtggacccctttgtggAggtcagctttgcggggaaaa	15	8	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:71755509A>C	ENST00000258104.3	+	13	1539	c.1262A>C	c.(1261-1263)gAg>gCg	p.E421A	DYSF_ENST00000413539.2_Missense_Mutation_p.E452A|DYSF_ENST00000429174.2_Missense_Mutation_p.E421A|DYSF_ENST00000410020.3_Missense_Mutation_p.E453A|DYSF_ENST00000409582.3_Missense_Mutation_p.E452A|DYSF_ENST00000409762.1_Missense_Mutation_p.E452A|DYSF_ENST00000409366.1_Missense_Mutation_p.E422A|DYSF_ENST00000409651.1_Missense_Mutation_p.E453A|DYSF_ENST00000410041.1_Missense_Mutation_p.E453A|DYSF_ENST00000394120.2_Missense_Mutation_p.E422A|DYSF_ENST00000409744.1_Missense_Mutation_p.E422A	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	421	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CCCTTTGTGGAGGTCAGCTTT	0.557																																					p.E453A		Atlas-SNP	.											.	DYSF	536	.	0			c.A1358C						.						95	82	86					2																	71755509		2203	4300	6503	SO:0001583	missense	8291	exon14			TTGTGGAGGTCAG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1262A>C	chr2.hg19:g.71755509A>C	ENSP00000258104:p.Glu421Ala	122.0	0.0		71.0	49.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.525293	0.85600	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45	4.82	4.82	0.62117	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.81322	0.4798	M	0.79926	2.475	0.54753	D	0.999986	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;0.998;1.0;0.998;1.0;0.999;0.999;0.968;0.992;0.998;0.999;0.999	D;D;D;D;D;D;D;D;D;P;D;D;D;D	0.97110	0.998;0.998;0.998;0.998;1.0;0.987;1.0;0.987;0.998;0.852;0.932;0.998;0.998;0.999	D	0.83610	0.0133	10	0.62326	D	0.03	-23.5455	12.6301	0.56653	1.0:0.0:0.0:0.0	.	453;453;422;422;453;422;452;421;452;452;421;421;422;421	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	A	452;452;452;421;421;453;422;422;422;453;453	ENSP00000407046:E452A;ENSP00000387137:E452A;ENSP00000386547:E452A;ENSP00000398305:E421A;ENSP00000258104:E421A;ENSP00000386683:E453A;ENSP00000377678:E422A;ENSP00000386285:E422A;ENSP00000386512:E422A;ENSP00000386881:E453A;ENSP00000386617:E453A	ENSP00000258104:E421A	E	+	2	0	DYSF	71609017	1.000000	0.71417	0.972000	0.41901	0.953000	0.61014	8.945000	0.92985	1.948000	0.56530	0.379000	0.24179	GAG	.	.		0.557	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		C	71755509	A	C	71755509	3	2	23	1	0	0	0	0	1	0	0	0	4861	304	11	5	1504	5	DYSF	2	71755509	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	15077	71755509	171443864	152	2218										
DYSF	8291	hgsc.bcm.edu	37	chr2	71766312	71766312	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctgactcacaatgacatcGtggctaccacctacctgagt	8	14	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:71766312G>A	ENST00000258104.3	+	16	1700	c.1423G>A	c.(1423-1425)Gtg>Atg	p.V475M	DYSF_ENST00000413539.2_Missense_Mutation_p.V506M|DYSF_ENST00000429174.2_Missense_Mutation_p.V475M|DYSF_ENST00000410020.3_Missense_Mutation_p.V507M|DYSF_ENST00000409582.3_Missense_Mutation_p.V506M|DYSF_ENST00000409762.1_Missense_Mutation_p.V506M|DYSF_ENST00000409366.1_Missense_Mutation_p.V476M|DYSF_ENST00000409651.1_Missense_Mutation_p.V507M|DYSF_ENST00000410041.1_Missense_Mutation_p.V507M|DYSF_ENST00000394120.2_Missense_Mutation_p.V476M|DYSF_ENST00000409744.1_Missense_Mutation_p.V476M	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	475	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CAATGACATCGTGGCTACCAC	0.557																																					p.V507M		Atlas-SNP	.											DYSF_ENST00000410020,bladder,carcinoma,0,2	DYSF	536	.	0			c.G1519A						.						164	137	146					2																	71766312		2203	4300	6503	SO:0001583	missense	8291	exon17			GACATCGTGGCTA	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1423G>A	chr2.hg19:g.71766312G>A	ENSP00000258104:p.Val475Met	63.0	0.0		47.0	33.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.968347	0.53614	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	5.05	5.05	0.67936	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.072041	0.64402	D	0.000016	T	0.75932	0.3917	L	0.43598	1.365	0.35605	D	0.808191	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.76494	0.999;0.999;0.998;0.996;0.999;0.999;0.999;0.995;0.999;0.999;0.997;0.996;0.998;0.997	D;D;D;P;D;D;D;D;D;D;P;D;D;D	0.71414	0.918;0.918;0.918;0.9;0.973;0.958;0.973;0.924;0.918;0.952;0.9;0.918;0.918;0.951	T	0.80446	-0.1379	10	0.59425	D	0.04	-28.6766	9.6381	0.39822	0.0927:0.0:0.9073:0.0	.	507;507;476;476;507;476;506;475;506;506;475;475;476;475	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	M	506;506;506;475;475;507;476;476;476;507;507	ENSP00000407046:V506M;ENSP00000387137:V506M;ENSP00000386547:V506M;ENSP00000398305:V475M;ENSP00000258104:V475M;ENSP00000386683:V507M;ENSP00000377678:V476M;ENSP00000386285:V476M;ENSP00000386512:V476M;ENSP00000386881:V507M;ENSP00000386617:V507M	ENSP00000258104:V475M	V	+	1	0	DYSF	71619820	0.997000	0.39634	0.994000	0.49952	0.472000	0.32918	2.236000	0.43052	2.786000	0.95864	0.563000	0.77884	GTG	.	.		0.557	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71766312	G	A	71766312	3	1	23	1	0	0	0	0	1	0	0	0	4861	1145	40	1	1677	1	DYSF	2	71766312	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	10803	71766312	171433061	153	2219										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73718037	73718038	+	Frame_Shift_Ins	INS	-	-	T													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaccaaatgaataaacaccaINSttttccccttcctcaaggtc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:73718037_73718038insT	ENST00000264448.6	+	10	9059_9060	c.8948_8949insT	c.(8947-8952)cattttfs	p.HF2983fs	AC096546.1_ENST00000408160.1_RNA|ALMS1_ENST00000409009.1_Frame_Shift_Ins_p.HF2941fs	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2983					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AATAAACACCATTTTCCCCTTC	0.391																																					p.H2983fs		Atlas-Indel,Pindel	.											.	ALMS1	384	.	0			c.8948_8949insT						.																																			SO:0001589	frameshift_variant	7840	exon10			.	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.8952dupT	chr2.hg19:g.73718041_73718041dupT	ENSP00000264448:p.His2983fs	187.0	0.0		193.0	80.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Frame_Shift_Ins	INS	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.391	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73718038	-	T	73718037	7	5	23	1	0	1	1	0	0	0	0	0	535	217	8	0	8986	0	ALMS1	2	73718037	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	1951725	73718037	169481336	154	2220										
DCTN1	1639	hgsc.bcm.edu	37	chr2	74593128	74593128	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcacgaagggcagcagcccgCagttcaaccggtggaggcta	15	12	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:74593128C>T	ENST00000361874.3	-	24	3095	c.2778G>A	c.(2776-2778)ctG>ctA	p.L926L	DCTN1_ENST00000495643.1_5'UTR|DCTN1_ENST00000394003.3_Silent_p.L919L|DCTN1_ENST00000409868.1_Silent_p.L909L|DCTN1_ENST00000409567.3_Silent_p.L906L|DCTN1_ENST00000409240.1_Silent_p.L889L|DCTN1_ENST00000409438.1_Silent_p.L792L|DCTN1_ENST00000407639.2_Silent_p.L792L|RP11-287D1.3_ENST00000451608.2_5'Flank	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	926					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CAGCAGCCCGCAGTTCAACCG	0.512																																					p.L926L		Atlas-SNP	.											DCTN1,right_upper_lobe,carcinoma,-2,1	DCTN1	110	.	0			c.G2778A						.						69	72	71					2																	74593128		2203	4300	6503	SO:0001819	synonymous_variant	1639	exon24			AGCCCGCAGTTCA		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"p150 glued homolog (Drosophila)"	601143	"dynactin 1 (p150, Glued (Drosophila) homolog)"			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.2778G>A	chr2.hg19:g.74593128C>T		60.0	0.0		81.0	37.0	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	hg19	CCDS1939.1																																																																																			.	.		0.512	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		T	74593128	C	T	74593128	2	4	23	1	0	0	0	0	0	0	0	1	4308	697	25	3		3	DCTN1	2	74593128	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	875091	74593128	168606245	155	2221										
C2orf65	130951	hgsc.bcm.edu	37	chr2	74789369	74789369	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cattcttaaggctatcatcaTgtgggtcctcaggtagcagg	11	9	4	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:74789369T>C	ENST00000290536.5	-	8	1372	c.1256A>G	c.(1255-1257)cAt>cGt	p.H419R	M1AP_ENST00000536235.1_Missense_Mutation_p.H419R|M1AP_ENST00000358434.2_Intron|M1AP_ENST00000409585.1_Missense_Mutation_p.H419R|M1AP_ENST00000464686.1_5'UTR	NM_001281296.1|NM_138804.3	NP_001268225.1|NP_620159.2	Q8TC57	M1AP_HUMAN	meiosis 1 associated protein	419					cell differentiation (GO:0030154)|chromatin assembly (GO:0031497)|female gamete generation (GO:0007292)|male meiosis chromosome separation (GO:0051308)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GCTATCATCATGTGGGTCCTC	0.557																																					p.H419R		Atlas-SNP	.											.	.	.	.	0			c.A1256G						.						139	126	130					2																	74789369		2203	4300	6503	SO:0001583	missense	130951	exon8			TCATCATGTGGGT		CCDS33229.1, CCDS62941.1	2p13.1	2013-02-05	2013-02-05	2013-01-16	ENSG00000159374	ENSG00000159374			25183	protein-coding gene	gene with protein product	"meiosis 1 arresting protein", "spermatogenesis associated 37"		"chromosome 2 open reading frame 65"	C2orf65		16881047, 23269666	Standard	NM_138804		Approved	D6Mm5e, SPATA37	uc002smy.3	Q8TC57	OTTHUMG00000152918	ENST00000290536.5:c.1256A>G	chr2.hg19:g.74789369T>C	ENSP00000290536:p.His419Arg	112.0	0.0		121.0	21.0	NM_138804	B7Z6E7|E9PGG8|Q6ZP30|Q96L07	Missense_Mutation	SNP	ENST00000290536.5	hg19	CCDS33229.1	.	.	.	.	.	.	.	.	.	.	T	2.905	-0.226739	0.06022	.	.	ENSG00000159374	ENST00000290536;ENST00000409585;ENST00000536235	T;T;T	0.40476	1.03;1.03;1.03	5.28	2.29	0.28610	.	0.335776	0.32473	N	0.006041	T	0.19604	0.0471	N	0.08118	0	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.14783	-1.0460	10	0.30078	T	0.28	-15.8409	7.4257	0.27098	0.0:0.1686:0.4955:0.3358	.	419;419;175	E9PGG8;Q8TC57;B3KX03	.;CB065_HUMAN;.	R	419	ENSP00000290536:H419R;ENSP00000386793:H419R;ENSP00000445662:H419R	ENSP00000290536:H419R	H	-	2	0	C2orf65	74642877	0.345000	0.24835	0.557000	0.28306	0.397000	0.30659	1.621000	0.36986	0.617000	0.30160	-1.228000	0.01579	CAT	.	.		0.557	M1AP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328569.1	NM_138804		C	74789369	T	C	74789369	3	2	23	1	0	0	0	0	1	0	0	0	2186	1464	51	2	352	2	C2orf65	2	74789369	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	196241	74789369	168410004	156	2222										
LRRTM4	80059	hgsc.bcm.edu	37	chr2	77746553	77746553	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttaaattgttcagattgcaAtgtctgaagcttattgtagg	9	4	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:77746553A>G	ENST00000409093.1	-	3	778	c.442T>C	c.(442-444)Ttg>Ctg	p.L148L	LRRTM4_ENST00000409884.1_Silent_p.L148L|LRRTM4_ENST00000409911.1_Silent_p.L149L|LRRTM4_ENST00000409088.3_Silent_p.L148L|LRRTM4_ENST00000409282.1_Silent_p.L149L			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	148					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		TCAGATTGCAATGTCTGAAGC	0.388																																					p.L148L		Atlas-SNP	.											.	LRRTM4	334	.	0			c.T442C						.						90	81	84					2																	77746553		1844	4082	5926	SO:0001819	synonymous_variant	80059	exon3			ATTGCAATGTCTG	AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.442T>C	chr2.hg19:g.77746553A>G		180.0	0.0		162.0	71.0	NM_024993	Q4FZ98|Q6UXJ7	Silent	SNP	ENST00000409093.1	hg19	CCDS46346.1																																																																																			.	.		0.388	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		G	77746553	A	G	77746553	2	3	23	1	0	0	0	0	0	0	0	1	9051	98	4	2		2	LRRTM4	2	77746553	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2957184	77746553	165452820	157	2223										
GGCX	2677	hgsc.bcm.edu	37	chr2	85788544	85788544	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccgcgcggacccggcagacAccgccattgctctgcggagg	14	16	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:85788544A>G	ENST00000233838.4	-	1	88	c.8T>C	c.(7-9)gTg>gCg	p.V3A	GGCX_ENST00000430215.3_Missense_Mutation_p.V3A|VAMP8_ENST00000432071.1_5'Flank	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	3					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	CCCGGCAGACACCGCCATTGC	0.701																																					p.V3A		Atlas-SNP	.											.	GGCX	44	.	0			c.T8C						.						6	8	7					2																	85788544		2109	4194	6303	SO:0001583	missense	2677	exon1			GCAGACACCGCCA		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"vitamin K-dependent gamma-carboxylase"	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.8T>C	chr2.hg19:g.85788544A>G	ENSP00000233838:p.Val3Ala	217.0	0.0		194.0	77.0	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Missense_Mutation	SNP	ENST00000233838.4	hg19	CCDS1978.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.049881	0.36181	.	.	ENSG00000115486	ENST00000233838;ENST00000430215	D;D	0.94280	-3.39;-3.22	2.56	-4.86	0.03132	.	1.066580	0.07375	N	0.886497	D	0.85522	0.5716	L	0.33485	1.01	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.70073	-0.4972	10	0.30854	T	0.27	0.012	4.497	0.11842	0.3193:0.0:0.4938:0.187	.	3;3	E9PEE1;P38435	.;VKGC_HUMAN	A	3	ENSP00000233838:V3A;ENSP00000408045:V3A	ENSP00000233838:V3A	V	-	2	0	GGCX	85642055	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-1.571000	0.02138	-1.174000	0.02754	0.454000	0.30748	GTG	.	.		0.701	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		G	85788544	A	G	85788544	3	3	23	1	0	0	0	0	1	0	0	0	6364	159	6	2	2328	2	GGCX	2	85788544	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	8041991	85788544	157410829	158	2224										
STARD7	56910	hgsc.bcm.edu	37	chr2	96852600	96852600	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcctttactttaatctccatAttcttggctttcagagtggc	6	10	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:96852600A>T	ENST00000337288.5	-	8	1364	c.981T>A	c.(979-981)aaT>aaA	p.N327K	STARD7_ENST00000462501.1_5'UTR	NM_020151.3	NP_064536.2	Q9NQZ5	STAR7_HUMAN	StAR-related lipid transfer (START) domain containing 7	327	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.					mitochondrion (GO:0005739)	lipid binding (GO:0008289)			endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|stomach(2)	14						TAATCTCCATATTCTTGGCTT	0.483																																					p.N327K		Atlas-SNP	.											.	STARD7	49	.	0			c.T981A						.						78	75	76					2																	96852600		2203	4300	6503	SO:0001583	missense	56910	exon8			CTCCATATTCTTG	AF270647	CCDS2017.2	2p11.1	2011-09-12	2007-08-16		ENSG00000084090	ENSG00000084090		"StAR-related lipid transfer (START) domain containing"	18063	protein-coding gene	gene with protein product			"START domain containing 7"				Standard	NM_020151		Approved	GTT1	uc002svm.4	Q9NQZ5	OTTHUMG00000130457	ENST00000337288.5:c.981T>A	chr2.hg19:g.96852600A>T	ENSP00000338030:p.Asn327Lys	152.0	0.0		161.0	74.0	NM_020151	D3DXG9|Q53T44|Q6GU43|Q969M6	Missense_Mutation	SNP	ENST00000337288.5	hg19	CCDS2017.2	.	.	.	.	.	.	.	.	.	.	A	22.7	4.319266	0.81469	.	.	ENSG00000084090	ENST00000337288	T	0.44482	0.92	5.84	3.08	0.35506	Lipid-binding START (2);	0.000000	0.85682	D	0.000000	T	0.35189	0.0923	L	0.51422	1.61	0.58432	D	0.999997	P	0.48589	0.912	B	0.43478	0.421	T	0.06552	-1.0820	10	0.19147	T	0.46	-30.1027	9.2388	0.37484	0.2406:0.0:0.7594:0.0	.	327	Q9NQZ5	STAR7_HUMAN	K	327	ENSP00000338030:N327K	ENSP00000338030:N327K	N	-	3	2	STARD7	96216327	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.239000	0.51360	0.375000	0.24679	-0.242000	0.12053	AAT	.	.		0.483	STARD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252848.2			T	96852600	A	T	96852600	3	4	23	1	0	0	0	0	1	0	0	0	15277	446	16	4	135	4	STARD7	2	96852600	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	11064056	96852600	146346773	159	2225										
FAM178B	51252	hgsc.bcm.edu	37	chr2	97587274	97587275	+	Frame_Shift_Ins	INS	-	-	T													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agaagctgctggaggtcaacINStttgggcagcaggcggagcc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:97587274_97587275insT	ENST00000417561.3	-	15	1847_1848	c.1848_1849insA	c.(1846-1851)aaagttfs	p.V617fs	FAM178B_ENST00000327896.3_Frame_Shift_Ins_p.V437fs|FAM178B_ENST00000490605.2_Frame_Shift_Ins_p.V469fs			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	617										large_intestine(1)|ovary(1)	2						TGGAGGTCAACTTTGGGCAGCA	0.619																																					p.V469fs		Atlas-Indel,Pindel	.											.	FAM178B	35	.	0			c.1405_1406insA						.																																			SO:0001589	frameshift_variant	51252	exon11			.	AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.1849dupA	chr2.hg19:g.97587277_97587277dupT	ENSP00000413245:p.Val617fs	270.0	0.0		281.0	107.0	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Frame_Shift_Ins	INS	ENST00000417561.3	hg19																																																																																				.	.		0.619	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490		T	97587275	-	T	97587274	7	5	23	1	0	1	1	0	0	0	0	0	5509	565	20	0	693	0	FAM178B	2	97587274	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	734674	97587274	145612099	160	2226										
TMEM131	23505	hgsc.bcm.edu	37	chr2	98382614	98382614	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actggaacggaatcccactcCggtggaggagagtctttttc	12	10	1	1	rs376329900		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:98382614C>T	ENST00000186436.5	-	35	4914	c.4686G>A	c.(4684-4686)ccG>ccA	p.P1562P		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1562						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						AATCCCACTCCGGTGGAGGAG	0.498																																					p.P1562P		Atlas-SNP	.											.	TMEM131	258	.	0			c.G4686A						.	C		0,3728		0,0,1864	87	87	87		4686	-11.6	0.3	2		87	1,8193		0,1,4096	no	coding-synonymous	TMEM131	NM_015348.1		0,1,5960	TT,TC,CC		0.0122,0.0,0.0084		1562/1884	98382614	1,11921	1864	4097	5961	SO:0001819	synonymous_variant	23505	exon35			CCACTCCGGTGGA	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.4686G>A	chr2.hg19:g.98382614C>T		238.0	0.0		213.0	86.0	NM_015348		Silent	SNP	ENST00000186436.5	hg19	CCDS46368.1																																																																																			.	.		0.498	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		T	98382614	C	T	98382614	2	4	23	1	0	0	0	0	0	0	0	1	16059	639	23	1		1	TMEM131	2	98382614	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	795340	98382614	144816759	161	2227										
MGAT4A	11320	hgsc.bcm.edu	37	chr2	99294779	99294779	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtttgtacctgaaaacttatTcaacgcatccttacttccat	4	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:99294779T>A	ENST00000264968.3	-	2	613	c.250A>T	c.(250-252)Aat>Tat	p.N84Y	MGAT4A_ENST00000409391.1_Missense_Mutation_p.N84Y|MGAT4A_ENST00000393487.1_Missense_Mutation_p.N84Y			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	84					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						GAAAACTTATTCAACGCATCC	0.294																																					p.N84Y		Atlas-SNP	.											.	MGAT4A	51	.	0			c.A250T						.						86	83	84					2																	99294779		2202	4300	6502	SO:0001583	missense	11320	exon3			ACTTATTCAACGC	AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	2.4.1.145	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7047	protein-coding gene	gene with protein product		604623	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A"			10024668	Standard	NM_001160154		Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.250A>T	chr2.hg19:g.99294779T>A	ENSP00000264968:p.Asn84Tyr	72.0	0.0		63.0	21.0	NM_012214	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Missense_Mutation	SNP	ENST00000264968.3	hg19	CCDS2036.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.768726	0.31320	.	.	ENSG00000071073	ENST00000393487;ENST00000264968;ENST00000409391	T;T;T	0.44482	0.92;0.92;0.92	5.44	4.29	0.51040	.	0.819623	0.11745	N	0.533589	T	0.38427	0.1040	L	0.40543	1.245	0.09310	N	1	B	0.26041	0.14	B	0.31547	0.132	T	0.37502	-0.9703	10	0.66056	D	0.02	.	10.3625	0.44003	0.0:0.0769:0.0:0.9231	.	84	Q9UM21	MGT4A_HUMAN	Y	84	ENSP00000377127:N84Y;ENSP00000264968:N84Y;ENSP00000386841:N84Y	ENSP00000264968:N84Y	N	-	1	0	MGAT4A	98661211	0.996000	0.38824	0.407000	0.26434	0.365000	0.29674	2.347000	0.44036	0.906000	0.36621	0.454000	0.30748	AAT	.	.		0.294	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214		A	99294779	T	A	99294779	3	1	23	1	0	0	0	0	1	0	0	0	9554	1783	62	4	1515	4	MGAT4A	2	99294779	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	912165	99294779	143904594	162	2228										
SLC9A2	6549	hgsc.bcm.edu	37	chr2	103311560	103311560	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggacattggggtcacaactTttggagagacaagtaagaag	13	5	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:103311560T>G	ENST00000233969.2	+	7	1716	c.1574T>G	c.(1573-1575)tTt>tGt	p.F525C	SLC9A2_ENST00000469286.1_3'UTR	NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	525					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						GGTCACAACTTTTGGAGAGAC	0.378																																					p.F525C		Atlas-SNP	.											.	SLC9A2	112	.	0			c.T1574G						.						212	211	211					2																	103311560		2203	4300	6503	SO:0001583	missense	6549	exon7			ACAACTTTTGGAG		CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"Solute carriers"	11072	protein-coding gene	gene with protein product		600530	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 2"	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.1574T>G	chr2.hg19:g.103311560T>G	ENSP00000233969:p.Phe525Cys	116.0	0.0		109.0	40.0	NM_003048	B2RMS2	Missense_Mutation	SNP	ENST00000233969.2	hg19	CCDS2062.1	.	.	.	.	.	.	.	.	.	.	T	18.62	3.663705	0.67700	.	.	ENSG00000115616	ENST00000233969	T	0.56275	0.47	5.91	5.91	0.95273	.	0.165493	0.56097	D	0.000031	T	0.54046	0.1834	L	0.40543	1.245	0.43756	D	0.996263	D	0.61080	0.989	P	0.52514	0.701	T	0.56763	-0.7925	10	0.56958	D	0.05	.	11.4321	0.50047	0.1345:0.0:0.0:0.8655	.	525	Q9UBY0	SL9A2_HUMAN	C	525	ENSP00000233969:F525C	ENSP00000233969:F525C	F	+	2	0	SLC9A2	102677992	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.403000	0.59729	2.254000	0.74563	0.533000	0.62120	TTT	.	.		0.378	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2			G	103311560	T	G	103311560	3	3	23	1	0	0	0	0	1	0	0	0	14727	1841	64	5	1600	5	SLC9A2	2	103311560	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	4016781	103311560	139887813	163	2229										
BUB1	699	hgsc.bcm.edu	37	chr2	111416240	111416240	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatggctgcactttggatggCgttgcctgaaccattcccag	12	11	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:111416240C>T	ENST00000302759.6	-	12	1474	c.1356G>A	c.(1354-1356)acG>acA	p.T452T	BUB1_ENST00000535254.1_Silent_p.T432T|BUB1_ENST00000409311.1_Silent_p.T452T	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	452					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.T452T(1)		breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		CTTTGGATGGCGTTGCCTGAA	0.433																																					p.T452T		Atlas-SNP	.											BUB1,colon,NS,0,1	BUB1	91	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1356A						.						226	192	204					2																	111416240		2203	4300	6503	SO:0001819	synonymous_variant	699	exon12			GGATGGCGTTGCC	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"budding uninhibited by benzimidazoles 1 (yeast homolog)", "budding uninhibited by benzimidazoles 1 homolog (yeast)"	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.1356G>A	chr2.hg19:g.111416240C>T		114.0	0.0		114.0	45.0	NM_004336	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Silent	SNP	ENST00000302759.6	hg19	CCDS33273.1																																																																																			.	.		0.433	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		T	111416240	C	T	111416240	2	4	23	1	0	0	0	0	0	0	0	1	1572	755	27	1		1	BUB1	2	111416240	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	8104680	111416240	131783133	164	2230										
RALB	5899	hgsc.bcm.edu	37	chr2	121036312	121036312	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atcatggttggcagcggaggCgttggcaagtcagccctgac	15	10	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:121036312C>T	ENST00000272519.5	+	2	342	c.72C>T	c.(70-72)ggC>ggT	p.G24G	RALB_ENST00000470417.1_Intron|RALB_ENST00000404963.3_Silent_p.G24G|RALB_ENST00000420510.1_Silent_p.G24G|RALB_ENST00000474855.2_Silent_p.G46G	NM_002881.2	NP_002872.1	P11234	RALB_HUMAN	v-ral simian leukemia viral oncogene homolog B	24					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of exocyst assembly (GO:0001928)|regulation of exocyst localization (GO:0060178)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(154;0.122)				GCAGCGGAGGCGTTGGCAAGT	0.577																																					p.G24G		Atlas-SNP	.											.	RALB	27	.	0			c.C72T						.						108	83	92					2																	121036312		2203	4300	6503	SO:0001819	synonymous_variant	5899	exon2			CGGAGGCGTTGGC		CCDS2131.1	2q14.2	2014-05-09	2013-07-09		ENSG00000144118	ENSG00000144118			9840	protein-coding gene	gene with protein product	"ras related GTP binding protein B"	179551					Standard	NM_002881		Approved		uc002tmk.3	P11234	OTTHUMG00000131435	ENST00000272519.5:c.72C>T	chr2.hg19:g.121036312C>T		97.0	0.0		68.0	25.0	NM_002881	B4E040|Q53T32|Q6ZS74	Silent	SNP	ENST00000272519.5	hg19	CCDS2131.1																																																																																			.	.		0.577	RALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254232.3	NM_002881		T	121036312	C	T	121036312	2	4	23	1	0	0	0	0	0	0	0	1	13026	755	27	1		1	RALB	2	121036312	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	9620072	121036312	122163061	165	2231										
GLI2	2736	hgsc.bcm.edu	37	chr2	121746146	121746146	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcaacctcacgccggcgcagCagtacagcctgcgggccaag	12	16	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:121746146C>T	ENST00000452319.1	+	14	2716	c.2656C>T	c.(2656-2658)Cag>Tag	p.Q886*	GLI2_ENST00000361492.4_Nonsense_Mutation_p.Q886*|GLI2_ENST00000314490.11_Nonsense_Mutation_p.Q558*					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GCCGGCGCAGCAGTACAGCCT	0.741																																					p.Q886X		Atlas-SNP	.											.	GLI2	187	.	0			c.C2656T						.						2	2	2					2																	121746146		1550	3232	4782	SO:0001587	stop_gained	2736	exon13			GCGCAGCAGTACA		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.2656C>T	chr2.hg19:g.121746146C>T	ENSP00000390436:p.Gln886*	138.0	0.0		158.0	67.0	NM_005270		Nonsense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	C	39	7.347207	0.98228	.	.	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	.	.	.	4.94	4.94	0.65067	.	0.231838	0.45126	D	0.000395	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.3616	0.90376	0.0:1.0:0.0:0.0	.	.	.	.	X	886;886;558	.	ENSP00000312694:Q558X	Q	+	1	0	GLI2	121462616	1.000000	0.71417	1.000000	0.80357	0.741000	0.42261	7.361000	0.79497	2.563000	0.86464	0.561000	0.74099	CAG	.	.		0.741	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121746146	C	T	121746146	4	4	23	1	0	0	0	0	0	1	0	0	6446	711	25	3	2706	3	GLI2	2	121746146	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	709834	121746146	121453227	166	2232										
WDR33	55339	hgsc.bcm.edu	37	chr2	128471170	128471170	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcccacctttcttctctgcGccctcgaaaacgtgggtcct	8	16	2	0	rs373594035		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:128471170G>A	ENST00000322313.4	-	18	3453	c.3295C>T	c.(3295-3297)Cgc>Tgc	p.R1099C		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	1099					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TCTTCTCTGCGCCCTCGAAAA	0.582																																					p.R1099C		Atlas-SNP	.											WDR33,NS,carcinoma,0,1	WDR33	136	.	0			c.C3295T						.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	124	129	128		3295	4.9	1	2		128	0,8600		0,0,4300	no	missense	WDR33	NM_018383.4	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1099/1337	128471170	1,13005	2203	4300	6503	SO:0001583	missense	55339	exon18			CTCTGCGCCCTCG		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.3295C>T	chr2.hg19:g.128471170G>A	ENSP00000325377:p.Arg1099Cys	132.0	1.0		81.0	25.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.810035	0.70797	2.27E-4	0.0	ENSG00000136709	ENST00000322313	D	0.91068	-2.78	5.81	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.83936	0.5362	N	0.08118	0	0.80722	D	1	D	0.69078	0.997	P	0.47603	0.551	D	0.86199	0.1617	10	0.49607	T	0.09	-8.0567	14.9159	0.70798	0.0:0.0:0.7541:0.2459	.	1099	Q9C0J8	WDR33_HUMAN	C	1099	ENSP00000325377:R1099C	ENSP00000325377:R1099C	R	-	1	0	WDR33	128187640	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.889000	0.48601	2.738000	0.93877	0.655000	0.94253	CGC	.	.		0.582	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		A	128471170	G	A	128471170	3	1	23	1	0	0	0	0	1	0	0	0	17302	1087	38	1	735	1	WDR33	2	128471170	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	6725024	128471170	114728203	167	2233										
CCDC74B	91409	hgsc.bcm.edu	37	chr2	130897479	130897479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttaccatttcttggagaggCtcttggtggagaccttgggg	14	8	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:130897479C>T	ENST00000310463.6	-	7	1129	c.992G>A	c.(991-993)aGc>aAc	p.S331N	MED15P9_ENST00000427638.1_RNA|CCDC74B_ENST00000409943.3_Missense_Mutation_p.S265N|CCDC74B_ENST00000392984.3_Missense_Mutation_p.S433N	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	331										endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					CTTGGAGAGGCTCTTGGTGGA	0.642																																					p.S331N		Atlas-SNP	.											.	CCDC74B	27	.	0			c.G992A						.						23	26	25					2																	130897479		2199	4275	6474	SO:0001583	missense	91409	exon7			GAGAGGCTCTTGG		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.992G>A	chr2.hg19:g.130897479C>T	ENSP00000308873:p.Ser331Asn	125.0	0.0		124.0	39.0	NM_207310	Q6NW18	Missense_Mutation	SNP	ENST00000310463.6	hg19	CCDS2155.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.006|0.006	-2.084878|-2.084878	0.00371|0.00371	.|.	.|.	ENSG00000152076|ENSG00000152076	ENST00000409488|ENST00000409943;ENST00000310463;ENST00000392984	.|T;T;T	.|0.30981	.|1.51;1.51;1.51	3.92|3.92	2.09|2.09	0.27110|0.27110	.|.	.|0.684728	.|0.11076	.|U	.|0.602420	T|T	0.12263|0.12263	0.0298|0.0298	N|N	0.05078|0.05078	-0.115|-0.115	0.09310|0.09310	N|N	1|1	.|B;B;P	.|0.50528	.|0.003;0.0;0.936	.|B;B;B	.|0.41236	.|0.004;0.001;0.351	T|T	0.04400|0.04400	-1.0954|-1.0954	6|10	0.31617|0.12430	T|T	0.26|0.62	.|.	5.6153|5.6153	0.17428|0.17428	0.0:0.7517:0.0:0.2483|0.0:0.7517:0.0:0.2483	.|.	.|433;265;331	.|E7ESC5;Q96LY2-2;Q96LY2	.|.;.;CC74B_HUMAN	T|N	229|265;331;433	.|ENSP00000386294:S265N;ENSP00000308873:S331N;ENSP00000376710:S433N	ENSP00000386250:A229T|ENSP00000308873:S331N	A|S	-|-	1|2	0|0	CCDC74B|CCDC74B	130613949|130613949	0.016000|0.016000	0.18221|0.18221	0.004000|0.004000	0.12327|0.12327	0.003000|0.003000	0.03518|0.03518	0.190000|0.190000	0.17057|0.17057	1.005000|1.005000	0.39183|0.39183	-0.401000|-0.401000	0.06369|0.06369	GCC|AGC	.	.		0.642	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310		T	130897479	C	T	130897479	3	4	23	1	0	0	0	0	1	0	0	0	2850	797	28	3	158	3	CCDC74B	2	130897479	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2426309	130897479	112301894	168	2234										
CCNT2	905	hgsc.bcm.edu	37	chr2	135711218	135711218	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggattacatcacagacctgAcaaaatttcagatcattctt	5	9	4	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:135711218A>T	ENST00000264157.5	+	9	1223	c.1193A>T	c.(1192-1194)gAc>gTc	p.D398V	CCNT2_ENST00000537343.1_Missense_Mutation_p.D223V|CCNT2_ENST00000295238.6_Missense_Mutation_p.D398V	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	398					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		CACAGACCTGACAAAATTTCA	0.413																																					p.D398V		Atlas-SNP	.											.	CCNT2	98	.	0			c.A1193T						.						80	81	81					2																	135711218		2203	4300	6503	SO:0001583	missense	905	exon9			GACCTGACAAAAT	AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.1193A>T	chr2.hg19:g.135711218A>T	ENSP00000264157:p.Asp398Val	286.0	0.0		154.0	107.0	NM_058241	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Missense_Mutation	SNP	ENST00000264157.5	hg19	CCDS2174.1	.	.	.	.	.	.	.	.	.	.	A	14.17	2.456750	0.43634	.	.	ENSG00000082258	ENST00000537343;ENST00000295238;ENST00000264157	T;T	0.28255	1.75;1.62	5.71	5.71	0.89125	.	0.175765	0.64402	D	0.000010	T	0.44008	0.1273	L	0.54323	1.7	0.80722	D	1	P;B;D	0.57571	0.665;0.036;0.98	P;B;P	0.53649	0.607;0.005;0.731	T	0.32851	-0.9891	10	0.52906	T	0.07	.	16.0044	0.80349	1.0:0.0:0.0:0.0	.	223;398;398	B4DH21;O60583;O60583-2	.;CCNT2_HUMAN;.	V	223;398;398	ENSP00000295238:D398V;ENSP00000264157:D398V	ENSP00000264157:D398V	D	+	2	0	CCNT2	135427688	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.602000	0.90868	2.191000	0.70037	0.528000	0.53228	GAC	.	.		0.413	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241		T	135711218	A	T	135711218	3	4	23	1	0	0	0	0	1	0	0	0	2937	275	10	4	1227	4	CCNT2	2	135711218	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	4813739	135711218	107488155	169	2235										
ZRANB3	84083	hgsc.bcm.edu	37	chr2	136029454	136029454	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccatctatcctaatgtaacGagtctagcatcaacaaggaa	6	10	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:136029454G>A	ENST00000264159.6	-	10	1206	c.1090C>T	c.(1090-1092)Cgt>Tgt	p.R364C	ZRANB3_ENST00000536680.1_Missense_Mutation_p.R364C|ZRANB3_ENST00000401392.1_Missense_Mutation_p.R364C	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	364	DNA annealing helicase activity.|Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		CTAATGTAACGAGTCTAGCAT	0.368																																					p.R364C		Atlas-SNP	.											.	ZRANB3	109	.	0			c.C1090T						.						68	65	66					2																	136029454		1870	4112	5982	SO:0001583	missense	84083	exon10			TGTAACGAGTCTA	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"Zinc fingers, RAN-binding domain containing"	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.1090C>T	chr2.hg19:g.136029454G>A	ENSP00000264159:p.Arg364Cys	65.0	0.0		39.0	29.0	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	hg19	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.218594	0.79464	.	.	ENSG00000121988	ENST00000401392;ENST00000264159;ENST00000536680;ENST00000397448	T;T;T	0.77358	-1.09;-1.09;-1.09	5.94	5.94	0.96194	Helicase, C-terminal (3);	0.153021	0.64402	D	0.000008	D	0.87398	0.6167	M	0.63208	1.945	0.58432	D	0.999999	D;D;D	0.89917	0.997;1.0;1.0	P;D;D	0.73380	0.613;0.98;0.962	D	0.87035	0.2137	10	0.66056	D	0.02	-10.0918	20.3593	0.98849	0.0:0.0:1.0:0.0	.	304;364;364	E9PBP0;Q5FWF4;Q5FWF4-3	.;ZRAB3_HUMAN;.	C	364;364;364;304	ENSP00000383979:R364C;ENSP00000264159:R364C;ENSP00000441320:R364C	ENSP00000264159:R364C	R	-	1	0	ZRANB3	135745924	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.377000	0.52425	2.807000	0.96579	0.591000	0.81541	CGT	.	.		0.368	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		A	136029454	G	A	136029454	3	1	23	1	0	0	0	0	1	0	0	0	18239	1058	37	1	2197	1	ZRANB3	2	136029454	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	318236	136029454	107169919	170	2236										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141232790	141232790	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtctacgattaacataatctAttgttagtgccataggtcta	7	7	3	0	rs377526659		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:141232790A>T	ENST00000389484.3	-	60	10513	c.9542T>A	c.(9541-9543)aTa>aAa	p.I3181K		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3181					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AACATAATCTATTGTTAGTGC	0.408										TSP Lung(27;0.18)																											p.I3181K	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T9542A						.						114	104	107					2																	141232790		2203	4300	6503	SO:0001583	missense	53353	exon60			TAATCTATTGTTA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.9542T>A	chr2.hg19:g.141232790A>T	ENSP00000374135:p.Ile3181Lys	190.0	0.0		131.0	99.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.209552	0.79240	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.94138	-3.36	5.63	5.63	0.86233	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.97526	0.9190	M	0.93283	3.4	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.98597	1.0657	10	0.87932	D	0	.	15.8229	0.78673	1.0:0.0:0.0:0.0	.	3181	Q9NZR2	LRP1B_HUMAN	K	3181;3119	ENSP00000374135:I3181K	ENSP00000374135:I3181K	I	-	2	0	LRP1B	140949260	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.282000	0.95840	2.142000	0.66516	0.528000	0.53228	ATA	.	.		0.408	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141232790	A	T	141232790	3	4	23	1	0	0	0	0	1	0	0	0	8964	449	16	4	4385	4	LRP1B	2	141232790	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	5203336	141232790	101966583	171	2237										
ARHGAP15	55843	hgsc.bcm.edu	37	chr2	144313999	144313999	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctagatgttgatggaatataTcgagttagtggcaatctggc	12	5	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:144313999T>C	ENST00000295095.6	+	11	1115	c.948T>C	c.(946-948)taT>taC	p.Y316Y	RP11-570L15.2_ENST00000546678.1_RNA|RP11-570L15.1_ENST00000553076.1_RNA	NM_018460.3	NP_060930.3	Q53QZ3	RHG15_HUMAN	Rho GTPase activating protein 15	316	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)			endometrium(1)|kidney(5)|large_intestine(8)|liver(2)|lung(15)|ovary(1)|skin(2)	34				BRCA - Breast invasive adenocarcinoma(221;0.151)		ATGGAATATATCGAGTTAGTG	0.318																																					p.Y316Y		Atlas-SNP	.											.	ARHGAP15	99	.	0			c.T948C						.						193	201	198					2																	144313999		2203	4298	6501	SO:0001819	synonymous_variant	55843	exon11			AATATATCGAGTT	AY219338	CCDS2184.1	2q22.2-q22.3	2013-01-10			ENSG00000075884	ENSG00000075884		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	21030	protein-coding gene	gene with protein product		610578				12650940, 11042152	Standard	NM_018460		Approved	BM046	uc002tvm.4	Q53QZ3	OTTHUMG00000131845	ENST00000295095.6:c.948T>C	chr2.hg19:g.144313999T>C		131.0	0.0		93.0	72.0	NM_018460	Q53R36|Q53RD7|Q53RT6|Q53SX9|Q584N9|Q6PJE6|Q86WP1|Q8IXX1|Q9NRL8|Q9NZ77|Q9NZ91	Silent	SNP	ENST00000295095.6	hg19	CCDS2184.1																																																																																			.	.		0.318	ARHGAP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254793.2	NM_018460		C	144313999	T	C	144313999	2	2	23	1	0	0	0	0	0	0	0	1	866	1442	50	2		2	ARHGAP15	2	144313999	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3081209	144313999	98885374	172	2238										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148674907	148674907	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagtttgcctggaatgaagcAtgagaacatattacagttca	9	7	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:148674907A>T	ENST00000241416.7	+	6	1364	c.728A>T	c.(727-729)cAt>cTt	p.H243L	ACVR2A_ENST00000404590.1_Missense_Mutation_p.H243L|ACVR2A_ENST00000535787.1_Missense_Mutation_p.H135L	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	243	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		GGAATGAAGCATGAGAACATA	0.383																																					p.H243L		Atlas-SNP	.											.	ACVR2A	125	.	0			c.A728T						.						110	91	98					2																	148674907		2203	4300	6503	SO:0001583	missense	92	exon6			TGAAGCATGAGAA		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.728A>T	chr2.hg19:g.148674907A>T	ENSP00000241416:p.His243Leu	244.0	0.0		125.0	91.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	A	32	5.137092	0.94517	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	T;T;T	0.78481	-1.18;-1.18;-1.18	5.68	5.68	0.88126	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92678	0.7673	H	0.97783	4.075	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95288	0.8392	10	0.87932	D	0	.	15.9354	0.79698	1.0:0.0:0.0:0.0	.	243	P27037	AVR2A_HUMAN	L	243;135;243	ENSP00000241416:H243L;ENSP00000439988:H135L;ENSP00000384338:H243L	ENSP00000241416:H243L	H	+	2	0	ACVR2A	148391377	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.313000	0.96297	2.182000	0.69389	0.533000	0.62120	CAT	.	.		0.383	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		T	148674907	A	T	148674907	3	4	23	1	0	0	0	0	1	0	0	0	223	217	8	4	750	4	ACVR2A	2	148674907	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	4360908	148674907	94524466	173	2239										
NEB	4703	hgsc.bcm.edu	37	chr2	152467281	152467281	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caggaaatctcttacttggcTgatattggcagaattactct							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:152467281delT	ENST00000172853.10	-	75	11323	c.11176delA	c.(11176-11178)agcfs	p.S3726fs	NEB_ENST00000427231.2_Frame_Shift_Del_p.S3969fs|NEB_ENST00000397345.3_Frame_Shift_Del_p.S3969fs|NEB_ENST00000604864.1_Frame_Shift_Del_p.S3969fs|NEB_ENST00000409198.1_Frame_Shift_Del_p.S3726fs|NEB_ENST00000603639.1_Frame_Shift_Del_p.S3969fs			P20929	NEBU_HUMAN	nebulin	3726					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTTACTTGGCTGATATTGGCA	0.413																																					p.S3969fs		Atlas-Indel,Pindel	.											.	NEB	1697	.	0			c.11906delG						.						73	67	69					2																	152467281		1905	4127	6032	SO:0001589	frameshift_variant	4703	exon79			.	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.11176delA	chr2.hg19:g.152467281delT	ENSP00000172853:p.Ser3726fs	124.0	0.0		70.0	32.0	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Frame_Shift_Del	DEL	ENST00000172853.10	hg19																																																																																				.	.		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		-	152467281	T	-	152467281	7	5	23	1	0	1	0	1	0	0	0	0	10311	1580	55	0	14197	0	NEB	2	152467281	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	3792374	152467281	90732092	174	2240										
PKP4	8502	hgsc.bcm.edu	37	chr2	159526240	159526240	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgccgttggcaggcaaatacGccatgcgagacctggtcaac	12	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:159526240G>A	ENST00000389759.3	+	17	2849	c.2737G>A	c.(2737-2739)Gcc>Acc	p.A913T	AC005042.4_ENST00000342892.4_RNA|PKP4_ENST00000389757.3_Missense_Mutation_p.A913T	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	913					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						AGGCAAATACGCCATGCGAGA	0.507										HNSCC(62;0.18)																											p.A913T		Atlas-SNP	.											.	PKP4	133	.	0			c.G2737A						.						49	52	51					2																	159526240		2203	4300	6503	SO:0001583	missense	8502	exon17			AAATACGCCATGC	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.2737G>A	chr2.hg19:g.159526240G>A	ENSP00000374409:p.Ala913Thr	270.0	0.0		114.0	73.0	NM_001005476	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.959642	0.92791	.	.	ENSG00000144283	ENST00000389757;ENST00000389759	T;T	0.51071	0.72;0.72	5.82	4.93	0.64822	Armadillo-like helical (1);Armadillo-type fold (1);	0.052613	0.85682	D	0.000000	T	0.67646	0.2915	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.985;1.0;1.0	P;D;D	0.91635	0.806;0.999;0.983	T	0.72067	-0.4402	10	0.87932	D	0	-12.3708	16.2419	0.82418	0.0:0.0:0.8661:0.1339	.	868;913;913	Q4W5T8;Q99569-2;Q99569	.;.;PKP4_HUMAN	T	913	ENSP00000374407:A913T;ENSP00000374409:A913T	ENSP00000374407:A913T	A	+	1	0	PKP4	159234486	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	9.756000	0.98918	1.450000	0.47717	0.650000	0.86243	GCC	.	.		0.507	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			A	159526240	G	A	159526240	3	1	23	1	0	0	0	0	1	0	0	0	11996	1087	38	1	2799	1	PKP4	2	159526240	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	7058959	159526240	83673133	175	2241										
COBLL1	22837	hgsc.bcm.edu	37	chr2	165556006	165556006	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcatatactacactgtgtggTtctctggaagatacgacatt	8	8	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:165556006T>G	ENST00000392717.2	-	12	1699	c.1695A>C	c.(1693-1695)gaA>gaC	p.E565D	COBLL1_ENST00000491126.2_5'Flank|COBLL1_ENST00000342193.4_Missense_Mutation_p.E527D|COBLL1_ENST00000194871.6_Missense_Mutation_p.E593D|COBLL1_ENST00000375458.2_Missense_Mutation_p.E488D|COBLL1_ENST00000409184.3_Missense_Mutation_p.E526D			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	565						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						CACTGTGTGGTTCTCTGGAAG	0.388																																					p.E527D		Atlas-SNP	.											.	COBLL1	122	.	0			c.A1581C						.						174	165	168					2																	165556006		2203	4298	6501	SO:0001583	missense	22837	exon11			GTGTGGTTCTCTG	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1695A>C	chr2.hg19:g.165556006T>G	ENSP00000376478:p.Glu565Asp	75.0	0.0		39.0	34.0	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	hg19		.	.	.	.	.	.	.	.	.	.	T	9.120	1.008719	0.19199	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	4.83	-1.74	0.08056	.	1.239710	0.05541	N	0.565694	T	0.20210	0.0486	N	0.08118	0	0.09310	N	1	P;B;B	0.34815	0.47;0.41;0.43	B;B;B	0.38296	0.139;0.071;0.27	T	0.23904	-1.0175	9	0.16896	T	0.51	-0.1507	8.9301	0.35666	0.0:0.419:0.0:0.581	.	565;593;526	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	D	488;527;526;565;593	.	ENSP00000194871:E593D	E	-	3	2	COBLL1	165264252	0.000000	0.05858	0.001000	0.08648	0.061000	0.15899	-0.120000	0.10660	-0.513000	0.06496	-0.250000	0.11733	GAA	.	.		0.388	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		G	165556006	T	G	165556006	3	3	23	1	0	0	0	0	1	0	0	0	3656	1722	60	5	1935	5	COBLL1	2	165556006	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	6029766	165556006	77643367	176	2242										
TTC21B	79809	hgsc.bcm.edu	37	chr2	166747435	166747435	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccattgagaaaaatcttgggAcatcctcgagttttccacat	7	10	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:166747435A>G	ENST00000243344.7	-	23	3151	c.3014T>C	c.(3013-3015)gTc>gCc	p.V1005A	TTC21B_ENST00000536175.1_5'Flank	NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	1005					forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)				breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						AAATCTTGGGACATCCTCGAG	0.343																																					p.V1005A		Atlas-SNP	.											.	TTC21B	130	.	0			c.T3014C						.						63	68	66					2																	166747435		2203	4300	6503	SO:0001583	missense	79809	exon23			CTTGGGACATCCT	AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"Tetratricopeptide (TTC) repeat domain containing", "Intraflagellar transport homologs"	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.3014T>C	chr2.hg19:g.166747435A>G	ENSP00000243344:p.Val1005Ala	250.0	0.0		142.0	6.0	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	hg19	CCDS33315.1	.	.	.	.	.	.	.	.	.	.	A	10.04	1.240432	0.22711	.	.	ENSG00000123607	ENST00000243344	T	0.24350	1.86	5.57	5.57	0.84162	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.168969	0.51477	D	0.000088	T	0.13157	0.0319	N	0.11106	0.095	0.80722	D	1	B	0.15141	0.012	B	0.09377	0.004	T	0.07693	-1.0759	10	0.02654	T	1	-25.0127	15.7265	0.77763	1.0:0.0:0.0:0.0	.	1005	Q7Z4L5	TT21B_HUMAN	A	1005	ENSP00000243344:V1005A	ENSP00000243344:V1005A	V	-	2	0	TTC21B	166455681	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.423000	0.66458	2.106000	0.64143	0.445000	0.29226	GTC	.	.		0.343	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753		G	166747435	A	G	166747435	3	3	23	1	0	0	0	0	1	0	0	0	16703	275	10	2	964	2	TTC21B	2	166747435	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1191429	166747435	76451938	177	2243										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166850833	166850833	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctggtcatctgtttccaccaTcattgtgaccatgttaagac	7	11	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:166850833T>G	ENST00000303395.4	-	25	4674	c.4675A>C	c.(4675-4677)Atg>Ctg	p.M1559L	SCN1A_ENST00000375405.3_Missense_Mutation_p.M1548L|SCN1A_ENST00000423058.2_Missense_Mutation_p.M1559L|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.M1531L|AC010127.3_ENST00000597623.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1559			Missing (in EIEE6). {ECO:0000269|PubMed:14738421}.		adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GTTTCCACCATCATTGTGACC	0.383																																					p.M1559L		Atlas-SNP	.											.	SCN1A	641	.	0			c.A4675C						.						145	120	128					2																	166850833		2203	4300	6503	SO:0001583	missense	6323	exon25			CCACCATCATTGT	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.4675A>C	chr2.hg19:g.166850833T>G	ENSP00000303540:p.Met1559Leu	225.0	0.0		125.0	12.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.915134	0.92178	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97303	-4.33;-4.33;-4.33;-4.33	5.9	5.9	0.94986	.	0.047303	0.85682	D	0.000000	D	0.98931	0.9637	H	0.95365	3.66	0.58432	D	0.999999	D	0.58268	0.982	D	0.72338	0.977	D	0.99486	1.0949	10	0.66056	D	0.02	.	16.3322	0.83039	0.0:0.0:0.0:1.0	.	1548	P35498-2	.	L	1559;1559;1548;1531	ENSP00000407030:M1559L;ENSP00000303540:M1559L;ENSP00000364554:M1548L;ENSP00000386312:M1531L	ENSP00000303540:M1559L	M	-	1	0	SCN1A	166559079	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.907000	0.87430	2.251000	0.74343	0.528000	0.53228	ATG	.	.		0.383	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166850833	T	G	166850833	3	3	23	1	0	0	0	0	1	0	0	0	13929	1435	50	5	1362	5	SCN1A	2	166850833	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	103398	166850833	76348540	178	2244										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166850895	166850895	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtcaaaaacttgtctggttAcgaagtcaaagaccattcct	7	9	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:166850895A>G	ENST00000303395.4	-	25	4612	c.4613T>C	c.(4612-4614)gTa>gCa	p.V1538A	SCN1A_ENST00000375405.3_Missense_Mutation_p.V1527A|SCN1A_ENST00000423058.2_Missense_Mutation_p.V1538A|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.V1510A|AC010127.3_ENST00000597623.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1538					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTGTCTGGTTACGAAGTCAAA	0.358																																					p.V1538A		Atlas-SNP	.											.	SCN1A	641	.	0			c.T4613C						.						111	100	104					2																	166850895		2203	4300	6503	SO:0001583	missense	6323	exon25			CTGGTTACGAAGT	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.4613T>C	chr2.hg19:g.166850895A>G	ENSP00000303540:p.Val1538Ala	190.0	0.0		93.0	34.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.182172	0.57800	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97279	-4.32;-4.32;-4.27;-4.25	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000002	D	0.96981	0.9014	M	0.77486	2.375	0.38301	D	0.942982	P	0.39181	0.663	B	0.42692	0.395	D	0.98718	1.0707	10	0.59425	D	0.04	.	16.0863	0.81056	1.0:0.0:0.0:0.0	.	1527	P35498-2	.	A	1538;1538;1527;1510	ENSP00000407030:V1538A;ENSP00000303540:V1538A;ENSP00000364554:V1527A;ENSP00000386312:V1510A	ENSP00000303540:V1538A	V	-	2	0	SCN1A	166559141	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.710000	0.68392	2.197000	0.70478	0.454000	0.30748	GTA	.	.		0.358	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166850895	A	G	166850895	3	3	23	1	0	0	0	0	1	0	0	0	13929	391	14	2	1424	2	SCN1A	2	166850895	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	62	166850895	76348478	179	2245										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168103817	168103817	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcaggttgctgtccagaggaAcaaaaatagtcttcttcagc	9	9	4	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:168103817A>G	ENST00000409195.1	+	9	6004	c.5915A>G	c.(5914-5916)aAc>aGc	p.N1972S	XIRP2_ENST00000295237.9_Missense_Mutation_p.N1972S|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.N1750S|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1797					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GTCCAGAGGAACAAAAATAGT	0.458																																					p.N1972S		Atlas-SNP	.											.	XIRP2	914	.	0			c.A5915G						.						42	41	41					2																	168103817		1913	4129	6042	SO:0001583	missense	129446	exon9			AGAGGAACAAAAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5915A>G	chr2.hg19:g.168103817A>G	ENSP00000386840:p.Asn1972Ser	245.0	0.0		167.0	67.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	2.136	-0.397954	0.04865	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02579	4.24;4.24;4.24	5.73	2.04	0.26737	.	0.562741	0.19002	N	0.125325	T	0.02156	0.0067	N	0.22421	0.69	0.09310	N	1	B;B;B	0.11235	0.003;0.004;0.0	B;B;B	0.10450	0.002;0.005;0.001	T	0.44742	-0.9308	10	0.37606	T	0.19	0.0057	6.1322	0.20211	0.7154:0.1378:0.1467:0.0	.	1797;1797;1750	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	1972;1972;1750	ENSP00000386840:N1972S;ENSP00000295237:N1972S;ENSP00000387255:N1750S	ENSP00000295237:N1972S	N	+	2	0	XIRP2	167812063	0.963000	0.33076	0.003000	0.11579	0.005000	0.04900	2.154000	0.42291	0.424000	0.26061	-0.274000	0.10170	AAC	.	.		0.458	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168103817	A	G	168103817	3	3	23	1	0	0	0	0	1	0	0	0	17445	43	2	2	5945	2	XIRP2	2	168103817	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1252922	168103817	75095556	180	2246										
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170396679	170396679	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agaaacactaatataaaaggAtccaatatacctaaaagaaa	4	6	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:170396679A>T	ENST00000453153.2	-	10	2173	c.1827T>A	c.(1825-1827)gaT>gaA	p.D609E	FASTKD1_ENST00000495505.1_5'Flank|FASTKD1_ENST00000453929.2_Missense_Mutation_p.D609E	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	609					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						ATATAAAAGGATCCAATATAC	0.289																																					p.D609E		Atlas-SNP	.											.	FASTKD1	86	.	0			c.T1827A						.						24	25	24					2																	170396679		2189	4273	6462	SO:0001583	missense	79675	exon10			AAAAGGATCCAAT	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1827T>A	chr2.hg19:g.170396679A>T	ENSP00000400513:p.Asp609Glu	532.0	2.0		342.0	243.0	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	hg19	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	A	6.793	0.515346	0.12944	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.40225	1.04;1.04	4.94	0.905	0.19307	FAST kinase leucine-rich (1);	0.145914	0.64402	N	0.000011	T	0.26557	0.0649	L	0.42632	1.34	0.49130	D	0.999751	B;B	0.23128	0.025;0.08	B;B	0.31337	0.05;0.128	T	0.05451	-1.0884	10	0.08179	T	0.78	-16.837	2.4517	0.04519	0.6038:0.1226:0.0889:0.1846	.	609;609	Q53R41-2;Q53R41	.;FAKD1_HUMAN	E	609	ENSP00000400513:D609E;ENSP00000403229:D609E	ENSP00000400513:D609E	D	-	3	2	FASTKD1	170104925	1.000000	0.71417	0.997000	0.53966	0.306000	0.27790	0.983000	0.29552	0.355000	0.24131	0.533000	0.62120	GAT	.	.		0.289	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		T	170396679	A	T	170396679	3	4	23	1	0	0	0	0	1	0	0	0	5693	330	12	4	740	4	FASTKD1	2	170396679	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2292862	170396679	72802694	181	2247										
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170403008	170403008	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaagtagtttcagttgtttcGcagtcatattatccaaatac	7	7	2	0	rs540349050		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:170403008G>A	ENST00000453153.2	-	8	1767	c.1421C>T	c.(1420-1422)gCg>gTg	p.A474V	FASTKD1_ENST00000453929.2_Missense_Mutation_p.A474V	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	474					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						CAGTTGTTTCGCAGTCATATT	0.383													G|||	1	0.000199681	0	0	5008	,	,		19733	0.001		0	False		,,,				2504	0				p.A474V		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C1421T						.						124	108	114					2																	170403008		2203	4300	6503	SO:0001583	missense	79675	exon8			TGTTTCGCAGTCA	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1421C>T	chr2.hg19:g.170403008G>A	ENSP00000400513:p.Ala474Val	265.0	1.0		148.0	111.0	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	hg19	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	G	7.034	0.561239	0.13498	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.17854	2.25;2.25	4.57	-0.413	0.12363	.	0.445361	0.27591	N	0.018695	T	0.06416	0.0165	N	0.22421	0.69	0.09310	N	0.999998	P;P	0.41643	0.566;0.758	B;B	0.31101	0.124;0.058	T	0.34079	-0.9843	10	0.29301	T	0.29	-0.5854	3.6131	0.08067	0.2361:0.4323:0.2342:0.0973	.	474;474	Q53R41-2;Q53R41	.;FAKD1_HUMAN	V	474	ENSP00000400513:A474V;ENSP00000403229:A474V	ENSP00000400513:A474V	A	-	2	0	FASTKD1	170111254	0.014000	0.17966	0.323000	0.25347	0.068000	0.16541	1.393000	0.34497	0.016000	0.14998	-1.826000	0.00596	GCG	.	.		0.383	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		A	170403008	G	A	170403008	3	1	23	1	0	0	0	0	1	0	0	0	5693	1087	38	1	1154	1	FASTKD1	2	170403008	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	6329	170403008	72796365	182	2248										
KIAA1715	80856	hgsc.bcm.edu	37	chr2	176802232	176802232	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttcaagaaaaaacagtaggcAcatcgaaaagctgcagagaa	9	7	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:176802232A>G	ENST00000272748.4	-	12	1141	c.894T>C	c.(892-894)tgT>tgC	p.C298C	KIAA1715_ENST00000535310.1_Silent_p.C223C|KIAA1715_ENST00000544803.1_Silent_p.C329C	NM_030650.1	NP_085153.1	Q9C0E8	LNP_HUMAN	KIAA1715	298					blood coagulation (GO:0007596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|limb development (GO:0060173)|regulation of chondrocyte differentiation (GO:0032330)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)	20			OV - Ovarian serous cystadenocarcinoma(117;0.0793)			AACAGTAGGCACATCGAAAAG	0.388																																					p.C298C		Atlas-SNP	.											.	KIAA1715	61	.	0			c.T894C						.						38	38	38					2																	176802232		2203	4299	6502	SO:0001819	synonymous_variant	80856	exon12			GTAGGCACATCGA	AB051502	CCDS33332.1	2q31	2014-06-27			ENSG00000144320	ENSG00000144320			21610	protein-coding gene	gene with protein product	"lunapark", "limb and neural patterns"	610236				11214970, 22729086	Standard	NM_030650		Approved	ulnaless, Ul, LNP1, LNP	uc002ukc.1	Q9C0E8	OTTHUMG00000154112	ENST00000272748.4:c.894T>C	chr2.hg19:g.176802232A>G		97.0	0.0		56.0	5.0	NM_030650	B7ZLA8|Q2M2V8|Q2YD99|Q658W8|Q8N5V9|Q96MS5	Silent	SNP	ENST00000272748.4	hg19	CCDS33332.1																																																																																			.	.		0.388	KIAA1715-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333949.3	XM_042834		G	176802232	A	G	176802232	2	3	23	1	0	0	0	0	0	0	0	1	8263	157	6	2		2	KIAA1715	2	176802232	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	6399224	176802232	66397141	183	2249										
TTN	7273	hgsc.bcm.edu	37	chr2	179411087	179411087	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaagagactttttcacagagAtctagctccttgtctccttt	6	10	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:179411087A>T	ENST00000591111.1	-	292	90272	c.90048T>A	c.(90046-90048)gaT>gaA	p.D30016E	TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586452.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D29089E|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D22592E|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D22784E|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D31657E|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D22717E|TTN-AS1_ENST00000590040.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30016	Ig-like 136.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTCACAGAGATCTAGCTCCT	0.438																																					p.D31657E		Atlas-SNP	.											.	TTN	18412	.	0			c.T94971A						.						142	140	140					2																	179411087		1954	4150	6104	SO:0001583	missense	7273	exon342			ACAGAGATCTAGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.90048T>A	chr2.hg19:g.179411087A>T	ENSP00000465570:p.Asp30016Glu	74.0	0.0		39.0	27.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.52	2.856810	0.51376	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.81	-2.51	0.06365	Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.34745	0.0908	N	0.11560	0.145	0.80722	D	1	B;B;B;B	0.12630	0.006;0.006;0.006;0.006	B;B;B;B	0.15484	0.013;0.013;0.013;0.013	T	0.04723	-1.0931	9	0.87932	D	0	.	3.4064	0.07343	0.346:0.1985:0.359:0.0965	.	22592;22717;22784;30016	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	29089;22592;22784;22717;22589	ENSP00000343764:D29089E;ENSP00000434586:D22592E;ENSP00000340554:D22784E;ENSP00000352154:D22717E	ENSP00000340554:D22784E	D	-	3	2	TTN	179119333	0.581000	0.26741	0.618000	0.29105	0.921000	0.55340	-0.067000	0.11579	-0.362000	0.08113	-0.290000	0.09829	GAT	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179411087	A	T	179411087	3	4	23	1	0	0	0	0	1	0	0	0	16750	330	12	4	13092	4	TTN	2	179411087	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2608855	179411087	63788286	184	2250										
ITGA4	3676	hgsc.bcm.edu	37	chr2	182399041	182399041	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgaaataagagcaacaggtTttccagagccaaatccaaga	8	8	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:182399041T>C	ENST00000397033.2	+	26	3257	c.2827T>C	c.(2827-2829)Ttt>Ctt	p.F943L		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	943					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	AGCAACAGGTTTTCCAGAGCC	0.338																																					p.F943L		Atlas-SNP	.											.	ITGA4	142	.	0			c.T2827C						.						76	69	71					2																	182399041		1835	4094	5929	SO:0001583	missense	3676	exon26			ACAGGTTTTCCAG		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2827T>C	chr2.hg19:g.182399041T>C	ENSP00000380227:p.Phe943Leu	537.0	2.0		283.0	191.0	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	hg19	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	T	9.786	1.176685	0.21704	.	.	ENSG00000115232	ENST00000397033	T	0.42513	0.97	5.96	4.74	0.60224	.	0.516425	0.22981	N	0.053303	T	0.25644	0.0624	N	0.14661	0.345	0.32806	D	0.500731	B	0.06786	0.001	B	0.04013	0.001	T	0.22800	-1.0206	10	0.28530	T	0.3	.	11.6696	0.51393	0.0:0.0:0.1476:0.8523	.	943	P13612	ITA4_HUMAN	L	943	ENSP00000380227:F943L	ENSP00000380227:F943L	F	+	1	0	ITGA4	182107286	0.998000	0.40836	1.000000	0.80357	0.320000	0.28249	3.266000	0.51569	2.279000	0.76181	0.533000	0.62120	TTT	.	.		0.338	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			C	182399041	T	C	182399041	3	2	23	1	0	0	0	0	1	0	0	0	7887	1841	64	2	2929	2	ITGA4	2	182399041	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2987954	182399041	60800332	185	2251										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187626496	187626496	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctatcagtcaatcaaaataAttactcaagaaacccaacac	2	11	5	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:187626496A>G	ENST00000304698.5	+	8	1630	c.1427A>G	c.(1426-1428)aAt>aGt	p.N476S		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	476						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						AATCAAAATAATTACTCAAGA	0.353																																					p.N476S		Atlas-SNP	.											.	FAM171B	146	.	0			c.A1427G						.						48	52	50					2																	187626496		2201	4299	6500	SO:0001583	missense	165215	exon8			AAAATAATTACTC	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.1427A>G	chr2.hg19:g.187626496A>G	ENSP00000304108:p.Asn476Ser	126.0	0.0		122.0	10.0	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	A	2.286	-0.363666	0.05103	.	.	ENSG00000144369	ENST00000304698	T	0.29655	1.56	5.7	0.0857	0.14443	.	0.638975	0.17586	N	0.168938	T	0.08758	0.0217	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33675	-0.9859	10	0.14252	T	0.57	-11.4546	5.0192	0.14352	0.4206:0.2829:0.2965:0.0	.	476;477	Q6P995;A8K122	F171B_HUMAN;.	S	476	ENSP00000304108:N476S	ENSP00000304108:N476S	N	+	2	0	FAM171B	187334741	0.939000	0.31865	0.983000	0.44433	0.973000	0.67179	0.509000	0.22707	0.087000	0.17167	0.533000	0.62120	AAT	.	.		0.353	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		G	187626496	A	G	187626496	3	3	23	1	0	0	0	0	1	0	0	0	5496	101	4	2	1457	2	FAM171B	2	187626496	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	5227455	187626496	55572877	186	2252										
SLC40A1	30061	hgsc.bcm.edu	37	chr2	190426694	190426694	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgtttcccagagtattttgGgcaaatcggaaatacataat	8	6	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:190426694G>A	ENST00000261024.2	-	8	2052	c.1626C>T	c.(1624-1626)gcC>gcT	p.A542A		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	542					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			GAGTATTTTGGGCAAATCGGA	0.418																																					p.A542A		Atlas-SNP	.											.	SLC40A1	51	.	0			c.C1626T						.						80	76	78					2																	190426694		2203	4300	6503	SO:0001819	synonymous_variant	30061	exon8			ATTTTGGGCAAAT	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"Solute carriers"	10909	protein-coding gene	gene with protein product	"ferroportin 1"	604653	"solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.1626C>T	chr2.hg19:g.190426694G>A		224.0	0.0		248.0	100.0	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Silent	SNP	ENST00000261024.2	hg19	CCDS2299.1																																																																																			.	.		0.418	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			A	190426694	G	A	190426694	2	1	23	1	0	0	0	0	0	0	0	1	14643	1219	43	3		3	SLC40A1	2	190426694	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2800198	190426694	52772679	187	2253										
ANKAR	150709	hgsc.bcm.edu	37	chr2	190585420	190585420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	taaatgtaatgaactgtataCgggtattgtgtataggaaat	10	2	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:190585420C>T	ENST00000520309.1	+	12	2630	c.2542C>T	c.(2542-2544)Cgg>Tgg	p.R848W	ANKAR_ENST00000281412.6_Missense_Mutation_p.R612W|ANKAR_ENST00000438402.2_Missense_Mutation_p.R848W|ANKAR_ENST00000431575.2_Missense_Mutation_p.R777W|ANKAR_ENST00000313581.4_Missense_Mutation_p.R848W	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	848						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			GAACTGTATACGGGTATTGTG	0.323																																					p.R848W		Atlas-SNP	.											.	ANKAR	184	.	0			c.C2542T						.						171	192	185					2																	190585420		2203	4300	6503	SO:0001583	missense	150709	exon12			TGTATACGGGTAT	AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"Ankyrin repeat domain containing", "Armadillo repeat containing"	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.2542C>T	chr2.hg19:g.190585420C>T	ENSP00000427882:p.Arg848Trp	121.0	0.0		113.0	5.0	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Missense_Mutation	SNP	ENST00000520309.1	hg19	CCDS33351.2	.	.	.	.	.	.	.	.	.	.	C	14.21	2.467624	0.43839	.	.	ENSG00000151687	ENST00000520309;ENST00000313581;ENST00000438402;ENST00000431575;ENST00000281412	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	4.84	3.92	0.45320	.	0.091025	0.41396	D	0.000896	T	0.42607	0.1210	M	0.64997	1.995	0.32027	N	0.600043	.	.	.	.	.	.	T	0.54497	-0.8285	8	0.72032	D	0.01	-8.4049	11.6577	0.51328	0.3035:0.6965:0.0:0.0	.	.	.	.	W	848;848;848;777;612	ENSP00000427882:R848W;ENSP00000313513:R848W;ENSP00000397243:R848W;ENSP00000393043:R777W;ENSP00000281412:R612W	ENSP00000281412:R612W	R	+	1	2	ANKAR	190293665	0.950000	0.32346	0.060000	0.19600	0.215000	0.24574	0.857000	0.27831	2.539000	0.85634	0.655000	0.94253	CGG	.	.		0.323	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		T	190585420	C	T	190585420	3	4	23	1	0	0	0	0	1	0	0	0	623	527	19	1	2584	1	ANKAR	2	190585420	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	158726	190585420	52613953	188	2254										
C2orf88	84281	hgsc.bcm.edu	37	chr2	191064799	191064799	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgtctcaggatatcttgtgTgatgccttgcagcaatgggc	12	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:191064799T>C	ENST00000340623.4	+	2	624	c.213T>C	c.(211-213)tgT>tgC	p.C71C	C2orf88_ENST00000409870.1_Silent_p.C71C|C2orf88_ENST00000443551.2_Silent_p.C71C|C2orf88_ENST00000396974.2_Silent_p.C71C	NM_001042519.1|NM_001042520.1|NM_001042521.1|NM_032321.2	NP_001035984.1|NP_001035985.1|NP_001035986.1|NP_115697.2	Q9BSF0	SMAKA_HUMAN	chromosome 2 open reading frame 88	71	PKA-RI-binding.					plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(1)	3						ATATCTTGTGTGATGCCTTGC	0.468																																					p.C71C		Atlas-SNP	.											.	C2orf88	7	.	0			c.T213C						.						195	192	193					2																	191064799		2019	4184	6203	SO:0001819	synonymous_variant	84281	exon2			CTTGTGTGATGCC	BC005083	CCDS42792.1	2q32.2	2014-02-12	2009-04-08		ENSG00000187699	ENSG00000187699			28191	protein-coding gene	gene with protein product	"small membrane AKAP"	615117				23996002	Standard	NM_032321		Approved	MGC13057, smAKAP	uc002urt.3	Q9BSF0	OTTHUMG00000154361	ENST00000340623.4:c.213T>C	chr2.hg19:g.191064799T>C		114.0	0.0		111.0	42.0	NM_001042519	D3DPI3|P0C876|Q53TC7	Silent	SNP	ENST00000340623.4	hg19	CCDS42792.1																																																																																			.	.		0.468	C2orf88-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334954.1	NM_032321		C	191064799	T	C	191064799	2	2	23	1	0	0	0	0	0	0	0	1	2204	1702	59	2		2	C2orf88	2	191064799	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	479379	191064799	52134574	189	2255										
NAB1	4664	hgsc.bcm.edu	37	chr2	191524471	191524471	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccaaaggagagcagtgaggCgctggatgctgctgctgcgc	16	11	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:191524471C>T	ENST00000337386.5	+	4	1030	c.569C>T	c.(568-570)gCg>gTg	p.A190V	NAB1_ENST00000357215.5_Missense_Mutation_p.A190V|NAB1_ENST00000409581.1_Missense_Mutation_p.A190V|NAB1_ENST00000409641.1_Missense_Mutation_p.A190V|NAB1_ENST00000545490.1_5'Flank	NM_005966.3	NP_005957.2	Q13506	NAB1_HUMAN	NGFI-A binding protein 1 (EGR1 binding protein 1)	190					endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of epidermis development (GO:0045682)|regulation of transcription, DNA-templated (GO:0006355)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)			AGCAGTGAGGCGCTGGATGCT	0.602																																					p.A190V		Atlas-SNP	.											.	NAB1	31	.	0			c.C569T						.						31	33	32					2																	191524471		2203	4300	6503	SO:0001583	missense	4664	exon4			GTGAGGCGCTGGA		CCDS2307.1	2q32.3-q33	2008-05-23			ENSG00000138386	ENSG00000138386			7626	protein-coding gene	gene with protein product	"EGR1 binding protein 1"	600800				7624335, 8668170, 9418898	Standard	XM_005246579		Approved		uc002usb.3	Q13506	OTTHUMG00000132689	ENST00000337386.5:c.569C>T	chr2.hg19:g.191524471C>T	ENSP00000336894:p.Ala190Val	211.0	0.0		243.0	93.0	NM_005966	O75383|O75384|Q6GTU1|Q9UEV1	Missense_Mutation	SNP	ENST00000337386.5	hg19	CCDS2307.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.088721	0.36855	.	.	ENSG00000138386	ENST00000409581;ENST00000337386;ENST00000357215;ENST00000409641	.	.	.	5.51	3.68	0.42216	NAB co-repressor, domain (1);	0.256387	0.45606	N	0.000346	T	0.31327	0.0793	N	0.16368	0.405	0.80722	D	1	B;B;B	0.29716	0.255;0.039;0.039	B;B;B	0.19946	0.027;0.012;0.012	T	0.06588	-1.0818	9	0.21540	T	0.41	-6.8587	10.6712	0.45760	0.0:0.8419:0.0:0.1581	.	190;190;190	F8W8J7;B8ZZS2;Q13506	.;.;NAB1_HUMAN	V	190	.	ENSP00000336894:A190V	A	+	2	0	NAB1	191232716	0.999000	0.42202	0.912000	0.35992	0.986000	0.74619	3.711000	0.54868	0.847000	0.35167	0.561000	0.74099	GCG	.	.		0.602	NAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255986.1	NM_005966		T	191524471	C	T	191524471	3	4	23	1	0	0	0	0	1	0	0	0	10140	768	27	1	571	1	NAB1	2	191524471	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	459672	191524471	51674902	190	2256										
GTF3C3	9330	hgsc.bcm.edu	37	chr2	197653948	197653948	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttgccatatctctagccagCtgcataaaacgttcgccatc	6	13	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:197653948C>T	ENST00000263956.3	-	6	962	c.873G>A	c.(871-873)caG>caA	p.Q291Q	GTF3C3_ENST00000470386.1_5'UTR|GTF3C3_ENST00000409364.3_Silent_p.Q291Q	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	291					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CTCTAGCCAGCTGCATAAAAC	0.378																																					p.Q291Q		Atlas-SNP	.											.	GTF3C3	96	.	0			c.G873A						.						113	105	108					2																	197653948		2203	4300	6503	SO:0001819	synonymous_variant	9330	exon6			AGCCAGCTGCATA	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.873G>A	chr2.hg19:g.197653948C>T		158.0	0.0		139.0	49.0	NM_001206774	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Silent	SNP	ENST00000263956.3	hg19	CCDS2316.1																																																																																			.	.		0.378	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			T	197653948	C	T	197653948	2	4	23	1	0	0	0	0	0	0	0	1	6883	796	28	3		3	GTF3C3	2	197653948	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	6129477	197653948	45545425	191	2257										
KCTD18	130535	hgsc.bcm.edu	37	chr2	201355178	201355178	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttgaaaccggtttgctgtcGccccagccgacgtctggatg	12	12	1	1	rs543025211		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:201355178G>A	ENST00000359878.3	-	7	1436	c.926C>T	c.(925-927)gCg>gTg	p.A309V	KCTD18_ENST00000409157.1_Missense_Mutation_p.A309V|KCTD18_ENST00000468413.1_5'Flank	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	309					protein homooligomerization (GO:0051260)					endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						GTTTGCTGTCGCCCCAGCCGA	0.592													G|||	1	0.000199681	8e-04	0	5008	,	,		17936	0		0	False		,,,				2504	0				p.A309V		Atlas-SNP	.											.	KCTD18	44	.	0			c.C926T						.						39	43	42					2																	201355178		2203	4300	6503	SO:0001583	missense	130535	exon7			GCTGTCGCCCCAG	AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 18"				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.926C>T	chr2.hg19:g.201355178G>A	ENSP00000352941:p.Ala309Val	72.0	0.0		50.0	27.0	NM_152387	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Missense_Mutation	SNP	ENST00000359878.3	hg19	CCDS2330.1	.	.	.	.	.	.	.	.	.	.	G	0.780	-0.762574	0.02996	.	.	ENSG00000155729	ENST00000359878;ENST00000409157	T;T	0.34275	1.37;1.37	4.14	-3.75	0.04372	.	1.124140	0.06730	N	0.776490	T	0.13927	0.0337	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26677	-1.0096	10	0.02654	T	1	-0.034	2.4717	0.04566	0.5529:0.1392:0.1681:0.1398	.	309	Q6PI47	KCD18_HUMAN	V	309	ENSP00000352941:A309V;ENSP00000386751:A309V	ENSP00000352941:A309V	A	-	2	0	KCTD18	201063423	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.303000	0.08210	-0.883000	0.03982	-1.619000	0.00793	GCG	.	.		0.592	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387		A	201355178	G	A	201355178	3	1	23	1	0	0	0	0	1	0	0	0	8114	1087	38	1	358	1	KCTD18	2	201355178	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3701230	201355178	41844195	192	2258										
ALS2CR8	79800	hgsc.bcm.edu	37	chr2	203846349	203846349	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggggttctttgtctcctgagCcaacccacttgctctcctca	8	15	4	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:203846349C>T	ENST00000402905.3	+	14	1951	c.1630C>T	c.(1630-1632)Cca>Tca	p.P544S	WDR12_ENST00000477723.1_Intron|CARF_ENST00000545253.1_Missense_Mutation_p.P456S|CARF_ENST00000545262.1_Missense_Mutation_p.P468S|CARF_ENST00000438828.2_Missense_Mutation_p.P544S|CARF_ENST00000414439.1_Missense_Mutation_p.P442S|CARF_ENST00000428585.1_Missense_Mutation_p.P468S|CARF_ENST00000320443.8_Missense_Mutation_p.P544S	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	544					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GTCTCCTGAGCCAACCCACTT	0.378																																					p.P544S		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.C1630T						.						100	98	99					2																	203846349		1834	4079	5913	SO:0001583	missense	79800	exon15			CCTGAGCCAACCC	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.1630C>T	chr2.hg19:g.203846349C>T	ENSP00000384006:p.Pro544Ser	703.0	2.0		603.0	222.0	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	hg19	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	C	13.18	2.161441	0.38119	.	.	ENSG00000138380	ENST00000402905;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000320443;ENST00000438828	.	.	.	5.7	2.64	0.31445	.	0.385237	0.25701	N	0.028870	T	0.34600	0.0903	L	0.44542	1.39	0.29329	N	0.866849	B;B;B	0.12630	0.006;0.002;0.006	B;B;B	0.12156	0.007;0.005;0.007	T	0.26395	-1.0104	9	0.51188	T	0.08	-5.3304	4.7953	0.13269	0.3186:0.4957:0.0:0.1857	.	456;468;544	B4DIA7;G3V1K7;Q8N187	.;.;AL2S8_HUMAN	S	544;442;468;456;468;544;544	.	ENSP00000316224:P544S	P	+	1	0	ALS2CR8	203554594	0.968000	0.33430	0.565000	0.28409	0.921000	0.55340	0.947000	0.29082	0.756000	0.33013	0.313000	0.20887	CCA	.	.		0.378	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		T	203846349	C	T	203846349	3	4	23	1	0	0	0	0	1	0	0	0	555	739	26	3	1676	3	ALS2CR8	2	203846349	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2491171	203846349	39353024	193	2259										
ABI2	10152	hgsc.bcm.edu	37	chr2	204281668	204281668	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaccgccacctgtggaagaAccagtctttgatgagtctcc	9	14	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:204281668A>G	ENST00000422511.2	+	10	1162	c.1131A>G	c.(1129-1131)gaA>gaG	p.E377E	ABI2_ENST00000424558.1_Silent_p.E404E|ABI2_ENST00000261018.7_Silent_p.E196E|ABI2_ENST00000430574.1_3'UTR|ABI2_ENST00000261017.5_Silent_p.E372E|ABI2_ENST00000430418.1_Silent_p.E355E|ABI2_ENST00000261016.6_Silent_p.E298E|ABI2_ENST00000295851.5_Silent_p.E410E|RAPH1_ENST00000457812.1_Intron			Q9NYB9	ABI2_HUMAN	abl-interactor 2	410	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						CTGTGGAAGAACCAGTCTTTG	0.463																																					p.E372E		Atlas-SNP	.											.	ABI2	44	.	0			c.A1116G						.						115	109	111					2																	204281668		2203	4300	6503	SO:0001819	synonymous_variant	10152	exon9			GGAAGAACCAGTC	AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443			24011	protein-coding gene	gene with protein product		606442				7590236, 10964520	Standard	XM_005246217		Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.1131A>G	chr2.hg19:g.204281668A>G		69.0	0.0		78.0	23.0	NM_005759	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	Silent	SNP	ENST00000422511.2	hg19		.	.	.	.	.	.	.	.	.	.	A	10.15	1.269860	0.23221	.	.	ENSG00000138443	ENST00000454023	.	.	.	6.03	-0.969	0.10310	.	.	.	.	.	T	0.63977	0.2557	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61113	-0.7128	4	.	.	.	-4.0586	13.0833	0.59125	0.3874:0.0:0.6126:0.0	.	.	.	.	S	190	.	.	N	+	2	0	ABI2	203989913	0.999000	0.42202	0.995000	0.50966	0.982000	0.71751	1.695000	0.37763	-0.138000	0.11434	-0.290000	0.09829	AAC	.	.		0.463	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000336179.2	NM_005759		G	204281668	A	G	204281668	2	3	23	1	0	0	0	0	0	0	0	1	89	40	2	2		2	ABI2	2	204281668	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	435319	204281668	38917705	194	2260										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207171520	207171520	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgacttttgattctgacccGcctcttctgtcagttactga	7	11	4	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:207171520G>A	ENST00000374423.3	+	5	2654	c.2268G>A	c.(2266-2268)ccG>ccA	p.P756P		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	756							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						ATTCTGACCCGCCTCTTCTGT	0.418																																					p.P756P		Atlas-SNP	.											.	ZDBF2	531	.	0			c.G2268A						.						185	188	187					2																	207171520		1899	4092	5991	SO:0001819	synonymous_variant	57683	exon5			TGACCCGCCTCTT	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.2268G>A	chr2.hg19:g.207171520G>A		74.0	0.0		73.0	26.0	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	hg19	CCDS46501.1																																																																																			.	.		0.418	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207171520	G	A	207171520	2	1	23	1	0	0	0	0	0	0	0	1	17614	1074	38	1		1	ZDBF2	2	207171520	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2889852	207171520	36027853	195	2261										
PLEKHM3	389072	hgsc.bcm.edu	37	chr2	208725985	208725985	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagccagctttccctctattAcctgcagaaagagaaatggg	10	10	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:208725985A>G	ENST00000427836.2	-	7	2441	c.1952T>C	c.(1951-1953)gTa>gCa	p.V651A	PLEKHM3_ENST00000389247.4_Splice_Site_p.V651A	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	651					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TCCCTCTATTACCTGCAGAAA	0.448																																					p.V651A		Atlas-SNP	.											.	PLEKHM3	101	.	0			c.T1952C						.						79	75	77					2																	208725985		1914	4139	6053	SO:0001630	splice_region_variant	389072	exon7			TCTATTACCTGCA	AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385		"Pleckstrin homology (PH) domain containing"	34006	protein-coding gene	gene with protein product	"differentiation associated protein"		"pleckstrin homology domain containing, family M, member 1-like"	PLEKHM1L		19028694	Standard	NM_001080475		Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.1951-1T>C	chr2.hg19:g.208725985A>G		108.0	0.0		112.0	57.0	NM_001080475	B9EKV2|Q8WW68	Missense_Mutation	SNP	ENST00000427836.2	hg19	CCDS42808.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.475136	0.84640	.	.	ENSG00000178385	ENST00000427836;ENST00000389247	D;D	0.87103	-2.18;-2.21	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	D	0.91962	0.7454	M	0.79805	2.47	0.80722	D	1	D	0.63880	0.993	P	0.57204	0.815	D	0.92903	0.6341	10	0.62326	D	0.03	.	15.3549	0.74421	1.0:0.0:0.0:0.0	.	651	Q6ZWE6	PKHM3_HUMAN	A	651	ENSP00000417003:V651A;ENSP00000373899:V651A	ENSP00000373899:V651A	V	-	2	0	PLEKHM3	208434230	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.087000	0.94110	2.265000	0.75225	0.533000	0.62120	GTA	.	.		0.448	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	NM_001080475	Missense_Mutation	G	208725985	A	G	208725985	5	3	23	1	0	0	0	0	0	0	1	0	12091	405	14	2	341	2	PLEKHM3	2	208725985	Splice_Site	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1554465	208725985	34473388	196	2262										
CRYGC	1420	hgsc.bcm.edu	37	chr2	208992994	208992994	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggccccccagtcctggcacCgcctgtactcttggggcctc	11	18	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:208992994C>T	ENST00000282141.3	-	3	495	c.458G>A	c.(457-459)cGg>cAg	p.R153Q		NM_020989.3	NP_066269.1	P07315	CRGC_HUMAN	crystallin, gamma C	153	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			NS(1)|endometrium(1)|large_intestine(2)|lung(5)	9				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		GTCCTGGCACCGCCTGTACTC	0.567																																					p.R153Q		Atlas-SNP	.											.	CRYGC	28	.	0			c.G458A						.						62	69	67					2																	208992994		2203	4300	6503	SO:0001583	missense	1420	exon3			TGGCACCGCCTGT		CCDS2379.1	2q33.3	2013-02-14			ENSG00000163254	ENSG00000163254			2410	protein-coding gene	gene with protein product		123680		CRYG3			Standard	NM_020989		Approved		uc002vco.4	P07315	OTTHUMG00000132942	ENST00000282141.3:c.458G>A	chr2.hg19:g.208992994C>T	ENSP00000282141:p.Arg153Gln	128.0	0.0		139.0	45.0	NM_020989	Q53R50	Missense_Mutation	SNP	ENST00000282141.3	hg19	CCDS2379.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484512	0.44147	.	.	ENSG00000163254	ENST00000282141	T	0.75154	-0.91	4.98	1.12	0.20585	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.190513	0.43260	N	0.000585	T	0.72277	0.3440	M	0.80746	2.51	0.09310	N	1	B	0.30634	0.288	B	0.33295	0.161	T	0.66504	-0.5907	10	0.72032	D	0.01	.	8.0289	0.30453	0.0:0.6458:0.0:0.3542	.	153	P07315	CRGC_HUMAN	Q	153	ENSP00000282141:R153Q	ENSP00000282141:R153Q	R	-	2	0	CRYGC	208701239	0.000000	0.05858	0.244000	0.24202	0.972000	0.66771	0.427000	0.21379	0.245000	0.21373	0.557000	0.71058	CGG	.	.		0.567	CRYGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256474.1	NM_020989		T	208992994	C	T	208992994	3	4	23	1	0	0	0	0	1	0	0	0	3918	652	23	1	70	1	CRYGC	2	208992994	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	267009	208992994	34206379	197	2263										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215852484	215852484	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccaataggaaggaagaattGgaaaataccagggagctgcc	12	7	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:215852484G>A	ENST00000272895.7	-	27	4082	c.3863C>T	c.(3862-3864)cCa>cTa	p.P1288L	ABCA12_ENST00000389661.4_Missense_Mutation_p.P970L	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1288					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AGGAAGAATTGGAAAATACCA	0.413																																					p.P1288L	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C3863T						.						55	50	52					2																	215852484		2203	4300	6503	SO:0001583	missense	26154	exon27			AGAATTGGAAAAT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.3863C>T	chr2.hg19:g.215852484G>A	ENSP00000272895:p.Pro1288Leu	262.0	0.0		236.0	95.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.578037	0.65878	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	T;T	0.62941	-0.01;-0.01	5.26	5.26	0.73747	.	0.000000	0.64402	D	0.000004	T	0.61527	0.2354	L	0.52364	1.645	0.80722	D	1	B;B	0.33299	0.348;0.407	B;B	0.35727	0.08;0.209	T	0.62680	-0.6803	10	0.48119	T	0.1	.	18.8492	0.92220	0.0:0.0:1.0:0.0	.	1288;970	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	L	1288;970	ENSP00000272895:P1288L;ENSP00000374312:P970L	ENSP00000272895:P1288L	P	-	2	0	ABCA12	215560729	1.000000	0.71417	0.997000	0.53966	0.950000	0.60333	5.664000	0.68045	2.464000	0.83262	0.561000	0.74099	CCA	.	.		0.413	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		A	215852484	G	A	215852484	3	1	23	1	0	0	0	0	1	0	0	0	30	1348	47	3	4032	3	ABCA12	2	215852484	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	6859490	215852484	27346889	198	2264										
ATIC	471	hgsc.bcm.edu	37	chr2	216197219	216197219	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgctgcctctttcaaacatgTcagcccagcaggtaaagctc	8	14	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:216197219T>C	ENST00000236959.9	+	8	1129	c.803T>C	c.(802-804)gTc>gCc	p.V268A	ATIC_ENST00000435675.1_Missense_Mutation_p.V267A|ATIC_ENST00000540518.1_Missense_Mutation_p.V209A	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	268					'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)		ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	TTCAAACATGTCAGCCCAGCA	0.428			T	ALK	ALCL																																p.V268A		Atlas-SNP	.		Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	.	ATIC	84	.	0			c.T803C						.						41	45	43					2																	216197219		2203	4300	6503	SO:0001583	missense	471	exon8			AACATGTCAGCCC		CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.803T>C	chr2.hg19:g.216197219T>C	ENSP00000236959:p.Val268Ala	88.0	0.0		65.0	22.0	NM_004044	A8K202|E9PBU3|Q13856|Q53S28	Missense_Mutation	SNP	ENST00000236959.9	hg19	CCDS2398.1	.	.	.	.	.	.	.	.	.	.	T	19.25	3.792392	0.70452	.	.	ENSG00000138363	ENST00000236959;ENST00000540518;ENST00000435675	T;T;T	0.76186	-1.0;-1.0;-1.0	5.94	4.78	0.61160	AICAR transformylase domain (1);Cytidine deaminase-like (1);	0.000000	0.85682	D	0.000000	D	0.83954	0.5366	M	0.77820	2.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81581	-0.0867	10	0.21014	T	0.42	-7.778	11.8202	0.52235	0.0:0.0691:0.0:0.9309	.	267;268	E9PBU3;P31939	.;PUR9_HUMAN	A	268;209;267	ENSP00000236959:V268A;ENSP00000440523:V209A;ENSP00000415935:V267A	ENSP00000236959:V268A	V	+	2	0	ATIC	215905464	1.000000	0.71417	0.998000	0.56505	0.595000	0.36748	7.894000	0.87336	1.067000	0.40740	-0.297000	0.09499	GTC	.	.		0.428	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	NM_004044		C	216197219	T	C	216197219	3	2	23	1	0	0	0	0	1	0	0	0	1105	1667	58	2	833	2	ATIC	2	216197219	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	344735	216197219	27002154	199	2265										
FN1	2335	hgsc.bcm.edu	37	chr2	216259426	216259426	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttgtaggggttgtggtaatTctataaccagtaatgtctgg	12	4	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:216259426T>A	ENST00000359671.1	-	24	3886	c.3621A>T	c.(3619-3621)agA>agT	p.R1207S	FN1_ENST00000432072.2_Missense_Mutation_p.R1207S|FN1_ENST00000357867.4_Missense_Mutation_p.R1207S|FN1_ENST00000354785.4_Missense_Mutation_p.R1207S|FN1_ENST00000323926.6_Missense_Mutation_p.R1207S|FN1_ENST00000356005.4_Missense_Mutation_p.R1207S|FN1_ENST00000443816.1_Missense_Mutation_p.R1207S|FN1_ENST00000346544.3_Missense_Mutation_p.R1207S|FN1_ENST00000446046.1_Missense_Mutation_p.R1207S|FN1_ENST00000357009.2_Missense_Mutation_p.R1207S|FN1_ENST00000336916.4_Missense_Mutation_p.R1207S|FN1_ENST00000345488.5_Missense_Mutation_p.R1207S|FN1_ENST00000421182.1_Missense_Mutation_p.R1207S			P02751	FINC_HUMAN	fibronectin 1	1207	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TTGTGGTAATTCTATAACCAG	0.448																																					p.R1207S		Atlas-SNP	.											.	FN1	521	.	0			c.A3621T						.						89	98	95					2																	216259426		2203	4300	6503	SO:0001583	missense	2335	exon24			GGTAATTCTATAA		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.3621A>T	chr2.hg19:g.216259426T>A	ENSP00000352696:p.Arg1207Ser	56.0	0.0		73.0	30.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	T	20.4	3.977855	0.74360	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000002	T	0.72423	0.3458	M	0.79926	2.475	0.58432	D	0.999999	D;P;D;D;D;D;D;D;D;P	0.89917	0.995;0.542;1.0;1.0;0.996;0.996;1.0;0.999;0.999;0.923	D;B;D;D;D;D;D;D;D;P	0.91635	0.991;0.279;0.998;0.999;0.958;0.973;0.999;0.996;0.996;0.79	T	0.75750	-0.3208	10	0.59425	D	0.04	.	12.1309	0.53942	0.1281:0.0:0.0:0.8719	.	1207;1207;1207;1207;1207;1207;1207;1207;1207;1207	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	S	1207	ENSP00000394423:R1207S;ENSP00000323534:R1207S;ENSP00000338200:R1207S;ENSP00000350534:R1207S;ENSP00000346839:R1207S;ENSP00000352696:R1207S;ENSP00000265312:R1207S;ENSP00000273049:R1207S;ENSP00000349509:R1207S;ENSP00000410422:R1207S;ENSP00000415018:R1207S;ENSP00000399538:R1207S;ENSP00000348285:R1207S	ENSP00000265313:R1207S	R	-	3	2	FN1	215967671	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.449000	0.44935	2.145000	0.66743	0.533000	0.62120	AGA	.	.		0.448	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		A	216259426	T	A	216259426	3	1	23	1	0	0	0	0	1	0	0	0	5970	1780	62	4	3904	4	FN1	2	216259426	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	62207	216259426	26939947	200	2266										
MARCH4	57574	hgsc.bcm.edu	37	chr2	217124185	217124186	+	Frame_Shift_Ins	INS	-	-	G													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtggccggcagcctgggcaINSgggccctgctcaggggcagg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:217124185_217124186insG	ENST00000273067.4	-	4	2848_2849	c.1082_1083insC	c.(1081-1083)cctfs	p.P361fs	AC012513.6_ENST00000417481.1_RNA	NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	361						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		CAGCCTGGGCAGGGCCCTGCTC	0.639																																					p.P361fs		Atlas-Indel,Pindel	.											.	MARCH4	50	.	0			c.1083_1084insC						.																																			SO:0001589	frameshift_variant	57574	exon4			.	AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	29269	protein-coding gene	gene with protein product		608208	"membrane-associated ring finger (C3HC4) 4"			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.1083dupC	chr2.hg19:g.217124188_217124188dupG	ENSP00000273067:p.Pro361fs	113.0	0.0		89.0	31.0	NM_020814	Q4KMN7|Q86WR8	Frame_Shift_Ins	INS	ENST00000273067.4	hg19	CCDS33376.1																																																																																			.	.		0.639	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814		G	217124186	-	G	217124185	7	5	23	1	0	1	1	0	0	0	0	0	9312	175	7	0	153	0	MARCH4	2	217124185	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	864759	217124185	26075188	201	2267										
C2orf62	375307	hgsc.bcm.edu	37	chr2	219222348	219222348	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggagagctgaccattgaggtGcagagagggaaataccagga	16	6	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:219222348G>A	ENST00000289388.3	+	3	239	c.210G>A	c.(208-210)gtG>gtA	p.V70V	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		70					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCATTGAGGTGCAGAGAGGGA	0.542																																					p.V70V		Atlas-SNP	.											.	C2orf62	28	.	0			c.G210A						.						61	54	56					2																	219222348		2203	4300	6503	SO:0001819	synonymous_variant	375307	exon3			TGAGGTGCAGAGA																												ENST00000289388.3:c.210G>A	chr2.hg19:g.219222348G>A		76.0	0.0		58.0	24.0	NM_198559		Silent	SNP	ENST00000289388.3	hg19	CCDS2414.1																																																																																			.	.		0.542	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			A	219222348	G	A	219222348	2	1	23	1	0	0	0	0	0	0	0	1	2183	1306	46	3		3	C2orf62	2	219222348	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2098163	219222348	23977025	202	2268										
STK36	27148	hgsc.bcm.edu	37	chr2	219563382	219563382	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgcccatcagccttctcacaCgcctggccctcatggatccc	7	19	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:219563382C>T	ENST00000295709.3	+	26	3394	c.3115C>T	c.(3115-3117)Cgc>Tgc	p.R1039C	STK36_ENST00000440309.1_Missense_Mutation_p.R1039C|STK36_ENST00000392106.2_Missense_Mutation_p.R1018C|STK36_ENST00000392105.3_Missense_Mutation_p.R1018C	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CCTTCTCACACGCCTGGCCCT	0.537																																					p.R1039C		Atlas-SNP	.											.	STK36	111	.	0			c.C3115T						.						212	186	194					2																	219563382		2203	4300	6503	SO:0001583	missense	27148	exon26			CTCACACGCCTGG	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"fused homolog (Drosophila)"	607652	"serine/threonine kinase 36 (fused homolog, Drosophila)"			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.3115C>T	chr2.hg19:g.219563382C>T	ENSP00000295709:p.Arg1039Cys	108.0	0.0		119.0	49.0	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	hg19	CCDS2421.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.960700	0.74016	.	.	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.75367	-0.93;-0.93;-0.17;-0.93	6.06	6.06	0.98353	.	0.691003	0.12632	N	0.452119	T	0.79764	0.4502	L	0.32530	0.975	0.58432	D	0.999993	D;D;D	0.76494	0.995;0.999;0.999	P;P;P	0.58077	0.661;0.832;0.802	T	0.79254	-0.1879	10	0.87932	D	0	-3.789	18.8014	0.92018	0.0:1.0:0.0:0.0	.	1018;1018;1039	A8MU99;Q9NRP7-2;Q9NRP7	.;.;STK36_HUMAN	C	1039;1018;1018;1039	ENSP00000295709:R1039C;ENSP00000375955:R1018C;ENSP00000375954:R1018C;ENSP00000394095:R1039C	ENSP00000295709:R1039C	R	+	1	0	STK36	219271626	0.999000	0.42202	0.927000	0.36925	0.349000	0.29174	5.327000	0.65881	2.882000	0.98803	0.655000	0.94253	CGC	.	.		0.537	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			T	219563382	C	T	219563382	3	4	23	1	0	0	0	0	1	0	0	0	15317	536	19	1	3213	1	STK36	2	219563382	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	341034	219563382	23635991	203	2269										
C2orf24	27013	hgsc.bcm.edu	37	chr2	220037323	220037323	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctacctagcctgggaaaacGaaagacttgaggcgagccag	12	11	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:220037323G>A	ENST00000409789.1	-	9	1645	c.1218C>T	c.(1216-1218)ttC>ttT	p.F406F	SLC23A3_ENST00000409878.3_5'Flank|SLC23A3_ENST00000396775.3_5'Flank|CNPPD1_ENST00000360507.5_Silent_p.F406F|SLC23A3_ENST00000295738.7_5'Flank|SLC23A3_ENST00000455516.2_5'Flank			Q9BV87	CNPD1_HUMAN	cyclin Pas1/PHO80 domain containing 1	406					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	integral component of membrane (GO:0016021)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	12						CTGGGAAAACGAAAGACTTGA	0.542																																					p.F406F		Atlas-SNP	.											.	CNPPD1	22	.	0			c.C1218T						.						112	113	113					2																	220037323		2203	4300	6503	SO:0001819	synonymous_variant	27013	exon8			GAAAACGAAAGAC	AF070638	CCDS2433.1	2q36	2011-03-23	2011-03-23	2011-03-23	ENSG00000115649	ENSG00000115649			25220	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 24"	C2orf24		8619474, 9110174	Standard	NM_015680		Approved	CGI-57	uc002vju.4	Q9BV87	OTTHUMG00000133132	ENST00000409789.1:c.1218C>T	chr2.hg19:g.220037323G>A		82.0	0.0		76.0	24.0	NM_015680	B2RC77|O75548|Q9H4N0|Q9UQN0	Silent	SNP	ENST00000409789.1	hg19	CCDS2433.1																																																																																			.	.		0.542	CNPPD1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336220.1	NM_015680		A	220037323	G	A	220037323	2	1	23	1	0	0	0	0	0	0	0	1	2161	1049	37	1		1	C2orf24	2	220037323	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	473941	220037323	23162050	204	2270										
ZFAND2B	130617	hgsc.bcm.edu	37	chr2	220073041	220073041	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actgtccccagcccaagtcaAaccatgccttcctgtacctc	5	18	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:220073041A>G	ENST00000289528.5	+	5	693	c.498A>G	c.(496-498)caA>caG	p.Q166Q	ZFAND2B_ENST00000444522.2_Silent_p.Q166Q|ZFAND2B_ENST00000409206.1_Silent_p.Q166Q|ZFAND2B_ENST00000409097.1_Silent_p.Q166Q|ZFAND2B_ENST00000409594.1_Silent_p.Q166Q|ZFAND2B_ENST00000409336.1_Silent_p.Q166Q|ZFAND2B_ENST00000409217.1_Silent_p.Q166Q	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	166						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCCAAGTCAAACCATGCCTT	0.542																																					p.Q166Q		Atlas-SNP	.											.	ZFAND2B	28	.	0			c.A498G						.						111	88	96					2																	220073041		2203	4300	6503	SO:0001819	synonymous_variant	130617	exon5			AAGTCAAACCATG	AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"Zinc fingers, AN1-type domain containing"	25206	protein-coding gene	gene with protein product	"arsenite inducible RNA associated protein-like"	613474	"zinc finger, AN1-type 2B"			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.498A>G	chr2.hg19:g.220073041A>G		190.0	0.0		147.0	45.0	NM_138802	Q8NB98	Silent	SNP	ENST00000289528.5	hg19	CCDS2435.1																																																																																			.	.		0.542	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802		G	220073041	A	G	220073041	2	3	23	1	0	0	0	0	0	0	0	1	17643	11	1	2		2	ZFAND2B	2	220073041	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	35718	220073041	23126332	205	2271										
TUBA4A	7277	hgsc.bcm.edu	37	chr2	220115838	220115838	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcacagtctgagtgctccaGggtggtgtgggtggtcagga	19	7	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:220115838G>T	ENST00000248437.4	-	4	756	c.583C>A	c.(583-585)Ctg>Atg	p.L195M	TUBA4A_ENST00000392088.2_Missense_Mutation_p.L180M|TUBA4A_ENST00000498660.1_5'UTR|TUBA4B_ENST00000490341.1_RNA	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	195					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	GAGTGCTCCAGGGTGGTGTGG	0.557																																					p.L195M		Atlas-SNP	.											.	TUBA4A	96	.	0			c.C583A						.						103	105	104					2																	220115838		2203	4300	6503	SO:0001583	missense	7277	exon4			GCTCCAGGGTGGT	AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"Tubulins"	12407	protein-coding gene	gene with protein product		191110	"tubulin, alpha 1 (testis specific)", "tubulin, alpha 1"	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.583C>A	chr2.hg19:g.220115838G>T	ENSP00000248437:p.Leu195Met	89.0	0.0		88.0	9.0	NM_006000	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	hg19	CCDS2438.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.613424	0.46631	.	.	ENSG00000127824	ENST00000248437;ENST00000392088;ENST00000398989;ENST00000427737	T;T;T;T	0.70869	-0.48;-0.48;-0.48;-0.52	5.28	5.28	0.74379	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.64402	D	0.000011	D	0.84822	0.5557	M	0.88906	2.99	0.80722	D	1	P	0.49559	0.925	P	0.61592	0.891	D	0.87145	0.2205	10	0.87932	D	0	.	14.3324	0.66566	0.0729:0.0:0.9271:0.0	.	195	P68366	TBA4A_HUMAN	M	195;180;42;180	ENSP00000248437:L195M;ENSP00000375938:L180M;ENSP00000396212:L42M;ENSP00000408194:L180M	ENSP00000248437:L195M	L	-	1	2	TUBA4A	219824082	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.374000	0.59543	2.755000	0.94549	0.655000	0.94253	CTG	.	.		0.557	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000		T	220115838	G	T	220115838	3	4	23	1	0	0	0	0	1	0	0	0	16764	991	35	3	767	3	TUBA4A	2	220115838	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	42797	220115838	23083535	206	2272										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220427202	220427202	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggagtcctcgagctggacagCgggcagcaccaggcggcgga	18	12	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:220427202C>T	ENST00000404537.1	-	8	2931	c.2875G>A	c.(2875-2877)Gct>Act	p.A959T	OBSL1_ENST00000373876.1_Missense_Mutation_p.A959T|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000603926.1_Missense_Mutation_p.A959T|OBSL1_ENST00000289656.3_Missense_Mutation_p.A546T|OBSL1_ENST00000265318.4_Missense_Mutation_p.A959T|OBSL1_ENST00000373873.4_Missense_Mutation_p.A959T	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	959	Ig-like 7.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		AGCTGGACAGCGGGCAGCACC	0.647																																					p.A959T		Atlas-SNP	.											.	OBSL1	120	.	0			c.G2875A						.						65	77	73					2																	220427202		2203	4300	6503	SO:0001583	missense	23363	exon8			GGACAGCGGGCAG	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.2875G>A	chr2.hg19:g.220427202C>T	ENSP00000385636:p.Ala959Thr	113.0	0.0		116.0	5.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	hg19	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	C	4.564	0.104704	0.08731	.	.	ENSG00000124006	ENST00000265318;ENST00000404537;ENST00000373876;ENST00000373873;ENST00000289656	T;T;T;T;T	0.04809	3.55;3.55;3.55;3.55;3.55	4.72	1.72	0.24424	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.05593	0.0147	L	0.35644	1.08	0.09310	N	1	P;P;P;B	0.38473	0.633;0.633;0.528;0.056	B;B;B;B	0.42522	0.39;0.39;0.145;0.027	T	0.40403	-0.9565	9	0.14252	T	0.57	.	10.5828	0.45265	0.5146:0.419:0.0:0.0664	.	960;959;546;959	A4KVA4;O75147;A8MSZ8;O75147-2	.;OBSL1_HUMAN;.;.	T	959;959;959;959;546	ENSP00000265318:A959T;ENSP00000385636:A959T;ENSP00000362983:A959T;ENSP00000362980:A959T;ENSP00000289656:A546T	ENSP00000265318:A959T	A	-	1	0	OBSL1	220135446	0.000000	0.05858	0.001000	0.08648	0.199000	0.23934	-0.249000	0.08842	-0.109000	0.12044	-0.808000	0.03180	GCT	.	.		0.647	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			T	220427202	C	T	220427202	3	4	23	1	0	0	0	0	1	0	0	0	10822	768	27	1	3023	1	OBSL1	2	220427202	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	311364	220427202	22772171	207	2273										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230652245	230652245	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttctatccaatctaggtgcAactctgctatcttgagaatc	6	10	4	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:230652245A>G	ENST00000283943.5	-	32	4924	c.4746T>C	c.(4744-4746)gtT>gtC	p.V1582V	TRIP12_ENST00000389044.4_Silent_p.V1630V|TRIP12_ENST00000389045.3_Silent_p.V1312V	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1582					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ATCTAGGTGCAACTCTGCTAT	0.343																																					p.V1582V		Atlas-SNP	.											.	TRIP12	207	.	0			c.T4746C						.						145	143	144					2																	230652245		2203	4300	6503	SO:0001819	synonymous_variant	9320	exon32			AGGTGCAACTCTG	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.4746T>C	chr2.hg19:g.230652245A>G		131.0	0.0		167.0	71.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.		0.343	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		G	230652245	A	G	230652245	2	3	23	1	0	0	0	0	0	0	0	1	16571	117	5	2		2	TRIP12	2	230652245	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	10225043	230652245	12547128	208	2274										
NMUR1	10316	hgsc.bcm.edu	37	chr2	232393179	232393179	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcatggcaagaccccagaCggccccaagcactcggcgca	12	16	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:232393179C>T	ENST00000305141.4	-	2	686	c.553G>A	c.(553-555)Gtc>Atc	p.V185I		NM_006056.4	NP_006047.3	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	185					activation of phospholipase C activity (GO:0007202)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|chloride transport (GO:0006821)|G-protein coupled receptor signaling pathway (GO:0007186)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|smooth muscle contraction (GO:0006939)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuromedin U receptor activity (GO:0001607)|neuropeptide receptor activity (GO:0008188)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(12)|pancreas(1)|skin(1)	24		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;8.37e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		AGACCCCAGACGGCCCCAAGC	0.687																																					p.V185I		Atlas-SNP	.											NMUR1,NS,carcinoma,0,1	NMUR1	46	.	0			c.G553A						.						36	33	34					2																	232393179		2203	4298	6501	SO:0001583	missense	10316	exon2			CCCAGACGGCCCC	AF044600	CCDS2486.1	2q37.1	2012-08-08	2004-05-27	2004-05-28	ENSG00000171596	ENSG00000171596		"GPCR / Class A : Neuromedin U receptors"	4518	protein-coding gene	gene with protein product		604153	"G protein-coupled receptor 66"	GPR66		9782091	Standard	NM_006056		Approved	GPC-R, FM-3, NMU1R	uc002vry.4	Q9HB89	OTTHUMG00000133225	ENST00000305141.4:c.553G>A	chr2.hg19:g.232393179C>T	ENSP00000305877:p.Val185Ile	94.0	0.0		99.0	58.0	NM_006056	O43664|Q7LDP6|Q8NE20	Missense_Mutation	SNP	ENST00000305141.4	hg19	CCDS2486.1	.	.	.	.	.	.	.	.	.	.	.	0.019	-1.459859	0.01062	.	.	ENSG00000171596	ENST00000305141	T	0.73152	-0.72	5.08	-7.44	0.01379	GPCR, rhodopsin-like superfamily (1);	0.529642	0.20465	N	0.091804	T	0.36690	0.0976	N	0.12443	0.215	0.09310	N	0.999995	B	0.21147	0.052	B	0.23150	0.044	T	0.50659	-0.8802	10	0.02654	T	1	-17.9982	7.5504	0.27793	0.0:0.3762:0.3266:0.2971	.	185	Q9HB89	NMUR1_HUMAN	I	185	ENSP00000305877:V185I	ENSP00000305877:V185I	V	-	1	0	NMUR1	232101423	0.000000	0.05858	0.011000	0.14972	0.018000	0.09664	-0.300000	0.08243	-0.760000	0.04677	0.456000	0.33151	GTC	.	.		0.687	NMUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256961.1	NM_006056		T	232393179	C	T	232393179	3	4	23	1	0	0	0	0	1	0	0	0	10515	536	19	1	735	1	NMUR1	2	232393179	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1740934	232393179	10806194	209	2275										
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233612329	233612329	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcttttctattctaggctcCgagctctgtccagtggtggg	12	10	4	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:233612329C>T	ENST00000409547.1	+	6	357	c.46C>T	c.(46-48)Cga>Tga	p.R16*	GIGYF2_ENST00000409480.1_Nonsense_Mutation_p.R16*|GIGYF2_ENST00000373566.3_Nonsense_Mutation_p.R16*|GIGYF2_ENST00000409451.3_Nonsense_Mutation_p.R16*|GIGYF2_ENST00000373563.4_Nonsense_Mutation_p.R16*|GIGYF2_ENST00000409196.3_Nonsense_Mutation_p.R16*	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	16					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		TTCTAGGCTCCGAGCTCTGTC	0.378																																					p.R16X		Atlas-SNP	.											.	GIGYF2	288	.	0			c.C46T						.						129	129	129					2																	233612329		2203	4300	6503	SO:0001587	stop_gained	26058	exon4			AGGCTCCGAGCTC	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.46C>T	chr2.hg19:g.233612329C>T	ENSP00000386537:p.Arg16*	82.0	0.0		95.0	4.0	NM_001103146	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Nonsense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	C	36	5.973652	0.97162	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000428883;ENST00000456491;ENST00000409480;ENST00000421433;ENST00000425040;ENST00000430720;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000429187;ENST00000440945	.	.	.	5.55	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.288	9.291	0.37786	0.1437:0.7835:0.0:0.0728	.	.	.	.	X	16	.	ENSP00000362664:R16X	R	+	1	2	GIGYF2	233320573	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.757000	0.62213	1.365000	0.46057	0.561000	0.74099	CGA	.	.		0.378	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		T	233612329	C	T	233612329	4	4	23	1	0	0	0	0	0	1	0	0	6386	644	23	1	52	1	GIGYF2	2	233612329	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1219150	233612329	9587044	210	2276										
NEU2	4759	hgsc.bcm.edu	37	chr2	233899090	233899090	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagcctaccgggagtggtccAcctttgcagtgggcccgggg	16	13	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:233899090A>G	ENST00000233840.3	+	2	466	c.466A>G	c.(466-468)Acc>Gcc	p.T156A		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	156					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	GGAGTGGTCCACCTTTGCAGT	0.657																																					p.T156A		Atlas-SNP	.											.	NEU2	42	.	0			c.A466G						.						46	51	49					2																	233899090		2203	4300	6503	SO:0001583	missense	4759	exon2			TGGTCCACCTTTG	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"N-acetyl-alpha-neuraminidase 2"	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.466A>G	chr2.hg19:g.233899090A>G	ENSP00000233840:p.Thr156Ala	69.0	0.0		60.0	6.0	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	hg19	CCDS2501.1	.	.	.	.	.	.	.	.	.	.	A	19.10	3.761504	0.69763	.	.	ENSG00000115488	ENST00000233840	D	0.84873	-1.91	4.88	4.88	0.63580	Neuraminidase (2);	0.000000	0.64402	D	0.000005	D	0.90556	0.7040	M	0.89601	3.045	0.53005	D	0.999967	P	0.50369	0.934	P	0.54759	0.76	D	0.89720	0.3918	10	0.12103	T	0.63	-29.9195	13.6972	0.62587	1.0:0.0:0.0:0.0	.	156	Q9Y3R4	NEUR2_HUMAN	A	156	ENSP00000233840:T156A	ENSP00000233840:T156A	T	+	1	0	NEU2	233607334	1.000000	0.71417	0.999000	0.59377	0.202000	0.24057	9.035000	0.93752	1.821000	0.53095	0.459000	0.35465	ACC	.	.		0.657	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383		G	233899090	A	G	233899090	3	3	23	1	0	0	0	0	1	0	0	0	10351	159	6	2	472	2	NEU2	2	233899090	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	286761	233899090	9300283	211	2277										
HDAC4	9759	hgsc.bcm.edu	37	chr2	240029867	240029867	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtgcttcagcatcagcgtgTcatacacgaggcctggggcg	15	11	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:240029867T>C	ENST00000345617.3	-	15	2767	c.1976A>G	c.(1975-1977)gAc>gGc	p.D659G	HDAC4_ENST00000543185.1_Missense_Mutation_p.D243G|HDAC4_ENST00000541256.1_Missense_Mutation_p.D633G	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	659	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CATCAGCGTGTCATACACGAG	0.692																																					p.D659G		Atlas-SNP	.											.	HDAC4	127	.	0			c.A1976G						.						22	21	21					2																	240029867		2192	4291	6483	SO:0001583	missense	9759	exon15			AGCGTGTCATACA	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.1976A>G	chr2.hg19:g.240029867T>C	ENSP00000264606:p.Asp659Gly	208.0	0.0		158.0	57.0	NM_006037	Q9UND6	Missense_Mutation	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.869275	0.72065	.	.	ENSG00000068024	ENST00000345617;ENST00000456922;ENST00000543185;ENST00000541256;ENST00000393621	T;T;T	0.78924	-0.91;-1.22;0.13	4.01	4.01	0.46588	Histone deacetylase domain (1);	0.000000	0.85682	D	0.000000	D	0.87390	0.6165	M	0.80616	2.505	0.80722	D	1	P;D;D;D;B;B	0.76494	0.549;0.998;0.999;0.998;0.262;0.134	B;D;D;D;B;B	0.79108	0.099;0.955;0.992;0.912;0.257;0.134	D	0.89202	0.3558	10	0.87932	D	0	.	13.2665	0.60137	0.0:0.0:0.0:1.0	.	659;542;633;633;627;659	B7Z8G5;F5H0Q9;F5H5W4;B7Z8I2;Q53SM2;P56524	.;.;.;.;.;HDAC4_HUMAN	G	659;547;243;633;542	ENSP00000264606:D659G;ENSP00000440481:D243G;ENSP00000443057:D633G	ENSP00000264606:D659G	D	-	2	0	HDAC4	239694804	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	7.623000	0.83113	1.598000	0.50083	0.460000	0.39030	GAC	.	.		0.692	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		C	240029867	T	C	240029867	3	2	23	1	0	0	0	0	1	0	0	0	7018	1667	58	2	1330	2	HDAC4	2	240029867	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	6130777	240029867	3169506	212	2278										
HDLBP	3069	hgsc.bcm.edu	37	chr2	242174657	242174657	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actgcagctcaggtgccgggAcatgtatgttcacctacgtg	12	11	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:242174657A>G	ENST00000391975.1	-	23	3250	c.3023T>C	c.(3022-3024)gTc>gCc	p.V1008A	HDLBP_ENST00000427183.2_Missense_Mutation_p.V975A|HDLBP_ENST00000310931.4_Missense_Mutation_p.V1008A|HDLBP_ENST00000391976.2_Missense_Mutation_p.V1008A	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1008	KH 12. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		AGGTGCCGGGACATGTATGTT	0.582																																					p.V1008A		Atlas-SNP	.											.	HDLBP	118	.	0			c.T3023C						.						77	74	75					2																	242174657		2203	4300	6503	SO:0001583	missense	3069	exon23			GCCGGGACATGTA		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.3023T>C	chr2.hg19:g.242174657A>G	ENSP00000375836:p.Val1008Ala	52.0	0.0		47.0	20.0	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	hg19	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.992974	0.74703	.	.	ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.79	4.62	0.57501	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.65407	0.2688	M	0.86178	2.8	0.80722	D	1	D;D	0.64830	0.987;0.994	D;P	0.67231	0.95;0.9	T	0.69351	-0.5168	10	0.59425	D	0.04	-29.4794	12.215	0.54402	0.8721:0.0:0.0:0.1279	.	975;1008	E7EM71;Q00341	.;VIGLN_HUMAN	A	1008;1008;1008;975	ENSP00000375836:V1008A;ENSP00000375837:V1008A;ENSP00000312042:V1008A;ENSP00000399139:V975A	ENSP00000312042:V1008A	V	-	2	0	HDLBP	241823330	1.000000	0.71417	0.022000	0.16811	0.677000	0.39632	9.220000	0.95180	0.995000	0.38917	0.455000	0.32223	GTC	.	.		0.582	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		G	242174657	A	G	242174657	3	3	23	1	0	0	0	0	1	0	0	0	7034	275	10	2	807	2	HDLBP	2	242174657	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2144790	242174657	1024716	213	2279										
C3orf32	51066	hgsc.bcm.edu	37	chr3	8671370	8671370	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgtgcccgccccgtggcagcCgctgcacttgtaccgcccac	11	20	0	0	rs532787180		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:8671370C>T	ENST00000317371.4	-	14	1727	c.502G>A	c.(502-504)Ggc>Agc	p.G168S	SSUH2_ENST00000544814.1_Missense_Mutation_p.G190S|SSUH2_ENST00000415132.1_Missense_Mutation_p.G168S|SSUH2_ENST00000341795.3_Missense_Mutation_p.G168S			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	168	Cys-rich.					cytoplasm (GO:0005737)											CCGTGGCAGCCGCTGCACTTG	0.627													C|||	1	0.000199681	0	0	5008	,	,		17694	0		0.001	False		,,,				2504	0				p.G190S		Atlas-SNP	.											.	.	.	.	0			c.G568A						.						82	86	85					3																	8671370		2203	4300	6503	SO:0001583	missense	51066	exon7			GGCAGCCGCTGCA	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 32"	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.502G>A	chr3.hg19:g.8671370C>T	ENSP00000324551:p.Gly168Ser	86.0	0.0		59.0	23.0	NM_001256748	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	hg19	CCDS2568.1	.	.	.	.	.	.	.	.	.	.	C	16.63	3.176932	0.57692	.	.	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132;ENST00000544814	T;T;T;T	0.40756	1.02;1.02;1.02;1.04	4.75	2.91	0.33838	.	0.301641	0.37857	N	0.001909	T	0.41971	0.1182	L	0.46157	1.445	0.30122	N	0.805604	D;D	0.67145	0.996;0.99	P;P	0.56823	0.807;0.651	T	0.35549	-0.9784	10	0.12103	T	0.63	-25.2349	6.0251	0.19650	0.1849:0.7162:0.0:0.0989	.	190;168	F5H2S5;Q9Y2M2	.;CC032_HUMAN	S	168;168;168;190	ENSP00000339150:G168S;ENSP00000324551:G168S;ENSP00000410757:G168S;ENSP00000439378:G190S	ENSP00000324551:G168S	G	-	1	0	C3orf32	8646370	0.542000	0.26426	0.611000	0.29010	0.837000	0.47467	0.867000	0.27968	0.404000	0.25506	0.467000	0.42956	GGC	.	.		0.627	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931		T	8671370	C	T	8671370	3	4	23	1	0	0	0	0	1	0	0	0	2224	652	23	1	583	1	C3orf32	3	8671370	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10		8671370	189351060	214	2280										
TMEM40	55287	hgsc.bcm.edu	37	chr3	12790175	12790175	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgaggaggaggaggatgaagAagatgaggaggatgaggagg	22	0	0	6			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:12790175A>G	ENST00000314124.7	-	3	546	c.190T>C	c.(190-192)Tct>Cct	p.S64P	TMEM40_ENST00000431022.2_Missense_Mutation_p.S80P|TMEM40_ENST00000435218.2_Missense_Mutation_p.S64P|TMEM40_ENST00000435575.1_Intron|TMEM40_ENST00000264728.8_Missense_Mutation_p.S64P	NM_001284406.1|NM_018306.2	NP_001271335.1|NP_060776.2	Q8WWA1	TMM40_HUMAN	transmembrane protein 40	64	Ser-rich.					integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(5)|urinary_tract(1)	10						gaggatgaagaagatgaggag	0.413																																					p.S64P		Atlas-SNP	.											.	TMEM40	22	.	0			c.T190C						.						156	149	151					3																	12790175		2203	4300	6503	SO:0001583	missense	55287	exon3			ATGAAGAAGATGA	BC020658	CCDS2613.1, CCDS68347.1, CCDS68348.1	3p25.2	2005-01-10			ENSG00000088726	ENSG00000088726			25620	protein-coding gene	gene with protein product						12477932	Standard	NM_018306		Approved	FLJ11036	uc003bxg.1	Q8WWA1	OTTHUMG00000129801	ENST00000314124.7:c.190T>C	chr3.hg19:g.12790175A>G	ENSP00000322837:p.Ser64Pro	27.0	0.0		32.0	18.0	NM_018306	C9JID5|Q8NAL4|Q9NUZ4	Missense_Mutation	SNP	ENST00000314124.7	hg19	CCDS2613.1	.	.	.	.	.	.	.	.	.	.	A	9.564	1.119136	0.20877	.	.	ENSG00000088726	ENST00000314124;ENST00000435218;ENST00000264728;ENST00000431022	.	.	.	3.29	3.29	0.37713	.	0.156430	0.30347	N	0.009840	T	0.48370	0.1496	L	0.31926	0.97	0.09310	N	1	D;B;D	0.76494	0.999;0.002;0.999	D;B;D	0.80764	0.994;0.004;0.994	T	0.20840	-1.0263	9	0.87932	D	0	.	8.3511	0.32303	1.0:0.0:0.0:0.0	.	80;64;64	B4DXI0;Q8WWA1-2;Q8WWA1	.;.;TMM40_HUMAN	P	64;64;64;80	.	ENSP00000264728:S64P	S	-	1	0	TMEM40	12765175	0.164000	0.22935	0.052000	0.19188	0.229000	0.25112	2.986000	0.49370	1.750000	0.51863	0.454000	0.30748	TCT	.	.		0.413	TMEM40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252029.2	NM_018306		G	12790175	A	G	12790175	3	3	23	1	0	0	0	0	1	0	0	0	16178	246	9	2	551	2	TMEM40	3	12790175	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	4118805	12790175	185232255	215	2281										
NUP210	23225	hgsc.bcm.edu	37	chr3	13368741	13368741	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caggctggtcagaacagtggCcagacagagcacgtccccca	12	14	1	3	rs199638243		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:13368741C>T	ENST00000254508.5	-	32	4565	c.4483G>A	c.(4483-4485)Gcc>Acc	p.A1495T		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1495					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					AGAACAGTGGCCAGACAGAGC	0.627																																					p.A1495T		Atlas-SNP	.											.	NUP210	182	.	0			c.G4483A						.						34	37	36					3																	13368741		2202	4300	6502	SO:0001583	missense	23225	exon32			CAGTGGCCAGACA	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.4483G>A	chr3.hg19:g.13368741C>T	ENSP00000254508:p.Ala1495Thr	67.0	0.0		48.0	8.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	C	11.53	1.667449	0.29604	.	.	ENSG00000132182	ENST00000254508	T	0.04758	3.56	5.88	1.3	0.21679	.	0.747393	0.12860	N	0.433231	T	0.03520	0.0101	L	0.34521	1.04	0.09310	N	0.999999	B	0.09022	0.002	B	0.09377	0.004	T	0.43621	-0.9380	10	0.33141	T	0.24	.	2.5038	0.04640	0.4424:0.2249:0.0:0.3326	.	1495	Q8TEM1	PO210_HUMAN	T	1495	ENSP00000254508:A1495T	ENSP00000254508:A1495T	A	-	1	0	NUP210	13343741	0.000000	0.05858	0.448000	0.26945	0.601000	0.36947	-0.434000	0.06939	0.317000	0.23160	0.655000	0.94253	GCC	.	.		0.627	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		T	13368741	C	T	13368741	3	4	23	1	0	0	0	0	1	0	0	0	10769	739	26	3	1216	3	NUP210	3	13368741	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	578566	13368741	184653689	216	2282										
C3orf20	84077	hgsc.bcm.edu	37	chr3	14724484	14724484	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaacccacctttgtgcaggtCcccacactgaagaagccact	8	15	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:14724484C>T	ENST00000253697.3	+	3	716	c.264C>T	c.(262-264)gtC>gtT	p.V88V	C3orf20_ENST00000435614.1_5'UTR|C3orf20_ENST00000412910.1_5'UTR	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	88						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						TTGTGCAGGTCCCCACACTGA	0.627																																					p.V88V		Atlas-SNP	.											.	C3orf20	109	.	0			c.C264T						.						60	55	56					3																	14724484		2203	4300	6503	SO:0001819	synonymous_variant	84077	exon3			GCAGGTCCCCACA	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.264C>T	chr3.hg19:g.14724484C>T		127.0	0.0		139.0	57.0	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Silent	SNP	ENST00000253697.3	hg19	CCDS33706.1																																																																																			.	.		0.627	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		T	14724484	C	T	14724484	2	4	23	1	0	0	0	0	0	0	0	1	2215	842	30	3		3	C3orf20	3	14724484	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1355743	14724484	183297946	217	2283										
NR2C2	7182	hgsc.bcm.edu	37	chr3	15057748	15057748	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagtactgtgtggtctgtggCgacaaagcctccggtatgta	14	8	1	0	rs369008989		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:15057748C>T	ENST00000425241.1	+	4	725	c.363C>T	c.(361-363)ggC>ggT	p.G121G	NR2C2_ENST00000406272.2_Silent_p.G121G|NR2C2_ENST00000323373.6_Silent_p.G140G|NR2C2_ENST00000393102.3_Silent_p.G121G			P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2	121					cell differentiation (GO:0030154)|gene expression (GO:0010467)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TGGTCTGTGGCGACAAAGCCT	0.507																																					p.G140G		Atlas-SNP	.											.	NR2C2	44	.	0			c.C420T						.	C		1,4405	2.1+/-5.4	0,1,2202	181	158	166		420	-6.4	0.6	3		166	0,8600		0,0,4300	no	coding-synonymous	NR2C2	NM_003298.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		140/616	15057748	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7182	exon5			CTGTGGCGACAAA	L27586	CCDS2621.1, CCDS74905.1	3p25	2013-01-16			ENSG00000177463	ENSG00000177463		"Nuclear hormone receptors"	7972	protein-coding gene	gene with protein product		601426		TR4		8661150, 8016112	Standard	XM_005265428		Approved	TAK1, TR2R1, hTAK1	uc003bzi.3	P49116	OTTHUMG00000129839	ENST00000425241.1:c.363C>T	chr3.hg19:g.15057748C>T		160.0	0.0		113.0	39.0	NM_003298	A8K3H5|B6ZGT8|P55092	Silent	SNP	ENST00000425241.1	hg19																																																																																				.	.		0.507	NR2C2-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000340729.1	NM_003298		T	15057748	C	T	15057748	2	4	23	1	0	0	0	0	0	0	0	1	10632	755	27	1		1	NR2C2	3	15057748	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	333264	15057748	182964682	218	2284										
ZFYVE20	64145	hgsc.bcm.edu	37	chr3	15116270	15116270	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgtggatctgctggaggagCgggtctgagtcctcactctg	15	9	4	1	rs551879008	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:15116270C>T	ENST00000253699.3	-	14	1987	c.1374G>A	c.(1372-1374)ccG>ccA	p.P458P	ZFYVE20_ENST00000476527.2_Silent_p.P458P	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	458	Necessary for the interaction with EHD1.|Necessary for the interaction with RAB4A.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						GCTGGAGGAGCGGGTCTGAGT	0.642													C|||	2	0.000399361	0	0.0014	5008	,	,		18852	0		0.001	False		,,,				2504	0				p.P458P		Atlas-SNP	.											.	ZFYVE20	61	.	0			c.G1374A						.						61	54	56					3																	15116270		2203	4300	6503	SO:0001819	synonymous_variant	64145	exon14			GAGGAGCGGGTCT	AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"Zinc fingers, FYVE domain containing"	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.1374G>A	chr3.hg19:g.15116270C>T		99.0	0.0		100.0	41.0	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Silent	SNP	ENST00000253699.3	hg19	CCDS2623.1																																																																																			.	.		0.642	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		T	15116270	C	T	15116270	2	4	23	1	0	0	0	0	0	0	0	1	17681	755	27	1		1	ZFYVE20	3	15116270	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	58522	15116270	182906160	219	2285										
DAZL	1618	hgsc.bcm.edu	37	chr3	16639957	16639957	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaatgaggtatgaatacaatAccctaacatcaattcctcca	4	10	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:16639957A>G	ENST00000399444.2	-	2	444		c.e2+1		DAZL_ENST00000250863.8_Splice_Site	NM_001351.3	NP_001342.2	Q92904	DAZL_HUMAN	deleted in azoospermia-like						female meiosis II (GO:0007147)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|oocyte maturation (GO:0001556)|positive regulation of meiosis (GO:0045836)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494)		RAF1/DAZL(2)	endometrium(1)|large_intestine(3)|lung(4)|prostate(3)	11						TGAATACAATACCCTAACATC	0.383																																					.		Atlas-SNP	.											.	DAZL	23	.	0			c.150+2T>C						.						155	150	152					3																	16639957		2203	4300	6503	SO:0001630	splice_region_variant	1618	exon3			TACAATACCCTAA	BC027595	CCDS43059.1, CCDS54556.1	3p24	2013-02-12			ENSG00000092345	ENSG00000092345		"RNA binding motif (RRM) containing"	2685	protein-coding gene	gene with protein product		601486		DAZLA		8896558	Standard	NM_001351		Approved	DAZH, SPGYLA, MGC26406, DAZL1	uc003cbb.3	Q92904	OTTHUMG00000157050	ENST00000399444.2:c.150+1T>C	chr3.hg19:g.16639957A>G		56.0	0.0		41.0	20.0	NM_001351	O15396|Q5HYB4|Q92909	Splice_Site	SNP	ENST00000399444.2	hg19	CCDS43059.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.521904	0.64747	.	.	ENSG00000092345	ENST00000250863;ENST00000399444;ENST00000454457	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5349	0.75996	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DAZL	16614961	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	7.320000	0.79064	2.142000	0.66516	0.482000	0.46254	.	.	.		0.383	DAZL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347261.2	NM_001351	Intron	G	16639957	A	G	16639957	5	3	23	1	0	0	0	0	0	0	1	0	4248	405	14	2	775	2	DAZL	3	16639957	Splice_Site	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1523687	16639957	181382473	220	2286										
UBE2E2	7325	hgsc.bcm.edu	37	chr3	23631290	23631290	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcagagcatgaccggatgGccagacagtggaccaagcgg	16	10	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:23631290G>A	ENST00000396703.1	+	6	754	c.574G>A	c.(574-576)Gcc>Acc	p.A192T	UBE2E2_ENST00000425792.1_Missense_Mutation_p.A192T	NM_152653.3	NP_689866.1	Q96LR5	UB2E2_HUMAN	ubiquitin-conjugating enzyme E2E 2	192					ISG15-protein conjugation (GO:0032020)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)		ATP binding (GO:0005524)|ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(2)	10						TGACCGGATGGCCAGACAGTG	0.602																																					p.A192T	GBM(85;1941 2083 9456)	Atlas-SNP	.											.	UBE2E2	24	.	0			c.G574A						.						97	82	87					3																	23631290		2203	4300	6503	SO:0001583	missense	7325	exon6			CGGATGGCCAGAC	AK057886	CCDS2637.1	3p24.2	2011-05-19	2011-05-19		ENSG00000182247	ENSG00000182247		"Ubiquitin-conjugating enzymes E2"	12478	protein-coding gene	gene with protein product		602163	"ubiquitin-conjugating enzyme E2E 2 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2E 2 (UBC4/5 homolog, yeast)"			9371400	Standard	NM_152653		Approved	UbcH8, FLJ25157	uc003ccg.2	Q96LR5	OTTHUMG00000130482	ENST00000396703.1:c.574G>A	chr3.hg19:g.23631290G>A	ENSP00000379931:p.Ala192Thr	364.0	0.0		347.0	141.0	NM_152653		Missense_Mutation	SNP	ENST00000396703.1	hg19	CCDS2637.1	.	.	.	.	.	.	.	.	.	.	G	33	5.267165	0.95399	.	.	ENSG00000182247	ENST00000425792;ENST00000396703	T;T	0.75154	-0.91;-0.91	5.45	5.45	0.79879	Ubiquitin-conjugating enzyme, E2 (1);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.64402	D	0.000007	D	0.91935	0.7446	H	0.98314	4.2	0.80722	D	1	D	0.69078	0.997	D	0.68192	0.956	D	0.94903	0.8058	10	0.87932	D	0	.	19.2915	0.94102	0.0:0.0:1.0:0.0	.	192	Q96LR5	UB2E2_HUMAN	T	192	ENSP00000401053:A192T;ENSP00000379931:A192T	ENSP00000379931:A192T	A	+	1	0	UBE2E2	23606294	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.970000	0.88000	2.562000	0.86427	0.655000	0.94253	GCC	.	.		0.602	UBE2E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252881.2	NM_152653		A	23631290	G	A	23631290	3	1	23	1	0	0	0	0	1	0	0	0	16868	1203	42	3	592	3	UBE2E2	3	23631290	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	6991333	23631290	174391140	221	2287										
PDCD6IP	10015	hgsc.bcm.edu	37	chr3	33885697	33885697	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggacaccatccaatgaactgTataagcctttaagagcaggt	9	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:33885697T>C	ENST00000307296.3	+	11	1830	c.1453T>C	c.(1453-1455)Tat>Cat	p.Y485H	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.Y490H			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	485	Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						CAATGAACTGTATAAGCCTTT	0.343																																					p.Y490H		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.T1468C						.						69	69	69					3																	33885697		2203	4298	6501	SO:0001583	missense	10015	exon11			GAACTGTATAAGC	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.1453T>C	chr3.hg19:g.33885697T>C	ENSP00000307387:p.Tyr485His	641.0	0.0		573.0	205.0	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	hg19	CCDS2660.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.177281	0.78564	.	.	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.30448	1.53;1.53	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.49762	0.1576	L	0.57536	1.79	0.80722	D	1	D;D;D	0.63880	0.976;0.993;0.987	D;D;D	0.70016	0.947;0.967;0.967	T	0.39272	-0.9622	10	0.27082	T	0.32	-10.0324	15.205	0.73173	0.0:0.0:0.0:1.0	.	266;490;485	B7Z5C1;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	H	485;490	ENSP00000307387:Y485H;ENSP00000411825:Y490H	ENSP00000307387:Y485H	Y	+	1	0	PDCD6IP	33860701	1.000000	0.71417	0.915000	0.36163	0.984000	0.73092	6.716000	0.74702	2.002000	0.58637	0.455000	0.32223	TAT	.	.		0.343	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			C	33885697	T	C	33885697	3	2	23	1	0	0	0	0	1	0	0	0	11633	1638	57	2	1510	2	PDCD6IP	3	33885697	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	10254407	33885697	164136733	222	2288										
TRANK1	9881	hgsc.bcm.edu	37	chr3	36872532	36872532	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagcttgccttcatcaatggCcgggtccaccttctcgtgga	10	14	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:36872532C>T	ENST00000429976.2	-	21	8657	c.8410G>A	c.(8410-8412)Gcc>Acc	p.A2804T	TRANK1_ENST00000428977.2_Missense_Mutation_p.A2254T|TRANK1_ENST00000301807.6_Missense_Mutation_p.A2254T	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2804							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						TCATCAATGGCCGGGTCCACC	0.532																																					p.A2804T		Atlas-SNP	.											.	TRANK1	398	.	0			c.G8410A						.						242	239	240					3																	36872532		2085	4203	6288	SO:0001583	missense	9881	exon21			CAATGGCCGGGTC	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.8410G>A	chr3.hg19:g.36872532C>T	ENSP00000416168:p.Ala2804Thr	116.0	0.0		102.0	7.0	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077639	0.36662	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.32272	1.46;1.88;1.46	5.48	3.61	0.41365	.	0.594227	0.16066	N	0.231255	T	0.15739	0.0379	L	0.27053	0.805	0.18873	N	0.999986	P	0.35433	0.501	B	0.27608	0.081	T	0.14671	-1.0464	10	0.37606	T	0.19	.	3.2309	0.06747	0.1427:0.5553:0.1386:0.1634	.	2804	O15050	TRNK1_HUMAN	T	2254;2804;2254	ENSP00000416826:A2254T;ENSP00000416168:A2804T;ENSP00000301807:A2254T	ENSP00000301807:A2254T	A	-	1	0	TRANK1	36847536	0.563000	0.26594	0.783000	0.31826	0.745000	0.42441	0.886000	0.28241	0.735000	0.32537	0.555000	0.69702	GCC	.	.		0.532	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		T	36872532	C	T	36872532	3	4	23	1	0	0	0	0	1	0	0	0	16469	739	26	3	379	3	TRANK1	3	36872532	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2986835	36872532	161149898	223	2289										
TRANK1	9881	hgsc.bcm.edu	37	chr3	36875360	36875360	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtaaaactgactggcagaaTaggagagcttggaaatggga	14	4	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:36875360T>C	ENST00000429976.2	-	21	5829	c.5582A>G	c.(5581-5583)tAt>tGt	p.Y1861C	TRANK1_ENST00000428977.2_Missense_Mutation_p.Y1311C|TRANK1_ENST00000301807.6_Missense_Mutation_p.Y1311C	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1861							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						ACTGGCAGAATAGGAGAGCTT	0.418																																					p.Y1861C		Atlas-SNP	.											.	TRANK1	398	.	0			c.A5582G						.						73	70	71					3																	36875360		1873	4099	5972	SO:0001583	missense	9881	exon21			GCAGAATAGGAGA	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.5582A>G	chr3.hg19:g.36875360T>C	ENSP00000416168:p.Tyr1861Cys	61.0	0.0		54.0	23.0	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	8.238	0.806179	0.16467	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.33865	1.39;1.81;1.39	5.27	4.1	0.47936	.	0.126578	0.36409	N	0.002616	T	0.21761	0.0524	N	0.19112	0.55	0.36433	D	0.865001	B	0.10296	0.003	B	0.06405	0.002	T	0.10776	-1.0615	10	0.34782	T	0.22	.	8.0264	0.30440	0.0:0.1749:0.0:0.8251	.	1861	O15050	TRNK1_HUMAN	C	1311;1861;1311	ENSP00000416826:Y1311C;ENSP00000416168:Y1861C;ENSP00000301807:Y1311C	ENSP00000301807:Y1311C	Y	-	2	0	TRANK1	36850364	0.996000	0.38824	0.998000	0.56505	0.985000	0.73830	1.717000	0.37991	0.940000	0.37473	0.448000	0.29417	TAT	.	.		0.418	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		C	36875360	T	C	36875360	3	2	23	1	0	0	0	0	1	0	0	0	16469	1406	49	2	3207	2	TRANK1	3	36875360	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2828	36875360	161147070	224	2290										
EPM2AIP1	9852	hgsc.bcm.edu	37	chr3	37032816	37032816	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catttcagttgtggcaacccGaaacagggcttggagatgct	12	9	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:37032816G>A	ENST00000322716.5	-	1	1979	c.1753C>T	c.(1753-1755)Cgg>Tgg	p.R585W	MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000539477.1_5'Flank|MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000455445.2_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	585					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						GTGGCAACCCGAAACAGGGCT	0.408																																					p.R585W		Atlas-SNP	.											.	EPM2AIP1	47	.	0			c.C1753T						.						83	82	82					3																	37032816		1864	4103	5967	SO:0001583	missense	9852	exon1			CAACCCGAAACAG	AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.1753C>T	chr3.hg19:g.37032816G>A	ENSP00000406027:p.Arg585Trp	182.0	0.0		166.0	9.0	NM_014805	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	hg19	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023385	0.54683	.	.	ENSG00000178567	ENST00000322716	T	0.22945	1.93	4.66	2.67	0.31697	.	.	.	.	.	T	0.48786	0.1519	M	0.73217	2.22	0.34659	D	0.722517	D	0.89917	1.0	D	0.97110	1.0	T	0.63229	-0.6684	9	0.87932	D	0	4.3078	13.3326	0.60497	0.0:0.0:0.8101:0.1899	.	585	Q7L775	EPMIP_HUMAN	W	585	ENSP00000406027:R585W	ENSP00000406027:R585W	R	-	1	2	EPM2AIP1	37007820	0.267000	0.24122	0.997000	0.53966	0.957000	0.61999	0.503000	0.22610	0.394000	0.25230	0.655000	0.94253	CGG	.	.		0.408	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805		A	37032816	G	A	37032816	3	1	23	1	0	0	0	0	1	0	0	0	5186	1057	37	1	74	1	EPM2AIP1	3	37032816	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	157456	37032816	160989614	225	2291										
ITGA9	3680	hgsc.bcm.edu	37	chr3	37821428	37821428	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaatttcttgcctaacagcAcactgtaactttagtgctct	7	10	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:37821428A>G	ENST00000264741.5	+	25	2959	c.2703A>G	c.(2701-2703)gcA>gcG	p.A901A	AC093415.2_ENST00000438136.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	901					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GCCTAACAGCACACTGTAACT	0.353																																					p.A901A		Atlas-SNP	.											.	ITGA9	98	.	0			c.A2703G						.						124	123	123					3																	37821428		2203	4300	6503	SO:0001819	synonymous_variant	3680	exon25			AACAGCACACTGT	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2703A>G	chr3.hg19:g.37821428A>G		109.0	0.0		78.0	25.0	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	hg19	CCDS2669.1																																																																																			.	.		0.353	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		G	37821428	A	G	37821428	2	3	23	1	0	0	0	0	0	0	0	1	7892	146	6	2		2	ITGA9	3	37821428	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	788612	37821428	160201002	226	2292										
WDR48	57599	hgsc.bcm.edu	37	chr3	39125659	39125659	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtataggcatgtaaagttgAagatctgggcaaagtggatt	13	3	1	2	rs112491258		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:39125659A>T	ENST00000302313.5	+	12	1215	c.1187A>T	c.(1186-1188)gAa>gTa	p.E396V	WDR48_ENST00000396258.3_Missense_Mutation_p.E314V|WDR48_ENST00000544962.1_Missense_Mutation_p.E121V|WDR48_ENST00000418020.1_De_novo_Start_OutOfFrame	NM_020839.2	NP_065890.1	Q8TAF3	WDR48_HUMAN	WD repeat domain 48	396					double-strand break repair via homologous recombination (GO:0000724)|embryonic organ development (GO:0048568)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|positive regulation of epithelial cell proliferation (GO:0050679)|protein deubiquitination (GO:0016579)|regulation of protein monoubiquitination (GO:1902525)|seminiferous tubule development (GO:0072520)|single fertilization (GO:0007338)|skeletal system morphogenesis (GO:0048705)|skin development (GO:0043588)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)				breast(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TGTAAAGTTGAAGATCTGGGC	0.299																																					p.E396V		Atlas-SNP	.											.	WDR48	41	.	0			c.A1187T						.						89	96	93					3																	39125659		2203	4297	6500	SO:0001583	missense	57599	exon12			AAGTTGAAGATCT	AF468833	CCDS33738.1	3p21.33	2014-06-16			ENSG00000114742	ENSG00000114742		"WD repeat domain containing"	30914	protein-coding gene	gene with protein product		612167				10819331, 12196293, 24482476	Standard	NM_020839		Approved	KIAA1449, P80, SPG60	uc003cit.3	Q8TAF3	OTTHUMG00000155972	ENST00000302313.5:c.1187A>T	chr3.hg19:g.39125659A>T	ENSP00000307491:p.Glu396Val	104.0	0.0		104.0	33.0	NM_020839	B4DM86|B4DQI2|B4DY84|Q63HJ2|Q658Y1|Q8N3Z1|Q9NSK8|Q9P279	Missense_Mutation	SNP	ENST00000302313.5	hg19	CCDS33738.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.928055	0.92389	.	.	ENSG00000114742	ENST00000302313;ENST00000544962;ENST00000396258	T;D;T	0.90133	1.01;-2.62;0.72	5.91	5.91	0.95273	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.94974	0.8374	M	0.75447	2.3	0.80722	D	1	D;P;D;D	0.61080	0.989;0.946;0.969;0.975	D;P;P;P	0.72625	0.978;0.754;0.754;0.841	D	0.95251	0.8360	10	0.66056	D	0.02	-1.8365	16.3483	0.83171	1.0:0.0:0.0:0.0	.	121;314;387;396	Q8TAF3-5;Q8TAF3-4;Q8TAF3-3;Q8TAF3	.;.;.;WDR48_HUMAN	V	396;121;314	ENSP00000307491:E396V;ENSP00000445187:E121V;ENSP00000379557:E314V	ENSP00000307491:E396V	E	+	2	0	WDR48	39100663	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.254000	0.74563	0.533000	0.62120	GAA	.	A|0.500;G|0.500		0.299	WDR48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342529.1	NM_020839		T	39125659	A	T	39125659	3	4	23	1	0	0	0	0	1	0	0	0	17316	246	9	4	1233	4	WDR48	3	39125659	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1304231	39125659	158896771	227	2293										
CCR8	1237	hgsc.bcm.edu	37	chr3	39374347	39374347	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctagtgttttaccaagtggcCtctgaagatggtgttctaca	10	8	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:39374347C>A	ENST00000326306.4	+	2	663	c.525C>A	c.(523-525)gcC>gcA	p.A175A	CCR8_ENST00000545843.1_Silent_p.A92A|CCR8_ENST00000414803.1_Missense_Mutation_p.L118I	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	175					cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)			NS(3)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)		ACCAAGTGGCCTCTGAAGATG	0.433																																					p.A175A		Atlas-SNP	.											.	CCR8	34	.	0			c.C525A						.						207	185	192					3																	39374347		2203	4300	6503	SO:0001819	synonymous_variant	1237	exon2			AGTGGCCTCTGAA	D49919	CCDS2684.1	3p22	2012-08-08			ENSG00000179934	ENSG00000179934		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1609	protein-coding gene	gene with protein product		601834		CMKBRL2, CMKBR8		8816377, 8886020	Standard	NM_005201		Approved	CY6, TER1, CKR-L1, GPR-CY6, CDw198	uc010hhr.2	P51685	OTTHUMG00000131290	ENST00000326306.4:c.525C>A	chr3.hg19:g.39374347C>A		86.0	0.0		94.0	24.0	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	Silent	SNP	ENST00000326306.4	hg19	CCDS2684.1	.	.	.	.	.	.	.	.	.	.	C	7.971	0.749096	0.15710	.	.	ENSG00000179934	ENST00000414803	T	0.54279	0.58	4.76	3.8	0.43715	.	.	.	.	.	T	0.54631	0.1870	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59568	-0.7430	6	0.87932	D	0	.	4.2069	0.10493	0.0:0.6097:0.2377:0.1525	.	.	.	.	I	118	ENSP00000390104:L118I	ENSP00000390104:L118I	L	+	1	0	CCR8	39349351	.	.	0.998000	0.56505	0.559000	0.35586	.	.	2.476000	0.83614	0.655000	0.94253	CTC	.	.		0.433	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201		A	39374347	C	A	39374347	2	1	23	1	0	0	0	0	0	0	0	1	2949	668	24	3		3	CCR8	3	39374347	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	248688	39374347	158648083	228	2294										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266137	41266137	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgccactaccacagctccttCtctgagtggtaaaggcaatc	8	13	1	1	rs121913409		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:41266137C>T	ENST00000349496.5	+	3	414	c.134C>T	c.(133-135)tCt>tTt	p.S45F	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45F(384)|p.S45del(53)|p.A5_A80del(53)|p.S45C(19)|p.S45Y(17)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.S45fs*2(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACAGCTCCTTCTCTGAGTGGT	0.498	S45F(HCC15_LUNG)|S45F(LS180_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+1,2	CTNNB1	4904	.	601	Substitution - Missense(421)|Deletion - In frame(152)|Complex - deletion inframe(20)|Unknown(7)|Deletion - Frameshift(1)	soft_tissue(233)|liver(141)|large_intestine(85)|kidney(74)|endometrium(16)|skin(11)|adrenal_gland(9)|stomach(7)|biliary_tract(5)|ovary(4)|lung(3)|central_nervous_system(2)|cervix(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(1)|pituitary(1)|prostate(1)|bone(1)|pancreas(1)	c.C134T						.						84	74	77					3																	41266137		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTCCTTCTCTGAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.134C>T	chr3.hg19:g.41266137C>T	ENSP00000344456:p.Ser45Phe	157.0	0.0		182.0	67.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569754	0.86439	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.68165	0.2971	M	0.65677	2.01	0.80722	D	1	D	0.67145	0.996	D	0.64687	0.928	T	0.68895	-0.5288	10	0.87932	D	0	-13.6823	20.2983	0.98569	0.0:1.0:0.0:0.0	.	45	P35222	CTNB1_HUMAN	F	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38F;ENSP00000385604:S45F;ENSP00000412219:S45F;ENSP00000379486:S45F;ENSP00000344456:S45F;ENSP00000411226:S38F;ENSP00000379488:S45F;ENSP00000409302:S45F;ENSP00000401599:S45F	ENSP00000344456:S45F	S	+	2	0	CTNNB1	41241141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266137	C	T	41266137	3	4	23	1	0	0	0	0	1	0	0	0	4018	913	32	3	140	3	CTNNB1	3	41266137	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1891790	41266137	156756293	229	2295										
FYCO1	79443	hgsc.bcm.edu	37	chr3	46008574	46008574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggccaactccctgttggcctTtctctgctgtgaggacctca	10	14	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:46008574T>C	ENST00000296137.2	-	8	2457	c.2252A>G	c.(2251-2253)aAa>aGa	p.K751R	FYCO1_ENST00000535325.1_Missense_Mutation_p.K751R	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	751					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CTGTTGGCCTTTCTCTGCTGT	0.622																																					p.K751R		Atlas-SNP	.											.,1	FYCO1	115	.	0			c.A2252G						.						92	91	91					3																	46008574		2203	4300	6503	SO:0001583	missense	79443	exon8			TGGCCTTTCTCTG	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.2252A>G	chr3.hg19:g.46008574T>C	ENSP00000296137:p.Lys751Arg	55.0	0.0		39.0	11.0	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	T	1.695	-0.503001	0.04261	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.25749	1.78;1.79	5.66	3.33	0.38152	.	0.329778	0.34959	N	0.003547	T	0.21387	0.0515	L	0.50333	1.59	0.09310	N	0.999996	B;B	0.16166	0.016;0.016	B;B	0.15484	0.013;0.007	T	0.14671	-1.0464	10	0.34782	T	0.22	-4.5521	8.2555	0.31754	0.0:0.154:0.0:0.846	.	751;751	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	R	751	ENSP00000296137:K751R;ENSP00000441178:K751R	ENSP00000296137:K751R	K	-	2	0	FYCO1	45983578	0.868000	0.29978	0.120000	0.21714	0.124000	0.20399	2.758000	0.47565	0.992000	0.38840	0.533000	0.62120	AAA	.	.		0.622	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		C	46008574	T	C	46008574	3	2	23	1	0	0	0	0	1	0	0	0	6133	1841	64	2	2228	2	FYCO1	3	46008574	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	4742437	46008574	152013856	230	2296										
CCR3	1232	hgsc.bcm.edu	37	chr3	46307586	46307586	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agaggttccggaagtacctgCgccacttcttccacaggcac	10	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:46307586C>T	ENST00000357422.2	+	4	1480	c.937C>T	c.(937-939)Cgc>Tgc	p.R313C	CCR3_ENST00000545097.1_Missense_Mutation_p.R334C|CCR3_ENST00000541018.1_Missense_Mutation_p.R313C|CCR3_ENST00000395940.2_Missense_Mutation_p.R313C|CCR3_ENST00000395942.2_Missense_Mutation_p.R313C			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	313					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		GAAGTACCTGCGCCACTTCTT	0.552																																					p.R334C		Atlas-SNP	.											.	CCR3	52	.	0			c.C1000T						.						106	88	94					3																	46307586		2203	4300	6503	SO:0001583	missense	1232	exon3			TACCTGCGCCACT	AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.937C>T	chr3.hg19:g.46307586C>T	ENSP00000350003:p.Arg313Cys	58.0	0.0		77.0	37.0	NM_178328	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Missense_Mutation	SNP	ENST00000357422.2	hg19	CCDS2738.1	.	.	.	.	.	.	.	.	.	.	C	8.150	0.787200	0.16189	.	.	ENSG00000183625	ENST00000357422;ENST00000545097;ENST00000541018;ENST00000395940;ENST00000395942	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.42	-0.218	0.13142	.	0.811875	0.10866	N	0.625524	T	0.26846	0.0657	L	0.31371	0.925	0.09310	N	0.999997	B;B	0.20550	0.046;0.027	B;B	0.20577	0.03;0.009	T	0.22103	-1.0226	10	0.30854	T	0.27	.	6.2461	0.20818	0.1228:0.4921:0.0:0.3851	.	334;313	F5GWL6;P51677	.;CCR3_HUMAN	C	313;334;313;313;313	ENSP00000350003:R313C;ENSP00000441600:R334C;ENSP00000440097:R313C;ENSP00000379271:R313C;ENSP00000379273:R313C	ENSP00000350003:R313C	R	+	1	0	CCR3	46282590	0.000000	0.05858	0.439000	0.26833	0.641000	0.38312	-0.349000	0.07731	0.016000	0.14998	-0.254000	0.11334	CGC	.	.		0.552	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2			T	46307586	C	T	46307586	3	4	23	1	0	0	0	0	1	0	0	0	2944	768	27	1	1006	1	CCR3	3	46307586	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	299012	46307586	151714844	231	2297										
TDGF1	6997	hgsc.bcm.edu	37	chr3	46619474	46619474	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaagctatggactgcaggaaGatggcccgcttctcttacag	11	10	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:46619474G>T	ENST00000296145.5	+	1	748	c.15G>T	c.(13-15)aaG>aaT	p.K5N	LRRC2_ENST00000296144.3_Intron|TDGF1_ENST00000542931.1_Intron	NM_003212.3	NP_003203.1	P13385	TDGF1_HUMAN	teratocarcinoma-derived growth factor 1	5					activation of MAPK activity (GO:0000187)|anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle cell differentiation (GO:0055007)|cell differentiation (GO:0030154)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-6 (GO:0071354)|cellular response to tumor necrosis factor (GO:0071356)|embryo development (GO:0009790)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of signal transduction (GO:0009966)|vasculogenesis (GO:0001570)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	growth factor activity (GO:0008083)|receptor binding (GO:0005102)			cervix(2)|endometrium(1)|kidney(1)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0173)|Kidney(197;0.0204)		ACTGCAGGAAGATGGCCCGCT	0.408																																					p.K5N		Atlas-SNP	.											.	TDGF1	17	.	0			c.G15T						.						205	197	200					3																	46619474		2203	4300	6503	SO:0001583	missense	6997	exon1			CAGGAAGATGGCC	M96955	CCDS2742.1, CCDS54575.1	3p21.31	2012-10-03			ENSG00000241186	ENSG00000241186			11701	protein-coding gene	gene with protein product		187395				1882841, 10393436	Standard	NM_003212		Approved	CRIPTO, CR, Cripto-1	uc021wxd.1	P13385	OTTHUMG00000133482	ENST00000296145.5:c.15G>T	chr3.hg19:g.46619474G>T	ENSP00000296145:p.Lys5Asn	69.0	0.0		66.0	25.0	NM_003212	Q8TCC1	Missense_Mutation	SNP	ENST00000296145.5	hg19	CCDS2742.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100438	0.56183	.	.	ENSG00000241186	ENST00000296145	T	0.67345	-0.26	4.16	2.31	0.28768	.	0.650011	0.13736	N	0.366333	T	0.53206	0.1782	L	0.44542	1.39	0.54753	D	0.999982	P	0.44877	0.845	B	0.38428	0.273	T	0.42666	-0.9438	10	0.18276	T	0.48	.	10.5559	0.45117	0.0:0.3817:0.6183:0.0	.	5	P13385	TDGF1_HUMAN	N	5	ENSP00000296145:K5N	ENSP00000296145:K5N	K	+	3	2	AC104304.1	46594478	0.984000	0.35163	0.631000	0.29282	0.509000	0.34042	0.957000	0.29215	0.675000	0.31264	0.655000	0.94253	AAG	.	.		0.408	TDGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257378.2	NM_003212		T	46619474	G	T	46619474	3	4	23	1	0	0	0	0	1	0	0	0	15741	933	33	3	17	3	TDGF1	3	46619474	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	311888	46619474	151402956	232	2298										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47047032	47047032	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcggcagcctggcaggcacGcctggagagccctgccgatg	17	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:47047032G>T	ENST00000450053.3	+	41	6793	c.6614G>T	c.(6613-6615)cGc>cTc	p.R2205L	NBEAL2_ENST00000383740.2_Missense_Mutation_p.R484L|NBEAL2_ENST00000292309.5_Missense_Mutation_p.R2021L	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2205	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TGGCAGGCACGCCTGGAGAGC	0.617																																					p.R2205L		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G6614T						.						17	19	18					3																	47047032		1932	4137	6069	SO:0001583	missense	23218	exon41			AGGCACGCCTGGA	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.6614G>T	chr3.hg19:g.47047032G>T	ENSP00000415034:p.Arg2205Leu	150.0	0.0		141.0	7.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.453|8.453	0.853450|0.853450	0.17106|0.17106	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000292309;ENST00000383740;ENST00000450053;ENST00000445550;ENST00000423436	.|T;T;T;T	.|0.78816	.|-1.21;-1.21;-1.21;-1.21	4.9|4.9	4.9|4.9	0.64082|0.64082	.|BEACH domain (4);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.43831|0.43831	0.1265|0.1265	N|N	0.00608|0.00608	-1.33|-1.33	0.58432|0.58432	D|D	0.999999|0.999999	.|P;B	.|0.40211	.|0.707;0.001	.|B;B	.|0.35550	.|0.205;0.013	T|T	0.63839|0.63839	-0.6546|-0.6546	5|10	.|0.02654	.|T	.|1	.|.	16.8148|16.8148	0.85730|0.85730	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2021;2205	.|Q6ZNJ1-2;Q6ZNJ1	.|.;NBEL2_HUMAN	S|L	1493|2021;484;2205;148;32	.|ENSP00000292309:R2021L;ENSP00000373246:R484L;ENSP00000415034:R2205L;ENSP00000415063:R32L	.|ENSP00000292309:R2021L	A|R	+|+	1|2	0|0	NBEAL2|NBEAL2	47022036|47022036	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.929000|0.929000	0.56500|0.56500	4.466000|4.466000	0.60148|0.60148	2.544000|2.544000	0.85801|0.85801	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.		0.617	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47047032	G	T	47047032	3	4	23	1	0	0	0	0	1	0	0	0	10198	1087	38	1	6776	1	NBEAL2	3	47047032	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	427558	47047032	150975398	233	2299										
PTPN23	25930	hgsc.bcm.edu	37	chr3	47451532	47451532	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgaggagctgcgcagcctCccccctgacatggtggctgg					rs77776224	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:47451532delC	ENST00000265562.4	+	20	2321	c.2244delC	c.(2242-2244)ctcfs	p.L748fs	PTPN23_ENST00000431726.1_Frame_Shift_Del_p.L622fs	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	748	Pro-rich.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGCGCAGCCTCCCCCCTGACA	0.701																																					p.L748fs		Atlas-Indel,Pindel	.											.	PTPN23	85	.	0			c.2243delT						.						35	34	35					3																	47451532		2203	4296	6499	SO:0001589	frameshift_variant	25930	exon20			.	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.2244delC	chr3.hg19:g.47451532delC	ENSP00000265562:p.Leu748fs	260.0	0.0		245.0	23.0	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Frame_Shift_Del	DEL	ENST00000265562.4	hg19	CCDS2754.1																																																																																			.	.		0.701	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		-	47451532	C	-	47451532	7	5	23	1	0	1	0	1	0	0	0	0	12803	842	30	0	2322	0	PTPN23	3	47451532	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	404500	47451532	150570898	234	2300										
SCAP	22937	hgsc.bcm.edu	37	chr3	47455478	47455481	+	Frame_Shift_Del	DEL	CTGT	CTGT	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actgttcttccccaggtagaCtgtctgtaacaggtccccgt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	CTGT	CTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:47455478_47455481delCTGT	ENST00000265565.5	-	23	4115_4118	c.3703_3706delACAG	c.(3703-3708)acagtcfs	p.TV1235fs	SCAP_ENST00000441517.2_Frame_Shift_Del_p.TV979fs|SCAP_ENST00000545718.1_Frame_Shift_Del_p.TV842fs	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	1235	Interaction with SREBF2. {ECO:0000250}.				aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		CCCAGGTAGACTGTCTGTAACAGG	0.583																																					p.1235_1236del	Pancreas(149;978 1908 29304 37806 46700)	Atlas-Indel,Pindel	.											.	SCAP	88	.	0			c.3704_3707del						.																																			SO:0001589	frameshift_variant	22937	exon23			.	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.3703_3706delACAG	chr3.hg19:g.47455482_47455485delCTGT	ENSP00000265565:p.Thr1235fs	77.0	0.0		90.0	36.0	NM_012235	Q8N2E0|Q8WUA1	Frame_Shift_Del	DEL	ENST00000265565.5	hg19	CCDS2755.2																																																																																			.	.		0.583	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		-	47455481	CTGT	-	47455478	7	5	23	1	0	1	0	1	0	0	0	0	13892	565	20	0	137	0	SCAP	3	47455478	Frame_Shift_Del	DEL	CTGT	TCGA-4R-AA8I-01A-11D-A382-10	3946	47455478	150566952	235	2301										
SCAP	22937	hgsc.bcm.edu	37	chr3	47461047	47461048	+	Frame_Shift_Ins	INS	-	-	G													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaggcagggtccgggtggctINSggggggcagcatgccactag							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:47461047_47461048insG	ENST00000265565.5	-	13	2122_2123	c.1710_1711insC	c.(1708-1713)cccagcfs	p.S571fs	SCAP_ENST00000465628.1_5'Flank|SCAP_ENST00000441517.2_Frame_Shift_Ins_p.S316fs|SCAP_ENST00000545718.1_Frame_Shift_Ins_p.S179fs	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	571					aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		TCCGGGTGGCTGGGGGGCAGCA	0.658																																					p.S571fs	Pancreas(149;978 1908 29304 37806 46700)	Atlas-Indel,Pindel	.											.	SCAP	88	.	0			c.1711_1712insC						.																																			SO:0001589	frameshift_variant	22937	exon13			.	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.1711dupC	chr3.hg19:g.47461053_47461053dupG	ENSP00000265565:p.Ser571fs	168.0	0.0		155.0	58.0	NM_012235	Q8N2E0|Q8WUA1	Frame_Shift_Ins	INS	ENST00000265565.5	hg19	CCDS2755.2																																																																																			.	.		0.658	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		G	47461048	-	G	47461047	7	5	23	1	0	1	1	0	0	0	0	0	13892	1580	55	0	2172	0	SCAP	3	47461047	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	5569	47461047	150561383	236	2302										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48605066	48605066	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctggcccggcacaccaggctCcccctggagaaaaaaagaca							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:48605066delC	ENST00000328333.8	-	108	8094	c.7987delG	c.(7987-7989)gagfs	p.E2663fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.E2631fs|COL7A1_ENST00000470076.1_5'Flank	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2663	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACACCAGGCTCCCCCTGGAGA	0.627																																					p.E2663fs		Pindel	.											.	COL7A1	320	.	0			c.7988delA						.						62	75	71					3																	48605066		2202	4300	6502	SO:0001589	frameshift_variant	1294	exon108			.	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.7987delG	chr3.hg19:g.48605066delC	ENSP00000332371:p.Glu2663fs	188.0	0.0		205.0	56.0	NM_000094	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.627	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		-	48605066	C	-	48605066	7	5	23	1	0	1	0	1	0	0	0	0	3706	864	30	0	891	0	COL7A1	3	48605066	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	1144019	48605066	149417364	237	2303										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48689914	48689914	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggagcctcctctgcactgcCggggggcaggcctcccacgt	14	16	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:48689914C>T	ENST00000164024.4	-	11	5987	c.5707G>A	c.(5707-5709)Ggc>Agc	p.G1903S	CELSR3_ENST00000544264.1_Missense_Mutation_p.G1903S	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1903	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TCTGCACTGCCGGGGGGCAGG	0.627																																					p.G1903S		Atlas-SNP	.											.,1	CELSR3	237	.	0			c.G5707A						.						56	56	56					3																	48689914		2203	4300	6503	SO:0001583	missense	1951	exon11			CACTGCCGGGGGG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.5707G>A	chr3.hg19:g.48689914C>T	ENSP00000164024:p.Gly1903Ser	109.0	0.0		93.0	42.0	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	C	4.631	0.117388	0.08881	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.79352	-1.26;-1.26	3.71	-3.02	0.05446	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.48750	0.1517	N	0.03608	-0.345	0.09310	N	1	B;B	0.12013	0.0;0.005	B;B	0.15870	0.001;0.014	T	0.40440	-0.9563	9	0.09084	T	0.74	.	9.3689	0.38241	0.0:0.5703:0.0:0.4297	.	1903;1973	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	S	1903	ENSP00000164024:G1903S;ENSP00000445694:G1903S	ENSP00000164024:G1903S	G	-	1	0	CELSR3	48664918	0.004000	0.15560	0.147000	0.22382	0.315000	0.28087	-0.320000	0.08028	-0.589000	0.05874	-0.367000	0.07326	GGC	.	.		0.627	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		T	48689914	C	T	48689914	3	4	23	1	0	0	0	0	1	0	0	0	3225	652	23	1	4331	1	CELSR3	3	48689914	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	84848	48689914	149332516	238	2304										
RNF123	63891	hgsc.bcm.edu	37	chr3	49751388	49751388	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctggcgccctatgagcagcgGccctgggcccagaccaactg	13	16	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:49751388G>A	ENST00000327697.6	+	30	3027	c.2883G>A	c.(2881-2883)cgG>cgA	p.R961R	RNF123_ENST00000433785.1_Silent_p.R73R	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	961					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		ATGAGCAGCGGCCCTGGGCCC	0.667																																					p.R961R		Atlas-SNP	.											.	RNF123	100	.	0			c.G2883A						.						63	67	66					3																	49751388		2203	4300	6503	SO:0001819	synonymous_variant	63891	exon30			GCAGCGGCCCTGG	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.2883G>A	chr3.hg19:g.49751388G>A		120.0	0.0		113.0	47.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	hg19	CCDS33758.1																																																																																			.	.		0.667	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		A	49751388	G	A	49751388	2	1	23	1	0	0	0	0	0	0	0	1	13448	1190	42	3		3	RNF123	3	49751388	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1061474	49751388	148271042	239	2305										
RBM5	10181	hgsc.bcm.edu	37	chr3	50145541	50145541	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcagtgttgactacagttaTctgcaaccaggtcaagatgg	12	8	2	2	rs148691467		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:50145541T>A	ENST00000347869.3	+	13	1255	c.1080T>A	c.(1078-1080)taT>taA	p.Y360*	RBM5_ENST00000441812.2_3'UTR	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	360	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACTACAGTTATCTGCAACCAG	0.408																																					p.Y360X		Atlas-SNP	.											.	RBM5	76	.	0			c.T1080A						.						212	181	192					3																	50145541		2203	4300	6503	SO:0001587	stop_gained	10181	exon13			CAGTTATCTGCAA	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"G patch domain containing", "RNA binding motif (RRM) containing"	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.1080T>A	chr3.hg19:g.50145541T>A	ENSP00000343054:p.Tyr360*	120.0	0.0		111.0	30.0	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Nonsense_Mutation	SNP	ENST00000347869.3	hg19	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	T	35	5.538428	0.96460	.	.	ENSG00000003756	ENST00000347869;ENST00000543047;ENST00000544851	.	.	.	5.88	-1.3	0.09259	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.5536	12.0826	0.53680	0.0:0.4905:0.0:0.5095	.	.	.	.	X	360;359;50	.	ENSP00000343054:Y360X	Y	+	3	2	RBM5	50120545	0.562000	0.26586	0.965000	0.40720	0.927000	0.56198	-0.387000	0.07361	-0.328000	0.08539	-0.366000	0.07423	TAT	.	T|1.000;C|0.000		0.408	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		A	50145541	T	A	50145541	4	1	23	1	0	0	0	0	0	1	0	0	13158	1442	50	4	1126	4	RBM5	3	50145541	Nonsense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	394153	50145541	147876889	240	2306										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52382985	52382985	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agccactggtggaagagctaCgggccaccattgccagtgcc	13	13	0	1	rs371359758		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:52382985C>T	ENST00000420323.2	+	13	2449	c.2188C>T	c.(2188-2190)Cgg>Tgg	p.R730W		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	730	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R730W(2)		cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGAAGAGCTACGGGCCACCAT	0.582																																					p.R730W		Atlas-SNP	.											DNAH1_ENST00000420323,NS,carcinoma,0,2	DNAH1	534	.	2	Substitution - Missense(2)	endometrium(2)	c.C2188T						.	C	TRP/ARG	1,4323		0,1,2161	112	119	117		2188	2.4	0.4	3		117	0,8534		0,0,4267	no	missense	DNAH1	NM_015512.4	101	0,1,6428	TT,TC,CC		0.0,0.0231,0.0078	possibly-damaging	730/4266	52382985	1,12857	2162	4267	6429	SO:0001583	missense	25981	exon13			GAGCTACGGGCCA	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.2188C>T	chr3.hg19:g.52382985C>T	ENSP00000401514:p.Arg730Trp	57.0	0.0		39.0	15.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.799648	0.50208	2.31E-4	0.0	ENSG00000114841	ENST00000420323	T	0.25579	1.79	5.24	2.39	0.29439	.	0.000000	0.47852	D	0.000220	T	0.50411	0.1614	M	0.87180	2.865	0.49915	D	0.999837	P;D	0.63880	0.871;0.993	B;P	0.60789	0.353;0.879	T	0.55211	-0.8176	10	0.41790	T	0.15	.	14.2149	0.65786	0.3916:0.6084:0.0:0.0	.	730;730	C9JXH6;Q9P2D7-3	.;.	W	730	ENSP00000401514:R730W	ENSP00000401514:R730W	R	+	1	2	DNAH1	52358025	0.994000	0.37717	0.358000	0.25811	0.142000	0.21351	1.415000	0.34748	0.188000	0.20168	0.655000	0.94253	CGG	.	.		0.582	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		T	52382985	C	T	52382985	3	4	23	1	0	0	0	0	1	0	0	0	4599	527	19	1	2234	1	DNAH1	3	52382985	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2237444	52382985	145639445	241	2307										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52428572	52428572	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcagaccgggcttggcgagAcatcctagcactctcgaacc	11	14	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:52428572A>T	ENST00000420323.2	+	67	10979	c.10718A>T	c.(10717-10719)gAc>gTc	p.D3573V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3638					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GCTTGGCGAGACATCCTAGCA	0.582																																					p.D3573V		Atlas-SNP	.											.	DNAH1	534	.	0			c.A10718T						.						100	109	106					3																	52428572		2049	4202	6251	SO:0001583	missense	25981	exon67			GGCGAGACATCCT	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.10718A>T	chr3.hg19:g.52428572A>T	ENSP00000401514:p.Asp3573Val	122.0	0.0		116.0	55.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.649719	0.87958	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.08720	3.06	5.15	5.15	0.70609	.	0.000000	0.64402	D	0.000001	T	0.31451	0.0797	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	0.985;1.0	P;D	0.87578	0.9;0.998	T	0.08827	-1.0703	10	0.87932	D	0	.	15.0069	0.71519	1.0:0.0:0.0:0.0	.	3573;3638	C9JXH6;Q9P2D7-2	.;.	V	3573;326	ENSP00000401514:D3573V	ENSP00000273600:D326V	D	+	2	0	DNAH1	52403612	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.305000	0.89960	1.957000	0.56846	0.533000	0.62120	GAC	.	.		0.582	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		T	52428572	A	T	52428572	3	4	23	1	0	0	0	0	1	0	0	0	4599	275	10	4	10980	4	DNAH1	3	52428572	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	45587	52428572	145593858	242	2308										
ITIH3	3699	hgsc.bcm.edu	37	chr3	52840398	52840398	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagccccaggcacagtgctgCgccttattcaggatgcagtc	11	13	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:52840398C>T	ENST00000449956.2	+	18	2038	c.2032C>T	c.(2032-2034)Cgc>Tgc	p.R678C	ITIH3_ENST00000416872.2_Intron	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	678					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CACAGTGCTGCGCCTTATTCA	0.612																																					p.R678C		Atlas-SNP	.											ITIH3_ENST00000449956,NS,carcinoma,-1,1	ITIH3	132	.	0			c.C2032T						.						45	45	45					3																	52840398		1966	4141	6107	SO:0001583	missense	3699	exon18			GTGCTGCGCCTTA		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.2032C>T	chr3.hg19:g.52840398C>T	ENSP00000415769:p.Arg678Cys	48.0	1.0		65.0	27.0	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	hg19	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	C	15.08	2.727264	0.48833	.	.	ENSG00000162267	ENST00000273291;ENST00000449956	T	0.01745	4.66	5.38	2.05	0.26809	.	0.337826	0.33496	N	0.004854	T	0.04907	0.0132	M	0.74881	2.28	0.40856	D	0.983796	D	0.54397	0.966	P	0.48677	0.586	T	0.38972	-0.9636	10	0.66056	D	0.02	-10.1344	12.7828	0.57487	0.6466:0.3534:0.0:0.0	.	678	Q06033	ITIH3_HUMAN	C	673;678	ENSP00000415769:R678C	ENSP00000273291:R673C	R	+	1	0	ITIH3	52815438	0.797000	0.28877	1.000000	0.80357	0.093000	0.18481	0.444000	0.21661	0.724000	0.32296	0.561000	0.74099	CGC	.	.		0.612	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		T	52840398	C	T	52840398	3	4	23	1	0	0	0	0	1	0	0	0	7914	768	27	1	2102	1	ITIH3	3	52840398	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	411826	52840398	145182032	243	2309										
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	54354484	54354484	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tacagaaatacaaagagtatGagaaagacgttgccatagaa							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:54354484delG	ENST00000474759.1	+	3	268	c.220delG	c.(220-222)gagfs	p.E74fs	CACNA2D3_ENST00000490478.1_5'UTR|CACNA2D3_ENST00000415676.2_Frame_Shift_Del_p.E74fs|CACNA2D3_ENST00000288197.5_Frame_Shift_Del_p.E74fs	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	74						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CAAAGAGTATGAGAAAGACGT	0.438																																					p.Y73X		Atlas-Indel,Pindel	.											.	CACNA2D3	159	.	0			c.219delT						.						62	57	58					3																	54354484		1913	4115	6028	SO:0001589	frameshift_variant	55799	exon3			.	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.220delG	chr3.hg19:g.54354484delG	ENSP00000419101:p.Glu74fs	84.0	0.0		85.0	38.0	NM_018398	B2RPL6|Q9NY16|Q9NY18	Frame_Shift_Del	DEL	ENST00000474759.1	hg19	CCDS54598.1																																																																																			.	.		0.438	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			-	54354484	G	-	54354484	7	5	23	1	0	1	0	1	0	0	0	0	2552	1291	45	0	230	0	CACNA2D3	3	54354484	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	1514086	54354484	143667946	244	2310										
LRTM1	57408	hgsc.bcm.edu	37	chr3	54958759	54958759	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgggcatggattccaggagcGctcgatcaagctgctgaagc	14	10	1	1	rs372086680		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:54958759G>A	ENST00000273286.5	-	2	653	c.491C>T	c.(490-492)gCg>gTg	p.A164V	CACNA2D3_ENST00000490478.1_Intron|LRTM1_ENST00000493075.1_Missense_Mutation_p.A88V|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000474759.1_Intron|CACNA2D3_ENST00000288197.5_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	164						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		TTCCAGGAGCGCTCGATCAAG	0.483																																					p.A164V		Atlas-SNP	.											.	LRTM1	52	.	0			c.C491T						.						98	99	99					3																	54958759		2203	4300	6503	SO:0001583	missense	57408	exon2			AGGAGCGCTCGAT	AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.491C>T	chr3.hg19:g.54958759G>A	ENSP00000273286:p.Ala164Val	136.0	0.0		100.0	46.0	NM_020678	Q8IUU2	Missense_Mutation	SNP	ENST00000273286.5	hg19	CCDS2876.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.645678	0.00792	.	.	ENSG00000144771	ENST00000273286;ENST00000493075	T;D	0.90133	4.29;-2.62	5.95	-3.18	0.05186	.	1.058120	0.07165	N	0.851454	T	0.78091	0.4229	N	0.20807	0.61	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.60900	-0.7171	10	0.29301	T	0.29	.	0.3837	0.00399	0.3326:0.1849:0.1341:0.3483	.	164	Q9HBL6	LRTM1_HUMAN	V	164;88	ENSP00000273286:A164V;ENSP00000419772:A88V	ENSP00000273286:A164V	A	-	2	0	LRTM1	54933799	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.609000	0.24238	-0.737000	0.04824	0.650000	0.86243	GCG	.	.		0.483	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678		A	54958759	G	A	54958759	3	1	23	1	0	0	0	0	1	0	0	0	9053	1087	38	1	554	1	LRTM1	3	54958759	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	604275	54958759	143063671	245	2311										
WNT5A	7474	hgsc.bcm.edu	37	chr3	55508545	55508545	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgcggcaggtccttggggcgCgcggcgcggctgcagccgca	19	15	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:55508545C>T	ENST00000474267.1	-	5	1025	c.504G>A	c.(502-504)gcG>gcA	p.A168A	WNT5A_ENST00000497027.1_Silent_p.A153A|WNT5A_ENST00000264634.4_Silent_p.A168A			P41221	WNT5A_HUMAN	wingless-type MMTV integration site family, member 5A	168					activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|ameboidal cell migration (GO:0001667)|anterior/posterior axis specification, embryo (GO:0008595)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular protein localization (GO:0034613)|cellular response to calcium ion (GO:0071277)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cervix development (GO:0060067)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|dopaminergic neuron differentiation (GO:0071542)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system development (GO:0048706)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|epithelial to mesenchymal transition (GO:0001837)|establishment of planar polarity (GO:0001736)|face development (GO:0060324)|genitalia development (GO:0048806)|heart looping (GO:0001947)|hematopoietic stem cell proliferation (GO:0071425)|hindgut morphogenesis (GO:0007442)|hypophysis morphogenesis (GO:0048850)|keratinocyte differentiation (GO:0030216)|lateral sprouting involved in mammary gland duct morphogenesis (GO:0060599)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|male gonad development (GO:0008584)|mammary gland branching involved in thelarche (GO:0060744)|mesenchymal-epithelial cell signaling (GO:0060638)|midgut development (GO:0007494)|negative chemotaxis (GO:0050919)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of mesenchymal cell proliferation (GO:0072201)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of synapse assembly (GO:0051964)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|olfactory bulb interneuron development (GO:0021891)|optic cup formation involved in camera-type eye development (GO:0003408)|palate development (GO:0060021)|planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:0061350)|planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:0061349)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar cell polarity pathway involved in outflow tract morphogenesis (GO:0061347)|planar cell polarity pathway involved in pericardium morphogenesis (GO:0061354)|planar cell polarity pathway involved in ventricular septum morphogenesis (GO:0061348)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of meiosis (GO:0045836)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ossification (GO:0045778)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of response to cytokine stimulus (GO:0060760)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|protein phosphorylation (GO:0006468)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|response to organic substance (GO:0010033)|somitogenesis (GO:0001756)|type B pancreatic cell development (GO:0003323)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vagina development (GO:0060068)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|wound healing (GO:0042060)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor tyrosine kinase-like orphan receptor binding (GO:0005115)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(1)|large_intestine(4)|lung(3)|prostate(2)|urinary_tract(1)	13				KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)		CCTTGGGGCGCGCGGCGCGGC	0.716																																					p.A168A		Atlas-SNP	.											.	WNT5A	43	.	0			c.G504A						.						4	6	6					3																	55508545		1752	3806	5558	SO:0001819	synonymous_variant	7474	exon4			GGGGCGCGCGGCG	L20861	CCDS46850.1, CCDS58835.1	3p21-p14	2013-02-28			ENSG00000114251	ENSG00000114251		"Wingless-type MMTV integration sites", "Endogenous ligands"	12784	protein-coding gene	gene with protein product	"WNT-5A protein"	164975				8288227	Standard	NM_001256105		Approved	hWNT5A	uc010hmw.4	P41221	OTTHUMG00000158361	ENST00000474267.1:c.504G>A	chr3.hg19:g.55508545C>T		56.0	0.0		78.0	28.0	NM_003392	A8K4A4|Q6P278	Silent	SNP	ENST00000474267.1	hg19	CCDS46850.1																																																																																			.	.		0.716	WNT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350793.3	NM_003392		T	55508545	C	T	55508545	2	4	23	1	0	0	0	0	0	0	0	1	17406	755	27	1		1	WNT5A	3	55508545	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	549786	55508545	142513885	246	2312										
LRIG1	26018	hgsc.bcm.edu	37	chr3	66449417	66449417	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgctccaggccttccagcccCgagaatgctctcttagccac	8	17	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:66449417C>T	ENST00000273261.3	-	10	1733	c.1209G>A	c.(1207-1209)tcG>tcA	p.S403S	LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Silent_p.S427S	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	403					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		CTTCCAGCCCCGAGAATGCTC	0.522																																					p.S403S		Atlas-SNP	.											.	LRIG1	138	.	0			c.G1209A						.						69	59	62					3																	66449417		2203	4300	6503	SO:0001819	synonymous_variant	26018	exon10			CAGCCCCGAGAAT	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1209G>A	chr3.hg19:g.66449417C>T		96.0	0.0		70.0	22.0	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	hg19	CCDS33783.1																																																																																			.	.		0.522	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		T	66449417	C	T	66449417	2	4	23	1	0	0	0	0	0	0	0	1	8953	639	23	1		1	LRIG1	3	66449417	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	10940872	66449417	131573013	247	2313										
CADM2	253559	hgsc.bcm.edu	37	chr3	85961535	85961536	+	Frame_Shift_Ins	INS	-	-	A													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttttcagatgtaaaatatttINSaaaagaagaggatgcaaatc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:85961535_85961536insA	ENST00000407528.2	+	5	577_578	c.515_516insA	c.(514-519)ttaaaafs	p.LK172fs	CADM2_ENST00000383699.3_Frame_Shift_Ins_p.LK181fs|CADM2_ENST00000405615.2_Frame_Shift_Ins_p.LK174fs	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	172	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		GTAAAATATTTAAAAGAAGAGG	0.386																																					p.L181fs		Atlas-Indel,Pindel	.											.	CADM2	195	.	0			c.542_543insA						.																																			SO:0001589	frameshift_variant	253559	exon6			.	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.519dupA	chr3.hg19:g.85961539_85961539dupA	ENSP00000384575:p.Leu172fs	389.0	0.0		397.0	145.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Frame_Shift_Ins	INS	ENST00000407528.2	hg19	CCDS54614.1																																																																																			.	.		0.386	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		A	85961536	-	A	85961535	7	5	23	1	0	1	1	0	0	0	0	0	2569	1764	61	0	604	0	CADM2	3	85961535	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	19512118	85961535	112060895	248	2314										
CADM2	253559	hgsc.bcm.edu	37	chr3	85961549	85961549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aatatttaaaagaagaggatGcaaatcgcaagacattcact	7	6	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:85961549G>A	ENST00000407528.2	+	5	591	c.529G>A	c.(529-531)Gca>Aca	p.A177T	CADM2_ENST00000383699.3_Missense_Mutation_p.A186T|CADM2_ENST00000405615.2_Missense_Mutation_p.A179T	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	177	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		AGAAGAGGATGCAAATCGCAA	0.383																																					p.A186T		Atlas-SNP	.											.	CADM2	195	.	0			c.G556A						.						69	57	61					3																	85961549		2203	4300	6503	SO:0001583	missense	253559	exon6			GAGGATGCAAATC	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.529G>A	chr3.hg19:g.85961549G>A	ENSP00000384575:p.Ala177Thr	465.0	1.0		464.0	176.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.519087	0.64634	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.75704	-0.96;-0.96;-0.96	5.6	5.6	0.85130	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.098719	0.64402	D	0.000001	T	0.68769	0.3037	L	0.27053	0.805	0.58432	D	0.999993	P;P;P	0.50528	0.581;0.702;0.936	B;B;P	0.51945	0.287;0.321;0.685	T	0.63175	-0.6696	10	0.12766	T	0.61	.	12.8969	0.58104	0.0743:0.0:0.9257:0.0	.	179;186;177	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	T	186;177;179	ENSP00000373200:A186T;ENSP00000384575:A177T;ENSP00000384193:A179T	ENSP00000373200:A186T	A	+	1	0	CADM2	86044239	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	5.309000	0.65774	2.640000	0.89533	0.591000	0.81541	GCA	.	.		0.383	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		A	85961549	G	A	85961549	3	1	23	1	0	0	0	0	1	0	0	0	2569	1319	46	3	618	3	CADM2	3	85961549	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	14	85961549	112060881	249	2315										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89462400	89462400	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccaccaacatatccattgaTaaagttgttggagcaggtaa	9	8	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:89462400T>A	ENST00000336596.2	+	10	2097	c.1872T>A	c.(1870-1872)gaT>gaA	p.D624E	EPHA3_ENST00000494014.1_Missense_Mutation_p.D624E	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	624	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TATCCATTGATAAAGTTGTTG	0.423										TSP Lung(6;0.00050)																											p.D624E		Atlas-SNP	.											.	EPHA3	501	.	0			c.T1872A						.						167	147	154					3																	89462400		2203	4299	6502	SO:0001583	missense	2042	exon10			CATTGATAAAGTT	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1872T>A	chr3.hg19:g.89462400T>A	ENSP00000337451:p.Asp624Glu	164.0	0.0		160.0	60.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	T	3.342	-0.134471	0.06711	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.61510	0.1;0.1	5.95	2.59	0.31030	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.52677	0.1749	N	0.11927	0.2	0.54753	D	0.999986	P	0.46952	0.887	D	0.65773	0.938	T	0.43734	-0.9373	9	.	.	.	.	8.3296	0.32178	0.0:0.4283:0.0:0.5717	.	624	P29320	EPHA3_HUMAN	E	624	ENSP00000337451:D624E;ENSP00000419190:D624E	.	D	+	3	2	EPHA3	89545090	0.986000	0.35501	1.000000	0.80357	0.991000	0.79684	0.182000	0.16900	0.176000	0.19873	-0.417000	0.06048	GAT	.	.		0.423	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		A	89462400	T	A	89462400	3	1	23	1	0	0	0	0	1	0	0	0	5170	1403	49	4	1936	4	EPHA3	3	89462400	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3500851	89462400	108560030	250	2316										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89499362	89499363	+	Frame_Shift_Ins	INS	-	-	C													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atgagggctatcgactgccaINSccccccatggactgcccagc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:89499362_89499363insC	ENST00000336596.2	+	15	2757_2758	c.2532_2533insC	c.(2533-2535)cccfs	p.P845fs	EPHA3_ENST00000494014.1_Frame_Shift_Ins_p.P845fs	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	845	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		ATCGACTGCCACCCCCCATGGA	0.465										TSP Lung(6;0.00050)																											p.P844fs		Atlas-Indel,Pindel	.											.	EPHA3	501	.	0			c.2532_2533insC						.																																			SO:0001589	frameshift_variant	2042	exon15			.	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2538dupC	chr3.hg19:g.89499368_89499368dupC	ENSP00000337451:p.Pro845fs	226.0	0.0		272.0	112.0	NM_005233	Q9H2V3|Q9H2V4	Frame_Shift_Ins	INS	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.		0.465	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		C	89499363	-	C	89499362	7	5	23	1	0	1	1	0	0	0	0	0	5170	146	6	0	2616	0	EPHA3	3	89499362	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	36962	89499362	108523068	251	2317										
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101383437	101383437	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtttgtgcattataagggcgTatcgtctctgaaaaaccatt	9	7	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:101383437T>C	ENST00000312938.4	-	5	2325	c.1745A>G	c.(1744-1746)tAc>tGc	p.Y582C	Y_RNA_ENST00000364251.1_RNA	NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	582					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TATAAGGGCGTATCGTCTCTG	0.353																																					p.Y582C		Atlas-SNP	.											.	ZBTB11	77	.	0			c.A1745G						.						248	234	239					3																	101383437		2202	4300	6502	SO:0001583	missense	27107	exon5			AGGGCGTATCGTC	U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.1745A>G	chr3.hg19:g.101383437T>C	ENSP00000326200:p.Tyr582Cys	138.0	0.0		121.0	43.0	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	hg19	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.394587	0.62066	.	.	ENSG00000066422	ENST00000312938	T	0.53640	0.61	5.69	5.69	0.88448	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.063950	0.64402	D	0.000004	T	0.63343	0.2503	L	0.49126	1.545	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.62450	-0.6852	10	0.44086	T	0.13	-20.1595	15.9526	0.79855	0.0:0.0:0.0:1.0	.	582	O95625	ZBT11_HUMAN	C	582	ENSP00000326200:Y582C	ENSP00000326200:Y582C	Y	-	2	0	ZBTB11	102866127	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	4.617000	0.61204	2.168000	0.68352	0.533000	0.62120	TAC	.	.		0.353	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		C	101383437	T	C	101383437	3	2	23	1	0	0	0	0	1	0	0	0	17539	1638	57	2	1444	2	ZBTB11	3	101383437	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	11884075	101383437	96638993	252	2318										
CD47	961	hgsc.bcm.edu	37	chr3	107798890	107798890	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccttctctggttaattctgtTacttcacaagtgtagtttcc	6	10	3	0	rs560443707		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:107798890T>G	ENST00000361309.5	-	2	453	c.348A>C	c.(346-348)gtA>gtC	p.V116V	CD47_ENST00000355354.7_Silent_p.V116V	NM_001777.3	NP_001768.1	Q08722	CD47_HUMAN	CD47 molecule	116	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|opsonization (GO:0008228)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of inflammatory response (GO:0050729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T cell activation (GO:0050870)|response to bacterium (GO:0009617)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(3;0.0191)|Epithelial(53;0.118)			TTAATTCTGTTACTTCACAAG	0.378																																					p.V116V		Atlas-SNP	.											.	CD47	37	.	0			c.A348C						.						237	210	218					3																	107798890		1879	4122	6001	SO:0001819	synonymous_variant	961	exon2			TTCTGTTACTTCA		CCDS43125.1, CCDS43126.1	3q13.1-q13.2	2013-01-11	2006-03-28		ENSG00000196776	ENSG00000196776		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1682	protein-coding gene	gene with protein product	"antigen identified by monoclonal antibody 1D8", "antigenic surface determinant protein OA3", "integrin associated protein", "Rh-related antigen", "leukocyte surface antigen CD47", "CD47 glycoprotein"	601028	"CD47 antigen (Rh-related antigen, integrin-associated signal transducer)"	MER6		8294396, 2277087	Standard	XM_005247908		Approved	IAP, OA3	uc003dwt.1	Q08722	OTTHUMG00000044216	ENST00000361309.5:c.348A>C	chr3.hg19:g.107798890T>G		146.0	0.0		161.0	65.0	NM_198793	A8K198|D3DN59|Q53Y71|Q96A60	Silent	SNP	ENST00000361309.5	hg19	CCDS43126.1																																																																																			.	.		0.378	CD47-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000102793.1	NM_001777		G	107798890	T	G	107798890	2	3	23	1	0	0	0	0	0	0	0	1	3021	1741	61	5		5	CD47	3	107798890	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	6415453	107798890	90223540	253	2319										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111898494	111898494	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcaattatcggaaaatcttTctcctttgactccaccattt	4	11	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:111898494T>C	ENST00000305815.5	-	23	3055	c.2803A>G	c.(2803-2805)Aaa>Gaa	p.K935E	SLC9C1_ENST00000487372.1_Missense_Mutation_p.K887E	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	935					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										GGAAAATCTTTCTCCTTTGAC	0.358																																					p.K935E		Atlas-SNP	.											.	.	.	.	0			c.A2803G						.						84	84	84					3																	111898494		2203	4299	6502	SO:0001583	missense	285335	exon23			AATCTTTCTCCTT	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2803A>G	chr3.hg19:g.111898494T>C	ENSP00000306627:p.Lys935Glu	62.0	0.0		85.0	38.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.483357	0.26598	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.77098	-1.07;-1.07	5.98	4.83	0.62350	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.215834	0.32503	N	0.006011	T	0.75170	0.3813	L	0.37750	1.13	0.21386	N	0.999705	B;D	0.56746	0.24;0.977	B;P	0.55011	0.096;0.766	T	0.65911	-0.6053	10	0.34782	T	0.22	-23.3858	8.0269	0.30442	0.0:0.0882:0.0:0.9118	.	887;935	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	E	935;887	ENSP00000306627:K935E;ENSP00000420688:K887E	ENSP00000306627:K935E	K	-	1	0	SLC9A10	113381184	0.933000	0.31639	0.355000	0.25773	0.023000	0.10783	4.037000	0.57311	2.289000	0.77006	0.421000	0.28195	AAA	.	.		0.358	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		C	111898494	T	C	111898494	3	2	23	1	0	0	0	0	1	0	0	0	14725	1792	62	2	758	2	SLC9A10	3	111898494	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	4099604	111898494	86123936	254	2320										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112358126	112358126	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggtccaggggctgctccagGatctggccctcgctggtgat	16	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:112358126G>A	ENST00000206423.3	-	2	1580	c.627C>T	c.(625-627)atC>atT	p.I209I	CCDC80_ENST00000439685.2_Silent_p.I209I|CCDC80_ENST00000475181.1_5'Flank	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	209					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						GCTGCTCCAGGATCTGGCCCT	0.582																																					p.I209I		Atlas-SNP	.											.	CCDC80	100	.	0			c.C627T						.						101	90	94					3																	112358126		2203	4300	6503	SO:0001819	synonymous_variant	151887	exon2			CTCCAGGATCTGG	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.627C>T	chr3.hg19:g.112358126G>A		85.0	0.0		99.0	31.0	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Silent	SNP	ENST00000206423.3	hg19	CCDS2968.1																																																																																			.	.		0.582	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		A	112358126	G	A	112358126	2	1	23	1	0	0	0	0	0	0	0	1	2856	1164	41	3		3	CCDC80	3	112358126	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	459632	112358126	85664304	255	2321										
CCDC52	152185	hgsc.bcm.edu	37	chr3	113188014	113188014	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttatttgtgactgggttgctAttttctgctgaatgtcagtc	10	6	2	2	rs558422433		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:113188014A>G	ENST00000295872.4	-	8	942	c.683T>C	c.(682-684)aTa>aCa	p.I228T		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	228					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						CTGGGTTGCTATTTTCTGCTG	0.393													A|||	1	0.000199681	8e-04	0	5008	,	,		11173	0		0	False		,,,				2504	0				p.I228T		Atlas-SNP	.											.	SPICE1	130	.	0			c.T683C						.						119	112	114					3																	113188014		2203	4300	6503	SO:0001583	missense	152185	exon8			GTTGCTATTTTCT	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.683T>C	chr3.hg19:g.113188014A>G	ENSP00000295872:p.Ile228Thr	118.0	0.0		151.0	31.0	NM_144718	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	hg19	CCDS2973.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.024|1.024	-0.684008|-0.684008	0.03353|0.03353	.|.	.|.	ENSG00000163611|ENSG00000163611	ENST00000295872|ENST00000467618	T|.	0.32023|.	1.47|.	4.91|4.91	2.3|2.3	0.28687|0.28687	.|.	0.838498|.	0.10836|.	N|.	0.628823|.	T|.	0.39306|.	0.1073|.	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	N|N	1|1	B;B|.	0.33238|.	0.403;0.275|.	B;B|.	0.31337|.	0.128;0.087|.	T|.	0.29366|.	-1.0014|.	10|.	0.45353|.	T|.	0.12|.	-2.906|-2.906	4.1692|4.1692	0.10322|0.10322	0.6525:0.0:0.0966:0.2509|0.6525:0.0:0.0966:0.2509	.|.	124;228|.	B3KX77;Q8N0Z3|.	.;SPICE_HUMAN|.	T|Q	228|40	ENSP00000295872:I228T|.	ENSP00000295872:I228T|.	I|X	-|-	2|1	0|0	SPICE1|SPICE1	114670704|114670704	0.513000|0.513000	0.26194|0.26194	0.336000|0.336000	0.25522|0.25522	0.408000|0.408000	0.30992|0.30992	0.646000|0.646000	0.24797|0.24797	0.806000|0.806000	0.34183|0.34183	0.482000|0.482000	0.46254|0.46254	ATA|TAG	.	.		0.393	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		G	113188014	A	G	113188014	3	3	23	1	0	0	0	0	1	0	0	0	2824	449	16	2	1928	2	CCDC52	3	113188014	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	829888	113188014	84834416	256	2322										
ZBTB20	26137	hgsc.bcm.edu	37	chr3	114070331	114070331	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggatccccgggaacacatcGcccacgttctgtgacacgat	10	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:114070331G>A	ENST00000474710.1	-	4	772	c.594C>T	c.(592-594)ggC>ggT	p.G198G	ZBTB20_ENST00000357258.3_Silent_p.G125G|ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20-AS1_ENST00000475939.1_RNA|ZBTB20_ENST00000462705.1_Silent_p.G125G|ZBTB20_ENST00000464560.1_Silent_p.G125G|ZBTB20_ENST00000471418.1_Silent_p.G125G|ZBTB20_ENST00000481632.1_Silent_p.G125G|ZBTB20-AS1_ENST00000467304.1_RNA|ZBTB20_ENST00000393785.2_Silent_p.G125G	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	198						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.G125G(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		GGAACACATCGCCCACGTTCT	0.647																																					p.G198G	NSCLC(69;748 1344 9802 11203 30933)	Atlas-SNP	.											ZBTB20,colon,carcinoma,0,1	ZBTB20	157	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C594T						.						74	62	66					3																	114070331		2203	4300	6503	SO:0001819	synonymous_variant	26137	exon4			CACATCGCCCACG	AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13503	protein-coding gene	gene with protein product		606025	"zinc finger protein 288"	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.594C>T	chr3.hg19:g.114070331G>A		89.0	0.0		76.0	9.0	NM_001164342	Q63HP6|Q8N6R5|Q9Y410	Silent	SNP	ENST00000474710.1	hg19	CCDS54626.1																																																																																			.	.		0.647	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		A	114070331	G	A	114070331	2	1	23	1	0	0	0	0	0	0	0	1	17544	1074	38	1		1	ZBTB20	3	114070331	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	882317	114070331	83952099	257	2323										
HCLS1	3059	hgsc.bcm.edu	37	chr3	121353148	121353148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagggctcctctttgtcacaGcctttcgctcctgttgcctc	8	16	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:121353148G>A	ENST00000314583.3	-	10	900	c.809C>T	c.(808-810)gCt>gTt	p.A270V	HCLS1_ENST00000428394.2_Missense_Mutation_p.A233V|HCLS1_ENST00000473883.1_5'UTR	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	270					actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		CTTTGTCACAGCCTTTCGCTC	0.577																																					p.A270V		Atlas-SNP	.											.	HCLS1	78	.	0			c.C809T						.						87	81	83					3																	121353148		2203	4300	6503	SO:0001583	missense	3059	exon10			GTCACAGCCTTTC		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"cortactin-like"	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.809C>T	chr3.hg19:g.121353148G>A	ENSP00000320176:p.Ala270Val	57.0	0.0		68.0	26.0	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Missense_Mutation	SNP	ENST00000314583.3	hg19	CCDS3003.1	.	.	.	.	.	.	.	.	.	.	G	7.714	0.695824	0.15106	.	.	ENSG00000180353	ENST00000314583;ENST00000428394	T;T	0.21191	2.04;2.02	5.38	3.46	0.39613	.	0.631964	0.17207	N	0.182890	T	0.17916	0.0430	L	0.50333	1.59	0.09310	N	1	B;B	0.23442	0.017;0.085	B;B	0.17098	0.01;0.017	T	0.13602	-1.0503	10	0.52906	T	0.07	-0.7608	6.6477	0.22945	0.212:0.0:0.788:0.0	.	233;270	E7EVW7;P14317	.;HCLS1_HUMAN	V	270;233	ENSP00000320176:A270V;ENSP00000387645:A233V	ENSP00000320176:A270V	A	-	2	0	HCLS1	122835838	0.726000	0.28059	0.616000	0.29078	0.075000	0.17131	3.059000	0.49947	1.506000	0.48736	-0.142000	0.14014	GCT	.	.		0.577	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335		A	121353148	G	A	121353148	3	1	23	1	0	0	0	0	1	0	0	0	7004	971	34	3	671	3	HCLS1	3	121353148	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	7282817	121353148	76669282	258	2324										
CSTA	1475	hgsc.bcm.edu	37	chr3	122060396	122060396	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gttgacaaaaacaaggatgaCgagctgacgggcttttagca	12	7	0	3	rs569377469		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:122060396C>T	ENST00000264474.3	+	3	328	c.279C>T	c.(277-279)gaC>gaT	p.D93D		NM_005213.3	NP_005204.1	P01040	CYTA_HUMAN	cystatin A (stefin A)	93					keratinocyte differentiation (GO:0030216)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|peptide cross-linking (GO:0018149)|single organismal cell-cell adhesion (GO:0016337)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			large_intestine(2)|lung(2)	4				GBM - Glioblastoma multiforme(114;0.155)		ACAAGGATGACGAGCTGACGG	0.393																																					p.D93D	Pancreas(26;157 1503 12440)	Atlas-SNP	.											CSTA,NS,carcinoma,0,1	CSTA	11	.	0			c.C279T						.						122	120	120					3																	122060396		2203	4300	6503	SO:0001819	synonymous_variant	1475	exon3			GGATGACGAGCTG		CCDS3011.1	3q21	2008-04-15			ENSG00000121552	ENSG00000121552			2481	protein-coding gene	gene with protein product		184600		STF1, STFA		1674139	Standard	NM_005213		Approved		uc003eex.3	P01040	OTTHUMG00000159488	ENST00000264474.3:c.279C>T	chr3.hg19:g.122060396C>T		163.0	0.0		174.0	29.0	NM_005213	Q6IB90	Silent	SNP	ENST00000264474.3	hg19	CCDS3011.1																																																																																			.	.		0.393	CSTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355751.1	NM_005213		T	122060396	C	T	122060396	2	4	23	1	0	0	0	0	0	0	0	1	3983	535	19	1		1	CSTA	3	122060396	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	707248	122060396	75962034	259	2325										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129284250	129284250	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctccaccacagactctgtgCgccgcagcatgagcttgggg	12	14	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:129284250C>T	ENST00000324093.4	-	25	4632	c.4454G>A	c.(4453-4455)cGc>cAc	p.R1485H	PLXND1_ENST00000393239.1_Missense_Mutation_p.R1485H	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1485					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.R1485H(1)	PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						AGACTCTGTGCGCCGCAGCAT	0.602																																					p.R1485H	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											PLXND1,colon,carcinoma,0,1	PLXND1	149	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4454A						.						115	102	106					3																	129284250		2203	4300	6503	SO:0001583	missense	23129	exon25			TCTGTGCGCCGCA	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.4454G>A	chr3.hg19:g.129284250C>T	ENSP00000317128:p.Arg1485His	115.0	1.0		103.0	40.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.537357	0.65085	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.17213	2.29;2.29	4.96	4.09	0.47781	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.300750	0.30620	N	0.009222	T	0.44582	0.1300	M	0.82823	2.61	0.58432	D	0.999996	D;D	0.89917	0.999;1.0	D;D	0.91635	0.987;0.999	T	0.50608	-0.8808	10	0.87932	D	0	.	13.4503	0.61167	0.0:0.9239:0.0:0.0761	.	80;1485	B4DRU3;Q9Y4D7	.;PLXD1_HUMAN	H	1485	ENSP00000317128:R1485H;ENSP00000376931:R1485H	ENSP00000317128:R1485H	R	-	2	0	PLXND1	130766940	0.999000	0.42202	1.000000	0.80357	0.257000	0.26127	7.800000	0.85949	1.083000	0.41159	-0.291000	0.09656	CGC	.	.		0.602	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		T	129284250	C	T	129284250	3	4	23	1	0	0	0	0	1	0	0	0	12136	768	27	1	1371	1	PLXND1	3	129284250	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	7223854	129284250	68738180	260	2326										
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132169658	132169658	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctctcagattatcaaggaggAttttgtatactttatggagg	10	5	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:132169658A>T	ENST00000260818.6	+	6	752	c.504A>T	c.(502-504)ggA>ggT	p.G168G	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	168					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						ATCAAGGAGGATTTTGTATAC	0.328																																					p.G168G		Atlas-SNP	.											.	DNAJC13	253	.	0			c.A504T						.						52	57	55					3																	132169658		2203	4300	6503	SO:0001819	synonymous_variant	23317	exon6			AGGAGGATTTTGT	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.504A>T	chr3.hg19:g.132169658A>T		230.0	0.0		194.0	83.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Silent	SNP	ENST00000260818.6	hg19	CCDS33857.1																																																																																			.	.		0.328	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132169658	A	T	132169658	2	4	23	1	0	0	0	0	0	0	0	1	4634	320	12	4		4	DNAJC13	3	132169658	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2885408	132169658	65852772	261	2327										
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135825069	135825069	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccaatcaggatgttgagaaCgatgggcctgagccctcaga	12	10	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:135825069C>T	ENST00000264977.3	+	13	3851	c.3234C>T	c.(3232-3234)aaC>aaT	p.N1078N	PPP2R3A_ENST00000490467.1_Silent_p.N342N|PPP2R3A_ENST00000334546.2_Silent_p.N457N|PPP2R3A_ENST00000469270.1_3'UTR	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	1078					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATGTTGAGAACGATGGGCCTG	0.463																																					p.N1078N		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.C3234T						.						65	66	66					3																	135825069		2203	4300	6503	SO:0001819	synonymous_variant	5523	exon13			TGAGAACGATGGG	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.3234C>T	chr3.hg19:g.135825069C>T		107.0	0.0		111.0	9.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	hg19	CCDS3087.1																																																																																			.	.		0.463	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		T	135825069	C	T	135825069	2	4	23	1	0	0	0	0	0	0	0	1	12400	535	19	1		1	PPP2R3A	3	135825069	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3655411	135825069	62197361	262	2328										
STAG1	10274	hgsc.bcm.edu	37	chr3	136141653	136141653	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agatttctaaatcaaaatacTgtgggatttgtagcaagttt	8	4	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:136141653T>G	ENST00000383202.2	-	18	2046	c.1790A>C	c.(1789-1791)cAg>cCg	p.Q597P	STAG1_ENST00000236698.5_Missense_Mutation_p.Q597P|STAG1_ENST00000536929.1_Missense_Mutation_p.Q181P|STAG1_ENST00000434713.2_Missense_Mutation_p.Q371P	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	597					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						ATCAAAATACTGTGGGATTTG	0.308																																					p.Q597P		Atlas-SNP	.											.	STAG1	135	.	0			c.A1790C						.						67	67	67					3																	136141653		2202	4299	6501	SO:0001583	missense	10274	exon18			AAATACTGTGGGA	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.1790A>C	chr3.hg19:g.136141653T>G	ENSP00000372689:p.Gln597Pro	187.0	0.0		164.0	7.0	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	hg19	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.217523	0.79352	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	5.66	5.66	0.87406	Armadillo-type fold (1);	0.055974	0.64402	D	0.000001	T	0.26195	0.0639	L	0.60957	1.885	0.80722	D	1	P;P;P	0.52692	0.819;0.955;0.91	P;P;P	0.52793	0.707;0.709;0.707	T	0.00651	-1.1626	10	0.35671	T	0.21	.	15.9375	0.79723	0.0:0.0:0.0:1.0	.	614;597;597	Q4LE48;Q6P275;Q8WVM7	.;.;STAG1_HUMAN	P	597;597;371;181	ENSP00000372689:Q597P;ENSP00000236698:Q597P;ENSP00000404396:Q371P;ENSP00000445787:Q181P	ENSP00000236698:Q597P	Q	-	2	0	STAG1	137624343	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.159000	0.67721	0.529000	0.55759	CAG	.	.		0.308	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		G	136141653	T	G	136141653	3	3	23	1	0	0	0	0	1	0	0	0	15257	1580	55	5	2054	5	STAG1	3	136141653	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	316584	136141653	61880777	263	2329										
ZBTB38	253461	hgsc.bcm.edu	37	chr3	141162007	141162007	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtgaagcccttgcagcgaaAccgaaaacatgccggaagcc	11	12	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:141162007A>G	ENST00000514251.1	+	4	1056	c.777A>G	c.(775-777)aaA>aaG	p.K259K	ZBTB38_ENST00000441582.2_Silent_p.K259K|ZBTB38_ENST00000321464.5_Silent_p.K260K					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						TTGCAGCGAAACCGAAAACAT	0.473																																					p.K259K		Atlas-SNP	.											.	ZBTB38	92	.	0			c.A777G						.						64	65	65					3																	141162007		1979	4177	6156	SO:0001819	synonymous_variant	253461	exon8			AGCGAAACCGAAA	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	26636	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 171"	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.777A>G	chr3.hg19:g.141162007A>G		109.0	0.0		112.0	39.0	NM_001080412		Silent	SNP	ENST00000514251.1	hg19	CCDS43157.1																																																																																			.	.		0.473	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2			G	141162007	A	G	141162007	2	3	23	1	0	0	0	0	0	0	0	1	17554	40	2	2		2	ZBTB38	3	141162007	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	5020354	141162007	56860423	264	2330										
GK5	256356	hgsc.bcm.edu	37	chr3	141901813	141901813	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtgttaatatccaaaaatgTcccagttcccatggttaatt	6	8	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:141901813T>A	ENST00000392993.2	-	10	1046	c.895A>T	c.(895-897)Aca>Tca	p.T299S		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	299					glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						TCCAAAAATGTCCCAGTTCCC	0.373																																					p.T299S		Atlas-SNP	.											.	GK5	45	.	0			c.A895T						.						93	88	90					3																	141901813		2203	4300	6503	SO:0001583	missense	256356	exon10			AAAATGTCCCAGT	BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066		"Glycerol kinases"	28635	protein-coding gene	gene with protein product						12477932	Standard	NM_001039547		Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.895A>T	chr3.hg19:g.141901813T>A	ENSP00000418001:p.Thr299Ser	128.0	0.0		119.0	43.0	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Missense_Mutation	SNP	ENST00000392993.2	hg19	CCDS33871.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.643855	0.29246	.	.	ENSG00000175066	ENST00000392993	D	0.84146	-1.81	5.69	5.69	0.88448	Carbohydrate kinase, FGGY, C-terminal (1);	0.157389	0.56097	D	0.000027	T	0.70500	0.3231	N	0.04063	-0.285	0.80722	D	1	B	0.15930	0.015	B	0.26517	0.07	T	0.68119	-0.5493	10	0.66056	D	0.02	-14.7751	8.9817	0.35970	0.2637:0.0:0.0:0.7362	.	299	Q6ZS86	GLPK5_HUMAN	S	299	ENSP00000418001:T299S	ENSP00000418001:T299S	T	-	1	0	GK5	143384503	0.995000	0.38212	0.932000	0.37286	0.690000	0.40134	2.543000	0.45752	2.162000	0.67917	0.533000	0.62120	ACA	.	.		0.373	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547		A	141901813	T	A	141901813	3	1	23	1	0	0	0	0	1	0	0	0	6430	1667	58	4	722	4	GK5	3	141901813	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	739806	141901813	56120617	265	2331										
ZIC1	7545	hgsc.bcm.edu	37	chr3	147128096	147128096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cggccagacggccttcacgtCgcaggcgccaggctacgcgg	15	16	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:147128096C>T	ENST00000282928.4	+	1	926	c.197C>T	c.(196-198)tCg>tTg	p.S66L		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	66					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						GCCTTCACGTCGCAGGCGCCA	0.697																																					p.S66L		Atlas-SNP	.											.	ZIC1	141	.	0			c.C197T						.						17	20	19					3																	147128096		2186	4293	6479	SO:0001583	missense	7545	exon1			TCACGTCGCAGGC	D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"Zinc fingers, C2H2-type"	12872	protein-coding gene	gene with protein product		600470	"Zic family member 1 (odd-paired Drosophila homolog)", "Zic family member 1 (odd-paired homolog, Drosophila)"			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.197C>T	chr3.hg19:g.147128096C>T	ENSP00000282928:p.Ser66Leu	90.0	0.0		92.0	34.0	NM_003412	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	hg19	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.467258	0.63625	.	.	ENSG00000152977	ENST00000282928	D	0.85861	-2.04	4.04	3.08	0.35506	.	0.000000	0.85682	D	0.000000	D	0.85605	0.5735	L	0.59436	1.845	0.58432	D	0.999998	D	0.57257	0.979	P	0.50378	0.639	D	0.87053	0.2148	10	0.59425	D	0.04	.	12.9438	0.58362	0.0:0.8358:0.1642:0.0	.	66	Q15915	ZIC1_HUMAN	L	66	ENSP00000282928:S66L	ENSP00000282928:S66L	S	+	2	0	ZIC1	148610786	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	5.412000	0.66392	1.806000	0.52798	0.442000	0.29010	TCG	.	.		0.697	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		T	147128096	C	T	147128096	3	4	23	1	0	0	0	0	1	0	0	0	17693	893	31	1	199	1	ZIC1	3	147128096	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5226283	147128096	50894334	266	2332										
CPA3	1359	hgsc.bcm.edu	37	chr3	148599317	148599317	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacctccgacaggcaaccaaAacttatgggagaaacaaaat	7	11	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:148599317A>C	ENST00000296046.3	+	7	637	c.585A>C	c.(583-585)aaA>aaC	p.K195N	RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)	195					angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			AGGCAACCAAAACTTATGGGA	0.338																																					p.K195N		Atlas-SNP	.											.	CPA3	75	.	0			c.A585C						.						96	95	96					3																	148599317		2203	4300	6503	SO:0001583	missense	1359	exon7			AACCAAAACTTAT		CCDS3138.1	3q24	2012-02-10			ENSG00000163751	ENSG00000163751	3.4.17.1		2298	protein-coding gene	gene with protein product	"mast cell carboxypeptidase A", "tissue carboxypeptidase A"	114851					Standard	NM_001870		Approved		uc003ewm.3	P15088	OTTHUMG00000159526	ENST00000296046.3:c.585A>C	chr3.hg19:g.148599317A>C	ENSP00000296046:p.Lys195Asn	100.0	0.0		111.0	43.0	NM_001870	Q96E94	Missense_Mutation	SNP	ENST00000296046.3	hg19	CCDS3138.1	.	.	.	.	.	.	.	.	.	.	A	8.576	0.881211	0.17467	.	.	ENSG00000163751	ENST00000296046	T	0.10382	2.88	5.06	3.92	0.45320	Peptidase M14, carboxypeptidase A (2);	0.354238	0.29579	N	0.011756	T	0.04588	0.0125	N	0.05177	-0.1	0.27807	N	0.942289	B	0.24576	0.106	B	0.24155	0.051	T	0.39981	-0.9587	10	0.15499	T	0.54	.	7.315	0.26495	0.8166:0.0:0.1834:0.0	.	195	P15088	CBPA3_HUMAN	N	195	ENSP00000296046:K195N	ENSP00000296046:K195N	K	+	3	2	CPA3	150082007	0.651000	0.27340	1.000000	0.80357	0.986000	0.74619	0.491000	0.22419	0.952000	0.37798	0.533000	0.62120	AAA	.	.		0.338	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	NM_001870		C	148599317	A	C	148599317	3	2	23	1	0	0	0	0	1	0	0	0	3793	11	1	5	611	5	CPA3	3	148599317	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1471221	148599317	49423113	267	2333										
GPR87	53836	hgsc.bcm.edu	37	chr3	151012803	151012803	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actatgtttttgagatagaaTatgaagctggttttattcct	8	4	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:151012803T>C	ENST00000260843.4	-	3	695	c.231A>G	c.(229-231)atA>atG	p.I77M	MED12L_ENST00000474524.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	77					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGAGATAGAATATGAAGCTGG	0.398																																					p.I77M		Atlas-SNP	.											.	GPR87	52	.	0			c.A231G						.						105	106	106					3																	151012803		2203	4300	6503	SO:0001583	missense	53836	exon3			ATAGAATATGAAG	AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"GPCR / Class A : Orphans"	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.231A>G	chr3.hg19:g.151012803T>C	ENSP00000260843:p.Ile77Met	129.0	0.0		93.0	35.0	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	hg19	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.968712	0.53614	.	.	ENSG00000138271	ENST00000260843	T	0.23348	1.91	5.31	1.22	0.21188	GPCR, rhodopsin-like superfamily (1);	0.061473	0.64402	D	0.000002	T	0.49133	0.1539	M	0.85197	2.74	0.42393	D	0.992534	D	0.76494	0.999	D	0.72338	0.977	T	0.46190	-0.9209	10	0.46703	T	0.11	-11.5763	9.9589	0.41684	0.1125:0.0:0.4646:0.4229	.	77	Q9BY21	GPR87_HUMAN	M	77	ENSP00000260843:I77M	ENSP00000260843:I77M	I	-	3	3	GPR87	152495493	0.000000	0.05858	0.999000	0.59377	0.994000	0.84299	-1.539000	0.02202	0.028000	0.15324	0.533000	0.62120	ATA	.	.		0.398	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1			C	151012803	T	C	151012803	3	2	23	1	0	0	0	0	1	0	0	0	6724	1396	49	2	849	2	GPR87	3	151012803	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2413486	151012803	47009627	268	2334										
P2RY13	53829	hgsc.bcm.edu	37	chr3	151046419	151046419	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaggtctgatgatcttgaggAatctgtcaaaggctatgagc	12	6	4	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:151046419A>G	ENST00000325602.5	-	2	444	c.425T>C	c.(424-426)tTc>tCc	p.F142S	MED12L_ENST00000474524.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron	NM_176894.2	NP_795713.2	Q9BPV8	P2Y13_HUMAN	purinergic receptor P2Y, G-protein coupled, 13	142					negative regulation of adenylate cyclase activity (GO:0007194)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(72;0.0189)|Lung(72;0.0278)			GATCTTGAGGAATCTGTCAAA	0.393																																					p.F142S		Atlas-SNP	.											.	P2RY13	80	.	0			c.T425C						.						51	51	51					3																	151046419		2203	4300	6503	SO:0001583	missense	53829	exon2			TTGAGGAATCTGT	AF295368	CCDS3158.2	3q24	2012-08-08	2004-07-12	2004-07-14	ENSG00000181631	ENSG00000181631		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	4537	protein-coding gene	gene with protein product		606380	"G protein-coupled receptor 86"	GPR94, GPR86		11273702, 11574155	Standard	NM_176894		Approved	FKSG77, P2Y13	uc003eyv.2	Q9BPV8	OTTHUMG00000155745	ENST00000325602.5:c.425T>C	chr3.hg19:g.151046419A>G	ENSP00000320376:p.Phe142Ser	246.0	0.0		285.0	89.0	NM_176894	B2R827|Q05C50|Q6DKN4|Q8IUT5|Q8TDU7|Q9BY61	Missense_Mutation	SNP	ENST00000325602.5	hg19	CCDS3158.2	.	.	.	.	.	.	.	.	.	.	A	17.47	3.397711	0.62177	.	.	ENSG00000181631	ENST00000325602	T	0.73681	-0.77	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.112777	0.64402	D	0.000008	D	0.82300	0.5007	L	0.59436	1.845	0.32849	D	0.506394	P	0.52316	0.952	P	0.60236	0.871	D	0.87620	0.2509	10	0.87932	D	0	-23.9887	15.5586	0.76219	1.0:0.0:0.0:0.0	.	142	Q9BPV8	P2Y13_HUMAN	S	142	ENSP00000320376:F142S	ENSP00000320376:F142S	F	-	2	0	P2RY13	152529109	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	0.936000	0.28938	2.075000	0.62263	0.455000	0.32223	TTC	.	.		0.393	P2RY13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341468.1	NM_023914		G	151046419	A	G	151046419	3	3	23	1	0	0	0	0	1	0	0	0	11359	246	9	2	643	2	P2RY13	3	151046419	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	33616	151046419	46976011	269	2335										
P2RY1	5028	hgsc.bcm.edu	37	chr3	152554282	152554282	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgctgattctgggctgttaCggattaattgtgagagcttt	13	5	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:152554282C>T	ENST00000305097.3	+	1	1547	c.711C>T	c.(709-711)taC>taT	p.Y237Y	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	237					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TGGGCTGTTACGGATTAATTG	0.453																																					p.Y237Y		Atlas-SNP	.											.	P2RY1	49	.	0			c.C711T						.						121	110	114					3																	152554282		2203	4300	6503	SO:0001819	synonymous_variant	5028	exon1			CTGTTACGGATTA	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.711C>T	chr3.hg19:g.152554282C>T		93.0	0.0		110.0	48.0	NM_002563		Silent	SNP	ENST00000305097.3	hg19	CCDS3169.1																																																																																			.	.		0.453	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		T	152554282	C	T	152554282	2	4	23	1	0	0	0	0	0	0	0	1	11355	547	19	1		1	P2RY1	3	152554282	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1507863	152554282	45468148	270	2336										
SGEF	26084	hgsc.bcm.edu	37	chr3	153912436	153912436	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttttatttcattacagactAtctgtcaaaaaacacctaag	3	9	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:153912436A>G	ENST00000356448.4	+	9	2058	c.1774A>G	c.(1774-1776)Atc>Gtc	p.I592V	ARHGEF26_ENST00000465817.1_Intron|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.I592V	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	592	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						ATTACAGACTATCTGTCAAAA	0.328																																					p.I592V	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.A1774G						.						57	54	55					3																	153912436		1816	4073	5889	SO:0001583	missense	26084	exon9			CAGACTATCTGTC	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.1774A>G	chr3.hg19:g.153912436A>G	ENSP00000348828:p.Ile592Val	181.0	0.0		189.0	69.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	hg19	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	a	18.00	3.525082	0.64747	.	.	ENSG00000114790	ENST00000356448;ENST00000465093	T;T	0.35789	1.29;1.29	5.7	5.7	0.88788	Dbl homology (DH) domain (5);	0.051159	0.85682	D	0.000000	T	0.52306	0.1726	L	0.42686	1.345	0.80722	D	1	D;D	0.69078	0.98;0.997	D;D	0.80764	0.961;0.994	T	0.46884	-0.9159	10	0.38643	T	0.18	-18.9384	16.0468	0.80725	1.0:0.0:0.0:0.0	.	592;592	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	V	592	ENSP00000348828:I592V;ENSP00000423418:I592V	ENSP00000348828:I592V	I	+	1	0	ARHGEF26	155395126	1.000000	0.71417	0.973000	0.42090	0.918000	0.54935	8.253000	0.89842	2.176000	0.68965	0.520000	0.50463	ATC	.	.		0.328	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		G	153912436	A	G	153912436	3	3	23	1	0	0	0	0	1	0	0	0	14220	449	16	2	1804	2	SGEF	3	153912436	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1358154	153912436	44109994	271	2337										
GPR149	344758	hgsc.bcm.edu	37	chr3	154146778	154146778	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aatcggtgagtgagtgggacTgagaggcccacgaggagtcc	17	8	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:154146778T>C	ENST00000389740.2	-	1	726	c.627A>G	c.(625-627)tcA>tcG	p.S209S		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	209					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TGAGTGGGACTGAGAGGCCCA	0.597																																					p.S209S		Atlas-SNP	.											.	GPR149	134	.	0			c.A627G						.						54	61	59					3																	154146778		1976	4152	6128	SO:0001819	synonymous_variant	344758	exon1			TGGGACTGAGAGG	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.627A>G	chr3.hg19:g.154146778T>C		262.0	0.0		219.0	88.0	NM_001038705		Silent	SNP	ENST00000389740.2	hg19	CCDS43162.1																																																																																			.	.		0.597	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		C	154146778	T	C	154146778	2	2	23	1	0	0	0	0	0	0	0	1	6662	1567	55	2		2	GPR149	3	154146778	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	234342	154146778	43875652	272	2338										
KCNAB1	7881	hgsc.bcm.edu	37	chr3	155861202	155861202	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagagcagagacgggcatgGcatacaggtactgctgattg	14	9	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:155861202G>A	ENST00000490337.1	+	1	339				KCNAB1_ENST00000389636.5_Intron|KCNAB1_ENST00000471742.1_Missense_Mutation_p.A79T	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1						learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GACGGGCATGGCATACAGGTA	0.453																																					p.A79T		Atlas-SNP	.											.	KCNAB1	176	.	0			c.G235A						.						110	108	108					3																	155861202		2203	4300	6503	SO:0001627	intron_variant	7881	exon1			GGCATGGCATACA	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.275+22527G>A	chr3.hg19:g.155861202G>A		126.0	0.0		85.0	43.0	NM_003471	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	hg19	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.095788	0.36952	.	.	ENSG00000169282	ENST00000471742	T	0.41758	0.99	5.29	0.157	0.14915	.	.	.	.	.	T	0.24774	0.0601	.	.	.	0.80722	D	1	B	0.15719	0.014	B	0.18871	0.023	T	0.06862	-1.0803	8	0.28530	T	0.3	.	4.1948	0.10438	0.3404:0.3191:0.3405:0.0	.	79	Q14722-3	.	T	79	ENSP00000418956:A79T	ENSP00000418956:A79T	A	+	1	0	KCNAB1	157343896	0.378000	0.25114	0.973000	0.42090	0.993000	0.82548	0.373000	0.20484	0.313000	0.23062	0.561000	0.74099	GCA	.	.		0.453	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		A	155861202	G	A	155861202	1	1	23	0	1	0	0	0	0	0	0	0	8018	1203	42	3		3	KCNAB1	3	155861202	Intron	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1714424	155861202	42161228	273	2339										
PLD1	5337	hgsc.bcm.edu	37	chr3	171453412	171453412	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgttaattcaatagtgtaaaGattaatacttggtacctaca	6	5	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:171453412G>A	ENST00000351298.4	-	4	430	c.304C>T	c.(304-306)Ctt>Ttt	p.L102F	PLD1_ENST00000356327.5_Missense_Mutation_p.L102F|PLD1_ENST00000340989.4_Missense_Mutation_p.L102F|PLD1_ENST00000342215.6_Missense_Mutation_p.L102F	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	102	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	ATAGTGTAAAGATTAATACTT	0.299																																					p.L102F	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.C304T						.						71	68	69					3																	171453412		2203	4300	6503	SO:0001583	missense	5337	exon4			TGTAAAGATTAAT	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"Pleckstrin homology (PH) domain containing"	9067	protein-coding gene	gene with protein product	"choline phosphatase 1"	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.304C>T	chr3.hg19:g.171453412G>A	ENSP00000342793:p.Leu102Phe	135.0	0.0		153.0	77.0	NM_002662		Missense_Mutation	SNP	ENST00000351298.4	hg19	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.177229	0.57692	.	.	ENSG00000075651	ENST00000356327;ENST00000351298;ENST00000342215;ENST00000340989;ENST00000418087	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.18	4.31	0.51392	Phox homologous domain (5);	0.199342	0.43416	D	0.000577	T	0.54319	0.1851	L	0.60067	1.865	0.32291	N	0.566369	P;B	0.45126	0.851;0.154	P;B	0.58820	0.846;0.261	T	0.64153	-0.6474	10	0.54805	T	0.06	-8.9613	9.7833	0.40662	0.0:0.3446:0.52:0.1354	.	125;102	Q59EA4;Q13393	.;PLD1_HUMAN	F	102	ENSP00000348681:L102F;ENSP00000342793:L102F;ENSP00000339936:L102F;ENSP00000340326:L102F;ENSP00000400639:L102F	ENSP00000340326:L102F	L	-	1	0	PLD1	172936106	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.787000	0.26858	1.158000	0.42547	0.563000	0.77884	CTT	.	.		0.299	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		A	171453412	G	A	171453412	3	1	23	1	0	0	0	0	1	0	0	0	12054	942	33	3	3016	3	PLD1	3	171453412	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	15592210	171453412	26569018	274	2340										
KCNMB2	10242	hgsc.bcm.edu	37	chr3	178525220	178525220	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtttatatggaccagtggccGgacctcttcatcttatagac	9	10	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:178525220G>A	ENST00000432997.1	+	2	375	c.23G>A	c.(22-24)cGg>cAg	p.R8Q	KCNMB2_ENST00000470361.2_3'UTR|RP11-385J1.2_ENST00000437488.1_RNA|KCNMB2_ENST00000452583.1_Missense_Mutation_p.R8Q|RP11-385J1.2_ENST00000425330.1_RNA|RP11-385J1.2_ENST00000451742.1_RNA|KCNMB2_ENST00000358316.3_Missense_Mutation_p.R8Q|KCNMB2_ENST00000420517.2_Missense_Mutation_p.R8Q|RP11-385J1.2_ENST00000432385.1_RNA	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	0					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	ACCAGTGGCCGGACCTCTTCA	0.438																																					p.R8Q		Atlas-SNP	.											.	KCNMB2	35	.	0			c.G23A						.						99	95	97					3																	178525220		2203	4300	6503	SO:0001583	missense	10242	exon3			GTGGCCGGACCTC	AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584		"Potassium channels"	6286	protein-coding gene	gene with protein product		605214				10097176	Standard	NM_181361		Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.23G>A	chr3.hg19:g.178525220G>A	ENSP00000407592:p.Arg8Gln	106.0	0.0		91.0	27.0	NM_005832	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000432997.1	hg19	CCDS3223.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766730	0.69878	.	.	ENSG00000197584	ENST00000437510;ENST00000420517;ENST00000452583;ENST00000432997;ENST00000455865;ENST00000358316;ENST00000457763	T;T;T;T;T;T	0.24538	2.17;3.04;3.04;3.04;1.85;3.04	5.41	5.41	0.78517	KCNMB2, ball/chain domain (2);	0.482489	0.23235	N	0.050420	T	0.36441	0.0967	N	0.14661	0.345	0.46701	D	0.999163	D;B	0.71674	0.998;0.039	D;B	0.79108	0.992;0.01	T	0.34477	-0.9827	10	0.62326	D	0.03	-19.7358	18.3237	0.90246	0.0:0.0:1.0:0.0	.	8;8	B5BNW9;Q9Y691	.;KCMB2_HUMAN	Q	8	ENSP00000395807:R8Q;ENSP00000408252:R8Q;ENSP00000397483:R8Q;ENSP00000407592:R8Q;ENSP00000399100:R8Q;ENSP00000351068:R8Q	ENSP00000351068:R8Q	R	+	2	0	KCNMB2	180007914	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.946000	0.70234	2.697000	0.92050	0.563000	0.77884	CGG	.	.		0.438	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348251.1	NM_181361		A	178525220	G	A	178525220	3	1	23	1	0	0	0	0	1	0	0	0	8084	1116	39	1	25	1	KCNMB2	3	178525220	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	7071808	178525220	19497210	275	2341										
USP13	8975	hgsc.bcm.edu	37	chr3	179448452	179448452	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggccagtattcaaagcctccGgtgaaatctgaactcattga	9	10	3	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:179448452G>A	ENST00000263966.3	+	10	1680	c.1209G>A	c.(1207-1209)ccG>ccA	p.P403P	USP13_ENST00000482333.1_3'UTR|USP13_ENST00000496897.1_Silent_p.P338P	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	403	USP.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			CAAAGCCTCCGGTGAAATCTG	0.458																																					p.P403P		Atlas-SNP	.											.	USP13	117	.	0			c.G1209A						.						56	54	55					3																	179448452		2203	4300	6503	SO:0001819	synonymous_variant	8975	exon10			GCCTCCGGTGAAA	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"Ubiquitin-specific peptidases"	12611	protein-coding gene	gene with protein product		603591	"ubiquitin specific protease 13 (isopeptidase T-3)"			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.1209G>A	chr3.hg19:g.179448452G>A		156.0	0.0		146.0	59.0	NM_003940	A8K2S3|B4DYF3|D3DNS2|Q96B25	Silent	SNP	ENST00000263966.3	hg19	CCDS3235.1																																																																																			.	.		0.458	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			A	179448452	G	A	179448452	2	1	23	1	0	0	0	0	0	0	0	1	17059	1103	39	1		1	USP13	3	179448452	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	923232	179448452	18573978	276	2342										
CCDC39	339829	hgsc.bcm.edu	37	chr3	180378451	180378451	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctaaccaggcctccaatgcTtgctggtcccagttcatttg	8	13	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:180378451T>G	ENST00000442201.2	-	4	542	c.423A>C	c.(421-423)caA>caC	p.Q141H	CCDC39_ENST00000273654.4_Missense_Mutation_p.Q225H	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	141					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CCTCCAATGCTTGCTGGTCCC	0.388																																					p.Q141H		Atlas-SNP	.											.	CCDC39	242	.	0			c.A423C						.						91	82	85					3																	180378451		1838	4087	5925	SO:0001583	missense	339829	exon4			CAATGCTTGCTGG	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.423A>C	chr3.hg19:g.180378451T>G	ENSP00000405708:p.Gln141His	86.0	0.0		93.0	39.0	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	hg19	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.376177	0.61735	.	.	ENSG00000145075	ENST00000273654;ENST00000442201	.	.	.	5.5	1.72	0.24424	.	0.107759	0.64402	D	0.000005	T	0.52948	0.1766	M	0.64997	1.995	0.39424	D	0.966967	D	0.53151	0.958	P	0.49140	0.601	T	0.54423	-0.8296	9	0.51188	T	0.08	-17.4904	8.7163	0.34414	0.0:0.4245:0.0:0.5755	.	141	Q9UFE4	CCD39_HUMAN	H	225;141	.	ENSP00000273654:Q225H	Q	-	3	2	CCDC39	181861145	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	0.357000	0.20199	0.388000	0.25054	0.477000	0.44152	CAA	.	.		0.388	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		G	180378451	T	G	180378451	3	3	23	1	0	0	0	0	1	0	0	0	2813	1606	56	5	2470	5	CCDC39	3	180378451	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	929999	180378451	17643979	277	2343										
B3GNT5	84002	hgsc.bcm.edu	37	chr3	182988028	182988028	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aactacaaagaaaactggctTgggaagatcaaaggtacaat	9	6	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:182988028T>C	ENST00000326505.3	+	2	972	c.442T>C	c.(442-444)Tgg>Cgg	p.W148R	B3GNT5_ENST00000460419.1_Missense_Mutation_p.W148R|MCF2L2_ENST00000473233.1_Intron|MCF2L2_ENST00000447025.2_Intron|MCF2L2_ENST00000328913.3_Intron|B3GNT5_ENST00000465010.1_Missense_Mutation_p.W148R	NM_032047.4	NP_114436.1	Q9BYG0	B3GN5_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	148					cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycolipid biosynthetic process (GO:0009247)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity (GO:0008457)|galactosyltransferase activity (GO:0008378)|lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase activity (GO:0047256)|lipopolysaccharide N-acetylglucosaminyltransferase activity (GO:0008917)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8	all_cancers(143;8.52e-13)|Ovarian(172;0.0355)		all cancers(12;4.52e-44)|Epithelial(37;8.82e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			AAAACTGGCTTGGGAAGATCA	0.378																																					p.W148R		Atlas-SNP	.											.	B3GNT5	26	.	0			c.T442C						.						55	54	54					3																	182988028		2203	4300	6503	SO:0001583	missense	84002	exon2			CTGGCTTGGGAAG	AB045278	CCDS3244.1	3q28	2013-02-21			ENSG00000176597	ENSG00000176597	2.4.1.206	"Beta 3-glycosyltransferases"	15684	protein-coding gene	gene with protein product	"lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase"	615333				11283017	Standard	XM_005247824		Approved	B3GN-T5, beta3Gn-T5	uc003flk.3	Q9BYG0	OTTHUMG00000158436	ENST00000326505.3:c.442T>C	chr3.hg19:g.182988028T>C	ENSP00000316173:p.Trp148Arg	157.0	0.0		154.0	61.0	NM_032047	D3DNS5|Q59FE3|Q7L9Z5|Q8WWP9	Missense_Mutation	SNP	ENST00000326505.3	hg19	CCDS3244.1	.	.	.	.	.	.	.	.	.	.	T	0.489	-0.876211	0.02550	.	.	ENSG00000176597	ENST00000326505;ENST00000460419;ENST00000465010	T;T;T	0.39056	1.1;1.1;1.1	5.91	-1.56	0.08532	.	0.822726	0.10930	N	0.618469	T	0.16981	0.0408	N	0.11364	0.135	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18587	-1.0332	10	0.24483	T	0.36	.	1.5143	0.02503	0.1981:0.1386:0.3664:0.297	.	148	Q9BYG0	B3GN5_HUMAN	R	148	ENSP00000316173:W148R;ENSP00000420778:W148R;ENSP00000417868:W148R	ENSP00000316173:W148R	W	+	1	0	B3GNT5	184470722	0.000000	0.05858	0.127000	0.21898	0.006000	0.05464	-0.593000	0.05740	0.114000	0.18032	-0.309000	0.09137	TGG	.	.		0.378	B3GNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351009.1	NM_032047		C	182988028	T	C	182988028	3	2	23	1	0	0	0	0	1	0	0	0	1260	1812	63	2	444	2	B3GNT5	3	182988028	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2609577	182988028	15034402	278	2344										
DGKG	1608	hgsc.bcm.edu	37	chr3	185975727	185975727	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtatcacggaaaaagttcaAcctgggaagaagaagaaagg	12	5	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:185975727A>C	ENST00000265022.3	-	17	1965	c.1426T>G	c.(1426-1428)Ttg>Gtg	p.L476V	DGKG_ENST00000344484.4_Splice_Site_p.L451V|DGKG_ENST00000382164.4_Splice_Site_p.L437V|DGKG_ENST00000544847.1_Splice_Site_p.L417V	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	476	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	AAAAAGTTCAACCTGGGAAGA	0.483																																					p.L476V		Atlas-SNP	.											.	DGKG	98	.	0			c.T1426G						.						91	83	86					3																	185975727		2203	4300	6503	SO:0001630	splice_region_variant	1608	exon17			AGTTCAACCTGGG	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.1425-1T>G	chr3.hg19:g.185975727A>C		105.0	0.0		98.0	6.0	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	hg19	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	A	17.93	3.509616	0.64522	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.33	0.017	0.14110	Diacylglycerol kinase, catalytic domain (3);	0.000000	0.64402	D	0.000009	T	0.54431	0.1858	M	0.87682	2.9	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.997;0.997	D;D;D;D	0.79108	0.992;0.992;0.979;0.988	T	0.56420	-0.7982	10	0.87932	D	0	.	9.6746	0.40032	0.7424:0.0:0.2576:0.0	.	417;451;437;476	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	V	476;451;437;417;440	ENSP00000265022:L476V;ENSP00000339777:L451V;ENSP00000371599:L437V;ENSP00000440507:L417V	ENSP00000265022:L476V	L	-	1	2	DGKG	187458421	0.160000	0.22878	0.917000	0.36280	0.785000	0.44390	0.513000	0.22770	-0.134000	0.11516	0.533000	0.62120	TTG	.	.		0.483	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3		Missense_Mutation	C	185975727	A	C	185975727	5	2	23	1	0	0	0	0	0	0	1	0	4471	57	2	5	985	5	DGKG	3	185975727	Splice_Site	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2987699	185975727	12046703	279	2345										
IL1RAP	3556	hgsc.bcm.edu	37	chr3	190338162	190338162	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aataatggaaattacacatgTgttgttacatatccagaaaa	6	5	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:190338162T>C	ENST00000412504.2	+	5	888	c.636T>C	c.(634-636)tgT>tgC	p.C212C	IL1RAP_ENST00000072516.3_Silent_p.C212C|IL1RAP_ENST00000422940.1_Silent_p.C212C|IL1RAP_ENST00000447382.1_Silent_p.C212C|IL1RAP_ENST00000422485.1_Silent_p.C212C|IL1RAP_ENST00000434491.1_Silent_p.C71C|IL1RAP_ENST00000443369.2_Silent_p.C212C|IL1RAP_ENST00000317757.3_Silent_p.C212C|IL1RAP_ENST00000439062.1_Silent_p.C212C			Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein	212	Ig-like C2-type 2.				immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-2 biosynthetic process (GO:0042094)|protein complex assembly (GO:0006461)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		ATTACACATGTGTTGTTACAT	0.353																																					p.C212C		Atlas-SNP	.											.	IL1RAP	96	.	0			c.T636C						.						124	114	117					3																	190338162		2203	4300	6503	SO:0001819	synonymous_variant	3556	exon5			CACATGTGTTGTT	AB006537	CCDS3298.1, CCDS46982.1, CCDS54696.1	3q28	2013-01-11			ENSG00000196083	ENSG00000196083		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5995	protein-coding gene	gene with protein product		602626				9479509, 9065432	Standard	NM_002182		Approved	IL-1RAcP, IL1R3, C3orf13	uc003fsq.3	Q9NPH3	OTTHUMG00000156211	ENST00000412504.2:c.636T>C	chr3.hg19:g.190338162T>C		135.0	0.0		95.0	20.0	NM_001167929	B1NLD0|D3DNW0|O14915|Q86WJ7	Silent	SNP	ENST00000412504.2	hg19	CCDS3298.1	.	.	.	.	.	.	.	.	.	.	T	10.55	1.381719	0.24944	.	.	ENSG00000196083	ENST00000412080	.	.	.	5.22	1.57	0.23409	.	.	.	.	.	T	0.53883	0.1824	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43845	-0.9366	4	.	.	.	.	6.4536	0.21918	0.0:0.2862:0.0:0.7138	.	.	.	.	A	49	.	.	V	+	2	0	IL1RAP	191820856	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	0.421000	0.21280	0.396000	0.25283	0.528000	0.53228	GTG	.	.		0.353	IL1RAP-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343497.1			C	190338162	T	C	190338162	2	2	23	1	0	0	0	0	0	0	0	1	7669	1702	59	2		2	IL1RAP	3	190338162	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	4362435	190338162	7684268	280	2346										
MUC4	4585	hgsc.bcm.edu	37	chr3	195475922	195475922	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catctgaagtaagccttcagCgtgctcacgttcactgtcgg	10	12	4	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:195475922C>T	ENST00000346145.4	-	23	3216	c.3177G>A	c.(3175-3177)acG>acA	p.T1059T	MUC4_ENST00000463781.3_Silent_p.T5295T|MUC4_ENST00000349607.4_Silent_p.T1008T|MUC4_ENST00000475231.1_Silent_p.T5243T	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2052					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGCCTTCAGCGTGCTCACGT	0.532																																					p.T5295T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G15885A						.						72	64	67					3																	195475922		2203	4300	6503	SO:0001819	synonymous_variant	4585	exon24			CTTCAGCGTGCTC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.3177G>A	chr3.hg19:g.195475922C>T		57.0	0.0		49.0	6.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	hg19	CCDS3310.1																																																																																			.	.		0.532	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		T	195475922	C	T	195475922	2	4	23	1	0	0	0	0	0	0	0	1	9987	755	27	1		1	MUC4	3	195475922	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5137760	195475922	2546508	281	2347										
PIGZ	80235	hgsc.bcm.edu	37	chr3	196674301	196674301	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacagggcccagtcctcagtCccccccatgtccaccacctc					rs200103570		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:196674301delC	ENST00000412723.1	-	3	1613	c.1467delG	c.(1465-1467)gggfs	p.G489fs		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	489					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		AGTCCTCAGTCCCCCCCATGT	0.627																																					p.T490fs		Atlas-Indel,Pindel	.											.	PIGZ	34	.	0			c.1468delA						.						65	64	64					3																	196674301		2203	4300	6503	SO:0001589	frameshift_variant	80235	exon3			.	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	30596	protein-coding gene	gene with protein product	"GPI mannosyltransferase 4", "dol-P-Man dependent GPI mannosyltransferase"	611671	"phosphatidylinositol glycan, class Z"			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.1467delG	chr3.hg19:g.196674301delC	ENSP00000413405:p.Gly489fs	64.0	0.0		56.0	17.0	NM_025163	Q9H9G6	Frame_Shift_Del	DEL	ENST00000412723.1	hg19	CCDS3324.1																																																																																			.	.		0.627	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163		-	196674301	C	-	196674301	7	5	23	1	0	1	0	1	0	0	0	0	11914	842	30	0	276	0	PIGZ	3	196674301	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	1198379	196674301	1348129	282	2348										
KIAA1530	57654	hgsc.bcm.edu	37	chr4	1343357	1343357	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctaccgcctgctgatagcAcagctgacccaggagcacgc	11	16	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:1343357A>G	ENST00000389851.4	+	3	591	c.144A>G	c.(142-144)gcA>gcG	p.A48A	UVSSA_ENST00000511216.1_Silent_p.A48A|UVSSA_ENST00000507531.1_Silent_p.A48A	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	48	VHS-like.				protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										TGCTGATAGCACAGCTGACCC	0.622																																					p.A48A		Atlas-SNP	.											.	.	.	.	0			c.A144G						.						74	66	69					4																	1343357		2203	4300	6503	SO:0001819	synonymous_variant	57654	exon3			GATAGCACAGCTG	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"KIAA1530"	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.144A>G	chr4.hg19:g.1343357A>G		87.0	0.0		78.0	32.0	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	hg19	CCDS33938.1																																																																																			.	.		0.622	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894		G	1343357	A	G	1343357	2	3	23	1	0	0	0	0	0	0	0	1	8250	146	6	2		2	KIAA1530	4	1343357	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10		1343357	189810919	283	2349										
HTT	3064	hgsc.bcm.edu	37	chr4	3241599	3241599	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acatgtcatcagcaggatggGcaagctggagcaggtggacg	16	8	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:3241599G>C	ENST00000355072.5	+	67	9387	c.9242G>C	c.(9241-9243)gGc>gCc	p.G3081A		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	3081					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AGCAGGATGGGCAAGCTGGAG	0.577																																					p.G3081A		Atlas-SNP	.											.	HTT	221	.	0			c.G9242C						.						27	28	28					4																	3241599		2141	4233	6374	SO:0001583	missense	3064	exon67			GGATGGGCAAGCT	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.9242G>C	chr4.hg19:g.3241599G>C	ENSP00000347184:p.Gly3081Ala	79.0	0.0		77.0	33.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875073	0.91664	.	.	ENSG00000197386	ENST00000355072	T	0.68025	-0.3	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.81336	0.4801	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.83690	0.0176	10	0.72032	D	0.01	.	17.272	0.87104	0.0:0.0:1.0:0.0	.	3081	P42858	HD_HUMAN	A	3081	ENSP00000347184:G3081A	ENSP00000347184:G3081A	G	+	2	0	HTT	3211397	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.848000	0.99507	2.284000	0.76573	0.655000	0.94253	GGC	.	.		0.577	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		C	3241599	G	C	3241599	3	2	23	1	0	0	0	0	1	0	0	0	7466	1203	42	4	9508	4	HTT	4	3241599	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1898242	3241599	187912677	284	2350										
EVC2	132884	hgsc.bcm.edu	37	chr4	5696122	5696122	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttcttaggccaggagggtatAaaagcaaataaggaatgagc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:5696122delA	ENST00000344408.5	-	3	443	c.390delT	c.(388-390)tttfs	p.F130fs	EVC2_ENST00000344938.1_Frame_Shift_Del_p.F130fs|EVC2_ENST00000310917.2_Frame_Shift_Del_p.F50fs	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	130					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						AGGAGGGTATAAAAGCAAATA	0.413																																					p.I131fs		Atlas-Indel,Pindel	.											.	EVC2	202	.	0			c.391delA						.						140	147	144					4																	5696122		2203	4300	6503	SO:0001589	frameshift_variant	132884	exon3			.	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.390delT	chr4.hg19:g.5696122delA	ENSP00000342144:p.Phe130fs	371.0	0.0		398.0	161.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Frame_Shift_Del	DEL	ENST00000344408.5	hg19	CCDS3382.2																																																																																			.	.		0.413	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		-	5696122	A	-	5696122	7	5	23	1	0	1	0	1	0	0	0	0	5288	359	13	0	3616	0	EVC2	4	5696122	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	2454523	5696122	185458154	285	2351										
AFAP1	60312	hgsc.bcm.edu	37	chr4	7783227	7783227	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acagcctagaggcctttctgTcagcaggagagtagcgggca	14	10	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:7783227T>A	ENST00000360265.4	-	12	1765				AFAP1_ENST00000420658.1_Missense_Mutation_p.D553V|AFAP1_ENST00000358461.2_Intron|AFAP1_ENST00000513842.1_5'UTR|AFAP1_ENST00000382543.3_Missense_Mutation_p.D553V|AFAP1-AS1_ENST00000608442.1_RNA			Q8N556	AFAP1_HUMAN	actin filament associated protein 1							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						GGCCTTTCTGTCAGCAGGAGA	0.537																																					p.D553V		Atlas-SNP	.											.	AFAP1	93	.	0			c.A1658T						.						125	119	120					4																	7783227		692	1591	2283	SO:0001627	intron_variant	60312	exon13			TTTCTGTCAGCAG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1531-2624A>T	chr4.hg19:g.7783227T>A		202.0	0.0		179.0	81.0	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	hg19	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.135403	0.37728	.	.	ENSG00000196526	ENST00000420658;ENST00000382543	T;T	0.15017	2.46;2.46	5.8	3.36	0.38483	.	.	.	.	.	T	0.11324	0.0276	N	0.22421	0.69	0.80722	D	1	B	0.27559	0.181	B	0.29440	0.102	T	0.15925	-1.0420	9	0.31617	T	0.26	.	8.7406	0.34556	0.0:0.0661:0.1291:0.8048	.	553	E9PDT7	.	V	553	ENSP00000410689:D553V;ENSP00000371983:D553V	ENSP00000371983:D553V	D	-	2	0	AFAP1	7834127	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.517000	0.45529	0.458000	0.26988	0.533000	0.62120	GAC	.	.		0.537	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		A	7783227	T	A	7783227	1	1	23	0	1	0	0	0	0	0	0	0	353	1667	58	4		4	AFAP1	4	7783227	Intron	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2087105	7783227	183371049	286	2352										
ABLIM2	84448	hgsc.bcm.edu	37	chr4	8031388	8031389	+	Frame_Shift_Ins	INS	-	-	G													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agggggccaagtacctggacINSggctgtagtgctgtggtgac					rs570874083|rs377709298		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:8031388_8031389insG	ENST00000341937.5	-	11	1226_1227	c.1162_1163insC	c.(1162-1164)cgtfs	p.R388fs	ABLIM2_ENST00000361581.5_Frame_Shift_Ins_p.R388fs|ABLIM2_ENST00000545242.1_Frame_Shift_Ins_p.R388fs|ABLIM2_ENST00000447017.2_Frame_Shift_Ins_p.R388fs|ABLIM2_ENST00000428004.2_Frame_Shift_Ins_p.R399fs|ABLIM2_ENST00000318888.4_Frame_Shift_Ins_p.R156fs|ABLIM2_ENST00000296372.8_Frame_Shift_Ins_p.R388fs|ABLIM2_ENST00000407564.3_Frame_Shift_Ins_p.R388fs|ABLIM2_ENST00000515079.1_5'UTR|ABLIM2_ENST00000546334.1_Frame_Shift_Ins_p.R399fs|ABLIM2_ENST00000361737.5_Frame_Shift_Ins_p.R399fs|ABLIM2_ENST00000514025.1_Frame_Shift_Ins_p.R156fs|ABLIM2_ENST00000505872.1_Frame_Shift_Ins_p.R388fs	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	388					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|myofibril (GO:0030016)	zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|pancreas(3)|prostate(2)|urinary_tract(1)	25						AGTACCTGGACGGCTGTAGTGC	0.53																																					p.R399fs		Pindel	.											.	ABLIM2	59	.	0			c.1196_1197insC						.																																			SO:0001589	frameshift_variant	84448	exon12			.	AB058711	CCDS47011.1, CCDS47012.1, CCDS47013.1, CCDS47014.1, CCDS47015.1, CCDS47016.1, CCDS54719.1, CCDS68669.1	4p16.1	2012-05-16			ENSG00000163995	ENSG00000163995			19195	protein-coding gene	gene with protein product		612544	"actin binding LIM protein 2"				Standard	NM_001130083		Approved	KIAA1808	uc003gkj.4	Q6H8Q1	OTTHUMG00000057427	ENST00000341937.5:c.1163dupC	chr4.hg19:g.8031390_8031390dupG	ENSP00000342813:p.Arg388fs	140.0	0.0		139.0	38.0	NM_001130087	E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Frame_Shift_Ins	INS	ENST00000341937.5	hg19	CCDS47013.1																																																																																			.	.		0.53	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083		G	8031389	-	G	8031388	7	5	23	1	0	1	1	0	0	0	0	0	95	536	19	0	835	0	ABLIM2	4	8031388	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	248161	8031388	183122888	287	2353										
LAP3	51056	hgsc.bcm.edu	37	chr4	17590466	17590466	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagtcttggattgaggaacaGgcaatgggatcattcctcag	12	7	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:17590466G>T	ENST00000226299.4	+	7	1003	c.729G>T	c.(727-729)caG>caT	p.Q243H	LAP3_ENST00000503467.1_3'UTR|LAP3_ENST00000606142.1_Missense_Mutation_p.Q212H|AC006160.5_ENST00000511010.1_RNA	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	243					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						TTGAGGAACAGGCAATGGGAT	0.438																																					p.Q243H		Atlas-SNP	.											.	LAP3	50	.	0			c.G729T						.						102	103	103					4																	17590466		2203	4300	6503	SO:0001583	missense	51056	exon7			GGAACAGGCAATG	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"peptidase S"	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.729G>T	chr4.hg19:g.17590466G>T	ENSP00000226299:p.Gln243His	339.0	0.0		337.0	137.0	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	hg19	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.836790	0.50951	.	.	ENSG00000002549	ENST00000226299;ENST00000513105	T;T	0.45668	0.89;0.89	5.12	1.13	0.20643	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.155036	0.64402	D	0.000017	T	0.53738	0.1815	M	0.64567	1.98	0.43047	D	0.994641	D	0.57899	0.981	D	0.63703	0.917	T	0.50849	-0.8779	10	0.45353	T	0.12	-18.0423	10.1037	0.42519	0.5372:0.0:0.4628:0.0	.	243	P28838	AMPL_HUMAN	H	243;77	ENSP00000226299:Q243H;ENSP00000424724:Q77H	ENSP00000226299:Q243H	Q	+	3	2	LAP3	17199564	0.998000	0.40836	0.520000	0.27837	0.926000	0.56050	0.483000	0.22292	0.200000	0.20447	0.557000	0.71058	CAG	.	.		0.438	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			T	17590466	G	T	17590466	3	4	23	1	0	0	0	0	1	0	0	0	8632	991	35	3	755	3	LAP3	4	17590466	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	9559078	17590466	173563810	288	2354										
GPR125	166647	hgsc.bcm.edu	37	chr4	22389385	22389385	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acattgccagtgctatcggtAccgagcaagggtccctcctg	11	13	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:22389385A>G	ENST00000334304.5	-	19	4178	c.3909T>C	c.(3907-3909)ggT>ggC	p.G1303G	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	1303					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				TGCTATCGGTACCGAGCAAGG	0.433																																					p.G1303G		Atlas-SNP	.											.	GPR125	118	.	0			c.T3909C						.						113	106	108					4																	22389385		2203	4300	6503	SO:0001819	synonymous_variant	166647	exon19			ATCGGTACCGAGC	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.3909T>C	chr4.hg19:g.22389385A>G		236.0	1.0		265.0	113.0	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Silent	SNP	ENST00000334304.5	hg19	CCDS33964.1																																																																																			.	.		0.433	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			G	22389385	A	G	22389385	2	3	23	1	0	0	0	0	0	0	0	1	6647	378	14	2		2	GPR125	4	22389385	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	4798919	22389385	168764891	289	2355										
PPARGC1A	10891	hgsc.bcm.edu	37	chr4	23833257	23833257	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actagcctcattgtcagtggTcacgtctccatctgtcagcg	9	13	6	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:23833257T>C	ENST00000264867.2	-	3	471	c.352A>G	c.(352-354)Acc>Gcc	p.T118A	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	118					androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				TTGTCAGTGGTCACGTCTCCA	0.537																																					p.T118A	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.A352G						.						415	325	355					4																	23833257		2203	4300	6503	SO:0001583	missense	10891	exon3			CAGTGGTCACGTC	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"RNA binding motif (RRM) containing"	9237	protein-coding gene	gene with protein product		604517	"peroxisome proliferative activated receptor, gamma, coactivator 1", "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.352A>G	chr4.hg19:g.23833257T>C	ENSP00000264867:p.Thr118Ala	129.0	0.0		110.0	5.0	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	hg19	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307209	0.40795	.	.	ENSG00000109819	ENST00000264867	T	0.23552	1.9	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.47414	0.1444	L	0.56769	1.78	0.80722	D	1	D	0.64830	0.994	D	0.70716	0.97	T	0.26258	-1.0108	10	0.36615	T	0.2	-6.5014	16.5582	0.84512	0.0:0.0:0.0:1.0	.	118	Q9UBK2	PRGC1_HUMAN	A	118	ENSP00000264867:T118A	ENSP00000264867:T118A	T	-	1	0	PPARGC1A	23442355	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.308000	0.77769	0.533000	0.62120	ACC	.	.		0.537	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261		C	23833257	T	C	23833257	3	2	23	1	0	0	0	0	1	0	0	0	12309	1667	58	2	2088	2	PPARGC1A	4	23833257	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1443872	23833257	167321019	290	2356										
LGI2	55203	hgsc.bcm.edu	37	chr4	25005399	25005399	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccgggagtccccgatgaagcGggtaagggaaaggtagaggg	19	7	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:25005399G>A	ENST00000382114.4	-	8	1497	c.1312C>T	c.(1312-1314)Cgc>Tgc	p.R438C		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	438						extracellular region (GO:0005576)		p.R438S(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				CCGATGAAGCGGGTAAGGGAA	0.547																																					p.R438C		Atlas-SNP	.											.	LGI2	62	.	1	Substitution - Missense(1)	lung(1)	c.C1312T						.						178	190	186					4																	25005399		2203	4300	6503	SO:0001583	missense	55203	exon8			TGAAGCGGGTAAG	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.1312C>T	chr4.hg19:g.25005399G>A	ENSP00000371548:p.Arg438Cys	163.0	0.0		207.0	96.0	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	hg19	CCDS3431.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255992	0.59321	.	.	ENSG00000153012	ENST00000382114;ENST00000282970	T	0.81163	-1.46	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.79015	0.4375	L	0.54323	1.7	0.80722	D	1	P	0.51791	0.948	P	0.45310	0.476	T	0.80986	-0.1137	10	0.59425	D	0.04	-24.2404	12.6604	0.56811	0.0:0.0:0.7238:0.2762	.	438	Q8N0V4	LGI2_HUMAN	C	438;86	ENSP00000371548:R438C	ENSP00000282970:R86C	R	-	1	0	LGI2	24614497	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.233000	0.58651	2.618000	0.88619	0.557000	0.71058	CGC	.	.		0.547	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1			A	25005399	G	A	25005399	3	1	23	1	0	0	0	0	1	0	0	0	8761	1116	39	1	329	1	LGI2	4	25005399	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1172142	25005399	166148877	291	2357										
RPL9	6133	hgsc.bcm.edu	37	chr4	39458043	39458043	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tacctggtctcatccgaaccCtgcggatatatttttcaccc	6	14	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:39458043C>A	ENST00000449470.2	-	4	822	c.374G>T	c.(373-375)aGg>aTg	p.R125M	LIAS_ENST00000340169.2_5'Flank|LIAS_ENST00000513731.1_5'Flank|RPL9_ENST00000295955.9_Missense_Mutation_p.R125M|LIAS_ENST00000261434.3_5'Flank|LIAS_ENST00000381846.1_5'Flank	NM_001024921.2	NP_001020092.1	P32969	RL9_HUMAN	ribosomal protein L9	125					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribosome (GO:0005840)	RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|skin(1)	8						CATCCGAACCCTGCGGATATA	0.408																																					p.R125M		Atlas-SNP	.											.	RPL9	16	.	0			c.G374T						.						48	50	50					4																	39458043		2203	4300	6503	SO:0001583	missense	6133	exon5			CGAACCCTGCGGA	D14531	CCDS3452.1	4p13	2011-04-06			ENSG00000163682	ENSG00000163682		"L ribosomal proteins"	10369	protein-coding gene	gene with protein product		603686				8597601, 8415001	Standard	XM_005262661		Approved	L9	uc021sso.1	P32969	OTTHUMG00000099367	ENST00000449470.2:c.374G>T	chr4.hg19:g.39458043C>A	ENSP00000400467:p.Arg125Met	690.0	0.0		608.0	247.0	NM_000661		Missense_Mutation	SNP	ENST00000449470.2	hg19	CCDS3452.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.69|18.69	3.678088|3.678088	0.68042|0.68042	.|.	.|.	ENSG00000163682|ENSG00000163682	ENST00000508595|ENST00000295955;ENST00000449470;ENST00000394452;ENST00000503040;ENST00000504470	.|.	.|.	.|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|Ribosomal protein L6, alpha-beta domain (3);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.70116|0.70116	0.3187|0.3187	M|M	0.73753|0.73753	2.245|2.245	0.80722|0.80722	D|D	1|1	.|P;P	.|0.48764	.|0.915;0.567	.|P;P	.|0.46253	.|0.474;0.509	T|T	0.74990|0.74990	-0.3475|-0.3475	5|9	.|0.72032	.|D	.|0.01	.|.	18.7279|18.7279	0.91722|0.91722	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|125;125	.|B4DLV8;P32969	.|.;RL9_HUMAN	H|M	121|125	.|.	.|ENSP00000346022:R125M	Q|R	-|-	3|2	2|0	RPL9|RPL9	39134438|39134438	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.262000|0.262000	0.26303|0.26303	7.741000|7.741000	0.84997|0.84997	2.665000|2.665000	0.90641|0.90641	0.561000|0.561000	0.74099|0.74099	CAG|AGG	.	.		0.408	RPL9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361018.1			A	39458043	C	A	39458043	3	1	23	1	0	0	0	0	1	0	0	0	13618	681	24	3	216	3	RPL9	4	39458043	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	14452644	39458043	151696233	292	2358										
PDS5A	23244	hgsc.bcm.edu	37	chr4	39891910	39891910	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgcacaggtgcgattctttcCaacagaaatttgaccatctc	7	11	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:39891910C>A	ENST00000303538.8	-	17	2384	c.1845G>T	c.(1843-1845)ttG>ttT	p.L615F		NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						CGATTCTTTCCAACAGAAATT	0.363																																					p.L615F		Atlas-SNP	.											.	PDS5A	114	.	0			c.G1845T						.						79	75	76					4																	39891910		1819	4086	5905	SO:0001583	missense	23244	exon17			TCTTTCCAACAGA	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.1845G>T	chr4.hg19:g.39891910C>A	ENSP00000303427:p.Leu615Phe	74.0	0.0		78.0	27.0	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058098	0.76074	.	.	ENSG00000121892	ENST00000303538	.	.	.	5.46	3.73	0.42828	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69691	0.3139	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.67848	-0.5564	8	.	.	.	-6.2637	10.3707	0.44053	0.0:0.7874:0.0:0.2126	.	615	Q29RF7	PDS5A_HUMAN	F	615	.	.	L	-	3	2	PDS5A	39568305	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.278000	0.51662	0.786000	0.33708	-0.140000	0.14226	TTG	.	.		0.363	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		A	39891910	C	A	39891910	3	1	23	1	0	0	0	0	1	0	0	0	11700	593	21	3	2236	3	PDS5A	4	39891910	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	433867	39891910	151262366	293	2359										
LIMCH1	22998	hgsc.bcm.edu	37	chr4	41621359	41621359	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaaagcaatcagacggcctaCgtccccgcgcctctgagaaa	9	14	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:41621359C>T	ENST00000313860.7	+	8	891	c.837C>T	c.(835-837)taC>taT	p.Y279Y	LIMCH1_ENST00000381753.4_Silent_p.Y125Y|LIMCH1_ENST00000509454.1_Silent_p.Y127Y|LIMCH1_ENST00000509638.1_Silent_p.Y120Y|LIMCH1_ENST00000503057.1_Silent_p.Y120Y|LIMCH1_ENST00000512632.1_Silent_p.Y279Y|LIMCH1_ENST00000512820.1_Silent_p.Y279Y|LIMCH1_ENST00000511496.1_Silent_p.Y120Y|LIMCH1_ENST00000513024.1_Silent_p.Y120Y|LIMCH1_ENST00000512946.1_Silent_p.Y279Y|LIMCH1_ENST00000509277.1_Silent_p.Y125Y|LIMCH1_ENST00000396595.3_Silent_p.Y125Y|LIMCH1_ENST00000514096.1_Silent_p.Y132Y|LIMCH1_ENST00000508501.1_Silent_p.Y279Y	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	279					actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						AGACGGCCTACGTCCCCGCGC	0.572																																					p.Y279Y		Atlas-SNP	.											.	LIMCH1	233	.	0			c.C837T						.						89	90	89					4																	41621359		2203	4300	6503	SO:0001819	synonymous_variant	22998	exon8			GGCCTACGTCCCC	AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.837C>T	chr4.hg19:g.41621359C>T		95.0	0.0		111.0	54.0	NM_014988	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Silent	SNP	ENST00000313860.7	hg19	CCDS33977.1	.	.	.	.	.	.	.	.	.	.	C	3.110	-0.182780	0.06340	.	.	ENSG00000064042	ENST00000508466	.	.	.	5.74	-5.27	0.02763	.	.	.	.	.	T	0.65481	0.2695	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65553	-0.6140	4	.	.	.	-15.6245	16.7172	0.85399	0.0:0.3074:0.0:0.6926	.	.	.	.	M	114	.	.	T	+	2	0	LIMCH1	41316116	0.002000	0.14202	0.488000	0.27440	0.379000	0.30106	-1.427000	0.02441	-1.497000	0.01826	-1.008000	0.02478	ACG	.	.		0.572	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988		T	41621359	C	T	41621359	2	4	23	1	0	0	0	0	0	0	0	1	8806	547	19	1		1	LIMCH1	4	41621359	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1729449	41621359	149532917	294	2360										
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57181271	57181271	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgagagacagaccatgcccCggccctacacgttccaggtg	11	15	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:57181271C>T	ENST00000504228.1	+	6	1708	c.1603C>T	c.(1603-1605)Cgg>Tgg	p.R535W	KIAA1211_ENST00000541073.1_Missense_Mutation_p.R528W|KIAA1211_ENST00000264229.6_Missense_Mutation_p.R535W			Q6ZU35	K1211_HUMAN	KIAA1211	535										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					GACCATGCCCCGGCCCTACAC	0.647																																					p.R535W		Atlas-SNP	.											.	KIAA1211	178	.	0			c.C1603T						.						15	21	19					4																	57181271		2064	4194	6258	SO:0001583	missense	57482	exon8			ATGCCCCGGCCCT	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1603C>T	chr4.hg19:g.57181271C>T	ENSP00000423366:p.Arg535Trp	266.0	1.0		305.0	124.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	hg19	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.823247	0.71143	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.02395	4.31;4.31;4.31	4.86	-1.26	0.09376	.	.	.	.	.	T	0.12347	0.0300	M	0.71581	2.175	0.49483	D	0.99979	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.01093	-1.1454	9	0.87932	D	0	-11.4339	14.7464	0.69492	0.386:0.614:0.0:0.0	.	528;528;535	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	W	535;535;528;445	ENSP00000264229:R535W;ENSP00000423366:R535W;ENSP00000444006:R528W	ENSP00000264229:R535W	R	+	1	2	KIAA1211	56876028	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	3.137000	0.50562	-0.121000	0.11787	-0.397000	0.06425	CGG	.	.		0.647	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		T	57181271	C	T	57181271	3	4	23	1	0	0	0	0	1	0	0	0	8224	643	23	1	1621	1	KIAA1211	4	57181271	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	15559912	57181271	133973005	295	2361										
REST	5978	hgsc.bcm.edu	37	chr4	57777460	57777460	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caagggccccattcgctgtgAccgctgcggctacaatacta	10	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:57777460A>G	ENST00000309042.7	+	2	970	c.656A>G	c.(655-657)gAc>gGc	p.D219G	REST_ENST00000514063.1_3'UTR	NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	219					cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					ATTCGCTGTGACCGCTGCGGC	0.488																																					p.D219G		Atlas-SNP	.											.	REST	104	.	0			c.A656G						.						54	51	52					4																	57777460		2203	4300	6503	SO:0001583	missense	5978	exon2			GCTGTGACCGCTG	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.656A>G	chr4.hg19:g.57777460A>G	ENSP00000311816:p.Asp219Gly	199.0	0.0		152.0	61.0	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	hg19	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306562	0.81247	.	.	ENSG00000084093	ENST00000456010;ENST00000309042;ENST00000358605	T	0.29142	1.58	5.25	5.25	0.73442	Zinc finger, C2H2-like (1);	0.077335	0.52532	D	0.000072	T	0.40862	0.1134	N	0.21545	0.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.981;1.0	T	0.18777	-1.0326	10	0.32370	T	0.25	-35.5772	14.9902	0.71381	1.0:0.0:0.0:0.0	.	219;219	Q13127-2;Q13127	.;REST_HUMAN	G	219	ENSP00000311816:D219G	ENSP00000311816:D219G	D	+	2	0	REST	57472217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.107000	0.94261	2.220000	0.72140	0.533000	0.62120	GAC	.	.		0.488	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		G	57777460	A	G	57777460	3	3	23	1	0	0	0	0	1	0	0	0	13249	275	10	2	658	2	REST	4	57777460	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	596189	57777460	133376816	296	2362										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62849207	62849207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tatcatgctggtggaggtttTtgagagtgaacattcacgta	12	5	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:62849207T>C	ENST00000514591.1	+	18	3247	c.2918T>C	c.(2917-2919)tTt>tCt	p.F973S	LPHN3_ENST00000545650.1_Missense_Mutation_p.F973S|LPHN3_ENST00000506720.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000506746.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000511324.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000507164.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000508693.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000506700.1_Missense_Mutation_p.F973S|LPHN3_ENST00000514157.1_Missense_Mutation_p.F973S|LPHN3_ENST00000507625.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000509896.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000514996.1_Missense_Mutation_p.F973S|LPHN3_ENST00000512091.2_Missense_Mutation_p.F973S|LPHN3_ENST00000508946.1_Missense_Mutation_p.F973S|LPHN3_ENST00000504896.1_Missense_Mutation_p.F973S			Q9HAR2	LPHN3_HUMAN	latrophilin 3	960					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GTGGAGGTTTTTGAGAGTGAA	0.478																																					p.F973S		Atlas-SNP	.											.	LPHN3	800	.	0			c.T2918C						.						201	191	195					4																	62849207		1950	4158	6108	SO:0001583	missense	23284	exon16			AGGTTTTTGAGAG	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.2918T>C	chr4.hg19:g.62849207T>C	ENSP00000422533:p.Phe973Ser	155.0	0.0		163.0	12.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.816145	0.90790	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17	5.72	5.72	0.89469	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.67859	0.2938	M	0.89785	3.06	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.83275	0.996;0.996;0.994	T	0.75651	-0.3244	10	0.87932	D	0	.	16.0129	0.80417	0.0:0.0:0.0:1.0	.	973;960;973	E9PE04;Q9HAR2;Q9HAR2-2	.;LPHN3_HUMAN;.	S	973;973;1041;1041;973;973;960;973;1041;1041;1041;973;973;973;1041;1041;973	ENSP00000423388:F973S;ENSP00000422533:F973S;ENSP00000423787:F1041S;ENSP00000425033:F1041S;ENSP00000424120:F973S;ENSP00000439831:F973S;ENSP00000421476:F1041S;ENSP00000424030:F1041S;ENSP00000421372:F1041S;ENSP00000425201:F973S;ENSP00000423434:F973S;ENSP00000421627:F973S;ENSP00000420931:F1041S;ENSP00000425884:F1041S;ENSP00000424258:F973S	ENSP00000280009:F973S	F	+	2	0	LPHN3	62531802	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.040000	0.89188	2.184000	0.69523	0.482000	0.46254	TTT	.	.		0.478	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			C	62849207	T	C	62849207	3	2	23	1	0	0	0	0	1	0	0	0	8926	1841	64	2	2980	2	LPHN3	4	62849207	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	5071747	62849207	128305069	297	2363										
CSN1S1	1446	hgsc.bcm.edu	37	chr4	70810695	70810695	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cactgctcatgaaaattatgAaaaaaataacgtcatgctac							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:70810695delA	ENST00000246891.4	+	15	579	c.530delA	c.(529-531)gaafs	p.E177fs	CSN1S1_ENST00000505782.1_Frame_Shift_Del_p.E161fs|CSN1S1_ENST00000444405.3_Frame_Shift_Del_p.E168fs|CSN1S1_ENST00000507772.1_Frame_Shift_Del_p.E169fs|CSN1S1_ENST00000507763.1_Frame_Shift_Del_p.E168fs	NM_001890.1	NP_001881.1	P47710	CASA1_HUMAN	casein alpha s1	177						extracellular region (GO:0005576)|extracellular space (GO:0005615)	transporter activity (GO:0005215)			lung(5)|prostate(1)|upper_aerodigestive_tract(1)	7						GAAAATTATGAAAAAAATAAC	0.393																																					p.E177fs		Atlas-Indel,Pindel	.											.	CSN1S1	20	.	0			c.529delG						.						165	155	158					4																	70810695		1858	4101	5959	SO:0001589	frameshift_variant	1446	exon15			.	X78416	CCDS47067.1, CCDS54769.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000126545	ENSG00000126545			2445	protein-coding gene	gene with protein product		115450	"casein, alpha"	CASA, CSN1		9050925, 7619062	Standard	NM_001890		Approved		uc003hep.1	P47710	OTTHUMG00000160843	ENST00000246891.4:c.530delA	chr4.hg19:g.70810695delA	ENSP00000246891:p.Glu177fs	141.0	0.0		154.0	68.0	NM_001890	A1A510|A1A511|E9PB60|Q4PNR5	Frame_Shift_Del	DEL	ENST00000246891.4	hg19	CCDS47067.1																																																																																			.	.		0.393	CSN1S1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362629.1			-	70810695	A	-	70810695	7	5	23	1	0	1	0	1	0	0	0	0	3949	246	9	0	584	0	CSN1S1	4	70810695	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	7961488	70810695	120343581	298	2364										
AMTN	401138	hgsc.bcm.edu	37	chr4	71394475	71394475	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcacacaacttggagcccaGgtaaaaattatgcttaatat	7	8	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:71394475G>A	ENST00000339336.4	+	6	460	c.330G>A	c.(328-330)caG>caA	p.Q110Q	AMTN_ENST00000504451.1_Splice_Site_p.Q109Q	NM_212557.2	NP_997722.1	Q6UX39	AMTN_HUMAN	amelotin	110					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|odontogenesis of dentin-containing tooth (GO:0042475)	basal lamina (GO:0005605)|cell-cell junction (GO:0005911)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)|skin(1)	19			Lung(101;0.235)			TTGGAGCCCAGGTAAAAATTA	0.333																																					p.Q110Q		Atlas-SNP	.											.	AMTN	28	.	0			c.G330A						.						86	90	89					4																	71394475		2202	4299	6501	SO:0001630	splice_region_variant	401138	exon6			AGCCCAGGTAAAA	AY358528	CCDS3542.1, CCDS68716.1	4q13.3	2006-12-12			ENSG00000187689	ENSG00000187689			33188	protein-coding gene	gene with protein product		610912				16304441	Standard	NM_001286731		Approved	UNQ689, RSTI689	uc003hfk.1	Q6UX39	OTTHUMG00000129906	ENST00000339336.4:c.330+1G>A	chr4.hg19:g.71394475G>A		211.0	0.0		256.0	93.0	NM_212557	Q0P503|Q0P506	Silent	SNP	ENST00000339336.4	hg19	CCDS3542.1																																																																																			.	.		0.333	AMTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252157.1	NM_212557	Silent	A	71394475	G	A	71394475	5	1	23	1	0	0	0	0	0	0	1	0	590	1014	35	3	348	3	AMTN	4	71394475	Splice_Site	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	583780	71394475	119759801	299	2365										
IGJ	3512	hgsc.bcm.edu	37	chr4	71532164	71532164	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctttcacatgaacagccttaAtaaaaaccgccaggactccc	5	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:71532164A>T	ENST00000254801.4	-	1	213	c.44T>A	c.(43-45)aTt>aAt	p.I15N	ENAM_ENST00000472903.1_Intron|IGJ_ENST00000543780.1_Missense_Mutation_p.I15N	NM_144646.3	NP_653247.1	P01591	IGJ_HUMAN	immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides	15					adaptive immune response (GO:0002250)|antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of respiratory burst (GO:0060267)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|dimeric IgA immunoglobulin complex (GO:0071750)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|pentameric IgM immunoglobulin complex (GO:0071756)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7			Lung(101;0.235)			AACAGCCTTAATAAAAACCGC	0.363																																					p.I15N		Atlas-SNP	.											.	IGJ	13	.	0			c.T44A						.						72	72	72					4																	71532164		2203	4300	6503	SO:0001583	missense	3512	exon1			GCCTTAATAAAAA	M12759	CCDS3545.1	4q21	2012-10-02			ENSG00000132465	ENSG00000132465		"Immunoglobulins / IGJ linker"	5713	protein-coding gene	gene with protein product	"immunoglobulin J chain", "IgJ chain"	147790				3016707, 2984306	Standard	NM_144646		Approved	IGCJ, JCH	uc003hfn.4	P01591	OTTHUMG00000129909	ENST00000254801.4:c.44T>A	chr4.hg19:g.71532164A>T	ENSP00000254801:p.Ile15Asn	209.0	0.0		223.0	11.0	NM_144646		Missense_Mutation	SNP	ENST00000254801.4	hg19	CCDS3545.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.387407	0.25031	.	.	ENSG00000132465	ENST00000254801;ENST00000510437;ENST00000543780;ENST00000510614;ENST00000391614;ENST00000470866	.	.	.	5.78	3.49	0.39957	.	0.722701	0.12334	N	0.478077	T	0.19046	0.0457	N	0.08118	0	0.19945	N	0.999941	B;B	0.23735	0.027;0.09	B;B	0.24394	0.029;0.053	T	0.16453	-1.0402	9	0.72032	D	0.01	.	5.7415	0.18096	0.6285:0.275:0.0965:0.0	.	15;15	D6RHJ6;P01591	.;IGJ_HUMAN	N	15	.	ENSP00000254801:I15N	I	-	2	0	IGJ	71751028	0.922000	0.31269	0.998000	0.56505	0.304000	0.27724	1.634000	0.37123	1.024000	0.39682	0.533000	0.62120	ATT	.	.		0.363	IGJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252160.1	NM_144646		T	71532164	A	T	71532164	3	4	23	1	0	0	0	0	1	0	0	0	7601	101	4	4	451	4	IGJ	4	71532164	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	137689	71532164	119622112	300	2366										
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73149372	73149372	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtatggagcagtatcgtgcCaacacttccatttgacagaa	10	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:73149372C>T	ENST00000286657.4	-	22	3135	c.3099G>A	c.(3097-3099)ttG>ttA	p.L1033L		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	1033	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGTATCGTGCCAACACTTCCA	0.408																																					p.L1033L	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											.	ADAMTS3	164	.	0			c.G3099A						.						99	92	94					4																	73149372		2203	4300	6503	SO:0001819	synonymous_variant	9508	exon22			TCGTGCCAACACT	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.3099G>A	chr4.hg19:g.73149372C>T		58.0	0.0		55.0	23.0	NM_014243	A1L3U9|Q9BXZ8	Silent	SNP	ENST00000286657.4	hg19	CCDS3553.1																																																																																			.	.		0.408	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			T	73149372	C	T	73149372	2	4	23	1	0	0	0	0	0	0	0	1	267	593	21	3		3	ADAMTS3	4	73149372	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1617208	73149372	118004904	301	2367										
PF4V1	5197	hgsc.bcm.edu	37	chr4	74719172	74719172	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgccagttgtggtcgccttCgccagaggtgagagcagaaa	14	10	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:74719172C>T	ENST00000226524.3	+	1	267	c.93C>T	c.(91-93)ttC>ttT	p.F31F		NM_002620.2	NP_002611.1	P10720	PF4V_HUMAN	platelet factor 4 variant 1	31					cell chemotaxis (GO:0060326)|immune response (GO:0006955)	extracellular space (GO:0005615)	heparin binding (GO:0008201)			endometrium(1)|liver(2)	3	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			TGGTCGCCTTCGCCAGAGGTG	0.662																																					p.F31F		Atlas-SNP	.											.	PF4V1	8	.	0			c.C93T						.						20	21	21					4																	74719172		2203	4300	6503	SO:0001819	synonymous_variant	5197	exon1			CGCCTTCGCCAGA	M26167	CCDS3561.1	4q12-q21	2008-08-15			ENSG00000109272	ENSG00000109272			8862	protein-coding gene	gene with protein product		173461				2725510	Standard	NM_002620		Approved	SCYB4V1, CXCL4V1, CXCL4L1	uc003hhg.1	P10720	OTTHUMG00000130177	ENST00000226524.3:c.93C>T	chr4.hg19:g.74719172C>T		230.0	0.0		227.0	86.0	NM_002620	A1L4S0	Silent	SNP	ENST00000226524.3	hg19	CCDS3561.1																																																																																			.	.		0.662	PF4V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252495.1			T	74719172	C	T	74719172	2	4	23	1	0	0	0	0	0	0	0	1	11762	883	31	1		1	PF4V1	4	74719172	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1569800	74719172	116435104	302	2368										
PPEF2	5470	hgsc.bcm.edu	37	chr4	76811198	76811198	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccccgtgtaactgtcgggtAcctctatggattcatagtca	10	11	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:76811198A>G	ENST00000286719.7	-	5	685	c.329T>C	c.(328-330)gTa>gCa	p.V110A	PPEF2_ENST00000510607.1_5'Flank	NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	110					detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			ACTGTCGGGTACCTCTATGGA	0.527																																					p.V110A	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.T329C						.						250	218	229					4																	76811198		2203	4300	6503	SO:0001583	missense	5470	exon5			TCGGGTACCTCTA	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9244	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, beta isozyme"	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.329T>C	chr4.hg19:g.76811198A>G	ENSP00000286719:p.Val110Ala	168.0	0.0		178.0	31.0	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	hg19	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.962355	0.74016	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.55760	0.5	4.8	4.8	0.61643	Serine/threonine phosphatase, PPP5 (1);	0.064498	0.64402	D	0.000008	T	0.76047	0.3933	M	0.89904	3.07	0.48696	D	0.99969	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.81331	-0.0981	10	0.87932	D	0	-4.9812	12.3127	0.54938	1.0:0.0:0.0:0.0	.	110;110	O14830-2;O14830	.;PPE2_HUMAN	A	110	ENSP00000286719:V110A	ENSP00000286719:V110A	V	-	2	0	PPEF2	77030222	1.000000	0.71417	0.929000	0.37066	0.586000	0.36452	6.939000	0.75911	1.808000	0.52836	0.260000	0.18958	GTA	.	.		0.527	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		G	76811198	A	G	76811198	3	3	23	1	0	0	0	0	1	0	0	0	12317	391	14	2	1984	2	PPEF2	4	76811198	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2092026	76811198	114343078	303	2369										
CCDC158	339965	hgsc.bcm.edu	37	chr4	77300543	77300543	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcatatacatagagttttggTttcttgcttgctctctaaga	8	7	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:77300543T>A	ENST00000388914.3	-	8	1081	c.929A>T	c.(928-930)aAc>aTc	p.N310I	CCDC158_ENST00000434846.2_Missense_Mutation_p.N310I	NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	310										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						AGAGTTTTGGTTTCTTGCTTG	0.388																																					p.N310I		Atlas-SNP	.											.	CCDC158	114	.	0			c.A929T						.						124	113	117					4																	77300543		1857	4099	5956	SO:0001583	missense	339965	exon8			TTTTGGTTTCTTG	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.929A>T	chr4.hg19:g.77300543T>A	ENSP00000373566:p.Asn310Ile	79.0	0.0		83.0	39.0	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	hg19	CCDS43242.1	.	.	.	.	.	.	.	.	.	.	T	14.92	2.678121	0.47886	.	.	ENSG00000163749	ENST00000388914;ENST00000318586;ENST00000434846	T;T	0.78924	-1.22;1.19	5.35	5.35	0.76521	.	0.000000	0.56097	D	0.000024	T	0.79251	0.4414	N	0.19112	0.55	0.39836	D	0.973033	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.80989	-0.1136	10	0.44086	T	0.13	.	12.876	0.57989	0.0:0.0:0.0:1.0	.	310;310	Q5M9N0-3;Q5M9N0	.;CD158_HUMAN	I	310	ENSP00000373566:N310I;ENSP00000401742:N310I	ENSP00000316815:N310I	N	-	2	0	CCDC158	77519567	1.000000	0.71417	1.000000	0.80357	0.160000	0.22226	2.785000	0.47782	2.024000	0.59613	0.528000	0.53228	AAC	.	.		0.388	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		A	77300543	T	A	77300543	3	1	23	1	0	0	0	0	1	0	0	0	2792	1725	60	4	2480	4	CCDC158	4	77300543	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	489345	77300543	113853733	304	2370										
HELQ	113510	hgsc.bcm.edu	37	chr4	84358187	84358187	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acaggacacaggttgccattGccaatattcttcaagttctt	7	10	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:84358187G>A	ENST00000295488.3	-	9	2034	c.1872C>T	c.(1870-1872)ggC>ggT	p.G624G	HELQ_ENST00000510985.1_Silent_p.G557G	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	624	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						GGTTGCCATTGCCAATATTCT	0.393								Other identified genes with known or suspected DNA repair function																													p.G624G		Atlas-SNP	.											.	HELQ	95	.	0			c.C1872T						.						152	147	149					4																	84358187		2203	4300	6503	SO:0001819	synonymous_variant	113510	exon9			GCCATTGCCAATA	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1872C>T	chr4.hg19:g.84358187G>A		137.0	0.0		179.0	76.0	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	hg19	CCDS3603.1																																																																																			.	.		0.393	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		A	84358187	G	A	84358187	2	1	23	1	0	0	0	0	0	0	0	1	7056	1306	46	3		3	HELQ	4	84358187	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	7057644	84358187	106796089	305	2371										
NKX6-1	4825	hgsc.bcm.edu	37	chr4	85419145	85419145	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggctgccgagggatgagagCccccccgtggccgggggctt					rs371770743		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:85419145delC	ENST00000295886.4	-	1	458	c.237delG	c.(235-237)gggfs	p.G79fs	NKX6-1_ENST00000515820.2_5'Flank	NM_006168.2	NP_006159.2	P78426	NKX61_HUMAN	NK6 homeobox 1	79					cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|cellular response to peptide hormone stimulus (GO:0071375)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|negative regulation of glial cell differentiation (GO:0045686)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|organ morphogenesis (GO:0009887)|pancreas development (GO:0031016)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of insulin secretion (GO:0032024)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of axon extension (GO:0030516)|regulation of neuron migration (GO:2001222)|regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification (GO:0021912)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)|response to drug (GO:0042493)|response to nicotine (GO:0035094)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	15		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.0013)		GGGATGAGAGCCCCCCCGTGG	0.746																																					p.L80fs		Atlas-Indel,Pindel	.											.,1	NKX6-1	38	.	0			c.238delC						.						5	8	7					4																	85419145		1946	3968	5914	SO:0001589	frameshift_variant	4825	exon1			.	AH007313	CCDS3607.1	4q21.33	2012-03-09	2007-07-09	2002-10-04	ENSG00000163623	ENSG00000163623		"Homeoboxes / ANTP class : NKL subclass"	7839	protein-coding gene	gene with protein product		602563	"NK homeobox (Drosophila), family 6, A", "NK6 transcription factor related, locus 1 (Drosophila)"	NKX6A		9119408	Standard	NM_006168		Approved	Nkx6.1	uc003hpa.1	P78426	OTTHUMG00000130426	ENST00000295886.4:c.237delG	chr4.hg19:g.85419145delC	ENSP00000295886:p.Gly79fs	71.0	0.0		89.0	40.0	NM_006168		Frame_Shift_Del	DEL	ENST00000295886.4	hg19	CCDS3607.1																																																																																			.	.		0.746	NKX6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252814.2	NM_006168		-	85419145	C	-	85419145	7	5	23	1	0	1	0	1	0	0	0	0	10466	726	26	0	878	0	NKX6-1	4	85419145	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	1060958	85419145	105735131	306	2372										
ARHGAP24	83478	hgsc.bcm.edu	37	chr4	86916149	86916149	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtaatgcagaaggtcttgagAaaacccaaaccacccccaat							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:86916149delA	ENST00000395184.1	+	9	1808	c.1342delA	c.(1342-1344)aaafs	p.K448fs	ARHGAP24_ENST00000395183.2_Frame_Shift_Del_p.K353fs|ARHGAP24_ENST00000264343.4_Frame_Shift_Del_p.K355fs	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	448					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		AGGTCTTGAGAAAACCCAAAC	0.498																																					p.E447fs		Atlas-Indel,Pindel	.											.	ARHGAP24	116	.	0			c.1341delG						.						59	66	64					4																	86916149		2203	4300	6503	SO:0001589	frameshift_variant	83478	exon9			.	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.1342delA	chr4.hg19:g.86916149delA	ENSP00000378611:p.Lys448fs	158.0	0.0		162.0	59.0	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Frame_Shift_Del	DEL	ENST00000395184.1	hg19	CCDS34025.1																																																																																			.	.		0.498	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		-	86916149	A	-	86916149	7	5	23	1	0	1	0	1	0	0	0	0	873	247	9	0	1488	0	ARHGAP24	4	86916149	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	1497004	86916149	104238127	307	2373										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87622823	87622823	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tatagccttggatatctttgGccctcagaaaatggatccaa	8	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:87622823G>A	ENST00000411767.2	+	7	1127	c.1064G>A	c.(1063-1065)gGc>gAc	p.G355D	PTPN13_ENST00000427191.2_Missense_Mutation_p.G355D|PTPN13_ENST00000511467.1_Missense_Mutation_p.G355D|PTPN13_ENST00000316707.6_Missense_Mutation_p.G355D|PTPN13_ENST00000436978.1_Missense_Mutation_p.G355D			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	355					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		GATATCTTTGGCCCTCAGAAA	0.453																																					p.G355D		Atlas-SNP	.											.	PTPN13	203	.	0			c.G1064A						.						86	83	84					4																	87622823		1909	4122	6031	SO:0001583	missense	5783	exon7			TCTTTGGCCCTCA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.1064G>A	chr4.hg19:g.87622823G>A	ENSP00000407249:p.Gly355Asp	216.0	0.0		194.0	83.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290675	0.59976	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	6.03	5.19	0.71726	.	0.000000	0.52532	D	0.000072	T	0.32194	0.0821	M	0.72894	2.215	0.51233	D	0.999917	B;B;B;B	0.32753	0.383;0.278;0.182;0.278	B;B;B;B	0.34093	0.175;0.126;0.059;0.126	T	0.08534	-1.0717	10	0.44086	T	0.13	.	15.1117	0.72362	0.0673:0.0:0.9327:0.0	.	355;355;355;355	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	D	355;355;355;355;355;323	ENSP00000408368:G355D;ENSP00000394794:G355D;ENSP00000322675:G355D;ENSP00000407249:G355D;ENSP00000426626:G355D	ENSP00000322675:G355D	G	+	2	0	PTPN13	87841847	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.109000	0.64615	1.561000	0.49584	0.655000	0.94253	GGC	.	.		0.453	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87622823	G	A	87622823	3	1	23	1	0	0	0	0	1	0	0	0	12795	1203	42	3	1086	3	PTPN13	4	87622823	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	706674	87622823	103531453	308	2374										
HSD17B13	345275	hgsc.bcm.edu	37	chr4	88239575	88239575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttcggcactcagctgcagttTcctccacaccgcgctgtaat	8	15	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:88239575T>C	ENST00000328546.4	-	2	288	c.224A>G	c.(223-225)gAa>gGa	p.E75G	RP11-529H2.2_ENST00000508163.1_RNA|HSD17B13_ENST00000302219.6_Intron	NM_178135.3	NP_835236.2	Q7Z5P4	DHB13_HUMAN	hydroxysteroid (17-beta) dehydrogenase 13	75						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	8		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.000308)		AGCTGCAGTTTCCTCCACACC	0.443																																					p.E75G		Atlas-SNP	.											.	HSD17B13	27	.	0			c.A224G						.						107	92	98					4																	88239575		2203	4300	6503	SO:0001583	missense	345275	exon2			GCAGTTTCCTCCA		CCDS3618.1, CCDS47097.1	4q22.1	2011-09-20			ENSG00000170509	ENSG00000170509	1.1.-.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	18685	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 16C, member 3"	612127				19027726	Standard	NM_178135		Approved	SCDR9, SDR16C3	uc003hqo.2	Q7Z5P4	OTTHUMG00000130602	ENST00000328546.4:c.224A>G	chr4.hg19:g.88239575T>C	ENSP00000333300:p.Glu75Gly	86.0	0.0		118.0	5.0	NM_178135	A8K9R9|Q2M1L5|Q86W22|Q86W23	Missense_Mutation	SNP	ENST00000328546.4	hg19	CCDS3618.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.857451	0.51376	.	.	ENSG00000170509	ENST00000328546	D	0.89415	-2.51	4.84	4.84	0.62591	NAD(P)-binding domain (1);	0.000000	0.64402	D	0.000005	D	0.93086	0.7799	M	0.73753	2.245	0.50171	D	0.999852	D	0.65815	0.995	P	0.62184	0.899	D	0.93873	0.7164	10	0.72032	D	0.01	.	14.2534	0.66035	0.0:0.0:0.0:1.0	.	75	Q7Z5P4	DHB13_HUMAN	G	75	ENSP00000333300:E75G	ENSP00000333300:E75G	E	-	2	0	HSD17B13	88458599	1.000000	0.71417	1.000000	0.80357	0.013000	0.08279	3.694000	0.54742	2.016000	0.59253	0.482000	0.46254	GAA	.	.		0.443	HSD17B13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253052.1	NM_178135		C	88239575	T	C	88239575	3	2	23	1	0	0	0	0	1	0	0	0	7391	1783	62	2	702	2	HSD17B13	4	88239575	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	616752	88239575	102914701	309	2375										
SPP1	6696	hgsc.bcm.edu	37	chr4	88903791	88903791	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acagttatgaaacgagtcagCtggatgaccagagtgctgaa	12	7	1	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:88903791C>T	ENST00000395080.3	+	7	815	c.688C>T	c.(688-690)Ctg>Ttg	p.L230L	SPP1_ENST00000237623.7_Silent_p.L216L|SPP1_ENST00000509659.1_3'UTR|SPP1_ENST00000360804.4_Silent_p.L203L	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	230					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|negative regulation of collateral sprouting of intact axon in response to injury (GO:0048685)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell-substrate adhesion (GO:0010811)|response to steroid hormone (GO:0048545)|response to vitamin D (GO:0033280)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix binding (GO:0050840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		AACGAGTCAGCTGGATGACCA	0.512																																					p.L243L		Atlas-SNP	.											.	SPP1	35	.	0			c.C727T						.						149	137	141					4																	88903791		2203	4300	6503	SO:0001819	synonymous_variant	6696	exon8			AGTCAGCTGGATG		CCDS3626.1, CCDS34027.1, CCDS43250.1	4q22.1	2014-01-30	2008-07-31		ENSG00000118785	ENSG00000118785		"Endogenous ligands"	11255	protein-coding gene	gene with protein product	"early T-lymphocyte activation 1"	166490	"osteopontin", "bone sialoprotein I"	BNSP, OPN		1575754	Standard	NM_001251829		Approved	BSPI, ETA-1	uc003hra.3	P10451	OTTHUMG00000130599	ENST00000395080.3:c.688C>T	chr4.hg19:g.88903791C>T		171.0	0.0		202.0	85.0	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Silent	SNP	ENST00000395080.3	hg19	CCDS43250.1																																																																																			.	.		0.512	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3			T	88903791	C	T	88903791	2	4	23	1	0	0	0	0	0	0	0	1	15101	796	28	3		3	SPP1	4	88903791	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	664216	88903791	102250485	310	2376										
NAP1L5	266812	hgsc.bcm.edu	37	chr4	89618583	89618583	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcttatagatgtcattatacTttttttccagagcctgaaat							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:89618583delT	ENST00000323061.5	-	1	803	c.323delA	c.(322-324)aagfs	p.K108fs	HERC3_ENST00000402738.1_Intron|HERC3_ENST00000543130.1_Intron|HERC3_ENST00000264345.3_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	108					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(123;0.000181)		GTCATTATACTTTTTTTCCAG	0.493																																					p.K108fs		Atlas-Indel,Pindel	.											.	NAP1L5	23	.	0			c.324delG						.						73	77	76					4																	89618583		2203	4300	6503	SO:0001589	frameshift_variant	266812	exon1			.	NM_153757	CCDS3632.1	4q21-q22	2006-04-12			ENSG00000177432	ENSG00000177432			19968	protein-coding gene	gene with protein product		612203				12383514	Standard	NM_153757		Approved	DRLM	uc003hrx.3	Q96NT1	OTTHUMG00000130950	ENST00000323061.5:c.323delA	chr4.hg19:g.89618583delT	ENSP00000320488:p.Lys108fs	72.0	0.0		83.0	31.0	NM_153757		Frame_Shift_Del	DEL	ENST00000323061.5	hg19	CCDS3632.1																																																																																			.	.		0.493	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757		-	89618583	T	-	89618583	7	5	23	1	0	1	0	1	0	0	0	0	10169	1609	56	0	229	0	NAP1L5	4	89618583	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	714792	89618583	101535693	311	2377										
FAM13A	10144	hgsc.bcm.edu	37	chr4	89689146	89689146	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaaattacctttcatcagacAtccattcaaaatcatcaggt	3	10	5	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:89689146A>G	ENST00000264344.5	-	12	1730	c.1523T>C	c.(1522-1524)aTg>aCg	p.M508T	FAM13A_ENST00000508369.1_Missense_Mutation_p.M182T|FAM13A_ENST00000503556.1_Missense_Mutation_p.M168T|FAM13A_ENST00000395002.2_Missense_Mutation_p.M182T|FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000511976.1_Missense_Mutation_p.M94T|FAM13A_ENST00000513837.1_Missense_Mutation_p.M154T	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	508					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						TTCATCAGACATCCATTCAAA	0.338																																					p.M508T		Atlas-SNP	.											.	FAM13A	181	.	0			c.T1523C						.						98	92	94					4																	89689146		2203	4300	6503	SO:0001583	missense	10144	exon12			TCAGACATCCATT	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.1523T>C	chr4.hg19:g.89689146A>G	ENSP00000264344:p.Met508Thr	244.0	0.0		227.0	65.0	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	hg19	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	A	3.400	-0.122379	0.06795	.	.	ENSG00000138640	ENST00000395002;ENST00000264344;ENST00000503556;ENST00000511976;ENST00000508369;ENST00000513837	T;T;T;T;T;T	0.62498	0.02;0.02;1.5;1.53;0.02;1.5	5.13	-0.215	0.13157	.	0.803358	0.12096	N	0.499947	T	0.45776	0.1359	L	0.50333	1.59	0.09310	N	1	B;B;B;B;B;B	0.30664	0.009;0.039;0.289;0.022;0.022;0.009	B;B;B;B;B;B	0.23275	0.014;0.023;0.045;0.014;0.014;0.014	T	0.22487	-1.0215	10	0.17832	T	0.49	.	5.306	0.15803	0.6421:0.1377:0.2201:0.0	.	154;94;508;182;168;182	O94988-6;E9PGM7;O94988;O94988-3;O94988-5;O94988-1	.;.;FA13A_HUMAN;.;.;.	T	182;508;168;94;182;154	ENSP00000378450:M182T;ENSP00000264344:M508T;ENSP00000427189:M168T;ENSP00000421914:M94T;ENSP00000421562:M182T;ENSP00000423252:M154T	ENSP00000264344:M508T	M	-	2	0	FAM13A	89908169	0.038000	0.19896	0.003000	0.11579	0.016000	0.09150	1.139000	0.31504	-0.141000	0.11374	-0.263000	0.10527	ATG	.	.		0.338	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			G	89689146	A	G	89689146	3	3	23	1	0	0	0	0	1	0	0	0	5457	217	8	2	1600	2	FAM13A	4	89689146	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	70563	89689146	101465130	312	2378										
FAM190A	401145	hgsc.bcm.edu	37	chr4	92519977	92519977	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acacagaacttacgggccacCgttgggcagagctctctgaa	11	12	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:92519977C>T	ENST00000509176.1	+	11	2760	c.2472C>T	c.(2470-2472)acC>acT	p.T824T	CCSER1_ENST00000333691.8_Silent_p.T824T	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	824																	TACGGGCCACCGTTGGGCAGA	0.478																																					p.T824T		Atlas-SNP	.											.	.	.	.	0			c.C2472T						.						88	77	81					4																	92519977		692	1591	2283	SO:0001819	synonymous_variant	401145	exon11			GGCCACCGTTGGG		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.2472C>T	chr4.hg19:g.92519977C>T		153.0	0.0		168.0	54.0	NM_001145065	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	hg19	CCDS47099.1																																																																																			.	.		0.478	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		T	92519977	C	T	92519977	2	4	23	1	0	0	0	0	0	0	0	1	5526	639	23	1		1	FAM190A	4	92519977	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2830831	92519977	98634299	313	2379										
NFKB1	4790	hgsc.bcm.edu	37	chr4	103498147	103498147	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctggactcttggtgcacccTgaccttgcctatttgcaagc	9	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:103498147T>G	ENST00000505458.1	+	7	796	c.519T>G	c.(517-519)ccT>ccG	p.P173P	NFKB1_ENST00000226574.4_Silent_p.P174P|NFKB1_ENST00000394820.4_Silent_p.P173P|NFKB1_ENST00000510638.1_3'UTR|NFKB1_ENST00000600343.1_5'Flank			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	173	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	TGGTGCACCCTGACCTTGCCT	0.493																																					p.P174P		Atlas-SNP	.											.	NFKB1	78	.	0			c.T522G						.						129	128	128					4																	103498147		2203	4300	6503	SO:0001819	synonymous_variant	4790	exon7			GCACCCTGACCTT	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.519T>G	chr4.hg19:g.103498147T>G		113.0	0.0		110.0	7.0	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	hg19	CCDS54783.1																																																																																			.	.		0.493	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			G	103498147	T	G	103498147	2	3	23	1	0	0	0	0	0	0	0	1	10384	1567	55	5		5	NFKB1	4	103498147	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	10978170	103498147	87656129	314	2380										
NFKB1	4790	hgsc.bcm.edu	37	chr4	103528382	103528382	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctggtggccgctggggctgAcgtcaatgctcaggagcaga	17	10	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:103528382A>G	ENST00000505458.1	+	18	2304	c.2027A>G	c.(2026-2028)gAc>gGc	p.D676G	NFKB1_ENST00000226574.4_Missense_Mutation_p.D677G|NFKB1_ENST00000394820.4_Missense_Mutation_p.D676G|NFKB1_ENST00000600343.1_Missense_Mutation_p.D496G			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	676	Essential for interaction with HIF1AN.|Interaction with CFLAR.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	GCTGGGGCTGACGTCAATGCT	0.577																																					p.D677G		Atlas-SNP	.											.	NFKB1	78	.	0			c.A2030G						.						94	92	93					4																	103528382		2203	4300	6503	SO:0001583	missense	4790	exon18			GGGCTGACGTCAA	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.2027A>G	chr4.hg19:g.103528382A>G	ENSP00000424790:p.Asp676Gly	190.0	0.0		173.0	63.0	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	hg19	CCDS54783.1	.	.	.	.	.	.	.	.	.	.	A	14.76	2.632558	0.47049	.	.	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000505458	T;T;T	0.43688	0.94;0.94;0.94	4.71	4.71	0.59529	Ankyrin repeat-containing domain (3);	0.124476	0.52532	D	0.000067	T	0.51261	0.1664	M	0.86097	2.795	0.36931	D	0.891897	P;P;P	0.41232	0.623;0.623;0.743	B;B;B	0.40825	0.341;0.223;0.281	T	0.67601	-0.5629	10	0.59425	D	0.04	.	14.4996	0.67711	1.0:0.0:0.0:0.0	.	496;676;677	B3KVE8;P19838;P19838-2	.;NFKB1_HUMAN;.	G	677;676;676	ENSP00000226574:D677G;ENSP00000378297:D676G;ENSP00000424790:D676G	ENSP00000226574:D677G	D	+	2	0	NFKB1	103747420	0.739000	0.28196	0.869000	0.34112	0.577000	0.36160	4.877000	0.63086	1.872000	0.54250	0.533000	0.62120	GAC	.	.		0.577	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			G	103528382	A	G	103528382	3	3	23	1	0	0	0	0	1	0	0	0	10384	275	10	2	2096	2	NFKB1	4	103528382	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	30235	103528382	87625894	315	2381										
TBCK	93627	hgsc.bcm.edu	37	chr4	107173107	107173107	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggttttttacttggcatgtgAtcagtggttttgaaaattcc	10	5	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:107173107A>T	ENST00000273980.5	-	7	960	c.513T>A	c.(511-513)gaT>gaA	p.D171E	TBCK_ENST00000361687.4_Missense_Mutation_p.D108E|TBCK_ENST00000394706.3_Intron|TBCK_ENST00000432496.2_Missense_Mutation_p.D171E|TBCK_ENST00000394708.2_Missense_Mutation_p.D171E					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TTGGCATGTGATCAGTGGTTT	0.368																																					p.D171E		Atlas-SNP	.											.	TBCK	89	.	0			c.T513A						.						106	105	105					4																	107173107		2203	4300	6503	SO:0001583	missense	93627	exon6			CATGTGATCAGTG		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.513T>A	chr4.hg19:g.107173107A>T	ENSP00000273980:p.Asp171Glu	108.0	0.0		115.0	36.0	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	hg19	CCDS54788.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.915315	0.52546	.	.	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394708	T;T;T;T	0.62498	0.02;0.02;3.81;0.02	5.74	3.02	0.34903	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043220	0.85682	D	0.000000	T	0.42200	0.1192	L	0.28649	0.875	0.38524	D	0.948791	B;B	0.09022	0.001;0.002	B;B	0.09377	0.004;0.002	T	0.22521	-1.0214	10	0.19590	T	0.45	.	5.0969	0.14739	0.6474:0.0:0.2206:0.1321	.	171;108	Q8TEA7;Q8TEA7-3	TBCK_HUMAN;.	E	171;171;108;171	ENSP00000273980:D171E;ENSP00000405847:D171E;ENSP00000355338:D108E;ENSP00000378198:D171E	ENSP00000273980:D171E	D	-	3	2	TBCK	107392556	0.996000	0.38824	0.998000	0.56505	0.977000	0.68977	0.578000	0.23773	1.023000	0.39654	0.533000	0.62120	GAT	.	.		0.368	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		T	107173107	A	T	107173107	3	4	23	1	0	0	0	0	1	0	0	0	15651	330	12	4	2252	4	TBCK	4	107173107	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3644725	107173107	83981169	316	2382										
LRIT3	345193	hgsc.bcm.edu	37	chr4	110791477	110791477	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgtattccaagtatggtggGaaggacctgctgctgttgaa	13	6	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:110791477G>A	ENST00000594814.1	+	4	1572	c.1572G>A	c.(1570-1572)ggG>ggA	p.G524G	LRIT3_ENST00000327908.3_Silent_p.G341G|LRIT3_ENST00000409621.2_Silent_p.G341G|LRIT3_ENST00000379920.3_Silent_p.G479G	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	524	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		AGTATGGTGGGAAGGACCTGC	0.483																																					p.G524G		Atlas-SNP	.											.	LRIT3	107	.	0			c.G1572A						.						137	126	129					4																	110791477		2203	4300	6503	SO:0001819	synonymous_variant	345193	exon4			TGGTGGGAAGGAC	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"Immunoglobulin superfamily / I-set domain containing"	24783	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 4"	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1572G>A	chr4.hg19:g.110791477G>A		135.0	0.0		179.0	75.0	NM_198506	C9J1C2|Q6ZTG1	Silent	SNP	ENST00000594814.1	hg19	CCDS3688.3																																																																																			.	.		0.483	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506		A	110791477	G	A	110791477	2	1	23	1	0	0	0	0	0	0	0	1	8958	1161	41	3		3	LRIT3	4	110791477	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3618370	110791477	80362799	317	2383										
FAT4	79633	hgsc.bcm.edu	37	chr4	126241913	126241913	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actgcacatgaccctgatgcAgacattaatggtcaactatc	7	11	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:126241913A>C	ENST00000394329.3	+	1	4360	c.4347A>C	c.(4345-4347)gcA>gcC	p.A1449A		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1449	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ACCCTGATGCAGACATTAATG	0.408																																					p.A1449A		Atlas-SNP	.											.	FAT4	1752	.	0			c.A4347C						.						142	130	134					4																	126241913		1910	4136	6046	SO:0001819	synonymous_variant	79633	exon1			TGATGCAGACATT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.4347A>C	chr4.hg19:g.126241913A>C		278.0	0.0		253.0	104.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.		0.408	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126241913	A	C	126241913	2	2	23	1	0	0	0	0	0	0	0	1	5700	175	7	5		5	FAT4	4	126241913	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	15450436	126241913	64912363	318	2384										
FAT4	79633	hgsc.bcm.edu	37	chr4	126412250	126412250	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagaagcaagagtcctcaggCcatggcatcacatggttcta	11	10	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:126412250C>T	ENST00000394329.3	+	17	14286	c.14273C>T	c.(14272-14274)gCc>gTc	p.A4758V	FAT4_ENST00000335110.5_Missense_Mutation_p.A2999V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4758	Necessary and sufficient for interaction with MPDZ. {ECO:0000250}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AGTCCTCAGGCCATGGCATCA	0.493																																					p.A4758V		Atlas-SNP	.											.	FAT4	1752	.	0			c.C14273T						.						55	54	54					4																	126412250		2203	4300	6503	SO:0001583	missense	79633	exon17			CTCAGGCCATGGC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.14273C>T	chr4.hg19:g.126412250C>T	ENSP00000377862:p.Ala4758Val	103.0	0.0		101.0	52.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	8.573	0.880562	0.17467	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.74106	-0.65;-0.81	4.87	4.02	0.46733	.	0.222293	0.22053	U	0.065298	T	0.57607	0.2065	N	0.14661	0.345	0.35823	D	0.824722	B;B;B	0.30634	0.288;0.19;0.288	B;B;B	0.29942	0.109;0.051;0.109	T	0.60110	-0.7327	10	0.23302	T	0.38	.	14.2568	0.66058	0.0:0.8501:0.1499:0.0	.	2999;4758;4757	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	V	4758;2999	ENSP00000377862:A4758V;ENSP00000335169:A2999V	ENSP00000335169:A2999V	A	+	2	0	FAT4	126631700	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	4.629000	0.61290	1.025000	0.39708	0.561000	0.74099	GCC	.	.		0.493	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126412250	C	T	126412250	3	4	23	1	0	0	0	0	1	0	0	0	5700	739	26	3	14339	3	FAT4	4	126412250	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	170337	126412250	64742026	319	2385										
MAML3	55534	hgsc.bcm.edu	37	chr4	140811112	140811123	+	In_Frame_Del	DEL	TGCTGCTGCTGT	TGCTGCTGCTGT	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctgctgctgctgctgctgcTgctgctgctgttgctgttgc					rs62344938|rs62344939		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TGCTGCTGCTGT	TGCTGCTGCTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:140811112_140811123delTGCTGCTGCTGT	ENST00000509479.2	-	2	2323_2334	c.1467_1478delACAGCAGCAGCA	c.(1465-1479)caacagcagcagcag>cag	p.489_493QQQQQ>Q	MAML3_ENST00000327122.5_In_Frame_Del_p.333_337QQQQQ>Q|MAML3_ENST00000398940.1_In_Frame_Del_p.28_32QQQQQ>Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					ctgctgctgctgctgctgctgttgctgttgct	0.547																																					p.490_493del		Atlas-INDEL	.											.	MAML3	192	.	0			c.1468_1479del						.			852,3360		97,658,1351						1.5	1		dbSNP_130	17	2205,5999		132,1941,2029	no	coding	MAML3	NM_018717.4		229,2599,3380	A1A1,A1R,RR		26.8771,20.2279,24.6215				3057,9359				SO:0001651	inframe_deletion	55534	exon2			.	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1467_1478delACAGCAGCAGCA	chr4.hg19:g.140811112_140811123delTGCTGCTGCTGT	ENSP00000421180:p.Gln505_Gln508del	70.0	0.0		80.0	12.0	NM_018717		In_Frame_Del	DEL	ENST00000509479.2	hg19	CCDS54805.1																																																																																			.	.		0.547	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			-	140811123	TGCTGCTGCTGT	-	140811112	7	5	23	1	0	1	0	1	0	0	0	0	9216	1580	55	0	1946	0	MAML3	4	140811112	In_Frame_Del	DEL	TGCTGCTGCTGT	TCGA-4R-AA8I-01A-11D-A382-10	14398862	140811112	50343164	320	2386										
USP38	84640	hgsc.bcm.edu	37	chr4	144135967	144135968	+	Frame_Shift_Ins	INS	-	-	A													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagcttatgtgcttttgtatINSaaaaaacagcatagtactaa							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:144135967_144135968insA	ENST00000307017.4	+	9	3344_3345	c.2838_2839insA	c.(2839-2841)aaafs	p.K947fs	USP38_ENST00000510377.1_Frame_Shift_Ins_p.K947fs	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	947	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					TGCTTTTGTATAAAAAACAGCA	0.371																																					p.Y946fs		Atlas-Indel,Pindel	.											.	USP38	92	.	0			c.2838_2839insA						.																																			SO:0001589	frameshift_variant	84640	exon9			.	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2844dupA	chr4.hg19:g.144135973_144135973dupA	ENSP00000303434:p.Lys947fs	313.0	0.0		280.0	107.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Frame_Shift_Ins	INS	ENST00000307017.4	hg19	CCDS3758.1																																																																																			.	.		0.371	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		A	144135968	-	A	144135967	7	5	23	1	0	1	1	0	0	0	0	0	17084	1413	49	0	2872	0	USP38	4	144135967	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	3324855	144135967	47018309	321	2387										
PET112L	5188	hgsc.bcm.edu	37	chr4	152622627	152622627	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acctgcgggcagagatgtggCgtcgtagagcaccaggggag	18	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:152622627C>T	ENST00000515812.1	-	8	944	c.928G>A	c.(928-930)Gcc>Acc	p.A310T	PET112_ENST00000263985.6_Missense_Mutation_p.A351T														p.A351T(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						AGAGATGTGGCGTCGTAGAGC	0.562																																					p.A351T		Atlas-SNP	.											PET112,NS,carcinoma,0,1	PET112	43	.	1	Substitution - Missense(1)	endometrium(1)	c.G1051A						.						59	57	58					4																	152622627		2203	4300	6503	SO:0001583	missense	5188	exon9			ATGTGGCGTCGTA																												ENST00000515812.1:c.928G>A	chr4.hg19:g.152622627C>T	ENSP00000426859:p.Ala310Thr	106.0	0.0		88.0	35.0	NM_004564		Missense_Mutation	SNP	ENST00000515812.1	hg19		.	.	.	.	.	.	.	.	.	.	C	7.751	0.703241	0.15172	.	.	ENSG00000059691	ENST00000263985;ENST00000515812	T;T	0.45668	0.91;0.89	5.7	-11.4	0.00090	.	0.993958	0.08184	N	0.984946	T	0.16854	0.0405	N	0.08118	0	0.33990	D	0.649014	B	0.09022	0.002	B	0.08055	0.003	T	0.15206	-1.0445	10	0.29301	T	0.29	-24.3714	10.0843	0.42408	0.4981:0.3826:0.0:0.1193	.	351	O75879	GATB_HUMAN	T	351;310	ENSP00000263985:A351T;ENSP00000426859:A310T	ENSP00000263985:A351T	A	-	1	0	PET112	152842077	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	-3.449000	0.00467	-3.065000	0.00255	-0.911000	0.02809	GCC	.	.		0.562	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1			T	152622627	C	T	152622627	3	4	23	1	0	0	0	0	1	0	0	0	11743	768	27	1	642	1	PET112L	4	152622627	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	8486660	152622627	38531649	322	2388										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153244121	153244121	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgcacacaccagctttgtgTttgaggctctgatccgccac	9	14	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:153244121T>C	ENST00000281708.4	-	12	3265	c.2036A>G	c.(2035-2037)aAc>aGc	p.N679S	FBXW7_ENST00000393956.3_Missense_Mutation_p.N503S|FBXW7_ENST00000263981.5_Missense_Mutation_p.N599S|FBXW7_ENST00000603548.1_Missense_Mutation_p.N679S|RP11-461L13.3_ENST00000603766.1_lincRNA|FBXW7_ENST00000603841.1_Missense_Mutation_p.N679S|FBXW7_ENST00000296555.5_Missense_Mutation_p.N561S	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	679					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CAGCTTTGTGTTTGAGGCTCT	0.493			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																p.N679S		Atlas-SNP	.		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	.	FBXW7	2157	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.A2036G						.						187	182	184					4																	153244121		2203	4300	6503	SO:0001583	missense	55294	exon12			TTTGTGTTTGAGG	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.2036A>G	chr4.hg19:g.153244121T>C	ENSP00000281708:p.Asn679Ser	198.0	0.0		198.0	90.0	NM_033632	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	hg19	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	2.458	-0.324730	0.05350	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.17528	2.27;2.27;2.27;2.27	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);	0.127285	0.64402	D	0.000001	T	0.11707	0.0285	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.13145	0.001;0.006;0.004;0.007	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.14282	-1.0478	10	0.25751	T	0.34	-17.8896	15.9087	0.79450	0.0:0.0:0.0:1.0	.	503;679;561;599	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	S	679;561;599;503	ENSP00000281708:N679S;ENSP00000296555:N561S;ENSP00000263981:N599S;ENSP00000377528:N503S	ENSP00000263981:N599S	N	-	2	0	FBXW7	153463571	1.000000	0.71417	0.986000	0.45419	0.991000	0.79684	8.015000	0.88690	2.165000	0.68154	0.533000	0.62120	AAC	.	.		0.493	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153244121	T	C	153244121	3	2	23	1	0	0	0	0	1	0	0	0	5777	1725	60	2	91	2	FBXW7	4	153244121	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	621494	153244121	37910155	323	2389										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155158059	155158059	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggaatattcaacatatgtgTtttcacgggtccagtcatgg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:155158059delT	ENST00000357232.4	-	25	6379	c.6380delA	c.(6379-6381)aacfs	p.N2127fs		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2127	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AACATATGTGTTTTCACGGGT	0.378																																					p.N2127fs		Atlas-Indel,Pindel	.											.	DCHS2	594	.	0			c.6381delC						.						133	129	131					4																	155158059		2203	4300	6503	SO:0001589	frameshift_variant	54798	exon25			.	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6380delA	chr4.hg19:g.155158059delT	ENSP00000349768:p.Asn2127fs	93.0	0.0		75.0	25.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Frame_Shift_Del	DEL	ENST00000357232.4	hg19	CCDS3785.1																																																																																			.	.		0.378	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		-	155158059	T	-	155158059	7	5	23	1	0	1	0	1	0	0	0	0	4290	1725	60	0	2374	0	DCHS2	4	155158059	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	1913938	155158059	35996217	324	2390										
NPY2R	4887	hgsc.bcm.edu	37	chr4	156135360	156135360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtaaccaactttttcattgCcaatctggctgtggcagatc	8	10	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:156135360C>T	ENST00000329476.3	+	2	758	c.269C>T	c.(268-270)gCc>gTc	p.A90V	NPY2R_ENST00000506608.1_Missense_Mutation_p.A90V	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	90					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	TTTTTCATTGCCAATCTGGCT	0.468																																					p.A90V		Atlas-SNP	.											.	NPY2R	87	.	0			c.C269T						.						109	109	109					4																	156135360		2203	4300	6503	SO:0001583	missense	4887	exon2			TCATTGCCAATCT	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"GPCR / Class A : Neuropeptide receptors : Y"	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.269C>T	chr4.hg19:g.156135360C>T	ENSP00000332591:p.Ala90Val	76.0	0.0		80.0	6.0	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation	SNP	ENST00000329476.3	hg19	CCDS3791.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.222658	0.39300	.	.	ENSG00000185149	ENST00000329476;ENST00000506608	T;T	0.69561	-0.41;-0.41	5.51	5.51	0.81932	GPCR, rhodopsin-like superfamily (1);	0.052025	0.85682	D	0.000000	T	0.41419	0.1158	N	0.11201	0.11	0.46542	D	0.999094	P	0.38300	0.626	B	0.36092	0.217	T	0.50189	-0.8857	10	0.02654	T	1	.	12.1441	0.54014	0.0:0.9216:0.0:0.0784	.	90	P49146	NPY2R_HUMAN	V	90	ENSP00000332591:A90V;ENSP00000426366:A90V	ENSP00000332591:A90V	A	+	2	0	NPY2R	156354810	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.002000	0.40835	2.732000	0.93576	0.643000	0.83706	GCC	.	.		0.468	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910		T	156135360	C	T	156135360	3	4	23	1	0	0	0	0	1	0	0	0	10618	739	26	3	271	3	NPY2R	4	156135360	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	977301	156135360	35018916	325	2391										
ETFDH	2110	hgsc.bcm.edu	37	chr4	159620153	159620153	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttaaggttggtctagactaTcagaatccatacctgagtcc	8	9	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:159620153T>A	ENST00000511912.1	+	9	1319	c.987T>A	c.(985-987)taT>taA	p.Y329*	U3_ENST00000607547.1_RNA|ETFDH_ENST00000307738.5_Nonsense_Mutation_p.Y282*	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	329					cellular metabolic process (GO:0044237)|electron transport chain (GO:0022900)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, oxidizing metal ions with flavin as acceptor (GO:0043783)|quinone binding (GO:0048038)|ubiquinone binding (GO:0048039)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|prostate(1)|skin(3)	28	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		GTCTAGACTATCAGAATCCAT	0.343																																					p.Y329X		Atlas-SNP	.											.	ETFDH	57	.	0			c.T987A						.						73	71	72					4																	159620153		2203	4300	6503	SO:0001587	stop_gained	2110	exon9			AGACTATCAGAAT	S69232	CCDS3800.1, CCDS64090.1	4q32-q35	2008-08-26			ENSG00000171503	ENSG00000171503			3483	protein-coding gene	gene with protein product		231675					Standard	NM_004453		Approved	ETFQO	uc003iqb.3	Q16134	OTTHUMG00000161684	ENST00000511912.1:c.987T>A	chr4.hg19:g.159620153T>A	ENSP00000426638:p.Tyr329*	403.0	0.0		373.0	145.0	NM_004453	B4E3R9|J3KND9|Q7Z347	Nonsense_Mutation	SNP	ENST00000511912.1	hg19	CCDS3800.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.150465	0.78001	.	.	ENSG00000171503	ENST00000511912;ENST00000507475;ENST00000307738	.	.	.	5.98	-0.254	0.12992	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.8195	10.2326	0.43264	0.0:0.3431:0.0:0.6569	.	.	.	.	X	329;164;282	.	ENSP00000303552:Y282X	Y	+	3	2	ETFDH	159839603	0.998000	0.40836	0.996000	0.52242	0.950000	0.60333	0.491000	0.22419	0.169000	0.19679	-0.326000	0.08463	TAT	.	.		0.343	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2			A	159620153	T	A	159620153	4	1	23	1	0	0	0	0	0	1	0	0	5273	1442	50	4	1021	4	ETFDH	4	159620153	Nonsense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3484793	159620153	31534123	326	2392										
RAPGEF2	9693	hgsc.bcm.edu	37	chr4	160264434	160264434	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctcctctgtcaatttcaggAaatgactcaaaagtagacgg	8	10	4	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:160264434A>T	ENST00000264431.4	+	16	3068	c.2649A>T	c.(2647-2649)ggA>ggT	p.G883G		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	883	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		CAATTTCAGGAAATGACTCAA	0.423																																					p.G883G		Atlas-SNP	.											.	RAPGEF2	171	.	0			c.A2649T						.						103	98	99					4																	160264434		1855	4093	5948	SO:0001630	splice_region_variant	9693	exon16			TTCAGGAAATGAC	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.2648-1A>T	chr4.hg19:g.160264434A>T		205.0	0.0		194.0	73.0	NM_014247	D3DP27	Silent	SNP	ENST00000264431.4	hg19	CCDS43277.1																																																																																			.	.		0.423	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	Silent	T	160264434	A	T	160264434	5	4	23	1	0	0	0	0	0	0	1	0	13059	260	9	4	2711	4	RAPGEF2	4	160264434	Splice_Site	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	644281	160264434	30889842	327	2393										
NPY1R	4886	hgsc.bcm.edu	37	chr4	164246566	164246566	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atcgtggacatggctattgtTtcataatcatcatcccgaga	8	9	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:164246566T>A	ENST00000296533.2	-	3	1575	c.1044A>T	c.(1042-1044)gaA>gaT	p.E348D	NPY1R_ENST00000509586.1_Missense_Mutation_p.E105D	NM_000909.5	NP_000900.1	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1	348					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose metabolic process (GO:0006006)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|regulation of blood pressure (GO:0008217)|regulation of multicellular organism growth (GO:0040014)|sensory perception of pain (GO:0019233)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			breast(1)|cervix(1)|large_intestine(4)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)	30	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TGGCTATTGTTTCATAATCAT	0.388																																					p.E348D		Atlas-SNP	.											.	NPY1R	72	.	0			c.A1044T						.						152	158	156					4																	164246566		2203	4300	6503	SO:0001583	missense	4886	exon3			TATTGTTTCATAA		CCDS34089.1	4q31.3-q32	2012-08-08				ENSG00000164128		"GPCR / Class A : Neuropeptide receptors : Y"	7956	protein-coding gene	gene with protein product		162641		NPYR		8095935	Standard	NM_000909		Approved		uc003iqm.2	P25929		ENST00000296533.2:c.1044A>T	chr4.hg19:g.164246566T>A	ENSP00000354652:p.Glu348Asp	140.0	0.0		140.0	53.0	NM_000909	B2R6H5	Missense_Mutation	SNP	ENST00000296533.2	hg19	CCDS34089.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.117630	0.37339	.	.	ENSG00000164128	ENST00000296533;ENST00000509586	T;T	0.37752	1.18;1.18	5.69	1.94	0.25998	.	0.220246	0.38663	N	0.001615	T	0.28632	0.0709	L	0.42632	1.34	0.49687	D	0.999814	B	0.22800	0.075	B	0.19391	0.025	T	0.07770	-1.0755	10	0.48119	T	0.1	.	10.0344	0.42120	0.0:0.7263:0.0:0.2737	.	348	P25929	NPY1R_HUMAN	D	348;105	ENSP00000354652:E348D;ENSP00000427284:E105D	ENSP00000354652:E348D	E	-	3	2	NPY1R	164466016	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.348000	0.33987	0.336000	0.23639	-0.177000	0.13119	GAA	.	.		0.388	NPY1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364685.1			A	164246566	T	A	164246566	3	1	23	1	0	0	0	0	1	0	0	0	10617	1838	64	4	114	4	NPY1R	4	164246566	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3982132	164246566	26907710	328	2394										
NPY5R	4889	hgsc.bcm.edu	37	chr4	164272694	164272694	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcctgttgtcttaatccaatTctatatgggtttcttaataa	5	7	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:164272694T>C	ENST00000515560.1	+	4	2791	c.1269T>C	c.(1267-1269)atT>atC	p.I423I	NPY5R_ENST00000338566.3_Silent_p.I423I|NPY5R_ENST00000506953.1_Silent_p.I423I			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	423					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				TTAATCCAATTCTATATGGGT	0.318																																					p.I423I	Melanoma(139;1287 1774 9781 19750 25599)	Atlas-SNP	.											.	NPY5R	101	.	0			c.T1269C						.						99	101	100					4																	164272694		2202	4300	6502	SO:0001819	synonymous_variant	4889	exon4			TCCAATTCTATAT	BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"GPCR / Class A : Neuropeptide receptors : Y"	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.1269T>C	chr4.hg19:g.164272694T>C		131.0	0.0		121.0	47.0	NM_006174	Q6GTR7|Q92916	Silent	SNP	ENST00000515560.1	hg19	CCDS3804.1																																																																																			.	.		0.318	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174		C	164272694	T	C	164272694	2	2	23	1	0	0	0	0	0	0	0	1	10619	1771	62	2		2	NPY5R	4	164272694	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	26128	164272694	26881582	329	2395										
TLL1	7092	hgsc.bcm.edu	37	chr4	166987010	166987010	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggcttcaaagcacatttttTctcaggtataagcattcaca	7	9	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:166987010T>C	ENST00000061240.2	+	16	2830	c.2183T>C	c.(2182-2184)tTc>tCc	p.F728S	TLL1_ENST00000507499.1_Missense_Mutation_p.F751S	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	728	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		GCACATTTTTTCTCAGGTATA	0.333																																					p.F728S		Atlas-SNP	.											.	TLL1	194	.	0			c.T2183C						.						103	101	102					4																	166987010		2203	4299	6502	SO:0001583	missense	7092	exon16			ATTTTTTCTCAGG	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2183T>C	chr4.hg19:g.166987010T>C	ENSP00000061240:p.Phe728Ser	135.0	0.0		134.0	49.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	hg19	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.259036	0.80246	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	T;D	0.81659	1.77;-1.52	6.02	6.02	0.97574	CUB (3);	0.000000	0.85682	U	0.000000	D	0.85071	0.5613	L	0.37561	1.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.83562	0.0107	10	0.32370	T	0.25	.	16.5446	0.84426	0.0:0.0:0.0:1.0	.	751;728	E9PD25;O43897	.;TLL1_HUMAN	S	728;751	ENSP00000061240:F728S;ENSP00000426082:F751S	ENSP00000061240:F728S	F	+	2	0	TLL1	167206460	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	7.997000	0.88414	2.311000	0.77944	0.533000	0.62120	TTC	.	.		0.333	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			C	166987010	T	C	166987010	3	2	23	1	0	0	0	0	1	0	0	0	15960	1783	62	2	2245	2	TLL1	4	166987010	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2714316	166987010	24167266	330	2396										
CLCN3	1182	hgsc.bcm.edu	37	chr4	170625277	170625277	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttaaggagtggtgtgaggtCggggctgattgcattacacc	15	6	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:170625277C>T	ENST00000513761.1	+	10	2251	c.1692C>T	c.(1690-1692)gtC>gtT	p.V564V	CLCN3_ENST00000347613.4_Silent_p.V564V|CLCN3_ENST00000360642.3_Silent_p.V537V|CLCN3_ENST00000504131.2_Silent_p.V547V	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	564					chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)			breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		GGTGTGAGGTCGGGGCTGATT	0.522																																					p.V564V		Atlas-SNP	.											.	CLCN3	85	.	0			c.C1692T						.						235	198	211					4																	170625277		2203	4300	6503	SO:0001819	synonymous_variant	1182	exon10			TGAGGTCGGGGCT	X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.1692C>T	chr4.hg19:g.170625277C>T		109.0	0.0		133.0	50.0	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Silent	SNP	ENST00000513761.1	hg19	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	C	9.300	1.052853	0.19907	.	.	ENSG00000109572	ENST00000515420	.	.	.	5.22	-9.53	0.00575	.	.	.	.	.	T	0.51686	0.1689	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63143	-0.6703	4	.	.	.	-1.8187	12.5309	0.56115	0.0:0.5393:0.0949:0.3658	.	.	.	.	L	219	.	.	S	+	2	0	CLCN3	170861852	0.001000	0.12720	0.880000	0.34516	0.941000	0.58515	-2.071000	0.01378	-1.434000	0.01975	-1.238000	0.01547	TCG	.	.		0.522	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			T	170625277	C	T	170625277	2	4	23	1	0	0	0	0	0	0	0	1	3466	871	31	1		1	CLCN3	4	170625277	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3638267	170625277	20528999	331	2397										
HAND2	9464	hgsc.bcm.edu	37	chr4	174450400	174450400	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caaacgggtagccctcgtggTgcaccaccgggtggtgggga	17	11	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:174450400T>C	ENST00000359562.4	-	1	980	c.41A>G	c.(40-42)cAc>cGc	p.H14R	HAND2-AS1_ENST00000512209.2_RNA|HAND2-AS1_ENST00000511196.1_RNA|HAND2-AS1_ENST00000502334.1_RNA|HAND2-AS1_ENST00000503474.1_RNA|HAND2-AS1_ENST00000508887.1_RNA|HAND2-AS1_ENST00000505817.1_RNA|HAND2-AS1_ENST00000514431.1_RNA|HAND2-AS1_ENST00000510339.1_RNA|HAND2-AS1_ENST00000503309.1_RNA|HAND2-AS1_ENST00000507571.1_RNA|HAND2-AS1_ENST00000515310.1_RNA|HAND2-AS1_ENST00000510268.1_RNA|HAND2-AS1_ENST00000509640.1_RNA|HAND2-AS1_ENST00000502941.1_RNA|HAND2-AS1_ENST00000504740.1_RNA|HAND2-AS1_ENST00000505621.1_RNA|HAND2-AS1_ENST00000507322.1_RNA|HAND2_ENST00000505300.1_5'UTR|HAND2-AS1_ENST00000512099.1_RNA|HAND2-AS1_ENST00000515350.1_RNA|HAND2-AS1_ENST00000507636.1_RNA|HAND2-AS1_ENST00000511728.1_RNA|HAND2-AS1_ENST00000503198.1_RNA|HAND2-AS1_ENST00000515376.1_RNA|HAND2-AS1_ENST00000512929.1_RNA|HAND2-AS1_ENST00000509866.1_RNA|HAND2-AS1_ENST00000510221.1_RNA|HAND2-AS1_ENST00000512246.1_RNA|HAND2-AS1_ENST00000502896.1_RNA|HAND2-AS1_ENST00000508534.1_RNA|HAND2-AS1_ENST00000504429.1_RNA|HAND2-AS1_ENST00000514673.1_RNA|HAND2-AS1_ENST00000507062.1_RNA|HAND2-AS1_ENST00000512943.1_RNA|HAND2-AS1_ENST00000515345.1_RNA|HAND2-AS1_ENST00000515741.1_RNA|HAND2-AS1_ENST00000505032.1_RNA	NM_021973.2	NP_068808.1	P61296	HAND2_HUMAN	heart and neural crest derivatives expressed 2	14					adult heart development (GO:0007512)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic process involved in heart morphogenesis (GO:0003278)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cardiac right ventricle formation (GO:0003219)|cartilage morphogenesis (GO:0060536)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|coronary artery morphogenesis (GO:0060982)|embryonic digit morphogenesis (GO:0042733)|heart development (GO:0007507)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mesenchymal cell proliferation (GO:0010463)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural crest cell development (GO:0014032)|noradrenergic neuron differentiation (GO:0003357)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peripheral nervous system neuron development (GO:0048935)|positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis (GO:2000764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process (GO:2000763)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|sympathetic nervous system development (GO:0048485)|thymus development (GO:0048538)|tongue development (GO:0043586)|visceral serous pericardium development (GO:0061032)	nuclear chromatin (GO:0000790)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|E-box binding (GO:0070888)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	13		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.37e-18)|Epithelial(43;5.5e-17)|OV - Ovarian serous cystadenocarcinoma(60;3.3e-10)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		GCCCTCGTGGTGCACCACCGG	0.741																																					p.H14R		Atlas-SNP	.											.	HAND2	25	.	0			c.A41G						.						2	3	3					4																	174450400		1327	2919	4246	SO:0001583	missense	9464	exon1			TCGTGGTGCACCA	AF087941	CCDS3819.1	4q34.1	2014-08-12			ENSG00000164107	ENSG00000164107		"Basic helix-loop-helix proteins"	4808	protein-coding gene	gene with protein product		602407				9878849	Standard	NM_021973		Approved	dHand, Thing2, Hed, bHLHa26	uc003ith.1	P61296	OTTHUMG00000160775	ENST00000359562.4:c.41A>G	chr4.hg19:g.174450400T>C	ENSP00000352565:p.His14Arg	63.0	0.0		50.0	19.0	NM_021973	B6ECG9|O95300|O95301|P97833|Q494T1	Missense_Mutation	SNP	ENST00000359562.4	hg19	CCDS3819.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030347	0.35797	.	.	ENSG00000164107	ENST00000359562;ENST00000393686	D	0.96745	-4.11	3.32	0.703	0.18116	.	0.056789	0.64402	D	0.000001	D	0.89639	0.6773	L	0.32530	0.975	0.47153	D	0.999333	B;P;B	0.47409	0.004;0.895;0.004	B;B;B	0.38056	0.004;0.264;0.007	T	0.82827	-0.0265	10	0.25106	T	0.35	-3.4584	5.6199	0.17451	0.0:0.0951:0.172:0.7329	.	14;14;14	B6ECG9;P61296;E9PCP7	.;HAND2_HUMAN;.	R	14	ENSP00000352565:H14R	ENSP00000352565:H14R	H	-	2	0	HAND2	174686975	1.000000	0.71417	0.447000	0.26932	0.942000	0.58702	4.109000	0.57824	-0.029000	0.13827	0.329000	0.21502	CAC	.	.		0.741	HAND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362241.3			C	174450400	T	C	174450400	3	2	23	1	0	0	0	0	1	0	0	0	6959	1696	59	2	620	2	HAND2	4	174450400	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3825123	174450400	16703876	332	2398										
NEIL3	55247	hgsc.bcm.edu	37	chr4	178283576	178283576	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaaaaacaatgcaatttttTccagtgggcagaaaatgggc	11	6	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:178283576T>C	ENST00000264596.3	+	10	1887	c.1769T>C	c.(1768-1770)tTc>tCc	p.F590S		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	590					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		TGCAATTTTTTCCAGTGGGCA	0.373								Base excision repair (BER), DNA glycosylases																													p.F590S		Atlas-SNP	.											.	NEIL3	89	.	0			c.T1769C						.						74	82	79					4																	178283576		2202	4300	6502	SO:0001583	missense	55247	exon10			ATTTTTTCCAGTG	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 3"	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.1769T>C	chr4.hg19:g.178283576T>C	ENSP00000264596:p.Phe590Ser	248.0	0.0		258.0	113.0	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	hg19	CCDS3828.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.454920	0.84209	.	.	ENSG00000109674	ENST00000264596	T	0.58940	0.3	5.16	5.16	0.70880	Zinc finger, GRF-type (1);	0.000000	0.85682	D	0.000000	D	0.83820	0.5337	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89525	0.3781	10	0.87932	D	0	-18.0468	15.3044	0.73982	0.0:0.0:0.0:1.0	.	590	Q8TAT5	NEIL3_HUMAN	S	590	ENSP00000264596:F590S	ENSP00000264596:F590S	F	+	2	0	NEIL3	178520570	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.811000	0.86092	2.096000	0.63516	0.402000	0.26972	TTC	.	.		0.373	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		C	178283576	T	C	178283576	3	2	23	1	0	0	0	0	1	0	0	0	10329	1783	62	2	1807	2	NEIL3	4	178283576	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3833176	178283576	12870700	333	2399										
DCTD	1635	hgsc.bcm.edu	37	chr4	183815749	183815749	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcatgatggcattcagctccGcatggcacactgtgggttga	12	10	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:183815749G>A	ENST00000438320.2	-	4	544	c.254C>T	c.(253-255)gCg>gTg	p.A85V	DCTD_ENST00000357067.3_Missense_Mutation_p.A96V|DCTD_ENST00000510370.1_Missense_Mutation_p.A85V	NM_001921.2	NP_001912.2	P32321	DCTD_HUMAN	dCMP deaminase	85					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	dCMP deaminase activity (GO:0004132)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|urinary_tract(1)	18		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)	Cytarabine(DB00987)	ATTCAGCTCCGCATGGCACAC	0.423																																					p.A96V		Atlas-SNP	.											.	DCTD	30	.	0			c.C287T						.						160	135	143					4																	183815749		2203	4300	6503	SO:0001583	missense	1635	exon4			AGCTCCGCATGGC	L12136	CCDS3831.1, CCDS34108.1	4q35.1	2008-08-01			ENSG00000129187	ENSG00000129187	3.5.4.12		2710	protein-coding gene	gene with protein product		607638					Standard	XM_005262778		Approved		uc003ivg.3	P32321	OTTHUMG00000160685	ENST00000438320.2:c.254C>T	chr4.hg19:g.183815749G>A	ENSP00000398194:p.Ala85Val	101.0	0.0		95.0	23.0	NM_001012732	B2R836|D3DP49|D3DP50|Q5M7Z8|Q9BVD8	Missense_Mutation	SNP	ENST00000438320.2	hg19	CCDS3831.1	.	.	.	.	.	.	.	.	.	.	G	18.01	3.527635	0.64860	.	.	ENSG00000129187	ENST00000357067;ENST00000438320;ENST00000510370;ENST00000503182;ENST00000510307;ENST00000512766;ENST00000514754	T;T;T;T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87	5.53	3.79	0.43588	APOBEC/CMP deaminase, zinc-binding (1);Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.094486	0.64402	D	0.000001	D	0.91693	0.7374	H	0.99464	4.58	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	D	0.93991	0.7267	10	0.87932	D	0	-2.1914	12.4035	0.55426	0.1389:0.0:0.8611:0.0	.	85;26;96;85	D6RBJ9;B4DDC2;P32321-2;P32321	.;.;.;DCTD_HUMAN	V	96;85;85;85;85;85;85	ENSP00000349576:A96V;ENSP00000398194:A85V;ENSP00000424017:A85V;ENSP00000422662:A85V;ENSP00000424050:A85V;ENSP00000423182:A85V;ENSP00000423894:A85V	ENSP00000349576:A96V	A	-	2	0	DCTD	184052743	1.000000	0.71417	0.068000	0.19968	0.426000	0.31534	9.813000	0.99286	1.337000	0.45525	0.650000	0.86243	GCG	.	.		0.423	DCTD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361743.2			A	183815749	G	A	183815749	3	1	23	1	0	0	0	0	1	0	0	0	4307	1087	38	1	294	1	DCTD	4	183815749	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	5532173	183815749	7338527	334	2400										
ADCY2	108	hgsc.bcm.edu	37	chr5	7706967	7706967	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtggcaatatgatgtgtggtCacatgatgtgaccttggcca	13	7	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:7706967C>A	ENST00000338316.4	+	8	1309	c.1220C>A	c.(1219-1221)tCa>tAa	p.S407*	RP11-711G10.1_ENST00000514105.2_RNA|ADCY2_ENST00000537121.1_Nonsense_Mutation_p.S227*	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	407					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						GATGTGTGGTCACATGATGTG	0.502																																					p.S407X		Atlas-SNP	.											.	ADCY2	337	.	0			c.C1220A						.						218	191	200					5																	7706967		2203	4300	6503	SO:0001587	stop_gained	108	exon8			TGTGGTCACATGA	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1220C>A	chr5.hg19:g.7706967C>A	ENSP00000342952:p.Ser407*	131.0	0.0		141.0	32.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Nonsense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	C	39	7.303778	0.98200	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.964	0.92687	0.0:1.0:0.0:0.0	.	.	.	.	X	407;258;227	.	ENSP00000342952:S407X	S	+	2	0	ADCY2	7759967	1.000000	0.71417	0.987000	0.45799	0.983000	0.72400	7.602000	0.82796	2.480000	0.83734	0.655000	0.94253	TCA	.	.		0.502	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7706967	C	A	7706967	4	1	23	1	0	0	0	0	0	1	0	0	294	838	29	3	1250	3	ADCY2	5	7706967	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10		7706967	173208293	335	2401										
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7867406	7867406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccactttttcagtacatgccTgcaagattctataaagggcc	7	11	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:7867406T>C	ENST00000264669.5	-	2	927	c.791A>G	c.(790-792)cAg>cGg	p.Q264R	MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000502509.1_Intron|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000341013.6_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	264					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						AGTACATGCCTGCAAGATTCT	0.353																																					p.Q264R		Atlas-SNP	.											.	FASTKD3	88	.	0			c.A791G						.						81	89	86					5																	7867406		2202	4300	6502	SO:0001583	missense	79072	exon2			CATGCCTGCAAGA	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.791A>G	chr5.hg19:g.7867406T>C	ENSP00000264669:p.Gln264Arg	57.0	0.0		64.0	27.0	NM_024091	Q9BVD3	Missense_Mutation	SNP	ENST00000264669.5	hg19	CCDS3873.1	.	.	.	.	.	.	.	.	.	.	T	19.85	3.904177	0.72754	.	.	ENSG00000124279	ENST00000264669	T	0.32753	1.44	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.50616	0.1626	M	0.76002	2.32	0.47374	D	0.999407	D	0.76494	0.999	D	0.66351	0.943	T	0.48758	-0.9007	10	0.15066	T	0.55	-21.4257	14.6078	0.68493	0.0:0.0:0.0:1.0	.	264	Q14CZ7	FAKD3_HUMAN	R	264	ENSP00000264669:Q264R	ENSP00000264669:Q264R	Q	-	2	0	FASTKD3	7920406	1.000000	0.71417	0.896000	0.35187	0.956000	0.61745	4.060000	0.57477	2.024000	0.59613	0.528000	0.53228	CAG	.	.		0.353	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		C	7867406	T	C	7867406	3	2	23	1	0	0	0	0	1	0	0	0	5695	1580	55	2	1221	2	FASTKD3	5	7867406	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	160439	7867406	173047854	336	2402										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13911493	13911493	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaattttattatacaacctAcatgaaggtcattagtctgc	7	7	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:13911493A>C	ENST00000265104.4	-	12	1749		c.e12+1			NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TATACAACCTACATGAAGGTC	0.363									Kartagener syndrome																												.		Atlas-SNP	.											.	DNAH5	868	.	0			c.1644+2T>G						.						116	113	114					5																	13911493		2202	4300	6502	SO:0001630	splice_region_variant	1767	exon13	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAACCTACATGAA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.1644+1T>G	chr5.hg19:g.13911493A>C		67.0	0.0		64.0	26.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Splice_Site	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306232	0.81247	.	.	ENSG00000039139	ENST00000265104	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0858	0.81049	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNAH5	13964493	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.320000	0.89995	2.264000	0.75181	0.533000	0.62120	.	.	.		0.363	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	Intron	C	13911493	A	C	13911493	5	2	23	1	0	0	0	0	0	0	1	0	4606	405	14	5	12500	5	DNAH5	5	13911493	Splice_Site	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	6044087	13911493	167003767	337	2403										
FBXL7	23194	hgsc.bcm.edu	37	chr5	15928504	15928504	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tacaccatcgcccagtgctgCcccgaactgaggcgactgga							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:15928504delC	ENST00000504595.1	+	3	1114	c.633delC	c.(631-633)tgcfs	p.C211fs	FBXL7_ENST00000329673.7_Frame_Shift_Del_p.C199fs|FBXL7_ENST00000510662.1_Frame_Shift_Del_p.C164fs	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	211					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						CCCAGTGCTGCCCCGAACTGA	0.587																																					p.C211fs		Atlas-Indel,Pindel	.											FBXL7,right_upper_lobe,carcinoma,0,1	FBXL7	138	.	0			c.632delG						.						67	68	67					5																	15928504		2074	4199	6273	SO:0001589	frameshift_variant	23194	exon3			.	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.633delC	chr5.hg19:g.15928504delC	ENSP00000423630:p.Cys211fs	124.0	0.0		126.0	20.0	NM_012304	B9EGF1|D6RDY7|O94926	Frame_Shift_Del	DEL	ENST00000504595.1	hg19	CCDS54833.1																																																																																			.	.		0.587	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		-	15928504	C	-	15928504	7	5	23	1	0	1	0	1	0	0	0	0	5732	747	26	0	643	0	FBXL7	5	15928504	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	2017011	15928504	164986756	338	2404										
MYO10	4651	hgsc.bcm.edu	37	chr5	16818199	16818199	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctgtcaaggacgccatgtcAtccacgccctcctcgttcgt	8	16	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:16818199A>G	ENST00000513610.1	-	3	652	c.198T>C	c.(196-198)gaT>gaC	p.D66D	MYO10_ENST00000507288.1_Silent_p.D66D	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	66	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						ACGCCATGTCATCCACGCCCT	0.468																																					p.D66D		Atlas-SNP	.											.	MYO10	198	.	0			c.T198C						.						70	70	70					5																	16818199		1986	4158	6144	SO:0001819	synonymous_variant	4651	exon3			CATGTCATCCACG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.198T>C	chr5.hg19:g.16818199A>G		77.0	0.0		67.0	29.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.468	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		G	16818199	A	G	16818199	2	3	23	1	0	0	0	0	0	0	0	1	10071	214	8	2		2	MYO10	5	16818199	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	889695	16818199	164097061	339	2405										
CDH10	1008	hgsc.bcm.edu	37	chr5	24509863	24509863	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctaggtaataaaaacggggAtctacatgggtgttttctgc	11	7	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:24509863A>T	ENST00000264463.4	-	7	1575	c.1068T>A	c.(1066-1068)gaT>gaA	p.D356E		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	356	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		AAAAACGGGGATCTACATGGG	0.373										HNSCC(23;0.051)																											p.D356E		Atlas-SNP	.											.	CDH10	391	.	0			c.T1068A						.						73	75	74					5																	24509863		2203	4300	6503	SO:0001583	missense	1008	exon7			ACGGGGATCTACA	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.1068T>A	chr5.hg19:g.24509863A>T	ENSP00000264463:p.Asp356Glu	238.0	0.0		246.0	57.0	NM_006727	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	hg19	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.358179	0.41801	.	.	ENSG00000040731	ENST00000264463	T	0.50001	0.76	5.03	1.21	0.21127	Cadherin (4);Cadherin-like (1);	0.047005	0.85682	D	0.000000	T	0.36580	0.0972	L	0.43554	1.36	0.34979	D	0.75387	B	0.17465	0.022	B	0.24394	0.053	T	0.31364	-0.9946	10	0.42905	T	0.14	.	8.0783	0.30729	0.6816:0.0:0.3184:0.0	.	356	Q9Y6N8	CAD10_HUMAN	E	356	ENSP00000264463:D356E	ENSP00000264463:D356E	D	-	3	2	CDH10	24545620	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	0.773000	0.26661	0.036000	0.15547	0.459000	0.35465	GAT	.	.		0.373	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		T	24509863	A	T	24509863	3	4	23	1	0	0	0	0	1	0	0	0	3098	330	12	4	1322	4	CDH10	5	24509863	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	7691664	24509863	156405397	340	2406										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32088757	32088757	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaacatggtaaatggcttgGaacatgacctgctagatgac	10	9	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:32088757G>T	ENST00000438447.1	+	20	5591	c.5203G>T	c.(5203-5205)Gaa>Taa	p.E1735*	PDZD2_ENST00000282493.3_Nonsense_Mutation_p.E1735*			O15018	PDZD2_HUMAN	PDZ domain containing 2	1735					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						AAATGGCTTGGAACATGACCT	0.493																																					p.E1735X		Atlas-SNP	.											PDZD2,NS,malignant_melanoma,0,1	PDZD2	306	.	0			c.G5203T						.						129	105	113					5																	32088757		2203	4300	6503	SO:0001587	stop_gained	23037	exon19			GGCTTGGAACATG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.5203G>T	chr5.hg19:g.32088757G>T	ENSP00000402033:p.Glu1735*	157.0	0.0		122.0	48.0	NM_178140	Q9BXD4	Nonsense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	46	12.771677	0.99695	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	.	.	.	5.84	5.84	0.93424	.	0.864075	0.10208	N	0.702481	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	15.6279	0.76878	0.0:0.0:1.0:0.0	.	.	.	.	X	1735;1536;1735	.	ENSP00000282493:E1735X	E	+	1	0	PDZD2	32124514	0.790000	0.28787	0.007000	0.13788	0.002000	0.02628	2.805000	0.47939	2.768000	0.95171	0.561000	0.74099	GAA	.	.		0.493	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32088757	G	T	32088757	4	4	23	1	0	0	0	0	0	1	0	0	11710	1175	41	3	5277	3	PDZD2	5	32088757	Nonsense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	7578894	32088757	148826503	341	2407										
DNAJC21	134218	hgsc.bcm.edu	37	chr5	34935891	34935891	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atgacagcttagatttgctaCgctatttcaccgttacctgt	7	10	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:34935891C>T	ENST00000342382.4	+	3	495	c.268C>T	c.(268-270)Cgc>Tgc	p.R90C	DNAJC21_ENST00000382021.2_Missense_Mutation_p.R90C|DNAJC21_ENST00000303525.7_Missense_Mutation_p.R90C			Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21	90					protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			AGATTTGCTACGCTATTTCAC	0.363																																					p.R90C		Atlas-SNP	.											.	DNAJC21	54	.	0			c.C268T						.						151	148	149					5																	34935891		2203	4300	6503	SO:0001583	missense	134218	exon3			TTGCTACGCTATT		CCDS3907.2, CCDS34144.1	5p13-p12	2012-10-05			ENSG00000168724	ENSG00000168724		"Heat shock proteins / DNAJ (HSP40)"	27030	protein-coding gene	gene with protein product	"JJJ1 DnaJ domain protein homolog (S. cerevisiae)"					15067379	Standard	XM_005248250		Approved	GS3, DNAJA5, JJJ1	uc003jjc.3	Q5F1R6	OTTHUMG00000074103	ENST00000342382.4:c.268C>T	chr5.hg19:g.34935891C>T	ENSP00000343728:p.Arg90Cys	122.0	0.0		115.0	46.0	NM_001012339	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	Missense_Mutation	SNP	ENST00000342382.4	hg19	CCDS34144.1	.	.	.	.	.	.	.	.	.	.	C	16.32	3.090522	0.55968	.	.	ENSG00000168724	ENST00000342382;ENST00000382021;ENST00000303525	T;T;T	0.73152	-0.72;-0.72;-0.72	5.62	4.75	0.60458	.	0.267930	0.44097	D	0.000488	T	0.58836	0.2150	L	0.31476	0.935	0.48975	D	0.999737	B;B	0.11235	0.002;0.004	B;B	0.06405	0.002;0.001	T	0.54827	-0.8235	10	0.37606	T	0.19	-3.5566	13.9574	0.64157	0.0:0.928:0.0:0.072	.	90;90	Q5F1R6;Q5F1R6-2	DJC21_HUMAN;.	C	90	ENSP00000343728:R90C;ENSP00000371451:R90C;ENSP00000306289:R90C	ENSP00000306289:R90C	R	+	1	0	DNAJC21	34971648	1.000000	0.71417	0.998000	0.56505	0.920000	0.55202	4.580000	0.60942	2.648000	0.89879	0.650000	0.86243	CGC	.	.		0.363	DNAJC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157337.1	NM_194283		T	34935891	C	T	34935891	3	4	23	1	0	0	0	0	1	0	0	0	4642	536	19	1	278	1	DNAJC21	5	34935891	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2847134	34935891	145979369	342	2408										
PLCXD3	345557	hgsc.bcm.edu	37	chr5	41382215	41382215	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttaaactaacttcctgggcAaaaatcgctgggcacatttt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:41382215delA	ENST00000377801.3	-	2	599	c.525delT	c.(523-525)tttfs	p.F175fs	PLCXD3_ENST00000328457.3_Frame_Shift_Del_p.F175fs			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	175	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						CTTCCTGGGCAAAAATCGCTG	0.443																																					p.A176fs		Atlas-Indel,Pindel	.											.	PLCXD3	86	.	0			c.526delG						.						96	96	96					5																	41382215		2202	4300	6502	SO:0001589	frameshift_variant	345557	exon2			.		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.525delT	chr5.hg19:g.41382215delA	ENSP00000367032:p.Phe175fs	170.0	0.0		149.0	56.0	NM_001005473	A6NL04	Frame_Shift_Del	DEL	ENST00000377801.3	hg19	CCDS34150.1																																																																																			.	.		0.443	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875		-	41382215	A	-	41382215	7	5	23	1	0	1	0	1	0	0	0	0	12052	127	5	0	448	0	PLCXD3	5	41382215	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	6446324	41382215	139533045	343	2409										
NAIP	4671	hgsc.bcm.edu	37	chr5	70280772	70280772	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	attaaactcaaagcaacatgAaaaaaaccctttcaaggcca							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:70280772delA	ENST00000517649.1	-	12	2394	c.2104delT	c.(2104-2106)tcafs	p.S702fs	NAIP_ENST00000503719.2_Frame_Shift_Del_p.S540fs|NAIP_ENST00000523981.1_Frame_Shift_Del_p.S540fs|NAIP_ENST00000194097.4_Frame_Shift_Del_p.S702fs|NAIP_ENST00000508426.2_Frame_Shift_Del_p.S702fs	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	702	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		AAGCAACATGAAAAAAACCCT	0.438																																					p.S702fs		Atlas-INDEL	.											.	NAIP	38	.	0			c.2105delC						.																																			SO:0001589	frameshift_variant	4671	exon12			.	U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"Baculoviral IAP repeat containing", "Nucleotide-binding domain and leucine rich repeat containing"	7634	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1", "NLR family, BIR domain containing 1"	600355	"baculoviral IAP repeat-containing 1"	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.2104delT	chr5.hg19:g.70280772delA	ENSP00000428657:p.Ser702fs	248.0	0.0		214.0	22.0	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Del	DEL	ENST00000517649.1	hg19	CCDS4009.1																																																																																			.	.		0.438	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536		-	70280772	A	-	70280772	7	5	23	1	0	1	0	1	0	0	0	0	10156	246	9	0	2131	0	NAIP	5	70280772	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	28898557	70280772	110634488	344	2410										
UTP15	84135	hgsc.bcm.edu	37	chr5	72864403	72864403	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatataagtgggagggctccCctcaggcagtttgaaggcca	14	9	1	1	rs112684902		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:72864403C>T	ENST00000296792.4	+	4	597	c.342C>T	c.(340-342)ccC>ccT	p.P114P	UTP15_ENST00000543251.1_5'UTR|UTP15_ENST00000508491.1_Silent_p.P95P|ANKRA2_ENST00000296785.3_5'Flank	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	114					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		GGAGGGCTCCCCTCAGGCAGT	0.423																																					p.P114P		Atlas-SNP	.											.	UTP15	30	.	0			c.C342T						.						83	85	85					5																	72864403		2203	4300	6503	SO:0001819	synonymous_variant	84135	exon4			GGCTCCCCTCAGG	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"WD repeat domain containing"	25758	protein-coding gene	gene with protein product			"UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.342C>T	chr5.hg19:g.72864403C>T		89.0	0.0		104.0	43.0	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Silent	SNP	ENST00000296792.4	hg19	CCDS34186.1	.	.	.	.	.	.	.	.	.	.	C	9.184	1.024234	0.19433	.	.	ENSG00000164338	ENST00000509005	T	0.60299	0.2	5.55	-6.61	0.01818	.	0.114641	0.64402	D	0.000004	T	0.39489	0.1080	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27123	-1.0083	6	.	.	.	.	1.4894	0.02453	0.1935:0.3001:0.2796:0.2268	.	.	.	.	L	141	ENSP00000421669:P141L	.	P	+	2	0	UTP15	72900159	0.009000	0.17119	0.933000	0.37362	0.999000	0.98932	-1.208000	0.03005	-0.892000	0.03935	0.655000	0.94253	CCC	.	C|0.500;T|0.500		0.423	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175		T	72864403	C	T	72864403	2	4	23	1	0	0	0	0	0	0	0	1	17112	610	22	3		3	UTP15	5	72864403	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2583631	72864403	108050857	345	2411										
RGNEF	64283	hgsc.bcm.edu	37	chr5	73128204	73128204	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaaaatccaagccgccctcgAcattgcttgctgcaggccgg	10	14	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:73128204A>G	ENST00000426542.2	+	9	1086	c.1066A>G	c.(1066-1068)Aca>Gca	p.T356A	ARHGEF28_ENST00000545377.1_Missense_Mutation_p.T356A|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.T356A|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.T356A|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.T356A|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.T43A|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.T356A			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	356					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GCCGCCCTCGACATTGCTTGC	0.443																																					p.T356A		Atlas-SNP	.											.	.	.	.	0			c.A1066G						.						82	74	77					5																	73128204		1904	4118	6022	SO:0001583	missense	64283	exon10			CCCTCGACATTGC		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.1066A>G	chr5.hg19:g.73128204A>G	ENSP00000412175:p.Thr356Ala	108.0	0.0		96.0	7.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	A	4.301	0.055104	0.08291	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.12879	2.9;2.9;2.9;2.64;2.9;2.9;2.77	5.48	-11.0	0.00169	.	.	.	.	.	T	0.04543	0.0124	N	0.10874	0.06	0.09310	N	1	B;B;B;B;B	0.09022	0.001;0.002;0.0;0.001;0.001	B;B;B;B;B	0.08055	0.002;0.003;0.002;0.003;0.003	T	0.30238	-0.9985	9	0.26408	T	0.33	.	4.6539	0.12608	0.2743:0.1912:0.4408:0.0937	.	43;356;356;356;356	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-2;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	A	356;356;356;356;356;356;43	ENSP00000296794:T356A;ENSP00000441913:T356A;ENSP00000441436:T356A;ENSP00000287898:T356A;ENSP00000411459:T356A;ENSP00000412175:T356A;ENSP00000296799:T43A	ENSP00000287898:T356A	T	+	1	0	RP11-428C6.1	73163960	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.004000	0.03678	-2.654000	0.00422	-0.263000	0.10527	ACA	.	.		0.443	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			G	73128204	A	G	73128204	3	3	23	1	0	0	0	0	1	0	0	0	13298	275	10	2	1100	2	RGNEF	5	73128204	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	263801	73128204	107787056	346	2412										
RGNEF	64283	hgsc.bcm.edu	37	chr5	73179659	73179659	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cattctgttggtcactcagcGtattacaaaataccctgtct	6	11	4	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:73179659G>A	ENST00000426542.2	+	23	3025	c.3005G>A	c.(3004-3006)cGt>cAt	p.R1002H	ARHGEF28_ENST00000512883.1_5'Flank|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.R1002H|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.R1002H|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.R1002H|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.R1002H|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.R689H|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.R1002H			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1002	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GTCACTCAGCGTATTACAAAA	0.363																																					p.R1002H		Atlas-SNP	.											.	.	.	.	0			c.G3005A						.						56	54	55					5																	73179659		1847	4074	5921	SO:0001583	missense	64283	exon24			CTCAGCGTATTAC		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.3005G>A	chr5.hg19:g.73179659G>A	ENSP00000412175:p.Arg1002His	175.0	0.0		144.0	61.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	G	34	5.388581	0.95988	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	D;D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	5.75	5.75	0.90469	Dbl homology (DH) domain (5);	.	.	.	.	D	0.95268	0.8465	M	0.91140	3.18	0.54753	D	0.999986	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.95620	0.8680	9	0.87932	D	0	.	19.9433	0.97172	0.0:0.0:1.0:0.0	.	689;1002;1002;1002	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	H	1002;1002;1002;1002;1002;1002;689	ENSP00000296794:R1002H;ENSP00000441913:R1002H;ENSP00000441436:R1002H;ENSP00000287898:R1002H;ENSP00000411459:R1002H;ENSP00000412175:R1002H;ENSP00000296799:R689H	ENSP00000287898:R1002H	R	+	2	0	RP11-428C6.1	73215415	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.390000	0.97246	2.716000	0.92895	0.655000	0.94253	CGT	.	.		0.363	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			A	73179659	G	A	73179659	3	1	23	1	0	0	0	0	1	0	0	0	13298	1145	40	1	3095	1	RGNEF	5	73179659	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	51455	73179659	107735601	347	2413										
HMGCR	3156	hgsc.bcm.edu	37	chr5	74650434	74650434	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaaactcatgagcgtggtgTatctattcgccgacagttac	11	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:74650434T>C	ENST00000287936.4	+	12	1631	c.1475T>C	c.(1474-1476)gTa>gCa	p.V492A	HMGCR_ENST00000511206.1_Missense_Mutation_p.V492A|HMGCR_ENST00000343975.5_Missense_Mutation_p.V492A	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	492	Catalytic.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	GAGCGTGGTGTATCTATTCGC	0.408																																					p.V492A		Atlas-SNP	.											.	HMGCR	53	.	0			c.T1475C						.						136	117	123					5																	74650434		2203	4300	6503	SO:0001583	missense	3156	exon12			GTGGTGTATCTAT		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"hydroxymethylglutaryl-CoA reductase", "3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"	142910	"3-hydroxy-3-methylglutaryl-Coenzyme A reductase"				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.1475T>C	chr5.hg19:g.74650434T>C	ENSP00000287936:p.Val492Ala	154.0	0.0		124.0	57.0	NM_001130996	B7Z3Y9|Q8N190	Missense_Mutation	SNP	ENST00000287936.4	hg19	CCDS4027.1	.	.	.	.	.	.	.	.	.	.	T	19.59	3.855882	0.71834	.	.	ENSG00000113161	ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975	T;T;T	0.48201	0.82;0.82;0.87	5.14	3.94	0.45596	Hydroxymethylglutaryl-CoA reductase, N-terminal (1);Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding (1);	0.000000	0.85682	D	0.000000	T	0.59569	0.2203	L	0.48935	1.535	0.80722	D	1	P;D;P	0.89917	0.474;1.0;0.474	P;D;P	0.87578	0.785;0.998;0.785	T	0.57093	-0.7870	10	0.42905	T	0.14	-12.7489	12.1695	0.54150	0.0:0.0:0.1432:0.8568	.	492;492;492	B2R649;P04035-2;P04035	.;.;HMDH_HUMAN	A	492;423;492;492	ENSP00000426745:V492A;ENSP00000287936:V492A;ENSP00000340816:V492A	ENSP00000287936:V492A	V	+	2	0	HMGCR	74686190	1.000000	0.71417	1.000000	0.80357	0.544000	0.35116	7.667000	0.83888	0.878000	0.35920	0.383000	0.25322	GTA	.	.		0.408	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			C	74650434	T	C	74650434	3	2	23	1	0	0	0	0	1	0	0	0	7240	1638	57	2	1517	2	HMGCR	5	74650434	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1470775	74650434	106264826	348	2414										
AGGF1	55109	hgsc.bcm.edu	37	chr5	76342271	76342271	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaaagaaggccaaaataggcAttcatcacaaaaatagtccc	6	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:76342271A>G	ENST00000312916.7	+	6	1352	c.970A>G	c.(970-972)Att>Gtt	p.I324V		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	324					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		CAAAATAGGCATTCATCACAA	0.363																																					p.I324V		Atlas-SNP	.											.	AGGF1	71	.	0			c.A970G						.						112	120	117					5																	76342271		2203	4300	6503	SO:0001583	missense	55109	exon6			ATAGGCATTCATC	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"G patch domain containing"	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.970A>G	chr5.hg19:g.76342271A>G	ENSP00000316109:p.Ile324Val	291.0	0.0		277.0	14.0	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	hg19	CCDS4035.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.357510	0.00214	.	.	ENSG00000164252	ENST00000312916	T	0.35236	1.32	5.29	0.123	0.14709	.	1.373260	0.04317	N	0.349998	T	0.20941	0.0504	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16808	-1.0390	10	0.27082	T	0.32	-26.3289	4.8384	0.13476	0.5717:0.0:0.297:0.1314	.	324	Q8N302	AGGF1_HUMAN	V	324	ENSP00000316109:I324V	ENSP00000316109:I324V	I	+	1	0	AGGF1	76378027	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	0.453000	0.21811	0.010000	0.14839	0.482000	0.46254	ATT	.	.		0.363	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046		G	76342271	A	G	76342271	3	3	23	1	0	0	0	0	1	0	0	0	382	217	8	2	992	2	AGGF1	5	76342271	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1691837	76342271	104572989	349	2415										
AP3B1	8546	hgsc.bcm.edu	37	chr5	77423904	77423904	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgggtcgggcgccacctctgGccaattagataattccaggt	12	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:77423904G>A	ENST00000255194.6	-	17	2093	c.1918C>T	c.(1918-1920)Cca>Tca	p.P640S	AP3B1_ENST00000519295.1_Missense_Mutation_p.P591S	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	640					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GCCACCTCTGGCCAATTAGAT	0.393									Hermansky-Pudlak syndrome																												p.P640S		Atlas-SNP	.											.	AP3B1	94	.	0			c.C1918T						.						74	76	75					5																	77423904		2203	4300	6503	SO:0001583	missense	8546	exon17	Familial Cancer Database	HPS, HPS1-8	CCTCTGGCCAATT	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1918C>T	chr5.hg19:g.77423904G>A	ENSP00000255194:p.Pro640Ser	106.0	0.0		113.0	39.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.910962	0.72983	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.58358	0.34;0.34	5.91	5.91	0.95273	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.77150	0.4088	M	0.88704	2.975	0.80722	D	1	D	0.60160	0.987	P	0.62298	0.9	T	0.80529	-0.1342	10	0.87932	D	0	-13.6369	20.2983	0.98569	0.0:0.0:1.0:0.0	.	640	O00203	AP3B1_HUMAN	S	640;591;640;544	ENSP00000255194:P640S;ENSP00000430597:P591S	ENSP00000255194:P640S	P	-	1	0	AP3B1	77459660	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.845000	0.99498	2.802000	0.96397	0.655000	0.94253	CCA	.	.		0.393	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			A	77423904	G	A	77423904	3	1	23	1	0	0	0	0	1	0	0	0	744	1203	42	3	1410	3	AP3B1	5	77423904	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1081633	77423904	103491356	350	2416										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79033682	79033682	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ataagacaaaagaagagataTccacagattcagaaactgat	7	6	1	6			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:79033682T>A	ENST00000446378.2	+	2	9125	c.9094T>A	c.(9094-9096)Tcc>Acc	p.S3032T		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3032					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AGAAGAGATATCCACAGATTC	0.313																																					p.S3032T		Atlas-SNP	.											.	CMYA5	643	.	0			c.T9094A						.						54	52	53					5																	79033682		1798	4067	5865	SO:0001583	missense	202333	exon2			GAGATATCCACAG	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.9094T>A	chr5.hg19:g.79033682T>A	ENSP00000394770:p.Ser3032Thr	473.0	0.0		440.0	179.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	T	6.040	0.375720	0.11409	.	.	ENSG00000164309	ENST00000446378	T	0.15952	2.38	5.93	-11.7	0.00046	.	1.351940	0.04712	N	0.417809	T	0.13286	0.0322	L	0.56769	1.78	0.09310	N	1	B	0.21381	0.055	B	0.20955	0.032	T	0.24048	-1.0171	10	0.59425	D	0.04	.	5.4465	0.16537	0.0849:0.3216:0.4121:0.1815	.	3032	Q8N3K9	CMYA5_HUMAN	T	3032	ENSP00000394770:S3032T	ENSP00000394770:S3032T	S	+	1	0	CMYA5	79069438	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-0.914000	0.04038	-2.465000	0.00533	-0.313000	0.08912	TCC	.	.		0.313	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79033682	T	A	79033682	3	1	23	1	0	0	0	0	1	0	0	0	3592	1435	50	4	9100	4	CMYA5	5	79033682	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1609778	79033682	101881578	351	2417										
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79734315	79734315	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aatagttgataaacaaaataCaatagaaaatggcctttctt	5	5	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:79734315C>T	ENST00000338008.5	+	3	1991	c.1811C>T	c.(1810-1812)aCa>aTa	p.T604I	ZFYVE16_ENST00000510158.1_Missense_Mutation_p.T604I|ZFYVE16_ENST00000505560.1_Missense_Mutation_p.T604I	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	604					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		AAACAAAATACAATAGAAAAT	0.323																																					p.T604I	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.C1811T						.						67	78	74					5																	79734315		2202	4295	6497	SO:0001583	missense	9765	exon4			AAAATACAATAGA	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"Zinc fingers, FYVE domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20756	protein-coding gene	gene with protein product	"endofin", "protein phosphatase 1, regulatory subunit 69"	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.1811C>T	chr5.hg19:g.79734315C>T	ENSP00000337159:p.Thr604Ile	418.0	0.0		456.0	202.0	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Missense_Mutation	SNP	ENST00000338008.5	hg19	CCDS4050.1	.	.	.	.	.	.	.	.	.	.	C	2.829	-0.242975	0.05906	.	.	ENSG00000039319	ENST00000338008;ENST00000510158;ENST00000505560	T;T;T	0.39592	1.07;1.07;1.07	5.42	-0.906	0.10524	.	1.075510	0.07096	N	0.839533	T	0.29716	0.0742	L	0.34521	1.04	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.32241	-0.9914	10	0.56958	D	0.05	0.35	5.4894	0.16767	0.1424:0.3281:0.0:0.5295	.	604;604	Q7Z3T8-3;Q7Z3T8	.;ZFY16_HUMAN	I	604	ENSP00000337159:T604I;ENSP00000423663:T604I;ENSP00000426848:T604I	ENSP00000337159:T604I	T	+	2	0	ZFYVE16	79770071	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	-0.198000	0.09505	-0.097000	0.12307	0.650000	0.86243	ACA	.	.		0.323	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		T	79734315	C	T	79734315	3	4	23	1	0	0	0	0	1	0	0	0	17679	478	17	3	1817	3	ZFYVE16	5	79734315	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	700633	79734315	101180945	352	2418										
NR2F1	7025	hgsc.bcm.edu	37	chr5	92923770	92923770	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctaccccacgtcgcgctacgGcagccagtgcatgcagccca	10	18	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:92923770G>A	ENST00000327111.3	+	2	2298	c.611G>A	c.(610-612)gGc>gAc	p.G204D	NR2F1-AS1_ENST00000513055.1_RNA	NM_005654.4	NP_005645.1	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	204					cerebral cortex regionalization (GO:0021796)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|retinoic acid-responsive element binding (GO:0044323)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|large_intestine(6)|lung(2)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	21		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		TCGCGCTACGGCAGCCAGTGC	0.657																																					p.G204D		Atlas-SNP	.											.	NR2F1	56	.	0			c.G611A						.						66	66	66					5																	92923770		2203	4299	6502	SO:0001583	missense	7025	exon2			GCTACGGCAGCCA	BC004154	CCDS4068.1	5q14	2013-01-16			ENSG00000175745	ENSG00000175745		"Nuclear hormone receptors"	7975	protein-coding gene	gene with protein product		132890		ERBAL3, TFCOUP1		8530078	Standard	NM_005654		Approved	EAR-3, COUP-TFI, TCFCOUP1, SVP44	uc003kkj.3	P10589	OTTHUMG00000119079	ENST00000327111.3:c.611G>A	chr5.hg19:g.92923770G>A	ENSP00000325819:p.Gly204Asp	179.0	0.0		193.0	80.0	NM_005654		Missense_Mutation	SNP	ENST00000327111.3	hg19	CCDS4068.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.994603	0.93167	.	.	ENSG00000175745	ENST00000327111	T	0.51574	0.7	4.39	4.39	0.52855	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	T	0.55847	0.1946	L	0.58583	1.82	0.80722	D	1	P	0.41673	0.759	P	0.49853	0.624	T	0.53613	-0.8414	10	0.30078	T	0.28	.	17.1166	0.86690	0.0:0.0:1.0:0.0	.	204	P10589	COT1_HUMAN	D	204	ENSP00000325819:G204D	ENSP00000325819:G204D	G	+	2	0	NR2F1	92949526	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	9.554000	0.98121	2.250000	0.74265	0.462000	0.41574	GGC	.	.		0.657	NR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239293.2	NM_005654		A	92923770	G	A	92923770	3	1	23	1	0	0	0	0	1	0	0	0	10636	1203	42	3	617	3	NR2F1	5	92923770	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	13189455	92923770	87991490	353	2419										
TRIM36	55521	hgsc.bcm.edu	37	chr5	114462349	114462349	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttcatctgatccatatcatAgaaatctactttgcctttat	3	9	4	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:114462349A>G	ENST00000282369.3	-	10	2159	c.2038T>C	c.(2038-2040)Tat>Cat	p.Y680H	TRIM36_ENST00000513154.1_Missense_Mutation_p.Y668H|TRIM36_ENST00000514154.1_Missense_Mutation_p.Y525H	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	680	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		TCCATATCATAGAAATCTACT	0.398																																					p.Y680H		Atlas-SNP	.											.	TRIM36	126	.	0			c.T2038C						.						98	90	93					5																	114462349		2202	4300	6502	SO:0001583	missense	55521	exon10			TATCATAGAAATC	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16280	protein-coding gene	gene with protein product	"zinc-binding protein Rbcc728", "tripartite motif protein 36", "RING finger protein 98"	609317	"tripartite motif-containing 36"			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.2038T>C	chr5.hg19:g.114462349A>G	ENSP00000282369:p.Tyr680His	141.0	0.0		136.0	62.0	NM_018700	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	hg19	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.112104	0.77210	.	.	ENSG00000152503	ENST00000282369;ENST00000513154;ENST00000514154	T;T;T	0.65549	-0.16;-0.16;-0.16	5.73	5.73	0.89815	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.058778	0.64402	D	0.000001	D	0.83050	0.5170	M	0.89785	3.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86561	0.1841	10	0.72032	D	0.01	.	16.3197	0.82945	1.0:0.0:0.0:0.0	.	668;680	E9PFI8;Q9NQ86	.;TRI36_HUMAN	H	680;668;525	ENSP00000282369:Y680H;ENSP00000423934:Y668H;ENSP00000424259:Y525H	ENSP00000282369:Y680H	Y	-	1	0	TRIM36	114490248	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.920000	0.75799	2.302000	0.77476	0.533000	0.62120	TAT	.	.		0.398	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		G	114462349	A	G	114462349	3	3	23	1	0	0	0	0	1	0	0	0	16525	420	15	2	152	2	TRIM36	5	114462349	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	21538579	114462349	66452911	354	2420										
SRFBP1	153443	hgsc.bcm.edu	37	chr5	121356208	121356208	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttgtgaagaggagaaggaaTattttgatgatagcacagaa	12	2	0	6			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:121356208T>A	ENST00000339397.4	+	6	850	c.778T>A	c.(778-780)Tat>Aat	p.Y260N		NM_152546.2	NP_689759.2			serum response factor binding protein 1											central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		GGAGAAGGAATATTTTGATGA	0.403																																					p.Y260N		Atlas-SNP	.											.	SRFBP1	47	.	0			c.T778A						.						132	119	123					5																	121356208		1876	4119	5995	SO:0001583	missense	153443	exon6			AAGGAATATTTTG	AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"BUD22 homolog (S. cerevisiae)"	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.778T>A	chr5.hg19:g.121356208T>A	ENSP00000341324:p.Tyr260Asn	284.0	0.0		300.0	118.0	NM_152546		Missense_Mutation	SNP	ENST00000339397.4	hg19	CCDS43354.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.852647	0.51270	.	.	ENSG00000151304	ENST00000339397	.	.	.	5.71	4.54	0.55810	.	0.055267	0.85682	D	0.000000	T	0.68531	0.3011	M	0.67397	2.05	0.58432	D	0.999992	D	0.61080	0.989	P	0.57057	0.812	T	0.71513	-0.4570	9	0.72032	D	0.01	-12.1589	13.0005	0.58672	0.0:0.0:0.1351:0.8649	.	260	Q8NEF9	SRFB1_HUMAN	N	260	.	ENSP00000341324:Y260N	Y	+	1	0	SRFBP1	121384107	1.000000	0.71417	0.975000	0.42487	0.491000	0.33493	4.744000	0.62118	0.974000	0.38366	0.460000	0.39030	TAT	.	.		0.403	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546		A	121356208	T	A	121356208	3	1	23	1	0	0	0	0	1	0	0	0	15159	1406	49	4	800	4	SRFBP1	5	121356208	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	6893859	121356208	59559052	355	2421										
FNIP1	96459	hgsc.bcm.edu	37	chr5	131007515	131007515	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttctgcttgttattttttgtAcacaatatttttgaaaactc	4	6	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:131007515A>G	ENST00000510461.1	-	14	2717	c.2622T>C	c.(2620-2622)tgT>tgC	p.C874C	CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Silent_p.C846C|FNIP1_ENST00000307954.8_Silent_p.C829C	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	874					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		TATTTTTTGTACACAATATTT	0.323																																					p.C874C		Atlas-SNP	.											.	FNIP1	104	.	0			c.T2622C						.						62	64	63					5																	131007515		2203	4300	6503	SO:0001819	synonymous_variant	96459	exon14			TTTTGTACACAAT	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.2622T>C	chr5.hg19:g.131007515A>G		114.0	0.0		103.0	6.0	NM_133372	D6RJH5|Q86T47|Q9BUT0	Silent	SNP	ENST00000510461.1	hg19	CCDS34227.1																																																																																			.	.		0.323	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		G	131007515	A	G	131007515	2	3	23	1	0	0	0	0	0	0	0	1	5983	389	14	2		2	FNIP1	5	131007515	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	9651307	131007515	49907745	356	2422										
KIF3A	11127	hgsc.bcm.edu	37	chr5	132069913	132069913	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttaccattgtagccttcaagTacagaatcaataataggtct	6	8	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:132069913T>A	ENST00000378746.4	-	2	482	c.264A>T	c.(262-264)gtA>gtT	p.V88V	KIF3A_ENST00000378735.1_Silent_p.V88V|KIF3A_ENST00000403231.1_Silent_p.V88V	NM_007054.5	NP_008985.3	Q9Y496	KIF3A_HUMAN	kinesin family member 3A	88	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterior/posterior pattern specification (GO:0009952)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|organelle organization (GO:0006996)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of receptor-mediated endocytosis (GO:0048260)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|neuron projection (GO:0043005)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|spectrin binding (GO:0030507)			endometrium(1)|kidney(4)|large_intestine(8)|lung(3)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	25		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGCCTTCAAGTACAGAATCAA	0.328																																					p.V88V		Atlas-SNP	.											.	KIF3A	117	.	0			c.A264T						.						98	101	100					5																	132069913		2203	4300	6503	SO:0001819	synonymous_variant	11127	exon2			TTCAAGTACAGAA	AF041853	CCDS34235.1, CCDS75295.1, CCDS75296.1	5q31	2012-08-01			ENSG00000131437	ENSG00000131437		"Kinesins"	6319	protein-coding gene	gene with protein product	"kinesin family protein 3A"	604683				1054846	Standard	XM_005271868		Approved	FLA10, KLP-20	uc003kxo.3	Q9Y496	OTTHUMG00000059725	ENST00000378746.4:c.264A>T	chr5.hg19:g.132069913T>A		183.0	0.0		177.0	71.0	NM_007054	A8MSW9|Q59EN1|Q86XE9|Q9Y6V4	Silent	SNP	ENST00000378746.4	hg19	CCDS34235.1																																																																																			.	.		0.328	KIF3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132788.3	NM_007054		A	132069913	T	A	132069913	2	1	23	1	0	0	0	0	0	0	0	1	8309	1625	57	4		4	KIF3A	5	132069913	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1062398	132069913	48845347	357	2423										
ANKRD43	134548	hgsc.bcm.edu	37	chr5	132150795	132150795	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atgctccaggacctggcccgAggcttgaagaagtcgagctc	13	12	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:132150795A>G	ENST00000378693.2	+	1	1763	c.1482A>G	c.(1480-1482)cgA>cgG	p.R494R	AC004775.5_ENST00000607389.1_lincRNA	NM_175873.4	NP_787069.3	Q2M3V2	SWAHA_HUMAN	sosondowah ankyrin repeat domain family member A	494																	ACCTGGCCCGAGGCTTGAAGA	0.612																																					p.R494R		Atlas-SNP	.											.	.	.	.	0			c.A1482G						.						44	46	45					5																	132150795		2203	4300	6503	SO:0001819	synonymous_variant	134548	exon1			GGCCCGAGGCTTG	AK090823	CCDS43361.1	5q23.3	2013-01-10	2012-01-12	2012-01-12	ENSG00000198944	ENSG00000198944		"Ankyrin repeat domain containing"	27033	protein-coding gene	gene with protein product			"ankyrin repeat domain 43"	ANKRD43		22234889	Standard	NM_175873		Approved		uc003kxw.3	Q2M3V2	OTTHUMG00000059844	ENST00000378693.2:c.1482A>G	chr5.hg19:g.132150795A>G		82.0	0.0		103.0	43.0	NM_175873	Q8NAE7	Silent	SNP	ENST00000378693.2	hg19	CCDS43361.1																																																																																			.	.		0.612	SOWAHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133062.1	NM_175873		G	132150795	A	G	132150795	2	3	23	1	0	0	0	0	0	0	0	1	671	291	11	2		2	ANKRD43	5	132150795	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	80882	132150795	48764465	358	2424										
SHROOM1	134549	hgsc.bcm.edu	37	chr5	132159057	132159057	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctctaggtcggccatgaacCggctgaaccgctccagctcc	11	16	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:132159057C>T	ENST00000378679.3	-	9	2915	c.2111G>A	c.(2110-2112)cGg>cAg	p.R704Q	SHROOM1_ENST00000319854.3_Missense_Mutation_p.R704Q|SHROOM1_ENST00000488072.1_5'UTR|SHROOM1_ENST00000378676.1_Missense_Mutation_p.R635Q	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	704	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGCCATGAACCGGCTGAACCG	0.736																																					p.R704Q		Atlas-SNP	.											.	SHROOM1	35	.	0			c.G2111A						.						13	15	14					5																	132159057		2175	4257	6432	SO:0001583	missense	134549	exon6			ATGAACCGGCTGA	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.2111G>A	chr5.hg19:g.132159057C>T	ENSP00000367950:p.Arg704Gln	72.0	0.0		65.0	24.0	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	hg19	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.668504	0.88348	.	.	ENSG00000164403	ENST00000378679;ENST00000319854;ENST00000378676	T;T;T	0.30714	1.52;1.52;1.52	4.91	4.04	0.47022	Apx/shroom, ASD2 (2);	0.258925	0.32314	N	0.006270	T	0.38719	0.1051	L	0.46741	1.465	0.28487	N	0.914656	D;D	0.89917	0.988;1.0	P;D	0.80764	0.737;0.994	T	0.24440	-1.0160	10	0.16420	T	0.52	-27.3311	5.52	0.16927	0.1996:0.7023:0.0:0.0982	.	704;704	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	Q	704;704;635	ENSP00000367950:R704Q;ENSP00000324245:R704Q;ENSP00000367947:R635Q	ENSP00000324245:R704Q	R	-	2	0	SHROOM1	132186956	0.060000	0.20803	1.000000	0.80357	0.981000	0.71138	1.570000	0.36439	2.673000	0.90976	0.555000	0.69702	CGG	.	.		0.736	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		T	132159057	C	T	132159057	3	4	23	1	0	0	0	0	1	0	0	0	14308	652	23	1	455	1	SHROOM1	5	132159057	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	8262	132159057	48756203	359	2425										
PKD2L2	27039	hgsc.bcm.edu	37	chr5	137228299	137228299	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgcagcataactgatttttgGaaggtaaagtatcttgtgac	10	6	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:137228299G>T	ENST00000508883.1	+	3	290	c.264G>T	c.(262-264)tgG>tgT	p.W88C	PKD2L2_ENST00000290431.5_Missense_Mutation_p.W88C|PKD2L2_ENST00000350250.4_Missense_Mutation_p.W54C|PKD2L2_ENST00000502810.1_Missense_Mutation_p.W88C|PKD2L2_ENST00000508638.1_Missense_Mutation_p.W88C			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	88					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTGATTTTTGGAAGGTAAAGT	0.378																																					p.W88C		Atlas-SNP	.											.	PKD2L2	68	.	0			c.G264T						.						142	136	138					5																	137228299		1884	4126	6010	SO:0001583	missense	27039	exon3			TTTTTGGAAGGTA	AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"Voltage-gated ion channels / Transient receptor potential cation channels"	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.264G>T	chr5.hg19:g.137228299G>T	ENSP00000424725:p.Trp88Cys	152.0	0.0		125.0	52.0	NM_001258448	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	hg19		.	.	.	.	.	.	.	.	.	.	G	24.6	4.546161	0.86022	.	.	ENSG00000078795	ENST00000350250;ENST00000508638;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73;-0.73	5.84	5.84	0.93424	Polycystin cation channel, PKD1/PKD2 (1);	0.000000	0.64402	D	0.000007	D	0.86723	0.6001	M	0.85777	2.775	0.80722	D	1	D;D;D	0.89917	0.997;1.0;0.994	D;D;P	0.85130	0.997;0.972;0.77	D	0.87797	0.2622	10	0.87932	D	0	-4.9854	19.7449	0.96248	0.0:0.0:1.0:0.0	.	88;88;88	Q9NZM6;E9PC91;Q9NZM6-5	PK2L2_HUMAN;.;.	C	54;88;88;88;88	ENSP00000344177:W54C;ENSP00000423382:W88C;ENSP00000425513:W88C;ENSP00000424725:W88C;ENSP00000290431:W88C	ENSP00000290431:W88C	W	+	3	0	PKD2L2	137256198	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.692000	0.91284	2.768000	0.95171	0.609000	0.83330	TGG	.	.		0.378	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		T	137228299	G	T	137228299	3	4	23	1	0	0	0	0	1	0	0	0	11977	1183	41	3	274	3	PKD2L2	5	137228299	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	5069242	137228299	43686961	360	2426										
APBB3	10307	hgsc.bcm.edu	37	chr5	139939980	139939980	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgcactggaagctctgacggCccaggtcagcgatgaggcca	14	13	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:139939980C>A	ENST00000357560.4	-	12	1585	c.1142G>T	c.(1141-1143)gGc>gTc	p.G381V	SRA1_ENST00000336283.6_5'Flank|APBB3_ENST00000508496.2_Missense_Mutation_p.G158V|APBB3_ENST00000507279.1_5'Flank|APBB3_ENST00000358580.5_3'UTR|APBB3_ENST00000354402.5_Missense_Mutation_p.G388V|APBB3_ENST00000356738.2_Missense_Mutation_p.G386V|SRA1_ENST00000520427.1_5'Flank|APBB3_ENST00000412920.3_Missense_Mutation_p.G379V	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	381	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTCTGACGGCCCAGGTCAGC	0.602																																					p.G388V		Atlas-SNP	.											.	APBB3	34	.	0			c.G1163T						.						59	53	55					5																	139939980		2203	4300	6503	SO:0001583	missense	10307	exon11			TGACGGCCCAGGT	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.1142G>T	chr5.hg19:g.139939980C>A	ENSP00000350171:p.Gly381Val	213.0	0.0		223.0	52.0	NM_006051	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	ENST00000357560.4	hg19	CCDS4229.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434687	0.83885	.	.	ENSG00000113108	ENST00000356738;ENST00000354402;ENST00000357560;ENST00000508496;ENST00000412920	T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.59252	0.2180	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.57177	-0.7856	9	.	.	.	-19.9488	18.9073	0.92467	0.0:1.0:0.0:0.0	.	379;386	O95704-2;O95704-3	.;.	V	386;388;381;158;379	ENSP00000349177:G386V;ENSP00000346378:G388V;ENSP00000350171:G381V;ENSP00000444013:G158V;ENSP00000402591:G379V	.	G	-	2	0	APBB3	139920164	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.678000	0.84035	2.468000	0.83385	0.655000	0.94253	GGC	.	.		0.602	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051		A	139939980	C	A	139939980	3	1	23	1	0	0	0	0	1	0	0	0	762	739	26	3	326	3	APBB3	5	139939980	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2711681	139939980	40975280	361	2427										
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140167660	140167660	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catgtggtggcgaaggtgcgCgcagtggacgccgactcggg	19	10	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140167660C>T	ENST00000504120.2	+	1	1785	c.1785C>T	c.(1783-1785)cgC>cgT	p.R595R	PCDHA1_ENST00000378133.3_Silent_p.R595R|PCDHA1_ENST00000394633.3_Intron	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	595	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGAAGGTGCGCGCAGTGGACG	0.692																																					p.R595R		Atlas-SNP	.											.	PCDHA1	387	.	0			c.C1785T						.						103	97	99					5																	140167660		2203	4299	6502	SO:0001819	synonymous_variant	56147	exon1			GGTGCGCGCAGTG	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"Cadherins / Protocadherins : Clustered"	8663	other	complex locus constituent	"KIAA0345-like 13"	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1785C>T	chr5.hg19:g.140167660C>T		126.0	0.0		153.0	60.0	NM_031410	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	hg19	CCDS54913.1																																																																																			.	.		0.692	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		T	140167660	C	T	140167660	2	4	23	1	0	0	0	0	0	0	0	1	11528	755	27	1		1	PCDHA1	5	140167660	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	227680	140167660	40747600	362	2428										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237443	140237443	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgctgactctggatacaacGcgtggctgtcgtatgaattg	12	9	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140237443G>T	ENST00000307360.5	+	1	1810	c.1810G>T	c.(1810-1812)Gcg>Tcg	p.A604S	PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	604	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGATACAACGCGTGGCTGTC	0.652																																					p.A604S		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1810T						.						90	91	91					5																	140237443		1323	2289	3612	SO:0001583	missense	56139	exon1			TACAACGCGTGGC	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1810G>T	chr5.hg19:g.140237443G>T	ENSP00000304234:p.Ala604Ser	165.0	0.0		141.0	65.0	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	hg19	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.733841	0.48939	.	.	ENSG00000250120	ENST00000307360	T	0.37752	1.18	3.68	3.68	0.42216	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.59985	0.2234	M	0.78801	2.425	0.39875	D	0.973556	D;D	0.89917	1.0;0.999	D;D	0.74674	0.954;0.984	T	0.66626	-0.5876	9	0.46703	T	0.11	.	15.9591	0.79914	0.0:0.0:1.0:0.0	.	604;604	Q9Y5I2-3;Q9Y5I2	.;PCDAA_HUMAN	S	604	ENSP00000304234:A604S	ENSP00000304234:A604S	A	+	1	0	PCDHA10	140217627	0.986000	0.35501	1.000000	0.80357	0.245000	0.25701	3.266000	0.51569	2.041000	0.60428	0.491000	0.48974	GCG	.	.		0.652	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140237443	G	T	140237443	3	4	23	1	0	0	0	0	1	0	0	0	11529	1087	38	1	1812	1	PCDHA10	5	140237443	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	69783	140237443	40677817	363	2429										
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140347456	140347456	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccccagaggtggtgctcacgGacctgtatagcccagtgcct	12	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140347456G>A	ENST00000289269.5	+	1	1637	c.1105G>A	c.(1105-1107)Gac>Aac	p.D369N	PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	369					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGCTCACGGACCTGTATAG	0.587																																					p.D369N	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.G1105A						.						93	78	83					5																	140347456		2203	4300	6503	SO:0001583	missense	56134	exon1			CTCACGGACCTGT	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"Cadherins / Protocadherins : Clustered"	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1105G>A	chr5.hg19:g.140347456G>A	ENSP00000289269:p.Asp369Asn	68.0	0.0		61.0	17.0	NM_031883	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	hg19	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.220364	0.39201	.	.	ENSG00000243232	ENST00000289269	T	0.67171	-0.25	5.6	5.6	0.85130	Cadherin-like (1);	0.000000	0.43747	D	0.000532	T	0.45438	0.1342	N	0.05510	-0.035	0.40517	D	0.980794	B;P	0.35174	0.352;0.488	B;B	0.30943	0.122;0.11	T	0.55724	-0.8096	10	0.72032	D	0.01	.	12.6865	0.56949	0.0:0.0:0.7245:0.2755	.	369;369	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	N	369	ENSP00000289269:D369N	ENSP00000289269:D369N	D	+	1	0	PCDHAC2	140327640	1.000000	0.71417	0.880000	0.34516	0.746000	0.42486	4.005000	0.57075	2.636000	0.89361	0.655000	0.94253	GAC	.	.		0.587	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		A	140347456	G	A	140347456	3	1	23	1	0	0	0	0	1	0	0	0	11542	1174	41	3	1107	3	PCDHAC2	5	140347456	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	110013	140347456	40567804	364	2430										
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140605037	140605037	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atggcgagcctcctcgctcgGccaccgccacgctgcacgtg	12	18	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140605037G>A	ENST00000239449.4	+	1	1960	c.1960G>A	c.(1960-1962)Gcc>Acc	p.A654T	PCDHB14_ENST00000515856.2_Missense_Mutation_p.A501T	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	654	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCTCGCTCGGCCACCGCCAC	0.721																																					p.A654T	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G1960A						.						16	20	18					5																	140605037		1894	3876	5770	SO:0001583	missense	56122	exon1			CGCTCGGCCACCG	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"Cadherins / Protocadherins : Clustered"	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.1960G>A	chr5.hg19:g.140605037G>A	ENSP00000239449:p.Ala654Thr	59.0	0.0		46.0	16.0	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	hg19	CCDS4256.1	.	.	.	.	.	.	.	.	.	.	N	8.920	0.960874	0.18583	.	.	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.51071	0.72;0.72	3.83	1.49	0.22878	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.42562	0.1208	L	0.40543	1.245	0.28057	N	0.933136	P	0.39424	0.673	P	0.44696	0.458	T	0.33574	-0.9863	9	0.46703	T	0.11	.	8.054	0.30593	0.3389:0.0:0.6611:0.0	.	654	Q9Y5E9	PCDBE_HUMAN	T	501;654	ENSP00000444518:A501T;ENSP00000239449:A654T	ENSP00000239449:A654T	A	+	1	0	PCDHB14	140585221	0.001000	0.12720	0.797000	0.32132	0.017000	0.09413	0.432000	0.21461	0.722000	0.32252	-0.199000	0.12753	GCC	.	.		0.721	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		A	140605037	G	A	140605037	3	1	23	1	0	0	0	0	1	0	0	0	11548	1203	42	3	1962	3	PCDHB14	5	140605037	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	257581	140605037	40310223	365	2431										
PCDHGA7	56108	hgsc.bcm.edu	37	chr5	140764204	140764204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctggcatggagctggcacccCgctccgcagagcccggctac	13	17	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140764204C>T	ENST00000518325.1	+	1	1738	c.1738C>T	c.(1738-1740)Cgc>Tgc	p.R580C	PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	580	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGGCACCCCGCTCCGCAGA	0.622																																					p.R580C		Atlas-SNP	.											PCDHGA7,NS,carcinoma,0,1	PCDHGA7	130	.	0			c.C1738T						.						83	98	93					5																	140764204		2202	4300	6502	SO:0001583	missense	56108	exon1			GCACCCCGCTCCG	AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"Cadherins / Protocadherins : Clustered"	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.1738C>T	chr5.hg19:g.140764204C>T	ENSP00000430024:p.Arg580Cys	103.0	0.0		129.0	50.0	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	hg19	CCDS54927.1	.	.	.	.	.	.	.	.	.	.	.	17.73	3.462042	0.63513	.	.	ENSG00000253537	ENST00000518325	T	0.59772	0.24	5.01	5.01	0.66863	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.81004	0.4733	H	0.95004	3.61	0.38846	D	0.95616	D;D	0.89917	1.0;1.0	D;D	0.79108	0.988;0.992	D	0.86378	0.1727	9	0.87932	D	0	.	11.8056	0.52152	0.0:0.9186:0.0:0.0814	.	580;580	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	C	580	ENSP00000430024:R580C	ENSP00000430024:R580C	R	+	1	0	PCDHGA7	140744388	0.937000	0.31787	0.959000	0.39883	0.972000	0.66771	2.006000	0.40874	2.484000	0.83849	0.655000	0.94253	CGC	.	.		0.622	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920		T	140764204	C	T	140764204	3	4	23	1	0	0	0	0	1	0	0	0	11568	652	23	1	1740	1	PCDHGA7	5	140764204	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	159167	140764204	40151056	366	2432										
DIAPH1	1729	hgsc.bcm.edu	37	chr5	140955840	140955840	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggcttcagatttctccaccTttgtcttatcaatcatttga	5	10	5	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140955840T>G	ENST00000398557.4	-	14	1558	c.1418A>C	c.(1417-1419)aAg>aCg	p.K473T	DIAPH1_ENST00000389054.3_Missense_Mutation_p.K473T|DIAPH1_ENST00000520569.1_Missense_Mutation_p.K419T|DIAPH1_ENST00000398562.2_Missense_Mutation_p.K464T|DIAPH1_ENST00000398566.3_Missense_Mutation_p.K464T|DIAPH1_ENST00000389057.5_Missense_Mutation_p.K464T|DIAPH1_ENST00000518047.1_Missense_Mutation_p.K464T|DIAPH1_ENST00000253811.6_Missense_Mutation_p.K473T	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	473					actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCTCCACCTTTGTCTTATC	0.363																																					p.K473T		Atlas-SNP	.											.	DIAPH1	64	.	0			c.A1418C						.						158	143	148					5																	140955840		1854	4101	5955	SO:0001583	missense	1729	exon14			TCCACCTTTGTCT	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.1418A>C	chr5.hg19:g.140955840T>G	ENSP00000381565:p.Lys473Thr	228.0	0.0		190.0	76.0	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.657790	0.88154	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047	T;T;T;T;T;T;T;T	0.22336	1.96;1.96;2.0;1.96;1.96;1.96;1.96;1.96	5.78	5.78	0.91487	Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.51143	0.1657	M	0.84948	2.725	0.58432	D	0.999995	D;D	0.69078	0.997;0.997	D;D	0.75020	0.985;0.985	T	0.58434	-0.7637	10	0.87932	D	0	.	15.0913	0.72195	0.0:0.0:0.0:1.0	.	464;473	E9PEZ2;O60610	.;DIAP1_HUMAN	T	473;419;464;464;464;473;473;464	ENSP00000373706:K473T;ENSP00000429282:K419T;ENSP00000381570:K464T;ENSP00000373709:K464T;ENSP00000381572:K464T;ENSP00000381565:K473T;ENSP00000253811:K473T;ENSP00000428268:K464T	ENSP00000253811:K473T	K	-	2	0	DIAPH1	140936024	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.356000	0.79445	2.204000	0.70986	0.528000	0.53228	AAG	.	.		0.363	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		G	140955840	T	G	140955840	3	3	23	1	0	0	0	0	1	0	0	0	4520	1609	56	5	2460	5	DIAPH1	5	140955840	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	191636	140955840	39959420	367	2433										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141336556	141336556	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgtccagcacctctggaggCatgtgcttactgaggaagaa	13	9	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:141336556C>A	ENST00000231484.3	-	1	2071	c.861G>T	c.(859-861)atG>atT	p.M287I	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	287	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTCTGGAGGCATGTGCTTAC	0.537																																					p.M287I		Atlas-SNP	.											.	PCDH12	133	.	0			c.G861T						.						99	92	94					5																	141336556		2203	4300	6503	SO:0001583	missense	51294	exon1			TGGAGGCATGTGC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.861G>T	chr5.hg19:g.141336556C>A	ENSP00000231484:p.Met287Ile	124.0	0.0		92.0	8.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	C	10.14	1.267319	0.23136	.	.	ENSG00000113555	ENST00000231484	T	0.50548	0.74	5.32	4.45	0.53987	Cadherin (4);Cadherin-like (1);	0.505224	0.22091	N	0.064750	T	0.21881	0.0527	N	0.02842	-0.48	0.22378	N	0.999151	B	0.02656	0.0	B	0.04013	0.001	T	0.13176	-1.0519	10	0.13108	T	0.6	.	11.6919	0.51521	0.0:0.9149:0.0:0.0851	.	287	Q9NPG4	PCD12_HUMAN	I	287	ENSP00000231484:M287I	ENSP00000231484:M287I	M	-	3	0	PCDH12	141316740	0.013000	0.17824	0.994000	0.49952	0.968000	0.65278	-0.866000	0.04245	1.471000	0.48121	0.655000	0.94253	ATG	.	.		0.537	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141336556	C	A	141336556	3	1	23	1	0	0	0	0	1	0	0	0	11519	710	25	3	2709	3	PCDH12	5	141336556	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	380716	141336556	39578704	368	2434										
RBM27	54439	hgsc.bcm.edu	37	chr5	145609290	145609290	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tatattataggacacgtgagAaaaaaagagaagacgggaaa							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:145609290delA	ENST00000265271.5	+	5	572	c.406delA	c.(406-408)aaafs	p.K137fs	RBM27_ENST00000506502.1_Frame_Shift_Del_p.K137fs	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	137	Arg-rich.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GACACGTGAGAAAAAAAGAGA	0.393																																					p.E135fs		Atlas-Indel,Pindel	.											.	RBM27	119	.	0			c.405delG						.						145	144	144					5																	145609290		1568	3582	5150	SO:0001589	frameshift_variant	54439	exon5			.	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.406delA	chr5.hg19:g.145609290delA	ENSP00000265271:p.Lys137fs	130.0	0.0		114.0	49.0	NM_018989	Q8IYW9	Frame_Shift_Del	DEL	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.		0.393	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		-	145609290	A	-	145609290	7	5	23	1	0	1	0	1	0	0	0	0	13142	247	9	0	424	0	RBM27	5	145609290	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	4272734	145609290	35305970	369	2435										
RBM27	54439	hgsc.bcm.edu	37	chr5	145634549	145634549	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aacccagaagctcctagtatTactagttctggtagatctca	7	10	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:145634549T>C	ENST00000265271.5	+	10	1654	c.1488T>C	c.(1486-1488)atT>atC	p.I496I	RBM27_ENST00000506502.1_Silent_p.I441I	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	496					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTCCTAGTATTACTAGTTCTG	0.403																																					p.I496I		Atlas-SNP	.											.	RBM27	119	.	0			c.T1488C						.						106	93	97					5																	145634549		1568	3582	5150	SO:0001819	synonymous_variant	54439	exon10			TAGTATTACTAGT	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1488T>C	chr5.hg19:g.145634549T>C		97.0	0.0		105.0	30.0	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.		0.403	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		C	145634549	T	C	145634549	2	2	23	1	0	0	0	0	0	0	0	1	13142	1742	61	2		2	RBM27	5	145634549	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	25259	145634549	35280711	370	2436										
C5orf46	389336	hgsc.bcm.edu	37	chr5	147281302	147281302	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttgggtctttgcccgagtcGtctggcttgtcgtctggctt	13	10	3	0	rs368375161		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:147281302G>A	ENST00000318315.4	-	2	105	c.105C>T	c.(103-105)gaC>gaT	p.D35D	C5orf46_ENST00000515291.1_Silent_p.D35D|C5orf46_ENST00000510432.1_5'UTR	NM_206966.2	NP_996849.2	Q6UWT4	CE046_HUMAN	chromosome 5 open reading frame 46	35						extracellular vesicular exosome (GO:0070062)				NS(1)|lung(1)|prostate(1)	3						TGCCCGAgtcgtctggcttgt	0.488																																					p.D35D		Atlas-SNP	.											.	C5orf46	8	.	0			c.C105T						.	A		2,4404	826.0+/-416.6	0,2,2201	226	200	208		105	-7.7	0.1	5		208	0,8600		0,0,4300	no	coding-synonymous	C5orf46	NM_206966.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		35/88	147281302	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	389336	exon2			CGAGTCGTCTGGC		CCDS34267.1	5q33.1	2013-12-13			ENSG00000178776	ENSG00000178776			33768	protein-coding gene	gene with protein product	"skin and saliva secreted protein 1"						Standard	NM_206966		Approved	MGC23985, SSSP1	uc003lou.3	Q6UWT4	OTTHUMG00000163420	ENST00000318315.4:c.105C>T	chr5.hg19:g.147281302G>A		178.0	0.0		195.0	73.0	NM_206966	A8K038|Q8WU04	Silent	SNP	ENST00000318315.4	hg19	CCDS34267.1																																																																																			.	.		0.488	C5orf46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373314.1	NM_206966		A	147281302	G	A	147281302	2	1	23	1	0	0	0	0	0	0	0	1	2307	1136	40	1		1	C5orf46	5	147281302	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1646753	147281302	33633958	371	2437										
PDE6A	5145	hgsc.bcm.edu	37	chr5	149324081	149324081	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcgctctcctccatgctgctCggggagtggtagttgctgaa	13	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:149324081C>T	ENST00000255266.5	-	1	275	c.156G>A	c.(154-156)ccG>ccA	p.P52P		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	52					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CCATGCTGCTCGGGGAGTGGT	0.517																																					p.P52P		Atlas-SNP	.											.	PDE6A	98	.	0			c.G156A						.						63	61	62					5																	149324081		2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			GCTGCTCGGGGAG		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.156G>A	chr5.hg19:g.149324081C>T		128.0	0.0		116.0	43.0	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	hg19	CCDS4299.1																																																																																			.	.		0.517	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			T	149324081	C	T	149324081	2	4	23	1	0	0	0	0	0	0	0	1	11654	871	31	1		1	PDE6A	5	149324081	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2042779	149324081	31591179	372	2438										
NDST1	3340	hgsc.bcm.edu	37	chr5	149901211	149901211	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cactgacaagggccgtggccGcttcgccctcatcatctatg	10	15	3	1	rs141135213		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:149901211G>A	ENST00000261797.6	+	2	897	c.395G>A	c.(394-396)cGc>cAc	p.R132H	NDST1_ENST00000523767.1_Missense_Mutation_p.R132H	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	132	Heparan sulfate N-deacetylase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGCCGTGGCCGCTTCGCCCTC	0.607																																					p.R132H		Atlas-SNP	.											.	NDST1	79	.	0			c.G395A						.	G	HIS/ARG	0,4406		0,0,2203	107	112	110		395	5.4	1	5	dbSNP_134	110	1,8599	1.2+/-3.3	0,1,4299	no	missense	NDST1	NM_001543.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	132/883	149901211	1,13005	2203	4300	6503	SO:0001583	missense	3340	exon2			GTGGCCGCTTCGC	U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"Sulfotransferases, membrane-bound"	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.395G>A	chr5.hg19:g.149901211G>A	ENSP00000261797:p.Arg132His	160.0	0.0		126.0	46.0	NM_001543	Q96E57	Missense_Mutation	SNP	ENST00000261797.6	hg19	CCDS34277.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.880758	0.91740	0.0	1.16E-4	ENSG00000070614	ENST00000519157;ENST00000523767;ENST00000261797	T;T;T	0.59083	0.29;0.58;0.91	5.39	5.39	0.77823	.	0.061246	0.64402	D	0.000001	T	0.78214	0.4248	M	0.81497	2.545	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74674	0.977;0.984;0.977	T	0.79381	-0.1827	10	0.54805	T	0.06	.	19.5078	0.95127	0.0:0.0:1.0:0.0	.	132;132;132	E7EVJ3;P52848-2;P52848	.;.;NDST1_HUMAN	H	132	ENSP00000427813:R132H;ENSP00000428604:R132H;ENSP00000261797:R132H	ENSP00000261797:R132H	R	+	2	0	NDST1	149881404	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.950000	0.87804	2.676000	0.91093	0.655000	0.94253	CGC	.	G|1.000;A|0.000		0.607	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543		A	149901211	G	A	149901211	3	1	23	1	0	0	0	0	1	0	0	0	10264	1087	38	1	397	1	NDST1	5	149901211	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	577130	149901211	31014049	373	2439										
TNIP1	10318	hgsc.bcm.edu	37	chr5	150410290	150410290	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtctcactgaggcccctcaCggtcattttttggagactct					rs199807288		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:150410290delC	ENST00000389378.2	-	18	2483	c.1895delG	c.(1894-1896)cgtfs	p.R632fs	TNIP1_ENST00000524280.1_Frame_Shift_Del_p.V536fs|TNIP1_ENST00000522226.1_Frame_Shift_Del_p.R632fs|TNIP1_ENST00000518977.1_Intron|TNIP1_ENST00000520931.1_Frame_Shift_Del_p.R579fs|TNIP1_ENST00000521591.1_Frame_Shift_Del_p.R632fs|TNIP1_ENST00000315050.7_Frame_Shift_Del_p.R632fs|TNIP1_ENST00000523200.1_Frame_Shift_Del_p.R568fs|TNIP1_ENST00000521423.1_5'Flank|TNIP1_ENST00000523338.1_Intron	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	632	Pro-rich.				defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGCCCCTCACGGTCATTTTT	0.438																																					p.R632fs		Atlas-Indel,Pindel	.											.	TNIP1	51	.	0			c.1896delT						.						81	81	81					5																	150410290		2203	4300	6503	SO:0001589	frameshift_variant	10318	exon18			.	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"virion-associated nuclear-shuttling protein", "Nef-associated factor 1 SNP"	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.1895delG	chr5.hg19:g.150410290delC	ENSP00000374029:p.Arg632fs	155.0	0.0		158.0	58.0	NM_001258454	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Frame_Shift_Del	DEL	ENST00000389378.2	hg19	CCDS34280.1																																																																																			.	.		0.438	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		-	150410290	C	-	150410290	7	5	23	1	0	1	0	1	0	0	0	0	16329	536	19	0	19	0	TNIP1	5	150410290	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	509079	150410290	30504970	374	2440										
SLC36A3	285641	hgsc.bcm.edu	37	chr5	150660598	150660598	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttagacagaccaaggctgagCggacagacaggtctacaaac	11	10	1	4	rs201585244		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:150660598C>T	ENST00000335230.3	-	9	1532	c.1121G>A	c.(1120-1122)cGc>cAc	p.R374H	SLC36A3_ENST00000377713.3_Missense_Mutation_p.R415H	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	374						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAAGGCTGAGCGGACAGACAG	0.552																																					p.R415H		Atlas-SNP	.											.	SLC36A3	54	.	0			c.G1244A						.						141	120	127					5																	150660598		2203	4300	6503	SO:0001583	missense	285641	exon10			GCTGAGCGGACAG	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"Solute carriers"	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.1121G>A	chr5.hg19:g.150660598C>T	ENSP00000334750:p.Arg374His	130.0	0.0		122.0	39.0	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Missense_Mutation	SNP	ENST00000335230.3	hg19	CCDS4314.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.345514	0.82022	.	.	ENSG00000186334	ENST00000335230;ENST00000377713	T;T	0.03920	3.76;3.76	3.82	2.95	0.34219	.	0.110120	0.64402	N	0.000010	T	0.28267	0.0698	H	0.94503	3.545	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.998	T	0.29852	-0.9998	10	0.87932	D	0	.	11.5293	0.50599	0.0:0.9119:0.0:0.0881	.	415;374;359	Q495N2-3;Q495N2;Q495N2-2	.;S36A3_HUMAN;.	H	374;415	ENSP00000334750:R374H;ENSP00000366942:R415H	ENSP00000334750:R374H	R	-	2	0	SLC36A3	150640791	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	3.880000	0.56145	0.955000	0.37878	0.561000	0.74099	CGC	.	C|1.000;A|0.000		0.552	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774		T	150660598	C	T	150660598	3	4	23	1	0	0	0	0	1	0	0	0	14610	768	27	1	299	1	SLC36A3	5	150660598	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	250308	150660598	30254662	375	2441										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153030021	153030021	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acctggagaagaaaaaggagCggctggtggtggtggactgt	18	5	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:153030021C>T	ENST00000285900.5	+	4	935	c.592C>T	c.(592-594)Cgg>Tgg	p.R198W	GRIA1_ENST00000340592.5_Missense_Mutation_p.R198W|GRIA1_ENST00000448073.4_Missense_Mutation_p.R208W|GRIA1_ENST00000518783.1_Missense_Mutation_p.R208W|GRIA1_ENST00000518142.1_Missense_Mutation_p.R118W|GRIA1_ENST00000518862.1_3'UTR|GRIA1_ENST00000521843.2_Missense_Mutation_p.R129W	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	198					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	GAAAAAGGAGCGGCTGGTGGT	0.542																																					p.R208W		Atlas-SNP	.											.	GRIA1	321	.	0			c.C622T						.						108	103	105					5																	153030021		2203	4300	6503	SO:0001583	missense	2890	exon4			AAGGAGCGGCTGG		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.592C>T	chr5.hg19:g.153030021C>T	ENSP00000285900:p.Arg198Trp	151.0	0.0		132.0	48.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.003695	0.54254	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38;1.38;1.38	5.33	-1.32	0.09201	Extracellular ligand-binding receptor (1);	0.055015	0.64402	D	0.000001	T	0.42877	0.1222	L	0.39898	1.24	0.45662	D	0.998588	D;D;D;D;D;D	0.89917	0.999;0.999;1.0;0.999;0.999;1.0	P;P;D;P;P;D	0.67103	0.901;0.901;0.949;0.901;0.841;0.949	T	0.07654	-1.0761	10	0.37606	T	0.19	.	11.2657	0.49110	0.6337:0.3015:0.0:0.0648	.	208;208;118;208;198;198	E7ESV8;B7Z9G9;B7Z3F6;B7Z2W8;P42261-2;P42261	.;.;.;.;.;GRIA1_HUMAN	W	198;198;118;152;198;129;129;208;208	ENSP00000285900:R198W;ENSP00000427920:R118W;ENSP00000339343:R198W;ENSP00000427864:R129W;ENSP00000442108:R129W;ENSP00000428994:R208W;ENSP00000415569:R208W	ENSP00000285900:R198W	R	+	1	2	GRIA1	153010214	0.634000	0.27190	0.814000	0.32528	0.577000	0.36160	-0.178000	0.09782	-0.654000	0.05394	-0.142000	0.14014	CGG	.	.		0.542	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			T	153030021	C	T	153030021	3	4	23	1	0	0	0	0	1	0	0	0	6776	759	27	1	606	1	GRIA1	5	153030021	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2369423	153030021	27885239	376	2442										
TIMD4	91937	hgsc.bcm.edu	37	chr5	156353300	156353300	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtttttgttgttttgttctGctcaggaactgctgtatcag	10	6	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:156353300G>A	ENST00000274532.2	-	6	924	c.868C>T	c.(868-870)Cag>Tag	p.Q290*	TIMD4_ENST00000406964.1_5'UTR|TIMD4_ENST00000407087.3_Nonsense_Mutation_p.Q262*	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	290						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTTTTGTTCTGCTCAGGAACT	0.373																																					p.Q290X		Atlas-SNP	.											.	TIMD4	94	.	0			c.C868T						.						178	159	165					5																	156353300		2203	4300	6503	SO:0001587	stop_gained	91937	exon6			TGTTCTGCTCAGG	BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850		"Immunoglobulin superfamily / V-set domain containing"	25132	protein-coding gene	gene with protein product		610096				12477932	Standard	NM_001146726		Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.868C>T	chr5.hg19:g.156353300G>A	ENSP00000274532:p.Gln290*	70.0	0.0		63.0	19.0	NM_138379	B5MCL9	Nonsense_Mutation	SNP	ENST00000274532.2	hg19	CCDS4332.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.638706	0.47153	.	.	ENSG00000145850	ENST00000274532;ENST00000407087	.	.	.	4.06	-0.165	0.13355	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	3.919	7.3801	0.26851	0.1019:0.5089:0.3892:0.0	.	.	.	.	X	290;262	.	ENSP00000274532:Q290X	Q	-	1	0	TIMD4	156285878	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.959000	0.03853	-0.153000	0.11137	0.650000	0.86243	CAG	.	.		0.373	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379		A	156353300	G	A	156353300	4	1	23	1	0	0	0	0	0	1	0	0	15918	1328	46	3	284	3	TIMD4	5	156353300	Nonsense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3323279	156353300	24561960	377	2443										
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156816337	156816337	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcccaccgcccaccaatggCgtcatgcacgtcgatgagtg	12	15	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:156816337C>T	ENST00000521420.1	+	28	3361	c.3270C>T	c.(3268-3270)ggC>ggT	p.G1090G	CYFIP2_ENST00000377576.3_Silent_p.G1116G|CYFIP2_ENST00000347377.6_Silent_p.G1116G|CYFIP2_ENST00000435847.2_Silent_p.G815G|CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000522463.1_Silent_p.G920G|CYFIP2_ENST00000318218.6_Silent_p.G1141G|CYFIP2_ENST00000541131.1_Silent_p.G1041G					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCACCAATGGCGTCATGCACG	0.617																																					p.G1116G		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C3348T						.						59	68	65					5																	156816337		2169	4284	6453	SO:0001819	synonymous_variant	26999	exon29			CAATGGCGTCATG	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.3270C>T	chr5.hg19:g.156816337C>T		71.0	0.0		79.0	18.0	NM_001037332		Silent	SNP	ENST00000521420.1	hg19																																																																																				.	.		0.617	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		T	156816337	C	T	156816337	2	4	23	1	0	0	0	0	0	0	0	1	4140	755	27	1		1	CYFIP2	5	156816337	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	463037	156816337	24098923	378	2444										
NUDCD2	134492	hgsc.bcm.edu	37	chr5	162887001	162887001	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaaggtctggtaccactggCcccacggggtcccgcacggt	13	16	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:162887001C>T	ENST00000302764.4	-	1	145	c.56G>A	c.(55-57)gGc>gAc	p.G19D	HMMR_ENST00000353866.3_5'Flank|NUDCD2_ENST00000519395.1_5'Flank|HMMR_ENST00000393915.4_5'Flank|HMMR_ENST00000358715.3_5'Flank|NUDCD2_ENST00000517501.1_Missense_Mutation_p.G19D|HMMR_ENST00000432118.2_5'Flank	NM_145266.4	NP_660309.1	Q8WVJ2	NUDC2_HUMAN	NudC domain containing 2	19	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)				large_intestine(1)|prostate(1)	2	Renal(175;0.000281)	Medulloblastoma(196;0.0207)|all_neural(177;0.0966)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0981)|OV - Ovarian serous cystadenocarcinoma(192;0.183)|Epithelial(171;0.247)		GTACCACTGGCCCCACGGGGT	0.687																																					p.G19D		Atlas-SNP	.											.	NUDCD2	12	.	0			c.G56A						.						78	92	87					5																	162887001		2203	4300	6503	SO:0001583	missense	134492	exon1			CACTGGCCCCACG	BX538290	CCDS4361.1	5q34	2008-02-05			ENSG00000170584	ENSG00000170584			30535	protein-coding gene	gene with protein product							Standard	NM_145266		Approved	DKFZp686E10109	uc003lze.3	Q8WVJ2	OTTHUMG00000130378	ENST00000302764.4:c.56G>A	chr5.hg19:g.162887001C>T	ENSP00000304854:p.Gly19Asp	413.0	0.0		408.0	163.0	NM_145266	B2R4V0	Missense_Mutation	SNP	ENST00000302764.4	hg19	CCDS4361.1	.	.	.	.	.	.	.	.	.	.	C	36	5.728119	0.96856	.	.	ENSG00000170584	ENST00000302764;ENST00000517501	T;T	0.42900	0.96;0.96	5.94	5.94	0.96194	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	0.000000	0.85682	D	0.000000	T	0.66982	0.2845	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63400	-0.6646	10	0.06891	T	0.86	0.0013	20.3736	0.98901	0.0:1.0:0.0:0.0	.	19	Q8WVJ2	NUDC2_HUMAN	D	19	ENSP00000304854:G19D;ENSP00000430347:G19D	ENSP00000304854:G19D	G	-	2	0	NUDCD2	162819579	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.207000	0.77899	2.820000	0.97059	0.650000	0.86243	GGC	.	.		0.687	NUDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252747.3	NM_145266		T	162887001	C	T	162887001	3	4	23	1	0	0	0	0	1	0	0	0	10732	739	26	3	433	3	NUDCD2	5	162887001	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	6070664	162887001	18028259	379	2445										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169116263	169116263	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttcttcccacagtgagaacTacctagtgcgatggggcagc	11	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:169116263T>C	ENST00000256935.8	+	9	849	c.769T>C	c.(769-771)Tac>Cac	p.Y257H		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	257					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAGTGAGAACTACCTAGTGCG	0.517																																					p.Y257H		Atlas-SNP	.											.	DOCK2	389	.	0			c.T769C						.						112	98	102					5																	169116263		2203	4300	6503	SO:0001583	missense	1794	exon9			GAGAACTACCTAG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.769T>C	chr5.hg19:g.169116263T>C	ENSP00000256935:p.Tyr257His	74.0	0.0		90.0	35.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.849042	0.91277	.	.	ENSG00000134516	ENST00000256935	T	0.17528	2.27	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.48040	0.1478	M	0.85710	2.77	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.54139	-0.8338	10	0.87932	D	0	.	16.4484	0.83959	0.0:0.0:0.0:1.0	.	257	Q92608	DOCK2_HUMAN	H	257	ENSP00000256935:Y257H	ENSP00000256935:Y257H	Y	+	1	0	DOCK2	169048841	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.965000	0.87945	2.285000	0.76669	0.533000	0.62120	TAC	.	.		0.517	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		C	169116263	T	C	169116263	3	2	23	1	0	0	0	0	1	0	0	0	4689	1522	53	2	803	2	DOCK2	5	169116263	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	6229262	169116263	11798997	380	2446										
GPRIN1	114787	hgsc.bcm.edu	37	chr5	176025680	176025680	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgtgtggccagacacaggacGcccctctcctgaggaggcag	14	14	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:176025680G>A	ENST00000303991.4	-	2	1333	c.1156C>T	c.(1156-1158)Cgt>Tgt	p.R386C		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	386					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GACACAGGACGCCCCTCTCCT	0.537																																					p.R386C		Atlas-SNP	.											GPRIN1,colon,carcinoma,0,1	GPRIN1	77	.	0			c.C1156T						.						61	57	58					5																	176025680		2203	4300	6503	SO:0001583	missense	114787	exon2			CAGGACGCCCCTC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.1156C>T	chr5.hg19:g.176025680G>A	ENSP00000305839:p.Arg386Cys	132.0	1.0		112.0	50.0	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	hg19	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.706135	0.30232	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.08720	3.06	4.72	0.659	0.17861	.	1.951490	0.03101	N	0.161082	T	0.08403	0.0209	L	0.36672	1.1	0.09310	N	1	P	0.39782	0.688	B	0.37780	0.258	T	0.29088	-1.0023	10	0.56958	D	0.05	14.3433	4.9434	0.13976	0.1413:0.3297:0.4452:0.0838	.	386	Q7Z2K8	GRIN1_HUMAN	C	386	ENSP00000305839:R386C	ENSP00000305839:R386C	R	-	1	0	GPRIN1	175958286	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.592000	0.05747	0.215000	0.20761	-1.576000	0.00868	CGT	.	.		0.537	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899		A	176025680	G	A	176025680	3	1	23	1	0	0	0	0	1	0	0	0	6738	1087	38	1	1874	1	GPRIN1	5	176025680	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	6909417	176025680	4889580	381	2447										
FGFR4	2264	hgsc.bcm.edu	37	chr5	176520464	176520464	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catccctggtacgaggcgtgCgtctctcctccagcggcccc	11	18	1	0	rs558220864	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:176520464C>T	ENST00000292408.4	+	10	1554	c.1309C>T	c.(1309-1311)Cgt>Tgt	p.R437C	FGFR4_ENST00000393637.1_Missense_Mutation_p.R397C|FGFR4_ENST00000292410.3_Missense_Mutation_p.R397C|FGFR4_ENST00000393648.2_Silent_p.C385C|FGFR4_ENST00000502906.1_Missense_Mutation_p.R437C	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	437					alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	ACGAGGCGTGCGTCTCTCCTC	0.627										TSP Lung(9;0.080)			C|||	2	0.000399361	0	0	5008	,	,		16618	0		0	False		,,,				2504	0.002				p.R437C		Atlas-SNP	.											.	FGFR4	174	.	0			c.C1309T						.						77	79	78					5																	176520464		2203	4299	6502	SO:0001583	missense	2264	exon10			GGCGTGCGTCTCT	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1309C>T	chr5.hg19:g.176520464C>T	ENSP00000292408:p.Arg437Cys	94.0	0.0		78.0	28.0	NM_002011	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.25|18.25	3.582520|3.582520	0.65992|0.65992	.|.	.|.	ENSG00000160867|ENSG00000160867	ENST00000511076|ENST00000292408;ENST00000502906;ENST00000292410;ENST00000393637;ENST00000377207	.|D;D;D;D	.|0.88664	.|-2.41;-2.41;-2.41;-2.41	4.44|4.44	3.57|3.57	0.40892|0.40892	.|.	.|0.103824	.|0.64402	.|D	.|0.000002	D|D	0.94598|0.94598	0.8259|0.8259	M|M	0.88450|0.88450	2.955|2.955	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.997;1.0	.|P;D	.|0.83275	.|0.681;0.996	D|D	0.94860|0.94860	0.8021|0.8021	5|10	.|0.87932	.|D	.|0	.|.	11.9644|11.9644	0.53027|0.53027	0.0:0.9148:0.0:0.0852|0.0:0.9148:0.0:0.0852	.|.	.|397;437	.|P22455-2;P22455	.|.;FGFR4_HUMAN	V|C	68|437;437;397;397;665	.|ENSP00000292408:R437C;ENSP00000424960:R437C;ENSP00000292410:R397C;ENSP00000377254:R397C	.|ENSP00000292408:R437C	A|R	+|+	2|1	0|0	FGFR4|FGFR4	176453070|176453070	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.204000|0.204000	0.24138|0.24138	5.863000|5.863000	0.69568|0.69568	1.097000|1.097000	0.41459|0.41459	0.555000|0.555000	0.69702|0.69702	GCG|CGT	.	.		0.627	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			T	176520464	C	T	176520464	3	4	23	1	0	0	0	0	1	0	0	0	5876	768	27	1	1413	1	FGFR4	5	176520464	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	494784	176520464	4394796	382	2448										
PFN3	345456	hgsc.bcm.edu	37	chr5	176827232	176827232	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gttgaggatgcccccatgtaCgccgcgtcggcccattagca	12	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:176827232C>T	ENST00000358571.2	-	1	405	c.346G>A	c.(346-348)Gta>Ata	p.V116I	F12_ENST00000514943.1_5'Flank	NM_001029886.2	NP_001025057.1	P60673	PROF3_HUMAN	profilin 3	116					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	lipid binding (GO:0008289)			lung(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCCCATGTACGCCGCGTCGG	0.726																																					p.V116I		Atlas-SNP	.											.	PFN3	4	.	0			c.G346A						.						17	19	18					5																	176827232		2076	4198	6274	SO:0001583	missense	345456	exon1			CATGTACGCCGCG	AC090063	CCDS34301.1	5q35.2	2008-08-26			ENSG00000196570	ENSG00000196570			18627	protein-coding gene	gene with protein product		612812				11867228	Standard	NM_001029886		Approved		uc003mgl.2	P60673	OTTHUMG00000163408	ENST00000358571.2:c.346G>A	chr5.hg19:g.176827232C>T	ENSP00000351379:p.Val116Ile	249.0	0.0		195.0	75.0	NM_001029886	A2RUL3	Missense_Mutation	SNP	ENST00000358571.2	hg19	CCDS34301.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.345624	0.61073	.	.	ENSG00000196570	ENST00000358571	D	0.86865	-2.18	4.76	4.76	0.60689	.	0.175856	0.37761	N	0.001954	T	0.80819	0.4696	L	0.44542	1.39	0.26464	N	0.975398	P	0.43431	0.807	B	0.35655	0.207	T	0.76055	-0.3099	10	0.42905	T	0.14	.	13.3416	0.60549	0.0:1.0:0.0:0.0	.	116	P60673	PROF3_HUMAN	I	116	ENSP00000351379:V116I	ENSP00000351379:V116I	V	-	1	0	PFN3	176759838	0.994000	0.37717	1.000000	0.80357	0.857000	0.48899	1.993000	0.40747	2.209000	0.71365	0.485000	0.47835	GTA	.	.		0.726	PFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373234.1	NM_001029886		T	176827232	C	T	176827232	3	4	23	1	0	0	0	0	1	0	0	0	11778	536	19	1	71	1	PFN3	5	176827232	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	306768	176827232	4088028	383	2449										
ZNF354B	117608	hgsc.bcm.edu	37	chr5	178310742	178310742	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgacttaatagacaccgaaTaattcatactggagagaaat	7	7	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:178310742T>A	ENST00000322434.3	+	5	1515	c.1289T>A	c.(1288-1290)aTa>aAa	p.I430K	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGACACCGAATAATTCATACT	0.358																																					p.I430K		Atlas-SNP	.											.	ZNF354B	67	.	0			c.T1289A						.						70	74	73					5																	178310742		2203	4300	6503	SO:0001583	missense	117608	exon5			ACCGAATAATTCA	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"Zinc fingers, C2H2-type", "-"	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.1289T>A	chr5.hg19:g.178310742T>A	ENSP00000327143:p.Ile430Lys	235.0	0.0		214.0	79.0	NM_058230	A8K0V2|Q5U5Z4	Missense_Mutation	SNP	ENST00000322434.3	hg19	CCDS4439.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.023794	0.35701	.	.	ENSG00000178338	ENST00000322434	T	0.12774	2.65	3.69	2.51	0.30379	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03011	0.0089	N	0.00315	-1.66	0.45490	D	0.998451	B	0.21905	0.062	B	0.23716	0.048	T	0.30090	-0.9990	9	0.41790	T	0.15	-1.6144	3.8088	0.08788	0.1987:0.0:0.2387:0.5626	.	430	Q96LW1	Z354B_HUMAN	K	430	ENSP00000327143:I430K	ENSP00000327143:I430K	I	+	2	0	ZNF354B	178243348	0.000000	0.05858	0.999000	0.59377	0.985000	0.73830	0.440000	0.21592	1.545000	0.49373	0.454000	0.30748	ATA	.	.		0.358	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230		A	178310742	T	A	178310742	3	1	23	1	0	0	0	0	1	0	0	0	17880	1406	49	4	1303	4	ZNF354B	5	178310742	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1483510	178310742	2604518	384	2450										
MAML1	9794	hgsc.bcm.edu	37	chr5	179201140	179201140	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagatagttgcccagcccccGccacaggccaccaatggaca	9	17	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:179201140G>A	ENST00000292599.3	+	5	2576	c.2313G>A	c.(2311-2313)ccG>ccA	p.P771P	MAML1_ENST00000503050.1_Intron	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCAGCCCCCGCCACAGGCCA	0.602																																					p.P771P		Atlas-SNP	.											.	MAML1	118	.	0			c.G2313A						.						38	39	39					5																	179201140		2203	4300	6503	SO:0001819	synonymous_variant	9794	exon5			GCCCCCGCCACAG	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.2313G>A	chr5.hg19:g.179201140G>A		70.0	0.0		52.0	18.0	NM_014757		Silent	SNP	ENST00000292599.3	hg19	CCDS34315.1																																																																																			.	.		0.602	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		A	179201140	G	A	179201140	2	1	23	1	0	0	0	0	0	0	0	1	9214	1074	38	1		1	MAML1	5	179201140	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	890398	179201140	1714120	385	2451										
BTNL9	153579	hgsc.bcm.edu	37	chr5	180472566	180472566	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcttgtcttcctcatgcaccTcctcctccttcagcctgggg	7	17	4	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:180472566T>C	ENST00000327705.9	+	2	308	c.77T>C	c.(76-78)cTc>cCc	p.L26P	BTNL9_ENST00000515271.1_Intron|BTNL9_ENST00000376841.2_Missense_Mutation_p.L26P|BTNL9_ENST00000376842.3_Missense_Mutation_p.L26P	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	26						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCATGCACCTCCTCCTCCTT	0.622																																					p.L26P		Atlas-SNP	.											.	BTNL9	58	.	0			c.T77C						.						114	97	103					5																	180472566		2203	4297	6500	SO:0001583	missense	153579	exon2			TGCACCTCCTCCT	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.77T>C	chr5.hg19:g.180472566T>C	ENSP00000330200:p.Leu26Pro	49.0	0.0		45.0	15.0	NM_152547	A6NL42|Q6P660|Q96DM5	Missense_Mutation	SNP	ENST00000327705.9	hg19	CCDS4460.2	.	.	.	.	.	.	.	.	.	.	T	16.36	3.101136	0.56183	.	.	ENSG00000165810	ENST00000376841;ENST00000327705;ENST00000376842;ENST00000376850	T;T;T	0.54279	3.81;0.6;0.58	4.73	4.73	0.59995	.	0.952130	0.08578	N	0.925046	T	0.66046	0.2750	M	0.64170	1.965	0.18873	N	0.999981	D	0.58970	0.984	P	0.57371	0.819	T	0.54682	-0.8257	10	0.87932	D	0	.	10.9292	0.47207	0.0:0.0:0.0:1.0	.	26	Q6UXG8	BTNL9_HUMAN	P	26	ENSP00000366037:L26P;ENSP00000330200:L26P;ENSP00000366038:L26P	ENSP00000330200:L26P	L	+	2	0	BTNL9	180405172	0.111000	0.22076	0.007000	0.13788	0.033000	0.12548	2.431000	0.44775	1.911000	0.55334	0.454000	0.30748	CTC	.	.		0.622	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547		C	180472566	T	C	180472566	3	2	23	1	0	0	0	0	1	0	0	0	1570	1551	54	2	79	2	BTNL9	5	180472566	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1271426	180472566	442694	386	2452										
RREB1	6239	hgsc.bcm.edu	37	chr6	7231535	7231535	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctgcccccgctggcctccaTtgcccagatcatctcatctg	8	18	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:7231535T>C	ENST00000349384.6	+	10	3517	c.3203T>C	c.(3202-3204)aTt>aCt	p.I1068T	RREB1_ENST00000334984.6_Missense_Mutation_p.I1068T|RREB1_ENST00000379938.2_Missense_Mutation_p.I1068T|RREB1_ENST00000379933.3_Missense_Mutation_p.I1068T	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1068					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CTGGCCTCCATTGCCCAGATC	0.642																																					p.I1068T		Atlas-SNP	.											.	RREB1	242	.	0			c.T3203C						.						37	44	42					6																	7231535		2203	4300	6503	SO:0001583	missense	6239	exon10			CCTCCATTGCCCA	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.3203T>C	chr6.hg19:g.7231535T>C	ENSP00000305560:p.Ile1068Thr	96.0	0.0		73.0	54.0	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	hg19	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.729279	0.89390	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.25579	1.95;1.94;1.95;1.79	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000009	T	0.42245	0.1194	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.36529	-0.9744	10	0.59425	D	0.04	-27.7182	16.2302	0.82332	0.0:0.0:0.0:1.0	.	1068;1068;1068	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	T	1068	ENSP00000369265:I1068T;ENSP00000369270:I1068T;ENSP00000305560:I1068T;ENSP00000335574:I1068T	ENSP00000335574:I1068T	I	+	2	0	RREB1	7176534	1.000000	0.71417	0.950000	0.38849	0.993000	0.82548	5.855000	0.69510	2.228000	0.72767	0.533000	0.62120	ATT	.	.		0.642	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			C	7231535	T	C	7231535	3	2	23	1	0	0	0	0	1	0	0	0	13694	1493	52	2	3229	2	RREB1	6	7231535	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10		7231535	163883532	387	2453										
MAK	4117	hgsc.bcm.edu	37	chr6	10764807	10764808	+	Frame_Shift_Ins	INS	-	-	C													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	taagtacgtcctgaaaactgINScccccgaccagtttttgtgt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:10764807_10764808insC	ENST00000313243.2	-	14	2131_2132	c.1749_1750insG	c.(1747-1752)gggcagfs	p.Q584fs	SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000354489.2_Frame_Shift_Ins_p.Q584fs|RP11-637O19.3_ENST00000480294.1_Intron|MAK_ENST00000538030.1_3'UTR|MAK_ENST00000474039.1_Frame_Shift_Ins_p.Q584fs			P20794	MAK_HUMAN	male germ cell-associated kinase	584					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				CCTGAAAACTGCCCCCGACCAG	0.411																																					p.Q609fs		Atlas-Indel,Pindel	.											.	MAK	47	.	0			c.1825_1826insG						.																																			SO:0001589	frameshift_variant	4117	exon15			.		CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1750dupG	chr6.hg19:g.10764812_10764812dupC	ENSP00000313021:p.Gln584fs	98.0	0.0		118.0	28.0	NM_001242957	F1T0K6|G1FL29|Q547D0|Q9NUH7	Frame_Shift_Ins	INS	ENST00000313243.2	hg19	CCDS4516.1																																																																																			.	.		0.411	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906		C	10764808	-	C	10764807	7	5	23	1	0	1	1	0	0	0	0	0	9206	1328	46	0	125	0	MAK	6	10764807	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	3533272	10764807	160350260	388	2454										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327684	16327684	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tattgcatgacgacctgggaGgggggccccagggtgagcgt					rs202200269	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:16327684delG	ENST00000244769.4	-	8	1794	c.858delC	c.(856-858)cccfs	p.P286fs	ATXN1_ENST00000436367.1_Frame_Shift_Del_p.P286fs	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	286					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CGACCTGGGAGGGGGGCCCCA	0.682																																					p.S287fs		Atlas-Indel,Pindel	.											.	ATXN1	117	.	0			c.859delT						.						31	34	33					6																	16327684		2203	4300	6503	SO:0001589	frameshift_variant	6310	exon8			.	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.858delC	chr6.hg19:g.16327684delG	ENSP00000244769:p.Pro286fs	174.0	0.0		206.0	58.0	NM_000332	Q17S02|Q9UJG2|Q9Y4J1	Frame_Shift_Del	DEL	ENST00000244769.4	hg19	CCDS34342.1																																																																																			.	.		0.682	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		-	16327684	G	-	16327684	7	5	23	1	0	1	0	1	0	0	0	0	1209	987	35	0	1597	0	ATXN1	6	16327684	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	5562877	16327684	154787383	389	2455										
MBOAT1	154141	hgsc.bcm.edu	37	chr6	20152967	20152967	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcgaaaccagaaagcagcaaAcagagcaacaagctggcata	10	10	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:20152967A>G	ENST00000324607.7	-	2	297	c.133T>C	c.(133-135)Ttt>Ctt	p.F45L	MBOAT1_ENST00000536798.1_Missense_Mutation_p.F45L|MBOAT1_ENST00000541730.1_5'UTR	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	45					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			AAAGCAGCAAACAGAGCAACA	0.428																																					p.F45L		Atlas-SNP	.											.	MBOAT1	48	.	0			c.T133C						.						92	91	91					6																	20152967		2203	4300	6503	SO:0001583	missense	154141	exon2			CAGCAAACAGAGC	AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197			21579	protein-coding gene	gene with protein product	"lysophosphatidylethanolamine acyltransferase 1"	611732	"O-acyltransferase (membrane bound) domain containing 1"	OACT1		18287005	Standard	NM_001080480		Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.133T>C	chr6.hg19:g.20152967A>G	ENSP00000324944:p.Phe45Leu	191.0	0.0		198.0	25.0	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Missense_Mutation	SNP	ENST00000324607.7	hg19	CCDS34346.1	.	.	.	.	.	.	.	.	.	.	A	3.231	-0.157379	0.06544	.	.	ENSG00000172197	ENST00000324607;ENST00000536798	T;T	0.21031	2.86;2.03	5.37	-4.69	0.03299	.	0.942499	0.09062	N	0.854219	T	0.01387	0.0045	N	0.02202	-0.64	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.46541	-0.9184	10	0.07482	T	0.82	-13.2751	6.7811	0.23646	0.4674:0.2126:0.3201:0.0	.	45	Q6ZNC8	MBOA1_HUMAN	L	45	ENSP00000324944:F45L;ENSP00000439814:F45L	ENSP00000324944:F45L	F	-	1	0	MBOAT1	20260946	0.000000	0.05858	0.013000	0.15412	0.831000	0.47069	-0.589000	0.05767	-0.745000	0.04772	0.533000	0.62120	TTT	.	.		0.428	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1			G	20152967	A	G	20152967	3	3	23	1	0	0	0	0	1	0	0	0	9365	43	2	2	1402	2	MBOAT1	6	20152967	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3825283	20152967	150962100	390	2456										
HDGFL1	154150	hgsc.bcm.edu	37	chr6	22570437	22570437	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcgcccctagcgagccgggCctggtctgcgagccgcctca	14	17	2	0	rs371376684		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:22570437C>T	ENST00000230012.3	+	1	760	c.633C>T	c.(631-633)ggC>ggT	p.G211G	HDGFL1_ENST00000510882.2_Silent_p.G211G	NM_138574.2	NP_612641.2	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1	211	Glu-rich.									kidney(1)|large_intestine(3)|lung(7)	11	Ovarian(93;0.163)					GCGAGCCGGGCCTGGTCTGCG	0.741																																					p.G211G		Atlas-SNP	.											.	HDGFL1	33	.	0			c.C633T						.						4	6	5					6																	22570437		1937	3989	5926	SO:0001819	synonymous_variant	154150	exon1			GCCGGGCCTGGTC	AK056824	CCDS34347.1	6p22.2	2008-02-05	2005-04-07	2005-04-07	ENSG00000112273	ENSG00000112273			21095	protein-coding gene	gene with protein product			"PWWP domain containing 1"	PWWP1			Standard	NM_138574		Approved	dJ309H15.1	uc003nds.3	Q5TGJ6	OTTHUMG00000016206	ENST00000230012.3:c.633C>T	chr6.hg19:g.22570437C>T		54.0	0.0		73.0	13.0	NM_138574	Q96MJ6	Silent	SNP	ENST00000230012.3	hg19	CCDS34347.1																																																																																			.	.		0.741	HDGFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043500.1	NM_138574		T	22570437	C	T	22570437	2	4	23	1	0	0	0	0	0	0	0	1	7028	726	26	3		3	HDGFL1	6	22570437	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2417470	22570437	148544630	391	2457										
LRRC16A	55604	hgsc.bcm.edu	37	chr6	25538179	25538179	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagatttaaaatcagcagagCggctcatgcgtgatgctaag	11	7	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:25538179C>T	ENST00000329474.6	+	25	2532	c.2164C>T	c.(2164-2166)Cgg>Tgg	p.R722W		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	722					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						ATCAGCAGAGCGGCTCATGCG	0.393																																					p.R722W		Atlas-SNP	.											.	LRRC16A	168	.	0			c.C2164T						.						50	48	48					6																	25538179		1889	4117	6006	SO:0001583	missense	55604	exon25			GCAGAGCGGCTCA	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"	609593	"leucine rich repeat containing 16"	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.2164C>T	chr6.hg19:g.25538179C>T	ENSP00000331983:p.Arg722Trp	48.0	0.0		57.0	11.0	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	hg19	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.167125	0.78339	.	.	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.16597	2.33	5.79	3.67	0.42095	.	0.090383	0.85682	D	0.000000	T	0.17662	0.0424	L	0.32530	0.975	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.70935	0.937;0.937;0.971;0.937	T	0.01492	-1.1341	10	0.66056	D	0.02	-18.7033	12.3661	0.55230	0.5598:0.4402:0.0:0.0	.	722;722;722;722	Q5VZK9;B2RTQ5;Q5VZK9-2;B8X1J0	LR16A_HUMAN;.;.;.	W	722	ENSP00000331983:R722W	ENSP00000331983:R722W	R	+	1	2	LRRC16A	25646158	1.000000	0.71417	0.961000	0.40146	0.991000	0.79684	3.670000	0.54569	0.614000	0.30107	0.591000	0.81541	CGG	.	.		0.393	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640		T	25538179	C	T	25538179	3	4	23	1	0	0	0	0	1	0	0	0	8980	759	27	1	2262	1	LRRC16A	6	25538179	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2967742	25538179	145576888	392	2458										
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056197	26056197	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttcttcgctttcttcggtgTtttcttagcgctcttcttcg	7	12	5	0	rs548795634		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:26056197T>C	ENST00000343677.2	-	1	502	c.460A>G	c.(460-462)Aca>Gca	p.T154A		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	154					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						TTCTTCGGTGTTTTCTTAGCG	0.562													T|||	1	0.000199681	0	0	5008	,	,		14270	0.001		0	False		,,,				2504	0				p.T154A		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.A460G						.						75	89	85					6																	26056197		2201	4297	6498	SO:0001583	missense	3006	exon1			TCGGTGTTTTCTT	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"Histones / Replication-dependent"	4716	protein-coding gene	gene with protein product		142710	"H1 histone family, member 2", "histone 1, H1c"	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.460A>G	chr6.hg19:g.26056197T>C	ENSP00000339566:p.Thr154Ala	118.0	0.0		146.0	40.0	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	hg19	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	T	2.271	-0.367071	0.05069	.	.	ENSG00000187837	ENST00000343677	T	0.15834	2.39	5.47	5.47	0.80525	.	0.381500	0.23472	N	0.047801	T	0.03520	0.0101	N	0.14661	0.345	0.34798	D	0.736415	B	0.30406	0.278	B	0.24974	0.057	T	0.38542	-0.9656	10	0.25751	T	0.34	-34.9918	9.5155	0.39102	0.0:0.0793:0.0:0.9207	.	154	P16403	H12_HUMAN	A	154	ENSP00000339566:T154A	ENSP00000339566:T154A	T	-	1	0	HIST1H1C	26164176	0.998000	0.40836	1.000000	0.80357	0.012000	0.07955	1.305000	0.33493	2.198000	0.70561	0.528000	0.53228	ACA	.	.		0.562	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		C	26056197	T	C	26056197	3	2	23	1	0	0	0	0	1	0	0	0	7133	1725	60	2	185	2	HIST1H1C	6	26056197	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	518018	26056197	145058870	393	2459										
ABT1	29777	hgsc.bcm.edu	37	chr6	26598247	26598247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtggagttccgtgacaagcGcatagccaagcgcgtggcgg	17	10	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:26598247G>A	ENST00000274849.1	+	2	378	c.347G>A	c.(346-348)cGc>cAc	p.R116H		NM_013375.3	NP_037507.1	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	116	RRM.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron differentiation (GO:0021522)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11						CGTGACAAGCGCATAGCCAAG	0.582																																					p.R116H		Atlas-SNP	.											.	ABT1	39	.	0			c.G347A						.						62	56	58					6																	26598247		2203	4300	6503	SO:0001583	missense	29777	exon2			ACAAGCGCATAGC	AB027258	CCDS4616.1	6p21.31	2008-07-07			ENSG00000146109	ENSG00000146109			17369	protein-coding gene	gene with protein product						10648625	Standard	NM_013375		Approved		uc003nii.3	Q9ULW3	OTTHUMG00000016319	ENST00000274849.1:c.347G>A	chr6.hg19:g.26598247G>A	ENSP00000274849:p.Arg116His	345.0	0.0		394.0	114.0	NM_013375		Missense_Mutation	SNP	ENST00000274849.1	hg19	CCDS4616.1	.	.	.	.	.	.	.	.	.	.	G	35	5.527269	0.96431	.	.	ENSG00000146109	ENST00000274849	T	0.43294	0.95	5.23	5.23	0.72850	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.60971	0.2310	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.64433	-0.6409	10	0.59425	D	0.04	-33.4763	16.6701	0.85263	0.0:0.0:1.0:0.0	.	116	Q9ULW3	ABT1_HUMAN	H	116	ENSP00000274849:R116H	ENSP00000274849:R116H	R	+	2	0	ABT1	26706226	1.000000	0.71417	0.959000	0.39883	0.903000	0.53119	8.296000	0.89940	2.629000	0.89072	0.563000	0.77884	CGC	.	.		0.582	ABT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043698.1			A	26598247	G	A	26598247	3	1	23	1	0	0	0	0	1	0	0	0	101	1087	38	1	353	1	ABT1	6	26598247	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	542050	26598247	144516820	394	2460										
HIST1H4I	8294	hgsc.bcm.edu	37	chr6	27107217	27107217	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccttgctcgccgcggcggcGtgaagcgcatttctggcctc	14	15	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:27107217G>A	ENST00000354348.2	+	1	142	c.130G>A	c.(130-132)Gtg>Atg	p.V44M	HIST1H2BK_ENST00000396891.4_Intron	NM_003495.2	NP_003486.1	P62805	H4_HUMAN	histone cluster 1, H4i	44					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(1)	1						CCGCGGCGGCGTGAAGCGCAT	0.642			T	BCL6	NHL																																p.V44M		Atlas-SNP	.		Dom	yes		6	6p21.3	8294	"histone 1, H4i (H4FM)"		L	.	HIST1H4I	26	.	0			c.G130A						.						57	59	58					6																	27107217		2203	4300	6503	SO:0001583	missense	8294	exon1			GGCGGCGTGAAGC	AB000905	CCDS4620.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198339	ENSG00000276180		"Histones / Replication-dependent"	4793	protein-coding gene	gene with protein product		602833	"H4 histone family, member M", "histone 1, H4i"	H4FM		8988030, 9439656, 12408966	Standard	NM_003495		Approved	H4/m	uc003niy.1	P62805	OTTHUMG00000014471	ENST00000354348.2:c.130G>A	chr6.hg19:g.27107217G>A	ENSP00000346316:p.Val44Met	202.0	0.0		254.0	41.0	NM_003495	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000354348.2	hg19	CCDS4620.1	.	.	.	.	.	.	.	.	.	.	.	17.13	3.309732	0.60414	.	.	ENSG00000198339	ENST00000354348	T	0.68624	-0.34	3.95	3.95	0.45737	.	0.000000	0.36444	U	0.002585	D	0.86171	0.5869	H	0.98089	4.145	0.48236	D	0.999618	.	.	.	.	.	.	D	0.90533	0.4497	8	0.62326	D	0.03	.	14.3124	0.66424	0.0:0.0:1.0:0.0	.	.	.	.	M	44	ENSP00000346316:V44M	ENSP00000346316:V44M	V	+	1	0	HIST1H4I	27215196	1.000000	0.71417	0.626000	0.29213	0.049000	0.14656	8.868000	0.92320	2.158000	0.67659	0.655000	0.94253	GTG	.	.		0.642	HIST1H4I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040139.1	NM_003495		A	27107217	G	A	27107217	3	1	23	1	0	0	0	0	1	0	0	0	7182	1145	40	1	132	1	HIST1H4I	6	27107217	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	508970	27107217	144007850	395	2461										
OR12D2	26529	hgsc.bcm.edu	37	chr6	29365183	29365183	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgtagcatgctctgtaaagCactgtccacttgtgcctccc	8	13	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:29365183C>T	ENST00000383555.2	+	1	768	c.707C>T	c.(706-708)gCa>gTa	p.A236V	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CTCTGTAAAGCACTGTCCACT	0.438																																					p.A236V		Atlas-SNP	.											.	OR12D2	42	.	0			c.C707T						.						223	216	218					6																	29365183		1511	2708	4219	SO:0001583	missense	26529	exon1			GTAAAGCACTGTC		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"GPCR / Class A : Olfactory receptors"	8178	protein-coding gene	gene with protein product			"olfactory receptor, family 12, subfamily D, member 2"				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.707C>T	chr6.hg19:g.29365183C>T	ENSP00000373047:p.Ala236Val	116.0	0.0		140.0	48.0	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	hg19	CCDS4659.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.394839	0.42512	.	.	ENSG00000168787	ENST00000383555	T	0.00342	8.03	3.94	3.94	0.45596	GPCR, rhodopsin-like superfamily (1);	0.213717	0.32736	N	0.005710	T	0.00440	0.0014	M	0.79614	2.46	0.37040	D	0.897106	D	0.64830	0.994	D	0.68765	0.96	T	0.76454	-0.2953	10	0.54805	T	0.06	.	15.7562	0.78030	0.0:1.0:0.0:0.0	.	236	P58182	O12D2_HUMAN	V	236	ENSP00000373047:A236V	ENSP00000373047:A236V	A	+	2	0	OR12D2	29473162	1.000000	0.71417	0.042000	0.18584	0.184000	0.23303	5.014000	0.64029	2.019000	0.59389	0.205000	0.17691	GCA	.	.		0.438	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2			T	29365183	C	T	29365183	3	4	23	1	0	0	0	0	1	0	0	0	10940	710	25	3	709	3	OR12D2	6	29365183	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2257966	29365183	141749884	396	2462										
HLA-G	3135	hgsc.bcm.edu	37	chr6	29797328	29797328	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggggaggaccagacccaggaCgtggagctcgtggagaccag	18	10	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:29797328C>T	ENST00000360323.6	+	4	777	c.753C>T	c.(751-753)gaC>gaT	p.D251D	HLA-G_ENST00000428701.1_Silent_p.D251D|HLA-G_ENST00000376828.2_Silent_p.D256D|HLA-G_ENST00000376818.3_Silent_p.D159D|HLA-G_ENST00000376815.3_Intron			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	251	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						AGACCCAGGACGTGGAGCTCG	0.617																																					p.D251D		Atlas-SNP	.											.	HLA-G	90	.	0			c.C753T						.						79	72	75					6																	29797328		2203	4300	6503	SO:0001819	synonymous_variant	3135	exon5			CCAGGACGTGGAG		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4964	protein-coding gene	gene with protein product	"b2 microglobulin"	142871	"HLA-G histocompatibility antigen, class I, G"				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.753C>T	chr6.hg19:g.29797328C>T		129.0	0.0		197.0	55.0	NM_002127		Silent	SNP	ENST00000360323.6	hg19	CCDS4668.1																																																																																			.	.		0.617	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		T	29797328	C	T	29797328	2	4	23	1	0	0	0	0	0	0	0	1	7221	535	19	1		1	HLA-G	6	29797328	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	432145	29797328	141317739	397	2463										
ZNRD1	30834	hgsc.bcm.edu	37	chr6	30029708	30029708	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgcagactttgaggggaagGttgtgaagacttcggttgtg	17	4	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:30029708G>A	ENST00000332435.5	+	2	431	c.160G>A	c.(160-162)Gtt>Att	p.V54I	ZNRD1_ENST00000376785.2_Missense_Mutation_p.V54I|ZNRD1_ENST00000376782.2_Missense_Mutation_p.V54I|ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1_ENST00000463141.1_Intron|ZNRD1-AS1_ENST00000376797.3_RNA|ZNRD1_ENST00000359374.4_Missense_Mutation_p.V54I|ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000421692.1_RNA|ZNRD1-AS1_ENST00000431012.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000452229.1_RNA|ZNRD1-AS1_ENST00000437417.1_RNA	NM_170783.2	NP_740753.1	Q9P1U0	RPA12_HUMAN	zinc ribbon domain containing 1	54					nucleobase-containing compound metabolic process (GO:0006139)|termination of RNA polymerase I transcription (GO:0006363)	DNA-directed RNA polymerase I complex (GO:0005736)	DNA-directed RNA polymerase activity (GO:0003899)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)										TGAGGGGAAGGTTGTGAAGAC	0.552																																					p.V54I		Atlas-SNP	.											.	.	.	.	0			c.G160A						.						191	196	194					6																	30029708		1511	2709	4220	SO:0001583	missense	30834	exon2			GGGAAGGTTGTGA	AF024617	CCDS4670.1	6p21	2011-02-18	2006-04-04		ENSG00000066379	ENSG00000066379			13182	protein-coding gene	gene with protein product		607525	"zinc ribbon domain containing, 1"			8938444, 10662553	Standard	NM_170783		Approved	hZR14, HTEX-6, tctex-6, RPA12	uc003npa.3	Q9P1U0	OTTHUMG00000031149	ENST00000332435.5:c.160G>A	chr6.hg19:g.30029708G>A	ENSP00000331111:p.Val54Ile	149.0	0.0		186.0	65.0	NM_170783		Missense_Mutation	SNP	ENST00000332435.5	hg19	CCDS4670.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730110	0.48939	.	.	ENSG00000066379	ENST00000332435;ENST00000376782;ENST00000359374;ENST00000376785	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.9	1.94	0.25998	.	0.295653	0.31246	N	0.008000	T	0.15739	0.0379	L	0.50333	1.59	0.39330	D	0.965392	B	0.11235	0.004	B	0.08055	0.003	T	0.04467	-1.0949	10	0.34782	T	0.22	-35.9902	5.7269	0.18018	0.1652:0.3046:0.5301:0.0	.	54	Q9P1U0	RPA12_HUMAN	I	54	ENSP00000331111:V54I;ENSP00000365978:V54I;ENSP00000352333:V54I;ENSP00000365981:V54I	ENSP00000331111:V54I	V	+	1	0	ZNRD1	30137687	0.998000	0.40836	0.958000	0.39756	0.993000	0.82548	1.193000	0.32162	0.404000	0.25506	0.637000	0.83480	GTT	.	.		0.552	ZNRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076272.2			A	30029708	G	A	30029708	3	1	23	1	0	0	0	0	1	0	0	0	18225	1261	44	3	166	3	ZNRD1	6	30029708	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	232380	30029708	141085359	398	2464										
RNF39	80352	hgsc.bcm.edu	37	chr6	30039027	30039027	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggccgtcgtagaaggccacgCggccccgctcccagtccagg	14	17	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:30039027C>T	ENST00000244360.6	-	4	1221	c.1124G>A	c.(1123-1125)cGc>cAc	p.R375H	RNF39_ENST00000376751.3_Intron	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	375	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										GAAGGCCACGCGGCCCCGCTC	0.726																																					p.R375H	NSCLC(8;188 360 1520 20207 31481)	Atlas-SNP	.											.	RNF39	27	.	0			c.G1124A						.						13	10	11					6																	30039027		1489	2677	4166	SO:0001583	missense	80352	exon4			GCCACGCGGCCCC	AF238315	CCDS4673.1, CCDS4674.1	6p21.3	2013-01-09			ENSG00000204618	ENSG00000204618		"RING-type (C3HC4) zinc fingers"	18064	protein-coding gene	gene with protein product		607524				11130983, 11716498	Standard	NM_170769		Approved	HZFw1, LIRF	uc003npe.3	Q9H2S5	OTTHUMG00000031288	ENST00000244360.6:c.1124G>A	chr6.hg19:g.30039027C>T	ENSP00000244360:p.Arg375His	148.0	0.0		224.0	9.0	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Missense_Mutation	SNP	ENST00000244360.6	hg19	CCDS4673.1	.	.	.	.	.	.	.	.	.	.	c	14.95	2.688513	0.48097	.	.	ENSG00000204618	ENST00000244360	T	0.69175	-0.38	4.43	4.43	0.53597	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.43579	D	0.000552	T	0.45357	0.1338	L	0.47716	1.5	0.29863	N	0.82749	B	0.31413	0.322	B	0.37780	0.258	T	0.38243	-0.9670	9	.	.	.	-17.3663	10.2818	0.43543	0.1975:0.8025:0.0:0.0	.	375	Q9H2S5	RNF39_HUMAN	H	375	ENSP00000244360:R375H	.	R	-	2	0	RNF39	30147006	0.000000	0.05858	0.974000	0.42286	0.251000	0.25915	0.140000	0.16056	2.195000	0.70347	0.282000	0.19409	CGC	.	.		0.726	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769		T	30039027	C	T	30039027	3	4	23	1	0	0	0	0	1	0	0	0	13506	768	27	1	142	1	RNF39	6	30039027	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	9319	30039027	141076040	399	2465										
TRIM15	89870	hgsc.bcm.edu	37	chr6	30139690	30139692	+	In_Frame_Del	DEL	AGA	AGA	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcagtgaggtacacccggcAgaagaagagcctgccagaca							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:30139690_30139692delAGA	ENST00000376694.4	+	7	1431_1433	c.962_964delAGA	c.(961-966)cagaag>cag	p.K323del	TRIM15_ENST00000376688.1_Intron	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	323	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|mesodermal cell fate determination (GO:0007500)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	14						TACACCCGGCAGAAGAAGAGCCT	0.67																																					p.321_321del		Atlas-Indel,Pindel	.											.	TRIM15	34	.	0			c.961_963del						.																																			SO:0001651	inframe_deletion	89870	exon7			.	AF220132, U34249	CCDS4677.1	6p21.33	2013-01-09	2011-01-25		ENSG00000204610	ENSG00000204610		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16284	protein-coding gene	gene with protein product			"zinc finger protein 178", "tripartite motif-containing 15"	ZNF178		11331580, 8304341, 8812418	Standard	NM_033229		Approved	ZNFB7, RNF93	uc010jrx.3	Q9C019	OTTHUMG00000031031	ENST00000376694.4:c.962_964delAGA	chr6.hg19:g.30139696_30139698delAGA	ENSP00000365884:p.Lys323del	275.0	0.0		375.0	108.0	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	In_Frame_Del	DEL	ENST00000376694.4	hg19	CCDS4677.1																																																																																			.	.		0.67	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229		-	30139692	AGA	-	30139690	7	5	23	1	0	1	0	1	0	0	0	0	16505	188	7	0	988	0	TRIM15	6	30139690	In_Frame_Del	DEL	AGA	TCGA-4R-AA8I-01A-11D-A382-10	100663	30139690	140975377	400	2466										
DDR1	780	hgsc.bcm.edu	37	chr6	30864468	30864468	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccccacctccccagaacagCgtcccccattatgccgaggc	7	21	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:30864468C>T	ENST00000324771.8	+	15	2243	c.1695C>T	c.(1693-1695)agC>agT	p.S565S	DDR1_ENST00000418800.2_Silent_p.S528S|DDR1_ENST00000376568.3_Silent_p.S565S|DDR1_ENST00000376575.3_Silent_p.S565S|DDR1_ENST00000508312.1_Silent_p.S546S|DDR1_ENST00000452441.1_Silent_p.S565S|DDR1_ENST00000376569.3_Silent_p.S528S|DDR1_ENST00000361741.4_Intron|DDR1_ENST00000376570.4_Silent_p.S528S|DDR1_ENST00000513240.1_Silent_p.S565S|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000376567.2_Silent_p.S528S|DDR1_ENST00000454612.2_Silent_p.S528S			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	565	Gly/Pro-rich.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CCCAGAACAGCGTCCCCCATT	0.642																																					p.S565S		Atlas-SNP	.											.	DDR1	213	.	0			c.C1695T						.						49	55	53					6																	30864468		2203	4300	6503	SO:0001819	synonymous_variant	780	exon12			GAACAGCGTCCCC	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"CD molecules"	2730	protein-coding gene	gene with protein product		600408	"discoidin domain receptor family, member 1"	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1695C>T	chr6.hg19:g.30864468C>T		250.0	0.0		309.0	60.0	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Silent	SNP	ENST00000324771.8	hg19	CCDS34385.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.377265	0.24944	.	.	ENSG00000204580	ENST00000514434	.	.	.	5.21	0.774	0.18521	.	.	.	.	.	T	0.38532	0.1044	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24404	-1.0161	4	.	.	.	.	6.739	0.23424	0.0:0.6021:0.1374:0.2606	.	.	.	.	C	57	.	.	R	+	1	0	DDR1	30972447	0.902000	0.30710	0.994000	0.49952	0.987000	0.75469	-0.032000	0.12266	0.205000	0.20568	0.561000	0.74099	CGT	.	.		0.642	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994		T	30864468	C	T	30864468	2	4	23	1	0	0	0	0	0	0	0	1	4338	767	27	1		1	DDR1	6	30864468	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	724778	30864468	140250599	401	2467										
GTF2H4	2968	hgsc.bcm.edu	37	chr6	30881751	30881751	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttttggaagcggcagaaacaTagctcctgagagcgcgggac	14	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:30881751T>G	ENST00000259895.4	+	14	1603	c.1380T>G	c.(1378-1380)caT>caG	p.H460Q	VARS2_ENST00000321897.5_5'Flank|VARS2_ENST00000541562.1_5'Flank|VARS2_ENST00000416670.2_5'Flank|VARS2_ENST00000542001.1_5'Flank|GTF2H4_ENST00000376316.2_Missense_Mutation_p.H460Q	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	460					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	ATP-dependent DNA helicase activity (GO:0004003)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						GGCAGAAACATAGCTCCTGAG	0.637								Nucleotide excision repair (NER)																													p.H460Q		Atlas-SNP	.											.	GTF2H4	38	.	0			c.T1380G						.						15	17	16					6																	30881751		1508	2707	4215	SO:0001583	missense	2968	exon14			GAAACATAGCTCC	Y07595	CCDS34386.1	6p21.3	2012-11-05	2002-08-29		ENSG00000213780	ENSG00000213780		"General transcription factors", "General transcription factor IIH complex subunits"	4658	protein-coding gene	gene with protein product		601760	"general transcription factor IIH, polypeptide 4 (52kD subunit)"			9118947	Standard	NM_001517		Approved	TFB2, TFIIH, P52	uc003nsa.1	Q92759	OTTHUMG00000031043	ENST00000259895.4:c.1380T>G	chr6.hg19:g.30881751T>G	ENSP00000259895:p.His460Gln	191.0	0.0		283.0	86.0	NM_001517	B4DTJ5|Q76KU4	Missense_Mutation	SNP	ENST00000259895.4	hg19	CCDS34386.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.035880	0.54896	.	.	ENSG00000213780	ENST00000259895;ENST00000376316	T;T	0.40476	1.03;1.03	5.86	5.0	0.66597	.	0.802978	0.11020	U	0.608480	T	0.08447	0.0210	N	0.02213	-0.635	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17018	-1.0383	10	0.29301	T	0.29	-4.7331	10.8614	0.46829	0.0:0.8469:0.0:0.1531	.	460	Q92759	TF2H4_HUMAN	Q	460	ENSP00000259895:H460Q;ENSP00000365493:H460Q	ENSP00000259895:H460Q	H	+	3	2	GTF2H4	30989730	1.000000	0.71417	1.000000	0.80357	0.660000	0.38997	1.143000	0.31553	0.845000	0.35118	-0.186000	0.12905	CAT	.	.		0.637	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517		G	30881751	T	G	30881751	3	3	23	1	0	0	0	0	1	0	0	0	6874	1403	49	5	1430	5	GTF2H4	6	30881751	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	17283	30881751	140233316	402	2468										
CDSN	170679	hgsc.bcm.edu	37	chr6	31084588	31084588	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgctacaggggggaccttgAaccactccaggggcaccaga	13	12	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:31084588A>C	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Silent_p.V268V	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GGGGACCTTGAACCACTCCAG	0.622																																					p.V268V		Atlas-SNP	.											.	CDSN	48	.	0			c.T804G						.						29	29	29					6																	31084588		2158	4232	6390	SO:0001627	intron_variant	1041	exon2			ACCTTGAACCACT	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"chromosome 6 open reading frame 16"	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1920A>C	chr6.hg19:g.31084588A>C		61.0	0.0		107.0	24.0	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	hg19	CCDS34390.1																																																																																			.	.		0.622	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		C	31084588	A	C	31084588	1	2	23	0	1	0	0	0	0	0	0	0	3181	233	9	5		5	CDSN	6	31084588	Intron	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	202837	31084588	140030479	403	2469										
BAT1	7919	hgsc.bcm.edu	37	chr6	31507027	31507027	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggacatccattcccagaatgGcctgagggatgcactcatgc	11	12	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:31507027G>A	ENST00000396172.1	-	3	866	c.236C>T	c.(235-237)gCc>gTc	p.A79V	DDX39B_ENST00000415382.2_Intron|DDX39B_ENST00000453105.2_Intron|DDX39B_ENST00000449074.2_Missense_Mutation_p.A79V|ATP6V1G2-DDX39B_ENST00000475917.1_5'Flank|DDX39B_ENST00000458640.1_Missense_Mutation_p.A79V|SNORD117_ENST00000364915.1_RNA|SNORD84_ENST00000584275.1_RNA|DDX39B_ENST00000376177.2_Missense_Mutation_p.A79V|DDX39B_ENST00000417556.2_Missense_Mutation_p.A79V|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	79	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)	p.A79V(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						TCCCAGAATGGCCTGAGGGAT	0.522																																					p.A79V		Atlas-SNP	.											DDX39B,face,carcinoma,0,1	DDX39B	38	.	1	Substitution - Missense(1)	skin(1)	c.C236T						.						117	122	120					6																	31507027		1511	2709	4220	SO:0001583	missense	7919	exon3			AGAATGGCCTGAG	Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"DEAD-boxes"	13917	protein-coding gene	gene with protein product	"U2AF65-associated protein 56"	142560	"HLA-B associated transcript 1"	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.236C>T	chr6.hg19:g.31507027G>A	ENSP00000379475:p.Ala79Val	92.0	0.0		143.0	48.0	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Missense_Mutation	SNP	ENST00000396172.1	hg19	CCDS4697.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504374	0.85176	.	.	ENSG00000198563	ENST00000376177;ENST00000458640;ENST00000396172;ENST00000417556;ENST00000427214;ENST00000428098;ENST00000419338;ENST00000456662;ENST00000449074;ENST00000428450;ENST00000449757;ENST00000456976;ENST00000418897;ENST00000419020;ENST00000458215	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.13901	2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55	5.53	5.53	0.82687	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.065486	0.64402	D	0.000017	T	0.11452	0.0279	L	0.41824	1.3	0.80722	D	1	P;B;P	0.47962	0.903;0.35;0.831	P;B;P	0.47470	0.521;0.177;0.548	T	0.01405	-1.1363	10	0.49607	T	0.09	-9.5406	16.9509	0.86245	0.0:0.0:1.0:0.0	.	99;79;79	Q59G92;Q13838;Q5STU3	.;DX39B_HUMAN;.	V	79;79;79;79;79;79;79;79;79;79;102;79;94;79;79	ENSP00000365347:A79V;ENSP00000416269:A79V;ENSP00000379475:A79V;ENSP00000412582:A79V;ENSP00000399371:A79V;ENSP00000392672:A79V;ENSP00000410313:A79V;ENSP00000416350:A79V;ENSP00000391946:A79V;ENSP00000405707:A79V;ENSP00000409426:A102V;ENSP00000393984:A79V;ENSP00000399841:A94V;ENSP00000405245:A79V	ENSP00000365347:A79V	A	-	2	0	DDX39B	31615006	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.262000	0.95591	2.592000	0.87571	0.563000	0.77884	GCC	.	.		0.522	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640		A	31507027	G	A	31507027	3	1	23	1	0	0	0	0	1	0	0	0	1318	1203	42	3	1086	3	BAT1	6	31507027	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	422439	31507027	139608040	404	2470										
LY6G6D	58530	hgsc.bcm.edu	37	chr6	31683313	31683313	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgctacaactgtggtggaagCcccagcagttcttgcaaaga							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:31683313delC	ENST00000375825.3	+	2	90	c.90delC	c.(88-90)agcfs	p.S30fs	XXbac-BPG32J3.20_ENST00000461287.1_5'Flank|MEGT1_ENST00000503322.1_Frame_Shift_Del_p.S279fs|LY6G6F_ENST00000556581.1_Frame_Shift_Del_p.S279fs|LY6G6E_ENST00000383418.4_5'Flank|LY6G6E_ENST00000409239.1_5'Flank	NM_021246.2	NP_067069.2	O95868	LY66D_HUMAN	lymphocyte antigen 6 complex, locus G6D	30	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|plasma membrane (GO:0005886)				central_nervous_system(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	5						GTGGTGGAAGCCCCAGCAGTT	0.622																																					p.S30fs		Atlas-INDEL	.											.	LY6G6D	11	.	0			c.89delG						.						78	73	75					6																	31683313		1511	2709	4220	SO:0001589	frameshift_variant	58530	exon2			.		CCDS34404.1	6p21.3	2008-08-29	2002-07-29	2002-08-01	ENSG00000244355	ENSG00000244355			13935	protein-coding gene	gene with protein product		606038	"chromosome 6 open reading frame 23"	C6orf23		12079290	Standard	NM_021246		Approved	MEGT1, Ly6-D, G6D, LY6-D, NG25		O95868	OTTHUMG00000137370	ENST00000375825.3:c.90delC	chr6.hg19:g.31683313delC	ENSP00000364985:p.Ser30fs	110.0	0.0		136.0	11.0	NM_021246	A2BEY8|B0UXC1|B0V019|B0V1Y6|Q4VX50	Frame_Shift_Del	DEL	ENST00000375825.3	hg19	CCDS34404.1																																																																																			.	.		0.622	LY6G6D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144875.2			-	31683313	C	-	31683313	7	5	23	1	0	1	0	1	0	0	0	0	9104	738	26	0	96	0	LY6G6D	6	31683313	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	176286	31683313	139431754	405	2471										
TNXB	7148	hgsc.bcm.edu	37	chr6	32029263	32029263	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atttgcgcccaggctccaggCcccccacggtgacctcgctc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:32029263delC	ENST00000375244.3	-	21	7604	c.7403delG	c.(7402-7404)ggcfs	p.G2468fs	TNXB_ENST00000375247.2_Frame_Shift_Del_p.G2468fs			P22105	TENX_HUMAN	tenascin XB	2528	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						AGGCTCCAGGCCCCCCACGGT	0.687																																					p.G2468fs		Pindel	.											.	TNXB	553	.	0			c.7404delC						.						75	88	84					6																	32029263		1262	2532	3794	SO:0001589	frameshift_variant	7148	exon21			.	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7403delG	chr6.hg19:g.32029263delC	ENSP00000364393:p.Gly2468fs	131.0	0.0		198.0	30.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Frame_Shift_Del	DEL	ENST00000375244.3	hg19																																																																																				.	.		0.687	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		-	32029263	C	-	32029263	7	5	23	1	0	1	0	1	0	0	0	0	16361	739	26	0	7406	0	TNXB	6	32029263	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	345950	32029263	139085804	406	2472										
AGPAT1	10554	hgsc.bcm.edu	37	chr6	32138331	32138331	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagccagcccacagtagctcGcgcttggcaatgggcacaca	12	14	0	0	rs528693769	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:32138331G>A	ENST00000395499.1	-	4	960	c.381C>T	c.(379-381)cgC>cgT	p.R127R	AGPAT1_ENST00000375107.3_Silent_p.R127R|AGPAT1_ENST00000412465.2_Silent_p.R15R|AGPAT1_ENST00000490711.1_Intron|AGPAT1_ENST00000395497.1_Silent_p.R127R|AGPAT1_ENST00000395496.1_Silent_p.R127R|AGPAT1_ENST00000375104.2_Silent_p.R127R|AGPAT1_ENST00000336984.6_Silent_p.R127R|PPT2-EGFL8_ENST00000422437.1_3'UTR			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	127					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			central_nervous_system(1)|large_intestine(3)|lung(6)|ovary(2)	12						ACAGTAGCTCGCGCTTGGCAA	0.637													G|||	2	0.000399361	0	0.0029	5008	,	,		18391	0		0	False		,,,				2504	0				p.R127R		Atlas-SNP	.											.	AGPAT1	22	.	0			c.C381T						.						64	70	67					6																	32138331		1510	2708	4218	SO:0001819	synonymous_variant	10554	exon4			TAGCTCGCGCTTG	U56417	CCDS4744.1	6p21.3	2013-02-05	2013-02-05		ENSG00000204310	ENSG00000204310	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	324	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, alpha"	603099	"1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)"			9461603, 9291118	Standard	NM_032741		Approved	LPAAT-alpha	uc003oae.3	Q99943	OTTHUMG00000031210	ENST00000395499.1:c.381C>T	chr6.hg19:g.32138331G>A		84.0	0.0		106.0	28.0	NM_006411	A2BFI5|Q5BL03	Silent	SNP	ENST00000395499.1	hg19	CCDS4744.1																																																																																			.	.		0.637	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411		A	32138331	G	A	32138331	2	1	23	1	0	0	0	0	0	0	0	1	386	1074	38	1		1	AGPAT1	6	32138331	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	109068	32138331	138976736	407	2473										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33608281	33608281	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctggtggatgaccgctgtgTggtggagcccgcggccgggg	21	10	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:33608281T>C	ENST00000374316.5	+	3	1170	c.110T>C	c.(109-111)gTg>gCg	p.V37A	ITPR3_ENST00000605930.1_Missense_Mutation_p.V37A			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	37					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GACCGCTGTGTGGTGGAGCCC	0.632																																					p.V37A		Atlas-SNP	.											.	ITPR3	409	.	0			c.T110C						.						148	161	157					6																	33608281		2203	4300	6503	SO:0001583	missense	3710	exon2			GCTGTGTGGTGGA	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.110T>C	chr6.hg19:g.33608281T>C	ENSP00000363435:p.Val37Ala	114.0	0.0		137.0	43.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.623529	0.87460	.	.	ENSG00000096433	ENST00000374316	D	0.98649	-5.05	5.15	5.15	0.70609	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);	0.000000	0.85682	D	0.000000	D	0.99180	0.9716	M	0.92459	3.31	0.44745	D	0.997747	D	0.89917	1.0	D	0.91635	0.999	D	0.99568	1.0970	10	0.87932	D	0	-30.931	11.3587	0.49630	0.0:0.0:0.0:1.0	.	37	Q14573	ITPR3_HUMAN	A	37	ENSP00000363435:V37A	ENSP00000363435:V37A	V	+	2	0	ITPR3	33716259	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.007000	0.70731	1.936000	0.56123	0.402000	0.26972	GTG	.	.		0.632	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		C	33608281	T	C	33608281	3	2	23	1	0	0	0	0	1	0	0	0	7931	1696	59	2	116	2	ITPR3	6	33608281	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1469950	33608281	137506786	408	2474										
IP6K3	117283	hgsc.bcm.edu	37	chr6	33693356	33693356	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agatccaggacacagggatgCgtgtactgtgacactacatt	11	9	0	2	rs200747722		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:33693356C>T	ENST00000293756.4	-	5	953	c.627G>A	c.(625-627)acG>acA	p.T209T	IP6K3_ENST00000451316.1_Silent_p.T209T	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	209					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						CACAGGGATGCGTGTACTGTG	0.552																																					p.T209T		Atlas-SNP	.											.	IP6K3	52	.	0			c.G627A						.						99	86	90					6																	33693356		2203	4300	6503	SO:0001819	synonymous_variant	117283	exon6			GGGATGCGTGTAC	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"inositol hexaphosphate kinase 3"	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.627G>A	chr6.hg19:g.33693356C>T		118.0	0.0		119.0	36.0	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	hg19	CCDS34435.1																																																																																			.	C|0.999;T|0.001		0.552	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111		T	33693356	C	T	33693356	2	4	23	1	0	0	0	0	0	0	0	1	7799	755	27	1		1	IP6K3	6	33693356	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	85075	33693356	137421711	409	2475										
C6orf89	221477	hgsc.bcm.edu	37	chr6	36867219	36867219	+	5'UTR	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagggattttatattggaagAcatggatcttgctgccaacg	11	7	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:36867219A>T	ENST00000480824.2	+	0	293				C6orf89_ENST00000510325.2_5'UTR|C6orf89_ENST00000359359.2_5'UTR|C6orf89_ENST00000373685.1_5'UTR|C6orf89_ENST00000355190.3_Missense_Mutation_p.D7V			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89						epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						ATATTGGAAGACATGGATCTT	0.418																																					p.D7V		Atlas-SNP	.											.	C6orf89	39	.	0			c.A20T						.						75	76	76					6																	36867219		2203	4300	6503	SO:0001623	5_prime_UTR_variant	221477	exon2			TGGAAGACATGGA	AK058086	CCDS4827.1, CCDS69100.1, CCDS75444.1	6p21.31	2013-03-14			ENSG00000198663	ENSG00000198663			21114	protein-coding gene	gene with protein product	"bombesin receptor activated protein"					21857995, 23460338	Standard	NM_152734		Approved	FLJ25357, BRAP	uc003omw.3	Q6UWU4	OTTHUMG00000014613	ENST00000480824.2:c.-2A>T	chr6.hg19:g.36867219A>T		113.0	0.0		54.0	23.0	NM_152734	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000480824.2	hg19		.	.	.	.	.	.	.	.	.	.	A	18.27	3.587111	0.66105	.	.	ENSG00000198663	ENST00000355190;ENST00000416621;ENST00000540072	.	.	.	5.91	3.32	0.38043	.	0.000000	0.56097	D	0.000033	T	0.26304	0.0642	L	0.36672	1.1	0.80722	D	1	P	0.39480	0.675	B	0.39258	0.295	T	0.15378	-1.0439	9	0.87932	D	0	-0.8288	7.8253	0.29311	0.7142:0.2102:0.0756:0.0	.	7	Q6UWU4-2	.	V	7;7;6	.	ENSP00000347322:D7V	D	+	2	0	C6orf89	36975197	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.146000	0.42216	1.023000	0.39654	0.533000	0.62120	GAC	.	.		0.418	C6orf89-004	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000040387.2	NM_152734		T	36867219	A	T	36867219	1	4	23	0	1	0	0	0	0	0	0	0	2375	275	10	4		4	C6orf89	6	36867219	5'UTR	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3173863	36867219	134247848	410	2476										
KCNK17	89822	hgsc.bcm.edu	37	chr6	39272281	39272281	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccccctcacctgccaggtgCcccccagcctgctggcccag							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:39272281delC	ENST00000373231.4	-	3	735	c.503delG	c.(502-504)ggcfs	p.G168fs	KCNK17_ENST00000453413.2_Frame_Shift_Del_p.G168fs	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	168					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						CTGCCAGGTGCCCCCCAGCCT	0.607																																					p.G168fs		Atlas-Indel,Pindel	.											.	KCNK17	61	.	0			c.504delC						.						53	58	56					6																	39272281		2203	4300	6503	SO:0001589	frameshift_variant	89822	exon3			.	AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.503delG	chr6.hg19:g.39272281delC	ENSP00000362328:p.Gly168fs	148.0	0.0		233.0	47.0	NM_001135111	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Frame_Shift_Del	DEL	ENST00000373231.4	hg19	CCDS4842.1																																																																																			.	.		0.607	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460		-	39272281	C	-	39272281	7	5	23	1	0	1	0	1	0	0	0	0	8073	739	26	0	639	0	KCNK17	6	39272281	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	2405062	39272281	131842786	411	2477										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42200601	42200601	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccccgtggatgcgggcatgGccattcagtgcctgtcggga	15	13	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:42200601G>A	ENST00000372922.4	-	17	3658	c.3096C>T	c.(3094-3096)ggC>ggT	p.G1032G	TRERF1_ENST00000340840.2_Silent_p.G961G|TRERF1_ENST00000354325.2_Silent_p.G949G|TRERF1_ENST00000372917.4_Silent_p.G961G|TRERF1_ENST00000541110.1_Silent_p.G1052G	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1032	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGCGGGCATGGCCATTCAGTG	0.562																																					p.G1032G		Atlas-SNP	.											.	TRERF1	124	.	0			c.C3096T						.						37	35	36					6																	42200601		2203	4300	6503	SO:0001819	synonymous_variant	55809	exon17			GGCATGGCCATTC	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.3096C>T	chr6.hg19:g.42200601G>A		55.0	0.0		127.0	19.0	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	hg19	CCDS4867.1																																																																																			.	.		0.562	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		A	42200601	G	A	42200601	2	1	23	1	0	0	0	0	0	0	0	1	16490	1190	42	3		3	TRERF1	6	42200601	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2928320	42200601	128914466	412	2478										
TBCC	6903	hgsc.bcm.edu	37	chr6	42713333	42713333	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgtatgctttcaactgccGgggggatgccaggagccgcg					rs201664636	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:42713333delG	ENST00000372876.1	-	1	501	c.479delC	c.(478-480)ccgfs	p.P160fs	TBCC_ENST00000244625.2_Frame_Shift_Del_p.P160fs	NM_003192.2	NP_003183	Q15814	TBCC_HUMAN	tubulin folding cofactor C	160					'de novo' posttranslational protein folding (GO:0051084)|cell morphogenesis (GO:0000902)|cellular protein metabolic process (GO:0044267)|GTP catabolic process (GO:0006184)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)	chaperone binding (GO:0051087)|GTPase activity (GO:0003924)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(3)	14	Colorectal(47;0.196)		all cancers(41;0.00122)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.125)			TTCAACTGCCGGGGGGATGCC	0.632																																					p.P160fs		Atlas-Indel,Pindel	.											.	TBCC	31	.	0			c.480delG						.																																			SO:0001589	frameshift_variant	6903	exon1			.	U61234	CCDS4872.1	6p21.1	2008-02-05	2006-11-21		ENSG00000124659	ENSG00000124659			11580	protein-coding gene	gene with protein product		602971	"tubulin-specific chaperone c"			8706133, 11847227	Standard	NM_003192		Approved	CFC	uc003osl.3	Q15814	OTTHUMG00000014704	ENST00000372876.1:c.479delC	chr6.hg19:g.42713333delG	ENSP00000361967:p.Pro160fs	173.0	0.0		488.0	85.0	NM_003192	Q53Y43|Q5T787	Frame_Shift_Del	DEL	ENST00000372876.1	hg19	CCDS4872.1																																																																																			.	.		0.632	TBCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040559.1	NM_003192		-	42713333	G	-	42713333	7	5	23	1	0	1	0	1	0	0	0	0	15646	1116	39	0	565	0	TBCC	6	42713333	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	512732	42713333	128401734	413	2479										
KIAA0240	23506	hgsc.bcm.edu	37	chr6	42796557	42796557	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctaattactcaggtcagacGctgcagcctataggggtgac	11	10	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:42796557G>A	ENST00000314073.5	+	6	662	c.486G>A	c.(484-486)acG>acA	p.T162T	GLTSCR1L_ENST00000394168.1_Silent_p.T162T			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	162																	CAGGTCAGACGCTGCAGCCTA	0.468																																					p.T162T		Atlas-SNP	.											.	.	.	.	0			c.G486A						.						134	124	128					6																	42796557		2203	4300	6503	SO:0001819	synonymous_variant	23506	exon5			TCAGACGCTGCAG	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"KIAA0240"	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.486G>A	chr6.hg19:g.42796557G>A		109.0	0.0		313.0	76.0	NM_015349	A1L3W2|Q5TFZ3|Q92514	Silent	SNP	ENST00000314073.5	hg19	CCDS34451.1																																																																																			.	.		0.468	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		A	42796557	G	A	42796557	2	1	23	1	0	0	0	0	0	0	0	1	8173	1074	38	1		1	KIAA0240	6	42796557	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	83224	42796557	128318510	414	2480										
PPP2R5D	5528	hgsc.bcm.edu	37	chr6	42975948	42975948	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcttccctcaggttcatctaCgagacggagcatcacaacgg	9	13	5	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:42975948C>T	ENST00000485511.1	+	8	1046	c.867C>T	c.(865-867)taC>taT	p.Y289Y	PPP2R5D_ENST00000394110.3_Silent_p.Y257Y|PPP2R5D_ENST00000461010.1_Silent_p.Y183Y|PPP2R5D_ENST00000472118.1_Silent_p.Y281Y	NM_001270476.1|NM_006245.3	NP_001257405.1|NP_006236.1	Q14738	2A5D_HUMAN	protein phosphatase 2, regulatory subunit B', delta	289					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of catalytic activity (GO:0050790)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	25			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			GGTTCATCTACGAGACGGAGC	0.582																																					p.Y289Y	Melanoma(63;587 1613 29742 31770)	Atlas-SNP	.											.	PPP2R5D	47	.	0			c.C867T						.						136	139	138					6																	42975948		2203	4300	6503	SO:0001819	synonymous_variant	5528	exon8			CATCTACGAGACG	L76702	CCDS4878.1, CCDS43464.1, CCDS55002.1	6p21.1	2010-06-18	2010-04-14		ENSG00000112640	ENSG00000112640		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9312	protein-coding gene	gene with protein product		601646	"protein phosphatase 2, regulatory subunit B (B56), delta isoform", "protein phosphatase 2, regulatory subunit B', delta isoform"			7592815	Standard	NM_006245		Approved	B56D	uc003oth.4	Q14738	OTTHUMG00000014716	ENST00000485511.1:c.867C>T	chr6.hg19:g.42975948C>T		133.0	0.0		281.0	36.0	NM_006245	A8K3I9|B5BUA6|O00494|O00696|Q15171|Q5TC39	Silent	SNP	ENST00000485511.1	hg19	CCDS4878.1	.	.	.	.	.	.	.	.	.	.	C	6.120	0.390354	0.11581	.	.	ENSG00000112640	ENST00000470467	.	.	.	5.84	-4.83	0.03161	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.3824	14.3121	0.66422	0.0:0.4819:0.0:0.5181	.	.	.	.	X	209	.	.	R	+	1	2	PPP2R5D	43083926	0.980000	0.34600	0.973000	0.42090	0.946000	0.59487	0.095000	0.15127	-0.641000	0.05487	-1.152000	0.01820	CGA	.	.		0.582	PPP2R5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040573.3	NM_006245		T	42975948	C	T	42975948	2	4	23	1	0	0	0	0	0	0	0	1	12407	547	19	1		1	PPP2R5D	6	42975948	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	179391	42975948	128139119	415	2481										
MRPL2	51069	hgsc.bcm.edu	37	chr6	43023917	43023917	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccggctgcccccagcaaccAgagctatgtctgctgaccta	9	16	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43023917A>G	ENST00000388752.3	-	4	846	c.422T>C	c.(421-423)cTg>cCg	p.L141P	MRPL2_ENST00000230413.5_Missense_Mutation_p.L141P|MRPL2_ENST00000489623.1_Intron|CUL7_ENST00000265348.3_5'Flank|CUL7_ENST00000535468.1_5'Flank	NM_015950.3	NP_057034.2	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2	141					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(2)	9		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		CCCAGCAACCAGAGCTATGTC	0.522																																					p.L141P		Atlas-SNP	.											.	MRPL2	30	.	0			c.T422C						.						113	104	107					6																	43023917		2203	4300	6503	SO:0001583	missense	51069	exon4			GCAACCAGAGCTA	AB051617	CCDS34454.1, CCDS75458.1	6p21.3	2012-09-13			ENSG00000112651	ENSG00000112651		"Mitochondrial ribosomal proteins / large subunits"	14056	protein-coding gene	gene with protein product		611822					Standard	XM_005249161		Approved	MRP-L14, RPML14, CGI-22	uc003ots.1	Q5T653	OTTHUMG00000014719	ENST00000388752.3:c.422T>C	chr6.hg19:g.43023917A>G	ENSP00000373404:p.Leu141Pro	72.0	0.0		172.0	67.0	NM_015950	B2RC56|Q8WUL1|Q96Q56|Q9Y311	Missense_Mutation	SNP	ENST00000388752.3	hg19	CCDS34454.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.535022	0.85812	.	.	ENSG00000112651	ENST00000388752;ENST00000230413	T	0.60040	0.22	5.7	5.7	0.88788	Nucleic acid-binding, OB-fold-like (1);Ribosomal Proteins L2, RNA binding domain (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.64402	D	0.000001	T	0.81283	0.4790	H	0.96604	3.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.87741	0.2585	10	0.87932	D	0	-12.5297	14.5373	0.67969	1.0:0.0:0.0:0.0	.	141;141	B4DVE2;Q5T653	.;RM02_HUMAN	P	141	ENSP00000373404:L141P	ENSP00000230413:L141P	L	-	2	0	MRPL2	43131895	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.831000	0.92068	2.170000	0.68504	0.533000	0.62120	CTG	.	.		0.522	MRPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040577.2			G	43023917	A	G	43023917	3	3	23	1	0	0	0	0	1	0	0	0	9794	188	7	2	511	2	MRPL2	6	43023917	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	47969	43023917	128091150	416	2482										
CUL9	23113	hgsc.bcm.edu	37	chr6	43190596	43190596	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtggagcagcagacagagaAcctggagctgcacaccaatg	14	10	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43190596A>G	ENST00000252050.4	+	38	7196	c.7112A>G	c.(7111-7113)aAc>aGc	p.N2371S	CUL9_ENST00000354495.3_Missense_Mutation_p.N2261S|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000372647.2_Missense_Mutation_p.N2343S	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2371					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CAGACAGAGAACCTGGAGCTG	0.642																																					p.N2371S		Atlas-SNP	.											.	CUL9	248	.	0			c.A7112G						.						88	89	89					6																	43190596		2203	4300	6503	SO:0001583	missense	23113	exon38			CAGAGAACCTGGA	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.7112A>G	chr6.hg19:g.43190596A>G	ENSP00000252050:p.Asn2371Ser	94.0	0.0		207.0	49.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	A	11.48	1.650741	0.29336	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.72282	-0.64;-0.64;-0.53	5.04	-3.13	0.05266	.	0.627181	0.16955	N	0.192706	T	0.22742	0.0549	N	0.08118	0	0.34091	D	0.660774	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.001;0.001	T	0.01781	-1.1275	10	0.25106	T	0.35	-3.2484	8.481	0.33043	0.4044:0.125:0.4706:0.0	.	2261;2343;2371	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	S	2371;2261;2343	ENSP00000252050:N2371S;ENSP00000346490:N2261S;ENSP00000361730:N2343S	ENSP00000252050:N2371S	N	+	2	0	CUL9	43298574	0.645000	0.27286	0.893000	0.35052	0.787000	0.44495	-0.025000	0.12413	-0.610000	0.05716	-0.366000	0.07423	AAC	.	.		0.642	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		G	43190596	A	G	43190596	3	3	23	1	0	0	0	0	1	0	0	0	4063	43	2	2	7258	2	CUL9	6	43190596	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	166679	43190596	127924471	417	2483										
SLC22A7	10864	hgsc.bcm.edu	37	chr6	43267678	43267678	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcaccgcaccgtggctggagTcctgagcagcaccttctgga	13	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43267678T>C	ENST00000372585.5	+	5	796	c.701T>C	c.(700-702)gTc>gCc	p.V234A	SLC22A7_ENST00000487175.1_3'UTR|SLC22A7_ENST00000372574.3_Missense_Mutation_p.V232A|SLC22A7_ENST00000372589.3_Missense_Mutation_p.V232A	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	234					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	GTGGCTGGAGTCCTGAGCAGC	0.617																																					p.V234A		Atlas-SNP	.											.	SLC22A7	69	.	0			c.T701C						.						152	121	131					6																	43267678		2203	4300	6503	SO:0001583	missense	10864	exon4			CTGGAGTCCTGAG	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.701T>C	chr6.hg19:g.43267678T>C	ENSP00000361666:p.Val234Ala	145.0	0.0		325.0	31.0	NM_153320	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	hg19	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	T	13.83	2.353384	0.41700	.	.	ENSG00000137204	ENST00000451757;ENST00000372589;ENST00000372585;ENST00000372574	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.68	5.68	0.88126	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.290888	0.32901	N	0.005504	T	0.51941	0.1704	M	0.66378	2.025	0.33870	D	0.634833	P;P;P	0.49862	0.929;0.913;0.913	P;P;P	0.59115	0.852;0.769;0.769	T	0.58239	-0.7671	10	0.42905	T	0.14	.	13.4565	0.61201	0.0:0.0:0.0:1.0	.	234;232;232	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	A	106;232;234;232	ENSP00000416052:V106A;ENSP00000361670:V232A;ENSP00000361666:V234A;ENSP00000361655:V232A	ENSP00000361655:V232A	V	+	2	0	SLC22A7	43375656	0.710000	0.27896	0.308000	0.25141	0.002000	0.02628	1.607000	0.36836	2.160000	0.67779	0.455000	0.32223	GTC	.	.		0.617	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			C	43267678	T	C	43267678	3	2	23	1	0	0	0	0	1	0	0	0	14474	1667	58	2	715	2	SLC22A7	6	43267678	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	77082	43267678	127847389	418	2484										
ABCC10	89845	hgsc.bcm.edu	37	chr6	43402386	43402386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagagctgctgagtggcattCgggtcatcaagttctgcggg	15	9	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43402386C>T	ENST00000372530.4	+	4	1623	c.1408C>T	c.(1408-1410)Cgg>Tgg	p.R470W	ABCC10_ENST00000443426.2_3'UTR|ABCC10_ENST00000244533.3_Missense_Mutation_p.R427W	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	470	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	GAGTGGCATTCGGGTCATCAA	0.612																																					p.R470W		Atlas-SNP	.											.	ABCC10	118	.	0			c.C1408T						.						100	105	103					6																	43402386		2203	4300	6503	SO:0001583	missense	89845	exon4			GGCATTCGGGTCA	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.1408C>T	chr6.hg19:g.43402386C>T	ENSP00000361608:p.Arg470Trp	53.0	0.0		193.0	21.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	hg19	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	32	5.160422	0.94727	.	.	ENSG00000124574	ENST00000372515;ENST00000372530;ENST00000244533	D;D;D	0.91843	-2.92;-2.92;-2.92	5.93	5.93	0.95920	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.96374	0.8817	M	0.88031	2.925	0.80722	D	1	D;D	0.89917	0.991;1.0	P;D	0.97110	0.786;1.0	D	0.96555	0.9411	10	0.87932	D	0	-25.7653	15.9036	0.79403	0.1357:0.8643:0.0:0.0	.	427;470	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	W	26;470;427	ENSP00000361593:R26W;ENSP00000361608:R470W;ENSP00000244533:R427W	ENSP00000244533:R427W	R	+	1	2	ABCC10	43510364	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	3.885000	0.56182	2.826000	0.97356	0.655000	0.94253	CGG	.	.		0.612	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		T	43402386	C	T	43402386	3	4	23	1	0	0	0	0	1	0	0	0	50	875	31	1	1285	1	ABCC10	6	43402386	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	134708	43402386	127712681	419	2485										
ABCC10	89845	hgsc.bcm.edu	37	chr6	43412531	43412531	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgtccccacccagccacgCggaacgctgctgactggtgg	12	17	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43412531C>T	ENST00000372530.4	+	13	2910	c.2695C>T	c.(2695-2697)Cgg>Tgg	p.R899W	ABCC10_ENST00000244533.3_Missense_Mutation_p.R871W	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	899	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.R871W(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	CCCAGCCACGCGGAACGCTGC	0.587																																					p.R899W		Atlas-SNP	.											ABCC10,bladder,carcinoma,0,1	ABCC10	118	.	1	Substitution - Missense(1)	urinary_tract(1)	c.C2695T						.						70	67	68					6																	43412531		2203	4300	6503	SO:0001583	missense	89845	exon13			GCCACGCGGAACG	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.2695C>T	chr6.hg19:g.43412531C>T	ENSP00000361608:p.Arg899Trp	55.0	1.0		139.0	24.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	hg19	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.445368	0.63178	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	T;T	0.42900	0.96;0.96	5.22	2.07	0.26955	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.351077	0.30043	N	0.010549	T	0.52419	0.1733	M	0.78285	2.405	0.42656	D	0.993467	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.98	T	0.56547	-0.7961	10	0.40728	T	0.16	-37.1748	13.796	0.63171	0.6701:0.3299:0.0:0.0	.	871;899	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	W	899;871	ENSP00000361608:R899W;ENSP00000244533:R871W	ENSP00000244533:R871W	R	+	1	2	ABCC10	43520509	0.735000	0.28153	0.244000	0.24202	0.947000	0.59692	1.451000	0.35145	0.448000	0.26722	0.563000	0.77884	CGG	.	.		0.587	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		T	43412531	C	T	43412531	3	4	23	1	0	0	0	0	1	0	0	0	50	759	27	1	2653	1	ABCC10	6	43412531	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	10145	43412531	127702536	420	2486										
DLK2	65989	hgsc.bcm.edu	37	chr6	43418413	43418413	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagggtagcaacagggtccaGgggggcagacaccccggcgc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43418413delG	ENST00000357338.3	-	6	1716	c.1016delC	c.(1015-1017)cctfs	p.P339fs	DLK2_ENST00000372488.3_Frame_Shift_Del_p.P339fs|DLK2_ENST00000372485.1_Frame_Shift_Del_p.P333fs|DLK2_ENST00000414245.1_Frame_Shift_Del_p.P333fs	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	339					negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			ACAGGGTCCAGGGGGGCAGAC	0.662																																					p.P339fs		Pindel	.											.	DLK2	22	.	0			c.1017delT						.						34	38	37					6																	43418413		2202	4297	6499	SO:0001589	frameshift_variant	65989	exon6			.	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"EGF-like-domain, multiple 9"	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.1016delC	chr6.hg19:g.43418413delG	ENSP00000349893:p.Pro339fs	222.0	0.0		599.0	71.0	NM_206539	B3KNZ7|Q5T3T8|Q9BQ54	Frame_Shift_Del	DEL	ENST00000357338.3	hg19	CCDS4897.1																																																																																			.	.		0.662	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932		-	43418413	G	-	43418413	7	5	23	1	0	1	0	1	0	0	0	0	4567	1000	35	0	139	0	DLK2	6	43418413	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	5882	43418413	127696654	421	2487										
XPO5	57510	hgsc.bcm.edu	37	chr6	43526266	43526266	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaagcattgaagtcctcatcGctatcaaaatcaaaccgaga	6	10	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43526266G>A	ENST00000265351.7	-	12	1494	c.1284C>T	c.(1282-1284)agC>agT	p.S428S	XPO5_ENST00000424378.2_5'UTR	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	428					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			AGTCCTCATCGCTATCAAAAT	0.408																																					p.S428S		Atlas-SNP	.											.	XPO5	79	.	0			c.C1284T						.						79	74	76					6																	43526266		1870	4097	5967	SO:0001819	synonymous_variant	57510	exon12			CTCATCGCTATCA	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.1284C>T	chr6.hg19:g.43526266G>A		168.0	0.0		459.0	49.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	hg19	CCDS47430.1																																																																																			.	.		0.408	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		A	43526266	G	A	43526266	2	1	23	1	0	0	0	0	0	0	0	1	17462	1078	38	1		1	XPO5	6	43526266	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	107853	43526266	127588801	422	2488										
RUNX2	860	hgsc.bcm.edu	37	chr6	45390466	45390466	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagcagcagcagcagcagcaAcagcagcagcagcagcagga	13	13	0	0	rs575896136	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:45390466A>G	ENST00000371438.1	+	2	553	c.195A>G	c.(193-195)caA>caG	p.Q65Q	RUNX2_ENST00000465038.2_Silent_p.Q65Q|RUNX2_ENST00000576263.1_Silent_p.Q65Q|RUNX2_ENST00000352853.5_Silent_p.Q133Q|RUNX2_ENST00000541979.1_Silent_p.Q133Q|RUNX2_ENST00000371432.3_Silent_p.Q51Q|RUNX2_ENST00000359524.5_Silent_p.Q51Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371436.6_Silent_p.Q65Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	65	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcaacagcagcagc	0.731													A|||	8	0.00159744	0.0023	0	5008	,	,		7675	0.002		0	False		,,,				2504	0.0031				p.Q65Q		Atlas-SNP	.											.	RUNX2	128	.	0			c.A195G						.						10	15	14					6																	45390466		1452	3071	4523	SO:0001819	synonymous_variant	860	exon3			GCAGCAACAGCAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.195A>G	chr6.hg19:g.45390466A>G		57.0	0.0		109.0	5.0	NM_001024630	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	hg19	CCDS43467.2																																																																																			.	.		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390466	A	G	45390466	2	3	23	1	0	0	0	0	0	0	0	1	13763	40	2	2		2	RUNX2	6	45390466	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1864200	45390466	125724601	423	2489										
TDRD6	221400	hgsc.bcm.edu	37	chr6	46656045	46656045	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcggccacgcgcggccagtgGgcgctgggcagcgcctcggc	19	16	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:46656045G>T	ENST00000316081.6	+	1	180	c.180G>T	c.(178-180)tgG>tgT	p.W60C	RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000434329.2_RNA|TDRD6_ENST00000544460.1_Missense_Mutation_p.W60C|RP11-446F17.3_ENST00000422284.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	60					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			GCGGCCAGTGGGCGCTGGGCA	0.741																																					p.W60C		Atlas-SNP	.											.	TDRD6	205	.	0			c.G180T						.						2	3	3					6																	46656045		1504	3094	4598	SO:0001583	missense	221400	exon1			CCAGTGGGCGCTG	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.180G>T	chr6.hg19:g.46656045G>T	ENSP00000346065:p.Trp60Cys	63.0	0.0		103.0	11.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	hg19	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.358668	0.24598	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.09255	3.0;3.0	5.2	4.32	0.51571	Maternal tudor protein (1);	0.879250	0.10003	N	0.728190	T	0.04227	0.0117	N	0.14661	0.345	0.18873	N	0.999987	P;D	0.53151	0.948;0.958	P;P	0.50754	0.517;0.649	T	0.33954	-0.9848	10	0.42905	T	0.14	-7.235	6.8771	0.24153	0.1443:0.1607:0.695:0.0	.	60;60	F5H5M3;O60522	.;TDRD6_HUMAN	C	60	ENSP00000443299:W60C;ENSP00000346065:W60C	ENSP00000346065:W60C	W	+	3	0	TDRD6	46764004	1.000000	0.71417	0.999000	0.59377	0.771000	0.43674	2.134000	0.42102	2.425000	0.82216	0.563000	0.77884	TGG	.	.		0.741	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		T	46656045	G	T	46656045	3	4	23	1	0	0	0	0	1	0	0	0	15749	1241	43	3	182	3	TDRD6	6	46656045	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1265579	46656045	124459022	424	2490										
GPR116	221395	hgsc.bcm.edu	37	chr6	46874483	46874483	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acatgaggcacaaagtggttCtccttggggatttcatgtct	11	8	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:46874483C>G	ENST00000283296.7	-	2	305	c.17G>C	c.(16-18)aGa>aCa	p.R6T	GPR116_ENST00000265417.7_Missense_Mutation_p.R6T|GPR116_ENST00000362015.4_Missense_Mutation_p.R6T|RP3-365O12.2_ENST00000451135.1_RNA|GPR116_ENST00000456426.2_Missense_Mutation_p.R6T	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	6					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R6I(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CAAAGTGGTTCTCCTTGGGGA	0.358																																					p.R6T	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											GPR116,colon,carcinoma,0,1	GPR116	133	.	1	Substitution - Missense(1)	large_intestine(1)	c.G17C						.						138	140	139					6																	46874483		2203	4300	6503	SO:0001583	missense	221395	exon2			GTGGTTCTCCTTG	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.17G>C	chr6.hg19:g.46874483C>G	ENSP00000283296:p.Arg6Thr	154.0	0.0		222.0	74.0	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	hg19	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	3.779	-0.046105	0.07407	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000265417	T;T;T;T	0.30182	1.54;1.92;1.6;1.54	5.73	2.6	0.31112	.	0.453074	0.19217	N	0.119775	T	0.04452	0.0122	N	0.12182	0.205	0.09310	N	0.999996	B;B;B	0.21381	0.055;0.017;0.004	B;B;B	0.12837	0.008;0.007;0.003	T	0.40327	-0.9569	10	0.25751	T	0.34	-0.5277	4.8602	0.13579	0.0:0.5998:0.1752:0.2251	.	6;6;6	A8K0D8;Q8IZF2-3;Q8IZF2	.;.;GP116_HUMAN	T	6	ENSP00000283296:R6T;ENSP00000354563:R6T;ENSP00000412866:R6T;ENSP00000265417:R6T	ENSP00000265417:R6T	R	-	2	0	GPR116	46982442	0.011000	0.17503	0.030000	0.17652	0.079000	0.17450	-0.122000	0.10627	0.280000	0.22209	0.557000	0.71058	AGA	.	.		0.358	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		G	46874483	C	G	46874483	3	3	23	1	0	0	0	0	1	0	0	0	6641	913	32	4	4103	4	GPR116	6	46874483	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	218438	46874483	124240584	425	2491										
GPR115	221393	hgsc.bcm.edu	37	chr6	47682484	47682484	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcattgctcatcatttatggAatattggtcattttccgtag	8	7	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:47682484A>G	ENST00000283303.2	+	6	1761	c.1503A>G	c.(1501-1503)ggA>ggG	p.G501G	GPR115_ENST00000327753.3_Silent_p.G501G|GPR115_ENST00000371220.1_Silent_p.G558G|RN7SKP116_ENST00000516902.1_RNA	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	501					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						TCATTTATGGAATATTGGTCA	0.423																																					p.G501G	GBM(22;431 510 9010 26644 32828)	Atlas-SNP	.											.	GPR115	140	.	0			c.A1503G						.						205	193	197					6																	47682484		2203	4300	6503	SO:0001819	synonymous_variant	221393	exon6			TTATGGAATATTG	AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.1503A>G	chr6.hg19:g.47682484A>G		75.0	0.0		155.0	54.0	NM_153838	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Silent	SNP	ENST00000283303.2	hg19	CCDS4922.2																																																																																			.	.		0.423	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		G	47682484	A	G	47682484	2	3	23	1	0	0	0	0	0	0	0	1	6640	233	9	2		2	GPR115	6	47682484	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	808001	47682484	123432583	426	2492										
COL19A1	1310	hgsc.bcm.edu	37	chr6	70866035	70866035	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttagaatttctgtggcaactGccaagccagtgtcccagggc	11	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:70866035G>A	ENST00000322773.4	+	32	2198	c.2096G>A	c.(2095-2097)tGc>tAc	p.C699Y	COL19A1_ENST00000393344.1_Missense_Mutation_p.C321Y	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	699					cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						TGTGGCAACTGCCAAGCCAGT	0.453																																					p.C699Y		Atlas-SNP	.											.	COL19A1	232	.	0			c.G2096A						.						70	64	66					6																	70866035		2203	4300	6503	SO:0001583	missense	1310	exon32			GCAACTGCCAAGC		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.2096G>A	chr6.hg19:g.70866035G>A	ENSP00000316030:p.Cys699Tyr	152.0	0.0		72.0	6.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	hg19	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.408196	0.42715	.	.	ENSG00000082293	ENST00000322773;ENST00000393344	D;D	0.92099	-2.97;-2.88	5.41	5.41	0.78517	.	0.062427	0.64402	D	0.000007	D	0.96846	0.8970	H	0.95712	3.71	0.50039	D	0.999846	D	0.71674	0.998	D	0.80764	0.994	D	0.96789	0.9581	10	0.46703	T	0.11	.	14.7103	0.69225	0.0:0.0:1.0:0.0	.	699	Q14993	COJA1_HUMAN	Y	699;321	ENSP00000316030:C699Y;ENSP00000377013:C321Y	ENSP00000316030:C699Y	C	+	2	0	COL19A1	70922756	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	4.422000	0.59854	2.546000	0.85860	0.563000	0.77884	TGC	.	.		0.453	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			A	70866035	G	A	70866035	3	1	23	1	0	0	0	0	1	0	0	0	3678	1319	46	3	2218	3	COL19A1	6	70866035	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	23183551	70866035	100249032	427	2493										
B3GAT2	135152	hgsc.bcm.edu	37	chr6	71603972	71603972	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggagaccttgcgggtggttcGcatctataaaaagggaaaag	14	6	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:71603972G>A	ENST00000230053.6	-	2	1203	c.595C>T	c.(595-597)Cga>Tga	p.R199*		NM_080742.2	NP_542780.1	Q9NPZ5	B3GA2_HUMAN	beta-1,3-glucuronyltransferase 2	199					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|metal ion binding (GO:0046872)	p.R199G(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						CGGGTGGTTCGCATCTATAAA	0.502																																					p.R199X		Atlas-SNP	.											B3GAT2,NS,carcinoma,0,1	B3GAT2	33	.	1	Substitution - Missense(1)	lung(1)	c.C595T						.						55	59	58					6																	71603972		2203	4300	6503	SO:0001587	stop_gained	135152	exon2			TGGTTCGCATCTA	AB075843	CCDS4974.1	6q12	2014-07-08	2014-07-08		ENSG00000112309	ENSG00000112309	2.4.1.135	"Beta-1,3-glucuronyltransferases"	922	protein-coding gene	gene with protein product	"glucuronosyltransferase S", "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2"	607497				12383500	Standard	NM_080742		Approved	GlcAT-S	uc003pfv.3	Q9NPZ5	OTTHUMG00000014997	ENST00000230053.6:c.595C>T	chr6.hg19:g.71603972G>A	ENSP00000230053:p.Arg199*	186.0	0.0		117.0	99.0	NM_080742	Q5JS09|Q8TF38|Q96NK4	Nonsense_Mutation	SNP	ENST00000230053.6	hg19	CCDS4974.1	.	.	.	.	.	.	.	.	.	.	G	40	8.154060	0.98680	.	.	ENSG00000112309	ENST00000230053	.	.	.	6.07	3.24	0.37175	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.3395	15.333	0.74229	0.0:0.0:0.634:0.366	.	.	.	.	X	199	.	ENSP00000230053:R199X	R	-	1	2	B3GAT2	71660693	1.000000	0.71417	1.000000	0.80357	0.079000	0.17450	3.976000	0.56867	0.392000	0.25172	0.650000	0.86243	CGA	.	.		0.502	B3GAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041150.2	NM_080742		A	71603972	G	A	71603972	4	1	23	1	0	0	0	0	0	1	0	0	1254	1095	38	1	388	1	B3GAT2	6	71603972	Nonsense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	737937	71603972	99511095	428	2494										
IBTK	25998	hgsc.bcm.edu	37	chr6	82891683	82891683	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aactatggctagtaacagacTttttttcttctagtaagaaa							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:82891683delT	ENST00000306270.7	-	26	4187	c.3638delA	c.(3637-3639)aagfs	p.K1213fs	IBTK_ENST00000503631.1_Frame_Shift_Del_p.K1012fs|IBTK_ENST00000510291.1_Frame_Shift_Del_p.K1198fs	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1213					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		AGTAACAGACTTTTTTTCTTC	0.343																																					p.K1213fs		Atlas-Indel,Pindel	.											.	IBTK	128	.	0			c.3639delG						.						51	53	52					6																	82891683		2203	4300	6503	SO:0001589	frameshift_variant	25998	exon26			.	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3638delA	chr6.hg19:g.82891683delT	ENSP00000305721:p.Lys1213fs	111.0	0.0		65.0	44.0	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Frame_Shift_Del	DEL	ENST00000306270.7	hg19	CCDS34490.1																																																																																			.	.		0.343	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		-	82891683	T	-	82891683	7	5	23	1	0	1	0	1	0	0	0	0	7485	1609	56	0	439	0	IBTK	6	82891683	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	11287711	82891683	88223384	429	2495										
SYNCRIP	10492	hgsc.bcm.edu	37	chr6	86333797	86333797	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aactgagatgcagacaccaaTatgttttccagaacgaattt	7	8	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:86333797T>C	ENST00000369622.3	-	7	1200	c.700A>G	c.(700-702)Att>Gtt	p.I234V	SYNCRIP_ENST00000355238.6_Missense_Mutation_p.I234V	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	234	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		CAGACACCAATATGTTTTCCA	0.323																																					p.I234V		Atlas-SNP	.											.	SYNCRIP	80	.	0			c.A700G						.						87	84	85					6																	86333797		2203	4300	6503	SO:0001583	missense	10492	exon7			CACCAATATGTTT	AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"RNA binding motif (RRM) containing"	16918	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein Q"					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.700A>G	chr6.hg19:g.86333797T>C	ENSP00000358635:p.Ile234Val	79.0	0.0		55.0	5.0	NM_006372	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Missense_Mutation	SNP	ENST00000369622.3	hg19	CCDS5005.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.348593	0.82132	.	.	ENSG00000135316	ENST00000355238;ENST00000369622	T;T	0.49139	1.12;0.79	5.75	5.75	0.90469	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.49201	0.1543	L	0.49571	1.57	0.54753	D	0.999982	P;P;P;P;B;P;P	0.50943	0.475;0.544;0.787;0.94;0.12;0.61;0.475	B;B;B;P;B;B;B	0.55011	0.196;0.439;0.387;0.766;0.219;0.358;0.196	T	0.54423	-0.8296	10	0.87932	D	0	.	16.066	0.80870	0.0:0.0:0.0:1.0	.	234;234;136;82;234;234;234	O60506;O60506-2;B7Z645;O60506-5;O60506-4;O60506-3;B2R8Z8	HNRPQ_HUMAN;.;.;.;.;.;.	V	234	ENSP00000347380:I234V;ENSP00000358635:I234V	ENSP00000347380:I234V	I	-	1	0	SYNCRIP	86390516	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.121000	0.64691	2.196000	0.70406	0.455000	0.32223	ATT	.	.		0.323	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372		C	86333797	T	C	86333797	3	2	23	1	0	0	0	0	1	0	0	0	15459	1406	49	2	1237	2	SYNCRIP	6	86333797	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3442114	86333797	84781270	430	2496										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138576784	138576784	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctatctattacatcgcagccGagctggtccggctggtgggg	14	11	1	0	rs370057378		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:138576784G>A	ENST00000251691.4	+	10	1148	c.982G>A	c.(982-984)Gag>Aag	p.E328K		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CATCGCAGCCGAGCTGGTCCG	0.662																																					p.E328K		Atlas-SNP	.											KIAA1244_ENST00000251691,NS,carcinoma,0,2	KIAA1244	236	.	0			c.G982A						.	G	LYS/GLU	0,4406		0,0,2203	27	28	27		982	5.7	1	6		27	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA1244	NM_020340.4	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	328/2178	138576784	1,13005	2203	4300	6503	SO:0001583	missense	57221	exon10			GCAGCCGAGCTGG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.982G>A	chr6.hg19:g.138576784G>A	ENSP00000251691:p.Glu328Lys	103.0	0.0		52.0	26.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	36	5.810796	0.96975	0.0	1.16E-4	ENSG00000112379	ENST00000251691	T	0.04654	3.58	5.68	5.68	0.88126	.	0.046372	0.85682	D	0.000000	T	0.15392	0.0371	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.00475	-1.1717	10	0.72032	D	0.01	-23.604	19.7964	0.96487	0.0:0.0:1.0:0.0	.	328	Q5TH69	BIG3_HUMAN	K	328	ENSP00000251691:E328K	ENSP00000251691:E328K	E	+	1	0	KIAA1244	138618477	1.000000	0.71417	0.976000	0.42696	0.935000	0.57460	9.869000	0.99810	2.702000	0.92279	0.655000	0.94253	GAG	.	.		0.662	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138576784	G	A	138576784	3	1	23	1	0	0	0	0	1	0	0	0	8226	1059	37	1	1020	1	KIAA1244	6	138576784	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	52242987	138576784	32538283	431	2497										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138584499	138584499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggactcgggcaggtccgacGtgtcagacattgggtcggac	16	10	1	1	rs376236619		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:138584499G>A	ENST00000251691.4	+	12	2045	c.1879G>A	c.(1879-1881)Gtg>Atg	p.V627M		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CAGGTCCGACGTGTCAGACAT	0.547																																					p.V627M		Atlas-SNP	.											.	KIAA1244	236	.	0			c.G1879A						.	G	MET/VAL	0,4406		0,0,2203	133	146	142		1879	5.3	1	6		142	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA1244	NM_020340.4	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	627/2178	138584499	1,13005	2203	4300	6503	SO:0001583	missense	57221	exon12			TCCGACGTGTCAG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.1879G>A	chr6.hg19:g.138584499G>A	ENSP00000251691:p.Val627Met	124.0	0.0		86.0	33.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	18.99	3.740392	0.69304	0.0	1.16E-4	ENSG00000112379	ENST00000251691	T	0.21734	1.99	5.32	5.32	0.75619	SEC7-like (1);	0.231513	0.34411	N	0.003983	T	0.18676	0.0448	L	0.57536	1.79	0.48185	D	0.999605	D	0.64830	0.994	P	0.48488	0.579	T	0.01114	-1.1447	10	0.54805	T	0.06	-22.0588	12.3695	0.55246	0.0773:0.0:0.9227:0.0	.	627	Q5TH69	BIG3_HUMAN	M	627	ENSP00000251691:V627M	ENSP00000251691:V627M	V	+	1	0	KIAA1244	138626192	1.000000	0.71417	0.962000	0.40283	0.649000	0.38597	7.524000	0.81866	2.482000	0.83794	0.655000	0.94253	GTG	.	.		0.547	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138584499	G	A	138584499	3	1	23	1	0	0	0	0	1	0	0	0	8226	1145	40	1	1925	1	KIAA1244	6	138584499	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	7715	138584499	32530568	432	2498										
ESR1	2099	hgsc.bcm.edu	37	chr6	152332874	152332874	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgatgattggtctcgtctggCgctccatggagcacccaggg	14	11	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:152332874C>T	ENST00000206249.3	+	5	1542	c.1180C>T	c.(1180-1182)Cgc>Tgc	p.R394C	ESR1_ENST00000443427.1_Missense_Mutation_p.R394C|ESR1_ENST00000427531.2_Missense_Mutation_p.R221C|ESR1_ENST00000456483.2_Missense_Mutation_p.R282C|ESR1_ENST00000406599.1_Intron|ESR1_ENST00000440973.1_Missense_Mutation_p.R394C|ESR1_ENST00000338799.5_Missense_Mutation_p.R394C	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	394	Interaction with AKAP13.|Self-association.|Steroid-binding.|Transactivation AF-2.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	TCTCGTCTGGCGCTCCATGGA	0.493																																					p.R394C		Atlas-SNP	.											.	ESR1	94	.	0			c.C1180T						.						142	127	132					6																	152332874		2203	4300	6503	SO:0001583	missense	2099	exon5			GTCTGGCGCTCCA	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"Nuclear hormone receptors"	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.1180C>T	chr6.hg19:g.152332874C>T	ENSP00000206249:p.Arg394Cys	117.0	0.0		69.0	17.0	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Missense_Mutation	SNP	ENST00000206249.3	hg19	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.483500	0.84854	.	.	ENSG00000091831	ENST00000440973;ENST00000338799;ENST00000456483;ENST00000431219;ENST00000443427;ENST00000206249;ENST00000431590;ENST00000544394;ENST00000415488	D;D;D;D;D;D;T	0.97256	-4.31;-4.31;-4.31;-4.31;-4.31;-4.31;0.35	5.42	5.42	0.78866	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.98535	0.9511	M	0.90814	3.15	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.997;0.998	D;D;D;D;P;D	0.97110	1.0;0.999;0.999;1.0;0.856;0.911	D	0.99513	1.0956	10	0.87932	D	0	.	14.0967	0.65027	0.1504:0.8495:0.0:0.0	.	298;175;89;393;394;394	B0QYW6;E7EVR3;C8CJL6;A8KAF4;G4XH65;P03372	.;.;.;.;.;ESR1_HUMAN	C	394;394;282;175;394;394;322;221;67	ENSP00000405330:R394C;ENSP00000342630:R394C;ENSP00000415934:R282C;ENSP00000387500:R394C;ENSP00000206249:R394C;ENSP00000445454:R221C;ENSP00000401995:R67C	ENSP00000206249:R394C	R	+	1	0	ESR1	152374567	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.719000	0.54926	2.541000	0.85698	0.591000	0.81541	CGC	.	.		0.493	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1			T	152332874	C	T	152332874	3	4	23	1	0	0	0	0	1	0	0	0	5258	768	27	1	1198	1	ESR1	6	152332874	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	13748375	152332874	18782193	433	2499										
TFB1M	51106	hgsc.bcm.edu	37	chr6	155578991	155578991	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tagagtctgtaattctctgcGtcatcctcttctttttcttc	5	11	6	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:155578991G>A	ENST00000367166.4	-	7	1075	c.1020C>T	c.(1018-1020)gaC>gaT	p.D340D	RP11-477D19.2_ENST00000435295.1_RNA	NM_016020.3	NP_057104.2	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	340					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)		AATTCTCTGCGTCATCCTCTT	0.418																																					p.D340D		Atlas-SNP	.											.	TFB1M	30	.	0			c.C1020T						.						104	94	97					6																	155578991		2203	4300	6503	SO:0001819	synonymous_variant	51106	exon7			CTCTGCGTCATCC	AF151833	CCDS5248.1	6q25.1-q25.3	2011-01-28			ENSG00000029639	ENSG00000029639			17037	protein-coding gene	gene with protein product	"dimethyladenosine transferase 1, mitochondrial"	607033				10810093, 11809803	Standard	NM_016020		Approved	mtTFB, CGI-75	uc003qqj.4	Q8WVM0	OTTHUMG00000015881	ENST00000367166.4:c.1020C>T	chr6.hg19:g.155578991G>A		73.0	0.0		54.0	27.0	NM_016020	Q05DR0|Q9Y384	Silent	SNP	ENST00000367166.4	hg19	CCDS5248.1																																																																																			.	.		0.418	TFB1M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042809.1			A	155578991	G	A	155578991	2	1	23	1	0	0	0	0	0	0	0	1	15808	1136	40	1		1	TFB1M	6	155578991	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3246117	155578991	15536076	434	2500										
TTLL2	83887	hgsc.bcm.edu	37	chr6	167754936	167754936	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagttacggagcaggcacacGcctcacaagacactcatgcc	9	14	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:167754936G>A	ENST00000239587.5	+	3	1636	c.1548G>A	c.(1546-1548)acG>acA	p.T516T		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	516					cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GCAGGCACACGCCTCACAAGA	0.577																																					p.T516T		Atlas-SNP	.											.	TTLL2	82	.	0			c.G1548A						.						147	120	129					6																	167754936		2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			GCACACGCCTCAC	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"Tubulin tyrosine ligase-like family"	21211	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 104"	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1548G>A	chr6.hg19:g.167754936G>A		135.0	0.0		61.0	40.0	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	hg19	CCDS5301.1																																																																																			.	.		0.577	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		A	167754936	G	A	167754936	2	1	23	1	0	0	0	0	0	0	0	1	16742	1074	38	1		1	TTLL2	6	167754936	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	12175945	167754936	3360131	435	2501										
PHF10	55274	hgsc.bcm.edu	37	chr6	170123958	170123959	+	Frame_Shift_Ins	INS	-	-	G													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	accttcggggactgcgctccINSgggggtggctgggtcgctgt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:170123958_170123959insG	ENST00000339209.4	-	1	192_193	c.69_70insC	c.(67-72)cccggafs	p.G24fs	RP1-266L20.4_ENST00000430250.1_RNA|RP1-266L20.2_ENST00000413088.1_RNA|PHF10_ENST00000366780.4_Frame_Shift_Ins_p.G24fs	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	24					nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		GACTGCGCTCCGGGGGTGGCTG	0.832																																					p.G24fs		Atlas-Indel,Pindel	.											.	PHF10	76	.	0			c.70_71insC						.																																			SO:0001589	frameshift_variant	55274	exon1			.	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"Zinc fingers, PHD-type"	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.70dupC	chr6.hg19:g.170123963_170123963dupG	ENSP00000341805:p.Gly24fs	21.0	0.0		29.0	19.0	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Frame_Shift_Ins	INS	ENST00000339209.4	hg19	CCDS5308.2																																																																																			.	.		0.832	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		G	170123959	-	G	170123958	7	5	23	1	0	1	1	0	0	0	0	0	11830	661	23	0	1474	0	PHF10	6	170123958	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	2369022	170123958	991109	436	2502										
PRKAR1B	5575	hgsc.bcm.edu	37	chr7	618965	618965	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctccatcttcaaactggacGggctccagcgcatccgccac	8	17	3	0	rs199622718		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:618965G>T	ENST00000406797.1	-	9	993	c.819C>A	c.(817-819)ccC>ccA	p.P273P	PRKAR1B_ENST00000544935.1_Silent_p.P273P|PRKAR1B_ENST00000360274.4_Silent_p.P273P|PRKAR1B_ENST00000403562.1_Silent_p.P273P|PRKAR1B_ENST00000537384.1_Silent_p.P273P	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	273					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CAAACTGGACGGGCTCCAGCG	0.627																																					p.P273P		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.C819A						.						130	102	111					7																	618965		2203	4296	6499	SO:0001819	synonymous_variant	5575	exon9			CTGGACGGGCTCC	M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	2.7.11.1		9390	protein-coding gene	gene with protein product		176911				1358799, 3479018	Standard	NM_002735		Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.819C>A	chr7.hg19:g.618965G>T		103.0	0.0		140.0	42.0	NM_001164760	Q8N422	Silent	SNP	ENST00000406797.1	hg19	CCDS34579.1	.	.	.	.	.	.	.	.	.	.	G	8.252	0.809138	0.16537	.	.	ENSG00000188191	ENST00000400758	T	0.71579	-0.58	5.14	-10.3	0.00346	.	0.057139	0.64402	U	0.000001	T	0.63283	0.2498	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70861	-0.4757	7	0.51188	T	0.08	-8.0692	6.2906	0.21057	0.2876:0.0998:0.5146:0.098	.	.	.	.	Q	134	ENSP00000383569:P134Q	ENSP00000383569:P134Q	P	-	2	0	PRKAR1B	585491	0.004000	0.15560	0.682000	0.30024	0.800000	0.45204	-1.351000	0.02622	-2.277000	0.00677	-1.104000	0.02111	CCG	.	G|1.000;A|0.000		0.627	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1			T	618965	G	T	618965	2	4	23	1	0	0	0	0	0	0	0	1	12516	1103	39	1		1	PRKAR1B	7	618965	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10		618965	158519698	437	2503										
INTS1	26173	hgsc.bcm.edu	37	chr7	1518116	1518116	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgacggaaggccagggcctCggccaggcgcaggagccccc	16	16	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:1518116C>T	ENST00000404767.3	-	33	4601	c.4516G>A	c.(4516-4518)Gag>Aag	p.E1506K	INTS1_ENST00000389470.4_Missense_Mutation_p.E1705K	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	1506					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GCCAGGGCCTCGGCCAGGCGC	0.697																																					p.E1506K		Atlas-SNP	.											.	INTS1	145	.	0			c.G4516A						.						23	30	27					7																	1518116		2114	4214	6328	SO:0001583	missense	26173	exon33			GGGCCTCGGCCAG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.4516G>A	chr7.hg19:g.1518116C>T	ENSP00000385722:p.Glu1506Lys	253.0	0.0		273.0	145.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.139569	0.37728	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.57907	0.54;0.37	4.51	3.62	0.41486	.	0.105841	0.64402	D	0.000005	T	0.37100	0.0991	L	0.34521	1.04	0.41207	D	0.986411	P	0.45428	0.858	B	0.34346	0.18	T	0.19778	-1.0295	10	0.36615	T	0.2	.	13.8353	0.63406	0.1542:0.8458:0.0:0.0	.	1506	Q8N201	INT1_HUMAN	K	1506;1705	ENSP00000385722:E1506K;ENSP00000374121:E1705K	ENSP00000374121:E1705K	E	-	1	0	INTS1	1484642	1.000000	0.71417	0.142000	0.22268	0.000000	0.00434	7.407000	0.80029	0.875000	0.35847	-0.310000	0.09108	GAG	.	.		0.697	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			T	1518116	C	T	1518116	3	4	23	1	0	0	0	0	1	0	0	0	7784	893	31	1	2120	1	INTS1	7	1518116	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	899151	1518116	157620547	438	2504										
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4825084	4825084	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actccgacctgcagaaagctGtaagtggctggggaccaggg	15	10	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:4825084G>C	ENST00000348624.4	+	8	1063		c.e8+1		AP5Z1_ENST00000401897.1_Splice_Site	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit						cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											GCAGAAAGCTGTAAGTGGCTG	0.632																																					.		Atlas-SNP	.											.	.	.	.	0			c.969+1G>C						.						37	44	42					7																	4825084		2132	4234	6366	SO:0001630	splice_region_variant	9907	exon8			AAAGCTGTAAGTG	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"KIAA0415"	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.969+1G>C	chr7.hg19:g.4825084G>C		101.0	0.0		119.0	31.0	NM_014855	Q8N3X2|Q96H80	Splice_Site	SNP	ENST00000348624.4	hg19	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.001907	0.54254	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3295	0.90263	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIAA0415	4791610	1.000000	0.71417	0.160000	0.22671	0.483000	0.33249	8.164000	0.89661	2.573000	0.86826	0.561000	0.74099	.	.	.		0.632	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		Intron	C	4825084	G	C	4825084	5	2	23	1	0	0	0	0	0	0	1	0	8184	1391	48	4	1000	4	KIAA0415	7	4825084	Splice_Site	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3306968	4825084	154313579	439	2505										
AIMP2	7965	hgsc.bcm.edu	37	chr7	6054890	6054890	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccaagatgattcaaacaccAgatgcagacttggatgtaac	8	9	1	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:6054890A>C	ENST00000223029.3	+	2	368	c.249A>C	c.(247-249)ccA>ccC	p.P83P	AIMP2_ENST00000400479.2_Silent_p.P5P|SNORA42_ENST00000384488.1_RNA|AIMP2_ENST00000395236.2_Intron	NM_006303.3	NP_006294.2	Q13155	AIMP2_HUMAN	aminoacyl tRNA synthetase complex-interacting multifunctional protein 2	83	Interaction with PARK2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|tRNA aminoacylation for protein translation (GO:0006418)|Type II pneumocyte differentiation (GO:0060510)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						TTCAAACACCAGATGCAGACT	0.458																																					p.P83P		Atlas-SNP	.											.	AIMP2	32	.	0			c.A249C						.						146	137	140					7																	6054890		2203	4300	6503	SO:0001819	synonymous_variant	7965	exon2			AACACCAGATGCA	U24169	CCDS5344.1	7p22.1	2009-05-29			ENSG00000106305	ENSG00000106305			20609	protein-coding gene	gene with protein product		600859				8666379, 18695251	Standard	NM_006303		Approved	p38, PRO0992, JTV-1, JTV1	uc003spo.3	Q13155	OTTHUMG00000122077	ENST00000223029.3:c.249A>C	chr7.hg19:g.6054890A>C		183.0	0.0		219.0	68.0	NM_006303	Q75MR1|Q96CZ5|Q9P1L2	Silent	SNP	ENST00000223029.3	hg19	CCDS5344.1																																																																																			.	.		0.458	AIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242834.2	NM_006303		C	6054890	A	C	6054890	2	2	23	1	0	0	0	0	0	0	0	1	434	175	7	5		5	AIMP2	7	6054890	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1229806	6054890	153083773	440	2506										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7412846	7412846	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcagtgatgaccaaggccacTttttttacacctggccttgc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:7412846delT	ENST00000399429.3	-	32	2831	c.2691delA	c.(2689-2691)aaafs	p.K897fs		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	897	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCAAGGCCACTTTTTTTACAC	0.478																																					p.V898fs		Pindel	.											.	COL28A1	113	.	0			c.2692delG						.						92	86	88					7																	7412846		1968	4159	6127	SO:0001589	frameshift_variant	340267	exon32			.	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2691delA	chr7.hg19:g.7412846delT	ENSP00000382356:p.Lys897fs	104.0	0.0		127.0	11.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Frame_Shift_Del	DEL	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.478	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		-	7412846	T	-	7412846	7	5	23	1	0	1	0	1	0	0	0	0	3688	1606	56	0	702	0	COL28A1	7	7412846	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	1357956	7412846	151725817	441	2507										
AVL9	23080	hgsc.bcm.edu	37	chr7	32612909	32612909	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcagactacctagtgaggcaCgtgactgagaatcgggatga	14	8	0	5			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:32612909C>T	ENST00000318709.4	+	12	1670	c.1449C>T	c.(1447-1449)caC>caT	p.H483H	AVL9_ENST00000404479.1_Intron|AVL9_ENST00000409301.1_Silent_p.H483H	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	483					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TAGTGAGGCACGTGACTGAGA	0.547																																					p.H483H		Atlas-SNP	.											.	AVL9	66	.	0			c.C1449T						.						141	107	118					7																	32612909		2203	4300	6503	SO:0001819	synonymous_variant	23080	exon12			GAGGCACGTGACT	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"KIAA0241"	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1449C>T	chr7.hg19:g.32612909C>T		177.0	0.0		209.0	119.0	NM_015060	Q92573	Silent	SNP	ENST00000318709.4	hg19	CCDS34613.1																																																																																			.	.		0.547	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		T	32612909	C	T	32612909	2	4	23	1	0	0	0	0	0	0	0	1	1228	535	19	1		1	AVL9	7	32612909	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	25200063	32612909	126525754	442	2508										
SEPT7	989	hgsc.bcm.edu	37	chr7	35913370	35913370	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgttgtttatacttcattgCtccttcaggacatgggtcag	10	8	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:35913370C>A	ENST00000435235.1	+	5	770	c.338C>A	c.(337-339)gCt>gAt	p.A113D	SEPT7_ENST00000469679.2_Missense_Mutation_p.A165D|SEPT7_ENST00000350320.6_Missense_Mutation_p.A165D|SEPT7_ENST00000399034.2_Missense_Mutation_p.A167D|SEPT7_ENST00000475109.1_3'UTR|SEPT7_ENST00000399035.3_Missense_Mutation_p.A165D|SEPT7_ENST00000494488.2_Missense_Mutation_p.A152D			Q16181	SEPT7_HUMAN	septin 7	166	Septin-type G.				cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						TACTTCATTGCTCCTTCAGGA	0.373																																					p.A165D		Atlas-SNP	.											.	SEPT7	24	.	0			c.C494A						.						101	92	95					7																	35913370		1913	4129	6042	SO:0001583	missense	989	exon5			TCATTGCTCCTTC	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"Septins"	1717	protein-coding gene	gene with protein product		603151	"CDC10 cell division cycle 10 homolog (S. cerevisiae)"	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.338C>A	chr7.hg19:g.35913370C>A	ENSP00000413507:p.Ala113Asp	136.0	0.0		212.0	76.0	NM_001011553	Q52M76|Q6NX50	Missense_Mutation	SNP	ENST00000435235.1	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.235523	0.95240	.	.	ENSG00000122545	ENST00000435235;ENST00000399034;ENST00000350320;ENST00000469679;ENST00000399035;ENST00000537785;ENST00000493670;ENST00000494488	T;T;T;T;T;T	0.69175	-0.38;2.2;2.2;2.2;2.2;2.2	5.09	5.09	0.68999	.	0.000000	0.85682	U	0.000000	T	0.78285	0.4259	L	0.60455	1.87	0.80722	D	1	D;D;D	0.53151	0.958;0.958;0.958	P;P;P	0.60541	0.876;0.876;0.876	T	0.80151	-0.1502	10	0.72032	D	0.01	.	18.918	0.92513	0.0:1.0:0.0:0.0	.	111;165;166	B4DNE4;E7EPK1;Q16181	.;.;SEPT7_HUMAN	D	113;167;165;165;165;111;113;152	ENSP00000413507:A113D;ENSP00000381992:A167D;ENSP00000344868:A165D;ENSP00000444501:A165D;ENSP00000381993:A165D;ENSP00000438395:A152D	ENSP00000344868:A165D	A	+	2	0	SEPT7	35879895	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.815000	0.86186	2.557000	0.86248	0.644000	0.83932	GCT	.	.		0.373	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788		A	35913370	C	A	35913370	3	1	23	1	0	0	0	0	1	0	0	0	14084	797	28	3	513	3	SEPT7	7	35913370	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3300461	35913370	123225293	443	2509										
STK17A	9263	hgsc.bcm.edu	37	chr7	43664380	43664380	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aatggagcaaaaggccatttCcaaacgatttaaatttgagg	9	6	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:43664380C>T	ENST00000319357.5	+	7	1363	c.1184C>T	c.(1183-1185)tCc>tTc	p.S395F		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	395					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						AAGGCCATTTCCAAACGATTT	0.343																																					p.S395F		Atlas-SNP	.											.	STK17A	31	.	0			c.C1184T						.						64	66	65					7																	43664380		2203	4300	6503	SO:0001583	missense	9263	exon7			CCATTTCCAAACG	AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"death-associated protein kinase-related 1"	604726	"serine/threonine kinase 17a (apoptosis-inducing)"			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.1184C>T	chr7.hg19:g.43664380C>T	ENSP00000319192:p.Ser395Phe	163.0	0.0		118.0	40.0	NM_004760	A4D1V6|Q8IVC8	Missense_Mutation	SNP	ENST00000319357.5	hg19	CCDS5470.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.451697	0.84209	.	.	ENSG00000164543	ENST00000319357	T	0.68479	-0.33	4.95	4.95	0.65309	.	0.000000	0.47455	D	0.000235	T	0.66684	0.2814	L	0.34521	1.04	0.80722	D	1	D	0.54207	0.965	P	0.50537	0.643	T	0.69745	-0.5062	10	0.51188	T	0.08	.	18.1719	0.89747	0.0:1.0:0.0:0.0	.	395	Q9UEE5	ST17A_HUMAN	F	395	ENSP00000319192:S395F	ENSP00000319192:S395F	S	+	2	0	STK17A	43630905	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.175000	0.71949	2.264000	0.75181	0.563000	0.77884	TCC	.	.		0.343	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760		T	43664380	C	T	43664380	3	4	23	1	0	0	0	0	1	0	0	0	15305	855	30	3	1210	3	STK17A	7	43664380	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	7751010	43664380	115474283	444	2510										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44556938	44556938	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtttttcaggggcttgtgaTaggccatgaacctggaggct							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:44556938delT	ENST00000289547.4	-	16	3291	c.3236delA	c.(3235-3237)tatfs	p.Y1079fs	NPC1L1_ENST00000381160.3_Frame_Shift_Del_p.Y1052fs|NPC1L1_ENST00000546276.1_Frame_Shift_Del_p.Y1006fs	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1079					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	GGGCTTGTGATAGGCCATGAA	0.562																																					p.Y1079fs		Pindel	.											.	NPC1L1	141	.	0			c.3237delT						.						102	97	99					7																	44556938		2203	4300	6503	SO:0001589	frameshift_variant	29881	exon16			.		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3236delA	chr7.hg19:g.44556938delT	ENSP00000289547:p.Tyr1079fs	51.0	0.0		48.0	15.0	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Frame_Shift_Del	DEL	ENST00000289547.4	hg19	CCDS5491.1																																																																																			.	.		0.562	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		-	44556938	T	-	44556938	7	5	23	1	0	1	0	1	0	0	0	0	10580	1406	49	0	863	0	NPC1L1	7	44556938	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	892558	44556938	114581725	445	2511										
ADCY1	107	hgsc.bcm.edu	37	chr7	45743231	45743231	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagtcctactcccaggtgggCgtcatgtttgcctccatccc	9	16	1	0	rs138836914		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:45743231C>T	ENST00000297323.7	+	16	2626	c.2604C>T	c.(2602-2604)ggC>ggT	p.G868G		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	868					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CCCAGGTGGGCGTCATGTTTG	0.567																																					p.G868G		Atlas-SNP	.											.	ADCY1	187	.	0			c.C2604T						.	C		0,4406		0,0,2203	138	117	124		2604	-2.2	1	7	dbSNP_134	124	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADCY1	NM_021116.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		868/1120	45743231	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	107	exon16			GGTGGGCGTCATG	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.2604C>T	chr7.hg19:g.45743231C>T		165.0	0.0		148.0	47.0	NM_021116	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	hg19	CCDS34631.1																																																																																			.	C|1.000;T|0.000		0.567	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		T	45743231	C	T	45743231	2	4	23	1	0	0	0	0	0	0	0	1	292	755	27	1		1	ADCY1	7	45743231	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1186293	45743231	113395432	446	2512										
IKZF1	10320	hgsc.bcm.edu	37	chr7	50467747	50467747	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acctgggggccgagtccctgCgcccgctggtgcagacgccc	15	17	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:50467747C>T	ENST00000331340.3	+	8	1137	c.982C>T	c.(982-984)Cgc>Tgc	p.R328C	IKZF1_ENST00000346667.4_Missense_Mutation_p.R98C|IKZF1_ENST00000357364.4_Missense_Mutation_p.R241C|IKZF1_ENST00000343574.5_Missense_Mutation_p.R241C|IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000439701.1_Missense_Mutation_p.R286C|IKZF1_ENST00000438033.1_Missense_Mutation_p.R241C|IKZF1_ENST00000359197.5_Missense_Mutation_p.R286C|IKZF1_ENST00000349824.4_Missense_Mutation_p.R185C	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	328					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(28)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				CGAGTCCCTGCGCCCGCTGGT	0.657			"D,T"	BCL6	"ALL, DLBCL"																																p.R328C		Atlas-SNP	.		"Rec,Dom"	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	28	Unknown(28)	haematopoietic_and_lymphoid_tissue(28)	c.C982T						.						19	21	20					7																	50467747		2076	4234	6310	SO:0001583	missense	10320	exon8			TCCCTGCGCCCGC	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13176	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 92"	603023	"zinc finger protein, subfamily 1A, 1 (Ikaros)"	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.982C>T	chr7.hg19:g.50467747C>T	ENSP00000331614:p.Arg328Cys	124.0	0.0		140.0	55.0	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.256041	0.95336	.	.	ENSG00000185811	ENST00000346667;ENST00000343574;ENST00000359197;ENST00000349824;ENST00000357364;ENST00000331340;ENST00000438033;ENST00000439701	T;T;T;T;T;T;T;T	0.08634	4.38;3.07;3.12;3.9;3.29;3.14;3.07;3.12	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.31765	0.0807	.	.	.	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.997;0.997;0.998	T	0.01090	-1.1455	9	0.52906	T	0.07	-22.584	19.3925	0.94590	0.0:1.0:0.0:0.0	.	241;98;241;286;328	Q13422-2;Q13422-6;Q13422-3;Q13422-7;Q13422	.;.;.;.;IKZF1_HUMAN	C	98;241;286;185;241;328;241;286	ENSP00000340080:R98C;ENSP00000342750:R241C;ENSP00000352123:R286C;ENSP00000342485:R185C;ENSP00000349928:R241C;ENSP00000331614:R328C;ENSP00000396554:R241C;ENSP00000413025:R286C	ENSP00000331614:R328C	R	+	1	0	IKZF1	50435241	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.757000	0.85209	2.591000	0.87537	0.650000	0.86243	CGC	.	.		0.657	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060		T	50467747	C	T	50467747	3	4	23	1	0	0	0	0	1	0	0	0	7623	768	27	1	1008	1	IKZF1	7	50467747	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	4724516	50467747	108670916	447	2513										
COBL	23242	hgsc.bcm.edu	37	chr7	51095511	51095511	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctctggacaacaggtttgaaTtttttcttcggcccaaaaat							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:51095511delT	ENST00000265136.7	-	10	3447	c.3282delA	c.(3280-3282)aaafs	p.K1094fs	COBL_ENST00000395542.2_Frame_Shift_Del_p.K1176fs	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1094					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					CAGGTTTGAATTTTTTCTTCG	0.488																																					p.F1095fs	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-Indel,Pindel	.											.	COBL	167	.	0			c.3283delT						.						173	158	163					7																	51095511		2203	4300	6503	SO:0001589	frameshift_variant	23242	exon10			.	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3282delA	chr7.hg19:g.51095511delT	ENSP00000265136:p.Lys1094fs	197.0	0.0		155.0	50.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Frame_Shift_Del	DEL	ENST00000265136.7	hg19	CCDS34637.1																																																																																			.	.		0.488	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		-	51095511	T	-	51095511	7	5	23	1	0	1	0	1	0	0	0	0	3655	1490	52	0	519	0	COBL	7	51095511	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	627764	51095511	108043152	448	2514										
POM121L12	285877	hgsc.bcm.edu	37	chr7	53103947	53103947	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaagcgctaggttcgacgggCcgttgtggttcgaggtctca	16	9	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:53103947C>T	ENST00000408890.4	+	1	599	c.583C>T	c.(583-585)Ccg>Tcg	p.P195S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	195										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GTTCGACGGGCCGTTGTGGTT	0.682																																					p.P195S		Atlas-SNP	.											POM121L12,NS,carcinoma,-2,1	POM121L12	146	.	0			c.C583T						.						48	56	53					7																	53103947		1973	4142	6115	SO:0001583	missense	285877	exon1			GACGGGCCGTTGT		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.583C>T	chr7.hg19:g.53103947C>T	ENSP00000386133:p.Pro195Ser	72.0	0.0		63.0	23.0	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	hg19	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.251504	0.39797	.	.	ENSG00000221900	ENST00000408890	T	0.12984	2.63	2.21	2.21	0.28008	.	.	.	.	.	T	0.26122	0.0637	L	0.46157	1.445	0.09310	N	1	D	0.71674	0.998	D	0.74023	0.982	T	0.03166	-1.1065	9	0.62326	D	0.03	.	8.0049	0.30319	0.0:1.0:0.0:0.0	.	195	Q8N7R1	P1L12_HUMAN	S	195	ENSP00000386133:P195S	ENSP00000386133:P195S	P	+	1	0	POM121L12	53071441	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.522000	0.22909	1.561000	0.49584	0.561000	0.74099	CCG	.	.		0.682	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		T	53103947	C	T	53103947	3	4	23	1	0	0	0	0	1	0	0	0	12250	739	26	3	585	3	POM121L12	7	53103947	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2008436	53103947	106034716	449	2515										
GUSB	2990	hgsc.bcm.edu	37	chr7	65426023	65426023	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctgccgagtgaagatccccTttttattccccagcactctc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:65426023delT	ENST00000304895.4	-	12	1947	c.1817delA	c.(1816-1818)aagfs	p.K606fs	GUSB_ENST00000345660.6_Frame_Shift_Del_p.K555fs|GUSB_ENST00000421103.1_Frame_Shift_Del_p.K460fs	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	606			K -> N (in MPS7). {ECO:0000269|PubMed:8644704}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						GAAGATCCCCTTTTTATTCCC	0.453																																					p.K606fs		Atlas-Indel,Pindel	.											.	GUSB	52	.	0			c.1818delG						.						191	186	188					7																	65426023		2203	4300	6503	SO:0001589	frameshift_variant	2990	exon12			.	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1817delA	chr7.hg19:g.65426023delT	ENSP00000302728:p.Lys606fs	72.0	0.0		80.0	31.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Frame_Shift_Del	DEL	ENST00000304895.4	hg19	CCDS5530.1																																																																																			.	.		0.453	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		-	65426023	T	-	65426023	7	5	23	1	0	1	0	1	0	0	0	0	6911	1609	56	0	142	0	GUSB	7	65426023	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	12322076	65426023	93712640	450	2516										
GUSB	2990	hgsc.bcm.edu	37	chr7	65440028	65440028	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtgtagaagtcagacacagGccccagtgacgtctgtgcag	13	10	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:65440028G>T	ENST00000304895.4	-	6	1073	c.943C>A	c.(943-945)Cct>Act	p.P315T	GUSB_ENST00000345660.6_Intron|GUSB_ENST00000476486.1_5'UTR|GUSB_ENST00000421103.1_Missense_Mutation_p.P169T	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	315					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TCAGACACAGGCCCCAGTGAC	0.587																																					p.P315T		Atlas-SNP	.											.	GUSB	52	.	0			c.C943A						.						84	78	80					7																	65440028		2203	4300	6503	SO:0001583	missense	2990	exon6			ACACAGGCCCCAG	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.943C>A	chr7.hg19:g.65440028G>T	ENSP00000302728:p.Pro315Thr	117.0	0.0		82.0	8.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Missense_Mutation	SNP	ENST00000304895.4	hg19	CCDS5530.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.271784	0.23221	.	.	ENSG00000169919	ENST00000304895;ENST00000421103	D;D	0.94897	-1.91;-3.55	4.99	-4.7	0.03288	Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich (2);Glycoside hydrolase, family 2/20, immunoglobulin-like beta-sandwich domain (1);	0.584044	0.18926	N	0.127351	D	0.84781	0.5548	N	0.21448	0.665	0.09310	N	0.999998	B;B	0.10296	0.003;0.0	B;B	0.08055	0.001;0.003	T	0.72587	-0.4248	10	0.14656	T	0.56	.	8.6134	0.33817	0.5727:0.0:0.3183:0.109	.	169;315	E9PCV0;P08236	.;BGLR_HUMAN	T	315;169	ENSP00000302728:P315T;ENSP00000391390:P169T	ENSP00000302728:P315T	P	-	1	0	GUSB	65077463	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.667000	0.05274	-0.772000	0.04602	0.511000	0.50034	CCT	.	.		0.587	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		T	65440028	G	T	65440028	3	4	23	1	0	0	0	0	1	0	0	0	6911	1203	42	3	1040	3	GUSB	7	65440028	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	14005	65440028	93698635	451	2517										
AUTS2	26053	hgsc.bcm.edu	37	chr7	70254962	70254962	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggccacctgcccgagaaggaCgggcacggccacgaggggcg	18	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:70254962C>T	ENST00000342771.4	+	19	3081	c.2760C>T	c.(2758-2760)gaC>gaT	p.D920D	AUTS2_ENST00000406775.2_Silent_p.D896D	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	920										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CCGAGAAGGACGGGCACGGCC	0.697																																					p.D920D		Atlas-SNP	.											.	AUTS2	173	.	0			c.C2760T						.						21	22	22					7																	70254962		2197	4294	6491	SO:0001819	synonymous_variant	26053	exon19			GAAGGACGGGCAC	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.2760C>T	chr7.hg19:g.70254962C>T		108.0	0.0		89.0	36.0	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	hg19	CCDS5539.1																																																																																			.	.		0.697	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			T	70254962	C	T	70254962	2	4	23	1	0	0	0	0	0	0	0	1	1225	535	19	1		1	AUTS2	7	70254962	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	4814934	70254962	88883701	452	2518										
DTX2	113878	hgsc.bcm.edu	37	chr7	76131756	76131756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgctgtgcctcctggccatgTactgcaacggcaataaggtg	12	11	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:76131756T>C	ENST00000324432.5	+	9	1882	c.1372T>C	c.(1372-1374)Tac>Cac	p.Y458H	DTX2_ENST00000430490.2_Missense_Mutation_p.Y458H|DTX2_ENST00000307569.8_Missense_Mutation_p.Y411H|DTX2_ENST00000446820.2_Missense_Mutation_p.Y411H|DTX2_ENST00000413936.2_Missense_Mutation_p.Y458H|DTX2_ENST00000446600.1_Missense_Mutation_p.Y367H	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	458					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						CCTGGCCATGTACTGCAACGG	0.662																																					p.Y458H		Atlas-SNP	.											.	DTX2	64	.	0			c.T1372C						.						59	43	48					7																	76131756		2201	4297	6498	SO:0001583	missense	113878	exon8			GCCATGTACTGCA		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"RING-type (C3HC4) zinc fingers"	15973	protein-coding gene	gene with protein product		613141	"deltex (Drosophila) homolog 2", "deltex homolog 2 (Drosophila)"			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.1372T>C	chr7.hg19:g.76131756T>C	ENSP00000322885:p.Tyr458His	128.0	0.0		110.0	42.0	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Missense_Mutation	SNP	ENST00000324432.5	hg19	CCDS5587.1	.	.	.	.	.	.	.	.	.	.	.	24.4	4.526779	0.85706	.	.	ENSG00000091073	ENST00000324432;ENST00000307569;ENST00000541989;ENST00000446600;ENST00000413936;ENST00000430490;ENST00000446820	T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.48	5.48	0.80851	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.122676	0.56097	D	0.000024	D	0.82628	0.5078	M	0.83012	2.62	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.991	D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;0.998	D	0.84817	0.0794	10	0.56958	D	0.05	-34.3157	14.7255	0.69341	0.0:0.0:0.0:1.0	.	367;89;367;411;458	F5GX89;Q6P2H0;E7ET89;Q86UW9-2;Q86UW9	.;.;.;.;DTX2_HUMAN	H	458;411;367;367;458;458;411	ENSP00000322885:Y458H;ENSP00000305242:Y411H;ENSP00000397648:Y367H;ENSP00000390218:Y458H;ENSP00000411986:Y458H;ENSP00000392545:Y411H	ENSP00000305242:Y411H	Y	+	1	0	AC005522.1	75969692	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	7.958000	0.87877	2.081000	0.62600	0.533000	0.62120	TAC	.	.		0.662	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2			C	76131756	T	C	76131756	3	2	23	1	0	0	0	0	1	0	0	0	4796	1638	57	2	1394	2	DTX2	7	76131756	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	5876794	76131756	83006907	453	2519										
UPK3B	80761	hgsc.bcm.edu	37	chr7	76140138	76140139	+	Frame_Shift_Ins	INS	-	-	C													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gattggaccctgggcgcccgINScccccctccgattgggagag					rs139989637|rs201668989	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:76140138_76140139insC	ENST00000257632.5	+	1	297_298	c.169_170insC	c.(169-171)gccfs	p.A57fs	UPK3B_ENST00000419923.2_Frame_Shift_Ins_p.A57fs|UPK3B_ENST00000394849.1_Intron|UPK3B_ENST00000448265.3_Frame_Shift_Ins_p.A57fs|UPK3B_ENST00000443097.2_Intron|UPK3B_ENST00000334348.3_Intron			Q9BT76	UPK3B_HUMAN	uroplakin 3B	57					negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				CTGGGCGCCCGCCCCCCTCCGA	0.708																																					p.A57fs		Atlas-Indel,Pindel	.											.	UPK3B	15	.	0			c.169_170insC						.																																			SO:0001589	frameshift_variant	80761	exon1			.	BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566			21444	protein-coding gene	gene with protein product	"uroplakin IIIb"	611887				12446744	Standard	XM_005250612		Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000257632.5:c.175dupC	chr7.hg19:g.76140144_76140144dupC	ENSP00000257632:p.Ala57fs	169.0	0.0		182.0	63.0	NM_030570	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Frame_Shift_Ins	INS	ENST00000257632.5	hg19	CCDS5588.1																																																																																			.	.		0.708	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570		C	76140139	-	C	76140138	7	5	23	1	0	1	1	0	0	0	0	0	17026	1087	38	0	171	0	UPK3B	7	76140138	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	8382	76140138	82998525	454	2520										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81579773	81579773	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaactggattccaatgatatAccacagggagggatttaatc	9	7	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:81579773A>G	ENST00000356253.5	-	39	3502	c.3247T>C	c.(3247-3249)Tat>Cat	p.Y1083H	CACNA2D1_ENST00000535308.1_Missense_Mutation_p.Y283H|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.Y1071H			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	1083					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CCAATGATATACCACAGGGAG	0.368																																					p.Y1071H		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.T3211C						.						82	81	82					7																	81579773		2203	4300	6503	SO:0001583	missense	781	exon39			TGATATACCACAG	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.3247T>C	chr7.hg19:g.81579773A>G	ENSP00000348589:p.Tyr1083His	114.0	0.0		111.0	38.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	hg19		.	.	.	.	.	.	.	.	.	.	A	4.185	0.033043	0.08101	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000535308	T;T;T	0.30714	3.27;3.27;1.52	4.89	2.4	0.29515	.	0.124078	0.56097	D	0.000027	T	0.13841	0.0335	N	0.08118	0	0.23823	N	0.996745	B;B	0.17038	0.02;0.02	B;B	0.13407	0.005;0.009	T	0.28490	-1.0042	10	0.15952	T	0.53	-7.9207	10.2042	0.43103	0.7348:0.0:0.0:0.2652	.	283;1071	B7Z658;P54289-2	.;.	H	1071;1090;1083;283	ENSP00000349320:Y1071H;ENSP00000348589:Y1083H;ENSP00000443124:Y283H	ENSP00000284088:Y1090H	Y	-	1	0	CACNA2D1	81417709	1.000000	0.71417	0.524000	0.27887	0.405000	0.30901	5.100000	0.64560	0.259000	0.21709	0.528000	0.53228	TAT	.	.		0.368	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				G	81579773	A	G	81579773	3	3	23	1	0	0	0	0	1	0	0	0	2550	391	14	2	68	2	CACNA2D1	7	81579773	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	5439635	81579773	77558890	455	2521										
DMTF1	9988	hgsc.bcm.edu	37	chr7	86817443	86817444	+	Frame_Shift_Ins	INS	-	-	A													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	taaacagttacatgagaaccINSaaaaaaacaacccaacgctt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:86817443_86817444insA	ENST00000394703.5	+	15	1800_1801	c.1237_1238insA	c.(1237-1239)caafs	p.Q413fs	DMTF1_ENST00000432937.2_Frame_Shift_Ins_p.Q325fs|DMTF1_ENST00000331242.7_Frame_Shift_Ins_p.Q413fs|DMTF1_ENST00000413276.2_Intron|DMTF1_ENST00000414194.2_Frame_Shift_Ins_p.Q147fs	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	413	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					ACATGAGAACCAAAAAAACAAC	0.411																																					p.Q413fs		Atlas-Indel,Pindel	.											.	DMTF1	48	.	0			c.1237_1238insA						.																																			SO:0001589	frameshift_variant	9988	exon13			.	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.1244dupA	chr7.hg19:g.86817450_86817450dupA	ENSP00000378193:p.Gln413fs	158.0	0.0		168.0	60.0	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Frame_Shift_Ins	INS	ENST00000394703.5	hg19	CCDS5601.1																																																																																			.	.		0.411	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145		A	86817444	-	A	86817443	7	5	23	1	0	1	1	0	0	0	0	0	4594	595	21	0	1279	0	DMTF1	7	86817443	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	5237670	86817443	72321220	456	2522										
CCDC132	55610	hgsc.bcm.edu	37	chr7	92970851	92970851	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gacatctggggatacgctgtAtgggttggcagaaagagtgg	17	5	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:92970851A>G	ENST00000305866.5	+	23	2299	c.2171A>G	c.(2170-2172)tAt>tGt	p.Y724C	CCDC132_ENST00000474412.1_3'UTR|CCDC132_ENST00000535481.1_Missense_Mutation_p.Y444C|CCDC132_ENST00000541136.1_Missense_Mutation_p.Y535C|CCDC132_ENST00000544910.1_Missense_Mutation_p.Y694C	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	724						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			GATACGCTGTATGGGTTGGCA	0.438																																					p.Y724C		Atlas-SNP	.											.	CCDC132	136	.	0			c.A2171G						.						131	139	137					7																	92970851		1953	4158	6111	SO:0001583	missense	55610	exon23			CGCTGTATGGGTT	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.2171A>G	chr7.hg19:g.92970851A>G	ENSP00000307666:p.Tyr724Cys	132.0	0.0		143.0	7.0	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.829345	0.71258	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481	.	.	.	5.69	5.69	0.88448	Protein of unknown function DUF2451, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79936	0.4532	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.997;0.997	T	0.82335	-0.0508	9	0.72032	D	0.01	-13.3761	16.2703	0.82612	1.0:0.0:0.0:0.0	.	444;694;724	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	C	724;694;535;444	.	ENSP00000307666:Y724C	Y	+	2	0	CCDC132	92808787	1.000000	0.71417	0.999000	0.59377	0.397000	0.30659	9.270000	0.95690	2.311000	0.77944	0.533000	0.62120	TAT	.	.		0.438	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		G	92970851	A	G	92970851	3	3	23	1	0	0	0	0	1	0	0	0	2769	449	16	2	2303	2	CCDC132	7	92970851	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	6153408	92970851	66167812	457	2523										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94052290	94052290	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtatttctggccctcctggtCcccctggtcctgctgggaaa					rs145355907		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:94052290delC	ENST00000297268.6	+	40	2896	c.2425delC	c.(2425-2427)cccfs	p.P810fs		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	810			Missing (in OI2). {ECO:0000269|PubMed:1339453}.|Missing (in OI2). {ECO:0000269|PubMed:18996919}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CCCTCCTGGTCCCCCTGGTCC	0.532										HNSCC(75;0.22)																											p.G808fs		Atlas-INDEL	.											.	COL1A2	240	.	0			c.2424delT						.						161	159	159					7																	94052290		2203	4300	6503	SO:0001589	frameshift_variant	1278	exon40			.	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.2425delC	chr7.hg19:g.94052290delC	ENSP00000297268:p.Pro810fs	169.0	0.0		178.0	11.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Frame_Shift_Del	DEL	ENST00000297268.6	hg19	CCDS34682.1																																																																																			.	.		0.532	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		-	94052290	C	-	94052290	7	5	23	1	0	1	0	1	0	0	0	0	3680	855	30	0	2583	0	COL1A2	7	94052290	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	1081439	94052290	65086373	458	2524										
BAIAP2L1	55971	hgsc.bcm.edu	37	chr7	97946608	97946608	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatcttcttcaactcagcttGggatttctccaaagactcta	6	11	6	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:97946608G>T	ENST00000005260.8	-	6	624	c.409C>A	c.(409-411)Caa>Aaa	p.Q137K	BAIAP2L1_ENST00000462558.1_5'UTR	NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	137	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			AACTCAGCTTGGGATTTCTCC	0.378																																					p.Q137K		Atlas-SNP	.											.	BAIAP2L1	61	.	0			c.C409A						.						259	247	251					7																	97946608		2203	4300	6503	SO:0001583	missense	55971	exon6			CAGCTTGGGATTT	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.409C>A	chr7.hg19:g.97946608G>T	ENSP00000005260:p.Gln137Lys	137.0	0.0		84.0	26.0	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Missense_Mutation	SNP	ENST00000005260.8	hg19	CCDS34687.1	.	.	.	.	.	.	.	.	.	.	G	16.04	3.011341	0.54361	.	.	ENSG00000006453	ENST00000005260	T	0.23552	1.9	5.53	5.53	0.82687	IRSp53/MIM homology domain (IMD) (3);	0.108634	0.64402	D	0.000005	T	0.22859	0.0552	L	0.39467	1.215	0.49798	D	0.999825	B	0.14012	0.009	B	0.17098	0.017	T	0.05321	-1.0892	10	0.14656	T	0.56	-5.5035	16.6084	0.84837	0.0:0.0:1.0:0.0	.	137	Q9UHR4	BI2L1_HUMAN	K	137	ENSP00000005260:Q137K	ENSP00000005260:Q137K	Q	-	1	0	AC093799.1	97784544	1.000000	0.71417	0.942000	0.38095	0.933000	0.57130	7.479000	0.81095	2.597000	0.87782	0.603000	0.83216	CAA	.	.		0.378	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842		T	97946608	G	T	97946608	3	4	23	1	0	0	0	0	1	0	0	0	1302	1357	47	3	1162	3	BAIAP2L1	7	97946608	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3894318	97946608	61192055	459	2525										
TAF6	6878	hgsc.bcm.edu	37	chr7	99706132	99706132	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgattgtcaggcggtgggCgcagctttgccagaacagga	15	10	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:99706132C>T	ENST00000344095.4	-	13	1841	c.1316G>A	c.(1315-1317)cGc>cAc	p.R439H	TAF6_ENST00000437822.2_Missense_Mutation_p.R476H|TAF6_ENST00000452041.1_Missense_Mutation_p.R439H|TAF6_ENST00000453269.2_Missense_Mutation_p.R439H|TAF6_ENST00000418432.2_Missense_Mutation_p.R363H|TAF6_ENST00000472509.1_Missense_Mutation_p.R496H|AP4M1_ENST00000421755.1_Intron	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	439					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGGCGGTGGGCGCAGCTTTGC	0.607																																					p.R476H		Atlas-SNP	.											.	TAF6	55	.	0			c.G1427A						.						61	68	66					7																	99706132		2203	4300	6503	SO:0001583	missense	6878	exon13			GGTGGGCGCAGCT		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD", "transcription initiation factor TFIID 70 kD subunit"	602955	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.1316G>A	chr7.hg19:g.99706132C>T	ENSP00000344537:p.Arg439His	84.0	0.0		100.0	43.0	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	hg19	CCDS5686.1	.	.	.	.	.	.	.	.	.	.	C	18.72	3.683357	0.68157	.	.	ENSG00000106290	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822	T;T;T;T;T	0.59906	0.3;0.23;0.3;0.3;0.24	5.69	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.48277	0.1491	L	0.43757	1.38	0.53005	D	0.999967	P;D;P;P;P	0.53462	0.933;0.96;0.933;0.933;0.933	B;B;B;B;B	0.40982	0.187;0.345;0.187;0.187;0.187	T	0.47886	-0.9082	10	0.38643	T	0.18	-11.6419	12.2687	0.54693	0.0:0.9179:0.0:0.0821	.	476;439;429;439;363	B4DT11;P49848-2;A4D299;P49848;B3KUR4	.;.;.;TAF6_HUMAN;.	H	439;496;439;439;363;476	ENSP00000389575:R439H;ENSP00000419760:R496H;ENSP00000416396:R439H;ENSP00000344537:R439H;ENSP00000399982:R476H	ENSP00000344537:R439H	R	-	2	0	TAF6	99544068	0.999000	0.42202	0.984000	0.44739	0.901000	0.52897	4.026000	0.57232	1.413000	0.46997	0.491000	0.48974	CGC	.	.		0.607	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		T	99706132	C	T	99706132	3	4	23	1	0	0	0	0	1	0	0	0	15545	768	27	1	729	1	TAF6	7	99706132	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1759524	99706132	59432531	460	2526										
C7orf51	222950	hgsc.bcm.edu	37	chr7	100084550	100084550	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgcggcgctccctcaggatgGgtttcatgacgatgcccgcc	13	14	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:100084550G>T	ENST00000300179.2	+	3	334	c.175G>T	c.(175-177)Ggt>Tgt	p.G59C	NYAP1_ENST00000423930.1_Missense_Mutation_p.G59C|NYAP1_ENST00000454988.1_Missense_Mutation_p.G2C	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	59					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CCTCAGGATGGGTTTCATGAC	0.741																																					p.G59C		Atlas-SNP	.											.	.	.	.	0			c.G175T						.						9	10	10					7																	100084550		2162	4247	6409	SO:0001583	missense	222950	exon3			AGGATGGGTTTCA	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.175G>T	chr7.hg19:g.100084550G>T	ENSP00000300179:p.Gly59Cys	160.0	0.0		162.0	11.0	NM_173564	Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	hg19	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.843378	0.91197	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.52295	0.67;0.67;0.67	5.03	5.03	0.67393	.	0.000000	0.52532	D	0.000078	T	0.65481	0.2695	L	0.58810	1.83	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67891	-0.5553	10	0.87932	D	0	-16.4094	15.8881	0.79269	0.0:0.0:1.0:0.0	.	59	Q6ZVC0	CG051_HUMAN	C	59;59;2	ENSP00000300179:G59C;ENSP00000411861:G59C;ENSP00000394424:G2C	ENSP00000300179:G59C	G	+	1	0	C7orf51	99922486	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.591000	0.74090	2.606000	0.88127	0.462000	0.41574	GGT	.	.		0.741	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		T	100084550	G	T	100084550	3	4	23	1	0	0	0	0	1	0	0	0	2402	1232	43	3	181	3	C7orf51	7	100084550	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	378418	100084550	59054113	461	2527										
AGFG2	3268	hgsc.bcm.edu	37	chr7	100159952	100159952	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagccaaacagcctcgcagaCgtgggcagcttcctgggacc	12	15	0	1	rs550739522		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:100159952C>T	ENST00000300176.4	+	7	1070	c.948C>T	c.(946-948)gaC>gaT	p.D316D	AGFG2_ENST00000262935.4_3'UTR|AGFG2_ENST00000474713.1_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	316					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.D316D(2)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCCTCGCAGACGTGGGCAGCT	0.637													C|||	1	0.000199681	0	0	5008	,	,		17703	0		0.001	False		,,,				2504	0				p.D316D		Atlas-SNP	.											AGFG2,NS,carcinoma,0,2	AGFG2	44	.	2	Substitution - coding silent(2)	lung(2)	c.C948T						.						43	47	46					7																	100159952		2203	4300	6503	SO:0001819	synonymous_variant	3268	exon7			CGCAGACGTGGGC	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"ADP-ribosylation factor GTPase activating proteins"	5177	protein-coding gene	gene with protein product		604019	"HIV-1 Rev binding protein-like"	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.948C>T	chr7.hg19:g.100159952C>T		156.0	0.0		132.0	56.0	NM_006076	O75429|Q96AB9|Q96GL4	Silent	SNP	ENST00000300176.4	hg19	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	C	3.110	-0.182952	0.06340	.	.	ENSG00000106351	ENST00000429987	.	.	.	4.61	-3.03	0.05429	.	.	.	.	.	T	0.47783	0.1464	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39418	-0.9615	4	.	.	.	-23.1344	5.1848	0.15178	0.0:0.3746:0.1604:0.465	.	.	.	.	M	58	.	.	T	+	2	0	AGFG2	99997888	0.140000	0.22579	0.373000	0.26003	0.380000	0.30137	-0.905000	0.04075	-0.629000	0.05575	-0.477000	0.04895	ACG	.	.		0.637	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076		T	100159952	C	T	100159952	2	4	23	1	0	0	0	0	0	0	0	1	381	535	19	1		1	AGFG2	7	100159952	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	75402	100159952	58978711	462	2528										
TRIP6	7205	hgsc.bcm.edu	37	chr7	100465745	100465746	+	Frame_Shift_Ins	INS	-	-	G													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcaggggctccctgcagacaINSgggggggccttcgccctgga					rs201628297	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:100465745_100465746insG	ENST00000200457.4	+	3	613_614	c.253_254insG	c.(253-255)aggfs	p.R85fs		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	85					focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					CCCTGCAGACAGGGGGGGCCTT	0.639																																					p.R85fs		Atlas-Indel,Pindel	.											.	TRIP6	45	.	0			c.253_254insG						.																																			SO:0001589	frameshift_variant	7205	exon3			.	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.260dupG	chr7.hg19:g.100465752_100465752dupG	ENSP00000200457:p.Arg85fs	206.0	0.0		202.0	82.0	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Frame_Shift_Ins	INS	ENST00000200457.4	hg19	CCDS5708.1																																																																																			.	.		0.639	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302		G	100465746	-	G	100465745	7	5	23	1	0	1	1	0	0	0	0	0	16574	179	7	0	263	0	TRIP6	7	100465745	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	305793	100465745	58672918	463	2529										
MUC17	140453	hgsc.bcm.edu	37	chr7	100678585	100678585	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgaccagtcctgaggctagCacccttttaacaactcctgt	8	13	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:100678585C>T	ENST00000306151.4	+	3	3952	c.3888C>T	c.(3886-3888)agC>agT	p.S1296S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1296	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CTGAGGCTAGCACCCTTTTAA	0.478																																					p.S1296S		Atlas-SNP	.											.	MUC17	804	.	0			c.C3888T						.						263	250	254					7																	100678585		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			GGCTAGCACCCTT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3888C>T	chr7.hg19:g.100678585C>T		83.0	0.0		49.0	24.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100678585	C	T	100678585	2	4	23	1	0	0	0	0	0	0	0	1	9983	709	25	3		3	MUC17	7	100678585	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	212840	100678585	58460078	464	2530										
PLOD3	8985	hgsc.bcm.edu	37	chr7	100856126	100856126	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggcacccccacctcacctgCccccccgggagtgtcctccg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:100856126delC	ENST00000223127.3	-	8	1274	c.876delG	c.(874-876)gggfs	p.G292fs		NM_001084.4	NP_001075.1	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	292					basement membrane assembly (GO:0070831)|cellular protein modification process (GO:0006464)|cellular response to hormone stimulus (GO:0032870)|collagen fibril organization (GO:0030199)|endothelial cell morphogenesis (GO:0001886)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|lung morphogenesis (GO:0060425)|neural tube development (GO:0021915)|protein localization (GO:0008104)|vasodilation (GO:0042311)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen galactosyltransferase activity (GO:0050211)|procollagen glucosyltransferase activity (GO:0033823)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	31	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)	ACCTCACCTGCCCCCCCGGGA	0.672																																					p.Q293fs		Pindel	.											.	PLOD3	79	.	0			c.877delC						.						28	29	29					7																	100856126		2203	4299	6502	SO:0001589	frameshift_variant	8985	exon8			.	AF046889	CCDS5715.1	7q22.1	2011-08-24			ENSG00000106397	ENSG00000106397	1.14.11.4		9083	protein-coding gene	gene with protein product	"lysyl hydroxlase 3"	603066				9724729, 9582318	Standard	NM_001084		Approved	LH3	uc003uyd.3	O60568	OTTHUMG00000157111	ENST00000223127.3:c.876delG	chr7.hg19:g.100856126delC	ENSP00000223127:p.Gly292fs	52.0	0.0		52.0	11.0	NM_001084	B2R6W6|Q540C3	Frame_Shift_Del	DEL	ENST00000223127.3	hg19	CCDS5715.1																																																																																			.	.		0.672	PLOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347470.1			-	100856126	C	-	100856126	7	5	23	1	0	1	0	1	0	0	0	0	12112	726	26	0	1388	0	PLOD3	7	100856126	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	177541	100856126	58282537	465	2531										
DNAJC2	27000	hgsc.bcm.edu	37	chr7	102953447	102953447	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccaggcaccgcttctgctaTtttttcccatctttcaggtg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:102953447delT	ENST00000379263.3	-	16	1988	c.1738delA	c.(1738-1740)atafs	p.I580fs	DNAJC2_ENST00000249270.7_Frame_Shift_Del_p.I527fs|PMPCB_ENST00000249269.4_3'UTR|PMPCB_ENST00000420236.2_Intron	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	580	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)			endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						GCTTCTGCTATTTTTTCCCAT	0.398																																					p.I580fs		Atlas-Indel,Pindel	.											.	DNAJC2	46	.	0			c.1739delT						.						267	247	253					7																	102953447		1852	4090	5942	SO:0001589	frameshift_variant	27000	exon16			.	X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"Heat shock proteins / DNAJ (HSP40)"	13192	protein-coding gene	gene with protein product		605502	"zuotin related factor 1"	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.1738delA	chr7.hg19:g.102953447delT	ENSP00000368565:p.Ile580fs	131.0	0.0		133.0	24.0	NM_014377	A4VCI0|Q9BVX1	Frame_Shift_Del	DEL	ENST00000379263.3	hg19	CCDS43628.1																																																																																			.	.		0.398	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1			-	102953447	T	-	102953447	7	5	23	1	0	1	0	1	0	0	0	0	4641	1493	52	0	135	0	DNAJC2	7	102953447	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	2097321	102953447	56185216	466	2532										
SLC26A5	375611	hgsc.bcm.edu	37	chr7	103014890	103014890	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcattgggctccaagtcctCctgggaagggggagccgagg	18	10	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:103014890C>T	ENST00000306312.3	-	20	2452	c.2191G>A	c.(2191-2193)Gag>Aag	p.E731K	SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000339444.6_Intron|SLC26A5_ENST00000393723.1_Missense_Mutation_p.E701K|SLC26A5_ENST00000393730.1_Missense_Mutation_p.E699K|SLC26A5_ENST00000354356.4_Missense_Mutation_p.E164K|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000432958.2_Missense_Mutation_p.E699K|SLC26A5_ENST00000393727.1_Missense_Mutation_p.E733K|SLC26A5_ENST00000393729.1_Missense_Mutation_p.E694K	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	731					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						TCCAAGTCCTCCTGGGAAGGG	0.527																																					p.E731K		Atlas-SNP	.											SLC26A5,NS,malignant_melanoma,0,1	SLC26A5	231	.	0			c.G2191A						.						59	52	55					7																	103014890		2203	4300	6503	SO:0001583	missense	375611	exon20			AGTCCTCCTGGGA	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.2191G>A	chr7.hg19:g.103014890C>T	ENSP00000304783:p.Glu731Lys	116.0	0.0		89.0	39.0	NM_198999	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Missense_Mutation	SNP	ENST00000306312.3	hg19	CCDS5733.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.331971	0.60853	.	.	ENSG00000170615	ENST00000306312;ENST00000393730;ENST00000432958;ENST00000354356;ENST00000393729;ENST00000393727;ENST00000393723	D;D;D;D;D;D;D	0.96232	-3.2;-3.22;-3.22;-3.95;-3.13;-3.2;-3.22	5.69	5.69	0.88448	.	0.330752	0.29587	N	0.011738	D	0.89280	0.6670	N	0.08118	0	0.28654	N	0.906519	B;B	0.27559	0.181;0.155	B;B	0.21360	0.024;0.034	T	0.83186	-0.0086	10	0.72032	D	0.01	.	8.3886	0.32516	0.0:0.8347:0.0:0.1653	.	731;699	P58743;Q496J2	S26A5_HUMAN;.	K	731;699;699;164;694;733;701	ENSP00000304783:E731K;ENSP00000377331:E699K;ENSP00000389733:E699K;ENSP00000346325:E164K;ENSP00000377330:E694K;ENSP00000377328:E733K;ENSP00000377324:E701K	ENSP00000304783:E731K	E	-	1	0	SLC26A5	102802126	0.996000	0.38824	1.000000	0.80357	0.665000	0.39181	2.163000	0.42377	2.699000	0.92147	0.454000	0.30748	GAG	.	.		0.527	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		T	103014890	C	T	103014890	3	4	23	1	0	0	0	0	1	0	0	0	14535	864	30	3	88	3	SLC26A5	7	103014890	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	61443	103014890	56123773	467	2533										
DOCK4	9732	hgsc.bcm.edu	37	chr7	111584884	111584884	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	accgattcggataatgtgcaCggtgatataaatgtcctttc	9	8	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:111584884C>T	ENST00000437633.1	-	10	1082	c.826G>A	c.(826-828)Gtg>Atg	p.V276M	DOCK4_ENST00000428084.1_Missense_Mutation_p.V276M|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	276					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				ATAATGTGCACGGTGATATAA	0.418																																					p.V276M		Atlas-SNP	.											.	DOCK4	365	.	0			c.G826A						.						136	130	132					7																	111584884		1913	4119	6032	SO:0001583	missense	9732	exon10			TGTGCACGGTGAT		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.826G>A	chr7.hg19:g.111584884C>T	ENSP00000404179:p.Val276Met	89.0	0.0		118.0	49.0	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.715839	0.89112	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	T;T	0.03272	3.99;3.99	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.12305	0.0299	L	0.50333	1.59	0.80722	D	1	D;D;D	0.69078	0.994;0.997;0.997	P;P;P	0.56088	0.791;0.791;0.791	T	0.00064	-1.2152	10	0.72032	D	0.01	.	20.2406	0.98372	0.0:1.0:0.0:0.0	.	276;276;276	A4D0S8;Q149N5;Q8N1I0	.;.;DOCK4_HUMAN	M	264;276;276;264;275	ENSP00000410746:V276M;ENSP00000404179:V276M	ENSP00000345432:V264M	V	-	1	0	DOCK4	111372120	1.000000	0.71417	0.978000	0.43139	0.993000	0.82548	6.730000	0.74780	2.857000	0.98124	0.650000	0.86243	GTG	.	.		0.418	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		T	111584884	C	T	111584884	3	4	23	1	0	0	0	0	1	0	0	0	4691	536	19	1	5246	1	DOCK4	7	111584884	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	8569994	111584884	47553779	468	2534										
AASS	10157	hgsc.bcm.edu	37	chr7	121733126	121733126	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttccaattcttttagtgctGgtgtgatgtagcttgcagtg	11	6	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:121733126G>A	ENST00000393376.1	-	15	1837	c.1742C>T	c.(1741-1743)cCa>cTa	p.P581L	AASS_ENST00000417368.2_Missense_Mutation_p.P581L|AASS_ENST00000473553.1_5'UTR			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	581	Saccharopine dehydrogenase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TTTTAGTGCTGGTGTGATGTA	0.368																																					p.P581L		Atlas-SNP	.											.	AASS	123	.	0			c.C1742T						.						173	177	176					7																	121733126		2203	4300	6503	SO:0001583	missense	10157	exon16			AGTGCTGGTGTGA	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.1742C>T	chr7.hg19:g.121733126G>A	ENSP00000377040:p.Pro581Leu	191.0	0.0		162.0	58.0	NM_005763	O95462	Missense_Mutation	SNP	ENST00000393376.1	hg19	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.824335	0.90955	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	T;T	0.44482	0.92;0.92	6.07	6.07	0.98685	NAD(P)-binding domain (1);	0.046355	0.85682	D	0.000000	T	0.71953	0.3401	M	0.92459	3.31	0.80722	D	1	D	0.55605	0.972	P	0.59825	0.864	T	0.77230	-0.2664	10	0.66056	D	0.02	-14.8046	20.2544	0.98414	0.0:0.0:1.0:0.0	.	581	Q9UDR5	AASS_HUMAN	L	581	ENSP00000377040:P581L;ENSP00000403768:P581L	ENSP00000351834:P581L	P	-	2	0	AASS	121520362	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	9.159000	0.94728	2.885000	0.99019	0.655000	0.94253	CCA	.	.		0.368	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		A	121733126	G	A	121733126	3	1	23	1	0	0	0	0	1	0	0	0	24	1348	47	3	1074	3	AASS	7	121733126	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	10148242	121733126	37405537	469	2535										
STRA8	346673	hgsc.bcm.edu	37	chr7	134931258	134931258	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcgctgcccatcgtctccgCggccatctcccacctgtggc	11	19	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:134931258C>T	ENST00000275764.3	+	6	536	c.536C>T	c.(535-537)gCg>gTg	p.A179V		NM_182489.1	NP_872295.1			stimulated by retinoic acid 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(1)	16						ATCGTCTCCGCGGCCATCTCC	0.642																																					p.A179V		Atlas-SNP	.											.	STRA8	39	.	0			c.C536T						.						13	13	13					7																	134931258		2194	4279	6473	SO:0001583	missense	346673	exon6			TCTCCGCGGCCAT	AF513502	CCDS5839.1	7q33	2012-12-07	2012-12-07		ENSG00000146857	ENSG00000146857			30653	protein-coding gene	gene with protein product		609987	"stimulated by retinoic acid gene 8 homolog (mouse)", "stimulated by retinoic acid 8 homolog (mouse)"			12489526	Standard	NM_182489		Approved		uc011kpx.2	Q7Z7C7	OTTHUMG00000155415	ENST00000275764.3:c.536C>T	chr7.hg19:g.134931258C>T	ENSP00000275764:p.Ala179Val	114.0	0.0		114.0	39.0	NM_182489		Missense_Mutation	SNP	ENST00000275764.3	hg19	CCDS5839.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.079253	0.76528	.	.	ENSG00000146857	ENST00000275764	.	.	.	5.92	5.92	0.95590	.	0.250984	0.33772	N	0.004569	T	0.49795	0.1578	M	0.63428	1.95	0.20074	N	0.999936	D	0.65815	0.995	P	0.48795	0.59	T	0.52697	-0.8541	9	0.56958	D	0.05	-20.8075	15.0829	0.72127	0.1417:0.8583:0.0:0.0	.	179	Q7Z7C7	STRA8_HUMAN	V	179	.	ENSP00000275764:A179V	A	+	2	0	STRA8	134581798	0.616000	0.27035	0.613000	0.29037	0.711000	0.40976	2.012000	0.40932	2.809000	0.96659	0.655000	0.94253	GCG	.	.		0.642	STRA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340028.1	NM_182489		T	134931258	C	T	134931258	3	4	23	1	0	0	0	0	1	0	0	0	15338	768	27	1	558	1	STRA8	7	134931258	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	13198132	134931258	24207405	470	2536										
FAM131B	9715	hgsc.bcm.edu	37	chr7	143055964	143055964	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgccatcgctgaggtcggagTaggcatccgtatccctgcgc	13	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:143055964T>C	ENST00000409408.1	-	4	2046	c.338A>G	c.(337-339)tAc>tGc	p.Y113C	FAM131B_ENST00000409578.1_Missense_Mutation_p.Y129C|FAM131B_ENST00000409222.3_Missense_Mutation_p.Y113C|FAM131B_ENST00000443739.2_Missense_Mutation_p.Y141C|FAM131B_ENST00000409346.1_Missense_Mutation_p.Y113C			Q86XD5	F131B_HUMAN	family with sequence similarity 131, member B	113										breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24	Melanoma(164;0.205)					GAGGTCGGAGTAGGCATCCGT	0.597																																					p.Y141C		Atlas-SNP	.											.	FAM131B	104	.	0			c.A422G						.						98	85	89					7																	143055964		2203	4300	6503	SO:0001583	missense	9715	exon5			TCGGAGTAGGCAT	BC045611	CCDS5882.1, CCDS47734.1	7q34	2007-03-20			ENSG00000159784	ENSG00000159784			22202	protein-coding gene	gene with protein product							Standard	NM_014690		Approved	KIAA0773	uc010lpa.3	Q86XD5	OTTHUMG00000152697	ENST00000409408.1:c.338A>G	chr7.hg19:g.143055964T>C	ENSP00000387017:p.Tyr113Cys	90.0	0.0		68.0	12.0	NM_001031690	A4D2H6|A6NDW3|A8K605|B8ZZN2|D3DXE3|J3KQX2|Q7L0D6|Q86T97	Missense_Mutation	SNP	ENST00000409408.1	hg19	CCDS5882.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.495513	0.64186	.	.	ENSG00000159784	ENST00000443739;ENST00000409578;ENST00000409346;ENST00000452076;ENST00000409408;ENST00000409222	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.26	5.26	0.73747	.	0.115379	0.64402	D	0.000009	T	0.63331	0.2502	M	0.71206	2.165	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.98	T	0.67558	-0.5640	10	0.87932	D	0	-15.5113	13.7328	0.62799	0.0:0.0:0.0:1.0	.	129;113	Q86XD5-2;Q86XD5	.;F131B_HUMAN	C	141;129;113;117;113;113	ENSP00000410603:Y141C;ENSP00000386568:Y129C;ENSP00000386984:Y113C;ENSP00000387017:Y113C;ENSP00000387147:Y113C	ENSP00000387147:Y113C	Y	-	2	0	FAM131B	142766086	1.000000	0.71417	1.000000	0.80357	0.349000	0.29174	7.686000	0.84128	1.977000	0.57605	0.459000	0.35465	TAC	.	.		0.597	FAM131B-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328057.1	NM_014690		C	143055964	T	C	143055964	3	2	23	1	0	0	0	0	1	0	0	0	5445	1638	57	2	672	2	FAM131B	7	143055964	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	8124706	143055964	16082699	471	2537										
TAS2R41	259287	hgsc.bcm.edu	37	chr7	143175777	143175777	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttactggccatggcaaattgCagtctacctgtgcatatctg	9	10	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:143175777C>T	ENST00000408916.1	+	1	812	c.812C>T	c.(811-813)gCa>gTa	p.A271V	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	271					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					TGGCAAATTGCAGTCTACCTG	0.478																																					p.A271V		Atlas-SNP	.											.	TAS2R41	43	.	0			c.C812T						.						148	142	144					7																	143175777		2061	4205	6266	SO:0001583	missense	259287	exon1			AAATTGCAGTCTA	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.812C>T	chr7.hg19:g.143175777C>T	ENSP00000386201:p.Ala271Val	127.0	0.0		111.0	42.0	NM_176883	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Missense_Mutation	SNP	ENST00000408916.1	hg19	CCDS43663.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.049140	0.00394	.	.	ENSG00000221855	ENST00000408916	T	0.35973	1.28	6.0	2.42	0.29668	.	2.338580	0.03182	U	0.172136	T	0.18923	0.0454	N	0.05467	-0.045	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.22977	-1.0201	10	0.02654	T	1	.	8.2919	0.31963	0.0:0.2292:0.0:0.7708	.	271	P59536	T2R41_HUMAN	V	271	ENSP00000386201:A271V	ENSP00000386201:A271V	A	+	2	0	TAS2R41	142885899	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.187000	0.16998	0.180000	0.19960	-0.302000	0.09304	GCA	.	.		0.478	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1			T	143175777	C	T	143175777	3	4	23	1	0	0	0	0	1	0	0	0	15594	710	25	3	814	3	TAS2R41	7	143175777	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	119813	143175777	15962886	472	2538										
KCNH2	3757	hgsc.bcm.edu	37	chr7	150648807	150648807	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctagccagtgcgcgatgagCgcaaaggtgcacatgagcaa	14	10	0	2	rs554855472	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:150648807C>T	ENST00000262186.5	-	7	2075	c.1674G>A	c.(1672-1674)gcG>gcA	p.A558A	KCNH2_ENST00000392968.2_Silent_p.A462A|KCNH2_ENST00000330883.4_Silent_p.A218A|KCNH2_ENST00000430723.3_Silent_p.A558A	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	558			A -> P (in LQT2). {ECO:0000269|PubMed:10220144}.		cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GCGCGATGAGCGCAAAGGTGC	0.647													C|||	2	0.000399361	0	0	5008	,	,		16943	0		0	False		,,,				2504	0.002				p.A558A	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.G1674A						.						77	63	68					7																	150648807		2203	4300	6503	SO:0001819	synonymous_variant	3757	exon7			GATGAGCGCAAAG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1674G>A	chr7.hg19:g.150648807C>T		97.0	0.0		87.0	33.0	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	hg19	CCDS5910.1																																																																																			.	.		0.647	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		T	150648807	C	T	150648807	2	4	23	1	0	0	0	0	0	0	0	1	8041	755	27	1		1	KCNH2	7	150648807	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	7473030	150648807	8489856	473	2539										
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150772569	150772569	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtcaaggagcagcgggtgaCggggctgctggttgccctgc	18	10	1	1	rs370805035		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:150772569C>T	ENST00000485713.1	+	20	4315	c.3275C>T	c.(3274-3276)aCg>aTg	p.T1092M	SLC4A2_ENST00000310317.5_Missense_Mutation_p.T1010M|SLC4A2_ENST00000413384.2_Missense_Mutation_p.T1092M|RP11-148K1.12_ENST00000485974.1_RNA|SLC4A2_ENST00000461735.1_Missense_Mutation_p.T1078M|SLC4A2_ENST00000392826.2_Missense_Mutation_p.T1083M|FASTK_ENST00000489884.1_5'Flank	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	1092	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGCGGGTGACGGGGCTGCTG	0.637																																					p.T1092M		Atlas-SNP	.											SLC4A2,NS,carcinoma,0,1	SLC4A2	98	.	0			c.C3275T						.	C	MET/THR,MET/THR,MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	136	145	142		3275,3248,3233,3275	5.1	1	7		142	0,8600		0,0,4300	no	missense,missense,missense,missense	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	81,81,81,81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1092/1242,1083/1233,1078/1228,1092/1242	150772569	1,13005	2203	4300	6503	SO:0001583	missense	6522	exon20			GGGTGACGGGGCT		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"Solute carriers"	11028	protein-coding gene	gene with protein product	"anion exchanger 2 type a", "anion exchanger 2 type b1", "anion exchanger 2 type b2"	109280	"erythrocyte membrane protein band 3-like 1", "solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.3275C>T	chr7.hg19:g.150772569C>T	ENSP00000419412:p.Thr1092Met	20.0	0.0		10.0	6.0	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	hg19	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.297317	0.81025	2.27E-4	0.0	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6	5.07	5.07	0.68467	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93684	0.7982	H	0.94306	3.52	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.993;0.993;0.996	D	0.95169	0.8288	10	0.87932	D	0	.	17.6106	0.88051	0.0:1.0:0.0:0.0	.	1083;1078;1092	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	M	1092;1092;1010;1083;1078	ENSP00000419412:T1092M;ENSP00000405600:T1092M;ENSP00000311402:T1010M;ENSP00000376571:T1083M;ENSP00000419164:T1078M	ENSP00000311402:T1010M	T	+	2	0	SLC4A2	150403502	1.000000	0.71417	0.958000	0.39756	0.958000	0.62258	5.934000	0.70138	2.639000	0.89480	0.561000	0.74099	ACG	.	.		0.637	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		T	150772569	C	T	150772569	3	4	23	1	0	0	0	0	1	0	0	0	14669	536	19	1	3349	1	SLC4A2	7	150772569	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	123762	150772569	8366094	474	2540										
FASTK	10922	hgsc.bcm.edu	37	chr7	150776623	150776623	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgcagacacacgtggatggTgtgaatgtcaaaggaggggc	17	6	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:150776623T>C	ENST00000297532.6	-	2	546	c.469A>G	c.(469-471)Acc>Gcc	p.T157A	FASTK_ENST00000353841.2_Intron|FASTK_ENST00000540185.1_Missense_Mutation_p.T123A|FASTK_ENST00000482571.1_Missense_Mutation_p.T157A|FASTK_ENST00000489884.1_Intron	NM_006712.4	NP_006703.1	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase	157					apoptotic signaling pathway (GO:0097190)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|Fas-activated serine/threonine kinase activity (GO:0033867)|protein serine/threonine kinase activity (GO:0004674)			lung(4)|stomach(2)	6			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)		ACGTGGATGGTGTGAATGTCA	0.577																																					p.T157A		Atlas-SNP	.											.	FASTK	29	.	0			c.A469G						.						63	59	60					7																	150776623		2202	4300	6502	SO:0001583	missense	10922	exon2			GGATGGTGTGAAT		CCDS5918.1, CCDS5919.1, CCDS59088.1	7q35	2006-07-06			ENSG00000164896	ENSG00000164896			24676	protein-coding gene	gene with protein product		606965				7544399, 15572676	Standard	NM_006712		Approved	FAST	uc003wix.2	Q14296	OTTHUMG00000158694	ENST00000297532.6:c.469A>G	chr7.hg19:g.150776623T>C	ENSP00000297532:p.Thr157Ala	259.0	1.0		246.0	98.0	NM_006712	A8K867|F8VTW9|Q59EM8|Q8IVA0	Missense_Mutation	SNP	ENST00000297532.6	hg19	CCDS5918.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.198786	0.58126	.	.	ENSG00000164896	ENST00000483105;ENST00000297530;ENST00000297532;ENST00000482571;ENST00000540185	T;T;T	0.45276	0.9;0.9;0.9	4.61	4.61	0.57282	.	0.268618	0.24779	N	0.035674	T	0.47451	0.1446	N	0.24115	0.695	0.41923	D	0.990523	D;P;P	0.67145	0.996;0.954;0.787	D;B;B	0.76071	0.987;0.446;0.219	T	0.40136	-0.9579	10	0.33141	T	0.24	-24.2934	12.1032	0.53796	0.0:0.0:0.0:1.0	.	123;157;157	G3V1R6;F8VTW9;Q14296	.;.;FASTK_HUMAN	A	157;157;157;157;123	ENSP00000297532:T157A;ENSP00000418516:T157A;ENSP00000444498:T123A	ENSP00000297530:T157A	T	-	1	0	FASTK	150407556	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.294000	0.65687	2.012000	0.59069	0.533000	0.62120	ACC	.	.		0.577	FASTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351832.2	NM_006712		C	150776623	T	C	150776623	3	2	23	1	0	0	0	0	1	0	0	0	5692	1696	59	2	1216	2	FASTK	7	150776623	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	4054	150776623	8362040	475	2541										
SMARCD3	6604	hgsc.bcm.edu	37	chr7	150938679	150938679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcctggacaatggctgagcGgctctgtgtgtgcagcccca	15	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:150938679G>A	ENST00000262188.8	-	8	1248	c.838C>T	c.(838-840)Cgc>Tgc	p.R280C	RP4-548D19.3_ENST00000607902.1_RNA|SMARCD3_ENST00000392811.2_Missense_Mutation_p.R267C|SMARCD3_ENST00000356800.2_Missense_Mutation_p.R267C|SMARCD3_ENST00000477169.1_5'Flank	NM_001003801.1	NP_001003801.1	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	280	SWIB.				cardiac right ventricle formation (GO:0003219)|cellular lipid metabolic process (GO:0044255)|chromatin remodeling (GO:0006338)|muscle cell differentiation (GO:0042692)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein binding (GO:0043393)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|secondary heart field specification (GO:0003139)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|receptor binding (GO:0005102)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATGGCTGAGCGGCTCTGTGTG	0.562																																					p.R280C		Atlas-SNP	.											.	SMARCD3	92	.	0			c.C838T						.						35	32	33					7																	150938679		2203	4300	6503	SO:0001583	missense	6604	exon8			CTGAGCGGCTCTG	U66619	CCDS5924.1, CCDS34780.1	7q35-q36	2008-07-18			ENSG00000082014	ENSG00000082014			11108	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60C", "Swp73-like protein", "SWI/SNF complex 60 kDa subunit C", "60kDa BRG-1/Brm associated factor subunit c"	601737				8804307, 9693044	Standard	NM_001003801		Approved	BAF60C, Rsc6p, CRACD3	uc003wjs.3	Q6STE5	OTTHUMG00000157431	ENST00000262188.8:c.838C>T	chr7.hg19:g.150938679G>A	ENSP00000262188:p.Arg280Cys	68.0	0.0		69.0	33.0	NM_001003801	D3DX10|Q2YD86|Q75MJ2|Q75MR8|Q92926|Q9BUH1	Missense_Mutation	SNP	ENST00000262188.8	hg19	CCDS34780.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.374349	0.82573	.	.	ENSG00000082014	ENST00000262188;ENST00000392811;ENST00000356800;ENST00000347683	T;T;T	0.56103	0.48;0.49;0.49	5.48	4.57	0.56435	SWIB domain (1);SWIB/MDM2 domain (2);	0.000000	0.85682	D	0.000000	T	0.76248	0.3961	M	0.90145	3.09	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.941	D;D;P	0.87578	0.998;0.992;0.584	T	0.81256	-0.1015	10	0.87932	D	0	-12.7736	13.5304	0.61619	0.0:0.0:0.8444:0.1556	.	280;267;280	B7Z4U8;Q6STE5-2;Q6STE5	.;.;SMRD3_HUMAN	C	280;267;267;232	ENSP00000262188:R280C;ENSP00000376558:R267C;ENSP00000349254:R267C	ENSP00000262188:R280C	R	-	1	0	SMARCD3	150569612	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.001000	0.88508	2.572000	0.86782	0.655000	0.94253	CGC	.	.		0.562	SMARCD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348825.1	NM_001003801		A	150938679	G	A	150938679	3	1	23	1	0	0	0	0	1	0	0	0	14794	1116	39	1	637	1	SMARCD3	7	150938679	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	162056	150938679	8199984	476	2542										
RHEB	6009	hgsc.bcm.edu	37	chr7	151188049	151188049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgttttctatggttggatcgTaggagtccacaaattggcct	11	7	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:151188049T>C	ENST00000262187.5	-	2	516	c.104A>G	c.(103-105)tAc>tGc	p.Y35C	RHEB_ENST00000472642.1_5'UTR|RHEB_ENST00000496004.1_5'UTR	NM_005614.3	NP_005605.1	Q15382	RHEB_HUMAN	Ras homolog enriched in brain	35					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|positive regulation of TOR signaling (GO:0032008)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)	14			OV - Ovarian serous cystadenocarcinoma(82;0.00306)	UCEC - Uterine corpus endometrioid carcinoma (81;0.174)		GGTTGGATCGTAGGAGTCCAC	0.358																																					p.Y35C	Pancreas(98;671 892 8111 15140 36556 39178 39939 44184)	Atlas-SNP	.											.	RHEB	30	.	0			c.A104G						.						103	100	101					7																	151188049		2203	4300	6503	SO:0001583	missense	6009	exon2			GGATCGTAGGAGT	D78132	CCDS5927.1	7q36	2014-05-09	2003-07-14	2003-07-14	ENSG00000106615	ENSG00000106615			10011	protein-coding gene	gene with protein product		601293	"Ras homolog enriched in brain 2"	RHEB2		8661031	Standard	NM_005614		Approved		uc003wkh.1	Q15382	OTTHUMG00000157330	ENST00000262187.5:c.104A>G	chr7.hg19:g.151188049T>C	ENSP00000262187:p.Tyr35Cys	106.0	0.0		99.0	5.0	NM_005614	B3KWN6|D3DX13|Q53Y56|Q99444	Missense_Mutation	SNP	ENST00000262187.5	hg19	CCDS5927.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.379908	0.82682	.	.	ENSG00000106615	ENST00000262187	D	0.81659	-1.52	5.42	5.42	0.78866	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90700	0.7082	M	0.88512	2.96	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92314	0.5860	10	0.87932	D	0	.	13.3975	0.60863	0.0:0.0:0.0:1.0	.	35	Q15382	RHEB_HUMAN	C	35	ENSP00000262187:Y35C	ENSP00000262187:Y35C	Y	-	2	0	RHEB	150818982	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.016000	0.76393	2.051000	0.60960	0.533000	0.62120	TAC	.	.		0.358	RHEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348468.2	NM_005614		C	151188049	T	C	151188049	3	2	23	1	0	0	0	0	1	0	0	0	13343	1638	57	2	478	2	RHEB	7	151188049	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	249370	151188049	7950614	477	2543										
LMBR1	64327	hgsc.bcm.edu	37	chr7	156521354	156521354	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttactgtctcaataagaaggAgaaccataacagcgggatac	9	8	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:156521354A>C	ENST00000353442.5	-	11	1135	c.899T>G	c.(898-900)cTc>cGc	p.L300R	LMBR1_ENST00000354505.4_Missense_Mutation_p.L341R|LMBR1_ENST00000359422.4_Missense_Mutation_p.L148R|LMBR1_ENST00000540390.1_Missense_Mutation_p.L279R	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	300					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		AATAAGAAGGAGAACCATAAC	0.333																																					p.L300R		Atlas-SNP	.											.	LMBR1	35	.	0			c.T899G						.						98	102	101					7																	156521354		2203	4299	6502	SO:0001583	missense	64327	exon11			AGAAGGAGAACCA	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"chromosome 7 open reading frame 2", "limb region 1 homolog (mouse)"	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.899T>G	chr7.hg19:g.156521354A>C	ENSP00000326604:p.Leu300Arg	314.0	0.0		280.0	93.0	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Missense_Mutation	SNP	ENST00000353442.5	hg19	CCDS5945.1	.	.	.	.	.	.	.	.	.	.	A	15.61	2.885158	0.51908	.	.	ENSG00000105983	ENST00000353442;ENST00000359422;ENST00000415428;ENST00000354505;ENST00000540390	T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41	4.83	4.83	0.62350	LMBR1-like membrane protein (1);	0.061993	0.64402	D	0.000004	T	0.50514	0.1620	L	0.60455	1.87	0.58432	D	0.999995	D;D;D	0.71674	0.986;0.998;0.979	P;D;P	0.70935	0.899;0.971;0.837	T	0.53641	-0.8410	10	0.72032	D	0.01	-10.086	14.0874	0.64968	1.0:0.0:0.0:0.0	.	279;341;300	B7Z633;Q8WVP7-3;Q8WVP7	.;.;LMBR1_HUMAN	R	300;148;339;341;279	ENSP00000326604:L300R;ENSP00000352392:L148R;ENSP00000408256:L339R;ENSP00000346500:L341R;ENSP00000445509:L279R	ENSP00000326604:L300R	L	-	2	0	LMBR1	156214115	1.000000	0.71417	0.969000	0.41365	0.335000	0.28730	7.780000	0.85658	1.806000	0.52798	0.533000	0.62120	CTC	.	.		0.333	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458		C	156521354	A	C	156521354	3	2	23	1	0	0	0	0	1	0	0	0	8849	304	11	5	601	5	LMBR1	7	156521354	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	5333305	156521354	2617309	478	2544										
FBXO25	26260	hgsc.bcm.edu	37	chr8	363195	363195	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgaaagagagaataaccgttGtaacatcagtcacagcatgt	9	7	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:363195G>A	ENST00000276326.5	+	2	235	c.116G>A	c.(115-117)tGt>tAt	p.C39Y	FBXO25_ENST00000350302.3_Missense_Mutation_p.C39Y|FBXO25_ENST00000352684.2_5'UTR|FBXO25_ENST00000382824.1_5'UTR	NM_183421.1	NP_904357.1	Q8TCJ0	FBX25_HUMAN	F-box protein 25	39	Interaction with beta-actin.				protein ubiquitination (GO:0016567)	nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		AATAACCGTTGTAACATCAGT	0.433																																					p.C39Y		Atlas-SNP	.											.	FBXO25	25	.	0			c.G116A						.						95	139	124					8																	363195		2203	4300	6503	SO:0001583	missense	26260	exon2			ACCGTTGTAACAT	AF174605	CCDS5952.1, CCDS5953.1, CCDS5954.1	8p23.3	2007-03-30	2004-06-15		ENSG00000147364	ENSG00000147364		"F-boxes /  "other""	13596	protein-coding gene	gene with protein product		609098	"F-box only protein 25"			10531035, 10531037	Standard	NM_012173		Approved	FBX25	uc003wox.3	Q8TCJ0	OTTHUMG00000090341	ENST00000276326.5:c.116G>A	chr8.hg19:g.363195G>A	ENSP00000276326:p.Cys39Tyr	179.0	0.0		175.0	52.0	NM_183420	Q6PJ83|Q7Z4V4|Q9UKB8	Missense_Mutation	SNP	ENST00000276326.5	hg19	CCDS5953.1	.	.	.	.	.	.	.	.	.	.	.	0.426	-0.905601	0.02453	.	.	ENSG00000147364	ENST00000518240;ENST00000350302;ENST00000276326;ENST00000447233	T;T;T	0.17854	2.25;2.25;2.25	3.45	1.57	0.23409	.	1.416530	0.04389	N	0.362038	T	0.19886	0.0478	M	0.80183	2.485	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.48636	-0.9018	10	0.02654	T	1	-13.5167	5.8083	0.18452	0.274:0.0:0.726:0.0	.	39;39	Q8TCJ0-2;Q8TCJ0	.;FBX25_HUMAN	Y	39	ENSP00000428872:C39Y;ENSP00000342077:C39Y;ENSP00000276326:C39Y	ENSP00000276326:C39Y	C	+	2	0	FBXO25	353195	0.000000	0.05858	0.000000	0.03702	0.943000	0.58893	0.506000	0.22658	0.113000	0.18004	0.298000	0.19748	TGT	.	.		0.433	FBXO25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206710.2	NM_012173		A	363195	G	A	363195	3	1	23	1	0	0	0	0	1	0	0	0	5744	1377	48	3	118	3	FBXO25	8	363195	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10		363195	146000827	479	2545										
CLN8	2055	hgsc.bcm.edu	37	chr8	1719730	1719730	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgctcctggagatgagcacGccctttacctgcgtttcctg	10	13	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:1719730G>A	ENST00000331222.4	+	2	757	c.510G>A	c.(508-510)acG>acA	p.T170T		NM_018941.3	NP_061764.2	Q9UBY8	CLN8_HUMAN	ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation)	170	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.		T -> M (in CLN8; associated with M-16 on the same allele; dbSNP:rs188259026). {ECO:0000269|PubMed:15024724}.		adult walking behavior (GO:0007628)|age-dependent response to oxidative stress (GO:0001306)|associative learning (GO:0008306)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|ceramide biosynthetic process (GO:0046513)|ceramide metabolic process (GO:0006672)|cholesterol metabolic process (GO:0008203)|L-glutamate uptake involved in synaptic transmission (GO:0051935)|lipid biosynthetic process (GO:0008610)|lipid transport (GO:0006869)|lysosome organization (GO:0007040)|mitochondrial membrane organization (GO:0007006)|musculoskeletal movement (GO:0050881)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteolysis (GO:0045861)|negative regulation of transferase activity (GO:0051348)|nervous system development (GO:0007399)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|phospholipid metabolic process (GO:0006644)|photoreceptor cell maintenance (GO:0045494)|protein catabolic process (GO:0030163)|regulation of cell size (GO:0008361)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic motor neuron differentiation (GO:0021523)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)		AGATGAGCACGCCCTTTACCT	0.493																																					p.T170T	Pancreas(155;338 1942 6138 10888 50612)	Atlas-SNP	.											.	CLN8	64	.	0			c.G510A						.						74	71	72					8																	1719730		2203	4300	6503	SO:0001819	synonymous_variant	2055	exon2			GAGCACGCCCTTT	AF123761	CCDS5956.1	8p23.3	2014-09-17			ENSG00000182372	ENSG00000182372			2079	protein-coding gene	gene with protein product		607837	"chromosome 8 open reading frame 61"	EPMR, C8orf61		10508524	Standard	NM_018941		Approved	FLJ39417	uc003wpo.4	Q9UBY8	OTTHUMG00000090343	ENST00000331222.4:c.510G>A	chr8.hg19:g.1719730G>A		61.0	0.0		47.0	6.0	NM_018941	Q86U71|Q96I95	Silent	SNP	ENST00000331222.4	hg19	CCDS5956.1																																																																																			.	.		0.493	CLN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206715.2	NM_018941		A	1719730	G	A	1719730	2	1	23	1	0	0	0	0	0	0	0	1	3548	1074	38	1		1	CLN8	8	1719730	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1356535	1719730	144644292	480	2546										
ARHGEF10	9639	hgsc.bcm.edu	37	chr8	1842674	1842674	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccactcgctatttcagatcgCgctggccagccgcgtttccg	10	16	1	1	rs144726787		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:1842674C>T	ENST00000398564.1	+	13	1451	c.1451C>T	c.(1450-1452)gCg>gTg	p.A484V	ARHGEF10_ENST00000518288.1_Missense_Mutation_p.A484V|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.A459V|ARHGEF10_ENST00000520359.1_Missense_Mutation_p.A421V|ARHGEF10_ENST00000398560.1_Missense_Mutation_p.A445V|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.A484V			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	484	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		TTTCAGATCGCGCTGGCCAGC	0.547																																					p.A459V		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.C1376T						.	C	VAL/ALA	0,4406		0,0,2203	83	74	77		1376	5.2	0.9	8	dbSNP_134	77	1,8599	1.2+/-3.3	0,1,4299	no	missense	ARHGEF10	NM_014629.2	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	459/1345	1842674	1,13005	2203	4300	6503	SO:0001583	missense	9639	exon13			AGATCGCGCTGGC	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"Rho guanine nucleotide exchange factors"	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.1451C>T	chr8.hg19:g.1842674C>T	ENSP00000381571:p.Ala484Val	116.0	0.0		119.0	29.0	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	hg19		.	.	.	.	.	.	.	.	.	.	C	32	5.122600	0.94429	0.0	1.16E-4	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398560;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.23	5.23	0.72850	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.82157	0.4976	M	0.84683	2.71	0.80722	D	1	D;D;D;D	0.89917	1.0;0.994;1.0;1.0	D;D;D;D	0.91635	0.999;0.911;0.999;0.998	D	0.85289	0.1066	10	0.87932	D	0	-44.9466	18.7871	0.91960	0.0:1.0:0.0:0.0	.	484;445;421;459	O15013;E9PB39;O15013-7;O15013-5	ARHGA_HUMAN;.;.;.	V	459;421;484;445;484;484;132	ENSP00000340297:A459V;ENSP00000427909:A421V;ENSP00000431012:A484V;ENSP00000381568:A445V;ENSP00000381571:A484V;ENSP00000262112:A484V;ENSP00000427768:A132V	ENSP00000262112:A484V	A	+	2	0	ARHGEF10	1830081	1.000000	0.71417	0.873000	0.34254	0.661000	0.39034	7.073000	0.76784	2.418000	0.82041	0.655000	0.94253	GCG	.	C|1.000;T|0.000		0.547	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding				T	1842674	C	T	1842674	3	4	23	1	0	0	0	0	1	0	0	0	894	768	27	1	1422	1	ARHGEF10	8	1842674	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	122944	1842674	144521348	481	2547										
AGPAT5	55326	hgsc.bcm.edu	37	chr8	6590108	6590108	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaatctatgtaaagcgcagTgccaaatttaacgagaaaga	10	6	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:6590108T>C	ENST00000285518.6	+	4	744	c.432T>C	c.(430-432)agT>agC	p.S144S		NM_018361.3	NP_060831.2	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	144					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		AGPAT5/MCPH1(2)	endometrium(2)|kidney(2)|large_intestine(4)|lung(3)	11			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		TAAAGCGCAGTGCCAAATTTA	0.423																																					p.S144S		Atlas-SNP	.											.	AGPAT5	31	.	0			c.T432C						.						69	66	67					8																	6590108		2203	4300	6503	SO:0001819	synonymous_variant	55326	exon4			GCGCAGTGCCAAA	AF375789	CCDS34796.1	8p23.1	2013-02-05	2013-02-05		ENSG00000155189	ENSG00000155189	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20886	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, epsilon"	614796	"1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"				Standard	NM_018361		Approved	FLJ11210, LPAAT-e, LPAAT-epsilon	uc003wqo.3	Q9NUQ2	OTTHUMG00000163656	ENST00000285518.6:c.432T>C	chr8.hg19:g.6590108T>C		539.0	0.0		569.0	37.0	NM_018361	Q8IZ47|Q9BQG4	Silent	SNP	ENST00000285518.6	hg19	CCDS34796.1																																																																																			.	.		0.423	AGPAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374684.1	NM_018361		C	6590108	T	C	6590108	2	2	23	1	0	0	0	0	0	0	0	1	390	1693	59	2		2	AGPAT5	8	6590108	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	4747434	6590108	139773914	482	2548										
C8orf79	57604	hgsc.bcm.edu	37	chr8	12879351	12879351	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agttgattccacagatttcaAcccagatgatacaatgtctg	7	9	2	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:12879351A>G	ENST00000524591.2	+	5	1652	c.1163A>G	c.(1162-1164)aAc>aGc	p.N388S	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	388							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						ACAGATTTCAACCCAGATGAT	0.433																																					p.N388S		Atlas-SNP	.											.	KIAA1456	20	.	0			c.A1163G						.						72	68	70					8																	12879351		1909	4140	6049	SO:0001583	missense	57604	exon5			ATTTCAACCCAGA	BC035082	CCDS47808.1	8p22	2013-10-04	2011-02-23	2011-02-23	ENSG00000250305	ENSG00000250305			26725	protein-coding gene	gene with protein product		615666	"chromosome 8 open reading frame 79"	C8orf79		23381944	Standard	NM_020844		Approved	FLJ36980	uc010lsq.3	Q8N9K7	OTTHUMG00000165477	ENST00000524591.2:c.1163A>G	chr8.hg19:g.12879351A>G	ENSP00000432695:p.Asn388Ser	154.0	0.0		156.0	48.0	NM_020844	Q96AW6	Missense_Mutation	SNP	ENST00000524591.2	hg19	CCDS47808.1	.	.	.	.	.	.	.	.	.	.	A	4.129	0.022214	0.08006	.	.	ENSG00000250305	ENST00000524591;ENST00000529978	T	0.08634	3.07	4.75	-4.95	0.03048	.	1.141070	0.06094	N	0.664072	T	0.05273	0.0140	L	0.48362	1.52	0.09310	N	1	B	0.16396	0.017	B	0.06405	0.002	T	0.45145	-0.9281	10	0.08599	T	0.76	-0.5598	1.3292	0.02131	0.1528:0.2811:0.1501:0.416	.	388	Q9P272	K1456_HUMAN	S	388;301	ENSP00000432695:N388S	ENSP00000432695:N388S	N	+	2	0	AC135352.2	12923722	0.000000	0.05858	0.003000	0.11579	0.084000	0.17831	0.125000	0.15749	-0.553000	0.06158	0.533000	0.62120	AAC	.	.		0.433	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677		G	12879351	A	G	12879351	3	3	23	1	0	0	0	0	1	0	0	0	2440	43	2	2	1173	2	C8orf79	8	12879351	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	6289243	12879351	133484671	483	2549										
PPP2R2A	5520	hgsc.bcm.edu	37	chr8	26223877	26223877	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgttcactgtatgaaaatgActgcatatttgacaaatttg	7	6	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:26223877A>G	ENST00000380737.3	+	9	1348	c.1019A>G	c.(1018-1020)gAc>gGc	p.D340G	PPP2R2A_ENST00000315985.7_Missense_Mutation_p.D350G	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	340					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		TATGAAAATGACTGCATATTT	0.308																																					p.D350G		Atlas-SNP	.											.	PPP2R2A	44	.	0			c.A1049G						.						136	136	136					8																	26223877		2203	4299	6502	SO:0001583	missense	5520	exon9			AAAATGACTGCAT	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9304	protein-coding gene	gene with protein product	"PP2A subunit B isoform alpha"	604941	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.1019A>G	chr8.hg19:g.26223877A>G	ENSP00000370113:p.Asp340Gly	112.0	0.0		106.0	34.0	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Missense_Mutation	SNP	ENST00000380737.3	hg19	CCDS34867.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.852848	0.91355	.	.	ENSG00000221914	ENST00000380737;ENST00000524169;ENST00000315985	T;T;T	0.71461	0.88;-0.57;0.86	5.96	5.96	0.96718	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	U	0.000000	D	0.87341	0.6153	M	0.91300	3.195	0.80722	D	1	D;D;D	0.69078	0.996;0.997;0.985	D;D;D	0.72338	0.946;0.946;0.977	D	0.89813	0.3983	10	0.66056	D	0.02	-13.965	16.4484	0.83959	1.0:0.0:0.0:0.0	.	350;340;341	B4E1T7;P63151;Q6ZP32	.;2ABA_HUMAN;.	G	340;119;350	ENSP00000370113:D340G;ENSP00000430320:D119G;ENSP00000325074:D350G	ENSP00000325074:D350G	D	+	2	0	PPP2R2A	26279794	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.285000	0.76669	0.533000	0.62120	GAC	.	.		0.308	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717		G	26223877	A	G	26223877	3	3	23	1	0	0	0	0	1	0	0	0	12396	275	10	2	1094	2	PPP2R2A	8	26223877	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	13344526	26223877	120140145	484	2550										
SCARA3	51435	hgsc.bcm.edu	37	chr8	27516318	27516318	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctctctgaaggacctcaccCaggagtgctacgatgtcaag	10	12	4	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:27516318C>A	ENST00000301904.3	+	5	651	c.631C>A	c.(631-633)Cag>Aag	p.Q211K	SCARA3_ENST00000337221.4_Missense_Mutation_p.Q211K	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	211					receptor-mediated endocytosis (GO:0006898)|response to oxidative stress (GO:0006979)|UV protection (GO:0009650)	collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)			breast(1)|large_intestine(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	9		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		GGACCTCACCCAGGAGTGCTA	0.607																																					p.Q211K		Atlas-SNP	.											.	SCARA3	93	.	0			c.C631A						.						36	37	37					8																	27516318		2203	4300	6503	SO:0001583	missense	51435	exon5			CTCACCCAGGAGT	AB007829	CCDS34870.1, CCDS34871.1	8p21	2010-03-24			ENSG00000168077	ENSG00000168077			19000	protein-coding gene	gene with protein product	"macrophage scavenger receptor-like 1"	602728				9747040, 9580669	Standard	NM_182826		Approved	CSR1, CSR, MSLR1, APC7, MSRL1	uc003xga.1	Q6AZY7	OTTHUMG00000163898	ENST00000301904.3:c.631C>A	chr8.hg19:g.27516318C>A	ENSP00000301904:p.Gln211Lys	123.0	0.0		152.0	7.0	NM_182826	Q9UM15|Q9UM16	Missense_Mutation	SNP	ENST00000301904.3	hg19	CCDS34871.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.764823	0.49574	.	.	ENSG00000168077	ENST00000337221;ENST00000301904	T;T	0.75367	-0.93;2.01	6.17	6.17	0.99709	.	0.102956	0.64402	D	0.000002	T	0.66799	0.2826	L	0.27053	0.805	0.43766	D	0.996289	P;P	0.46859	0.885;0.817	P;B	0.44946	0.465;0.275	T	0.61676	-0.7014	10	0.12430	T	0.62	-18.7305	18.3732	0.90420	0.0:1.0:0.0:0.0	.	211;211	Q6AZY7-2;Q6AZY7	.;SCAR3_HUMAN	K	211	ENSP00000337985:Q211K;ENSP00000301904:Q211K	ENSP00000301904:Q211K	Q	+	1	0	SCARA3	27572237	0.992000	0.36948	1.000000	0.80357	0.994000	0.84299	2.839000	0.48207	2.941000	0.99782	0.655000	0.94253	CAG	.	.		0.607	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240		A	27516318	C	A	27516318	3	1	23	1	0	0	0	0	1	0	0	0	13894	595	21	3	649	3	SCARA3	8	27516318	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1292441	27516318	118847704	485	2551										
ESCO2	157570	hgsc.bcm.edu	37	chr8	27646450	27646450	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaccctgaagatgaaatgcaGcatgtacagcatcaccacag	8	11	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:27646450G>A	ENST00000305188.8	+	7	1456	c.1218G>A	c.(1216-1218)caG>caA	p.Q406Q	ESCO2_ENST00000397418.2_Silent_p.Q54Q	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	406					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		ATGAAATGCAGCATGTACAGC	0.413									SC Phocomelia syndrome																												p.Q406Q		Atlas-SNP	.											.	ESCO2	50	.	0			c.G1218A						.						128	117	121					8																	27646450		2203	4300	6503	SO:0001819	synonymous_variant	157570	exon7	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	AATGCAGCATGTA	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"Roberts syndrome", "establishment of cohesion 1 homolog 2 (S. cerevisiae)"	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.1218G>A	chr8.hg19:g.27646450G>A		82.0	0.0		108.0	40.0	NM_001017420	B3KW59|Q49AP4	Silent	SNP	ENST00000305188.8	hg19	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	G	9.386	1.074229	0.20227	.	.	ENSG00000171320	ENST00000518262	.	.	.	6.03	-1.5	0.08691	.	.	.	.	.	T	0.57403	0.2051	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54794	-0.8240	4	.	.	.	-10.9913	10.9164	0.47139	0.7521:0.0:0.2479:0.0	.	.	.	.	N	111	.	.	S	+	2	0	ESCO2	27702369	0.986000	0.35501	0.975000	0.42487	0.992000	0.81027	0.115000	0.15540	-0.140000	0.11394	-0.137000	0.14449	AGC	.	.		0.413	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420		A	27646450	G	A	27646450	2	1	23	1	0	0	0	0	0	0	0	1	5251	962	34	3		3	ESCO2	8	27646450	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	130132	27646450	118717572	486	2552										
PBK	55872	hgsc.bcm.edu	37	chr8	27667883	27667883	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaggacgatctttagggtctTcattagtgcatacagagaag	11	6	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:27667883T>A	ENST00000301905.4	-	8	1371	c.908A>T	c.(907-909)gAa>gTa	p.E303V	PBK_ENST00000522944.1_Missense_Mutation_p.E314V|ESCO2_ENST00000397418.2_Intron	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	303	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		TTTAGGGTCTTCATTAGTGCA	0.423																																					p.E303V		Atlas-SNP	.											.	PBK	29	.	0			c.A908T						.						168	138	149					8																	27667883		2203	4300	6503	SO:0001583	missense	55872	exon8			GGGTCTTCATTAG	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"T-LAK cell-originated protein kinase", "cancer/testis antigen 84"	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.908A>T	chr8.hg19:g.27667883T>A	ENSP00000301905:p.Glu303Val	114.0	0.0		103.0	51.0	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Missense_Mutation	SNP	ENST00000301905.4	hg19	CCDS6063.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.180811	0.78677	.	.	ENSG00000168078	ENST00000301905;ENST00000522944	T;T	0.33216	1.42;1.42	6.11	6.11	0.99139	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.37433	0.1003	L	0.39245	1.2	0.80722	D	1	P;P	0.51057	0.883;0.941	P;P	0.51657	0.676;0.676	T	0.04333	-1.0959	10	0.37606	T	0.19	-28.0105	14.6542	0.68820	0.0:0.0:0.0:1.0	.	314;303	B4DX68;Q96KB5	.;TOPK_HUMAN	V	303;314	ENSP00000301905:E303V;ENSP00000428489:E314V	ENSP00000301905:E303V	E	-	2	0	PBK	27723802	1.000000	0.71417	0.996000	0.52242	0.624000	0.37722	7.765000	0.85310	2.343000	0.79666	0.533000	0.62120	GAA	.	.		0.423	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492		A	27667883	T	A	27667883	3	1	23	1	0	0	0	0	1	0	0	0	11497	1783	62	4	64	4	PBK	8	27667883	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	21433	27667883	118696139	487	2553										
EXTL3	2137	hgsc.bcm.edu	37	chr8	28608212	28608212	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttccgatgcccaggatgcccTcaggccctgtctcatgatga	10	14	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:28608212T>C	ENST00000220562.4	+	7	3491	c.2589T>C	c.(2587-2589)ccT>ccC	p.P863P	EXTL3_ENST00000519886.1_Intron|EXTL3_ENST00000523149.1_Silent_p.P479P	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	863					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)			biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		CAGGATGCCCTCAGGCCCTGT	0.562																																					p.P863P		Atlas-SNP	.											.	EXTL3	83	.	0			c.T2589C						.						146	115	125					8																	28608212		2203	4300	6503	SO:0001819	synonymous_variant	2137	exon7			ATGCCCTCAGGCC	U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"Exostosin glycosyltransferase family"	3518	protein-coding gene	gene with protein product	"REG receptor", "glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"	605744	"exostoses (multiple)-like 3"			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.2589T>C	chr8.hg19:g.28608212T>C		66.0	0.0		48.0	21.0	NM_001440	D3DST8|O00225|Q53XT3	Silent	SNP	ENST00000220562.4	hg19	CCDS6070.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.325950	0.24080	.	.	ENSG00000012232	ENST00000521473	.	.	.	5.61	-7.8	0.01214	.	.	.	.	.	T	0.36690	0.0976	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45571	-0.9252	4	.	.	.	-20.6994	3.7169	0.08441	0.0924:0.2857:0.375:0.2469	.	.	.	.	P	154	.	.	S	+	1	0	EXTL3	28664131	0.780000	0.28664	0.965000	0.40720	0.902000	0.53008	-0.181000	0.09740	-0.895000	0.03920	-0.478000	0.04885	TCA	.	.		0.562	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440		C	28608212	T	C	28608212	2	2	23	1	0	0	0	0	0	0	0	1	5329	1538	54	2		2	EXTL3	8	28608212	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	940329	28608212	117755810	488	2554										
TMEM66	51669	hgsc.bcm.edu	37	chr8	29924389	29924389	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atccttgttgtcctgtaaaaGcactgccaaaaccagaagtt	7	10	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:29924389G>A	ENST00000256255.6	-	4	1003	c.746C>T	c.(745-747)gCt>gTt	p.A249V	TMEM66_ENST00000545648.1_Missense_Mutation_p.A77V|TMEM66_ENST00000536273.1_Missense_Mutation_p.A77V	NM_016127.4	NP_057211.4	Q96BY9	SARAF_HUMAN		249					calcium ion transport (GO:0006816)|regulation of store-operated calcium entry (GO:2001256)	integral component of endoplasmic reticulum membrane (GO:0030176)				endometrium(2)|large_intestine(1)|lung(11)	14				KIRC - Kidney renal clear cell carcinoma(542;0.0993)|Kidney(114;0.119)		TCCTGTAAAAGCACTGCCAAA	0.393																																					p.A249V		Atlas-SNP	.											.	TMEM66	23	.	0			c.C746T						.						147	143	144					8																	29924389		2203	4300	6503	SO:0001583	missense	51669	exon4			GTAAAAGCACTGC																												ENST00000256255.6:c.746C>T	chr8.hg19:g.29924389G>A	ENSP00000256255:p.Ala249Val	165.0	0.0		183.0	19.0	NM_016127	B3KQQ4|B7Z9J1|D3DSU7|H9MHJ8|H9MHJ9|Q53HE8|Q9UNZ3|Q9Y683	Missense_Mutation	SNP	ENST00000256255.6	hg19	CCDS6074.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.47|19.47	3.832781|3.832781	0.71258|0.71258	.|.	.|.	ENSG00000133872|ENSG00000133872	ENST00000256255;ENST00000545648;ENST00000541035;ENST00000536273;ENST00000523127|ENST00000521265	T;T;T;T|.	0.44482|.	0.92;0.92;0.92;0.92|.	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	0.470266|.	0.24217|.	N|.	0.040472|.	T|T	0.50650|0.50650	0.1628|0.1628	L|L	0.55103|0.55103	1.725|1.725	0.29310|0.29310	N|N	0.868108|0.868108	P;P|.	0.52170|.	0.951;0.951|.	P;P|.	0.52646|.	0.705;0.705|.	T|T	0.50338|0.50338	-0.8840|-0.8840	10|5	0.48119|.	T|.	0.1|.	-20.6171|-20.6171	9.8225|9.8225	0.40891|0.40891	0.0936:0.0:0.9064:0.0|0.0936:0.0:0.9064:0.0	.|.	249;249|.	B3KQQ4;Q96BY9|.	.;TMM66_HUMAN|.	V|F	249;77;213;77;147|249	ENSP00000256255:A249V;ENSP00000441351:A77V;ENSP00000441723:A77V;ENSP00000428323:A147V|.	ENSP00000256255:A249V|.	A|L	-|-	2|1	0|0	TMEM66|TMEM66	30043931|30043931	0.980000|0.980000	0.34600|0.34600	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	1.720000|1.720000	0.38022|0.38022	2.442000|2.442000	0.82660|0.82660	0.580000|0.580000	0.79431|0.79431	GCT|CTT	.	.		0.393	TMEM66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257254.4			A	29924389	G	A	29924389	3	1	23	1	0	0	0	0	1	0	0	0	16210	971	34	3	285	3	TMEM66	8	29924389	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1316177	29924389	116439633	489	2555										
UNC5D	137970	hgsc.bcm.edu	37	chr8	35541099	35541099	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaatgaagagcccattgactCtgaacaagacgagaacattg	9	8	1	6			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:35541099C>A	ENST00000404895.2	+	5	933	c.605C>A	c.(604-606)tCt>tAt	p.S202Y	UNC5D_ENST00000416672.1_Missense_Mutation_p.S202Y|UNC5D_ENST00000453357.2_Missense_Mutation_p.S197Y|UNC5D_ENST00000287272.2_Missense_Mutation_p.S202Y|UNC5D_ENST00000420357.1_Missense_Mutation_p.S202Y	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	202	Ig-like C2-type.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		CCCATTGACTCTGAACAAGAC	0.448																																					p.S202Y		Atlas-SNP	.											.	UNC5D	393	.	0			c.C605A						.						94	83	87					8																	35541099		2203	4300	6503	SO:0001583	missense	137970	exon5			TTGACTCTGAACA	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.605C>A	chr8.hg19:g.35541099C>A	ENSP00000385143:p.Ser202Tyr	124.0	0.0		121.0	53.0	NM_080872	Q8WYP7	Missense_Mutation	SNP	ENST00000404895.2	hg19	CCDS6093.2	.	.	.	.	.	.	.	.	.	.	C	20.3	3.963810	0.74131	.	.	ENSG00000156687	ENST00000404895;ENST00000420357;ENST00000287272;ENST00000416672;ENST00000453357	T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46	5.39	5.39	0.77823	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.051625	0.85682	D	0.000000	T	0.68705	0.3030	L	0.37561	1.115	0.80722	D	1	P;P	0.44241	0.823;0.829	P;P	0.48795	0.59;0.544	T	0.71856	-0.4466	10	0.87932	D	0	-16.6379	19.5354	0.95251	0.0:1.0:0.0:0.0	.	197;202	Q6UXZ4-2;Q6UXZ4	.;UNC5D_HUMAN	Y	202;202;202;202;197	ENSP00000385143:S202Y;ENSP00000392739:S202Y;ENSP00000287272:S202Y;ENSP00000412652:S202Y;ENSP00000394303:S197Y	ENSP00000287272:S202Y	S	+	2	0	UNC5D	35660641	1.000000	0.71417	0.994000	0.49952	0.863000	0.49368	5.905000	0.69893	2.709000	0.92574	0.655000	0.94253	TCT	.	.		0.448	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			A	35541099	C	A	35541099	3	1	23	1	0	0	0	0	1	0	0	0	17010	913	32	3	623	3	UNC5D	8	35541099	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5616710	35541099	110822923	490	2556										
WHSC1L1	54904	hgsc.bcm.edu	37	chr8	38184373	38184373	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttctgttttgttaccaattCcctttaaaataaggcaaaag	5	7	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:38184373C>T	ENST00000317025.8	-	7	2100	c.1583G>A	c.(1582-1584)gGa>gAa	p.G528E	WHSC1L1_ENST00000527502.1_Splice_Site_p.G528E|WHSC1L1_ENST00000433384.2_Splice_Site_p.G528E|WHSC1L1_ENST00000316985.3_Splice_Site_p.G528E	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	528					histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			GTTACCAATTCCCTTTAAAAT	0.368			T	NUP98	AML																																p.G528E		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.G1583A						.						112	99	103					8																	38184373		2203	4300	6503	SO:0001630	splice_region_variant	54904	exon7			CCAATTCCCTTTA	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.1582-1G>A	chr8.hg19:g.38184373C>T		73.0	0.0		87.0	34.0	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	hg19	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.842584	0.51057	.	.	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985	D;D;D;T	0.94537	-3.42;-3.45;-3.45;0.01	5.79	5.79	0.91817	.	0.000000	0.47093	U	0.000245	D	0.89382	0.6699	N	0.19112	0.55	0.46437	D	0.999041	B;B;B;B	0.29301	0.012;0.082;0.241;0.049	B;B;B;B	0.30855	0.009;0.039;0.121;0.018	D	0.86763	0.1968	10	0.40728	T	0.16	.	13.2527	0.60060	0.0:0.9276:0.0:0.0724	.	528;528;528;528	B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95	.;.;.;NSD3_HUMAN	E	528;528;465;528;528	ENSP00000393284:G528E;ENSP00000313983:G528E;ENSP00000434730:G528E;ENSP00000313410:G528E	ENSP00000313410:G528E	G	-	2	0	WHSC1L1	38303530	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.655000	0.54460	2.718000	0.92993	0.655000	0.94253	GGA	.	.		0.368	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	Missense_Mutation	T	38184373	C	T	38184373	5	4	23	1	0	0	0	0	0	0	1	0	17378	869	30	3	2889	3	WHSC1L1	8	38184373	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2643274	38184373	108179649	491	2557										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53555118	53555118	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttttcttttcctcaagcaaaCgagctcgatcttcagaaagt	6	10	4	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:53555118C>T	ENST00000025008.5	-	18	4653	c.4130G>A	c.(4129-4131)cGt>cAt	p.R1377H	RB1CC1_ENST00000539297.1_Missense_Mutation_p.R1377H|RB1CC1_ENST00000435644.2_Missense_Mutation_p.R1377H|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1377					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				CTCAAGCAAACGAGCTCGATC	0.358																																					p.R1377H	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.G4130A						.						80	76	77					8																	53555118		2203	4300	6503	SO:0001583	missense	9821	exon18			AGCAAACGAGCTC	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.4130G>A	chr8.hg19:g.53555118C>T	ENSP00000025008:p.Arg1377His	110.0	0.0		103.0	30.0	NM_001083617	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	hg19	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831119	0.91036	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.15487	2.42;2.42;2.42	5.61	5.61	0.85477	.	0.053357	0.85682	D	0.000000	T	0.30823	0.0777	L	0.32530	0.975	0.44104	D	0.996878	D;D	0.76494	0.999;0.998	P;P	0.61592	0.891;0.781	T	0.01460	-1.1349	10	0.72032	D	0.01	-13.615	18.6201	0.91318	0.0:1.0:0.0:0.0	.	1377;1377	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	H	1377	ENSP00000025008:R1377H;ENSP00000396067:R1377H;ENSP00000445960:R1377H	ENSP00000025008:R1377H	R	-	2	0	RB1CC1	53717671	0.998000	0.40836	0.994000	0.49952	0.998000	0.95712	3.761000	0.55242	2.632000	0.89209	0.655000	0.94253	CGT	.	.		0.358	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		T	53555118	C	T	53555118	3	4	23	1	0	0	0	0	1	0	0	0	13114	536	19	1	682	1	RB1CC1	8	53555118	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	15370745	53555118	92808904	492	2558										
NSMAF	8439	hgsc.bcm.edu	37	chr8	59511898	59511898	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgctttccaatgcatctttgCtcttctggagaaagtcctcg	8	11	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:59511898C>T	ENST00000038176.3	-	19	1690	c.1478G>A	c.(1477-1479)aGc>aAc	p.S493N	NSMAF_ENST00000427130.2_Missense_Mutation_p.S524N|NSMAF_ENST00000519858.1_5'Flank	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	493	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TGCATCTTTGCTCTTCTGGAG	0.398																																					p.S524N		Atlas-SNP	.											.	NSMAF	156	.	0			c.G1571A						.						139	139	139					8																	59511898		2203	4300	6503	SO:0001583	missense	8439	exon19			TCTTTGCTCTTCT	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.1478G>A	chr8.hg19:g.59511898C>T	ENSP00000038176:p.Ser493Asn	93.0	0.0		89.0	37.0	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	hg19	CCDS6173.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.558695	0.27827	.	.	ENSG00000035681	ENST00000038176;ENST00000427130	T;T	0.78595	-1.19;-1.19	6.17	4.37	0.52481	BEACH domain (4);	0.181464	0.64402	N	0.000006	T	0.38321	0.1036	N	0.00178	-1.915	0.32582	N	0.528327	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.001	T	0.42430	-0.9452	9	.	.	.	.	9.386	0.38342	0.0:0.7848:0.0:0.2152	.	524;493	Q92636-2;Q92636	.;FAN_HUMAN	N	493;524	ENSP00000038176:S493N;ENSP00000411012:S524N	.	S	-	2	0	NSMAF	59674452	1.000000	0.71417	0.999000	0.59377	0.864000	0.49448	2.248000	0.43160	0.923000	0.37045	0.655000	0.94253	AGC	.	.		0.398	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		T	59511898	C	T	59511898	3	4	23	1	0	0	0	0	1	0	0	0	10683	797	28	3	1327	3	NSMAF	8	59511898	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5956780	59511898	86852124	493	2559										
PDE7A	5150	hgsc.bcm.edu	37	chr8	66651737	66651737	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aatgggttagaatcacttacCtaaaaatctacgaagtttca	6	7	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:66651737C>A	ENST00000401827.3	-	6	1038	c.595G>T	c.(595-597)Gtt>Ttt	p.V199F	PDE7A_ENST00000396642.3_Splice_Site_p.V199F|PDE7A_ENST00000518667.1_5'UTR|PDE7A_ENST00000379419.4_Splice_Site_p.V173F	NM_001242318.2	NP_001229247.1	Q13946	PDE7A_HUMAN	phosphodiesterase 7A	199	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			large_intestine(5)|lung(3)|stomach(1)|urinary_tract(1)	10			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	AATCACTTACCTAAAAATCTA	0.289																																					p.V199F		Atlas-SNP	.											.	PDE7A	78	.	0			c.G595T						.						55	56	56					8																	66651737		2195	4292	6487	SO:0001630	splice_region_variant	5150	exon6			ACTTACCTAAAAA	L12052	CCDS34901.1, CCDS56538.1	8q13	2008-03-18				ENSG00000205268	3.1.4.17	"Phosphodiesterases"	8791	protein-coding gene	gene with protein product		171885				8389765, 9521885	Standard	NM_001242318		Approved	HCP1	uc003xvq.3	Q13946		ENST00000401827.3:c.595+1G>T	chr8.hg19:g.66651737C>A		268.0	0.0		239.0	92.0	NM_001242318	A0AVH6|A8K436|A8K9G5|O15380|Q96T72	Missense_Mutation	SNP	ENST00000401827.3	hg19	CCDS56538.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756829	0.89843	.	.	ENSG00000205268	ENST00000401827;ENST00000379419;ENST00000396642	T;T;T	0.76316	-1.01;-1.01;-0.44	5.37	5.37	0.77165	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	D	0.85405	0.5689	L	0.52573	1.65	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.81914	0.995;0.952;0.995	D	0.84150	0.0422	9	.	.	.	.	19.107	0.93300	0.0:1.0:0.0:0.0	.	199;199;173	Q13946-3;Q13946;Q13946-2	.;PDE7A_HUMAN;.	F	199;173;199	ENSP00000385632:V199F;ENSP00000368730:V173F;ENSP00000379881:V199F	.	V	-	1	0	PDE7A	66814291	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.565000	0.82337	2.502000	0.84385	0.655000	0.94253	GTT	.	.		0.289	PDE7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378905.1		Missense_Mutation	A	66651737	C	A	66651737	5	1	23	1	0	0	0	0	0	0	1	0	11660	695	24	3	917	3	PDE7A	8	66651737	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	7139839	66651737	79712285	494	2560										
PREX2	80243	hgsc.bcm.edu	37	chr8	69020402	69020402	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	taaacaggccaaatctaaaaTctccccactgcacagcagtg	6	13	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:69020402T>A	ENST00000288368.4	+	24	3051	c.2774T>A	c.(2773-2775)aTc>aAc	p.I925N		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	925					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AAATCTAAAATCTCCCCACTG	0.408																																					p.I925N		Atlas-SNP	.											.	PREX2	614	.	0			c.T2774A						.						93	83	86					8																	69020402		2203	4300	6503	SO:0001583	missense	80243	exon24			CTAAAATCTCCCC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2774T>A	chr8.hg19:g.69020402T>A	ENSP00000288368:p.Ile925Asn	87.0	0.0		114.0	40.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.964171	0.53507	.	.	ENSG00000046889	ENST00000288368;ENST00000396539	T	0.34667	1.35	5.85	5.85	0.93711	.	0.184790	0.48767	D	0.000170	T	0.24890	0.0604	N	0.22421	0.69	0.41335	D	0.987262	P;B	0.35944	0.529;0.047	B;B	0.36922	0.236;0.042	T	0.09952	-1.0651	10	0.22706	T	0.39	.	10.5554	0.45114	0.0:0.0716:0.0:0.9284	.	990;925	Q70Z35-2;Q70Z35	.;PREX2_HUMAN	N	925;991	ENSP00000288368:I925N	ENSP00000288368:I925N	I	+	2	0	PREX2	69182956	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.162000	0.64942	2.238000	0.73509	0.533000	0.62120	ATC	.	.		0.408	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		A	69020402	T	A	69020402	3	1	23	1	0	0	0	0	1	0	0	0	12489	1435	50	4	3097	4	PREX2	8	69020402	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2368665	69020402	77343620	495	2561										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77776151	77776151	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgttgttccattcgtcaagTatgagtttatatgcagaaag	9	6	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:77776151T>C	ENST00000521891.2	+	11	10649	c.10201T>C	c.(10201-10203)Tat>Cat	p.Y3401H	ZFHX4_ENST00000518282.1_Missense_Mutation_p.Y3375H|ZFHX4_ENST00000050961.6_Missense_Mutation_p.Y3352H|ZFHX4_ENST00000455469.2_Missense_Mutation_p.Y3356H	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3352					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ATTCGTCAAGTATGAGTTTAT	0.398										HNSCC(33;0.089)																											p.Y3401H		Atlas-SNP	.											.	ZFHX4	878	.	0			c.T10201C						.						48	45	46					8																	77776151		1876	4116	5992	SO:0001583	missense	79776	exon11			GTCAAGTATGAGT		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.10201T>C	chr8.hg19:g.77776151T>C	ENSP00000430497:p.Tyr3401His	70.0	0.0		71.0	31.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	T	6.636	0.485890	0.12641	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.51817	0.69;0.75;0.72;0.71	4.85	4.85	0.62838	.	0.000000	0.40469	U	0.001088	T	0.26412	0.0645	N	0.05510	-0.035	0.36159	D	0.847962	B	0.09022	0.002	B	0.11329	0.006	T	0.20706	-1.0267	10	0.37606	T	0.19	.	9.1643	0.37041	0.0:0.0811:0.0:0.9189	.	3356	Q86UP3-4	.	H	3401;3385;3356;3352;3375	ENSP00000430497:Y3401H;ENSP00000399605:Y3356H;ENSP00000050961:Y3352H;ENSP00000430848:Y3375H	ENSP00000050961:Y3352H	Y	+	1	0	ZFHX4	77938706	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.142000	0.50601	2.056000	0.61249	0.496000	0.49642	TAT	.	.		0.398	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77776151	T	C	77776151	3	2	23	1	0	0	0	0	1	0	0	0	17650	1638	57	2	10239	2	ZFHX4	8	77776151	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	8755749	77776151	68587871	496	2562										
PSKH2	85481	hgsc.bcm.edu	37	chr8	87076416	87076416	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagtcaccactttttttcccGgagtatgccaaaccaaaatc	5	13	1	0	rs376242267		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:87076416G>A	ENST00000276616.2	-	2	704	c.630C>T	c.(628-630)tcC>tcT	p.S210S	PSKH2_ENST00000517981.1_5'UTR	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	210	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			TTTTTTTCCCGGAGTATGCCA	0.423																																					p.S210S		Atlas-SNP	.											PSKH2,rectum,carcinoma,0,1	PSKH2	79	.	0			c.C630T						.	G		1,4405	2.1+/-5.4	0,1,2202	72	76	75		630	-1.9	1	8		75	0,8600		0,0,4300	no	coding-synonymous	PSKH2	NM_033126.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		210/386	87076416	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	85481	exon2			TTTCCCGGAGTAT	AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.630C>T	chr8.hg19:g.87076416G>A		127.0	0.0		130.0	52.0	NM_033126	A0AV22	Silent	SNP	ENST00000276616.2	hg19	CCDS6240.1																																																																																			.	.		0.423	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126		A	87076416	G	A	87076416	2	1	23	1	0	0	0	0	0	0	0	1	12677	1103	39	1		1	PSKH2	8	87076416	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	9300265	87076416	59287606	497	2563										
SLC26A7	115111	hgsc.bcm.edu	37	chr8	92352747	92352747	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcttgctcaaggatctgccAaaaaattcaaatattcaatt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:92352747delA	ENST00000276609.3	+	8	1233	c.994delA	c.(994-996)aaafs	p.K333fs	SLC26A7_ENST00000523719.1_Frame_Shift_Del_p.K333fs|SLC26A7_ENST00000309536.2_Frame_Shift_Del_p.K333fs	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7									p.K333fs*20(1)		breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			AGGATCTGCCAAAAAATTCAA	0.502																																					p.A331fs		Atlas-Indel,Pindel	.											.	SLC26A7	207	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.993delC						.						97	90	92					8																	92352747		2203	4300	6503	SO:0001589	frameshift_variant	115111	exon8			.	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"Solute carriers"	14467	protein-coding gene	gene with protein product		608479	"solute carrier family 26, member 7"			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.994delA	chr8.hg19:g.92352747delA	ENSP00000276609:p.Lys333fs	77.0	0.0		80.0	33.0	NM_052832		Frame_Shift_Del	DEL	ENST00000276609.3	hg19	CCDS6254.1																																																																																			.	.		0.502	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1			-	92352747	A	-	92352747	7	5	23	1	0	1	0	1	0	0	0	0	14537	131	5	0	1020	0	SLC26A7	8	92352747	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	5276331	92352747	54011275	498	2564										
ESRP1	54845	hgsc.bcm.edu	37	chr8	95680213	95680213	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcccagtttctctccaaggAaaatcaagtcattgtccgca	7	12	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:95680213A>G	ENST00000433389.2	+	10	1158	c.968A>G	c.(967-969)gAa>gGa	p.E323G	ESRP1_ENST00000454170.2_Missense_Mutation_p.E323G|ESRP1_ENST00000358397.5_Missense_Mutation_p.E323G|ESRP1_ENST00000423620.2_Missense_Mutation_p.E323G	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	323					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						CTCTCCAAGGAAAATCAAGTC	0.468																																					p.E323G		Atlas-SNP	.											.	ESRP1	148	.	0			c.A968G						.						60	58	58					8																	95680213		1849	4088	5937	SO:0001583	missense	54845	exon10			CCAAGGAAAATCA	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"RNA binding motif (RRM) containing"	25966	protein-coding gene	gene with protein product		612959	"RNA binding motif protein 35A"	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.968A>G	chr8.hg19:g.95680213A>G	ENSP00000405738:p.Glu323Gly	131.0	0.0		121.0	45.0	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Missense_Mutation	SNP	ENST00000433389.2	hg19	CCDS47897.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.588378	0.46110	.	.	ENSG00000104413	ENST00000423620;ENST00000433389;ENST00000358397;ENST00000454170;ENST00000517610	T;T;T;T;T	0.29397	1.57;3.39;3.39;2.8;3.39	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.36608	0.0973	N	0.16567	0.415	0.80722	D	1	P;D;B;B;B;B	0.56746	0.589;0.977;0.005;0.003;0.014;0.431	B;D;B;B;B;B	0.64506	0.346;0.926;0.029;0.013;0.029;0.254	T	0.13575	-1.0504	10	0.19147	T	0.46	-14.893	16.1146	0.81295	1.0:0.0:0.0:0.0	.	323;323;323;323;323;323	D7PBN3;Q6NXG1-4;Q6NXG1-2;E9PB47;Q6NXG1-3;Q6NXG1	.;.;.;.;.;ESRP1_HUMAN	G	323;323;323;323;182	ENSP00000407349:E323G;ENSP00000405738:E323G;ENSP00000351168:E323G;ENSP00000402766:E323G;ENSP00000429125:E182G	ENSP00000351168:E323G	E	+	2	0	ESRP1	95749389	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.200000	0.70718	0.460000	0.39030	GAA	.	.		0.468	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697		G	95680213	A	G	95680213	3	3	23	1	0	0	0	0	1	0	0	0	5260	246	9	2	1006	2	ESRP1	8	95680213	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3327466	95680213	50683809	499	2565										
CTHRC1	115908	hgsc.bcm.edu	37	chr8	104394725	104394725	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aattggtgctggattagtggAtgttgctatctgggttggta	15	3	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:104394725A>T	ENST00000330295.5	+	4	771	c.629A>T	c.(628-630)gAt>gTt	p.D210V	RNU6-1011P_ENST00000384668.1_RNA|CTHRC1_ENST00000520880.1_Missense_Mutation_p.D80V|CTHRC1_ENST00000520337.1_Missense_Mutation_p.D196V|RP11-1C8.6_ENST00000577199.1_lincRNA	NM_138455.3	NP_612464.1	Q96CG8	CTHR1_HUMAN	collagen triple helix repeat containing 1	210					cell migration (GO:0016477)|cochlea morphogenesis (GO:0090103)|establishment of planar polarity involved in neural tube closure (GO:0090177)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|ossification involved in bone remodeling (GO:0043932)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein binding (GO:0032092)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)				endometrium(1)|large_intestine(5)|lung(4)|ovary(1)|urinary_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)			GGATTAGTGGATGTTGCTATC	0.378																																					p.D210V		Atlas-SNP	.											.	CTHRC1	29	.	0			c.A629T						.						306	289	295					8																	104394725		2203	4300	6503	SO:0001583	missense	115908	exon4			TAGTGGATGTTGC	BC014245	CCDS6299.1, CCDS59110.1	8q22.3	2008-08-07			ENSG00000164932	ENSG00000164932			18831	protein-coding gene	gene with protein product		610635				15618538	Standard	NM_138455		Approved		uc003ylk.4	Q96CG8	OTTHUMG00000164887	ENST00000330295.5:c.629A>T	chr8.hg19:g.104394725A>T	ENSP00000330523:p.Asp210Val	152.0	0.0		121.0	48.0	NM_138455	G3V141|Q6UW91|Q8IX63	Missense_Mutation	SNP	ENST00000330295.5	hg19	CCDS6299.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.418834	0.83559	.	.	ENSG00000164932	ENST00000330295;ENST00000520337;ENST00000297577;ENST00000520880	T;T	0.66815	-0.23;0.8	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.80934	0.4719	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.83202	-0.0078	10	0.72032	D	0.01	-10.7745	15.4021	0.74849	1.0:0.0:0.0:0.0	.	210	Q96CG8	CTHR1_HUMAN	V	210;196;196;80	ENSP00000330523:D210V;ENSP00000430550:D196V	ENSP00000297577:D196V	D	+	2	0	CTHRC1	104463901	1.000000	0.71417	0.991000	0.47740	0.991000	0.79684	8.962000	0.93254	2.048000	0.60808	0.533000	0.62120	GAT	.	.		0.378	CTHRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380792.1	NM_138455		T	104394725	A	T	104394725	3	4	23	1	0	0	0	0	1	0	0	0	4012	333	12	4	643	4	CTHRC1	8	104394725	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	8714512	104394725	41969297	500	2566										
DCAF13	25879	hgsc.bcm.edu	37	chr8	104447934	104447934	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atctgcagtgcttgatgtggAttactctcccactgggaagg	12	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:104447934A>G	ENST00000297579.5	+	8	1599	c.1322A>G	c.(1321-1323)gAt>gGt	p.D441G	DCAF13_ENST00000521999.1_3'UTR	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	289					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						CTTGATGTGGATTACTCTCCC	0.398																																					p.D441G		Atlas-SNP	.											.	DCAF13	66	.	0			c.A1322G						.						150	129	136					8																	104447934		2203	4300	6503	SO:0001583	missense	25879	exon8			ATGTGGATTACTC	AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24535	protein-coding gene	gene with protein product			"WD repeats and SOF1 domain containing"	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.1322A>G	chr8.hg19:g.104447934A>G	ENSP00000297579:p.Asp441Gly	46.0	0.0		63.0	24.0	NM_015420	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	hg19	CCDS34934.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.530671	0.85706	.	.	ENSG00000164934	ENST00000297579	T	0.61510	0.1	4.99	4.99	0.66335	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.74268	0.3694	M	0.73217	2.22	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.78097	-0.2337	10	0.87932	D	0	-23.3527	14.9911	0.71390	1.0:0.0:0.0:0.0	.	289	Q9NV06	DCA13_HUMAN	G	441	ENSP00000297579:D441G	ENSP00000297579:D441G	D	+	2	0	DCAF13	104517110	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.906000	0.92626	1.998000	0.58463	0.528000	0.53228	GAT	.	.		0.398	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420		G	104447934	A	G	104447934	3	3	23	1	0	0	0	0	1	0	0	0	4268	333	12	2	1352	2	DCAF13	8	104447934	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	53209	104447934	41916088	501	2567										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124340665	124340665	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgtttccggtctcattatgAtctacacttgtgtcttgagt	9	8	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:124340665A>T	ENST00000287394.5	-	25	3740	c.3633T>A	c.(3631-3633)gaT>gaA	p.D1211E	ATAD2_ENST00000521903.1_Missense_Mutation_p.D529E	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	1211					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			TCTCATTATGATCTACACTTG	0.383																																					p.D1211E		Atlas-SNP	.											.	ATAD2	160	.	0			c.T3633A						.						175	165	169					8																	124340665		2203	4300	6503	SO:0001583	missense	29028	exon25			ATTATGATCTACA	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.3633T>A	chr8.hg19:g.124340665A>T	ENSP00000287394:p.Asp1211Glu	124.0	0.0		141.0	58.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	A	10.13	1.266032	0.23136	.	.	ENSG00000156802	ENST00000287394;ENST00000521903	D;T	0.91792	-2.91;1.53	5.03	-1.74	0.08056	.	1.645960	0.02670	N	0.108427	T	0.79924	0.4530	N	0.08118	0	0.31420	N	0.674386	B	0.06786	0.001	B	0.06405	0.002	T	0.74140	-0.3761	10	0.07990	T	0.79	-4.3289	4.8821	0.13685	0.5084:0.253:0.2385:0.0	.	1211	Q6PL18	ATAD2_HUMAN	E	1211;529	ENSP00000287394:D1211E;ENSP00000429213:D529E	ENSP00000287394:D1211E	D	-	3	2	ATAD2	124409846	0.422000	0.25473	0.876000	0.34364	0.946000	0.59487	-0.469000	0.06648	-0.095000	0.12351	-0.345000	0.07892	GAT	.	.		0.383	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		T	124340665	A	T	124340665	3	4	23	1	0	0	0	0	1	0	0	0	1071	330	12	4	555	4	ATAD2	8	124340665	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	19892731	124340665	22023357	502	2568										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124383532	124383532	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttctctcattcgctgtctacGcatcttcttcatgtcatcca	4	14	7	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:124383532G>A	ENST00000287394.5	-	5	690	c.583C>T	c.(583-585)Cgt>Tgt	p.R195C	ATAD2_ENST00000521903.1_5'UTR|ATAD2_ENST00000534257.1_5'Flank	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	195					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			CGCTGTCTACGCATCTTCTTC	0.313																																					p.R195C		Atlas-SNP	.											.	ATAD2	160	.	0			c.C583T						.						94	92	93					8																	124383532		2203	4298	6501	SO:0001583	missense	29028	exon5			GTCTACGCATCTT	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.583C>T	chr8.hg19:g.124383532G>A	ENSP00000287394:p.Arg195Cys	212.0	0.0		198.0	71.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.984142	0.74474	.	.	ENSG00000156802	ENST00000287394	T	0.08102	3.13	5.06	4.16	0.48862	.	3.441010	0.01712	U	0.027766	T	0.33904	0.0879	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00003	-1.2586	10	0.87932	D	0	-11.072	13.9126	0.63876	0.0:0.0:0.8343:0.1657	.	25;195	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	C	195	ENSP00000287394:R195C	ENSP00000287394:R195C	R	-	1	0	ATAD2	124452713	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.008000	0.70739	1.057000	0.40506	0.555000	0.69702	CGT	.	.		0.313	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		A	124383532	G	A	124383532	3	1	23	1	0	0	0	0	1	0	0	0	1071	1087	38	1	3685	1	ATAD2	8	124383532	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	42867	124383532	21980490	503	2569										
TMEM71	137835	hgsc.bcm.edu	37	chr8	133764034	133764034	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	taatatgctctgcttacctaActaagttctccttatacata	3	10	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:133764034A>C	ENST00000356838.3	-	4	453	c.311T>G	c.(310-312)gTt>gGt	p.V104G	TMEM71_ENST00000517538.1_5'UTR|TMEM71_ENST00000523829.1_Missense_Mutation_p.V104G|TMEM71_ENST00000377901.4_Missense_Mutation_p.V104G	NM_144649.2	NP_653250.2	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	104						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TGCTTACCTAACTAAGTTCTC	0.378																																					p.V104G		Atlas-SNP	.											.	TMEM71	55	.	0			c.T311G						.						131	120	124					8																	133764034		2203	4300	6503	SO:0001583	missense	137835	exon4			TACCTAACTAAGT	AK057631	CCDS6366.1, CCDS47921.1	8q24.22	2005-09-02				ENSG00000165071			26572	protein-coding gene	gene with protein product						12477932	Standard	NM_144649		Approved	FLJ33069	uc003ytn.3	Q6P5X7		ENST00000356838.3:c.311T>G	chr8.hg19:g.133764034A>C	ENSP00000349296:p.Val104Gly	126.0	0.0		119.0	40.0	NM_144649	Q3KRC2|Q8WVZ4|Q96LX9	Missense_Mutation	SNP	ENST00000356838.3	hg19	CCDS6366.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.352347	0.61293	.	.	ENSG00000165071	ENST00000523829;ENST00000356838;ENST00000377901;ENST00000522334;ENST00000519016	.	.	.	5.95	5.95	0.96441	.	0.073213	0.53938	D	0.000046	T	0.79311	0.4424	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.993;0.962;0.999	T	0.81906	-0.0718	9	0.87932	D	0	.	14.1698	0.65503	1.0:0.0:0.0:0.0	.	104;104;104	Q6P5X7;Q6P5X7-3;Q6P5X7-2	TMM71_HUMAN;.;.	G	104;104;104;7;7	.	ENSP00000349296:V104G	V	-	2	0	TMEM71	133833216	0.996000	0.38824	0.989000	0.46669	0.252000	0.25951	5.934000	0.70138	2.282000	0.76494	0.533000	0.62120	GTT	.	.		0.378	TMEM71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379591.1	NM_144649		C	133764034	A	C	133764034	3	2	23	1	0	0	0	0	1	0	0	0	16215	43	2	5	604	5	TMEM71	8	133764034	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	9380502	133764034	12599988	504	2570										
PHF20L1	51105	hgsc.bcm.edu	37	chr8	133848922	133848922	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atgctcttaatgaaattgtgCgatgtatttgtgagatggat	11	3	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:133848922C>T	ENST00000395386.2	+	16	2346	c.2047C>T	c.(2047-2049)Cga>Tga	p.R683*	AF230666.2_ENST00000608375.1_RNA|PHF20L1_ENST00000395390.2_Nonsense_Mutation_p.R658*|PHF20L1_ENST00000220847.7_Nonsense_Mutation_p.R70*|AF230666.2_ENST00000429151.1_RNA	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	683							zinc ion binding (GO:0008270)	p.R657*(2)		breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TGAAATTGTGCGATGTATTTG	0.408																																					p.R683X		Atlas-SNP	.											Q86U89_HUMAN,NS,carcinoma,0,4	PHF20L1	129	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C2047T						.						190	183	185					8																	133848922		1969	4147	6116	SO:0001587	stop_gained	51105	exon16			ATTGTGCGATGTA	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2047C>T	chr8.hg19:g.133848922C>T	ENSP00000378784:p.Arg683*	159.0	0.0		158.0	55.0	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Nonsense_Mutation	SNP	ENST00000395386.2	hg19	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	C	38	7.083629	0.98051	.	.	ENSG00000129292	ENST00000395386;ENST00000220847;ENST00000395390	.	.	.	5.14	3.02	0.34903	.	0.103999	0.38111	U	0.001810	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6783	12.4875	0.55881	0.3889:0.6111:0.0:0.0	.	.	.	.	X	683;70;658	.	ENSP00000220847:R70X	R	+	1	2	PHF20L1	133918104	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	2.219000	0.42899	1.289000	0.44618	0.544000	0.68410	CGA	.	.		0.408	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		T	133848922	C	T	133848922	4	4	23	1	0	0	0	0	0	1	0	0	11841	760	27	1	2201	1	PHF20L1	8	133848922	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	84888	133848922	12515100	505	2571										
LYNX1	66004	hgsc.bcm.edu	37	chr8	143857040	143857040	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggtcatgcagtaggcaaccAtagccgggcagcgcatgggg	16	10	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:143857040A>G	ENST00000335822.5	-	3	752	c.125T>C	c.(124-126)aTg>aCg	p.M42T	LYNX1_ENST00000522906.1_Intron|LYNX1_ENST00000523332.1_Missense_Mutation_p.M42T|LYNX1_ENST00000345173.6_Missense_Mutation_p.M42T|LYNX1_ENST00000395192.2_Missense_Mutation_p.M42T|LYNX1_ENST00000398906.1_Missense_Mutation_p.M42T	NM_023946.2	NP_076435.1	Q9BZG9	LYNX1_HUMAN	Ly6/neurotoxin 1	42						anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|lung(2)|skin(1)	4	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GTAGGCAACCATAGCCGGGCA	0.657																																					p.M42T		Atlas-SNP	.											.	LYNX1	40	.	0			c.T125C						.						73	59	64					8																	143857040		2201	4299	6500	SO:0001583	missense	66004	exon3			GCAACCATAGCCG	AF321824	CCDS6389.1, CCDS34951.1, CCDS34952.1	8q24.3	2008-03-12			ENSG00000180155	ENSG00000180155			29604	protein-coding gene	gene with protein product		606110				12573258, 10402197	Standard	NM_023946		Approved	SLURP2	uc003yxd.1	Q9BZG9	OTTHUMG00000164694	ENST00000335822.5:c.125T>C	chr8.hg19:g.143857040A>G	ENSP00000337950:p.Met42Thr	116.0	0.0		99.0	40.0	NM_177477	D3DWI7|G3XAC2|Q86SR0	Missense_Mutation	SNP	ENST00000335822.5	hg19	CCDS34951.1	.	.	.	.	.	.	.	.	.	.	a	11.89	1.774863	0.31411	.	.	ENSG00000180155	ENST00000523332;ENST00000335822;ENST00000395192;ENST00000398906;ENST00000345173;ENST00000522929;ENST00000520131	T;T;T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06;2.06;2.06	4.82	3.51	0.40186	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	1.465370	0.03948	N	0.288053	T	0.26738	0.0654	N	0.22421	0.69	0.09310	N	1	P;D	0.56968	0.802;0.978	B;P	0.53649	0.43;0.731	T	0.26883	-1.0090	10	0.72032	D	0.01	-19.2184	8.1989	0.31413	0.808:0.0:0.0:0.192	.	42;42	Q9BZG9;G3XAC2	LYNX1_HUMAN;.	T	42	ENSP00000428713:M42T;ENSP00000337950:M42T;ENSP00000378618:M42T;ENSP00000381878:M42T;ENSP00000332495:M42T;ENSP00000429261:M42T;ENSP00000428157:M42T	ENSP00000337950:M42T	M	-	2	0	LYNX1	143854042	0.996000	0.38824	0.992000	0.48379	0.602000	0.36980	2.589000	0.46145	1.827000	0.53221	0.529000	0.55759	ATG	.	.		0.657	LYNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379786.3	NM_177476		G	143857040	A	G	143857040	3	3	23	1	0	0	0	0	1	0	0	0	9117	217	8	2	539	2	LYNX1	8	143857040	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	10008118	143857040	2506982	506	2572										
FAM83H	286077	hgsc.bcm.edu	37	chr8	144809309	144809309	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccccccacggcacctggggcCgccacctcttcccgccacgc	9	24	1	0	rs566224492		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:144809309C>T	ENST00000388913.3	-	5	2447	c.2322G>A	c.(2320-2322)gcG>gcA	p.A774A		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	774					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CACCTGGGGCCGCCACCTCTT	0.741													c|||	1	0.000199681	0	0	5008	,	,		10370	0		0	False		,,,				2504	0.001				p.A774A		Atlas-SNP	.											.	FAM83H	68	.	0			c.G2322A						.						2	3	2					8																	144809309		1498	3149	4647	SO:0001819	synonymous_variant	286077	exon5			TGGGGCCGCCACC	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.2322G>A	chr8.hg19:g.144809309C>T		914.0	1.0		952.0	247.0	NM_198488	A0JLS2|Q8N4W0	Silent	SNP	ENST00000388913.3	hg19	CCDS6410.2																																																																																			.	.		0.741	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		T	144809309	C	T	144809309	2	4	23	1	0	0	0	0	0	0	0	1	5648	639	23	1		1	FAM83H	8	144809309	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	952269	144809309	1554713	507	2573										
FAM83H	286077	hgsc.bcm.edu	37	chr8	144812634	144812634	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaagcggctgtaggcctccGagccaccctcggccagtgca	14	15	0	0	rs371078447		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:144812634G>A	ENST00000388913.3	-	2	244	c.119C>T	c.(118-120)tCg>tTg	p.S40L	MIR4664_ENST00000583819.1_RNA	NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	40					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GTAGGCCTCCGAGCCACCCTC	0.647																																					p.S40L		Atlas-SNP	.											.	FAM83H	68	.	0			c.C119T						.	G	LEU/SER	1,3997		0,1,1998	29	33	32		119	3	0	8		32	0,8314		0,0,4157	no	missense	FAM83H	NM_198488.3	145	0,1,6155	AA,AG,GG		0.0,0.025,0.0081	benign	40/1180	144812634	1,12311	1999	4157	6156	SO:0001583	missense	286077	exon2			GCCTCCGAGCCAC	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.119C>T	chr8.hg19:g.144812634G>A	ENSP00000373565:p.Ser40Leu	1440.0	2.0		1310.0	554.0	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	hg19	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	g	3.815	-0.038928	0.07497	2.5E-4	0.0	ENSG00000180921	ENST00000388913	T	0.11277	2.79	4.87	2.97	0.34412	.	0.602886	0.15663	N	0.250787	T	0.02970	0.0088	N	0.00521	-1.4	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.44097	-0.9350	10	0.23302	T	0.38	.	9.5268	0.39169	0.0:0.1291:0.575:0.2959	.	40	Q6ZRV2	FA83H_HUMAN	L	40	ENSP00000373565:S40L	ENSP00000373565:S40L	S	-	2	0	FAM83H	144884622	0.000000	0.05858	0.015000	0.15790	0.181000	0.23173	0.271000	0.18626	0.517000	0.28361	0.561000	0.74099	TCG	.	.		0.647	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		A	144812634	G	A	144812634	3	1	23	1	0	0	0	0	1	0	0	0	5648	1059	37	1	3436	1	FAM83H	8	144812634	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3325	144812634	1551388	508	2574										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144942558	144942558	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgcctcctccacggtcagctTccggttctccacggggtcga	11	17	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:144942558T>A	ENST00000525985.1	-	2	4935	c.4864A>T	c.(4864-4866)Aag>Tag	p.K1622*				P58107	EPIPL_HUMAN	epiplakin 1	1622						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ACGGTCAGCTTCCGGTTCTCC	0.642																																					p.K1622X		Atlas-SNP	.											.	EPPK1	199	.	0			c.A4864T						.						50	57	55					8																	144942558		2037	4186	6223	SO:0001587	stop_gained	83481	exon1			TCAGCTTCCGGTT	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4864A>T	chr8.hg19:g.144942558T>A	ENSP00000436337:p.Lys1622*	73.0	0.0		90.0	15.0	NM_031308	Q76E58|Q9NSU9	Nonsense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	T	44	11.034399	0.99506	.	.	ENSG00000227184	ENST00000525985	.	.	.	4.41	1.91	0.25777	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5429	0.39262	0.0:0.0:0.3414:0.6586	.	.	.	.	X	1622	.	ENSP00000436337:K1622X	K	-	1	0	EPPK1	145014546	0.817000	0.29147	0.537000	0.28052	0.847000	0.48162	1.977000	0.40589	0.204000	0.20548	0.482000	0.46254	AAG	.	.		0.642	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144942558	T	A	144942558	4	1	23	1	0	0	0	0	0	1	0	0	5192	1792	62	4	2402	4	EPPK1	8	144942558	Nonsense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	129924	144942558	1421464	509	2575										
SPATC1	375686	hgsc.bcm.edu	37	chr8	145095689	145095689	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccacctcccccaccacctcCcccacggtcaccgtccttgc	4	26	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145095689C>T	ENST00000377470.3	+	3	1089	c.987C>T	c.(985-987)tcC>tcT	p.S329S	SPATC1_ENST00000447830.2_Silent_p.S329S	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	329						centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ccaccacctcccccacggtca	0.677																																					p.S329S		Atlas-SNP	.											.	SPATC1	77	.	0			c.C987T						.						67	29	42					8																	145095689		2198	4289	6487	SO:0001819	synonymous_variant	375686	exon3			CACCTCCCCCACG	BC053547	CCDS6413.2, CCDS47937.1	8q24.3	2005-01-11			ENSG00000186583	ENSG00000186583			30510	protein-coding gene	gene with protein product		610874				15280373	Standard	NM_198572		Approved	MGC61633, SPATA15, SPERIOLIN	uc011lkw.2	Q76KD6	OTTHUMG00000156976	ENST00000377470.3:c.987C>T	chr8.hg19:g.145095689C>T		134.0	0.0		125.0	40.0	NM_001134374	B4DWW9|Q5U5I8|Q7Z6L7	Silent	SNP	ENST00000377470.3	hg19	CCDS6413.2																																																																																			.	.		0.677	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	NM_198572		T	145095689	C	T	145095689	2	4	23	1	0	0	0	0	0	0	0	1	15032	610	22	3		3	SPATC1	8	145095689	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	153131	145095689	1268333	510	2576										
VPS28	51160	hgsc.bcm.edu	37	chr8	145649444	145649444	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cactggctgaccgtctggcgGccctcaaagtcgggtgggag	16	12	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145649444G>A	ENST00000526054.1	-	8	565	c.528C>T	c.(526-528)ggC>ggT	p.G176G	VPS28_ENST00000377348.2_Silent_p.G176G|VPS28_ENST00000529182.1_Silent_p.G176G|VPS28_ENST00000526734.1_5'Flank|VPS28_ENST00000292510.4_Silent_p.G176G			Q9UK41	VPS28_HUMAN	vacuolar protein sorting 28 homolog (S. cerevisiae)	176	VPS28 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00642}.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|negative regulation of protein ubiquitination (GO:0031397)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			CCGTCTGGCGGCCCTCAAAGT	0.697																																					p.G176G		Atlas-SNP	.											.	VPS28	23	.	0			c.C528T						.						49	57	54					8																	145649444		2203	4298	6501	SO:0001819	synonymous_variant	51160	exon9			CTGGCGGCCCTCA	AF316887	CCDS6425.1, CCDS34967.1	8q24.3	2014-08-12	2006-04-04		ENSG00000160948	ENSG00000160948			18178	protein-coding gene	gene with protein product		611952	"vacuolar protein sorting 28 (yeast)"				Standard	NM_183057		Approved		uc003zct.1	Q9UK41	OTTHUMG00000165209	ENST00000526054.1:c.528C>T	chr8.hg19:g.145649444G>A		145.0	0.0		139.0	62.0	NM_016208	Q86VK0	Silent	SNP	ENST00000526054.1	hg19	CCDS6425.1																																																																																			.	.		0.697	VPS28-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382694.1			A	145649444	G	A	145649444	2	1	23	1	0	0	0	0	0	0	0	1	17214	1190	42	3		3	VPS28	8	145649444	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	553755	145649444	714578	511	2577										
FOXH1	8928	hgsc.bcm.edu	37	chr8	145700399	145700399	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggctcacgtcgaccgcccagAagttgcccttggcctggggc	14	15	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145700399A>G	ENST00000377317.4	-	3	898	c.320T>C	c.(319-321)tTc>tCc	p.F107S	FOXH1_ENST00000525197.1_5'UTR	NM_003923.2	NP_003914.1	O75593	FOXH1_HUMAN	forkhead box H1	107					aorta morphogenesis (GO:0035909)|axial mesoderm development (GO:0048318)|cardiac right ventricle morphogenesis (GO:0003215)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|heart looping (GO:0001947)|negative regulation of androgen receptor activity (GO:2000824)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|secondary heart field specification (GO:0003139)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular trabecula myocardium morphogenesis (GO:0003222)	activin responsive factor complex (GO:0032444)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|bHLH transcription factor binding (GO:0043425)|co-SMAD binding (GO:0070410)|enhancer binding (GO:0035326)|protein domain specific binding (GO:0019904)|R-SMAD binding (GO:0070412)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.76e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GACCGCCCAGAAGTTGCCCTT	0.677																																					p.F107S		Atlas-SNP	.											.	FOXH1	17	.	0			c.T320C						.						15	12	13					8																	145700399		2189	4271	6460	SO:0001583	missense	8928	exon3			GCCCAGAAGTTGC	AF076292	CCDS6428.1	8q24.3	2014-08-12			ENSG00000160973			"Forkhead boxes"	3814	protein-coding gene	gene with protein product		603621				9702198	Standard	NM_003923		Approved	FAST1	uc003zdc.3	O75593	OTTHUMG00000165172	ENST00000377317.4:c.320T>C	chr8.hg19:g.145700399A>G	ENSP00000366534:p.Phe107Ser	72.0	0.0		96.0	42.0	NM_003923	D3DWM4	Missense_Mutation	SNP	ENST00000377317.4	hg19	CCDS6428.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.267893	0.80469	.	.	ENSG00000160973	ENST00000377317;ENST00000292541	D	0.95588	-3.75	4.63	3.38	0.38709	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.96463	0.8846	M	0.69248	2.105	0.49915	D	0.999839	D	0.89917	1.0	D	0.77557	0.99	D	0.95942	0.8947	10	0.87932	D	0	-47.1348	8.3518	0.32307	0.6509:0.349:0.0:0.0	.	107	O75593	FOXH1_HUMAN	S	107;134	ENSP00000366534:F107S	ENSP00000292541:F134S	F	-	2	0	FOXH1	145671207	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.947000	0.63583	1.723000	0.51488	0.379000	0.24179	TTC	.	.		0.677	FOXH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382451.1			G	145700399	A	G	145700399	3	3	23	1	0	0	0	0	1	0	0	0	6016	246	9	2	781	2	FOXH1	8	145700399	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	50955	145700399	663623	512	2578										
LRRC14	9684	hgsc.bcm.edu	37	chr8	145746113	145746113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggatggcgaggacaacttccGctacttccttgcccagatgg	12	12	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145746113G>A	ENST00000292524.1	+	3	967	c.821G>A	c.(820-822)cGc>cAc	p.R274H	LRRC14_ENST00000529022.1_Missense_Mutation_p.R274H|RECQL4_ENST00000532237.1_5'Flank|RECQL4_ENST00000428558.2_5'Flank	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	274										endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GACAACTTCCGCTACTTCCTT	0.632																																					p.R274H		Atlas-SNP	.											.	LRRC14	25	.	0			c.G821A						.						56	52	53					8																	145746113		2202	4300	6502	SO:0001583	missense	9684	exon4			ACTTCCGCTACTT	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179	ENST00000292524.1:c.821G>A	chr8.hg19:g.145746113G>A	ENSP00000292524:p.Arg274His	18.0	0.0		19.0	9.0	NM_001272036	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.599259	0.46318	.	.	ENSG00000160959	ENST00000527730;ENST00000529022;ENST00000292524	T;T;T	0.53640	0.61;0.61;0.61	4.44	1.2	0.21068	.	0.165156	0.45606	D	0.000344	T	0.42854	0.1221	L	0.55990	1.75	0.20638	N	0.99987	D	0.69078	0.997	P	0.50708	0.648	T	0.24870	-1.0148	10	0.35671	T	0.21	.	2.9598	0.05889	0.1838:0.0:0.3831:0.4331	.	274	Q15048	LRC14_HUMAN	H	274	ENSP00000436452:R274H;ENSP00000434768:R274H;ENSP00000292524:R274H	ENSP00000292524:R274H	R	+	2	0	LRRC14	145716921	0.309000	0.24518	0.938000	0.37757	0.947000	0.59692	1.385000	0.34408	0.446000	0.26666	0.313000	0.20887	CGC	.	.		0.632	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		A	145746113	G	A	145746113	3	1	23	1	0	0	0	0	1	0	0	0	8977	1087	38	1	827	1	LRRC14	8	145746113	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	45714	145746113	617909	513	2579										
LRRC14	9684	hgsc.bcm.edu	37	chr8	145746554	145746554	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cactacccatcctgactcagTgcgccagtctccggtacctt	7	17	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145746554T>C	ENST00000292524.1	+	4	1320	c.1174T>C	c.(1174-1176)Tgc>Cgc	p.C392R	LRRC14_ENST00000529022.1_Missense_Mutation_p.C392R	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	392										endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CCTGACTCAGTGCGCCAGTCT	0.607																																					p.C392R		Atlas-SNP	.											.	LRRC14	25	.	0			c.T1174C						.						79	68	71					8																	145746554		2203	4300	6503	SO:0001583	missense	9684	exon5			ACTCAGTGCGCCA	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179	ENST00000292524.1:c.1174T>C	chr8.hg19:g.145746554T>C	ENSP00000292524:p.Cys392Arg	71.0	0.0		49.0	15.0	NM_001272036	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.821321	0.32237	.	.	ENSG00000160959	ENST00000529022;ENST00000292524	T;T	0.12984	2.63;2.63	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.42966	0.1226	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.52162	-0.8612	10	0.87932	D	0	.	11.9975	0.53212	0.0:0.0:0.0:1.0	.	392	Q15048	LRC14_HUMAN	R	392	ENSP00000434768:C392R;ENSP00000292524:C392R	ENSP00000292524:C392R	C	+	1	0	LRRC14	145717362	0.989000	0.36119	0.036000	0.18154	0.001000	0.01503	2.808000	0.47963	1.932000	0.55993	0.533000	0.62120	TGC	.	.		0.607	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		C	145746554	T	C	145746554	3	2	23	1	0	0	0	0	1	0	0	0	8977	1696	59	2	1184	2	LRRC14	8	145746554	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	441	145746554	617468	514	2580										
LRRC24	441381	hgsc.bcm.edu	37	chr8	145750253	145750253	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcgcaaccgcagggcgccacActccaccgtggcgctgtagc	13	17	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145750253A>G	ENST00000529415.2	-	2	223	c.106T>C	c.(106-108)Tgt>Cgt	p.C36R	LRRC14_ENST00000292524.1_3'UTR|LRRC24_ENST00000533758.1_Missense_Mutation_p.C36R			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	36	LRRNT.					integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			AGGGCGCCACACTCCACCGTG	0.746																																					p.C36R		Atlas-SNP	.											.	LRRC24	11	.	0			c.T106C						.						3	4	4					8																	145750253		1503	2917	4420	SO:0001583	missense	441381	exon2			CGCCACACTCCAC	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"Immunoglobulin superfamily / I-set domain containing"	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.106T>C	chr8.hg19:g.145750253A>G	ENSP00000434849:p.Cys36Arg	62.0	0.0		67.0	21.0	NM_001024678		Missense_Mutation	SNP	ENST00000529415.2	hg19	CCDS34969.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677044	0.88445	.	.	ENSG00000254402	ENST00000529415;ENST00000533758	T;T	0.53857	0.6;3.97	4.84	4.84	0.62591	Leucine-rich repeat-containing N-terminal (1);	0.059704	0.64402	D	0.000002	T	0.77445	0.4131	M	0.93854	3.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.82548	-0.0402	10	0.87932	D	0	.	10.7106	0.45982	1.0:0.0:0.0:0.0	.	36;36	G3V1D8;Q50LG9	.;LRC24_HUMAN	R	36	ENSP00000434849:C36R;ENSP00000435653:C36R	ENSP00000434849:C36R	C	-	1	0	LRRC24	145721061	1.000000	0.71417	0.989000	0.46669	0.682000	0.39822	3.478000	0.53158	2.022000	0.59522	0.533000	0.62120	TGT	.	.		0.746	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678		G	145750253	A	G	145750253	3	3	23	1	0	0	0	0	1	0	0	0	8988	159	6	2	1451	2	LRRC24	8	145750253	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3699	145750253	613769	515	2581										
MGC70857	414919	hgsc.bcm.edu	37	chr8	145752948	145752948	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcggccaggggcagcaggcgCgccggctcgaagggcacggc	20	14	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145752948C>T	ENST00000524821.1	-	3	644	c.429G>A	c.(427-429)gcG>gcA	p.A143A	C8orf82_ENST00000313465.5_3'UTR|LRRC24_ENST00000529415.2_5'Flank|LRRC24_ENST00000533758.1_5'Flank			Q6P1X6	CH082_HUMAN	chromosome 8 open reading frame 82	143										endometrium(1)|urinary_tract(1)	2						GCAGCAGGCGCGCCGGCTCGA	0.776																																					p.A143A		Atlas-SNP	.											.	C8orf82	7	.	0			c.G429A						.						1	2	2					8																	145752948		924	2176	3100	SO:0001819	synonymous_variant	414919	exon3			CAGGCGCGCCGGC		CCDS34970.1	8q24	2012-04-18			ENSG00000213563	ENSG00000213563			33826	protein-coding gene	gene with protein product						12477932	Standard	NM_001001795		Approved	MGC70857	uc003zdp.1	Q6P1X6	OTTHUMG00000165181	ENST00000524821.1:c.429G>A	chr8.hg19:g.145752948C>T		15.0	0.0		8.0	7.0	NM_001001795	Q6GMR2|Q6P2Q7	Silent	SNP	ENST00000524821.1	hg19	CCDS34970.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.686159	0.29962	.	.	ENSG00000213563	ENST00000532827	.	.	.	3.96	-0.875	0.10628	.	0.118857	0.34932	U	0.003561	T	0.49609	0.1567	.	.	.	0.58432	D	0.999991	.	.	.	.	.	.	T	0.30327	-0.9982	6	0.31617	T	0.26	-11.1577	5.177	0.15141	0.5791:0.3077:0.0:0.1131	.	.	.	.	T	188	.	ENSP00000437092:A188T	A	-	1	0	C8orf82	145723756	0.009000	0.17119	0.857000	0.33713	0.944000	0.59088	0.076000	0.14712	-0.008000	0.14320	-0.262000	0.10625	GCG	.	.		0.776	C8orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382503.1	NM_001001795		T	145752948	C	T	145752948	2	4	23	1	0	0	0	0	0	0	0	1	9562	755	27	1		1	MGC70857	8	145752948	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2695	145752948	611074	516	2582										
ZNF517	340385	hgsc.bcm.edu	37	chr8	146033090	146033090	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgcgagcggccctacgcatgCggcgagtgcggcaaggcctt	16	14	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:146033090C>T	ENST00000531720.1	+	4	834	c.789C>T	c.(787-789)tgC>tgT	p.C263C	ZNF517_ENST00000359971.3_Silent_p.C263C|ZNF517_ENST00000525105.1_Intron|ZNF517_ENST00000526178.1_Intron			Q6ZMY9	ZN517_HUMAN	zinc finger protein 517	263					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			CCTACGCATGCGGCGAGTGCG	0.697																																					p.C263C		Atlas-SNP	.											.	ZNF517	30	.	0			c.C789T						.						22	23	22					8																	146033090		2201	4298	6499	SO:0001819	synonymous_variant	340385	exon5			CGCATGCGGCGAG	AK096527	CCDS6434.1	8q24.3	2013-01-08				ENSG00000197363		"Zinc fingers, C2H2-type", "-"	27984	protein-coding gene	gene with protein product							Standard	NM_213605		Approved		uc003zed.1	Q6ZMY9		ENST00000531720.1:c.789C>T	chr8.hg19:g.146033090C>T		83.0	0.0		69.0	29.0	NM_213605		Silent	SNP	ENST00000531720.1	hg19	CCDS6434.1	.	.	.	.	.	.	.	.	.	.	C	0.046	-1.264883	0.01433	.	.	ENSG00000197363	ENST00000529429	.	.	.	2.37	-2.12	0.07165	.	.	.	.	.	T	0.52141	0.1716	.	.	.	0.53005	D	0.999962	.	.	.	.	.	.	T	0.45644	-0.9247	4	.	.	.	.	8.1165	0.30946	0.0:0.2622:0.0:0.7378	.	.	.	.	V	230	.	.	A	+	2	0	ZNF517	146003894	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.344000	0.02639	-0.443000	0.07180	0.462000	0.41574	GCG	.	.		0.697	ZNF517-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382642.1	XM_291261		T	146033090	C	T	146033090	2	4	23	1	0	0	0	0	0	0	0	1	17976	776	27	1		1	ZNF517	8	146033090	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	280142	146033090	330932	517	2583										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2047346	2047346	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccgcccgcggccgcagtgcCcgggccctcagtgccgcagc	15	20	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:2047346C>A	ENST00000382203.1	+	5	1117	c.908C>A	c.(907-909)cCc>cAc	p.P303H	SMARCA2_ENST00000382194.1_Missense_Mutation_p.P303H|SMARCA2_ENST00000349721.2_Missense_Mutation_p.P303H|SMARCA2_ENST00000357248.2_Missense_Mutation_p.P303H|RP11-264I13.2_ENST00000426860.1_RNA			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	303					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		gccgcAGTGCCCGGGCCCTCA	0.801																																					p.P303H		Atlas-SNP	.											.	SMARCA2	313	.	0			c.C908A						.						4	5	4					9																	2047346		1937	3815	5752	SO:0001583	missense	6595	exon5			CAGTGCCCGGGCC	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.908C>A	chr9.hg19:g.2047346C>A	ENSP00000371638:p.Pro303His	367.0	0.0		358.0	17.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	C	17.91	3.505499	0.64410	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000450198;ENST00000382203;ENST00000382194	D;D;T;D;D	0.87256	-2.23;-2.23;0.7;-2.23;-2.23	5.72	4.82	0.62117	.	0.844539	0.10410	N	0.677990	D	0.83514	0.5271	L	0.38175	1.15	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.75731	-0.3215	10	0.66056	D	0.02	-9.6039	14.4802	0.67576	0.0:0.9288:0.0:0.0712	.	303;303	P51531-2;P51531	.;SMCA2_HUMAN	H	303	ENSP00000265773:P303H;ENSP00000349788:P303H;ENSP00000392081:P303H;ENSP00000371638:P303H;ENSP00000371629:P303H	ENSP00000265773:P303H	P	+	2	0	SMARCA2	2037346	1.000000	0.71417	0.532000	0.27989	0.390000	0.30446	3.327000	0.52045	1.435000	0.47434	0.551000	0.68910	CCC	.	.		0.801	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2047346	C	A	2047346	3	1	23	1	0	0	0	0	1	0	0	0	14784	623	22	3	922	3	SMARCA2	9	2047346	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10		2047346	139166085	518	2584										
GLIS3	169792	hgsc.bcm.edu	37	chr9	4118184	4118184	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcccgggaactcctccaggcGttcggtcttgaacaggccgg	14	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:4118184G>A	ENST00000324333.10	-	3	1022	c.829C>T	c.(829-831)Cgc>Tgc	p.R277C	GLIS3_ENST00000381971.3_Missense_Mutation_p.R432C	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	277					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TCCTCCAGGCGTTCGGTCTTG	0.726																																					p.R432C		Atlas-SNP	.											.	GLIS3	152	.	0			c.C1294T						.						6	8	7					9																	4118184		1687	3372	5059	SO:0001583	missense	169792	exon4			CCAGGCGTTCGGT	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"Zinc fingers, C2H2-type"	28510	protein-coding gene	gene with protein product		610192	"zinc finger protein 515"	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.829C>T	chr9.hg19:g.4118184G>A	ENSP00000325494:p.Arg277Cys	114.0	0.0		111.0	42.0	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	hg19	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.688228	0.48097	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.11604	2.78;2.76	5.51	5.51	0.81932	.	0.000000	0.45606	D	0.000358	T	0.12518	0.0304	M	0.63428	1.95	0.37725	D	0.925057	B;B	0.21381	0.055;0.033	B;B	0.12156	0.007;0.003	T	0.04522	-1.0945	10	0.51188	T	0.08	.	8.7194	0.34432	0.0757:0.0:0.7731:0.1512	.	432;277	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	C	277;432	ENSP00000325494:R277C;ENSP00000371398:R432C	ENSP00000325494:R277C	R	-	1	0	GLIS3	4108184	0.998000	0.40836	1.000000	0.80357	0.688000	0.40055	3.821000	0.55700	2.583000	0.87209	0.655000	0.94253	CGC	.	.		0.726	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		A	4118184	G	A	4118184	3	1	23	1	0	0	0	0	1	0	0	0	6455	1145	40	1	1530	1	GLIS3	9	4118184	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2070838	4118184	137095247	519	2585										
KIAA1432	57589	hgsc.bcm.edu	37	chr9	5772941	5772941	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtgcctagactggtgcatcGttataggcctgattcttaga	12	8	1	3	rs565348578		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:5772941G>A	ENST00000414202.2	+	25	4035	c.3844G>A	c.(3844-3846)Gtt>Att	p.V1282I	KIAA1432_ENST00000449720.2_Missense_Mutation_p.V1166I|KIAA1432_ENST00000418622.3_Missense_Mutation_p.V1203I	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		CTGGTGCATCGTTATAGGCCT	0.358													G|||	1	0.000199681	0	0	5008	,	,		17787	0		0	False		,,,				2504	0.001				p.V1282I		Atlas-SNP	.											.	KIAA1432	97	.	0			c.G3844A						.						114	107	110					9																	5772941		2203	4300	6503	SO:0001583	missense	57589	exon25			TGCATCGTTATAG																												ENST00000414202.2:c.3844G>A	chr9.hg19:g.5772941G>A	ENSP00000416696:p.Val1282Ile	93.0	0.0		88.0	35.0	NM_020829		Missense_Mutation	SNP	ENST00000414202.2	hg19	CCDS34982.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.92|11.92	1.781261|1.781261	0.31502|0.31502	.|.	.|.	ENSG00000107036|ENSG00000107036	ENST00000545641|ENST00000414202;ENST00000418622;ENST00000449720;ENST00000490816	.|.	.|.	.|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.125811	.|0.53938	.|D	.|0.000053	T|T	0.40322|0.40322	0.1112|0.1112	N|N	0.21583|0.21583	0.68|0.68	0.80722|0.80722	D|D	1|1	.|B;B	.|0.16166	.|0.016;0.016	.|B;B	.|0.09377	.|0.004;0.004	T|T	0.25606|0.25606	-1.0127|-1.0127	5|9	.|0.27785	.|T	.|0.31	-17.6829|-17.6829	9.3842|9.3842	0.38333|0.38333	0.1974:0.0:0.8026:0.0|0.1974:0.0:0.8026:0.0	.|.	.|1166;1282	.|B7ZM67;Q4ADV7	.|.;RIC1_HUMAN	H|I	1173|1282;1203;1166;101	.|.	.|ENSP00000416696:V1282I	R|V	+|+	2|1	0|0	KIAA1432|KIAA1432	5762941|5762941	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.991000|0.991000	0.79684|0.79684	3.349000|3.349000	0.52217|0.52217	2.590000|2.590000	0.87494|0.87494	0.555000|0.555000	0.69702|0.69702	CGT|GTT	.	.		0.358	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3			A	5772941	G	A	5772941	3	1	23	1	0	0	0	0	1	0	0	0	8242	1145	40	1	3775	1	KIAA1432	9	5772941	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1654757	5772941	135440490	520	2586										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8521421	8521421	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttcaggtgtcagatcttctgCccccaacatccactttacat							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:8521421delC	ENST00000381196.4	-	17	1360	c.817delG	c.(817-819)gcafs	p.A273fs	PTPRD_ENST00000397611.3_Frame_Shift_Del_p.A270fs|PTPRD_ENST00000537002.1_Frame_Shift_Del_p.A270fs|PTPRD_ENST00000360074.4_Frame_Shift_Del_p.A260fs|PTPRD_ENST00000397606.3_Frame_Shift_Del_p.A263fs|PTPRD_ENST00000358503.5_Frame_Shift_Del_p.A260fs|PTPRD_ENST00000355233.5_Frame_Shift_Del_p.A273fs|PTPRD_ENST00000486161.1_Frame_Shift_Del_p.A273fs|PTPRD_ENST00000397617.3_Frame_Shift_Del_p.A263fs|PTPRD_ENST00000540109.1_Frame_Shift_Del_p.A273fs|PTPRD_ENST00000356435.5_Frame_Shift_Del_p.A273fs	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	273	Ig-like C2-type 3.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		AGATCTTCTGCCCCCAACATC	0.453										TSP Lung(15;0.13)																											p.A273fs		Atlas-Indel,Pindel	.											.	PTPRD	1348	.	0			c.818delC						.						178	158	165					9																	8521421		2203	4300	6503	SO:0001589	frameshift_variant	5789	exon9			.	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.817delG	chr9.hg19:g.8521421delC	ENSP00000370593:p.Ala273fs	96.0	0.0		85.0	35.0	NM_130391	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Frame_Shift_Del	DEL	ENST00000381196.4	hg19	CCDS43786.1																																																																																			.	.		0.453	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			-	8521421	C	-	8521421	7	5	23	1	0	1	0	1	0	0	0	0	12814	739	26	0	5097	0	PTPRD	9	8521421	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	2748480	8521421	132692010	521	2587										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13192209	13192209	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtggcacagttcgacgacagCacaccattgtcacttctata	8	12	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:13192209C>T	ENST00000319217.7	-	15	2136	c.1889G>A	c.(1888-1890)tGc>tAc	p.C630Y	MPDZ_ENST00000381022.2_Missense_Mutation_p.C630Y|MPDZ_ENST00000381015.4_Missense_Mutation_p.C630Y|MPDZ_ENST00000447879.1_Missense_Mutation_p.C630Y|MPDZ_ENST00000536827.1_Missense_Mutation_p.C630Y|MPDZ_ENST00000546205.1_Missense_Mutation_p.C630Y|MPDZ_ENST00000541718.1_Missense_Mutation_p.C630Y	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	630	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TCGACGACAGCACACCATTGT	0.398																																					p.C630Y		Atlas-SNP	.											.	MPDZ	324	.	0			c.G1889A						.						132	123	126					9																	13192209		1926	4138	6064	SO:0001583	missense	8777	exon15			CGACAGCACACCA	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.1889G>A	chr9.hg19:g.13192209C>T	ENSP00000320006:p.Cys630Tyr	110.0	0.0		110.0	39.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	C	24.9	4.580177	0.86645	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13;1.13;1.13	5.77	5.77	0.91146	.	0.000000	0.49305	D	0.000160	T	0.71710	0.3372	M	0.86953	2.85	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.75838	-0.3176	10	0.87932	D	0	.	19.9915	0.97366	0.0:1.0:0.0:0.0	.	630;630;630	B7ZMI4;O75970-3;O75970-2	.;.;.	Y	630	ENSP00000320006:C630Y;ENSP00000439807:C630Y;ENSP00000370410:C630Y;ENSP00000444151:C630Y;ENSP00000415208:C630Y;ENSP00000370403:C630Y;ENSP00000446358:C630Y	ENSP00000320006:C630Y	C	-	2	0	MPDZ	13182209	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	7.487000	0.81328	2.723000	0.93209	0.655000	0.94253	TGC	.	.		0.398	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		T	13192209	C	T	13192209	3	4	23	1	0	0	0	0	1	0	0	0	9731	710	25	3	4364	3	MPDZ	9	13192209	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	4670788	13192209	128021222	522	2588										
ACO1	48	hgsc.bcm.edu	37	chr9	32450103	32450103	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tacatgatccgcaagatggcCaagtaggagacgtgcacttg	12	9	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:32450103C>G	ENST00000309951.6	+	21	2802	c.2664C>G	c.(2662-2664)gcC>gcG	p.A888A	ACO1_ENST00000379923.1_Silent_p.A888A|ACO1_ENST00000541043.1_Silent_p.A789A	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	888					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		GCAAGATGGCCAAGTAGGAGA	0.607																																					p.A888A		Atlas-SNP	.											.	ACO1	149	.	0			c.C2664G						.						106	95	98					9																	32450103		2203	4300	6503	SO:0001819	synonymous_variant	48	exon21			GATGGCCAAGTAG	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.2664C>G	chr9.hg19:g.32450103C>G		163.0	0.0		130.0	60.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	hg19	CCDS6525.1																																																																																			.	.		0.607	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		G	32450103	C	G	32450103	2	3	23	1	0	0	0	0	0	0	0	1	146	581	21	4		4	ACO1	9	32450103	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	19257894	32450103	108763328	523	2589										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35399263	35399263	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagaggatgattgttctgccCccactcactgaccagacggt	11	12	2	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:35399263C>A	ENST00000378495.3	+	33	4155	c.3933C>A	c.(3931-3933)ccC>ccA	p.P1311P	UNC13B_ENST00000396787.1_Silent_p.P1323P|UNC13B_ENST00000378496.4_Silent_p.P1311P	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1311	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TTGTTCTGCCCCCACTCACTG	0.562																																					p.P1311P		Atlas-SNP	.											.	UNC13B	153	.	0			c.C3933A						.						190	167	175					9																	35399263		2203	4300	6503	SO:0001819	synonymous_variant	10497	exon33			TCTGCCCCCACTC	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.3933C>A	chr9.hg19:g.35399263C>A		138.0	0.0		147.0	53.0	NM_006377	Q5VYM8	Silent	SNP	ENST00000378495.3	hg19	CCDS6579.1																																																																																			.	.		0.562	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		A	35399263	C	A	35399263	2	1	23	1	0	0	0	0	0	0	0	1	17000	610	22	3		3	UNC13B	9	35399263	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2949160	35399263	105814168	524	2590										
RUSC2	9853	hgsc.bcm.edu	37	chr9	35558293	35558293	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgctggaggatgggctcaagGcctttgtactggacgtcatc	14	9	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:35558293G>A	ENST00000455600.1	+	7	3729	c.3160G>A	c.(3160-3162)Gcc>Acc	p.A1054T		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1054	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			TGGGCTCAAGGCCTTTGTACT	0.592																																					p.A1054T		Atlas-SNP	.											.	RUSC2	88	.	0			c.G3160A						.						102	89	94					9																	35558293		2203	4300	6503	SO:0001583	missense	9853	exon7			CTCAAGGCCTTTG	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.3160G>A	chr9.hg19:g.35558293G>A	ENSP00000393922:p.Ala1054Thr	64.0	0.0		53.0	11.0	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Missense_Mutation	SNP	ENST00000455600.1	hg19	CCDS35008.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.019289	0.75275	.	.	ENSG00000198853	ENST00000361226;ENST00000455600	T;T	0.30182	1.54;1.54	5.72	2.75	0.32379	RUN (2);	0.235880	0.42053	D	0.000764	T	0.28366	0.0701	L	0.44542	1.39	0.47183	D	0.999348	B	0.31752	0.338	B	0.37015	0.239	T	0.05699	-1.0869	10	0.59425	D	0.04	-6.8154	9.9291	0.41512	0.0:0.1246:0.4483:0.4271	.	1054	Q8N2Y8	RUSC2_HUMAN	T	1054	ENSP00000355177:A1054T;ENSP00000393922:A1054T	ENSP00000355177:A1054T	A	+	1	0	RUSC2	35548293	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	2.263000	0.43293	0.283000	0.22279	0.655000	0.94253	GCC	.	.		0.592	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		A	35558293	G	A	35558293	3	1	23	1	0	0	0	0	1	0	0	0	13766	1203	42	3	3182	3	RUSC2	9	35558293	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	159030	35558293	105655138	525	2591										
CA9	768	hgsc.bcm.edu	37	chr9	35674060	35674060	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actgctgcttctggtgcctgTccatccccagaggttgcccc	10	16	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:35674060T>G	ENST00000378357.4	+	1	208	c.104T>G	c.(103-105)gTc>gGc	p.V35G	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	35					bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	CTGGTGCCTGTCCATCCCCAG	0.647																																					p.V35G		Atlas-SNP	.											.	CA9	48	.	0			c.T104G						.						61	56	57					9																	35674060		2203	4300	6503	SO:0001583	missense	768	exon1			TGCCTGTCCATCC	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"Carbonic anhydrases"	1383	protein-coding gene	gene with protein product	"carbonic dehydratase", "RCC-associated protein G250"	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.104T>G	chr9.hg19:g.35674060T>G	ENSP00000367608:p.Val35Gly	84.0	0.0		91.0	32.0	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	hg19	CCDS6585.1	.	.	.	.	.	.	.	.	.	.	T	6.793	0.515345	0.12944	.	.	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.63417	-0.04	5.01	0.922	0.19408	.	1.897240	0.02339	N	0.074648	T	0.45558	0.1348	N	0.14661	0.345	0.29156	N	0.878054	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40365	-0.9567	10	0.72032	D	0.01	.	4.4005	0.11385	0.0:0.5452:0.1616:0.2932	.	35;35	F5H404;Q16790	.;CAH9_HUMAN	G	35	ENSP00000367608:V35G	ENSP00000367608:V35G	V	+	2	0	CA9	35664060	0.116000	0.22171	0.979000	0.43373	0.020000	0.10135	0.458000	0.21892	0.001000	0.14605	-2.130000	0.00343	GTC	.	.		0.647	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216		G	35674060	T	G	35674060	3	3	23	1	0	0	0	0	1	0	0	0	2526	1667	58	5	106	5	CA9	9	35674060	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	115767	35674060	105539371	526	2592										
TLN1	7094	hgsc.bcm.edu	37	chr9	35705588	35705588	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccgctgcaggcttggcctccGaggccagacggccatagtca	13	15	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:35705588G>A	ENST00000314888.9	-	43	6046	c.5693C>T	c.(5692-5694)tCg>tTg	p.S1898L	TLN1_ENST00000540444.1_Intron|TLN1_ENST00000464379.1_Intron	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1898	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CTTGGCCTCCGAGGCCAGACG	0.577																																					p.S1898L		Atlas-SNP	.											.	TLN1	185	.	0			c.C5693T						.						61	63	62					9																	35705588		2203	4299	6502	SO:0001583	missense	7094	exon43			GCCTCCGAGGCCA	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.5693C>T	chr9.hg19:g.35705588G>A	ENSP00000316029:p.Ser1898Leu	80.0	0.0		80.0	37.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	G	5.199	0.222180	0.09863	.	.	ENSG00000137076	ENST00000314888	T	0.14640	2.49	5.66	1.26	0.21427	Vinculin-binding site-containing domain (1);	0.834466	0.11111	N	0.598613	T	0.07369	0.0186	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39781	-0.9597	10	0.27082	T	0.32	-0.6165	5.1951	0.15232	0.3907:0.0:0.446:0.1633	.	1898	Q9Y490	TLN1_HUMAN	L	1898	ENSP00000316029:S1898L	ENSP00000316029:S1898L	S	-	2	0	TLN1	35695588	0.400000	0.25295	0.336000	0.25522	0.931000	0.56810	0.836000	0.27545	0.342000	0.23796	0.555000	0.69702	TCG	.	.		0.577	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35705588	G	A	35705588	3	1	23	1	0	0	0	0	1	0	0	0	15962	1059	37	1	1992	1	TLN1	9	35705588	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	31528	35705588	105507843	527	2593										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37707440	37707440	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gttgctgcagctgatgggccCgccaggaacccaactcagac	12	14	1	2	rs139243880	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:37707440C>T	ENST00000539465.1	+	3	722	c.129C>T	c.(127-129)ccC>ccT	p.P43P	FRMPD1_ENST00000377765.3_Silent_p.P43P|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	43						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CTGATGGGCCCGCCAGGAACC	0.498													C|||	2	0.000399361	0	0	5008	,	,		18943	0		0.001	False		,,,				2504	0.001				p.P43P		Atlas-SNP	.											.	FRMPD1	237	.	0			c.C129T						.	C		0,4406		0,0,2203	91	93	92		129	0.8	0.1	9	dbSNP_134	92	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FRMPD1	NM_014907.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		43/1579	37707440	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	22844	exon3			TGGGCCCGCCAGG	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.129C>T	chr9.hg19:g.37707440C>T		115.0	0.0		155.0	68.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	hg19	CCDS6612.1																																																																																			.	C|1.000;T|0.000		0.498	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		T	37707440	C	T	37707440	2	4	23	1	0	0	0	0	0	0	0	1	6065	639	23	1		1	FRMPD1	9	37707440	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2001852	37707440	103505991	528	2594										
MCART1	92014	hgsc.bcm.edu	37	chr9	37888305	37888305	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aatgggggaaggattccacgAtacaaatttcgaaatccatc	9	8	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:37888305A>T	ENST00000377716.2	-	3	986	c.243T>A	c.(241-243)taT>taA	p.Y81*	SLC25A51_ENST00000242275.6_Nonsense_Mutation_p.Y81*|SLC25A51_ENST00000496760.1_Intron|SLC25A51_ENST00000380590.3_Nonsense_Mutation_p.Y81*|RP11-613M10.9_ENST00000540557.1_Intron			Q9H1U9	S2551_HUMAN	solute carrier family 25, member 51	81					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											GGATTCCACGATACAAATTTC	0.448																																					p.Y81X		Atlas-SNP	.											.	.	.	.	0			c.T243A						.						119	106	110					9																	37888305		2203	4300	6503	SO:0001587	stop_gained	92014	exon3			TCCACGATACAAA	BC008500	CCDS6614.1	9p13.3-p12	2013-05-22	2012-03-29	2012-03-29	ENSG00000122696	ENSG00000122696		"Solute carriers"	23323	protein-coding gene	gene with protein product			"mitochondrial carrier triple repeat 1"	MCART1		12477932	Standard	NM_033412		Approved	MGC14836, CG7943	uc004aav.2	Q9H1U9	OTTHUMG00000019935	ENST00000377716.2:c.243T>A	chr9.hg19:g.37888305A>T	ENSP00000366945:p.Tyr81*	144.0	0.0		159.0	52.0	NM_033412		Nonsense_Mutation	SNP	ENST00000377716.2	hg19	CCDS6614.1	.	.	.	.	.	.	.	.	.	.	.	41	8.893163	0.98992	.	.	ENSG00000122696	ENST00000380590;ENST00000377716;ENST00000242275	.	.	.	4.94	-3.85	0.04243	.	0.078063	0.53938	D	0.000059	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7727	0.69691	0.2702:0.0:0.7298:0.0	.	.	.	.	X	81	.	ENSP00000242275:Y81X	Y	-	3	2	MCART1	37878305	0.979000	0.34478	0.988000	0.46212	0.918000	0.54935	0.140000	0.16056	-0.554000	0.06150	-0.361000	0.07541	TAT	.	.		0.448	SLC25A51-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313746.1	NM_033412		T	37888305	A	T	37888305	4	4	23	1	0	0	0	0	0	1	0	0	9378	340	12	4	654	4	MCART1	9	37888305	Nonsense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	180865	37888305	103325126	529	2595										
FAM75A1	647060	hgsc.bcm.edu	37	chr9	39361342	39361342	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgagagccaaaaaacagtgAaaaacagatcatgtgtgtac							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:39361342delA	ENST00000377647.3	+	4	3609	c.3580delA	c.(3580-3582)aaafs	p.K1194fs		NM_001085452.1	NP_001078921.1	Q5TZJ5	S31A1_HUMAN	SPATA31 subfamily A, member 1	1194					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AAAAACAGTGAAAAACAGATC	0.448																																					p.V1193fs		Atlas-INDEL	.											.	.	.	.	0			c.3579delG						.						1	1	1					9																	39361342		77	181	258	SO:0001589	frameshift_variant	647060	exon4			.		CCDS43808.1	9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000204849	ENSG00000204849			23394	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 36", "family with sequence similarity 75, member A1"	C9orf36, FAM75A1		20850414	Standard	XM_006716851		Approved	DKFZP434B204, C9orf36A, OTTHUMG00000013156		Q5TZJ5	OTTHUMG00000013156	ENST00000377647.3:c.3580delA	chr9.hg19:g.39361342delA	ENSP00000366875:p.Lys1194fs	146.0	0.0		163.0	28.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000377647.3	hg19	CCDS43808.1																																																																																			.	.		0.448	SPATA31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036910.1	NM_001085452		-	39361342	A	-	39361342	7	5	23	1	0	1	0	1	0	0	0	0	5627	247	9	0	3594	0	FAM75A1	9	39361342	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	1473037	39361342	101852089	530	2596										
FAM75A1	642265	hgsc.bcm.edu	37	chr9	39890593	39890593	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgagagccaaaaaacagtgAaaaacagatcatgtgtgtac							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:39890593delA	ENST00000456183.2	+	4	3609	c.3580delA	c.(3580-3582)aaafs	p.K1194fs		NM_001040065.1	NP_001035154.1	Q5RGS2	S31A2_HUMAN	SPATA31 subfamily A, member 2	1194					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AAAAACAGTGAAAAACAGATC	0.448																																					p.V1193fs		Atlas-INDEL	.											.	.	.	.	0			c.3579delG						.						1	1	1					9																	39890593		1	3	4	SO:0001589	frameshift_variant	647060	exon4			.			9p13.1	2012-10-15	2012-10-12	2012-10-12	ENSG00000204848				32002	protein-coding gene	gene with protein product			"family with sequence similarity 75, member A2"	FAM75A2		20850414	Standard			Approved	OTTHUMG00000013563	uc004abm.3	Q5RGS2	OTTHUMG00000013563	ENST00000456183.2:c.3580delA	chr9.hg19:g.39890593delA	ENSP00000406957:p.Lys1194fs	119.0	0.0		139.0	34.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000456183.2	hg19	CCDS43809.1																																																																																			.	.		0.448	SPATA31A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037739.1	NM_001040065		-	39890593	A	-	39890593	7	5	23	1	0	1	0	1	0	0	0	0	5627	247	9	0	7654	0	FAM75A1	9	39890593	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	529251	39890593	101322838	531	2597										
C9orf135	138255	hgsc.bcm.edu	37	chr9	72435841	72435841	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggactggtgcgacaggaagCaacactggttggagatcgga	16	7	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:72435841C>T	ENST00000377197.3	+	1	133	c.46C>T	c.(46-48)Caa>Taa	p.Q16*	C9orf135_ENST00000527647.1_Nonsense_Mutation_p.Q16*|C9orf135_ENST00000466872.2_3'UTR|C9orf135-AS1_ENST00000439418.1_lincRNA	NM_001010940.1	NP_001010940.1	Q5VTT2	CI135_HUMAN	chromosome 9 open reading frame 135	16						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						CGACAGGAAGCAACACTGGTT	0.592																																					p.Q16X		Atlas-SNP	.											.	C9orf135	25	.	0			c.C46T						.						76	66	69					9																	72435841		2203	4300	6503	SO:0001587	stop_gained	138255	exon1			AGGAAGCAACACT		CCDS35041.1	9q21.11	2013-06-07	2013-06-07	2013-06-07	ENSG00000204711	ENSG00000204711			31422	protein-coding gene	gene with protein product							Standard	XM_005251705		Approved		uc004ahl.3	Q5VTT2	OTTHUMG00000019985	ENST00000377197.3:c.46C>T	chr9.hg19:g.72435841C>T	ENSP00000366402:p.Gln16*	84.0	0.0		82.0	24.0	NM_001010940	A7E2U4|B2RN61	Nonsense_Mutation	SNP	ENST00000377197.3	hg19	CCDS35041.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.123022	0.56613	.	.	ENSG00000204711	ENST00000377197;ENST00000527647	.	.	.	4.5	-1.42	0.08913	.	1.087950	0.07217	N	0.860239	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-8.5176	10.4441	0.44483	0.1434:0.2605:0.5961:0.0	.	.	.	.	X	16	.	ENSP00000366402:Q16X	Q	+	1	0	C9orf135	71625661	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.284000	0.08422	-0.054000	0.13266	-0.176000	0.13171	CAA	.	.		0.592	C9orf135-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052591.1	NM_001010940		T	72435841	C	T	72435841	4	4	23	1	0	0	0	0	0	1	0	0	2460	711	25	3	48	3	C9orf135	9	72435841	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	32545248	72435841	68777590	532	2598										
ALDH1A1	216	hgsc.bcm.edu	37	chr9	75567885	75567885	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcttcaaatcggtgagtaggAcaggtaagtctggcgtgcct	13	8	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:75567885A>T	ENST00000297785.3	-	1	86	c.32T>A	c.(31-33)gTc>gAc	p.V11D	ALDH1A1_ENST00000482210.1_5'Flank|ALDH1A1_ENST00000376939.1_Missense_Mutation_p.V11D	NM_000689.4	NP_000680.2	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1 family, member A1	11					cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|positive regulation of Ras GTPase activity (GO:0032320)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|androgen binding (GO:0005497)|Ras GTPase activator activity (GO:0005099)|retinal dehydrogenase activity (GO:0001758)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)	17					Tretinoin(DB00755)|Vitamin A(DB00162)	GGTGAGTAGGACAGGTAAGTC	0.418																																					p.V11D		Atlas-SNP	.											.	ALDH1A1	98	.	0			c.T32A						.						116	105	109					9																	75567885		2203	4299	6502	SO:0001583	missense	216	exon1			AGTAGGACAGGTA	K03000	CCDS6644.1	9q21.13	2010-08-05			ENSG00000165092	ENSG00000165092	1.2.1.36, 1.2.1.3	"Aldehyde dehydrogenases"	402	protein-coding gene	gene with protein product	"retinaldehyde dehydrogenase 1"	100640		PUMB1, ALDH1		1709013	Standard	NM_000689		Approved	RALDH1	uc004ajd.3	P00352	OTTHUMG00000020019	ENST00000297785.3:c.32T>A	chr9.hg19:g.75567885A>T	ENSP00000297785:p.Val11Asp	136.0	0.0		142.0	51.0	NM_000689	O00768|Q5SYR1	Missense_Mutation	SNP	ENST00000297785.3	hg19	CCDS6644.1	.	.	.	.	.	.	.	.	.	.	A	5.234	0.228572	0.09916	.	.	ENSG00000165092	ENST00000297785;ENST00000376939;ENST00000428593;ENST00000419959;ENST00000446946	T;T;T;T	0.76060	-0.99;-0.34;-0.27;0.01	5.96	-11.3	0.00108	Aldehyde/histidinol dehydrogenase (1);	1.017990	0.07854	N	0.965112	T	0.51601	0.1684	N	0.03608	-0.345	0.23806	N	0.996792	B	0.18968	0.032	B	0.15484	0.013	T	0.50065	-0.8871	10	0.33141	T	0.24	.	24.0269	0.99987	0.0905:0.0:0.8261:0.0834	.	11	P00352	AL1A1_HUMAN	D	11;11;25;11;11	ENSP00000297785:V11D;ENSP00000366138:V11D;ENSP00000388026:V11D;ENSP00000401361:V11D	ENSP00000297785:V11D	V	-	2	0	ALDH1A1	74757705	0.125000	0.22332	0.001000	0.08648	0.118000	0.20060	-0.686000	0.05161	-2.366000	0.00606	-1.054000	0.02325	GTC	.	.		0.418	ALDH1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052679.1			T	75567885	A	T	75567885	3	4	23	1	0	0	0	0	1	0	0	0	490	275	10	4	1525	4	ALDH1A1	9	75567885	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3132044	75567885	65645546	533	2599										
TLE4	7091	hgsc.bcm.edu	37	chr9	82333837	82333837	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggctgcgtcaaggtctgggAcatcagccacccaggcaata	13	12	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:82333837A>T	ENST00000376552.2	+	15	2559	c.1541A>T	c.(1540-1542)gAc>gTc	p.D514V	TLE4_ENST00000376544.3_Missense_Mutation_p.D445V|TLE4_ENST00000265284.6_Missense_Mutation_p.D489V|TLE4_ENST00000376537.4_Missense_Mutation_p.D546V|TLE4_ENST00000376520.4_Missense_Mutation_p.D546V|TLE4_ENST00000376534.4_Missense_Mutation_p.D151V	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	514					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						AAGGTCTGGGACATCAGCCAC	0.552																																					p.D514V		Atlas-SNP	.											.	TLE4	187	.	0			c.A1541T						.						109	108	109					9																	82333837		2203	4300	6503	SO:0001583	missense	7091	exon15			TCTGGGACATCAG	M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"WD repeat domain containing"	11840	protein-coding gene	gene with protein product		605132	"transducin-like enhancer of split 4, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.1541A>T	chr9.hg19:g.82333837A>T	ENSP00000365735:p.Asp514Val	122.0	0.0		151.0	66.0	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	hg19	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	A	33	5.290764	0.95546	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000376537;ENST00000376534;ENST00000265284	T;T;T;T;T;T	0.17370	2.28;2.28;2.28;2.28;2.28;2.28	6.07	6.07	0.98685	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.49474	0.1559	M	0.87547	2.89	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.995;0.998;1.0;0.997	T	0.56613	-0.7950	10	0.87932	D	0	-27.0888	16.6288	0.85011	1.0:0.0:0.0:0.0	.	489;445;546;514	F8W6T6;Q04727-2;Q04727-3;Q04727	.;.;.;TLE4_HUMAN	V	514;445;546;546;151;489	ENSP00000365735:D514V;ENSP00000365727:D445V;ENSP00000365703:D546V;ENSP00000365720:D546V;ENSP00000365717:D151V;ENSP00000265284:D489V	ENSP00000265284:D489V	D	+	2	0	TLE4	81523657	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.326000	0.78906	0.533000	0.62120	GAC	.	.		0.552	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237		T	82333837	A	T	82333837	3	4	23	1	0	0	0	0	1	0	0	0	15956	275	10	4	1599	4	TLE4	9	82333837	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	6765952	82333837	58879594	534	2600										
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84607569	84607569	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctatctgtgtcagagagaatTcatggaccgttaaatatctc	8	8	4	2	rs145735905	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:84607569T>A	ENST00000344803.2	+	4	2231	c.2184T>A	c.(2182-2184)atT>atA	p.I728I		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	728					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CAGAGAGAATTCATGGACCGT	0.488																																					p.I728I		Atlas-SNP	.											.	.	.	.	0			c.T2184A						.						70	62	65					9																	84607569		1852	4099	5951	SO:0001819	synonymous_variant	389763	exon4			GAGAATTCATGGA		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.2184T>A	chr9.hg19:g.84607569T>A		330.0	0.0		342.0	139.0	NM_001001670		Silent	SNP	ENST00000344803.2	hg19	CCDS47986.1																																																																																			.	T|0.998;C|0.002		0.488	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84607569	T	A	84607569	2	1	23	1	0	0	0	0	0	0	0	1	5940	1771	62	4		4	FLJ46321	9	84607569	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2273732	84607569	56605862	535	2601										
KIF27	55582	hgsc.bcm.edu	37	chr9	86495341	86495341	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acactctgctctagctcattAgcacgtttctcattttggat	6	11	4	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:86495341A>G	ENST00000297814.2	-	11	2657	c.2514T>C	c.(2512-2514)gcT>gcC	p.A838A	KIF27_ENST00000376347.1_Silent_p.A229A|KIF27_ENST00000334204.2_Silent_p.A838A|KIF27_ENST00000413982.1_Intron	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	838					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						CTAGCTCATTAGCACGTTTCT	0.358																																					p.A838A		Atlas-SNP	.											.	KIF27	103	.	0			c.T2514C						.						211	189	197					9																	86495341		2203	4300	6503	SO:0001819	synonymous_variant	55582	exon11			CTCATTAGCACGT	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"Kinesins"	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.2514T>C	chr9.hg19:g.86495341A>G		50.0	0.0		60.0	27.0	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Silent	SNP	ENST00000297814.2	hg19	CCDS6665.1																																																																																			.	.		0.358	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		G	86495341	A	G	86495341	2	3	23	1	0	0	0	0	0	0	0	1	8305	407	15	2		2	KIF27	9	86495341	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1887772	86495341	54718090	536	2602										
LOC645961	645961	hgsc.bcm.edu	37	chr9	90747272	90747272	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaggaggagtgaagcctttcGgaggaggcggagagcaggcc	20	7	0	2	rs373582239		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:90747272G>A								U6 (134022 upstream) : U3 (241911 downstream)																							GAAGCCTTTCGGAGGAGGCGG	0.587																																					p.P227L		Atlas-SNP	.											.	.	.	.	0			c.C680T						.	G	LEU/PRO	2,1382		0,2,690	92	82	85		680	0.1	0	9		85	0,3182		0,0,1591	no	missense	FAM75C2	NM_001166137.1	98	0,2,2281	AA,AG,GG		0.0,0.1445,0.0438	probably-damaging	227/1135	90747272	2,4564	692	1591	2283	SO:0001628	intergenic_variant	645961	exon4			CCTTTCGGAGGAG																													chr9.hg19:g.90747272G>A		103.0	0.0		106.0	42.0	NM_001166137		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.587									A	90747272	G	A	90747272	1	1	23	0	1	0	0	0	0	0	0	0	8892	1116	39	1		1	LOC645961	9	90747272	IGR	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	4251931	90747272	50466159	537	2603										
NXNL2	158046	hgsc.bcm.edu	37	chr9	91150438	91150438	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctgcagaacaaggtggtggCactgtacttcgcggcggccc	15	12	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:91150438C>T	ENST00000375854.3	+	1	423	c.89C>T	c.(88-90)gCa>gTa	p.A30V	NXNL2_ENST00000487646.2_3'UTR|NXNL2_ENST00000375855.3_Missense_Mutation_p.A30V	NM_001161625.1	NP_001155097.1	Q5VZ03	NXNL2_HUMAN	nucleoredoxin-like 2	30	Thioredoxin.				photoreceptor cell maintenance (GO:0045494)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)					lung(3)	3						AAGGTGGTGGCACTGTACTTC	0.711																																					p.A30V		Atlas-SNP	.											.	NXNL2	13	.	0			c.C89T						.						32	36	34					9																	91150438		2200	4297	6497	SO:0001583	missense	158046	exon1			TGGTGGCACTGTA	BC022521	CCDS6679.1, CCDS55325.1	9q22.2	2008-02-05	2007-08-16	2007-08-16	ENSG00000130045	ENSG00000130045			30482	protein-coding gene	gene with protein product		615299	"chromosome 9 open reading frame 121"	C9orf121		12477932	Standard	NM_001161625		Approved		uc011ltj.2	Q5VZ03	OTTHUMG00000020170	ENST00000375854.3:c.89C>T	chr9.hg19:g.91150438C>T	ENSP00000365014:p.Ala30Val	171.0	0.0		122.0	50.0	NM_145283	B1AMD0|Q8TBG6	Missense_Mutation	SNP	ENST00000375854.3	hg19	CCDS55325.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.411271	0.83340	.	.	ENSG00000130045	ENST00000375854;ENST00000375855	T;T	0.80738	1.36;-1.41	3.95	3.0	0.34707	Thioredoxin-like fold (2);	0.194164	0.42420	D	0.000702	T	0.77136	0.4086	L	0.33293	1	0.44024	D	0.996742	P;D	0.62365	0.669;0.991	B;P	0.53593	0.355;0.73	T	0.75402	-0.3330	10	0.36615	T	0.2	-9.6255	10.7547	0.46230	0.0:0.5395:0.4605:0.0	.	30;30	Q5VZ03;Q5VZ03-3	NXNL2_HUMAN;.	V	30	ENSP00000365014:A30V;ENSP00000365015:A30V	ENSP00000365014:A30V	A	+	2	0	NXNL2	90340258	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	4.960000	0.63673	2.040000	0.60383	0.491000	0.48974	GCA	.	.		0.711	NXNL2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145283		T	91150438	C	T	91150438	3	4	23	1	0	0	0	0	1	0	0	0	10798	710	25	3	91	3	NXNL2	9	91150438	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	403166	91150438	50062993	538	2604										
S1PR3	1903	hgsc.bcm.edu	37	chr9	91617238	91617238	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgcagcacttcagaatgggAtcttctgcaactgatcgtct	9	11	4	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:91617238A>T	ENST00000375846.3	+	1	5818	c.1123A>T	c.(1123-1125)Atc>Ttc	p.I375F	S1PR3_ENST00000358157.2_Missense_Mutation_p.I375F			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	375					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						TCAGAATGGGATCTTCTGCAA	0.557																																					p.I375F		Atlas-SNP	.											.	S1PR3	49	.	0			c.A1123T						.						68	65	66					9																	91617238		2203	4300	6503	SO:0001583	missense	1903	exon2			AATGGGATCTTCT	AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3167	protein-coding gene	gene with protein product	"sphingosine-1-phosphate receptor 3"	601965	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.1123A>T	chr9.hg19:g.91617238A>T	ENSP00000365006:p.Ile375Phe	92.0	0.0		103.0	40.0	NM_005226	Q5SQD8|Q7Z5I2	Missense_Mutation	SNP	ENST00000375846.3	hg19	CCDS6680.1	.	.	.	.	.	.	.	.	.	.	A	7.650	0.682612	0.14907	.	.	ENSG00000213694	ENST00000358157;ENST00000375846	T;T	0.68903	-0.36;-0.36	5.07	-1.31	0.09230	.	0.891383	0.09228	N	0.831015	T	0.44644	0.1303	N	0.14661	0.345	0.23192	N	0.998142	B	0.26400	0.148	B	0.24541	0.054	T	0.30387	-0.9980	10	0.54805	T	0.06	.	5.8187	0.18516	0.587:0.1298:0.2832:0.0	.	375	Q99500	S1PR3_HUMAN	F	375	ENSP00000350878:I375F;ENSP00000365006:I375F	ENSP00000350878:I375F	I	+	1	0	S1PR3	90807058	0.072000	0.21174	0.280000	0.24747	0.027000	0.11550	0.123000	0.15708	-0.386000	0.07821	0.402000	0.26972	ATC	.	.		0.557	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226		T	91617238	A	T	91617238	3	4	23	1	0	0	0	0	1	0	0	0	13810	333	12	4	1125	4	S1PR3	9	91617238	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	466800	91617238	49596193	539	2605										
IARS	3376	hgsc.bcm.edu	37	chr9	95021242	95021242	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctcttctttaaagcggaggTtttctgctctcaccacaggg	9	12	4	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:95021242T>C	ENST00000375643.3	-	19	2176	c.1910A>G	c.(1909-1911)aAc>aGc	p.N637S	IARS_ENST00000443024.2_Missense_Mutation_p.N637S|IARS_ENST00000447699.2_Missense_Mutation_p.N527S|IARS_ENST00000375629.3_5'UTR	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	637					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	AAAGCGGAGGTTTTCTGCTCT	0.433																																					p.N637S		Atlas-SNP	.											.	IARS	74	.	0			c.A1910G						.						77	70	72					9																	95021242		2203	4300	6503	SO:0001583	missense	3376	exon19			CGGAGGTTTTCTG	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	5330	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 1, cytoplasmic"	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.1910A>G	chr9.hg19:g.95021242T>C	ENSP00000364794:p.Asn637Ser	86.0	0.0		78.0	33.0	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	hg19	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	T	12.80	2.045461	0.36085	.	.	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000447699;ENST00000375660	T;T;T	0.21031	2.03;2.03;2.03	5.45	5.45	0.79879	Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.85682	D	0.000000	T	0.25717	0.0626	M	0.69463	2.115	0.80722	D	1	B;B	0.32653	0.226;0.379	B;B	0.37091	0.241;0.241	T	0.04481	-1.0948	10	0.09338	T	0.73	-26.181	15.1695	0.72858	0.0:0.0:0.0:1.0	.	637;482	P41252;Q6P0M4	SYIC_HUMAN;.	S	637;637;527;637	ENSP00000364794:N637S;ENSP00000406448:N637S;ENSP00000415020:N527S	ENSP00000364794:N637S	N	-	2	0	IARS	94061063	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.004000	0.70709	2.072000	0.62099	0.459000	0.35465	AAC	.	.		0.433	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161		C	95021242	T	C	95021242	3	2	23	1	0	0	0	0	1	0	0	0	7482	1725	60	2	1942	2	IARS	9	95021242	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3404004	95021242	46192189	540	2606										
ECM2	1842	hgsc.bcm.edu	37	chr9	95263292	95263292	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttgggtagataggacgggaCgtgatagagcttgttgtagg	17	4	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:95263292C>T	ENST00000344604.5	-	9	1797	c.1648G>A	c.(1648-1650)Gtc>Atc	p.V550I	ECM2_ENST00000444490.2_Missense_Mutation_p.V528I|CENPP_ENST00000375587.3_Intron	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	550					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						TAGGACGGGACGTGATAGAGC	0.483																																					p.V550I		Atlas-SNP	.											.	ECM2	147	.	0			c.G1648A						.						141	129	133					9																	95263292		2203	4300	6503	SO:0001583	missense	1842	exon9			ACGGGACGTGATA	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"matrix glycoprotein SC1/ECM2"	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.1648G>A	chr9.hg19:g.95263292C>T	ENSP00000344758:p.Val550Ile	159.0	0.0		147.0	50.0	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Missense_Mutation	SNP	ENST00000344604.5	hg19	CCDS6698.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.439466	0.83885	.	.	ENSG00000106823	ENST00000444490;ENST00000344604	T;T	0.20332	2.08;5.7	5.35	5.35	0.76521	.	0.115628	0.64402	D	0.000016	T	0.37571	0.1008	L	0.39566	1.225	0.80722	D	1	D;D;D	0.69078	0.996;0.997;0.997	D;D;D	0.67103	0.949;0.945;0.946	T	0.01500	-1.1339	10	0.27785	T	0.31	.	19.4519	0.94871	0.0:1.0:0.0:0.0	.	550;528;528	O94769;B4DK93;O94769-2	ECM2_HUMAN;.;.	I	528;550	ENSP00000393971:V528I;ENSP00000344758:V550I	ENSP00000344758:V550I	V	-	1	0	ECM2	94303113	1.000000	0.71417	0.926000	0.36857	0.751000	0.42716	5.740000	0.68629	2.676000	0.91093	0.591000	0.81541	GTC	.	.		0.483	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393		T	95263292	C	T	95263292	3	4	23	1	0	0	0	0	1	0	0	0	4900	536	19	1	459	1	ECM2	9	95263292	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	242050	95263292	45950139	541	2607										
ZNF510	22869	hgsc.bcm.edu	37	chr9	99521523	99521523	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttctctgatgtattctgaggTttgacttctggccaaatgtt	9	7	3	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:99521523T>G	ENST00000375231.1	-	6	2239	c.1589A>C	c.(1588-1590)aAc>aCc	p.N530T	ZNF510_ENST00000223428.4_Missense_Mutation_p.N530T			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	530					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				TATTCTGAGGTTTGACTTCTG	0.403																																					p.N530T		Atlas-SNP	.											.	ZNF510	59	.	0			c.A1589C						.						161	161	161					9																	99521523		2203	4300	6503	SO:0001583	missense	22869	exon6			CTGAGGTTTGACT	AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"Zinc fingers, C2H2-type", "-"	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.1589A>C	chr9.hg19:g.99521523T>G	ENSP00000364379:p.Asn530Thr	101.0	0.0		91.0	6.0	NM_014930	Q5SZP5	Missense_Mutation	SNP	ENST00000375231.1	hg19	CCDS35074.1	.	.	.	.	.	.	.	.	.	.	T	8.090	0.774401	0.16051	.	.	ENSG00000081386	ENST00000375231;ENST00000223428	T;T	0.22134	1.97;1.97	3.02	0.676	0.17958	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09555	0.0235	N	0.12961	0.28	0.09310	N	1	B	0.33103	0.397	B	0.29353	0.101	T	0.33727	-0.9857	9	0.21014	T	0.42	.	6.0406	0.19732	0.0:0.2425:0.0:0.7575	.	530	Q9Y2H8	ZN510_HUMAN	T	530	ENSP00000364379:N530T;ENSP00000223428:N530T	ENSP00000223428:N530T	N	-	2	0	ZNF510	98561344	0.000000	0.05858	0.923000	0.36655	0.978000	0.69477	0.141000	0.16076	0.120000	0.18254	0.533000	0.62120	AAC	.	.		0.403	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930		G	99521523	T	G	99521523	3	3	23	1	0	0	0	0	1	0	0	0	17969	1725	60	5	466	5	ZNF510	9	99521523	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	4258231	99521523	41691908	542	2608										
ZNF782	158431	hgsc.bcm.edu	37	chr9	99580289	99580289	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catttatcacatttatagggTttctcccctgtgtgagttct	7	9	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:99580289T>C	ENST00000481138.1	-	6	2677	c.2016A>G	c.(2014-2016)aaA>aaG	p.K672K	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Silent_p.K540K	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	672					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				ATTTATAGGGTTTCTCCCCTG	0.413																																					p.K672K		Atlas-SNP	.											.	ZNF782	64	.	0			c.A2016G						.						101	102	102					9																	99580289		2203	4300	6503	SO:0001819	synonymous_variant	158431	exon6			ATAGGGTTTCTCC	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"Zinc fingers, C2H2-type", "-"	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.2016A>G	chr9.hg19:g.99580289T>C		166.0	0.0		160.0	10.0	NM_001001662	B2RNR0	Silent	SNP	ENST00000481138.1	hg19	CCDS35075.1	.	.	.	.	.	.	.	.	.	.	t	7.291	0.611092	0.14066	.	.	ENSG00000196597	ENST00000289032	.	.	.	2.64	0.247	0.15521	.	.	.	.	.	T	0.51466	0.1676	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38067	-0.9678	4	.	.	.	.	5.8842	0.18872	0.0:0.2581:0.0:0.7419	.	.	.	.	A	661	.	.	T	-	1	0	ZNF782	98620110	0.001000	0.12720	0.991000	0.47740	0.996000	0.88848	-0.239000	0.08965	0.028000	0.15324	0.533000	0.62120	ACC	.	.		0.413	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		C	99580289	T	C	99580289	2	2	23	1	0	0	0	0	0	0	0	1	18170	1722	60	2		2	ZNF782	9	99580289	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	58766	99580289	41633142	543	2609										
FOXE1	2304	hgsc.bcm.edu	37	chr9	100617015	100617015	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	accggggcccggccggccaaCccctccgcctatgcggctgc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:100617015delC	ENST00000375123.3	+	1	1480	c.819delC	c.(817-819)aacfs	p.N273fs		NM_004473.3	NP_004464.2	O00358	FOXE1_HUMAN	forkhead box E1 (thyroid transcription factor 2)	273	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|cell migration (GO:0016477)|embryonic organ morphogenesis (GO:0048562)|hair follicle morphogenesis (GO:0031069)|hard palate development (GO:0060022)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pharynx development (GO:0060465)|positive regulation of transcription, DNA-templated (GO:0045893)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(62;0.158)				GGCCGGCCAACCCCTCCGCCT	0.791																																					p.N273fs		Atlas-Indel,Pindel	.											.	FOXE1	19	.	0			c.818delA						.						1	1	1					9																	100617015		636	1543	2179	SO:0001589	frameshift_variant	2304	exon1			.	U89995	CCDS35078.1	9q22	2008-09-05			ENSG00000178919	ENSG00000178919		"Forkhead boxes"	3806	protein-coding gene	gene with protein product		602617	"forkhead box E2"	FKHL15, TITF2, FOXE2		9169137, 9697705	Standard	NM_004473		Approved	TTF-2, HFKH4	uc004axu.3	O00358	OTTHUMG00000020333	ENST00000375123.3:c.819delC	chr9.hg19:g.100617015delC	ENSP00000364265:p.Asn273fs	234.0	0.0		162.0	29.0	NM_004473	O75765|Q5T109|Q99526	Frame_Shift_Del	DEL	ENST00000375123.3	hg19	CCDS35078.1																																																																																			.	.		0.791	FOXE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053341.1			-	100617015	C	-	100617015	7	5	23	1	0	1	0	1	0	0	0	0	6011	506	18	0	821	0	FOXE1	9	100617015	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	1036726	100617015	40596416	544	2610										
INVS	27130	hgsc.bcm.edu	37	chr9	103054739	103054739	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgagacagctggcgatgagCggtgtgcaaaggggaaaggc	19	6	0	2	rs370949695		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:103054739C>T	ENST00000262457.2	+	14	2385	c.2200C>T	c.(2200-2202)Cgg>Tgg	p.R734W	INVS_ENST00000541287.1_Missense_Mutation_p.R638W|INVS_ENST00000262456.2_Intron	NM_014425.3	NP_055240.2	Q9Y283	INVS_HUMAN	inversin	734					embryonic heart tube left/right pattern formation (GO:0060971)|kidney development (GO:0001822)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|pancreas development (GO:0031016)|post-embryonic development (GO:0009791)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Acute lymphoblastic leukemia(62;0.056)				TGGCGATGAGCGGTGTGCAAA	0.577																																					p.R734W		Atlas-SNP	.											INVS,NS,carcinoma,0,1	INVS	81	.	0			c.C2200T						.	C	TRP/ARG,	1,4405	2.1+/-5.4	0,1,2202	67	56	60		2200,	3.7	0	9		60	0,8600		0,0,4300	no	missense,intron	INVS	NM_014425.2,NM_183245.1	101,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,	734/1066,	103054739	1,13005	2203	4300	6503	SO:0001583	missense	27130	exon14			GATGAGCGGTGTG	AF039217	CCDS6746.1, CCDS6747.1	9q31	2013-01-10	2003-08-11		ENSG00000119509	ENSG00000119509		"Ankyrin repeat domain containing"	17870	protein-coding gene	gene with protein product	"nephrocystin 2"	243305	"nephronophthisis 2 (infantile)"	NPHP2		12872123	Standard	NM_014425		Approved		uc004bap.2	Q9Y283	OTTHUMG00000020364	ENST00000262457.2:c.2200C>T	chr9.hg19:g.103054739C>T	ENSP00000262457:p.Arg734Trp	250.0	0.0		223.0	91.0	NM_014425	A2A2Y2|Q2NKL0|Q5W0T6|Q8IVX8|Q9BRB9|Q9Y488|Q9Y498	Missense_Mutation	SNP	ENST00000262457.2	hg19	CCDS6746.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.686349	0.47991	2.27E-4	0.0	ENSG00000119509	ENST00000262457;ENST00000541287	T;T	0.41065	1.01;1.03	5.55	3.69	0.42338	.	1.744500	0.02657	N	0.107102	T	0.38799	0.1054	N	0.24115	0.695	0.09310	N	1	D;D	0.65815	0.995;0.964	P;B	0.46975	0.533;0.232	T	0.27640	-1.0068	10	0.72032	D	0.01	.	7.2451	0.26117	0.1671:0.7459:0.0:0.087	.	638;734	F5GZH2;Q9Y283	.;INVS_HUMAN	W	734;638	ENSP00000262457:R734W;ENSP00000444454:R638W	ENSP00000262457:R734W	R	+	1	2	INVS	102094560	0.055000	0.20627	0.011000	0.14972	0.199000	0.23934	4.128000	0.57951	0.680000	0.31366	0.650000	0.86243	CGG	.	.		0.577	INVS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053407.1	NM_014425		T	103054739	C	T	103054739	3	4	23	1	0	0	0	0	1	0	0	0	7796	759	27	1	2250	1	INVS	9	103054739	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2437724	103054739	38158692	545	2611										
LPPR1	54886	hgsc.bcm.edu	37	chr9	104079724	104079724	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgaggatccccgtggagtAcccctaatggctttcccaag	10	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:104079724A>G	ENST00000374874.3	+	7	1330	c.891A>G	c.(889-891)gtA>gtG	p.V297V	LPPR1_ENST00000395056.2_Silent_p.V297V	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		297					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										CCCGTGGAGTACCCCTAATGG	0.483																																					p.V297V		Atlas-SNP	.											.	.	.	.	0			c.A891G						.						122	129	127					9																	104079724		2203	4300	6503	SO:0001819	synonymous_variant	0	exon7			TGGAGTACCCCTA																												ENST00000374874.3:c.891A>G	chr9.hg19:g.104079724A>G		196.0	0.0		155.0	62.0	NM_207299	Q5VX23|Q9NXE2	Silent	SNP	ENST00000374874.3	hg19	CCDS6751.1																																																																																			.	.		0.483	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1			G	104079724	A	G	104079724	2	3	23	1	0	0	0	0	0	0	0	1	8933	378	14	2		2	LPPR1	9	104079724	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1024985	104079724	37133707	546	2612										
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104340102	104340102	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgcttttcctctataaatgAtgtatttattgctctgtgta	6	7	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:104340102A>T	ENST00000361820.3	-	8	3556	c.2956T>A	c.(2956-2958)Tca>Aca	p.S986T		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	986	PPP2CB binding site. {ECO:0000250}.				calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	TCTATAAATGATGTATTTATT	0.368																																					p.S986T		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T2956A						.						147	140	142					9																	104340102		2203	4300	6503	SO:0001583	missense	116443	exon8			TAAATGATGTATT		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2956T>A	chr9.hg19:g.104340102A>T	ENSP00000355155:p.Ser986Thr	63.0	0.0		45.0	12.0	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	A	8.832	0.940030	0.18281	.	.	ENSG00000198785	ENST00000361820	T	0.10477	2.87	5.64	5.64	0.86602	.	0.386476	0.24056	N	0.041955	T	0.10252	0.0251	L	0.39898	1.24	0.38326	D	0.943667	B	0.11235	0.004	B	0.08055	0.003	T	0.13098	-1.0522	10	0.09084	T	0.74	.	15.8494	0.78916	1.0:0.0:0.0:0.0	.	986	Q8TCU5	NMD3A_HUMAN	T	986	ENSP00000355155:S986T	ENSP00000355155:S986T	S	-	1	0	GRIN3A	103379923	0.999000	0.42202	0.999000	0.59377	0.996000	0.88848	3.981000	0.56902	2.148000	0.66965	0.533000	0.62120	TCA	.	.		0.368	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			T	104340102	A	T	104340102	3	4	23	1	0	0	0	0	1	0	0	0	6792	333	12	4	399	4	GRIN3A	9	104340102	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	260378	104340102	36873329	547	2613										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114176260	114176260	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaatagacagtacataaccGgcaaacctaaataagaattc	5	10	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:114176260G>A	ENST00000338205.5	-	19	2213	c.1994C>T	c.(1993-1995)cCg>cTg	p.P665L	RNA5SP294_ENST00000411306.1_RNA|KIAA0368_ENST00000259335.4_Missense_Mutation_p.P843L			Q5VYK3	ECM29_HUMAN	KIAA0368	671					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						GTACATAACCGGCAAACCTAA	0.353																																					p.P843L		Atlas-SNP	.											.	KIAA0368	144	.	0			c.C2528T						.						60	51	54					9																	114176260		1834	4087	5921	SO:0001583	missense	23392	exon21			ATAACCGGCAAAC	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1994C>T	chr9.hg19:g.114176260G>A	ENSP00000339889:p.Pro665Leu	80.0	0.0		91.0	23.0	NM_001080398	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	hg19		.	.	.	.	.	.	.	.	.	.	G	12.49	1.953603	0.34471	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	T	0.63417	-0.04	5.53	5.53	0.82687	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.51160	0.1658	L	0.44542	1.39	0.80722	D	1	B;B	0.32731	0.382;0.27	B;B	0.20384	0.029;0.015	T	0.51076	-0.8751	10	0.36615	T	0.2	.	14.3268	0.66526	0.0:0.0:0.8516:0.1484	.	671;140	Q5VYK3;B3KXF2	ECM29_HUMAN;.	L	665;843;140	ENSP00000259335:P843L	ENSP00000259335:P843L	P	-	2	0	KIAA0368	113216081	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.126000	0.77201	2.607000	0.88179	0.563000	0.77884	CCG	.	.		0.353	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		A	114176260	G	A	114176260	3	1	23	1	0	0	0	0	1	0	0	0	8180	1116	39	1	3649	1	KIAA0368	9	114176260	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	9836158	114176260	27037171	548	2614										
SLC46A2	57864	hgsc.bcm.edu	37	chr9	115648748	115648748	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcccatcctacctaattggAatgatggccaggaaggagag	11	10	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:115648748A>T	ENST00000374228.4	-	3	1593	c.1362T>A	c.(1360-1362)atT>atA	p.I454I	RP11-408O19.5_ENST00000605480.1_RNA	NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	454					negative regulation of T cell apoptotic process (GO:0070233)|regulation of T cell differentiation (GO:0045580)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(1)	18						ACCTAATTGGAATGATGGCCA	0.517																																					p.I454I		Atlas-SNP	.											.	SLC46A2	30	.	0			c.T1362A						.						111	106	108					9																	115648748		2203	4300	6503	SO:0001819	synonymous_variant	57864	exon3			AATTGGAATGATG	AF242557	CCDS6786.1	9q32	2013-05-22	2007-03-29	2007-03-29	ENSG00000119457	ENSG00000119457		"Solute carriers"	16055	protein-coding gene	gene with protein product		608956	"thymic stromal co-transporter"	TSCOT		10978518, 12826694	Standard	NM_033051		Approved	Ly110	uc004bgk.3	Q9BY10	OTTHUMG00000020513	ENST00000374228.4:c.1362T>A	chr9.hg19:g.115648748A>T		148.0	0.0		164.0	60.0	NM_033051	B1ALK1|Q86VT0|Q96NE2	Silent	SNP	ENST00000374228.4	hg19	CCDS6786.1																																																																																			.	.		0.517	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051		T	115648748	A	T	115648748	2	4	23	1	0	0	0	0	0	0	0	1	14660	242	9	4		4	SLC46A2	9	115648748	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1472488	115648748	25564683	549	2615										
ALAD	210	hgsc.bcm.edu	37	chr9	116153902	116153902	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttccagccgcttcacaccatAcctgtgtgggtgtgggtaga	12	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:116153902A>G	ENST00000409155.3	-	4	362	c.166T>C	c.(166-168)Tat>Cat	p.Y56H	ALAD_ENST00000482001.1_5'UTR|ALAD_ENST00000277315.5_Splice_Site_p.Y39H	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	56					cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1)	9					Aminolevulinic acid(DB00855)	TTCACACCATACCTGTGTGGG	0.587																																					p.Y56H		Atlas-SNP	.											.	ALAD	36	.	0			c.T166C						.						65	61	62					9																	116153902		2203	4300	6503	SO:0001630	splice_region_variant	210	exon4			CACCATACCTGTG	M13928	CCDS6794.2	9q32	2010-04-29	2010-04-29		ENSG00000148218	ENSG00000148218	4.2.1.24		395	protein-coding gene	gene with protein product	"porphobilinogen synthase"	125270	"aminolevulinate, delta-, dehydratase"			6839527, 6378062	Standard	NM_000031		Approved	ALADH, PBGS	uc011lxf.2	P13716	OTTHUMG00000020522	ENST00000409155.3:c.165-1T>C	chr9.hg19:g.116153902A>G		79.0	0.0		64.0	28.0	NM_000031	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Missense_Mutation	SNP	ENST00000409155.3	hg19	CCDS6794.2	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184733	0.78677	.	.	ENSG00000148218	ENST00000409155;ENST00000277315;ENST00000448137	D;D;D	0.87179	-2.22;-2.16;-2.22	5.65	5.65	0.86999	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.86343	0.5910	L	0.49778	1.585	0.80722	D	1	B;B;B	0.26935	0.015;0.054;0.164	B;B;B	0.37304	0.115;0.086;0.246	T	0.82798	-0.0279	10	0.28530	T	0.3	-7.3993	15.072	0.72046	1.0:0.0:0.0:0.0	.	56;39;85	P13716;B7Z3I9;P13716-2	HEM2_HUMAN;.;.	H	56;39;65	ENSP00000386284:Y56H;ENSP00000277315:Y39H;ENSP00000392748:Y65H	ENSP00000277315:Y39H	Y	-	1	0	ALAD	115193723	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	6.741000	0.74837	2.146000	0.66826	0.533000	0.62120	TAT	.	.		0.587	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945	Missense_Mutation	G	116153902	A	G	116153902	5	3	23	1	0	0	0	0	0	0	1	0	483	405	14	2	862	2	ALAD	9	116153902	Splice_Site	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	505154	116153902	25059529	550	2616										
PAPPA	5069	hgsc.bcm.edu	37	chr9	119130003	119130003	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aacgtgaccgtgcgtgacatCccccactggctgaaccccac							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:119130003delC	ENST00000328252.3	+	19	4944	c.4575delC	c.(4573-4575)atcfs	p.I1525fs	PAPPA_ENST00000534838.1_Frame_Shift_Del_p.I563fs	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1525	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						TGCGTGACATCCCCCACTGGC	0.572																																					p.I1525fs		Atlas-Indel,Pindel	.											.	PAPPA	243	.	0			c.4574delT						.						127	83	98					9																	119130003		2203	4300	6503	SO:0001589	frameshift_variant	5069	exon19			.		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.4575delC	chr9.hg19:g.119130003delC	ENSP00000330658:p.Ile1525fs	165.0	0.0		150.0	23.0	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Frame_Shift_Del	DEL	ENST00000328252.3	hg19	CCDS6813.1																																																																																			.	.		0.572	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		-	119130003	C	-	119130003	7	5	23	1	0	1	0	1	0	0	0	0	11441	845	30	0	4649	0	PAPPA	9	119130003	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	2976101	119130003	22083428	551	2617										
FBXW2	26190	hgsc.bcm.edu	37	chr9	123533666	123533666	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaagtcccactggtagagacCaagtgctgaactacagacaa	9	10	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:123533666C>T	ENST00000608872.1	-	7	1223	c.1036G>A	c.(1036-1038)Ggt>Agt	p.G346S	FBXW2_ENST00000493559.1_5'UTR|FBXW2_ENST00000340778.5_Missense_Mutation_p.G281S	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	346					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)			ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						TGGTAGAGACCAAGTGCTGAA	0.423																																					p.G346S		Atlas-SNP	.											.	FBXW2	34	.	0			c.G1036A						.						98	89	92					9																	123533666		1903	4127	6030	SO:0001583	missense	26190	exon7			AGAGACCAAGTGC	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"F-boxes / WD-40 domains", "WD repeat domain containing"	13608	protein-coding gene	gene with protein product		609071	"F-box and WD-40 domain protein 2"			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1036G>A	chr9.hg19:g.123533666C>T	ENSP00000476369:p.Gly346Ser	108.0	0.0		98.0	33.0	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Missense_Mutation	SNP	ENST00000608872.1	hg19	CCDS43872.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.983146	0.74474	.	.	ENSG00000119402	ENST00000373926;ENST00000340778;ENST00000444833	T;T	0.24350	1.86;1.86	5.77	5.77	0.91146	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.093477	0.85682	D	0.000000	T	0.45577	0.1349	L	0.55481	1.735	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.994;0.997;0.997	T	0.05903	-1.0857	10	0.15499	T	0.54	-10.6657	17.8518	0.88748	0.0:1.0:0.0:0.0	.	281;346;346	Q9UKT8-2;B2RAW3;Q9UKT8	.;.;FBXW2_HUMAN	S	346;281;346	ENSP00000363036:G346S;ENSP00000341161:G281S	ENSP00000341161:G281S	G	-	1	0	FBXW2	122573487	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.885000	0.99019	0.655000	0.94253	GGT	.	.		0.423	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2			T	123533666	C	T	123533666	3	4	23	1	0	0	0	0	1	0	0	0	5774	594	21	3	336	3	FBXW2	9	123533666	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	4403663	123533666	17679765	552	2618										
DAB2IP	153090	hgsc.bcm.edu	37	chr9	124534910	124534910	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atagatttcacccggttaccGtctccaacccccgaaaacaa	5	15	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:124534910G>A	ENST00000408936.3	+	12	2285	c.2103G>A	c.(2101-2103)ccG>ccA	p.P701P	DAB2IP_ENST00000259371.2_Silent_p.P673P|DAB2IP_ENST00000309989.1_Silent_p.P577P			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	701	Necessary for interaction with AKT1.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						CCCGGTTACCGTCTCCAACCC	0.557																																					p.P673P		Atlas-SNP	.											DAB2IP_ENST00000259371,NS,carcinoma,0,2	DAB2IP	150	.	0			c.G2019A						.						101	96	98					9																	124534910		2203	4300	6503	SO:0001819	synonymous_variant	153090	exon12			GTTACCGTCTCCA	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.2103G>A	chr9.hg19:g.124534910G>A		95.0	0.0		80.0	27.0	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Silent	SNP	ENST00000408936.3	hg19																																																																																				.	.		0.557	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		A	124534910	G	A	124534910	2	1	23	1	0	0	0	0	0	0	0	1	4221	1132	40	1		1	DAB2IP	9	124534910	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1001244	124534910	16678521	553	2619										
ANGPTL2	23452	hgsc.bcm.edu	37	chr9	129854031	129854031	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagtcacccgcattgccatgGtagcgccccagccgcagctt	11	16	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:129854031G>A	ENST00000373425.3	-	4	1817	c.1200C>T	c.(1198-1200)taC>taT	p.Y400Y	RALGPS1_ENST00000373436.1_Intron|RALGPS1_ENST00000424082.2_Intron|ANGPTL2_ENST00000373417.1_Silent_p.Y98Y|RALGPS1_ENST00000394022.3_Intron|RALGPS1_ENST00000259351.5_Intron|RALGPS1_ENST00000373434.1_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	400	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						CATTGCCATGGTAGCGCCCCA	0.542																																					p.Y400Y		Atlas-SNP	.											.	ANGPTL2	46	.	0			c.C1200T						.						175	173	173					9																	129854031		2203	4300	6503	SO:0001819	synonymous_variant	23452	exon4			GCCATGGTAGCGC	AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"Fibrinogen C domain containing"	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.1200C>T	chr9.hg19:g.129854031G>A		110.0	0.0		99.0	32.0	NM_012098	Q5JT58|Q8NCH7	Silent	SNP	ENST00000373425.3	hg19	CCDS6868.1																																																																																			.	.		0.542	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098		A	129854031	G	A	129854031	2	1	23	1	0	0	0	0	0	0	0	1	614	1256	44	3		3	ANGPTL2	9	129854031	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	5319121	129854031	11359400	554	2620										
GARNL3	84253	hgsc.bcm.edu	37	chr9	130027161	130027161	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcagccctttttgcaaatggTagttgatttttgcagaaggt	11	6	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:130027161T>C	ENST00000373387.4	+	1	357	c.5T>C	c.(4-6)gTa>gCa	p.V2A	GARNL3_ENST00000435213.2_Intron|GARNL3_ENST00000314904.5_Missense_Mutation_p.V2A	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	2					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						TTGCAAATGGTAGTTGATTTT	0.502																																					p.V2A		Atlas-SNP	.											.	GARNL3	83	.	0			c.T5C						.						136	134	135					9																	130027161		2203	4300	6503	SO:0001583	missense	84253	exon1			AAATGGTAGTTGA	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.5T>C	chr9.hg19:g.130027161T>C	ENSP00000362485:p.Val2Ala	129.0	0.0		113.0	47.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	hg19	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	T	12.62	1.992302	0.35131	.	.	ENSG00000136895	ENST00000314904;ENST00000373387	D;D	0.87650	-2.28;-2.26	5.35	4.19	0.49359	.	.	.	.	.	T	0.71160	0.3307	N	0.08118	0	0.21527	N	0.99965	B	0.02656	0.0	B	0.04013	0.001	T	0.56486	-0.7971	8	.	.	.	.	6.0035	0.19533	0.0:0.0825:0.3214:0.5961	.	2	Q5VVW2	GARL3_HUMAN	A	2	ENSP00000313970:V2A;ENSP00000362485:V2A	.	V	+	2	0	GARNL3	129066982	1.000000	0.71417	0.972000	0.41901	0.991000	0.79684	1.451000	0.35145	0.840000	0.34995	0.529000	0.55759	GTA	.	.		0.502	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		C	130027161	T	C	130027161	3	2	23	1	0	0	0	0	1	0	0	0	6249	1638	57	2	7	2	GARNL3	9	130027161	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	173130	130027161	11186270	555	2621										
CDK9	1025	hgsc.bcm.edu	37	chr9	130551527	130551527	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caagggccagaagcggaaggTgaaggacaggctgaaggcct	17	8	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:130551527T>C	ENST00000373264.4	+	7	924	c.824T>C	c.(823-825)gTg>gCg	p.V275A	CDK9_ENST00000373265.2_Missense_Mutation_p.V392A	NM_001261.3	NP_001252.1	P50750	CDK9_HUMAN	cyclin-dependent kinase 9	275	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|DNA repair (GO:0006281)|gene expression (GO:0010467)|negative regulation of cell cycle arrest (GO:0071157)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of DNA repair (GO:0006282)|regulation of histone modification (GO:0031056)|replication fork arrest (GO:0043111)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|positive transcription elongation factor complex b (GO:0008024)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|DNA binding (GO:0003677)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			lung(1)	1						AAGCGGAAGGTGAAGGACAGG	0.587																																					p.V275A		Atlas-SNP	.											.	CDK9	22	.	0			c.T824C						.						160	100	120					9																	130551527		2203	4300	6503	SO:0001583	missense	1025	exon7			GGAAGGTGAAGGA	L25676	CCDS6879.1	9q34.1	2011-11-08	2007-11-21		ENSG00000136807	ENSG00000136807		"Cyclin-dependent kinases"	1780	protein-coding gene	gene with protein product		603251	"cyclin-dependent kinase 9 (CDC2-related kinase)"	CDC2L4		8170997, 9356449	Standard	NM_001261		Approved	PITALRE, C-2k, TAK	uc004bse.2	P50750	OTTHUMG00000020715	ENST00000373264.4:c.824T>C	chr9.hg19:g.130551527T>C	ENSP00000362361:p.Val275Ala	93.0	0.0		109.0	45.0	NM_001261	Q5JU24|Q5JU25|Q5U006|Q96TF1	Missense_Mutation	SNP	ENST00000373264.4	hg19	CCDS6879.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.788860	0.90367	.	.	ENSG00000136807	ENST00000373265;ENST00000373264	T;T	0.43294	0.95;0.95	5.43	5.43	0.79202	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.51924	0.1703	N	0.25426	0.745	0.80722	D	1	D	0.63880	0.993	D	0.75484	0.986	T	0.56709	-0.7934	10	0.87932	D	0	-13.9615	14.633	0.68671	0.0:0.0:0.0:1.0	.	275	P50750	CDK9_HUMAN	A	392;275	ENSP00000362362:V392A;ENSP00000362361:V275A	ENSP00000362361:V275A	V	+	2	0	CDK9	129591348	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.798000	0.85924	2.058000	0.61347	0.482000	0.46254	GTG	.	.		0.587	CDK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054235.1			C	130551527	T	C	130551527	3	2	23	1	0	0	0	0	1	0	0	0	3153	1696	59	2	850	2	CDK9	9	130551527	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	524366	130551527	10661904	556	2622										
NAIF1	203245	hgsc.bcm.edu	37	chr9	130829075	130829075	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcccaggccccccagctccGtcctcctcagtgggccccgg	11	21	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:130829075G>A	ENST00000373078.4	-	1	525	c.306C>T	c.(304-306)gaC>gaT	p.D102D	SLC25A25_ENST00000373068.2_5'Flank|NAIF1_ENST00000488519.1_5'Flank|SLC25A25_ENST00000373069.5_5'Flank	NM_197956.3	NP_931045.1	Q69YI7	NAIF1_HUMAN	nuclear apoptosis inducing factor 1	102	Gly-rich.				negative regulation of cell growth (GO:0030308)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CCCCAGCTCCGTCCTCCTCAG	0.682																																					p.D102D		Atlas-SNP	.											.	NAIF1	36	.	0			c.C306T						.						33	35	34					9																	130829075		2200	4298	6498	SO:0001819	synonymous_variant	203245	exon1			AGCTCCGTCCTCC	AK122729	CCDS6889.1	9q34.11	2008-04-10	2008-04-10	2008-04-10	ENSG00000171169	ENSG00000171169			25446	protein-coding gene	gene with protein product	"nuclear apoptosis-inducing factor 1"	610673	"chromosome 9 open reading frame 90"	C9orf90		14702039, 16378748	Standard	NM_197956		Approved	DKFZp762G199, bA379C10.2	uc004bta.3	Q69YI7	OTTHUMG00000020727	ENST00000373078.4:c.306C>T	chr9.hg19:g.130829075G>A		90.0	0.0		72.0	29.0	NM_197956	B3KV81|Q8WU12	Silent	SNP	ENST00000373078.4	hg19	CCDS6889.1																																																																																			.	.		0.682	NAIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054330.1	NM_197956		A	130829075	G	A	130829075	2	1	23	1	0	0	0	0	0	0	0	1	10155	1136	40	1		1	NAIF1	9	130829075	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	277548	130829075	10384356	557	2623										
USP20	10868	hgsc.bcm.edu	37	chr9	132637022	132637022	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctctcggtcatctgccaccaCggcacggcaggcagtgagtc	12	15	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:132637022C>T	ENST00000315480.4	+	18	2066	c.1908C>T	c.(1906-1908)caC>caT	p.H636H	USP20_ENST00000358355.1_Silent_p.H636H|USP20_ENST00000372429.3_Silent_p.H636H			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	636	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				TCTGCCACCACGGCACGGCAG	0.657																																					p.H636H		Atlas-SNP	.											.	USP20	186	.	0			c.C1908T						.						77	84	81					9																	132637022		2146	4245	6391	SO:0001819	synonymous_variant	10868	exon18			CCACCACGGCACG	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.1908C>T	chr9.hg19:g.132637022C>T		90.0	0.0		78.0	33.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Silent	SNP	ENST00000315480.4	hg19	CCDS43892.1																																																																																			.	.		0.657	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			T	132637022	C	T	132637022	2	4	23	1	0	0	0	0	0	0	0	1	17067	535	19	1		1	USP20	9	132637022	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1807947	132637022	8576409	558	2624										
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134353960	134353960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtcctgaccaagaagcagcGccgcctgctggaggaagaga	14	11	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:134353960G>A	ENST00000357304.4	+	17	4767	c.4712G>A	c.(4711-4713)cGc>cAc	p.R1571H	PRRC2B_ENST00000405995.1_Missense_Mutation_p.R877H|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Missense_Mutation_p.R877H	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1571							poly(A) RNA binding (GO:0044822)	p.R1571H(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						AAGAAGCAGCGCCGCCTGCTG	0.637											OREG0019562	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R1571H		Atlas-SNP	.											PRRC2B_ENST00000357304,rectum,carcinoma,0,2	PRRC2B	266	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4712A						.						67	74	72					9																	134353960		1880	4109	5989	SO:0001583	missense	84726	exon17			AGCAGCGCCGCCT	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4712G>A	chr9.hg19:g.134353960G>A	ENSP00000349856:p.Arg1571His	114.0	0.0	1610	93.0	46.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	hg19	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.908653	0.92107	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550	T;T;T	0.03124	4.04;4.3;4.04	5.42	5.42	0.78866	.	0.000000	0.42682	U	0.000676	T	0.15219	0.0367	L	0.52573	1.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.991	T	0.00134	-1.2009	10	0.72032	D	0.01	-44.0546	18.2062	0.89855	0.0:0.0:1.0:0.0	.	304;1571	Q5JSZ8;Q5JSZ5	.;PRC2B_HUMAN	H	877;1571;877	ENSP00000384606:R877H;ENSP00000349856:R1571H;ENSP00000398853:R877H	ENSP00000349856:R1571H	R	+	2	0	PRRC2B	133343781	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.655000	0.67981	2.549000	0.85964	0.561000	0.74099	CGC	.	.		0.637	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134353960	G	A	134353960	3	1	23	1	0	0	0	0	1	0	0	0	1320	1087	38	1	4778	1	BAT2L1	9	134353960	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1716938	134353960	6859471	559	2625										
SETX	23064	hgsc.bcm.edu	37	chr9	135140223	135140223	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtctggacccctctggggcTatggtaggagggtgagtgag	19	7	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:135140223T>C	ENST00000224140.5	-	26	7619	c.7437A>G	c.(7435-7437)atA>atG	p.I2479M	SETX_ENST00000477049.1_5'UTR|SETX_ENST00000372169.2_Missense_Mutation_p.I2508M|SETX_ENST00000393220.1_Missense_Mutation_p.I2446M	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2479					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		CCTCTGGGGCTATGGTAGGAG	0.498																																					p.I2479M		Atlas-SNP	.											.,1	SETX	234	.	0			c.A7437G						.						100	104	103					9																	135140223		2203	4300	6503	SO:0001583	missense	23064	exon26			TGGGGCTATGGTA	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.7437A>G	chr9.hg19:g.135140223T>C	ENSP00000224140:p.Ile2479Met	100.0	0.0		103.0	50.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.131366	0.56828	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.90900	-2.09;-2.75;-2.23;-1.84	4.83	-9.65	0.00537	.	1.549250	0.04012	N	0.298360	D	0.85305	0.5666	L	0.44542	1.39	0.09310	N	1	P;P;P	0.44946	0.763;0.761;0.846	B;B;P	0.45610	0.28;0.293;0.487	T	0.82139	-0.0605	10	0.44086	T	0.13	.	4.9238	0.13883	0.0965:0.1923:0.4924:0.2189	.	2446;2479;2508	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	M	2479;750;2508;2446	ENSP00000224140:I2479M;ENSP00000409143:I750M;ENSP00000361242:I2508M;ENSP00000376913:I2446M	ENSP00000224140:I2479M	I	-	3	3	SETX	134130044	0.000000	0.05858	0.000000	0.03702	0.380000	0.30137	-4.012000	0.00314	-3.100000	0.00245	0.459000	0.35465	ATA	.	.		0.498	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		C	135140223	T	C	135140223	3	2	23	1	0	0	0	0	1	0	0	0	14156	1512	53	2	600	2	SETX	9	135140223	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	786263	135140223	6073208	560	2626										
C9orf7	11094	hgsc.bcm.edu	37	chr9	136330530	136330530	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacagtggcggagaaggtggAccggctgcgctcctggcaga	17	11	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:136330530A>T	ENST00000316948.4	+	3	361	c.281A>T	c.(280-282)gAc>gTc	p.D94V	CACFD1_ENST00000489519.1_3'UTR|CACFD1_ENST00000542192.1_Intron|CACFD1_ENST00000540581.1_Missense_Mutation_p.D94V|CACFD1_ENST00000291722.7_Intron	NM_017586.3	NP_060056.1	Q9UGQ2	FLOWR_HUMAN	calcium channel flower domain containing 1	94					synaptic vesicle endocytosis (GO:0048488)	integral component of synaptic vesicle membrane (GO:0030285)	calcium channel activity (GO:0005262)										GAGAAGGTGGACCGGCTGCGC	0.582																																					p.D94V		Atlas-SNP	.											.	CACFD1	1	.	0			c.A281T						.						111	105	107					9																	136330530		2203	4300	6503	SO:0001583	missense	11094	exon3			AGGTGGACCGGCT		CCDS6974.1, CCDS48051.1, CCDS56591.1, CCDS56592.1	9q34	2012-03-06	2012-03-06	2012-03-06	ENSG00000160325	ENSG00000160325			1365	protein-coding gene	gene with protein product		613104	"chromosome 9 open reading frame 7"	C9orf7		19737521	Standard	NM_001242370		Approved	D9S2135, flower	uc011mdh.1	Q9UGQ2	OTTHUMG00000020875	ENST00000316948.4:c.281A>T	chr9.hg19:g.136330530A>T	ENSP00000317121:p.Asp94Val	90.0	0.0		69.0	31.0	NM_017586	B7Z3T8|B7Z5E1|F5GXX4|Q5SXD4|Q8NBM6	Missense_Mutation	SNP	ENST00000316948.4	hg19	CCDS6974.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.520414	0.85495	.	.	ENSG00000160325	ENST00000535514;ENST00000316948;ENST00000540581;ENST00000444798	T;T;T	0.46819	0.86;0.86;0.86	5.35	5.35	0.76521	Membrane protein, Golgi apparatus TVP18/Calcium channel flower (1);	0.096847	0.64402	D	0.000002	T	0.69815	0.3153	M	0.80183	2.485	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.982;0.99	T	0.74722	-0.3569	10	0.72032	D	0.01	-41.932	14.5099	0.67776	1.0:0.0:0.0:0.0	.	94;94	F5GXX4;Q9UGQ2	.;FLOWR_HUMAN	V	84;94;94;66	ENSP00000317121:D94V;ENSP00000440832:D94V;ENSP00000414495:D66V	ENSP00000317121:D94V	D	+	2	0	C9orf7	135320351	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	8.896000	0.92521	2.025000	0.59659	0.402000	0.26972	GAC	.	.		0.582	CACFD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054915.1	NM_017586		T	136330530	A	T	136330530	3	4	23	1	0	0	0	0	1	0	0	0	2495	275	10	4	291	4	C9orf7	9	136330530	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1190307	136330530	4882901	561	2627										
GPSM1	26086	hgsc.bcm.edu	37	chr9	139231495	139231495	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcacctgccgcccgatgtcCgagagaccctgtgcaaggcc	13	16	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:139231495C>T	ENST00000440944.1	+	4	764	c.544C>T	c.(544-546)Cga>Tga	p.R182*	GPSM1_ENST00000392945.3_Nonsense_Mutation_p.R182*	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	182	Mediates association with membranes. {ECO:0000250}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GCCCGATGTCCGAGAGACCCT	0.647																																					p.R182X		Atlas-SNP	.											.	GPSM1	50	.	0			c.C544T						.						36	34	34					9																	139231495		2111	4156	6267	SO:0001587	stop_gained	26086	exon4			GATGTCCGAGAGA	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"Tetratricopeptide (TTC) repeat domain containing"	17858	protein-coding gene	gene with protein product	"AGS3 homolog (C. elegans)"	609491	"G-protein signalling modulator 1 (AGS3-like, C. elegans)"			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.544C>T	chr9.hg19:g.139231495C>T	ENSP00000392828:p.Arg182*	122.0	0.0		89.0	29.0	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Nonsense_Mutation	SNP	ENST00000440944.1	hg19	CCDS48055.1	.	.	.	.	.	.	.	.	.	.	C	37	6.421558	0.97555	.	.	ENSG00000160360	ENST00000392945;ENST00000440944;ENST00000354753	.	.	.	3.79	1.57	0.23409	.	0.127086	0.51477	U	0.000091	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.7884	9.5393	0.39242	0.6145:0.3855:0.0:0.0	.	.	.	.	X	182;182;159	.	ENSP00000346797:R159X	R	+	1	2	GPSM1	138351316	0.996000	0.38824	0.025000	0.17156	0.792000	0.44763	2.604000	0.46274	0.821000	0.34540	0.563000	0.77884	CGA	.	.		0.647	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		T	139231495	C	T	139231495	4	4	23	1	0	0	0	0	0	1	0	0	6743	644	23	1	558	1	GPSM1	9	139231495	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2900965	139231495	1981936	562	2628										
SNAPC4	6621	hgsc.bcm.edu	37	chr9	139288750	139288750	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caggcggtcactcaccactgActttcggagcaaggcctttt	10	13	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:139288750A>G	ENST00000298532.2	-	6	951	c.583T>C	c.(583-585)Tca>Cca	p.S195P		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		CTCACCACTGACTTTCGGAGC	0.547																																					p.S195P		Atlas-SNP	.											.	SNAPC4	82	.	0			c.T583C						.						163	156	159					9																	139288750		2203	4300	6503	SO:0001583	missense	6621	exon6			CCACTGACTTTCG	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"small nuclear RNA activating complex, polypeptide 4, 190kD"			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.583T>C	chr9.hg19:g.139288750A>G	ENSP00000298532:p.Ser195Pro	86.0	0.0		86.0	35.0	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	hg19	CCDS6998.1	.	.	.	.	.	.	.	.	.	.	A	16.43	3.122312	0.56613	.	.	ENSG00000165684	ENST00000298532	T	0.32272	1.46	4.9	2.41	0.29592	SANT domain, DNA binding (1);	0.450738	0.22316	N	0.061677	T	0.37972	0.1023	M	0.62723	1.935	0.30814	N	0.738492	P	0.52170	0.951	P	0.49226	0.603	T	0.45862	-0.9232	10	0.72032	D	0.01	-3.9617	11.1655	0.48541	0.5364:0.4636:0.0:0.0	.	195	Q5SXM2	SNPC4_HUMAN	P	195	ENSP00000298532:S195P	ENSP00000298532:S195P	S	-	1	0	SNAPC4	138408571	0.896000	0.30565	0.216000	0.23742	0.773000	0.43773	0.866000	0.27954	0.194000	0.20326	0.529000	0.55759	TCA	.	.		0.547	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086		G	139288750	A	G	139288750	3	3	23	1	0	0	0	0	1	0	0	0	14852	275	10	2	3894	2	SNAPC4	9	139288750	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	57255	139288750	1924681	563	2629										
EGFL7	51162	hgsc.bcm.edu	37	chr9	139564144	139564144	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgccccggctggaagaggaCcagcgggcttcctggggcct	16	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:139564144C>T	ENST00000371699.1	+	5	1195	c.284C>T	c.(283-285)aCc>aTc	p.T95I	EGFL7_ENST00000406555.3_Missense_Mutation_p.T95I|MIR126_ENST00000362291.1_RNA|EGFL7_ENST00000492002.1_3'UTR|EGFL7_ENST00000371698.3_Missense_Mutation_p.T95I|EGFL7_ENST00000308874.7_Missense_Mutation_p.T95I			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	95	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.				angiogenesis (GO:0001525)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|negative regulation of cell migration (GO:0030336)|negative regulation of Notch signaling pathway (GO:0045746)|positive regulation of endothelial cell proliferation (GO:0001938)|vasculogenesis (GO:0001570)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)			kidney(2)|ovary(1)|prostate(2)|urinary_tract(1)	6	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		TGGAAGAGGACCAGCGGGCTT	0.682																																					p.T95I		Atlas-SNP	.											.	EGFL7	11	.	0			c.C284T						.						14	16	16					9																	139564144		2182	4287	6469	SO:0001583	missense	51162	exon6			AGAGGACCAGCGG	AF186111	CCDS7002.1	9q34.3	2008-02-05			ENSG00000172889	ENSG00000172889			20594	protein-coding gene	gene with protein product		608582					Standard	NM_016215		Approved	ZNEU1	uc004cih.3	Q9UHF1	OTTHUMG00000020938	ENST00000371699.1:c.284C>T	chr9.hg19:g.139564144C>T	ENSP00000360764:p.Thr95Ile	113.0	0.0		107.0	6.0	NM_016215	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	ENST00000371699.1	hg19	CCDS7002.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.495338	0.26774	.	.	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	4.06	3.1	0.35709	EMI domain (2);	0.486110	0.21645	N	0.071267	T	0.26882	0.0658	L	0.35414	1.06	0.27529	N	0.951145	P	0.39809	0.689	B	0.37091	0.241	T	0.07809	-1.0753	10	0.30078	T	0.28	-17.256	6.9329	0.24451	0.0:0.7258:0.1777:0.0965	.	95	Q9UHF1	EGFL7_HUMAN	I	95	ENSP00000360764:T95I;ENSP00000307843:T95I;ENSP00000385639:T95I;ENSP00000360763:T95I	ENSP00000307843:T95I	T	+	2	0	EGFL7	138683965	0.012000	0.17670	0.696000	0.30242	0.300000	0.27592	1.251000	0.32862	2.089000	0.63090	0.313000	0.20887	ACC	.	.		0.682	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215		T	139564144	C	T	139564144	3	4	23	1	0	0	0	0	1	0	0	0	4966	507	18	3	294	3	EGFL7	9	139564144	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	275394	139564144	1649287	564	2630										
ZMYND19	116225	hgsc.bcm.edu	37	chr9	140477533	140477533	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccgttggcattataataccGggtcacatttaggacaggaa	10	9	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:140477533G>A	ENST00000298585.2	-	5	668	c.442C>T	c.(442-444)Cgg>Tgg	p.R148W		NM_138462.2	NP_612471.1	Q96E35	ZMY19_HUMAN	zinc finger, MYND-type containing 19	148						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|synapse (GO:0045202)	metal ion binding (GO:0046872)	p.R148R(1)		endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	13	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.000275)|Epithelial(140;0.00047)		TTATAATACCGGGTCACATTT	0.473																																					p.R148W		Atlas-SNP	.											.	ZMYND19	16	.	1	Substitution - coding silent(1)	lung(1)	c.C442T						.						274	253	260					9																	140477533		2203	4300	6503	SO:0001583	missense	116225	exon5			AATACCGGGTCAC	BC012948	CCDS7048.1	9q34.3	2008-02-05			ENSG00000165724	ENSG00000165724		"Zinc fingers, MYND-type"	21146	protein-coding gene	gene with protein product		611424					Standard	NM_138462		Approved	MIZIP	uc004cno.1	Q96E35	OTTHUMG00000020992	ENST00000298585.2:c.442C>T	chr9.hg19:g.140477533G>A	ENSP00000298585:p.Arg148Trp	107.0	0.0		98.0	19.0	NM_138462	Q5T366	Missense_Mutation	SNP	ENST00000298585.2	hg19	CCDS7048.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.552503	0.86127	.	.	ENSG00000165724	ENST00000298585	.	.	.	5.29	4.39	0.52855	.	0.060469	0.64402	D	0.000002	T	0.68109	0.2965	M	0.62723	1.935	0.54753	D	0.999984	D	0.76494	0.999	P	0.62014	0.897	T	0.70502	-0.4854	9	0.87932	D	0	-36.7711	9.8258	0.40910	0.0947:0.0:0.9053:0.0	.	148	Q96E35	ZMY19_HUMAN	W	148	.	ENSP00000298585:R148W	R	-	1	2	ZMYND19	139597354	1.000000	0.71417	0.957000	0.39632	0.973000	0.67179	7.808000	0.86044	1.228000	0.43614	0.561000	0.74099	CGG	.	.		0.473	ZMYND19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055356.1	NM_138462		A	140477533	G	A	140477533	3	1	23	1	0	0	0	0	1	0	0	0	17725	1115	39	1	249	1	ZMYND19	9	140477533	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	913389	140477533	735898	565	2631										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140881287	140881287	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttcgacaccttccctgccgCcatcctcactgtcttccagg	6	19	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:140881287C>A	ENST00000371372.1	+	15	2100	c.1955C>A	c.(1954-1956)gCc>gAc	p.A652D	CACNA1B_ENST00000371357.1_Missense_Mutation_p.A653D|CACNA1B_ENST00000277551.2_Missense_Mutation_p.A652D|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371363.1_Missense_Mutation_p.A652D|CACNA1B_ENST00000371355.4_Missense_Mutation_p.A653D	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	652					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TTCCCTGCCGCCATCCTCACT	0.602																																					p.A652D		Atlas-SNP	.											.	CACNA1B	266	.	0			c.C1955A						.						187	202	197					9																	140881287		2082	4212	6294	SO:0001583	missense	774	exon15			CTGCCGCCATCCT	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1955C>A	chr9.hg19:g.140881287C>A	ENSP00000360423:p.Ala652Asp	82.0	0.0		66.0	21.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.844506	0.51164	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.98914	-5.23;-5.23;-5.23;-5.23;-5.23	4.12	4.12	0.48240	.	0.112726	0.64402	D	0.000012	D	0.99489	0.9818	H	0.98068	4.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97855	1.0277	10	0.87932	D	0	.	16.8462	0.85981	0.0:1.0:0.0:0.0	.	652;652	B1AQK4;B1AQK6	.;.	D	652;652;652;653;653	ENSP00000360423:A652D;ENSP00000277551:A652D;ENSP00000360414:A652D;ENSP00000360408:A653D;ENSP00000360406:A653D	ENSP00000277551:A652D	A	+	2	0	CACNA1B	140001108	1.000000	0.71417	0.995000	0.50966	0.291000	0.27294	7.538000	0.82048	2.210000	0.71456	0.448000	0.29417	GCC	.	.		0.602	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		A	140881287	C	A	140881287	3	1	23	1	0	0	0	0	1	0	0	0	2541	739	26	3	2013	3	CACNA1B	9	140881287	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	403754	140881287	332144	566	2632										
GDI2	2665	hgsc.bcm.edu	37	chr10	5827986	5827986	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acactaggaatttcctgaagCgacgtttttcaaacaatccc	6	11	1	1	rs376781352		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:5827986C>T	ENST00000380191.4	-	5	706	c.416G>A	c.(415-417)cGc>cAc	p.R139H	GDI2_ENST00000380181.3_Missense_Mutation_p.R94H|GDI2_ENST00000380132.4_Missense_Mutation_p.R143H	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2	139					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|Rab GDP-dissociation inhibitor activity (GO:0005093)|Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|large_intestine(1)|lung(6)|urinary_tract(1)	10						TTTCCTGAAGCGACGTTTTTC	0.373																																					p.R139H		Atlas-SNP	.											.	GDI2	26	.	0			c.G416A						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	100	99	99		281,416	4.3	1	10		99	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GDI2	NM_001115156.1,NM_001494.3	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	94/401,139/446	5827986	1,13005	2203	4300	6503	SO:0001583	missense	2665	exon5			CTGAAGCGACGTT	D13988	CCDS7071.1, CCDS44352.1	10p15	2010-03-16			ENSG00000057608	ENSG00000057608			4227	protein-coding gene	gene with protein product	"rab GDP-dissociation"	600767				9434952	Standard	NM_001494		Approved	RABGDIB	uc001iil.4	P50395	OTTHUMG00000017607	ENST00000380191.4:c.416G>A	chr10.hg19:g.5827986C>T	ENSP00000369538:p.Arg139His	60.0	0.0		36.0	13.0	NM_001494	O43928|Q5SX88|Q9UQM6	Missense_Mutation	SNP	ENST00000380191.4	hg19	CCDS7071.1	.	.	.	.	.	.	.	.	.	.	C	19.49	3.836798	0.71373	0.0	1.16E-4	ENSG00000057608	ENST00000380191;ENST00000380132;ENST00000380181;ENST00000456041;ENST00000418688;ENST00000380127	D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	5.17	4.26	0.50523	.	0.000000	0.85682	D	0.000000	D	0.91878	0.7429	M	0.85777	2.775	0.80722	D	1	B;P;P	0.40660	0.151;0.726;0.48	B;P;B	0.46825	0.049;0.528;0.067	D	0.92440	0.5961	10	0.62326	D	0.03	0.609	13.7496	0.62899	0.0:0.9244:0.0:0.0756	.	143;94;139	E7EU23;Q5SX88;P50395	.;.;GDIB_HUMAN	H	139;143;94;129;103;143	ENSP00000369538:R139H;ENSP00000369475:R143H;ENSP00000369528:R94H;ENSP00000401733:R129H;ENSP00000394177:R103H;ENSP00000369470:R143H	ENSP00000369470:R143H	R	-	2	0	GDI2	5867992	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.664000	0.83830	1.315000	0.45114	0.655000	0.94253	CGC	.	.		0.373	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	NM_001494		T	5827986	C	T	5827986	3	4	23	1	0	0	0	0	1	0	0	0	6329	768	27	1	949	1	GDI2	10	5827986	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10		5827986	129706761	567	2633										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7608361	7608361	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccccaattaactctccgttcActgtgacacctcaaaggcca	5	16	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:7608361A>G	ENST00000256861.6	-	13	2237	c.2159T>C	c.(2158-2160)gTg>gCg	p.V720A	ITIH5_ENST00000298441.6_Missense_Mutation_p.V506A|ITIH5_ENST00000446830.2_Missense_Mutation_p.V502A|ITIH5_ENST00000397146.2_Intron	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	720					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CTCTCCGTTCACTGTGACACC	0.522																																					p.V720A		Atlas-SNP	.											.	ITIH5	343	.	0			c.T2159C						.						58	59	58					10																	7608361		2203	4300	6503	SO:0001583	missense	80760	exon13			CCGTTCACTGTGA			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.2159T>C	chr10.hg19:g.7608361A>G	ENSP00000256861:p.Val720Ala	84.0	0.0		35.0	21.0	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	A	16.29	3.082855	0.55861	.	.	ENSG00000123243	ENST00000256861;ENST00000298441;ENST00000446830	T;T;T	0.26810	1.71;1.71;1.71	5.84	5.84	0.93424	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.051547	0.85682	D	0.000000	T	0.53916	0.1826	.	.	.	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.58584	-0.7611	9	0.87932	D	0	-34.9487	16.1928	0.82004	1.0:0.0:0.0:0.0	.	720;506	Q86UX2;Q86UX2-3	ITIH5_HUMAN;.	A	720;506;502	ENSP00000256861:V720A;ENSP00000298441:V506A;ENSP00000387969:V502A	ENSP00000256861:V720A	V	-	2	0	ITIH5	7648367	1.000000	0.71417	0.997000	0.53966	0.086000	0.17979	7.011000	0.76359	2.216000	0.71823	0.533000	0.62120	GTG	.	.		0.522	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		G	7608361	A	G	7608361	3	3	23	1	0	0	0	0	1	0	0	0	7916	159	6	2	719	2	ITIH5	10	7608361	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1780375	7608361	127926386	568	2634										
RPP38	10557	hgsc.bcm.edu	37	chr10	15145341	15145341	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagctcctcaagcaccggggCggggatctctccgtaagacg	13	14	2	1	rs138934702		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:15145341C>T	ENST00000378197.4	+	3	542	c.28C>T	c.(28-30)Cgg>Tgg	p.R10W	NMT2_ENST00000466201.1_5'UTR|RPP38_ENST00000378202.5_Missense_Mutation_p.R10W|RPP38_ENST00000451677.1_Intron	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	10					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)	8						AGCACCGGGGCGGGGATCTCT	0.483																																					p.R10W	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.C28T						.	C	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	65	70	68		28,28,28	-1.6	0	10	dbSNP_134	68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	101,101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	10/284,10/284,10/284	15145341	1,13005	2203	4300	6503	SO:0001583	missense	10557	exon2			CCGGGGCGGGGAT	U77664	CCDS7108.1	10p13	2012-05-21			ENSG00000152464	ENSG00000152464			30329	protein-coding gene	gene with protein product		606116				9037013, 9630247	Standard	NM_183005		Approved		uc001inx.5	P78345	OTTHUMG00000017728	ENST00000378197.4:c.28C>T	chr10.hg19:g.15145341C>T	ENSP00000367439:p.Arg10Trp	130.0	0.0		79.0	37.0	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Missense_Mutation	SNP	ENST00000378197.4	hg19	CCDS7108.1	.	.	.	.	.	.	.	.	.	.	C	12.51	1.959700	0.34565	0.0	1.16E-4	ENSG00000152464	ENST00000378203;ENST00000378201;ENST00000378202;ENST00000378197;ENST00000441850	T;T;T;T	0.26373	2.73;2.73;2.73;1.74	5.75	-1.56	0.08532	.	0.113772	0.56097	D	0.000030	T	0.45236	0.1332	M	0.68317	2.08	0.21064	N	0.999796	D	0.89917	1.0	D	0.69479	0.964	T	0.51044	-0.8755	10	0.87932	D	0	-27.85	16.3068	0.82852	0.2668:0.7332:0.0:0.0	.	10	P78345	RPP38_HUMAN	W	10	ENSP00000367445:R10W;ENSP00000367444:R10W;ENSP00000367439:R10W;ENSP00000402635:R10W	ENSP00000367439:R10W	R	+	1	2	RPP38	15185347	0.137000	0.22531	0.022000	0.16811	0.059000	0.15707	0.938000	0.28965	-0.545000	0.06224	-0.271000	0.10264	CGG	.	C|1.000;T|0.000		0.483	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414		T	15145341	C	T	15145341	3	4	23	1	0	0	0	0	1	0	0	0	13628	759	27	1	30	1	RPP38	10	15145341	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	7536980	15145341	120389406	569	2635										
ITGA8	8516	hgsc.bcm.edu	37	chr10	15590538	15590538	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtcgtcccactgcacaggaGatttgtaaacactcgatatt	8	10	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:15590538G>A	ENST00000378076.3	-	27	3149	c.2796C>T	c.(2794-2796)atC>atT	p.I932I		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	932					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						CTGCACAGGAGATTTGTAAAC	0.453																																					p.I932I		Atlas-SNP	.											.	ITGA8	230	.	0			c.C2796T						.						138	116	124					10																	15590538		2203	4300	6503	SO:0001819	synonymous_variant	8516	exon27			ACAGGAGATTTGT	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.2796C>T	chr10.hg19:g.15590538G>A		90.0	0.0		76.0	35.0	NM_003638	B0YJ31|Q5VX94	Silent	SNP	ENST00000378076.3	hg19	CCDS31155.1																																																																																			.	.		0.453	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		A	15590538	G	A	15590538	2	1	23	1	0	0	0	0	0	0	0	1	7891	932	33	3		3	ITGA8	10	15590538	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	445197	15590538	119944209	570	2636										
CUBN	8029	hgsc.bcm.edu	37	chr10	16877086	16877086	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaaagagggaaatggtgtggTtctggggggctgtgagagta	19	2	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:16877086T>C	ENST00000377833.4	-	64	10354	c.10289A>G	c.(10288-10290)aAc>aGc	p.N3430S		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3430	CUB 26. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AATGGTGTGGTTCTGGGGGGC	0.448																																					p.N3430S		Atlas-SNP	.											.	CUBN	515	.	0			c.A10289G						.						162	137	146					10																	16877086		2203	4300	6503	SO:0001583	missense	8029	exon64			GTGTGGTTCTGGG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.10289A>G	chr10.hg19:g.16877086T>C	ENSP00000367064:p.Asn3430Ser	153.0	0.0		111.0	8.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.373093	0.61624	.	.	ENSG00000107611	ENST00000377833;ENST00000545090	T	0.34667	1.35	4.84	4.84	0.62591	CUB (5);	0.000000	0.47093	D	0.000243	T	0.48333	0.1494	L	0.43554	1.36	0.80722	D	1	D	0.61080	0.989	D	0.63488	0.915	T	0.34875	-0.9811	10	0.30854	T	0.27	.	14.5848	0.68317	0.0:0.0:0.0:1.0	.	3430	O60494	CUBN_HUMAN	S	3430;271	ENSP00000367064:N3430S	ENSP00000367064:N3430S	N	-	2	0	CUBN	16917092	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	1.964000	0.40462	2.028000	0.59812	0.459000	0.35465	AAC	.	.		0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16877086	T	C	16877086	3	2	23	1	0	0	0	0	1	0	0	0	4053	1725	60	2	598	2	CUBN	10	16877086	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1286548	16877086	118657661	571	2637										
C10orf140	387640	hgsc.bcm.edu	37	chr10	21804625	21804625	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccctttgtatcattgcactcGcactttagcttatttgtaaa	5	10	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:21804625G>A	ENST00000449193.2	-	4	4379	c.2127C>T	c.(2125-2127)tgC>tgT	p.C709C	SKIDA1_ENST00000444772.3_Silent_p.C630C	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	628						nucleus (GO:0005634)											CATTGCACTCGCACTTTAGCT	0.393																																					p.C709C		Atlas-SNP	.											C10orf140_ENST00000449193,colon,carcinoma,0,2	.	.	.	0			c.C2127T						.						213	215	215					10																	21804625		1933	4132	6065	SO:0001819	synonymous_variant	387640	exon4			GCACTCGCACTTT	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 140"	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.2127C>T	chr10.hg19:g.21804625G>A		109.0	1.0		107.0	29.0	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	ENST00000449193.2	hg19	CCDS44363.1																																																																																			.	.		0.393	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		A	21804625	G	A	21804625	2	1	23	1	0	0	0	0	0	0	0	1	1597	1079	38	1		1	C10orf140	10	21804625	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	4927539	21804625	113730122	572	2638										
ARMC3	219681	hgsc.bcm.edu	37	chr10	23326257	23326257	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcgcggagagtacggtagagCgtggaatgaagtcatgctgc	16	7	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:23326257C>T	ENST00000298032.5	+	19	2552	c.2468C>T	c.(2467-2469)gCg>gTg	p.A823V	ARMC3_ENST00000409983.3_Missense_Mutation_p.A816V|ARMC3_ENST00000376528.4_Missense_Mutation_p.A560V	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	823						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TACGGTAGAGCGTGGAATGAA	0.542																																					p.A823V		Atlas-SNP	.											.	ARMC3	102	.	0			c.C2468T						.						123	116	118					10																	23326257		2203	4300	6503	SO:0001583	missense	219681	exon19			GTAGAGCGTGGAA	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"Armadillo repeat containing"	30964	protein-coding gene	gene with protein product	"cancer/testis antigen 81"	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.2468C>T	chr10.hg19:g.23326257C>T	ENSP00000298032:p.Ala823Val	124.0	0.0		133.0	52.0	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Missense_Mutation	SNP	ENST00000298032.5	hg19	CCDS7142.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.395601	0.62177	.	.	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000376528	T;T;T	0.50548	0.74;0.74;1.99	5.68	4.76	0.60689	.	0.061426	0.64402	D	0.000005	T	0.71542	0.3352	M	0.87682	2.9	0.58432	D	0.999993	D;D	0.89917	1.0;0.999	D;D	0.65010	0.928;0.931	T	0.78698	-0.2103	10	0.87932	D	0	-25.4588	16.305	0.82844	0.0:0.8631:0.1369:0.0	.	816;823	Q5W041-4;Q5W041	.;ARMC3_HUMAN	V	823;816;560	ENSP00000298032:A823V;ENSP00000386943:A816V;ENSP00000365711:A560V	ENSP00000298032:A823V	A	+	2	0	ARMC3	23366263	0.998000	0.40836	0.727000	0.30756	0.005000	0.04900	3.693000	0.54735	1.360000	0.45960	0.655000	0.94253	GCG	.	.		0.542	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		T	23326257	C	T	23326257	3	4	23	1	0	0	0	0	1	0	0	0	952	768	27	1	2538	1	ARMC3	10	23326257	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1521632	23326257	112208490	573	2639										
SVIL	6840	hgsc.bcm.edu	37	chr10	29769474	29769474	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcgctcactaacctgccgtgCtcaccatgaacttccacttg	7	16	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:29769474C>T	ENST00000355867.4	-	29	6121	c.5369G>A	c.(5368-5370)aGc>aAc	p.S1790N	SVIL_ENST00000375398.2_Missense_Mutation_p.S1790N|SVIL_ENST00000460007.1_Intron|SVIL_ENST00000535393.1_Missense_Mutation_p.S704N|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000375400.3_Missense_Mutation_p.S1364N|SVIL_ENST00000538146.1_Missense_Mutation_p.S582N|PTCHD3P1_ENST00000413405.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1790					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				ACCTGCCGTGCTCACCATGAA	0.562																																					p.S1790N		Atlas-SNP	.											.	SVIL	226	.	0			c.G5369A						.						95	87	90					10																	29769474		2203	4300	6503	SO:0001583	missense	6840	exon29			GCCGTGCTCACCA	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.5369G>A	chr10.hg19:g.29769474C>T	ENSP00000348128:p.Ser1790Asn	117.0	0.0		116.0	42.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.404653	0.83230	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;1.7	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.47414	0.1444	L	0.58101	1.795	0.80722	D	1	B;B;B;B	0.32040	0.02;0.004;0.164;0.353	B;B;B;B	0.32211	0.029;0.018;0.142;0.118	T	0.51568	-0.8689	10	0.46703	T	0.11	-11.6278	17.4706	0.87645	0.0:1.0:0.0:0.0	.	704;582;1364;1790	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	N	1364;1790;1790;704;744;582	ENSP00000364549:S1364N;ENSP00000364547:S1790N;ENSP00000348128:S1790N;ENSP00000445472:S704N;ENSP00000440343:S582N	ENSP00000348128:S1790N	S	-	2	0	SVIL	29809480	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	5.779000	0.68948	2.337000	0.79520	0.561000	0.74099	AGC	.	.		0.562	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			T	29769474	C	T	29769474	3	4	23	1	0	0	0	0	1	0	0	0	15436	797	28	3	1315	3	SVIL	10	29769474	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	6443217	29769474	105765273	574	2640										
EPC1	80314	hgsc.bcm.edu	37	chr10	32581987	32581987	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atttgtgctggaaccatctcGcttctcttgttttactgatg	8	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:32581987G>A	ENST00000263062.8	-	4	864	c.595C>T	c.(595-597)Cga>Tga	p.R199*	EPC1_ENST00000375110.2_Nonsense_Mutation_p.R149*|EPC1_ENST00000319778.6_Nonsense_Mutation_p.R199*	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	199					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				GAACCATCTCGCTTCTCTTGT	0.338																																					p.R199X		Atlas-SNP	.											EPC1,colon,carcinoma,0,1	EPC1	74	.	0			c.C595T						.						72	73	73					10																	32581987		2202	4300	6502	SO:0001587	stop_gained	80314	exon4			CATCTCGCTTCTC	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.595C>T	chr10.hg19:g.32581987G>A	ENSP00000263062:p.Arg199*	92.0	0.0		87.0	33.0	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Nonsense_Mutation	SNP	ENST00000263062.8	hg19	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	G	38	6.729400	0.97796	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	.	.	.	6.08	2.88	0.33553	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.8674	16.7515	0.85488	0.0:0.0:0.6531:0.3469	.	.	.	.	X	149;199;199	.	ENSP00000263062:R199X	R	-	1	2	EPC1	32621993	1.000000	0.71417	0.997000	0.53966	0.797000	0.45037	3.544000	0.53640	0.871000	0.35750	-0.230000	0.12252	CGA	.	.		0.338	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			A	32581987	G	A	32581987	4	1	23	1	0	0	0	0	0	1	0	0	5162	1095	38	1	1963	1	EPC1	10	32581987	Nonsense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2812513	32581987	102952760	575	2641										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37447483	37447483	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctattccaactaaagccttAgaattgaaggacatgcaaac	6	9	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:37447483A>G	ENST00000602533.1	+	15	1800	c.1701A>G	c.(1699-1701)ttA>ttG	p.L567L	ANKRD30A_ENST00000361713.1_Silent_p.L567L|ANKRD30A_ENST00000374660.1_Silent_p.L567L			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	623					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CTAAAGCCTTAGAATTGAAGG	0.294																																					p.L567L		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.A1701G						.						100	92	94					10																	37447483		1799	4071	5870	SO:0001819	synonymous_variant	91074	exon15			AGCCTTAGAATTG	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1701A>G	chr10.hg19:g.37447483A>G		268.0	0.0		290.0	119.0	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	hg19																																																																																				.	.		0.294	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		G	37447483	A	G	37447483	2	3	23	1	0	0	0	0	0	0	0	1	658	417	15	2		2	ANKRD30A	10	37447483	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	4865496	37447483	98087264	576	2642										
ALOX5	240	hgsc.bcm.edu	37	chr10	45924153	45924153	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcacactccagttcctggccGctcccatctgcttgctgtat	8	16	1	0	rs28395872		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:45924153G>A	ENST00000374391.2	+	7	975	c.922G>A	c.(922-924)Gct>Act	p.A308T	ALOX5_ENST00000542434.1_Missense_Mutation_p.A308T	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	308	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	GTTCCTGGCCGCTCCCATCTG	0.557																																					p.A308T		Atlas-SNP	.											.	ALOX5	88	.	0			c.G922A						.						118	103	108					10																	45924153		2203	4300	6503	SO:0001583	missense	240	exon7			CTGGCCGCTCCCA	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"Arachidonate lipoxygenases"	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.922G>A	chr10.hg19:g.45924153G>A	ENSP00000363512:p.Ala308Thr	142.0	0.0		130.0	43.0	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Missense_Mutation	SNP	ENST00000374391.2	hg19	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.045635	0.93685	.	.	ENSG00000012779	ENST00000542434;ENST00000374391	D;D	0.95853	-3.83;-3.83	5.28	5.28	0.74379	Lipoxygenase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.97586	0.9209	M	0.93016	3.37	0.80722	D	1	D;D;D	0.63046	0.985;0.983;0.992	P;P;P	0.54401	0.704;0.751;0.704	D	0.98366	1.0551	10	0.66056	D	0.02	-31.2213	16.4137	0.83727	0.0:0.0:1.0:0.0	.	308;308;308	B7ZLS0;E5FPY8;P09917	.;.;LOX5_HUMAN	T	308	ENSP00000437634:A308T;ENSP00000363512:A308T	ENSP00000363512:A308T	A	+	1	0	ALOX5	45244159	1.000000	0.71417	0.102000	0.21198	0.903000	0.53119	9.798000	0.99111	2.470000	0.83445	0.655000	0.94253	GCT	.	G|0.973;T|0.027		0.557	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1			A	45924153	G	A	45924153	3	1	23	1	0	0	0	0	1	0	0	0	540	1087	38	1	948	1	ALOX5	10	45924153	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	8476670	45924153	89610594	577	2643										
PPYR1	5540	hgsc.bcm.edu	37	chr10	47087814	47087814	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctgacttgccagcagagcgCccccctggaggagtcggagc					rs555663093	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:47087814delC	ENST00000395716.1	+	2	1116	c.1031delC	c.(1030-1032)gccfs	p.A344fs	NPY4R_ENST00000374312.1_Frame_Shift_Del_p.A344fs			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	344					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										CAGCAGAGCGCCCCCCTGGAG	0.562													CCCCCC|CCCCCC|CCCCC|deletion	14	0.00279553	0.0091	0.0029	5008	,	,		42658	0		0	False		,,,				2504	0				p.A344fs		Atlas-Indel,Pindel	.											.	PPYR1	54	.	0			c.1030delG						.			74,4188		23,28,2080	126	128	127			-9.9	0	10		127	104,8148		50,4,4072	no	frameshift	PPYR1	NM_005972.4		73,32,6152	A1A1,A1R,RR		1.2603,1.7363,1.4224			47087814	178,12336	2203	4300	6503	SO:0001589	frameshift_variant	5540	exon3			.		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"GPCR / Class A : Neuropeptide receptors : Y"	9329	protein-coding gene	gene with protein product		601790	"pancreatic polypeptide receptor 1"	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.1031delC	chr10.hg19:g.47087814delC	ENSP00000379066:p.Ala344fs	215.0	0.0		224.0	25.0	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Frame_Shift_Del	DEL	ENST00000395716.1	hg19	CCDS31193.1																																																																																			.	.		0.562	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1			-	47087814	C	-	47087814	7	5	23	1	0	1	0	1	0	0	0	0	12428	739	26	0	1033	0	PPYR1	10	47087814	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	1163661	47087814	88446933	578	2644										
RBP3	5949	hgsc.bcm.edu	37	chr10	48388542	48388542	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggttgtagcgcaggtcgatcAccagcgcagccgtgtccacc	13	14	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:48388542A>G	ENST00000224600.4	-	1	2449	c.2336T>C	c.(2335-2337)gTg>gCg	p.V779A	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	779	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	CAGGTCGATCACCAGCGCAGC	0.622																																					p.V779A		Atlas-SNP	.											.	RBP3	152	.	0			c.T2336C						.						32	29	30					10																	48388542		2201	4300	6501	SO:0001583	missense	5949	exon1			TCGATCACCAGCG	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.2336T>C	chr10.hg19:g.48388542A>G	ENSP00000224600:p.Val779Ala	126.0	0.0		110.0	43.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	hg19	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	A	10.71	1.426805	0.25726	.	.	ENSG00000107618	ENST00000224600	T	0.72725	-0.68	5.34	5.34	0.76211	Interphotoreceptor retinol-binding (2);	0.618333	0.14333	N	0.326219	T	0.73297	0.3569	M	0.72894	2.215	0.32287	N	0.566875	P	0.43938	0.822	B	0.42495	0.389	T	0.81147	-0.1065	10	0.87932	D	0	-9.2725	14.5119	0.67794	1.0:0.0:0.0:0.0	.	779	P10745	RET3_HUMAN	A	779	ENSP00000224600:V779A	ENSP00000224600:V779A	V	-	2	0	RBP3	48008548	1.000000	0.71417	0.109000	0.21407	0.030000	0.12068	8.563000	0.90723	2.029000	0.59856	0.533000	0.62120	GTG	.	.		0.622	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		G	48388542	A	G	48388542	3	3	23	1	0	0	0	0	1	0	0	0	13172	159	6	2	1423	2	RBP3	10	48388542	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1300728	48388542	87146205	579	2645										
GDF2	2658	hgsc.bcm.edu	37	chr10	48414329	48414329	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgtagcactatcccaggcaTctgttccatccagaacatca	6	14	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:48414329T>C	ENST00000249598.1	-	2	698	c.539A>G	c.(538-540)gAt>gGt	p.D180G		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	180					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						ATCCCAGGCATCTGTTCCATC	0.537																																					p.D180G		Atlas-SNP	.											.	GDF2	77	.	0			c.A539G						.						79	66	70					10																	48414329		2203	4300	6503	SO:0001583	missense	2658	exon2			CAGGCATCTGTTC	AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"Endogenous ligands"	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.539A>G	chr10.hg19:g.48414329T>C	ENSP00000249598:p.Asp180Gly	80.0	0.0		96.0	37.0	NM_016204	Q5VSQ9|Q9Y571	Missense_Mutation	SNP	ENST00000249598.1	hg19	CCDS7219.1	.	.	.	.	.	.	.	.	.	.	T	9.419	1.082480	0.20309	.	.	ENSG00000128802	ENST00000249598	T	0.64991	-0.13	5.32	0.18	0.15068	Transforming growth factor-beta, N-terminal (1);	0.508313	0.19993	N	0.101504	T	0.53126	0.1777	M	0.63428	1.95	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.41734	-0.9492	10	0.22706	T	0.39	.	10.1783	0.42952	0.0:0.345:0.0:0.655	.	180	Q9UK05	GDF2_HUMAN	G	180	ENSP00000249598:D180G	ENSP00000249598:D180G	D	-	2	0	GDF2	48034335	0.211000	0.23529	0.000000	0.03702	0.845000	0.48019	1.812000	0.38952	-0.212000	0.10109	0.482000	0.46254	GAT	.	.		0.537	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204		C	48414329	T	C	48414329	3	2	23	1	0	0	0	0	1	0	0	0	6322	1435	50	2	754	2	GDF2	10	48414329	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	25787	48414329	87120418	580	2646										
MAPK8	5599	hgsc.bcm.edu	37	chr10	49628362	49628362	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcatgggctacaaggaaaaCggtcagcacacacatttatt	10	9	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:49628362C>T	ENST00000374189.1	+	6	796	c.615C>T	c.(613-615)aaC>aaT	p.N205N	MAPK8_ENST00000374174.1_Splice_Site_p.N205N|MAPK8_ENST00000360332.3_Splice_Site_p.N205N|MAPK8_ENST00000395611.3_Splice_Site_p.N205N|MAPK8_ENST00000374182.3_Splice_Site_p.N205N			P45983	MK08_HUMAN	mitogen-activated protein kinase 8	205	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nitric oxide (GO:0071732)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|programmed necrotic cell death (GO:0097300)|regulation of histone deacetylation (GO:0031063)|regulation of protein localization (GO:0032880)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to cadmium ion (GO:0046686)|response to stress (GO:0006950)|response to UV (GO:0009411)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|JUN kinase activity (GO:0004705)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	34		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		ACAAGGAAAACGGTCAGCACA	0.393																																					p.N205N		Atlas-SNP	.											.	MAPK8	118	.	0			c.C615T						.						128	121	123					10																	49628362		2203	4300	6503	SO:0001630	splice_region_variant	5599	exon5			GGAAAACGGTCAG	L26318	CCDS7223.1, CCDS7224.1, CCDS7225.1, CCDS7226.1, CCDS60527.1	10q11	2011-06-09			ENSG00000107643	ENSG00000107643	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6881	protein-coding gene	gene with protein product	"JUN N-terminal kinase"	601158		PRKM8		8137421, 8654373	Standard	NM_002750		Approved	JNK, JNK1, SAPK1	uc001jgp.3	P45983	OTTHUMG00000018172	ENST00000374189.1:c.616+1C>T	chr10.hg19:g.49628362C>T		108.0	0.0		99.0	7.0	NM_139047	B5BTZ5|B7ZLV4|D3DX88|D3DX92|Q15709|Q15712|Q15713|Q308M2	Silent	SNP	ENST00000374189.1	hg19	CCDS7224.1																																																																																			.	.		0.393	MAPK8-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047931.1		Silent	T	49628362	C	T	49628362	5	4	23	1	0	0	0	0	0	0	1	0	9292	550	19	1	633	1	MAPK8	10	49628362	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1214033	49628362	85906385	581	2647										
CHAT	1103	hgsc.bcm.edu	37	chr10	50854625	50854625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctggacgcgccaggaggcGtggagctcagcgacacccac	15	15	1	0	rs536359684		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:50854625G>A	ENST00000337653.2	+	8	1339	c.1186G>A	c.(1186-1188)Gtg>Atg	p.V396M	CHAT_ENST00000395559.2_Missense_Mutation_p.V278M|CHAT_ENST00000351556.3_Missense_Mutation_p.V278M|CHAT_ENST00000339797.1_Missense_Mutation_p.V278M|CHAT_ENST00000455728.2_Missense_Mutation_p.V278M|CHAT_ENST00000395562.2_Missense_Mutation_p.V314M	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	396				V -> L (in Ref. 6; AAB23557). {ECO:0000305}.	adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	GCCAGGAGGCGTGGAGCTCAG	0.632													G|||	1	0.000199681	0	0	5008	,	,		21243	0		0	False		,,,				2504	0.001				p.V396M		Atlas-SNP	.											.	CHAT	162	.	0			c.G1186A						.						98	87	91					10																	50854625		2203	4300	6503	SO:0001583	missense	1103	exon8			GGAGGCGTGGAGC	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.1186G>A	chr10.hg19:g.50854625G>A	ENSP00000337103:p.Val396Met	149.0	0.0		161.0	76.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	hg19	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	G	7.773	0.707778	0.15239	.	.	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	D;D;D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59;-2.59;-2.59	5.27	-0.828	0.10799	.	0.845545	0.10704	N	0.643710	T	0.80979	0.4728	L	0.43646	1.37	0.09310	N	1	B;B	0.22346	0.001;0.068	B;B	0.10450	0.001;0.005	T	0.65327	-0.6195	10	0.33940	T	0.23	-2.3264	5.1433	0.14971	0.2791:0.0:0.476:0.2449	.	278;396	F8W8I2;P28329	.;CLAT_HUMAN	M	278;278;278;396;314;278	ENSP00000343486:V278M;ENSP00000345878:V278M;ENSP00000378926:V278M;ENSP00000337103:V396M;ENSP00000378929:V314M;ENSP00000390521:V278M	ENSP00000337103:V396M	V	+	1	0	CHAT	50524631	0.000000	0.05858	0.045000	0.18777	0.665000	0.39181	-0.417000	0.07088	-0.055000	0.13244	-0.136000	0.14681	GTG	.	.		0.632	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		A	50854625	G	A	50854625	3	1	23	1	0	0	0	0	1	0	0	0	3315	1145	40	1	1260	1	CHAT	10	50854625	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1226263	50854625	84680122	582	2648										
A1CF	29974	hgsc.bcm.edu	37	chr10	52587939	52587939	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aatcatctcttcagaggtagAcagcataagatttcttacat	6	8	4	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:52587939A>G	ENST00000373993.1	-	5	765	c.721T>C	c.(721-723)Tct>Cct	p.S241P	A1CF_ENST00000395489.2_Missense_Mutation_p.S234P|A1CF_ENST00000282641.2_Missense_Mutation_p.S241P|A1CF_ENST00000493415.1_5'UTR|A1CF_ENST00000374001.2_Missense_Mutation_p.S241P|A1CF_ENST00000373997.3_Missense_Mutation_p.S241P|A1CF_ENST00000395495.1_Intron|A1CF_ENST00000373995.3_Missense_Mutation_p.S249P			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	241	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						TCAGAGGTAGACAGCATAAGA	0.358																																					p.S249P		Atlas-SNP	.											.	A1CF	190	.	0			c.T745C						.						135	131	132					10																	52587939		2203	4300	6503	SO:0001583	missense	29974	exon8			AGGTAGACAGCAT	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"RNA binding motif (RRM) containing"	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.721T>C	chr10.hg19:g.52587939A>G	ENSP00000363105:p.Ser241Pro	58.0	0.0		63.0	20.0	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	hg19	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.320777	0.41096	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395488;ENST00000395489	T;T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88;2.88	5.48	4.34	0.51931	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.234804	0.44688	N	0.000421	T	0.10594	0.0259	L	0.56199	1.76	0.40079	D	0.976116	B;B;B;B	0.14438	0.01;0.003;0.001;0.005	B;B;B;B	0.17433	0.008;0.008;0.002;0.018	T	0.11060	-1.0603	10	0.45353	T	0.12	.	5.0867	0.14687	0.7553:0.0:0.0856:0.1591	.	234;241;241;249	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	P	241;241;241;249;241;224;234	ENSP00000363113:S241P;ENSP00000363105:S241P;ENSP00000363109:S241P;ENSP00000363107:S249P;ENSP00000282641:S241P;ENSP00000378868:S234P	ENSP00000282641:S241P	S	-	1	0	A1CF	52257945	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	3.758000	0.55220	0.910000	0.36722	0.460000	0.39030	TCT	.	.		0.358	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576		G	52587939	A	G	52587939	3	3	23	1	0	0	0	0	1	0	0	0	2	275	10	2	1091	2	A1CF	10	52587939	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1733314	52587939	82946808	583	2649										
CSTF2T	23283	hgsc.bcm.edu	37	chr10	53458564	53458564	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctgcatcagaggaggaatgTccttcacaggtcttctagcc	10	11	5	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:53458564T>A	ENST00000331173.4	-	1	791	c.746A>T	c.(745-747)gAc>gTc	p.D249V	PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron|PRKG1_ENST00000373980.4_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	249					mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		AGGAGGAATGTCCTTCACAGG	0.572																																					p.D249V		Atlas-SNP	.											.	CSTF2T	64	.	0			c.A746T						.						40	44	43					10																	53458564		2203	4300	6503	SO:0001583	missense	23283	exon1			GGAATGTCCTTCA	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"RNA binding motif (RRM) containing"	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.746A>T	chr10.hg19:g.53458564T>A	ENSP00000332444:p.Asp249Val	85.0	0.0		65.0	24.0	NM_015235	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Missense_Mutation	SNP	ENST00000331173.4	hg19	CCDS7245.1	.	.	.	.	.	.	.	.	.	.	T	16.16	3.044253	0.55110	.	.	ENSG00000177613	ENST00000331173	T	0.21543	2.0	4.8	3.68	0.42216	.	0.054486	0.64402	D	0.000001	T	0.17746	0.0426	N	0.08118	0	0.58432	D	0.999996	D	0.69078	0.997	P	0.60117	0.869	T	0.03051	-1.1078	10	0.49607	T	0.09	-23.1109	5.4405	0.16507	0.0:0.1872:0.0:0.8128	.	249	Q9H0L4	CSTFT_HUMAN	V	249	ENSP00000332444:D249V	ENSP00000332444:D249V	D	-	2	0	CSTF2T	53128570	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	2.194000	0.42668	2.149000	0.67028	0.533000	0.62120	GAC	.	.		0.572	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235		A	53458564	T	A	53458564	3	1	23	1	0	0	0	0	1	0	0	0	3987	1667	58	4	1108	4	CSTF2T	10	53458564	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	870625	53458564	82076183	584	2650										
SIRT1	23411	hgsc.bcm.edu	37	chr10	69672422	69672422	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttactgaaaaacctccacgaAcacaaaaagaattggcttat	5	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:69672422A>G	ENST00000212015.6	+	8	1602	c.1549A>G	c.(1549-1551)Aca>Gca	p.T517A	SIRT1_ENST00000432464.1_Missense_Mutation_p.T222A|SIRT1_ENST00000406900.1_Missense_Mutation_p.T214A|SIRT1_ENST00000403579.1_Missense_Mutation_p.T214A	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	517	Interaction with CCAR2.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						ACCTCCACGAACACAAAAAGA	0.388																																					p.T517A		Atlas-SNP	.											.	SIRT1	38	.	0			c.A1549G						.						76	76	76					10																	69672422		2203	4300	6503	SO:0001583	missense	23411	exon8			CCACGAACACAAA	AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1", "sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.1549A>G	chr10.hg19:g.69672422A>G	ENSP00000212015:p.Thr517Ala	182.0	0.0		175.0	73.0	NM_012238	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Missense_Mutation	SNP	ENST00000212015.6	hg19	CCDS7273.1	.	.	.	.	.	.	.	.	.	.	A	9.115	1.007529	0.19199	.	.	ENSG00000096717	ENST00000212015;ENST00000432464;ENST00000406900;ENST00000403579	T;T;T;T	0.22336	2.53;1.97;1.96;1.96	5.68	0.102	0.14522	.	0.492715	0.20777	N	0.085863	T	0.14270	0.0345	L	0.31476	0.935	0.24340	N	0.994965	B;B	0.15141	0.001;0.012	B;B	0.13407	0.005;0.009	T	0.29792	-1.0000	10	0.09084	T	0.74	-2.3804	16.9373	0.86206	0.3923:0.6077:0.0:0.0	.	214;517	B0QZ35;Q96EB6	.;SIRT1_HUMAN	A	517;222;214;214	ENSP00000212015:T517A;ENSP00000409208:T222A;ENSP00000384508:T214A;ENSP00000384063:T214A	ENSP00000212015:T517A	T	+	1	0	SIRT1	69342428	0.970000	0.33590	0.999000	0.59377	0.995000	0.86356	0.263000	0.18478	0.058000	0.16222	0.528000	0.53228	ACA	.	.		0.388	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1			G	69672422	A	G	69672422	3	3	23	1	0	0	0	0	1	0	0	0	14352	43	2	2	1579	2	SIRT1	10	69672422	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	16213858	69672422	65862325	585	2651										
SAR1A	56681	hgsc.bcm.edu	37	chr10	71912317	71912317	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acatgaacacttccatggggCgagcattcagctccttcagg	10	12	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:71912317C>T	ENST00000373242.2	-	8	708	c.512G>A	c.(511-513)cGc>cAc	p.R171H	SAR1A_ENST00000373241.4_Missense_Mutation_p.R171H|SAR1A_ENST00000373238.1_Missense_Mutation_p.R171H|SAR1A_ENST00000431664.2_Missense_Mutation_p.R171H|SAR1A_ENST00000458634.2_Missense_Mutation_p.R128H	NM_001142648.1	NP_001136120.1	Q9NR31	SAR1A_HUMAN	secretion associated, Ras related GTPase 1A	171					intracellular protein transport (GO:0006886)|negative regulation of cargo loading into COPII-coated vesicle (GO:1901303)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)	6						TTCCATGGGGCGAGCATTCAG	0.502																																					p.R171H		Atlas-SNP	.											.	SAR1A	19	.	0			c.G512A						.						76	66	69					10																	71912317		2203	4300	6503	SO:0001583	missense	56681	exon7			ATGGGGCGAGCAT		CCDS7298.1	10q22.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000079332	ENSG00000079332			10534	protein-coding gene	gene with protein product		607691	"SAR1a gene homolog (S. cerevisiae) 1", "SAR1a gene homolog 1 (S. cerevisiae)", "SAR1 homolog A (S. cerevisiae)"	SARA1		10871277	Standard	NM_020150		Approved	SAR1, Sara	uc010qji.2	Q9NR31	OTTHUMG00000018400	ENST00000373242.2:c.512G>A	chr10.hg19:g.71912317C>T	ENSP00000362339:p.Arg171His	92.0	0.0		83.0	38.0	NM_020150	B4DQ19	Missense_Mutation	SNP	ENST00000373242.2	hg19	CCDS7298.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.432073	0.83776	.	.	ENSG00000079332	ENST00000373241;ENST00000373239;ENST00000373238;ENST00000373242;ENST00000431664;ENST00000458634;ENST00000395026	T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27	5.61	4.68	0.58851	.	0.051164	0.64402	D	0.000001	T	0.71617	0.3361	M	0.75615	2.305	0.80722	D	1	D	0.60575	0.988	P	0.47075	0.536	T	0.76686	-0.2868	10	0.66056	D	0.02	.	14.8863	0.70572	0.0:0.8556:0.1444:0.0	.	171	Q9NR31	SAR1A_HUMAN	H	171;171;171;171;171;128;90	ENSP00000362338:R171H;ENSP00000362335:R171H;ENSP00000362339:R171H;ENSP00000399698:R171H;ENSP00000437979:R128H	ENSP00000362335:R171H	R	-	2	0	SAR1A	71582323	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	1.316000	0.45131	0.585000	0.79938	CGC	.	.		0.502	SAR1A-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048500.2			T	71912317	C	T	71912317	3	4	23	1	0	0	0	0	1	0	0	0	13854	768	27	1	88	1	SAR1A	10	71912317	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2239895	71912317	63622430	586	2652										
PSAP	5660	hgsc.bcm.edu	37	chr10	73594212	73594212	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttcacattctggcaccacaCtgccgagcccctggtgcatt	8	16	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:73594212C>G	ENST00000394936.3	-	2	238	c.91G>C	c.(91-93)Gtg>Ctg	p.V31L	PSAP_ENST00000394934.1_Missense_Mutation_p.V31L			P07602	SAP_HUMAN	prosaposin	31	Saposin A-type 1. {ECO:0000255|PROSITE- ProRule:PRU00414}.				blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						TGGCACCACACTGCCGAGCCC	0.582																																					p.V31L		Atlas-SNP	.											.	PSAP	43	.	0			c.G91C						.						47	42	44					10																	73594212		2203	4300	6503	SO:0001583	missense	5660	exon2			ACCACACTGCCGA	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"Endogenous ligands"	9498	protein-coding gene	gene with protein product	"variant Gaucher disease and variant metachromatic leukodystrophy"	176801	"sphingolipid activator protein-1"	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.91G>C	chr10.hg19:g.73594212C>G	ENSP00000378394:p.Val31Leu	99.0	0.0		72.0	28.0	NM_001042466	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Missense_Mutation	SNP	ENST00000394936.3	hg19	CCDS7311.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.848757	0.91277	.	.	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000394929;ENST00000404083	T;T	0.57436	0.4;0.4	5.67	5.67	0.87782	Saposin type A (3);	0.183599	0.48286	D	0.000188	T	0.69396	0.3106	M	0.65975	2.015	0.38631	D	0.951371	D	0.56287	0.975	P	0.62184	0.899	T	0.68685	-0.5343	10	0.37606	T	0.19	-18.5668	18.5336	0.91001	0.0:1.0:0.0:0.0	.	31	P07602	SAP_HUMAN	L	31;31;31;31;31;34	ENSP00000378394:V31L;ENSP00000378392:V31L	ENSP00000350063:V31L	V	-	1	0	PSAP	73264218	0.990000	0.36364	0.960000	0.40013	0.978000	0.69477	2.870000	0.48451	2.680000	0.91292	0.563000	0.77884	GTG	.	.		0.582	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778		G	73594212	C	G	73594212	3	3	23	1	0	0	0	0	1	0	0	0	12655	565	20	4	1551	4	PSAP	10	73594212	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1681895	73594212	61940535	587	2653										
CHST3	9469	hgsc.bcm.edu	37	chr10	73767711	73767711	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcgacccccgggccgtgctgGcctcgcgcatggtggccttc	15	17	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:73767711G>A	ENST00000373115.4	+	3	1359	c.922G>A	c.(922-924)Gcc>Acc	p.A308T		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	308					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						GGCCGTGCTGGCCTCGCGCAT	0.701																																					p.A308T		Atlas-SNP	.											.	CHST3	36	.	0			c.G922A						.						5	6	6					10																	73767711		1903	3753	5656	SO:0001583	missense	9469	exon3			GTGCTGGCCTCGC	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"Sulfotransferases, membrane-bound"	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.922G>A	chr10.hg19:g.73767711G>A	ENSP00000362207:p.Ala308Thr	202.0	0.0		195.0	89.0	NM_004273	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	hg19	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	G	35	5.491125	0.96339	.	.	ENSG00000122863	ENST00000373115	D	0.83163	-1.69	5.55	5.55	0.83447	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.88683	0.6503	M	0.66506	2.035	0.80722	D	1	D	0.56746	0.977	P	0.57425	0.82	D	0.88319	0.2961	10	0.48119	T	0.1	-28.5478	18.5034	0.90889	0.0:0.0:1.0:0.0	.	308	Q7LGC8	CHST3_HUMAN	T	308	ENSP00000362207:A308T	ENSP00000362207:A308T	A	+	1	0	CHST3	73437717	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.855000	0.99526	2.630000	0.89119	0.561000	0.74099	GCC	.	.		0.701	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273		A	73767711	G	A	73767711	3	1	23	1	0	0	0	0	1	0	0	0	3407	1203	42	3	928	3	CHST3	10	73767711	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	173499	73767711	61767036	588	2654										
MYST4	23522	hgsc.bcm.edu	37	chr10	76784946	76784949	+	Frame_Shift_Del	DEL	ACAA	ACAA	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catcagcctgggaagaaaagAcaaacagaggaagaggaagg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	ACAA	ACAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:76784946_76784949delACAA	ENST00000287239.4	+	17	4092_4095	c.3603_3606delACAA	c.(3601-3606)agacaafs	p.RQ1201fs	KAT6B_ENST00000372725.1_Frame_Shift_Del_p.RQ909fs|KAT6B_ENST00000490365.1_3'UTR|KAT6B_ENST00000372711.1_Frame_Shift_Del_p.RQ1018fs|RP11-77G23.2_ENST00000413431.1_RNA|KAT6B_ENST00000372724.1_Frame_Shift_Del_p.RQ909fs|RP11-77G23.5_ENST00000436608.1_RNA|KAT6B_ENST00000372714.1_Frame_Shift_Del_p.RQ909fs	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1201					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GGAAGAAAAGACAAACAGAGGAAG	0.451																																					p.1201_1202del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.3602_3605del						.																																			SO:0001589	frameshift_variant	23522	exon17			.	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.3603_3606delACAA	chr10.hg19:g.76784946_76784949delACAA	ENSP00000287239:p.Arg1201fs	272.0	0.0		211.0	73.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Frame_Shift_Del	DEL	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.451	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		-	76784949	ACAA	-	76784946	7	5	23	1	0	1	0	1	0	0	0	0	10114	272	10	0	3661	0	MYST4	10	76784946	Frame_Shift_Del	DEL	ACAA	TCGA-4R-AA8I-01A-11D-A382-10	3017235	76784946	58749801	589	2655										
ZNF503	84858	hgsc.bcm.edu	37	chr10	77159849	77159849	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgaaacacccccgccgccgCccccgccaccgccaccgcct							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:77159849delC	ENST00000372524.4	-	2	1085	c.599delG	c.(598-600)ggcfs	p.G204fs	ZNF503-AS2_ENST00000486015.1_RNA|RP11-399K21.11_ENST00000418818.2_lincRNA|ZNF503-AS2_ENST00000466942.2_RNA|ZNF503_ENST00000535216.1_Frame_Shift_Del_p.G204fs|ZNF503-AS2_ENST00000425916.3_RNA	NM_032772.4	NP_116161.2	Q96F45	ZN503_HUMAN	zinc finger protein 503	204	Gly-rich.				G1 to G0 transition involved in cell differentiation (GO:0070315)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|neural precursor cell proliferation (GO:0061351)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			lung(4)|ovary(1)|skin(1)	6	all_cancers(46;0.105)|all_epithelial(25;0.00449)|Prostate(51;0.0112)|Ovarian(15;0.088)					Cccgccgccgcccccgccacc	0.692																																					p.G200fs		Atlas-Indel,Pindel	.											.	ZNF503	25	.	0			c.600delC						.						2	2	2					10																	77159849		1491	3151	4642	SO:0001589	frameshift_variant	84858	exon2			.	AK127647	CCDS7350.1	10q22.3	2011-02-09			ENSG00000165655	ENSG00000165655		"Zinc fingers, C2H2-type"	23589	protein-coding gene	gene with protein product		613902				12477932	Standard	NM_032772		Approved	FLJ45745, MGC2555	uc001jxg.3	Q96F45	OTTHUMG00000018526	ENST00000372524.4:c.599delG	chr10.hg19:g.77159849delC	ENSP00000361602:p.Gly204fs	75.0	0.0		74.0	28.0	NM_032772	Q8NAC5|Q96E25|Q96IJ0	Frame_Shift_Del	DEL	ENST00000372524.4	hg19	CCDS7350.1																																																																																			.	.		0.692	ZNF503-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048826.1	NM_032772		-	77159849	C	-	77159849	7	5	23	1	0	1	0	1	0	0	0	0	17966	739	26	0	1345	0	ZNF503	10	77159849	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	374903	77159849	58374898	590	2656										
ZMIZ1	57178	hgsc.bcm.edu	37	chr10	81065903	81065903	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atcccacgtgcagctggcggCcggtgcccatcaagtcggac	13	15	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:81065903C>T	ENST00000334512.5	+	22	3042	c.2470C>T	c.(2470-2472)Ccg>Tcg	p.P824S	ZMIZ1_ENST00000446377.2_5'Flank	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	824					artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CAGCTGGCGGCCGGTGCCCAT	0.607																																					p.P824S		Atlas-SNP	.											.	ZMIZ1	101	.	0			c.C2470T						.						69	58	61					10																	81065903		2203	4300	6503	SO:0001583	missense	57178	exon22			TGGCGGCCGGTGC	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"Zinc fingers, MIZ-type"	16493	protein-coding gene	gene with protein product		607159	"retinoic acid induced 17"	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.2470C>T	chr10.hg19:g.81065903C>T	ENSP00000334474:p.Pro824Ser	51.0	0.0		42.0	14.0	NM_020338	Q5JSH9|Q7Z7E6	Missense_Mutation	SNP	ENST00000334512.5	hg19	CCDS7357.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.422601	0.83559	.	.	ENSG00000108175	ENST00000334512;ENST00000360331;ENST00000372347	T	0.39997	1.05	4.6	4.6	0.57074	.	0.000000	0.41396	D	0.000894	T	0.66703	0.2816	M	0.80183	2.485	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	T	0.72520	-0.4268	10	0.62326	D	0.03	-7.5952	17.8001	0.88584	0.0:1.0:0.0:0.0	.	824	Q9ULJ6	ZMIZ1_HUMAN	S	824;754;726	ENSP00000334474:P824S	ENSP00000334474:P824S	P	+	1	0	ZMIZ1	80735909	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.458000	0.80787	2.275000	0.75901	0.491000	0.48974	CCG	.	.		0.607	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338		T	81065903	C	T	81065903	3	4	23	1	0	0	0	0	1	0	0	0	17711	739	26	3	2540	3	ZMIZ1	10	81065903	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3906054	81065903	54468844	591	2657										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88197700	88197700	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagattcataaaactcaaaaAttttttgagcatctctgtca	5	7	4	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:88197700A>T	ENST00000298767.5	-	18	3956	c.3484T>A	c.(3484-3486)Ttt>Att	p.F1162I	WAPAL_ENST00000263070.7_Missense_Mutation_p.F374I|WAPAL_ENST00000484070.1_5'UTR|WAPAL_ENST00000372075.1_Missense_Mutation_p.F374I	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	1162	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						AAACTCAAAAATTTTTTGAGC	0.318																																					p.F1162I		Atlas-SNP	.											.	WAPAL	81	.	0			c.T3484A						.						54	61	59					10																	88197700		2203	4300	6503	SO:0001583	missense	23063	exon18			TCAAAAATTTTTT	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.3484T>A	chr10.hg19:g.88197700A>T	ENSP00000298767:p.Phe1162Ile	497.0	0.0		415.0	133.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	A	35	5.443210	0.96187	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076;ENST00000372075;ENST00000263070	T;T;T	0.40476	1.03;1.03;1.03	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.65760	0.2722	M	0.75615	2.305	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;1.0	D;D;D;D	0.87578	0.986;0.998;0.986;0.996	T	0.69826	-0.5040	10	0.87932	D	0	.	16.0204	0.80478	1.0:0.0:0.0:0.0	.	1156;1200;1162;1199	B2RTX8;E9PH12;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	I	1247;1162;1247;374;374	ENSP00000298767:F1162I;ENSP00000361145:F374I;ENSP00000263070:F374I	ENSP00000263070:F374I	F	-	1	0	WAPAL	88187680	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.950000	0.93019	2.174000	0.68829	0.533000	0.62120	TTT	.	.		0.318	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		T	88197700	A	T	88197700	3	4	23	1	0	0	0	0	1	0	0	0	17263	101	4	4	96	4	WAPAL	10	88197700	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	7131797	88197700	47337047	592	2658										
PANK1	53354	hgsc.bcm.edu	37	chr10	91371568	91371568	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgaacctgtgcatagcacagCtgggaaagcggatgaagtgc	14	8	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:91371568C>A	ENST00000307534.4	-	2	1096	c.941G>T	c.(940-942)aGc>aTc	p.S314I	PANK1_ENST00000342512.3_Missense_Mutation_p.S89I|PANK1_ENST00000322191.6_Missense_Mutation_p.S89I|PANK1_ENST00000371774.2_Missense_Mutation_p.S116I	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	314					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell periphery (GO:0071944)|clathrin coat (GO:0030118)|cytosol (GO:0005829)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			cervix(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	11						CATAGCACAGCTGGGAAAGCG	0.527																																					p.S314I		Atlas-SNP	.											.	PANK1	35	.	0			c.G941T						.						92	79	83					10																	91371568		2203	4300	6503	SO:0001583	missense	53354	exon2			GCACAGCTGGGAA	AF355198	CCDS7405.1, CCDS7406.1, CCDS31244.1	10q23.31	2008-05-14	2002-11-13	2002-11-15	ENSG00000152782	ENSG00000152782			8598	protein-coding gene	gene with protein product		606160	"pantothenate kinase"	PANK		11809413	Standard	NM_148977		Approved	MGC24596, PANK1a, PANK1b	uc001kgp.2	Q8TE04	OTTHUMG00000018718	ENST00000307534.4:c.941G>T	chr10.hg19:g.91371568C>A	ENSP00000302108:p.Ser314Ile	134.0	0.0		128.0	51.0	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Missense_Mutation	SNP	ENST00000307534.4	hg19	CCDS31244.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.011705	0.54468	.	.	ENSG00000152782	ENST00000342512;ENST00000322191;ENST00000371774;ENST00000307534;ENST00000371775	D;D;D;D	0.99503	-6.03;-6.03;-6.03;-6.03	6.11	4.11	0.48088	.	0.133324	0.64402	D	0.000001	D	0.98845	0.9610	L	0.35854	1.095	0.41211	D	0.986442	B;D;B;B	0.58620	0.215;0.983;0.0;0.215	B;P;B;B	0.55923	0.067;0.787;0.003;0.067	D	0.99816	1.1044	10	0.72032	D	0.01	.	16.7682	0.85529	0.0:0.5528:0.4472:0.0	.	116;314;89;89	Q8TE04-4;Q8TE04;Q8TE04-3;Q8TE04-2	.;PANK1_HUMAN;.;.	I	89;89;116;314;177	ENSP00000345118:S89I;ENSP00000318526:S89I;ENSP00000360839:S116I;ENSP00000302108:S314I	ENSP00000302108:S314I	S	-	2	0	PANK1	91361548	0.992000	0.36948	1.000000	0.80357	0.997000	0.91878	1.911000	0.39937	1.459000	0.47892	0.655000	0.94253	AGC	.	.		0.527	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	91371568	C	A	91371568	3	1	23	1	0	0	0	0	1	0	0	0	11425	797	28	3	879	3	PANK1	10	91371568	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3173868	91371568	44163179	593	2659										
KIF20B	9585	hgsc.bcm.edu	37	chr10	91520371	91520371	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acctctatcgacaagttttgAaatttccagaaataaaatag	5	7	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:91520371A>T	ENST00000371728.3	+	28	4834	c.4769A>T	c.(4768-4770)gAa>gTa	p.E1590V	KIF20B_ENST00000416354.1_Missense_Mutation_p.E1620V|KIF20B_ENST00000260753.4_Missense_Mutation_p.E1550V|KIF20B_ENST00000394289.2_Missense_Mutation_p.E1590V|KIF20B_ENST00000478929.1_3'UTR	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1590	Interaction with PIN1.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						ACAAGTTTTGAAATTTCCAGA	0.353																																					p.E1550V		Atlas-SNP	.											.	KIF20B	191	.	0			c.A4649T						.						56	55	55					10																	91520371		2203	4300	6503	SO:0001583	missense	9585	exon28			GTTTTGAAATTTC	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.4769A>T	chr10.hg19:g.91520371A>T	ENSP00000360793:p.Glu1590Val	307.0	0.0		257.0	97.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	hg19		.	.	.	.	.	.	.	.	.	.	A	13.94	2.386794	0.42308	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	4.7	4.7	0.59300	.	0.132784	0.34178	N	0.004193	T	0.49150	0.1540	L	0.42245	1.32	0.33487	D	0.588244	D;D	0.61697	0.964;0.99	P;P	0.59487	0.601;0.858	T	0.60840	-0.7183	10	0.42905	T	0.14	-10.075	10.7268	0.46072	1.0:0.0:0.0:0.0	.	1590;1550	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	V	1550;1620;1590;1590	ENSP00000260753:E1550V;ENSP00000411545:E1620V;ENSP00000377830:E1590V;ENSP00000360793:E1590V	ENSP00000260753:E1550V	E	+	2	0	KIF20B	91510351	1.000000	0.71417	0.991000	0.47740	0.351000	0.29236	3.735000	0.55044	2.112000	0.64535	0.482000	0.46254	GAA	.	.		0.353	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		T	91520371	A	T	91520371	3	4	23	1	0	0	0	0	1	0	0	0	8296	246	9	4	4755	4	KIF20B	10	91520371	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	148803	91520371	44014376	594	2660										
ANKRD1	27063	hgsc.bcm.edu	37	chr10	92675939	92675939	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaggaataccttatctcgggCgctaatttttgctcctttat	7	9	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:92675939C>T	ENST00000371697.3	-	6	888	c.640G>A	c.(640-642)Gcc>Acc	p.A214T		NM_014391.2	NP_055206.2	Q15327	ANKR1_HUMAN	ankyrin repeat domain 1 (cardiac muscle)	214					cardiac muscle tissue morphogenesis (GO:0055008)|cellular lipid metabolic process (GO:0044255)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|skeletal muscle cell differentiation (GO:0035914)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I band (GO:0031674)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|p53 binding (GO:0002039)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|titin binding (GO:0031432)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|prostate(3)|skin(1)	27		Colorectal(252;0.0475)				TTATCTCGGGCGCTAATTTTT	0.527																																					p.A214T		Atlas-SNP	.											.	ANKRD1	50	.	0			c.G640A						.						84	81	82					10																	92675939		2203	4300	6503	SO:0001583	missense	27063	exon6			CTCGGGCGCTAAT	X83703	CCDS7412.1	10q23.33	2014-09-17			ENSG00000148677	ENSG00000148677		"Ankyrin repeat domain containing"	15819	protein-coding gene	gene with protein product		609599				7730328	Standard	NM_014391		Approved	C-193, ALRP, CARP, CVARP, MCARP	uc001khe.1	Q15327	OTTHUMG00000018734	ENST00000371697.3:c.640G>A	chr10.hg19:g.92675939C>T	ENSP00000360762:p.Ala214Thr	113.0	0.0		76.0	17.0	NM_014391	Q96LE7	Missense_Mutation	SNP	ENST00000371697.3	hg19	CCDS7412.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.941171	0.53079	.	.	ENSG00000148677	ENST00000371697	T	0.65364	-0.15	5.35	4.44	0.53790	Ankyrin repeat-containing domain (4);	0.075470	0.56097	D	0.000039	T	0.55768	0.1941	L	0.52573	1.65	0.48135	D	0.999596	B	0.18863	0.031	B	0.21917	0.037	T	0.52555	-0.8560	10	0.30854	T	0.27	.	13.4315	0.61057	0.0:0.9243:0.0:0.0757	.	214	Q15327	ANKR1_HUMAN	T	214	ENSP00000360762:A214T	ENSP00000360762:A214T	A	-	1	0	ANKRD1	92665919	0.868000	0.29978	0.996000	0.52242	0.966000	0.64601	1.646000	0.37249	2.511000	0.84671	0.484000	0.47621	GCC	.	.		0.527	ANKRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049357.1	NM_014391		T	92675939	C	T	92675939	3	4	23	1	0	0	0	0	1	0	0	0	637	768	27	1	335	1	ANKRD1	10	92675939	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1155568	92675939	42858808	595	2661										
RRP12	23223	hgsc.bcm.edu	37	chr10	99131898	99131898	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcagcacacggagccaaggCcacgaccaggtccaggacag	13	14	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:99131898C>G	ENST00000370992.4	-	20	2386	c.2275G>C	c.(2275-2277)Gcc>Ccc	p.A759P	RRP12_ENST00000414986.1_Missense_Mutation_p.A698P|RRP12_ENST00000315563.6_Missense_Mutation_p.A659P|RRP12_ENST00000536831.1_Missense_Mutation_p.A477P|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	759						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GGAGCCAAGGCCACGACCAGG	0.612																																					p.A759P		Atlas-SNP	.											.	RRP12	97	.	0			c.G2275C						.						85	68	73					10																	99131898		2203	4300	6503	SO:0001583	missense	23223	exon20			CCAAGGCCACGAC		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"KIAA0690"	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.2275G>C	chr10.hg19:g.99131898C>G	ENSP00000360031:p.Ala759Pro	75.0	0.0		77.0	17.0	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	hg19	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.917972	0.92249	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	5.47	5.47	0.80525	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81484	0.4832	M	0.81942	2.565	0.80722	D	1	D;D;D;D	0.89917	0.999;0.996;1.0;0.998	D;D;D;D	0.75020	0.941;0.953;0.985;0.921	D	0.83454	0.0050	10	0.66056	D	0.02	-21.4836	13.5966	0.61994	0.0:0.9258:0.0:0.0742	.	698;659;477;759	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	P	759;659;698;477	ENSP00000360031:A759P;ENSP00000324315:A659P;ENSP00000414863:A698P;ENSP00000446184:A477P	ENSP00000324315:A659P	A	-	1	0	RRP12	99121888	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.492000	0.66893	2.568000	0.86640	0.655000	0.94253	GCC	.	.		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		G	99131898	C	G	99131898	3	3	23	1	0	0	0	0	1	0	0	0	13701	739	26	4	1678	4	RRP12	10	99131898	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	6455959	99131898	36402849	596	2662										
PKD2L1	9033	hgsc.bcm.edu	37	chr10	102058491	102058491	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catgttctcatagtagatgaAggagtgggagccatggccca	13	8	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:102058491A>G	ENST00000318222.3	-	4	941	c.559T>C	c.(559-561)Ttc>Ctc	p.F187L	PKD2L1_ENST00000353274.3_Missense_Mutation_p.F187L|PKD2L1_ENST00000338519.3_Missense_Mutation_p.F187L	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	187					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)			NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		TAGTAGATGAAGGAGTGGGAG	0.547																																					p.F187L		Atlas-SNP	.											.	PKD2L1	103	.	0			c.T559C						.						83	83	83					10																	102058491		2203	4300	6503	SO:0001583	missense	9033	exon4			AGATGAAGGAGTG	AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"Voltage-gated ion channels / Transient receptor potential cation channels"	9011	protein-coding gene	gene with protein product	"transient receptor potential cation channel, subfamily P, member 3"	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.559T>C	chr10.hg19:g.102058491A>G	ENSP00000325296:p.Phe187Leu	130.0	0.0		131.0	35.0	NM_016112	O75972|Q5W039|Q9UP35|Q9UPA2	Missense_Mutation	SNP	ENST00000318222.3	hg19	CCDS7492.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.850504	0.71719	.	.	ENSG00000107593	ENST00000338519;ENST00000353274;ENST00000318222;ENST00000339977	T;T;T	0.69040	-0.37;-0.37;-0.37	5.32	5.32	0.75619	Polycystin cation channel, PKD1/PKD2 (1);	0.048691	0.85682	D	0.000000	T	0.58366	0.2117	L	0.41236	1.265	0.50632	D	0.999888	B;B	0.22480	0.07;0.004	B;B	0.26969	0.075;0.029	T	0.53954	-0.8365	10	0.21540	T	0.41	-21.7473	14.4704	0.67512	1.0:0.0:0.0:0.0	.	140;187	Q1L4F0;Q9P0L9	.;PK2L1_HUMAN	L	187	ENSP00000345068:F187L;ENSP00000266049:F187L;ENSP00000325296:F187L	ENSP00000325296:F187L	F	-	1	0	PKD2L1	102048481	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.449000	0.80643	2.015000	0.59207	0.459000	0.35465	TTC	.	.		0.547	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112		G	102058491	A	G	102058491	3	3	23	1	0	0	0	0	1	0	0	0	11976	72	3	2	1910	2	PKD2L1	10	102058491	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2926593	102058491	33476256	597	2663										
SEMA4G	57715	hgsc.bcm.edu	37	chr10	102740362	102740362	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctggatccacaaggccgtagTcctgggctctgggatgcaca	13	12	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:102740362T>A	ENST00000370250.4	+	11	1752	c.1379T>A	c.(1378-1380)gTc>gAc	p.V460D	MRPL43_ENST00000318325.2_Intron|MRPL43_ENST00000370242.4_Intron|RP11-108L7.4_ENST00000447344.1_RNA|MRPL43_ENST00000370241.3_Intron|SEMA4G_ENST00000517724.1_Missense_Mutation_p.V460D|SEMA4G_ENST00000210633.3_Missense_Mutation_p.V460D	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	460	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		AAGGCCGTAGTCCTGGGCTCT	0.507																																					p.V460D		Atlas-SNP	.											.	SEMA4G	55	.	0			c.T1379A						.						119	111	114					10																	102740362		2203	4300	6503	SO:0001583	missense	57715	exon11			CCGTAGTCCTGGG	AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.1379T>A	chr10.hg19:g.102740362T>A	ENSP00000359270:p.Val460Asp	108.0	0.0		117.0	43.0	NM_001203244	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Missense_Mutation	SNP	ENST00000370250.4	hg19		.	.	.	.	.	.	.	.	.	.	T	13.40	2.226411	0.39300	.	.	ENSG00000095539	ENST00000519649;ENST00000457585;ENST00000370250;ENST00000517724;ENST00000210633	T;T;T;T	0.12147	2.71;2.71;2.71;2.71	5.02	5.02	0.67125	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.700209	0.14484	N	0.316768	T	0.13415	0.0325	L	0.37850	1.14	0.58432	D	0.999998	B;B;B	0.27594	0.14;0.182;0.148	B;B;B	0.32533	0.055;0.147;0.039	T	0.09618	-1.0666	10	0.15066	T	0.55	.	13.5579	0.61770	0.0:0.0:0.0:1.0	.	460;460;460	Q9NTN9;A1A5C6;Q9NTN9-2	SEM4G_HUMAN;.;.	D	460	ENSP00000428896:V460D;ENSP00000359270:V460D;ENSP00000430175:V460D;ENSP00000210633:V460D	ENSP00000210633:V460D	V	+	2	0	SEMA4G	102730352	1.000000	0.71417	0.996000	0.52242	0.881000	0.50899	2.782000	0.47758	1.888000	0.54679	0.254000	0.18369	GTC	.	.		0.507	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2			A	102740362	T	A	102740362	3	1	23	1	0	0	0	0	1	0	0	0	14051	1667	58	4	1421	4	SEMA4G	10	102740362	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	681871	102740362	32794385	598	2664										
LDB1	8861	hgsc.bcm.edu	37	chr10	103870859	103870859	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgaagccgtttgttaagctcAaatattctgtagtcagtttg	9	6	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:103870859A>G	ENST00000425280.1	-	4	558	c.216T>C	c.(214-216)ttT>ttC	p.F72F	LDB1_ENST00000361198.5_Silent_p.F36F|LDB1_ENST00000490751.1_5'UTR	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	72					anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		TGTTAAGCTCAAATATTCTGT	0.542																																					p.F72F		Atlas-SNP	.											.	LDB1	61	.	0			c.T216C						.						162	160	161					10																	103870859		2203	4300	6503	SO:0001819	synonymous_variant	8861	exon4			AAGCTCAAATATT	AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"carboxy terminal LIM domain protein 2"	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.216T>C	chr10.hg19:g.103870859A>G		71.0	0.0		67.0	37.0	NM_001113407	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Silent	SNP	ENST00000425280.1	hg19	CCDS44472.1																																																																																			.	.		0.542	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407		G	103870859	A	G	103870859	2	3	23	1	0	0	0	0	0	0	0	1	8704	127	5	2		2	LDB1	10	103870859	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1130497	103870859	31663888	599	2665										
LOC729020	729020	hgsc.bcm.edu	37	chr10	105005831	105005831	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggggccaagtgcctccagatGctagactctggggccgatta	14	11	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:105005831G>A	ENST00000441178.2	+	1	188	c.78G>A	c.(76-78)atG>atA	p.M26I		NM_001143909.1	NP_001137381.1																					GCCTCCAGATGCTAGACTCTG	0.542																																					p.M26I		Atlas-SNP	.											.	.	.	.	0			c.G78A						.						113	97	102					10																	105005831		692	1591	2283	SO:0001583	missense	0	exon1			CCAGATGCTAGAC																												ENST00000441178.2:c.78G>A	chr10.hg19:g.105005831G>A	ENSP00000476672:p.Met26Ile	151.0	0.0		157.0	52.0	NM_001143909		Missense_Mutation	SNP	ENST00000441178.2	hg19																																																																																				.	.		0.542	RP11-332O19.5-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050120.2			A	105005831	G	A	105005831	3	1	23	1	0	0	0	0	1	0	0	0	8897	1319	46	3	80	3	LOC729020	10	105005831	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1134972	105005831	30528916	600	2666										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105182857	105182857	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttcagtgggggtccagtgccCgacctggtcctgaaagccag	14	12	1	1	rs141472462		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:105182857C>A	ENST00000369797.3	+	18	2704	c.2610C>A	c.(2608-2610)ccC>ccA	p.P870P		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	870					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GTCCAGTGCCCGACCTGGTCC	0.572																																					p.P870P		Atlas-SNP	.											.	PDCD11	160	.	0			c.C2610A						.						139	120	127					10																	105182857		2203	4300	6503	SO:0001819	synonymous_variant	22984	exon18			AGTGCCCGACCTG	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.2610C>A	chr10.hg19:g.105182857C>A		158.0	0.0		133.0	58.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	hg19	CCDS31276.1																																																																																			.	C|1.000;T|0.000		0.572	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			A	105182857	C	A	105182857	2	1	23	1	0	0	0	0	0	0	0	1	11626	639	23	1		1	PDCD11	10	105182857	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	177026	105182857	30351890	601	2667										
SLK	9748	hgsc.bcm.edu	37	chr10	105762305	105762305	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaaaagagaataatataatgAtaaccttagaaacaaatatt	5	3	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:105762305A>T	ENST00000369755.3	+	9	1914	c.1369A>T	c.(1369-1371)Ata>Tta	p.I457L	SLK_ENST00000335753.4_Missense_Mutation_p.I457L	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	457	Glu-rich.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TAATATAATGATAACCTTAGA	0.333																																					p.I457L	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.A1369T						.						63	71	68					10																	105762305		2201	4294	6495	SO:0001583	missense	9748	exon9			ATAATGATAACCT		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.1369A>T	chr10.hg19:g.105762305A>T	ENSP00000358770:p.Ile457Leu	107.0	0.0		101.0	46.0	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	hg19	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	5.939	0.357297	0.11239	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.68025	-0.3;-0.3	5.81	-0.969	0.10310	Protein kinase-like domain (1);	0.553031	0.18895	N	0.128204	T	0.51058	0.1652	L	0.36672	1.1	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.13407	0.009;0.002	T	0.34502	-0.9826	10	0.28530	T	0.3	.	10.9001	0.47047	0.5569:0.0:0.4431:0.0	.	457;457	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	L	457	ENSP00000336824:I457L;ENSP00000358770:I457L	ENSP00000336824:I457L	I	+	1	0	SLK	105752295	0.000000	0.05858	0.022000	0.16811	0.947000	0.59692	-0.165000	0.09968	-0.402000	0.07633	0.454000	0.30748	ATA	.	.		0.333	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		T	105762305	A	T	105762305	3	4	23	1	0	0	0	0	1	0	0	0	14763	333	12	4	1403	4	SLK	10	105762305	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	579448	105762305	29772442	602	2668										
ITPRIP	85450	hgsc.bcm.edu	37	chr10	106075738	106075738	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggactgtggcgttctcccgCgggaacagcagcgggtggtt	18	10	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:106075738C>T	ENST00000337478.1	-	2	243	c.72G>A	c.(70-72)ccG>ccA	p.P24P	RP11-127L20.5_ENST00000472915.2_RNA|ITPRIP_ENST00000278071.2_Silent_p.P24P|ITPRIP_ENST00000358187.2_Silent_p.P24P	NM_001272013.1	NP_001258942.1	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein	24						membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(9)|upper_aerodigestive_tract(1)	20						CGTTCTCCCGCGGGAACAGCA	0.627																																					p.P24P		Atlas-SNP	.											.	ITPRIP	44	.	0			c.G72A						.						59	54	56					10																	106075738		2203	4300	6503	SO:0001819	synonymous_variant	85450	exon2			CTCCCGCGGGAAC	AB051541	CCDS7557.1	10q25.1	2011-04-28	2011-04-28	2008-08-11	ENSG00000148841	ENSG00000148841			29370	protein-coding gene	gene with protein product			"KIAA1754", "inositol 1,4,5-triphosphate receptor interacting protein"	KIAA1754		11214970, 16990268	Standard	NM_001272012		Approved	bA127L20.2, DANGER	uc001kye.4	Q8IWB1	OTTHUMG00000019003	ENST00000337478.1:c.72G>A	chr10.hg19:g.106075738C>T		52.0	0.0		52.0	17.0	NM_001272013	D3DRA5|Q5JU17|Q96MS8|Q9C0A9	Silent	SNP	ENST00000337478.1	hg19	CCDS7557.1																																																																																			.	.		0.627	ITPRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050204.1	NM_033397		T	106075738	C	T	106075738	2	4	23	1	0	0	0	0	0	0	0	1	7932	755	27	1		1	ITPRIP	10	106075738	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	313433	106075738	29459009	603	2669										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106401491	106401491	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaggagtcgccgggcgcagCccccaatcacccaggaacgc					rs373150688		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:106401491delC	ENST00000369701.3	+	1	633	c.406delC	c.(406-408)cccfs	p.P137fs		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	137					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CCGGGCGCAGCCCCCAATCAC	0.716																																					p.Q135fs	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-Indel,Pindel	.											.	SORCS3	282	.	0			c.405delG						.						3	3	3					10																	106401491		1634	3275	4909	SO:0001589	frameshift_variant	22986	exon1			.	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.406delC	chr10.hg19:g.106401491delC	ENSP00000358715:p.Pro137fs	68.0	0.0		72.0	30.0	NM_014978	Q5VXF9|Q9NQJ2	Frame_Shift_Del	DEL	ENST00000369701.3	hg19	CCDS7558.1																																																																																			.	.		0.716	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		-	106401491	C	-	106401491	7	5	23	1	0	1	0	1	0	0	0	0	14947	739	26	0	408	0	SORCS3	10	106401491	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	325753	106401491	29133256	604	2670										
SMC3	9126	hgsc.bcm.edu	37	chr10	112337617	112337617	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ataaagaggaagtttcacttCgaagagttattggtgccaaa	10	5	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:112337617C>T	ENST00000361804.4	+	6	421	c.295C>T	c.(295-297)Cga>Tga	p.R99*	snoU13_ENST00000458966.1_RNA|SMC3_ENST00000462899.1_3'UTR	NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	99					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		AGTTTCACTTCGAAGAGTTAT	0.279																																					p.R99X		Atlas-SNP	.											SMC3,NS,carcinoma,0,2	SMC3	103	.	0			c.C295T						.						75	79	78					10																	112337617		2203	4300	6503	SO:0001587	stop_gained	9126	exon6			TCACTTCGAAGAG	AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.295C>T	chr10.hg19:g.112337617C>T	ENSP00000354720:p.Arg99*	88.0	0.0		59.0	24.0	NM_005445	A8K156|O60464|Q5T482	Nonsense_Mutation	SNP	ENST00000361804.4	hg19	CCDS31285.1	.	.	.	.	.	.	.	.	.	.	C	37	6.011302	0.97200	.	.	ENSG00000108055	ENST00000361804	.	.	.	5.67	3.75	0.43078	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7855	0.40673	0.25:0.6835:0.0:0.0665	.	.	.	.	X	99	.	ENSP00000354720:R99X	R	+	1	2	SMC3	112327607	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.597000	0.61062	0.687000	0.31509	0.460000	0.39030	CGA	.	.		0.279	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		T	112337617	C	T	112337617	4	4	23	1	0	0	0	0	0	1	0	0	14799	876	31	1	317	1	SMC3	10	112337617	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5936126	112337617	23197130	605	2671										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114900984	114900984	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagcaccctcaccatgtccaCcccctcacgcctcttatcac							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:114900984delC	ENST00000355995.4	+	6	1101	c.594delC	c.(592-594)cacfs	p.H198fs	TCF7L2_ENST00000369395.1_Frame_Shift_Del_p.H223fs|TCF7L2_ENST00000352065.5_Frame_Shift_Del_p.H175fs|TCF7L2_ENST00000543371.1_Frame_Shift_Del_p.H198fs|TCF7L2_ENST00000538897.1_Frame_Shift_Del_p.H198fs|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000355717.4_Frame_Shift_Del_p.H222fs|TCF7L2_ENST00000545257.1_Frame_Shift_Del_p.H198fs|TCF7L2_ENST00000369397.4_Frame_Shift_Del_p.H175fs|TCF7L2_ENST00000369389.1_5'Flank|TCF7L2_ENST00000349937.2_Frame_Shift_Del_p.H198fs|TCF7L2_ENST00000536810.1_Frame_Shift_Del_p.H198fs|TCF7L2_ENST00000534894.1_Frame_Shift_Del_p.H198fs			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	198	Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		ACCATGTCCACCCCCTCACGC	0.572			T	VTI1A	colorectal																																p.H222fs		Atlas-Indel,Pindel	.		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	.	TCF7L2	298	.	0			c.665delA						.						184	154	164					10																	114900984		2203	4300	6503	SO:0001589	frameshift_variant	6934	exon6			.	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.594delC	chr10.hg19:g.114900984delC	ENSP00000348274:p.His198fs	148.0	0.0		127.0	42.0	NM_001146283	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Frame_Shift_Del	DEL	ENST00000355995.4	hg19																																																																																				.	.		0.572	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		-	114900984	C	-	114900984	7	5	23	1	0	1	0	1	0	0	0	0	15713	506	18	0	761	0	TCF7L2	10	114900984	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	2563367	114900984	20633763	606	2672										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114901029	114901029	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcaatgaacacttcacgccGggaaacccacctccacactt	6	16	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:114901029G>A	ENST00000355995.4	+	6	1146	c.639G>A	c.(637-639)ccG>ccA	p.P213P	TCF7L2_ENST00000369395.1_Silent_p.P238P|TCF7L2_ENST00000352065.5_Silent_p.P190P|TCF7L2_ENST00000543371.1_Silent_p.P213P|TCF7L2_ENST00000538897.1_Silent_p.P213P|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000355717.4_Silent_p.P237P|TCF7L2_ENST00000545257.1_Silent_p.P213P|TCF7L2_ENST00000369397.4_Silent_p.P190P|TCF7L2_ENST00000369389.1_5'Flank|TCF7L2_ENST00000349937.2_Silent_p.P213P|TCF7L2_ENST00000536810.1_Silent_p.P213P|TCF7L2_ENST00000534894.1_Silent_p.P213P			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	213	Mediates interaction with MAD2L2.|Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		ACTTCACGCCGGGAAACCCAC	0.587			T	VTI1A	colorectal																																p.P237P		Atlas-SNP	.		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	.	TCF7L2	298	.	0			c.G711A						.						157	130	139					10																	114901029		2203	4300	6503	SO:0001819	synonymous_variant	6934	exon6			CACGCCGGGAAAC	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.639G>A	chr10.hg19:g.114901029G>A		138.0	0.0		104.0	32.0	NM_001146283	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Silent	SNP	ENST00000355995.4	hg19																																																																																				.	.		0.587	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		A	114901029	G	A	114901029	2	1	23	1	0	0	0	0	0	0	0	1	15713	1103	39	1		1	TCF7L2	10	114901029	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	45	114901029	20633718	607	2673										
C10orf96	374355	hgsc.bcm.edu	37	chr10	118116936	118116936	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtagccagttaaatgaacttCaaaaacaaaagagtgaattg	8	5	1	3	rs201464805		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:118116936C>T	ENST00000333254.3	+	6	744	c.493C>T	c.(493-495)Caa>Taa	p.Q165*		NM_198515.2	NP_940917.1	P0C7W6	CC172_HUMAN	coiled-coil domain containing 172	165																	AAATGAACTTCAAAAACAAAA	0.274																																					p.Q165X		Atlas-SNP	.											.	.	.	.	0			c.C493T						.						41	43	42					10																	118116936		2185	4273	6458	SO:0001587	stop_gained	374355	exon6			GAACTTCAAAAAC	BC044830	CCDS31291.1	10q26.11-q26.12	2012-05-31	2012-05-31	2012-05-31	ENSG00000182645	ENSG00000182645			30524	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 96"	C10orf96		12477932	Standard	NM_198515		Approved	MGC35062	uc001lck.3	P0C7W6	OTTHUMG00000019098	ENST00000333254.3:c.493C>T	chr10.hg19:g.118116936C>T	ENSP00000329860:p.Gln165*	249.0	0.0		229.0	10.0	NM_198515		Nonsense_Mutation	SNP	ENST00000333254.3	hg19	CCDS31291.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.685066	0.88639	.	.	ENSG00000182645	ENST00000333254	.	.	.	5.6	4.64	0.57946	.	0.215967	0.39407	N	0.001379	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-12.8496	15.2862	0.73831	0.1407:0.8593:0.0:0.0	.	.	.	.	X	165	.	ENSP00000329860:Q165X	Q	+	1	0	C10orf96	118106926	1.000000	0.71417	1.000000	0.80357	0.306000	0.27790	3.429000	0.52800	2.635000	0.89317	0.655000	0.94253	CAA	.	.		0.274	CCDC172-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050516.2	NM_198515		T	118116936	C	T	118116936	4	4	23	1	0	0	0	0	0	1	0	0	1629	827	29	3	511	3	C10orf96	10	118116936	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3215907	118116936	17417811	608	2674										
VAX1	11023	hgsc.bcm.edu	37	chr10	118896110	118896110	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgaaggacgtgcgcgtcctcTtaggccggtccaagtccagg	14	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:118896110T>G	ENST00000369206.5	-	2	301	c.302A>C	c.(301-303)aAg>aCg	p.K101T	VAX1_ENST00000277905.2_Missense_Mutation_p.K101T	NM_001112704.1	NP_001106175.1	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1	101					axon guidance (GO:0007411)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|palate development (GO:0060021)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(8)|ovary(2)	12				all cancers(201;0.0108)		GCGCGTCCTCTTAGGCCGGTC	0.657																																					p.K101T		Atlas-SNP	.											.	VAX1	50	.	0			c.A302C						.						52	46	48					10																	118896110		2203	4300	6503	SO:0001583	missense	11023	exon2			GTCCTCTTAGGCC	AK127095	CCDS7597.1, CCDS44483.1	10q26.11	2011-06-20			ENSG00000148704	ENSG00000148704		"Homeoboxes / ANTP class : NKL subclass"	12660	protein-coding gene	gene with protein product		604294				9636075, 10485894	Standard	NM_199131		Approved		uc009xyx.3	Q5SQQ9	OTTHUMG00000019117	ENST00000369206.5:c.302A>C	chr10.hg19:g.118896110T>G	ENSP00000358207:p.Lys101Thr	109.0	0.0		123.0	59.0	NM_001112704	B1AVW5|Q6ZSX0	Missense_Mutation	SNP	ENST00000369206.5	hg19	CCDS44483.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.144273	0.57044	.	.	ENSG00000148704	ENST00000277905;ENST00000369206	D;D	0.97041	-4.22;-4.22	4.03	4.03	0.46877	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.055699	0.64402	D	0.000001	D	0.98147	0.9388	M	0.90650	3.135	0.58432	D	0.999999	D;D	0.58620	0.983;0.979	P;P	0.57502	0.822;0.801	D	0.98871	1.0766	10	0.87932	D	0	-4.7467	13.1035	0.59233	0.0:0.0:0.0:1.0	.	101;101	Q5SQQ9;Q5SQQ9-2	VAX1_HUMAN;.	T	101	ENSP00000277905:K101T;ENSP00000358207:K101T	ENSP00000277905:K101T	K	-	2	0	VAX1	118886100	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.431000	0.80335	1.691000	0.51100	0.374000	0.22700	AAG	.	.		0.657	VAX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050559.3	XM_301242		G	118896110	T	G	118896110	3	3	23	1	0	0	0	0	1	0	0	0	17149	1609	56	5	850	5	VAX1	10	118896110	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	779174	118896110	16638637	609	2675										
ATHL1	80162	hgsc.bcm.edu	37	chr11	294325	294325	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtcggggatctccagagtgAgcgtctccggcatcttctac	12	12	4	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:294325A>C	ENST00000409548.2	+	13	1982	c.1867A>C	c.(1867-1869)Agc>Cgc	p.S623R	ATHL1_ENST00000409479.1_Missense_Mutation_p.S650R|ATHL1_ENST00000409655.1_Missense_Mutation_p.S375R	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	623					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		CTCCAGAGTGAGCGTCTCCGG	0.622																																					p.S623R		Atlas-SNP	.											.	ATHL1	88	.	0			c.A1867C						.						73	78	76					11																	294325		2203	4300	6503	SO:0001583	missense	80162	exon13			AGAGTGAGCGTCT	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.1867A>C	chr11.hg19:g.294325A>C	ENSP00000387185:p.Ser623Arg	101.0	0.0		157.0	71.0	NM_025092	Q658X8|Q8TEG9|Q9H635	Missense_Mutation	SNP	ENST00000409548.2	hg19	CCDS31322.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.91|10.91	1.484496|1.484496	0.26598|0.26598	.|.	.|.	ENSG00000142102|ENSG00000142102	ENST00000397660|ENST00000409548;ENST00000409655;ENST00000409479	.|.	.|.	.|.	4.04|4.04	-8.08|-8.08	0.01094|0.01094	.|Six-hairpin glycosidase-like (1);	.|1.140950	.|0.06247	.|N	.|0.691374	T|T	0.20981|0.20981	0.0505|0.0505	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.15206|0.15206	-1.0445|-1.0445	5|9	.|0.33940	.|T	.|0.23	.|.	3.525|3.525	0.07756|0.07756	0.4002:0.3816:0.0986:0.1195|0.4002:0.3816:0.0986:0.1195	.|.	.|623;375	.|Q32M88;B8ZZ60	.|ATHL1_HUMAN;.	A|R	83|623;375;650	.|.	.|ENSP00000387099:S650R	E|S	+|+	2|1	0|0	ATHL1|ATHL1	284325|284325	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.109000|0.109000	0.19521|0.19521	-2.224000|-2.224000	0.01213|0.01213	-1.656000|-1.656000	0.01495|0.01495	0.379000|0.379000	0.24179|0.24179	GAG|AGC	.	.		0.622	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092		C	294325	A	C	294325	3	2	23	1	0	0	0	0	1	0	0	0	1104	304	11	5	1913	5	ATHL1	11	294325	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10		294325	134712191	610	2676										
C11orf35	256329	hgsc.bcm.edu	37	chr11	554999	554999	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctaggcgccgcggcaggtgTccgcggtgaccggcaggcag	18	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:554999T>C	ENST00000329451.3	-	14	1948	c.1886A>G	c.(1885-1887)gAc>gGc	p.D629G	RP11-496I9.1_ENST00000527620.1_RNA	NM_173573.2	NP_775844.2	Q8IXW0	LMTD2_HUMAN		629										NS(1)|breast(1)|central_nervous_system(1)|lung(4)|pancreas(1)	8		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCGGCAGGTGTCCGCGGTGAC	0.741																																					p.D629G		Atlas-SNP	.											.	C11orf35	22	.	0			c.A1886G						.						6	7	7					11																	554999		1809	3658	5467	SO:0001583	missense	256329	exon14			CAGGTGTCCGCGG																												ENST00000329451.3:c.1886A>G	chr11.hg19:g.554999T>C	ENSP00000331167:p.Asp629Gly	100.0	0.0		104.0	32.0	NM_173573		Missense_Mutation	SNP	ENST00000329451.3	hg19	CCDS7701.1	.	.	.	.	.	.	.	.	.	.	t	17.64	3.438947	0.63067	.	.	ENSG00000185522	ENST00000329451	T	0.52057	0.68	4.64	0.813	0.18749	.	0.379512	0.19440	N	0.114219	T	0.23688	0.0573	N	0.12182	0.205	0.09310	N	1	B	0.21821	0.061	B	0.19666	0.026	T	0.14282	-1.0478	10	0.72032	D	0.01	-14.6999	2.7658	0.05320	0.1906:0.2122:0.0:0.5972	.	629	Q8IXW0	CK035_HUMAN	G	629	ENSP00000331167:D629G	ENSP00000331167:D629G	D	-	2	0	C11orf35	544999	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	-0.114000	0.10757	0.210000	0.20664	0.449000	0.29647	GAC	.	.		0.741	C11orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254973.2			C	554999	T	C	554999	3	2	23	1	0	0	0	0	1	0	0	0	1640	1667	58	2	22	2	C11orf35	11	554999	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	260674	554999	134451517	611	2677										
PHRF1	57661	hgsc.bcm.edu	37	chr11	609548	609548	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccagttccccggatgtggcGcctgcggggaaggaagacag	16	12	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:609548G>A	ENST00000264555.5	+	14	4220	c.4092G>A	c.(4090-4092)gcG>gcA	p.A1364A	PHRF1_ENST00000413872.2_Silent_p.A1362A|PHRF1_ENST00000416188.2_Silent_p.A1363A|PHRF1_ENST00000533464.1_Silent_p.A1360A	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1364					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CGGATGTGGCGCCTGCGGGGA	0.692																																					p.A1363A		Atlas-SNP	.											.	PHRF1	188	.	0			c.G4089A						.						17	22	21					11																	609548		2011	4159	6170	SO:0001819	synonymous_variant	57661	exon14			TGTGGCGCCTGCG	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.4092G>A	chr11.hg19:g.609548G>A		53.0	0.0		51.0	17.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	hg19																																																																																				.	.		0.692	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		A	609548	G	A	609548	2	1	23	1	0	0	0	0	0	0	0	1	11870	1074	38	1		1	PHRF1	11	609548	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	54549	609548	134396968	612	2678										
PHRF1	57661	hgsc.bcm.edu	37	chr11	610607	610607	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catccttcaggggagcctgcCgctagtgggctgtggggcag	17	11	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:610607C>T	ENST00000264555.5	+	16	4651	c.4523C>T	c.(4522-4524)cCg>cTg	p.P1508L	PHRF1_ENST00000413872.2_Missense_Mutation_p.P1506L|PHRF1_ENST00000416188.2_Missense_Mutation_p.P1507L|PHRF1_ENST00000533464.1_Missense_Mutation_p.P1504L	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1508					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GGGAGCCTGCCGCTAGTGGGC	0.706																																					p.P1507L		Atlas-SNP	.											.	PHRF1	188	.	0			c.C4520T						.						15	20	19					11																	610607		2002	4143	6145	SO:0001583	missense	57661	exon16			GCCTGCCGCTAGT	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.4523C>T	chr11.hg19:g.610607C>T	ENSP00000264555:p.Pro1508Leu	97.0	0.0		111.0	45.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	C	12.95	2.090799	0.36855	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	D;D;D;D	0.82344	-1.59;-1.59;-1.6;-1.59	3.82	3.82	0.43975	.	0.000000	0.35555	N	0.003122	D	0.88760	0.6524	L	0.60455	1.87	0.19775	N	0.999955	D;D;D;D	0.76494	0.999;0.996;0.998;0.997	D;P;D;D	0.70935	0.956;0.852;0.971;0.936	T	0.82339	-0.0506	10	0.72032	D	0.01	-25.937	16.2035	0.82105	0.0:1.0:0.0:0.0	.	1504;1506;1507;1508	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	L	1508;1506;1507;1504	ENSP00000264555:P1508L;ENSP00000388589:P1506L;ENSP00000410626:P1507L;ENSP00000431870:P1504L	ENSP00000264555:P1508L	P	+	2	0	PHRF1	600607	0.115000	0.22152	0.010000	0.14722	0.008000	0.06430	3.200000	0.51051	2.074000	0.62210	0.491000	0.48974	CCG	.	.		0.706	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		T	610607	C	T	610607	3	4	23	1	0	0	0	0	1	0	0	0	11870	652	23	1	4578	1	PHRF1	11	610607	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1059	610607	134395909	613	2679										
EPS8L2	64787	hgsc.bcm.edu	37	chr11	721123	721123	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctcctccccagggcccggCgcccatccccttccagcacc	8	24	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:721123C>T	ENST00000533256.1	+	9	992	c.617C>T	c.(616-618)gCg>gTg	p.A206V	EPS8L2_ENST00000530636.1_Missense_Mutation_p.A206V|EPS8L2_ENST00000318562.8_Missense_Mutation_p.A206V|EPS8L2_ENST00000526198.1_Missense_Mutation_p.A222V|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	206					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGGGCCCGGCGCCCATCCCC	0.736																																					p.A206V		Atlas-SNP	.											.	EPS8L2	42	.	0			c.C617T						.						9	10	10					11																	721123		2067	4079	6146	SO:0001583	missense	64787	exon8			GCCCGGCGCCCAT	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.617C>T	chr11.hg19:g.721123C>T	ENSP00000435585:p.Ala206Val	103.0	0.0		115.0	17.0	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Missense_Mutation	SNP	ENST00000533256.1	hg19	CCDS31328.1	.	.	.	.	.	.	.	.	.	.	c	17.29	3.352367	0.61293	.	.	ENSG00000177106	ENST00000318562;ENST00000533256;ENST00000530636;ENST00000526198	T;T;T;T	0.24723	1.93;1.93;1.93;1.84	3.38	3.38	0.38709	.	0.482476	0.17660	U	0.166358	T	0.23054	0.0557	L	0.53249	1.67	0.45354	D	0.998345	P;D;P	0.54772	0.614;0.968;0.614	B;B;B	0.38106	0.091;0.265;0.091	T	0.17930	-1.0353	10	0.66056	D	0.02	-14.7971	12.1482	0.54036	0.0:1.0:0.0:0.0	.	222;250;206	B7ZKL3;B4DFD2;Q9H6S3	.;.;ES8L2_HUMAN	V	206;206;206;222	ENSP00000320828:A206V;ENSP00000435585:A206V;ENSP00000436035:A206V;ENSP00000436230:A222V	ENSP00000320828:A206V	A	+	2	0	EPS8L2	711123	1.000000	0.71417	0.103000	0.21229	0.137000	0.21094	3.423000	0.52756	1.912000	0.55364	0.556000	0.70494	GCG	.	.		0.736	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		T	721123	C	T	721123	3	4	23	1	0	0	0	0	1	0	0	0	5198	768	27	1	643	1	EPS8L2	11	721123	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	110516	721123	134285393	614	2680										
SLC25A22	79751	hgsc.bcm.edu	37	chr11	792953	792953	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcaggtgccagccccacagCccgccagcatctctttaagc	10	17	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:792953C>T	ENST00000320230.5	-	6	810	c.329G>A	c.(328-330)gGc>gAc	p.G110D	SLC25A22_ENST00000531214.1_Missense_Mutation_p.G110D|CEND1_ENST00000330106.4_5'Flank|CEND1_ENST00000524587.1_5'Flank	NM_001191061.1|NM_024698.5	NP_001177990.1|NP_078974.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22	110					L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCCCCACAGCCCGCCAGCAT	0.652																																					p.G110D	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											.	SLC25A22	19	.	0			c.G329A						.						40	35	37					11																	792953		2203	4298	6501	SO:0001583	missense	79751	exon6			CCACAGCCCGCCA	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"Solute carriers"	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310	ENST00000320230.5:c.329G>A	chr11.hg19:g.792953C>T	ENSP00000322020:p.Gly110Asp	81.0	0.0		98.0	44.0	NM_001191061	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Missense_Mutation	SNP	ENST00000320230.5	hg19	CCDS7715.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.294378	0.60086	.	.	ENSG00000177542	ENST00000320230;ENST00000531214;ENST00000481290;ENST00000531437;ENST00000533385;ENST00000526152;ENST00000528606;ENST00000527723;ENST00000531514;ENST00000528936	D;D;D;D;D;D;D;D;D;D	0.92249	-3.0;-3.0;-3.0;-3.0;-3.0;-1.88;-1.88;-1.88;-1.88;-1.88	4.14	4.14	0.48551	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.97654	0.9231	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99755	1.1019	10	0.87932	D	0	-22.1587	16.7938	0.85596	0.0:1.0:0.0:0.0	.	110	Q9H936	GHC1_HUMAN	D	110;110;135;106;110;110;110;110;110;110	ENSP00000322020:G110D;ENSP00000437236:G110D;ENSP00000431829:G135D;ENSP00000435862:G106D;ENSP00000434287:G110D;ENSP00000436745:G110D;ENSP00000437045:G110D;ENSP00000434479:G110D;ENSP00000433780:G110D;ENSP00000432817:G110D	ENSP00000322020:G110D	G	-	2	0	SLC25A22	782953	1.000000	0.71417	0.662000	0.29724	0.058000	0.15608	4.732000	0.62029	2.027000	0.59764	0.591000	0.81541	GGC	.	.		0.652	SLC25A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257107.2			T	792953	C	T	792953	3	4	23	1	0	0	0	0	1	0	0	0	14500	739	26	3	662	3	SLC25A22	11	792953	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	71830	792953	134213563	615	2681										
AP2A2	161	hgsc.bcm.edu	37	chr11	972110	972110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actcaaacagtgagctgatcCgcctgatcaacaacgccatc	7	14	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:972110C>T	ENST00000448903.2	+	4	469	c.328C>T	c.(328-330)Cgc>Tgc	p.R110C	AP2A2_ENST00000534328.1_Missense_Mutation_p.R110C|AP2A2_ENST00000332231.5_Missense_Mutation_p.R110C	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	110					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		TGAGCTGATCCGCCTGATCAA	0.557																																					p.R110C		Atlas-SNP	.											.	AP2A2	50	.	0			c.C328T						.						88	82	84					11																	972110		2086	4220	6306	SO:0001583	missense	161	exon4			CTGATCCGCCTGA	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.328C>T	chr11.hg19:g.972110C>T	ENSP00000413234:p.Arg110Cys	51.0	0.0		66.0	30.0	NM_012305	O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	ENST00000448903.2	hg19	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.412342	0.42817	.	.	ENSG00000183020	ENST00000534328;ENST00000417081;ENST00000448903;ENST00000332231;ENST00000448757;ENST00000529125;ENST00000452310;ENST00000531548;ENST00000534485;ENST00000527024;ENST00000526753;ENST00000530801;ENST00000524559	T;T;T;T;T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74	3.24	2.33	0.28932	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.46718	0.1407	M	0.80332	2.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.971	T	0.42716	-0.9435	10	0.62326	D	0.03	-12.8407	6.6073	0.22731	0.177:0.7279:0.0:0.0951	.	110;110	O94973-2;O94973	.;AP2A2_HUMAN	C	110;110;110;110;110;110;110;116;100;104;34;34;34	ENSP00000436059:R110C;ENSP00000413234:R110C;ENSP00000327694:R110C;ENSP00000433498:R116C;ENSP00000435756:R100C;ENSP00000434563:R104C;ENSP00000435863:R34C;ENSP00000434553:R34C;ENSP00000434432:R34C	ENSP00000327694:R110C	R	+	1	0	AP2A2	962110	1.000000	0.71417	0.983000	0.44433	0.398000	0.30690	3.436000	0.52856	0.957000	0.37930	-0.136000	0.14681	CGC	.	.		0.557	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		T	972110	C	T	972110	3	4	23	1	0	0	0	0	1	0	0	0	740	652	23	1	342	1	AP2A2	11	972110	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	179157	972110	134034406	616	2682										
MUC6	4588	hgsc.bcm.edu	37	chr11	1015776	1015776	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acttaccgggtgaggtgggcGtaggtgtcccgagagaagat	17	7	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:1015776G>A	ENST00000421673.2	-	31	7075	c.7025C>T	c.(7024-7026)aCg>aTg	p.T2342M		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2342	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGAGGTGGGCGTAGGTGTCCC	0.627																																					p.T2342M		Atlas-SNP	.											MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	.	0			c.C7025T						.						61	69	66					11																	1015776		2147	4253	6400	SO:0001583	missense	4588	exon31			GTGGGCGTAGGTG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.7025C>T	chr11.hg19:g.1015776G>A	ENSP00000406861:p.Thr2342Met	137.0	0.0		190.0	73.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	6.274	0.418687	0.11870	.	.	ENSG00000184956	ENST00000421673	T	0.18810	2.19	3.22	-2.25	0.06888	.	.	.	.	.	T	0.08537	0.0212	N	0.14661	0.345	0.09310	N	1	D	0.56035	0.974	B	0.40134	0.32	T	0.14699	-1.0463	9	0.42905	T	0.14	.	1.3153	0.02106	0.2334:0.1645:0.4348:0.1673	.	2342	Q6W4X9	MUC6_HUMAN	M	2342	ENSP00000406861:T2342M	ENSP00000406861:T2342M	T	-	2	0	MUC6	1005776	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.153000	0.10144	-0.612000	0.05701	0.448000	0.29417	ACG	.	.		0.627	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1015776	G	A	1015776	3	1	23	1	0	0	0	0	1	0	0	0	9989	1145	40	1	306	1	MUC6	11	1015776	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	43666	1015776	133990740	617	2683										
CARS	833	hgsc.bcm.edu	37	chr11	3026609	3026612	+	Frame_Shift_Del	DEL	TCTC	TCTC	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tactcacccgtctcttttctTctctctcttttaataaggtg					rs541100565		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:3026609_3026612delTCTC	ENST00000397111.5	-	19	2197_2200	c.1952_1955delGAGA	c.(1951-1956)agagaafs	p.RE651fs	CARS_ENST00000278224.9_Frame_Shift_Del_p.RE651fs|CARS_ENST00000380525.4_Frame_Shift_Del_p.RE734fs|CARS_ENST00000470221.2_5'UTR|CARS_ENST00000401769.3_Frame_Shift_Del_p.RE664fs|CARS_ENST00000397114.3_Frame_Shift_Del_p.RE641fs			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	651					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.R734T(1)|p.R651T(1)	CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	TCTCTTTTCTTCTCTCTCTTTTAA	0.397			T	ALK	ALCL																																p.734_735del	Ovarian(61;932 1157 5961 20446 52152)	Atlas-Indel,Pindel	.		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	.	CARS	114	.	2	Substitution - Missense(2)	lung(2)	c.2202_2205del						.																																			SO:0001589	frameshift_variant	833	exon20			.	AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"Aminoacyl tRNA synthetases / Class I"	1493	protein-coding gene	gene with protein product	"cysteine tRNA ligase 1, cytoplasmic"	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.1952_1955delGAGA	chr11.hg19:g.3026613_3026616delTCTC	ENSP00000380300:p.Arg651fs	109.0	0.0		99.0	40.0	NM_001014437	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Frame_Shift_Del	DEL	ENST00000397111.5	hg19	CCDS7742.1																																																																																			.	.		0.397	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751		-	3026612	TCTC	-	3026609	7	5	23	1	0	1	0	1	0	0	0	0	2659	1783	62	0	315	0	CARS	11	3026609	Frame_Shift_Del	DEL	TCTC	TCGA-4R-AA8I-01A-11D-A382-10	2010833	3026609	131979907	618	2684										
RHOG	391	hgsc.bcm.edu	37	chr11	3848965	3848965	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgctgcggtgtgatgggcGcctggccctgctccttgagg	16	13	0	2	rs535699358		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:3848965G>A	ENST00000351018.4	-	2	561	c.404C>T	c.(403-405)gCg>gTg	p.A135V	RHOG_ENST00000396978.1_Missense_Mutation_p.A135V|RHOG_ENST00000533217.1_Missense_Mutation_p.A135V|RHOG_ENST00000396979.1_Missense_Mutation_p.A135V	NM_001665.3	NP_001656.2	P84095	RHOG_HUMAN	ras homolog family member G	135					actin cytoskeleton organization (GO:0030036)|activation of Rac GTPase activity (GO:0032863)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|GTP catabolic process (GO:0006184)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of transcription, DNA-templated (GO:0045893)|Rac protein signal transduction (GO:0016601)|regulation of ruffle assembly (GO:1900027)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)	2		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0349)|LUSC - Lung squamous cell carcinoma(625;0.194)		TGTGATGGGCGCCTGGCCCTG	0.642													G|||	1	0.000199681	0	0.0014	5008	,	,		19567	0		0	False		,,,				2504	0				p.A135V		Atlas-SNP	.											.	RHOG	13	.	0			c.C404T						.						50	46	47					11																	3848965		2201	4298	6499	SO:0001583	missense	391	exon2			ATGGGCGCCTGGC	X61587	CCDS7748.1	11p15.5-p15.4	2012-02-27	2012-02-27	2004-03-24	ENSG00000177105	ENSG00000177105			672	protein-coding gene	gene with protein product		179505	"ras homolog gene family, member G (rho G)"	ARHG		8325658	Standard	NM_001665		Approved	RhoG, MGC125835, MGC125836	uc001lyu.2	P84095	OTTHUMG00000012287	ENST00000351018.4:c.404C>T	chr11.hg19:g.3848965G>A	ENSP00000339467:p.Ala135Val	98.0	0.0		63.0	24.0	NM_001665	P35238|Q8NI04	Missense_Mutation	SNP	ENST00000351018.4	hg19	CCDS7748.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.089368	0.36855	.	.	ENSG00000177105	ENST00000351018;ENST00000396979;ENST00000396978;ENST00000533217	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.45	3.58	0.41010	Small GTP-binding protein domain (1);	0.392675	0.30455	N	0.009589	T	0.57066	0.2028	N	0.12182	0.205	0.41724	D	0.989528	B	0.15473	0.013	B	0.08055	0.003	T	0.53704	-0.8401	10	0.46703	T	0.11	.	6.4443	0.21867	0.2747:0.0:0.7253:0.0	.	135	P84095	RHOG_HUMAN	V	135	ENSP00000339467:A135V;ENSP00000380176:A135V;ENSP00000380175:A135V;ENSP00000436932:A135V	ENSP00000339467:A135V	A	-	2	0	RHOG	3805541	0.996000	0.38824	0.970000	0.41538	0.978000	0.69477	2.379000	0.44318	1.285000	0.44548	0.563000	0.77884	GCG	.	.		0.642	RHOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034125.2	NM_001665		A	3848965	G	A	3848965	3	1	23	1	0	0	0	0	1	0	0	0	13354	1087	38	1	175	1	RHOG	11	3848965	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	822356	3848965	131157551	619	2685										
RIC3	79608	hgsc.bcm.edu	37	chr11	8159886	8159887	+	Frame_Shift_Ins	INS	-	-	T													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctctgcagttgttttccccINStttgagagctgagaattgaa							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:8159886_8159887insT	ENST00000309737.6	-	3	358_359	c.359_360insA	c.(358-360)aagfs	p.K120fs	RIC3_ENST00000539720.1_Frame_Shift_Ins_p.K71fs|RIC3_ENST00000335425.7_Intron|RIC3_ENST00000343202.4_Frame_Shift_Ins_p.K120fs|RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000425599.2_Frame_Shift_Ins_p.K120fs			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	120					cellular protein complex assembly (GO:0043623)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein folding (GO:0006457)|synaptic transmission, cholinergic (GO:0007271)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.K120N(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)	17				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		TTGTTTTCCCCTTTGAGAGCTG	0.441																																					p.K120fs		Atlas-Indel,Pindel	.											.	RIC3	42	.	1	Substitution - Missense(1)	lung(1)	c.360_361insA						.																																			SO:0001589	frameshift_variant	79608	exon3			.		CCDS7788.1, CCDS44533.1, CCDS55741.1, CCDS55742.1	11p15.4	2013-08-05	2013-08-05		ENSG00000166405	ENSG00000166405			30338	protein-coding gene	gene with protein product		610509	"resistance to inhibitors of cholinesterase 3 homolog (C. elegans)"			12821669	Standard	NM_024557		Approved	FLJ11608, PRO1385, AYST720	uc001mgd.2	Q7Z5B4	OTTHUMG00000165694	ENST00000309737.6:c.360dupA	chr11.hg19:g.8159889_8159889dupT	ENSP00000308820:p.Lys120fs	62.0	0.0		60.0	26.0	NM_001206672	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Frame_Shift_Ins	INS	ENST00000309737.6	hg19	CCDS55742.1																																																																																			.	.		0.441	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557		T	8159887	-	T	8159886	7	5	23	1	0	1	1	0	0	0	0	0	13369	680	24	0	762	0	RIC3	11	8159886	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	4310921	8159886	126846630	620	2686										
ST5	6764	hgsc.bcm.edu	37	chr11	8751983	8751983	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggacctgttcaattttctggAtccggctcagcactgctgag	11	11	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:8751983A>G	ENST00000534127.1	-	6	1239	c.854T>C	c.(853-855)aTc>aCc	p.I285T	ST5_ENST00000357665.1_Missense_Mutation_p.I285T|ST5_ENST00000313726.6_Missense_Mutation_p.I285T|ST5_ENST00000526757.1_Intron|ST5_ENST00000530438.1_Intron	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	285					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		AATTTTCTGGATCCGGCTCAG	0.642																																					p.I285T		Atlas-SNP	.											.	ST5	85	.	0			c.T854C						.						42	51	48					11																	8751983		2187	4280	6467	SO:0001583	missense	6764	exon6			TTCTGGATCCGGC	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"DENN/MADD domain containing"	11350	protein-coding gene	gene with protein product	"DENN/MADD domain containing 2B"	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.854T>C	chr11.hg19:g.8751983A>G	ENSP00000433528:p.Ile285Thr	48.0	0.0		42.0	11.0	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	hg19	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.442880	0.83993	.	.	ENSG00000166444	ENST00000534127;ENST00000313726;ENST00000357665	T;T;T	0.23950	1.88;1.88;1.88	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.45054	0.1323	M	0.63843	1.955	0.80722	D	1	D	0.60575	0.988	P	0.57204	0.815	T	0.38243	-0.9670	10	0.87932	D	0	-17.9635	16.8222	0.85835	1.0:0.0:0.0:0.0	.	285	P78524	ST5_HUMAN	T	285	ENSP00000433528:I285T;ENSP00000319678:I285T;ENSP00000350294:I285T	ENSP00000319678:I285T	I	-	2	0	ST5	8708559	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.901000	0.92560	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.642	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		G	8751983	A	G	8751983	3	3	23	1	0	0	0	0	1	0	0	0	15235	333	12	2	2631	2	ST5	11	8751983	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	592097	8751983	126254533	621	2687										
DENND5A	23258	hgsc.bcm.edu	37	chr11	9161225	9161225	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggtgctgggaggtcagatgTcgatgcccttgacaagggac	16	8	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:9161225T>G	ENST00000328194.3	-	23	4177	c.3857A>C	c.(3856-3858)gAc>gCc	p.D1286A	DENND5A_ENST00000527700.1_Missense_Mutation_p.D629A|DENND5A_ENST00000530044.1_3'UTR|SCUBE2_ENST00000534295.1_5'Flank	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	1286					positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						AGGTCAGATGTCGATGCCCTT	0.512																																					p.D1286A		Atlas-SNP	.											.	DENND5A	84	.	0			c.A3857C						.						111	76	88					11																	9161225		2201	4296	6497	SO:0001583	missense	23258	exon23			CAGATGTCGATGC	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"DENN/MADD domain containing"	19344	protein-coding gene	gene with protein product			"RAB6 interacting protein 1"	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.3857A>C	chr11.hg19:g.9161225T>G	ENSP00000328524:p.Asp1286Ala	30.0	0.0		39.0	13.0	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	hg19	CCDS31423.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.62|14.62	2.588559|2.588559	0.46110|0.46110	.|.	.|.	ENSG00000184014|ENSG00000184014	ENST00000328194;ENST00000527700|ENST00000528725;ENST00000533737	T;T|.	0.20598|.	3.58;2.06|.	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	0.092310|.	0.85682|.	D|.	0.000000|.	T|T	0.62889|0.62889	0.2465|0.2465	L|L	0.56769|0.56769	1.78|1.78	0.42395|0.42395	D|D	0.992548|0.992548	B|.	0.31790|.	0.34|.	B|.	0.32465|.	0.146|.	T|T	0.62886|0.62886	-0.6759|-0.6759	10|5	0.66056|.	D|.	0.02|.	.|.	10.6809|10.6809	0.45813|0.45813	0.0:0.0747:0.0:0.9253|0.0:0.0747:0.0:0.9253	.|.	1286|.	Q6IQ26|.	DEN5A_HUMAN|.	A|P	1286;629|185;194	ENSP00000328524:D1286A;ENSP00000432549:D629A|.	ENSP00000328524:D1286A|.	D|T	-|-	2|1	0|0	DENND5A|DENND5A	9117801|9117801	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	3.788000|3.788000	0.55446|0.55446	2.064000|2.064000	0.61679|0.61679	0.460000|0.460000	0.39030|0.39030	GAC|ACA	.	.		0.512	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		G	9161225	T	G	9161225	3	3	23	1	0	0	0	0	1	0	0	0	4438	1667	58	5	10	5	DENND5A	11	9161225	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	409242	9161225	125845291	622	2688										
IPO7	10527	hgsc.bcm.edu	37	chr11	9435806	9435806	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtattcctactcaaaggtatAaaaaaccagaggagcggagt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:9435806delA	ENST00000379719.3	+	5	626	c.484delA	c.(484-486)aaafs	p.K163fs		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	163					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		TCAAAGGTATAAAAAACCAGA	0.328																																					p.Y161X		Atlas-Indel,Pindel	.											.	IPO7	72	.	0			c.483delT						.						63	61	62					11																	9435806		2201	4296	6497	SO:0001589	frameshift_variant	10527	exon5			.	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.484delA	chr11.hg19:g.9435806delA	ENSP00000369042:p.Lys163fs	83.0	0.0		97.0	23.0	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Frame_Shift_Del	DEL	ENST00000379719.3	hg19	CCDS31425.1																																																																																			.	.		0.328	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		-	9435806	A	-	9435806	7	5	23	1	0	1	0	1	0	0	0	0	7806	363	13	0	502	0	IPO7	11	9435806	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	274581	9435806	125570710	623	2689										
SPON1	10418	hgsc.bcm.edu	37	chr11	14264943	14264943	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctggcagcctctcaacgtGtaagtaacacaagtcccttg	9	13	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:14264943G>A	ENST00000310358.7	+	0	1425							Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	21				Epithelial(150;0.00898)		CTCTCAACGTGTAAGTAACAC	0.488																																					.		Atlas-SNP	.											.	SPON1	65	.	0			c.889+1G>A						.						43	49	47					11																	14264943		2004	4167	6171			10418	exon7			CAACGTGTAAGTA	AB018305	CCDS73262.1	11p15.2	2014-05-06	2004-03-05		ENSG00000152268	ENSG00000262655			11252	protein-coding gene	gene with protein product		604989	"spondin 1, (f-spondin) extracellular matrix protein"			9872452	Standard	NM_006108		Approved	KIAA0762, f-spondin	uc001mle.3	Q9HCB6	OTTHUMG00000181576		chr11.hg19:g.14264943G>A		103.0	0.0		56.0	25.0	NM_006108	A8K6W5|O94862|Q8NCD7|Q8WUR5	Splice_Site	SNP	ENST00000310358.7	hg19		.	.	.	.	.	.	.	.	.	.	G	23.4	4.408592	0.83340	.	.	ENSG00000152268	ENST00000310358	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2499	0.66013	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SPON1	14221519	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.447000	0.80620	2.422000	0.82143	0.555000	0.69702	.	.	.		0.488	SPON1-201	KNOWN	basic	processed_transcript	processed_transcript		NM_145584		A	14264943	G	A	14264943	1	1	23	0	1	0	0	0	0	0	0	0	15097	1391	48	3		3	SPON1	11	14264943	RNA	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	4829137	14264943	120741573	624	2690										
NAV2	89797	hgsc.bcm.edu	37	chr11	20119177	20119177	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tagggctgaattcagacagcGttcttggctacagcattgga	12	8	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:20119177G>A	ENST00000396087.3	+	34	6343	c.6244G>A	c.(6244-6246)Gtt>Att	p.V2082I	NAV2_ENST00000533917.1_Missense_Mutation_p.V1087I|NAV2_ENST00000349880.4_Missense_Mutation_p.V2023I|NAV2_ENST00000396085.1_Missense_Mutation_p.V2026I|NAV2_ENST00000527559.2_Missense_Mutation_p.V2011I|NAV2_ENST00000311043.8_Missense_Mutation_p.V1087I|NAV2_ENST00000360655.4_Missense_Mutation_p.V1959I|NAV2_ENST00000540292.1_Missense_Mutation_p.V2013I	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2082					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TTCAGACAGCGTTCTTGGCTA	0.458																																					p.V2082I		Atlas-SNP	.											.	NAV2	255	.	0			c.G6244A						.						109	105	106					11																	20119177		2203	4300	6503	SO:0001583	missense	89797	exon33			GACAGCGTTCTTG	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.6244G>A	chr11.hg19:g.20119177G>A	ENSP00000379396:p.Val2082Ile	126.0	0.0		95.0	33.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	hg19	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	G	5.485	0.274451	0.10403	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000311043	T;T;T;T;T;T;T;T	0.22336	1.99;2.09;2.1;2.07;1.96;1.96;3.62;3.62	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000015	T	0.14657	0.0354	N	0.02286	-0.61	0.80722	D	1	P;P;P;D	0.52996	0.832;0.939;0.782;0.957	B;B;B;P	0.48738	0.252;0.406;0.436;0.588	T	0.33111	-0.9881	9	.	.	.	.	19.9617	0.97254	0.0:0.0:1.0:0.0	.	2026;1087;2023;1959	A7E2D6;Q8IVL1-5;Q8IVL1-3;Q8IVL1-4	.;.;.;.	I	1959;2026;2023;2082;2011;2013;1087;1087	ENSP00000353871:V1959I;ENSP00000379394:V2026I;ENSP00000309577:V2023I;ENSP00000379396:V2082I;ENSP00000435395:V2011I;ENSP00000443489:V2013I;ENSP00000437316:V1087I;ENSP00000312169:V1087I	.	V	+	1	0	NAV2	20075753	1.000000	0.71417	0.157000	0.22605	0.332000	0.28634	6.732000	0.74790	2.894000	0.99253	0.655000	0.94253	GTT	.	.		0.458	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		A	20119177	G	A	20119177	3	1	23	1	0	0	0	0	1	0	0	0	10193	1145	40	1	6307	1	NAV2	11	20119177	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	5854234	20119177	114887339	625	2691										
NELL1	4745	hgsc.bcm.edu	37	chr11	21135203	21135203	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtgtgtcaaccttcctgggTtatatcgctgtgactgtgtc	11	9	1	1	rs561468649		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:21135203T>C	ENST00000357134.5	+	13	1521	c.1369T>C	c.(1369-1371)Tta>Cta	p.L457L	NELL1_ENST00000532434.1_Silent_p.L457L|NELL1_ENST00000325319.5_Silent_p.L400L|NELL1_ENST00000298925.5_Silent_p.L485L	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	457	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						CCTTCCTGGGTTATATCGCTG	0.393																																					p.L457L		Atlas-SNP	.											.	NELL1	179	.	0			c.T1369C						.						353	303	320					11																	21135203		2203	4300	6503	SO:0001819	synonymous_variant	4745	exon13			CCTGGGTTATATC	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.1369T>C	chr11.hg19:g.21135203T>C		148.0	0.0		177.0	71.0	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	hg19	CCDS7855.1																																																																																			.	.		0.393	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		C	21135203	T	C	21135203	2	2	23	1	0	0	0	0	0	0	0	1	10342	1722	60	2		2	NELL1	11	21135203	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1016026	21135203	113871313	626	2692										
C11orf46	120534	hgsc.bcm.edu	37	chr11	30354502	30354502	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaaactggtaaaagagaaaaAagaaggcttacaaaaaatgc	9	4	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:30354502A>G	ENST00000282032.3	+	3	731	c.516A>G	c.(514-516)aaA>aaG	p.K172K		NM_152316.1	NP_689529.1	Q8N8R7	AL14E_HUMAN	ADP-ribosylation factor-like 14 effector protein	172						cytoplasm (GO:0005737)											AAAGAGAAAAAAGAAGGCTTA	0.408																																					p.K172K		Atlas-SNP	.											.	.	.	.	0			c.A516G						.						68	65	66					11																	30354502		2202	4299	6501	SO:0001819	synonymous_variant	120534	exon3			AGAAAAAAGAAGG	AK096287	CCDS7869.1	11p14.1	2014-09-17	2012-07-09	2012-07-09	ENSG00000152219	ENSG00000152219			26798	protein-coding gene	gene with protein product		612295	"chromosome 11 open reading frame 46"	C11orf46		21458045	Standard	XM_005252792		Approved	FLJ38968, ARF7EP	uc001mso.1	Q8N8R7	OTTHUMG00000166154	ENST00000282032.3:c.516A>G	chr11.hg19:g.30354502A>G		64.0	0.0		85.0	37.0	NM_152316	Q5HYH9	Silent	SNP	ENST00000282032.3	hg19	CCDS7869.1																																																																																			.	.		0.408	ARL14EP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388129.1	NM_152316		G	30354502	A	G	30354502	2	3	23	1	0	0	0	0	0	0	0	1	1645	11	1	2		2	C11orf46	11	30354502	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	9219299	30354502	104652014	627	2693										
MPPED2	744	hgsc.bcm.edu	37	chr11	30435807	30435807	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caccaaacacatggagcttgGgccggactcgcctctgaacc	10	15	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:30435807G>A	ENST00000358117.5	-	5	856	c.734C>T	c.(733-735)cCc>cTc	p.P245L	MPPED2_ENST00000524667.1_5'UTR|MPPED2_ENST00000448418.2_Missense_Mutation_p.P245L	NM_001584.2	NP_001575.1	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	245					nervous system development (GO:0007399)		hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(15)|skin(2)|upper_aerodigestive_tract(2)	33						ATGGAGCTTGGGCCGGACTCG	0.478																																					p.P245L		Atlas-SNP	.											.	MPPED2	106	.	0			c.C734T						.						122	109	114					11																	30435807		2202	4299	6501	SO:0001583	missense	744	exon5			AGCTTGGGCCGGA	U57911	CCDS7870.1, CCDS44560.1	11p13	2008-07-18	2005-10-10	2005-10-10	ENSG00000066382	ENSG00000066382			1180	protein-coding gene	gene with protein product		600911	"chromosome 11 open reading frame 8"	C11orf8		8666403, 9266672	Standard	NM_001584		Approved	239FB, D11S302E, Hs.46638, FAM1B, dJ873F21.1, dJ1024C24.1	uc001msr.3	Q15777	OTTHUMG00000166159	ENST00000358117.5:c.734C>T	chr11.hg19:g.30435807G>A	ENSP00000350833:p.Pro245Leu	130.0	0.0		102.0	44.0	NM_001584	D3DQZ5|E9PB10|Q59GE6	Missense_Mutation	SNP	ENST00000358117.5	hg19	CCDS7870.1	.	.	.	.	.	.	.	.	.	.	G	34	5.346944	0.95807	.	.	ENSG00000066382	ENST00000448418;ENST00000358117	T;T	0.73575	-0.76;-0.76	5.92	5.92	0.95590	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	D	0.88544	0.6465	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.991;0.999	D	0.88708	0.3220	10	0.62326	D	0.03	-8.8258	20.3206	0.98668	0.0:0.0:1.0:0.0	.	245;245	Q15777;E9PB10	MPPD2_HUMAN;.	L	245	ENSP00000388258:P245L;ENSP00000350833:P245L	ENSP00000350833:P245L	P	-	2	0	MPPED2	30392383	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.813000	0.96785	0.561000	0.74099	CCC	.	.		0.478	MPPED2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388155.2	NM_001584		A	30435807	G	A	30435807	3	1	23	1	0	0	0	0	1	0	0	0	9751	1232	43	3	230	3	MPPED2	11	30435807	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	81305	30435807	104570709	628	2694										
PRDM11	56981	hgsc.bcm.edu	37	chr11	45241211	45241211	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttccgggcgtgcagggacatCcggcctggggagtggctgcg	19	11	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:45241211C>T	ENST00000530656.1	+	6	747	c.747C>T	c.(745-747)atC>atT	p.I249I	CTD-2560E9.3_ENST00000527450.1_RNA|PRDM11_ENST00000424263.2_Silent_p.I215I|PRDM11_ENST00000528980.1_3'UTR|PRDM11_ENST00000263765.4_Silent_p.I249I			Q9NQV5	PRD11_HUMAN	PR domain containing 11	249	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						GCAGGGACATCCGGCCTGGGG	0.632																																					p.I215I	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											.	PRDM11	53	.	0			c.C645T						.						72	58	63					11																	45241211		2203	4299	6502	SO:0001819	synonymous_variant	56981	exon6			GGACATCCGGCCT	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"PR-domain containing protein 11"						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.747C>T	chr11.hg19:g.45241211C>T		90.0	0.0		76.0	24.0	NM_001256695	Q8N9F1	Silent	SNP	ENST00000530656.1	hg19																																																																																				.	.		0.632	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229		T	45241211	C	T	45241211	2	4	23	1	0	0	0	0	0	0	0	1	12464	845	30	3		3	PRDM11	11	45241211	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	14805404	45241211	89765305	629	2695										
DDB2	1643	hgsc.bcm.edu	37	chr11	47238524	47238524	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccaactcaccccagcactgTggctgtgggttccaaagggg	12	14	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:47238524T>C	ENST00000256996.4	+	3	575	c.380T>C	c.(379-381)gTg>gCg	p.V127A	DDB2_ENST00000378600.3_Missense_Mutation_p.V127A|DDB2_ENST00000378601.3_Missense_Mutation_p.V127A|DDB2_ENST00000378603.3_Intron	NM_000107.2	NP_000098.1	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2, 48kDa	127					DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|pyrimidine dimer repair (GO:0006290)|response to UV (GO:0009411)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(1)	17						CCCAGCACTGTGGCTGTGGGT	0.527			"Mis, N"			"skin basal cell, skin squamous cell, melanoma"		Direct reversal of damage;Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.V127A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (E)	11	11p12	1643	damage-specific DNA binding protein 2		E	.	DDB2	31	.	0			c.T380C						.						64	59	61					11																	47238524		2201	4298	6499	SO:0001583	missense	1643	exon3	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GCACTGTGGCTGT		CCDS7927.1, CCDS73284.1	11p12-p11	2014-09-17	2002-08-29			ENSG00000134574		"WD repeat domain containing"	2718	protein-coding gene	gene with protein product	"xeroderma pigmentosum group E protein", "UV-damaged DNA-binding protein 2", "DDB p48 subunit"	600811	"damage-specific DNA binding protein 2 (48kD)"			8407967, 8530102	Standard	NM_000107		Approved	DDBB, UV-DDB2, FLJ34321	uc001neb.2	Q92466		ENST00000256996.4:c.380T>C	chr11.hg19:g.47238524T>C	ENSP00000256996:p.Val127Ala	160.0	0.0		145.0	11.0	NM_000107	B2R875|Q76E54|Q76E55|Q76E56|Q76E57	Missense_Mutation	SNP	ENST00000256996.4	hg19	CCDS7927.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.928234	0.73327	.	.	ENSG00000134574	ENST00000256996;ENST00000378600;ENST00000378601	T;T;T	0.68479	-0.33;-0.16;1.46	5.78	5.78	0.91487	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.295779	0.32518	N	0.005987	T	0.67429	0.2892	M	0.61703	1.905	0.47698	D	0.999497	B;B;P	0.36199	0.287;0.287;0.543	B;B;B	0.37888	0.124;0.167;0.26	T	0.71126	-0.4683	10	0.72032	D	0.01	-16.4465	15.7819	0.78267	0.0:0.0:0.0:1.0	.	127;127;127	Q92466-3;Q92466-2;Q92466	.;.;DDB2_HUMAN	A	127	ENSP00000256996:V127A;ENSP00000367863:V127A;ENSP00000367864:V127A	ENSP00000256996:V127A	V	+	2	0	DDB2	47195100	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	7.331000	0.79192	2.205000	0.71048	0.533000	0.62120	GTG	.	.		0.527	DDB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000107		C	47238524	T	C	47238524	3	2	23	1	0	0	0	0	1	0	0	0	4326	1696	59	2	390	2	DDB2	11	47238524	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1997313	47238524	87767992	630	2696										
SPI1	6688	hgsc.bcm.edu	37	chr11	47376855	47376855	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaactggtaggtgagcttctTcttcaccttcttgacctcgc	9	12	4	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:47376855T>C	ENST00000378538.3	-	5	958	c.736A>G	c.(736-738)Aag>Gag	p.K246E	MYBPC3_ENST00000256993.4_5'Flank|MYBPC3_ENST00000399249.2_5'Flank|SPI1_ENST00000227163.4_Missense_Mutation_p.K247E|MYBPC3_ENST00000545968.1_5'Flank|SPI1_ENST00000533030.1_3'UTR	NM_001080547.1|NM_003120.2	NP_001074016.1|NP_003111.2	P17947	SPI1_HUMAN	Spi-1 proto-oncogene	246					anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|histone H3 acetylation (GO:0043966)|hypermethylation of CpG island (GO:0044027)|lymphocyte differentiation (GO:0030098)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of erythrocyte differentiation (GO:0045646)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somatic stem cell maintenance (GO:0035019)	nuclear chromatin (GO:0000790)	core promoter binding (GO:0001047)|NFAT protein binding (GO:0051525)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(4)|ovary(1)	8				Lung(87;0.0967)		GTGAGCTTCTTCTTCACCTTC	0.692																																					p.K247E		Atlas-SNP	.											.	SPI1	21	.	0			c.A739G						.						73	58	63					11																	47376855		2201	4298	6499	SO:0001583	missense	6688	exon5			GCTTCTTCTTCAC	X52056	CCDS7933.2, CCDS44591.1	11p12-p11.22	2014-06-25	2014-06-25		ENSG00000066336	ENSG00000066336			11241	protein-coding gene	gene with protein product	"hematopoietic transcription factor PU.1", "31 kDa transforming protein"	165170	"spleen focus forming virus (SFFV) proviral integration oncogene"			1693183	Standard	NM_003120		Approved	PU.1, SPI-A, OF, SFPI1, SPI-1	uc001nfb.1	P17947	OTTHUMG00000150150	ENST00000378538.3:c.736A>G	chr11.hg19:g.47376855T>C	ENSP00000367799:p.Lys246Glu	32.0	0.0		42.0	9.0	NM_001080547		Missense_Mutation	SNP	ENST00000378538.3	hg19	CCDS7933.2	.	.	.	.	.	.	.	.	.	.	t	27.8	4.861439	0.91433	.	.	ENSG00000066336	ENST00000378538;ENST00000227163	T;T	0.24538	1.85;1.85	4.11	4.11	0.48088	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.85682	D	0.000000	T	0.41488	0.1161	M	0.63208	1.945	0.80722	D	1	P;P	0.51449	0.945;0.867	P;P	0.56216	0.794;0.733	T	0.39292	-0.9621	10	0.66056	D	0.02	-26.9315	13.462	0.61233	0.0:0.0:0.0:1.0	.	246;247	P17947;P17947-2	SPI1_HUMAN;.	E	246;247	ENSP00000367799:K246E;ENSP00000227163:K247E	ENSP00000227163:K247E	K	-	1	0	SPI1	47333431	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.868000	0.63021	1.639000	0.50556	0.393000	0.25936	AAG	.	.		0.692	SPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316571.1	NM_003120		C	47376855	T	C	47376855	3	2	23	1	0	0	0	0	1	0	0	0	15064	1792	62	2	80	2	SPI1	11	47376855	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	138331	47376855	87629661	631	2697										
C1QTNF4	114900	hgsc.bcm.edu	37	chr11	47611408	47611408	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggccccgaggcccggcggggCggcgggggcgaggtcggggt	25	12	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:47611408C>T	ENST00000302514.3	-	2	1471	c.955G>A	c.(955-957)Gcc>Acc	p.A319T		NM_031909.2	NP_114115.2	Q9BXJ3	C1QT4_HUMAN	C1q and tumor necrosis factor related protein 4	319						extracellular space (GO:0005615)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						cccggcggggcggcgggggcg	0.731																																					p.A319T		Atlas-SNP	.											.	C1QTNF4	19	.	0			c.G955A						.						27	35	32					11																	47611408		1920	3768	5688	SO:0001583	missense	114900	exon2			GCGGGGCGGCGGG	AF329838	CCDS7942.1	11q11	2008-07-18				ENSG00000172247			14346	protein-coding gene	gene with protein product	"complement-c1q tumor necrosis factor-related protein 4"	614911				16094384	Standard	NM_031909		Approved	CTRP4, ZACRP4	uc001ngc.2	Q9BXJ3		ENST00000302514.3:c.955G>A	chr11.hg19:g.47611408C>T	ENSP00000302274:p.Ala319Thr	136.0	0.0		173.0	78.0	NM_031909	Q8IV25	Missense_Mutation	SNP	ENST00000302514.3	hg19	CCDS7942.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243010	0.39697	.	.	ENSG00000172247	ENST00000302514	T	0.74947	-0.89	4.4	1.39	0.22231	.	6.789180	0.01907	U	0.039580	T	0.53174	0.1780	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.12156	0.007	T	0.37934	-0.9684	10	0.21540	T	0.41	.	3.025	0.06087	0.1633:0.5316:0.2005:0.1046	.	319	Q9BXJ3	C1QT4_HUMAN	T	319	ENSP00000302274:A319T	ENSP00000302274:A319T	A	-	1	0	C1QTNF4	47567984	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.304000	0.08199	0.054000	0.16065	-0.258000	0.10820	GCC	.	.		0.731	C1QTNF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391772.1	NM_031909		T	47611408	C	T	47611408	3	4	23	1	0	0	0	0	1	0	0	0	1967	768	27	1	38	1	C1QTNF4	11	47611408	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	234553	47611408	87395108	632	2698										
C1QTNF4	114900	hgsc.bcm.edu	37	chr11	47612245	47612245	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catctccgacgtgccctccaGgggggtggtgcgtgccgccg					rs371580513		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:47612245delG	ENST00000302514.3	-	2	634	c.118delC	c.(118-120)ctgfs	p.L40fs		NM_031909.2	NP_114115.2	Q9BXJ3	C1QT4_HUMAN	C1q and tumor necrosis factor related protein 4	40	C1q 1. {ECO:0000255|PROSITE- ProRule:PRU00368}.					extracellular space (GO:0005615)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						GTGCCCTCCAGGGGGGTGGTG	0.726																																					p.L40fs		Atlas-Indel,Pindel	.											C1QTNF4,NS,carcinoma,0,1	C1QTNF4	19	.	0			c.119delT						.			10,4238		4,2,2118	17	17	17			4.3	0.9	11		17	27,8189		12,3,4093	no	frameshift	C1QTNF4	NM_031909.2		16,5,6211	A1A1,A1R,RR		0.3286,0.2354,0.2969			47612245	37,12427	2194	4289	6483	SO:0001589	frameshift_variant	114900	exon2			.	AF329838	CCDS7942.1	11q11	2008-07-18				ENSG00000172247			14346	protein-coding gene	gene with protein product	"complement-c1q tumor necrosis factor-related protein 4"	614911				16094384	Standard	NM_031909		Approved	CTRP4, ZACRP4	uc001ngc.2	Q9BXJ3		ENST00000302514.3:c.118delC	chr11.hg19:g.47612245delG	ENSP00000302274:p.Leu40fs	128.0	0.0		156.0	52.0	NM_031909	Q8IV25	Frame_Shift_Del	DEL	ENST00000302514.3	hg19	CCDS7942.1																																																																																			.	.		0.726	C1QTNF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391772.1	NM_031909		-	47612245	G	-	47612245	7	5	23	1	0	1	0	1	0	0	0	0	1967	991	35	0	875	0	C1QTNF4	11	47612245	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	837	47612245	87394271	633	2699										
AGBL2	79841	hgsc.bcm.edu	37	chr11	47701557	47701557	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggatcacaaaagtccagaaGggtgtcacagacatgataac							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:47701557delG	ENST00000525123.1	-	13	2269	c.1984delC	c.(1984-1986)cttfs	p.L663fs	AGBL2_ENST00000529712.1_5'UTR|AGBL2_ENST00000528244.1_Frame_Shift_Del_p.L625fs|AGBL2_ENST00000357610.3_Frame_Shift_Del_p.L663fs|AGBL2_ENST00000298861.4_Frame_Shift_Del_p.L663fs	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	663						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						AAGTCCAGAAGGGTGTCACAG	0.428																																					p.L662fs		Atlas-Indel,Pindel	.											.	AGBL2	73	.	0			c.1985delT						.						111	106	107					11																	47701557		2201	4298	6499	SO:0001589	frameshift_variant	79841	exon13			.		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"cytoplasmic carboxypeptidase 2"					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.1984delC	chr11.hg19:g.47701557delG	ENSP00000435582:p.Leu663fs	140.0	0.0		109.0	45.0	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Frame_Shift_Del	DEL	ENST00000525123.1	hg19	CCDS7944.1																																																																																			.	.		0.428	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783		-	47701557	G	-	47701557	7	5	23	1	0	1	0	1	0	0	0	0	376	1000	35	0	752	0	AGBL2	11	47701557	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	89312	47701557	87304959	634	2700										
OR4C11	219429	hgsc.bcm.edu	37	chr11	55371494	55371494	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tacagatggccacatagcgaTcaacagccatgagaatgagg	11	9	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55371494T>A	ENST00000302231.4	-	1	380	c.356A>T	c.(355-357)gAt>gTt	p.D119V		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	119						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						CACATAGCGATCAACAGCCAT	0.433																																					p.D119V		Atlas-SNP	.											.	OR4C11	73	.	0			c.A356T						.						93	77	83					11																	55371494		2179	4007	6186	SO:0001583	missense	219429	exon1			TAGCGATCAACAG	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"GPCR / Class A : Olfactory receptors"	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.356A>T	chr11.hg19:g.55371494T>A	ENSP00000306651:p.Asp119Val	138.0	0.0		155.0	64.0	NM_001004700	B9EIL4|Q8NGL8	Missense_Mutation	SNP	ENST00000302231.4	hg19	CCDS31503.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.761642	0.49468	.	.	ENSG00000172188	ENST00000302231	T	0.02158	4.42	4.34	4.34	0.51931	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	U	0.000122	T	0.21468	0.0517	H	0.98238	4.18	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.22068	-1.0227	10	0.87932	D	0	.	11.7877	0.52051	0.0:0.0:0.0:1.0	.	119	Q6IEV9	OR4CB_HUMAN	V	119	ENSP00000306651:D119V	ENSP00000306651:D119V	D	-	2	0	OR4C11	55128070	1.000000	0.71417	0.975000	0.42487	0.132000	0.20833	5.063000	0.64332	1.962000	0.57031	0.391000	0.25812	GAT	.	.		0.433	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700		A	55371494	T	A	55371494	3	1	23	1	0	0	0	0	1	0	0	0	11054	1435	50	4	578	4	OR4C11	11	55371494	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	7669937	55371494	79635022	635	2701										
OR5D13	390142	hgsc.bcm.edu	37	chr11	55541296	55541296	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttatgaccgttttgtggcagTttgtaaacccttgctgtata							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55541296delT	ENST00000361760.1	+	1	383	c.383delT	c.(382-384)gttfs	p.V128fs		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				TTTGTGGCAGTTTGTAAACCC	0.443																																					p.V128fs		Atlas-Indel,Pindel	.											.	OR5D13	96	.	0			c.382delG						.						240	234	236					11																	55541296		2200	4296	6496	SO:0001589	frameshift_variant	390142	exon1			.	BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"GPCR / Class A : Olfactory receptors"	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.383delT	chr11.hg19:g.55541296delT	ENSP00000354800:p.Val128fs	134.0	0.0		156.0	62.0	NM_001001967	Q6IF68|Q6IFC9	Frame_Shift_Del	DEL	ENST00000361760.1	hg19	CCDS31507.1																																																																																			.	.		0.443	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967		-	55541296	T	-	55541296	7	5	23	1	0	1	0	1	0	0	0	0	11163	1725	60	0	385	0	OR5D13	11	55541296	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	169802	55541296	79465220	636	2702										
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579121	55579121	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcggctccacacccccatgtActttttcctcagccacttgt	5	17	1	0	rs142577076		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55579121A>T	ENST00000333973.2	+	1	268	c.179A>T	c.(178-180)tAc>tTc	p.Y60F		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				ACCCCCATGTACTTTTTCCTC	0.463																																					p.Y60F		Atlas-SNP	.											OR5L1,NS,carcinoma,0,1	OR5L1	145	.	0			c.A179T						.						284	253	264					11																	55579121		2200	4296	6496	SO:0001583	missense	219437	exon1			CCATGTACTTTTT	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.179A>T	chr11.hg19:g.55579121A>T	ENSP00000335529:p.Tyr60Phe	103.0	0.0		153.0	62.0	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	hg19	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	a	15.79	2.938177	0.52972	.	.	ENSG00000186117	ENST00000333973	T	0.14391	2.51	4.32	4.32	0.51571	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44483	D	0.000451	T	0.44808	0.1311	M	0.92317	3.295	0.36280	D	0.855733	D	0.71674	0.998	D	0.72338	0.977	T	0.65134	-0.6242	10	0.87932	D	0	-46.0803	12.3887	0.55347	1.0:0.0:0.0:0.0	.	60	Q8NGL2	OR5L1_HUMAN	F	60	ENSP00000335529:Y60F	ENSP00000335529:Y60F	Y	+	2	0	OR5L1	55335697	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	6.889000	0.75627	1.608000	0.50180	0.358000	0.22013	TAC	.	A|1.000;G|0.000		0.463	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		T	55579121	A	T	55579121	3	4	23	1	0	0	0	0	1	0	0	0	11179	391	14	4	181	4	OR5L1	11	55579121	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	37825	55579121	79427395	637	2703										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587264	55587264	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	attgtgatcatcaaaatcaaCcccaaactgcatacccccat							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55587264delC	ENST00000333976.4	+	1	179	c.159delC	c.(157-159)aacfs	p.N53fs		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				TCAAAATCAACCCCAAACTGC	0.448																																					p.N53fs		Atlas-Indel,Pindel	.											.	OR5D18	121	.	0			c.158delA						.						238	218	224					11																	55587264		2200	4296	6496	SO:0001589	frameshift_variant	219438	exon1			.	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.159delC	chr11.hg19:g.55587264delC	ENSP00000335025:p.Asn53fs	112.0	0.0		143.0	32.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Frame_Shift_Del	DEL	ENST00000333976.4	hg19	CCDS31510.1																																																																																			.	.		0.448	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		-	55587264	C	-	55587264	7	5	23	1	0	1	0	1	0	0	0	0	11166	506	18	0	161	0	OR5D18	11	55587264	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	8143	55587264	79419252	638	2704										
OR5D16	390144	hgsc.bcm.edu	37	chr11	55606628	55606628	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catttgcaatcctctgctctAcacagttgccatctcccaga	5	15	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55606628A>G	ENST00000378396.1	+	1	401	c.401A>G	c.(400-402)tAc>tGc	p.Y134C		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	134						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				CCTCTGCTCTACACAGTTGCC	0.463																																					p.Y134C		Atlas-SNP	.											.	OR5D16	94	.	0			c.A401G						.						128	116	120					11																	55606628		2201	4296	6497	SO:0001583	missense	390144	exon1			TGCTCTACACAGT	AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"GPCR / Class A : Olfactory receptors"	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.401A>G	chr11.hg19:g.55606628A>G	ENSP00000367649:p.Tyr134Cys	106.0	0.0		84.0	37.0	NM_001005496	Q6IF65|Q96RB4	Missense_Mutation	SNP	ENST00000378396.1	hg19	CCDS31512.1	.	.	.	.	.	.	.	.	.	.	.	11.63	1.695124	0.30052	.	.	ENSG00000205029	ENST00000378396	T	0.33865	1.39	4.47	2.05	0.26809	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.69797	0.3151	H	0.97340	3.985	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59994	-0.7349	9	0.87932	D	0	-24.1127	8.3681	0.32399	0.83:0.0:0.17:0.0	.	134	Q8NGK9	OR5DG_HUMAN	C	134	ENSP00000367649:Y134C	ENSP00000367649:Y134C	Y	+	2	0	OR5D16	55363204	1.000000	0.71417	0.002000	0.10522	0.207000	0.24258	5.675000	0.68123	0.213000	0.20722	-0.528000	0.04320	TAC	.	.		0.463	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496		G	55606628	A	G	55606628	3	3	23	1	0	0	0	0	1	0	0	0	11165	391	14	2	403	2	OR5D16	11	55606628	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	19364	55606628	79399888	639	2705										
OR8I2	120586	hgsc.bcm.edu	37	chr11	55860942	55860942	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgttaatcagaatggattcTcagcttcacacccctatgta	6	11	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55860942T>G	ENST00000302124.2	+	1	190	c.159T>G	c.(157-159)tcT>tcG	p.S53S		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					GAATGGATTCTCAGCTTCACA	0.368																																					p.S53S		Atlas-SNP	.											.	OR8I2	119	.	0			c.T159G						.						253	243	247					11																	55860942		2201	4296	6497	SO:0001819	synonymous_variant	120586	exon1			GGATTCTCAGCTT	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.159T>G	chr11.hg19:g.55860942T>G		72.0	0.0		71.0	36.0	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Silent	SNP	ENST00000302124.2	hg19	CCDS31517.1																																																																																			.	.		0.368	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		G	55860942	T	G	55860942	2	3	23	1	0	0	0	0	0	0	0	1	11249	1538	54	5		5	OR8I2	11	55860942	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	254314	55860942	79145574	640	2706										
OR8H3	390152	hgsc.bcm.edu	37	chr11	55890135	55890135	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caactatatttccttcacggGctgctttgcccagatgttct	7	12	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55890135G>A	ENST00000313472.3	+	1	287	c.287G>A	c.(286-288)gGc>gAc	p.G96D		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	96						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TCCTTCACGGGCTGCTTTGCC	0.443																																					p.G96D		Atlas-SNP	.											.	OR8H3	92	.	0			c.G287A						.						336	328	331					11																	55890135		2201	4296	6497	SO:0001583	missense	390152	exon1			TCACGGGCTGCTT	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"GPCR / Class A : Olfactory receptors"	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.287G>A	chr11.hg19:g.55890135G>A	ENSP00000323928:p.Gly96Asp	99.0	0.0		120.0	7.0	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	hg19	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	G	7.838	0.721222	0.15372	.	.	ENSG00000181761	ENST00000313472	T	0.09723	2.95	3.44	2.52	0.30459	GPCR, rhodopsin-like superfamily (1);	0.331079	0.26542	N	0.023795	T	0.12860	0.0312	M	0.64170	1.965	0.26439	N	0.975809	B	0.20368	0.044	B	0.21151	0.033	T	0.14309	-1.0477	10	0.52906	T	0.07	.	10.6985	0.45913	0.0976:0.0:0.9024:0.0	.	96	Q8N146	OR8H3_HUMAN	D	96	ENSP00000323928:G96D	ENSP00000323928:G96D	G	+	2	0	OR8H3	55646711	0.003000	0.15002	0.239000	0.24122	0.272000	0.26649	0.201000	0.17276	0.548000	0.28955	0.173000	0.16961	GGC	.	.		0.443	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201		A	55890135	G	A	55890135	3	1	23	1	0	0	0	0	1	0	0	0	11248	1203	42	3	289	3	OR8H3	11	55890135	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	29193	55890135	79116381	641	2707										
OR5AR1	219493	hgsc.bcm.edu	37	chr11	56432083	56432083	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcaaaaagctaattggaaaaAaatctcaataataacacaaa	3	6	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:56432083A>G	ENST00000302969.2	+	1	946	c.922A>G	c.(922-924)Aaa>Gaa	p.K308E		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	308						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						AATTGGAAAAAAATCTCAATA	0.343																																					p.K308E		Atlas-SNP	.											.	OR5AR1	68	.	0			c.A922G						.						24	25	24					11																	56432083		2201	4296	6497	SO:0001583	missense	219493	exon1			GGAAAAAAATCTC	AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"GPCR / Class A : Olfactory receptors"	15260	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily AR, member 1"				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.922A>G	chr11.hg19:g.56432083A>G	ENSP00000302639:p.Lys308Glu	56.0	0.0		56.0	23.0	NM_001004730	Q6IF61	Missense_Mutation	SNP	ENST00000302969.2	hg19	CCDS31535.1	.	.	.	.	.	.	.	.	.	.	A	5.691	0.312126	0.10789	.	.	ENSG00000172459	ENST00000302969	T	0.39406	1.08	4.63	4.63	0.57726	.	1.008850	0.07975	N	0.984696	T	0.37732	0.1014	L	0.43923	1.385	0.09310	N	1	B	0.26081	0.141	B	0.19391	0.025	T	0.20107	-1.0285	10	0.48119	T	0.1	.	10.6087	0.45408	1.0:0.0:0.0:0.0	.	308	Q8NGP9	O5AR1_HUMAN	E	308	ENSP00000302639:K308E	ENSP00000302639:K308E	K	+	1	0	OR5AR1	56188659	0.000000	0.05858	0.021000	0.16686	0.021000	0.10359	0.769000	0.26604	2.074000	0.62210	0.467000	0.42956	AAA	.	.		0.343	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730		G	56432083	A	G	56432083	3	3	23	1	0	0	0	0	1	0	0	0	11154	15	1	2	924	2	OR5AR1	11	56432083	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	541948	56432083	78574433	642	2708										
PRG2	5553	hgsc.bcm.edu	37	chr11	57155302	57155302	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagtatgcaaagttccagcGgctgccgtcaacccactgaa	9	14	1	1	rs142359007		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:57155302G>A	ENST00000311862.5	-	5	608	c.535C>T	c.(535-537)Cgc>Tgc	p.R179C	PRG2_ENST00000525955.1_Missense_Mutation_p.R179C|PRG2_ENST00000533605.1_Missense_Mutation_p.R168C	NM_001243245.1|NM_002728.4	NP_001230174.1|NP_002719.3	P13727	PRG2_HUMAN	proteoglycan 2, bone marrow (natural killer cell activator, eosinophil granule major basic protein)	179	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		R -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)	p.R179C(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Sargramostim(DB00020)	AAGTTCCAGCGGCTGCCGTCA	0.637																																					p.R179C		Atlas-SNP	.											PRG2_ENST00000311862,colon,carcinoma,0,1	PRG2	65	.	1	Substitution - Missense(1)	large_intestine(1)	c.C535T						.	G	CYS/ARG	0,4396		0,0,2198	18	18	18		535	-9.9	0	11	dbSNP_134	18	1,8581		0,1,4290	no	missense	PRG2	NM_002728.4	180	0,1,6488	AA,AG,GG		0.0117,0.0,0.0077		179/223	57155302	1,12977	2198	4291	6489	SO:0001583	missense	5553	exon5			TCCAGCGGCTGCC	BC005929	CCDS7955.1, CCDS58133.1	11q12	2005-11-25				ENSG00000186652			9362	protein-coding gene	gene with protein product		605601				1565101	Standard	NM_001243245		Approved	MBP, BMPG		P13727		ENST00000311862.5:c.535C>T	chr11.hg19:g.57155302G>A	ENSP00000312134:p.Arg179Cys	202.0	0.0		161.0	65.0	NM_002728	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Missense_Mutation	SNP	ENST00000311862.5	hg19	CCDS7955.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265585	0.40095	0.0	1.17E-4	ENSG00000186652	ENST00000311862;ENST00000533605;ENST00000525955	T;T;T	0.19669	2.13;2.13;2.13	4.98	-9.95	0.00446	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.531680	0.04767	N	0.427360	T	0.15825	0.0381	L	0.58510	1.815	0.09310	N	1	B;B	0.17852	0.001;0.024	B;B	0.09377	0.002;0.004	T	0.11036	-1.0604	10	0.36615	T	0.2	.	4.9516	0.14017	0.1525:0.4452:0.31:0.0923	.	168;179	A6XMW0;P13727	.;PRG2_HUMAN	C	179;168;179	ENSP00000312134:R179C;ENSP00000433231:R168C;ENSP00000433016:R179C	ENSP00000312134:R179C	R	-	1	0	PRG2	56911878	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-2.542000	0.00935	-2.572000	0.00467	-0.355000	0.07637	CGC	.	G|1.000;A|0.000		0.637	PRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392468.1	NM_002728		A	57155302	G	A	57155302	3	1	23	1	0	0	0	0	1	0	0	0	12491	1116	39	1	141	1	PRG2	11	57155302	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	723219	57155302	77851214	643	2709										
VPS37C	55048	hgsc.bcm.edu	37	chr11	60899319	60899319	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaggccaggcaggccccggCggtggtgggaacccataggg	18	13	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:60899319C>T	ENST00000301765.5	-	5	1273	c.1041G>A	c.(1039-1041)ccG>ccA	p.P347P		NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)	347	Pro-rich.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						CAGGCCCCGGCGGTGGTGGGA	0.697																																					p.P347P		Atlas-SNP	.											.	VPS37C	30	.	0			c.G1041A						.						4	4	4					11																	60899319		1916	3926	5842	SO:0001819	synonymous_variant	55048	exon5			CCCCGGCGGTGGT	AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"vacuolar protein sorting 37C (yeast)"			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.1041G>A	chr11.hg19:g.60899319C>T		23.0	0.0		33.0	14.0	NM_017966	Q8N3K4	Silent	SNP	ENST00000301765.5	hg19	CCDS31573.1																																																																																			.	.		0.697	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966		T	60899319	C	T	60899319	2	4	23	1	0	0	0	0	0	0	0	1	17222	755	27	1		1	VPS37C	11	60899319	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3744017	60899319	74107197	644	2710										
C11orf66	220004	hgsc.bcm.edu	37	chr11	61249285	61249285	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccctgccccacagcatcatgAtggggaaactccccctgggg	11	16	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:61249285A>T	ENST00000338608.2	+	2	129	c.4A>T	c.(4-6)Atg>Ttg	p.M2L	RP11-286N22.8_ENST00000544880.1_Intron|PPP1R32_ENST00000432063.2_Missense_Mutation_p.M2L|RP11-286N22.8_ENST00000543044.1_3'UTR	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	2							phosphatase binding (GO:0019902)										CAGCATCATGATGGGGAAACT	0.632																																					p.M2L		Atlas-SNP	.											.	.	.	.	0			c.A4T						.						18	20	20					11																	61249285		2201	4298	6499	SO:0001583	missense	220004	exon2			ATCATGATGGGGA	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	28869	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 66"	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.4A>T	chr11.hg19:g.61249285A>T	ENSP00000344140:p.Met2Leu	74.0	0.0		58.0	22.0	NM_001170753	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	hg19	CCDS8008.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.934765	0.73442	.	.	ENSG00000256591;ENSG00000162148;ENSG00000162148	ENST00000541135;ENST00000432063;ENST00000338608	T;T;T	0.75589	-0.95;0.37;0.93	4.73	3.57	0.40892	.	0.108731	0.41294	N	0.000906	T	0.73249	0.3563	M	0.72894	2.215	0.80722	D	1	P;P	0.45078	0.85;0.85	B;B	0.43809	0.432;0.432	T	0.73202	-0.4057	10	0.66056	D	0.02	-3.6751	9.2926	0.37795	0.8179:0.1821:0.0:0.0	.	2;2	Q7Z5V6-2;Q7Z5V6	.;PPR32_HUMAN	L	154;2;2	ENSP00000443130:M154L;ENSP00000391560:M2L;ENSP00000344140:M2L	ENSP00000344140:M2L	M	+	1	0	C11orf66;RP11-286N22.8	61005861	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.736000	0.38187	0.653000	0.30826	0.329000	0.21502	ATG	.	.		0.632	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017		T	61249285	A	T	61249285	3	4	23	1	0	0	0	0	1	0	0	0	1658	333	12	4	6	4	C11orf66	11	61249285	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	349966	61249285	73757231	645	2711										
FEN1	2237	hgsc.bcm.edu	37	chr11	61563849	61563849	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaaggcagcacccagggccGcctggatgatttcttcaagg	12	13	2	1	rs573495657		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:61563849G>A	ENST00000305885.2	+	2	1429	c.1016G>A	c.(1015-1017)cGc>cAc	p.R339H	FADS2_ENST00000574708.1_Intron	NM_004111.5	NP_004102.1			flap structure-specific endonuclease 1											endometrium(1)|large_intestine(4)|lung(1)|ovary(1)	7						ACCCAGGGCCGCCTGGATGAT	0.552								Editing and processing nucleases					G|||	1	0.000199681	0	0	5008	,	,		17828	0		0	False		,,,				2504	0.001				p.R339H		Atlas-SNP	.											FEN1,colon,carcinoma,0,1	FEN1	15	.	0			c.G1016A						.						30	33	32					11																	61563849		2202	4299	6501	SO:0001583	missense	2237	exon2			AGGGCCGCCTGGA	L37374	CCDS8010.1	11q12	2013-05-08			ENSG00000168496	ENSG00000168496			3650	protein-coding gene	gene with protein product	"maturation factor-1", "DNase IV"	600393		RAD2		7774922	Standard	NM_004111		Approved	FEN-1, MF1	uc001nsg.3	P39748	OTTHUMG00000168162	ENST00000305885.2:c.1016G>A	chr11.hg19:g.61563849G>A	ENSP00000305480:p.Arg339His	227.0	0.0		190.0	72.0	NM_004111		Missense_Mutation	SNP	ENST00000305885.2	hg19	CCDS8010.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.300983	0.81136	.	.	ENSG00000168496	ENST00000305885	T	0.33654	1.4	5.44	4.54	0.55810	-3&apos (1); exonuclease, C-terminal domain (1);5&apos (1);	0.000000	0.85682	D	0.000000	T	0.68238	0.2979	M	0.92507	3.315	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77747	-0.2472	10	0.87932	D	0	-31.7275	14.568	0.68191	0.0703:0.0:0.9297:0.0	.	339	P39748	FEN1_HUMAN	H	339	ENSP00000305480:R339H	ENSP00000305480:R339H	R	+	2	0	FEN1	61320425	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	9.324000	0.96373	1.446000	0.47643	-0.258000	0.10820	CGC	.	.		0.552	FEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398526.1	NM_004111		A	61563849	G	A	61563849	3	1	23	1	0	0	0	0	1	0	0	0	5820	1087	38	1	1018	1	FEN1	11	61563849	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	314564	61563849	73442667	646	2712										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62303477	62303477	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgtcacctcctgcacaaagaCgccgtcgtccctctgggcga	10	17	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:62303477C>T	ENST00000378024.4	-	3	368	c.94G>A	c.(94-96)Gtc>Atc	p.V32I	RP11-864I4.3_ENST00000544108.1_RNA|AHNAK_ENST00000257247.7_Missense_Mutation_p.V32I|AHNAK_ENST00000530124.1_Missense_Mutation_p.V32I	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	32	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGCACAAAGACGCCGTCGTCC	0.652																																					p.V32I		Atlas-SNP	.											.	AHNAK	532	.	0			c.G94A						.						61	58	59					11																	62303477		2202	4299	6501	SO:0001583	missense	79026	exon3			CAAAGACGCCGTC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.94G>A	chr11.hg19:g.62303477C>T	ENSP00000367263:p.Val32Ile	45.0	0.0		62.0	33.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	C	9.454	1.091281	0.20471	.	.	ENSG00000124942	ENST00000530124;ENST00000257247;ENST00000533365;ENST00000378024;ENST00000530285;ENST00000528508;ENST00000531324	T;T;T;T;T;T;T	0.41065	1.83;1.83;1.83;1.01;1.83;1.83;1.83	5.36	5.36	0.76844	PDZ/DHR/GLGF (3);	0.127761	0.31427	U	0.007679	T	0.31857	0.0810	N	0.00926	-1.1	0.35379	D	0.78977	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	T	0.37957	-0.9683	10	0.02654	T	1	-29.8375	17.8806	0.88839	0.0:1.0:0.0:0.0	.	32;32	Q09666;A1A586	AHNK_HUMAN;.	I	32	ENSP00000433789:V32I;ENSP00000257247:V32I;ENSP00000433635:V32I;ENSP00000367263:V32I;ENSP00000433286:V32I;ENSP00000435357:V32I;ENSP00000436845:V32I	ENSP00000257247:V32I	V	-	1	0	AHNAK	62060053	0.996000	0.38824	0.955000	0.39395	0.249000	0.25844	3.220000	0.51207	2.512000	0.84698	0.655000	0.94253	GTC	.	.		0.652	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62303477	C	T	62303477	3	4	23	1	0	0	0	0	1	0	0	0	414	536	19	1	17706	1	AHNAK	11	62303477	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	739628	62303477	72703039	647	2713										
EML3	256364	hgsc.bcm.edu	37	chr11	62370721	62370721	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagcctccagccacgtccccTggggagagggagcccgccca	13	18	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:62370721T>G	ENST00000394773.2	-	20	2565		c.e20-2		EML3_ENST00000531557.1_Splice_Site|EML3_ENST00000529309.1_Splice_Site|RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000438258.1_5'Flank|EML3_ENST00000278845.4_Splice_Site|MTA2_ENST00000527204.1_5'Flank|EML3_ENST00000494176.2_Splice_Site|MTA2_ENST00000278823.2_5'Flank	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3							cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						CCACGTCCCCTGGGGAGAGGG	0.612																																					.		Atlas-SNP	.											.	EML3	61	.	0			c.2258-2A>C						.						57	60	59					11																	62370721		2202	4299	6501	SO:0001630	splice_region_variant	256364	exon21			GTCCCCTGGGGAG	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"WD repeat domain containing"	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.2258-2A>C	chr11.hg19:g.62370721T>G		30.0	0.0		25.0	11.0	NM_153265	Q6ZQW7|Q8NA55	Splice_Site	SNP	ENST00000394773.2	hg19	CCDS8023.2	.	.	.	.	.	.	.	.	.	.	T	17.88	3.498349	0.64186	.	.	ENSG00000149499	ENST00000439994;ENST00000394773;ENST00000394776;ENST00000278845;ENST00000531557;ENST00000494176;ENST00000529309	.	.	.	4.78	4.78	0.61160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2655	0.54676	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EML3	62127297	1.000000	0.71417	0.863000	0.33907	0.897000	0.52465	7.717000	0.84732	1.787000	0.52448	0.459000	0.35465	.	.	.		0.612	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265	Intron	G	62370721	T	G	62370721	5	3	23	1	0	0	0	0	0	0	1	0	5100	1594	55	5	446	5	EML3	11	62370721	Splice_Site	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	67244	62370721	72635795	648	2714										
CHRM1	1128	hgsc.bcm.edu	37	chr11	62677349	62677349	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggttgatggtgctgttgacGtagcacagccagtagcccag	15	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:62677349G>A	ENST00000306960.3	-	2	1765	c.1224C>T	c.(1222-1224)taC>taT	p.Y408Y	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	408					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	TGCTGTTGACGTAGCACAGCC	0.582																																					p.Y408Y		Atlas-SNP	.											.	CHRM1	29	.	0			c.C1224T						.						158	136	143					11																	62677349		2201	4298	6499	SO:0001819	synonymous_variant	1128	exon2			GTTGACGTAGCAC	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1950	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 1"	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1224C>T	chr11.hg19:g.62677349G>A		150.0	0.0		128.0	44.0	NM_000738	Q96RH1	Silent	SNP	ENST00000306960.3	hg19	CCDS8040.1																																																																																			.	.		0.582	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738		A	62677349	G	A	62677349	2	1	23	1	0	0	0	0	0	0	0	1	3378	1140	40	1		1	CHRM1	11	62677349	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	306628	62677349	72329167	649	2715										
MAP4K2	5871	hgsc.bcm.edu	37	chr11	64557055	64557055	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggatgtagaggttgctgtgcGcctctgggttgtcagtggga	18	6	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:64557055G>A	ENST00000294066.2	-	32	2508	c.2417C>T	c.(2416-2418)gCg>gTg	p.A806V	MAP4K2_ENST00000377350.3_Missense_Mutation_p.A798V	NM_004579.3	NP_004570.2	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase kinase 2	806					activation of JUN kinase activity (GO:0007257)|immune response (GO:0006955)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|positive regulation of JNK cascade (GO:0046330)|protein phosphorylation (GO:0006468)|vesicle targeting (GO:0006903)	Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(1)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(2)	8						GTTGCTGTGCGCCTCTGGGTT	0.632																																					p.A806V		Atlas-SNP	.											.	MAP4K2	83	.	0			c.C2417T						.						96	84	88					11																	64557055		2201	4297	6498	SO:0001583	missense	5871	exon32			CTGTGCGCCTCTG	BC047865	CCDS8082.1	11q13.1	2011-06-09			ENSG00000168067	ENSG00000168067		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6864	protein-coding gene	gene with protein product		603166		RAB8IP		7515885	Standard	NM_004579		Approved	GCK, BL44	uc001obh.3	Q12851	OTTHUMG00000045328	ENST00000294066.2:c.2417C>T	chr11.hg19:g.64557055G>A	ENSP00000294066:p.Ala806Val	130.0	0.0		114.0	29.0	NM_004579	Q86VU3	Missense_Mutation	SNP	ENST00000294066.2	hg19	CCDS8082.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117851	0.77323	.	.	ENSG00000168067	ENST00000294066;ENST00000377350	T;T	0.71103	-0.54;-0.5	5.19	5.19	0.71726	.	0.058733	0.64402	D	0.000003	T	0.81754	0.4889	M	0.68952	2.095	0.58432	D	0.999993	D;D	0.76494	0.999;0.999	D;D	0.73380	0.97;0.98	T	0.82812	-0.0272	10	0.56958	D	0.05	.	14.2799	0.66205	0.0:0.0:1.0:0.0	.	798;806	Q86VU3;Q12851	.;M4K2_HUMAN	V	806;798	ENSP00000294066:A806V;ENSP00000366567:A798V	ENSP00000294066:A806V	A	-	2	0	MAP4K2	64313631	1.000000	0.71417	0.877000	0.34402	0.248000	0.25809	8.251000	0.89838	2.446000	0.82766	0.555000	0.69702	GCG	.	.		0.632	MAP4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105239.1	NM_004579		A	64557055	G	A	64557055	3	1	23	1	0	0	0	0	1	0	0	0	9269	1087	38	1	49	1	MAP4K2	11	64557055	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1879706	64557055	70449461	650	2716										
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64592001	64592001	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcttcggggccgttctgagaCctgcaggagaaagaaaagga	15	8	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:64592001C>T	ENST00000342711.5	-	37	4599	c.4600G>A	c.(4600-4602)Gtc>Atc	p.V1534I		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						CGTTCTGAGACCTGCAGGAGA	0.577																																					p.V1534I		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.G4600A						.						42	46	45					11																	64592001		2201	4297	6498	SO:0001630	splice_region_variant	55561	exon37			CTGAGACCTGCAG	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"Pleckstrin homology (PH) domain containing"	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.4600-1G>A	chr11.hg19:g.64592001C>T		347.0	0.0		358.0	138.0	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	hg19	CCDS31601.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.081619	0.36758	.	.	ENSG00000171219	ENST00000342711	T	0.66638	-0.22	4.33	3.14	0.36123	.	0.000000	0.34879	N	0.003617	T	0.62768	0.2455	L	0.36672	1.1	0.24694	N	0.993299	P	0.44690	0.841	P	0.58820	0.846	T	0.53085	-0.8488	10	0.10111	T	0.7	.	5.3771	0.16172	0.0:0.8079:0.0:0.1921	.	1534	Q6DT37	MRCKG_HUMAN	I	1534	ENSP00000345133:V1534I	ENSP00000345133:V1534I	V	-	1	0	CDC42BPG	64348577	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	2.275000	0.43399	2.152000	0.67230	0.555000	0.69702	GTC	.	.		0.577	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	Missense_Mutation	T	64592001	C	T	64592001	5	4	23	1	0	0	0	0	0	0	1	0	3076	521	18	3	59	3	CDC42BPG	11	64592001	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	34946	64592001	70414515	651	2717										
EHD1	10938	hgsc.bcm.edu	37	chr11	64622239	64622239	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caccatcaccatcagccgcgCgatgtcgttggccagcatgt	10	15	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:64622239C>T	ENST00000320631.3	-	5	1425	c.1171G>A	c.(1171-1173)Gcg>Acg	p.A391T	EHD1_ENST00000488711.1_5'UTR|EHD1_ENST00000359393.2_Missense_Mutation_p.A391T	NM_001282445.1|NM_006795.2	NP_001269374.1|NP_006786.2	Q9H4M9	EHD1_HUMAN	EH-domain containing 1	391					blood coagulation (GO:0007596)|cellular response to nerve growth factor stimulus (GO:1990090)|cholesterol homeostasis (GO:0042632)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|low-density lipoprotein particle clearance (GO:0034383)|neuron projection development (GO:0031175)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein homooligomerization (GO:0051260)	early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12						ATCAGCCGCGCGATGTCGTTG	0.642																																					p.A391T		Atlas-SNP	.											.	EHD1	31	.	0			c.G1171A						.						215	199	205					11																	64622239		2201	4297	6498	SO:0001583	missense	10938	exon5			GCCGCGCGATGTC	AF099011	CCDS8084.1, CCDS73315.1	11q13	2013-01-10			ENSG00000110047	ENSG00000110047		"EF-hand domain containing"	3242	protein-coding gene	gene with protein product	"testilin"	605888		PAST1		10395801, 10673336	Standard	NM_001282444		Approved	H-PAST, HPAST1, FLJ42622, FLJ44618	uc001obu.1	Q9H4M9	OTTHUMG00000066832	ENST00000320631.3:c.1171G>A	chr11.hg19:g.64622239C>T	ENSP00000320516:p.Ala391Thr	32.0	0.0		29.0	10.0	NM_006795	O14611|Q2M3Q4|Q9UNR3	Missense_Mutation	SNP	ENST00000320631.3	hg19	CCDS8084.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.838589	0.71373	.	.	ENSG00000110047	ENST00000320631;ENST00000359393;ENST00000541001;ENST00000421510	T;T;T	0.47177	2.19;2.19;0.85	4.56	4.56	0.56223	.	0.098802	0.64402	D	0.000002	T	0.47655	0.1457	M	0.71581	2.175	0.80722	D	1	B;B	0.27656	0.184;0.184	B;B	0.19391	0.025;0.025	T	0.52253	-0.8600	10	0.52906	T	0.07	.	14.8614	0.70384	0.0:1.0:0.0:0.0	.	391;391	B2R5U3;Q9H4M9	.;EHD1_HUMAN	T	391;391;367;255	ENSP00000320516:A391T;ENSP00000352354:A391T;ENSP00000391429:A255T	ENSP00000320516:A391T	A	-	1	0	EHD1	64378815	1.000000	0.71417	0.649000	0.29536	0.895000	0.52256	7.576000	0.82467	2.381000	0.81170	0.561000	0.74099	GCG	.	.		0.642	EHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143229.2	NM_006795		T	64622239	C	T	64622239	3	4	23	1	0	0	0	0	1	0	0	0	4979	768	27	1	437	1	EHD1	11	64622239	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	30238	64622239	70384277	652	2718										
NAALADL1	10004	hgsc.bcm.edu	37	chr11	64813529	64813529	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccttctgcagtgttgatatgCgttggcccaaggctgcagct	12	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:64813529C>T	ENST00000358658.3	-	16	1940	c.1913G>A	c.(1912-1914)cGc>cAc	p.R638H	NAALADL1_ENST00000526799.1_5'UTR|NAALADL1_ENST00000339885.2_3'UTR|NAALADL1_ENST00000355721.3_Missense_Mutation_p.R597H|NAALADL1_ENST00000528884.1_5'UTR|NAALADL1_ENST00000340252.4_Missense_Mutation_p.R689H|NAALADL1_ENST00000355369.2_3'UTR|NAALADL1_ENST00000356632.3_Missense_Mutation_p.R603H	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	638						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						TGTTGATATGCGTTGGCCCAA	0.632																																					p.R638H		Atlas-SNP	.											.	NAALADL1	58	.	0			c.G1913A						.						55	51	52					11																	64813529		2201	4297	6498	SO:0001583	missense	10004	exon16			GATATGCGTTGGC	AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"ileal peptidase I100"	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.1913G>A	chr11.hg19:g.64813529C>T	ENSP00000351484:p.Arg638His	46.0	0.0		52.0	20.0	NM_005468	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Missense_Mutation	SNP	ENST00000358658.3	hg19	CCDS31604.1	.	.	.	.	.	.	.	.	.	.	C	5.797	0.331378	0.10956	.	.	ENSG00000168060	ENST00000533753;ENST00000358658;ENST00000453486;ENST00000340252;ENST00000355721;ENST00000356632	T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34	4.98	-6.83	0.01693	Transferrin receptor-like, dimerisation domain (3);	0.970926	0.08538	N	0.931048	T	0.30166	0.0756	N	0.20610	0.595	0.09310	N	0.999999	B	0.06786	0.001	B	0.10450	0.005	T	0.24225	-1.0166	10	0.26408	T	0.33	-6.1261	8.7798	0.34785	0.1205:0.1896:0.0:0.6899	.	638	Q9UQQ1	NALDL_HUMAN	H	45;638;638;689;597;603	ENSP00000434225:R45H;ENSP00000351484:R638H;ENSP00000344244:R689H;ENSP00000347955:R597H;ENSP00000349045:R603H	ENSP00000344244:R689H	R	-	2	0	NAALADL1	64570105	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.936000	0.01549	-0.899000	0.03901	-0.367000	0.07326	CGC	.	.		0.632	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468		T	64813529	C	T	64813529	3	4	23	1	0	0	0	0	1	0	0	0	10138	768	27	1	321	1	NAALADL1	11	64813529	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	191290	64813529	70192987	653	2719										
RELA	5970	hgsc.bcm.edu	37	chr11	65426225	65426225	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acacagtaggaagatctcatCcccaccgaggcagctgccag	10	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:65426225C>A	ENST00000406246.3	-	7	889	c.628G>T	c.(628-630)Gat>Tat	p.D210Y	RELA_ENST00000308639.9_Missense_Mutation_p.D207Y|RELA_ENST00000525693.1_Missense_Mutation_p.D210Y	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	210	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						AAGATCTCATCCCCACCGAGG	0.567																																					p.D210Y		Atlas-SNP	.											.	RELA	44	.	0			c.G628T						.						140	120	126					11																	65426225		2201	4297	6498	SO:0001583	missense	5970	exon7			TCTCATCCCCACC	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.628G>T	chr11.hg19:g.65426225C>A	ENSP00000384273:p.Asp210Tyr	78.0	0.0		57.0	38.0	NM_021975	Q6GTV1|Q6SLK1	Missense_Mutation	SNP	ENST00000406246.3	hg19	CCDS31609.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.770269	0.90108	.	.	ENSG00000173039	ENST00000406246;ENST00000525693;ENST00000308639;ENST00000426617;ENST00000545816;ENST00000532999;ENST00000534558;ENST00000527749	T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36	5.13	5.13	0.70059	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.68265	0.2982	M	0.91612	3.225	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.998;1.0;1.0;0.999;0.999;0.997	T	0.76688	-0.2867	10	0.87932	D	0	-12.0034	16.0771	0.80976	0.0:1.0:0.0:0.0	.	210;197;207;210;221;210	Q04206-3;Q04206-2;Q04206-4;Q04206;B4E082;Q2TAM5	.;.;.;TF65_HUMAN;.;.	Y	210;210;207;210;221;221;201;179	ENSP00000384273:D210Y;ENSP00000432537:D210Y;ENSP00000311508:D207Y;ENSP00000433526:D221Y;ENSP00000434372:D201Y;ENSP00000436545:D179Y	ENSP00000311508:D207Y	D	-	1	0	RELA	65182801	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.634000	0.83273	2.387000	0.81309	0.655000	0.94253	GAT	.	.		0.567	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		A	65426225	C	A	65426225	3	1	23	1	0	0	0	0	1	0	0	0	13231	855	30	3	1047	3	RELA	11	65426225	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	612696	65426225	69580291	654	2720										
RBM4	5936	hgsc.bcm.edu	37	chr11	66411228	66411228	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtggcagctgcagctgcctcCgtgtataattacgcagagca	12	11	0	1	rs372104227		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:66411228C>T	ENST00000409406.1	+	2	1497	c.720C>T	c.(718-720)tcC>tcT	p.S240S	RBM4_ENST00000506523.2_Intron|RBM4_ENST00000396053.4_Intron|RBM4_ENST00000408993.2_Silent_p.S240S|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000578778.1_Intron|RBM4_ENST00000530235.1_Intron|RBM4_ENST00000398692.4_Intron|RBM4_ENST00000514361.3_Silent_p.S215S|RBM4_ENST00000503028.2_Silent_p.S240S|RBM4_ENST00000515838.2_3'UTR|RBM14-RBM4_ENST00000412278.2_Silent_p.S215S|RBM4_ENST00000310092.7_Silent_p.S240S			Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	240	Interaction with TNPO3.				cap-independent translational initiation (GO:0002190)|cell differentiation (GO:0030154)|circadian regulation of translation (GO:0097167)|entrainment of circadian clock by photoperiod (GO:0043153)|IRES-dependent translational initiation (GO:0002192)|mRNA processing (GO:0006397)|negative regulation of translation (GO:0017148)|negative regulation of translation in response to stress (GO:0032055)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of nucleocytoplasmic transport (GO:0046822)|response to arsenic-containing substance (GO:0046685)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|stress-activated MAPK cascade (GO:0051403)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	miRNA binding (GO:0035198)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|pre-mRNA intronic pyrimidine-rich binding (GO:0097158)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		CAGCTGCCTCCGTGTATAATT	0.562																																					p.S240S		Atlas-SNP	.											.	RBM4	34	.	0			c.C720T						.	C	,,,,	1,4091		0,1,2045	37	44	42		,,645,,720	-4.4	1	11		42	1,8423		0,1,4211	no	intron,intron,coding-synonymous,intron,coding-synonymous	RBM4,RBM14-RBM4	NM_001198843.1,NM_001198844.1,NM_001198845.1,NM_001198846.1,NM_002896.3	,,,,	0,2,6256	TT,TC,CC		0.0119,0.0244,0.016	,,,,	,,215/340,,240/365	66411228	2,12514	2046	4212	6258	SO:0001819	synonymous_variant	5936	exon3			TGCCTCCGTGTAT	U89505	CCDS41676.1, CCDS55776.1, CCDS55777.1	11q13	2013-02-12			ENSG00000173933	ENSG00000173933		"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	9901	protein-coding gene	gene with protein product		602571				9169144, 16260624	Standard	NM_002896		Approved	LARK, RBM4A, ZCRB3A, ZCCHC21		Q9BWF3	OTTHUMG00000154171	ENST00000409406.1:c.720C>T	chr11.hg19:g.66411228C>T		50.0	0.0		49.0	24.0	NM_002896	B3KUN0|B4E1U0|E7EQS3|O02916|Q4VC48|Q6P1P2|Q8WU85	Silent	SNP	ENST00000409406.1	hg19	CCDS41676.1																																																																																			.	.		0.562	RBM4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334212.1	NM_002896		T	66411228	C	T	66411228	2	4	23	1	0	0	0	0	0	0	0	1	13149	639	23	1		1	RBM4	11	66411228	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	985003	66411228	68595288	655	2721										
ANKRD13D	338692	hgsc.bcm.edu	37	chr11	67069033	67069033	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acagcgtgctgggcatggagCgcaacgagcccctccgggac	15	14	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:67069033C>T	ENST00000447274.2	+	13	2337	c.1162C>T	c.(1162-1164)Cgc>Tgc	p.R388C	SSH3_ENST00000376757.5_5'Flank|ANKRD13D_ENST00000514166.1_Missense_Mutation_p.R388C|ANKRD13D_ENST00000511455.2_Missense_Mutation_p.R475C|ANKRD13D_ENST00000308440.6_Missense_Mutation_p.R388C|ANKRD13D_ENST00000515828.1_Missense_Mutation_p.R125C|ANKRD13D_ENST00000504236.1_3'UTR|SSH3_ENST00000308298.7_5'Flank|SSH3_ENST00000308127.4_5'Flank			Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	388						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			GGGCATGGAGCGCAACGAGCC	0.662																																					p.R475C		Atlas-SNP	.											.	ANKRD13D	71	.	0			c.C1423T						.						56	56	56					11																	67069033		2200	4294	6494	SO:0001583	missense	338692	exon13			ATGGAGCGCAACG	AK027313	CCDS31616.1, CCDS31616.2	11q13.2	2013-01-11		2005-08-09	ENSG00000172932	ENSG00000172932		"Ankyrin repeat domain containing"	27880	protein-coding gene	gene with protein product		615126					Standard	NM_207354		Approved		uc001okd.2	Q6ZTN6	OTTHUMG00000162929	ENST00000447274.2:c.1162C>T	chr11.hg19:g.67069033C>T	ENSP00000402616:p.Arg388Cys	85.0	0.0		109.0	42.0	NM_207354	D6RCN6|Q0VAK0|Q0VGC3|Q6ZVD0|Q86SU1	Missense_Mutation	SNP	ENST00000447274.2	hg19		.	.	.	.	.	.	.	.	.	.	C	18.05	3.536345	0.65085	.	.	ENSG00000172932	ENST00000447274;ENST00000511455;ENST00000308440;ENST00000514166;ENST00000515828	T;T;T;T;T	0.51071	1.35;1.53;1.35;1.35;0.72	4.71	4.71	0.59529	.	0.379294	0.27591	N	0.018681	T	0.66247	0.2770	M	0.79011	2.435	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.70716	0.917;0.97;0.943	T	0.69705	-0.5073	10	0.72032	D	0.01	-28.8024	11.0229	0.47728	0.0:0.9138:0.0:0.0862	.	125;475;388	Q6ZTN6-2;Q6ZTN6-3;Q6ZTN6	.;.;AN13D_HUMAN	C	388;475;388;388;125	ENSP00000402616:R388C;ENSP00000427130:R475C;ENSP00000310874:R388C;ENSP00000444404:R388C;ENSP00000443977:R125C	ENSP00000310874:R388C	R	+	1	0	ANKRD13D	66825609	0.969000	0.33509	1.000000	0.80357	0.546000	0.35178	2.376000	0.44292	2.440000	0.82611	0.561000	0.74099	CGC	.	.		0.662	ANKRD13D-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000371067.2	NM_207354		T	67069033	C	T	67069033	3	4	23	1	0	0	0	0	1	0	0	0	644	768	27	1	1473	1	ANKRD13D	11	67069033	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	657805	67069033	67937483	656	2722										
MRGPRF	116535	hgsc.bcm.edu	37	chr11	68772834	68772834	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccccagctcagcgccgtccCgcagggcccgctggaagacc	12	20	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:68772834C>T	ENST00000309099.6	-	3	1326	c.944G>A	c.(943-945)cGg>cAg	p.R315Q	RP11-554A11.5_ENST00000562506.1_RNA|MRGPRF_ENST00000441623.1_Missense_Mutation_p.R315Q	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	315						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			AGCGCCGTCCCGCAGGGCCCG	0.692																																					p.R315Q		Atlas-SNP	.											.	MRGPRF	22	.	0			c.G944A						.						13	11	11					11																	68772834		2178	4270	6448	SO:0001583	missense	116535	exon3			CCGTCCCGCAGGG	AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"GPCR / Class A : Orphans"	24828	protein-coding gene	gene with protein product		607233	"G protein-coupled receptor 168", "G protein-coupled receptor 140"	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.944G>A	chr11.hg19:g.68772834C>T	ENSP00000309782:p.Arg315Gln	47.0	0.0		35.0	12.0	NM_001098515	B3KV43|Q8NBK8	Missense_Mutation	SNP	ENST00000309099.6	hg19	CCDS8188.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.490531	0.84962	.	.	ENSG00000172935	ENST00000441623;ENST00000309099;ENST00000421543	T;T	0.04970	3.52;3.52	5.21	4.3	0.51218	.	0.000000	0.34580	N	0.003849	T	0.10551	0.0258	N	0.25332	0.735	0.31714	N	0.639157	D	0.89917	1.0	D	0.76575	0.988	T	0.00964	-1.1498	10	0.05351	T	0.99	-14.2746	11.9025	0.52692	0.0:0.8246:0.1754:0.0	.	315	Q96AM1	MRGRF_HUMAN	Q	315;315;287	ENSP00000403660:R315Q;ENSP00000309782:R315Q	ENSP00000309782:R315Q	R	-	2	0	MRGPRF	68529410	0.022000	0.18835	0.976000	0.42696	0.973000	0.67179	1.490000	0.35573	1.175000	0.42826	0.561000	0.74099	CGG	.	.		0.692	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015		T	68772834	C	T	68772834	3	4	23	1	0	0	0	0	1	0	0	0	9774	652	23	1	91	1	MRGPRF	11	68772834	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1703801	68772834	66233682	657	2723										
SHANK2	22941	hgsc.bcm.edu	37	chr11	70332826	70332826	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggccggctgtgccgctgctcGcggagggcactgctgggctg	19	13	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:70332826G>A	ENST00000423696.2	-	15	2471	c.2435C>T	c.(2434-2436)gCg>gTg	p.A812V	SHANK2_ENST00000409161.1_Missense_Mutation_p.A595V|SHANK2_ENST00000338508.4_Missense_Mutation_p.A1192V|SHANK2_ENST00000449833.2_Missense_Mutation_p.A596V			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	812					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			GCCGCTGCTCGCGGAGGGCAC	0.706																																					p.A603V		Atlas-SNP	.											.	SHANK2	340	.	0			c.C1808T						.						20	26	24					11																	70332826		2193	4290	6483	SO:0001583	missense	22941	exon10			CTGCTCGCGGAGG	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14295	protein-coding gene	gene with protein product		603290	"cortactin binding protein 1"	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.2435C>T	chr11.hg19:g.70332826G>A	ENSP00000394536:p.Ala812Val	92.0	0.0		73.0	29.0	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	hg19		.	.	.	.	.	.	.	.	.	.	G	0.402	-0.917591	0.02396	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92	3.62	1.21	0.21127	.	1.993000	0.03565	U	0.227639	T	0.29652	0.0740	L	0.29908	0.895	0.37959	D	0.932906	B;B;B	0.21309	0.018;0.054;0.054	B;B;B	0.09377	0.001;0.002;0.004	T	0.13229	-1.0517	10	0.15499	T	0.54	.	6.0032	0.19531	0.0:0.0925:0.1739:0.7336	.	812;1191;596	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	V	596;595;470;1192;812;830;815	ENSP00000399423:A596V;ENSP00000386491:A595V;ENSP00000402944:A470V;ENSP00000345193:A1192V;ENSP00000394536:A812V;ENSP00000294018:A815V	ENSP00000294018:A815V	A	-	2	0	SHANK2	70010474	1.000000	0.71417	0.001000	0.08648	0.001000	0.01503	3.744000	0.55112	-0.046000	0.13446	-0.397000	0.06425	GCG	.	.		0.706	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		A	70332826	G	A	70332826	3	1	23	1	0	0	0	0	1	0	0	0	14280	1087	38	1	1985	1	SHANK2	11	70332826	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1559992	70332826	64673690	658	2724										
ARAP1	116985	hgsc.bcm.edu	37	chr11	72437830	72437830	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcctccggggcgggatgggtGgggcagcggggagcccctca							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:72437830delG	ENST00000393609.3	-	3	546	c.344delC	c.(343-345)ccafs	p.P116fs	ARAP1_ENST00000359373.5_Frame_Shift_Del_p.P116fs|ARAP1_ENST00000455638.2_Frame_Shift_Del_p.P116fs	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	116					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						CGGGATGGGTGGGGCAGCGGG	0.697																																					p.P115fs	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-Indel,Pindel	.											.	ARAP1	168	.	0			c.345delA						.						8	10	9					11																	72437830		1787	3854	5641	SO:0001589	frameshift_variant	116985	exon3			.	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16925	protein-coding gene	gene with protein product		606646	"centaurin, delta 2"	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.344delC	chr11.hg19:g.72437830delG	ENSP00000377233:p.Pro116fs	166.0	0.0		174.0	59.0	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Frame_Shift_Del	DEL	ENST00000393609.3	hg19	CCDS41687.1																																																																																			.	.		0.697	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		-	72437830	G	-	72437830	7	5	23	1	0	1	0	1	0	0	0	0	838	1348	47	0	4140	0	ARAP1	11	72437830	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	2105004	72437830	62568686	659	2725										
DNAJB13	374407	hgsc.bcm.edu	37	chr11	73675956	73675956	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agaaggaagtgaggtagattTgaactttggggggctccagg	17	4	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:73675956T>A	ENST00000339764.1	+	4	1119	c.368T>A	c.(367-369)tTg>tAg	p.L123*	RP11-167N4.2_ENST00000537019.1_RNA|DNAJB13_ENST00000543947.1_5'Flank|RP11-167N4.2_ENST00000540886.1_RNA|DNAJB13_ENST00000537753.1_5'UTR	NM_153614.2	NP_705842.2	P59910	DJB13_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 13	123					protein folding (GO:0006457)					large_intestine(3)|lung(2)	5	Breast(11;7.42e-05)					GAGGTAGATTTGAACTTTGGG	0.552											OREG0021218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L123X		Atlas-SNP	.											.	DNAJB13	28	.	0			c.T368A						.						47	53	51					11																	73675956		2200	4293	6493	SO:0001587	stop_gained	374407	exon4			TAGATTTGAACTT	AF516185	CCDS8227.1	11q13.3	2011-09-02	2010-04-21		ENSG00000187726	ENSG00000187726		"Heat shock proteins / DNAJ (HSP40)"	30718	protein-coding gene	gene with protein product	"radial spoke 16 homolog A (Chlamydomonas)"	610263	"DnaJ (Hsp40) related, subfamily B, member 13"				Standard	NM_153614		Approved	TSARG6, RSPH16A	uc001ouo.3	P59910	OTTHUMG00000168093	ENST00000339764.1:c.368T>A	chr11.hg19:g.73675956T>A	ENSP00000344431:p.Leu123*	103.0	0.0	1147	97.0	30.0	NM_153614	B3LEP4|Q8IZW5	Nonsense_Mutation	SNP	ENST00000339764.1	hg19	CCDS8227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	23.8|23.8	4.456187|4.456187	0.84209|0.84209	.|.	.|.	ENSG00000187726|ENSG00000187726	ENST00000542350|ENST00000339764	.|.	.|.	.|.	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	.|1.310620	.|0.04974	.|N	.|0.464465	T|.	0.37348|.	0.1000|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.16276|.	-1.0408|.	4|.	.|0.07990	.|T	.|0.79	.|.	8.5178|8.5178	0.33257|0.33257	0.0:0.0881:0.0:0.9119|0.0:0.0881:0.0:0.9119	.|.	.|.	.|.	.|.	L|X	23|123	.|.	.|ENSP00000344431:L123X	F|L	+|+	3|2	2|0	DNAJB13|DNAJB13	73353604|73353604	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.765000|0.765000	0.43378|0.43378	1.908000|1.908000	0.39907|0.39907	1.951000|1.951000	0.56629|0.56629	0.369000|0.369000	0.22263|0.22263	TTT|TTG	.	.		0.552	DNAJB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398100.1	NM_153614		A	73675956	T	A	73675956	4	1	23	1	0	0	0	0	0	1	0	0	4620	1821	63	4	382	4	DNAJB13	11	73675956	Nonsense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1238126	73675956	61330560	660	2726										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73801915	73801915	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggactgagatggaaacagttCgggcagcaagaactccctct	12	10	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:73801915C>T	ENST00000334126.7	-	20	3810	c.3584G>A	c.(3583-3585)cGa>cAa	p.R1195Q	C2CD3_ENST00000313663.7_Missense_Mutation_p.R1195Q			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1195	C2 1.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GGAAACAGTTCGGGCAGCAAG	0.493																																					p.R1195Q		Atlas-SNP	.											.	C2CD3	288	.	0			c.G3584A						.						131	110	117					11																	73801915		2200	4293	6493	SO:0001583	missense	26005	exon20			ACAGTTCGGGCAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.3584G>A	chr11.hg19:g.73801915C>T	ENSP00000334379:p.Arg1195Gln	94.0	0.0		99.0	41.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	15.52	2.859200	0.51376	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.15603	2.9;2.91;2.41	5.7	3.73	0.42828	.	0.520355	0.20720	N	0.086921	T	0.18841	0.0452	N	0.22421	0.69	0.33718	D	0.61657	D	0.76494	0.999	P	0.62649	0.905	T	0.23440	-1.0188	10	0.27082	T	0.32	-8.3216	4.6413	0.12550	0.0:0.6101:0.1746:0.2153	.	1195	Q4AC94-1	.	Q	1195;1195;1195;3	ENSP00000334379:R1195Q;ENSP00000323339:R1195Q;ENSP00000388750:R3Q	ENSP00000323339:R1195Q	R	-	2	0	C2CD3	73479563	0.031000	0.19500	0.993000	0.49108	0.929000	0.56500	0.295000	0.19065	1.434000	0.47414	0.484000	0.47621	CGA	.	.		0.493	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		T	73801915	C	T	73801915	3	4	23	1	0	0	0	0	1	0	0	0	2156	884	31	1	2355	1	C2CD3	11	73801915	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	125959	73801915	61204601	661	2727										
ARRB1	408	hgsc.bcm.edu	37	chr11	74984011	74984011	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaggatctcacggttggcaCcttccctcaacctgcaaagt	8	15	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:74984011C>T	ENST00000420843.2	-	12	1023	c.926G>A	c.(925-927)gGt>gAt	p.G309D	ARRB1_ENST00000393505.4_Missense_Mutation_p.G309D|ARRB1_ENST00000360025.3_Missense_Mutation_p.G309D	NM_004041.4	NP_004032.2	P49407	ARRB1_HUMAN	arrestin, beta 1	309					activation of MAPK activity (GO:0000187)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|Notch signaling pathway (GO:0007219)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of GTPase activity (GO:0043547)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-Golgi vesicle-mediated transport (GO:0006892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)|transcription from RNA polymerase II promoter (GO:0006366)	basolateral plasma membrane (GO:0016323)|chromatin (GO:0000785)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|pseudopodium (GO:0031143)	angiotensin receptor binding (GO:0031701)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme inhibitor activity (GO:0004857)|GTPase activator activity (GO:0005096)|insulin-like growth factor receptor binding (GO:0005159)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|large_intestine(2)|lung(4)|prostate(1)	11						ACGGTTGGCACCTTCCCTCAA	0.612																																					p.G309D		Atlas-SNP	.											.	ARRB1	37	.	0			c.G926A						.						94	82	86					11																	74984011		2200	4293	6493	SO:0001583	missense	408	exon12			TTGGCACCTTCCC	BC003636	CCDS31640.1, CCDS44684.1	11q13	2008-12-11			ENSG00000137486	ENSG00000137486			711	protein-coding gene	gene with protein product	"arrestin 2"	107940		ARR1		8486659	Standard	NM_004041		Approved		uc001owe.2	P49407	OTTHUMG00000165444	ENST00000420843.2:c.926G>A	chr11.hg19:g.74984011C>T	ENSP00000409581:p.Gly309Asp	92.0	0.0		89.0	37.0	NM_020251	B6V9G8|O75625|O75630|Q2PP20|Q9BTK8	Missense_Mutation	SNP	ENST00000420843.2	hg19	CCDS44684.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.016742	0.75161	.	.	ENSG00000137486	ENST00000420843;ENST00000393505;ENST00000360025	T;T;T	0.10477	2.87;2.87;2.87	5.27	5.27	0.74061	Immunoglobulin E-set (1);Arrestin, C-terminal (1);Arrestin-like, C-terminal (1);	0.072206	0.53938	D	0.000057	T	0.30510	0.0767	M	0.76574	2.34	0.50813	D	0.999892	D;D	0.59357	0.966;0.985	P;P	0.60789	0.692;0.879	T	0.01087	-1.1456	10	0.44086	T	0.13	-13.6043	16.3875	0.83521	0.0:1.0:0.0:0.0	.	309;309	P49407-2;P49407	.;ARRB1_HUMAN	D	309	ENSP00000409581:G309D;ENSP00000377141:G309D;ENSP00000353124:G309D	ENSP00000353124:G309D	G	-	2	0	ARRB1	74661659	1.000000	0.71417	0.948000	0.38648	0.797000	0.45037	5.978000	0.70501	2.471000	0.83476	0.561000	0.74099	GGT	.	.		0.612	ARRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384092.3	NM_004041		T	74984011	C	T	74984011	3	4	23	1	0	0	0	0	1	0	0	0	980	507	18	3	350	3	ARRB1	11	74984011	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1182096	74984011	60022505	662	2728										
B3GNT6	192134	hgsc.bcm.edu	37	chr11	76751049	76751049	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctacggcgggcggccagtgCgccgcctctttctattgggc	15	14	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:76751049C>T	ENST00000533140.1	+	2	592	c.454C>T	c.(454-456)Cgc>Tgc	p.R152C	B3GNT6_ENST00000354301.5_Missense_Mutation_p.R152C|B3GNT6_ENST00000421061.1_Missense_Mutation_p.R63C			O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						GCGGCCAGTGCGCCGCCTCTT	0.746																																					p.R152C		Atlas-SNP	.											.	B3GNT6	27	.	0			c.C454T						.						4	5	5					11																	76751049		1612	3616	5228	SO:0001583	missense	192134	exon2			CCAGTGCGCCGCC	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"Beta 3-glycosyltransferases"	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000533140.1:c.454C>T	chr11.hg19:g.76751049C>T	ENSP00000435352:p.Arg152Cys	23.0	0.0		35.0	10.0	NM_138706	Q4TTN0	Missense_Mutation	SNP	ENST00000533140.1	hg19	CCDS53681.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.999444	0.35320	.	.	ENSG00000198488	ENST00000533140;ENST00000354301;ENST00000421061	T;T;T	0.44881	0.91;0.91;0.91	3.28	1.38	0.22167	.	0.203439	0.41001	D	0.000971	T	0.50086	0.1595	H	0.94925	3.6	0.38408	D	0.945851	P	0.41393	0.748	B	0.42138	0.377	T	0.52859	-0.8519	10	0.59425	D	0.04	.	2.7636	0.05314	0.224:0.527:0.0:0.249	.	152	Q6ZMB0	B3GN6_HUMAN	C	152;152;63	ENSP00000435352:R152C;ENSP00000346256:R152C;ENSP00000403463:R63C	ENSP00000346256:R152C	R	+	1	0	B3GNT6	76428697	1.000000	0.71417	0.985000	0.45067	0.179000	0.23085	1.880000	0.39628	0.384000	0.24942	0.462000	0.41574	CGC	.	.		0.746	B3GNT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382740.2	NM_138706		T	76751049	C	T	76751049	3	4	23	1	0	0	0	0	1	0	0	0	1261	768	27	1	456	1	B3GNT6	11	76751049	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1767038	76751049	58255467	663	2729										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76919769	76919769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccctcactcacctaccaggTgttcttcatgaagaagctgt	8	13	4	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:76919769T>C	ENST00000409709.3	+	44	6244	c.5972T>C	c.(5971-5973)gTg>gCg	p.V1991A	MYO7A_ENST00000409619.2_Missense_Mutation_p.V1942A|MYO7A_ENST00000458637.2_Missense_Mutation_p.V1953A|MYO7A_ENST00000605744.1_3'UTR	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1991	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						ACCTACCAGGTGTTCTTCATG	0.592																																					p.V1991A		Atlas-SNP	.											.	MYO7A	164	.	0			c.T5972C						.						58	66	63					11																	76919769		2083	4207	6290	SO:0001583	missense	4647	exon44			ACCAGGTGTTCTT	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.5972T>C	chr11.hg19:g.76919769T>C	ENSP00000386331:p.Val1991Ala	46.0	0.0		48.0	23.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.517748	0.64634	.	.	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169;ENST00000544424	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	4.37	4.37	0.52481	Band 4.1 domain (1);FERM domain (1);	0.129984	0.51477	D	0.000095	D	0.85487	0.5708	M	0.89095	3.005	0.80722	D	1	D;B	0.54601	0.967;0.108	P;B	0.58013	0.831;0.092	D	0.88713	0.3224	10	0.87932	D	0	.	13.7401	0.62842	0.0:0.0:0.0:1.0	.	1953;1991	F8VUN5;Q13402	.;MYO7A_HUMAN	A	1991;1953;1942;1164;1990;1960;1867;1133;606	ENSP00000386331:V1991A;ENSP00000392185:V1953A;ENSP00000386635:V1942A;ENSP00000417017:V1133A	ENSP00000345075:V1867A	V	+	2	0	MYO7A	76597417	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.503000	0.81632	1.850000	0.53721	0.254000	0.18369	GTG	.	.		0.592	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		C	76919769	T	C	76919769	3	2	23	1	0	0	0	0	1	0	0	0	10091	1696	59	2	6176	2	MYO7A	11	76919769	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	168720	76919769	58086747	664	2730										
RSF1	51773	hgsc.bcm.edu	37	chr11	77411876	77411876	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcatcttctccttcccctcTttttttatcagctttctgat							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:77411876delT	ENST00000308488.6	-	6	2700	c.2398delA	c.(2398-2400)agafs	p.R800fs	RSF1_ENST00000360355.2_Frame_Shift_Del_p.R769fs|RSF1_ENST00000480887.1_Frame_Shift_Del_p.R548fs			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	800					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			CCTTCCCCTCTTTTTTTATCA	0.368																																					p.R800fs		Atlas-Indel,Pindel	.											.	RSF1	105	.	0			c.2399delG						.						145	145	145					11																	77411876		2200	4292	6492	SO:0001589	frameshift_variant	51773	exon6			.	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"Zinc fingers, PHD-type"	18118	protein-coding gene	gene with protein product		608522	"hepatitis B virus x associated protein"	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.2398delA	chr11.hg19:g.77411876delT	ENSP00000311513:p.Arg800fs	40.0	0.0		36.0	14.0	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Frame_Shift_Del	DEL	ENST00000308488.6	hg19	CCDS8253.1																																																																																			.	.		0.368	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		-	77411876	T	-	77411876	7	5	23	1	0	1	0	1	0	0	0	0	13714	1617	56	0	1971	0	RSF1	11	77411876	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	492107	77411876	57594640	665	2731										
GAB2	9846	hgsc.bcm.edu	37	chr11	77930356	77930356	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaaggctctgaggactgccGcacgtctgtccactcctgca	12	14	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:77930356G>A	ENST00000361507.4	-	10	2078	c.1993C>T	c.(1993-1995)Cgg>Tgg	p.R665W	GAB2_ENST00000340149.2_Missense_Mutation_p.R627W	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	665					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			GAGGACTGCCGCACGTCTGTC	0.602																																					p.R665W		Atlas-SNP	.											.	GAB2	63	.	0			c.C1993T						.						123	99	107					11																	77930356		2200	4292	6492	SO:0001583	missense	9846	exon10			ACTGCCGCACGTC	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"Pleckstrin homology (PH) domain containing"	14458	protein-coding gene	gene with protein product	"Grb2-associated binder 2"	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.1993C>T	chr11.hg19:g.77930356G>A	ENSP00000354952:p.Arg665Trp	80.0	0.0		73.0	30.0	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Missense_Mutation	SNP	ENST00000361507.4	hg19	CCDS8259.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.007303	0.93287	.	.	ENSG00000033327	ENST00000340149;ENST00000361507	T;T	0.24538	1.85;1.85	5.38	4.46	0.54185	.	0.000000	0.64402	U	0.000001	T	0.56046	0.1959	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65689	-0.6107	10	0.87932	D	0	-16.6452	15.85	0.78924	0.0:0.0:0.8632:0.1368	.	665	Q9UQC2	GAB2_HUMAN	W	627;665	ENSP00000343959:R627W;ENSP00000354952:R665W	ENSP00000343959:R627W	R	-	1	2	GAB2	77608004	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.957000	0.87870	1.384000	0.46424	0.563000	0.77884	CGG	.	.		0.602	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		A	77930356	G	A	77930356	3	1	23	1	0	0	0	0	1	0	0	0	6157	1086	38	1	41	1	GAB2	11	77930356	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	518480	77930356	57076160	666	2732										
CCDC81	60494	hgsc.bcm.edu	37	chr11	86126223	86126223	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgagggtgaactgatggtggAaaagcaaaagcgagaacaaa	14	4	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:86126223A>G	ENST00000445632.2	+	13	1831	c.1559A>G	c.(1558-1560)gAa>gGa	p.E520G	CCDC81_ENST00000278487.3_Missense_Mutation_p.E255G|CCDC81_ENST00000528728.1_Missense_Mutation_p.E255G|CCDC81_ENST00000354755.1_Missense_Mutation_p.E430G	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	520										kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				CTGATGGTGGAAAAGCAAAAG	0.493																																					p.E520G		Atlas-SNP	.											.	CCDC81	89	.	0			c.A1559G						.						71	68	69					11																	86126223		2202	4299	6501	SO:0001583	missense	60494	exon13			TGGTGGAAAAGCA	AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.1559A>G	chr11.hg19:g.86126223A>G	ENSP00000415528:p.Glu520Gly	226.0	0.0		216.0	80.0	NM_001156474	A0AVL7|Q53FW3|Q9H5E5	Missense_Mutation	SNP	ENST00000445632.2	hg19	CCDS53691.1	.	.	.	.	.	.	.	.	.	.	A	12.47	1.946835	0.34377	.	.	ENSG00000149201	ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	5.46	3.14	0.36123	.	0.431103	0.23365	N	0.048962	T	0.31979	0.0814	L	0.43152	1.355	0.20873	N	0.999833	B;B;B	0.15473	0.003;0.013;0.011	B;B;B	0.11329	0.002;0.006;0.003	T	0.19289	-1.0310	9	.	.	.	-0.3586	9.165	0.37046	0.8474:0.0:0.1526:0.0	.	255;520;430	Q6ZN84-3;Q6ZN84;Q6ZN84-2	.;CCD81_HUMAN;.	G	430;255;520;255	ENSP00000346800:E430G;ENSP00000278487:E255G;ENSP00000415528:E520G;ENSP00000437165:E255G	.	E	+	2	0	CCDC81	85803871	0.919000	0.31177	0.009000	0.14445	0.009000	0.06853	2.081000	0.41596	0.367000	0.24454	-0.421000	0.06004	GAA	.	.		0.493	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827		G	86126223	A	G	86126223	3	3	23	1	0	0	0	0	1	0	0	0	2857	246	9	2	1609	2	CCDC81	11	86126223	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	8195867	86126223	48880293	667	2733										
GPR83	10888	hgsc.bcm.edu	37	chr11	94113391	94113391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gttgggaggtgggcaggaggTtattggcaaggggagccctc	20	6	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:94113391T>C	ENST00000243673.2	-	4	1367	c.1196A>G	c.(1195-1197)aAc>aGc	p.N399S	GPR83_ENST00000539203.2_Missense_Mutation_p.N357S	NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83	399					response to glucocorticoid (GO:0051384)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GGGCAGGAGGTTATTGGCAAG	0.582																																					p.N399S		Atlas-SNP	.											.	GPR83	47	.	0			c.A1196G						.						75	77	77					11																	94113391		2201	4298	6499	SO:0001583	missense	10888	exon4			AGGAGGTTATTGG	AF236081	CCDS8297.1	11q21	2012-08-21	2003-07-30	2003-08-01	ENSG00000123901	ENSG00000123901		"GPCR / Class A : Orphans"	4523	protein-coding gene	gene with protein product		605569	"G protein-coupled receptor 72"	GPR72		10760605, 11060465	Standard	NM_016540		Approved		uc001pet.2	Q9NYM4	OTTHUMG00000167779	ENST00000243673.2:c.1196A>G	chr11.hg19:g.94113391T>C	ENSP00000243673:p.Asn399Ser	154.0	0.0		132.0	47.0	NM_016540	B0M0K5|Q6NWR4|Q9P1Y8	Missense_Mutation	SNP	ENST00000243673.2	hg19	CCDS8297.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.092963	0.00364	.	.	ENSG00000123901	ENST00000243673;ENST00000539203	T;T	0.60797	0.16;0.27	5.75	2.17	0.27698	.	0.768897	0.12985	N	0.422940	T	0.28300	0.0699	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20672	-1.0268	10	0.07175	T	0.84	.	1.2577	0.01995	0.1358:0.2417:0.1405:0.482	.	399	Q9NYM4	GPR83_HUMAN	S	399;357	ENSP00000243673:N399S;ENSP00000441550:N357S	ENSP00000243673:N399S	N	-	2	0	GPR83	93753039	0.905000	0.30787	0.001000	0.08648	0.001000	0.01503	0.541000	0.23207	0.120000	0.18254	-0.250000	0.11733	AAC	.	.		0.582	GPR83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396232.1	NM_016540		C	94113391	T	C	94113391	3	2	23	1	0	0	0	0	1	0	0	0	6721	1725	60	2	79	2	GPR83	11	94113391	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	7987168	94113391	40893125	668	2734										
CEP57	9702	hgsc.bcm.edu	37	chr11	95562468	95562468	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaagcaaaagccaaccaaatAactaaagttcgaaaatacca	5	9	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:95562468A>G	ENST00000325542.5	+	10	1483	c.1245A>G	c.(1243-1245)atA>atG	p.I415M	CEP57_ENST00000541150.1_Missense_Mutation_p.I406M|CEP57_ENST00000325486.5_Missense_Mutation_p.I389M|CEP57_ENST00000537677.1_Missense_Mutation_p.I388M	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	415	Mediates interaction with microtubules. {ECO:0000250}.				fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CCAACCAAATAACTAAAGTTC	0.363									Mosaic Variegated Aneuploidy Syndrome																												p.I415M		Atlas-SNP	.											.	CEP57	40	.	0			c.A1245G						.						187	194	191					11																	95562468		2201	4298	6499	SO:0001583	missense	9702	exon10	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	CCAAATAACTAAA	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.1245A>G	chr11.hg19:g.95562468A>G	ENSP00000317902:p.Ile415Met	131.0	0.0		157.0	8.0	NM_014679	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Missense_Mutation	SNP	ENST00000325542.5	hg19	CCDS8304.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.2|20.2	3.948644|3.948644	0.73787|0.73787	.|.	.|.	ENSG00000166037|ENSG00000166037	ENST00000537677;ENST00000325542;ENST00000325486;ENST00000541150|ENST00000535224	T;T;T;T|.	0.56941|.	0.49;0.43;0.43;0.43|.	5.54|5.54	4.35|4.35	0.52113|0.52113	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72326|0.72326	0.3446|0.3446	M|M	0.76838|0.76838	2.35|2.35	0.46874|0.46874	D|D	0.99923|0.99923	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.997;1.0;0.999|.	T|T	0.73642|0.73642	-0.3918|-0.3918	10|5	0.87932|.	D|.	0|.	-26.7924|-26.7924	10.9427|10.9427	0.47283|0.47283	0.6535:0.3465:0.0:0.0|0.6535:0.3465:0.0:0.0	.|.	406;389;415|.	F5H5F7;Q86XR8-2;Q86XR8|.	.;.;CEP57_HUMAN|.	M|D	388;415;389;406|205	ENSP00000441392:I388M;ENSP00000317902:I415M;ENSP00000317487:I389M;ENSP00000443436:I406M|.	ENSP00000317487:I389M|.	I|N	+|+	3|1	3|0	CEP57|CEP57	95202116|95202116	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	2.297000|2.297000	0.43593|0.43593	2.111000|2.111000	0.64477|0.64477	0.402000|0.402000	0.26972|0.26972	ATA|AAC	.	.		0.363	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679		G	95562468	A	G	95562468	3	3	23	1	0	0	0	0	1	0	0	0	3258	352	13	2	1283	2	CEP57	11	95562468	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1449077	95562468	39444048	669	2735										
MTMR2	8898	hgsc.bcm.edu	37	chr11	95580973	95580973	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctccttaagttttcgtaatgAttctctcataacatgaatat	4	8	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:95580973A>T	ENST00000346299.5	-	10	1424	c.1084T>A	c.(1084-1086)Tca>Aca	p.S362T	MTMR2_ENST00000409459.1_Missense_Mutation_p.S290T|MTMR2_ENST00000393223.3_Missense_Mutation_p.S290T|MTMR2_ENST00000352297.7_Missense_Mutation_p.S290T|MTMR2_ENST00000484818.1_5'Flank	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	362	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TTTCGTAATGATTCTCTCATA	0.388																																					p.S362T		Atlas-SNP	.											.	MTMR2	79	.	0			c.T1084A						.						150	141	144					11																	95580973		2201	4298	6499	SO:0001583	missense	8898	exon10			GTAATGATTCTCT	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.1084T>A	chr11.hg19:g.95580973A>T	ENSP00000345752:p.Ser362Thr	157.0	0.0		138.0	41.0	NM_016156	A6NN98|Q9UPS9	Missense_Mutation	SNP	ENST00000346299.5	hg19	CCDS8305.1	.	.	.	.	.	.	.	.	.	.	A	16.47	3.131856	0.56828	.	.	ENSG00000087053	ENST00000346299;ENST00000393223;ENST00000409459;ENST00000352297;ENST00000444541	D;D;D;D;D	0.95035	-3.59;-3.59;-3.59;-3.59;-3.59	5.65	5.65	0.86999	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.98074	0.9365	H	0.95224	3.64	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.982	D	0.99376	1.0921	10	0.87932	D	0	.	15.882	0.79211	1.0:0.0:0.0:0.0	.	362;362	A8K5G2;Q13614	.;MTMR2_HUMAN	T	362;290;290;290;290	ENSP00000345752:S362T;ENSP00000376915:S290T;ENSP00000386882:S290T;ENSP00000343737:S290T;ENSP00000396020:S290T	ENSP00000345752:S362T	S	-	1	0	MTMR2	95220621	1.000000	0.71417	0.456000	0.27044	0.201000	0.24016	7.253000	0.78320	2.155000	0.67459	0.533000	0.62120	TCA	.	.		0.388	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156		T	95580973	A	T	95580973	3	4	23	1	0	0	0	0	1	0	0	0	9953	333	12	4	871	4	MTMR2	11	95580973	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	18505	95580973	39425543	670	2736										
MMP20	9313	hgsc.bcm.edu	37	chr11	102482511	102482511	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttttcaaaagatatcataatAtccgcttctcctgagtttat	4	8	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:102482511A>T	ENST00000260228.2	-	3	510	c.498T>A	c.(496-498)gaT>gaA	p.D166E	RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	169					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	ATATCATAATATCCGCTTCTC	0.438																																					p.D166E		Atlas-SNP	.											.	MMP20	52	.	0			c.T498A						.						71	70	71					11																	102482511		2203	4299	6502	SO:0001583	missense	9313	exon3			CATAATATCCGCT	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"enamelysin"	604629	"matrix metalloproteinase 20 (enamelysin)"			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.498T>A	chr11.hg19:g.102482511A>T	ENSP00000260228:p.Asp166Glu	54.0	0.0		38.0	18.0	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	hg19	CCDS8318.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.113437	0.77210	.	.	ENSG00000137674	ENST00000260228	T	0.33865	1.39	5.35	-2.98	0.05513	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.62011	0.2393	M	0.91717	3.235	0.45733	D	0.998637	D	0.76494	0.999	D	0.87578	0.998	T	0.68138	-0.5488	10	0.87932	D	0	.	12.8338	0.57761	0.4615:0.0:0.5385:0.0	.	166	O60882	MMP20_HUMAN	E	166	ENSP00000260228:D166E	ENSP00000260228:D166E	D	-	3	2	MMP20	101987721	0.895000	0.30542	0.422000	0.26621	0.970000	0.65996	0.006000	0.13152	-0.661000	0.05345	-0.250000	0.11733	GAT	.	.		0.438	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1			T	102482511	A	T	102482511	3	4	23	1	0	0	0	0	1	0	0	0	9668	446	16	4	985	4	MMP20	11	102482511	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	6901538	102482511	32524005	671	2737										
POU2AF1	5450	hgsc.bcm.edu	37	chr11	111225251	111225251	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggtgaggggtgcctggtgcTctgggccctccagcgggggc	20	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:111225251T>C	ENST00000393067.3	-	5	1020	c.506A>G	c.(505-507)gAg>gGg	p.E169G		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	169					humoral immune response (GO:0006959)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(2)|lung(2)	5		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		TGCCTGGTGCTCTGGGCCCTC	0.662			T	BCL6	NHL																																p.E169G		Atlas-SNP	.		Dom	yes		11	11q23.1	5450	"POU domain, class 2, associating factor 1 (OBF1)"		L	.	POU2AF1	23	.	0			c.A506G						.						26	34	31					11																	111225251		2199	4297	6496	SO:0001583	missense	5450	exon5			TGGTGCTCTGGGC		CCDS31675.1	11q23.1	2011-06-01	2007-07-13			ENSG00000110777			9211	protein-coding gene	gene with protein product		601206	"POU domain class 2, associating factor 1"			8617501	Standard	NM_006235		Approved	OBF1	uc001plg.4	Q16633		ENST00000393067.3:c.506A>G	chr11.hg19:g.111225251T>C	ENSP00000376786:p.Glu169Gly	113.0	0.0		126.0	50.0	NM_006235	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	hg19	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.528384	0.85706	.	.	ENSG00000110777	ENST00000393067	T	0.37411	1.2	4.87	4.87	0.63330	.	0.063541	0.64402	D	0.000009	T	0.52757	0.1754	L	0.54323	1.7	0.40643	D	0.981962	D	0.64830	0.994	D	0.64595	0.927	T	0.56553	-0.7960	10	0.59425	D	0.04	-20.1092	14.3077	0.66395	0.0:0.0:0.0:1.0	.	169	Q16633	OBF1_HUMAN	G	169	ENSP00000376786:E169G	ENSP00000376786:E169G	E	-	2	0	POU2AF1	110730461	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	5.646000	0.67916	2.043000	0.60533	0.460000	0.39030	GAG	.	.		0.662	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235		C	111225251	T	C	111225251	3	2	23	1	0	0	0	0	1	0	0	0	12279	1551	54	2	268	2	POU2AF1	11	111225251	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	8742740	111225251	23781265	672	2738										
ZW10	9183	hgsc.bcm.edu	37	chr11	113609090	113609090	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagttcacctttctgtgcccGcatttgggccaaaaagcatt	8	11	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:113609090G>A	ENST00000200135.3	-	13	1924	c.1780C>T	c.(1780-1782)Cgg>Tgg	p.R594W		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	594					ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		TTCTGTGCCCGCATTTGGGCC	0.388																																					p.R594W		Atlas-SNP	.											.	ZW10	49	.	0			c.C1780T						.						79	75	76					11																	113609090		2201	4296	6497	SO:0001583	missense	9183	exon13			GTGCCCGCATTTG	U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"ZW10 (Drosophila) homolog, centromere/kinetochore protein", "ZW10, kinetochore associated, homolog (Drosophila)"			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.1780C>T	chr11.hg19:g.113609090G>A	ENSP00000200135:p.Arg594Trp	82.0	0.0		73.0	33.0	NM_004724	A1A528	Missense_Mutation	SNP	ENST00000200135.3	hg19	CCDS8363.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.675261	0.47781	.	.	ENSG00000086827	ENST00000200135	T	0.46819	0.86	5.08	2.96	0.34315	.	0.179894	0.47852	D	0.000203	T	0.44519	0.1297	M	0.66939	2.045	0.41954	D	0.99067	P	0.36712	0.566	B	0.29862	0.108	T	0.57051	-0.7877	10	0.72032	D	0.01	-6.8325	15.292	0.73872	0.0:0.0:0.7337:0.2663	.	594	O43264	ZW10_HUMAN	W	594	ENSP00000200135:R594W	ENSP00000200135:R594W	R	-	1	2	ZW10	113114300	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.086000	0.50159	1.123000	0.41961	0.563000	0.77884	CGG	.	.		0.388	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724		A	113609090	G	A	113609090	3	1	23	1	0	0	0	0	1	0	0	0	18262	1086	38	1	575	1	ZW10	11	113609090	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2383839	113609090	21397426	673	2739										
MLL	4297	hgsc.bcm.edu	37	chr11	118377321	118377321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagttcttctgaagcacacAttccagaccaagaaacgaca	6	13	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:118377321A>G	ENST00000389506.5	+	27	10705	c.10705A>G	c.(10705-10707)Att>Gtt	p.I3569V	KMT2A_ENST00000354520.4_Missense_Mutation_p.I3531V|KMT2A_ENST00000534358.1_Missense_Mutation_p.I3572V			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3569					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TGAAGCACACATTCCAGACCA	0.478																																					p.I3572V		Atlas-SNP	.											.	MLL	548	.	0			c.A10714G						.						98	95	96					11																	118377321		2200	4295	6495	SO:0001583	missense	4297	exon27			GCACACATTCCAG	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.10705A>G	chr11.hg19:g.118377321A>G	ENSP00000374157:p.Ile3569Val	151.0	0.0		183.0	81.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	10.21	1.288120	0.23478	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	T;T;T	0.81078	-1.45;-1.45;-1.42	5.85	1.12	0.20585	.	0.430925	0.25919	N	0.027446	T	0.52500	0.1738	N	0.04508	-0.205	0.24694	N	0.993294	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41034	-0.9531	10	0.06099	T	0.92	.	8.4852	0.33067	0.4573:0.0:0.5427:0.0	.	3572;3569	E9PQG7;Q03164	.;MLL1_HUMAN	V	3572;3569;3531;2479	ENSP00000436786:I3572V;ENSP00000374157:I3569V;ENSP00000346516:I3531V	ENSP00000346516:I3531V	I	+	1	0	MLL	117882531	0.316000	0.24580	1.000000	0.80357	0.998000	0.95712	0.125000	0.15749	0.158000	0.19367	0.477000	0.44152	ATT	.	.		0.478	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		G	118377321	A	G	118377321	3	3	23	1	0	0	0	0	1	0	0	0	9629	217	8	2	10811	2	MLL	11	118377321	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	4768231	118377321	16629195	674	2740										
BCL9L	283149	hgsc.bcm.edu	37	chr11	118779169	118779169	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccatggttccccgcccccacGcccttcgagcccacgttgca	8	21	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:118779169G>A	ENST00000334801.3	-	2	1186	c.222C>T	c.(220-222)ggC>ggT	p.G74G	BCL9L_ENST00000526143.1_5'UTR|MIR4492_ENST00000581627.1_RNA	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	74					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		CCGCCCCCACGCCCTTCGAGC	0.587																																					p.G74G		Atlas-SNP	.											.	BCL9L	254	.	0			c.C222T						.						89	92	91					11																	118779169		2200	4295	6495	SO:0001819	synonymous_variant	283149	exon2			CCCCACGCCCTTC	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.222C>T	chr11.hg19:g.118779169G>A		117.0	0.0		100.0	38.0	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	hg19	CCDS8403.1																																																																																			.	.		0.587	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		A	118779169	G	A	118779169	2	1	23	1	0	0	0	0	0	0	0	1	1382	1074	38	1		1	BCL9L	11	118779169	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	401848	118779169	16227347	675	2741										
CBL	867	hgsc.bcm.edu	37	chr11	119169140	119169140	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaatgaggatgatgggtatgAtgtcccaaagccacctgtgc	12	8	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:119169140A>T	ENST00000264033.4	+	15	2700	c.2324A>T	c.(2323-2325)gAt>gTt	p.D775V		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	775	Asp/Glu-rich (acidic).|Interaction with CD2AP.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		GATGGGTATGATGTCCCAAAG	0.532			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																												p.D775V		Atlas-SNP	.		"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.A2324T						.						97	88	91					11																	119169140		2199	4295	6494	SO:0001583	missense	867	exon15	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	GGTATGATGTCCC	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2324A>T	chr11.hg19:g.119169140A>T	ENSP00000264033:p.Asp775Val	130.0	0.0		156.0	71.0	NM_005188	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	hg19	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	A	19.33	3.807631	0.70797	.	.	ENSG00000110395	ENST00000264033	D	0.84589	-1.87	5.59	5.59	0.84812	.	0.095529	0.64402	D	0.000001	D	0.88969	0.6582	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.90294	0.4325	10	0.87932	D	0	-42.7633	15.777	0.78228	1.0:0.0:0.0:0.0	.	775	P22681	CBL_HUMAN	V	775	ENSP00000264033:D775V	ENSP00000264033:D775V	D	+	2	0	CBL	118674350	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	8.137000	0.89612	2.120000	0.65058	0.528000	0.53228	GAT	.	.		0.532	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		T	119169140	A	T	119169140	3	4	23	1	0	0	0	0	1	0	0	0	2702	333	12	4	2382	4	CBL	11	119169140	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	389971	119169140	15837376	676	2742										
TECTA	7007	hgsc.bcm.edu	37	chr11	121039544	121039544	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttttgtggttggagctgacgCcacacatttaatcctaacac	8	10	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:121039544C>T	ENST00000392793.1	+	20	6180	c.5909C>T	c.(5908-5910)gCc>gTc	p.A1970V	TECTA_ENST00000264037.2_Missense_Mutation_p.A1970V			O75443	TECTA_HUMAN	tectorin alpha	1970	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GGAGCTGACGCCACACATTTA	0.468																																					p.A1970V		Atlas-SNP	.											.	TECTA	329	.	0			c.C5909T						.						186	174	178					11																	121039544		2203	4299	6502	SO:0001583	missense	7007	exon19			CTGACGCCACACA	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.5909C>T	chr11.hg19:g.121039544C>T	ENSP00000376543:p.Ala1970Val	184.0	0.0		156.0	21.0	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558091	0.65538	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	D;D	0.82526	-1.62;-1.62	5.81	5.81	0.92471	Endoglin/CD105 antigen conserved site (1);Zona pellucida sperm-binding protein (3);	0.565601	0.19263	N	0.118624	T	0.75019	0.3793	N	0.12569	0.235	0.27018	N	0.964539	B	0.20887	0.049	B	0.24974	0.057	T	0.67499	-0.5655	10	0.62326	D	0.03	.	20.0812	0.97776	0.0:1.0:0.0:0.0	.	1970	O75443	TECTA_HUMAN	V	1970	ENSP00000376543:A1970V;ENSP00000264037:A1970V	ENSP00000264037:A1970V	A	+	2	0	TECTA	120544754	0.819000	0.29175	0.882000	0.34594	0.941000	0.58515	4.739000	0.62080	2.752000	0.94435	0.557000	0.71058	GCC	.	.		0.468	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		T	121039544	C	T	121039544	3	4	23	1	0	0	0	0	1	0	0	0	15762	739	26	3	5983	3	TECTA	11	121039544	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1870404	121039544	13966972	677	2743										
TMEM225	338661	hgsc.bcm.edu	37	chr11	123754903	123754903	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgatatagtatgagtgcccaGagcagagagatacctgatgt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:123754903delG	ENST00000375026.2	-	3	558	c.342delC	c.(340-342)ctcfs	p.L114fs		NM_001013743.1	NP_001013765.1	Q6GV28	TM225_HUMAN	transmembrane protein 225	114					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	28						TGAGTGCCCAGAGCAGAGAGA	0.368																																					p.W115fs		Atlas-Indel,Pindel	.											.	TMEM225	56	.	0			c.343delT						.						108	103	105					11																	123754903		2202	4299	6501	SO:0001589	frameshift_variant	338661	exon3			.	AY634366	CCDS31697.1	11q24.1	2014-06-13			ENSG00000204300	ENSG00000204300			32390	protein-coding gene	gene with protein product	"PMP22 claudin domain containing", "protein phosphatase 1, regulatory subunit 154"						Standard	XM_006718832		Approved	PMP22CD, PPP1R154	uc001pzi.3	Q6GV28	OTTHUMG00000165959	ENST00000375026.2:c.342delC	chr11.hg19:g.123754903delG	ENSP00000364166:p.Leu114fs	61.0	0.0		65.0	24.0	NM_001013743		Frame_Shift_Del	DEL	ENST00000375026.2	hg19	CCDS31697.1																																																																																			.	.		0.368	TMEM225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387260.1	NM_001013743		-	123754903	G	-	123754903	7	5	23	1	0	1	0	1	0	0	0	0	16162	929	33	0	343	0	TMEM225	11	123754903	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	2715359	123754903	11251613	678	2744										
OR8B4	283162	hgsc.bcm.edu	37	chr11	124294491	124294491	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgagtcatacatcccacatAagagatgatactttctgaaa	6	9	2	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:124294491A>G	ENST00000356130.3	-	1	298	c.277T>C	c.(277-279)Tat>Cat	p.Y93H		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CATCCCACATAAGAGATGATA	0.383																																					p.Y93H		Atlas-SNP	.											.	OR8B4	60	.	0			c.T277C						.						99	97	98					11																	124294491		2201	4299	6500	SO:0001583	missense	283162	exon1			CCACATAAGAGAT	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"GPCR / Class A : Olfactory receptors"	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.277T>C	chr11.hg19:g.124294491A>G	ENSP00000348449:p.Tyr93His	139.0	0.0		135.0	55.0	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	hg19	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	a	13.96	2.394406	0.42410	.	.	ENSG00000198657	ENST00000356130	T	0.00397	7.57	4.61	4.61	0.57282	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000199	T	0.00784	0.0026	M	0.80508	2.5	0.28667	N	0.905807	D	0.63880	0.993	P	0.61070	0.883	T	0.36986	-0.9725	10	0.51188	T	0.08	.	10.3205	0.43762	0.8349:0.1651:0.0:0.0	.	93	Q96RC9	OR8B4_HUMAN	H	93	ENSP00000348449:Y93H	ENSP00000348449:Y93H	Y	-	1	0	OR8B4	123799701	0.000000	0.05858	0.872000	0.34217	0.960000	0.62799	1.365000	0.34182	2.070000	0.61991	0.528000	0.53228	TAT	.	.		0.383	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196		G	124294491	A	G	124294491	3	3	23	1	0	0	0	0	1	0	0	0	11238	362	13	2	654	2	OR8B4	11	124294491	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	539588	124294491	10712025	679	2745										
SIAE	54414	hgsc.bcm.edu	37	chr11	124509754	124509754	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgagctcttcttagacaaatCtgaagataactagaaagcag	8	7	3	5			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:124509754C>T	ENST00000263593.3	-	8	1148	c.976G>A	c.(976-978)Gat>Aat	p.D326N	SIAE_ENST00000545756.1_Missense_Mutation_p.D291N			Q9HAT2	SIAE_HUMAN	sialic acid acetylesterase	326					carbohydrate metabolic process (GO:0005975)|regulation of immune system process (GO:0002682)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	sialate O-acetylesterase activity (GO:0001681)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	15	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)		TTAGACAAATCTGAAGATAAC	0.433																																					p.D326N		Atlas-SNP	.											.	SIAE	37	.	0			c.G976A						.						131	122	125					11																	124509754		2201	4299	6500	SO:0001583	missense	54414	exon8			ACAAATCTGAAGA	AF300796	CCDS8449.1, CCDS55795.1	11q24	2005-12-15	2005-12-15	2005-12-15		ENSG00000110013			18187	protein-coding gene	gene with protein product	"sialic acid-specific acetylesterase II"	610079	"Ysg2 homolog (mouse)"	YSG2		10464298	Standard	NM_001199922		Approved	CSE-C, MGC87009, LSE	uc001qan.3	Q9HAT2		ENST00000263593.3:c.976G>A	chr11.hg19:g.124509754C>T	ENSP00000263593:p.Asp326Asn	56.0	0.0		60.0	20.0	NM_170601	B3KPB0|Q8IUT9|Q9HAU7|Q9NT71	Missense_Mutation	SNP	ENST00000263593.3	hg19	CCDS8449.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.323895	0.24080	.	.	ENSG00000110013	ENST00000263593;ENST00000545756	D;D	0.94576	-3.46;-3.46	5.4	-2.97	0.05530	Esterase, SGNH hydrolase-type (1);	0.761579	0.12850	N	0.434009	T	0.78253	0.4254	N	0.01048	-1.04	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.70908	-0.4744	10	0.45353	T	0.12	-0.4514	4.7711	0.13157	0.3345:0.4636:0.0773:0.1245	.	326	Q9HAT2	SIAE_HUMAN	N	326;291	ENSP00000263593:D326N;ENSP00000437877:D291N	ENSP00000263593:D326N	D	-	1	0	SIAE	124014964	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-0.675000	0.05227	-0.312000	0.08741	-0.974000	0.02594	GAT	.	.		0.433	SIAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387070.1	NM_170601		T	124509754	C	T	124509754	3	4	23	1	0	0	0	0	1	0	0	0	14313	913	32	3	607	3	SIAE	11	124509754	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	215263	124509754	10496762	680	2746										
HEPACAM	641654	hgsc.bcm.edu	37	chr11	124791252	124791252	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cggcgagcggccgggcacggCgggagacacggagtagccgg	21	12	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:124791252C>T	ENST00000408930.5	+	0	1428				HEPACAM_ENST00000298251.4_Missense_Mutation_p.A345T	NM_001037558.2	NP_001032647.2	Q6WQI6	HEPN1_HUMAN	hepatocellular carcinoma, down-regulated 1							cytoplasm (GO:0005737)				large_intestine(1)|lung(1)|stomach(1)	3	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0287)		CCGGGCACGGCGGGAGACACG	0.781																																					p.A345T		Atlas-SNP	.											.	HEPACAM	64	.	0			c.G1033A						.						1	1	1					11																	124791252		712	1792	2504	SO:0001628	intergenic_variant	220296	exon7			GCACGGCGGGAGA	BC148521	CCDS41729.1	11q24	2013-07-02	2011-02-11		ENSG00000221932	ENSG00000221932			34400	protein-coding gene	gene with protein product	"cancer susceptibility gene HEPN1"	611641	"HEPACAM opposite strand 1"			12971969, 23548416	Standard	NM_001037558		Approved		uc001qbj.1	Q6WQI6	OTTHUMG00000165939		chr11.hg19:g.124791252C>T		307.0	0.0		261.0	100.0	NM_152722		Missense_Mutation	SNP	ENST00000408930.5	hg19	CCDS41729.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.359324	0.24598	.	.	ENSG00000165478	ENST00000298251	T	0.44482	0.92	5.46	0.083	0.14431	.	0.361788	0.30809	N	0.008839	T	0.21761	0.0524	N	0.19112	0.55	0.09310	N	1	B	0.25105	0.118	B	0.10450	0.005	T	0.10382	-1.0632	10	0.38643	T	0.18	-6.7065	6.7462	0.23462	0.0:0.2776:0.4516:0.2709	.	345	Q14CZ8	HECAM_HUMAN	T	345	ENSP00000298251:A345T	ENSP00000298251:A345T	A	-	1	0	HEPACAM	124296462	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.153000	0.10144	-0.011000	0.14247	-0.165000	0.13383	GCC	.	.		0.781	HEPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387129.1	NM_001037558		T	124791252	C	T	124791252	1	4	23	0	1	0	0	0	0	0	0	0	7061	768	27	1		1	HEPACAM	11	124791252	IGR	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	281498	124791252	10215264	681	2747										
CHEK1	1111	hgsc.bcm.edu	37	chr11	125514027	125514027	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagttctcagccagaaccccGcacaggtctttccttatggg	9	14	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:125514027G>A	ENST00000534070.1	+	10	1220	c.965G>A	c.(964-966)cGc>cAc	p.R322H	CHEK1_ENST00000278916.3_Missense_Mutation_p.R322H|CHEK1_ENST00000438015.1_Missense_Mutation_p.R322H|CHEK1_ENST00000532449.1_3'UTR|CHEK1_ENST00000524737.1_Missense_Mutation_p.R322H|CHEK1_ENST00000428830.2_Missense_Mutation_p.R322H|CHEK1_ENST00000544373.1_Missense_Mutation_p.R322H|CHEK1_ENST00000427383.2_Missense_Mutation_p.R338H	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	322					cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		CCAGAACCCCGCACAGGTCTT	0.408								Other conserved DNA damage response genes																													p.R322H		Atlas-SNP	.											CHEK1,colon,carcinoma,0,1	CHEK1	44	.	0			c.G965A						.						109	107	108					11																	125514027		2201	4299	6500	SO:0001583	missense	1111	exon10			AACCCCGCACAGG	AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"CHK1 (checkpoint, S.pombe) homolog", "CHK1 checkpoint homolog (S. pombe)"			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.965G>A	chr11.hg19:g.125514027G>A	ENSP00000435371:p.Arg322His	188.0	0.0		152.0	65.0	NM_001244846	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Missense_Mutation	SNP	ENST00000534070.1	hg19	CCDS8459.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.568815	0.45798	.	.	ENSG00000149554	ENST00000438015;ENST00000427383;ENST00000428830;ENST00000544373;ENST00000534070;ENST00000524737;ENST00000278916	T;T;T;T;T;T;T	0.72942	-0.7;-0.38;-0.7;-0.67;-0.7;-0.7;-0.66	5.58	3.69	0.42338	Protein kinase-like domain (1);	0.360905	0.28796	N	0.014119	T	0.59059	0.2166	L	0.43923	1.385	0.41168	D	0.986146	B;B;B;B	0.15719	0.004;0.014;0.012;0.012	B;B;B;B	0.14023	0.003;0.01;0.009;0.009	T	0.52895	-0.8514	10	0.13853	T	0.58	-5.7233	11.7534	0.51862	0.1485:0.0:0.8515:0.0	.	322;338;322;322	F5H7S4;E7EPP6;B5BTY6;O14757	.;.;.;CHK1_HUMAN	H	322;338;322;322;322;322;322	ENSP00000388648:R322H;ENSP00000391090:R338H;ENSP00000412504:R322H;ENSP00000442317:R322H;ENSP00000435371:R322H;ENSP00000432890:R322H;ENSP00000278916:R322H	ENSP00000278916:R322H	R	+	2	0	CHEK1	125019237	0.745000	0.28261	0.985000	0.45067	0.861000	0.49209	2.323000	0.43823	1.370000	0.46153	0.655000	0.94253	CGC	.	.		0.408	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274		A	125514027	G	A	125514027	3	1	23	1	0	0	0	0	1	0	0	0	3336	1087	38	1	999	1	CHEK1	11	125514027	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	722775	125514027	9492489	682	2748										
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128936699	128936699	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atcttcggtcataaatacacAgatgaagatgtttatcaagt	7	6	3	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:128936699A>C	ENST00000310343.9	-	6	553	c.554T>G	c.(553-555)cTg>cGg	p.L185R	ARHGAP32_ENST00000524655.1_Missense_Mutation_p.L111R	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	185	PX; atypical.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						ATAAATACACAGATGAAGATG	0.368																																					p.L185R		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.T554G						.						81	77	79					11																	128936699		1566	3578	5144	SO:0001583	missense	9743	exon6			ATACACAGATGAA	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.554T>G	chr11.hg19:g.128936699A>C	ENSP00000310561:p.Leu185Arg	90.0	0.0		95.0	42.0	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	A	7.520	0.656446	0.14580	.	.	ENSG00000134909	ENST00000310343;ENST00000524655;ENST00000457677;ENST00000525234	T;T;T	0.34859	1.34;1.34;1.34	5.05	5.05	0.67936	Phox homologous domain (3);	.	.	.	.	T	0.40886	0.1135	N	0.16656	0.425	0.80722	D	1	B;D	0.89917	0.211;1.0	B;D	0.74023	0.241;0.982	T	0.19353	-1.0308	9	0.21014	T	0.42	.	13.9074	0.63845	1.0:0.0:0.0:0.0	.	119;185	Q86T64;A7KAX9	.;RHG32_HUMAN	R	185;111;119;159	ENSP00000310561:L185R;ENSP00000432468:L111R;ENSP00000432303:L159R	ENSP00000310561:L185R	L	-	2	0	ARHGAP32	128441909	1.000000	0.71417	0.903000	0.35520	0.993000	0.82548	6.763000	0.74955	2.126000	0.65437	0.460000	0.39030	CTG	.	.		0.368	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		C	128936699	A	C	128936699	3	2	23	1	0	0	0	0	1	0	0	0	881	188	7	5	5777	5	ARHGAP32	11	128936699	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3422672	128936699	6069817	683	2749										
NFRKB	4798	hgsc.bcm.edu	37	chr11	129734929	129734929	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaggaaactaacaggcttatTgccagcaatgagcttagtgc	11	8	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:129734929T>C	ENST00000446488.3	-	25	3809	c.3706A>G	c.(3706-3708)Aat>Gat	p.N1236D	NFRKB_ENST00000304521.5_Missense_Mutation_p.N1236D|NFRKB_ENST00000524746.1_Missense_Mutation_p.N1236D|NFRKB_ENST00000524794.1_Missense_Mutation_p.N1261D	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	1236					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		ACAGGCTTATTGCCAGCAATG	0.532																																					p.N1261D		Atlas-SNP	.											.	NFRKB	101	.	0			c.A3781G						.						122	111	115					11																	129734929		2201	4297	6498	SO:0001583	missense	4798	exon24			GCTTATTGCCAGC		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"INO80 complex subunits"	7802	protein-coding gene	gene with protein product	"nuclear factor related to kappa B binding protein", "DNA-binding protein R kappa B", "INO80 complex subunit G"	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.3706A>G	chr11.hg19:g.129734929T>C	ENSP00000400476:p.Asn1236Asp	136.0	0.0		126.0	56.0	NM_006165	Q12869|Q15312|Q9H048	Missense_Mutation	SNP	ENST00000446488.3	hg19	CCDS44770.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.978030	0.92982	.	.	ENSG00000170322	ENST00000304521;ENST00000446488;ENST00000524794;ENST00000524746	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.63733	0.2536	N	0.19112	0.55	0.58432	D	0.999993	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.80764	0.968;0.994;0.994	T	0.67070	-0.5763	9	0.51188	T	0.08	-27.296	16.1388	0.81509	0.0:0.0:0.0:1.0	.	1236;1235;1261	Q6P4R8;Q6P4R8-3;Q6P4R8-2	NFRKB_HUMAN;.;.	D	1236;1236;1261;1236	.	ENSP00000303800:N1236D	N	-	1	0	NFRKB	129240139	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	6.101000	0.71479	2.205000	0.71048	0.528000	0.53228	AAT	.	.		0.532	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		C	129734929	T	C	129734929	3	2	23	1	0	0	0	0	1	0	0	0	10393	1812	63	2	201	2	NFRKB	11	129734929	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	798230	129734929	5271587	684	2750										
SNX19	399979	hgsc.bcm.edu	37	chr11	130784447	130784447	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagcaaagctgtaacagagGcggtaacatctccttgttct	9	11	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:130784447G>A	ENST00000265909.4	-	1	1957	c.1388C>T	c.(1387-1389)gCc>gTc	p.A463V	SNX19_ENST00000530356.1_Intron|SNX19_ENST00000539184.1_Intron|SNX19_ENST00000533318.1_Intron|SNX19_ENST00000533214.1_Missense_Mutation_p.A463V|SNX19_ENST00000528555.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	463					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		TGTAACAGAGGCGGTAACATC	0.522																																					p.A463V		Atlas-SNP	.											.	SNX19	84	.	0			c.C1388T						.						106	103	104					11																	130784447		2201	4297	6498	SO:0001583	missense	399979	exon1			ACAGAGGCGGTAA	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1388C>T	chr11.hg19:g.130784447G>A	ENSP00000265909:p.Ala463Val	88.0	0.0		85.0	30.0	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	hg19	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	G	6.076	0.382292	0.11524	.	.	ENSG00000120451	ENST00000265909;ENST00000533214	T;T	0.20738	2.05;2.05	5.1	3.14	0.36123	.	0.996378	0.08150	N	0.990184	T	0.12092	0.0294	N	0.08118	0	0.09310	N	0.999999	B;B	0.20052	0.012;0.041	B;B	0.19391	0.015;0.025	T	0.34976	-0.9807	10	0.31617	T	0.26	.	9.2251	0.37402	0.0:0.1594:0.6751:0.1655	.	463;463	E9PKB9;Q92543	.;SNX19_HUMAN	V	463	ENSP00000265909:A463V;ENSP00000435390:A463V	ENSP00000265909:A463V	A	-	2	0	SNX19	130289657	0.007000	0.16637	0.001000	0.08648	0.143000	0.21401	1.559000	0.36320	0.666000	0.31087	0.650000	0.86243	GCC	.	.		0.522	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		A	130784447	G	A	130784447	3	1	23	1	0	0	0	0	1	0	0	0	14905	1203	42	3	1634	3	SNX19	11	130784447	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1049518	130784447	4222069	685	2751										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133814238	133814238	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgttccagccgcagagatgCcttatcatgaagactggccc	10	12	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:133814238C>T	ENST00000321016.8	-	3	516	c.286G>A	c.(286-288)Gca>Aca	p.A96T	IGSF9B_ENST00000533871.2_Missense_Mutation_p.A96T			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	96	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CGCAGAGATGCCTTATCATGA	0.582																																					p.A96T		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G286A						.						62	66	64					11																	133814238		2020	4186	6206	SO:0001583	missense	22997	exon3			GAGATGCCTTATC	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.286G>A	chr11.hg19:g.133814238C>T	ENSP00000317980:p.Ala96Thr	100.0	0.0		60.0	22.0	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	28.7	4.942764	0.92526	.	.	ENSG00000080854	ENST00000321016;ENST00000527648;ENST00000533160;ENST00000526663	T;T;T;T	0.27720	1.65;1.65;1.65;1.86	5.69	4.78	0.61160	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.091985	0.41194	D	0.000922	T	0.42966	0.1226	M	0.64676	1.99	0.47737	D	0.999508	P	0.39003	0.654	P	0.46172	0.506	T	0.41016	-0.9532	10	0.59425	D	0.04	.	16.125	0.81386	0.1347:0.8653:0.0:0.0	.	96	Q9UPX0	TUTLB_HUMAN	T	96;96;86;143	ENSP00000317980:A96T;ENSP00000436576:A96T;ENSP00000434026:A86T;ENSP00000435989:A143T	ENSP00000317980:A96T	A	-	1	0	IGSF9B	133319448	1.000000	0.71417	0.949000	0.38748	0.844000	0.47949	5.968000	0.70413	1.392000	0.46585	0.563000	0.77884	GCA	.	.		0.582	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		T	133814238	C	T	133814238	3	4	23	1	0	0	0	0	1	0	0	0	7615	739	26	3	3831	3	IGSF9B	11	133814238	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3029791	133814238	1192278	686	2752										
TEAD4	7004	hgsc.bcm.edu	37	chr12	3131073	3131073	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctacagcgacccctacctcGaagccgtggacatccgccaa	9	17	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:3131073G>A	ENST00000397122.2	+	8	685	c.400G>A	c.(400-402)Gaa>Aaa	p.E134K	TEAD4_ENST00000359864.2_Missense_Mutation_p.E263K|TEAD4_ENST00000358409.2_Missense_Mutation_p.E220K	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4	263					gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			CCCCTACCTCGAAGCCGTGGA	0.542																																					p.E263K		Atlas-SNP	.											TEAD4,NS,carcinoma,0,1	TEAD4	45	.	0			c.G787A						.						132	130	131					12																	3131073		2203	4300	6503	SO:0001583	missense	7004	exon10			TACCTCGAAGCCG	X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561		ENST00000397122.2:c.400G>A	chr12.hg19:g.3131073G>A	ENSP00000380311:p.Glu134Lys	157.0	0.0		143.0	65.0	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Missense_Mutation	SNP	ENST00000397122.2	hg19	CCDS41737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.211382|5.211382	0.95069|0.95069	.|.	.|.	ENSG00000197905|ENSG00000197905	ENST00000358409;ENST00000359864;ENST00000397122|ENST00000544666	T;T;T|.	0.35236|.	1.32;1.32;1.32|.	4.19|4.19	4.19|4.19	0.49359|0.49359	.|.	0.196140|.	0.43579|.	D|.	0.000541|.	D|D	0.86151|0.86151	0.5864|0.5864	H|H	0.94264|0.94264	3.515|3.515	0.80722|0.80722	D|D	1|1	P|.	0.52577|.	0.954|.	B|.	0.41646|.	0.362|.	D|D	0.90541|0.90541	0.4502|0.4502	10|5	0.87932|.	D|.	0|.	-6.5462|-6.5462	15.6724|15.6724	0.77289|0.77289	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	263|.	Q15561|.	TEAD4_HUMAN|.	K|Q	220;263;134|185	ENSP00000351184:E220K;ENSP00000352926:E263K;ENSP00000380311:E134K|.	ENSP00000351184:E220K|.	E|R	+|+	1|2	0|0	TEAD4|TEAD4	3001334|3001334	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.884000|0.884000	0.51177|0.51177	7.770000|7.770000	0.85390|0.85390	2.167000|2.167000	0.68274|0.68274	0.655000|0.655000	0.94253|0.94253	GAA|CGA	.	.		0.542	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213		A	3131073	G	A	3131073	3	1	23	1	0	0	0	0	1	0	0	0	15756	1059	37	1	817	1	TEAD4	12	3131073	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10		3131073	130720822	687	2753										
VWF	7450	hgsc.bcm.edu	37	chr12	6128578	6128578	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcgccgcagctctgacggtcGcttccggtccttgagcccga	13	16	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:6128578G>A	ENST00000261405.5	-	28	4260	c.4006C>T	c.(4006-4008)Cga>Tga	p.R1336*		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1336	VWFA 1; binding site for platelet glycoprotein Ib. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	TCTGACGGTCGCTTCCGGTCC	0.622																																					p.R1336X		Atlas-SNP	.											.	VWF	338	.	0			c.C4006T						.						42	41	41					12																	6128578		2201	4300	6501	SO:0001587	stop_gained	7450	exon28			ACGGTCGCTTCCG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.4006C>T	chr12.hg19:g.6128578G>A	ENSP00000261405:p.Arg1336*	104.0	0.0		86.0	32.0	NM_000552	Q8TCE8|Q99806	Nonsense_Mutation	SNP	ENST00000261405.5	hg19	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	.	42	9.615016	0.99220	.	.	ENSG00000110799	ENST00000261405	.	.	.	4.98	4.98	0.66077	.	0.189630	0.26086	N	0.026431	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.9727	0.47448	0.0:0.0:0.7098:0.2902	.	.	.	.	X	1336	.	ENSP00000261405:R1336X	R	-	1	2	VWF	5998839	1.000000	0.71417	1.000000	0.80357	0.389000	0.30415	1.476000	0.35420	2.605000	0.88082	0.555000	0.69702	CGA	.	.		0.622	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6128578	G	A	6128578	4	1	23	1	0	0	0	0	0	1	0	0	17261	1095	38	1	4535	1	VWF	12	6128578	Nonsense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2997505	6128578	127723317	688	2754										
TAPBPL	55080	hgsc.bcm.edu	37	chr12	6562348	6562348	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtgaggacagggcaagggcCtcccttgtgctgaagcaggt	16	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:6562348C>A	ENST00000266556.7	+	2	345	c.180C>A	c.(178-180)gcC>gcA	p.A60A	CD27-AS1_ENST00000399492.2_RNA|TAPBPL_ENST00000545700.1_3'UTR|CD27-AS1_ENST00000545339.1_RNA|TAPBPL_ENST00000544021.1_Intron	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	60					negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						GGGCAAGGGCCTCCCTTGTGC	0.632																																					p.A60A		Atlas-SNP	.											.	TAPBPL	21	.	0			c.C180A						.						59	48	52					12																	6562348		2203	4300	6503	SO:0001819	synonymous_variant	55080	exon2			AAGGGCCTCCCTT	AK001005	CCDS8546.1	12p13.31	2013-01-11						"Immunoglobulin superfamily / C1-set domain containing"	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.180C>A	chr12.hg19:g.6562348C>A		146.0	0.0		123.0	43.0	NM_018009	Q9NWB8	Silent	SNP	ENST00000266556.7	hg19	CCDS8546.1																																																																																			.	.		0.632	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009		A	6562348	C	A	6562348	2	1	23	1	0	0	0	0	0	0	0	1	15568	668	24	3		3	TAPBPL	12	6562348	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	433770	6562348	127289547	689	2755										
IFFO1	25900	hgsc.bcm.edu	37	chr12	6657862	6657862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcatgcgctgcatctcctCgttgatgctgagggctgtgc	14	11	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:6657862C>T	ENST00000396840.2	-	5	1242	c.1201G>A	c.(1201-1203)Gag>Aag	p.E401K	IFFO1_ENST00000465801.1_Missense_Mutation_p.E97K|IFFO1_ENST00000336604.4_Missense_Mutation_p.E404K|IFFO1_ENST00000436152.2_Missense_Mutation_p.E97K|IFFO1_ENST00000356896.4_Missense_Mutation_p.E404K			Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan 1	401						intermediate filament (GO:0005882)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	20						TGCATCTCCTCGTTGATGCTG	0.692																																					p.E412K		Atlas-SNP	.											.	IFFO1	55	.	0			c.G1234A						.						79	74	76					12																	6657862		2203	4300	6503	SO:0001583	missense	25900	exon6			TCTCCTCGTTGAT	AF124432	CCDS8550.1, CCDS41741.1, CCDS8550.2, CCDS73425.1	12p13.31	2013-01-16	2008-09-11	2008-09-11	ENSG00000010295	ENSG00000010295		"Intermediate filament family orphans"	24970	protein-coding gene	gene with protein product		610495	"intermediate filament family orphan"	IFFO		8771189, 3052284	Standard	NM_001193457		Approved	HOM-TES-103	uc010sfe.2	Q0D2I5	OTTHUMG00000141264	ENST00000396840.2:c.1201G>A	chr12.hg19:g.6657862C>T	ENSP00000380052:p.Glu401Lys	119.0	0.0		120.0	38.0	NM_001193457	Q24JT6|Q7L5J9|Q7Z5X4|Q9BQ46	Missense_Mutation	SNP	ENST00000396840.2	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.374289	0.95923	.	.	ENSG00000010295	ENST00000436152;ENST00000465801;ENST00000336604;ENST00000396840;ENST00000356896;ENST00000423501	D;D;D;D;D	0.92752	-2.93;-3.1;-2.82;-2.81;-2.88	4.55	4.55	0.56014	.	0.000000	0.64402	D	0.000002	D	0.95027	0.8390	L	0.60455	1.87	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.995;0.999;0.999;0.999;0.999	D;P;D;D;D;D	0.78314	0.991;0.819;0.991;0.991;0.991;0.941	D	0.95587	0.8651	10	0.66056	D	0.02	-21.5766	17.3158	0.87224	0.0:1.0:0.0:0.0	.	403;96;404;401;404;105	Q0D2I5-7;Q6P593;Q0D2I5-4;Q0D2I5;Q0D2I5-5;B4DQQ1	.;.;.;IFFO1_HUMAN;.;.	K	97;97;404;401;404;41	ENSP00000390721:E97K;ENSP00000436261:E97K;ENSP00000337593:E404K;ENSP00000380052:E401K;ENSP00000349364:E404K	ENSP00000337593:E404K	E	-	1	0	IFFO1	6528123	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.643000	0.83403	2.072000	0.62099	0.655000	0.94253	GAG	.	.		0.692	IFFO1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000280428.1	NM_080730		T	6657862	C	T	6657862	3	4	23	1	0	0	0	0	1	0	0	0	7519	893	31	1	501	1	IFFO1	12	6657862	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	95514	6657862	127194033	690	2756										
PTPN6	5777	hgsc.bcm.edu	37	chr12	7069305	7069305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagatggtgcgggcgcagcGctcgggcatggtgcagacgg	19	11	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:7069305G>A	ENST00000318974.9	+	13	1728	c.1484G>A	c.(1483-1485)cGc>cAc	p.R495H	PTPN6_ENST00000399448.1_Missense_Mutation_p.R497H|PTPN6_ENST00000456013.1_Missense_Mutation_p.R495H|PTPN6_ENST00000539029.1_3'UTR|PTPN6_ENST00000447931.2_Missense_Mutation_p.R456H	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	495	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|apoptotic process (GO:0006915)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|natural killer cell mediated cytotoxicity (GO:0042267)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell proliferation (GO:0008285)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein dephosphorylation (GO:0006470)|regulation of B cell differentiation (GO:0045577)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|type I interferon signaling pathway (GO:0060337)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|prostate(3)	18						CGGGCGCAGCGCTCGGGCATG	0.592																																					p.R497H		Atlas-SNP	.											.	PTPN6	42	.	0			c.G1490A						.						49	57	55					12																	7069305		2157	4271	6428	SO:0001583	missense	5777	exon13			CGCAGCGCTCGGG		CCDS41744.1, CCDS44820.1, CCDS44821.1	12p13.31	2013-02-14			ENSG00000111679	ENSG00000111679		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9658	protein-coding gene	gene with protein product		176883				1639416	Standard	NM_080548		Approved	HCP, HCPH, PTP-1C, SHP-1, SHP1	uc001qsa.1	P29350	OTTHUMG00000168518	ENST00000318974.9:c.1484G>A	chr12.hg19:g.7069305G>A	ENSP00000326010:p.Arg495His	99.0	0.0		78.0	11.0	NM_080548	A8K306|G3V0F8|Q969V8|Q9UK67	Missense_Mutation	SNP	ENST00000318974.9	hg19	CCDS44820.1	.	.	.	.	.	.	.	.	.	.	G	34	5.401697	0.96030	.	.	ENSG00000111679	ENST00000399448;ENST00000447931;ENST00000318974;ENST00000456013	D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24	4.79	4.79	0.61399	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.98479	0.9493	H	0.99764	4.76	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.99737	1.1014	10	0.87932	D	0	.	18.0266	0.89271	0.0:0.0:1.0:0.0	.	483;456;495;495;497	B4DPS0;P29350-2;G3V0F8;P29350;Q53XS4	.;.;.;PTN6_HUMAN;.	H	497;456;495;495	ENSP00000382376:R497H;ENSP00000415979:R456H;ENSP00000326010:R495H;ENSP00000391592:R495H	ENSP00000326010:R495H	R	+	2	0	PTPN6	6939566	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.533000	0.98059	2.497000	0.84241	0.561000	0.74099	CGC	.	.		0.592	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831		A	7069305	G	A	7069305	3	1	23	1	0	0	0	0	1	0	0	0	12807	1087	38	1	1552	1	PTPN6	12	7069305	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	411443	7069305	126782590	691	2757										
LRP6	4040	hgsc.bcm.edu	37	chr12	12300444	12300444	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtcccatccaaagcagcccGttcaattttaggagaccttt	7	12	1	1	rs143966208		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:12300444G>A	ENST00000261349.4	-	15	3329	c.3253C>T	c.(3253-3255)Cgg>Tgg	p.R1085W	LRP6_ENST00000543091.1_Missense_Mutation_p.R1085W	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1085	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				AAAGCAGCCCGTTCAATTTTA	0.413																																					p.R1085W		Atlas-SNP	.											LRP6,NS,carcinoma,0,1	LRP6	170	.	0			c.C3253T						.	G	TRP/ARG	0,4406		0,0,2203	125	132	130		3253	3.7	1	12	dbSNP_134	130	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRP6	NM_002336.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1085/1614	12300444	1,13005	2203	4300	6503	SO:0001583	missense	4040	exon15			CAGCCCGTTCAAT	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.3253C>T	chr12.hg19:g.12300444G>A	ENSP00000261349:p.Arg1085Trp	177.0	1.0		177.0	61.0	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.961442	0.74016	0.0	1.16E-4	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.96300	-3.97;-3.97	5.69	3.68	0.42216	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	U	0.000018	D	0.97823	0.9285	M	0.84156	2.68	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.969;0.996	D	0.98274	1.0505	10	0.87932	D	0	.	12.1502	0.54046	0.0:0.0:0.4196:0.5804	.	1085;1085	F5H7J9;O75581	.;LRP6_HUMAN	W	1085	ENSP00000261349:R1085W;ENSP00000442472:R1085W	ENSP00000261349:R1085W	R	-	1	2	LRP6	12191711	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.110000	0.31147	1.387000	0.46486	0.563000	0.77884	CGG	.	G|1.000;A|0.000		0.413	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			A	12300444	G	A	12300444	3	1	23	1	0	0	0	0	1	0	0	0	8971	1144	40	1	1624	1	LRP6	12	12300444	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	5231139	12300444	121551451	692	2758										
DUSP16	80824	hgsc.bcm.edu	37	chr12	12633224	12633224	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatagcgatggtggcggagcGggagatcccagctaaacagt	16	8	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:12633224G>A	ENST00000228862.2	-	6	1379	c.748C>T	c.(748-750)Cgc>Tgc	p.R250C	DUSP16_ENST00000298573.4_3'UTR|DUSP16_ENST00000545864.1_Intron	NM_030640.2	NP_085143.1	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	250	Tyrosine-protein phosphatase.				dephosphorylation (GO:0016311)|inactivation of MAPK activity (GO:0000188)|MAPK export from nucleus (GO:0045204)|MAPK phosphatase export from nucleus, leptomycin B sensitive (GO:0045209)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(7)|kidney(2)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(3)	26		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		GTGGCGGAGCGGGAGATCCCA	0.448																																					p.R250C	Ovarian(158;443 1896 15437 36069 46477)	Atlas-SNP	.											.	DUSP16	64	.	0			c.C748T						.						224	207	213					12																	12633224		2203	4300	6503	SO:0001583	missense	80824	exon6			CGGAGCGGGAGAT	AB052156	CCDS8650.1	12p13	2011-06-09				ENSG00000111266		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	17909	protein-coding gene	gene with protein product	"MAPK phosphatase-7"	607175				11359773, 11489891, 15888437	Standard	NM_030640		Approved	MKP-7, KIAA1700, MKP7	uc001rao.2	Q9BY84		ENST00000228862.2:c.748C>T	chr12.hg19:g.12633224G>A	ENSP00000228862:p.Arg250Cys	109.0	0.0		104.0	37.0	NM_030640	Q547C7|Q96QS2|Q9C0G3	Missense_Mutation	SNP	ENST00000228862.2	hg19	CCDS8650.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.449088	0.84101	.	.	ENSG00000111266	ENST00000228862	D	0.98381	-4.9	5.66	5.66	0.87406	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.99459	0.9808	H	0.98487	4.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	D	0.98171	1.0452	10	0.87932	D	0	.	19.7516	0.96271	0.0:0.0:1.0:0.0	.	250;250	Q9BY84;Q96N49	DUS16_HUMAN;.	C	250	ENSP00000228862:R250C	ENSP00000228862:R250C	R	-	1	0	DUSP16	12524491	1.000000	0.71417	0.961000	0.40146	0.809000	0.45718	7.834000	0.86773	2.656000	0.90262	0.655000	0.94253	CGC	.	.		0.448	DUSP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400311.1	NM_030640		A	12633224	G	A	12633224	3	1	23	1	0	0	0	0	1	0	0	0	4818	1116	39	1	1257	1	DUSP16	12	12633224	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	332780	12633224	121218671	693	2759										
RERG	85004	hgsc.bcm.edu	37	chr12	15262428	15262428	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccttccccccatcgcatgtgCccctccctctgaatggtatc	6	19	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:15262428C>T	ENST00000256953.2	-	5	552	c.216G>A	c.(214-216)ggG>ggA	p.G72G	RERG_ENST00000538313.1_Silent_p.G72G|RERG_ENST00000536465.1_Silent_p.G72G|RERG-IT1_ENST00000539734.1_RNA|RERG_ENST00000546331.1_Silent_p.G53G	NM_032918.2	NP_116307.1	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor	72					negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to hormone (GO:0009725)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	estrogen receptor binding (GO:0030331)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16						ATCGCATGTGCCCCTCCCTCT	0.458																																					p.G72G		Atlas-SNP	.											.	RERG	30	.	0			c.G216A						.						250	261	257					12																	15262428		2203	4300	6503	SO:0001819	synonymous_variant	85004	exon5			CATGTGCCCCTCC	AF339750	CCDS8673.1, CCDS53753.1	12p13.1	2014-05-09			ENSG00000134533	ENSG00000134533			15980	protein-coding gene	gene with protein product		612664				11533059	Standard	NM_032918		Approved	MGC15754	uc001rct.3	Q96A58	OTTHUMG00000168745	ENST00000256953.2:c.216G>A	chr12.hg19:g.15262428C>T		173.0	0.0		140.0	56.0	NM_032918	B2R9R0|B4DI02	Silent	SNP	ENST00000256953.2	hg19	CCDS8673.1																																																																																			.	.		0.458	RERG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400882.1	NM_032918		T	15262428	C	T	15262428	2	4	23	1	0	0	0	0	0	0	0	1	13247	726	26	3		3	RERG	12	15262428	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2629204	15262428	118589467	694	2760										
SLCO1B3	28234	hgsc.bcm.edu	37	chr12	20968682	20968682	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtagtttaataatggaccaaCatcaacatttgaataaaaca	5	6	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:20968682C>A	ENST00000381545.3	+	3	229	c.10C>A	c.(10-12)Cat>Aat	p.H4N	SLCO1B3_ENST00000553473.1_Missense_Mutation_p.H4N|LST3_ENST00000381541.3_Missense_Mutation_p.H4N|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.H4N|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.H4N|LST3_ENST00000540229.1_Missense_Mutation_p.H4N	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	4					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	AATGGACCAACATCAACATTT	0.308																																					p.H4N		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.C10A						.						53	52	53					12																	20968682		2203	4294	6497	SO:0001583	missense	28234	exon3			GACCAACATCAAC		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.10C>A	chr12.hg19:g.20968682C>A	ENSP00000370956:p.His4Asn	75.0	0.0		56.0	30.0	NM_019844	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	hg19	CCDS8684.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.032114	0.00406	.	.	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046;ENSG00000257046;ENSG00000205754	ENST00000540853;ENST00000261196;ENST00000381545;ENST00000553473;ENST00000381541;ENST00000540229;ENST00000554957	T;T;T;T;T;T;T	0.36699	1.24;1.31;1.31;1.32;1.33;1.32;1.33	2.15	-0.511	0.11970	Major facilitator superfamily domain, general substrate transporter (1);	1.405570	0.04707	N	0.416865	T	0.07773	0.0195	N	0.00237	-1.79	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.28396	-1.0045	10	0.07175	T	0.84	.	2.6745	0.05077	0.462:0.2905:0.0:0.2475	.	4;4;4	F5H094;Q5JAR4;Q9NPD5	.;.;SO1B3_HUMAN	N	4	ENSP00000442000:H4N;ENSP00000261196:H4N;ENSP00000370956:H4N;ENSP00000451758:H4N;ENSP00000370952:H4N;ENSP00000441269:H4N;ENSP00000452013:H4N	ENSP00000370952:H4N	H	+	1	0	SLCO1B3;SLCO1B7;RP11-545J16.1	20859949	0.054000	0.20591	0.033000	0.17914	0.278000	0.26855	0.844000	0.27654	-0.109000	0.12044	0.305000	0.20034	CAT	.	.		0.308	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		A	20968682	C	A	20968682	3	1	23	1	0	0	0	0	1	0	0	0	14739	478	17	3	12	3	SLCO1B3	12	20968682	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5706254	20968682	112883213	695	2761										
BHLHE41	79365	hgsc.bcm.edu	37	chr12	26275589	26275590	+	In_Frame_Ins	INS	-	-	GCT													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggccgccgccgctgccgccINSgccgcgggaatccagcttca							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:26275589_26275590insGCT	ENST00000242728.4	-	5	1205_1206	c.858_859insAGC	c.(856-861)ggcggc>ggcAGCggc	p.286_287GG>GSG	RP11-283G6.3_ENST00000545819.1_RNA|RP11-283G6.3_ENST00000535914.1_RNA	NM_030762.2	NP_110389.1	Q9C0J9	BHE41_HUMAN	basic helix-loop-helix family, member e41	286					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|MRF binding (GO:0043426)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)	5						ccgctgccgccgccgcGGGAAT	0.787																																					p.G287delinsSG		Atlas-INDEL	.											.	BHLHE41	20	.	0			c.859_860insAGC						.																																			SO:0001652	inframe_insertion	79365	exon5			.	AB044088	CCDS8706.1	12p12.1	2011-12-05	2009-01-12	2009-01-12	ENSG00000123095	ENSG00000123095		"Basic helix-loop-helix proteins"	16617	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 2", "Enhancer-of-split and hairy-related protein 1"	606200	"basic helix-loop-helix domain containing, class B, 3"	BHLHB3		11162494, 18557763	Standard	NM_030762		Approved	DEC2, SHARP-1, SHARP1, bHLHe41	uc001rhb.3	Q9C0J9	OTTHUMG00000169174	ENST00000242728.4:c.858_859insAGC	chr12.hg19:g.26275589_26275590insGCT	ENSP00000242728:p.Gly286_Gly287insSer	46.0	0.0		26.0	10.0	NM_030762	A2I2N8	In_Frame_Ins	INS	ENST00000242728.4	hg19	CCDS8706.1																																																																																			.	.		0.787	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762		GCT	26275590	-	GCT	26275589	7	5	23	1	0	1	1	0	0	0	0	0	1424	652	23	0	593	0	BHLHE41	12	26275589	In_Frame_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	5306907	26275589	107576306	696	2762										
CAPRIN2	65981	hgsc.bcm.edu	37	chr12	30863317	30863317	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catccacaggggtcatgctaCgggagtctccttgtccagag	12	12	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:30863317C>T	ENST00000298892.5	-	17	3503	c.2753G>A	c.(2752-2754)cGt>cAt	p.R918H	CAPRIN2_ENST00000308433.5_Missense_Mutation_p.R634H|CAPRIN2_ENST00000417045.1_3'UTR|CAPRIN2_ENST00000395805.2_3'UTR|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.R968H	NM_023925.3	NP_076414.2			caprin family member 2											breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					GGTCATGCTACGGGAGTCTCC	0.522																																					p.R968H		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.G2903A						.						227	230	229					12																	30863317		2203	4300	6503	SO:0001583	missense	65981	exon18			ATGCTACGGGAGT	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000298892.5:c.2753G>A	chr12.hg19:g.30863317C>T	ENSP00000298892:p.Arg918His	89.0	0.0		105.0	43.0	NM_001002259		Missense_Mutation	SNP	ENST00000298892.5	hg19	CCDS8720.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599263	0.87055	.	.	ENSG00000110888	ENST00000298892;ENST00000251071;ENST00000308433	T;T;T	0.76448	-0.67;-0.72;-1.02	5.7	5.7	0.88788	.	0.119796	0.64402	D	0.000019	D	0.82356	0.5019	N	0.24115	0.695	0.50039	D	0.999844	D;D	0.89917	1.0;1.0	D;D	0.77004	0.982;0.989	D	0.84372	0.0544	10	0.72032	D	0.01	-8.6597	19.8253	0.96616	0.0:1.0:0.0:0.0	.	968;918	Q6IMN6;Q6IMN6-2	CAPR2_HUMAN;.	H	918;968;634	ENSP00000298892:R918H;ENSP00000251071:R968H;ENSP00000309785:R634H	ENSP00000251071:R968H	R	-	2	0	CAPRIN2	30754584	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	6.055000	0.71103	2.682000	0.91365	0.655000	0.94253	CGT	.	.		0.522	CAPRIN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402778.1	NM_023925		T	30863317	C	T	30863317	3	4	23	1	0	0	0	0	1	0	0	0	2638	536	19	1	484	1	CAPRIN2	12	30863317	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	4587728	30863317	102988578	697	2763										
FGD4	121512	hgsc.bcm.edu	37	chr12	32793225	32793225	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttaggacgtcagagcccagGccaccattccacttctgggc	10	14	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:32793225G>A	ENST00000427716.2	+	17	2483	c.2059G>A	c.(2059-2061)Gcc>Acc	p.A687T	FGD4_ENST00000534526.2_Missense_Mutation_p.A824T|FGD4_ENST00000531134.1_Missense_Mutation_p.A772T|FGD4_ENST00000525053.1_Missense_Mutation_p.A799T|FGD4_ENST00000546442.1_Missense_Mutation_p.A594T	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	687	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					CAGAGCCCAGGCCACCATTCC	0.488																																					p.A687T		Atlas-SNP	.											.	FGD4	86	.	0			c.G2059A						.						136	131	133					12																	32793225		2203	4300	6503	SO:0001583	missense	121512	exon17			GCCCAGGCCACCA	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.2059G>A	chr12.hg19:g.32793225G>A	ENSP00000394487:p.Ala687Thr	136.0	0.0		111.0	41.0	NM_139241	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	hg19	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	G	8.819	0.937095	0.18206	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000427716;ENST00000546442;ENST00000525053	T;T;T;T;T	0.12774	2.65;2.65;2.65;2.65;2.65	5.31	4.38	0.52667	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.124137	0.36066	N	0.002809	T	0.11580	0.0282	L	0.38838	1.175	0.80722	D	1	B;B;B	0.14012	0.002;0.001;0.009	B;B;B	0.15484	0.013;0.013;0.011	T	0.09122	-1.0689	10	0.22109	T	0.4	-5.6503	12.5212	0.56060	0.0856:0.0:0.9144:0.0	.	799;772;687	E9PJX4;B7Z493;Q96M96	.;.;FGD4_HUMAN	T	824;772;687;594;799	ENSP00000449273:A824T;ENSP00000431323:A772T;ENSP00000394487:A687T;ENSP00000446695:A594T;ENSP00000433666:A799T	ENSP00000394487:A687T	A	+	1	0	FGD4	32684492	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	3.838000	0.55828	1.143000	0.42306	0.563000	0.77884	GCC	.	.		0.488	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		A	32793225	G	A	32793225	3	1	23	1	0	0	0	0	1	0	0	0	5843	1203	42	3	2117	3	FGD4	12	32793225	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1929908	32793225	101058670	698	2764										
SLC2A13	114134	hgsc.bcm.edu	37	chr12	40441899	40441899	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaaggctccatcaacaacacTtgcaaagaactgccctcctg	7	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:40441899T>G	ENST00000280871.4	-	2	720	c.670A>C	c.(670-672)Agt>Cgt	p.S224R	SLC2A13_ENST00000380858.1_Missense_Mutation_p.S224R	NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	224					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				TCAACAACACTTGCAAAGAAC	0.428										HNSCC(50;0.14)																											p.S224R		Atlas-SNP	.											.	SLC2A13	91	.	0			c.A670C						.						169	160	163					12																	40441899		2203	4300	6503	SO:0001583	missense	114134	exon2			CAACACTTGCAAA	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.670A>C	chr12.hg19:g.40441899T>G	ENSP00000280871:p.Ser224Arg	129.0	0.0		86.0	43.0	NM_052885	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	hg19	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	T	18.65	3.669579	0.67814	.	.	ENSG00000151229	ENST00000280871;ENST00000380858	T;T	0.59638	0.25;0.25	5.65	5.65	0.86999	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.080853	0.85682	D	0.000000	T	0.70141	0.3190	M	0.83774	2.66	0.48288	D	0.99962	P;D	0.57257	0.84;0.979	P;P	0.54590	0.673;0.756	T	0.74355	-0.3692	10	0.54805	T	0.06	-27.107	10.2561	0.43399	0.0:0.0735:0.0:0.9265	.	224;224	Q96QE2;E9PE47	MYCT_HUMAN;.	R	224	ENSP00000280871:S224R;ENSP00000370239:S224R	ENSP00000280871:S224R	S	-	1	0	SLC2A13	38728166	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	5.820000	0.69250	2.156000	0.67533	0.533000	0.62120	AGT	.	.		0.428	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			G	40441899	T	G	40441899	3	3	23	1	0	0	0	0	1	0	0	0	14557	1609	56	5	1312	5	SLC2A13	12	40441899	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	7648674	40441899	93409996	699	2765										
IRAK4	51135	hgsc.bcm.edu	37	chr12	44161948	44161948	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	taacaccatcaacatatgtgCgctgcctcaatgttggacta	7	11	2	0	rs377584435		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:44161948C>T	ENST00000448290.2	+	2	105	c.34C>T	c.(34-36)Cgc>Tgc	p.R12C	IRAK4_ENST00000551736.1_Missense_Mutation_p.R12C|IRAK4_ENST00000440781.2_Intron|IRAK4_ENST00000431837.1_5'UTR	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	12					cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		AACATATGTGCGCTGCCTCAA	0.343																																					p.R12C		Atlas-SNP	.											IRAK4_ENST00000448290,caecum,carcinoma,0,5	IRAK4	77	.	0			c.C34T						.	C	CYS/ARG,,,,CYS/ARG	0,4406		0,0,2203	78	77	77		34,,,,34	4.6	1	12		77	1,8599	1.2+/-3.3	0,1,4299	no	missense,utr-5,utr-5,intron,missense	IRAK4	NM_001114182.2,NM_001145256.1,NM_001145257.1,NM_001145258.1,NM_016123.3	180,,,,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,,,,probably-damaging	12/461,,,,12/461	44161948	1,13005	2203	4300	6503	SO:0001583	missense	51135	exon2			TATGTGCGCTGCC	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		ENST00000448290.2:c.34C>T	chr12.hg19:g.44161948C>T	ENSP00000390651:p.Arg12Cys	213.0	0.0		219.0	38.0	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	hg19	CCDS8744.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.250977	0.80135	0.0	1.16E-4	ENSG00000198001	ENST00000550616;ENST00000448290;ENST00000551736;ENST00000356669	T;T;T	0.78003	-1.14;-1.14;-1.14	5.5	4.56	0.56223	DEATH-like (2);	0.000000	0.85682	D	0.000000	D	0.87669	0.6235	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88359	0.2986	10	0.59425	D	0.04	-10.9971	15.9279	0.79635	0.1352:0.8648:0.0:0.0	.	12	Q9NWZ3	IRAK4_HUMAN	C	12	ENSP00000446571:R12C;ENSP00000390651:R12C;ENSP00000446490:R12C	ENSP00000349096:R12C	R	+	1	0	IRAK4	42448215	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	3.230000	0.51286	2.751000	0.94390	0.650000	0.86243	CGC	.	.		0.343	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1			T	44161948	C	T	44161948	3	4	23	1	0	0	0	0	1	0	0	0	7834	768	27	1	36	1	IRAK4	12	44161948	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3720049	44161948	89689947	700	2766										
ANO6	196527	hgsc.bcm.edu	37	chr12	45725118	45725118	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgactccctcttttttaatgAtggccagcgaagaattgact	8	9	1	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:45725118A>T	ENST00000320560.8	+	3	393	c.191A>T	c.(190-192)gAt>gTt	p.D64V	ANO6_ENST00000425752.2_Missense_Mutation_p.D64V|ANO6_ENST00000435642.1_Missense_Mutation_p.D64V|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000441606.2_Missense_Mutation_p.D46V|ANO6_ENST00000423947.3_Missense_Mutation_p.D85V	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	64					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						TTTTTTAATGATGGCCAGCGA	0.294																																					p.D85V		Atlas-SNP	.											.	ANO6	163	.	0			c.A254T						.						67	71	70					12																	45725118		2203	4298	6501	SO:0001583	missense	196527	exon4			TTAATGATGGCCA	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.191A>T	chr12.hg19:g.45725118A>T	ENSP00000320087:p.Asp64Val	565.0	0.0		527.0	218.0	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202517	0.79127	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	D	0.85461	0.5702	M	0.92412	3.305	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.996;0.997;0.997	D	0.89046	0.3452	10	0.87932	D	0	.	14.69	0.69080	1.0:0.0:0.0:0.0	.	46;85;64;64	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	V	64;85;64;64;46	ENSP00000391417:D64V;ENSP00000409126:D85V;ENSP00000413840:D64V;ENSP00000320087:D64V;ENSP00000413137:D46V	ENSP00000320087:D64V	D	+	2	0	ANO6	44011385	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.235000	0.78143	2.254000	0.74563	0.482000	0.46254	GAT	.	.		0.294	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743		T	45725118	A	T	45725118	3	4	23	1	0	0	0	0	1	0	0	0	701	333	12	4	221	4	ANO6	12	45725118	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1563170	45725118	88126777	701	2767										
SLC38A2	54407	hgsc.bcm.edu	37	chr12	46760702	46760702	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caccaaaggcaactcatattTcactatgaagaggtagcttg	8	9	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:46760702T>C	ENST00000256689.5	-	7	952	c.508A>G	c.(508-510)Aaa>Gaa	p.K170E	SLC38A2_ENST00000547252.1_5'UTR|SLC38A2_ENST00000551374.1_5'Flank	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	170					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		AACTCATATTTCACTATGAAG	0.383																																					p.K170E	Ovarian(9;448 492 8335 28722 40361)	Atlas-SNP	.											.	SLC38A2	36	.	0			c.A508G						.						87	83	85					12																	46760702		2203	4300	6503	SO:0001583	missense	54407	exon7			CATATTTCACTAT	AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"Solute carriers"	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.508A>G	chr12.hg19:g.46760702T>C	ENSP00000256689:p.Lys170Glu	72.0	0.0		85.0	34.0	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Missense_Mutation	SNP	ENST00000256689.5	hg19	CCDS8749.1	.	.	.	.	.	.	.	.	.	.	T	34	5.349087	0.95830	.	.	ENSG00000134294	ENST00000256689	T	0.02323	4.34	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.22166	0.0534	M	0.92026	3.265	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.02004	-1.1231	10	0.72032	D	0.01	-15.3943	16.8222	0.85835	0.0:0.0:0.0:1.0	.	70;170	Q96QD8-2;Q96QD8	.;S38A2_HUMAN	E	170	ENSP00000256689:K170E	ENSP00000256689:K170E	K	-	1	0	SLC38A2	45046969	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	AAA	.	.		0.383	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1			C	46760702	T	C	46760702	3	2	23	1	0	0	0	0	1	0	0	0	14619	1792	62	2	1052	2	SLC38A2	12	46760702	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1035584	46760702	87091193	702	2768										
MLL2	8085	hgsc.bcm.edu	37	chr12	49427950	49427950	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggccagcttttttggcagtgCgctgcttggcacacagagcc	13	12	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:49427950C>T	ENST00000301067.7	-	38	10639	c.10640G>A	c.(10639-10641)cGc>cAc	p.R3547H	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3547	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R3547H(1)|p.R3277H(1)									TTTGGCAGTGCGCTGCTTGGC	0.542																																					p.R3547H		Atlas-SNP	.											MLL2_ENST00000301067,NS,carcinoma,0,4	MLL2	1173	.	2	Substitution - Missense(2)	prostate(2)	c.G10640A						.						83	81	82					12																	49427950		2023	4198	6221	SO:0001583	missense	8085	exon38			GCAGTGCGCTGCT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.10640G>A	chr12.hg19:g.49427950C>T	ENSP00000301067:p.Arg3547His	63.0	0.0		47.0	24.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.508596	0.44660	.	.	ENSG00000167548	ENST00000301067	T	0.43688	0.94	5.38	5.38	0.77491	.	0.000000	0.36893	N	0.002344	T	0.62048	0.2396	L	0.54323	1.7	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.63355	-0.6656	10	0.87932	D	0	.	18.2915	0.90131	0.0:1.0:0.0:0.0	.	3547	O14686	MLL2_HUMAN	H	3547	ENSP00000301067:R3547H	ENSP00000301067:R3547H	R	-	2	0	MLL2	47714217	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.818000	0.86416	2.711000	0.92665	0.563000	0.77884	CGC	.	.		0.542	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49427950	C	T	49427950	3	4	23	1	0	0	0	0	1	0	0	0	9630	768	27	1	6041	1	MLL2	12	49427950	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2667248	49427950	84423945	703	2769										
AQP6	363	hgsc.bcm.edu	37	chr12	50367033	50367033	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttggaaagccatcagcagggCgctgtttgcagagttcctgg	14	9	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:50367033C>T	ENST00000315520.5	+	1	414	c.77C>T	c.(76-78)gCg>gTg	p.A26V	AQP6_ENST00000551733.1_Intron	NM_001652.3	NP_001643.2	Q13520	AQP6_HUMAN	aquaporin 6, kidney specific	26					anion transport (GO:0006820)|excretion (GO:0007588)|odontogenesis (GO:0042476)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	integral component of plasma membrane (GO:0005887)|transport vesicle membrane (GO:0030658)	anion channel activity (GO:0005253)|water channel activity (GO:0015250)			endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(2)	13						ATCAGCAGGGCGCTGTTTGCA	0.617																																					p.A26V		Atlas-SNP	.											.	AQP6	25	.	0			c.C77T						.						138	118	125					12																	50367033		2203	4300	6503	SO:0001583	missense	363	exon1			GCAGGGCGCTGTT	AL137716	CCDS31798.1	12q13	2005-09-20			ENSG00000086159	ENSG00000086159		"Ion channels / Aquaporins"	639	protein-coding gene	gene with protein product		601383		AQP2L		8812490	Standard	XM_006719375		Approved		uc001rvr.1	Q13520	OTTHUMG00000133548	ENST00000315520.5:c.77C>T	chr12.hg19:g.50367033C>T	ENSP00000320247:p.Ala26Val	91.0	0.0		51.0	13.0	NM_001652		Missense_Mutation	SNP	ENST00000315520.5	hg19	CCDS31798.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.251172	0.80135	.	.	ENSG00000086159	ENST00000315520	D	0.86769	-2.17	5.37	4.48	0.54585	Aquaporin-like (2);	0.101360	0.39909	N	0.001228	D	0.94251	0.8154	M	0.92459	3.31	0.50039	D	0.999841	D	0.89917	1.0	D	0.67103	0.949	D	0.95201	0.8317	10	0.87932	D	0	-21.477	13.1013	0.59222	0.1608:0.8392:0.0:0.0	.	26	Q13520	AQP6_HUMAN	V	26	ENSP00000320247:A26V	ENSP00000320247:A26V	A	+	2	0	AQP6	48653300	0.760000	0.28428	0.362000	0.25862	0.707000	0.40811	0.875000	0.28079	1.412000	0.46977	0.561000	0.74099	GCG	.	.		0.617	AQP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257528.2	NM_001652, NM_053286		T	50367033	C	T	50367033	3	4	23	1	0	0	0	0	1	0	0	0	830	768	27	1	79	1	AQP6	12	50367033	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	939083	50367033	83484862	704	2770										
AQP6	363	hgsc.bcm.edu	37	chr12	50368266	50368266	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cactgggccacctcattgggGtaaggaacagaggggacacc	14	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:50368266G>T	ENST00000315520.5	+	2	898		c.e2+1		AQP6_ENST00000551733.1_Splice_Site	NM_001652.3	NP_001643.2	Q13520	AQP6_HUMAN	aquaporin 6, kidney specific						anion transport (GO:0006820)|excretion (GO:0007588)|odontogenesis (GO:0042476)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	integral component of plasma membrane (GO:0005887)|transport vesicle membrane (GO:0030658)	anion channel activity (GO:0005253)|water channel activity (GO:0015250)			endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(2)	13						CCTCATTGGGGTAAGGAACAG	0.637											OREG0021809	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	AQP6	25	.	0			c.561+1G>T						.						61	50	53					12																	50368266		2203	4300	6503	SO:0001630	splice_region_variant	363	exon2			ATTGGGGTAAGGA	AL137716	CCDS31798.1	12q13	2005-09-20			ENSG00000086159	ENSG00000086159		"Ion channels / Aquaporins"	639	protein-coding gene	gene with protein product		601383		AQP2L		8812490	Standard	XM_006719375		Approved		uc001rvr.1	Q13520	OTTHUMG00000133548	ENST00000315520.5:c.561+1G>T	chr12.hg19:g.50368266G>T		46.0	0.0	969	46.0	24.0	NM_001652		Splice_Site	SNP	ENST00000315520.5	hg19	CCDS31798.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.819608	0.71028	.	.	ENSG00000086159	ENST00000551733;ENST00000315520	.	.	.	4.18	4.18	0.49190	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8902	0.63733	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AQP6	48654533	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.162000	0.77515	2.344000	0.79699	0.491000	0.48974	.	.	.		0.637	AQP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257528.2	NM_001652, NM_053286	Intron	T	50368266	G	T	50368266	5	4	23	1	0	0	0	0	0	0	1	0	830	1275	44	3	568	3	AQP6	12	50368266	Splice_Site	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1233	50368266	83483629	705	2771										
LASS5	91012	hgsc.bcm.edu	37	chr12	50537820	50537820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctcgatgccaatacagagtGcacagggtttggcaataaat	10	9	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:50537820G>A	ENST00000317551.6	-	2	342	c.218C>T	c.(217-219)gCa>gTa	p.A73V	CERS5_ENST00000422340.2_Missense_Mutation_p.A15V	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	73					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AATACAGAGTGCACAGGGTTT	0.378																																					p.A73V		Atlas-SNP	.											.	.	.	.	0			c.C218T						.						119	117	118					12																	50537820		2203	4300	6503	SO:0001583	missense	91012	exon2			CAGAGTGCACAGG		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"Homeoboxes / CERS class"	23749	protein-coding gene	gene with protein product		615335	"LAG1 longevity assurance homolog 5 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 5"	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.218C>T	chr12.hg19:g.50537820G>A	ENSP00000325485:p.Ala73Val	60.0	0.0		76.0	11.0	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	hg19	CCDS8801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.7|23.7	4.446218|4.446218	0.84101|0.84101	.|.	.|.	ENSG00000139624|ENSG00000139624	ENST00000317551;ENST00000422340|ENST00000547800	T;T|.	0.22336|.	1.96;2.48|.	4.0|4.0	3.11|3.11	0.35812|0.35812	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73931|0.73931	0.3650|0.3650	M|M	0.79805|0.79805	2.47|2.47	0.58432|0.58432	D|D	0.999999|0.999999	D;P|.	0.71674|.	0.998;0.787|.	D;B|.	0.66847|.	0.947;0.271|.	T|T	0.75858|0.75858	-0.3169|-0.3169	10|5	0.66056|.	D|.	0.02|.	-7.0865|-7.0865	12.6364|12.6364	0.56685|0.56685	0.0826:0.0:0.9174:0.0|0.0826:0.0:0.9174:0.0	.|.	15;73|.	B4DV54;Q8N5B7|.	.;CERS5_HUMAN|.	V|Y	73;15|8	ENSP00000325485:A73V;ENSP00000389050:A15V|.	ENSP00000325485:A73V|.	A|H	-|-	2|1	0|0	CERS5|CERS5	48824087|48824087	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.856000|0.856000	0.48823|0.48823	9.046000|9.046000	0.93817|0.93817	1.271000|1.271000	0.44313|0.44313	-0.140000|-0.140000	0.14226|0.14226	GCA|CAC	.	.		0.378	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190		A	50537820	G	A	50537820	3	1	23	1	0	0	0	0	1	0	0	0	8651	1319	46	3	996	3	LASS5	12	50537820	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	169554	50537820	83314075	706	2772										
TFCP2	7024	hgsc.bcm.edu	37	chr12	51512404	51512404	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgaatgaggaagcatctaacCttgattgagatacgttaggg	12	5	1	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:51512404C>A	ENST00000257915.5	-	2	732	c.274G>T	c.(274-276)Gga>Tga	p.G92*	TFCP2_ENST00000549867.1_Splice_Site_p.G92*|TFCP2_ENST00000548115.1_Splice_Site_p.G92*|TFCP2_ENST00000307660.4_Splice_Site_p.G92*	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	92				G -> A (in Ref. 1; M84810/AA sequence). {ECO:0000305}.	regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						AGCATCTAACCTTGATTGAGA	0.393																																					p.G92X		Atlas-SNP	.											.	TFCP2	49	.	0			c.G274T						.						160	148	152					12																	51512404		2203	4300	6503	SO:0001630	splice_region_variant	7024	exon2			TCTAACCTTGATT	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.274+1G>T	chr12.hg19:g.51512404C>A		100.0	0.0		89.0	16.0	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Nonsense_Mutation	SNP	ENST00000257915.5	hg19	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	C	40	8.060487	0.98635	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000549867;ENST00000548115	.	.	.	5.51	4.62	0.57501	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.4074	13.7046	0.62631	0.0:0.9239:0.0:0.0761	.	.	.	.	X	92	.	.	G	-	1	0	TFCP2	49798671	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	7.731000	0.84895	1.472000	0.48140	0.591000	0.81541	GGA	.	.		0.393	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653	Nonsense_Mutation	A	51512404	C	A	51512404	5	1	23	1	0	0	0	0	0	0	1	0	15810	695	24	3	1290	3	TFCP2	12	51512404	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	974584	51512404	82339491	707	2773										
SMAGP	57228	hgsc.bcm.edu	37	chr12	51663059	51663059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggagtagtcaggaggctggTcattgtcactagtggttgag	16	5	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:51663059T>C	ENST00000603798.1	-	2	676	c.4A>G	c.(4-6)Acc>Gcc	p.T2A	SMAGP_ENST00000604188.1_Missense_Mutation_p.T2A|SMAGP_ENST00000603864.1_Missense_Mutation_p.T2A|SMAGP_ENST00000605627.1_5'UTR|SMAGP_ENST00000398453.3_Missense_Mutation_p.T2A|DAZAP2_ENST00000604900.1_Intron|SMAGP_ENST00000603838.1_Missense_Mutation_p.T2A	NM_001031628.1	NP_001026798.1	Q0VAQ4	SMAGP_HUMAN	small cell adhesion glycoprotein	2						cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)											AGGAGGCTGGTCATTGTCACT	0.517																																					p.T2A		Atlas-SNP	.											.	SMAGP	7	.	0			c.A4G						.						128	131	130					12																	51663059		1944	4151	6095	SO:0001583	missense	57228	exon2			GGCTGGTCATTGT		CCDS44889.1	12q13.13	2010-02-17			ENSG00000170545	ENSG00000170545			26918	protein-coding gene	gene with protein product	"small trans-membrane and glycosylated protein"					15021913	Standard	NM_001031628		Approved	MGC149453, MGC149454, hSMAGP	uc001rye.1	Q0VAQ4		ENST00000603798.1:c.4A>G	chr12.hg19:g.51663059T>C	ENSP00000475068:p.Thr2Ala	104.0	0.0		96.0	35.0	NM_001031628	A6NIL5	Missense_Mutation	SNP	ENST00000603798.1	hg19	CCDS44889.1	.	.	.	.	.	.	.	.	.	.	T	4.081	0.012870	0.07912	.	.	ENSG00000170545	ENST00000380103;ENST00000398453	T	0.40476	1.03	4.38	-0.912	0.10504	.	0.613383	0.11234	U	0.585315	T	0.25121	0.0610	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.18999	-1.0319	9	0.46703	T	0.11	-23.8773	3.2584	0.06840	0.1805:0.3326:0.0:0.4869	.	2	Q0VAQ4	SMAGP_HUMAN	A	2	ENSP00000381471:T2A	ENSP00000369446:T2A	T	-	1	0	SMAGP	49949326	0.625000	0.27111	0.112000	0.21494	0.103000	0.19146	-0.009000	0.12765	-0.144000	0.11314	-0.408000	0.06270	ACC	.	.		0.517	SMAGP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469789.1	NM_020467		C	51663059	T	C	51663059	3	2	23	1	0	0	0	0	1	0	0	0	14780	1667	58	2	301	2	SMAGP	12	51663059	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	150655	51663059	82188836	708	2774										
NR4A1	3164	hgsc.bcm.edu	37	chr12	52448156	52448156	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgggacaccagcaccgagtcCgggaccccgtgaccacctgg	13	16	0	1	rs375396767		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:52448156C>T	ENST00000243050.1	+	3	358	c.44C>T	c.(43-45)cCg>cTg	p.P15L	NR4A1_ENST00000360284.3_Missense_Mutation_p.P28L|NR4A1_ENST00000550082.1_Missense_Mutation_p.P28L|NR4A1_ENST00000547206.1_3'UTR|NR4A1_ENST00000545748.1_Missense_Mutation_p.P69L|NR4A1_ENST00000394824.2_Missense_Mutation_p.P15L|NR4A1_ENST00000548232.1_Missense_Mutation_p.P15L|NR4A1_ENST00000394825.1_Missense_Mutation_p.P15L	NM_002135.4	NP_002126.2	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	15					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell chemotaxis (GO:0035767)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)	16				BRCA - Breast invasive adenocarcinoma(357;0.0967)		GCACCGAGTCCGGGACCCCGT	0.642																																					p.P28L		Atlas-SNP	.											.	NR4A1	77	.	0			c.C83T						.						52	49	50					12																	52448156		2203	4300	6503	SO:0001583	missense	3164	exon3			CGAGTCCGGGACC	L13740	CCDS8818.1, CCDS55828.1, CCDS73471.1	12q13	2013-01-16			ENSG00000123358	ENSG00000123358		"Nuclear hormone receptors"	7980	protein-coding gene	gene with protein product		139139		HMR, GFRP1		2626032	Standard	NM_002135		Approved	TR3, N10, NAK-1, NGFIB, NUR77	uc001rzt.3	P22736	OTTHUMG00000150393	ENST00000243050.1:c.44C>T	chr12.hg19:g.52448156C>T	ENSP00000243050:p.Pro15Leu	61.0	0.0		72.0	12.0	NM_001202233	B4DML7|Q15627|Q53Y00|Q6IBU8	Missense_Mutation	SNP	ENST00000243050.1	hg19	CCDS8818.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638295	0.47153	.	.	ENSG00000123358	ENST00000360284;ENST00000545748;ENST00000550082;ENST00000243050;ENST00000394825;ENST00000550763;ENST00000394824;ENST00000548232	D;D;D;D;D;T;D;D	0.92699	-3.02;-3.05;-3.02;-3.02;-3.02;0.86;-3.02;-3.09	4.43	4.43	0.53597	.	1.044700	0.07454	N	0.899528	D	0.87653	0.6231	N	0.14661	0.345	0.51012	D	0.999903	P;P;D	0.58620	0.645;0.856;0.983	B;B;P	0.45119	0.089;0.081;0.47	D	0.83674	0.0168	10	0.87932	D	0	.	12.7862	0.57507	0.0:0.8337:0.1663:0.0	.	28;15;15	B4DML7;P22736;Q15627	.;NR4A1_HUMAN;.	L	28;69;28;15;15;15;15;15	ENSP00000353427:P28L;ENSP00000440864:P69L;ENSP00000449539:P28L;ENSP00000243050:P15L;ENSP00000378302:P15L;ENSP00000449858:P15L;ENSP00000378301:P15L;ENSP00000449587:P15L	ENSP00000243050:P15L	P	+	2	0	NR4A1	50734423	0.001000	0.12720	1.000000	0.80357	0.619000	0.37552	1.330000	0.33781	2.451000	0.82905	0.561000	0.74099	CCG	.	.		0.642	NR4A1-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317922.2			T	52448156	C	T	52448156	3	4	23	1	0	0	0	0	1	0	0	0	10641	652	23	1	46	1	NR4A1	12	52448156	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	785097	52448156	81403739	709	2775										
KRT82	3888	hgsc.bcm.edu	37	chr12	52799999	52799999	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	accatccggggcatgacagcCgagtatgagctgaaactctg	12	11	1	3	rs558524531		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:52799999C>T	ENST00000257974.2	-	1	140	c.63G>A	c.(61-63)tcG>tcA	p.S21S	RP11-1020M18.10_ENST00000548135.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	21	Head.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		GCATGACAGCCGAGTATGAGC	0.632													C|||	1	0.000199681	8e-04	0	5008	,	,		18226	0		0	False		,,,				2504	0				p.S21S		Atlas-SNP	.											.	KRT82	45	.	0			c.G63A						.						36	32	33					12																	52799999		2202	4298	6500	SO:0001819	synonymous_variant	3888	exon1			GACAGCCGAGTAT	Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"-", "Intermediate filaments type II, keratins (basic)"	6459	protein-coding gene	gene with protein product	"hard keratin type II 2"	601078	"keratin, hair, basic, 2"	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.63G>A	chr12.hg19:g.52799999C>T		53.0	0.0		73.0	5.0	NM_033033		Silent	SNP	ENST00000257974.2	hg19	CCDS8826.1																																																																																			.	.		0.632	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033		T	52799999	C	T	52799999	2	4	23	1	0	0	0	0	0	0	0	1	8505	639	23	1		1	KRT82	12	52799999	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	351843	52799999	81051896	710	2776										
KRT2	3849	hgsc.bcm.edu	37	chr12	53041638	53041638	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagtcacctggagctcctcaTactgatatggggagaagagg	13	9	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:53041638T>C	ENST00000309680.3	-	6	1145	c.1124A>G	c.(1123-1125)tAt>tGt	p.Y375C		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	375	Coil 2.|Rod.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		GAGCTCCTCATACTGATATGG	0.547																																					p.Y375C		Atlas-SNP	.											.	KRT2	94	.	0			c.A1124G						.						62	52	55					12																	53041638		2203	4300	6503	SO:0001630	splice_region_variant	3849	exon6			TCCTCATACTGAT		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.1123-1A>G	chr12.hg19:g.53041638T>C		62.0	0.0		70.0	31.0	NM_000423	Q4VAQ2	Missense_Mutation	SNP	ENST00000309680.3	hg19	CCDS8835.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.154708	0.57259	.	.	ENSG00000172867	ENST00000309680	T	0.75367	-0.93	5.03	5.03	0.67393	Filament (1);	.	.	.	.	D	0.84419	0.5468	M	0.72894	2.215	0.47737	D	0.999509	D	0.89917	1.0	D	0.79108	0.992	D	0.84191	0.0445	9	0.38643	T	0.18	.	15.0736	0.72059	0.0:0.0:0.0:1.0	.	375	P35908	K22E_HUMAN	C	375	ENSP00000310861:Y375C	ENSP00000310861:Y375C	Y	-	2	0	KRT2	51327905	0.584000	0.26766	1.000000	0.80357	0.351000	0.29236	0.855000	0.27805	2.046000	0.60703	0.455000	0.32223	TAT	.	.		0.547	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423	Missense_Mutation	C	53041638	T	C	53041638	5	2	23	1	0	0	0	0	0	0	1	0	8466	1420	49	2	811	2	KRT2	12	53041638	Splice_Site	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	241639	53041638	80810257	711	2777										
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56575357	56575357	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtttccccccttcttgtcccGtcgatctgaatctgggctgt	9	14	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:56575357G>A	ENST00000267064.4	-	10	951	c.865C>T	c.(865-867)Cgg>Tgg	p.R289W	SMARCC2_ENST00000550164.1_Missense_Mutation_p.R289W|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000550859.1_5'Flank|SMARCC2_ENST00000394023.3_Missense_Mutation_p.R289W|SMARCC2_ENST00000347471.4_Missense_Mutation_p.R289W	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	289					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			TTCTTGTCCCGTCGATCTGAA	0.483																																					p.R289W		Atlas-SNP	.											.	SMARCC2	212	.	0			c.C865T						.						97	96	97					12																	56575357		2203	4300	6503	SO:0001583	missense	6601	exon10			TGTCCCGTCGATC	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.865C>T	chr12.hg19:g.56575357G>A	ENSP00000267064:p.Arg289Trp	156.0	0.0		119.0	46.0	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.306806	0.60305	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T	0.48836	0.83;0.84;0.8	4.19	2.31	0.28768	.	0.000000	0.85682	D	0.000000	T	0.63307	0.2500	M	0.66939	2.045	0.38593	D	0.950475	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.76575	0.973;0.988;0.973;0.973;0.988	T	0.68221	-0.5466	10	0.87932	D	0	-12.6371	11.4917	0.50385	0.0:0.0:0.5333:0.4667	.	178;289;294;289;289	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	W	289	ENSP00000449396:R289W;ENSP00000302919:R289W;ENSP00000267064:R289W	ENSP00000267064:R289W	R	-	1	2	SMARCC2	54861624	0.995000	0.38212	1.000000	0.80357	0.992000	0.81027	1.236000	0.32683	0.680000	0.31366	-0.314000	0.08810	CGG	.	.		0.483	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			A	56575357	G	A	56575357	3	1	23	1	0	0	0	0	1	0	0	0	14791	1144	40	1	2952	1	SMARCC2	12	56575357	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3533719	56575357	77276538	712	2778										
IL23A	51561	hgsc.bcm.edu	37	chr12	56733288	56733288	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagatggctgtgacccccaaGgactcagggacaacagtcag	13	11	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:56733288G>T	ENST00000228534.4	+	2	407	c.241G>T	c.(241-243)Gga>Tga	p.G81*	STAT2_ENST00000556539.1_5'Flank	NM_016584.2	NP_057668.1	Q9NPF7	IL23A_HUMAN	interleukin 23, alpha subunit p19	81					defense response to Gram-negative bacterium (GO:0050829)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|T cell proliferation (GO:0042098)|tissue remodeling (GO:0048771)	interleukin-23 complex (GO:0070743)				kidney(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	5						TGACCCCCAAGGACTCAGGGA	0.512																																					p.G81X		Atlas-SNP	.											IL23A,NS,carcinoma,0,1	IL23A	12	.	0			c.G241T						.						87	74	78					12																	56733288		2203	4300	6503	SO:0001587	stop_gained	51561	exon2			CCCCAAGGACTCA	AB030000	CCDS8916.1	12q13.13	2011-07-15				ENSG00000110944		"Interleukins and interleukin receptors"	15488	protein-coding gene	gene with protein product	"interleukin-six, G-CSF related factor"	605580				11114383	Standard	NM_016584		Approved	SGRF, IL23P19, IL-23, IL-23A, P19	uc001sla.3	Q9NPF7		ENST00000228534.4:c.241G>T	chr12.hg19:g.56733288G>T	ENSP00000228534:p.Gly81*	119.0	1.0		103.0	29.0	NM_016584	Q6NZ80|Q6NZ82|Q9H2A5	Nonsense_Mutation	SNP	ENST00000228534.4	hg19	CCDS8916.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.765175	0.90020	.	.	ENSG00000110944	ENST00000228534	.	.	.	5.73	4.83	0.62350	.	0.000000	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-10.6862	11.2915	0.49252	0.0878:0.0:0.9122:0.0	.	.	.	.	X	81	.	ENSP00000228534:G81X	G	+	1	0	IL23A	55019555	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.243000	0.51392	2.882000	0.98803	0.655000	0.94253	GGA	.	.		0.512	IL23A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_016584		T	56733288	G	T	56733288	4	4	23	1	0	0	0	0	0	1	0	0	7684	1001	35	3	247	3	IL23A	12	56733288	Nonsense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	157931	56733288	77118607	713	2779										
APOF	319	hgsc.bcm.edu	37	chr12	56755672	56755672	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cggtagagctgtagctgtagAgcccaaacatcagcctgaca	11	11	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:56755672A>C	ENST00000398189.3	-	2	395	c.318T>G	c.(316-318)gcT>gcG	p.A106A	STAT2_ENST00000314128.4_5'Flank|STAT2_ENST00000418572.2_5'Flank|STAT2_ENST00000557235.1_5'Flank|APOF_ENST00000541105.1_Silent_p.A88A	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	106					cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|high-density lipoprotein particle (GO:0034364)|low-density lipoprotein particle (GO:0034362)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)|receptor binding (GO:0005102)			breast(1)|lung(3)|prostate(1)|stomach(1)	6						GTAGCTGTAGAGCCCAAACAT	0.557																																					p.A106A		Atlas-SNP	.											.	APOF	13	.	0			c.T318G						.						62	63	63					12																	56755672		2090	4242	6332	SO:0001819	synonymous_variant	319	exon2			CTGTAGAGCCCAA	L27050	CCDS44923.1	12q13	2013-01-24				ENSG00000175336		"Apolipoproteins"	615	protein-coding gene	gene with protein product		107760				8093033	Standard	NM_001638		Approved		uc001sle.1	Q13790		ENST00000398189.3:c.318T>G	chr12.hg19:g.56755672A>C		149.0	0.0		133.0	9.0	NM_001638	Q8TC13	Silent	SNP	ENST00000398189.3	hg19	CCDS44923.1																																																																																			.	.		0.557	APOF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410076.1			C	56755672	A	C	56755672	2	2	23	1	0	0	0	0	0	0	0	1	803	291	11	5		5	APOF	12	56755672	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	22384	56755672	77096223	714	2780										
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56814391	56814391	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccgaacccctagcttgcgcaAcagctgctgaaactgttcgt	9	14	0	1	rs267603583		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:56814391A>G	ENST00000553532.1	-	26	3340	c.3190T>C	c.(3190-3192)Ttg>Ctg	p.L1064L	TIMELESS_ENST00000229201.4_Silent_p.L1063L|TIMELESS_ENST00000554616.1_Silent_p.L561L					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						AGCTTGCGCAACAGCTGCTGA	0.512																																					p.L1064L		Atlas-SNP	.											.	TIMELESS	107	.	0			c.T3190C						.						133	110	117					12																	56814391		2203	4300	6503	SO:0001819	synonymous_variant	8914	exon26			TGCGCAACAGCTG	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1"	603887	"timeless (Drosophila) homolog", "timeless homolog (Drosophila)"			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.3190T>C	chr12.hg19:g.56814391A>G		112.0	0.0		107.0	46.0	NM_003920		Silent	SNP	ENST00000553532.1	hg19	CCDS8918.1																																																																																			.	.		0.512	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		G	56814391	A	G	56814391	2	3	23	1	0	0	0	0	0	0	0	1	15919	40	2	2		2	TIMELESS	12	56814391	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	58719	56814391	77037504	715	2781										
LRP1	4035	hgsc.bcm.edu	37	chr12	57556223	57556223	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aacggggtgtaggaggcgcaCcccccactgtgacccttctg					rs34108076		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:57556223delC	ENST00000243077.3	+	14	2792	c.2326delC	c.(2326-2328)cccfs	p.P777fs		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	777					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	AGGAGGCGCACCCCCCACTGT	0.607																																					p.A775fs		Atlas-Indel,Pindel	.											.	LRP1	428	.	0			c.2325delA						.						150	122	132					12																	57556223		2203	4300	6503	SO:0001589	frameshift_variant	4035	exon14			.	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.2326delC	chr12.hg19:g.57556223delC	ENSP00000243077:p.Pro777fs	72.0	0.0		68.0	28.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Frame_Shift_Del	DEL	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.607	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		-	57556223	C	-	57556223	7	5	23	1	0	1	0	1	0	0	0	0	8960	507	18	0	2380	0	LRP1	12	57556223	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	741832	57556223	76295672	716	2782										
GLI1	2735	hgsc.bcm.edu	37	chr12	57865761	57865761	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ataccccacctccctctgggCcccccaacatggctgtgggc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:57865761delC	ENST00000228682.2	+	12	3329	c.3238delC	c.(3238-3240)cccfs	p.P1081fs	GLI1_ENST00000546141.1_Frame_Shift_Del_p.P1040fs|GLI1_ENST00000543426.1_Frame_Shift_Del_p.P953fs	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	1081					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			TCCCTCTGGGCCCCCCAACAT	0.557																																					p.G1079fs	Pancreas(157;841 1936 10503 41495 50368)	Atlas-Indel,Pindel	.											.	GLI1	141	.	0			c.3237delG						.						84	85	84					12																	57865761		2203	4300	6503	SO:0001589	frameshift_variant	2735	exon12			.		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.3238delC	chr12.hg19:g.57865761delC	ENSP00000228682:p.Pro1081fs	149.0	0.0		129.0	56.0	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Frame_Shift_Del	DEL	ENST00000228682.2	hg19	CCDS8940.1																																																																																			.	.		0.557	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		-	57865761	C	-	57865761	7	5	23	1	0	1	0	1	0	0	0	0	6445	739	26	0	3280	0	GLI1	12	57865761	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	309538	57865761	75986134	717	2783										
DTX3	196403	hgsc.bcm.edu	37	chr12	58001004	58001004	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcaccctgagatgcaccgcGcaggcccaccccctctccga	9	20	1	1	rs373278710		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:58001004G>A	ENST00000548198.1	+	3	1862	c.358G>A	c.(358-360)Gca>Aca	p.A120T	DTX3_ENST00000548804.1_Missense_Mutation_p.A120T|DTX3_ENST00000337737.3_Missense_Mutation_p.A120T|DTX3_ENST00000551632.1_Missense_Mutation_p.A123T|ARHGEF25_ENST00000333972.7_5'Flank			Q8N9I9	DTX3_HUMAN	deltex 3, E3 ubiquitin ligase	120					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(6)|urinary_tract(1)	12	Melanoma(17;0.122)					GATGCACCGCGCAGGCCCACC	0.687																																					p.A120T		Atlas-SNP	.											.	DTX3	27	.	0			c.G358A						.	G	THR/ALA	0,3736		0,0,1868	14	17	16		358	1.9	1	12		16	1,8173		0,1,4086	no	missense	DTX3	NM_178502.2	58	0,1,5954	AA,AG,GG		0.0122,0.0,0.0084	benign	120/348	58001004	1,11909	1868	4087	5955	SO:0001583	missense	196403	exon5			CACCGCGCAGGCC	AK094385	CCDS41800.1, CCDS66410.1	12q13.2	2014-01-28	2014-01-28			ENSG00000178498		"RING-type (C3HC4) zinc fingers"	24457	protein-coding gene	gene with protein product		613142	"deltex 3 homolog (Drosophila)", "deltex homolog 3 (Drosophila)"			12670957	Standard	XM_005268697		Approved	FLJ34766, RNF154	uc001sow.1	Q8N9I9		ENST00000548198.1:c.358G>A	chr12.hg19:g.58001004G>A	ENSP00000447873:p.Ala120Thr	95.0	0.0		67.0	24.0	NM_178502	Q53ZZ2|Q8NAU6|Q8NDS8	Missense_Mutation	SNP	ENST00000548198.1	hg19	CCDS41800.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.682289	0.29872	0.0	1.22E-4	ENSG00000178498	ENST00000548804;ENST00000549583;ENST00000337737;ENST00000548198;ENST00000551632;ENST00000548478	T;T;T;T;T;T	0.43294	1.55;0.95;1.55;1.55;1.55;0.96	4.0	1.94	0.25998	.	0.326263	0.20948	N	0.082808	T	0.19005	0.0456	N	0.08118	0	0.19775	N	0.99996	B	0.26120	0.142	B	0.15052	0.012	T	0.17471	-1.0368	10	0.12766	T	0.61	-4.8237	11.5041	0.50454	0.0:0.6464:0.3536:0.0	.	120	Q8N9I9	DTX3_HUMAN	T	120;123;120;120;123;113	ENSP00000449294:A120T;ENSP00000449688:A123T;ENSP00000338050:A120T;ENSP00000447873:A120T;ENSP00000448696:A123T;ENSP00000448224:A113T	ENSP00000338050:A120T	A	+	1	0	DTX3	56287271	0.998000	0.40836	1.000000	0.80357	0.985000	0.73830	0.322000	0.19576	0.805000	0.34159	-0.599000	0.04106	GCA	.	.		0.687	DTX3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407848.1	NM_178502		A	58001004	G	A	58001004	3	1	23	1	0	0	0	0	1	0	0	0	4797	1087	38	1	364	1	DTX3	12	58001004	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	135243	58001004	75850891	718	2784										
USP15	9958	hgsc.bcm.edu	37	chr12	62785110	62785110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgggacacaaaaaacgattgTttacattccagttcaacaac	6	10	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:62785110T>C	ENST00000280377.5	+	16	2192	c.2134T>C	c.(2134-2136)Ttt>Ctt	p.F712L	USP15_ENST00000353364.3_Missense_Mutation_p.F683L|USP15_ENST00000393654.3_Missense_Mutation_p.F687L	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	712	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		AAAACGATTGTTTACATTCCA	0.378																																					p.F712L	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.T2134C						.						116	114	114					12																	62785110		2203	4300	6503	SO:0001583	missense	9958	exon16			CGATTGTTTACAT	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2134T>C	chr12.hg19:g.62785110T>C	ENSP00000280377:p.Phe712Leu	269.0	0.0		279.0	105.0	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Missense_Mutation	SNP	ENST00000280377.5	hg19	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.730107	0.89390	.	.	ENSG00000135655	ENST00000353364;ENST00000280377;ENST00000393654	T;T;T	0.19938	2.13;2.11;2.12	5.59	5.59	0.84812	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.37812	0.1017	L	0.39633	1.23	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.04467	-1.0949	9	.	.	.	-13.6337	15.7764	0.78224	0.0:0.0:0.0:1.0	.	712;683	Q9Y4E8;Q9Y4E8-2	UBP15_HUMAN;.	L	683;712;687	ENSP00000258123:F683L;ENSP00000280377:F712L;ENSP00000377264:F687L	.	F	+	1	0	USP15	61071377	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.447000	0.80620	2.135000	0.66039	0.460000	0.39030	TTT	.	.		0.378	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		C	62785110	T	C	62785110	3	2	23	1	0	0	0	0	1	0	0	0	17061	1725	60	2	2105	2	USP15	12	62785110	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	4784106	62785110	71066785	719	2785										
MON2	23041	hgsc.bcm.edu	37	chr12	62938760	62938760	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	taaagcaggattaacatttaAccatgatcctccactctcac	4	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:62938760A>G	ENST00000393632.2	+	21	2940	c.2549A>G	c.(2548-2550)aAc>aGc	p.N850S	MON2_ENST00000393629.2_Missense_Mutation_p.N850S|MON2_ENST00000546600.1_Missense_Mutation_p.N850S|MON2_ENST00000552115.1_Missense_Mutation_p.N850S|MON2_ENST00000552738.1_Missense_Mutation_p.N827S|MON2_ENST00000280379.6_Missense_Mutation_p.N851S|MON2_ENST00000393630.3_Missense_Mutation_p.N851S|RNU6-399P_ENST00000365164.1_RNA	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	850					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TTAACATTTAACCATGATCCT	0.333																																					p.N850S		Atlas-SNP	.											.	MON2	160	.	0			c.A2549G						.						66	65	65					12																	62938760		2203	4300	6503	SO:0001583	missense	23041	exon21			CATTTAACCATGA		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.2549A>G	chr12.hg19:g.62938760A>G	ENSP00000377252:p.Asn850Ser	406.0	0.0		392.0	155.0	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	A	12.61	1.991003	0.35131	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629;ENST00000552115	T;T;T;T;T;T;T	0.54675	0.56;0.57;0.57;0.56;0.56;0.56;1.58	5.59	-4.85	0.03142	.	0.502543	0.22866	N	0.054681	T	0.26666	0.0652	N	0.08118	0	0.09310	N	0.999999	B;B;B;B	0.13145	0.005;0.007;0.002;0.007	B;B;B;B	0.18263	0.021;0.012;0.007;0.02	T	0.11542	-1.0583	9	.	.	.	-0.6927	14.9276	0.70890	0.494:0.0:0.506:0.0	.	850;827;850;850	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-4	.;.;.;.	S	850;851;851;850;827;850;850	ENSP00000377252:N850S;ENSP00000377250:N851S;ENSP00000280379:N851S;ENSP00000447407:N850S;ENSP00000449215:N827S;ENSP00000377249:N850S;ENSP00000446635:N850S	.	N	+	2	0	MON2	61225027	0.743000	0.28239	0.520000	0.27837	0.993000	0.82548	0.540000	0.23191	-1.269000	0.02436	-0.261000	0.10672	AAC	.	.		0.333	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		G	62938760	A	G	62938760	3	3	23	1	0	0	0	0	1	0	0	0	9709	43	2	2	2631	2	MON2	12	62938760	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	153650	62938760	70913135	720	2786										
AVPR1A	552	hgsc.bcm.edu	37	chr12	63541343	63541343	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcttgaaggagatggccactAaaaaacatgtatatccaggg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:63541343delA	ENST00000299178.2	-	2	1158	c.1053delT	c.(1051-1053)tttfs	p.F351fs		NM_000706.4	NP_000697.1	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	351					activation of phospholipase C activity (GO:0007202)|blood circulation (GO:0008015)|calcium-mediated signaling (GO:0019722)|cellular response to water deprivation (GO:0042631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|grooming behavior (GO:0007625)|maternal aggressive behavior (GO:0002125)|maternal behavior (GO:0042711)|myotube differentiation (GO:0014902)|negative regulation of female receptivity (GO:0007621)|negative regulation of transmission of nerve impulse (GO:0051970)|penile erection (GO:0043084)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glutamate secretion (GO:0014049)|positive regulation of heart rate (GO:0010460)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of vasoconstriction (GO:0045907)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to corticosterone (GO:0051412)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|telencephalon development (GO:0021537)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|prostate(2)|skin(1)	26			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	GATGGCCACTAAAAAACATGT	0.398																																					p.S352fs		Atlas-Indel,Pindel	.											.	AVPR1A	85	.	0			c.1054delA						.						152	145	148					12																	63541343		2203	4300	6503	SO:0001589	frameshift_variant	552	exon2			.	L25615	CCDS8965.1	12q14-q15	2012-08-08				ENSG00000166148		"GPCR / Class A : Vasopressin and oxytocin receptors"	895	protein-coding gene	gene with protein product		600821		AVPR1		8106369	Standard	NM_000706		Approved		uc001sro.2	P37288		ENST00000299178.2:c.1053delT	chr12.hg19:g.63541343delA	ENSP00000299178:p.Phe351fs	155.0	0.0		173.0	63.0	NM_000706		Frame_Shift_Del	DEL	ENST00000299178.2	hg19	CCDS8965.1																																																																																			.	.		0.398	AVPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406734.1			-	63541343	A	-	63541343	7	5	23	1	0	1	0	1	0	0	0	0	1231	359	13	0	207	0	AVPR1A	12	63541343	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	602583	63541343	70310552	721	2787										
SLC35E3	55508	hgsc.bcm.edu	37	chr12	69145879	69145879	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctgtactaccaggctccgaTgtcatctgccatgttgctgg	11	12	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:69145879T>C	ENST00000398004.2	+	3	853	c.581T>C	c.(580-582)aTg>aCg	p.M194T		NM_018656.2	NP_061126.2	Q7Z769	S35E3_HUMAN	solute carrier family 35, member E3	194						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12	Breast(13;2.31e-06)|Renal(347;0.0684)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00372)			CAGGCTCCGATGTCATCTGCC	0.463																																					p.M194T		Atlas-SNP	.											.	SLC35E3	23	.	0			c.T581C						.						235	225	228					12																	69145879		2017	4183	6200	SO:0001583	missense	55508	exon3			CTCCGATGTCATC	AF148713, AY358943	CCDS41808.1	12q15	2014-09-04			ENSG00000175782	ENSG00000175782		"Solute carriers"	20864	protein-coding gene	gene with protein product						12975309	Standard	XM_005269006		Approved	BLOV1	uc001suh.3	Q7Z769	OTTHUMG00000169282	ENST00000398004.2:c.581T>C	chr12.hg19:g.69145879T>C	ENSP00000381089:p.Met194Thr	123.0	0.0		100.0	42.0	NM_018656	A8K0T0|Q0P5Y5|Q9P0V1	Missense_Mutation	SNP	ENST00000398004.2	hg19	CCDS41808.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.296189	0.60086	.	.	ENSG00000175782	ENST00000398004;ENST00000431174	T;T	0.63744	-0.06;1.29	5.59	5.59	0.84812	Domain of unknown function DUF250 (1);	0.041255	0.85682	D	0.000000	T	0.53706	0.1813	L	0.37630	1.12	0.58432	D	0.999999	B	0.15930	0.015	B	0.23150	0.044	T	0.48068	-0.9067	9	.	.	.	-0.3555	16.0729	0.80948	0.0:0.0:0.0:1.0	.	194	Q7Z769	S35E3_HUMAN	T	194;4	ENSP00000381089:M194T;ENSP00000403769:M4T	.	M	+	2	0	SLC35E3	67432146	1.000000	0.71417	0.994000	0.49952	0.968000	0.65278	7.698000	0.84413	2.266000	0.75297	0.454000	0.30748	ATG	.	.		0.463	SLC35E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403241.1	NM_018656		C	69145879	T	C	69145879	3	2	23	1	0	0	0	0	1	0	0	0	14601	1464	51	2	591	2	SLC35E3	12	69145879	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	5604536	69145879	64706016	722	2788										
RAB3IP	117177	hgsc.bcm.edu	37	chr12	70188991	70188991	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagttctccaacatcacctaCgcaggagcctttgccaggtg	9	14	2	0	rs575263311	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:70188991C>T	ENST00000247833.7	+	6	1131	c.755C>T	c.(754-756)aCg>aTg	p.T252M	RAB3IP_ENST00000550536.1_Missense_Mutation_p.T268M|RAB3IP_ENST00000483530.2_Missense_Mutation_p.T252M|RAB3IP_ENST00000325555.9_Missense_Mutation_p.T46M|RAB3IP_ENST00000551641.1_Missense_Mutation_p.T46M|RAB3IP_ENST00000553099.1_Missense_Mutation_p.T46M|RAB3IP_ENST00000362025.5_Missense_Mutation_p.T268M|RAB3IP_ENST00000378815.6_Missense_Mutation_p.T252M|RAB3IP_ENST00000550847.1_5'Flank					RAB3A interacting protein											NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			ACATCACCTACGCAGGAGCCT	0.428													C|||	2	0.000399361	0.0015	0	5008	,	,		20028	0		0	False		,,,				2504	0				p.T268M		Atlas-SNP	.											.	RAB3IP	48	.	0			c.C803T						.						106	103	104					12																	70188991		2203	4300	6503	SO:0001583	missense	117177	exon6			CACCTACGCAGGA		CCDS8993.1, CCDS8995.1, CCDS8996.1, CCDS41811.1, CCDS44942.1	12q15	2013-01-22	2013-01-22		ENSG00000127328	ENSG00000127328			16508	protein-coding gene	gene with protein product	"rabin3"	608686					Standard	NM_175623		Approved	RABIN3	uc001svm.3	Q96QF0	OTTHUMG00000169437	ENST00000247833.7:c.755C>T	chr12.hg19:g.70188991C>T	ENSP00000247833:p.Thr252Met	246.0	0.0		221.0	74.0	NM_175623		Missense_Mutation	SNP	ENST00000247833.7	hg19	CCDS8995.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633427	0.47049	.	.	ENSG00000127328	ENST00000247833;ENST00000378815;ENST00000483530;ENST00000325555;ENST00000550536;ENST00000362025;ENST00000551641;ENST00000553099	T;T;T;T;T	0.47177	0.86;0.9;0.85;0.9;0.9	5.84	3.59	0.41128	.	0.442527	0.27881	N	0.017470	T	0.52853	0.1760	L	0.43152	1.355	0.09310	N	0.999996	P;D;P;D	0.61080	0.929;0.989;0.88;0.972	P;P;P;P	0.56788	0.541;0.806;0.541;0.503	T	0.44997	-0.9291	10	0.44086	T	0.13	.	12.8738	0.57980	0.0:0.8377:0.0:0.1623	.	268;268;252;252	Q96QF0-4;Q96QF0;Q96QF0-3;Q96QF0-7	.;RAB3I_HUMAN;.;.	M	252;252;252;46;268;268;46;46	ENSP00000247833:T252M;ENSP00000323349:T46M;ENSP00000447300:T268M;ENSP00000448773:T46M;ENSP00000448027:T46M	ENSP00000247833:T252M	T	+	2	0	RAB3IP	68475258	0.552000	0.26505	0.066000	0.19879	0.888000	0.51559	2.521000	0.45563	1.386000	0.46466	-0.355000	0.07637	ACG	.	.		0.428	RAB3IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280671.2	NM_022456		T	70188991	C	T	70188991	3	4	23	1	0	0	0	0	1	0	0	0	12953	536	19	1	825	1	RAB3IP	12	70188991	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1043112	70188991	63662904	723	2789										
KCNMB4	27345	hgsc.bcm.edu	37	chr12	70824288	70824288	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agatgatgtgcttctgcatcGcactcatgatgagattgtcc	10	9	2	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:70824288G>A	ENST00000258111.4	+	3	947	c.488G>A	c.(487-489)cGc>cAc	p.R163H		NM_014505.5	NP_055320.4	Q86W47	KCMB4_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 4	163					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of neurotransmitter secretion (GO:0046928)|regulation of vasoconstriction (GO:0019229)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)			kidney(1)|large_intestine(4)|lung(5)	10	Renal(347;0.236)		Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)		Miconazole(DB01110)|Procaine(DB00721)	CTTCTGCATCGCACTCATGAT	0.488																																					p.R163H		Atlas-SNP	.											KCNMB4,caecum,carcinoma,0,3	KCNMB4	27	.	0			c.G488A						.						204	188	193					12																	70824288		2203	4300	6503	SO:0001583	missense	27345	exon3			TGCATCGCACTCA	AF207992	CCDS8997.1	12q15	2006-06-10			ENSG00000135643	ENSG00000135643		"Potassium channels"	6289	protein-coding gene	gene with protein product		605223				10692449, 10828459	Standard	NM_014505		Approved		uc001svx.3	Q86W47	OTTHUMG00000167586	ENST00000258111.4:c.488G>A	chr12.hg19:g.70824288G>A	ENSP00000258111:p.Arg163His	68.0	0.0		52.0	21.0	NM_014505	Q8IVR3|Q9NPA4|Q9P0G5	Missense_Mutation	SNP	ENST00000258111.4	hg19	CCDS8997.1	.	.	.	.	.	.	.	.	.	.	G	33	5.268925	0.95429	.	.	ENSG00000135643	ENST00000258111	T	0.15834	2.39	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	M	0.63843	1.955	0.58432	D	0.999997	D	0.89917	1.0	D	0.85130	0.997	T	0.12682	-1.0538	10	0.66056	D	0.02	-23.5357	20.1653	0.98150	0.0:0.0:1.0:0.0	.	163	Q86W47	KCMB4_HUMAN	H	163	ENSP00000258111:R163H	ENSP00000258111:R163H	R	+	2	0	KCNMB4	69110555	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.440000	0.73435	2.768000	0.95171	0.655000	0.94253	CGC	.	.		0.488	KCNMB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395208.1	NM_014505		A	70824288	G	A	70824288	3	1	23	1	0	0	0	0	1	0	0	0	8086	1087	38	1	498	1	KCNMB4	12	70824288	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	635297	70824288	63027607	724	2790										
GLIPR1L2	144321	hgsc.bcm.edu	37	chr12	75816819	75816843	+	Intron	DEL	GAAAAATAAGCGATTGAACACTAGT	GAAAAATAAGCGATTGAACACTAGT	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atgcataatggattggacaaGaaaaataagcgattgaacac					rs200555586|rs75261424|rs77365041	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	GAAAAATAAGCGATTGAACACTAGT	GAAAAATAAGCGATTGAACACTAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:75816819_75816843delGAAAAATAAGCGATTGAACACTAGT	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000320460.4_Frame_Shift_Del_p.KKNKRLNTS240fs|GLIPR1L2_ENST00000378692.3_Intron|GLIPR1L2_ENST00000441218.1_Intron|GLIPR1L2_ENST00000435775.1_Intron	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2							integral component of membrane (GO:0016021)		p.K240N(1)		kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						GATTGGACAAGAAAAATAAGCGATTGAACACTAGTTTTTTATGGT	0.302																																					p.240_248del		Pindel	.											.	GLIPR1L2	54	.	1	Substitution - Missense(1)	large_intestine(1)	c.719_743del						.																																			SO:0001627	intron_variant	144321	exon4			.	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.670+50GAAAAATAAGCGATTGAACACTAGT>-	chr12.hg19:g.75816819_75816843delGAAAAATAAGCGATTGAACACTAGT		158.0	0.0		125.0	27.0	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Frame_Shift_Del	DEL	ENST00000550916.1	hg19	CCDS58258.1																																																																																			.	.		0.302	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436		-	75816843	GAAAAATAAGCGATTGAACACTAGT	-	75816819	6	5	23	0	1	1	0	1	0	0	0	0	6451	933	33	0		0	GLIPR1L2	12	75816819	Intron	DEL	GAAAAATAAGCGATTGAACACTAGT	TCGA-4R-AA8I-01A-11D-A382-10	4992531	75816819	58035076	725	2791										
BBS10	79738	hgsc.bcm.edu	37	chr12	76740856	76740856	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atgagcaattttacattctgActatgtagatgtttcattat	6	5	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:76740856A>G	ENST00000393262.3	-	2	992	c.909T>C	c.(907-909)agT>agC	p.S303S		NM_024685.3	NP_078961.3	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	303					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|regulation of protein complex assembly (GO:0043254)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell projection (GO:0042995)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)	19						TTACATTCTGACTATGTAGAT	0.338									Bardet-Biedl syndrome																												p.S303S		Atlas-SNP	.											.	BBS10	46	.	0			c.T909C						.						118	105	109					12																	76740856		2203	4300	6503	SO:0001819	synonymous_variant	79738	exon2	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	ATTCTGACTATGT	BC026355	CCDS9014.2	12q21.2	2014-06-17	2006-04-28	2006-04-28	ENSG00000179941	ENSG00000179941		"Heat Shock Proteins / Chaperonins"	26291	protein-coding gene	gene with protein product		610148	"chromosome 12 open reading frame 58"	C12orf58		16582908	Standard	NM_024685		Approved	FLJ23560	uc001syd.1	Q8TAM1	OTTHUMG00000147352	ENST00000393262.3:c.909T>C	chr12.hg19:g.76740856A>G		75.0	0.0		64.0	24.0	NM_024685	Q96CW2|Q9H5D2	Silent	SNP	ENST00000393262.3	hg19	CCDS9014.2																																																																																			.	.		0.338	BBS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303983.2	NM_024685		G	76740856	A	G	76740856	2	3	23	1	0	0	0	0	0	0	0	1	1336	272	10	2		2	BBS10	12	76740856	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	924037	76740856	57111039	726	2792										
E2F7	144455	hgsc.bcm.edu	37	chr12	77417817	77417817	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtcagcgccgccgctggggAtttctagtctcctctgggcc	13	14	4	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:77417817A>T	ENST00000322886.7	-	13	2949	c.2714T>A	c.(2713-2715)aTc>aAc	p.I905N	E2F7_ENST00000416496.2_3'UTR	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	905					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						GCCGCTGGGGATTTCTAGTCT	0.597																																					p.I905N		Atlas-SNP	.											.	E2F7	201	.	0			c.T2714A						.						102	107	106					12																	77417817		2203	4300	6503	SO:0001583	missense	144455	exon13			CTGGGGATTTCTA	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.2714T>A	chr12.hg19:g.77417817A>T	ENSP00000323246:p.Ile905Asn	84.0	0.0		69.0	32.0	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	hg19	CCDS9016.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.786609	0.49997	.	.	ENSG00000165891	ENST00000322886;ENST00000339887	T	0.24723	1.84	5.91	5.91	0.95273	.	0.128916	0.49916	D	0.000134	T	0.41834	0.1176	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.29882	-0.9997	10	0.87932	D	0	-21.5712	14.0893	0.64980	1.0:0.0:0.0:0.0	.	905	Q96AV8	E2F7_HUMAN	N	905;376	ENSP00000323246:I905N	ENSP00000323246:I905N	I	-	2	0	E2F7	75941948	1.000000	0.71417	0.365000	0.25901	0.009000	0.06853	5.736000	0.68597	2.254000	0.74563	0.533000	0.62120	ATC	.	.		0.597	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		T	77417817	A	T	77417817	3	4	23	1	0	0	0	0	1	0	0	0	4874	333	12	4	25	4	E2F7	12	77417817	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	676961	77417817	56434078	727	2793										
NTS	4922	hgsc.bcm.edu	37	chr12	86276037	86276037	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttcttgatactggaaatgacAaaaatggaaaggaagaagtc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:86276037delA	ENST00000256010.6	+	4	504	c.397delA	c.(397-399)aaafs	p.K133fs	NTS_ENST00000551529.1_Frame_Shift_Del_p.K58fs	NM_006183.4	NP_006174.1	P30990	NEUT_HUMAN	neurotensin	133					regulation of blood vessel size (GO:0050880)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)				large_intestine(2)|lung(6)	8						TGGAAATGACAAAAATGGAAA	0.323																																					p.D132fs		Atlas-Indel,Pindel	.											.	NTS	25	.	0			c.396delC						.						65	71	69					12																	86276037		2203	4293	6496	SO:0001589	frameshift_variant	4922	exon4			.		CCDS9029.1	12q21.31	2013-02-26			ENSG00000133636	ENSG00000133636		"Endogenous ligands"	8038	protein-coding gene	gene with protein product	"neuromedin N", "pro-neurotensin/neuromedin"	162650					Standard	NM_006183		Approved		uc001tag.3	P30990	OTTHUMG00000169832	ENST00000256010.6:c.397delA	chr12.hg19:g.86276037delA	ENSP00000256010:p.Lys133fs	372.0	0.0		378.0	122.0	NM_006183		Frame_Shift_Del	DEL	ENST00000256010.6	hg19	CCDS9029.1																																																																																			.	.		0.323	NTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406111.2			-	86276037	A	-	86276037	7	5	23	1	0	1	0	1	0	0	0	0	10718	131	5	0	411	0	NTS	12	86276037	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	8858220	86276037	47575858	728	2794										
MGAT4C	25834	hgsc.bcm.edu	37	chr12	86377408	86377408	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catagcgttctgaattcagtTgatgtgtggatgtttccctt	10	7	2	2	rs35652293		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:86377408T>C	ENST00000604798.1	-	7	1392	c.188A>G	c.(187-189)cAa>cGa	p.Q63R	MGAT4C_ENST00000548651.1_Missense_Mutation_p.Q63R|MGAT4C_ENST00000552435.2_Missense_Mutation_p.Q63R|MGAT4C_ENST00000549405.2_Missense_Mutation_p.Q63R|MGAT4C_ENST00000332156.1_Missense_Mutation_p.Q63R|MGAT4C_ENST00000552808.2_Missense_Mutation_p.Q63R|MGAT4C_ENST00000393205.2_Missense_Mutation_p.Q92R			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	63					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TGAATTCAGTTGATGTGTGGA	0.348																																					p.Q63R		Atlas-SNP	.											.	MGAT4C	110	.	0			c.A188G						.						138	137	137					12																	86377408		2203	4300	6503	SO:0001583	missense	25834	exon6			TTCAGTTGATGTG		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	30871	protein-coding gene	gene with protein product		607385	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.188A>G	chr12.hg19:g.86377408T>C	ENSP00000474896:p.Gln63Arg	106.0	0.0		91.0	4.0	NM_013244	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	hg19	CCDS9030.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.115001	0.77210	.	.	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225;ENST00000552435	T;T;T;T;T;T	0.46063	1.48;1.45;1.48;1.48;1.48;0.88	5.44	5.44	0.79542	.	0.078589	0.53938	D	0.000051	T	0.43188	0.1236	L	0.44542	1.39	0.34850	D	0.741548	P;P	0.47191	0.891;0.891	B;P	0.48368	0.412;0.575	T	0.50980	-0.8763	10	0.18710	T	0.47	4.0E-4	15.502	0.75705	0.0:0.0:0.0:1.0	.	92;63	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	R	63;92;63;63;63;63;63;63	ENSP00000331664:Q63R;ENSP00000376900:Q92R;ENSP00000449022:Q63R;ENSP00000446647:Q63R;ENSP00000447253:Q63R;ENSP00000449172:Q63R	ENSP00000331664:Q63R	Q	-	2	0	MGAT4C	84901539	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	6.104000	0.71498	2.071000	0.62044	0.460000	0.39030	CAA	.	.		0.348	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		C	86377408	T	C	86377408	3	2	23	1	0	0	0	0	1	0	0	0	9556	1812	63	2	1256	2	MGAT4C	12	86377408	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	101371	86377408	47474487	729	2795										
TMTC3	160418	hgsc.bcm.edu	37	chr12	88582677	88582677	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	taaaaatttaaatagaaccaAagaagctgaagaatcttaca	5	5	1	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:88582677A>G	ENST00000266712.6	+	11	1710	c.1490A>G	c.(1489-1491)aAa>aGa	p.K497R		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	497					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						AATAGAACCAAAGAAGCTGAA	0.299																																					p.K497R		Atlas-SNP	.											.	TMTC3	75	.	0			c.A1490G						.						75	81	79					12																	88582677		2202	4286	6488	SO:0001583	missense	160418	exon11			GAACCAAAGAAGC		CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"Tetratricopeptide (TTC) repeat domain containing"	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.1490A>G	chr12.hg19:g.88582677A>G	ENSP00000266712:p.Lys497Arg	462.0	0.0		433.0	101.0	NM_181783	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Missense_Mutation	SNP	ENST00000266712.6	hg19	CCDS9032.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.219074	0.39201	.	.	ENSG00000139324	ENST00000266712	T	0.54479	0.57	5.37	2.75	0.32379	.	0.133494	0.64402	N	0.000002	T	0.41351	0.1155	L	0.42581	1.335	0.36341	D	0.859478	B	0.02656	0.0	B	0.08055	0.003	T	0.34229	-0.9837	10	0.25106	T	0.35	-12.3542	10.5278	0.44958	0.8997:0.0:0.1003:0.0	.	497	Q6ZXV5-2	.	R	497	ENSP00000266712:K497R	ENSP00000266712:K497R	K	+	2	0	TMTC3	87106808	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.051000	0.57412	0.241000	0.21283	0.533000	0.62120	AAA	.	.		0.299	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783		G	88582677	A	G	88582677	3	3	23	1	0	0	0	0	1	0	0	0	16277	14	1	2	1528	2	TMTC3	12	88582677	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2205269	88582677	45269218	730	2796										
LUM	4060	hgsc.bcm.edu	37	chr12	91497984	91497984	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcaacacgtagacattcataCatatccggtggaagactggt	10	9	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:91497984C>A	ENST00000266718.4	-	3	1429	c.975G>T	c.(973-975)atG>atT	p.M325I	LUM_ENST00000548071.1_5'UTR	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	325					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						GACATTCATACATATCCGGTG	0.398																																					p.M325I		Atlas-SNP	.											.	LUM	65	.	0			c.G975T						.						117	111	113					12																	91497984		2203	4300	6503	SO:0001583	missense	4060	exon3			TTCATACATATCC	BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6724	protein-coding gene	gene with protein product	"lumican proteoglycan"	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.975G>T	chr12.hg19:g.91497984C>A	ENSP00000266718:p.Met325Ile	91.0	0.0		125.0	56.0	NM_002345	B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	hg19	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	C	8.773	0.926379	0.18056	.	.	ENSG00000139329	ENST00000266718	T	0.16897	2.31	5.19	4.29	0.51040	.	0.188883	0.52532	D	0.000064	T	0.12475	0.0303	L	0.31294	0.92	0.44409	D	0.997325	B	0.06786	0.001	B	0.08055	0.003	T	0.09335	-1.0679	10	0.16896	T	0.51	-19.136	13.6563	0.62339	0.0:0.9231:0.0:0.0769	.	325	P51884	LUM_HUMAN	I	325	ENSP00000266718:M325I	ENSP00000266718:M325I	M	-	3	0	LUM	90022115	1.000000	0.71417	0.997000	0.53966	0.547000	0.35210	2.105000	0.41825	2.398000	0.81561	0.591000	0.81541	ATG	.	.		0.398	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345		A	91497984	C	A	91497984	3	1	23	1	0	0	0	0	1	0	0	0	9094	478	17	3	45	3	LUM	12	91497984	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2915307	91497984	42353911	731	2797										
ELK3	2004	hgsc.bcm.edu	37	chr12	96617510	96617510	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaaacaaaacaaatatgaacTatgataagctgagcagagcc	7	7	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:96617510T>C	ENST00000228741.3	+	2	492	c.166T>C	c.(166-168)Tat>Cat	p.Y56H	ELK3_ENST00000552142.1_Missense_Mutation_p.Y56H|RP11-394J1.2_ENST00000551844.1_RNA	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	56					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|wound healing (GO:0042060)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	purine-rich negative regulatory element binding (GO:0032422)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(5)|ovary(2)|prostate(1)|stomach(2)	20	all_cancers(2;0.00173)					AAATATGAACTATGATAAGCT	0.488																																					p.Y56H		Atlas-SNP	.											.	ELK3	36	.	0			c.T166C						.						76	72	73					12																	96617510		2203	4300	6503	SO:0001583	missense	2004	exon2			ATGAACTATGATA	BC017371	CCDS9060.1	12q23	2006-12-30				ENSG00000111145			3325	protein-coding gene	gene with protein product		600247				7851904	Standard	NM_005230		Approved	ERP, NET, SAP2	uc001teo.1	P41970		ENST00000228741.3:c.166T>C	chr12.hg19:g.96617510T>C	ENSP00000228741:p.Tyr56His	106.0	0.0		106.0	47.0	NM_005230	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Missense_Mutation	SNP	ENST00000228741.3	hg19	CCDS9060.1	.	.	.	.	.	.	.	.	.	.	t	26.2	4.717535	0.89205	.	.	ENSG00000111145	ENST00000228741;ENST00000552142;ENST00000547860	T;T;T	0.72282	-0.64;-0.64;-0.64	5.48	5.48	0.80851	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (5);	0.000000	0.85682	D	0.000000	D	0.89777	0.6813	H	0.97611	4.04	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.93360	0.6726	10	0.87932	D	0	.	15.5812	0.76445	0.0:0.0:0.0:1.0	.	56	P41970	ELK3_HUMAN	H	56	ENSP00000228741:Y56H;ENSP00000449430:Y56H;ENSP00000447857:Y56H	ENSP00000228741:Y56H	Y	+	1	0	ELK3	95141641	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	8.036000	0.88901	2.094000	0.63399	0.459000	0.35465	TAT	.	.		0.488	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408694.1	NM_005230		C	96617510	T	C	96617510	3	2	23	1	0	0	0	0	1	0	0	0	5062	1522	53	2	168	2	ELK3	12	96617510	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	5119526	96617510	37234385	732	2798										
SCYL2	55681	hgsc.bcm.edu	37	chr12	100708368	100708368	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagtttttcaaaggactgccAaaggttctaccaaaactgcc	7	11	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:100708368A>G	ENST00000360820.2	+	8	1508	c.1071A>G	c.(1069-1071)ccA>ccG	p.P357P		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	357			P -> L (in dbSNP:rs33968174). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						AAGGACTGCCAAAGGTTCTAC	0.323																																					p.P357P		Atlas-SNP	.											.	SCYL2	99	.	0			c.A1071G						.						65	65	65					12																	100708368		2203	4297	6500	SO:0001819	synonymous_variant	55681	exon8			ACTGCCAAAGGTT	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.1071A>G	chr12.hg19:g.100708368A>G		578.0	0.0		486.0	195.0	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Silent	SNP	ENST00000360820.2	hg19	CCDS9076.1																																																																																			.	.		0.323	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		G	100708368	A	G	100708368	2	3	23	1	0	0	0	0	0	0	0	1	13963	117	5	2		2	SCYL2	12	100708368	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	4090858	100708368	33143527	733	2799										
PMCH	5367	hgsc.bcm.edu	37	chr12	102591388	102591388	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcaataactgatttttctGcagtgtcttccttctgaaag	8	8	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:102591388G>A	ENST00000329406.4	-	1	235	c.161C>T	c.(160-162)gCa>gTa	p.A54V		NM_002674.2	NP_002665.2	P20382	MCH_HUMAN	pro-melanin-concentrating hormone	54					cell differentiation (GO:0030154)|feeding behavior (GO:0007631)|multicellular organismal development (GO:0007275)|neuropeptide signaling pathway (GO:0007218)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|nucleus (GO:0005634)				large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	6						TGATTTTTCTGCAGTGTCTTC	0.358																																					p.A54V		Atlas-SNP	.											.	PMCH	10	.	0			c.C161T						.						112	108	109					12																	102591388		2201	4300	6501	SO:0001583	missense	5367	exon1			TTTTCTGCAGTGT	M57703	CCDS31885.1	12q23.2	2013-02-26			ENSG00000183395	ENSG00000183395		"Endogenous ligands"	9109	protein-coding gene	gene with protein product		176795				2149166	Standard	NM_002674		Approved	MCH	uc001tjl.3	P20382	OTTHUMG00000170479	ENST00000329406.4:c.161C>T	chr12.hg19:g.102591388G>A	ENSP00000332225:p.Ala54Val	90.0	0.0		82.0	15.0	NM_002674	Q16044|Q8WVG0	Missense_Mutation	SNP	ENST00000329406.4	hg19	CCDS31885.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710462	0.30322	.	.	ENSG00000183395	ENST00000329406	.	.	.	5.76	2.99	0.34606	.	0.316543	0.30028	N	0.010591	T	0.26268	0.0641	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16424	-1.0403	9	0.46703	T	0.11	.	5.776	0.18279	0.2626:0.0:0.6122:0.1252	.	54	P20382	MCH_HUMAN	V	54	.	ENSP00000332225:A54V	A	-	2	0	PMCH	101115518	0.825000	0.29262	0.981000	0.43875	0.978000	0.69477	2.274000	0.43390	0.378000	0.24764	0.655000	0.94253	GCA	.	.		0.358	PMCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409337.1	NM_002674		A	102591388	G	A	102591388	3	1	23	1	0	0	0	0	1	0	0	0	12140	1319	46	3	348	3	PMCH	12	102591388	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1883020	102591388	31260507	734	2800										
HCFC2	29915	hgsc.bcm.edu	37	chr12	104476618	104476618	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tatttttggagtggaagagaTggctacaaaaaagcactgaa	11	4	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:104476618T>C	ENST00000229330.4	+	7	1106	c.1002T>C	c.(1000-1002)gaT>gaC	p.D334D		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	334					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						GTGGAAGAGATGGCTACAAAA	0.378																																					p.D334D	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-SNP	.											.	HCFC2	94	.	0			c.T1002C						.						81	82	82					12																	104476618		2203	4300	6503	SO:0001819	synonymous_variant	29915	exon7			AAGAGATGGCTAC	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1002T>C	chr12.hg19:g.104476618T>C		132.0	0.0		129.0	53.0	NM_013320	B2R8Q5|C0H5X3	Silent	SNP	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.378	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		C	104476618	T	C	104476618	2	2	23	1	0	0	0	0	0	0	0	1	7002	1461	51	2		2	HCFC2	12	104476618	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1885230	104476618	29375277	735	2801										
CMKLR1	1240	hgsc.bcm.edu	37	chr12	108685651	108685651	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtctccctctcattcatagaAgtcctctcattcattgatga	5	12	5	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:108685651A>G	ENST00000312143.7	-	3	1452	c.1089T>C	c.(1087-1089)acT>acC	p.T363T	CMKLR1_ENST00000397688.2_Silent_p.T361T|CMKLR1_ENST00000550402.1_Silent_p.T363T|CMKLR1_ENST00000552995.1_Silent_p.T361T|CMKLR1_ENST00000412676.1_Silent_p.T363T	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	363					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						CATTCATAGAAGTCCTCTCAT	0.488																																					p.T363T		Atlas-SNP	.											.	CMKLR1	67	.	0			c.T1089C						.						120	124	123					12																	108685651		1922	4136	6058	SO:0001819	synonymous_variant	1240	exon3			CATAGAAGTCCTC	U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"GPCR / Class A : Resolvin receptors"	2121	protein-coding gene	gene with protein product	"resolvin E1 receptor", "chemerin receptor"	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.1089T>C	chr12.hg19:g.108685651A>G		137.0	0.0		116.0	49.0	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Silent	SNP	ENST00000312143.7	hg19	CCDS44965.1																																																																																			.	.		0.488	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1			G	108685651	A	G	108685651	2	3	23	1	0	0	0	0	0	0	0	1	3581	59	3	2		2	CMKLR1	12	108685651	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	4209033	108685651	25166244	736	2802										
RBM19	9904	hgsc.bcm.edu	37	chr12	114397139	114397139	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagcatccaggccatcattcGcccaagtggctgcctgcgcc	10	17	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:114397139G>A	ENST00000545145.2	-	5	527	c.449C>T	c.(448-450)gCg>gTg	p.A150V	RBM19_ENST00000261741.5_Missense_Mutation_p.A150V|RBM19_ENST00000392561.3_Missense_Mutation_p.A150V	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	150					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GCCATCATTCGCCCAAGTGGC	0.602																																					p.A150V		Atlas-SNP	.											.	RBM19	117	.	0			c.C449T						.						87	81	83					12																	114397139		2203	4300	6503	SO:0001583	missense	9904	exon5			TCATTCGCCCAAG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"RNA binding motif (RRM) containing"	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.449C>T	chr12.hg19:g.114397139G>A	ENSP00000442053:p.Ala150Val	80.0	0.0		84.0	32.0	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	hg19	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.830482	0.32329	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.06849	3.25;3.25;3.25	5.27	4.38	0.52667	.	0.162158	0.56097	D	0.000040	T	0.12561	0.0305	M	0.79926	2.475	0.42178	D	0.991676	B	0.24258	0.1	B	0.17433	0.018	T	0.02190	-1.1198	10	0.46703	T	0.11	-31.3027	9.0416	0.36321	0.0743:0.0:0.7801:0.1456	.	150	Q9Y4C8	RBM19_HUMAN	V	150	ENSP00000442053:A150V;ENSP00000376344:A150V;ENSP00000261741:A150V	ENSP00000261741:A150V	A	-	2	0	RBM19	112881522	1.000000	0.71417	0.837000	0.33122	0.134000	0.20937	4.999000	0.63934	1.230000	0.43646	-0.143000	0.13931	GCG	.	.		0.602	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		A	114397139	G	A	114397139	3	1	23	1	0	0	0	0	1	0	0	0	13136	1087	38	1	2513	1	RBM19	12	114397139	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	5711488	114397139	19454756	737	2803										
MED13L	23389	hgsc.bcm.edu	37	chr12	116420407	116420407	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tattctctccctttctgtaaCactggagagagagtcacttg	8	10	3	2	rs151181388		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:116420407C>T	ENST00000281928.3	-	22	5163	c.4957G>A	c.(4957-4959)Gtt>Att	p.V1653I		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1653						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		CTTTCTGTAACACTGGAGAGA	0.458																																					p.V1653I		Atlas-SNP	.											.	MED13L	193	.	0			c.G4957A						.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	64	56	58		4957	5	1	12	dbSNP_134	58	0,8600		0,0,4300	no	missense-near-splice	MED13L	NM_015335.4	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	1653/2211	116420407	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	23389	exon22			CTGTAACACTGGA	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.4956-1G>A	chr12.hg19:g.116420407C>T		118.0	0.0		124.0	46.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.605349	0.66445	2.27E-4	0.0	ENSG00000123066	ENST00000281928	T	0.74106	-0.81	5.87	4.96	0.65561	.	0.297369	0.38436	N	0.001692	T	0.59321	0.2185	N	0.19112	0.55	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.55496	-0.8132	10	0.44086	T	0.13	.	10.7911	0.46434	0.0:0.7948:0.0:0.2052	.	1653	Q71F56	MD13L_HUMAN	I	1653	ENSP00000281928:V1653I	ENSP00000281928:V1653I	V	-	1	0	MED13L	114904790	0.950000	0.32346	0.999000	0.59377	0.947000	0.59692	0.525000	0.22956	1.427000	0.47276	0.591000	0.81541	GTT	.	C|1.000;T|0.000		0.458	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		Missense_Mutation	T	116420407	C	T	116420407	5	4	23	1	0	0	0	0	0	0	1	0	9440	492	17	3	1715	3	MED13L	12	116420407	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2023268	116420407	17431488	738	2804										
SUDS3	64426	hgsc.bcm.edu	37	chr12	118848915	118848915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccatctatctggagtcaaagGacaaccagaaactgagctgc	9	11	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:118848915G>A	ENST00000543473.1	+	11	1153	c.841G>A	c.(841-843)Gac>Aac	p.D281N	SUDS3_ENST00000541280.1_3'UTR|SUDS3_ENST00000397564.2_Missense_Mutation_p.D282N	NM_022491.2	NP_071936.2	Q9H7L9	SDS3_HUMAN	suppressor of defective silencing 3 homolog (S. cerevisiae)	281					apoptotic process (GO:0006915)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)			breast(1)|lung(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGAGTCAAAGGACAACCAGAA	0.468																																					p.D281N		Atlas-SNP	.											.	SUDS3	26	.	0			c.G841A						.						47	44	45					12																	118848915		1921	4139	6060	SO:0001583	missense	64426	exon11			TCAAAGGACAACC	AK023801	CCDS44993.1	12q24.23	2006-02-13	2006-02-13		ENSG00000111707	ENSG00000111707			29545	protein-coding gene	gene with protein product	"sin3A-associated protein, 45kDa"	608250	"suppressor of defective silencing 3 homolog (SDS3, S. cerevisiae)"			11909966	Standard	NM_022491		Approved	SDS3, FLJ00052, SAP45	uc001twz.3	Q9H7L9	OTTHUMG00000168884	ENST00000543473.1:c.841G>A	chr12.hg19:g.118848915G>A	ENSP00000443988:p.Asp281Asn	63.0	0.0		71.0	21.0	NM_022491	Q4KMQ5|Q8N6H0|Q9H8D2	Missense_Mutation	SNP	ENST00000543473.1	hg19	CCDS44993.1	.	.	.	.	.	.	.	.	.	.	G	30	5.054496	0.93793	.	.	ENSG00000111707	ENST00000543473;ENST00000397564	.	.	.	5.91	5.91	0.95273	.	0.135771	0.64402	D	0.000002	T	0.61274	0.2334	L	0.46157	1.445	0.80722	D	1	B	0.29531	0.247	B	0.31191	0.125	T	0.60964	-0.7158	9	0.87932	D	0	-19.6053	19.8936	0.96942	0.0:0.0:1.0:0.0	.	281	Q9H7L9	SDS3_HUMAN	N	281;282	.	ENSP00000380695:D282N	D	+	1	0	SUDS3	117333298	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.180000	0.94867	2.793000	0.96121	0.655000	0.94253	GAC	.	.		0.468	SUDS3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401504.1	NM_022491		A	118848915	G	A	118848915	3	1	23	1	0	0	0	0	1	0	0	0	15382	1174	41	3	883	3	SUDS3	12	118848915	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2428508	118848915	15002980	739	2805										
CIT	11113	hgsc.bcm.edu	37	chr12	120151400	120151400	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcatattcagcaggcaagcCgcaggtggctggcaagcacg	15	11	1	0	rs370080702		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:120151400C>T	ENST00000261833.7	-	33	4286	c.4234G>A	c.(4234-4236)Ggc>Agc	p.G1412S	CIT_ENST00000392521.2_Missense_Mutation_p.G1454S|CIT_ENST00000537607.1_5'UTR|MIR1178_ENST00000408396.1_RNA	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1412					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.G1440S(1)		breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		GCAGGCAAGCCGCAGGTGGCT	0.577																																					p.G1454S		Atlas-SNP	.											CIT_ENST00000392521,colon,carcinoma,+1,1	CIT	535	.	1	Substitution - Missense(1)	ovary(1)	c.G4360A						.	C	SER/GLY,SER/GLY	0,4406		0,0,2203	89	77	81		4360,4234	6.1	1	12		81	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CIT	NM_001206999.1,NM_007174.2	56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1454/2070,1412/2028	120151400	1,13005	2203	4300	6503	SO:0001583	missense	11113	exon34			GCAAGCCGCAGGT	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.4234G>A	chr12.hg19:g.120151400C>T	ENSP00000261833:p.Gly1412Ser	96.0	0.0		95.0	35.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	C	35	5.525819	0.96431	0.0	1.16E-4	ENSG00000122966	ENST00000392521;ENST00000261833	D;D	0.84516	-1.86;-1.86	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.93465	0.7915	M	0.82193	2.58	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.993	D	0.93270	0.6651	10	0.87932	D	0	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	1454;1412;930	Q2M5E1;O14578;O14578-3	.;CTRO_HUMAN;.	S	1454;1412	ENSP00000376306:G1454S;ENSP00000261833:G1412S	ENSP00000261833:G1412S	G	-	1	0	CIT	118635783	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.610000	0.82949	2.884000	0.98904	0.655000	0.94253	GGC	.	.		0.577	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120151400	C	T	120151400	3	4	23	1	0	0	0	0	1	0	0	0	3440	652	23	1	1909	1	CIT	12	120151400	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1302485	120151400	13700495	740	2806										
UNC119B	84747	hgsc.bcm.edu	37	chr12	121157763	121157763	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccttacgagacccgctctgaCagcttctactttgttgacaa	7	13	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:121157763C>A	ENST00000344651.4	+	5	724	c.684C>A	c.(682-684)gaC>gaA	p.D228E	RP11-173P15.5_ENST00000544939.1_RNA	NM_001080533.1	NP_001074002.1	A6NIH7	U119B_HUMAN	unc-119 homolog B (C. elegans)	228					cilium morphogenesis (GO:0060271)|lipoprotein transport (GO:0042953)	ciliary transition zone (GO:0035869)	lipid binding (GO:0008289)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)	9	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCCGCTCTGACAGCTTCTACT	0.448																																					p.D228E		Atlas-SNP	.											.	UNC119B	21	.	0			c.C684A						.						90	83	85					12																	121157763		2203	4300	6503	SO:0001583	missense	84747	exon5			CTCTGACAGCTTC		CCDS31914.1	12q24	2014-06-16	2001-11-28		ENSG00000175970	ENSG00000175970			16488	protein-coding gene	gene with protein product	"POC7 centriolar protein homolog B (Chlamydomonas)"		"unc119 (C.elegans) homolog B"				Standard	NM_001080533		Approved	MGC5139, POC7B	uc001tyz.4	A6NIH7	OTTHUMG00000169201	ENST00000344651.4:c.684C>A	chr12.hg19:g.121157763C>A	ENSP00000344942:p.Asp228Glu	77.0	0.0		91.0	40.0	NM_001080533		Missense_Mutation	SNP	ENST00000344651.4	hg19	CCDS31914.1	.	.	.	.	.	.	.	.	.	.	C	36	5.723254	0.96847	.	.	ENSG00000175970	ENST00000344651;ENST00000537794	.	.	.	6.07	6.07	0.98685	Immunoglobulin E-set (1);	0.000000	0.85682	D	0.000000	D	0.90181	0.6931	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92100	0.5687	9	0.87932	D	0	-8.4568	20.6439	0.99570	0.0:1.0:0.0:0.0	.	228	A6NIH7	U119B_HUMAN	E	228	.	ENSP00000344942:D228E	D	+	3	2	UNC119B	119642146	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.792000	0.85828	2.884000	0.98904	0.655000	0.94253	GAC	.	.		0.448	UNC119B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402857.1	NM_001080533		A	121157763	C	A	121157763	3	1	23	1	0	0	0	0	1	0	0	0	16998	477	17	3	702	3	UNC119B	12	121157763	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1006363	121157763	12694132	741	2807										
DIABLO	56616	hgsc.bcm.edu	37	chr12	122693101	122693101	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagctgaatgtgattcctggCggttatagaggcctgatctg	13	8	1	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:122693101C>T	ENST00000443649.3	-	7	1364	c.547G>A	c.(547-549)Gcc>Acc	p.A183T	DIABLO_ENST00000464942.2_Missense_Mutation_p.A130T|DIABLO_ENST00000413918.1_Missense_Mutation_p.A139T|DIABLO_ENST00000353548.6_Missense_Mutation_p.A139T|RP11-512M8.5_ENST00000535844.1_3'UTR|B3GNT4_ENST00000545141.1_3'UTR|B3GNT4_ENST00000546192.1_3'UTR|DIABLO_ENST00000267169.6_Missense_Mutation_p.A130T	NM_019887.4	NP_063940.1	Q9NR28	DBLOH_HUMAN	diablo, IAP-binding mitochondrial protein	183					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)				breast(1)|endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	7	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000302)|Epithelial(86;0.00051)|BRCA - Breast invasive adenocarcinoma(302;0.223)		TGATTCCTGGCGGTTATAGAG	0.577																																					p.A183T		Atlas-SNP	.											.	DIABLO	16	.	0			c.G547A						.						65	56	59					12																	122693101		2203	4300	6503	SO:0001583	missense	56616	exon7			TCCTGGCGGTTAT	AF262240	CCDS9228.1, CCDS9229.1, CCDS73541.1	12q24.31	2011-08-02	2011-03-11		ENSG00000184047	ENSG00000184047			21528	protein-coding gene	gene with protein product	"second mitochondria-derived activator of caspase"	605219				12749848, 17237824, 21722859	Standard	NM_019887		Approved	SMAC, DIABLO-S, FLJ25049, FLJ10537, DFNA64	uc010tab.2	Q9NR28	OTTHUMG00000157014	ENST00000443649.3:c.547G>A	chr12.hg19:g.122693101C>T	ENSP00000398495:p.Ala183Thr	42.0	0.0		46.0	22.0	NM_019887	B2RDQ0|Q6W3F3|Q96LV0|Q9BT11|Q9HAV6	Missense_Mutation	SNP	ENST00000443649.3	hg19	CCDS9228.1	.	.	.	.	.	.	.	.	.	.	c	21.8	4.203149	0.79127	.	.	ENSG00000184047	ENST00000413918;ENST00000443649;ENST00000353548;ENST00000464942;ENST00000267169;ENST00000541273;ENST00000474004;ENST00000540535;ENST00000541656	T;T;T;T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	5.77	4.88	0.63580	Smac/DIABLO-like (1);	0.345133	0.33813	N	0.004534	D	0.82508	0.5052	L	0.60455	1.87	0.29397	N	0.86218	D;D;P	0.71674	0.998;0.994;0.744	P;P;B	0.59703	0.862;0.721;0.262	T	0.79055	-0.1960	10	0.48119	T	0.1	-5.989	11.8481	0.52395	0.0:0.8577:0.0:0.1423	.	139;183;130	Q6W3F3;Q9NR28;Q502X2	.;DBLOH_HUMAN;.	T	139;183;139;130;130;86;110;110;110	ENSP00000411638:A139T;ENSP00000398495:A183T;ENSP00000320343:A139T;ENSP00000442360:A130T;ENSP00000267169:A130T;ENSP00000440971:A86T;ENSP00000442669:A110T;ENSP00000441139:A110T;ENSP00000440653:A110T	ENSP00000267169:A130T	A	-	1	0	DIABLO	121259054	0.875000	0.30112	0.889000	0.34880	0.938000	0.57974	1.671000	0.37513	1.453000	0.47775	-0.127000	0.14921	GCC	.	.		0.577	DIABLO-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347102.2	NM_019887		T	122693101	C	T	122693101	3	4	23	1	0	0	0	0	1	0	0	0	4519	768	27	1	176	1	DIABLO	12	122693101	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1535338	122693101	11158794	742	2808										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124403305	124403305	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctaccggccagcagccaggaGgggggccatcctgttcttcg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:124403305delG	ENST00000409039.3	+	64	10986	c.10961delG	c.(10960-10962)aggfs	p.R3654fs		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3654					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCAGCCAGGAGGGGGGCCATC	0.567																																					p.R3654fs		Atlas-Indel,Pindel	.											.	DNAH10	888	.	0			c.10960delA						.						37	41	40					12																	124403305		1932	4133	6065	SO:0001589	frameshift_variant	196385	exon64			.	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.10961delG	chr12.hg19:g.124403305delG	ENSP00000386770:p.Arg3654fs	76.0	0.0		97.0	23.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Frame_Shift_Del	DEL	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.567	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			-	124403305	G	-	124403305	7	5	23	1	0	1	0	1	0	0	0	0	4600	1000	35	0	11215	0	DNAH10	12	124403305	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	1710204	124403305	9448590	743	2809										
GALNT9	50614	hgsc.bcm.edu	37	chr12	132905784	132905784	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gttcggatcttcctggccacCgccatgaacacggctgcagc	11	15	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:132905784C>T	ENST00000328957.8	-	1	5	c.6G>A	c.(4-6)gcG>gcA	p.A2A	RP13-895J2.7_ENST00000537720.1_RNA	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	2					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		TCCTGGCCACCGCCATGAACA	0.682																																					p.A2A	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.G6A						.						16	19	18					12																	132905784		692	1589	2281	SO:0001819	synonymous_variant	50614	exon1			GGCCACCGCCATG	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4131	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 9"	606251	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.6G>A	chr12.hg19:g.132905784C>T		114.0	0.0		89.0	38.0	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	hg19																																																																																				.	.		0.682	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636		T	132905784	C	T	132905784	2	4	23	1	0	0	0	0	0	0	0	1	6228	639	23	1		1	GALNT9	12	132905784	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	8502479	132905784	946111	744	2810										
MIPEP	4285	hgsc.bcm.edu	37	chr13	24413824	24413824	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctcgctgaaaaaaatcacaGtaaatgtaccccaacaatcc	5	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:24413824G>A	ENST00000382172.3	-	12	1400	c.1302C>T	c.(1300-1302)taC>taT	p.Y434Y		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	434					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		AAAAATCACAGTAAATGTACC	0.368																																					p.Y434Y		Atlas-SNP	.											.	MIPEP	53	.	0			c.C1302T						.						107	105	106					13																	24413824		2203	4300	6503	SO:0001819	synonymous_variant	4285	exon12			ATCACAGTAAATG		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1302C>T	chr13.hg19:g.24413824G>A		91.0	0.0		56.0	38.0	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Silent	SNP	ENST00000382172.3	hg19	CCDS9303.1																																																																																			.	.		0.368	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1			A	24413824	G	A	24413824	2	1	23	1	0	0	0	0	0	0	0	1	9601	1024	36	3		3	MIPEP	13	24413824	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10		24413824	90756054	745	2811										
MIPEP	4285	hgsc.bcm.edu	37	chr13	24413861	24413861	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atccttcagattcatgaacaAcagcctagaaaaaaaaattt	4	8	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:24413861A>G	ENST00000382172.3	-	12	1363	c.1265T>C	c.(1264-1266)gTt>gCt	p.V422A		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	422					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		TTCATGAACAACAGCCTAGAA	0.358																																					p.V422A		Atlas-SNP	.											.	MIPEP	53	.	0			c.T1265C						.						75	76	75					13																	24413861		2203	4300	6503	SO:0001583	missense	4285	exon12			TGAACAACAGCCT		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1265T>C	chr13.hg19:g.24413861A>G	ENSP00000371607:p.Val422Ala	63.0	0.0		41.0	25.0	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	hg19	CCDS9303.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.321734	0.81580	.	.	ENSG00000027001	ENST00000382172	T	0.24723	1.84	5.2	5.2	0.72013	Metallopeptidase, catalytic domain (1);	0.368225	0.30168	N	0.010244	T	0.52256	0.1723	M	0.77313	2.365	0.58432	D	0.999997	D	0.65815	0.995	D	0.70935	0.971	T	0.57906	-0.7730	10	0.87932	D	0	-1.5937	15.3646	0.74510	1.0:0.0:0.0:0.0	.	422	Q99797	MIPEP_HUMAN	A	422	ENSP00000371607:V422A	ENSP00000371607:V422A	V	-	2	0	MIPEP	23311861	1.000000	0.71417	0.981000	0.43875	0.864000	0.49448	9.146000	0.94640	2.096000	0.63516	0.523000	0.50628	GTT	.	.		0.358	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1			G	24413861	A	G	24413861	3	3	23	1	0	0	0	0	1	0	0	0	9601	43	2	2	908	2	MIPEP	13	24413861	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	37	24413861	90756017	746	2812										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24858385	24858385	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctcggtacctgcagcccggCggggagcagctggccatcaa	14	15	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:24858385C>T	ENST00000382095.4	+	4	809	c.402C>T	c.(400-402)ggC>ggT	p.G134G	SPATA13_ENST00000424834.2_Silent_p.G759G|SPATA13_ENST00000399949.2_Silent_p.G56G|SPATA13_ENST00000409126.1_Silent_p.G56G|RP11-307N16.6_ENST00000382141.4_Silent_p.G637G|SPATA13_ENST00000382108.3_Silent_p.G759G|SPATA13_ENST00000343003.6_Silent_p.G78G	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	134	ABR (APC-binding region) domain.				cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		TGCAGCCCGGCGGGGAGCAGC	0.552																																					p.G759G		Atlas-SNP	.											.	SPATA13	92	.	0			c.C2277T						.						41	37	38					13																	24858385		2203	4300	6503	SO:0001819	synonymous_variant	221178	exon5			GCCCGGCGGGGAG	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.402C>T	chr13.hg19:g.24858385C>T		75.0	0.0		33.0	5.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	hg19	CCDS9305.1	.	.	.	.	.	.	.	.	.	.	C	9.245	1.039321	0.19669	.	.	ENSG00000182957	ENST00000424834	.	.	.	5.65	-10.2	0.00374	.	.	.	.	.	T	0.33556	0.0867	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40289	-0.9571	4	.	.	.	.	2.3715	0.04331	0.3825:0.1979:0.067:0.3526	.	.	.	.	W	797	.	.	R	+	1	2	SPATA13	23756385	0.010000	0.17322	0.145000	0.22337	0.877000	0.50540	-1.316000	0.02710	-2.009000	0.00954	-0.140000	0.14226	CGG	.	.		0.552	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		T	24858385	C	T	24858385	2	4	23	1	0	0	0	0	0	0	0	1	15015	755	27	1		1	SPATA13	13	24858385	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	444524	24858385	90311493	747	2813										
NBEA	26960	hgsc.bcm.edu	37	chr13	35615180	35615180	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatgtaacatgtcaagcagaAatatggagcatgtttacagc	10	6	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:35615180A>T	ENST00000400445.3	+	2	939	c.405A>T	c.(403-405)gaA>gaT	p.E135D	NBEA_ENST00000310336.4_Missense_Mutation_p.E135D|NBEA_ENST00000540320.1_Missense_Mutation_p.E135D|NBEA_ENST00000379939.2_Missense_Mutation_p.E135D	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	135					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GTCAAGCAGAAATATGGAGCA	0.383																																					p.E135D		Atlas-SNP	.											.	NBEA	340	.	0			c.A405T						.						126	115	119					13																	35615180		1896	4150	6046	SO:0001583	missense	26960	exon2			AGCAGAAATATGG	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.405A>T	chr13.hg19:g.35615180A>T	ENSP00000383295:p.Glu135Asp	123.0	0.0		54.0	45.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.215312	0.79352	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.53640	0.61;0.61;0.61;0.61	5.43	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.65491	0.2696	M	0.80982	2.52	0.80722	D	1	D	0.63880	0.993	D	0.70016	0.967	T	0.65425	-0.6171	10	0.49607	T	0.09	.	8.3159	0.32100	0.8491:0.0:0.1509:0.0	.	135	Q5T321	.	D	135	ENSP00000440951:E135D;ENSP00000383295:E135D;ENSP00000369271:E135D;ENSP00000308534:E135D	ENSP00000308534:E135D	E	+	3	2	NBEA	34513180	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.175000	0.31944	0.910000	0.36722	0.477000	0.44152	GAA	.	.		0.383	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35615180	A	T	35615180	3	4	23	1	0	0	0	0	1	0	0	0	10196	11	1	4	411	4	NBEA	13	35615180	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	10756795	35615180	79554698	748	2814										
ENOX1	55068	hgsc.bcm.edu	37	chr13	43843689	43843689	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttctgactttttgttgtttaActcctcctggatggttagca	8	8	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:43843689A>C	ENST00000261488.6	-	13	2048	c.1471T>G	c.(1471-1473)Tta>Gta	p.L491V	ENOX1_ENST00000412891.1_Missense_Mutation_p.L491V	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	491					rhythmic process (GO:0048511)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(3)|large_intestine(7)|lung(18)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(1)	34		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		TTGTTGTTTAACTCCTCCTGG	0.373																																					p.L491V		Atlas-SNP	.											.	ENOX1	158	.	0			c.T1471G						.						289	239	256					13																	43843689		2203	4300	6503	SO:0001583	missense	55068	exon13			TGTTTAACTCCTC	EF432052	CCDS9389.1	13q14.11	2013-02-12			ENSG00000120658	ENSG00000120658		"RNA binding motif (RRM) containing"	25474	protein-coding gene	gene with protein product		610914				11360993	Standard	NM_001127615		Approved	FLJ10094, PIG38, CNOX, cCNOX	uc001uza.4	Q8TC92	OTTHUMG00000016818	ENST00000261488.6:c.1471T>G	chr13.hg19:g.43843689A>C	ENSP00000261488:p.Leu491Val	72.0	0.0		32.0	26.0	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	hg19	CCDS9389.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.404205	0.62288	.	.	ENSG00000120658	ENST00000261488;ENST00000412891	T;T	0.49139	0.79;0.79	5.95	2.3	0.28687	.	0.000000	0.85682	D	0.000000	T	0.61311	0.2337	M	0.66939	2.045	0.80722	D	1	D	0.63880	0.993	D	0.76071	0.987	T	0.55159	-0.8184	10	0.38643	T	0.18	-8.3657	9.2761	0.37700	0.5578:0.0:0.4422:0.0	.	491	Q8TC92	ENOX1_HUMAN	V	491	ENSP00000261488:L491V;ENSP00000415054:L491V	ENSP00000261488:L491V	L	-	1	2	ENOX1	42741689	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	1.877000	0.39598	0.064000	0.16427	0.533000	0.62120	TTA	.	.		0.373	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993		C	43843689	A	C	43843689	3	2	23	1	0	0	0	0	1	0	0	0	5128	40	2	5	480	5	ENOX1	13	43843689	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	8228509	43843689	71326189	749	2815										
PCDH9	5101	hgsc.bcm.edu	37	chr13	67799558	67799558	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtctggtgtgtaaggggccCtttgtcttgaagcctccttg	13	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:67799558C>A	ENST00000377865.2	-	1	3149	c.3015G>T	c.(3013-3015)aaG>aaT	p.K1005N	PCDH9_ENST00000377861.3_Missense_Mutation_p.K1005N|PCDH9_ENST00000328454.5_Missense_Mutation_p.K1005N|PCDH9_ENST00000456367.1_Missense_Mutation_p.K1005N|PCDH9_ENST00000544246.1_Missense_Mutation_p.K1005N			Q9HC56	PCDH9_HUMAN	protocadherin 9	1005					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GTAAGGGGCCCTTTGTCTTGA	0.478																																					p.K1005N		Atlas-SNP	.											.	PCDH9	252	.	0			c.G3015T						.						111	100	104					13																	67799558		2203	4300	6503	SO:0001583	missense	5101	exon2			GGGGCCCTTTGTC	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.3015G>T	chr13.hg19:g.67799558C>A	ENSP00000367096:p.Lys1005Asn	157.0	0.0		177.0	82.0	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	C	7.879	0.729818	0.15507	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.54071	0.63;0.63;0.59;0.59;0.59	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.33147	0.0853	N	0.08118	0	0.58432	D	0.999998	P;P;P;P	0.45902	0.791;0.478;0.868;0.791	B;B;P;B	0.45037	0.277;0.191;0.467;0.277	T	0.15378	-1.0439	10	0.07990	T	0.79	.	12.6988	0.57020	0.0:0.9241:0.0:0.0759	.	1005;1005;1005;1005	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	N	1005	ENSP00000442186:K1005N;ENSP00000367096:K1005N;ENSP00000401699:K1005N;ENSP00000332060:K1005N;ENSP00000367092:K1005N	ENSP00000332060:K1005N	K	-	3	2	PCDH9	66697559	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.595000	0.61048	2.651000	0.90000	0.655000	0.94253	AAG	.	.		0.478	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		A	67799558	C	A	67799558	3	1	23	1	0	0	0	0	1	0	0	0	11527	680	24	3	714	3	PCDH9	13	67799558	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	23955869	67799558	47370320	750	2816										
SLITRK6	84189	hgsc.bcm.edu	37	chr13	86369655	86369655	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctttgcagttacaaggaataGggcagtaaggtcctggaagt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:86369655delG	ENST00000400286.2	-	2	1587	c.989delC	c.(988-990)cctfs	p.P330fs		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	330	LRRNT 2.				adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		ACAAGGAATAGGGCAGTAAGG	0.443																																					p.P330fs		Atlas-Indel,Pindel	.											.	SLITRK6	150	.	0			c.990delT						.						146	134	138					13																	86369655		1935	4130	6065	SO:0001589	frameshift_variant	84189	exon2			.	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.989delC	chr13.hg19:g.86369655delG	ENSP00000383143:p.Pro330fs	61.0	0.0		62.0	26.0	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Frame_Shift_Del	DEL	ENST00000400286.2	hg19	CCDS41903.1																																																																																			.	.		0.443	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		-	86369655	G	-	86369655	7	5	23	1	0	1	0	1	0	0	0	0	14762	1000	35	0	1540	0	SLITRK6	13	86369655	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	18570097	86369655	28800223	751	2817										
DZIP1	22873	hgsc.bcm.edu	37	chr13	96239850	96239850	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcttccctcggtcccgtccgCgtcacttttcactgtgttct	8	16	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:96239850C>T	ENST00000376829.2	-	20	3012	c.2161G>A	c.(2161-2163)Gcg>Acg	p.A721T	DZIP1_ENST00000347108.3_Missense_Mutation_p.A721T|DZIP1_ENST00000361156.3_Missense_Mutation_p.A702T|DZIP1_ENST00000361396.2_Missense_Mutation_p.A702T	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	721					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			GTCCCGTCCGCGTCACTTTTC	0.562																																					p.A721T		Atlas-SNP	.											.	DZIP1	195	.	0			c.G2161A						.						173	147	156					13																	96239850		2203	4300	6503	SO:0001583	missense	22873	exon20			CGTCCGCGTCACT	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.2161G>A	chr13.hg19:g.96239850C>T	ENSP00000366025:p.Ala721Thr	102.0	0.0		107.0	43.0	NM_198968	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	hg19	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	C	0.068	-1.207475	0.01568	.	.	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.27720	1.65;1.65;1.65;1.65	5.35	2.81	0.32909	.	1.015710	0.07822	N	0.959900	T	0.05364	0.0142	N	0.00119	-2.075	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.41270	-0.9518	10	0.02654	T	1	-7.3955	3.6649	0.08252	0.1635:0.1909:0.0:0.6456	.	702;721	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	T	721;702;702;721	ENSP00000257312:A721T;ENSP00000355018:A702T;ENSP00000355175:A702T;ENSP00000366025:A721T	ENSP00000257312:A721T	A	-	1	0	DZIP1	95037851	0.023000	0.18921	0.932000	0.37286	0.075000	0.17131	0.150000	0.16263	0.877000	0.35895	-0.302000	0.09304	GCG	.	.		0.562	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		T	96239850	C	T	96239850	3	4	23	1	0	0	0	0	1	0	0	0	4865	768	27	1	458	1	DZIP1	13	96239850	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	9870195	96239850	18930028	752	2818										
DZIP1	22873	hgsc.bcm.edu	37	chr13	96274617	96274617	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgactatcaagaagctgcaTgacattatggaaatcctggg	10	8	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:96274617T>C	ENST00000376829.2	-	9	1941	c.1090A>G	c.(1090-1092)Atg>Gtg	p.M364V	DZIP1_ENST00000347108.3_Missense_Mutation_p.M364V|DZIP1_ENST00000361156.3_Missense_Mutation_p.M364V|DZIP1_ENST00000361396.2_Missense_Mutation_p.M364V	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	364					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			AGAAGCTGCATGACATTATGG	0.433																																					p.M364V		Atlas-SNP	.											.	DZIP1	195	.	0			c.A1090G						.						215	178	191					13																	96274617		2203	4300	6503	SO:0001583	missense	22873	exon9			GCTGCATGACATT	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.1090A>G	chr13.hg19:g.96274617T>C	ENSP00000366025:p.Met364Val	66.0	0.0		86.0	18.0	NM_014934	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	hg19	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	T	1.642	-0.516340	0.04200	.	.	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.03	-0.721	0.11189	.	0.585038	0.20068	N	0.099936	T	0.15998	0.0385	N	0.08118	0	0.23762	N	0.996911	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.25572	-1.0128	10	0.10377	T	0.69	-7.991	6.0699	0.19883	0.0:0.1661:0.4259:0.408	.	364;364	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	V	364	ENSP00000257312:M364V;ENSP00000355018:M364V;ENSP00000355175:M364V;ENSP00000366025:M364V	ENSP00000257312:M364V	M	-	1	0	DZIP1	95072618	0.947000	0.32204	0.998000	0.56505	0.413000	0.31143	0.501000	0.22578	0.030000	0.15379	-1.089000	0.02181	ATG	.	.		0.433	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		C	96274617	T	C	96274617	3	2	23	1	0	0	0	0	1	0	0	0	4865	1464	51	2	1573	2	DZIP1	13	96274617	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	34767	96274617	18895261	753	2819										
COL4A1	1282	hgsc.bcm.edu	37	chr13	110864792	110864792	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cattgcatcctggaatacctGgggggcctggcgggccgtct							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:110864792delG	ENST00000375820.4	-	6	480	c.359delC	c.(358-360)ccafs	p.P120fs	COL4A1_ENST00000543140.1_Frame_Shift_Del_p.P120fs	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	120					axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)	p.P120Q(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TGGAATACCTGGGGGGCCTGG	0.453																																					p.P120fs		Atlas-Indel,Pindel	.											.	COL4A1	372	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.360delA						.						133	156	148					13																	110864792		2203	4300	6503	SO:0001589	frameshift_variant	1282	exon6			.	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.359delC	chr13.hg19:g.110864792delG	ENSP00000364979:p.Pro120fs	107.0	0.0		103.0	46.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Frame_Shift_Del	DEL	ENST00000375820.4	hg19	CCDS9511.1																																																																																			.	.		0.453	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			-	110864792	G	-	110864792	7	5	23	1	0	1	0	1	0	0	0	0	3691	1348	47	0	4838	0	COL4A1	13	110864792	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	14590175	110864792	4305086	754	2820										
MCF2L	23263	hgsc.bcm.edu	37	chr13	113718636	113718636	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggtcataatgctgagctccGtaccagacttacacggttac	9	11	1	2	rs563320301		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:113718636G>A	ENST00000375608.3	+	7	656	c.598G>A	c.(598-600)Gta>Ata	p.V200I	MCF2L_ENST00000421756.1_Missense_Mutation_p.V174I|MCF2L_ENST00000535094.2_Missense_Mutation_p.V170I|MCF2L_ENST00000423482.2_Missense_Mutation_p.V168I|MCF2L_ENST00000397030.1_Missense_Mutation_p.V203I|MCF2L_ENST00000375597.4_Missense_Mutation_p.V168I|MCF2L_ENST00000434480.2_Missense_Mutation_p.V176I|MCF2L_ENST00000375604.2_Missense_Mutation_p.V227I|MCF2L_ENST00000442652.2_Missense_Mutation_p.V200I|MCF2L_ENST00000375601.3_Missense_Mutation_p.V174I			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	200	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				GCTGAGCTCCGTACCAGACTT	0.567													G|||	1	0.000199681	0	0	5008	,	,		18820	0		0	False		,,,				2504	0.001				p.V170I		Atlas-SNP	.											.	MCF2L	182	.	0			c.G508A						.						168	135	146					13																	113718636		2203	4300	6503	SO:0001583	missense	23263	exon6			AGCTCCGTACCAG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.598G>A	chr13.hg19:g.113718636G>A	ENSP00000364758:p.Val200Ile	78.0	0.0		62.0	16.0	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	hg19		.	.	.	.	.	.	.	.	.	.	G	10.63	1.405376	0.25378	.	.	ENSG00000126217	ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000430480;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000423251;ENST00000440749	T;T;T;T;T;T;T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02	5.26	5.26	0.73747	Cellular retinaldehyde-binding/triple function, C-terminal (3);	0.195605	0.45606	D	0.000350	T	0.51975	0.1706	L	0.38838	1.175	0.31522	N	0.662231	P;P;P;P;B;P	0.37466	0.453;0.596;0.453;0.509;0.307;0.509	B;B;B;B;B;B	0.34242	0.064;0.178;0.064;0.129;0.064;0.106	T	0.62854	-0.6766	10	0.44086	T	0.13	.	15.2767	0.73748	0.0:0.1404:0.8596:0.0	.	168;170;227;132;168;200	E9PDN8;O15068-9;G5E9A1;E2QRA2;O15068-4;O15068	.;.;.;.;.;MCF2L_HUMAN	I	200;200;227;203;170;170;174;174;176;168;168;90;11	ENSP00000364758:V200I;ENSP00000401422:V200I;ENSP00000364754:V227I;ENSP00000380225:V203I;ENSP00000440374:V170I;ENSP00000397285:V174I;ENSP00000364751:V174I;ENSP00000407722:V176I;ENSP00000405639:V168I;ENSP00000364747:V168I;ENSP00000405996:V90I	ENSP00000364747:V168I	V	+	1	0	MCF2L	112766637	0.909000	0.30893	0.906000	0.35671	0.067000	0.16453	1.376000	0.34306	2.456000	0.83038	0.555000	0.69702	GTA	.	.		0.567	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			A	113718636	G	A	113718636	3	1	23	1	0	0	0	0	1	0	0	0	9388	1145	40	1	796	1	MCF2L	13	113718636	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2853844	113718636	1451242	755	2821										
RASA3	22821	hgsc.bcm.edu	37	chr13	114784388	114784388	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	accattgtcccggggctggaGgaagtacctgggtgggaggg	19	8	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:114784388G>T	ENST00000334062.7	-	10	914	c.793C>A	c.(793-795)Ctc>Atc	p.L265I	RASA3_ENST00000542651.1_3'UTR|RASA3_ENST00000389544.4_Missense_Mutation_p.L233I	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	265					calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			CGGGGCTGGAGGAAGTACCTG	0.597																																					p.L265I		Atlas-SNP	.											.	RASA3	83	.	0			c.C793A						.						103	92	96					13																	114784388		2203	4300	6503	SO:0001583	missense	22821	exon10			GCTGGAGGAAGTA		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"Pleckstrin homology (PH) domain containing"	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.793C>A	chr13.hg19:g.114784388G>T	ENSP00000335029:p.Leu265Ile	117.0	0.0		102.0	49.0	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	hg19	CCDS32016.1	.	.	.	.	.	.	.	.	.	.	G	19.90	3.912115	0.72983	.	.	ENSG00000185989	ENST00000334062;ENST00000389544	T;T	0.81078	-1.45;-1.45	4.62	4.62	0.57501	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.90960	0.7158	M	0.89287	3.02	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.92590	0.6082	9	.	.	.	.	16.2114	0.82164	0.0:0.0:1.0:0.0	.	265	Q14644	RASA3_HUMAN	I	265;233	ENSP00000335029:L265I;ENSP00000374195:L233I	.	L	-	1	0	RASA3	113802490	1.000000	0.71417	0.995000	0.50966	0.300000	0.27592	6.498000	0.73679	2.066000	0.61787	0.467000	0.42956	CTC	.	.		0.597	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368		T	114784388	G	T	114784388	3	4	23	1	0	0	0	0	1	0	0	0	13077	1000	35	3	1771	3	RASA3	13	114784388	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1065752	114784388	385490	756	2822										
TTC5	91875	hgsc.bcm.edu	37	chr14	20757848	20757848	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctgctggatccctgaggctTcccattcaccactagcagga	10	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:20757848T>A	ENST00000258821.3	-	10	1317	c.1261A>T	c.(1261-1263)Aag>Tag	p.K421*	TTC5_ENST00000556592.1_5'Flank	NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	421					DNA repair (GO:0006281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		CCCTGAGGCTTCCCATTCACC	0.527																																					p.K421X		Atlas-SNP	.											.	TTC5	34	.	0			c.A1261T						.						82	63	69					14																	20757848		2203	4300	6503	SO:0001587	stop_gained	91875	exon10			GAGGCTTCCCATT	BC008647	CCDS9546.1	14q11.2	2013-01-11			ENSG00000136319	ENSG00000136319		"Tetratricopeptide (TTC) repeat domain containing"	19274	protein-coding gene	gene with protein product						11511361	Standard	NM_138376		Approved	Strap	uc001vwt.3	Q8N0Z6	OTTHUMG00000029506	ENST00000258821.3:c.1261A>T	chr14.hg19:g.20757848T>A	ENSP00000258821:p.Lys421*	89.0	0.0		78.0	28.0	NM_138376	A8MQ18|Q96HF9	Nonsense_Mutation	SNP	ENST00000258821.3	hg19	CCDS9546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.8|24.8	4.570075|4.570075	0.86542|0.86542	.|.	.|.	ENSG00000136319|ENSG00000136319	ENST00000423949|ENST00000258821	.|.	.|.	.|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.35653|.	0.0939|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.20107|.	-1.0285|.	4|.	.|0.02654	.|T	.|1	.|.	12.8401|12.8401	0.57797|0.57797	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	V|X	365|421	.|.	.|ENSP00000258821:K421X	E|K	-|-	2|1	0|0	TTC5|TTC5	19827688|19827688	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.786000|0.786000	0.44442|0.44442	5.252000|5.252000	0.65445|0.65445	2.224000|2.224000	0.72417|0.72417	0.528000|0.528000	0.53228|0.53228	GAA|AAG	.	.		0.527	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376		A	20757848	T	A	20757848	4	1	23	1	0	0	0	0	0	1	0	0	16726	1792	62	4	65	4	TTC5	14	20757848	Nonsense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10		20757848	86591692	757	2823										
RNASE7	84659	hgsc.bcm.edu	37	chr14	21511475	21511475	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggggccgtgtccctgaccatGtgtaagctcacctcagggaa	13	12	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:21511475G>A	ENST00000298690.4	+	2	581	c.324G>A	c.(322-324)atG>atA	p.M108I	NDRG2_ENST00000403829.3_Intron	NM_032572.3	NP_115961	Q9H1E1	RNAS7_HUMAN	ribonuclease, RNase A family, 7	108					antibacterial humoral response (GO:0019731)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|membrane disruption in other organism (GO:0051673)|response to bacterium (GO:0009617)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|lipopolysaccharide binding (GO:0001530)|nucleic acid binding (GO:0003676)|peptidoglycan binding (GO:0042834)|ribonuclease activity (GO:0004540)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	6	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;3.42e-11)|Epithelial(56;5.57e-09)|all cancers(55;2.36e-08)	GBM - Glioblastoma multiforme(265;0.0191)		CCCTGACCATGTGTAAGCTCA	0.547																																					p.M108I		Atlas-SNP	.											.	RNASE7	18	.	0			c.G324A						.						113	109	110					14																	21511475		2203	4300	6503	SO:0001583	missense	84659	exon2			GACCATGTGTAAG	AJ131212	CCDS41914.1	14q11.1	2013-02-15			ENSG00000165799	ENSG00000165799		"Ribonucleases, RNase A"	19278	protein-coding gene	gene with protein product		612484				12244054, 12527768	Standard	NM_032572		Approved		uc001vzk.4	Q9H1E1	OTTHUMG00000171358	ENST00000298690.4:c.324G>A	chr14.hg19:g.21511475G>A	ENSP00000298690:p.Met108Ile	103.0	0.0		92.0	42.0	NM_032572	P80927|P83685|Q546N3	Missense_Mutation	SNP	ENST00000298690.4	hg19	CCDS41914.1	.	.	.	.	.	.	.	.	.	.	G	7.704	0.693799	0.15039	.	.	ENSG00000165799	ENST00000298690	T	0.12672	2.66	4.94	-1.93	0.07594	Ribonuclease A, domain (4);	3.249820	0.01107	U	0.005496	T	0.09555	0.0235	N	0.25789	0.76	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.25676	-1.0125	10	0.22109	T	0.4	4.1987	5.1682	0.15096	0.344:0.3222:0.3338:0.0	.	108	Q9H1E1	RNAS7_HUMAN	I	108	ENSP00000298690:M108I	ENSP00000298690:M108I	M	+	3	0	RNASE7	20581315	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-1.835000	0.01692	-0.282000	0.09128	-0.150000	0.13652	ATG	.	.		0.547	RNASE7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313936.1	NM_032572		A	21511475	G	A	21511475	3	1	23	1	0	0	0	0	1	0	0	0	13423	1377	48	3	326	3	RNASE7	14	21511475	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	753627	21511475	85838065	758	2824										
ZNF219	51222	hgsc.bcm.edu	37	chr14	21560611	21560611	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaaaccaagactgtgtaaagCtctggccgcacacttggcag	11	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:21560611C>A	ENST00000360947.3	-	3	1256	c.845G>T	c.(844-846)aGc>aTc	p.S282I	ZNF219_ENST00000451119.2_Missense_Mutation_p.S282I|ZNF219_ENST00000556101.1_5'Flank|ZNF219_ENST00000421093.2_Missense_Mutation_p.S282I|RP11-998D10.7_ENST00000554733.2_lincRNA	NM_016423.2	NP_057507.2	Q9P2Y4	ZN219_HUMAN	zinc finger protein 219	282					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurotransmitter levels (GO:0001505)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histamine receptor activity (GO:0004969)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(2)	8	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;9.86e-11)|Epithelial(56;1.27e-08)|all cancers(55;6.06e-08)	GBM - Glioblastoma multiforme(265;0.0191)		CTGTGTAAAGCTCTGGCCGCA	0.657											OREG0022565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S282I		Atlas-SNP	.											.	ZNF219	28	.	0			c.G845T						.						19	19	19					14																	21560611		2179	4273	6452	SO:0001583	missense	51222	exon3			GTAAAGCTCTGGC	AB015427	CCDS9568.1	14q11	2013-01-08			ENSG00000165804	ENSG00000165804		"Zinc fingers, C2H2-type"	13011	protein-coding gene	gene with protein product		605036				10819330	Standard	NM_016423		Approved		uc001vzs.2	Q9P2Y4	OTTHUMG00000029647	ENST00000360947.3:c.845G>T	chr14.hg19:g.21560611C>A	ENSP00000354206:p.Ser282Ile	99.0	0.0	749	87.0	34.0	NM_001102454	D3DS16|Q53Y57|Q8IYC1|Q9BW28	Missense_Mutation	SNP	ENST00000360947.3	hg19	CCDS9568.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.063011	0.76187	.	.	ENSG00000165804	ENST00000360947;ENST00000451119;ENST00000421093	T;T;T	0.56275	0.47;0.47;0.47	4.65	4.65	0.58169	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.053653	0.64402	D	0.000001	T	0.53334	0.1790	L	0.48877	1.53	0.38614	D	0.95097	P	0.49253	0.921	P	0.47251	0.542	T	0.62053	-0.6935	10	0.62326	D	0.03	-25.2119	15.0771	0.72084	0.0:1.0:0.0:0.0	.	282	Q9P2Y4	ZN219_HUMAN	I	282	ENSP00000354206:S282I;ENSP00000388558:S282I;ENSP00000392401:S282I	ENSP00000354206:S282I	S	-	2	0	ZNF219	20630451	0.007000	0.16637	1.000000	0.80357	0.985000	0.73830	0.373000	0.20484	2.414000	0.81942	0.467000	0.42956	AGC	.	.		0.657	ZNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073931.2			A	21560611	C	A	21560611	3	1	23	1	0	0	0	0	1	0	0	0	17788	797	28	3	1335	3	ZNF219	14	21560611	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	49136	21560611	85788929	759	2825										
OR4E2	26686	hgsc.bcm.edu	37	chr14	22133945	22133945	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtttcttggccgtggtcaccTcctatatggtcatcctggtt	10	11	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:22133945T>A	ENST00000408935.1	+	1	649	c.649T>A	c.(649-651)Tcc>Acc	p.S217T		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		CGTGGTCACCTCCTATATGGT	0.512																																					p.S217T		Atlas-SNP	.											.	OR4E2	44	.	0			c.T649A						.						154	142	146					14																	22133945		1973	4159	6132	SO:0001583	missense	26686	exon1			GTCACCTCCTATA		CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"GPCR / Class A : Olfactory receptors"	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.649T>A	chr14.hg19:g.22133945T>A	ENSP00000386195:p.Ser217Thr	153.0	0.0		187.0	9.0	NM_001001912	Q6IET6|Q96R62	Missense_Mutation	SNP	ENST00000408935.1	hg19	CCDS41916.1	.	.	.	.	.	.	.	.	.	.	T	14.47	2.544075	0.45280	.	.	ENSG00000221977	ENST00000408935	T	0.42900	0.96	5.59	5.59	0.84812	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37955	U	0.001878	T	0.68732	0.3033	M	0.87827	2.91	0.38657	D	0.951984	D	0.89917	1.0	D	0.87578	0.998	T	0.76997	-0.2751	10	0.87932	D	0	.	13.9921	0.64374	0.0:0.0:0.0:1.0	.	217	Q8NGC2	OR4E2_HUMAN	T	217	ENSP00000386195:S217T	ENSP00000386195:S217T	S	+	1	0	OR4E2	21203785	0.998000	0.40836	0.988000	0.46212	0.120000	0.20174	2.928000	0.48908	2.244000	0.73946	0.482000	0.46254	TCC	.	.		0.512	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1			A	22133945	T	A	22133945	3	1	23	1	0	0	0	0	1	0	0	0	11069	1551	54	4	651	4	OR4E2	14	22133945	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	573334	22133945	85215595	760	2826										
MMP14	4323	hgsc.bcm.edu	37	chr14	23315224	23315224	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggcgactgctctactgccaGcgttccctgctggacaaggt	12	13	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:23315224G>A	ENST00000311852.6	+	10	1986	c.1725G>A	c.(1723-1725)caG>caA	p.Q575Q	MMP14_ENST00000548162.1_Intron	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	575					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	TCTACTGCCAGCGTTCCCTGC	0.657																																					p.Q575Q		Atlas-SNP	.											.	MMP14	40	.	0			c.G1725A						.						14	14	14					14																	23315224		2165	4253	6418	SO:0001819	synonymous_variant	4323	exon10			CTGCCAGCGTTCC		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"membrane type 1 metalloprotease"	600754	"matrix metalloproteinase 14 (membrane-inserted)"			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.1725G>A	chr14.hg19:g.23315224G>A		64.0	0.0		54.0	14.0	NM_004995	A8K5L0|Q6GSF3|Q92678	Silent	SNP	ENST00000311852.6	hg19	CCDS9577.1																																																																																			.	.		0.657	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995		A	23315224	G	A	23315224	2	1	23	1	0	0	0	0	0	0	0	1	9662	962	34	3		3	MMP14	14	23315224	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1181279	23315224	84034316	761	2827										
SLC7A8	23428	hgsc.bcm.edu	37	chr14	23652042	23652042	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tactccgccccctccggaacCagcctcggggctggcgtccg	12	19	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:23652042C>G	ENST00000316902.7	-	1	807	c.82G>C	c.(82-84)Ggt>Cgt	p.G28R	C14orf164_ENST00000399910.1_5'Flank|SLC7A8_ENST00000469263.1_Missense_Mutation_p.G28R	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	28					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	CCTCCGGAACCAGCCTCGGGG	0.592																																					p.G28R		Atlas-SNP	.											.	SLC7A8	54	.	0			c.G82C						.						119	118	118					14																	23652042		2203	4300	6503	SO:0001583	missense	23428	exon1			CGGAACCAGCCTC	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"Solute carriers"	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.82G>C	chr14.hg19:g.23652042C>G	ENSP00000320378:p.Gly28Arg	75.0	0.0		70.0	24.0	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000316902.7	hg19	CCDS9590.1	.	.	.	.	.	.	.	.	.	.	C	9.958	1.221909	0.22457	.	.	ENSG00000092068	ENST00000316902;ENST00000469263;ENST00000524758;ENST00000525062	D;D;D;D	0.94758	-2.66;-3.01;-2.82;-3.51	5.45	3.61	0.41365	.	2.000960	0.02338	N	0.074602	D	0.89364	0.6694	N	0.19112	0.55	0.19300	N	0.999978	B;B	0.25955	0.138;0.037	B;B	0.21917	0.037;0.019	T	0.78150	-0.2316	10	0.17832	T	0.49	.	8.043	0.30532	0.0:0.7462:0.0:0.2538	.	28;28	E9PLV9;Q9UHI5	.;LAT2_HUMAN	R	28	ENSP00000320378:G28R;ENSP00000435114:G28R;ENSP00000434352:G28R;ENSP00000436665:G28R	ENSP00000320378:G28R	G	-	1	0	SLC7A8	22721882	0.002000	0.14202	0.001000	0.08648	0.565000	0.35776	0.845000	0.27668	0.654000	0.30846	0.462000	0.41574	GGT	.	.		0.592	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3			G	23652042	C	G	23652042	3	3	23	1	0	0	0	0	1	0	0	0	14719	594	21	4	1569	4	SLC7A8	14	23652042	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	336818	23652042	83697498	762	2828										
MYH6	4624	hgsc.bcm.edu	37	chr14	23863388	23863388	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcgtctctttgatgcgcccGaactcttccttcatggtggc	10	13	3	1	rs148596692		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:23863388G>A	ENST00000356287.3	-	20	2603	c.2574C>T	c.(2572-2574)ttC>ttT	p.F858F	MYH6_ENST00000405093.3_Silent_p.F858F			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	858					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TGATGCGCCCGAACTCTTCCT	0.572																																					p.F858F		Atlas-SNP	.											MYH6,NS,adenoma,0,1	MYH6	274	.	0			c.C2574T						.	G		1,4405	2.1+/-5.4	0,1,2202	137	120	126		2574	-5.9	0.8	14	dbSNP_134	126	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MYH6	NM_002471.3		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		858/1940	23863388	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon21			GCGCCCGAACTCT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.2574C>T	chr14.hg19:g.23863388G>A		111.0	0.0		101.0	51.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	hg19	CCDS9600.1																																																																																			.	G|1.000;A|0.000		0.572	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23863388	G	A	23863388	2	1	23	1	0	0	0	0	0	0	0	1	10047	1049	37	1		1	MYH6	14	23863388	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	211346	23863388	83486152	763	2829										
DHRS4L2	317749	hgsc.bcm.edu	37	chr14	24470144	24470144	+	Splice_Site	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagaaatggagaaacgagggTacagagagtgagagagagcc					rs375757538		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:24470144delT	ENST00000335125.6	+	4	605		c.e4+2		DHRS4L2_ENST00000382755.4_Splice_Site|DHRS4L2_ENST00000545240.1_Intron|DHRS4L2_ENST00000397071.1_Intron|DHRS4L2_ENST00000543805.1_Intron|DHRS4L2_ENST00000537912.1_Intron|DHRS4L2_ENST00000534993.1_Intron|DHRS4L2_ENST00000558753.1_Intron	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2							extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		GAAACGAGGGTACAGAGAGTG	0.552																																					.		Atlas-Indel,Pindel	.											.	DHRS4L2	29	.	0			c.176+1T>-						.						90	95	94					14																	24470144		2196	4299	6495	SO:0001630	splice_region_variant	317749	exon4			.		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	19731	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 25C, member 3"	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.479+2T>-	chr14.hg19:g.24470144delT		555.0	0.0		577.0	209.0	NM_001193636	Q3YLD4	Splice_Site	DEL	ENST00000335125.6	hg19	CCDS9606.2																																																																																			.	.		0.552	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		Intron	-	24470144	T	-	24470144	8	5	23	1	0	1	0	1	0	0	1	0	4496	1652	57	0	495	0	DHRS4L2	14	24470144	Splice_Site	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	606756	24470144	82879396	764	2830										
CPNE6	9362	hgsc.bcm.edu	37	chr14	24542179	24542179	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agatgggatgggtgcctgagCccccaaccatgacgctgggg	16	11	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:24542179C>G	ENST00000397016.2	+	3	345	c.34C>G	c.(34-36)Ccc>Gcc	p.P12A	CPNE6_ENST00000216775.2_Missense_Mutation_p.P12A|CPNE6_ENST00000560092.1_Intron|CPNE6_ENST00000537691.1_Missense_Mutation_p.P67A	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	12					lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		GGTGCCTGAGCCCCCAACCAT	0.652																																					p.P12A		Atlas-SNP	.											.	CPNE6	40	.	0			c.C34G						.						36	31	33					14																	24542179		2203	4300	6503	SO:0001583	missense	9362	exon2			CCTGAGCCCCCAA	AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.34C>G	chr14.hg19:g.24542179C>G	ENSP00000380211:p.Pro12Ala	51.0	0.0		63.0	23.0	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Missense_Mutation	SNP	ENST00000397016.2	hg19	CCDS9607.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.952545	0.34471	.	.	ENSG00000100884	ENST00000537691;ENST00000397016;ENST00000216775	T;T;T	0.07908	3.15;3.23;3.23	4.58	4.58	0.56647	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.45361	D	0.000375	T	0.03871	0.0109	N	0.02539	-0.55	0.34692	D	0.725858	B;P	0.37141	0.32;0.584	B;B	0.35114	0.119;0.196	T	0.43376	-0.9395	10	0.51188	T	0.08	-12.8409	13.0802	0.59109	0.0:1.0:0.0:0.0	.	67;12	F5GXN1;O95741	.;CPNE6_HUMAN	A	67;12;12	ENSP00000440077:P67A;ENSP00000380211:P12A;ENSP00000216775:P12A	ENSP00000216775:P12A	P	+	1	0	CPNE6	23612019	0.224000	0.23674	1.000000	0.80357	0.998000	0.95712	0.455000	0.21843	2.543000	0.85770	0.563000	0.77884	CCC	.	.		0.652	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5			G	24542179	C	G	24542179	3	3	23	1	0	0	0	0	1	0	0	0	3818	739	26	4	36	4	CPNE6	14	24542179	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	72035	24542179	82807361	765	2831										
RIPK3	11035	hgsc.bcm.edu	37	chr14	24806911	24806911	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggcactcaccgtggagacaGcagcattcatattgttctcc	9	12	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:24806911G>A	ENST00000216274.5	-	7	1108	c.890C>T	c.(889-891)gCt>gTt	p.A297V	RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000396747.3_5'Flank|RP11-934B9.3_ENST00000555591.1_5'Flank|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000418030.2_5'Flank|ADCY4_ENST00000554068.2_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	297					activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		CGTGGAGACAGCAGCATTCAT	0.532																																					p.A297V	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C890T						.						152	129	136					14																	24806911		2203	4300	6503	SO:0001583	missense	11035	exon7			GAGACAGCAGCAT	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.890C>T	chr14.hg19:g.24806911G>A	ENSP00000216274:p.Ala297Val	130.0	0.0		109.0	37.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	hg19	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.523546	0.44866	.	.	ENSG00000129465	ENST00000216274	T	0.79141	-1.24	4.67	4.67	0.58626	Protein kinase-like domain (1);	0.269320	0.26891	N	0.021972	T	0.73521	0.3597	L	0.34521	1.04	0.09310	N	0.999991	D	0.60160	0.987	P	0.49528	0.614	T	0.67624	-0.5623	10	0.48119	T	0.1	-5.7202	13.3819	0.60773	0.0:0.0:1.0:0.0	.	297	Q9Y572	RIPK3_HUMAN	V	297	ENSP00000216274:A297V	ENSP00000216274:A297V	A	-	2	0	RIPK3	23876751	0.048000	0.20356	0.224000	0.23877	0.009000	0.06853	2.340000	0.43974	2.876000	0.98609	0.655000	0.94253	GCT	.	.		0.532	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		A	24806911	G	A	24806911	3	1	23	1	0	0	0	0	1	0	0	0	13397	971	34	3	682	3	RIPK3	14	24806911	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	264732	24806911	82542629	766	2832										
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24877520	24877520	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttcggcatctctgactcccActccgatccggaggttctaa	8	15	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:24877520A>G	ENST00000382554.3	+	3	962	c.644A>G	c.(643-645)cAc>cGc	p.H215R		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	215					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						TCTGACTCCCACTCCGATCCG	0.637																																					p.H215R		Atlas-SNP	.											.	NYNRIN	120	.	0			c.A644G						.						38	45	43					14																	24877520		2080	4221	6301	SO:0001583	missense	57523	exon3			ACTCCCACTCCGA	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.644A>G	chr14.hg19:g.24877520A>G	ENSP00000371994:p.His215Arg	23.0	0.0		38.0	17.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.186074	0.00305	.	.	ENSG00000205978	ENST00000382554	T	0.08984	3.03	4.85	-5.98	0.02220	.	2.517910	0.01251	N	0.008885	T	0.02230	0.0069	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38436	-0.9661	10	0.02654	T	1	.	3.6155	0.08075	0.2548:0.1101:0.4928:0.1423	.	215	Q9P2P1	NYNRI_HUMAN	R	215	ENSP00000371994:H215R	ENSP00000371994:H215R	H	+	2	0	NYNRIN	23947360	0.000000	0.05858	0.000000	0.03702	0.283000	0.27025	-0.224000	0.09164	-0.839000	0.04212	0.533000	0.62120	CAC	.	.		0.637	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			G	24877520	A	G	24877520	3	3	23	1	0	0	0	0	1	0	0	0	10805	159	6	2	650	2	NYNRIN	14	24877520	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	70609	24877520	82472020	767	2833										
C14orf126	112487	hgsc.bcm.edu	37	chr14	31926576	31926576	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtaggagcgcccgggcctgAggaatccggctaccctcagc	14	14	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:31926576A>C	ENST00000310850.4	-	1	140	c.24T>G	c.(22-24)ccT>ccG	p.P8P	DTD2_ENST00000356180.4_Silent_p.P8P|RP11-176H8.1_ENST00000547378.1_Silent_p.P8P	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	8					D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)										CCCGGGCCTGAGGAATCCGGC	0.697																																					p.P8P		Atlas-SNP	.											.	.	.	.	0			c.T24G						.						12	13	13					14																	31926576		2189	4279	6468	SO:0001819	synonymous_variant	112487	exon1			GGCCTGAGGAATC	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 126"	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.24T>G	chr14.hg19:g.31926576A>C		223.0	0.0		220.0	88.0	NM_080664	D3DS87	Silent	SNP	ENST00000310850.4	hg19	CCDS9643.1																																																																																			.	.		0.697	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664		C	31926576	A	C	31926576	2	2	23	1	0	0	0	0	0	0	0	1	1745	291	11	5		5	C14orf126	14	31926576	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	7049056	31926576	75422964	768	2834										
PRPF39	55015	hgsc.bcm.edu	37	chr14	45579384	45579384	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tacatctcccaaagaaacccAtggtgcatatgctttgggca	8	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:45579384A>G	ENST00000355765.6	+	9	1434	c.1264A>G	c.(1264-1266)Atg>Gtg	p.M422V	SNORD127_ENST00000458892.1_RNA	NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	422					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						AAAGAAACCCATGGTGCATAT	0.403																																					p.M422V		Atlas-SNP	.											.	PRPF39	46	.	0			c.A1264G						.						122	119	120					14																	45579384		2203	4300	6503	SO:0001583	missense	55015	exon9			AAACCCATGGTGC	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"PRP39 pre-mRNA processing factor 39 homolog (yeast)", "PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.1264A>G	chr14.hg19:g.45579384A>G	ENSP00000348010:p.Met422Val	205.0	0.0		180.0	66.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	A	11.07	1.530724	0.27387	.	.	ENSG00000185246	ENST00000355765	T	0.32023	1.47	5.53	4.39	0.52855	Tetratricopeptide-like helical (1);	0.238501	0.51477	N	0.000084	T	0.22781	0.0550	L	0.36672	1.1	0.38234	D	0.94111	B;B	0.16802	0.0;0.019	B;B	0.18871	0.001;0.023	T	0.08534	-1.0717	10	0.16420	T	0.52	-1.9165	11.0638	0.47964	0.9263:0.0:0.0737:0.0	.	26;422	Q86UA1-2;Q86UA1	.;PRP39_HUMAN	V	422	ENSP00000348010:M422V	ENSP00000348010:M422V	M	+	1	0	PRPF39	44649134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.239000	0.65371	0.937000	0.37394	0.460000	0.39030	ATG	.	.		0.403	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			G	45579384	A	G	45579384	3	3	23	1	0	0	0	0	1	0	0	0	12581	217	8	2	1294	2	PRPF39	14	45579384	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	13652808	45579384	61770156	769	2835										
SOS2	6655	hgsc.bcm.edu	37	chr14	50597348	50597348	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagctcagtttcagcaatccGactaaagcttattttacatg	6	10	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:50597348G>A	ENST00000216373.5	-	20	3482	c.3208C>T	c.(3208-3210)Cgg>Tgg	p.R1070W	SOS2_ENST00000543680.1_Missense_Mutation_p.R1037W	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	1070					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					TCAGCAATCCGACTAAAGCTT	0.448																																					p.R1070W		Atlas-SNP	.											.	SOS2	195	.	0			c.C3208T						.						191	164	173					14																	50597348		2203	4300	6503	SO:0001583	missense	6655	exon20			CAATCCGACTAAA	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11188	protein-coding gene	gene with protein product		601247	"son of sevenless (Drosophilia) homolog 2"			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.3208C>T	chr14.hg19:g.50597348G>A	ENSP00000216373:p.Arg1070Trp	206.0	0.0		213.0	90.0	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	hg19	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546139	0.65198	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.80909	-1.43;-1.3	5.62	4.72	0.59763	.	0.046560	0.85682	D	0.000000	D	0.86276	0.5894	L	0.59436	1.845	0.48696	D	0.999699	D;D	0.76494	0.999;0.999	D;D	0.63793	0.918;0.918	D	0.87554	0.2467	10	0.87932	D	0	.	13.7891	0.63128	0.0:0.0:0.6073:0.3927	.	1037;1070	B7ZKT6;Q07890	.;SOS2_HUMAN	W	1070;1037	ENSP00000216373:R1070W;ENSP00000445328:R1037W	ENSP00000216373:R1070W	R	-	1	2	SOS2	49667098	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.776000	0.38594	1.357000	0.45904	0.484000	0.47621	CGG	.	.		0.448	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2			A	50597348	G	A	50597348	3	1	23	1	0	0	0	0	1	0	0	0	14952	1057	37	1	806	1	SOS2	14	50597348	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	5017964	50597348	56752192	770	2836										
PTGER2	5732	hgsc.bcm.edu	37	chr14	52781730	52781730	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcgcgctccgggggcctggCcgtgctgcctgtcatctatg	14	15	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:52781730C>A	ENST00000245457.5	+	1	618	c.464C>A	c.(463-465)gCc>gAc	p.A155D	PTGER2_ENST00000557436.1_Intron	NM_000956.3	NP_000947.2	P43116	PE2R2_HUMAN	prostaglandin E receptor 2 (subtype EP2), 53kDa	155					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular response to prostaglandin E stimulus (GO:0071380)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cell proliferation (GO:0042127)|response to lipopolysaccharide (GO:0032496)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(41;0.0639)|all_epithelial(31;0.0729)				Alprostadil(DB00770)|Dinoprostone(DB00917)|Misoprostol(DB00929)	GGGGGCCTGGCCGTGCTGCCT	0.657																																					p.A155D		Atlas-SNP	.											.	PTGER2	27	.	0			c.C464A						.						59	64	62					14																	52781730		2203	4300	6503	SO:0001583	missense	5732	exon1			GCCTGGCCGTGCT		CCDS9708.1	14q22	2012-08-08	2002-08-29		ENSG00000125384	ENSG00000125384		"GPCR / Class A : Prostanoid receptors"	9594	protein-coding gene	gene with protein product		176804	"prostaglandin E receptor 2 (subtype EP2), 53kD"			8250933, 7759114	Standard	NM_000956		Approved	EP2	uc001wzr.3	P43116	OTTHUMG00000140300	ENST00000245457.5:c.464C>A	chr14.hg19:g.52781730C>A	ENSP00000245457:p.Ala155Asp	61.0	0.0		54.0	26.0	NM_000956	D3DSC0|Q52LG8	Missense_Mutation	SNP	ENST00000245457.5	hg19	CCDS9708.1	.	.	.	.	.	.	.	.	.	.	C	13.78	2.340399	0.41498	.	.	ENSG00000125384	ENST00000245457	T	0.73681	-0.77	5.23	0.765	0.18470	GPCR, rhodopsin-like superfamily (1);	0.529807	0.21022	N	0.081481	T	0.74749	0.3757	L	0.58810	1.83	0.21719	N	0.999577	P	0.44281	0.831	P	0.52386	0.697	T	0.65245	-0.6215	10	0.66056	D	0.02	-1.6751	6.6937	0.23187	0.0:0.461:0.0:0.539	.	155	P43116	PE2R2_HUMAN	D	155	ENSP00000245457:A155D	ENSP00000245457:A155D	A	+	2	0	PTGER2	51851480	0.001000	0.12720	0.510000	0.27712	0.115000	0.19883	-0.016000	0.12613	0.306000	0.22856	0.563000	0.77884	GCC	.	.		0.657	PTGER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276890.1			A	52781730	C	A	52781730	3	1	23	1	0	0	0	0	1	0	0	0	12756	739	26	3	466	3	PTGER2	14	52781730	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2184382	52781730	54567810	771	2837										
KTN1	3895	hgsc.bcm.edu	37	chr14	56094630	56094630	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cattgctttctcaattgcagTcaagtaagggagaattgact	9	7	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:56094630T>A	ENST00000395314.3	+	6	1032	c.964T>A	c.(964-966)Tca>Aca	p.S322T	KTN1_ENST00000395308.1_Splice_Site_p.S322T|KTN1_ENST00000395309.3_Splice_Site_p.S322T|KTN1_ENST00000416613.1_Splice_Site_p.S322T|KTN1_ENST00000438792.2_Splice_Site_p.S322T|KTN1_ENST00000395311.1_Splice_Site_p.S322T|KTN1_ENST00000413890.2_Splice_Site_p.S322T	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	322					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TCAATTGCAGTCAAGTAAGGG	0.388			T	RET	papillary thryoid																																p.S322T		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.T964A						.						103	87	92					14																	56094630		2203	4300	6503	SO:0001630	splice_region_variant	3895	exon6			TTGCAGTCAAGTA		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.964-1T>A	chr14.hg19:g.56094630T>A		142.0	0.0		144.0	56.0	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	T	10.83	1.461999	0.26248	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613	T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.8	3.28	0.37604	.	0.861201	0.09829	N	0.750471	T	0.29126	0.0724	L	0.29908	0.895	0.29135	N	0.879405	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.24083	-1.0170	9	.	.	.	-0.1021	7.0935	0.25297	0.1172:0.0:0.3281:0.5547	.	322;322;322;322	B4DZ88;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;KTN1_HUMAN	T	322	ENSP00000394992:S322T;ENSP00000378720:S322T;ENSP00000391964:S322T;ENSP00000378725:S322T;ENSP00000378719:S322T;ENSP00000378722:S322T;ENSP00000388807:S322T	.	S	+	1	0	KTN1	55164383	1.000000	0.71417	0.859000	0.33776	0.147000	0.21601	3.031000	0.49728	0.994000	0.38892	0.533000	0.62120	TCA	.	.		0.388	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		Missense_Mutation	A	56094630	T	A	56094630	5	1	23	1	0	0	0	0	0	0	1	0	8594	1681	58	4	982	4	KTN1	14	56094630	Splice_Site	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3312900	56094630	51254910	772	2838										
C14orf101	54916	hgsc.bcm.edu	37	chr14	57051736	57051736	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caggggaactgatcacagccGcacatgagcttggagtaagt	13	9	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:57051736G>A	ENST00000261556.6	+	2	300	c.178G>A	c.(178-180)Gca>Aca	p.A60T	TMEM260_ENST00000538838.1_Missense_Mutation_p.A60T|TMEM260_ENST00000536419.1_5'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	60						integral component of membrane (GO:0016021)											GATCACAGCCGCACATGAGCT	0.318																																					p.A60T		Atlas-SNP	.											.	.	.	.	0			c.G178A						.						99	96	97					14																	57051736		2203	4298	6501	SO:0001583	missense	0	exon2			ACAGCCGCACATG	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 101"	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.178G>A	chr14.hg19:g.57051736G>A	ENSP00000261556:p.Ala60Thr	115.0	0.0		90.0	34.0	NM_017799	A8KAN4|B3KPF5|Q86XE1	Missense_Mutation	SNP	ENST00000261556.6	hg19	CCDS9727.2	.	.	.	.	.	.	.	.	.	.	G	21.2	4.116927	0.77323	.	.	ENSG00000070269	ENST00000556810;ENST00000261556;ENST00000538838	T;T	0.57273	0.98;0.41	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.75882	0.3910	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.79787	-0.1656	10	0.72032	D	0.01	-10.5261	18.8103	0.92056	0.0:0.0:1.0:0.0	.	60	Q9NX78	CN101_HUMAN	T	23;60;60	ENSP00000261556:A60T;ENSP00000441934:A60T	ENSP00000261556:A60T	A	+	1	0	C14orf101	56121489	1.000000	0.71417	0.995000	0.50966	0.933000	0.57130	9.434000	0.97515	2.444000	0.82710	0.650000	0.86243	GCA	.	.		0.318	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799		A	57051736	G	A	57051736	3	1	23	1	0	0	0	0	1	0	0	0	1736	1087	38	1	184	1	C14orf101	14	57051736	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	957106	57051736	50297804	773	2839										
MUDENG	55745	hgsc.bcm.edu	37	chr14	57747061	57747061	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tagtattgatgcaatggatgActctgcatttagtgggcctt	11	6	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:57747061A>G	ENST00000261558.3	+	3	1275	c.869A>G	c.(868-870)gAc>gGc	p.D290G	AP5M1_ENST00000431972.2_Missense_Mutation_p.D304G|AP5M1_ENST00000556723.1_3'UTR	NM_018229.3	NP_060699.3	Q9H0R1	AP5M1_HUMAN	adaptor-related protein complex 5, mu 1 subunit	290	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytosol (GO:0005829)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)											GCAATGGATGACTCTGCATTT	0.413																																					p.D290G		Atlas-SNP	.											.	.	.	.	0			c.A869G						.						219	192	201					14																	57747061		2203	4300	6503	SO:0001583	missense	55745	exon3			TGGATGACTCTGC	AF094583	CCDS9729.1	14q22.2	2012-03-20	2012-03-20	2012-03-20	ENSG00000053770	ENSG00000053770			20192	protein-coding gene	gene with protein product	"Mu-2 related death-inducing gene"	614368	"chromosome 14 open reading frame 108", "MU-2/AP1M2 domain containing, death-inducing"	C14orf108, MUDENG		18395520	Standard	NM_018229		Approved	FLJ10813, MuD, mu5	uc001xcv.3	Q9H0R1	OTTHUMG00000140318	ENST00000261558.3:c.869A>G	chr14.hg19:g.57747061A>G	ENSP00000261558:p.Asp290Gly	144.0	0.0		121.0	60.0	NM_018229	O95354|Q6ZMD7|Q96DX3|Q9NVC5	Missense_Mutation	SNP	ENST00000261558.3	hg19	CCDS9729.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.244038	0.39697	.	.	ENSG00000053770	ENST00000261558;ENST00000431972	T;T	0.19105	2.17;2.17	5.96	5.96	0.96718	Clathrin adaptor, mu subunit, C-terminal (3);	0.044985	0.85682	D	0.000000	T	0.15176	0.0366	N	0.16743	0.435	0.58432	D	0.999997	B	0.02656	0.0	B	0.09377	0.004	T	0.07986	-1.0744	10	0.26408	T	0.33	.	16.4356	0.83874	1.0:0.0:0.0:0.0	.	290	Q9H0R1	MUDEN_HUMAN	G	290;304	ENSP00000261558:D290G;ENSP00000390531:D304G	ENSP00000261558:D290G	D	+	2	0	MUDENG	56816814	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.158000	0.77470	2.280000	0.76307	0.496000	0.49642	GAC	.	.		0.413	AP5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276922.1	NM_018229		G	57747061	A	G	57747061	3	3	23	1	0	0	0	0	1	0	0	0	9992	275	10	2	879	2	MUDENG	14	57747061	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	695325	57747061	49602479	774	2840										
DACT1	51339	hgsc.bcm.edu	37	chr14	59113492	59113492	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgccctacgccagcccctaCgcctacgtggctagcgactc	9	19	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:59113492C>T	ENST00000335867.4	+	4	2175	c.2151C>T	c.(2149-2151)taC>taT	p.Y717Y	DACT1_ENST00000556859.1_Silent_p.Y436Y|DACT1_ENST00000541264.2_Silent_p.Y436Y|DACT1_ENST00000395153.3_Silent_p.Y680Y			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	717					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						CCAGCCCCTACGCCTACGTGG	0.652																																					p.Y717Y		Atlas-SNP	.											DACT1,NS,carcinoma,0,1	DACT1	119	.	0			c.C2151T						.						39	41	40					14																	59113492		2203	4300	6503	SO:0001819	synonymous_variant	51339	exon4			CCCCTACGCCTAC	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"dapper homolog 1, antagonist of beta-catenin (xenopus)", "dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.2151C>T	chr14.hg19:g.59113492C>T		94.0	0.0		74.0	24.0	NM_016651	A8MYJ2|Q86TY0	Silent	SNP	ENST00000335867.4	hg19	CCDS9736.1																																																																																			.	.		0.652	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651		T	59113492	C	T	59113492	2	4	23	1	0	0	0	0	0	0	0	1	4224	547	19	1		1	DACT1	14	59113492	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1366431	59113492	48236048	775	2841										
C14orf149	112849	hgsc.bcm.edu	37	chr14	59950530	59950530	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaggtcccgcccattacctgTggccagcacgaaggccggga	13	14	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:59950530T>C	ENST00000247194.4	-	1	618	c.505A>G	c.(505-507)Aca>Gca	p.T169A	JKAMP_ENST00000425728.2_5'Flank|JKAMP_ENST00000356057.5_5'Flank|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000261247.9_5'Flank|L3HYPDH_ENST00000487285.1_5'Flank|JKAMP_ENST00000554271.1_5'Flank|JKAMP_ENST00000556985.1_5'Flank	NM_144581.1	NP_653182.1	Q96EM0	T3HPD_HUMAN	L-3-hydroxyproline dehydratase (trans-)	169					metabolic process (GO:0008152)		hydro-lyase activity (GO:0016836)|trans-L-3-hydroxyproline dehydratase activity (GO:0050346)									L-Proline(DB00172)	CCATTACCTGTGGCCAGCACG	0.647											OREG0022712	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T169A		Atlas-SNP	.											.	.	.	.	0			c.A505G						.						8	9	9					14																	59950530		2108	4156	6264	SO:0001583	missense	112849	exon1			TACCTGTGGCCAG	AI762327	CCDS9739.1	14q23.1	2012-08-15	2012-08-15	2012-08-15	ENSG00000126790	ENSG00000126790	4.2.1.77		20488	protein-coding gene	gene with protein product	"trans-L-3-hydroxyproline dehydratase"	614811	"chromosome 14 open reading frame 149"	C14orf149		22528483	Standard	NM_144581		Approved	FLJ25436	uc001xee.1	Q96EM0	OTTHUMG00000028941	ENST00000247194.4:c.505A>G	chr14.hg19:g.59950530T>C	ENSP00000247194:p.Thr169Ala	40.0	0.0	1042	31.0	16.0	NM_144581	Q96LJ5	Missense_Mutation	SNP	ENST00000247194.4	hg19	CCDS9739.1	.	.	.	.	.	.	.	.	.	.	T	6.818	0.520079	0.13005	.	.	ENSG00000126790	ENST00000247194	T	0.16324	2.35	5.58	0.142	0.14816	.	0.254626	0.45126	N	0.000385	T	0.09730	0.0239	L	0.39692	1.235	0.80722	D	1	B;B	0.15930	0.015;0.001	B;B	0.18561	0.022;0.006	T	0.25745	-1.0123	10	0.08837	T	0.75	.	4.7938	0.13261	0.2711:0.1393:0.0:0.5896	.	169;169	B4DGY8;Q96EM0	.;PRCM_HUMAN	A	169	ENSP00000247194:T169A	ENSP00000247194:T169A	T	-	1	0	C14orf149	59020283	1.000000	0.71417	0.991000	0.47740	0.496000	0.33645	0.769000	0.26604	0.041000	0.15688	-0.379000	0.06801	ACA	.	.		0.647	L3HYPDH-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072254.5	NM_144581		C	59950530	T	C	59950530	3	2	23	1	0	0	0	0	1	0	0	0	1754	1696	59	2	579	2	C14orf149	14	59950530	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	837038	59950530	47399010	776	2842										
MTHFD1	4522	hgsc.bcm.edu	37	chr14	64921459	64921459	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agggctttgggaatctccccAtctgcatggctaaaacacac	9	12	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:64921459A>C	ENST00000545908.1	+	26	2981	c.2752A>C	c.(2752-2754)Atc>Ctc	p.I918L	ZBTB25_ENST00000555220.1_Intron|MTHFD1_ENST00000216605.8_Missense_Mutation_p.I862L|ZBTB25_ENST00000555424.1_Intron|MTHFD1_ENST00000556284.1_3'UTR			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	862	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	GAATCTCCCCATCTGCATGGC	0.517																																					p.I862L	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.A2584C						.						110	97	102					14																	64921459		2203	4300	6503	SO:0001583	missense	4522	exon26			CTCCCCATCTGCA	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2752A>C	chr14.hg19:g.64921459A>C	ENSP00000438588:p.Ile918Leu	101.0	0.0		106.0	26.0	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.19	2.759082	0.49468	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605	T;T;T	0.26810	1.71;1.71;1.71	4.65	3.5	0.40072	.	0.173902	0.51477	D	0.000095	T	0.35913	0.0948	M	0.88181	2.935	0.80722	D	1	B;B	0.22480	0.07;0.052	B;B	0.29716	0.106;0.074	T	0.29212	-1.0019	10	0.66056	D	0.02	-13.5966	7.7201	0.28727	0.8363:0.0:0.1637:0.0	.	918;862	F5H2F4;G3V2B8	.;.	L	918;862;918	ENSP00000438588:I918L;ENSP00000450560:I862L;ENSP00000216605:I918L	ENSP00000216605:I862L	I	+	1	0	MTHFD1	63991212	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	2.805000	0.47939	0.915000	0.36847	0.460000	0.39030	ATC	.	.		0.517	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			C	64921459	A	C	64921459	3	2	23	1	0	0	0	0	1	0	0	0	9936	217	8	5	2686	5	MTHFD1	14	64921459	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	4970929	64921459	42428081	777	2843										
PLEK2	26499	hgsc.bcm.edu	37	chr14	67864501	67864501	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtacaccagcgtgttctgccGaaggatgaaccatcgcgcct	11	13	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:67864501G>A	ENST00000216446.4	-	2	225	c.85C>T	c.(85-87)Cgg>Tgg	p.R29W	PLEK2_ENST00000557388.1_5'UTR	NM_016445.1	NP_057529.1	Q9NYT0	PLEK2_HUMAN	pleckstrin 2	29	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	15				all cancers(60;0.000728)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.00953)		GTGTTCTGCCGAAGGATGAAC	0.597																																					p.R29W		Atlas-SNP	.											.	PLEK2	23	.	0			c.C85T						.						58	47	51					14																	67864501		2203	4300	6503	SO:0001583	missense	26499	exon2			TCTGCCGAAGGAT	AF228603	CCDS9782.1	14q23.3	2014-08-12			ENSG00000100558	ENSG00000100558		"Pleckstrin homology (PH) domain containing"	19238	protein-coding gene	gene with protein product		608007				11911883, 17658464	Standard	NM_016445		Approved		uc001xjh.1	Q9NYT0	OTTHUMG00000171247	ENST00000216446.4:c.85C>T	chr14.hg19:g.67864501G>A	ENSP00000216446:p.Arg29Trp	118.0	0.0		108.0	47.0	NM_016445	Q96JT0	Missense_Mutation	SNP	ENST00000216446.4	hg19	CCDS9782.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.425310	0.62733	.	.	ENSG00000100558	ENST00000216446	T	0.77358	-1.09	5.6	4.59	0.56863	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.507527	0.21430	N	0.074661	T	0.78266	0.4256	M	0.84326	2.69	0.09310	N	1	P	0.51057	0.941	B	0.43360	0.417	T	0.75895	-0.3156	10	0.72032	D	0.01	-11.1157	8.572	0.33576	0.0794:0.0:0.7238:0.1968	.	29	Q9NYT0	PLEK2_HUMAN	W	29	ENSP00000216446:R29W	ENSP00000216446:R29W	R	-	1	2	PLEK2	66934254	0.066000	0.20996	0.985000	0.45067	0.997000	0.91878	1.961000	0.40432	2.793000	0.96121	0.563000	0.77884	CGG	.	.		0.597	PLEK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412547.2			A	67864501	G	A	67864501	3	1	23	1	0	0	0	0	1	0	0	0	12063	1057	37	1	1008	1	PLEK2	14	67864501	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2943042	67864501	39485039	778	2844										
MAP3K9	4293	hgsc.bcm.edu	37	chr14	71199865	71199865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcggtggtgggcaccgccccGcttgaggctgttggttggcg	19	11	0	1	rs145221753	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:71199865G>A	ENST00000554752.2	-	11	2220	c.2221C>T	c.(2221-2223)Cgg>Tgg	p.R741W	MAP3K9_ENST00000555993.2_Missense_Mutation_p.R755W|MAP3K9_ENST00000553414.1_Missense_Mutation_p.R474W|MAP3K9_ENST00000554146.1_Missense_Mutation_p.R469W|MAP3K9_ENST00000381250.4_Missense_Mutation_p.R718W	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	741					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		GCACCGCCCCGCTTGAGGCTG	0.652													G|||	2	0.000399361	0.0015	0	5008	,	,		16255	0		0	False		,,,				2504	0				p.R755W	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.C2263T						.	G	TRP/ARG	0,4406		0,0,2203	38	43	42		2263	3.8	1	14	dbSNP_134	42	1,8599	1.2+/-3.3	0,1,4299	no	missense	MAP3K9	NM_033141.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	755/1119	71199865	1,13005	2203	4300	6503	SO:0001583	missense	4293	exon12			CGCCCCGCTTGAG	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.2221C>T	chr14.hg19:g.71199865G>A	ENSP00000451612:p.Arg741Trp	92.0	0.0		84.0	15.0	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	ENST00000554752.2	hg19		.	.	.	.	.	.	.	.	.	.	G	17.70	3.453363	0.63290	0.0	1.16E-4	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	4.77	3.83	0.44106	.	0.176165	0.47455	D	0.000227	T	0.56217	0.1970	M	0.64997	1.995	0.48511	D	0.999668	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.999;0.999	T	0.60767	-0.7198	10	0.87932	D	0	.	14.5039	0.67741	0.0:0.0:0.8533:0.1467	.	469;741;755;474	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	W	741;755;474;718;469;457	ENSP00000451612:R741W;ENSP00000451038:R474W;ENSP00000370649:R718W;ENSP00000451921:R469W	ENSP00000005198:R755W	R	-	1	2	MAP3K9	70269618	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	2.694000	0.47035	2.478000	0.83669	0.561000	0.74099	CGG	.	G|1.000;A|0.000		0.652	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			A	71199865	G	A	71199865	3	1	23	1	0	0	0	0	1	0	0	0	9266	1086	38	1	1101	1	MAP3K9	14	71199865	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3335364	71199865	36149675	779	2845										
ACOT4	122970	hgsc.bcm.edu	37	chr14	74062092	74062092	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ataactggagaagtgagttgTatgcccaaacagtctctgaa	10	7	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:74062092T>C	ENST00000326303.4	+	3	1254	c.1000T>C	c.(1000-1002)Tat>Cat	p.Y334H		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	334					acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		AAGTGAGTTGTATGCCCAAAC	0.507																																					p.Y334H		Atlas-SNP	.											.	ACOT4	25	.	0			c.T1000C						.						88	77	81					14																	74062092		2203	4300	6503	SO:0001583	missense	122970	exon3			GAGTTGTATGCCC	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"Acyl CoA thioesterases"	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.1000T>C	chr14.hg19:g.74062092T>C	ENSP00000323071:p.Tyr334His	135.0	0.0		126.0	35.0	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	hg19	CCDS9817.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.639304	0.47153	.	.	ENSG00000177465	ENST00000326303	T	0.30182	1.54	5.63	4.47	0.54385	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.669756	0.16037	N	0.232576	T	0.46444	0.1393	L	0.48642	1.525	0.42153	D	0.991568	D	0.89917	1.0	D	0.87578	0.998	T	0.14448	-1.0472	10	0.30078	T	0.28	0.2696	11.6923	0.51523	0.1329:0.0:0.0:0.8671	.	334	Q8N9L9	ACOT4_HUMAN	H	334	ENSP00000323071:Y334H	ENSP00000323071:Y334H	Y	+	1	0	ACOT4	73131845	0.578000	0.26717	0.142000	0.22268	0.749000	0.42624	4.450000	0.60041	0.936000	0.37367	0.459000	0.35465	TAT	.	.		0.507	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331		C	74062092	T	C	74062092	3	2	23	1	0	0	0	0	1	0	0	0	153	1638	57	2	1010	2	ACOT4	14	74062092	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2862227	74062092	33287448	780	2846										
TMEM90A	646658	hgsc.bcm.edu	37	chr14	74876101	74876101	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cataggacacagtctggatgGtgacattctctgcagcttgg	12	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:74876101G>A	ENST00000554823.1	-	1	408	c.347C>T	c.(346-348)aCc>aTc	p.T116I	SYNDIG1L_ENST00000331628.3_Missense_Mutation_p.T116I			A6NDD5	SYN1L_HUMAN	synapse differentiation inducing 1-like	116					response to biotic stimulus (GO:0009607)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(8)|pancreas(1)|prostate(1)|skin(1)	14						AGTCTGGATGGTGACATTCTC	0.587																																					p.T116I		Atlas-SNP	.											.	SYNDIG1L	24	.	0			c.C347T						.						85	89	88					14																	74876101		2038	4202	6240	SO:0001583	missense	646658	exon2			TGGATGGTGACAT		CCDS41970.1	14q24.3	2011-06-30	2011-06-30	2011-06-30		ENSG00000183379			32388	protein-coding gene	gene with protein product	"caudate-and putamen-enriched sequence", "interferon induced transmembrane protein domain containing 4"	609999	"transmembrane protein 90A"	TMEM90A		16359841	Standard	NM_001105579		Approved	capucin, IFITMD4	uc001xpx.2	A6NDD5		ENST00000554823.1:c.347C>T	chr14.hg19:g.74876101G>A	ENSP00000450439:p.Thr116Ile	53.0	0.0		61.0	21.0	NM_001105579		Missense_Mutation	SNP	ENST00000554823.1	hg19	CCDS41970.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267015	0.40095	.	.	ENSG00000183379	ENST00000331628;ENST00000554823	D;D	0.95272	-3.66;-3.66	4.63	3.66	0.41972	.	0.524136	0.19671	N	0.108749	D	0.87803	0.6269	N	0.22421	0.69	0.25431	N	0.988183	B	0.23735	0.09	B	0.21360	0.034	T	0.79519	-0.1770	10	0.62326	D	0.03	-9.9873	6.7756	0.23619	0.0:0.1714:0.5472:0.2813	.	116	A6NDD5	SYN1L_HUMAN	I	116	ENSP00000331474:T116I;ENSP00000450439:T116I	ENSP00000331474:T116I	T	-	2	0	SYNDIG1L	73945854	0.998000	0.40836	0.929000	0.37066	0.819000	0.46315	3.050000	0.49877	2.402000	0.81655	0.467000	0.42956	ACC	.	.		0.587	SYNDIG1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412341.1	XM_938515		A	74876101	G	A	74876101	3	1	23	1	0	0	0	0	1	0	0	0	16233	1261	44	3	381	3	TMEM90A	14	74876101	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	814009	74876101	32473439	781	2847										
KIAA0317	9870	hgsc.bcm.edu	37	chr14	75130470	75130470	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcgctgatggccagctgcaGcatcctgtgcacctcttcat	9	15	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:75130470G>A	ENST00000356357.4	-	20	2940	c.2425C>T	c.(2425-2427)Ctg>Ttg	p.L809L	AREL1_ENST00000557401.1_Intron	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	809	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GCCAGCTGCAGCATCCTGTGC	0.537																																					p.L809L		Atlas-SNP	.											.	KIAA0317	68	.	0			c.C2425T						.						136	142	140					14																	75130470		2160	4265	6425	SO:0001819	synonymous_variant	9870	exon20			GCTGCAGCATCCT	AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"KIAA0317"	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.2425C>T	chr14.hg19:g.75130470G>A		95.0	0.0		87.0	41.0	NM_001039479	B4E2C7|Q7LDY1|Q8IYY9	Silent	SNP	ENST00000356357.4	hg19	CCDS41971.1																																																																																			.	.		0.537	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821		A	75130470	G	A	75130470	2	1	23	1	0	0	0	0	0	0	0	1	8176	962	34	3		3	KIAA0317	14	75130470	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	254369	75130470	32219070	782	2848										
EIF2B2	8892	hgsc.bcm.edu	37	chr14	75471454	75471454	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttacagaagggacaatggagAacattgcagcccaggctctg	12	9	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:75471454A>G	ENST00000266126.5	+	4	528	c.448A>G	c.(448-450)Aac>Gac	p.N150D	RP11-950C14.3_ENST00000554430.1_RNA	NM_014239.3	NP_055054.1	P49770	EI2BB_HUMAN	eukaryotic translation initiation factor 2B, subunit 2 beta, 39kDa	150					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|central nervous system development (GO:0007417)|gene expression (GO:0010467)|myelination (GO:0042552)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|translation initiation factor activity (GO:0003743)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(234;0.00661)		GACAATGGAGAACATTGCAGC	0.373																																					p.N150D		Atlas-SNP	.											.	EIF2B2	22	.	0			c.A448G						.						67	64	65					14																	75471454		2203	4300	6503	SO:0001583	missense	8892	exon4			ATGGAGAACATTG		CCDS9836.1	14q24.3	2008-08-11	2002-08-29			ENSG00000119718			3258	protein-coding gene	gene with protein product		606454	"eukaryotic translation initiation factor 2B, subunit 2 (beta, 39kD)"			8887689	Standard	NM_014239		Approved	EIF2B, EIF-2Bbeta	uc001xrc.2	P49770		ENST00000266126.5:c.448A>G	chr14.hg19:g.75471454A>G	ENSP00000266126:p.Asn150Asp	63.0	0.0		43.0	17.0	NM_014239	O43201	Missense_Mutation	SNP	ENST00000266126.5	hg19	CCDS9836.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.062865	0.76187	.	.	ENSG00000119718	ENST00000266126	D	0.92495	-3.05	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.93360	0.7883	L	0.59436	1.845	0.80722	D	1	P	0.37636	0.603	P	0.49528	0.614	D	0.92663	0.6143	10	0.41790	T	0.15	-26.0731	15.827	0.78718	1.0:0.0:0.0:0.0	.	150	P49770	EI2BB_HUMAN	D	150	ENSP00000266126:N150D	ENSP00000266126:N150D	N	+	1	0	EIF2B2	74541207	1.000000	0.71417	1.000000	0.80357	0.619000	0.37552	9.065000	0.93941	2.324000	0.78689	0.533000	0.62120	AAC	.	.		0.373	EIF2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414993.1	NM_014239		G	75471454	A	G	75471454	3	3	23	1	0	0	0	0	1	0	0	0	5003	246	9	2	462	2	EIF2B2	14	75471454	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	340984	75471454	31878086	783	2849										
KIAA1737	85457	hgsc.bcm.edu	37	chr14	77580248	77580248	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtctgaccttcgcttcccccGccagtcctgtctgcgcatca	8	18	3	1	rs201665496		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:77580248G>A	ENST00000361786.2	+	4	1104	c.787G>A	c.(787-789)Gcc>Acc	p.A263T	RP11-463C8.4_ENST00000557752.1_Intron	NM_033426.2	NP_219494.2	Q9C0C6	CIPC_HUMAN		263					negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(2)|lung(4)|prostate(3)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		CGCTTCCCCCGCCAGTCCTGT	0.572																																					p.A263T		Atlas-SNP	.											KIAA1737,NS,carcinoma,0,1	KIAA1737	26	.	0			c.G787A						.						86	73	78					14																	77580248		2203	4300	6503	SO:0001583	missense	85457	exon4			TCCCCCGCCAGTC																												ENST00000361786.2:c.787G>A	chr14.hg19:g.77580248G>A	ENSP00000355319:p.Ala263Thr	73.0	0.0		81.0	32.0	NM_033426	B2RCI1|Q8N389|Q8NDZ1	Missense_Mutation	SNP	ENST00000361786.2	hg19	CCDS9855.1	.	.	.	.	.	.	.	.	.	.	G	16.10	3.026280	0.54683	.	.	ENSG00000198894	ENST00000361786	T	0.33216	1.42	5.58	4.63	0.57726	.	0.505693	0.21867	N	0.067941	T	0.34890	0.0913	L	0.51422	1.61	0.39356	D	0.965849	D;D	0.62365	0.991;0.991	P;P	0.52109	0.69;0.69	T	0.02533	-1.1145	10	0.30078	T	0.28	-22.2881	8.9275	0.35650	0.0:0.1491:0.6748:0.1761	.	263;165	Q9C0C6;B3KU75	K1737_HUMAN;.	T	263	ENSP00000355319:A263T	ENSP00000355319:A263T	A	+	1	0	KIAA1737	76650001	0.999000	0.42202	0.996000	0.52242	0.995000	0.86356	2.124000	0.42006	2.792000	0.96026	0.555000	0.69702	GCC	.	G|1.000;C|0.000		0.572	KIAA1737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414278.1			A	77580248	G	A	77580248	3	1	23	1	0	0	0	0	1	0	0	0	8264	1087	38	1	797	1	KIAA1737	14	77580248	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2108794	77580248	29769292	784	2850										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86088965	86088965	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgacccccggcctgcctctCttcaccccagccccaagtac	6	22	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:86088965C>A	ENST00000330753.4	+	2	1874	c.1107C>A	c.(1105-1107)ctC>ctA	p.L369L	FLRT2_ENST00000554746.1_Silent_p.L369L	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	369					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		GCCTGCCTCTCTTCACCCCAG	0.557																																					p.L369L		Atlas-SNP	.											.	FLRT2	168	.	0			c.C1107A						.						83	90	88					14																	86088965		2203	4300	6503	SO:0001819	synonymous_variant	23768	exon2			GCCTCTCTTCACC	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1107C>A	chr14.hg19:g.86088965C>A		69.0	0.0		71.0	26.0	NM_013231	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	hg19	CCDS9877.1																																																																																			.	.		0.557	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			A	86088965	C	A	86088965	2	1	23	1	0	0	0	0	0	0	0	1	5947	900	32	3		3	FLRT2	14	86088965	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	8508717	86088965	21260575	785	2851										
ZC3H14	79882	hgsc.bcm.edu	37	chr14	89039079	89039079	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggagaatcccttatctcagAaaaaacctacagtgacactt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:89039079delA	ENST00000251038.5	+	6	814	c.589delA	c.(589-591)aaafs	p.K198fs	ZC3H14_ENST00000557607.1_Frame_Shift_Del_p.K43fs|ZC3H14_ENST00000302216.8_Frame_Shift_Del_p.K198fs|ZC3H14_ENST00000336693.4_Frame_Shift_Del_p.K164fs|ZC3H14_ENST00000393514.5_Frame_Shift_Del_p.K198fs|ZC3H14_ENST00000359301.3_Frame_Shift_Del_p.K164fs|ZC3H14_ENST00000556945.1_Frame_Shift_Del_p.K198fs|ZC3H14_ENST00000555755.1_Frame_Shift_Del_p.K198fs	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	198						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						CTTATCTCAGAAAAAACCTAC	0.413																																					p.Q196fs		Atlas-Indel,Pindel	.											.	ZC3H14	71	.	0			c.588delG						.						172	177	176					14																	89039079		2203	4300	6503	SO:0001589	frameshift_variant	79882	exon6			.	AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"Zinc fingers, CCCH-type domain containing"	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.589delA	chr14.hg19:g.89039079delA	ENSP00000251038:p.Lys198fs	176.0	0.0		156.0	58.0	NM_001160104	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Frame_Shift_Del	DEL	ENST00000251038.5	hg19	CCDS32133.1																																																																																			.	.		0.413	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824		-	89039079	A	-	89039079	7	5	23	1	0	1	0	1	0	0	0	0	17581	247	9	0	611	0	ZC3H14	14	89039079	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	2950114	89039079	18310461	786	2852										
TTC7B	145567	hgsc.bcm.edu	37	chr14	91155976	91155976	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcgtccagaggtgactggcaCggtggatcctccagagggtt	15	10	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:91155976C>T	ENST00000328459.6	-	7	979	c.858G>A	c.(856-858)ccG>ccA	p.P286P	TTC7B_ENST00000357056.2_Silent_p.P286P	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	286										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				GTGACTGGCACGGTGGATCCT	0.527																																					p.P286P		Atlas-SNP	.											.	TTC7B	93	.	0			c.G858A						.						118	97	104					14																	91155976		2203	4300	6503	SO:0001819	synonymous_variant	145567	exon7			CTGGCACGGTGGA	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"Tetratricopeptide (TTC) repeat domain containing"	19858	protein-coding gene	gene with protein product			"tetratricopeptide repeat domain 7 like 1"	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.858G>A	chr14.hg19:g.91155976C>T		114.0	0.0		131.0	65.0	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	hg19	CCDS32140.1																																																																																			.	.		0.527	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2			T	91155976	C	T	91155976	2	4	23	1	0	0	0	0	0	0	0	1	16728	523	19	1		1	TTC7B	14	91155976	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2116897	91155976	16193564	787	2853										
CHGA	1113	hgsc.bcm.edu	37	chr14	93397934	93397934	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaagagagaagaggaggaggAggaggaggaggaggctgagg	23	1	0	4	rs71430778		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:93397934A>C	ENST00000216492.5	+	6	975	c.695A>C	c.(694-696)gAg>gCg	p.E232A	CHGA_ENST00000334654.4_Intron|CHGA_ENST00000553866.1_3'UTR	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)	232					regulation of blood pressure (GO:0008217)	extracellular region (GO:0005576)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)				cervix(1)|large_intestine(1)|lung(3)|skin(3)	8		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		gaggaggaggaggaggaggag	0.637																																					p.E232A	Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)	Atlas-SNP	.											.	CHGA	32	.	0			c.A695C						.						33	39	37					14																	93397934		2203	4300	6503	SO:0001583	missense	1113	exon6			AGGAGGAGGAGGA		CCDS9906.1	14q32	2012-10-02			ENSG00000100604	ENSG00000100604			1929	protein-coding gene	gene with protein product	"vasostatin", "pancreastatin", "parastatin"	118910				3403545	Standard	NM_001275		Approved		uc001ybc.4	P10645		ENST00000216492.5:c.695A>C	chr14.hg19:g.93397934A>C	ENSP00000216492:p.Glu232Ala	174.0	0.0		169.0	69.0	NM_001275	B2R9E9|Q53FA8|Q6NR84|Q96E84|Q96GL7|Q9BQB5	Missense_Mutation	SNP	ENST00000216492.5	hg19	CCDS9906.1	.	.	.	.	.	.	.	.	.	.	A	9.231	1.035830	0.19590	.	.	ENSG00000100604	ENST00000216492	T	0.01584	4.75	4.55	3.4	0.38934	.	0.495175	0.19758	N	0.106736	T	0.04952	0.0133	M	0.64997	1.995	0.80722	D	1	D	0.55605	0.972	P	0.54238	0.746	T	0.34104	-0.9842	10	0.66056	D	0.02	.	7.8352	0.29365	0.9015:0.0:0.0985:0.0	.	232	P10645	CMGA_HUMAN	A	232	ENSP00000216492:E232A	ENSP00000216492:E232A	E	+	2	0	CHGA	92467687	0.962000	0.33011	0.113000	0.21522	0.259000	0.26198	2.363000	0.44178	0.713000	0.32060	0.374000	0.22700	GAG	.	A|0.500;T|0.500		0.637	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	NM_001275		C	93397934	A	C	93397934	3	2	23	1	0	0	0	0	1	0	0	0	3340	304	11	5	717	5	CHGA	14	93397934	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2241958	93397934	13951606	788	2854										
BDKRB1	623	hgsc.bcm.edu	37	chr14	96730967	96730967	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtaatttatgtctttgtgggCcggctcttcaggaccaaggt	12	8	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:96730967C>T	ENST00000216629.6	+	3	1554	c.948C>T	c.(946-948)ggC>ggT	p.G316G	RP11-404P21.3_ENST00000553638.1_RNA|BDKRB1_ENST00000553356.1_Silent_p.G250G	NM_000710.3	NP_000701.2	P46663	BKRB1_HUMAN	bradykinin receptor B1	316					cell migration (GO:0016477)|inflammatory response (GO:0006954)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell growth (GO:0030308)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|peptide binding (GO:0042277)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(4)|skin(1)|urinary_tract(1)	16		all_cancers(154;0.0677)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.208)|Epithelial(152;0.226)		TCTTTGTGGGCCGGCTCTTCA	0.453																																					p.G316G		Atlas-SNP	.											.	BDKRB1	41	.	0			c.C948T						.						141	149	146					14																	96730967		2203	4300	6503	SO:0001819	synonymous_variant	623	exon3			TGTGGGCCGGCTC	L42383	CCDS9943.1	14q32.1-q32.2	2012-08-08				ENSG00000100739		"GPCR / Class A : Bradykinin receptors"	1029	protein-coding gene	gene with protein product		600337				8808279	Standard	NM_000710		Approved	BKR1, B1BKR, bradyb1	uc001yfh.3	P46663		ENST00000216629.6:c.948C>T	chr14.hg19:g.96730967C>T		111.0	0.0		108.0	44.0	NM_000710	A8K7F5|Q546S7|Q8N0Y8	Silent	SNP	ENST00000216629.6	hg19	CCDS9943.1																																																																																			.	.		0.453	BDKRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413300.1			T	96730967	C	T	96730967	2	4	23	1	0	0	0	0	0	0	0	1	1392	726	26	3		3	BDKRB1	14	96730967	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3333033	96730967	10618573	789	2855										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96781801	96781801	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actgtctcctccaactccatCtgaagaagttttactgaggc	7	12	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:96781801C>T	ENST00000359933.4	-	22	4374	c.3481G>A	c.(3481-3483)Gat>Aat	p.D1161N		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1161					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		CCAACTCCATCTGAAGAAGTT	0.418																																					p.D1161N		Atlas-SNP	.											.	ATG2B	169	.	0			c.G3481A						.						59	57	58					14																	96781801		2203	4300	6503	SO:0001583	missense	55102	exon22			CTCCATCTGAAGA	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.3481G>A	chr14.hg19:g.96781801C>T	ENSP00000353010:p.Asp1161Asn	366.0	0.0		377.0	26.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	C	13.63	2.294599	0.40594	.	.	ENSG00000066739	ENST00000359933	T	0.09723	2.95	5.61	5.61	0.85477	.	0.355513	0.22282	U	0.062107	T	0.07188	0.0182	N	0.16478	0.41	0.39419	D	0.966897	B	0.06786	0.001	B	0.06405	0.002	T	0.36672	-0.9738	10	0.15952	T	0.53	.	12.9138	0.58195	0.0:0.9257:0.0:0.0743	.	1161	Q96BY7	ATG2B_HUMAN	N	1161	ENSP00000353010:D1161N	ENSP00000353010:D1161N	D	-	1	0	ATG2B	95851554	1.000000	0.71417	0.980000	0.43619	0.949000	0.60115	3.972000	0.56838	2.654000	0.90174	0.591000	0.81541	GAT	.	.		0.418	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		T	96781801	C	T	96781801	3	4	23	1	0	0	0	0	1	0	0	0	1094	913	32	3	2839	3	ATG2B	14	96781801	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	50834	96781801	10567739	790	2856										
C14orf177	283598	hgsc.bcm.edu	37	chr14	99183450	99183450	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caggtgagtgctctacctgtTtctgtacagaagagaaatca	10	8	3	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:99183450T>C	ENST00000325812.2	+	4	636	c.217T>C	c.(217-219)Ttc>Ctc	p.F73L		NM_182560.2	NP_872366.2	Q52M58	CN177_HUMAN	chromosome 14 open reading frame 177	73										endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	13		Melanoma(154;0.128)				CTCTACCTGTTTCTGTACAGA	0.488																																					p.F73L		Atlas-SNP	.											.	C14orf177	37	.	0			c.T217C						.						96	87	90					14																	99183450		2203	4300	6503	SO:0001583	missense	283598	exon4			ACCTGTTTCTGTA	AK098639	CCDS9948.1	14q32.2	2012-05-30			ENSG00000176605	ENSG00000176605			26375	protein-coding gene	gene with protein product						12477932	Standard	NM_182560		Approved	FLJ25773	uc001yfz.2	Q52M58	OTTHUMG00000167745	ENST00000325812.2:c.217T>C	chr14.hg19:g.99183450T>C	ENSP00000321360:p.Phe73Leu	92.0	0.0		81.0	29.0	NM_182560	Q8N7D2	Missense_Mutation	SNP	ENST00000325812.2	hg19	CCDS9948.1	.	.	.	.	.	.	.	.	.	.	T	8.607	0.888275	0.17540	.	.	ENSG00000176605	ENST00000325812;ENST00000541516	T;T	0.38722	1.23;1.12	3.23	-0.664	0.11406	.	.	.	.	.	T	0.18882	0.0453	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18967	-1.0320	9	0.87932	D	0	.	2.2474	0.04034	0.4498:0.1553:0.0:0.3949	.	73	Q52M58	CN177_HUMAN	L	73	ENSP00000321360:F73L;ENSP00000440687:F73L	ENSP00000321360:F73L	F	+	1	0	C14orf177	98253203	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.194000	0.17135	-0.132000	0.11557	0.533000	0.62120	TTC	.	.		0.488	C14orf177-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396078.1	NM_182560		C	99183450	T	C	99183450	3	2	23	1	0	0	0	0	1	0	0	0	1762	1841	64	2	223	2	C14orf177	14	99183450	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2401649	99183450	8166090	791	2857										
SETD3	84193	hgsc.bcm.edu	37	chr14	99929899	99929899	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cactcttttcctgggccaggCgccggactgctgcattctgt	11	14	2	0	rs146095518		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:99929899C>T	ENST00000331768.5	-	3	279	c.120G>A	c.(118-120)gcG>gcA	p.A40A	SETD3_ENST00000436070.2_Silent_p.A40A|SETD3_ENST00000329331.3_Silent_p.A40A|SETD3_ENST00000453938.1_5'UTR	NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	40					histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				CTGGGCCAGGCGCCGGACTGC	0.433																																					p.A40A		Atlas-SNP	.											.	SETD3	56	.	0			c.G120A						.	C	,	0,4406		0,0,2203	70	60	64		120,120	-9.8	0	14	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SETD3	NM_032233.2,NM_199123.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	40/595,40/297	99929899	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	84193	exon3			GCCAGGCGCCGGA	AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"chromosome 14 open reading frame 154"	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.120G>A	chr14.hg19:g.99929899C>T		46.0	0.0		36.0	14.0	NM_032233	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Silent	SNP	ENST00000331768.5	hg19	CCDS9951.1																																																																																			.	C|1.000;T|0.000		0.433	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233		T	99929899	C	T	99929899	2	4	23	1	0	0	0	0	0	0	0	1	14147	755	27	1		1	SETD3	14	99929899	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	746449	99929899	7419641	792	2858										
WDR20	91833	hgsc.bcm.edu	37	chr14	102675272	102675272	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttgactcagtggagctgcaCggtacgatgaaaagctactt	11	8	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:102675272C>T	ENST00000342702.3	+	3	796	c.765C>T	c.(763-765)caC>caT	p.H255H	WDR20_ENST00000322340.5_Intron|WDR20_ENST00000556511.2_Silent_p.H194H|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000499851.2_5'UTR|WDR20_ENST00000454394.2_Silent_p.H286H|WDR20_ENST00000545563.1_Silent_p.H82H|WDR20_ENST00000424963.2_Silent_p.H131H|WDR20_ENST00000335263.5_Silent_p.H255H|WDR20_ENST00000556807.1_Silent_p.H194H	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	255										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						TGGAGCTGCACGGTACGATGA	0.557																																					p.H286H		Atlas-SNP	.											.	WDR20	35	.	0			c.C858T						.						78	67	70					14																	102675272		2203	4300	6503	SO:0001819	synonymous_variant	91833	exon4			GCTGCACGGTACG	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.765C>T	chr14.hg19:g.102675272C>T		107.0	0.0		113.0	7.0	NM_001242417	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Silent	SNP	ENST00000342702.3	hg19	CCDS9969.1	.	.	.	.	.	.	.	.	.	.	C	3.389	-0.124819	0.06795	.	.	ENSG00000140153	ENST00000556511	.	.	.	5.83	3.03	0.35002	.	.	.	.	.	T	0.57315	0.2045	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49652	-0.8917	4	.	.	.	.	7.8045	0.29193	0.0:0.566:0.0:0.434	.	.	.	.	W	186	.	.	R	+	1	2	WDR20	101745025	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	0.617000	0.24359	0.388000	0.25054	0.655000	0.94253	CGG	.	.		0.557	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		T	102675272	C	T	102675272	2	4	23	1	0	0	0	0	0	0	0	1	17295	535	19	1		1	WDR20	14	102675272	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2745373	102675272	4674268	793	2859										
INF2	64423	hgsc.bcm.edu	37	chr14	105168020	105168020	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acctgcgtcagctgcgtgcgCgccgtcatgaactcgcggca	13	15	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:105168020C>T	ENST00000392634.4	+	2	430	c.318C>T	c.(316-318)cgC>cgT	p.R106R	INF2_ENST00000330634.7_Silent_p.R106R|INF2_ENST00000398337.4_Silent_p.R106R	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	106	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		GCTGCGTGCGCGCCGTCATGA	0.706																																					p.R106R		Atlas-SNP	.											.	INF2	148	.	0			c.C318T						.						8	11	10					14																	105168020		2076	4175	6251	SO:0001819	synonymous_variant	64423	exon2			CGTGCGCGCCGTC	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"inverted formin 2"	610982	"chromosome 14 open reading frame 151", "chromosome 14 open reading frame 173"	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.318C>T	chr14.hg19:g.105168020C>T		66.0	0.0		54.0	13.0	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Silent	SNP	ENST00000392634.4	hg19	CCDS9989.2																																																																																			.	.		0.706	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		T	105168020	C	T	105168020	2	4	23	1	0	0	0	0	0	0	0	1	7743	755	27	1		1	INF2	14	105168020	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2492748	105168020	2181520	794	2860										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414171	105414171	+	Missense_Mutation	SNP	G	G	T													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggccagcctggacctccagGtcagcggaagggggctgaat							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:105414171G>T	ENST00000333244.5	-	7	7736	c.7617C>A	c.(7615-7617)gaC>gaA	p.D2539E	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2539						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGACCTCCAGGTCAGCGGAAG	0.662																																					p.D2539E		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C7617A						.						108	121	117					14																	105414171		1889	4103	5992	SO:0001583	missense	113146	exon7			CTCCAGGTCAGCG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7617C>A	chr14.hg19:g.105414171G>T	ENSP00000353114:p.Asp2539Glu	217.0	0.0		170.0	11.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	15.90	2.969777	0.53614	.	.	ENSG00000185567	ENST00000333244	T	0.01139	5.28	3.7	-7.39	0.01402	.	.	.	.	.	T	0.00906	0.0030	L	0.33245	0.995	0.09310	N	1	B	0.19817	0.039	B	0.25140	0.058	T	0.49634	-0.8919	9	0.05833	T	0.94	.	9.9132	0.41419	0.3594:0.5343:0.1063:0.0	.	2539	Q8IVF2	AHNK2_HUMAN	E	2539	ENSP00000353114:D2539E	ENSP00000353114:D2539E	D	-	3	2	AHNAK2	104485216	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-2.249000	0.01188	-1.218000	0.02601	0.306000	0.20318	GAC	.	.		0.662	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105414171	G	T	105414171	3	4	23	1	0	0	0	0	1	0	0	0	415	1252	44	3	9774	3	AHNAK2	14	105414171	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	246151	105414171	1935369	795	2861	10	3								
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414174	105414174	+	Silent	SNP	A	A	G													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagcctggacctccaggtcAgcggaagggggctgaatgct					rs374363751		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:105414174A>G	ENST00000333244.5	-	7	7733	c.7614T>C	c.(7612-7614)gcT>gcC	p.A2538A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2538						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCTCCAGGTCAGCGGAAGGGG	0.667																																					p.A2538A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T7614C						.						108	121	117					14																	105414174		1889	4105	5994	SO:0001819	synonymous_variant	113146	exon7			CAGGTCAGCGGAA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7614T>C	chr14.hg19:g.105414174A>G		227.0	0.0		165.0	11.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.667	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		G	105414174	A	G	105414174	2	3	23	1	0	0	0	0	0	0	0	1	415	175	7	2		2	AHNAK2	14	105414174	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3	105414174	1935366	796	2862	10	3								
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414177	105414177	+	Silent	SNP	G	G	A													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctggacctccaggtcagcGgaagggggctgaatgctgag					rs368398841	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:105414177G>A	ENST00000333244.5	-	7	7730	c.7611C>T	c.(7609-7611)tcC>tcT	p.S2537S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2537						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCAGGTCAGCGGAAGGGGGCT	0.667													.|||	2	0.000399361	8e-04	0	5008	,	,		16640	0		0	False		,,,				2504	0.001				p.S2537S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C7611T						.	A		4,3784		0,4,1890	110	123	119		7611	-7.4	0	14		119	1,8217		0,1,4108	no	coding-synonymous	AHNAK2	NM_138420.2		0,5,5998	AA,AG,GG		0.0122,0.1056,0.0416		2537/5796	105414177	5,12001	1894	4109	6003	SO:0001819	synonymous_variant	113146	exon7			GTCAGCGGAAGGG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7611C>T	chr14.hg19:g.105414177G>A		225.0	0.0		173.0	11.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.667	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105414177	G	A	105414177	2	1	23	1	0	0	0	0	0	0	0	1	415	1103	39	1		1	AHNAK2	14	105414177	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3	105414177	1935363	797	2863	10	3								
CYFIP1	81614	hgsc.bcm.edu	37	chr15	23003033	23003033	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catccaccagtccctcgccaGcagctgagggcacgcgctgc	11	18	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:23003033G>A	ENST00000337451.3	-	0	3233				CYFIP1_ENST00000560848.1_Missense_Mutation_p.S1252N|CYFIP1_ENST00000435939.2_Missense_Mutation_p.S821N|CYFIP1_ENST00000313077.7_Missense_Mutation_p.S1252N	NM_030922.6	NP_112184.4	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 2							early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(4)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		TCCCTCGCCAGCAGCTGAGGG	0.542																																					p.S1252N		Atlas-SNP	.											.	CYFIP1	159	.	0			c.G3755A						.						33	30	31					15																	23003033		2203	4300	6503	SO:0001628	intergenic_variant	23191	exon31			TCGCCAGCAGCTG	AY732242	CCDS73693.1, CCDS73694.1	15q11.2	2008-02-05			ENSG00000140157	ENSG00000140157			17044	protein-coding gene	gene with protein product		608146				14508708	Standard	NM_001008860		Approved		uc001yuz.3	Q8N8Q9	OTTHUMG00000129101		chr15.hg19:g.23003033G>A		120.0	0.0		95.0	41.0	NM_014608	F8W7Y8|Q96F03|Q9BVS2	Missense_Mutation	SNP	ENST00000337451.3	hg19	CCDS10010.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.934067	0.52866	.	.	ENSG00000068793	ENST00000313077;ENST00000412127;ENST00000435939	T;T	0.33654	2.19;1.4	6.17	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.31979	0.0814	L	0.33485	1.01	0.80722	D	1	B;B	0.13145	0.007;0.002	B;B	0.23852	0.049;0.004	T	0.04991	-1.0913	10	0.23891	T	0.37	-27.8302	17.7372	0.88397	0.0:0.1223:0.8776:0.0	.	821;1252	Q7L576-2;Q7L576	.;CYFP1_HUMAN	N	1252;1254;821	ENSP00000324549:S1252N;ENSP00000405956:S821N	ENSP00000324549:S1252N	S	+	2	0	CYFIP1	20554474	1.000000	0.71417	1.000000	0.80357	0.635000	0.38103	7.931000	0.87625	1.611000	0.50210	0.655000	0.94253	AGC	.	.		0.542	NIPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251137.1	NM_030922		A	23003033	G	A	23003033	1	1	23	0	1	0	0	0	0	0	0	0	4139	971	34	3		3	CYFIP1	15	23003033	IGR	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10		23003033	79528359	798	2864										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24921255	24921255	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccctcgggctgcggccgccCctctgggggtcctgccggct	15	18	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:24921255C>T	ENST00000329468.2	+	1	715	c.241C>T	c.(241-243)Cct>Tct	p.P81S		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	81					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											TGCGGCCGCCCCTCTGGGGGT	0.701																																					p.P81S		Atlas-SNP	.											.	.	.	.	0			c.C241T						.						16	18	17					15																	24921255		2117	4170	6287	SO:0001583	missense	23742	exon1			GCCGCCCCTCTGG	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.241C>T	chr15.hg19:g.24921255C>T	ENSP00000333735:p.Pro81Ser	109.0	0.0		97.0	42.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	10.85	1.466117	0.26335	.	.	ENSG00000185823	ENST00000329468	T	0.06768	3.26	1.96	-2.28	0.06826	.	1.189390	0.06402	N	0.718990	T	0.05868	0.0153	L	0.38175	1.15	0.09310	N	1	B	0.27166	0.17	B	0.21708	0.036	T	0.40794	-0.9544	10	0.33940	T	0.23	.	2.2894	0.04135	0.2371:0.386:0.0:0.3769	.	81	Q9NZP6	CO002_HUMAN	S	81	ENSP00000333735:P81S	ENSP00000333735:P81S	P	+	1	0	C15orf2	22472348	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.427000	0.06999	-0.577000	0.05967	-0.719000	0.03609	CCT	.	.		0.701	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24921255	C	T	24921255	3	4	23	1	0	0	0	0	1	0	0	0	1786	623	22	3	243	3	C15orf2	15	24921255	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1918222	24921255	77610137	799	2865										
APBA2	321	hgsc.bcm.edu	37	chr15	29406202	29406202	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agaagatagtccaagctctgTccaactcggtcggagaggta	12	9	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:29406202T>A	ENST00000558402.1	+	15	2760	c.2161T>A	c.(2161-2163)Tcc>Acc	p.S721T	APBA2_ENST00000561069.1_Missense_Mutation_p.S721T|APBA2_ENST00000411764.1_Missense_Mutation_p.S709T|APBA2_ENST00000558259.1_Missense_Mutation_p.S721T|APBA2_ENST00000558330.1_Missense_Mutation_p.S709T			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	721	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CCAAGCTCTGTCCAACTCGGT	0.637																																					p.S721T		Atlas-SNP	.											.	APBA2	132	.	0			c.T2161A						.						131	98	109					15																	29406202		2203	4300	6503	SO:0001583	missense	321	exon13			GCTCTGTCCAACT	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.2161T>A	chr15.hg19:g.29406202T>A	ENSP00000453293:p.Ser721Thr	94.0	0.0		87.0	37.0	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	hg19	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.490877	0.64074	.	.	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.26660	1.72	4.48	4.48	0.54585	PDZ/DHR/GLGF (4);	0.383779	0.22569	N	0.058372	T	0.25901	0.0631	N	0.03891	-0.335	0.80722	D	1	D;B	0.54207	0.965;0.124	D;B	0.70487	0.969;0.078	T	0.29822	-0.9999	10	0.33940	T	0.23	.	12.9729	0.58524	0.0:0.0:0.0:1.0	.	709;721	E9PGI4;Q99767	.;APBA2_HUMAN	T	709;721	ENSP00000409312:S709T	ENSP00000219865:S721T	S	+	1	0	APBA2	27193494	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.842000	0.86851	1.651000	0.50673	0.459000	0.35465	TCC	.	.		0.637	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		A	29406202	T	A	29406202	3	1	23	1	0	0	0	0	1	0	0	0	757	1667	58	4	2203	4	APBA2	15	29406202	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	4484947	29406202	73125190	800	2866										
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32908462	32908462	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgttgcagcatctgcgggCcttctatggtattaaggtga	12	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:32908462C>T	ENST00000361627.3	+	1	772	c.50C>T	c.(49-51)gCc>gTc	p.A17V	ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.A17V|AC123768.4_ENST00000576873.1_lincRNA|ARHGAP11A_ENST00000543522.1_Intron|RP11-1000B6.5_ENST00000500941.2_lincRNA|ARHGAP11A_ENST00000565905.1_Intron|ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.A17V	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	17					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		CATCTGCGGGCCTTCTATGGT	0.547																																					p.A17V	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.C50T						.						77	74	75					15																	32908462		2201	4300	6501	SO:0001583	missense	9824	exon1			TGCGGGCCTTCTA	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.50C>T	chr15.hg19:g.32908462C>T	ENSP00000355090:p.Ala17Val	192.0	0.0		202.0	76.0	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	hg19	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	16.29	3.081246	0.55753	.	.	ENSG00000198826	ENST00000361627	T	0.10005	2.92	3.72	3.72	0.42706	.	0.755248	0.11694	N	0.538556	T	0.07007	0.0178	N	0.24115	0.695	0.80722	D	1	P	0.38617	0.64	B	0.27170	0.077	T	0.42716	-0.9435	10	0.35671	T	0.21	.	12.7189	0.57131	0.0:1.0:0.0:0.0	.	17	Q6P4F7	RHGBA_HUMAN	V	17	ENSP00000355090:A17V	ENSP00000355090:A17V	A	+	2	0	ARHGAP11A	30695754	0.818000	0.29161	0.632000	0.29296	0.965000	0.64279	4.266000	0.58871	2.071000	0.62044	0.478000	0.44815	GCC	.	.		0.547	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		T	32908462	C	T	32908462	3	4	23	1	0	0	0	0	1	0	0	0	863	739	26	3	52	3	ARHGAP11A	15	32908462	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3502260	32908462	69622930	801	2867										
GJD2	57369	hgsc.bcm.edu	37	chr15	35044813	35044813	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacagccagcttgatcttgcGccatcccaggtggttgagtt	11	12	1	2	rs113904860		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:35044813G>A	ENST00000290374.4	-	2	1308	c.832C>T	c.(832-834)Cgc>Tgc	p.R278C	RP11-814P5.1_ENST00000558707.1_RNA|RP11-814P5.1_ENST00000503496.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	278					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TTGATCTTGCGCCATCCCAGG	0.512																																					p.R278C		Atlas-SNP	.											GJD2,NS,carcinoma,+1,1	GJD2	49	.	0			c.C832T						.						130	107	115					15																	35044813		2201	4298	6499	SO:0001583	missense	57369	exon2			TCTTGCGCCATCC	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"Ion channels / Gap junction proteins (connexins)"	19154	protein-coding gene	gene with protein product	"connexin 36"	607058	"gap junction protein, alpha 9, 36kDa"	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.832C>T	chr15.hg19:g.35044813G>A	ENSP00000290374:p.Arg278Cys	164.0	0.0		152.0	61.0	NM_020660	Q2M241|Q9P2R0	Missense_Mutation	SNP	ENST00000290374.4	hg19	CCDS10040.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.480981	0.63849	.	.	ENSG00000159248	ENST00000290374	D	0.98313	-4.86	5.86	5.86	0.93980	.	0.089867	0.43416	D	0.000568	D	0.97015	0.9025	L	0.27053	0.805	0.80722	D	1	D	0.76494	0.999	P	0.53689	0.732	D	0.97229	0.9883	10	0.72032	D	0.01	.	14.8465	0.70264	0.0:0.0:0.8224:0.1776	.	278	Q9UKL4	CXD2_HUMAN	C	278	ENSP00000290374:R278C	ENSP00000290374:R278C	R	-	1	0	GJD2	32832105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.960000	0.56752	2.781000	0.95711	0.650000	0.86243	CGC	.	.		0.512	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2			A	35044813	G	A	35044813	3	1	23	1	0	0	0	0	1	0	0	0	6425	1087	38	1	137	1	GJD2	15	35044813	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2136351	35044813	67486579	802	2868										
THBS1	7057	hgsc.bcm.edu	37	chr15	39874935	39874935	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctccgcatcgcaaaggggggCgtcaatgacaatttccaggt	12	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:39874935C>T	ENST00000260356.5	+	3	774	c.609C>T	c.(607-609)ggC>ggT	p.G203G		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	203	Laminin G-like.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CAAAGGGGGGCGTCAATGACA	0.557																																					p.G203G		Atlas-SNP	.											.	THBS1	106	.	0			c.C609T						.						38	36	37					15																	39874935		2200	4296	6496	SO:0001819	synonymous_variant	7057	exon3			GGGGGGCGTCAAT		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.609C>T	chr15.hg19:g.39874935C>T		35.0	0.0		33.0	13.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	hg19	CCDS32194.1																																																																																			.	.		0.557	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		T	39874935	C	T	39874935	2	4	23	1	0	0	0	0	0	0	0	1	15868	755	27	1		1	THBS1	15	39874935	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	4830122	39874935	62656457	803	2869										
THBS1	7057	hgsc.bcm.edu	37	chr15	39881519	39881519	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttcaccggctcacagcccttCggccagggtgtcgaacatgc	11	15	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:39881519C>T	ENST00000260356.5	+	12	2055	c.1890C>T	c.(1888-1890)ttC>ttT	p.F630F		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	630					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CACAGCCCTTCGGCCAGGGTG	0.577																																					p.F630F		Atlas-SNP	.											.	THBS1	106	.	0			c.C1890T						.						68	72	71					15																	39881519		2200	4297	6497	SO:0001819	synonymous_variant	7057	exon12			GCCCTTCGGCCAG		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1890C>T	chr15.hg19:g.39881519C>T		92.0	0.0		91.0	34.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	1.559	-0.537237	0.04082	.	.	ENSG00000137801	ENST00000397593	.	.	.	5.64	-6.1	0.02138	.	.	.	.	.	T	0.76054	0.3934	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.79838	-0.1634	5	0.87932	D	0	-13.2719	18.2928	0.90136	0.0:0.2884:0.0:0.7116	.	.	.	.	L	64	.	ENSP00000380721:S64L	S	+	2	0	THBS1	37668811	0.013000	0.17824	0.216000	0.23742	0.063000	0.16089	-0.813000	0.04491	-1.693000	0.01427	-1.731000	0.00696	TCG	.	.		0.577	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		T	39881519	C	T	39881519	2	4	23	1	0	0	0	0	0	0	0	1	15868	883	31	1		1	THBS1	15	39881519	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	6584	39881519	62649873	804	2870										
THBS1	7057	hgsc.bcm.edu	37	chr15	39885371	39885371	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atgaccctaactgggttgtaCgccatcagggtaaagaactc	10	10	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:39885371C>T	ENST00000260356.5	+	18	3103	c.2938C>T	c.(2938-2940)Cgc>Tgc	p.R980C	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	980	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CTGGGTTGTACGCCATCAGGG	0.488																																					p.R980C		Atlas-SNP	.											.	THBS1	106	.	0			c.C2938T						.						72	63	66					15																	39885371		2200	4297	6497	SO:0001583	missense	7057	exon18			GTTGTACGCCATC		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2938C>T	chr15.hg19:g.39885371C>T	ENSP00000260356:p.Arg980Cys	102.0	0.0		89.0	39.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.128312	0.77549	.	.	ENSG00000137801	ENST00000260356	D	0.95412	-3.7	5.68	5.68	0.88126	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.36665	N	0.002479	D	0.97318	0.9123	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97222	0.9878	10	0.54805	T	0.06	-28.2234	14.5836	0.68308	0.1461:0.8539:0.0:0.0	.	895;980	B4E3J7;P07996	.;TSP1_HUMAN	C	980	ENSP00000260356:R980C	ENSP00000260356:R980C	R	+	1	0	THBS1	37672663	0.998000	0.40836	0.999000	0.59377	0.999000	0.98932	3.748000	0.55142	2.667000	0.90743	0.655000	0.94253	CGC	.	.		0.488	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		T	39885371	C	T	39885371	3	4	23	1	0	0	0	0	1	0	0	0	15868	536	19	1	3004	1	THBS1	15	39885371	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3852	39885371	62646021	805	2871										
DISP2	85455	hgsc.bcm.edu	37	chr15	40660890	40660890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctggggcctgacctctgctgCggccactcggacttcccctg	12	17	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:40660890C>T	ENST00000267889.3	+	8	2664	c.2577C>T	c.(2575-2577)tgC>tgT	p.C859C	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	859					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		ACCTCTGCTGCGGCCACTCGG	0.667																																					p.C859C		Atlas-SNP	.											.	DISP2	86	.	0			c.C2577T						.						18	22	21					15																	40660890		2201	4299	6500	SO:0001819	synonymous_variant	85455	exon8			CTGCTGCGGCCAC	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2577C>T	chr15.hg19:g.40660890C>T		85.0	0.0		75.0	27.0	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	hg19	CCDS10056.1																																																																																			.	.		0.667	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		T	40660890	C	T	40660890	2	4	23	1	0	0	0	0	0	0	0	1	4542	776	27	1		1	DISP2	15	40660890	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	775519	40660890	61870502	806	2872										
LTK	4058	hgsc.bcm.edu	37	chr15	41804450	41804450	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctttgccgcccgcggctcCgtaggctgagatcctgcggg	15	15	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:41804450C>T	ENST00000263800.6	-	4	469	c.373G>A	c.(373-375)Gga>Aga	p.G125R	LTK_ENST00000453182.2_Missense_Mutation_p.G125R|LTK_ENST00000561619.1_Intron|LTK_ENST00000355166.5_Missense_Mutation_p.G125R	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	125					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CCCGCGGCTCCGTAGGCTGAG	0.667										TSP Lung(18;0.14)																											p.G125R		Atlas-SNP	.											.	LTK	117	.	0			c.G373A						.						26	32	30					15																	41804450		2203	4299	6502	SO:0001583	missense	4058	exon4			CGGCTCCGTAGGC	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.373G>A	chr15.hg19:g.41804450C>T	ENSP00000263800:p.Gly125Arg	223.0	0.0		243.0	90.0	NM_001135685	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	C	33	5.236788	0.95240	.	.	ENSG00000062524	ENST00000360087;ENST00000355166;ENST00000263800;ENST00000453182	D;D;D	0.91945	-2.94;-2.94;-2.94	4.28	4.28	0.50868	.	0.000000	0.34110	U	0.004257	D	0.96531	0.8868	M	0.89163	3.01	0.43084	D	0.994747	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.986;0.999	D	0.97670	1.0166	10	0.87932	D	0	.	16.5404	0.84383	0.0:1.0:0.0:0.0	.	125;125;125	E9PFX4;P29376-4;P29376	.;.;LTK_HUMAN	R	125	ENSP00000347293:G125R;ENSP00000263800:G125R;ENSP00000392196:G125R	ENSP00000263800:G125R	G	-	1	0	LTK	39591742	1.000000	0.71417	0.852000	0.33557	0.988000	0.76386	2.135000	0.42112	2.220000	0.72140	0.561000	0.74099	GGA	.	.		0.667	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			T	41804450	C	T	41804450	3	4	23	1	0	0	0	0	1	0	0	0	9089	661	23	1	2289	1	LTK	15	41804450	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1143560	41804450	60726942	807	2873										
TGM5	9333	hgsc.bcm.edu	37	chr15	43545733	43545733	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caccactctgctgacgtagaCggggcttccccgcagagcac	11	16	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:43545733C>T	ENST00000220420.5	-	5	662	c.655G>A	c.(655-657)Gtc>Atc	p.V219I	TGM5_ENST00000349114.4_Missense_Mutation_p.V137I	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	219					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	CTGACGTAGACGGGGCTTCCC	0.607																																					p.V219I		Atlas-SNP	.											.	TGM5	88	.	0			c.G655A						.						72	64	67					15																	43545733		2202	4299	6501	SO:0001583	missense	9333	exon5			CGTAGACGGGGCT	AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"Transglutaminases"	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.655G>A	chr15.hg19:g.43545733C>T	ENSP00000220420:p.Val219Ile	50.0	0.0		46.0	15.0	NM_201631	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	hg19	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.430780	0.43122	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	D;D	0.92249	-3.0;-3.0	5.31	3.42	0.39159	.	0.000000	0.85682	D	0.000000	D	0.89904	0.6850	L	0.39147	1.195	0.33801	D	0.626706	D;D	0.59767	0.986;0.975	P;B	0.54100	0.742;0.41	D	0.88890	0.3345	10	0.17832	T	0.49	-40.1078	9.6247	0.39743	0.0:0.8284:0.0:0.1716	.	137;219	O43548-2;O43548	.;TGM5_HUMAN	I	219;137;218	ENSP00000220420:V219I;ENSP00000220419:V137I	ENSP00000220420:V219I	V	-	1	0	TGM5	41333025	0.174000	0.23070	0.849000	0.33467	0.583000	0.36354	0.776000	0.26704	1.383000	0.46405	-0.137000	0.14449	GTC	.	.		0.607	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		T	43545733	C	T	43545733	3	4	23	1	0	0	0	0	1	0	0	0	15848	536	19	1	1543	1	TGM5	15	43545733	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1741283	43545733	58985659	808	2874										
TUBGCP4	27229	hgsc.bcm.edu	37	chr15	43668752	43668752	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggttacatggaatctacctgCgggccttctgcacagggctg	13	11	2	0	rs200951264		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:43668752C>T	ENST00000260383.7	+	3	513	c.259C>T	c.(259-261)Cgg>Tgg	p.R87W	TUBGCP4_ENST00000564079.1_Missense_Mutation_p.R87W|TUBGCP4_ENST00000399460.3_5'UTR|TUBGCP4_ENST00000570081.1_3'UTR			Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	87					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|spindle pole (GO:0000922)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(4)|prostate(2)|upper_aerodigestive_tract(2)	21		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		AATCTACCTGCGGGCCTTCTG	0.493											OREG0023088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R87W		Atlas-SNP	.											.	TUBGCP4	48	.	0			c.C259T						.						132	126	128					15																	43668752		1901	4120	6021	SO:0001583	missense	27229	exon3			TACCTGCGGGCCT	AJ249677	CCDS42030.1, CCDS66745.1	15q15.3	2014-08-12			ENSG00000137822	ENSG00000137822			16691	protein-coding gene	gene with protein product		609610				10562286	Standard	NM_001286414		Approved	76P, FLJ14797	uc001zrn.3	Q9UGJ1	OTTHUMG00000176647	ENST00000260383.7:c.259C>T	chr15.hg19:g.43668752C>T	ENSP00000260383:p.Arg87Trp	140.0	0.0	918	118.0	42.0	NM_014444	B3KNK6|Q969X3|Q9NVF0	Missense_Mutation	SNP	ENST00000260383.7	hg19		.	.	.	.	.	.	.	.	.	.	c	21.2	4.112382	0.77210	.	.	ENSG00000137822	ENST00000260383	T	0.09255	3.0	5.38	2.89	0.33648	.	0.000000	0.85682	D	0.000000	T	0.28928	0.0718	M	0.67397	2.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.988	T	0.03608	-1.1020	10	0.72032	D	0.01	-15.6209	12.7941	0.57551	0.5737:0.4263:0.0:0.0	.	87;87	Q9UGJ1;Q9UGJ1-2	GCP4_HUMAN;.	W	87	ENSP00000260383:R87W	ENSP00000260383:R87W	R	+	1	2	TUBGCP4	41456044	1.000000	0.71417	0.938000	0.37757	0.991000	0.79684	4.186000	0.58337	0.993000	0.38866	-0.259000	0.10710	CGG	.	C|0.999;A|0.001		0.493	TUBGCP4-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000432970.1	NM_014444		T	43668752	C	T	43668752	3	4	23	1	0	0	0	0	1	0	0	0	16783	759	27	1	269	1	TUBGCP4	15	43668752	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	123019	43668752	58862640	809	2875										
MAP1A	4130	hgsc.bcm.edu	37	chr15	43820753	43820753	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgaggattgtgcagccaatgGcccaactgaaaccagcccta	10	12	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:43820753G>A	ENST00000300231.5	+	4	7532	c.7082G>A	c.(7081-7083)gGc>gAc	p.G2361D	MAP1A_ENST00000382031.1_Missense_Mutation_p.G2599D|MAP1A_ENST00000399453.1_Missense_Mutation_p.G2361D			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2361					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GCAGCCAATGGCCCAACTGAA	0.637																																					p.G2361D		Atlas-SNP	.											.	MAP1A	189	.	0			c.G7082A						.						31	35	33					15																	43820753		2002	4155	6157	SO:0001583	missense	4130	exon4			CCAATGGCCCAAC	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.7082G>A	chr15.hg19:g.43820753G>A	ENSP00000300231:p.Gly2361Asp	73.0	0.0		69.0	28.0	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.251906	0.22880	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01705	4.68;4.68;4.68	4.59	4.59	0.56863	.	0.000000	0.34603	N	0.003828	T	0.04407	0.0121	L	0.36672	1.1	0.42855	D	0.994096	D	0.56521	0.976	P	0.53006	0.715	T	0.51513	-0.8696	10	0.72032	D	0.01	-12.0978	17.5779	0.87956	0.0:0.0:1.0:0.0	.	2361	P78559	MAP1A_HUMAN	D	2599;2361;2361	ENSP00000371462:G2599D;ENSP00000382380:G2361D;ENSP00000300231:G2361D	ENSP00000300231:G2361D	G	+	2	0	MAP1A	41608045	1.000000	0.71417	1.000000	0.80357	0.452000	0.32318	4.715000	0.61909	2.392000	0.81423	0.561000	0.74099	GGC	.	.		0.637	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		A	43820753	G	A	43820753	3	1	23	1	0	0	0	0	1	0	0	0	9236	1203	42	3	7084	3	MAP1A	15	43820753	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	152001	43820753	58710639	810	2876										
DUOXA1	90527	hgsc.bcm.edu	37	chr15	45413420	45413420	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcagaactgaaattcacagCtgtggttggggagttggaca	13	7	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:45413420C>T	ENST00000560572.1	-	3	211		c.e3-1		DUOXA1_ENST00000430224.2_Intron|DUOXA1_ENST00000558996.1_Intron|DUOXA1_ENST00000559014.1_Splice_Site|DUOXA1_ENST00000267803.4_Splice_Site|DUOXA1_ENST00000558422.1_Intron	NM_001276266.1	NP_001263195.1	Q1HG43	DOXA1_HUMAN	dual oxidase maturation factor 1						hydrogen peroxide metabolic process (GO:0042743)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)		AAATTCACAGCTGTGGTTGGG	0.493																																					.		Atlas-SNP	.											.	DUOXA1	32	.	0			c.206-1G>A						.						88	69	76					15																	45413420		2198	4298	6496	SO:0001630	splice_region_variant	90527	exon7			TCACAGCTGTGGT	BC029819	CCDS10119.1, CCDS61619.1, CCDS61620.1, CCDS61621.1	15q21.1	2006-11-29	2006-01-23	2006-07-25	ENSG00000140254	ENSG00000140254			26507	protein-coding gene	gene with protein product		612771				16651268	Standard	NM_144565		Approved	FLJ32334, NUMBIP, NIP, mol	uc010bec.4	Q1HG43	OTTHUMG00000131352	ENST00000560572.1:c.206-1G>A	chr15.hg19:g.45413420C>T		148.0	0.0		131.0	24.0	NM_001276264	Q8N6K9|Q96MI4	Splice_Site	SNP	ENST00000560572.1	hg19		.	.	.	.	.	.	.	.	.	.	C	20.2	3.944379	0.73672	.	.	ENSG00000140254	ENST00000267803	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7142	0.88331	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DUOXA1	43200712	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	6.980000	0.76160	2.674000	0.91012	0.650000	0.86243	.	.	.		0.493	DUOXA1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000416242.1	NM_144565	Intron	T	45413420	C	T	45413420	5	4	23	1	0	0	0	0	0	0	1	0	4804	811	28	3	1270	3	DUOXA1	15	45413420	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1592667	45413420	57117972	811	2877										
SPATA5L1	79029	hgsc.bcm.edu	37	chr15	45695622	45695622	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gttgacgctgctggacggcgCcagtggggaccgcgaggtcg	19	11	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:45695622C>A	ENST00000305560.6	+	1	1094	c.995C>A	c.(994-996)gCc>gAc	p.A332D	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.A332D|GATM_ENST00000458245.5_5'Flank	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	332						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		CTGGACGGCGCCAGTGGGGAC	0.667																																					p.A332D		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.C995A						.						22	27	25					15																	45695622		2194	4287	6481	SO:0001583	missense	79029	exon1			ACGGCGCCAGTGG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"ATPases / AAA-type"	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.995C>A	chr15.hg19:g.45695622C>A	ENSP00000305494:p.Ala332Asp	121.0	0.0		127.0	63.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	hg19	CCDS10123.1	.	.	.	.	.	.	.	.	.	.	C	10.78	1.446875	0.25987	.	.	ENSG00000171763	ENST00000305560	D	0.94862	-3.54	4.55	2.22	0.28083	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.840508	0.10929	N	0.618658	D	0.92241	0.7539	L	0.50333	1.59	0.09310	N	1	P	0.41080	0.737	B	0.42851	0.4	D	0.84275	0.0491	10	0.87932	D	0	-36.6425	7.7622	0.28959	0.0:0.1833:0.0:0.8167	.	332	Q9BVQ7	SPA5L_HUMAN	D	332	ENSP00000305494:A332D	ENSP00000305494:A332D	A	+	2	0	SPATA5L1	43482914	0.746000	0.28272	0.011000	0.14972	0.041000	0.13682	3.620000	0.54203	0.274000	0.22072	-0.323000	0.08544	GCC	.	.		0.667	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		A	45695622	C	A	45695622	3	1	23	1	0	0	0	0	1	0	0	0	15027	739	26	3	997	3	SPATA5L1	15	45695622	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	282202	45695622	56835770	812	2878										
CEP152	22995	hgsc.bcm.edu	37	chr15	49030737	49030737	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctgtatctgaaagataaccGgatggtgaaaactgtttgga	11	5	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:49030737G>A	ENST00000380950.2	-	27	5029	c.4842C>T	c.(4840-4842)tcC>tcT	p.S1614S	CEP152_ENST00000399334.3_Silent_p.S1558S	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1614					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		AAAGATAACCGGATGGTGAAA	0.378																																					p.S1614S		Atlas-SNP	.											.	CEP152	145	.	0			c.C4842T						.						100	99	99					15																	49030737		1904	4130	6034	SO:0001819	synonymous_variant	22995	exon27			ATAACCGGATGGT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.4842C>T	chr15.hg19:g.49030737G>A		102.0	0.0		122.0	38.0	NM_001194998	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.		0.378	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		A	49030737	G	A	49030737	2	1	23	1	0	0	0	0	0	0	0	1	3250	1103	39	1		1	CEP152	15	49030737	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3335115	49030737	53500655	813	2879										
GALK2	2585	hgsc.bcm.edu	37	chr15	49584596	49584596	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggtgcaggctaaactagggAttagtctagaagaaatgctg	13	5	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:49584596A>T	ENST00000560031.1	+	8	1136	c.829A>T	c.(829-831)Att>Ttt	p.I277F	GALK2_ENST00000396509.2_Missense_Mutation_p.I253F|GALK2_ENST00000559454.1_Missense_Mutation_p.I253F|GALK2_ENST00000544523.1_Missense_Mutation_p.I253F|GALK2_ENST00000543495.1_Missense_Mutation_p.I148F|GALK2_ENST00000561014.1_3'UTR|GALK2_ENST00000327171.3_Missense_Mutation_p.I266F			Q01415	GALK2_HUMAN	galactokinase 2	277					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		TAAACTAGGGATTAGTCTAGA	0.463																																					p.I277F		Atlas-SNP	.											.	GALK2	78	.	0			c.A829T						.						125	131	129					15																	49584596		2196	4295	6491	SO:0001583	missense	2585	exon8			CTAGGGATTAGTC		CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.829A>T	chr15.hg19:g.49584596A>T	ENSP00000453129:p.Ile277Phe	121.0	0.0		128.0	44.0	NM_002044	Q7Z4Q4	Missense_Mutation	SNP	ENST00000560031.1	hg19	CCDS42034.1	.	.	.	.	.	.	.	.	.	.	A	5.621	0.299216	0.10622	.	.	ENSG00000156958	ENST00000327171;ENST00000396509;ENST00000543495;ENST00000544523	D;T;D	0.85702	-2.02;-0.49;-2.02	5.45	-2.76	0.05896	.	0.416052	0.28653	N	0.014597	T	0.67618	0.2912	L	0.29908	0.895	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.50448	-0.8827	10	0.28530	T	0.3	-32.7812	2.0306	0.03528	0.2066:0.1023:0.4838:0.2072	.	277;266	Q01415;Q7Z4Q4	GALK2_HUMAN;.	F	266;277;148;253	ENSP00000316632:I266F;ENSP00000443220:I148F;ENSP00000440312:I253F	ENSP00000316632:I266F	I	+	1	0	GALK2	47371888	0.639000	0.27234	0.057000	0.19452	0.120000	0.20174	0.644000	0.24766	-0.471000	0.06891	-1.223000	0.01593	ATT	.	.		0.463	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1			T	49584596	A	T	49584596	3	4	23	1	0	0	0	0	1	0	0	0	6212	333	12	4	883	4	GALK2	15	49584596	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	553859	49584596	52946796	814	2880										
ATP8B4	79895	hgsc.bcm.edu	37	chr15	50331023	50331023	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgattatcactcttgtggcGaaactgaaaaatcaaagtgt	8	6	3	2	rs372854928		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:50331023G>A	ENST00000284509.6	-	6	445	c.304C>T	c.(304-306)Cgc>Tgc	p.R102C	ATP8B4_ENST00000558959.1_5'UTR|ATP8B4_ENST00000559829.1_Missense_Mutation_p.R102C	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	102						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		CTCTTGTGGCGAAACTGAAAA	0.363																																					p.R102C		Atlas-SNP	.											.	ATP8B4	173	.	0			c.C304T						.	G	CYS/ARG	0,4392		0,0,2196	132	116	121		304	5.4	1	15		121	1,8587	1.2+/-3.3	0,1,4293	no	missense	ATP8B4	NM_024837.2	180	0,1,6489	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	102/1193	50331023	1,12979	2196	4294	6490	SO:0001583	missense	79895	exon6			TGTGGCGAAACTG	AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"ATPases / P-type"	13536	protein-coding gene	gene with protein product		609123	"ATPase, Class I, type 8B, member 4"			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.304C>T	chr15.hg19:g.50331023G>A	ENSP00000284509:p.Arg102Cys	141.0	0.0		94.0	28.0	NM_024837	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	hg19	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.348741	0.82132	0.0	1.16E-4	ENSG00000104043	ENST00000284509	D	0.85861	-2.04	5.39	5.39	0.77823	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.95787	0.8629	H	0.99058	4.415	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.97412	1.0003	10	0.87932	D	0	.	17.0049	0.86390	0.0:0.0:1.0:0.0	.	102	Q8TF62	AT8B4_HUMAN	C	102	ENSP00000284509:R102C	ENSP00000284509:R102C	R	-	1	0	ATP8B4	48118315	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.429000	0.80309	2.690000	0.91761	0.655000	0.94253	CGC	.	.		0.363	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837		A	50331023	G	A	50331023	3	1	23	1	0	0	0	0	1	0	0	0	1197	1058	37	1	3366	1	ATP8B4	15	50331023	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	746427	50331023	52200369	815	2881										
TRPM7	54822	hgsc.bcm.edu	37	chr15	50884115	50884115	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgccaaacttacctacaaaTgctccaaattctgtattatc	3	11	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:50884115T>C	ENST00000313478.7	-	26	4598	c.4317A>G	c.(4315-4317)gcA>gcG	p.A1439A	TRPM7_ENST00000560955.1_Silent_p.A1439A	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1439					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		TACCTACAAATGCTCCAAATT	0.323																																					p.A1439A		Atlas-SNP	.											.	TRPM7	145	.	0			c.A4317G						.						78	73	75					15																	50884115		1803	4068	5871	SO:0001819	synonymous_variant	54822	exon26			TACAAATGCTCCA	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.4317A>G	chr15.hg19:g.50884115T>C		112.0	0.0		94.0	4.0	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Silent	SNP	ENST00000313478.7	hg19	CCDS42035.1																																																																																			.	.		0.323	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		C	50884115	T	C	50884115	2	2	23	1	0	0	0	0	0	0	0	1	16606	1451	51	2		2	TRPM7	15	50884115	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	553092	50884115	51647277	816	2882										
ADAM10	102	hgsc.bcm.edu	37	chr15	58936169	58936169	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtatcaatcgctttaacatgActggatatctatgatttaaa	6	6	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:58936169A>G	ENST00000260408.3	-	7	1187	c.744T>C	c.(742-744)agT>agC	p.S248S	ADAM10_ENST00000396140.2_Intron|ADAM10_ENST00000561288.1_Intron|ADAM10_ENST00000402627.1_Intron	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	248	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		CTTTAACATGACTGGATATCT	0.303																																					p.S248S		Atlas-SNP	.											.	ADAM10	59	.	0			c.T744C						.						99	99	99					15																	58936169		2192	4292	6484	SO:0001819	synonymous_variant	102	exon7			AACATGACTGGAT	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"ADAM metallopeptidase domain containing", "CD molecules"	188	protein-coding gene	gene with protein product		602192	"a disintegrin and metalloproteinase domain 10"			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.744T>C	chr15.hg19:g.58936169A>G		100.0	0.0		110.0	5.0	NM_001110	B4DU28|Q10742|Q92650	Silent	SNP	ENST00000260408.3	hg19	CCDS10167.1																																																																																			.	.		0.303	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110		G	58936169	A	G	58936169	2	3	23	1	0	0	0	0	0	0	0	1	234	272	10	2		2	ADAM10	15	58936169	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	8052054	58936169	43595223	817	2883										
SLTM	79811	hgsc.bcm.edu	37	chr15	59175873	59175873	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgcccggccgtcacccattCgcctcgtatcatgatagcta	8	16	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:59175873C>T	ENST00000380516.2	-	20	3035	c.2948G>A	c.(2947-2949)cGa>cAa	p.R983Q	SLTM_ENST00000536328.1_Missense_Mutation_p.R552Q	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	983					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GTCACCCATTCGCCTCGTATC	0.517																																					p.R983Q		Atlas-SNP	.											.	SLTM	90	.	0			c.G2948A						.						217	189	198					15																	59175873		2192	4292	6484	SO:0001583	missense	79811	exon20			CCCATTCGCCTCG	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"RNA binding motif (RRM) containing"	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.2948G>A	chr15.hg19:g.59175873C>T	ENSP00000369887:p.Arg983Gln	133.0	0.0		131.0	58.0	NM_024755	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000380516.2	hg19	CCDS10168.2	.	.	.	.	.	.	.	.	.	.	C	36	5.607455	0.96626	.	.	ENSG00000137776	ENST00000380516;ENST00000432750;ENST00000536328	T	0.28895	1.59	6.02	6.02	0.97574	.	0.000000	0.49305	D	0.000149	T	0.55016	0.1894	L	0.53249	1.67	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.99	T	0.51718	-0.8670	10	0.87932	D	0	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	983;552	Q9NWH9;A8K5V8	SLTM_HUMAN;.	Q	983;549;552	ENSP00000369887:R983Q	ENSP00000369887:R983Q	R	-	2	0	SLTM	56963165	1.000000	0.71417	0.997000	0.53966	0.911000	0.54048	5.987000	0.70571	2.857000	0.98124	0.650000	0.86243	CGA	.	.		0.517	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755		T	59175873	C	T	59175873	3	4	23	1	0	0	0	0	1	0	0	0	14769	884	31	1	164	1	SLTM	15	59175873	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	239704	59175873	43355519	818	2884										
TLN2	83660	hgsc.bcm.edu	37	chr15	63009820	63009820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagccacacagaccatcgccGcctcccagaatgcagctgtt	8	17	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:63009820G>A	ENST00000561311.1	+	23	3039	c.2809G>A	c.(2809-2811)Gcc>Acc	p.A937T	TLN2_ENST00000306829.6_Missense_Mutation_p.A937T			Q9Y4G6	TLN2_HUMAN	talin 2	937	Ala-rich.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						GACCATCGCCGCCTCCCAGAA	0.567																																					p.A937T		Atlas-SNP	.											.	TLN2	253	.	0			c.G2809A						.						30	27	28					15																	63009820		2203	4295	6498	SO:0001583	missense	83660	exon21			ATCGCCGCCTCCC	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.2809G>A	chr15.hg19:g.63009820G>A	ENSP00000453508:p.Ala937Thr	236.0	0.0		224.0	81.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	G	34	5.344071	0.95807	.	.	ENSG00000171914	ENST00000306829	T	0.70869	-0.52	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.86594	0.5970	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85108	0.0961	10	0.35671	T	0.21	-21.3073	19.9855	0.97347	0.0:0.0:1.0:0.0	.	937	Q9Y4G6	TLN2_HUMAN	T	937	ENSP00000303476:A937T	ENSP00000303476:A937T	A	+	1	0	TLN2	60797112	1.000000	0.71417	0.977000	0.42913	0.626000	0.37791	9.751000	0.98889	2.806000	0.96561	0.655000	0.94253	GCC	.	.		0.567	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63009820	G	A	63009820	3	1	23	1	0	0	0	0	1	0	0	0	15963	1087	38	1	2891	1	TLN2	15	63009820	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3833947	63009820	39521572	819	2885										
PIF1	80119	hgsc.bcm.edu	37	chr15	65111379	65111379	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgggcatccagggtactggcCagctcagggttgctgtccat	14	11	1	0	rs374363106		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:65111379C>T	ENST00000268043.4	-	9	1471	c.1377G>A	c.(1375-1377)ctG>ctA	p.L459L	PIF1_ENST00000333425.6_Silent_p.L459L|PIF1_ENST00000559239.1_Silent_p.L459L					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						GGGTACTGGCCAGCTCAGGGT	0.542																																					p.L459L		Atlas-SNP	.											.	PIF1	43	.	0			c.G1377A						.	C		0,4404		0,0,2202	45	41	43		1377	-5.4	0.3	15		43	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PIF1	NM_025049.2		0,1,6500	TT,TC,CC		0.0116,0.0,0.0077		459/642	65111379	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	80119	exon9			ACTGGCCAGCTCA	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"chromosome 15 open reading frame 20", "PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.1377G>A	chr15.hg19:g.65111379C>T		221.0	0.0		210.0	91.0	NM_025049		Silent	SNP	ENST00000268043.4	hg19	CCDS10195.2																																																																																			.	.		0.542	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049		T	65111379	C	T	65111379	2	4	23	1	0	0	0	0	0	0	0	1	11892	581	21	3		3	PIF1	15	65111379	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2101559	65111379	37420013	820	2886										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72338646	72338646	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agccattcggggccacagcaTcattcgctgaactggacaat	10	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:72338646T>A	ENST00000356056.5	-	2	731	c.259A>T	c.(259-261)Atg>Ttg	p.M87L	MYO9A_ENST00000444904.1_Missense_Mutation_p.M87L|RNU2-65P_ENST00000410162.1_RNA|MYO9A_ENST00000564571.1_Missense_Mutation_p.M87L|MYO9A_ENST00000424560.1_Missense_Mutation_p.M87L|MYO9A_ENST00000566885.1_Intron|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	87	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GGCCACAGCATCATTCGCTGA	0.428																																					p.M87L		Atlas-SNP	.											.	MYO9A	203	.	0			c.A259T						.						85	83	84					15																	72338646		2199	4297	6496	SO:0001583	missense	4649	exon2			ACAGCATCATTCG	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.259A>T	chr15.hg19:g.72338646T>A	ENSP00000348349:p.Met87Leu	95.0	0.0		108.0	45.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	t	10.86	1.469781	0.26423	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864;ENST00000446448	T;T;T	0.14640	2.49;2.49;2.49	5.33	4.18	0.49190	Ras-association (3);	.	.	.	.	T	0.08358	0.0208	N	0.21097	0.63	0.54753	D	0.999984	B;B;B	0.23316	0.003;0.003;0.083	B;B;B	0.24394	0.002;0.005;0.053	T	0.09143	-1.0688	9	0.02654	T	1	.	12.2501	0.54593	0.0:0.0:0.142:0.858	.	87;87;87	B2RTY4-3;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	L	87	ENSP00000348349:M87L;ENSP00000399162:M87L;ENSP00000398250:M87L	ENSP00000261864:M87L	M	-	1	0	MYO9A	70125700	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.304000	0.51866	0.832000	0.34804	0.372000	0.22366	ATG	.	.		0.428	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		A	72338646	T	A	72338646	3	1	23	1	0	0	0	0	1	0	0	0	10093	1435	50	4	7551	4	MYO9A	15	72338646	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	7227267	72338646	30192746	821	2887										
PML	5371	hgsc.bcm.edu	37	chr15	74337203	74337203	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctgcagaccaccacgttgCcccctgcccagcctgctttc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:74337203delC	ENST00000268058.3	+	9	2599	c.2503delC	c.(2503-2505)cccfs	p.P836fs	PML_ENST00000565898.1_Frame_Shift_Del_p.P788fs	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	836					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CACCACGTTGCCCCCTGCCCA	0.637			T	"RARA, PAX5"	"APL, ALL"																																p.L834fs		Atlas-Indel,Pindel	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.2502delG						.						45	47	46					15																	74337203		2196	4294	6490	SO:0001589	frameshift_variant	5371	exon9			.	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.2503delC	chr15.hg19:g.74337203delC	ENSP00000268058:p.Pro836fs	75.0	0.0		82.0	28.0	NM_033238	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Frame_Shift_Del	DEL	ENST00000268058.3	hg19	CCDS10255.1																																																																																			.	.		0.637	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		-	74337203	C	-	74337203	7	5	23	1	0	1	0	1	0	0	0	0	12144	739	26	0	3554	0	PML	15	74337203	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	1998557	74337203	28194189	822	2888										
ISLR2	57611	hgsc.bcm.edu	37	chr15	74426101	74426101	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caccgcgcttcctggccctcGcaaatggctccctgttggtg	11	16	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:74426101G>A	ENST00000361742.3	+	4	1775	c.1006G>A	c.(1006-1008)Gca>Aca	p.A336T	ISLR2_ENST00000419208.1_Missense_Mutation_p.A336T|ISLR2_ENST00000453268.2_Missense_Mutation_p.A336T|ISLR2_ENST00000445793.1_Missense_Mutation_p.A336T|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000565159.1_Missense_Mutation_p.A336T|ISLR2_ENST00000435464.1_Missense_Mutation_p.A336T|ISLR2_ENST00000565540.1_Missense_Mutation_p.A336T	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	336	Ig-like.				positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A336P(1)		breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						CCTGGCCCTCGCAAATGGCTC	0.642																																					p.A336T		Atlas-SNP	.											ISLR2,NS,carcinoma,0,1	ISLR2	78	.	1	Substitution - Missense(1)	lung(1)	c.G1006A						.						21	22	22					15																	74426101		2198	4297	6495	SO:0001583	missense	57611	exon4			GCCCTCGCAAATG		CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.1006G>A	chr15.hg19:g.74426101G>A	ENSP00000355402:p.Ala336Thr	122.0	0.0		113.0	47.0	NM_001130138	A8K352|Q9P263	Missense_Mutation	SNP	ENST00000361742.3	hg19	CCDS10259.1	.	.	.	.	.	.	.	.	.	.	G	1.031	-0.681696	0.03353	.	.	ENSG00000167178	ENST00000445793;ENST00000361742;ENST00000435464;ENST00000453268;ENST00000419208	T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7	4.7	0.893	0.19236	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.591333	0.16795	N	0.199204	T	0.11580	0.0282	N	0.21240	0.645	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.25187	-1.0139	10	0.15499	T	0.54	.	1.9626	0.03389	0.3129:0.1302:0.4102:0.1467	.	336	Q6UXK2	ISLR2_HUMAN	T	336	ENSP00000403244:A336T;ENSP00000355402:A336T;ENSP00000411443:A336T;ENSP00000411834:A336T;ENSP00000408872:A336T	ENSP00000355402:A336T	A	+	1	0	ISLR2	72213154	0.000000	0.05858	0.022000	0.16811	0.534000	0.34807	0.182000	0.16900	0.290000	0.22444	0.195000	0.17529	GCA	.	.		0.642	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851		A	74426101	G	A	74426101	3	1	23	1	0	0	0	0	1	0	0	0	7868	1087	38	1	1008	1	ISLR2	15	74426101	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	88898	74426101	28105291	823	2889										
EDC3	80153	hgsc.bcm.edu	37	chr15	74932931	74932931	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagctttttatgcagctcatAggaaatacttgggacaacca	8	9	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:74932931A>G	ENST00000315127.4	-	5	1031	c.850T>C	c.(850-852)Tat>Cat	p.Y284H	EDC3_ENST00000426797.3_Missense_Mutation_p.Y284H|EDC3_ENST00000568176.1_Missense_Mutation_p.Y284H	NM_001142444.1|NM_025083.3	NP_001135916.1|NP_079359.2	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	284	Required for interaction with DDX6. {ECO:0000250}.|YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|membrane (GO:0016020)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						TGCAGCTCATAGGAAATACTT	0.498																																					p.Y284H		Atlas-SNP	.											.	EDC3	32	.	0			c.T850C						.						88	73	78					15																	74932931		2197	4296	6493	SO:0001583	missense	80153	exon6			GCTCATAGGAAAT	BC011534	CCDS10267.1	15q24.1	2013-05-02	2013-05-02	2006-07-07	ENSG00000179151	ENSG00000179151			26114	protein-coding gene	gene with protein product		609842	"yjeF domain containing (E.coli)", "LSM16 homolog (EDC3, S. cerevisiae)", "enhancer of mRNA decapping 3 homolog (S. cerevisiae)"	YJDC, LSM16		15225602, 17533573, 22483619	Standard	NM_025083		Approved	FLJ21128, hYjeF_N2-15q23, YJEFN2	uc002aym.3	Q96F86	OTTHUMG00000142815	ENST00000315127.4:c.850T>C	chr15.hg19:g.74932931A>G	ENSP00000320503:p.Tyr284His	112.0	0.0		114.0	43.0	NM_001142444	B3KPH0|D3DW61|Q9H797	Missense_Mutation	SNP	ENST00000315127.4	hg19	CCDS10267.1	.	.	.	.	.	.	.	.	.	.	A	16.79	3.219139	0.58560	.	.	ENSG00000179151	ENST00000315127;ENST00000426797	T;T	0.42900	0.96;0.96	5.82	5.82	0.92795	YjeF-related protein, N-terminal (2);	0.056460	0.64402	D	0.000001	T	0.41743	0.1172	L	0.38175	1.15	0.80722	D	1	B	0.33940	0.433	B	0.43386	0.418	T	0.18745	-1.0327	10	0.15952	T	0.53	-20.8694	15.3675	0.74535	1.0:0.0:0.0:0.0	.	284	Q96F86	EDC3_HUMAN	H	284	ENSP00000320503:Y284H;ENSP00000401343:Y284H	ENSP00000320503:Y284H	Y	-	1	0	EDC3	72719984	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	8.589000	0.90817	2.225000	0.72522	0.533000	0.62120	TAT	.	.		0.498	EDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286399.1	NM_025083		G	74932931	A	G	74932931	3	3	23	1	0	0	0	0	1	0	0	0	4909	420	15	2	688	2	EDC3	15	74932931	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	506830	74932931	27598461	824	2890										
SGK269	79834	hgsc.bcm.edu	37	chr15	77471265	77471265	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctagccttgctctgatccaCactgagctggccttgagcag	10	14	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:77471265C>T	ENST00000560626.2	-	4	3479	c.3004G>A	c.(3004-3006)Gtg>Atg	p.V1002M	PEAK1_ENST00000312493.4_Missense_Mutation_p.V1002M|PEAK1_ENST00000558305.1_Missense_Mutation_p.V1002M			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1002					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CTCTGATCCACACTGAGCTGG	0.527																																					p.V1002M		Atlas-SNP	.											.	.	.	.	0			c.G3004A						.						135	134	135					15																	77471265		2118	4233	6351	SO:0001583	missense	0	exon5			GATCCACACTGAG		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3004G>A	chr15.hg19:g.77471265C>T	ENSP00000452796:p.Val1002Met	55.0	0.0		76.0	29.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.709952	0.30322	.	.	ENSG00000173517	ENST00000312493	T	0.70282	-0.47	5.75	2.86	0.33363	.	0.370320	0.24479	N	0.038179	T	0.48589	0.1508	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.40059	-0.9583	10	0.56958	D	0.05	-6.477	5.22	0.15364	0.1309:0.5924:0.0:0.2766	.	1002	Q9H792	PEAK1_HUMAN	M	1002	ENSP00000309230:V1002M	ENSP00000309230:V1002M	V	-	1	0	AC087465.1	75258320	0.000000	0.05858	0.174000	0.22961	0.915000	0.54546	0.023000	0.13533	0.794000	0.33899	0.655000	0.94253	GTG	.	.		0.527	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			T	77471265	C	T	77471265	3	4	23	1	0	0	0	0	1	0	0	0	14226	478	17	3	2252	3	SGK269	15	77471265	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2538334	77471265	25060127	825	2891										
AP3B2	8120	hgsc.bcm.edu	37	chr15	83350208	83350208	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggcgtgggcagctgttttcCgcacatagggtgacatgtcc	14	10	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:83350208C>T	ENST00000261722.3	-	5	692	c.485G>A	c.(484-486)cGg>cAg	p.R162Q	AP3B2_ENST00000535359.1_Missense_Mutation_p.R162Q|AP3B2_ENST00000535348.1_Missense_Mutation_p.R130Q|RP11-752G15.3_ENST00000560650.1_RNA	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	162					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			AGCTGTTTTCCGCACATAGGG	0.582																																					p.R162Q		Atlas-SNP	.											.	AP3B2	103	.	0			c.G485A						.						103	105	105					15																	83350208		2073	4201	6274	SO:0001583	missense	8120	exon5			GTTTTCCGCACAT	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.485G>A	chr15.hg19:g.83350208C>T	ENSP00000261722:p.Arg162Gln	76.0	0.0		80.0	38.0	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Missense_Mutation	SNP	ENST00000261722.3	hg19	CCDS45331.1	.	.	.	.	.	.	.	.	.	.	C	37	6.151902	0.97329	.	.	ENSG00000103723	ENST00000261722;ENST00000535348;ENST00000535359;ENST00000541693	T;T;T;T	0.25912	1.77;1.77;1.77;1.77	5.09	5.09	0.68999	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.058253	0.64402	D	0.000002	T	0.68723	0.3032	H	0.97806	4.08	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.994;1.0;1.0	T	0.81824	-0.0755	10	0.87932	D	0	-16.9628	18.6878	0.91571	0.0:1.0:0.0:0.0	.	130;162;162	B7ZKR7;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	Q	162;130;162;118	ENSP00000261722:R162Q;ENSP00000438721:R130Q;ENSP00000440984:R162Q;ENSP00000441961:R118Q	ENSP00000261722:R162Q	R	-	2	0	AP3B2	81147262	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.627000	0.83176	2.642000	0.89623	0.563000	0.77884	CGG	.	.		0.582	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			T	83350208	C	T	83350208	3	4	23	1	0	0	0	0	1	0	0	0	745	652	23	1	2775	1	AP3B2	15	83350208	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5878943	83350208	19181184	826	2892										
ALPK3	57538	hgsc.bcm.edu	37	chr15	85403072	85403072	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccccgtagactgcggtgtgtAtcggtgcaccatccacaatg	11	13	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:85403072A>G	ENST00000258888.5	+	8	4804	c.4637A>G	c.(4636-4638)tAt>tGt	p.Y1546C		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1546	Ig-like 2.				heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			TGCGGTGTGTATCGGTGCACC	0.687																																					p.Y1546C		Atlas-SNP	.											.	ALPK3	289	.	0			c.A4637G						.						48	45	46					15																	85403072		2203	4299	6502	SO:0001583	missense	57538	exon8			GTGTGTATCGGTG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4637A>G	chr15.hg19:g.85403072A>G	ENSP00000258888:p.Tyr1546Cys	95.0	0.0		82.0	31.0	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	hg19	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.633489	0.87660	.	.	ENSG00000136383	ENST00000258888	T	0.79247	-1.25	5.52	5.52	0.82312	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	D	0.87180	0.6113	M	0.76170	2.325	0.54753	D	0.999987	D	0.89917	1.0	D	0.87578	0.998	D	0.88634	0.3171	10	0.87932	D	0	-8.3972	13.5898	0.61953	1.0:0.0:0.0:0.0	.	1546	Q96L96	ALPK3_HUMAN	C	1546	ENSP00000258888:Y1546C	ENSP00000258888:Y1546C	Y	+	2	0	ALPK3	83204076	1.000000	0.71417	0.853000	0.33588	0.986000	0.74619	6.667000	0.74451	2.101000	0.63845	0.460000	0.39030	TAT	.	.		0.687	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		G	85403072	A	G	85403072	3	3	23	1	0	0	0	0	1	0	0	0	546	449	16	2	4667	2	ALPK3	15	85403072	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2052864	85403072	17128320	827	2893										
MFGE8	4240	hgsc.bcm.edu	37	chr15	89449105	89449105	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaacaggttgacatgcaccgCgtttttgttccagttaccca	8	11	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:89449105C>T	ENST00000566497.1	-	5	629	c.568G>A	c.(568-570)Gcg>Acg	p.A190T	MFGE8_ENST00000539437.1_Missense_Mutation_p.A182T|MFGE8_ENST00000268151.7_Missense_Mutation_p.A190T|MFGE8_ENST00000268150.8_Missense_Mutation_p.A190T|MFGE8_ENST00000542878.1_Missense_Mutation_p.A146T|MFGE8_ENST00000559997.1_Intron			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	190	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					ACATGCACCGCGTTTTTGTTC	0.562																																					p.A190T		Atlas-SNP	.											.	MFGE8	60	.	0			c.G568A						.						136	121	126					15																	89449105		2200	4299	6499	SO:0001583	missense	4240	exon5			GCACCGCGTTTTT	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"sperm surface protein hP47"	602281	"sperm associated antigen 10"	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.568G>A	chr15.hg19:g.89449105C>T	ENSP00000456281:p.Ala190Thr	163.0	0.0		140.0	56.0	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Missense_Mutation	SNP	ENST00000566497.1	hg19	CCDS10347.1	.	.	.	.	.	.	.	.	.	.	C	2.803	-0.248735	0.05867	.	.	ENSG00000140545	ENST00000268150;ENST00000268151;ENST00000539437;ENST00000542878	D;D;D;T	0.96685	-4.09;-4.09;-4.09;-1.45	4.97	-0.939	0.10408	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.692542	0.16168	N	0.226449	T	0.77631	0.4159	N	0.00098	-2.145	0.09310	N	1	B;B;B;B;B	0.24258	0.048;0.1;0.036;0.002;0.017	B;B;B;B;B	0.24006	0.018;0.05;0.01;0.004;0.01	T	0.76683	-0.2869	10	0.02654	T	1	-12.7145	10.1991	0.43073	0.0:0.4537:0.0:0.5463	.	182;146;182;190;190	B3KTQ2;F5GZN3;F5H7N9;Q08431-3;Q08431	.;.;.;.;MFGM_HUMAN	T	190;190;182;146	ENSP00000268150:A190T;ENSP00000268151:A190T;ENSP00000442386:A182T;ENSP00000444332:A146T	ENSP00000268150:A190T	A	-	1	0	MFGE8	87250109	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.141000	0.10327	-0.227000	0.09884	-1.093000	0.02169	GCG	.	.		0.562	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928		T	89449105	C	T	89449105	3	4	23	1	0	0	0	0	1	0	0	0	9529	768	27	1	611	1	MFGE8	15	89449105	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	4046033	89449105	13082287	828	2894										
ABHD2	11057	hgsc.bcm.edu	37	chr15	89698708	89698708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctatcggtgcgccgtgctgAaccacctgggtgccctgccc	13	16	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:89698708A>G	ENST00000352732.5	+	5	1001	c.481A>G	c.(481-483)Aac>Gac	p.N161D	ABHD2_ENST00000565973.1_Missense_Mutation_p.N161D|ABHD2_ENST00000355100.3_Missense_Mutation_p.N161D	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	161					negative regulation of cell migration (GO:0030336)|response to wounding (GO:0009611)	integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|soft_tissue(1)	23	Lung NSC(78;0.0472)|all_lung(78;0.089)					CGCCGTGCTGAACCACCTGGG	0.527																																					p.N161D	Colon(11;252 417 24570 33239 41878)	Atlas-SNP	.											.	ABHD2	55	.	0			c.A481G						.						161	133	142					15																	89698708		2200	4299	6499	SO:0001583	missense	11057	exon9			GTGCTGAACCACC	X12433	CCDS10348.1	15q26.1	2006-10-06			ENSG00000140526	ENSG00000140526		"Abhydrolase domain containing"	18717	protein-coding gene	gene with protein product		612196					Standard	NM_152924		Approved	LABH2	uc002bnk.2	P08910	OTTHUMG00000148684	ENST00000352732.5:c.481A>G	chr15.hg19:g.89698708A>G	ENSP00000268129:p.Asn161Asp	143.0	0.0		136.0	68.0	NM_007011	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Missense_Mutation	SNP	ENST00000352732.5	hg19	CCDS10348.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.967918	0.92855	.	.	ENSG00000140526	ENST00000352732;ENST00000355100	T;T	0.25250	1.81;1.81	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.28863	0.0716	L	0.31207	0.915	0.80722	D	1	B	0.31893	0.345	B	0.41813	0.367	T	0.10706	-1.0618	10	0.56958	D	0.05	-1.0008	15.8956	0.79333	1.0:0.0:0.0:0.0	.	161	P08910	ABHD2_HUMAN	D	161	ENSP00000268129:N161D;ENSP00000347217:N161D	ENSP00000268129:N161D	N	+	1	0	ABHD2	87499712	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	9.183000	0.94887	2.198000	0.70561	0.533000	0.62120	AAC	.	.		0.527	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2			G	89698708	A	G	89698708	3	3	23	1	0	0	0	0	1	0	0	0	82	246	9	2	491	2	ABHD2	15	89698708	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	249603	89698708	12832684	829	2895										
MESP2	145873	hgsc.bcm.edu	37	chr15	90320134	90320134	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caggcggaggggcaggggcaAgggcaggggcaggggcaggg	26	7	0	0	rs56192595|rs200021459|rs199821487	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:90320134A>G	ENST00000341735.3	+	1	546	c.546A>G	c.(544-546)caA>caG	p.Q182Q	MESP2_ENST00000558723.1_Intron|MESP2_ENST00000560219.1_Intron	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	182	13 X 2 AA tandem repeats of G-Q.				mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q198_G205delQGQGQGQG(1)		kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			ggcaggggcaagggcaggggc	0.786																																					p.Q182Q		Atlas-SNP	.											MESP2,NS,carcinoma,0,1	MESP2	20	.	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.A546G						.						3	3	3					15																	90320134		1211	2942	4153	SO:0001819	synonymous_variant	145873	exon1			GGGGCAAGGGCAG		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"Basic helix-loop-helix proteins"	29659	protein-coding gene	gene with protein product		605195	"mesoderm posterior 2 homolog (mouse)"			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.546A>G	chr15.hg19:g.90320134A>G		50.0	1.0		20.0	4.0	NM_001039958	Q7RTU2	Silent	SNP	ENST00000341735.3	hg19	CCDS42078.1																																																																																			.	.		0.786	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		G	90320134	A	G	90320134	2	3	23	1	0	0	0	0	0	0	0	1	9492	69	3	2		2	MESP2	15	90320134	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	621426	90320134	12211258	830	2896										
ASB7	140460	hgsc.bcm.edu	37	chr15	101152549	101152549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggctattccccgaatggccGagatgcgaatggctggactc	13	11	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:101152549G>A	ENST00000332783.7	+	4	913	c.128G>A	c.(127-129)cGa>cAa	p.R43Q	ASB7_ENST00000558747.1_Missense_Mutation_p.R43Q|ASB7_ENST00000343276.4_Missense_Mutation_p.R43Q	NM_198243.2	NP_937886.1	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box containing 7	43					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)	16	Lung NSC(78;0.00121)|all_lung(78;0.00152)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00168)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)			CCGAATGGCCGAGATGCGAAT	0.522																																					p.R43Q		Atlas-SNP	.											.	ASB7	32	.	0			c.G128A						.						138	135	136					15																	101152549		2203	4300	6503	SO:0001583	missense	140460	exon4			ATGGCCGAGATGC		CCDS10387.1, CCDS10388.1	15q26.3	2013-01-10	2011-01-25		ENSG00000183475	ENSG00000183475		"Ankyrin repeat domain containing"	17182	protein-coding gene	gene with protein product		615052	"ankyrin repeat and SOCS box-containing 7"				Standard	NM_024708		Approved		uc002bwk.3	Q9H672	OTTHUMG00000149868	ENST00000332783.7:c.128G>A	chr15.hg19:g.101152549G>A	ENSP00000328327:p.Arg43Gln	149.0	0.0		177.0	76.0	NM_024708	A8K1E5|Q6GSJ6|Q7Z4S3	Missense_Mutation	SNP	ENST00000332783.7	hg19	CCDS10387.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.719202	0.89205	.	.	ENSG00000183475	ENST00000332783;ENST00000343276	T;T	0.65549	-0.16;0.61	5.9	5.9	0.94986	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.70430	0.3223	L	0.28192	0.835	0.80722	D	1	D;B	0.63046	0.992;0.447	D;B	0.70227	0.968;0.018	T	0.68674	-0.5346	10	0.41790	T	0.15	-8.6224	20.2822	0.98520	0.0:0.0:1.0:0.0	.	43;43	Q9H672;Q9H672-2	ASB7_HUMAN;.	Q	43	ENSP00000328327:R43Q;ENSP00000339819:R43Q	ENSP00000328327:R43Q	R	+	2	0	ASB7	98970072	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.296000	0.96104	2.806000	0.96561	0.655000	0.94253	CGA	.	.		0.522	ASB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313617.1	NM_024708		A	101152549	G	A	101152549	3	1	23	1	0	0	0	0	1	0	0	0	1028	1058	37	1	130	1	ASB7	15	101152549	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	10832415	101152549	1378843	831	2897										
SOLH	6650	hgsc.bcm.edu	37	chr16	599385	599385	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagagggcgcctaccaggtgCggctgtgcaaggacggcacg	17	12	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:599385C>T	ENST00000219611.2	+	6	2119	c.1756C>T	c.(1756-1758)Cgg>Tgg	p.R586W	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	586	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CTACCAGGTGCGGCTGTGCAA	0.701																																					p.R586W		Atlas-SNP	.											.	SOLH	47	.	0			c.C1756T						.						26	18	21					16																	599385		2171	4272	6443	SO:0001583	missense	6650	exon6			CAGGTGCGGCTGT	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"small optic lobes (Drosophila) homolog", "small optic lobes homolog (Drosophila)"	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.1756C>T	chr16.hg19:g.599385C>T	ENSP00000219611:p.Arg586Trp	50.0	0.0		56.0	13.0	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	hg19	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	c	21.8	4.205289	0.79127	.	.	ENSG00000103326	ENST00000219611	D	0.89552	-2.53	5.04	5.04	0.67666	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.85682	D	0.000000	D	0.94748	0.8305	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95469	0.8550	10	0.87932	D	0	.	16.9735	0.86306	0.0:1.0:0.0:0.0	.	586	O75808	CAN15_HUMAN	W	586	ENSP00000219611:R586W	ENSP00000219611:R586W	R	+	1	2	SOLH	539386	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	5.403000	0.66338	2.347000	0.79759	0.556000	0.70494	CGG	.	.		0.701	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		T	599385	C	T	599385	3	4	23	1	0	0	0	0	1	0	0	0	14940	759	27	1	1766	1	SOLH	16	599385	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10		599385	89755368	832	2898										
SOX8	30812	hgsc.bcm.edu	37	chr16	1033875	1033875	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcgactccgactcgggcgcGgagctgggaccccaccctgg	15	16	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:1033875G>A	ENST00000293894.3	+	2	685	c.570G>A	c.(568-570)gcG>gcA	p.A190A	RP11-161M6.2_ENST00000565467.1_lincRNA	NM_014587.3	NP_055402.2	P57073	SOX8_HUMAN	SRY (sex determining region Y)-box 8	190					adipose tissue development (GO:0060612)|astrocyte fate commitment (GO:0060018)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|enteric nervous system development (GO:0048484)|fat cell differentiation (GO:0045444)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of gliogenesis (GO:0014015)|positive regulation of kidney development (GO:0090184)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone levels (GO:0010817)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|ureter morphogenesis (GO:0072197)	cytoplasm (GO:0005737)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|kidney(1)|lung(5)|prostate(2)|skin(1)	10		Hepatocellular(780;0.00308)				ACTCGGGCGCGGAGCTGGGAC	0.682																																					p.A190A		Atlas-SNP	.											.	SOX8	29	.	0			c.G570A						.						26	27	27					16																	1033875		2194	4295	6489	SO:0001819	synonymous_variant	30812	exon2			GGGCGCGGAGCTG	AF164104	CCDS10428.1	16p13.3	2008-05-23			ENSG00000005513	ENSG00000005513		"SRY (sex determining region Y)-boxes"	11203	protein-coding gene	gene with protein product		605923				10662550, 10684944	Standard	NM_014587		Approved		uc002ckn.3	P57073	OTTHUMG00000122101	ENST00000293894.3:c.570G>A	chr16.hg19:g.1033875G>A		225.0	0.0		209.0	94.0	NM_014587	Q9NZW2	Silent	SNP	ENST00000293894.3	hg19	CCDS10428.1																																																																																			.	.		0.682	SOX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242867.1			A	1033875	G	A	1033875	2	1	23	1	0	0	0	0	0	0	0	1	14972	1103	39	1		1	SOX8	16	1033875	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	434490	1033875	89320878	833	2899										
SOX8	30812	hgsc.bcm.edu	37	chr16	1034924	1034924	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagtacctgcccctgggcggCcccgccccacccgagccggg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:1034924delC	ENST00000293894.3	+	3	994	c.879delC	c.(877-879)ggcfs	p.G293fs		NM_014587.3	NP_055402.2	P57073	SOX8_HUMAN	SRY (sex determining region Y)-box 8	293					adipose tissue development (GO:0060612)|astrocyte fate commitment (GO:0060018)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|enteric nervous system development (GO:0048484)|fat cell differentiation (GO:0045444)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of gliogenesis (GO:0014015)|positive regulation of kidney development (GO:0090184)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone levels (GO:0010817)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|ureter morphogenesis (GO:0072197)	cytoplasm (GO:0005737)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|kidney(1)|lung(5)|prostate(2)|skin(1)	10		Hepatocellular(780;0.00308)				CCCTGGGCGGCCCCGCCCCAC	0.701																																					p.G293fs		Atlas-Indel,Pindel	.											.	SOX8	29	.	0			c.878delG						.						15	16	15					16																	1034924		2184	4279	6463	SO:0001589	frameshift_variant	30812	exon3			.	AF164104	CCDS10428.1	16p13.3	2008-05-23			ENSG00000005513	ENSG00000005513		"SRY (sex determining region Y)-boxes"	11203	protein-coding gene	gene with protein product		605923				10662550, 10684944	Standard	NM_014587		Approved		uc002ckn.3	P57073	OTTHUMG00000122101	ENST00000293894.3:c.879delC	chr16.hg19:g.1034924delC	ENSP00000293894:p.Gly293fs	232.0	0.0		209.0	19.0	NM_014587	Q9NZW2	Frame_Shift_Del	DEL	ENST00000293894.3	hg19	CCDS10428.1																																																																																			.	.		0.701	SOX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242867.1			-	1034924	C	-	1034924	7	5	23	1	0	1	0	1	0	0	0	0	14972	726	26	0	889	0	SOX8	16	1034924	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	1049	1034924	89319829	834	2900										
UNKL	64718	hgsc.bcm.edu	37	chr16	1464671	1464671	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccgctcagcgccgctgccgCcgctttcgaaaccgacggca	11	19	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:1464671C>G	ENST00000389221.4	-	1	21	c.22G>C	c.(22-24)Gcg>Ccg	p.A8P	UNKL_ENST00000397462.1_Missense_Mutation_p.A8P|LA16c-312E8.2_ENST00000568554.1_RNA|UNKL_ENST00000503648.1_5'UTR|UNKL_ENST00000508903.2_Missense_Mutation_p.A8P|UNKL_ENST00000301712.5_Missense_Mutation_p.A8P	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	8	Poly-Ala.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Hepatocellular(780;0.0893)				GCCGCTGCCGCCGCTTTCGAA	0.751																																					p.A8P		Atlas-SNP	.											.	UNKL	46	.	0			c.G22C						.						3	4	4					16																	1464671		1671	3626	5297	SO:0001583	missense	64718	exon1			CTGCCGCCGCTTT	BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145		"Zinc fingers, CCCH-type domain containing"	14184	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 28", "unkempt homolog (Drosophila)-like"	C16orf28		20148946	Standard	NM_001193389		Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000389221.4:c.22G>C	chr16.hg19:g.1464671C>G	ENSP00000373873:p.Ala8Pro	62.0	0.0		81.0	33.0	NM_001193388	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Missense_Mutation	SNP	ENST00000389221.4	hg19	CCDS53981.1	.	.	.	.	.	.	.	.	.	.	C	8.247	0.808071	0.16467	.	.	ENSG00000059145	ENST00000389221;ENST00000508903;ENST00000397462;ENST00000301712	T	0.65549	-0.16	2.14	1.14	0.20703	.	0.318901	0.20036	U	0.100605	T	0.49898	0.1584	N	0.08118	0	0.23277	N	0.997991	D	0.62365	0.991	D	0.63703	0.917	T	0.30592	-0.9973	10	0.33940	T	0.23	.	3.8286	0.08865	0.0:0.768:0.0:0.232	.	8	Q9H9P5-5	.	P	8	ENSP00000373873:A8P	ENSP00000301712:A8P	A	-	1	0	UNKL	1404672	0.106000	0.21978	1.000000	0.80357	0.746000	0.42486	0.351000	0.20096	1.133000	0.42147	0.185000	0.17295	GCG	.	.		0.751	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125		G	1464671	C	G	1464671	3	3	23	1	0	0	0	0	1	0	0	0	17016	739	26	4	1550	4	UNKL	16	1464671	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	429747	1464671	88890082	835	2901										
NTHL1	4913	hgsc.bcm.edu	37	chr16	2093714	2093714	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggcgctggtctgcttgatgTatttcaccttgctctgaaag	11	9	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:2093714T>C	ENST00000219066.1	-	4	581	c.563A>G	c.(562-564)tAc>tGc	p.Y188C	NTHL1_ENST00000562951.1_5'UTR	NM_002528.5	NP_002519.1			nth endonuclease III-like 1 (E. coli)											lung(1)	1						CTGCTTGATGTATTTCACCTT	0.637								Base excision repair (BER), DNA glycosylases																													p.Y188C		Atlas-SNP	.											.	NTHL1	24	.	0			c.A563G						.						93	69	77					16																	2093714		2196	4299	6495	SO:0001583	missense	4913	exon4			TTGATGTATTTCA	U81285	CCDS10457.1	16p13.3	2008-02-05	2001-11-28		ENSG00000065057	ENSG00000065057			8028	protein-coding gene	gene with protein product		602656	"nth (E.coli endonuclease III)-like 1"			9045706, 8990169	Standard	NM_002528		Approved	NTH1, OCTS3	uc002col.1	P78549	OTTHUMG00000128744	ENST00000219066.1:c.563A>G	chr16.hg19:g.2093714T>C	ENSP00000219066:p.Tyr188Cys	46.0	0.0		35.0	15.0	NM_002528		Missense_Mutation	SNP	ENST00000219066.1	hg19	CCDS10457.1	.	.	.	.	.	.	.	.	.	.	T	16.58	3.161675	0.57368	.	.	ENSG00000065057	ENST00000219066	D	0.88975	-2.45	5.32	-0.18	0.13295	HhH-GPD domain (2);DNA glycosylase (2);	0.256859	0.40144	N	0.001163	D	0.93301	0.7865	H	0.97587	4.035	0.58432	D	0.999999	P;P	0.39022	0.655;0.655	P;P	0.45428	0.48;0.48	D	0.92323	0.5867	10	0.72032	D	0.01	-8.9262	10.9829	0.47506	0.41:0.0:0.0:0.59	.	188;188	E5KTI5;P78549	.;NTHL1_HUMAN	C	188	ENSP00000219066:Y188C	ENSP00000219066:Y188C	Y	-	2	0	NTHL1	2033715	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	1.346000	0.33964	-0.024000	0.13941	0.402000	0.26972	TAC	.	.		0.637	NTHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250656.1	NM_002528		C	2093714	T	C	2093714	3	2	23	1	0	0	0	0	1	0	0	0	10707	1638	57	2	387	2	NTHL1	16	2093714	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	629043	2093714	88261039	836	2902										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2818134	2818134	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcggcggagttcctcctcGtcgtcgtcgtcctctagctc	12	15	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:2818134G>C	ENST00000301740.8	+	11	8154	c.7605G>C	c.(7603-7605)tcG>tcC	p.S2535S	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2535	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						GTtcctcctcgtcgtcgtcgt	0.617																																					p.S2535S		Atlas-SNP	.											SRRM2,bladder,carcinoma,+1,1	SRRM2	263	.	0			c.G7605C						.						61	54	56					16																	2818134		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			CTCCTCGTCGTCG	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.7605G>C	chr16.hg19:g.2818134G>C		43.0	0.0		60.0	16.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.		0.617	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			C	2818134	G	C	2818134	2	2	23	1	0	0	0	0	0	0	0	1	15184	1132	40	4		4	SRRM2	16	2818134	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	724420	2818134	87536619	837	2903										
CLDN9	9080	hgsc.bcm.edu	37	chr16	3063895	3063895	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgcactgcttatgctgggcGgggggctcctctgctgcacg					rs374732646		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:3063895delG	ENST00000445369.2	+	1	1439	c.532delG	c.(532-534)gggfs	p.G179fs		NM_020982.3	NP_066192.1	O95484	CLD9_HUMAN	claudin 9	179					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(1)|lung(5)|prostate(2)	10						TATGCTGGGCGGGGGGCTCCT	0.721																																					p.G177fs		Atlas-Indel,Pindel	.											.	CLDN9	33	.	0			c.531delC						.						16	21	19					16																	3063895		2174	4262	6436	SO:0001589	frameshift_variant	9080	exon1			.	AJ130941	CCDS10487.1	16p13.3	2008-08-01			ENSG00000213937	ENSG00000213937		"Claudins"	2051	protein-coding gene	gene with protein product		615799				9441748, 18234789	Standard	NM_020982		Approved		uc010uwo.1	O95484	OTTHUMG00000129000	ENST00000445369.2:c.532delG	chr16.hg19:g.3063895delG	ENSP00000398017:p.Gly179fs	72.0	0.0		77.0	36.0	NM_020982		Frame_Shift_Del	DEL	ENST00000445369.2	hg19	CCDS10487.1																																																																																			.	.		0.721	CLDN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250989.1	NM_020982		-	3063895	G	-	3063895	7	5	23	1	0	1	0	1	0	0	0	0	3494	1116	39	0	534	0	CLDN9	16	3063895	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	245761	3063895	87290858	838	2904										
MEFV	4210	hgsc.bcm.edu	37	chr16	3293875	3293875	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttaccagcatgtgcctgagCgccaatcagctccggaacta	9	14	1	1	rs375665850		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:3293875C>T	ENST00000219596.1	-	9	1816	c.1777G>A	c.(1777-1779)Gct>Act	p.A593T	MEFV_ENST00000339854.4_Missense_Mutation_p.A413T|MEFV_ENST00000536379.1_Missense_Mutation_p.A382T|MEFV_ENST00000541159.1_Missense_Mutation_p.R440H	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	593	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						TGTGCCTGAGCGCCAATCAGC	0.512																																					p.A593T		Atlas-SNP	.											.	MEFV	170	.	0			c.G1777A						.						48	50	49					16																	3293875		2197	4300	6497	SO:0001583	missense	4210	exon9			CCTGAGCGCCAAT	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1777G>A	chr16.hg19:g.3293875C>T	ENSP00000219596:p.Ala593Thr	216.0	0.0		194.0	72.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	hg19	CCDS10498.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.47|12.47	1.948409|1.948409	0.34377|0.34377	.|.	.|.	ENSG00000103313|ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000536379|ENST00000541159	T;T;T|T	0.64260|0.63417	-0.09;0.34;0.34|-0.04	4.92|4.92	4.92|4.92	0.64577|0.64577	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);|.	0.723385|.	0.12438|.	N|.	0.468915|.	T|T	0.68595|0.68595	0.3018|0.3018	M|M	0.63843|0.63843	1.955|1.955	0.21184|0.21184	N|N	0.999767|0.999767	D|.	0.89917|.	1.0|.	P|.	0.56163|.	0.793|.	T|T	0.60831|0.60831	-0.7185|-0.7185	10|7	0.37606|0.38643	T|T	0.19|0.18	-36.0955|-36.0955	13.8235|13.8235	0.63338|0.63338	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	593|.	O15553|.	MEFV_HUMAN|.	T|H	593;593;413;382|440	ENSP00000219596:A593T;ENSP00000339639:A413T;ENSP00000445079:A382T|ENSP00000438711:R440H	ENSP00000219596:A593T|ENSP00000438711:R440H	A|R	-|-	1|2	0|0	MEFV|MEFV	3233876|3233876	0.805000|0.805000	0.28982|0.28982	0.573000|0.573000	0.28510|0.28510	0.039000|0.039000	0.13416|0.13416	2.355000|2.355000	0.44107|0.44107	2.725000|2.725000	0.93324|0.93324	0.655000|0.655000	0.94253|0.94253	GCT|CGC	.	.		0.512	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		T	3293875	C	T	3293875	3	4	23	1	0	0	0	0	1	0	0	0	9468	768	27	1	576	1	MEFV	16	3293875	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	229980	3293875	87060878	839	2905										
TRAP1	10131	hgsc.bcm.edu	37	chr16	3712966	3712966	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttctctgataggcactcggCggctgcggaagagcaggcga	15	11	1	2	rs549044388	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:3712966C>T	ENST00000246957.5	-	15	1799	c.1711G>A	c.(1711-1713)Gcc>Acc	p.A571T	TRAP1_ENST00000538171.1_Missense_Mutation_p.A518T|DNASE1_ENST00000414110.2_Intron|TRAP1_ENST00000575671.1_Missense_Mutation_p.A362T|DNASE1_ENST00000575152.1_3'UTR	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	571					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				AGGCACTCGGCGGCTGCGGAA	0.642													C|||	2	0.000399361	8e-04	0	5008	,	,		17870	0		0	False		,,,				2504	0.001				p.A571T		Atlas-SNP	.											TRAP1,colon,carcinoma,0,1	TRAP1	53	.	0			c.G1711A						.						64	49	54					16																	3712966		2197	4300	6497	SO:0001583	missense	10131	exon15			ACTCGGCGGCTGC	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"Heat shock proteins / HSPC"	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.1711G>A	chr16.hg19:g.3712966C>T	ENSP00000246957:p.Ala571Thr	16.0	0.0		25.0	8.0	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Missense_Mutation	SNP	ENST00000246957.5	hg19	CCDS10508.1	.	.	.	.	.	.	.	.	.	.	C	8.864	0.947740	0.18356	.	.	ENSG00000126602	ENST00000246957;ENST00000538171	T;T	0.14266	2.52;2.52	5.45	-0.454	0.12197	.	0.735859	0.13582	N	0.377261	T	0.04543	0.0124	N	0.04508	-0.205	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.37056	-0.9722	10	0.30854	T	0.27	-0.8126	2.2713	0.04091	0.1244:0.4432:0.1216:0.3109	.	518;571	F5H897;Q12931	.;TRAP1_HUMAN	T	571;518	ENSP00000246957:A571T;ENSP00000442070:A518T	ENSP00000246957:A571T	A	-	1	0	TRAP1	3652967	0.015000	0.18098	0.000000	0.03702	0.003000	0.03518	0.217000	0.17603	0.289000	0.22422	0.650000	0.86243	GCC	.	.		0.642	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292		T	3712966	C	T	3712966	3	4	23	1	0	0	0	0	1	0	0	0	16470	768	27	1	419	1	TRAP1	16	3712966	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	419091	3712966	86641787	840	2906										
ZNF500	26048	hgsc.bcm.edu	37	chr16	4802884	4802885	+	Frame_Shift_Ins	INS	-	-	G													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggaagcccgtcttcctggtINSggggggccgcctcttggctg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:4802884_4802885insG	ENST00000219478.6	-	6	1234_1235	c.935_936insC	c.(934-936)ccafs	p.P312fs	ZNF500_ENST00000545009.1_Frame_Shift_Ins_p.P312fs|RP11-127I20.7_ENST00000588099.1_RNA|ZNF500_ENST00000591026.1_5'UTR			O60304	ZN500_HUMAN	zinc finger protein 500	312					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	21						GTCTTCCTGGTGGGGGGCCGCC	0.663																																					p.P312fs		Atlas-Indel,Pindel	.											.	ZNF500	45	.	0			c.936_937insC						.																																			SO:0001589	frameshift_variant	26048	exon6			.	AB011129	CCDS32383.1	16p13.3	2013-01-09				ENSG00000103199		"Zinc fingers, C2H2-type", "-", "-", "-"	23716	protein-coding gene	gene with protein product						9628581	Standard	XM_005255243		Approved	ZKSCAN18, KIAA0557, ZSCAN50	uc002cxp.1	O60304		ENST00000219478.6:c.936dupC	chr16.hg19:g.4802890_4802890dupG	ENSP00000219478:p.Pro312fs	52.0	0.0		73.0	24.0	NM_021646	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Frame_Shift_Ins	INS	ENST00000219478.6	hg19	CCDS32383.1																																																																																			.	.		0.663	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507		G	4802885	-	G	4802884	7	5	23	1	0	1	1	0	0	0	0	0	17963	1683	59	0	510	0	ZNF500	16	4802884	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	1089918	4802884	85551869	841	2907										
GSPT1	2935	hgsc.bcm.edu	37	chr16	11981478	11981478	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaatcatatttgggacaaaActcttgtggccaggggcatc	10	10	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:11981478A>G	ENST00000563468.1	-	5	518	c.492T>C	c.(490-492)agT>agC	p.S164S	GSPT1_ENST00000420576.2_Silent_p.S164S|GSPT1_ENST00000439887.2_Silent_p.S301S|GSPT1_ENST00000434724.2_Silent_p.S302S|RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000564790.1_5'Flank			P15170	ERF3A_HUMAN	G1 to S phase transition 1	164	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				G1/S transition of mitotic cell cycle (GO:0000082)|GTP catabolic process (GO:0006184)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|translational termination (GO:0006415)	intracellular (GO:0005622)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation release factor activity (GO:0003747)			breast(1)|central_nervous_system(1)|kidney(4)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	14						TTGGGACAAAACTCTTGTGGC	0.443																																					p.S302S		Atlas-SNP	.											.	GSPT1	71	.	0			c.T906C						.						149	153	152					16																	11981478		2197	4298	6495	SO:0001819	synonymous_variant	2935	exon7			GACAAAACTCTTG	BC008391	CCDS45412.1, CCDS45413.1, CCDS45414.1	16p13.1	2008-08-01							4621	protein-coding gene	gene with protein product		139259				2511002, 17700517	Standard	NM_002094		Approved	GST1, ETF3A, eRF3a	uc002dbt.3	P15170		ENST00000563468.1:c.492T>C	chr16.hg19:g.11981478A>G		212.0	0.0		190.0	78.0	NM_002094	J3KQG6|Q96GF2	Silent	SNP	ENST00000563468.1	hg19	CCDS45414.1																																																																																			.	.		0.443	GSPT1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421513.1	NM_002094		G	11981478	A	G	11981478	2	3	23	1	0	0	0	0	0	0	0	1	6835	40	2	2		2	GSPT1	16	11981478	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	7178594	11981478	78373275	842	2908										
ERCC4	2072	hgsc.bcm.edu	37	chr16	14041629	14041629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctccagaaatgtgcgtggagCgcaagagtatcagtgattta	12	7	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:14041629C>T	ENST00000311895.7	+	11	2185	c.2176C>T	c.(2176-2178)Cgc>Tgc	p.R726C		NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	726	ERCC4.|Nuclease.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						GTGCGTGGAGCGCAAGAGTAT	0.498			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.R726C		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"excision repair cross-complementing rodent repair deficiency, complementation group 4"		E	.	ERCC4	100	.	0			c.C2176T						.						92	89	90					16																	14041629		2197	4300	6497	SO:0001583	missense	2072	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GTGGAGCGCAAGA	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"xeroderma pigmentosum, complementation group F"	133520	"excision repair cross-complementing rodent repair deficiency, complementation group 4"	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.2176C>T	chr16.hg19:g.14041629C>T	ENSP00000310520:p.Arg726Cys	93.0	0.0		106.0	34.0	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Missense_Mutation	SNP	ENST00000311895.7	hg19	CCDS32390.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.423764	0.62733	.	.	ENSG00000175595	ENST00000311895;ENST00000389138	T	0.62941	-0.01	5.58	3.42	0.39159	DNA repair nuclease, XPF-type/Helicase (1);Restriction endonuclease, type II-like (1);ERCC4 domain (2);	0.050473	0.85682	D	0.000000	D	0.86083	0.5848	H	0.98901	4.365	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89713	0.3913	10	0.87932	D	0	-21.909	11.3027	0.49316	0.2224:0.6665:0.1111:0.0	.	726	Q92889	XPF_HUMAN	C	726;714	ENSP00000310520:R726C	ENSP00000310520:R726C	R	+	1	0	ERCC4	13949130	1.000000	0.71417	1.000000	0.80357	0.582000	0.36321	2.660000	0.46749	1.346000	0.45694	-0.165000	0.13383	CGC	.	.		0.498	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236		T	14041629	C	T	14041629	3	4	23	1	0	0	0	0	1	0	0	0	5217	768	27	1	2218	1	ERCC4	16	14041629	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2060151	14041629	76313124	843	2909										
PARN	5073	hgsc.bcm.edu	37	chr16	14721031	14721031	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaaaacatagaagttaaatgActtcgttatatacctgggat	8	5	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:14721031A>C	ENST00000437198.2	-	5	400	c.259T>G	c.(259-261)Tca>Gca	p.S87A	PARN_ENST00000566021.1_5'UTR|PARN_ENST00000420015.2_Intron|PARN_ENST00000341484.7_Missense_Mutation_p.S26A|PARN_ENST00000539279.1_Intron	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN	poly(A)-specific ribonuclease	87					female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						AAGTTAAATGACTTCGTTATA	0.363																																					p.S87A		Atlas-SNP	.											.	PARN	72	.	0			c.T259G						.						72	68	70					16																	14721031		1854	4087	5941	SO:0001583	missense	5073	exon5			TAAATGACTTCGT	AJ005698	CCDS45419.1, CCDS45420.1, CCDS58425.1	16p13	2014-08-08	2011-07-07		ENSG00000140694	ENSG00000140694	3.1.13.4		8609	protein-coding gene	gene with protein product	"deadenylation nuclease"	604212	"poly(A)-specific ribonuclease (deadenylation nuclease)"			10640832	Standard	NM_002582		Approved	DAN	uc010uzd.2	O95453	OTTHUMG00000173199	ENST00000437198.2:c.259T>G	chr16.hg19:g.14721031A>C	ENSP00000387911:p.Ser87Ala	142.0	0.0		164.0	61.0	NM_002582	B2RCB3|B4DDG8|B4DWR4|B4E1H6	Missense_Mutation	SNP	ENST00000437198.2	hg19	CCDS45419.1	.	.	.	.	.	.	.	.	.	.	A	11.76	1.734373	0.30774	.	.	ENSG00000140694	ENST00000437198;ENST00000341484	T;T	0.24151	1.87;1.87	5.86	5.86	0.93980	Ribonuclease H-like (1);	0.126644	0.56097	D	0.000030	T	0.18215	0.0437	N	0.16656	0.425	0.80722	D	1	B	0.06786	0.001	B	0.21546	0.035	T	0.08889	-1.0700	10	0.20519	T	0.43	-13.1429	15.448	0.75248	1.0:0.0:0.0:0.0	.	87	O95453	PARN_HUMAN	A	87;26	ENSP00000387911:S87A;ENSP00000345456:S26A	ENSP00000345456:S26A	S	-	1	0	PARN	14628532	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.035000	0.57297	2.240000	0.73641	0.533000	0.62120	TCA	.	.		0.363	PARN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422383.1	NM_002582		C	14721031	A	C	14721031	3	2	23	1	0	0	0	0	1	0	0	0	11462	275	10	5	1740	5	PARN	16	14721031	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	679402	14721031	75633722	844	2910										
NTAN1	123803	hgsc.bcm.edu	37	chr16	15131931	15131931	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttcccacaagccatcttcaTtttttttgtagagtagggct	7	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:15131931T>G	ENST00000287706.3	-	10	982	c.890A>C	c.(889-891)aAt>aCt	p.N297T	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	297					adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						GCCATCTTCATTTTTTTTGTA	0.383																																					p.N297T		Atlas-SNP	.											.,1	NTAN1	21	.	0			c.A890C						.						88	91	90					16																	15131931		2197	4299	6496	SO:0001583	missense	123803	exon10			TCTTCATTTTTTT	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.890A>C	chr16.hg19:g.15131931T>G	ENSP00000287706:p.Asn297Thr	145.0	0.0		126.0	10.0	NM_173474	Q7Z4Z0	Missense_Mutation	SNP	ENST00000287706.3	hg19	CCDS10558.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.484142	0.44147	.	.	ENSG00000157045	ENST00000287706	T	0.28069	1.63	5.87	5.87	0.94306	.	0.165305	0.56097	D	0.000034	T	0.31606	0.0802	L	0.37630	1.12	0.39621	D	0.970034	P	0.51933	0.949	P	0.46543	0.52	T	0.04078	-1.0979	10	0.32370	T	0.25	-17.8893	15.7569	0.78037	0.0:0.0:0.0:1.0	.	297	Q96AB6	NTAN1_HUMAN	T	297	ENSP00000287706:N297T	ENSP00000287706:N297T	N	-	2	0	NTAN1	15039432	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	2.778000	0.47726	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.383	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474		G	15131931	T	G	15131931	3	3	23	1	0	0	0	0	1	0	0	0	10704	1493	52	5	46	5	NTAN1	16	15131931	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	410900	15131931	75222822	845	2911										
ABCC1	4363	hgsc.bcm.edu	37	chr16	16177388	16177388	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagtggggatcggacagagAttggcgagaaggtcagtata	16	6	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:16177388A>T	ENST00000399410.3	+	17	2456	c.2281A>T	c.(2281-2283)Att>Ttt	p.I761F	ABCC1_ENST00000349029.5_Intron|ABCC1_ENST00000346370.5_Missense_Mutation_p.I761F|ABCC1_ENST00000399408.2_Missense_Mutation_p.I761F|ABCC1_ENST00000345148.5_Missense_Mutation_p.I761F|ABCC1_ENST00000351154.5_Intron	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	761	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	TCGGACAGAGATTGGCGAGAA	0.537																																					p.I761F		Atlas-SNP	.											.	ABCC1	156	.	0			c.A2281T						.						80	82	81					16																	16177388		2070	4216	6286	SO:0001583	missense	4363	exon17			ACAGAGATTGGCG	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.2281A>T	chr16.hg19:g.16177388A>T	ENSP00000382342:p.Ile761Phe	161.0	0.0		131.0	27.0	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	hg19	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.647814	0.87958	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000345148;ENST00000536381	D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91	5.38	5.38	0.77491	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.96491	0.8855	M	0.88310	2.945	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.997;0.995	D	0.97228	0.9882	10	0.87932	D	0	-17.4158	14.5874	0.68335	1.0:0.0:0.0:0.0	.	761;761;761;761	P33527-4;P33527-3;P33527;P33527-9	.;.;MRP1_HUMAN;.	F	761;761;761;761;435	ENSP00000382342:I761F;ENSP00000382340:I761F;ENSP00000263019:I761F;ENSP00000263014:I761F	ENSP00000263014:I761F	I	+	1	0	ABCC1	16084889	1.000000	0.71417	0.998000	0.56505	0.828000	0.46876	9.230000	0.95299	2.048000	0.60808	0.460000	0.39030	ATT	.	.		0.537	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		T	16177388	A	T	16177388	3	4	23	1	0	0	0	0	1	0	0	0	49	333	12	4	2347	4	ABCC1	16	16177388	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1045457	16177388	74177365	846	2912										
OTOA	146183	hgsc.bcm.edu	37	chr16	21702950	21702950	+	Silent	SNP	C	C	T													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gacaaaacctcggctcattcCcagagagctctctattcctg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:21702950C>T	ENST00000286149.4	+	8	682	c.681C>T	c.(679-681)tcC>tcT	p.S227S	OTOA_ENST00000388958.3_Silent_p.S227S|OTOA_ENST00000388956.4_Silent_p.S148S			Q7RTW8	OTOAN_HUMAN	otoancorin	227					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CGGCTCATTCCCAGAGAGCTC	0.488																																					p.S227S		Atlas-SNP	.											.	OTOA	144	.	0			c.C681T						.						101	91	95					16																	21702950		2199	4300	6499	SO:0001819	synonymous_variant	146183	exon8			TCATTCCCAGAGA	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.681C>T	chr16.hg19:g.21702950C>T		86.0	0.0		117.0	20.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Silent	SNP	ENST00000286149.4	hg19																																																																																				.	.		0.488	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			T	21702950	C	T	21702950	2	4	23	1	0	0	0	0	0	0	0	1	11311	610	22	3		3	OTOA	16	21702950	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5525562	21702950	68651803	847	2913	11	2								
OTOA	146183	hgsc.bcm.edu	37	chr16	21702955	21702955	+	Missense_Mutation	SNP	G	G	A													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aacctcggctcattcccagaGagctctctattcctggatga							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:21702955G>A	ENST00000286149.4	+	8	687	c.686G>A	c.(685-687)aGa>aAa	p.R229K	OTOA_ENST00000388958.3_Missense_Mutation_p.R229K|OTOA_ENST00000388956.4_Missense_Mutation_p.R150K			Q7RTW8	OTOAN_HUMAN	otoancorin	229					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CATTCCCAGAGAGCTCTCTAT	0.488																																					p.R229K		Atlas-SNP	.											.	OTOA	144	.	0			c.G686A						.						99	90	93					16																	21702955		2199	4300	6499	SO:0001583	missense	146183	exon8			CCCAGAGAGCTCT	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.686G>A	chr16.hg19:g.21702955G>A	ENSP00000286149:p.Arg229Lys	86.0	0.0		121.0	21.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	hg19		.	.	.	.	.	.	.	.	.	.	G	10.70	1.424300	0.25639	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956	T;T;T	0.12147	2.71;2.71;2.71	5.27	2.23	0.28157	.	0.167421	0.50627	N	0.000103	T	0.10895	0.0266	L	0.52364	1.645	0.80722	D	1	P;P	0.38223	0.623;0.623	B;B	0.36186	0.219;0.219	T	0.18713	-1.0328	10	0.26408	T	0.33	-1.9773	6.27	0.20949	0.1621:0.0:0.6887:0.1492	.	150;229	B3KWU3;E9PF51	.;.	K	229;229;150	ENSP00000373610:R229K;ENSP00000286149:R229K;ENSP00000373608:R150K	ENSP00000286149:R229K	R	+	2	0	OTOA	21610456	1.000000	0.71417	0.757000	0.31301	0.086000	0.17979	1.581000	0.36558	0.225000	0.20959	0.556000	0.70494	AGA	.	.		0.488	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			A	21702955	G	A	21702955	3	1	23	1	0	0	0	0	1	0	0	0	11311	942	33	3	750	3	OTOA	16	21702955	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	5	21702955	68651798	848	2914	11	2								
OTOA	146183	hgsc.bcm.edu	37	chr16	21721362	21721362	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccatctccaccctcaaccagGtctcaggttgggccaagagc	9	16	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:21721362G>A	ENST00000286149.4	+	12	1301	c.1300G>A	c.(1300-1302)Gtc>Atc	p.V434I	OTOA_ENST00000388958.3_Missense_Mutation_p.V420I|OTOA_ENST00000388956.4_Missense_Mutation_p.V341I|OTOA_ENST00000388957.3_Missense_Mutation_p.V96I			Q7RTW8	OTOAN_HUMAN	otoancorin	434					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CCTCAACCAGGTCTCAGGTTG	0.522																																					p.V420I		Atlas-SNP	.											.	OTOA	144	.	0			c.G1258A						.						71	58	63					16																	21721362		2199	4300	6499	SO:0001583	missense	146183	exon12			AACCAGGTCTCAG	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.1300G>A	chr16.hg19:g.21721362G>A	ENSP00000286149:p.Val434Ile	120.0	0.0		151.0	49.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	hg19		.	.	.	.	.	.	.	.	.	.	G	15.15	2.747220	0.49257	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956;ENST00000388957	T;T;T;T	0.78364	2.81;2.81;2.81;-1.17	5.21	4.24	0.50183	.	0.215069	0.39544	N	0.001329	T	0.73636	0.3612	M	0.66939	2.045	0.43890	D	0.996512	B;B;B;B	0.29232	0.238;0.238;0.238;0.238	B;B;B;B	0.31495	0.079;0.112;0.131;0.079	T	0.67352	-0.5692	10	0.17832	T	0.49	-17.6608	11.8567	0.52441	0.0869:0.0:0.9131:0.0	.	434;341;96;420	Q7RTW8;B3KWU3;Q7RTW8-2;E9PF51	OTOAN_HUMAN;.;.;.	I	420;434;341;96	ENSP00000373610:V420I;ENSP00000286149:V434I;ENSP00000373608:V341I;ENSP00000373609:V96I	ENSP00000286149:V434I	V	+	1	0	OTOA	21628863	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.330000	0.65899	1.143000	0.42306	0.643000	0.83706	GTC	.	.		0.522	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			A	21721362	G	A	21721362	3	1	23	1	0	0	0	0	1	0	0	0	11311	1261	44	3	1350	3	OTOA	16	21721362	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	18407	21721362	68633391	849	2915										
RBBP6	5930	hgsc.bcm.edu	37	chr16	24580479	24580479	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgactttagagacccatttgAaaaagaacgctaccgagaat							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:24580479delA	ENST00000319715.4	+	17	2900	c.2468delA	c.(2467-2469)gaafs	p.E823fs	RBBP6_ENST00000381039.3_Intron|RBBP6_ENST00000348022.2_Frame_Shift_Del_p.E789fs	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	823					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		GACCCATTTGAAAAAGAACGC	0.378																																					p.E823fs		Atlas-Indel,Pindel	.											.	RBBP6	158	.	0			c.2467delG						.						51	54	53					16																	24580479		2195	4300	6495	SO:0001589	frameshift_variant	5930	exon17			.		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.2468delA	chr16.hg19:g.24580479delA	ENSP00000317872:p.Glu823fs	336.0	0.0		317.0	119.0	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Frame_Shift_Del	DEL	ENST00000319715.4	hg19	CCDS10621.1																																																																																			.	.		0.378	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		-	24580479	A	-	24580479	7	5	23	1	0	1	0	1	0	0	0	0	13118	246	9	0	2588	0	RBBP6	16	24580479	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	2859117	24580479	65774274	850	2916										
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27752080	27752080	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggggaccagccggagtgtcaAcaccaaggagagaccccaga	14	12	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:27752080A>G	ENST00000261588.4	+	15	2481	c.2462A>G	c.(2461-2463)aAc>aGc	p.N821S		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	821						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						CGGAGTGTCAACACCAAGGAG	0.602																																					p.N821S		Atlas-SNP	.											.	KIAA0556	348	.	0			c.A2462G						.						45	48	47					16																	27752080		2197	4300	6497	SO:0001583	missense	23247	exon15			GTGTCAACACCAA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.2462A>G	chr16.hg19:g.27752080A>G	ENSP00000261588:p.Asn821Ser	133.0	0.0		143.0	53.0	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	A	10.85	1.467670	0.26335	.	.	ENSG00000047578	ENST00000261588	T	0.09723	2.95	5.15	0.0363	0.14191	.	0.307133	0.33290	N	0.005065	T	0.05410	0.0143	N	0.19112	0.55	0.09310	N	1	B	0.19817	0.039	B	0.18871	0.023	T	0.28459	-1.0043	10	0.49607	T	0.09	-22.8944	3.1277	0.06413	0.3324:0.3125:0.0:0.3551	.	821	O60303	K0556_HUMAN	S	821	ENSP00000261588:N821S	ENSP00000261588:N821S	N	+	2	0	KIAA0556	27659581	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.029000	0.13666	0.006000	0.14734	-0.527000	0.04329	AAC	.	.		0.602	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		G	27752080	A	G	27752080	3	3	23	1	0	0	0	0	1	0	0	0	8192	43	2	2	2520	2	KIAA0556	16	27752080	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3171601	27752080	62602673	851	2917										
MVP	9961	hgsc.bcm.edu	37	chr16	29848108	29848108	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggagtgtcccgccgcactggGgaggagtggctggtaacagt	18	9	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:29848108G>A	ENST00000357402.5	+	7	876	c.738G>A	c.(736-738)ggG>ggA	p.G246G	MVP_ENST00000395353.1_Silent_p.G246G|MVP_ENST00000452209.2_Missense_Mutation_p.G61R	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	246					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						GCCGCACTGGGGAGGAGTGGC	0.642																																					p.G246G		Atlas-SNP	.											.	MVP	80	.	0			c.G738A						.						47	46	46					16																	29848108		2197	4300	6497	SO:0001819	synonymous_variant	9961	exon7			CACTGGGGAGGAG	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"lung resistance-related protein"	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.738G>A	chr16.hg19:g.29848108G>A		106.0	0.0		119.0	45.0	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Silent	SNP	ENST00000357402.5	hg19	CCDS10656.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.835504	0.50951	.	.	ENSG00000013364	ENST00000452209	T	0.64438	-0.1	5.47	1.12	0.20585	.	0.000000	0.85682	D	0.000000	T	0.56441	0.1985	.	.	.	0.23162	N	0.998194	.	.	.	.	.	.	T	0.52320	-0.8591	7	0.87932	D	0	-13.119	5.0154	0.14333	0.3406:0.1497:0.5098:0.0	.	.	.	.	R	61	ENSP00000387916:G61R	ENSP00000387916:G61R	G	+	1	0	MVP	29755609	0.972000	0.33761	0.999000	0.59377	0.954000	0.61252	-0.046000	0.11983	0.321000	0.23259	0.462000	0.41574	GGA	.	.		0.642	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115		A	29848108	G	A	29848108	2	1	23	1	0	0	0	0	0	0	0	1	10005	1219	43	3		3	MVP	16	29848108	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2096028	29848108	60506645	852	2918										
PRR14	78994	hgsc.bcm.edu	37	chr16	30667498	30667498	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccgtggggtccgggctgcaGggggcaggactgttcctccc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:30667498delG	ENST00000542965.2	+	11	2080	c.1624delG	c.(1624-1626)gggfs	p.G543fs	PRR14_ENST00000300835.4_Frame_Shift_Del_p.G543fs|FBRS_ENST00000356166.6_5'Flank			Q9BWN1	PRR14_HUMAN	proline rich 14	543										breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			CCGGGCTGCAGGGGGCAGGAC	0.637																																					p.A541fs		Atlas-Indel,Pindel	.											.	PRR14	45	.	0			c.1623delA						.						53	61	58					16																	30667498		2197	4300	6497	SO:0001589	frameshift_variant	78994	exon12			.	AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.1624delG	chr16.hg19:g.30667498delG	ENSP00000441641:p.Gly543fs	91.0	0.0		86.0	38.0	NM_024031	Q8WTX2	Frame_Shift_Del	DEL	ENST00000542965.2	hg19	CCDS10687.1																																																																																			.	.		0.637	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031		-	30667498	G	-	30667498	7	5	23	1	0	1	0	1	0	0	0	0	12598	1000	35	0	1666	0	PRR14	16	30667498	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	819390	30667498	59687255	853	2919										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30727435	30727435	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttaaggtggatgttgagaagCagatgcccaaaaagtacgag	13	5	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:30727435C>T	ENST00000262518.4	+	17	2927	c.2542C>T	c.(2542-2544)Cag>Tag	p.Q848*	SRCAP_ENST00000395059.2_Nonsense_Mutation_p.Q848*|SRCAP_ENST00000344771.4_Nonsense_Mutation_p.Q848*	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	848					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TGTTGAGAAGCAGATGCCCAA	0.498																																					p.Q848X		Atlas-SNP	.											.	SRCAP	298	.	0			c.C2542T						.						148	126	133					16																	30727435		2197	4300	6497	SO:0001587	stop_gained	10847	exon17			GAGAAGCAGATGC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.2542C>T	chr16.hg19:g.30727435C>T	ENSP00000262518:p.Gln848*	95.0	0.0		87.0	29.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Nonsense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	39	7.810078	0.98501	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	.	.	.	5.25	5.25	0.73442	.	0.000000	0.51477	D	0.000082	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-12.6405	17.783	0.88529	0.0:1.0:0.0:0.0	.	.	.	.	X	848	.	ENSP00000262518:Q848X	Q	+	1	0	SRCAP	30634936	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.500000	0.81588	2.726000	0.93360	0.561000	0.74099	CAG	.	.		0.498	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30727435	C	T	30727435	4	4	23	1	0	0	0	0	0	1	0	0	15150	711	25	3	2600	3	SRCAP	16	30727435	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	59937	30727435	59627318	854	2920										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30734920	30734920	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cacagcttcagcccccggagCtgcccccttgaccatctctt	7	19	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:30734920C>A	ENST00000262518.4	+	25	4560	c.4175C>A	c.(4174-4176)gCt>gAt	p.A1392D	SRCAP_ENST00000395059.2_Missense_Mutation_p.A1330D|SRCAP_ENST00000344771.4_Missense_Mutation_p.A1234D	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1392	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GCCCCCGGAGCTGCCCCCTTG	0.572																																					p.A1392D		Atlas-SNP	.											.	SRCAP	298	.	0			c.C4175A						.						141	134	136					16																	30734920		2197	4300	6497	SO:0001583	missense	10847	exon25			CCGGAGCTGCCCC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.4175C>A	chr16.hg19:g.30734920C>A	ENSP00000262518:p.Ala1392Asp	73.0	0.0		82.0	30.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	2.967	-0.213287	0.06140	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91577	-2.78;-2.87;-2.86	5.65	4.69	0.59074	.	0.370343	0.23429	N	0.048274	T	0.80314	0.4600	N	0.08118	0	0.18873	N	0.999983	B;B;B	0.30361	0.096;0.277;0.181	B;B;B	0.28638	0.092;0.092;0.042	T	0.74748	-0.3560	10	0.87932	D	0	-1.8765	11.6028	0.51012	0.0:0.9144:0.0:0.0856	.	1234;1330;1392	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	D	1392;1330;1234	ENSP00000262518:A1392D;ENSP00000378499:A1330D;ENSP00000343042:A1234D	ENSP00000262518:A1392D	A	+	2	0	SRCAP	30642421	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	2.044000	0.41241	2.658000	0.90341	0.555000	0.69702	GCT	.	.		0.572	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30734920	C	A	30734920	3	1	23	1	0	0	0	0	1	0	0	0	15150	797	28	3	4265	3	SRCAP	16	30734920	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	7485	30734920	59619833	855	2921										
STX1B	112755	hgsc.bcm.edu	37	chr16	31008338	31008338	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttggactgggtcgcgttatAttcggtcattacctccacga	10	11	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:31008338A>T	ENST00000215095.5	-	6	628	c.397T>A	c.(397-399)Tat>Aat	p.Y133N	STX1B_ENST00000565419.1_Missense_Mutation_p.Y133N	NM_052874.3	NP_443106.1	P61266	STX1B_HUMAN	syntaxin 1B	133					intracellular protein transport (GO:0006886)|neurotransmitter transport (GO:0006836)|regulation of exocytosis (GO:0017157)|regulation of gene expression (GO:0010468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|large_intestine(5)|lung(5)	13						GTCGCGTTATATTCGGTCATT	0.627																																					p.Y133N		Atlas-SNP	.											.	STX1B	26	.	0			c.T397A						.						44	41	42					16																	31008338		2197	4300	6497	SO:0001583	missense	112755	exon6			CGTTATATTCGGT	AY028792	CCDS10699.1	16p12-p11	2008-02-05	2007-06-20	2007-06-20	ENSG00000099365	ENSG00000099365			18539	protein-coding gene	gene with protein product		601485	"syntaxin 1B1", "syntaxin 1B2"	STX1B1, STX1B2			Standard	NM_052874		Approved		uc010cad.2	P61266	OTTHUMG00000132391	ENST00000215095.5:c.397T>A	chr16.hg19:g.31008338A>T	ENSP00000215095:p.Tyr133Asn	64.0	0.0		74.0	25.0	NM_052874	Q15531|Q2VPS2	Missense_Mutation	SNP	ENST00000215095.5	hg19	CCDS10699.1	.	.	.	.	.	.	.	.	.	.	A	35	5.572248	0.96553	.	.	ENSG00000099365	ENST00000215095	T	0.31769	1.48	4.86	4.86	0.63082	t-SNARE (1);Syntaxin, N-terminal (1);	0.000000	0.64402	D	0.000001	T	0.63920	0.2552	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73799	-0.3869	10	0.87932	D	0	.	13.5675	0.61826	1.0:0.0:0.0:0.0	.	133;133	Q2VPS2;P61266	.;STX1B_HUMAN	N	133	ENSP00000215095:Y133N	ENSP00000215095:Y133N	Y	-	1	0	STX1B	30915839	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.139000	0.94554	2.051000	0.60960	0.454000	0.30748	TAT	.	.		0.627	STX1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255521.2			T	31008338	A	T	31008338	3	4	23	1	0	0	0	0	1	0	0	0	15359	449	16	4	489	4	STX1B	16	31008338	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	273418	31008338	59346415	856	2922										
FUS	2521	hgsc.bcm.edu	37	chr16	31196408	31196408	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggggtggcagtggtggcggCggcggcggcggcggtggtgg	27	7	0	0	rs533399799	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:31196408C>T	ENST00000254108.7	+	6	777	c.672C>T	c.(670-672)ggC>ggT	p.G224G	RP11-388M20.6_ENST00000564743.1_RNA|FUS_ENST00000380244.3_Silent_p.G223G|FUS_ENST00000568685.1_Silent_p.G224G	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	224	Gly-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		gtggtggcggcggcggcggcg	0.672			T	"DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"	"liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"								C|||	4	0.000798722	0.0015	0	5008	,	,		10664	0.001		0	False		,,,				2504	0.001				p.G224G		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"fusion, derived from t(12;16) malignant liposarcoma"		"M, L"	.	FUS	52	.	0			c.C672T						.						20	19	19					16																	31196408		2193	4291	6484	SO:0001819	synonymous_variant	2521	exon6			TGGCGGCGGCGGC	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"RNA binding motif (RRM) containing"	4010	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein P2", "translocated in liposarcoma"	137070	"fusion, derived from t(12;16) malignant liposarcoma", "amyotrophic lateral sclerosis 6", "fusion (involved in t(12;16) in malignant liposarcoma)", "fused in sarcoma"	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.672C>T	chr16.hg19:g.31196408C>T		72.0	0.0		73.0	29.0	NM_004960	Q9H4A8	Silent	SNP	ENST00000254108.7	hg19	CCDS10707.1																																																																																			.	.		0.672	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960		T	31196408	C	T	31196408	2	4	23	1	0	0	0	0	0	0	0	1	6108	755	27	1		1	FUS	16	31196408	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	188070	31196408	59158345	857	2923										
SALL1	6299	hgsc.bcm.edu	37	chr16	51173443	51173443	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggatgaatcattggtcaggAcatccccctcgatggaccca	10	12	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:51173443A>G	ENST00000251020.4	-	2	2723	c.2690T>C	c.(2689-2691)gTc>gCc	p.V897A	SALL1_ENST00000440970.1_Missense_Mutation_p.V800A|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	897					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			ATTGGTCAGGACATCCCCCTC	0.542																																					p.V897A	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.T2690C						.						98	77	84					16																	51173443		2198	4300	6498	SO:0001583	missense	6299	exon2			GTCAGGACATCCC	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2690T>C	chr16.hg19:g.51173443A>G	ENSP00000251020:p.Val897Ala	82.0	0.0		110.0	49.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.531823	0.00951	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.80824	-1.42;-1.42	5.5	4.34	0.51931	.	0.305299	0.36338	N	0.002655	T	0.67335	0.2882	L	0.29908	0.895	0.23473	N	0.997601	B	0.24317	0.101	B	0.21360	0.034	T	0.51228	-0.8732	10	0.16420	T	0.52	.	11.2091	0.48786	0.7174:0.2826:0.0:0.0	.	897	Q9NSC2	SALL1_HUMAN	A	897;800;861	ENSP00000251020:V897A;ENSP00000407914:V800A	ENSP00000251020:V897A	V	-	2	0	SALL1	49730944	0.301000	0.24444	1.000000	0.80357	0.057000	0.15508	2.369000	0.44231	2.085000	0.62840	0.455000	0.32223	GTC	.	.		0.542	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		G	51173443	A	G	51173443	3	3	23	1	0	0	0	0	1	0	0	0	13825	275	10	2	1292	2	SALL1	16	51173443	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	19977035	51173443	39181310	858	2924										
CPNE2	221184	hgsc.bcm.edu	37	chr16	57144691	57144691	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgggggtgccccagcagcgGgggcagcccccatgggcccc	18	16	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:57144691G>A	ENST00000535318.2	+	3	398	c.37G>A	c.(37-39)Ggg>Agg	p.G13R	CPNE2_ENST00000290776.8_Missense_Mutation_p.G13R|CPNE2_ENST00000537605.1_5'UTR|CPNE2_ENST00000565874.1_Missense_Mutation_p.G13R			Q96FN4	CPNE2_HUMAN	copine II	13	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5)	21		all_neural(199;0.224)				CCCAGCAGCGGGGGCAGCCCC	0.647																																					p.G13R		Atlas-SNP	.											.	CPNE2	48	.	0			c.G37A						.						33	30	31					16																	57144691		2198	4299	6497	SO:0001583	missense	221184	exon2			GCAGCGGGGGCAG		CCDS10774.1	16q13	2008-02-05			ENSG00000140848	ENSG00000140848			2315	protein-coding gene	gene with protein product		604206				9430674	Standard	NM_152727		Approved	CPN2	uc002eks.2	Q96FN4	OTTHUMG00000133471	ENST00000535318.2:c.37G>A	chr16.hg19:g.57144691G>A	ENSP00000439018:p.Gly13Arg	156.0	0.0		124.0	50.0	NM_152727	Q68D19|Q719H8|Q86XP9	Missense_Mutation	SNP	ENST00000535318.2	hg19	CCDS10774.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.764349	0.69878	.	.	ENSG00000140848	ENST00000290776;ENST00000535318	T;T	0.04706	3.57;3.57	4.22	4.22	0.49857	C2 calcium/lipid-binding domain, CaLB (1);	0.547211	0.19070	N	0.123526	T	0.03477	0.0100	N	0.08118	0	0.80722	D	1	B;B	0.12630	0.006;0.001	B;B	0.06405	0.002;0.001	T	0.50734	-0.8793	10	0.54805	T	0.06	-1.0409	14.5079	0.67764	0.0:0.1478:0.8522:0.0	.	13;13	A8K8A4;Q96FN4	.;CPNE2_HUMAN	R	13	ENSP00000290776:G13R;ENSP00000439018:G13R	ENSP00000290776:G13R	G	+	1	0	CPNE2	55702192	0.998000	0.40836	0.873000	0.34254	0.279000	0.26890	2.742000	0.47434	2.655000	0.90218	0.650000	0.86243	GGG	.	.		0.647	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727		A	57144691	G	A	57144691	3	1	23	1	0	0	0	0	1	0	0	0	3814	1232	43	3	39	3	CPNE2	16	57144691	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	5971248	57144691	33210062	859	2925										
KIFC3	3801	hgsc.bcm.edu	37	chr16	57794959	57794959	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctgccactctcacccgtgGtgcggaggcctgtgctgcag	14	15	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:57794959G>A	ENST00000379655.4	-	15	2254	c.1997C>T	c.(1996-1998)aCc>aTc	p.T666I	KIFC3_ENST00000543930.1_Missense_Mutation_p.T524I|KIFC3_ENST00000541240.1_Missense_Mutation_p.T688I|KIFC3_ENST00000445690.2_Missense_Mutation_p.T666I|KIFC3_ENST00000465878.2_Missense_Mutation_p.T527I|KIFC3_ENST00000540079.2_Missense_Mutation_p.T564I|KIFC3_ENST00000421376.2_Missense_Mutation_p.T527I|KIFC3_ENST00000539578.1_Missense_Mutation_p.T608I|KIFC3_ENST00000562903.1_Missense_Mutation_p.T527I	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	666	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				CTCACCCGTGGTGCGGAGGCC	0.672																																					p.T666I		Atlas-SNP	.											.	KIFC3	55	.	0			c.C1997T						.						57	52	53					16																	57794959		2198	4299	6497	SO:0001583	missense	3801	exon15			CCCGTGGTGCGGA	BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"Kinesins"	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.1997C>T	chr16.hg19:g.57794959G>A	ENSP00000368976:p.Thr666Ile	40.0	0.0		29.0	11.0	NM_001130100	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Missense_Mutation	SNP	ENST00000379655.4	hg19	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	G	15.91	2.972637	0.53614	.	.	ENSG00000140859	ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578	T;T;T;T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94;-0.94;-0.94;-0.94	5.21	5.21	0.72293	Kinesin, motor domain (4);	0.103125	0.64402	D	0.000003	T	0.76737	0.4029	L	0.41356	1.27	0.80722	D	1	P;D;P;B;P;P	0.54601	0.953;0.967;0.751;0.324;0.866;0.84	P;P;B;B;P;B	0.52823	0.71;0.455;0.267;0.064;0.62;0.274	T	0.78518	-0.2173	10	0.54805	T	0.06	.	17.7443	0.88415	0.0:0.0:1.0:0.0	.	688;608;524;564;666;527	B7Z484;F5H4I9;B7Z896;F5H3M2;Q9BVG8;A8K6S2	.;.;.;.;KIFC3_HUMAN;.	I	666;666;527;688;564;524;608	ENSP00000368976:T666I;ENSP00000401696:T666I;ENSP00000396399:T527I;ENSP00000442008:T688I;ENSP00000438805:T564I;ENSP00000444012:T524I;ENSP00000444884:T608I	ENSP00000368976:T666I	T	-	2	0	KIFC3	56352460	1.000000	0.71417	1.000000	0.80357	0.239000	0.25481	9.498000	0.97972	2.460000	0.83146	0.205000	0.17691	ACC	.	.		0.672	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550		A	57794959	G	A	57794959	3	1	23	1	0	0	0	0	1	0	0	0	8323	1261	44	3	533	3	KIFC3	16	57794959	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	650268	57794959	32559794	860	2926										
CNGB1	1258	hgsc.bcm.edu	37	chr16	57918254	57918254	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtggagaccccgggggctcGgggggcgtccggggcgcggg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:57918254delG	ENST00000251102.8	-	33	3630	c.3570delC	c.(3568-3570)cccfs	p.P1190fs	CNGB1_ENST00000564448.1_Frame_Shift_Del_p.P1184fs	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	1190					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						CCGGGGGCTCGGGGGGCGTCC	0.741																																					p.E1191fs	Colon(156;1293 1853 16336 28962 38659)	Atlas-Indel,Pindel	.											.	CNGB1	105	.	0			c.3571delG						.						10	12	12					16																	57918254		1713	3794	5507	SO:0001589	frameshift_variant	1258	exon33			.	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2151	protein-coding gene	gene with protein product	"glutamic acid-rich protein"	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.3570delC	chr16.hg19:g.57918254delG	ENSP00000251102:p.Pro1190fs	73.0	0.0		75.0	27.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Frame_Shift_Del	DEL	ENST00000251102.8	hg19	CCDS42169.1																																																																																			.	.		0.741	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		-	57918254	G	-	57918254	7	5	23	1	0	1	0	1	0	0	0	0	3602	1103	39	0	189	0	CNGB1	16	57918254	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	123295	57918254	32436499	861	2927										
CNGB1	1258	hgsc.bcm.edu	37	chr16	57937813	57937813	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatcttgtagaaattcatgtActtcaccgtgctgtccatgc	8	10	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:57937813A>G	ENST00000251102.8	-	27	2767	c.2707T>C	c.(2707-2709)Tac>Cac	p.Y903H	CNGB1_ENST00000564448.1_Missense_Mutation_p.Y897H	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	903					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						AAATTCATGTACTTCACCGTG	0.572																																					p.Y903H	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.T2707C						.						131	139	136					16																	57937813		2086	4197	6283	SO:0001583	missense	1258	exon27			TCATGTACTTCAC	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2151	protein-coding gene	gene with protein product	"glutamic acid-rich protein"	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2707T>C	chr16.hg19:g.57937813A>G	ENSP00000251102:p.Tyr903His	71.0	0.0		72.0	30.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	hg19	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.319897	0.81469	.	.	ENSG00000070729	ENST00000251102	D	0.97731	-4.51	4.82	3.69	0.42338	Cyclic nucleotide-binding-like (1);	0.076454	0.53938	D	0.000046	D	0.98573	0.9523	M	0.87269	2.87	0.80722	D	1	D;P	0.89917	1.0;0.784	D;P	0.91635	0.999;0.686	D	0.98532	1.0628	10	0.66056	D	0.02	.	10.7068	0.45960	0.8395:0.1605:0.0:0.0	.	275;903	Q14028-2;Q14028	.;CNGB1_HUMAN	H	903	ENSP00000251102:Y903H	ENSP00000251102:Y903H	Y	-	1	0	CNGB1	56495314	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.336000	0.96533	0.656000	0.30886	0.460000	0.39030	TAC	.	.		0.572	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		G	57937813	A	G	57937813	3	3	23	1	0	0	0	0	1	0	0	0	3602	391	14	2	1076	2	CNGB1	16	57937813	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	19559	57937813	32416940	862	2928										
B3GNT9	80262	hgsc.bcm.edu	37	chr16	67184217	67184217	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggctgcacccgcgtcgggtaActggaacgcgcggggtccgg	18	13	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:67184217A>G	ENST00000219139.3	+	0	2865				B3GNT9_ENST00000449549.3_Silent_p.L58L	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70											cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		GCGTCGGGTAACTGGAACGCG	0.756																																					p.L58L		Atlas-SNP	.											.	B3GNT9	25	.	0			c.T172C						.						7	9	8					16																	67184217		1763	3973	5736	SO:0001628	intergenic_variant	84752	exon2			CGGGTAACTGGAA	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 6"	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510		chr16.hg19:g.67184217A>G		138.0	0.0		108.0	39.0	NM_033309	Q9HA86	Silent	SNP	ENST00000219139.3	hg19	CCDS10828.1																																																																																			.	.		0.756	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		G	67184217	A	G	67184217	1	3	23	0	1	0	0	0	0	0	0	0	1264	40	2	2		2	B3GNT9	16	67184217	IGR	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	9246404	67184217	23170536	863	2929										
RLTPR	146206	hgsc.bcm.edu	37	chr16	67683180	67683180	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaccctggacgacgtcctgcAccggattgtccagctcatgc	11	15	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:67683180A>G	ENST00000334583.6	+	19	2040	c.1712A>G	c.(1711-1713)cAc>cGc	p.H571R	RLTPR_ENST00000545661.1_Missense_Mutation_p.H535R	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	571					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		GACGTCCTGCACCGGATTGTC	0.627																																					p.H571R		Atlas-SNP	.											.	RLTPR	124	.	0			c.A1712G						.						57	64	61					16																	67683180		2017	4164	6181	SO:0001583	missense	146206	exon19			TCCTGCACCGGAT	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.1712A>G	chr16.hg19:g.67683180A>G	ENSP00000334958:p.His571Arg	59.0	0.0		48.0	19.0	NM_001013838	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	hg19	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.399064	0.83120	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	T;T	0.51574	0.7;0.7	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.54532	0.1864	L	0.38838	1.175	0.43417	D	0.995569	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.991	T	0.47459	-0.9116	10	0.16420	T	0.52	-16.3245	12.6465	0.56738	1.0:0.0:0.0:0.0	.	535;571	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	R	571;535	ENSP00000334958:H571R;ENSP00000441481:H535R	ENSP00000334958:H571R	H	+	2	0	RLTPR	66240681	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.386000	0.66238	1.817000	0.53016	0.459000	0.35465	CAC	.	.		0.627	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		G	67683180	A	G	67683180	3	3	23	1	0	0	0	0	1	0	0	0	13409	159	6	2	1786	2	RLTPR	16	67683180	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	498963	67683180	22671573	864	2930										
RLTPR	146206	hgsc.bcm.edu	37	chr16	67688265	67688265	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaggaggacccggccactgaGgggggcgccactcctgtccc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:67688265delG	ENST00000334583.6	+	31	3580	c.3252delG	c.(3250-3252)gagfs	p.E1084fs	RLTPR_ENST00000545661.1_Frame_Shift_Del_p.E1048fs	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	1084					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		CGGCCACTGAGGGGGGCGCCA	0.652																																					p.E1084fs		Atlas-Indel,Pindel	.											.	RLTPR	124	.	0			c.3251delA						.						14	17	16					16																	67688265		1931	4087	6018	SO:0001589	frameshift_variant	146206	exon31			.	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.3252delG	chr16.hg19:g.67688265delG	ENSP00000334958:p.Glu1084fs	137.0	0.0		128.0	65.0	NM_001013838	B8X2Z3	Frame_Shift_Del	DEL	ENST00000334583.6	hg19	CCDS45513.1																																																																																			.	.		0.652	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		-	67688265	G	-	67688265	7	5	23	1	0	1	0	1	0	0	0	0	13409	991	35	0	3374	0	RLTPR	16	67688265	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	5085	67688265	22666488	865	2931										
RANBP10	57610	hgsc.bcm.edu	37	chr16	67765413	67765413	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgcctgttcttcctgaatcGgggtttcagtcattcgagca	10	11	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:67765413G>A	ENST00000317506.3	-	7	966	c.851C>T	c.(850-852)cCg>cTg	p.P284L	RANBP10_ENST00000602677.1_Missense_Mutation_p.P284L|RANBP10_ENST00000411657.2_Missense_Mutation_p.P167L|RANBP10_ENST00000448631.2_Missense_Mutation_p.P228L|RANBP10_ENST00000536251.1_Missense_Mutation_p.P55L|RANBP10_ENST00000425512.2_Missense_Mutation_p.P152L	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	284	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.				microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.P284Q(1)		endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		TTCCTGAATCGGGGTTTCAGT	0.478																																					p.P284L		Atlas-SNP	.											RANBP10,NS,lymphoid_neoplasm,0,1	RANBP10	56	.	1	Substitution - Missense(1)	lung(1)	c.C851T						.						147	134	138					16																	67765413		2198	4300	6498	SO:0001583	missense	57610	exon7			TGAATCGGGGTTT	AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.851C>T	chr16.hg19:g.67765413G>A	ENSP00000316589:p.Pro284Leu	169.0	0.0		117.0	49.0	NM_020850	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	Missense_Mutation	SNP	ENST00000317506.3	hg19	CCDS32469.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.825099	0.50739	.	.	ENSG00000141084	ENST00000317506;ENST00000448631;ENST00000536251;ENST00000411657;ENST00000425512	D	0.88046	-2.33	5.78	5.78	0.91487	LisH dimerisation motif (2);	0.297907	0.35096	N	0.003442	T	0.80788	0.4690	N	0.19112	0.55	0.46849	D	0.999229	B;B;B;B;B	0.11235	0.004;0.003;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.002;0.001;0.0;0.0;0.001	T	0.73219	-0.4052	10	0.33141	T	0.24	-20.3522	19.6088	0.95594	0.0:0.0:1.0:0.0	.	152;284;167;228;284	B4DHL9;B4E1Y2;B4DID0;B4DQH9;Q6VN20	.;.;.;.;RBP10_HUMAN	L	284;228;55;167;152	ENSP00000410617:P152L	ENSP00000316589:P284L	P	-	2	0	RANBP10	66322914	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.274000	0.65569	2.734000	0.93682	0.563000	0.77884	CCG	.	.		0.478	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467896.1	NM_020850		A	67765413	G	A	67765413	3	1	23	1	0	0	0	0	1	0	0	0	13041	1116	39	1	1043	1	RANBP10	16	67765413	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	77148	67765413	22589340	866	2932										
PSKH1	5681	hgsc.bcm.edu	37	chr16	67943147	67943147	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtggaggtgttcgagacacaGgagcgggtgtacatggtgat	18	5	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:67943147G>T	ENST00000291041.5	+	2	665	c.495G>T	c.(493-495)caG>caT	p.Q165H		NM_006742.2	NP_006733.1	P11801	KPSH1_HUMAN	protein serine kinase H1	165	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|large_intestine(1)|lung(7)|pancreas(1)	12		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0044)|Epithelial(162;0.0197)|all cancers(182;0.128)		TCGAGACACAGGAGCGGGTGT	0.632																																					p.Q165H		Atlas-SNP	.											.	PSKH1	28	.	0			c.G495T						.						109	102	105					16																	67943147		2198	4300	6498	SO:0001583	missense	5681	exon2			GACACAGGAGCGG	M14504	CCDS10851.1	16q22.1	2008-02-05			ENSG00000159792	ENSG00000159792			9529	protein-coding gene	gene with protein product		177015				8268911	Standard	NM_006742		Approved		uc002euv.3	P11801	OTTHUMG00000137548	ENST00000291041.5:c.495G>T	chr16.hg19:g.67943147G>T	ENSP00000291041:p.Gln165His	129.0	0.0		115.0	37.0	NM_006742	Q9NY19	Missense_Mutation	SNP	ENST00000291041.5	hg19	CCDS10851.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.293653	0.40594	.	.	ENSG00000159792	ENST00000291041	T	0.39592	1.07	5.21	3.25	0.37280	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.113455	0.64402	D	0.000010	T	0.28234	0.0697	N	0.17674	0.51	0.42502	D	0.992931	B	0.22800	0.075	B	0.25759	0.063	T	0.11817	-1.0572	10	0.51188	T	0.08	-21.6908	10.6928	0.45882	0.1565:0.0:0.8435:0.0	.	165	P11801	KPSH1_HUMAN	H	165	ENSP00000291041:Q165H	ENSP00000291041:Q165H	Q	+	3	2	PSKH1	66500648	1.000000	0.71417	0.997000	0.53966	0.467000	0.32768	0.821000	0.27338	1.222000	0.43521	0.655000	0.94253	CAG	.	.		0.632	PSKH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268882.3	NM_006742		T	67943147	G	T	67943147	3	4	23	1	0	0	0	0	1	0	0	0	12676	991	35	3	497	3	PSKH1	16	67943147	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	177734	67943147	22411606	867	2933										
TERF2	7014	hgsc.bcm.edu	37	chr16	69418537	69418537	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actgcttctgtcagtgtaaaTtccgttttaatcatctccag	6	10	4	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:69418537T>A	ENST00000254942.3	-	3	568	c.552A>T	c.(550-552)gaA>gaT	p.E184D	TERF2_ENST00000567296.2_Missense_Mutation_p.E184D|TERF2_ENST00000569611.2_5'UTR|TERF2_ENST00000603068.1_Missense_Mutation_p.E142D	NM_005652.3	NP_005643.2	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2	184	TRFH dimerization.				age-dependent telomere shortening (GO:0001309)|cell cycle (GO:0007049)|cellular senescence (GO:0090398)|in utero embryonic development (GO:0001701)|negative regulation of telomere maintenance (GO:0032205)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|positive regulation of telomere maintenance (GO:0032206)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|telomere capping (GO:0016233)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)|telomeric loop formation (GO:0031627)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded telomeric DNA binding (GO:0003691)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			NS(2)|breast(1)|large_intestine(3)|lung(1)	7		Ovarian(137;0.101)				TCAGTGTAAATTCCGTTTTAA	0.398																																					p.E184D	Ovarian(13;63 524 30420 31710 34037)	Atlas-SNP	.											.	TERF2	24	.	0			c.A552T						.						111	105	107					16																	69418537		2198	4300	6498	SO:0001583	missense	7014	exon3			TGTAAATTCCGTT		CCDS10879.1, CCDS10879.2	16q22.1	2008-02-05			ENSG00000132604	ENSG00000132604			11729	protein-coding gene	gene with protein product		602027		TRBF2		9326950, 10226653	Standard	NM_005652		Approved	TRF2	uc002exd.4	Q15554	OTTHUMG00000137566	ENST00000254942.3:c.552A>T	chr16.hg19:g.69418537T>A	ENSP00000254942:p.Glu184Asp	91.0	0.0		98.0	39.0	NM_005652		Missense_Mutation	SNP	ENST00000254942.3	hg19		.	.	.	.	.	.	.	.	.	.	T	18.71	3.681753	0.68042	.	.	ENSG00000132604	ENST00000254942	.	.	.	5.48	1.15	0.20763	Telomere repeat-binding factor, dimerisation domain (4);	0.148438	0.50627	D	0.000107	T	0.49898	0.1584	N	0.16656	0.425	0.44677	D	0.997668	B;D	0.58620	0.046;0.983	B;D	0.72982	0.069;0.979	T	0.38373	-0.9664	9	0.33940	T	0.23	-16.4594	8.5205	0.33273	0.0:0.5361:0.0:0.4639	.	142;142	Q15554-2;Q15554	.;TERF2_HUMAN	D	142	.	ENSP00000254942:E142D	E	-	3	2	TERF2	67976038	0.997000	0.39634	0.994000	0.49952	0.881000	0.50899	0.104000	0.15313	0.242000	0.21303	0.477000	0.44152	GAA	.	.		0.398	TERF2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000268944.2			A	69418537	T	A	69418537	3	1	23	1	0	0	0	0	1	0	0	0	15777	1490	52	4	1108	4	TERF2	16	69418537	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1475390	69418537	20936216	868	2934										
MTSS1L	92154	hgsc.bcm.edu	37	chr16	70708260	70708260	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggggcttggagtaggtggcGtcctgggagacgaagccaga	20	7	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:70708260G>A	ENST00000338779.6	-	11	1276	c.1002C>T	c.(1000-1002)gaC>gaT	p.D334D		NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	334	Ser-rich.				filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						AGTAGGTGGCGTCCTGGGAGA	0.642																																					p.D334D		Atlas-SNP	.											.	MTSS1L	22	.	0			c.C1002T						.						70	71	71					16																	70708260		2198	4300	6498	SO:0001819	synonymous_variant	92154	exon11			GGTGGCGTCCTGG		CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613			25094	protein-coding gene	gene with protein product	"actin-bundling protein with BAIAP2 homology"					12477932	Standard	XM_006721335		Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.1002C>T	chr16.hg19:g.70708260G>A		123.0	0.0		102.0	42.0	NM_138383	A6NJI7|Q9BUA8	Silent	SNP	ENST00000338779.6	hg19	CCDS32476.1																																																																																			.	.		0.642	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434927.3	NM_138383		A	70708260	G	A	70708260	2	1	23	1	0	0	0	0	0	0	0	1	9972	1136	40	1		1	MTSS1L	16	70708260	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1289723	70708260	19646493	869	2935										
HYDIN	54768	hgsc.bcm.edu	37	chr16	71094473	71094474	+	Frame_Shift_Del	DEL	TT	TT	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgagaatcctggaagagtcTtttaggacgtagatattccc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:71094473_71094474delTT	ENST00000393567.2	-	18	2612_2613	c.2462_2463delAA	c.(2461-2463)aaafs	p.K821fs	HYDIN_ENST00000448691.1_Frame_Shift_Del_p.K821fs|HYDIN_ENST00000541601.1_Frame_Shift_Del_p.K838fs|HYDIN_ENST00000538248.1_Frame_Shift_Del_p.K848fs|HYDIN_ENST00000321489.5_Frame_Shift_Del_p.K821fs|HYDIN_ENST00000448089.2_Frame_Shift_Del_p.K821fs	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	821					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGGAAGAGTCTTTTAGGACGTA	0.475																																					p.848_849del		Atlas-INDEL	.											.	HYDIN	788	.	0			c.2544_2545del						.																																			SO:0001589	frameshift_variant	54768	exon18			.	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.2462_2463delAA	chr16.hg19:g.71094475_71094476delTT	ENSP00000377197:p.Lys821fs	156.0	0.0		133.0	18.0	NM_001198542	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Frame_Shift_Del	DEL	ENST00000393567.2	hg19	CCDS59269.1																																																																																			.	.		0.475	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			-	71094474	TT	-	71094473	7	5	23	1	0	1	0	1	0	0	0	0	7476	1606	56	0	13187	0	HYDIN	16	71094473	Frame_Shift_Del	DEL	TT	TCGA-4R-AA8I-01A-11D-A382-10	386213	71094473	19260280	870	2936										
ZNF19	7567	hgsc.bcm.edu	37	chr16	71509598	71509598	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgccgaagtaggggtgaattAccaacaaaagctttgccaca	10	9	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:71509598A>G	ENST00000288177.5	-	6	1107	c.852T>C	c.(850-852)ggT>ggC	p.G284G	ZNF19_ENST00000567225.1_Intron|ZNF19_ENST00000565637.1_Silent_p.G242G|ZNF19_ENST00000564230.1_Silent_p.G284G|ZNF19_ENST00000565100.2_Silent_p.G214G|AC010547.9_ENST00000561908.1_Intron	NM_006961.3	NP_008892.2	P17023	ZNF19_HUMAN	zinc finger protein 19	284					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|prostate(1)|stomach(1)	22		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		GGGGTGAATTACCAACAAAAG	0.443																																					p.G284G		Atlas-SNP	.											.	ZNF19	46	.	0			c.T852C						.						93	91	92					16																	71509598		2198	4300	6498	SO:0001819	synonymous_variant	7567	exon6			TGAATTACCAACA	X52343	CCDS10901.1	16q22	2013-01-08	2006-05-10		ENSG00000157429	ENSG00000157429		"Zinc fingers, C2H2-type", "-"	12981	protein-coding gene	gene with protein product		194525	"zinc finger protein 19 (KOX 12)"			1505991, 1946370	Standard	NM_006961		Approved	KOX12, MGC51021	uc002fam.1	P17023	OTTHUMG00000137593	ENST00000288177.5:c.852T>C	chr16.hg19:g.71509598A>G		110.0	0.0		111.0	45.0	NM_006961	A8K895|Q86Y66|Q8NDE2|Q96M79|Q96NE5	Silent	SNP	ENST00000288177.5	hg19	CCDS10901.1																																																																																			.	.		0.443	ZNF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268993.2	NM_006961		G	71509598	A	G	71509598	2	3	23	1	0	0	0	0	0	0	0	1	17770	378	14	2		2	ZNF19	16	71509598	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	415125	71509598	18845155	871	2937										
PMFBP1	83449	hgsc.bcm.edu	37	chr16	72157448	72157448	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttcctcccatactcacttcTgctgttttgcccattgctcc	4	16	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:72157448T>C	ENST00000537792.1	-	2	187	c.188A>G	c.(187-189)cAg>cGg	p.Q63R	PMFBP1_ENST00000237353.10_Missense_Mutation_p.Q897R|PMFBP1_ENST00000355636.6_Missense_Mutation_p.Q752R|PMFBP1_ENST00000537465.1_Missense_Mutation_p.Q902R			Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	902						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TACTCACTTCTGCTGTTTTGC	0.562																																					p.Q897R		Atlas-SNP	.											.	PMFBP1	101	.	0			c.A2690G						.						117	99	105					16																	72157448		2198	4300	6498	SO:0001583	missense	83449	exon18			CACTTCTGCTGTT	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000537792.1:c.188A>G	chr16.hg19:g.72157448T>C	ENSP00000443366:p.Gln63Arg	81.0	0.0		99.0	32.0	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000537792.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.52	3.641325	0.67244	.	.	ENSG00000118557	ENST00000537792;ENST00000537465;ENST00000237353;ENST00000355636	T;T;T;T	0.62498	0.02;1.46;1.45;1.52	4.95	4.95	0.65309	.	0.000000	0.46145	D	0.000309	T	0.74366	0.3707	M	0.72118	2.19	0.45883	D	0.998739	D;D;D	0.67145	0.989;0.996;0.981	D;D;D	0.78314	0.979;0.991;0.969	T	0.72124	-0.4385	10	0.25751	T	0.34	.	10.9428	0.47283	0.0:0.0:0.0:1.0	.	902;897;902	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	R	63;902;897;752	ENSP00000443366:Q63R;ENSP00000443817:Q902R;ENSP00000237353:Q897R;ENSP00000347854:Q752R	ENSP00000237353:Q897R	Q	-	2	0	PMFBP1	70714949	1.000000	0.71417	1.000000	0.80357	0.697000	0.40408	3.432000	0.52824	2.088000	0.63022	0.528000	0.53228	CAG	.	.		0.562	PMFBP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000396523.1	NM_031293		C	72157448	T	C	72157448	3	2	23	1	0	0	0	0	1	0	0	0	12143	1580	55	2	409	2	PMFBP1	16	72157448	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	647850	72157448	18197305	872	2938										
ZNRF1	84937	hgsc.bcm.edu	37	chr16	75033762	75033762	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcatggaccccagcacggccGggggggtgccctttggcctc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:75033762delG	ENST00000335325.4	+	1	835	c.193delG	c.(193-195)gggfs	p.G66fs	ZNRF1_ENST00000567962.1_Frame_Shift_Del_p.G66fs|ZNRF1_ENST00000320619.6_Frame_Shift_Del_p.G66fs|ZNRF1_ENST00000566250.1_Frame_Shift_Del_p.G66fs|WDR59_ENST00000562331.1_5'Flank	NM_032268.4	NP_115644.1	Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase	66					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)	1						CAGCACGGCCGGGGGGGTGCC	0.756																																					p.A64fs		Pindel	.											.	ZNRF1	6	.	0			c.192delC						.			23,3159		4,15,1572	3	4	4			2.8	1	16		3	35,6275		5,25,3125	no	frameshift	ZNRF1	NM_032268.4		9,40,4697	A1A1,A1R,RR		0.5547,0.7228,0.611			75033762	58,9434	1796	3541	5337	SO:0001589	frameshift_variant	84937	exon1			.	AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187		"RING-type (C3HC4) zinc fingers"	18452	protein-coding gene	gene with protein product		612060	"zinc and ring finger 1"				Standard	NM_032268		Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606	ENST00000335325.4:c.193delG	chr16.hg19:g.75033762delG	ENSP00000335091:p.Gly66fs	57.0	0.0		70.0	18.0	NM_032268	D3DUJ9|Q9H083	Frame_Shift_Del	DEL	ENST00000335325.4	hg19	CCDS10912.1																																																																																			.	.		0.756	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2			-	75033762	G	-	75033762	7	5	23	1	0	1	0	1	0	0	0	0	18226	1116	39	0	195	0	ZNRF1	16	75033762	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	2876314	75033762	15320991	873	2939										
ZNRF1	84937	hgsc.bcm.edu	37	chr16	75033861	75033861	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgcgtccgactccacctatGcccatggcaatggttaccag	9	15	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:75033861G>A	ENST00000335325.4	+	1	934	c.292G>A	c.(292-294)Gcc>Acc	p.A98T	ZNRF1_ENST00000567962.1_Missense_Mutation_p.A98T|ZNRF1_ENST00000320619.6_Missense_Mutation_p.A98T|ZNRF1_ENST00000566250.1_Missense_Mutation_p.A98T|WDR59_ENST00000562331.1_5'Flank	NM_032268.4	NP_115644.1	Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase	98					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)	1						CTCCACCTATGCCCATGGCAA	0.701																																					p.A98T		Atlas-SNP	.											.	ZNRF1	6	.	0			c.G292A						.						20	19	19					16																	75033861		2189	4283	6472	SO:0001583	missense	84937	exon1			ACCTATGCCCATG	AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187		"RING-type (C3HC4) zinc fingers"	18452	protein-coding gene	gene with protein product		612060	"zinc and ring finger 1"				Standard	NM_032268		Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606	ENST00000335325.4:c.292G>A	chr16.hg19:g.75033861G>A	ENSP00000335091:p.Ala98Thr	93.0	0.0		74.0	21.0	NM_032268	D3DUJ9|Q9H083	Missense_Mutation	SNP	ENST00000335325.4	hg19	CCDS10912.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.962988	0.53507	.	.	ENSG00000186187	ENST00000320619;ENST00000335325	.	.	.	4.93	4.93	0.64822	.	0.429360	0.23752	N	0.044919	T	0.25975	0.0633	N	0.08118	0	0.38241	D	0.94133	B;P;B	0.39311	0.002;0.667;0.001	B;B;B	0.33254	0.001;0.16;0.0	T	0.18304	-1.0341	9	0.23302	T	0.38	-10.6251	15.3624	0.74487	0.0:0.0:1.0:0.0	.	98;98;98	B4DG67;Q8ND25-2;Q8ND25	.;.;ZNRF1_HUMAN	T	98	.	ENSP00000323362:A98T	A	+	1	0	ZNRF1	73591362	0.928000	0.31464	1.000000	0.80357	0.996000	0.88848	0.593000	0.23999	2.701000	0.92244	0.650000	0.86243	GCC	.	.		0.701	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2			A	75033861	G	A	75033861	3	1	23	1	0	0	0	0	1	0	0	0	18226	1319	46	3	294	3	ZNRF1	16	75033861	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	99	75033861	15320892	874	2940										
GAN	8139	hgsc.bcm.edu	37	chr16	81411036	81411036	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttaggtaccaattacgactaCgtgcgtgagtttaaaagaag	10	6	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:81411036C>T	ENST00000568107.2	+	11	1791	c.1629C>T	c.(1627-1629)taC>taT	p.Y543Y		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	543					cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				ATTACGACTACGTGCGTGAGT	0.468																																					p.Y543Y	GBM(106;1239 1507 7582 9741 33976)	Atlas-SNP	.											.	GAN	59	.	0			c.C1629T						.						173	157	163					16																	81411036		2201	4300	6501	SO:0001819	synonymous_variant	8139	exon11			CGACTACGTGCGT	AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"Kelch-like", "BTB/POZ domain containing"	4137	protein-coding gene	gene with protein product	"kelch-like family member 16"	605379	"giant axonal neuropathy (gigaxonin)"			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.1629C>T	chr16.hg19:g.81411036C>T		113.0	0.0		136.0	11.0	NM_022041		Silent	SNP	ENST00000568107.2	hg19	CCDS10935.1																																																																																			.	.		0.468	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3			T	81411036	C	T	81411036	2	4	23	1	0	0	0	0	0	0	0	1	6240	547	19	1		1	GAN	16	81411036	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	6377175	81411036	8943717	875	2941										
IL17C	27189	hgsc.bcm.edu	37	chr16	88705522	88705522	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaactgcccctcggccaggCccccccacacctgctggctc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:88705522delC	ENST00000244241.4	+	2	189	c.140delC	c.(139-141)gccfs	p.A47fs		NM_013278.3	NP_037410.1	Q9P0M4	IL17C_HUMAN	interleukin 17C	47					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|neutrophil differentiation (GO:0030223)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)	p.H50fs*68(1)		large_intestine(1)|lung(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0477)		CTCGGCCAGGCCCCCCCACAC	0.687																																					p.A47fs		Atlas-Indel,Pindel	.											.,1	IL17C	6	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.139delG						.						39	47	45					16																	88705522		1993	4143	6136	SO:0001589	frameshift_variant	27189	exon2			.	AF152099	CCDS42217.1	16q24	2011-07-14			ENSG00000124391	ENSG00000124391		"Interleukins and interleukin receptors"	5983	protein-coding gene	gene with protein product		604628				10639155	Standard	NM_013278		Approved	IL-17C, CX2, IL-21, MGC126884, MGC138401	uc002fla.3	Q9P0M4		ENST00000244241.4:c.140delC	chr16.hg19:g.88705522delC	ENSP00000244241:p.Ala47fs	96.0	0.0		107.0	45.0	NM_013278	Q3MIG8|Q9HC75	Frame_Shift_Del	DEL	ENST00000244241.4	hg19	CCDS42217.1																																																																																			.	.		0.687	IL17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422575.1	NM_013278		-	88705522	C	-	88705522	7	5	23	1	0	1	0	1	0	0	0	0	7645	739	26	0	146	0	IL17C	16	88705522	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	7294486	88705522	1649231	876	2942										
CTU2	9780	hgsc.bcm.edu	37	chr16	88779224	88779224	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccccagaacctggcaagaccGcctgcccctgcccagactga	9	19	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:88779224G>A	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Silent_p.P216P|CTU2_ENST00000567949.1_Silent_p.P287P|CTU2_ENST00000312060.5_Silent_p.P216P|CTU2_ENST00000378384.3_Silent_p.P129P	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						TGGCAAGACCGCCTGCCCCTG	0.672																																					p.P216P		Atlas-SNP	.											.	CTU2	66	.	0			c.G648A						.						19	22	21					16																	88779224		2184	4283	6467	SO:0001628	intergenic_variant	348180	exon7			AAGACCGCCTGCC	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"family with sequence similarity 38, member A"	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776		chr16.hg19:g.88779224G>A		128.0	0.0		120.0	44.0	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	hg19	CCDS54058.1																																																																																			.	.		0.672	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745		A	88779224	G	A	88779224	1	1	23	0	1	0	0	0	0	0	0	0	4050	1074	38	1		1	CTU2	16	88779224	IGR	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	73702	88779224	1575529	877	2943										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89348566	89348568	+	In_Frame_Del	DEL	TCT	TCT	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttctccctgtgtttctctcTcttcttcttctcttttagga							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:89348566_89348568delTCT	ENST00000301030.4	-	9	4842_4844	c.4382_4384delAGA	c.(4381-4386)aagaga>aga	p.K1461del	ANKRD11_ENST00000378330.2_In_Frame_Del_p.K1461del	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1461	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		tgtttctctctcttcttcttctc	0.483																																					p.1461_1462del		Atlas-Indel,Pindel	.											.	ANKRD11	195	.	0			c.4383_4385del						.			0,4264		0,0,2132						5.1	0			86	3,8251		1,1,4125	no	coding	ANKRD11	NM_013275.4		1,1,6257	A1A1,A1R,RR		0.0363,0.0,0.024				3,12515				SO:0001651	inframe_deletion	29123	exon10			.	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.4382_4384delAGA	chr16.hg19:g.89348575_89348577delTCT	ENSP00000301030:p.Lys1461del	70.0	0.0		63.0	29.0	NM_001256182	Q6NTG1|Q6QMF8	In_Frame_Del	DEL	ENST00000301030.4	hg19	CCDS32513.1																																																																																			.	.		0.483	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		-	89348568	TCT	-	89348566	7	5	23	1	0	1	0	1	0	0	0	0	639	1559	54	0	3627	0	ANKRD11	16	89348566	In_Frame_Del	DEL	TCT	TCGA-4R-AA8I-01A-11D-A382-10	569342	89348566	1006187	878	2944										
ZNF276	92822	hgsc.bcm.edu	37	chr16	89804261	89804261	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtggacaaaccttcaagcagCggaagcaccttctcgtccac	9	14	2	0	rs149209309		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:89804261C>T	ENST00000443381.2	+	10	1619	c.1522C>T	c.(1522-1524)Cgg>Tgg	p.R508W	FANCA_ENST00000389301.3_3'UTR|ZNF276_ENST00000446326.2_Missense_Mutation_p.R294W|ZNF276_ENST00000568064.1_Missense_Mutation_p.R416W|ZNF276_ENST00000289816.5_Missense_Mutation_p.R433W	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	508					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)	14		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		CTTCAAGCAGCGGAAGCACCT	0.587																																					p.R508W		Atlas-SNP	.											.	ZNF276	70	.	0			c.C1522T						.						137	122	127					16																	89804261		2198	4300	6498	SO:0001583	missense	92822	exon10			AAGCAGCGGAAGC	AK026482	CCDS10986.1, CCDS45554.1	16q24.3	2014-02-17	2006-02-10	2006-02-10	ENSG00000158805	ENSG00000158805		"Zinc fingers, C2H2-type"	23330	protein-coding gene	gene with protein product	"centromere protein Z", "zinc finger, AD-type"	608460	"zinc finger protein 276 homolog (mouse)"	ZFP276		10936049, 20813266	Standard	NM_152287		Approved	MGC45417, ZNF477, CENPZ, CENP-Z, ZADT	uc002fos.4	Q8N554	OTTHUMG00000138050	ENST00000443381.2:c.1522C>T	chr16.hg19:g.89804261C>T	ENSP00000415836:p.Arg508Trp	156.0	0.0		166.0	7.0	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Missense_Mutation	SNP	ENST00000443381.2	hg19	CCDS45554.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561125	0.65538	.	.	ENSG00000158805	ENST00000446326;ENST00000289816;ENST00000443381	T;T;T	0.52754	0.65;0.65;0.65	5.62	4.66	0.58398	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.63331	0.2502	L	0.49640	1.575	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.999	T	0.66881	-0.5811	10	0.87932	D	0	-37.2611	14.9466	0.71035	0.144:0.856:0.0:0.0	.	346;508;294;433	B4DIT3;Q8N554;A8K186;Q8N554-2	.;ZN276_HUMAN;.;.	W	294;433;508	ENSP00000415999:R294W;ENSP00000289816:R433W;ENSP00000415836:R508W	ENSP00000289816:R433W	R	+	1	2	ZNF276	88331762	1.000000	0.71417	1.000000	0.80357	0.652000	0.38707	1.591000	0.36665	1.352000	0.45808	0.555000	0.69702	CGG	.	C|1.000;G|0.000		0.587	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287		T	89804261	C	T	89804261	3	4	23	1	0	0	0	0	1	0	0	0	17826	759	27	1	1560	1	ZNF276	16	89804261	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	455695	89804261	550492	879	2945										
CENPBD1	92806	hgsc.bcm.edu	37	chr16	90037950	90037950	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctctccgtttgagaaccttcGccatgttcacgctgtaagtc	8	13	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:90037950G>A	ENST00000314994.3	-	1	992	c.381C>T	c.(379-381)ggC>ggT	p.G127G	CENPBD1_ENST00000567035.1_Intron|RP11-566K11.5_ENST00000565150.1_RNA|AFG3L1P_ENST00000437774.1_RNA	NM_145039.3	NP_659476.2	B2RD01	CENP1_HUMAN	CENPB DNA-binding domains containing 1	127	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(2)	3						gagaaccttcgccatgttcac	0.532																																					p.G127G		Atlas-SNP	.											.	CENPBD1	18	.	0			c.C381T						.						84	85	85					16																	90037950		1858	3692	5550	SO:0001819	synonymous_variant	92806	exon1			ACCTTCGCCATGT	AK056131	CCDS45556.1	16q24.3	2009-08-26			ENSG00000177946	ENSG00000177946			28272	protein-coding gene	gene with protein product							Standard	NM_145039		Approved	MGC16385	uc002fpr.3	B2RD01		ENST00000314994.3:c.381C>T	chr16.hg19:g.90037950G>A		215.0	0.0		188.0	67.0	NM_145039		Silent	SNP	ENST00000314994.3	hg19	CCDS45556.1																																																																																			.	.		0.532	CENPBD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421897.1	NM_145039		A	90037950	G	A	90037950	2	1	23	1	0	0	0	0	0	0	0	1	3230	1074	38	1		1	CENPBD1	16	90037950	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	233689	90037950	316803	880	2946										
NXN	64359	hgsc.bcm.edu	37	chr17	726873	726874	+	Splice_Site	INS	-	-	A													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggggtccaaacactcacccINSaatgtgcggagaaatagacg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:726873_726874insA	ENST00000336868.3	-	3	701_702	c.610_611insT	c.(610-612)tgg>tTgg	p.W204fs	NXN_ENST00000538650.1_5'Flank|NXN_ENST00000537628.2_5'UTR|NXN_ENST00000577098.1_5'Flank|NXN_ENST00000575801.1_Splice_Site_p.W96fs	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	204	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		AACACTCACCCAATGTGCGGAG	0.584																																					p.W204fs		Atlas-Indel,Pindel	.											.	NXN	32	.	0			c.611_612insT						.																																			SO:0001630	splice_region_variant	64359	exon3			.		CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693			18008	protein-coding gene	gene with protein product		612895					Standard	NM_022463		Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.612+1->T	chr17.hg19:g.726875_726875dupA		125.0	0.0		74.0	52.0	NM_022463	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	Frame_Shift_Ins	INS	ENST00000336868.3	hg19	CCDS10998.1																																																																																			.	.		0.584	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206669.1		Frame_Shift_Ins	A	726874	-	A	726873	8	5	23	1	0	1	1	0	0	0	1	0	10796	608	21	0	720	0	NXN	17	726873	Splice_Site	INS	-	TCGA-4R-AA8I-01A-11D-A382-10		726873	80468337	881	2947										
SRR	63826	hgsc.bcm.edu	37	chr17	2227123	2227123	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctcctccataacttgggtgAagcaggctgaaaggccagct	11	12	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:2227123A>G	ENST00000344595.5	+	8	1297	c.979A>G	c.(979-981)Aag>Gag	p.K327E	TSR1_ENST00000301364.5_3'UTR|SRR_ENST00000576848.1_Missense_Mutation_p.K101E	NM_021947.1	NP_068766.1	Q9GZT4	SRR_HUMAN	serine racemase	327					aging (GO:0007568)|brain development (GO:0007420)|D-serine biosynthetic process (GO:0070179)|D-serine metabolic process (GO:0070178)|L-serine metabolic process (GO:0006563)|protein homotetramerization (GO:0051289)|pyruvate biosynthetic process (GO:0042866)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|serine family amino acid metabolic process (GO:0009069)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|D-serine ammonia-lyase activity (GO:0008721)|glycine binding (GO:0016594)|L-serine ammonia-lyase activity (GO:0003941)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|serine racemase activity (GO:0030378)|threonine racemase activity (GO:0018114)			NS(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;3.24e-06)|READ - Rectum adenocarcinoma(1115;0.0649)	L-Serine(DB00133)	AACTTGGGTGAAGCAGGCTGA	0.393																																					p.K327E		Atlas-SNP	.											.	SRR	21	.	0			c.A979G						.						75	71	72					17																	2227123		2203	4300	6503	SO:0001583	missense	63826	exon8			TGGGTGAAGCAGG	AF169974	CCDS11017.1	17p13	2007-01-18			ENSG00000167720	ENSG00000167720			14398	protein-coding gene	gene with protein product		606477				17067558, 15953485, 15193426	Standard	NM_021947		Approved	ILV1, ISO1	uc002fue.1	Q9GZT4	OTTHUMG00000090583	ENST00000344595.5:c.979A>G	chr17.hg19:g.2227123A>G	ENSP00000339435:p.Lys327Glu	99.0	0.0		67.0	6.0	NM_021947	D3DTI5|Q6IA55	Missense_Mutation	SNP	ENST00000344595.5	hg19	CCDS11017.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.397930	0.25205	.	.	ENSG00000167720	ENST00000344595	D	0.99376	-5.79	5.26	1.7	0.24286	.	0.396760	0.31071	N	0.008311	D	0.94729	0.8299	N	0.08118	0	0.53688	D	0.999973	B	0.06786	0.001	B	0.04013	0.001	D	0.89397	0.3693	10	0.07813	T	0.8	0.8681	8.5224	0.33285	0.7649:0.0:0.2351:0.0	.	327	Q9GZT4	SRR_HUMAN	E	327	ENSP00000339435:K327E	ENSP00000339435:K327E	K	+	1	0	SRR	2173873	1.000000	0.71417	0.922000	0.36590	0.496000	0.33645	3.305000	0.51873	0.310000	0.22990	0.455000	0.32223	AAG	.	.		0.393	SRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207129.2	NM_021947		G	2227123	A	G	2227123	3	3	23	1	0	0	0	0	1	0	0	0	15181	247	9	2	1005	2	SRR	17	2227123	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1500250	2227123	78968087	882	2948										
RAP1GAP2	23108	hgsc.bcm.edu	37	chr17	2911342	2911342	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctcctggacaaccttcacgAtgagctccacgcccacacac	6	19	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:2911342A>G	ENST00000254695.8	+	17	1487	c.1397A>G	c.(1396-1398)gAt>gGt	p.D466G	RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.D451G|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.D466G|RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.D447G	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	466					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						AACCTTCACGATGAGCTCCAC	0.597																																					p.D466G		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.A1397G						.						61	67	65					17																	2911342		2077	4202	6279	SO:0001583	missense	23108	exon17			TTCACGATGAGCT	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 4", "GTPase activating Rap/RanGAP domain-like 4"	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1397A>G	chr17.hg19:g.2911342A>G	ENSP00000254695:p.Asp466Gly	116.0	0.0		52.0	42.0	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	hg19	CCDS45573.1	.	.	.	.	.	.	.	.	.	.	A	17.53	3.411652	0.62399	.	.	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.95573	0.8561	M	0.73598	2.24	0.80722	D	1	D;D	0.63046	0.992;0.986	P;P	0.60286	0.872;0.731	D	0.95599	0.8661	10	0.54805	T	0.06	-6.186	14.0619	0.64804	1.0:0.0:0.0:0.0	.	451;466	Q684P5-2;Q684P5	.;RPGP2_HUMAN	G	466;451;447;466	ENSP00000254695:D466G;ENSP00000389824:D451G;ENSP00000439688:D447G;ENSP00000444890:D466G	ENSP00000254695:D466G	D	+	2	0	RAP1GAP2	2858092	1.000000	0.71417	0.929000	0.37066	0.939000	0.58152	9.339000	0.96797	1.909000	0.55274	0.379000	0.24179	GAT	.	.		0.597	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2			G	2911342	A	G	2911342	3	3	23	1	0	0	0	0	1	0	0	0	13053	333	12	2	1463	2	RAP1GAP2	17	2911342	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	684219	2911342	78283868	883	2949										
OR1A1	8383	hgsc.bcm.edu	37	chr17	3119841	3119841	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttcaacaagagaatctcctcGtaaccaatgtgagggcctac	8	11	2	2	rs142898585		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:3119841G>A	ENST00000304094.1	+	1	927	c.927G>A	c.(925-927)tcG>tcA	p.S309S		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						GAATCTCCTCGTAACCAATGT	0.473													G|||	1	0.000199681	0	0	5008	,	,		19470	0		0.001	False		,,,				2504	0				p.S309S		Atlas-SNP	.											.	OR1A1	54	.	0			c.G927A						.	G		0,4406		0,0,2203	61	59	60		927	-1.8	0	17	dbSNP_134	60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR1A1	NM_014565.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		309/310	3119841	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8383	exon1			CTCCTCGTAACCA	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"GPCR / Class A : Olfactory receptors"	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.927G>A	chr17.hg19:g.3119841G>A		72.0	0.0		28.0	18.0	NM_014565	A5D914|Q6IFM1|Q6NTA9|Q96R87	Silent	SNP	ENST00000304094.1	hg19	CCDS11022.1																																																																																			.	G|1.000;A|0.000		0.473	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565		A	3119841	G	A	3119841	2	1	23	1	0	0	0	0	0	0	0	1	10958	1159	40	1		1	OR1A1	17	3119841	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	208499	3119841	78075369	884	2950										
TM4SF5	9032	hgsc.bcm.edu	37	chr17	4686302	4686302	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctggtgaacgcgaccattggTgtcttctgcggcgattgcag	14	10	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:4686302T>C	ENST00000270560.3	+	4	580	c.549T>C	c.(547-549)ggT>ggC	p.G183G		NM_003963.2	NP_003954.2	O14894	T4S5_HUMAN	transmembrane 4 L six family member 5	183						integral component of plasma membrane (GO:0005887)				large_intestine(2)|lung(3)|ovary(1)	6						CGACCATTGGTGTCTTCTGCG	0.562																																					p.G183G		Atlas-SNP	.											.	TM4SF5	26	.	0			c.T549C						.						144	118	127					17																	4686302		2203	4300	6503	SO:0001819	synonymous_variant	9032	exon4			CATTGGTGTCTTC	AF027204	CCDS11054.1	17p13.3	2007-01-06	2005-03-21		ENSG00000142484	ENSG00000142484			11857	protein-coding gene	gene with protein product		604657	"transmembrane 4 superfamily member 5"			9479038	Standard	NM_003963		Approved		uc002fyw.1	O14894	OTTHUMG00000090776	ENST00000270560.3:c.549T>C	chr17.hg19:g.4686302T>C		197.0	0.0		95.0	28.0	NM_003963	Q17RW9|Q6IB79	Silent	SNP	ENST00000270560.3	hg19	CCDS11054.1																																																																																			.	.		0.562	TM4SF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207558.2			C	4686302	T	C	4686302	2	2	23	1	0	0	0	0	0	0	0	1	15986	1683	59	2		2	TM4SF5	17	4686302	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1566461	4686302	76508908	885	2951										
DVL2	1856	hgsc.bcm.edu	37	chr17	7130768	7130768	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttgagccacatgcggtcccGgacttccagtccagactctg	10	15	1	2	rs372746877		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:7130768G>A	ENST00000005340.5	-	12	1600	c.1318C>T	c.(1318-1320)Cgg>Tgg	p.R440W	DVL2_ENST00000575458.1_Missense_Mutation_p.R434W|DVL2_ENST00000574642.1_5'Flank	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	440	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						ATGCGGTCCCGGACTTCCAGT	0.612																																					p.R440W		Atlas-SNP	.											.	DVL2	49	.	0			c.C1318T						.	G	TRP/ARG	0,4406		0,0,2203	68	71	70		1318	4.8	1	17		70	1,8599	1.2+/-3.3	0,1,4299	no	missense	DVL2	NM_004422.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	440/737	7130768	1,13005	2203	4300	6503	SO:0001583	missense	1856	exon12			GGTCCCGGACTTC	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"Dishevelled homologs"	3086	protein-coding gene	gene with protein product		602151	"dishevelled 2 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 2 (Drosophila)"			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.1318C>T	chr17.hg19:g.7130768G>A	ENSP00000005340:p.Arg440Trp	105.0	0.0		51.0	39.0	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	hg19	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.302374	0.81136	0.0	1.16E-4	ENSG00000004975	ENST00000005340	T	0.17370	2.28	4.76	4.76	0.60689	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	M	0.90814	3.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.60125	-0.7324	10	0.87932	D	0	-12.4618	15.2834	0.73806	0.0:0.0:1.0:0.0	.	434;440	B4DLQ0;O14641	.;DVL2_HUMAN	W	440	ENSP00000005340:R440W	ENSP00000005340:R440W	R	-	1	2	DVL2	7071492	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.475000	0.53136	2.482000	0.83794	0.655000	0.94253	CGG	.	.		0.612	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422		A	7130768	G	A	7130768	3	1	23	1	0	0	0	0	1	0	0	0	4838	1115	39	1	908	1	DVL2	17	7130768	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2444466	7130768	74064442	886	2952										
TP53	7157	hgsc.bcm.edu	37	chr17	7578275	7578277	+	In_Frame_Del	DEL	GAG	GAG	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttccactcggataagatgctGaggaggggccagacctaaga					rs587778718		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:7578275_7578277delGAG	ENST00000269305.4	-	6	761_763	c.572_574delCTC	c.(571-576)cctcag>cag	p.P191del	TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_In_Frame_Del_p.P191del|TP53_ENST00000359597.4_In_Frame_Del_p.P191del|TP53_ENST00000445888.2_In_Frame_Del_p.P191del|TP53_ENST00000420246.2_In_Frame_Del_p.P191del|TP53_ENST00000413465.2_In_Frame_Del_p.P191del	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	191	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> R (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q192*(83)|p.0?(8)|p.P191del(7)|p.Q99*(6)|p.?(6)|p.Q60*(6)|p.P191delP(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.P191L(2)|p.P191R(2)|p.G187fs*16(2)|p.P59delP(2)|p.P98delP(2)|p.P191fs*56(1)|p.P191fs*6(1)|p.A189_Q192>E(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P191H(1)|p.P191P(1)|p.P191_Q192delPQ(1)|p.D186_P191delDGLAPP(1)|p.Q192K(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.Q192fs*56(1)|p.Q192del(1)|p.Q192fs*16(1)|p.L188_P191del(1)|p.Q192fs*30(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATAAGATGCTGAGGAGGGGCCAG	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.191_192del	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,-1,2	TP53	33396	.	156	Substitution - Nonsense(95)|Deletion - In frame(23)|Deletion - Frameshift(8)|Whole gene deletion(8)|Complex - deletion inframe(6)|Unknown(6)|Substitution - Missense(6)|Insertion - Frameshift(2)|Complex - frameshift(1)|Substitution - coding silent(1)	breast(27)|ovary(21)|urinary_tract(15)|lung(13)|upper_aerodigestive_tract(12)|large_intestine(9)|skin(9)|oesophagus(8)|biliary_tract(7)|haematopoietic_and_lymphoid_tissue(6)|kidney(6)|stomach(5)|liver(5)|bone(4)|central_nervous_system(3)|pancreas(2)|cervix(1)|endometrium(1)|eye(1)|prostate(1)	c.573_575del	GRCh37	CD972478	TP53	D		.																																			SO:0001651	inframe_deletion	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.572_574delCTC	chr17.hg19:g.7578278_7578280delGAG	ENSP00000269305:p.Pro191del	215.0	0.0		85.0	63.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	In_Frame_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7578277	GAG	-	7578275	7	5	23	1	0	1	0	1	0	0	0	0	16396	1299	45	0	720	0	TP53	17	7578275	In_Frame_Del	DEL	GAG	TCGA-4R-AA8I-01A-11D-A382-10	447507	7578275	73616935	887	2953										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7667529	7667529	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggccaacgtggagactcagAtccctcccatacacgagcaa	9	14	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:7667529A>T	ENST00000572933.1	+	20	4734	c.3274A>T	c.(3274-3276)Atc>Ttc	p.I1092F	DNAH2_ENST00000389173.2_Missense_Mutation_p.I1092F			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1092	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GGAGACTCAGATCCCTCCCAT	0.552																																					p.I1092F		Atlas-SNP	.											.	DNAH2	498	.	0			c.A3274T						.						198	177	184					17																	7667529		2203	4300	6503	SO:0001583	missense	146754	exon19			ACTCAGATCCCTC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.3274A>T	chr17.hg19:g.7667529A>T	ENSP00000458355:p.Ile1092Phe	408.0	0.0		219.0	149.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	4.310	0.056889	0.08339	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.22336	1.96	4.66	4.66	0.58398	.	0.000000	0.64402	D	0.000002	T	0.08088	0.0202	N	0.03948	-0.315	0.80722	D	1	B	0.09022	0.002	B	0.13407	0.009	T	0.14364	-1.0475	10	0.02654	T	1	.	11.6042	0.51022	1.0:0.0:0.0:0.0	.	1092	Q9P225	DYH2_HUMAN	F	1092	ENSP00000373825:I1092F	ENSP00000353818:I1092F	I	+	1	0	DNAH2	7608254	1.000000	0.71417	1.000000	0.80357	0.592000	0.36648	8.156000	0.89645	1.732000	0.51606	0.454000	0.30748	ATC	.	.		0.552	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7667529	A	T	7667529	3	4	23	1	0	0	0	0	1	0	0	0	4604	333	12	4	3348	4	DNAH2	17	7667529	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	89254	7667529	73527681	888	2954										
C17orf59	54785	hgsc.bcm.edu	37	chr17	8092992	8092992	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gacggctggagaacgagcggCcggctctgctgcccgcggcc	17	15	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:8092992C>T	ENST00000389017.4	-	1	572	c.467G>A	c.(466-468)gGc>gAc	p.G156D	MIR3676_ENST00000579470.1_RNA	NM_017622.2	NP_060092.2	Q96GS4	CQ059_HUMAN	chromosome 17 open reading frame 59	156										large_intestine(2)|lung(3)|urinary_tract(1)	6						GAACGAGCGGCCGGCTCTGCT	0.726																																					p.G156D		Atlas-SNP	.											.	C17orf59	19	.	0			c.G467A						.						11	15	13					17																	8092992		2086	4132	6218	SO:0001583	missense	54785	exon1			GAGCGGCCGGCTC	BC018880	CCDS11133.2	17p13.1	2005-12-16			ENSG00000196544	ENSG00000196544			25939	protein-coding gene	gene with protein product						12477932	Standard	NM_017622		Approved	FLJ20014	uc010vut.2	Q96GS4	OTTHUMG00000153930	ENST00000389017.4:c.467G>A	chr17.hg19:g.8092992C>T	ENSP00000373669:p.Gly156Asp	30.0	0.0		23.0	10.0	NM_017622	Q53HS4|Q9NXW8	Missense_Mutation	SNP	ENST00000389017.4	hg19	CCDS11133.2	.	.	.	.	.	.	.	.	.	.	C	13.64	2.298762	0.40694	.	.	ENSG00000196544	ENST00000389017	.	.	.	4.83	3.87	0.44632	.	0.672971	0.13547	N	0.379765	T	0.27098	0.0664	L	0.29908	0.895	0.18873	N	0.999984	P	0.40602	0.723	B	0.38562	0.276	T	0.11690	-1.0577	9	0.72032	D	0.01	-7.7334	8.7548	0.34639	0.0:0.8981:0.0:0.1019	.	156	Q96GS4	CQ059_HUMAN	D	156	.	ENSP00000373669:G156D	G	-	2	0	C17orf59	8033717	0.127000	0.22367	0.229000	0.23960	0.071000	0.16799	1.524000	0.35942	1.281000	0.44480	0.561000	0.74099	GGC	.	.		0.726	C17orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333072.1	NM_017622		T	8092992	C	T	8092992	3	4	23	1	0	0	0	0	1	0	0	0	1869	739	26	3	610	3	C17orf59	17	8092992	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	425463	8092992	73102218	889	2955										
MYH1	4619	hgsc.bcm.edu	37	chr17	10408257	10408257	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caaattcttccttcatgttgGccatctccttctctgtctct	4	14	5	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:10408257G>A	ENST00000226207.5	-	22	2655	c.2561C>T	c.(2560-2562)gCc>gTc	p.A854V	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	854					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CTTCATGTTGGCCATCTCCTT	0.443																																					p.A854V		Atlas-SNP	.											.	MYH1	403	.	0			c.C2561T						.						155	144	148					17																	10408257		2203	4300	6503	SO:0001583	missense	4619	exon22			ATGTTGGCCATCT		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2561C>T	chr17.hg19:g.10408257G>A	ENSP00000226207:p.Ala854Val	114.0	0.0		166.0	43.0	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953120	0.73902	.	.	ENSG00000109061	ENST00000226207	D	0.93488	-3.23	5.48	5.48	0.80851	.	0.000000	0.42964	U	0.000638	D	0.94152	0.8124	M	0.87456	2.885	0.38141	D	0.938453	B	0.30511	0.282	B	0.34038	0.174	D	0.94392	0.7615	10	0.66056	D	0.02	.	14.5454	0.68027	0.0:0.0:0.8537:0.1463	.	854	P12882	MYH1_HUMAN	V	854	ENSP00000226207:A854V	ENSP00000226207:A854V	A	-	2	0	MYH1	10348982	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.396000	0.66297	2.749000	0.94314	0.655000	0.94253	GCC	.	.		0.443	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		A	10408257	G	A	10408257	3	1	23	1	0	0	0	0	1	0	0	0	10038	1203	42	3	3334	3	MYH1	17	10408257	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2315265	10408257	70786953	890	2956										
ELAC2	60528	hgsc.bcm.edu	37	chr17	12906873	12906873	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	accaccaaggccacgggggcAtctgcctttccttggtacct	10	15	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:12906873A>G	ENST00000338034.4	-	12	1241	c.1002T>C	c.(1000-1002)gaT>gaC	p.D334D	ELAC2_ENST00000426905.3_Silent_p.D294D|ELAC2_ENST00000609345.1_5'UTR|ELAC2_ENST00000395962.2_Silent_p.D315D	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	334					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						CCACGGGGGCATCTGCCTTTC	0.597											OREG0024189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D334D		Atlas-SNP	.											.	ELAC2	48	.	0			c.T1002C						.						117	95	102					17																	12906873		2203	4300	6503	SO:0001819	synonymous_variant	60528	exon12			GGGGGCATCTGCC	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"tRNase Z (long form)"	605367	"elaC (E. coli) homolog 2", "elaC homolog 2 (E. coli)"			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1002T>C	chr17.hg19:g.12906873A>G		59.0	0.0	683	65.0	23.0	NM_173717	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Silent	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	A	7.391	0.630710	0.14322	.	.	ENSG00000006744	ENST00000446899	.	.	.	5.19	-10.4	0.00318	.	.	.	.	.	T	0.14830	0.0358	.	.	.	0.23765	N	0.996904	.	.	.	.	.	.	T	0.10823	-1.0613	4	.	.	.	-5.6271	2.4027	0.04405	0.1234:0.3613:0.2621:0.2532	.	.	.	.	R	114	.	.	C	-	1	0	ELAC2	12847598	0.000000	0.05858	0.000000	0.03702	0.867000	0.49689	-0.464000	0.06688	-2.343000	0.00623	0.533000	0.62120	TGC	.	.		0.597	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5			G	12906873	A	G	12906873	2	3	23	1	0	0	0	0	0	0	0	1	5049	214	8	2		2	ELAC2	17	12906873	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2498616	12906873	68288337	891	2957										
ELAC2	60528	hgsc.bcm.edu	37	chr17	12919138	12919138	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagcccggtttcctttaaagTaagaatcattcctaaaaagg	7	8	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:12919138T>C	ENST00000338034.4	-	4	618	c.379A>G	c.(379-381)Act>Gct	p.T127A	ELAC2_ENST00000426905.3_Missense_Mutation_p.T127A|ELAC2_ENST00000609345.1_5'UTR|ELAC2_ENST00000395962.2_Missense_Mutation_p.T108A|ELAC2_ENST00000578071.1_Missense_Mutation_p.T127A	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	127					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						TCCTTTAAAGTAAGAATCATT	0.398																																					p.T127A		Atlas-SNP	.											.	ELAC2	48	.	0			c.A379G						.						106	109	108					17																	12919138		2203	4300	6503	SO:0001583	missense	60528	exon4			TTAAAGTAAGAAT	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"tRNase Z (long form)"	605367	"elaC (E. coli) homolog 2", "elaC homolog 2 (E. coli)"			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.379A>G	chr17.hg19:g.12919138T>C	ENSP00000337445:p.Thr127Ala	123.0	0.0		132.0	17.0	NM_001165962	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Missense_Mutation	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.284565	0.40394	.	.	ENSG00000006744	ENST00000426905;ENST00000338034;ENST00000395962	T;T;T	0.55234	0.53;0.53;0.53	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.66177	0.2763	M	0.77103	2.36	0.80722	D	1	P;D;D;P	0.59357	0.866;0.985;0.982;0.866	B;P;P;B	0.56278	0.341;0.786;0.795;0.414	T	0.71467	-0.4584	10	0.72032	D	0.01	-19.2318	11.7192	0.51672	0.0:0.0:0.0:1.0	.	127;110;108;127	B4DPL9;E9PGJ0;G5E9D5;Q9BQ52	.;.;.;RNZ2_HUMAN	A	127;127;108	ENSP00000405223:T127A;ENSP00000337445:T127A;ENSP00000379291:T108A	ENSP00000337445:T127A	T	-	1	0	ELAC2	12859863	1.000000	0.71417	0.786000	0.31890	0.997000	0.91878	6.774000	0.75012	1.855000	0.53841	0.528000	0.53228	ACT	.	.		0.398	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5			C	12919138	T	C	12919138	3	2	23	1	0	0	0	0	1	0	0	0	5049	1638	57	2	2185	2	ELAC2	17	12919138	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	12265	12919138	68276072	892	2958										
ELAC2	60528	hgsc.bcm.edu	37	chr17	12921261	12921261	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagcagcgagcaaagcgcccAcatgcgcccgtctccaccaa	9	18	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:12921261A>G	ENST00000338034.4	-	1	243	c.4T>C	c.(4-6)Tgg>Cgg	p.W2R	ELAC2_ENST00000426905.3_Missense_Mutation_p.W2R|ELAC2_ENST00000609345.1_5'Flank|ELAC2_ENST00000395962.2_Missense_Mutation_p.W2R|ELAC2_ENST00000578071.1_Missense_Mutation_p.W2R	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	2					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						CAAAGCGCCCACATGCGCCCG	0.697																																					p.W2R		Atlas-SNP	.											.	ELAC2	48	.	0			c.T4C						.						3	3	3					17																	12921261		1663	3368	5031	SO:0001583	missense	60528	exon1			GCGCCCACATGCG	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"tRNase Z (long form)"	605367	"elaC (E. coli) homolog 2", "elaC homolog 2 (E. coli)"			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.4T>C	chr17.hg19:g.12921261A>G	ENSP00000337445:p.Trp2Arg	72.0	0.0		46.0	8.0	NM_001165962	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Missense_Mutation	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.392730	0.83011	.	.	ENSG00000006744	ENST00000426905;ENST00000338034;ENST00000395962	T;T;T	0.65178	0.3;-0.08;-0.14	4.88	4.88	0.63580	.	0.063071	0.64402	D	0.000002	T	0.60090	0.2242	N	0.08118	0	0.35694	D	0.815067	D;D;D;D	0.71674	0.997;0.997;0.998;0.997	D;D;D;D	0.70935	0.936;0.936;0.971;0.936	T	0.71797	-0.4484	10	0.54805	T	0.06	-13.2928	12.7538	0.57323	1.0:0.0:0.0:0.0	.	2;2;2;2	B4DPL9;E9PGJ0;G5E9D5;Q9BQ52	.;.;.;RNZ2_HUMAN	R	2	ENSP00000405223:W2R;ENSP00000337445:W2R;ENSP00000379291:W2R	ENSP00000337445:W2R	W	-	1	0	ELAC2	12861986	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	1.763000	0.38461	2.164000	0.68074	0.533000	0.62120	TGG	.	.		0.697	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5			G	12921261	A	G	12921261	3	3	23	1	0	0	0	0	1	0	0	0	5049	159	6	2	2572	2	ELAC2	17	12921261	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2123	12921261	68273949	893	2959										
LLGL1	3996	hgsc.bcm.edu	37	chr17	18138832	18138832	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggcccaggagccgtcacagCgagggctgctgctgacgggg	18	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:18138832C>T	ENST00000316843.4	+	11	1429	c.1333C>T	c.(1333-1335)Cga>Tga	p.R445*		NM_004140.3	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1 (Drosophila)	445					axonogenesis (GO:0007409)|cortical actin cytoskeleton organization (GO:0030866)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|maintenance of apical/basal cell polarity (GO:0035090)|positive regulation of Rab GTPase activity (GO:0032851)|protein complex assembly (GO:0006461)	cell projection (GO:0042995)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome membrane (GO:0031901)|Golgi cis cisterna (GO:0000137)|myelin sheath abaxonal region (GO:0035748)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)|structural molecule activity (GO:0005198)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_neural(463;0.228)					GCCGTCACAGCGAGGGCTGCT	0.637																																					p.R445X		Atlas-SNP	.											.	LLGL1	61	.	0			c.C1333T						.						87	78	81					17																	18138832		2203	4300	6503	SO:0001587	stop_gained	3996	exon11			TCACAGCGAGGGC		CCDS32586.1	17p11.2	2013-01-10	2001-11-28		ENSG00000131899	ENSG00000131899		"WD repeat domain containing"	6628	protein-coding gene	gene with protein product		600966	"lethal giant larvae (Drosophila) homolog 1"	DLG4, LLGL, HUGL, HUGL-1		7542763, 8565641	Standard	XM_005256643		Approved		uc002gsp.3	Q15334	OTTHUMG00000059396	ENST00000316843.4:c.1333C>T	chr17.hg19:g.18138832C>T	ENSP00000321537:p.Arg445*	55.0	0.0		83.0	34.0	NM_004140	A7MBM7|O00188|Q58F11|Q86UK6	Nonsense_Mutation	SNP	ENST00000316843.4	hg19	CCDS32586.1	.	.	.	.	.	.	.	.	.	.	C	37	6.043830	0.97231	.	.	ENSG00000131899	ENST00000316843	.	.	.	5.19	1.91	0.25777	.	0.244039	0.40385	N	0.001113	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.1751	7.7692	0.28997	0.3714:0.5498:0.0:0.0788	.	.	.	.	X	445	.	ENSP00000321537:R445X	R	+	1	2	LLGL1	18079557	0.997000	0.39634	0.989000	0.46669	0.483000	0.33249	0.819000	0.27308	0.883000	0.36040	0.650000	0.86243	CGA	.	.		0.637	LLGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132067.3			T	18138832	C	T	18138832	4	4	23	1	0	0	0	0	0	1	0	0	8842	760	27	1	1375	1	LLGL1	17	18138832	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5217571	18138832	63056378	894	2960										
MAPK7	5598	hgsc.bcm.edu	37	chr17	19284128	19284128	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcaagattggtgactttggTatggctcgtggcctgtgcac	13	9	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:19284128T>C	ENST00000308406.5	+	4	992	c.606T>C	c.(604-606)ggT>ggC	p.G202G	MAPK7_ENST00000571657.1_Intron|MFAP4_ENST00000574313.2_5'Flank|B9D1_ENST00000468679.3_5'Flank|MAPK7_ENST00000395604.3_Silent_p.G202G|MAPK7_ENST00000299612.7_Silent_p.G63G|B9D1_ENST00000477478.2_5'Flank|B9D1_ENST00000575403.1_5'Flank|MAPK7_ENST00000395602.4_Silent_p.G202G	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	202	Necessary for oligomerization. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)			autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					GTGACTTTGGTATGGCTCGTG	0.557																																					p.G202G		Atlas-SNP	.											.	MAPK7	72	.	0			c.T606C						.						128	107	114					17																	19284128		2203	4300	6503	SO:0001819	synonymous_variant	5598	exon4			CTTTGGTATGGCT	U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"Mitogen-activated protein kinase cascade / Kinases"	6880	protein-coding gene	gene with protein product	"BMK1 kinase", "extracellular-signal-regulated kinase 5"	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.606T>C	chr17.hg19:g.19284128T>C		108.0	0.0		128.0	61.0	NM_002749	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Silent	SNP	ENST00000308406.5	hg19	CCDS11206.1																																																																																			.	.		0.557	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033		C	19284128	T	C	19284128	2	2	23	1	0	0	0	0	0	0	0	1	9291	1625	57	2		2	MAPK7	17	19284128	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1145296	19284128	61911082	895	2961										
NOS2	4843	hgsc.bcm.edu	37	chr17	26096024	26096024	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgaaggtttgcacggcccaGctgcggaaggcgtcctcctg	14	12	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:26096024G>T	ENST00000313735.6	-	17	2246	c.2013C>A	c.(2011-2013)agC>agA	p.S671R		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	671	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GCACGGCCCAGCTGCGGAAGG	0.612																																					p.S671R		Atlas-SNP	.											.	NOS2	113	.	0			c.C2013A						.						51	45	47					17																	26096024		2203	4299	6502	SO:0001583	missense	4843	exon17			GGCCCAGCTGCGG	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"nitric oxide synthase 2A (inducible, hepatocytes)"	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2013C>A	chr17.hg19:g.26096024G>T	ENSP00000327251:p.Ser671Arg	27.0	0.0		34.0	15.0	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	hg19	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.788330	0.49997	.	.	ENSG00000007171	ENST00000313735;ENST00000379105;ENST00000302153	T	0.59224	0.28	5.16	5.16	0.70880	Flavodoxin/nitric oxide synthase (2);	0.332353	0.32884	N	0.005540	T	0.50718	0.1632	L	0.31526	0.94	0.42957	D	0.994392	B;P	0.38129	0.032;0.619	B;B	0.43123	0.075;0.409	T	0.48703	-0.9012	10	0.30078	T	0.28	.	14.2421	0.65963	0.0:0.0:0.8507:0.1493	.	636;671	F8WEM3;P35228	.;NOS2_HUMAN	R	671;632;636	ENSP00000327251:S671R	ENSP00000305638:S636R	S	-	3	2	NOS2	23120151	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.442000	0.44873	2.397000	0.81536	0.462000	0.41574	AGC	.	.		0.612	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		T	26096024	G	T	26096024	3	4	23	1	0	0	0	0	1	0	0	0	10552	962	34	3	1492	3	NOS2	17	26096024	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	6811896	26096024	55099186	896	2962										
SLC46A1	113235	hgsc.bcm.edu	37	chr17	26731651	26731651	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tacctgtgaacatgagaggcGtgatagtggcaaaggcaaag	14	6	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:26731651G>A	ENST00000440501.1	-	2	1159	c.1064C>T	c.(1063-1065)aCg>aTg	p.T355M	SLC46A1_ENST00000321666.5_Missense_Mutation_p.T355M|CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000584729.1_5'UTR|CTD-2350C19.2_ENST00000580714.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	355					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	CATGAGAGGCGTGATAGTGGC	0.592																																					p.T355M		Atlas-SNP	.											.	SLC46A1	17	.	0			c.C1064T						.						41	40	40					17																	26731651		2006	4178	6184	SO:0001583	missense	113235	exon2			AGAGGCGTGATAG	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"Solute carriers"	30521	protein-coding gene	gene with protein product	"heme carrier protein 1", "proton-coupled folate transporter"	611672	"solute carrier family 46, member 1"			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.1064C>T	chr17.hg19:g.26731651G>A	ENSP00000395653:p.Thr355Met	96.0	0.0		99.0	45.0	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Missense_Mutation	SNP	ENST00000440501.1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.74	3.883402	0.72410	.	.	ENSG00000076351	ENST00000440501;ENST00000321666	T;T	0.57752	0.38;0.38	5.11	5.11	0.69529	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.72969	0.3527	.	.	.	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.72899	-0.4152	9	0.39692	T	0.17	-6.3156	18.5385	0.91019	0.0:0.0:1.0:0.0	.	355;355;355	B4DJ17;Q96NT5-2;Q96NT5	.;.;PCFT_HUMAN	M	355	ENSP00000395653:T355M;ENSP00000318828:T355M	ENSP00000318828:T355M	T	-	2	0	SLC46A1	23755778	1.000000	0.71417	0.997000	0.53966	0.702000	0.40608	9.444000	0.97578	2.360000	0.80028	0.563000	0.77884	ACG	.	.		0.592	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		A	26731651	G	A	26731651	3	1	23	1	0	0	0	0	1	0	0	0	14659	1145	40	1	332	1	SLC46A1	17	26731651	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	635627	26731651	54463559	897	2963										
SLC46A1	113235	hgsc.bcm.edu	37	chr17	26732401	26732401	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccacactgtcgctccaagctCccagcagggtggacgagaag	12	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:26732401C>T	ENST00000440501.1	-	2	409	c.314G>A	c.(313-315)gGa>gAa	p.G105E	SLC46A1_ENST00000321666.5_Missense_Mutation_p.G105E|CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000584729.1_5'UTR|CTD-2350C19.2_ENST00000580714.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	105					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	GCTCCAAGCTCCCAGCAGGGT	0.642																																					p.G105E		Atlas-SNP	.											.	SLC46A1	17	.	0			c.G314A						.						11	15	14					17																	26732401		2027	4173	6200	SO:0001583	missense	113235	exon2			CAAGCTCCCAGCA	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"Solute carriers"	30521	protein-coding gene	gene with protein product	"heme carrier protein 1", "proton-coupled folate transporter"	611672	"solute carrier family 46, member 1"			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.314G>A	chr17.hg19:g.26732401C>T	ENSP00000395653:p.Gly105Glu	180.0	0.0		182.0	72.0	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Missense_Mutation	SNP	ENST00000440501.1	hg19		.	.	.	.	.	.	.	.	.	.	c	16.21	3.059212	0.55325	.	.	ENSG00000076351	ENST00000440501;ENST00000321666	T;T	0.73469	-0.75;-0.75	5.38	5.38	0.77491	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Sugar transporter, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.87430	0.6175	.	.	.	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.998;1.0	D	0.88579	0.3135	9	0.87932	D	0	-8.5213	19.0886	0.93217	0.0:1.0:0.0:0.0	.	105;105;105	B4DJ17;Q96NT5-2;Q96NT5	.;.;PCFT_HUMAN	E	105	ENSP00000395653:G105E;ENSP00000318828:G105E	ENSP00000318828:G105E	G	-	2	0	SLC46A1	23756528	1.000000	0.71417	0.999000	0.59377	0.950000	0.60333	7.391000	0.79828	2.685000	0.91497	0.556000	0.70494	GGA	.	.		0.642	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		T	26732401	C	T	26732401	3	4	23	1	0	0	0	0	1	0	0	0	14659	855	30	3	1082	3	SLC46A1	17	26732401	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	750	26732401	54462809	898	2964										
NEK8	284086	hgsc.bcm.edu	37	chr17	27061037	27061037	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgcgaaaggctgaccagaaGctggtgatcatcaagcagat	12	9	2	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:27061037G>T	ENST00000268766.6	+	2	118	c.84G>T	c.(82-84)aaG>aaT	p.K28N	AC010761.6_ENST00000584779.1_RNA|NEK8_ENST00000593261.1_3'UTR	NM_178170.2	NP_835464.1	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	28	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				organ morphogenesis (GO:0009887)|regulation of hippo signaling (GO:0035330)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|primary cilium (GO:0072372)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Lung NSC(42;0.0158)					CTGACCAGAAGCTGGTGATCA	0.572																																					p.K28N	NSCLC(6;19 293 14866 25253 49845)	Atlas-SNP	.											.	NEK8	76	.	0			c.G84T						.						94	84	88					17																	27061037		2203	4300	6503	SO:0001583	missense	284086	exon2			CCAGAAGCTGGTG	AY267371	CCDS32597.1	17q11.1	2012-11-15	2012-11-15			ENSG00000160602			13387	protein-coding gene	gene with protein product		609799	"NIMA (never in mitosis gene a)- related kinase 8"			18199800	Standard	NM_178170		Approved	NPHP9	uc002hcp.3	Q86SG6		ENST00000268766.6:c.84G>T	chr17.hg19:g.27061037G>T	ENSP00000268766:p.Lys28Asn	89.0	0.0		90.0	24.0	NM_178170	A6NIC5|Q14CL7|Q2M1S6|Q8NDH1	Missense_Mutation	SNP	ENST00000268766.6	hg19	CCDS32597.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.360634	0.41801	.	.	ENSG00000160602	ENST00000543014;ENST00000268766	T;T	0.67698	-0.28;-0.28	4.92	3.93	0.45458	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.107611	0.64402	D	0.000006	T	0.59376	0.2189	L	0.39467	1.215	0.43321	D	0.995347	B	0.23128	0.08	B	0.29942	0.109	T	0.61964	-0.6954	10	0.56958	D	0.05	.	12.7217	0.57146	0.0814:0.0:0.9186:0.0	.	28	Q86SG6	NEK8_HUMAN	N	28	ENSP00000465859:K28N;ENSP00000268766:K28N	ENSP00000268766:K28N	K	+	3	2	NEK8	24085164	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.319000	0.33655	2.267000	0.75376	0.313000	0.20887	AAG	.	.		0.572	NEK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446467.2			T	27061037	G	T	27061037	3	4	23	1	0	0	0	0	1	0	0	0	10339	962	34	3	90	3	NEK8	17	27061037	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	328636	27061037	54134173	899	2965										
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28419089	28419089	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagccaacgtgaaactagtgCgtgacatcctgaaggcggtt	12	9	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:28419089C>T	ENST00000394835.3	+	21	4330	c.4138C>T	c.(4138-4140)Cgt>Tgt	p.R1380C	RP11-1148O4.2_ENST00000582938.1_RNA|EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000320856.5_Missense_Mutation_p.R1256C	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1380							calcium ion binding (GO:0005509)	p.R1380C(1)		breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						GAAACTAGTGCGTGACATCCT	0.388																																					p.R1380C		Atlas-SNP	.											EFCAB5,NS,carcinoma,0,1	EFCAB5	122	.	1	Substitution - Missense(1)	lung(1)	c.C4138T						.						85	86	86					17																	28419089		1906	4126	6032	SO:0001583	missense	374786	exon21			CTAGTGCGTGACA	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.4138C>T	chr17.hg19:g.28419089C>T	ENSP00000378312:p.Arg1380Cys	163.0	0.0		143.0	43.0	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	hg19	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	C	15.94	2.980031	0.53827	.	.	ENSG00000176927	ENST00000394835;ENST00000320856;ENST00000419434	T;T;T	0.10477	2.87;2.87;2.88	5.75	5.75	0.90469	.	0.521011	0.21036	N	0.081252	T	0.08758	0.0217	N	0.08118	0	0.80722	D	1	D;D	0.57257	0.979;0.979	B;B	0.43123	0.409;0.409	T	0.24083	-1.0170	10	0.87932	D	0	-0.1214	18.943	0.92611	0.0:1.0:0.0:0.0	.	1256;1380	E7EVS9;A4FU69	.;EFCB5_HUMAN	C	1380;1256;1062	ENSP00000378312:R1380C;ENSP00000322003:R1256C;ENSP00000417009:R1062C	ENSP00000322003:R1256C	R	+	1	0	EFCAB5	25443215	0.063000	0.20901	0.011000	0.14972	0.025000	0.11179	2.608000	0.46308	2.714000	0.92807	0.655000	0.94253	CGT	.	.		0.388	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		T	28419089	C	T	28419089	3	4	23	1	0	0	0	0	1	0	0	0	4940	768	27	1	4387	1	EFCAB5	17	28419089	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1358052	28419089	52776121	900	2966										
PSMD11	5717	hgsc.bcm.edu	37	chr17	30806365	30806365	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tactagaacagaatctgatcCgagtcattgagcctttttcc	7	10	2	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:30806365C>T	ENST00000261712.3	+	10	1272	c.1009C>T	c.(1009-1011)Cga>Tga	p.R337*	PSMD11_ENST00000457654.2_Nonsense_Mutation_p.R337*	NM_001270482.1|NM_002815.3	NP_001257411.1|NP_002806.2	O00231	PSD11_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	337	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome assembly (GO:0043248)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stem cell differentiation (GO:0048863)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			GAATCTGATCCGAGTCATTGA	0.517																																					p.R337X	Ovarian(130;1038 1716 9294 11987 19279)	Atlas-SNP	.											.	PSMD11	41	.	0			c.C1009T						.						136	131	132					17																	30806365		2203	4300	6503	SO:0001587	stop_gained	5717	exon10			CTGATCCGAGTCA	AB003102	CCDS11272.1	17q12	2008-05-22			ENSG00000108671	ENSG00000108671		"Proteasome (prosome, macropain) subunits"	9556	protein-coding gene	gene with protein product		604449				9426256, 9119060	Standard	NM_001270482		Approved	S9, p44.5, MGC3844, Rpn6	uc010cta.2	O00231	OTTHUMG00000132811	ENST00000261712.3:c.1009C>T	chr17.hg19:g.30806365C>T	ENSP00000261712:p.Arg337*	136.0	0.0		93.0	36.0	NM_002815	A8K3I7|E1P663|O00495|Q53FT5	Nonsense_Mutation	SNP	ENST00000261712.3	hg19	CCDS11272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.459853|5.459853	0.96240|0.96240	.|.	.|.	ENSG00000108671|ENSG00000108671	ENST00000457654|ENST00000261712	.|.	.|.	.|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.43875|.	0.1267|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.36504|.	-0.9745|.	3|.	.|0.02654	.|T	.|1	-2.6927|-2.6927	16.7464|16.7464	0.85473|0.85473	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	L|X	74|337	.|.	.|ENSP00000261712:R337X	P|R	+|+	2|1	0|2	PSMD11|PSMD11	27830478|27830478	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	1.912000|1.912000	0.39946|0.39946	2.826000|2.826000	0.97356|0.97356	0.561000|0.561000	0.74099|0.74099	CCG|CGA	.	.		0.517	PSMD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256252.2	NM_002815		T	30806365	C	T	30806365	4	4	23	1	0	0	0	0	0	1	0	0	12706	644	23	1	1047	1	PSMD11	17	30806365	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2387276	30806365	50388845	901	2967										
LIG3	3980	hgsc.bcm.edu	37	chr17	33325644	33325644	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtacatatgagcctgggaagCggcactggctgaaagtgaag	15	7	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:33325644C>T	ENST00000378526.4	+	14	2144	c.2011C>T	c.(2011-2013)Cgg>Tgg	p.R671W	LIG3_ENST00000262327.5_Missense_Mutation_p.R671W	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	671					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	GCCTGGGAAGCGGCACTGGCT	0.532								Other BER factors			OREG0024326	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R671W		Atlas-SNP	.											.	LIG3	164	.	0			c.C2011T						.						119	128	125					17																	33325644		2203	4300	6503	SO:0001583	missense	3980	exon14			GGGAAGCGGCACT		CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"ligase II, DNA, ATP-dependent"	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.2011C>T	chr17.hg19:g.33325644C>T	ENSP00000367787:p.Arg671Trp	84.0	0.0	839	83.0	33.0	NM_013975	Q16714|Q6NVK3	Missense_Mutation	SNP	ENST00000378526.4	hg19	CCDS11284.2	.	.	.	.	.	.	.	.	.	.	C	27.5	4.841329	0.91197	.	.	ENSG00000005156	ENST00000378526;ENST00000262327	D;D	0.87334	-2.24;-2.24	5.27	4.29	0.51040	DNA ligase, ATP-dependent, central (2);DNA ligase, ATP-dependent, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.96207	0.8763	H	0.98901	4.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97697	1.0182	10	0.87932	D	0	-8.4847	14.4308	0.67249	0.1483:0.8517:0.0:0.0	.	671;671	P49916;E5KLB6	DNLI3_HUMAN;.	W	671	ENSP00000367787:R671W;ENSP00000262327:R671W	ENSP00000262327:R671W	R	+	1	2	LIG3	30349757	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.745000	0.68672	1.426000	0.47256	0.655000	0.94253	CGG	.	.		0.532	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975		T	33325644	C	T	33325644	3	4	23	1	0	0	0	0	1	0	0	0	8791	759	27	1	2061	1	LIG3	17	33325644	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2519279	33325644	47869566	902	2968										
LIG3	3980	hgsc.bcm.edu	37	chr17	33329755	33329755	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggccacaaagtcttctccaGtgaaagtaggggagaagcgg	14	8	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:33329755G>T	ENST00000378526.4	+	19	2876	c.2743G>T	c.(2743-2745)Gtg>Ttg	p.V915L	RP5-837J1.2_ENST00000578488.1_RNA|LIG3_ENST00000262327.5_Missense_Mutation_p.V915L	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	915					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	GTCTTCTCCAGTGAAAGTAGG	0.552								Other BER factors																													p.V915L		Atlas-SNP	.											.	LIG3	164	.	0			c.G2743T						.						66	54	58					17																	33329755		2203	4300	6503	SO:0001583	missense	3980	exon19			TCTCCAGTGAAAG		CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"ligase II, DNA, ATP-dependent"	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.2743G>T	chr17.hg19:g.33329755G>T	ENSP00000367787:p.Val915Leu	234.0	0.0		224.0	89.0	NM_013975	Q16714|Q6NVK3	Missense_Mutation	SNP	ENST00000378526.4	hg19	CCDS11284.2	.	.	.	.	.	.	.	.	.	.	G	9.380	1.072830	0.20147	.	.	ENSG00000005156	ENST00000378526;ENST00000262327	T;T	0.61742	0.22;0.08	3.51	2.52	0.30459	.	0.704560	0.13672	N	0.370811	T	0.43897	0.1268	L	0.43152	1.355	0.24286	N	0.995189	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.25502	-1.0130	10	0.13470	T	0.59	-6.2242	8.27	0.31838	0.0:0.0:0.7635:0.2365	.	915;915	P49916;E5KLB6	DNLI3_HUMAN;.	L	915	ENSP00000367787:V915L;ENSP00000262327:V915L	ENSP00000262327:V915L	V	+	1	0	LIG3	30353868	.	.	0.285000	0.24819	0.753000	0.42808	.	.	1.033000	0.39918	0.563000	0.77884	GTG	.	.		0.552	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975		T	33329755	G	T	33329755	3	4	23	1	0	0	0	0	1	0	0	0	8791	1029	36	3	2813	3	LIG3	17	33329755	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	4111	33329755	47865455	903	2969										
CCL15	6359	hgsc.bcm.edu	37	chr17	34324830	34324830	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagtagggcttcagctttttCatgcaatcctgaactcccgg	10	11	2	1	rs551984257	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:34324830C>T	ENST00000354059.4	-	4	867	c.315G>A	c.(313-315)atG>atA	p.M105I	CCL14_ENST00000536149.1_5'UTR|CCL15-CCL14_ENST00000481427.2_Missense_Mutation_p.M105I	NM_032965.4	NP_116741.1	Q16663	CCL15_HUMAN	chemokine (C-C motif) ligand 15	105					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|immune response (GO:0006955)|positive chemotaxis (GO:0050918)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)|receptor binding (GO:0005102)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCAGCTTTTTCATGCAATCCT	0.468													C|||	2	0.000399361	0	0	5008	,	,		16643	0		0	False		,,,				2504	0.002				p.M105I		Atlas-SNP	.											.	CCL15	15	.	0			c.G315A						.						78	74	76					17																	34324830		2203	4300	6503	SO:0001583	missense	6359	exon4			CTTTTTCATGCAA	AF031587	CCDS11304.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000267596	ENSG00000275718		"Chemokine ligands", "Endogenous ligands"	10613	protein-coding gene	gene with protein product	"leukotactin 1", "CC chemokine 3", "macrophage inflammatory protein 5", "chemokine CC-2", "MIP-1 delta"	601393	"small inducible cytokine subfamily A (Cys-Cys), member 15"	SCYA15		8661057	Standard	NM_032965		Approved	HCC-2, NCC-3, SCYL3, MIP-5, Lkn-1, MIP-1d, HMRP-2B	uc010wcu.2	Q16663	OTTHUMG00000188406	ENST00000354059.4:c.315G>A	chr17.hg19:g.34324830C>T	ENSP00000293276:p.Met105Ile	76.0	0.0		103.0	7.0	NM_032965	B2RU34|E1P651|Q9UM74	Missense_Mutation	SNP	ENST00000354059.4	hg19	CCDS11304.1	.	.	.	.	.	.	.	.	.	.	C	0.230	-1.022123	0.02061	.	.	ENSG00000161574	ENST00000354059	T	0.04194	3.68	4.72	-3.32	0.04973	Chemokine interleukin-8-like domain (3);	1.213440	0.06406	N	0.719711	T	0.01800	0.0057	N	0.05534	-0.03	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.43925	-0.9361	10	0.06099	T	0.92	.	0.8665	0.01205	0.1487:0.2889:0.2735:0.289	.	105	Q16663	CCL15_HUMAN	I	105	ENSP00000293276:M105I	ENSP00000293276:M105I	M	-	3	0	CCL15	31348943	0.033000	0.19621	0.050000	0.19076	0.009000	0.06853	-0.032000	0.12266	-0.640000	0.05495	-0.469000	0.05056	ATG	.	.		0.468	CCL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256584.2	NM_004167		T	34324830	C	T	34324830	3	4	23	1	0	0	0	0	1	0	0	0	2888	826	29	3	30	3	CCL15	17	34324830	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	995075	34324830	46870380	904	2970										
AATF	26574	hgsc.bcm.edu	37	chr17	35310201	35310201	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtagatgaggaaatatctgAtgaggaagggtctggagatg	16	2	2	5			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:35310201A>G	ENST00000225402.5	+	3	550	c.299A>G	c.(298-300)gAt>gGt	p.D100G		NM_012138.3	NP_036270.1	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor	100	Glu-rich.				apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|embryonic cleavage (GO:0040016)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of apoptotic process (GO:0043066)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of superoxide anion generation (GO:0032929)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mitotic cell cycle (GO:0007346)|ribosome biogenesis (GO:0042254)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	leucine zipper domain binding (GO:0043522)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)	18		Breast(25;0.00607)				GAAATATCTGATGAGGAAGGG	0.453																																					p.D100G	NSCLC(49;901 1159 19183 41572 46244)	Atlas-SNP	.											.	AATF	36	.	0			c.A299G						.						77	80	79					17																	35310201		2203	4300	6503	SO:0001583	missense	26574	exon3			TATCTGATGAGGA	AF083208	CCDS32632.1	17q12	2014-05-06			ENSG00000108270	ENSG00000275700			19235	protein-coding gene	gene with protein product		608463				11027528, 10783144	Standard	NM_012138		Approved	DED, CHE-1, CHE1, BFR2	uc002hni.3	Q9NY61	OTTHUMG00000188458	ENST00000225402.5:c.299A>G	chr17.hg19:g.35310201A>G	ENSP00000225402:p.Asp100Gly	156.0	0.0		165.0	55.0	NM_012138	A6NCJ6|B3KQ26|Q9P0A4|Q9UNX5	Missense_Mutation	SNP	ENST00000225402.5	hg19	CCDS32632.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.782088	0.31502	.	.	ENSG00000108270	ENST00000225402	T	0.31247	1.5	5.84	4.75	0.60458	.	0.147974	0.64402	D	0.000016	T	0.32194	0.0821	M	0.64997	1.995	0.45554	D	0.998507	P	0.39060	0.657	B	0.37650	0.255	T	0.07616	-1.0763	10	0.52906	T	0.07	-2.2421	11.5879	0.50929	0.8509:0.1491:0.0:0.0	.	100	Q9NY61	AATF_HUMAN	G	100	ENSP00000225402:D100G	ENSP00000225402:D100G	D	+	2	0	AATF	32384314	1.000000	0.71417	0.379000	0.26080	0.006000	0.05464	4.056000	0.57448	1.003000	0.39130	0.533000	0.62120	GAT	.	.		0.453	AATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451543.1	NM_012138		G	35310201	A	G	35310201	3	3	23	1	0	0	0	0	1	0	0	0	25	333	12	2	309	2	AATF	17	35310201	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	985371	35310201	45885009	905	2971										
AATF	26574	hgsc.bcm.edu	37	chr17	35346611	35346611	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	attctgatggacaaagagagAttacttcgaaggacacagac	10	7	1	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:35346611A>T	ENST00000225402.5	+	7	1466	c.1215A>T	c.(1213-1215)agA>agT	p.R405S		NM_012138.3	NP_036270.1	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor	405	RB1 and SP1 binding.				apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|embryonic cleavage (GO:0040016)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of apoptotic process (GO:0043066)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of superoxide anion generation (GO:0032929)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mitotic cell cycle (GO:0007346)|ribosome biogenesis (GO:0042254)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	leucine zipper domain binding (GO:0043522)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)	18		Breast(25;0.00607)				ACAAAGAGAGATTACTTCGAA	0.493																																					p.R405S	NSCLC(49;901 1159 19183 41572 46244)	Atlas-SNP	.											.	AATF	36	.	0			c.A1215T						.						279	270	273					17																	35346611		2203	4300	6503	SO:0001583	missense	26574	exon7			AGAGAGATTACTT	AF083208	CCDS32632.1	17q12	2014-05-06			ENSG00000108270	ENSG00000275700			19235	protein-coding gene	gene with protein product		608463				11027528, 10783144	Standard	NM_012138		Approved	DED, CHE-1, CHE1, BFR2	uc002hni.3	Q9NY61	OTTHUMG00000188458	ENST00000225402.5:c.1215A>T	chr17.hg19:g.35346611A>T	ENSP00000225402:p.Arg405Ser	89.0	0.0		73.0	25.0	NM_012138	A6NCJ6|B3KQ26|Q9P0A4|Q9UNX5	Missense_Mutation	SNP	ENST00000225402.5	hg19	CCDS32632.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.980851	0.74474	.	.	ENSG00000108270	ENST00000225402	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.80303	0.4598	M	0.88105	2.93	0.54753	D	0.999985	D	0.89917	1.0	D	0.76071	0.987	T	0.83111	-0.0123	9	0.62326	D	0.03	-15.7616	10.3345	0.43841	0.8532:0.0:0.0:0.1467	.	405	Q9NY61	AATF_HUMAN	S	405	.	ENSP00000225402:R405S	R	+	3	2	AATF	32420724	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	1.316000	0.33620	1.963000	0.57068	0.383000	0.25322	AGA	.	.		0.493	AATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451543.1	NM_012138		T	35346611	A	T	35346611	3	4	23	1	0	0	0	0	1	0	0	0	25	330	12	4	1241	4	AATF	17	35346611	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	36410	35346611	45848599	906	2972										
ACACA	31	hgsc.bcm.edu	37	chr17	35620662	35620662	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aataatcttctgatgcctgcGttgtacagagcaatcacgac	8	10	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:35620662G>A	ENST00000394406.2	-	11	1334	c.1144C>T	c.(1144-1146)Cgc>Tgc	p.R382C	ACACA_ENST00000353139.5_Missense_Mutation_p.R419C|ACACA_ENST00000335166.5_Missense_Mutation_p.R304C|ACACA_ENST00000360679.3_Missense_Mutation_p.R324C	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	382	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TGATGCCTGCGTTGTACAGAG	0.418																																					p.R419C	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											ACACA_ENST00000353139,NS,malignant_melanoma,0,2	ACACA	395	.	0			c.C1255T						.						259	235	243					17																	35620662		2203	4300	6503	SO:0001583	missense	31	exon11			GCCTGCGTTGTAC	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.1144C>T	chr17.hg19:g.35620662G>A	ENSP00000377928:p.Arg382Cys	123.0	0.0		142.0	62.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	hg19	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.930444	0.92389	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	D;D;D;D	0.97924	-4.61;-4.61;-4.61;-4.61	5.78	4.78	0.61160	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.000000	0.85682	D	0.000000	D	0.99390	0.9785	H	0.99689	4.705	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97936	1.0323	10	0.87932	D	0	-10.3882	16.221	0.82258	0.0:0.0:0.8665:0.1335	.	419;382;324	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	C	419;324;382;406;304	ENSP00000344789:R419C;ENSP00000353898:R324C;ENSP00000377928:R382C;ENSP00000335323:R304C	ENSP00000335323:R304C	R	-	1	0	ACACA	32694775	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	6.744000	0.74854	2.722000	0.93159	0.655000	0.94253	CGC	.	.		0.418	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		A	35620662	G	A	35620662	3	1	23	1	0	0	0	0	1	0	0	0	106	1145	40	1	6080	1	ACACA	17	35620662	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	274051	35620662	45574548	907	2973										
MED1	5469	hgsc.bcm.edu	37	chr17	37584012	37584012	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcatccagtaggtcagaaggAgagacatagtacttcaggtt	11	7	3	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:37584012A>G	ENST00000394287.3	-	10	886	c.681T>C	c.(679-681)tcT>tcC	p.S227S	MED1_ENST00000300651.6_Silent_p.S227S			O95243	MBD4_HUMAN	mediator complex subunit 1	112					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		GGTCAGAAGGAGAGACATAGT	0.318										HNSCC(31;0.082)																											p.S227S	Pancreas(21;279 768 2492 4877 24026)	Atlas-SNP	.											.	MED1	123	.	0			c.T681C						.						96	95	96					17																	37584012		2203	4300	6503	SO:0001819	synonymous_variant	5469	exon10			AGAAGGAGAGACA	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"PPAR binding protein"	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000394287.3:c.681T>C	chr17.hg19:g.37584012A>G		88.0	0.0		96.0	36.0	NM_004774	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Silent	SNP	ENST00000394287.3	hg19																																																																																				.	.		0.318	MED1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000256944.1	NM_004774		G	37584012	A	G	37584012	2	3	23	1	0	0	0	0	0	0	0	1	9434	291	11	2		2	MED1	17	37584012	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1963350	37584012	43611198	908	2974										
MED24	9862	hgsc.bcm.edu	37	chr17	38183700	38183700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agatgtcaaacagcagggccCggacggaggccggtttggct	16	10	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:38183700C>T	ENST00000394128.2	-	16	1547	c.1466G>A	c.(1465-1467)cGg>cAg	p.R489Q	MED24_ENST00000394127.2_Missense_Mutation_p.R476Q|MED24_ENST00000501516.3_Missense_Mutation_p.R508Q|SNORD124_ENST00000459577.1_RNA|MED24_ENST00000394126.1_Missense_Mutation_p.R514Q|MED24_ENST00000356271.3_Missense_Mutation_p.R476Q	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	489					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.R489L(1)		autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CAGCAGGGCCCGGACGGAGGC	0.647											OREG0024386	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R489Q		Atlas-SNP	.											MED24,NS,carcinoma,0,1	MED24	89	.	1	Substitution - Missense(1)	lung(1)	c.G1466A						.						33	32	33					17																	38183700		2203	4300	6503	SO:0001583	missense	9862	exon16			AGGGCCCGGACGG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1466G>A	chr17.hg19:g.38183700C>T	ENSP00000377686:p.Arg489Gln	167.0	0.0	876	112.0	53.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	hg19	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.527162	0.64860	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000431269	T;T;T	0.61980	0.06;0.06;0.06	4.89	4.89	0.63831	Mediator complex, subunit Med24, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.78855	0.4349	M	0.72894	2.215	0.80722	D	1	P;D;D;D;D;D	0.89917	0.953;0.998;1.0;0.998;0.998;1.0	P;P;D;D;D;D	0.81914	0.543;0.845;0.995;0.986;0.992;0.995	T	0.81230	-0.1027	10	0.72032	D	0.01	-6.9283	18.2773	0.90087	0.0:1.0:0.0:0.0	.	430;439;399;476;489;431	B4DSQ6;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;MED24_HUMAN;.	Q	489;489;489;439;476;431;399	ENSP00000377686:R489Q;ENSP00000443344:R439Q;ENSP00000377685:R476Q	ENSP00000348610:R489Q	R	-	2	0	MED24	35437226	1.000000	0.71417	0.097000	0.21041	0.175000	0.22909	4.792000	0.62467	2.534000	0.85438	0.655000	0.94253	CGG	.	.		0.647	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		T	38183700	C	T	38183700	3	4	23	1	0	0	0	0	1	0	0	0	9451	652	23	1	1547	1	MED24	17	38183700	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	599688	38183700	43011510	909	2975										
KRT20	54474	hgsc.bcm.edu	37	chr17	39034421	39034421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgtcttctccttccagaaggCggcggtaagtagcaatttcc	10	12	2	1	rs377652428		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:39034421C>T	ENST00000167588.3	-	6	1156	c.1115G>A	c.(1114-1116)cGc>cAc	p.R372H		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	372	Coil 2.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				TTCCAGAAGGCGGCGGTAAGT	0.418																																					p.R372H		Atlas-SNP	.											.	KRT20	38	.	0			c.G1115A						.	C	HIS/ARG	0,4406		0,0,2203	241	210	220		1115	0.9	0.9	17		220	1,8599	1.2+/-3.3	0,1,4299	no	missense	KRT20	NM_019010.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	372/425	39034421	1,13005	2203	4300	6503	SO:0001583	missense	54474	exon6			AGAAGGCGGCGGT	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"-", "Intermediate filaments type I, keratins (acidic)"	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.1115G>A	chr17.hg19:g.39034421C>T	ENSP00000167588:p.Arg372His	97.0	0.0		90.0	39.0	NM_019010	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	hg19	CCDS11379.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.854326	0.71719	0.0	1.16E-4	ENSG00000171431	ENST00000167588	D	0.89810	-2.57	5.27	0.929	0.19449	Filament (1);Intermediate filament protein, conserved site (1);	0.195280	0.36591	N	0.002513	D	0.91043	0.7182	M	0.66939	2.045	0.23309	N	0.997932	D	0.89917	1.0	D	0.72625	0.978	T	0.82210	-0.0570	10	0.54805	T	0.06	.	5.4275	0.16433	0.1237:0.5308:0.0:0.3456	.	372	P35900	K1C20_HUMAN	H	372	ENSP00000167588:R372H	ENSP00000167588:R372H	R	-	2	0	KRT20	36287947	0.413000	0.25400	0.908000	0.35775	0.997000	0.91878	0.893000	0.28336	-0.029000	0.13827	0.591000	0.81541	CGC	.	.		0.418	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2			T	39034421	C	T	39034421	3	4	23	1	0	0	0	0	1	0	0	0	8467	768	27	1	171	1	KRT20	17	39034421	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	850721	39034421	42160789	910	2976										
KRT20	54474	hgsc.bcm.edu	37	chr17	39041125	39041125	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cggggcgttggtttcgtaccActgcttgatttgcacttcaa	11	10	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:39041125A>C	ENST00000167588.3	-	1	354	c.313T>G	c.(313-315)Tgg>Ggg	p.W105G		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	105	Coil 1A.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				GTTTCGTACCACTGCTTGATT	0.502																																					p.W105G		Atlas-SNP	.											.	KRT20	38	.	0			c.T313G						.						114	102	106					17																	39041125		2203	4300	6503	SO:0001583	missense	54474	exon1			CGTACCACTGCTT	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"-", "Intermediate filaments type I, keratins (acidic)"	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.313T>G	chr17.hg19:g.39041125A>C	ENSP00000167588:p.Trp105Gly	117.0	0.0		122.0	6.0	NM_019010	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	hg19	CCDS11379.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.800851	0.50315	.	.	ENSG00000171431	ENST00000167588	D	0.88975	-2.45	5.65	5.65	0.86999	Filament (1);	0.000000	0.56097	D	0.000035	D	0.95338	0.8487	M	0.89601	3.045	0.46478	D	0.999069	D	0.76494	0.999	D	0.72338	0.977	D	0.96110	0.9076	10	0.72032	D	0.01	.	15.8704	0.79115	1.0:0.0:0.0:0.0	.	105	P35900	K1C20_HUMAN	G	105	ENSP00000167588:W105G	ENSP00000167588:W105G	W	-	1	0	KRT20	36294651	1.000000	0.71417	1.000000	0.80357	0.106000	0.19336	7.257000	0.78362	2.141000	0.66446	0.533000	0.62120	TGG	.	.		0.502	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2			C	39041125	A	C	39041125	3	2	23	1	0	0	0	0	1	0	0	0	8467	159	6	5	993	5	KRT20	17	39041125	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	6704	39041125	42154085	911	2977										
KRT31	3881	hgsc.bcm.edu	37	chr17	39551555	39551555	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgactgtgcgtctcagctcgAtgatctccgcctggtaggac	12	12	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:39551555A>T	ENST00000251645.2	-	5	870	c.818T>A	c.(817-819)aTc>aAc	p.I273N		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	273	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				TCTCAGCTCGATGATCTCCGC	0.582																																					p.I273N		Atlas-SNP	.											.	KRT31	158	.	0			c.T818A						.						123	112	115					17																	39551555		2203	4300	6503	SO:0001583	missense	3881	exon5			AGCTCGATGATCT	X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"-", "Intermediate filaments type I, keratins (acidic)"	6448	protein-coding gene	gene with protein product	"hard keratin type I 1"	601077	"keratin, hair, acidic, 1"	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.818T>A	chr17.hg19:g.39551555A>T	ENSP00000251645:p.Ile273Asn	107.0	0.0		105.0	42.0	NM_002277	Q9UE12	Missense_Mutation	SNP	ENST00000251645.2	hg19	CCDS11391.1	.	.	.	.	.	.	.	.	.	.	a	16.02	3.005161	0.54254	.	.	ENSG00000094796	ENST00000251645	T	0.75938	-0.98	5.36	4.27	0.50696	Filament (1);	0.000000	0.64402	D	0.000006	T	0.75496	0.3857	L	0.33339	1.005	0.35822	D	0.824646	D	0.67145	0.996	D	0.67900	0.954	T	0.79577	-0.1746	10	0.87932	D	0	.	6.6752	0.23090	0.739:0.0:0.261:0.0	.	273	Q15323	K1H1_HUMAN	N	273	ENSP00000251645:I273N	ENSP00000251645:I273N	I	-	2	0	KRT31	36805081	1.000000	0.71417	0.977000	0.42913	0.679000	0.39708	3.951000	0.56684	0.853000	0.35312	0.456000	0.33151	ATC	.	.		0.582	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277		T	39551555	A	T	39551555	3	4	23	1	0	0	0	0	1	0	0	0	8476	333	12	4	444	4	KRT31	17	39551555	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	510430	39551555	41643655	912	2978										
NT5C3L	115024	hgsc.bcm.edu	37	chr17	39983842	39983842	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agagctgttcttgttgtatgTgtgtatgagctggcccttaa	12	6	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:39983842T>C	ENST00000435506.2	-	8	673	c.604A>G	c.(604-606)Aca>Gca	p.T202A	NT5C3B_ENST00000269534.8_Missense_Mutation_p.T194A|NT5C3B_ENST00000521789.1_Intron			Q969T7	5NT3B_HUMAN	5'-nucleotidase, cytosolic IIIB	202					nucleotide metabolic process (GO:0009117)	cytoplasm (GO:0005737)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)										TTGTTGTATGTGTGTATGAGC	0.502																																					p.T202A		Atlas-SNP	.											.	.	.	.	0			c.A604G						.						155	147	150					17																	39983842		2203	4300	6503	SO:0001583	missense	115024	exon8			TGTATGTGTGTAT		CCDS11410.1, CCDS11410.2	17q21.2	2013-01-31	2013-01-31	2013-01-31	ENSG00000141698	ENSG00000141698	3.1.3.5		28300	protein-coding gene	gene with protein product			"5'-nucleotidase, cytosolic III-like"	NT5C3L		23223233	Standard	NM_052935		Approved	MGC20781	uc021txo.1	Q969T7	OTTHUMG00000133499	ENST00000435506.2:c.604A>G	chr17.hg19:g.39983842T>C	ENSP00000389948:p.Thr202Ala	209.0	0.0		184.0	60.0	NM_052935	A8MWB9|C9JKC4|Q7L3B7	Missense_Mutation	SNP	ENST00000435506.2	hg19	CCDS11410.2	.	.	.	.	.	.	.	.	.	.	T	17.17	3.320204	0.60634	.	.	ENSG00000141698	ENST00000269534;ENST00000393911;ENST00000435506;ENST00000415460	D;D;D	0.82619	-1.63;-1.63;-1.63	5.07	5.07	0.68467	HAD-like domain (2);	0.104097	0.64402	D	0.000004	D	0.83903	0.5355	M	0.67625	2.065	0.46849	D	0.999222	P;P	0.40144	0.704;0.704	P;P	0.45071	0.468;0.468	T	0.82147	-0.0601	10	0.26408	T	0.33	1.7022	14.6635	0.68891	0.0:0.0:0.0:1.0	.	202;194	C9JKC4;Q969T7	.;5NT3L_HUMAN	A	194;236;202;172	ENSP00000269534:T194A;ENSP00000389948:T202A;ENSP00000397742:T172A	ENSP00000269534:T194A	T	-	1	0	NT5C3L	37237368	1.000000	0.71417	0.994000	0.49952	0.969000	0.65631	3.282000	0.51693	2.131000	0.65755	0.379000	0.24179	ACA	.	.		0.502	NT5C3B-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257430.2	NM_052935		C	39983842	T	C	39983842	3	2	23	1	0	0	0	0	1	0	0	0	10698	1696	59	2	306	2	NT5C3L	17	39983842	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	432287	39983842	41211368	913	2979										
DHX58	79132	hgsc.bcm.edu	37	chr17	40263791	40263791	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccatccacagtctctaggtgCcgcttggccacataagcagc	9	15	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:40263791C>A	ENST00000251642.3	-	3	342	c.120G>T	c.(118-120)cgG>cgT	p.R40R		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	40	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TCTCTAGGTGCCGCTTGGCCA	0.597																																					p.R40R		Atlas-SNP	.											.	DHX58	39	.	0			c.G120T						.						127	114	118					17																	40263791		2203	4300	6503	SO:0001819	synonymous_variant	79132	exon3			TAGGTGCCGCTTG	BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"RNA helicase LGP2"	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.120G>T	chr17.hg19:g.40263791C>A		87.0	0.0		108.0	29.0	NM_024119	Q9HAM6	Silent	SNP	ENST00000251642.3	hg19	CCDS11416.1																																																																																			.	.		0.597	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119		A	40263791	C	A	40263791	2	1	23	1	0	0	0	0	0	0	0	1	4516	726	26	3		3	DHX58	17	40263791	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	279949	40263791	40931419	914	2980										
VPS25	84313	hgsc.bcm.edu	37	chr17	40928326	40928326	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aactgactaatggggaagacAcagaggatgagggtaatgcc	14	6	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:40928326A>G	ENST00000253794.2	+	5	446	c.406A>G	c.(406-408)Aca>Gca	p.T136A		NM_032353.2	NP_115729.1	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25 homolog (S. cerevisiae)	136					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)	5		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		TGGGGAAGACACAGAGGATGA	0.423																																					p.T136A		Atlas-SNP	.											.	VPS25	11	.	0			c.A406G						.						97	92	94					17																	40928326		2203	4300	6503	SO:0001583	missense	84313	exon5			GAAGACACAGAGG	AB014763	CCDS11438.1	17q21.31	2014-02-12	2006-04-04		ENSG00000131475	ENSG00000131475			28122	protein-coding gene	gene with protein product		610907	"vacuolar protein sorting 25 (yeast)"			15511219	Standard	NM_032353		Approved	MGC10540, EAP20, DERP9	uc002ibi.3	Q9BRG1		ENST00000253794.2:c.406A>G	chr17.hg19:g.40928326A>G	ENSP00000253794:p.Thr136Ala	153.0	0.0		145.0	52.0	NM_032353	B2R581	Missense_Mutation	SNP	ENST00000253794.2	hg19	CCDS11438.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.377327	0.61735	.	.	ENSG00000131475	ENST00000253794	T	0.51325	0.71	5.4	5.4	0.78164	ESCRT-II complex, Vps25 subunit, C-terminal winged helix (1);	0.000000	0.85682	D	0.000000	T	0.48995	0.1531	M	0.65498	2.005	0.80722	D	1	P	0.42518	0.782	B	0.40101	0.319	T	0.52472	-0.8571	10	0.42905	T	0.14	-3.3437	15.0877	0.72167	1.0:0.0:0.0:0.0	.	136	Q9BRG1	VPS25_HUMAN	A	136	ENSP00000253794:T136A	ENSP00000253794:T136A	T	+	1	0	VPS25	38181852	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	8.931000	0.92884	2.050000	0.60909	0.454000	0.30748	ACA	.	.		0.423	VPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452383.1	NM_032353		G	40928326	A	G	40928326	3	3	23	1	0	0	0	0	1	0	0	0	17211	159	6	2	424	2	VPS25	17	40928326	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	664535	40928326	40266884	915	2981										
MPP3	4356	hgsc.bcm.edu	37	chr17	41907454	41907454	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcatcactgtgcacggaggCggcctgcaactcctccatca	9	16	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:41907454C>T	ENST00000398389.4	-	6	409	c.244G>A	c.(244-246)Gcc>Acc	p.A82T	MPP3_ENST00000398393.1_Missense_Mutation_p.A107T	NM_001932.4	NP_001923.2	Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	82	L27 2. {ECO:0000255|PROSITE- ProRule:PRU00365}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	guanylate kinase activity (GO:0004385)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		TGCACGGAGGCGGCCTGCAAC	0.622																																					p.A82T		Atlas-SNP	.											.	MPP3	42	.	0			c.G244A						.						34	43	40					17																	41907454		2149	4260	6409	SO:0001583	missense	4356	exon6			CGGAGGCGGCCTG		CCDS42344.1	17q12-q21	2008-07-18			ENSG00000161647	ENSG00000161647			7221	protein-coding gene	gene with protein product	"MAGUK p55 subfamily member 3", "discs, large (Drosophila) homolog 3", "membrane protein palmitoylated 3"	601114		DLG3		8824795	Standard	NR_003562		Approved		uc002iei.4	Q13368	OTTHUMG00000133838	ENST00000398389.4:c.244G>A	chr17.hg19:g.41907454C>T	ENSP00000381425:p.Ala82Thr	37.0	0.0		47.0	25.0	NM_001932	B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	Missense_Mutation	SNP	ENST00000398389.4	hg19	CCDS42344.1	.	.	.	.	.	.	.	.	.	.	C	9.185	1.024601	0.19433	.	.	ENSG00000161647	ENST00000398393;ENST00000398389;ENST00000356492	T;T	0.15834	2.39;2.4	4.78	3.81	0.43845	L27, C-terminal (1);L27 (2);	0.256058	0.39475	N	0.001349	T	0.10981	0.0268	N	0.05306	-0.075	0.37641	D	0.92203	D;B;B	0.63046	0.992;0.006;0.011	P;B;B	0.51324	0.666;0.014;0.014	T	0.25710	-1.0124	10	0.15952	T	0.53	.	8.9554	0.35814	0.0:0.8296:0.0:0.1704	.	107;82;107	B4DS20;Q13368;D3DX46	.;MPP3_HUMAN;.	T	107;82;107	ENSP00000381430:A107T;ENSP00000381425:A82T	ENSP00000348885:A107T	A	-	1	0	MPP3	39262980	0.984000	0.35163	0.998000	0.56505	0.899000	0.52679	1.249000	0.32839	1.231000	0.43661	0.462000	0.41574	GCC	.	.		0.622	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1	NM_001932		T	41907454	C	T	41907454	3	4	23	1	0	0	0	0	1	0	0	0	9744	768	27	1	1573	1	MPP3	17	41907454	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	979128	41907454	39287756	916	2982										
TMEM101	84336	hgsc.bcm.edu	37	chr17	42089395	42089395	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcaacacgccgcgtgttgtgCcagtaagcaacattgccatc	9	13	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:42089395C>A	ENST00000589334.1	-	5	990	c.675G>T	c.(673-675)tgG>tgT	p.W225C	TMEM101_ENST00000206380.3_Missense_Mutation_p.W225C|TMEM101_ENST00000542039.1_Missense_Mutation_p.W167C			Q96IK0	TM101_HUMAN	transmembrane protein 101	225					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Breast(137;0.0264)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCGTGTTGTGCCAGTAAGCAA	0.562																																					p.W225C		Atlas-SNP	.											.	TMEM101	18	.	0			c.G675T						.						115	91	99					17																	42089395		2203	4300	6503	SO:0001583	missense	84336	exon4			GTTGTGCCAGTAA	AK172826	CCDS11474.1	17q21.31	2005-12-16							28653	protein-coding gene	gene with protein product						12761501	Standard	NM_032376		Approved	MGC4251, FLJ23987	uc002ieu.3	Q96IK0		ENST00000589334.1:c.675G>T	chr17.hg19:g.42089395C>A	ENSP00000468025:p.Trp225Cys	81.0	0.0		88.0	40.0	NM_032376	B2R9N6	Missense_Mutation	SNP	ENST00000589334.1	hg19	CCDS11474.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.412091	0.83340	.	.	ENSG00000091947	ENST00000206380;ENST00000542039	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.68016	0.2955	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.70680	-0.4805	9	0.87932	D	0	-5.1077	17.0298	0.86458	0.0:1.0:0.0:0.0	.	225	Q96IK0	TM101_HUMAN	C	225;167	.	ENSP00000206380:W225C	W	-	3	0	TMEM101	39444921	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.707000	0.84623	2.615000	0.88500	0.484000	0.47621	TGG	.	.		0.562	TMEM101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457665.1	NM_032376		A	42089395	C	A	42089395	3	1	23	1	0	0	0	0	1	0	0	0	16031	740	26	3	102	3	TMEM101	17	42089395	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	181941	42089395	39105815	917	2983										
HDAC5	10014	hgsc.bcm.edu	37	chr17	42157801	42157801	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggtactccacgtctccaatGggggggtccacacctcctgt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:42157801delG	ENST00000393622.2	-	22	3124	c.2793delC	c.(2791-2793)cccfs	p.P931fs	HDAC5_ENST00000225983.6_Frame_Shift_Del_p.P932fs|HDAC5_ENST00000586802.1_Frame_Shift_Del_p.P931fs|HDAC5_ENST00000336057.5_Frame_Shift_Del_p.P846fs	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	931	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		CGTCTCCAATGGGGGGGTCCA	0.607																																					p.I933fs		Atlas-Indel,Pindel	.											.	HDAC5	67	.	0			c.2797delA						.						103	98	99					17																	42157801		2203	4300	6503	SO:0001589	frameshift_variant	10014	exon22			.	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.2793delC	chr17.hg19:g.42157801delG	ENSP00000377244:p.Pro931fs	79.0	0.0		84.0	39.0	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Frame_Shift_Del	DEL	ENST00000393622.2	hg19	CCDS45696.1																																																																																			.	.		0.607	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		-	42157801	G	-	42157801	7	5	23	1	0	1	0	1	0	0	0	0	7019	1335	47	0	599	0	HDAC5	17	42157801	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	68406	42157801	39037409	918	2984										
HDAC5	10014	hgsc.bcm.edu	37	chr17	42171119	42171119	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agagcccaccagagccccccGtagctccacagggctggggc	13	17	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:42171119G>A	ENST00000393622.2	-	4	509	c.178C>T	c.(178-180)Cgg>Tgg	p.R60W	HDAC5_ENST00000225983.6_Missense_Mutation_p.R61W|HDAC5_ENST00000586802.1_Missense_Mutation_p.R60W|HDAC5_ENST00000336057.5_Missense_Mutation_p.R60W	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	60					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		AGAGCCCCCCGTAGCTCCACA	0.667																																					p.R61W		Atlas-SNP	.											HDAC5,NS,carcinoma,0,1	HDAC5	67	.	0			c.C181T						.						13	15	15					17																	42171119		2197	4295	6492	SO:0001583	missense	10014	exon4			CCCCCCGTAGCTC	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.178C>T	chr17.hg19:g.42171119G>A	ENSP00000377244:p.Arg60Trp	118.0	0.0		143.0	58.0	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	hg19	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.604577	0.66445	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.50001	0.78;0.78;0.76	4.14	4.14	0.48551	.	0.240511	0.26859	N	0.022121	T	0.56891	0.2016	L	0.32530	0.975	0.42561	D	0.993142	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.69654	0.965;0.924;0.965;0.924	T	0.63189	-0.6693	10	0.87932	D	0	-23.2017	15.156	0.72743	0.0:0.0:1.0:0.0	.	60;60;61;60	Q9UQL6-2;B4DGT4;Q9UQL6-3;Q9UQL6	.;.;.;HDAC5_HUMAN	W	61;60;60	ENSP00000225983:R61W;ENSP00000377244:R60W;ENSP00000337290:R60W	ENSP00000225983:R61W	R	-	1	2	HDAC5	39526645	0.996000	0.38824	0.992000	0.48379	0.875000	0.50365	3.362000	0.52314	1.858000	0.53909	0.462000	0.41574	CGG	.	.		0.667	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		A	42171119	G	A	42171119	3	1	23	1	0	0	0	0	1	0	0	0	7019	1144	40	1	3286	1	HDAC5	17	42171119	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	13318	42171119	39024091	919	2985										
NMT1	4836	hgsc.bcm.edu	37	chr17	43171104	43171104	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcctgacaaggacaatatccGccaggagccctacaccctgc	9	16	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:43171104G>A	ENST00000592782.1	+	5	568	c.437G>A	c.(436-438)cGc>cAc	p.R146H	NMT1_ENST00000258960.2_Missense_Mutation_p.R146H|NMT1_ENST00000590114.1_3'UTR			P30419	NMT1_HUMAN	N-myristoyltransferase 1	146					apoptotic process (GO:0006915)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	8		Prostate(33;0.155)				GACAATATCCGCCAGGAGCCC	0.627																																					p.R146H		Atlas-SNP	.											.	NMT1	31	.	0			c.G437A						.						69	61	64					17																	43171104		2203	4300	6503	SO:0001583	missense	4836	exon4			ATATCCGCCAGGA		CCDS11494.1	17q21.31	2012-10-02			ENSG00000136448	ENSG00000136448			7857	protein-coding gene	gene with protein product	"alternative, short form NMT-S", "myristoyl-CoA:protein N-myristoyltransferase", "long form, NMT-L"	160993				1570339	Standard	NM_021079		Approved	NMT	uc002ihz.3	P30419	OTTHUMG00000180003	ENST00000592782.1:c.437G>A	chr17.hg19:g.43171104G>A	ENSP00000468424:p.Arg146His	66.0	0.0		71.0	26.0	NM_021079	A8K7C1|Q9UE09	Missense_Mutation	SNP	ENST00000592782.1	hg19	CCDS11494.1	.	.	.	.	.	.	.	.	.	.	G	35	5.542206	0.96474	.	.	ENSG00000136448	ENST00000258960	T	0.49720	0.77	5.02	5.02	0.67125	Acyl-CoA N-acyltransferase (2);Myristoyl-CoA:protein N-myristoyltransferase, N-terminal (1);	0.048417	0.85682	N	0.000000	T	0.79082	0.4386	H	0.95187	3.635	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.85347	0.1099	10	0.87932	D	0	-15.1227	18.8925	0.92410	0.0:0.0:1.0:0.0	.	146	P30419	NMT1_HUMAN	H	146	ENSP00000258960:R146H	ENSP00000258960:R146H	R	+	2	0	NMT1	40526630	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.601000	0.98297	2.767000	0.95098	0.655000	0.94253	CGC	.	.		0.627	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079		A	43171104	G	A	43171104	3	1	23	1	0	0	0	0	1	0	0	0	10512	1087	38	1	451	1	NMT1	17	43171104	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	999985	43171104	38024106	920	2986										
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44108889	44108889	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggctgctgccaccagatgccGactcttgagggggacaatgg	15	11	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:44108889G>A	ENST00000262419.6	-	15	3741	c.3271C>T	c.(3271-3273)Cgg>Tgg	p.R1091W	KANSL1_ENST00000575318.1_Missense_Mutation_p.R1027W|KANSL1_ENST00000574590.1_Missense_Mutation_p.R1091W|KANSL1_ENST00000432791.1_Missense_Mutation_p.R1091W|KANSL1_ENST00000393476.3_Missense_Mutation_p.R385W|KANSL1_ENST00000572904.1_Missense_Mutation_p.R1091W	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	1091	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.R1091W(1)									ACCAGATGCCGACTCTTGAGG	0.612																																					p.R1091W		Atlas-SNP	.											KIAA1267,face,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	skin(1)	c.C3271T						.						25	23	24					17																	44108889		2203	4300	6503	SO:0001583	missense	284058	exon15			GATGCCGACTCTT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"centromere protein 36"	612452	"KIAA1267"	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.3271C>T	chr17.hg19:g.44108889G>A	ENSP00000262419:p.Arg1091Trp	98.0	0.0		88.0	30.0	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	hg19	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.445331	0.63178	.	.	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.28255	2.43;2.43;1.62	5.72	3.53	0.40419	.	0.000000	0.51477	D	0.000086	T	0.33585	0.0868	N	0.19112	0.55	0.39056	D	0.960425	D;D;D;D	0.71674	0.994;0.994;0.998;0.998	P;P;P;P	0.59546	0.629;0.629;0.859;0.859	T	0.29852	-0.9998	10	0.66056	D	0.02	-3.8111	11.5213	0.50553	0.0:0.1263:0.7277:0.146	.	359;422;1091;1091	B3KT49;Q7Z3B3-2;C9JHY2;Q7Z3B3	.;.;.;K1267_HUMAN	W	1091;1091;385	ENSP00000262419:R1091W;ENSP00000387393:R1091W;ENSP00000377117:R385W	ENSP00000262419:R1091W	R	-	1	2	KIAA1267	41464736	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	4.125000	0.57931	1.414000	0.47017	0.561000	0.74099	CGG	.	.		0.612	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		A	44108889	G	A	44108889	3	1	23	1	0	0	0	0	1	0	0	0	8228	1057	37	1	50	1	KIAA1267	17	44108889	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	937785	44108889	37086321	921	2987										
ITGB3	3690	hgsc.bcm.edu	37	chr17	45363766	45363766	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agagggtggctttgatgccaTcatgcaggctacagtctgtg	14	8	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:45363766T>C	ENST00000559488.1	+	5	771	c.755T>C	c.(754-756)aTc>aCc	p.I252T	ITGB3_ENST00000560629.1_Silent_p.H240H|ITGB3_ENST00000571680.1_Missense_Mutation_p.I252T|ITGB3_ENST00000435993.2_Missense_Mutation_p.I205T	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	252	VWFA.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	tttgatgccaTCATGCAGGCT	0.532																																					p.I252T		Atlas-SNP	.											.	ITGB3	157	.	0			c.T755C						.						101	84	90					17																	45363766		2203	4300	6503	SO:0001583	missense	3690	exon5			ATGCCATCATGCA		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.755T>C	chr17.hg19:g.45363766T>C	ENSP00000452786:p.Ile252Thr	79.0	0.0		88.0	32.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	hg19	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.528815	0.85706	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.98296	-4.85	5.01	5.01	0.66863	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.048416	0.85682	D	0.000000	D	0.99020	0.9665	M	0.89968	3.075	0.80722	D	1	P;D	0.58268	0.701;0.982	P;D	0.74348	0.694;0.983	D	0.99589	1.0975	10	0.87932	D	0	.	13.9843	0.64324	0.0:0.0:0.0:1.0	.	252;252	P05106;Q2YFE1	ITB3_HUMAN;.	T	252;205	ENSP00000407801:I205T	ENSP00000262017:I252T	I	+	2	0	C17orf57	42718765	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.997000	0.88414	2.006000	0.58801	0.459000	0.35465	ATC	.	.		0.532	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		C	45363766	T	C	45363766	3	2	23	1	0	0	0	0	1	0	0	0	7904	1435	50	2	773	2	ITGB3	17	45363766	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1254877	45363766	35831444	922	2988										
OSBPL7	114881	hgsc.bcm.edu	37	chr17	45895948	45895948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcggtgggcacgcagctgcGccacccagctctggaatagg	16	13	1	0	rs368110786		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:45895948G>A	ENST00000007414.3	-	6	595	c.404C>T	c.(403-405)gCg>gTg	p.A135V	OSBPL7_ENST00000392507.3_Missense_Mutation_p.A135V	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	135	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						ACGCAGCTGCGCCACCCAGCT	0.617																																					p.A135V		Atlas-SNP	.											.	OSBPL7	65	.	0			c.C404T						.	G	VAL/ALA	0,4404		0,0,2202	27	31	30		404	6	1	17		30	1,8595		0,1,4297	no	missense	OSBPL7	NM_145798.2	64	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	benign	135/843	45895948	1,12999	2202	4298	6500	SO:0001583	missense	114881	exon6			AGCTGCGCCACCC	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.404C>T	chr17.hg19:g.45895948G>A	ENSP00000007414:p.Ala135Val	72.0	0.0		81.0	36.0	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	hg19	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	G	19.59	3.856095	0.71834	0.0	1.16E-4	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.17854	2.25;2.25	5.97	5.97	0.96955	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.344395	0.34110	N	0.004253	T	0.13543	0.0328	N	0.20483	0.58	0.42564	D	0.993156	B	0.25743	0.133	B	0.25140	0.058	T	0.12041	-1.0563	10	0.27785	T	0.31	-9.7525	17.3447	0.87307	0.0:0.0:1.0:0.0	.	135	Q9BZF2	OSBL7_HUMAN	V	135	ENSP00000007414:A135V;ENSP00000376295:A135V	ENSP00000007414:A135V	A	-	2	0	OSBPL7	43250947	0.998000	0.40836	0.997000	0.53966	0.993000	0.82548	3.929000	0.56514	2.837000	0.97791	0.655000	0.94253	GCG	.	.		0.617	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		A	45895948	G	A	45895948	3	1	23	1	0	0	0	0	1	0	0	0	11291	1087	38	1	2196	1	OSBPL7	17	45895948	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	532182	45895948	35299262	923	2989										
OSBPL7	114881	hgsc.bcm.edu	37	chr17	45896429	45896429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatggacatgaccgacagccGgacatcgatggagccatgga	14	10	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:45896429G>A	ENST00000007414.3	-	5	483	c.292C>T	c.(292-294)Cgg>Tgg	p.R98W	OSBPL7_ENST00000392507.3_Missense_Mutation_p.R98W	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	98	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						ACCGACAGCCGGACATCGATG	0.552																																					p.R98W		Atlas-SNP	.											.	OSBPL7	65	.	0			c.C292T						.						154	122	133					17																	45896429		2203	4300	6503	SO:0001583	missense	114881	exon5			ACAGCCGGACATC	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.292C>T	chr17.hg19:g.45896429G>A	ENSP00000007414:p.Arg98Trp	110.0	0.0		102.0	35.0	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	hg19	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.104875	0.37145	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.19250	2.16;2.16	5.35	5.35	0.76521	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.105384	0.64402	D	0.000004	T	0.42359	0.1199	L	0.55213	1.73	0.41193	D	0.986315	D	0.89917	1.0	D	0.73708	0.981	T	0.26883	-1.0090	10	0.72032	D	0.01	-23.0732	15.9951	0.80234	0.0:0.0:1.0:0.0	.	98	Q9BZF2	OSBL7_HUMAN	W	98	ENSP00000007414:R98W;ENSP00000376295:R98W	ENSP00000007414:R98W	R	-	1	2	OSBPL7	43251428	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	0.914000	0.28624	2.504000	0.84457	0.655000	0.94253	CGG	.	.		0.552	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		A	45896429	G	A	45896429	3	1	23	1	0	0	0	0	1	0	0	0	11291	1115	39	1	2312	1	OSBPL7	17	45896429	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	481	45896429	35298781	924	2990										
HOXB7	3217	hgsc.bcm.edu	37	chr17	46687954	46687954	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagtccctctgctccttggcGcccgccgccttggcggagtc	13	17	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:46687954G>A	ENST00000239165.7	-	1	425	c.327C>T	c.(325-327)ggC>ggT	p.G109G	HOXB7_ENST00000567101.2_Intron	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN	homeobox B7	109					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						GCTCCTTGGCGCCCGCCGCCT	0.657																																					p.G109G		Atlas-SNP	.											.	HOXB7	15	.	0			c.C327T						.						7	7	7					17																	46687954		2098	4146	6244	SO:0001819	synonymous_variant	3217	exon1			CTTGGCGCCCGCC		CCDS11532.1	17q21.32	2013-05-22	2005-12-22					"Homeoboxes / ANTP class : HOXL subclass"	5118	protein-coding gene	gene with protein product		142962	"homeo box B7"	HOX2, HOX2C		1973146, 1358459	Standard	NM_004502		Approved		uc002inv.3	P09629	OTTHUMG00000170231	ENST00000239165.7:c.327C>T	chr17.hg19:g.46687954G>A		198.0	0.0		199.0	83.0	NM_004502	A8K3N8|Q15957|Q53FN3|Q96BQ6	Silent	SNP	ENST00000239165.7	hg19	CCDS11532.1																																																																																			.	.		0.657	HOXB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358097.3			A	46687954	G	A	46687954	2	1	23	1	0	0	0	0	0	0	0	1	7315	1074	38	1		1	HOXB7	17	46687954	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	791525	46687954	34507256	925	2991										
HOXB13	10481	hgsc.bcm.edu	37	chr17	46805444	46805444	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agccaccagcgagagcccaaGactggtaactgtccacaggc	11	14	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:46805444G>T	ENST00000290295.7	-	1	1096	c.512C>A	c.(511-513)tCt>tAt	p.S171Y	PRAC2_ENST00000422730.2_RNA	NM_006361.5	NP_006352.2	Q92826	HXB13_HUMAN	homeobox B13	171					angiogenesis (GO:0001525)|epidermis development (GO:0008544)|epithelial cell maturation involved in prostate gland development (GO:0060743)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|response to wounding (GO:0009611)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|lung(6)|prostate(1)	11						GAGAGCCCAAGACTGGTAACT	0.567																																					p.S171Y		Atlas-SNP	.											.	HOXB13	28	.	0			c.C512A						.						77	73	74					17																	46805444		2203	4300	6503	SO:0001583	missense	10481	exon1			GCCCAAGACTGGT	U57052	CCDS11536.1	17q21.32	2014-09-17	2005-12-22		ENSG00000159184	ENSG00000159184		"Homeoboxes / ANTP class : HOXL subclass"	5112	protein-coding gene	gene with protein product		604607	"homeo box B13"			8756292, 9665387	Standard	NM_006361		Approved		uc002ioa.3	Q92826	OTTHUMG00000159900	ENST00000290295.7:c.512C>A	chr17.hg19:g.46805444G>T	ENSP00000290295:p.Ser171Tyr	112.0	0.0		146.0	71.0	NM_006361	B2R878|Q96QM4|Q99810	Missense_Mutation	SNP	ENST00000290295.7	hg19	CCDS11536.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.110888	0.56398	.	.	ENSG00000159184	ENST00000290295	D	0.91740	-2.9	4.79	4.79	0.61399	.	0.118436	0.64402	D	0.000015	D	0.87700	0.6243	L	0.29908	0.895	0.39184	D	0.962838	B	0.16802	0.019	B	0.04013	0.001	D	0.85599	0.1251	10	0.72032	D	0.01	.	16.5918	0.84767	0.0:0.0:1.0:0.0	.	171	Q92826	HXB13_HUMAN	Y	171	ENSP00000290295:S171Y	ENSP00000290295:S171Y	S	-	2	0	HOXB13	44160443	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	5.167000	0.64972	2.498000	0.84270	0.561000	0.74099	TCT	.	.		0.567	HOXB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358087.3	NM_006361		T	46805444	G	T	46805444	3	4	23	1	0	0	0	0	1	0	0	0	7309	942	33	3	350	3	HOXB13	17	46805444	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	117490	46805444	34389766	926	2992										
ZNF652	22834	hgsc.bcm.edu	37	chr17	47389292	47389292	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtagcacattccttacctcGcatctaaagggcttctctcc	7	14	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:47389292G>A	ENST00000362063.2	-	4	1479	c.1161C>T	c.(1159-1161)tgC>tgT	p.C387C	ZNF652_ENST00000430262.2_Silent_p.C387C	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	387					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			TCCTTACCTCGCATCTAAAGG	0.512																																					p.C387C		Atlas-SNP	.											ZNF652,colon,carcinoma,0,1	ZNF652	54	.	0			c.C1161T						.						163	130	141					17																	47389292		2203	4300	6503	SO:0001819	synonymous_variant	22834	exon4			TACCTCGCATCTA	AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740		"Zinc fingers, C2H2-type"	29147	protein-coding gene	gene with protein product		613907				10231032	Standard	NM_014897		Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.1161C>T	chr17.hg19:g.47389292G>A		121.0	0.0		116.0	31.0	NM_001145365	A4QPD9|Q5H9Q0	Silent	SNP	ENST00000362063.2	hg19	CCDS32677.1																																																																																			.	.		0.512	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897		A	47389292	G	A	47389292	2	1	23	1	0	0	0	0	0	0	0	1	18080	1079	38	1		1	ZNF652	17	47389292	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	583848	47389292	33805918	927	2993										
SAMD14	201191	hgsc.bcm.edu	37	chr17	48191303	48191303	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccacctttagtttgcttccGtccagctgcagcagctgcgg	10	15	0	0	rs367685385		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:48191303G>A	ENST00000330175.4	-	9	1400	c.1083C>T	c.(1081-1083)gaC>gaT	p.D361D	SAMD14_ENST00000503734.1_5'Flank|SAMD14_ENST00000503131.1_Silent_p.D389D	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	361	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						GTTTGCTTCCGTCCAGCTGCA	0.572																																					p.D389D		Atlas-SNP	.											.	SAMD14	36	.	0			c.C1167T						.	G		0,4406		0,0,2203	50	49	49		1167	-6.4	0.9	17		49	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SAMD14	NM_174920.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		389/446	48191303	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	201191	exon10			GCTTCCGTCCAGC		CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"Sterile alpha motif (SAM) domain containing"	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.1083C>T	chr17.hg19:g.48191303G>A		154.0	0.0		167.0	79.0	NM_174920	A5D8V1|Q8N2X0	Silent	SNP	ENST00000330175.4	hg19	CCDS58562.1																																																																																			.	.		0.572	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920		A	48191303	G	A	48191303	2	1	23	1	0	0	0	0	0	0	0	1	13834	1136	40	1		1	SAMD14	17	48191303	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	802011	48191303	33003907	928	2994										
COL1A1	1277	hgsc.bcm.edu	37	chr17	48276626	48276626	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccgggaggtccggggggtccGgggggtccgggaagtccagg					rs72667016		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:48276626delG	ENST00000225964.5	-	5	550	c.432delC	c.(430-432)cccfs	p.P144fs		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	144					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	cggggggtccggggggtccgg	0.682			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.G145fs		Atlas-Indel,Pindel	.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1	158	.	0			c.433delG	GRCh37	CD063493	COL1A1	D	rs72667016	.			10,2100		3,4,1048	1	2	2	http://www.ncbi.nlm.nih.gov/sites/varvu?gene		5.2	0.3	17	dbSNP_130	2	13,4777		4,5,2386	no	frameshift	COL1A1	NM_000088.3		7,9,3434	A1A1,A1R,RR		0.2714,0.4739,0.3333			48276626	23,6877	1258	2831	4089	SO:0001589	frameshift_variant	1277	exon5			.	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.432delC	chr17.hg19:g.48276626delG	ENSP00000225964:p.Pro144fs	287.0	0.0		260.0	54.0	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Frame_Shift_Del	DEL	ENST00000225964.5	hg19	CCDS11561.1																																																																																			.	.		0.682	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			-	48276626	G	-	48276626	7	5	23	1	0	1	0	1	0	0	0	0	3679	1103	39	0	4150	0	COL1A1	17	48276626	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	85323	48276626	32918584	929	2995										
EME1	146956	hgsc.bcm.edu	37	chr17	48452870	48452870	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttcctctggctcaaaggcttAcatgtaagtttctgacccac	7	12	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:48452870A>G	ENST00000338165.4	+	2	383	c.301A>G	c.(301-303)Aca>Gca	p.T101A	MRPL27_ENST00000503633.1_5'Flank|MRPL27_ENST00000507088.1_5'Flank|MRPL27_ENST00000442592.3_5'Flank|EME1_ENST00000511648.2_Missense_Mutation_p.T101A|EME1_ENST00000393271.2_Missense_Mutation_p.T101A|MRPL27_ENST00000225969.4_5'Flank	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	101					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			TCAAAGGCTTACATGTAAGTT	0.428								Direct reversal of damage;Homologous recombination																													p.T101A		Atlas-SNP	.											.	EME1	39	.	0			c.A301G						.						82	85	84					17																	48452870		2203	4300	6503	SO:0001583	missense	146956	exon2			AGGCTTACATGTA	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"	610885	"essential meiotic endonuclease 1 homolog 1 (S. pombe)"			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.301A>G	chr17.hg19:g.48452870A>G	ENSP00000339897:p.Thr101Ala	180.0	0.0		156.0	71.0	NM_152463	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	hg19	CCDS11565.1	.	.	.	.	.	.	.	.	.	.	A	0.684	-0.797025	0.02862	.	.	ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511519;ENST00000511648	T;T;T;T	0.18502	2.92;2.91;2.21;2.91	4.84	-0.259	0.12971	.	1.055010	0.07445	N	0.897984	T	0.11410	0.0278	L	0.29908	0.895	0.09310	N	1	B;B	0.23937	0.034;0.094	B;B	0.21708	0.036;0.026	T	0.38415	-0.9662	10	0.30078	T	0.28	.	5.3177	0.15864	0.5715:0.2784:0.15:0.0	.	101;101	Q96AY2-2;Q96AY2	.;EME1_HUMAN	A	101	ENSP00000339897:T101A;ENSP00000376952:T101A;ENSP00000423029:T101A;ENSP00000421700:T101A	ENSP00000339897:T101A	T	+	1	0	EME1	45807869	0.001000	0.12720	0.000000	0.03702	0.018000	0.09664	1.178000	0.31981	0.037000	0.15575	-0.912000	0.02778	ACA	.	.		0.428	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463		G	48452870	A	G	48452870	3	3	23	1	0	0	0	0	1	0	0	0	5090	391	14	2	303	2	EME1	17	48452870	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	176244	48452870	32742340	930	2996										
NME1	4830	hgsc.bcm.edu	37	chr17	49233116	49233116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttttgagcagaaaggattccGccttgttggtctgaaattca	10	7	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:49233116G>A	ENST00000393196.3	+	2	232	c.101G>A	c.(100-102)cGc>cAc	p.R34H	NME2_ENST00000555572.1_Missense_Mutation_p.R59H|NME2_ENST00000376392.6_Missense_Mutation_p.R34H|NME1_ENST00000336097.3_Missense_Mutation_p.R59H|NME1-NME2_ENST00000608447.1_Missense_Mutation_p.R59H|NME1_ENST00000511355.1_Missense_Mutation_p.R34H|NME1_ENST00000480143.1_Missense_Mutation_p.R59H|NME1-NME2_ENST00000393198.3_Missense_Mutation_p.R34H|NME1_ENST00000013034.3_Missense_Mutation_p.R59H|NME2_ENST00000393193.2_Missense_Mutation_p.R34H	NM_000269.2	NP_000260.1	P15531	NDKA_HUMAN	NME/NM23 nucleoside diphosphate kinase 1	34					cellular response to drug (GO:0035690)|cellular response to fatty acid (GO:0071398)|cellular response to glucose stimulus (GO:0071333)|CTP biosynthetic process (GO:0006241)|DNA catabolic process (GO:0006308)|endocytosis (GO:0006897)|GTP biosynthetic process (GO:0006183)|hippocampus development (GO:0021766)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amine (GO:0014075)|response to cAMP (GO:0051591)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|deoxyribonuclease activity (GO:0004536)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|nucleoside diphosphate kinase activity (GO:0004550)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|single-stranded DNA binding (GO:0003697)			endometrium(1)|large_intestine(1)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)		Adefovir Dipivoxil(DB00718)|Lamivudine(DB00709)|Tenofovir(DB00300)	AAAGGATTCCGCCTTGTTGGT	0.458																																					p.R59H	GBM(176;1298 2890 6639 30062)	Atlas-SNP	.											.	NME1	12	.	0			c.G176A						.						211	181	191					17																	49233116		2203	4300	6503	SO:0001583	missense	4830	exon3			GATTCCGCCTTGT	AL360191, X17620	CCDS11578.1, CCDS11579.1	17q21.33	2013-04-29	2012-05-18		ENSG00000239672	ENSG00000239672			7849	protein-coding gene	gene with protein product		156490	"non-metastatic cells 1, protein (NM23A) expressed in"			8270257, 19852809	Standard	NM_000269		Approved	NM23, NM23-H1, NDPKA		P15531	OTTHUMG00000137474	ENST00000393196.3:c.101G>A	chr17.hg19:g.49233116G>A	ENSP00000376892:p.Arg34His	138.0	0.0		139.0	32.0	NM_198175	Q6FGK3|Q86XQ2|Q9UDJ6	Missense_Mutation	SNP	ENST00000393196.3	hg19	CCDS11579.1	.	.	.	.	.	.	.	.	.	.	G	9.471	1.095664	0.20471	.	.	ENSG00000239672;ENSG00000239672;ENSG00000239672;ENSG00000239672;ENSG00000239672;ENSG00000239672;ENSG00000011052;ENSG00000011052;ENSG00000243678;ENSG00000243678	ENST00000393196;ENST00000336097;ENST00000480143;ENST00000511355;ENST00000013034;ENST00000456492;ENST00000376392;ENST00000555572;ENST00000393193;ENST00000393198	T;T;T;T;T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48;0.48;0.48;0.48;0.48	4.93	-2.4	0.06583	.	.	.	.	.	T	0.37128	0.0992	L	0.41824	1.3	0.09310	N	1	B;B;B;B	0.26120	0.142;0.018;0.033;0.1	B;B;B;B	0.23018	0.043;0.002;0.018;0.025	T	0.29181	-1.0020	9	0.54805	T	0.06	.	5.2607	0.15571	0.4413:0.0:0.3435:0.2152	.	59;59;34;59	E7ERL0;Q32Q12;P15531;P15531-2	.;.;NDKA_HUMAN;.	H	34;59;59;34;59;59;34;59;34;59	ENSP00000376892:R34H;ENSP00000337060:R59H;ENSP00000429318:R59H;ENSP00000428553:R34H;ENSP00000013034:R59H;ENSP00000387682:R59H;ENSP00000365572:R34H;ENSP00000451932:R59H;ENSP00000376889:R34H	ENSP00000013034:R59H	R	+	2	0	NME2;NME1-NME2;NME1	46588115	0.001000	0.12720	0.112000	0.21494	0.045000	0.14185	0.033000	0.13754	-0.407000	0.07576	-0.749000	0.03505	CGC	.	.		0.458	NME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268662.2	NM_000269		A	49233116	G	A	49233116	3	1	23	1	0	0	0	0	1	0	0	0	10498	1087	38	1	182	1	NME1	17	49233116	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	780246	49233116	31962094	931	2997										
PPM1D	8493	hgsc.bcm.edu	37	chr17	58740416	58740416	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	accatatacctgccctggttCgtagcaatgccttctcagag	8	13	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:58740416C>T	ENST00000305921.3	+	6	1553	c.1321C>T	c.(1321-1323)Cgt>Tgt	p.R441C	RNU6-623P_ENST00000363143.1_RNA	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	441					G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of cell proliferation (GO:0008285)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			TGCCCTGGTTCGTAGCAATGC	0.408											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.R441C		Atlas-SNP	.											PPM1D,colon,carcinoma,0,1	PPM1D	50	.	0			c.C1321T						.						109	109	109					17																	58740416		2203	4300	6503	SO:0001583	missense	8493	exon6			CTGGTTCGTAGCA	U78305	CCDS11625.1	17q23.3	2014-09-17	2010-03-05		ENSG00000170836	ENSG00000170836		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9277	protein-coding gene	gene with protein product	"wild-type p53-induced phosphatase 1", "protein phosphatase 2C, delta isoform"	605100	"protein phosphatase 1D magnesium-dependent, delta isoform"			9177166	Standard	NM_003620		Approved	Wip1, PP2C-DELTA	uc002iyt.2	O15297		ENST00000305921.3:c.1321C>T	chr17.hg19:g.58740416C>T	ENSP00000306682:p.Arg441Cys	148.0	0.0	1033	160.0	65.0	NM_003620	Q53XP4|Q6P991|Q8IVR6	Missense_Mutation	SNP	ENST00000305921.3	hg19	CCDS11625.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.170723	0.78452	.	.	ENSG00000170836	ENST00000305921	T	0.55413	0.52	5.78	4.75	0.60458	.	0.103267	0.64402	D	0.000005	T	0.56455	0.1986	L	0.29908	0.895	0.54753	D	0.999989	D	0.89917	1.0	P	0.57846	0.828	T	0.56529	-0.7964	10	0.51188	T	0.08	-6.7846	15.9796	0.80097	0.1353:0.8647:0.0:0.0	.	441	O15297	PPM1D_HUMAN	C	441	ENSP00000306682:R441C	ENSP00000306682:R441C	R	+	1	0	PPM1D	56095198	0.980000	0.34600	1.000000	0.80357	0.913000	0.54294	2.592000	0.46171	2.894000	0.99253	0.591000	0.81541	CGT	.	.		0.408	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620		T	58740416	C	T	58740416	3	4	23	1	0	0	0	0	1	0	0	0	12349	884	31	1	1343	1	PPM1D	17	58740416	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	9507300	58740416	22454794	932	2998										
CD79B	974	hgsc.bcm.edu	37	chr17	62007735	62007735	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggctctgccagatccgcgaAcaagcactacctgtgggtgc	13	13	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:62007735A>G	ENST00000006750.3	-	3	221	c.129T>C	c.(127-129)tgT>tgC	p.C43C	CD79B_ENST00000349817.2_Intron|CD79B_ENST00000392795.3_Silent_p.C44C	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	43	Ig-like V-type.				B cell receptor signaling pathway (GO:0050853)|immune response (GO:0006955)|signal transduction (GO:0007165)	B cell receptor complex (GO:0019815)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						AGATCCGCGAACAAGCACTAC	0.612			"Mis, O"		DLBCL																																p.C44C		Atlas-SNP	.		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	.	CD79B	38	.	0			c.T132C						.						41	34	36					17																	62007735		2203	4300	6503	SO:0001819	synonymous_variant	974	exon3			CCGCGAACAAGCA	L27587	CCDS11655.1, CCDS11656.1, CCDS42372.1	17q23	2014-09-17	2006-03-28			ENSG00000007312		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1699	protein-coding gene	gene with protein product		147245	"CD79B antigen (immunoglobulin-associated beta)"	IGB		9545642	Standard	XM_005257858		Approved	B29	uc002jdp.1	P40259		ENST00000006750.3:c.129T>C	chr17.hg19:g.62007735A>G		62.0	0.0		81.0	28.0	NM_001039933	Q53FS2|Q9BU06	Silent	SNP	ENST00000006750.3	hg19	CCDS11655.1																																																																																			.	.		0.612	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			G	62007735	A	G	62007735	2	3	23	1	0	0	0	0	0	0	0	1	3039	41	2	2		2	CD79B	17	62007735	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3267319	62007735	19187475	933	2999										
BPTF	2186	hgsc.bcm.edu	37	chr17	65862621	65862621	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaatgaaaagaaaatttggtAttacagcacaaaggtccaac	7	6	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:65862621A>G	ENST00000321892.4	+	3	1539	c.1478A>G	c.(1477-1479)tAt>tGt	p.Y493C	BPTF_ENST00000424123.3_Missense_Mutation_p.Y354C|BPTF_ENST00000306378.6_Missense_Mutation_p.Y493C|BPTF_ENST00000335221.5_Missense_Mutation_p.Y493C			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	493					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAAATTTGGTATTACAGCACA	0.333																																					p.Y493C		Atlas-SNP	.											.	BPTF	415	.	0			c.A1478G						.						81	93	89					17																	65862621		2203	4300	6503	SO:0001583	missense	2186	exon3			TTTGGTATTACAG	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.1478A>G	chr17.hg19:g.65862621A>G	ENSP00000315454:p.Tyr493Cys	175.0	0.0		152.0	71.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	A	16.44	3.123571	0.56613	.	.	ENSG00000171634	ENST00000544491;ENST00000306378;ENST00000335221;ENST00000321892;ENST00000544778	T;T;T;D	0.86769	-1.26;-1.37;-1.31;-2.17	5.84	5.84	0.93424	.	.	.	.	.	D	0.94082	0.8103	M	0.84846	2.72	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.998;0.999	D	0.94854	0.8016	9	0.87932	D	0	.	16.2302	0.82332	1.0:0.0:0.0:0.0	.	493;493;493	Q12830;Q12830-2;Q12830-4	BPTF_HUMAN;.;.	C	398;493;493;493;354	ENSP00000307208:Y493C;ENSP00000334351:Y493C;ENSP00000315454:Y493C;ENSP00000440854:Y354C	ENSP00000307208:Y493C	Y	+	2	0	BPTF	63293083	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.095000	0.89535	2.228000	0.72767	0.533000	0.62120	TAT	.	.		0.333	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65862621	A	G	65862621	3	3	23	1	0	0	0	0	1	0	0	0	1497	449	16	2	1488	2	BPTF	17	65862621	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3854886	65862621	15332589	934	3000										
ABCA9	10350	hgsc.bcm.edu	37	chr17	66972304	66972304	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggtagactgtgagaggctgTactcctccaggtcgaaactc	13	10	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:66972304T>C	ENST00000340001.4	-	38	4959	c.4748A>G	c.(4747-4749)tAc>tGc	p.Y1583C	ABCA9_ENST00000453985.2_Missense_Mutation_p.Y1545C|ABCA9_ENST00000370732.2_3'UTR	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1583					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					TGAGAGGCTGTACTCCTCCAG	0.393																																					p.Y1583C		Atlas-SNP	.											.	ABCA9	192	.	0			c.A4748G						.						97	89	92					17																	66972304		2203	4300	6503	SO:0001583	missense	10350	exon38			AGGCTGTACTCCT	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.4748A>G	chr17.hg19:g.66972304T>C	ENSP00000342216:p.Tyr1583Cys	197.0	0.0		217.0	59.0	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	hg19	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.915024	0.52546	.	.	ENSG00000154258	ENST00000340001;ENST00000453985	D	0.89343	-2.5	4.92	4.92	0.64577	.	0.000000	0.42682	D	0.000666	D	0.96396	0.8824	H	0.97240	3.965	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97625	1.0138	10	0.87932	D	0	.	13.7627	0.62977	0.0:0.0:0.0:1.0	.	1583	Q8IUA7	ABCA9_HUMAN	C	1583;1528	ENSP00000342216:Y1583C	ENSP00000342216:Y1583C	Y	-	2	0	ABCA9	64483899	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	5.261000	0.65496	1.854000	0.53819	0.496000	0.49642	TAC	.	.		0.393	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		C	66972304	T	C	66972304	3	2	23	1	0	0	0	0	1	0	0	0	39	1638	57	2	134	2	ABCA9	17	66972304	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1109683	66972304	14222906	935	3001										
GRIN2C	2905	hgsc.bcm.edu	37	chr17	72840513	72840513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaggcgaagaccagcagggCcagccccatggccaccagca	12	17	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:72840513C>T	ENST00000293190.5	-	12	2631	c.2485G>A	c.(2485-2487)Gcc>Acc	p.A829T	GRIN2C_ENST00000347612.4_Missense_Mutation_p.A829T	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	829					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ACCAGCAGGGCCAGCCCCATG	0.597																																					p.A829T		Atlas-SNP	.											.	GRIN2C	144	.	0			c.G2485A						.						114	103	107					17																	72840513		2203	4300	6503	SO:0001583	missense	2905	exon12			GCAGGGCCAGCCC		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.2485G>A	chr17.hg19:g.72840513C>T	ENSP00000293190:p.Ala829Thr	135.0	0.0		133.0	52.0	NM_000835	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	hg19	CCDS32724.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.543653	0.45280	.	.	ENSG00000161509	ENST00000293190;ENST00000347612	T	0.44083	0.93	4.79	3.74	0.42951	.	0.119523	0.53938	D	0.000047	T	0.21387	0.0515	N	0.08118	0	0.44380	D	0.997289	B;B	0.32573	0.376;0.273	B;B	0.36666	0.214;0.23	T	0.09100	-1.0690	10	0.87932	D	0	.	3.2291	0.06742	0.223:0.5647:0.0:0.2124	.	863;829	Q8IW23;Q14957	.;NMDE3_HUMAN	T	829;863	ENSP00000293190:A829T	ENSP00000293190:A829T	A	-	1	0	GRIN2C	70352108	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.903000	0.63272	2.360000	0.80028	0.561000	0.74099	GCC	.	.		0.597	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1			T	72840513	C	T	72840513	3	4	23	1	0	0	0	0	1	0	0	0	6790	739	26	3	1224	3	GRIN2C	17	72840513	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5868209	72840513	8354697	936	3002										
ICT1	3396	hgsc.bcm.edu	37	chr17	73008822	73008822	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcgctggggcctgagccgagCcggagtctggctgctcccac							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:73008822delC	ENST00000301585.5	+	1	54	c.41delC	c.(40-42)gccfs	p.A14fs		NM_001545.1	NP_001536.1	Q14197	ICT1_HUMAN	immature colon carcinoma transcript 1	14					mitochondrial translational termination (GO:0070126)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	aminoacyl-tRNA hydrolase activity (GO:0004045)|translation release factor activity, codon nonspecific (GO:0016150)			NS(1)|central_nervous_system(1)|lung(2)|ovary(1)|urinary_tract(1)	6	all_lung(278;0.226)					CTGAGCCGAGCCGGAGTCTGG	0.687											OREG0024724	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A14fs		Atlas-Indel,Pindel	.											.	ICT1	17	.	0			c.40delG						.						12	11	11					17																	73008822		2168	4256	6424	SO:0001589	frameshift_variant	3396	exon1			.	X81788	CCDS11711.1	17q25	2014-02-12				ENSG00000167862			5359	protein-coding gene	gene with protein product		603000				8575443, 20186120	Standard	NM_001545		Approved	DS-1	uc002jmm.3	Q14197		ENST00000301585.5:c.41delC	chr17.hg19:g.73008822delC	ENSP00000301585:p.Ala14fs	88.0	0.0	1142	82.0	33.0	NM_001545	B2RAD1|Q53HM7|Q53Y11	Frame_Shift_Del	DEL	ENST00000301585.5	hg19	CCDS11711.1																																																																																			.	.		0.687	ICT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445314.1	NM_001545		-	73008822	C	-	73008822	7	5	23	1	0	1	0	1	0	0	0	0	7497	739	26	0	43	0	ICT1	17	73008822	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	168309	73008822	8186388	937	3003										
KIAA0195	9772	hgsc.bcm.edu	37	chr17	73490855	73490855	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caacgcctgcatccgctttgTctacttctctttggaggatg	9	12	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:73490855T>C	ENST00000314256.7	+	19	2949	c.2555T>C	c.(2554-2556)gTc>gCc	p.V852A	KIAA0195_ENST00000375248.5_Missense_Mutation_p.V862A|KIAA0195_ENST00000579208.1_Missense_Mutation_p.V503A|AC100787.1_ENST00000579379.1_RNA	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	852						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			ATCCGCTTTGTCTACTTCTCT	0.567																																					p.V852A		Atlas-SNP	.											.	KIAA0195	102	.	0			c.T2555C						.						102	93	96					17																	73490855		2203	4300	6503	SO:0001583	missense	9772	exon19			GCTTTGTCTACTT		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.2555T>C	chr17.hg19:g.73490855T>C	ENSP00000313885:p.Val852Ala	116.0	0.0		127.0	46.0	NM_014738	O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	hg19	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.088382	0.55968	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	T;T	0.69685	-0.42;-0.42	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.82655	0.5084	M	0.81341	2.54	0.80722	D	1	D;D;D	0.71674	0.993;0.998;0.997	D;D;D	0.77557	0.967;0.99;0.978	D	0.85196	0.1012	10	0.87932	D	0	-42.2554	16.1298	0.81418	0.0:0.0:0.0:1.0	.	862;862;852	B4DGC6;C9JL75;Q12767	.;.;K0195_HUMAN	A	852;862	ENSP00000313885:V852A;ENSP00000364397:V862A	ENSP00000313885:V852A	V	+	2	0	KIAA0195	71002450	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.954000	0.87848	2.208000	0.71279	0.482000	0.46254	GTC	.	.		0.567	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738		C	73490855	T	C	73490855	3	2	23	1	0	0	0	0	1	0	0	0	8169	1667	58	2	2625	2	KIAA0195	17	73490855	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	482033	73490855	7704355	938	3004										
GALK1	2584	hgsc.bcm.edu	37	chr17	73754367	73754367	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agccaccgaagccaccgcccGtcatgcggctgccataaacc	9	18	1	0	rs371517491		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:73754367G>A	ENST00000588479.1	-	7	1605	c.1031C>T	c.(1030-1032)aCg>aTg	p.T344M	GALK1_ENST00000225614.2_Missense_Mutation_p.T344M|GALK1_ENST00000437911.1_Missense_Mutation_p.T374M			P51570	GALK1_HUMAN	galactokinase 1	344					carbohydrate metabolic process (GO:0005975)|galactitol metabolic process (GO:0019402)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|galactose binding (GO:0005534)			endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	5	all_cancers(13;1.5e-07)		all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCCACCGCCCGTCATGCGGCT	0.672																																					p.T344M		Atlas-SNP	.											.	GALK1	17	.	0			c.C1031T	GRCh37	CM993835	GALK1	M		.	G	MET/THR	0,4354		0,0,2177	14	17	16		1031	4.5	0.9	17		16	1,8555		0,1,4277	no	missense	GALK1	NM_000154.1	81	0,1,6454	AA,AG,GG		0.0117,0.0,0.0077	probably-damaging	344/393	73754367	1,12909	2177	4278	6455	SO:0001583	missense	2584	exon7			CCGCCCGTCATGC		CCDS11728.1	17q25.1	2013-09-19			ENSG00000108479	ENSG00000108479	2.7.1.6		4118	protein-coding gene	gene with protein product		604313		GALK		7670469	Standard	NM_000154		Approved		uc002jpk.3	P51570	OTTHUMG00000179832	ENST00000588479.1:c.1031C>T	chr17.hg19:g.73754367G>A	ENSP00000465930:p.Thr344Met	90.0	0.0		94.0	32.0	NM_000154	B2RC07|B4E1G6	Missense_Mutation	SNP	ENST00000588479.1	hg19	CCDS11728.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.847209	0.91277	0.0	1.17E-4	ENSG00000108479	ENST00000225614;ENST00000437911	D;D	0.91631	-2.88;-2.88	4.46	4.46	0.54185	GHMP kinase, C-terminal (1);	.	.	.	.	D	0.95749	0.8617	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96383	0.9283	9	0.87932	D	0	-11.08	17.3028	0.87187	0.0:0.0:1.0:0.0	.	344	P51570	GALK1_HUMAN	M	344;374	ENSP00000225614:T344M;ENSP00000406305:T374M	ENSP00000225614:T344M	T	-	2	0	GALK1	71265962	1.000000	0.71417	0.946000	0.38457	0.973000	0.67179	9.060000	0.93907	2.317000	0.78254	0.563000	0.77884	ACG	.	.		0.672	GALK1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448430.1			A	73754367	G	A	73754367	3	1	23	1	0	0	0	0	1	0	0	0	6211	1145	40	1	155	1	GALK1	17	73754367	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	263512	73754367	7440843	939	3005										
FBF1	85302	hgsc.bcm.edu	37	chr17	73910972	73910972	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggcgccgccgctcctccccGcacttgagcatgacagactt	10	17	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:73910972G>A	ENST00000586717.1	-	24	2901	c.2628C>T	c.(2626-2628)tgC>tgT	p.C876C	RP11-552F3.12_ENST00000587556.1_5'Flank|FBF1_ENST00000389570.4_Silent_p.C876C|FBF1_ENST00000319129.5_Silent_p.C875C			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	876					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						GCTCCTCCCCGCACTTGAGCA	0.677																																					p.C875C		Atlas-SNP	.											.	FBF1	48	.	0			c.C2625T						.						24	29	27					17																	73910972		2102	4209	6311	SO:0001819	synonymous_variant	85302	exon24			CTCCCCGCACTTG	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.2628C>T	chr17.hg19:g.73910972G>A		75.0	0.0		81.0	28.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	hg19																																																																																				.	.		0.677	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		A	73910972	G	A	73910972	2	1	23	1	0	0	0	0	0	0	0	1	5703	1079	38	1		1	FBF1	17	73910972	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	156605	73910972	7284238	940	3006										
GALR2	8811	hgsc.bcm.edu	37	chr17	74072920	74072920	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccgcgccatggacatctgcaCcttcgtcttcagctacctgc	8	17	3	0	rs534747980		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:74072920C>A	ENST00000329003.3	+	2	662	c.572C>A	c.(571-573)aCc>aAc	p.T191N	ZACN_ENST00000334586.5_5'Flank|ZACN_ENST00000392503.2_5'Flank	NM_003857.2	NP_003848.1	O43603	GALR2_HUMAN	galanin receptor 2	191					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell surface receptor signaling pathway (GO:0007166)|digestion (GO:0007586)|feeding behavior (GO:0007631)|learning or memory (GO:0007611)|multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|negative regulation of adenylate cyclase activity (GO:0007194)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of large conductance calcium-activated potassium channel activity (GO:1902608)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|peptide hormone binding (GO:0017046)			cervix(1)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	8						GACATCTGCACCTTCGTCTTC	0.697																																					p.T191N		Atlas-SNP	.											.	GALR2	17	.	0			c.C572A						.						45	32	36					17																	74072920		2200	4299	6499	SO:0001583	missense	8811	exon2			TCTGCACCTTCGT	AF040630	CCDS11739.1	17q25.3	2012-08-08			ENSG00000182687	ENSG00000182687		"GPCR / Class A : Galanin receptors"	4133	protein-coding gene	gene with protein product		603691				9685625, 9832121	Standard	NM_003857		Approved	GALNR2	uc002jqm.1	O43603	OTTHUMG00000167479	ENST00000329003.3:c.572C>A	chr17.hg19:g.74072920C>A	ENSP00000329684:p.Thr191Asn	51.0	0.0		52.0	21.0	NM_003857	A5JUU4|Q32MN8	Missense_Mutation	SNP	ENST00000329003.3	hg19	CCDS11739.1	.	.	.	.	.	.	.	.	.	.	C	32	5.165023	0.94727	.	.	ENSG00000182687	ENST00000329003	T	0.72505	-0.66	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.81922	0.4925	L	0.60012	1.86	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82161	-0.0594	10	0.46703	T	0.11	.	17.8276	0.88671	0.0:1.0:0.0:0.0	.	191	O43603	GALR2_HUMAN	N	191	ENSP00000329684:T191N	ENSP00000329684:T191N	T	+	2	0	GALR2	71584515	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	7.706000	0.84615	2.308000	0.77769	0.462000	0.41574	ACC	.	.		0.697	GALR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394760.1			A	74072920	C	A	74072920	3	1	23	1	0	0	0	0	1	0	0	0	6236	507	18	3	578	3	GALR2	17	74072920	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	161948	74072920	7122290	941	3007										
ENGASE	64772	hgsc.bcm.edu	37	chr17	77081342	77081342	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caagctcaagacacagcctcCgacccctccgggtgcccccc	8	21	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:77081342C>T	ENST00000579016.1	+	12	1618	c.1618C>T	c.(1618-1620)Cga>Tga	p.R540*		NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	540						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						ACACAGCCTCCGACCCCTCCG	0.607																																					p.R540X		Atlas-SNP	.											.	ENGASE	55	.	0			c.C1618T						.						31	35	34					17																	77081342		1945	4141	6086	SO:0001587	stop_gained	64772	exon12			AGCCTCCGACCCC	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1618C>T	chr17.hg19:g.77081342C>T	ENSP00000462333:p.Arg540*	502.0	1.0		262.0	198.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Nonsense_Mutation	SNP	ENST00000579016.1	hg19	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	C	37	6.587067	0.97684	.	.	ENSG00000167280	ENST00000545583	.	.	.	5.03	1.63	0.23807	.	1.128810	0.06486	N	0.733791	.	.	.	.	.	.	0.20638	N	0.999875	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-21.8065	6.45	0.21898	0.4837:0.4293:0.0:0.087	.	.	.	.	X	540	.	ENSP00000438577:R540X	R	+	1	2	ENGASE	74592937	0.000000	0.05858	0.121000	0.21740	0.843000	0.47879	0.106000	0.15354	0.449000	0.26747	0.561000	0.74099	CGA	.	.		0.607	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		T	77081342	C	T	77081342	4	4	23	1	0	0	0	0	0	1	0	0	5120	644	23	1	1664	1	ENGASE	17	77081342	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3008422	77081342	4113868	942	3008										
ANAPC11	51529	hgsc.bcm.edu	37	chr17	79857927	79857927	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccatgtgccgccaggaatggAagttcaaggagtgaggcccg	15	10	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:79857927A>T	ENST00000575195.2	+	2	421	c.241A>T	c.(241-243)Aag>Tag	p.K81*	ANAPC11_ENST00000574924.2_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000571874.2_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000571024.2_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000578544.1_3'UTR|ANAPC11_ENST00000357385.3_Missense_Mutation_p.E181V|ANAPC11_ENST00000583839.1_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000572851.2_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000344877.5_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000572639.1_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000579978.1_Nonsense_Mutation_p.K81*|NPB_ENST00000573081.1_5'Flank|ANAPC11_ENST00000392376.3_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000578550.1_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000577747.1_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000577425.1_3'UTR|ANAPC11_ENST00000579133.1_3'UTR|ANAPC11_ENST00000571570.1_Nonsense_Mutation_p.K81*|NPB_ENST00000333383.7_5'Flank			Q9NYG5	APC11_HUMAN	anaphase promoting complex subunit 11	81					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)	2	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			CCAGGAATGGAAGTTCAAGGA	0.642																																					p.K81X		Atlas-SNP	.											.	ANAPC11	1	.	0			c.A241T						.						61	50	54					17																	79857927		2200	4300	6500	SO:0001587	stop_gained	51529	exon3			GAATGGAAGTTCA	AF247565	CCDS11789.1, CCDS32769.1, CCDS74180.1	17q25.3	2011-06-15	2008-10-30			ENSG00000141552		"Anaphase promoting complex subunits"	14452	protein-coding gene	gene with protein product		614534	"anaphase promoting complex subunit 11 (yeast APC11 homolog)"			10922056	Standard	NM_001002245		Approved	HSPC214, APC11, Apc11p, MGC882	uc002kby.1	Q9NYG5		ENST00000575195.2:c.241A>T	chr17.hg19:g.79857927A>T	ENSP00000458515:p.Lys81*	97.0	0.0		50.0	34.0	NM_001002247	A8MTT2|B7ZW64|Q502X9|Q9BW64|Q9P0R2	Nonsense_Mutation	SNP	ENST00000575195.2	hg19	CCDS11789.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	36|36	5.807083|5.807083	0.96967|0.96967	.|.	.|.	ENSG00000141552|ENSG00000141552	ENST00000357385|ENST00000344877;ENST00000392376	.|.	.|.	.|.	5.16|5.16	5.16|5.16	0.70880|0.70880	.|.	0.291843|.	0.25958|.	U|.	0.027215|.	T|.	0.27866|.	0.0686|.	.|.	.|.	.|.	0.28144|0.28144	N|N	0.929673|0.929673	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|.	0.09292|.	-1.0681|.	8|.	0.87932|0.07482	D|T	0|0.82	.|.	14.9859|14.9859	0.71348|0.71348	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	181|.	Q9NYG5-2|.	.|.	V|X	181|81	.|.	ENSP00000349957:E181V|ENSP00000339695:K81X	E|K	+|+	2|1	0|0	ANAPC11|ANAPC11	77451219|77451219	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	8.187000|8.187000	0.89708|0.89708	1.954000|1.954000	0.56735|0.56735	0.460000|0.460000	0.39030|0.39030	GAA|AAG	.	.		0.642	ANAPC11-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440106.2	NM_016476		T	79857927	A	T	79857927	4	4	23	1	0	0	0	0	0	1	0	0	600	247	9	4	552	4	ANAPC11	17	79857927	Nonsense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2776585	79857927	1337283	943	3009										
FOXK2	3607	hgsc.bcm.edu	37	chr17	80521292	80521293	+	Frame_Shift_Del	DEL	AG	AG	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cactgccctgtccagcgagaAgagagagaagcaggaggcgt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:80521292_80521293delAG	ENST00000335255.5	+	2	656_657	c.482_483delAG	c.(481-483)aagfs	p.K161fs		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	161					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			TCCAGCGAGAAGAGAGAGAAGC	0.535																																					p.161_161del		Atlas-Indel,Pindel	.											.	FOXK2	46	.	0			c.481_482del						.																																			SO:0001589	frameshift_variant	3607	exon2			.	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.482_483delAG	chr17.hg19:g.80521298_80521299delAG	ENSP00000335677:p.Lys161fs	140.0	0.0		73.0	45.0	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Frame_Shift_Del	DEL	ENST00000335255.5	hg19	CCDS11813.1																																																																																			.	.		0.535	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		-	80521293	AG	-	80521292	7	5	23	1	0	1	0	1	0	0	0	0	6023	72	3	0	488	0	FOXK2	17	80521292	Frame_Shift_Del	DEL	AG	TCGA-4R-AA8I-01A-11D-A382-10	663365	80521292	673918	944	3010										
ENOSF1	55556	hgsc.bcm.edu	37	chr18	675343	675343	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgggaggcatgtaggaagccCgctggatcatcacgggatac	15	9	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:675343C>T	ENST00000251101.7	-	15	1296	c.1208G>A	c.(1207-1209)cGg>cAg	p.R403Q	ENOSF1_ENST00000383578.3_Missense_Mutation_p.R321Q|ENOSF1_ENST00000340116.7_Missense_Mutation_p.R410Q|ENOSF1_ENST00000583973.1_5'UTR|ENOSF1_ENST00000580982.1_Missense_Mutation_p.R327Q|ENOSF1_ENST00000319815.6_Missense_Mutation_p.R173Q	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	403					cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						GTAGGAAGCCCGCTGGATCAT	0.557																																					p.R410Q		Atlas-SNP	.											.	ENOSF1	44	.	0			c.G1229A						.						83	69	74					18																	675343		2203	4300	6503	SO:0001583	missense	55556	exon14			GAAGCCCGCTGGA	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.1208G>A	chr18.hg19:g.675343C>T	ENSP00000251101:p.Arg403Gln	103.0	0.0		126.0	57.0	NM_202758	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Missense_Mutation	SNP	ENST00000251101.7	hg19	CCDS11822.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.693600	0.30052	.	.	ENSG00000132199	ENST00000383578;ENST00000319815;ENST00000251101;ENST00000340116	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.97	4.83	0.62350	.	0.521550	0.23296	N	0.049728	T	0.27169	0.0666	N	0.20685	0.6	0.80722	D	1	B;B;B;B;B	0.16802	0.01;0.0;0.019;0.001;0.0	B;B;B;B;B	0.11329	0.004;0.001;0.006;0.003;0.001	T	0.06075	-1.0847	10	0.51188	T	0.08	.	8.0276	0.30446	0.0:0.1621:0.0:0.8379	.	410;222;434;403;321	A6NMP3;B3KXE4;Q6ZS08;Q7L5Y1;Q7L5Y1-2	.;.;.;ENOF1_HUMAN;.	Q	321;173;403;410	ENSP00000373072:R321Q;ENSP00000313346:R173Q;ENSP00000251101:R403Q;ENSP00000345974:R410Q	ENSP00000251101:R403Q	R	-	2	0	ENOSF1	665343	0.970000	0.33590	0.907000	0.35723	0.756000	0.42949	1.955000	0.40372	1.088000	0.41272	-0.312000	0.09012	CGG	.	.		0.557	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512		T	675343	C	T	675343	3	4	23	1	0	0	0	0	1	0	0	0	5127	652	23	1	131	1	ENOSF1	18	675343	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10		675343	77401905	945	3011										
CHMP1B	57132	hgsc.bcm.edu	37	chr18	11851635	11851635	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aattaaaaaggccattcagaAgggcaacatggaagttgcga	11	6	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:11851635A>C	ENST00000526991.2	+	1	241	c.125A>C	c.(124-126)aAg>aCg	p.K42T	GNAL_ENST00000334049.6_Intron|GNAL_ENST00000423027.3_Intron|GNAL_ENST00000269162.5_Intron|RP11-78A19.3_ENST00000586474.1_RNA|GNAL_ENST00000535121.1_Intron	NM_020412.4	NP_065145.2	Q7LBR1	CHM1B_HUMAN	charged multivesicular body protein 1B	42					cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|protein transport (GO:0015031)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)			endometrium(1)|lung(1)|urinary_tract(1)	3						GCCATTCAGAAGGGCAACATG	0.488																																					p.K42T		Atlas-SNP	.											.	CHMP1B	16	.	0			c.A125C						.						57	58	58					18																	11851635		2022	4186	6208	SO:0001583	missense	57132	exon1			TTCAGAAGGGCAA	AF306520	CCDS54180.1	18p11.21	2011-09-21	2011-09-21		ENSG00000255112	ENSG00000255112		"Charged multivesicular body proteins"	24287	protein-coding gene	gene with protein product		606486	"chromatin modifying protein 1B"			15537668	Standard	NM_020412		Approved	CHMP1.5, C18orf2, Vps46B	uc002kqe.3	Q7LBR1	OTTHUMG00000165820	ENST00000526991.2:c.125A>C	chr18.hg19:g.11851635A>C	ENSP00000432279:p.Lys42Thr	91.0	0.0		107.0	6.0	NM_020412	Q96E89|Q9HD41	Missense_Mutation	SNP	ENST00000526991.2	hg19	CCDS54180.1	.	.	.	.	.	.	.	.	.	.	A	31	5.078484	0.94000	.	.	ENSG00000255112	ENST00000526991	T	0.73469	-0.75	5.54	5.54	0.83059	.	.	.	.	.	D	0.88448	0.6439	H	0.94385	3.53	0.80722	D	1	D	0.57571	0.98	P	0.60541	0.876	D	0.91445	0.5177	9	0.87932	D	0	.	13.9287	0.63981	1.0:0.0:0.0:0.0	.	42	Q7LBR1	CHM1B_HUMAN	T	42	ENSP00000432279:K42T	ENSP00000432279:K42T	K	+	2	0	CHMP1B	11841635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.155000	0.77445	2.235000	0.73313	0.533000	0.62120	AAG	.	.		0.488	CHMP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386375.2	NM_020412		C	11851635	A	C	11851635	3	2	23	1	0	0	0	0	1	0	0	0	3355	72	3	5	127	5	CHMP1B	18	11851635	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	11176292	11851635	66225613	946	3012										
ROCK1	6093	hgsc.bcm.edu	37	chr18	18625320	18625320	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttctgcagtatagaatcgtgCccatttttcaggcacatcat	7	10	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:18625320C>T	ENST00000399799.2	-	5	1463	c.523G>A	c.(523-525)Gca>Aca	p.A175T		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	175	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TAGAATCGTGCCCATTTTTCA	0.373																																					p.A175T		Atlas-SNP	.											.	ROCK1	162	.	0			c.G523A						.						128	117	121					18																	18625320		2203	4300	6503	SO:0001583	missense	6093	exon5			ATCGTGCCCATTT		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.523G>A	chr18.hg19:g.18625320C>T	ENSP00000382697:p.Ala175Thr	52.0	0.0		69.0	23.0	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	hg19	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	C	36	5.730189	0.96856	.	.	ENSG00000067900	ENST00000399799	T	0.68025	-0.3	5.36	5.36	0.76844	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77811	0.4186	L	0.45137	1.4	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.79024	-0.1972	10	0.87932	D	0	.	19.2924	0.94105	0.0:1.0:0.0:0.0	.	175	Q13464	ROCK1_HUMAN	T	175	ENSP00000382697:A175T	ENSP00000382697:A175T	A	-	1	0	ROCK1	16879318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.559000	0.82265	2.783000	0.95769	0.655000	0.94253	GCA	.	.		0.373	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		T	18625320	C	T	18625320	3	4	23	1	0	0	0	0	1	0	0	0	13532	739	26	3	3657	3	ROCK1	18	18625320	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	6773685	18625320	59451928	947	3013										
NPC1	4864	hgsc.bcm.edu	37	chr18	21136382	21136382	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaggcgagcctggctgctgGgggctgaccagaggtcaact	16	12	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:21136382G>A	ENST00000269228.5	-	8	1705	c.1151C>T	c.(1150-1152)cCc>cTc	p.P384L	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Missense_Mutation_p.P134L	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	384					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CTGGCTGCTGGGGGCTGACCA	0.557																																					p.P384L		Atlas-SNP	.											.	NPC1	114	.	0			c.C1151T						.						48	49	48					18																	21136382		2203	4300	6503	SO:0001583	missense	4864	exon8			CTGCTGGGGGCTG	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.1151C>T	chr18.hg19:g.21136382G>A	ENSP00000269228:p.Pro384Leu	175.0	0.0		182.0	84.0	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	hg19	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.321058	0.81580	.	.	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.97404	-4.37;-4.37	5.97	5.97	0.96955	.	0.099552	0.64402	D	0.000001	D	0.98213	0.9409	M	0.87097	2.86	0.80722	D	1	P;P	0.50369	0.934;0.837	P;P	0.52710	0.707;0.707	D	0.98669	1.0687	10	0.87932	D	0	-19.4693	20.428	0.99075	0.0:0.0:1.0:0.0	.	395;384	Q59GR1;O15118	.;NPC1_HUMAN	L	384;134;229	ENSP00000269228:P384L;ENSP00000408606:P134L	ENSP00000269228:P384L	P	-	2	0	NPC1	19390380	1.000000	0.71417	0.310000	0.25168	0.226000	0.24999	9.863000	0.99569	2.837000	0.97791	0.655000	0.94253	CCC	.	.		0.557	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		A	21136382	G	A	21136382	3	1	23	1	0	0	0	0	1	0	0	0	10579	1232	43	3	2757	3	NPC1	18	21136382	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	2511062	21136382	56940866	948	3014										
DSC3	1825	hgsc.bcm.edu	37	chr18	28584133	28584133	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcagtgctatacccagtaaTattgcaaggattgcccattt	8	9	0	0	rs527772600		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:28584133T>A	ENST00000360428.4	-	13	2168	c.2088A>T	c.(2086-2088)atA>atT	p.I696I	DSC3_ENST00000434452.1_Silent_p.I696I	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	696					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			TACCCAGTAATATTGCAAGGA	0.333																																					p.I696I		Atlas-SNP	.											.	DSC3	225	.	0			c.A2088T						.						98	92	94					18																	28584133		2203	4300	6503	SO:0001819	synonymous_variant	1825	exon13			CAGTAATATTGCA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"Cadherins / Major cadherins"	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.2088A>T	chr18.hg19:g.28584133T>A		115.0	0.0		115.0	41.0	NM_024423	A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	hg19	CCDS32810.1																																																																																			.	.		0.333	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		A	28584133	T	A	28584133	2	1	23	1	0	0	0	0	0	0	0	1	4769	1396	49	4		4	DSC3	18	28584133	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	7447751	28584133	49493115	949	3015										
SETBP1	26040	hgsc.bcm.edu	37	chr18	42532195	42532195	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggaggagctaatcaccaagTtccaagtgttcagaatctcc	9	10	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:42532195T>C	ENST00000282030.5	+	4	3186	c.2890T>C	c.(2890-2892)Ttc>Ctc	p.F964L		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	964						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AATCACCAAGTTCCAAGTGTT	0.483									Schinzel-Giedion syndrome																												p.F964L		Atlas-SNP	.											.	SETBP1	577	.	0			c.T2890C						.						84	82	82					18																	42532195		2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	ACCAAGTTCCAAG	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.2890T>C	chr18.hg19:g.42532195T>C	ENSP00000282030:p.Phe964Leu	176.0	0.0		150.0	11.0	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	hg19	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	T	8.737	0.917947	0.17982	.	.	ENSG00000152217	ENST00000282030	T	0.80994	-1.44	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.56819	0.2011	N	0.03608	-0.345	0.38853	D	0.956315	B	0.33022	0.394	B	0.27796	0.083	T	0.64702	-0.6345	10	0.02654	T	1	.	16.3512	0.83208	0.0:0.0:0.0:1.0	.	964	Q9Y6X0	SETBP_HUMAN	L	964	ENSP00000282030:F964L	ENSP00000282030:F964L	F	+	1	0	SETBP1	40786193	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.107000	0.57811	2.266000	0.75297	0.533000	0.62120	TTC	.	.		0.483	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		C	42532195	T	C	42532195	3	2	23	1	0	0	0	0	1	0	0	0	14144	1725	60	2	3093	2	SETBP1	18	42532195	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	13948062	42532195	35545053	950	3016										
TCF4	6925	hgsc.bcm.edu	37	chr18	52895534	52895534	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagagagggggaggctctgaGgacaccttctcttcctccct	13	12	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:52895534G>A	ENST00000356073.4	-	19	2537	c.1926C>T	c.(1924-1926)tcC>tcT	p.S642S	TCF4_ENST00000457482.3_Silent_p.S486S|TCF4_ENST00000564228.1_Silent_p.S571S|TCF4_ENST00000354452.3_Silent_p.S646S|TCF4_ENST00000540999.1_Silent_p.S618S|TCF4_ENST00000537856.3_Silent_p.S512S|TCF4_ENST00000570177.2_Silent_p.S512S|TCF4_ENST00000564999.1_Silent_p.S642S|TCF4_ENST00000570287.2_Silent_p.S482S|TCF4_ENST00000564403.2_Silent_p.S652S|TCF4_ENST00000398339.1_Silent_p.S748S|TCF4_ENST00000543082.1_Silent_p.S600S|TCF4_ENST00000566279.1_Silent_p.S586S|TCF4_ENST00000561831.3_Silent_p.S482S|TCF4_ENST00000537578.1_Silent_p.S622S|TCF4_ENST00000568740.1_Silent_p.S617S|TCF4_ENST00000567880.1_Silent_p.S582S|TCF4_ENST00000544241.2_Silent_p.S575S|TCF4_ENST00000568673.1_Silent_p.S622S|TCF4_ENST00000566286.1_Silent_p.S639S|TCF4_ENST00000561992.1_Silent_p.S512S|TCF4_ENST00000565018.2_Silent_p.S646S	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	642	Class A specific domain.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GAGGCTCTGAGGACACCTTCT	0.507																																					p.S748S		Atlas-SNP	.											.	TCF4	178	.	0			c.C2244T						.						127	118	121					18																	52895534		2203	4300	6503	SO:0001819	synonymous_variant	6925	exon20			CTCTGAGGACACC	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1926C>T	chr18.hg19:g.52895534G>A		65.0	0.0		74.0	15.0	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Silent	SNP	ENST00000356073.4	hg19	CCDS11960.1																																																																																			.	.		0.507	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		A	52895534	G	A	52895534	2	1	23	1	0	0	0	0	0	0	0	1	15710	987	35	3		3	TCF4	18	52895534	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	10363339	52895534	25181714	951	3017										
ST8SIA3	51046	hgsc.bcm.edu	37	chr18	55024435	55024435	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcccctacggaggctttccaAagagatgttggaagaaaaac	11	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:55024435A>G	ENST00000324000.3	+	3	2628	c.594A>G	c.(592-594)caA>caG	p.Q198Q		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	198					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		AGGCTTTCCAAAGAGATGTTG	0.413																																					p.Q198Q		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.A594G						.						72	76	75					18																	55024435		2203	4300	6503	SO:0001819	synonymous_variant	51046	exon3			TTTCCAAAGAGAT	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"Sialyltransferases"	14269	protein-coding gene	gene with protein product	"ST8Sia III"	609478	"sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.594A>G	chr18.hg19:g.55024435A>G		158.0	0.0		151.0	47.0	NM_015879	A8K0F2|Q6B085|Q9NS41	Silent	SNP	ENST00000324000.3	hg19	CCDS32834.1																																																																																			.	.		0.413	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879		G	55024435	A	G	55024435	2	3	23	1	0	0	0	0	0	0	0	1	15248	11	1	2		2	ST8SIA3	18	55024435	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	2128901	55024435	23052813	952	3018										
VPS4B	9525	hgsc.bcm.edu	37	chr18	61071042	61071042	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	actccatttcacatttggtcGttctataacaatggcacctg	6	11	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:61071042G>A	ENST00000238497.5	-	5	585	c.382C>T	c.(382-384)Cga>Tga	p.R128*	VPS4B_ENST00000591383.1_5'UTR	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	128					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						ACATTTGGTCGTTCTATAACA	0.348																																					p.R128X		Atlas-SNP	.											.	VPS4B	33	.	0			c.C382T						.						69	62	64					18																	61071042		2203	4300	6503	SO:0001587	stop_gained	9525	exon5			TTGGTCGTTCTAT	AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"ATPases / AAA-type"	10895	protein-coding gene	gene with protein product		609983	"suppressor of K+ transport defect 1", "vacuolar protein sorting 4B (yeast)"	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.382C>T	chr18.hg19:g.61071042G>A	ENSP00000238497:p.Arg128*	66.0	0.0		67.0	25.0	NM_004869	Q69HW4|Q9GZS7	Nonsense_Mutation	SNP	ENST00000238497.5	hg19	CCDS11983.1	.	.	.	.	.	.	.	.	.	.	G	38	6.963087	0.97967	.	.	ENSG00000119541	ENST00000238497	.	.	.	5.69	3.83	0.44106	.	0.137128	0.52532	D	0.000068	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-12.3543	14.618	0.68562	0.0:0.0:0.5113:0.4887	.	.	.	.	X	128	.	ENSP00000238497:R128X	R	-	1	2	VPS4B	59222022	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.386000	0.44380	1.394000	0.46624	0.650000	0.86243	CGA	.	.		0.348	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869		A	61071042	G	A	61071042	4	1	23	1	0	0	0	0	0	1	0	0	17228	1153	40	1	980	1	VPS4B	18	61071042	Nonsense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	6046607	61071042	17006206	953	3019										
TMX3	54495	hgsc.bcm.edu	37	chr18	66377257	66377257	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ataaactaagtgaaggcttaCtagaataggaagtagcatcc	9	6	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:66377257C>G	ENST00000299608.2	-	4	582		c.e4+1		TMX3_ENST00000443099.2_Splice_Site|TMX3_ENST00000562706.1_Splice_Site	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3						cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						TGAAGGCTTACTAGAATAGGA	0.358																																					.		Atlas-SNP	.											.	TMX3	44	.	0			c.265+1G>C						.						105	99	101					18																	66377257		2203	4300	6503	SO:0001630	splice_region_variant	54495	exon5			GGCTTACTAGAAT	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"Protein disulfide isomerases"	24718	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 13"		"thioredoxin domain containing 10"	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.265+1G>C	chr18.hg19:g.66377257C>G		96.0	0.0		90.0	17.0	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Splice_Site	SNP	ENST00000299608.2	hg19	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.393874	0.83011	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1057	0.89519	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMX3	64528237	1.000000	0.71417	0.988000	0.46212	0.980000	0.70556	7.407000	0.80029	2.619000	0.88677	0.563000	0.77884	.	.	.		0.358	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022	Intron	G	66377257	C	G	66377257	5	3	23	1	0	0	0	0	0	0	1	0	16283	579	20	4	1150	4	TMX3	18	66377257	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	5306215	66377257	11699991	954	3020										
CD226	10666	hgsc.bcm.edu	37	chr18	67614087	67614087	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaagaaaagagtcatgttatTggaagccatcgttgaattca	9	5	2	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:67614087T>C	ENST00000280200.4	-	3	533	c.265A>G	c.(265-267)Aat>Gat	p.N89D	CD226_ENST00000582621.1_Missense_Mutation_p.N89D|CD226_ENST00000581982.1_Intron|CD226_ENST00000577287.1_Intron	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	89	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)|cytokine production (GO:0001816)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	24		Esophageal squamous(42;0.129)				GTCATGTTATTGGAAGCCATC	0.448																																					p.N89D	NSCLC(184;838 2130 8673 21498 50749)	Atlas-SNP	.											.	CD226	51	.	0			c.A265G						.						115	101	106					18																	67614087		2203	4300	6503	SO:0001583	missense	10666	exon3			TGTTATTGGAAGC	U56102	CCDS11997.1	18q22.3	2013-01-11	2006-03-28		ENSG00000150637	ENSG00000150637		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	16961	protein-coding gene	gene with protein product		605397	"CD226 antigen"			8673704	Standard	NM_006566		Approved	DNAM-1, DNAM1, PTA1, TLiSA1	uc002lkm.4	Q15762	OTTHUMG00000132809	ENST00000280200.4:c.265A>G	chr18.hg19:g.67614087T>C	ENSP00000280200:p.Asn89Asp	245.0	0.0		210.0	18.0	NM_006566	B2R818	Missense_Mutation	SNP	ENST00000280200.4	hg19	CCDS11997.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.693802	0.48202	.	.	ENSG00000150637	ENST00000280200	T	0.02737	4.18	5.51	2.68	0.31781	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.533834	0.22044	N	0.065415	T	0.05777	0.0151	L	0.56769	1.78	0.09310	N	1	P	0.48589	0.912	P	0.47603	0.551	T	0.19647	-1.0299	10	0.44086	T	0.13	.	10.551	0.45087	0.0:0.0:0.4514:0.5486	.	89	Q15762	CD226_HUMAN	D	89	ENSP00000280200:N89D	ENSP00000280200:N89D	N	-	1	0	CD226	65765067	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	-0.187000	0.09656	0.269000	0.21961	0.533000	0.62120	AAT	.	.		0.448	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566		C	67614087	T	C	67614087	3	2	23	1	0	0	0	0	1	0	0	0	2988	1812	63	2	765	2	CD226	18	67614087	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	1236830	67614087	10463161	955	3021										
ZNF236	7776	hgsc.bcm.edu	37	chr18	74587535	74587535	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	catgatcaagcacacaggtgAaaaaccccatgcctgtgcct							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:74587535delA	ENST00000253159.8	+	6	947	c.749delA	c.(748-750)gaafs	p.E250fs	ZNF236_ENST00000320610.9_Frame_Shift_Del_p.E252fs	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	250					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		CACACAGGTGAAAAACCCCAT	0.527											OREG0025069	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E250fs		Pindel	.											.	ZNF236	325	.	0			c.748delG						.						123	126	125					18																	74587535		2013	4177	6190	SO:0001589	frameshift_variant	7776	exon6			.	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"Zinc fingers, C2H2-type"	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.749delA	chr18.hg19:g.74587535delA	ENSP00000253159:p.Glu250fs	117.0	0.0	1154	134.0	42.0	NM_007345	B2RTX9|Q9UL37	Frame_Shift_Del	DEL	ENST00000253159.8	hg19	CCDS42447.1																																																																																			.	.		0.527	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			-	74587535	A	-	74587535	7	5	23	1	0	1	0	1	0	0	0	0	17804	246	9	0	771	0	ZNF236	18	74587535	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	6973448	74587535	3489713	956	3022										
CTDP1	9150	hgsc.bcm.edu	37	chr18	77488909	77488909	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctatgaaattcctttcagagCggttccgccaccccagccgc	8	16	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:77488909C>T	ENST00000299543.7	+	11	2567	c.2420C>T	c.(2419-2421)gCg>gTg	p.A807V	CTDP1_ENST00000075430.7_Intron	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	807					exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		CCTTTCAGAGCGGTTCCGCCA	0.552																																					p.A807V		Atlas-SNP	.											CTDP1,NS,carcinoma,0,1	CTDP1	67	.	0			c.C2420T						.						158	179	172					18																	77488909		2203	4300	6503	SO:0001583	missense	9150	exon11			TCAGAGCGGTTCC	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.2420C>T	chr18.hg19:g.77488909C>T	ENSP00000299543:p.Ala807Val	67.0	0.0		53.0	9.0	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	hg19	CCDS12017.1	.	.	.	.	.	.	.	.	.	.	C	4.726	0.135042	0.09032	.	.	ENSG00000060069	ENST00000299543	T	0.46451	0.87	5.01	-0.0294	0.13918	FCP1-like phosphatase, C-terminal (1);	1.078290	0.07078	N	0.836606	T	0.20495	0.0493	N	0.04043	-0.29	0.80722	D	1	B;B	0.17667	0.023;0.006	B;B	0.10450	0.003;0.005	T	0.12319	-1.0552	10	0.19147	T	0.46	-0.0228	9.0808	0.36550	0.0:0.1879:0.0:0.8121	.	688;807	Q9Y5B0-3;Q9Y5B0	.;CTDP1_HUMAN	V	807	ENSP00000299543:A807V	ENSP00000299543:A807V	A	+	2	0	CTDP1	75589897	1.000000	0.71417	0.356000	0.25785	0.053000	0.15095	1.891000	0.39738	-0.263000	0.09378	-0.199000	0.12753	GCG	.	.		0.552	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715		T	77488909	C	T	77488909	3	4	23	1	0	0	0	0	1	0	0	0	4004	768	27	1	2462	1	CTDP1	18	77488909	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2901374	77488909	588339	957	3023										
ADNP2	22850	hgsc.bcm.edu	37	chr18	77895803	77895803	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccaaaggagaagcttggggAgcgggaagtctacttggcaa	16	7	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:77895803A>T	ENST00000262198.4	+	4	2962	c.2507A>T	c.(2506-2508)gAg>gTg	p.E836V		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	836					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		AAGCTTGGGGAGCGGGAAGTC	0.527																																					p.E836V		Atlas-SNP	.											.	ADNP2	102	.	0			c.A2507T						.						66	66	66					18																	77895803		2203	4300	6503	SO:0001583	missense	22850	exon4			TTGGGGAGCGGGA	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	23803	protein-coding gene	gene with protein product			"zinc finger protein 508"	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.2507A>T	chr18.hg19:g.77895803A>T	ENSP00000262198:p.Glu836Val	48.0	0.0		49.0	13.0	NM_014913	A8K951|O94943|Q9H9P3	Missense_Mutation	SNP	ENST00000262198.4	hg19	CCDS32853.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.425753	0.83667	.	.	ENSG00000101544	ENST00000262198	.	.	.	5.18	5.18	0.71444	.	0.241133	0.35378	N	0.003259	T	0.73682	0.3618	M	0.62723	1.935	0.49130	D	0.999754	D	0.63046	0.992	P	0.61800	0.894	T	0.74153	-0.3757	8	.	.	.	-27.8706	15.1957	0.73084	1.0:0.0:0.0:0.0	.	836	Q6IQ32	ADNP2_HUMAN	V	836	.	.	E	+	2	0	ADNP2	75996794	1.000000	0.71417	0.988000	0.46212	0.940000	0.58332	4.082000	0.57635	2.171000	0.68590	0.533000	0.62120	GAG	.	.		0.527	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913		T	77895803	A	T	77895803	3	4	23	1	0	0	0	0	1	0	0	0	324	304	11	4	2517	4	ADNP2	18	77895803	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	406894	77895803	181445	958	3024										
SHC2	25759	hgsc.bcm.edu	37	chr19	438994	438994	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttcttccaggatccccggacGccaggcacggcctcatggag	12	15	2	0	rs372414911		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:438994G>A	ENST00000264554.6	-	3	575	c.576C>T	c.(574-576)ggC>ggT	p.G192G		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	192	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATCCCCGGACGCCAGGCACGG	0.672																																					p.G192G		Atlas-SNP	.											.	SHC2	47	.	0			c.C576T						.	G		0,3714		0,0,1857	22	23	23		576	-2.2	0.9	19		23	2,8158		0,2,4078	no	coding-synonymous	SHC2	NM_012435.2		0,2,5935	AA,AG,GG		0.0245,0.0,0.0168		192/583	438994	2,11872	1857	4080	5937	SO:0001819	synonymous_variant	25759	exon3			CCGGACGCCAGGC	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"SH2 domain containing"	29869	protein-coding gene	gene with protein product	"neuronal Shc adaptor homolog"	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.576C>T	chr19.hg19:g.438994G>A		244.0	0.0		145.0	95.0	NM_012435	O60230|Q9NPL5|Q9UCX4	Silent	SNP	ENST00000264554.6	hg19	CCDS45891.1																																																																																			.	.		0.672	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3			A	438994	G	A	438994	2	1	23	1	0	0	0	0	0	0	0	1	14286	1074	38	1		1	SHC2	19	438994	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10		438994	58689989	959	3025										
PTBP1	5725	hgsc.bcm.edu	37	chr19	804698	804698	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtgaccctggatgtgctgcAccaggtgaggtggtcccatc	14	11	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:804698A>G	ENST00000349038.4	+	6	675	c.602A>G	c.(601-603)cAc>cGc	p.H201R	PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000356948.6_Missense_Mutation_p.H201R|PTBP1_ENST00000394601.4_Missense_Mutation_p.H201R|MIR4745_ENST00000577608.1_RNA	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	201	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GATGTGCTGCACCAGGTGAGG	0.687																																					p.H201R		Atlas-SNP	.											.	PTBP1	43	.	0			c.A602G						.						58	56	57					19																	804698		2203	4300	6503	SO:0001583	missense	5725	exon6			TGCTGCACCAGGT	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"RNA binding motif (RRM) containing"	9583	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein I"	600693	"polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.602A>G	chr19.hg19:g.804698A>G	ENSP00000014112:p.His201Arg	68.0	0.0		32.0	19.0	NM_031990	Q9BUQ0	Missense_Mutation	SNP	ENST00000349038.4	hg19	CCDS32859.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.009406	0.54361	.	.	ENSG00000011304	ENST00000356948;ENST00000394601;ENST00000349038	T;T;T	0.53640	0.61;0.67;1.01	4.65	4.65	0.58169	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.051377	0.85682	D	0.000000	T	0.47469	0.1447	L	0.47716	1.5	0.80722	D	1	P;B;B	0.34815	0.47;0.038;0.051	B;B;B	0.40702	0.338;0.078;0.17	T	0.53294	-0.8459	10	0.87932	D	0	-48.146	13.2834	0.60228	1.0:0.0:0.0:0.0	.	201;201;201	P26599;P26599-2;Q9BUQ0	PTBP1_HUMAN;.;.	R	201	ENSP00000349428:H201R;ENSP00000408096:H201R;ENSP00000014112:H201R	ENSP00000014112:H201R	H	+	2	0	PTBP1	755698	1.000000	0.71417	0.996000	0.52242	0.495000	0.33615	7.186000	0.77722	1.739000	0.51704	0.533000	0.62120	CAC	.	.		0.687	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1			G	804698	A	G	804698	3	3	23	1	0	0	0	0	1	0	0	0	12737	159	6	2	624	2	PTBP1	19	804698	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	365704	804698	58324285	960	3026										
STK11	6794	hgsc.bcm.edu	37	chr19	1218439	1218439	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aattcaactactgaggaggtTacggcacaaaaatgtcatcc	8	9	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:1218439T>G	ENST00000326873.7	+	2	1487	c.314T>G	c.(313-315)tTa>tGa	p.L105*	STK11_ENST00000585748.1_3'UTR	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	105	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.?(3)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGAGGAGGTTACGGCACAAA	0.547		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																											p.L105X		Atlas-SNP	.	yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	.	STK11	410	.	23	Whole gene deletion(20)|Unknown(2)|Deletion - Frameshift(1)	cervix(15)|lung(4)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.T314G						.						167	173	171					19																	1218439		2010	4168	6178	SO:0001587	stop_gained	6794	exon2	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	GGAGGTTACGGCA	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"polarization-related protein LKB1"	602216	"serine/threonine kinase 11 (Peutz-Jeghers syndrome)"			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.314T>G	chr19.hg19:g.1218439T>G	ENSP00000324856:p.Leu105*	94.0	0.0		70.0	31.0	NM_000455	B2RBX7|E7EW76	Nonsense_Mutation	SNP	ENST00000326873.7	hg19	CCDS45896.1	.	.	.	.	.	.	.	.	.	.	T	46	12.840858	0.99700	.	.	ENSG00000118046	ENST00000326873;ENST00000405031	.	.	.	4.1	4.1	0.47936	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.0596	12.2854	0.54789	0.0:0.0:0.0:1.0	.	.	.	.	X	105	.	ENSP00000324856:L105X	L	+	2	0	STK11	1169439	0.999000	0.42202	0.117000	0.21633	0.785000	0.44390	7.837000	0.86796	1.506000	0.48736	0.402000	0.26972	TTA	.	.		0.547	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		G	1218439	T	G	1218439	4	3	23	1	0	0	0	0	0	1	0	0	15302	1764	61	5	320	5	STK11	19	1218439	Nonsense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	413741	1218439	57910544	961	3027										
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1434830	1434830	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtccctccgtgccagggtcGgggggcccccccgccggcgg					rs368917206		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:1434830delG	ENST00000233078.4	+	12	1304	c.1143delG	c.(1141-1143)tcgfs	p.S381fs	DAZAP1_ENST00000336761.6_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	381	Pro-rich.		S -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCCAGGGTcggggggccccc	0.711																																					p.S381fs		Pindel	.											DAZAP1,colon,carcinoma,0,1	DAZAP1	52	.	0			c.1142delC						.						12	16	15					19																	1434830		2200	4293	6493	SO:0001589	frameshift_variant	26528	exon12			.		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"RNA binding motif (RRM) containing"	2683	protein-coding gene	gene with protein product	"deleted in azoospermia associated protein 1"	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.1143delG	chr19.hg19:g.1434830delG	ENSP00000233078:p.Ser381fs	126.0	0.0		83.0	14.0	NM_018959	Q96MJ3|Q9NRR9	Frame_Shift_Del	DEL	ENST00000233078.4	hg19	CCDS12065.1																																																																																			.	.		0.711	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		-	1434830	G	-	1434830	7	5	23	1	0	1	0	1	0	0	0	0	4246	1103	39	0	1282	0	DAZAP1	19	1434830	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	216391	1434830	57694153	962	3028										
ADAMTSL5	339366	hgsc.bcm.edu	37	chr19	1510710	1510710	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcgggtccaggacacccacGgggtccactcgcccggaccc	13	18	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:1510710G>A	ENST00000413997.2	-	3	148	c.149C>T	c.(148-150)cCg>cTg	p.P50L	CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000330475.4_Missense_Mutation_p.P40L|ADAMTSL5_ENST00000395467.2_5'UTR|ADAMTSL5_ENST00000590562.1_5'UTR			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	50	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGACACCCACGGGGTCCACTC	0.716																																					p.P40L		Atlas-SNP	.											.	ADAMTSL5	24	.	0			c.C119T						.						5	5	5					19																	1510710		2002	3897	5899	SO:0001583	missense	339366	exon3			ACCCACGGGGTCC	BC040620	CCDS12071.1	19p13.3	2008-02-05	2006-02-07	2006-02-07		ENSG00000185761			27912	protein-coding gene	gene with protein product			"thrombospondin, type I, domain containing 6"	THSD6			Standard	NM_213604		Approved		uc002ltd.2	Q6ZMM2		ENST00000413997.2:c.149C>T	chr19.hg19:g.1510710G>A	ENSP00000399364:p.Pro50Leu	206.0	0.0		84.0	52.0	NM_213604	B4DXK7|Q8IW95	Missense_Mutation	SNP	ENST00000413997.2	hg19		.	.	.	.	.	.	.	.	.	.	G	10.35	1.325261	0.24080	.	.	ENSG00000185761	ENST00000413997;ENST00000330475	T;T	0.54479	0.57;0.57	3.43	1.18	0.20946	.	0.682392	0.14384	N	0.322928	T	0.40862	0.1134	L	0.45581	1.43	0.23113	N	0.998277	B;B	0.18863	0.031;0.031	B;B	0.14578	0.011;0.011	T	0.27434	-1.0074	10	0.38643	T	0.18	.	6.6092	0.22741	0.2373:0.0:0.7627:0.0	.	50;40	B4DXK7;Q6ZMM2	.;ATL5_HUMAN	L	50;40	ENSP00000399364:P50L;ENSP00000327608:P40L	ENSP00000327608:P40L	P	-	2	0	ADAMTSL5	1461710	0.015000	0.18098	0.014000	0.15608	0.647000	0.38526	1.583000	0.36579	0.156000	0.19299	0.456000	0.33151	CCG	.	.		0.716	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding		XM_294919		A	1510710	G	A	1510710	3	1	23	1	0	0	0	0	1	0	0	0	278	1116	39	1	1336	1	ADAMTSL5	19	1510710	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	75880	1510710	57618273	963	3029										
TCF3	6929	hgsc.bcm.edu	37	chr19	1625583	1625583	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaccccgctcacctaggctgCcgtctgccgctctccgccgg	11	20	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:1625583C>T	ENST00000262965.5	-	7	835	c.491G>A	c.(490-492)gGc>gAc	p.G164D	TCF3_ENST00000588136.1_Missense_Mutation_p.G164D|TCF3_ENST00000453954.2_Missense_Mutation_p.G80D|TCF3_ENST00000395423.3_Missense_Mutation_p.G113D|TCF3_ENST00000344749.5_Missense_Mutation_p.G164D	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCTAGGCTGCCGTCTGCCGC	0.697			T	"PBX1, HLF, TFPT"	pre B-ALL																																p.G164D		Atlas-SNP	.		Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	.	TCF3	72	.	0			c.G491A						.						9	11	10					19																	1625583		2163	4269	6432	SO:0001583	missense	6929	exon7			AGGCTGCCGTCTG	M65214	CCDS12074.1, CCDS45899.1	19p13.3	2014-02-13	2013-02-26		ENSG00000071564	ENSG00000071564		"Basic helix-loop-helix proteins"	11633	protein-coding gene	gene with protein product	"transcription factor E2-alpha", "immunoglobulin transcription factor 1", "kappa-E2-binding factor", "E2A immunoglobulin enhancer-binding factor E12/E47", "VDR interacting repressor"	147141				2308859, 1967983	Standard	NM_003200		Approved	E2A, ITF1, MGC129647, MGC129648, bHLHb21, VDIR, E47	uc002ltt.4	P15923	OTTHUMG00000180031	ENST00000262965.5:c.491G>A	chr19.hg19:g.1625583C>T	ENSP00000262965:p.Gly164Asp	169.0	0.0		127.0	87.0	NM_003200	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000262965.5	hg19	CCDS12074.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.505246	0.26949	.	.	ENSG00000071564	ENST00000262965;ENST00000344749;ENST00000453954;ENST00000395423	T;T;T	0.40476	1.03;1.03;1.03	4.52	4.52	0.55395	.	0.476605	0.22677	N	0.056981	T	0.36331	0.0963	N	0.16790	0.44	0.19945	N	0.999948	D;P;B	0.61697	0.99;0.954;0.016	P;B;B	0.53861	0.736;0.356;0.003	T	0.16600	-1.0397	10	0.11182	T	0.66	-2.4508	13.9503	0.64113	0.0:1.0:0.0:0.0	.	164;164;113	P15923-2;P15923;Q2TB39	.;TFE2_HUMAN;.	D	164;164;164;113	ENSP00000262965:G164D;ENSP00000344375:G164D;ENSP00000378813:G113D	ENSP00000262965:G164D	G	-	2	0	TCF3	1576583	0.058000	0.20735	0.009000	0.14445	0.017000	0.09413	3.330000	0.52068	2.049000	0.60858	0.561000	0.74099	GGC	.	.		0.697	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1	NM_003200		T	1625583	C	T	1625583	3	4	23	1	0	0	0	0	1	0	0	0	15709	739	26	3	1756	3	TCF3	19	1625583	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	114873	1625583	57503400	964	3030										
REXO1	57455	hgsc.bcm.edu	37	chr19	1827184	1827184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagagggccacacgctcggcAcccctggccctgcggcctcg	13	19	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:1827184A>G	ENST00000170168.4	-	2	1698	c.1604T>C	c.(1603-1605)gTg>gCg	p.V535A	CTB-31O20.4_ENST00000587741.1_RNA|REXO1_ENST00000587524.1_5'Flank|CTB-31O20.4_ENST00000593201.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	535	Interacts with TCEB3.					nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACGCTCGGCACCCCTGGCCC	0.716																																					p.V535A		Atlas-SNP	.											.	REXO1	55	.	0			c.T1604C						.						6	6	6					19																	1827184		1997	3963	5960	SO:0001583	missense	57455	exon2			CTCGGCACCCCTG	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"elongin A binding protein 1"	609614	"transcription elongation factor B polypeptide 3 binding protein 1"	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.1604T>C	chr19.hg19:g.1827184A>G	ENSP00000170168:p.Val535Ala	61.0	0.0		28.0	18.0	NM_020695	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	hg19	CCDS32866.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.240958	0.00274	.	.	ENSG00000079313	ENST00000170168	T	0.10668	2.85	3.93	0.408	0.16377	.	591.051000	0.00687	N	0.000710	T	0.03564	0.0102	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32955	-0.9887	10	0.07644	T	0.81	-3.1855	1.9791	0.03422	0.12:0.1999:0.4747:0.2054	.	535	Q8N1G1	REXO1_HUMAN	A	535	ENSP00000170168:V535A	ENSP00000170168:V535A	V	-	2	0	REXO1	1778184	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-0.065000	0.11617	-0.008000	0.14320	-0.475000	0.04921	GTG	.	.		0.716	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		G	1827184	A	G	1827184	3	3	23	1	0	0	0	0	1	0	0	0	13256	159	6	2	2121	2	REXO1	19	1827184	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	201601	1827184	57301799	965	3031										
DOT1L	84444	hgsc.bcm.edu	37	chr19	2193778	2193778	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agacatcccggccaagtatgCggaggtgagcggatctgagg	16	9	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:2193778C>T	ENST00000398665.3	+	6	620	c.584C>T	c.(583-585)gCg>gTg	p.A195V		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	195	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCAAGTATGCGGAGGTGAGC	0.607																																					p.A195V		Atlas-SNP	.											.	DOT1L	205	.	0			c.C584T						.						87	90	89					19																	2193778		2179	4268	6447	SO:0001583	missense	84444	exon6			AGTATGCGGAGGT	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.584C>T	chr19.hg19:g.2193778C>T	ENSP00000381657:p.Ala195Val	54.0	0.0		26.0	16.0	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817061	0.90790	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000452696	T;T	0.37235	1.21;1.21	4.34	4.34	0.51931	.	0.112447	0.64402	D	0.000012	T	0.68329	0.2989	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.78375	-0.2228	10	0.87932	D	0	-11.0759	15.988	0.80176	0.0:1.0:0.0:0.0	.	195	Q8TEK3-2	.	V	195;195;171	ENSP00000381657:A195V;ENSP00000404284:A171V	ENSP00000221482:A195V	A	+	2	0	DOT1L	2144778	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	5.528000	0.67129	2.249000	0.74217	0.561000	0.74099	GCG	.	.		0.607	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2193778	C	T	2193778	3	4	23	1	0	0	0	0	1	0	0	0	4711	768	27	1	606	1	DOT1L	19	2193778	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	366594	2193778	56935205	966	3032										
LINGO3	645191	hgsc.bcm.edu	37	chr19	2290416	2290416	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcacgcgcgcccggcccgCgctggtggccgtcaccggcc	16	19	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:2290416C>T	ENST00000585527.1	-	1	1607	c.1360G>A	c.(1360-1362)Gcg>Acg	p.A454T	LINGO3_ENST00000404279.1_Missense_Mutation_p.A454T			P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3	454	Ig-like C2-type.					integral component of membrane (GO:0016021)				lung(1)|urinary_tract(1)	2						GCCCGGCCCGCGCTGGTGGCC	0.791																																					p.A454T		Atlas-SNP	.											.	LINGO3	19	.	0			c.G1360A						.						1	1	1					19																	2290416		545	1142	1687	SO:0001583	missense	645191	exon2			GGCCCGCGCTGGT	AK091795	CCDS45905.1	19p13.3	2013-01-11	2007-02-01	2007-02-01		ENSG00000220008		"Immunoglobulin superfamily / I-set domain containing"	21206	protein-coding gene	gene with protein product		609792	"leucine rich repeat neuronal 6B"	LRRN6B		14686891	Standard	NM_001101391		Approved	LERN2	uc010dsx.1	P0C6S8		ENST00000585527.1:c.1360G>A	chr19.hg19:g.2290416C>T	ENSP00000467753:p.Ala454Thr	25.0	0.0		13.0	11.0	NM_001101391		Missense_Mutation	SNP	ENST00000585527.1	hg19	CCDS45905.1	.	.	.	.	.	.	.	.	.	.	c	0.466	-0.886868	0.02511	.	.	ENSG00000220008	ENST00000404279	T	0.77750	-1.12	4.12	-0.116	0.13555	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.42854	0.1221	N	0.02142	-0.665	0.20196	N	0.999928	B	0.02656	0.0	B	0.04013	0.001	T	0.32079	-0.9920	9	0.10902	T	0.67	.	1.5461	0.02565	0.1488:0.4158:0.2211:0.2143	.	454	P0C6S8	LIGO3_HUMAN	T	454	ENSP00000384979:A454T	ENSP00000384979:A454T	A	-	1	0	LINGO3	2241416	0.014000	0.17966	0.605000	0.28930	0.075000	0.17131	-0.010000	0.12743	0.116000	0.18110	0.462000	0.41574	GCG	.	.		0.791	LINGO3-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451291.2	NM_001101391		T	2290416	C	T	2290416	3	4	23	1	0	0	0	0	1	0	0	0	8825	768	27	1	422	1	LINGO3	19	2290416	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	96638	2290416	56838567	967	3033										
DIRAS1	148252	hgsc.bcm.edu	37	chr19	2717762	2717762	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctcttgcccacgccgcccgCcccgaacaccaccacgcggt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:2717762delC	ENST00000323469.4	-	2	226	c.43delG	c.(43-45)gcgfs	p.A15fs	DIRAS1_ENST00000585334.1_Frame_Shift_Del_p.A15fs	NM_145173.3	NP_660156.1	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1	15					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|lung(2)|ovary(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGCCGCCCGCCCCGAACACC	0.682																																					p.A15fs		Atlas-Indel,Pindel	.											DIRAS1,NS,carcinoma,0,1	DIRAS1	26	.	0			c.44delC						.						48	46	46					19																	2717762		2203	4298	6501	SO:0001589	frameshift_variant	148252	exon2			.	BC030660	CCDS12092.1	19p13.3	2014-05-09				ENSG00000176490			19127	protein-coding gene	gene with protein product		607862				12107278	Standard	NM_145173		Approved	Di-Ras1, GBTS1, RIG	uc002lwf.3	O95057		ENST00000323469.4:c.43delG	chr19.hg19:g.2717762delC	ENSP00000325836:p.Ala15fs	46.0	0.0		23.0	17.0	NM_145173		Frame_Shift_Del	DEL	ENST00000323469.4	hg19	CCDS12092.1																																																																																			.	.		0.682	DIRAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451350.1			-	2717762	C	-	2717762	7	5	23	1	0	1	0	1	0	0	0	0	4532	739	26	0	557	0	DIRAS1	19	2717762	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	427346	2717762	56411221	968	3034										
SEMA6B	10501	hgsc.bcm.edu	37	chr19	4548377	4548377	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaacttgaggaccgtccccGcctcagaacccaggaagaca	11	14	1	3	rs145507498		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:4548377G>A	ENST00000586582.1	-	13	1662	c.1352C>T	c.(1351-1353)gCg>gTg	p.A451V	RN7SL121P_ENST00000584223.1_RNA|SEMA6B_ENST00000301293.3_Missense_Mutation_p.A451V|SEMA6B_ENST00000586965.1_Missense_Mutation_p.A451V	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	451	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		GACCGTCCCCGCCTCAGAACC	0.662																																					p.A451V		Atlas-SNP	.											.	SEMA6B	51	.	0			c.C1352T						.	G	VAL/ALA	2,4404		0,2,2201	55	55	55		1352	0.1	0.1	19	dbSNP_134	55	0,8600		0,0,4300	no	missense	SEMA6B	NM_032108.3	64	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	451/889	4548377	2,13004	2203	4300	6503	SO:0001583	missense	10501	exon13			GTCCCCGCCTCAG	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"Semaphorins"	10739	protein-coding gene	gene with protein product	"Sema VIb", "semaphorin Z", "semaphorin VIB"	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.1352C>T	chr19.hg19:g.4548377G>A	ENSP00000467290:p.Ala451Val	122.0	0.0		140.0	61.0	NM_032108	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	hg19	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	.	9.156	1.017611	0.19355	4.54E-4	0.0	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.10573	2.86	4.01	0.0592	0.14331	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.358123	0.30556	N	0.009370	T	0.05502	0.0145	N	0.11698	0.16	0.09310	N	1	B;B	0.15930	0.015;0.006	B;B	0.13407	0.009;0.009	T	0.32824	-0.9892	10	0.48119	T	0.1	.	8.6381	0.33962	0.284:0.0:0.716:0.0	.	451;451	B4DT36;Q9H3T3	.;SEM6B_HUMAN	V	451	ENSP00000301293:A451V	ENSP00000301292:A451V	A	-	2	0	SEMA6B	4499377	0.003000	0.15002	0.129000	0.21949	0.573000	0.36030	0.904000	0.28491	-0.093000	0.12396	0.485000	0.47835	GCG	.	G|1.000;A|0.000		0.662	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108		A	4548377	G	A	4548377	3	1	23	1	0	0	0	0	1	0	0	0	14055	1087	38	1	1334	1	SEMA6B	19	4548377	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1830615	4548377	54580606	969	3035										
ARRDC5	645432	hgsc.bcm.edu	37	chr19	4891359	4891359	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctcgctgctgtccagccgaGaccgccgctctgcactgggc	13	17	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:4891359G>A	ENST00000381781.2	-	3	727	c.728C>T	c.(727-729)tCt>tTt	p.S243F	AC027319.1_ENST00000408608.1_RNA	NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	243										endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		GTCCAGCCGAGACCGCCGCTC	0.592																																					p.S243F		Atlas-SNP	.											.	ARRDC5	19	.	0			c.C728T						.						56	68	64					19																	4891359		2099	4205	6304	SO:0001583	missense	645432	exon3			AGCCGAGACCGCC		CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.728C>T	chr19.hg19:g.4891359G>A	ENSP00000371200:p.Ser243Phe	56.0	0.0		48.0	17.0	NM_001080523		Missense_Mutation	SNP	ENST00000381781.2	hg19	CCDS45929.1	.	.	.	.	.	.	.	.	.	.	G	7.436	0.639764	0.14386	.	.	ENSG00000205784	ENST00000381781	T	0.18338	2.22	4.92	-2.96	0.05547	Immunoglobulin E-set (1);Arrestin-like, C-terminal (1);	2.609720	0.01383	N	0.013012	T	0.09949	0.0244	N	0.24115	0.695	0.09310	N	1	P	0.40266	0.71	B	0.38378	0.272	T	0.09640	-1.0665	10	0.33940	T	0.23	3.5095	0.6696	0.00856	0.2503:0.1522:0.3619:0.2355	.	243	A6NEK1	ARRD5_HUMAN	F	243	ENSP00000371200:S243F	ENSP00000371200:S243F	S	-	2	0	ARRDC5	4842359	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.152000	0.10159	-0.426000	0.07360	-0.961000	0.02630	TCT	.	.		0.592	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1	XM_292803		A	4891359	G	A	4891359	3	1	23	1	0	0	0	0	1	0	0	0	986	942	33	3	304	3	ARRDC5	19	4891359	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	342982	4891359	54237624	970	3036										
ARRDC5	645432	hgsc.bcm.edu	37	chr19	4891371	4891371	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagccgagaccgccgctctGcactgggcgtgaagccctcg	13	17	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:4891371G>T	ENST00000381781.2	-	3	715	c.716C>A	c.(715-717)gCa>gAa	p.A239E	AC027319.1_ENST00000408608.1_RNA	NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	239										endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		CCGCCGCTCTGCACTGGGCGT	0.577																																					p.A239E		Atlas-SNP	.											.	ARRDC5	19	.	0			c.C716A						.						68	76	73					19																	4891371		2084	4215	6299	SO:0001583	missense	645432	exon3			CGCTCTGCACTGG		CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.716C>A	chr19.hg19:g.4891371G>T	ENSP00000371200:p.Ala239Glu	55.0	0.0		51.0	17.0	NM_001080523		Missense_Mutation	SNP	ENST00000381781.2	hg19	CCDS45929.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.576065	0.45902	.	.	ENSG00000205784	ENST00000381781	T	0.16324	2.35	4.92	4.92	0.64577	Immunoglobulin E-set (1);Arrestin-like, C-terminal (1);	0.266274	0.19834	U	0.105015	T	0.25568	0.0622	L	0.29908	0.895	0.09310	N	0.999999	D	0.58620	0.983	P	0.60415	0.874	T	0.10428	-1.0630	10	0.22109	T	0.4	-32.0156	15.8766	0.79170	0.0:0.0:1.0:0.0	.	239	A6NEK1	ARRD5_HUMAN	E	239	ENSP00000371200:A239E	ENSP00000371200:A239E	A	-	2	0	ARRDC5	4842371	0.141000	0.22595	0.011000	0.14972	0.001000	0.01503	3.260000	0.51523	2.667000	0.90743	0.655000	0.94253	GCA	.	.		0.577	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1	XM_292803		T	4891371	G	T	4891371	3	4	23	1	0	0	0	0	1	0	0	0	986	1319	46	3	316	3	ARRDC5	19	4891371	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	12	4891371	54237612	971	3037										
KDM4B	23030	hgsc.bcm.edu	37	chr19	5119732	5119732	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caagttccctggggagggtaCggctggggcagcgctcctag	17	11	0	0	rs374489612	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:5119732C>T	ENST00000159111.4	+	11	1402	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M	KDM4B_ENST00000536461.1_Missense_Mutation_p.T429M	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	395					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						GGGGAGGGTACGGCTGGGGCA	0.672													C|||	2	0.000399361	0.0015	0	5008	,	,		14792	0		0	False		,,,				2504	0				p.T395M		Atlas-SNP	.											.	KDM4B	120	.	0			c.C1184T						.	C	MET/THR	2,4274		0,2,2136	25	18	21		1184	-0.4	0	19		21	0,8426		0,0,4213	no	missense	KDM4B	NM_015015.2	81	0,2,6349	TT,TC,CC		0.0,0.0468,0.0157	benign	395/1097	5119732	2,12700	2138	4213	6351	SO:0001583	missense	23030	exon11			AGGGTACGGCTGG	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1184C>T	chr19.hg19:g.5119732C>T	ENSP00000159111:p.Thr395Met	194.0	1.0		181.0	155.0	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	hg19	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	C	5.454	0.268823	0.10349	4.68E-4	0.0	ENSG00000127663	ENST00000159111;ENST00000536461	T;T	0.16897	2.32;2.31	4.76	-0.385	0.12470	.	2.196000	0.02115	N	0.055111	T	0.10294	0.0252	N	0.11427	0.14	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.04013	0.001;0.0	T	0.30238	-0.9985	10	0.45353	T	0.12	-2.9184	6.6216	0.22806	0.0:0.3429:0.0:0.6571	.	429;395	F5GX28;O94953	.;KDM4B_HUMAN	M	395;429	ENSP00000159111:T395M;ENSP00000440495:T429M	ENSP00000159111:T395M	T	+	2	0	KDM4B	5070732	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.588000	0.23924	0.104000	0.17725	-0.258000	0.10820	ACG	.	.		0.672	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		T	5119732	C	T	5119732	3	4	23	1	0	0	0	0	1	0	0	0	8138	536	19	1	1218	1	KDM4B	19	5119732	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	228361	5119732	54009251	972	3038										
PTPRS	5802	hgsc.bcm.edu	37	chr19	5221076	5221076	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagccgtcagcatcaggcttGggggcgacgctgggcttgcc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:5221076delG	ENST00000587303.1	-	19	3489	c.3390delC	c.(3388-3390)cccfs	p.P1130fs	PTPRS_ENST00000592099.1_Frame_Shift_Del_p.P699fs|PTPRS_ENST00000372412.4_Frame_Shift_Del_p.P1131fs|PTPRS_ENST00000348075.2_Frame_Shift_Del_p.P1108fs|PTPRS_ENST00000353284.2_Frame_Shift_Del_p.P699fs|PTPRS_ENST00000357368.4_Frame_Shift_Del_p.P1130fs|PTPRS_ENST00000588012.1_Frame_Shift_Del_p.P1108fs|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Frame_Shift_Del_p.P1126fs			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1130					cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	CATCAGGCTTGGGGGCGACGC	0.637																																					p.K1131fs		Atlas-Indel,Pindel	.											.	PTPRS	169	.	0			c.3391delA						.						105	97	100					19																	5221076		2203	4300	6503	SO:0001589	frameshift_variant	5802	exon20			.	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.3390delC	chr19.hg19:g.5221076delG	ENSP00000467537:p.Pro1130fs	71.0	0.0		46.0	16.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Frame_Shift_Del	DEL	ENST00000587303.1	hg19	CCDS45930.1																																																																																			.	.		0.637	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			-	5221076	G	-	5221076	7	5	23	1	0	1	0	1	0	0	0	0	12826	1335	47	0	2532	0	PTPRS	19	5221076	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	101344	5221076	53907907	973	3039										
SAFB2	9667	hgsc.bcm.edu	37	chr19	5604862	5604862	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatggctgatgcacttggtcGcctcgtcagatgtcgacatg	13	10	1	2	rs142026681		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:5604862G>A	ENST00000252542.4	-	10	1646	c.1382C>T	c.(1381-1383)gCg>gTg	p.A461V	SAFB2_ENST00000591310.1_5'UTR	NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	461	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		GCACTTGGTCGCCTCGTCAGA	0.547													G|||	1	0.000199681	8e-04	0	5008	,	,		17190	0		0	False		,,,				2504	0				p.A461V	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.C1382T						.	G	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	87	70	76		1382	5.3	1	19	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	no	missense	SAFB2	NM_014649.2	64	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	461/954	5604862	2,13004	2203	4300	6503	SO:0001583	missense	9667	exon10			TTGGTCGCCTCGT	D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"RNA binding motif (RRM) containing"	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.1382C>T	chr19.hg19:g.5604862G>A	ENSP00000252542:p.Ala461Val	83.0	0.0		62.0	18.0	NM_014649	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	hg19	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805080	0.70682	2.27E-4	1.16E-4	ENSG00000130254	ENST00000434962;ENST00000415313;ENST00000394625;ENST00000252542	D	0.83591	-1.74	5.34	5.34	0.76211	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.56097	D	0.000025	D	0.88377	0.6420	M	0.80422	2.495	0.80722	D	1	P	0.41947	0.766	P	0.49799	0.622	D	0.86308	0.1684	10	0.25751	T	0.34	-25.2929	19.0382	0.92987	0.0:0.0:1.0:0.0	.	461	Q14151	SAFB2_HUMAN	V	357;212;461;461	ENSP00000252542:A461V	ENSP00000252542:A461V	A	-	2	0	SAFB2	5555862	1.000000	0.71417	0.983000	0.44433	0.655000	0.38815	9.746000	0.98859	2.505000	0.84491	0.555000	0.69702	GCG	.	G|1.000;A|0.000		0.547	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		A	5604862	G	A	5604862	3	1	23	1	0	0	0	0	1	0	0	0	13822	1087	38	1	1527	1	SAFB2	19	5604862	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	383786	5604862	53524121	974	3040										
SAFB	6294	hgsc.bcm.edu	37	chr19	5661679	5661679	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcgggaacggctggagcgCgaacgcatgcacgtggagca	18	10	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:5661679C>T	ENST00000292123.5	+	15	2120	c.2013C>T	c.(2011-2013)cgC>cgT	p.R671R	SAFB_ENST00000538656.1_Silent_p.R513R|SAFB_ENST00000433404.1_Silent_p.R501R|SAFB_ENST00000454510.1_Silent_p.R602R|SAFB_ENST00000592224.1_Silent_p.R670R|SAFB_ENST00000588852.1_Silent_p.R671R	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	671	Arg-rich.|Glu-rich.|Interaction with POLR2A.|Interaction with SAFB2.				chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GGCTGGAGCGCGAACGCATGC	0.701																																					p.R671R	Colon(88;338 1345 6184 8214 20897)	Atlas-SNP	.											.	SAFB	74	.	0			c.C2013T						.						17	20	19					19																	5661679		2198	4292	6490	SO:0001819	synonymous_variant	6294	exon15			GGAGCGCGAACGC	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"RNA binding motif (RRM) containing"	10520	protein-coding gene	gene with protein product	"Hsp27 ERE-TATA binding protein"	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.2013C>T	chr19.hg19:g.5661679C>T		129.0	0.0		118.0	10.0	NM_002967	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Silent	SNP	ENST00000292123.5	hg19	CCDS12142.1																																																																																			.	.		0.701	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2			T	5661679	C	T	5661679	2	4	23	1	0	0	0	0	0	0	0	1	13821	755	27	1		1	SAFB	19	5661679	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	56817	5661679	53467304	975	3041										
TRIP10	9322	hgsc.bcm.edu	37	chr19	6743585	6743585	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cggctagaccaggatatcaaCgccaccaaggctgatgtgga	12	11	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:6743585C>T	ENST00000313244.9	+	6	524	c.489C>T	c.(487-489)aaC>aaT	p.N163N	TRIP10_ENST00000600428.1_Silent_p.N55N|TRIP10_ENST00000313285.8_Silent_p.N163N|TRIP10_ENST00000596758.1_Silent_p.N163N			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	163	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						AGGATATCAACGCCACCAAGG	0.622																																					p.N163N		Atlas-SNP	.											.	TRIP10	104	.	0			c.C489T						.						62	61	61					19																	6743585		2202	4300	6502	SO:0001819	synonymous_variant	9322	exon6			TATCAACGCCACC	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"Cdc42-interacting protein"	604504	"salt tolerator"	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.489C>T	chr19.hg19:g.6743585C>T		53.0	0.0		65.0	20.0	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Silent	SNP	ENST00000313244.9	hg19																																																																																				.	.		0.622	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2			T	6743585	C	T	6743585	2	4	23	1	0	0	0	0	0	0	0	1	16569	535	19	1		1	TRIP10	19	6743585	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1081906	6743585	52385398	976	3042										
ZNF358	140467	hgsc.bcm.edu	37	chr19	7585482	7585482	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgctcggctctggcttgggcCtcagccctggcaccagctct	12	16	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:7585482C>A	ENST00000597229.1	+	2	1524	c.1354C>A	c.(1354-1356)Ctc>Atc	p.L452I	ZNF358_ENST00000394341.2_Missense_Mutation_p.L452I|CTD-2207O23.11_ENST00000602083.1_RNA|MCOLN1_ENST00000264079.6_5'Flank	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN	zinc finger protein 358	452					embryonic forelimb morphogenesis (GO:0035115)|neural tube development (GO:0021915)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|lung(1)|skin(2)	8						tggcttgggcctcagccctgg	0.687																																					p.L452I		Atlas-SNP	.											.	ZNF358	41	.	0			c.C1354A						.						21	23	22					19																	7585482		2058	4066	6124	SO:0001583	missense	140467	exon2			TTGGGCCTCAGCC	AK001252	CCDS32890.2	19p13.2	2013-01-08			ENSG00000198816	ENSG00000198816		"Zinc fingers, C2H2-type"	16838	protein-coding gene	gene with protein product							Standard	NM_018083		Approved	FLJ10390, ZFEND	uc002mgn.2	Q9NW07		ENST00000597229.1:c.1354C>A	chr19.hg19:g.7585482C>A	ENSP00000472305:p.Leu452Ile	93.0	0.0		110.0	49.0	NM_018083	Q9BTM7	Missense_Mutation	SNP	ENST00000597229.1	hg19	CCDS32890.2	.	.	.	.	.	.	.	.	.	.	C	12.36	1.914796	0.33815	.	.	ENSG00000198816	ENST00000361576;ENST00000394341	T	0.08370	3.1	2.94	0.697	0.18081	.	.	.	.	.	T	0.03178	0.0093	N	0.08118	0	0.24609	N	0.99374	P	0.34522	0.455	B	0.27170	0.077	T	0.40757	-0.9546	9	0.36615	T	0.2	-16.2488	3.2665	0.06867	0.2585:0.5979:0.0:0.1436	.	452	Q9NW07	ZN358_HUMAN	I	452	ENSP00000377873:L452I	ENSP00000354703:L452I	L	+	1	0	ZNF358	7491482	0.001000	0.12720	0.143000	0.22291	0.306000	0.27790	0.032000	0.13732	0.249000	0.21456	0.462000	0.41574	CTC	.	.		0.687	ZNF358-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316747.1			A	7585482	C	A	7585482	3	1	23	1	0	0	0	0	1	0	0	0	17882	681	24	3	1356	3	ZNF358	19	7585482	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	841897	7585482	51543501	977	3043										
XAB2	56949	hgsc.bcm.edu	37	chr19	7687717	7687717	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctccgcactgacaccacacGcttgccaggtcatccacctg	7	18	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:7687717G>A	ENST00000358368.4	-	10	1339	c.1302C>T	c.(1300-1302)agC>agT	p.S434S	XAB2_ENST00000534844.1_Silent_p.S431S	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	434					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						GACACCACACGCTTGCCAGGT	0.657								Direct reversal of damage;Nucleotide excision repair (NER)																													p.S434S		Atlas-SNP	.											XAB2,NS,carcinoma,0,2	XAB2	69	.	0			c.C1302T						.						79	62	68					19																	7687717		2203	4300	6503	SO:0001819	synonymous_variant	56949	exon10			CCACACGCTTGCC	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"SYF1 homolog, RNA splicing factor (S. cerevisiae)", "SYF1 pre-mRNA-splicing factor"	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.1302C>T	chr19.hg19:g.7687717G>A		101.0	0.0		103.0	9.0	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	hg19	CCDS32892.1																																																																																			.	.		0.657	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		A	7687717	G	A	7687717	2	1	23	1	0	0	0	0	0	0	0	1	17433	1078	38	1		1	XAB2	19	7687717	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	102235	7687717	51441266	978	3044										
LASS4	79603	hgsc.bcm.edu	37	chr19	8320763	8320763	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcctctcggtcctgtaccaCgtgagtataccagagtatag	11	11	1	2	rs368700192		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:8320763C>T	ENST00000251363.5	+	6	768	c.468C>T	c.(466-468)caC>caT	p.H156H	CERS4_ENST00000559336.1_Splice_Site_p.H156H|CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000559450.1_Splice_Site_p.H156H|CERS4_ENST00000558331.1_Splice_Site_p.H105H	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	156	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										TCCTGTACCACGTGAGTATAC	0.587																																					p.H156H		Atlas-SNP	.											.	.	.	.	0			c.C468T						.	C		1,4405	2.1+/-5.4	0,1,2202	79	71	74		468	0.5	1	19		74	0,8600		0,0,4300	no	coding-synonymous-near-splice	CERS4	NM_024552.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		156/395	8320763	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	79603	exon6			GTACCACGTGAGT		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"Homeoboxes / CERS class"	23747	protein-coding gene	gene with protein product		615334	"LAG1 longevity assurance homolog 4 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 4"	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.468+1C>T	chr19.hg19:g.8320763C>T		47.0	0.0		52.0	19.0	NM_024552	D6W665	Silent	SNP	ENST00000251363.5	hg19	CCDS12197.1																																																																																			.	.		0.587	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	Silent	T	8320763	C	T	8320763	5	4	23	1	0	0	0	0	0	0	1	0	8650	550	19	1	482	1	LASS4	19	8320763	Splice_Site	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	633046	8320763	50808220	979	3045										
MUC16	94025	hgsc.bcm.edu	37	chr19	9071612	9071612	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaagggtactgtgcgatgcAgactcaggaggacttgcttg	16	7	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:9071612A>G	ENST00000397910.4	-	3	16037	c.15834T>C	c.(15832-15834)tcT>tcC	p.S5278S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5280	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGTGCGATGCAGACTCAGGAG	0.512																																					p.S5278S		Atlas-SNP	.											.	MUC16	4315	.	0			c.T15834C						.						177	172	174					19																	9071612		2069	4214	6283	SO:0001819	synonymous_variant	94025	exon3			CGATGCAGACTCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15834T>C	chr19.hg19:g.9071612A>G		93.0	0.0		116.0	5.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9071612	A	G	9071612	2	3	23	1	0	0	0	0	0	0	0	1	9982	175	7	2		2	MUC16	19	9071612	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	750849	9071612	50057371	980	3046										
ZNF266	10781	hgsc.bcm.edu	37	chr19	9524021	9524021	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aactggaagaactgaaggctTtcccgcactccttacattca	7	12	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:9524021T>G	ENST00000592904.1	-	5	3656	c.1580A>C	c.(1579-1581)aAa>aCa	p.K527T	ZNF266_ENST00000592292.1_Missense_Mutation_p.K527T|ZNF266_ENST00000361151.1_Missense_Mutation_p.K527T|ZNF266_ENST00000588221.1_Missense_Mutation_p.K527T|ZNF266_ENST00000361451.2_Missense_Mutation_p.K527T|ZNF266_ENST00000590306.1_Missense_Mutation_p.K527T|ZNF266_ENST00000588933.1_Missense_Mutation_p.K527T			Q14584	ZN266_HUMAN	zinc finger protein 266	527					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						ACTGAAGGCTTTCCCGCACTC	0.443																																					p.K527T		Atlas-SNP	.											.	ZNF266	65	.	0			c.A1580C						.						92	81	85					19																	9524021		2203	4300	6503	SO:0001583	missense	10781	exon11			AAGGCTTTCCCGC	X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"Zinc fingers, C2H2-type"	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.1580A>C	chr19.hg19:g.9524021T>G	ENSP00000466714:p.Lys527Thr	127.0	0.0		124.0	43.0	NM_001271314	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	hg19	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.445700	0.84101	.	.	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.27890	1.64;1.64	2.4	2.4	0.29515	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.54447	0.1859	M	0.84326	2.69	0.26605	N	0.972956	D	0.89917	1.0	D	0.79784	0.993	T	0.38757	-0.9646	9	0.87932	D	0	.	8.6374	0.33957	0.0:0.0:0.0:1.0	.	527	Q14584	ZN266_HUMAN	T	527	ENSP00000354680:K527T;ENSP00000355047:K527T	ENSP00000355047:K527T	K	-	2	0	ZNF266	9385021	0.994000	0.37717	0.025000	0.17156	0.702000	0.40608	2.799000	0.47892	1.352000	0.45808	0.374000	0.22700	AAA	.	.		0.443	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			G	9524021	T	G	9524021	3	3	23	1	0	0	0	0	1	0	0	0	17820	1841	64	5	73	5	ZNF266	19	9524021	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	452409	9524021	49604962	981	3047										
ICAM5	7087	hgsc.bcm.edu	37	chr19	10405166	10405166	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgctggcctgcgccgcccggGgtcgcccttccccaggagtg	15	18	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:10405166G>A	ENST00000221980.4	+	9	2143	c.2080G>A	c.(2080-2082)Ggt>Agt	p.G694S		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	694	Ig-like C2-type 8.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CGCCGCCCGGGGTCGCCCTTC	0.677																																					p.G694S		Atlas-SNP	.											.	ICAM5	53	.	0			c.G2080A						.						22	24	24					19																	10405166		2202	4298	6500	SO:0001583	missense	7087	exon9			GCCCGGGGTCGCC	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5348	protein-coding gene	gene with protein product	"telencephalin"	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.2080G>A	chr19.hg19:g.10405166G>A	ENSP00000221980:p.Gly694Ser	142.0	0.0		130.0	51.0	NM_003259	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	hg19	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.628501	0.67015	.	.	ENSG00000105376	ENST00000221980	T	0.14391	2.51	5.45	5.45	0.79879	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000065	T	0.47303	0.1438	M	0.92077	3.27	0.38983	D	0.958981	D	0.89917	1.0	D	0.97110	1.0	T	0.60732	-0.7205	10	0.72032	D	0.01	-18.9075	14.7756	0.69729	0.0:0.0:1.0:0.0	.	694	Q9UMF0	ICAM5_HUMAN	S	694	ENSP00000221980:G694S	ENSP00000221980:G694S	G	+	1	0	ICAM5	10266166	1.000000	0.71417	0.997000	0.53966	0.177000	0.22998	5.023000	0.64084	2.574000	0.86865	0.542000	0.68232	GGT	.	.		0.677	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		A	10405166	G	A	10405166	3	1	23	1	0	0	0	0	1	0	0	0	7492	1232	43	3	2114	3	ICAM5	19	10405166	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	881145	10405166	48723817	982	3048										
SLC44A2	57153	hgsc.bcm.edu	37	chr19	10748543	10748543	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcctccagattgccatctaCggcaccaatttctgcacctc	5	17	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:10748543C>T	ENST00000335757.5	+	18	2083	c.1707C>T	c.(1705-1707)taC>taT	p.Y569Y	SLC44A2_ENST00000586078.1_Silent_p.Y569Y|SLC44A2_ENST00000407327.4_Silent_p.Y567Y|SLC44A2_ENST00000588214.1_3'UTR			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	569					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	TTGCCATCTACGGCACCAATT	0.582																																					p.Y569Y		Atlas-SNP	.											.	SLC44A2	56	.	0			c.C1707T						.						159	145	150					19																	10748543		2203	4300	6503	SO:0001819	synonymous_variant	57153	exon18			CATCTACGGCACC	AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"Solute carriers"	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000335757.5:c.1707C>T	chr19.hg19:g.10748543C>T		118.0	0.0		99.0	34.0	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Silent	SNP	ENST00000335757.5	hg19	CCDS12245.1																																																																																			.	.		0.582	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1			T	10748543	C	T	10748543	2	4	23	1	0	0	0	0	0	0	0	1	14651	547	19	1		1	SLC44A2	19	10748543	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	343377	10748543	48380440	983	3049										
LDLR	3949	hgsc.bcm.edu	37	chr19	11217304	11217304	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aaactgcatccatggcagccGgcagtgtgaccgggaatatg	13	10	0	1	rs139507589		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:11217304G>A	ENST00000558518.1	+	5	945	c.758G>A	c.(757-759)cGg>cAg	p.R253Q	LDLR_ENST00000535915.1_Missense_Mutation_p.R212Q|LDLR_ENST00000545707.1_Missense_Mutation_p.R126Q|LDLR_ENST00000455727.2_Intron|LDLR_ENST00000557933.1_Missense_Mutation_p.R253Q|LDLR_ENST00000558013.1_Missense_Mutation_p.R253Q	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	253	LDL-receptor class A 6. {ECO:0000255|PROSITE-ProRule:PRU00124}.		R -> W (may contribute to familial hypercholesterolemia). {ECO:0000269|PubMed:10882754}.		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	CATGGCAGCCGGCAGTGTGAC	0.527																																					p.R253Q	GBM(18;201 575 7820 21545)	Atlas-SNP	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.G758A						.	G	GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	140	124	130		758,758,635,,395,377	4	1	19	dbSNP_134	130	0,8600		0,0,4300	no	missense,missense,missense,intron,missense,missense	LDLR	NM_000527.4,NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195802.1,NM_001195803.1	43,43,43,,43,43	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	253/861,253/859,212/820,,132/740,126/683	11217304	2,13004	2203	4300	6503	SO:0001583	missense	3949	exon5			GCAGCCGGCAGTG	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"Low density lipoprotein receptors"	6547	protein-coding gene	gene with protein product	"familial hypercholesterolemia"	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.758G>A	chr19.hg19:g.11217304G>A	ENSP00000454071:p.Arg253Gln	136.0	0.0		118.0	46.0	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	hg19	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.455809	0.43634	4.54E-4	0.0	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000535915	D;D	0.94897	-3.55;-3.55	5.1	4.0	0.46444	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.231332	0.28748	N	0.014264	D	0.89891	0.6846	N	0.25957	0.775	0.42200	D	0.991769	B;B;B;B;B	0.33512	0.301;0.415;0.24;0.275;0.415	B;B;B;B;B	0.40565	0.215;0.191;0.191;0.333;0.114	D	0.85575	0.1236	10	0.33940	T	0.23	.	7.2448	0.26115	0.0998:0.0:0.7375:0.1627	.	126;132;212;265;253	B4DJZ8;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;LDLR_HUMAN	Q	253;126;212	ENSP00000437639:R126Q;ENSP00000440520:R212Q	ENSP00000252444:R253Q	R	+	2	0	LDLR	11078304	0.900000	0.30661	0.996000	0.52242	0.619000	0.37552	1.193000	0.32162	1.010000	0.39314	0.462000	0.41574	CGG	.	G|1.000;A|0.000		0.527	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2			A	11217304	G	A	11217304	3	1	23	1	0	0	0	0	1	0	0	0	8713	1116	39	1	776	1	LDLR	19	11217304	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	468761	11217304	47911679	984	3050										
ZNF700	90592	hgsc.bcm.edu	37	chr19	12059373	12059373	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagaaagccttcaggtatcgCccatccattagaacacaaga	7	11	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:12059373C>T	ENST00000254321.5	+	4	677	c.534C>T	c.(532-534)cgC>cgT	p.R178R	ZNF763_ENST00000591944.1_Intron|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF700_ENST00000482090.1_Silent_p.R160R|ZNF763_ENST00000538752.1_Intron|ZNF763_ENST00000590798.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	178					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						TCAGGTATCGCCCATCCATTA	0.408																																					p.R181R		Atlas-SNP	.											.	ZNF700	81	.	0			c.C543T						.						97	97	97					19																	12059373		2203	4300	6503	SO:0001819	synonymous_variant	90592	exon4			GTATCGCCCATCC	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"Zinc fingers, C2H2-type", "-"	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.534C>T	chr19.hg19:g.12059373C>T		156.0	0.0		161.0	8.0	NM_001271848	B9EGU4	Silent	SNP	ENST00000254321.5	hg19	CCDS32915.1																																																																																			.	.		0.408	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		T	12059373	C	T	12059373	2	4	23	1	0	0	0	0	0	0	0	1	18119	726	26	3		3	ZNF700	19	12059373	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	842069	12059373	47069610	985	3051										
ZNF490	57474	hgsc.bcm.edu	37	chr19	12692077	12692077	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agggtttctctccagtgtgaTttttttcatggcgccgaaga							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:12692077delT	ENST00000311437.6	-	5	934	c.812delA	c.(811-813)aatfs	p.N271fs	CTD-2192J16.20_ENST00000593682.1_5'Flank|ZNF490_ENST00000465656.1_5'Flank	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						TCCAGTGTGATTTTTTTCATG	0.413																																					p.N271fs		Atlas-Indel,Pindel	.											.	ZNF490	42	.	0			c.813delT						.						87	86	87					19																	12692077		2203	4300	6503	SO:0001589	frameshift_variant	57474	exon5			.	AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"Zinc fingers, C2H2-type", "-"	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.812delA	chr19.hg19:g.12692077delT	ENSP00000311521:p.Asn271fs	82.0	0.0		83.0	29.0	NM_020714		Frame_Shift_Del	DEL	ENST00000311437.6	hg19	CCDS12272.1																																																																																			.	.		0.413	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714		-	12692077	T	-	12692077	7	5	23	1	0	1	0	1	0	0	0	0	17956	1493	52	0	781	0	ZNF490	19	12692077	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	632704	12692077	46436906	986	3052										
NANOS3	342977	hgsc.bcm.edu	37	chr19	13988407	13988407	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gactacgtgtgtccccagtgCggcgccacacgtgagcgcgc	14	15	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:13988407C>T	ENST00000397555.2	+	2	288	c.288C>T	c.(286-288)tgC>tgT	p.C96C	MIR181D_ENST00000384853.1_RNA|NANOS3_ENST00000591727.1_Intron|MIR181C_ENST00000384881.1_RNA|NANOS3_ENST00000339133.5_Silent_p.C115C	NM_001098622.2	NP_001092092.1	P60323	NANO3_HUMAN	nanos homolog 3 (Drosophila)	96					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	7			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			GTCCCCAGTGCGGCGCCACAC	0.662																																					p.C115C		Atlas-SNP	.											.	NANOS3	19	.	0			c.C345T						.						30	35	33					19																	13988407		2159	4263	6422	SO:0001819	synonymous_variant	342977	exon1			CCAGTGCGGCGCC	BM702754	CCDS42511.1	19p13.13	2003-12-01				ENSG00000187556			22048	protein-coding gene	gene with protein product		608229					Standard	NM_001098622		Approved	NANOS1L, NOS3	uc002mxj.4	P60323		ENST00000397555.2:c.288C>T	chr19.hg19:g.13988407C>T		69.0	0.0		56.0	24.0	NM_001098622	Q495E5	Silent	SNP	ENST00000397555.2	hg19																																																																																				.	.		0.662	NANOS3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_292819		T	13988407	C	T	13988407	2	4	23	1	0	0	0	0	0	0	0	1	10162	776	27	1		1	NANOS3	19	13988407	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1296330	13988407	45140576	987	3053										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14024359	14024359	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccagccggcccctagaatcgCgtcagccccagagcccaggg	12	18	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:14024359C>T	ENST00000318003.7	+	6	897	c.656C>T	c.(655-657)gCg>gTg	p.A219V	CC2D1A_ENST00000589606.1_Missense_Mutation_p.A219V	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	219	Pro-rich.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)	p.A219V(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			CCTAGAATCGCGTCAGCCCCA	0.667																																					p.A219V		Atlas-SNP	.											CC2D1A,NS,carcinoma,0,1	CC2D1A	67	.	1	Substitution - Missense(1)	endometrium(1)	c.C656T						.						29	37	35					19																	14024359		1965	4121	6086	SO:0001583	missense	54862	exon6			GAATCGCGTCAGC	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.656C>T	chr19.hg19:g.14024359C>T	ENSP00000313601:p.Ala219Val	180.0	1.0		171.0	64.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	hg19	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	C	9.837	1.189970	0.21954	.	.	ENSG00000132024	ENST00000318003;ENST00000254346;ENST00000389233	T	0.21932	1.98	2.95	-5.0	0.03001	.	1.588220	0.04137	N	0.318934	T	0.10380	0.0254	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.001;0.005	B;B	0.06405	0.0;0.002	T	0.24835	-1.0149	10	0.33141	T	0.24	-1.3178	4.3426	0.11117	0.1638:0.2978:0.0:0.5384	.	219;219	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	V	219;57;194	ENSP00000313601:A219V	ENSP00000254346:A57V	A	+	2	0	CC2D1A	13885359	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.035000	0.01423	-0.956000	0.03631	-0.448000	0.05591	GCG	.	.		0.667	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		T	14024359	C	T	14024359	3	4	23	1	0	0	0	0	1	0	0	0	2728	768	27	1	678	1	CC2D1A	19	14024359	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	35952	14024359	45104624	988	3054										
AKAP8	10270	hgsc.bcm.edu	37	chr19	15483896	15483896	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gacgcagcggggggcacgaaGgggtcgctgcgcatgaaggt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:15483896delG	ENST00000269701.2	-	5	687	c.627delC	c.(625-627)cccfs	p.P209fs		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	209					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						GGGGCACGAAGGGGTCGCTGC	0.731																																					p.F210fs	GBM(190;1671 2163 3274 27186 30476)	Atlas-Indel,Pindel	.											.	AKAP8	68	.	0			c.628delT						.						10	13	12					19																	15483896		2188	4271	6459	SO:0001589	frameshift_variant	10270	exon5			.	Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"A-kinase anchor proteins"	378	protein-coding gene	gene with protein product	"A-kinase anchor protein, 95kDa"	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.627delC	chr19.hg19:g.15483896delG	ENSP00000269701:p.Pro209fs	151.0	0.0		175.0	66.0	NM_005858		Frame_Shift_Del	DEL	ENST00000269701.2	hg19	CCDS12329.1																																																																																			.	.		0.731	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858		-	15483896	G	-	15483896	7	5	23	1	0	1	0	1	0	0	0	0	457	987	35	0	1491	0	AKAP8	19	15483896	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	1459537	15483896	43645087	989	3055										
TPM4	7171	hgsc.bcm.edu	37	chr19	16192750	16192750	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgatgtggccgccctcaacCgacgcatccagctcgttgag	12	14	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:16192750C>T	ENST00000300933.4	+	2	420	c.160C>T	c.(160-162)Cga>Tga	p.R54*	TPM4_ENST00000344824.6_Nonsense_Mutation_p.R90*|TPM4_ENST00000538887.1_Nonsense_Mutation_p.R90*	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4	54					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)		TPM4/ALK(12)	breast(1)|large_intestine(3)	4						CGCCCTCAACCGACGCATCCA	0.612			T	ALK	ALCL																																p.R90X		Atlas-SNP	.		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	.	TPM4	28	.	0			c.C268T						.						46	47	47					19																	16192750		2203	4300	6503	SO:0001587	stop_gained	7171	exon3			CTCAACCGACGCA		CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"Tropomyosins"	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134	ENST00000300933.4:c.160C>T	chr19.hg19:g.16192750C>T	ENSP00000300933:p.Arg54*	55.0	0.0		48.0	23.0	NM_001145160	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Nonsense_Mutation	SNP	ENST00000300933.4	hg19	CCDS12338.1	.	.	.	.	.	.	.	.	.	.	C	37	6.056672	0.97241	.	.	ENSG00000167460	ENST00000344824;ENST00000538887;ENST00000300933	.	.	.	4.62	3.57	0.40892	.	0.000000	0.52532	U	0.000080	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.1957	12.0321	0.53403	0.3305:0.6695:0.0:0.0	.	.	.	.	X	90;90;54	.	ENSP00000300933:R54X	R	+	1	2	TPM4	16053750	0.908000	0.30866	0.925000	0.36789	0.931000	0.56810	1.047000	0.30367	1.026000	0.39733	0.591000	0.81541	CGA	.	.		0.612	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290		T	16192750	C	T	16192750	4	4	23	1	0	0	0	0	0	1	0	0	16423	644	23	1	414	1	TPM4	19	16192750	Nonsense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	708854	16192750	42936233	990	3056										
TMEM38A	79041	hgsc.bcm.edu	37	chr19	16797152	16797152	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttcaccctccagcagacccGctggctcccagtgtccaaag	8	18	1	1	rs78725797		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:16797152G>A	ENST00000187762.2	+	5	699	c.608G>A	c.(607-609)cGc>cAc	p.R203H		NM_024074.1	NP_076979.1	Q9H6F2	TM38A_HUMAN	transmembrane protein 38A	203						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)	15						CAGCAGACCCGCTGGCTCCCA	0.562																																					p.R203H		Atlas-SNP	.											.	TMEM38A	32	.	0			c.G608A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	131	95	107		608	3.8	1	19	dbSNP_131	107	0,8600		0,0,4300	no	missense	TMEM38A	NM_024074.1	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	203/300	16797152	1,13005	2203	4300	6503	SO:0001583	missense	79041	exon5			AGACCCGCTGGCT	AK025981	CCDS12349.1	19p13.11	2013-05-23				ENSG00000072954			28462	protein-coding gene	gene with protein product		611235				17611541	Standard	NM_024074		Approved	MGC3169, TRIC-A	uc002nes.3	Q9H6F2		ENST00000187762.2:c.608G>A	chr19.hg19:g.16797152G>A	ENSP00000187762:p.Arg203His	48.0	0.0		44.0	13.0	NM_024074	A8K9P9	Missense_Mutation	SNP	ENST00000187762.2	hg19	CCDS12349.1	.	.	.	.	.	.	.	.	.	.	g	9.106	1.005306	0.19199	2.27E-4	0.0	ENSG00000072954	ENST00000187762	.	.	.	4.87	3.84	0.44239	.	0.110837	0.64402	D	0.000011	T	0.15349	0.0370	N	0.00869	-1.13	0.36185	D	0.849713	B	0.11235	0.004	B	0.08055	0.003	T	0.09907	-1.0653	9	0.33940	T	0.23	-42.5728	5.1808	0.15160	0.2785:0.0:0.7215:0.0	.	203	Q9H6F2	TM38A_HUMAN	H	203	.	ENSP00000187762:R203H	R	+	2	0	TMEM38A	16658152	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.170000	0.58229	2.257000	0.74773	0.655000	0.94253	CGC	.	.		0.562	TMEM38A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462841.1	NM_024074		A	16797152	G	A	16797152	3	1	23	1	0	0	0	0	1	0	0	0	16174	1087	38	1	626	1	TMEM38A	19	16797152	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	604402	16797152	42331831	991	3057										
ANO8	57719	hgsc.bcm.edu	37	chr19	17434419	17434419	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggggatccgaggtgggcggTagcggtgggggcgggaggct	25	6	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:17434419T>C	ENST00000159087.4	-	18	3764	c.3606A>G	c.(3604-3606)ctA>ctG	p.L1202L		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	1202	Pro-rich.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						aggtgggcggtagcggtgggg	0.751																																					p.L1202L		Atlas-SNP	.											.	ANO8	67	.	0			c.A3606G						.						4	6	5					19																	17434419		1263	2728	3991	SO:0001819	synonymous_variant	57719	exon18			GGGCGGTAGCGGT	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	29329	protein-coding gene	gene with protein product		610216	"KIAA1623", "transmembrane protein 16H"	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.3606A>G	chr19.hg19:g.17434419T>C		48.0	0.0		44.0	4.0	NM_020959	A6NIJ0	Silent	SNP	ENST00000159087.4	hg19	CCDS32949.1																																																																																			.	.		0.751	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644		C	17434419	T	C	17434419	2	2	23	1	0	0	0	0	0	0	0	1	703	1625	57	2		2	ANO8	19	17434419	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	637267	17434419	41694564	992	3058										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22155265	22155265	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcacatttgtagggtttctcTccagtatgaattaccttatg	7	8	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:22155265T>C	ENST00000397126.4	-	4	2719	c.2571A>G	c.(2569-2571)ggA>ggG	p.G857G	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	857					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGGGTTTCTCTCCAGTATGAA	0.373																																					p.G857G		Atlas-SNP	.											.	ZNF208	817	.	0			c.A2571G						.						39	41	41					19																	22155265		2024	4204	6228	SO:0001819	synonymous_variant	7757	exon4			TTTCTCTCCAGTA	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2571A>G	chr19.hg19:g.22155265T>C		52.0	0.0		42.0	15.0	NM_007153		Silent	SNP	ENST00000397126.4	hg19	CCDS54240.1																																																																																			.	.		0.373	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		C	22155265	T	C	22155265	2	2	23	1	0	0	0	0	0	0	0	1	17781	1538	54	2		2	ZNF208	19	22155265	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	4720846	22155265	36973718	993	3059										
C19orf2	8725	hgsc.bcm.edu	37	chr19	30503420	30503420	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aatcaaaagaaacttttgccCttatcagtaacacctgaggt	6	9	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:30503420C>A	ENST00000542441.2	+	10	1704	c.1407C>A	c.(1405-1407)ccC>ccA	p.P469P	URI1_ENST00000392271.1_Silent_p.P393P|URI1_ENST00000312051.6_Silent_p.P429P|URI1_ENST00000360605.4_Silent_p.P451P			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	469					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)										AACTTTTGCCCTTATCAGTAA	0.368																																					p.P469P		Atlas-SNP	.											.	.	.	.	0			c.C1407A						.						67	72	70					19																	30503420		2203	4300	6503	SO:0001819	synonymous_variant	8725	exon10			TTTGCCCTTATCA	AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.1407C>A	chr19.hg19:g.30503420C>A		88.0	0.0		106.0	41.0	NM_003796	A8K805|H7BY42|Q8TC23|Q9UNU3	Silent	SNP	ENST00000542441.2	hg19	CCDS12420.1																																																																																			.	.		0.368	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		A	30503420	C	A	30503420	2	1	23	1	0	0	0	0	0	0	0	1	1913	668	24	3		3	C19orf2	19	30503420	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	8348155	30503420	28625563	994	3060										
CHST8	64377	hgsc.bcm.edu	37	chr19	34263780	34263780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acttcttcctgagcctcatcCgcgcgccgcggaacctgacc	9	18	2	2	rs557313187		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:34263780C>T	ENST00000262622.4	+	4	1845	c.1087C>T	c.(1087-1089)Cgc>Tgc	p.R363C	CHST8_ENST00000438847.3_Missense_Mutation_p.R363C|CHST8_ENST00000434302.1_Missense_Mutation_p.R363C	NM_022467.3	NP_071912.2	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8	363					carbohydrate biosynthetic process (GO:0016051)|central nervous system development (GO:0007417)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(5)	27	Esophageal squamous(110;0.162)					GAGCCTCATCCGCGCGCCGCG	0.632													C|||	1	0.000199681	8e-04	0	5008	,	,		18248	0		0	False		,,,				2504	0				p.R363C		Atlas-SNP	.											.	CHST8	70	.	0			c.C1087T						.						64	52	56					19																	34263780		2203	4300	6503	SO:0001583	missense	64377	exon5			CTCATCCGCGCGC	AB047801	CCDS12433.1	19q13.1	2008-02-05				ENSG00000124302		"Sulfotransferases, membrane-bound"	15993	protein-coding gene	gene with protein product		610190				10988300, 11001942	Standard	NM_001127895		Approved	GALNAC-4-ST1	uc002nut.4	Q9H2A9		ENST00000262622.4:c.1087C>T	chr19.hg19:g.34263780C>T	ENSP00000262622:p.Arg363Cys	102.0	0.0		91.0	41.0	NM_001127895	Q9H3N2	Missense_Mutation	SNP	ENST00000262622.4	hg19	CCDS12433.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.662745	0.67700	.	.	ENSG00000124302	ENST00000434302;ENST00000438847;ENST00000262622	T;T;T	0.74002	-0.8;-0.8;-0.8	5.01	3.93	0.45458	.	0.812256	0.11161	N	0.593112	T	0.74076	0.3669	L	0.39898	1.24	0.37014	D	0.895879	D	0.61080	0.989	P	0.51453	0.67	T	0.77051	-0.2731	10	0.87932	D	0	-23.0001	11.4741	0.50286	0.0:0.5906:0.4093:0.0	.	363	Q9H2A9	CHST8_HUMAN	C	363	ENSP00000392604:R363C;ENSP00000393879:R363C;ENSP00000262622:R363C	ENSP00000262622:R363C	R	+	1	0	CHST8	38955620	0.973000	0.33851	0.560000	0.28344	0.527000	0.34593	6.047000	0.71038	2.331000	0.79229	0.297000	0.19635	CGC	.	.		0.632	CHST8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451453.1	NM_022467		T	34263780	C	T	34263780	3	4	23	1	0	0	0	0	1	0	0	0	3412	652	23	1	1097	1	CHST8	19	34263780	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3760360	34263780	24865203	995	3061										
UBA2	10054	hgsc.bcm.edu	37	chr19	34949675	34949675	+	Splice_Site	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgttatttctcctccaaagaTttttttgaataaacaaccaa							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:34949675delT	ENST00000246548.4	+	13	1317	c.1247delT	c.(1246-1248)att>at	p.I416fs	UBA2_ENST00000592791.1_5'UTR|UBA2_ENST00000439527.2_Splice_Site_p.I320fs	NM_005499.2	NP_005490.1	Q9UBT2	SAE2_HUMAN	ubiquitin-like modifier activating enzyme 2	416					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|SUMO activating enzyme complex (GO:0031510)	ATP binding (GO:0005524)|enzyme activator activity (GO:0008047)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SUMO activating enzyme activity (GO:0019948)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	20	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			CCTCCAAAGATTTTTTTGAAT	0.388																																					p.I416fs		Atlas-Indel,Pindel	.											.	UBA2	53	.	0			c.1246delA						.						88	91	90					19																	34949675		2203	4300	6503	SO:0001630	splice_region_variant	10054	exon13			.	BC003153	CCDS12439.1	19q13.11	2008-02-05	2007-11-30	2007-11-30		ENSG00000126261		"Ubiquitin-like modifier activating enzymes"	30661	protein-coding gene	gene with protein product	"UBA2, ubiquitin-activating enzyme E1 homolog (yeast)"	613295	"SUMO1 activating enzyme subunit 2"	SAE2		10187858, 9920803	Standard	NM_005499		Approved	FLJ13058, HRIHFB2115, ARX	uc002nvk.3	Q9UBT2		ENST00000246548.4:c.1246-1T>-	chr19.hg19:g.34949675delT		170.0	0.0		142.0	12.0	NM_005499	B3KWB9|O95605|Q59H87|Q6IBP6|Q9NTJ1|Q9UED2	Frame_Shift_Del	DEL	ENST00000246548.4	hg19	CCDS12439.1																																																																																			.	.		0.388	UBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459257.3	NM_005499	Frame_Shift_Del	-	34949675	T	-	34949675	8	5	23	1	0	1	0	1	0	0	1	0	16843	1507	52	0	1297	0	UBA2	19	34949675	Splice_Site	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10	685895	34949675	24179308	996	3062										
MLL4	9757	hgsc.bcm.edu	37	chr19	36223002	36223002	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcgccatcccggaggcccttGgggggtgtctcctttggccc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:36223002delG	ENST00000222270.7	+	27	5631	c.5631delG	c.(5629-5631)ttgfs	p.L1877fs	KMT2B_ENST00000420124.1_Frame_Shift_Del_p.L1877fs|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1877					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G1881fs*16(1)									GGAGGCCCTTGGGGGGTGTCT	0.672																																					p.L1877fs		Atlas-Indel,Pindel	.											.	MLL4	229	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.5630delT						.						11	12	12					19																	36223002		1860	4086	5946	SO:0001589	frameshift_variant	8085	exon27			.	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5631delG	chr19.hg19:g.36223002delG	ENSP00000222270:p.Leu1877fs	90.0	0.0		66.0	27.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Frame_Shift_Del	DEL	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.672	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		-	36223002	G	-	36223002	7	5	23	1	0	1	0	1	0	0	0	0	9632	1339	47	0	5737	0	MLL4	19	36223002	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	1273327	36223002	22905981	997	3063										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36357195	36357195	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccctaccttctatgacttcaAcccacacctgggcatggtcc	6	17	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:36357195A>G	ENST00000360202.5	+	15	2126	c.1928A>G	c.(1927-1929)aAc>aGc	p.N643S	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Intron|KIRREL2_ENST00000262625.7_Intron|APLP1_ENST00000221891.4_5'Flank|APLP1_ENST00000537454.2_5'Flank|KIRREL2_ENST00000592409.1_Missense_Mutation_p.N608S	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	643	Pro-rich.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TATGACTTCAACCCACACCTG	0.622																																					p.N643S		Atlas-SNP	.											.	KIRREL2	170	.	0			c.A1928G						.						72	75	74					19																	36357195		2203	4300	6503	SO:0001583	missense	84063	exon15			ACTTCAACCCACA	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.1928A>G	chr19.hg19:g.36357195A>G	ENSP00000353331:p.Asn643Ser	67.0	0.0		82.0	33.0	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	hg19	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	A	0.210	-1.037379	0.02013	.	.	ENSG00000126259	ENST00000360202;ENST00000341658;ENST00000270294	T	0.63255	-0.03	5.1	0.204	0.15199	.	0.711674	0.12648	N	0.450717	T	0.33585	0.0868	N	0.08118	0	0.26540	N	0.974093	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.001;0.003;0.002	T	0.17137	-1.0379	9	.	.	.	-1.7079	4.7512	0.13061	0.3311:0.2578:0.4111:0.0	.	643;623;643	F1T0I2;Q6UWL6-4;Q6UWL6	.;.;KIRR2_HUMAN	S	643;623;154	ENSP00000353331:N643S	.	N	+	2	0	KIRREL2	41049035	0.189000	0.23263	0.208000	0.23602	0.843000	0.47879	0.401000	0.20948	0.026000	0.15269	0.459000	0.35465	AAC	.	.		0.622	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		G	36357195	A	G	36357195	3	3	23	1	0	0	0	0	1	0	0	0	8334	43	2	2	1986	2	KIRREL2	19	36357195	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	134193	36357195	22771788	998	3064										
ZNF461	92283	hgsc.bcm.edu	37	chr19	37130266	37130266	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cattgcttacattcatagggTttttcaccagtatgaagtct	7	8	3	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:37130266T>G	ENST00000588268.1	-	6	1208	c.981A>C	c.(979-981)aaA>aaC	p.K327N	ZNF461_ENST00000360357.4_Missense_Mutation_p.K304N|ZNF461_ENST00000540605.2_5'UTR	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATTCATAGGGTTTTTCACCAG	0.413																																					p.K327N		Atlas-SNP	.											.	ZNF461	73	.	0			c.A981C						.						53	59	57					19																	37130266		2201	4300	6501	SO:0001583	missense	92283	exon6			ATAGGGTTTTTCA	BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"Zinc fingers, C2H2-type", "-"	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.981A>C	chr19.hg19:g.37130266T>G	ENSP00000467931:p.Lys327Asn	117.0	0.0		104.0	38.0	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	hg19	CCDS54257.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.139342	0.56936	.	.	ENSG00000197808	ENST00000396893;ENST00000396896;ENST00000360357;ENST00000540605	T	0.26067	1.76	3.6	3.6	0.41247	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47040	0.1424	M	0.75447	2.3	0.29751	N	0.836322	D;D;D	0.89917	0.996;1.0;1.0	D;D;D	0.91635	0.993;0.999;0.988	T	0.42327	-0.9458	9	0.87932	D	0	.	7.151	0.25610	0.0:0.1116:0.0:0.8884	.	304;249;327	B4DRP8;Q59G30;Q8TAF7	.;.;ZN461_HUMAN	N	327;58;304;200	ENSP00000353515:K304N	ENSP00000353515:K304N	K	-	3	2	ZNF461	41822106	0.006000	0.16342	1.000000	0.80357	0.992000	0.81027	-0.567000	0.05916	1.632000	0.50472	0.477000	0.44152	AAA	.	.		0.413	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		G	37130266	T	G	37130266	3	3	23	1	0	0	0	0	1	0	0	0	17940	1722	60	5	714	5	ZNF461	19	37130266	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	773071	37130266	21998717	999	3065										
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38573540	38573540	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcgcaacgtgagcttctcCcgggcttccgtgggctcccc	13	16	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:38573540C>T	ENST00000222345.6	+	3	1844	c.1335C>T	c.(1333-1335)tcC>tcT	p.S445S		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	445					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TGAGCTTCTCCCGGGCTTCCG	0.667																																					p.S445S		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.C1335T						.						45	49	48					19																	38573540		2202	4300	6502	SO:0001819	synonymous_variant	23094	exon3			CTTCTCCCGGGCT	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.1335C>T	chr19.hg19:g.38573540C>T		96.0	0.0		85.0	39.0	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	hg19	CCDS33007.1																																																																																			.	.		0.667	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		T	38573540	C	T	38573540	2	4	23	1	0	0	0	0	0	0	0	1	14346	610	22	3		3	SIPA1L3	19	38573540	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1443274	38573540	20555443	1000	3066										
FAM98C	147965	hgsc.bcm.edu	37	chr19	38893823	38893823	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgaaggcggaagcgtgggaGggggccgcggtggcccagga							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:38893823delG	ENST00000252530.5	+	1	49	c.30delG	c.(28-30)gagfs	p.E10fs	FAM98C_ENST00000588262.1_Frame_Shift_Del_p.E10fs|FAM98C_ENST00000343358.7_Frame_Shift_Del_p.E10fs	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	10										endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AAGCGTGGGAGGGGGCCGCGG	0.726																																					p.E10fs		Atlas-Indel,Pindel	.											.	FAM98C	39	.	0			c.29delA						.						15	23	20					19																	38893823		2016	4153	6169	SO:0001589	frameshift_variant	147965	exon1			.		CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.30delG	chr19.hg19:g.38893823delG	ENSP00000252530:p.Glu10fs	123.0	0.0		105.0	52.0	NM_174905	A6NMW3|Q66K45	Frame_Shift_Del	DEL	ENST00000252530.5	hg19	CCDS42562.1																																																																																			.	.		0.726	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905		-	38893823	G	-	38893823	7	5	23	1	0	1	0	1	0	0	0	0	5666	991	35	0	32	0	FAM98C	19	38893823	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	320283	38893823	20235160	1001	3067										
MAP4K1	11184	hgsc.bcm.edu	37	chr19	39096218	39096218	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcccattacctgaatgggcGgtgaggtgggggctgctggt	18	8	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:39096218G>A	ENST00000591517.1	-	18	1381	c.1353C>T	c.(1351-1353)acC>acT	p.T451T	MAP4K1_ENST00000423454.2_Silent_p.T113T|MAP4K1_ENST00000586296.1_Intron|MAP4K1_ENST00000396857.2_Silent_p.T451T|MAP4K1_ENST00000589002.1_5'Flank|MAP4K1_ENST00000589130.1_Silent_p.T447T	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	451					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CTGAATGGGCGGTGAGGTGGG	0.672																																					p.T451T		Atlas-SNP	.											.	MAP4K1	165	.	0			c.C1353T						.						4	4	4					19																	39096218		1693	3833	5526	SO:0001819	synonymous_variant	11184	exon18			ATGGGCGGTGAGG	U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6863	protein-coding gene	gene with protein product	"hematopoietic progenitor kinase 1"	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.1353C>T	chr19.hg19:g.39096218G>A		108.0	0.0		81.0	33.0	NM_007181		Silent	SNP	ENST00000591517.1	hg19	CCDS59385.1																																																																																			.	.		0.672	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600		A	39096218	G	A	39096218	2	1	23	1	0	0	0	0	0	0	0	1	9268	1103	39	1		1	MAP4K1	19	39096218	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	202395	39096218	20032765	1002	3068										
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39329068	39329068	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tctcctcggtcacctccagcGgggcgttgaagaagtgcagc	13	13	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:39329068G>A	ENST00000221419.5	-	10	1892	c.1526C>T	c.(1525-1527)cCg>cTg	p.P509L	AC104534.3_ENST00000594769.1_Missense_Mutation_p.R126C|HNRNPL_ENST00000600873.1_Missense_Mutation_p.P376L	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	509	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			CACCTCCAGCGGGGCGTTGAA	0.597																																					p.P509L		Atlas-SNP	.											.	HNRNPL	67	.	0			c.C1526T						.						67	58	61					19																	39329068		2203	4300	6503	SO:0001583	missense	3191	exon10			TCCAGCGGGGCGT	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1526C>T	chr19.hg19:g.39329068G>A	ENSP00000221419:p.Pro509Leu	78.0	0.0		109.0	39.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	hg19	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.183061	0.78677	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750	.	.	.	5.87	5.87	0.94306	Nucleotide-binding, alpha-beta plait (1);	0.051568	0.85682	D	0.000000	D	0.83562	0.5281	M	0.82823	2.61	0.80722	D	1	D;D;D	0.89917	0.994;1.0;0.999	B;D;P	0.68765	0.364;0.96;0.662	D	0.84732	0.0746	9	0.87932	D	0	.	19.3531	0.94398	0.0:0.0:1.0:0.0	.	509;478;492	P14866;B2R959;Q6NTA2	HNRPL_HUMAN;.;.	L	509;376;376	.	ENSP00000221419:P509L	P	-	2	0	HNRNPL	44020908	1.000000	0.71417	0.993000	0.49108	0.963000	0.63663	5.429000	0.66495	2.941000	0.99782	0.655000	0.94253	CCG	.	.		0.597	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			A	39329068	G	A	39329068	3	1	23	1	0	0	0	0	1	0	0	0	7279	1116	39	1	259	1	HNRNPL	19	39329068	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	232850	39329068	19799915	1003	3069										
ADCK4	79934	hgsc.bcm.edu	37	chr19	41219998	41219998	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agttggccaagcggctgatgCgggaggcaggcaccttgcgt	17	10	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:41219998C>T	ENST00000324464.3	-	4	564	c.263G>A	c.(262-264)cGc>cAc	p.R88H	ADCK4_ENST00000450541.1_Missense_Mutation_p.R88H|ADCK4_ENST00000243583.6_Missense_Mutation_p.R88H	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	88						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			GCGGCTGATGCGGGAGGCAGG	0.562																																					p.R88H		Atlas-SNP	.											.	ADCK4	92	.	0			c.G263A						.						89	83	85					19																	41219998		2203	4300	6503	SO:0001583	missense	79934	exon4			CTGATGCGGGAGG	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.263G>A	chr19.hg19:g.41219998C>T	ENSP00000315118:p.Arg88His	145.0	0.0		142.0	28.0	NM_001142555	Q8TAJ1|Q9HA52	Missense_Mutation	SNP	ENST00000324464.3	hg19	CCDS12562.1	.	.	.	.	.	.	.	.	.	.	c	35	5.508631	0.96386	.	.	ENSG00000123815	ENST00000324464;ENST00000450541;ENST00000243583	T;T;T	0.80393	-1.17;-1.37;-1.37	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.90920	0.7146	M	0.91354	3.2	0.58432	D	0.999999	D;D	0.69078	0.994;0.997	P;D	0.63381	0.717;0.914	D	0.92570	0.6065	10	0.66056	D	0.02	-2.9595	16.2208	0.82257	0.0:1.0:0.0:0.0	.	88;88	Q96D53;Q96D53-2	ADCK4_HUMAN;.	H	88	ENSP00000315118:R88H;ENSP00000412839:R88H;ENSP00000243583:R88H	ENSP00000243583:R88H	R	-	2	0	ADCK4	45911838	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.567000	0.73983	2.567000	0.86603	0.556000	0.70494	CGC	.	.		0.562	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876		T	41219998	C	T	41219998	3	4	23	1	0	0	0	0	1	0	0	0	290	768	27	1	1419	1	ADCK4	19	41219998	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1890930	41219998	17908985	1004	3070										
SNRPA	6626	hgsc.bcm.edu	37	chr19	41268862	41268862	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caccacatgccgggccagccGccctacatgccgccccctgg	10	21	0	0	rs374030639		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:41268862G>A	ENST00000243563.3	+	4	1033	c.483G>A	c.(481-483)ccG>ccA	p.P161P		NM_004596.4	NP_004587.1	P09012	SNRPA_HUMAN	small nuclear ribonucleoprotein polypeptide A	161	Pro-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snRNA binding (GO:0017069)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CGGGCCAGCCGCCCTACATGC	0.677																																					p.P161P		Atlas-SNP	.											.	SNRPA	20	.	0			c.G483A						.	G		0,4402		0,0,2201	28	27	28		483	-11.1	0.4	19		28	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	SNRPA	NM_004596.4		0,1,6499	AA,AG,GG		0.0116,0.0,0.0077		161/283	41268862	1,12999	2201	4299	6500	SO:0001819	synonymous_variant	6626	exon4			CCAGCCGCCCTAC	X06347	CCDS12565.1	19q13.1	2013-02-12				ENSG00000077312		"RNA binding motif (RRM) containing"	11151	protein-coding gene	gene with protein product		182285				1701111	Standard	NM_004596		Approved	U1A, U1-A, Mud1	uc002ooz.3	P09012		ENST00000243563.3:c.483G>A	chr19.hg19:g.41268862G>A		125.0	0.0		154.0	7.0	NM_004596		Silent	SNP	ENST00000243563.3	hg19	CCDS12565.1																																																																																			.	.		0.677	SNRPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463118.2	NM_004596		A	41268862	G	A	41268862	2	1	23	1	0	0	0	0	0	0	0	1	14874	1074	38	1		1	SNRPA	19	41268862	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	48864	41268862	17860121	1005	3071										
EGLN2	112398	hgsc.bcm.edu	37	chr19	41307129	41307129	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggccctcaaacggggtgggCgcctgcgagacgggcagcta	17	12	1	1	rs140368149		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:41307129C>T	ENST00000593726.1	+	1	1680	c.652C>T	c.(652-654)Cgc>Tgc	p.R218C	EGLN2_ENST00000303961.4_Missense_Mutation_p.R218C|EGLN2_ENST00000594140.1_5'Flank|RAB4B-EGLN2_ENST00000594136.1_3'UTR|CTC-490E21.12_ENST00000601627.1_5'Flank|EGLN2_ENST00000406058.2_Missense_Mutation_p.R218C			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	218					cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	ACGGGGTGGGCGCCTGCGAGA	0.682																																					p.R218C		Atlas-SNP	.											.	EGLN2	31	.	0			c.C652T						.	C	CYS/ARG,CYS/ARG	0,4404		0,0,2202	50	54	52		652,652	4.1	1	19	dbSNP_134	52	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense	EGLN2	NM_053046.3,NM_080732.3	180,180	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	218/408,218/408	41307129	1,12999	2202	4298	6500	SO:0001583	missense	112398	exon2			GGTGGGCGCCTGC	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"HIF prolyl hydroxylase 1"	606424	"EGL nine (C.elegans) homolog 2", "egl nine homolog 2 (C. elegans)"				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.652C>T	chr19.hg19:g.41307129C>T	ENSP00000469686:p.Arg218Cys	118.0	0.0		125.0	63.0	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Missense_Mutation	SNP	ENST00000593726.1	hg19	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.830995	0.71258	0.0	1.16E-4	ENSG00000171570	ENST00000303961;ENST00000406058	T;T	0.26067	1.76;1.76	4.05	4.05	0.47172	Prolyl 4-hydroxylase, alpha subunit (1);	0.077318	0.49916	D	0.000135	T	0.17450	0.0419	L	0.29908	0.895	0.52099	D	0.999949	B	0.27559	0.181	B	0.24848	0.056	T	0.04976	-1.0914	10	0.38643	T	0.18	-10.4218	9.5003	0.39013	0.3315:0.6685:0.0:0.0	.	218	Q96KS0	EGLN2_HUMAN	C	218	ENSP00000307080:R218C;ENSP00000385253:R218C	ENSP00000307080:R218C	R	+	1	0	EGLN2	45998969	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.981000	0.40628	2.263000	0.75096	0.591000	0.81541	CGC	.	C|1.000;T|0.000		0.682	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1			T	41307129	C	T	41307129	3	4	23	1	0	0	0	0	1	0	0	0	4971	768	27	1	654	1	EGLN2	19	41307129	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	38267	41307129	17821854	1006	3072										
CEACAM5	1048	hgsc.bcm.edu	37	chr19	42224866	42224866	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gccggacacccccatcatttCccccccagactcgtcttacc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:42224866delC	ENST00000221992.6	+	8	1910	c.1796delC	c.(1795-1797)tccfs	p.S599fs	CEA_ENST00000598976.1_Intron|CEACAM5_ENST00000398599.4_Frame_Shift_Del_p.S598fs|CEACAM5_ENST00000405816.1_Frame_Shift_Del_p.S599fs	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	599	Ig-like 7.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CCCATCATTTCCCCCCCAGAC	0.547																																					p.S599fs		Atlas-Indel,Pindel	.											.	CEACAM5	84	.	0			c.1795delT						.						136	141	139					19																	42224866		2203	4300	6503	SO:0001589	frameshift_variant	1048	exon8			.	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1796delC	chr19.hg19:g.42224866delC	ENSP00000221992:p.Ser599fs	156.0	0.0		176.0	64.0	NM_004363	H9KVA7	Frame_Shift_Del	DEL	ENST00000221992.6	hg19	CCDS12584.1																																																																																			.	.		0.547	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363		-	42224866	C	-	42224866	7	5	23	1	0	1	0	1	0	0	0	0	3197	855	30	0	1826	0	CEACAM5	19	42224866	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	917737	42224866	16904117	1007	3073										
GSK3A	2931	hgsc.bcm.edu	37	chr19	42744195	42744195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtacacgaccccaaatgagCcattgccaatcactttgatg	8	12	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:42744195C>T	ENST00000222330.3	-	2	510	c.383G>A	c.(382-384)gGc>gAc	p.G128D	AC006486.1_ENST00000378108.1_5'Flank|GSK3A_ENST00000398249.4_Missense_Mutation_p.G46D|AC006486.9_ENST00000594664.1_Missense_Mutation_p.G41D	NM_019884.2	NP_063937.2	P49840	GSK3A_HUMAN	glycogen synthase kinase 3 alpha	128	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cardiac left ventricle morphogenesis (GO:0003214)|cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|cellular response to interleukin-3 (GO:0036016)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transferase activity (GO:0051348)|negative regulation of type B pancreatic cell development (GO:2000077)|negative regulation of UDP-glucose catabolic process (GO:0010905)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of heart contraction (GO:0045823)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein phosphorylation (GO:0006468)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of systemic arterial blood pressure (GO:0003073)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cytosol (GO:0005829)	ATP binding (GO:0005524)|protein kinase A catalytic subunit binding (GO:0034236)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(3)|large_intestine(3)|lung(6)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	19		Prostate(69;0.00682)				CCCAAATGAGCCATTGCCAAT	0.572																																					p.G128D		Atlas-SNP	.											.	GSK3A	45	.	0			c.G383A						.						165	121	136					19																	42744195		2203	4300	6503	SO:0001583	missense	2931	exon2			AATGAGCCATTGC		CCDS12599.1	19q13	2008-02-15			ENSG00000105723	ENSG00000105723			4616	protein-coding gene	gene with protein product		606784				9809441	Standard	NM_019884		Approved		uc002otb.1	P49840	OTTHUMG00000150722	ENST00000222330.3:c.383G>A	chr19.hg19:g.42744195C>T	ENSP00000222330:p.Gly128Asp	129.0	0.0		111.0	12.0	NM_019884	O14959	Missense_Mutation	SNP	ENST00000222330.3	hg19	CCDS12599.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148837	0.94603	.	.	ENSG00000105723	ENST00000222330;ENST00000398249;ENST00000544315	D;D	0.91180	-2.8;-2.8	5.22	5.22	0.72569	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.96781	0.8949	H	0.94808	3.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97712	1.0191	10	0.87932	D	0	-6.3289	17.9284	0.88990	0.0:1.0:0.0:0.0	.	128;46	P49840;A8MT37	GSK3A_HUMAN;.	D	128;46;73	ENSP00000222330:G128D;ENSP00000381301:G46D	ENSP00000222330:G128D	G	-	2	0	GSK3A	47436035	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.273000	0.78527	2.622000	0.88805	0.555000	0.69702	GGC	.	.		0.572	GSK3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319782.1			T	42744195	C	T	42744195	3	4	23	1	0	0	0	0	1	0	0	0	6832	739	26	3	1108	3	GSK3A	19	42744195	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	519329	42744195	16384788	1008	3074										
CNFN	84518	hgsc.bcm.edu	37	chr19	42893103	42893103	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggcatgtcgttgcagcagtcCgtgagacctgtgtgccagtc	14	11	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:42893103C>T	ENST00000222032.5	-	2	136	c.87G>A	c.(85-87)acG>acA	p.T29T	CNFN_ENST00000597255.1_Silent_p.T29T	NM_032488.3	NP_115877.2	Q9BYD5	CNFN_HUMAN	cornifelin	29					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				lung(1)|prostate(1)	2		Prostate(69;0.00899)				TGCAGCAGTCCGTGAGACCTG	0.617																																					p.T29T		Atlas-SNP	.											.	CNFN	5	.	0			c.G87A						.						128	96	106					19																	42893103		2203	4300	6503	SO:0001819	synonymous_variant	84518	exon2			GCAGTCCGTGAGA	AB049591	CCDS12606.1	19q13.31	2006-01-11				ENSG00000105427			30183	protein-coding gene	gene with protein product		611764					Standard	NM_032488		Approved	PLAC8L2	uc002otp.4	Q9BYD5		ENST00000222032.5:c.87G>A	chr19.hg19:g.42893103C>T		39.0	0.0		39.0	19.0	NM_032488	B2R569	Silent	SNP	ENST00000222032.5	hg19	CCDS12606.1																																																																																			.	.		0.617	CNFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463859.1	NM_032488		T	42893103	C	T	42893103	2	4	23	1	0	0	0	0	0	0	0	1	3597	639	23	1		1	CNFN	19	42893103	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	148908	42893103	16235880	1009	3075										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44739561	44739561	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggagagaagtcttatagatgCgacagttgcggcaagggatt	15	5	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:44739561C>T	ENST00000313040.7	+	6	1183	c.978C>T	c.(976-978)tgC>tgT	p.C326C	ZNF227_ENST00000589005.1_Silent_p.C275C|ZNF227_ENST00000391961.2_Silent_p.C275C	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	326					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				CTTATAGATGCGACAGTTGCG	0.393																																					p.C326C		Atlas-SNP	.											ZNF227,NS,carcinoma,0,1	ZNF227	62	.	0			c.C978T						.						66	68	67					19																	44739561		2203	4300	6503	SO:0001819	synonymous_variant	7770	exon6			TAGATGCGACAGT	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.978C>T	chr19.hg19:g.44739561C>T		77.0	0.0		57.0	27.0	NM_182490	B3KRU7|B7Z5P9	Silent	SNP	ENST00000313040.7	hg19	CCDS12636.1																																																																																			.	.		0.393	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		T	44739561	C	T	44739561	2	4	23	1	0	0	0	0	0	0	0	1	17796	776	27	1		1	ZNF227	19	44739561	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1846458	44739561	14389422	1010	3076										
ZNF235	9310	hgsc.bcm.edu	37	chr19	44791785	44791785	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aatcgcttctgacatgcatcAcacttgaatggtttttcccc	6	12	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:44791785A>G	ENST00000291182.4	-	5	1905	c.1803T>C	c.(1801-1803)tgT>tgC	p.C601C	ZNF235_ENST00000589799.1_Intron|ZNF235_ENST00000589248.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	601					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				GACATGCATCACACTTGAATG	0.473																																					p.C601C		Atlas-SNP	.											.	ZNF235	60	.	0			c.T1803C						.						162	148	152					19																	44791785		2203	4300	6503	SO:0001819	synonymous_variant	9310	exon5			TGCATCACACTTG	X78929	CCDS33048.1	19q13.2	2013-01-08	2002-11-04	2002-11-08	ENSG00000159917	ENSG00000159917		"Zinc fingers, C2H2-type", "-"	12866	protein-coding gene	gene with protein product		604749	"zinc finger protein homologous to Zfp93 in mouse"	ZNF270, ZFP93		7865130, 9570955	Standard	NM_004234		Approved	HZF6, ANF270	uc002oza.4	Q14590		ENST00000291182.4:c.1803T>C	chr19.hg19:g.44791785A>G		161.0	0.0		159.0	74.0	NM_004234	B4DTQ7|O14898|O14899|Q17RR8	Silent	SNP	ENST00000291182.4	hg19	CCDS33048.1																																																																																			.	.		0.473	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1			G	44791785	A	G	44791785	2	3	23	1	0	0	0	0	0	0	0	1	17803	157	6	2		2	ZNF235	19	44791785	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	52224	44791785	14337198	1011	3077										
PVR	5817	hgsc.bcm.edu	37	chr19	45162189	45162189	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgagcatcaccagagctgcCgtaattgagcacctactacg	10	12	1	3	rs35385129	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:45162189C>T	ENST00000425690.3	+	6	1449				PVR_ENST00000406449.4_Missense_Mutation_p.R391C|PVR_ENST00000403059.4_Intron|PVR_ENST00000344956.4_Intron|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor						adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		CCagagctgccgtaattgagc	0.532																																					p.R391C		Atlas-SNP	.											.	PVR	23	.	0			c.C1171T						.						73	74	73					19																	45162189		2203	4300	6503	SO:0001627	intron_variant	5817	exon6			AGCTGCCGTAATT	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9705	protein-coding gene	gene with protein product	"nectin-like 5"	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.1150+21C>T	chr19.hg19:g.45162189C>T		64.0	0.0		68.0	31.0	NM_001135770	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	hg19	CCDS12640.1	.	.	.	.	.	.	.	.	.	.	C	8.729	0.916225	0.17907	.	.	ENSG00000073008	ENST00000406449	D	0.88046	-2.33	2.11	0.956	0.19608	.	.	.	.	.	T	0.75664	0.3880	.	.	.	0.09310	N	1	D	0.54772	0.968	B	0.36959	0.237	T	0.65212	-0.6223	7	.	.	.	.	6.1885	0.20510	0.0:0.6791:0.3209:0.0	.	391	P15151-4	.	C	391	ENSP00000383907:R391C	.	R	+	1	0	PVR	49854029	0.001000	0.12720	0.000000	0.03702	0.205000	0.24178	0.662000	0.25038	0.397000	0.25310	0.555000	0.69702	CGT	.	C|0.834;A|0.166		0.532	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505		T	45162189	C	T	45162189	1	4	23	0	1	0	0	0	0	0	0	0	12852	652	23	1		1	PVR	19	45162189	Intron	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	370404	45162189	13966794	1012	3078										
APOE	348	hgsc.bcm.edu	37	chr19	45411140	45411140	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcgcttttgggattacctgcGctgggtgcagacactgtctg	13	10	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:45411140G>A	ENST00000252486.4	+	3	278	c.167G>A	c.(166-168)cGc>cAc	p.R56H		NM_000041.2	NP_000032.1	P02649	APOE_HUMAN	apolipoprotein E	56					aging (GO:0007568)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|artery morphogenesis (GO:0048844)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cellular response to interleukin-1 (GO:0071347)|cGMP-mediated signaling (GO:0019934)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|cytoskeleton organization (GO:0007010)|fatty acid homeostasis (GO:0055089)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|intracellular transport (GO:0046907)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|long-chain fatty acid transport (GO:0015909)|low-density lipoprotein particle remodeling (GO:0034374)|maintenance of location in cell (GO:0051651)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of blood coagulation (GO:0030195)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cholesterol biosynthetic process (GO:0045541)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of dendritic spine development (GO:0061000)|negative regulation of dendritic spine maintenance (GO:1902951)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of inflammatory response (GO:0050728)|negative regulation of lipid biosynthetic process (GO:0051055)|negative regulation of lipid transport across blood brain barrier (GO:1903001)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of phospholipid efflux (GO:1902999)|negative regulation of platelet activation (GO:0010544)|negative regulation of postsynaptic membrane organization (GO:1901627)|negative regulation of presynaptic membrane organization (GO:1901630)|nitric oxide mediated signal transduction (GO:0007263)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system axon regeneration (GO:0014012)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of axon extension (GO:0045773)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of dendritic spine maintenance (GO:1902952)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of lipid transport across blood brain barrier (GO:1903002)|positive regulation of low-density lipoprotein particle receptor catabolic process (GO:0032805)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipid efflux (GO:1902995)|positive regulation of postsynaptic membrane organization (GO:1901628)|positive regulation of presynaptic membrane organization (GO:1901631)|protein import (GO:0017038)|receptor-mediated endocytosis (GO:0006898)|regulation of axon extension (GO:0030516)|regulation of beta-amyloid clearance (GO:1900221)|regulation of Cdc42 protein signal transduction (GO:0032489)|regulation of neuron death (GO:1901214)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of tau-protein kinase activity (GO:1902947)|response to dietary excess (GO:0002021)|response to ethanol (GO:0045471)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)|response to retinoic acid (GO:0032526)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|synaptic transmission, cholinergic (GO:0007271)|triglyceride metabolic process (GO:0006641)|vasodilation (GO:0042311)|very-low-density lipoprotein particle clearance (GO:0034447)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|high-density lipoprotein particle (GO:0034364)|intermediate-density lipoprotein particle (GO:0034363)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)|vesicle (GO:0031982)	antioxidant activity (GO:0016209)|beta-amyloid binding (GO:0001540)|cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle receptor binding (GO:0050750)|metal chelating activity (GO:0046911)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)|tau protein binding (GO:0048156)|very-low-density lipoprotein particle receptor binding (GO:0070326)			large_intestine(1)|lung(2)|prostate(1)	4	Lung NSC(12;0.0018)|all_lung(12;0.00481)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)	Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	GATTACCTGCGCTGGGTGCAG	0.657																																					p.R56H		Atlas-SNP	.											.	APOE	11	.	0			c.G167A						.						43	42	42					19																	45411140		2203	4300	6503	SO:0001583	missense	348	exon3			ACCTGCGCTGGGT	K00396	CCDS12647.1	19q13.31	2013-01-24			ENSG00000130203	ENSG00000130203		"Apolipoproteins"	613	protein-coding gene	gene with protein product		107741	"Alzheimer disease 2 (APOE*E4-associated, late onset)"	AD2		10662539	Standard	NM_000041		Approved		uc002pab.3	P02649	OTTHUMG00000128901	ENST00000252486.4:c.167G>A	chr19.hg19:g.45411140G>A	ENSP00000252486:p.Arg56His	106.0	0.0		107.0	46.0	NM_000041	B2RC15|C0JYY5|Q9P2S4	Missense_Mutation	SNP	ENST00000252486.4	hg19	CCDS12647.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.557019	0.45590	.	.	ENSG00000130203	ENST00000252486;ENST00000446996;ENST00000434152;ENST00000425718	T;T;T	0.79653	-1.29;-1.29;-1.29	4.85	-0.0363	0.13888	Apolipoprotein/apolipophorin (1);	0.594848	0.15262	N	0.271759	T	0.75459	0.3852	M	0.81802	2.56	0.27077	N	0.963178	B	0.15930	0.015	B	0.08055	0.003	T	0.68142	-0.5487	10	0.59425	D	0.04	-13.5464	3.2725	0.06887	0.3015:0.0:0.5146:0.1839	.	56	P02649	APOE_HUMAN	H	56;56;101;56	ENSP00000252486:R56H;ENSP00000413135:R56H;ENSP00000410423:R56H	ENSP00000252486:R56H	R	+	2	0	APOE	50102980	0.984000	0.35163	1.000000	0.80357	0.897000	0.52465	0.635000	0.24629	0.564000	0.29238	0.561000	0.74099	CGC	.	.		0.657	APOE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250865.2	NM_000041		A	45411140	G	A	45411140	3	1	23	1	0	0	0	0	1	0	0	0	802	1087	38	1	173	1	APOE	19	45411140	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	248951	45411140	13717843	1013	3079										
NOVA2	4858	hgsc.bcm.edu	37	chr19	46476610	46476610	+	5'UTR	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccggggcctcgggctccatGgggggggcctggggcggcgg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:46476610delG	ENST00000263257.5	-	0	194				NOVA2_ENST00000599462.1_5'Flank	NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2						regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		CGGGCTCCATGGGGGGGGCCT	0.761																																					p.M1fs		Atlas-INDEL	.											.	NOVA2	38	.	0			c.1delA						.						2	3	3					19																	46476610		1128	2587	3715	SO:0001623	5_prime_UTR_variant	4858	exon1			.	U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"neuro-oncological ventral antigen 3"	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.-1C>-	chr19.hg19:g.46476610delG		36.0	0.0		27.0	11.0	NM_002516	O43267|Q9UEA1	Frame_Shift_Del	DEL	ENST00000263257.5	hg19	CCDS12679.1																																																																																			.	.		0.761	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516		-	46476610	G	-	46476610	6	5	23	0	1	1	0	1	0	0	0	0	10564	1363	47	0		0	NOVA2	19	46476610	5'UTR	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	1065470	46476610	12652373	1014	3080										
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48202008	48202008	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccctaccatgtctaccagggCgccctcccctcccccagtga	7	21	1	1	rs371897707		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:48202008C>T	ENST00000396720.3	+	12	3560	c.3366C>T	c.(3364-3366)ggC>ggT	p.G1122G	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1122										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		TCTACCAGGGCGCCCTCCCCT	0.672											OREG0025594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G1122G		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.C3366T						.	C		1,3927		0,1,1963	29	31	30		3366	-8.5	0.2	19		30	0,8282		0,0,4141	no	coding-synonymous	GLTSCR1	NM_015711.3		0,1,6104	TT,TC,CC		0.0,0.0255,0.0082		1122/1561	48202008	1,12209	1964	4141	6105	SO:0001819	synonymous_variant	29998	exon12			CCAGGGCGCCCTC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.3366C>T	chr19.hg19:g.48202008C>T		67.0	0.0	952	47.0	22.0	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	hg19	CCDS46134.1																																																																																			.	.		0.672	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		T	48202008	C	T	48202008	2	4	23	1	0	0	0	0	0	0	0	1	6482	755	27	1		1	GLTSCR1	19	48202008	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1725398	48202008	10926975	1015	3081										
CA11	770	hgsc.bcm.edu	37	chr19	49148722	49148722	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agtcctcggggtcaggtgctGgtccgatgtgagctgggaag	18	8	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:49148722G>A	ENST00000084798.4	-	2	759	c.80C>T	c.(79-81)cCa>cTa	p.P27L	SEC1P_ENST00000430145.2_RNA	NM_001217.3	NP_001208.2	O75493	CAH11_HUMAN	carbonic anhydrase XI	27						basolateral plasma membrane (GO:0016323)|extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	14		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000103)|all cancers(93;0.000119)|GBM - Glioblastoma multiforme(486;0.00634)|Epithelial(262;0.016)	Zonisamide(DB00909)	GTCAGGTGCTGGTCCGATGTG	0.652																																					p.P27L		Atlas-SNP	.											.	CA11	29	.	0			c.C80T						.						66	61	63					19																	49148722		2203	4300	6503	SO:0001583	missense	770	exon2			GGTGCTGGTCCGA	AF067662	CCDS12729.1	19q13.3	2012-07-02			ENSG00000063180	ENSG00000063180		"Carbonic anhydrases"	1370	protein-coding gene	gene with protein product	"CA-RP XI", "carbonic anhydrase-related protein XI", "carbonic anhydrase-related protein 2"	604644				9878252	Standard	XR_243956		Approved	CARP2, CARPX1	uc002pjz.1	O75493		ENST00000084798.4:c.80C>T	chr19.hg19:g.49148722G>A	ENSP00000084798:p.Pro27Leu	82.0	0.0		88.0	31.0	NM_001217	O60596|Q6FHI1|Q9UEC4	Missense_Mutation	SNP	ENST00000084798.4	hg19	CCDS12729.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163080	0.78226	.	.	ENSG00000063180	ENST00000084798	T	0.70631	-0.5	3.84	3.84	0.44239	.	0.100808	0.39834	N	0.001244	T	0.63861	0.2547	N	0.08118	0	0.44424	D	0.997344	D	0.64830	0.994	D	0.73708	0.981	T	0.57602	-0.7783	10	0.10636	T	0.68	.	11.5626	0.50785	0.0:0.0:1.0:0.0	.	27	O75493	CAH11_HUMAN	L	27	ENSP00000084798:P27L	ENSP00000084798:P27L	P	-	2	0	CA11	53840534	0.992000	0.36948	0.993000	0.49108	0.993000	0.82548	4.729000	0.62008	2.435000	0.82474	0.462000	0.41574	CCA	.	.		0.652	CA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466172.1	NM_001217		A	49148722	G	A	49148722	3	1	23	1	0	0	0	0	1	0	0	0	2514	1348	47	3	938	3	CA11	19	49148722	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	946714	49148722	9980261	1016	3082										
FUT1	2523	hgsc.bcm.edu	37	chr19	49254381	49254381	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tacccggcaggcagaagatgGccactgggggtgtcaccagg	16	11	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:49254381G>T	ENST00000310160.3	-	4	1132	c.158C>A	c.(157-159)gCc>gAc	p.A53D	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	53					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		GCAGAAGATGGCCACTGGGGG	0.602																																					p.A53D		Atlas-SNP	.											.	FUT1	44	.	0			c.C158A						.						49	50	50					19																	49254381		2203	4300	6503	SO:0001583	missense	2523	exon4			AAGATGGCCACTG		CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"Blood group antigens", "Fucosyltransferases"	4012	protein-coding gene	gene with protein product		211100	"fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)", "fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.158C>A	chr19.hg19:g.49254381G>T	ENSP00000312021:p.Ala53Asp	142.0	0.0		113.0	43.0	NM_000148	O14505|O14506|O14507	Missense_Mutation	SNP	ENST00000310160.3	hg19	CCDS12733.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.859363	0.51376	.	.	ENSG00000174951	ENST00000310160;ENST00000539428	D	0.97016	-4.21	4.53	3.46	0.39613	.	0.231427	0.30639	N	0.009190	D	0.96065	0.8718	M	0.63428	1.95	0.33636	D	0.606606	P	0.51653	0.947	P	0.54210	0.745	D	0.96781	0.9575	10	0.42905	T	0.14	-7.8449	10.4627	0.44590	0.0:0.1974:0.8026:0.0	.	53	P19526	FUT1_HUMAN	D	53	ENSP00000312021:A53D	ENSP00000312021:A53D	A	-	2	0	FUT1	53946193	0.807000	0.29009	0.999000	0.59377	0.204000	0.24138	0.964000	0.29306	1.223000	0.43536	0.655000	0.94253	GCC	.	.		0.602	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148		T	49254381	G	T	49254381	3	4	23	1	0	0	0	0	1	0	0	0	6109	1203	42	3	943	3	FUT1	19	49254381	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	105659	49254381	9874602	1017	3083										
ALDH16A1	126133	hgsc.bcm.edu	37	chr19	49965147	49965147	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggggggtccctaggaagggCgtgcccttcgacggagcctg	19	11	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:49965147C>T	ENST00000293350.4	+	7	929	c.766C>T	c.(766-768)Cgt>Tgt	p.R256C	CTD-3148I10.9_ENST00000599536.1_5'Flank|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.R93C|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.R91C|ALDH16A1_ENST00000455361.2_Intron	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	256						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CTAGGAAGGGCGTGCCCTTCG	0.721																																					p.R256C		Atlas-SNP	.											ALDH16A1,colon,carcinoma,0,1	ALDH16A1	54	.	0			c.C766T						.						16	18	17					19																	49965147		2183	4280	6463	SO:0001583	missense	126133	exon7			GAAGGGCGTGCCC	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"Aldehyde dehydrogenases"	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.766C>T	chr19.hg19:g.49965147C>T	ENSP00000293350:p.Arg256Cys	137.0	0.0		149.0	67.0	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	hg19	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.377297	0.61735	.	.	ENSG00000161618	ENST00000293350;ENST00000540132;ENST00000433981	T;T;T	0.79033	-1.23;-1.23;-1.23	4.65	4.65	0.58169	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.759301	0.12974	N	0.423860	D	0.90521	0.7030	M	0.93150	3.385	0.50813	D	0.999893	D;D	0.89917	1.0;1.0	D;D	0.68621	0.953;0.959	D	0.91378	0.5125	10	0.87932	D	0	-8.4781	13.7969	0.63177	0.0:1.0:0.0:0.0	.	93;256	F5H4B6;Q8IZ83	.;A16A1_HUMAN	C	256;93;91	ENSP00000293350:R256C;ENSP00000445088:R93C;ENSP00000398675:R91C	ENSP00000293350:R256C	R	+	1	0	ALDH16A1	54656959	0.125000	0.22332	0.997000	0.53966	0.373000	0.29922	1.112000	0.31172	2.536000	0.85505	0.585000	0.79938	CGT	.	.		0.721	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		T	49965147	C	T	49965147	3	4	23	1	0	0	0	0	1	0	0	0	488	768	27	1	792	1	ALDH16A1	19	49965147	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	710766	49965147	9163836	1018	3084										
TBC1D17	79735	hgsc.bcm.edu	37	chr19	50391714	50391714	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgtgcaggagatcctggggCtggccccgcccgcagagccc	15	16	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:50391714C>T	ENST00000221543.5	+	17	2079	c.1780C>T	c.(1780-1782)Ctg>Ttg	p.L594L	MIR4750_ENST00000584564.1_RNA|TBC1D17_ENST00000535102.2_Silent_p.L561L	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	594					autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		GATCCTGGGGCTGGCCCCGCC	0.736																																					p.L594L		Atlas-SNP	.											.	TBC1D17	39	.	0			c.C1780T						.						9	10	10					19																	50391714		2073	3992	6065	SO:0001819	synonymous_variant	79735	exon17			CTGGGGCTGGCCC	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.1780C>T	chr19.hg19:g.50391714C>T		99.0	0.0		81.0	11.0	NM_024682	B4DT12|B9A6L8|F5H1W7	Silent	SNP	ENST00000221543.5	hg19	CCDS12785.1																																																																																			.	.		0.736	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682		T	50391714	C	T	50391714	2	4	23	1	0	0	0	0	0	0	0	1	15621	796	28	3		3	TBC1D17	19	50391714	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	426567	50391714	8737269	1019	3085										
ZNF473	25888	hgsc.bcm.edu	37	chr19	50542425	50542425	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tactgtgtttcaggaatttgTgaccctcaaggatgtcggca	11	8	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:50542425T>C	ENST00000595661.1	+	4	512	c.17T>C	c.(16-18)gTg>gCg	p.V6A	ZNF473_ENST00000270617.3_Missense_Mutation_p.V6A|ZNF473_ENST00000601364.1_Missense_Mutation_p.V6A|ZNF473_ENST00000445728.3_5'UTR|ZNF473_ENST00000391821.2_Missense_Mutation_p.V6A			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	6	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		CAGGAATTTGTGACCCTCAAG	0.577																																					p.V6A		Atlas-SNP	.											.	ZNF473	86	.	0			c.T17C						.						163	143	150					19																	50542425		2203	4300	6503	SO:0001583	missense	25888	exon3			AATTTGTGACCCT	AB032967	CCDS33077.1	19q13.33	2013-01-08						"Zinc fingers, C2H2-type", "-"	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.17T>C	chr19.hg19:g.50542425T>C	ENSP00000472808:p.Val6Ala	103.0	0.0		76.0	28.0	NM_015428	A8K8T7|Q9ULS9|Q9Y4Q7	Missense_Mutation	SNP	ENST00000595661.1	hg19	CCDS33077.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.489092	0.44249	.	.	ENSG00000142528	ENST00000270617;ENST00000391821	T;T	0.05717	3.4;3.4	5.11	-7.21	0.01490	Krueppel-associated box (4);	1.795830	0.03316	N	0.191109	T	0.10637	0.0260	M	0.88842	2.985	0.09310	N	0.999996	B	0.09022	0.002	B	0.12156	0.007	T	0.41680	-0.9495	10	0.87932	D	0	0.645	2.6942	0.05129	0.1976:0.4028:0.1069:0.2927	.	6	Q8WTR7	ZN473_HUMAN	A	6	ENSP00000270617:V6A;ENSP00000375697:V6A	ENSP00000270617:V6A	V	+	2	0	ZNF473	55234237	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.824000	0.04438	-1.786000	0.01269	0.528000	0.53228	GTG	.	.		0.577	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390		C	50542425	T	C	50542425	3	2	23	1	0	0	0	0	1	0	0	0	17946	1696	59	2	23	2	ZNF473	19	50542425	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	150711	50542425	8586558	1020	3086										
MYH14	79784	hgsc.bcm.edu	37	chr19	50794187	50794187	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggatgaggagcggaagcagcGcactctggccgtggctgccc	17	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:50794187G>A	ENST00000596571.1	+	33	4886	c.4886G>A	c.(4885-4887)cGc>cAc	p.R1629H	MYH14_ENST00000440075.2_Missense_Mutation_p.R1670H|MYH14_ENST00000262269.8_Missense_Mutation_p.R1670H|MYH14_ENST00000425460.1_Missense_Mutation_p.R1637H|MYH14_ENST00000376970.2_Missense_Mutation_p.R1662H|MYH14_ENST00000601313.1_Missense_Mutation_p.R1670H|MYH14_ENST00000598205.1_Missense_Mutation_p.R1637H			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1629					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CGGAAGCAGCGCACTCTGGCC	0.657																																					p.R1670H		Atlas-SNP	.											MYH14_ENST00000262269,colon,carcinoma,0,1	MYH14	261	.	0			c.G5009A						.						19	25	23					19																	50794187		2066	4197	6263	SO:0001583	missense	79784	exon36			AGCAGCGCACTCT	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.4886G>A	chr19.hg19:g.50794187G>A	ENSP00000472819:p.Arg1629His	117.0	0.0		137.0	54.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.983989	0.74474	.	.	ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47	4.42	4.42	0.53409	Myosin tail (1);	.	.	.	.	D	0.89132	0.6628	M	0.77406	2.37	0.49051	D	0.999747	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90495	0.4470	9	0.87932	D	0	.	14.8871	0.70579	0.0:0.0:1.0:0.0	.	1670;1629;1637	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	H	1670;1662;1637;1413;1670	ENSP00000406273:R1670H;ENSP00000366169:R1662H;ENSP00000407879:R1637H;ENSP00000262269:R1670H	ENSP00000262269:R1670H	R	+	2	0	MYH14	55485999	0.997000	0.39634	1.000000	0.80357	0.325000	0.28411	7.474000	0.81024	2.447000	0.82792	0.491000	0.48974	CGC	.	.		0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		A	50794187	G	A	50794187	3	1	23	1	0	0	0	0	1	0	0	0	10042	1087	38	1	5147	1	MYH14	19	50794187	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	251762	50794187	8334796	1021	3087										
POLD1	5424	hgsc.bcm.edu	37	chr19	50905061	50905061	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgcagcctgtgcctggggggCccccaccatcccgcggctcc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:50905061delC	ENST00000440232.2	+	4	396	c.343delC	c.(343-345)cccfs	p.P117fs	POLD1_ENST00000599857.1_Frame_Shift_Del_p.P117fs|POLD1_ENST00000595904.1_Frame_Shift_Del_p.P117fs	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	117					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		GCCTGGGGGGCCCCCACCATC	0.662								DNA polymerases (catalytic subunits)																													p.G114fs		Atlas-Indel,Pindel	.											.	POLD1	174	.	0			c.342delG						.						31	36	35					19																	50905061		2200	4293	6493	SO:0001589	frameshift_variant	5424	exon4			.		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.343delC	chr19.hg19:g.50905061delC	ENSP00000406046:p.Pro117fs	90.0	0.0		77.0	28.0	NM_002691	Q8NER3|Q96H98	Frame_Shift_Del	DEL	ENST00000440232.2	hg19	CCDS12795.1																																																																																			.	.		0.662	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			-	50905061	C	-	50905061	7	5	23	1	0	1	0	1	0	0	0	0	12199	739	26	0	353	0	POLD1	19	50905061	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	110874	50905061	8223922	1022	3088										
KLK10	5655	hgsc.bcm.edu	37	chr19	51520382	51520382	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctacttgtttccgcagtgcgCggccgtcagcacccaactct	9	16	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:51520382C>T	ENST00000309958.3	-	3	471	c.253G>A	c.(253-255)Gcg>Acg	p.A85T	CTC-518B2.12_ENST00000596286.1_RNA|KLK10_ENST00000358789.3_Missense_Mutation_p.A85T|KLK10_ENST00000391805.1_Missense_Mutation_p.A85T	NM_002776.4	NP_002767.2	O43240	KLK10_HUMAN	kallikrein-related peptidase 10	85	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		CCGCAGTGCGCGGCCGTCAGC	0.706											OREG0025646	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A85T		Atlas-SNP	.											.	KLK10	32	.	0			c.G253A						.						21	21	21					19																	51520382		2202	4296	6498	SO:0001583	missense	5655	exon3			AGTGCGCGGCCGT	AF024605	CCDS12817.1	19q13	2011-03-07	2006-10-27			ENSG00000129451		"Kallikreins"	6358	protein-coding gene	gene with protein product		602673	"kallikrein 10"	PRSSL1		8764136, 9533035, 16800724, 16800723, 10675891	Standard	NM_145888		Approved	NES1	uc002pva.3	O43240		ENST00000309958.3:c.253G>A	chr19.hg19:g.51520382C>T	ENSP00000311746:p.Ala85Thr	117.0	0.0	978	149.0	64.0	NM_145888	A6NC12|Q53YL3|Q99920|Q9GZW9	Missense_Mutation	SNP	ENST00000309958.3	hg19	CCDS12817.1	.	.	.	.	.	.	.	.	.	.	c	27.7	4.856623	0.91355	.	.	ENSG00000129451	ENST00000391805;ENST00000309958;ENST00000358789	D;D;D	0.96940	-4.18;-4.18;-4.18	4.43	4.43	0.53597	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.34460	N	0.003956	D	0.98604	0.9533	H	0.96208	3.785	0.35355	D	0.787717	D	0.89917	1.0	D	0.97110	1.0	D	0.99968	1.1923	10	0.87932	D	0	.	12.8949	0.58093	0.0:1.0:0.0:0.0	.	85	O43240	KLK10_HUMAN	T	85	ENSP00000375681:A85T;ENSP00000311746:A85T;ENSP00000351640:A85T	ENSP00000311746:A85T	A	-	1	0	KLK10	56212194	0.998000	0.40836	0.984000	0.44739	0.990000	0.78478	5.361000	0.66092	2.167000	0.68274	0.491000	0.48974	GCG	.	.		0.706	KLK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464337.2	NM_002776		T	51520382	C	T	51520382	3	4	23	1	0	0	0	0	1	0	0	0	8407	768	27	1	593	1	KLK10	19	51520382	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	615321	51520382	7608601	1023	3089										
SIGLEC6	946	hgsc.bcm.edu	37	chr19	52034864	52034864	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agcaggggcagcagcagcggTagcatctctgaggcggaggc	18	10	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:52034864T>C	ENST00000425629.3	-	1	193	c.39A>G	c.(37-39)ctA>ctG	p.L13L	SIGLEC6_ENST00000359982.4_Silent_p.L13L|SIGLEC6_ENST00000346477.3_Silent_p.L13L|SIGLEC6_ENST00000436458.1_Silent_p.L13L|SIGLEC6_ENST00000391797.3_Silent_p.L13L|SIGLEC6_ENST00000343300.4_Silent_p.L13L	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	13					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GCAGCAGCGGTAGCATCTCTG	0.687																																					p.L13L		Atlas-SNP	.											.	SIGLEC6	142	.	0			c.A39G						.						17	21	20					19																	52034864		2160	4271	6431	SO:0001819	synonymous_variant	946	exon1			CAGCGGTAGCATC	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.39A>G	chr19.hg19:g.52034864T>C		213.0	0.0		188.0	62.0	NM_001177549	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Silent	SNP	ENST00000425629.3	hg19	CCDS12834.3																																																																																			.	.		0.687	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245		C	52034864	T	C	52034864	2	2	23	1	0	0	0	0	0	0	0	1	14327	1625	57	2		2	SIGLEC6	19	52034864	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	514482	52034864	7094119	1024	3090										
SIGLEC5	8778	hgsc.bcm.edu	37	chr19	52133551	52133551	+	Splice_Site	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcctccctcagctcactcaCccccccacagcaggggcagc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:52133551delC	ENST00000534261.2	-	2	437		c.e2+1		SIGLEC5_ENST00000429354.3_Intron|SIGLEC5_ENST00000599649.1_Intron|SIGLEC5_ENST00000570106.2_Splice_Site|SIGLEC5_ENST00000222107.4_Intron			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5						cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		AGCTCACTCACCCCCCCACAG	0.677																																					.		Atlas-INDEL	.											.	SIGLEC5	67	.	0			c.37+2G>-						.						1	1	1					19																	52133551		662	1813	2475	SO:0001630	splice_region_variant	8778	exon2			.	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.37+1G>-	chr19.hg19:g.52133551delC		159.0	0.0		142.0	28.0	NM_003830		Splice_Site	DEL	ENST00000534261.2	hg19	CCDS33088.1																																																																																			.	.		0.677	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	Intron	-	52133551	C	-	52133551	8	5	23	1	0	1	0	1	0	0	1	0	14326	521	18	0	1653	0	SIGLEC5	19	52133551	Splice_Site	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	98687	52133551	6995432	1025	3091										
ZNF841	284371	hgsc.bcm.edu	37	chr19	52569919	52569919	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccgtttaaaggttttgccacAttcattacatttgtagggtt	8	7	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:52569919A>G	ENST00000426391.2	-	5	1419	c.868T>C	c.(868-870)Tgt>Cgt	p.C290R	ZNF841_ENST00000359973.2_Missense_Mutation_p.C290R|ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000389534.4_Missense_Mutation_p.C406R|ZNF841_ENST00000594295.1_Missense_Mutation_p.C406R|CTC-471J1.2_ENST00000569091.1_RNA			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	290					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						GTTTTGCCACATTCATTACAT	0.388																																					p.C406R		Atlas-SNP	.											.	ZNF841	183	.	0			c.T1216C						.						119	103	108					19																	52569919		692	1591	2283	SO:0001583	missense	284371	exon7			TGCCACATTCATT	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"Zinc fingers, C2H2-type", "-"	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.868T>C	chr19.hg19:g.52569919A>G	ENSP00000415453:p.Cys290Arg	96.0	0.0		112.0	50.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	hg19		.	.	.	.	.	.	.	.	.	.	A	21.1	4.104998	0.77096	.	.	ENSG00000197608	ENST00000389534;ENST00000426391;ENST00000359973	D;D;D	0.85955	-2.05;-2.05;-2.05	2.26	2.26	0.28386	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94248	0.8153	H	0.97852	4.09	0.52501	D	0.999954	D;D;D	0.89917	0.998;1.0;0.993	D;D;D	0.78314	0.991;0.991;0.985	D	0.93759	0.7065	9	0.87932	D	0	.	9.2133	0.37331	1.0:0.0:0.0:0.0	.	406;290;290	Q6ZN19-3;Q6ZN19-2;Q6ZN19	.;.;ZN841_HUMAN	R	406;290;290	ENSP00000374185:C406R;ENSP00000415453:C290R;ENSP00000353060:C290R	ENSP00000353060:C290R	C	-	1	0	ZNF841	57261731	0.398000	0.25279	0.017000	0.16124	0.848000	0.48234	2.561000	0.45905	1.031000	0.39867	0.260000	0.18958	TGT	.	.		0.388	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		G	52569919	A	G	52569919	3	3	23	1	0	0	0	0	1	0	0	0	18204	217	8	2	1562	2	ZNF841	19	52569919	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	436368	52569919	6559064	1026	3092										
ZNF578	147660	hgsc.bcm.edu	37	chr19	53014578	53014578	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcacactggtgagaaaccttAcaagtgtaatgaatgtggaa	10	6	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:53014578A>G	ENST00000421239.2	+	6	1188	c.944A>G	c.(943-945)tAc>tGc	p.Y315C	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GAGAAACCTTACAAGTGTAAT	0.408																																					p.Y315C		Atlas-SNP	.											.	.	.	.	0			c.A944G						.						99	103	101					19																	53014578		2203	4300	6503	SO:0001583	missense	147660	exon6			AACCTTACAAGTG	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.944A>G	chr19.hg19:g.53014578A>G	ENSP00000459216:p.Tyr315Cys	160.0	0.0		177.0	71.0	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	hg19	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	11.94	1.787735	0.31593	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.37	1.37	0.22104	.	.	.	.	.	T	0.58566	0.2131	M	0.82433	2.59	0.09310	N	1	D	0.76494	0.999	D	0.65323	0.934	T	0.45160	-0.9280	7	.	.	.	.	4.2923	0.10885	0.487:0.0:0.0:0.513	.	315	G3V4F6	.	C	315	.	.	Y	+	2	0	ZNF578	57706390	0.000000	0.05858	0.031000	0.17742	0.372000	0.29890	-0.421000	0.07053	0.640000	0.30582	0.246000	0.17985	TAC	.	.		0.408	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		G	53014578	A	G	53014578	3	3	23	1	0	0	0	0	1	0	0	0	18025	391	14	2	954	2	ZNF578	19	53014578	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	444659	53014578	6114405	1027	3093										
LILRB3	11025	hgsc.bcm.edu	37	chr19	54721271	54721271	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagtgaggagggaggagaggCcatttctctcctaggactgg	16	8	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:54721271C>T	ENST00000391750.1	-	13	1802	c.1666G>A	c.(1666-1668)Gcc>Acc	p.A556T	LILRB3_ENST00000245620.9_Missense_Mutation_p.A557T|LILRB3_ENST00000469273.1_5'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.A573T|LILRA6_ENST00000270464.5_Missense_Mutation_p.A557T|LILRB3_ENST00000346401.6_Missense_Mutation_p.A568T|LILRB3_ENST00000424807.1_Missense_Mutation_p.A556T|LILRA6_ENST00000419410.2_Missense_Mutation_p.A557T|LILRA6_ENST00000440558.2_Missense_Mutation_p.A556T|LILRA6_ENST00000391735.3_3'UTR			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	556					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGAGGAGAGGCCATTTCTCTC	0.577																																					p.A557T		Atlas-SNP	.											.	LILRB3	67	.	0			c.G1669A						.						128	129	129					19																	54721271		2202	4300	6502	SO:0001583	missense	11025	exon12			GAGAGGCCATTTC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1666G>A	chr19.hg19:g.54721271C>T	ENSP00000375630:p.Ala556Thr	235.0	0.0		217.0	52.0	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	hg19	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.103359	0.37145	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00500	6.97;6.97;6.96;6.98;7.02;6.97;6.97;6.99	2.45	-4.91	0.03085	.	.	.	.	.	T	0.00637	0.0021	L	0.44542	1.39	0.09310	N	1	D;B;B;P;B;B;P	0.89917	1.0;0.021;0.026;0.916;0.003;0.004;0.652	D;B;B;B;B;B;P	0.85130	0.997;0.03;0.017;0.434;0.01;0.008;0.646	T	0.41963	-0.9479	9	0.18276	T	0.48	.	0.6035	0.00748	0.1746:0.276:0.1725:0.3769	.	573;556;557;568;573;556;557	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	T	556;556;568;557;573;556;557;557	ENSP00000375630:A556T;ENSP00000412771:A556T;ENSP00000345184:A568T;ENSP00000245620:A557T;ENSP00000384274:A573T;ENSP00000390120:A556T;ENSP00000270464:A557T;ENSP00000411227:A557T	ENSP00000270464:A557T	A	-	1	0	LILRB3;LILRA6	59413083	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-1.210000	0.02999	-1.009000	0.03400	0.121000	0.15741	GCC	.	.		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		T	54721271	C	T	54721271	3	4	23	1	0	0	0	0	1	0	0	0	8801	739	26	3	237	3	LILRB3	19	54721271	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1706693	54721271	4407712	1028	3094										
LILRB5	10990	hgsc.bcm.edu	37	chr19	54754663	54754664	+	Frame_Shift_Ins	INS	-	-	G													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgtgggctagtggatggccaINSggggggcgtagatgctgggt							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:54754663_54754664insG	ENST00000316219.5	-	13	1866_1867	c.1759_1760insC	c.(1759-1761)ctgfs	p.L587fs	LILRB5_ENST00000449561.2_Frame_Shift_Ins_p.L588fs|LILRB5_ENST00000345866.6_Frame_Shift_Ins_p.L488fs|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000450632.1_3'UTR	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	587					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTGGATGGCCAGGGGGGCGTAG	0.604																																					p.L588fs		Atlas-Indel,Pindel	.											.	LILRB5	176	.	0			c.1763_1764insC						.																																			SO:0001589	frameshift_variant	10990	exon13			.	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1760dupC	chr19.hg19:g.54754669_54754669dupG	ENSP00000320390:p.Leu587fs	94.0	0.0		120.0	44.0	NM_001081442	Q8N760	Frame_Shift_Ins	INS	ENST00000316219.5	hg19	CCDS12885.1																																																																																			.	.		0.604	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			G	54754664	-	G	54754663	7	5	23	1	0	1	1	0	0	0	0	0	8803	188	7	0	16	0	LILRB5	19	54754663	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	33392	54754663	4374320	1029	3095										
LENG8	114823	hgsc.bcm.edu	37	chr19	54967527	54967527	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctcccactcagactccgacaGctcctactcagggaatgagt	8	15	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:54967527G>A	ENST00000326764.5	+	10	1807	c.1328G>A	c.(1327-1329)aGc>aAc	p.S443N	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	406										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GACTCCGACAGCTCCTACTCA	0.672																																					p.S443N		Atlas-SNP	.											.	LENG8	73	.	0			c.G1328A						.						53	57	56					19																	54967527		2203	4300	6503	SO:0001583	missense	114823	exon10			CCGACAGCTCCTA	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1328G>A	chr19.hg19:g.54967527G>A	ENSP00000318374:p.Ser443Asn	62.0	0.0		60.0	26.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	hg19	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	G	18.65	3.670567	0.67814	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000376526;ENST00000431846	T;T;T	0.36699	1.28;1.28;1.24	4.52	4.52	0.55395	.	0.109881	0.64402	D	0.000003	T	0.33381	0.0861	L	0.27053	0.805	0.42244	D	0.991949	B;P	0.46784	0.449;0.884	B;P	0.47864	0.185;0.559	T	0.03887	-1.0995	10	0.26408	T	0.33	-7.2268	15.6069	0.76679	0.0:0.0:1.0:0.0	.	443;406	Q96PV6-2;F8W9Q9	.;.	N	443;406;406;443	ENSP00000318374:S443N;ENSP00000365709:S406N;ENSP00000388053:S443N	ENSP00000301196:S406N	S	+	2	0	LENG8	59659339	1.000000	0.71417	0.985000	0.45067	0.986000	0.74619	5.566000	0.67372	2.466000	0.83321	0.555000	0.69702	AGC	.	.		0.672	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		A	54967527	G	A	54967527	3	1	23	1	0	0	0	0	1	0	0	0	8733	971	34	3	1362	3	LENG8	19	54967527	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	212864	54967527	4161456	1030	3096										
LILRA2	11027	hgsc.bcm.edu	37	chr19	55087325	55087325	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcagccggtccccacagtagCcccaggaaagaacgtgaccc					rs537955715		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:55087325delC	ENST00000251377.3	+	7	1137	c.1004delC	c.(1003-1005)gccfs	p.A335fs	LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000251376.3_Frame_Shift_Del_p.A335fs|LILRA2_ENST00000391738.3_Frame_Shift_Del_p.A335fs|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA2_ENST00000391737.1_Frame_Shift_Del_p.A323fs			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	335	Ig-like C2-type 4.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		CCCACAGTAGCCCCAGGAAAG	0.592																																					p.A335fs		Atlas-Indel,Pindel	.											.	LILRA2	99	.	0			c.1003delG						.						65	57	60					19																	55087325		2203	4300	6503	SO:0001589	frameshift_variant	11027	exon6			.	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.1004delC	chr19.hg19:g.55087325delC	ENSP00000251377:p.Ala335fs	116.0	0.0		135.0	53.0	NM_001130917	O75020	Frame_Shift_Del	DEL	ENST00000251377.3	hg19	CCDS46179.1																																																																																			.	.		0.592	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			-	55087325	C	-	55087325	7	5	23	1	0	1	0	1	0	0	0	0	8794	739	26	0	1026	0	LILRA2	19	55087325	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	119798	55087325	4041658	1031	3097										
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55591068	55591068	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccgtaccagcacctggtgaCgttctgcctgggtgaggacg	14	12	1	2	rs373089208		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:55591068C>T	ENST00000201647.6	+	5	184	c.128C>T	c.(127-129)aCg>aTg	p.T43M	EPS8L1_ENST00000588359.1_5'Flank|EPS8L1_ENST00000540810.1_5'UTR|EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000586329.1_Missense_Mutation_p.T25M|EPS8L1_ENST00000245618.5_5'Flank	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	43					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CACCTGGTGACGTTCTGCCTG	0.582																																					p.T43M	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.C128T						.	C	MET/THR	0,4406		0,0,2203	91	72	79		128	3.8	1	19		79	1,8599	1.2+/-3.3	0,1,4299	no	missense	EPS8L1	NM_133180.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	43/724	55591068	1,13005	2203	4300	6503	SO:0001583	missense	54869	exon5			TGGTGACGTTCTG	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.128C>T	chr19.hg19:g.55591068C>T	ENSP00000201647:p.Thr43Met	110.0	0.0		94.0	30.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	hg19	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055187	0.75960	0.0	1.16E-4	ENSG00000131037	ENST00000310075;ENST00000201647	T	0.41400	1.0	3.85	3.85	0.44370	Pleckstrin homology-type (1);Tensin phosphotyrosine-binding domain (1);	0.073341	0.53938	D	0.000045	T	0.65923	0.2738	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.72821	-0.4177	10	0.87932	D	0	-22.5488	13.6399	0.62243	0.0:1.0:0.0:0.0	.	25;43	Q8TE68-3;Q8TE68	.;ES8L1_HUMAN	M	25;43	ENSP00000201647:T43M	ENSP00000201647:T43M	T	+	2	0	EPS8L1	60282880	1.000000	0.71417	0.992000	0.48379	0.816000	0.46133	6.675000	0.74493	1.860000	0.53959	0.313000	0.20887	ACG	.	.		0.582	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		T	55591068	C	T	55591068	3	4	23	1	0	0	0	0	1	0	0	0	5197	536	19	1	142	1	EPS8L1	19	55591068	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	503743	55591068	3537915	1032	3098										
PTPRH	5794	hgsc.bcm.edu	37	chr19	55693151	55693151	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caacttgtgggcctggatggCggccacgttctcgtagatga	14	10	1	2	rs201369294		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:55693151C>T	ENST00000376350.3	-	20	3341	c.3319G>A	c.(3319-3321)Gcc>Acc	p.A1107T	SYT5_ENST00000590851.1_5'Flank|PTPRH_ENST00000263434.5_Missense_Mutation_p.A929T|SYT5_ENST00000354308.3_5'Flank|SYT5_ENST00000537500.1_5'Flank	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	1107					apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		GCCTGGATGGCGGCCACGTTC	0.602																																					p.A1107T		Atlas-SNP	.											.	PTPRH	139	.	0			c.G3319A						.						128	125	126					19																	55693151		2203	4300	6503	SO:0001583	missense	5794	exon20			GGATGGCGGCCAC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.3319G>A	chr19.hg19:g.55693151C>T	ENSP00000365528:p.Ala1107Thr	116.0	0.0		95.0	40.0	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	hg19	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.037159	0.54896	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.06371	3.31;4.31	4.16	1.99	0.26369	.	0.000000	0.35466	N	0.003200	T	0.04815	0.0130	L	0.27053	0.805	0.09310	N	1	P;P	0.51933	0.949;0.949	B;P	0.44561	0.358;0.453	T	0.37174	-0.9717	10	0.38643	T	0.18	.	5.7617	0.18203	0.0:0.6497:0.1866:0.1637	.	929;1107	C9JCH2;Q9HD43	.;PTPRH_HUMAN	T	1107;929	ENSP00000365528:A1107T;ENSP00000263434:A929T	ENSP00000263434:A929T	A	-	1	0	PTPRH	60384963	0.002000	0.14202	0.021000	0.16686	0.030000	0.12068	0.700000	0.25601	1.046000	0.40249	0.650000	0.86243	GCC	.	C|0.999;T|0.001		0.602	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			T	55693151	C	T	55693151	3	4	23	1	0	0	0	0	1	0	0	0	12818	768	27	1	32	1	PTPRH	19	55693151	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	102083	55693151	3435832	1033	3099										
RPL28	6158	hgsc.bcm.edu	37	chr19	55899324	55899324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaagcctgccacctcctatGtgcggaccaccatcaacaag	9	15	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:55899324G>A	ENST00000344063.2	+	4	861	c.232G>A	c.(232-234)Gtg>Atg	p.V78M	RPL28_ENST00000558815.1_Missense_Mutation_p.V78M|RPL28_ENST00000559463.1_Missense_Mutation_p.V78M|RPL28_ENST00000560583.1_Missense_Mutation_p.V78M|RPL28_ENST00000560055.1_Missense_Mutation_p.V78M|RPL28_ENST00000558131.1_Missense_Mutation_p.M71I|RPL28_ENST00000458349.2_Missense_Mutation_p.V78M			P46779	RL28_HUMAN	ribosomal protein L28	78					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)	6	Breast(117;0.191)	Renal(1328;0.245)	LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CACCTCCTATGTGCGGACCAC	0.612																																					p.V78M		Atlas-SNP	.											.	RPL28	31	.	0			c.G232A						.						87	86	86					19																	55899324		2203	4300	6503	SO:0001583	missense	6158	exon4			TCCTATGTGCGGA	U14969	CCDS12924.1, CCDS46189.1, CCDS46190.1, CCDS46191.1, CCDS46192.1	19q13.4	2011-04-06				ENSG00000108107		"L ribosomal proteins"	10330	protein-coding gene	gene with protein product	"60S ribosomal protein L28"	603638				7772601, 9582194	Standard	NM_001136134		Approved	FLJ43307, L28	uc010yga.2	P46779		ENST00000344063.2:c.232G>A	chr19.hg19:g.55899324G>A	ENSP00000342787:p.Val78Met	89.0	0.0		80.0	33.0	NM_000991	B2R4A6|B4DEP9|C9JB50|E9PB24|G5E9L2|Q6IAY0|Q96FX1|Q9BWQ0	Missense_Mutation	SNP	ENST00000344063.2	hg19	CCDS12924.1	.	.	.	.	.	.	.	.	.	.	G	14.53	2.563526	0.45694	.	.	ENSG00000108107	ENST00000344063;ENST00000426763;ENST00000458349	T;T	0.45668	0.89;0.89	3.44	3.44	0.39384	.	0.673867	0.13775	N	0.363655	T	0.48095	0.1481	M	0.78285	2.405	0.26786	N	0.969502	P;P;B	0.42010	0.623;0.768;0.149	B;B;B	0.41988	0.268;0.372;0.122	T	0.47535	-0.9110	10	0.48119	T	0.1	.	13.1887	0.59697	0.0:0.0:1.0:0.0	.	78;78;78	B4DEP9;E9PB24;P46779	.;.;RL28_HUMAN	M	78	ENSP00000342787:V78M;ENSP00000401450:V78M	ENSP00000342787:V78M	V	+	1	0	RPL28	60591136	1.000000	0.71417	0.933000	0.37362	0.975000	0.68041	5.866000	0.69590	1.864000	0.54056	0.462000	0.41574	GTG	.	.		0.612	RPL28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416277.2	NM_000991		A	55899324	G	A	55899324	3	1	23	1	0	0	0	0	1	0	0	0	13592	1377	48	3	310	3	RPL28	19	55899324	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	206173	55899324	3229659	1034	3100										
ZNF628	89887	hgsc.bcm.edu	37	chr19	55992668	55992668	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgccccggcggcccagtaCgaatgtggggagtgtggcaa	16	12	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:55992668C>T	ENST00000598519.1	+	3	661	c.108C>T	c.(106-108)taC>taT	p.Y36Y	ZNF628_ENST00000391718.2_Silent_p.Y32Y			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	36					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		CGGCCCAGTACGAATGTGGGG	0.711																																					p.Y36Y		Atlas-SNP	.											.	ZNF628	75	.	0			c.C108T						.						22	23	23					19																	55992668		2199	4295	6494	SO:0001819	synonymous_variant	89887	exon3			CCAGTACGAATGT	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"Zinc fingers, C2H2-type"	28054	protein-coding gene	gene with protein product	"Zinc finger expressed in Embryonal cells and Certain adult organs"	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.108C>T	chr19.hg19:g.55992668C>T		129.0	0.0		148.0	56.0	NM_033113	Q86X34	Silent	SNP	ENST00000598519.1	hg19	CCDS33116.3																																																																																			.	.		0.711	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		T	55992668	C	T	55992668	2	4	23	1	0	0	0	0	0	0	0	1	18067	547	19	1		1	ZNF628	19	55992668	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	93344	55992668	3136315	1035	3101										
U2AF2	11338	hgsc.bcm.edu	37	chr19	56185355	56185355	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaaagccatgcagggcctgaCgggccgcaagttcgccaaca	13	13	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:56185355C>T	ENST00000308924.4	+	12	1389	c.1349C>T	c.(1348-1350)aCg>aTg	p.T450M	CTD-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.13_ENST00000592252.1_RNA|EPN1_ENST00000411543.2_5'Flank|U2AF2_ENST00000450554.2_Missense_Mutation_p.T446M|CTD-2537I9.12_ENST00000585940.1_RNA|U2AF2_ENST00000590551.1_Missense_Mutation_p.T282M|EPN1_ENST00000085079.7_5'Flank|EPN1_ENST00000270460.6_5'Flank			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	450	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T450M(1)		biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CAGGGCCTGACGGGCCGCAAG	0.577																																					p.T450M		Atlas-SNP	.											U2AF2,bile_duct,carcinoma,0,1	U2AF2	62	.	1	Substitution - Missense(1)	biliary_tract(1)	c.C1349T						.						89	84	86					19																	56185355		2203	4300	6503	SO:0001583	missense	11338	exon12			GCCTGACGGGCCG	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"RNA binding motif (RRM) containing"	23156	protein-coding gene	gene with protein product	"U2 small nuclear ribonucleoprotein auxiliary factor (65kD)", "splicing factor U2AF 65 kD subunit", "U2 snRNP auxiliary factor large subunit"	191318	"U2 (RNU2) small nuclear RNA auxiliary factor 2"			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.1349C>T	chr19.hg19:g.56185355C>T	ENSP00000307863:p.Thr450Met	117.0	0.0		99.0	37.0	NM_007279	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	hg19	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373101	0.82573	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	T;T	0.16324	2.35;2.35	4.42	4.42	0.53409	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	U	0.000000	T	0.40619	0.1124	M	0.71871	2.18	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72625	0.978;0.943	T	0.24190	-1.0167	10	0.42905	T	0.14	-22.4265	16.161	0.81712	0.0:1.0:0.0:0.0	.	450;446	P26368;P26368-2	U2AF2_HUMAN;.	M	450;446	ENSP00000307863:T450M;ENSP00000388475:T446M	ENSP00000307863:T450M	T	+	2	0	U2AF2	60877167	1.000000	0.71417	0.951000	0.38953	0.990000	0.78478	5.200000	0.65158	2.173000	0.68751	0.478000	0.44815	ACG	.	.		0.577	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		T	56185355	C	T	56185355	3	4	23	1	0	0	0	0	1	0	0	0	16838	536	19	1	1395	1	U2AF2	19	56185355	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	192687	56185355	2943628	1036	3102										
ZNF835	90485	hgsc.bcm.edu	37	chr19	57175770	57175770	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtggatgcgctggtggcggAtgagcgctgaggagaagcgg	21	6	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:57175770A>T	ENST00000537055.2	-	2	1028	c.797T>A	c.(796-798)aTc>aAc	p.I266N		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	266					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CTGGTGGCGGATGAGCGCTGA	0.677																																					p.I266N		Atlas-SNP	.											.	ZNF835	106	.	0			c.T797A						.						31	32	31					19																	57175770		2203	4300	6503	SO:0001583	missense	90485	exon2			TGGCGGATGAGCG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.797T>A	chr19.hg19:g.57175770A>T	ENSP00000444747:p.Ile266Asn	128.0	0.0		123.0	51.0	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	hg19	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	A	14.24	2.475900	0.44044	.	.	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.07114	3.22	2.12	-0.00638	0.14013	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08088	0.0202	N	0.04959	-0.14	0.09310	N	1	D	0.59357	0.985	P	0.61477	0.889	T	0.33266	-0.9875	9	0.45353	T	0.12	.	5.3168	0.15860	0.6931:0.0:0.3069:0.0	.	288	Q9Y2P0	ZN835_HUMAN	N	288;266	ENSP00000444747:I266N	ENSP00000341756:I288N	I	-	2	0	ZNF835	61867582	0.000000	0.05858	0.000000	0.03702	0.719000	0.41307	-2.552000	0.00927	-0.066000	0.12998	0.459000	0.35465	ATC	.	.		0.677	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		T	57175770	A	T	57175770	3	4	23	1	0	0	0	0	1	0	0	0	18201	333	12	4	818	4	ZNF835	19	57175770	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	990415	57175770	1953213	1037	3103										
ZNF814	730051	hgsc.bcm.edu	37	chr19	58384994	58384994	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgatggctcctaaggtgcccGattgaactaaaagatttccc	9	10	0	3	rs562476717		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:58384994G>A	ENST00000435989.2	-	3	1998	c.1764C>T	c.(1762-1764)atC>atT	p.I588I	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	588					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TAAGGTGCCCGATTGAACTAA	0.453																																					p.I588I		Atlas-SNP	.											.	ZNF814	93	.	0			c.C1764T						.						93	75	81					19																	58384994		692	1591	2283	SO:0001819	synonymous_variant	730051	exon3			GTGCCCGATTGAA		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1764C>T	chr19.hg19:g.58384994G>A		122.0	0.0		102.0	47.0	NM_001144989	A6NF35	Silent	SNP	ENST00000435989.2	hg19	CCDS46212.1																																																																																			.	.		0.453	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		A	58384994	G	A	58384994	2	1	23	1	0	0	0	0	0	0	0	1	18191	1048	37	1		1	ZNF814	19	58384994	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1209224	58384994	743989	1038	3104										
ZNF544	27300	hgsc.bcm.edu	37	chr19	58773536	58773536	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctggagagaagccctatgagTgcaacctgtgtgggaaatcc	13	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:58773536T>C	ENST00000596652.1	+	6	1798	c.1564T>C	c.(1564-1566)Tgc>Cgc	p.C522R	ZNF544_ENST00000596825.1_3'UTR|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000269829.4_Missense_Mutation_p.C522R|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000415203.2_Missense_Mutation_p.C494R|ZNF544_ENST00000599953.1_Missense_Mutation_p.C380R|ZNF544_ENST00000600220.1_Missense_Mutation_p.C494R|ZNF544_ENST00000600044.1_Missense_Mutation_p.C494R			Q6NX49	ZN544_HUMAN	zinc finger protein 544	522					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		GCCCTATGAGTGCAACCTGTG	0.438																																					p.C522R		Atlas-SNP	.											.	ZNF544	57	.	0			c.T1564C						.						80	83	82					19																	58773536		2203	4300	6503	SO:0001583	missense	27300	exon7			TATGAGTGCAACC	AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.1564T>C	chr19.hg19:g.58773536T>C	ENSP00000469635:p.Cys522Arg	165.0	0.0		158.0	59.0	NM_014480	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	hg19	CCDS12973.1	.	.	.	.	.	.	.	.	.	.	T	13.52	2.262069	0.39995	.	.	ENSG00000198131	ENST00000269829;ENST00000415203	D;D	0.85258	-1.96;-1.96	2.8	1.72	0.24424	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94059	0.8096	H	0.97940	4.11	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.91846	0.5487	9	0.87932	D	0	.	7.4777	0.27387	0.1925:0.0:0.0:0.8075	.	494;494;522	B7ZAY1;B4DL50;Q6NX49	.;.;ZN544_HUMAN	R	522;494	ENSP00000269829:C522R;ENSP00000394341:C494R	ENSP00000269829:C522R	C	+	1	0	ZNF544	63465348	1.000000	0.71417	0.001000	0.08648	0.005000	0.04900	4.949000	0.63596	0.282000	0.22254	0.421000	0.28195	TGC	.	.		0.438	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		C	58773536	T	C	58773536	3	2	23	1	0	0	0	0	1	0	0	0	17992	1696	59	2	1578	2	ZNF544	19	58773536	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	388542	58773536	355447	1039	3105										
SLC27A5	10998	hgsc.bcm.edu	37	chr19	59011917	59011917	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttgcccagggccccgcagcGccccacatagttgactaagc	10	17	0	1	rs558863851		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:59011917G>A	ENST00000263093.2	-	5	1448	c.1339C>T	c.(1339-1341)Cgc>Tgc	p.R447C	SLC27A5_ENST00000594786.1_5'Flank|SLC27A5_ENST00000601355.1_Missense_Mutation_p.R363C|SLC27A5_ENST00000599700.1_5'Flank	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	447					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		GCCCCGCAGCGCCCCACATAG	0.602													G|||	1	0.000199681	8e-04	0	5008	,	,		17577	0		0	False		,,,				2504	0				p.R447C		Atlas-SNP	.											.	SLC27A5	58	.	0			c.C1339T						.						80	72	75					19																	59011917		2203	4300	6503	SO:0001583	missense	10998	exon5			CGCAGCGCCCCAC	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"Acyl-CoA synthetase family", "Solute carriers"	10999	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 3"	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.1339C>T	chr19.hg19:g.59011917G>A	ENSP00000263093:p.Arg447Cys	65.0	0.0		56.0	18.0	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	hg19	CCDS12983.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.408143	0.62399	.	.	ENSG00000083807	ENST00000263093	T	0.43294	0.95	5.33	4.28	0.50868	AMP-dependent synthetase/ligase (1);	0.377730	0.28393	N	0.015502	T	0.63954	0.2555	M	0.83118	2.625	0.30853	N	0.734336	D	0.76494	0.999	D	0.67725	0.953	T	0.70288	-0.4913	10	0.87932	D	0	-13.0742	11.6284	0.51160	0.0:0.0:0.822:0.178	.	447	Q9Y2P5	S27A5_HUMAN	C	447	ENSP00000263093:R447C	ENSP00000263093:R447C	R	-	1	0	SLC27A5	63703729	0.029000	0.19370	0.314000	0.25224	0.647000	0.38526	1.920000	0.40025	1.363000	0.46019	0.563000	0.77884	CGC	.	.		0.602	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		A	59011917	G	A	59011917	3	1	23	1	0	0	0	0	1	0	0	0	14544	1087	38	1	757	1	SLC27A5	19	59011917	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	238381	59011917	117066	1040	3106										
TRIM28	10155	hgsc.bcm.edu	37	chr19	59059077	59059077	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcaccaaggaggttcgcaGctcgtaagtgtgggttctgg	16	8	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:59059077G>A	ENST00000253024.5	+	5	1125	c.836G>A	c.(835-837)aGc>aAc	p.S279N	TRIM28_ENST00000341753.6_Missense_Mutation_p.S197N	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28	279	Interaction with MAGEC2.|Leucine zipper alpha helical coiled-coil region.|RBCC domain.				convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GAGGTTCGCAGCTCGTAAGTG	0.602																																					p.S279N		Atlas-SNP	.											.	TRIM28	46	.	0			c.G836A						.						118	98	105					19																	59059077		2203	4300	6503	SO:0001583	missense	10155	exon5			TTCGCAGCTCGTA		CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	16384	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 157"	601742	"tripartite motif-containing 28"			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.836G>A	chr19.hg19:g.59059077G>A	ENSP00000253024:p.Ser279Asn	165.0	0.0		125.0	39.0	NM_005762	O00677|Q7Z632|Q93040|Q96IM1	Missense_Mutation	SNP	ENST00000253024.5	hg19	CCDS12985.1	.	.	.	.	.	.	.	.	.	.	G	8.588	0.883850	0.17467	.	.	ENSG00000130726	ENST00000253024;ENST00000341753	T;T	0.67523	-0.04;-0.27	4.99	3.89	0.44902	B-box, C-terminal (1);	0.117868	0.56097	D	0.000035	T	0.45478	0.1344	N	0.11427	0.14	0.34896	D	0.746054	P;P	0.40731	0.728;0.608	B;B	0.43445	0.42;0.188	T	0.53415	-0.8442	10	0.02654	T	1	-34.7179	12.6235	0.56616	0.0:0.2675:0.7325:0.0	.	197;279	Q13263-2;Q13263	.;TIF1B_HUMAN	N	279;197	ENSP00000253024:S279N;ENSP00000342232:S197N	ENSP00000253024:S279N	S	+	2	0	TRIM28	63750889	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.331000	0.33793	2.499000	0.84300	0.555000	0.69702	AGC	.	.		0.602	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467074.1	NM_005762		A	59059077	G	A	59059077	3	1	23	1	0	0	0	0	1	0	0	0	16517	971	34	3	854	3	TRIM28	19	59059077	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	47160	59059077	69906	1041	3107										
SIRPB1	10326	hgsc.bcm.edu	37	chr20	1600524	1600524	+	Frame_Shift_Del	DEL	T	T	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcagtgctcacctgtgagtcTccccagcagtagcgtcatca					rs1535882	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:1600524delT	ENST00000381605.4	-	1	131	c.67delA	c.(67-69)agafs	p.R23fs	SIRPB1_ENST00000381603.3_Frame_Shift_Del_p.R23fs|SIRPB1_ENST00000279477.7_Frame_Shift_Del_p.R23fs|RP4-576H24.4_ENST00000564763.1_Frame_Shift_Del_p.R23fs|SIRPB1_ENST00000568365.1_Frame_Shift_Del_p.R23fs|SIRPB1_ENST00000381596.1_5'UTR	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	23			R -> G (in dbSNP:rs1535882).		cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CCTGTGAGTCTCCCCAGCAGT	0.562																																					p.R23fs		Atlas-Indel,Pindel	.											.	SIRPB1	83	.	0			c.68delG						.						97	87	90					20																	1600524		2203	4300	6503	SO:0001589	frameshift_variant	10326	exon1			.	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.67delA	chr20.hg19:g.1600524delT	ENSP00000371018:p.Arg23fs	99.0	0.0		96.0	39.0	NM_001083910	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Frame_Shift_Del	DEL	ENST00000381605.4	hg19	CCDS13019.1																																																																																			.	.		0.562	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		-	1600524	T	-	1600524	7	5	23	1	0	1	0	1	0	0	0	0	14348	1559	54	0	2286	0	SIRPB1	20	1600524	Frame_Shift_Del	DEL	T	TCGA-4R-AA8I-01A-11D-A382-10		1600524	61424996	1042	3108										
NOP56	10528	hgsc.bcm.edu	37	chr20	2635511	2635511	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagttaagtttaatgtgaacCgggtggacaatatgatcatc	10	5	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:2635511C>T	ENST00000329276.5	+	5	1003	c.487C>T	c.(487-489)Cgg>Tgg	p.R163W	SNORA51_ENST00000606420.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORD110_ENST00000408189.1_RNA|SNORD56_ENST00000413522.1_RNA|SNORD86_ENST00000391196.1_RNA|SNORD57_ENST00000448188.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	163					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						TAATGTGAACCGGGTGGACAA	0.507																																					p.R163W		Atlas-SNP	.											.	NOP56	73	.	0			c.C487T						.						173	168	170					20																	2635511		2203	4300	6503	SO:0001583	missense	10528	exon5			GTGAACCGGGTGG	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"spinocerebellar ataxia 36"	614154	"nucleolar protein 5A (56kD with KKE/D repeat)", "nucleolar protein 5A (56kDa with KKE/D repeat)", "NOP56 ribonucleoprotein homolog (yeast)"	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.487C>T	chr20.hg19:g.2635511C>T	ENSP00000370589:p.Arg163Trp	102.0	0.0		95.0	29.0	NM_006392	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	hg19	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.236678	0.39498	.	.	ENSG00000101361	ENST00000329276;ENST00000445139	T;T	0.77750	-1.12;-1.12	5.89	3.79	0.43588	.	0.000000	0.85682	D	0.000000	D	0.88912	0.6566	M	0.93106	3.38	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89514	0.3773	10	0.87932	D	0	-15.3937	8.3385	0.32230	0.2177:0.6984:0.0:0.0839	.	163	O00567	NOP56_HUMAN	W	163	ENSP00000370589:R163W;ENSP00000388497:R163W	ENSP00000370589:R163W	R	+	1	2	NOP56	2583511	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	1.509000	0.35780	1.494000	0.48533	-0.266000	0.10368	CGG	.	.		0.507	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392		T	2635511	C	T	2635511	3	4	23	1	0	0	0	0	1	0	0	0	10548	643	23	1	505	1	NOP56	20	2635511	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1034987	2635511	60390009	1043	3109										
UBOX5	22888	hgsc.bcm.edu	37	chr20	3102753	3102753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	accgccgcctgtcacatgggTgatacagatccttaagtggg	12	11	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:3102753T>C	ENST00000217173.2	-	3	1003	c.532A>G	c.(532-534)Acc>Gcc	p.T178A	UBOX5_ENST00000348031.2_Missense_Mutation_p.T178A|UBOX5-AS1_ENST00000446537.1_RNA	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5											endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						GTCACATGGGTGATACAGATC	0.577																																					p.T178A		Atlas-SNP	.											.	UBOX5	47	.	0			c.A532G						.						68	61	63					20																	3102753		2203	4300	6503	SO:0001583	missense	22888	exon3			CATGGGTGATACA	AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"RING-type (C3HC4) zinc fingers", "U-box domain containing"	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.532A>G	chr20.hg19:g.3102753T>C	ENSP00000217173:p.Thr178Ala	110.0	0.0		99.0	42.0	NM_014948		Missense_Mutation	SNP	ENST00000217173.2	hg19	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	T	8.988	0.977004	0.18812	.	.	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.48836	0.8;0.8	5.19	5.19	0.71726	.	0.124327	0.53938	U	0.000048	T	0.36193	0.0958	L	0.35288	1.05	0.39081	D	0.960917	B;B;B	0.32350	0.366;0.361;0.366	B;B;B	0.23574	0.047;0.042;0.047	T	0.31392	-0.9945	10	0.41790	T	0.15	-17.3227	15.0487	0.71846	0.0:0.0:0.0:1.0	.	178;178;178	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	A	178	ENSP00000217173:T178A;ENSP00000311726:T178A	ENSP00000217173:T178A	T	-	1	0	UBOX5	3050753	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	4.739000	0.62080	1.950000	0.56595	0.379000	0.24179	ACC	.	.		0.577	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		C	3102753	T	C	3102753	3	2	23	1	0	0	0	0	1	0	0	0	16909	1696	59	2	1105	2	UBOX5	20	3102753	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	467242	3102753	59922767	1044	3110										
ProSAPiP1	9762	hgsc.bcm.edu	37	chr20	3145661	3145663	+	In_Frame_Del	DEL	CTT	CTT	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggctgagcagctgctcctcCttctcccgcagcgaagcccg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:3145661_3145663delCTT	ENST00000329152.3	-	3	2856_2858	c.1459_1461delAAG	c.(1459-1461)aagdel	p.K487del	LZTS3_ENST00000360342.3_In_Frame_Del_p.K441del|LZTS3_ENST00000337576.5_In_Frame_Del_p.K441del			O60299	LZTS3_HUMAN		487						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)											GCTGCTCCTCCTTCTCCCGCAGC	0.685																																					p.487_488del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1460_1462del						.																																			SO:0001651	inframe_deletion	0	exon3			.																												ENST00000329152.3:c.1459_1461delAAG	chr20.hg19:g.3145661_3145663delCTT	ENSP00000332123:p.Lys487del	74.0	0.0		56.0	18.0	NM_014731	A2A2Q7|D3DVX6|Q8IXX8	In_Frame_Del	DEL	ENST00000329152.3	hg19	CCDS13049.1																																																																																			.	.		0.685	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2			-	3145663	CTT	-	3145661	7	5	23	1	0	1	0	1	0	0	0	0	12885	680	24	0	564	0	ProSAPiP1	20	3145661	In_Frame_Del	DEL	CTT	TCGA-4R-AA8I-01A-11D-A382-10	42908	3145661	59879859	1045	3111										
ATRN	8455	hgsc.bcm.edu	37	chr20	3556555	3556555	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgactgccactggtgcaatgAccattgtgtccccaggaacc	10	13	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:3556555A>C	ENST00000262919.5	+	13	2242	c.2174A>C	c.(2173-2175)gAc>gCc	p.D725A	ATRN_ENST00000446916.2_Missense_Mutation_p.D725A	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	725	PSI 1.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						TGGTGCAATGACCATTGTGTC	0.453																																					p.D725A		Atlas-SNP	.											.	ATRN	118	.	0			c.A2174C						.						95	84	88					20																	3556555		2203	4300	6503	SO:0001583	missense	8455	exon13			GCAATGACCATTG	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"mahogany protein"	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.2174A>C	chr20.hg19:g.3556555A>C	ENSP00000262919:p.Asp725Ala	66.0	0.0		67.0	26.0	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	hg19	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.959695	0.74016	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.18502	3.39;2.21	5.79	5.79	0.91817	.	0.204186	0.50627	D	0.000103	T	0.23249	0.0562	M	0.65498	2.005	0.43868	D	0.996477	B;P	0.42296	0.372;0.775	B;B	0.39771	0.309;0.225	T	0.01697	-1.1293	10	0.44086	T	0.13	-25.0048	15.797	0.78420	1.0:0.0:0.0:0.0	.	725;725	O75882;O75882-2	ATRN_HUMAN;.	A	725;725;651	ENSP00000262919:D725A;ENSP00000416587:D725A	ENSP00000262919:D725A	D	+	2	0	ATRN	3504555	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.976000	0.63785	2.204000	0.70986	0.460000	0.39030	GAC	.	.		0.453	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321		C	3556555	A	C	3556555	3	2	23	1	0	0	0	0	1	0	0	0	1206	275	10	5	2224	5	ATRN	20	3556555	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	410894	3556555	59468965	1046	3112										
ATRN	8455	hgsc.bcm.edu	37	chr20	3575207	3575207	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caccaagggcgtcaagggggAcgagtgccagctgtgagtac	16	10	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:3575207A>G	ENST00000262919.5	+	20	3472	c.3404A>G	c.(3403-3405)gAc>gGc	p.D1135G	ATRN_ENST00000446916.2_Missense_Mutation_p.D1135G	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	1135	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						GTCAAGGGGGACGAGTGCCAG	0.597																																					p.D1135G		Atlas-SNP	.											.	ATRN	118	.	0			c.A3404G						.						85	70	75					20																	3575207		2203	4300	6503	SO:0001583	missense	8455	exon20			AGGGGGACGAGTG	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"mahogany protein"	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.3404A>G	chr20.hg19:g.3575207A>G	ENSP00000262919:p.Asp1135Gly	146.0	0.0		145.0	41.0	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	hg19	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	A	31	5.085824	0.94100	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.55588	0.51;0.51	5.85	5.85	0.93711	EGF-like, laminin (1);	0.229658	0.50627	D	0.000114	T	0.70448	0.3225	M	0.88775	2.98	0.80722	D	1	P;P	0.49090	0.919;0.801	P;B	0.51453	0.67;0.393	T	0.77056	-0.2729	10	0.66056	D	0.02	-13.6339	15.8975	0.79346	1.0:0.0:0.0:0.0	.	1135;1135	O75882;O75882-2	ATRN_HUMAN;.	G	1135;1135;1061	ENSP00000262919:D1135G;ENSP00000416587:D1135G	ENSP00000262919:D1135G	D	+	2	0	ATRN	3523207	1.000000	0.71417	0.974000	0.42286	0.999000	0.98932	9.197000	0.94985	2.237000	0.73441	0.528000	0.53228	GAC	.	.		0.597	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321		G	3575207	A	G	3575207	3	3	23	1	0	0	0	0	1	0	0	0	1206	275	10	2	3482	2	ATRN	20	3575207	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	18652	3575207	59450313	1047	3113										
BMP2	650	hgsc.bcm.edu	37	chr20	6759209	6759209	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtggactgcacagggacacGccaaccatggattcgtggtg	15	10	0	0	rs140884062		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:6759209G>A	ENST00000378827.4	+	3	1883	c.664G>A	c.(664-666)Gcc>Acc	p.A222T		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	222					activation of MAPK activity (GO:0000187)|atrioventricular valve morphogenesis (GO:0003181)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|bone mineralization (GO:0030282)|bone mineralization involved in bone maturation (GO:0035630)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiocyte differentiation (GO:0035051)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation (GO:0002062)|corticotropin hormone secreting cell differentiation (GO:0060128)|embryo development (GO:0009790)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchyme development (GO:0060485)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of calcium-independent cell-cell adhesion (GO:0051042)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|pericardium development (GO:0060039)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of odontogenesis (GO:0042482)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of Wnt signaling pathway by BMP signaling pathway (GO:0060804)|protein destabilization (GO:0031648)|protein phosphorylation (GO:0006468)|proteoglycan metabolic process (GO:0006029)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP receptor binding (GO:0070700)|phosphatase activator activity (GO:0019211)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)|retinol dehydrogenase activity (GO:0004745)|SMAD binding (GO:0046332)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	13						ACAGGGACACGCCAACCATGG	0.517																																					p.A222T		Atlas-SNP	.											BMP2,caecum,carcinoma,0,1	BMP2	45	.	0			c.G664A						.	G	THR/ALA	0,4406		0,0,2203	54	48	50		664	-1.5	0	20	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	no	missense	BMP2	NM_001200.2	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	222/397	6759209	1,13005	2203	4300	6503	SO:0001583	missense	650	exon3			GGACACGCCAACC		CCDS13099.1	20p12	2014-01-30			ENSG00000125845	ENSG00000125845		"Bone morphogenetic proteins", "Endogenous ligands"	1069	protein-coding gene	gene with protein product		112261		BMP2A		2376592	Standard	NM_001200		Approved		uc002wmu.1	P12643	OTTHUMG00000031833	ENST00000378827.4:c.664G>A	chr20.hg19:g.6759209G>A	ENSP00000368104:p.Ala222Thr	133.0	1.0		116.0	5.0	NM_001200		Missense_Mutation	SNP	ENST00000378827.4	hg19	CCDS13099.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.727275	0.30593	0.0	1.16E-4	ENSG00000125845	ENST00000378827	T	0.62498	0.02	5.76	-1.45	0.08828	Transforming growth factor-beta, N-terminal (1);	0.842625	0.11159	N	0.593292	T	0.41903	0.1179	L	0.27053	0.805	0.20563	N	0.999887	B	0.06786	0.001	B	0.04013	0.001	T	0.21552	-1.0242	10	0.23891	T	0.37	.	6.7317	0.23387	0.4242:0.2291:0.3467:0.0	.	222	P12643	BMP2_HUMAN	T	222	ENSP00000368104:A222T	ENSP00000368104:A222T	A	+	1	0	BMP2	6707209	0.011000	0.17503	0.040000	0.18447	0.956000	0.61745	0.262000	0.18460	-0.086000	0.12550	-0.312000	0.09012	GCC	.	G|1.000;A|0.000		0.517	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3			A	6759209	G	A	6759209	3	1	23	1	0	0	0	0	1	0	0	0	1459	1087	38	1	670	1	BMP2	20	6759209	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3184002	6759209	56266311	1048	3114										
JAG1	182	hgsc.bcm.edu	37	chr20	10620156	10620156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccgcggtctgctatacgatgTactccattcggtttaagctc	9	12	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:10620156T>C	ENST00000254958.5	-	26	4162	c.3647A>G	c.(3646-3648)tAc>tGc	p.Y1216C	JAG1_ENST00000423891.2_Missense_Mutation_p.Y1057C	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	1216					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						CTATACGATGTACTCCATTCG	0.532									Alagille Syndrome																												p.Y1216C		Atlas-SNP	.											.	JAG1	213	.	0			c.A3647G						.						186	165	172					20																	10620156		2203	4300	6503	SO:0001583	missense	182	exon26	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	ACGATGTACTCCA	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"CD molecules"	6188	protein-coding gene	gene with protein product		601920	"Alagille syndrome"	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.3647A>G	chr20.hg19:g.10620156T>C	ENSP00000254958:p.Tyr1216Cys	128.0	0.0		120.0	46.0	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	hg19	CCDS13112.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.123379	0.56613	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.87491	-2.24;-2.26	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.89815	0.6824	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.91190	0.4983	10	0.87932	D	0	.	16.383	0.83481	0.0:0.0:0.0:1.0	.	1216	P78504	JAG1_HUMAN	C	1216;1057	ENSP00000254958:Y1216C;ENSP00000389519:Y1057C	ENSP00000254958:Y1216C	Y	-	2	0	JAG1	10568156	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.630000	0.83225	2.326000	0.78906	0.533000	0.62120	TAC	.	.		0.532	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		C	10620156	T	C	10620156	3	2	23	1	0	0	0	0	1	0	0	0	7943	1638	57	2	13	2	JAG1	20	10620156	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	3860947	10620156	52405364	1049	3115										
FLRT3	23767	hgsc.bcm.edu	37	chr20	14307168	14307168	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttggcacatgagcccacgcaCgttgaccttcacaggtagtg	11	12	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:14307168C>T	ENST00000378053.3	-	2	1241	c.985G>A	c.(985-987)Gtg>Atg	p.V329M	FLRT3_ENST00000341420.4_Missense_Mutation_p.V329M|FLRT3_ENST00000462077.1_5'Flank|MACROD2_ENST00000217246.4_Intron|MACROD2_ENST00000310348.4_Intron	NM_013281.3	NP_037413.1	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	329	LRRCT.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		AGCCCACGCACGTTGACCTTC	0.463																																					p.V329M		Atlas-SNP	.											.	FLRT3	67	.	0			c.G985A						.						126	112	117					20																	14307168		2203	4300	6503	SO:0001583	missense	23767	exon2			CACGCACGTTGAC	AF169677	CCDS13121.1	20p11	2013-02-11			ENSG00000125848	ENSG00000125848		"Fibronectin type III domain containing"	3762	protein-coding gene	gene with protein product		604808				10644439	Standard	NM_198391		Approved		uc002wow.2	Q9NZU0	OTTHUMG00000031914	ENST00000378053.3:c.985G>A	chr20.hg19:g.14307168C>T	ENSP00000367292:p.Val329Met	221.0	0.0		210.0	77.0	NM_013281	D3DW20|Q542Z9|Q96K39|Q96K42|Q96KB1|Q9P259	Missense_Mutation	SNP	ENST00000378053.3	hg19	CCDS13121.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698854	0.68501	.	.	ENSG00000125848	ENST00000378053;ENST00000341420;ENST00000541882	T;T	0.61510	0.1;0.1	6.06	6.06	0.98353	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77075	0.4077	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.76364	-0.2986	10	0.62326	D	0.03	-9.9021	20.6397	0.99537	0.0:1.0:0.0:0.0	.	329	Q9NZU0	FLRT3_HUMAN	M	329	ENSP00000367292:V329M;ENSP00000339912:V329M	ENSP00000339912:V329M	V	-	1	0	FLRT3	14255168	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.818000	0.86416	2.880000	0.98712	0.650000	0.86243	GTG	.	.		0.463	FLRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078075.1	NM_013281		T	14307168	C	T	14307168	3	4	23	1	0	0	0	0	1	0	0	0	5948	536	19	1	968	1	FLRT3	20	14307168	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3687012	14307168	48718352	1050	3116										
C20orf12	55184	hgsc.bcm.edu	37	chr20	18365673	18365673	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gacataccccagtaaagtggCggtgctctctcttcctgcaa	9	13	2	0	rs143185709		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:18365673C>T	ENST00000358866.6	-	19	2102	c.2080G>A	c.(2080-2082)Gcc>Acc	p.A694T	DZANK1_ENST00000329494.5_Missense_Mutation_p.A672T|DZANK1_ENST00000357236.4_Missense_Mutation_p.A580T|DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000262547.5_Missense_Mutation_p.A694T			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	694							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						AGTAAAGTGGCGGTGCTCTCT	0.493																																					p.A694T		Atlas-SNP	.											DZANK1,caecum,carcinoma,0,4	DZANK1	65	.	0			c.G2080A						.						23	26	25					20																	18365673		1868	4077	5945	SO:0001583	missense	55184	exon20			AAGTGGCGGTGCT	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.2080G>A	chr20.hg19:g.18365673C>T	ENSP00000351734:p.Ala694Thr	100.0	0.0		88.0	29.0	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Missense_Mutation	SNP	ENST00000358866.6	hg19	CCDS46582.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.293171	0.23564	.	.	ENSG00000089091	ENST00000377630;ENST00000262547;ENST00000329494;ENST00000414623;ENST00000377637;ENST00000357236	T;T;T;T	0.70631	0.64;0.64;-0.5;0.64	5.17	1.09	0.20402	.	0.652897	0.14669	N	0.305449	T	0.50137	0.1598	L	0.35341	1.055	0.09310	N	1	B;B;B;B	0.33238	0.152;0.403;0.039;0.089	B;B;B;B	0.19148	0.011;0.024;0.011;0.007	T	0.21999	-1.0229	10	0.16420	T	0.52	-0.2673	9.2467	0.37529	0.0:0.6975:0.0:0.3025	.	713;580;694;479	B7Z631;Q9NVP4-4;Q9NVP4;A6NKD0	.;.;DZAN1_HUMAN;.	T	527;694;672;526;479;580	ENSP00000366857:A527T;ENSP00000262547:A694T;ENSP00000328866:A672T;ENSP00000349774:A580T	ENSP00000262547:A694T	A	-	1	0	C20orf12	18313673	0.027000	0.19231	0.001000	0.08648	0.902000	0.53008	0.112000	0.15479	-0.024000	0.13941	-0.150000	0.13652	GCC	.	.		0.493	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		T	18365673	C	T	18365673	3	4	23	1	0	0	0	0	1	0	0	0	2087	768	27	1	186	1	C20orf12	20	18365673	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	4058505	18365673	44659847	1051	3117										
PAX1	5075	hgsc.bcm.edu	37	chr20	21687178	21687178	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgtggagctggcgcagctggGcatccgaccctgtgacatca	14	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:21687178G>A	ENST00000398485.2	+	2	443	c.389G>A	c.(388-390)gGc>gAc	p.G130D	PAX1_ENST00000460221.1_Intron|PAX1_ENST00000444366.2_Missense_Mutation_p.G106D	NM_001257096.1|NM_006192.4	NP_001244025.1|NP_006183.2	P15863	PAX1_HUMAN	paired box 1	130	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				bone morphogenesis (GO:0060349)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|parathyroid gland development (GO:0060017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sclerotome development (GO:0061056)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(21)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	38						GCGCAGCTGGGCATCCGACCC	0.662																																					p.G130D		Atlas-SNP	.											.	PAX1	152	.	0			c.G389A						.						38	40	39					20																	21687178		2203	4298	6501	SO:0001583	missense	5075	exon2			AGCTGGGCATCCG		CCDS13146.2, CCDS74709.1	20p11.22	2007-07-12	2007-07-12		ENSG00000125813	ENSG00000125813		"Paired boxes"	8615	protein-coding gene	gene with protein product		167411	"paired box gene 1"			1358810	Standard	NM_006192		Approved		uc002wsj.3	P15863	OTTHUMG00000032034	ENST00000398485.2:c.389G>A	chr20.hg19:g.21687178G>A	ENSP00000381499:p.Gly130Asp	72.0	0.0		86.0	27.0	NM_006192	B4E0D6|Q642X9|Q6NTC0|Q9Y558	Missense_Mutation	SNP	ENST00000398485.2	hg19	CCDS13146.2	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579920	0.65992	.	.	ENSG00000125813	ENST00000398485;ENST00000444366	D;D	0.99795	-6.78;-6.78	5.14	5.14	0.70334	Paired box protein, N-terminal (4);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	H	0.94847	3.59	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.96619	0.9458	10	0.87932	D	0	.	18.2175	0.89890	0.0:0.0:1.0:0.0	.	106;36;130	P15863-2;C9J775;P15863	.;.;PAX1_HUMAN	D	130;106	ENSP00000381499:G130D;ENSP00000410355:G106D	ENSP00000381499:G130D	G	+	2	0	PAX1	21635178	1.000000	0.71417	1.000000	0.80357	0.006000	0.05464	9.654000	0.98509	2.382000	0.81193	0.655000	0.94253	GGC	.	.		0.662	PAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078282.3			A	21687178	G	A	21687178	3	1	23	1	0	0	0	0	1	0	0	0	11487	1203	42	3	395	3	PAX1	20	21687178	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3321505	21687178	41338342	1052	3118										
NANP	140838	hgsc.bcm.edu	37	chr20	25604493	25604493	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcgccatgggtggggacgttAcctccaacatgcctctcctg	12	14	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:25604493A>T	ENST00000304788.3	-	1	317		c.e1+1		RP4-694B14.5_ENST00000428254.1_RNA|RP4-694B14.5_ENST00000414393.1_RNA|RP4-694B14.5_ENST00000439498.1_RNA|RP4-694B14.5_ENST00000420803.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA	NM_152667.2	NP_689880.1	Q8TBE9	NANP_HUMAN	N-acetylneuraminic acid phosphatase						carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate biosynthetic process (GO:0046380)		N-acylneuraminate-9-phosphatase activity (GO:0050124)			endometrium(2)|lung(2)|prostate(1)	5						TGGGGACGTTACCTCCAACAT	0.697																																					.		Atlas-SNP	.											.	NANP	10	.	0			c.90+2T>A						.						32	33	33					20																	25604493		2200	4299	6499	SO:0001630	splice_region_variant	140838	exon2			GACGTTACCTCCA	AL031673	CCDS13173.1	20p11.1	2006-10-24	2006-01-24	2006-01-24	ENSG00000170191	ENSG00000170191			16140	protein-coding gene	gene with protein product		610763	"chromosome 20 open reading frame 147", "haloacid dehalogenase-like hydrolase domain containing 4"	C20orf147, HDHD4		16237198	Standard	NM_152667		Approved	dJ694B14.3, MGC26833	uc002wuy.3	Q8TBE9	OTTHUMG00000032132	ENST00000304788.3:c.90+1T>A	chr20.hg19:g.25604493A>T		155.0	0.0		143.0	47.0	NM_152667	B3KP12|Q5JYN8|Q8TE97|Q9Y3N0	Splice_Site	SNP	ENST00000304788.3	hg19	CCDS13173.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.001319	0.74818	.	.	ENSG00000170191	ENST00000304788	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6532	0.56774	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NANP	25552493	1.000000	0.71417	0.994000	0.49952	0.668000	0.39293	6.461000	0.73522	1.866000	0.54105	0.459000	0.35465	.	.	.		0.697	NANP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078457.2	NM_152667	Intron	T	25604493	A	T	25604493	5	4	23	1	0	0	0	0	0	0	1	0	10163	405	14	4	662	4	NANP	20	25604493	Splice_Site	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3917315	25604493	37421027	1053	3119										
C20orf186	149954	hgsc.bcm.edu	37	chr20	31671633	31671633	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaggagggggtgtcctgggCgtgctcggcgagggtggcat	23	7	0	0	rs578066819		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:31671633C>T	ENST00000375483.3	+	3	630	c.630C>T	c.(628-630)ggC>ggT	p.G210G		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	210	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										GTGTCCTGGGCGTGCTCGGCG	0.642													C|||	1	0.000199681	8e-04	0	5008	,	,		17430	0		0	False		,,,				2504	0				p.G210G		Atlas-SNP	.											.	.	.	.	0			c.C630T						.						36	42	40					20																	31671633		2198	4293	6491	SO:0001819	synonymous_variant	149954	exon3			CCTGGGCGTGCTC	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"BPI fold containing"	16179	protein-coding gene	gene with protein product		615718	"chromosome 20 open reading frame 186"	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.630C>T	chr20.hg19:g.31671633C>T		88.0	0.0		87.0	28.0	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	hg19	CCDS13213.2																																																																																			.	.		0.642	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		T	31671633	C	T	31671633	2	4	23	1	0	0	0	0	0	0	0	1	2100	755	27	1		1	C20orf186	20	31671633	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	6067140	31671633	31353887	1054	3120										
CBFA2T2	9139	hgsc.bcm.edu	37	chr20	32224505	32224505	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acgtacctgtggagttttggAaaaaaacaggtatgtgtctg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:32224505delA	ENST00000346541.3	+	10	1852	c.1315delA	c.(1315-1317)aaafs	p.K440fs	CBFA2T2_ENST00000375279.2_Frame_Shift_Del_p.K440fs|CBFA2T2_ENST00000359606.3_Frame_Shift_Del_p.K450fs|CBFA2T2_ENST00000543126.1_5'Flank|CBFA2T2_ENST00000492345.1_Frame_Shift_Del_p.K411fs|CBFA2T2_ENST00000342704.6_Frame_Shift_Del_p.K431fs|CBFA2T2_ENST00000397800.1_Frame_Shift_Del_p.K411fs	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	440					epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						GGAGTTTTGGAAAAAAACAGG	0.448																																					p.W438X	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-Indel,Pindel	.											CBFA2T2_ENST00000342704,colon,carcinoma,0,2	CBFA2T2	93	.	0			c.1314delG						.																																			SO:0001589	frameshift_variant	9139	exon10			.	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"Zinc fingers, MYND-type"	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.1315delA	chr20.hg19:g.32224505delA	ENSP00000262653:p.Lys440fs	79.0	0.0		92.0	47.0	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Frame_Shift_Del	DEL	ENST00000346541.3	hg19	CCDS13221.1																																																																																			.	.		0.448	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		-	32224505	A	-	32224505	7	5	23	1	0	1	0	1	0	0	0	0	2699	247	9	0	1387	0	CBFA2T2	20	32224505	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	552872	32224505	30801015	1055	3121										
MYH7B	26133	hgsc.bcm.edu	37	chr20	33588879	33588879	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gacgctggagcagacggtgcGcgagctccaggcccgccttg	16	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:33588879G>A	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Missense_Mutation_p.R1840H			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein						calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			CAGACGGTGCGCGAGCTCCAG	0.642																																					p.R1840H		Atlas-SNP	.											.	MYH7B	145	.	0			c.G5519A						.						35	46	42					20																	33588879		2201	4300	6501	SO:0001628	intergenic_variant	57644	exon41			CGGTGCGCGAGCT	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319		chr20.hg19:g.33588879G>A		201.0	0.0		243.0	100.0	NM_020884	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	hg19	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.107039	0.77096	.	.	ENSG00000078814	ENST00000262873	T	0.80824	-1.42	4.55	4.55	0.56014	Myosin tail (1);	0.000000	0.34628	N	0.003817	T	0.74566	0.3733	L	0.37750	1.13	0.35897	D	0.830083	D	0.59767	0.986	P	0.49597	0.616	T	0.79899	-0.1608	10	0.66056	D	0.02	.	5.3998	0.16288	0.2473:0.0:0.7527:0.0	.	1798	A7E2Y1	MYH7B_HUMAN	H	1840	ENSP00000262873:R1840H	ENSP00000262873:R1840H	R	+	2	0	MYH7B	33052540	1.000000	0.71417	0.948000	0.38648	0.818000	0.46254	7.439000	0.80444	2.368000	0.80403	0.462000	0.41574	CGC	.	.		0.642	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		A	33588879	G	A	33588879	1	1	23	0	1	0	0	0	0	0	0	0	10049	1087	38	1		1	MYH7B	20	33588879	IGR	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1364374	33588879	29436641	1056	3122										
EDEM2	55741	hgsc.bcm.edu	37	chr20	33719574	33719574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttgccagtgagcacatcaaTgtggttgccgacctgagaga	12	10	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:33719574T>C	ENST00000374492.3	-	7	820	c.715A>G	c.(715-717)Att>Gtt	p.I239V	EDEM2_ENST00000374491.3_Missense_Mutation_p.I202V|EDEM2_ENST00000541621.1_Missense_Mutation_p.I18V|EDEM2_ENST00000542871.1_5'UTR|EDEM2_ENST00000540582.1_Missense_Mutation_p.I198V	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	239					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			AGCACATCAATGTGGTTGCCG	0.587																																					p.I239V	Esophageal Squamous(51;906 1021 24535 36410 39145)	Atlas-SNP	.											.	EDEM2	46	.	0			c.A715G						.						95	94	94					20																	33719574		2203	4300	6503	SO:0001583	missense	55741	exon7			CATCAATGTGGTT	AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"chromosome 20 open reading frame 31"	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.715A>G	chr20.hg19:g.33719574T>C	ENSP00000363616:p.Ile239Val	111.0	0.0		102.0	32.0	NM_018217	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Missense_Mutation	SNP	ENST00000374492.3	hg19	CCDS13247.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.477501	0.44044	.	.	ENSG00000088298	ENST00000374491;ENST00000374492;ENST00000541621;ENST00000540582	T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72	5.6	5.6	0.85130	.	0.043964	0.85682	D	0.000000	T	0.61949	0.2388	L	0.41415	1.275	0.58432	D	0.999994	B;B;B;B	0.27286	0.048;0.174;0.142;0.172	B;B;B;B	0.33392	0.086;0.163;0.125;0.143	T	0.60224	-0.7305	10	0.37606	T	0.19	-14.0668	8.2659	0.31813	0.0:0.1478:0.0:0.8522	.	198;18;202;239	F5GZ44;G3V1Q0;Q9BV94-2;Q9BV94	.;.;.;EDEM2_HUMAN	V	202;239;18;198	ENSP00000363615:I202V;ENSP00000363616:I239V;ENSP00000443528:I18V;ENSP00000441548:I198V	ENSP00000363615:I202V	I	-	1	0	EDEM2	33183235	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.131000	0.64751	2.122000	0.65172	0.528000	0.53228	ATT	.	.		0.587	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217		C	33719574	T	C	33719574	3	2	23	1	0	0	0	0	1	0	0	0	4914	1464	51	2	1041	2	EDEM2	20	33719574	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	130695	33719574	29305946	1057	3123										
CEP250	11190	hgsc.bcm.edu	37	chr20	34090970	34090970	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acccagagagtggctttgacCcaccttacgctggacctaga	10	13	0	3	rs562343473		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:34090970C>T	ENST00000397527.1	+	30	5493	c.4773C>T	c.(4771-4773)acC>acT	p.T1591T	CEP250_ENST00000342580.4_Silent_p.T1535T	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1591	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			TGGCTTTGACCCACCTTACGC	0.562													C|||	1	0.000199681	0	0.0014	5008	,	,		19629	0		0	False		,,,				2504	0				p.T1591T		Atlas-SNP	.											.	CEP250	141	.	0			c.C4773T						.						38	35	36					20																	34090970		2203	4300	6503	SO:0001819	synonymous_variant	11190	exon30			TTTGACCCACCTT	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.4773C>T	chr20.hg19:g.34090970C>T		124.0	0.0		128.0	51.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	hg19	CCDS13255.1																																																																																			.	.		0.562	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34090970	C	T	34090970	2	4	23	1	0	0	0	0	0	0	0	1	3254	610	22	3		3	CEP250	20	34090970	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	371396	34090970	28934550	1058	3124										
C20orf152	140894	hgsc.bcm.edu	37	chr20	34618504	34618504	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atggcaccccagaaatacctCcccccattgaggattgtcca							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:34618504delC	ENST00000373973.3	+	12	1838	c.1665delC	c.(1663-1665)ctcfs	p.L555fs	CNBD2_ENST00000538900.1_3'UTR|CNBD2_ENST00000349339.1_Frame_Shift_Del_p.L551fs			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	555																	AGAAATACCTCCCCCCATTGA	0.458																																					p.L551fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1652delT						.						222	216	218					20																	34618504		2203	4300	6503	SO:0001589	frameshift_variant	140894	exon12			.	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 152", "cyclic nucleotide (cNMP) binding domain containing 1"	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.1665delC	chr20.hg19:g.34618504delC	ENSP00000363084:p.Leu555fs	294.0	0.0		219.0	69.0	NM_080834	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Frame_Shift_Del	DEL	ENST00000373973.3	hg19																																																																																				.	.		0.458	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834		-	34618504	C	-	34618504	7	5	23	1	0	1	0	1	0	0	0	0	2094	842	30	0	1699	0	C20orf152	20	34618504	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	527534	34618504	28407016	1059	3125										
RPN2	6185	hgsc.bcm.edu	37	chr20	35860726	35860726	+	Frame_Shift_Del	DEL	C	C	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccgcgagcctgagaagaggCcccccaccgtggtgtccaat							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:35860726delC	ENST00000237530.6	+	14	1920	c.1609delC	c.(1609-1611)cccfs	p.P538fs	RPN2_ENST00000470352.1_Intron|RPN2_ENST00000373622.5_Frame_Shift_Del_p.P506fs	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II	538					aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				TGAGAAGAGGCCCCCCACCGT	0.577																																					p.R536fs		Atlas-Indel,Pindel	.											.	RPN2	45	.	0			c.1608delG						.						213	186	195					20																	35860726		2203	4300	6503	SO:0001589	frameshift_variant	6185	exon14			.	Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"oligosaccharyltransferase complex subunit (non-catalytic)"	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.1609delC	chr20.hg19:g.35860726delC	ENSP00000237530:p.Pro538fs	72.0	0.0		81.0	33.0	NM_002951	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Frame_Shift_Del	DEL	ENST00000237530.6	hg19	CCDS13291.1																																																																																			.	.		0.577	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079076.2	NM_002951		-	35860726	C	-	35860726	7	5	23	1	0	1	0	1	0	0	0	0	13623	739	26	0	1663	0	RPN2	20	35860726	Frame_Shift_Del	DEL	C	TCGA-4R-AA8I-01A-11D-A382-10	1242222	35860726	27164794	1060	3126										
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37182643	37182643	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agttacggattgcaagccccCgcctcctgcccaggaattcc	9	16	0	0	rs138852733		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:37182643C>T	ENST00000262879.6	+	22	3580	c.3296C>T	c.(3295-3297)cCg>cTg	p.P1099L	RALGAPB_ENST00000397040.1_Missense_Mutation_p.P1099L|RALGAPB_ENST00000397042.3_Missense_Mutation_p.P1095L|RALGAPB_ENST00000397038.1_Missense_Mutation_p.P877L			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1099					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TGCAAGCCCCCGCCTCCTGCC	0.453																																					p.P1099L		Atlas-SNP	.											.	RALGAPB	134	.	0			c.C3296T						.						92	93	93					20																	37182643		2203	4300	6503	SO:0001583	missense	57148	exon22			AGCCCCCGCCTCC	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"KIAA1219"	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.3296C>T	chr20.hg19:g.37182643C>T	ENSP00000262879:p.Pro1099Leu	176.0	0.0		208.0	47.0	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	hg19	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	C	34	5.307384	0.95629	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000397038;ENST00000397040;ENST00000438490	D;D;D;D;D	0.92965	-3.14;-3.14;-3.14;-3.14;-3.14	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.94000	0.8078	L	0.33339	1.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	D	0.93539	0.6876	10	0.46703	T	0.11	.	20.0851	0.97797	0.0:1.0:0.0:0.0	.	1095;1099	A2A2E9;Q86X10	.;RLGPB_HUMAN	L	1099;1095;877;1099;927	ENSP00000262879:P1099L;ENSP00000380235:P1095L;ENSP00000380231:P877L;ENSP00000380233:P1099L;ENSP00000416646:P927L	ENSP00000262879:P1099L	P	+	2	0	RALGAPB	36616057	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.664000	0.61540	2.758000	0.94735	0.650000	0.86243	CCG	.	C|1.000;A|0.000		0.453	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		T	37182643	C	T	37182643	3	4	23	1	0	0	0	0	1	0	0	0	13030	652	23	1	3378	1	RALGAPB	20	37182643	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1321917	37182643	25842877	1061	3127										
PPP1R16B	26051	hgsc.bcm.edu	37	chr20	37536807	37536807	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acaacggggacatcagggagAccaggacagaccaagagaat	13	9	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:37536807A>T	ENST00000299824.1	+	10	1354	c.1165A>T	c.(1165-1167)Acc>Tcc	p.T389S	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.T347S	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	389					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				CATCAGGGAGACCAGGACAGA	0.597																																					p.T389S		Atlas-SNP	.											.	PPP1R16B	103	.	0			c.A1165T						.						100	91	94					20																	37536807		2203	4300	6503	SO:0001583	missense	26051	exon10			AGGGAGACCAGGA	AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	15850	protein-coding gene	gene with protein product	"TGF-beta-inhibited membrane-associated protein", "ankyrin repeat domain protein 4"	613275	"protein phosphatase 1, regulatory (inhibitor) subunit 16B"			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1165A>T	chr20.hg19:g.37536807A>T	ENSP00000299824:p.Thr389Ser	373.0	0.0		338.0	126.0	NM_015568	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Missense_Mutation	SNP	ENST00000299824.1	hg19	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.995|7.995	0.754180|0.754180	0.15778|0.15778	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000438192|ENST00000299824;ENST00000373331	.|T;T	.|0.71222	.|-0.31;-0.55	5.79|5.79	3.54|3.54	0.40534|0.40534	.|.	.|0.355587	.|0.33670	.|N	.|0.004672	T|T	0.42314|0.42314	0.1197|0.1197	N|N	0.08118|0.08118	0|0	0.28938|0.28938	N|N	0.891184|0.891184	.|P;B	.|0.37688	.|0.605;0.07	.|B;B	.|0.34093	.|0.175;0.044	T|T	0.38972|0.38972	-0.9636|-0.9636	5|10	.|0.10377	.|T	.|0.69	.|.	8.375|8.375	0.32438|0.32438	0.7984:0.1336:0.068:0.0|0.7984:0.1336:0.068:0.0	.|.	.|347;389	.|E9PFS8;Q96T49	.|.;PP16B_HUMAN	S|S	289|389;347	.|ENSP00000299824:T389S;ENSP00000362428:T347S	.|ENSP00000299824:T389S	R|T	+|+	3|1	2|0	PPP1R16B|PPP1R16B	36970221|36970221	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.734000|2.734000	0.47368|0.47368	1.021000|1.021000	0.39600|0.39600	0.524000|0.524000	0.50904|0.50904	AGA|ACC	.	.		0.597	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568		T	37536807	A	T	37536807	3	4	23	1	0	0	0	0	1	0	0	0	12378	275	10	4	1199	4	PPP1R16B	20	37536807	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	354164	37536807	25488713	1062	3128										
SNX21	90203	hgsc.bcm.edu	37	chr20	44469566	44469566	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcgtgctgccggagctgcggCgggcacagagcctcacctgt	15	14	1	1	rs563427177		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:44469566C>T	ENST00000491381.1	+	4	804	c.736C>T	c.(736-738)Cgg>Tgg	p.R246W	SNX21_ENST00000462307.1_3'UTR|SNX21_ENST00000344780.4_3'UTR|SNX21_ENST00000372542.1_Missense_Mutation_p.R237W|SNX21_ENST00000342644.5_Intron			Q969T3	SNX21_HUMAN	sorting nexin family member 21	246	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				GGAGCTGCGGCGGGCACAGAG	0.662													C|||	1	0.000199681	0	0	5008	,	,		13806	0.001		0	False		,,,				2504	0				p.R246W		Atlas-SNP	.											.	SNX21	23	.	0			c.C736T						.						20	23	22					20																	44469566		2197	4267	6464	SO:0001583	missense	90203	exon4			CTGCGGCGGGCAC	AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"Sorting nexins", "Tetratricopeptide (TTC) repeat domain containing"	16154	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 161"	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.736C>T	chr20.hg19:g.44469566C>T	ENSP00000418593:p.Arg246Trp	84.0	0.0		73.0	39.0	NM_033421	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Missense_Mutation	SNP	ENST00000491381.1	hg19	CCDS13377.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.874668	0.51695	.	.	ENSG00000124104	ENST00000491381;ENST00000372542	T;T	0.66638	-0.22;-0.22	4.32	3.36	0.38483	Phox homologous domain (2);Tetratricopeptide-like helical (1);	0.276731	0.36134	N	0.002777	T	0.50205	0.1602	L	0.39898	1.24	0.23524	N	0.997492	P;P	0.51537	0.946;0.946	B;B	0.37422	0.249;0.249	T	0.51576	-0.8688	10	0.72032	D	0.01	-9.0455	7.0255	0.24938	0.3236:0.4945:0.1818:0.0	.	237;246	Q5JZH3;Q969T3	.;SNX21_HUMAN	W	246;237	ENSP00000418593:R246W;ENSP00000361620:R237W	ENSP00000361620:R237W	R	+	1	2	SNX21	43902973	0.961000	0.32948	0.982000	0.44146	0.837000	0.47467	2.223000	0.42936	1.012000	0.39366	0.462000	0.41574	CGG	.	.		0.662	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421		T	44469566	C	T	44469566	3	4	23	1	0	0	0	0	1	0	0	0	14908	759	27	1	765	1	SNX21	20	44469566	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	6932759	44469566	18555954	1063	3129										
ZNF335	63925	hgsc.bcm.edu	37	chr20	44596429	44596429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgtggccttggtgctgctcCggtactggcacatcttgcat	13	11	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:44596429C>T	ENST00000322927.2	-	5	858	c.758G>A	c.(757-759)cGg>cAg	p.R253Q	ZNF335_ENST00000426788.1_Missense_Mutation_p.R98Q|ZNF335_ENST00000494955.1_5'UTR	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	253					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				GGTGCTGCTCCGGTACTGGCA	0.637																																					p.R253Q		Atlas-SNP	.											ZNF335,colon,carcinoma,0,1	ZNF335	115	.	0			c.G758A						.						67	63	65					20																	44596429		2203	4300	6503	SO:0001583	missense	63925	exon5			CTGCTCCGGTACT	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.758G>A	chr20.hg19:g.44596429C>T	ENSP00000325326:p.Arg253Gln	56.0	0.0		57.0	28.0	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	hg19	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.856930	0.91433	.	.	ENSG00000198026	ENST00000322927;ENST00000426788	T;T	0.28666	1.6;1.6	4.78	4.78	0.61160	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.079918	0.52532	D	0.000063	T	0.22859	0.0552	N	0.19112	0.55	0.36281	D	0.855805	D;D	0.59357	0.981;0.985	P;P	0.48873	0.458;0.593	T	0.08722	-1.0708	10	0.37606	T	0.19	-27.6024	6.5587	0.22474	0.0:0.8062:0.0:0.1938	.	98;253	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	Q	253;98	ENSP00000325326:R253Q;ENSP00000397098:R98Q	ENSP00000325326:R253Q	R	-	2	0	ZNF335	44029836	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.475000	0.66787	2.469000	0.83416	0.561000	0.74099	CGG	.	.		0.637	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		T	44596429	C	T	44596429	3	4	23	1	0	0	0	0	1	0	0	0	17867	652	23	1	3366	1	ZNF335	20	44596429	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	126863	44596429	18429091	1064	3130										
CD40	958	hgsc.bcm.edu	37	chr20	44750964	44750964	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tagacacctggaacagagagAcacactgccaccagcacaaa	8	13	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:44750964A>G	ENST00000372285.3	+	3	295	c.223A>G	c.(223-225)Aca>Gca	p.T75A	CD40_ENST00000489304.1_3'UTR|CD40_ENST00000372276.3_Missense_Mutation_p.T75A	NM_001250.4	NP_001241.1	P25942	TNR5_HUMAN	CD40 molecule, TNF receptor superfamily member 5	75					B cell proliferation (GO:0042100)|cellular calcium ion homeostasis (GO:0006874)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|protein complex assembly (GO:0006461)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	CD40 receptor complex (GO:0035631)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|enzyme binding (GO:0019899)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		Myeloproliferative disorder(115;0.0122)				GAACAGAGAGACACACTGCCA	0.532									Immune Deficiency with Hyper-IgM																												p.T75A		Atlas-SNP	.											.	CD40	33	.	0			c.A223G						.						93	81	85					20																	44750964		2203	4300	6503	SO:0001583	missense	958	exon3	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	AGAGAGACACACT	X60592	CCDS13393.1, CCDS13394.1	20q12-q13.2	2014-09-17	2006-03-28	2005-01-14	ENSG00000101017	ENSG00000101017		"Tumor necrosis factor receptor superfamily", "CD molecules"	11919	protein-coding gene	gene with protein product		109535	"tumor necrosis factor receptor superfamily, member 5"	TNFRSF5		7687385, 2998589	Standard	XM_005260617		Approved	p50, Bp50	uc002xrg.1	P25942	OTTHUMG00000033053	ENST00000372285.3:c.223A>G	chr20.hg19:g.44750964A>G	ENSP00000361359:p.Thr75Ala	119.0	0.0		102.0	39.0	NM_152854	E1P5S9|Q53GN5|Q5JY15|Q5U007|Q7M4Q8|Q86YK5|Q9BYU0	Missense_Mutation	SNP	ENST00000372285.3	hg19	CCDS13393.1	.	.	.	.	.	.	.	.	.	.	a	4.782	0.145441	0.09134	.	.	ENSG00000101017	ENST00000372285;ENST00000372276	T;T	0.70399	-0.48;-0.48	4.55	0.636	0.17729	TNFR/CD27/30/40/95 cysteine-rich region (2);	1.368000	0.04645	N	0.405978	T	0.56775	0.2008	L	0.28400	0.85	0.09310	N	1	B;B;B;B	0.29378	0.005;0.243;0.017;0.029	B;B;B;B	0.27608	0.012;0.081;0.006;0.015	T	0.31888	-0.9927	10	0.09590	T	0.72	0.1609	9.9895	0.41863	0.4695:0.5305:0.0:0.0	.	58;75;75;75	Q09LL4;P25942-2;P25942;Q6P2H9	.;.;TNR5_HUMAN;.	A	75	ENSP00000361359:T75A;ENSP00000361350:T75A	ENSP00000361350:T75A	T	+	1	0	CD40	44184371	0.003000	0.15002	0.018000	0.16275	0.018000	0.09664	0.742000	0.26216	-0.011000	0.14247	0.378000	0.23410	ACA	.	.		0.532	CD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080376.1	NM_001250		G	44750964	A	G	44750964	3	3	23	1	0	0	0	0	1	0	0	0	3017	275	10	2	233	2	CD40	20	44750964	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	154535	44750964	18274556	1065	3131										
SULF2	55959	hgsc.bcm.edu	37	chr20	46307534	46307534	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggccaggtcaatgttgaggAcgatgtggggattcctgggg	19	6	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:46307534A>G	ENST00000359930.4	-	8	1930	c.1079T>C	c.(1078-1080)gTc>gCc	p.V360A	CTD-2653D5.1_ENST00000526566.2_RNA|SULF2_ENST00000361612.4_Missense_Mutation_p.V360A|SULF2_ENST00000484875.1_Missense_Mutation_p.V360A|SULF2_ENST00000467815.1_Missense_Mutation_p.V360A	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	360					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						AATGTTGAGGACGATGTGGGG	0.627																																					p.V360A		Atlas-SNP	.											.	SULF2	131	.	0			c.T1079C						.						92	84	87					20																	46307534		2203	4300	6503	SO:0001583	missense	55959	exon8			TTGAGGACGATGT	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.1079T>C	chr20.hg19:g.46307534A>G	ENSP00000353007:p.Val360Ala	34.0	0.0		56.0	29.0	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	hg19	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	a	22.5	4.301289	0.81136	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815	D;D;D;D	0.97114	-4.25;-4.25;-4.25;-4.25	5.26	5.26	0.73747	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.96947	0.9003	M	0.64997	1.995	0.58432	D	0.999999	D;P	0.56521	0.976;0.915	P;P	0.51516	0.672;0.604	D	0.97168	0.9842	10	0.62326	D	0.03	-28.6635	15.1843	0.72986	1.0:0.0:0.0:0.0	.	360;360	Q8IWU5-2;Q8IWU5	.;SULF2_HUMAN	A	360	ENSP00000353007:V360A;ENSP00000418290:V360A;ENSP00000354662:V360A;ENSP00000418442:V360A	ENSP00000353007:V360A	V	-	2	0	SULF2	45740941	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.573000	0.82421	1.994000	0.58287	0.375000	0.23000	GTC	.	.		0.627	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		G	46307534	A	G	46307534	3	3	23	1	0	0	0	0	1	0	0	0	15386	275	10	2	1589	2	SULF2	20	46307534	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	1556570	46307534	16717986	1066	3132										
PTGIS	5740	hgsc.bcm.edu	37	chr20	48156217	48156217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggcctggctttcatgggtgCgtggcagcgcctcaattccg	15	12	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:48156217C>T	ENST00000244043.4	-	5	592	c.563G>A	c.(562-564)cGc>cAc	p.R188H	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	188					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	TTCATGGGTGCGTGGCAGCGC	0.647																																					p.R188H		Atlas-SNP	.											PTGIS,NS,carcinoma,0,1	PTGIS	60	.	0			c.G563A						.						50	48	48					20																	48156217		2203	4300	6503	SO:0001583	missense	5740	exon5			TGGGTGCGTGGCA		CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"Cytochrome P450s"	9603	protein-coding gene	gene with protein product	"cytochrome P450, family 8, subfamily A, polypeptide 1"	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.563G>A	chr20.hg19:g.48156217C>T	ENSP00000244043:p.Arg188His	41.0	0.0		49.0	20.0	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Missense_Mutation	SNP	ENST00000244043.4	hg19	CCDS13419.1	.	.	.	.	.	.	.	.	.	.	C	8.624	0.892030	0.17613	.	.	ENSG00000124212	ENST00000244043	T	0.68624	-0.34	5.15	-0.819	0.10829	.	0.930319	0.08935	N	0.872410	T	0.47563	0.1452	N	0.25890	0.77	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.29088	-1.0023	10	0.35671	T	0.21	-26.1822	4.6513	0.12596	0.0:0.3708:0.2821:0.3471	.	188	Q16647	PTGIS_HUMAN	H	188	ENSP00000244043:R188H	ENSP00000244043:R188H	R	-	2	0	PTGIS	47589624	0.807000	0.29009	0.929000	0.37066	0.814000	0.46013	1.043000	0.30316	-0.075000	0.12798	0.561000	0.74099	CGC	.	.		0.647	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2			T	48156217	C	T	48156217	3	4	23	1	0	0	0	0	1	0	0	0	12765	768	27	1	963	1	PTGIS	20	48156217	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1848683	48156217	14869303	1067	3133										
KCNG1	3755	hgsc.bcm.edu	37	chr20	49626762	49626762	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgctgcgcccggcggtagaaCgcgcccttgatggcctggcg	16	15	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:49626762C>T	ENST00000371571.4	-	2	399	c.114G>A	c.(112-114)gcG>gcA	p.A38A	KCNG1_ENST00000506387.1_5'Flank|KCNG1_ENST00000396017.3_Silent_p.A38A|RP5-955M13.4_ENST00000424566.1_RNA	NM_002237.3	NP_002228.2	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G, member 1	38					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GGCGGTAGAACGCGCCCTTGA	0.697																																					p.A38A		Atlas-SNP	.											.	KCNG1	86	.	0			c.G114A						.						19	22	21					20																	49626762		2192	4269	6461	SO:0001819	synonymous_variant	3755	exon2			GTAGAACGCGCCC	AF033383	CCDS13436.1	20q13	2011-07-05			ENSG00000026559	ENSG00000026559		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6248	protein-coding gene	gene with protein product		603788		KCNG		9434767, 16382104	Standard	NM_002237		Approved	Kv6.1, kH2, K13	uc002xwa.4	Q9UIX4	OTTHUMG00000032745	ENST00000371571.4:c.114G>A	chr20.hg19:g.49626762C>T		40.0	0.0		30.0	9.0	NM_002237	A8K3S4|O43528|Q5JXL5|Q9BRC1	Silent	SNP	ENST00000371571.4	hg19	CCDS13436.1																																																																																			.	.		0.697	KCNG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079726.4	NM_002237		T	49626762	C	T	49626762	2	4	23	1	0	0	0	0	0	0	0	1	8036	523	19	1		1	KCNG1	20	49626762	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1470545	49626762	13398758	1068	3134										
SALL4	57167	hgsc.bcm.edu	37	chr20	50408386	50408386	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagatctgctcgaggacccaCgggatgctgttggcaccagg	14	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:50408386C>T	ENST00000217086.4	-	2	747	c.636G>A	c.(634-636)ccG>ccA	p.P212P	SALL4_ENST00000395997.3_Silent_p.P212P|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	212					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CGAGGACCCACGGGATGCTGT	0.627																																					p.P212P		Atlas-SNP	.											.	SALL4	168	.	0			c.G636A						.						68	69	69					20																	50408386		2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			GACCCACGGGATG	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.636G>A	chr20.hg19:g.50408386C>T		42.0	0.0		51.0	29.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	hg19	CCDS13438.1																																																																																			.	.		0.627	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			T	50408386	C	T	50408386	2	4	23	1	0	0	0	0	0	0	0	1	13828	523	19	1		1	SALL4	20	50408386	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	781624	50408386	12617134	1069	3135										
SALL4	57167	hgsc.bcm.edu	37	chr20	50408677	50408678	+	Frame_Shift_Ins	INS	-	-	A													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggctcagtacagctccggagINSaagtcttctgaaggcacagg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:50408677_50408678insA	ENST00000217086.4	-	2	455_456	c.344_345insT	c.(343-345)ttcfs	p.F115fs	SALL4_ENST00000395997.3_Frame_Shift_Ins_p.F115fs|SALL4_ENST00000483130.1_5'UTR|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	115					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CAGCTCCGGAGAAGTCTTCTGA	0.53																																					p.F115fs		Atlas-Indel,Pindel	.											SALL4,NS,carcinoma,0,1	SALL4	168	.	0			c.345_346insT						.																																			SO:0001589	frameshift_variant	57167	exon2			.	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.345dupT	chr20.hg19:g.50408679_50408679dupA	ENSP00000217086:p.Phe115fs	278.0	0.0		287.0	113.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Frame_Shift_Ins	INS	ENST00000217086.4	hg19	CCDS13438.1																																																																																			.	.		0.53	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			A	50408678	-	A	50408677	7	5	23	1	0	1	1	0	0	0	0	0	13828	933	33	0	2828	0	SALL4	20	50408677	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	291	50408677	12616843	1070	3136										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52192757	52192757	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttttgtcttatccggtgcaGgggaaacactggttttagga	12	6	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:52192757G>A	ENST00000371471.2	-	4	2971	c.2546C>T	c.(2545-2547)cCt>cTt	p.P849L	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.P849L			O75362	ZN217_HUMAN	zinc finger protein 217	849					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			ATCCGGTGCAGGGGAAACACT	0.517																																					p.P849L		Atlas-SNP	.											.	ZNF217	227	.	0			c.C2546T						.						95	98	97					20																	52192757		2203	4300	6503	SO:0001583	missense	7764	exon3			GGTGCAGGGGAAA	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2546C>T	chr20.hg19:g.52192757G>A	ENSP00000360526:p.Pro849Leu	87.0	0.0		65.0	33.0	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	hg19	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.376112	0.24857	.	.	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000395971	T;T	0.10477	2.87;2.87	5.1	2.08	0.27032	.	0.651039	0.14769	N	0.299494	T	0.08846	0.0219	L	0.43152	1.355	0.09310	N	1	P	0.38922	0.651	B	0.33392	0.163	T	0.18209	-1.0344	10	0.66056	D	0.02	-11.4983	7.9334	0.29916	0.1478:0.1327:0.7196:0.0	.	849	O75362	ZN217_HUMAN	L	849;849;9	ENSP00000360526:P849L;ENSP00000304308:P849L	ENSP00000304308:P849L	P	-	2	0	ZNF217	51626164	0.175000	0.23083	0.001000	0.08648	0.003000	0.03518	1.649000	0.37281	0.181000	0.19994	-0.172000	0.13284	CCT	.	.		0.517	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		A	52192757	G	A	52192757	3	1	23	1	0	0	0	0	1	0	0	0	17787	1000	35	3	608	3	ZNF217	20	52192757	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1784080	52192757	10832763	1071	3137										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52198883	52198883	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggctccttgaatcttcttccGcacatgttacacccgtaagt	7	13	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:52198883G>A	ENST00000371471.2	-	2	908	c.483C>T	c.(481-483)tgC>tgT	p.C161C	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Silent_p.C161C			O75362	ZN217_HUMAN	zinc finger protein 217	161					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			ATCTTCTTCCGCACATGTTAC	0.448																																					p.C161C		Atlas-SNP	.											ZNF217_ENST00000371471,colon,carcinoma,0,2	ZNF217	227	.	0			c.C483T						.						155	154	154					20																	52198883		2203	4300	6503	SO:0001819	synonymous_variant	7764	exon1			TCTTCCGCACATG	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.483C>T	chr20.hg19:g.52198883G>A		94.0	0.0		79.0	34.0	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	hg19	CCDS13443.1																																																																																			.	.		0.448	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		A	52198883	G	A	52198883	2	1	23	1	0	0	0	0	0	0	0	1	17787	1079	38	1		1	ZNF217	20	52198883	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	6126	52198883	10826637	1072	3138										
CSTF1	1477	hgsc.bcm.edu	37	chr20	54978541	54978541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caggcgcgggtttaagtggaCgccaggtgcaccggacacag	16	11	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:54978541C>T	ENST00000217109.4	+	6	1406	c.1054C>T	c.(1054-1056)Cgc>Tgc	p.R352C	CSTF1_ENST00000493039.1_3'UTR	NM_001033521.1|NM_001324.2	NP_001028693.1|NP_001315.1	Q05048	CSTF1_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa	352					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R352C(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	15			Colorectal(105;0.202)			TTTAAGTGGACGCCAGGTGCA	0.527																																					p.R352C		Atlas-SNP	.											CSTF1,NS,carcinoma,0,1	CSTF1	29	.	1	Substitution - Missense(1)	prostate(1)	c.C1054T						.						90	81	84					20																	54978541		2203	4300	6503	SO:0001583	missense	1477	exon6			AGTGGACGCCAGG		CCDS13452.1	20q13.31	2013-01-10	2002-08-29		ENSG00000101138	ENSG00000101138		"WD repeat domain containing"	2483	protein-coding gene	gene with protein product		600369	"cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kD"			1358884, 11257228	Standard	NM_001033521		Approved		uc002xxl.1	Q05048	OTTHUMG00000032791	ENST00000217109.4:c.1054C>T	chr20.hg19:g.54978541C>T	ENSP00000217109:p.Arg352Cys	103.0	0.0		102.0	42.0	NM_001033522	Q5QPD8	Missense_Mutation	SNP	ENST00000217109.4	hg19	CCDS13452.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.830246	0.50845	.	.	ENSG00000101138	ENST00000217109;ENST00000425890	T	0.59364	0.27	5.45	4.49	0.54785	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.39172	0.1068	N	0.22421	0.69	0.80722	D	1	P	0.50710	0.938	B	0.34346	0.18	T	0.46386	-0.9195	10	0.72032	D	0.01	-20.0546	13.5181	0.61551	0.284:0.716:0.0:0.0	.	352	Q05048	CSTF1_HUMAN	C	352;339	ENSP00000217109:R352C	ENSP00000217109:R352C	R	+	1	0	CSTF1	54411948	0.997000	0.39634	0.988000	0.46212	0.815000	0.46073	3.566000	0.53805	1.397000	0.46682	0.650000	0.86243	CGC	.	.		0.527	CSTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079794.2	NM_001033521		T	54978541	C	T	54978541	3	4	23	1	0	0	0	0	1	0	0	0	3985	536	19	1	1072	1	CSTF1	20	54978541	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2779658	54978541	8046979	1073	3139										
STX16	8675	hgsc.bcm.edu	37	chr20	57242608	57242608	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatccagaagcagcgattggTgtgacaaaacggccacctcc	11	12	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:57242608T>C	ENST00000371141.4	+	3	931	c.207T>C	c.(205-207)ggT>ggC	p.G69G	STX16_ENST00000361770.5_Silent_p.G52G|STX16_ENST00000496003.1_3'UTR|STX16-NPEPL1_ENST00000530122.1_Silent_p.G69G|STX16_ENST00000361830.3_Silent_p.G69G|STX16_ENST00000358029.4_Silent_p.G65G|STX16_ENST00000359617.4_Silent_p.G16G|STX16_ENST00000355957.5_Silent_p.G52G|STX16_ENST00000371132.4_Silent_p.G48G	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	69					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			CAGCGATTGGTGTGACAAAAC	0.413																																					p.G69G		Atlas-SNP	.											.	STX16	36	.	0			c.T207C						.						147	137	140					20																	57242608		2203	4300	6503	SO:0001819	synonymous_variant	8675	exon3			GATTGGTGTGACA	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.207T>C	chr20.hg19:g.57242608T>C		121.0	0.0		146.0	70.0	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Silent	SNP	ENST00000371141.4	hg19	CCDS13468.1																																																																																			.	.		0.413	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433		C	57242608	T	C	57242608	2	2	23	1	0	0	0	0	0	0	0	1	15354	1683	59	2		2	STX16	20	57242608	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2264067	57242608	5782912	1074	3140										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60885264	60885264	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtcacctgcaactgcaagtaGgggggcgtccgggcctggcc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:60885264delG	ENST00000252999.3	-	77	10770	c.10704delC	c.(10702-10704)cccfs	p.P3568fs	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3568	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			ACTGCAAGTAGGGGGGCGTCC	0.647																																					p.Y3569fs		Atlas-Indel,Pindel	.											.	LAMA5	268	.	0			c.10705delT						.						35	41	39					20																	60885264		2200	4294	6494	SO:0001589	frameshift_variant	3911	exon77			.	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.10704delC	chr20.hg19:g.60885264delG	ENSP00000252999:p.Pro3568fs	74.0	0.0		78.0	18.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Frame_Shift_Del	DEL	ENST00000252999.3	hg19	CCDS33502.1																																																																																			.	.		0.647	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		-	60885264	G	-	60885264	7	5	23	1	0	1	0	1	0	0	0	0	8618	987	35	0	399	0	LAMA5	20	60885264	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	3642656	60885264	2140256	1075	3141										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60887270	60887270	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagggcactgtcctgggcgcTgtggaagccgaagccggagt	17	11	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:60887270T>G	ENST00000252999.3	-	69	9529	c.9463A>C	c.(9463-9465)Agc>Cgc	p.S3155R	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3155	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TCCTGGGCGCTGTGGAAGCCG	0.682																																					p.S3155R		Atlas-SNP	.											.	LAMA5	268	.	0			c.A9463C						.						32	35	34					20																	60887270		2194	4291	6485	SO:0001583	missense	3911	exon69			GGGCGCTGTGGAA	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.9463A>C	chr20.hg19:g.60887270T>G	ENSP00000252999:p.Ser3155Arg	231.0	0.0		175.0	72.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	t	15.31	2.795012	0.50208	.	.	ENSG00000130702	ENST00000252999	T	0.78003	-1.14	4.06	1.58	0.23477	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.210351	0.48286	D	0.000185	T	0.74261	0.3693	L	0.54323	1.7	0.80722	D	1	P	0.48998	0.918	P	0.49387	0.609	T	0.72786	-0.4188	10	0.87932	D	0	.	5.5549	0.17111	0.1524:0.0935:0.0:0.754	.	3155	O15230	LAMA5_HUMAN	R	3155	ENSP00000252999:S3155R	ENSP00000252999:S3155R	S	-	1	0	LAMA5	60320665	0.003000	0.15002	0.997000	0.53966	0.071000	0.16799	0.746000	0.26275	0.735000	0.32537	0.454000	0.30748	AGC	.	.		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		G	60887270	T	G	60887270	3	3	23	1	0	0	0	0	1	0	0	0	8618	1580	55	5	1672	5	LAMA5	20	60887270	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2006	60887270	2138250	1076	3142										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61527589	61527589	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gacaccaggcacacacctgaTttttagggtccttcaggttg	10	11	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:61527589T>A	ENST00000266070.4	-	8	2535	c.2210A>T	c.(2209-2211)aAt>aTt	p.N737I	DIDO1_ENST00000395335.2_Missense_Mutation_p.N737I|DIDO1_ENST00000395340.1_Missense_Mutation_p.N737I|DIDO1_ENST00000395343.1_Missense_Mutation_p.N737I	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	737	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					ACACACCTGATTTTTAGGGTC	0.423																																					p.N737I	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.A2210T						.						184	167	173					20																	61527589		2203	4300	6503	SO:0001583	missense	11083	exon8			ACCTGATTTTTAG	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.2210A>T	chr20.hg19:g.61527589T>A	ENSP00000266070:p.Asn737Ile	117.0	0.0		128.0	47.0	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.000211	0.93227	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.7	5.7	0.88788	Transcription elongation factor S-IIM (1);Transcription elongation factor S-II, central domain (4);	0.000000	0.46145	D	0.000315	D	0.86435	0.5932	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90029	0.4133	10	0.87932	D	0	-38.3716	15.9774	0.80079	0.0:0.0:0.0:1.0	.	737;737	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	I	737	ENSP00000266070:N737I;ENSP00000378752:N737I;ENSP00000378749:N737I;ENSP00000378744:N737I	ENSP00000266070:N737I	N	-	2	0	DIDO1	60998034	1.000000	0.71417	0.910000	0.35882	0.955000	0.61496	7.927000	0.87577	2.179000	0.69175	0.533000	0.62120	AAT	.	.		0.423	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		A	61527589	T	A	61527589	3	1	23	1	0	0	0	0	1	0	0	0	4524	1493	52	4	4577	4	DIDO1	20	61527589	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	640319	61527589	1497931	1077	3143										
SLC17A9	63910	hgsc.bcm.edu	37	chr20	61588143	61588143	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gtgccaggcatggacggggaCgctgctgctgggcacatgcc	17	12	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:61588143C>T	ENST00000370351.4	+	2	217	c.86C>T	c.(85-87)aCg>aTg	p.T29M	SLC17A9_ENST00000488738.1_3'UTR|SLC17A9_ENST00000370349.3_Missense_Mutation_p.T23M	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	29					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						TGGACGGGGACGCTGCTGCTG	0.652																																					p.T29M		Atlas-SNP	.											.	SLC17A9	54	.	0			c.C86T						.						23	27	26					20																	61588143		2097	4216	6313	SO:0001583	missense	63910	exon2			CGGGGACGCTGCT	AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"Solute carriers"	16192	protein-coding gene	gene with protein product		612107	"chromosome 20 open reading frame 59", "solute carrier family 17, member 9"	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.86C>T	chr20.hg19:g.61588143C>T	ENSP00000359376:p.Thr29Met	65.0	0.0		54.0	21.0	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Missense_Mutation	SNP	ENST00000370351.4	hg19	CCDS42901.1	.	.	.	.	.	.	.	.	.	.	C	1.930	-0.446286	0.04604	.	.	ENSG00000101194	ENST00000370351;ENST00000370349;ENST00000411611	T;T;T	0.58797	0.31;0.31;0.31	4.91	0.72	0.18214	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.674794	0.15589	N	0.254520	T	0.39545	0.1082	L	0.32530	0.975	0.09310	N	1	B;B;B	0.20459	0.045;0.016;0.027	B;B;B	0.23018	0.012;0.019;0.043	T	0.25152	-1.0140	10	0.09843	T	0.71	.	8.7004	0.34323	0.0:0.517:0.0:0.483	.	49;29;23	B4DPU8;Q9BYT1;Q9BYT1-2	.;S17A9_HUMAN;.	M	29;23;49	ENSP00000359376:T29M;ENSP00000359374:T23M;ENSP00000388215:T49M	ENSP00000359374:T23M	T	+	2	0	SLC17A9	61058588	0.926000	0.31397	0.000000	0.03702	0.009000	0.06853	1.599000	0.36751	0.269000	0.21961	-0.140000	0.14226	ACG	.	.		0.652	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082		T	61588143	C	T	61588143	3	4	23	1	0	0	0	0	1	0	0	0	14439	536	19	1	92	1	SLC17A9	20	61588143	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	60554	61588143	1437377	1078	3144										
YTHDF1	54915	hgsc.bcm.edu	37	chr20	61834090	61834090	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	acttaatggagcggtggatgTcgtcctcagagtagctcttg	13	8	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:61834090T>C	ENST00000370339.3	-	4	1543	c.1202A>G	c.(1201-1203)gAc>gGc	p.D401G	YTHDF1_ENST00000370333.4_Missense_Mutation_p.D351G|YTHDF1_ENST00000370334.4_Intron	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	401	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.						N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						GCGGTGGATGTCGTCCTCAGA	0.542																																					p.D401G		Atlas-SNP	.											.	YTHDF1	66	.	0			c.A1202G						.						99	87	91					20																	61834090		2203	4300	6503	SO:0001583	missense	54915	exon4			TGGATGTCGTCCT	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"YTH domain family 1"	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.1202A>G	chr20.hg19:g.61834090T>C	ENSP00000359364:p.Asp401Gly	91.0	0.0		106.0	39.0	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Missense_Mutation	SNP	ENST00000370339.3	hg19	CCDS13511.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.221784	0.58560	.	.	ENSG00000149658	ENST00000370339;ENST00000370333	T;T	0.34859	1.34;1.34	4.72	4.72	0.59763	YTH domain (2);	0.000000	0.85682	D	0.000000	T	0.71409	0.3336	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81901	-0.0720	10	0.87932	D	0	-42.5169	14.5032	0.67737	0.0:0.0:0.0:1.0	.	401	Q9BYJ9	YTHD1_HUMAN	G	401;351	ENSP00000359364:D401G;ENSP00000359358:D351G	ENSP00000359358:D351G	D	-	2	0	YTHDF1	61304535	1.000000	0.71417	0.216000	0.23742	0.492000	0.33523	7.875000	0.87205	1.896000	0.54893	0.482000	0.46254	GAC	.	.		0.542	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798		C	61834090	T	C	61834090	3	2	23	1	0	0	0	0	1	0	0	0	17513	1667	58	2	485	2	YTHDF1	20	61834090	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	245947	61834090	1191430	1079	3145										
PRIC285	85441	hgsc.bcm.edu	37	chr20	62198473	62198473	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atgaagctgacaatggcgtcCgtgcagcggtagttctcgtg	14	9	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:62198473C>T	ENST00000467148.1	-	6	2307	c.2238G>A	c.(2236-2238)acG>acA	p.T746T	HELZ2_ENST00000427522.2_Silent_p.T177T	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	746	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CAATGGCGTCCGTGCAGCGGT	0.662																																					p.T746T		Atlas-SNP	.											.	.	.	.	0			c.G2238A						.						63	61	62					20																	62198473		2202	4299	6501	SO:0001819	synonymous_variant	85441	exon7			GGCGTCCGTGCAG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.2238G>A	chr20.hg19:g.62198473C>T		79.0	0.0		51.0	4.0	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	hg19	CCDS33508.1																																																																																			.	.		0.662	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		T	62198473	C	T	62198473	2	4	23	1	0	0	0	0	0	0	0	1	12497	639	23	1		1	PRIC285	20	62198473	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	364383	62198473	827047	1080	3146										
TCP10L	140290	hgsc.bcm.edu	37	chr21	33951121	33951121	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctgacagaggtgaaattttTccaaaagcaggttccaatgc	10	8	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:33951121T>A	ENST00000300258.3	-	4	494	c.381A>T	c.(379-381)ggA>ggT	p.G127G	LINC00846_ENST00000334165.4_lincRNA|TCP10L_ENST00000472557.1_Silent_p.G41G	NM_144659.5	NP_653260.1	Q8TDR4	TCP1L_HUMAN	t-complex 10-like	127					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	protein self-association (GO:0043621)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)			breast(1)|central_nervous_system(1)|liver(1)|skin(1)	4						GTGAAATTTTTCCAAAAGCAG	0.368																																					p.G127G		Atlas-SNP	.											.	TCP10L	24	.	0			c.A381T						.						118	111	113					21																	33951121		2203	4300	6503	SO:0001819	synonymous_variant	140290	exon4			AATTTTTCCAAAA	AF115967	CCDS13616.1	21p22.11	2012-09-20	2012-09-20		ENSG00000242220	ENSG00000242220			11657	protein-coding gene	gene with protein product		608365	"t-complex 10 (a murine tcp homolog)-like", "t-complex 10 (mouse)-like"			10830953	Standard	NM_144659		Approved	PRED77		Q8TDR4	OTTHUMG00000064901	ENST00000300258.3:c.381A>T	chr21.hg19:g.33951121T>A		242.0	0.0		223.0	80.0	NM_144659	Q53EW0|Q96LN5	Silent	SNP	ENST00000300258.3	hg19	CCDS13616.1																																																																																			.	.		0.368	TCP10L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139350.1	NM_144659		A	33951121	T	A	33951121	2	1	23	1	0	0	0	0	0	0	0	1	15726	1770	62	4		4	TCP10L	21	33951121	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10		33951121	14178774	1081	3147										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37600040	37600040	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caggtgctcggctgcctggtGcagcctcttgctgaggacat	14	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:37600040G>A	ENST00000399151.3	+	13	1615	c.1530G>A	c.(1528-1530)gtG>gtA	p.V510V		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	510					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GCTGCCTGGTGCAGCCTCTTG	0.502																																					p.V510V		Atlas-SNP	.											.	DOPEY2	184	.	0			c.G1530A						.						75	65	69					21																	37600040		2203	4300	6503	SO:0001819	synonymous_variant	9980	exon13			CCTGGTGCAGCCT	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.1530G>A	chr21.hg19:g.37600040G>A		81.0	0.0		49.0	19.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	hg19	CCDS13643.1																																																																																			.	.		0.502	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		A	37600040	G	A	37600040	2	1	23	1	0	0	0	0	0	0	0	1	4710	1306	46	3		3	DOPEY2	21	37600040	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3648919	37600040	10529855	1082	3148										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37603120	37603120	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccaatgattccagcaggaagAactcttgggagcccaagccc	10	13	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:37603120A>G	ENST00000399151.3	+	14	2123	c.2038A>G	c.(2038-2040)Aac>Gac	p.N680D		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	680					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CAGCAGGAAGAACTCTTGGGA	0.547																																					p.N680D		Atlas-SNP	.											.	DOPEY2	184	.	0			c.A2038G						.						83	75	78					21																	37603120		2203	4300	6503	SO:0001583	missense	9980	exon14			AGGAAGAACTCTT	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.2038A>G	chr21.hg19:g.37603120A>G	ENSP00000382104:p.Asn680Asp	131.0	0.0		138.0	66.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.596630	0.28445	.	.	ENSG00000142197	ENST00000399151	T	0.11385	2.78	5.43	1.68	0.24146	.	0.648666	0.16682	N	0.203888	T	0.07279	0.0184	L	0.36672	1.1	0.20764	N	0.99985	B;B	0.23249	0.082;0.049	B;B	0.20767	0.031;0.014	T	0.40608	-0.9554	10	0.19590	T	0.45	.	5.4609	0.16615	0.6557:0.1353:0.209:0.0	.	680;680	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	D	680	ENSP00000382104:N680D	ENSP00000382104:N680D	N	+	1	0	DOPEY2	36524990	0.000000	0.05858	0.799000	0.32177	0.547000	0.35210	0.316000	0.19469	0.106000	0.17784	0.402000	0.26972	AAC	.	.		0.547	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		G	37603120	A	G	37603120	3	3	23	1	0	0	0	0	1	0	0	0	4710	246	9	2	2088	2	DOPEY2	21	37603120	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	3080	37603120	10526775	1083	3149										
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38852951	38852951	+	Frame_Shift_Del	DEL	A	A	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcatttcaggtttactatgcAaaaaagaagcgaagacacca							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:38852951delA	ENST00000398960.2	+	4	414	c.339delA	c.(337-339)gcafs	p.A113fs	DYRK1A_ENST00000462274.1_3'UTR|DYRK1A_ENST00000338785.3_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000398956.2_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000321219.8_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000339659.4_Frame_Shift_Del_p.A104fs|DYRK1A_ENST00000451934.1_Frame_Shift_Del_p.A113fs	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	113					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TTTACTATGCAAAAAAGAAGC	0.363																																					p.A113fs	Melanoma(114;464 1602 31203 43785 45765)	Atlas-Indel,Pindel	.											.	DYRK1A	85	.	0			c.338delC						.						98	97	98					21																	38852951		2203	4300	6503	SO:0001589	frameshift_variant	1859	exon4			.	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.339delA	chr21.hg19:g.38852951delA	ENSP00000381932:p.Ala113fs	216.0	0.0		225.0	70.0	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Frame_Shift_Del	DEL	ENST00000398960.2	hg19	CCDS42925.1																																																																																			.	.		0.363	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		-	38852951	A	-	38852951	7	5	23	1	0	1	0	1	0	0	0	0	4856	117	5	0	353	0	DYRK1A	21	38852951	Frame_Shift_Del	DEL	A	TCGA-4R-AA8I-01A-11D-A382-10	1249831	38852951	9276944	1084	3150										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46910776	46910776	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aagggagacagaggcagccgGggagaaaaggtgagtgtccc	18	7	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:46910776G>A	ENST00000359759.4	+	20	3324	c.3303G>A	c.(3301-3303)cgG>cgA	p.R1101R	COL18A1_ENST00000355480.5_Silent_p.R866R|COL18A1_ENST00000400337.2_Silent_p.R686R			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1101	Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GAGGCAGCCGGGGAGAAAAGG	0.647																																					p.R866R		Atlas-SNP	.											.	COL18A1	129	.	0			c.G2598A						.						13	15	14					21																	46910776		1448	3162	4610	SO:0001819	synonymous_variant	80781	exon20			CAGCCGGGGAGAA		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3303G>A	chr21.hg19:g.46910776G>A		142.0	0.0		169.0	83.0	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	hg19																																																																																				.	.		0.647	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			A	46910776	G	A	46910776	2	1	23	1	0	0	0	0	0	0	0	1	3677	1219	43	3		3	COL18A1	21	46910776	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	8057825	46910776	1219119	1085	3151										
COL6A1	1291	hgsc.bcm.edu	37	chr21	47414118	47414119	+	Frame_Shift_Ins	INS	-	-	C													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtgatcagggaagagaaggINSccccgttggtgtccctggag							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:47414118_47414119insC	ENST00000361866.3	+	20	1487_1488	c.1373_1374insC	c.(1372-1377)ggccccfs	p.GP458fs		NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	458	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		GGAAGAGAAGGCCCCGTTGGTG	0.639																																					p.G458fs		Atlas-Indel,Pindel	.											.	COL6A1	101	.	0			c.1373_1374insC						.																																			SO:0001589	frameshift_variant	1291	exon20			.	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"Collagens"	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.1377dupC	chr21.hg19:g.47414122_47414122dupC	ENSP00000355180:p.Gly458fs	263.0	0.0		255.0	87.0	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Frame_Shift_Ins	INS	ENST00000361866.3	hg19	CCDS13727.1																																																																																			.	.		0.639	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		C	47414119	-	C	47414118	7	5	23	1	0	1	1	0	0	0	0	0	3701	1203	42	0	1451	0	COL6A1	21	47414118	Frame_Shift_Ins	INS	-	TCGA-4R-AA8I-01A-11D-A382-10	503342	47414118	715777	1086	3152										
COL6A1	1291	hgsc.bcm.edu	37	chr21	47422161	47422161	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagcctgcagtggatggcggGcggcaccttcacgggggagg	20	10	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:47422161G>A	ENST00000361866.3	+	32	2210	c.2096G>A	c.(2095-2097)gGc>gAc	p.G699D	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	699	C-terminal globular domain.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		TGGATGGCGGGCGGCACCTTC	0.697																																					p.G699D		Atlas-SNP	.											.	COL6A1	101	.	0			c.G2096A						.						11	11	11					21																	47422161		2162	4263	6425	SO:0001583	missense	1291	exon32			TGGCGGGCGGCAC	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"Collagens"	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2096G>A	chr21.hg19:g.47422161G>A	ENSP00000355180:p.Gly699Asp	90.0	0.0		97.0	21.0	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	hg19	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.022783	0.54683	.	.	ENSG00000142156	ENST00000361866	D	0.86366	-2.11	4.63	4.63	0.57726	von Willebrand factor, type A (3);	0.069270	0.64402	D	0.000018	D	0.94463	0.8218	M	0.91038	3.17	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	D	0.94825	0.7990	10	0.42905	T	0.14	-22.672	17.4727	0.87650	0.0:0.0:1.0:0.0	.	699	P12109	CO6A1_HUMAN	D	699	ENSP00000355180:G699D	ENSP00000355180:G699D	G	+	2	0	COL6A1	46246589	1.000000	0.71417	0.197000	0.23402	0.183000	0.23260	6.641000	0.74324	2.134000	0.65973	0.462000	0.41574	GGC	.	.		0.697	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		A	47422161	G	A	47422161	3	1	23	1	0	0	0	0	1	0	0	0	3701	1203	42	3	2222	3	COL6A1	21	47422161	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	8043	47422161	707734	1087	3153										
COL6A2	1292	hgsc.bcm.edu	37	chr21	47551948	47551948	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccgagcggctgggtgagcagAacttccacaaggcccggcgc	15	14	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:47551948A>G	ENST00000300527.4	+	28	2646	c.2542A>G	c.(2542-2544)Aac>Gac	p.N848D		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	848	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		GGGTGAGCAGAACTTCCACAA	0.701																																					p.N848D		Atlas-SNP	.											.	COL6A2	351	.	0			c.A2542G						.						18	19	18					21																	47551948		2192	4292	6484	SO:0001583	missense	1292	exon28			GAGCAGAACTTCC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"Collagens"	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2542A>G	chr21.hg19:g.47551948A>G	ENSP00000300527:p.Asn848Asp	107.0	0.0		112.0	54.0	NM_001849	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	hg19	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.924200	0.52653	.	.	ENSG00000142173	ENST00000300527	T	0.78924	-1.22	4.18	4.18	0.49190	von Willebrand factor, type A (3);	0.051650	0.64402	D	0.000001	T	0.80281	0.4594	M	0.75447	2.3	0.80722	D	1	P	0.43701	0.815	P	0.45998	0.5	T	0.81647	-0.0838	10	0.48119	T	0.1	-35.6117	13.2466	0.60026	1.0:0.0:0.0:0.0	.	848	P12110	CO6A2_HUMAN	D	848	ENSP00000300527:N848D	ENSP00000300527:N848D	N	+	1	0	COL6A2	46376376	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	6.023000	0.70848	1.541000	0.49316	0.260000	0.18958	AAC	.	.		0.701	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			G	47551948	A	G	47551948	3	3	23	1	0	0	0	0	1	0	0	0	3702	246	9	2	2978	2	COL6A2	21	47551948	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	129787	47551948	577947	1088	3154										
PCNT	5116	hgsc.bcm.edu	37	chr21	47848330	47848330	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagacctgcaggaaaagtccCtggagcatcttcgcttgccg	12	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:47848330C>T	ENST00000359568.5	+	35	7623	c.7516C>T	c.(7516-7518)Ctg>Ttg	p.L2506L	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2506					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GGAAAAGTCCCTGGAGCATCT	0.657																																					p.L2506L		Atlas-SNP	.											.	PCNT	283	.	0			c.C7516T						.						42	32	36					21																	47848330		2202	4298	6500	SO:0001819	synonymous_variant	5116	exon35			AAGTCCCTGGAGC	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7516C>T	chr21.hg19:g.47848330C>T		127.0	0.0		114.0	48.0	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	hg19	CCDS33592.1																																																																																			.	.		0.657	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47848330	C	T	47848330	2	4	23	1	0	0	0	0	0	0	0	1	11599	680	24	3		3	PCNT	21	47848330	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	296382	47848330	281565	1089	3155										
PCNT	5116	hgsc.bcm.edu	37	chr21	47848382	47848382	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgctgtccgagatccaggCgctgcgtgcccagctgcgca	13	16	0	1	rs368569999		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:47848382C>A	ENST00000359568.5	+	35	7675	c.7568C>A	c.(7567-7569)gCg>gAg	p.A2523E	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2523					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GAGATCCAGGCGCTGCGTGCC	0.662																																					p.A2523E		Atlas-SNP	.											.	PCNT	283	.	0			c.C7568A						.						34	27	30					21																	47848382		2201	4299	6500	SO:0001583	missense	5116	exon35			TCCAGGCGCTGCG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7568C>A	chr21.hg19:g.47848382C>A	ENSP00000352572:p.Ala2523Glu	107.0	0.0		91.0	43.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.291281	0.59976	.	.	ENSG00000160299	ENST00000359568	T	0.01548	4.78	4.39	4.39	0.52855	.	0.000000	0.32190	N	0.006460	T	0.04182	0.0116	L	0.49350	1.555	0.31121	N	0.708795	D;D	0.61697	0.99;0.974	P;P	0.61397	0.888;0.875	T	0.02553	-1.1142	10	0.02654	T	1	.	10.9292	0.47207	0.2909:0.7091:0.0:0.0	.	2405;2523	O95613-2;O95613	.;PCNT_HUMAN	E	2523	ENSP00000352572:A2523E	ENSP00000352572:A2523E	A	+	2	0	PCNT	46672810	0.986000	0.35501	0.995000	0.50966	0.648000	0.38561	2.616000	0.46376	2.375000	0.81037	0.563000	0.77884	GCG	.	.		0.662	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		A	47848382	C	A	47848382	3	1	23	1	0	0	0	0	1	0	0	0	11599	768	27	1	7706	1	PCNT	21	47848382	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	52	47848382	281513	1090	3156										
IL17RA	23765	hgsc.bcm.edu	37	chr22	17588634	17588634	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cagggcctggaagtgaaaaaTacagtgatgacaccaaatac	10	8	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:17588634T>A	ENST00000319363.6	+	12	1196	c.1063T>A	c.(1063-1065)Tac>Aac	p.Y355N		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	355					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		AAGTGAAAAATACAGTGATGA	0.468																																					p.Y355N		Atlas-SNP	.											.	IL17RA	62	.	0			c.T1063A						.						125	123	123					22																	17588634		2203	4300	6503	SO:0001583	missense	23765	exon12			GAAAAATACAGTG	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"Interleukins and interleukin receptors", "CD molecules"	5985	protein-coding gene	gene with protein product		605461	"interleukin 17 receptor"	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.1063T>A	chr22.hg19:g.17588634T>A	ENSP00000320936:p.Tyr355Asn	110.0	0.0		86.0	32.0	NM_014339	O43844|Q20WK1	Missense_Mutation	SNP	ENST00000319363.6	hg19	CCDS13739.1	.	.	.	.	.	.	.	.	.	.	T	4.881	0.163755	0.09287	.	.	ENSG00000177663	ENST00000319363	T	0.05513	3.43	3.83	-4.53	0.03462	.	2.187910	0.01505	N	0.017658	T	0.06962	0.0177	L	0.44542	1.39	0.09310	N	1	B	0.18610	0.029	B	0.16722	0.016	T	0.35748	-0.9776	10	0.29301	T	0.29	0.8733	8.9589	0.35834	0.0:0.6318:0.1535:0.2147	.	355	Q96F46	I17RA_HUMAN	N	355	ENSP00000320936:Y355N	ENSP00000320936:Y355N	Y	+	1	0	IL17RA	15968634	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.687000	0.05156	-1.083000	0.03097	-1.563000	0.00883	TAC	.	.		0.468	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339		A	17588634	T	A	17588634	3	1	23	1	0	0	0	0	1	0	0	0	7648	1406	49	4	1109	4	IL17RA	22	17588634	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10		17588634	33715932	1091	3157										
SLC25A1	6576	hgsc.bcm.edu	37	chr22	19165655	19165655	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccctcctcaccgatgccccGgtaccgcggcgggtgcgagc	13	19	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:19165655G>A	ENST00000215882.5	-	2	349	c.193C>T	c.(193-195)Cgg>Tgg	p.R65W	SLC25A1_ENST00000451283.1_5'UTR|SLC25A1_ENST00000461267.1_5'UTR|CLTCL1_ENST00000442042.2_5'Flank	NM_005984.3	NP_005975.1	P53007	TXTP_HUMAN	solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1	65					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|citrate transport (GO:0015746)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	citrate transmembrane transporter activity (GO:0015137)			cervix(1)|lung(1)	2	Colorectal(54;0.0993)	all_lung(157;9.94e-09)		Lung(27;0.124)		CCGATGCCCCGGTACCGCGGC	0.756																																					p.R72W		Atlas-SNP	.											.	SLC25A1	14	.	0			c.C214T						.						5	7	6					22																	19165655		2037	4032	6069	SO:0001583	missense	6576	exon1			TGCCCCGGTACCG	U25147	CCDS13758.1, CCDS74817.1	22q11	2013-05-22			ENSG00000100075	ENSG00000100075		"Solute carriers"	10979	protein-coding gene	gene with protein product		190315	"solute carrier family 20 (mitochondrial citrate transporter), member 3"	SLC20A3		8666394, 9254007	Standard	NM_001256534		Approved	CTP	uc002zoz.4	P53007	OTTHUMG00000150123	ENST00000215882.5:c.193C>T	chr22.hg19:g.19165655G>A	ENSP00000215882:p.Arg65Trp	132.0	0.0		117.0	8.0	NM_001256534	A8K8E8|Q9BSK6	Missense_Mutation	SNP	ENST00000215882.5	hg19	CCDS13758.1	.	.	.	.	.	.	.	.	.	.	G	32	5.116777	0.94385	.	.	ENSG00000100075	ENST00000215882	T	0.79940	-1.32	4.77	2.46	0.29980	Mitochondrial carrier domain (2);	0.113003	0.56097	D	0.000031	D	0.89424	0.6711	M	0.92691	3.335	0.80722	D	1	D	0.71674	0.998	P	0.58970	0.849	D	0.91248	0.5027	10	0.87932	D	0	-2.5554	12.2745	0.54726	0.0:0.0:0.5691:0.4309	.	65	P53007	TXTP_HUMAN	W	65	ENSP00000215882:R65W	ENSP00000215882:R65W	R	-	1	2	SLC25A1	17545655	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.510000	0.53393	0.947000	0.37659	0.549000	0.68633	CGG	.	.		0.756	SLC25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316441.1	NM_005984		A	19165655	G	A	19165655	3	1	23	1	0	0	0	0	1	0	0	0	14486	1115	39	1	774	1	SLC25A1	22	19165655	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1577021	19165655	32138911	1092	3158										
C22orf29	79680	hgsc.bcm.edu	37	chr22	19839777	19839777	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctgctgacggcaccggccaCgaggcatgctgggagcacag	15	14	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:19839777C>T	ENST00000405640.1	-	2	676	c.8G>A	c.(7-9)cGt>cAt	p.R3H	C22orf29_ENST00000484072.1_Intron|GNB1L_ENST00000405009.1_Intron|GNB1L_ENST00000329517.6_Intron|C22orf29_ENST00000328554.4_Missense_Mutation_p.R3H|C22orf29_ENST00000407472.1_Missense_Mutation_p.R3H|GNB1L_ENST00000403325.1_Intron|GNB1L_ENST00000460402.1_Intron			Q7L3V2	BOP_HUMAN	chromosome 22 open reading frame 29	3					mitochondrial outer membrane permeabilization (GO:0097345)|regulation of mitochondrial membrane potential (GO:0051881)	mitochondrion (GO:0005739)				NS(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	7	Colorectal(54;0.0993)					GCACCGGCCACGAGGCATGCT	0.632																																					p.R3H		Atlas-SNP	.											.	C22orf29	23	.	0			c.G8A						.						46	48	48					22																	19839777		2191	4268	6459	SO:0001583	missense	79680	exon3			CGGCCACGAGGCA	BX640998	CCDS13769.1	22q11.21	2006-07-05			ENSG00000215012	ENSG00000215012			26112	protein-coding gene	gene with protein product						12477932	Standard	NM_024627		Approved	FLJ21125	uc002zqh.3	Q7L3V2	OTTHUMG00000030314	ENST00000405640.1:c.8G>A	chr22.hg19:g.19839777C>T	ENSP00000384924:p.Arg3His	155.0	0.0		144.0	52.0	NM_024627	A8K5E7|D3DX21|Q6MZM8|Q6N000|Q9H7A0	Missense_Mutation	SNP	ENST00000405640.1	hg19	CCDS13769.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.849042	0.32699	.	.	ENSG00000215012	ENST00000407472;ENST00000328554;ENST00000405640;ENST00000416337	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	3.69	-3.65	0.04502	.	.	.	.	.	T	0.14313	0.0346	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.26916	-1.0089	9	0.62326	D	0.03	0.0166	8.8206	0.35023	0.0:0.3949:0.0:0.6051	.	3	Q7L3V2	CV029_HUMAN	H	3	ENSP00000386111:R3H;ENSP00000330596:R3H;ENSP00000384924:R3H;ENSP00000392994:R3H	ENSP00000330596:R3H	R	-	2	0	C22orf29	18219777	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.581000	0.02119	-0.624000	0.05611	-0.768000	0.03414	CGT	.	.		0.632	C22orf29-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317290.2	NM_024627		T	19839777	C	T	19839777	3	4	23	1	0	0	0	0	1	0	0	0	2143	536	19	1	1090	1	C22orf29	22	19839777	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	674122	19839777	31464789	1093	3159										
DGCR8	54487	hgsc.bcm.edu	37	chr22	20074009	20074009	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttggtgacggggtaggcataGggggtgagagtgctgataag							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:20074009delG	ENST00000351989.3	+	2	952	c.523delG	c.(523-525)gggfs	p.G176fs	DGCR8_ENST00000383024.2_Frame_Shift_Del_p.G176fs|MIR3618_ENST00000580330.1_RNA|MIR1306_ENST00000408439.1_RNA|DGCR8_ENST00000407755.1_Frame_Shift_Del_p.G176fs	NM_022720.6	NP_073557.3	Q8WYQ5	DGCR8_HUMAN	DGCR8 microprocessor complex subunit	176	Necessary for interaction with NCL.|Necessary for nuclear localization and retention.				gene expression (GO:0010467)|primary miRNA processing (GO:0031053)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			NS(2)|breast(1)|endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	Colorectal(54;0.0993)					GGTAGGCATAGGGGGTGAGAG	0.552																																					p.I174fs		Atlas-Indel,Pindel	.											.	DGCR8	53	.	0			c.522delA						.						139	131	134					22																	20074009		2203	4300	6503	SO:0001589	frameshift_variant	54487	exon2			.	AF165527, AB050770	CCDS13773.1, CCDS54501.1	22q11.2	2013-05-02	2013-05-02		ENSG00000128191	ENSG00000128191			2847	protein-coding gene	gene with protein product		609030	"chromosome 22 open reading frame 12", "DiGeorge syndrome critical region gene 8"	C22orf12		21454614	Standard	NM_001190326		Approved	DGCRK6, Gy1, pasha	uc002zri.3	Q8WYQ5	OTTHUMG00000150503	ENST00000351989.3:c.523delG	chr22.hg19:g.20074009delG	ENSP00000263209:p.Gly176fs	70.0	0.0		67.0	20.0	NM_001190326	B2R8G1|Q6DCB2|Q6MZE9|Q6Y2L0|Q96G39|Q96GP8|Q9H6L8|Q9H6T7|Q9NRW2	Frame_Shift_Del	DEL	ENST00000351989.3	hg19	CCDS13773.1																																																																																			.	.		0.552	DGCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318654.1			-	20074009	G	-	20074009	7	5	23	1	0	1	0	1	0	0	0	0	4466	1000	35	0	525	0	DGCR8	22	20074009	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	234232	20074009	31230557	1094	3160										
RTN4R	65078	hgsc.bcm.edu	37	chr22	20229291	20229291	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggcccaggggggtgaggctGcaggtgaggctgggtagggc	23	7	0	2	rs374126911		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:20229291G>A	ENST00000043402.7	-	2	1803	c.1365C>T	c.(1363-1365)tgC>tgT	p.C455C	RTN4R_ENST00000469601.1_5'Flank	NM_023004.5	NP_075380.1	Q9BZR6	RTN4R_HUMAN	reticulon 4 receptor	455					axonogenesis (GO:0007409)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			lung(1)|ovary(1)|prostate(1)	3	Colorectal(54;0.0993)					GGGTGAGGCTGCAGGTGAGGC	0.692																																					p.C455C		Atlas-SNP	.											.	RTN4R	14	.	0			c.C1365T						.	G		0,4196		0,0,2098	10	7	8		1365	0.8	0.9	22		8	1,8319		0,1,4159	no	coding-synonymous	RTN4R	NM_023004.5		0,1,6257	AA,AG,GG		0.012,0.0,0.0080		455/474	20229291	1,12515	2098	4160	6258	SO:0001819	synonymous_variant	65078	exon2			GAGGCTGCAGGTG	AF283463	CCDS13777.1	22q11	2008-05-02			ENSG00000040608	ENSG00000040608			18601	protein-coding gene	gene with protein product		605566				11201742	Standard	NM_023004		Approved	NOGOR	uc002zrv.3	Q9BZR6	OTTHUMG00000150572	ENST00000043402.7:c.1365C>T	chr22.hg19:g.20229291G>A		136.0	0.0		139.0	57.0	NM_023004	D3DX28	Silent	SNP	ENST00000043402.7	hg19	CCDS13777.1	.	.	.	.	.	.	.	.	.	.	G	2.979	-0.210662	0.06140	0.0	1.2E-4	ENSG00000040608	ENST00000416372;ENST00000425986	.	.	.	3.02	0.841	0.18918	.	.	.	.	.	T	0.51363	0.1670	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37454	-0.9705	4	.	.	.	.	5.1608	0.15060	0.2921:0.0:0.7079:0.0	.	.	.	.	V	475;541	.	.	A	-	2	0	RTN4R	18609291	0.004000	0.15560	0.933000	0.37362	0.453000	0.32348	0.597000	0.24059	0.146000	0.19002	0.305000	0.20034	GCA	.	.		0.692	RTN4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318950.2			A	20229291	G	A	20229291	2	1	23	1	0	0	0	0	0	0	0	1	13745	1311	46	3		3	RTN4R	22	20229291	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	155282	20229291	31075275	1095	3161										
RIMBP3	85376	hgsc.bcm.edu	37	chr22	20458139	20458139	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggcagccgcacctccacccGcgcccggtagtgcgtgccgg	14	18	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:20458139G>A	ENST00000426804.1	-	1	3647	c.3163C>T	c.(3163-3165)Cgg>Tgg	p.R1055W	SCARNA18_ENST00000516215.1_RNA|SCARNA17_ENST00000516762.1_RNA|RN7SKP131_ENST00000363006.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1055	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.									breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			ACCTCCACCCGCGCCCGGTAG	0.637																																					p.R1055W		Atlas-SNP	.											.	RIMBP3	42	.	0			c.C3163T						.						71	92	85					22																	20458139		2131	4250	6381	SO:0001583	missense	85376	exon1			CCACCCGCGCCCG	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3163C>T	chr22.hg19:g.20458139G>A	ENSP00000391564:p.Arg1055Trp	1061.0	0.0		1049.0	170.0	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	hg19	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	G	4.244	0.044204	0.08196	.	.	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.59638	0.25	3.56	-3.28	0.05033	Fibronectin, type III (2);	0.376219	0.25657	N	0.029179	T	0.43612	0.1255	M	0.68952	2.095	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.38714	-0.9648	10	0.87932	D	0	-1.125	1.0843	0.01649	0.4062:0.1452:0.2911:0.1575	.	961	Q9UFD9	RIM3A_HUMAN	W	961;1055	ENSP00000391564:R1055W	ENSP00000347318:R961W	R	-	1	2	RIMBP3	18838139	0.005000	0.15991	0.001000	0.08648	0.030000	0.12068	1.052000	0.30429	-0.673000	0.05259	-0.552000	0.04208	CGG	.	.		0.637	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672		A	20458139	G	A	20458139	3	1	23	1	0	0	0	0	1	0	0	0	13379	1086	38	1	1760	1	RIMBP3	22	20458139	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	228848	20458139	30846427	1096	3162										
GNAZ	2781	hgsc.bcm.edu	37	chr22	23438309	23438309	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggcacaggcctgcttcagcCgctccagcgagtaccacctg	12	16	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:23438309C>T	ENST00000248996.4	+	2	1093	c.427C>T	c.(427-429)Cgc>Tgc	p.R143C	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	143					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		CTGCTTCAGCCGCTCCAGCGA	0.657																																					p.R143C		Atlas-SNP	.											.	GNAZ	45	.	0			c.C427T						.						61	52	55					22																	23438309		2203	4300	6503	SO:0001583	missense	2781	exon2			TTCAGCCGCTCCA		CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.427C>T	chr22.hg19:g.23438309C>T	ENSP00000248996:p.Arg143Cys	74.0	0.0		42.0	8.0	NM_002073	B2R6C1|Q4QRJ6	Missense_Mutation	SNP	ENST00000248996.4	hg19	CCDS13804.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.850237	0.91277	.	.	ENSG00000128266	ENST00000248996;ENST00000456059	D	0.90504	-2.68	4.85	4.85	0.62838	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.93229	0.7843	H	0.94886	3.595	0.80722	D	1	D	0.65815	0.995	B	0.41299	0.353	D	0.95381	0.8473	10	0.87932	D	0	.	17.3371	0.87285	0.0:1.0:0.0:0.0	.	143	P19086	GNAZ_HUMAN	C	143;91	ENSP00000248996:R143C	ENSP00000248996:R143C	R	+	1	0	GNAZ	21768309	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.613000	0.61176	2.428000	0.82296	0.655000	0.94253	CGC	.	.		0.657	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073		T	23438309	C	T	23438309	3	4	23	1	0	0	0	0	1	0	0	0	6522	652	23	1	429	1	GNAZ	22	23438309	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	2980170	23438309	27866257	1097	3163										
SLC2A11	66035	hgsc.bcm.edu	37	chr22	24219966	24219966	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggccagctgcctggtgcccGgggcgctccagctcgcctcc	14	18	0	0	rs144951215		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:24219966G>A	ENST00000345044.6	+	6	863	c.595G>A	c.(595-597)Ggg>Agg	p.G199R	SLC2A11_ENST00000316185.8_Missense_Mutation_p.G202R|SLC2A11_ENST00000398356.2_Missense_Mutation_p.G206R|AP000350.10_ENST00000433835.3_Intron|SLC2A11_ENST00000467660.1_3'UTR|RN7SL268P_ENST00000491172.2_RNA			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	199					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						CCTGGTGCCCGGGGCGCTCCA	0.677																																					p.G206R		Atlas-SNP	.											.	SLC2A11	32	.	0			c.G616A						.	G	ARG/GLY,ARG/GLY,ARG/GLY	0,4406		0,0,2203	20	18	18		595,604,616	1.4	0	22	dbSNP_134	18	1,8599		0,1,4299	no	missense,missense,missense	SLC2A11	NM_001024938.2,NM_001024939.2,NM_030807.3	125,125,125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	199/497,202/500,206/504	24219966	1,13005	2203	4300	6503	SO:0001583	missense	66035	exon7			GTGCCCGGGGCGC	AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"Solute carriers"	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.595G>A	chr22.hg19:g.24219966G>A	ENSP00000342542:p.Gly199Arg	126.0	0.0		106.0	38.0	NM_030807	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Missense_Mutation	SNP	ENST00000345044.6	hg19	CCDS46673.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018991	0.35606	0.0	1.16E-4	ENSG00000133460	ENST00000345044;ENST00000398356;ENST00000398359;ENST00000407566;ENST00000316185	T;T;T	0.73897	-0.79;-0.79;-0.79	3.52	1.39	0.22231	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.256061	0.37530	N	0.002046	T	0.81550	0.4846	M	0.76328	2.33	0.09310	N	1	D;D;D;D;D	0.76494	0.999;0.999;0.997;0.999;0.999	P;D;D;D;D	0.71656	0.905;0.956;0.947;0.974;0.974	T	0.69591	-0.5104	10	0.87932	D	0	.	7.0897	0.25277	0.2391:0.0:0.7609:0.0	.	206;202;199;206;206	E7ENI4;Q9BYW1-3;Q9BYW1;E9PH55;Q6P4C1	.;.;GTR11_HUMAN;.;.	R	199;206;206;206;202	ENSP00000342542:G199R;ENSP00000381399:G206R;ENSP00000326748:G202R	ENSP00000326748:G202R	G	+	1	0	SLC2A11	22549966	0.888000	0.30383	0.039000	0.18376	0.126000	0.20510	4.498000	0.60373	0.785000	0.33685	0.603000	0.83216	GGG	.	G|1.000;A|0.000		0.677	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807		A	24219966	G	A	24219966	3	1	23	1	0	0	0	0	1	0	0	0	14555	1116	39	1	697	1	SLC2A11	22	24219966	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	781657	24219966	27084600	1098	3164										
GGT5	2687	hgsc.bcm.edu	37	chr22	24628858	24628858	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaaacggctgaggacaggggCcaccacatgcccccctcgga	13	15	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:24628858C>T	ENST00000327365.4	-	4	945	c.529G>A	c.(529-531)Gcc>Acc	p.A177T	GGT5_ENST00000263112.7_Missense_Mutation_p.A145T|GGT5_ENST00000398292.3_Missense_Mutation_p.A177T|GGT5_ENST00000418439.2_Missense_Mutation_p.G101D	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	177					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						AGGACAGGGGCCACCACATGC	0.701																																					p.A177T		Atlas-SNP	.											.	GGT5	61	.	0			c.G529A						.						34	37	36					22																	24628858		2193	4293	6486	SO:0001583	missense	2687	exon4			CAGGGGCCACCAC	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"Gamma-glutamyltransferases"	4260	protein-coding gene	gene with protein product		137168	"gamma-glutamyltransferase-like activity 1"	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.529G>A	chr22.hg19:g.24628858C>T	ENSP00000330080:p.Ala177Thr	256.0	0.0		220.0	72.0	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Missense_Mutation	SNP	ENST00000327365.4	hg19	CCDS13825.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.53|12.53	1.964787|1.964787	0.34659|0.34659	.|.	.|.	ENSG00000099998|ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000438024;ENST00000398292|ENST00000418439	T;T;T|T	0.20598|0.21031	2.06;2.06;2.06|2.03	3.64|3.64	0.217|0.217	0.15264|0.15264	.|.	0.280853|.	0.35151|.	N|.	0.003404|.	T|T	0.05686|0.05686	0.0149|0.0149	N|N	0.02876|0.02876	-0.465|-0.465	0.09310|0.09310	N|N	1|1	B;B;B;B|B	0.15141|0.29909	0.01;0.012;0.0;0.012|0.261	B;B;B;B|B	0.28305|0.20955	0.053;0.088;0.007;0.088|0.032	T|T	0.36187|0.36187	-0.9758|-0.9758	10|9	0.20519|0.08837	T|T	0.43|0.75	-38.1671|-38.1671	3.7817|3.7817	0.08683|0.08683	0.3159:0.1896:0.4946:0.0|0.3159:0.1896:0.4946:0.0	.|.	145;177;177;177|101	P36269-2;Q53XM9;Q6GMP0;P36269|E7EUG3	.;.;.;GGT5_HUMAN|.	T|D	177;145;92;177|101	ENSP00000330080:A177T;ENSP00000263112:A145T;ENSP00000381340:A177T|ENSP00000392146:G101D	ENSP00000263112:A145T|ENSP00000392146:G101D	A|G	-|-	1|2	0|0	GGT5|GGT5	22958858|22958858	0.990000|0.990000	0.36364|0.36364	0.237000|0.237000	0.24090|0.24090	0.036000|0.036000	0.12997|0.12997	2.004000|2.004000	0.40854|0.40854	0.173000|0.173000	0.19788|0.19788	-1.426000|-1.426000	0.01102|0.01102	GCC|GGC	.	.		0.701	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121		T	24628858	C	T	24628858	3	4	23	1	0	0	0	0	1	0	0	0	6370	739	26	3	1270	3	GGT5	22	24628858	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	408892	24628858	26675708	1099	3165										
ADRBK2	157	hgsc.bcm.edu	37	chr22	26100174	26100174	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cggctgggctgtcacggaggCgggtaggccattgttcctgc	17	11	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:26100174C>T	ENST00000324198.6	+	15	1518	c.1326C>T	c.(1324-1326)ggC>ggT	p.G442G		NM_005160.3	NP_005151.2	P35626	ARBK2_HUMAN	adrenergic, beta, receptor kinase 2	442	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				receptor internalization (GO:0031623)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)		ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|skin(3)|stomach(2)	32					Adenosine triphosphate(DB00171)	GTCACGGAGGCGGGTAGGCCA	0.463																																					p.G442G		Atlas-SNP	.											.	ADRBK2	78	.	0			c.C1326T						.						66	65	65					22																	26100174		2203	4300	6503	SO:0001819	synonymous_variant	157	exon15			CGGAGGCGGGTAG	X69117	CCDS13832.1	22q11	2013-01-10			ENSG00000100077	ENSG00000100077		"Pleckstrin homology (PH) domain containing"	290	protein-coding gene	gene with protein product		109636				7695743	Standard	NM_005160		Approved	GRK3, BARK2	uc003abx.4	P35626	OTTHUMG00000150280	ENST00000324198.6:c.1326C>T	chr22.hg19:g.26100174C>T		166.0	0.0		134.0	58.0	NM_005160	Q9UGW9	Silent	SNP	ENST00000324198.6	hg19	CCDS13832.1																																																																																			.	.		0.463	ADRBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317296.4	NM_005160		T	26100174	C	T	26100174	2	4	23	1	0	0	0	0	0	0	0	1	344	755	27	1		1	ADRBK2	22	26100174	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1471316	26100174	25204392	1100	3166										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26306993	26306993	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagaagcaagatttggaaggCttgatcggaaccctctgtga	13	7	1	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:26306993C>A	ENST00000407587.2	+	33	5512	c.5343C>A	c.(5341-5343)ggC>ggA	p.G1781G	MYO18B_ENST00000536101.1_Silent_p.G1780G|MYO18B_ENST00000335473.7_Silent_p.G1780G			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1780	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						ATTTGGAAGGCTTGATCGGAA	0.498																																					p.G1780G		Atlas-SNP	.											.	MYO18B	322	.	0			c.C5340A						.						70	71	71					22																	26306993		1972	4153	6125	SO:0001819	synonymous_variant	84700	exon33			GGAAGGCTTGATC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.5343C>A	chr22.hg19:g.26306993C>A		104.0	0.0		100.0	29.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.		0.498	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26306993	C	A	26306993	2	1	23	1	0	0	0	0	0	0	0	1	10075	784	28	3		3	MYO18B	22	26306993	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	206819	26306993	24997573	1101	3167										
GAS2L1	10633	hgsc.bcm.edu	37	chr22	29706652	29706652	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgaggagccacgtgatggtgCgagtgggtggtggctgggac	21	6	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:29706652C>T	ENST00000216101.6	-	0	1490				GAS2L1_ENST00000360113.2_Nonsense_Mutation_p.R256*|GAS2L1_ENST00000341313.6_Nonsense_Mutation_p.R256*|GAS2L1_ENST00000407647.2_Nonsense_Mutation_p.R256*|GAS2L1_ENST00000406549.3_Nonsense_Mutation_p.R256*|RASL10A_ENST00000608559.1_5'Flank|GAS2L1_ENST00000407854.1_Nonsense_Mutation_p.R256*|GAS2L1_ENST00000471961.1_Nonsense_Mutation_p.R256*|GAS2L1_ENST00000403764.1_Nonsense_Mutation_p.R256*	NM_006477.4	NP_006468.1	Q92737	RSLAA_HUMAN	RAS-like, family 10, member A						small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)	1						CGTGATGGTGCGAGTGGGTGG	0.711																																					p.R256X		Atlas-SNP	.											.	GAS2L1	54	.	0			c.C766T						.						54	54	54					22																	29706652		2202	4295	6497	SO:0001628	intergenic_variant	10634	exon4			ATGGTGCGAGTGG	Y07847	CCDS13854.1	22q12.2	2014-05-09			ENSG00000100276	ENSG00000100276			16954	protein-coding gene	gene with protein product		602220				8975699, 15731001	Standard	NM_006477		Approved	RRP22	uc031rxl.1	Q92737	OTTHUMG00000151106		chr22.hg19:g.29706652C>T		63.0	0.0		47.0	24.0	NM_152237	Q49AU5|Q6PI03	Nonsense_Mutation	SNP	ENST00000216101.6	hg19	CCDS13854.1	.	.	.	.	.	.	.	.	.	.	c	36	5.853070	0.97030	.	.	ENSG00000185340	ENST00000407647;ENST00000333679;ENST00000406549;ENST00000360113;ENST00000341313;ENST00000403764;ENST00000471961;ENST00000407854	.	.	.	4.17	1.78	0.24846	.	0.180905	0.35179	N	0.003395	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.949	10.6805	0.45811	0.1541:0.7123:0.1336:0.0	.	.	.	.	X	256	.	ENSP00000332834:R256X	R	+	1	2	GAS2L1	28036652	1.000000	0.71417	0.958000	0.39756	0.946000	0.59487	4.363000	0.59473	0.902000	0.36520	0.306000	0.20318	CGA	.	.		0.711	RASL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321342.1			T	29706652	C	T	29706652	1	4	23	0	1	0	0	0	0	0	0	0	6254	760	27	1		1	GAS2L1	22	29706652	IGR	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3399659	29706652	21597914	1102	3168										
SF3A1	10291	hgsc.bcm.edu	37	chr22	30736780	30736782	+	In_Frame_Del	DEL	CTT	CTT	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggtgggggcactttctgccCttcttcttcatcatctgaac							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:30736780_30736782delCTT	ENST00000215793.8	-	8	1245_1247	c.1091_1093delAAG	c.(1090-1095)gaaggg>ggg	p.E364del	SF3A1_ENST00000439242.1_In_Frame_Del_p.E299del	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	364					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						ACTTTCTGCCCTTCTTCTTCATC	0.571																																					p.364_365del		Atlas-Indel,Pindel	.											.	SF3A1	61	.	0			c.1092_1094del						.																																			SO:0001651	inframe_deletion	10291	exon8			.	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"splicing factor 3a, subunit 1, 120kD"			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.1091_1093delAAG	chr22.hg19:g.30736786_30736788delCTT	ENSP00000215793:p.Glu364del	88.0	0.0		65.0	20.0	NM_005877	E9PAW1	In_Frame_Del	DEL	ENST00000215793.8	hg19	CCDS13875.1																																																																																			.	.		0.571	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877		-	30736782	CTT	-	30736780	7	5	23	1	0	1	0	1	0	0	0	0	14161	681	24	0	1324	0	SF3A1	22	30736780	In_Frame_Del	DEL	CTT	TCGA-4R-AA8I-01A-11D-A382-10	1030128	30736780	20567786	1103	3169										
SLC35E4	339665	hgsc.bcm.edu	37	chr22	31042723	31042723	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcccactgctggcgactctcGcctctgggcctgcatcctgc	11	18	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:31042723G>A	ENST00000343605.4	+	2	1557	c.758G>A	c.(757-759)cGc>cAc	p.R253H	SLC35E4_ENST00000406566.1_Intron|SLC35E4_ENST00000300385.8_Intron	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	253	Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						GGCGACTCTCGCCTCTGGGCC	0.667																																					p.R253H		Atlas-SNP	.											.	SLC35E4	22	.	0			c.G758A						.						49	36	40					22																	31042723		2203	4300	6503	SO:0001583	missense	339665	exon2			ACTCTCGCCTCTG		CCDS13882.1	22q12.2	2013-05-22			ENSG00000100036	ENSG00000100036		"Solute carriers"	17058	protein-coding gene	gene with protein product							Standard	NM_001001479		Approved		uc003ais.1	Q6ICL7	OTTHUMG00000151110	ENST00000343605.4:c.758G>A	chr22.hg19:g.31042723G>A	ENSP00000339626:p.Arg253His	61.0	0.0		59.0	29.0	NM_001001479	Q567P0	Missense_Mutation	SNP	ENST00000343605.4	hg19	CCDS13882.1	.	.	.	.	.	.	.	.	.	.	G	9.981	1.228147	0.22542	.	.	ENSG00000100036	ENST00000343605	T	0.65549	-0.16	5.02	-1.51	0.08664	Domain of unknown function DUF250 (1);	0.304838	0.34291	N	0.004098	T	0.45498	0.1345	L	0.41961	1.31	0.41875	D	0.990296	B	0.11235	0.004	B	0.10450	0.005	T	0.27434	-1.0074	10	0.12430	T	0.62	-16.2139	10.0811	0.42391	0.4756:0.0:0.5244:0.0	.	253	Q6ICL7	S35E4_HUMAN	H	253	ENSP00000339626:R253H	ENSP00000339626:R253H	R	+	2	0	SLC35E4	29372723	0.018000	0.18449	0.901000	0.35422	0.751000	0.42716	0.282000	0.18829	-0.010000	0.14271	-0.258000	0.10820	CGC	.	.		0.667	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973		A	31042723	G	A	31042723	3	1	23	1	0	0	0	0	1	0	0	0	14602	1087	38	1	764	1	SLC35E4	22	31042723	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	305943	31042723	20261843	1104	3170										
DUSP18	150290	hgsc.bcm.edu	37	chr22	31059555	31059555	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gatgagctgctcccaaaagcCgctgttgggtcggatgatgg	15	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:31059555C>T	ENST00000334679.3	-	2	941	c.436G>A	c.(436-438)Ggc>Agc	p.G146S	DUSP18_ENST00000461301.1_Intron|DUSP18_ENST00000404885.1_Missense_Mutation_p.G146S|DUSP18_ENST00000403268.1_Missense_Mutation_p.R109Q|DUSP18_ENST00000407308.1_Missense_Mutation_p.G146S	NM_152511.3	NP_689724.3	Q8NEJ0	DUS18_HUMAN	dual specificity phosphatase 18	146	Tyrosine-protein phosphatase.				peptidyl-tyrosine dephosphorylation (GO:0035335)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			large_intestine(1)|lung(1)|prostate(1)|skin(1)	4						TCCCAAAAGCCGCTGTTGGGT	0.557																																					p.G146S		Atlas-SNP	.											DUSP18,NS,carcinoma,0,1	DUSP18	10	.	0			c.G436A						.						109	96	101					22																	31059555		2203	4300	6503	SO:0001583	missense	150290	exon2			AAAAGCCGCTGTT	AF461689	CCDS13883.1	22q12.1	2011-06-09				ENSG00000167065		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	18484	protein-coding gene	gene with protein product		611446				12408986	Standard	NM_152511		Approved	DUSP20	uc003aiw.1	Q8NEJ0		ENST00000334679.3:c.436G>A	chr22.hg19:g.31059555C>T	ENSP00000333917:p.Gly146Ser	102.0	1.0		108.0	41.0	NM_152511	B3KPA4	Missense_Mutation	SNP	ENST00000334679.3	hg19	CCDS13883.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.422402|5.422402	0.96111|0.96111	.|.	.|.	ENSG00000167065|ENSG00000167065	ENST00000404885;ENST00000407308;ENST00000334679;ENST00000342474|ENST00000403268	D;D;D;D|.	0.85484|.	-1.99;-1.99;-1.99;-1.99|.	5.27|5.27	5.27|5.27	0.74061|0.74061	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.81197|0.81197	0.4772|0.4772	M|M	0.85197|0.85197	2.74|2.74	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.65773|.	0.938|.	T|T	0.79196|0.79196	-0.1903|-0.1903	10|6	0.40728|0.24483	T|T	0.16|0.36	.|.	18.5145|18.5145	0.90931|0.90931	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	146|.	Q8NEJ0|.	DUS18_HUMAN|.	S|Q	146|109	ENSP00000385463:G146S;ENSP00000386063:G146S;ENSP00000333917:G146S;ENSP00000340795:G146S|.	ENSP00000333917:G146S|ENSP00000384946:R109Q	G|R	-|-	1|2	0|0	DUSP18|DUSP18	29389555|29389555	1.000000|1.000000	0.71417|0.71417	0.944000|0.944000	0.38274|0.38274	0.897000|0.897000	0.52465|0.52465	4.890000|4.890000	0.63178|0.63178	2.471000|2.471000	0.83476|0.83476	0.655000|0.655000	0.94253|0.94253	GGC|CGG	.	.		0.557	DUSP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321400.1			T	31059555	C	T	31059555	3	4	23	1	0	0	0	0	1	0	0	0	4819	652	23	1	134	1	DUSP18	22	31059555	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	16832	31059555	20245011	1105	3171										
SMTN	6525	hgsc.bcm.edu	37	chr22	31484696	31484696	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tacccacagttgcgaagcgcTggtgagtatgaggagcgcaa	14	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:31484696T>C	ENST00000347557.2	+	5	524	c.306T>C	c.(304-306)gcT>gcC	p.A102A	SMTN_ENST00000333137.7_Silent_p.A102A|SMTN_ENST00000475548.1_3'UTR|SMTN_ENST00000358743.1_Silent_p.A102A	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	102					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						TGCGAAGCGCTGGTGAGTATG	0.657																																					p.A158A		Atlas-SNP	.											.	SMTN	219	.	0			c.T474C						.						63	54	57					22																	31484696		2201	4300	6501	SO:0001819	synonymous_variant	6525	exon4			AAGCGCTGGTGAG	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.306T>C	chr22.hg19:g.31484696T>C		172.0	0.0		154.0	13.0	NM_001207018	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Silent	SNP	ENST00000347557.2	hg19	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	T	4.327	0.060099	0.08339	.	.	ENSG00000183963	ENST00000438223	.	.	.	4.79	-9.57	0.00562	.	.	.	.	.	T	0.71013	0.3290	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.79713	-0.1688	4	.	.	.	-13.5919	20.9408	0.99941	0.0:0.8283:0.0782:0.0935	.	.	.	.	R	157	.	.	W	+	1	0	SMTN	29814696	0.001000	0.12720	0.000000	0.03702	0.395000	0.30598	-1.951000	0.01529	-3.031000	0.00266	-0.904000	0.02843	TGG	.	.		0.657	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		C	31484696	T	C	31484696	2	2	23	1	0	0	0	0	0	0	0	1	14829	1567	55	2		2	SMTN	22	31484696	Silent	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	425141	31484696	19819870	1106	3172										
RFPL2	10739	hgsc.bcm.edu	37	chr22	32586994	32586994	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccccactcgctgtaacttgCggtctacgaagaggaaagtc	10	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:32586994C>T	ENST00000400237.1	-	5	1837	c.902G>A	c.(901-903)cGc>cAc	p.R301H	RFPL2_ENST00000489846.1_5'UTR|RFPL2_ENST00000400236.3_Missense_Mutation_p.R211H|RFPL2_ENST00000248980.4_Missense_Mutation_p.R240H|RFPL2_ENST00000248983.4_Missense_Mutation_p.R211H			O75678	RFPL2_HUMAN	ret finger protein-like 2	301	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	21						CTGTAACTTGCGGTCTACGAA	0.512																																					p.R301H		Atlas-SNP	.											.	RFPL2	81	.	0			c.G902A						.						41	61	54					22																	32586994		2202	4294	6496	SO:0001583	missense	10739	exon5			AACTTGCGGTCTA	AJ010231	CCDS43009.1, CCDS46694.1, CCDS43009.2	22q12.3	2008-06-12				ENSG00000128253		"RING-type (C3HC4) zinc fingers"	9979	protein-coding gene	gene with protein product		605969				10508838	Standard	NM_001098527		Approved	RNF79	uc003amg.3	O75678		ENST00000400237.1:c.902G>A	chr22.hg19:g.32586994C>T	ENSP00000383096:p.Arg301His	234.0	0.0		218.0	108.0	NM_001098527		Missense_Mutation	SNP	ENST00000400237.1	hg19	CCDS43009.2	.	.	.	.	.	.	.	.	.	.	C	5.006	0.186849	0.09547	.	.	ENSG00000128253	ENST00000248980;ENST00000248983;ENST00000400236;ENST00000400237	T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35	0.351	-0.702	0.11265	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.50701	0.1631	L	0.33710	1.025	0.09310	N	1	B;B	0.15473	0.013;0.0	B;B	0.18561	0.022;0.005	T	0.37056	-0.9722	9	0.54805	T	0.06	.	5.6019	0.17359	0.0:0.6559:0.344:0.0	.	301;240	O75678;O75678-3	RFPL2_HUMAN;.	H	240;211;211;301	ENSP00000248980:R240H;ENSP00000248983:R211H;ENSP00000383095:R211H;ENSP00000383096:R301H	ENSP00000248980:R240H	R	-	2	0	RFPL2	30916994	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-3.805000	0.00362	-0.711000	0.04995	-0.714000	0.03626	CGC	.	.		0.512	RFPL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075262.2	NM_006605		T	32586994	C	T	32586994	3	4	23	1	0	0	0	0	1	0	0	0	13269	768	27	1	238	1	RFPL2	22	32586994	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1102298	32586994	18717572	1107	3173										
GGA1	26088	hgsc.bcm.edu	37	chr22	38016853	38016853	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgaccccaagcttccagatgAcactacctttccccttcctc	4	19	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:38016853A>G	ENST00000343632.4	+	6	847	c.461A>G	c.(460-462)gAc>gGc	p.D154G	GGA1_ENST00000406772.1_Missense_Mutation_p.D81G|GGA1_ENST00000381756.5_Missense_Mutation_p.D171G|GGA1_ENST00000325180.8_Missense_Mutation_p.D154G|GGA1_ENST00000337437.4_Missense_Mutation_p.D121G	NM_001172687.1|NM_013365.4	NP_001166158.1|NP_037497.1	Q9UJY5	GGA1_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 1	154	Interaction with ARF3.				intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	10	Melanoma(58;0.0574)					CTTCCAGATGACACTACCTTT	0.522																																					p.D154G		Atlas-SNP	.											.	GGA1	39	.	0			c.A461G						.						159	129	139					22																	38016853		2203	4300	6503	SO:0001583	missense	26088	exon6			CAGATGACACTAC	AF190862	CCDS13951.1, CCDS33643.1, CCDS54526.1	22q13.31	2010-02-12	2010-02-12		ENSG00000100083	ENSG00000100083			17842	protein-coding gene	gene with protein product		606004				10747088, 10747089, 16407204	Standard	NM_013365		Approved		uc003atc.3	Q9UJY5	OTTHUMG00000030985	ENST00000343632.4:c.461A>G	chr22.hg19:g.38016853A>G	ENSP00000341344:p.Asp154Gly	118.0	0.0		110.0	37.0	NM_001001560	A8K3D3|B0QYR7|Q5TG07|Q86YA9|Q8NCS6|Q9BW94|Q9UG00|Q9UGW0|Q9UGW1	Missense_Mutation	SNP	ENST00000343632.4	hg19	CCDS13951.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.891503	0.52014	.	.	ENSG00000100083	ENST00000343632;ENST00000381756;ENST00000429218;ENST00000325180;ENST00000337437;ENST00000449944;ENST00000406772;ENST00000413251;ENST00000423024	T;T;T;T;T;T	0.38887	2.17;1.89;2.24;1.11;1.28;1.15	5.56	4.52	0.55395	.	0.092463	0.64402	D	0.000001	T	0.38081	0.1027	L	0.54323	1.7	0.80722	D	1	B;B;B	0.29835	0.258;0.034;0.013	B;B;B	0.31245	0.126;0.015;0.022	T	0.25398	-1.0133	10	0.37606	T	0.19	-21.3779	10.8912	0.46996	0.9266:0.0:0.0734:0.0	.	171;154;154	Q6IC75;Q86YA9;Q9UJY5	.;.;GGA1_HUMAN	G	154;171;81;154;121;146;81;81;81	ENSP00000341344:D154G;ENSP00000371175:D171G;ENSP00000321288:D154G;ENSP00000338647:D121G;ENSP00000390416:D146G;ENSP00000385287:D81G	ENSP00000321288:D154G	D	+	2	0	GGA1	36346799	1.000000	0.71417	0.617000	0.29091	0.955000	0.61496	5.285000	0.65633	2.102000	0.63906	0.460000	0.39030	GAC	.	.		0.522	GGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075873.3	NM_013365		G	38016853	A	G	38016853	3	3	23	1	0	0	0	0	1	0	0	0	6360	275	10	2	549	2	GGA1	22	38016853	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	5429859	38016853	13287713	1108	3174										
MICALL1	85377	hgsc.bcm.edu	37	chr22	38315101	38315101	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	caccggccagacccccagcaGcacgtgcgcagcctgccagc	11	20	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:38315101G>A	ENST00000215957.6	+	5	611	c.485G>A	c.(484-486)aGc>aAc	p.S162N		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	162	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					ACCCCCAGCAGCACGTGCGCA	0.672																																					p.S162N		Atlas-SNP	.											.	MICALL1	53	.	0			c.G485A						.						13	11	12					22																	38315101		2152	4176	6328	SO:0001583	missense	85377	exon5			CCAGCAGCACGTG	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"molecule interacting with Rab13"					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.485G>A	chr22.hg19:g.38315101G>A	ENSP00000215957:p.Ser162Asn	96.0	0.0		101.0	47.0	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	hg19	CCDS13961.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111079	0.77210	.	.	ENSG00000100139	ENST00000445494;ENST00000215957	T;T	0.74209	-0.82;0.37	4.99	4.99	0.66335	Zinc finger, LIM-type (2);	0.000000	0.64402	D	0.000003	D	0.87924	0.6300	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	D	0.89597	0.3832	10	0.62326	D	0.03	.	18.4596	0.90734	0.0:0.0:1.0:0.0	.	162	Q8N3F8	MILK1_HUMAN	N	78;162	ENSP00000404543:S78N;ENSP00000215957:S162N	ENSP00000215957:S162N	S	+	2	0	MICALL1	36645047	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	7.544000	0.82117	2.570000	0.86706	0.563000	0.77884	AGC	.	.		0.672	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		A	38315101	G	A	38315101	3	1	23	1	0	0	0	0	1	0	0	0	9582	971	34	3	503	3	MICALL1	22	38315101	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	298248	38315101	12989465	1109	3175										
PICK1	9463	hgsc.bcm.edu	37	chr22	38470413	38470413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gcgcccgcttctcccagatgCgcaaggatgtgctggagaag	14	12	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:38470413C>T	ENST00000404072.3	+	12	1281	c.934C>T	c.(934-936)Cgc>Tgc	p.R312C	PICK1_ENST00000356976.3_Missense_Mutation_p.R312C|RP5-1039K5.13_ENST00000445483.1_RNA	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	312	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					CTCCCAGATGCGCAAGGATGT	0.652																																					p.R312C		Atlas-SNP	.											.	PICK1	30	.	0			c.C934T						.						35	37	36					22																	38470413		2203	4300	6503	SO:0001583	missense	9463	exon12			CAGATGCGCAAGG	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"protein kinase C, alpha binding protein", "protein interacting with PRKCA"	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.934C>T	chr22.hg19:g.38470413C>T	ENSP00000385205:p.Arg312Cys	200.0	0.0		191.0	42.0	NM_012407	B3KS52|O95906	Missense_Mutation	SNP	ENST00000404072.3	hg19	CCDS13965.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.124859	0.77436	.	.	ENSG00000100151	ENST00000404072;ENST00000356976	D;D	0.81821	-1.54;-1.54	4.57	3.48	0.39840	Arfaptin-like (3);	0.047265	0.85682	D	0.000000	D	0.89273	0.6668	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90458	0.4444	10	0.87932	D	0	-16.8451	11.8046	0.52147	0.3177:0.6823:0.0:0.0	.	312	Q9NRD5	PICK1_HUMAN	C	312	ENSP00000385205:R312C;ENSP00000349465:R312C	ENSP00000349465:R312C	R	+	1	0	PICK1	36800359	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.645000	0.54389	2.251000	0.74343	0.563000	0.77884	CGC	.	.		0.652	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407		T	38470413	C	T	38470413	3	4	23	1	0	0	0	0	1	0	0	0	11890	768	27	1	976	1	PICK1	22	38470413	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	155312	38470413	12834153	1110	3176										
GTPBP1	9567	hgsc.bcm.edu	37	chr22	39125562	39125562	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cccctgacgaaacgagacgaGgggggcccgtctggtgggcc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:39125562delG	ENST00000216044.5	+	11	2045	c.1812delG	c.(1810-1812)gagfs	p.E604fs		NM_004286.4	NP_004277.2	O00178	GTPB1_HUMAN	GTP binding protein 1	604					GTP catabolic process (GO:0006184)|immune response (GO:0006955)|positive regulation of mRNA catabolic process (GO:0061014)|signal transduction (GO:0007165)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	18	Melanoma(58;0.04)					AACGAGACGAGGGGGGCCCGT	0.607																																					p.E604fs		Pindel	.											.	GTPBP1	51	.	0			c.1811delA						.						29	27	27					22																	39125562		2202	4300	6502	SO:0001589	frameshift_variant	9567	exon11			.	U87964	CCDS13977.2	22q13.1	2008-07-01			ENSG00000100226	ENSG00000100226			4669	protein-coding gene	gene with protein product		602245				9070279	Standard	XM_005261857		Approved	GP-1, HSPC018	uc003awg.3	O00178	OTTHUMG00000151002	ENST00000216044.5:c.1812delG	chr22.hg19:g.39125562delG	ENSP00000216044:p.Glu604fs	179.0	0.0		180.0	20.0	NM_004286	Q6IC67	Frame_Shift_Del	DEL	ENST00000216044.5	hg19	CCDS13977.2																																																																																			.	.		0.607	GTPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075532.1	NM_004286		-	39125562	G	-	39125562	7	5	23	1	0	1	0	1	0	0	0	0	6887	991	35	0	1854	0	GTPBP1	22	39125562	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	655149	39125562	12179004	1111	3177										
CBX6	23466	hgsc.bcm.edu	37	chr22	39262901	39262901	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ccggcgcccccgccgccagcGcccttgtcgatcaccttcag	10	21	2	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:39262901G>A	ENST00000407418.3	-	5	675	c.552C>T	c.(550-552)ggC>ggT	p.G184G	CBX6_ENST00000216083.6_Silent_p.G166G			O95503	CBX6_HUMAN	chromobox homolog 6	184					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6	Melanoma(58;0.04)					cgccgccAGCGCCCTTGTCGA	0.677																																					p.G184G		Atlas-SNP	.											.	CBX6	26	.	0			c.C552T						.						10	11	11					22																	39262901		2189	4252	6441	SO:0001819	synonymous_variant	23466	exon5			GCCAGCGCCCTTG		CCDS13980.1	22q13.1	2013-04-23			ENSG00000183741	ENSG00000183741			1556	protein-coding gene	gene with protein product							Standard	NM_014292		Approved		uc003awl.3	O95503	OTTHUMG00000150456	ENST00000407418.3:c.552C>T	chr22.hg19:g.39262901G>A		86.0	0.0		73.0	17.0	NM_014292	A8KAH0|Q96EM5	Silent	SNP	ENST00000407418.3	hg19	CCDS13980.1																																																																																			.	.		0.677	CBX6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318190.1	NM_014292		A	39262901	G	A	39262901	2	1	23	1	0	0	0	0	0	0	0	1	2724	1074	38	1		1	CBX6	22	39262901	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	137339	39262901	12041665	1112	3178										
SMCR7L	54471	hgsc.bcm.edu	37	chr22	39908399	39908399	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcgggccaagcaagctgctgTggacatatgtgccgagctcc	13	12	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:39908399T>C	ENST00000325301.2	+	5	909	c.485T>C	c.(484-486)gTg>gCg	p.V162A	MIEF1_ENST00000402881.1_Missense_Mutation_p.V162A|MIEF1_ENST00000404569.1_Missense_Mutation_p.V162A	NM_019008.4	NP_061881.2	Q9NQG6	MID51_HUMAN	mitochondrial elongation factor 1	162	Dimerization.|Important for interaction with DNM1L.				mitochondrial fission (GO:0000266)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|GDP binding (GO:0019003)|identical protein binding (GO:0042802)										CAAGCTGCTGTGGACATATGT	0.597																																					p.V162A		Atlas-SNP	.											.	SMCR7L	33	.	0			c.T485C						.						51	49	50					22																	39908399		2203	4300	6503	SO:0001583	missense	54471	exon5			CTGCTGTGGACAT	AL365515	CCDS13995.1	22q13.1	2013-09-23	2013-09-23	2013-09-23	ENSG00000100335	ENSG00000100335			25979	protein-coding gene	gene with protein product		615497	"Smith-Magenis syndrome chromosome region, candidate 7-like"	SMCR7L		21508961, 21701560	Standard	NM_019008		Approved	FLJ20232, MiD51	uc003axx.3	Q9NQG6	OTTHUMG00000151105	ENST00000325301.2:c.485T>C	chr22.hg19:g.39908399T>C	ENSP00000327124:p.Val162Ala	58.0	0.0		64.0	23.0	NM_019008	Q7L890|Q9BUI3	Missense_Mutation	SNP	ENST00000325301.2	hg19	CCDS13995.1	.	.	.	.	.	.	.	.	.	.	T	12.41	1.929634	0.34096	.	.	ENSG00000100335	ENST00000402881;ENST00000325301;ENST00000404569	T;T;T	0.11712	2.75;2.77;2.77	5.67	5.67	0.87782	.	0.064498	0.64402	D	0.000007	T	0.10252	0.0251	L	0.36672	1.1	0.54753	D	0.999985	B;P	0.44006	0.231;0.824	B;B	0.41202	0.055;0.35	T	0.17471	-1.0368	10	0.09084	T	0.74	-20.4286	15.9007	0.79373	0.0:0.0:0.0:1.0	.	162;162	Q9NQG6;B0QY95	MID51_HUMAN;.	A	162	ENSP00000385110:V162A;ENSP00000327124:V162A;ENSP00000385191:V162A	ENSP00000327124:V162A	V	+	2	0	SMCR7L	38238345	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.009000	0.88606	2.158000	0.67659	0.477000	0.44152	GTG	.	.		0.597	MIEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321325.1	NM_019008		C	39908399	T	C	39908399	3	2	23	1	0	0	0	0	1	0	0	0	14806	1696	59	2	495	2	SMCR7L	22	39908399	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	645498	39908399	11396167	1113	3179										
ATF4	468	hgsc.bcm.edu	37	chr22	39918267	39918267	+	Frame_Shift_Del	DEL	G	G	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tcagcacagcccctctaccaGgggctctccaaataggagcc							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:39918267delG	ENST00000337304.2	+	2	1598	c.716delG	c.(715-717)aggfs	p.R239fs	ATF4_ENST00000396680.1_Frame_Shift_Del_p.R239fs|ATF4_ENST00000404241.2_Frame_Shift_Del_p.R239fs	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	239					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	CCCTCTACCAGGGGCTCTCCA	0.537																																					p.R239fs		Atlas-Indel,Pindel	.											.	ATF4	27	.	0			c.715delA						.						19	20	19					22																	39918267		2203	4299	6502	SO:0001589	frameshift_variant	468	exon3			.	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"basic leucine zipper proteins"	786	protein-coding gene	gene with protein product	"tax-responsive enhancer element B67"	604064	"activating transcription factor 4 (tax-responsive enhancer element B67)"	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.716delG	chr22.hg19:g.39918267delG	ENSP00000336790:p.Arg239fs	411.0	0.0		348.0	136.0	NM_182810	Q9UH31	Frame_Shift_Del	DEL	ENST00000337304.2	hg19	CCDS13996.1																																																																																			.	.		0.537	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		-	39918267	G	-	39918267	7	5	23	1	0	1	0	1	0	0	0	0	1082	1000	35	0	722	0	ATF4	22	39918267	Frame_Shift_Del	DEL	G	TCGA-4R-AA8I-01A-11D-A382-10	9868	39918267	11386299	1114	3180										
EFCAB6	64800	hgsc.bcm.edu	37	chr22	44067890	44067890	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgttaaaaatggacagaagaCgtgcatgattttcttgaaat	9	5	1	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:44067890C>T	ENST00000262726.7	-	15	1856	c.1603G>A	c.(1603-1605)Gtc>Atc	p.V535I	EFCAB6_ENST00000396231.2_Missense_Mutation_p.V383I	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	535	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				GGACAGAAGACGTGCATGATT	0.353																																					p.V535I		Atlas-SNP	.											.	EFCAB6	177	.	0			c.G1603A						.						104	101	102					22																	44067890		2203	4300	6503	SO:0001583	missense	64800	exon15			AGAAGACGTGCAT	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.1603G>A	chr22.hg19:g.44067890C>T	ENSP00000262726:p.Val535Ile	174.0	0.0		156.0	58.0	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	hg19	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	0.076	-1.193115	0.01607	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.30714	1.52;1.52	5.04	0.534	0.17127	EF-hand-like domain (1);	1.335570	0.04589	N	0.396360	T	0.20007	0.0481	N	0.17082	0.46	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.25082	-1.0142	10	0.36615	T	0.2	-2.2762	7.3377	0.26619	0.0:0.4606:0.0:0.5394	.	535	Q5THR3	EFCB6_HUMAN	I	383;535	ENSP00000379533:V383I;ENSP00000262726:V535I	ENSP00000262726:V535I	V	-	1	0	EFCAB6	42399223	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.238000	0.08977	-0.110000	0.12022	-0.367000	0.07326	GTC	.	.		0.353	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		T	44067890	C	T	44067890	3	4	23	1	0	0	0	0	1	0	0	0	4941	536	19	1	2974	1	EFCAB6	22	44067890	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	4149623	44067890	7236676	1115	3181										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46829297	46829297	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gggcccatcttaccttgttgTagtactgcacctgcacagag	10	12	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:46829297T>C	ENST00000262738.3	-	5	4603	c.4604A>G	c.(4603-4605)tAc>tGc	p.Y1535C		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1535	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TACCTTGTTGTAGTACTGCAC	0.647																																					p.Y1535C		Atlas-SNP	.											.	CELSR1	242	.	0			c.A4604G						.						65	56	59					22																	46829297		2203	4300	6503	SO:0001583	missense	9620	exon5			TTGTTGTAGTACT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.4604A>G	chr22.hg19:g.46829297T>C	ENSP00000262738:p.Tyr1535Cys	51.0	0.0		42.0	11.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.231476	0.79688	.	.	ENSG00000075275	ENST00000262738	T	0.78246	-1.16	4.62	4.62	0.57501	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.64402	U	0.000007	D	0.88145	0.6358	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89696	0.3901	10	0.62326	D	0.03	.	13.9979	0.64414	0.0:0.0:0.0:1.0	.	1535	Q9NYQ6	CELR1_HUMAN	C	1535	ENSP00000262738:Y1535C	ENSP00000262738:Y1535C	Y	-	2	0	CELSR1	45207961	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.335000	0.79234	1.857000	0.53885	0.533000	0.62120	TAC	.	.		0.647	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		C	46829297	T	C	46829297	3	2	23	1	0	0	0	0	1	0	0	0	3223	1638	57	2	4564	2	CELSR1	22	46829297	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2761407	46829297	4475269	1116	3182										
PLCXD1	55344	hgsc.bcm.edu	37	chrX	209880	209880	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaccatgaagagctgcggccGcccaggtaccaggtcgcccc	13	16	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:209880G>A	ENST00000381657.2	+	6	1242	c.728G>A	c.(727-729)cGc>cAc	p.R243H	PLCXD1_ENST00000399012.1_Missense_Mutation_p.R243H|PLCXD1_ENST00000381663.3_Missense_Mutation_p.R243H	NM_018390.3	NP_060860.1	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 1	243					lipid metabolic process (GO:0006629)		phosphoric diester hydrolase activity (GO:0008081)			endometrium(3)|large_intestine(1)|lung(7)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGCTGCGGCCGCCCAGGTACC	0.647																																					p.R243H		Atlas-SNP	.											.	PLCXD1	18	.	0			c.G728A						.						81	72	75					X																	209880		2203	4296	6499	SO:0001583	missense	55344	exon6			GCGGCCGCCCAGG	AK002185	CCDS14103.1	Xp22.33 and Yp11.32	2010-07-28			ENSG00000182378	ENSG00000182378		"Pseudoautosomal regions / PAR1"	23148	protein-coding gene	gene with protein product							Standard	NM_018390		Approved	FLJ11323	uc004cpc.3	Q9NUJ7	OTTHUMG00000022693	ENST00000381657.2:c.728G>A	chrX.hg19:g.209880G>A	ENSP00000371073:p.Arg243His	208.0	0.0		181.0	38.0	NM_018390	A2BH51|A2BH52	Missense_Mutation	SNP	ENST00000381657.2	hg19	CCDS14103.1	.	.	.	.	.	.	.	.	.	.	.	11.30	1.596973	0.28445	.	.	ENSG00000182378	ENST00000399012;ENST00000381657;ENST00000381663	T;T;T	0.31247	1.5;1.5;1.5	1.45	1.45	0.22620	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.124124	0.52532	N	0.000062	T	0.16854	0.0405	.	.	.	0.09310	N	1	P	0.51147	0.942	B	0.36134	0.218	T	0.16958	-1.0385	9	0.35671	T	0.21	-29.046	8.4059	0.32614	0.0:0.0:1.0:0.0	.	243	Q9NUJ7	PLCX1_HUMAN	H	243	ENSP00000381976:R243H;ENSP00000371073:R243H;ENSP00000371079:R243H	ENSP00000371073:R243H	R	+	2	0	PLCXD1	149880	0.998000	0.40836	0.572000	0.28498	0.390000	0.30446	5.640000	0.67875	0.768000	0.33290	0.394000	0.25966	CGC	.	.		0.647	PLCXD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058879.2	NM_018390		A	209880	G	A	209880	3	1	23	1	0	0	0	0	1	0	0	0	12050	1087	38	1	746	1	PLCXD1	23	209880	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10		209880	155060680	1117	3183										
CSF2RA	1438	hgsc.bcm.edu	37	chrX	1424529	1424529	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cttctccaccagatgggaccGcagcgtcaccaccggtgtgg	12	15	2	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:1424529G>A	ENST00000381524.3	+	12	1311				CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000432318.2_Intron|CSF2RA_ENST00000361536.3_Intron|CSF2RA_ENST00000501036.2_Intron|CSF2RA_ENST00000417535.2_Intron|CSF2RA_ENST00000355805.2_Intron|CSF2RA_ENST00000381500.1_Intron|CSF2RA_ENST00000355432.3_Intron|CSF2RA_ENST00000381509.3_Silent_p.P378P|CSF2RA_ENST00000381529.3_Intron|CSF2RA_ENST00000498153.1_Intron			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)						response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	AGATGGGACCGCAGCGTCACC	0.637																																					p.P378P	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.G1134A						.						121	127	125					X																	1424529		692	1591	2283	SO:0001627	intron_variant	1438	exon13			GGGACCGCAGCGT	M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"CD molecules", "Pseudoautosomal regions / PAR1"	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.1125+109G>A	chrX.hg19:g.1424529G>A		600.0	0.0		576.0	250.0	NM_001161531	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Silent	SNP	ENST00000381524.3	hg19	CCDS35191.1																																																																																			.	.		0.637	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2			A	1424529	G	A	1424529	1	1	23	0	1	0	0	0	0	0	0	0	3936	1074	38	1		1	CSF2RA	23	1424529	Intron	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1214649	1424529	153846031	1118	3184										
SHROOM2	357	hgsc.bcm.edu	37	chrX	9866241	9866241	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cctttgcaggaagcttctgtCgaactgcgaaggcaggcagg	14	10	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:9866241C>T	ENST00000380913.3	+	5	2892	c.2802C>T	c.(2800-2802)gtC>gtT	p.V934V	SHROOM2_ENST00000493668.1_3'UTR	NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	934					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				AAGCTTCTGTCGAACTGCGAA	0.577																																					p.V934V		Atlas-SNP	.											.	SHROOM2	139	.	0			c.C2802T						.						12	11	11					X																	9866241		2172	4266	6438	SO:0001819	synonymous_variant	357	exon5			TTCTGTCGAACTG	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"apical protein, Xenopus laevis-like", "apical protein-like (Xenopus laevis)"	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.2802C>T	chrX.hg19:g.9866241C>T		268.0	0.0		244.0	137.0	NM_001649	B9EIQ7	Silent	SNP	ENST00000380913.3	hg19	CCDS14135.1																																																																																			.	.		0.577	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649		T	9866241	C	T	9866241	2	4	23	1	0	0	0	0	0	0	0	1	14309	871	31	1		1	SHROOM2	23	9866241	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	8441712	9866241	145404319	1119	3185										
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765564	27765564	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gagacatctgccctgccccgAcctcgctggcaggtcgttac	11	16	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:27765564A>G	ENST00000451261.2	+	5	951	c.552A>G	c.(550-552)cgA>cgG	p.R184R		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	184										central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						CCCTGCCCCGACCTCGCTGGC	0.602																																					p.R184R		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.A552G						.						47	43	44					X																	27765564		692	1591	2283	SO:0001819	synonymous_variant	347442	exon1			GCCCCGACCTCGC		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.552A>G	chrX.hg19:g.27765564A>G		136.0	1.0		109.0	87.0	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.602	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		G	27765564	A	G	27765564	2	3	23	1	0	0	0	0	0	0	0	1	4280	262	10	2		2	DCAF8L2	23	27765564	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	17899323	27765564	127504996	1120	3186										
DMD	1756	hgsc.bcm.edu	37	chrX	31496268	31496268	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agagagtcaatgaggagatcGcccacgggctgccaggatcc	14	11	1	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:31496268G>A	ENST00000357033.4	-	59	9098	c.8892C>T	c.(8890-8892)ggC>ggT	p.G2964G	DMD_ENST00000445312.1_5'Flank|DMD_ENST00000378677.2_Silent_p.G2960G|DMD_ENST00000343523.2_Silent_p.G504G|DMD_ENST00000474231.1_Silent_p.G504G|DMD_ENST00000541735.1_Silent_p.G504G|DMD_ENST00000378707.3_Silent_p.G504G|DMD_ENST00000359836.1_Silent_p.G504G	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2964					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TGAGGAGATCGCCCACGGGCT	0.532																																					p.G2964G		Atlas-SNP	.											.	DMD	2127	.	0			c.C8892T						.						57	47	50					X																	31496268		2202	4300	6502	SO:0001819	synonymous_variant	1756	exon59			GAGATCGCCCACG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.8892C>T	chrX.hg19:g.31496268G>A		56.0	0.0		48.0	35.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	0.194	-1.050338	0.01981	.	.	ENSG00000198947	ENST00000465285	.	.	.	5.4	-10.8	0.00216	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6471	0.17596	0.1701:0.1452:0.4746:0.21	.	.	.	.	X	693	.	.	R	-	1	2	DMD	31406189	0.000000	0.05858	0.017000	0.16124	0.324000	0.28378	-2.946000	0.00680	-4.954000	0.00026	-1.515000	0.00940	CGA	.	.		0.532	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	31496268	G	A	31496268	2	1	23	1	0	0	0	0	0	0	0	1	4582	1074	38	1		1	DMD	23	31496268	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3730704	31496268	123774292	1121	3187										
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49127168	49127168	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ctgggccaacaaccacggccGcaactacacagtcctgctcc	8	18	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:49127168G>A	ENST00000055335.6	+	1	852	c.836G>A	c.(835-837)cGc>cAc	p.R279H	LL0XNC01-7P3.1_ENST00000602455.1_lincRNA|PPP1R3F_ENST00000495799.1_Intron|PPP1R3F_ENST00000438316.1_5'UTR|PPP1R3F_ENST00000466508.1_5'UTR	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	279	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)	p.R279H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					AACCACGGCCGCAACTACACA	0.682													G|||	1	0.000264901	0	0	3775	,	,		11622	0		0	False		,,,				2504	0.001				p.R279H		Atlas-SNP	.											.	PPP1R3F	56	.	1	Substitution - Missense(1)	endometrium(1)	c.G836A						.						31	20	24					X																	49127168		2200	4295	6495	SO:0001583	missense	89801	exon1			ACGGCCGCAACTA		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14944	protein-coding gene	gene with protein product			"protein phosphatase 1, regulatory (inhibitor) subunit 3F"			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.836G>A	chrX.hg19:g.49127168G>A	ENSP00000055335:p.Arg279His	78.0	0.0		83.0	66.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	hg19	CCDS35254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.99|15.99	2.995935|2.995935	0.54147|0.54147	.|.	.|.	ENSG00000049769|ENSG00000049769	ENST00000471261|ENST00000055335	.|T	.|0.64803	.|-0.12	4.06|4.06	3.09|3.09	0.35607|0.35607	.|Putative phosphatase regulatory subunit (2);	.|.	.|.	.|.	.|.	T|T	0.51432|0.51432	0.1674|0.1674	N|N	0.26092|0.26092	0.79|0.79	0.80722|0.80722	D|D	1|1	.|D	.|0.58620	.|0.983	.|P	.|0.49597	.|0.616	T|T	0.53995|0.53995	-0.8359|-0.8359	5|9	.|0.66056	.|D	.|0.02	-2.3334|-2.3334	4.9887|4.9887	0.14203|0.14203	0.177:0.0:0.823:0.0|0.177:0.0:0.823:0.0	.|.	.|279	.|Q6ZSY5	.|PPR3F_HUMAN	T|H	29|279	.|ENSP00000055335:R279H	.|ENSP00000055335:R279H	A|R	+|+	1|2	0|0	PPP1R3F|PPP1R3F	49014112|49014112	0.994000|0.994000	0.37717|0.37717	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	0.942000|0.942000	0.29017|0.29017	1.843000|1.843000	0.53566|0.53566	0.513000|0.513000	0.50165|0.50165	GCA|CGC	.	.		0.682	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		A	49127168	G	A	49127168	3	1	23	1	0	0	0	0	1	0	0	0	12387	1087	38	1	838	1	PPP1R3F	23	49127168	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	17630900	49127168	106143392	1122	3188										
WNK3	65267	hgsc.bcm.edu	37	chrX	54321142	54321142	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	agggaatacattccccatagActtgcactgagaatccctgc	8	12	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:54321142A>T	ENST00000375159.2	-	7	1536	c.1537T>A	c.(1537-1539)Tct>Act	p.S513T	WNK3_ENST00000354646.2_Missense_Mutation_p.S513T|WNK3_ENST00000375169.3_Missense_Mutation_p.S513T			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	513					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						TTCCCCATAGACTTGCACTGA	0.478																																					p.S513T		Atlas-SNP	.											.	WNK3	218	.	0			c.T1537A						.						94	84	87					X																	54321142		2203	4300	6503	SO:0001583	missense	65267	exon8			CCATAGACTTGCA	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.1537T>A	chrX.hg19:g.54321142A>T	ENSP00000364301:p.Ser513Thr	42.0	0.0		49.0	46.0	NM_001002838	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	hg19	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	A	4.087	0.014155	0.07959	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.70986	-0.5;-0.53;-0.53	4.74	3.47	0.39725	.	0.854177	0.09985	N	0.730552	T	0.54367	0.1854	L	0.27053	0.805	0.09310	N	1	B;B	0.31730	0.337;0.147	B;B	0.31614	0.133;0.063	T	0.43798	-0.9369	10	0.33141	T	0.24	-1.7498	5.4726	0.16678	0.6545:0.1741:0.0:0.1715	.	513;513	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	T	513	ENSP00000364312:S513T;ENSP00000346667:S513T;ENSP00000364301:S513T	ENSP00000346667:S513T	S	-	1	0	WNK3	54337867	0.000000	0.05858	0.477000	0.27303	0.282000	0.26991	-0.257000	0.08745	1.662000	0.50781	0.481000	0.45027	TCT	.	.		0.478	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		T	54321142	A	T	54321142	3	4	23	1	0	0	0	0	1	0	0	0	17394	275	10	4	3933	4	WNK3	23	54321142	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	5193974	54321142	100949418	1123	3189										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73963111	73963111	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccagggaattagcaagatgGccctgctttggattcttaag	11	8	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:73963111G>A	ENST00000055682.6	-	3	1892	c.1281C>T	c.(1279-1281)ggC>ggT	p.G427G		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	427					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						TAGCAAGATGGCCCTGCTTTG	0.428																																					p.G427G		Atlas-SNP	.											.	KIAA2022	262	.	0			c.C1281T						.						180	147	158					X																	73963111		2203	4300	6503	SO:0001819	synonymous_variant	340533	exon3			AAGATGGCCCTGC		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.1281C>T	chrX.hg19:g.73963111G>A		44.0	0.0		47.0	39.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Silent	SNP	ENST00000055682.6	hg19	CCDS35337.1																																																																																			.	.		0.428	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		A	73963111	G	A	73963111	2	1	23	1	0	0	0	0	0	0	0	1	8278	1190	42	3		3	KIAA2022	23	73963111	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	19641969	73963111	81307449	1124	3190										
ATRX	546	hgsc.bcm.edu	37	chrX	76920179	76920179	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgttttccagttcttttttTcccttcttctggctcatcat	4	11	5	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:76920179T>C	ENST00000373344.5	-	11	4112	c.3898A>G	c.(3898-3900)Aaa>Gaa	p.K1300E	ATRX_ENST00000395603.3_Missense_Mutation_p.K1262E|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1300	Interaction with DAXX.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						GTTCTTTTTTTCCCTTCTTCT	0.373			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.K1300E		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.A3898G						.						184	165	171					X																	76920179		2203	4296	6499	SO:0001583	missense	546	exon11			TTTTTTTCCCTTC	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.3898A>G	chrX.hg19:g.76920179T>C	ENSP00000362441:p.Lys1300Glu	58.0	0.0		34.0	25.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	hg19	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	T	10.27	1.303879	0.23736	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.92299	-3.01;-3.01	4.89	3.7	0.42460	.	0.081603	0.47852	U	0.000203	D	0.94169	0.8129	M	0.62723	1.935	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.80764	0.994;0.991;0.98	D	0.92170	0.5743	10	0.39692	T	0.17	-11.9863	10.3878	0.44152	0.149:0.0:0.0:0.851	.	1232;1262;1300	P46100-6;P46100-4;P46100	.;.;ATRX_HUMAN	E	1300;1262;1227	ENSP00000362441:K1300E;ENSP00000378967:K1262E	ENSP00000362441:K1300E	K	-	1	0	ATRX	76806835	1.000000	0.71417	0.679000	0.29978	0.174000	0.22865	3.566000	0.53805	0.611000	0.30052	-0.391000	0.06502	AAA	.	.		0.373	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		C	76920179	T	C	76920179	3	2	23	1	0	0	0	0	1	0	0	0	1208	1792	62	2	3680	2	ATRX	23	76920179	Missense_Mutation	SNP	T	TCGA-4R-AA8I-01A-11D-A382-10	2957068	76920179	78350381	1125	3191										
BRWD3	254065	hgsc.bcm.edu	37	chrX	79965042	79965042	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gacgtttgcgctgtgtcctgCgtaaagaacgcccacagcta	11	12	0	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:79965042C>T	ENST00000373275.4	-	21	2576	c.2360G>A	c.(2359-2361)cGc>cAc	p.R787H	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	787					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						CTGTGTCCTGCGTAAAGAACG	0.388																																					p.R787H		Atlas-SNP	.											.	BRWD3	251	.	0			c.G2360A						.						151	105	121					X																	79965042		2203	4300	6503	SO:0001583	missense	254065	exon21			GTCCTGCGTAAAG		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.2360G>A	chrX.hg19:g.79965042C>T	ENSP00000362372:p.Arg787His	72.0	0.0		87.0	64.0	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	hg19	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	C	18.42	3.619414	0.66787	.	.	ENSG00000165288	ENST00000373275	T	0.30182	1.54	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.38321	0.1036	M	0.79258	2.445	0.47407	D	0.999411	B	0.24721	0.11	B	0.18561	0.022	T	0.20907	-1.0261	9	.	.	.	-8.7575	18.3472	0.90326	0.0:1.0:0.0:0.0	.	787	Q6RI45	BRWD3_HUMAN	H	787	ENSP00000362372:R787H	.	R	-	2	0	BRWD3	79851698	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	5.628000	0.67791	2.273000	0.75805	0.600000	0.82982	CGC	.	.		0.388	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		T	79965042	C	T	79965042	3	4	23	1	0	0	0	0	1	0	0	0	1528	768	27	1	3132	1	BRWD3	23	79965042	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	3044863	79965042	75305518	1126	3192										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86877225	86877225	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttctaggaacacttcattgaGgtaataaaaaaccaagaatt	6	6	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:86877225G>T	ENST00000373119.4	+	5	1084	c.939G>T	c.(937-939)gaG>gaT	p.E313D	KLHL4_ENST00000373114.4_Missense_Mutation_p.E313D	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	313						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						ACTTCATTGAGGTAATAAAAA	0.323																																					p.E313D		Atlas-SNP	.											.	KLHL4	263	.	0			c.G939T						.						61	54	56					X																	86877225		2203	4300	6503	SO:0001583	missense	56062	exon5			CATTGAGGTAATA	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.939G>T	chrX.hg19:g.86877225G>T	ENSP00000362211:p.Glu313Asp	273.0	0.0		247.0	172.0	NM_019117	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	hg19	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.747727	0.30955	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.70749	-0.51;-0.51	5.48	1.5	0.22942	BTB/Kelch-associated (2);	0.112471	0.64402	N	0.000016	T	0.55625	0.1932	L	0.38649	1.16	0.47276	D	0.999373	B;B	0.20887	0.025;0.049	B;B	0.28916	0.074;0.096	T	0.37197	-0.9716	10	0.39692	T	0.17	.	3.7946	0.08734	0.2392:0.0:0.3173:0.4435	.	313;313	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	D	313	ENSP00000362211:E313D;ENSP00000362206:E313D	ENSP00000362206:E313D	E	+	3	2	KLHL4	86763881	1.000000	0.71417	0.925000	0.36789	0.901000	0.52897	2.111000	0.41883	-0.137000	0.11455	-0.322000	0.08575	GAG	.	.		0.323	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			T	86877225	G	T	86877225	3	4	23	1	0	0	0	0	1	0	0	0	8400	991	35	3	957	3	KLHL4	23	86877225	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	6912183	86877225	68393335	1127	3193										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91873881	91873881	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tttgacaaccttcactccacGccaacaggccagaccgtcca	6	17	1	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:91873881G>A	ENST00000373094.1	+	7	4831	c.3986G>A	c.(3985-3987)cGc>cAc	p.R1329H	PCDH11X_ENST00000373088.1_Missense_Mutation_p.R1292H|PCDH11X_ENST00000298274.8_Missense_Mutation_p.R1292H|PCDH11X_ENST00000361655.2_Missense_Mutation_p.R1311H|PCDH11X_ENST00000406881.1_Missense_Mutation_p.R1321H|PCDH11X_ENST00000373097.1_Missense_Mutation_p.R1319H|PCDH11X_ENST00000504220.2_3'UTR	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1329					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						TTCACTCCACGCCAACAGGCC	0.403																																					p.R1329H	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.G3986A						.						135	128	130					X																	91873881		2203	4300	6503	SO:0001583	missense	27328	exon7			CTCCACGCCAACA	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3986G>A	chrX.hg19:g.91873881G>A	ENSP00000362186:p.Arg1329His	225.0	0.0		199.0	24.0	NM_032968	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	hg19	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	G	6.890	0.533717	0.13188	.	.	ENSG00000102290	ENST00000373094;ENST00000373097;ENST00000373088;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T	0.54279	0.61;0.62;0.63;0.58;0.61;0.63	4.57	3.69	0.42338	.	.	.	.	.	T	0.29158	0.0725	N	0.08118	0	0.09310	N	1	P;P;P;P;P	0.49358	0.923;0.923;0.923;0.923;0.875	B;B;B;B;B	0.34722	0.188;0.188;0.188;0.188;0.092	T	0.03651	-1.1016	9	0.49607	T	0.09	.	12.3924	0.55366	0.0:0.3405:0.6595:0.0	.	1292;1311;1321;1319;1329	Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7	.;.;.;.;PC11X_HUMAN	H	1329;1319;1292;1311;1321;1329;1292	ENSP00000362186:R1329H;ENSP00000362189:R1319H;ENSP00000362180:R1292H;ENSP00000355105:R1311H;ENSP00000384758:R1321H;ENSP00000298274:R1292H	ENSP00000298274:R1292H	R	+	2	0	PCDH11X	91760537	0.004000	0.15560	0.005000	0.12908	0.074000	0.17049	1.310000	0.33551	0.704000	0.31869	0.459000	0.35465	CGC	.	.		0.403	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		A	91873881	G	A	91873881	3	1	23	1	0	0	0	0	1	0	0	0	11517	1087	38	1	4134	1	PCDH11X	23	91873881	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	4996656	91873881	63396679	1128	3194										
GUCY2F	2986	hgsc.bcm.edu	37	chrX	108691376	108691376	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ttgggtcctttgatcaactgGattttatttatacgacgcct	8	8	1	1			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:108691376G>A	ENST00000218006.2	-	6	1782	c.1491C>T	c.(1489-1491)atC>atT	p.I497I		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	497					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						TGATCAACTGGATTTTATTTA	0.408																																					p.I497I		Atlas-SNP	.											.	GUCY2F	178	.	0			c.C1491T						.						120	104	110					X																	108691376		2203	4300	6503	SO:0001819	synonymous_variant	2986	exon6			CAACTGGATTTTA	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.1491C>T	chrX.hg19:g.108691376G>A		76.0	0.0		73.0	63.0	NM_001522	Q9UJF1	Silent	SNP	ENST00000218006.2	hg19	CCDS14545.1																																																																																			.	.		0.408	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		A	108691376	G	A	108691376	2	1	23	1	0	0	0	0	0	0	0	1	6907	1164	41	3		3	GUCY2F	23	108691376	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	16817495	108691376	46579184	1129	3195										
NXT2	55916	hgsc.bcm.edu	37	chrX	108779154	108779154	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggtctcagggagacagagaaGgataccaaagaagaagtaac	13	6	1	4	rs142540133	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:108779154G>T	ENST00000372106.1	+	0	0				NXT2_ENST00000372107.1_5'Flank|NXT2_ENST00000218004.1_Nonsense_Mutation_p.G15*|NXT2_ENST00000372103.1_5'Flank	NM_001242617.1	NP_001229546.1	Q9NPJ8	NXT2_HUMAN	nuclear transport factor 2-like export factor 2						mRNA transport (GO:0051028)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	6						AGACAGAGAAGGATACCAAAG	0.393																																					p.G15X		Atlas-SNP	.											.	NXT2	16	.	0			c.G43T						.						67	58	61					X																	108779154		2203	4300	6503	SO:0001631	upstream_gene_variant	55916	exon1			AGAGAAGGATACC	AF246127	CCDS14546.1, CCDS56605.1, CCDS56606.1	Xq22.3	2008-02-05			ENSG00000101888	ENSG00000101888			18151	protein-coding gene	gene with protein product		300320				11073998	Standard	NM_018698		Approved	P15-2	uc004eoe.2	Q9NPJ8	OTTHUMG00000022185		chrX.hg19:g.108779154G>T	Exception_encountered	373.0	0.0		394.0	31.0	NM_018698	D3DUY1|Q0VAN8|Q5JYV5|Q5JYV6|Q5JYV7|Q9H8U0|Q9NQ64|Q9NRL7|Q9Y3M4|Q9Y3M5	Nonsense_Mutation	SNP	ENST00000372106.1	hg19	CCDS56605.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.000689	0.54254	.	.	ENSG00000101888	ENST00000218004	.	.	.	4.18	-5.42	0.02640	.	1.115670	0.06935	N	0.811772	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.0526	0.03574	0.2432:0.4283:0.1873:0.1412	.	.	.	.	X	15	.	ENSP00000218004:G15X	G	+	1	0	NXT2	108665810	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.162000	0.10012	-1.176000	0.02747	-0.384000	0.06662	GGA	.	G|1.000;C|0.000		0.393	NXT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057886.1	NM_018698		T	108779154	G	T	108779154	1	4	23	0	1	0	0	0	0	0	0	0	10804	1001	35	3		3	NXT2	23	108779154	5'Flank	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	87778	108779154	46491406	1130	3196										
AMOT	154796	hgsc.bcm.edu	37	chrX	112033910	112033910	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gctcccactttgtcatatcaGcttccagagccagaatcctc	6	15	2	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:112033910G>T	ENST00000524145.1	-	8	2101	c.2027C>A	c.(2026-2028)gCt>gAt	p.A676D	AMOT_ENST00000304758.1_Missense_Mutation_p.A267D|AMOT_ENST00000371959.3_Missense_Mutation_p.A676D|AMOT_ENST00000371958.1_Missense_Mutation_p.A444D|AMOT_ENST00000371962.1_Missense_Mutation_p.A444D			Q4VCS5	AMOT_HUMAN	angiomotin	676					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						TGTCATATCAGCTTCCAGAGC	0.498																																					p.A676D		Atlas-SNP	.											.	AMOT	204	.	0			c.C2027A						.						202	182	189					X																	112033910		2203	4300	6503	SO:0001583	missense	154796	exon7			ATATCAGCTTCCA	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.2027C>A	chrX.hg19:g.112033910G>T	ENSP00000429013:p.Ala676Asp	108.0	0.0		98.0	73.0	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	hg19	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	G	32	5.110473	0.94292	.	.	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145;ENST00000371958	T;T;T;T;T	0.29142	2.01;1.84;2.09;1.84;1.58	6.08	6.08	0.98989	Angiomotin, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.57666	0.2069	M	0.79123	2.44	0.80722	D	1	D	0.56968	0.978	D	0.65443	0.935	T	0.56768	-0.7924	10	0.48119	T	0.1	-13.2289	18.3623	0.90379	0.0:0.0:1.0:0.0	.	676	Q4VCS5	AMOT_HUMAN	D	267;676;444;676;444	ENSP00000305557:A267D;ENSP00000361027:A676D;ENSP00000361030:A444D;ENSP00000429013:A676D;ENSP00000361026:A444D	ENSP00000305557:A267D	A	-	2	0	AMOT	111920566	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.562000	0.86427	0.600000	0.82982	GCT	.	.		0.498	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		T	112033910	G	T	112033910	3	4	23	1	0	0	0	0	1	0	0	0	582	971	34	3	1247	3	AMOT	23	112033910	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	3254756	112033910	43236650	1131	3197										
BCORL1	63035	hgsc.bcm.edu	37	chrX	129185838	129185838	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atatgctccccttacagaggAaaaagacgggtttgcctgtg	11	9	0	2			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:129185838A>G	ENST00000218147.7	+	12	4897	c.4700A>G	c.(4699-4701)gAa>gGa	p.E1567G	BCORL1_ENST00000303743.5_Missense_Mutation_p.E1641G|BCORL1_ENST00000359304.2_Missense_Mutation_p.E1437G|BCORL1_ENST00000540052.1_Missense_Mutation_p.E1567G			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	1567					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						CTTACAGAGGAAAAAGACGGG	0.473																																					p.E1567G		Atlas-SNP	.											.	BCORL1	213	.	0			c.A4700G						.						202	188	192					X																	129185838		2203	4300	6503	SO:0001583	missense	63035	exon11			CAGAGGAAAAAGA	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.4700A>G	chrX.hg19:g.129185838A>G	ENSP00000218147:p.Glu1567Gly	91.0	0.0		102.0	91.0	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Missense_Mutation	SNP	ENST00000218147.7	hg19	CCDS14616.1	.	.	.	.	.	.	.	.	.	.	A	1.979	-0.434698	0.04669	.	.	ENSG00000085185	ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052;ENST00000456822	T;T;T;T;T	0.41065	1.01;1.44;1.01;1.01;1.5	5.53	1.67	0.24075	.	0.478772	0.15564	N	0.255788	T	0.09862	0.0242	N	0.00436	-1.5	0.21386	N	0.99971	B;B	0.06786	0.001;0.0	B;B	0.04013	0.0;0.001	T	0.29971	-0.9994	10	0.14656	T	0.56	0.3218	3.558	0.07871	0.3209:0.2323:0.4468:0.0	.	1641;1567	Q5H9F3-3;Q5H9F3	.;BCORL_HUMAN	G	1567;1641;1437;1567;1241	ENSP00000218147:E1567G;ENSP00000307541:E1641G;ENSP00000352253:E1437G;ENSP00000437775:E1567G;ENSP00000399483:E1241G	ENSP00000218147:E1567G	E	+	2	0	BCORL1	129013519	1.000000	0.71417	0.399000	0.26333	0.831000	0.47069	2.055000	0.41345	0.210000	0.20664	0.417000	0.27973	GAA	.	.		0.473	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		G	129185838	A	G	129185838	3	3	23	1	0	0	0	0	1	0	0	0	1387	246	9	2	4968	2	BCORL1	23	129185838	Missense_Mutation	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10	17151928	129185838	26084722	1132	3198										
GPR101	83550	hgsc.bcm.edu	37	chrX	136112908	136112909	+	Frame_Shift_Del	DEL	CT	CT	-													0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	cgtcgctggccaccgtgctgCtctctctgacctcctcgctg							TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:136112908_136112909delCT	ENST00000298110.1	-	1	924_925	c.925_926delAG	c.(925-927)agcfs	p.S310fs		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	310						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					CACCGTGCTGCTCTCTCTGACC	0.599																																					p.309_309del		Atlas-Indel,Pindel	.											.	GPR101	96	.	0			c.926_927del						.																																			SO:0001589	frameshift_variant	83550	exon1			.	AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.925_926delAG	chrX.hg19:g.136112914_136112915delCT	ENSP00000298110:p.Ser310fs	51.0	0.0		47.0	40.0	NM_054021	Q5JSM8|Q8NG93	Frame_Shift_Del	DEL	ENST00000298110.1	hg19	CCDS14662.1																																																																																			.	.		0.599	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			-	136112909	CT	-	136112908	7	5	23	1	0	1	0	1	0	0	0	0	6630	797	28	0	603	0	GPR101	23	136112908	Frame_Shift_Del	DEL	CT	TCGA-4R-AA8I-01A-11D-A382-10	6927070	136112908	19157652	1133	3199										
PNMA5	114824	hgsc.bcm.edu	37	chrX	152158844	152158844	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	atggccccagcccctgcctcGtttcccaactcctctcctgc	6	21	1	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:152158844G>A	ENST00000439251.1	-	2	1737	c.1299C>T	c.(1297-1299)aaC>aaT	p.N433N	PNMA5_ENST00000361887.5_Silent_p.N433N|PNMA5_ENST00000535214.1_Silent_p.N433N|PNMA5_ENST00000452693.1_Silent_p.N433N	NM_001103150.1	NP_001096620.1	Q96PV4	PNMA5_HUMAN	paraneoplastic Ma antigen family member 5	433					positive regulation of apoptotic process (GO:0043065)					breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					CCCCTGCCTCGTTTCCCAACT	0.612																																					p.N433N		Atlas-SNP	.											.	PNMA5	63	.	0			c.C1299T						.						102	81	88					X																	152158844		2203	4300	6503	SO:0001819	synonymous_variant	114824	exon2			TGCCTCGTTTCCC	AB067521	CCDS14718.1	Xq28	2012-02-09	2012-02-09		ENSG00000198883	ENSG00000198883		"Paraneoplastic Ma antigens"	18743	protein-coding gene	gene with protein product	"paraneoplastic antigen family 5"	300916	"paraneoplastic antigen like 5"			16214224	Standard	NM_052926		Approved	KIAA1934	uc004fgy.4	Q96PV4	OTTHUMG00000024184	ENST00000439251.1:c.1299C>T	chrX.hg19:g.152158844G>A		61.0	0.0		70.0	51.0	NM_001103150	B4DI72|B7Z9Y9|Q495L5|Q8NET3	Silent	SNP	ENST00000439251.1	hg19	CCDS14718.1																																																																																			.	.		0.612	PNMA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060925.1	NM_052926		A	152158844	G	A	152158844	2	1	23	1	0	0	0	0	0	0	0	1	12165	1136	40	1		1	PNMA5	23	152158844	Silent	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	16045936	152158844	3111716	1134	3200										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153138119	153138119	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggaagacaaccaggcgccgtGgagactgttccgtgatgaca	14	10	0	4			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:153138119G>A	ENST00000370060.1	-	4	314	c.125C>T	c.(124-126)cCa>cTa	p.P42L	L1CAM_ENST00000538883.1_Missense_Mutation_p.P44L|L1CAM_ENST00000361699.4_Missense_Mutation_p.P42L|L1CAM_ENST00000370055.1_Missense_Mutation_p.P37L|L1CAM_ENST00000361981.3_Missense_Mutation_p.P37L|L1CAM_ENST00000543994.1_Missense_Mutation_p.P44L|L1CAM_ENST00000370057.3_Missense_Mutation_p.P42L	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	42	Ig-like C2-type 1.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGCGCCGTGGAGACTGTTC	0.602																																					p.P42L		Atlas-SNP	.											.	L1CAM	189	.	0			c.C125T						.						112	82	92					X																	153138119		2203	4300	6503	SO:0001583	missense	3897	exon3			CGCCGTGGAGACT	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.125C>T	chrX.hg19:g.153138119G>A	ENSP00000359077:p.Pro42Leu	115.0	0.0		101.0	73.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	hg19	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.629893	0.87660	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699;ENST00000439496;ENST00000407935;ENST00000420165;ENST00000458029	T;T;T;T;T;T;T;T;T;T;D	0.96491	-1.34;-1.34;-1.34;-1.34;-1.34;-1.34;-1.34;-1.34;-1.34;-1.34;-4.03	4.69	4.69	0.59074	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000011	D	0.96759	0.8942	M	0.78456	2.415	0.80722	D	1	P;P;P	0.52577	0.944;0.858;0.954	P;P;P	0.53266	0.696;0.661;0.722	D	0.96651	0.9481	10	0.62326	D	0.03	.	11.2495	0.49017	0.0:0.0:0.8168:0.1832	.	37;42;42	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	L	42;44;42;44;37;37;42;42;37;37;42	ENSP00000359077:P42L;ENSP00000438430:P44L;ENSP00000359074:P42L;ENSP00000439645:P44L;ENSP00000354712:P37L;ENSP00000359072:P37L;ENSP00000355380:P42L;ENSP00000402407:P42L;ENSP00000384902:P37L;ENSP00000392524:P37L;ENSP00000396079:P42L	ENSP00000355380:P42L	P	-	2	0	L1CAM	152791313	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	3.707000	0.54838	2.176000	0.68965	0.529000	0.55759	CCA	.	.		0.602	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		A	153138119	G	A	153138119	3	1	23	1	0	0	0	0	1	0	0	0	8597	1348	47	3	3752	3	L1CAM	23	153138119	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	979275	153138119	2132441	1135	3201										
MECP2	4204	hgsc.bcm.edu	37	chrX	153296806	153296806	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	ggctccctctcccagttaccGtgaagtcaaaatcattaggg	9	12	3	1	rs28934906		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:153296806G>A	ENST00000303391.6	-	4	722	c.473C>T	c.(472-474)aCg>aTg	p.T158M	MECP2_ENST00000460227.1_5'Flank|MECP2_ENST00000407218.1_Intron|MECP2_ENST00000453960.2_Missense_Mutation_p.T170M	NM_004992.3	NP_004983.1	P51608	MECP2_HUMAN	methyl CpG binding protein 2	158	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.		T -> A (in RTT). {ECO:0000269|PubMed:11269512, ECO:0000269|PubMed:15057977}.|T -> M (in RTT; dbSNP:rs28934906). {ECO:0000269|PubMed:10508514, ECO:0000269|PubMed:10577905, ECO:0000269|PubMed:10745042, ECO:0000269|PubMed:10767337, ECO:0000269|PubMed:10814719, ECO:0000269|PubMed:10944854, ECO:0000269|PubMed:10991688, ECO:0000269|PubMed:10991689, ECO:0000269|PubMed:11055898, ECO:0000269|PubMed:11241840, ECO:0000269|PubMed:11269512, ECO:0000269|PubMed:11376998, ECO:0000269|PubMed:11402105, ECO:0000269|PubMed:11738883, ECO:0000269|PubMed:12567420, ECO:0000269|PubMed:12966523, ECO:0000269|PubMed:15057977}.		adult locomotory behavior (GO:0008344)|behavioral fear response (GO:0001662)|cardiolipin metabolic process (GO:0032048)|catecholamine secretion (GO:0050432)|cerebellum development (GO:0021549)|chromatin silencing (GO:0006342)|dendrite development (GO:0016358)|glucocorticoid metabolic process (GO:0008211)|glutamine metabolic process (GO:0006541)|histone acetylation (GO:0016573)|histone methylation (GO:0016571)|inositol metabolic process (GO:0006020)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone methylation (GO:0031061)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron maturation (GO:0042551)|pathogenesis (GO:0009405)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|proprioception (GO:0019230)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|startle response (GO:0001964)|synapse assembly (GO:0007416)|transcription, DNA-templated (GO:0006351)|ventricular system development (GO:0021591)|visual learning (GO:0008542)	cytosol (GO:0005829)|extracellular space (GO:0005615)|heterochromatin (GO:0000792)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|siRNA binding (GO:0035197)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCAGTTACCGTGAAGTCAAA	0.562																																					p.T170M		Atlas-SNP	.											.	MECP2	41	.	0			c.C509T	GRCh37	CM992178	MECP2	M	rs28934906	.						71	68	69					X																	153296806		2203	4300	6503	SO:0001583	missense	4204	exon3			GTTACCGTGAAGT	AF158180	CCDS14741.1, CCDS48193.1	Xq28	2014-09-17	2014-06-18		ENSG00000169057	ENSG00000169057			6990	protein-coding gene	gene with protein product		300005	"mental retardation, X-linked 16", "mental retardation, X-linked 79", "Rett syndrome", "methyl CpG binding protein 2 (Rett syndrome)"	RTT, MRX16, MRX79		1606614, 10508514	Standard	NM_004992		Approved		uc004fjw.2	P51608	OTTHUMG00000024229	ENST00000303391.6:c.473C>T	chrX.hg19:g.153296806G>A	ENSP00000301948:p.Thr158Met	98.0	0.0		79.0	68.0	NM_001110792	O15233|Q6QHH9|Q7Z384	Missense_Mutation	SNP	ENST00000303391.6	hg19	CCDS14741.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.860099	0.71834	.	.	ENSG00000169057	ENST00000303391;ENST00000545451;ENST00000453960;ENST00000369964	D;D	0.99436	-5.9;-5.9	5.48	5.48	0.80851	Methyl-CpG DNA binding (4);DNA-binding, integrase-type (1);	0.000000	0.85682	D	0.000000	D	0.99290	0.9752	L	0.50333	1.59	0.80722	A	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99758	1.1020	9	0.87932	D	0	-12.1252	17.0301	0.86458	0.0:0.0:1.0:0.0	rs28934906	170;158	P51608-2;P51608	.;MECP2_HUMAN	M	158;158;170;158	ENSP00000301948:T158M;ENSP00000395535:T170M	ENSP00000301948:T158M	T	-	2	0	MECP2	152950000	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.283000	0.95860	2.285000	0.76669	0.600000	0.82982	ACG	.	G|1.000;|0.000		0.562	MECP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061144.1	NM_004992		A	153296806	G	A	153296806	3	1	23	1	0	0	0	0	1	0	0	0	9432	1145	40	1	991	1	MECP2	23	153296806	Missense_Mutation	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	158687	153296806	1973754	1136	3202										
FLNA	2316	hgsc.bcm.edu	37	chrX	153599342	153599342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tgggccgctggttgtgcttgCggtgcatcttcttctggctg	15	10	3	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:153599342C>T	ENST00000369850.3	-	2	508	c.272G>A	c.(271-273)cGc>cAc	p.R91H	FLNA_ENST00000344736.4_Missense_Mutation_p.R91H|FLNA_ENST00000422373.1_Missense_Mutation_p.R91H|FLNA_ENST00000360319.4_Missense_Mutation_p.R91H	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	91	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GTTGTGCTTGCGGTGCATCTT	0.607																																					p.R91H		Atlas-SNP	.											.	FLNA	373	.	0			c.G272A						.						55	52	53					X																	153599342		2201	4298	6499	SO:0001583	missense	2316	exon2			TGCTTGCGGTGCA	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.272G>A	chrX.hg19:g.153599342C>T	ENSP00000358866:p.Arg91His	87.0	0.0		86.0	4.0	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	hg19	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.856260	0.71834	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.94931	-3.56;-3.56;-3.56;-3.56	5.13	5.13	0.70059	Calponin homology domain (5);	0.071778	0.52532	D	0.000062	D	0.96024	0.8705	L	0.57536	1.79	0.80722	D	1	B;D	0.69078	0.063;0.997	B;P	0.60473	0.016;0.875	D	0.96469	0.9347	10	0.66056	D	0.02	.	17.3547	0.87332	0.0:1.0:0.0:0.0	.	91;91	P21333-2;P21333	.;FLNA_HUMAN	H	91;64;91;91;91	ENSP00000353467:R91H;ENSP00000416926:R91H;ENSP00000358866:R91H;ENSP00000358863:R91H	ENSP00000358863:R91H	R	-	2	0	FLNA	153252536	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.630000	0.83225	2.131000	0.65755	0.525000	0.51046	CGC	.	.		0.607	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			T	153599342	C	T	153599342	3	4	23	1	0	0	0	0	1	0	0	0	5941	768	27	1	7859	1	FLNA	23	153599342	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	302536	153599342	1671218	1137	3203										
SPRY3	10251	hgsc.bcm.edu	37	chrX	155004148	155004148	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tccactgatgatgaagacaaCtgtgctgatgagccctgctc	10	11	0	6			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:155004148C>T	ENST00000302805.2	+	2	1046	c.615C>T	c.(613-615)aaC>aaT	p.N205N		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	205	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)						all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ATGAAGACAACTGTGCTGATG	0.562																																					p.N205N		Atlas-SNP	.											.	SPRY3	52	.	0			c.C615T						.	C		0,4406		0,0,2203	265	235	245		615	2.9	1	X		245	1,8591		0,1,4295	no	coding-synonymous	SPRY3	NM_005840.1		0,1,6498	TT,TC,CC		0.0116,0.0,0.0077		205/289	155004148	1,12997	2203	4296	6499	SO:0001819	synonymous_variant	10251	exon2			AGACAACTGTGCT	AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"Pseudoautosomal regions / PAR2"	11271	protein-coding gene	gene with protein product	"antagonist of FGF signaling"	300531	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.615C>T	chrX.hg19:g.155004148C>T		154.0	0.0		154.0	57.0	NM_005840	A8K0H8	Silent	SNP	ENST00000302805.2	hg19	CCDS14769.4	.	.	.	.	.	.	.	.	.	.	C	4.447	0.082729	0.08533	0.0	1.16E-4	ENSG00000168939	ENST00000369437	.	.	.	2.94	2.94	0.34122	.	.	.	.	.	T	0.46483	0.1395	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.40213	-0.9575	5	0.87932	D	0	-14.1758	10.9825	0.47504	0.0:1.0:0.0:0.0	.	.	.	.	I	106	.	ENSP00000358445:T106I	T	+	2	0	SPRY3	154657342	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	1.648000	0.37271	1.494000	0.48533	0.279000	0.19357	ACT	.	.		0.562	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840		T	155004148	C	T	155004148	2	4	23	1	0	0	0	0	0	0	0	1	15122	564	20	3		3	SPRY3	23	155004148	Silent	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	1404806	155004148	266412	1138	3204										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	5369160	5369160	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	gaaagcagcagtgatggtggActgggagaccatgatgcagg	17	6	0	3			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrY:5369160A>T	ENST00000215473.6	+	3	3192	c.3192A>T	c.(3190-3192)ggA>ggT	p.G1064G				Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	1064					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						GTGATGGTGGACTGGGAGACC	0.532																																					p.G1064G		Atlas-SNP	.											.	PCDH11Y	163	.	0			c.A3192T						.																																			SO:0001819	synonymous_variant	83259	exon3			TGGTGGACTGGGA	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000215473.6:c.3192A>T	chrY.hg19:g.5369160A>T		413.0	2.0		411.0	288.0	NM_032973	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Silent	SNP	ENST00000215473.6	hg19																																																																																				.	.		0.532	PCDH11Y-201	KNOWN	basic	protein_coding	protein_coding		NM_032973		T	5369160	A	T	5369160	2	4	23	1	0	0	0	0	0	0	0	1	11518	262	10	4		4	PCDH11Y	24	5369160	Silent	SNP	A	TCGA-4R-AA8I-01A-11D-A382-10		5369160	54004406	1139	3205										
DDX3Y	8653	hgsc.bcm.edu	37	chrY	15026814	15026814	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	aggaaaatggaaggtatgggCgccgcaaacaatatccaata	11	7	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrY:15026814C>T	ENST00000336079.3	+	9	884	c.778C>T	c.(778-780)Cgc>Tgc	p.R260C	DDX3Y_ENST00000463199.1_3'UTR|DDX3Y_ENST00000360160.4_Missense_Mutation_p.R260C	NM_001122665.1|NM_004660.3	NP_001116137.1|NP_004651.2	O15523	DDX3Y_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, Y-linked	260	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			kidney(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	5						AAGGTATGGGCGCCGCAAACA	0.308																																					p.R260C		Atlas-SNP	.											.	DDX3Y	13	.	0			c.C778T						.						31	31	31					Y																	15026814		580	1901	2481	SO:0001583	missense	8653	exon9			TATGGGCGCCGCA	AF000984	CCDS14782.1	Yq11	2013-07-16	2013-07-16	2003-06-20	ENSG00000067048	ENSG00000067048		"DEAD-boxes"	2699	protein-coding gene	gene with protein product		400010	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide, Y chromosome", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked"	DBY		9381176	Standard	NM_004660		Approved		uc004fsv.2	O15523	OTTHUMG00000036324	ENST00000336079.3:c.778C>T	chrY.hg19:g.15026814C>T	ENSP00000336725:p.Arg260Cys	179.0	0.0		148.0	121.0	NM_004660	B4DK29|B4DXX7|Q8IYV7	Missense_Mutation	SNP	ENST00000336079.3	hg19	CCDS14782.1																																																																																			.	.		0.308	DDX3Y-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088407.1	NM_004660		T	15026814	C	T	15026814	3	4	23	1	0	0	0	0	1	0	0	0	4361	768	27	1	812	1	DDX3Y	24	15026814	Missense_Mutation	SNP	C	TCGA-4R-AA8I-01A-11D-A382-10	9657654	15026814	44346752	1140	3206										
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16942179	16942179	+	3'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0105448154657293	12	1	0.193452155445821	1.08615324776352	0.166141988185624	0.0116425658138673	0.241259836031806	0	tggccaccgccgacctgcacGcgcagtacggctcccccacc	10	21	0	0			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrY:16942179G>A	ENST00000476359.1	+	0	1926							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						CGACCTGCACGCGCAGTACGG	0.617																																					p.A461T		Atlas-SNP	.											.	NLGN4Y	44	.	0			c.G1381A						.																																			SO:0001624	3_prime_UTR_variant	22829	exon5			CTGCACGCGCAGT		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*1923G>A	chrY.hg19:g.16942179G>A		247.0	0.0		197.0	163.0	NM_014893	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Missense_Mutation	SNP	ENST00000476359.1	hg19																																																																																				.	.		0.617	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		A	16942179	G	A	16942179	1	1	23	0	1	0	0	0	0	0	0	0	10474	1087	38	1		1	NLGN4Y	24	16942179	3'UTR	SNP	G	TCGA-4R-AA8I-01A-11D-A382-10	1915365	16942179	42431387	1141	3207										
CDA	978	hgsc.bcm.edu	37	chr1	20940339	20940339	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttctttgcttccccagtgacAtgcaagatgattttatctct	6	10	2	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:20940339A>G	ENST00000375071.3	+	3	453	c.271A>G	c.(271-273)Atg>Gtg	p.M91V	CDA_ENST00000461985.1_Intron	NM_001785.2	NP_001776.1	P32320	CDD_HUMAN	cytidine deaminase	91	CMP/dCMP deaminase zinc-binding.				cell surface receptor signaling pathway (GO:0007166)|cytidine deamination (GO:0009972)|cytosine metabolic process (GO:0019858)|negative regulation of cell growth (GO:0030308)|negative regulation of nucleotide metabolic process (GO:0045980)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine-containing compound salvage (GO:0008655)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	cytidine deaminase activity (GO:0004126)|nucleoside binding (GO:0001882)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)	CCCCAGTGACATGCAAGATGA	0.468																																					p.M91V	Pancreas(74;49 1356 2772 27818 40529)	Atlas-SNP	.											.	CDA	19	.	0			c.A271G						.						133	111	119					1																	20940339		2203	4300	6503	SO:0001583	missense	978	exon3			AGTGACATGCAAG	BC054036	CCDS210.1	1p36.2-p35	2008-02-05			ENSG00000158825	ENSG00000158825	3.5.4.5		1712	protein-coding gene	gene with protein product		123920				8422236, 9878810	Standard	NM_001785		Approved	CDD	uc001bdk.3	P32320	OTTHUMG00000002845	ENST00000375071.3:c.271A>G	chr1.hg19:g.20940339A>G	ENSP00000364212:p.Met91Val	80.0	0.0		68.0	6.0	NM_001785		Missense_Mutation	SNP	ENST00000375071.3	hg19	CCDS210.1	.	.	.	.	.	.	.	.	.	.	A	1.698	-0.502234	0.04261	.	.	ENSG00000158825	ENST00000375071	T	0.41065	1.01	5.38	-10.1	0.00402	APOBEC/CMP deaminase, zinc-binding (1);Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.426630	0.24182	N	0.040793	T	0.10637	0.0260	N	0.12422	0.21	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.42515	-0.9447	10	0.02654	T	1	.	1.7827	0.03035	0.3143:0.3583:0.1065:0.2208	.	91	P32320	CDD_HUMAN	V	91	ENSP00000364212:M91V	ENSP00000364212:M91V	M	+	1	0	CDA	20812926	0.000000	0.05858	0.894000	0.35097	0.770000	0.43624	-4.067000	0.00302	-1.137000	0.02888	-0.669000	0.03829	ATG	.	.		0.468	CDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007965.1	NM_001785		G	20940339	A	G	20940339	3	3	24	1	0	0	0	0	1	0	0	0	3054	217	8	2	281	2	CDA	1	20940339	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10		20940339	228310282	1	3208										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70300494	70300494	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gcttcacacagctcctaaacCtgacccagctctacctgaat	5	16	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:70300494C>T	ENST00000035383.5	+	4	448	c.418C>T	c.(418-420)Ctg>Ttg	p.L140L	LRRC7_ENST00000370958.1_Silent_p.L178L|LRRC7_ENST00000310961.5_Silent_p.L145L|LRRC7_ENST00000415775.2_5'UTR	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	140						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						GCTCCTAAACCTGACCCAGCT	0.348																																					p.L140L		Atlas-SNP	.											.	LRRC7	400	.	0			c.C418T						.						156	146	149					1																	70300494		2203	4300	6503	SO:0001819	synonymous_variant	57554	exon4			CTAAACCTGACCC		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.418C>T	chr1.hg19:g.70300494C>T		96.0	0.0		106.0	18.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Silent	SNP	ENST00000035383.5	hg19	CCDS645.1																																																																																			.	.		0.348	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		T	70300494	C	T	70300494	2	4	24	1	0	0	0	0	0	0	0	1	9029	680	24	3		3	LRRC7	1	70300494	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	49360155	70300494	178950127	2	3209										
TNNI3K	100144878	hgsc.bcm.edu	37	chr1	74957809	74957809	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tcctgcatcaagtaacagcaGtgggtctctctcaccttctt	7	13	4	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:74957809G>A	ENST00000294635.4	-	2	89				TNNI3K_ENST00000370891.2_Missense_Mutation_p.S838N|TNNI3K_ENST00000326637.3_Missense_Mutation_p.S737N|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.S851N			A6NM62	LRC53_HUMAN	leucine rich repeat containing 53							integral component of membrane (GO:0016021)				NS(1)|breast(1)|lung(2)	4						AGTAACAGCAGTGGGTCTCTC	0.463																																					p.S838N		Atlas-SNP	.											.	.	.	.	0			c.G2513A						.						203	204	203					1																	74957809		2203	4300	6503	SO:0001627	intron_variant	100526835	exon25			ACAGCAGTGGGTC			1p31.3	2010-08-31			ENSG00000162621	ENSG00000162621			25255	protein-coding gene	gene with protein product							Standard			Approved			A6NM62	OTTHUMG00000009621	ENST00000294635.4:c.26-8750C>T	chr1.hg19:g.74957809G>A		151.0	0.0		117.0	29.0	NM_001112808		Missense_Mutation	SNP	ENST00000294635.4	hg19		.	.	.	.	.	.	.	.	.	.	G	30	5.052662	0.93793	.	.	ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000557284;ENST00000370891;ENST00000326637	T;T;T	0.75050	-0.9;-0.9;-0.88	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.72309	0.3444	N	0.19112	0.55	0.58432	D	0.999995	D;D	0.67145	0.993;0.996	D;D	0.75484	0.968;0.986	T	0.69525	-0.5122	10	0.25106	T	0.35	.	19.8247	0.96612	0.0:0.0:1.0:0.0	.	737;838	Q59H18;Q59H18-1	TNI3K_HUMAN;.	N	838;838;737	ENSP00000450895:S838N;ENSP00000359928:S838N;ENSP00000322251:S737N	ENSP00000322251:S737N	S	+	2	0	RP11-653A5.2;AC093158.1	74730397	1.000000	0.71417	0.991000	0.47740	0.954000	0.61252	5.987000	0.70571	2.696000	0.92011	0.655000	0.94253	AGT	.	.		0.463	LRRC53-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000026515.2			A	74957809	G	A	74957809	1	1	24	0	1	0	0	0	0	0	0	0	16344	1029	36	3		3	TNNI3K	1	74957809	Intron	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	4657315	74957809	174292812	3	3210										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117156546	117156546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gaggcggaaggtggtcctccCcagcttgtccagccgcacct	13	15	0	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:117156546C>T	ENST00000369486.3	-	4	1438	c.673G>A	c.(673-675)Ggg>Agg	p.G225R	IGSF3_ENST00000369483.1_Missense_Mutation_p.G225R|IGSF3_ENST00000318837.6_Missense_Mutation_p.G225R	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	225	Ig-like C2-type 2.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		GTGGTCCTCCCCAGCTTGTCC	0.627																																					p.G225R		Atlas-SNP	.											.	IGSF3	294	.	0			c.G673A						.						34	34	34					1																	117156546		2202	4295	6497	SO:0001583	missense	3321	exon4			TCCTCCCCAGCTT	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.673G>A	chr1.hg19:g.117156546C>T	ENSP00000358498:p.Gly225Arg	138.0	0.0		124.0	27.0	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.069490	0.76301	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.22539	1.95;1.95;1.95	4.77	4.77	0.60923	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054090	0.85682	D	0.000000	T	0.38374	0.1038	M	0.75085	2.285	0.46336	D	0.99899	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.17198	-1.0377	10	0.52906	T	0.07	-49.4997	15.3267	0.74168	0.0:1.0:0.0:0.0	.	225;225	O75054;A6NJZ6	IGSF3_HUMAN;.	R	225	ENSP00000358498:G225R;ENSP00000358495:G225R;ENSP00000321184:G225R	ENSP00000321184:G225R	G	-	1	0	IGSF3	116958069	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.743000	0.47442	2.470000	0.83445	0.557000	0.71058	GGG	.	.		0.627	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		T	117156546	C	T	117156546	3	4	24	1	0	0	0	0	1	0	0	0	7610	623	22	3	3007	3	IGSF3	1	117156546	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	42198737	117156546	132094075	4	3211										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144868126	144868126	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gaagagtcggcttccaagtcGttgctcagcaatgtagctgt	12	9	1	1	rs369950064		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:144868126G>A	ENST00000369354.3	-	33	5502	c.5313C>T	c.(5311-5313)aaC>aaT	p.N1771N	PDE4DIP_ENST00000313382.9_Silent_p.N1665N|PDE4DIP_ENST00000369359.4_Silent_p.N1907N|PDE4DIP_ENST00000369356.4_Silent_p.N1771N|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000530740.1_Silent_p.N1856N|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1771					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTTCCAAGTCGTTGCTCAGCA	0.522			T	PDGFRB	MPD								.|||	1	0.000199681	0	0	5008	,	,		37801	0		0	False		,,,				2504	0.001				p.N1771N		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C5313T						.	G	,,	0,4406		0,0,2203	123	127	126		4995,5313,5313	1.1	0.1	1		126	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	,,	1665/2241,1771/2363,1771/2347	144868126	1,12997	2203	4296	6499	SO:0001819	synonymous_variant	9659	exon33			CAAGTCGTTGCTC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.5313C>T	chr1.hg19:g.144868126G>A		99.0	0.0		185.0	9.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	hg19	CCDS30824.1																																																																																			.	.		0.522	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		A	144868126	G	A	144868126	2	1	24	1	0	0	0	0	0	0	0	1	11652	1136	40	1		1	PDE4DIP	1	144868126	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	27711580	144868126	104382495	5	3212										
TCHH	7062	hgsc.bcm.edu	37	chr1	152080721	152080721	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gtcgtgacgcagctgttgttCgcgctcctggcggcgcagct	15	13	0	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:152080721C>T	ENST00000368804.1	-	2	4971	c.4972G>A	c.(4972-4974)Gaa>Aaa	p.E1658K		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1658	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCTGTTGTTCGCGCTCCTGG	0.607																																					p.E1658K		Atlas-SNP	.											.	TCHH	275	.	0			c.G4972A						.						68	69	69					1																	152080721		1905	4126	6031	SO:0001583	missense	7062	exon3			GTTGTTCGCGCTC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.4972G>A	chr1.hg19:g.152080721C>T	ENSP00000357794:p.Glu1658Lys	114.0	0.0		232.0	24.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.409197	0.25378	.	.	ENSG00000159450	ENST00000368804	T	0.08282	3.11	3.47	3.47	0.39725	.	.	.	.	.	T	0.08670	0.0215	M	0.73217	2.22	0.09310	N	1	D	0.71674	0.998	P	0.52856	0.711	T	0.18085	-1.0348	9	0.23302	T	0.38	-6.1047	12.459	0.55721	0.0:1.0:0.0:0.0	.	1658	Q07283	TRHY_HUMAN	K	1658	ENSP00000357794:E1658K	ENSP00000357794:E1658K	E	-	1	0	TCHH	150347345	0.001000	0.12720	0.010000	0.14722	0.029000	0.11900	0.018000	0.13422	1.790000	0.52503	0.411000	0.27672	GAA	.	.		0.607	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		T	152080721	C	T	152080721	3	4	24	1	0	0	0	0	1	0	0	0	15715	893	31	1	863	1	TCHH	1	152080721	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	7212595	152080721	97169900	6	3213										
LCE1F	353137	hgsc.bcm.edu	37	chr1	152749024	152749025	+	In_Frame_Ins	INS	-	-	TGCAGCTCTGGGGGCTGC													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gctccagctctgggggctgcINStgcagctctgggggtggtgg							TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:152749024_152749025insTGCAGCTCTGGGGGCTGC	ENST00000334371.2	+	1	177_178	c.177_178insTGCAGCTCTGGGGGCTGC	c.(178-180)tgc>TGCAGCTCTGGGGGCTGCtgc	p.60_60C>CSSGGCC		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	60					keratinization (GO:0031424)			p.C59C(1)		kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGGGGGCTGCTGCAGCTCTGG	0.678																																					p.C59delinsCCSSGGC		Atlas-INDEL	.											LCE1F,colon,carcinoma,0,1	LCE1F	42	.	1	Substitution - coding silent(1)	large_intestine(1)	c.177_178insTGCAGCTCTGGGGGCTGC						.																																			SO:0001652	inframe_insertion	353137	exon1			.		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"Late cornified envelopes"	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	Exception_encountered	chr1.hg19:g.152749024_152749025insTGCAGCTCTGGGGGCTGC	ENSP00000334187:p.SerSerGlyGlyCysCys60dup	202.0	0.0		366.0	81.0	NM_178354		In_Frame_Ins	INS	ENST00000334371.2	hg19	CCDS1023.1																																																																																			.	.		0.678	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354		TGCAGCTCTGGGGGCTGC	152749025	-	TGCAGCTCTGGGGGCTGC	152749024	7	5	24	1	0	1	1	0	0	0	0	0	8673	805	28	0	179	0	LCE1F	1	152749024	In_Frame_Ins	INS	-	TCGA-5C-A9VG-01A-11D-A36X-10	668303	152749024	96501597	7	3214										
IVL	3713	hgsc.bcm.edu	37	chr1	152882767	152882767	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gcaggaggggcacctgaagcAcctagagcagcaggagggac	17	10	0	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:152882767A>C	ENST00000368764.3	+	2	558	c.494A>C	c.(493-495)cAc>cCc	p.H165P	IVL_ENST00000392667.2_Missense_Mutation_p.H19P			P07476	INVO_HUMAN	involucrin	165	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			cacctgaagcacctagagcag	0.602																																					p.H165P		Atlas-SNP	.											.	IVL	100	.	0			c.A494C						.						33	36	35					1																	152882767		2203	4300	6503	SO:0001583	missense	3713	exon2			TGAAGCACCTAGA	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.494A>C	chr1.hg19:g.152882767A>C	ENSP00000357753:p.His165Pro	244.0	1.0		402.0	177.0	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	hg19	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	A	10.16	1.272630	0.23221	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.10668	3.08;2.85	3.42	-4.4	0.03600	.	.	.	.	.	T	0.01421	0.0046	N	0.24115	0.695	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.46925	-0.9156	9	0.28530	T	0.3	.	2.2701	0.04088	0.2656:0.4459:0.1055:0.183	.	165	P07476	INVO_HUMAN	P	165;19	ENSP00000357753:H165P;ENSP00000376435:H19P	ENSP00000357753:H165P	H	+	2	0	IVL	151149391	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.002000	0.03686	-0.886000	0.03966	-0.782000	0.03352	CAC	.	.		0.602	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		C	152882767	A	C	152882767	3	2	24	1	0	0	0	0	1	0	0	0	7938	159	6	5	496	5	IVL	1	152882767	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	133743	152882767	96367854	8	3215										
IVL	3713	hgsc.bcm.edu	37	chr1	152883444	152883444	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	agcacctggaggaggaggagGggcagctgaagcacctggtg	19	8	0	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:152883444G>A	ENST00000368764.3	+	2	1235	c.1171G>A	c.(1171-1173)Ggg>Agg	p.G391R	IVL_ENST00000392667.2_Missense_Mutation_p.G245R			P07476	INVO_HUMAN	involucrin	391	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ggaggaggaggggcagctgaa	0.657																																					p.G391R		Atlas-SNP	.											.	IVL	100	.	0			c.G1171A						.																																			SO:0001583	missense	3713	exon2			GAGGAGGGGCAGC	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1171G>A	chr1.hg19:g.152883444G>A	ENSP00000357753:p.Gly391Arg	131.0	0.0		235.0	19.0	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	hg19	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.855193	0.32791	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.24538	2.13;1.85	4.22	-8.45	0.00946	.	.	.	.	.	T	0.03220	0.0094	N	0.24115	0.695	0.09310	N	1	B	0.21905	0.062	B	0.21360	0.034	T	0.33624	-0.9861	9	0.16896	T	0.51	.	5.757	0.18178	0.2041:0.5081:0.1987:0.0892	.	391	P07476	INVO_HUMAN	R	391;245	ENSP00000357753:G391R;ENSP00000376435:G245R	ENSP00000357753:G391R	G	+	1	0	IVL	151150068	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	0.922000	0.28734	-1.815000	0.01222	-0.309000	0.09137	GGG	.	.		0.657	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		A	152883444	G	A	152883444	3	1	24	1	0	0	0	0	1	0	0	0	7938	1232	43	3	1173	3	IVL	1	152883444	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	677	152883444	96367177	9	3216										
CKS1B	1163	hgsc.bcm.edu	37	chr1	154950543	154950543	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	atctgaatggaggaatcttgGcgttcagcagagtcagggat	14	6	4	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:154950543G>A	ENST00000308987.5	+	2	187	c.140G>A	c.(139-141)gGc>gAc	p.G47D	CKS1B_ENST00000368436.1_Missense_Mutation_p.G47D|CKS1B_ENST00000368439.1_Missense_Mutation_p.G31D|CKS1B_ENST00000471245.1_3'UTR|MIR4258_ENST00000580920.1_RNA	NM_001826.2	NP_001817.1	P61024	CKS1_HUMAN	CDC28 protein kinase regulatory subunit 1B	47					cell division (GO:0051301)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	nucleoplasm (GO:0005654)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|large_intestine(1)|lung(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			AGGAATCTTGGCGTTCAGCAG	0.468																																					p.G47D		Atlas-SNP	.											.	CKS1B	5	.	0			c.G140A						.						66	60	63					1																	154950543		2203	4297	6500	SO:0001583	missense	1163	exon2			ATCTTGGCGTTCA	BC007751	CCDS1077.1	1q21.2	2011-04-28	2002-10-07		ENSG00000173207	ENSG00000173207			19083	protein-coding gene	gene with protein product		116900	"CDC28 protein kinase 1B"			2227411	Standard	NM_001826		Approved	ckshs1, CKS1	uc001fgb.3	P61024	OTTHUMG00000037413	ENST00000308987.5:c.140G>A	chr1.hg19:g.154950543G>A	ENSP00000311083:p.Gly47Asp	125.0	0.0		188.0	27.0	NM_001826	P33551	Missense_Mutation	SNP	ENST00000308987.5	hg19	CCDS1077.1	.	.	.	.	.	.	.	.	.	.	G	35	5.448626	0.96205	.	.	ENSG00000173207	ENST00000368439;ENST00000368436;ENST00000308987	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.81814	0.4902	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82261	-0.0545	8	0.87932	D	0	.	19.6509	0.95805	0.0:0.0:1.0:0.0	.	47	P61024	CKS1_HUMAN	D	31;47;47	.	ENSP00000311083:G47D	G	+	2	0	CKS1B	153217167	1.000000	0.71417	0.970000	0.41538	0.971000	0.66376	9.256000	0.95535	2.941000	0.99782	0.655000	0.94253	GGC	.	.		0.468	CKS1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091078.1	NM_001826		A	154950543	G	A	154950543	3	1	24	1	0	0	0	0	1	0	0	0	3454	1203	42	3	146	3	CKS1B	1	154950543	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	2067099	154950543	94300078	10	3217										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158646066	158646066	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	aaagtgtcagcttctctgctTtagcacataactccttcacc	5	13	3	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:158646066T>G	ENST00000368147.4	-	8	1157	c.977A>C	c.(976-978)aAa>aCa	p.K326T		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	326					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CTTCTCTGCTTTAGCACATAA	0.478																																					p.K326T		Atlas-SNP	.											.	SPTA1	720	.	0			c.A977C						.						192	180	184					1																	158646066		1919	4136	6055	SO:0001583	missense	6708	exon8			TCTGCTTTAGCAC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.977A>C	chr1.hg19:g.158646066T>G	ENSP00000357129:p.Lys326Thr	82.0	0.0		149.0	15.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.205185	0.79127	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.46819	0.86;0.86	5.24	5.24	0.73138	.	0.000000	0.34067	N	0.004297	T	0.27098	0.0664	L	0.28556	0.865	0.44660	D	0.997644	P	0.36495	0.556	B	0.41917	0.37	T	0.08827	-1.0703	10	0.25751	T	0.34	.	14.1225	0.65198	0.0:0.0:0.0:1.0	.	326	P02549	SPTA1_HUMAN	T	326	ENSP00000357130:K326T;ENSP00000357129:K326T	ENSP00000357129:K326T	K	-	2	0	SPTA1	156912690	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.129000	0.64739	2.186000	0.69663	0.533000	0.62120	AAA	.	.		0.478	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		G	158646066	T	G	158646066	3	3	24	1	0	0	0	0	1	0	0	0	15131	1841	64	5	6462	5	SPTA1	1	158646066	Missense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	3695523	158646066	90604555	11	3218										
NR1I3	9970	hgsc.bcm.edu	37	chr1	161205749	161205749	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	aaggggcaggtgggaccaatGcttttgctgactgttctcct	13	9	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:161205749G>C	ENST00000367982.4	-	3	281	c.126C>G	c.(124-126)agC>agG	p.S42R	NR1I3_ENST00000504010.1_Missense_Mutation_p.S13R|NR1I3_ENST00000367983.4_Missense_Mutation_p.S42R|NR1I3_ENST00000428574.2_Missense_Mutation_p.S42R|NR1I3_ENST00000367985.3_Missense_Mutation_p.S42R|NR1I3_ENST00000437437.2_Missense_Mutation_p.S13R|NR1I3_ENST00000412844.2_Missense_Mutation_p.S13R|NR1I3_ENST00000515452.1_Missense_Mutation_p.S42R|NR1I3_ENST00000506209.1_Missense_Mutation_p.S13R|NR1I3_ENST00000508387.1_Missense_Mutation_p.S13R|NR1I3_ENST00000515621.1_5'UTR|NR1I3_ENST00000502985.1_Missense_Mutation_p.S42R|NR1I3_ENST00000511748.1_Missense_Mutation_p.S13R|NR1I3_ENST00000511676.1_Missense_Mutation_p.S13R|NR1I3_ENST00000367984.4_Missense_Mutation_p.S42R|NR1I3_ENST00000442691.2_Missense_Mutation_p.S42R|NR1I3_ENST00000367979.2_Missense_Mutation_p.S42R|NR1I3_ENST00000505005.1_Missense_Mutation_p.S42R|NR1I3_ENST00000367980.2_Missense_Mutation_p.S42R|NR1I3_ENST00000511944.1_Missense_Mutation_p.S42R|NR1I3_ENST00000512372.1_Missense_Mutation_p.S13R|NR1I3_ENST00000508740.1_Missense_Mutation_p.S13R|NR1I3_ENST00000367981.3_Missense_Mutation_p.S13R			Q14994	NR1I3_HUMAN	nuclear receptor subfamily 1, group I, member 3	42					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	15	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TGGGACCAATGCTTTTGCTGA	0.532																																					p.S42R		Atlas-SNP	.											.	NR1I3	74	.	0			c.C126G						.						91	82	85					1																	161205749		2203	4300	6503	SO:0001583	missense	9970	exon3			ACCAATGCTTTTG	Z30425	CCDS1228.1, CCDS41427.1, CCDS41428.1, CCDS41429.1, CCDS41430.1, CCDS44260.1, CCDS44261.1, CCDS44262.1, CCDS53405.1, CCDS53406.1, CCDS53407.1, CCDS53408.1, CCDS53409.1, CCDS53410.1, CCDS53411.1	1q23.3	2013-01-16			ENSG00000143257	ENSG00000143257		"Nuclear hormone receptors"	7969	protein-coding gene	gene with protein product	"constitutive androstane receptor"	603881				8114692	Standard	NM_001077480		Approved	MB67, CAR1, CAR	uc001fzp.3	Q14994	OTTHUMG00000034347	ENST00000367982.4:c.126C>G	chr1.hg19:g.161205749G>C	ENSP00000356961:p.Ser42Arg	69.0	0.0		125.0	7.0	NM_005122	E9PB75|E9PC13|E9PDU3|E9PGH6|E9PH10|E9PHC8|E9PHN4|F1D8Q0|F1D8Q1|Q0VAC9|Q4U0F0|Q5VTW5|Q5VTW6|Q6GZ68|Q6GZ76|Q6GZ77|Q6GZ78|Q6GZ79|Q6GZ82|Q6GZ83|Q6GZ84|Q6GZ85|Q6GZ87|Q6GZ89	Missense_Mutation	SNP	ENST00000367982.4	hg19	CCDS41430.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.053648	0.36277	.	.	ENSG00000143257	ENST00000512372;ENST00000367983;ENST00000367980;ENST00000437437;ENST00000442691;ENST00000412844;ENST00000428574;ENST00000505005;ENST00000508740;ENST00000367982;ENST00000508387;ENST00000504010;ENST00000511676;ENST00000502985;ENST00000367981;ENST00000511944;ENST00000511748;ENST00000367984;ENST00000367985;ENST00000367979;ENST00000506209;ENST00000515452	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96396	-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0	5.33	-2.65	0.06095	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	1.262690	0.04830	N	0.438628	D	0.90577	0.7046	L	0.43152	1.355	0.32520	N	0.536328	B;B;P;B;P;B;B;B;P;B;P;B;B;P;B;P;B;P;P	0.50443	0.071;0.27;0.584;0.036;0.714;0.172;0.172;0.172;0.584;0.259;0.935;0.172;0.43;0.714;0.172;0.585;0.298;0.584;0.584	B;B;B;B;B;B;B;B;B;B;P;B;B;B;B;P;B;B;B	0.49953	0.156;0.315;0.438;0.062;0.34;0.188;0.188;0.188;0.345;0.133;0.627;0.188;0.111;0.438;0.142;0.487;0.111;0.34;0.345	D	0.83977	0.0330	9	0.62326	D	0.03	.	1.96	0.03384	0.3158:0.1734:0.3963:0.1145	.	42;13;13;42;42;42;42;42;42;13;42;42;13;13;13;13;13;13;42	B7Z8R7;E9PCF2;E9PHN4;Q6GZ85;E9PHC8;Q0VAC9;F1D8Q1;Q14994;E9PC13;Q6GZ70;Q6GZ72;Q4U0F0;Q6GZ87;E9PDU3;Q6GZ68;E9PH10;Q6GZ84;E9PGH6;E9PB75	.;.;.;.;.;.;.;NR1I3_HUMAN;.;.;.;.;.;.;.;.;.;.;.	R	13;42;42;13;42;13;42;42;13;42;13;13;13;42;13;42;13;42;42;42;13;42	ENSP00000425417:S13R;ENSP00000356962:S42R;ENSP00000356959:S42R;ENSP00000407446:S13R;ENSP00000406493:S42R;ENSP00000399361:S13R;ENSP00000412672:S42R;ENSP00000424934:S42R;ENSP00000423666:S13R;ENSP00000356961:S42R;ENSP00000422982:S13R;ENSP00000424345:S13R;ENSP00000427175:S13R;ENSP00000421374:S42R;ENSP00000356960:S13R;ENSP00000426292:S42R;ENSP00000427600:S13R;ENSP00000356963:S42R;ENSP00000356965:S42R;ENSP00000356958:S42R;ENSP00000423089:S13R;ENSP00000427034:S42R	ENSP00000356958:S42R	S	-	3	2	NR1I3	159472373	0.000000	0.05858	0.000000	0.03702	0.329000	0.28539	-0.424000	0.07025	0.005000	0.14708	-0.373000	0.07131	AGC	.	.		0.532	NR1I3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083048.2			C	161205749	G	C	161205749	3	2	24	1	0	0	0	0	1	0	0	0	10630	1310	46	4	1070	4	NR1I3	1	161205749	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	2559683	161205749	88044872	12	3219										
MAEL	84944	hgsc.bcm.edu	37	chr1	166958660	166958660	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gaagatccccgaactacggcGacgaggcctgcctgtggctc	13	14	0	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:166958660G>A	ENST00000367872.4	+	1	315	c.71G>A	c.(70-72)cGa>cAa	p.R24Q	MAEL_ENST00000367870.2_Missense_Mutation_p.R24Q	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	24					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						GAACTACGGCGACGAGGCCTG	0.612																																					p.R24Q		Atlas-SNP	.											.	MAEL	95	.	0			c.G71A						.						46	38	41					1																	166958660		2203	4298	6501	SO:0001583	missense	84944	exon1			TACGGCGACGAGG	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"cancer/testis antigen 128", "spermatogenesis associated 35"	611368	"maelstrom homolog (Drosophila)"			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.71G>A	chr1.hg19:g.166958660G>A	ENSP00000356846:p.Arg24Gln	84.0	0.0		160.0	18.0	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Missense_Mutation	SNP	ENST00000367872.4	hg19	CCDS1257.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.839097	0.32513	.	.	ENSG00000143194	ENST00000367872;ENST00000367870;ENST00000447624	T;T;T	0.14640	2.49;2.49;2.49	5.49	4.58	0.56647	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);Domain of unknown function DUF1898 (1);	0.341713	0.25106	N	0.033093	T	0.03095	0.0091	N	0.14661	0.345	0.41059	D	0.985363	B;B	0.33103	0.341;0.397	B;B	0.26416	0.05;0.069	T	0.44174	-0.9345	10	0.31617	T	0.26	.	13.113	0.59285	0.0775:0.0:0.9225:0.0	.	24;24	E9JVC3;Q96JY0	.;MAEL_HUMAN	Q	24	ENSP00000356846:R24Q;ENSP00000356844:R24Q;ENSP00000402143:R24Q	ENSP00000356844:R24Q	R	+	2	0	MAEL	165225284	0.912000	0.30974	0.565000	0.28409	0.198000	0.23893	1.982000	0.40638	1.562000	0.49601	0.655000	0.94253	CGA	.	.		0.612	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858		A	166958660	G	A	166958660	3	1	24	1	0	0	0	0	1	0	0	0	9163	1058	37	1	73	1	MAEL	1	166958660	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	5752911	166958660	82291961	13	3220										
FAM129A	116496	hgsc.bcm.edu	37	chr1	184801016	184801016	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	agtgatcatttcccaggaacCatagtgacccttctcctgtc	7	13	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:184801016C>T	ENST00000367511.3	-	6	875	c.682G>A	c.(682-684)Ggt>Agt	p.G228S	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	228					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						TCCCAGGAACCATAGTGACCC	0.423																																					p.G228S		Atlas-SNP	.											.	FAM129A	98	.	0			c.G682A						.						111	108	109					1																	184801016		2203	4300	6503	SO:0001583	missense	116496	exon6			AGGAACCATAGTG	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"cell growth inhibiting protein 39"		"chromosome 1 open reading frame 24"	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.682G>A	chr1.hg19:g.184801016C>T	ENSP00000356481:p.Gly228Ser	190.0	0.0		275.0	29.0	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	hg19	CCDS1364.1	.	.	.	.	.	.	.	.	.	.	C	33	5.287556	0.95517	.	.	ENSG00000135842	ENST00000367511	T	0.17691	2.26	5.61	5.61	0.85477	.	0.153223	0.64402	D	0.000015	T	0.45357	0.1338	M	0.77313	2.365	0.51233	D	0.999915	D	0.89917	1.0	D	0.97110	1.0	T	0.29181	-1.0020	10	0.52906	T	0.07	-27.5979	17.7743	0.88502	0.0:1.0:0.0:0.0	.	228	Q9BZQ8	NIBAN_HUMAN	S	228	ENSP00000356481:G228S	ENSP00000356481:G228S	G	-	1	0	FAM129A	183067639	1.000000	0.71417	0.990000	0.47175	0.989000	0.77384	5.999000	0.70665	2.793000	0.96121	0.655000	0.94253	GGT	.	.		0.423	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			T	184801016	C	T	184801016	3	4	24	1	0	0	0	0	1	0	0	0	5441	594	21	3	2140	3	FAM129A	1	184801016	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	17842356	184801016	64449605	14	3221										
TRIM67	440730	hgsc.bcm.edu	37	chr1	231299711	231299711	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tgcctggaggagggccggcaCgccaagcacgaggtgaagcc	17	12	0	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:231299711C>T	ENST00000366653.5	+	1	996	c.996C>T	c.(994-996)caC>caT	p.H332H	TRIM67_ENST00000366652.2_Silent_p.H332H|TRIM67_ENST00000449018.3_Silent_p.H270H|TRIM67_ENST00000444294.3_Silent_p.H332H			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	332					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				AGGGCCGGCACGCCAAGCACG	0.632																																					p.H332H		Atlas-SNP	.											.	TRIM67	160	.	0			c.C996T						.						16	19	18					1																	231299711		2047	4196	6243	SO:0001819	synonymous_variant	440730	exon1			CCGGCACGCCAAG	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.996C>T	chr1.hg19:g.231299711C>T		108.0	0.0		174.0	35.0	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	hg19	CCDS44333.1																																																																																			.	.		0.632	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		T	231299711	C	T	231299711	2	4	24	1	0	0	0	0	0	0	0	1	16555	535	19	1		1	TRIM67	1	231299711	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	46498695	231299711	17950910	15	3222										
WDR33	55339	hgsc.bcm.edu	37	chr2	128480544	128480544	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tctcttacccatctgttcttGttccatagctaattttagtt	4	10	3	0	rs200713285		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr2:128480544G>T	ENST00000322313.4	-	13	1524	c.1366C>A	c.(1366-1368)Caa>Aaa	p.Q456K		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	456					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		ATCTGTTCTTGTTCCATAGCT	0.328																																					p.Q456K		Atlas-SNP	.											.	WDR33	136	.	0			c.C1366A						.						135	120	125					2																	128480544		2203	4300	6503	SO:0001583	missense	55339	exon13			GTTCTTGTTCCAT		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.1366C>A	chr2.hg19:g.128480544G>T	ENSP00000325377:p.Gln456Lys	144.0	0.0		147.0	29.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.786664	0.70337	.	.	ENSG00000136709	ENST00000322313	D	0.88818	-2.43	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.90710	0.7085	L	0.36672	1.1	0.80722	D	1	P	0.49447	0.924	P	0.59424	0.857	D	0.89556	0.3803	10	0.34782	T	0.22	-10.532	18.7096	0.91651	0.0:0.0:1.0:0.0	.	456	Q9C0J8	WDR33_HUMAN	K	456	ENSP00000325377:Q456K	ENSP00000325377:Q456K	Q	-	1	0	WDR33	128197014	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.155000	0.94700	2.484000	0.83849	0.650000	0.86243	CAA	.	G|1.000;C|0.000		0.328	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		T	128480544	G	T	128480544	3	4	24	1	0	0	0	0	1	0	0	0	17302	1386	48	3	2684	3	WDR33	2	128480544	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10		128480544	114718829	16	3223										
MAP2	4133	hgsc.bcm.edu	37	chr2	210560690	210560690	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	acctgggtgtctcaggtgccAgggaggaatttgtggagacc	16	8	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr2:210560690A>C	ENST00000360351.4	+	7	4302	c.3796A>C	c.(3796-3798)Agg>Cgg	p.R1266R	MAP2_ENST00000199940.6_Intron|MAP2_ENST00000447185.1_Silent_p.R1262R|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1266					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	CTCAGGTGCCAGGGAGGAATT	0.483																																					p.R1266R	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.A3796C						.						119	122	121					2																	210560690		2203	4300	6503	SO:0001819	synonymous_variant	4133	exon7			GGTGCCAGGGAGG		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.3796A>C	chr2.hg19:g.210560690A>C		111.0	0.0		130.0	22.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.		0.483	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		C	210560690	A	C	210560690	2	2	24	1	0	0	0	0	0	0	0	1	9244	179	7	5		5	MAP2	2	210560690	Silent	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	82080146	210560690	32638683	17	3224										
CPS1	1373	hgsc.bcm.edu	37	chr2	211473265	211473444	+	Splice_Site	DEL	TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	-													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tctagccgaattggtagctcTatgaaaagtgtaggagaggt					rs553030521|rs542398928|rs141106588|rs59741271|rs376315320	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr2:211473265_211473444delTATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	ENST00000233072.5	+	19	2569_2587	c.2373_2391delTATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	c.(2371-2391)tctatgaaaagtgtaggagag>tc	p.SMKSVGE791del	CPS1_ENST00000451903.2_Splice_Site_p.SMKSVGE340del|CPS1_ENST00000430249.2_Splice_Site_p.SMKSVGE797del	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	791					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TTGGTAGCTCTATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAATATGCTAACA	0.392																																					p.797_803del		Pindel	.											.	CPS1	485	.	0			c.2390_2409del						.																																			SO:0001630	splice_region_variant	1373	exon20			.	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2391+1TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA>-	chr2.hg19:g.211473265_211473444delTATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA		81.0	0.0		60.0	18.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Frame_Shift_Del	DEL	ENST00000233072.5	hg19	CCDS2393.1																																																																																			.	.		0.392	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		In_Frame_Del	-	211473444	TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	-	211473265	8	5	24	1	0	1	0	1	0	0	1	0	3825	1509	53	0	2469	0	CPS1	2	211473265	Splice_Site	DEL	TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	TCGA-5C-A9VG-01A-11D-A36X-10	912575	211473265	31726108	18	3225										
CPS1	1373	hgsc.bcm.edu	37	chr2	211525234	211525234	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tgagtgtaacttgagagcttCtcgatccttcccctttgttt	8	10	1	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr2:211525234C>T	ENST00000233072.5	+	32	3978	c.3782C>T	c.(3781-3783)tCt>tTt	p.S1261F	CPS1_ENST00000451903.2_Missense_Mutation_p.S810F|CPS1_ENST00000430249.2_Missense_Mutation_p.S1267F	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1261	ATP-grasp 2.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TTGAGAGCTTCTCGATCCTTC	0.398																																					p.S1267F		Atlas-SNP	.											.	CPS1	485	.	0			c.C3800T						.						271	249	257					2																	211525234		2203	4300	6503	SO:0001583	missense	1373	exon33			GAGCTTCTCGATC	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3782C>T	chr2.hg19:g.211525234C>T	ENSP00000233072:p.Ser1261Phe	143.0	0.0		121.0	26.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.934509	0.92458	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.98313	-4.86;-4.86;-4.86	5.98	5.98	0.97165	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	H	0.99090	4.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97880	1.0291	10	0.72032	D	0.01	-10.4337	20.4434	0.99119	0.0:1.0:0.0:0.0	.	1271;1261	Q59HF8;P31327	.;CPSM_HUMAN	F	1267;1269;1261;810	ENSP00000402608:S1267F;ENSP00000233072:S1261F;ENSP00000406136:S810F	ENSP00000233072:S1261F	S	+	2	0	CPS1	211233479	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.398000	0.79919	2.838000	0.97847	0.655000	0.94253	TCT	.	.		0.398	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211525234	C	T	211525234	3	4	24	1	0	0	0	0	1	0	0	0	3825	913	32	3	3930	3	CPS1	2	211525234	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	51969	211525234	31674139	19	3226										
AZI2	64343	hgsc.bcm.edu	37	chr3	28382058	28382058	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gtcactgtatctctcttatgGgctttttcatgattcagaat	7	8	5	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:28382058G>A	ENST00000479665.1	-	2	582	c.51C>T	c.(49-51)gcC>gcT	p.A17A	AZI2_ENST00000457172.1_Silent_p.A17A|AZI2_ENST00000334100.6_Silent_p.A17A|AZI2_ENST00000295748.3_5'UTR|AZI2_ENST00000420543.2_Silent_p.A17A	NM_022461.3	NP_071906.1	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2	17	Homodimerization. {ECO:0000250}.				dendritic cell differentiation (GO:0097028)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-alpha production (GO:0032607)|interferon-gamma production (GO:0032609)|interleukin-6 production (GO:0032635)|mitotic cell cycle (GO:0000278)|T cell activation (GO:0042110)|tumor necrosis factor production (GO:0032640)	cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15						CTCTCTTATGGGCTTTTTCAT	0.348																																					p.A17A		Atlas-SNP	.											.	AZI2	33	.	0			c.C51T						.						103	106	105					3																	28382058		2203	4300	6503	SO:0001819	synonymous_variant	64343	exon2			CTTATGGGCTTTT	AC093142	CCDS2647.1, CCDS46782.1, CCDS46783.1	3p23	2006-03-01			ENSG00000163512	ENSG00000163512			24002	protein-coding gene	gene with protein product		609916				10580148	Standard	NM_001134432		Approved	NAP1, FLJ21939, AZ2	uc003ceb.4	Q9H6S1	OTTHUMG00000130573	ENST00000479665.1:c.51C>T	chr3.hg19:g.28382058G>A		208.0	0.0		194.0	43.0	NM_001134432	A8K3M2|C9JB40|H7BXU6|Q86W99|Q9BQF1	Silent	SNP	ENST00000479665.1	hg19	CCDS2647.1																																																																																			.	.		0.348	AZI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252998.2	NM_203326		A	28382058	G	A	28382058	2	1	24	1	0	0	0	0	0	0	0	1	1241	1219	43	3		3	AZI2	3	28382058	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10		28382058	169640372	20	3227										
RBMS3	27303	hgsc.bcm.edu	37	chr3	29938929	29938929	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gattccacagacatctatcaCgccattcattgctgcttccc	5	15	3	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:29938929C>T	ENST00000383767.2	+	9	1187	c.851C>T	c.(850-852)aCg>aTg	p.T284M	RBMS3_ENST00000273139.9_Missense_Mutation_p.T284M|RBMS3_ENST00000396583.3_Missense_Mutation_p.T297M|RBMS3_ENST00000452462.1_Missense_Mutation_p.T284M|RBMS3_ENST00000434693.2_Missense_Mutation_p.T283M|RBMS3_ENST00000383766.2_Missense_Mutation_p.T283M|RBMS3_ENST00000456853.1_Missense_Mutation_p.T297M			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	284					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				ACATCTATCACGCCATTCATT	0.418																																					p.T297M		Atlas-SNP	.											RBMS3_ENST00000383767,NS,carcinoma,0,1	RBMS3	62	.	0			c.C890T						.						277	251	260					3																	29938929		2203	4300	6503	SO:0001583	missense	27303	exon10			CTATCACGCCATT	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"RNA binding motif (RRM) containing"	13427	protein-coding gene	gene with protein product	"RNA-binding protein"	605786	"RNA binding motif, single stranded interacting protein"			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.851C>T	chr3.hg19:g.29938929C>T	ENSP00000373277:p.Thr284Met	110.0	0.0		103.0	20.0	NM_001177712	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Missense_Mutation	SNP	ENST00000383767.2	hg19	CCDS33724.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.914916	0.92178	.	.	ENSG00000144642	ENST00000434693;ENST00000396583;ENST00000383767;ENST00000273139;ENST00000383766;ENST00000452462;ENST00000456853	T;T;T;T;T;T;T	0.27402	1.71;1.67;1.71;1.71;1.79;1.7;1.68	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.44456	0.1294	L	0.39633	1.23	0.80722	D	1	P;D;D;P	0.63046	0.614;0.992;0.992;0.679	B;P;P;B	0.60286	0.228;0.872;0.872;0.174	T	0.15809	-1.0424	9	.	.	.	.	18.754	0.91825	0.0:1.0:0.0:0.0	.	284;297;283;284	G5E9J9;Q6XE24-2;Q6XE24-3;Q6XE24	.;.;.;RBMS3_HUMAN	M	283;297;284;284;283;284;297	ENSP00000395592:T283M;ENSP00000379828:T297M;ENSP00000373277:T284M;ENSP00000273139:T284M;ENSP00000373276:T283M;ENSP00000397926:T284M;ENSP00000400519:T297M	.	T	+	2	0	RBMS3	29913933	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.433000	0.82419	0.655000	0.94253	ACG	.	.		0.418	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792		T	29938929	C	T	29938929	3	4	24	1	0	0	0	0	1	0	0	0	13165	536	19	1	928	1	RBMS3	3	29938929	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	1556871	29938929	168083501	21	3228										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266113	41266113	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cctggactctggaatccattCtggtgccactaccacagctc	8	15	2	0	rs121913416|rs121913403		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:41266113C>T	ENST00000349496.5	+	3	390	c.110C>T	c.(109-111)tCt>tTt	p.S37F	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S30F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S37F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S37F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S37F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S37F(172)|p.S37C(141)|p.A5_A80del(53)|p.S37Y(31)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGAATCCATTCTGGTGCCACT	0.498	S37C(JHUEM2_ENDOMETRIUM)|S37C(SNU398_LIVER)|S37F(HUTU80_SMALL_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S37F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	474	Substitution - Missense(344)|Deletion - In frame(102)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(145)|endometrium(64)|stomach(38)|skin(34)|ovary(33)|central_nervous_system(28)|pancreas(28)|large_intestine(22)|pituitary(22)|lung(21)|biliary_tract(15)|thyroid(4)|soft_tissue(4)|urinary_tract(4)|small_intestine(3)|oesophagus(3)|adrenal_gland(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)|breast(1)	c.C110T						.						93	78	83					3																	41266113		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TCCATTCTGGTGC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.110C>T	chr3.hg19:g.41266113C>T	ENSP00000344456:p.Ser37Phe	165.0	0.0		141.0	31.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.513375	0.85389	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75297	-0.3367	10	0.87932	D	0	-15.9763	19.9596	0.97236	0.0:1.0:0.0:0.0	.	37	P35222	CTNB1_HUMAN	F	30;37;37;37;37;30;37;37;37	ENSP00000400508:S30F;ENSP00000385604:S37F;ENSP00000412219:S37F;ENSP00000379486:S37F;ENSP00000344456:S37F;ENSP00000411226:S30F;ENSP00000379488:S37F;ENSP00000409302:S37F;ENSP00000401599:S37F	ENSP00000344456:S37F	S	+	2	0	CTNNB1	41241117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266113	C	T	41266113	3	4	24	1	0	0	0	0	1	0	0	0	4018	913	32	3	116	3	CTNNB1	3	41266113	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	11327184	41266113	156756317	22	3229										
ULK4	54986	hgsc.bcm.edu	37	chr3	41831172	41831172	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ccttttcttggattagtcttTgaagatgaatcccacaggac	8	9	2	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:41831172T>A	ENST00000301831.4	-	21	2636	c.2174A>T	c.(2173-2175)cAa>cTa	p.Q725L		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	725					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		GATTAGTCTTTGAAGATGAAT	0.388																																					p.Q725L		Atlas-SNP	.											.	ULK4	150	.	0			c.A2174T						.						94	89	90					3																	41831172		1886	4109	5995	SO:0001583	missense	54986	exon21			AGTCTTTGAAGAT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2174A>T	chr3.hg19:g.41831172T>A	ENSP00000301831:p.Gln725Leu	113.0	0.0		123.0	24.0	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	hg19	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.021352	0.75275	.	.	ENSG00000168038	ENST00000301831	T	0.61274	0.12	5.91	5.91	0.95273	Armadillo-like helical (1);Armadillo-type fold (2);	0.206736	0.42053	U	0.000777	T	0.61986	0.2391	L	0.52573	1.65	0.80722	D	1	P;D	0.55172	0.947;0.97	P;P	0.50934	0.576;0.654	T	0.59532	-0.7437	10	0.31617	T	0.26	.	16.3453	0.83126	0.0:0.0:0.0:1.0	.	725;725	B4E2M4;Q96C45	.;ULK4_HUMAN	L	725	ENSP00000301831:Q725L	ENSP00000301831:Q725L	Q	-	2	0	ULK4	41806176	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	6.369000	0.73109	2.261000	0.74972	0.533000	0.62120	CAA	.	.		0.388	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		A	41831172	T	A	41831172	3	1	24	1	0	0	0	0	1	0	0	0	16993	1812	63	4	1721	4	ULK4	3	41831172	Missense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	565059	41831172	156191258	23	3230										
LZTFL1	54585	hgsc.bcm.edu	37	chr3	45875746	45875746	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttacctttttgtttgaagatGtaatctctgctttttcaaat	5	6	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:45875746G>A	ENST00000296135.6	-	4	542	c.368C>T	c.(367-369)aCa>aTa	p.T123I	LZTFL1_ENST00000536047.1_Missense_Mutation_p.T106I|LZTFL1_ENST00000539217.1_Missense_Mutation_p.T119I|LZTFL1_ENST00000490463.1_5'UTR	NM_001276378.1|NM_020347.2	NP_001263307.1|NP_065080.1	Q9NQ48	LZTL1_HUMAN	leucine zipper transcription factor-like 1	123					establishment of protein localization to organelle (GO:0072594)	BBSome (GO:0034464)|cytoplasm (GO:0005737)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	8				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		GTTTGAAGATGTAATCTCTGC	0.269																																					p.T123I		Atlas-SNP	.											.	LZTFL1	37	.	0			c.C368T						.						47	49	48					3																	45875746		2195	4294	6489	SO:0001583	missense	54585	exon4			GAAGATGTAATCT	AJ297351	CCDS2731.1, CCDS63608.1, CCDS63609.1	3p21.3	2014-01-28			ENSG00000163818	ENSG00000163818			6741	protein-coding gene	gene with protein product		606568				11352561, 22510444	Standard	NM_020347		Approved	BBS17	uc003cox.2	Q9NQ48	OTTHUMG00000133452	ENST00000296135.6:c.368C>T	chr3.hg19:g.45875746G>A	ENSP00000296135:p.Thr123Ile	92.0	0.0		86.0	6.0	NM_020347	B3KSI9|B4E0K7|Q8TC61|Q9NQ56	Missense_Mutation	SNP	ENST00000296135.6	hg19	CCDS2731.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.776451	0.31411	.	.	ENSG00000163818	ENST00000296135;ENST00000536047;ENST00000539217	T;T;T	0.25749	1.78;1.78;1.78	5.96	2.17	0.27698	.	0.403999	0.31347	N	0.007802	T	0.24812	0.0602	L	0.59436	1.845	0.27164	N	0.961093	B	0.06786	0.001	B	0.09377	0.004	T	0.18053	-1.0349	10	0.52906	T	0.07	-8.0E-4	10.8925	0.47004	0.2517:0.0:0.7483:0.0	.	123	Q9NQ48	LZTL1_HUMAN	I	123;106;119	ENSP00000296135:T123I;ENSP00000439522:T106I;ENSP00000441784:T119I	ENSP00000296135:T123I	T	-	2	0	LZTFL1	45850750	0.990000	0.36364	0.868000	0.34077	0.726000	0.41606	0.497000	0.22514	0.120000	0.18254	-0.140000	0.14226	ACA	.	.		0.269	LZTFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257326.3	NM_020347		A	45875746	G	A	45875746	3	1	24	1	0	0	0	0	1	0	0	0	9145	1377	48	3	559	3	LZTFL1	3	45875746	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	4044574	45875746	152146684	24	3231										
CCR3	1232	hgsc.bcm.edu	37	chr3	46307580	46307580	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttggagagaggttccggaagTacctgcgccacttcttccac	11	12	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:46307580T>A	ENST00000357422.2	+	4	1474	c.931T>A	c.(931-933)Tac>Aac	p.Y311N	CCR3_ENST00000395940.2_Missense_Mutation_p.Y311N|CCR3_ENST00000541018.1_Missense_Mutation_p.Y311N|CCR3_ENST00000545097.1_Missense_Mutation_p.Y332N|CCR3_ENST00000395942.2_Missense_Mutation_p.Y311N			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	311					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		GTTCCGGAAGTACCTGCGCCA	0.552																																					p.Y332N		Atlas-SNP	.											.	CCR3	52	.	0			c.T994A						.						109	91	97					3																	46307580		2203	4300	6503	SO:0001583	missense	1232	exon3			CGGAAGTACCTGC	AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.931T>A	chr3.hg19:g.46307580T>A	ENSP00000350003:p.Tyr311Asn	73.0	0.0		64.0	13.0	NM_178328	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Missense_Mutation	SNP	ENST00000357422.2	hg19	CCDS2738.1	.	.	.	.	.	.	.	.	.	.	T	10.53	1.375870	0.24857	.	.	ENSG00000183625	ENST00000357422;ENST00000545097;ENST00000541018;ENST00000395940;ENST00000395942	T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21	5.55	0.263	0.15602	.	0.486738	0.18614	N	0.136063	T	0.36026	0.0952	M	0.69823	2.125	0.31785	N	0.630359	B;B	0.22541	0.071;0.042	B;B	0.32624	0.149;0.071	T	0.40459	-0.9562	10	0.72032	D	0.01	.	5.3126	0.15839	0.1281:0.3515:0.0:0.5204	.	332;311	F5GWL6;P51677	.;CCR3_HUMAN	N	311;332;311;311;311	ENSP00000350003:Y311N;ENSP00000441600:Y332N;ENSP00000440097:Y311N;ENSP00000379271:Y311N;ENSP00000379273:Y311N	ENSP00000350003:Y311N	Y	+	1	0	CCR3	46282584	0.011000	0.17503	0.611000	0.29010	0.350000	0.29205	-0.103000	0.10940	-0.186000	0.10533	-0.250000	0.11733	TAC	.	.		0.552	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2			A	46307580	T	A	46307580	3	1	24	1	0	0	0	0	1	0	0	0	2944	1638	57	4	1000	4	CCR3	3	46307580	Missense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	431834	46307580	151714850	25	3232										
GBE1	2632	hgsc.bcm.edu	37	chr3	81630426	81630426	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	atctttaaactctttaagtaGctagacacaagagagaaaaa	6	6	2	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:81630426G>A	ENST00000429644.2	-	11	1979	c.1336C>T	c.(1336-1338)Cta>Tta	p.L446L	GBE1_ENST00000489715.1_Splice_Site_p.L405L	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	446					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		TCTTTAAGTAGCTAGACACAA	0.343									Glycogen Storage Disease, type IV																												p.L446L		Atlas-SNP	.											.	GBE1	111	.	0			c.C1336T						.						106	95	98					3																	81630426		1832	4088	5920	SO:0001630	splice_region_variant	2632	exon11	Familial Cancer Database	Andersen Disease, Brancher deficiency	TAAGTAGCTAGAC		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"glycogen branching enzyme", "Andersen disease", "glycogen storage disease type IV"	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.1336-1C>T	chr3.hg19:g.81630426G>A		77.0	0.0		86.0	9.0	NM_000158	B3KWV3|Q96EN0	Silent	SNP	ENST00000429644.2	hg19	CCDS54612.1																																																																																			.	.		0.343	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		Silent	A	81630426	G	A	81630426	5	1	24	1	0	0	0	0	0	0	1	0	6278	985	34	3	796	3	GBE1	3	81630426	Splice_Site	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	35322846	81630426	116392004	26	3233										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89528604	89528604	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cagaagaagatcatcagtagCattaaagctctagaaacgca	8	8	3	4			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:89528604C>T	ENST00000336596.2	+	17	3129	c.2904C>T	c.(2902-2904)agC>agT	p.S968S	EPHA3_ENST00000494014.1_3'UTR	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	968	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TCATCAGTAGCATTAAAGCTC	0.463										TSP Lung(6;0.00050)																											p.S968S		Atlas-SNP	.											.	EPHA3	501	.	0			c.C2904T						.						100	88	92					3																	89528604		2203	4300	6503	SO:0001819	synonymous_variant	2042	exon17			CAGTAGCATTAAA	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2904C>T	chr3.hg19:g.89528604C>T		292.0	0.0		314.0	13.0	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.		0.463	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89528604	C	T	89528604	2	4	24	1	0	0	0	0	0	0	0	1	5170	709	25	3		3	EPHA3	3	89528604	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	7898178	89528604	108493826	27	3234										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134898792	134898793	+	Frame_Shift_Ins	INS	-	-	T													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gccaaggagattgatgtatcINSttttgtgaaaattgaagagg							TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:134898792_134898793insT	ENST00000398015.3	+	10	2220_2221	c.1850_1851insT	c.(1849-1854)tcttttfs	p.SF617fs	EPHB1_ENST00000493838.1_Frame_Shift_Ins_p.SF178fs	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	617					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						ATTGATGTATCTTTTGTGAAAA	0.485																																					p.S617fs		Atlas-Indel,Pindel	.											.	EPHB1	519	.	0			c.1850_1851insT						.																																			SO:0001589	frameshift_variant	2047	exon10			.	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.1854dupT	chr3.hg19:g.134898796_134898796dupT	ENSP00000381097:p.Ser617fs	131.0	0.0		131.0	47.0	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Frame_Shift_Ins	INS	ENST00000398015.3	hg19	CCDS46921.1																																																																																			.	.		0.485	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		T	134898793	-	T	134898792	7	5	24	1	0	1	1	0	0	0	0	0	5176	913	32	0	1888	0	EPHB1	3	134898792	Frame_Shift_Ins	INS	-	TCGA-5C-A9VG-01A-11D-A36X-10	45370188	134898792	63123638	28	3235										
PLOD2	5352	hgsc.bcm.edu	37	chr3	145824364	145824364	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttagtgtaaaagagctgatcAtcatcattatcctggagatt	8	6	3	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:145824364A>T	ENST00000360060.3	-	5	747	c.570T>A	c.(568-570)gaT>gaA	p.D190E	PLOD2_ENST00000494950.1_Missense_Mutation_p.D135E|PLOD2_ENST00000282903.5_Missense_Mutation_p.D190E|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	190					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	AGAGCTGATCATCATCATTAT	0.343																																					p.D190E		Atlas-SNP	.											.	PLOD2	81	.	0			c.T570A						.						161	159	159					3																	145824364		2203	4300	6503	SO:0001583	missense	5352	exon5			CTGATCATCATCA	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"lysyl hydroxlase 2"	601865	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.570T>A	chr3.hg19:g.145824364A>T	ENSP00000353170:p.Asp190Glu	147.0	0.0		141.0	11.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	hg19	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.414748	0.83449	.	.	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000494950;ENST00000469350	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	5.24	-1.66	0.08265	.	0.000000	0.85682	D	0.000000	T	0.60431	0.2268	M	0.90595	3.13	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.987	D;D;D	0.91635	0.994;0.999;0.928	T	0.62478	-0.6846	10	0.87932	D	0	-20.3189	10.1756	0.42937	0.6636:0.0:0.3364:0.0	.	135;190;190	E7ETU9;O00469;O00469-2	.;PLOD2_HUMAN;.	E	190;190;135;162	ENSP00000282903:D190E;ENSP00000353170:D190E;ENSP00000420094:D135E;ENSP00000419963:D162E	ENSP00000282903:D190E	D	-	3	2	PLOD2	147307054	0.920000	0.31207	0.984000	0.44739	0.998000	0.95712	0.164000	0.16542	-0.562000	0.06086	0.533000	0.62120	GAT	.	.		0.343	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		T	145824364	A	T	145824364	3	4	24	1	0	0	0	0	1	0	0	0	12111	214	8	4	1770	4	PLOD2	3	145824364	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	10925572	145824364	52198066	29	3236										
FNDC3B	64778	hgsc.bcm.edu	37	chr3	171944729	171944729	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttcatgtgcctccaggttatAtctcacaggtaatccatttg	7	10	2	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:171944729A>C	ENST00000336824.4	+	4	355	c.256A>C	c.(256-258)Atc>Ctc	p.I86L	FNDC3B_ENST00000415807.2_Missense_Mutation_p.I86L|FNDC3B_ENST00000416957.1_Missense_Mutation_p.I86L	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	86					cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		TCCAGGTTATATCTCACAGGT	0.443																																					p.I86L		Atlas-SNP	.											.	FNDC3B	118	.	0			c.A256C						.						145	130	135					3																	171944729		2203	4300	6503	SO:0001583	missense	64778	exon4			GGTTATATCTCAC	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.256A>C	chr3.hg19:g.171944729A>C	ENSP00000338523:p.Ile86Leu	82.0	0.0		104.0	27.0	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	hg19	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.590756	0.66219	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957;ENST00000443501	T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69	5.95	5.95	0.96441	.	0.043534	0.85682	D	0.000000	T	0.80523	0.4639	L	0.54323	1.7	0.80722	D	1	P;B	0.51147	0.942;0.435	D;B	0.64595	0.927;0.155	T	0.79541	-0.1761	10	0.42905	T	0.14	-25.5664	16.4237	0.83790	1.0:0.0:0.0:0.0	.	86;86	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	L	86;86;86;59	ENSP00000411242:I86L;ENSP00000338523:I86L;ENSP00000389094:I86L;ENSP00000389064:I59L	ENSP00000338523:I86L	I	+	1	0	FNDC3B	173427423	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	5.224000	0.65288	2.279000	0.76181	0.533000	0.62120	ATC	.	.		0.443	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		C	171944729	A	C	171944729	3	2	24	1	0	0	0	0	1	0	0	0	5978	449	16	5	266	5	FNDC3B	3	171944729	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	26120365	171944729	26077701	30	3237										
N4BP2	55728	hgsc.bcm.edu	37	chr4	40122641	40122641	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ctaagtaaaaagagtcatggGcaacacacatcgttgcctct	8	10	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:40122641G>A	ENST00000261435.6	+	9	3326	c.2910G>A	c.(2908-2910)ggG>ggA	p.G970G		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	970					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						AGAGTCATGGGCAACACACAT	0.418																																					p.G970G		Atlas-SNP	.											.	N4BP2	166	.	0			c.G2910A						.						87	85	86					4																	40122641		2203	4300	6503	SO:0001819	synonymous_variant	55728	exon9			TCATGGGCAACAC	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.2910G>A	chr4.hg19:g.40122641G>A		142.0	0.0		147.0	33.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Silent	SNP	ENST00000261435.6	hg19	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.902404	0.00512	.	.	ENSG00000078177	ENST00000513269	.	.	.	4.99	-3.09	0.05331	.	.	.	.	.	T	0.17450	0.0419	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25572	-1.0128	4	.	.	.	0.0169	0.5399	0.00644	0.3149:0.2013:0.2877:0.1962	.	.	.	.	T	617	.	.	A	+	1	0	N4BP2	39799036	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.765000	0.04730	-0.437000	0.07243	0.655000	0.94253	GCA	.	.		0.418	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		A	40122641	G	A	40122641	2	1	24	1	0	0	0	0	0	0	0	1	10119	1190	42	3		3	N4BP2	4	40122641	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10		40122641	151031635	31	3238										
AFM	173	hgsc.bcm.edu	37	chr4	74357714	74357714	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tcaaacaaagatgatagaccAaaggatttatctctaagaga	7	6	2	4			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:74357714A>G	ENST00000226355.3	+	8	1062	c.969A>G	c.(967-969)ccA>ccG	p.P323P		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	323	Albumin 2. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATGATAGACCAAAGGATTTAT	0.378																																					p.P323P		Atlas-SNP	.											.	AFM	101	.	0			c.A969G						.						82	85	84					4																	74357714		2203	4300	6503	SO:0001819	synonymous_variant	173	exon8			TAGACCAAAGGAT	L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.969A>G	chr4.hg19:g.74357714A>G		472.0	0.0		400.0	92.0	NM_001133	A8K3E1|Q32MR3|Q4W5C5	Silent	SNP	ENST00000226355.3	hg19	CCDS3557.1																																																																																			.	.		0.378	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			G	74357714	A	G	74357714	2	3	24	1	0	0	0	0	0	0	0	1	361	117	5	2		2	AFM	4	74357714	Silent	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	34235073	74357714	116796562	32	3239										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87556471	87556471	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	accacttcaggaggaagaaaTatgggctgtattaaatcaaa	9	6	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:87556471T>C	ENST00000411767.2	+	2	125	c.62T>C	c.(61-63)aTa>aCa	p.I21T	PTPN13_ENST00000427191.2_Missense_Mutation_p.I21T|PTPN13_ENST00000436978.1_Missense_Mutation_p.I21T|PTPN13_ENST00000316707.6_Missense_Mutation_p.I21T|PTPN13_ENST00000511467.1_Missense_Mutation_p.I21T|PTPN13_ENST00000502971.1_Missense_Mutation_p.I21T			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	21	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		GAGGAAGAAATATGGGCTGTA	0.453																																					p.I21T		Atlas-SNP	.											.	PTPN13	203	.	0			c.T62C						.						61	63	63					4																	87556471		1928	4128	6056	SO:0001583	missense	5783	exon2			AAGAAATATGGGC		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.62T>C	chr4.hg19:g.87556471T>C	ENSP00000407249:p.Ile21Thr	129.0	0.0		95.0	16.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.335229	0.81801	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000502971;ENST00000316707;ENST00000411767;ENST00000507902;ENST00000511467	T;T;T;T;T;T;T	0.33438	2.02;2.02;1.41;2.02;2.02;2.02;2.02	5.54	5.54	0.83059	KIND (2);	0.103582	0.42294	D	0.000735	T	0.45597	0.1350	L	0.42245	1.32	0.43317	D	0.995332	D;B;B;B	0.60575	0.988;0.374;0.258;0.374	P;B;B;B	0.61201	0.885;0.354;0.193;0.354	T	0.42155	-0.9468	10	0.72032	D	0.01	.	15.3531	0.74405	0.0:0.0:0.0:1.0	.	21;21;21;21	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	T	21	ENSP00000408368:I21T;ENSP00000394794:I21T;ENSP00000423531:I21T;ENSP00000322675:I21T;ENSP00000407249:I21T;ENSP00000422835:I21T;ENSP00000426626:I21T	ENSP00000322675:I21T	I	+	2	0	PTPN13	87775495	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.354000	0.79424	2.086000	0.62901	0.528000	0.53228	ATA	.	.		0.453	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			C	87556471	T	C	87556471	3	2	24	1	0	0	0	0	1	0	0	0	12795	1406	49	2	64	2	PTPN13	4	87556471	Missense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	13198757	87556471	103597805	33	3240										
PKD2	5311	hgsc.bcm.edu	37	chr4	88996722	88996722	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	agcttcccagatcagtcatgGtttaggcacgccagtgggac	12	11	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:88996722G>T	ENST00000508588.1	+	10	1432	c.1037G>T	c.(1036-1038)gGt>gTt	p.G346V	PKD2_ENST00000237596.2_Missense_Mutation_p.G928V|PKD2_ENST00000502363.1_Missense_Mutation_p.G346V|PKD2_ENST00000511337.1_3'UTR			Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	0					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		ATCAGTCATGGTTTAGGCACG	0.532																																					p.G928V		Atlas-SNP	.											.	PKD2	82	.	0			c.G2783T						.						164	149	154					4																	88996722		2203	4300	6503	SO:0001583	missense	5311	exon15			GTCATGGTTTAGG	U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"Voltage-gated ion channels / Transient receptor potential cation channels", "EF-hand domain containing"	9009	protein-coding gene	gene with protein product	"transient receptor potential cation channel, subfamily P, member 2"	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000508588.1:c.1037G>T	chr4.hg19:g.88996722G>T	ENSP00000427131:p.Gly346Val	140.0	0.0		101.0	20.0	NM_000297	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000508588.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.81	1.749711	0.30955	.	.	ENSG00000118762	ENST00000237596;ENST00000508588;ENST00000502363	T;D;D	0.91843	-0.14;-2.92;-2.92	5.2	5.2	0.72013	.	0.435283	0.27048	N	0.021190	D	0.85548	0.5722	N	0.22421	0.69	0.33176	D	0.548938	P	0.39391	0.671	B	0.32289	0.143	D	0.87601	0.2497	10	0.30078	T	0.28	-10.9556	18.7273	0.91718	0.0:0.0:1.0:0.0	.	928	Q13563	PKD2_HUMAN	V	928;346;346	ENSP00000237596:G928V;ENSP00000427131:G346V;ENSP00000425289:G346V	ENSP00000237596:G928V	G	+	2	0	PKD2	89215746	0.990000	0.36364	0.027000	0.17364	0.597000	0.36814	4.424000	0.59868	2.409000	0.81822	0.585000	0.79938	GGT	.	.		0.532	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297		T	88996722	G	T	88996722	3	4	24	1	0	0	0	0	1	0	0	0	11975	1261	44	3	2841	3	PKD2	4	88996722	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	1440251	88996722	102157554	34	3241										
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125631232	125631232	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	actgctggatcccttagcttGtcctcatatccttggagtag	9	11	1	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:125631232G>C	ENST00000504087.1	-	2	1472	c.435C>G	c.(433-435)gaC>gaG	p.D145E	ANKRD50_ENST00000515641.1_Intron	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	145										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						CCCTTAGCTTGTCCTCATATC	0.483																																					p.D145E		Atlas-SNP	.											.	ANKRD50	136	.	0			c.C435G						.						74	75	74					4																	125631232		2203	4300	6503	SO:0001583	missense	57182	exon2			TAGCTTGTCCTCA	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.435C>G	chr4.hg19:g.125631232G>C	ENSP00000425658:p.Asp145Glu	44.0	0.0		69.0	29.0	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	hg19	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	G	0.301	-0.973918	0.02215	.	.	ENSG00000151458	ENST00000504087	T	0.16897	2.31	5.16	3.37	0.38596	.	0.056907	0.64402	D	0.000002	T	0.06234	0.0161	N	0.03917	-0.325	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.26950	-1.0088	10	0.05721	T	0.95	.	10.7728	0.46332	0.1604:0.0:0.8396:0.0	.	145	Q9ULJ7	ANR50_HUMAN	E	145	ENSP00000425658:D145E	ENSP00000425658:D145E	D	-	3	2	ANKRD50	125850682	1.000000	0.71417	1.000000	0.80357	0.326000	0.28443	3.157000	0.50716	0.519000	0.28406	0.462000	0.41574	GAC	.	.		0.483	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		C	125631232	G	C	125631232	3	2	24	1	0	0	0	0	1	0	0	0	677	1368	48	4	3866	4	ANKRD50	4	125631232	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	36634510	125631232	65523044	35	3242										
KLKB1	3818	hgsc.bcm.edu	37	chr4	187158050	187158051	+	Frame_Shift_Ins	INS	-	-	T													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ccagtaacattcgctgccagINStttttttcatatgccacgca					rs560588447	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:187158050_187158051insT	ENST00000264690.6	+	5	631_632	c.444_445insT	c.(445-447)tttfs	p.F149fs	KLKB1_ENST00000513864.1_Frame_Shift_Ins_p.F149fs	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	149	Apple 2. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		TTCGCTGCCAGTTTTTTTCATA	0.401													|||unknown(NO_COVERAGE)	18	0.00359425	0.0136	0	5008	,	,		14583	0		0	False		,,,				2504	0				p.Q148fs		Pindel	.											.	KLKB1	155	.	0			c.444_445insT						.			65,4201		1,63,2069						-9.8	0.3			116	2,8252		0,2,4125	no	frameshift	KLKB1	NM_000892.3		1,65,6194	A1A1,A1R,RR		0.0242,1.5237,0.5351				67,12453				SO:0001589	frameshift_variant	3818	exon5			.	M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"Kallikreins"	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.451dupT	chr4.hg19:g.187158057_187158057dupT	ENSP00000264690:p.Phe149fs	125.0	0.0		133.0	17.0	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Frame_Shift_Ins	INS	ENST00000264690.6	hg19	CCDS34120.1																																																																																			.	.		0.401	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892		T	187158051	-	T	187158050	7	5	24	1	0	1	1	0	0	0	0	0	8421	1020	36	0	458	0	KLKB1	4	187158050	Frame_Shift_Ins	INS	-	TCGA-5C-A9VG-01A-11D-A36X-10	61526818	187158050	3996226	36	3243										
CDH9	1007	hgsc.bcm.edu	37	chr5	26902786	26902786	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	atcgtggatcagggtgagtgTtacttgcatccactcttaaa	10	8	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:26902786T>G	ENST00000231021.4	-	7	1224	c.1052A>C	c.(1051-1053)aAc>aCc	p.N351T		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	351	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						AGGGTGAGTGTTACTTGCATC	0.353																																					p.N351T	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											CDH9,NS,carcinoma,0,1	CDH9	305	.	0			c.A1052C						.						90	89	89					5																	26902786		2203	4300	6503	SO:0001583	missense	1007	exon7			TGAGTGTTACTTG	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1052A>C	chr5.hg19:g.26902786T>G	ENSP00000231021:p.Asn351Thr	109.0	0.0		93.0	17.0	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.457689	0.84317	.	.	ENSG00000113100	ENST00000231021	T	0.55052	0.54	5.62	5.62	0.85841	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.81616	0.4860	H	0.96576	3.845	0.54753	D	0.999986	D	0.89917	1.0	D	0.91635	0.999	D	0.87790	0.2618	9	.	.	.	.	14.6446	0.68751	0.0:0.0:0.0:1.0	.	351	Q9ULB4	CADH9_HUMAN	T	351	ENSP00000231021:N351T	.	N	-	2	0	CDH9	26938543	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.671000	0.83941	2.139000	0.66308	0.528000	0.53228	AAC	.	.		0.353	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		G	26902786	T	G	26902786	3	3	24	1	0	0	0	0	1	0	0	0	3119	1725	60	5	1341	5	CDH9	5	26902786	Missense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10		26902786	154012474	37	3244										
NUP155	9631	hgsc.bcm.edu	37	chr5	37352900	37352900	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tctacaggggtcgccaaaacCaggaggtgtcgcacatgagg	14	10	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:37352900C>A	ENST00000231498.3	-	5	698	c.495G>T	c.(493-495)ctG>ctT	p.L165L	NUP155_ENST00000381843.2_Silent_p.L106L|NUP155_ENST00000513532.1_Silent_p.L165L	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	165					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TCGCCAAAACCAGGAGGTGTC	0.393																																					p.L165L		Atlas-SNP	.											.	NUP155	116	.	0			c.G495T						.						88	84	85					5																	37352900		2203	4300	6503	SO:0001819	synonymous_variant	9631	exon5			CAAAACCAGGAGG	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.495G>T	chr5.hg19:g.37352900C>A		161.0	0.0		163.0	27.0	NM_153485	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	hg19	CCDS3921.1																																																																																			.	.		0.393	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		A	37352900	C	A	37352900	2	1	24	1	0	0	0	0	0	0	0	1	10765	581	21	3		3	NUP155	5	37352900	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	10450114	37352900	143562360	38	3245										
PELO	53918	hgsc.bcm.edu	37	chr5	52097577	52097577	+	Frame_Shift_Del	DEL	A	A	-													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tagtcttcacgtttctggggAacagctcagccagttgactg							TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:52097577delA	ENST00000274311.2	+	3	2046	c.1061delA	c.(1060-1062)gaafs	p.E354fs	ITGA1_ENST00000282588.6_Intron|ITGA1_ENST00000504086.1_Intron|PELO_ENST00000506949.1_3'UTR	NM_015946.4	NP_057030.3	Q9BRX2	PELO_HUMAN	pelota homolog (Drosophila)	354					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA catabolic process, non-stop decay (GO:0070481)|RNA surveillance (GO:0071025)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	11		Lung NSC(810;4.94e-05)|Breast(144;0.0848)				GTTTCTGGGGAACAGCTCAGC	0.517																																					p.E354fs		Atlas-Indel,Pindel	.											.	PELO	25	.	0			c.1060delG						.						65	61	62					5																	52097577		2203	4300	6503	SO:0001589	frameshift_variant	53918	exon3			.		CCDS3956.1	5q11.2	2008-07-18	2001-11-28		ENSG00000152684	ENSG00000152684			8829	protein-coding gene	gene with protein product		605757	"pelota (Drosophila) homolog"			11060452	Standard	NM_015946		Approved		uc003jos.3	Q9BRX2	OTTHUMG00000096973	ENST00000274311.2:c.1061delA	chr5.hg19:g.52097577delA	ENSP00000274311:p.Glu354fs	106.0	0.0		127.0	16.0	NM_015946	Q9GZS6|Q9Y306	Frame_Shift_Del	DEL	ENST00000274311.2	hg19	CCDS3956.1																																																																																			.	.		0.517	PELO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214040.1	NM_015946		-	52097577	A	-	52097577	7	5	24	1	0	1	0	1	0	0	0	0	11733	246	9	0	1067	0	PELO	5	52097577	Frame_Shift_Del	DEL	A	TCGA-5C-A9VG-01A-11D-A36X-10	14744677	52097577	128817683	39	3246										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54649070	54649070	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gttttatttacaaatgcccgCaaatttgatgggaaggattt	9	5	0	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:54649070C>G	ENST00000230640.5	+	14	1760	c.1506C>G	c.(1504-1506)cgC>cgG	p.R502R	SKIV2L2_ENST00000545714.1_Silent_p.R401R	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	502	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				CAAATGCCCGCAAATTTGATG	0.328																																					p.R502R	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.C1506G						.						85	91	89					5																	54649070		2203	4300	6503	SO:0001819	synonymous_variant	23517	exon14			TGCCCGCAAATTT	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.1506C>G	chr5.hg19:g.54649070C>G		92.0	0.0		99.0	7.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	hg19	CCDS3967.1																																																																																			.	.		0.328	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			G	54649070	C	G	54649070	2	3	24	1	0	0	0	0	0	0	0	1	14375	697	25	4		4	SKIV2L2	5	54649070	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	2551493	54649070	126266190	40	3247										
CCNB1	891	hgsc.bcm.edu	37	chr5	68470853	68470853	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	aagcaccaaatcagacagatGgaaatgaagattctaagagc	9	7	2	5			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:68470853G>A	ENST00000256442.5	+	6	1108	c.855G>A	c.(853-855)atG>atA	p.M285I	snoU13_ENST00000459230.1_RNA	NM_031966.3	NP_114172.1	P14635	CCNB1_HUMAN	cyclin B1	285					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to iron(III) ion (GO:0071283)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle checkpoint (GO:0071174)|mitotic spindle stabilization (GO:0043148)|negative regulation of gene expression (GO:0010629)|negative regulation of protein phosphorylation (GO:0001933)|oocyte maturation (GO:0001556)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of chromosome condensation (GO:0060623)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to DDT (GO:0046680)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|spermatogenesis (GO:0007283)|tissue regeneration (GO:0042246)|ventricular cardiac muscle cell development (GO:0055015)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase activity (GO:0016301)|patched binding (GO:0005113)|protein kinase binding (GO:0019901)			large_intestine(2)|lung(5)|skin(1)	8		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TCAGACAGATGGAAATGAAGA	0.403																																					p.M285I		Atlas-SNP	.											.	CCNB1	36	.	0			c.G855A						.						140	142	141					5																	68470853		2203	4300	6503	SO:0001583	missense	891	exon6			ACAGATGGAAATG	U22364	CCDS3997.1	5q12	2008-07-18			ENSG00000134057	ENSG00000134057			1579	protein-coding gene	gene with protein product	"G2/mitotic-specific cyclin B1"	123836		CCNB		1386342	Standard	NM_031966		Approved		uc003jvm.3	P14635	OTTHUMG00000097817	ENST00000256442.5:c.855G>A	chr5.hg19:g.68470853G>A	ENSP00000256442:p.Met285Ile	145.0	0.0		177.0	23.0	NM_031966	A8K066|Q5TZP9	Missense_Mutation	SNP	ENST00000256442.5	hg19	CCDS3997.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.452138	0.84209	.	.	ENSG00000134057	ENST00000256442;ENST00000506572;ENST00000508407;ENST00000505500;ENST00000507798	T;T;T;T;T	0.15487	2.42;2.42;2.42;2.42;2.42	6.16	6.16	0.99307	Cyclin, N-terminal (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.56775	0.2008	H	0.95470	3.675	0.80722	D	1	P;D;D	0.64830	0.857;0.96;0.994	P;P;D	0.67548	0.785;0.887;0.952	T	0.67902	-0.5550	10	0.87932	D	0	.	19.6313	0.95704	0.0:0.0:1.0:0.0	.	285;285;285	E9PC90;Q5TZP9;P14635	.;.;CCNB1_HUMAN	I	285;285;232;285;101	ENSP00000256442:M285I;ENSP00000423387:M285I;ENSP00000426092:M232I;ENSP00000424588:M285I;ENSP00000426230:M101I	ENSP00000256442:M285I	M	+	3	0	CCNB1	68506609	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.941000	0.87700	2.937000	0.99478	0.650000	0.86243	ATG	.	.		0.403	CCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215084.1	NM_031966		A	68470853	G	A	68470853	3	1	24	1	0	0	0	0	1	0	0	0	2913	1348	47	3	877	3	CCNB1	5	68470853	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	13821783	68470853	112444407	41	3248										
EDIL3	10085	hgsc.bcm.edu	37	chr5	83239361	83239361	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	atgacattttttctgtgagtGtcattgtcaaaatttccctg	7	7	3	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:83239361G>A	ENST00000296591.5	-	11	1738	c.1320C>T	c.(1318-1320)gaC>gaT	p.D440D	EDIL3_ENST00000380138.3_Silent_p.D430D	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	440	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		TTCTGTGAGTGTCATTGTCAA	0.418																																					p.D440D		Atlas-SNP	.											.	EDIL3	94	.	0			c.C1320T						.						126	120	122					5																	83239361		2203	4300	6503	SO:0001819	synonymous_variant	10085	exon11			GTGAGTGTCATTG	U70312	CCDS4062.1, CCDS64195.1	5q14	2008-02-05			ENSG00000164176	ENSG00000164176			3173	protein-coding gene	gene with protein product		606018				9420328	Standard	NM_005711		Approved	DEL1	uc003kio.1	O43854	OTTHUMG00000119047	ENST00000296591.5:c.1320C>T	chr5.hg19:g.83239361G>A		118.0	0.0		117.0	21.0	NM_005711	B2R763|O43855|Q5D094|Q8N610	Silent	SNP	ENST00000296591.5	hg19	CCDS4062.1																																																																																			.	.		0.418	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711		A	83239361	G	A	83239361	2	1	24	1	0	0	0	0	0	0	0	1	4917	1368	48	3		3	EDIL3	5	83239361	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	14768508	83239361	97675899	42	3249										
LARP1	23367	hgsc.bcm.edu	37	chr5	154172335	154172335	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	atggagatgaggattgccagCgaggcgggcagaagaagaaa	17	5	0	5			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:154172335C>T	ENST00000336314.4	+	4	511	c.487C>T	c.(487-489)Cga>Tga	p.R163*		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	240					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GGATTGCCAGCGAGGCGGGCA	0.512																																					p.R163X		Atlas-SNP	.											.,2	LARP1	187	.	0			c.C487T						.						109	109	109					5																	154172335		2203	4300	6503	SO:0001587	stop_gained	23367	exon4			TGCCAGCGAGGCG	AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"La ribonucleoprotein domain containing"	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.487C>T	chr5.hg19:g.154172335C>T	ENSP00000336721:p.Arg163*	105.0	0.0		110.0	11.0	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Nonsense_Mutation	SNP	ENST00000336314.4	hg19	CCDS4328.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.169644|8.169644	0.98688|0.98688	.|.	.|.	ENSG00000155506|ENSG00000155506	ENST00000517616;ENST00000518194|ENST00000336314;ENST00000518297;ENST00000519931;ENST00000524248;ENST00000523163	.|.	.|.	.|.	5.63|5.63	3.52|3.52	0.40303|0.40303	.|.	.|0.120525	.|0.53938	.|D	.|0.000045	T|.	0.27900|.	0.0687|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.28996|.	-1.0026|.	3|.	.|0.05525	.|T	.|0.97	-6.0673|-6.0673	12.1582|12.1582	0.54089|0.54089	0.5659:0.4341:0.0:0.0|0.5659:0.4341:0.0:0.0	.|.	.|.	.|.	.|.	V|X	142;1|163;240;35;35;15	.|.	.|ENSP00000336721:R163X	A|R	+|+	2|1	0|2	LARP1|LARP1	154152528|154152528	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.616000|4.616000	0.61197|0.61197	1.438000|1.438000	0.47492|0.47492	0.655000|0.655000	0.94253|0.94253	GCG|CGA	.	.		0.512	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		T	154172335	C	T	154172335	4	4	24	1	0	0	0	0	0	1	0	0	8637	760	27	1	501	1	LARP1	5	154172335	Nonsense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	70932974	154172335	26742925	43	3250										
HLA-B	3106	hgsc.bcm.edu	37	chr6	31323270	31323270	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cctcgccatcccgctgccagGtcagtgtgatctccgcaggg	12	16	2	1	rs151341351		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:31323270G>A	ENST00000412585.2	-	4	747	c.719C>T	c.(718-720)aCc>aTc	p.T240I		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	240	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CCGCTGCCAGGTCAGTGTGAT	0.607									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.T240I		Atlas-SNP	.											.	HLA-B	54	.	0			c.C719T						.						92	86	88					6																	31323270		2203	4300	6503	SO:0001583	missense	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	TGCCAGGTCAGTG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4932	protein-coding gene	gene with protein product		142830	"ankylosing spondylitis"	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.719C>T	chr6.hg19:g.31323270G>A	ENSP00000399168:p.Thr240Ile	129.0	0.0		152.0	31.0	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	hg19	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	12.54	1.969553	0.34754	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596	T	0.03358	3.96	3.06	3.06	0.35304	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.452724	0.16632	U	0.206027	T	0.06508	0.0167	M	0.64630	1.985	0.28228	N	0.926237	D	0.89917	1.0	D	0.91635	0.999	T	0.09640	-1.0665	10	0.87932	D	0	.	7.6422	0.28300	0.0:0.0:0.7472:0.2528	.	240	P01889	1B07_HUMAN	I	240;119;119	ENSP00000399168:T240I	ENSP00000399168:T240I	T	-	2	0	HLA-B	31431249	0.609000	0.26975	0.999000	0.59377	0.838000	0.47535	-0.280000	0.08468	1.742000	0.51746	0.442000	0.29010	ACC	.	.		0.607	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		A	31323270	G	A	31323270	3	1	24	1	0	0	0	0	1	0	0	0	7205	1261	44	3	385	3	HLA-B	6	31323270	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10		31323270	139791797	44	3251										
VARS	7407	hgsc.bcm.edu	37	chr6	31747209	31747209	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gcctgaggctcacagtcaggCcggatccgggtgaggttgta	16	10	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:31747209C>A	ENST00000375663.3	-	28	3833	c.3393G>T	c.(3391-3393)cgG>cgT	p.R1131R	VWA7_ENST00000375688.4_5'Flank|VWA7_ENST00000447450.1_5'Flank|VWA7_ENST00000375686.3_5'Flank|VWA7_ENST00000467576.1_5'Flank|Y_RNA_ENST00000364685.1_RNA|VARS_ENST00000482996.1_5'Flank	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	1131					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	CACAGTCAGGCCGGATCCGGG	0.667																																					p.R1131R		Atlas-SNP	.											.	VARS	76	.	0			c.G3393T						.						41	34	36					6																	31747209		1509	2706	4215	SO:0001819	synonymous_variant	7407	exon28			GTCAGGCCGGATC	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	12651	protein-coding gene	gene with protein product	"valine tRNA ligase 1, cytoplasmic"	192150	"valyl-tRNA synthetase 2"	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.3393G>T	chr6.hg19:g.31747209C>A		89.0	0.0		77.0	25.0	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Silent	SNP	ENST00000375663.3	hg19	CCDS34412.1																																																																																			.	.		0.667	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295		A	31747209	C	A	31747209	2	1	24	1	0	0	0	0	0	0	0	1	17138	726	26	3		3	VARS	6	31747209	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	423939	31747209	139367858	45	3252										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33631619	33631619	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gcctctctctttgagctggaCcccaccaccttgcagaaaac	7	16	2	2	rs2229630	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:33631619C>G	ENST00000374316.5	+	12	2170	c.1110C>G	c.(1108-1110)gaC>gaG	p.D370E	ITPR3_ENST00000605930.1_Missense_Mutation_p.D370E			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	370	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TTGAGCTGGACCCCACCACCT	0.612																																					p.D370E		Atlas-SNP	.											.	ITPR3	409	.	0			c.C1110G						.						79	76	77					6																	33631619		2203	4300	6503	SO:0001583	missense	3710	exon11			GCTGGACCCCACC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.1110C>G	chr6.hg19:g.33631619C>G	ENSP00000363435:p.Asp370Glu	65.0	0.0		94.0	29.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.553799	0.65425	.	.	ENSG00000096433	ENST00000374316	D	0.87256	-2.23	4.74	0.62	0.17637	MIR motif (2);MIR (2);	0.111192	0.64402	D	0.000010	D	0.88779	0.6529	M	0.78456	2.415	0.50632	D	0.999889	D	0.67145	0.996	D	0.69479	0.964	D	0.87333	0.2326	10	0.48119	T	0.1	-39.8685	10.1744	0.42931	0.0:0.6136:0.0:0.3864	.	370	Q14573	ITPR3_HUMAN	E	370	ENSP00000363435:D370E	ENSP00000363435:D370E	D	+	3	2	ITPR3	33739597	1.000000	0.71417	0.999000	0.59377	0.868000	0.49771	2.001000	0.40825	0.221000	0.20879	0.484000	0.47621	GAC	.	C|0.995;T|0.005		0.612	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		G	33631619	C	G	33631619	3	3	24	1	0	0	0	0	1	0	0	0	7931	506	18	4	1152	4	ITPR3	6	33631619	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	1884410	33631619	137483448	46	3253										
MOCS1	4337	hgsc.bcm.edu	37	chr6	39881105	39881105	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	agcgcacatccagggggaggCcctcagtcaaggccgcaaag	14	13	2	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:39881105C>T	ENST00000340692.5	-	6	716	c.713G>A	c.(712-714)gGc>gAc	p.G238D	MOCS1_ENST00000373195.3_Missense_Mutation_p.G151D|MOCS1_ENST00000308559.7_Missense_Mutation_p.G238D|MOCS1_ENST00000432280.2_Missense_Mutation_p.G209D|MOCS1_ENST00000373175.4_Missense_Mutation_p.G209D|MOCS1_ENST00000425303.2_Missense_Mutation_p.G238D|MOCS1_ENST00000373186.4_Missense_Mutation_p.G238D|MOCS1_ENST00000373188.2_Missense_Mutation_p.G238D			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	238	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					CAGGGGGAGGCCCTCAGTCAA	0.587																																					p.G238D	NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	Atlas-SNP	.											.	MOCS1	87	.	0			c.G713A						.						109	95	100					6																	39881105		2203	4300	6503	SO:0001583	missense	4337	exon5			GGGAGGCCCTCAG	AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.713G>A	chr6.hg19:g.39881105C>T	ENSP00000344794:p.Gly238Asp	114.0	0.0		122.0	25.0	NM_005943	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	hg19		.	.	.	.	.	.	.	.	.	.	C	0.011	-1.722757	0.00700	.	.	ENSG00000124615	ENST00000373186;ENST00000308559;ENST00000373175;ENST00000373188;ENST00000373195;ENST00000340692;ENST00000425303;ENST00000432280	T;T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99	4.68	3.81	0.43845	Elongator protein 3/MiaB/NifB (1);Aldolase-type TIM barrel (1);	0.354601	0.30193	N	0.010183	T	0.02342	0.0072	N	0.00102	-2.13	0.34074	D	0.658831	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.002;0.001;0.002;0.002	T	0.36383	-0.9750	9	.	.	.	-15.5051	6.1159	0.20126	0.0:0.6601:0.0:0.3399	.	238;238;238;238;238	Q9NZB8-2;Q9NZB8-5;Q9NZB8;Q9NZB8-8;Q9NZB8-6	.;.;MOCS1_HUMAN;.;.	D	238;238;209;238;151;238;238;209	ENSP00000362282:G238D;ENSP00000309843:G238D;ENSP00000362270:G209D;ENSP00000362284:G238D;ENSP00000362291:G151D;ENSP00000344794:G238D;ENSP00000416478:G238D;ENSP00000410809:G209D	.	G	-	2	0	MOCS1	39989083	0.910000	0.30920	0.875000	0.34327	0.062000	0.15995	1.586000	0.36611	0.980000	0.38523	0.655000	0.94253	GGC	.	.		0.587	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943		T	39881105	C	T	39881105	3	4	24	1	0	0	0	0	1	0	0	0	9699	739	26	3	464	3	MOCS1	6	39881105	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	6249486	39881105	131233962	47	3254										
KCNQ5	56479	hgsc.bcm.edu	37	chr6	73787165	73787165	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cctccgcatggtgcgcatggAccgaaggggaggcacttgga	16	11	0	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:73787165A>G	ENST00000370398.1	+	4	846	c.737A>G	c.(736-738)gAc>gGc	p.D246G	KCNQ5_ENST00000403813.2_Missense_Mutation_p.D246G|KCNQ5_ENST00000402622.2_Missense_Mutation_p.D246G|KCNQ5_ENST00000355194.4_Missense_Mutation_p.D246G|KCNQ5_ENST00000414165.2_Missense_Mutation_p.D246G|KCNQ5_ENST00000370392.1_Missense_Mutation_p.D246G|KCNQ5_ENST00000355635.3_Missense_Mutation_p.D246G|KCNQ5_ENST00000342056.2_Missense_Mutation_p.D246G	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	246					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	GTGCGCATGGACCGAAGGGGA	0.428																																					p.D246G	GBM(142;1375 1859 14391 23261 44706)	Atlas-SNP	.											.	KCNQ5	153	.	0			c.A737G						.						77	74	75					6																	73787165		2203	4300	6503	SO:0001583	missense	56479	exon4			GCATGGACCGAAG	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.737A>G	chr6.hg19:g.73787165A>G	ENSP00000359425:p.Asp246Gly	84.0	0.0		105.0	8.0	NM_001160132	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	hg19	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.714811	0.89112	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000370392;ENST00000402622;ENST00000355635;ENST00000403813;ENST00000414165	D;D;D;D;D;D;D;D	0.98455	-4.94;-4.94;-4.94;-4.94;-4.94;-4.94;-4.94;-4.94	5.84	5.84	0.93424	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98333	0.9447	L	0.52905	1.665	0.80722	D	1	P;D;D;D;D;D	0.89917	0.712;1.0;0.989;0.986;1.0;0.985	P;D;D;D;D;D	0.81914	0.493;0.986;0.929;0.962;0.995;0.972	D	0.99904	1.1174	10	0.72032	D	0.01	.	16.2194	0.82247	1.0:0.0:0.0:0.0	.	246;246;246;246;246;246	F5GZV0;Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82;Q9NR82-4	.;.;.;.;KCNQ5_HUMAN;.	G	246	ENSP00000345055:D246G;ENSP00000347326:D246G;ENSP00000359425:D246G;ENSP00000359419:D246G;ENSP00000385501:D246G;ENSP00000347853:D246G;ENSP00000384453:D246G;ENSP00000409861:D246G	ENSP00000345055:D246G	D	+	2	0	KCNQ5	73843886	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.234000	0.73211	0.528000	0.53228	GAC	.	.		0.428	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		G	73787165	A	G	73787165	3	3	24	1	0	0	0	0	1	0	0	0	8095	275	10	2	751	2	KCNQ5	6	73787165	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	33906060	73787165	97327902	48	3255										
SENP6	26054	hgsc.bcm.edu	37	chr6	76423528	76423528	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	atatgtattgcagtatgtagAgagcttttttgaggtgggtt	13	2	0	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:76423528A>G	ENST00000447266.2	+	23	3594	c.3116A>G	c.(3115-3117)gAg>gGg	p.E1039G	SENP6_ENST00000370010.2_Missense_Mutation_p.E1032G|SENP6_ENST00000370014.3_Missense_Mutation_p.E1039G|SENP6_ENST00000541192.1_3'UTR	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	1039	Protease.				protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				CAGTATGTAGAGAGCTTTTTT	0.318																																					p.E1039G		Atlas-SNP	.											.	SENP6	189	.	0			c.A3116G						.						99	91	93					6																	76423528		1820	4077	5897	SO:0001583	missense	26054	exon23			ATGTAGAGAGCTT		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.3116A>G	chr6.hg19:g.76423528A>G	ENSP00000402527:p.Glu1039Gly	182.0	0.0		222.0	71.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	hg19	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.359393	0.82353	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000447266	T;T;T	0.40756	1.02;1.02;1.02	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.67183	0.2866	M	0.93854	3.465	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.72338	0.935;0.977	T	0.77981	-0.2383	10	0.87932	D	0	-7.1117	14.9661	0.71196	1.0:0.0:0.0:0.0	.	1032;1039	Q9GZR1-2;Q9GZR1	.;SENP6_HUMAN	G	1032;1039;1039	ENSP00000359027:E1032G;ENSP00000359031:E1039G;ENSP00000402527:E1039G	ENSP00000359027:E1032G	E	+	2	0	SENP6	76480248	1.000000	0.71417	1.000000	0.80357	0.655000	0.38815	8.910000	0.92685	2.005000	0.58758	0.460000	0.39030	GAG	.	.		0.318	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		G	76423528	A	G	76423528	3	3	24	1	0	0	0	0	1	0	0	0	14065	304	11	2	3206	2	SENP6	6	76423528	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	2636363	76423528	94691539	49	3256										
RSPO3	84870	hgsc.bcm.edu	37	chr6	127440418	127440418	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	agccaaaacgcctcccggggAaggcgccagcgaagaagtaa	13	12	0	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:127440418A>T	ENST00000356698.4	+	1	670	c.81A>T	c.(79-81)ggA>ggT	p.G27G	RSPO3_ENST00000368317.3_Silent_p.G27G	NM_032784.3	NP_116173.2	Q9BXY4	RSPO3_HUMAN	R-spondin 3	27					branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)	extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)		PTPRK/RSPO3(10)	breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17				GBM - Glioblastoma multiforme(226;0.0555)		CCTCCCGGGGAAGGCGCCAGC	0.537																																					p.G27G		Atlas-SNP	.											.	RSPO3	32	.	0			c.A81T						.						150	164	160					6																	127440418		2203	4300	6503	SO:0001819	synonymous_variant	84870	exon1			CCGGGGAAGGCGC	BC022367	CCDS5135.1	6q22.33	2013-02-28	2011-06-29	2005-08-08	ENSG00000146374	ENSG00000146374		"Endogenous ligands"	20866	protein-coding gene	gene with protein product		610574	"thrombospondin, type I, domain containing 2", "R-spondin 3 homolog (Xenopus laevis)"	THSD2		10842357, 15469841	Standard	NM_032784		Approved	FLJ14440	uc003qar.3	Q9BXY4	OTTHUMG00000015521	ENST00000356698.4:c.81A>T	chr6.hg19:g.127440418A>T		137.0	0.0		163.0	16.0	NM_032784	B2RC27|Q5VTV4|Q96K87	Silent	SNP	ENST00000356698.4	hg19	CCDS5135.1																																																																																			.	.		0.537	RSPO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042111.1	NM_032784		T	127440418	A	T	127440418	2	4	24	1	0	0	0	0	0	0	0	1	13726	233	9	4		4	RSPO3	6	127440418	Silent	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	51016890	127440418	43674649	50	3257										
TXLNB	167838	hgsc.bcm.edu	37	chr6	139609802	139609802	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ggccctggcagagccctcttTccctgctgtgctggcagcag	13	15	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:139609802T>A	ENST00000358430.3	-	2	467	c.235A>T	c.(235-237)Aaa>Taa	p.K79*	RP11-445F6.2_ENST00000441249.1_RNA|RP11-445F6.2_ENST00000440518.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	79						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		GAGCCCTCTTTCCCTGCTGTG	0.527																																					p.K79X		Atlas-SNP	.											.	TXLNB	96	.	0			c.A235T						.						113	111	111					6																	139609802		2203	4300	6503	SO:0001587	stop_gained	167838	exon2			CCTCTTTCCCTGC		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"chromosome 6 open reading frame 198"	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.235A>T	chr6.hg19:g.139609802T>A	ENSP00000351206:p.Lys79*	129.0	0.0		128.0	47.0	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Nonsense_Mutation	SNP	ENST00000358430.3	hg19	CCDS34545.1	.	.	.	.	.	.	.	.	.	.	T	34	5.314079	0.95655	.	.	ENSG00000164440	ENST00000358430	.	.	.	5.98	-0.911	0.10507	.	1.115670	0.06832	N	0.794182	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.3354	6.5519	0.22438	0.0:0.1984:0.4327:0.3689	.	.	.	.	X	79	.	.	K	-	1	0	TXLNB	139651495	0.687000	0.27671	0.001000	0.08648	0.002000	0.02628	-0.488000	0.06497	-0.130000	0.11599	-1.123000	0.02005	AAA	.	.		0.527	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235		A	139609802	T	A	139609802	4	1	24	1	0	0	0	0	0	1	0	0	16803	1792	62	4	1855	4	TXLNB	6	139609802	Nonsense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	12169384	139609802	31505265	51	3258										
MICALL2	79778	hgsc.bcm.edu	37	chr7	1484651	1484651	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cagccgctgctgtgcacgggGcagctgacgaccagcccatc	13	16	0	1	rs375853882		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:1484651G>A	ENST00000297508.7	-	6	1230	c.1055C>T	c.(1054-1056)gCc>gTc	p.A352V	MICALL2_ENST00000405088.4_Missense_Mutation_p.A140V	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	352	Mediates targeting to the cell plasma membrane. {ECO:0000250}.|Necessary and sufficient for interaction with actinins. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		TGTGCACGGGGCAGCTGACGA	0.736																																					p.A352V		Atlas-SNP	.											.	MICALL2	63	.	0			c.C1055T						.		VAL/ALA	1,4099		0,1,2049	8	7	8		1055	2.1	0	7		8	0,8082		0,0,4041	no	missense	MICALL2	NM_182924.3	64	0,1,6090	AA,AG,GG		0.0,0.0244,0.0082	possibly-damaging	352/905	1484651	1,12181	2050	4041	6091	SO:0001583	missense	79778	exon6			CACGGGGCAGCTG	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"junctional Rab13-binding protein"					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.1055C>T	chr7.hg19:g.1484651G>A	ENSP00000297508:p.Ala352Val	66.0	0.0		70.0	6.0	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	hg19	CCDS5324.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.115906	0.56505	2.44E-4	0.0	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.69040	2.38;-0.37	3.99	2.12	0.27331	.	0.759254	0.10766	N	0.636615	T	0.66327	0.2778	L	0.32530	0.975	0.09310	N	1	D	0.67145	0.996	D	0.63381	0.914	T	0.52290	-0.8595	10	0.29301	T	0.29	.	5.5566	0.17119	0.118:0.2202:0.6618:0.0	.	352	Q8IY33	MILK2_HUMAN	V	140;352	ENSP00000385928:A140V;ENSP00000297508:A352V	ENSP00000297508:A352V	A	-	2	0	MICALL2	1451177	0.012000	0.17670	0.002000	0.10522	0.003000	0.03518	1.192000	0.32150	0.271000	0.22005	0.561000	0.74099	GCC	.	.		0.736	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924		A	1484651	G	A	1484651	3	1	24	1	0	0	0	0	1	0	0	0	9583	1203	42	3	1707	3	MICALL2	7	1484651	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10		1484651	157654012	52	3259										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83014671	83014671	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	taactttcgcttgtaaagatCgtggggtacattccagcaaa	9	8	0	1	rs145707650		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:83014671C>A	ENST00000307792.3	-	16	2281	c.1814G>T	c.(1813-1815)cGa>cTa	p.R605L	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R545L	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	605	Ig-like C2-type.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TTGTAAAGATCGTGGGGTACA	0.398																																					p.R605L		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G1814T						.	C	LEU/ARG,LEU/ARG	0,4406		0,0,2203	203	182	189		1634,1814	5.5	1	7	dbSNP_134	189	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SEMA3E	NM_001178129.1,NM_012431.2	102,102	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	545/716,605/776	83014671	1,13005	2203	4300	6503	SO:0001583	missense	9723	exon16			AAAGATCGTGGGG	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1814G>T	chr7.hg19:g.83014671C>A	ENSP00000303212:p.Arg605Leu	162.0	0.0		203.0	40.0	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.573826	0.86542	0.0	1.16E-4	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.21734	1.99;1.99	5.54	5.54	0.83059	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.45776	0.1359	M	0.78456	2.415	0.58432	D	0.999999	P	0.51449	0.945	D	0.62955	0.909	T	0.21484	-1.0244	10	0.30854	T	0.27	.	16.4843	0.84180	0.0:0.8692:0.1308:0.0	.	605	O15041	SEM3E_HUMAN	L	605;545;605	ENSP00000303212:R605L;ENSP00000405052:R545L	ENSP00000303212:R605L	R	-	2	0	SEMA3E	82852607	0.997000	0.39634	0.977000	0.42913	0.990000	0.78478	4.558000	0.60789	2.597000	0.87782	0.650000	0.86243	CGA	.	C|1.000;A|0.000		0.398	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		A	83014671	C	A	83014671	3	1	24	1	0	0	0	0	1	0	0	0	14043	884	31	1	521	1	SEMA3E	7	83014671	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	81530020	83014671	76123992	53	3260										
ACHE	43	hgsc.bcm.edu	37	chr7	100490028	100490028	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ctcctctgccgtgtagtttcGagaggggtccagggggatcc	15	11	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:100490028G>A	ENST00000412389.1	-	2	1635	c.1480C>T	c.(1480-1482)Cga>Tga	p.R494*	ACHE_ENST00000241069.5_Nonsense_Mutation_p.R494*|ACHE_ENST00000419336.2_Nonsense_Mutation_p.R406*|ACHE_ENST00000411582.1_Nonsense_Mutation_p.R494*|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000302913.4_Nonsense_Mutation_p.R494*|ACHE_ENST00000428317.1_Nonsense_Mutation_p.R494*			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	494					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	GTGTAGTTTCGAGAGGGGTCC	0.597																																					p.R494X		Atlas-SNP	.											.	ACHE	80	.	0			c.C1480T						.						48	47	48					7																	100490028		2203	4300	6503	SO:0001587	stop_gained	43	exon3			AGTTTCGAGAGGG		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"Blood group antigens"	108	protein-coding gene	gene with protein product	"Yt blood group"	100740	"acetylcholinesterase (YT blood group)", "acetylcholinesterase (Yt blood group)", "acetylcholinesterase"	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1480C>T	chr7.hg19:g.100490028G>A	ENSP00000394976:p.Arg494*	131.0	0.0		162.0	22.0	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Nonsense_Mutation	SNP	ENST00000412389.1	hg19	CCDS5709.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122826	0.77436	.	.	ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000302913;ENST00000412389;ENST00000411582;ENST00000422451	.	.	.	3.92	3.0	0.34707	.	0.269718	0.29493	N	0.011991	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	5.8005	0.18412	0.2592:0.0:0.7408:0.0	.	.	.	.	X	406;494;494;494;494;494;494	.	ENSP00000241069:R494X	R	-	1	2	ACHE	100327964	0.964000	0.33143	0.869000	0.34112	0.560000	0.35617	2.190000	0.42630	0.942000	0.37525	0.491000	0.48974	CGA	.	.		0.597	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831		A	100490028	G	A	100490028	4	1	24	1	0	0	0	0	0	1	0	0	141	1066	37	1	511	1	ACHE	7	100490028	Nonsense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	17475357	100490028	58648635	54	3261										
MLL5	55904	hgsc.bcm.edu	37	chr7	104730539	104730539	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttctgaatccatggaaaataTcaatagtggttatgagacca	8	6	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:104730539T>C	ENST00000311117.3	+	14	1987	c.1442T>C	c.(1441-1443)aTc>aCc	p.I481T	KMT2E_ENST00000257745.4_Missense_Mutation_p.I481T|KMT2E_ENST00000476671.1_Missense_Mutation_p.I481T|KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000334877.4_Missense_Mutation_p.I481T	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	481					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										ATGGAAAATATCAATAGTGGT	0.353																																					p.I481T		Atlas-SNP	.											.	MLL5	173	.	0			c.T1442C						.						106	120	115					7																	104730539		2202	4298	6500	SO:0001583	missense	55904	exon13			AAAATATCAATAG	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.1442T>C	chr7.hg19:g.104730539T>C	ENSP00000312379:p.Ile481Thr	427.0	0.0		539.0	189.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.312204	0.60414	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000478990;ENST00000476671;ENST00000537308	D;D;D;D;D	0.95724	-2.91;-2.53;-2.91;-3.79;-3.26	5.83	5.83	0.93111	.	0.063289	0.64402	D	0.000005	D	0.93239	0.7846	L	0.34521	1.04	0.80722	D	1	D;P	0.59357	0.985;0.867	P;B	0.50537	0.643;0.288	D	0.91244	0.5024	10	0.11182	T	0.66	.	14.7838	0.69787	0.0:0.0:0.0:1.0	.	481;481	Q8IZD2;Q8IZD2-3	MLL5_HUMAN;.	T	481;481;481;481;481;339;481;415	ENSP00000312379:I481T;ENSP00000335599:I481T;ENSP00000257745:I481T;ENSP00000419883:I339T;ENSP00000417888:I481T	ENSP00000257745:I481T	I	+	2	0	MLL5	104517775	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.319000	0.79040	2.236000	0.73375	0.533000	0.62120	ATC	.	.		0.353	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			C	104730539	T	C	104730539	3	2	24	1	0	0	0	0	1	0	0	0	9633	1435	50	2	1488	2	MLL5	7	104730539	Missense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	4240511	104730539	54408124	55	3262										
IFRD1	3475	hgsc.bcm.edu	37	chr7	112102091	112102091	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ctggaatgtttggaaaatatCttcactaaatcctatctcaa	5	8	3	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:112102091C>T	ENST00000403825.3	+	7	915	c.654C>T	c.(652-654)atC>atT	p.I218I	IFRD1_ENST00000005558.4_Silent_p.I218I|IFRD1_ENST00000486688.1_3'UTR|IFRD1_ENST00000535603.1_Silent_p.I168I	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	218					adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						TGGAAAATATCTTCACTAAAT	0.343																																					p.I218I		Atlas-SNP	.											.	IFRD1	46	.	0			c.C654T						.						105	102	103					7																	112102091		2203	4300	6503	SO:0001819	synonymous_variant	3475	exon8			AAATATCTTCACT	Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.654C>T	chr7.hg19:g.112102091C>T		106.0	0.0		153.0	35.0	NM_001007245	B7Z5G1|O75234|Q5U013|Q9BVE4	Silent	SNP	ENST00000403825.3	hg19	CCDS34736.1																																																																																			.	.		0.343	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550		T	112102091	C	T	112102091	2	4	24	1	0	0	0	0	0	0	0	1	7562	903	32	3		3	IFRD1	7	112102091	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	7371552	112102091	47036572	56	3263										
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138601674	138601674	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	acttgcggcgtcacccatcaGggtggagtcgaggggaccac	15	12	2	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:138601674G>A	ENST00000422774.1	-	2	2746	c.2698C>T	c.(2698-2700)Ctg>Ttg	p.L900L	KIAA1549_ENST00000440172.1_Silent_p.L900L|KIAA1549_ENST00000242365.4_Silent_p.L850L			Q9HCM3	K1549_HUMAN	KIAA1549	900						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TCACCCATCAGGGTGGAGTCG	0.632			O	BRAF	pilocytic astrocytoma																																p.L900L	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C2698T						.						31	38	36					7																	138601674		2124	4223	6347	SO:0001819	synonymous_variant	57670	exon2			CCATCAGGGTGGA		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.2698C>T	chr7.hg19:g.138601674G>A		82.0	0.0		102.0	14.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	hg19	CCDS56513.1																																																																																			.	.		0.632	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			A	138601674	G	A	138601674	2	1	24	1	0	0	0	0	0	0	0	1	8253	991	35	3		3	KIAA1549	7	138601674	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	26499583	138601674	20536989	57	3264										
ARHGEF10	9639	hgsc.bcm.edu	37	chr8	1905384	1905384	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cagccccaccaggaagagctGgcgccgaccgtcatggtctg	13	15	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:1905384G>T	ENST00000398564.1	+	29	4065	c.4065G>T	c.(4063-4065)ctG>ctT	p.L1355L	ARHGEF10_ENST00000262112.6_Silent_p.L1326L|ARHGEF10_ENST00000349830.3_Silent_p.L1330L|ARHGEF10_ENST00000520359.1_Silent_p.L1292L|ARHGEF10_ENST00000518288.1_Silent_p.L1354L			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1355					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		AGGAAGAGCTGGCGCCGACCG	0.627																																					p.L1330L		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.G3990T						.																																			SO:0001819	synonymous_variant	9639	exon29			AGAGCTGGCGCCG	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"Rho guanine nucleotide exchange factors"	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.4065G>T	chr8.hg19:g.1905384G>T		78.0	0.0		65.0	12.0	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	hg19																																																																																				.	.		0.627	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding				T	1905384	G	T	1905384	2	4	24	1	0	0	0	0	0	0	0	1	894	1335	47	3		3	ARHGEF10	8	1905384	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10		1905384	144458638	58	3265										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321956	52321956	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cgaaggcggtcagcgccgcgCcccacgtgggctgctgcagg	17	15	1	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:52321956C>T	ENST00000356297.4	-	17	2328	c.2228G>A	c.(2227-2229)gGc>gAc	p.G743D	PXDNL_ENST00000543296.1_Missense_Mutation_p.G743D	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	743					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CAGCGCCGCGCCCCACGTGGG	0.721																																					p.G743D		Atlas-SNP	.											.	PXDNL	414	.	0			c.G2228A						.						14	16	15					8																	52321956		1958	4127	6085	SO:0001583	missense	137902	exon17			GCCGCGCCCCACG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2228G>A	chr8.hg19:g.52321956C>T	ENSP00000348645:p.Gly743Asp	51.0	0.0		60.0	26.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442651	0.63067	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.96300	-3.97;-3.97	3.71	3.71	0.42584	.	.	.	.	.	D	0.98912	0.9631	H	0.99104	4.43	0.45239	D	0.998242	D	0.89917	1.0	D	0.97110	1.0	D	0.98713	1.0705	9	0.87932	D	0	.	13.2908	0.60270	0.0:1.0:0.0:0.0	.	743	A1KZ92	PXDNL_HUMAN	D	743	ENSP00000348645:G743D;ENSP00000444865:G743D	ENSP00000348645:G743D	G	-	2	0	PXDNL	52484509	1.000000	0.71417	0.126000	0.21872	0.260000	0.26232	4.946000	0.63576	1.779000	0.52309	0.555000	0.69702	GGC	.	.		0.721	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		T	52321956	C	T	52321956	3	4	24	1	0	0	0	0	1	0	0	0	12863	739	26	3	2191	3	PXDNL	8	52321956	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	50416572	52321956	94042066	59	3266										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72936129	72936130	+	Frame_Shift_Ins	INS	-	-	A													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttatttccccagtgcaaaatINSaaaaaacagaatatatgctg							TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:72936129_72936130insA	ENST00000262209.4	-	26	3275_3276	c.3068_3069insT	c.(3067-3069)ttafs	p.L1023fs	RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	1023					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CAGTGCAAAATAAAAAACAGAA	0.302																																					p.L1023fs		Atlas-Indel,Pindel	.											.,1	TRPA1	256	.	0			c.3069_3070insT						.																																			SO:0001589	frameshift_variant	8989	exon26			.	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.3069dupT	chr8.hg19:g.72936135_72936135dupA	ENSP00000262209:p.Leu1023fs	238.0	0.0		374.0	86.0	NM_007332	A6NIN6	Frame_Shift_Ins	INS	ENST00000262209.4	hg19	CCDS34908.1																																																																																			.	.		0.302	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		A	72936130	-	A	72936129	7	5	24	1	0	1	1	0	0	0	0	0	16592	1403	49	0	298	0	TRPA1	8	72936129	Frame_Shift_Ins	INS	-	TCGA-5C-A9VG-01A-11D-A36X-10	20614173	72936129	73427893	60	3267										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77618110	77618110	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ccagcatggctttaccccgaGtactcctggcacaccagggc	10	16	0	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:77618110G>A	ENST00000521891.2	+	2	2235	c.1787G>A	c.(1786-1788)aGt>aAt	p.S596N	ZFHX4_ENST00000050961.6_Missense_Mutation_p.S596N|ZFHX4_ENST00000518282.1_Missense_Mutation_p.S596N|ZFHX4_ENST00000455469.2_Missense_Mutation_p.S596N|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	596					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TTTACCCCGAGTACTCCTGGC	0.582										HNSCC(33;0.089)																											p.S596N		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G1787A						.						70	76	74					8																	77618110		2107	4222	6329	SO:0001583	missense	79776	exon2			CCCCGAGTACTCC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.1787G>A	chr8.hg19:g.77618110G>A	ENSP00000430497:p.Ser596Asn	122.0	0.0		164.0	48.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	11.47	1.648758	0.29336	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.51071	0.72;0.77;0.73;0.72	5.65	5.65	0.86999	.	0.000000	0.52532	U	0.000066	T	0.44244	0.1284	L	0.44542	1.39	0.38445	D	0.946816	B;P;P;B	0.35272	0.361;0.493;0.493;0.185	B;B;B;B	0.33620	0.075;0.167;0.157;0.117	T	0.37244	-0.9714	10	0.34782	T	0.22	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	596;596;596;596	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	N	596	ENSP00000430497:S596N;ENSP00000399605:S596N;ENSP00000050961:S596N;ENSP00000430848:S596N	ENSP00000050961:S596N	S	+	2	0	ZFHX4	77780665	0.986000	0.35501	0.010000	0.14722	0.104000	0.19210	4.713000	0.61895	2.941000	0.99782	0.655000	0.94253	AGT	.	.		0.582	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77618110	G	A	77618110	3	1	24	1	0	0	0	0	1	0	0	0	17650	1029	36	3	1789	3	ZFHX4	8	77618110	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	4681981	77618110	68745912	61	3268										
EIF2C2	27161	hgsc.bcm.edu	37	chr8	141595331	141595331	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tgtaatttgattgttctcccGgaggtcccaaagtcgggtct	11	9	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:141595331G>A	ENST00000220592.5	-	2	214	c.102C>T	c.(100-102)tcC>tcT	p.S34S	AGO2_ENST00000519980.1_Silent_p.S34S|AGO2_ENST00000517293.1_5'UTR	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	34					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										TTGTTCTCCCGGAGGTCCCAA	0.507																																					p.S34S		Atlas-SNP	.											.	.	.	.	0			c.C102T						.						77	79	78					8																	141595331		2203	4300	6503	SO:0001819	synonymous_variant	27161	exon2			TCTCCCGGAGGTC	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"Argonaute/PIWI family"	3263	protein-coding gene	gene with protein product	"argonaute 2"	606229	"eukaryotic translation initiation factor 2C, 2"	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.102C>T	chr8.hg19:g.141595331G>A		141.0	0.0		211.0	53.0	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Silent	SNP	ENST00000220592.5	hg19	CCDS6380.1																																																																																			.	.		0.507	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4			A	141595331	G	A	141595331	2	1	24	1	0	0	0	0	0	0	0	1	5008	1103	39	1		1	EIF2C2	8	141595331	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	63977221	141595331	4768691	62	3269										
TSNARE1	203062	hgsc.bcm.edu	37	chr8	143395792	143395792	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	aagcagcgctctggacttttCtgcaattttctgttgaaaaa	8	8	3	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:143395792C>G	ENST00000307180.3	-	9	1201	c.1084G>C	c.(1084-1086)Gaa>Caa	p.E362Q	TSNARE1_ENST00000519651.1_Missense_Mutation_p.E142Q|TSNARE1_ENST00000518928.1_5'UTR|TSNARE1_ENST00000524325.1_Missense_Mutation_p.E361Q|TSNARE1_ENST00000520166.1_Missense_Mutation_p.E361Q	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	362					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CTGGACTTTTCTGCAATTTTC	0.522																																					p.E362Q		Atlas-SNP	.											.	TSNARE1	59	.	0			c.G1084C						.						58	55	56					8																	143395792		2203	4300	6503	SO:0001583	missense	203062	exon9			ACTTTTCTGCAAT			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.1084G>C	chr8.hg19:g.143395792C>G	ENSP00000303437:p.Glu362Gln	84.0	0.0		101.0	46.0	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490894	0.64074	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	4.27	4.27	0.50696	t-SNARE (1);	0.000000	0.32608	U	0.005866	T	0.49355	0.1552	M	0.77820	2.39	0.24415	N	0.994649	D;D;D;D	0.89917	0.998;1.0;0.998;0.998	D;D;D;D	0.80764	0.991;0.994;0.991;0.991	T	0.39921	-0.9590	10	0.46703	T	0.11	.	12.201	0.54326	0.0:1.0:0.0:0.0	.	361;142;362;362	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	Q	361;362;361;142	ENSP00000428763:E361Q;ENSP00000303437:E362Q;ENSP00000427770:E361Q;ENSP00000429679:E142Q	ENSP00000303437:E362Q	E	-	1	0	TSNARE1	143393699	0.946000	0.32159	0.979000	0.43373	0.993000	0.82548	3.506000	0.53364	1.915000	0.55452	0.655000	0.94253	GAA	.	.		0.522	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003		G	143395792	C	G	143395792	3	3	24	1	0	0	0	0	1	0	0	0	16645	922	32	4	477	4	TSNARE1	8	143395792	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	1800461	143395792	2968230	63	3270										
LRRC24	441381	hgsc.bcm.edu	37	chr8	145748697	145748698	+	Frame_Shift_Del	DEL	AT	AT	-													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ggcgcgggggctctgcacacAtgatcttcctgtccctggag							TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:145748697_145748698delAT	ENST00000529415.2	-	5	820_821	c.703_704delAT	c.(703-705)atgfs	p.M235fs	LRRC14_ENST00000528528.1_3'UTR|LRRC24_ENST00000533758.1_Frame_Shift_Del_p.M232fs|LRRC14_ENST00000292524.1_3'UTR			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	235	LRRCT.					integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CTCTGCACACATGATCTTCCTG	0.658																																					p.235_235del		Atlas-Indel,Pindel	.											.	LRRC24	11	.	0			c.704_705del						.																																			SO:0001589	frameshift_variant	441381	exon5			.	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"Immunoglobulin superfamily / I-set domain containing"	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.703_704delAT	chr8.hg19:g.145748697_145748698delAT	ENSP00000434849:p.Met235fs	85.0	0.0		111.0	25.0	NM_001024678		Frame_Shift_Del	DEL	ENST00000529415.2	hg19	CCDS34969.1																																																																																			.	.		0.658	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678		-	145748698	AT	-	145748697	7	5	24	1	0	1	0	1	0	0	0	0	8988	217	8	0	841	0	LRRC24	8	145748697	Frame_Shift_Del	DEL	AT	TCGA-5C-A9VG-01A-11D-A36X-10	2352905	145748697	615325	64	3271										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8733790	8733790	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	aatggcttactctcagcatcCgtgcggaggaagaaagtgag	13	8	1	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr9:8733790C>T	ENST00000381196.4	-	9	597	c.54G>A	c.(52-54)acG>acA	p.T18T	PTPRD_ENST00000397606.3_Silent_p.T18T|PTPRD_ENST00000356435.5_Silent_p.T18T|PTPRD_ENST00000358503.5_Silent_p.T18T|PTPRD_ENST00000360074.4_Silent_p.T18T|PTPRD_ENST00000537002.1_Silent_p.T18T|PTPRD_ENST00000397611.3_Silent_p.T18T|PTPRD_ENST00000486161.1_Silent_p.T18T|PTPRD_ENST00000540109.1_Silent_p.T18T|PTPRD_ENST00000355233.5_Silent_p.T18T|PTPRD_ENST00000463477.1_Silent_p.T18T|PTPRD_ENST00000397617.3_Silent_p.T18T	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	18					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TCTCAGCATCCGTGCGGAGGA	0.567										TSP Lung(15;0.13)																											p.T18T		Atlas-SNP	.											.	PTPRD	1348	.	0			c.G54A						.						67	54	59					9																	8733790		2167	4230	6397	SO:0001819	synonymous_variant	5789	exon1			AGCATCCGTGCGG	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.54G>A	chr9.hg19:g.8733790C>T		82.0	0.0		92.0	24.0	NM_001040712	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	hg19	CCDS43786.1																																																																																			.	.		0.567	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			T	8733790	C	T	8733790	2	4	24	1	0	0	0	0	0	0	0	1	12814	639	23	1		1	PTPRD	9	8733790	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10		8733790	132479641	65	3272										
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134357810	134357810	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cgttgacttgagtgccgagtCtcgggagtcgtctgcgacct	14	11	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr9:134357810C>A	ENST00000357304.4	+	20	5091	c.5036C>A	c.(5035-5037)tCt>tAt	p.S1679Y	PRRC2B_ENST00000458550.1_Missense_Mutation_p.S985Y|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000405995.1_Missense_Mutation_p.S985Y	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1679							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						AGTGCCGAGTCTCGGGAGTCG	0.592																																					p.S1679Y		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C5036A						.						148	155	153					9																	134357810		1992	4172	6164	SO:0001583	missense	84726	exon20			CCGAGTCTCGGGA	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.5036C>A	chr9.hg19:g.134357810C>A	ENSP00000349856:p.Ser1679Tyr	187.0	0.0		184.0	41.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	hg19	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.768602	0.69878	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550	T;T;T	0.04809	3.55;3.93;3.55	4.92	4.92	0.64577	.	0.000000	0.41605	U	0.000852	T	0.20414	0.0491	M	0.68593	2.085	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.78314	0.967;0.991	T	0.00350	-1.1797	10	0.72032	D	0.01	-23.5277	17.105	0.86660	0.0:1.0:0.0:0.0	.	411;1679	Q5JSZ8;Q5JSZ5	.;PRC2B_HUMAN	Y	985;1679;985	ENSP00000384606:S985Y;ENSP00000349856:S1679Y;ENSP00000398853:S985Y	ENSP00000349856:S1679Y	S	+	2	0	PRRC2B	133347631	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	4.343000	0.59348	2.275000	0.75901	0.561000	0.74099	TCT	.	.		0.592	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134357810	C	A	134357810	3	1	24	1	0	0	0	0	1	0	0	0	1320	913	32	3	5114	3	BAT2L1	9	134357810	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	125624020	134357810	6855621	66	3273										
ANK3	288	hgsc.bcm.edu	37	chr10	62149211	62149211	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tccgatcccgggaccgtttgCggtgtttcctttttttctca	9	12	1	0	rs373407780		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:62149211C>T	ENST00000280772.2	-	1	277	c.86G>A	c.(85-87)cGc>cAc	p.R29H	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	29					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GGACCGTTTGCGGTGTTTCCT	0.398																																					p.R29H		Atlas-SNP	.											.	ANK3	703	.	0			c.G86A						.	C	,,HIS/ARG	0,4406		0,0,2203	172	165	168		,,86	6	1	10		168	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,missense	ANK3	NM_001204403.1,NM_001204404.1,NM_020987.3	,,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,possibly-damaging	,,29/4378	62149211	1,13005	2203	4300	6503	SO:0001583	missense	288	exon1			CGTTTGCGGTGTT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.86G>A	chr10.hg19:g.62149211C>T	ENSP00000280772:p.Arg29His	81.0	0.0		100.0	6.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.039705	0.55003	0.0	1.16E-4	ENSG00000151150	ENST00000280772	T	0.64618	-0.11	5.96	5.96	0.96718	.	0.000000	0.33959	U	0.004385	T	0.65302	0.2678	N	0.08118	0	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.72472	-0.4283	10	0.66056	D	0.02	.	19.4101	0.94667	0.0:1.0:0.0:0.0	.	29	Q12955	ANK3_HUMAN	H	29	ENSP00000280772:R29H	ENSP00000280772:R29H	R	-	2	0	ANK3	61819217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.931000	0.70113	2.832000	0.97577	0.655000	0.94253	CGC	.	.		0.398	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	62149211	C	T	62149211	3	4	24	1	0	0	0	0	1	0	0	0	622	768	27	1	13552	1	ANK3	10	62149211	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10		62149211	73385536	67	3274										
SEC24C	9632	hgsc.bcm.edu	37	chr10	75528787	75528787	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	atccgtgctgtagatttcttTggagctttctacatgagcaa	9	8	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:75528787T>C	ENST00000339365.2	+	18	2463	c.2301T>C	c.(2299-2301)ttT>ttC	p.F767F	SEC24C_ENST00000345254.4_Silent_p.F767F|SEC24C_ENST00000496827.1_3'UTR|SEC24C_ENST00000540668.1_Silent_p.F15F|SEC24C_ENST00000535742.1_Silent_p.F15F|SEC24C_ENST00000411652.2_Silent_p.F648F	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	767					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					TAGATTTCTTTGGAGCTTTCT	0.512																																					p.F767F		Atlas-SNP	.											SEC24C,colon,carcinoma,0,1	SEC24C	86	.	0			c.T2301C						.						101	90	93					10																	75528787		2203	4300	6503	SO:0001819	synonymous_variant	9632	exon17			TTTCTTTGGAGCT	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"SEC24 (S. cerevisiae) related gene family, member C", "SEC24 family, member C (S. cerevisiae)"			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.2301T>C	chr10.hg19:g.75528787T>C		106.0	0.0		136.0	31.0	NM_198597	B4DZT4|Q8WV25	Silent	SNP	ENST00000339365.2	hg19	CCDS7332.1																																																																																			.	.		0.512	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			C	75528787	T	C	75528787	2	2	24	1	0	0	0	0	0	0	0	1	14011	1809	63	2		2	SEC24C	10	75528787	Silent	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	13379576	75528787	60005960	68	3275										
LIPJ	142910	hgsc.bcm.edu	37	chr10	90356037	90356037	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tatatcttattttattttagGtttcataacattttctacta	2	5	3	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:90356037G>A	ENST00000371939.3	+	7	754	c.440G>A	c.(439-441)gGt>gAt	p.G147D		NM_001010939.2	NP_001010939.2	Q5W064	LIPJ_HUMAN	lipase, family member J	147					lipid catabolic process (GO:0016042)		hydrolase activity, acting on ester bonds (GO:0016788)			large_intestine(4)|lung(4)|ovary(1)	9		all_cancers(4;2.79e-10)|Prostate(4;1.68e-15)|all_epithelial(4;1.43e-09)|Colorectal(252;0.0381)|Breast(4;0.141)|Melanoma(5;0.2)|all_hematologic(4;0.222)		Colorectal(12;1.02e-05)|COAD - Colon adenocarcinoma(12;1.54e-05)		TTTATTTTAGGTTTCATAACA	0.264																																					p.G147D		Atlas-SNP	.											.	LIPJ	32	.	0			c.G440A						.						12	12	12					10																	90356037		2099	4175	6274	SO:0001630	splice_region_variant	142910	exon7			TTTTAGGTTTCAT	BC031219	CCDS31240.1	10q23.31	2008-02-04	2008-02-04	2007-02-27	ENSG00000204022	ENSG00000204022			21773	protein-coding gene	gene with protein product		613921	"lipase-like, ab-hydrolase domain containing 1", "lipase, family member J"	LIPL1			Standard	NM_001010939		Approved	bA425M17.2	uc001kff.3	Q5W064	OTTHUMG00000018691	ENST00000371939.3:c.440-1G>A	chr10.hg19:g.90356037G>A		359.0	0.0		508.0	52.0	NM_001010939	A8MT98|Q0P671	Missense_Mutation	SNP	ENST00000371939.3	hg19	CCDS31240.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.242293	0.39598	.	.	ENSG00000204022	ENST00000371939;ENST00000531458	T;T	0.71817	-0.6;-0.6	4.46	-5.17	0.02849	Alpha/beta hydrolase fold-1 (1);	0.686580	0.12597	N	0.455039	T	0.77089	0.4079	M	0.65320	2	0.26196	N	0.979516	D	0.64830	0.994	P	0.61592	0.891	T	0.73924	-0.3829	9	.	.	.	.	16.5221	0.84320	0.0977:0.2467:0.6555:0.0	.	147	Q5W064	LIPJ_HUMAN	D	147;11	ENSP00000361007:G147D;ENSP00000434211:G11D	.	G	+	2	0	LIPJ	90346017	0.045000	0.20229	0.213000	0.23690	0.432000	0.31715	-0.294000	0.08309	-0.777000	0.04572	-0.142000	0.14014	GGT	.	.		0.264	LIPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049248.2	XM_084377	Missense_Mutation	A	90356037	G	A	90356037	5	1	24	1	0	0	0	0	0	0	1	0	8835	1275	44	3	458	3	LIPJ	10	90356037	Splice_Site	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	14827250	90356037	45178710	69	3276										
MYOF	26509	hgsc.bcm.edu	37	chr10	95134586	95134586	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gccagtgtggacttcacatcTgtggcttccgacctcatcct	9	14	3	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:95134586T>A	ENST00000359263.4	-	23	2234	c.2235A>T	c.(2233-2235)acA>acT	p.T745T	MYOF_ENST00000371501.4_Silent_p.T745T|MYOF_ENST00000371502.4_Silent_p.T745T|MYOF_ENST00000358334.5_Silent_p.T732T	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	745					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						ACTTCACATCTGTGGCTTCCG	0.483																																					p.T745T		Atlas-SNP	.											.	MYOF	177	.	0			c.A2235T						.						76	79	78					10																	95134586		1922	4134	6056	SO:0001819	synonymous_variant	26509	exon23			CACATCTGTGGCT	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.2235A>T	chr10.hg19:g.95134586T>A		128.0	0.0		148.0	47.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Silent	SNP	ENST00000359263.4	hg19	CCDS41551.1																																																																																			.	.		0.483	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		A	95134586	T	A	95134586	2	1	24	1	0	0	0	0	0	0	0	1	10098	1567	55	4		4	MYOF	10	95134586	Silent	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	4778549	95134586	40400161	70	3277										
CWF19L1	55280	hgsc.bcm.edu	37	chr10	102013179	102013179	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	agaatgaaatgctactcaccGatatggaagcctctcataat	7	9	2	2	rs150239404		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:102013179G>A	ENST00000354105.4	-	6	708	c.622C>T	c.(622-624)Cga>Tga	p.R208*	CWF19L1_ENST00000478047.1_5'UTR	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	208							catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		GCTACTCACCGATATGGAAGC	0.383																																					p.R208X		Atlas-SNP	.											.	CWF19L1	39	.	0			c.C622T						.	G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	113	115	114		622	5.4	1	10	dbSNP_134	114	2,8598	2.2+/-6.3	0,2,4298	yes	stop-gained-near-splice	CWF19L1	NM_018294.4		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		208/539	102013179	3,13003	2203	4300	6503	SO:0001630	splice_region_variant	55280	exon6			CTCACCGATATGG	AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.623+1C>T	chr10.hg19:g.102013179G>A		104.0	0.0		104.0	18.0	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Nonsense_Mutation	SNP	ENST00000354105.4	hg19	CCDS7489.1	.	.	.	.	.	.	.	.	.	.	G	36	5.749544	0.96890	2.27E-4	2.33E-4	ENSG00000095485	ENST00000354105	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.254	11.7084	0.51610	0.0:0.0:0.8235:0.1765	.	.	.	.	X	208	.	ENSP00000326411:R208X	R	-	1	2	CWF19L1	102003169	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.735000	0.62051	2.516000	0.84829	0.561000	0.74099	CGA	.	G|1.000;A|0.000		0.383	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	Nonsense_Mutation	A	102013179	G	A	102013179	5	1	24	1	0	0	0	0	0	0	1	0	4073	1072	37	1	1030	1	CWF19L1	10	102013179	Splice_Site	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	6878593	102013179	33521568	71	3278										
INA	9118	hgsc.bcm.edu	37	chr10	105037736	105037736	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gccgaggtggacgtgactgtGgctaaaccagacctgacctc	13	12	0	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:105037736G>T	ENST00000369849.4	+	1	817	c.768G>T	c.(766-768)gtG>gtT	p.V256V		NM_032727.3	NP_116116.1	Q16352	AINX_HUMAN	internexin neuronal intermediate filament protein, alpha	256	Linker 2.|Rod.				cell differentiation (GO:0030154)|neurofilament cytoskeleton organization (GO:0060052)|substantia nigra development (GO:0021762)	cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular space (GO:0005615)|neurofilament (GO:0005883)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)	13				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		ACGTGACTGTGGCTAAACCAG	0.647																																					p.V256V		Atlas-SNP	.											.	INA	34	.	0			c.G768T						.						38	32	34					10																	105037736		2201	4299	6500	SO:0001819	synonymous_variant	9118	exon1			GACTGTGGCTAAA	S78296	CCDS7545.1	10q24	2013-01-16			ENSG00000148798	ENSG00000148798		"Intermediate filaments type IV"	6057	protein-coding gene	gene with protein product		605338		NEF5		7769995	Standard	NM_032727		Approved	NF-66	uc001kws.3	Q16352	OTTHUMG00000018986	ENST00000369849.4:c.768G>T	chr10.hg19:g.105037736G>T		165.0	0.0		170.0	27.0	NM_032727	B1AQK0|Q9BRC5	Silent	SNP	ENST00000369849.4	hg19	CCDS7545.1																																																																																			.	.		0.647	INA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050145.1	NM_032727		T	105037736	G	T	105037736	2	4	24	1	0	0	0	0	0	0	0	1	7739	1335	47	3		3	INA	10	105037736	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	3024557	105037736	30497011	72	3279										
LHPP	64077	hgsc.bcm.edu	37	chr10	126205791	126205791	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tcgtgggcgacgtcggcggtGcccagcggtgtggaatgaga	19	9	0	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:126205791G>T	ENST00000368842.5	+	6	695	c.667G>T	c.(667-669)Gcc>Tcc	p.A223S	LHPP_ENST00000368839.1_Intron	NM_022126.3	NP_071409.3	Q9H008	LHPP_HUMAN	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	223					phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|phosphohistidine phosphatase activity (GO:0008969)|protein homodimerization activity (GO:0042803)			large_intestine(2)|lung(2)	4		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)		CGTCGGCGGTGCCCAGCGGTG	0.577																																					p.A223S	GBM(165;1980 2715 15999 18454)	Atlas-SNP	.											LHPP,NS,carcinoma,0,1	LHPP	18	.	0			c.G667T						.						80	72	75					10																	126205791		2203	4299	6502	SO:0001583	missense	64077	exon6			GGCGGTGCCCAGC	AB049629	CCDS7640.1, CCDS53587.1	10q26.2	2010-02-17			ENSG00000107902	ENSG00000107902	3.6.1.1		30042	protein-coding gene	gene with protein product						12801912, 16430861	Standard	NM_022126		Approved	HDHD2B	uc001lhs.2	Q9H008	OTTHUMG00000019214	ENST00000368842.5:c.667G>T	chr10.hg19:g.126205791G>T	ENSP00000357835:p.Ala223Ser	68.0	0.0		77.0	17.0	NM_022126	B3KP20|Q2TBE9|Q5VUV9|Q5VUW0	Missense_Mutation	SNP	ENST00000368842.5	hg19	CCDS7640.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.874671	0.91664	.	.	ENSG00000107902	ENST00000368842	T	0.52526	0.66	4.83	4.83	0.62350	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.73410	0.3583	M	0.90425	3.115	0.80722	D	1	D	0.62365	0.991	D	0.67900	0.954	T	0.80165	-0.1496	10	0.72032	D	0.01	-16.3445	16.4736	0.84125	0.0:0.0:1.0:0.0	.	223	Q9H008	LHPP_HUMAN	S	223	ENSP00000357835:A223S	ENSP00000357835:A223S	A	+	1	0	LHPP	126195781	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.106000	0.77039	2.404000	0.81709	0.484000	0.47621	GCC	.	.		0.577	LHPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050870.1	NM_022126		T	126205791	G	T	126205791	3	4	24	1	0	0	0	0	1	0	0	0	8778	1319	46	3	689	3	LHPP	10	126205791	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	21168055	126205791	9328956	73	3280										
OR51G2	81282	hgsc.bcm.edu	37	chr11	4936102	4936102	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tttccaaagcgatggatgacAgagaggccaatcatgggagt	13	7	1	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:4936102A>G	ENST00000322013.3	-	1	820	c.792T>C	c.(790-792)tcT>tcC	p.S264S	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGGATGACAGAGAGGCCAA	0.517																																					p.S264S		Atlas-SNP	.											.	OR51G2	70	.	0			c.T792C						.						139	122	128					11																	4936102		2201	4298	6499	SO:0001819	synonymous_variant	81282	exon1			GATGACAGAGAGG	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"GPCR / Class A : Olfactory receptors"	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.792T>C	chr11.hg19:g.4936102A>G		163.0	0.0		164.0	37.0	NM_001005238	Q6IFH7	Silent	SNP	ENST00000322013.3	hg19	CCDS31365.1																																																																																			.	.		0.517	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		G	4936102	A	G	4936102	2	3	24	1	0	0	0	0	0	0	0	1	11108	175	7	2		2	OR51G2	11	4936102	Silent	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10		4936102	130070414	74	3281										
ABTB2	25841	hgsc.bcm.edu	37	chr11	34192494	34192494	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cccatccggacccaaggcctCgatggcttggttgatgaggt	13	12	0	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:34192494C>T	ENST00000435224.2	-	5	1946	c.1522G>A	c.(1522-1524)Gag>Aag	p.E508K	ABTB2_ENST00000530814.1_5'Flank|ABTB2_ENST00000298992.2_Missense_Mutation_p.E322K	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	508					cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				CCCAAGGCCTCGATGGCTTGG	0.567																																					p.E508K		Atlas-SNP	.											.	ABTB2	101	.	0			c.G1522A						.						109	93	98					11																	34192494		2202	4298	6500	SO:0001583	missense	25841	exon5			AGGCCTCGATGGC	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.1522G>A	chr11.hg19:g.34192494C>T	ENSP00000410157:p.Glu508Lys	85.0	0.0		81.0	11.0	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Missense_Mutation	SNP	ENST00000435224.2	hg19	CCDS7890.2	.	.	.	.	.	.	.	.	.	.	C	12.83	2.054543	0.36277	.	.	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.66638	-0.22;-0.22	5.03	5.03	0.67393	Ankyrin repeat-containing domain (1);	0.663526	0.15490	N	0.259639	T	0.52709	0.1751	N	0.25031	0.7	0.30151	N	0.803068	B	0.24533	0.105	B	0.20955	0.032	T	0.50499	-0.8821	10	0.28530	T	0.3	-1.0545	14.0228	0.64568	0.0:0.8486:0.1514:0.0	.	322	Q8N961	ABTB2_HUMAN	K	508;322	ENSP00000410157:E508K;ENSP00000298992:E322K	ENSP00000298992:E322K	E	-	1	0	ABTB2	34149070	0.200000	0.23398	0.996000	0.52242	0.359000	0.29487	2.092000	0.41700	2.329000	0.79093	0.491000	0.48974	GAG	.	.		0.567	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804		T	34192494	C	T	34192494	3	4	24	1	0	0	0	0	1	0	0	0	103	893	31	1	1607	1	ABTB2	11	34192494	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	29256392	34192494	100814022	75	3282										
OR5M10	390167	hgsc.bcm.edu	37	chr11	56344374	56344374	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tcaaaaaagtataaaagactGcaattattttggactcctct	5	7	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:56344374G>A	ENST00000526812.2	-	1	889	c.824C>T	c.(823-825)gCa>gTa	p.A275V		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						ATAAAAGACTGCAATTATTTT	0.413																																					p.A275V		Atlas-SNP	.											.	OR5M10	56	.	0			c.C824T						.						202	197	198					11																	56344374		1832	4087	5919	SO:0001583	missense	390167	exon1			AAGACTGCAATTA	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"GPCR / Class A : Olfactory receptors"	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.824C>T	chr11.hg19:g.56344374G>A	ENSP00000436004:p.Ala275Val	308.0	0.0		276.0	55.0	NM_001004741	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	hg19	CCDS53630.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629812	0.46944	.	.	ENSG00000254834	ENST00000526812	T	0.00202	8.56	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00580	0.0019	M	0.79011	2.435	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.54132	-0.8339	9	0.72032	D	0.01	.	15.6851	0.77402	0.0:0.0:1.0:0.0	.	275	Q6IEU7	OR5MA_HUMAN	V	275	ENSP00000436004:A275V	ENSP00000436004:A275V	A	-	2	0	OR5M10	56100950	0.696000	0.27757	0.101000	0.21167	0.437000	0.31866	4.921000	0.63397	2.316000	0.78162	0.632000	0.83419	GCA	.	.		0.413	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		A	56344374	G	A	56344374	3	1	24	1	0	0	0	0	1	0	0	0	11182	1319	46	3	127	3	OR5M10	11	56344374	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	22151880	56344374	78662142	76	3283										
C11orf24	53838	hgsc.bcm.edu	37	chr11	68029219	68029219	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gggcaaacaaaaccaagactGtgatgaaaagggtcaccccg	11	10	1	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:68029219G>C	ENST00000304271.6	-	4	1646	c.1244C>G	c.(1243-1245)aCa>aGa	p.T415R	C11orf24_ENST00000533310.1_Intron|C11orf24_ENST00000530166.1_5'Flank	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	415						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						AACCAAGACTGTGATGAAAAG	0.527																																					p.T415R	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.C1244G						.						111	105	107					11																	68029219		2200	4294	6494	SO:0001583	missense	53838	exon4			AAGACTGTGATGA	AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.1244C>G	chr11.hg19:g.68029219G>C	ENSP00000307264:p.Thr415Arg	127.0	0.0		142.0	19.0	NM_022338	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	hg19	CCDS8180.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.040772	0.75732	.	.	ENSG00000171067	ENST00000304271	T	0.34472	1.36	4.89	1.87	0.25490	.	0.719989	0.11457	N	0.562140	T	0.46425	0.1392	L	0.43152	1.355	0.09310	N	0.999998	D	0.76494	0.999	D	0.65010	0.931	T	0.25293	-1.0136	10	0.72032	D	0.01	-0.4645	8.0294	0.30457	0.1461:0.1304:0.7235:0.0	.	415	Q96F05	CK024_HUMAN	R	415	ENSP00000307264:T415R	ENSP00000307264:T415R	T	-	2	0	C11orf24	67785795	0.739000	0.28196	0.001000	0.08648	0.987000	0.75469	2.777000	0.47717	0.488000	0.27723	0.484000	0.47621	ACA	.	.		0.527	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338		C	68029219	G	C	68029219	3	2	24	1	0	0	0	0	1	0	0	0	1637	1377	48	4	109	4	C11orf24	11	68029219	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	11684845	68029219	66977297	77	3284										
PAK1	5058	hgsc.bcm.edu	37	chr11	77060308	77060308	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tgtcctgtggccacatccatTgctgtgtacacggtgcctga	11	12	0	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:77060308T>A	ENST00000356341.3	-	9	1392	c.861A>T	c.(859-861)gcA>gcT	p.A287A	PAK1_ENST00000278568.4_Silent_p.A287A|PAK1_ENST00000528203.1_Silent_p.A189A|PAK1_ENST00000530617.1_Silent_p.A287A|PAK1_ENST00000525542.1_5'UTR	NM_002576.4	NP_002567.3	Q13153	PAK1_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 1	287	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to insulin stimulus (GO:0032869)|dendrite development (GO:0016358)|exocytosis (GO:0006887)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor clustering (GO:0043113)|response to hypoxia (GO:0001666)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|wound healing (GO:0042060)	axon (GO:0030424)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|Z disc (GO:0030018)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1)	29	all_cancers(14;1.75e-18)					CCACATCCATTGCTGTGTACA	0.428																																					p.A287A		Atlas-SNP	.											.	PAK1	89	.	0			c.A861T						.						79	62	68					11																	77060308		2200	4292	6492	SO:0001819	synonymous_variant	5058	exon9			ATCCATTGCTGTG	U51120	CCDS8250.1, CCDS44687.1	11q13-q14	2008-06-17	2008-06-17						8590	protein-coding gene	gene with protein product	"STE20 homolog, yeast"	602590	"p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)", "p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)"			8805275, 9533029	Standard	NM_002576		Approved		uc001oyg.4	Q13153		ENST00000356341.3:c.861A>T	chr11.hg19:g.77060308T>A		122.0	0.0		86.0	18.0	NM_001128620	O75561|Q13567|Q32M53|Q32M54|Q86W79	Silent	SNP	ENST00000356341.3	hg19	CCDS8250.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.785341	0.31593	.	.	ENSG00000149269	ENST00000533285	.	.	.	5.91	-0.562	0.11781	.	.	.	.	.	T	0.38878	0.1057	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25779	-1.0122	4	.	.	.	.	0.1874	0.00130	0.2304:0.2046:0.237:0.3281	.	.	.	.	Y	9	.	.	N	-	1	0	PAK1	76737956	0.841000	0.29509	0.997000	0.53966	0.987000	0.75469	-0.164000	0.09983	-0.109000	0.12044	0.533000	0.62120	AAT	.	.		0.428	PAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382083.2	NM_002576		A	77060308	T	A	77060308	2	1	24	1	0	0	0	0	0	0	0	1	11408	1799	63	4		4	PAK1	11	77060308	Silent	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	9031089	77060308	57946208	78	3285										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78387340	78387340	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gacggtgccagccagcaagtGgggctcagtctgcagcgcca	15	13	2	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:78387340G>C	ENST00000278550.7	-	30	5815	c.5353C>G	c.(5353-5355)Cac>Gac	p.H1785D		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1785					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										GCCAGCAAGTGGGGCTCAGTC	0.642																																					p.H1785D		Atlas-SNP	.											.	.	.	.	0			c.C5353G						.						31	38	35					11																	78387340		2157	4249	6406	SO:0001583	missense	26011	exon30			GCAAGTGGGGCTC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5353C>G	chr11.hg19:g.78387340G>C	ENSP00000278550:p.His1785Asp	60.0	0.0		62.0	10.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.855005	0.91355	.	.	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.90197	-2.63;0.81	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.94686	0.8286	M	0.72118	2.19	0.80722	D	1	D	0.63880	0.993	D	0.72338	0.977	D	0.94188	0.7438	9	.	.	.	.	18.2069	0.89858	0.0:0.0:1.0:0.0	.	1785	Q6N022	TEN4_HUMAN	D	1785;249	ENSP00000278550:H1785D;ENSP00000431711:H249D	.	H	-	1	0	ODZ4	78064988	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.580000	0.98207	2.584000	0.87258	0.650000	0.86243	CAC	.	.		0.642	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			C	78387340	G	C	78387340	3	2	24	1	0	0	0	0	1	0	0	0	10846	1348	47	4	2976	4	ODZ4	11	78387340	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	1327032	78387340	56619176	79	3286										
FAT3	120114	hgsc.bcm.edu	37	chr11	92533209	92533209	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttcacatagatagctcaagtGgcttaatcctgacagcacga	8	10	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:92533209G>A	ENST00000298047.6	+	9	7047	c.7030G>A	c.(7030-7032)Ggc>Agc	p.G2344S	FAT3_ENST00000409404.2_Missense_Mutation_p.G2344S|FAT3_ENST00000525166.1_Missense_Mutation_p.G2194S			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2344	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TAGCTCAAGTGGCTTAATCCT	0.398										TCGA Ovarian(4;0.039)																											p.G2344S		Atlas-SNP	.											.	FAT3	1822	.	0			c.G7030A						.						98	92	94					11																	92533209		1955	4145	6100	SO:0001583	missense	120114	exon9			TCAAGTGGCTTAA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.7030G>A	chr11.hg19:g.92533209G>A	ENSP00000298047:p.Gly2344Ser	103.0	0.0		113.0	5.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	22.6	4.309725	0.81247	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.69561	-0.41;-0.41;-0.41	5.95	5.95	0.96441	.	.	.	.	.	D	0.90277	0.6959	H	0.98818	4.34	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93438	0.6791	9	0.87932	D	0	.	20.3931	0.98965	0.0:0.0:1.0:0.0	.	2344	Q8TDW7-3	.	S	2344;2344;2194	ENSP00000298047:G2344S;ENSP00000387040:G2344S;ENSP00000432586:G2194S	ENSP00000298047:G2344S	G	+	1	0	FAT3	92172857	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.787000	0.99055	2.824000	0.97209	0.655000	0.94253	GGC	.	.		0.398	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92533209	G	A	92533209	3	1	24	1	0	0	0	0	1	0	0	0	5699	1348	47	3	7064	3	FAT3	11	92533209	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	14145869	92533209	42473307	80	3287										
HTR3B	9177	hgsc.bcm.edu	37	chr11	113803709	113803709	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cccagaagacattcagcatgAcaaaaaggcgtttttgaatg	9	8	1	4			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:113803709A>G	ENST00000260191.2	+	6	847	c.590A>G	c.(589-591)gAc>gGc	p.D197G	HTR3B_ENST00000537778.1_Missense_Mutation_p.D186G	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	197					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	ATTCAGCATGACAAAAAGGCG	0.473																																					p.D197G		Atlas-SNP	.											.	HTR3B	50	.	0			c.A590G						.						141	129	133					11																	113803709		2201	4296	6497	SO:0001583	missense	9177	exon6			AGCATGACAAAAA	AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5298	protein-coding gene	gene with protein product		604654	"5-hydroxytryptamine (serotonin) receptor 3B"			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.590A>G	chr11.hg19:g.113803709A>G	ENSP00000260191:p.Asp197Gly	102.0	0.0		123.0	42.0	NM_006028	B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	hg19	CCDS8364.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.02|19.02	3.746905|3.746905	0.69418|0.69418	.|.	.|.	ENSG00000149305|ENSG00000149305	ENST00000260191;ENST00000537778|ENST00000543092	T;T|.	0.80909|.	-1.43;-1.43|.	6.17|6.17	6.17|6.17	0.99709|0.99709	Neurotransmitter-gated ion-channel ligand-binding (3);|.	0.049670|.	0.85682|.	D|.	0.000000|.	D|D	0.86928|0.86928	0.6051|0.6051	H|H	0.94698|0.94698	3.57|3.57	0.80722|0.80722	D|D	1|1	D;D|.	0.67145|.	0.996;0.987|.	D;P|.	0.65233|.	0.933;0.831|.	D|D	0.90300|0.90300	0.4329|0.4329	10|5	0.87932|.	D|.	0|.	-9.1491|-9.1491	15.8048|15.8048	0.78491|0.78491	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	186;197|.	O95264-2;O95264|.	.;5HT3B_HUMAN|.	G|A	197;186|126	ENSP00000260191:D197G;ENSP00000443118:D186G|.	ENSP00000260191:D197G|.	D|T	+|+	2|1	0|0	HTR3B|HTR3B	113308919|113308919	1.000000|1.000000	0.71417|0.71417	0.848000|0.848000	0.33437|0.33437	0.327000|0.327000	0.28475|0.28475	8.181000|8.181000	0.89696|0.89696	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.		0.473	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028		G	113803709	A	G	113803709	3	3	24	1	0	0	0	0	1	0	0	0	7454	275	10	2	612	2	HTR3B	11	113803709	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	21270500	113803709	21202807	81	3288										
ROBO4	54538	hgsc.bcm.edu	37	chr11	124756912	124756912	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cactgagttccaagcacaggGctacctcctcaggggtcagc	11	14	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:124756912G>A	ENST00000306534.3	-	15	2881	c.2396C>T	c.(2395-2397)gCc>gTc	p.A799V	RP11-664I21.5_ENST00000524453.1_RNA|ROBO4_ENST00000533054.1_Missense_Mutation_p.A654V	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	799					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		CAAGCACAGGGCTACCTCCTC	0.592																																					p.A799V		Atlas-SNP	.											.	ROBO4	130	.	0			c.C2396T						.						79	80	80					11																	124756912		2201	4299	6500	SO:0001583	missense	54538	exon15			CACAGGGCTACCT	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.2396C>T	chr11.hg19:g.124756912G>A	ENSP00000304945:p.Ala799Val	157.0	0.0		132.0	33.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	hg19	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	g	19.79	3.893829	0.72639	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.71934	-0.61;-0.31	4.83	4.83	0.62350	.	0.000000	0.36034	N	0.002826	D	0.82802	0.5116	M	0.71581	2.175	0.33596	D	0.601664	P;D;D	0.76494	0.954;0.999;0.999	D;D;D	0.72075	0.943;0.976;0.946	D	0.88109	0.2824	10	0.56958	D	0.05	.	16.5107	0.84284	0.0:0.0:1.0:0.0	.	799;689;799	Q8WZ75-2;Q8WZ75-3;Q8WZ75	.;.;ROBO4_HUMAN	V	799;689;654	ENSP00000304945:A799V;ENSP00000437129:A654V	ENSP00000304945:A799V	A	-	2	0	ROBO4	124262122	1.000000	0.71417	0.999000	0.59377	0.742000	0.42306	3.239000	0.51360	2.231000	0.72958	0.651000	0.88453	GCC	.	.		0.592	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		A	124756912	G	A	124756912	3	1	24	1	0	0	0	0	1	0	0	0	13531	1203	42	3	643	3	ROBO4	11	124756912	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	10953203	124756912	10249604	82	3289										
GPR162	27239	hgsc.bcm.edu	37	chr12	6933599	6933599	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tctccaagatcggcctcggcTttggcgtttgcttcagcctc	10	14	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:6933599T>G	ENST00000311268.3	+	2	1322	c.535T>G	c.(535-537)Ttt>Gtt	p.F179V	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						CGGCCTCGGCTTTGGCGTTTG	0.597																																					p.F179V		Atlas-SNP	.											.	GPR162	55	.	0			c.T535G						.						86	82	83					12																	6933599		2203	4300	6503	SO:0001583	missense	27239	exon2			CTCGGCTTTGGCG	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"GPCR / Class A : Orphans"	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.535T>G	chr12.hg19:g.6933599T>G	ENSP00000311528:p.Phe179Val	82.0	0.0		93.0	17.0	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	hg19	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.688914	0.88735	.	.	ENSG00000250510	ENST00000311268	T	0.69561	-0.41	4.33	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.71143	0.3305	L	0.34521	1.04	0.80722	D	1	D;P	0.59767	0.986;0.856	D;P	0.64144	0.922;0.635	T	0.75139	-0.3423	9	0.87932	D	0	.	13.6533	0.62323	0.0:0.0:0.0:1.0	.	179;179	B7Z3U3;Q16538	.;GP162_HUMAN	V	179	ENSP00000311528:F179V	ENSP00000311528:F179V	F	+	1	0	GPR162	6803860	1.000000	0.71417	0.738000	0.30950	0.883000	0.51084	7.858000	0.86971	1.826000	0.53198	0.402000	0.26972	TTT	.	.		0.597	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		G	6933599	T	G	6933599	3	3	24	1	0	0	0	0	1	0	0	0	6674	1609	56	5	556	5	GPR162	12	6933599	Missense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10		6933599	126918296	83	3290										
GPR162	27239	hgsc.bcm.edu	37	chr12	6933713	6933713	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	cccggagggctcggcaggccCggagagtggggggtggtggg	24	9	0	1	rs375616091		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:6933713C>T	ENST00000311268.3	+	2	1436	c.649C>T	c.(649-651)Cgg>Tgg	p.R217W	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						TCGGCAGGCCCGGAGAGTGGG	0.662																																					p.R217W		Atlas-SNP	.											GPR162,trunk,malignant_melanoma,-1,1	GPR162	55	.	0			c.C649T						.	C	,TRP/ARG	1,4405		0,1,2202	31	37	35		,649	3.6	1	12		35	0,8598		0,0,4299	no	intron,missense	GPR162	NM_014449.1,NM_019858.1	,101	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	,benign	,217/589	6933713	1,13003	2203	4299	6502	SO:0001583	missense	27239	exon2			CAGGCCCGGAGAG	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"GPCR / Class A : Orphans"	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.649C>T	chr12.hg19:g.6933713C>T	ENSP00000311528:p.Arg217Trp	65.0	1.0		68.0	21.0	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	hg19	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.804265	0.70682	2.27E-4	0.0	ENSG00000250510	ENST00000311268	T	0.73469	-0.75	4.48	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.57373	0.2049	N	0.14661	0.345	0.80722	D	1	B;B	0.15141	0.001;0.012	B;B	0.08055	0.002;0.003	T	0.56044	-0.8044	9	0.72032	D	0.01	.	10.6787	0.45802	0.0:0.9108:0.0:0.0892	.	217;217	B7Z3U3;Q16538	.;GP162_HUMAN	W	217	ENSP00000311528:R217W	ENSP00000311528:R217W	R	+	1	2	GPR162	6803974	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	1.176000	0.31957	1.117000	0.41842	0.491000	0.48974	CGG	.	.		0.662	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		T	6933713	C	T	6933713	3	4	24	1	0	0	0	0	1	0	0	0	6674	643	23	1	670	1	GPR162	12	6933713	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	114	6933713	126918182	84	3291										
ITGB7	3695	hgsc.bcm.edu	37	chr12	53585410	53585410	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tgatggcacttttgtagagaGgattactgtcctggagaaag	13	5	0	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:53585410G>A	ENST00000267082.5	-	16	2558	c.2327C>T	c.(2326-2328)cCt>cTt	p.P776L	ITGB7_ENST00000550743.2_Missense_Mutation_p.P628L|ITGB7_ENST00000422257.3_Missense_Mutation_p.P776L|ITGB7_ENST00000338737.4_Missense_Mutation_p.P628L	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	776					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTTGTAGAGAGGATTACTGTC	0.498																																					p.P776L		Atlas-SNP	.											.	ITGB7	60	.	0			c.C2327T						.						174	161	165					12																	53585410		2203	4300	6503	SO:0001583	missense	3695	exon16			TAGAGAGGATTAC		CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"Integrins"	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.2327C>T	chr12.hg19:g.53585410G>A	ENSP00000267082:p.Pro776Leu	114.0	0.0		111.0	20.0	NM_000889	Q9UCP7|Q9UCS7	Missense_Mutation	SNP	ENST00000267082.5	hg19	CCDS8849.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.169747	0.78452	.	.	ENSG00000139626	ENST00000422257;ENST00000267082;ENST00000338737	D;D;D	0.99737	-6.59;-6.59;-6.59	4.05	4.05	0.47172	Integrin beta subunit, cytoplasmic (2);	0.000000	0.37348	N	0.002128	D	0.99739	0.9897	M	0.92268	3.29	0.45995	D	0.998801	D	0.89917	1.0	D	0.91635	0.999	D	0.97017	0.9740	10	0.87932	D	0	.	14.5236	0.67870	0.0:0.0:1.0:0.0	.	776	P26010	ITB7_HUMAN	L	776;776;628	ENSP00000408741:P776L;ENSP00000267082:P776L;ENSP00000345501:P628L	ENSP00000267082:P776L	P	-	2	0	ITGB7	51871677	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	7.352000	0.79404	2.571000	0.86741	0.563000	0.77884	CCT	.	.		0.498	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			A	53585410	G	A	53585410	3	1	24	1	0	0	0	0	1	0	0	0	7909	1000	35	3	73	3	ITGB7	12	53585410	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	46651697	53585410	80266485	85	3292										
MON2	23041	hgsc.bcm.edu	37	chr12	62902146	62902146	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tctccaaatataaagttcagAcaaggttccagcacctcatc	5	12	3	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:62902146A>G	ENST00000393632.2	+	8	1261	c.870A>G	c.(868-870)agA>agG	p.R290R	MON2_ENST00000549378.1_3'UTR|MON2_ENST00000393630.3_Silent_p.R290R|MON2_ENST00000546600.1_Silent_p.R290R|MON2_ENST00000393629.2_Silent_p.R290R|MON2_ENST00000280379.6_Silent_p.R290R|MON2_ENST00000552115.1_Silent_p.R290R|MON2_ENST00000552738.1_Silent_p.R290R	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	290					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TAAAGTTCAGACAAGGTTCCA	0.388																																					p.R290R		Atlas-SNP	.											.	MON2	160	.	0			c.A870G						.						125	118	120					12																	62902146		2202	4300	6502	SO:0001819	synonymous_variant	23041	exon8			GTTCAGACAAGGT		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.870A>G	chr12.hg19:g.62902146A>G		167.0	0.0		225.0	9.0	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Silent	SNP	ENST00000393632.2	hg19	CCDS31849.1																																																																																			.	.		0.388	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		G	62902146	A	G	62902146	2	3	24	1	0	0	0	0	0	0	0	1	9709	272	10	2		2	MON2	12	62902146	Silent	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	9316736	62902146	70949749	86	3293										
MYF6	4618	hgsc.bcm.edu	37	chr12	81101722	81101722	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gcagcctccacactgccccgGccagtgtctgatctgggctt	11	16	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:81101722G>A	ENST00000228641.3	+	1	446	c.224G>A	c.(223-225)gGc>gAc	p.G75D		NM_002469.2	NP_002460.1	P23409	MYF6_HUMAN	myogenic factor 6 (herculin)	75					muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|skin(1)	26						CACTGCCCCGGCCAGTGTCTG	0.647																																					p.G75D		Atlas-SNP	.											.	MYF6	74	.	0			c.G224A						.						29	36	33					12																	81101722		2202	4300	6502	SO:0001583	missense	4618	exon1			GCCCCGGCCAGTG		CCDS9019.1	12q21	2013-05-21				ENSG00000111046		"Basic helix-loop-helix proteins"	7566	protein-coding gene	gene with protein product	"muscle-specific regulatory factor 4"	159991				8978788	Standard	NM_002469		Approved	MRF4, bHLHc4	uc001szf.2	P23409		ENST00000228641.3:c.224G>A	chr12.hg19:g.81101722G>A	ENSP00000228641:p.Gly75Asp	64.0	0.0		104.0	25.0	NM_002469	B2R898|Q53X80|Q6FHI9	Missense_Mutation	SNP	ENST00000228641.3	hg19	CCDS9019.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.755048	0.89843	.	.	ENSG00000111046	ENST00000228641	D	0.91351	-2.83	5.62	5.62	0.85841	Myogenic basic muscle-specific protein (2);	0.000000	0.85682	D	0.000000	D	0.96018	0.8703	M	0.85777	2.775	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96185	0.9133	10	0.87932	D	0	-14.9884	19.6517	0.95819	0.0:0.0:1.0:0.0	.	75	P23409	MYF6_HUMAN	D	75	ENSP00000228641:G75D	ENSP00000228641:G75D	G	+	2	0	MYF6	79625853	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	9.476000	0.97823	2.662000	0.90505	0.655000	0.94253	GGC	.	.		0.647	MYF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407756.1	NM_002469		A	81101722	G	A	81101722	3	1	24	1	0	0	0	0	1	0	0	0	10037	1203	42	3	226	3	MYF6	12	81101722	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	18199576	81101722	52750173	87	3294										
BTBD11	121551	hgsc.bcm.edu	37	chr12	108013779	108013779	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ccaggcgtcccgtggactctGcacacgtggctggagtcttt	13	13	2	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:108013779G>A	ENST00000280758.5	+	11	2997	c.2469G>A	c.(2467-2469)ctG>ctA	p.L823L	BTBD11_ENST00000420571.2_Silent_p.L704L|BTBD11_ENST00000490090.2_Silent_p.L823L|RP11-128P10.1_ENST00000548473.1_RNA|BTBD11_ENST00000357167.4_Silent_p.L360L	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	823						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CGTGGACTCTGCACACGTGGC	0.602																																					p.L823L		Atlas-SNP	.											.	BTBD11	122	.	0			c.G2469A						.						32	30	31					12																	108013779		2203	4300	6503	SO:0001819	synonymous_variant	121551	exon11			GACTCTGCACACG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2469G>A	chr12.hg19:g.108013779G>A		50.0	0.0		68.0	6.0	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	hg19	CCDS31893.1																																																																																			.	.		0.602	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		A	108013779	G	A	108013779	2	1	24	1	0	0	0	0	0	0	0	1	1541	1306	46	3		3	BTBD11	12	108013779	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	26912057	108013779	25838116	88	3295										
ARPC3	10094	hgsc.bcm.edu	37	chr12	110874389	110874389	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ctgtttgtttgcaggtttggCataaattgcgttaagtggaa	12	4	0	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:110874389C>T	ENST00000228825.7	-	5	498	c.352G>A	c.(352-354)Gcc>Acc	p.A118T	RP11-478C19.2_ENST00000550231.1_RNA	NM_001278556.1|NM_005719.2	NP_001265485.1|NP_005710.1	O15145	ARPC3_HUMAN	actin related protein 2/3 complex, subunit 3, 21kDa	118					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			lung(1)|ovary(1)	2						GCAGGTTTGGCATAAATTGCG	0.428																																					p.A118T		Atlas-SNP	.											.	ARPC3	7	.	0			c.G352A						.						189	173	179					12																	110874389		2203	4300	6503	SO:0001583	missense	10094	exon5			GTTTGGCATAAAT	AF006086	CCDS9146.1	12q24	2011-07-06	2002-08-29		ENSG00000111229	ENSG00000111229		"Actin related protein 2/3 complex subunits"	706	protein-coding gene	gene with protein product		604225	"actin related protein 2/3 complex, subunit 3 (21 kD)"			9230079, 9359840	Standard	NM_001278556		Approved	p21-Arc, ARC21	uc001tqq.3	O15145	OTTHUMG00000134333	ENST00000228825.7:c.352G>A	chr12.hg19:g.110874389C>T	ENSP00000228825:p.Ala118Thr	46.0	0.0		65.0	8.0	NM_005719	O00554	Missense_Mutation	SNP	ENST00000228825.7	hg19	CCDS9146.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372719	0.61624	.	.	ENSG00000111229	ENST00000228825;ENST00000392683	.	.	.	5.95	5.95	0.96441	.	0.140386	0.64402	D	0.000004	T	0.55909	0.1950	L	0.28694	0.88	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.50849	-0.8779	9	0.87932	D	0	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	118	O15145	ARPC3_HUMAN	T	118	.	ENSP00000228825:A118T	A	-	1	0	ARPC3	109358772	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.444000	0.80532	2.824000	0.97209	0.655000	0.94253	GCC	.	.		0.428	ARPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259487.2			T	110874389	C	T	110874389	3	4	24	1	0	0	0	0	1	0	0	0	972	710	25	3	196	3	ARPC3	12	110874389	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	2860610	110874389	22977506	89	3296										
CCDC60	160777	hgsc.bcm.edu	37	chr12	119957988	119957988	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	taaggaaatgcagaccactcTcaaatcaaggtaggaaagcc	9	9	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:119957988T>C	ENST00000327554.2	+	9	1496	c.1031T>C	c.(1030-1032)cTc>cCc	p.L344P	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	344										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CAGACCACTCTCAAATCAAGG	0.507																																					p.L344P		Atlas-SNP	.											.	CCDC60	84	.	0			c.T1031C						.						125	124	124					12																	119957988		2203	4300	6503	SO:0001583	missense	160777	exon9			CCACTCTCAAATC	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.1031T>C	chr12.hg19:g.119957988T>C	ENSP00000333374:p.Leu344Pro	68.0	0.0		72.0	13.0	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	hg19	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	T	0.128	-1.116803	0.01799	.	.	ENSG00000183273	ENST00000327554	T	0.24151	1.87	3.94	-7.87	0.01183	.	2.297300	0.01611	N	0.022527	T	0.13586	0.0329	N	0.22421	0.69	0.09310	N	1	P	0.34757	0.467	B	0.31686	0.134	T	0.08973	-1.0696	9	.	.	.	6.0E-4	6.1289	0.20194	0.1612:0.0:0.3382:0.5006	.	344	Q8IWA6	CCD60_HUMAN	P	344	ENSP00000333374:L344P	.	L	+	2	0	CCDC60	118442371	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.430000	0.02434	-2.578000	0.00464	-2.093000	0.00369	CTC	.	.		0.507	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		C	119957988	T	C	119957988	3	2	24	1	0	0	0	0	1	0	0	0	2833	1551	54	2	1065	2	CCDC60	12	119957988	Missense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	9083599	119957988	13893907	90	3297										
PABPC3	5042	hgsc.bcm.edu	37	chr13	25671865	25671865	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tccacggtataaatatgctgCgggagttcgcaatcctcagc	10	11	1	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr13:25671865C>T	ENST00000281589.3	+	1	1566	c.1529C>T	c.(1528-1530)gCg>gTg	p.A510V		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	510					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AAATATGCTGCGGGAGTTCGC	0.527																																					p.A510V		Atlas-SNP	.											.	PABPC3	129	.	0			c.C1529T						.						64	60	62					13																	25671865		2203	4300	6503	SO:0001583	missense	5042	exon1			ATGCTGCGGGAGT	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1529C>T	chr13.hg19:g.25671865C>T	ENSP00000281589:p.Ala510Val	70.0	0.0		71.0	13.0	NM_030979	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	hg19	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.254611	0.22965	.	.	ENSG00000151846	ENST00000281589	T	0.43688	0.94	1.0	0.0783	0.14411	Polyadenylate-binding protein/Hyperplastic disc protein (1);	0.134298	0.31381	N	0.007744	T	0.24928	0.0605	L	0.31752	0.955	0.34986	D	0.754589	B	0.06786	0.001	B	0.01281	0.0	T	0.08554	-1.0716	10	0.36615	T	0.2	.	6.1155	0.20124	0.3017:0.6983:0.0:0.0	.	510	Q9H361	PABP3_HUMAN	V	510	ENSP00000281589:A510V	ENSP00000281589:A510V	A	+	2	0	PABPC3	24569865	0.988000	0.35896	0.503000	0.27626	0.034000	0.12701	3.257000	0.51500	0.003000	0.14656	-0.361000	0.07541	GCG	.	.		0.527	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		T	25671865	C	T	25671865	3	4	24	1	0	0	0	0	1	0	0	0	11374	768	27	1	1531	1	PABPC3	13	25671865	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10		25671865	89498013	91	3298										
OLFM4	10562	hgsc.bcm.edu	37	chr13	53603061	53603061	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gatgtgggacctccaattccCagccccggcttcagctcttt	9	15	2	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr13:53603061C>A	ENST00000219022.2	+	1	168	c.90C>A	c.(88-90)ccC>ccA	p.P30P		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	30					cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		CTCCAATTCCCAGCCCCGGCT	0.607																																					p.P30P		Atlas-SNP	.											.	OLFM4	94	.	0			c.C90A						.						104	110	108					13																	53603061		2203	4300	6503	SO:0001819	synonymous_variant	10562	exon1			AATTCCCAGCCCC	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.90C>A	chr13.hg19:g.53603061C>A		91.0	0.0		65.0	12.0	NM_006418	O95362|Q5VWG0|Q86T22	Silent	SNP	ENST00000219022.2	hg19	CCDS9440.1																																																																																			.	.		0.607	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418		A	53603061	C	A	53603061	2	1	24	1	0	0	0	0	0	0	0	1	10864	581	21	3		3	OLFM4	13	53603061	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	27931196	53603061	61566817	92	3299										
SCEL	8796	hgsc.bcm.edu	37	chr13	78211328	78211328	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ctgtttattcaacttctgatAggtgagtatgtctttatttc	7	6	3	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr13:78211328A>T	ENST00000349847.3	+	30	1921	c.1837A>T	c.(1837-1839)Agg>Tgg	p.R613W	SCEL_ENST00000377246.3_Splice_Site_p.R593W|SCEL_ENST00000535157.1_Splice_Site_p.R571W	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	613					embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		AACTTCTGATAGGTGAGTATG	0.328																																					p.R613W		Atlas-SNP	.											.	SCEL	85	.	0			c.A1837T						.						87	81	83					13																	78211328		2203	4298	6501	SO:0001630	splice_region_variant	8796	exon30			TCTGATAGGTGAG	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.1838+1A>T	chr13.hg19:g.78211328A>T		55.0	0.0		58.0	9.0	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	hg19	CCDS9459.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.289698	0.80914	.	.	ENSG00000136155	ENST00000535157;ENST00000377246;ENST00000349847	D;D;D	0.81659	-1.52;-1.52;-1.52	5.93	4.69	0.59074	.	0.000000	0.64402	D	0.000004	T	0.81163	0.4765	L	0.38953	1.18	0.42116	D	0.991407	P;P;D	0.56521	0.949;0.949;0.976	P;P;D	0.63877	0.889;0.879;0.919	T	0.81885	-0.0727	10	0.72032	D	0.01	-12.9835	6.396	0.21613	0.682:0.1624:0.0:0.1556	.	571;593;613	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	W	571;593;613	ENSP00000437895:R571W;ENSP00000366454:R593W;ENSP00000302579:R613W	ENSP00000302579:R613W	R	+	1	2	SCEL	77109329	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.402000	0.34600	2.263000	0.75096	0.533000	0.62120	AGG	.	.		0.328	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777	Missense_Mutation	T	78211328	A	T	78211328	5	4	24	1	0	0	0	0	0	0	1	0	13903	434	15	4	1951	4	SCEL	13	78211328	Splice_Site	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	24608267	78211328	36958550	93	3300										
RNASE12	493901	hgsc.bcm.edu	37	chr14	21058715	21058715	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttacaagtgtggtcaggttcCctgataactctttgtatgat	9	7	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr14:21058715C>T	ENST00000556526.1	-	1	267	c.168G>A	c.(166-168)agG>agA	p.R56R	RNASE11_ENST00000555283.1_Intron|RP11-14J7.6_ENST00000554993.1_RNA|RP11-14J7.6_ENST00000554006.1_RNA|RNASE11_ENST00000555841.1_5'Flank|RNASE11_ENST00000610205.1_5'Flank|RNASE11_ENST00000398009.2_5'Flank|RNASE11_ENST00000553849.1_5'Flank|RNASE11_ENST00000432835.2_5'Flank|RNASE11_ENST00000398008.2_5'Flank|RP11-14J7.6_ENST00000556487.1_RNA|RP11-14J7.6_ENST00000554529.1_RNA|RP11-14J7.6_ENST00000553604.1_RNA	NM_001024822.2	NP_001019993.1	Q5GAN4	RNS12_HUMAN	ribonuclease, RNase A family, 12 (non-active)	56						extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			kidney(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(95;0.00238)		Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.013)		GGTCAGGTTCCCTGATAACTC	0.438																																					p.R56R		Atlas-SNP	.											.	RNASE12	19	.	0			c.G168A						.						149	123	132					14																	21058715		2203	4300	6503	SO:0001819	synonymous_variant	493901	exon1			AGGTTCCCTGATA		CCDS32037.1	14q11.1	2012-10-05			ENSG00000258436	ENSG00000258436		"Ribonucleases, RNase A"	24211	protein-coding gene	gene with protein product							Standard	NM_001024822		Approved		uc001vxt.3	Q5GAN4	OTTHUMG00000170991	ENST00000556526.1:c.168G>A	chr14.hg19:g.21058715C>T		165.0	0.0		119.0	22.0	NM_001024822		Silent	SNP	ENST00000556526.1	hg19	CCDS32037.1																																																																																			.	.		0.438	RNASE12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411107.1			T	21058715	C	T	21058715	2	4	24	1	0	0	0	0	0	0	0	1	13417	622	22	3		3	RNASE12	14	21058715	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10		21058715	86290825	94	3301										
C14orf93	60686	hgsc.bcm.edu	37	chr14	23467696	23467696	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	caccctgggagccgcatgtcCctctgagttgctgggaagcc	13	14	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr14:23467696C>T	ENST00000299088.6	-	2	966	c.537G>A	c.(535-537)agG>agA	p.R179R	C14orf93_ENST00000397382.4_Silent_p.R179R|RP11-298I3.4_ENST00000556503.1_RNA|C14orf93_ENST00000397379.3_Silent_p.R179R|RP11-298I3.4_ENST00000555294.1_RNA|C14orf93_ENST00000557513.1_5'Flank|C14orf93_ENST00000397377.1_5'UTR|C14orf93_ENST00000341470.4_Silent_p.R179R|C14orf93_ENST00000406429.2_Silent_p.R179R	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93	179						extracellular region (GO:0005576)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	17	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		GCCGCATGTCCCTCTGAGTTG	0.657																																					p.R179R		Atlas-SNP	.											.	C14orf93	33	.	0			c.G537A						.						16	17	17					14																	23467696		2203	4296	6499	SO:0001819	synonymous_variant	60686	exon2			CATGTCCCTCTGA	AK023026	CCDS9583.1, CCDS61399.1, CCDS61400.1	14q11.1	2012-09-25			ENSG00000100802	ENSG00000100802			20162	protein-coding gene	gene with protein product							Standard	XM_005267971		Approved	FLJ12154	uc001wih.3	Q9H972	OTTHUMG00000028712	ENST00000299088.6:c.537G>A	chr14.hg19:g.23467696C>T		155.0	0.0		152.0	26.0	NM_021944	B7WP03|D3DS38|D3DS39|Q86SE6|Q96CF7|Q9HA68	Silent	SNP	ENST00000299088.6	hg19	CCDS9583.1																																																																																			.	.		0.657	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	NM_021944		T	23467696	C	T	23467696	2	4	24	1	0	0	0	0	0	0	0	1	1784	622	22	3		3	C14orf93	14	23467696	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	2408981	23467696	83881844	95	3302										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42356164	42356164	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttgaatagcaacagattgacTaaaattacaaatgatatgtt	6	4	0	4			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr14:42356164T>G	ENST00000298119.4	+	3	1525	c.336T>G	c.(334-336)acT>acG	p.T112T	LRFN5_ENST00000554120.1_Silent_p.T112T|LRFN5_ENST00000554171.1_Silent_p.T112T	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	112						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		ACAGATTGACTAAAATTACAA	0.358										HNSCC(30;0.082)																											p.T112T		Atlas-SNP	.											.	LRFN5	269	.	0			c.T336G						.						65	65	65					14																	42356164		2203	4300	6503	SO:0001819	synonymous_variant	145581	exon3			ATTGACTAAAATT	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.336T>G	chr14.hg19:g.42356164T>G		150.0	0.0		144.0	24.0	NM_152447	B3KU78|Q86XL2	Silent	SNP	ENST00000298119.4	hg19	CCDS9678.1																																																																																			.	.		0.358	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		G	42356164	T	G	42356164	2	3	24	1	0	0	0	0	0	0	0	1	8950	1509	53	5		5	LRFN5	14	42356164	Silent	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	18888468	42356164	64993376	96	3303										
ESRRB	2103	hgsc.bcm.edu	37	chr14	76957890	76957890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	taccgctcgctgccctatgaCgacaagctggtgtacgctga	11	13	0	2	rs139812473		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr14:76957890C>T	ENST00000509242.1	+	7	986	c.888C>T	c.(886-888)gaC>gaT	p.D296D	ESRRB_ENST00000380887.2_Silent_p.D296D|ESRRB_ENST00000261532.7_Silent_p.D296D|ESRRB_ENST00000556177.1_Silent_p.D296D	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	296					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		TGCCCTATGACGACAAGCTGG	0.617																																					p.D296D		Atlas-SNP	.											.	ESRRB	114	.	0			c.C888T						.	C		1,4403		0,1,2201	61	46	51		888	-8.9	0.2	14	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous	ESRRB	NM_004452.3		0,1,6501	TT,TC,CC		0.0,0.0227,0.0077		296/509	76957890	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	2103	exon8			CTATGACGACAAG	X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715		"Nuclear hormone receptors"	3473	protein-coding gene	gene with protein product		602167	"deafness, autosomal recessive 35"	ESRL2, DFNB35		3267207, 9344655, 18179891	Standard	NM_004452		Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000509242.1:c.888C>T	chr14.hg19:g.76957890C>T		136.0	0.0		110.0	19.0	NM_004452	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Silent	SNP	ENST00000509242.1	hg19	CCDS9850.2																																																																																			.	C|1.000;T|0.000		0.617	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1			T	76957890	C	T	76957890	2	4	24	1	0	0	0	0	0	0	0	1	5263	535	19	1		1	ESRRB	14	76957890	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	34601726	76957890	30391650	97	3304										
RYR3	6263	hgsc.bcm.edu	37	chr15	33954906	33954906	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gagttccagtttgtgcctgtGctgaaactcattggaaccct	10	10	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:33954906G>T	ENST00000389232.4	+	35	5245	c.5175G>T	c.(5173-5175)gtG>gtT	p.V1725V	RYR3_ENST00000415757.3_Silent_p.V1725V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1725	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTGTGCCTGTGCTGAAACTCA	0.557																																					p.V1725V		Atlas-SNP	.											.	RYR3	760	.	0			c.G5175T						.						96	103	101					15																	33954906		2141	4267	6408	SO:0001819	synonymous_variant	6263	exon35			GCCTGTGCTGAAA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.5175G>T	chr15.hg19:g.33954906G>T		109.0	0.0		115.0	19.0	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.557	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33954906	G	T	33954906	2	4	24	1	0	0	0	0	0	0	0	1	13785	1306	46	3		3	RYR3	15	33954906	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10		33954906	68576486	98	3305										
MEIS2	4212	hgsc.bcm.edu	37	chr15	37242602	37242602	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tcttcggaagggtacggatgCtaatggaaaaacaaatgttt	11	5	1	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:37242602C>T	ENST00000561208.1	-	9	1319		c.e9-1		MEIS2_ENST00000557796.2_Splice_Site|MEIS2_ENST00000397620.2_Splice_Site|MEIS2_ENST00000340545.5_Splice_Site|MEIS2_ENST00000444725.1_Splice_Site|MEIS2_ENST00000559561.1_Splice_Site|MEIS2_ENST00000219869.9_Splice_Site|MEIS2_ENST00000559085.1_Splice_Site|MEIS2_ENST00000397624.3_Splice_Site|MEIS2_ENST00000424352.2_Splice_Site|MEIS2_ENST00000382766.2_Splice_Site|MEIS2_ENST00000338564.5_Splice_Site			O14770	MEIS2_HUMAN	Meis homeobox 2						eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		GGTACGGATGCTAATGGAAAA	0.378																																					.		Atlas-SNP	.											.	MEIS2	99	.	0			c.901-1G>A						.						160	152	155					15																	37242602		2201	4297	6498	SO:0001630	splice_region_variant	4212	exon10			CGGATGCTAATGG	AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"Homeoboxes / TALE class"	7001	protein-coding gene	gene with protein product		601740	"Meis (mouse) homolog 2", "Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.901-1G>A	chr15.hg19:g.37242602C>T		99.0	0.0		140.0	14.0	NM_170677	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Splice_Site	SNP	ENST00000561208.1	hg19	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719292	0.68844	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766;ENST00000424352;ENST00000444725;ENST00000340545;ENST00000397624;ENST00000397620;ENST00000219869	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5721	0.95425	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MEIS2	35029894	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.651000	0.83577	2.857000	0.98124	0.650000	0.86243	.	.	.		0.378	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677	Intron	T	37242602	C	T	37242602	5	4	24	1	0	0	0	0	0	0	1	0	9477	811	28	3	612	3	MEIS2	15	37242602	Splice_Site	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	3287696	37242602	65288790	99	3306										
MGA	23269	hgsc.bcm.edu	37	chr15	41988636	41988636	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tatctggagccctgtgctgtCaccagaagcacagttaagat	10	10	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:41988636C>T	ENST00000570161.1	+	2	1428	c.1428C>T	c.(1426-1428)gtC>gtT	p.V476V	MGA_ENST00000219905.7_Silent_p.V476V|MGA_ENST00000545763.1_Silent_p.V476V|MGA_ENST00000566586.1_Silent_p.V476V|MGA_ENST00000389936.4_Silent_p.V476V|MGA_ENST00000568630.1_3'UTR			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CCTGTGCTGTCACCAGAAGCA	0.423																																					p.V476V		Atlas-SNP	.											.	MGA	264	.	0			c.C1428T						.						72	69	70					15																	41988636		1847	4096	5943	SO:0001819	synonymous_variant	23269	exon3			TGCTGTCACCAGA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1428C>T	chr15.hg19:g.41988636C>T		103.0	0.0		148.0	27.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.423	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	41988636	C	T	41988636	2	4	24	1	0	0	0	0	0	0	0	1	9549	813	29	3		3	MGA	15	41988636	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	4746034	41988636	60542756	100	3307										
ATP8B4	79895	hgsc.bcm.edu	37	chr15	50223353	50223354	+	Frame_Shift_Ins	INS	-	-	A													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttctggtgttgttgaaatccINSaaaaaggcaagtaattgata					rs146835330	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:50223353_50223354insA	ENST00000284509.6	-	16	1745_1746	c.1604_1605insT	c.(1603-1605)ttgfs	p.L535fs	ATP8B4_ENST00000559829.1_Frame_Shift_Ins_p.L535fs	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	535						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		TGTTGAAATCCAAAAAGGCAAG	0.371																																					p.L535fs		Atlas-Indel,Pindel	.											.	ATP8B4	173	.	0			c.1605_1606insT						.																																			SO:0001589	frameshift_variant	79895	exon16			.	AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"ATPases / P-type"	13536	protein-coding gene	gene with protein product		609123	"ATPase, Class I, type 8B, member 4"			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.1605dupT	chr15.hg19:g.50223358_50223358dupA	ENSP00000284509:p.Leu535fs	160.0	0.0		212.0	36.0	NM_024837	Q9H727	Frame_Shift_Ins	INS	ENST00000284509.6	hg19	CCDS32238.1																																																																																			.	.		0.371	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837		A	50223354	-	A	50223353	7	5	24	1	0	1	1	0	0	0	0	0	1197	593	21	0	2025	0	ATP8B4	15	50223353	Frame_Shift_Ins	INS	-	TCGA-5C-A9VG-01A-11D-A36X-10	8234717	50223353	52308039	101	3308										
ARID3B	10620	hgsc.bcm.edu	37	chr15	74836644	74836644	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	aggctgcttcaaaatattttCatgtgcagaaagtagctcgc	9	8	2	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:74836644C>T	ENST00000346246.5	+	2	598	c.367C>T	c.(367-369)Cat>Tat	p.H123Y		NM_006465.2	NP_006456.1	Q8IVW6	ARI3B_HUMAN	AT rich interactive domain 3B (BRIGHT-like)	123						nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(2)	14						AAAATATTTTCATGTGCAGAA	0.502																																					p.H123Y		Atlas-SNP	.											.	ARID3B	35	.	0			c.C367T						.						31	30	30					15																	74836644		2197	4292	6489	SO:0001583	missense	10620	exon2			TATTTTCATGTGC		CCDS10264.1	15q24	2013-02-07	2006-11-08		ENSG00000179361	ENSG00000179361		"-"	14350	protein-coding gene	gene with protein product		612457	"AT rich interactive domain 3B (BRIGHT- like)"				Standard	NM_006465		Approved	BDP, DRIL2	uc002ayd.3	Q8IVW6	OTTHUMG00000141321	ENST00000346246.5:c.367C>T	chr15.hg19:g.74836644C>T	ENSP00000343126:p.His123Tyr	216.0	0.0		288.0	24.0	NM_006465	O95443|Q59HC9|Q6P9C9	Missense_Mutation	SNP	ENST00000346246.5	hg19	CCDS10264.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.823804	0.71143	.	.	ENSG00000179361	ENST00000382537;ENST00000346246;ENST00000395077	T	0.52295	0.67	5.5	4.58	0.56647	.	0.327366	0.32093	N	0.006584	T	0.55386	0.1917	L	0.32530	0.975	0.35248	D	0.778469	D;D;D	0.63880	0.993;0.991;0.993	D;P;D	0.70227	0.968;0.851;0.968	T	0.61505	-0.7049	10	0.25106	T	0.35	-2.8674	14.7359	0.69414	0.0:0.8557:0.1443:0.0	.	123;123;123	Q8IVW6;Q8IVW6-4;B4DQB0	ARI3B_HUMAN;.;.	Y	123	ENSP00000343126:H123Y	ENSP00000343126:H123Y	H	+	1	0	ARID3B	72623697	0.757000	0.28394	0.854000	0.33618	0.915000	0.54546	2.363000	0.44178	1.310000	0.45006	0.650000	0.86243	CAT	.	.		0.502	ARID3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280688.2	NM_006465		T	74836644	C	T	74836644	3	4	24	1	0	0	0	0	1	0	0	0	917	826	29	3	369	3	ARID3B	15	74836644	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	24613291	74836644	27694748	102	3309										
FAM108C1	58489	hgsc.bcm.edu	37	chr15	81046707	81046707	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	atctcacgaacttcctaattCctgaagacaacaacttgatc	4	12	1	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:81046707C>G	ENST00000258884.4	+	3	1113	c.986C>G	c.(985-987)tCc>tGc	p.S329C	ABHD17C_ENST00000559506.1_3'UTR|ABHD17C_ENST00000560609.1_Missense_Mutation_p.S94C|ABHD17C_ENST00000558464.1_Missense_Mutation_p.S295C	NM_021214.1	NP_067037.1	Q6PCB6	AB17C_HUMAN	abhydrolase domain containing 17C	329							hydrolase activity (GO:0016787)										CTTCCTAATTCCTGAAGACAA	0.413																																					p.S329C		Atlas-SNP	.											.	FAM108C1	12	.	0			c.C986G						.						53	51	51					15																	81046707		1903	4128	6031	SO:0001583	missense	58489	exon3			CTAATTCCTGAAG		CCDS45323.1	15q25.1	2013-03-15	2013-03-15	2013-03-15	ENSG00000136379	ENSG00000136379		"Abhydrolase domain containing"	26925	protein-coding gene	gene with protein product			"family with sequence similarity 108, member C1"	FAM108C1			Standard	NM_021214		Approved		uc002bfu.3	Q6PCB6		ENST00000258884.4:c.986C>G	chr15.hg19:g.81046707C>G	ENSP00000258884:p.Ser329Cys	76.0	0.0		83.0	30.0	NM_021214	Q1RMD6|Q9NPM1	Missense_Mutation	SNP	ENST00000258884.4	hg19	CCDS45323.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.211228	0.58343	.	.	ENSG00000136379	ENST00000258884	T	0.34667	1.35	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.39784	0.1091	N	0.08118	0	0.58432	D	0.999996	D;D	0.71674	0.992;0.998	P;D	0.63113	0.751;0.911	T	0.54296	-0.8315	10	0.87932	D	0	.	18.21	0.89867	0.0:1.0:0.0:0.0	.	329;295	Q6PCB6;Q6PCB6-2	F108C_HUMAN;.	C	329	ENSP00000258884:S329C	ENSP00000258884:S329C	S	+	2	0	FAM108C1	78833762	1.000000	0.71417	0.994000	0.49952	0.514000	0.34195	4.230000	0.58632	2.297000	0.77311	0.555000	0.69702	TCC	.	.		0.413	ABHD17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417652.1	NM_021214		G	81046707	C	G	81046707	3	3	24	1	0	0	0	0	1	0	0	0	5398	855	30	4	996	4	FAM108C1	15	81046707	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	6210063	81046707	21484685	103	3310										
C16orf11	146325	hgsc.bcm.edu	37	chr16	613614	613614	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gcaaccccagggagcacggcCcacaggtgctgcccccgcgc	13	19	0	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:613614C>A	ENST00000409413.3	+	2	599	c.320C>A	c.(319-321)cCc>cAc	p.P107H		NM_145270.2	NP_660313.1	P0CG20	PRR35_HUMAN		107	Pro-rich.									central_nervous_system(1)|endometrium(1)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10						GGAGCACGGCCCACAGGTGCT	0.746																																					p.P107H		Atlas-SNP	.											.	C16orf11	27	.	0			c.C320A						.						14	14	14					16																	613614		1895	4082	5977	SO:0001583	missense	146325	exon2			CACGGCCCACAGG																												ENST00000409413.3:c.320C>A	chr16.hg19:g.613614C>A	ENSP00000386499:p.Pro107His	48.0	0.0		47.0	5.0	NM_145270	B8ZZ27|Q8N233|Q96AX3|Q96S23	Missense_Mutation	SNP	ENST00000409413.3	hg19	CCDS45365.1	.	.	.	.	.	.	.	.	.	.	C	7.201	0.593465	0.13875	.	.	ENSG00000161992	ENST00000409413	.	.	.	1.83	-0.627	0.11541	.	1.619920	0.04669	U	0.410413	T	0.17619	0.0423	L	0.36672	1.1	0.09310	N	1	P	0.43352	0.804	B	0.28784	0.094	T	0.24621	-1.0155	9	0.38643	T	0.18	.	4.2979	0.10910	0.0:0.5055:0.0:0.4945	.	107	P0CG20	CP011_HUMAN	H	107	.	ENSP00000386499:P107H	P	+	2	0	C16orf11	553615	0.003000	0.15002	0.001000	0.08648	0.000000	0.00434	-0.154000	0.10130	0.016000	0.14998	-0.384000	0.06662	CCC	.	.		0.746	C16orf11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000333913.1			A	613614	C	A	613614	3	1	24	1	0	0	0	0	1	0	0	0	1812	623	22	3	322	3	C16orf11	16	613614	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10		613614	89741139	104	3311										
PRSS27	83886	hgsc.bcm.edu	37	chr16	2764244	2764244	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tggtacagggggttgctctcCacctgcctcacccgggcata	12	14	2	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:2764244C>T	ENST00000302641.3	-	4	384	c.330G>A	c.(328-330)gtG>gtA	p.V110V	AC092117.1_ENST00000410123.1_RNA	NM_031948.3	NP_114154.1	Q9BQR3	PRS27_HUMAN	protease, serine 27	110	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8						GGTTGCTCTCCACCTGCCTCA	0.657																																					p.V110V		Atlas-SNP	.											.	PRSS27	20	.	0			c.G330A						.						39	35	36					16																	2764244		2198	4300	6498	SO:0001819	synonymous_variant	83886	exon4			GCTCTCCACCTGC	AB056161	CCDS10476.1	16p13.3	2010-05-07			ENSG00000172382	ENSG00000172382		"Serine peptidases / Serine peptidases"	15475	protein-coding gene	gene with protein product		608018					Standard	NM_031948		Approved	MPN, pancreasin, CAPH2, marapsin	uc002crf.3	Q9BQR3	OTTHUMG00000128929	ENST00000302641.3:c.330G>A	chr16.hg19:g.2764244C>T		41.0	0.0		41.0	10.0	NM_031948		Silent	SNP	ENST00000302641.3	hg19	CCDS10476.1																																																																																			.	.		0.657	PRSS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250908.1	NM_031948		T	2764244	C	T	2764244	2	4	24	1	0	0	0	0	0	0	0	1	12633	581	21	3		3	PRSS27	16	2764244	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	2150630	2764244	87590509	105	3312										
MEFV	4210	hgsc.bcm.edu	37	chr16	3296531	3296531	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ggacctcgctgtacctgtgcAagatgtctccaatgtcctag	10	12	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:3296531A>G	ENST00000219596.1	-	6	1643	c.1604T>C	c.(1603-1605)tTg>tCg	p.L535S	MEFV_ENST00000536379.1_Missense_Mutation_p.L324S|MEFV_ENST00000339854.4_Missense_Mutation_p.L355S|MEFV_ENST00000541159.1_Missense_Mutation_p.L324S	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	535	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GTACCTGTGCAAGATGTCTCC	0.557																																					p.L535S		Atlas-SNP	.											.	MEFV	170	.	0			c.T1604C						.						86	81	83					16																	3296531		2197	4300	6497	SO:0001583	missense	4210	exon6			CTGTGCAAGATGT	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1604T>C	chr16.hg19:g.3296531A>G	ENSP00000219596:p.Leu535Ser	44.0	0.0		60.0	8.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	hg19	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	A	15.79	2.937014	0.52972	.	.	ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000541159;ENST00000536379;ENST00000534868	T;T;T;T	0.70399	-0.48;-0.05;-0.31;-0.02	5.41	5.41	0.78517	.	0.000000	0.41938	D	0.000785	D	0.83644	0.5299	M	0.80616	2.505	0.38573	D	0.949999	D	0.89917	1.0	D	0.71870	0.975	D	0.87288	0.2297	10	0.87932	D	0	-25.6511	13.6884	0.62531	1.0:0.0:0.0:0.0	.	535	O15553	MEFV_HUMAN	S	535;535;355;324;324;324	ENSP00000219596:L535S;ENSP00000339639:L355S;ENSP00000438711:L324S;ENSP00000445079:L324S	ENSP00000219596:L535S	L	-	2	0	MEFV	3236532	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	5.608000	0.67654	2.188000	0.69820	0.533000	0.62120	TTG	.	.		0.557	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		G	3296531	A	G	3296531	3	3	24	1	0	0	0	0	1	0	0	0	9468	131	5	2	761	2	MEFV	16	3296531	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	532287	3296531	87058222	106	3313										
TMC7	79905	hgsc.bcm.edu	37	chr16	19056299	19056299	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gatgacacatgtgacctttgCggctacaaccagaaactcta	8	11	1	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:19056299C>T	ENST00000304381.5	+	10	1561	c.1431C>T	c.(1429-1431)tgC>tgT	p.C477C	TMC7_ENST00000421369.3_Silent_p.C367C|TMC7_ENST00000569532.1_Silent_p.C477C	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	477					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						GTGACCTTTGCGGCTACAACC	0.562																																					p.C477C		Atlas-SNP	.											.	TMC7	75	.	0			c.C1431T						.						117	113	115					16																	19056299		2197	4300	6497	SO:0001819	synonymous_variant	79905	exon10			CCTTTGCGGCTAC	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1431C>T	chr16.hg19:g.19056299C>T		86.0	0.0		113.0	32.0	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Silent	SNP	ENST00000304381.5	hg19	CCDS10573.1																																																																																			.	.		0.562	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847		T	19056299	C	T	19056299	2	4	24	1	0	0	0	0	0	0	0	1	16005	776	27	1		1	TMC7	16	19056299	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	15759768	19056299	71298454	107	3314										
RBBP6	5930	hgsc.bcm.edu	37	chr16	24583041	24583041	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	acaaagccacttatgatactAaacggccaaatgaagagaca	7	9	0	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:24583041A>G	ENST00000319715.4	+	18	5086	c.4654A>G	c.(4654-4656)Aaa>Gaa	p.K1552E	RBBP6_ENST00000381039.3_Missense_Mutation_p.K712E|RBBP6_ENST00000348022.2_Missense_Mutation_p.K1518E	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1552					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TTATGATACTAAACGGCCAAA	0.368																																					p.K1552E		Atlas-SNP	.											RBBP6,bladder,carcinoma,0,1	RBBP6	158	.	0			c.A4654G						.						60	56	57					16																	24583041		2197	4300	6497	SO:0001583	missense	5930	exon18			GATACTAAACGGC		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.4654A>G	chr16.hg19:g.24583041A>G	ENSP00000317872:p.Lys1552Glu	428.0	0.0		495.0	85.0	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	hg19	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.149581	0.57151	.	.	ENSG00000122257	ENST00000381039;ENST00000319715;ENST00000348022	T;T;T	0.21543	2.0;2.39;2.35	6.03	6.03	0.97812	.	0.138745	0.51477	D	0.000090	T	0.16981	0.0408	L	0.32530	0.975	0.29183	N	0.876348	P;P;P	0.52316	0.952;0.952;0.919	B;B;B	0.43413	0.419;0.419;0.152	T	0.08229	-1.0732	10	0.11485	T	0.65	-26.416	13.011	0.58731	0.8657:0.1343:0.0:0.0	.	712;1518;1552	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9	.;.;RBBP6_HUMAN	E	712;1552;1518	ENSP00000370427:K712E;ENSP00000317872:K1552E;ENSP00000316291:K1518E	ENSP00000317872:K1552E	K	+	1	0	RBBP6	24490542	1.000000	0.71417	0.990000	0.47175	0.890000	0.51754	7.541000	0.82084	2.313000	0.78055	0.455000	0.32223	AAA	.	.		0.368	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		G	24583041	A	G	24583041	3	3	24	1	0	0	0	0	1	0	0	0	13118	363	13	2	4778	2	RBBP6	16	24583041	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	5526742	24583041	65771712	108	3315										
MVP	9961	hgsc.bcm.edu	37	chr16	29858633	29858633	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ggctgaggtggaggtgaagaAgttcaagcagatgacagagg	18	4	1	6	rs555637285		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:29858633A>C	ENST00000357402.5	+	14	2519	c.2381A>C	c.(2380-2382)aAg>aCg	p.K794T	MVP_ENST00000395353.1_Missense_Mutation_p.K794T	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	794					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						GAGGTGAAGAAGTTCAAGCAG	0.602													A|||	1	0.000199681	0	0	5008	,	,		19421	0.001		0	False		,,,				2504	0				p.K794T		Atlas-SNP	.											.	MVP	80	.	0			c.A2381C						.						62	53	56					16																	29858633		2197	4300	6497	SO:0001583	missense	9961	exon14			TGAAGAAGTTCAA	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"lung resistance-related protein"	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.2381A>C	chr16.hg19:g.29858633A>C	ENSP00000349977:p.Lys794Thr	56.0	0.0		66.0	8.0	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	hg19	CCDS10656.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.396759	0.83120	.	.	ENSG00000013364	ENST00000357402;ENST00000395353	T;T	0.49432	0.78;0.78	6.17	6.17	0.99709	.	0.046352	0.85682	D	0.000000	T	0.60573	0.2279	M	0.71581	2.175	0.80722	D	1	D	0.59357	0.985	P	0.52856	0.711	T	0.65261	-0.6211	10	0.87932	D	0	-41.6928	14.7743	0.69713	1.0:0.0:0.0:0.0	.	794	Q14764	MVP_HUMAN	T	794	ENSP00000349977:K794T;ENSP00000378760:K794T	ENSP00000349977:K794T	K	+	2	0	MVP	29766134	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.041000	0.64196	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.602	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115		C	29858633	A	C	29858633	3	2	24	1	0	0	0	0	1	0	0	0	10005	72	3	5	2431	5	MVP	16	29858633	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	5275592	29858633	60496120	109	3316										
NRN1L	123904	hgsc.bcm.edu	37	chr16	67920015	67920015	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttgcacactctgtgcggtgcCccggtgcatgttcgggagcg	15	12	1	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:67920015C>A	ENST00000339176.3	+	3	450	c.351C>A	c.(349-351)gcC>gcA	p.A117A	NRN1L_ENST00000576147.1_Missense_Mutation_p.P44H|CTC-479C5.10_ENST00000572067.1_lincRNA	NM_198443.1	NP_940845.1	Q496H8	NRN1L_HUMAN	neuritin 1-like	117					nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)		TGTGCGGTGCCCCGGTGCATG	0.662																																					p.A117A		Atlas-SNP	.											.	NRN1L	13	.	0			c.C351A						.						38	35	36					16																	67920015		2197	4300	6497	SO:0001819	synonymous_variant	123904	exon3			CGGTGCCCCGGTG	AY358782	CCDS10850.1	16q22.1	2008-02-05			ENSG00000188038	ENSG00000188038			29811	protein-coding gene	gene with protein product						12975309	Standard	NM_198443		Approved	UNQ2446, MRCC2446	uc002euu.3	Q496H8	OTTHUMG00000137541	ENST00000339176.3:c.351C>A	chr16.hg19:g.67920015C>A		28.0	0.0		42.0	7.0	NM_198443	Q6UWH7	Silent	SNP	ENST00000339176.3	hg19	CCDS10850.1																																																																																			.	.		0.662	NRN1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268872.2	NM_198443		A	67920015	C	A	67920015	2	1	24	1	0	0	0	0	0	0	0	1	10668	610	22	3		3	NRN1L	16	67920015	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	38061382	67920015	22434738	110	3317										
LRRC50	123872	hgsc.bcm.edu	37	chr16	84188219	84188219	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	aacctggaagagtacacaggGctgcgctgtctctggctgca	13	11	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:84188219G>A	ENST00000378553.5	+	4	514	c.390G>A	c.(388-390)ggG>ggA	p.G130G	DNAAF1_ENST00000334315.5_Silent_p.G130G	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	130					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						AGTACACAGGGCTGCGCTGTC	0.507																																					p.G130G		Atlas-SNP	.											.	DNAAF1	81	.	0			c.G390A						.						98	93	95					16																	84188219		2200	4300	6500	SO:0001819	synonymous_variant	123872	exon4			CACAGGGCTGCGC	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"outer row dynein assembly 7 homolog (Chlamydomonas)"	613190	"leucine rich repeat containing 50"	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.390G>A	chr16.hg19:g.84188219G>A		102.0	0.0		122.0	43.0	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Silent	SNP	ENST00000378553.5	hg19	CCDS10943.2																																																																																			.	.		0.507	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452		A	84188219	G	A	84188219	2	1	24	1	0	0	0	0	0	0	0	1	9018	1190	42	3		3	LRRC50	16	84188219	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	16268204	84188219	6166534	111	3318										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89347979	89347979	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gcggcaggtggaataggagtCgactctttgagctttttgtc	14	7	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:89347979C>T	ENST00000301030.4	-	9	5431	c.4971G>A	c.(4969-4971)tcG>tcA	p.S1657S	ANKRD11_ENST00000378330.2_Silent_p.S1657S	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1657					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GAATAGGAGTCGACTCTTTGA	0.562																																					p.S1657S		Atlas-SNP	.											.	ANKRD11	195	.	0			c.G4971A						.						131	143	139					16																	89347979		2198	4300	6498	SO:0001819	synonymous_variant	29123	exon9			AGGAGTCGACTCT	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.4971G>A	chr16.hg19:g.89347979C>T		76.0	0.0		123.0	13.0	NM_001256183	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	hg19	CCDS32513.1																																																																																			.	.		0.562	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		T	89347979	C	T	89347979	2	4	24	1	0	0	0	0	0	0	0	1	639	871	31	1		1	ANKRD11	16	89347979	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	5159760	89347979	1006774	112	3319										
CHRNB1	1140	hgsc.bcm.edu	37	chr17	7359261	7359261	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	aacaggaggaccacgatgcgGtatgtccaacgggggtggaa	16	8	0	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:7359261G>C	ENST00000306071.2	+	10	1432		c.e10+1		CHRNB1_ENST00000575379.1_Splice_Site|CHRNB1_ENST00000536404.2_Splice_Site|CHRNB1_ENST00000576360.1_Splice_Site	NM_000747.2	NP_000738.2	P11230	ACHB_HUMAN	cholinergic receptor, nicotinic, beta 1 (muscle)						behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|neurological system process (GO:0050877)|neuromuscular synaptic transmission (GO:0007274)|postsynaptic membrane organization (GO:0001941)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|ligand-gated ion channel activity (GO:0015276)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(3)	23		Prostate(122;0.157)			Galantamine(DB00674)	CCACGATGCGGTATGTCCAAC	0.582																																					.		Atlas-SNP	.											.	CHRNB1	46	.	0			c.1365+1G>C						.						57	50	52					17																	7359261		2203	4300	6503	SO:0001630	splice_region_variant	1140	exon10			GATGCGGTATGTC	X14830	CCDS11106.1	17p13.1	2012-02-11	2006-02-01		ENSG00000170175	ENSG00000170175		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1961	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 1 (muscle)"	100710	"cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)"	CHRNB			Standard	NM_000747		Approved		uc002ghb.3	P11230	OTTHUMG00000108139	ENST00000306071.2:c.1365+1G>C	chr17.hg19:g.7359261G>C		82.0	0.0		125.0	10.0	NM_000747	B7Z5H1|Q8IZ46|Q96FB8	Splice_Site	SNP	ENST00000306071.2	hg19	CCDS11106.1	.	.	.	.	.	.	.	.	.	.	G	9.570	1.120824	0.20877	.	.	ENSG00000170175	ENST00000306071;ENST00000536404	.	.	.	5.37	4.38	0.52667	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0982	0.59206	0.0:0.0:0.8381:0.1619	.	.	.	.	.	-1	.	.	.	+	.	.	CHRNB1	7299985	1.000000	0.71417	0.845000	0.33349	0.004000	0.04260	6.696000	0.74598	1.231000	0.43661	-0.719000	0.03609	.	.	.		0.582	CHRNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226942.3		Intron	C	7359261	G	C	7359261	5	2	24	1	0	0	0	0	0	0	1	0	3392	1275	44	4	1404	4	CHRNB1	17	7359261	Splice_Site	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10		7359261	73835949	113	3320										
NKIRAS2	28511	hgsc.bcm.edu	37	chr17	40174526	40174543	+	In_Frame_Del	DEL	GGCCGAACTGCCCCGACA	GGCCGAACTGCCCCGACA	-													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	acccgggggctccgagatggGgccgaactgccccgacactg							TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	GGCCGAACTGCCCCGACA	GGCCGAACTGCCCCGACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:40174526_40174543delGGCCGAACTGCCCCGACA	ENST00000307641.5	+	3	825_842	c.204_221delGGCCGAACTGCCCCGACA	c.(202-222)ggggccgaactgccccgacac>ggc	p.AELPRH69del	NKIRAS2_ENST00000462043.2_Intron|NKIRAS2_ENST00000316082.4_In_Frame_Del_p.AELPRH69del|NKIRAS2_ENST00000393884.2_In_Frame_Del_p.AELPRH67del|NKIRAS2_ENST00000393880.1_In_Frame_Del_p.AELPRH69del|NKIRAS2_ENST00000393881.3_In_Frame_Del_p.AELPRH69del|NKIRAS2_ENST00000479407.1_Intron|NKIRAS2_ENST00000449471.4_Intron|NKIRAS2_ENST00000393885.4_In_Frame_Del_p.AELPRH69del	NM_001001349.2	NP_001001349.1	Q9NYR9	KBRS2_HUMAN	NFKB inhibitor interacting Ras-like 2	69	Small GTPase-like.				I-kappaB kinase/NF-kappaB signaling (GO:0007249)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R73Q(1)		large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	9		all_cancers(22;1.1e-05)|Breast(137;0.000143)|all_epithelial(22;0.000319)				TCCGAGATGGGGCCGAACTGCCCCGACACTGCTTCTCT	0.569																																					p.68_74del		Atlas-INDEL	.											.	NKIRAS2	15	.	1	Substitution - Missense(1)	large_intestine(1)	c.203_220del						.																																			SO:0001651	inframe_deletion	28511	exon3			.	AF229840	CCDS11415.1, CCDS45679.1, CCDS45680.1	17q21.31	2014-05-09	2004-05-20		ENSG00000168256	ENSG00000168256			17898	protein-coding gene	gene with protein product		604497	"NFKB inhibitor interacting Ras-like protein 2"			10657303	Standard	NM_001001349		Approved	KBRAS2, DKFZP434N1526, kappaB-Ras2	uc002hys.3	Q9NYR9	OTTHUMG00000133503	ENST00000307641.5:c.204_221delGGCCGAACTGCCCCGACA	chr17.hg19:g.40174526_40174543delGGCCGAACTGCCCCGACA	ENSP00000303580:p.Ala69_His74del	60.0	0.0		73.0	12.0	NM_017595	A6NCZ5|B3KNN0|B4DNM3|Q6PK52|Q96KC7|Q9NSX1	In_Frame_Del	DEL	ENST00000307641.5	hg19	CCDS11415.1																																																																																			.	.		0.569	NKIRAS2-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257457.1	NM_017595		-	40174543	GGCCGAACTGCCCCGACA	-	40174526	7	5	24	1	0	1	0	1	0	0	0	0	10454	1219	43	0	210	0	NKIRAS2	17	40174526	In_Frame_Del	DEL	GGCCGAACTGCCCCGACA	TCGA-5C-A9VG-01A-11D-A36X-10	32815265	40174526	41020684	114	3321										
VPS25	84313	hgsc.bcm.edu	37	chr17	40925774	40925774	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	acaaccgaatgtggacactcGgcagaagcagctggccgcct	12	13	0	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:40925774G>T	ENST00000253794.2	+	2	117	c.77G>T	c.(76-78)cGg>cTg	p.R26L		NM_032353.2	NP_115729.1	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25 homolog (S. cerevisiae)	26					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)	5		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		GTGGACACTCGGCAGAAGCAG	0.617																																					p.R26L		Atlas-SNP	.											.	VPS25	11	.	0			c.G77T						.						78	82	81					17																	40925774		2203	4300	6503	SO:0001583	missense	84313	exon2			ACACTCGGCAGAA	AB014763	CCDS11438.1	17q21.31	2014-02-12	2006-04-04		ENSG00000131475	ENSG00000131475			28122	protein-coding gene	gene with protein product		610907	"vacuolar protein sorting 25 (yeast)"			15511219	Standard	NM_032353		Approved	MGC10540, EAP20, DERP9	uc002ibi.3	Q9BRG1		ENST00000253794.2:c.77G>T	chr17.hg19:g.40925774G>T	ENSP00000253794:p.Arg26Leu	66.0	0.0		81.0	13.0	NM_032353	B2R581	Missense_Mutation	SNP	ENST00000253794.2	hg19	CCDS11438.1	.	.	.	.	.	.	.	.	.	.	G	36	5.647018	0.96714	.	.	ENSG00000131475	ENST00000253794	T	0.51574	0.7	5.5	5.5	0.81552	ESCRT-II complex, Vps25 subunit, N-terminal winged helix (1);	0.000000	0.85682	D	0.000000	T	0.49898	0.1584	M	0.67517	2.055	0.80722	D	1	D	0.52996	0.957	B	0.41988	0.372	T	0.51403	-0.8710	10	0.30854	T	0.27	-32.2901	18.975	0.92731	0.0:0.0:1.0:0.0	.	26	Q9BRG1	VPS25_HUMAN	L	26	ENSP00000253794:R26L	ENSP00000253794:R26L	R	+	2	0	VPS25	38179300	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.241000	0.78201	2.584000	0.87258	0.655000	0.94253	CGG	.	.		0.617	VPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452383.1	NM_032353		T	40925774	G	T	40925774	3	4	24	1	0	0	0	0	1	0	0	0	17211	1116	39	1	83	1	VPS25	17	40925774	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	751248	40925774	40269436	115	3322										
APOH	350	hgsc.bcm.edu	37	chr17	64219853	64219853	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tccgggctccattttccttcCtcagtgcacttggcagaatc	8	14	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:64219853C>T	ENST00000205948.6	-	4	415	c.378G>A	c.(376-378)gaG>gaA	p.E126E		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	126	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			ATTTTCCTTCCTCAGTGCACT	0.443																																					p.E126E	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.G378A						.						110	107	108					17																	64219853		2203	4300	6503	SO:0001819	synonymous_variant	350	exon4			TCCTTCCTCAGTG		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"Apolipoproteins"	616	protein-coding gene	gene with protein product	"beta-2-glycoprotein I"	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.378G>A	chr17.hg19:g.64219853C>T		115.0	0.0		114.0	22.0	NM_000042	B2R9M3|Q9UCN7	Silent	SNP	ENST00000205948.6	hg19	CCDS11663.1																																																																																			.	.		0.443	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042		T	64219853	C	T	64219853	2	4	24	1	0	0	0	0	0	0	0	1	804	680	24	3		3	APOH	17	64219853	Silent	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	23294079	64219853	16975357	116	3323										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76567433	76567433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ggctttctctaggatctcaaCaatcttgttcactttgggtc	8	10	4	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:76567433C>T	ENST00000585328.1	-	5	884	c.760G>A	c.(760-762)Gtt>Att	p.V254I	DNAH17_ENST00000389840.5_Missense_Mutation_p.V254I	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	254	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			AGGATCTCAACAATCTTGTTC	0.502																																					p.V254I		Atlas-SNP	.											.	DNAH17	347	.	0			c.G760A						.						96	93	94					17																	76567433		2019	4189	6208	SO:0001583	missense	8632	exon5			TCTCAACAATCTT	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.760G>A	chr17.hg19:g.76567433C>T	ENSP00000465516:p.Val254Ile	159.0	0.0		181.0	20.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.04	1.241185	0.22711	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.55588	0.51	4.58	4.58	0.56647	.	.	.	.	.	T	0.48150	0.1484	L	0.40543	1.245	0.09310	N	1	.	.	.	.	.	.	T	0.34675	-0.9819	7	0.21014	T	0.42	.	11.6264	0.51147	0.1776:0.8224:0.0:0.0	.	.	.	.	I	254	ENSP00000374490:V254I	ENSP00000300671:V254I	V	-	1	0	DNAH17	74079028	0.591000	0.26824	0.232000	0.24009	0.936000	0.57629	2.064000	0.41432	2.267000	0.75376	0.561000	0.74099	GTT	.	.		0.502	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		T	76567433	C	T	76567433	3	4	24	1	0	0	0	0	1	0	0	0	4603	478	17	3	12936	3	DNAH17	17	76567433	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	12347580	76567433	4627777	117	3324										
NPLOC4	55666	hgsc.bcm.edu	37	chr17	79556001	79556011	+	Frame_Shift_Del	DEL	CTGCTAGACTC	CTGCTAGACTC	-													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	catcaggcacgtactgctcaCtgctagactccttggcgtag							TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	CTGCTAGACTC	CTGCTAGACTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:79556001_79556011delCTGCTAGACTC	ENST00000331134.6	-	12	1455_1465	c.1240_1250delGAGTCTAGCAG	c.(1240-1251)gagtctagcagtfs	p.ESSS414fs	NPLOC4_ENST00000374747.5_Frame_Shift_Del_p.ESSS414fs|NPLOC4_ENST00000539314.1_Frame_Shift_Del_p.ESSS253fs	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	414					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GTACTGCTCACTGCTAGACTCCTTGGCGTAG	0.483																																					p.414_417del		Atlas-Indel,Pindel	.											.	NPLOC4	27	.	0			c.1241_1251del						.																																			SO:0001589	frameshift_variant	55666	exon12			.	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.1240_1250delGAGTCTAGCAG	chr17.hg19:g.79556001_79556011delCTGCTAGACTC	ENSP00000331487:p.Glu414fs	128.0	0.0		131.0	12.0	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Frame_Shift_Del	DEL	ENST00000331134.6	hg19	CCDS45812.1																																																																																			.	.		0.483	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1			-	79556011	CTGCTAGACTC	-	79556001	7	5	24	1	0	1	0	1	0	0	0	0	10595	565	20	0	600	0	NPLOC4	17	79556001	Frame_Shift_Del	DEL	CTGCTAGACTC	TCGA-5C-A9VG-01A-11D-A36X-10	2988568	79556001	1639209	118	3325										
L3MBTL4	91133	hgsc.bcm.edu	37	chr18	6263997	6263997	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gccttctgttctttcaagtaCcactcccaagaccatgctcc	5	16	3	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr18:6263997C>G	ENST00000284898.6	-	5	368	c.168G>C	c.(166-168)tgG>tgC	p.W56C	L3MBTL4_ENST00000400104.3_Missense_Mutation_p.W56C|L3MBTL4_ENST00000317931.7_Missense_Mutation_p.W56C|L3MBTL4_ENST00000400105.2_Missense_Mutation_p.W56C	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	56					chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				CTTTCAAGTACCACTCCCAAG	0.438																																					p.W56C	Esophageal Squamous(41;748 902 17366 28959 43175)	Atlas-SNP	.											.	L3MBTL4	87	.	0			c.G168C						.						87	89	89					18																	6263997		2203	4300	6503	SO:0001583	missense	91133	exon5			CAAGTACCACTCC	BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"Sterile alpha motif (SAM) domain containing"	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.168G>C	chr18.hg19:g.6263997C>G	ENSP00000284898:p.Trp56Cys	111.0	0.0		108.0	10.0	NM_173464	A8MTL8|Q8IXS3	Missense_Mutation	SNP	ENST00000284898.6	hg19	CCDS11839.2	.	.	.	.	.	.	.	.	.	.	C	10.64	1.406748	0.25378	.	.	ENSG00000154655	ENST00000400105;ENST00000317931;ENST00000284898;ENST00000400104	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	5.04	5.04	0.67666	.	0.187021	0.34676	N	0.003775	T	0.69975	0.3171	N	0.14661	0.345	0.80722	D	1	B	0.28324	0.207	B	0.16722	0.016	T	0.71341	-0.4622	10	0.66056	D	0.02	.	14.2378	0.65938	0.0:1.0:0.0:0.0	.	56	Q8NA19	LMBL4_HUMAN	C	56	ENSP00000382976:W56C;ENSP00000318543:W56C;ENSP00000284898:W56C;ENSP00000382975:W56C	ENSP00000284898:W56C	W	-	3	0	L3MBTL4	6253997	0.310000	0.24527	1.000000	0.80357	0.978000	0.69477	0.617000	0.24359	2.519000	0.84933	0.650000	0.86243	TGG	.	.		0.438	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464		G	6263997	C	G	6263997	3	3	24	1	0	0	0	0	1	0	0	0	8603	508	18	4	1767	4	L3MBTL4	18	6263997	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10		6263997	71813251	119	3326										
C19orf29	58509	hgsc.bcm.edu	37	chr19	3626733	3626733	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gccccggcgacccgcggaccGcgagcgcgagcgtgtgtccc	16	18	0	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:3626733G>A	ENST00000429344.2	-	1	80	c.28C>T	c.(28-30)Cgg>Tgg	p.R10W	CACTIN_ENST00000248420.5_Missense_Mutation_p.R10W|CACTIN_ENST00000221899.3_5'UTR	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	10					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CCCGCGGACCGCGAGCGCGAG	0.741																																					p.R10W		Atlas-SNP	.											.	.	.	.	0			c.C28T						.						3	4	3					19																	3626733		1709	3746	5455	SO:0001583	missense	58509	exon1			CGGACCGCGAGCG	BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"NY REN 24 antigen", "functional spliceosome-associated protein c", "cactin homolog (Drosophila)"		"chromosome 19 open reading frame 29"	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.28C>T	chr19.hg19:g.3626733G>A	ENSP00000415078:p.Arg10Trp	66.0	0.0		53.0	19.0	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Missense_Mutation	SNP	ENST00000429344.2	hg19	CCDS45920.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.607780	0.46527	.	.	ENSG00000105298	ENST00000429344;ENST00000248420;ENST00000446452	.	.	.	4.21	4.21	0.49690	.	.	.	.	.	T	0.51278	0.1665	N	0.08118	0	0.35815	D	0.824164	D	0.89917	1.0	D	0.75020	0.985	T	0.64867	-0.6306	8	0.72032	D	0.01	.	12.249	0.54587	0.0:0.0:1.0:0.0	.	10	Q8WUQ7	CS029_HUMAN	W	10	.	ENSP00000248420:R10W	R	-	1	2	C19orf29	3577733	0.973000	0.33851	0.993000	0.49108	0.220000	0.24768	2.369000	0.44231	2.352000	0.79861	0.555000	0.69702	CGG	.	.		0.741	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2			A	3626733	G	A	3626733	3	1	24	1	0	0	0	0	1	0	0	0	1920	1086	38	1	2288	1	C19orf29	19	3626733	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10		3626733	55502250	120	3327										
FEM1A	55527	hgsc.bcm.edu	37	chr19	4793065	4793065	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ccgttacaggggtgccgtgtAcgccgactcgggcaatttcg	14	12	0	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:4793065A>G	ENST00000269856.3	+	1	1338	c.1199A>G	c.(1198-1200)tAc>tGc	p.Y400C	AC005523.2_ENST00000596170.1_RNA|AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000601192.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	400					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GGTGCCGTGTACGCCGACTCG	0.622																																					p.Y400C		Atlas-SNP	.											.	FEM1A	41	.	0			c.A1199G						.						55	52	53					19																	4793065		2203	4300	6503	SO:0001583	missense	55527	exon1			CCGTGTACGCCGA	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"Ankyrin repeat domain containing"	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1199A>G	chr19.hg19:g.4793065A>G	ENSP00000269856:p.Tyr400Cys	49.0	0.0		53.0	6.0	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Missense_Mutation	SNP	ENST00000269856.3	hg19	CCDS12135.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.391030	0.62066	.	.	ENSG00000141965	ENST00000269856	T	0.68181	-0.31	4.88	4.88	0.63580	Tetratricopeptide-like helical (1);	0.000000	0.64402	U	0.000002	T	0.82263	0.4999	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84180	0.0439	10	0.49607	T	0.09	-22.1428	14.4967	0.67694	1.0:0.0:0.0:0.0	.	400	Q9BSK4	FEM1A_HUMAN	C	400	ENSP00000269856:Y400C	ENSP00000269856:Y400C	Y	+	2	0	FEM1A	4744065	1.000000	0.71417	0.989000	0.46669	0.681000	0.39784	9.119000	0.94362	1.824000	0.53156	0.402000	0.26972	TAC	.	.		0.622	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1			G	4793065	A	G	4793065	3	3	24	1	0	0	0	0	1	0	0	0	5817	391	14	2	1201	2	FEM1A	19	4793065	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	1166332	4793065	54335918	121	3328										
SAFB2	9667	hgsc.bcm.edu	37	chr19	5592867	5592867	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tcggtcctccattgccacacGctttccttctggccaatagg	8	15	1	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:5592867G>A	ENST00000252542.4	-	16	2503	c.2239C>T	c.(2239-2241)Cgt>Tgt	p.R747C		NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	747	Arg-rich.|Interacts with SAFB1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		ATTGCCACACGCTTTCCTTCT	0.498																																					p.R747C	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											SAFB2,NS,carcinoma,0,1	SAFB2	90	.	0			c.C2239T						.						140	108	119					19																	5592867		2203	4300	6503	SO:0001583	missense	9667	exon16			CCACACGCTTTCC	D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"RNA binding motif (RRM) containing"	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.2239C>T	chr19.hg19:g.5592867G>A	ENSP00000252542:p.Arg747Cys	101.0	0.0		113.0	16.0	NM_014649	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	hg19	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.979611	0.34942	.	.	ENSG00000130254	ENST00000252542	T	0.16073	2.37	4.7	2.35	0.29111	.	0.000000	0.51477	D	0.000087	T	0.37100	0.0991	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.23261	-1.0193	10	0.87932	D	0	-13.958	11.8841	0.52592	0.0:0.0:0.5478:0.4522	.	747	Q14151	SAFB2_HUMAN	C	747	ENSP00000252542:R747C	ENSP00000252542:R747C	R	-	1	0	SAFB2	5543867	1.000000	0.71417	0.134000	0.22075	0.153000	0.21895	2.719000	0.47244	0.928000	0.37168	0.561000	0.74099	CGT	.	.		0.498	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		A	5592867	G	A	5592867	3	1	24	1	0	0	0	0	1	0	0	0	13822	1087	38	1	646	1	SAFB2	19	5592867	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	799802	5592867	53536116	122	3329										
RAVER1	125950	hgsc.bcm.edu	37	chr19	10431330	10431330	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gagctgcagccaggcactcaCcgaggggtagtcgaagctgt	15	11	1	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:10431330C>T	ENST00000293677.6	-	9	1903		c.e9+1		CTD-2369P2.12_ENST00000586529.1_Splice_Site	NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1							cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	18			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)			CAGGCACTCACCGAGGGGTAG	0.597																																					.		Atlas-SNP	.											.	RAVER1	67	.	0			c.1821+1G>A						.						6	6	6					19																	10431330		1986	4163	6149	SO:0001630	splice_region_variant	125950	exon10			CACTCACCGAGGG		CCDS45960.1	19p13.2	2013-02-12				ENSG00000161847		"RNA binding motif (RRM) containing"	30296	protein-coding gene	gene with protein product		609950				11853319, 11724819	Standard	NM_133452		Approved	KIAA1978	uc002moa.3	Q8IY67		ENST00000293677.6:c.1821+1G>A	chr19.hg19:g.10431330C>T		114.0	0.0		116.0	12.0	NM_133452	A6NMU4|Q8IY60|Q8TF24	Splice_Site	SNP	ENST00000293677.6	hg19	CCDS45960.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484246	0.44147	.	.	ENSG00000161847	ENST00000293677	.	.	.	4.29	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2398	0.54536	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RAVER1	10292330	1.000000	0.71417	0.998000	0.56505	0.491000	0.33493	4.226000	0.58606	1.951000	0.56629	0.561000	0.74099	.	.	.		0.597	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452	Intron	T	10431330	C	T	10431330	5	4	24	1	0	0	0	0	0	0	1	0	13109	521	18	3	468	3	RAVER1	19	10431330	Splice_Site	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	4838463	10431330	48697653	123	3330										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13476260	13476260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	agggatcatcgccttcatgaTcgacttcaggacgacttgta	10	10	3	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:13476260T>C	ENST00000360228.5	-	5	654	c.655A>G	c.(655-657)Atc>Gtc	p.I219V	CACNA1A_ENST00000573710.2_Missense_Mutation_p.I219V	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	219					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GCCTTCATGATCGACTTCAGG	0.488																																					p.I219V		Atlas-SNP	.											.	CACNA1A	715	.	0			c.A655G						.						56	56	56					19																	13476260		1921	4135	6056	SO:0001583	missense	773	exon5			TCATGATCGACTT	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.655A>G	chr19.hg19:g.13476260T>C	ENSP00000353362:p.Ile219Val	187.0	0.0		255.0	51.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.756994	0.49362	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98400	-4.91	5.55	5.55	0.83447	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98175	0.9397	L	0.46157	1.445	0.48696	D	0.999694	D;D	0.63880	0.958;0.993	D;D	0.76071	0.97;0.987	D	0.98068	1.0397	10	0.30854	T	0.27	.	14.6926	0.69096	0.0:0.0:0.0:1.0	.	219;219	O00555;Q9NS88	CAC1A_HUMAN;.	V	219	ENSP00000353362:I219V	ENSP00000317661:I219V	I	-	1	0	CACNA1A	13337260	1.000000	0.71417	0.980000	0.43619	0.998000	0.95712	7.800000	0.85949	2.105000	0.64084	0.533000	0.62120	ATC	.	.		0.488	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		C	13476260	T	C	13476260	3	2	24	1	0	0	0	0	1	0	0	0	2540	1435	50	2	7151	2	CACNA1A	19	13476260	Missense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	3044930	13476260	45652723	124	3331										
SIN3B	23309	hgsc.bcm.edu	37	chr19	16952599	16952599	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gagaattcgcacaaccacggGgacggtgcagaggacttcaa	13	10	1	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:16952599G>C	ENST00000248054.5	+	4	423	c.402G>C	c.(400-402)ggG>ggC	p.G134G	SIN3B_ENST00000379803.1_Silent_p.G134G|CTD-2538G9.5_ENST00000600987.1_RNA|SIN3B_ENST00000596802.1_Silent_p.G134G					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						ACAACCACGGGGACGGTGCAG	0.552																																					p.G134G		Atlas-SNP	.											.	SIN3B	90	.	0			c.G402C						.						91	86	87					19																	16952599		2203	4300	6503	SO:0001819	synonymous_variant	23309	exon4			CCACGGGGACGGT	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.402G>C	chr19.hg19:g.16952599G>C		147.0	0.0		172.0	23.0	NM_015260		Silent	SNP	ENST00000248054.5	hg19																																																																																				.	.		0.552	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		C	16952599	G	C	16952599	2	2	24	1	0	0	0	0	0	0	0	1	14341	1219	43	4		4	SIN3B	19	16952599	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	3476339	16952599	42176384	125	3332										
MPV17L2	84769	hgsc.bcm.edu	37	chr19	18306856	18306856	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tgtgtggccctggacacccgAgcagactgaactgtctgctt	12	12	1	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:18306856A>C	ENST00000599612.2	+	5	712	c.612A>C	c.(610-612)cgA>cgC	p.R204R		NM_032683.2	NP_116072.2	Q567V2	M17L2_HUMAN	MPV17 mitochondrial membrane protein-like 2	204						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				large_intestine(1)|lung(2)|urinary_tract(1)	4						TGGACACCCGAGCAGACTGAA	0.612																																					p.R204R		Atlas-SNP	.											.	MPV17L2	12	.	0			c.A612C						.						96	106	102					19																	18306856		2069	4192	6261	SO:0001819	synonymous_variant	84769	exon5			CACCCGAGCAGAC	AK094091	CCDS42522.1	19p13.11	2011-05-26			ENSG00000254858	ENSG00000254858			28177	protein-coding gene	gene with protein product						12477932	Standard	NM_032683		Approved	FKSG24, MGC12972	uc002nid.3	Q567V2	OTTHUMG00000165628	ENST00000599612.2:c.612A>C	chr19.hg19:g.18306856A>C		51.0	0.0		70.0	30.0	NM_032683	Q96P34|Q96QA0|Q9BSG4	Silent	SNP	ENST00000599612.2	hg19	CCDS42522.1																																																																																			.	.		0.612	MPV17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466294.2	NM_032683		C	18306856	A	C	18306856	2	2	24	1	0	0	0	0	0	0	0	1	9756	291	11	5		5	MPV17L2	19	18306856	Silent	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	1354257	18306856	40822127	126	3333										
ZNF626	199777	hgsc.bcm.edu	37	chr19	20807134	20807300	+	Frame_Shift_Del	DEL	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	-													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ggtgtgaggaccgcttgaagGctttgccacattcttcacat					rs200411264|rs4808252|rs4808251|rs190319020|rs4809071|rs4809072|rs547337333|rs76605719|rs10408597|rs71332197|rs549423118|rs78715171|rs4808250|rs376295094|rs78217174|rs375690494|rs35575803|rs71174721	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:20807134_20807300delGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	ENST00000601440.1	-	4	1529_1695	c.1383_1549delTTTTAAGTGCTCCTCTAACCTTACTACACATAAGAAAATTCATACTGGAGAGAGACCCTACAAATGTGAAGAATGTGGCAAAGCCTTCAACCAGTCCTCAATCCTTACTACACATGAGAGAATCATACTGGAGAGAAATTCTACAAATGTGAAGAATGTGGCAAAGC	c.(1381-1551)gcttttaagtgctcctctaaccttactacacataagaaaattcatactggagagagaccctacaaatgtgaagaatgtggcaaagccttcaaccagtcctcaatccttactacacatgagagaatcatactggagagaaattctacaaatgtgaagaatgtggcaaagcctfs	p.FKCSSNLTTHKKIHTGERPYKCEECGKAFNQSSILTTHERIILERNSTNVKNVAKP462fs	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	462					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K473R(2)|p.E484K(1)|p.I502F(1)		breast(1)|endometrium(1)|lung(3)|skin(1)	6						CCGCTTGAAGGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAAGCTTTGCCAC	0.384																																					p.462_517del		Pindel	.											.	ZNF626	121	.	4	Substitution - Missense(4)	lung(3)|central_nervous_system(1)	c.1384_1550del						.																																			SO:0001589	frameshift_variant	199777	exon4			.	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"Zinc fingers, C2H2-type", "-"	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.1383_1549delTTTTAAGTGCTCCTCTAACCTTACTACACATAAGAAAATTCATACTGGAGAGAGACCCTACAAATGTGAAGAATGTGGCAAAGCCTTCAACCAGTCCTCAATCCTTACTACACATGAGAGAATCATACTGGAGAGAAATTCTACAAATGTGAAGAATGTGGCAAAGC	chr19.hg19:g.20807134_20807300delGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	ENSP00000469958:p.Phe462fs	35.0	0.0		32.0	19.0	NM_001076675	Q8N8T4|Q96QM1	Frame_Shift_Del	DEL	ENST00000601440.1	hg19	CCDS42535.1																																																																																			.	.		0.384	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		-	20807300	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	-	20807134	7	5	24	1	0	1	0	1	0	0	0	0	18065	1203	42	0	41	0	ZNF626	19	20807134	Frame_Shift_Del	DEL	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	TCGA-5C-A9VG-01A-11D-A36X-10	2500278	20807134	38321849	127	3334										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40368475	40368475	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	acatgagcatggcaggtggtGaaggggccccctgtgccaga	16	10	0	3			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:40368475G>A	ENST00000221347.6	-	28	12880	c.12873C>T	c.(12871-12873)ttC>ttT	p.F4291F		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4291	VWFD 10. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGCAGGTGGTGAAGGGGCCCC	0.617																																					p.F4291F		Atlas-SNP	.											.	FCGBP	416	.	0			c.C12873T						.						104	99	101					19																	40368475		2203	4298	6501	SO:0001819	synonymous_variant	8857	exon28			GGTGGTGAAGGGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12873C>T	chr19.hg19:g.40368475G>A		104.0	0.0		146.0	16.0	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.		0.617	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40368475	G	A	40368475	2	1	24	1	0	0	0	0	0	0	0	1	5786	1281	45	3		3	FCGBP	19	40368475	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	19561341	40368475	18760508	128	3335										
CYP2B6	1555	hgsc.bcm.edu	37	chr19	41512811	41512811	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	acctgctgcttcttcctaggGgccctcatggaccccacctt	8	17	2	0	rs150862336	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:41512811G>T	ENST00000324071.4	+	4	493	c.486G>T	c.(484-486)ggG>ggT	p.G162G	CYP2B6_ENST00000330446.5_Intron|CYP2B6_ENST00000598834.1_3'UTR|CYP2B6_ENST00000593831.1_Intron	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	162					cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	TCTTCCTAGGGGCCCTCATGG	0.512																																					p.G162G		Atlas-SNP	.											.	CYP2B6	79	.	0			c.G486T						.						58	54	56					19																	41512811		2203	4300	6503	SO:0001630	splice_region_variant	1555	exon4			CCTAGGGGCCCTC	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"Cytochrome P450s"	2615	protein-coding gene	gene with protein product		123930	"cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6", "cytochrome P450, family 2, subfamily B", "cytochrome P450, subfamily IIB (phenobarbital-inducible)"	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.485-1G>T	chr19.hg19:g.41512811G>T		54.0	0.0		74.0	10.0	NM_000767	B4DWP3|Q2V565|Q9UK46	Silent	SNP	ENST00000324071.4	hg19	CCDS12570.1																																																																																			.	G|0.999;A|0.001		0.512	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	Silent	T	41512811	G	T	41512811	5	4	24	1	0	0	0	0	0	0	1	0	4166	1246	43	3	500	3	CYP2B6	19	41512811	Splice_Site	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	1144336	41512811	17616172	129	3336										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53854546	53854546	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tcattactcacacaaaagcaGgaagtacacatgagagaaaa	7	8	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:53854546G>A	ENST00000595091.1	+	5	837	c.618G>A	c.(616-618)caG>caA	p.Q206Q	ZNF845_ENST00000458035.1_Silent_p.Q206Q			Q96IR2	ZN845_HUMAN	zinc finger protein 845	206					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						CACAAAAGCAGGAAGTACACA	0.353																																					p.Q206Q		Atlas-SNP	.											.	ZNF845	101	.	0			c.G618A						.						60	45	50					19																	53854546		692	1591	2283	SO:0001819	synonymous_variant	91664	exon4			AAAGCAGGAAGTA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.618G>A	chr19.hg19:g.53854546G>A		159.0	0.0		160.0	28.0	NM_138374		Silent	SNP	ENST00000595091.1	hg19	CCDS46170.1																																																																																			.	.		0.353	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		A	53854546	G	A	53854546	2	1	24	1	0	0	0	0	0	0	0	1	18206	991	35	3		3	ZNF845	19	53854546	Silent	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	12341735	53854546	5274437	130	3337										
RBL1	5933	hgsc.bcm.edu	37	chr20	35695127	35695127	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tctaattataagtacagtacCttcctgtcaaagagttttga	6	7	2	2			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:35695127C>G	ENST00000373664.3	-	6	912	c.846G>C	c.(844-846)aaG>aaC	p.K282N	RBL1_ENST00000344359.3_Splice_Site_p.K282N	NM_002895.2	NP_002886.2	P28749	RBL1_HUMAN	retinoblastoma-like 1	282					chromatin modification (GO:0016568)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(7)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	42		Myeloproliferative disorder(115;0.00878)				AGTACAGTACCTTCCTGTCAA	0.343																																					p.K282N		Atlas-SNP	.											.	RBL1	114	.	0			c.G846C						.						91	93	92					20																	35695127		2203	4300	6503	SO:0001630	splice_region_variant	5933	exon6			CAGTACCTTCCTG	L14812	CCDS13289.1, CCDS13290.1	20q11.23	2014-03-11	2014-03-11		ENSG00000080839	ENSG00000080839			9893	protein-coding gene	gene with protein product		116957				1833063	Standard	NM_183404		Approved	p107, cp107, PRB1	uc002xgi.3	P28749	OTTHUMG00000032406	ENST00000373664.3:c.846+1G>C	chr20.hg19:g.35695127C>G		91.0	0.0		121.0	45.0	NM_183404	A8K2W5|Q4VXA0|Q8N5K6|Q9H1L5|Q9H1M1	Missense_Mutation	SNP	ENST00000373664.3	hg19	CCDS13289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.22|18.22	3.576476|3.576476	0.65878|0.65878	.|.	.|.	ENSG00000080839|ENSG00000080839	ENST00000373664;ENST00000344359|ENST00000525052	D;D|.	0.93076|.	-2.94;-3.16|.	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	0.206543|.	0.49916|.	D|.	0.000126|.	T|T	0.67268|0.67268	0.2875|0.2875	L|L	0.43152|0.43152	1.355|1.355	0.53688|0.53688	D|D	0.999975|0.999975	P;B|.	0.35684|.	0.515;0.031|.	B;B|.	0.41299|.	0.353;0.037|.	T|T	0.63585|0.63585	-0.6604|-0.6604	9|5	.|.	.|.	.|.	-7.0251|-7.0251	18.3499|18.3499	0.90335|0.90335	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	282;282|.	P28749-2;P28749|.	.;RBL1_HUMAN|.	N|T	282|87	ENSP00000362768:K282N;ENSP00000343646:K282N|.	.|.	K|R	-|-	3|2	2|0	RBL1|RBL1	35128541|35128541	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.823000|0.823000	0.46562|0.46562	5.660000|5.660000	0.68018|0.68018	2.575000|2.575000	0.86900|0.86900	0.313000|0.313000	0.20887|0.20887	AAG|AGA	.	.		0.343	RBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079067.2	NM_002895	Missense_Mutation	G	35695127	C	G	35695127	5	3	24	1	0	0	0	0	0	0	1	0	13124	695	24	4	2437	4	RBL1	20	35695127	Splice_Site	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10		35695127	27330393	131	3338										
PCIF1	63935	hgsc.bcm.edu	37	chr20	44574977	44574977	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tcaactgctacttccgccagTactgttctgccttccccgac	6	17	2	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:44574977T>C	ENST00000372409.3	+	14	1931	c.1567T>C	c.(1567-1569)Tac>Cac	p.Y523H	PCIF1_ENST00000479348.1_3'UTR	NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	523					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						CTTCCGCCAGTACTGTTCTGC	0.632																																					p.Y523H		Atlas-SNP	.											PCIF1,colon,carcinoma,0,1	PCIF1	51	.	0			c.T1567C						.						122	116	118					20																	44574977		2203	4300	6503	SO:0001583	missense	63935	exon14			CGCCAGTACTGTT	AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 121"		"chromosome 20 open reading frame 67"	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.1567T>C	chr20.hg19:g.44574977T>C	ENSP00000361486:p.Tyr523His	55.0	0.0		49.0	17.0	NM_022104	E1P5P1|Q54AB9|Q9NT85	Missense_Mutation	SNP	ENST00000372409.3	hg19	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.212107	0.79240	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.06	3.97	0.46021	Phosphorylated CTD interacting factor 1, WW domain (1);	0.134024	0.52532	D	0.000074	T	0.80417	0.4619	M	0.89601	3.045	0.53688	D	0.999976	D	0.89917	1.0	D	0.79108	0.992	T	0.82214	-0.0568	9	0.87932	D	0	-23.2464	9.6689	0.40000	0.0:0.0809:0.0:0.9191	.	523	Q9H4Z3	PCIF1_HUMAN	H	523	.	ENSP00000361486:Y523H	Y	+	1	0	PCIF1	44008384	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.640000	0.83355	0.972000	0.38314	0.379000	0.24179	TAC	.	.		0.632	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104		C	44574977	T	C	44574977	3	2	24	1	0	0	0	0	1	0	0	0	11589	1638	57	2	1613	2	PCIF1	20	44574977	Missense_Mutation	SNP	T	TCGA-5C-A9VG-01A-11D-A36X-10	8879850	44574977	18450543	132	3339										
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47601303	47601303	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	agagggggatccagtttctcCaggagcagggcatgctggga	17	8	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:47601303C>T	ENST00000371917.4	+	15	1996	c.1996C>T	c.(1996-1998)Cag>Tag	p.Q666*		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	666	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			CCAGTTTCTCCAGGAGCAGGG	0.512																																					p.Q666X	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.C1996T						.						133	133	133					20																	47601303		2203	4300	6503	SO:0001587	stop_gained	10564	exon15			TTTCTCCAGGAGC	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1996C>T	chr20.hg19:g.47601303C>T	ENSP00000360985:p.Gln666*	156.0	0.0		199.0	31.0	NM_006420	Q5TFT9|Q9NTS1	Nonsense_Mutation	SNP	ENST00000371917.4	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	C	39	7.589342	0.98374	.	.	ENSG00000124198	ENST00000538445;ENST00000371917	.	.	.	5.85	5.85	0.93711	.	0.162448	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	20.1588	0.98128	0.0:1.0:0.0:0.0	.	.	.	.	X	666	.	ENSP00000360985:Q666X	Q	+	1	0	ARFGEF2	47034710	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.818000	0.86416	2.770000	0.95276	0.563000	0.77884	CAG	.	.		0.512	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		T	47601303	C	T	47601303	4	4	24	1	0	0	0	0	0	1	0	0	853	595	21	3	2054	3	ARFGEF2	20	47601303	Nonsense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	3026326	47601303	15424217	133	3340										
SALL4	57167	hgsc.bcm.edu	37	chr20	50408507	50408507	+	Missense_Mutation	SNP	G	G	C													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tgttggccactttgcctttgGctaaatagcttatgtcctgg							TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:50408507G>C	ENST00000217086.4	-	2	626	c.515C>G	c.(514-516)gCc>gGc	p.A172G	SALL4_ENST00000395997.3_Missense_Mutation_p.A172G|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	172					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTTGCCTTTGGCTAAATAGCT	0.587																																					p.A172G		Atlas-SNP	.											.	SALL4	168	.	0			c.C515G						.						130	129	130					20																	50408507		2203	4300	6503	SO:0001583	missense	57167	exon2			CCTTTGGCTAAAT	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.515C>G	chr20.hg19:g.50408507G>C	ENSP00000217086:p.Ala172Gly	72.0	0.0		75.0	13.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	hg19	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	G	4.897	0.166660	0.09339	.	.	ENSG00000101115	ENST00000217086;ENST00000395997	T;T	0.08370	3.1;3.34	5.29	5.29	0.74685	.	0.155634	0.30714	N	0.009023	T	0.04048	0.0113	N	0.02539	-0.55	0.80722	D	1	B;B	0.14438	0.01;0.01	B;B	0.13407	0.005;0.009	T	0.42292	-0.9460	10	0.08179	T	0.78	-34.4665	18.9212	0.92526	0.0:0.0:1.0:0.0	.	172;172	A2A2D8;Q9UJQ4	.;SALL4_HUMAN	G	172	ENSP00000217086:A172G;ENSP00000379319:A172G	ENSP00000217086:A172G	A	-	2	0	SALL4	49841914	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	3.104000	0.50306	2.466000	0.83321	0.655000	0.94253	GCC	.	.		0.587	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			C	50408507	G	C	50408507	3	2	24	1	0	0	0	0	1	0	0	0	13828	1203	42	4	2658	4	SALL4	20	50408507	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	2807204	50408507	12617013	134	3341	12	2								
SALL4	57167	hgsc.bcm.edu	37	chr20	50408510	50408510	+	Frame_Shift_Del	DEL	A	A	-													0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tggccactttgcctttggctAaatagcttatgtcctggggg							TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:50408510delA	ENST00000217086.4	-	2	623	c.512delT	c.(511-513)ttafs	p.L171fs	SALL4_ENST00000395997.3_Frame_Shift_Del_p.L171fs|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	171					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GCCTTTGGCTAAATAGCTTAT	0.592																																					p.L171fs		Atlas-INDEL	.											.	SALL4	168	.	0			c.513delA						.						130	130	130					20																	50408510		2203	4300	6503	SO:0001589	frameshift_variant	57167	exon2			.	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.512delT	chr20.hg19:g.50408510delA	ENSP00000217086:p.Leu171fs	73.0	0.0		76.0	13.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Frame_Shift_Del	DEL	ENST00000217086.4	hg19	CCDS13438.1																																																																																			.	.		0.592	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			-	50408510	A	-	50408510	7	5	24	1	0	1	0	1	0	0	0	0	13828	372	13	0	2661	0	SALL4	20	50408510	Frame_Shift_Del	DEL	A	TCGA-5C-A9VG-01A-11D-A36X-10	3	50408510	12617010	135	3342	12	2								
GNAS	2778	hgsc.bcm.edu	37	chr20	57484420	57484420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ttcaggacctgcttcgctgcCgtgtcctgacttctggaatc	10	13	2	1	rs11554273		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:57484420C>T	ENST00000371085.3	+	8	1025	c.601C>T	c.(601-603)Cgt>Tgt	p.R201C	GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186C|GNAS_ENST00000371102.4_Missense_Mutation_p.R830C|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000354359.7_Missense_Mutation_p.R202C|GNAS_ENST00000371100.4_Missense_Mutation_p.R844C|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000306090.10_Missense_Mutation_p.R187C|GNAS_ENST00000371095.3_Missense_Mutation_p.R187C	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	201			R -> C (in MAS and somatotrophinoma; dbSNP:rs11554273). {ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> G (in MAS). {ECO:0000269|PubMed:10571700}.|R -> H (in MAS, somatotrophinoma and AIMAH1). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:1594625, ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> L (in non-MAS endocrine tumors). {ECO:0000269|PubMed:7751320}.|R -> S (in AIMAH1, pituitary tumor and polyostotic fibrous dysplasia). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:8766942, ECO:0000269|PubMed:9267696}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R201C(228)|p.R844C(9)|p.R201S(5)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCTTCGCTGCCGTGTCCTGAC	0.428			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.R844C	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	GNAS_ENST00000371100,NS,adenocarcinoma,0,338	GNAS	867	.	242	Substitution - Missense(242)	pituitary(141)|pancreas(35)|large_intestine(14)|ovary(12)|thyroid(10)|adrenal_gland(7)|biliary_tract(6)|parathyroid(5)|liver(3)|kidney(3)|testis(2)|upper_aerodigestive_tract(2)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)	c.C2530T						.						80	78	79					20																	57484420		2203	4300	6503	SO:0001583	missense	2778	exon8			CGCTGCCGTGTCC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.601C>T	chr20.hg19:g.57484420C>T	ENSP00000360126:p.Arg201Cys	135.0	0.0		119.0	34.0	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371085.3	hg19	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215896	0.79352	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99466	-5.95;-5.95;-5.95;-5.95;-5.95;-2.99;-5.95	5.53	4.53	0.55603	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99775	0.9907	H	0.99732	4.735	0.80722	D	1	D;D;D;D	0.89917	0.999;0.983;0.979;1.0	D;P;P;D	0.97110	0.939;0.845;0.643;1.0	D	0.96814	0.9599	10	0.87932	D	0	.	13.0593	0.58997	0.2437:0.7563:0.0:0.0	rs11554273	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	C	844;830;187;201;202;186;187	ENSP00000360141:R844C;ENSP00000360143:R830C;ENSP00000360136:R187C;ENSP00000360126:R201C;ENSP00000346328:R202C;ENSP00000265620:R186C;ENSP00000304472:R187C	ENSP00000265620:R186C	R	+	1	0	GNAS	56917815	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	4.055000	0.57441	2.596000	0.87737	0.563000	0.77884	CGT	.	C|1.000		0.428	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516		T	57484420	C	T	57484420	3	4	24	1	0	0	0	0	1	0	0	0	6518	652	23	1	3448	1	GNAS	20	57484420	Missense_Mutation	SNP	C	TCGA-5C-A9VG-01A-11D-A36X-10	7075910	57484420	5541100	136	3343										
LIPI	149998	hgsc.bcm.edu	37	chr21	15535777	15535777	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ccacttgtatccaaaaacacAgtggtcctaagaggtcttcc	7	12	1	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr21:15535777A>T	ENST00000536861.1	-	7	968	c.969T>A	c.(967-969)acT>acA	p.T323T	LIPI_ENST00000344577.2_Silent_p.T344T			Q6XZB0	LIPI_HUMAN	lipase, member I	323					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		CCAAAAACACAGTGGTCCTAA	0.299																																					p.T344T		Atlas-SNP	.											.	LIPI	95	.	0			c.T1032A						.						112	118	116					21																	15535777		2203	4297	6500	SO:0001819	synonymous_variant	149998	exon7			AAACACAGTGGTC	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.969T>A	chr21.hg19:g.15535777A>T		168.0	0.0		195.0	20.0	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Silent	SNP	ENST00000536861.1	hg19																																																																																				.	.		0.299	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		T	15535777	A	T	15535777	2	4	24	1	0	0	0	0	0	0	0	1	8834	175	7	4		4	LIPI	21	15535777	Silent	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10		15535777	32594118	137	3344										
ETS2	2114	hgsc.bcm.edu	37	chr21	40186286	40186286	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ctaccttcagtggcttcaaaAaggaacagcggcgcctgggc	12	12	2	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr21:40186286A>C	ENST00000360214.3	+	5	734	c.274A>C	c.(274-276)Aag>Cag	p.K92Q	ETS2_ENST00000360938.3_Missense_Mutation_p.K92Q	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	92	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				TGGCTTCAAAAAGGAACAGCG	0.493																																					p.K232Q		Atlas-SNP	.											.	ETS2	87	.	0			c.A694C						.						73	75	74					21																	40186286		2203	4300	6503	SO:0001583	missense	2114	exon5			TTCAAAAAGGAAC		CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.274A>C	chr21.hg19:g.40186286A>C	ENSP00000353344:p.Lys92Gln	97.0	0.0		109.0	19.0	NM_001256295	A6NM68|D3DSH6|Q53Y89	Missense_Mutation	SNP	ENST00000360214.3	hg19	CCDS13659.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.340215	0.41398	.	.	ENSG00000157557	ENST00000360214;ENST00000360938;ENST00000432278;ENST00000456966	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.77	5.77	0.91146	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.095829	0.64402	D	0.000001	T	0.58177	0.2104	M	0.86651	2.83	0.58432	D	0.999994	D;P	0.69078	0.997;0.536	P;B	0.59889	0.865;0.329	T	0.66217	-0.5979	10	0.72032	D	0.01	.	16.383	0.83481	1.0:0.0:0.0:0.0	.	92;92	P15036;C9JAG2	ETS2_HUMAN;.	Q	92	ENSP00000353344:K92Q;ENSP00000354194:K92Q;ENSP00000401273:K92Q;ENSP00000411086:K92Q	ENSP00000353344:K92Q	K	+	1	0	ETS2	39108156	1.000000	0.71417	0.946000	0.38457	0.013000	0.08279	8.537000	0.90631	2.326000	0.78906	0.533000	0.62120	AAG	.	.		0.493	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1			C	40186286	A	C	40186286	3	2	24	1	0	0	0	0	1	0	0	0	5278	15	1	5	284	5	ETS2	21	40186286	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10	24650509	40186286	7943609	138	3345										
EP300	2033	hgsc.bcm.edu	37	chr22	41523630	41523630	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	tgttctccttttgcatgctcAcaagtgccagcgccgggaac	10	13	2	0			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr22:41523630A>G	ENST00000263253.7	+	4	2265	c.1046A>G	c.(1045-1047)cAc>cGc	p.H349R		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	349					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TTGCATGCTCACAAGTGCCAG	0.547			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.H349R		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.A1046G						.						109	104	106					22																	41523630		2203	4300	6503	SO:0001583	missense	2033	exon4	Familial Cancer Database	Broad Thumb-Hallux syndrome	ATGCTCACAAGTG	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.1046A>G	chr22.hg19:g.41523630A>G	ENSP00000263253:p.His349Arg	146.0	0.0		146.0	22.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.004834	0.93287	.	.	ENSG00000100393	ENST00000263253	D	0.81659	-1.52	6.02	6.02	0.97574	Zinc finger, TAZ-type (5);	0.000000	0.51477	D	0.000095	D	0.86497	0.5947	L	0.48935	1.535	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.85146	0.0983	10	0.35671	T	0.21	-12.8324	16.542	0.84395	1.0:0.0:0.0:0.0	.	349	Q09472	EP300_HUMAN	R	349	ENSP00000263253:H349R	ENSP00000263253:H349R	H	+	2	0	EP300	39853576	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	2.304000	0.77564	0.528000	0.53228	CAC	.	.		0.547	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41523630	A	G	41523630	3	3	24	1	0	0	0	0	1	0	0	0	5150	159	6	2	1060	2	EP300	22	41523630	Missense_Mutation	SNP	A	TCGA-5C-A9VG-01A-11D-A36X-10		41523630	9780936	139	3346										
CYP2D6	1565	hgsc.bcm.edu	37	chr22	42522650	42522650	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	gacaccatggtggctgggccGgggctgtccagtgggcaccg	18	12	0	0	rs185772085		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr22:42522650G>A	ENST00000360608.5	-	9	1534	c.1420C>T	c.(1420-1422)Cgg>Tgg	p.R474W	NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.R423W|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.R474W|NDUFA6-AS1_ENST00000416037.2_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	474					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TGGCTGGGCCGGGGCTGTCCA	0.637																																					p.R474W		Atlas-SNP	.											.	CYP2D6	104	.	0			c.C1420T						.						28	24	26					22																	42522650		2192	4298	6490	SO:0001583	missense	1565	exon9			TGGGCCGGGGCTG	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"Cytochrome P450s"	2625	protein-coding gene	gene with protein product		124030	"cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6", "cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2", "cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2", "cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2", "cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1420C>T	chr22.hg19:g.42522650G>A	ENSP00000353820:p.Arg474Trp	195.0	0.0		167.0	22.0	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	hg19	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	G	16.17	3.047842	0.55110	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.69040	-0.37;-0.37;-0.37	4.85	1.21	0.21127	.	0.980175	0.08291	N	0.968458	T	0.79112	0.4391	M	0.70595	2.14	0.24748	N	0.992996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.979;0.987;0.979	T	0.63550	-0.6612	10	0.87932	D	0	.	9.0849	0.36574	0.0:0.1323:0.4633:0.4044	.	474;423;474	C1ID54;Q6NXU8;Q6NWU0	.;.;.	W	474;474;420;423;423	ENSP00000353820:R474W;ENSP00000374620:R474W;ENSP00000351927:R423W	ENSP00000351927:R423W	R	-	1	2	CYP2D6	40852594	0.000000	0.05858	0.656000	0.29637	0.011000	0.07611	-0.224000	0.09164	0.384000	0.24942	0.555000	0.69702	CGG	.	G|1.000;T|0.000		0.637	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1			A	42522650	G	A	42522650	3	1	24	1	0	0	0	0	1	0	0	0	4171	1115	39	1	77	1	CYP2D6	22	42522650	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10	999020	42522650	8781916	140	3347										
ZIC3	7547	hgsc.bcm.edu	37	chrX	136649430	136649430	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	7	1	0.724402601330913	0.655411877394636	0.737338362068966	0.0405594405594406	0.387914649453111	0	ggctgcgtggggagctgttcGgccgtgctgacccataccgc	16	13	0	1			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chrX:136649430G>T	ENST00000287538.5	+	1	1130	c.580G>T	c.(580-582)Ggc>Tgc	p.G194C	RP1-137H15.2_ENST00000442841.1_RNA|ZIC3_ENST00000370606.3_Missense_Mutation_p.G194C	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	194					anterior/posterior pattern specification (GO:0009952)|cell differentiation (GO:0030154)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of left/right asymmetry in nervous system (GO:0035545)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|heart looping (GO:0001947)|lung development (GO:0030324)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					GGAGCTGTTCGGCCGTGCTGA	0.677																																					p.G194C		Atlas-SNP	.											.	ZIC3	93	.	0			c.G580T						.						24	27	26					X																	136649430		2184	4239	6423	SO:0001583	missense	7547	exon1			CTGTTCGGCCGTG	AF028706	CCDS14663.1	Xq24-q27.1	2013-01-08	2011-05-19		ENSG00000156925	ENSG00000156925		"Zinc fingers, C2H2-type"	12874	protein-coding gene	gene with protein product		300265	"heterotaxy 1", "Zic family member 3 (odd-paired homolog, Drosophila)"	HTX1		8298651, 7747776	Standard	NM_003413		Approved	HTX, ZNF203	uc004fak.3	O60481	OTTHUMG00000022525	ENST00000287538.5:c.580G>T	chrX.hg19:g.136649430G>T	ENSP00000287538:p.Gly194Cys	109.0	0.0		120.0	34.0	NM_003413	B2CNW4|Q14DE5|Q5JY75	Missense_Mutation	SNP	ENST00000287538.5	hg19	CCDS14663.1	.	.	.	.	.	.	.	.	.	.	g	21.3	4.129498	0.77549	.	.	ENSG00000156925	ENST00000287538;ENST00000370606	T;T	0.61510	0.1;0.1	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.73860	0.3641	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77593	-0.2530	10	0.87932	D	0	.	15.2367	0.73436	0.0:0.0:1.0:0.0	.	194	O60481	ZIC3_HUMAN	C	194	ENSP00000287538:G194C;ENSP00000359638:G194C	ENSP00000287538:G194C	G	+	1	0	ZIC3	136477096	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	9.189000	0.94928	2.155000	0.67459	0.597000	0.82753	GGC	.	.		0.677	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1			T	136649430	G	T	136649430	3	4	24	1	0	0	0	0	1	0	0	0	17695	1116	39	1	582	1	ZIC3	23	136649430	Missense_Mutation	SNP	G	TCGA-5C-A9VG-01A-11D-A36X-10		136649430	18621130	141	3348										
C1orf59	113802	hgsc.bcm.edu	37	chr1	109191371	109191371	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	aaaaatttatctccaacacaGaagggtgtgggagagttctc	10	7	2	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:109191371G>A	ENST00000370032.5	-	8	1419	c.999C>T	c.(997-999)ttC>ttT	p.F333F	HENMT1_ENST00000370031.1_Silent_p.F364F|HENMT1_ENST00000402983.1_Silent_p.F333F|HENMT1_ENST00000493676.1_5'Flank	NM_144584.2	NP_653185.2	Q5T8I9	HENMT_HUMAN	HEN1 methyltransferase homolog 1 (Arabidopsis)	333					gene silencing by RNA (GO:0031047)|piRNA metabolic process (GO:0034587)|RNA methylation (GO:0001510)	P granule (GO:0043186)	metal ion binding (GO:0046872)|O-methyltransferase activity (GO:0008171)|RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	16						CTCCAACACAGAAGGGTGTGG	0.478																																					p.F333F		Atlas-SNP	.											.	HENMT1	38	.	0			c.C999T						.						115	108	110					1																	109191371		2203	4300	6503	SO:0001819	synonymous_variant	113802	exon8			AACACAGAAGGGT		CCDS787.1	1p13.3	2011-01-28	2011-01-28	2011-01-28	ENSG00000162639	ENSG00000162639			26400	protein-coding gene	gene with protein product	"HEN1 methyltransferase homolog (Arabidopsis)"	612178	"chromosome 1 open reading frame 59"	C1orf59			Standard	NM_144584		Approved	FLJ30525, HEN1	uc001dvt.4	Q5T8I9	OTTHUMG00000011123	ENST00000370032.5:c.999C>T	chr1.hg19:g.109191371G>A		180.0	1.0		77.0	51.0	NM_144584	A8MRR6|B1AM16|B1AM17|Q96EJ7|Q96NN0	Silent	SNP	ENST00000370032.5	hg19	CCDS787.1																																																																																			.	.		0.478	HENMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030592.1	NM_144584		A	109191371	G	A	109191371	2	1	25	1	0	0	0	0	0	0	0	1	2053	933	33	3		3	C1orf59	1	109191371	Silent	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10		109191371	140059250	1	3349										
VPS45	11311	hgsc.bcm.edu	37	chr1	150053492	150053492	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cggattgatctttccagagtGccgggaatcagtaaagactt	11	8	2	3	rs375831361		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:150053492G>T	ENST00000369130.3	+	8	1302	c.756G>T	c.(754-756)gtG>gtT	p.V252V	VPS45_ENST00000369128.5_Silent_p.V147V|VPS45_ENST00000535106.1_Silent_p.V183V	NM_001279354.1|NM_007259.3	NP_001266283.1|NP_009190.2	Q9NRW7	VPS45_HUMAN	vacuolar protein sorting 45 homolog (S. cerevisiae)	252					blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|vesicle docking involved in exocytosis (GO:0006904)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			TTTCCAGAGTGCCGGGAATCA	0.348																																					p.V252V		Atlas-SNP	.											.	VPS45	47	.	0			c.G756T						.	G		0,4406		0,0,2203	90	92	92		756	2.1	1	1		92	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	VPS45	NM_007259.3		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		252/571	150053492	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11311	exon8			CAGAGTGCCGGGA	U35246	CCDS944.1, CCDS60244.1, CCDS72904.1	1q21.2	2008-02-05	2006-12-19	2006-12-19	ENSG00000136631	ENSG00000136631			14579	protein-coding gene	gene with protein product		610035	"vacuolar protein sorting 45A (yeast homolog)", "vacuolar protein sorting 45A (yeast)"	VPS45B, VPS45A		8996080	Standard	NM_007259		Approved	h-vps45, H1	uc001etp.3	Q9NRW7	OTTHUMG00000012511	ENST00000369130.3:c.756G>T	chr1.hg19:g.150053492G>T		144.0	0.0		194.0	47.0	NM_007259	D3DUZ9|F5H8K1|Q15715|Q53FR8|Q5T4P6|Q9Y4Z6	Silent	SNP	ENST00000369130.3	hg19	CCDS944.1																																																																																			.	.		0.348	VPS45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034964.1	NM_007259		T	150053492	G	T	150053492	2	4	25	1	0	0	0	0	0	0	0	1	17226	1306	46	3		3	VPS45	1	150053492	Silent	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	40862121	150053492	99197129	2	3350										
UBAP2L	9898	hgsc.bcm.edu	37	chr1	154201144	154201144	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tgtgtgattgctttgcatgaCtgcaatggagatgtcaacag	12	6	1	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:154201144C>T	ENST00000361546.2	+	3	264	c.222C>T	c.(220-222)gaC>gaT	p.D74D	UBAP2L_ENST00000428931.1_Silent_p.D74D|UBAP2L_ENST00000343815.6_Silent_p.D74D|UBAP2L_ENST00000271877.7_Silent_p.D74D			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	74	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CTTTGCATGACTGCAATGGAG	0.423																																					p.D74D		Atlas-SNP	.											.	UBAP2L	197	.	0			c.C222T						.						215	189	198					1																	154201144		2203	4300	6503	SO:0001819	synonymous_variant	9898	exon4			GCATGACTGCAAT	BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.222C>T	chr1.hg19:g.154201144C>T		44.0	0.0		62.0	12.0	NM_001127320	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Silent	SNP	ENST00000361546.2	hg19	CCDS1063.1																																																																																			.	.		0.423	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		T	154201144	C	T	154201144	2	4	25	1	0	0	0	0	0	0	0	1	16853	564	20	3		3	UBAP2L	1	154201144	Silent	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	4147652	154201144	95049477	3	3351										
FLAD1	80308	hgsc.bcm.edu	37	chr1	154962718	154962718	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tgagctggaacagtttctacAggacactatcaagaggtact	10	8	2	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:154962718A>T	ENST00000292180.3	+	4	1671	c.1349A>T	c.(1348-1350)cAg>cTg	p.Q450L	FLAD1_ENST00000405236.2_Missense_Mutation_p.R302W|FLAD1_ENST00000295530.2_Missense_Mutation_p.R134W|FLAD1_ENST00000315144.10_Missense_Mutation_p.Q353L|FLAD1_ENST00000368433.1_Missense_Mutation_p.Q450L|FLAD1_ENST00000368428.1_De_novo_Start_OutOfFrame|FLAD1_ENST00000368432.1_Missense_Mutation_p.Q353L	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	450	FAD synthase.				FAD biosynthetic process (GO:0006747)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|FMN adenylyltransferase activity (GO:0003919)			endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|ovary(3)|skin(3)	22	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CAGTTTCTACAGGACACTATC	0.522																																					p.Q450L		Atlas-SNP	.											.	FLAD1	52	.	0			c.A1349T						.						138	143	141					1																	154962718		2203	4300	6503	SO:0001583	missense	80308	exon4			TTCTACAGGACAC		CCDS1078.1, CCDS1079.1, CCDS53371.1, CCDS53372.1	1q22	2013-03-05	2013-03-05		ENSG00000160688	ENSG00000160688	2.7.7.2		24671	protein-coding gene	gene with protein product		610595	"Fad1, flavin adenine dinucleotide synthetase, homolog (yeast)", "FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae)", "flavin adenine dinucleotide synthetase"				Standard	NM_001184891		Approved	PP591, FAD1	uc001fgf.2	Q8NFF5	OTTHUMG00000037416	ENST00000292180.3:c.1349A>T	chr1.hg19:g.154962718A>T	ENSP00000292180:p.Gln450Leu	134.0	0.0		215.0	94.0	NM_025207	Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Missense_Mutation	SNP	ENST00000292180.3	hg19	CCDS1078.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.51|16.51	3.144692|3.144692	0.57044|0.57044	.|.	.|.	ENSG00000160688|ENSG00000160688	ENST00000368433;ENST00000315144;ENST00000368432;ENST00000292180|ENST00000405236;ENST00000295530	.|.	.|.	.|.	5.37|5.37	5.37|5.37	0.77165|0.77165	Phosphoadenosine phosphosulphate reductase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);|.	0.057589|.	0.64402|.	D|.	0.000001|.	T|T	0.51719|0.51719	0.1691|0.1691	M|M	0.64404|0.64404	1.975|1.975	0.25793|0.25793	N|N	0.984597|0.984597	B|D	0.28584|0.69078	0.216|0.997	B|D	0.31390|0.71870	0.129|0.975	T|T	0.51803|0.51803	-0.8659|-0.8659	9|8	0.32370|0.87932	T|D	0.25|0	-25.5623|-25.5623	9.4334|9.4334	0.38624|0.38624	0.918:0.0:0.082:0.0|0.918:0.0:0.082:0.0	.|.	450|134	Q8NFF5|Q5T191	FAD1_HUMAN|.	L|W	450;353;353;450|302;134	.|.	ENSP00000292180:Q450L|ENSP00000295530:R134W	Q|R	+|+	2|1	0|2	FLAD1|FLAD1	153229342|153229342	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	5.316000|5.316000	0.65815|0.65815	2.254000|2.254000	0.74563|0.74563	0.533000|0.533000	0.62120|0.62120	CAG|AGG	.	.		0.522	FLAD1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091089.1	NM_025207		T	154962718	A	T	154962718	3	4	25	1	0	0	0	0	1	0	0	0	5928	188	7	4	1503	4	FLAD1	1	154962718	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	761574	154962718	94287903	4	3352										
TBX19	9095	hgsc.bcm.edu	37	chr1	168250458	168250458	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cggagaagcaacttcagatcAtcctggaggatgcacctctc	10	12	3	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:168250458A>G	ENST00000367821.3	+	1	181	c.130A>G	c.(130-132)Atc>Gtc	p.I44V		NM_005149.2	NP_005140.1	O60806	TBX19_HUMAN	T-box 19	44					anatomical structure morphogenesis (GO:0009653)|cell fate commitment (GO:0045165)|pituitary gland development (GO:0021983)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(11)|prostate(2)|skin(2)|urinary_tract(1)	34	all_hematologic(923;0.215)					ACTTCAGATCATCCTGGAGGA	0.537																																					p.I44V		Atlas-SNP	.											.	TBX19	68	.	0			c.A130G						.						126	114	118					1																	168250458		2203	4300	6503	SO:0001583	missense	9095	exon1			CAGATCATCCTGG	AJ010277	CCDS1272.1	1q23-q24	2008-02-05			ENSG00000143178	ENSG00000143178		"T-boxes"	11596	protein-coding gene	gene with protein product	"TBS 19"	604614				9888994	Standard	NM_005149		Approved	dj747L4.1, TPIT	uc001gfl.3	O60806	OTTHUMG00000034648	ENST00000367821.3:c.130A>G	chr1.hg19:g.168250458A>G	ENSP00000356795:p.Ile44Val	174.0	0.0		232.0	53.0	NM_005149	Q52M53	Missense_Mutation	SNP	ENST00000367821.3	hg19	CCDS1272.1	.	.	.	.	.	.	.	.	.	.	A	8.387	0.838766	0.16891	.	.	ENSG00000143178	ENST00000367821	D	0.87256	-2.23	5.72	0.901	0.19284	p53-like transcription factor, DNA-binding (1);	0.654011	0.16384	N	0.216785	T	0.47507	0.1449	N	0.04018	-0.295	0.26629	N	0.972502	B	0.09022	0.002	B	0.08055	0.003	T	0.07271	-1.0781	9	0.23891	T	0.37	.	5.159	0.15050	0.5262:0.1496:0.3243:0.0	.	44	O60806	TBX19_HUMAN	V	44	ENSP00000356795:I44V	ENSP00000356795:I44V	I	+	1	0	TBX19	166517082	0.995000	0.38212	0.997000	0.53966	0.994000	0.84299	0.664000	0.25068	0.111000	0.17947	0.533000	0.62120	ATC	.	.		0.537	TBX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083825.1	NM_005149		G	168250458	A	G	168250458	3	3	25	1	0	0	0	0	1	0	0	0	15669	217	8	2	132	2	TBX19	1	168250458	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	13287740	168250458	81000163	5	3353										
FMO2	2327	hgsc.bcm.edu	37	chr1	171176859	171176859	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	caaccttttattccttaggcTtgtgtagcctgccctcagag	8	12	1	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:171176859T>C	ENST00000209929.7	+	8	1344	c.1186T>C	c.(1186-1188)Ttg>Ctg	p.L396L	RP1-127D3.4_ENST00000445909.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA|FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Silent_p.L396L			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	395					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TTCCTTAGGCTTGTGTAGCCT	0.313																																					p.L396L		Atlas-SNP	.											.	FMO2	66	.	0			c.T1186C						.						98	103	101					1																	171176859		2203	4300	6503	SO:0001819	synonymous_variant	2327	exon8			TTAGGCTTGTGTA	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"flavin containing monooxygenase 2"			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.1186T>C	chr1.hg19:g.171176859T>C		283.0	0.0		423.0	98.0	NM_001460	Q53XR0	Silent	SNP	ENST00000209929.7	hg19	CCDS1293.1																																																																																			.	.		0.313	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		C	171176859	T	C	171176859	2	2	25	1	0	0	0	0	0	0	0	1	5963	1606	56	2		2	FMO2	1	171176859	Silent	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10	2926401	171176859	78073762	6	3354										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176564000	176564000	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gaggatgggcactatttccgTggacacctgggcacactggt	14	10	0	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:176564000T>C	ENST00000367662.3	+	3	2424	c.1260T>C	c.(1258-1260)cgT>cgC	p.R420R	PAPPA2_ENST00000367661.3_Silent_p.R420R	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	420					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						ACTATTTCCGTGGACACCTGG	0.572																																					p.R420R		Atlas-SNP	.											.	PAPPA2	665	.	0			c.T1260C						.						109	112	111					1																	176564000		2097	4215	6312	SO:0001819	synonymous_variant	60676	exon3			TTTCCGTGGACAC	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1260T>C	chr1.hg19:g.176564000T>C		104.0	0.0		161.0	39.0	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.		0.572	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			C	176564000	T	C	176564000	2	2	25	1	0	0	0	0	0	0	0	1	11442	1683	59	2		2	PAPPA2	1	176564000	Silent	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10	5387141	176564000	72686621	7	3355										
NUAK2	81788	hgsc.bcm.edu	37	chr1	205290603	205290626	+	In_Frame_Del	DEL	GGTGCCGCAGGTTGTGCTTGTGGT	GGTGCCGCAGGTTGTGCTTGTGGT	-													0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ggtctccaggaactcgtagcGgtgccgcaggttgtgcttgt							TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	GGTGCCGCAGGTTGTGCTTGTGGT	GGTGCCGCAGGTTGTGCTTGTGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:205290603_205290626delGGTGCCGCAGGTTGTGCTTGTGGT	ENST00000367157.3	-	1	257_280	c.131_154delACCACAAGCACAACCTGCGGCACC	c.(130-156)caccacaagcacaacctgcggcaccgc>cgc	p.HHKHNLRH44del		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2									p.H45Y(2)		breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			AACTCGTAGCGGTGCCGCAGGTTGTGCTTGTGGTGGTGCCGCTT	0.679																																					p.44_52del		Pindel	.											.	NUAK2	107	.	2	Substitution - Missense(2)	kidney(2)	c.132_155del						.																																			SO:0001651	inframe_deletion	81788	exon1			.	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"SNF1/AMP activated protein kinase"	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.131_154delACCACAAGCACAACCTGCGGCACC	chr1.hg19:g.205290603_205290626delGGTGCCGCAGGTTGTGCTTGTGGT	ENSP00000356125:p.His44_His51del	148.0	0.0		147.0	12.0	NM_030952		In_Frame_Del	DEL	ENST00000367157.3	hg19	CCDS1453.1																																																																																			.	.		0.679	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		-	205290626	GGTGCCGCAGGTTGTGCTTGTGGT	-	205290603	7	5	25	1	0	1	0	1	0	0	0	0	10722	1116	39	0	1760	0	NUAK2	1	205290603	In_Frame_Del	DEL	GGTGCCGCAGGTTGTGCTTGTGGT	TCGA-5C-A9VH-01A-11D-A36X-10	28726603	205290603	43960018	8	3356										
TGFB2	7042	hgsc.bcm.edu	37	chr1	218578606	218578606	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cttccaatttggtgaaagcaGagttcagagtctttcgtttg	10	7	2	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:218578606G>C	ENST00000366930.4	+	2	909	c.442G>C	c.(442-444)Gag>Cag	p.E148Q	TGFB2_ENST00000366929.4_Missense_Mutation_p.E176Q	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	148					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		GGTGAAAGCAGAGTTCAGAGT	0.433																																					p.E176Q		Atlas-SNP	.											.	TGFB2	102	.	0			c.G526C						.						216	208	211					1																	218578606		2203	4300	6503	SO:0001583	missense	7042	exon3			AAAGCAGAGTTCA	M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.442G>C	chr1.hg19:g.218578606G>C	ENSP00000355897:p.Glu148Gln	135.0	0.0		160.0	30.0	NM_001135599	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	hg19	CCDS1521.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.895590	0.72639	.	.	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.72051	-0.62;-0.62	5.09	5.09	0.68999	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84763	0.5544	M	0.88377	2.95	0.80722	D	1	P;D;D	0.63880	0.95;0.983;0.993	P;P;P	0.59761	0.652;0.831;0.863	D	0.85736	0.1334	10	0.37606	T	0.19	.	18.5292	0.90984	0.0:0.0:1.0:0.0	.	176;148;177	P61812-2;P61812;Q59EG9	.;TGFB2_HUMAN;.	Q	148;176	ENSP00000355897:E148Q;ENSP00000355896:E176Q	ENSP00000355896:E176Q	E	+	1	0	TGFB2	216645229	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	9.675000	0.98638	2.363000	0.80096	0.650000	0.86243	GAG	.	.		0.433	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		C	218578606	G	C	218578606	3	2	25	1	0	0	0	0	1	0	0	0	15833	943	33	4	536	4	TGFB2	1	218578606	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	13288003	218578606	30672015	9	3357										
ITPKB	3707	hgsc.bcm.edu	37	chr1	226923826	226923826	+	Frame_Shift_Del	DEL	C	C	-													0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	agcccagcgttggggaccctCcctccactctgtcggagagc							TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:226923826delC	ENST00000272117.3	-	1	1333	c.1334delG	c.(1333-1335)ggafs	p.G446fs	ITPKB_ENST00000429204.1_Frame_Shift_Del_p.G446fs|ITPKB_ENST00000366784.1_Frame_Shift_Del_p.G446fs			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	446					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				TGGGGACCCTCCCTCCACTCT	0.706																																					p.G445fs	Colon(84;110 1851 5306 33547)	Atlas-Indel,Pindel	.											.	ITPKB	158	.	0			c.1335delA						.						18	23	21					1																	226923826		2182	4282	6464	SO:0001589	frameshift_variant	3707	exon2			.	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"inositol 1,4,5-trisphosphate 3-kinase B"			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1334delG	chr1.hg19:g.226923826delC	ENSP00000272117:p.Gly446fs	84.0	0.0		87.0	13.0	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Frame_Shift_Del	DEL	ENST00000272117.3	hg19	CCDS1555.1																																																																																			.	.		0.706	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		-	226923826	C	-	226923826	7	5	25	1	0	1	0	1	0	0	0	0	7927	855	30	0	1534	0	ITPKB	1	226923826	Frame_Shift_Del	DEL	C	TCGA-5C-A9VH-01A-11D-A36X-10	8345220	226923826	22326795	10	3358										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245862336	245862336	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	atcccaacaagtggctcagtGaatgtaaggccggggtgcct	13	10	1	1	rs367835473		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr1:245862336G>C	ENST00000407071.2	+	14	6615	c.6175G>C	c.(6175-6177)Gaa>Caa	p.E2059Q	KIF26B_ENST00000366518.4_Missense_Mutation_p.E1678Q	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	2059					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GTGGCTCAGTGAATGTAAGGC	0.597																																					p.E2059Q		Atlas-SNP	.											.	KIF26B	343	.	0			c.G6175C						.						76	83	80					1																	245862336		2107	4219	6326	SO:0001583	missense	55083	exon14			CTCAGTGAATGTA	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.6175G>C	chr1.hg19:g.245862336G>C	ENSP00000385545:p.Glu2059Gln	102.0	0.0		148.0	67.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910478	0.52439	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	D;D	0.82526	-1.62;-1.61	5.73	5.73	0.89815	.	.	.	.	.	D	0.87188	0.6115	L	0.38175	1.15	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	T	0.82839	-0.0259	9	0.19147	T	0.46	.	19.9017	0.96988	0.0:0.0:1.0:0.0	.	2059	Q2KJY2	KI26B_HUMAN	Q	2059;1678;1675	ENSP00000385545:E2059Q;ENSP00000355475:E1678Q	ENSP00000355475:E1678Q	E	+	1	0	KIF26B	243928959	1.000000	0.71417	0.993000	0.49108	0.843000	0.47879	9.838000	0.99474	2.707000	0.92482	0.561000	0.74099	GAA	.	.		0.597	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		C	245862336	G	C	245862336	3	2	25	1	0	0	0	0	1	0	0	0	8304	1291	45	4	6229	4	KIF26B	1	245862336	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	18938510	245862336	3388285	11	3359										
PQLC3	130814	hgsc.bcm.edu	37	chr2	11300609	11300609	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cagattcctggtgtttctgcGgtaccagtgttactatgggt	12	8	1	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr2:11300609G>T	ENST00000295083.3	+	2	336	c.161G>T	c.(160-162)cGg>cTg	p.R54L	PQLC3_ENST00000402361.1_Missense_Mutation_p.R54L|PQLC3_ENST00000476787.1_3'UTR|PQLC3_ENST00000441908.2_Missense_Mutation_p.R54L	NM_152391.3	NP_689604.1	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3	54						integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		GTGTTTCTGCGGTACCAGTGT	0.602																																					p.R54L		Atlas-SNP	.											.	PQLC3	8	.	0			c.G161T						.						145	123	130					2																	11300609		2203	4300	6503	SO:0001583	missense	130814	exon2			TTCTGCGGTACCA	BC027625	CCDS1679.1, CCDS62856.1, CCDS62857.1	2p25.1	2004-02-05	2005-07-19	2005-07-19	ENSG00000162976	ENSG00000162976			28503	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 22"	C2orf22		12477932	Standard	NM_001282711		Approved	MGC33602	uc002rbc.3	Q8N755	OTTHUMG00000119055	ENST00000295083.3:c.161G>T	chr2.hg19:g.11300609G>T	ENSP00000295083:p.Arg54Leu	73.0	0.0		52.0	16.0	NM_152391	B2R8K1|B4DWA4	Missense_Mutation	SNP	ENST00000295083.3	hg19	CCDS1679.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.295929	0.40594	.	.	ENSG00000162976	ENST00000445402;ENST00000295083;ENST00000441908;ENST00000402361	D;D;D;D	0.97352	-4.35;-4.35;-4.35;-4.35	5.01	5.01	0.66863	.	0.139116	0.47455	D	0.000238	D	0.96225	0.8769	L	0.36672	1.1	0.40465	D	0.980283	D;D	0.60575	0.974;0.988	P;P	0.57846	0.776;0.828	D	0.94737	0.7915	10	0.15499	T	0.54	-25.082	15.2439	0.73490	0.0:0.0:1.0:0.0	.	54;54	B4DWA4;Q8N755	.;PQLC3_HUMAN	L	77;54;54;54	ENSP00000410430:R77L;ENSP00000295083:R54L;ENSP00000406148:R54L;ENSP00000384129:R54L	ENSP00000295083:R54L	R	+	2	0	PQLC3	11218060	1.000000	0.71417	0.996000	0.52242	0.701000	0.40568	2.641000	0.46587	2.307000	0.77673	0.561000	0.74099	CGG	.	.		0.602	PQLC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239266.4	NM_152391		T	11300609	G	T	11300609	3	4	25	1	0	0	0	0	1	0	0	0	12432	1116	39	1	167	1	PQLC3	2	11300609	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10		11300609	231898764	12	3360										
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74900921	74900921	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	agcatttgactcatacgagcGcattaaagtcccacgggtgg	11	10	1	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr2:74900921G>A	ENST00000357877.2	+	7	937	c.788G>A	c.(787-789)cGc>cAc	p.R263H	SEMA4F_ENST00000339773.5_Intron	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	263	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						TCATACGAGCGCATTAAAGTC	0.557																																					p.R263H		Atlas-SNP	.											SEMA4F,NS,carcinoma,0,1	SEMA4F	89	.	0			c.G788A						.						109	117	114					2																	74900921		2203	4300	6503	SO:0001583	missense	10505	exon7			ACGAGCGCATTAA	AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.788G>A	chr2.hg19:g.74900921G>A	ENSP00000350547:p.Arg263His	71.0	0.0		58.0	24.0	NM_004263	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	hg19	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.309276	0.40895	.	.	ENSG00000135622	ENST00000357877	T	0.10860	2.83	5.03	-4.74	0.03249	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.796333	0.11605	N	0.547387	T	0.04227	0.0117	N	0.13272	0.32	0.09310	N	0.999996	B	0.11235	0.004	B	0.10450	0.005	T	0.37454	-0.9705	10	0.31617	T	0.26	.	2.1447	0.03784	0.4596:0.2354:0.1855:0.1195	.	263	O95754	SEM4F_HUMAN	H	263	ENSP00000350547:R263H	ENSP00000350547:R263H	R	+	2	0	SEMA4F	74754429	0.000000	0.05858	0.035000	0.18076	0.962000	0.63368	0.222000	0.17699	-0.592000	0.05851	0.462000	0.41574	CGC	.	.		0.557	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		A	74900921	G	A	74900921	3	1	25	1	0	0	0	0	1	0	0	0	14050	1087	38	1	814	1	SEMA4F	2	74900921	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	63600312	74900921	168298452	13	3361										
PROC	5624	hgsc.bcm.edu	37	chr2	128184696	128184696	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tccaggtggtcctgctggacTcaaagaagaagctggcctgc	13	11	1	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr2:128184696T>A	ENST00000234071.3	+	8	781	c.694T>A	c.(694-696)Tca>Aca	p.S232T	PROC_ENST00000422777.3_Missense_Mutation_p.S232T|PROC_ENST00000409048.1_Missense_Mutation_p.S266T|PROC_ENST00000453608.2_Missense_Mutation_p.S287T	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	232	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood coagulation (GO:0030195)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	CCTGCTGGACTCAAAGAAGAA	0.597																																					p.S232T		Atlas-SNP	.											.	PROC	31	.	0			c.T694A						.						117	118	118					2																	128184696		2203	4300	6503	SO:0001583	missense	5624	exon8			CTGGACTCAAAGA	X02750	CCDS2145.1	2q13-q14	2014-01-30			ENSG00000115718	ENSG00000115718		"Endogenous ligands"	9451	protein-coding gene	gene with protein product	"prepro-protein C"	612283				2991887, 2437584	Standard	NM_000312		Approved		uc002tok.3	P04070	OTTHUMG00000131528	ENST00000234071.3:c.694T>A	chr2.hg19:g.128184696T>A	ENSP00000234071:p.Ser232Thr	56.0	0.0		53.0	22.0	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Missense_Mutation	SNP	ENST00000234071.3	hg19	CCDS2145.1	.	.	.	.	.	.	.	.	.	.	T	5.450	0.268052	0.10349	.	.	ENSG00000115718	ENST00000234071;ENST00000537436;ENST00000453608;ENST00000409048;ENST00000422777	D;D;D;D	0.93366	-3.21;-3.21;-3.21;-3.21	5.48	5.48	0.80851	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.40064	N	0.001199	D	0.86037	0.5837	L	0.35593	1.075	0.23361	N	0.997836	B;B;B;B	0.18610	0.015;0.026;0.009;0.029	B;B;B;B	0.21360	0.034;0.014;0.011;0.018	T	0.69420	-0.5150	10	0.09338	T	0.73	.	6.0256	0.19652	0.208:0.0751:0.0:0.7169	.	287;288;266;232	B4DPQ7;B4DPQ3;E7END6;P04070	.;.;.;PROC_HUMAN	T	232;191;287;266;232	ENSP00000234071:S232T;ENSP00000404030:S287T;ENSP00000386679:S266T;ENSP00000409543:S232T	ENSP00000234071:S232T	S	+	1	0	PROC	127901166	0.051000	0.20477	0.996000	0.52242	0.314000	0.28054	0.295000	0.19065	2.074000	0.62210	0.533000	0.62120	TCA	.	.		0.597	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312		A	128184696	T	A	128184696	3	1	25	1	0	0	0	0	1	0	0	0	12557	1551	54	4	720	4	PROC	2	128184696	Missense_Mutation	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10	53283775	128184696	115014677	14	3362										
TTN	7273	hgsc.bcm.edu	37	chr2	179596477	179596477	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cacctcattggtcacccgacActggtattcgccagcatctg	8	15	3	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr2:179596477A>G	ENST00000591111.1	-	56	16398	c.16174T>C	c.(16174-16176)Tgt>Cgt	p.C5392R	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.C4465R|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.C5709R			Q8WZ42	TITIN_HUMAN	titin	12211	Ig-like 34.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCACCCGACACTGGTATTCG	0.493																																					p.C5709R		Atlas-SNP	.											.	TTN	18412	.	0			c.T17125C						.						101	102	102					2																	179596477		1951	4147	6098	SO:0001583	missense	7273	exon58			CCCGACACTGGTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.16174T>C	chr2.hg19:g.179596477A>G	ENSP00000465570:p.Cys5392Arg	93.0	0.0		73.0	26.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	11.86	1.763649	0.31228	.	.	ENSG00000155657	ENST00000342992	T	0.64803	-0.12	5.93	5.93	0.95920	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.87237	0.6127	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91917	0.5544	9	0.87932	D	0	.	16.3943	0.83563	1.0:0.0:0.0:0.0	.	5392	Q8WZ42	TITIN_HUMAN	R	4465	ENSP00000343764:C4465R	ENSP00000343764:C4465R	C	-	1	0	TTN	179304722	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.281000	0.76405	0.533000	0.62120	TGT	.	.		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179596477	A	G	179596477	3	3	25	1	0	0	0	0	1	0	0	0	16750	159	6	2	87624	2	TTN	2	179596477	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	51411781	179596477	63602896	15	3363										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204031020	204031020	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gcagcattgaaaaagaagatGgtgaggagttctggaaaaaa	13	3	1	4			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr2:204031020G>A	ENST00000449802.1	+	36	6109	c.5776G>A	c.(5776-5778)Gga>Aga	p.G1926R		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1926										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AAAAGAAGATGGTGAGGAGTT	0.303																																					p.G1926R		Atlas-SNP	.											.	NBEAL1	266	.	0			c.G5776A						.						70	63	65					2																	204031020		1821	4071	5892	SO:0001630	splice_region_variant	65065	exon36			GAAGATGGTGAGG	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.5776+1G>A	chr2.hg19:g.204031020G>A		218.0	0.0		216.0	55.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.228276	0.58777	.	.	ENSG00000144426	ENST00000449802;ENST00000340268	T	0.56941	0.43	5.12	5.12	0.69794	PH-BEACH domain (1);	0.119705	0.56097	D	0.000036	T	0.50565	0.1623	L	0.60067	1.865	0.58432	D	0.999995	P;P	0.35050	0.482;0.482	B;B	0.30029	0.11;0.11	T	0.55347	-0.8155	10	0.51188	T	0.08	.	18.5162	0.90936	0.0:0.0:1.0:0.0	.	1926;1915	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	R	1926	ENSP00000399903:G1926R	ENSP00000344985:G1926R	G	+	1	0	NBEAL1	203739265	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	6.664000	0.74437	2.549000	0.85964	0.467000	0.42956	GGA	.	.		0.303	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		Missense_Mutation	A	204031020	G	A	204031020	5	1	25	1	0	0	0	0	0	0	1	0	10197	1362	47	3	5914	3	NBEAL1	2	204031020	Splice_Site	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	24434543	204031020	39168353	16	3364										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238253721	238253721	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ggcatttatctttgatgcttTggatgagggcacattgcttt	11	6	1	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr2:238253721T>C	ENST00000295550.4	-	34	7594	c.7142A>G	c.(7141-7143)cAa>cGa	p.Q2381R	COL6A3_ENST00000472056.1_Missense_Mutation_p.Q1774R|COL6A3_ENST00000346358.4_Missense_Mutation_p.Q2181R|COL6A3_ENST00000347401.3_Missense_Mutation_p.Q2180R|COL6A3_ENST00000353578.4_Missense_Mutation_p.Q2175R|COL6A3_ENST00000409809.1_Missense_Mutation_p.Q2175R	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2381	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTTGATGCTTTGGATGAGGGC	0.358																																					p.Q2381R		Atlas-SNP	.											.	COL6A3	608	.	0			c.A7142G						.						93	90	91					2																	238253721		2203	4300	6503	SO:0001583	missense	1293	exon34			ATGCTTTGGATGA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7142A>G	chr2.hg19:g.238253721T>C	ENSP00000295550:p.Gln2381Arg	223.0	0.0		183.0	89.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	T	9.243	1.038787	0.19669	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.95690	-3.78;-3.78;-3.78;-3.78;-3.78;-3.78	5.31	4.13	0.48395	.	0.000000	0.51477	D	0.000082	D	0.92453	0.7604	M	0.64567	1.98	0.32379	N	0.55485	B;B;B;B	0.31413	0.001;0.001;0.002;0.322	B;B;B;B	0.33454	0.002;0.002;0.004;0.164	D	0.88835	0.3308	10	0.21014	T	0.42	.	6.8527	0.24024	0.0:0.1183:0.1374:0.7443	.	1774;1774;2175;2381	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	R	2381;2180;2175;1774;2175;2181	ENSP00000295550:Q2381R;ENSP00000315609:Q2180R;ENSP00000315873:Q2175R;ENSP00000418285:Q1774R;ENSP00000386844:Q2175R;ENSP00000295546:Q2181R	ENSP00000295550:Q2381R	Q	-	2	0	COL6A3	237918460	0.903000	0.30736	0.087000	0.20705	0.828000	0.46876	1.153000	0.31676	0.824000	0.34613	0.533000	0.62120	CAA	.	.		0.358	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		C	238253721	T	C	238253721	3	2	25	1	0	0	0	0	1	0	0	0	3703	1812	63	2	2435	2	COL6A3	2	238253721	Missense_Mutation	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10	34222701	238253721	4945652	17	3365										
SHISA5	51246	hgsc.bcm.edu	37	chr3	48520585	48520585	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cagccagcaggctttacttaCcctgacatggggtcgttgta	11	11	0	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr3:48520585C>T	ENST00000296444.2	-	3	651		c.e3+1		SHISA5_ENST00000443308.2_Splice_Site|SHISA5_ENST00000442747.1_Splice_Site|SHISA5_ENST00000444115.1_Splice_Site	NM_001272065.1|NM_016479.3	NP_001258994.1|NP_057563.3	Q8N114	SHSA5_HUMAN	shisa family member 5						intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			large_intestine(1)|lung(1)	2						GCTTTACTTACCCTGACATGG	0.602																																					.		Atlas-SNP	.											.	SHISA5	10	.	0			c.314+1G>A						.						41	35	37					3																	48520585		2202	4299	6501	SO:0001630	splice_region_variant	51246	exon4			TACTTACCCTGAC	AF520698	CCDS2770.1, CCDS63621.1, CCDS63622.1, CCDS63623.1	3p21.31	2013-07-31	2013-07-31		ENSG00000164054	ENSG00000164054		"Shisa homologs"	30376	protein-coding gene	gene with protein product		607290	"shisa homolog 5 (Xenopus laevis)"			11042152, 12135983	Standard	NM_016479		Approved	SCOTIN, hShisa5	uc011bbk.1	Q8N114	OTTHUMG00000133529	ENST00000296444.2:c.314+1G>A	chr3.hg19:g.48520585C>T		59.0	0.0		55.0	19.0	NM_016479	B3KW99|F8W9N8|Q69YY9|Q7Z433|Q8NHL9|Q96MW8|Q9BV58	Splice_Site	SNP	ENST00000296444.2	hg19	CCDS2770.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.933405	0.34096	.	.	ENSG00000164054	ENST00000296444;ENST00000444115;ENST00000442747;ENST00000443308;ENST00000417841	.	.	.	3.39	2.49	0.30216	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.9827	0.30194	0.2437:0.7563:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SHISA5	48495589	1.000000	0.71417	0.997000	0.53966	0.153000	0.21895	2.991000	0.49409	0.982000	0.38575	0.484000	0.47621	.	.	.		0.602	SHISA5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257504.3	NM_016479	Intron	T	48520585	C	T	48520585	5	4	25	1	0	0	0	0	0	0	1	0	14298	521	18	3	423	3	SHISA5	3	48520585	Splice_Site	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10		48520585	149501845	18	3366										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77147199	77147199	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	caggaggactttcccccgcgGattgtggagcatccttccga	12	13	0	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr3:77147199G>A	ENST00000461745.1	+	2	996	c.96G>A	c.(94-96)cgG>cgA	p.R32R	ROBO2_ENST00000332191.8_Silent_p.R32R|ROBO2_ENST00000487694.3_Silent_p.R48R	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	32	Ig-like C2-type 1.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		TTCCCCCGCGGATTGTGGAGC	0.532																																					p.R32R		Atlas-SNP	.											.	ROBO2	527	.	0			c.G96A						.						47	49	48					3																	77147199		1945	4135	6080	SO:0001819	synonymous_variant	6092	exon2			CCCGCGGATTGTG	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.96G>A	chr3.hg19:g.77147199G>A		116.0	0.0		86.0	34.0	NM_002942	O43608|Q19AB4|Q19AB5	Silent	SNP	ENST00000461745.1	hg19	CCDS43109.1																																																																																			.	.		0.532	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		A	77147199	G	A	77147199	2	1	25	1	0	0	0	0	0	0	0	1	13529	1174	41	3		3	ROBO2	3	77147199	Silent	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	28626614	77147199	120875231	19	3367										
TRAT1	50852	hgsc.bcm.edu	37	chr3	108572654	108572654	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cccagaaagccaggcagtagAggaaaacattcatgatgatc	10	9	1	4			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr3:108572654A>G	ENST00000295756.6	+	6	721	c.491A>G	c.(490-492)gAg>gGg	p.E164G	TRAT1_ENST00000426646.1_Missense_Mutation_p.E127G	NM_016388.2	NP_057472.2	Q6PIZ9	TRAT1_HUMAN	T cell receptor associated transmembrane adaptor 1	164					cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of receptor recycling (GO:0001920)|negative regulation of transport (GO:0051051)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell receptor signaling pathway (GO:0050862)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(3)	28						CAGGCAGTAGAGGAAAACATT	0.438																																					p.E164G		Atlas-SNP	.											.	TRAT1	48	.	0			c.A491G						.						93	95	94					3																	108572654		2203	4300	6503	SO:0001583	missense	50852	exon6			CAGTAGAGGAAAA	AJ240084	CCDS33813.1	3q13	2005-05-04	2005-05-04	2005-05-04	ENSG00000163519	ENSG00000163519			30698	protein-coding gene	gene with protein product		604962	"T cell receptor interacting molecule"	TCRIM		10663578, 9687533	Standard	NM_016388		Approved	HSPC062, TRIM	uc003dxi.1	Q6PIZ9	OTTHUMG00000159198	ENST00000295756.6:c.491A>G	chr3.hg19:g.108572654A>G	ENSP00000295756:p.Glu164Gly	393.0	0.0		280.0	107.0	NM_016388	Q9NZX5	Missense_Mutation	SNP	ENST00000295756.6	hg19	CCDS33813.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.354682	0.61293	.	.	ENSG00000163519	ENST00000295756;ENST00000426646	T;T	0.34667	1.36;1.35	5.85	5.85	0.93711	.	0.092833	0.47093	D	0.000242	T	0.57519	0.2059	M	0.65975	2.015	0.36196	D	0.850405	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.67734	-0.5594	10	0.62326	D	0.03	-17.3146	12.6339	0.56673	1.0:0.0:0.0:0.0	.	127;164	C9JF66;Q6PIZ9	.;TRAT1_HUMAN	G	164;127	ENSP00000295756:E164G;ENSP00000410097:E127G	ENSP00000295756:E164G	E	+	2	0	TRAT1	110055344	1.000000	0.71417	0.996000	0.52242	0.330000	0.28571	2.435000	0.44811	2.234000	0.73211	0.533000	0.62120	GAG	.	.		0.438	TRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353794.1	NM_016388		G	108572654	A	G	108572654	3	3	25	1	0	0	0	0	1	0	0	0	16481	304	11	2	513	2	TRAT1	3	108572654	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	31425455	108572654	89449776	20	3368										
STK32B	55351	hgsc.bcm.edu	37	chr4	5399957	5399957	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	catcaagccagacaatatccTgctggatgaacacggtaagc	9	11	1	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr4:5399957T>C	ENST00000282908.5	+	5	880	c.458T>C	c.(457-459)cTg>cCg	p.L153P	STK32B_ENST00000512636.1_Missense_Mutation_p.L106P|STK32B_ENST00000510398.1_Missense_Mutation_p.L106P	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						GACAATATCCTGCTGGATGAA	0.493																																					p.L153P		Atlas-SNP	.											.	STK32B	87	.	0			c.T458C						.						151	140	144					4																	5399957		2203	4300	6503	SO:0001583	missense	55351	exon5			ATATCCTGCTGGA	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.458T>C	chr4.hg19:g.5399957T>C	ENSP00000282908:p.Leu153Pro	87.0	0.0		68.0	27.0	NM_018401		Missense_Mutation	SNP	ENST00000282908.5	hg19	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	T	15.45	2.836187	0.50951	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.58797	0.31;0.31;0.31	4.4	4.4	0.53042	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.33591	U	0.004747	D	0.82986	0.5156	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87284	0.2294	10	0.87932	D	0	.	10.1832	0.42982	0.0:0.0:0.0:1.0	.	153	Q9NY57	ST32B_HUMAN	P	153;106;106	ENSP00000282908:L153P;ENSP00000423209:L106P;ENSP00000420984:L106P	ENSP00000282908:L153P	L	+	2	0	STK32B	5450858	0.967000	0.33354	0.811000	0.32455	0.668000	0.39293	3.155000	0.50700	1.975000	0.57531	0.533000	0.62120	CTG	.	.		0.493	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		C	5399957	T	C	5399957	3	2	25	1	0	0	0	0	1	0	0	0	15313	1580	55	2	476	2	STK32B	4	5399957	Missense_Mutation	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10		5399957	185754319	21	3369										
WDR19	57728	hgsc.bcm.edu	37	chr4	39280267	39280267	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ctgcgaacggaggaggaactGtgattggcacgtgcaggtga	17	7	0	2	rs371200402		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr4:39280267G>C	ENST00000399820.3	+	36	4180	c.4026G>C	c.(4024-4026)ctG>ctC	p.L1342L	WDR19_ENST00000288634.7_Silent_p.L1182L	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	1342					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						AGGAGGAACTGTGATTGGCAC	0.527																																					p.L1342L		Atlas-SNP	.											.	WDR19	96	.	0			c.G4026C						.						64	63	63					4																	39280267		2083	4221	6304	SO:0001819	synonymous_variant	57728	exon36			GGAACTGTGATTG	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"WD repeat domain containing", "Intraflagellar transport homologs"	18340	protein-coding gene	gene with protein product	"intraflagellar transport 144 homolog (Chlamydomonas)"	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.4026G>C	chr4.hg19:g.39280267G>C		187.0	0.0		157.0	70.0	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.		0.527	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			C	39280267	G	C	39280267	2	2	25	1	0	0	0	0	0	0	0	1	17294	1364	48	4		4	WDR19	4	39280267	Silent	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	33880310	39280267	151874009	22	3370										
BEND4	389206	hgsc.bcm.edu	37	chr4	42154069	42154069	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ccagcgccggtctcttgctgGggaacgtcttgaggacgctg	15	12	2	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr4:42154069G>T	ENST00000502486.1	-	2	671	c.92C>A	c.(91-93)cCc>cAc	p.P31H	BEND4_ENST00000504360.1_Missense_Mutation_p.P27H	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	31										NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						TCTCTTGCTGGGGAACGTCTT	0.716																																					p.P31H		Atlas-SNP	.											BEND4,NS,carcinoma,0,1	BEND4	67	.	0			c.C92A						.						9	12	11					4																	42154069		1845	3930	5775	SO:0001583	missense	389206	exon2			TTGCTGGGGAACG	AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"BEN domain containing"	23815	protein-coding gene	gene with protein product			"coiled-coil domain containing 4"	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.92C>A	chr4.hg19:g.42154069G>T	ENSP00000421169:p.Pro31His	113.0	0.0		82.0	29.0	NM_001159547	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Missense_Mutation	SNP	ENST00000502486.1	hg19	CCDS47048.1	.	.	.	.	.	.	.	.	.	.	G	17.24	3.338345	0.60963	.	.	ENSG00000188848	ENST00000411720;ENST00000502486;ENST00000504360	.	.	.	3.12	3.12	0.35913	.	0.470207	0.17105	U	0.186837	T	0.62183	0.2407	L	0.29908	0.895	0.45962	D	0.998785	D;D	0.71674	0.991;0.998	P;D	0.64237	0.779;0.923	T	0.65647	-0.6117	9	0.87932	D	0	.	12.9238	0.58247	0.0:0.0:1.0:0.0	.	31;31	Q6ZU67;Q6ZU67-2	BEND4_HUMAN;.	H	27;31;27	.	ENSP00000412495:P27H	P	-	2	0	BEND4	41848826	1.000000	0.71417	0.993000	0.49108	0.985000	0.73830	3.924000	0.56476	1.240000	0.43803	0.313000	0.20887	CCC	.	.		0.716	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406		T	42154069	G	T	42154069	3	4	25	1	0	0	0	0	1	0	0	0	1400	1232	43	3	1532	3	BEND4	4	42154069	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	2873802	42154069	149000207	23	3371										
TACR3	6870	hgsc.bcm.edu	37	chr4	104640792	104640792	+	Frame_Shift_Del	DEL	C	C	-													0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cgtctgcacccacgcctccaCccccgtctatccaggtttct							TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr4:104640792delC	ENST00000304883.2	-	1	181	c.41delG	c.(40-42)ggtfs	p.G16fs		NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	16					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		CACGCCTCCACCCCCGTCTAT	0.677																																					p.G14fs		Atlas-Indel,Pindel	.											.	TACR3	102	.	0			c.42delT						.						36	42	40					4																	104640792		2200	4296	6496	SO:0001589	frameshift_variant	6870	exon1			.	M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"GPCR / Class A : Tachykinin receptors"	11528	protein-coding gene	gene with protein product	"neurokinin beta receptor"	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.41delG	chr4.hg19:g.104640792delC	ENSP00000303325:p.Gly16fs	55.0	0.0		46.0	18.0	NM_001059	Q0P510	Frame_Shift_Del	DEL	ENST00000304883.2	hg19	CCDS3664.1																																																																																			.	.		0.677	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		-	104640792	C	-	104640792	7	5	25	1	0	1	0	1	0	0	0	0	15522	507	18	0	1376	0	TACR3	4	104640792	Frame_Shift_Del	DEL	C	TCGA-5C-A9VH-01A-11D-A36X-10	62486723	104640792	86513484	24	3372										
GSTCD	79807	hgsc.bcm.edu	37	chr4	106766631	106766631	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gtgcttggtggatctggatcGagcaagagctgcagaagaat	15	6	1	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr4:106766631G>T	ENST00000515279.1	+	12	2019	c.1799G>T	c.(1798-1800)cGa>cTa	p.R600L	GSTCD_ENST00000515255.1_3'UTR|GSTCD_ENST00000394730.3_Missense_Mutation_p.R513L|GSTCD_ENST00000360505.5_Missense_Mutation_p.R600L|GSTCD_ENST00000394728.3_Missense_Mutation_p.R600L			Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain containing	600						extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	14		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)		GATCTGGATCGAGCAAGAGCT	0.453																																					p.R600L		Atlas-SNP	.											.	GSTCD	69	.	0			c.G1799T						.						110	109	109					4																	106766631		1973	4175	6148	SO:0001583	missense	79807	exon12			TGGATCGAGCAAG	BC032942	CCDS3672.2, CCDS43257.1	4q24	2008-02-05	2006-05-09		ENSG00000138780	ENSG00000138780			25806	protein-coding gene	gene with protein product		615912	"Glutathione S-transferase, C-terminal domain containing"			12477932	Standard	NM_001031720		Approved	FLJ13273	uc003hxz.4	Q8NEC7	OTTHUMG00000131211	ENST00000515279.1:c.1799G>T	chr4.hg19:g.106766631G>T	ENSP00000422354:p.Arg600Leu	78.0	0.0		74.0	30.0	NM_001031720	A8K8J0|A8MVD3|H9KV97|Q9H8S3	Missense_Mutation	SNP	ENST00000515279.1	hg19	CCDS43257.1	.	.	.	.	.	.	.	.	.	.	G	31	5.095948	0.94197	.	.	ENSG00000138780	ENST00000394730;ENST00000515279;ENST00000360505;ENST00000394728	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.83940	0.5363	M	0.82716	2.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86281	0.1667	9	0.87932	D	0	-8.7287	19.0547	0.93058	0.0:0.0:1.0:0.0	.	600;223	Q8NEC7;B7Z8J7	GSTCD_HUMAN;.	L	513;600;600;600	.	ENSP00000353695:R600L	R	+	2	0	GSTCD	106986080	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.038000	0.93771	2.480000	0.83734	0.650000	0.86243	CGA	.	.		0.453	GSTCD-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363981.1	NM_024751		T	106766631	G	T	106766631	3	4	25	1	0	0	0	0	1	0	0	0	6844	1058	37	1	1841	1	GSTCD	4	106766631	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	2125839	106766631	84387645	25	3373										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186544464	186544464	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tttcctccggaaaggcacagGactgactagaaaagcaagtt	10	9	0	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr4:186544464G>T	ENST00000284776.7	-	13	2616	c.2107C>A	c.(2107-2109)Cct>Act	p.P703T	SORBS2_ENST00000355634.5_Missense_Mutation_p.P803T|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000431808.1_Missense_Mutation_p.P703T|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.P607T|SORBS2_ENST00000448662.2_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	703					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		AAAGGCACAGGACTGACTAGA	0.453																																					p.P803T	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.C2407A						.						132	144	140					4																	186544464		2203	4300	6503	SO:0001583	missense	8470	exon16			GCACAGGACTGAC		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.2107C>A	chr4.hg19:g.186544464G>T	ENSP00000284776:p.Pro703Thr	56.0	0.0		44.0	18.0	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	hg19	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.922135	0.52653	.	.	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.74421	-0.71;-0.71;-0.72;-0.84	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.86163	0.5867	M	0.68593	2.085	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.996;0.997	D	0.85980	0.1482	10	0.66056	D	0.02	-21.1686	20.2405	0.98372	0.0:0.0:1.0:0.0	.	607;803;703	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	T	703;703;607;803	ENSP00000284776:P703T;ENSP00000411764:P703T;ENSP00000397482:P607T;ENSP00000347852:P803T	ENSP00000284776:P703T	P	-	1	0	SORBS2	186781458	1.000000	0.71417	0.995000	0.50966	0.072000	0.16883	9.869000	0.99810	2.797000	0.96272	0.561000	0.74099	CCT	.	.		0.453	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		T	186544464	G	T	186544464	3	4	25	1	0	0	0	0	1	0	0	0	14943	1174	41	3	1231	3	SORBS2	4	186544464	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	79777833	186544464	4609812	26	3374										
RAI14	26064	hgsc.bcm.edu	37	chr5	34823606	34823607	+	Frame_Shift_Del	DEL	GA	GA	-													0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gaaagaaataaagagaaagtGagagagttagaggaaaaact							TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr5:34823606_34823607delGA	ENST00000265109.3	+	15	1946_1947	c.1659_1660delGA	c.(1657-1662)gtgagafs	p.R554fs	RAI14_ENST00000503673.1_Frame_Shift_Del_p.R554fs|RAI14_ENST00000506376.1_Frame_Shift_Del_p.R546fs|RAI14_ENST00000512629.1_Frame_Shift_Del_p.R525fs|RAI14_ENST00000515799.1_Frame_Shift_Del_p.R557fs|RAI14_ENST00000397449.1_Frame_Shift_Del_p.R547fs|RAI14_ENST00000428746.2_Frame_Shift_Del_p.R554fs	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	554						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					aagagaaagtgagagagttaga	0.406																																					p.556_556del		Atlas-Indel,Pindel	.											.	RAI14	100	.	0			c.1667_1668del						.																																			SO:0001589	frameshift_variant	26064	exon17			.	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.1659_1660delGA	chr5.hg19:g.34823610_34823611delGA	ENSP00000265109:p.Arg554fs	133.0	0.0		142.0	52.0	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Frame_Shift_Del	DEL	ENST00000265109.3	hg19	CCDS34142.1																																																																																			.	.		0.406	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		-	34823607	GA	-	34823606	7	5	25	1	0	1	0	1	0	0	0	0	13023	1277	45	0	1778	0	RAI14	5	34823606	Frame_Shift_Del	DEL	GA	TCGA-5C-A9VH-01A-11D-A36X-10		34823606	146091654	27	3375										
GDNF	2668	hgsc.bcm.edu	37	chr5	37834855	37834855	+	Frame_Shift_Del	DEL	T	T	-													0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gcgggaaggcggacgcggtgTggagcagcaccaggcagaca							TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr5:37834855delT	ENST00000326524.2	-	2	243	c.44delA	c.(43-45)cacfs	p.H15fs	GDNF_ENST00000515058.1_Frame_Shift_Del_p.H15fs|GDNF_ENST00000381826.4_Frame_Shift_Del_p.H32fs|GDNF_ENST00000344622.4_Frame_Shift_Del_p.H15fs|GDNF_ENST00000427982.1_Frame_Shift_Del_p.H32fs	NM_000514.3	NP_000505.1	P39905	GDNF_HUMAN	glial cell derived neurotrophic factor	15					adult locomotory behavior (GO:0008344)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|enteric nervous system development (GO:0048484)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|metanephros development (GO:0001656)|mRNA stabilization (GO:0048255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|organ induction (GO:0001759)|peristalsis (GO:0030432)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|postganglionic parasympathetic nervous system development (GO:0021784)|postsynaptic membrane organization (GO:0001941)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of morphogenesis of a branching structure (GO:0060688)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|ureteric bud formation (GO:0060676)	extracellular region (GO:0005576)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(8)|skin(2)	15	all_lung(31;0.00118)					GGACGCGGTGTGGAGCAGCAC	0.726																																					p.H32fs		Atlas-Indel,Pindel	.											.	GDNF	56	.	0			c.96delC						.						26	28	27					5																	37834855		2202	4299	6501	SO:0001589	frameshift_variant	2668	exon2			.		CCDS3922.1, CCDS3923.1, CCDS54845.1, CCDS54846.1, CCDS75237.1	5p13.1-p12	2014-01-30			ENSG00000168621	ENSG00000168621		"Endogenous ligands"	4232	protein-coding gene	gene with protein product	"astrocyte-derived trophic factor", "glial cell line derived neurotrophic factor", "glial derived neurotrophic factor"	600837				8493557	Standard	NM_199231		Approved	ATF1, ATF2, HFB1-GDNF	uc011cpg.2	P39905	OTTHUMG00000090809	ENST00000326524.2:c.44delA	chr5.hg19:g.37834855delT	ENSP00000317145:p.His15fs	209.0	0.0		187.0	47.0	NM_001190469	B7WPK7|O95448|O95449|O95986|Q6FH33|Q96L44|Q9UD32|Q9UD33|Q9UMV2|Q9UP67|Q9UP97	Frame_Shift_Del	DEL	ENST00000326524.2	hg19	CCDS3922.1																																																																																			.	.		0.726	GDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207606.1	NM_000514		-	37834855	T	-	37834855	7	5	25	1	0	1	0	1	0	0	0	0	6330	1696	59	0	598	0	GDNF	5	37834855	Frame_Shift_Del	DEL	T	TCGA-5C-A9VH-01A-11D-A36X-10	3011249	37834855	143080405	28	3376										
TMEM174	134288	hgsc.bcm.edu	37	chr5	72469952	72469952	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ggaggcctgtgcctgcttctCtcctcccccttatgaagaaa	9	14	1	2	rs556952520		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr5:72469952C>G	ENST00000296776.5	+	2	741	c.692C>G	c.(691-693)tCt>tGt	p.S231C	TMEM174_ENST00000511737.1_Intron	NM_153217.2	NP_694949.1	Q8WUU8	TM174_HUMAN	transmembrane protein 174	231						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-54)		GCCTGCTTCTCTCCTCCCCCT	0.473																																					p.S231C		Atlas-SNP	.											TMEM174,NS,malignant_melanoma,0,1	TMEM174	22	.	0			c.C692G						.						117	114	115					5																	72469952		2203	4300	6503	SO:0001583	missense	134288	exon2			GCTTCTCTCCTCC	BC019346	CCDS4018.1	5q13.2	2008-02-05			ENSG00000164325	ENSG00000164325			28187	protein-coding gene	gene with protein product		614909				12477932	Standard	NM_153217		Approved	MGC13034, FLJ31268	uc010izc.3	Q8WUU8	OTTHUMG00000131268	ENST00000296776.5:c.692C>G	chr5.hg19:g.72469952C>G	ENSP00000296776:p.Ser231Cys	122.0	0.0		106.0	29.0	NM_153217	B2RDA0|Q96N81	Missense_Mutation	SNP	ENST00000296776.5	hg19	CCDS4018.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.580424	0.46006	.	.	ENSG00000164325	ENST00000296776	.	.	.	5.24	5.24	0.73138	.	0.210963	0.41938	D	0.000800	T	0.75664	0.3880	M	0.69823	2.125	0.43338	D	0.995389	D	0.65815	0.995	P	0.61132	0.884	T	0.77099	-0.2713	9	0.56958	D	0.05	-14.3656	16.1353	0.81481	0.0:1.0:0.0:0.0	.	231	Q8WUU8	TM174_HUMAN	C	231	.	ENSP00000296776:S231C	S	+	2	0	TMEM174	72505708	1.000000	0.71417	1.000000	0.80357	0.129000	0.20672	2.698000	0.47068	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.473	TMEM174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254036.1	NM_153217		G	72469952	C	G	72469952	3	3	25	1	0	0	0	0	1	0	0	0	16105	913	32	4	698	4	TMEM174	5	72469952	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	34635097	72469952	108445308	29	3377										
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140589288	140589288	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cgtctcagcctgggatttagActctggaacaaacagtgaac	10	10	2	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr5:140589288A>T	ENST00000239450.2	+	1	998	c.809A>T	c.(808-810)gAc>gTc	p.D270V	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	270	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGGATTTAGACTCTGGAACA	0.428																																					p.D270V		Atlas-SNP	.											.	PCDHB12	179	.	0			c.A809T						.						135	141	139					5																	140589288		2203	4300	6503	SO:0001583	missense	56124	exon1			ATTTAGACTCTGG	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.809A>T	chr5.hg19:g.140589288A>T	ENSP00000239450:p.Asp270Val	132.0	0.0		115.0	44.0	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	hg19	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	A	16.10	3.027167	0.54683	.	.	ENSG00000120328	ENST00000239450	T	0.74737	-0.87	4.16	4.16	0.48862	Cadherin (5);Cadherin-like (1);	.	.	.	.	D	0.91593	0.7344	H	0.99357	4.53	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94377	0.7601	9	0.87932	D	0	.	13.1424	0.59442	1.0:0.0:0.0:0.0	.	270	Q9Y5F1	PCDBC_HUMAN	V	270	ENSP00000239450:D270V	ENSP00000239450:D270V	D	+	2	0	PCDHB12	140569472	1.000000	0.71417	0.455000	0.27031	0.524000	0.34500	9.187000	0.94912	1.648000	0.50643	0.402000	0.26972	GAC	.	.		0.428	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		T	140589288	A	T	140589288	3	4	25	1	0	0	0	0	1	0	0	0	11546	275	10	4	811	4	PCDHB12	5	140589288	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	68119336	140589288	40325972	30	3378										
PCDH1	5097	hgsc.bcm.edu	37	chr5	141248468	141248468	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	catcacggtctgaagccagcGggatggggaagagtgagccg	17	9	2	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr5:141248468G>A	ENST00000394536.3	-	2	708	c.569C>T	c.(568-570)cCg>cTg	p.P190L	PCDH1_ENST00000456271.1_Missense_Mutation_p.P190L|PCDH1_ENST00000287008.3_Missense_Mutation_p.P190L|PCDH1_ENST00000536585.1_Missense_Mutation_p.P168L|PCDH1_ENST00000511044.1_5'Flank|PCDH1_ENST00000503492.1_Missense_Mutation_p.P190L	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	190	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		TGAAGCCAGCGGGATGGGGAA	0.577																																					p.P190L	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.C569T						.						290	277	281					5																	141248468		2203	4300	6503	SO:0001583	missense	5097	exon2			GCCAGCGGGATGG	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"Cadherins / Protocadherins : Non-clustered"	8655	protein-coding gene	gene with protein product		603626	"protocadherin 1 (cadherin-like 1)"			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.569C>T	chr5.hg19:g.141248468G>A	ENSP00000378043:p.Pro190Leu	185.0	0.0		182.0	77.0	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000394536.3	hg19	CCDS43375.1	.	.	.	.	.	.	.	.	.	.	g	22.5	4.302915	0.81136	.	.	ENSG00000156453	ENST00000503492;ENST00000287008;ENST00000394536;ENST00000456271;ENST00000357517;ENST00000536585	T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0	4.91	4.91	0.64330	Cadherin (4);Cadherin-like (1);	0.000000	0.51477	D	0.000093	T	0.58148	0.2102	L	0.47190	1.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.989;0.994	T	0.61148	-0.7121	10	0.87932	D	0	.	15.985	0.80144	0.0:0.0:1.0:0.0	.	190;190	Q08174;Q08174-2	PCDH1_HUMAN;.	L	190;190;190;190;201;168	ENSP00000424667:P190L;ENSP00000287008:P190L;ENSP00000378043:P190L;ENSP00000403497:P190L;ENSP00000350122:P201L;ENSP00000438825:P168L	ENSP00000287008:P190L	P	-	2	0	PCDH1	141228652	1.000000	0.71417	0.989000	0.46669	0.985000	0.73830	6.535000	0.73838	2.442000	0.82660	0.550000	0.68814	CCG	.	.		0.577	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420		A	141248468	G	A	141248468	3	1	25	1	0	0	0	0	1	0	0	0	11515	1116	39	1	3244	1	PCDH1	5	141248468	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	659180	141248468	39666792	31	3379										
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12121246	12121246	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ccaaaaaaacaaggaaaataTatttgtgagtattgcaatag	7	4	0	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr6:12121246T>C	ENST00000379388.2	+	4	1550	c.1218T>C	c.(1216-1218)taT>taC	p.Y406Y		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	406					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				AAGGAAAATATATTTGTGAGT	0.403																																					p.Y406Y		Atlas-SNP	.											.	HIVEP1	242	.	0			c.T1218C						.						81	77	78					6																	12121246		1923	4131	6054	SO:0001819	synonymous_variant	3096	exon4			AAAATATATTTGT	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.1218T>C	chr6.hg19:g.12121246T>C		91.0	0.0		84.0	29.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Silent	SNP	ENST00000379388.2	hg19	CCDS43426.1																																																																																			.	.		0.403	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		C	12121246	T	C	12121246	2	2	25	1	0	0	0	0	0	0	0	1	7195	1413	49	2		2	HIVEP1	6	12121246	Silent	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10		12121246	158993821	32	3380										
SLC17A3	10786	hgsc.bcm.edu	37	chr6	25850803	25850803	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tatggaccaaatgggtagagAtctgagcatagctttgatgg	13	5	1	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr6:25850803A>G	ENST00000360657.3	-	7	928	c.643T>C	c.(643-645)Tct>Cct	p.S215P	SLC17A3_ENST00000361703.6_Missense_Mutation_p.S215P|SLC17A3_ENST00000397060.4_Missense_Mutation_p.S293P			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	215					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						ATGGGTAGAGATCTGAGCATA	0.423																																					p.S293P		Atlas-SNP	.											.	SLC17A3	95	.	0			c.T877C						.						142	129	133					6																	25850803		2203	4300	6503	SO:0001583	missense	10786	exon8			GTAGAGATCTGAG	U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"Solute carriers"	10931	protein-coding gene	gene with protein product		611034	"solute carrier family 17 (sodium phosphate), member 3"			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.643T>C	chr6.hg19:g.25850803A>G	ENSP00000353873:p.Ser215Pro	119.0	0.0		114.0	39.0	NM_001098486	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Missense_Mutation	SNP	ENST00000360657.3	hg19	CCDS4566.2	.	.	.	.	.	.	.	.	.	.	A	12.17	1.856427	0.32791	.	.	ENSG00000124564	ENST00000397060;ENST00000360657;ENST00000361703	T;T;T	0.60672	0.17;0.17;0.17	3.53	3.53	0.40419	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.46145	D	0.000318	T	0.72260	0.3438	M	0.93328	3.405	0.21473	N	0.999676	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.998	T	0.64791	-0.6324	10	0.87932	D	0	.	8.7361	0.34530	1.0:0.0:0.0:0.0	.	215;293;215	B7Z531;B7Z511;O00476	.;.;NPT4_HUMAN	P	293;215;215	ENSP00000380250:S293P;ENSP00000353873:S215P;ENSP00000355307:S215P	ENSP00000353873:S215P	S	-	1	0	SLC17A3	25958782	0.685000	0.27652	0.023000	0.16930	0.077000	0.17291	5.078000	0.64425	1.823000	0.53134	0.477000	0.44152	TCT	.	.		0.423	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2			G	25850803	A	G	25850803	3	3	25	1	0	0	0	0	1	0	0	0	14433	333	12	2	639	2	SLC17A3	6	25850803	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	13729557	25850803	145264264	33	3381										
ZSCAN16	80345	hgsc.bcm.edu	37	chr6	28093436	28093445	+	Frame_Shift_Del	DEL	CAGAATGCCA	CAGAATGCCA	-													0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ctgccgtcagtggctgaggcCagaatgccacaccaaggagc							TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	CAGAATGCCA	CAGAATGCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr6:28093436_28093445delCAGAATGCCA	ENST00000340487.4	+	2	364_373	c.215_224delCAGAATGCCA	c.(214-225)ccagaatgccacfs	p.PECH72fs	ZSCAN16-AS1_ENST00000600652.1_RNA|ZSCAN16-AS1_ENST00000602810.1_RNA	NM_025231.1	NP_079507.1	Q9H4T2	ZSC16_HUMAN	zinc finger and SCAN domain containing 16	72	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|liver(1)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						TGGCTGAGGCCAGAATGCCACACCAAGGAG	0.538																																					p.72_75del		Atlas-Indel,Pindel	.											.	ZSCAN16	24	.	0			c.214_223del						.																																			SO:0001589	frameshift_variant	80345	exon2			.	AK025844	CCDS4644.1	6p21.33	2013-01-08	2007-02-20	2007-02-20	ENSG00000196812	ENSG00000196812		"-", "Zinc fingers, C2H2-type"	20813	protein-coding gene	gene with protein product			"zinc finger protein 392", "zinc finger protein 435"	ZNF392, ZNF435			Standard	NM_025231		Approved	FLJ22191, dJ265C24.3	uc003nkm.3	Q9H4T2	OTTHUMG00000014509	ENST00000340487.4:c.215_224delCAGAATGCCA	chr6.hg19:g.28093436_28093445delCAGAATGCCA	ENSP00000366527:p.Pro72fs	177.0	0.0		123.0	29.0	NM_025231	Q9H6K2	Frame_Shift_Del	DEL	ENST00000340487.4	hg19	CCDS4644.1																																																																																			.	.		0.538	ZSCAN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040177.1	NM_025231		-	28093445	CAGAATGCCA	-	28093436	7	5	25	1	0	1	0	1	0	0	0	0	18244	594	21	0	217	0	ZSCAN16	6	28093436	Frame_Shift_Del	DEL	CAGAATGCCA	TCGA-5C-A9VH-01A-11D-A36X-10	2242633	28093436	143021631	34	3382										
PRRT1	80863	hgsc.bcm.edu	37	chr6	32117406	32117406	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	catgtagtcgtgtggcgggcGcctcggctccagtagggcca	16	12	0	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr6:32117406G>T	ENST00000211413.5	-	3	776	c.652C>A	c.(652-654)Cgc>Agc	p.R218S	PRRT1_ENST00000375152.2_Missense_Mutation_p.R137S|PRRT1_ENST00000467780.1_5'UTR|PRRT1_ENST00000375150.2_Missense_Mutation_p.R137S	NM_030651.3	NP_085154.3	Q99946	PRRT1_HUMAN	proline-rich transmembrane protein 1	218					response to biotic stimulus (GO:0009607)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						TGTGGCGGGCGCCTCGGCTCC	0.672																																					p.R218S		Atlas-SNP	.											.	PRRT1	14	.	0			c.C652A						.						41	42	41					6																	32117406		1507	2708	4215	SO:0001583	missense	80863	exon3			GCGGGCGCCTCGG	AK054885	CCDS4739.1	6p21.32	2011-10-10	2005-07-24	2005-07-24		ENSG00000204314		"Proline-rich transmembrane proteins"	13943	protein-coding gene	gene with protein product	"interferon induced transmembrane protein domain containing 7"		"chromosome 6 open reading frame 31"	C6orf31			Standard	XM_006715221		Approved	NG5, IFITMD7	uc003nzt.3	Q99946		ENST00000211413.5:c.652C>A	chr6.hg19:g.32117406G>T	ENSP00000211413:p.Arg218Ser	89.0	0.0		61.0	30.0	NM_030651	A6ND08|A6ND40|B0S869|Q5SSW4|Q5SSX7|Q5STI1|Q96DW3|Q96NQ8	Missense_Mutation	SNP	ENST00000211413.5	hg19	CCDS4739.1	.	.	.	.	.	.	.	.	.	.	G	32	5.170636	0.94807	.	.	ENSG00000204314	ENST00000211413;ENST00000375150;ENST00000375152	D;D;D	0.85556	-2.0;-2.0;-2.0	5.03	5.03	0.67393	.	.	.	.	.	T	0.78065	0.4225	N	0.12569	0.235	0.53688	D	0.999977	D;D	0.89917	0.997;1.0	D;D	0.85130	0.993;0.997	T	0.76035	-0.3106	9	0.09338	T	0.73	-1.509	15.8661	0.79067	0.0:0.0:1.0:0.0	.	218;137	Q99946;Q99946-2	PRRT1_HUMAN;.	S	218;137;137	ENSP00000211413:R218S;ENSP00000364292:R137S;ENSP00000364294:R137S	ENSP00000211413:R218S	R	-	1	0	PRRT1	32225384	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.263000	0.65507	2.354000	0.79902	0.650000	0.86243	CGC	.	.		0.672	PRRT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076255.2	NM_030651		T	32117406	G	T	32117406	3	4	25	1	0	0	0	0	1	0	0	0	12621	1087	38	1	276	1	PRRT1	6	32117406	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	4023970	32117406	138997661	35	3383										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32190405	32190405	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	aagcttggcctggcatctctCaccagtgaagccagggaggc	13	12	2	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr6:32190405C>T	ENST00000375023.3	-	3	472	c.334G>A	c.(334-336)Gag>Aag	p.E112K		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	112	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TGGCATCTCTCACCAGTGAAG	0.632																																					p.E112K		Atlas-SNP	.											.	NOTCH4	201	.	0			c.G334A						.						72	75	74					6																	32190405		2203	4300	6503	SO:0001583	missense	4855	exon3			ATCTCTCACCAGT		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.334G>A	chr6.hg19:g.32190405C>T	ENSP00000364163:p.Glu112Lys	172.0	0.0		153.0	51.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	C	9.454	1.091386	0.20471	.	.	ENSG00000204301	ENST00000375023	T	0.40756	1.02	4.14	0.959	0.19624	Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	1.004830	0.08021	N	0.991897	T	0.04724	0.0128	N	0.04090	-0.28	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.16289	0.015;0.01	T	0.35773	-0.9775	10	0.13108	T	0.6	.	0.7382	0.00969	0.1951:0.3913:0.1868:0.2268	.	112;112	Q6P3V5;Q99466	.;NOTC4_HUMAN	K	112	ENSP00000364163:E112K	ENSP00000364163:E112K	E	-	1	0	NOTCH4	32298383	0.000000	0.05858	0.469000	0.27204	0.610000	0.37248	0.243000	0.18106	0.381000	0.24851	0.561000	0.74099	GAG	.	.		0.632	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			T	32190405	C	T	32190405	3	4	25	1	0	0	0	0	1	0	0	0	10560	835	29	3	5789	3	NOTCH4	6	32190405	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	72999	32190405	138924662	36	3384										
GLP1R	2740	hgsc.bcm.edu	37	chr6	39048499	39048500	+	Nonsense_Mutation	DNP	GC	GC	AA													0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gatggtggccatattatactGctttgtcaacaatgaggtaa							TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr6:39048499_39048500GC>AA	ENST00000373256.4	+	12	1251_1252	c.1208_1209GC>AA	c.(1207-1209)tGC>tAA	p.C403*		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	403					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)			breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	ATATTATACTGCTTTGTCAACA	0.569																																					p.C403Y|p.C403X		Atlas-SNP	.											.	GLP1R	64	.	0			c.G1208A|c.C1209A						.																																			SO:0001587	stop_gained	2740	exon12			TATACTGCTTTGT|ATACTGCTTTGTC		CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"GPCR / Class B : Glucagon receptors"	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	Exception_encountered	chr6.hg19:g.39048499_39048500delinsAA	ENSP00000362353:p.Cys403*	83.0|82.0	0.0		70.0	23.0	NM_002062	Q2M229|Q99669	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000373256.4	hg19	CCDS4839.1																																																																																			.	.		0.569	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1			AA	39048500	GC	AA	39048499	4	1	25	1	0	0	0	0	0	1	0	0	6460	1319	46	3	1254	3	GLP1R	6	39048499	Nonsense_Mutation	DNP	GC	TCGA-5C-A9VH-01A-11D-A36X-10	6858094	39048499	132066568	37	3385										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76023250	76023250	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gtcagattgagaacctcctgCcccatgtttttgttcttatt	7	10	2	2	rs147346630		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr6:76023250C>T	ENST00000237172.7	-	5	2628	c.2298G>A	c.(2296-2298)ggG>ggA	p.G766G	FILIP1_ENST00000393004.2_Silent_p.G766G|FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Silent_p.G667G	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	766										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GAACCTCCTGCCCCATGTTTT	0.413																																					p.G766G		Atlas-SNP	.											.	FILIP1	173	.	0			c.G2298A						.						127	131	129					6																	76023250		2203	4300	6503	SO:0001819	synonymous_variant	27145	exon5			CTCCTGCCCCATG	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.2298G>A	chr6.hg19:g.76023250C>T		113.0	0.0		79.0	27.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Silent	SNP	ENST00000237172.7	hg19	CCDS4984.1																																																																																			.	C|1.000;A|0.000		0.413	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		T	76023250	C	T	76023250	2	4	25	1	0	0	0	0	0	0	0	1	5902	726	26	3		3	FILIP1	6	76023250	Silent	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	36974751	76023250	95091817	38	3386										
TNS3	64759	hgsc.bcm.edu	37	chr7	47408695	47408695	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tcagataggagtgagttctgGctgctcttgtggcaggtgaa	15	6	3	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr7:47408695G>T	ENST00000398879.1	-	17	1914	c.1548C>A	c.(1546-1548)agC>agA	p.S516R	TNS3_ENST00000355730.3_Missense_Mutation_p.S276R|TNS3_ENST00000311160.9_Missense_Mutation_p.S516R			Q68CZ2	TENS3_HUMAN	tensin 3	516					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						GTGAGTTCTGGCTGCTCTTGT	0.632																																					p.S516R		Atlas-SNP	.											.	TNS3	140	.	0			c.C1548A						.						42	47	46					7																	47408695		2003	4154	6157	SO:0001583	missense	64759	exon17			GTTCTGGCTGCTC	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.1548C>A	chr7.hg19:g.47408695G>T	ENSP00000381854:p.Ser516Arg	78.0	0.0		78.0	23.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	hg19	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546694	0.65198	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000457718	D;D;D;D	0.94723	-3.12;-3.12;-3.5;-3.28	5.59	2.35	0.29111	.	0.920814	0.09433	N	0.802805	D	0.96355	0.8811	M	0.69823	2.125	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.92761	0.6224	10	0.87932	D	0	-30.3011	7.8351	0.29365	0.3634:0.0:0.6366:0.0	.	516	Q68CZ2	TENS3_HUMAN	R	516;626;516;276;619	ENSP00000312143:S516R;ENSP00000381854:S516R;ENSP00000347968:S276R;ENSP00000414358:S619R	ENSP00000312143:S516R	S	-	3	2	TNS3	47375220	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.359000	0.34113	0.709000	0.31976	0.655000	0.94253	AGC	.	.		0.632	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		T	47408695	G	T	47408695	3	4	25	1	0	0	0	0	1	0	0	0	16359	1194	42	3	2849	3	TNS3	7	47408695	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10		47408695	111729968	39	3387										
MLL3	58508	hgsc.bcm.edu	37	chr7	152132847	152132847	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cggcggctgcggctgctccaCgctcttgtcctcctccgacg	12	18	1	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr7:152132847C>T	ENST00000262189.6	-	1	243	c.25G>A	c.(25-27)Gtg>Atg	p.V9M	KMT2C_ENST00000355193.2_Missense_Mutation_p.V9M|FABP5P3_ENST00000477993.1_RNA	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	9					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GGCTGCTCCACGCTCTTGTCC	0.741																																					p.V9M		Atlas-SNP	.											.	MLL3	1564	.	0			c.G25A						.						4	5	5					7																	152132847		2031	4061	6092	SO:0001583	missense	58508	exon1			GCTCCACGCTCTT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.25G>A	chr7.hg19:g.152132847C>T	ENSP00000262189:p.Val9Met	141.0	0.0		137.0	42.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	c	12.38	1.919802	0.33908	.	.	ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000452749	D;D	0.84730	-1.89;-1.89	2.07	2.07	0.26955	.	.	.	.	.	T	0.65217	0.2670	N	0.08118	0	0.80722	D	1	B	0.33073	0.396	B	0.17098	0.017	T	0.62831	-0.6771	9	0.62326	D	0.03	.	7.5514	0.27800	0.0:0.7307:0.2693:0.0	.	9	Q8NEZ4	MLL3_HUMAN	M	9	ENSP00000262189:V9M;ENSP00000347325:V9M	ENSP00000262189:V9M	V	-	1	0	MLL3	151763780	0.905000	0.30787	0.978000	0.43139	0.930000	0.56654	1.020000	0.30027	0.667000	0.31107	0.282000	0.19409	GTG	.	.		0.741	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	152132847	C	T	152132847	3	4	25	1	0	0	0	0	1	0	0	0	9631	536	19	1	14946	1	MLL3	7	152132847	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	104724152	152132847	7005816	40	3388										
PINX1	54984	hgsc.bcm.edu	37	chr8	10690495	10690495	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tgctcctgagcccctaaaccCtgtggagattaaacacagag	9	12	0	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr8:10690495C>T	ENST00000314787.3	-	3	249		c.e3-1		SOX7_ENST00000554914.1_Splice_Site|SOX7_ENST00000553390.1_Splice_Site|PINX1_ENST00000519088.1_Splice_Site|PINX1_ENST00000426190.2_Splice_Site|PINX1_ENST00000520018.2_Splice_Site	NM_017884.4	NP_060354.4	Q96BK5	PINX1_HUMAN	PIN2/TERF1 interacting, telomerase inhibitor 1						mitotic metaphase plate congression (GO:0007080)|negative regulation of cell proliferation (GO:0008285)|negative regulation of telomerase activity (GO:0051974)|regulation of telomerase activity (GO:0051972)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|spindle (GO:0005819)	telomerase inhibitor activity (GO:0010521)|telomeric RNA binding (GO:0070034)			kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17				Kidney(29;0.0595)|COAD - Colon adenocarcinoma(149;0.105)|KIRC - Kidney renal clear cell carcinoma(542;0.201)		CCCCTAAACCCTGTGGAGATT	0.453																																					.		Atlas-SNP	.											.	PINX1	38	.	0			c.130-1G>A						.						88	78	81					8																	10690495		1886	4112	5998	SO:0001630	splice_region_variant	54984	exon4			TAAACCCTGTGGA	AF418553	CCDS47801.1, CCDS64825.1	8p23	2013-01-28				ENSG00000254093		"G patch domain containing"	30046	protein-coding gene	gene with protein product	"PIN2 interacting protein 1", "liver-related putative tumor suppressor"	606505				11003615, 11701125	Standard	NM_001284356		Approved	PinX1, LPTL, LPTS, FLJ20565, MGC8850		Q96BK5		ENST00000314787.3:c.130-1G>A	chr8.hg19:g.10690495C>T		76.0	0.0		29.0	13.0	NM_017884	B2R9B1|Q548A5|Q6QWG9|Q7Z7J8|Q96QD7|Q9HBU7|Q9NWW2	Splice_Site	SNP	ENST00000314787.3	hg19	CCDS47801.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529315	0.64860	.	.	ENSG00000171056;ENSG00000258724;ENSG00000254093;ENSG00000254093;ENSG00000254093;ENSG00000254093	ENST00000553390;ENST00000554914;ENST00000314787;ENST00000426190;ENST00000519088;ENST00000524114	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8069	0.78520	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SOX7;CTD-2135J3.4;PINX1	10727905	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.661000	0.74422	2.585000	0.87301	0.655000	0.94253	.	.	.		0.453	PINX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375683.1	NM_017884	Intron	T	10690495	C	T	10690495	5	4	25	1	0	0	0	0	0	0	1	0	11942	695	24	3	877	3	PINX1	8	10690495	Splice_Site	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10		10690495	135673527	41	3389										
MCM4	4173	hgsc.bcm.edu	37	chr8	48883923	48883923	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tgggatcatctgtcagctcaAtgcgcgcacctctgtcctgg	11	13	5	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr8:48883923A>T	ENST00000262105.2	+	12	2032	c.1823A>T	c.(1822-1824)aAt>aTt	p.N608I	MCM4_ENST00000523944.1_Missense_Mutation_p.N608I	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	608	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			biliary_tract(1)|breast(1)|endometrium(7)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	44		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				TGTCAGCTCAATGCGCGCACC	0.498																																					p.N608I		Atlas-SNP	.											.	MCM4	97	.	0			c.A1823T						.						98	92	94					8																	48883923		2203	4300	6503	SO:0001583	missense	4173	exon13			AGCTCAATGCGCG		CCDS6143.1	8q12-q13	2008-02-05	2007-04-04		ENSG00000104738	ENSG00000104738			6947	protein-coding gene	gene with protein product		602638	"MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)"	CDC21		7601140	Standard	NM_005914		Approved	CDC54, hCdc21, P1-Cdc21, MGC33310	uc003xql.2	P33991	OTTHUMG00000164205	ENST00000262105.2:c.1823A>T	chr8.hg19:g.48883923A>T	ENSP00000262105:p.Asn608Ile	86.0	0.0		152.0	31.0	NM_182746	Q8NEH1|Q99658	Missense_Mutation	SNP	ENST00000262105.2	hg19	CCDS6143.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.156830	0.78114	.	.	ENSG00000104738	ENST00000523944;ENST00000262105;ENST00000396826;ENST00000429229	T;T	0.08634	3.07;3.07	6.17	5.02	0.67125	ATPase, AAA+ type, core (1);	0.123647	0.85682	D	0.000000	T	0.46870	0.1415	H	0.99182	4.46	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.76071	0.987;0.987	T	0.67102	-0.5755	10	0.87932	D	0	-36.8898	12.3678	0.55238	0.9348:0.0:0.0652:0.0	.	608;608	B3KMX0;P33991	.;MCM4_HUMAN	I	608;608;595;568	ENSP00000430194:N608I;ENSP00000262105:N608I	ENSP00000262105:N608I	N	+	2	0	MCM4	49046476	1.000000	0.71417	0.994000	0.49952	0.589000	0.36550	9.300000	0.96151	1.159000	0.42565	0.533000	0.62120	AAT	.	.		0.498	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377791.1	NM_005914		T	48883923	A	T	48883923	3	4	25	1	0	0	0	0	1	0	0	0	9398	101	4	4	1869	4	MCM4	8	48883923	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	38193428	48883923	97480099	42	3390										
JRK	8629	hgsc.bcm.edu	37	chr8	143747230	143747230	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ccaggtgctccagcttgggcGtgtgcagcgtgcgccgctgc	16	14	0	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr8:143747230G>A	ENST00000507178.2	-	0	580							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				cagcttgggcgtgtgcagcgt	0.672																																					p.T83M		Atlas-SNP	.											.	.	.	.	0			c.C248T						.						29	36	34					8																	143747230		2130	4241	6371			8629	exon2			TTGGGCGTGTGCA	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"jerky (mouse) homolog", "jerky homolog (mouse)"			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			chr8.hg19:g.143747230G>A		62.0	0.0		112.0	23.0	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	hg19																																																																																				.	.		0.672	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		A	143747230	G	A	143747230	1	1	25	0	1	0	0	0	0	0	0	0	7973	1145	40	1		1	JRK	8	143747230	RNA	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	94863307	143747230	2616792	43	3391										
TIGD5	84948	hgsc.bcm.edu	37	chr8	144681433	144681433	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	acttcatgcgcagcttcatgCtcaaggacatgctctacctg	8	13	4	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr8:144681433C>A	ENST00000504548.2	+	1	1360	c.1360C>A	c.(1360-1362)Ctc>Atc	p.L454I	EEF1D_ENST00000531770.1_5'Flank|EEF1D_ENST00000531621.1_5'Flank|RP11-661A12.14_ENST00000606452.1_lincRNA|EEF1D_ENST00000524624.1_5'Flank|TIGD5_ENST00000321385.3_Missense_Mutation_p.L405I|EEF1D_ENST00000423316.2_5'Flank|EEF1D_ENST00000317198.6_5'Flank|EEF1D_ENST00000419152.2_5'Flank|EEF1D_ENST00000529272.1_5'Flank|EEF1D_ENST00000395119.3_5'Flank|EEF1D_ENST00000532400.1_5'Flank|EEF1D_ENST00000442189.2_5'Flank|EEF1D_ENST00000528610.1_5'Flank|EEF1D_ENST00000526838.1_5'Flank	NM_032862.4	NP_116251.4	Q53EQ6	TIGD5_HUMAN	tigger transposable element derived 5	454	DDE 2.					nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	7	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			CAGCTTCATGCTCAAGGACAT	0.667																																					p.L454I		Atlas-SNP	.											.	TIGD5	22	.	0			c.C1360A						.						23	24	23					8																	144681433		2189	4290	6479	SO:0001583	missense	84948	exon1			TTCATGCTCAAGG	AK027832	CCDS6406.1, CCDS6406.2	8q24.3	2008-02-01				ENSG00000179886			18336	protein-coding gene	gene with protein product							Standard	NM_032862		Approved	FLJ14926	uc003yyx.2	Q53EQ6		ENST00000504548.2:c.1360C>A	chr8.hg19:g.144681433C>A	ENSP00000421489:p.Leu454Ile	98.0	0.0		174.0	37.0	NM_032862	E7EWS2|Q6NT83|Q8N5A1|Q96JW8	Missense_Mutation	SNP	ENST00000504548.2	hg19	CCDS6406.2	.	.	.	.	.	.	.	.	.	.	C	20.6	4.025090	0.75390	.	.	ENSG00000179886	ENST00000504548;ENST00000321385	T;T	0.46451	0.87;0.87	4.3	4.3	0.51218	.	0.000000	0.50627	U	0.000114	T	0.49609	0.1567	L	0.32530	0.975	0.27089	N	0.962908	D	0.71674	0.998	D	0.70227	0.968	T	0.42999	-0.9418	10	0.14252	T	0.57	.	15.7834	0.78281	0.0:1.0:0.0:0.0	.	405	Q53EQ6	TIGD5_HUMAN	I	454;405	ENSP00000421489:L454I;ENSP00000315906:L405I	ENSP00000315906:L405I	L	+	1	0	TIGD5	144752576	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.953000	0.49105	1.926000	0.55796	0.655000	0.94253	CTC	.	.		0.667	TIGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368269.1	NM_032862		A	144681433	C	A	144681433	3	1	25	1	0	0	0	0	1	0	0	0	15914	797	28	3	1362	3	TIGD5	8	144681433	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	934203	144681433	1682589	44	3392										
IFNB1	3456	hgsc.bcm.edu	37	chr9	21077442	21077442	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cctcccataatatcttttcaGgtgcagactgctcatgagtt	7	11	3	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr9:21077442G>T	ENST00000380232.2	-	1	501	c.427C>A	c.(427-429)Ctg>Atg	p.L143M		NM_002176.2	NP_002167.1	P01574	IFNB_HUMAN	interferon, beta 1, fibroblast	143					adaptive immune response (GO:0002250)|B cell activation involved in immune response (GO:0002312)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of viral genome replication (GO:0045071)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	12				GBM - Glioblastoma multiforme(5;7.45e-142)|Lung(24;2.42e-17)|LUSC - Lung squamous cell carcinoma(38;7.17e-11)		TATCTTTTCAGGTGCAGACTG	0.433																																					p.L143M		Atlas-SNP	.											.	IFNB1	33	.	0			c.C427A						.						180	183	182					9																	21077442		2203	4300	6503	SO:0001583	missense	3456	exon1			TTTTCAGGTGCAG		CCDS6495.1	9p22	2008-07-21			ENSG00000171855	ENSG00000171855		"Interferons"	5434	protein-coding gene	gene with protein product		147640		IFNB			Standard	NM_002176		Approved	IFB, IFF	uc003zok.3	P01574	OTTHUMG00000019652	ENST00000380232.2:c.427C>A	chr9.hg19:g.21077442G>T	ENSP00000369581:p.Leu143Met	159.0	0.0		71.0	41.0	NM_002176	Q5VWC9	Missense_Mutation	SNP	ENST00000380232.2	hg19	CCDS6495.1	.	.	.	.	.	.	.	.	.	.	G	13.80	2.346573	0.41599	.	.	ENSG00000171855	ENST00000380232	T	0.27104	1.69	5.42	2.54	0.30619	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.195950	0.34484	N	0.003925	T	0.44993	0.1320	M	0.79123	2.44	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.23547	-1.0185	10	0.52906	T	0.07	-10.0403	5.3225	0.15889	0.1767:0.3212:0.5021:0.0	.	143	P01574	IFNB_HUMAN	M	143	ENSP00000369581:L143M	ENSP00000369581:L143M	L	-	1	2	IFNB1	21067442	0.617000	0.27043	0.011000	0.14972	0.019000	0.09904	0.791000	0.26915	0.386000	0.24997	0.650000	0.86243	CTG	.	.		0.433	IFNB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051881.1	NM_002176		T	21077442	G	T	21077442	3	4	25	1	0	0	0	0	1	0	0	0	7555	991	35	3	140	3	IFNB1	9	21077442	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10		21077442	120135989	45	3393										
ST8SIA6	338596	hgsc.bcm.edu	37	chr10	17363172	17363172	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ccagatctttcaggtacttgGgatggaaaaatagaaccttt	9	7	2	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr10:17363172G>A	ENST00000377602.4	-	8	976	c.902C>T	c.(901-903)cCc>cTc	p.P301L		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	301					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						CAGGTACTTGGGATGGAAAAA	0.468																																					p.P301L		Atlas-SNP	.											.	ST8SIA6	85	.	0			c.C902T						.						185	188	187					10																	17363172		2203	4300	6503	SO:0001583	missense	338596	exon8			TACTTGGGATGGA		CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.902C>T	chr10.hg19:g.17363172G>A	ENSP00000366827:p.Pro301Leu	195.0	0.0		128.0	54.0	NM_001004470	B0YJ97|B9EH72|Q5VZH4	Missense_Mutation	SNP	ENST00000377602.4	hg19	CCDS31158.1	.	.	.	.	.	.	.	.	.	.	G	32	5.130943	0.94473	.	.	ENSG00000148488	ENST00000377602	T	0.59906	0.23	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.76652	0.4017	M	0.76433	2.335	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75147	-0.3420	10	0.42905	T	0.14	-17.476	19.2559	0.93945	0.0:0.0:1.0:0.0	.	301	P61647	SIA8F_HUMAN	L	301	ENSP00000366827:P301L	ENSP00000366827:P301L	P	-	2	0	ST8SIA6	17403178	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.601000	0.98297	2.861000	0.98227	0.650000	0.86243	CCC	.	.		0.468	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		A	17363172	G	A	17363172	3	1	25	1	0	0	0	0	1	0	0	0	15251	1232	43	3	298	3	ST8SIA6	10	17363172	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10		17363172	118171575	46	3394										
PRKG1	5592	hgsc.bcm.edu	37	chr10	54042015	54042015	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	agatcatcctgaacaaaggcCatgacatttcagccgactac	7	12	2	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr10:54042015C>T	ENST00000401604.2	+	14	1797	c.1603C>T	c.(1603-1605)Cat>Tat	p.H535Y	PRKG1_ENST00000373985.1_Missense_Mutation_p.H523Y|PRKG1_ENST00000373980.4_Missense_Mutation_p.H550Y|PRKG1-AS1_ENST00000426785.2_RNA|PRKG1_ENST00000373975.2_Missense_Mutation_p.H253Y|PRKG1-AS1_ENST00000452247.2_RNA			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	535	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.H550Y(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		GAACAAAGGCCATGACATTTC	0.423																																					p.H550Y		Atlas-SNP	.											PRKG1,ear,carcinoma,0,1	PRKG1	167	.	1	Substitution - Missense(1)	skin(1)	c.C1648T						.						112	103	106					10																	54042015		2203	4300	6503	SO:0001583	missense	5592	exon14			AAAGGCCATGACA		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.1603C>T	chr10.hg19:g.54042015C>T	ENSP00000384200:p.His535Tyr	164.0	0.0		109.0	41.0	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	hg19	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.897084	0.91962	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193;ENST00000373975	T;T;T	0.04603	3.59;3.59;3.59	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.07098	0.0180	N	0.01515	-0.825	0.80722	D	1	D;D;D	0.89917	0.993;1.0;1.0	D;D;D	0.97110	0.979;1.0;1.0	T	0.65594	-0.6130	10	0.32370	T	0.25	-18.3413	19.3218	0.94245	0.0:1.0:0.0:0.0	.	253;550;535	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	Y	535;523;550;253;147	ENSP00000384200:H535Y;ENSP00000363097:H523Y;ENSP00000363092:H550Y	ENSP00000327642:H253Y	H	+	1	0	PRKG1	53712021	1.000000	0.71417	0.987000	0.45799	0.998000	0.95712	7.770000	0.85390	2.727000	0.93392	0.563000	0.77884	CAT	.	.		0.423	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	54042015	C	T	54042015	3	4	25	1	0	0	0	0	1	0	0	0	12534	594	21	3	1972	3	PRKG1	10	54042015	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	36678843	54042015	81492732	47	3395										
DDIT4	54541	hgsc.bcm.edu	37	chr10	74034129	74034129	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ctccacgagcctggagagctCggactgcgagtccctggaca	13	14	0	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr10:74034129C>G	ENST00000307365.3	+	2	356	c.155C>G	c.(154-156)tCg>tGg	p.S52W	RP11-442H21.2_ENST00000491934.2_RNA	NM_019058.2	NP_061931.1	Q9NX09	DDIT4_HUMAN	DNA-damage-inducible transcript 4	52					brain development (GO:0007420)|cell proliferation (GO:0008283)|defense response to virus (GO:0051607)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of glycolytic process (GO:0045820)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of TOR signaling (GO:0032007)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron death (GO:1901216)|protein complex disassembly (GO:0043241)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|mitochondrion (GO:0005739)				cervix(1)|endometrium(2)|lung(5)|pancreas(1)|prostate(2)|urinary_tract(1)	12						CTGGAGAGCTCGGACTGCGAG	0.721																																					p.S52W		Atlas-SNP	.											.	DDIT4	14	.	0			c.C155G						.						29	31	31					10																	74034129		2203	4298	6501	SO:0001583	missense	54541	exon2			AGAGCTCGGACTG	AK000507	CCDS7315.1	10q22.1	2008-05-14			ENSG00000168209	ENSG00000168209			24944	protein-coding gene	gene with protein product	"HIF-1 responsive RTP801"	607729				11884613	Standard	NM_019058		Approved	RTP801, FLJ20500, REDD-1, REDD1, Dig2	uc001jsx.1	Q9NX09	OTTHUMG00000018435	ENST00000307365.3:c.155C>G	chr10.hg19:g.74034129C>G	ENSP00000307305:p.Ser52Trp	40.0	0.0		45.0	20.0	NM_019058	Q9H0S3	Missense_Mutation	SNP	ENST00000307365.3	hg19	CCDS7315.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.670725	0.88348	.	.	ENSG00000168209	ENST00000307365	T	0.51817	0.69	5.33	5.33	0.75918	.	0.415784	0.26788	N	0.022486	T	0.58836	0.2150	L	0.27053	0.805	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.62914	-0.6753	10	0.87932	D	0	-13.0136	19.0232	0.92922	0.0:1.0:0.0:0.0	.	52	Q9NX09	DDIT4_HUMAN	W	52	ENSP00000307305:S52W	ENSP00000307305:S52W	S	+	2	0	DDIT4	73704135	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.230000	0.51286	2.652000	0.90054	0.655000	0.94253	TCG	.	.		0.721	DDIT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048577.1	NM_019058		G	74034129	C	G	74034129	3	3	25	1	0	0	0	0	1	0	0	0	4333	893	31	4	157	4	DDIT4	10	74034129	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	19992114	74034129	61500618	48	3396										
SH3PXD2A	9644	hgsc.bcm.edu	37	chr10	105361743	105361743	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ctcgtagtctgcgatagagaCgtacacatctttgaggttat	10	8	2	2	rs561681082		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr10:105361743C>T	ENST00000369774.4	-	15	3508	c.3232G>A	c.(3232-3234)Gtc>Atc	p.V1078I	SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000538130.1_Missense_Mutation_p.V913I|SH3PXD2A_ENST00000540321.1_Missense_Mutation_p.V945I|SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000355946.2_Missense_Mutation_p.V1050I			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	1078	SH3 5. {ECO:0000255|PROSITE- ProRule:PRU00192}.				superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		GCGATAGAGACGTACACATCT	0.577													C|||	1	0.000199681	0	0	5008	,	,		17603	0.001		0	False		,,,				2504	0				p.V1050I		Atlas-SNP	.											.	SH3PXD2A	90	.	0			c.G3148A						.						129	131	130					10																	105361743		2203	4300	6503	SO:0001583	missense	9644	exon14			TAGAGACGTACAC	AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"five SH3 domains"		"SH3 multiple domains 1"	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.3232G>A	chr10.hg19:g.105361743C>T	ENSP00000358789:p.Val1078Ile	74.0	0.0		70.0	29.0	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Missense_Mutation	SNP	ENST00000369774.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.558|5.558	0.287830|0.287830	0.10513|0.10513	.|.	.|.	ENSG00000107957|ENSG00000107957	ENST00000420222|ENST00000369774;ENST00000355946;ENST00000315994;ENST00000536035;ENST00000540321;ENST00000538130	.|T;T;T;T	.|0.31510	.|1.49;1.49;1.49;1.49	5.39|5.39	2.25|2.25	0.28309|0.28309	.|Src homology-3 domain (2);	.|0.251698	.|0.39759	.|N	.|0.001277	T|T	0.23611|0.23611	0.0571|0.0571	L|L	0.52206|0.52206	1.635|1.635	0.38176|0.38176	D|D	0.939463|0.939463	.|B;B;B;B	.|0.18013	.|0.003;0.015;0.019;0.025	.|B;B;B;B	.|0.14578	.|0.003;0.005;0.007;0.011	T|T	0.10730|0.10730	-1.0617|-1.0617	5|10	.|0.18710	.|T	.|0.47	-21.6886|-21.6886	8.487|8.487	0.33078|0.33078	0.0:0.6687:0.0:0.3313|0.0:0.6687:0.0:0.3313	.|.	.|1078;927;923;1050	.|Q5TCZ1;B7Z9L8;B7Z3B0;Q5TCZ1-3	.|SPD2A_HUMAN;.;.;.	H|I	1004|1078;1050;885;910;945;913	.|ENSP00000358789:V1078I;ENSP00000348215:V1050I;ENSP00000443663:V945I;ENSP00000441514:V913I	.|ENSP00000318135:V885I	R|V	-|-	2|1	0|0	SH3PXD2A|SH3PXD2A	105351733|105351733	0.051000|0.051000	0.20477|0.20477	0.118000|0.118000	0.21660|0.21660	0.135000|0.135000	0.20990|0.20990	0.296000|0.296000	0.19083|0.19083	0.156000|0.156000	0.19299|0.19299	-0.367000|-0.367000	0.07326|0.07326	CGT|GTC	.	.		0.577	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631		T	105361743	C	T	105361743	3	4	25	1	0	0	0	0	1	0	0	0	14271	536	19	1	173	1	SH3PXD2A	10	105361743	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	31327614	105361743	30173004	49	3397										
CCDC147	159686	hgsc.bcm.edu	37	chr10	106163548	106163548	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ggacacgctgccgagccctgGaggaggagctggagaatccc	16	12	0	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr10:106163548G>A	ENST00000369704.3	+	14	2235	c.2101G>A	c.(2101-2103)Gag>Aag	p.E701K		NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		701						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		CCGAGCCCTGGAGGAGGAGCT	0.488																																					p.E701K		Atlas-SNP	.											.	CCDC147	137	.	0			c.G2101A						.						64	65	65					10																	106163548		2203	4300	6503	SO:0001583	missense	159686	exon14			GCCCTGGAGGAGG																												ENST00000369704.3:c.2101G>A	chr10.hg19:g.106163548G>A	ENSP00000358718:p.Glu701Lys	88.0	0.0		78.0	35.0	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	hg19	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.495854	0.85069	.	.	ENSG00000120051	ENST00000369704	T	0.51071	0.72	5.5	5.5	0.81552	.	0.104953	0.64402	D	0.000006	T	0.63546	0.2520	M	0.79475	2.455	0.80722	D	1	P	0.49961	0.93	P	0.56042	0.79	T	0.58370	-0.7648	10	0.15952	T	0.53	-27.5186	17.9465	0.89040	0.0:0.0:1.0:0.0	.	701	Q5T655	CC147_HUMAN	K	701	ENSP00000358718:E701K	ENSP00000358718:E701K	E	+	1	0	CCDC147	106153538	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.212000	0.65225	2.735000	0.93741	0.655000	0.94253	GAG	.	.		0.488	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			A	106163548	G	A	106163548	3	1	25	1	0	0	0	0	1	0	0	0	2783	1175	41	3	2155	3	CCDC147	10	106163548	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	801805	106163548	29371199	50	3398										
MRGPRX4	117196	hgsc.bcm.edu	37	chr11	18195075	18195075	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	attacgcctcatcaatatcaGccatctcatccgcaaaatcc	3	15	4	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr11:18195075G>C	ENST00000314254.3	+	1	692	c.272G>C	c.(271-273)aGc>aCc	p.S91T	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						ATCAATATCAGCCATCTCATC	0.512																																					p.S91T		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.G272C						.						124	96	106					11																	18195075		2199	4293	6492	SO:0001583	missense	117196	exon1			ATATCAGCCATCT	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"GPCR / Class A : Orphans"	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.272G>C	chr11.hg19:g.18195075G>C	ENSP00000314042:p.Ser91Thr	105.0	0.0		90.0	27.0	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	hg19	CCDS7831.1	.	.	.	.	.	.	.	.	.	.	G	0.093	-1.164358	0.01673	.	.	ENSG00000179817	ENST00000314254	T	0.42131	0.98	2.7	-1.99	0.07457	GPCR, rhodopsin-like superfamily (1);	3.243040	0.00654	N	0.000579	T	0.29817	0.0745	L	0.41824	1.3	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.03287	-1.1052	10	0.21540	T	0.41	.	1.2322	0.01946	0.1774:0.1204:0.3655:0.3368	.	91	Q96LA9	MRGX4_HUMAN	T	91	ENSP00000314042:S91T	ENSP00000314042:S91T	S	+	2	0	MRGPRX4	18151651	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.490000	0.02304	-0.576000	0.05974	-3.271000	0.00048	AGC	.	.		0.512	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032		C	18195075	G	C	18195075	3	2	25	1	0	0	0	0	1	0	0	0	9778	971	34	4	274	4	MRGPRX4	11	18195075	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10		18195075	116811441	51	3399										
ARFGAP2	84364	hgsc.bcm.edu	37	chr11	47193261	47193261	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	atcggctgcctgctgctcacGgagcttctctgccacctgag	11	15	2	1	rs138040761	byFrequency	TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr11:47193261G>A	ENST00000524782.1	-	9	991	c.763C>T	c.(763-765)Cgt>Tgt	p.R255C	ARFGAP2_ENST00000319543.6_5'UTR|RP11-390K5.6_ENST00000524412.1_RNA|ARFGAP2_ENST00000395449.3_5'UTR|ARFGAP2_ENST00000419701.2_Missense_Mutation_p.R148C|ARFGAP2_ENST00000426335.2_Missense_Mutation_p.R119C	NM_001242832.1|NM_032389.4	NP_001229761.1|NP_115765.2	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating protein 2	255	Required for interaction with coatomer.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						TGCTGCTCACGGAGCTTCTCT	0.622													G|||	14	0.00279553	0	0	5008	,	,		15707	0		0	False		,,,				2504	0.0143				p.R255C		Atlas-SNP	.											.	ARFGAP2	43	.	0			c.C763T						.	G	CYS/ARG,CYS/ARG	0,4402		0,0,2201	65	68	67		679,763	5.9	1	11	dbSNP_134	67	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	ARFGAP2	NM_001242832.1,NM_032389.4	180,180	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	227/494,255/522	47193261	1,12999	2201	4299	6500	SO:0001583	missense	84364	exon9			GCTCACGGAGCTT	AK027482	CCDS7926.1, CCDS73283.1	11p11.2-p11.12	2012-10-05	2008-01-09	2008-01-09	ENSG00000149182	ENSG00000149182		"ADP-ribosylation factor GTPase activating proteins"	13504	protein-coding gene	gene with protein product		606908	"zinc finger protein 289, ID1 regulated"	ZNF289		11278321, 14690497	Standard	NM_032389		Approved	IRZ, Zfp289, FLJ14576	uc001ndt.3	Q8N6H7	OTTHUMG00000166773	ENST00000524782.1:c.763C>T	chr11.hg19:g.47193261G>A	ENSP00000434442:p.Arg255Cys	46.0	0.0		54.0	5.0	NM_032389	B4DX29|B7Z9M7|D3DQQ9|Q3LIF2|Q8N3I1|Q96SX7	Missense_Mutation	SNP	ENST00000524782.1	hg19	CCDS7926.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.143951	0.57044	0.0	1.16E-4	ENSG00000149182	ENST00000426335;ENST00000524782;ENST00000419701;ENST00000527927;ENST00000525398	T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.67524	0.2902	M	0.78801	2.425	0.80722	D	1	D;B;D	0.89917	1.0;0.081;0.999	D;B;P	0.67103	0.949;0.006;0.891	T	0.70167	-0.4946	10	0.72032	D	0.01	-8.5939	13.2963	0.60298	0.0:0.0:0.7402:0.2598	.	148;119;255	B4DX29;G5E9L0;Q8N6H7	.;.;ARFG2_HUMAN	C	119;255;148;119;269	ENSP00000400226:R119C;ENSP00000434442:R255C;ENSP00000389264:R148C;ENSP00000434433:R119C;ENSP00000431939:R269C	ENSP00000389264:R148C	R	-	1	0	ARFGAP2	47149837	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.465000	0.60141	2.824000	0.97209	0.655000	0.94253	CGT	.	G|1.000;A|0.000		0.622	ARFGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391425.1	NM_032389		A	47193261	G	A	47193261	3	1	25	1	0	0	0	0	1	0	0	0	850	1116	39	1	834	1	ARFGAP2	11	47193261	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	28998186	47193261	87813255	52	3400										
OR1S1	219959	hgsc.bcm.edu	37	chr11	57983067	57983067	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cactcaccctgaggacactgAtaagattggtgctgtcctat	9	11	1	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr11:57983067A>T	ENST00000309433.6	+	1	851	c.851A>T	c.(850-852)gAt>gTt	p.D284V		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	284						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				GAGGACACTGATAAGATTGGT	0.473																																					p.D284V		Atlas-SNP	.											.	OR1S1	139	.	0			c.A851T						.						136	123	127					11																	57983067		2201	4293	6494	SO:0001583	missense	219959	exon1			ACACTGATAAGAT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"GPCR / Class A : Olfactory receptors"	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.851A>T	chr11.hg19:g.57983067A>T	ENSP00000311688:p.Asp284Val	141.0	0.0		107.0	27.0	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	hg19	CCDS31546.1	.	.	.	.	.	.	.	.	.	.	A	12.41	1.930780	0.34096	.	.	ENSG00000172774	ENST00000309433	T	0.00253	8.43	3.23	3.23	0.37069	GPCR, rhodopsin-like superfamily (1);	0.409624	0.20658	N	0.088067	T	0.00552	0.0018	M	0.87971	2.92	0.09310	N	0.999995	D	0.89917	1.0	D	0.76071	0.987	T	0.36065	-0.9763	10	0.56958	D	0.05	.	7.6674	0.28439	0.8888:0.0:0.1112:0.0	.	284	Q8NH92	OR1S1_HUMAN	V	284	ENSP00000311688:D284V	ENSP00000311688:D284V	D	+	2	0	OR1S1	57739643	0.000000	0.05858	0.184000	0.23157	0.758000	0.43043	1.286000	0.33273	1.345000	0.45676	0.392000	0.25879	GAT	.	.		0.473	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458		T	57983067	A	T	57983067	3	4	25	1	0	0	0	0	1	0	0	0	10981	333	12	4	853	4	OR1S1	11	57983067	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	10789806	57983067	77023449	53	3401										
CHRM1	1128	hgsc.bcm.edu	37	chr11	62677923	62677927	+	Frame_Shift_Del	DEL	TTCTC	TTCTC	-													0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ctgccagctcccgtgctcggTtctctgtctcccggtagatg							TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	TTCTC	TTCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr11:62677923_62677927delTTCTC	ENST00000306960.3	-	2	1187_1191	c.646_650delGAGAA	c.(646-651)gagaacfs	p.EN216fs	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	216					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	CCGTGCTCGGTTCTCTGTCTCCCGG	0.639																																					p.216_217del		Atlas-Indel,Pindel	.											.	CHRM1	29	.	0			c.647_651del						.																																			SO:0001589	frameshift_variant	1128	exon2			.	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1950	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 1"	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.646_650delGAGAA	chr11.hg19:g.62677923_62677927delTTCTC	ENSP00000306490:p.Glu216fs	60.0	0.0		37.0	18.0	NM_000738	Q96RH1	Frame_Shift_Del	DEL	ENST00000306960.3	hg19	CCDS8040.1																																																																																			.	.		0.639	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738		-	62677927	TTCTC	-	62677923	7	5	25	1	0	1	0	1	0	0	0	0	3378	1725	60	0	736	0	CHRM1	11	62677923	Frame_Shift_Del	DEL	TTCTC	TCGA-5C-A9VH-01A-11D-A36X-10	4694856	62677923	72328593	54	3402										
MFRP	83552	hgsc.bcm.edu	37	chr11	119213689	119213689	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tggtgcgaggagacgaggtgGgggggtggctctgctccaca	20	8	1	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr11:119213689G>T	ENST00000530681.1	-	10	1293	c.1149C>A	c.(1147-1149)ccC>ccA	p.P383P	MFRP_ENST00000449574.2_Silent_p.P383P|C1QTNF5_ENST00000528368.1_5'Flank|C1QTNF5_ENST00000445041.2_5'UTR|C1QTNF5_ENST00000525657.1_5'Flank|MFRP_ENST00000529147.1_5'Flank|MFRP_ENST00000360167.4_Missense_Mutation_p.P308H|MFRP_ENST00000555262.1_Silent_p.P383P	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	383	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				embryo development (GO:0009790)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|urinary_tract(1)	18		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		AGACGAGGTGGGGGGGTGGCT	0.622																																					p.P383P		Atlas-SNP	.											.	MFRP	63	.	0			c.C1149A						.						33	27	29					11																	119213689		2196	4293	6489	SO:0001819	synonymous_variant	83552	exon10			GAGGTGGGGGGGT	AB055505	CCDS8421.1	11q23.3	2014-01-28			ENSG00000235718	ENSG00000235718			18121	protein-coding gene	gene with protein product	"membrane-type frizzled-related protein", "complement C1q tumor necrosis factor-related protein 5 precursor variant 1"	606227				11263980	Standard	NM_031433		Approved	FLJ30570, rd6, NNO2, C1QTNF5	uc001pwj.2	Q9BY79		ENST00000530681.1:c.1149C>A	chr11.hg19:g.119213689G>T		74.0	0.0		50.0	21.0	NM_031433	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Silent	SNP	ENST00000530681.1	hg19	CCDS8421.1	.	.	.	.	.	.	.	.	.	.	G	0.213	-1.035170	0.02029	.	.	ENSG00000235718	ENST00000360167	T	0.25085	1.82	4.84	-9.68	0.00528	.	0.274308	0.34411	N	0.003982	T	0.11024	0.0269	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.05886	-1.0858	9	0.42905	T	0.14	-0.9876	3.3846	0.07266	0.1173:0.3353:0.2036:0.3438	.	308	B4DHN8	.	H	308	ENSP00000353291:P308H	ENSP00000353291:P308H	P	-	2	0	MFRP	118718899	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	-1.766000	0.01797	-3.385000	0.00174	-1.153000	0.01818	CCC	.	.		0.622	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433		T	119213689	G	T	119213689	2	4	25	1	0	0	0	0	0	0	0	1	9535	1219	43	3		3	MFRP	11	119213689	Silent	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	56535766	119213689	15792827	55	3403										
BLID	414899	hgsc.bcm.edu	37	chr11	121986326	121986326	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	acagggcctcagcagaggaaTtgcataacaatgtaacttgt	10	8	1	1	rs375451446		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr11:121986326T>A	ENST00000560104.1	-	1	597	c.305A>T	c.(304-306)aAt>aTt	p.N102I		NM_001001786.2	NP_001001786.2	Q8IZY5	BLID_HUMAN	BH3-like motif containing, cell death inducer	102					apoptotic process (GO:0006915)	mitochondrion (GO:0005739)				NS(1)|large_intestine(4)|lung(6)|pancreas(1)	12		Breast(109;0.0164)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;2.08e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.101)		AGCAGAGGAATTGCATAACAA	0.453																																					p.N102I		Atlas-SNP	.											.	BLID	20	.	0			c.A305T						.						105	101	102					11																	121986326		2202	4299	6501	SO:0001583	missense	414899	exon1			GAGGAATTGCATA	AF303179	CCDS31693.1	11q24.1	2007-06-22				ENSG00000259571			33495	protein-coding gene	gene with protein product	"breast cancer cell 2"	608853				15069058, 17220890	Standard	NM_001001786		Approved	BRCC2	uc001pyf.3	Q8IZY5		ENST00000560104.1:c.305A>T	chr11.hg19:g.121986326T>A	ENSP00000453153:p.Asn102Ile	107.0	0.0		100.0	41.0	NM_001001786	A1L416	Missense_Mutation	SNP	ENST00000560104.1	hg19	CCDS31693.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.756516	0.49362	.	.	ENSG00000258606;ENSG00000258574	ENST00000553434;ENST00000556841	.	.	.	3.76	1.44	0.22558	.	.	.	.	.	T	0.19127	0.0459	N	0.08118	0	0.09310	N	0.999999	P	0.44429	0.835	P	0.46917	0.531	T	0.10132	-1.0643	8	0.87932	D	0	.	5.3091	0.15821	0.0:0.2371:0.0:0.7629	.	102	Q8IZY5	BLID_HUMAN	I	102	.	ENSP00000448995:N102I	N	-	2	0	BLID;AP001924.1	121491536	0.123000	0.22298	0.240000	0.24138	0.719000	0.41307	0.696000	0.25541	0.296000	0.22592	0.482000	0.46254	AAT	.	.		0.453	BLID-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387656.1	NM_001001786		A	121986326	T	A	121986326	3	1	25	1	0	0	0	0	1	0	0	0	1443	1493	52	4	25	4	BLID	11	121986326	Missense_Mutation	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10	2772637	121986326	13020190	56	3404										
ESAM	90952	hgsc.bcm.edu	37	chr11	124626226	124626226	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tgcccccacatggggcacacCctggagacggcaggatggag	15	13	0	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr11:124626226C>A	ENST00000278927.5	-	4	613	c.484G>T	c.(484-486)Ggt>Tgt	p.G162C	RP11-677M14.3_ENST00000504932.2_RNA|ESAM_ENST00000442070.2_Intron	NM_138961.2	NP_620411.2	Q96AP7	ESAM_HUMAN	endothelial cell adhesion molecule	162	Ig-like C2-type.				blood coagulation (GO:0007596)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)|single organismal cell-cell adhesion (GO:0016337)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.022)		TGGGGCACACCCTGGAGACGG	0.607																																					p.G162C		Atlas-SNP	.											.	ESAM	31	.	0			c.G484T						.						35	30	32					11																	124626226		2201	4299	6500	SO:0001583	missense	90952	exon4			GCACACCCTGGAG	AK075396	CCDS8453.1	11q24.2	2013-01-29			ENSG00000149564	ENSG00000149564		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17474	protein-coding gene	gene with protein product		614281				11279107, 11906820	Standard	NM_138961		Approved	W117m	uc001qav.4	Q96AP7	OTTHUMG00000151986	ENST00000278927.5:c.484G>T	chr11.hg19:g.124626226C>A	ENSP00000278927:p.Gly162Cys	59.0	0.0		40.0	10.0	NM_138961	B4DVN8|Q96T50	Missense_Mutation	SNP	ENST00000278927.5	hg19	CCDS8453.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.536261	0.45176	.	.	ENSG00000149564	ENST00000278927;ENST00000435477	T;T	0.16324	2.35;2.35	5.37	4.45	0.53987	Immunoglobulin-like fold (1);	0.052629	0.85682	D	0.000000	T	0.48352	0.1495	M	0.92317	3.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.995;0.996;0.999	T	0.57213	-0.7850	10	0.87932	D	0	.	10.4642	0.44598	0.0:0.9097:0.0:0.0903	.	162;162;35	F8WDW9;Q96AP7;C9JIE7	.;ESAM_HUMAN;.	C	162;35	ENSP00000278927:G162C;ENSP00000415893:G35C	ENSP00000278927:G162C	G	-	1	0	ESAM	124131436	0.634000	0.27190	0.276000	0.24689	0.221000	0.24807	3.014000	0.49590	2.509000	0.84616	0.655000	0.94253	GGT	.	.		0.607	ESAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324686.1	NM_138961		A	124626226	C	A	124626226	3	1	25	1	0	0	0	0	1	0	0	0	5249	623	22	3	704	3	ESAM	11	124626226	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	2639900	124626226	10380290	57	3405										
ZNF384	171017	hgsc.bcm.edu	37	chr12	6787570	6787570	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cgaaatggggaaggtctgagCtgatgatgctgtggtcacaa	15	6	2	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr12:6787570C>A	ENST00000396801.3	-	6	616	c.409G>T	c.(409-411)Gct>Tct	p.A137S	ZNF384_ENST00000396799.2_Missense_Mutation_p.A137S|ZNF384_ENST00000396795.1_Missense_Mutation_p.A137S|ZNF384_ENST00000319770.3_Missense_Mutation_p.A121S|ZNF384_ENST00000361959.3_Missense_Mutation_p.A137S|ZNF384_ENST00000355772.4_Intron	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	137					nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)		EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						AAGGTCTGAGCTGATGATGCT	0.547			T	"EWSR1, TAF15 "	ALL																																p.A137S		Atlas-SNP	.		Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	.	ZNF384	102	.	0			c.G409T						.						37	36	36					12																	6787570		2203	4300	6503	SO:0001583	missense	171017	exon6			TCTGAGCTGATGA	U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"Zinc fingers, C2H2-type"	11955	protein-coding gene	gene with protein product		609951	"trinucleotide repeat containing 1"	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.409G>T	chr12.hg19:g.6787570C>A	ENSP00000380019:p.Ala137Ser	117.0	0.0		116.0	38.0	NM_133476	O15407|Q7Z722|Q8N938	Missense_Mutation	SNP	ENST00000396801.3	hg19	CCDS44817.1	.	.	.	.	.	.	.	.	.	.	C	9.295	1.051654	0.19827	.	.	ENSG00000126746	ENST00000319770;ENST00000396795;ENST00000396801;ENST00000361959;ENST00000396799;ENST00000417772;ENST00000436774;ENST00000542796;ENST00000540915;ENST00000535485	T;T;T;T;T;T	0.08282	3.16;3.21;3.11;3.11;3.21;3.47	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000002	T	0.04137	0.0115	N	0.03050	-0.425	0.45822	D	0.998692	B;B;B	0.28378	0.209;0.123;0.123	B;B;B	0.18871	0.021;0.015;0.023	T	0.53940	-0.8367	10	0.21014	T	0.42	-7.7809	17.4978	0.87723	0.0:1.0:0.0:0.0	.	137;121;137	Q8TF68;F8W6Q3;Q8TF68-2	ZN384_HUMAN;.;.	S	121;137;137;137;137;137;121;121;137;121	ENSP00000321650:A121S;ENSP00000380013:A137S;ENSP00000380019:A137S;ENSP00000354592:A137S;ENSP00000380017:A137S;ENSP00000412911:A121S	ENSP00000321650:A121S	A	-	1	0	ZNF384	6657831	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.009000	0.40903	2.560000	0.86352	0.591000	0.81541	GCT	.	.		0.547	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400712.1			A	6787570	C	A	6787570	3	1	25	1	0	0	0	0	1	0	0	0	17890	797	28	3	1348	3	ZNF384	12	6787570	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10		6787570	127064325	58	3406										
TAS2R20	259295	hgsc.bcm.edu	37	chr12	11150332	11150332	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tggagactgccagagcagcaAtaatttgatcagctgaggag	13	7	1	4			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr12:11150332A>G	ENST00000538986.1	-	1	142	c.143T>C	c.(142-144)aTt>aCt	p.I48T	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	48					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						CAGAGCAGCAATAATTTGATC	0.358																																					p.I48T		Atlas-SNP	.											.	TAS2R20	17	.	0			c.T143C						.						42	47	45					12																	11150332		2202	4299	6501	SO:0001583	missense	259295	exon1			GCAGCAATAATTT	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19109	protein-coding gene	gene with protein product		613962	"taste receptor, type 2, member 49"	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.143T>C	chr12.hg19:g.11150332A>G	ENSP00000441624:p.Ile48Thr	292.0	0.0		218.0	80.0	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	hg19	CCDS8639.1	.	.	.	.	.	.	.	.	.	.	A	12.07	1.827179	0.32329	.	.	ENSG00000255837	ENST00000538986	T	0.00840	5.63	2.77	2.77	0.32553	.	0.353536	0.21366	U	0.075710	T	0.01592	0.0051	M	0.64404	1.975	0.09310	N	1	P	0.37731	0.607	B	0.39465	0.3	T	0.38993	-0.9635	10	0.87932	D	0	.	8.9683	0.35890	1.0:0.0:0.0:0.0	.	48	P59543	T2R20_HUMAN	T	48	ENSP00000441624:I48T	ENSP00000441624:I48T	I	-	2	0	TAS2R20	11041599	0.374000	0.25081	0.004000	0.12327	0.033000	0.12548	2.971000	0.49248	1.279000	0.44446	0.482000	0.46254	ATT	.	.		0.358	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889		G	11150332	A	G	11150332	3	3	25	1	0	0	0	0	1	0	0	0	15586	101	4	2	790	2	TAS2R20	12	11150332	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	4362762	11150332	122701563	59	3407										
DAZAP2	9802	hgsc.bcm.edu	37	chr12	51634874	51634874	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	atgcaggtgccagatttggaGctggggctactgctggcaac	15	9	0	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr12:51634874G>T	ENST00000412716.3	+	3	968	c.352G>T	c.(352-354)Gct>Tct	p.A118S	DAZAP2_ENST00000551534.1_3'UTR|DAZAP2_ENST00000425012.2_Missense_Mutation_p.A118S|DAZAP2_ENST00000439799.2_Intron|DAZAP2_ENST00000604900.1_Missense_Mutation_p.A118S|DAZAP2_ENST00000551313.1_Missense_Mutation_p.A58S|DAZAP2_ENST00000549555.1_Intron|DAZAP2_ENST00000449723.3_Missense_Mutation_p.A96S|DAZAP2_ENST00000549732.2_Missense_Mutation_p.A86S			Q15038	DAZP2_HUMAN	DAZ associated protein 2	118	Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	WW domain binding (GO:0050699)			haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)	6						CAGATTTGGAGCTGGGGCTAC	0.473																																					p.A118S		Atlas-SNP	.											.	DAZAP2	6	.	0			c.G352T						.						88	80	83					12																	51634874		2203	4300	6503	SO:0001583	missense	9802	exon3			TTTGGAGCTGGGG	D31767	CCDS8809.1, CCDS44884.1, CCDS44885.1, CCDS44886.1, CCDS44887.1, CCDS44888.1	12q13.13	2012-04-04			ENSG00000183283	ENSG00000183283			2684	protein-coding gene	gene with protein product		607431				10857750, 7584044	Standard	NM_014764		Approved	KIAA0058	uc010snd.2	Q15038	OTTHUMG00000169649	ENST00000412716.3:c.352G>T	chr12.hg19:g.51634874G>T	ENSP00000394699:p.Ala118Ser	52.0	0.0		31.0	12.0	NM_001136269	A8K254|B4DDT5|B4E1G3|C9JA96|C9JP84|E9PB45|F8VU62	Missense_Mutation	SNP	ENST00000412716.3	hg19	CCDS8809.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.365959	0.82463	.	.	ENSG00000183283	ENST00000412716;ENST00000425012;ENST00000549732;ENST00000449723;ENST00000551313	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	4.13	4.13	0.48395	.	0.118043	0.56097	D	0.000032	T	0.43010	0.1228	N	0.11927	0.2	0.35056	D	0.761059	D;D;D	0.63046	0.975;0.978;0.992	P;D;D	0.74348	0.79;0.918;0.983	T	0.40421	-0.9564	10	0.13108	T	0.6	.	16.3716	0.83364	0.0:0.0:1.0:0.0	.	118;86;118	B4DDT5;C9JP84;Q15038	.;.;DAZP2_HUMAN	S	118;118;86;96;58	ENSP00000394699:A118S;ENSP00000408251:A118S;ENSP00000446554:A86S;ENSP00000412812:A96S;ENSP00000447842:A58S	ENSP00000394699:A118S	A	+	1	0	DAZAP2	49921141	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.472000	0.60189	2.589000	0.87451	0.655000	0.94253	GCT	.	.		0.473	DAZAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405259.2	NM_014764		T	51634874	G	T	51634874	3	4	25	1	0	0	0	0	1	0	0	0	4247	971	34	3	362	3	DAZAP2	12	51634874	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	40484542	51634874	82217021	60	3408										
CSAD	51380	hgsc.bcm.edu	37	chr12	53566426	53566426	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ctcctcaggctccttccactCacagacctaggaagagagcc	8	16	2	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr12:53566426C>G	ENST00000444623.1	-	5	400	c.133G>C	c.(133-135)Gag>Cag	p.E45Q	CSAD_ENST00000491654.1_5'UTR|CSAD_ENST00000542115.1_Missense_Mutation_p.E45Q|CSAD_ENST00000379843.3_Intron|CSAD_ENST00000453446.2_Missense_Mutation_p.E45Q|CSAD_ENST00000267085.4_Missense_Mutation_p.E72Q|CSAD_ENST00000379846.1_Intron	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	45					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	TCCTTCCACTCACAGACCTAG	0.617																																					p.E72Q	Ovarian(109;252 1546 16882 28524 44645)	Atlas-SNP	.											.	CSAD	66	.	0			c.G214C						.						21	23	22					12																	53566426		2203	4300	6503	SO:0001583	missense	51380	exon5			TCCACTCACAGAC	AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"P-selectin cytoplasmic tail-associated protein"					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.133G>C	chr12.hg19:g.53566426C>G	ENSP00000415485:p.Glu45Gln	43.0	0.0		23.0	10.0	NM_015989	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Missense_Mutation	SNP	ENST00000444623.1	hg19	CCDS58235.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.52|17.52	3.410027|3.410027	0.62399|0.62399	.|.	.|.	ENSG00000139631|ENSG00000139631	ENST00000308926;ENST00000267085;ENST00000544139;ENST00000444623;ENST00000398047;ENST00000453446;ENST00000542115;ENST00000437073;ENST00000424990|ENST00000379850	T;T;T;T;T;T|.	0.39056|.	1.1;1.1;1.1;1.1;1.1;1.1|.	4.67|4.67	4.67|4.67	0.58626|0.58626	Pyridoxal phosphate-dependent transferase, major domain (1);|.	0.102798|.	0.64402|.	D|.	0.000003|.	T|.	0.75384|.	0.3842|.	M|M	0.74647|0.74647	2.275|2.275	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D|.	0.71674|.	0.997;0.998;0.988|.	D;D;P|.	0.70016|.	0.933;0.967;0.88|.	T|.	0.75958|.	-0.3134|.	10|.	0.26408|.	T|.	0.33|.	-28.7401|-28.7401	16.888|16.888	0.86080|0.86080	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	45;72;45|.	B4DL84;Q9Y600-3;Q9Y600|.	.;.;CSAD_HUMAN|.	Q|S	134;72;45;45;45;45;45;45;45|70	ENSP00000267085:E72Q;ENSP00000415485:E45Q;ENSP00000410648:E45Q;ENSP00000439419:E45Q;ENSP00000415314:E45Q;ENSP00000401078:E45Q|.	ENSP00000267085:E72Q|.	E|X	-|-	1|2	0|2	CSAD|CSAD	51852693|51852693	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.881000|0.881000	0.50899|0.50899	6.909000|6.909000	0.75735|0.75735	2.604000|2.604000	0.88044|0.88044	0.555000|0.555000	0.69702|0.69702	GAG|TGA	.	.		0.617	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343697.1	NM_015989		G	53566426	C	G	53566426	3	3	25	1	0	0	0	0	1	0	0	0	3927	835	29	4	1400	4	CSAD	12	53566426	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	1931552	53566426	80285469	61	3409										
SRGAP1	57522	hgsc.bcm.edu	37	chr12	64377754	64377754	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	agctcaactggtagaacaacAaaaatgcctggagcagcaaa	9	9	1	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr12:64377754A>T	ENST00000355086.3	+	2	619	c.95A>T	c.(94-96)cAa>cTa	p.Q32L	SRGAP1_ENST00000357825.3_Missense_Mutation_p.Q32L|SRGAP1_ENST00000543397.1_5'UTR	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	32	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		GTAGAACAACAAAAATGCCTG	0.413																																					p.Q32L		Atlas-SNP	.											.	SRGAP1	146	.	0			c.A95T						.						78	83	81					12																	64377754		2203	4300	6503	SO:0001583	missense	57522	exon2			AACAACAAAAATG	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.95A>T	chr12.hg19:g.64377754A>T	ENSP00000347198:p.Gln32Leu	83.0	0.0		82.0	38.0	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	hg19	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	A	3.909	-0.020495	0.07634	.	.	ENSG00000196935	ENST00000355086;ENST00000357825	T;T	0.13778	2.56;2.56	4.89	3.71	0.42584	Fps/Fes/Fer/CIP4 homology (3);	0.000000	0.33591	U	0.004750	T	0.02267	0.0070	N	0.00065	-2.305	0.58432	D	0.999999	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.001	T	0.34054	-0.9844	9	.	.	.	.	11.075	0.48025	0.861:0.0:0.0:0.139	.	32;32	Q7Z6B7;Q7Z6B7-2	SRGP1_HUMAN;.	L	32	ENSP00000347198:Q32L;ENSP00000350480:Q32L	.	Q	+	2	0	SRGAP1	62664021	1.000000	0.71417	0.914000	0.36105	0.993000	0.82548	5.077000	0.64419	0.786000	0.33708	0.477000	0.44152	CAA	.	.		0.413	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			T	64377754	A	T	64377754	3	4	25	1	0	0	0	0	1	0	0	0	15160	130	5	4	101	4	SRGAP1	12	64377754	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	10811328	64377754	69474141	62	3410										
RNF17	56163	hgsc.bcm.edu	37	chr13	25378454	25378454	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cacaatcactaagaagtcacTttgaaaaaaatactacttta	3	8	2	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr13:25378454T>A	ENST00000255324.5	+	15	2030	c.1978T>A	c.(1978-1980)Ttt>Att	p.F660I	RNF17_ENST00000381921.1_Missense_Mutation_p.F660I|RNF17_ENST00000255325.6_Intron	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	660					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		AAGAAGTCACTTTGAAAAAAA	0.378																																					p.F660I		Atlas-SNP	.											.	RNF17	259	.	0			c.T1978A						.						88	87	87					13																	25378454		2200	4299	6499	SO:0001583	missense	56163	exon15			AGTCACTTTGAAA	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.1978T>A	chr13.hg19:g.25378454T>A	ENSP00000255324:p.Phe660Ile	103.0	0.0		81.0	29.0	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	hg19	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	T	9.150	1.015945	0.19355	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047	T;T	0.20598	2.06;2.06	5.49	-3.84	0.04256	.	1.261360	0.05418	N	0.543777	T	0.07593	0.0191	N	0.08118	0	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30563	-0.9974	10	0.17369	T	0.5	.	0.7527	0.00993	0.1635:0.2446:0.2884:0.3035	.	660;660	B7Z7S1;Q9BXT8	.;RNF17_HUMAN	I	660;660;519	ENSP00000255324:F660I;ENSP00000371346:F660I	ENSP00000255324:F660I	F	+	1	0	RNF17	24276454	0.002000	0.14202	0.056000	0.19401	0.580000	0.36256	0.156000	0.16382	-0.307000	0.08804	0.477000	0.44152	TTT	.	.		0.378	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		A	25378454	T	A	25378454	3	1	25	1	0	0	0	0	1	0	0	0	13476	1609	56	4	2036	4	RNF17	13	25378454	Missense_Mutation	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10		25378454	89791424	63	3411										
OLFM4	10562	hgsc.bcm.edu	37	chr13	53608515	53608515	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ttcaccggctccgtggatgaCcgtgggacctgccagtgctc	13	14	1	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr13:53608515C>T	ENST00000219022.2	+	2	315	c.237C>T	c.(235-237)gaC>gaT	p.D79D		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	79					cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		CCGTGGATGACCGTGGGACCT	0.478																																					p.D79D		Atlas-SNP	.											.	OLFM4	94	.	0			c.C237T						.						137	118	124					13																	53608515		2203	4300	6503	SO:0001819	synonymous_variant	10562	exon2			GGATGACCGTGGG	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.237C>T	chr13.hg19:g.53608515C>T		103.0	0.0		68.0	18.0	NM_006418	O95362|Q5VWG0|Q86T22	Silent	SNP	ENST00000219022.2	hg19	CCDS9440.1																																																																																			.	.		0.478	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418		T	53608515	C	T	53608515	2	4	25	1	0	0	0	0	0	0	0	1	10864	506	18	3		3	OLFM4	13	53608515	Silent	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	28230061	53608515	61561363	64	3412										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77836229	77836229	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tagcgcaaactctcgtcctgCaccaagaattgctgactcct	7	14	1	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr13:77836229C>T	ENST00000544440.2	-	11	1509	c.1492G>A	c.(1492-1494)Gca>Aca	p.A498T	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Missense_Mutation_p.A498T|MYCBP2_ENST00000407578.2_Missense_Mutation_p.A536T					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TCTCGTCCTGCACCAAGAATT	0.323																																					p.A536T		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.G1606A						.						87	84	85					13																	77836229		2203	4299	6502	SO:0001583	missense	23077	exon11			GTCCTGCACCAAG	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.1492G>A	chr13.hg19:g.77836229C>T	ENSP00000444596:p.Ala498Thr	44.0	0.0		44.0	13.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	C	27.0	4.791602	0.90367	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	D;D;D	0.81739	-1.53;-1.53;-1.53	5.29	5.29	0.74685	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.64402	D	0.000001	D	0.84061	0.5389	L	0.38175	1.15	0.58432	D	0.999998	D	0.63880	0.993	D	0.70935	0.971	D	0.83786	0.0228	10	0.44086	T	0.13	.	14.2069	0.65739	0.0:0.9263:0.0:0.0737	.	498	O75592	MYCB2_HUMAN	T	498;536;498	ENSP00000349892:A498T;ENSP00000384288:A536T;ENSP00000444596:A498T	ENSP00000349892:A498T	A	-	1	0	MYCBP2	76734230	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.341000	0.52151	2.468000	0.83385	0.591000	0.81541	GCA	.	.		0.323	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		T	77836229	C	T	77836229	3	4	25	1	0	0	0	0	1	0	0	0	10027	710	25	3	12722	3	MYCBP2	13	77836229	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	24227714	77836229	37333649	65	3413										
GZMH	2999	hgsc.bcm.edu	37	chr14	25076509	25076509	+	Frame_Shift_Del	DEL	C	C	-													0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	aagtgctcattgagacataaCcccagccagccacactgcac							TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr14:25076509delC	ENST00000216338.4	-	4	487	c.443delG	c.(442-444)ggtfs	p.G148fs	GZMH_ENST00000382548.4_Intron|GZMH_ENST00000557220.2_Intron|RP11-104E19.1_ENST00000555300.1_RNA|RP11-104E19.1_ENST00000557736.1_RNA	NM_033423.4	NP_219491.1	P20718	GRAH_HUMAN	granzyme H (cathepsin G-like 2, protein h-CCPX)	148	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)	membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)	12				GBM - Glioblastoma multiforme(265;0.0267)		TGAGACATAACCCCAGCCAGC	0.562																																					p.G148fs		Atlas-Indel,Pindel	.											GZMH,NS,carcinoma,0,1	GZMH	24	.	0			c.444delT						.						89	81	84					14																	25076509		2203	4300	6503	SO:0001589	frameshift_variant	2999	exon4			.	M72150	CCDS9632.1, CCDS59243.1	14q11.2	2003-10-20			ENSG00000100450	ENSG00000100450			4710	protein-coding gene	gene with protein product		116831		CTSGL2		2049336	Standard	NM_033423		Approved	CGL-2, CCP-X, CTLA1, CSP-C	uc001wpr.2	P20718	OTTHUMG00000140185	ENST00000216338.4:c.443delG	chr14.hg19:g.25076509delC	ENSP00000216338:p.Gly148fs	40.0	0.0		32.0	16.0	NM_033423	G3V2C5|Q6XGZ0|Q6XGZ1	Frame_Shift_Del	DEL	ENST00000216338.4	hg19	CCDS9632.1																																																																																			.	.		0.562	GZMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276538.2	NM_033423		-	25076509	C	-	25076509	7	5	25	1	0	1	0	1	0	0	0	0	6926	507	18	0	305	0	GZMH	14	25076509	Frame_Shift_Del	DEL	C	TCGA-5C-A9VH-01A-11D-A36X-10		25076509	82273031	66	3414										
SPATA7	55812	hgsc.bcm.edu	37	chr14	88857749	88857749	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	agcaacctctgtccttcccaGatatggtccaccgtgcctat	7	15	1	1	rs200551653		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr14:88857749G>T	ENST00000393545.4	+	2	333	c.44G>T	c.(43-45)aGa>aTa	p.R15I	SPATA7_ENST00000045347.7_Missense_Mutation_p.R15I|SPATA7_ENST00000554102.1_3'UTR|SPATA7_ENST00000356583.5_Missense_Mutation_p.R15I|SPATA7_ENST00000556553.1_Missense_Mutation_p.R15I	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	15					response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						GTCCTTCCCAGATATGGTCCA	0.348																																					p.R15I		Atlas-SNP	.											.	SPATA7	58	.	0			c.G44T						.						82	76	78					14																	88857749		2203	4300	6503	SO:0001583	missense	55812	exon2			TTCCCAGATATGG	AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"Leber congenital amaurosis 3"	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.44G>T	chr14.hg19:g.88857749G>T	ENSP00000377176:p.Arg15Ile	93.0	0.0		69.0	25.0	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Missense_Mutation	SNP	ENST00000393545.4	hg19	CCDS9883.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.504020	0.44558	.	.	ENSG00000042317	ENST00000556553;ENST00000393545;ENST00000356583;ENST00000553885;ENST00000045347	T;T;T;T;T	0.26067	1.76;1.76;1.76;1.76;1.76	4.97	-0.167	0.13347	.	0.806182	0.11408	N	0.567045	T	0.27933	0.0688	M	0.62723	1.935	0.45390	D	0.998374	B;P	0.37276	0.358;0.589	B;B	0.42422	0.299;0.387	T	0.21484	-1.0244	10	0.87932	D	0	-0.9809	5.1818	0.15163	0.2442:0.2811:0.4748:0.0	.	15;15	Q9P0W8-2;Q9P0W8	.;SPAT7_HUMAN	I	15	ENSP00000451128:R15I;ENSP00000377176:R15I;ENSP00000348991:R15I;ENSP00000450606:R15I;ENSP00000045347:R15I	ENSP00000045347:R15I	R	+	2	0	SPATA7	87927502	1.000000	0.71417	0.639000	0.29394	0.984000	0.73092	1.596000	0.36718	-0.014000	0.14175	-0.234000	0.12200	AGA	.	G|0.999;C|0.001		0.348	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1			T	88857749	G	T	88857749	3	4	25	1	0	0	0	0	1	0	0	0	15029	942	33	3	50	3	SPATA7	14	88857749	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	63781240	88857749	18491791	67	3415										
DUOXA2	405753	hgsc.bcm.edu	37	chr15	45410034	45410034	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ccaggagagagggggctcacCtcttatcctcggcgacccac	12	15	2	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr15:45410034C>T	ENST00000323030.5	+	6	1175	c.890C>T	c.(889-891)cCt>cTt	p.P297L	DUOXA1_ENST00000267803.4_Intron|DUOXA1_ENST00000430224.2_Intron|DUOXA1_ENST00000559014.1_Intron|DUOXA1_ENST00000558996.1_3'UTR	NM_207581.3	NP_997464.2	Q1HG44	DOXA2_HUMAN	dual oxidase maturation factor 2	297					hydrogen peroxide metabolic process (GO:0042743)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)							all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		GGGGGCTCACCTCTTATCCTC	0.607											OREG0023102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P297L		Atlas-SNP	.											.	DUOXA2	38	.	0			c.C890T						.						63	71	68					15																	45410034		2198	4298	6496	SO:0001583	missense	405753	exon6			GCTCACCTCTTAT	BX537581	CCDS10118.2	15q21.1	2008-10-30		2006-07-25	ENSG00000140274	ENSG00000140274			32698	protein-coding gene	gene with protein product		612772				16651268	Standard	NM_207581		Approved		uc001zuo.3	Q1HG44	OTTHUMG00000131354	ENST00000323030.5:c.890C>T	chr15.hg19:g.45410034C>T	ENSP00000319705:p.Pro297Leu	106.0	0.0	931	77.0	39.0	NM_207581	B2RPI9|H0YNQ6	Missense_Mutation	SNP	ENST00000323030.5	hg19	CCDS10118.2	.	.	.	.	.	.	.	.	.	.	C	14.47	2.546483	0.45383	.	.	ENSG00000140274	ENST00000323030	T	0.55760	0.5	5.26	4.34	0.51931	.	0.408629	0.27558	N	0.018821	T	0.28034	0.0691	N	0.08118	0	0.29538	N	0.852329	P	0.40875	0.731	B	0.33750	0.169	T	0.11792	-1.0573	10	0.28530	T	0.3	-5.4342	11.7399	0.51786	0.1756:0.8244:0.0:0.0	.	297	Q1HG44	DOXA2_HUMAN	L	297	ENSP00000319705:P297L	ENSP00000319705:P297L	P	+	2	0	DUOXA2	43197326	0.000000	0.05858	0.039000	0.18376	0.036000	0.12997	0.381000	0.20619	1.336000	0.45506	0.561000	0.74099	CCT	.	.		0.607	DUOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254142.1	NM_207581		T	45410034	C	T	45410034	3	4	25	1	0	0	0	0	1	0	0	0	4805	681	24	3	912	3	DUOXA2	15	45410034	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10		45410034	57121358	68	3416										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75968199	75968199	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gatgatgacgctgaacatgtTggcctcaaggaagctcagga	13	8	2	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr15:75968199T>C	ENST00000308508.5	-	10	6753	c.6661A>G	c.(6661-6663)Aac>Gac	p.N2221D	CTD-2026K11.1_ENST00000569467.1_RNA|AC105020.1_ENST00000435356.1_5'Flank	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	2221	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTGAACATGTTGGCCTCAAGG	0.617																																					p.N2221D		Atlas-SNP	.											.	CSPG4	175	.	0			c.A6661G						.						92	89	90					15																	75968199		2197	4294	6491	SO:0001583	missense	1464	exon10			ACATGTTGGCCTC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.6661A>G	chr15.hg19:g.75968199T>C	ENSP00000312506:p.Asn2221Asp	38.0	0.0		30.0	9.0	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	hg19	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	T	17.30	3.355422	0.61293	.	.	ENSG00000173546	ENST00000308508;ENST00000537176	T	0.20738	2.05	5.33	4.18	0.49190	.	0.077653	0.52532	D	0.000062	T	0.31389	0.0795	L	0.49126	1.545	0.38925	D	0.957817	D	0.67145	0.996	P	0.57204	0.815	T	0.04635	-1.0937	10	0.38643	T	0.18	.	10.6126	0.45432	0.0:0.0:0.3099:0.6901	.	2221	Q6UVK1	CSPG4_HUMAN	D	2221;253	ENSP00000312506:N2221D	ENSP00000312506:N2221D	N	-	1	0	CSPG4	73755254	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.418000	0.34782	0.842000	0.35045	0.459000	0.35465	AAC	.	.		0.617	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		C	75968199	T	C	75968199	3	2	25	1	0	0	0	0	1	0	0	0	3962	1812	63	2	311	2	CSPG4	15	75968199	Missense_Mutation	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10	30558165	75968199	26563193	69	3417										
GP2	2813	hgsc.bcm.edu	37	chr16	20335564	20335564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cccatacgaactggcttcaaTggggtttccataacctggga	10	11	1	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr16:20335564T>C	ENST00000381362.4	-	3	185	c.109A>G	c.(109-111)Att>Gtt	p.I37V	GP2_ENST00000381360.5_Intron|GP2_ENST00000341642.5_Intron|GP2_ENST00000302555.5_Missense_Mutation_p.I37V|GP2_ENST00000573897.1_5'Flank	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	37					antigen transcytosis by M cells in mucosal-associated lymphoid tissue (GO:0002412)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						CTGGCTTCAATGGGGTTTCCA	0.522																																					p.I37V		Atlas-SNP	.											.	GP2	122	.	0			c.A109G						.						40	38	39					16																	20335564		2203	4300	6503	SO:0001583	missense	2813	exon3			CTTCAATGGGGTT	U36221	CCDS10582.2, CCDS42128.1, CCDS45432.1, CCDS45433.1	16p12.3	2008-02-05			ENSG00000169347	ENSG00000169347			4441	protein-coding gene	gene with protein product		602977				9605860	Standard	XM_005255259		Approved		uc002dgw.3	P55259	OTTHUMG00000131489	ENST00000381362.4:c.109A>G	chr16.hg19:g.20335564T>C	ENSP00000370767:p.Ile37Val	199.0	0.0		143.0	65.0	NM_001502	A6NFM9|A6NJA8|Q13338|Q9UIF1	Missense_Mutation	SNP	ENST00000381362.4	hg19	CCDS42128.1	.	.	.	.	.	.	.	.	.	.	t	5.609	0.297047	0.10622	.	.	ENSG00000169347	ENST00000302555;ENST00000381362	D;D	0.99226	-5.59;-5.59	4.78	-9.56	0.00566	.	.	.	.	.	D	0.93572	0.7948	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.0	D	0.90471	0.4453	9	0.18710	T	0.47	9.8097	2.3862	0.04366	0.2586:0.212:0.399:0.1304	.	37;37	P55259-3;P55259	.;GP2_HUMAN	V	37	ENSP00000304044:I37V;ENSP00000370767:I37V	ENSP00000304044:I37V	I	-	1	0	GP2	20243065	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.459000	0.01000	-2.245000	0.00705	-1.325000	0.01285	ATT	.	.		0.522	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295		C	20335564	T	C	20335564	3	2	25	1	0	0	0	0	1	0	0	0	6590	1464	51	2	1544	2	GP2	16	20335564	Missense_Mutation	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10		20335564	70019189	70	3418										
ITFG1	81533	hgsc.bcm.edu	37	chr16	47292650	47292650	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gcactacaatgtccaagattCcctggaaaaaaacaaacaaa	5	10	0	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr16:47292650C>A	ENST00000320640.6	-	12	1451	c.1223G>T	c.(1222-1224)gGa>gTa	p.G408V	ITFG1_ENST00000568047.1_5'UTR|ITFG1_ENST00000544001.2_Splice_Site_p.G295V	NM_030790.3	NP_110417.2	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	408						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	19		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				GTCCAAGATTCCCTGGAAAAA	0.274																																					p.G408V		Atlas-SNP	.											.	ITFG1	49	.	0			c.G1223T						.						63	64	63					16																	47292650		2200	4296	6496	SO:0001630	splice_region_variant	81533	exon12			AAGATTCCCTGGA	AF503339	CCDS10728.1	16q12.1	2008-02-05			ENSG00000129636	ENSG00000129636			30697	protein-coding gene	gene with protein product	"T cell immunomodulatory protein"	611803				12598909	Standard	NM_030790		Approved	CDA08, TIP	uc002eet.3	Q8TB96	OTTHUMG00000133103	ENST00000320640.6:c.1222-1G>T	chr16.hg19:g.47292650C>A		40.0	0.0		42.0	8.0	NM_030790	Q96SR4|Q9BRE2|Q9H2V9	Missense_Mutation	SNP	ENST00000320640.6	hg19	CCDS10728.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.451052	0.84209	.	.	ENSG00000129636	ENST00000320640;ENST00000537184;ENST00000542691;ENST00000544001	T;T	0.80824	-1.42;0.6	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.91670	0.7367	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.92720	0.6190	10	0.87932	D	0	-0.4478	19.2105	0.93753	0.0:1.0:0.0:0.0	.	295;408	F5GXC5;Q8TB96	.;TIP_HUMAN	V	408;68;153;295	ENSP00000319918:G408V;ENSP00000441062:G295V	ENSP00000319918:G408V	G	-	2	0	ITFG1	45850151	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.330000	0.79181	2.712000	0.92718	0.585000	0.79938	GGA	.	.		0.274	ITFG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256768.3	NM_030790	Missense_Mutation	A	47292650	C	A	47292650	5	1	25	1	0	0	0	0	0	0	1	0	7878	869	30	3	643	3	ITFG1	16	47292650	Splice_Site	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	26957086	47292650	43062103	71	3419										
VPS4A	27183	hgsc.bcm.edu	37	chr16	69356497	69356497	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tcgcaccaaccccagcatgaTgattgatgacctcctgactc	7	15	0	5			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr16:69356497T>C	ENST00000254950.11	+	10	1262	c.1106T>C	c.(1105-1107)aTg>aCg	p.M369T	COG8_ENST00000564419.1_Intron	NM_013245.2	NP_037377.1			vacuolar protein sorting 4 homolog A (S. cerevisiae)											NS(1)|central_nervous_system(1)|large_intestine(2)|lung(3)	7		Ovarian(137;0.101)				CCCAGCATGATGATTGATGAC	0.587																																					p.M369T		Atlas-SNP	.											.	VPS4A	18	.	0			c.T1106C						.						85	88	87					16																	69356497		2058	4222	6280	SO:0001583	missense	27183	exon10			GCATGATGATTGA	AF112215	CCDS45517.1	16q23.1	2010-04-21	2006-04-04		ENSG00000132612	ENSG00000132612		"ATPases / AAA-type"	13488	protein-coding gene	gene with protein product		609982	"vacuolar protein sorting 4A (yeast homolog)", "vacuolar protein sorting 4A (yeast)"			10637304, 11563910	Standard	NM_013245		Approved	VPS4, VPS4-1, FLJ22197, SKD2, SKD1, SKD1A	uc002eww.3	Q9UN37		ENST00000254950.11:c.1106T>C	chr16.hg19:g.69356497T>C	ENSP00000254950:p.Met369Thr	85.0	0.0		64.0	5.0	NM_013245		Missense_Mutation	SNP	ENST00000254950.11	hg19	CCDS45517.1	.	.	.	.	.	.	.	.	.	.	T	0.217	-1.031696	0.02029	.	.	ENSG00000132612	ENST00000254950	D	0.94687	-3.49	5.62	4.52	0.55395	.	0.202829	0.64402	N	0.000016	D	0.83732	0.5318	N	0.05199	-0.095	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.74842	-0.3527	10	0.08179	T	0.78	-13.6267	8.6393	0.33968	0.0:0.1558:0.0:0.8442	.	369	Q9UN37	VPS4A_HUMAN	T	369	ENSP00000254950:M369T	ENSP00000254950:M369T	M	+	2	0	VPS4A	67913998	0.956000	0.32656	0.975000	0.42487	0.022000	0.10575	2.605000	0.46283	0.949000	0.37715	-0.290000	0.09829	ATG	.	.		0.587	VPS4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430563.3	NM_013245		C	69356497	T	C	69356497	3	2	25	1	0	0	0	0	1	0	0	0	17227	1464	51	2	1144	2	VPS4A	16	69356497	Missense_Mutation	SNP	T	TCGA-5C-A9VH-01A-11D-A36X-10	22063847	69356497	20998256	72	3420										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81232485	81232485	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gctccaccaagtggactgtaAtgtttctggagattgtagag	12	7	1	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr16:81232485A>G	ENST00000525539.1	-	0	1324				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GTGGACTGTAATGTTTCTGGA	0.557																																					p.I442T		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T1325C						.						176	181	179					16																	81232485		1991	4143	6134			114780	exon7			ACTGTAATGTTTC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		chr16.hg19:g.81232485A>G		191.0	0.0		145.0	43.0	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.32	1.316534	0.23908	.	.	ENSG00000166473	ENST00000337114	T	0.01455	4.87	4.98	4.98	0.66077	Egg jelly receptor, REJ-like (1);	0.573831	0.17233	N	0.181845	T	0.03263	0.0095	.	.	.	0.21740	N	0.999564	P;B	0.35272	0.493;0.361	B;B	0.39258	0.295;0.036	T	0.33137	-0.9880	9	0.87932	D	0	-5.6646	14.6886	0.69068	1.0:0.0:0.0:0.0	.	442;442	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	T	442	ENSP00000337397:I442T	ENSP00000337397:I442T	I	-	2	0	PKD1L2	79789986	0.979000	0.34478	0.032000	0.17829	0.010000	0.07245	6.830000	0.75319	1.884000	0.54569	0.448000	0.29417	ATT	.	.		0.557	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			G	81232485	A	G	81232485	1	3	25	0	1	0	0	0	0	0	0	0	11974	101	4	2		2	PKD1L2	16	81232485	RNA	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	11875988	81232485	9122268	73	3421										
ATAD5	79915	hgsc.bcm.edu	37	chr17	29162604	29162604	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cagagagggaaacactcaaaAgaaagaaacaacctttttct	7	8	2	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr17:29162604A>G	ENST00000321990.4	+	2	1883	c.1505A>G	c.(1504-1506)aAg>aGg	p.K502R	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	502					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AACACTCAAAAGAAAGAAACA	0.303																																					p.K502R		Atlas-SNP	.											.	ATAD5	150	.	0			c.A1505G						.						52	60	57					17																	29162604		2202	4295	6497	SO:0001583	missense	79915	exon2			CTCAAAAGAAAGA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.1505A>G	chr17.hg19:g.29162604A>G	ENSP00000313171:p.Lys502Arg	240.0	0.0		205.0	87.0	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	A	7.096	0.573139	0.13623	.	.	ENSG00000176208	ENST00000321990	T	0.09723	2.95	5.85	0.743	0.18347	.	0.649731	0.14873	N	0.293452	T	0.08492	0.0211	L	0.53249	1.67	0.09310	N	1	B;P	0.36222	0.418;0.544	B;B	0.33521	0.165;0.079	T	0.25779	-1.0122	10	0.51188	T	0.08	.	1.6687	0.02807	0.333:0.1141:0.1114:0.4415	.	502;502	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	R	502	ENSP00000313171:K502R	ENSP00000313171:K502R	K	+	2	0	ATAD5	26186730	0.087000	0.21565	0.845000	0.33349	0.852000	0.48524	0.711000	0.25764	0.410000	0.25675	0.533000	0.62120	AAG	.	.		0.303	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		G	29162604	A	G	29162604	3	3	25	1	0	0	0	0	1	0	0	0	1076	72	3	2	1511	2	ATAD5	17	29162604	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10		29162604	52032606	74	3422										
PIGW	284098	hgsc.bcm.edu	37	chr17	34893442	34893442	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	aaaactgagctctatgggacAggagcaatggattttggagt	13	5	1	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr17:34893442A>G	ENST00000592983.1	+	2	1072	c.492A>G	c.(490-492)acA>acG	p.T164T	MYO19_ENST00000590081.1_Intron|MYO19_ENST00000544606.1_5'Flank|MYO19_ENST00000268852.9_5'Flank|MYO19_ENST00000431794.3_5'Flank|PIGW_ENST00000328396.2_Silent_p.T164T|MYO19_ENST00000586007.1_5'Flank			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	164					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCTATGGGACAGGAGCAATGG	0.433																																					p.T164T		Atlas-SNP	.											.	PIGW	50	.	0			c.A492G						.						207	216	213					17																	34893442		2203	4300	6503	SO:0001819	synonymous_variant	284098	exon2			TGGGACAGGAGCA	AB097818	CCDS11313.1	17q21.1	2014-05-06	2006-06-28		ENSG00000184886	ENSG00000277161		"Phosphatidylinositol glycan anchor biosynthesis"	23213	protein-coding gene	gene with protein product		610275	"phosphatidylinositol glycan, class W"			14517336, 12714589	Standard	XM_005257238		Approved	Gwt1, FLJ37433	uc002hmz.1	Q7Z7B1	OTTHUMG00000188438	ENST00000592983.1:c.492A>G	chr17.hg19:g.34893442A>G		135.0	0.0		102.0	32.0	NM_178517	Q8N9G3	Silent	SNP	ENST00000592983.1	hg19	CCDS11313.1																																																																																			.	.		0.433	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517		G	34893442	A	G	34893442	2	3	25	1	0	0	0	0	0	0	0	1	11911	175	7	2		2	PIGW	17	34893442	Silent	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	5730838	34893442	46301768	75	3423										
SOCS7	30837	hgsc.bcm.edu	37	chr17	36508540	36508541	+	Missense_Mutation	DNP	GC	GC	AG													0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ctgctcggaagaggagctcaGcagcccgggtcgcggaggag							TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr17:36508540_36508541GC>AG	ENST00000577233.1	+	1	413_414	c.413_414GC>AG	c.(412-414)aGC>aAG	p.S138K	SOCS7_ENST00000331159.5_Missense_Mutation_p.S138K	NM_014598.2	NP_055413.1	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	138	Mediates interaction with SORBS3.				fat cell differentiation (GO:0045444)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of signal transduction (GO:0009968)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			central_nervous_system(1)|endometrium(1)|kidney(1)|prostate(1)|skin(5)	9	Breast(7;3.47e-17)					GAGGAGCTCAGCAGCCCGGGTC	0.683																																					p.S138N|p.S138R		Atlas-SNP	.											.	SOCS7	22	.	0			c.G413A|c.C414G						.																																			SO:0001583	missense	30837	exon1			AGCTCAGCAGCCC|GCTCAGCAGCCCG	AB005216	CCDS32637.1	17q12	2014-08-12			ENSG00000274211	ENSG00000274211		"Suppressors of cytokine signaling", "SH2 domain containing"	29846	protein-coding gene	gene with protein product	"Nck, Ash and phospholipase C binding protein", "NCK-associated protein 4"	608788				9344857, 12076535	Standard	XM_005257264		Approved	NAP4, NCKAP4	uc002hqa.3	O14512	OTTHUMG00000188546	Exception_encountered	chr17.hg19:g.36508540_36508541delinsAG	ENSP00000464034:p.Ser138Lys	217.0|220.0	0.0		194.0|189.0	81.0|80.0	NM_014598	A2VCU2|Q0IJ63	Missense_Mutation	SNP	ENST00000577233.1	hg19	CCDS32637.1																																																																																			.	.		0.683	SOCS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440486.4	XM_371052		AG	36508541	GC	AG	36508540	3	1	25	1	0	0	0	0	1	0	0	0	14934	971	34	3	415	3	SOCS7	17	36508540	Missense_Mutation	DNP	GC	TCGA-5C-A9VH-01A-11D-A36X-10	1615098	36508540	44686670	76	3424										
BRCA1	672	hgsc.bcm.edu	37	chr17	41246777	41246777	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ctaccctgatacttttctggAtgcctctcagctgcacgctt	7	14	2	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr17:41246777A>G	ENST00000357654.3	-	10	889	c.771T>C	c.(769-771)caT>caC	p.H257H	BRCA1_ENST00000346315.3_Silent_p.H257H|BRCA1_ENST00000493795.1_Silent_p.H210H|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000491747.2_Silent_p.H257H|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000471181.2_Silent_p.H257H|BRCA1_ENST00000309486.4_5'UTR|BRCA1_ENST00000468300.1_Silent_p.H257H|BRCA1_ENST00000354071.3_Silent_p.H257H|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000591849.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	257					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		ACTTTTCTGGATGCCTCTCAG	0.423			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.H257H		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.T771C						.						97	89	92					17																	41246777		2203	4300	6503	SO:0001819	synonymous_variant	672	exon9	Familial Cancer Database		TTCTGGATGCCTC	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.771T>C	chr17.hg19:g.41246777A>G		71.0	0.0		53.0	25.0	NM_007298	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	hg19	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	A	6.620	0.482881	0.12581	.	.	ENSG00000012048	ENST00000473961	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	T	0.61035	0.2315	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59511	-0.7441	4	.	.	.	.	10.1432	0.42747	0.8328:0.1672:0.0:0.0	.	.	.	.	T	123	.	.	I	-	2	0	BRCA1	38500303	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	2.912000	0.48782	2.116000	0.64780	0.533000	0.62120	ATC	.	.		0.423	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		G	41246777	A	G	41246777	2	3	25	1	0	0	0	0	0	0	0	1	1500	330	12	2		2	BRCA1	17	41246777	Silent	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	4738237	41246777	39948433	77	3425										
HELZ	9931	hgsc.bcm.edu	37	chr17	65174829	65174829	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tataaagaaggtcatgtaacCgtgactgatagttgctcttg	10	6	2	3			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr17:65174829C>G	ENST00000358691.5	-	13	1542	c.1376G>C	c.(1375-1377)cGg>cCg	p.R459P	HELZ_ENST00000580168.1_Missense_Mutation_p.R459P	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	459						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R459L(1)		NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					GTCATGTAACCGTGACTGATA	0.378																																					p.R459P		Atlas-SNP	.											HELZ,NS,carcinoma,0,2	HELZ	160	.	1	Substitution - Missense(1)	kidney(1)	c.G1376C						.						121	115	117					17																	65174829		1853	4101	5954	SO:0001583	missense	9931	exon13			TGTAACCGTGACT	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.1376G>C	chr17.hg19:g.65174829C>G	ENSP00000351524:p.Arg459Pro	126.0	0.0		78.0	21.0	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.054269	0.55218	.	.	ENSG00000198265	ENST00000358691	D	0.86030	-2.06	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.92688	0.7676	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.983	D	0.92372	0.5906	10	0.87932	D	0	-20.6865	20.6525	0.99598	0.0:1.0:0.0:0.0	.	459;459	B7ZLW2;P42694	.;HELZ_HUMAN	P	459	ENSP00000351524:R459P	ENSP00000351524:R459P	R	-	2	0	HELZ	62605291	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.385000	0.79763	2.890000	0.99128	0.585000	0.79938	CGG	.	.		0.378	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		G	65174829	C	G	65174829	3	3	25	1	0	0	0	0	1	0	0	0	7058	652	23	4	4536	4	HELZ	17	65174829	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	23928052	65174829	16020381	78	3426										
CBX4	8535	hgsc.bcm.edu	37	chr17	77808906	77808906	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gcaggtggggctgggcgcctCcttgtggccgccctggtact	17	13	0	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr17:77808906C>A	ENST00000269397.4	-	5	712	c.535G>T	c.(535-537)Gag>Tag	p.E179*	CBX4_ENST00000448310.1_3'UTR	NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	179	Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			CTGGGCGCCTCCTTGTGGCCG	0.662											OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E179X		Atlas-SNP	.											.	CBX4	40	.	0			c.G535T						.						56	58	57					17																	77808906		2203	4300	6503	SO:0001587	stop_gained	8535	exon5			GCGCCTCCTTGTG	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"NS5ATP1-binding protein 16", "Pc class 2 homolog (Drosophila)"	603079	"chromobox homolog 4 (Drosophila Pc class)"			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.535G>T	chr17.hg19:g.77808906C>A	ENSP00000269397:p.Glu179*	61.0	0.0	1178	49.0	17.0	NM_003655	B1PJR7|Q6TPI8|Q96C04	Nonsense_Mutation	SNP	ENST00000269397.4	hg19	CCDS32758.1	.	.	.	.	.	.	.	.	.	.	c	37	6.078027	0.97262	.	.	ENSG00000141582	ENST00000269397	.	.	.	4.16	4.16	0.48862	.	0.303964	0.25511	U	0.030180	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	0.2304	16.4918	0.84203	0.0:1.0:0.0:0.0	.	.	.	.	X	179	.	ENSP00000269397:E179X	E	-	1	0	CBX4	75423501	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.437000	0.66544	1.891000	0.54761	0.298000	0.19748	GAG	.	.		0.662	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655		A	77808906	C	A	77808906	4	1	25	1	0	0	0	0	0	1	0	0	2722	864	30	3	1151	3	CBX4	17	77808906	Nonsense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	12634077	77808906	3386304	79	3427										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48604747	48604747	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	agcatcaaagaaacaccttgCtggattgaaattcacttaca	6	9	2	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr18:48604747C>G	ENST00000342988.3	+	12	2107	c.1569C>G	c.(1567-1569)tgC>tgG	p.C523W	SMAD4_ENST00000588745.1_Missense_Mutation_p.C427W|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Missense_Mutation_p.C523W	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	523	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.C523W(2)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		AAACACCTTGCTGGATTGAAA	0.478																																					p.C523W		Atlas-SNP	.											SMAD4,NS,carcinoma,0,3	SMAD4	822	.	40	Whole gene deletion(36)|Substitution - Missense(2)|Unknown(2)	pancreas(27)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|biliary_tract(1)|oesophagus(1)	c.C1569G						.						93	90	91					18																	48604747		2203	4300	6503	SO:0001583	missense	4089	exon12			ACCTTGCTGGATT	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1569C>G	chr18.hg19:g.48604747C>G	ENSP00000341551:p.Cys523Trp	103.0	0.0		52.0	33.0	NM_005359	A8K405	Missense_Mutation	SNP	ENST00000342988.3	hg19	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	13.63	2.295153	0.40594	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.98264	-4.83;-4.83	6.08	3.39	0.38822	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.085248	0.85682	D	0.000000	D	0.99029	0.9668	H	0.95539	3.685	0.80722	D	1	D	0.64830	0.994	D	0.64595	0.927	D	0.98837	1.0753	10	0.87932	D	0	.	9.9615	0.41699	0.0:0.7371:0.0:0.2629	.	523	Q13485	SMAD4_HUMAN	W	523	ENSP00000341551:C523W;ENSP00000381452:C523W	ENSP00000341551:C523W	C	+	3	2	SMAD4	46858745	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.497000	0.35649	0.475000	0.27415	0.655000	0.94253	TGC	.	.		0.478	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48604747	C	G	48604747	3	3	25	1	0	0	0	0	1	0	0	0	14775	805	28	4	1611	4	SMAD4	18	48604747	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10		48604747	29472501	80	3428										
CTDP1	9150	hgsc.bcm.edu	37	chr18	77474844	77474844	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ccagcgacagcgagagcagcAgtgagtccgagggcacgaag	16	11	0	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr18:77474844A>T	ENST00000299543.7	+	8	1531	c.1384A>T	c.(1384-1386)Agt>Tgt	p.S462C	CTDP1_ENST00000075430.7_Missense_Mutation_p.S462C	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	462	Ser-rich.				exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		CGAGAGCAGCAGTGAGTCCGA	0.677																																					p.S462C		Atlas-SNP	.											.	CTDP1	67	.	0			c.A1384T						.						13	14	13					18																	77474844		2186	4277	6463	SO:0001583	missense	9150	exon8			AGCAGCAGTGAGT	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.1384A>T	chr18.hg19:g.77474844A>T	ENSP00000299543:p.Ser462Cys	152.0	0.0		58.0	31.0	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	hg19	CCDS12017.1	.	.	.	.	.	.	.	.	.	.	A	11.81	1.748712	0.30955	.	.	ENSG00000060069	ENST00000299543;ENST00000075430	T;T	0.11604	2.76;2.76	3.1	1.87	0.25490	.	1.094360	0.06762	N	0.781942	T	0.15219	0.0367	L	0.39898	1.24	0.21967	N	0.999445	P;D;P	0.63046	0.954;0.992;0.923	P;P;B	0.53146	0.54;0.719;0.338	T	0.18935	-1.0321	10	0.59425	D	0.04	-0.3262	3.6391	0.08160	0.5782:0.2005:0.2213:0.0	.	343;462;462	Q9Y5B0-3;Q9Y5B0-4;Q9Y5B0	.;.;CTDP1_HUMAN	C	462	ENSP00000299543:S462C;ENSP00000075430:S462C	ENSP00000075430:S462C	S	+	1	0	CTDP1	75575832	0.266000	0.24112	0.972000	0.41901	0.170000	0.22686	0.638000	0.24674	0.224000	0.20940	-0.460000	0.05396	AGT	.	.		0.677	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715		T	77474844	A	T	77474844	3	4	25	1	0	0	0	0	1	0	0	0	4004	188	7	4	1414	4	CTDP1	18	77474844	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10	28870097	77474844	602404	81	3429										
LPPR3	79948	hgsc.bcm.edu	37	chr19	813388	813388	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ctcctcttcctcttcgtcctCctcctcttcctcctcctccg	2	23	3	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr19:813388C>T	ENST00000520876.3	-	8	1417	c.1339G>A	c.(1339-1341)Gag>Aag	p.E447K	MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Missense_Mutation_p.E475K	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		447	Glu-rich.					integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										tcttcgtcctcctcctcttcc	0.756																																					p.E475K		Atlas-SNP	.											.	.	.	.	0			c.G1423A						.						2	2	2					19																	813388		1593	3295	4888	SO:0001583	missense	0	exon7			CGTCCTCCTCCTC																												ENST00000520876.3:c.1339G>A	chr19.hg19:g.813388C>T	ENSP00000430297:p.Glu447Lys	36.0	0.0		34.0	13.0	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	hg19	CCDS58636.1	.	.	.	.	.	.	.	.	.	.	c	0.008	-1.883951	0.00532	.	.	ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876	T;T	0.20463	2.07;2.07	.	.	.	.	0.615099	0.14392	U	0.322434	T	0.15046	0.0363	L	0.34521	1.04	0.24542	N	0.994062	B;B;B	0.30281	0.275;0.227;0.275	B;B;B	0.34301	0.109;0.179;0.087	T	0.21861	-1.0233	8	0.51188	T	0.08	-15.4211	.	.	.	.	448;447;475	Q6T4P5-2;Q6T4P5;Q6T4P5-3	.;LPPR3_HUMAN;.	K	448;475;447	ENSP00000352962:E475K;ENSP00000430297:E447K	ENSP00000300947:E448K	E	-	1	0	AC006273.1	764388	0.957000	0.32711	0.996000	0.52242	0.177000	0.22998	4.203000	0.58453	0.149000	0.19098	0.152000	0.16155	GAG	.	.		0.756	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3			T	813388	C	T	813388	3	4	25	1	0	0	0	0	1	0	0	0	8935	864	30	3	821	3	LPPR3	19	813388	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10		813388	58315595	82	3430										
NFIC	4782	hgsc.bcm.edu	37	chr19	3449113	3449113	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ccagcttcacccagcaccacCggcccgtcatcgccgtgcac	8	21	2	0			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr19:3449113C>T	ENST00000443272.2	+	7	1111	c.1060C>T	c.(1060-1062)Cgg>Tgg	p.R354W	NFIC_ENST00000586919.1_Missense_Mutation_p.R321W|NFIC_ENST00000589123.1_Missense_Mutation_p.R345W|NFIC_ENST00000346156.5_Missense_Mutation_p.R321W|NFIC_ENST00000395111.3_Missense_Mutation_p.R345W|NFIC_ENST00000590282.1_Missense_Mutation_p.R354W|NFIC_ENST00000341919.3_Missense_Mutation_p.R354W	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	354					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		CCAGCACCACCGGCCCGTCAT	0.682																																					p.R354W		Atlas-SNP	.											.	NFIC	36	.	0			c.C1060T						.						77	55	62					19																	3449113		2203	4300	6503	SO:0001583	missense	4782	exon7			CACCACCGGCCCG	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.1060C>T	chr19.hg19:g.3449113C>T	ENSP00000396843:p.Arg354Trp	82.0	0.0		65.0	29.0	NM_001245004	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	hg19	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.732683	0.69189	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T;T	0.51574	0.73;0.7;0.7;0.7	3.96	2.87	0.33458	.	0.000000	0.64402	D	0.000001	T	0.60702	0.2289	M	0.63843	1.955	0.40665	D	0.982162	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.997;0.994;0.996;0.917;0.997	T	0.57585	-0.7786	10	0.35671	T	0.21	.	9.4621	0.38792	0.3995:0.6005:0.0:0.0	.	354;354;345;354;345	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	W	345;345;321;354;354;354	ENSP00000396843:R345W;ENSP00000378543:R345W;ENSP00000301935:R321W;ENSP00000342194:R354W	ENSP00000269778:R354W	R	+	1	2	NFIC	3400113	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.175000	0.50855	0.581000	0.29539	0.561000	0.74099	CGG	.	.		0.682	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597		T	3449113	C	T	3449113	3	4	25	1	0	0	0	0	1	0	0	0	10381	643	23	1	1093	1	NFIC	19	3449113	Missense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	2635725	3449113	55679870	83	3431										
FCER2	2208	hgsc.bcm.edu	37	chr19	7763670	7763670	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	agcccagcccacagagcggcGgtcaccagccccagcagcac	11	19	1	1	rs376326260		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr19:7763670G>T	ENST00000346664.5	-	3	305	c.93C>A	c.(91-93)acC>acA	p.T31T	FCER2_ENST00000360067.4_Silent_p.T30T|FCER2_ENST00000597921.1_Silent_p.T31T	NM_001220500.1|NM_002002.4	NP_001207429.1|NP_001993.2	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor for (CD23)	31					Notch signaling pathway (GO:0007219)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	10						ACAGAGCGGCGGTCACCAGCC	0.652																																					p.T31T		Atlas-SNP	.											.	FCER2	19	.	0			c.C93A						.						44	39	41					19																	7763670		2196	4296	6492	SO:0001819	synonymous_variant	2208	exon3			AGCGGCGGTCACC	M15059	CCDS12184.1	19p13.3	2011-08-30	2006-03-09			ENSG00000104921		"C-type lectin domain containing", "CD molecules"	3612	protein-coding gene	gene with protein product		151445	"Fc fragment of IgE, low affinity II, receptor for (CD23A)"	CD23A, FCE2			Standard	NM_002002		Approved	CLEC4J, CD23	uc002mhm.2	P06734		ENST00000346664.5:c.93C>A	chr19.hg19:g.7763670G>T		113.0	0.0		101.0	35.0	NM_002002		Silent	SNP	ENST00000346664.5	hg19	CCDS12184.1																																																																																			.	.		0.652	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002		T	7763670	G	T	7763670	2	4	25	1	0	0	0	0	0	0	0	1	5784	1103	39	1		1	FCER2	19	7763670	Silent	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	4314557	7763670	51365313	84	3432										
C19orf57	79173	hgsc.bcm.edu	37	chr19	14006250	14006250	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	ggaacaggtcccaatttgccCtctggctcctcagggtgatg	12	12	2	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr19:14006250C>T	ENST00000586783.1	-	2	140	c.141G>A	c.(139-141)gaG>gaA	p.E47E	C19orf57_ENST00000346736.2_Silent_p.E47E|C19orf57_ENST00000454313.1_Silent_p.E47E|C19orf57_ENST00000591586.1_Silent_p.E47E			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	47					multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			CCAATTTGCCCTCTGGCTCCT	0.567																																					p.E47E		Atlas-SNP	.											.	C19orf57	34	.	0			c.G141A						.						188	184	186					19																	14006250		2203	4300	6503	SO:0001819	synonymous_variant	79173	exon3			TTTGCCCTCTGGC	BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.141G>A	chr19.hg19:g.14006250C>T		163.0	0.0		113.0	44.0	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Silent	SNP	ENST00000586783.1	hg19																																																																																				.	.		0.567	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323		T	14006250	C	T	14006250	2	4	25	1	0	0	0	0	0	0	0	1	1941	680	24	3		3	C19orf57	19	14006250	Silent	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	6242580	14006250	45122733	85	3433										
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39915656	39915656	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	agagcctggctcggcggcagGggcctgggggaggggccccc	21	13	0	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr19:39915656G>C	ENST00000409794.3	+	19	4733	c.3883G>C	c.(3883-3885)Ggg>Cgg	p.G1295R	CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000458508.2_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.G1266R|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000409797.2_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	1295					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TCGGCGGCAGGGGCCTGGGGG	0.716																																					p.G1295R		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G3883C						.						19	22	21					19																	39915656		2189	4278	6467	SO:0001583	missense	64857	exon19			CGGCAGGGGCCTG	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.3883G>C	chr19.hg19:g.39915656G>C	ENSP00000386733:p.Gly1295Arg	65.0	0.0		40.0	19.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	hg19	CCDS33022.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.35|19.35	3.811229|3.811229	0.70797|0.70797	.|.	.|.	ENSG00000090924|ENSG00000090924	ENST00000409794;ENST00000425673|ENST00000205135	T;T|.	0.81415|.	-1.39;-1.49|.	5.14|5.14	4.1|4.1	0.47936|0.47936	.|.	0.215507|.	0.24436|.	N|.	0.038550|.	T|T	0.63570|0.63570	0.2522|0.2522	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.999|.	T|T	0.62020|0.62020	-0.6942|-0.6942	9|5	.|.	.|.	.|.	.|.	9.3585|9.3585	0.38182|0.38182	0.0991:0.0:0.9009:0.0|0.0991:0.0:0.9009:0.0	.|.	1266;1295|.	Q9H7P9-3;Q9H7P9|.	.;PKHG2_HUMAN|.	R|S	1295;1266|1162	ENSP00000386733:G1295R;ENSP00000392906:G1266R|.	.|.	G|R	+|+	1|3	0|2	PLEKHG2|PLEKHG2	44607496|44607496	1.000000|1.000000	0.71417|0.71417	0.964000|0.964000	0.40570|0.40570	0.980000|0.980000	0.70556|0.70556	2.196000|2.196000	0.42686|0.42686	1.171000|1.171000	0.42768|0.42768	0.561000|0.561000	0.74099|0.74099	GGG|AGG	.	.		0.716	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		C	39915656	G	C	39915656	3	2	25	1	0	0	0	0	1	0	0	0	12078	1232	43	4	3953	4	PLEKHG2	19	39915656	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	25909406	39915656	19213327	86	3434										
C20orf70	140683	hgsc.bcm.edu	37	chr20	31760750	31760750	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tttggcaggcatccttgagaAactgaaggtcgacctaggag	13	8	0	2	rs542770426		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr20:31760750A>G	ENST00000253362.2	+	3	316	c.170A>G	c.(169-171)aAa>aGa	p.K57R	BPIFA2_ENST00000354932.5_Missense_Mutation_p.K57R			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	57						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										ATCCTTGAGAAACTGAAGGTC	0.488													A|||	1	0.000199681	0	0	5008	,	,		19050	0.001		0	False		,,,				2504	0				p.K57R		Atlas-SNP	.											.	.	.	.	0			c.A170G						.						84	79	81					20																	31760750		2203	4300	6503	SO:0001583	missense	140683	exon3			TTGAGAAACTGAA	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"BPI fold containing"	16203	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 70"	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.170A>G	chr20.hg19:g.31760750A>G	ENSP00000253362:p.Lys57Arg	101.0	0.0		83.0	33.0	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	hg19	CCDS13214.1	.	.	.	.	.	.	.	.	.	.	A	13.95	2.390386	0.42410	.	.	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.13196	2.61;2.61	3.87	2.77	0.32553	.	1.606950	0.03350	N	0.196028	T	0.21590	0.0520	M	0.65975	2.015	0.09310	N	1	B	0.33280	0.405	B	0.39617	0.305	T	0.26916	-1.0089	10	0.36615	T	0.2	-23.2357	6.0224	0.19636	0.8827:0.0:0.1173:0.0	.	57	Q96DR5	BPIA2_HUMAN	R	57	ENSP00000253362:K57R;ENSP00000347012:K57R	ENSP00000253362:K57R	K	+	2	0	BPIFA2	31224411	0.003000	0.15002	0.003000	0.11579	0.015000	0.08874	2.008000	0.40893	0.835000	0.34877	0.459000	0.35465	AAA	.	.		0.488	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574		G	31760750	A	G	31760750	3	3	25	1	0	0	0	0	1	0	0	0	2118	14	1	2	176	2	C20orf70	20	31760750	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10		31760750	31264770	87	3435										
DLGAP4	22839	hgsc.bcm.edu	37	chr20	35060202	35060202	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	agcccctgtttgcagggaccGaccgcaacccctacctgctg	10	17	0	0	rs374922768		TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr20:35060202G>A	ENST00000373907.2	+	2	281	c.82G>A	c.(82-84)Gac>Aac	p.D28N	DLGAP4_ENST00000373913.3_Missense_Mutation_p.D28N|DLGAP4_ENST00000339266.5_Missense_Mutation_p.D28N|DLGAP4_ENST00000401952.2_Missense_Mutation_p.D28N			Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4	28					cell-cell signaling (GO:0007267)	membrane (GO:0016020)|synapse (GO:0045202)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				TGCAGGGACCGACCGCAACCC	0.697																																					p.D28N		Atlas-SNP	.											.	DLGAP4	111	.	0			c.G82A						.						31	33	33					20																	35060202		2203	4296	6499	SO:0001583	missense	22839	exon2			GGGACCGACCGCA	AF088030	CCDS13274.1, CCDS13275.1	20q11.23	2010-02-05			ENSG00000080845	ENSG00000080845			24476	protein-coding gene	gene with protein product						9115257	Standard	XM_005260329		Approved	DAP4, KIAA0964, SAPAP4	uc010zvp.2	Q9Y2H0	OTTHUMG00000032390	ENST00000373907.2:c.82G>A	chr20.hg19:g.35060202G>A	ENSP00000363014:p.Asp28Asn	250.0	0.0		197.0	98.0	NM_014902	E1P5T5|Q5QPG4|Q5T2Y4|Q5T2Y5|Q9H137|Q9H138|Q9H1L7	Missense_Mutation	SNP	ENST00000373907.2	hg19		.	.	.	.	.	.	.	.	.	.	G	23.4	4.411160	0.83340	.	.	ENSG00000080845	ENST00000373913;ENST00000401952;ENST00000373907;ENST00000339266	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	5.67	4.73	0.59995	.	0.332695	0.36374	N	0.002631	T	0.60301	0.2258	L	0.54323	1.7	0.35797	D	0.822827	D	0.71674	0.998	P	0.54312	0.748	T	0.71494	-0.4576	10	0.56958	D	0.05	.	13.6837	0.62502	0.0737:0.0:0.9263:0.0	.	28	Q9Y2H0-1	.	N	28	ENSP00000363023:D28N;ENSP00000384954:D28N;ENSP00000363014:D28N;ENSP00000341633:D28N	ENSP00000341633:D28N	D	+	1	0	DLGAP4	34493616	1.000000	0.71417	0.997000	0.53966	0.893000	0.52053	5.682000	0.68182	1.409000	0.46915	0.561000	0.74099	GAC	.	.		0.697	DLGAP4-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000079025.2	NM_014902		A	35060202	G	A	35060202	3	1	25	1	0	0	0	0	1	0	0	0	4564	1058	37	1	84	1	DLGAP4	20	35060202	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10	3299452	35060202	27965318	88	3436										
NCAM2	4685	hgsc.bcm.edu	37	chr21	22782741	22782741	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	acctgctaaaaacacgaccaAtttaaagacttatagtacag	5	9	0	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chr21:22782741A>G	ENST00000400546.1	+	10	1592	c.1343A>G	c.(1342-1344)aAt>aGt	p.N448S	NCAM2_ENST00000284894.7_Missense_Mutation_p.N306S	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	448	Ig-like C2-type 5.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AACACGACCAATTTAAAGACT	0.313																																					p.N448S		Atlas-SNP	.											.	NCAM2	220	.	0			c.A1343G						.						75	76	76					21																	22782741		1822	4075	5897	SO:0001583	missense	4685	exon10			CGACCAATTTAAA		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1343A>G	chr21.hg19:g.22782741A>G	ENSP00000383392:p.Asn448Ser	318.0	1.0		245.0	95.0	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	hg19	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.909325	0.52439	.	.	ENSG00000154654	ENST00000400546;ENST00000284894	T;T	0.66638	-0.22;-0.22	4.75	4.75	0.60458	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.203608	0.50627	D	0.000120	T	0.57242	0.2040	L	0.47016	1.485	0.80722	D	1	P;P	0.36587	0.559;0.559	B;B	0.29785	0.107;0.073	T	0.63976	-0.6515	10	0.72032	D	0.01	-17.7111	13.3568	0.60633	1.0:0.0:0.0:0.0	.	306;448	B7Z5K2;O15394	.;NCAM2_HUMAN	S	448;306	ENSP00000383392:N448S;ENSP00000284894:N306S	ENSP00000284894:N306S	N	+	2	0	NCAM2	21704612	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.624000	0.83124	1.893000	0.54813	0.383000	0.25322	AAT	.	.		0.313	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		G	22782741	A	G	22782741	3	3	25	1	0	0	0	0	1	0	0	0	10212	101	4	2	1381	2	NCAM2	21	22782741	Missense_Mutation	SNP	A	TCGA-5C-A9VH-01A-11D-A36X-10		22782741	25347154	89	3437										
UPRT	139596	hgsc.bcm.edu	37	chrX	74494410	74494410	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	gaactctcccggcagatcggGgcgcagcttaagctgctgcc	13	14	1	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chrX:74494410G>T	ENST00000373383.4	+	1	488	c.321G>T	c.(319-321)ggG>ggT	p.G107G	UPRT_ENST00000530743.1_5'Flank|UPRT_ENST00000373379.1_Silent_p.G107G|UPRT_ENST00000531704.1_3'UTR	NM_145052.3	NP_659489.1	Q96BW1	UPP_HUMAN	uracil phosphoribosyltransferase (FUR1) homolog (S. cerevisiae)	107					female pregnancy (GO:0007565)|lactation (GO:0007595)|response to insulin (GO:0032868)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(4)|lung(4)	18						GGCAGATCGGGGCGCAGCTTA	0.552																																					p.G107G		Atlas-SNP	.											.	UPRT	46	.	0			c.G321T						.						29	22	24					X																	74494410		2203	4300	6503	SO:0001819	synonymous_variant	139596	exon1			GATCGGGGCGCAG	BC015116	CCDS14429.1	Xq13.3	2009-01-14			ENSG00000094841	ENSG00000094841			28334	protein-coding gene	gene with protein product		300656				12477932	Standard	NM_145052		Approved	DKFZp781E1243, MGC23937, FUR1, RP11-311P8.3	uc004ecb.2	Q96BW1	OTTHUMG00000021864	ENST00000373383.4:c.321G>T	chrX.hg19:g.74494410G>T		157.0	0.0		102.0	86.0	NM_145052	Q5JRL1|Q5JRL3|Q68DN0|Q96MW2	Silent	SNP	ENST00000373383.4	hg19	CCDS14429.1																																																																																			.	.		0.552	UPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057278.1	NM_145052		T	74494410	G	T	74494410	2	4	25	1	0	0	0	0	0	0	0	1	17029	1219	43	3		3	UPRT	23	74494410	Silent	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10		74494410	80776150	90	3438										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151818999	151818999	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	cactattacctcttggatatCgttttggatgaactatgatt	7	7	1	2			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chrX:151818999C>A	ENST00000370306.2	+	7	877	c.857C>A	c.(856-858)tCg>tAg	p.S286*		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	286					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)	p.S286L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCTTGGATATCGTTTTGGATG	0.453																																					p.S286X		Atlas-SNP	.											.	GABRQ	131	.	1	Substitution - Missense(1)	large_intestine(1)	c.C857A						.						359	303	322					X																	151818999		2203	4300	6503	SO:0001587	stop_gained	55879	exon7			GGATATCGTTTTG	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.857C>A	chrX.hg19:g.151818999C>A	ENSP00000359329:p.Ser286*	118.0	0.0		115.0	83.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Nonsense_Mutation	SNP	ENST00000370306.2	hg19	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.963616	0.92791	.	.	ENSG00000147402	ENST00000370306	.	.	.	6.08	6.08	0.98989	.	0.163737	0.29572	N	0.011766	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.7366	0.85448	0.0:1.0:0.0:0.0	.	.	.	.	X	286	.	ENSP00000359329:S286X	S	+	2	0	GABRQ	151569655	1.000000	0.71417	0.341000	0.25589	0.302000	0.27658	7.798000	0.85924	2.562000	0.86427	0.600000	0.82982	TCG	.	.		0.453	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		A	151818999	C	A	151818999	4	1	25	1	0	0	0	0	0	1	0	0	6183	893	31	1	883	1	GABRQ	23	151818999	Nonsense_Mutation	SNP	C	TCGA-5C-A9VH-01A-11D-A36X-10	77324589	151818999	3451561	91	3439										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	4967469	4967469	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	6	1	1.29410334346505	3.01957446808511	0.603914893617021	0.592074592074592	1	0	tgtcccagaaaaccttccaaGgcatggtacagtaggactaa	9	10	0	1			TCGA-5C-A9VH-01A-11D-A36X-10	TCGA-5C-A9VH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	44e358dc-cbf5-4177-89a4-3d0d0fe2ff38	b56ae97e-c498-4223-a583-2b86e313f4bb	g.chrY:4967469G>A	ENST00000333703.4	+	5	2330	c.1817G>A	c.(1816-1818)aGg>aAg	p.R606K	PCDH11Y_ENST00000215473.6_Missense_Mutation_p.R617K|PCDH11Y_ENST00000362095.5_Missense_Mutation_p.R617K	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	617	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						AACCTTCCAAGGCATGGTACA	0.383																																					p.R617K		Atlas-SNP	.											.	PCDH11Y	163	.	0			c.G1850A						.																																			SO:0001583	missense	83259	exon2			TTCCAAGGCATGG	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000333703.4:c.1817G>A	chrY.hg19:g.4967469G>A	ENSP00000330552:p.Arg606Lys	226.0	0.0		154.0	109.0	NM_032972	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000333703.4	hg19	CCDS14776.1																																																																																			.	.		0.383	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	NM_032973		A	4967469	G	A	4967469	3	1	25	1	0	0	0	0	1	0	0	0	11518	1000	35	3	1892	3	PCDH11Y	24	4967469	Missense_Mutation	SNP	G	TCGA-5C-A9VH-01A-11D-A36X-10		4967469	54406097	92	3440										
MEGF6	1953	hgsc.bcm.edu	37	chr1	3417558	3417558	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	cagctaaagccggtccacccGggggcacagctgcagtgtcc	13	15	0	0			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:3417558G>C	ENST00000356575.4	-	20	2773	c.2547C>G	c.(2545-2547)ccC>ccG	p.P849P	MEGF6_ENST00000294599.4_Silent_p.P744P	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	849	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		CGGTCCACCCGGGGGCACAGC	0.642																																					p.P849P	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C2547G						.						35	44	41					1																	3417558		2000	4177	6177	SO:0001819	synonymous_variant	1953	exon20			CCACCCGGGGGCA	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"EGF-like-domain, multiple 3"	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.2547C>G	chr1.hg19:g.3417558G>C		152.0	0.0		254.0	112.0	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	hg19	CCDS41237.1																																																																																			.	.		0.642	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		C	3417558	G	C	3417558	2	2	26	1	0	0	0	0	0	0	0	1	9471	1103	39	4		4	MEGF6	1	3417558	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10		3417558	245833063	1	3441										
TP73	7161	hgsc.bcm.edu	37	chr1	3599745	3599745	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gcatgactacatctgtcatgGtgagtgggggggctgccctc	15	10	2	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:3599745G>A	ENST00000378295.4	+	3	341		c.e3+1		TP73_ENST00000354437.4_Splice_Site|TP73_ENST00000604074.1_Splice_Site|TP73_ENST00000346387.4_Splice_Site|TP73_ENST00000357733.3_Splice_Site|TP73_ENST00000604479.1_Splice_Site|TP73_ENST00000603362.1_Splice_Site	NM_001204185.1|NM_005427.3	NP_001191114.1|NP_005418.1	O15350	P73_HUMAN	tumor protein p73						activation of MAPK activity (GO:0000187)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|cerebrospinal fluid secretion (GO:0033326)|digestive tract morphogenesis (GO:0048546)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|hippocampus development (GO:0021766)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|kidney development (GO:0001822)|mismatch repair (GO:0006298)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell size (GO:0045793)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein tetramerization (GO:0051262)|release of cytochrome c from mitochondria (GO:0001836)|response to gamma radiation (GO:0010332)|response to organonitrogen compound (GO:0010243)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|lung(8)|ovary(1)|prostate(1)	20	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)		ATCTGTCATGGTGAGTGGGGG	0.592																																					.		Atlas-SNP	.											.	TP73	54	.	0			c.186+1G>A						.						73	74	74					1																	3599745		2203	4300	6503	SO:0001630	splice_region_variant	7161	exon3			GTCATGGTGAGTG	AB055065	CCDS49.1, CCDS44049.1, CCDS44050.1, CCDS44051.1, CCDS55566.1, CCDS55567.1, CCDS55568.1, CCDS55569.1, CCDS59965.1	1p36.3	2010-06-15			ENSG00000078900	ENSG00000078900			12003	protein-coding gene	gene with protein product		601990				9296498, 9288759	Standard	NM_001204186		Approved	P73	uc001akp.3	O15350	OTTHUMG00000000610	ENST00000378295.4:c.186+1G>A	chr1.hg19:g.3599745G>A		103.0	0.0		162.0	55.0	NM_001204188	B7Z7J4|B7Z8Z1|B7Z9C1|C9J521|O15351|Q17RN8|Q5TBV5|Q5TBV6|Q8NHW9|Q8TDY5|Q8TDY6|Q9NTK8	Splice_Site	SNP	ENST00000378295.4	hg19	CCDS49.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967158	0.53507	.	.	ENSG00000078900	ENST00000378295;ENST00000354437;ENST00000357733;ENST00000346387	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7783	0.85557	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TP73	3589605	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	5.479000	0.66813	2.250000	0.74265	0.563000	0.77884	.	.	.		0.592	TP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001468.4	NM_005427	Intron	A	3599745	G	A	3599745	5	1	26	1	0	0	0	0	0	0	1	0	16408	1275	44	3	193	3	TP73	1	3599745	Splice_Site	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	182187	3599745	245650876	2	3442										
RERE	473	hgsc.bcm.edu	37	chr1	8416253	8416255	+	In_Frame_Del	DEL	GGT	GGT	-													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	cgggtaggggaagcgagccaGgtggggaccggcagtcaggg							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	GGT	GGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:8416253_8416255delGGT	ENST00000337907.3	-	22	5025_5027	c.4391_4393delACC	c.(4390-4395)cacctg>ctg	p.H1464del	RERE_ENST00000476556.1_In_Frame_Del_p.H910del|RERE_ENST00000400907.2_Intron|RERE_ENST00000377464.1_In_Frame_Del_p.H1196del|RERE_ENST00000400908.2_In_Frame_Del_p.H1464del	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1464	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		AAGCGAGCCAGGTGGGGACCGGC	0.626																																					p.1464_1465del		Atlas-Indel,Pindel	.											.	RERE	129	.	0			c.4392_4394del						.																																			SO:0001651	inframe_deletion	473	exon22			.	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.4391_4393delACC	chr1.hg19:g.8416253_8416255delGGT	ENSP00000338629:p.His1464del	105.0	0.0		185.0	57.0	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	In_Frame_Del	DEL	ENST00000337907.3	hg19	CCDS95.1																																																																																			.	.		0.626	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			-	8416255	GGT	-	8416253	7	5	26	1	0	1	0	1	0	0	0	0	13246	991	35	0	319	0	RERE	1	8416253	In_Frame_Del	DEL	GGT	TCGA-5C-AAPD-01A-21D-A38X-10	4816508	8416253	240834368	3	3443										
IL23R	149233	hgsc.bcm.edu	37	chr1	67666504	67666505	+	Frame_Shift_Ins	INS	-	-	T													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tacaaggtggcaagaagtacINSttggtttgggtccaagcagc							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:67666504_67666505insT	ENST00000347310.5	+	5	747_748	c.576_577insT	c.(577-579)ttgfs	p.L193fs	IL23R_ENST00000371002.1_Frame_Shift_Ins_p.L193fs|C1orf141_ENST00000371007.2_Intron	NM_144701.2	NP_653302.2	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor	193	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|interleukin-23-mediated signaling pathway (GO:0038155)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)	interleukin-23 receptor complex (GO:0072536)|receptor complex (GO:0043235)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	21						GCAAGAAGTACTTGGTTTGGGT	0.371																																					p.Y192fs		Atlas-Indel,Pindel	.											.	IL23R	52	.	0			c.576_577insT						.																																			SO:0001589	frameshift_variant	149233	exon5			.	AF461422	CCDS637.1	1p31.2	2008-02-05			ENSG00000162594	ENSG00000162594			19100	protein-coding gene	gene with protein product		607562				12023369	Standard	NM_144701		Approved	IL-23R	uc001ddo.3	Q5VWK5	OTTHUMG00000009092	ENST00000347310.5:c.578dupT	chr1.hg19:g.67666506_67666506dupT	ENSP00000321345:p.Leu193fs	360.0	0.0		296.0	83.0	NM_144701	C9JGX4|Q4VGP1|Q4VGP2|Q4VGP3|Q4VGP4|Q4VGP5|Q4VGP6|Q5VWK7|Q8IW84|Q8NFQ9|Q96AS1	Frame_Shift_Ins	INS	ENST00000347310.5	hg19	CCDS637.1																																																																																			.	.		0.371	IL23R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025199.2	NM_144701		T	67666505	-	T	67666504	7	5	26	1	0	1	1	0	0	0	0	0	7685	576	20	0	590	0	IL23R	1	67666504	Frame_Shift_Ins	INS	-	TCGA-5C-AAPD-01A-21D-A38X-10	59250251	67666504	181584117	4	3444										
WDR47	22911	hgsc.bcm.edu	37	chr1	109538417	109538417	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gctgatacctcattaccaagGccatccattccaatatttaa	4	12	1	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:109538417G>C	ENST00000369962.3	-	8	1698	c.1476C>G	c.(1474-1476)ggC>ggG	p.G492G	WDR47_ENST00000369965.4_Silent_p.G493G|WDR47_ENST00000357672.3_Silent_p.G464G|WDR47_ENST00000361054.3_Silent_p.G464G|WDR47_ENST00000400794.3_Silent_p.G500G			O94967	WDR47_HUMAN	WD repeat domain 47	492					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		CATTACCAAGGCCATCCATTC	0.343																																					p.G500G		Atlas-SNP	.											.	WDR47	56	.	0			c.C1500G						.						153	153	153					1																	109538417		2203	4296	6499	SO:0001819	synonymous_variant	22911	exon8			ACCAAGGCCATCC	AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433		"WD repeat domain containing"	29141	protein-coding gene	gene with protein product		615734				10048485	Standard	NM_014969		Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369962.3:c.1476C>G	chr1.hg19:g.109538417G>C		154.0	0.0		159.0	42.0	NM_001142550	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Silent	SNP	ENST00000369962.3	hg19	CCDS44187.1																																																																																			.	.		0.343	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032414.2	NM_014969		C	109538417	G	C	109538417	2	2	26	1	0	0	0	0	0	0	0	1	17315	1190	42	4		4	WDR47	1	109538417	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	41871913	109538417	139712204	5	3445										
TUFT1	7286	hgsc.bcm.edu	37	chr1	151546817	151546817	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	cagagagaggaggacagagtGgagcagaaagaggcagaagt	18	4	0	6			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:151546817G>T	ENST00000368849.3	+	8	728	c.666G>T	c.(664-666)gtG>gtT	p.V222V	TUFT1_ENST00000392712.3_Silent_p.V167V|TUFT1_ENST00000538902.1_Silent_p.V241V|TUFT1_ENST00000368848.2_Silent_p.V197V|TUFT1_ENST00000353024.3_Silent_p.V163V	NM_020127.2	NP_064512.1	Q9NNX1	TUFT1_HUMAN	tuftelin 1	222					bone mineralization (GO:0030282)|odontogenesis (GO:0042476)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	structural constituent of tooth enamel (GO:0030345)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGGACAGAGTGGAGCAGAAAG	0.542											OREG0003906	type=REGULATORY REGION|Gene=TUFT1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.V222V		Atlas-SNP	.											.	TUFT1	32	.	0			c.G666T						.						111	101	104					1																	151546817		2203	4300	6503	SO:0001819	synonymous_variant	7286	exon8			CAGAGTGGAGCAG	AF254260	CCDS1000.1, CCDS44223.1	1q21	2008-02-05			ENSG00000143367	ENSG00000143367			12422	protein-coding gene	gene with protein product		600087				7919663	Standard	NM_020127		Approved		uc001eyl.3	Q9NNX1	OTTHUMG00000012536	ENST00000368849.3:c.666G>T	chr1.hg19:g.151546817G>T		300.0	0.0	1741	384.0	87.0	NM_020127	B2RD57|D3DV21|D3DV22|Q5T384|Q5T385|Q9BU28|Q9H5L1	Silent	SNP	ENST00000368849.3	hg19	CCDS1000.1																																																																																			.	.		0.542	TUFT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035022.1	NM_020127		T	151546817	G	T	151546817	2	4	26	1	0	0	0	0	0	0	0	1	16787	1335	47	3		3	TUFT1	1	151546817	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	42008400	151546817	97703804	6	3446										
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156520099	156520099	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ttggctctgaccactccctgGcggatctcctcaagccacag	9	16	3	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:156520099G>A	ENST00000361170.2	-	16	1789	c.1779C>T	c.(1777-1779)cgC>cgT	p.R593R		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	593					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCACTCCCTGGCGGATCTCCT	0.552																																					p.R593R		Atlas-SNP	.											.	IQGAP3	146	.	0			c.C1779T						.						82	71	75					1																	156520099		2203	4300	6503	SO:0001819	synonymous_variant	128239	exon16			TCCCTGGCGGATC	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.1779C>T	chr1.hg19:g.156520099G>A		68.0	0.0		95.0	46.0	NM_178229	Q5T3H8	Silent	SNP	ENST00000361170.2	hg19	CCDS1144.1																																																																																			.	.		0.552	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		A	156520099	G	A	156520099	2	1	26	1	0	0	0	0	0	0	0	1	7825	1190	42	3		3	IQGAP3	1	156520099	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	4973282	156520099	92730522	7	3447										
FCRL1	115350	hgsc.bcm.edu	37	chr1	157772291	157772291	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tactctgctgtcagtgaacgCtgggtctttgactgaaggtt	12	8	3	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:157772291C>T	ENST00000368176.3	-	4	550	c.483G>A	c.(481-483)caG>caA	p.Q161Q	FCRL1_ENST00000358292.3_Silent_p.Q161Q|FCRL1_ENST00000491942.1_Silent_p.Q161Q|FCRL1_ENST00000489998.1_5'UTR	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	161	Ig-like C2-type 2.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TCAGTGAACGCTGGGTCTTTG	0.498																																					p.Q161Q	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.G483A						.						115	95	102					1																	157772291		2203	4300	6503	SO:0001819	synonymous_variant	115350	exon4			TGAACGCTGGGTC	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.483G>A	chr1.hg19:g.157772291C>T		133.0	0.0		136.0	29.0	NM_001159397	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Silent	SNP	ENST00000368176.3	hg19	CCDS1170.1																																																																																			.	.		0.498	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938		T	157772291	C	T	157772291	2	4	26	1	0	0	0	0	0	0	0	1	5802	796	28	3		3	FCRL1	1	157772291	Silent	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	1252192	157772291	91478330	8	3448										
KCNJ10	3766	hgsc.bcm.edu	37	chr1	160012115	160012115	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tgcaaaggtcgcagagaagaGcagaagcttgtagcgccact	13	9	0	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:160012115G>A	ENST00000368089.3	-	2	434	c.208C>T	c.(208-210)Ctc>Ttc	p.L70F	KCNJ10_ENST00000509700.1_5'Flank	NM_002241.4	NP_002232.2	P78508	KCJ10_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 10	70					adult walking behavior (GO:0007628)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|L-glutamate uptake involved in synaptic transmission (GO:0051935)|membrane hyperpolarization (GO:0060081)|optic nerve development (GO:0021554)|potassium ion homeostasis (GO:0055075)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of resting membrane potential (GO:0060075)|regulation of sensory perception of pain (GO:0051930)|response to blue light (GO:0009637)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)		Yohimbine(DB01392)	GCAGAGAAGAGCAGAAGCTTG	0.572																																					p.L70F	GBM(167;1368 2014 14817 36425 43215)	Atlas-SNP	.											.	KCNJ10	58	.	0			c.C208T						.						176	151	159					1																	160012115		2203	4300	6503	SO:0001583	missense	3766	exon2			AGAAGAGCAGAAG	U52155	CCDS1193.1	1q23.2	2011-07-05			ENSG00000177807	ENSG00000177807		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6256	protein-coding gene	gene with protein product		602208				9367690, 8995301, 16382105	Standard	NM_002241		Approved	Kir4.1, Kir1.2	uc001fuw.2	P78508	OTTHUMG00000024073	ENST00000368089.3:c.208C>T	chr1.hg19:g.160012115G>A	ENSP00000357068:p.Leu70Phe	123.0	0.0		106.0	19.0	NM_002241	A3KME7|Q5VUT9|Q8N4I7|Q92808	Missense_Mutation	SNP	ENST00000368089.3	hg19	CCDS1193.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.519921	0.44866	.	.	ENSG00000177807	ENST00000368089	D	0.94966	-3.57	5.17	4.23	0.50019	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.95079	0.8406	L	0.53671	1.685	0.53005	D	0.999968	D	0.69078	0.997	D	0.76575	0.988	D	0.94360	0.7587	10	0.52906	T	0.07	.	11.9518	0.52959	0.0869:0.0:0.9131:0.0	.	70	P78508	IRK10_HUMAN	F	70	ENSP00000357068:L70F	ENSP00000357068:L70F	L	-	1	0	KCNJ10	158278739	0.940000	0.31905	1.000000	0.80357	0.998000	0.95712	1.401000	0.34589	2.688000	0.91661	0.591000	0.81541	CTC	.	.		0.572	KCNJ10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060629.1	NM_002241		A	160012115	G	A	160012115	3	1	26	1	0	0	0	0	1	0	0	0	8053	971	34	3	935	3	KCNJ10	1	160012115	Missense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	2239824	160012115	89238506	9	3449										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167095331	167095331	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gaagaggaggacgacagcgcCagccacctgagtggctcctc	14	13	0	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:167095331C>A	ENST00000361200.2	+	6	1129	c.963C>A	c.(961-963)gcC>gcA	p.A321A	DUSP27_ENST00000271385.5_Silent_p.A321A|DUSP27_ENST00000443333.1_Silent_p.A321A|DUSP27_ENST00000485151.1_3'UTR			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	321					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						ACGACAGCGCCAGCCACCTGA	0.667																																					p.A321A		Atlas-SNP	.											.	DUSP27	235	.	0			c.C963A						.						23	26	25					1																	167095331		2202	4299	6501	SO:0001819	synonymous_variant	92235	exon5			CAGCGCCAGCCAC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.963C>A	chr1.hg19:g.167095331C>A		69.0	0.0		61.0	25.0	NM_001080426	A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	hg19	CCDS30932.1																																																																																			.	.		0.667	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		A	167095331	C	A	167095331	2	1	26	1	0	0	0	0	0	0	0	1	4826	581	21	3		3	DUSP27	1	167095331	Silent	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	7083216	167095331	82155290	10	3450										
KISS1	3814	hgsc.bcm.edu	37	chr1	204159709	204159709	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	agttgtagttcggcaggtccTtctcccgctgcaccagcacc	10	15	1	0			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr1:204159709T>G	ENST00000367194.4	-	3	468	c.320A>C	c.(319-321)aAg>aCg	p.K107T		NM_002256.3	NP_002247.3	Q15726	KISS1_HUMAN	KiSS-1 metastasis-suppressor	107					cytoskeleton organization (GO:0007010)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of luteinizing hormone secretion (GO:0033686)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of synaptic transmission (GO:0050806)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				large_intestine(1)|lung(1)|ovary(1)	3	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)	Breast(1374;9.42e-05)	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.069)|Kidney(21;0.0934)|Epithelial(59;0.239)	Colorectal(1306;0.0129)		CGGCAGGTCCTTCTCCCGCTG	0.736																																					p.K107T		Atlas-SNP	.											.	KISS1	6	.	0			c.A320C						.						7	7	7					1																	204159709		1829	3973	5802	SO:0001583	missense	3814	exon3			AGGTCCTTCTCCC	U43527	CCDS41454.1	1q32	2014-01-30			ENSG00000170498	ENSG00000170498		"Endogenous ligands"	6341	protein-coding gene	gene with protein product	"prepro-kisspeptin", "kisspeptin"	603286				9192814, 9806840	Standard	NM_002256		Approved		uc001har.3	Q15726	OTTHUMG00000036060	ENST00000367194.4:c.320A>C	chr1.hg19:g.204159709T>G	ENSP00000356162:p.Lys107Thr	105.0	0.0		129.0	30.0	NM_002256	A8K6N0|Q9HBP1	Missense_Mutation	SNP	ENST00000367194.4	hg19	CCDS41454.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.246875	0.59103	.	.	ENSG00000170498	ENST00000367194	D	0.84223	-1.82	4.98	3.82	0.43975	.	0.000000	0.50627	D	0.000106	D	0.89986	0.6874	M	0.76002	2.32	0.38582	D	0.950206	D	0.71674	0.998	D	0.71656	0.974	D	0.89618	0.3846	10	0.72032	D	0.01	-18.2005	7.6564	0.28377	0.0:0.0991:0.0:0.9009	.	107	Q15726	KISS1_HUMAN	T	107	ENSP00000356162:K107T	ENSP00000356162:K107T	K	-	2	0	KISS1	202426332	1.000000	0.71417	0.883000	0.34634	0.347000	0.29111	1.272000	0.33109	0.706000	0.31912	0.418000	0.28097	AAG	.	.		0.736	KISS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087892.1	NM_002256		G	204159709	T	G	204159709	3	3	26	1	0	0	0	0	1	0	0	0	8336	1609	56	5	100	5	KISS1	1	204159709	Missense_Mutation	SNP	T	TCGA-5C-AAPD-01A-21D-A38X-10	37064378	204159709	45090912	11	3451										
NBAS	51594	hgsc.bcm.edu	37	chr2	15651378	15651378	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ttagtaacctgcttataataCggtgatcctgaaagaactct	7	8	1	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr2:15651378C>T	ENST00000281513.5	-	10	868	c.843G>A	c.(841-843)ccG>ccA	p.P281P	NBAS_ENST00000441750.1_Silent_p.P281P	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	281					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						GCTTATAATACGGTGATCCTG	0.428																																					p.P281P		Atlas-SNP	.											.	NBAS	246	.	0			c.G843A						.						155	156	156					2																	15651378		2203	4300	6503	SO:0001819	synonymous_variant	51594	exon10			ATAATACGGTGAT	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.843G>A	chr2.hg19:g.15651378C>T		258.0	0.0		228.0	62.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	hg19	CCDS1685.1																																																																																			.	.		0.428	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15651378	C	T	15651378	2	4	26	1	0	0	0	0	0	0	0	1	10195	523	19	1		1	NBAS	2	15651378	Silent	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10		15651378	227547995	12	3452										
RAD51AP2	729475	hgsc.bcm.edu	37	chr2	17698736	17698737	+	Frame_Shift_Ins	INS	-	-	T													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	aatgttttccgcttctacagINStttttttatcattctgtaac							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr2:17698736_17698737insT	ENST00000399080.2	-	1	969_970	c.946_947insA	c.(946-948)actfs	p.T316fs		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	316										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CGCTTCTACAGTTTTTTTATCA	0.332																																					p.T316fs		Atlas-Indel,Pindel	.											.,2	RAD51AP2	134	.	0			c.947_948insA						.			1,3493		0,1,1746						-5.6	0			116	1,7797		0,1,3898	no	frameshift	RAD51AP2	NM_001099218.2		0,2,5644	A1A1,A1R,RR		0.0128,0.0286,0.0177				2,11290				SO:0001589	frameshift_variant	729475	exon1			.	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.947dupA	chr2.hg19:g.17698743_17698743dupT	ENSP00000382030:p.Thr316fs	89.0	0.0		68.0	22.0	NM_001099218		Frame_Shift_Ins	INS	ENST00000399080.2	hg19	CCDS42656.1																																																																																			.	.		0.332	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		T	17698737	-	T	17698736	7	5	26	1	0	1	1	0	0	0	0	0	13002	1029	36	0	2544	0	RAD51AP2	2	17698736	Frame_Shift_Ins	INS	-	TCGA-5C-AAPD-01A-21D-A38X-10	2047358	17698736	225500637	13	3453										
PUM2	23369	hgsc.bcm.edu	37	chr2	20490528	20490528	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tgattgggagtaagaggacgCtgacctgctccagcacggag	15	9	0	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr2:20490528C>T	ENST00000361078.2	-	9	1198	c.1176G>A	c.(1174-1176)caG>caA	p.Q392Q	PUM2_ENST00000536417.1_Silent_p.Q336Q|PUM2_ENST00000319801.5_Silent_p.Q392Q|PUM2_ENST00000403432.1_Silent_p.Q392Q|PUM2_ENST00000338086.5_Silent_p.Q392Q			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	392	Ala-rich.|Gln-rich.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAAGAGGACGCTGACCTGCTC	0.423																																					p.Q392Q		Atlas-SNP	.											.	PUM2	91	.	0			c.G1176A						.						67	60	63					2																	20490528		2203	4300	6503	SO:0001819	synonymous_variant	23369	exon9			AGGACGCTGACCT	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"pumilio (Drosphila) homolog 2", "pumilio homolog 2 (Drosophila)"			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.1176G>A	chr2.hg19:g.20490528C>T		209.0	0.0		171.0	43.0	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Silent	SNP	ENST00000361078.2	hg19																																																																																				.	.		0.423	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		T	20490528	C	T	20490528	2	4	26	1	0	0	0	0	0	0	0	1	12841	796	28	3		3	PUM2	2	20490528	Silent	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	2791792	20490528	222708845	14	3454										
VIT	5212	hgsc.bcm.edu	37	chr2	37041407	37041407	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	cactcaccccgccagagaccActccttctttgtggacgagt	8	16	2	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr2:37041407A>C	ENST00000389975.3	+	15	2242	c.1940A>C	c.(1939-1941)cAc>cCc	p.H647P	VIT_ENST00000379241.3_Missense_Mutation_p.H625P|VIT_ENST00000379242.3_Missense_Mutation_p.H662P|VIT_ENST00000401530.1_Missense_Mutation_p.H626P|VIT_ENST00000404084.1_Missense_Mutation_p.H599P|VIT_ENST00000497382.1_Missense_Mutation_p.H316P	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	647	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				GCCAGAGACCACTCCTTCTTT	0.517																																					p.H662P		Atlas-SNP	.											.	VIT	138	.	0			c.A1985C						.						133	110	118					2																	37041407		2203	4300	6503	SO:0001583	missense	5212	exon16			GAGACCACTCCTT	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.1940A>C	chr2.hg19:g.37041407A>C	ENSP00000374625:p.His647Pro	110.0	0.0		88.0	21.0	NM_053276	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	hg19	CCDS54347.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.745451	0.89663	.	.	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000497382;ENST00000404084;ENST00000379241;ENST00000401530	D;D;D;D;D;D	0.84873	-1.91;-1.91;-1.91;-1.91;-1.91;-1.91	5.52	5.52	0.82312	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.94866	0.8341	H	0.95917	3.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.96277	0.9203	10	0.66056	D	0.02	-19.8221	15.6637	0.77209	1.0:0.0:0.0:0.0	.	626;625;647;662	E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4	.;.;VITRN_HUMAN;.	P	662;647;316;599;625;626	ENSP00000368544:H662P;ENSP00000374625:H647P;ENSP00000417874:H316P;ENSP00000384154:H599P;ENSP00000368543:H625P;ENSP00000385658:H626P	ENSP00000368543:H625P	H	+	2	0	VIT	36894911	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	9.300000	0.96151	2.095000	0.63458	0.533000	0.62120	CAC	.	.		0.517	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				C	37041407	A	C	37041407	3	2	26	1	0	0	0	0	1	0	0	0	17186	159	6	5	2168	5	VIT	2	37041407	Missense_Mutation	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10	16550879	37041407	206157966	15	3455										
DHX57	90957	hgsc.bcm.edu	37	chr2	39046078	39046104	+	Splice_Site	DEL	CTTCTTTTGTACTTAGCTGCCATCCCT	CTTCTTTTGTACTTAGCTGCCATCCCT	-													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	attataacttgcacgcacgcCttcttttgtacttagctgcc					rs147441334		TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	CTTCTTTTGTACTTAGCTGCCATCCCT	CTTCTTTTGTACTTAGCTGCCATCCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr2:39046078_39046104delCTTCTTTTGTACTTAGCTGCCATCCCT	ENST00000295373.6	-	19	3514_3538	c.3388_3412delAGGGATGGCAGCTAAGTACAAAAGAAG	c.(3388-3414)agggatggcagctaagtacaaaagaag>ag	p.RDGS*VQKK1130del		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1130							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				GCACGCACGCCTTCTTTTGTACTTAGCTGCCATCCCTAAATTTTGGA	0.366																																					p.1130_1138del	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-Indel,Pindel	.											.	DHX57	127	.	0			c.3388_3413del						.																																			SO:0001630	splice_region_variant	90957	exon19			.	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3388-1AGGGATGGCAGCTAAGTACAAAAGAAG>-	chr2.hg19:g.39046078_39046104delCTTCTTTTGTACTTAGCTGCCATCCCT		114.0	0.0		80.0	11.0	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Frame_Shift_Del	DEL	ENST00000295373.6	hg19	CCDS1800.1																																																																																			.	.		0.366	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	In_Frame_Del	-	39046104	CTTCTTTTGTACTTAGCTGCCATCCCT	-	39046078	8	5	26	1	0	1	0	1	0	0	1	0	4515	681	24	0	772	0	DHX57	2	39046078	Splice_Site	DEL	CTTCTTTTGTACTTAGCTGCCATCCCT	TCGA-5C-AAPD-01A-21D-A38X-10	2004671	39046078	204153295	16	3456										
TNFAIP6	7130	hgsc.bcm.edu	37	chr2	152235980	152235981	+	Frame_Shift_Ins	INS	-	-	A													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gtatccaaatccagtcaaggINSaaaaaatacaagtactactt							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr2:152235980_152235981insA	ENST00000243347.3	+	6	842_843	c.767_768insA	c.(766-771)ggaaaafs	p.GK256fs		NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	256					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	TCCAGTCAAGGAAAAAATACAA	0.337																																					p.G256fs		Atlas-Indel,Pindel	.											.	TNFAIP6	98	.	0			c.767_768insA						.																																			SO:0001589	frameshift_variant	7130	exon6			.		CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	ENST00000243347.3:c.773dupA	chr2.hg19:g.152235986_152235986dupA	ENSP00000243347:p.Gly256fs	172.0	0.0		165.0	34.0	NM_007115	Q53TI7|Q8WWI9	Frame_Shift_Ins	INS	ENST00000243347.3	hg19	CCDS2193.1																																																																																			.	.		0.337	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115		A	152235981	-	A	152235980	7	5	26	1	0	1	1	0	0	0	0	0	16290	1174	41	0	789	0	TNFAIP6	2	152235980	Frame_Shift_Ins	INS	-	TCGA-5C-AAPD-01A-21D-A38X-10	113189902	152235980	90963393	17	3457										
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172650192	172650192	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	cattcagggcgctgactctgGgtcccgtggtgatctctcca	12	13	3	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr2:172650192G>T	ENST00000422440.2	-	14	1428	c.1391C>A	c.(1390-1392)cCc>cAc	p.P464H	SLC25A12_ENST00000392592.4_Missense_Mutation_p.P357H	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	464					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	GCTGACTCTGGGTCCCGTGGT	0.468																																					p.P464H		Atlas-SNP	.											.	SLC25A12	59	.	0			c.C1391A						.						82	83	83					2																	172650192		2203	4300	6503	SO:0001583	missense	8604	exon14			ACTCTGGGTCCCG	Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"Solute carriers", "EF-hand domain containing"	10982	protein-coding gene	gene with protein product		603667	"solute carrier family 25 (mitochondrial carrier, Aralar), member 12"			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.1391C>A	chr2.hg19:g.172650192G>T	ENSP00000388658:p.Pro464His	127.0	0.0		118.0	23.0	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	hg19	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.835266	0.91117	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	T;T	0.79454	-1.27;-1.27	5.31	5.31	0.75309	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.87958	0.6309	M	0.77313	2.365	0.80722	D	1	D;P	0.60160	0.987;0.953	D;P	0.64687	0.928;0.895	D	0.89181	0.3544	10	0.72032	D	0.01	-10.381	18.9718	0.92718	0.0:0.0:1.0:0.0	.	357;464	B3KR64;O75746	.;CMC1_HUMAN	H	464;357	ENSP00000388658:P464H;ENSP00000376371:P357H	ENSP00000376371:P357H	P	-	2	0	SLC25A12	172358438	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.835000	0.99442	2.480000	0.83734	0.655000	0.94253	CCC	.	.		0.468	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		T	172650192	G	T	172650192	3	4	26	1	0	0	0	0	1	0	0	0	14489	1232	43	3	665	3	SLC25A12	2	172650192	Missense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	20414212	172650192	70549181	18	3458										
WHSC1	7468	hgsc.bcm.edu	37	chr4	1961231	1961231	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	acgggaaagtccagatctacAcagcggatatttcagaaatc	9	9	2	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr4:1961231A>G	ENST00000382895.3	+	19	3450	c.3019A>G	c.(3019-3021)Aca>Gca	p.T1007A	WHSC1_ENST00000382888.3_Missense_Mutation_p.T355A|WHSC1_ENST00000382892.2_Missense_Mutation_p.T1007A|WHSC1_ENST00000382891.5_Missense_Mutation_p.T1007A|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000508803.1_Missense_Mutation_p.T1007A	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	1007					anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		CCAGATCTACACAGCGGATAT	0.488			T	IGH@	MM																																p.T1007A		Atlas-SNP	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.A3019G						.						65	57	60					4																	1961231		2203	4300	6503	SO:0001583	missense	7468	exon17			ATCTACACAGCGG	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"Zinc fingers, PHD-type"	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.3019A>G	chr4.hg19:g.1961231A>G	ENSP00000372351:p.Thr1007Ala	195.0	0.0		143.0	62.0	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	hg19	CCDS33940.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.750564	0.49257	.	.	ENSG00000109685	ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895;ENST00000382888	D;D;D;D;D	0.97138	-3.67;-3.67;-3.67;-3.67;-4.26	5.45	5.45	0.79879	.	0.000000	0.56097	D	0.000039	D	0.93334	0.7875	N	0.21508	0.67	0.80722	D	1	B;B	0.13594	0.0;0.008	B;B	0.14023	0.001;0.01	D	0.90252	0.4294	10	0.27082	T	0.32	.	15.806	0.78513	1.0:0.0:0.0:0.0	.	355;1007	A2A2T2;O96028	.;NSD2_HUMAN	A	1007;1007;1007;1007;355	ENSP00000423972:T1007A;ENSP00000372347:T1007A;ENSP00000372348:T1007A;ENSP00000372351:T1007A;ENSP00000372344:T355A	ENSP00000372344:T355A	T	+	1	0	WHSC1	1931029	1.000000	0.71417	0.519000	0.27824	0.952000	0.60782	6.136000	0.71703	2.196000	0.70406	0.533000	0.62120	ACA	.	.		0.488	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		G	1961231	A	G	1961231	3	3	26	1	0	0	0	0	1	0	0	0	17377	159	6	2	3157	2	WHSC1	4	1961231	Missense_Mutation	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10		1961231	189193045	19	3459										
TLR6	10333	hgsc.bcm.edu	37	chr4	38829121	38829121	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tctaggtaaggtaccaattcActtttcacccaggcagaatc	7	11	3	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr4:38829121A>T	ENST00000381950.1	-	1	2039	c.1974T>A	c.(1972-1974)agT>agA	p.S658R	TLR6_ENST00000436693.2_Missense_Mutation_p.S658R			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	658	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GTACCAATTCACTTTTCACCC	0.403																																					p.S658R		Atlas-SNP	.											.	TLR6	67	.	0			c.T1974A						.						94	99	98					4																	38829121		2203	4300	6503	SO:0001583	missense	10333	exon2			CAATTCACTTTTC		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"CD molecules"	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.1974T>A	chr4.hg19:g.38829121A>T	ENSP00000371376:p.Ser658Arg	137.0	0.0		87.0	43.0	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	hg19	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	A	9.177	1.022504	0.19433	.	.	ENSG00000174130	ENST00000436693;ENST00000381950	T;T	0.02498	4.27;4.27	4.55	1.93	0.25924	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.393883	0.25419	N	0.030804	T	0.01523	0.0049	N	0.02765	-0.5	0.09310	N	1	B	0.13594	0.008	B	0.16722	0.016	T	0.46303	-0.9201	10	0.87932	D	0	.	8.8328	0.35093	0.7667:0.0:0.2333:0.0	.	658	Q9Y2C9	TLR6_HUMAN	R	658	ENSP00000389600:S658R;ENSP00000371376:S658R	ENSP00000371376:S658R	S	-	3	2	TLR6	38505516	0.000000	0.05858	0.984000	0.44739	0.665000	0.39181	0.174000	0.16743	0.734000	0.32515	0.459000	0.35465	AGT	.	.		0.403	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			T	38829121	A	T	38829121	3	4	26	1	0	0	0	0	1	0	0	0	15970	156	6	4	420	4	TLR6	4	38829121	Missense_Mutation	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10	36867890	38829121	152325155	20	3460										
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140255592	140255592	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	taagtctaaatgagaattttGagcttaaaataaaaacaaaa	5	3	1	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr5:140255592G>T	ENST00000398631.2	+	1	535	c.535G>T	c.(535-537)Gag>Tag	p.E179*	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	179	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAGAATTTTGAGCTTAAAAT	0.378																																					p.E179X	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.G535T						.						47	51	50					5																	140255592		1959	4186	6145	SO:0001587	stop_gained	56137	exon1			AATTTTGAGCTTA	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.535G>T	chr5.hg19:g.140255592G>T	ENSP00000381628:p.Glu179*	185.0	0.0		101.0	37.0	NM_018903	O75278|Q2M1N8	Nonsense_Mutation	SNP	ENST00000398631.2	hg19	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	9.172	1.021408	0.19433	.	.	ENSG00000251664	ENST00000398631	.	.	.	5.07	-4.33	0.03677	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	4.8766	0.13658	0.4124:0.0:0.1962:0.3914	.	.	.	.	X	179	.	ENSP00000381628:E179X	E	+	1	0	PCDHA12	140235776	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-2.792000	0.00766	-0.442000	0.07190	0.591000	0.81541	GAG	.	.		0.378	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		T	140255592	G	T	140255592	4	4	26	1	0	0	0	0	0	1	0	0	11531	1291	45	3	537	3	PCDHA12	5	140255592	Nonsense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10		140255592	40659668	21	3461										
FOXC1	2296	hgsc.bcm.edu	37	chr6	1612016	1612016	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gcagctcgtcgtccctgagtCacggcggcggcggcggcggc	18	15	1	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr6:1612016C>G	ENST00000380874.2	+	1	1336	c.1336C>G	c.(1336-1338)Cac>Gac	p.H446D		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	446					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		GTCCCTGAGTCAcggcggcgg	0.781																																					p.H446D	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.C1336G						.						1	1	1					6																	1612016		321	808	1129	SO:0001583	missense	2296	exon1			CTGAGTCACGGCG	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"Forkhead boxes"	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.1336C>G	chr6.hg19:g.1612016C>G	ENSP00000370256:p.His446Asp	157.0	0.0		120.0	5.0	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Missense_Mutation	SNP	ENST00000380874.2	hg19	CCDS4473.1	.	.	.	.	.	.	.	.	.	.	C	4.868	0.161390	0.09287	.	.	ENSG00000054598	ENST00000380874	T	0.36878	1.23	2.69	2.69	0.31865	.	2.064780	0.03070	U	0.157019	T	0.15825	0.0381	L	0.34521	1.04	0.45791	D	0.998674	B	0.15930	0.015	B	0.06405	0.002	T	0.09907	-1.0653	10	0.27082	T	0.32	.	12.2364	0.54518	0.0:1.0:0.0:0.0	.	446	Q12948	FOXC1_HUMAN	D	446	ENSP00000370256:H446D	ENSP00000370256:H446D	H	+	1	0	FOXC1	1557015	0.998000	0.40836	0.998000	0.56505	0.852000	0.48524	3.555000	0.53727	1.380000	0.46344	0.281000	0.19383	CAC	.	.		0.781	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			G	1612016	C	G	1612016	3	3	26	1	0	0	0	0	1	0	0	0	6002	826	29	4	1338	4	FOXC1	6	1612016	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10		1612016	169503051	22	3462										
SCAND3	114821	hgsc.bcm.edu	37	chr6	28539781	28539781	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ctcaggggataatgtatattTaaactgtttctatgttttgt	8	4	2	0			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr6:28539781T>G	ENST00000452236.2	-	4	4502	c.3885A>C	c.(3883-3885)ttA>ttC	p.L1295F		NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						aatgtatatttaaactgtttc	0.343																																					p.L1295F		Atlas-SNP	.											.	SCAND3	156	.	0			c.A3885C						.						84	83	83					6																	28539781		2203	4300	6503	SO:0001583	missense	114821	exon4			TATATTTAAACTG																												ENST00000452236.2:c.3885A>C	chr6.hg19:g.28539781T>G	ENSP00000395259:p.Leu1295Phe	211.0	0.0		230.0	52.0	NM_052923		Missense_Mutation	SNP	ENST00000452236.2	hg19	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	T	14.70	2.612241	0.46631	.	.	ENSG00000232040	ENST00000452236	T	0.45668	0.89	2.63	1.44	0.22558	HAT dimerisation (1);Ribonuclease H-like (1);	0.000000	0.44688	U	0.000426	T	0.47021	0.1423	M	0.84433	2.695	0.25078	N	0.990944	D	0.69078	0.997	D	0.83275	0.996	T	0.30765	-0.9967	10	0.62326	D	0.03	.	4.5595	0.12152	0.0:0.1559:0.0:0.8441	.	1295	Q6R2W3	SCND3_HUMAN	F	1295	ENSP00000395259:L1295F	ENSP00000395259:L1295F	L	-	3	2	SCAND3	28647760	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.773000	0.26661	0.415000	0.25817	0.533000	0.62120	TTA	.	.		0.343	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			G	28539781	T	G	28539781	3	3	26	1	0	0	0	0	1	0	0	0	13891	1751	61	5	96	5	SCAND3	6	28539781	Missense_Mutation	SNP	T	TCGA-5C-AAPD-01A-21D-A38X-10	26927765	28539781	142575286	23	3463										
GUCA1A	2978	hgsc.bcm.edu	37	chr6	42146134	42146134	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gatgtagatggcaacggctgCattgaccgcgatgagctgct	14	9	0	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr6:42146134C>T	ENST00000394237.1	+	4	1294	c.318C>T	c.(316-318)tgC>tgT	p.C106C	GUCA1A_ENST00000053469.4_Silent_p.C106C|GUCA1A_ENST00000372958.1_Silent_p.C106C|GUCA1A_ENST00000541991.1_Silent_p.C106C			P43080	GUC1A_HUMAN	guanylate cyclase activator 1A (retina)	106	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				phototransduction, visible light (GO:0007603)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;5.54e-05)|Epithelial(12;0.000167)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GCAACGGCTGCATTGACCGCG	0.622																																					p.C106C		Atlas-SNP	.											.	GUCA1A	18	.	0			c.C318T						.						120	111	114					6																	42146134		2203	4300	6503	SO:0001819	synonymous_variant	2978	exon4			CGGCTGCATTGAC		CCDS4864.1	6p21.1	2013-06-06			ENSG00000048545	ENSG00000048545		"EF-hand domain containing"	4678	protein-coding gene	gene with protein product	"cone dystrophy 3"	600364	"chromosome 6 open reading frame 131"	GUCA, GUCA1, C6orf131		9425234	Standard	NM_000409		Approved	GCAP, GCAP1, COD3, dJ139D8.6, CORD14	uc003orx.3	P43080	OTTHUMG00000014696	ENST00000394237.1:c.318C>T	chr6.hg19:g.42146134C>T		79.0	0.0		57.0	15.0	NM_000409	B3KWT4|Q7Z6T1|Q9NU14	Silent	SNP	ENST00000394237.1	hg19	CCDS4864.1																																																																																			.	.		0.622	GUCA1A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316582.1			T	42146134	C	T	42146134	2	4	26	1	0	0	0	0	0	0	0	1	6897	718	25	3		3	GUCA1A	6	42146134	Silent	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	13606353	42146134	128968933	24	3464										
VEGFA	7422	hgsc.bcm.edu	37	chr6	43738861	43738875	+	5'Flank	DEL	GCCCGGGCCTCGGGC	GCCCGGGCCTCGGGC	-													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	cgcgcgctccccaggccctgGcccgggcctcgggccgggga							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	GCCCGGGCCTCGGGC	GCCCGGGCCTCGGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr6:43738861_43738875delGCCCGGGCCTCGGGC	ENST00000523873.1	+	0	0				VEGFA_ENST00000372067.3_In_Frame_Del_p.ARASG140del|VEGFA_ENST00000417285.2_In_Frame_Del_p.ARASG140del|VEGFA_ENST00000230480.6_5'Flank|RP1-261G23.7_ENST00000607600.1_RNA|VEGFA_ENST00000523950.1_5'Flank|VEGFA_ENST00000518689.1_5'Flank|VEGFA_ENST00000324450.6_In_Frame_Del_p.ARASG140del|VEGFA_ENST00000372077.4_5'UTR|VEGFA_ENST00000372064.4_In_Frame_Del_p.ARASG140del|VEGFA_ENST00000520948.1_5'UTR|VEGFA_ENST00000372055.4_In_Frame_Del_p.ARASG140del|VEGFA_ENST00000518824.1_5'Flank|VEGFA_ENST00000482630.2_In_Frame_Del_p.ARASG140del|VEGFA_ENST00000413642.3_In_Frame_Del_p.ARASG140del|VEGFA_ENST00000523125.1_5'Flank|VEGFA_ENST00000425836.2_In_Frame_Del_p.ARASG140del|VEGFA_ENST00000457104.2_5'Flank			P15692	VEGFA_HUMAN	vascular endothelial growth factor A						activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|artery morphogenesis (GO:0048844)|basophil chemotaxis (GO:0002575)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|camera-type eye morphogenesis (GO:0048593)|cardiac muscle fiber development (GO:0048739)|cardiac vascular smooth muscle cell development (GO:0060948)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to hypoxia (GO:0071456)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|dopaminergic neuron differentiation (GO:0071542)|endothelial cell chemotaxis (GO:0035767)|epithelial cell differentiation (GO:0030855)|eye photoreceptor cell development (GO:0042462)|growth (GO:0040007)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|induction of positive chemotaxis (GO:0050930)|kidney development (GO:0001822)|lactation (GO:0007595)|lung development (GO:0030324)|lymph vessel morphogenesis (GO:0036303)|macrophage differentiation (GO:0030225)|mammary gland alveolus development (GO:0060749)|mesoderm development (GO:0007498)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|outflow tract morphogenesis (GO:0003151)|ovarian follicle development (GO:0001541)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cellular component movement (GO:0051272)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine autophosphorylation (GO:1900086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein localization to early endosome (GO:1902966)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor internalization (GO:0002092)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular permeability (GO:0043117)|post-embryonic camera-type eye development (GO:0031077)|primitive erythrocyte differentiation (GO:0060319)|regulation of cell shape (GO:0008360)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)|surfactant homeostasis (GO:0043129)|tube formation (GO:0035148)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|VEGF-activated neuropilin signaling pathway (GO:0038190)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|neuropilin binding (GO:0038191)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor agonist activity (GO:0048018)|vascular endothelial growth factor receptor 1 binding (GO:0043183)|vascular endothelial growth factor receptor 2 binding (GO:0043184)|vascular endothelial growth factor receptor binding (GO:0005172)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9	all_cancers(18;5.46e-07)|all_epithelial(2;5.96e-08)|Lung NSC(15;0.000157)|all_lung(25;0.000486)|Hepatocellular(11;0.00309)		all cancers(41;0.000413)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0742)|OV - Ovarian serous cystadenocarcinoma(102;0.196)		Aflibercept(DB08885)|Bevacizumab(DB00112)|Carvedilol(DB01136)|Dalteparin(DB06779)|Gliclazide(DB01120)|Minocycline(DB01017)|Ranibizumab(DB01270)|Vandetanib(DB05294)	CCAGGCCCTGGCCCGGGCCTCGGGCCGGGGAGGAA	0.791																																					p.139_144del		Atlas-INDEL	.											.	VEGFA	21	.	0			c.417_431del						.																																			SO:0001631	upstream_gene_variant	7422	exon1			.	AB021221	CCDS34457.1, CCDS4907.2, CCDS34458.1, CCDS47432.1, CCDS47433.1, CCDS47434.1, CCDS47435.1, CCDS55007.1, CCDS55008.1, CCDS55009.1, CCDS55010.1, CCDS55011.1, CCDS55012.1, CCDS55013.1, CCDS55014.1, CCDS55015.1, CCDS69125.1	6p12	2008-02-05	2006-10-31	2006-10-31	ENSG00000112715	ENSG00000112715			12680	protein-coding gene	gene with protein product		192240	"vascular endothelial growth factor"	VEGF		8786112	Standard	NM_001025366		Approved	VEGF-A, VPF	uc003owh.3	P15692	OTTHUMG00000014745		chr6.hg19:g.43738861_43738875delGCCCGGGCCTCGGGC	Exception_encountered	56.0	0.0		46.0	10.0	NM_001204385	B5BU86|H0Y2S8|H0Y407|H0Y414|H0Y462|H0Y8N2|H3BLW7|O60720|O75875|Q074Z4|Q16889|Q5UB46|Q6P0P5|Q96KJ0|Q96L82|Q96NW5|Q9H1W8|Q9H1W9|Q9UH58|Q9UL23	In_Frame_Del	DEL	ENST00000523873.1	hg19	CCDS55010.1																																																																																			.	.		0.791	VEGFA-021	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374460.1	NM_001025366		-	43738875	GCCCGGGCCTCGGGC	-	43738861	6	5	26	0	1	1	0	1	0	0	0	0	17165	1203	42	0		0	VEGFA	6	43738861	5'Flank	DEL	GCCCGGGCCTCGGGC	TCGA-5C-AAPD-01A-21D-A38X-10	1592727	43738861	127376206	25	3465										
CAPN11	11131	hgsc.bcm.edu	37	chr6	44148397	44148397	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tgtttaagatagtggcaggaGaggtgagcaggccacgagcg	17	6	0	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr6:44148397G>T	ENST00000398776.1	+	16	1782	c.1744G>T	c.(1744-1746)Gag>Tag	p.E582*	CAPN11_ENST00000542245.1_Nonsense_Mutation_p.E582*	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	582	Domain IV.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AGTGGCAGGAGAGGTGAGCAG	0.597																																					p.E582X		Atlas-SNP	.											.	CAPN11	66	.	0			c.G1744T						.						34	38	36					6																	44148397		1910	4124	6034	SO:0001587	stop_gained	11131	exon16			GCAGGAGAGGTGA	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1744G>T	chr6.hg19:g.44148397G>T	ENSP00000381758:p.Glu582*	111.0	0.0		126.0	28.0	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Nonsense_Mutation	SNP	ENST00000398776.1	hg19	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	g	38	7.091783	0.98059	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	.	.	.	4.54	-0.771	0.11002	.	1.288740	0.05432	N	0.546089	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	8.0704	0.30687	0.1513:0.4039:0.4448:0.0	.	.	.	.	X	582	.	ENSP00000381758:E582X	E	+	1	0	CAPN11	44256375	0.870000	0.30015	0.787000	0.31911	0.861000	0.49209	0.640000	0.24705	-0.249000	0.09569	0.493000	0.49557	GAG	.	.		0.597	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			T	44148397	G	T	44148397	4	4	26	1	0	0	0	0	0	1	0	0	2626	943	33	3	1806	3	CAPN11	6	44148397	Nonsense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	409536	44148397	126966670	26	3466										
PHF3	23469	hgsc.bcm.edu	37	chr6	64408443	64408443	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tcgggacacagatgctaaatAtaagaacaaatatagaagtt	8	5	0	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr6:64408443A>G	ENST00000262043.3	+	8	3270	c.2930A>G	c.(2929-2931)tAt>tGt	p.Y977C	PHF3_ENST00000393387.1_Missense_Mutation_p.Y977C			Q92576	PHF3_HUMAN	PHD finger protein 3	977	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GATGCTAAATATAAGAACAAA	0.328																																					p.Y977C	GBM(135;136 1820 29512 34071 46235)	Atlas-SNP	.											.	PHF3	191	.	0			c.A2930G						.						38	45	43					6																	64408443		2198	4291	6489	SO:0001583	missense	23469	exon7			CTAAATATAAGAA	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.2930A>G	chr6.hg19:g.64408443A>G	ENSP00000262043:p.Tyr977Cys	497.0	0.0		479.0	119.0	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	hg19	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	A	16.50	3.140395	0.56936	.	.	ENSG00000118482	ENST00000506783;ENST00000515594;ENST00000262043;ENST00000393387	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.49	5.49	0.81192	Transcription elongation factor S-IIM (1);Transcription elongation factor S-II, central domain (4);	0.000000	0.36002	N	0.002859	D	0.82435	0.5036	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87750	0.2591	10	0.87932	D	0	-15.7394	15.8791	0.79189	1.0:0.0:0.0:0.0	.	977	Q92576	PHF3_HUMAN	C	791;246;977;977	ENSP00000424694:Y791C;ENSP00000425338:Y246C;ENSP00000262043:Y977C;ENSP00000377048:Y977C	ENSP00000262043:Y977C	Y	+	2	0	PHF3	64466402	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.229000	0.95273	2.213000	0.71641	0.397000	0.26171	TAT	.	.		0.328	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			G	64408443	A	G	64408443	3	3	26	1	0	0	0	0	1	0	0	0	11845	449	16	2	2956	2	PHF3	6	64408443	Missense_Mutation	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10	20260046	64408443	106706624	27	3467										
DAGLB	221955	hgsc.bcm.edu	37	chr7	6474641	6474641	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ggaaaccactgtggcagcgaTgatgatccaactgcaagaca	11	10	0	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr7:6474641T>C	ENST00000297056.6	-	4	599	c.430A>G	c.(430-432)Atc>Gtc	p.I144V	DAGLB_ENST00000421761.2_Intron|DAGLB_ENST00000428902.2_Missense_Mutation_p.I17V|DAGLB_ENST00000425398.2_Intron|DAGLB_ENST00000479922.2_5'Flank|DAGLB_ENST00000436575.1_Missense_Mutation_p.I103V	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	144					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		GTGGCAGCGATGATGATCCAA	0.562																																					p.I144V		Atlas-SNP	.											.	DAGLB	74	.	0			c.A430G						.						64	66	65					7																	6474641		2203	4300	6503	SO:0001583	missense	221955	exon4			CAGCGATGATGAT	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.430A>G	chr7.hg19:g.6474641T>C	ENSP00000297056:p.Ile144Val	119.0	0.0		110.0	26.0	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Missense_Mutation	SNP	ENST00000297056.6	hg19	CCDS5350.1	.	.	.	.	.	.	.	.	.	.	T	12.16	1.856023	0.32791	.	.	ENSG00000164535	ENST00000297056;ENST00000436575;ENST00000471132;ENST00000428902	T;T	0.47177	0.88;0.85	5.34	5.34	0.76211	.	0.139516	0.51477	N	0.000099	T	0.45597	0.1350	M	0.64170	1.965	0.80722	D	1	P	0.35612	0.512	B	0.32677	0.15	T	0.43048	-0.9415	10	0.33940	T	0.23	-10.0322	15.3197	0.74112	0.0:0.0:0.0:1.0	.	144	Q8NCG7	DGLB_HUMAN	V	144;103;144;17	ENSP00000297056:I144V;ENSP00000404785:I103V	ENSP00000297056:I144V	I	-	1	0	DAGLB	6441166	1.000000	0.71417	0.988000	0.46212	0.570000	0.35934	5.836000	0.69375	2.008000	0.58898	0.472000	0.43445	ATC	.	.		0.562	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179		C	6474641	T	C	6474641	3	2	26	1	0	0	0	0	1	0	0	0	4229	1464	51	2	1636	2	DAGLB	7	6474641	Missense_Mutation	SNP	T	TCGA-5C-AAPD-01A-21D-A38X-10		6474641	152664022	28	3468										
HOXA10	3206	hgsc.bcm.edu	37	chr7	27211712	27211712	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	cttctccagctccagtgtctGgtgcttcgtgtaggggcagc	13	12	2	0			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr7:27211712G>T	ENST00000283921.4	-	2	1038	c.1039C>A	c.(1039-1041)Cag>Aag	p.Q347K	MIR196B_ENST00000384852.1_RNA|HOXA10_ENST00000396344.4_Missense_Mutation_p.Q31K|HOXA-AS4_ENST00000523790.1_RNA|HOXA-AS4_ENST00000519694.1_RNA|RP1-170O19.20_ENST00000470747.4_Intron|HOXA-AS4_ENST00000519935.1_RNA|RP1-170O19.20_ENST00000465941.1_Intron|HOXA9_ENST00000497089.1_5'Flank|HOXA10_ENST00000521421.1_5'UTR	NM_018951.3	NP_061824.3	P31260	HXA10_HUMAN	homeobox A10	347					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|male gonad development (GO:0008584)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	9						TCCAGTGTCTGGTGCTTCGTG	0.527																																					p.Q347K		Atlas-SNP	.											.	HOXA10	55	.	0			c.C1039A						.						103	98	99					7																	27211712		2203	4300	6503	SO:0001583	missense	3206	exon2			GTGTCTGGTGCTT		CCDS5410.2	7p15.2	2011-06-20	2005-12-22		ENSG00000253293	ENSG00000253293		"Homeoboxes / ANTP class : HOXL subclass"	5100	protein-coding gene	gene with protein product		142957	"homeo box A10"	HOX1H, HOX1		1973146, 1358459	Standard	NR_037939		Approved		uc011jzm.2	P31260	OTTHUMG00000023436	ENST00000283921.4:c.1039C>A	chr7.hg19:g.27211712G>T	ENSP00000283921:p.Gln347Lys	165.0	0.0		129.0	39.0	NM_018951	O43370|O43605|Q15949|Q504T1	Missense_Mutation	SNP	ENST00000283921.4	hg19	CCDS5410.2	.	.	.	.	.	.	.	.	.	.	G	20.1	3.937710	0.73557	.	.	ENSG00000253293	ENST00000283921;ENST00000396344	D;D	0.97941	-4.62;-4.62	5.7	5.7	0.88788	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000001	D	0.99306	0.9757	H	0.97635	4.045	0.58432	D	0.999992	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.999	D	0.98683	1.0693	10	0.87932	D	0	.	19.8362	0.96658	0.0:0.0:1.0:0.0	.	347;31	P31260;Q504T1	HXA10_HUMAN;.	K	347;31	ENSP00000283921:Q347K;ENSP00000379633:Q31K	ENSP00000283921:Q347K	Q	-	1	0	HOXA10	27178237	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.984000	0.88150	2.690000	0.91761	0.563000	0.77884	CAG	.	.		0.527	HOXA10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358724.2			T	27211712	G	T	27211712	3	4	26	1	0	0	0	0	1	0	0	0	7298	1357	47	3	197	3	HOXA10	7	27211712	Missense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	20737071	27211712	131926951	29	3469										
ASB10	136371	hgsc.bcm.edu	37	chr7	150883974	150883974	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	atcaaagacggaatcaggagCcaggccagtactggagtccg	13	10	2	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr7:150883974C>G	ENST00000420175.2	-	1	268	c.244G>C	c.(244-246)Gct>Cct	p.A82P	ASB10_ENST00000377867.3_Intron|ASB10_ENST00000434669.1_Missense_Mutation_p.A127P|ASB10_ENST00000422024.1_Missense_Mutation_p.A127P|ASB10_ENST00000275838.1_Missense_Mutation_p.A82P			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	82					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAATCAGGAGCCAGGCCAGTA	0.642																																					p.A82P		Atlas-SNP	.											.	ASB10	99	.	0			c.G244C						.						45	48	47					7																	150883974		2203	4300	6503	SO:0001583	missense	136371	exon1			CAGGAGCCAGGCC	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"Ankyrin repeat domain containing"	17185	protein-coding gene	gene with protein product		615054	"ankyrin repeat and SOCS box-containing 10", "glaucoma 1, open angle, F (adult-onset)"	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.244G>C	chr7.hg19:g.150883974C>G	ENSP00000391137:p.Ala82Pro	118.0	0.0		111.0	30.0	NM_001142459	A0AVH0|Q6ZUL6	Missense_Mutation	SNP	ENST00000420175.2	hg19	CCDS47750.2	.	.	.	.	.	.	.	.	.	.	C	11.79	1.744342	0.30865	.	.	ENSG00000146926	ENST00000275838;ENST00000422024;ENST00000434669;ENST00000420175	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	4.37	3.47	0.39725	Ankyrin repeat-containing domain (1);	.	.	.	.	T	0.29389	0.0732	N	0.05230	-0.09	0.22112	N	0.999356	B;B	0.16166	0.016;0.011	B;B	0.18561	0.015;0.022	T	0.09122	-1.0689	9	0.30854	T	0.27	-4.4497	8.1794	0.31302	0.0:0.7484:0.1608:0.0908	.	82;127	Q8WXI3;D5MNW9	ASB10_HUMAN;.	P	82;127;127;82	ENSP00000275838:A82P;ENSP00000401369:A127P;ENSP00000398247:A127P;ENSP00000391137:A82P	ENSP00000275838:A82P	A	-	1	0	ASB10	150514907	0.924000	0.31332	0.999000	0.59377	0.940000	0.58332	0.734000	0.26101	2.143000	0.66587	0.491000	0.48974	GCT	.	.		0.642	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871		G	150883974	C	G	150883974	3	3	26	1	0	0	0	0	1	0	0	0	1014	739	26	4	1179	4	ASB10	7	150883974	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	123672262	150883974	8254689	30	3470										
CDH17	1015	hgsc.bcm.edu	37	chr8	95161092	95161092	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ccaacctcttgtgtctccccTcagtgaatagcttcatcaaa	5	14	5	1	rs558415835		TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr8:95161092T>A	ENST00000027335.3	-	14	1931	c.1807A>T	c.(1807-1809)Agg>Tgg	p.R603W	CDH17_ENST00000450165.2_Missense_Mutation_p.R603W|CDH17_ENST00000441892.2_Missense_Mutation_p.R389W	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	603	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			GTGTCTCCCCTCAGTGAATAG	0.428																																					p.R603W		Atlas-SNP	.											.	CDH17	119	.	0			c.A1807T						.						107	91	96					8																	95161092		2203	4300	6503	SO:0001583	missense	1015	exon14			CTCCCCTCAGTGA	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1807A>T	chr8.hg19:g.95161092T>A	ENSP00000027335:p.Arg603Trp	73.0	0.0		68.0	14.0	NM_004063	Q15336|Q2M2E0	Missense_Mutation	SNP	ENST00000027335.3	hg19	CCDS6260.1	.	.	.	.	.	.	.	.	.	.	T	18.73	3.687113	0.68157	.	.	ENSG00000079112	ENST00000027335;ENST00000441892;ENST00000450165	T;T;T	0.52057	0.68;0.68;0.68	5.91	3.59	0.41128	Cadherin (4);Cadherin-like (1);	0.863480	0.10335	N	0.687002	T	0.56499	0.1989	L	0.39898	1.24	0.25742	N	0.985142	D;D	0.69078	0.997;0.996	D;D	0.73380	0.98;0.928	T	0.41052	-0.9530	10	0.72032	D	0.01	-2.0689	6.6607	0.23012	0.0:0.1787:0.0:0.8213	.	389;603	E7EN24;Q12864	.;CAD17_HUMAN	W	603;389;603	ENSP00000027335:R603W;ENSP00000392811:R389W;ENSP00000401468:R603W	ENSP00000027335:R603W	R	-	1	2	CDH17	95230268	0.758000	0.28405	0.708000	0.30435	0.131000	0.20780	0.855000	0.27805	1.076000	0.40961	0.379000	0.24179	AGG	.	.		0.428	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		A	95161092	T	A	95161092	3	1	26	1	0	0	0	0	1	0	0	0	3104	1550	54	4	711	4	CDH17	8	95161092	Missense_Mutation	SNP	T	TCGA-5C-AAPD-01A-21D-A38X-10		95161092	51202930	31	3471										
SNX31	169166	hgsc.bcm.edu	37	chr8	101624286	101624286	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	acttccaagactaacataagGgagttcaaagtcagccaatt	7	9	2	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr8:101624286G>A	ENST00000311812.2	-	7	703	c.553C>T	c.(553-555)Cct>Tct	p.P185S	SNX31_ENST00000428383.2_Missense_Mutation_p.P86S	NM_152628.3	NP_689841.3	Q8N9S9	SNX31_HUMAN	sorting nexin 31	185					protein transport (GO:0015031)	protein complex (GO:0043234)	phosphatidylinositol binding (GO:0035091)	p.P185S(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|skin(3)|urinary_tract(1)	26	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)			CTAACATAAGGGAGTTCAAAG	0.418																																					p.P185S		Atlas-SNP	.											SNX31,extremity,malignant_melanoma,0,2	SNX31	66	.	1	Substitution - Missense(1)	skin(1)	c.C553T						.						87	88	88					8																	101624286		2203	4300	6503	SO:0001583	missense	169166	exon7			CATAAGGGAGTTC		CCDS6288.1	8q22.3	2011-05-03			ENSG00000174226	ENSG00000174226		"Sorting nexins"	28605	protein-coding gene	gene with protein product						16782399	Standard	NM_152628		Approved	MGC39715	uc003yjr.3	Q8N9S9	OTTHUMG00000164725	ENST00000311812.2:c.553C>T	chr8.hg19:g.101624286G>A	ENSP00000312368:p.Pro185Ser	130.0	1.0		121.0	13.0	NM_152628	C9J6L9|Q8N0U9	Missense_Mutation	SNP	ENST00000311812.2	hg19	CCDS6288.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002348	0.74932	.	.	ENSG00000174226	ENST00000311812;ENST00000428383;ENST00000520352	T;T;T	0.76060	1.91;1.41;-0.99	5.92	5.04	0.67666	.	0.095774	0.44483	D	0.000444	D	0.87220	0.6123	M	0.86953	2.85	0.51012	D	0.999904	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.89208	0.3562	10	0.87932	D	0	-2.5239	13.1125	0.59281	0.0:0.1604:0.8396:0.0	.	86;185	Q8N9S9-2;Q8N9S9	.;SNX31_HUMAN	S	185;86;119	ENSP00000312368:P185S;ENSP00000405024:P86S;ENSP00000428210:P119S	ENSP00000312368:P185S	P	-	1	0	SNX31	101693462	1.000000	0.71417	0.995000	0.50966	0.884000	0.51177	4.973000	0.63763	1.500000	0.48636	0.650000	0.86243	CCT	.	.		0.418	SNX31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379910.1	NM_152628		A	101624286	G	A	101624286	3	1	26	1	0	0	0	0	1	0	0	0	14916	1232	43	3	801	3	SNX31	8	101624286	Missense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	6463194	101624286	44739736	32	3472										
ANKRD20A1	84210	hgsc.bcm.edu	37	chr9	67930803	67930803	+	Frame_Shift_Del	DEL	T	T	-													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ctcactggcagaaaaactgcTttcccatggtgcacatattg							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr9:67930803delT	ENST00000377477.2	+	3	570	c.458delT	c.(457-459)cttfs	p.L153fs		NM_032250.3	NP_115626.2	Q5TYW2	A20A1_HUMAN	ankyrin repeat domain 20 family, member A1	153						plasma membrane (GO:0005886)				kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	11						GAAAAACTGCTTTCCCATGGT	0.418																																					p.L153fs		Atlas-INDEL	.											.	.	.	.	0			c.457delC						.						3	4	4					9																	67930803		307	944	1251	SO:0001589	frameshift_variant	441425	exon3			.	AL136793	CCDS6620.1	9p12	2014-04-16	2005-08-23	2005-08-23	ENSG00000196774	ENSG00000260691		"Ankyrin repeat domain containing"	23665	protein-coding gene	gene with protein product			"ankyrin repeat domain 20A"	ANKRD20A			Standard	NM_032250		Approved	DKFZp434A171		Q5TYW2	OTTHUMG00000188594	ENST00000377477.2:c.458delT	chr9.hg19:g.67930803delT	ENSP00000366697:p.Leu153fs	83.0	0.0		87.0	15.0	NM_001012419	Q9H0H6	Frame_Shift_Del	DEL	ENST00000377477.2	hg19	CCDS6620.1																																																																																			.	.		0.418	ANKRD20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083800.1			-	67930803	T	-	67930803	7	5	26	1	0	1	0	1	0	0	0	0	648	1609	56	0	468	0	ANKRD20A1	9	67930803	Frame_Shift_Del	DEL	T	TCGA-5C-AAPD-01A-21D-A38X-10		67930803	73282628	33	3473										
ANKRD20A4	728747	hgsc.bcm.edu	37	chr9	69386021	69386021	+	Frame_Shift_Del	DEL	T	T	-													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ctcactggcagaaaaactgcTttcccatggtgcacatattg							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr9:69386021delT	ENST00000357336.3	+	3	739	c.458delT	c.(457-459)cttfs	p.L153fs		NM_001098805.1	NP_001092275.1	Q4UJ75	A20A4_HUMAN	ankyrin repeat domain 20 family, member A4	153										breast(1)|large_intestine(1)|liver(1)|lung(9)|pancreas(2)|skin(2)	16						GAAAAACTGCTTTCCCATGGT	0.418																																					p.L153fs		Atlas-INDEL	.											.	ANKRD20A4	38	.	0			c.457delC						.						1	1	1					9																	69386021		76	174	250	SO:0001589	frameshift_variant	728747	exon3			.		CCDS43828.1	9q21.11	2013-01-10			ENSG00000172014	ENSG00000172014		"Ankyrin repeat domain containing"	31982	protein-coding gene	gene with protein product							Standard	NM_001098805		Approved	OTTHUMG00000066855	uc004afn.3	Q4UJ75	OTTHUMG00000066855	ENST00000357336.3:c.458delT	chr9.hg19:g.69386021delT	ENSP00000349891:p.Leu153fs	124.0	0.0		116.0	13.0	NM_001098805		Frame_Shift_Del	DEL	ENST00000357336.3	hg19	CCDS43828.1																																																																																			.	.		0.418	ANKRD20A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143287.3	NM_001098805		-	69386021	T	-	69386021	7	5	26	1	0	1	0	1	0	0	0	0	650	1609	56	0	468	0	ANKRD20A4	9	69386021	Frame_Shift_Del	DEL	T	TCGA-5C-AAPD-01A-21D-A38X-10	1455218	69386021	71827410	34	3474										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77401029	77401029	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ttgggtaaacttcccaggttCtgaaatacagatctaaaaga	8	7	2	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr9:77401029C>T	ENST00000360774.1	-	21	2917	c.2680G>A	c.(2680-2682)Gaa>Aaa	p.E894K	TRPM6_ENST00000361255.3_Missense_Mutation_p.E889K|TRPM6_ENST00000449912.2_Missense_Mutation_p.E889K|TRPM6_ENST00000451710.3_Missense_Mutation_p.E894K|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.E894K|TRPM6_ENST00000376872.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	894					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TTCCCAGGTTCTGAAATACAG	0.393																																					p.E894K		Atlas-SNP	.											.	TRPM6	377	.	0			c.G2680A						.						90	90	90					9																	77401029		2203	4300	6503	SO:0001583	missense	140803	exon21			CAGGTTCTGAAAT	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.2680G>A	chr9.hg19:g.77401029C>T	ENSP00000354006:p.Glu894Lys	201.0	0.0		158.0	44.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	C	19.01	3.744081	0.69418	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07	5.14	5.14	0.70334	Ion transport (1);	0.090386	0.85682	D	0.000000	D	0.83238	0.5211	M	0.89904	3.07	0.80722	D	1	D;P;D	0.76494	0.966;0.836;0.999	P;P;D	0.74023	0.89;0.794;0.982	D	0.86666	0.1907	10	0.87932	D	0	.	18.7871	0.91960	0.0:1.0:0.0:0.0	.	557;894;889	F5H7D1;Q9BX84;Q9BX84-3	.;TRPM6_HUMAN;.	K	894;894;889;889;894;557;557	ENSP00000354006:E894K;ENSP00000407341:E894K;ENSP00000396672:E889K;ENSP00000354962:E889K;ENSP00000366060:E894K	ENSP00000309693:E557K	E	-	1	0	TRPM6	76590849	1.000000	0.71417	1.000000	0.80357	0.056000	0.15407	7.602000	0.82796	2.669000	0.90835	0.549000	0.68633	GAA	.	.		0.393	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		T	77401029	C	T	77401029	3	4	26	1	0	0	0	0	1	0	0	0	16605	922	32	3	3464	3	TRPM6	9	77401029	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	8015008	77401029	63812402	35	3475										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77427340	77427340	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	atctgacattgcttgttccaGggcatcaggcttcagaaagc	10	10	3	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr9:77427340G>T	ENST00000360774.1	-	12	1555	c.1318C>A	c.(1318-1320)Ctg>Atg	p.L440M	TRPM6_ENST00000361255.3_Missense_Mutation_p.L435M|TRPM6_ENST00000449912.2_Missense_Mutation_p.L435M|TRPM6_ENST00000451710.3_Missense_Mutation_p.L440M|TRPM6_ENST00000376871.3_Missense_Mutation_p.L440M|TRPM6_ENST00000376864.4_Missense_Mutation_p.L440M|TRPM6_ENST00000376872.3_Missense_Mutation_p.L440M	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	440					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						GCTTGTTCCAGGGCATCAGGC	0.353																																					p.L440M		Atlas-SNP	.											.	TRPM6	377	.	0			c.C1318A						.						77	72	74					9																	77427340		2203	4300	6503	SO:0001583	missense	140803	exon12			GTTCCAGGGCATC	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.1318C>A	chr9.hg19:g.77427340G>T	ENSP00000354006:p.Leu440Met	93.0	0.0		99.0	4.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.727154	0.48833	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22;0.22;0.22	5.7	3.63	0.41609	.	0.000000	0.85682	D	0.000000	T	0.77246	0.4102	M	0.93375	3.41	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;0.999;1.0	T	0.77960	-0.2391	10	0.87932	D	0	.	4.2243	0.10574	0.4623:0.0:0.5377:0.0	.	440;440;440;435	Q9BX84-6;Q9BX84-5;Q9BX84;Q9BX84-3	.;.;TRPM6_HUMAN;.	M	440;440;440;440;435;435;440;103;103	ENSP00000354006:L440M;ENSP00000407341:L440M;ENSP00000366068:L440M;ENSP00000366067:L440M;ENSP00000396672:L435M;ENSP00000354962:L435M;ENSP00000366060:L440M	ENSP00000309693:L103M	L	-	1	2	TRPM6	76617160	0.893000	0.30496	0.825000	0.32803	0.459000	0.32528	1.730000	0.38125	1.405000	0.46838	0.650000	0.86243	CTG	.	.		0.353	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		T	77427340	G	T	77427340	3	4	26	1	0	0	0	0	1	0	0	0	16605	991	35	3	4862	3	TRPM6	9	77427340	Missense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	26311	77427340	63786091	36	3476										
RALGPS1	9649	hgsc.bcm.edu	37	chr9	129831597	129831597	+	Frame_Shift_Del	DEL	T	T	-													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	caagcggacacgggaatataTccgaagcctgaagatggttc							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr9:129831597delT	ENST00000259351.5	+	8	839	c.572delT	c.(571-573)atcfs	p.I191fs	RALGPS1_ENST00000373436.1_Frame_Shift_Del_p.I191fs|RALGPS1_ENST00000373434.1_Frame_Shift_Del_p.I191fs|RALGPS1_ENST00000394022.3_Frame_Shift_Del_p.I191fs|RALGPS1_ENST00000424082.2_Frame_Shift_Del_p.I191fs	NM_014636.2	NP_055451.1	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1	191	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ral GTPase activity (GO:0032852)|regulation of Ral protein signal transduction (GO:0032485)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ral guanyl-nucleotide exchange factor activity (GO:0008321)			kidney(2)|large_intestine(6)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19						CGGGAATATATCCGAAGCCTG	0.368																																					p.I191fs		Atlas-Indel,Pindel	.											.	RALGPS1	86	.	0			c.571delA						.						108	111	110					9																	129831597		2203	4300	6503	SO:0001589	frameshift_variant	9649	exon8			.	AB002349	CCDS35143.1, CCDS55344.1, CCDS55345.1, CCDS55346.1	9q33.3	2013-01-10			ENSG00000136828	ENSG00000136828		"Pleckstrin homology (PH) domain containing"	16851	protein-coding gene	gene with protein product		614444				9205841, 10747847	Standard	NM_001190728		Approved	RALGPS1A, RALGEF2, KIAA0351	uc004bqo.2	Q5JS13	OTTHUMG00000020696	ENST00000259351.5:c.572delT	chr9.hg19:g.129831597delT	ENSP00000259351:p.Ile191fs	113.0	0.0		94.0	28.0	NM_001190729	B4DR86|E9PBQ5|O15059|Q5JT60|Q5JT65|Q5JUG5|Q8N4S6|Q8N5H4|Q8WUV7|Q9NZ16	Frame_Shift_Del	DEL	ENST00000259351.5	hg19	CCDS35143.1																																																																																			.	.		0.368	RALGPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054133.1	NM_014636		-	129831597	T	-	129831597	7	5	26	1	0	1	0	1	0	0	0	0	13032	1435	50	0	598	0	RALGPS1	9	129831597	Frame_Shift_Del	DEL	T	TCGA-5C-AAPD-01A-21D-A38X-10	52404257	129831597	11381834	37	3477										
ST6GALNAC6	30815	hgsc.bcm.edu	37	chr9	130649801	130649801	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	accatgccatagacatgcacGtggtcacacaactccaccgc	7	16	1	1	rs145170753		TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr9:130649801G>A	ENST00000373146.1	-	6	953	c.774C>T	c.(772-774)caC>caT	p.H258H	ST6GALNAC6_ENST00000373141.1_Silent_p.H224H|RP11-203J24.9_ENST00000476274.2_RNA|ST6GALNAC6_ENST00000291839.5_Silent_p.H258H|ST6GALNAC6_ENST00000542456.1_Silent_p.H58H|ST6GALNAC6_ENST00000485320.1_5'UTR|ST6GALNAC6_ENST00000373142.1_Silent_p.H258H|ST6GALNAC6_ENST00000373144.3_Silent_p.H224H			Q969X2	SIA7F_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	258					cell-cell recognition (GO:0009988)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						AGACATGCACGTGGTCACACA	0.612																																					p.H258H		Atlas-SNP	.											.	ST6GALNAC6	36	.	0			c.C774T						.	G		1,4405	2.1+/-5.4	0,1,2202	167	96	120		774	-6.5	0.9	9	dbSNP_134	120	0,8600		0,0,4300	no	coding-synonymous	ST6GALNAC6	NM_013443.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		258/334	130649801	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	30815	exon6			ATGCACGTGGTCA	BC006564	CCDS6882.1, CCDS69668.1, CCDS69669.1, CCDS75908.1	9q34.13	2013-03-01		2005-02-07	ENSG00000160408	ENSG00000160408		"Sialyltransferases"	23364	protein-coding gene	gene with protein product		610135	"sialytransferase 7 ((alpha-N-acetylneuraminyl 2,3-betagalactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialytransferase) F"	SIAT7F		12668675	Standard	XM_005251952		Approved	ST6GALNACVI	uc004bso.1	Q969X2	OTTHUMG00000020718	ENST00000373146.1:c.774C>T	chr9.hg19:g.130649801G>A		120.0	0.0		147.0	15.0	NM_013443	B3KQ01|Q5T9C4|Q5T9C5|Q9H8A2|Q9ULB8	Silent	SNP	ENST00000373146.1	hg19	CCDS6882.1																																																																																			.	G|1.000;A|0.000		0.612	ST6GALNAC6-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054278.1	NM_013443		A	130649801	G	A	130649801	2	1	26	1	0	0	0	0	0	0	0	1	15243	1136	40	1		1	ST6GALNAC6	9	130649801	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	818204	130649801	10563630	38	3478										
OR2D2	120776	hgsc.bcm.edu	37	chr11	6913415	6913415	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	cgcactgggtacacccaaaaAtgaggaaaaagagaagtcga	11	8	0	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr11:6913415A>T	ENST00000299459.2	-	1	415	c.317T>A	c.(316-318)aTt>aAt	p.I106N		NM_003700.1	NP_003691.1	Q9H210	OR2D2_HUMAN	olfactory receptor, family 2, subfamily D, member 2	106					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	18		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		ACACCCAAAAATGAGGAAAAA	0.468																																					p.I106N		Atlas-SNP	.											.	OR2D2	52	.	0			c.T317A						.						115	94	101					11																	6913415		2201	4296	6497	SO:0001583	missense	120776	exon1			CCAAAAATGAGGA	AB065824	CCDS31416.1	11p15.4	2012-08-09			ENSG00000166368	ENSG00000166368		"GPCR / Class A : Olfactory receptors"	8244	protein-coding gene	gene with protein product		608494		OR2D1		9787077	Standard	NM_003700		Approved	OR11-610, hg27	uc010rau.2	Q9H210	OTTHUMG00000165741	ENST00000299459.2:c.317T>A	chr11.hg19:g.6913415A>T	ENSP00000299459:p.Ile106Asn	281.0	0.0		152.0	34.0	NM_003700	B9EIL5|O95224|Q6IF28|Q8NGH4|Q96R52	Missense_Mutation	SNP	ENST00000299459.2	hg19	CCDS31416.1	.	.	.	.	.	.	.	.	.	.	a	8.937	0.964800	0.18583	.	.	ENSG00000166368	ENST00000299459	T	0.01323	5.01	5.23	5.23	0.72850	GPCR, rhodopsin-like superfamily (1);	0.134994	0.33515	N	0.004822	T	0.01976	0.0062	L	0.46614	1.455	0.09310	N	1	P	0.43885	0.82	B	0.42555	0.391	T	0.50996	-0.8761	10	0.37606	T	0.19	-21.1989	7.9016	0.29738	0.9104:0.0:0.0896:0.0	.	106	Q9H210	OR2D2_HUMAN	N	106	ENSP00000299459:I106N	ENSP00000299459:I106N	I	-	2	0	OR2D2	6869991	0.112000	0.22096	0.007000	0.13788	0.433000	0.31745	3.913000	0.56394	2.337000	0.79520	0.524000	0.50904	ATT	.	.		0.468	OR2D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385986.1	NM_003700		T	6913415	A	T	6913415	3	4	26	1	0	0	0	0	1	0	0	0	11003	101	4	4	612	4	OR2D2	11	6913415	Missense_Mutation	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10		6913415	128093101	39	3479										
EEF1G	1937	hgsc.bcm.edu	37	chr11	62327913	62327913	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gtacttgcgcttaaattcatCcaacacaaaggtactaagag	7	9	1	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr11:62327913C>T	ENST00000329251.4	-	8	1001	c.871G>A	c.(871-873)Gat>Aat	p.D291N	EEF1G_ENST00000378019.3_Missense_Mutation_p.D341N|MIR3654_ENST00000496634.2_3'UTR	NM_001404.4	NP_001395.1	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1 gamma	291	EF-1-gamma C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00519}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to virus (GO:0009615)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	translation elongation factor activity (GO:0003746)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TTAAATTCATCCAACACAAAG	0.458																																					p.D291N		Atlas-SNP	.											.	EEF1G	33	.	0			c.G871A						.						32	29	30					11																	62327913		1917	4120	6037	SO:0001583	missense	1937	exon8			ATTCATCCAACAC	X63526	CCDS44626.1	11q12.3	2008-02-05			ENSG00000254772	ENSG00000254772			3213	protein-coding gene	gene with protein product		130593				1598220, 1461723	Standard	NM_001404		Approved	EF1G	uc001ntm.1	P26641	OTTHUMG00000167567	ENST00000329251.4:c.871G>A	chr11.hg19:g.62327913C>T	ENSP00000331901:p.Asp291Asn	118.0	0.0		66.0	16.0	NM_001404	B4DTG2|Q6PJ62|Q6PK31|Q96CU2|Q9P196	Missense_Mutation	SNP	ENST00000329251.4	hg19	CCDS44626.1	.	.	.	.	.	.	.	.	.	.	C	19.85	3.903395	0.72754	.	.	ENSG00000254772	ENST00000329251;ENST00000378019;ENST00000424909	T;T	0.35973	1.37;1.28	4.7	4.7	0.59300	Translation elongation factor EF1B, gamma chain, conserved (4);	0.000000	0.85682	D	0.000000	T	0.59542	0.2201	M	0.89658	3.05	0.80722	D	1	B;B;B	0.25904	0.105;0.137;0.119	B;B;B	0.43445	0.187;0.42;0.38	T	0.66056	-0.6018	10	0.66056	D	0.02	.	15.2077	0.73192	0.0:1.0:0.0:0.0	.	341;60;291	B4DTG2;B4DUP0;P26641	.;.;EF1G_HUMAN	N	291;341;60	ENSP00000331901:D291N;ENSP00000367258:D341N	ENSP00000331901:D291N	D	-	1	0	EEF1G	62084489	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.485000	0.81204	2.465000	0.83290	0.550000	0.68814	GAT	.	.		0.458	EEF1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395047.1	NM_001404		T	62327913	C	T	62327913	3	4	26	1	0	0	0	0	1	0	0	0	4930	855	30	3	454	3	EEF1G	11	62327913	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	55414498	62327913	72678603	40	3480										
MACROD1	28992	hgsc.bcm.edu	37	chr11	63767228	63767228	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gcgatgggccccactgtgtgGatgacgtctacggggggcga	18	10	1	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr11:63767228G>T	ENST00000255681.6	-	6	738	c.672C>A	c.(670-672)atC>atA	p.I224I	OTUB1_ENST00000535715.1_Intron	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1	224	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						CCACTGTGTGGATGACGTCTA	0.706																																					p.I224I		Atlas-SNP	.											.	MACROD1	17	.	0			c.C672A						.						11	15	13					11																	63767228		2152	4216	6368	SO:0001819	synonymous_variant	28992	exon6			TGTGTGGATGACG	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.672C>A	chr11.hg19:g.63767228G>T		109.0	0.0		59.0	12.0	NM_014067	Q9UH96	Silent	SNP	ENST00000255681.6	hg19	CCDS8056.1																																																																																			.	.		0.706	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		T	63767228	G	T	63767228	2	4	26	1	0	0	0	0	0	0	0	1	9154	1164	41	3		3	MACROD1	11	63767228	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	1439315	63767228	71239288	41	3481										
AKAP3	10566	hgsc.bcm.edu	37	chr12	4736121	4736121	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	atcttggtcagcccagaaagGgcaccaggggtctcatcatc	11	12	4	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr12:4736121G>T	ENST00000545990.2	-	5	2471	c.1947C>A	c.(1945-1947)gcC>gcA	p.A649A	AKAP3_ENST00000228850.1_Silent_p.A649A|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	649					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						GCCCAGAAAGGGCACCAGGGG	0.522																																					p.A649A		Atlas-SNP	.											.	AKAP3	212	.	0			c.C1947A						.						54	48	50					12																	4736121		2203	4300	6503	SO:0001819	synonymous_variant	10566	exon4			AGAAAGGGCACCA	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.1947C>A	chr12.hg19:g.4736121G>T		76.0	0.0		77.0	24.0	NM_006422	O75945|Q86X01|Q9UM61	Silent	SNP	ENST00000545990.2	hg19	CCDS8531.1																																																																																			.	.		0.522	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		T	4736121	G	T	4736121	2	4	26	1	0	0	0	0	0	0	0	1	452	1219	43	3		3	AKAP3	12	4736121	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10		4736121	129115774	42	3482										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48368646	48368646	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ggggtcaatccagtagtctcCtgcagggggaagaggcagca	16	9	2	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr12:48368646C>T	ENST00000380518.3	-	52	4051		c.e52-1		COL2A1_ENST00000493991.1_Splice_Site|COL2A1_ENST00000337299.6_Splice_Site	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1						axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CAGTAGTCTCCTGCAGGGGGA	0.572																																					.		Atlas-SNP	.											.	COL2A1	368	.	0			c.3680-1G>A						.						67	67	67					12																	48368646		2203	4300	6503	SO:0001630	splice_region_variant	1280	exon52			AGTCTCCTGCAGG	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.3887-1G>A	chr12.hg19:g.48368646C>T		66.0	0.0		55.0	16.0	NM_033150	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Splice_Site	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.349141	0.82132	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.095	0.89487	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL2A1	46654913	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.770000	0.85390	2.444000	0.82710	0.561000	0.74099	.	.	.		0.572	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	Intron	T	48368646	C	T	48368646	5	4	26	1	0	0	0	0	0	0	1	0	3689	695	24	3	589	3	COL2A1	12	48368646	Splice_Site	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	43632525	48368646	85483249	43	3483										
SPATS2	65244	hgsc.bcm.edu	37	chr12	49884489	49884489	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tgccagtgaagtactcaaagAatggacagtaacaggcaaga	11	7	1	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr12:49884489A>G	ENST00000553127.1	+	7	752	c.239A>G	c.(238-240)gAa>gGa	p.E80G	SPATS2_ENST00000321898.6_Missense_Mutation_p.E80G|SPATS2_ENST00000552557.1_3'UTR|SPATS2_ENST00000552918.1_Missense_Mutation_p.E80G			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	80						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						GTACTCAAAGAATGGACAGTA	0.353																																					p.E80G		Atlas-SNP	.											.	SPATS2	43	.	0			c.A239G						.						122	113	116					12																	49884489		2203	4300	6503	SO:0001583	missense	65244	exon6			TCAAAGAATGGAC	AK023179	CCDS31794.1	12q13.12	2009-06-12							18650	protein-coding gene	gene with protein product		611667				11944913, 17989879	Standard	NM_023071		Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000553127.1:c.239A>G	chr12.hg19:g.49884489A>G	ENSP00000448228:p.Glu80Gly	77.0	0.0		81.0	21.0	NM_023071	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	Missense_Mutation	SNP	ENST00000553127.1	hg19	CCDS31794.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.801910	0.90538	.	.	ENSG00000123352	ENST00000550997;ENST00000553127;ENST00000321898;ENST00000552918;ENST00000395063	.	.	.	5.24	5.24	0.73138	UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.69459	0.3113	L	0.58101	1.795	0.80722	D	1	D	0.89917	1.0	D	0.66084	0.941	T	0.72721	-0.4208	9	0.87932	D	0	-20.8127	11.5475	0.50702	1.0:0.0:0.0:0.0	.	80	Q86XZ4	SPAS2_HUMAN	G	80	.	ENSP00000326841:E80G	E	+	2	0	SPATS2	48170756	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.714000	0.84703	1.974000	0.57490	0.472000	0.43445	GAA	.	.		0.353	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404023.1	NM_023071		G	49884489	A	G	49884489	3	3	26	1	0	0	0	0	1	0	0	0	15034	246	9	2	253	2	SPATS2	12	49884489	Missense_Mutation	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10	1515843	49884489	83967406	44	3484										
HSD17B6	8630	hgsc.bcm.edu	37	chr12	57180989	57180989	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	actgcatggaacatgctctgAcatcggtgcatccgcgaact	10	12	1	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr12:57180989A>C	ENST00000554643.1	+	6	1166	c.817A>C	c.(817-819)Aca>Cca	p.T273P	HSD17B6_ENST00000554150.1_Missense_Mutation_p.T273P|HSD17B6_ENST00000555159.1_Missense_Mutation_p.T273P|HSD17B6_ENST00000555805.1_Missense_Mutation_p.T273P|HSD17B6_ENST00000322165.1_Missense_Mutation_p.T273P			O14756	H17B6_HUMAN	hydroxysteroid (17-beta) dehydrogenase 6	273					androgen biosynthetic process (GO:0006702)|androgen catabolic process (GO:0006710)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|intracellular (GO:0005622)|membrane (GO:0016020)	catalytic activity (GO:0003824)|electron carrier activity (GO:0009055)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|oxidoreductase activity (GO:0016491)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			endometrium(1)|large_intestine(2)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10					Succinic acid(DB00139)	ACATGCTCTGACATCGGTGCA	0.408																																					p.T273P		Atlas-SNP	.											.	HSD17B6	26	.	0			c.A817C						.						143	123	130					12																	57180989		2203	4300	6503	SO:0001583	missense	8630	exon5			GCTCTGACATCGG	AF016509	CCDS8925.1	12q13.3	2012-12-07	2012-12-07		ENSG00000025423	ENSG00000025423	1.1.1.62, 1.1.1.63, 1.1.1.105	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	23316	protein-coding gene	gene with protein product	"oxidative 3-alpha-hydroxysteroid-dehydrogenase", "3(alpha->beta)-hydroxysteroid epimerasel", "retinol dehydrogenase", "oxidoreductase", "NAD+ -dependent 3 alpha-hydroxysteroid dehydrogenase", "3-hydroxysteroid epimerase", "short chain dehydrogenase/reductase family 9C, member 6"	606623	"hydroxysteroid (17-beta) dehydrogenase 6", "hydroxysteroid (17-beta) dehydrogenase 6 homolog (mouse)"			11165032, 19027726	Standard	XM_005269207		Approved	HSE, RODH, SDR9C6	uc001smg.1	O14756	OTTHUMG00000170854	ENST00000554643.1:c.817A>C	chr12.hg19:g.57180989A>C	ENSP00000451406:p.Thr273Pro	128.0	0.0		79.0	18.0	NM_003725	O43275	Missense_Mutation	SNP	ENST00000554643.1	hg19	CCDS8925.1	.	.	.	.	.	.	.	.	.	.	a	18.15	3.561025	0.65538	.	.	ENSG00000025423	ENST00000555159;ENST00000555805;ENST00000554643;ENST00000554150;ENST00000322165	D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18	4.97	3.83	0.44106	NAD(P)-binding domain (1);	0.356817	0.23995	N	0.042535	D	0.93641	0.7969	M	0.93678	3.445	0.32712	N	0.511418	D	0.63880	0.993	D	0.63033	0.91	D	0.94324	0.7556	10	0.54805	T	0.06	.	9.6529	0.39908	0.9158:0.0:0.0842:0.0	.	273	O14756	H17B6_HUMAN	P	273	ENSP00000450698:T273P;ENSP00000451753:T273P;ENSP00000451406:T273P;ENSP00000452273:T273P;ENSP00000318631:T273P	ENSP00000318631:T273P	T	+	1	0	HSD17B6	55467256	1.000000	0.71417	0.760000	0.31359	0.865000	0.49528	3.500000	0.53318	0.912000	0.36772	0.529000	0.55759	ACA	.	.		0.408	HSD17B6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410714.1	NM_003725		C	57180989	A	C	57180989	3	2	26	1	0	0	0	0	1	0	0	0	7396	275	10	5	831	5	HSD17B6	12	57180989	Missense_Mutation	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10	7296500	57180989	76670906	45	3485										
RASSF9	9182	hgsc.bcm.edu	37	chr12	86198626	86198626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	aatctccccattgctactggGaacctcagattccttcgctc	6	15	2	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr12:86198626G>A	ENST00000361228.3	-	2	1530	c.1162C>T	c.(1162-1164)Ccc>Tcc	p.P388S		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	388					endosomal transport (GO:0016197)|protein targeting (GO:0006605)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|trans-Golgi network transport vesicle membrane (GO:0012510)	transporter activity (GO:0005215)			endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TTGCTACTGGGAACCTCAGAT	0.418																																					p.P388S		Atlas-SNP	.											.	RASSF9	100	.	0			c.C1162T						.						182	176	178					12																	86198626		1909	4139	6048	SO:0001583	missense	9182	exon2			TACTGGGAACCTC		CCDS44950.1	12q21.31	2008-02-22	2008-02-22	2008-02-22		ENSG00000198774			15739	protein-coding gene	gene with protein product		610383	"peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor"	PAMCI		9837933, 18272789	Standard	NM_005447		Approved	P-CIP1	uc001taf.1	O75901	OTTHUMG00000169831	ENST00000361228.3:c.1162C>T	chr12.hg19:g.86198626G>A	ENSP00000354884:p.Pro388Ser	168.0	0.0		146.0	40.0	NM_005447	B3KMQ4|Q8N5U8	Missense_Mutation	SNP	ENST00000361228.3	hg19	CCDS44950.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.730573	0.00687	.	.	ENSG00000198774	ENST00000361228	T	0.43294	0.95	5.29	-3.56	0.04626	.	1.610810	0.03755	N	0.257253	T	0.23054	0.0557	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.08554	-1.0716	10	0.33940	T	0.23	-9.833	1.3355	0.02144	0.4052:0.1646:0.2774:0.1527	.	388	O75901	RASF9_HUMAN	S	388	ENSP00000354884:P388S	ENSP00000354884:P388S	P	-	1	0	RASSF9	84722757	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.288000	0.08377	-0.623000	0.05618	-1.847000	0.00572	CCC	.	.		0.418	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406109.1			A	86198626	G	A	86198626	3	1	26	1	0	0	0	0	1	0	0	0	13108	1174	41	3	149	3	RASSF9	12	86198626	Missense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	29017637	86198626	47653269	46	3486										
BRAP	8315	hgsc.bcm.edu	37	chr12	112082089	112082089	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gctcgaggccgaggccatggCgatgttgatctgtccctcct	13	13	1	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr12:112082089C>T	ENST00000327551.6	-	12	1743	c.1603G>A	c.(1603-1605)Gcc>Acc	p.A535T	BRAP_ENST00000539060.1_Missense_Mutation_p.A386T|BRAP_ENST00000419234.4_Missense_Mutation_p.A565T			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	0					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						GAGGCCATGGCGATGTTGATC	0.612																																					p.A565T	Pancreas(146;846 1904 7830 25130 26065)	Atlas-SNP	.											.	BRAP	42	.	0			c.G1693A						.						127	103	111					12																	112082089		2203	4300	6503	SO:0001583	missense	8315	exon12			CCATGGCGATGTT	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"RING-type (C3HC4) zinc fingers"	1099	protein-coding gene	gene with protein product	"impedes mitogenic signal propagation", "galectin-2-binding protein"	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.1603G>A	chr12.hg19:g.112082089C>T	ENSP00000330813:p.Ala535Thr	80.0	0.0		75.0	18.0	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000327551.6	hg19		.	.	.	.	.	.	.	.	.	.	C	19.15	3.772596	0.69992	.	.	ENSG00000089234	ENST00000419234;ENST00000539060;ENST00000327551	T;T;T	0.46063	0.88;0.9;0.89	5.8	-1.07	0.09968	.	0.430676	0.25380	N	0.031099	T	0.38161	0.1030	L	0.55103	1.725	0.37325	D	0.909745	B;P	0.43909	0.327;0.821	B;B	0.38500	0.05;0.275	T	0.44651	-0.9314	10	0.20046	T	0.44	-0.0437	21.6149	0.99957	0.0:0.3762:0.6238:0.0	.	386;565	B4DRM1;Q7Z569	.;BRAP_HUMAN	T	565;386;535	ENSP00000403524:A565T;ENSP00000441659:A386T;ENSP00000330813:A535T	ENSP00000330813:A535T	A	-	1	0	BRAP	110566472	0.426000	0.25506	0.151000	0.22473	0.957000	0.61999	0.661000	0.25023	-0.501000	0.06605	-0.264000	0.10439	GCC	.	.		0.612	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			T	112082089	C	T	112082089	3	4	26	1	0	0	0	0	1	0	0	0	1499	768	27	1	89	1	BRAP	12	112082089	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	25883463	112082089	21769806	47	3487										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112638476	112638476	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gttggtattgtccagtgtgaCcagcccattggtggcagtcc	13	10	0	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr12:112638476C>G	ENST00000430131.2	-	54	8412	c.7267G>C	c.(7267-7269)Gtc>Ctc	p.V2423L	HECTD4_ENST00000550722.1_Missense_Mutation_p.V2699L|HECTD4_ENST00000377560.5_Missense_Mutation_p.V2673L			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2423					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TCCAGTGTGACCAGCCCATTG	0.517																																					p.V2711L		Atlas-SNP	.											.	.	.	.	0			c.G8131C						.						141	137	138					12																	112638476		2011	4176	6187	SO:0001583	missense	283450	exon55			GTGTGACCAGCCC	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.7267G>C	chr12.hg19:g.112638476C>G	ENSP00000404379:p.Val2423Leu	191.0	0.0		162.0	48.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	C	35	5.544317	0.96488	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722;ENST00000548896	T;T;T	0.46819	0.86;0.86;0.86	5.86	5.86	0.93980	.	.	.	.	.	T	0.56601	0.1996	N	0.24115	0.695	0.58432	D	0.999999	P	0.44690	0.841	P	0.58820	0.846	T	0.57676	-0.7770	9	0.87932	D	0	.	20.5632	0.99335	0.0:1.0:0.0:0.0	.	2423	Q9Y4D8	K0614_HUMAN	L	2673;2423;2699;54	ENSP00000366783:V2673L;ENSP00000404379:V2423L;ENSP00000449784:V2699L	ENSP00000366783:V2673L	V	-	1	0	C12orf51	111122859	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.226000	0.78060	2.937000	0.99478	0.650000	0.86243	GTC	.	.		0.517	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		G	112638476	C	G	112638476	3	3	26	1	0	0	0	0	1	0	0	0	1698	507	18	4	4811	4	C12orf51	12	112638476	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	556387	112638476	21213419	48	3488										
GOLGA3	2802	hgsc.bcm.edu	37	chr12	133358980	133358980	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tgcgttggactgaccgaggcCcgtaagcttccctttctcgt	11	13	1	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr12:133358980C>T	ENST00000450791.2	-	16	3550	c.3367G>A	c.(3367-3369)Ggc>Agc	p.G1123S	GOLGA3_ENST00000456883.2_Missense_Mutation_p.G1123S|GOLGA3_ENST00000204726.3_Missense_Mutation_p.G1123S			Q08378	GOGA3_HUMAN	golgin A3	1123					intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		TGACCGAGGCCCGTAAGCTTC	0.502																																					p.G1123S		Atlas-SNP	.											.	GOLGA3	234	.	0			c.G3367A						.						225	206	212					12																	133358980		2203	4300	6503	SO:0001583	missense	2802	exon17			CGAGGCCCGTAAG	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"SY2/SY10 protein", "Golgi complex-associated protein of 170 kD"	602581	"golgi autoantigen, golgin subfamily a, 3"			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.3367G>A	chr12.hg19:g.133358980C>T	ENSP00000410378:p.Gly1123Ser	115.0	0.0		123.0	33.0	NM_005895	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	hg19	CCDS9281.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.523369	0.85600	.	.	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883	T;T;T	0.68903	-0.36;-0.36;-0.31	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.74496	0.3724	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.75593	-0.3264	10	0.59425	D	0.04	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	1123;1123	Q08378-2;Q08378	.;GOGA3_HUMAN	S	1123	ENSP00000204726:G1123S;ENSP00000410378:G1123S;ENSP00000409303:G1123S	ENSP00000204726:G1123S	G	-	1	0	GOLGA3	131869053	1.000000	0.71417	0.886000	0.34754	0.046000	0.14306	7.629000	0.83207	2.884000	0.98904	0.655000	0.94253	GGC	.	.		0.502	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895		T	133358980	C	T	133358980	3	4	26	1	0	0	0	0	1	0	0	0	6562	623	22	3	1161	3	GOLGA3	12	133358980	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	20720504	133358980	492915	49	3489										
RB1	5925	hgsc.bcm.edu	37	chr13	49037924	49037924	+	Frame_Shift_Del	DEL	A	A	-													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	agaatatagaccttaaattcAaaatcattgtaacagcatac					rs587778849		TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr13:49037924delA	ENST00000267163.4	+	21	2302	c.2164delA	c.(2164-2166)aaafs	p.K722fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	722	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.I703_E737del(2)|p.C712_A727del(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CCTTAAATTCAAAATCATTGT	0.294		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.F721fs		Pindel	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	28	Whole gene deletion(15)|Unknown(10)|Deletion - In frame(3)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|ovary(1)|prostate(1)|liver(1)	c.2163delC	GRCh37	CM030514	RB1	M		.						109	115	112					13																	49037924		2203	4288	6491	SO:0001589	frameshift_variant	5925	exon21	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2164delA	chr13.hg19:g.49037924delA	ENSP00000267163:p.Lys722fs	443.0	0.0		397.0	115.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Del	DEL	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.294	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			-	49037924	A	-	49037924	7	5	26	1	0	1	0	1	0	0	0	0	13113	131	5	0	2246	0	RB1	13	49037924	Frame_Shift_Del	DEL	A	TCGA-5C-AAPD-01A-21D-A38X-10		49037924	66131954	50	3490										
ATL1	51062	hgsc.bcm.edu	37	chr14	51060573	51060573	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tctttatcaaggtatataacTtatcccaaaatgtccaggag	6	8	2	0			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr14:51060573T>G	ENST00000358385.6	+	5	773	c.532T>G	c.(532-534)Tta>Gta	p.L178V	ATL1_ENST00000441560.2_Missense_Mutation_p.L178V|ATL1_ENST00000357032.3_Missense_Mutation_p.L178V|ATL1_ENST00000354525.4_Missense_Mutation_p.L178V	NM_015915.4	NP_056999.2	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	178	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						GGTATATAACTTATCCCAAAA	0.313																																					p.L178V		Atlas-SNP	.											.	ATL1	46	.	0			c.T532G						.						117	117	117					14																	51060573		2203	4299	6502	SO:0001583	missense	51062	exon5			TATAACTTATCCC	AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513			11231	protein-coding gene	gene with protein product	"atlastin"	606439	"spastic paraplegia 3A (autosomal dominant)"	SPG3, SPG3A		8252041, 7825576	Standard	NM_015915		Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000358385.6:c.532T>G	chr14.hg19:g.51060573T>G	ENSP00000351155:p.Leu178Val	68.0	0.0		39.0	8.0	NM_015915	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000358385.6	hg19	CCDS9700.1	.	.	.	.	.	.	.	.	.	.	T	13.32	2.202210	0.38905	.	.	ENSG00000198513	ENST00000441560;ENST00000358385;ENST00000357032;ENST00000354525;ENST00000554886	T;T;T;T;T	0.60797	0.16;0.16;0.16;0.16;0.16	5.46	1.79	0.24919	Guanylate-binding protein, N-terminal (1);	0.060050	0.64402	D	0.000003	T	0.45498	0.1345	L	0.35723	1.085	0.52099	D	0.999945	B;B	0.16802	0.019;0.015	B;B	0.33339	0.162;0.1	T	0.14699	-1.0463	10	0.19147	T	0.46	-10.1854	8.143	0.31095	0.0:0.2493:0.0:0.7507	.	178;178	Q8WXF7;G5E9T1	ATLA1_HUMAN;.	V	178;178;178;178;34	ENSP00000413675:L178V;ENSP00000351155:L178V;ENSP00000349534:L178V;ENSP00000346522:L178V;ENSP00000452074:L34V	ENSP00000346522:L178V	L	+	1	2	ATL1	50130323	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.886000	0.39688	0.436000	0.26393	0.533000	0.62120	TTA	.	.		0.313	ATL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276884.2			G	51060573	T	G	51060573	3	3	26	1	0	0	0	0	1	0	0	0	1106	1606	56	5	550	5	ATL1	14	51060573	Missense_Mutation	SNP	T	TCGA-5C-AAPD-01A-21D-A38X-10		51060573	56288967	51	3491										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96752158	96752158	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tctggcctaatttggtttctCatgccacccagcacgtttga	8	12	2	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr14:96752158C>A	ENST00000359933.4	-	42	7064	c.6171G>T	c.(6169-6171)atG>atT	p.M2057I		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	2057					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TTTGGTTTCTCATGCCACCCA	0.547																																					p.M2057I		Atlas-SNP	.											.	ATG2B	169	.	0			c.G6171T						.						141	108	119					14																	96752158		2203	4300	6503	SO:0001583	missense	55102	exon42			GTTTCTCATGCCA	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.6171G>T	chr14.hg19:g.96752158C>A	ENSP00000353010:p.Met2057Ile	141.0	0.0		87.0	33.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	C	36	5.614511	0.96649	.	.	ENSG00000066739	ENST00000359933	T	0.09630	2.96	5.76	5.76	0.90799	Autophagy-related, C-terminal (1);	0.080494	0.85682	D	0.000000	T	0.26448	0.0646	L	0.41492	1.28	0.80722	D	1	D	0.60575	0.988	D	0.74348	0.983	T	0.00304	-1.1832	10	0.30854	T	0.27	.	19.976	0.97309	0.0:1.0:0.0:0.0	.	2057	Q96BY7	ATG2B_HUMAN	I	2057	ENSP00000353010:M2057I	ENSP00000353010:M2057I	M	-	3	0	ATG2B	95821911	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.468000	0.80943	2.713000	0.92767	0.655000	0.94253	ATG	.	.		0.547	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		A	96752158	C	A	96752158	3	1	26	1	0	0	0	0	1	0	0	0	1094	826	29	3	69	3	ATG2B	14	96752158	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	45691585	96752158	10597382	52	3492										
WDR90	197335	hgsc.bcm.edu	37	chr16	701923	701923	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	cggatggccccggtttccatAgccttgagccctgggcccag	13	15	0	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr16:701923A>C	ENST00000293879.4	+	9	937	c.937A>C	c.(937-939)Agc>Cgc	p.S313R	WDR90_ENST00000549091.1_Missense_Mutation_p.S313R|AL022341.3_ENST00000455294.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	313										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CGGTTTCCATAGCCTTGAGCC	0.701																																					p.S313R		Atlas-SNP	.											.	WDR90	107	.	0			c.A937C						.						15	20	18					16																	701923		2046	4181	6227	SO:0001583	missense	197335	exon9			TTCCATAGCCTTG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.937A>C	chr16.hg19:g.701923A>C	ENSP00000293879:p.Ser313Arg	69.0	0.0		44.0	9.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	A	3.478	-0.106403	0.06924	.	.	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.28069	1.66;1.63	3.21	-6.42	0.01932	.	1.775110	0.04139	U	0.319296	T	0.18341	0.0440	L	0.38531	1.155	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.001;0.001;0.003	T	0.17228	-1.0376	10	0.15499	T	0.54	.	4.2291	0.10594	0.2912:0.0:0.4127:0.2961	.	313;314;313	Q96KV7;C9JMK1;Q96KV7-3	WDR90_HUMAN;.;.	R	313	ENSP00000448122:S313R;ENSP00000293879:S313R	ENSP00000293879:S313R	S	+	1	0	WDR90	641924	0.004000	0.15560	0.000000	0.03702	0.003000	0.03518	0.970000	0.29383	-1.990000	0.00978	-0.558000	0.04189	AGC	.	.		0.701	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		C	701923	A	C	701923	3	2	26	1	0	0	0	0	1	0	0	0	17352	420	15	5	971	5	WDR90	16	701923	Missense_Mutation	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10		701923	89652830	53	3493										
ZNF423	23090	hgsc.bcm.edu	37	chr16	49671334	49671334	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gtgcttggtgagtttcaggaTggagccaaagatgggggagt	18	4	1	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr16:49671334T>A	ENST00000561648.1	-	4	1782	c.1729A>T	c.(1729-1731)Atc>Ttc	p.I577F	ZNF423_ENST00000562520.1_Missense_Mutation_p.I517F|ZNF423_ENST00000262383.2_Missense_Mutation_p.I577F|ZNF423_ENST00000535559.1_Missense_Mutation_p.I460F|ZNF423_ENST00000563137.2_Missense_Mutation_p.I517F|ZNF423_ENST00000562871.1_Missense_Mutation_p.I517F|ZNF423_ENST00000567169.1_Missense_Mutation_p.I460F	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	577					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				AGTTTCAGGATGGAGCCAAAG	0.567																																					p.I577F		Atlas-SNP	.											.	ZNF423	463	.	0			c.A1729T						.						138	123	128					16																	49671334		2198	4300	6498	SO:0001583	missense	23090	exon4			TCAGGATGGAGCC	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1729A>T	chr16.hg19:g.49671334T>A	ENSP00000455426:p.Ile577Phe	135.0	0.0		64.0	27.0	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	T	10.54	1.379998	0.24944	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.08720	3.06;3.08	4.99	3.82	0.43975	Zinc finger, C2H2-like (1);	0.116446	0.64402	D	0.000015	T	0.03783	0.0107	N	0.03608	-0.345	0.47153	D	0.999339	B	0.27068	0.167	B	0.28465	0.09	T	0.50311	-0.8843	9	.	.	.	.	11.4301	0.50034	0.0:0.0:0.1509:0.8491	.	577	Q2M1K9	ZN423_HUMAN	F	577;460	ENSP00000262383:I577F;ENSP00000442321:I460F	.	I	-	1	0	ZNF423	48228835	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.332000	0.52083	1.881000	0.54492	0.459000	0.35465	ATC	.	.		0.567	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		A	49671334	T	A	49671334	3	1	26	1	0	0	0	0	1	0	0	0	17913	1464	51	4	2145	4	ZNF423	16	49671334	Missense_Mutation	SNP	T	TCGA-5C-AAPD-01A-21D-A38X-10	48969411	49671334	40683419	54	3494										
TP53	7157	hgsc.bcm.edu	37	chr17	7579559	7579559	+	Frame_Shift_Del	DEL	A	A	-													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tatcgtccggggacagcatcAaatcatccattgcttgggac							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr17:7579559delA	ENST00000269305.4	-	4	317	c.128delT	c.(127-129)ttgfs	p.L43fs	TP53_ENST00000413465.2_Frame_Shift_Del_p.L43fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.L43fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.L43fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Del_p.L43fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.L43fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	43	Interaction with HRMT1L2.|Transcription activation (acidic).		L -> S (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.S37fs*79(1)|p.L43fs*7(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGACAGCATCAAATCATCCAT	0.597		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.L43fs	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	.	TP53	33396	.	12	Whole gene deletion(8)|Deletion - Frameshift(4)	bone(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|ovary(1)|prostate(1)	c.129delG						.						169	166	167					17																	7579559		2203	4300	6503	SO:0001589	frameshift_variant	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.128delT	chr17.hg19:g.7579559delA	ENSP00000269305:p.Leu43fs	92.0	0.0		58.0	26.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.597	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7579559	A	-	7579559	7	5	26	1	0	1	0	1	0	0	0	0	16396	131	5	0	1174	0	TP53	17	7579559	Frame_Shift_Del	DEL	A	TCGA-5C-AAPD-01A-21D-A38X-10		7579559	73615651	55	3495										
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833448	56833448	+	Silent	SNP	G	G	A													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ggaccgtgcggcggcggcgaGccggagccggaacccgaacc							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr17:56833448G>A	ENST00000308249.2	+	1	219	c.90G>A	c.(88-90)gaG>gaA	p.E30E		NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	0	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			GCGGCGGcgagccggagccgg	0.667																																					p.E30E		Atlas-SNP	.											.	PPM1E	97	.	0			c.G90A						.						14	19	17					17																	56833448		2178	4275	6453	SO:0001819	synonymous_variant	22843	exon1			CGGCGAGCCGGAG	AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19322	protein-coding gene	gene with protein product	"partner of PIX 1", "nuclear calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1E (PP2C domain containing)"			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.90G>A	chr17.hg19:g.56833448G>A		212.0	0.0		230.0	12.0	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	CCDS11613.1																																																																																			.	.		0.667	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		A	56833448	G	A	56833448	2	1	26	1	0	0	0	0	0	0	0	1	12350	962	34	3		3	PPM1E	17	56833448	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	49253889	56833448	24361762	56	3496	13	2								
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833451	56833451	+	Silent	SNP	G	G	C													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ccgtgcggcggcggcgagccGgagccggaacccgaacccga							TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr17:56833451G>C	ENST00000308249.2	+	1	222	c.93G>C	c.(91-93)ccG>ccC	p.P31P		NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	0	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			GCGGcgagccggagccggaac	0.672																																					p.P31P		Atlas-SNP	.											.	PPM1E	97	.	0			c.G93C						.						14	20	18					17																	56833451		2180	4278	6458	SO:0001819	synonymous_variant	22843	exon1			CGAGCCGGAGCCG	AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19322	protein-coding gene	gene with protein product	"partner of PIX 1", "nuclear calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1E (PP2C domain containing)"			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.93G>C	chr17.hg19:g.56833451G>C		209.0	0.0		226.0	17.0	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	CCDS11613.1																																																																																			.	.		0.672	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		C	56833451	G	C	56833451	2	2	26	1	0	0	0	0	0	0	0	1	12350	1103	39	4		4	PPM1E	17	56833451	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	3	56833451	24361759	57	3497	13	2								
TLK2	11011	hgsc.bcm.edu	37	chr17	60679436	60679436	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	agtaaatggtacagcgtgtgGagagataaaaattacagatt	11	3	0	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr17:60679436G>T	ENST00000326270.9	+	20	2088	c.1820G>T	c.(1819-1821)gGa>gTa	p.G607V	TLK2_ENST00000582809.1_Missense_Mutation_p.G436V|TLK2_ENST00000542523.1_Missense_Mutation_p.G553V|TLK2_ENST00000343388.7_Missense_Mutation_p.G553V|TLK2_ENST00000346027.5_Missense_Mutation_p.G585V	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	607	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						ACAGCGTGTGGAGAGATAAAA	0.343																																					p.G585V		Atlas-SNP	.											.	TLK2	223	.	0			c.G1754T						.						91	87	88					17																	60679436		2203	4300	6503	SO:0001583	missense	11011	exon19			CGTGTGGAGAGAT	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.1820G>T	chr17.hg19:g.60679436G>T	ENSP00000316512:p.Gly607Val	84.0	0.0		109.0	31.0	NM_006852	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	hg19		.	.	.	.	.	.	.	.	.	.	G	13.61	2.289612	0.40494	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	T;T;T;T	0.25085	1.82;1.82;1.82;1.82	5.78	4.82	0.62117	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.51007	0.1649	M	0.75884	2.315	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;0.982;0.999	D;D;D;D	0.97110	1.0;0.977;0.941;0.995	T	0.56189	-0.8020	10	0.87932	D	0	.	13.8848	0.63702	0.0729:0.0:0.9271:0.0	.	607;553;585;585	Q86UE8;Q86UE8-3;Q86UE8-2;D3DU05	TLK2_HUMAN;.;.;.	V	585;553;607;553	ENSP00000275780:G585V;ENSP00000340800:G553V;ENSP00000316512:G607V;ENSP00000442311:G553V	ENSP00000316512:G607V	G	+	2	0	TLK2	58033168	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	1.450000	0.47717	0.561000	0.74099	GGA	.	.		0.343	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852		T	60679436	G	T	60679436	3	4	26	1	0	0	0	0	1	0	0	0	15959	1174	41	3	1824	3	TLK2	17	60679436	Missense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	3845985	60679436	20515774	58	3498										
TEX2	55852	hgsc.bcm.edu	37	chr17	62265633	62265633	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	atgtacacgctgtagtcgagAagcatcttctgccgcacgct	10	12	2	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr17:62265633A>C	ENST00000583097.1	-	5	2491	c.2319T>G	c.(2317-2319)ctT>ctG	p.L773L	TEX2_ENST00000258991.3_Silent_p.L780L|TEX2_ENST00000584379.1_Silent_p.L773L			Q8IWB9	TEX2_HUMAN	testis expressed 2	773					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TGTAGTCGAGAAGCATCTTCT	0.627																																					p.L780L		Atlas-SNP	.											.	TEX2	89	.	0			c.T2340G						.						101	82	88					17																	62265633		2203	4300	6503	SO:0001819	synonymous_variant	55852	exon5			GTCGAGAAGCATC	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"transmembrane protein 96"		"testis expressed sequence 2"			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.2319T>G	chr17.hg19:g.62265633A>C		74.0	0.0		50.0	20.0	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Silent	SNP	ENST00000583097.1	hg19																																																																																				.	.		0.627	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		C	62265633	A	C	62265633	2	2	26	1	0	0	0	0	0	0	0	1	15796	233	9	5		5	TEX2	17	62265633	Silent	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10	1586197	62265633	18929577	59	3499										
APCDD1	147495	hgsc.bcm.edu	37	chr18	10471890	10471890	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tgtgagtgcaccaaggccgtGaactttgccatgcatgaact	11	10	0	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr18:10471890G>A	ENST00000355285.5	+	3	960	c.606G>A	c.(604-606)gtG>gtA	p.V202V	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		CCAAGGCCGTGAACTTTGCCA	0.602																																					p.V202V		Atlas-SNP	.											.	APCDD1	57	.	0			c.G606A						.						146	134	138					18																	10471890		2203	4300	6503	SO:0001819	synonymous_variant	147495	exon3			GGCCGTGAACTTT	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.606G>A	chr18.hg19:g.10471890G>A		127.0	0.0		89.0	47.0	NM_153000		Silent	SNP	ENST00000355285.5	hg19	CCDS11849.1																																																																																			.	.		0.602	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		A	10471890	G	A	10471890	2	1	26	1	0	0	0	0	0	0	0	1	765	1277	45	3		3	APCDD1	18	10471890	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10		10471890	67605358	60	3500										
ZNF396	252884	hgsc.bcm.edu	37	chr18	32949594	32949594	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	aagtcttttgccttgaagcaGatttcacatttgtagttttg	8	6	2	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr18:32949594G>T	ENST00000589332.1	-	4	724	c.593C>A	c.(592-594)tCt>tAt	p.S198Y	ZNF396_ENST00000306346.1_Missense_Mutation_p.S198Y			Q96N95	ZN396_HUMAN	zinc finger protein 396	198					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)	7						CCTTGAAGCAGATTTCACATT	0.363																																					p.S198Y		Atlas-SNP	.											.	ZNF396	28	.	0			c.C593A						.						101	99	99					18																	32949594		2203	4300	6503	SO:0001583	missense	252884	exon4			GAAGCAGATTTCA	AK055775	CCDS11913.1	18p12	2013-01-09			ENSG00000186496	ENSG00000186496		"-", "Zinc fingers, C2H2-type"	18824	protein-coding gene	gene with protein product		609600					Standard	NM_145756		Approved	ZSCAN14, FLJ31213	uc010xcf.1	Q96N95	OTTHUMG00000132562	ENST00000589332.1:c.593C>A	chr18.hg19:g.32949594G>T	ENSP00000466500:p.Ser198Tyr	103.0	0.0		83.0	38.0	NM_145756	A1L3V0|Q8NF98|Q8TD80	Missense_Mutation	SNP	ENST00000589332.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.42	1.344948	0.24426	.	.	ENSG00000186496	ENST00000306346;ENST00000399057	T	0.08807	3.05	4.41	3.54	0.40534	.	0.670897	0.11710	U	0.537013	T	0.14485	0.0350	L	0.32530	0.975	0.43222	D	0.995103	D	0.67145	0.996	D	0.65874	0.939	T	0.15435	-1.0437	10	0.20519	T	0.43	.	8.1514	0.31143	0.107:0.0:0.893:0.0	.	198	Q96N95-3	.	Y	198	ENSP00000302310:S198Y	ENSP00000302310:S198Y	S	-	2	0	ZNF396	31203592	0.001000	0.12720	0.003000	0.11579	0.004000	0.04260	0.855000	0.27805	1.451000	0.47736	0.650000	0.86243	TCT	.	.		0.363	ZNF396-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255766.1	NM_145756		T	32949594	G	T	32949594	3	4	26	1	0	0	0	0	1	0	0	0	17897	942	33	3	416	3	ZNF396	18	32949594	Missense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	22477704	32949594	45127654	61	3501										
ZNF441	126068	hgsc.bcm.edu	37	chr19	11891848	11891848	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gggaaagcctttagtgatttCtattactttcgaaatcatga	8	6	2	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr19:11891848C>G	ENST00000357901.4	+	4	1311	c.1209C>G	c.(1207-1209)ttC>ttG	p.F403L	ZNF441_ENST00000454339.2_Missense_Mutation_p.F336L	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	403					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TTAGTGATTTCTATTACTTTC	0.378																																					p.F403L		Atlas-SNP	.											ZNF441_ENST00000357901,NS,carcinoma,0,2	ZNF441	123	.	0			c.C1209G						.						46	48	47					19																	11891848		2203	4300	6503	SO:0001583	missense	126068	exon4			TGATTTCTATTAC	AK095956	CCDS12266.2	19p13.13	2013-01-08			ENSG00000197044	ENSG00000197044		"Zinc fingers, C2H2-type", "-"	20875	protein-coding gene	gene with protein product							Standard	NM_152355		Approved	FLJ38637	uc010dyj.3	Q8N8Z8	OTTHUMG00000154449	ENST00000357901.4:c.1209C>G	chr19.hg19:g.11891848C>G	ENSP00000350576:p.Phe403Leu	87.0	0.0		77.0	20.0	NM_152355		Missense_Mutation	SNP	ENST00000357901.4	hg19	CCDS12266.2	.	.	.	.	.	.	.	.	.	.	-	8.650	0.898135	0.17686	.	.	ENSG00000197044	ENST00000409902;ENST00000357901;ENST00000454339	T;T	0.07021	3.23;3.23	1.06	-1.96	0.07525	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.	.	.	.	T	0.02193	0.0068	N	0.02296	-0.605	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.45190	-0.9278	9	0.15066	T	0.55	.	0.1783	0.00120	0.2122:0.2385:0.2107:0.3385	.	403	Q8N8Z8	ZN441_HUMAN	L	359;403;336	ENSP00000350576:F403L;ENSP00000403738:F336L	ENSP00000350576:F403L	F	+	3	2	ZNF441	11752848	0.000000	0.05858	0.000000	0.03702	0.934000	0.57294	-5.767000	0.00099	-0.483000	0.06772	0.298000	0.19748	TTC	.	.		0.378	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355		G	11891848	C	G	11891848	3	3	26	1	0	0	0	0	1	0	0	0	17929	912	32	4	1223	4	ZNF441	19	11891848	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10		11891848	47237135	62	3502										
SYDE1	85360	hgsc.bcm.edu	37	chr19	15221118	15221118	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tggcgtgagaaggcaccggcCctgtgcccagggcaccgtgc	16	14	0	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr19:15221118C>T	ENST00000342784.2	+	3	1065	c.1034C>T	c.(1033-1035)cCc>cTc	p.P345L	SYDE1_ENST00000600252.1_5'UTR|SYDE1_ENST00000600440.1_Missense_Mutation_p.P278L	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	345					activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)			endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						AGGCACCGGCCCTGTGCCCAG	0.716																																					p.P345L		Atlas-SNP	.											.	SYDE1	44	.	0			c.C1034T						.						6	9	8					19																	15221118		1891	3647	5538	SO:0001583	missense	85360	exon3			ACCGGCCCTGTGC	BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.1034C>T	chr19.hg19:g.15221118C>T	ENSP00000341489:p.Pro345Leu	45.0	0.0		40.0	11.0	NM_033025	Q7L2I8|Q8N6J2|Q9H8K4	Missense_Mutation	SNP	ENST00000342784.2	hg19	CCDS12324.1	.	.	.	.	.	.	.	.	.	.	c	1.023	-0.684263	0.03353	.	.	ENSG00000105137	ENST00000342784	T	0.07567	3.18	3.83	2.79	0.32731	C2 calcium/lipid-binding domain, CaLB (1);	0.361722	0.26586	N	0.023549	T	0.02807	0.0084	N	0.02315	-0.6	0.33534	D	0.593957	B;B	0.13145	0.007;0.001	B;B	0.08055	0.001;0.003	T	0.30060	-0.9991	10	0.24483	T	0.36	.	5.9307	0.19138	0.0:0.76:0.0:0.24	.	278;345	Q6ZW31-2;Q6ZW31	.;SYDE1_HUMAN	L	345	ENSP00000341489:P345L	ENSP00000341489:P345L	P	+	2	0	SYDE1	15082118	0.996000	0.38824	0.999000	0.59377	0.010000	0.07245	2.405000	0.44548	0.833000	0.34828	-0.359000	0.07587	CCC	.	.		0.716	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025		T	15221118	C	T	15221118	3	4	26	1	0	0	0	0	1	0	0	0	15450	623	22	3	1044	3	SYDE1	19	15221118	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	3329270	15221118	43907865	63	3503										
MAP1S	55201	hgsc.bcm.edu	37	chr19	17837234	17837234	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gcctgcgaggccgcgtcgcgGctggcgcgcggcgaggatga	20	13	0	1			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr19:17837234G>T	ENST00000324096.4	+	5	1192	c.1041G>T	c.(1039-1041)cgG>cgT	p.R347R	MAP1S_ENST00000544059.2_Silent_p.R321R|CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000597681.1_Intron	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	347	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CCGCGTCGCGGCTGGCGCGCG	0.721																																					p.R347R		Atlas-SNP	.											.	MAP1S	74	.	0			c.G1041T						.						5	6	5					19																	17837234		1975	3888	5863	SO:0001819	synonymous_variant	55201	exon5			GTCGCGGCTGGCG	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.1041G>T	chr19.hg19:g.17837234G>T		25.0	0.0		26.0	11.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Silent	SNP	ENST00000324096.4	hg19	CCDS32954.1																																																																																			.	.		0.721	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		T	17837234	G	T	17837234	2	4	26	1	0	0	0	0	0	0	0	1	9243	1190	42	3		3	MAP1S	19	17837234	Silent	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	2616116	17837234	41291749	64	3504										
ZNF781	163115	hgsc.bcm.edu	37	chr19	38160695	38160695	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ggccttccaacattgcttacAtttataaggtttctcaccag	6	11	1	0			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr19:38160695A>G	ENST00000590008.1	-	5	1207	c.355T>C	c.(355-357)Tgt>Cgt	p.C119R	ZNF781_ENST00000593040.1_5'Flank|ZNF781_ENST00000358582.4_Missense_Mutation_p.C119R|ZFP30_ENST00000586732.1_Intron			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	119					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						CATTGCTTACATTTATAAGGT	0.383																																					p.C119R		Atlas-SNP	.											.	ZNF781	66	.	0			c.T355C						.						122	121	121					19																	38160695		2203	4300	6503	SO:0001583	missense	163115	exon4			GCTTACATTTATA	AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"Zinc fingers, C2H2-type"	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.355T>C	chr19.hg19:g.38160695A>G	ENSP00000466370:p.Cys119Arg	84.0	0.0		93.0	28.0	NM_152605	Q2VPJ8	Missense_Mutation	SNP	ENST00000590008.1	hg19	CCDS12507.1	.	.	.	.	.	.	.	.	.	.	A	11.23	1.577208	0.28092	.	.	ENSG00000196381	ENST00000358582;ENST00000545586	D	0.85258	-1.96	2.23	1.13	0.20643	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.92786	0.7706	M	0.92880	3.355	0.09310	N	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.83865	0.0270	9	0.87932	D	0	.	8.2999	0.32008	0.875:0.0:0.125:0.0	.	119	Q8N8C0	ZN781_HUMAN	R	119	ENSP00000351391:C119R	ENSP00000351391:C119R	C	-	1	0	ZNF781	42852535	0.985000	0.35326	0.003000	0.11579	0.001000	0.01503	3.784000	0.55416	-0.269000	0.09298	-1.446000	0.01064	TGT	.	.		0.383	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605		G	38160695	A	G	38160695	3	3	26	1	0	0	0	0	1	0	0	0	18169	217	8	2	632	2	ZNF781	19	38160695	Missense_Mutation	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10	20323461	38160695	20968288	65	3505										
TGFB1	80776	hgsc.bcm.edu	37	chr19	41858864	41858864	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tagtcttgcaggtggatagtCccgcggccggccggccaggc	16	13	1	0	rs199758510|rs66551611	byFrequency	TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr19:41858864C>T	ENST00000243578.3	-	0	1027				CTC-435M10.3_ENST00000604424.1_Intron|TMEM91_ENST00000604123.1_5'Flank|TMEM91_ENST00000539627.1_Intron|TGFB1_ENST00000221930.5_Missense_Mutation_p.G29E	NM_030578.3	NP_085055.2	Q9BPU9	B9D2_HUMAN	B9 protein domain 2						cilium assembly (GO:0042384)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)	gamma-tubulin binding (GO:0043015)			large_intestine(1)|ovary(1)	2						GGTGGATAGTCCCGCGGCCGG	0.711													C|||	2	0.000399361	8e-04	0	5008	,	,		12405	0		0.001	False		,,,				2504	0				p.G29E		Atlas-SNP	.											.	TGFB1	27	.	0			c.G86A	GRCh37	CM090931|CM090932	TGFB1	M		.	C	GLU/GLY	2,4240		0,2,2119	13	10	11		86	1.3	1	19		11	3,8293		0,3,4145	yes	missense	TGFB1	NM_000660.4	98	0,5,6264	TT,TC,CC		0.0362,0.0471,0.0399	possibly-damaging	29/391	41858864	5,12533	2121	4148	6269	SO:0001628	intergenic_variant	7040	exon1			GATAGTCCCGCGG	BC004157	CCDS12579.1	19q13.2	2014-01-28				ENSG00000123810			28636	protein-coding gene	gene with protein product		611951				21763481	Standard	NM_030578		Approved	MGC4093, MKS10	uc002oqj.2	Q9BPU9			chr19.hg19:g.41858864C>T		77.0	0.0		68.0	17.0	NM_000660		Missense_Mutation	SNP	ENST00000243578.3	hg19	CCDS12579.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.735595	0.69189	4.71E-4	3.62E-4	ENSG00000105329	ENST00000221930	T	0.31769	1.48	3.74	1.29	0.21616	Transforming growth factor-beta, N-terminal (1);	0.473959	0.22160	N	0.063783	T	0.33585	0.0868	M	0.62723	1.935	0.80722	D	1	P	0.42161	0.772	B	0.43575	0.424	T	0.30149	-0.9988	10	0.49607	T	0.09	-15.6854	12.0894	0.53717	0.0:0.5772:0.4228:0.0	.	29	P01137	TGFB1_HUMAN	E	29	ENSP00000221930:G29E	ENSP00000221930:G29E	G	-	2	0	TGFB1	46550704	0.004000	0.15560	0.981000	0.43875	0.943000	0.58893	0.541000	0.23207	0.724000	0.32296	0.462000	0.41574	GGA	.	.		0.711	B9D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463489.1	NM_030578		T	41858864	C	T	41858864	1	4	26	0	1	0	0	0	0	0	0	0	15831	855	30	3		3	TGFB1	19	41858864	IGR	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	3698169	41858864	17270119	66	3506										
KLK12	43849	hgsc.bcm.edu	37	chr19	51534168	51534168	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	tgaggcactggagcagatccGggaatgggtctggagagaga	18	6	1	4			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr19:51534168G>T	ENST00000525263.1	-	4	586	c.467C>A	c.(466-468)cCg>cAg	p.P156Q	CTC-518B2.9_ENST00000594910.1_RNA|KLK11_ENST00000319720.7_5'Flank|KLK12_ENST00000529888.1_Silent_p.P69P|KLK12_ENST00000250351.4_Missense_Mutation_p.P156Q|KLK12_ENST00000319590.4_Missense_Mutation_p.P156Q|KLK11_ENST00000391804.3_5'Flank|KLK12_ENST00000250352.11_Missense_Mutation_p.P46Q			Q9UKR0	KLK12_HUMAN	kallikrein-related peptidase 12	156	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	12		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)		GAGCAGATCCGGGAATGGGTC	0.592																																					p.P156Q		Atlas-SNP	.											.	KLK12	30	.	0			c.C467A						.						162	152	156					19																	51534168		2203	4300	6503	SO:0001583	missense	43849	exon5			AGATCCGGGAATG		CCDS12820.1, CCDS12821.1, CCDS54298.1	19q13.33	2008-02-05	2006-10-27		ENSG00000186474	ENSG00000186474		"Kallikreins"	6360	protein-coding gene	gene with protein product		605539	"kallikrein 12"			16800724, 16800723	Standard	NM_019598		Approved	KLK-L5	uc002pvh.1	Q9UKR0	OTTHUMG00000165806	ENST00000525263.1:c.467C>A	chr19.hg19:g.51534168G>T	ENSP00000436458:p.Pro156Gln	117.0	0.0		82.0	19.0	NM_019598	Q9UKR1|Q9UKR2	Missense_Mutation	SNP	ENST00000525263.1	hg19	CCDS12821.1	.	.	.	.	.	.	.	.	.	.	g	15.19	2.759872	0.49468	.	.	ENSG00000186474	ENST00000525263;ENST00000319590;ENST00000250352;ENST00000250351	D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51	4.62	4.62	0.57501	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.450566	0.16616	N	0.206692	D	0.93877	0.8041	M	0.79475	2.455	0.32947	D	0.519266	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	1.0;0.999;0.999;0.971	D	0.94969	0.8115	10	0.87932	D	0	.	12.8167	0.57669	0.0:0.0:1.0:0.0	.	46;46;156;156	B9EGA9;Q49AM7;Q9UKR0-2;Q9UKR0	.;.;.;KLK12_HUMAN	Q	156;156;46;156	ENSP00000436458:P156Q;ENSP00000324181:P156Q;ENSP00000250352:P46Q;ENSP00000250351:P156Q	ENSP00000250351:P156Q	P	-	2	0	KLK12	56225980	1.000000	0.71417	0.861000	0.33841	0.318000	0.28184	5.638000	0.67861	2.395000	0.81488	0.555000	0.69702	CCG	.	.		0.592	KLK12-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386288.1	NM_019598		T	51534168	G	T	51534168	3	4	26	1	0	0	0	0	1	0	0	0	8409	1116	39	1	349	1	KLK12	19	51534168	Missense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	9675304	51534168	7594815	67	3507										
MAVS	57506	hgsc.bcm.edu	37	chr20	3845305	3845305	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gccttctaatgcgctcaccaAtccagcaccatccaaattgc	5	16	2	0			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr20:3845305A>G	ENST00000428216.2	+	6	1156	c.1028A>G	c.(1027-1029)aAt>aGt	p.N343S	MAVS_ENST00000416600.2_Missense_Mutation_p.N202S|MAVS_ENST00000358134.6_3'UTR	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	343					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						GCGCTCACCAATCCAGCACCA	0.557																																					p.N343S		Atlas-SNP	.											.	MAVS	34	.	0			c.A1028G						.						138	125	129					20																	3845305		2203	4300	6503	SO:0001583	missense	57506	exon6			TCACCAATCCAGC	DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"virus-induced signaling adaptor", "IFN-B promoter stimulator 1", "CARD adaptor inducing IFN-beta"	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.1028A>G	chr20.hg19:g.3845305A>G	ENSP00000401980:p.Asn343Ser	84.0	0.0		65.0	19.0	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Missense_Mutation	SNP	ENST00000428216.2	hg19	CCDS33437.1	.	.	.	.	.	.	.	.	.	.	A	9.862	1.196692	0.22037	.	.	ENSG00000088888	ENST00000416600;ENST00000428216	T;T	0.32515	1.45;2.46	3.73	-2.66	0.06077	.	1.390520	0.04818	N	0.436369	T	0.13543	0.0328	N	0.11201	0.11	0.09310	N	1	B	0.27625	0.183	B	0.25140	0.058	T	0.23726	-1.0180	10	0.05620	T	0.96	-1.1473	8.4884	0.33084	0.4964:0.0:0.5036:0.0	.	343	Q7Z434	MAVS_HUMAN	S	202;343	ENSP00000413749:N202S;ENSP00000401980:N343S	ENSP00000413749:N202S	N	+	2	0	MAVS	3793305	0.000000	0.05858	0.000000	0.03702	0.786000	0.44442	-0.159000	0.10056	-0.476000	0.06842	0.402000	0.26972	AAT	.	.		0.557	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746		G	3845305	A	G	3845305	3	3	26	1	0	0	0	0	1	0	0	0	9347	101	4	2	1046	2	MAVS	20	3845305	Missense_Mutation	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10		3845305	59180215	68	3508										
TRMT6	51605	hgsc.bcm.edu	37	chr20	5919267	5919267	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	agtgcttgcattagatttgaGgctggtgtctgctttaaggt	13	5	1	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr20:5919267G>A	ENST00000203001.2	-	11	1538	c.1408C>T	c.(1408-1410)Ctc>Ttc	p.L470F	TRMT6_ENST00000473131.1_5'UTR|TRMT6_ENST00000453074.2_Missense_Mutation_p.L300F	NM_015939.3	NP_057023.2	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6 homolog (S. cerevisiae)	470					regulation of translational initiation (GO:0006446)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	15						TTAGATTTGAGGCTGGTGTCT	0.473																																					p.L470F		Atlas-SNP	.											.	TRMT6	28	.	0			c.C1408T						.						134	131	132					20																	5919267		2203	4300	6503	SO:0001583	missense	51605	exon11			ATTTGAGGCTGGT	AK000613	CCDS13093.1, CCDS63225.1	20p12.3	2009-01-12			ENSG00000089195	ENSG00000089195			20900	protein-coding gene	gene with protein product						16043508	Standard	NM_001281467		Approved	GCD10, MGC5029, Gcd10p, CGI-09	uc002wmh.1	Q9UJA5	OTTHUMG00000031816	ENST00000203001.2:c.1408C>T	chr20.hg19:g.5919267G>A	ENSP00000203001:p.Leu470Phe	93.0	0.0		95.0	24.0	NM_015939	B4DUV6|Q76P92|Q9BQV5|Q9ULR7|Q9Y2Z8	Missense_Mutation	SNP	ENST00000203001.2	hg19	CCDS13093.1	.	.	.	.	.	.	.	.	.	.	G	10.05	1.243252	0.22796	.	.	ENSG00000089195	ENST00000203001;ENST00000453074	T;T	0.24151	1.88;1.87	5.65	4.69	0.59074	.	0.153525	0.30969	N	0.008516	T	0.20170	0.0485	N	0.22421	0.69	0.09310	N	1	B	0.25169	0.119	B	0.26517	0.07	T	0.19031	-1.0318	10	0.54805	T	0.06	-2.8296	14.6958	0.69121	0.0:0.4016:0.5984:0.0	.	470	Q9UJA5	TRM6_HUMAN	F	470;300	ENSP00000203001:L470F;ENSP00000392070:L300F	ENSP00000203001:L470F	L	-	1	0	TRMT6	5867267	0.006000	0.16342	0.308000	0.25141	0.125000	0.20455	1.678000	0.37586	1.507000	0.48752	0.650000	0.86243	CTC	.	.		0.473	TRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077889.2			A	5919267	G	A	5919267	3	1	26	1	0	0	0	0	1	0	0	0	16583	1000	35	3	89	3	TRMT6	20	5919267	Missense_Mutation	SNP	G	TCGA-5C-AAPD-01A-21D-A38X-10	2073962	5919267	57106253	69	3509										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35422556	35422556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	agcctccgtccaggcgctgcCgtgagaagttgcagagccac	13	14	0	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr20:35422556C>T	ENST00000357779.3	-	14	3541	c.3215G>A	c.(3214-3216)cGg>cAg	p.R1072Q	SOGA1_ENST00000456801.2_Missense_Mutation_p.R913Q|SOGA1_ENST00000279034.6_Intron|SOGA1_ENST00000237536.4_Missense_Mutation_p.R1310Q			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	1072					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						CAGGCGCTGCCGTGAGAAGTT	0.652																																					p.R1310Q		Atlas-SNP	.											.	SOGA1	136	.	0			c.G3929A						.						30	30	30					20																	35422556		692	1591	2283	SO:0001583	missense	140710	exon14			CGCTGCCGTGAGA	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.3215G>A	chr20.hg19:g.35422556C>T	ENSP00000350424:p.Arg1072Gln	90.0	0.0		83.0	21.0	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	hg19		.	.	.	.	.	.	.	.	.	.	C	15.82	2.945960	0.53079	.	.	ENSG00000149639	ENST00000237536;ENST00000456801;ENST00000357779	T;T;T	0.18016	2.24;2.26;2.25	5.3	4.29	0.51040	.	0.529373	0.20551	N	0.090115	T	0.19967	0.0480	L	0.52126	1.63	0.30214	N	0.797445	.	.	.	.	.	.	T	0.05550	-1.0878	8	0.45353	T	0.12	-40.9805	5.3258	0.15905	0.0:0.7579:0.0:0.2421	.	.	.	.	Q	1310;913;1072	ENSP00000237536:R1310Q;ENSP00000413886:R913Q;ENSP00000350424:R1072Q	ENSP00000237536:R1310Q	R	-	2	0	KIAA0889	34855970	0.993000	0.37304	1.000000	0.80357	0.996000	0.88848	2.423000	0.44705	2.748000	0.94277	0.655000	0.94253	CGG	.	.		0.652	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		T	35422556	C	T	35422556	3	4	26	1	0	0	0	0	1	0	0	0	2085	652	23	1	1126	1	C20orf117	20	35422556	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	29503289	35422556	27602964	70	3510										
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47558450	47558450	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	acttcattgaagctgacaagTattttcttccattcgagcta	6	9	2	2			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr20:47558450T>C	ENST00000371917.4	+	3	202	c.202T>C	c.(202-204)Tat>Cat	p.Y68H		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	68	DCB; DCB:DCB domain and DCB:HUS domain interaction.				endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			AGCTGACAAGTATTTTCTTCC	0.473																																					p.Y68H	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.T202C						.						174	159	164					20																	47558450		2203	4300	6503	SO:0001583	missense	10564	exon3			GACAAGTATTTTC	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.202T>C	chr20.hg19:g.47558450T>C	ENSP00000360985:p.Tyr68His	65.0	0.0		68.0	17.0	NM_006420	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.832285	0.91036	.	.	ENSG00000124198	ENST00000538445;ENST00000371917	T	0.26373	1.74	5.74	5.74	0.90152	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.42743	0.1216	M	0.73598	2.24	0.80722	D	1	D	0.61080	0.989	P	0.51701	0.677	T	0.38415	-0.9662	10	0.48119	T	0.1	.	16.0314	0.80579	0.0:0.0:0.0:1.0	.	68	Q9Y6D5	BIG2_HUMAN	H	68	ENSP00000360985:Y68H	ENSP00000360985:Y68H	Y	+	1	0	ARFGEF2	46991857	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.955000	0.87856	2.193000	0.70182	0.402000	0.26972	TAT	.	.		0.473	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		C	47558450	T	C	47558450	3	2	26	1	0	0	0	0	1	0	0	0	853	1638	57	2	212	2	ARFGEF2	20	47558450	Missense_Mutation	SNP	T	TCGA-5C-AAPD-01A-21D-A38X-10	12135894	47558450	15467070	71	3511										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26348383	26348383	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	cagaaggtgcagattaagagAtttgaggtacgtagtgattc	13	4	0	5			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr22:26348383A>G	ENST00000407587.2	+	38	6136	c.5967A>G	c.(5965-5967)agA>agG	p.R1989R	MYO18B_ENST00000335473.7_Silent_p.R1988R|MYO18B_ENST00000536101.1_Silent_p.R1988R			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1988	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AGATTAAGAGATTTGAGGTAC	0.483																																					p.R1988R		Atlas-SNP	.											.	MYO18B	322	.	0			c.A5964G						.						64	68	66					22																	26348383		2025	4192	6217	SO:0001819	synonymous_variant	84700	exon38			TAAGAGATTTGAG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.5967A>G	chr22.hg19:g.26348383A>G		127.0	0.0		125.0	43.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.		0.483	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26348383	A	G	26348383	2	3	26	1	0	0	0	0	0	0	0	1	10075	330	12	2		2	MYO18B	22	26348383	Silent	SNP	A	TCGA-5C-AAPD-01A-21D-A38X-10		26348383	24956183	72	3512										
TRMU	55687	hgsc.bcm.edu	37	chr22	46733707	46733707	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	acaggggtgtttatgaagaaCtgggactcactggatgaaca	13	6	1	3			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chr22:46733707C>A	ENST00000290846.4	+	2	454	c.114C>A	c.(112-114)aaC>aaA	p.N38K	TRMU_ENST00000424260.2_Missense_Mutation_p.N3K|TRMU_ENST00000381019.3_Missense_Mutation_p.N38K	NM_018006.4	NP_060476.2	O75648	MTU1_HUMAN	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	38					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|sulfurtransferase activity (GO:0016783)|tRNA binding (GO:0000049)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)	10		Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00449)|LUAD - Lung adenocarcinoma(64;0.248)		TTATGAAGAACTGGGACTCAC	0.458																																					p.N38K		Atlas-SNP	.											.	TRMU	23	.	0			c.C114A						.						125	106	112					22																	46733707		2203	4300	6503	SO:0001583	missense	55687	exon2			GAAGAACTGGGAC	AY062123	CCDS14075.1, CCDS63510.1	22q13	2005-08-11	2005-08-11	2005-08-11	ENSG00000100416	ENSG00000100416	2.1.1.61		25481	protein-coding gene	gene with protein product		610230	"tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase "	TRMT		14746906	Standard	XM_005261678		Approved	FLJ10140, MTO2	uc003bhp.3	O75648	OTTHUMG00000150424	ENST00000290846.4:c.114C>A	chr22.hg19:g.46733707C>A	ENSP00000290846:p.Asn38Lys	127.0	0.0		123.0	35.0	NM_018006	A8K3U7|Q05C99|Q5W9C8|Q66K31|Q6ICC3|Q9NWC1	Missense_Mutation	SNP	ENST00000290846.4	hg19	CCDS14075.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.223688	0.79576	.	.	ENSG00000100416	ENST00000290846;ENST00000381019;ENST00000424260	T;T;T	0.72394	-0.08;-0.08;-0.65	4.91	4.91	0.64330	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.88934	0.6572	H	0.97265	3.97	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.998;1.0	D	0.91950	0.5570	10	0.87932	D	0	-44.7634	12.2442	0.54560	0.0:0.9166:0.0:0.0834	.	38;38;38	B4DHM1;O75648-2;O75648	.;.;MTU1_HUMAN	K	38;38;3	ENSP00000290846:N38K;ENSP00000370407:N38K;ENSP00000406038:N3K	ENSP00000290846:N38K	N	+	3	2	TRMU	45112371	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.527000	0.53517	2.256000	0.74724	0.557000	0.71058	AAC	.	.		0.458	TRMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318042.2	NM_018006		A	46733707	C	A	46733707	3	1	26	1	0	0	0	0	1	0	0	0	16586	564	20	3	120	3	TRMU	22	46733707	Missense_Mutation	SNP	C	TCGA-5C-AAPD-01A-21D-A38X-10	20385324	46733707	4570859	73	3513										
ARSD	414	hgsc.bcm.edu	37	chrX	2827944	2827966	+	Frame_Shift_Del	DEL	GGCCGGGAGCACCCCCGGCCAGT	GGCCGGGAGCACCCCCGGCCAGT	-													0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	ggctctccaatcactcggccGgccgggagcacccccggcca					rs144863992		TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	GGCCGGGAGCACCCCCGGCCAGT	GGCCGGGAGCACCCCCGGCCAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chrX:2827944_2827966delGGCCGGGAGCACCCCCGGCCAGT	ENST00000381154.1	-	8	1265_1287	c.1190_1212delACTGGCCGGGGGTGCTCCCGGCC	c.(1189-1212)cactggccgggggtgctcccggccfs	p.HWPGVLPA397fs		NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	397					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TCACTCGGCCGGCCGGGAGCACCCCCGGCCAGTGGAAGATCCC	0.619																																					p.397_405del		Atlas-Indel,Pindel	.											.	ARSD	47	.	0			c.1191_1213del						.																																			SO:0001589	frameshift_variant	414	exon8			.	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"Arylsulfatase family"	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.1190_1212delACTGGCCGGGGGTGCTCCCGGCC	chrX.hg19:g.2827944_2827966delGGCCGGGAGCACCCCCGGCCAGT	ENSP00000370546:p.His397fs	283.0	0.0		287.0	135.0	NM_001669	Q9UHJ8	Frame_Shift_Del	DEL	ENST00000381154.1	hg19	CCDS35196.1																																																																																			.	.		0.619	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1			-	2827966	GGCCGGGAGCACCCCCGGCCAGT	-	2827944	7	5	26	1	0	1	0	1	0	0	0	0	989	1103	39	0	581	0	ARSD	23	2827944	Frame_Shift_Del	DEL	GGCCGGGAGCACCCCCGGCCAGT	TCGA-5C-AAPD-01A-21D-A38X-10		2827944	152442616	74	3514										
RIBC1	158787	hgsc.bcm.edu	37	chrX	53457918	53457918	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.11216158143532	2.4096834264432	0.722905027932961	1	1	0	gcccagtatcaccagcagttTaacaccagcagccgctaagt	8	14	1	0			TCGA-5C-AAPD-01A-21D-A38X-10	TCGA-5C-AAPD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fb2728b8-fc2d-4f40-98b0-649f020fd475	94fbe599-361a-4bfb-9e37-dae2c10b4ddd	g.chrX:53457918T>C	ENST00000375327.3	+	8	1275	c.1122T>C	c.(1120-1122)ttT>ttC	p.F374F	HSD17B10_ENST00000495986.1_5'Flank|RP3-339A18.6_ENST00000418049.1_RNA	NM_001031745.2	NP_001026915.1	Q8N443	RIBC1_HUMAN	RIB43A domain with coiled-coils 1	374										lung(2)	2						ACCAGCAGTTTAACACCAGCA	0.468																																					p.F374F		Atlas-SNP	.											.	RIBC1	20	.	0			c.T1122C						.						201	155	171					X																	53457918		2203	4300	6503	SO:0001819	synonymous_variant	158787	exon8			GCAGTTTAACACC	AK057345	CCDS14353.1, CCDS35299.1, CCDS59168.1	Xp11.23	2006-04-12			ENSG00000158423	ENSG00000158423			26537	protein-coding gene	gene with protein product							Standard	NM_144968		Approved	FLJ32783	uc004dsk.4	Q8N443	OTTHUMG00000021615	ENST00000375327.3:c.1122T>C	chrX.hg19:g.53457918T>C		108.0	0.0		163.0	53.0	NM_001031745	B4E297|E9PDU2|Q5H931|Q96A80	Silent	SNP	ENST00000375327.3	hg19	CCDS35299.1																																																																																			.	.		0.468	RIBC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056762.1	NM_144968		C	53457918	T	C	53457918	2	2	26	1	0	0	0	0	0	0	0	1	13367	1751	61	2		2	RIBC1	23	53457918	Silent	SNP	T	TCGA-5C-AAPD-01A-21D-A38X-10	50629974	53457918	101812642	75	3515										
CROCC	4237	hgsc.bcm.edu	37	chr1	17298042	17298042	+	IGR	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gcagcagctggagctgcagcAggaggtggagcggctgcgca	19	10	0	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr1:17298042A>T	ENST00000375535.3	-	0	1260				CROCC_ENST00000375541.5_Missense_Mutation_p.Q1956L|MFAP2_ENST00000490075.1_5'Flank			P55001	MFAP2_HUMAN	microfibrillar-associated protein 2						extracellular matrix organization (GO:0030198)|platelet formation (GO:0030220)	extracellular region (GO:0005576)|microfibril (GO:0001527)				kidney(1)|lung(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000118)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000538)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|COAD - Colon adenocarcinoma(227;1.07e-05)|BRCA - Breast invasive adenocarcinoma(304;3.04e-05)|Kidney(64;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00544)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GAGCTGCAGCAGGAGGTGGAG	0.731																																					p.Q1956L		Atlas-SNP	.											.	CROCC	185	.	0			c.A5867T						.						5	6	5					1																	17298042		1971	3830	5801	SO:0001628	intergenic_variant	9696	exon36			TGCAGCAGGAGGT	BC015039	CCDS174.1, CCDS44071.1	1p36.1-p35	2008-02-05			ENSG00000117122	ENSG00000117122			7033	protein-coding gene	gene with protein product		156790				7759096	Standard	NM_017459		Approved	MAGP, MAGP-1	uc001azw.3	P55001	OTTHUMG00000002290		chr1.hg19:g.17298042A>T		117.0	0.0		75.0	28.0	NM_014675	Q53X60|Q5JXY0	Missense_Mutation	SNP	ENST00000375535.3	hg19	CCDS174.1	.	.	.	.	.	.	.	.	.	.	A	11.32	1.605096	0.28623	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.09911	2.93	4.52	2.18	0.27775	.	.	.	.	.	T	0.04543	0.0124	N	0.10916	0.065	0.34564	D	0.712698	B;B;B	0.22346	0.068;0.068;0.019	B;B;B	0.19391	0.025;0.025;0.025	T	0.33369	-0.9871	9	0.23891	T	0.37	.	2.7668	0.05322	0.601:0.0:0.2094:0.1896	.	1837;1259;1956	B1AKD8;Q5TZA2-2;Q5TZA2	.;.;CROCC_HUMAN	L	1956;1837	ENSP00000364691:Q1956L	ENSP00000364691:Q1956L	Q	+	2	0	CROCC	17170629	0.994000	0.37717	1.000000	0.80357	0.793000	0.44817	0.293000	0.19029	0.599000	0.29845	0.402000	0.26972	CAG	.	.		0.731	MFAP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006609.1	NM_002403		T	17298042	A	T	17298042	1	4	27	0	1	0	0	0	0	0	0	0	3895	188	7	4		4	CROCC	1	17298042	IGR	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10		17298042	231952579	1	3516										
RCAN3	11123	hgsc.bcm.edu	37	chr1	24859580	24859580	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tcgctccctgcaggtgcagaTgtccggcgaagtgcgggaca	15	12	0	1	rs537312929		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr1:24859580T>C	ENST00000374395.4	+	4	690	c.377T>C	c.(376-378)aTg>aCg	p.M126T	RCAN3_ENST00000436717.2_Intron|RCAN3_ENST00000538532.1_Missense_Mutation_p.M68T|RCAN3_ENST00000374393.2_Intron|RCAN3_ENST00000412742.2_Intron	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3	126					anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		CAGGTGCAGATGTCCGGCGAA	0.552													T|||	1	0.000199681	0	0	5008	,	,		13003	0		0	False		,,,				2504	0.001				p.M126T		Atlas-SNP	.											.	RCAN3	22	.	0			c.T377C						.						53	46	49					1																	24859580		2203	4300	6503	SO:0001583	missense	11123	exon4			TGCAGATGTCCGG		CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"Down syndrome critical region gene 1-like 2"	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.377T>C	chr1.hg19:g.24859580T>C	ENSP00000363516:p.Met126Thr	98.0	0.0		64.0	25.0	NM_001251979	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Missense_Mutation	SNP	ENST00000374395.4	hg19	CCDS254.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.726501	0.00694	.	.	ENSG00000117602	ENST00000374395;ENST00000538532	T;T	0.41065	1.09;1.01	5.08	-1.65	0.08291	.	0.723471	0.14800	N	0.297716	T	0.09247	0.0228	N	0.00332	-1.63	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44065	-0.9352	10	0.05721	T	0.95	-16.5523	10.0284	0.42085	0.0:0.3978:0.0:0.6022	.	68;126	A4GU14;Q9UKA8	.;RCAN3_HUMAN	T	126;68	ENSP00000363516:M126T;ENSP00000445401:M68T	ENSP00000363516:M126T	M	+	2	0	RCAN3	24732167	1.000000	0.71417	0.073000	0.20177	0.038000	0.13279	2.015000	0.40961	-0.370000	0.08016	-0.410000	0.06199	ATG	.	.		0.552	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2			C	24859580	T	C	24859580	3	2	27	1	0	0	0	0	1	0	0	0	13185	1464	51	2	387	2	RCAN3	1	24859580	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	7561538	24859580	224391041	2	3517										
NCDN	23154	hgsc.bcm.edu	37	chr1	36029507	36029507	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	cccggctccttagcacctctCcaggtaagaactggggatcc	10	15	1	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr1:36029507C>A	ENST00000373243.2	+	6	2133	c.1750C>A	c.(1750-1752)Cca>Aca	p.P584T	NCDN_ENST00000373253.3_Missense_Mutation_p.P567T|NCDN_ENST00000356090.4_Missense_Mutation_p.P584T	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	584					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TAGCACCTCTCCAGGTAAGAA	0.562																																					p.P584T		Atlas-SNP	.											.	NCDN	79	.	0			c.C1750A						.						40	39	40					1																	36029507		2203	4300	6503	SO:0001583	missense	23154	exon6			ACCTCTCCAGGTA	AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.1750C>A	chr1.hg19:g.36029507C>A	ENSP00000362340:p.Pro584Thr	65.0	0.0		54.0	32.0	NM_014284	D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Missense_Mutation	SNP	ENST00000373243.2	hg19	CCDS392.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.045917	0.36085	.	.	ENSG00000020129	ENST00000373253;ENST00000356090;ENST00000373243	.	.	.	4.39	4.39	0.52855	.	0.221552	0.38058	N	0.001821	T	0.27169	0.0666	N	0.22421	0.69	0.37629	D	0.921616	B	0.34372	0.451	B	0.30029	0.11	T	0.17137	-1.0379	9	0.23302	T	0.38	.	6.6022	0.22707	0.0:0.6976:0.2012:0.1012	.	584	Q9UBB6	NCDN_HUMAN	T	567;584;584	.	ENSP00000348394:P584T	P	+	1	0	NCDN	35802094	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.003000	0.40844	1.993000	0.58246	0.462000	0.41574	CCA	.	.		0.562	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284		A	36029507	C	A	36029507	3	1	27	1	0	0	0	0	1	0	0	0	10223	855	30	3	1772	3	NCDN	1	36029507	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	11169927	36029507	213221114	3	3518										
EPS8L3	79574	hgsc.bcm.edu	37	chr1	110293318	110293318	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	acagcctccagccgggacagGattcgtggggcctcctgtgg	15	13	0	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr1:110293318G>A	ENST00000361965.4	-	18	1840	c.1734C>T	c.(1732-1734)atC>atT	p.I578I	EPS8L3_ENST00000369805.3_Silent_p.I579I|EPS8L3_ENST00000361852.4_Silent_p.I548I|RP4-735C1.4_ENST00000431955.1_RNA	NM_133181.3	NP_573444.2	Q8TE67	ES8L3_HUMAN	EPS8-like 3	578						cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	32		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		GCCGGGACAGGATTCGTGGGG	0.612																																					p.I579I		Atlas-SNP	.											.	EPS8L3	73	.	0			c.C1737T						.						62	49	53					1																	110293318		2203	4300	6503	SO:0001819	synonymous_variant	79574	exon18			GGACAGGATTCGT	AK025175	CCDS813.1, CCDS814.1, CCDS815.1	1p13.2	2008-02-05			ENSG00000198758	ENSG00000198758			21297	protein-coding gene	gene with protein product		614989				12620401	Standard	NM_139053		Approved	FLJ21522, MGC16817	uc001dyq.2	Q8TE67	OTTHUMG00000011651	ENST00000361965.4:c.1734C>T	chr1.hg19:g.110293318G>A		127.0	0.0		97.0	5.0	NM_139053	A8K833|Q5T8Q6|Q5T8Q7|Q5T8Q8|Q96E47|Q9H719	Silent	SNP	ENST00000361965.4	hg19	CCDS814.1																																																																																			.	.		0.612	EPS8L3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032234.1	NM_024526		A	110293318	G	A	110293318	2	1	27	1	0	0	0	0	0	0	0	1	5199	1164	41	3		3	EPS8L3	1	110293318	Silent	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	74263811	110293318	138957303	4	3519										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842095	154842095	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	agggtggaggatggcggtggAgttggacgaagggggggccc	24	5	0	0	rs76110919		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr1:154842095A>T	ENST00000271915.4	-	1	661	c.346T>A	c.(346-348)Tcc>Acc	p.S116T	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	121					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	ATGGCGGTGGAGTTGGACGAA	0.632																																					p.S116T		Atlas-SNP	.											.	KCNN3	141	.	0			c.T346A						.						48	40	43					1																	154842095		2203	4300	6503	SO:0001583	missense	3782	exon1			CGGTGGAGTTGGA	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.346T>A	chr1.hg19:g.154842095A>T	ENSP00000271915:p.Ser116Thr	213.0	0.0		260.0	17.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.41|13.41	2.229373|2.229373	0.39399|0.39399	.|.	.|.	ENSG00000143603|ENSG00000143603	ENST00000539103|ENST00000271915	.|D	.|0.96365	.|-3.99	5.02|5.02	5.02|5.02	0.67125|0.67125	.|.	.|0.165944	.|0.29172	.|N	.|0.012936	D|D	0.86272|0.86272	0.5893|0.5893	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	D|D	1|1	.|P;B	.|0.48764	.|0.915;0.378	.|B;B	.|0.36959	.|0.237;0.073	D|D	0.88373|0.88373	0.2996|0.2996	6|10	0.87932|0.39692	D|T	0|0.17	-26.9966|-26.9966	12.737|12.737	0.57230|0.57230	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|122;121	.|Q6JXY2;Q9UGI6	.|.;KCNN3_HUMAN	H|T	210|116	.|ENSP00000271915:S116T	ENSP00000442214:L210H|ENSP00000271915:S116T	L|S	-|-	2|1	0|0	KCNN3|KCNN3	153108719|153108719	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	3.358000|3.358000	0.52284|0.52284	2.110000|2.110000	0.64415|0.64415	0.460000|0.460000	0.39030|0.39030	CTC|TCC	.	.		0.632	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154842095	A	T	154842095	3	4	27	1	0	0	0	0	1	0	0	0	8089	304	11	4	1903	4	KCNN3	1	154842095	Missense_Mutation	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10	44548777	154842095	94408526	5	3520										
SHC1	6464	hgsc.bcm.edu	37	chr1	154940971	154940971	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gtctgcccaccttcaccaacCtgtttgcagtctgcggccat	8	16	3	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr1:154940971C>A	ENST00000368445.5	-	4	964	c.750G>T	c.(748-750)caG>caT	p.Q250H	SHC1_ENST00000368453.4_Splice_Site_p.Q140H|SHC1_ENST00000368449.4_Splice_Site_p.Q21H|SHC1_ENST00000490667.1_5'Flank|SHC1_ENST00000448116.2_Splice_Site_p.Q250H|SHC1_ENST00000368450.1_Splice_Site_p.Q140H|SHC1_ENST00000606391.1_Splice_Site_p.Q51H	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	250	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|Ras protein signal transduction (GO:0007265)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of growth (GO:0040008)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|Shc-EGFR complex (GO:0070435)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phospholipid binding (GO:0005543)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	20	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CTTCACCAACCTGTTTGCAGT	0.542																																					p.Q250H	NSCLC(4;32 234 1864 2492 3259 13747 17376)	Atlas-SNP	.											.	SHC1	91	.	0			c.G750T						.						215	226	223					1																	154940971		2203	4300	6503	SO:0001630	splice_region_variant	6464	exon4			ACCAACCTGTTTG	U73377	CCDS1076.1, CCDS30881.1, CCDS44233.1, CCDS44234.1	1q21	2013-02-14	2002-01-14		ENSG00000160691	ENSG00000160691		"SH2 domain containing"	10840	protein-coding gene	gene with protein product		600560	"SHC (Src homology 2 domain-containing) transforming protein 1"	SHC		1623525	Standard	NM_003029		Approved	p66	uc001ffw.3	P29353	OTTHUMG00000037295	ENST00000368445.5:c.750+1G>T	chr1.hg19:g.154940971C>A		83.0	0.0		104.0	68.0	NM_183001	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Missense_Mutation	SNP	ENST00000368445.5	hg19	CCDS30881.1	.	.	.	.	.	.	.	.	.	.	C	32	5.171568	0.94807	.	.	ENSG00000160691	ENST00000368445;ENST00000448116;ENST00000368449;ENST00000368453;ENST00000368450;ENST00000368443;ENST00000414115;ENST00000444179;ENST00000412170	T;T;T;T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06;2.49;2.06;2.06	5.51	5.51	0.81932	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.39253	0.1071	M	0.81942	2.565	0.80722	D	1	P;P;P	0.48407	0.91;0.693;0.538	P;P;P	0.58391	0.838;0.69;0.591	T	0.14144	-1.0483	9	.	.	.	.	19.4272	0.94746	0.0:1.0:0.0:0.0	.	29;250;250	Q59HB0;P29353-6;P29353	.;.;SHC1_HUMAN	H	250;250;51;140;140;186;21;21;140	ENSP00000357430:Q250H;ENSP00000401303:Q250H;ENSP00000357434:Q51H;ENSP00000357438:Q140H;ENSP00000357435:Q140H;ENSP00000404908:Q21H;ENSP00000398864:Q21H;ENSP00000398441:Q140H	.	Q	-	3	2	SHC1	153207595	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.276000	0.78559	2.590000	0.87494	0.467000	0.42956	CAG	.	.		0.542	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001	Missense_Mutation	A	154940971	C	A	154940971	5	1	27	1	0	0	0	0	0	0	1	0	14285	695	24	3	1040	3	SHC1	1	154940971	Splice_Site	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	98876	154940971	94309650	6	3521										
DARC	2532	hgsc.bcm.edu	37	chr1	159176208	159176208	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ccctccctgaaggatggtctTctcatctggacacccttgga	9	14	3	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr1:159176208T>A	ENST00000368122.2	+	2	1658	c.979T>A	c.(979-981)Tct>Act	p.S327T	DARC_ENST00000537147.1_Missense_Mutation_p.S327T|CTA-134P22.2_ENST00000609696.1_RNA|DARC_ENST00000368121.2_Missense_Mutation_p.S329T	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		327					chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					AGGATGGTCTTCTCATCTGGA	0.532																																					p.S329T		Atlas-SNP	.											.	DARC	76	.	0			c.T985A						.						213	230	225					1																	159176208		2203	4300	6503	SO:0001583	missense	2532	exon1			TGGTCTTCTCATC																												ENST00000368122.2:c.979T>A	chr1.hg19:g.159176208T>A	ENSP00000357104:p.Ser327Thr	111.0	0.0		132.0	36.0	NM_001122951	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Missense_Mutation	SNP	ENST00000368122.2	hg19	CCDS1183.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.372147	0.61624	.	.	ENSG00000213088	ENST00000368122;ENST00000537147;ENST00000359381;ENST00000368121	T;T;T	0.02369	4.33;4.33;4.32	5.4	3.11	0.35812	.	.	.	.	.	T	0.02083	0.0065	L	0.39898	1.24	0.09310	N	0.999999	D;D	0.54772	0.968;0.968	P;P	0.53450	0.726;0.726	T	0.46048	-0.9219	9	0.87932	D	0	-5.3364	6.8845	0.24191	0.0:0.1832:0.0:0.8168	.	329;327	Q5Y7A1;Q16570	.;DUFFY_HUMAN	T	327;327;327;329	ENSP00000357104:S327T;ENSP00000441985:S327T;ENSP00000357103:S329T	ENSP00000352341:S327T	S	+	1	0	DARC	157442832	0.479000	0.25925	0.255000	0.24374	0.740000	0.42216	0.466000	0.22019	0.457000	0.26962	0.533000	0.62120	TCT	.	.		0.532	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2			A	159176208	T	A	159176208	3	1	27	1	0	0	0	0	1	0	0	0	4242	1783	62	4	1012	4	DARC	1	159176208	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	4235237	159176208	90074413	7	3522										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185986178	185986179	+	Frame_Shift_Ins	INS	-	-	C													0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ggagctagattgtcatgtgaINScaggctctcccccaccaact							TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr1:185986178_185986179insC	ENST00000271588.4	+	33	5504_5505	c.5275_5276insC	c.(5275-5277)acafs	p.T1759fs	HMCN1_ENST00000367492.2_Frame_Shift_Ins_p.T1759fs	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1759	Ig-like C2-type 15.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TTGTCATGTGACAGGCTCTCCC	0.396																																					p.T1759fs		Atlas-Indel,Pindel	.											.	HMCN1	797	.	0			c.5275_5276insC						.																																			SO:0001589	frameshift_variant	83872	exon33			.	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.5276dupC	chr1.hg19:g.185986179_185986179dupC	ENSP00000271588:p.Thr1759fs	148.0	0.0		250.0	112.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Frame_Shift_Ins	INS	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.396	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	185986179	-	C	185986178	7	5	27	1	0	1	1	0	0	0	0	0	7229	275	10	0	5405	0	HMCN1	1	185986178	Frame_Shift_Ins	INS	-	TCGA-5R-AA1C-01A-11D-A40R-10	26809970	185986178	63264443	8	3523										
PRG4	10216	hgsc.bcm.edu	37	chr1	186281352	186281352	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	taaacaggaacctgtacagaAgtgccctggaagaaggcctg	12	9	0	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr1:186281352A>G	ENST00000445192.2	+	11	3884	c.3839A>G	c.(3838-3840)aAg>aGg	p.K1280R	TPR_ENST00000367478.4_3'UTR|PRG4_ENST00000367484.3_Missense_Mutation_p.K809R|PRG4_ENST00000367485.4_Missense_Mutation_p.K1187R|PRG4_ENST00000367483.4_Missense_Mutation_p.K1239R|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367486.3_Missense_Mutation_p.K1237R	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1280					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCTGTACAGAAGTGCCCTGGA	0.398																																					p.K1280R		Atlas-SNP	.											.	PRG4	259	.	0			c.A3839G						.						97	97	97					1																	186281352		2203	4300	6503	SO:0001583	missense	10216	exon11			TACAGAAGTGCCC	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.3839A>G	chr1.hg19:g.186281352A>G	ENSP00000399679:p.Lys1280Arg	144.0	0.0		199.0	128.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	hg19	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	A	11.08	1.534293	0.27475	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.06449	3.3;3.43;3.39;3.3;3.42	5.38	4.24	0.50183	Hemopexin/matrixin (2);	0.137606	0.32459	N	0.006077	T	0.07188	0.0182	L	0.42245	1.32	0.23366	N	0.997823	P;P;P;P	0.40050	0.694;0.694;0.7;0.694	B;B;B;P	0.44623	0.37;0.37;0.357;0.455	T	0.25187	-1.0139	10	0.34782	T	0.22	-5.4422	3.1118	0.06361	0.6349:0.148:0.0756:0.1416	.	1146;1187;1280;1239	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	R	1237;809;1239;1187;1280	ENSP00000356456:K1237R;ENSP00000356454:K809R;ENSP00000356453:K1239R;ENSP00000356455:K1187R;ENSP00000399679:K1280R	ENSP00000356453:K1239R	K	+	2	0	PRG4	184547975	0.976000	0.34144	0.907000	0.35723	0.653000	0.38743	1.429000	0.34903	0.962000	0.38057	0.477000	0.44152	AAG	.	.		0.398	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		G	186281352	A	G	186281352	3	3	27	1	0	0	0	0	1	0	0	0	12493	72	3	2	3877	2	PRG4	1	186281352	Missense_Mutation	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10	295174	186281352	62969269	9	3524										
RRM2	6241	hgsc.bcm.edu	37	chr2	10262771	10262797	+	5'Flank	DEL	AGCCAATGGGAAGGGCCGGGGCACCAA	AGCCAATGGGAAGGGCCGGGGCACCAA	-													0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	aagggtcggaggcatggcacAgccaatgggaagggccgggg							TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	AGCCAATGGGAAGGGCCGGGGCACCAA	AGCCAATGGGAAGGGCCGGGGCACCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr2:10262771_10262797delAGCCAATGGGAAGGGCCGGGGCACCAA	ENST00000304567.5	+	0	0				RP11-254F7.4_ENST00000607140.1_lincRNA|RRM2_ENST00000360566.2_In_Frame_Del_p.PMGRAGAPK10del	NM_001034.3	NP_001025.1	P31350	RIR2_HUMAN	ribonucleotide reductase M2						deoxyribonucleoside diphosphate metabolic process (GO:0009186)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|skin(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.188)|OV - Ovarian serous cystadenocarcinoma(76;0.221)	Cladribine(DB00242)|Gallium nitrate(DB05260)	GGCATGGCACAGCCAATGGGAAGGGCCGGGGCACCAAAGCCAATGGG	0.705																																					p.9_17del		Atlas-Indel,Pindel	.											.	RRM2	63	.	0			c.25_51del						.																																			SO:0001631	upstream_gene_variant	6241	exon1			.		CCDS1669.1, CCDS54334.1	2p25-p24	2012-10-02	2009-07-10		ENSG00000171848	ENSG00000171848	1.17.4.1		10452	protein-coding gene	gene with protein product		180390	"ribonucleotide reductase M2 polypeptide"				Standard	NM_001034		Approved		uc021vdr.1	P31350	OTTHUMG00000090449		chr2.hg19:g.10262771_10262797delAGCCAATGGGAAGGGCCGGGGCACCAA	Exception_encountered	265.0	0.0		192.0	45.0	NM_001165931	B2R9B5|J3KP43|Q5WRU7	In_Frame_Del	DEL	ENST00000304567.5	hg19	CCDS1669.1																																																																																			.	.		0.705	RRM2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364902.2			-	10262797	AGCCAATGGGAAGGGCCGGGGCACCAA	-	10262771	6	5	27	0	1	1	0	1	0	0	0	0	13697	188	7	0		0	RRM2	2	10262771	5'Flank	DEL	AGCCAATGGGAAGGGCCGGGGCACCAA	TCGA-5R-AA1C-01A-11D-A40R-10		10262771	232936602	10	3525										
PQLC3	130814	hgsc.bcm.edu	37	chr2	11317882	11317882	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gttcttctacgttttgtgatCatgctggctttaaatatatg	8	6	3	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr2:11317882C>T	ENST00000295083.3	+	7	712	c.537C>T	c.(535-537)atC>atT	p.I179I	PQLC3_ENST00000402361.1_3'UTR|PQLC3_ENST00000441908.2_Silent_p.I165I	NM_152391.3	NP_689604.1	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3	179						integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		GTTTTGTGATCATGCTGGCTT	0.368																																					p.I179I		Atlas-SNP	.											.	PQLC3	8	.	0			c.C537T						.						85	84	84					2																	11317882		2203	4300	6503	SO:0001819	synonymous_variant	130814	exon7			TGTGATCATGCTG	BC027625	CCDS1679.1, CCDS62856.1, CCDS62857.1	2p25.1	2004-02-05	2005-07-19	2005-07-19	ENSG00000162976	ENSG00000162976			28503	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 22"	C2orf22		12477932	Standard	NM_001282711		Approved	MGC33602	uc002rbc.3	Q8N755	OTTHUMG00000119055	ENST00000295083.3:c.537C>T	chr2.hg19:g.11317882C>T		51.0	0.0		54.0	30.0	NM_152391	B2R8K1|B4DWA4	Silent	SNP	ENST00000295083.3	hg19	CCDS1679.1																																																																																			.	.		0.368	PQLC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239266.4	NM_152391		T	11317882	C	T	11317882	2	4	27	1	0	0	0	0	0	0	0	1	12432	816	29	3		3	PQLC3	2	11317882	Silent	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	1055111	11317882	231881491	11	3526										
EMILIN1	11117	hgsc.bcm.edu	37	chr2	27305559	27305559	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gcaggctggatgtcgtggccGgctcagtgacagtgctgagt	17	9	1	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr2:27305559G>A	ENST00000380320.4	+	4	1619	c.1120G>A	c.(1120-1122)Ggc>Agc	p.G374S		NM_007046.3	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1	374					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(14)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	26	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTCGTGGCCGGCTCAGTGAC	0.726																																					p.G374S		Atlas-SNP	.											.	EMILIN1	75	.	0			c.G1120A						.						7	6	6					2																	27305559		2070	4081	6151	SO:0001583	missense	11117	exon4			GTGGCCGGCTCAG	AF088916	CCDS1733.1	2p23.3-p23.2	2008-02-05			ENSG00000138080	ENSG00000138080		"EMI domain containing"	19880	protein-coding gene	gene with protein product		130660					Standard	NM_007046		Approved	DKFZp586M121, gp115	uc002rii.4	Q9Y6C2	OTTHUMG00000097069	ENST00000380320.4:c.1120G>A	chr2.hg19:g.27305559G>A	ENSP00000369677:p.Gly374Ser	114.0	0.0		103.0	24.0	NM_007046	A5PL03|H0Y7A0|Q53SY9|Q96G58|Q96IH6|Q9UG76	Missense_Mutation	SNP	ENST00000380320.4	hg19	CCDS1733.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.465105	0.43839	.	.	ENSG00000138080	ENST00000380320	T	0.64260	-0.09	5.25	4.38	0.52667	.	0.077352	0.51477	D	0.000083	T	0.40619	0.1124	L	0.27053	0.805	0.42202	D	0.991778	P	0.36438	0.553	B	0.23574	0.047	T	0.28586	-1.0039	10	0.14252	T	0.57	-19.2585	11.4969	0.50413	0.0881:0.0:0.9119:0.0	.	374	Q9Y6C2	EMIL1_HUMAN	S	374	ENSP00000369677:G374S	ENSP00000369677:G374S	G	+	1	0	EMILIN1	27159063	0.973000	0.33851	0.958000	0.39756	0.299000	0.27559	1.613000	0.36900	1.227000	0.43598	0.407000	0.27541	GGC	.	.		0.726	EMILIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214185.1	NM_007046		A	27305559	G	A	27305559	3	1	27	1	0	0	0	0	1	0	0	0	5095	1116	39	1	1134	1	EMILIN1	2	27305559	Missense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	15987677	27305559	215893814	12	3527										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	catggccgggcgagctggagGaggaggaggaggaggaggag	24	5	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						.						3	4	4					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	239.0	0.0		273.0	11.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73613036	G	C	73613036	3	2	27	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	46307477	73613036	169586337	13	3528										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196681579	196681579	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ttctgagaaatctcattagcCaaggccttggaggaagataa	10	7	2	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr2:196681579C>A	ENST00000312428.6	-	51	9634	c.9534G>T	c.(9532-9534)ttG>ttT	p.L3178F		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3178	AAA 5. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TCTCATTAGCCAAGGCCTTGG	0.398																																					p.L3178F		Atlas-SNP	.											.	DNAH7	512	.	0			c.G9534T						.						103	104	104					2																	196681579		1857	4097	5954	SO:0001583	missense	56171	exon51			ATTAGCCAAGGCC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.9534G>T	chr2.hg19:g.196681579C>A	ENSP00000311273:p.Leu3178Phe	489.0	1.0		494.0	133.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	19.11	3.762967	0.69763	.	.	ENSG00000118997	ENST00000312428	T	0.54479	0.57	5.26	2.29	0.28610	.	0.000000	0.64402	D	0.000002	T	0.72358	0.3450	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74506	-0.3643	10	0.52906	T	0.07	.	10.7938	0.46449	0.0:0.7561:0.0:0.2439	.	3178	Q8WXX0	DYH7_HUMAN	F	3178	ENSP00000311273:L3178F	ENSP00000311273:L3178F	L	-	3	2	DNAH7	196389824	0.989000	0.36119	0.996000	0.52242	0.993000	0.82548	0.381000	0.20619	0.794000	0.33899	0.591000	0.81541	TTG	.	.		0.398	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196681579	C	A	196681579	3	1	27	1	0	0	0	0	1	0	0	0	4608	593	21	3	2600	3	DNAH7	2	196681579	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	123068543	196681579	46517794	14	3529										
COL4A3	1285	hgsc.bcm.edu	37	chr2	228141161	228141161	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	cccaccaggacctccagggcCccctggccatcctggccccc	9	23	0	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr2:228141161C>T	ENST00000396578.3	+	27	2150	c.1988C>T	c.(1987-1989)cCc>cTc	p.P663L	AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000433324.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	663	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		CCTCCAGGGCCCCCTGGCCAT	0.527																																					p.P663L		Atlas-SNP	.											.	COL4A3	293	.	0			c.C1988T						.						56	59	58					2																	228141161		1929	4126	6055	SO:0001583	missense	1285	exon27			CAGGGCCCCCTGG		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.1988C>T	chr2.hg19:g.228141161C>T	ENSP00000379823:p.Pro663Leu	98.0	0.0		121.0	65.0	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	hg19	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	C	4.746	0.138703	0.09083	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.94931	-3.56	5.33	0.926	0.19430	.	0.992308	0.08186	N	0.984716	D	0.87807	0.6270	L	0.28694	0.88	0.23095	N	0.998308	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.001;0.002;0.002	T	0.73052	-0.4104	10	0.10111	T	0.7	.	6.4894	0.22107	0.0:0.5469:0.0:0.4531	.	663;663;663;663	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	L	663	ENSP00000379823:P663L	ENSP00000323334:P663L	P	+	2	0	COL4A3	227849405	0.000000	0.05858	0.766000	0.31476	0.677000	0.39632	0.125000	0.15749	0.327000	0.23409	0.655000	0.94253	CCC	.	.		0.527	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		T	228141161	C	T	228141161	3	4	27	1	0	0	0	0	1	0	0	0	3693	623	22	3	2094	3	COL4A3	2	228141161	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	31459582	228141161	15058212	15	3530										
SH3BP4	23677	hgsc.bcm.edu	37	chr2	235949591	235949591	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ctttcggaaatgcaaaggaaGtgattgcgatcaaggactat	11	6	1	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr2:235949591G>T	ENST00000409212.1	+	4	685	c.178G>T	c.(178-180)Gtg>Ttg	p.V60L	SH3BP4_ENST00000344528.4_Missense_Mutation_p.V60L|SH3BP4_ENST00000392011.2_Missense_Mutation_p.V60L			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	60	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		TGCAAAGGAAGTGATTGCGAT	0.522																																					p.V60L		Atlas-SNP	.											.	SH3BP4	109	.	0			c.G178T						.						143	137	139					2																	235949591		2203	4300	6503	SO:0001583	missense	23677	exon4			AAGGAAGTGATTG	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.178G>T	chr2.hg19:g.235949591G>T	ENSP00000386862:p.Val60Leu	113.0	0.0		119.0	68.0	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	hg19	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.192849	0.78902	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000416021;ENST00000409212;ENST00000344528;ENST00000446904	T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33	5.44	5.44	0.79542	Src homology-3 domain (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	M	0.79011	2.435	0.80722	D	1	D;D	0.61080	0.989;0.989	D;D	0.70227	0.968;0.968	T	0.65796	-0.6081	10	0.66056	D	0.02	-0.0082	17.8307	0.88682	0.0:0.0:1.0:0.0	.	60;60	A8K594;Q9P0V3	.;SH3B4_HUMAN	L	60	ENSP00000375867:V60L;ENSP00000403251:V60L;ENSP00000386862:V60L;ENSP00000340237:V60L;ENSP00000415391:V60L	ENSP00000340237:V60L	V	+	1	0	SH3BP4	235614330	1.000000	0.71417	1.000000	0.80357	0.167000	0.22549	9.549000	0.98106	2.549000	0.85964	0.655000	0.94253	GTG	.	.		0.522	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			T	235949591	G	T	235949591	3	4	27	1	0	0	0	0	1	0	0	0	14261	1029	36	3	184	3	SH3BP4	2	235949591	Missense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	7808430	235949591	7249782	16	3531										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37396591	37396591	+	Splice_Site	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	catctcttgtttttcttgtaGaccatggcaaaagttataac	6	8	2	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr3:37396591G>A	ENST00000361924.2	+	22	6950		c.e22-1		GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Splice_Site	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4						Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TTTTCTTGTAGACCATGGCAA	0.408																																					.		Atlas-SNP	.											.	GOLGA4	173	.	0			c.6622-1G>A						.						151	146	148					3																	37396591		2203	4299	6502	SO:0001630	splice_region_variant	2803	exon22			CTTGTAGACCATG	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.6577-1G>A	chr3.hg19:g.37396591G>A		87.0	0.0		127.0	30.0	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Splice_Site	SNP	ENST00000361924.2	hg19	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.055800	0.55325	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1086	0.97902	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GOLGA4	37371595	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	6.056000	0.71111	2.756000	0.94617	0.563000	0.77884	.	.	.		0.408	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	Intron	A	37396591	G	A	37396591	5	1	27	1	0	0	0	0	0	0	1	0	6563	956	33	3	6732	3	GOLGA4	3	37396591	Splice_Site	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10		37396591	160625839	17	3532										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266137	41266137	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tgccactaccacagctccttCtctgagtggtaaaggcaatc	8	13	1	1	rs121913409		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr3:41266137C>A	ENST00000349496.5	+	3	414	c.134C>A	c.(133-135)tCt>tAt	p.S45Y	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45Y|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38Y|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45Y|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45Y	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45F(384)|p.S45del(53)|p.A5_A80del(53)|p.S45C(19)|p.S45Y(17)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.S45fs*2(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACAGCTCCTTCTCTGAGTGGT	0.498	S45F(HCC15_LUNG)|S45F(LS180_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45Y	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+1,2	CTNNB1	4904	.	601	Substitution - Missense(421)|Deletion - In frame(152)|Complex - deletion inframe(20)|Unknown(7)|Deletion - Frameshift(1)	soft_tissue(233)|liver(141)|large_intestine(85)|kidney(74)|endometrium(16)|skin(11)|adrenal_gland(9)|stomach(7)|biliary_tract(5)|ovary(4)|lung(3)|central_nervous_system(2)|cervix(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(1)|pituitary(1)|prostate(1)|bone(1)|pancreas(1)	c.C134A						.						84	74	77					3																	41266137		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTCCTTCTCTGAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.134C>A	chr3.hg19:g.41266137C>A	ENSP00000344456:p.Ser45Tyr	209.0	0.0		174.0	95.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519229	0.85495	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.68659	0.3025	M	0.65677	2.01	0.80722	D	1	D	0.76494	0.999	D	0.67231	0.95	T	0.69320	-0.5176	10	0.87932	D	0	-13.6823	20.2983	0.98569	0.0:1.0:0.0:0.0	.	45	P35222	CTNB1_HUMAN	Y	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38Y;ENSP00000385604:S45Y;ENSP00000412219:S45Y;ENSP00000379486:S45Y;ENSP00000344456:S45Y;ENSP00000411226:S38Y;ENSP00000379488:S45Y;ENSP00000409302:S45Y;ENSP00000401599:S45Y	ENSP00000344456:S45Y	S	+	2	0	CTNNB1	41241141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266137	C	A	41266137	3	1	27	1	0	0	0	0	1	0	0	0	4018	913	32	3	140	3	CTNNB1	3	41266137	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	3869546	41266137	156756293	18	3533										
SACM1L	22908	hgsc.bcm.edu	37	chr3	45751119	45751119	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	acactagtcctgaattccaaGaaatgagtctcttggaaagg	9	8	1	3			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr3:45751119G>C	ENST00000389061.5	+	5	667	c.463G>C	c.(463-465)Gaa>Caa	p.E155Q	SACM1L_ENST00000541314.1_Missense_Mutation_p.E94Q|SACM1L_ENST00000418611.1_Missense_Mutation_p.E52Q|SACM1L_ENST00000464524.1_3'UTR	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	155	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		TGAATTCCAAGAAATGAGTCT	0.333																																					p.E155Q		Atlas-SNP	.											.	SACM1L	38	.	0			c.G463C						.						86	81	83					3																	45751119		2203	4300	6503	SO:0001583	missense	22908	exon5			TTCCAAGAAATGA	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.463G>C	chr3.hg19:g.45751119G>C	ENSP00000373713:p.Glu155Gln	126.0	0.0		127.0	27.0	NM_014016	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	hg19	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.510582	0.64522	.	.	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000438671;ENST00000541314	T;T;T;T	0.58506	0.33;0.33;0.33;0.33	6.08	6.08	0.98989	Synaptojanin, N-terminal (2);	0.051390	0.85682	D	0.000000	T	0.45796	0.1360	N	0.16790	0.44	0.80722	D	1	B;B	0.18310	0.027;0.013	B;B	0.24701	0.042;0.055	T	0.34453	-0.9828	10	0.13853	T	0.58	-15.7407	20.6721	0.99693	0.0:0.0:1.0:0.0	.	94;155	B4DK71;Q9NTJ5	.;SAC1_HUMAN	Q	52;155;94;94	ENSP00000396387:E52Q;ENSP00000373713:E155Q;ENSP00000411966:E94Q;ENSP00000443373:E94Q	ENSP00000373713:E155Q	E	+	1	0	SACM1L	45726123	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.459000	0.97638	2.894000	0.99253	0.591000	0.81541	GAA	.	.		0.333	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016		C	45751119	G	C	45751119	3	2	27	1	0	0	0	0	1	0	0	0	13818	943	33	4	481	4	SACM1L	3	45751119	Missense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	4484982	45751119	152271311	19	3534										
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73433952	73433952	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tgcggtggcgtcgtcgccatTgttctcttgctccgagctct	12	13	2	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr3:73433952T>G	ENST00000263666.4	-	10	1879	c.1765A>C	c.(1765-1767)Aat>Cat	p.N589H	PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000479530.1_Missense_Mutation_p.N306H|PDZRN3_ENST00000535920.1_Missense_Mutation_p.N311H|PDZRN3_ENST00000462146.2_Missense_Mutation_p.N246H|PDZRN3_ENST00000466780.1_Missense_Mutation_p.N246H	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	589					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TCGTCGCCATTGTTCTCTTGC	0.632																																					p.N589H		Atlas-SNP	.											.	PDZRN3	196	.	0			c.A1765C						.						87	78	81					3																	73433952		2203	4300	6503	SO:0001583	missense	23024	exon10			CGCCATTGTTCTC	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.1765A>C	chr3.hg19:g.73433952T>G	ENSP00000263666:p.Asn589His	70.0	0.0		79.0	21.0	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	hg19	CCDS33789.1	.	.	.	.	.	.	.	.	.	.	T	9.111	1.006508	0.19199	.	.	ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530;ENST00000416926;ENST00000492909	T;T;T;T;T;T	0.09723	2.95;3.64;3.53;3.53;3.65;3.64	4.77	4.77	0.60923	.	0.948643	0.08842	N	0.885715	T	0.11367	0.0277	L	0.44542	1.39	0.40950	D	0.984538	B;B;B;B	0.18863	0.001;0.007;0.002;0.031	B;B;B;B	0.12156	0.007;0.004;0.003;0.007	T	0.09930	-1.0652	10	0.24483	T	0.36	.	10.3295	0.43814	0.0:0.0:0.165:0.835	.	311;306;306;589	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7	.;.;.;PZRN3_HUMAN	H	589;311;246;246;306;589;287	ENSP00000263666:N589H;ENSP00000442026:N311H;ENSP00000418168:N246H;ENSP00000418484:N246H;ENSP00000418624:N306H;ENSP00000419250:N287H	ENSP00000263666:N589H	N	-	1	0	PDZRN3	73516642	1.000000	0.71417	0.998000	0.56505	0.767000	0.43475	3.124000	0.50461	1.995000	0.58328	0.533000	0.62120	AAT	.	.		0.632	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		G	73433952	T	G	73433952	3	3	27	1	0	0	0	0	1	0	0	0	11718	1812	63	5	1439	5	PDZRN3	3	73433952	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	27682833	73433952	124588478	20	3535										
C3orf37	56941	hgsc.bcm.edu	37	chr3	129017267	129017267	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ggacaactggaggctgctgaCaatggccgggatctttgact	14	9	1	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr3:129017267C>T	ENST00000383463.4	+	5	613	c.524C>T	c.(523-525)aCa>aTa	p.T175I	HMCES_ENST00000389735.3_Missense_Mutation_p.T175I|HMCES_ENST00000417226.2_Missense_Mutation_p.T133I|HMCES_ENST00000502878.2_Missense_Mutation_p.T175I	NM_020187.2	NP_064572.2	Q96FZ2	HMCES_HUMAN	5-hydroxymethylcytosine (hmC) binding, ES cell-specific	175							DNA binding (GO:0003677)|peptidase activity (GO:0008233)										AGGCTGCTGACAATGGCCGGG	0.507																																					p.T175I		Atlas-SNP	.											.	C3orf37	27	.	0			c.C524T						.						112	102	106					3																	129017267		2203	4300	6503	SO:0001583	missense	56941	exon5			TGCTGACAATGGC	AF201934	CCDS33852.1	3q21.3	2013-08-30	2013-08-30	2013-08-30	ENSG00000183624	ENSG00000183624			24446	protein-coding gene	gene with protein product	"SOS response associated peptidase domain containing 1"		"chromosome 3 open reading frame 37"	C3orf37		23434322, 23945014	Standard	XM_005247636		Approved	DC12, SRAPD1	uc003elt.3	Q96FZ2	OTTHUMG00000159452	ENST00000383463.4:c.524C>T	chr3.hg19:g.129017267C>T	ENSP00000372955:p.Thr175Ile	214.0	1.0		195.0	103.0	NM_020187	A6NJR9|Q96G34|Q9NRP3	Missense_Mutation	SNP	ENST00000383463.4	hg19	CCDS33852.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.337138	0.81801	.	.	ENSG00000183624	ENST00000509042;ENST00000383463;ENST00000417226;ENST00000510314;ENST00000502878;ENST00000389735;ENST00000509551;ENST00000511665	.	.	.	4.73	4.73	0.59995	.	0.102570	0.64402	D	0.000003	T	0.79684	0.4488	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82808	-0.0274	9	0.66056	D	0.02	-19.4031	15.1904	0.73038	0.0:1.0:0.0:0.0	.	133;175	E7EMP6;Q96FZ2	.;CC037_HUMAN	I	127;175;133;85;175;175;175;85	.	ENSP00000372955:T175I	T	+	2	0	C3orf37	130499957	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.179000	0.77665	2.165000	0.68154	0.585000	0.79938	ACA	.	.		0.507	HMCES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355470.2	NM_020187		T	129017267	C	T	129017267	3	4	27	1	0	0	0	0	1	0	0	0	2229	478	17	3	538	3	C3orf37	3	129017267	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	55583315	129017267	69005163	21	3536										
PDE6B	5158	hgsc.bcm.edu	37	chr4	661717	661717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	acaataggaaagagtggaagGcgctggctgatgagtatgag	16	4	0	4			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr4:661717G>A	ENST00000496514.1	+	21	2446	c.2425G>A	c.(2425-2427)Gcg>Acg	p.A809T	PDE6B_ENST00000255622.6_Missense_Mutation_p.A809T|PDE6B_ENST00000429163.2_Missense_Mutation_p.A530T			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	809					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	AGAGTGGAAGGCGCTGGCTGA	0.562																																					p.A809T	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.G2425A						.						140	145	143					4																	661717		2203	4300	6503	SO:0001583	missense	5158	exon21			TGGAAGGCGCTGG	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"Phosphodiesterases"	8786	protein-coding gene	gene with protein product	"congenital stationary night blindness 3, autosomal dominant"	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.2425G>A	chr4.hg19:g.661717G>A	ENSP00000420295:p.Ala809Thr	89.0	0.0		77.0	24.0	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	hg19	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	g	13.26	2.185372	0.38609	.	.	ENSG00000133256	ENST00000255622;ENST00000496514;ENST00000429163	T;T;T	0.77489	-1.1;-1.1;-1.1	4.7	2.95	0.34219	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.126462	0.51477	N	0.000093	T	0.65322	0.2680	L	0.33753	1.03	0.39314	D	0.965121	B;B	0.14012	0.005;0.009	B;B	0.20767	0.031;0.031	T	0.56944	-0.7895	10	0.30854	T	0.27	.	9.4703	0.38837	0.1804:0.0:0.8196:0.0	.	809;809	P35913;P35913-2	PDE6B_HUMAN;.	T	809;809;530	ENSP00000255622:A809T;ENSP00000420295:A809T;ENSP00000406334:A530T	ENSP00000255622:A809T	A	+	1	0	PDE6B	651717	1.000000	0.71417	0.925000	0.36789	0.890000	0.51754	3.418000	0.52721	0.517000	0.28361	-0.141000	0.14075	GCG	.	.		0.562	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		A	661717	G	A	661717	3	1	27	1	0	0	0	0	1	0	0	0	11655	1203	42	3	2507	3	PDE6B	4	661717	Missense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10		661717	190492559	22	3537										
STK32B	55351	hgsc.bcm.edu	37	chr4	5500781	5500781	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gcaacaacaacctcctcaccCacacctgcacccgtggctgc	6	20	1	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr4:5500781C>T	ENST00000282908.5	+	12	1638	c.1216C>T	c.(1216-1218)Cac>Tac	p.H406Y	STK32B_ENST00000512636.1_Missense_Mutation_p.H329Y|STK32B_ENST00000510398.1_Missense_Mutation_p.H359Y|STK32B_ENST00000508728.1_3'UTR	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						CCTCCTCACCCACACCTGCAC	0.647																																					p.H406Y		Atlas-SNP	.											.	STK32B	87	.	0			c.C1216T						.						138	101	114					4																	5500781		2203	4300	6503	SO:0001583	missense	55351	exon12			CTCACCCACACCT	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.1216C>T	chr4.hg19:g.5500781C>T	ENSP00000282908:p.His406Tyr	323.0	0.0		219.0	97.0	NM_018401		Missense_Mutation	SNP	ENST00000282908.5	hg19	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	C	1.863	-0.462098	0.04508	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.67698	-0.21;0.1;-0.28	4.97	2.23	0.28157	.	0.179933	0.25984	U	0.027052	T	0.55529	0.1926	L	0.51422	1.61	0.09310	N	1	B	0.27068	0.167	B	0.28011	0.085	T	0.40887	-0.9539	10	0.25751	T	0.34	.	7.8806	0.29621	0.2825:0.6341:0.0:0.0834	.	406	Q9NY57	ST32B_HUMAN	Y	406;329;359	ENSP00000282908:H406Y;ENSP00000423209:H329Y;ENSP00000420984:H359Y	ENSP00000282908:H406Y	H	+	1	0	STK32B	5551682	0.006000	0.16342	0.001000	0.08648	0.001000	0.01503	0.437000	0.21543	-0.097000	0.12307	-2.600000	0.00162	CAC	.	.		0.647	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		T	5500781	C	T	5500781	3	4	27	1	0	0	0	0	1	0	0	0	15313	594	21	3	1262	3	STK32B	4	5500781	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	4839064	5500781	185653495	23	3538										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46067487	46067487	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gtttctgaagaaagtgtcagGaatccaaatttttccaacca	7	8	2	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr4:46067487G>T	ENST00000295452.4	-	4	603	c.436C>A	c.(436-438)Cct>Act	p.P146T		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	146					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.P146T(1)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AAAGTGTCAGGAATCCAAATT	0.358																																					p.P146T		Atlas-SNP	.											GABRG1,NS,carcinoma,0,1	GABRG1	172	.	1	Substitution - Missense(1)	lung(1)	c.C436A						.						85	85	85					4																	46067487		2203	4300	6503	SO:0001583	missense	2565	exon4			TGTCAGGAATCCA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.436C>A	chr4.hg19:g.46067487G>T	ENSP00000295452:p.Pro146Thr	80.0	0.0		93.0	39.0	NM_173536	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.596088	0.86953	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	D	0.98550	-4.99	5.08	5.08	0.68730	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.99384	0.9783	H	0.97732	4.065	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98440	1.0586	10	0.87932	D	0	.	17.8218	0.88652	0.0:0.0:1.0:0.0	.	146	Q8N1C3	GBRG1_HUMAN	T	146	ENSP00000295452:P146T	ENSP00000295452:P146T	P	-	1	0	GABRG1	45762244	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.792000	0.99085	2.513000	0.84729	0.508000	0.49915	CCT	.	.		0.358	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		T	46067487	G	T	46067487	3	4	27	1	0	0	0	0	1	0	0	0	6179	1174	41	3	985	3	GABRG1	4	46067487	Missense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	40566706	46067487	145086789	24	3539										
CXCL13	10563	hgsc.bcm.edu	37	chr4	78528986	78528986	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tggttgtccaagaaaagaaaTcatgtaagtttcaagagaaa	9	4	2	3			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr4:78528986T>C	ENST00000286758.4	+	3	272	c.194T>C	c.(193-195)aTc>aCc	p.I65T		NM_006419.2	NP_006410.1	O43927	CXL13_HUMAN	chemokine (C-X-C motif) ligand 13	65					activation of Rap GTPase activity (GO:0032861)|B cell chemotaxis (GO:0035754)|B cell chemotaxis across high endothelial venule (GO:0035769)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|chronic inflammatory response (GO:0002544)|defense response to bacterium (GO:0042742)|endothelial cell chemotaxis to fibroblast growth factor (GO:0035768)|germinal center formation (GO:0002467)|immune response (GO:0006955)|lymph node development (GO:0048535)|lymphocyte chemotaxis across high endothelial venule (GO:0002518)|negative regulation of endothelial cell chemotaxis to fibroblast growth factor (GO:2000545)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of integrin activation (GO:0033625)|positive regulation of T cell chemotaxis (GO:0010820)|regulation of angiogenesis (GO:0045765)|regulation of humoral immune response (GO:0002920)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR10 chemokine receptor binding (GO:0031735)|chemokine activity (GO:0008009)|CXCR3 chemokine receptor binding (GO:0048248)|CXCR5 chemokine receptor binding (GO:0031724)|fibroblast growth factor binding (GO:0017134)|heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|receptor agonist activity (GO:0048018)			large_intestine(1)|ovary(1)|skin(1)|urinary_tract(1)	4						AGAAAAGAAATCATGTAAGTT	0.378																																					p.I65T		Atlas-SNP	.											.	CXCL13	9	.	0			c.T194C						.						76	73	74					4																	78528986		2203	4300	6503	SO:0001583	missense	10563	exon3			AAGAAATCATGTA	AJ002211	CCDS3582.1	4q21	2013-02-25	2008-08-29	2002-08-23	ENSG00000156234	ENSG00000156234		"Endogenous ligands"	10639	protein-coding gene	gene with protein product	"B-cell chemoattractant"	605149	"small inducible cytokine B subfamily (Cys-X-Cys motif), member 13 (B-cell chemoattractant)"	SCYB13		9463416, 9486651	Standard	NM_006419		Approved	BLC, BCA-1, BLR1L, ANGIE, ANGIE2	uc003hkr.3	O43927	OTTHUMG00000130201	ENST00000286758.4:c.194T>C	chr4.hg19:g.78528986T>C	ENSP00000286758:p.Ile65Thr	108.0	0.0		90.0	13.0	NM_006419		Missense_Mutation	SNP	ENST00000286758.4	hg19	CCDS3582.1	.	.	.	.	.	.	.	.	.	.	T	14.00	2.405102	0.42613	.	.	ENSG00000156234	ENST00000286758	T	0.07216	3.21	4.74	3.54	0.40534	CXC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.479361	0.21446	N	0.074405	T	0.28863	0.0716	M	0.87328	2.875	0.24173	N	0.995617	D	0.76494	0.999	D	0.72625	0.978	T	0.08046	-1.0741	10	0.87932	D	0	-11.6691	7.7838	0.29080	0.1855:0.0:0.0:0.8145	.	65	O43927	CXL13_HUMAN	T	65	ENSP00000286758:I65T	ENSP00000286758:I65T	I	+	2	0	CXCL13	78748010	0.810000	0.29049	0.739000	0.30968	0.479000	0.33129	1.964000	0.40462	0.924000	0.37069	0.460000	0.39030	ATC	.	.		0.378	CXCL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252519.1			C	78528986	T	C	78528986	3	2	27	1	0	0	0	0	1	0	0	0	4083	1435	50	2	200	2	CXCL13	4	78528986	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	32461499	78528986	112625290	25	3540										
HEXB	3074	hgsc.bcm.edu	37	chr5	73981154	73981154	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ctgctgttggcgacactgctGgcggcgatgttggcgctgct	16	11	0	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr5:73981154G>A	ENST00000261416.7	+	1	186	c.69G>A	c.(67-69)ctG>ctA	p.L23L	HEXB_ENST00000511181.1_Intron	NM_000521.3	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B (beta polypeptide)	23					astrocyte cell migration (GO:0043615)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|ganglioside catabolic process (GO:0006689)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|lipid storage (GO:0019915)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|male courtship behavior (GO:0008049)|myelination (GO:0042552)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|oogenesis (GO:0048477)|penetration of zona pellucida (GO:0007341)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(3)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		CGACACTGCTGGCGGCGATGT	0.751																																					p.L23L	Melanoma(66;841 1270 13391 18706 27225)	Atlas-SNP	.											.	HEXB	34	.	0			c.G69A						.						5	6	6					5																	73981154		2054	4046	6100	SO:0001819	synonymous_variant	3074	exon1			ACTGCTGGCGGCG	M13519	CCDS4022.1	5q13.3	2012-10-02			ENSG00000049860	ENSG00000049860	3.2.1.52		4879	protein-coding gene	gene with protein product		606873				2579389, 3013851	Standard	NM_000521		Approved		uc003kdf.4	P07686	OTTHUMG00000102057	ENST00000261416.7:c.69G>A	chr5.hg19:g.73981154G>A		104.0	0.0		97.0	49.0	NM_000521		Silent	SNP	ENST00000261416.7	hg19	CCDS4022.1																																																																																			.	.		0.751	HEXB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219859.6	NM_000521		A	73981154	G	A	73981154	2	1	27	1	0	0	0	0	0	0	0	1	7083	1335	47	3		3	HEXB	5	73981154	Silent	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10		73981154	106934106	26	3541										
GFM2	84340	hgsc.bcm.edu	37	chr5	74021934	74021934	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	aagatgccttttgtctcctaAagttctatctaaggtatctg	7	8	4	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr5:74021934A>C	ENST00000296805.3	-	18	2201	c.1744T>G	c.(1744-1746)Tta>Gta	p.L582V	GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000345239.2_Missense_Mutation_p.L535V|RNU6-658P_ENST00000384606.1_RNA|GFM2_ENST00000509430.1_Missense_Mutation_p.L582V	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		TTGTCTCCTAAAGTTCTATCT	0.358																																					p.L582V		Atlas-SNP	.											.	GFM2	38	.	0			c.T1744G						.						104	98	100					5																	74021934		2203	4300	6503	SO:0001583	missense	84340	exon18			CTCCTAAAGTTCT	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1744T>G	chr5.hg19:g.74021934A>C	ENSP00000296805:p.Leu582Val	61.0	0.0		44.0	10.0	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	A	6.291	0.421778	0.11928	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000509430	T;T;T	0.29397	1.57;1.57;1.57	5.7	0.5	0.16919	Ribosomal protein S5 domain 2-type fold (1);Translation elongation factor EFG/EF2, domain IV (2);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.226724	0.35772	N	0.002991	T	0.18173	0.0436	L	0.29908	0.895	0.50039	D	0.999843	B;B;B	0.18013	0.007;0.025;0.008	B;B;B	0.26864	0.03;0.046;0.074	T	0.08432	-1.0722	10	0.72032	D	0.01	-2.6368	2.1389	0.03770	0.3416:0.3336:0.2193:0.1055	.	582;535;582	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	V	582;535;582	ENSP00000296805:L582V;ENSP00000296804:L535V;ENSP00000427004:L582V	ENSP00000296805:L582V	L	-	1	2	GFM2	74057690	0.040000	0.19996	0.950000	0.38849	0.631000	0.37964	0.378000	0.20569	0.101000	0.17610	-0.371000	0.07208	TTA	.	.		0.358	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		C	74021934	A	C	74021934	3	2	27	1	0	0	0	0	1	0	0	0	6350	11	1	5	611	5	GFM2	5	74021934	Missense_Mutation	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10	40780	74021934	106893326	27	3542										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169412919	169412919	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ggatggccatgagcatggttCaaaacaggtgagctgctacc	13	9	1	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr5:169412919C>T	ENST00000256935.8	+	29	3066	c.2986C>T	c.(2986-2988)Caa>Taa	p.Q996*	DOCK2_ENST00000540750.1_Nonsense_Mutation_p.Q57*|DOCK2_ENST00000520908.1_Nonsense_Mutation_p.Q488*|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	996	Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAGCATGGTTCAAAACAGGTG	0.453																																					p.Q996X		Atlas-SNP	.											.	DOCK2	389	.	0			c.C2986T						.						219	207	211					5																	169412919		2203	4300	6503	SO:0001587	stop_gained	1794	exon29			ATGGTTCAAAACA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2986C>T	chr5.hg19:g.169412919C>T	ENSP00000256935:p.Gln996*	164.0	0.0		107.0	33.0	NM_004946	Q2M3I0|Q96AK7	Nonsense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	49	15.080676	0.99821	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	19.0483	0.93030	0.0:1.0:0.0:0.0	.	.	.	.	X	996;488;57	.	ENSP00000256935:Q996X	Q	+	1	0	DOCK2	169345497	1.000000	0.71417	0.989000	0.46669	0.309000	0.27889	7.776000	0.85560	2.495000	0.84180	0.655000	0.94253	CAA	.	.		0.453	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169412919	C	T	169412919	4	4	27	1	0	0	0	0	0	1	0	0	4689	827	29	3	3100	3	DOCK2	5	169412919	Nonsense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	95390985	169412919	11502341	28	3543										
HIST1H2AH	85235	hgsc.bcm.edu	37	chr6	27114964	27114964	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gccaaggccaagacccgctcTtctcgggctgggcttcagtt	12	14	3	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr6:27114964T>C	ENST00000377459.1	+	1	104	c.57T>C	c.(55-57)tcT>tcC	p.S19S	HIST1H2BK_ENST00000396891.4_5'Flank|HIST1H2BK_ENST00000356950.1_5'Flank|MIR3143_ENST00000584253.1_RNA	NM_080596.1	NP_542163.1	Q96KK5	H2A1H_HUMAN	histone cluster 1, H2ah	19						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|prostate(1)|skin(1)	12						AGACCCGCTCTTCTCGGGCTG	0.622																																					p.S19S		Atlas-SNP	.											.	HIST1H2AH	26	.	0			c.T57C						.						63	71	68					6																	27114964		2203	4300	6503	SO:0001819	synonymous_variant	85235	exon1			CCGCTCTTCTCGG	AY131988	CCDS4622.1	6p22.1	2011-01-27	2006-10-11			ENSG00000274997		"Histones / Replication-dependent"	13671	protein-coding gene	gene with protein product		615013	"histone 1, H2ah"			12408966	Standard	NM_080596		Approved	H2AFALii, dJ86C11.1, H2A/S	uc003niz.4	Q96KK5		ENST00000377459.1:c.57T>C	chr6.hg19:g.27114964T>C		268.0	0.0		266.0	54.0	NM_080596		Silent	SNP	ENST00000377459.1	hg19	CCDS4622.1																																																																																			.	.		0.622	HIST1H2AH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040136.1	NM_080596		C	27114964	T	C	27114964	2	2	27	1	0	0	0	0	0	0	0	1	7143	1596	56	2		2	HIST1H2AH	6	27114964	Silent	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10		27114964	144000103	29	3544										
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31927872	31927872	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	atccccagcctggctgcctcTgcatggtgtggagcactcag	12	14	2	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr6:31927872T>A	ENST00000375394.2	+	3	325	c.212T>A	c.(211-213)cTg>cAg	p.L71Q	NELFE_ENST00000375425.5_5'Flank|NELFE_ENST00000375429.3_5'Flank|SKIV2L_ENST00000488648.1_3'UTR|SKIV2L_ENST00000544581.1_Intron|NELFE_ENST00000444811.2_5'Flank	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	71					ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						TGGCTGCCTCTGCATGGTGTG	0.572																																					p.L71Q		Atlas-SNP	.											.	SKIV2L	97	.	0			c.T212A						.						69	69	69					6																	31927872		1509	2709	4218	SO:0001583	missense	6499	exon3			TGCCTCTGCATGG		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.212T>A	chr6.hg19:g.31927872T>A	ENSP00000364543:p.Leu71Gln	92.0	0.0		120.0	41.0	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.443581	0.63067	.	.	ENSG00000204351	ENST00000375394	T	0.44482	0.92	4.61	4.61	0.57282	.	0.174295	0.39146	N	0.001451	T	0.28466	0.0704	L	0.36672	1.1	0.80722	D	1	D	0.56968	0.978	P	0.52267	0.694	T	0.02813	-1.1107	10	0.24483	T	0.36	-12.0315	11.6576	0.51328	0.0:0.0:0.0:1.0	.	71	Q15477	SKIV2_HUMAN	Q	71	ENSP00000364543:L71Q	ENSP00000364543:L71Q	L	+	2	0	SKIV2L	32035851	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.294000	0.59043	1.944000	0.56390	0.533000	0.62120	CTG	.	.		0.572	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			A	31927872	T	A	31927872	3	1	27	1	0	0	0	0	1	0	0	0	14374	1580	55	4	222	4	SKIV2L	6	31927872	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	4812908	31927872	139187195	30	3545										
TEAD3	7005	hgsc.bcm.edu	37	chr6	35443156	35443156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gcacgctgttcatcatgtacTtctcgggcaggtgcttcagc	11	12	4	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr6:35443156T>C	ENST00000402886.3	-	10	1124	c.971A>G	c.(970-972)aAg>aGg	p.K324R	TEAD3_ENST00000338863.7_Missense_Mutation_p.K384R			Q99594	TEAD3_HUMAN	TEA domain family member 3	384	Transcriptional activation. {ECO:0000255}.				female pregnancy (GO:0007565)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	10						CATCATGTACTTCTCGGGCAG	0.592																																					p.K384R		Atlas-SNP	.											.	TEAD3	52	.	0			c.A1151G						.						101	95	97					6																	35443156		2203	4300	6503	SO:0001583	missense	7005	exon12			ATGTACTTCTCGG	X94439	CCDS47414.1	6p21.2	2008-07-28			ENSG00000007866	ENSG00000007866			11716	protein-coding gene	gene with protein product		603170		TEAD5		9889009, 9148898	Standard	NM_003214		Approved	TEF-5, ETFR-1	uc003oku.4	Q99594	OTTHUMG00000014571	ENST00000402886.3:c.971A>G	chr6.hg19:g.35443156T>C	ENSP00000384577:p.Lys324Arg	64.0	0.0		58.0	24.0	NM_003214	O95910|Q5BJG7|Q8N6Y4	Missense_Mutation	SNP	ENST00000402886.3	hg19		.	.	.	.	.	.	.	.	.	.	T	19.56	3.849889	0.71603	.	.	ENSG00000007866	ENST00000338863;ENST00000402886;ENST00000373905	T;T	0.34275	1.37;1.37	5.61	5.61	0.85477	.	0.055638	0.64402	D	0.000001	T	0.44767	0.1309	M	0.69185	2.1	0.58432	D	0.999998	P;D;P	0.57899	0.867;0.981;0.79	P;D;P	0.68353	0.519;0.957;0.508	T	0.33904	-0.9850	10	0.20519	T	0.43	-30.5472	14.6427	0.68737	0.0:0.0:0.0:1.0	.	324;400;384	B5MCM0;Q7Z6V0;Q99594	.;.;TEAD3_HUMAN	R	384;324;400	ENSP00000345772:K384R;ENSP00000384577:K324R	ENSP00000345772:K384R	K	-	2	0	TEAD3	35551134	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	6.235000	0.72332	2.132000	0.65825	0.528000	0.53228	AAG	.	.		0.592	TEAD3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316961.2			C	35443156	T	C	35443156	3	2	27	1	0	0	0	0	1	0	0	0	15755	1609	56	2	164	2	TEAD3	6	35443156	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	3515284	35443156	135671911	31	3546										
TJAP1	93643	hgsc.bcm.edu	37	chr6	43473578	43473578	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	acccaggcccaggagcagggCaacctgctcaactagggccc	12	16	1	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr6:43473578C>G	ENST00000372445.5	+	11	2035	c.1659C>G	c.(1657-1659)ggC>ggG	p.G553G	TJAP1_ENST00000438588.2_Silent_p.G553G|TJAP1_ENST00000372444.2_Silent_p.G543G|TJAP1_ENST00000372449.1_Silent_p.G553G|TJAP1_ENST00000372452.1_Silent_p.G543G|TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000436109.2_Silent_p.G543G|TJAP1_ENST00000259751.1_Silent_p.G543G	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	553					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			AGGAGCAGGGCAACCTGCTCA	0.672																																					p.G553G		Atlas-SNP	.											.	TJAP1	35	.	0			c.C1659G						.						6	7	6					6																	43473578		2122	4191	6313	SO:0001819	synonymous_variant	93643	exon11			GCAGGGCAACCTG	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.1659C>G	chr6.hg19:g.43473578C>G		54.0	0.0		73.0	23.0	NM_001146016	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Silent	SNP	ENST00000372445.5	hg19	CCDS55004.1																																																																																			.	.		0.672	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		G	43473578	C	G	43473578	2	3	27	1	0	0	0	0	0	0	0	1	15943	697	25	4		4	TJAP1	6	43473578	Silent	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	8030422	43473578	127641489	32	3547										
TFAP2B	7021	hgsc.bcm.edu	37	chr6	50803851	50803851	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gaggcatgtctgtcaacaccGgcgaggtgttttgctccgtc	13	11	2	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr6:50803851G>C	ENST00000393655.3	+	4	848	c.679G>C	c.(679-681)Ggc>Cgc	p.G227R	TFAP2B_ENST00000263046.4_Missense_Mutation_p.G236R	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	227					aorta morphogenesis (GO:0035909)|calcium ion homeostasis (GO:0055074)|cellular ammonia homeostasis (GO:0097275)|cellular creatinine homeostasis (GO:0097276)|cellular urea homeostasis (GO:0097277)|collecting duct development (GO:0072044)|distal tubule development (GO:0072017)|ductus arteriosus closure (GO:0097070)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hindlimb morphogenesis (GO:0035137)|kidney development (GO:0001822)|magnesium ion homeostasis (GO:0010960)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphate ion homeostasis (GO:0055062)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|potassium ion homeostasis (GO:0055075)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell differentiation (GO:0045595)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|renal water homeostasis (GO:0003091)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|retina layer formation (GO:0010842)|skin development (GO:0043588)|sodium ion homeostasis (GO:0055078)|sympathetic nervous system development (GO:0048485)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)	40	Lung NSC(77;0.156)					TGTCAACACCGGCGAGGTGTT	0.502																																					p.G227R	Pancreas(116;1373 2332 5475 10752)	Atlas-SNP	.											.	TFAP2B	91	.	0			c.G679C						.						107	109	108					6																	50803851		2203	4300	6503	SO:0001583	missense	7021	exon4			AACACCGGCGAGG	X95694	CCDS4934.2	6p12	2008-02-05	2001-11-28		ENSG00000008196	ENSG00000008196			11743	protein-coding gene	gene with protein product		601601	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)"			7555706, 8661133	Standard	NM_003221		Approved	AP2-B	uc003pag.3	Q92481	OTTHUMG00000014836	ENST00000393655.3:c.679G>C	chr6.hg19:g.50803851G>C	ENSP00000377265:p.Gly227Arg	110.0	0.0		155.0	10.0	NM_003221	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	hg19	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	G	15.80	2.941381	0.53079	.	.	ENSG00000008196	ENST00000393655;ENST00000263046	D;D	0.97232	-4.3;-4.29	5.44	5.44	0.79542	.	0.161988	0.56097	D	0.000033	D	0.93736	0.7998	L	0.40543	1.245	0.49483	D	0.999791	P	0.38535	0.635	B	0.42959	0.403	D	0.93957	0.7237	10	0.51188	T	0.08	-13.0556	12.5994	0.56489	0.0759:0.0:0.9241:0.0	.	227	Q92481	AP2B_HUMAN	R	227;236	ENSP00000377265:G227R;ENSP00000263046:G236R	ENSP00000263046:G236R	G	+	1	0	TFAP2B	50911810	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.131000	0.71670	2.561000	0.86390	0.650000	0.86243	GGC	.	.		0.502	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221		C	50803851	G	C	50803851	3	2	27	1	0	0	0	0	1	0	0	0	15803	1116	39	4	693	4	TFAP2B	6	50803851	Missense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	7330273	50803851	120311216	33	3548										
HCRTR2	3062	hgsc.bcm.edu	37	chr6	55120007	55120007	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gtggtatgcaatctgtcaccCtttgatgtttaagagcacag	10	8	2	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr6:55120007C>T	ENST00000370862.3	+	3	812	c.476C>T	c.(475-477)cCt>cTt	p.P159L		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	159					circadian sleep/wake cycle process (GO:0022410)|feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|orexin receptor activity (GO:0016499)			breast(3)|endometrium(2)|kidney(1)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	46	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			ATCTGTCACCCTTTGATGTTT	0.468																																					p.P159L		Atlas-SNP	.											.	HCRTR2	112	.	0			c.C476T						.						162	136	145					6																	55120007		2203	4300	6503	SO:0001583	missense	3062	exon3			GTCACCCTTTGAT	AF041245	CCDS4956.1	6p12.1	2012-09-20			ENSG00000137252	ENSG00000137252		"GPCR / Class A : Hypocretin (orexin) receptors"	4849	protein-coding gene	gene with protein product		602393				9491897	Standard	NM_001526		Approved	OX2R	uc003pcl.3	O43614	OTTHUMG00000016150	ENST00000370862.3:c.476C>T	chr6.hg19:g.55120007C>T	ENSP00000359899:p.Pro159Leu	81.0	0.0		132.0	70.0	NM_001526	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	hg19	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.965998	0.92855	.	.	ENSG00000137252	ENST00000370862	T	0.61274	0.12	5.05	5.05	0.67936	GPCR, rhodopsin-like superfamily (1);	0.103102	0.64402	D	0.000002	D	0.83806	0.5334	H	0.98111	4.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90329	0.4350	10	0.87932	D	0	.	18.3959	0.90497	0.0:1.0:0.0:0.0	.	159;159	Q548Y0;O43614	.;OX2R_HUMAN	L	159	ENSP00000359899:P159L	ENSP00000359899:P159L	P	+	2	0	HCRTR2	55227966	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.345000	0.79718	0.484000	0.47621	CCT	.	.		0.468	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			T	55120007	C	T	55120007	3	4	27	1	0	0	0	0	1	0	0	0	7011	681	24	3	486	3	HCRTR2	6	55120007	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	4316156	55120007	115995060	34	3549										
HMGCLL1	54511	hgsc.bcm.edu	37	chr6	55300495	55300495	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ggcttgtgctactttagagtTtgtggttttattcacagctt	10	6	1	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr6:55300495T>A	ENST00000398661.2	-	10	1209	c.1078A>T	c.(1078-1080)Aac>Tac	p.N360Y	HMGCLL1_ENST00000508459.1_Missense_Mutation_p.N164Y|HMGCLL1_ENST00000370850.2_Missense_Mutation_p.N227Y|HMGCLL1_ENST00000274901.4_Missense_Mutation_p.N330Y|HMGCLL1_ENST00000308161.4_Missense_Mutation_p.N298Y|HMGCLL1_ENST00000507223.1_5'UTR	NM_019036.2	NP_061909.2	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1	360					ketone body biosynthetic process (GO:0046951)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)			ACTTTAGAGTTTGTGGTTTTA	0.393																																					p.N360Y	Ovarian(35;840 893 7837 15538 42887)	Atlas-SNP	.											.	HMGCLL1	70	.	0			c.A1078T						.						142	144	143					6																	55300495		1861	4094	5955	SO:0001583	missense	54511	exon10			TAGAGTTTGTGGT	AK055075	CCDS43474.1, CCDS43475.1, CCDS75472.1, CCDS75473.1	6p12.1	2010-04-30	2010-04-30		ENSG00000146151	ENSG00000146151			21359	protein-coding gene	gene with protein product			"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1"			8619474, 9110174	Standard	NM_001042406		Approved	DKFZP434G1411, bA418P12.1	uc003pcn.3	Q8TB92	OTTHUMG00000014902	ENST00000398661.2:c.1078A>T	chr6.hg19:g.55300495T>A	ENSP00000381654:p.Asn360Tyr	122.0	0.0		117.0	32.0	NM_019036	B1AQ42|B3KNV0|B7Z1S7|F8W793|Q6ZSA9	Missense_Mutation	SNP	ENST00000398661.2	hg19	CCDS43475.1	.	.	.	.	.	.	.	.	.	.	T	19.87	3.908274	0.72868	.	.	ENSG00000146151	ENST00000274901;ENST00000398661;ENST00000370850;ENST00000508459;ENST00000308161	D;D;D;D;D	0.98164	-4.76;-4.76;-4.4;-4.76;-4.76	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.98686	0.9559	M	0.84846	2.72	0.80722	D	1	D;D;D;B;B	0.65815	0.995;0.995;0.958;0.313;0.402	P;P;P;B;B	0.62014	0.897;0.854;0.772;0.227;0.438	D	0.99544	1.0964	10	0.72032	D	0.01	-3.3409	15.1716	0.72878	0.0:0.0:0.0:1.0	.	164;227;298;330;360	B7Z4D4;B7Z212;F8W793;Q8TB92-2;Q8TB92	.;.;.;.;HMGC2_HUMAN	Y	330;360;227;164;298	ENSP00000274901:N330Y;ENSP00000381654:N360Y;ENSP00000359887:N227Y;ENSP00000424309:N164Y;ENSP00000309737:N298Y	ENSP00000274901:N330Y	N	-	1	0	HMGCLL1	55408454	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.138000	0.64795	1.986000	0.57962	0.533000	0.62120	AAC	.	.		0.393	HMGCLL1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360290.1	XM_166383		A	55300495	T	A	55300495	3	1	27	1	0	0	0	0	1	0	0	0	7239	1841	64	4	38	4	HMGCLL1	6	55300495	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	180488	55300495	115814572	35	3550										
BAI3	577	hgsc.bcm.edu	37	chr6	70071152	70071152	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	aaagaagaaagcaaaatgaaTattggcatggaaaccttgcc	9	6	0	3			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr6:70071152T>C	ENST00000370598.1	+	29	4808	c.3987T>C	c.(3985-3987)aaT>aaC	p.N1329N	BAI3_ENST00000238918.8_Silent_p.N535N|BAI3_ENST00000546190.1_Silent_p.N293N	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1329					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				GCAAAATGAATATTGGCATGG	0.383																																					p.N1329N		Atlas-SNP	.											.	BAI3	451	.	0			c.T3987C						.						69	64	66					6																	70071152		2203	4299	6502	SO:0001819	synonymous_variant	577	exon29			AATGAATATTGGC	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.3987T>C	chr6.hg19:g.70071152T>C		109.0	0.0		77.0	35.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	hg19	CCDS4968.1																																																																																			.	.		0.383	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			C	70071152	T	C	70071152	2	2	27	1	0	0	0	0	0	0	0	1	1300	1403	49	2		2	BAI3	6	70071152	Silent	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	14770657	70071152	101043915	36	3551										
ATG5	9474	hgsc.bcm.edu	37	chr6	106764056	106764058	+	In_Frame_Del	DEL	CTC	CTC	-													0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	aattcgtccaaaccacacatCtcgaagcacatctttgtcat							TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr6:106764056_106764058delCTC	ENST00000369076.3	-	2	349_351	c.26_28delGAG	c.(25-30)cgagat>cat	p.9_10RD>H	ATG5_ENST00000369070.1_5'UTR|ATG5_ENST00000360666.4_In_Frame_Del_p.9_10RD>H|ATG5_ENST00000343245.3_In_Frame_Del_p.9_10RD>H	NM_004849.2	NP_004840.1	Q9H1Y0	ATG5_HUMAN	autophagy related 5	9					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|blood vessel remodeling (GO:0001974)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of type I interferon production (GO:0032480)|negative stranded viral RNA replication (GO:0039689)|otolith development (GO:0048840)|post-translational protein modification (GO:0043687)|regulation of cilium assembly (GO:1902017)|regulation of cytokine secretion involved in immune response (GO:0002739)|response to drug (GO:0042493)|response to fungus (GO:0009620)|vasodilation (GO:0042311)|ventricular cardiac muscle cell development (GO:0055015)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|membrane (GO:0016020)|pre-autophagosomal structure membrane (GO:0034045)				endometrium(1)|large_intestine(5)|lung(1)|prostate(1)	8	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		AACCACACATCTCGAAGCACATC	0.379																																					p.9_10del		Atlas-Indel,Pindel	.											.	ATG5	23	.	0			c.27_29del						.																																			SO:0001651	inframe_deletion	9474	exon2			.	Y11588	CCDS5055.1, CCDS69159.1, CCDS75498.1	6q21	2014-02-12	2012-06-06	2005-09-11	ENSG00000057663	ENSG00000057663			589	protein-coding gene	gene with protein product		604261	"APG5 (autophagy 5, S. cerevisiae)-like", "APG5 autophagy 5-like (S. cerevisiae)", "ATG5 autophagy related 5 homolog (S. cerevisiae)"	APG5L		9563500, 11349150, 15778222	Standard	NM_001286111		Approved	ASP, APG5, hAPG5	uc003prf.3	Q9H1Y0	OTTHUMG00000016193	ENST00000369076.3:c.26_28delGAG	chr6.hg19:g.106764056_106764058delCTC	ENSP00000358072:p.Arg9_Asp10delinsHis	117.0	0.0		39.0	28.0	NM_004849	O60875|Q5JVR2|Q68DI4|Q9H2B8|Q9HCZ7	In_Frame_Del	DEL	ENST00000369076.3	hg19	CCDS5055.1																																																																																			.	.		0.379	ATG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043476.1	NM_004849		-	106764058	CTC	-	106764056	7	5	27	1	0	1	0	1	0	0	0	0	1100	913	32	0	827	0	ATG5	6	106764056	In_Frame_Del	DEL	CTC	TCGA-5R-AA1C-01A-11D-A40R-10	36692904	106764056	64351011	37	3552										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152831461	152831461	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gtccacggaggatgcgctgcTggacaaagactggagctggg	17	9	0	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr6:152831461T>G	ENST00000367255.5	-	8	1049	c.448A>C	c.(448-450)Agc>Cgc	p.S150R	SYNE1_ENST00000466159.2_Missense_Mutation_p.S150R|SYNE1_ENST00000423061.1_Missense_Mutation_p.S157R|SYNE1_ENST00000448038.1_Missense_Mutation_p.S157R|SYNE1_ENST00000413186.2_Missense_Mutation_p.S150R|SYNE1_ENST00000367248.3_Missense_Mutation_p.S157R|SYNE1_ENST00000367253.4_Missense_Mutation_p.S150R|SYNE1_ENST00000341594.5_Missense_Mutation_p.S150R|SYNE1_ENST00000265368.4_Missense_Mutation_p.S150R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	150	Actin-binding.				cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GATGCGCTGCTGGACAAAGAC	0.468										HNSCC(10;0.0054)																											p.S157R		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A469C						.						107	94	99					6																	152831461		2203	4300	6503	SO:0001583	missense	23345	exon8			CGCTGCTGGACAA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.448A>C	chr6.hg19:g.152831461T>G	ENSP00000356224:p.Ser150Arg	175.0	0.0		92.0	64.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	20.6	4.024026	0.75390	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000466159;ENST00000537750	T;T;T;T;T;D;D;D;D;D	0.92299	0.39;0.32;0.29;0.32;0.53;-2.43;-2.6;-2.55;-2.84;-3.01	5.66	1.88	0.25563	Calponin homology domain (1);	0.246735	0.35585	N	0.003116	D	0.90998	0.7169	M	0.66378	2.025	0.80722	D	1	P;P;P;P;P	0.51147	0.884;0.904;0.553;0.84;0.942	P;P;P;P;P	0.58013	0.678;0.562;0.566;0.461;0.831	D	0.89613	0.3843	10	0.72032	D	0.01	.	8.6257	0.33888	0.0:0.2426:0.0:0.7574	.	150;150;150;150;157	B3W695;Q8NF91;F5H4Q0;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.	R	150;157;150;157;150;150;157;150;150;150	ENSP00000356224:S150R;ENSP00000396024:S157R;ENSP00000265368:S150R;ENSP00000390975:S157R;ENSP00000341887:S150R;ENSP00000356222:S150R;ENSP00000356217:S157R;ENSP00000414510:S150R;ENSP00000446021:S150R;ENSP00000441264:S150R	ENSP00000265368:S150R	S	-	1	0	SYNE1	152873154	1.000000	0.71417	0.994000	0.49952	0.933000	0.57130	2.877000	0.48506	0.085000	0.17107	-0.312000	0.09012	AGC	.	.		0.468	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152831461	T	G	152831461	3	3	27	1	0	0	0	0	1	0	0	0	15460	1580	55	5	26574	5	SYNE1	6	152831461	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	46067405	152831461	18283606	38	3553										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5352817	5352817	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gctgctgctgctgctgctgcTactgctgccactactgctgc	11	15	0	0	rs548772421	byFrequency	TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr7:5352817T>C	ENST00000430969.1	-	27	8053	c.7705A>G	c.(7705-7707)Agc>Ggc	p.S2569G	TNRC18_ENST00000399537.4_Missense_Mutation_p.S2569G	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2569	Ser-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		ctgctgctgctactgctgcca	0.672													T|||	9	0.00179712	0	0	5008	,	,		8638	0.001		0.003	False		,,,				2504	0.0051				p.S2569G		Atlas-SNP	.											.	TNRC18	311	.	0			c.A7705G						.																																			SO:0001583	missense	84629	exon27			TGCTGCTACTGCT	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7705A>G	chr7.hg19:g.5352817T>C	ENSP00000395538:p.Ser2569Gly	64.0	0.0		49.0	12.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	13.83|13.83	2.353299|2.353299	0.41700|0.41700	.|.	.|.	ENSG00000182095|ENSG00000182095	ENST00000399537;ENST00000430969|ENST00000328270	T;T|.	0.06449|.	3.3;3.3|.	4.66|4.66	2.25|2.25	0.28309|0.28309	.|.	0.370157|.	0.19843|.	N|.	0.104820|.	T|.	0.33731|.	0.0873|.	L|L	0.34521|0.34521	1.04|1.04	0.19300|0.19300	N|N	0.999978|0.999978	B|.	0.31318|.	0.319|.	B|.	0.22880|.	0.042|.	T|.	0.21827|.	-1.0234|.	10|.	0.22706|.	T|.	0.39|.	.|.	8.4207|8.4207	0.32698|0.32698	0.0:0.1633:0.0:0.8367|0.0:0.1633:0.0:0.8367	.|.	2569|.	O15417|.	TNC18_HUMAN|.	G|W	2569|382	ENSP00000382452:S2569G;ENSP00000395538:S2569G|.	ENSP00000382452:S2569G|.	S|X	-|-	1|2	0|0	TNRC18|TNRC18	5319343|5319343	0.089000|0.089000	0.21612|0.21612	0.998000|0.998000	0.56505|0.56505	0.874000|0.874000	0.50279|0.50279	0.201000|0.201000	0.17276|0.17276	0.242000|0.242000	0.21303|0.21303	0.454000|0.454000	0.30748|0.30748	AGC|TAG	.	.		0.672	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	5352817	T	C	5352817	3	2	27	1	0	0	0	0	1	0	0	0	16354	1522	53	2	1217	2	TNRC18	7	5352817	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10		5352817	153785846	39	3554										
FLNC	2318	hgsc.bcm.edu	37	chr7	128494870	128494870	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gggaggctggcgctgggggcCtgtccattgctgtggagggt	21	8	0	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr7:128494870C>T	ENST00000325888.8	+	42	7300	c.7039C>T	c.(7039-7041)Ctg>Ttg	p.L2347L	FLNC_ENST00000346177.6_Silent_p.L2314L|RP11-309L24.2_ENST00000469965.1_RNA	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2347					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CGCTGGGGGCCTGTCCATTGC	0.612																																					p.L2347L		Atlas-SNP	.											.	FLNC	339	.	0			c.C7039T						.						69	79	76					7																	128494870		2053	4202	6255	SO:0001819	synonymous_variant	2318	exon42			GGGGGCCTGTCCA	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.7039C>T	chr7.hg19:g.128494870C>T		155.0	0.0		89.0	35.0	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.612	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128494870	C	T	128494870	2	4	27	1	0	0	0	0	0	0	0	1	5943	680	24	3		3	FLNC	7	128494870	Silent	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	123142053	128494870	30643793	40	3555										
CNOT4	4850	hgsc.bcm.edu	37	chr7	135099083	135099083	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	caagaggactatattaccttAagtgttctgccatctactac	6	10	2	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr7:135099083A>T	ENST00000315544.5	-	5	837	c.558T>A	c.(556-558)ctT>ctA	p.L186L	CNOT4_ENST00000451834.1_Silent_p.L186L|CNOT4_ENST00000541284.1_Silent_p.L186L|CNOT4_ENST00000428680.2_Silent_p.L186L|CNOT4_ENST00000361528.4_Silent_p.L186L|CNOT4_ENST00000423368.2_Silent_p.L186L|CNOT4_ENST00000356162.4_Silent_p.L186L|CNOT4_ENST00000414802.1_Silent_p.L186L	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	186	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						ATATTACCTTAAGTGTTCTGC	0.363																																					p.L186L	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.T558A						.						153	146	148					7																	135099083		1859	4100	5959	SO:0001819	synonymous_variant	4850	exon5			TACCTTAAGTGTT	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"RNA binding motif (RRM) containing"	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.558T>A	chr7.hg19:g.135099083A>T		74.0	0.0		74.0	29.0	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Silent	SNP	ENST00000315544.5	hg19	CCDS55166.1																																																																																			.	.		0.363	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		T	135099083	A	T	135099083	2	4	27	1	0	0	0	0	0	0	0	1	3623	349	13	4		4	CNOT4	7	135099083	Silent	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10	6604213	135099083	24039580	41	3556										
SSPO	23145	hgsc.bcm.edu	37	chr7	149518154	149518154	+	RNA	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ctgtgcctggagccactggtCggcctggagtccctgcagcc	14	15	0	0	rs563749259		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr7:149518154C>A	ENST00000378016.2	+	0	12497							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AGCCACTGGTCGGCCTGGAGT	0.682																																					p.S4166X		Atlas-SNP	.											.	.	.	.	0			c.C12497A						.						4	7	6					7																	149518154		1926	4030	5956			23145	exon87			ACTGGTCGGCCTG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149518154C>A		55.0	0.0		43.0	13.0	NM_198455	Q76B61	Nonsense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.682	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149518154	C	A	149518154	1	1	27	0	1	0	0	0	0	0	0	0	15204	893	31	1		1	SSPO	7	149518154	RNA	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	14419071	149518154	9620509	42	3557										
HTR5A	3361	hgsc.bcm.edu	37	chr7	154876098	154876098	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tggaaaagcatcttcctgtgGcttggctactccaactcctt	8	12	1	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr7:154876098G>C	ENST00000287907.2	+	2	1551	c.975G>C	c.(973-975)tgG>tgC	p.W325C	HTR5A_ENST00000486819.1_3'UTR	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	325					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	TCTTCCTGTGGCTTGGCTACT	0.512																																					p.W325C		Atlas-SNP	.											.	HTR5A	114	.	0			c.G975C						.						196	185	189					7																	154876098		2203	4300	6503	SO:0001583	missense	3361	exon2			CCTGTGGCTTGGC		CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5300	protein-coding gene	gene with protein product		601305	"5-hydroxytryptamine (serotonin) receptor 5A"			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.975G>C	chr7.hg19:g.154876098G>C	ENSP00000287907:p.Trp325Cys	170.0	0.0		120.0	48.0	NM_024012	Q2M2D2	Missense_Mutation	SNP	ENST00000287907.2	hg19	CCDS5936.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.614064	0.66672	.	.	ENSG00000157219	ENST00000287907	T	0.73789	-0.78	4.93	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.86847	0.6031	H	0.94306	3.52	0.80722	D	1	P	0.41673	0.759	P	0.48815	0.591	D	0.90690	0.4612	10	0.87932	D	0	.	18.1526	0.89679	0.0:0.0:1.0:0.0	.	325	P47898	5HT5A_HUMAN	C	325	ENSP00000287907:W325C	ENSP00000287907:W325C	W	+	3	0	HTR5A	154507031	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.438000	0.97539	2.274000	0.75844	0.655000	0.94253	TGG	.	.		0.512	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012		C	154876098	G	C	154876098	3	2	27	1	0	0	0	0	1	0	0	0	7459	1212	42	4	981	4	HTR5A	7	154876098	Missense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	5357944	154876098	4262565	43	3558										
XKR4	114786	hgsc.bcm.edu	37	chr8	56015588	56015588	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gaggacagcgccacggccgcTgctgcctccagctgcccgca	13	18	0	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr8:56015588T>A	ENST00000327381.6	+	1	640	c.540T>A	c.(538-540)gcT>gcA	p.A180A		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	180						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			CCACGGCCGCTGCTGCCTCCA	0.652																																					p.A180A		Atlas-SNP	.											.	XKR4	104	.	0			c.T540A						.						26	23	24					8																	56015588		2192	4286	6478	SO:0001819	synonymous_variant	114786	exon1			GGCCGCTGCTGCC	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 4"				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.540T>A	chr8.hg19:g.56015588T>A		106.0	0.0		89.0	38.0	NM_052898	Q96PZ8	Silent	SNP	ENST00000327381.6	hg19	CCDS34893.1																																																																																			.	.		0.652	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		A	56015588	T	A	56015588	2	1	27	1	0	0	0	0	0	0	0	1	17448	1567	55	4		4	XKR4	8	56015588	Silent	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10		56015588	90348434	44	3559										
TMEM67	91147	hgsc.bcm.edu	37	chr8	94770709	94770709	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	cattttttttcttttaatttAgaaaggtgttacagaagatg	7	3	1	3			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr8:94770709A>G	ENST00000453321.3	+	3	370		c.e3-1		TMEM67_ENST00000409623.3_Intron	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67						cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			CTTTTAATTTAGAAAGGTGTT	0.333																																					.		Atlas-SNP	.											.	TMEM67	187	.	0			c.313-2A>G						.						72	75	74					8																	94770709		2203	4300	6503	SO:0001630	splice_region_variant	91147	exon3			TAATTTAGAAAGG	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.313-1A>G	chr8.hg19:g.94770709A>G		91.0	0.0		114.0	66.0	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Splice_Site	SNP	ENST00000453321.3	hg19	CCDS6258.2	.	.	.	.	.	.	.	.	.	.	A	17.55	3.418729	0.62622	.	.	ENSG00000164953	ENST00000452276;ENST00000453321;ENST00000453906;ENST00000521517	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3966	0.55389	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM67	94839885	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	5.011000	0.64011	2.190000	0.69967	0.533000	0.62120	.	.	.		0.333	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704	Intron	G	94770709	A	G	94770709	5	3	27	1	0	0	0	0	0	0	1	0	16211	434	15	2	321	2	TMEM67	8	94770709	Splice_Site	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10	38755121	94770709	51593313	45	3560										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95550552	95550552	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gttgaagaataagtctaattGaaatgtatggggagatgtct	12	2	2	4			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr8:95550552G>A	ENST00000297591.5	-	3	277	c.202C>T	c.(202-204)Caa>Taa	p.Q68*	KIAA1429_ENST00000437199.1_Nonsense_Mutation_p.Q68*|KIAA1429_ENST00000421249.2_Nonsense_Mutation_p.Q68*	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	68					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			AAGTCTAATTGAAATGTATGG	0.353																																					p.Q68X		Atlas-SNP	.											.	KIAA1429	176	.	0			c.C202T						.						121	116	118					8																	95550552		2203	4300	6503	SO:0001587	stop_gained	25962	exon3			CTAATTGAAATGT	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.202C>T	chr8.hg19:g.95550552G>A	ENSP00000297591:p.Gln68*	110.0	0.0		141.0	41.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Nonsense_Mutation	SNP	ENST00000297591.5	hg19	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	G	36	5.701936	0.96812	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	.	.	.	5.57	5.57	0.84162	.	0.064299	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-10.1825	19.5403	0.95271	0.0:0.0:1.0:0.0	.	.	.	.	X	68	.	ENSP00000297591:Q68X	Q	-	1	0	KIAA1429	95619728	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.066000	0.93949	2.623000	0.88846	0.561000	0.74099	CAA	.	.		0.353	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		A	95550552	G	A	95550552	4	1	27	1	0	0	0	0	0	1	0	0	8240	1299	45	3	5378	3	KIAA1429	8	95550552	Nonsense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	779843	95550552	50813470	46	3561										
AZIN1	51582	hgsc.bcm.edu	37	chr8	103855817	103855817	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	atagttatcaataacatttcCaaggtttgttccttcatcca	4	9	2	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr8:103855817C>A	ENST00000337198.5	-	3	1227	c.64G>T	c.(64-66)Gga>Tga	p.G22*	AZIN1_ENST00000522311.1_5'UTR|AZIN1_ENST00000347770.4_Nonsense_Mutation_p.G22*	NM_148174.2	NP_680479.1	O14977	AZIN1_HUMAN	antizyme inhibitor 1	22					cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|negative regulation of protein catabolic process (GO:0042177)|polyamine biosynthetic process (GO:0006596)|positive regulation of polyamine transmembrane transport (GO:1902269)|regulation of cellular amino acid metabolic process (GO:0006521)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|enzyme inhibitor activity (GO:0004857)|ornithine decarboxylase activator activity (GO:0042978)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	9	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)			ATAACATTTCCAAGGTTTGTT	0.383																																					p.G22X		Atlas-SNP	.											.	AZIN1	26	.	0			c.G64T						.						172	158	163					8																	103855817		2203	4300	6503	SO:0001587	stop_gained	51582	exon4			CATTTCCAAGGTT	AAC25391	CCDS6295.1	8p22-q21.3	2005-03-21	2005-03-21	2005-03-21		ENSG00000155096			16432	protein-coding gene	gene with protein product	"ornithine decarboxylase 1-like"	607909	"ornithine decarboxylase antizyme inhibitor"	OAZIN		9349715, 9110174	Standard	XM_005250969		Approved	OAZI, ODC1L	uc003yky.3	O14977		ENST00000337198.5:c.64G>T	chr8.hg19:g.103855817C>A	ENSP00000337180:p.Gly22*	166.0	0.0		194.0	20.0	NM_015878	A6NCD5|Q6IBQ7|Q96D20	Nonsense_Mutation	SNP	ENST00000337198.5	hg19	CCDS6295.1	.	.	.	.	.	.	.	.	.	.	C	37	6.085814	0.97271	.	.	ENSG00000155096	ENST00000337198;ENST00000347770;ENST00000520402;ENST00000518353	.	.	.	5.96	5.96	0.96718	.	0.214946	0.48286	D	0.000191	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-10.986	13.5795	0.61893	0.0:0.9291:0.0:0.0709	.	.	.	.	X	22	.	ENSP00000337180:G22X	G	-	1	0	AZIN1	103924993	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.032000	0.41127	2.820000	0.97059	0.655000	0.94253	GGA	.	.		0.383	AZIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380133.1			A	103855817	C	A	103855817	4	1	27	1	0	0	0	0	0	1	0	0	1242	603	21	3	1322	3	AZIN1	8	103855817	Nonsense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	8305265	103855817	42508205	47	3562										
EIF2C2	27161	hgsc.bcm.edu	37	chr8	141559371	141559371	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gcatgccggcgtctctcgagAtctttctgagctgctctgtg	12	12	4	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr8:141559371A>T	ENST00000220592.5	-	12	1542	c.1430T>A	c.(1429-1431)aTc>aAc	p.I477N	AGO2_ENST00000519980.1_Missense_Mutation_p.I477N	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	477					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										GTCTCTCGAGATCTTTCTGAG	0.612																																					p.I477N		Atlas-SNP	.											.	.	.	.	0			c.T1430A						.						44	41	42					8																	141559371		2203	4300	6503	SO:0001583	missense	27161	exon12			CTCGAGATCTTTC	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"Argonaute/PIWI family"	3263	protein-coding gene	gene with protein product	"argonaute 2"	606229	"eukaryotic translation initiation factor 2C, 2"	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1430T>A	chr8.hg19:g.141559371A>T	ENSP00000220592:p.Ile477Asn	65.0	0.0		64.0	42.0	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Missense_Mutation	SNP	ENST00000220592.5	hg19	CCDS6380.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.600344	0.87055	.	.	ENSG00000123908	ENST00000220592;ENST00000519980	T;T	0.05199	3.48;3.48	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.31040	0.0784	M	0.92317	3.295	0.80722	D	1	D;P	0.56035	0.974;0.956	P;P	0.60609	0.877;0.757	T	0.37291	-0.9712	10	0.87932	D	0	-15.5008	15.5084	0.75760	1.0:0.0:0.0:0.0	.	477;477	Q9UKV8-2;Q9UKV8	.;AGO2_HUMAN	N	477	ENSP00000220592:I477N;ENSP00000430176:I477N	ENSP00000220592:I477N	I	-	2	0	EIF2C2	141628553	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	9.190000	0.94934	2.134000	0.65973	0.460000	0.39030	ATC	.	.		0.612	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4			T	141559371	A	T	141559371	3	4	27	1	0	0	0	0	1	0	0	0	5008	333	12	4	1181	4	EIF2C2	8	141559371	Missense_Mutation	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10	37703554	141559371	4804651	48	3563										
JAK2	3717	hgsc.bcm.edu	37	chr9	5044434	5044434	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ctcgttggtattgcagtggcAgcaacagagcctatcggcat	12	10	0	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr9:5044434A>T	ENST00000381652.3	+	5	876	c.382A>T	c.(382-384)Agc>Tgc	p.S128C	JAK2_ENST00000544510.1_5'UTR|JAK2_ENST00000539801.1_Missense_Mutation_p.S128C	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	128	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with cytokine/interferon/growth hormone receptors. {ECO:0000250}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TTGCAGTGGCAGCAACAGAGC	0.373		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.S128C		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.A382T						.						140	131	134					9																	5044434		2203	4300	6503	SO:0001583	missense	3717	exon5	Familial Cancer Database		AGTGGCAGCAACA		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.382A>T	chr9.hg19:g.5044434A>T	ENSP00000371067:p.Ser128Cys	102.0	0.0		102.0	34.0	NM_004972	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	hg19	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.196534	0.38806	.	.	ENSG00000096968	ENST00000539801;ENST00000381652	T;T	0.57436	0.4;0.4	5.35	2.99	0.34606	Band 4.1 domain (1);FERM domain (1);	0.460963	0.26272	N	0.025331	T	0.32224	0.0822	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11867	-1.0570	10	0.54805	T	0.06	-3.8034	9.464	0.38802	0.8548:0.0:0.1452:0.0	.	128	O60674	JAK2_HUMAN	C	128	ENSP00000440387:S128C;ENSP00000371067:S128C	ENSP00000371067:S128C	S	+	1	0	JAK2	5034434	0.029000	0.19370	1.000000	0.80357	0.804000	0.45430	0.863000	0.27913	0.958000	0.37956	0.533000	0.62120	AGC	.	.		0.373	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			T	5044434	A	T	5044434	3	4	27	1	0	0	0	0	1	0	0	0	7947	188	7	4	392	4	JAK2	9	5044434	Missense_Mutation	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10		5044434	136168997	49	3564										
ZMYND11	10771	hgsc.bcm.edu	37	chr10	226050	226050	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gaaccagaagcagattgccaAcattgaccgtattacaaagt	8	9	0	3			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr10:226050A>G	ENST00000397962.3	+	2	526	c.98A>G	c.(97-99)aAc>aGc	p.N33S	ZMYND11_ENST00000381604.4_5'UTR|ZMYND11_ENST00000397959.3_Missense_Mutation_p.N33S|ZMYND11_ENST00000309776.4_5'UTR|ZMYND11_ENST00000381607.4_5'UTR|ZMYND11_ENST00000602682.1_Missense_Mutation_p.N33S|ZMYND11_ENST00000381591.1_Missense_Mutation_p.N33S|ZMYND11_ENST00000402736.1_Missense_Mutation_p.N33S|ZMYND11_ENST00000403354.1_Missense_Mutation_p.N33S|ZMYND11_ENST00000381584.1_5'UTR|ZMYND11_ENST00000509513.2_Missense_Mutation_p.N33S|ZMYND11_ENST00000558098.2_Missense_Mutation_p.N33S|ZMYND11_ENST00000381602.4_5'UTR			Q15326	ZMY11_HUMAN	zinc finger, MYND-type containing 11	33					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription elongation from RNA polymerase II promoter (GO:0034243)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	24		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CAGATTGCCAACATTGACCGT	0.378																																					p.N33S		Atlas-SNP	.											.	ZMYND11	72	.	0			c.A98G						.						122	110	114					10																	226050		1568	3582	5150	SO:0001583	missense	10771	exon2			TTGCCAACATTGA	X86098	CCDS7052.1, CCDS7053.1, CCDS7052.2, CCDS55696.1, CCDS55697.1, CCDS7053.2, CCDS73060.1, CCDS73061.1	10p14	2011-01-26	2011-01-26		ENSG00000015171	ENSG00000015171		"Zinc fingers, MYND-type"	16966	protein-coding gene	gene with protein product		608668	"zinc finger, MYND domain containing 11"			7621829, 10734313	Standard	NM_006624		Approved	BS69	uc010pzx.2	Q15326	OTTHUMG00000017526	ENST00000397962.3:c.98A>G	chr10.hg19:g.226050A>G	ENSP00000381053:p.Asn33Ser	129.0	0.0		113.0	44.0	NM_001202465	B2R6G8|B7Z293|F6UH50|Q2LD45|Q2LD46|Q2LD47|Q2LD48|Q5VUI1|Q8N4B3	Missense_Mutation	SNP	ENST00000397962.3	hg19	CCDS7052.2	.	.	.	.	.	.	.	.	.	.	A	12.96	2.093310	0.36952	.	.	ENSG00000015171	ENST00000439456;ENST00000397962;ENST00000509513;ENST00000397959;ENST00000381591;ENST00000403354;ENST00000402736;ENST00000397955	.	.	.	6.02	6.02	0.97574	.	0.164028	0.38548	N	0.001645	T	0.60753	0.2293	L	0.29908	0.895	0.29737	N	0.83744	B;P;B;B;B;B;B	0.52842	0.002;0.956;0.0;0.002;0.003;0.001;0.002	B;P;B;B;B;B;B	0.62184	0.002;0.899;0.001;0.004;0.003;0.003;0.004	T	0.54536	-0.8279	8	0.07990	T	0.79	-12.4953	16.5494	0.84464	1.0:0.0:0.0:0.0	.	33;33;33;33;33;33;33	Q2LD45;B7Z293;B7Z2J6;Q2LD48;Q2LD46;Q2LD47;E7ENI9	.;.;.;.;.;.;.	S	33	.	ENSP00000371003:N33S	N	+	2	0	ZMYND11	216050	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.910000	0.92685	2.299000	0.77371	0.528000	0.53228	AAC	.	.		0.378	ZMYND11-206	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046382.4	NM_006624		G	226050	A	G	226050	3	3	27	1	0	0	0	0	1	0	0	0	17721	43	2	2	100	2	ZMYND11	10	226050	Missense_Mutation	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10		226050	135308697	50	3565										
UPF2	26019	hgsc.bcm.edu	37	chr10	12041933	12041933	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tcagatctcggttgacacagTtgggtaactgctgtaggaaa	12	7	2	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr10:12041933T>G	ENST00000356352.2	-	6	2203	c.1730A>C	c.(1729-1731)aAc>aCc	p.N577T	UPF2_ENST00000397053.2_Missense_Mutation_p.N577T|UPF2_ENST00000357604.5_Missense_Mutation_p.N577T			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	577	MIF4G 2.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				GTTGACACAGTTGGGTAACTG	0.388																																					p.N577T		Atlas-SNP	.											.	UPF2	111	.	0			c.A1730C						.						164	139	148					10																	12041933		2203	4300	6503	SO:0001583	missense	26019	exon7			ACACAGTTGGGTA	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.1730A>C	chr10.hg19:g.12041933T>G	ENSP00000348708:p.Asn577Thr	124.0	0.0		80.0	31.0	NM_080599	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Missense_Mutation	SNP	ENST00000356352.2	hg19	CCDS7086.1	.	.	.	.	.	.	.	.	.	.	T	16.98	3.272571	0.59649	.	.	ENSG00000151461	ENST00000356352;ENST00000357604;ENST00000379172;ENST00000397053;ENST00000313977	T;T;T	0.34072	1.38;1.38;1.38	5.19	5.19	0.71726	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.47395	0.1443	L	0.33137	0.985	0.80722	D	1	D;B	0.61080	0.989;0.374	D;B	0.70487	0.969;0.289	T	0.33240	-0.9876	10	0.30854	T	0.27	.	15.0023	0.71483	0.0:0.0:0.0:1.0	.	547;577	Q9HAU5-2;Q9HAU5	.;RENT2_HUMAN	T	577;577;547;577;547	ENSP00000348708:N577T;ENSP00000350221:N577T;ENSP00000380244:N577T	ENSP00000313617:N547T	N	-	2	0	UPF2	12081939	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.630000	0.83225	2.087000	0.62958	0.379000	0.24179	AAC	.	.		0.388	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			G	12041933	T	G	12041933	3	3	27	1	0	0	0	0	1	0	0	0	17019	1725	60	5	2152	5	UPF2	10	12041933	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	11815883	12041933	123492814	51	3566										
C10orf71	118461	hgsc.bcm.edu	37	chr10	50534397	50534397	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tccctcacacccctgcccgcGtaccccgccacccagaaggt	7	22	1	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr10:50534397G>A	ENST00000374144.3	+	3	4095	c.3807G>A	c.(3805-3807)gcG>gcA	p.A1269A	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1269				A -> T (in Ref. 2; AL833265). {ECO:0000305}.						endometrium(1)	1						CCCTGCCCGCGTACCCCGCCA	0.667																																					p.A1269A		Atlas-SNP	.											.	C10orf71	179	.	0			c.G3807A						.						3	6	5					10																	50534397		624	1495	2119	SO:0001819	synonymous_variant	118461	exon3			GCCCGCGTACCCC	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.3807G>A	chr10.hg19:g.50534397G>A		175.0	0.0		114.0	38.0	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	hg19	CCDS44387.1																																																																																			.	.		0.667	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		A	50534397	G	A	50534397	2	1	27	1	0	0	0	0	0	0	0	1	1616	1132	40	1		1	C10orf71	10	50534397	Silent	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	38492464	50534397	85000350	52	3567										
ADAM12	8038	hgsc.bcm.edu	37	chr10	127753571	127753571	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gctgttcctgcaggcttcagCtggaaggagagggccattta	14	9	1	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr10:127753571C>A	ENST00000368679.4	-	14	1732		c.e14-1		ADAM12_ENST00000368676.4_Splice_Site|ADAM12_ENST00000467145.1_Splice_Site	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12						cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CAGGCTTCAGCTGGAAGGAGA	0.602																																					.		Atlas-SNP	.											.	ADAM12	388	.	0			c.1423-1G>T						.						49	49	49					10																	127753571		2203	4300	6503	SO:0001630	splice_region_variant	8038	exon15			CTTCAGCTGGAAG	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1423-1G>T	chr10.hg19:g.127753571C>A		38.0	0.0		31.0	14.0	NM_003474	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Splice_Site	SNP	ENST00000368679.4	hg19	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.371248	0.82573	.	.	ENSG00000148848	ENST00000368679;ENST00000368676	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0783	0.93171	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADAM12	127743561	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.537000	0.82033	2.731000	0.93534	0.650000	0.86243	.	.	.		0.602	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		Intron	A	127753571	C	A	127753571	5	1	27	1	0	0	0	0	0	0	1	0	236	811	28	3	1455	3	ADAM12	10	127753571	Splice_Site	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	77219174	127753571	7781176	53	3568										
KRTAP5-1	387264	hgsc.bcm.edu	37	chr11	1606214	1606214	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tggatcccccacaagagccaCagccccccttgcagcctcca	7	20	0	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr11:1606214C>T	ENST00000382171.2	-	1	299	c.266G>A	c.(265-267)tGt>tAt	p.C89Y	KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	89	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACAAGAGCCACAGCCCCCCTT	0.672																																					p.C89Y		Atlas-SNP	.											.	KRTAP5-1	74	.	0			c.G266A						.						36	52	47					11																	1606214		2201	4292	6493	SO:0001583	missense	387264	exon1			GAGCCACAGCCCC	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"Keratin associated proteins"	23596	protein-coding gene	gene with protein product		148022	"keratin, cuticle, ultrahigh sulphur 1-like"	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.266G>A	chr11.hg19:g.1606214C>T	ENSP00000371606:p.Cys89Tyr	190.0	0.0		127.0	44.0	NM_001005922		Missense_Mutation	SNP	ENST00000382171.2	hg19	CCDS31330.1	.	.	.	.	.	.	.	.	.	.	C	4.603	0.112000	0.08831	.	.	ENSG00000205869	ENST00000382171	T	0.06528	3.29	3.69	3.69	0.42338	.	.	.	.	.	T	0.25158	0.0611	M	0.83118	2.625	0.27245	N	0.959036	D	0.64830	0.994	D	0.64877	0.93	T	0.03139	-1.1068	9	0.62326	D	0.03	.	13.0905	0.59164	0.0:1.0:0.0:0.0	.	89	Q6L8H4	KRA51_HUMAN	Y	89	ENSP00000371606:C89Y	ENSP00000371606:C89Y	C	-	2	0	KRTAP5-1	1562790	0.018000	0.18449	0.878000	0.34440	0.003000	0.03518	1.365000	0.34182	1.632000	0.50472	0.442000	0.29010	TGT	.	.		0.672	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922		T	1606214	C	T	1606214	3	4	27	1	0	0	0	0	1	0	0	0	8567	478	17	3	574	3	KRTAP5-1	11	1606214	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10		1606214	133400302	54	3569										
MAP3K11	10089	hgsc.bcm.edu	37	chr11	65365864	65365864	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	aaggggttggcaggtggggaGtcccagaaggggtctgagtc	20	6	1	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr11:65365864G>T	ENST00000340313.4	-	0	0				KCNK7_ENST00000394216.2_5'Flank|KCNK7_ENST00000394217.2_5'Flank|KCNK7_ENST00000342202.4_5'Flank|MAP3K11_ENST00000530153.1_Missense_Mutation_p.D557E|MAP3K11_ENST00000534432.1_5'Flank|MAP3K11_ENST00000309100.3_Missense_Mutation_p.D814E|MAP3K11_ENST00000532507.1_Missense_Mutation_p.D230E	NM_033347.1	NP_203133.1	Q9Y2U2	KCNK7_HUMAN	potassium channel, subfamily K, member 7						potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|liver(1)|lung(1)	3						CAGGTGGGGAGTCCCAGAAGG	0.687																																					p.D814E		Atlas-SNP	.											.	MAP3K11	67	.	0			c.C2442A						.						29	30	29					11																	65365864		2201	4297	6498	SO:0001631	upstream_gene_variant	4296	exon10			TGGGGAGTCCCAG	AF110522	CCDS8106.1, CCDS31608.1, CCDS41673.1	11q13	2012-03-07			ENSG00000173338	ENSG00000173338		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6282	protein-coding gene	gene with protein product		603940				10206991, 11256078, 16382106	Standard	NM_033347		Approved	K2p7.1	uc001oes.3	Q9Y2U2	OTTHUMG00000166528		chr11.hg19:g.65365864G>T	Exception_encountered	218.0	0.0		127.0	42.0	NM_002419	Q3SYI2|Q9Y2U3|Q9Y2U4	Missense_Mutation	SNP	ENST00000340313.4	hg19	CCDS31608.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.527042	0.85706	.	.	ENSG00000173327	ENST00000309100;ENST00000532507;ENST00000530153	T;T	0.74842	-0.79;-0.88	5.3	5.3	0.74995	.	0.000000	0.64402	D	0.000001	T	0.75012	0.3792	N	0.22421	0.69	0.32192	N	0.578959	D;D	0.61697	0.99;0.984	D;D	0.75484	0.986;0.935	T	0.69967	-0.5001	10	0.10636	T	0.68	.	14.7718	0.69684	0.0:0.0:1.0:0.0	.	303;814	B3KQY4;Q16584	.;M3K11_HUMAN	E	814;230;557	ENSP00000309597:D814E;ENSP00000433886:D557E	ENSP00000309597:D814E	D	-	3	2	MAP3K11	65122440	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.052000	0.41316	2.633000	0.89246	0.655000	0.94253	GAC	.	.		0.687	KCNK7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390206.1	NM_005714		T	65365864	G	T	65365864	1	4	27	0	1	0	0	0	0	0	0	0	9254	1020	36	3		3	MAP3K11	11	65365864	5'Flank	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	63759650	65365864	69640652	55	3570										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43833794	43833794	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	caataacagttcttgttcctTgcacattgatttcttttttt	4	8	2	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr12:43833794T>C	ENST00000389420.3	-	17	2368	c.2369A>G	c.(2368-2370)cAa>cGa	p.Q790R	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.Q790R|ADAMTS20_ENST00000395541.2_5'Flank	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	790	Spacer.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TCTTGTTCCTTGCACATTGAT	0.308																																					p.Q790R		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A2369G						.						83	71	75					12																	43833794		2198	4290	6488	SO:0001583	missense	80070	exon17			GTTCCTTGCACAT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2369A>G	chr12.hg19:g.43833794T>C	ENSP00000374071:p.Gln790Arg	87.0	0.0		56.0	22.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	6.323	0.427626	0.11987	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.51325	0.71;0.71	5.19	4.03	0.46877	ADAM-TS Spacer 1 (1);	0.256819	0.27577	N	0.018744	T	0.34483	0.0899	N	0.24115	0.695	0.80722	D	1	P	0.35383	0.498	B	0.40329	0.326	T	0.04946	-1.0916	10	0.11485	T	0.65	.	11.5753	0.50858	0.0:0.0714:0.0:0.9286	.	790	P59510	ATS20_HUMAN	R	790	ENSP00000374071:Q790R;ENSP00000448341:Q790R	ENSP00000374068:Q790R	Q	-	2	0	ADAMTS20	42120061	1.000000	0.71417	0.999000	0.59377	0.163000	0.22366	3.863000	0.56016	1.057000	0.40506	-0.297000	0.09499	CAA	.	.		0.308	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		C	43833794	T	C	43833794	3	2	27	1	0	0	0	0	1	0	0	0	266	1812	63	2	3454	2	ADAMTS20	12	43833794	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10		43833794	90018101	56	3571										
SYCP3	50511	hgsc.bcm.edu	37	chr12	102125389	102125389	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gtttaattgttttcaatctcTggctctgaacaattctagat	6	7	4	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr12:102125389T>A	ENST00000392927.3	-	7	640	c.509A>T	c.(508-510)cAg>cTg	p.Q170L	SYCP3_ENST00000392924.1_Missense_Mutation_p.Q170L|SYCP3_ENST00000266743.2_Missense_Mutation_p.Q170L	NM_001177948.1|NM_001177949.1|NM_153694.4	NP_001171419.1|NP_001171420.1|NP_710161.1	Q8IZU3	SYCP3_HUMAN	synaptonemal complex protein 3	170	Gln-rich.				male meiosis I (GO:0007141)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.Q170R(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	11						TTTCAATCTCTGGCTCTGAAC	0.279																																					p.Q170L		Atlas-SNP	.											SYCP3,NS,carcinoma,0,1	SYCP3	19	.	1	Substitution - Missense(1)	lung(1)	c.A509T						.						58	58	58					12																	102125389		2201	4270	6471	SO:0001583	missense	50511	exon7			AATCTCTGGCTCT	AF492003, AI075991	CCDS9087.1	12q23.2	2007-02-05			ENSG00000139351	ENSG00000139351			18130	protein-coding gene	gene with protein product		604759				12213195, 10854409	Standard	NM_153694		Approved		uc001tis.3	Q8IZU3	OTTHUMG00000150132	ENST00000392927.3:c.509A>T	chr12.hg19:g.102125389T>A	ENSP00000376658:p.Gln170Leu	60.0	0.0		39.0	12.0	NM_001177949		Missense_Mutation	SNP	ENST00000392927.3	hg19	CCDS9087.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.785978	0.70337	.	.	ENSG00000139351	ENST00000266743;ENST00000392927;ENST00000392924	.	.	.	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.79476	0.4452	M	0.86651	2.83	0.51482	D	0.999925	D	0.76494	0.999	D	0.77004	0.989	T	0.82159	-0.0595	9	0.62326	D	0.03	-0.8602	10.5266	0.44952	0.0:0.0:0.1622:0.8378	.	170	Q8IZU3	SYCP3_HUMAN	L	170	.	ENSP00000266743:Q170L	Q	-	2	0	SYCP3	100649520	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.283000	0.65621	2.023000	0.59567	0.254000	0.18369	CAG	.	.		0.279	SYCP3-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316478.2	NM_153694		A	102125389	T	A	102125389	3	1	27	1	0	0	0	0	1	0	0	0	15449	1580	55	4	213	4	SYCP3	12	102125389	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	58291595	102125389	31726506	57	3572										
OLFM4	10562	hgsc.bcm.edu	37	chr13	53624703	53624703	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gtggggttctgtatgccaccCgtactatgaacaccagaaca	10	11	1	2	rs542614490	byFrequency	TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr13:53624703C>A	ENST00000219022.2	+	5	1408	c.1330C>A	c.(1330-1332)Cgt>Agt	p.R444S		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	444	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		GTATGCCACCCGTACTATGAA	0.413																																					p.R444S		Atlas-SNP	.											.	OLFM4	94	.	0			c.C1330A						.						137	124	129					13																	53624703		2203	4300	6503	SO:0001583	missense	10562	exon5			GCCACCCGTACTA	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.1330C>A	chr13.hg19:g.53624703C>A	ENSP00000219022:p.Arg444Ser	161.0	0.0		117.0	43.0	NM_006418	O95362|Q5VWG0|Q86T22	Missense_Mutation	SNP	ENST00000219022.2	hg19	CCDS9440.1	.	.	.	.	.	.	.	.	.	.	C	16.31	3.088572	0.55968	.	.	ENSG00000102837	ENST00000219022	D	0.89196	-2.48	5.92	4.13	0.48395	Olfactomedin-like (3);	0.043912	0.85682	D	0.000000	D	0.92417	0.7593	M	0.66560	2.04	0.48511	D	0.999668	D	0.89917	1.0	D	0.91635	0.999	D	0.92233	0.5794	10	0.72032	D	0.01	.	8.9069	0.35530	0.3087:0.6165:0.0:0.0748	.	444	Q6UX06	OLFM4_HUMAN	S	444	ENSP00000219022:R444S	ENSP00000219022:R444S	R	+	1	0	OLFM4	52522704	0.771000	0.28555	0.899000	0.35326	0.463000	0.32649	1.607000	0.36836	1.500000	0.48636	0.650000	0.86243	CGT	.	.		0.413	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418		A	53624703	C	A	53624703	3	1	27	1	0	0	0	0	1	0	0	0	10864	652	23	1	1348	1	OLFM4	13	53624703	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10		53624703	61545175	58	3573										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31597196	31597196	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	aaattagggaaactctgagcAcccataagaggagaagctaa	10	7	1	3			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr14:31597196A>G	ENST00000399332.1	-	26	5264	c.4776T>C	c.(4774-4776)ggT>ggC	p.G1592G	HECTD1_ENST00000553700.1_Silent_p.G1592G	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1592	Ser-rich.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		AACTCTGAGCACCCATAAGAG	0.373																																					p.G1592G		Atlas-SNP	.											.	HECTD1	159	.	0			c.T4776C						.						83	75	77					14																	31597196		1884	4115	5999	SO:0001819	synonymous_variant	25831	exon26			CTGAGCACCCATA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.4776T>C	chr14.hg19:g.31597196A>G		106.0	0.0		79.0	29.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	A	3.680	-0.065670	0.07273	.	.	ENSG00000092148	ENST00000557369	.	.	.	6.16	4.98	0.66077	.	.	.	.	.	T	0.59878	0.2226	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58267	-0.7666	4	.	.	.	-16.3884	8.8367	0.35117	0.7421:0.132:0.0:0.1259	.	.	.	.	R	144	.	.	C	-	1	0	HECTD1	30666947	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.578000	0.36525	2.367000	0.80283	0.528000	0.53228	TGC	.	.		0.373	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			G	31597196	A	G	31597196	2	3	27	1	0	0	0	0	0	0	0	1	7048	146	6	2		2	HECTD1	14	31597196	Silent	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10		31597196	75752344	59	3574										
MTHFD1	4522	hgsc.bcm.edu	37	chr14	64920556	64920556	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tacttcccgaagctcaacacAaagctgaagtctacacgaag	7	12	2	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr14:64920556A>C	ENST00000545908.1	+	25	2939	c.2710A>C	c.(2710-2712)Aaa>Caa	p.K904Q	MTHFD1_ENST00000556284.1_3'UTR|ZBTB25_ENST00000555424.1_Intron|MTHFD1_ENST00000216605.8_Missense_Mutation_p.K848Q|ZBTB25_ENST00000555220.1_Intron			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	848	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	AGCTCAACACAAAGCTGAAGT	0.443																																					p.K848Q	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.A2542C						.						165	132	144					14																	64920556		2203	4300	6503	SO:0001583	missense	4522	exon25			CAACACAAAGCTG	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2710A>C	chr14.hg19:g.64920556A>C	ENSP00000438588:p.Lys904Gln	139.0	0.0		127.0	52.0	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	hg19		.	.	.	.	.	.	.	.	.	.	A	11.83	1.756720	0.31137	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605	T;T;T	0.22336	1.96;1.96;1.96	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.19446	0.0467	L	0.35793	1.09	0.80722	D	1	P;B	0.36249	0.545;0.058	B;B	0.39617	0.305;0.106	T	0.04347	-1.0958	10	0.20519	T	0.43	-20.9854	14.5157	0.67818	1.0:0.0:0.0:0.0	.	904;848	F5H2F4;G3V2B8	.;.	Q	904;848;904	ENSP00000438588:K904Q;ENSP00000450560:K848Q;ENSP00000216605:K904Q	ENSP00000216605:K848Q	K	+	1	0	MTHFD1	63990309	1.000000	0.71417	0.992000	0.48379	0.207000	0.24258	9.083000	0.94067	2.064000	0.61679	0.477000	0.44152	AAA	.	.		0.443	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			C	64920556	A	C	64920556	3	2	27	1	0	0	0	0	1	0	0	0	9936	131	5	5	2640	5	MTHFD1	14	64920556	Missense_Mutation	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10	33323360	64920556	42428984	60	3575										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94139742	94139742	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gtagtgttgttctagaacttCtgcaggccctaaagctcaaa	9	9	3	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr14:94139742C>T	ENST00000393151.2	+	42	6799	c.6799C>T	c.(6799-6801)Ctg>Ttg	p.L2267L	UNC79_ENST00000256339.4_Silent_p.L2090L|UNC79_ENST00000555664.1_Silent_p.L2228L|UNC79_ENST00000553484.1_Silent_p.L2289L			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2267					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TCTAGAACTTCTGCAGGCCCT	0.358																																					p.L2090L		Atlas-SNP	.											.	UNC79	366	.	0			c.C6268T						.						183	176	178					14																	94139742		2203	4300	6503	SO:0001819	synonymous_variant	57578	exon42			GAACTTCTGCAGG	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.6799C>T	chr14.hg19:g.94139742C>T		98.0	0.0		84.0	23.0	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	hg19																																																																																				.	.		0.358	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94139742	C	T	94139742	2	4	27	1	0	0	0	0	0	0	0	1	8239	912	32	3		3	KIAA1409	14	94139742	Silent	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	29219186	94139742	13209798	61	3576										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105411351	105411351	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gacaccccgaaggagggcatCttgaacttgggcattttgaa	12	9	1	2	rs556676336		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr14:105411351C>T	ENST00000333244.5	-	7	10556	c.10437G>A	c.(10435-10437)aaG>aaA	p.K3479K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3479						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			AGGAGGGCATCTTGAACTTGG	0.622																																					p.K3479K		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G10437A						.						226	241	236					14																	105411351		1976	4148	6124	SO:0001819	synonymous_variant	113146	exon7			GGGCATCTTGAAC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.10437G>A	chr14.hg19:g.105411351C>T		98.0	0.0		83.0	17.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105411351	C	T	105411351	2	4	27	1	0	0	0	0	0	0	0	1	415	912	32	3		3	AHNAK2	14	105411351	Silent	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	11271609	105411351	1938189	62	3577										
BAHD1	22893	hgsc.bcm.edu	37	chr15	40751536	40751536	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tctgcaactccttgtgggccAtccgtccagccatctcatca	7	16	3	0	rs144909314	byFrequency	TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr15:40751536A>G	ENST00000416165.1	+	2	944	c.873A>G	c.(871-873)ccA>ccG	p.P291P	BAHD1_ENST00000560846.1_Silent_p.P291P|BAHD1_ENST00000561234.1_Silent_p.P291P	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	291	Pro-rich.				heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		CTTGTGGGCCATCCGTCCAGC	0.662																																					p.P291P		Atlas-SNP	.											.	BAHD1	68	.	0			c.A873G						.						46	47	47					15																	40751536		2202	4295	6497	SO:0001819	synonymous_variant	22893	exon2			TGGGCCATCCGTC	AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.873A>G	chr15.hg19:g.40751536A>G		147.0	0.0		106.0	47.0	NM_014952	Q8NDF7|Q9Y2F4	Silent	SNP	ENST00000416165.1	hg19	CCDS10058.1																																																																																			.	A|0.997;C|0.003		0.662	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		G	40751536	A	G	40751536	2	3	27	1	0	0	0	0	0	0	0	1	1297	204	8	2		2	BAHD1	15	40751536	Silent	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10		40751536	61779856	63	3578										
CORO2B	10391	hgsc.bcm.edu	37	chr15	69011783	69011783	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	atgtctttgaaagaaggctaTaagaagtcctcaaaaatggt	9	5	2	3			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr15:69011783T>C	ENST00000566799.1	+	11	1232	c.1203T>C	c.(1201-1203)taT>taC	p.Y401Y	CORO2B_ENST00000543950.1_Silent_p.Y396Y|CORO2B_ENST00000540068.1_Silent_p.Y396Y|CORO2B_ENST00000261861.5_Silent_p.Y396Y			Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B	401					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			kidney(3)|large_intestine(13)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						AAGAAGGCTATAAGAAGTCCT	0.453																																					p.Y401Y		Atlas-SNP	.											.	CORO2B	68	.	0			c.T1203C						.						142	137	139					15																	69011783		2200	4298	6498	SO:0001819	synonymous_variant	10391	exon11			AGGCTATAAGAAG	AB010098	CCDS53952.1, CCDS10229.2	15q22.31	2013-01-10	2001-11-28		ENSG00000103647	ENSG00000103647		"Coronins", "WD repeat domain containing"	2256	protein-coding gene	gene with protein product	"clipin C", "coronin, actin-binding, 2B"	605002	"coronin, actin-binding protein, 2B"			10224093, 10231032	Standard	NM_001190456		Approved	ClipinC, KIAA0925	uc021spj.1	Q9UQ03	OTTHUMG00000133288	ENST00000566799.1:c.1203T>C	chr15.hg19:g.69011783T>C		191.0	0.0		127.0	54.0	NM_006091	A8K0W3|O94767|Q8TAN1	Silent	SNP	ENST00000566799.1	hg19	CCDS10229.2																																																																																			.	.		0.453	CORO2B-203	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006091		C	69011783	T	C	69011783	2	2	27	1	0	0	0	0	0	0	0	1	3759	1413	49	2		2	CORO2B	15	69011783	Silent	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	28260247	69011783	33519609	64	3579										
RCN2	5955	hgsc.bcm.edu	37	chr15	77224707	77224707	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	cgcttccccctaaaggaagaTgtggatgaatatgttaaact	9	8	0	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr15:77224707T>A	ENST00000394885.3	+	2	373	c.150T>A	c.(148-150)gaT>gaA	p.D50E	RCN2_ENST00000394883.3_Intron|RCN2_ENST00000320963.5_Missense_Mutation_p.D50E	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	50						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						TAAAGGAAGATGTGGATGAAT	0.473																																					p.D50E		Atlas-SNP	.											.	RCN2	16	.	0			c.T150A						.						64	55	58					15																	77224707		2196	4294	6490	SO:0001583	missense	5955	exon2			GGAAGATGTGGAT	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"EF-hand domain containing"	9935	protein-coding gene	gene with protein product	"Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.150T>A	chr15.hg19:g.77224707T>A	ENSP00000378349:p.Asp50Glu	68.0	0.0		67.0	23.0	NM_002902	A8MTG6|F8WCY5|Q53XN8	Missense_Mutation	SNP	ENST00000394885.3	hg19	CCDS10291.1	.	.	.	.	.	.	.	.	.	.	T	7.036	0.561666	0.13498	.	.	ENSG00000117906	ENST00000394885;ENST00000320963	T;T	0.73363	-0.74;0.36	5.45	0.164	0.14990	.	0.329961	0.35525	N	0.003142	T	0.33440	0.0863	N	0.01081	-1.03	0.80722	D	1	B;B	0.10296	0.003;0.001	B;B	0.13407	0.009;0.001	T	0.37865	-0.9687	10	0.02654	T	1	-5.953	4.7914	0.13250	0.6145:0.2183:0.066:0.1011	.	50;50	F8WCY5;Q14257	.;RCN2_HUMAN	E	50	ENSP00000378349:D50E;ENSP00000319739:D50E	ENSP00000319739:D50E	D	+	3	2	RCN2	75011762	1.000000	0.71417	0.996000	0.52242	0.856000	0.48823	0.861000	0.27885	-0.237000	0.09739	-0.649000	0.03915	GAT	.	.		0.473	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902		A	77224707	T	A	77224707	3	1	27	1	0	0	0	0	1	0	0	0	13195	1461	51	4	156	4	RCN2	15	77224707	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	8212924	77224707	25306685	65	3580										
PRPF8	10594	hgsc.bcm.edu	37	chr17	1584082	1584082	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	aaagtagaaagctggcaagtCaggatcctcagttttgatga	11	6	2	3			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr17:1584082C>A	ENST00000572621.1	-	7	1301	c.1036G>T	c.(1036-1038)Gac>Tac	p.D346Y	PRPF8_ENST00000304992.6_Missense_Mutation_p.D346Y			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	346					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GCTGGCAAGTCAGGATCCTCA	0.473																																					p.D346Y		Atlas-SNP	.											.	PRPF8	169	.	0			c.G1036T						.						133	127	129					17																	1584082		2203	4300	6503	SO:0001583	missense	10594	exon8			GCAAGTCAGGATC	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.1036G>T	chr17.hg19:g.1584082C>A	ENSP00000460348:p.Asp346Tyr	170.0	0.0		119.0	52.0	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.181343	0.78677	.	.	ENSG00000174231	ENST00000304992	D	0.81659	-1.52	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.90662	0.7071	M	0.85945	2.785	0.80722	D	1	D	0.64830	0.994	D	0.64506	0.926	D	0.91594	0.5289	10	0.87932	D	0	-14.5378	19.7207	0.96142	0.0:1.0:0.0:0.0	.	346	Q6P2Q9	PRP8_HUMAN	Y	346	ENSP00000304350:D346Y	ENSP00000304350:D346Y	D	-	1	0	PRPF8	1530832	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.780000	0.85658	2.647000	0.89833	0.650000	0.86243	GAC	.	.		0.473	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			A	1584082	C	A	1584082	3	1	27	1	0	0	0	0	1	0	0	0	12587	826	29	3	6115	3	PRPF8	17	1584082	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10		1584082	79611128	66	3581										
MAP2K4	6416	hgsc.bcm.edu	37	chr17	12016647	12016648	+	Frame_Shift_Del	DEL	AA	AA	-													0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gtggactctattgccaagacAagagatgctggctgtaggcc							TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr17:12016647_12016648delAA	ENST00000353533.5	+	7	846_847	c.783_784delAA	c.(781-786)acaagafs	p.R262fs	MAP2K4_ENST00000581941.1_3'UTR|MAP2K4_ENST00000415385.3_Frame_Shift_Del_p.R273fs	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	262	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TTGCCAAGACAAGAGATGCTGG	0.465			"D, Mis, N"		"pancreatic, breast, colorectal"																																p.261_261del		Atlas-Indel,Pindel	.		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	MAP2K4	176	.	11	Whole gene deletion(10)|Unknown(1)	ovary(4)|breast(4)|biliary_tract(1)|large_intestine(1)|pancreas(1)	c.782_783del						.																																			SO:0001589	frameshift_variant	6416	exon7			.	L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.783_784delAA	chr17.hg19:g.12016647_12016648delAA	ENSP00000262445:p.Arg262fs	93.0	0.0		66.0	23.0	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Frame_Shift_Del	DEL	ENST00000353533.5	hg19	CCDS11162.1																																																																																			.	.		0.465	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			-	12016648	AA	-	12016647	7	5	27	1	0	1	0	1	0	0	0	0	9248	117	5	0	809	0	MAP2K4	17	12016647	Frame_Shift_Del	DEL	AA	TCGA-5R-AA1C-01A-11D-A40R-10	10432565	12016647	69178563	67	3582										
TTC19	54902	hgsc.bcm.edu	37	chr17	15903501	15903501	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gggagccgacggggccgctgCcgaggacggggcggacgagg	23	11	0	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr17:15903501C>T	ENST00000261647.5	+	2	723	c.254C>T	c.(253-255)gCc>gTc	p.A85V	TTC19_ENST00000497842.2_3'UTR|ZSWIM7_ENST00000399280.2_5'Flank|ZSWIM7_ENST00000486655.1_5'Flank|ZSWIM7_ENST00000399277.1_5'Flank|TTC19_ENST00000486880.2_Missense_Mutation_p.A206V|ZSWIM7_ENST00000472495.1_5'Flank	NM_001271420.1|NM_017775.3	NP_001258349.1|NP_060245.3	Q6DKK2	TTC19_HUMAN	tetratricopeptide repeat domain 19	85					cytokinesis (GO:0000910)|mitochondrial respiratory chain complex III assembly (GO:0034551)	centrosome (GO:0005813)|midbody (GO:0030496)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				central_nervous_system(1)|lung(2)|skin(1)|stomach(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		GGGGCCGCTGCCGAGGACGGG	0.741																																					p.A85V		Atlas-SNP	.											.	TTC19	10	.	0			c.C254T						.						9	14	13					17																	15903501		2144	4195	6339	SO:0001583	missense	54902	exon2			CCGCTGCCGAGGA	AK094819	CCDS11174.1, CCDS11174.2	17p11.2	2013-01-11			ENSG00000011295	ENSG00000011295		"Tetratricopeptide (TTC) repeat domain containing"	26006	protein-coding gene	gene with protein product		613814					Standard	NM_017775		Approved	FLJ20343, MGC19520	uc002gph.3	Q6DKK2	OTTHUMG00000059306	ENST00000261647.5:c.254C>T	chr17.hg19:g.15903501C>T	ENSP00000261647:p.Ala85Val	1107.0	0.0		867.0	91.0	NM_017775	A8MZ52|B3KP62|B4DN65|Q2M248|Q7L3U8|Q9H6G3|Q9NXB2	Missense_Mutation	SNP	ENST00000261647.5	hg19	CCDS11174.2	.	.	.	.	.	.	.	.	.	.	C	11.78	1.740517	0.30865	.	.	ENSG00000011295	ENST00000261647;ENST00000555605;ENST00000395886	D	0.83992	-1.79	3.98	1.74	0.24563	.	0.882556	0.09519	N	0.791185	T	0.67487	0.2898	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.60732	-0.7205	8	0.56958	D	0.05	0.0576	6.2913	0.21061	0.2127:0.581:0.2063:0.0	.	.	.	.	V	85;206;85	ENSP00000261647:A85V	ENSP00000261647:A206V	A	+	2	0	TTC19	15844226	0.000000	0.05858	0.013000	0.15412	0.484000	0.33280	0.222000	0.17699	1.005000	0.39183	0.498000	0.49722	GCC	.	.		0.741	TTC19-001	NOVEL	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000131725.6	NM_017775		T	15903501	C	T	15903501	3	4	27	1	0	0	0	0	1	0	0	0	16701	739	26	3	623	3	TTC19	17	15903501	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	3886854	15903501	65291709	68	3583										
NCOR1	9611	hgsc.bcm.edu	37	chr17	16029431	16029435	+	Frame_Shift_Del	DEL	TTTCT	TTTCT	-													0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	tcatctttttcctcttcatcTttcttttcttcttctttttt							TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	TTTCT	TTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr17:16029431_16029435delTTTCT	ENST00000268712.3	-	15	1852_1856	c.1595_1599delAGAAA	c.(1594-1599)aagaaafs	p.KK532fs	NCOR1_ENST00000395848.1_Frame_Shift_Del_p.KK423fs|NCOR1_ENST00000395851.1_Frame_Shift_Del_p.KK532fs	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	532					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		cctcttcatctttcttttcttcttc	0.268																																					p.532_534del		Atlas-Indel,Pindel	.											.	NCOR1	240	.	0			c.1596_1600del						.																																			SO:0001589	frameshift_variant	9611	exon14			.	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.1595_1599delAGAAA	chr17.hg19:g.16029436_16029440delTTTCT	ENSP00000268712:p.Lys532fs	314.0	0.0		292.0	21.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Frame_Shift_Del	DEL	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.		0.268	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		-	16029435	TTTCT	-	16029431	7	5	27	1	0	1	0	1	0	0	0	0	10244	1606	56	0	5851	0	NCOR1	17	16029431	Frame_Shift_Del	DEL	TTTCT	TCGA-5R-AA1C-01A-11D-A40R-10	125930	16029431	65165779	69	3584										
TAOK1	57551	hgsc.bcm.edu	37	chr17	27849536	27849536	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	acaacagcctaagagtttgaAggtatggttagcctaagctt	10	7	0	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr17:27849536A>T	ENST00000261716.3	+	17	2666	c.2147A>T	c.(2146-2148)aAg>aTg	p.K716M	TAOK1_ENST00000536202.1_Intron	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	716					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|execution phase of apoptosis (GO:0097194)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of cytoskeleton organization (GO:0051493)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28			Colorectal(6;0.198)			AAGAGTTTGAAGGTATGGTTA	0.388																																					p.K716M		Atlas-SNP	.											.	TAOK1	151	.	0			c.A2147T						.						102	99	100					17																	27849536		2203	4300	6503	SO:0001630	splice_region_variant	57551	exon17			GTTTGAAGGTATG	AB037782	CCDS32601.1, CCDS56024.1	17q11.2	2014-01-28				ENSG00000160551			29259	protein-coding gene	gene with protein product		610266				10718198, 14517247	Standard	NM_020791		Approved	KIAA1361, MARKK, PSK2, MAP3K16, FLJ14314, TAO1	uc002hdz.2	Q7L7X3		ENST00000261716.3:c.2148+1A>T	chr17.hg19:g.27849536A>T		180.0	0.0		114.0	13.0	NM_020791	A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Missense_Mutation	SNP	ENST00000261716.3	hg19	CCDS32601.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.326220	0.81580	.	.	ENSG00000160551	ENST00000261716	T	0.61980	0.06	5.81	5.81	0.92471	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.80374	0.4611	M	0.87547	2.89	0.80722	D	1	P	0.52692	0.955	P	0.60286	0.872	D	0.84033	0.0360	10	0.87932	D	0	.	16.1631	0.81732	1.0:0.0:0.0:0.0	.	716	Q7L7X3	TAOK1_HUMAN	M	716	ENSP00000261716:K716M	ENSP00000261716:K716M	K	+	2	0	TAOK1	24873662	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.570000	0.82390	2.217000	0.71921	0.523000	0.50628	AAG	.	.		0.388	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791	Missense_Mutation	T	27849536	A	T	27849536	5	4	27	1	0	0	0	0	0	0	1	0	15562	86	3	4	2209	4	TAOK1	17	27849536	Splice_Site	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10	11820105	27849536	53345674	70	3585										
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40650998	40650998	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	aactcctttaagatgaagatGtctgttatccttggtatcat	7	7	2	3			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr17:40650998G>A	ENST00000343619.4	+	15	1740	c.1617G>A	c.(1615-1617)atG>atA	p.M539I	ATP6V0A1_ENST00000544137.1_Missense_Mutation_p.M185I|ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.M539I|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.M496I|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.M546I|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.M539I|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.M496I|RP11-194N12.2_ENST00000591343.1_RNA	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	539					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		AGATGAAGATGTCTGTTATCC	0.368																																					p.M546I		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.G1638A						.						246	221	230					17																	40650998		2203	4300	6503	SO:0001583	missense	535	exon15			GAAGATGTCTGTT	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"ATPases / V-type"	865	protein-coding gene	gene with protein product		192130	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 1", "ATPase, H+ transporting, lysosomal V0 subunit A1"	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.1617G>A	chr17.hg19:g.40650998G>A	ENSP00000342951:p.Met539Ile	171.0	0.0		112.0	41.0	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	hg19	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	G	17.46	3.394617	0.62066	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728;ENST00000544137	D;D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05;-2.05;-2.05	5.76	4.8	0.61643	.	0.035003	0.85682	D	0.000000	D	0.86314	0.5903	M	0.76170	2.325	0.80722	D	1	B;B;B;B;B	0.33044	0.001;0.001;0.001;0.134;0.395	B;B;B;B;B	0.38683	0.004;0.013;0.008;0.111;0.279	D	0.85101	0.0957	10	0.40728	T	0.16	-24.1107	14.7293	0.69368	0.0693:0.0:0.9307:0.0	.	496;496;546;539;539	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1	.;.;.;VPP1_HUMAN;.	I	539;539;539;546;496;185	ENSP00000342951:M539I;ENSP00000444676:M539I;ENSP00000377415:M539I;ENSP00000264649:M546I;ENSP00000443991:M496I;ENSP00000446377:M185I	ENSP00000264649:M546I	M	+	3	0	ATP6V0A1	37904524	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.724000	0.74747	1.443000	0.47586	0.655000	0.94253	ATG	.	.		0.368	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020		A	40650998	G	A	40650998	3	1	27	1	0	0	0	0	1	0	0	0	1168	1377	48	3	1692	3	ATP6V0A1	17	40650998	Missense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	12801462	40650998	40544212	71	3586										
ABCA5	23461	hgsc.bcm.edu	37	chr17	67285417	67285417	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ttgatagtctgcatgtctaaAtctagtaaaaccttctgcac	6	9	4	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr17:67285417A>C	ENST00000392676.3	-	14	1867	c.1803T>G	c.(1801-1803)gaT>gaG	p.D601E	ABCA5_ENST00000588877.1_Missense_Mutation_p.D601E|ABCA5_ENST00000392677.2_Missense_Mutation_p.D601E			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	601	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	GCATGTCTAAATCTAGTAAAA	0.289																																					p.D601E		Atlas-SNP	.											.	ABCA5	162	.	0			c.T1803G						.						86	83	84					17																	67285417		2202	4298	6500	SO:0001583	missense	23461	exon13			GTCTAAATCTAGT	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.1803T>G	chr17.hg19:g.67285417A>C	ENSP00000376443:p.Asp601Glu	84.0	0.0		62.0	29.0	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	hg19	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	A	9.538	1.112497	0.20795	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.93189	-3.18;-3.18	5.09	5.09	0.68999	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.64402	D	0.000009	D	0.90487	0.7020	N	0.03016	-0.435	0.54753	D	0.999984	D;D	0.89917	0.999;1.0	D;D	0.77004	0.973;0.989	D	0.90276	0.4311	9	.	.	.	.	14.5684	0.68194	1.0:0.0:0.0:0.0	.	601;601	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	E	601	ENSP00000376444:D601E;ENSP00000376443:D601E	.	D	-	3	2	ABCA5	64797012	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.443000	0.52907	1.935000	0.56089	0.397000	0.26171	GAT	.	.		0.289	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		C	67285417	A	C	67285417	3	2	27	1	0	0	0	0	1	0	0	0	35	98	4	5	3229	5	ABCA5	17	67285417	Missense_Mutation	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10	26634419	67285417	13909793	72	3587										
SBNO2	22904	hgsc.bcm.edu	37	chr19	1109536	1109536	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ggtagaagccgtcataggggCccgtcagcgccagcgacttg	15	12	2	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr19:1109536C>T	ENST00000361757.3	-	28	3422	c.3185G>A	c.(3184-3186)gGc>gAc	p.G1062D	SBNO2_ENST00000587024.1_Missense_Mutation_p.G1052D|SBNO2_ENST00000438103.2_Missense_Mutation_p.G1005D	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	1062					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCATAGGGGCCCGTCAGCGC	0.721																																					p.G1062D		Atlas-SNP	.											.	SBNO2	112	.	0			c.G3185A						.						7	9	8					19																	1109536		1854	4036	5890	SO:0001583	missense	22904	exon28			TAGGGGCCCGTCA	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.3185G>A	chr19.hg19:g.1109536C>T	ENSP00000354733:p.Gly1062Asp	176.0	0.0		106.0	37.0	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Missense_Mutation	SNP	ENST00000361757.3	hg19	CCDS45894.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.566936	0.45694	.	.	ENSG00000064932	ENST00000361757;ENST00000438103;ENST00000250872	D;D	0.83250	-1.7;-1.7	4.62	4.62	0.57501	.	0.056069	0.64402	D	0.000001	T	0.76849	0.4045	L	0.51422	1.61	0.32387	N	0.553836	P;P	0.39131	0.531;0.661	B;B	0.38378	0.14;0.272	T	0.79729	-0.1681	10	0.29301	T	0.29	-34.4199	10.1785	0.42952	0.0:0.9078:0.0:0.0922	.	1062;1005	Q9Y2G9;Q9Y2G9-3	SBNO2_HUMAN;.	D	1062;1005;1080	ENSP00000354733:G1062D;ENSP00000400762:G1005D	ENSP00000250872:G1080D	G	-	2	0	SBNO2	1060536	0.735000	0.28153	0.057000	0.19452	0.592000	0.36648	2.687000	0.46976	2.121000	0.65114	0.462000	0.41574	GGC	.	.		0.721	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		T	1109536	C	T	1109536	3	4	27	1	0	0	0	0	1	0	0	0	13878	739	26	3	935	3	SBNO2	19	1109536	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10		1109536	58019447	73	3588										
PTPRS	5802	hgsc.bcm.edu	37	chr19	5244107	5244107	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ggtgtagtagacgcggtagcCgcggatcaggccgttgggct	18	9	1	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr19:5244107C>A	ENST00000587303.1	-	10	1474	c.1375G>T	c.(1375-1377)Ggc>Tgc	p.G459C	PTPRS_ENST00000592099.1_Missense_Mutation_p.G446C|PTPRS_ENST00000372412.4_Missense_Mutation_p.G460C|PTPRS_ENST00000348075.2_Missense_Mutation_p.G446C|PTPRS_ENST00000353284.2_Missense_Mutation_p.G446C|PTPRS_ENST00000357368.4_Missense_Mutation_p.G459C|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Missense_Mutation_p.G455C|PTPRS_ENST00000588012.1_Missense_Mutation_p.G446C			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	459	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	ACGCGGTAGCCGCGGATCAGG	0.677																																					p.G459C		Atlas-SNP	.											.	PTPRS	169	.	0			c.G1375T						.						87	81	83					19																	5244107		2203	4300	6503	SO:0001583	missense	5802	exon11			GGTAGCCGCGGAT	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.1375G>T	chr19.hg19:g.5244107C>A	ENSP00000467537:p.Gly459Cys	55.0	0.0		40.0	15.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	hg19	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.018157	0.54576	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08	3.84	3.84	0.44239	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	U	0.000002	D	0.84960	0.5588	H	0.98612	4.28	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.994;0.997;0.992;1.0;1.0;0.996	D	0.91511	0.5227	10	0.87932	D	0	.	15.9215	0.79580	0.0:1.0:0.0:0.0	.	459;446;450;446;459;472	F8W800;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;PTPRS_HUMAN;.	C	472;460;459;459;459;455;446;459;450;446	ENSP00000361489:G460C;ENSP00000349932:G459C;ENSP00000262963:G455C;ENSP00000269907:G446C;ENSP00000327313:G446C	ENSP00000262963:G455C	G	-	1	0	PTPRS	5195107	1.000000	0.71417	0.995000	0.50966	0.097000	0.18754	7.509000	0.81698	1.999000	0.58509	0.462000	0.41574	GGC	.	.		0.677	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			A	5244107	C	A	5244107	3	1	27	1	0	0	0	0	1	0	0	0	12826	652	23	1	4583	1	PTPRS	19	5244107	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	4134571	5244107	53884876	74	3589										
FUT6	2528	hgsc.bcm.edu	37	chr19	5832522	5832522	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	atcagcagctgaaacagcagCgtggtcagacagcagcgcca	12	12	2	2	rs371867552		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr19:5832522C>A	ENST00000318336.4	-	3	1251	c.57G>T	c.(55-57)acG>acT	p.T19T	FUT6_ENST00000592563.1_Silent_p.T19T|FUT6_ENST00000524754.1_Silent_p.T19T|FUT6_ENST00000286955.5_Silent_p.T19T|FUT6_ENST00000527106.1_Silent_p.T19T	NM_000150.2	NP_000141.1	P51993	FUT6_HUMAN	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	19					fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)	6						GAAACAGCAGCGTGGTCAGAC	0.582																																					p.T19T		Atlas-SNP	.											.	FUT6	30	.	0			c.G57T						.						37	31	33					19																	5832522		2203	4300	6503	SO:0001819	synonymous_variant	2528	exon3			CAGCAGCGTGGTC		CCDS12152.1	19p13.3	2013-02-26			ENSG00000156413	ENSG00000156413	2.4.1.65	"Fucosyltransferases"	4017	protein-coding gene	gene with protein product	"alpha-(1,3)-fucosyltransferase", "galactoside 3-L-fucosyltransferase"	136836				1520296, 7782074	Standard	NM_001040701		Approved	FT1A, FCT3A, FucT-VI, FLJ40754	uc002mdh.1	P51993	OTTHUMG00000167335	ENST00000318336.4:c.57G>T	chr19.hg19:g.5832522C>A		183.0	0.0		113.0	35.0	NM_000150	A6NEX0|D6W637|Q9UND8	Silent	SNP	ENST00000318336.4	hg19	CCDS12152.1																																																																																			.	.		0.582	FUT6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394218.2	NM_000150		A	5832522	C	A	5832522	2	1	27	1	0	0	0	0	0	0	0	1	6116	755	27	1		1	FUT6	19	5832522	Silent	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	588415	5832522	53296461	75	3590										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13616903	13616903	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	cattgactgcttgtacatccTttgcgccccgggctgcccgc	10	16	0	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr19:13616903T>G	ENST00000360228.5	-	1	135	c.136A>C	c.(136-138)Agg>Cgg	p.R46R	CACNA1A_ENST00000573710.2_Silent_p.R46R	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	46					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TTGTACATCCTTTGCGCCCCG	0.706																																					p.R46R		Atlas-SNP	.											.	CACNA1A	715	.	0			c.A136C						.						69	73	72					19																	13616903		2046	4189	6235	SO:0001819	synonymous_variant	773	exon1			ACATCCTTTGCGC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.136A>C	chr19.hg19:g.13616903T>G		1172.0	1.0		935.0	368.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	hg19	CCDS45998.1																																																																																			.	.		0.706	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		G	13616903	T	G	13616903	2	3	27	1	0	0	0	0	0	0	0	1	2540	1608	56	5		5	CACNA1A	19	13616903	Silent	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10	7784381	13616903	45512080	76	3591										
CEACAM5	1048	hgsc.bcm.edu	37	chr19	42221465	42221465	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	acctgtgaacctgagattcaGaacacaacctacctgtggtg	9	11	1	3			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr19:42221465G>A	ENST00000221992.6	+	5	1164	c.1050G>A	c.(1048-1050)caG>caA	p.Q350Q	CEACAM5_ENST00000405816.1_Silent_p.Q350Q|CEACAM5_ENST00000398599.4_Silent_p.Q349Q|CEA_ENST00000598976.1_Intron	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	350	Ig-like 4.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CTGAGATTCAGAACACAACCT	0.532																																					p.Q350Q		Atlas-SNP	.											.	CEACAM5	84	.	0			c.G1050A						.						177	167	170					19																	42221465		2203	4300	6503	SO:0001819	synonymous_variant	1048	exon5			GATTCAGAACACA	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1050G>A	chr19.hg19:g.42221465G>A		133.0	0.0		89.0	31.0	NM_004363	H9KVA7	Silent	SNP	ENST00000221992.6	hg19	CCDS12584.1	.	.	.	.	.	.	.	.	.	.	G	5.471	0.272029	0.10349	.	.	ENSG00000105388	ENST00000398599	.	.	.	2.77	-2.34	0.06704	.	.	.	.	.	T	0.21468	0.0517	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30736	-0.9968	4	.	.	.	.	4.3211	0.11018	0.0:0.2213:0.3319:0.4468	.	.	.	.	K	346	.	.	E	+	1	0	CEACAM5	46913305	0.000000	0.05858	0.000000	0.03702	0.370000	0.29829	-0.120000	0.10660	-0.052000	0.13311	0.479000	0.44913	GAA	.	.		0.532	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363		A	42221465	G	A	42221465	2	1	27	1	0	0	0	0	0	0	0	1	3197	933	33	3		3	CEACAM5	19	42221465	Silent	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	28604562	42221465	16907518	77	3592										
LILRB3	11025	hgsc.bcm.edu	37	chr19	54726002	54726002	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gggtgggtttgctgtaggctCctaggagagaaagaggcacc	17	7	0	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr19:54726002C>A	ENST00000391750.1	-	5	492	c.356G>T	c.(355-357)gGa>gTa	p.G119V	LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000424807.1_Splice_Site_p.G119V|LILRB3_ENST00000346401.6_Splice_Site_p.G119V|LILRB3_ENST00000245620.9_Splice_Site_p.G119V|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000407860.2_Splice_Site_p.G119V|CTB-83J4.1_ENST00000601161.1_lincRNA			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	119	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCTGTAGGCTCCTAGGAGAGA	0.622																																					p.G119V		Atlas-SNP	.											.	LILRB3	67	.	0			c.G356T						.						62	40	48					19																	54726002		2132	3924	6056	SO:0001630	splice_region_variant	11025	exon4			TAGGCTCCTAGGA	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.356-1G>T	chr19.hg19:g.54726002C>A		214.0	0.0		141.0	18.0	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	hg19	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.844770	0.32606	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000445347	T;T;T;T;T;T	0.14266	2.52;2.52;2.52;2.52;2.52;2.52	2.87	0.59	0.17458	Immunoglobulin-like fold (1);	0.256125	0.27500	N	0.019096	T	0.42787	0.1218	H	0.97023	3.925	0.23150	N	0.99821	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.993;0.995;0.999;0.985;0.999	T	0.27468	-1.0073	10	0.87932	D	0	.	3.9673	0.09437	0.0:0.6062:0.2496:0.1442	.	119;119;119;119;119	B5MCX0;F8WD89;O75022-2;O75022;O75022-3	.;.;.;LIRB3_HUMAN;.	V	119	ENSP00000375630:G119V;ENSP00000412771:G119V;ENSP00000345184:G119V;ENSP00000245620:G119V;ENSP00000384274:G119V;ENSP00000388199:G119V	ENSP00000245620:G119V	G	-	2	0	LILRB3	59417814	0.108000	0.22018	0.177000	0.23020	0.074000	0.17049	1.354000	0.34056	0.253000	0.21552	-0.253000	0.11424	GGA	.	.		0.622	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	Missense_Mutation	A	54726002	C	A	54726002	5	1	27	1	0	0	0	0	0	0	1	0	8801	869	30	3	1582	3	LILRB3	19	54726002	Splice_Site	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	12504537	54726002	4402981	78	3593										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20144770	20144770	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	cagtaggagcttggcatcgcTcgtactgcctgaagagcccg	13	12	0	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr20:20144770T>C	ENST00000245957.5	+	11	1179	c.1103T>C	c.(1102-1104)cTc>cCc	p.L368P	C20orf26_ENST00000377306.1_Missense_Mutation_p.L368P|C20orf26_ENST00000451767.2_Missense_Mutation_p.L368P|C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000389656.3_5'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		368										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		TTGGCATCGCTCGTACTGCCT	0.493																																					p.L368P		Atlas-SNP	.											.	C20orf26	188	.	0			c.T1103C						.						131	121	125					20																	20144770		2203	4300	6503	SO:0001583	missense	26074	exon11			CATCGCTCGTACT																												ENST00000245957.5:c.1103T>C	chr20.hg19:g.20144770T>C	ENSP00000245957:p.Leu368Pro	65.0	0.0		67.0	24.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	hg19	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	T	13.22	2.171453	0.38315	.	.	ENSG00000089101	ENST00000340348;ENST00000389655;ENST00000245957;ENST00000377306;ENST00000451767	T;T;T	0.09911	2.93;2.93;2.93	5.05	-1.14	0.09741	.	1.337740	0.04852	N	0.442440	T	0.12092	0.0294	L	0.47716	1.5	0.09310	N	0.999997	P;B;B;B	0.49559	0.925;0.009;0.115;0.255	P;B;B;B	0.45610	0.487;0.023;0.048;0.061	T	0.30707	-0.9969	10	0.33940	T	0.23	.	5.0756	0.14630	0.0:0.384:0.1914:0.4246	.	368;368;323;368	Q8NHU2-3;F8W6K4;F8W6E2;Q8NHU2	.;.;.;CT026_HUMAN	P	323;368;368;368;368	ENSP00000245957:L368P;ENSP00000366521:L368P;ENSP00000414537:L368P	ENSP00000245957:L368P	L	+	2	0	C20orf26	20092770	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.128000	0.10531	-0.103000	0.12175	-0.256000	0.11100	CTC	.	.		0.493	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			C	20144770	T	C	20144770	3	2	27	1	0	0	0	0	1	0	0	0	2108	1551	54	2	1141	2	C20orf26	20	20144770	Missense_Mutation	SNP	T	TCGA-5R-AA1C-01A-11D-A40R-10		20144770	42880750	79	3594										
SYS1	90196	hgsc.bcm.edu	37	chr20	43995750	43995750	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	actcagcccctaaatccaatGtctagaatcaggccctttgg	7	13	3	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr20:43995750G>A	ENST00000243918.5	+	4	757	c.466G>A	c.(466-468)Gtc>Atc	p.V156I	SYS1_ENST00000372727.1_Missense_Mutation_p.V156I|SYS1_ENST00000414310.1_Missense_Mutation_p.V135I|SYS1-DBNDD2_ENST00000452133.1_Intron|SYS1_ENST00000426004.1_Intron|SYS1-DBNDD2_ENST00000475242.1_Intron|SYS1_ENST00000479779.1_3'UTR	NM_033542.3	NP_291020.1	Q8N2H4	SYS1_HUMAN	Sys1 golgi trafficking protein	156					protein transport (GO:0015031)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|large_intestine(2)|prostate(1)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				TAAATCCAATGTCTAGAATCA	0.567																																					p.V156I		Atlas-SNP	.											.	SYS1	15	.	0			c.G466A						.						97	98	98					20																	43995750		2203	4300	6503	SO:0001583	missense	90196	exon5			TCCAATGTCTAGA	AL021578	CCDS13351.1, CCDS56192.1	20q13.12	2014-05-07	2014-05-07	2006-11-06	ENSG00000204070	ENSG00000204070			16162	protein-coding gene	gene with protein product		612979	"chromosome 20 open reading frame 169", "SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)"	C20orf169		15077113	Standard	NM_001197129		Approved	dJ453C12.4	uc002xnv.3	Q8N2H4	OTTHUMG00000032579	ENST00000243918.5:c.466G>A	chr20.hg19:g.43995750G>A	ENSP00000243918:p.Val156Ile	106.0	0.0		79.0	35.0	NM_001197129	C9JFB3|E1P620|Q5QPU7|Q96SD8|Q9BQZ2|Q9BQZ4|Q9H1F7	Missense_Mutation	SNP	ENST00000243918.5	hg19	CCDS13351.1	.	.	.	.	.	.	.	.	.	.	G	19.53	3.844763	0.71603	.	.	ENSG00000204070	ENST00000372727;ENST00000414310;ENST00000243918	.	.	.	6.17	6.17	0.99709	.	0.066463	0.64402	D	0.000010	T	0.62221	0.2410	L	0.54323	1.7	0.39460	D	0.96755	B	0.32302	0.363	B	0.31946	0.138	T	0.61773	-0.6994	9	0.51188	T	0.08	-0.0156	19.8676	0.96824	0.0:0.0:1.0:0.0	.	156	Q8N2H4	SYS1_HUMAN	I	156;135;156	.	ENSP00000243918:V156I	V	+	1	0	SYS1	43429164	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.855000	0.62925	2.941000	0.99782	0.655000	0.94253	GTC	.	.		0.567	SYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079453.2	NM_033542		A	43995750	G	A	43995750	3	1	27	1	0	0	0	0	1	0	0	0	15479	1377	48	3	476	3	SYS1	20	43995750	Missense_Mutation	SNP	G	TCGA-5R-AA1C-01A-11D-A40R-10	23850980	43995750	19029770	80	3595										
KCNB1	3745	hgsc.bcm.edu	37	chr20	47990403	47990403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gaggggctacggggctggggAtactctccatttcaagttct	14	9	3	0			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr20:47990403A>G	ENST00000371741.4	-	2	1860	c.1694T>C	c.(1693-1695)aTc>aCc	p.I565T		NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1	565					energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	GGGGCTGGGGATACTCTCCAT	0.493																																					p.I565T		Atlas-SNP	.											.	KCNB1	142	.	0			c.T1694C						.						117	100	106					20																	47990403		2203	4300	6503	SO:0001583	missense	3745	exon2			CTGGGGATACTCT	AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.1694T>C	chr20.hg19:g.47990403A>G	ENSP00000360806:p.Ile565Thr	110.0	0.0		94.0	33.0	NM_004975	Q14193	Missense_Mutation	SNP	ENST00000371741.4	hg19	CCDS13418.1	.	.	.	.	.	.	.	.	.	.	A	5.981	0.364907	0.11296	.	.	ENSG00000158445	ENST00000371741;ENST00000538812	T	0.26660	1.72	6.07	6.07	0.98685	.	1.730570	0.02606	N	0.101553	T	0.31327	0.0793	L	0.40543	1.245	0.25230	N	0.989838	B	0.23377	0.084	B	0.22753	0.041	T	0.43925	-0.9361	10	0.31617	T	0.26	.	16.3023	0.82830	1.0:0.0:0.0:0.0	.	565	Q14721	KCNB1_HUMAN	T	565;520	ENSP00000360806:I565T	ENSP00000360806:I565T	I	-	2	0	KCNB1	47423810	1.000000	0.71417	0.935000	0.37517	0.221000	0.24807	8.962000	0.93254	2.326000	0.78906	0.533000	0.62120	ATC	.	.		0.493	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975		G	47990403	A	G	47990403	3	3	27	1	0	0	0	0	1	0	0	0	8021	333	12	2	886	2	KCNB1	20	47990403	Missense_Mutation	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10	3994653	47990403	15035117	81	3596										
BACH1	571	hgsc.bcm.edu	37	chr21	30701998	30701998	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	ctgtatacagaatcttgaatCagaaattgagaagctggtaa	9	5	2	4			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr21:30701998C>A	ENST00000399921.1	+	4	2003	c.1760C>A	c.(1759-1761)tCa>tAa	p.S587*	BACH1_ENST00000286800.3_Nonsense_Mutation_p.S587*	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0					DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						AATCTTGAATCAGAAATTGAG	0.343																																					p.S587X		Atlas-SNP	.											.	BACH1	66	.	0			c.C1760A						.						23	23	23					21																	30701998		2203	4300	6503	SO:0001587	stop_gained	571	exon4			TTGAATCAGAAAT	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"BTB/POZ domain containing", "basic leucine zipper proteins"	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.1760C>A	chr21.hg19:g.30701998C>A	ENSP00000382805:p.Ser587*	175.0	0.0		78.0	40.0	NM_206866	Q3MJE2|Q8NCI5	Nonsense_Mutation	SNP	ENST00000399921.1	hg19	CCDS13585.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.779927|7.779927	0.98486|0.98486	.|.	.|.	ENSG00000156273|ENSG00000156273	ENST00000551628|ENST00000286800;ENST00000399921	.|.	.|.	.|.	5.64|5.64	4.57|4.57	0.56435|0.56435	.|.	.|0.185391	.|0.38217	.|N	.|0.001764	T|.	0.35098|.	0.0920|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.13150|.	-1.0520|.	4|.	.|0.06365	.|T	.|0.9	-15.5547|-15.5547	10.9688|10.9688	0.47428|0.47428	0.0:0.7883:0.1331:0.0786|0.0:0.7883:0.1331:0.0786	.|.	.|.	.|.	.|.	K|X	81|587	.|.	.|ENSP00000286800:S587X	Q|S	+|+	1|2	0|0	BACH1|BACH1	29623869|29623869	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	2.121000|2.121000	0.41977|0.41977	2.660000|2.660000	0.90430|0.90430	0.650000|0.650000	0.86243|0.86243	CAG|TCA	.	.		0.343	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		A	30701998	C	A	30701998	4	1	27	1	0	0	0	0	0	1	0	0	1283	838	29	3	1770	3	BACH1	21	30701998	Nonsense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10		30701998	17427897	82	3597										
IFNAR2	3455	hgsc.bcm.edu	37	chr21	34635391	34635391	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gaggttgatgtggagctcccCacgatgccaaaggacagccc	13	12	0	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr21:34635391C>T	ENST00000342136.4	+	9	1460	c.1134C>T	c.(1132-1134)ccC>ccT	p.P378P	IFNAR2_ENST00000404220.3_3'UTR|IFNAR2_ENST00000382241.3_Silent_p.P378P|IL10RB-AS1_ENST00000411998.1_RNA|IFNAR2_ENST00000342101.3_3'UTR|AP000295.9_ENST00000433395.2_Intron			P48551	INAR2_HUMAN	interferon (alpha, beta and omega) receptor 2	378					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|type I interferon binding (GO:0019962)|type I interferon receptor activity (GO:0004905)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	11					"""Interferon Alfa-2a(DB00034)|""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"	TGGAGCTCCCCACGATGCCAA	0.587																																					p.P378P		Atlas-SNP	.											.	IFNAR2	44	.	0			c.C1134T						.						63	67	65					21																	34635391		2203	4300	6503	SO:0001819	synonymous_variant	3455	exon9			GCTCCCCACGATG		CCDS13621.1, CCDS13622.1, CCDS74782.1	21q22.1	2010-08-17			ENSG00000159110	ENSG00000159110		"Interferons"	5433	protein-coding gene	gene with protein product		602376		IFNABR		8181059	Standard	NM_207585		Approved		uc002yrd.3	P48551	OTTHUMG00000065127	ENST00000342136.4:c.1134C>T	chr21.hg19:g.34635391C>T		138.0	0.0		66.0	42.0	NM_207585	A8KAJ4|D3DSE8|D3DSE9|Q15467|Q6FHD7	Silent	SNP	ENST00000342136.4	hg19	CCDS13621.1																																																																																			.	.		0.587	IFNAR2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139825.1			T	34635391	C	T	34635391	2	4	27	1	0	0	0	0	0	0	0	1	7554	581	21	3		3	IFNAR2	21	34635391	Silent	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10	3933393	34635391	13494504	83	3598										
SFI1	9814	hgsc.bcm.edu	37	chr22	32009644	32009644	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	gccacgctctggaaacagaaAgtgctgggccggggcgggaa	17	10	1	1			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chr22:32009644A>G	ENST00000400288.2	+	27	2904	c.2799A>G	c.(2797-2799)aaA>aaG	p.K933K	SFI1_ENST00000443326.1_Silent_p.K851K|SFI1_ENST00000540643.1_Silent_p.K878K|SFI1_ENST00000414585.1_Silent_p.K780K|SFI1_ENST00000443011.1_Silent_p.K780K|SFI1_ENST00000400289.1_Silent_p.K851K|SFI1_ENST00000432498.1_Silent_p.K902K	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	933					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GGAAACAGAAAGTGCTGGGCC	0.642																																					p.K933K		Atlas-SNP	.											.	SFI1	78	.	0			c.A2799G						.						17	21	20					22																	32009644		2034	4175	6209	SO:0001819	synonymous_variant	9814	exon27			ACAGAAAGTGCTG	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.2799A>G	chr22.hg19:g.32009644A>G		135.0	0.0		110.0	35.0	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Silent	SNP	ENST00000400288.2	hg19	CCDS43004.1																																																																																			.	.		0.642	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		G	32009644	A	G	32009644	2	3	27	1	0	0	0	0	0	0	0	1	14171	69	3	2		2	SFI1	22	32009644	Silent	SNP	A	TCGA-5R-AA1C-01A-11D-A40R-10		32009644	19294922	84	3599										
AFF2	2334	hgsc.bcm.edu	37	chrX	148037839	148037839	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0941176470588235	8	1	2.24186498300146	1.62535211267606	2.37030516431925	0.0237358101135191	0.304738562091504	0	aatctgtggtgccagcctgaCcctcagcaccttaatgagta	9	12	2	2			TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	g.chrX:148037839C>T	ENST00000370460.2	+	11	2743	c.2264C>T	c.(2263-2265)aCc>aTc	p.T755I	AFF2_ENST00000286437.5_Missense_Mutation_p.T396I|AFF2_ENST00000370457.5_Missense_Mutation_p.T722I|AFF2_ENST00000342251.3_Missense_Mutation_p.T722I	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	755					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)	p.T755N(2)|p.T396N(1)		breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GCCAGCCTGACCCTCAGCACC	0.453																																					p.T755I		Atlas-SNP	.											.	AFF2	679	.	3	Substitution - Missense(3)	lung(3)	c.C2264T						.						95	86	89					X																	148037839		2203	4300	6503	SO:0001583	missense	2334	exon11			GCCTGACCCTCAG	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.2264C>T	chrX.hg19:g.148037839C>T	ENSP00000359489:p.Thr755Ile	128.0	0.0		162.0	69.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	hg19	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	C	5.362	0.252128	0.10185	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	5.93	3.0	0.34707	.	0.372648	0.27193	N	0.020496	T	0.45994	0.1370	L	0.40543	1.245	0.09310	N	1	B;B;B;B;B;B	0.10296	0.003;0.002;0.002;0.002;0.002;0.003	B;B;B;B;B;B	0.13407	0.009;0.005;0.005;0.005;0.005;0.009	T	0.17776	-1.0358	10	0.40728	T	0.16	.	4.0132	0.09632	0.1239:0.4075:0.374:0.0947	.	396;720;722;716;745;755	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	I	755;722;722;396	ENSP00000359489:T755I;ENSP00000359486:T722I;ENSP00000345459:T722I;ENSP00000286437:T396I	ENSP00000286437:T396I	T	+	2	0	AFF2	147845539	1.000000	0.71417	0.016000	0.15963	0.042000	0.13812	2.973000	0.49264	2.498000	0.84270	0.600000	0.82982	ACC	.	.		0.453	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		T	148037839	C	T	148037839	3	4	27	1	0	0	0	0	1	0	0	0	357	507	18	3	2361	3	AFF2	23	148037839	Missense_Mutation	SNP	C	TCGA-5R-AA1C-01A-11D-A40R-10		148037839	7232721	85	3600										
WNT7A	7476	hgsc.bcm.edu	37	chr3	13921289	13921289	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	gctgagaaagaggtggcccaGgcagcgccgcgctttccggt	16	12	0	2	rs145718587	byFrequency	TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr3:13921289G>C	ENST00000285018.4	-	1	329	c.25C>G	c.(25-27)Ctg>Gtg	p.L9V	WNT7A_ENST00000497808.1_5'Flank	NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	9					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						AGGTGGCCCAGGCAGCGCCGC	0.697																																					p.L9V		Atlas-SNP	.											.	WNT7A	70	.	0			c.C25G						.						45	45	45					3																	13921289		2203	4300	6503	SO:0001583	missense	7476	exon1			GGCCCAGGCAGCG	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"Wingless-type MMTV integration sites"	12786	protein-coding gene	gene with protein product	"proto-oncogene Wnt7a protein"	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.25C>G	chr3.hg19:g.13921289G>C	ENSP00000285018:p.Leu9Val	232.0	0.0		223.0	37.0	NM_004625	Q96H90|Q9Y560	Missense_Mutation	SNP	ENST00000285018.4	hg19	CCDS2616.1	.	.	.	.	.	.	.	.	.	.	G	9.589	1.125520	0.20959	.	.	ENSG00000154764	ENST00000285018	T	0.75938	-0.98	3.71	0.473	0.16763	.	0.078049	0.51477	D	0.000093	T	0.47021	0.1423	N	0.08118	0	0.24291	N	0.995163	B	0.02656	0.0	B	0.04013	0.001	T	0.32771	-0.9894	10	0.51188	T	0.08	.	3.4506	0.07496	0.2418:0.0:0.4479:0.3102	.	9	O00755	WNT7A_HUMAN	V	9	ENSP00000285018:L9V	ENSP00000285018:L9V	L	-	1	2	WNT7A	13896290	1.000000	0.71417	1.000000	0.80357	0.163000	0.22366	2.565000	0.45939	0.254000	0.21573	-0.142000	0.14014	CTG	.	G|1.000;A|0.000		0.697	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625		C	13921289	G	C	13921289	3	2	28	1	0	0	0	0	1	0	0	0	17409	991	35	4	1040	4	WNT7A	3	13921289	Missense_Mutation	SNP	G	TCGA-5R-AA1D-01A-11D-A382-10		13921289	184101141	1	3601										
CDH9	1007	hgsc.bcm.edu	37	chr5	26885762	26885762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	gagtagaatcgcaacgagagCtcccgtgctcaggccggctg	14	12	1	2			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr5:26885762C>T	ENST00000231021.4	-	11	2015	c.1843G>A	c.(1843-1845)Gct>Act	p.A615T		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	615					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						GCAACGAGAGCTCCCGTGCTC	0.507																																					p.A615T	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											CDH9,right_upper_lobe,carcinoma,0,1	CDH9	305	.	0			c.G1843A						.						77	66	70					5																	26885762		2203	4300	6503	SO:0001583	missense	1007	exon11			CGAGAGCTCCCGT	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1843G>A	chr5.hg19:g.26885762C>T	ENSP00000231021:p.Ala615Thr	162.0	0.0		160.0	29.0	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	34	5.327459	0.95733	.	.	ENSG00000113100	ENST00000231021	T	0.59638	0.25	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.83427	0.5252	H	0.94582	3.555	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.79108	0.979;0.992	D	0.87302	0.2306	9	.	.	.	.	18.82	0.92092	0.0:1.0:0.0:0.0	.	208;615	B4DFP0;Q9ULB4	.;CADH9_HUMAN	T	615	ENSP00000231021:A615T	.	A	-	1	0	CDH9	26921519	1.000000	0.71417	0.231000	0.23993	0.971000	0.66376	7.781000	0.85668	2.797000	0.96272	0.563000	0.77884	GCT	.	.		0.507	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26885762	C	T	26885762	3	4	28	1	0	0	0	0	1	0	0	0	3119	797	28	3	534	3	CDH9	5	26885762	Missense_Mutation	SNP	C	TCGA-5R-AA1D-01A-11D-A382-10		26885762	154029498	2	3602										
PON2	5445	hgsc.bcm.edu	37	chr7	95040997	95040997	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	tcatgtttgactgttttcagAtgcaacagagaattttctgc	8	7	3	3			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr7:95040997A>C	ENST00000222572.3	-	5	708	c.462T>G	c.(460-462)caT>caG	p.H154Q	PON2_ENST00000433091.2_Missense_Mutation_p.H142Q|PON2_ENST00000536183.1_Missense_Mutation_p.H175Q|PON2_ENST00000483292.1_5'UTR			Q15165	PON2_HUMAN	paraoxonase 2	154					aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			CTGTTTTCAGATGCAACAGAG	0.363																																					p.H154Q	GBM(42;803 823 13649 23368 31463)	Atlas-SNP	.											.	PON2	32	.	0			c.T462G						.						76	78	78					7																	95040997		2203	4300	6503	SO:0001583	missense	5445	exon5			TTTCAGATGCAAC	M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"Paraoxonases"	9205	protein-coding gene	gene with protein product	"paraoxonase nirs", "arylesterase 2"	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.462T>G	chr7.hg19:g.95040997A>C	ENSP00000222572:p.His154Gln	168.0	0.0		149.0	27.0	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	hg19	CCDS5640.1	.	.	.	.	.	.	.	.	.	.	A	13.15	2.152480	0.38021	.	.	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.42513	2.32;0.97;2.32	4.94	-3.32	0.04973	Six-bladed beta-propeller, TolB-like (1);	0.093439	0.64402	D	0.000001	T	0.65344	0.2682	M	0.88241	2.94	0.51482	D	0.999924	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.73304	-0.4025	10	0.72032	D	0.01	-21.5209	15.3323	0.74223	0.3835:0.0:0.6165:0.0	.	154;154	A4D1H7;Q15165	.;PON2_HUMAN	Q	175;152;142;154	ENSP00000440282:H175Q;ENSP00000404622:H142Q;ENSP00000222572:H154Q	ENSP00000222572:H154Q	H	-	3	2	PON2	94878933	0.999000	0.42202	0.971000	0.41717	0.003000	0.03518	0.560000	0.23500	-0.448000	0.07128	0.528000	0.53228	CAT	.	.		0.363	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305		C	95040997	A	C	95040997	3	2	28	1	0	0	0	0	1	0	0	0	12258	330	12	5	622	5	PON2	7	95040997	Missense_Mutation	SNP	A	TCGA-5R-AA1D-01A-11D-A382-10		95040997	64097666	3	3603										
NLRP6	171389	hgsc.bcm.edu	37	chr11	281192	281192	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	ctcagcaaaaaggagctgccGggcgtgctggagacagaggt	16	9	1	2			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr11:281192G>T	ENST00000312165.5	+	4	1458	c.1458G>T	c.(1456-1458)ccG>ccT	p.P486P	NLRP6_ENST00000534750.1_Silent_p.P486P	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	486	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGGAGCTGCCGGGCGTGCTGG	0.612																																					p.P486P		Atlas-SNP	.											.	NLRP6	4	.	0			c.G1458T						.						79	79	79					11																	281192		2203	4300	6503	SO:0001819	synonymous_variant	171389	exon4			GCTGCCGGGCGTG	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"Nucleotide-binding domain and leucine rich repeat containing"	22944	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"	609650	"NACHT, leucine rich repeat and PYD containing 6"	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.1458G>T	chr11.hg19:g.281192G>T		133.0	0.0		103.0	18.0	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	hg19	CCDS7693.1																																																																																			.	.		0.612	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		T	281192	G	T	281192	2	4	28	1	0	0	0	0	0	0	0	1	10490	1103	39	1		1	NLRP6	11	281192	Silent	SNP	G	TCGA-5R-AA1D-01A-11D-A382-10		281192	134725324	4	3604										
SAA4	6291	hgsc.bcm.edu	37	chr11	18254009	18254009	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	atcatagtttccccgagcatAgagatatctgtttgaatttt	7	7	2	2			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr11:18254009A>T	ENST00000278222.4	-	3	343	c.163T>A	c.(163-165)Tat>Aat	p.Y55N	SAA2-SAA4_ENST00000524555.1_RNA	NM_006512.3	NP_006503.2	P35542	SAA4_HUMAN	serum amyloid A4, constitutive	55					acute-phase response (GO:0006953)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(1)|stomach(1)	13						CCCCGAGCATAGAGATATCTG	0.468																																					p.Y133N		Atlas-SNP	.											.	.	.	.	0			c.T397A						.						179	175	176					11																	18254009		2199	4293	6492	SO:0001583	missense	100528017	exon5			GAGCATAGAGATA	M81349	CCDS7832.1	11p15.1-p14	2008-07-21			ENSG00000148965	ENSG00000148965			10516	protein-coding gene	gene with protein product		104752				8325654	Standard	NM_006512		Approved	C-SAA, CSAA		P35542	OTTHUMG00000166483	ENST00000278222.4:c.163T>A	chr11.hg19:g.18254009A>T	ENSP00000278222:p.Tyr55Asn	131.0	0.0		103.0	18.0	NM_001199744	Q6FHJ4	Missense_Mutation	SNP	ENST00000278222.4	hg19	CCDS7832.1	.	.	.	.	.	.	.	.	.	.	A	10.76	1.440836	0.25900	.	.	ENSG00000148965	ENST00000278222	T	0.09817	2.94	3.26	0.932	0.19466	.	.	.	.	.	T	0.08891	0.0220	L	0.43152	1.355	0.33002	D	0.526322	P	0.43826	0.818	B	0.38985	0.287	T	0.24905	-1.0147	9	0.87932	D	0	-8.8289	5.6276	0.17490	0.3224:0.0:0.6776:0.0	.	55	P35542	SAA4_HUMAN	N	55	ENSP00000278222:Y55N	ENSP00000278222:Y55N	Y	-	1	0	SAA4	18210585	1.000000	0.71417	0.114000	0.21550	0.084000	0.17831	2.247000	0.43151	-0.129000	0.11620	-0.456000	0.05471	TAT	.	.		0.468	SAA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389988.1	NM_006512		T	18254009	A	T	18254009	3	4	28	1	0	0	0	0	1	0	0	0	13815	420	15	4	237	4	SAA4	11	18254009	Missense_Mutation	SNP	A	TCGA-5R-AA1D-01A-11D-A382-10	17972817	18254009	116752507	5	3605										
OTUB1	55611	hgsc.bcm.edu	37	chr11	63753947	63753947	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.125	2	1	1.4	3.5	0.875	1	1	0	agatggcggcggaggaacctCagcagcagaagcaggagccg	17	10	1	2			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr11:63753947C>T	ENST00000538426.1	+	1	63	c.19C>T	c.(19-21)Cag>Tag	p.Q7*	OTUB1_ENST00000428192.2_Nonsense_Mutation_p.Q7*|AP000721.4_ENST00000535431.1_Missense_Mutation_p.S150L|OTUB1_ENST00000422031.2_Nonsense_Mutation_p.Q44*|OTUB1_ENST00000535715.1_Nonsense_Mutation_p.Q7*|OTUB1_ENST00000536443.1_3'UTR|OTUB1_ENST00000543004.1_Nonsense_Mutation_p.Q7*|OTUB1_ENST00000541478.1_Nonsense_Mutation_p.Q7*|OTUB1_ENST00000543988.1_5'Flank	NM_017670.2	NP_060140.2	Q96FW1	OTUB1_HUMAN	OTU deubiquitinase, ubiquitin aldehyde binding 1	7					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|immune system process (GO:0002376)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein K48-linked deubiquitination (GO:0071108)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	NEDD8-specific protease activity (GO:0019784)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	6						GGAGGAACCTCAGCAGCAGAA	0.672																																					p.Q7X		Atlas-SNP	.											.	OTUB1	19	.	0			c.C19T						.						27	30	29					11																	63753947		2132	4179	6311	SO:0001587	stop_gained	55611	exon1			GAACCTCAGCAGC	AY177200	CCDS8055.1	11q13.1	2014-02-24	2014-02-24			ENSG00000167770		"OTU domain containing"	23077	protein-coding gene	gene with protein product		608337	"OTU domain, ubiquitin aldehyde binding 1"			12704427, 19383985	Standard	NM_017670		Approved	FLJ20113, FLJ40710	uc001nyf.1	Q96FW1		ENST00000538426.1:c.19C>T	chr11.hg19:g.63753947C>T	ENSP00000444357:p.Gln7*	159.0	0.0		124.0	15.0	NM_017670	Q32Q78|Q96II3|Q9NXQ4|Q9P0B8	Nonsense_Mutation	SNP	ENST00000538426.1	hg19	CCDS8055.1	.	.	.	.	.	.	.	.	.	.	c	35	5.521842	0.96416	.	.	ENSG00000167770	ENST00000541478;ENST00000535715;ENST00000428192;ENST00000422031;ENST00000538426;ENST00000543004	.	.	.	4.36	4.36	0.52297	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	12.8577	0.57894	0.0:1.0:0.0:0.0	.	.	.	.	X	7;7;7;44;7;7	.	ENSP00000416973:Q44X	Q	+	1	0	OTUB1	63510523	1.000000	0.71417	1.000000	0.80357	0.695000	0.40330	1.417000	0.34770	2.155000	0.67459	0.552000	0.68991	CAG	.	.		0.672	OTUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396277.1	NM_017670		T	63753947	C	T	63753947	4	4	28	1	0	0	0	0	0	1	0	0	11320	827	29	3	21	3	OTUB1	11	63753947	Nonsense_Mutation	SNP	C	TCGA-5R-AA1D-01A-11D-A382-10	45499938	63753947	71252569	6	3606										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43748039	43748039	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	acttgaattgggagaccagtAgtcatgtgaggaagacactt	12	6	1	4			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr12:43748039A>G	ENST00000389420.3	-	39	5705	c.5706T>C	c.(5704-5706)acT>acC	p.T1902T		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1902	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		GGAGACCAGTAGTCATGTGAG	0.398																																					p.T1902T		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T5706C						.						67	59	61					12																	43748039		2202	4299	6501	SO:0001819	synonymous_variant	80070	exon39			ACCAGTAGTCATG	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.5706T>C	chr12.hg19:g.43748039A>G		84.0	0.0		84.0	17.0	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.		0.398	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43748039	A	G	43748039	2	3	28	1	0	0	0	0	0	0	0	1	266	407	15	2		2	ADAMTS20	12	43748039	Silent	SNP	A	TCGA-5R-AA1D-01A-11D-A382-10		43748039	90103856	7	3607										
APOF	319	hgsc.bcm.edu	37	chr12	56755172	56755172	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	ccctcaaaccctccttggtgGtctccggctgagagatgttt	10	13	2	2			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr12:56755172G>A	ENST00000398189.3	-	2	895	c.818C>T	c.(817-819)aCc>aTc	p.T273I	STAT2_ENST00000314128.4_5'Flank|STAT2_ENST00000418572.2_5'Flank|APOF_ENST00000541105.1_Missense_Mutation_p.T255I|STAT2_ENST00000557235.1_5'Flank	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	273					cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|high-density lipoprotein particle (GO:0034364)|low-density lipoprotein particle (GO:0034362)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)|receptor binding (GO:0005102)			breast(1)|lung(3)|prostate(1)|stomach(1)	6						CTCCTTGGTGGTCTCCGGCTG	0.473																																					p.T273I		Atlas-SNP	.											.	APOF	13	.	0			c.C818T						.						100	102	101					12																	56755172		1964	4152	6116	SO:0001583	missense	319	exon2			TTGGTGGTCTCCG	L27050	CCDS44923.1	12q13	2013-01-24				ENSG00000175336		"Apolipoproteins"	615	protein-coding gene	gene with protein product		107760				8093033	Standard	NM_001638		Approved		uc001sle.1	Q13790		ENST00000398189.3:c.818C>T	chr12.hg19:g.56755172G>A	ENSP00000381250:p.Thr273Ile	105.0	0.0		84.0	7.0	NM_001638	Q8TC13	Missense_Mutation	SNP	ENST00000398189.3	hg19	CCDS44923.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.546661	0.27652	.	.	ENSG00000175336	ENST00000398189;ENST00000541105	T;T	0.47869	0.83;0.84	5.12	-0.345	0.12624	.	1.274100	0.05849	N	0.620904	T	0.30978	0.0782	L	0.41236	1.265	0.09310	N	1	B	0.19583	0.037	B	0.17433	0.018	T	0.14615	-1.0466	10	0.09843	T	0.71	-0.4661	1.3687	0.02206	0.1962:0.3183:0.3226:0.1629	.	273	Q13790	APOF_HUMAN	I	273;255	ENSP00000381250:T273I;ENSP00000440997:T255I	ENSP00000381250:T273I	T	-	2	0	APOF	55041439	0.003000	0.15002	0.000000	0.03702	0.200000	0.23975	0.829000	0.27449	0.033000	0.15463	0.655000	0.94253	ACC	.	.		0.473	APOF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410076.1			A	56755172	G	A	56755172	3	1	28	1	0	0	0	0	1	0	0	0	803	1261	44	3	166	3	APOF	12	56755172	Missense_Mutation	SNP	G	TCGA-5R-AA1D-01A-11D-A382-10	13007133	56755172	77096723	8	3608										
HHIPL1	84439	hgsc.bcm.edu	37	chr14	100135258	100135258	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	gccgttcattttacagtggtGgaaatgagcacaaagacacg	11	8	1	2			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr14:100135258G>A	ENST00000330710.5	+	7	1828				HHIPL1_ENST00000357223.2_Nonsense_Mutation_p.W607*	NM_001127258.1	NP_001120730.1	Q96JK4	HIPL1_HUMAN	HHIP-like 1						carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|skin(2)	15		Melanoma(154;0.128)				ttacagtggtggaaatgagca	0.607																																					p.W607X		Atlas-SNP	.											.	HHIPL1	86	.	0			c.G1820A						.						61	55	57					14																	100135258		2203	4300	6503	SO:0001627	intron_variant	84439	exon8			AGTGGTGGAAATG	AB058725	CCDS9953.1, CCDS45162.1	14q32	2008-01-16	2008-01-16	2008-01-16		ENSG00000182218			19710	protein-coding gene	gene with protein product			"KIAA1822"	KIAA1822			Standard	NM_032425		Approved		uc010avs.3	Q96JK4		ENST00000330710.5:c.1730+618G>A	chr14.hg19:g.100135258G>A		56.0	0.0		45.0	12.0	NM_032425	A2RUF8|B2RN09|Q6UXX2	Nonsense_Mutation	SNP	ENST00000330710.5	hg19	CCDS45162.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.808904	0.50421	.	.	ENSG00000182218	ENST00000357223	.	.	.	1.49	0.549	0.17213	.	5.116030	0.00868	U	0.001997	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.8652	0.09013	0.2445:0.0:0.7555:0.0	.	.	.	.	X	607	.	ENSP00000349757:W607X	W	+	2	0	HHIPL1	99205011	0.000000	0.05858	0.008000	0.14137	0.040000	0.13550	-0.511000	0.06321	0.172000	0.19760	0.462000	0.41574	TGG	.	.		0.607	HHIPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413811.1	XM_041566		A	100135258	G	A	100135258	1	1	28	0	1	0	0	0	0	0	0	0	7102	1357	47	3		3	HHIPL1	14	100135258	Intron	SNP	G	TCGA-5R-AA1D-01A-11D-A382-10		100135258	7214282	9	3609										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24921813	24921813	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	cagcgccccctgagccagccGttggctgctccctgctgcag	12	18	0	1			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr15:24921813G>A	ENST00000329468.2	+	1	1273	c.799G>A	c.(799-801)Gtt>Att	p.V267I		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	267					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											TGAGCCAGCCGTTGGCTGCTC	0.632																																					p.V267I		Atlas-SNP	.											C15orf2,NS,carcinoma,0,1	.	.	.	0			c.G799A						.						33	36	35					15																	24921813		2198	4293	6491	SO:0001583	missense	23742	exon1			CCAGCCGTTGGCT	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.799G>A	chr15.hg19:g.24921813G>A	ENSP00000333735:p.Val267Ile	87.0	0.0		80.0	7.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	6.795	0.515772	0.12944	.	.	ENSG00000185823	ENST00000329468	T	0.11821	2.74	1.39	0.392	0.16288	.	1.238710	0.06258	N	0.693365	T	0.06416	0.0165	N	0.08118	0	0.09310	N	1	B	0.30526	0.283	B	0.16289	0.015	T	0.34304	-0.9834	10	0.66056	D	0.02	.	5.3252	0.15903	0.0:0.6174:0.3826:0.0	.	267	Q9NZP6	CO002_HUMAN	I	267	ENSP00000333735:V267I	ENSP00000333735:V267I	V	+	1	0	C15orf2	22472906	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.832000	0.01696	0.143000	0.18926	-0.662000	0.03851	GTT	.	.		0.632	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24921813	G	A	24921813	3	1	28	1	0	0	0	0	1	0	0	0	1786	1145	40	1	801	1	C15orf2	15	24921813	Missense_Mutation	SNP	G	TCGA-5R-AA1D-01A-11D-A382-10		24921813	77609579	10	3610										
OTUD7A	161725	hgsc.bcm.edu	37	chr15	31776670	31776670	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	atcttgccgtgcaccaggccGccgaggccgcccatgttttt	11	15	1	0			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr15:31776670G>A	ENST00000307050.4	-	11	1700	c.1608C>T	c.(1606-1608)ggC>ggT	p.G536G	OTUD7A_ENST00000382902.1_Silent_p.G543G	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	536					protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		GCACCAGGCCGCCGAGGCCGC	0.647																																					p.G536G		Atlas-SNP	.											.	OTUD7A	89	.	0			c.C1608T						.						59	56	57					15																	31776670		2202	4300	6502	SO:0001819	synonymous_variant	161725	exon11			CAGGCCGCCGAGG	AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918		"OTU domain containing"	20718	protein-coding gene	gene with protein product		612024	"chromosome 15 open reading frame 16", "OTU domain containing 7", "OTU domain containing 7A"	C15orf16, OTUD7		23827681	Standard	NM_130901		Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.1608C>T	chr15.hg19:g.31776670G>A		18.0	0.0		27.0	7.0	NM_130901	Q8IWK5	Silent	SNP	ENST00000307050.4	hg19	CCDS10026.1																																																																																			.	.		0.647	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901		A	31776670	G	A	31776670	2	1	28	1	0	0	0	0	0	0	0	1	11327	1074	38	1		1	OTUD7A	15	31776670	Silent	SNP	G	TCGA-5R-AA1D-01A-11D-A382-10	6854857	31776670	70754722	11	3611										
HIRIP3	8479	hgsc.bcm.edu	37	chr16	30006907	30006907	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	agctacgggtgaactcctgcAtctccttctcccgcgccatt	8	16	2	1			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr16:30006907A>G	ENST00000279392.3	-	1	850	c.20T>C	c.(19-21)aTg>aCg	p.M7T	INO80E_ENST00000567705.1_5'Flank|INO80E_ENST00000563197.1_5'UTR|HIRIP3_ENST00000566471.1_5'UTR|HIRIP3_ENST00000564026.1_Missense_Mutation_p.M7T|INO80E_ENST00000304516.7_5'Flank|INO80E_ENST00000567254.1_5'Flank	NM_003609.4	NP_003600.2	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3	7					chromatin assembly or disassembly (GO:0006333)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(9)	17						GAACTCCTGCATCTCCTTCTC	0.652																																					p.M7T		Atlas-SNP	.											.	HIRIP3	45	.	0			c.T20C						.						77	73	74					16																	30006907		2197	4300	6497	SO:0001583	missense	8479	exon1			TCCTGCATCTCCT	AJ223351	CCDS10664.1, CCDS58449.1	16p12.1	2008-02-05	2001-11-29		ENSG00000149929	ENSG00000149929			4917	protein-coding gene	gene with protein product		603365	"HIRA-interacting protein 3"			9710638	Standard	NM_003609		Approved		uc002dve.3	Q9BW71	OTTHUMG00000132118	ENST00000279392.3:c.20T>C	chr16.hg19:g.30006907A>G	ENSP00000279392:p.Met7Thr	116.0	0.0		105.0	26.0	NM_001197323	H3BSR3|O75707|O75708	Missense_Mutation	SNP	ENST00000279392.3	hg19	CCDS10664.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.219737	0.79464	.	.	ENSG00000149929	ENST00000279392;ENST00000352552	T	0.38240	1.15	5.45	5.45	0.79879	.	0.109676	0.64402	D	0.000013	T	0.47600	0.1454	M	0.61703	1.905	0.80722	D	1	P;D	0.63880	0.952;0.993	P;P	0.52109	0.521;0.69	T	0.50591	-0.8810	10	0.66056	D	0.02	-15.9284	13.5297	0.61615	1.0:0.0:0.0:0.0	.	7;7	B2R6A9;Q9BW71	.;HIRP3_HUMAN	T	7	ENSP00000279392:M7T	ENSP00000279392:M7T	M	-	2	0	HIRIP3	29914408	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.992000	0.49417	2.288000	0.76882	0.528000	0.53228	ATG	.	.		0.652	HIRIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255160.2	NM_003609		G	30006907	A	G	30006907	3	3	28	1	0	0	0	0	1	0	0	0	7130	217	8	2	1678	2	HIRIP3	16	30006907	Missense_Mutation	SNP	A	TCGA-5R-AA1D-01A-11D-A382-10		30006907	60347846	12	3612										
CLTC	1213	hgsc.bcm.edu	37	chr17	57761270	57761270	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	actggtgaaaccgtatttgcGttcagttcagaaccataaca	8	9	2	2			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr17:57761270G>A	ENST00000269122.3	+	28	4632	c.4358G>A	c.(4357-4359)cGt>cAt	p.R1453H	CLTC_ENST00000579456.1_Missense_Mutation_p.R390H|CLTC_ENST00000393043.1_Missense_Mutation_p.R1453H	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	1453	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CCGTATTTGCGTTCAGTTCAG	0.328			T	"ALK, TFE3"	"ALCL, renal "																																p.R1453H		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.G4358A						.						73	69	71					17																	57761270		2203	4300	6503	SO:0001583	missense	1213	exon28			ATTTGCGTTCAGT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.4358G>A	chr17.hg19:g.57761270G>A	ENSP00000269122:p.Arg1453His	194.0	0.0		195.0	8.0	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.052072	0.75960	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.20463	2.07;2.07	5.55	5.55	0.83447	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.53981	0.1830	M	0.87547	2.89	0.80722	D	1	D;B	0.71674	0.998;0.048	D;B	0.74023	0.982;0.046	T	0.55768	-0.8089	10	0.45353	T	0.12	.	19.8621	0.96787	0.0:0.0:1.0:0.0	.	1453;1453	Q00610;Q00610-2	CLH1_HUMAN;.	H	1453	ENSP00000269122:R1453H;ENSP00000376763:R1453H	ENSP00000269122:R1453H	R	+	2	0	CLTC	55116052	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.770000	0.95276	0.563000	0.77884	CGT	.	.		0.328	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		A	57761270	G	A	57761270	3	1	28	1	0	0	0	0	1	0	0	0	3568	1145	40	1	4468	1	CLTC	17	57761270	Missense_Mutation	SNP	G	TCGA-5R-AA1D-01A-11D-A382-10		57761270	23433940	13	3613										
RYR1	6261	hgsc.bcm.edu	37	chr19	38964339	38964340	+	Frame_Shift_Ins	INS	-	-	GGGGG													0.125	2	1	1.4	3.5	0.875	1	1	0	cccgggggcaccccgcaggcINSggggggagaggcgcagcccg							TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr19:38964339_38964340insGGGGG	ENST00000359596.3	+	28	4088_4089	c.4088_4089insGGGGG	c.(4087-4092)gcggggfs	p.-1365fs	RYR1_ENST00000360985.3_Frame_Shift_Ins_p.-1365fs|RYR1_ENST00000355481.4_Frame_Shift_Ins_p.-1365fs			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)						calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACCCCGCAGGCGGGGGGAGAGG	0.678																																					p.A1363fs		Atlas-INDEL	.											.	RYR1	708	.	0			c.4088_4089insGGGGG						.																																			SO:0001589	frameshift_variant	6261	exon28			.	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.4089_4093dupGGGGG	chr19.hg19:g.38964340_38964344dupGGGGG	ENSP00000352608:p.Gly1365fs	326.0	0.0		241.0	20.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Frame_Shift_Ins	INS	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.678	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			GGGGG	38964340	-	GGGGG	38964339	7	5	28	1	0	1	1	0	0	0	0	0	13783	768	27	0	4198	0	RYR1	19	38964339	Frame_Shift_Ins	INS	-	TCGA-5R-AA1D-01A-11D-A382-10		38964339	20164644	14	3614										
RALY	22913	hgsc.bcm.edu	37	chr20	32664865	32664865	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.125	2	1	1.4	3.5	0.875	1	1	0	aagggtgatggaggtggcgcCggcggcggcggcggtggtgg	25	7	0	1	rs57852506	byFrequency	TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr20:32664865C>T	ENST00000246194.3	+	8	1192	c.690C>T	c.(688-690)gcC>gcT	p.A230A	RALY_ENST00000375114.3_Silent_p.A214A	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	230	Epitope (recognized by BKRF1 antibodies).|Poly-Gly.			A -> AS (in Ref. 2; AAC28898). {ECO:0000305}.	mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						GAggtggcgccggcggcggcg	0.662																																					p.A230A		Atlas-SNP	.											.,1	RALY	44	.	0			c.C690T						.						6	8	7					20																	32664865		2110	4142	6252	SO:0001819	synonymous_variant	22913	exon8			TGGCGCCGGCGGC	AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"RNA binding motif (RRM) containing"	15921	protein-coding gene	gene with protein product		614663	"RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)", "RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	ENST00000246194.3:c.690C>T	chr20.hg19:g.32664865C>T		126.0	0.0		112.0	0.0	NM_016732	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	Silent	SNP	ENST00000246194.3	hg19	CCDS13230.1																																																																																			.	.		0.662	RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1			T	32664865	C	T	32664865	2	4	28	1	0	0	0	0	0	0	0	1	13034	639	23	1		1	RALY	20	32664865	Silent	SNP	C	TCGA-5R-AA1D-01A-11D-A382-10		32664865	30360655	15	3615										
FAM3A	60343	hgsc.bcm.edu	37	chrX	153735650	153735650	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.125	2	1	1.4	3.5	0.875	1	1	0	actgaagagctttctggtctCttcattcatcctgcagcatg	8	11	4	2			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chrX:153735650C>G	ENST00000447601.2	-	8	947	c.481G>C	c.(481-483)Gag>Cag	p.E161Q	FAM3A_ENST00000369643.1_Missense_Mutation_p.E161Q|FAM3A_ENST00000492763.1_5'Flank|FAM3A_ENST00000359889.5_Missense_Mutation_p.E161Q|FAM3A_ENST00000393572.1_Missense_Mutation_p.E123Q|FAM3A_ENST00000369641.3_Missense_Mutation_p.E168Q|FAM3A_ENST00000434658.2_Missense_Mutation_p.E144Q	NM_021806.2	NP_068578.2	P98173	FAM3A_HUMAN	family with sequence similarity 3, member A	161						extracellular region (GO:0005576)				kidney(2)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TTTCTGGTCTCTTCATTCATC	0.602																																					p.E161Q		Atlas-SNP	.											.	FAM3A	11	.	0			c.G481C						.						64	53	57					X																	153735650		2203	4300	6503	SO:0001583	missense	60343	exon9			TGGTCTCTTCATT	X74610	CCDS35453.1, CCDS55542.1, CCDS55543.1, CCDS76060.1	Xq28	2008-07-29			ENSG00000071889	ENSG00000071889			13749	protein-coding gene	gene with protein product		300492				8733135, 8281148	Standard	NM_021806		Approved	DXS560S, 2-19, XAP-7	uc004fls.2	P98173	OTTHUMG00000013418	ENST00000447601.2:c.481G>C	chrX.hg19:g.153735650C>G	ENSP00000416146:p.Glu161Gln	128.0	0.0		99.0	13.0	NM_001171132	A6QRH6|B2RBI7|B4DFI8|D3DWX4|Q5HY76|Q96H51	Missense_Mutation	SNP	ENST00000447601.2	hg19	CCDS35453.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.753475	0.89753	.	.	ENSG00000071889	ENST00000434658;ENST00000359889;ENST00000369643;ENST00000447601;ENST00000369641;ENST00000393572	T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88	5.06	5.06	0.68205	.	0.050323	0.85682	D	0.000000	T	0.50069	0.1594	M	0.72894	2.215	0.58432	D	0.999999	D;D;D;D	0.76494	0.961;0.997;0.999;0.987	P;D;D;D	0.71184	0.756;0.972;0.972;0.913	T	0.51576	-0.8688	10	0.51188	T	0.08	-18.7323	16.2748	0.82638	0.0:1.0:0.0:0.0	.	144;168;175;161	B4DFI8;Q5HY75;D3DWX8;P98173	.;.;.;FAM3A_HUMAN	Q	144;161;161;161;168;123	ENSP00000396243:E144Q;ENSP00000352955:E161Q;ENSP00000358657:E161Q;ENSP00000416146:E161Q;ENSP00000358655:E168Q;ENSP00000377202:E123Q	ENSP00000352955:E161Q	E	-	1	0	FAM3A	153388844	1.000000	0.71417	0.990000	0.47175	0.990000	0.78478	5.610000	0.67668	2.094000	0.63399	0.529000	0.55759	GAG	.	.		0.602	FAM3A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037362.2			G	153735650	C	G	153735650	3	3	28	1	0	0	0	0	1	0	0	0	5564	922	32	4	219	4	FAM3A	23	153735650	Missense_Mutation	SNP	C	TCGA-5R-AA1D-01A-11D-A382-10		153735650	1534910	16	3616										
EPHA2	1969	hgsc.bcm.edu	37	chr1	16464471	16464471	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ctccaggtcgctcactgtcaCactggtgcgggtcagtccgt	12	14	3	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:16464471C>T	ENST00000358432.5	-	5	1343	c.1189G>A	c.(1189-1191)Gtg>Atg	p.V397M		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	397	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	CTCACTGTCACACTGGTGCGG	0.647																																					p.V397M		Atlas-SNP	.											.	EPHA2	102	.	0			c.G1189A						.						64	60	61					1																	16464471		2203	4300	6503	SO:0001583	missense	1969	exon5			CTGTCACACTGGT	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3386	protein-coding gene	gene with protein product		176946	"EphA2"	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.1189G>A	chr1.hg19:g.16464471C>T	ENSP00000351209:p.Val397Met	81.0	0.0		52.0	7.0	NM_004431	B5A968|Q8N3Z2	Missense_Mutation	SNP	ENST00000358432.5	hg19	CCDS169.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.949706	0.53186	.	.	ENSG00000142627	ENST00000358432	T	0.60424	0.19	4.97	3.04	0.35103	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.434432	0.19393	N	0.115344	T	0.71953	0.3401	M	0.86097	2.795	0.53005	D	0.999967	D;P	0.61697	0.99;0.482	P;B	0.60286	0.872;0.22	T	0.72408	-0.4303	10	0.87932	D	0	.	8.0626	0.30642	0.0:0.3706:0.5279:0.1016	.	397;397	B5A968;P29317	.;EPHA2_HUMAN	M	397	ENSP00000351209:V397M	ENSP00000351209:V397M	V	-	1	0	EPHA2	16337058	0.920000	0.31207	0.965000	0.40720	0.542000	0.35054	2.129000	0.42055	0.593000	0.29745	0.561000	0.74099	GTG	.	.		0.647	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431		T	16464471	C	T	16464471	3	4	29	1	0	0	0	0	1	0	0	0	5169	478	17	3	1793	3	EPHA2	1	16464471	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10		16464471	232786150	1	3617										
INADL	10207	hgsc.bcm.edu	37	chr1	62232108	62232108	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gtggaccccgaagttgggaaAtgaagactttaactcagtca	11	8	2	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:62232108A>G	ENST00000371158.2	+	4	461	c.347A>G	c.(346-348)aAt>aGt	p.N116S	INADL_ENST00000316485.6_Missense_Mutation_p.N116S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	116					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AAGTTGGGAAATGAAGACTTT	0.398																																					p.N116S		Atlas-SNP	.											.	INADL	179	.	0			c.A347G						.						101	98	99					1																	62232108		2203	4300	6503	SO:0001583	missense	10207	exon4			TGGGAAATGAAGA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.347A>G	chr1.hg19:g.62232108A>G	ENSP00000360200:p.Asn116Ser	78.0	0.0		73.0	22.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	3.841	-0.033772	0.07543	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.11604	2.89;2.76	6.08	3.72	0.42706	.	0.397923	0.26173	N	0.025908	T	0.06962	0.0177	L	0.36672	1.1	0.80722	D	1	B;B;B	0.15473	0.01;0.006;0.013	B;B;B	0.14023	0.01;0.003;0.003	T	0.22347	-1.0219	10	0.07325	T	0.83	.	5.8951	0.18935	0.7139:0.0:0.1368:0.1493	.	116;116;116	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	S	116	ENSP00000360200:N116S;ENSP00000326199:N116S	ENSP00000255202:N116S	N	+	2	0	INADL	62004696	1.000000	0.71417	0.999000	0.59377	0.716000	0.41182	1.692000	0.37731	0.512000	0.28257	0.482000	0.46254	AAT	.	.		0.398	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62232108	A	G	62232108	3	3	29	1	0	0	0	0	1	0	0	0	7740	101	4	2	357	2	INADL	1	62232108	Missense_Mutation	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10	45767637	62232108	187018513	2	3618										
CHIA	27159	hgsc.bcm.edu	37	chr1	111854972	111854972	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	atcaccaccatcgaatggaaTgatgtgactctctaccaagc	7	12	2	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:111854972T>G	ENST00000369740.1	+	4	319	c.216T>G	c.(214-216)aaT>aaG	p.N72K	CHIA_ENST00000353665.6_Intron|CHIA_ENST00000451398.2_Intron|CHIA_ENST00000343320.6_Missense_Mutation_p.N72K|CHIA_ENST00000430615.1_Intron|CHIA_ENST00000483391.1_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	72					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TCGAATGGAATGATGTGACTC	0.468																																					p.N72K		Atlas-SNP	.											.	CHIA	115	.	0			c.T216G						.						121	116	118					1																	111854972		1987	4156	6143	SO:0001583	missense	27159	exon4			ATGGAATGATGTG	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.216T>G	chr1.hg19:g.111854972T>G	ENSP00000358755:p.Asn72Lys	94.0	0.0		105.0	16.0	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	hg19	CCDS41368.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.692421	0.48202	.	.	ENSG00000134216	ENST00000369740;ENST00000343320	T;T	0.05319	3.46;3.46	4.93	0.785	0.18584	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.163676	0.37577	U	0.002031	T	0.05502	0.0145	M	0.76938	2.355	0.80722	D	1	B	0.33135	0.399	P	0.44897	0.463	T	0.13495	-1.0507	10	0.51188	T	0.08	-2.086	3.7062	0.08401	0.1626:0.2275:0.0:0.6098	.	72	Q9BZP6	CHIA_HUMAN	K	72	ENSP00000358755:N72K;ENSP00000341828:N72K	ENSP00000341828:N72K	N	+	3	2	CHIA	111656495	0.183000	0.23186	0.946000	0.38457	0.689000	0.40095	-0.524000	0.06222	0.280000	0.22209	-0.274000	0.10170	AAT	.	.		0.468	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			G	111854972	T	G	111854972	3	3	29	1	0	0	0	0	1	0	0	0	3344	1461	51	5	226	5	CHIA	1	111854972	Missense_Mutation	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	49622864	111854972	137395649	3	3619										
ZNF687	57592	hgsc.bcm.edu	37	chr1	151258832	151258832	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ctttgacatccctgacattgAtgcgaatgaagccatccatt	7	11	0	4			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:151258832A>G	ENST00000368879.2	+	2	163	c.65A>G	c.(64-66)gAt>gGt	p.D22G		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	22					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CCTGACATTGATGCGAATGAA	0.512																																					p.D22G		Atlas-SNP	.											.	ZNF687	94	.	0			c.A65G						.						101	104	103					1																	151258832		2203	4300	6503	SO:0001583	missense	57592	exon2			ACATTGATGCGAA		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.65A>G	chr1.hg19:g.151258832A>G	ENSP00000357874:p.Asp22Gly	89.0	0.0		85.0	13.0	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Missense_Mutation	SNP	ENST00000368879.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.38	3.107408	0.56291	.	.	ENSG00000143373	ENST00000443959;ENST00000336715;ENST00000324048;ENST00000368879	T;T;T	0.01998	4.51;4.51;4.8	4.43	3.28	0.37604	.	0.000000	0.36555	N	0.002538	T	0.05318	0.0141	M	0.74881	2.28	0.44985	D	0.998	D;D;D	0.71674	0.998;0.993;0.996	D;D;D	0.81914	0.995;0.984;0.993	T	0.06698	-1.0812	10	0.87932	D	0	.	9.4423	0.38677	0.8407:0.0:0.0:0.1593	.	22;22;22	Q8N1G0-2;Q8N1G0;F8WCX2	.;ZN687_HUMAN;.	G	31;22;22;22	ENSP00000336620:D22G;ENSP00000319829:D22G;ENSP00000357874:D22G	ENSP00000319829:D22G	D	+	2	0	ZNF687	149525456	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	5.787000	0.69013	0.725000	0.32318	0.260000	0.18958	GAT	.	.		0.512	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		G	151258832	A	G	151258832	3	3	29	1	0	0	0	0	1	0	0	0	18107	333	12	2	67	2	ZNF687	1	151258832	Missense_Mutation	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10	39403860	151258832	97991789	4	3620										
CD1B	910	hgsc.bcm.edu	37	chr1	158299379	158299379	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gaatcctgagacatggcacaCaagctgcagacggccaggtc	12	12	0	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:158299379C>T	ENST00000368168.3	-	4	774	c.667G>A	c.(667-669)Gtg>Atg	p.V223M		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	223	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					ACATGGCACACAAGCTGCAGA	0.572																																					p.V223M		Atlas-SNP	.											.	CD1B	78	.	0			c.G667A						.						75	73	74					1																	158299379		2203	4300	6503	SO:0001583	missense	910	exon4			GGCACACAAGCTG	M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1635	protein-coding gene	gene with protein product		188360	"CD1B antigen, b polypeptide", "CD1b antigen"	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.667G>A	chr1.hg19:g.158299379C>T	ENSP00000357150:p.Val223Met	157.0	0.0		141.0	7.0	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Missense_Mutation	SNP	ENST00000368168.3	hg19	CCDS1176.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.06|17.06	3.292699|3.292699	0.59976|0.59976	.|.	.|.	ENSG00000158485|ENSG00000158485	ENST00000451207|ENST00000368168	.|T	.|0.03413	.|3.94	4.26|4.26	2.13|2.13	0.27403|0.27403	.|Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	.|0.202721	.|0.24698	.|N	.|0.036334	T|T	0.11110|0.11110	0.0271|0.0271	M|M	0.89601|0.89601	3.045|3.045	0.30264|0.30264	N|N	0.792917|0.792917	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.83275	.|0.996;0.987	T|T	0.01182|0.01182	-1.1426|-1.1426	5|10	.|0.72032	.|D	.|0.01	-22.564|-22.564	9.9076|9.9076	0.41386|0.41386	0.0:0.5921:0.4079:0.0|0.0:0.5921:0.4079:0.0	.|.	.|223;223	.|P29016;P29016-2	.|CD1B_HUMAN;.	Y|M	190|223	.|ENSP00000357150:V223M	.|ENSP00000357150:V223M	C|V	-|-	2|1	0|0	CD1B|CD1B	156566003|156566003	0.722000|0.722000	0.28017|0.28017	0.999000|0.999000	0.59377|0.59377	0.968000|0.968000	0.65278|0.65278	0.581000|0.581000	0.23819|0.23819	1.078000|1.078000	0.41014|0.41014	0.655000|0.655000	0.94253|0.94253	TGT|GTG	.	.		0.572	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764		T	158299379	C	T	158299379	3	4	29	1	0	0	0	0	1	0	0	0	2977	478	17	3	346	3	CD1B	1	158299379	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	7040547	158299379	90951242	5	3621										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158585118	158585118	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tttgatatcaaggatcagagCgtcttccaagttgtccccca	8	11	3	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:158585118C>T	ENST00000368147.4	-	48	6856	c.6676G>A	c.(6676-6678)Gct>Act	p.A2226T		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2226					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGGATCAGAGCGTCTTCCAAG	0.498																																					p.A2226T		Atlas-SNP	.											SPTA1,caecum,carcinoma,0,2	SPTA1	720	.	0			c.G6676A						.						188	190	189					1																	158585118		2014	4196	6210	SO:0001583	missense	6708	exon48			TCAGAGCGTCTTC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6676G>A	chr1.hg19:g.158585118C>T	ENSP00000357129:p.Ala2226Thr	111.0	0.0		122.0	16.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.157605	0.78114	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.52526	0.66;0.66	5.54	5.54	0.83059	.	0.000000	0.32120	N	0.006555	T	0.46833	0.1413	M	0.67953	2.075	0.52099	D	0.999943	P	0.51537	0.946	P	0.51777	0.679	T	0.28299	-1.0048	10	0.15066	T	0.55	.	18.234	0.89944	0.0:1.0:0.0:0.0	.	2226	P02549	SPTA1_HUMAN	T	2226;2223	ENSP00000357130:A2226T;ENSP00000357129:A2223T	ENSP00000357129:A2223T	A	-	1	0	SPTA1	156851742	1.000000	0.71417	1.000000	0.80357	0.358000	0.29455	7.104000	0.77024	2.884000	0.98904	0.655000	0.94253	GCT	.	.		0.498	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158585118	C	T	158585118	3	4	29	1	0	0	0	0	1	0	0	0	15131	768	27	1	603	1	SPTA1	1	158585118	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	285739	158585118	90665503	6	3622										
ATP1A4	480	hgsc.bcm.edu	37	chr1	160128807	160128807	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	catagcaagctctggtaattCgaggaggagagaagatgcaa	13	6	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:160128807C>A	ENST00000368081.4	+	5	1012	c.541C>A	c.(541-543)Cga>Aga	p.R181R		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	181					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TCTGGTAATTCGAGGAGGAGA	0.468																																					p.R181R		Atlas-SNP	.											.	ATP1A4	167	.	0			c.C541A						.						94	84	87					1																	160128807		2203	4300	6503	SO:0001819	synonymous_variant	480	exon5			GTAATTCGAGGAG	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.541C>A	chr1.hg19:g.160128807C>A		133.0	0.0		125.0	48.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	hg19	CCDS1197.1																																																																																			.	.		0.468	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		A	160128807	C	A	160128807	2	1	29	1	0	0	0	0	0	0	0	1	1131	876	31	1		1	ATP1A4	1	160128807	Silent	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	1543689	160128807	89121814	7	3623										
C1orf114	57821	hgsc.bcm.edu	37	chr1	169391306	169391306	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ataatatatctccttacttcCtcatcctcttcctcctccaa	0	16	3	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:169391306C>G	ENST00000367806.3	-	3	515	c.363G>C	c.(361-363)gaG>gaC	p.E121D	CCDC181_ENST00000545005.1_Missense_Mutation_p.E121D|CCDC181_ENST00000367805.3_Missense_Mutation_p.E121D|CCDC181_ENST00000491570.1_5'UTR	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	121	Poly-Glu.					nucleus (GO:0005634)											TCCTTACTTCCTCATCCTCTT	0.383																																					p.E121D		Atlas-SNP	.											.	C1orf114	67	.	0			c.G363C						.						79	81	80					1																	169391306		2203	4300	6503	SO:0001583	missense	57821	exon3			TACTTCCTCATCC	AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 114"	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.363G>C	chr1.hg19:g.169391306C>G	ENSP00000356780:p.Glu121Asp	97.0	0.0		98.0	9.0	NM_021179	O60780|Q53FD5|Q5TID9|Q8TC48	Missense_Mutation	SNP	ENST00000367806.3	hg19		.	.	.	.	.	.	.	.	.	.	C	13.41	2.228427	0.39399	.	.	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005;ENST00000456107	T;T;T;T	0.55930	1.24;1.24;1.24;0.49	5.34	2.48	0.30137	.	0.000000	0.85682	D	0.000000	T	0.48484	0.1502	L	0.56769	1.78	0.34676	D	0.724226	D;D;D	0.89917	0.968;1.0;1.0	P;D;D	0.83275	0.708;0.996;0.996	T	0.46456	-0.9190	9	0.27082	T	0.32	-17.1823	7.3304	0.26580	0.0:0.5185:0.0:0.4815	.	121;121;121	Q5TID7-2;Q5TID7;Q5TID7-3	.;CA114_HUMAN;.	D	121	ENSP00000356779:E121D;ENSP00000356780:E121D;ENSP00000442297:E121D;ENSP00000411000:E121D	ENSP00000356779:E121D	E	-	3	2	C1orf114	167657930	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	0.670000	0.25157	0.258000	0.21686	0.563000	0.77884	GAG	.	.		0.383	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179		G	169391306	C	G	169391306	3	3	29	1	0	0	0	0	1	0	0	0	1989	680	24	4	1179	4	C1orf114	1	169391306	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	9262499	169391306	79859315	8	3624										
NR5A2	2494	hgsc.bcm.edu	37	chr1	200008803	200008803	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	caggtgctgggcttccggacCgacacggatcccccatcccc	11	18	0	0	rs537463980		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:200008803C>T	ENST00000367362.3	+	2	328	c.82C>T	c.(82-84)Cga>Tga	p.R28*	NR5A2_ENST00000544748.1_5'Flank|NR5A2_ENST00000236914.3_Intron	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	28					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					GCTTCCGGACCGACACGGATC	0.652																																					p.C28C	Melanoma(179;1138 2773 15678 26136)	Atlas-SNP	.											.	NR5A2	83	.	0			c.T82T						.						52	60	57					1																	200008803		2203	4300	6503	SO:0001587	stop_gained	2494	exon2			CCGGACCGACACG	U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"Nuclear hormone receptors"	7984	protein-coding gene	gene with protein product	"liver receptor homolog-1"	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.82C>T	chr1.hg19:g.200008803C>T	ENSP00000356331:p.Arg28*	169.0	0.0		191.0	51.0	NM_205860	B4E2P3|O95642|Q147U3	Silent	SNP	ENST00000367362.3	hg19	CCDS1401.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.43|11.43	1.636687|1.636687	0.29068|0.29068	.|.	.|.	ENSG00000116833|ENSG00000116833	ENST00000447034|ENST00000367362;ENST00000542116	.|.	.|.	.|.	5.02|5.02	-1.91|-1.91	0.07641|0.07641	.|.	.|0.569224	.|0.14329	.|N	.|0.326478	T|.	0.42966|.	0.1226|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.28038|.	-1.0056|.	4|.	.|.	.|.	.|.	.|.	4.0574|4.0574	0.09823|0.09823	0.1795:0.4258:0.3028:0.0919|0.1795:0.4258:0.3028:0.0919	.|.	.|.	.|.	.|.	L|X	40|28;52	.|.	.|.	P|R	+|+	2|1	0|2	NR5A2|NR5A2	198275426|198275426	0.020000|0.020000	0.18652|0.18652	0.396000|0.396000	0.26296|0.26296	0.173000|0.173000	0.22820|0.22820	0.061000|0.061000	0.14366|0.14366	-0.384000|-0.384000	0.07845|0.07845	-0.142000|-0.142000	0.14014|0.14014	CCG|CGA	.	.		0.652	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2			T	200008803	C	T	200008803	4	4	29	1	0	0	0	0	0	1	0	0	10645	644	23	1	88	1	NR5A2	1	200008803	Nonsense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	30617497	200008803	49241818	9	3625										
USH2A	7399	hgsc.bcm.edu	37	chr1	215848027	215848027	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gagagtaaggctgcaggtggGaaaccagcaggcacaggccc	16	10	0	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:215848027G>A	ENST00000307340.3	-	63	13612	c.13226C>T	c.(13225-13227)tCc>tTc	p.S4409F	USH2A_ENST00000366943.2_Missense_Mutation_p.S4409F	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4409	Fibronectin type-III 29. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTGCAGGTGGGAAACCAGCAG	0.483										HNSCC(13;0.011)																											p.S4409F		Atlas-SNP	.											USH2A,NS,malignant_melanoma,0,1	USH2A	1168	.	0			c.C13226T						.						71	73	72					1																	215848027		2203	4300	6503	SO:0001583	missense	7399	exon63			AGGTGGGAAACCA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.13226C>T	chr1.hg19:g.215848027G>A	ENSP00000305941:p.Ser4409Phe	61.0	0.0		94.0	29.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.911594	0.52439	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.58940	0.3;0.3	4.82	4.82	0.62117	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41938	U	0.000793	T	0.73125	0.3547	M	0.86651	2.83	0.23023	N	0.998418	D	0.54772	0.968	P	0.55999	0.789	T	0.68985	-0.5265	10	0.56958	D	0.05	.	12.7065	0.57063	0.0798:0.0:0.9202:0.0	.	4409	O75445	USH2A_HUMAN	F	4409	ENSP00000305941:S4409F;ENSP00000355910:S4409F	ENSP00000305941:S4409F	S	-	2	0	USH2A	213914650	0.985000	0.35326	0.012000	0.15200	0.873000	0.50193	3.689000	0.54706	2.384000	0.81235	0.467000	0.42956	TCC	.	.		0.483	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	215848027	G	A	215848027	3	1	29	1	0	0	0	0	1	0	0	0	17051	1174	41	3	2422	3	USH2A	1	215848027	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	15839224	215848027	33402594	10	3626										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227222368	227222369	+	Frame_Shift_Ins	INS	-	-	C													0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ctcttacctcatgtcaatcaINScttgactaatgacaacactg							TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:227222368_227222369insC	ENST00000366769.3	-	25	4649_4650	c.3358_3359insG	c.(3358-3360)gtgfs	p.V1120fs	CDC42BPA_ENST00000366766.2_Frame_Shift_Ins_p.V1155fs|CDC42BPA_ENST00000334218.5_Frame_Shift_Ins_p.V1120fs|CDC42BPA_ENST00000366767.3_Frame_Shift_Ins_p.V1039fs|CDC42BPA_ENST00000366764.2_Frame_Shift_Ins_p.V1092fs|CDC42BPA_ENST00000366765.3_Frame_Shift_Ins_p.V1133fs|CDC42BPA_ENST00000535525.1_Frame_Shift_Ins_p.V1100fs	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				CATGTCAATCACTTGACTAATG	0.371																																					p.V1120fs		Atlas-Indel,Pindel	.											.	CDC42BPA	528	.	0			c.3359_3360insG						.																																			SO:0001589	frameshift_variant	8476	exon25			.	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.3359dupG	chr1.hg19:g.227222369_227222369dupC	ENSP00000355731:p.Val1120fs	52.0	0.0		54.0	15.0	NM_003607		Frame_Shift_Ins	INS	ENST00000366769.3	hg19	CCDS1558.1																																																																																			.	.		0.371	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		C	227222369	-	C	227222368	7	5	29	1	0	1	1	0	0	0	0	0	3074	159	6	0	1848	0	CDC42BPA	1	227222368	Frame_Shift_Ins	INS	-	TCGA-5R-AAAM-01A-12D-A40R-10	11374341	227222368	22028253	11	3627										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32750591	32750591	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	acctcgcccaccatccaggaGggggaggacaatacctgata	11	13	0	1	rs553403645		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:32750591G>A	ENST00000421745.2	+	59	11950	c.11816G>A	c.(11815-11817)aGg>aAg	p.R3939K		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3939					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CCATCCAGGAGGGGGAGGACA	0.448																																					p.R3939K	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.G11816A						.						94	91	92					2																	32750591		2203	4300	6503	SO:0001583	missense	57448	exon59			CCAGGAGGGGGAG	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.11816G>A	chr2.hg19:g.32750591G>A	ENSP00000393596:p.Arg3939Lys	158.0	0.0		165.0	9.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	16.58	3.163074	0.57476	.	.	ENSG00000115760	ENST00000421745	T	0.73152	-0.72	5.62	4.73	0.59995	.	0.111765	0.64402	D	0.000018	T	0.57242	0.2040	L	0.27053	0.805	0.58432	D	0.999993	P	0.46656	0.882	B	0.41236	0.351	T	0.55347	-0.8155	10	0.09843	T	0.71	.	16.4961	0.84246	0.0:0.1312:0.8688:0.0	.	3939	Q9NR09	BIRC6_HUMAN	K	3939	ENSP00000393596:R3939K	ENSP00000393596:R3939K	R	+	2	0	BIRC6	32604095	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.160000	0.94734	1.362000	0.46000	0.561000	0.74099	AGG	.	.		0.448	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		A	32750591	G	A	32750591	3	1	29	1	0	0	0	0	1	0	0	0	1438	1000	35	3	12050	3	BIRC6	2	32750591	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10		32750591	210448782	12	3628										
FER1L5	90342	hgsc.bcm.edu	37	chr2	97357320	97357320	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ccaacaaggacaagggcatcGcgcccatattcctcctggag	10	14	0	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:97357320G>A	ENST00000457909.1	+	0	1505							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						CAAGGGCATCGCGCCCATATT	0.667																																					p.A1009T		Atlas-SNP	.											FER1L5,caecum,carcinoma,0,1	FER1L5	113	.	0			c.G3025A						.						33	40	38					2																	97357320		692	1591	2283			90342	exon28			GGCATCGCGCCCA	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		chr2.hg19:g.97357320G>A		186.0	0.0		165.0	21.0	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	hg19		.	.	.	.	.	.	.	.	.	.	G	3.278	-0.147649	0.06627	.	.	ENSG00000214272	ENST00000414152;ENST00000436930	.	.	.	5.41	4.45	0.53987	.	.	.	.	.	T	0.64450	0.2599	M	0.68952	2.095	.	.	.	D	0.67145	0.996	P	0.50314	0.637	T	0.76870	-0.2799	7	0.87932	D	0	-10.5851	14.0812	0.64922	0.0:0.0:0.8392:0.1608	.	1009	A0AVI2	FR1L5_HUMAN	T	1009;1001	.	ENSP00000444148:A1009T	A	+	1	0	FER1L5	96721047	0.988000	0.35896	0.033000	0.17914	0.005000	0.04900	2.830000	0.48136	2.543000	0.85770	0.655000	0.94253	GCG	.	.		0.667	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		A	97357320	G	A	97357320	1	1	29	0	1	0	0	0	0	0	0	0	5822	1087	38	1		1	FER1L5	2	97357320	RNA	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	64606729	97357320	145842053	13	3629										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141473604	141473604	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ccttgggaaataattacataAcggaaagaaccattgagtct	8	7	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:141473604A>G	ENST00000389484.3	-	37	6932	c.5961T>C	c.(5959-5961)cgT>cgC	p.R1987R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1987					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TAATTACATAACGGAAAGAAC	0.348										TSP Lung(27;0.18)																											p.R1987R	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,colon,carcinoma,-2,2	LRP1B	1315	.	0			c.T5961C						.						114	120	118					2																	141473604		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon37			TACATAACGGAAA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.5961T>C	chr2.hg19:g.141473604A>G		226.0	1.0		253.0	11.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.		0.348	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141473604	A	G	141473604	2	3	29	1	0	0	0	0	0	0	0	1	8964	30	2	2		2	LRP1B	2	141473604	Silent	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10	44116284	141473604	101725769	14	3630										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098806	178098806	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gaattgggagaaattcacctGtctcttcatctagttgtaac	8	8	4	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:178098806G>A	ENST00000397062.3	-	2	793	c.239C>T	c.(238-240)aCa>aTa	p.T80I	NFE2L2_ENST00000423513.1_Missense_Mutation_p.T64I|NFE2L2_ENST00000446151.2_Missense_Mutation_p.T64I|NFE2L2_ENST00000464747.1_Missense_Mutation_p.T64I|NFE2L2_ENST00000397063.4_Missense_Mutation_p.T64I	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	80					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T80K(3)|p.T80R(2)|p.T80I(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AAATTCACCTGTCTCTTCATC	0.443			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.T80I		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,0,8	NFE2L2	225	.	6	Substitution - Missense(6)	lung(2)|oesophagus(2)|upper_aerodigestive_tract(1)|endometrium(1)	c.C239T						.						146	145	145					2																	178098806		1901	4109	6010	SO:0001583	missense	4780	exon2			TCACCTGTCTCTT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.239C>T	chr2.hg19:g.178098806G>A	ENSP00000380252:p.Thr80Ile	58.0	0.0		76.0	24.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758048	0.69648	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37;1.37	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.68109	0.2965	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.997;0.996;0.999;0.997	T	0.72623	-0.4237	10	0.87932	D	0	.	19.9976	0.97389	0.0:0.0:1.0:0.0	.	64;64;64;80	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	I	64;80;64;64;64;64;64	ENSP00000380253:T64I;ENSP00000380252:T80I;ENSP00000411575:T64I;ENSP00000391590:T64I;ENSP00000400073:T64I;ENSP00000412191:T64I;ENSP00000410015:T64I	ENSP00000380252:T80I	T	-	2	0	NFE2L2	177807052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.229000	0.95273	2.737000	0.93849	0.563000	0.77884	ACA	.	.		0.443	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		A	178098806	G	A	178098806	3	1	29	1	0	0	0	0	1	0	0	0	10377	1377	48	3	1594	3	NFE2L2	2	178098806	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	36625202	178098806	65100567	15	3631										
TTN	7273	hgsc.bcm.edu	37	chr2	179436587	179436587	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tgcatttactctagttgtctGcttcagtggtacattatctt	7	8	4	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:179436587G>A	ENST00000591111.1	-	276	69573	c.69349C>T	c.(69349-69351)Cag>Tag	p.Q23117*	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.Q15885*|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.Q24758*|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.Q15693*|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.Q22190*|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.Q15818*			Q8WZ42	TITIN_HUMAN	titin	23117	Ig-like 118.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTAGTTGTCTGCTTCAGTGGT	0.438																																					p.Q24758X		Atlas-SNP	.											.	TTN	18412	.	0			c.C74272T						.						91	96	94					2																	179436587		1926	4136	6062	SO:0001587	stop_gained	7273	exon326			TTGTCTGCTTCAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.69349C>T	chr2.hg19:g.179436587G>A	ENSP00000465570:p.Gln23117*	131.0	0.0		124.0	39.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	63	73.990175	0.99992	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	6.07	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.9885	0.86347	0.0:0.0:0.8717:0.1283	.	.	.	.	X	22190;15693;15885;15818;15691	.	ENSP00000340554:Q15885X	Q	-	1	0	TTN	179144833	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	6.054000	0.71096	1.556000	0.49512	0.650000	0.86243	CAG	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179436587	G	A	179436587	4	1	29	1	0	0	0	0	0	1	0	0	16750	1328	46	3	33855	3	TTN	2	179436587	Nonsense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	1337781	179436587	63762786	16	3632										
PAX3	5077	hgsc.bcm.edu	37	chr2	223086027	223086027	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cagtgggagggaaccccccgGgaatgagatggttgaaagcc	16	9	0	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:223086027G>T	ENST00000350526.4	-	6	1008	c.872C>A	c.(871-873)cCc>cAc	p.P291H	PAX3_ENST00000336840.6_Missense_Mutation_p.P291H|PAX3_ENST00000409551.3_Missense_Mutation_p.P290H|PAX3_ENST00000464706.1_5'UTR|PAX3_ENST00000392069.2_Missense_Mutation_p.P291H|PAX3_ENST00000392070.2_Missense_Mutation_p.P291H|PAX3_ENST00000344493.4_Missense_Mutation_p.P291H	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	291					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GAACCCCCCGGGAATGAGATG	0.522			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.P291H		Atlas-SNP	.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	PAX3	106	.	0			c.C872A						.						155	164	161					2																	223086027		2203	4300	6503	SO:0001583	missense	5077	exon6			CCCCCGGGAATGA		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.872C>A	chr2.hg19:g.223086027G>T	ENSP00000343052:p.Pro291His	142.0	0.0		161.0	26.0	NM_181457	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Missense_Mutation	SNP	ENST00000350526.4	hg19	CCDS42826.1	.	.	.	.	.	.	.	.	.	.	G	32	5.132879	0.94517	.	.	ENSG00000135903	ENST00000392069;ENST00000344493;ENST00000350526;ENST00000392070;ENST00000336840;ENST00000409551;ENST00000464706;ENST00000555548	D;D;D;D;D;D	0.95103	-3.6;-3.6;-3.59;-3.58;-3.61;-3.59	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.96728	0.8932	L	0.60455	1.87	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.994;1.0;0.999;0.999	D;P;D;D;D	0.72625	0.928;0.707;0.961;0.978;0.912	D	0.96034	0.9019	10	0.52906	T	0.07	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	291;290;291;291;291	P23760;Q494Z4;P23760-4;P23760-5;G5E9C1	PAX3_HUMAN;.;.;.;.	H	291;291;291;291;291;290;8;8	ENSP00000375921:P291H;ENSP00000342092:P291H;ENSP00000343052:P291H;ENSP00000375922:P291H;ENSP00000338767:P291H;ENSP00000386750:P290H	ENSP00000338767:P291H	P	-	2	0	PAX3	222794271	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.414000	0.97362	2.882000	0.98803	0.655000	0.94253	CCC	.	.		0.522	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			T	223086027	G	T	223086027	3	4	29	1	0	0	0	0	1	0	0	0	11489	1232	43	3	693	3	PAX3	2	223086027	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	43649440	223086027	20113346	17	3633										
ATG16L1	55054	hgsc.bcm.edu	37	chr2	234173607	234173607	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gacctgcgcactaagctttgTgaccttgaaagagccaacca	9	12	0	3			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:234173607T>C	ENST00000392017.4	+	5	716	c.459T>C	c.(457-459)tgT>tgC	p.C153C	ATG16L1_ENST00000347464.5_Intron|ATG16L1_ENST00000392020.4_Silent_p.C153C|ATG16L1_ENST00000392018.1_Silent_p.C153C|ATG16L1_ENST00000373525.5_Intron	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	153					autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		CTAAGCTTTGTGACCTTGAAA	0.473																																					p.C153C		Atlas-SNP	.											.	ATG16L1	83	.	0			c.T459C						.						128	118	121					2																	234173607		2203	4300	6503	SO:0001819	synonymous_variant	55054	exon5			GCTTTGTGACCTT	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"WD repeat domain containing"	21498	protein-coding gene	gene with protein product		610767	"APG16 autophagy 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like 1 (S. cerevisiae)"	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.459T>C	chr2.hg19:g.234173607T>C		137.0	0.0		128.0	17.0	NM_017974	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Silent	SNP	ENST00000392017.4	hg19	CCDS2503.2																																																																																			.	.		0.473	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974		C	234173607	T	C	234173607	2	2	29	1	0	0	0	0	0	0	0	1	1091	1702	59	2		2	ATG16L1	2	234173607	Silent	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	11087580	234173607	9025766	18	3634										
GRM7	2917	hgsc.bcm.edu	37	chr3	6903173	6903173	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cgcgctggcggcggcggcgcGcggccaggagatgtacgccc	19	15	0	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr3:6903173G>A	ENST00000357716.4	+	1	372	c.98G>A	c.(97-99)cGc>cAc	p.R33H	GRM7_ENST00000403881.1_Missense_Mutation_p.R33H|GRM7_ENST00000486284.1_Missense_Mutation_p.R33H|GRM7_ENST00000389336.4_Missense_Mutation_p.R33H|GRM7_ENST00000402647.2_Missense_Mutation_p.R33H	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	33					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)	p.R33H(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						GCGGCGGCGCGCGGCCAGGAG	0.692																																					p.R33H		Atlas-SNP	.											GRM7,NS,carcinoma,0,1	GRM7	223	.	1	Substitution - Missense(1)	lung(1)	c.G98A						.						9	9	9					3																	6903173		2118	4167	6285	SO:0001583	missense	2917	exon1			CGGCGCGCGGCCA	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.98G>A	chr3.hg19:g.6903173G>A	ENSP00000350348:p.Arg33His	118.0	0.0		114.0	12.0	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	hg19	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	G	3.232	-0.157146	0.06544	.	.	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647;ENST00000413492	D;D;D;D;D	0.89415	-2.47;-2.51;-2.51;-2.51;-2.51	5.23	1.98	0.26296	.	0.420263	0.21050	N	0.081012	T	0.70404	0.3220	N	0.01352	-0.895	0.28094	N	0.931708	B;B;D	0.64830	0.001;0.0;0.994	B;B;P	0.51415	0.0;0.0;0.669	T	0.66300	-0.5958	10	0.16420	T	0.52	.	1.0944	0.01670	0.2192:0.3258:0.2877:0.1673	.	33;33;33	Q14831-5;Q14831;Q14831-2	.;GRM7_HUMAN;.	H	33	ENSP00000350348:R33H;ENSP00000417536:R33H;ENSP00000373987:R33H;ENSP00000385664:R33H;ENSP00000384585:R33H	ENSP00000350348:R33H	R	+	2	0	GRM7	6878173	0.709000	0.27886	1.000000	0.80357	0.239000	0.25481	0.784000	0.26816	0.575000	0.29434	-0.312000	0.09012	CGC	.	.		0.692	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		A	6903173	G	A	6903173	3	1	29	1	0	0	0	0	1	0	0	0	6811	1087	38	1	100	1	GRM7	3	6903173	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10		6903173	191119257	19	3635										
CNBP	7555	hgsc.bcm.edu	37	chr3	128889414	128889414	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	catgaccagtttcaccacacCtaaaaaagaaattaaaagtt	4	9	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr3:128889414C>T	ENST00000422453.2	-	5	577		c.e5-1		CNBP_ENST00000504813.1_Splice_Site|CNBP_ENST00000500450.2_Splice_Site|CNBP_ENST00000446936.2_Splice_Site|CNBP_ENST00000451728.2_Splice_Site|CNBP_ENST00000502976.1_Splice_Site|CNBP_ENST00000441626.2_Splice_Site	NM_001127192.1|NM_001127193.1|NM_003418.4	NP_001120664.1|NP_001120665.1|NP_003409.1	P62633	CNBP_HUMAN	CCHC-type zinc finger, nucleic acid binding protein						cholesterol biosynthetic process (GO:0006695)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			biliary_tract(1)|endometrium(1)|kidney(1)|lung(2)	5						TTCACCACACCTAAAAAAGAA	0.443																																					.		Atlas-SNP	.											.	CNBP	12	.	0			c.417-1G>A						.						121	117	118					3																	128889414		2203	4300	6503	SO:0001630	splice_region_variant	7555	exon6			CCACACCTAAAAA	U19765	CCDS3056.1, CCDS46906.1, CCDS46907.1, CCDS46908.1, CCDS54637.1	3q21	2013-01-09	2006-06-29	2006-06-29				"RING-type (C3HC4) zinc fingers", "Zinc fingers, CCHC domain containing"	13164	protein-coding gene	gene with protein product		116955	"zinc finger protein 9 (a cellular retroviral nucleic acid binding protein)", "zinc finger protein 9"	DM2, ZNF9		2249857, 11486088	Standard	NM_003418		Approved	RNF163, ZCCHC22, CNBP1	uc021xdw.1	P62633		ENST00000422453.2:c.417-1G>A	chr3.hg19:g.128889414C>T		118.0	0.0		107.0	12.0	NM_003418	A8K7V4|B2RAV9|B4DP17|D3DNB9|D3DNC0|D3DNC1|E9PDR7|P20694|Q4JGY0|Q4JGY1|Q5QJR0|Q5U0E9|Q6PJI7|Q96NV3	Splice_Site	SNP	ENST00000422453.2	hg19	CCDS3056.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.668973	0.47677	.	.	ENSG00000169714	ENST00000502976;ENST00000422453;ENST00000451728;ENST00000446936;ENST00000500450;ENST00000504813;ENST00000441626	.	.	.	5.92	4.13	0.48395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.278	0.49178	0.1429:0.7197:0.1374:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CNBP	130372104	1.000000	0.71417	0.928000	0.36995	0.940000	0.58332	7.373000	0.79623	0.848000	0.35191	0.467000	0.42956	.	.	.		0.443	CNBP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358419.1	NM_003418	Intron	T	128889414	C	T	128889414	5	4	29	1	0	0	0	0	0	0	1	0	3594	695	24	3	121	3	CNBP	3	128889414	Splice_Site	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	121986241	128889414	69133016	20	3636										
C3orf79	152118	hgsc.bcm.edu	37	chr3	153220256	153220256	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gcaaaccagtatcaaacagaTgccagtcacttgtaacatct	6	11	3	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr3:153220256T>C	ENST00000446603.2	+	3	350	c.288T>C	c.(286-288)gaT>gaC	p.D96D	RP11-23D24.2_ENST00000493214.2_RNA	NM_001101337.1	NP_001094807.1	P0CE67	CC079_HUMAN	chromosome 3 open reading frame 79	96										endometrium(1)|large_intestine(3)	4						ATCAAACAGATGCCAGTCACT	0.393																																					p.D96D		Atlas-SNP	.											.	C3orf79	13	.	0			c.T288C						.						103	101	102					3																	153220256		1865	4100	5965	SO:0001819	synonymous_variant	152118	exon3			AACAGATGCCAGT	AF086445	CCDS46937.1	3q25.2	2009-09-30			ENSG00000237787	ENSG00000237787			37259	protein-coding gene	gene with protein product							Standard	NM_001101337		Approved		uc003ezt.3	P0CE67	OTTHUMG00000159629	ENST00000446603.2:c.288T>C	chr3.hg19:g.153220256T>C		82.0	0.0		102.0	13.0	NM_001101337		Silent	SNP	ENST00000446603.2	hg19	CCDS46937.1																																																																																			.	.		0.393	C3orf79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356570.1	NM_001101337		C	153220256	T	C	153220256	2	2	29	1	0	0	0	0	0	0	0	1	2248	1461	51	2		2	C3orf79	3	153220256	Silent	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	24330842	153220256	44802174	21	3637										
ACAP2	23527	hgsc.bcm.edu	37	chr3	195029516	195029516	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ttcatttattaacacctaccTtaaattttttctggtaaacc	2	9	2	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr3:195029516T>A	ENST00000326793.6	-	11	1138	c.908A>T	c.(907-909)aAg>aTg	p.K303M		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	303	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						AACACCTACCTTAAATTTTTT	0.289																																					p.K303M		Atlas-SNP	.											.	ACAP2	72	.	0			c.A908T						.						53	55	54					3																	195029516		2200	4290	6490	SO:0001630	splice_region_variant	23527	exon11			CCTACCTTAAATT		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.909+1A>T	chr3.hg19:g.195029516T>A		119.0	0.0		98.0	8.0	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	hg19	CCDS33924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.3|20.3	3.968611|3.968611	0.74131|0.74131	.|.	.|.	ENSG00000114331|ENSG00000114331	ENST00000326793|ENST00000439758	T|.	0.78246|.	-1.16|.	5.76|5.76	5.76|5.76	0.90799|0.90799	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.70666|.	0.3250|.	M|M	0.64170|0.64170	1.965|1.965	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|.	0.70011|.	-0.4989|.	10|.	0.51188|.	T|.	0.08|.	.|.	13.8133|13.8133	0.63276|0.63276	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	303|.	Q15057|.	ACAP2_HUMAN|.	M|Y	303|177	ENSP00000324287:K303M|.	ENSP00000324287:K303M|.	K|X	-|-	2|3	0|2	ACAP2|ACAP2	196510805|196510805	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	5.869000|5.869000	0.69613|0.69613	2.189000|2.189000	0.69895|0.69895	0.528000|0.528000	0.53228|0.53228	AAG|TAA	.	.		0.289	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287	Missense_Mutation	A	195029516	T	A	195029516	5	1	29	1	0	0	0	0	0	0	1	0	119	1623	56	4	1480	4	ACAP2	3	195029516	Splice_Site	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	41809260	195029516	2992914	22	3638										
WDR19	57728	hgsc.bcm.edu	37	chr4	39229946	39229946	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tatgatgatgataaggtgtaCacttatgtctttcacaagga	9	5	2	3	rs539697450		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:39229946C>T	ENST00000399820.3	+	16	1900	c.1746C>T	c.(1744-1746)taC>taT	p.Y582Y	WDR19_ENST00000288634.7_Silent_p.Y422Y	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	582					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						ATAAGGTGTACACTTATGTCT	0.348													C|||	1	0.000199681	0	0	5008	,	,		21314	0		0	False		,,,				2504	0.001				p.Y582Y		Atlas-SNP	.											.	WDR19	96	.	0			c.C1746T						.						87	82	84					4																	39229946		1866	4108	5974	SO:0001819	synonymous_variant	57728	exon16			GGTGTACACTTAT	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"WD repeat domain containing", "Intraflagellar transport homologs"	18340	protein-coding gene	gene with protein product	"intraflagellar transport 144 homolog (Chlamydomonas)"	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.1746C>T	chr4.hg19:g.39229946C>T		118.0	0.0		119.0	14.0	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.		0.348	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			T	39229946	C	T	39229946	2	4	29	1	0	0	0	0	0	0	0	1	17294	489	17	3		3	WDR19	4	39229946	Silent	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10		39229946	151924330	23	3639										
ODAM	54959	hgsc.bcm.edu	37	chr4	71063815	71063815	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ttgcccaaggagcccaggcaGgccaagttgatcccttacag	11	13	0	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:71063815G>T	ENST00000396094.2	+	4	364	c.316G>T	c.(316-318)Ggc>Tgc	p.G106C		NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN	odontogenic, ameloblast asssociated	106	Gln-rich.				biomineral tissue development (GO:0031214)|odontogenesis of dentin-containing tooth (GO:0042475)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|fibril (GO:0043205)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(3)|skin(2)	20						AGCCCAGGCAGGCCAAGTTGA	0.517																																					p.G106C		Atlas-SNP	.											.	ODAM	38	.	0			c.G316T						.						135	140	138					4																	71063815		1940	4133	6073	SO:0001583	missense	54959	exon4			CAGGCAGGCCAAG	AK000520	CCDS3536.2	4q13.3	2010-11-23			ENSG00000109205	ENSG00000109205			26043	protein-coding gene	gene with protein product		614843				14647039	Standard	NM_017855		Approved	APin, FLJ20513	uc003hfc.3	A1E959	OTTHUMG00000129406	ENST00000396094.2:c.316G>T	chr4.hg19:g.71063815G>T	ENSP00000379401:p.Gly106Cys	105.0	0.0		102.0	9.0	NM_017855	Q8WWE5|Q9NWZ9	Missense_Mutation	SNP	ENST00000396094.2	hg19	CCDS3536.2	.	.	.	.	.	.	.	.	.	.	G	10.10	1.257197	0.22965	.	.	ENSG00000109205	ENST00000396094;ENST00000510709;ENST00000514097	T;T	0.46819	0.86;0.86	4.79	2.15	0.27550	.	.	.	.	.	T	0.54791	0.1880	L	0.50333	1.59	0.09310	N	1	D	0.69078	0.997	D	0.63192	0.912	T	0.39014	-0.9634	9	0.46703	T	0.11	3.1135	6.7114	0.23280	0.2947:0.0:0.7053:0.0	.	106	A1E959	ODAM_HUMAN	C	106;92;59	ENSP00000379401:G106C;ENSP00000426106:G59C	ENSP00000379401:G106C	G	+	1	0	ODAM	71098404	0.000000	0.05858	0.000000	0.03702	0.247000	0.25773	0.208000	0.17415	0.253000	0.21552	0.561000	0.74099	GGC	.	.		0.517	ODAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251562.1	NM_017855		T	71063815	G	T	71063815	3	4	29	1	0	0	0	0	1	0	0	0	10833	1000	35	3	330	3	ODAM	4	71063815	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	31833869	71063815	120090461	24	3640										
STBD1	100631383	hgsc.bcm.edu	37	chr4	77231109	77231148	+	Frame_Shift_Del	DEL	GGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	GGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	-													0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gcaatagattcctagaaactGgccatgaggataaagtggtt					rs199743271|rs527950885|rs561957942|rs144679126|rs148507767	byFrequency	TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	GGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	GGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:77231109_77231148delGGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	ENST00000237642.6	+	2	1777_1816	c.1033_1072delGGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	c.(1033-1074)ggccatgaggataaagtggttcacgcatggtgggggattcacfs	p.GHEDKVVHAWWGIH345fs	FAM47E_ENST00000515604.1_3'UTR|FAM47E-STBD1_ENST00000539752.1_Frame_Shift_Del_p.GHEDKVVHAWWGIH196fs	NM_003943.4	NP_003934.1			FAM47E-STBD1 readthrough									p.W355L(1)									CCTAGAAACTGGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTCACTGATTCAG	0.463																																					p.344_357del		Pindel	.											.	STBD1	22	.	1	Substitution - Missense(1)	lung(1)	c.1032_1071del						.																																			SO:0001589	frameshift_variant	8987	exon2			.		CCDS58908.1	4q21.1	2013-04-23			ENSG00000118804	ENSG00000118804			44667	other	readthrough							Standard	NM_001242939		Approved				OTTHUMG00000160966	ENST00000237642.6:c.1033_1072delGGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	chr4.hg19:g.77231109_77231148delGGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	ENSP00000237642:p.Gly345fs	32.0	0.0		23.0	10.0	NM_003943		Frame_Shift_Del	DEL	ENST00000237642.6	hg19	CCDS3578.1																																																																																			.	.		0.463	FAM47E-STBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252415.2			-	77231148	GGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	-	77231109	7	5	29	1	0	1	0	1	0	0	0	0	15289	1348	47	0	1039	0	STBD1	4	77231109	Frame_Shift_Del	DEL	GGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	TCGA-5R-AAAM-01A-12D-A40R-10	6167294	77231109	113923167	25	3641										
SEC24D	9871	hgsc.bcm.edu	37	chr4	119653989	119653989	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ttcatcagttgagatctctgGtctgctgagtagtacacagt	10	8	4	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:119653989G>C	ENST00000280551.6	-	20	2813	c.2575C>G	c.(2575-2577)Cca>Gca	p.P859A	SEC24D_ENST00000429811.2_3'UTR|SEC24D_ENST00000379735.5_Missense_Mutation_p.P860A|SEC24D_ENST00000511481.1_Missense_Mutation_p.P490A|SEC24D_ENST00000505134.1_5'UTR			O94855	SC24D_HUMAN	SEC24 family member D	859					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						GAGATCTCTGGTCTGCTGAGT	0.423																																					p.P859A		Atlas-SNP	.											.	SEC24D	96	.	0			c.C2575G						.						195	163	174					4																	119653989		2203	4300	6503	SO:0001583	missense	9871	exon20			TCTCTGGTCTGCT	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"SEC24 (S. cerevisiae) related gene family, member D", "SEC24 family, member D (S. cerevisiae)"			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.2575C>G	chr4.hg19:g.119653989G>C	ENSP00000280551:p.Pro859Ala	142.0	0.0		135.0	43.0	NM_014822	Q8IYI7	Missense_Mutation	SNP	ENST00000280551.6	hg19	CCDS3710.1	.	.	.	.	.	.	.	.	.	.	G	1.842	-0.467082	0.04476	.	.	ENSG00000150961	ENST00000280551;ENST00000379735;ENST00000511481	D;D;D	0.88431	-2.38;-2.38;-2.38	5.62	4.77	0.60923	Sec23/Sec24, helical domain (2);	0.214881	0.49305	D	0.000152	T	0.78991	0.4371	L	0.27053	0.805	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.69595	-0.5103	10	0.07175	T	0.84	-4.9602	10.5038	0.44821	0.071:0.1327:0.7962:0.0	.	21;860;859	Q9NWP5;O94855-2;O94855	.;.;SC24D_HUMAN	A	859;860;490	ENSP00000280551:P859A;ENSP00000369059:P860A;ENSP00000425491:P490A	ENSP00000280551:P859A	P	-	1	0	SEC24D	119873437	1.000000	0.71417	0.845000	0.33349	0.990000	0.78478	2.122000	0.41987	1.340000	0.45581	0.591000	0.81541	CCA	.	.		0.423	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4			C	119653989	G	C	119653989	3	2	29	1	0	0	0	0	1	0	0	0	14012	1261	44	4	539	4	SEC24D	4	119653989	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	42422880	119653989	71500287	26	3642										
SLC25A31	83447	hgsc.bcm.edu	37	chr4	128651788	128651788	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	accttctggccggcggagtcGcggcagctgtgtccaagaca	14	13	1	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:128651788G>A	ENST00000281154.4	+	1	256	c.88G>A	c.(88-90)Gcg>Acg	p.A30T		NM_031291.2	NP_112581.1	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	30					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|nucleus (GO:0005634)	transporter activity (GO:0005215)			NS(1)|breast(1)|large_intestine(10)|lung(8)|skin(2)	22						CGGCGGAGTCGCGGCAGCTGT	0.622																																					p.A30T		Atlas-SNP	.											.	SLC25A31	42	.	0			c.G88A						.						50	48	49					4																	128651788		2203	4300	6503	SO:0001583	missense	83447	exon1			GGAGTCGCGGCAG	AL136857	CCDS3733.1	4q28	2013-05-22			ENSG00000151475	ENSG00000151475		"Solute carriers"	25319	protein-coding gene	gene with protein product		610796				15670820	Standard	NM_031291		Approved	DKFZP434N1235, ANT4	uc003ifl.3	Q9H0C2	OTTHUMG00000133300	ENST00000281154.4:c.88G>A	chr4.hg19:g.128651788G>A	ENSP00000281154:p.Ala30Thr	213.0	0.0		226.0	46.0	NM_031291		Missense_Mutation	SNP	ENST00000281154.4	hg19	CCDS3733.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.389167	0.61956	.	.	ENSG00000151475	ENST00000281154	D	0.87103	-2.21	4.96	4.96	0.65561	Mitochondrial carrier domain (2);	0.140508	0.32901	N	0.005508	D	0.91181	0.7222	M	0.90814	3.15	0.43814	D	0.996373	D	0.67145	0.996	P	0.47864	0.559	D	0.93160	0.6557	10	0.87932	D	0	-0.5605	15.2429	0.73485	0.0:0.0:1.0:0.0	.	30	Q9H0C2	ADT4_HUMAN	T	30	ENSP00000281154:A30T	ENSP00000281154:A30T	A	+	1	0	SLC25A31	128871238	1.000000	0.71417	0.125000	0.21846	0.007000	0.05969	4.772000	0.62324	2.575000	0.86900	0.655000	0.94253	GCG	.	.		0.622	SLC25A31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257094.2	NM_031291		A	128651788	G	A	128651788	3	1	29	1	0	0	0	0	1	0	0	0	14510	1087	38	1	90	1	SLC25A31	4	128651788	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	8997799	128651788	62502488	27	3643										
MAML3	55534	hgsc.bcm.edu	37	chr4	140811125	140811125	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ctgctgctgctgctgctgttGctgttgctgtttctgctgca	12	11	1	0	rs62344940		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:140811125G>T	ENST00000509479.2	-	2	2321	c.1465C>A	c.(1465-1467)Caa>Aaa	p.Q489K	MAML3_ENST00000327122.5_Missense_Mutation_p.Q333K|MAML3_ENST00000398940.1_Missense_Mutation_p.Q28K	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					tgctgctgttgctgttgctgt	0.552																																					p.Q489K		Atlas-SNP	.											.	MAML3	192	.	0			c.C1465A						.						17	20	19					4																	140811125		2194	4294	6488	SO:0001583	missense	55534	exon2			GCTGTTGCTGTTG	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1465C>A	chr4.hg19:g.140811125G>T	ENSP00000421180:p.Gln489Lys	55.0	0.0		59.0	8.0	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	hg19	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	G	3.000	-0.206260	0.06180	.	.	ENSG00000196782	ENST00000509479;ENST00000327122;ENST00000398940	T;T	0.76448	0.83;-1.02	2.61	2.61	0.31194	.	0.000000	0.64402	D	0.000001	T	0.66607	0.2806	N	0.08118	0	0.31344	N	0.683255	P	0.43392	0.805	P	0.59424	0.857	T	0.64106	-0.6485	10	0.05436	T	0.98	.	8.8799	0.35367	0.0:0.0:1.0:0.0	rs62344940	489	Q96JK9	MAML3_HUMAN	K	489;333;28	ENSP00000421180:Q489K;ENSP00000313316:Q333K	ENSP00000313316:Q333K	Q	-	1	0	MAML3	141030575	1.000000	0.71417	1.000000	0.80357	0.631000	0.37964	3.291000	0.51764	1.788000	0.52465	0.484000	0.47621	CAA	.	.		0.552	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811125	G	T	140811125	3	4	29	1	0	0	0	0	1	0	0	0	9216	1328	46	3	1959	3	MAML3	4	140811125	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	12159337	140811125	50343151	28	3644										
FGB	2244	hgsc.bcm.edu	37	chr4	155487708	155487708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	acaggaaaggccaatcagaaAtagtgttgatgagttaaata	10	4	1	3			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:155487708A>G	ENST00000302068.4	+	3	437	c.374A>G	c.(373-375)aAt>aGt	p.N125S	FGB_ENST00000509493.1_Intron|FGB_ENST00000502545.1_3'UTR	NM_005141.4	NP_005132.2	P02675	FIBB_HUMAN	fibrinogen beta chain	125					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|cellular response to interleukin-1 (GO:0071347)|cellular response to leptin stimulus (GO:0044320)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	chaperone binding (GO:0051087)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(22)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	CCAATCAGAAATAGTGTTGAT	0.418																																					p.N125S	NSCLC(106;1133 1613 21870 46110 52656)	Atlas-SNP	.											.	FGB	71	.	0			c.A374G						.						159	149	152					4																	155487708		2203	4300	6503	SO:0001583	missense	2244	exon3			TCAGAAATAGTGT		CCDS3786.1	4q28	2014-09-17			ENSG00000171564	ENSG00000171564		"Fibrinogen C domain containing", "Endogenous ligands"	3662	protein-coding gene	gene with protein product		134830	"fibrinogen, B beta polypeptide"				Standard	NM_005141		Approved		uc003ioa.4	P02675	OTTHUMG00000150331	ENST00000302068.4:c.374A>G	chr4.hg19:g.155487708A>G	ENSP00000306099:p.Asn125Ser	137.0	0.0		135.0	22.0	NM_005141	A0JLR9|B2R7G3|Q32Q65|Q3KPF2	Missense_Mutation	SNP	ENST00000302068.4	hg19	CCDS3786.1	.	.	.	.	.	.	.	.	.	.	A	0.052	-1.246284	0.01481	.	.	ENSG00000171564	ENST00000302068;ENST00000537843	D	0.81659	-1.52	5.27	0.923	0.19413	Fibrinogen, alpha/beta/gamma chain, coiled coil domain (2);	0.674999	0.15593	N	0.254288	T	0.56108	0.1963	N	0.08118	0	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37865	-0.9687	10	0.13853	T	0.58	.	6.3655	0.21453	0.6481:0.181:0.1709:0.0	.	108;125	B4E1D3;P02675	.;FIBB_HUMAN	S	125;108	ENSP00000306099:N125S	ENSP00000306099:N125S	N	+	2	0	FGB	155707158	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.382000	0.20635	0.055000	0.16094	-1.162000	0.01777	AAT	.	.		0.418	FGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317595.1	NM_005141		G	155487708	A	G	155487708	3	3	29	1	0	0	0	0	1	0	0	0	5839	101	4	2	384	2	FGB	4	155487708	Missense_Mutation	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10	14676583	155487708	35666568	29	3645										
PAPD7	11044	hgsc.bcm.edu	37	chr5	6753104	6753104	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	catgtcttccccggccattcCctcagcgtcccccaacccgc	6	22	2	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:6753104C>A	ENST00000230859.6	+	12	1517	c.1388C>A	c.(1387-1389)cCc>cAc	p.P463H		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	693	PAP-associated.				double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)			cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CCGGCCATTCCCTCAGCGTCC	0.562																																					p.P463H	NSCLC(7;212 333 5667 23379 46547)	Atlas-SNP	.											.	PAPD7	69	.	0			c.C1388A						.						154	142	146					5																	6753104		2203	4300	6503	SO:0001583	missense	11044	exon12			CCATTCCCTCAGC	AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"topoisomerase-related function protein 4-1", "polymerase (DNA-directed) sigma", "DNA polymerase kappa", "TUTase5"	605198	"polymerase (DNA directed) sigma"	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.1388C>A	chr5.hg19:g.6753104C>A	ENSP00000230859:p.Pro463His	118.0	0.0		122.0	7.0	NM_001171805	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Missense_Mutation	SNP	ENST00000230859.6	hg19	CCDS3871.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.444058	0.43429	.	.	ENSG00000112941	ENST00000230859	T	0.33654	1.4	5.24	5.24	0.73138	.	0.190471	0.45867	D	0.000330	T	0.39911	0.1096	L	0.27053	0.805	0.42241	D	0.991937	D;D	0.67145	0.996;0.996	P;P	0.54372	0.75;0.75	T	0.24440	-1.0160	10	0.49607	T	0.09	1.0E-4	15.5482	0.76126	0.0:1.0:0.0:0.0	.	463;463	B7ZLL4;Q5XG87	.;PAPD7_HUMAN	H	463	ENSP00000230859:P463H	ENSP00000230859:P463H	P	+	2	0	PAPD7	6806104	0.855000	0.29742	0.111000	0.21465	0.405000	0.30901	2.935000	0.48963	2.438000	0.82558	0.655000	0.94253	CCC	.	.		0.562	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		A	6753104	C	A	6753104	3	1	29	1	0	0	0	0	1	0	0	0	11435	623	22	3	1430	3	PAPD7	5	6753104	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10		6753104	174162156	30	3646										
CARD6	84674	hgsc.bcm.edu	37	chr5	40852639	40852639	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gtcaaacatgtatcagtgccAgtttgctcttcccctgctac	7	13	3	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:40852639A>C	ENST00000254691.5	+	3	1404	c.1205A>C	c.(1204-1206)cAg>cCg	p.Q402P	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	402					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						TATCAGTGCCAGTTTGCTCTT	0.453																																					p.Q402P		Atlas-SNP	.											.	CARD6	141	.	0			c.A1205C						.						73	70	71					5																	40852639		2203	4300	6503	SO:0001583	missense	84674	exon3			AGTGCCAGTTTGC	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.1205A>C	chr5.hg19:g.40852639A>C	ENSP00000254691:p.Gln402Pro	98.0	0.0		98.0	30.0	NM_032587	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	hg19	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.869137	0.51588	.	.	ENSG00000132357	ENST00000254691;ENST00000509771	T	0.58210	0.35	5.49	-1.45	0.08828	.	1.203030	0.05872	N	0.624793	T	0.49355	0.1552	M	0.72894	2.215	0.80722	D	1	B	0.25048	0.117	B	0.20184	0.028	T	0.44802	-0.9304	10	0.87932	D	0	0.3299	5.9549	0.19267	0.5768:0.129:0.2941:0.0	.	402	Q9BX69	CARD6_HUMAN	P	402	ENSP00000254691:Q402P	ENSP00000254691:Q402P	Q	+	2	0	CARD6	40888396	1.000000	0.71417	0.860000	0.33809	0.997000	0.91878	1.242000	0.32755	-0.356000	0.08187	0.533000	0.62120	CAG	.	.		0.453	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			C	40852639	A	C	40852639	3	2	29	1	0	0	0	0	1	0	0	0	2652	188	7	5	1215	5	CARD6	5	40852639	Missense_Mutation	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10	34099535	40852639	140062621	31	3647										
C5orf51	285636	hgsc.bcm.edu	37	chr5	41912232	41912232	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ttatcgatgtcctatccagtTaaatgaaggagtttctttcc	7	8	1	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:41912232T>G	ENST00000381647.2	+	5	567	c.548T>G	c.(547-549)tTa>tGa	p.L183*		NM_175921.4	NP_787117.3	A6NDU8	CE051_HUMAN	chromosome 5 open reading frame 51	183										endometrium(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						CCTATCCAGTTAAATGAAGGA	0.323																																					p.L183X		Atlas-SNP	.											.	C5orf51	28	.	0			c.T548G						.						165	168	167					5																	41912232		2203	4298	6501	SO:0001587	stop_gained	285636	exon5			TCCAGTTAAATGA	AL833916, AK094002	CCDS34151.1	5p13.1	2008-07-18			ENSG00000205765	ENSG00000205765			27750	protein-coding gene	gene with protein product						14702039	Standard	NM_175921		Approved	LOC285636	uc003jmo.3	A6NDU8	OTTHUMG00000162084	ENST00000381647.2:c.548T>G	chr5.hg19:g.41912232T>G	ENSP00000371061:p.Leu183*	59.0	0.0		56.0	6.0	NM_175921	A2RRM9	Nonsense_Mutation	SNP	ENST00000381647.2	hg19	CCDS34151.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.679979	0.88542	.	.	ENSG00000205765	ENST00000381647	.	.	.	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-38.0925	9.9804	0.41811	0.0:0.0755:0.0:0.9245	.	.	.	.	X	183	.	ENSP00000371061:L183X	L	+	2	0	C5orf51	41947989	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.641000	0.61375	2.233000	0.73108	0.454000	0.30748	TTA	.	.		0.323	C5orf51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367144.1	NM_175921		G	41912232	T	G	41912232	4	3	29	1	0	0	0	0	0	1	0	0	2310	1764	61	5	566	5	C5orf51	5	41912232	Nonsense_Mutation	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	1059593	41912232	139003028	32	3648										
PDE8B	8622	hgsc.bcm.edu	37	chr5	76722294	76722294	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tgcacatctgccagccctgaTgcaacatttggctgacaact	8	13	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:76722294T>A	ENST00000264917.5	+	22	2618	c.2573T>A	c.(2572-2574)aTg>aAg	p.M858K	WDR41_ENST00000512033.1_5'Flank|PDE8B_ENST00000346042.3_Missense_Mutation_p.M761K|PDE8B_ENST00000340978.3_Missense_Mutation_p.M811K|PDE8B_ENST00000342343.4_Missense_Mutation_p.M838K|PDE8B_ENST00000505283.1_Missense_Mutation_p.M323K|PDE8B_ENST00000333194.4_Missense_Mutation_p.M803K	NM_003719.3	NP_003710.1	O95263	PDE8B_HUMAN	phosphodiesterase 8B	858	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|negative regulation of insulin secretion (GO:0046676)|negative regulation of steroid hormone biosynthetic process (GO:0090032)|phosphorelay signal transduction system (GO:0000160)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)		GMDS/PDE8B(2)	NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(15)|ovary(1)|prostate(2)|skin(3)	40		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)	Caffeine(DB00201)|Ketotifen(DB00920)	CCAGCCCTGATGCAACATTTG	0.468																																					p.M858K		Atlas-SNP	.											.	PDE8B	103	.	0			c.T2573A						.						87	77	80					5																	76722294		2203	4300	6503	SO:0001583	missense	8622	exon22			CCCTGATGCAACA	AF079529	CCDS4037.1, CCDS34190.1, CCDS34191.1, CCDS34192.1, CCDS34193.1	5q14.1	2008-05-15			ENSG00000113231	ENSG00000113231	3.1.4.17	"Phosphodiesterases"	8794	protein-coding gene	gene with protein product		603390				9784418	Standard	NM_003719		Approved		uc003kfa.3	O95263	OTTHUMG00000102170	ENST00000264917.5:c.2573T>A	chr5.hg19:g.76722294T>A	ENSP00000264917:p.Met858Lys	171.0	0.0		199.0	8.0	NM_003719	Q5J7V7|Q86XK8|Q8IUJ7|Q8IUJ8|Q8IUJ9|Q8IUK0|Q8N3T2	Missense_Mutation	SNP	ENST00000264917.5	hg19	CCDS4037.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.030352	0.93575	.	.	ENSG00000113231	ENST00000340978;ENST00000346042;ENST00000264917;ENST00000342343;ENST00000333194;ENST00000505283	T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	5.63	5.63	0.86233	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.036230	0.85682	D	0.000000	D	0.87577	0.6212	M	0.80183	2.485	0.80722	D	1	P;D;D;D;D	0.60160	0.818;0.984;0.984;0.984;0.987	P;P;P;P;D	0.63283	0.635;0.858;0.858;0.858;0.913	D	0.89308	0.3631	10	0.87932	D	0	.	16.1413	0.81528	0.0:0.0:0.0:1.0	.	761;811;803;838;858	O95263-2;O95263-6;O95263-3;O95263-4;O95263	.;.;.;.;PDE8B_HUMAN	K	811;761;858;838;803;323	ENSP00000345446:M811K;ENSP00000330428:M761K;ENSP00000264917:M858K;ENSP00000345646:M838K;ENSP00000331336:M803K;ENSP00000423461:M323K	ENSP00000264917:M858K	M	+	2	0	PDE8B	76758050	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.997000	0.88414	2.270000	0.75569	0.482000	0.46254	ATG	.	.		0.468	PDE8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000220015.3	NM_003719		A	76722294	T	A	76722294	3	1	29	1	0	0	0	0	1	0	0	0	11663	1464	51	4	2659	4	PDE8B	5	76722294	Missense_Mutation	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	34810062	76722294	104192966	33	3649										
PCDHB6	56130	hgsc.bcm.edu	37	chr5	140532159	140532159	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gattatgcccaacttccctcCtcagggcactgagagagaaa	9	12	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:140532159C>T	ENST00000231136.1	+	1	2321	c.2321C>T	c.(2320-2322)cCt>cTt	p.P774L	PCDHB6_ENST00000543635.1_Missense_Mutation_p.P638L	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	774					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AACTTCCCTCCTCAGGGCACT	0.473																																					p.P774L		Atlas-SNP	.											.	PCDHB6	161	.	0			c.C2321T						.						109	118	115					5																	140532159		2202	4300	6502	SO:0001583	missense	56130	exon1			TCCCTCCTCAGGG	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.2321C>T	chr5.hg19:g.140532159C>T	ENSP00000231136:p.Pro774Leu	191.0	0.0		216.0	27.0	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	hg19	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	C	8.963	0.971165	0.18659	.	.	ENSG00000113211	ENST00000543635;ENST00000231136	T;T	0.13307	2.6;2.6	4.51	-0.855	0.10700	.	.	.	.	.	T	0.06416	0.0165	N	0.17631	0.505	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41822	-0.9487	9	0.21014	T	0.42	.	1.8217	0.03112	0.1317:0.4228:0.1292:0.3163	.	774	Q9Y5E3	PCDB6_HUMAN	L	638;774	ENSP00000438466:P638L;ENSP00000231136:P774L	ENSP00000231136:P774L	P	+	2	0	PCDHB6	140512343	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.023000	0.03607	-0.147000	0.11254	-0.314000	0.08810	CCT	.	.		0.473	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		T	140532159	C	T	140532159	3	4	29	1	0	0	0	0	1	0	0	0	11555	681	24	3	2323	3	PCDHB6	5	140532159	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	63809865	140532159	40383101	34	3650										
PCDHGB1	56104	hgsc.bcm.edu	37	chr5	140731361	140731361	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cgcagagcggggtggtgttcGcgcagcgcgccttcgaccac	16	14	0	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:140731361G>A	ENST00000523390.1	+	1	1534	c.1534G>A	c.(1534-1536)Gcg>Acg	p.A512T	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	512	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGTGTTCGCGCAGCGCGC	0.682																																					p.A512T		Atlas-SNP	.											PCDHGB1_ENST00000523390,NS,carcinoma,0,2	PCDHGB1	198	.	0			c.G1534A						.						38	44	42					5																	140731361		2012	4186	6198	SO:0001583	missense	56104	exon1			GTGTTCGCGCAGC	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"Cadherins / Protocadherins : Clustered"	8708	other	protocadherin	"protocadherin gamma subfamily B, 1, isoform 2"	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1534G>A	chr5.hg19:g.140731361G>A	ENSP00000429273:p.Ala512Thr	100.0	0.0		68.0	5.0	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	hg19	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	21.7	4.181064	0.78677	.	.	ENSG00000254221	ENST00000523390	T	0.42513	0.97	5.49	5.49	0.81192	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.54240	0.1846	L	0.31926	0.97	0.33144	D	0.544792	D;D	0.89917	1.0;0.996	D;D	0.76575	0.988;0.917	T	0.63545	-0.6613	9	0.87932	D	0	.	15.0291	0.71694	0.0:0.0:0.8571:0.1429	.	512;512	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	T	512	ENSP00000429273:A512T	ENSP00000429273:A512T	A	+	1	0	PCDHGB1	140711545	0.050000	0.20438	1.000000	0.80357	0.985000	0.73830	1.472000	0.35376	2.740000	0.93945	0.563000	0.77884	GCG	.	.		0.682	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922		A	140731361	G	A	140731361	3	1	29	1	0	0	0	0	1	0	0	0	11571	1087	38	1	1536	1	PCDHGB1	5	140731361	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	199202	140731361	40183899	35	3651										
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156819926	156819926	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cctgaacaaatacatgaagtCcgtggagacagacagttcca	9	10	0	4			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:156819926C>A	ENST00000521420.1	+	30	3693	c.3602C>A	c.(3601-3603)tCc>tAc	p.S1201Y	CYFIP2_ENST00000377576.3_Missense_Mutation_p.S1227Y|CYFIP2_ENST00000318218.6_Missense_Mutation_p.S1252Y|CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000347377.6_Missense_Mutation_p.S1227Y|CYFIP2_ENST00000541131.1_Missense_Mutation_p.S1152Y|CYFIP2_ENST00000522463.1_Missense_Mutation_p.S1031Y|CYFIP2_ENST00000435847.2_Missense_Mutation_p.S926Y					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TACATGAAGTCCGTGGAGACA	0.522																																					p.S1227Y		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C3680A						.						90	97	95					5																	156819926		2151	4274	6425	SO:0001583	missense	26999	exon31			TGAAGTCCGTGGA	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.3602C>A	chr5.hg19:g.156819926C>A	ENSP00000430904:p.Ser1201Tyr	86.0	0.0		78.0	14.0	NM_001037332		Missense_Mutation	SNP	ENST00000521420.1	hg19		.	.	.	.	.	.	.	.	.	.	C	28.4	4.917065	0.92249	.	.	ENSG00000055163	ENST00000318218;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576;ENST00000541131;ENST00000435847	T;T;T;T;T;T;T	0.25749	2.11;2.11;2.11;2.11;2.11;2.11;1.78	5.38	5.38	0.77491	.	0.166812	0.53938	D	0.000048	T	0.39708	0.1088	L	0.27053	0.805	0.80722	D	1	P;P;P;D;P;P	0.89917	0.923;0.763;0.608;1.0;0.732;0.894	P;P;B;D;P;B	0.71184	0.655;0.563;0.157;0.972;0.459;0.202	T	0.10636	-1.0621	10	0.40728	T	0.16	-19.7475	19.5107	0.95140	0.0:1.0:0.0:0.0	.	1091;1031;1201;1227;1227;1252	A8MUM2;E7EW33;E7EVJ5;E7EVF4;Q96F07-2;Q96F07	.;.;.;.;.;CYFP2_HUMAN	Y	1252;1031;1201;1227;1227;1152;926	ENSP00000325817:S1252Y;ENSP00000428009:S1031Y;ENSP00000430904:S1201Y;ENSP00000313567:S1227Y;ENSP00000366799:S1227Y;ENSP00000444645:S1152Y;ENSP00000403793:S926Y	ENSP00000325817:S1252Y	S	+	2	0	CYFIP2	156752504	1.000000	0.71417	0.970000	0.41538	0.848000	0.48234	7.776000	0.85560	2.679000	0.91253	0.655000	0.94253	TCC	.	.		0.522	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		A	156819926	C	A	156819926	3	1	29	1	0	0	0	0	1	0	0	0	4140	855	30	3	3798	3	CYFIP2	5	156819926	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	16088565	156819926	24095334	36	3652										
HIST1H3J	8356	hgsc.bcm.edu	37	chr6	27858205	27858205	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cgcgcaagctggatgtccttAggcataatagtgacacgctt	11	10	0	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr6:27858205A>C	ENST00000359303.2	-	1	365	c.366T>G	c.(364-366)ccT>ccG	p.P122P	HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000479986.1_5'Flank	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	122				P -> L (in Ref. 13; AAH66884). {ECO:0000305}.	blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	8						GGATGTCCTTAGGCATAATAG	0.527																																					p.P122P		Atlas-SNP	.											.	HIST1H3J	16	.	0			c.T366G						.						65	65	65					6																	27858205		2203	4300	6503	SO:0001819	synonymous_variant	8356	exon1			GTCCTTAGGCATA	Z83737	CCDS4638.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197153	ENSG00000197153		"Histones / Replication-dependent"	4774	protein-coding gene	gene with protein product		602817	"H3 histone family, member J", "histone 1, H3j"	H3FJ		9439656, 12408966	Standard	NM_003535		Approved	H3/j	uc003nka.3	P68431	OTTHUMG00000016185	ENST00000359303.2:c.366T>G	chr6.hg19:g.27858205A>C		108.0	0.0		109.0	38.0	NM_003535	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000359303.2	hg19	CCDS4638.1																																																																																			.	.		0.527	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043453.2	NM_003535		C	27858205	A	C	27858205	2	2	29	1	0	0	0	0	0	0	0	1	7173	407	15	5		5	HIST1H3J	6	27858205	Silent	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10		27858205	143256862	37	3653										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51491853	51491853	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gattctcggcgtttggatgaGatgtggatatgaatattttg	13	3	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr6:51491853G>C	ENST00000371117.3	-	66	12002	c.11727C>G	c.(11725-11727)atC>atG	p.I3909M		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3909					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GTTTGGATGAGATGTGGATAT	0.418																																					p.I3909M		Atlas-SNP	.											.	PKHD1	927	.	0			c.C11727G						.						291	281	284					6																	51491853		2203	4300	6503	SO:0001583	missense	5314	exon66			GGATGAGATGTGG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11727C>G	chr6.hg19:g.51491853G>C	ENSP00000360158:p.Ile3909Met	130.0	0.0		89.0	34.0	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	8.108	0.778177	0.16120	.	.	ENSG00000170927	ENST00000371117	D	0.86030	-2.06	4.44	1.6	0.23607	.	2.030180	0.02516	N	0.092055	T	0.49966	0.1588	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.47724	-0.9095	10	0.46703	T	0.11	.	7.0109	0.24861	0.0951:0.3583:0.5466:0.0	.	3909	P08F94	PKHD1_HUMAN	M	3909	ENSP00000360158:I3909M	ENSP00000360158:I3909M	I	-	3	3	PKHD1	51599812	0.003000	0.15002	0.016000	0.15963	0.023000	0.10783	0.017000	0.13399	0.347000	0.23924	0.655000	0.94253	ATC	.	.		0.418	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		C	51491853	G	C	51491853	3	2	29	1	0	0	0	0	1	0	0	0	11980	932	33	4	505	4	PKHD1	6	51491853	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	23633648	51491853	119623214	38	3654										
EPHA7	2045	hgsc.bcm.edu	37	chr6	93967865	93967865	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	aacattcgggtggtcaaactGccccatgatgcttgcttcac	9	12	2	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr6:93967865G>A	ENST00000369303.4	-	11	2246	c.2062C>T	c.(2062-2064)Cag>Tag	p.Q688*		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	688	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TGGTCAAACTGCCCCATGATG	0.388																																					p.Q688X		Atlas-SNP	.											.	EPHA7	251	.	0			c.C2062T						.						126	125	125					6																	93967865		2203	4300	6503	SO:0001587	stop_gained	2045	exon11			CAAACTGCCCCAT	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2062C>T	chr6.hg19:g.93967865G>A	ENSP00000358309:p.Gln688*	64.0	0.0		46.0	17.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Nonsense_Mutation	SNP	ENST00000369303.4	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	G	41	8.647399	0.98899	.	.	ENSG00000135333	ENST00000369303	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	.	.	.	X	688	.	ENSP00000358309:Q688X	Q	-	1	0	EPHA7	94024586	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.894000	0.99253	0.591000	0.81541	CAG	.	.		0.388	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			A	93967865	G	A	93967865	4	1	29	1	0	0	0	0	0	1	0	0	5174	1328	46	3	962	3	EPHA7	6	93967865	Nonsense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	42476012	93967865	77147202	39	3655										
TRDN	10345	hgsc.bcm.edu	37	chr6	123658784	123658784	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ctttatctttcagaattgaaGaagtcttcccagatttttct	5	8	4	4			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr6:123658784G>A	ENST00000398178.3	-	22	1421	c.1400C>T	c.(1399-1401)tCt>tTt	p.S467F	TRDN_ENST00000334268.4_Missense_Mutation_p.S467F	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	467					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		CAGAATTGAAGAAGTCTTCCC	0.289																																					p.S467F		Atlas-SNP	.											.	TRDN	88	.	0			c.C1400T						.						24	22	23					6																	123658784		1163	2539	3702	SO:0001583	missense	10345	exon22			ATTGAAGAAGTCT	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1400C>T	chr6.hg19:g.123658784G>A	ENSP00000381240:p.Ser467Phe	205.0	0.0		178.0	30.0	NM_006073	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	hg19	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.824110	0.32237	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.20069	2.1;2.11	4.68	4.68	0.58851	.	0.000000	0.41605	D	0.000860	T	0.20536	0.0494	N	0.24115	0.695	0.80722	D	1	D	0.69078	0.997	D	0.66196	0.942	T	0.01762	-1.1279	10	0.62326	D	0.03	-6.0861	13.2958	0.60296	0.0:0.0:1.0:0.0	.	467	Q13061	TRDN_HUMAN	F	467;469;467	ENSP00000381240:S467F;ENSP00000333984:S467F	ENSP00000333984:S467F	S	-	2	0	TRDN	123700483	1.000000	0.71417	0.980000	0.43619	0.037000	0.13140	4.759000	0.62227	2.608000	0.88229	0.650000	0.86243	TCT	.	.		0.289	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	123658784	G	A	123658784	3	1	29	1	0	0	0	0	1	0	0	0	16483	942	33	3	869	3	TRDN	6	123658784	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	29690919	123658784	47456283	40	3656										
C7orf10	79783	hgsc.bcm.edu	37	chr7	40174633	40174633	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gcacgcgatgctggcgacgcTggcgagggtggcagctctgc	18	12	1	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr7:40174633T>A	ENST00000335693.4	+	1	58	c.35T>A	c.(34-36)cTg>cAg	p.L12Q	MPLKIP_ENST00000306984.6_5'Flank|C7orf10_ENST00000540834.1_Missense_Mutation_p.L5Q|C7orf10_ENST00000309930.5_Missense_Mutation_p.L12Q|C7orf10_ENST00000401647.2_Missense_Mutation_p.L12Q	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		12					metabolic process (GO:0008152)	mitochondrion (GO:0005739)	succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369)			endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)	18						CTGGCGACGCTGGCGAGGGTG	0.736																																					p.L12Q		Atlas-SNP	.											.	C7orf10	99	.	0			c.T35A						.						6	9	8					7																	40174633		1955	4073	6028	SO:0001583	missense	79783	exon1			CGACGCTGGCGAG																												ENST00000335693.4:c.35T>A	chr7.hg19:g.40174633T>A	ENSP00000338475:p.Leu12Gln	176.0	0.0		165.0	25.0	NM_001193313	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	Missense_Mutation	SNP	ENST00000335693.4	hg19	CCDS55105.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.765|8.765	0.924496|0.924496	0.18056|0.18056	.|.	.|.	ENSG00000175600|ENSG00000175600	ENST00000309930;ENST00000401647;ENST00000335693;ENST00000540834|ENST00000413931;ENST00000416370	T;T;T;T|.	0.73575|.	0.87;0.84;0.87;-0.76|.	3.38|3.38	2.2|2.2	0.27929|0.27929	.|.	2.083540|.	0.03763|.	U|.	0.258475|.	T|T	0.16342|0.16342	0.0393|0.0393	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	P;P;P|.	0.48503|.	0.61;0.61;0.911|.	B;B;P|.	0.49421|.	0.193;0.193;0.61|.	T|T	0.24799|0.24799	-1.0150|-1.0150	10|5	0.62326|.	D|.	0.03|.	0.0534|0.0534	5.4743|5.4743	0.16688|0.16688	0.0:0.1337:0.0:0.8663|0.0:0.1337:0.0:0.8663	.|.	12;12;12|.	Q4KMW8;Q9HAC7;Q9HAC7-2|.	.;CG010_HUMAN;.|.	Q|R	12;12;12;5|7	ENSP00000312054:L12Q;ENSP00000385222:L12Q;ENSP00000338475:L12Q;ENSP00000445521:L5Q|.	ENSP00000312054:L12Q|.	L|W	+|+	2|1	0|0	C7orf10|C7orf10	40141158|40141158	0.003000|0.003000	0.15002|0.15002	0.015000|0.015000	0.15790|0.15790	0.025000|0.025000	0.11179|0.11179	-0.364000|-0.364000	0.07583|0.07583	0.487000|0.487000	0.27698|0.27698	0.450000|0.450000	0.29827|0.29827	CTG|TGG	.	.		0.736	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338388.1			A	40174633	T	A	40174633	3	1	29	1	0	0	0	0	1	0	0	0	2378	1580	55	4	37	4	C7orf10	7	40174633	Missense_Mutation	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10		40174633	118964030	41	3657										
C7orf25	79020	hgsc.bcm.edu	37	chr7	42949520	42949520	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ttcgcttaattaacacagtgGccctctctctctccccaggt	6	15	2	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr7:42949520G>A	ENST00000350427.4	-	2	1255	c.980C>T	c.(979-981)gCc>gTc	p.A327V	C7orf25_ENST00000447342.1_Missense_Mutation_p.A327V|PSMA2_ENST00000442788.1_3'UTR|C7orf25_ENST00000438029.1_Missense_Mutation_p.A327V|C7orf25_ENST00000431882.2_Missense_Mutation_p.A385V			Q9BPX7	CG025_HUMAN	chromosome 7 open reading frame 25	327										endometrium(6)|kidney(1)|large_intestine(7)|lung(2)|skin(1)	17						TAACACAGTGGCCCTCTCTCT	0.448																																					p.A385V		Atlas-SNP	.											.	C7orf25	36	.	0			c.C1154T						.						89	84	86					7																	42949520		2203	4300	6503	SO:0001583	missense	79020	exon2			ACAGTGGCCCTCT	BC001845	CCDS5466.1, CCDS47576.1	7p14.1	2011-11-24			ENSG00000136197	ENSG00000136197			21703	protein-coding gene	gene with protein product							Standard	NM_024054		Approved	MGC2821	uc003thx.4	Q9BPX7	OTTHUMG00000128869	ENST00000350427.4:c.980C>T	chr7.hg19:g.42949520G>A	ENSP00000343364:p.Ala327Val	190.0	0.0		173.0	15.0	NM_001099858	A4D1V2|J3KR36|Q9H779	Missense_Mutation	SNP	ENST00000350427.4	hg19	CCDS5466.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.363477	0.82353	.	.	ENSG00000136197	ENST00000350427;ENST00000447342;ENST00000431882;ENST00000438029	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.71117	0.3302	M	0.76727	2.345	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.91635	0.999;0.934	T	0.71649	-0.4529	10	0.59425	D	0.04	-5.28	20.0212	0.97504	0.0:0.0:1.0:0.0	.	385;327	B4DQM3;Q9BPX7	.;CG025_HUMAN	V	327;327;385;327	ENSP00000343364:A327V;ENSP00000413029:A327V;ENSP00000416290:A385V;ENSP00000396597:A327V	ENSP00000343364:A327V	A	-	2	0	C7orf25	42916045	1.000000	0.71417	0.967000	0.41034	0.902000	0.53008	9.434000	0.97515	2.735000	0.93741	0.561000	0.74099	GCC	.	.		0.448	C7orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250814.2	NM_024054		A	42949520	G	A	42949520	3	1	29	1	0	0	0	0	1	0	0	0	2382	1203	42	3	289	3	C7orf25	7	42949520	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	2774887	42949520	116189143	42	3658										
GIMAP1	170575	hgsc.bcm.edu	37	chr7	150417974	150417974	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ttctgggtgctgctccacagGcggtggtcggaggccgttgc	17	11	1	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr7:150417974G>T	ENST00000307194.5	+	3	1022	c.882G>T	c.(880-882)agG>agT	p.R294S		NM_130759.3	NP_570115.1	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	294					B cell differentiation (GO:0030183)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGCTCCACAGGCGGTGGTCGG	0.652																																					p.R294S		Atlas-SNP	.											.	GIMAP1	61	.	0			c.G882T						.						13	13	13					7																	150417974		1894	3819	5713	SO:0001583	missense	170575	exon3			CCACAGGCGGTGG	AJ306287	CCDS5906.1	7q36.1	2014-04-04			ENSG00000213203	ENSG00000213203		"GTPases, IMAP"	23237	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 2"	608084				15474311, 18701445	Standard	NM_130759		Approved	HIMAP1, IMAP38, IMAP1, IAN2		Q8WWP7	OTTHUMG00000157489	ENST00000307194.5:c.882G>T	chr7.hg19:g.150417974G>T	ENSP00000302833:p.Arg294Ser	85.0	0.0		85.0	28.0	NM_130759	B2RCI3|Q8NAZ0	Missense_Mutation	SNP	ENST00000307194.5	hg19	CCDS5906.1	.	.	.	.	.	.	.	.	.	.	G	10.11	1.259425	0.23051	.	.	ENSG00000213203	ENST00000307194	T	0.06449	3.3	2.87	-3.77	0.04346	.	35.744600	0.01164	U	0.006710	T	0.04182	0.0116	L	0.29908	0.895	0.09310	N	1	P	0.43750	0.816	B	0.36719	0.231	T	0.23940	-1.0174	10	0.41790	T	0.15	.	1.2107	0.01904	0.454:0.1691:0.2222:0.1547	.	294	Q8WWP7	GIMA1_HUMAN	S	294	ENSP00000302833:R294S	ENSP00000302833:R294S	R	+	3	2	GIMAP1	150048907	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.856000	0.04290	-1.085000	0.03088	-0.142000	0.14014	AGG	.	.		0.652	GIMAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348951.2	NM_130759		T	150417974	G	T	150417974	3	4	29	1	0	0	0	0	1	0	0	0	6387	1194	42	3	888	3	GIMAP1	7	150417974	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	107468454	150417974	8720689	43	3659										
MYBL1	4603	hgsc.bcm.edu	37	chr8	67478976	67478976	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cctgattcttctttttcccaAttatctaagactagtgattt	4	9	3	3			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr8:67478976A>G	ENST00000522677.3	-	14	2303	c.1893T>C	c.(1891-1893)aaT>aaC	p.N631N	MYBL1_ENST00000522419.1_5'UTR|MYBL1_ENST00000517885.1_Silent_p.N289N|MYBL1_ENST00000524176.2_Silent_p.N631N	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	631					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			CTTTTTCCCAATTATCTAAGA	0.338																																					p.N631N		Atlas-SNP	.											.	MYBL1	73	.	0			c.T1893C						.						109	104	105					8																	67478976		1812	4077	5889	SO:0001819	synonymous_variant	4603	exon14			TTCCCAATTATCT	X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.1893T>C	chr8.hg19:g.67478976A>G		100.0	0.0		151.0	59.0	NM_001080416	E7EW29|Q495F9	Silent	SNP	ENST00000522677.3	hg19	CCDS47867.1																																																																																			.	.		0.338	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		G	67478976	A	G	67478976	2	3	29	1	0	0	0	0	0	0	0	1	10018	98	4	2		2	MYBL1	8	67478976	Silent	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10		67478976	78885046	44	3660										
SLCO5A1	81796	hgsc.bcm.edu	37	chr8	70674091	70674091	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cccactgcagggccaagtgcTcccatgacatacatgatggc	10	14	0	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr8:70674091T>A	ENST00000260126.4	-	3	1633	c.927A>T	c.(925-927)ggA>ggT	p.G309G	SLCO5A1_ENST00000528658.1_5'UTR|SLCO5A1_ENST00000524945.1_Silent_p.G309G|SLCO5A1_ENST00000530307.1_Silent_p.G309G	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			GGCCAAGTGCTCCCATGACAT	0.423																																					p.G309G		Atlas-SNP	.											.	SLCO5A1	142	.	0			c.A927T						.						89	85	86					8																	70674091		2203	4300	6503	SO:0001819	synonymous_variant	81796	exon3			AAGTGCTCCCATG	AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"Solute carriers"	19046	protein-coding gene	gene with protein product		613543	"solute carrier family 21 (organic anion transporter), member 15"	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.927A>T	chr8.hg19:g.70674091T>A		69.0	0.0		101.0	22.0	NM_030958	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Silent	SNP	ENST00000260126.4	hg19	CCDS6205.1																																																																																			.	.		0.423	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958		A	70674091	T	A	70674091	2	1	29	1	0	0	0	0	0	0	0	1	14746	1538	54	4		4	SLCO5A1	8	70674091	Silent	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	3195115	70674091	75689931	45	3661										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100287443	100287443	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cagatttgatggccttcacaAtccaagttccacaatatatt	5	10	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr8:100287443A>G	ENST00000358544.2	+	19	2896	c.2785A>G	c.(2785-2787)Atc>Gtc	p.I929V	VPS13B_ENST00000395996.1_Missense_Mutation_p.I929V|VPS13B_ENST00000357162.2_Missense_Mutation_p.I929V	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	929					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GGCCTTCACAATCCAAGTTCC	0.393																																					p.I929V	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A2785G						.						148	150	149					8																	100287443		2203	4300	6503	SO:0001583	missense	157680	exon19			TTCACAATCCAAG	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.2785A>G	chr8.hg19:g.100287443A>G	ENSP00000351346:p.Ile929Val	96.0	0.0		122.0	11.0	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	7.506	0.653672	0.14580	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.68479	-0.33;-0.33;-0.04	5.43	3.04	0.35103	.	0.255369	0.32736	N	0.005702	T	0.41026	0.1141	N	0.12182	0.205	0.33665	D	0.610241	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.39722	-0.9600	10	0.13108	T	0.6	.	7.2037	0.25895	0.5697:0.0:0.4303:0.0	.	929;929;929;929	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	V	929	ENSP00000349685:I929V;ENSP00000351346:I929V;ENSP00000379318:I929V	ENSP00000349685:I929V	I	+	1	0	VPS13B	100356619	0.989000	0.36119	0.975000	0.42487	0.992000	0.81027	0.280000	0.18790	1.098000	0.41479	0.482000	0.46254	ATC	.	.		0.393	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100287443	A	G	100287443	3	3	29	1	0	0	0	0	1	0	0	0	17205	101	4	2	2978	2	VPS13B	8	100287443	Missense_Mutation	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10	29613352	100287443	46076579	46	3662										
ROR2	4920	hgsc.bcm.edu	37	chr9	94493238	94493238	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	atgcgtacgtttttattctgCgtaaagcaccaggggccctc	10	11	1	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr9:94493238C>T	ENST00000375708.3	-	7	1335	c.1137G>A	c.(1135-1137)acG>acA	p.T379T	ROR2_ENST00000375715.1_Silent_p.T239T|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	379	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						TTTTATTCTGCGTAAAGCACC	0.527																																					p.T379T		Atlas-SNP	.											.	ROR2	167	.	0			c.G1137A						.						86	78	81					9																	94493238		2203	4300	6503	SO:0001819	synonymous_variant	4920	exon7			ATTCTGCGTAAAG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.1137G>A	chr9.hg19:g.94493238C>T		132.0	0.0		99.0	23.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	hg19	CCDS6691.1																																																																																			.	.		0.527	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			T	94493238	C	T	94493238	2	4	29	1	0	0	0	0	0	0	0	1	13542	755	27	1		1	ROR2	9	94493238	Silent	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10		94493238	46720193	47	3663										
TNC	3371	hgsc.bcm.edu	37	chr9	117853261	117853261	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	agcgagggcaaggaaagcaaGaaagacacctgccaacagct	12	10	0	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr9:117853261G>T	ENST00000350763.4	-	2	448	c.37C>A	c.(37-39)Ctt>Att	p.L13I	TNC_ENST00000537320.1_Missense_Mutation_p.L13I|TNC_ENST00000341037.4_Missense_Mutation_p.L13I|TNC_ENST00000535648.1_Missense_Mutation_p.L13I|TNC_ENST00000345230.3_Missense_Mutation_p.L13I|TNC_ENST00000423613.2_Missense_Mutation_p.L13I|TNC_ENST00000346706.3_Missense_Mutation_p.L13I|TNC_ENST00000542877.1_Missense_Mutation_p.L13I|TNC_ENST00000340094.3_Missense_Mutation_p.L13I	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	13					bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						AGGAAAGCAAGAAAGACACCT	0.587																																					p.L13I		Atlas-SNP	.											.	TNC	282	.	0			c.C37A						.						42	42	42					9																	117853261		2203	4300	6503	SO:0001583	missense	3371	exon2			AAGCAAGAAAGAC		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.37C>A	chr9.hg19:g.117853261G>T	ENSP00000265131:p.Leu13Ile	33.0	0.0		49.0	10.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.640089	0.29157	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877;ENST00000534839	T;T;T;T;T;T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35	5.58	2.17	0.27698	.	0.758451	0.12410	N	0.471341	T	0.23611	0.0571	L	0.31065	0.9	0.09310	N	1	B;B	0.27791	0.189;0.004	B;B	0.25987	0.065;0.009	T	0.18871	-1.0323	10	0.48119	T	0.1	.	5.0289	0.14400	0.0759:0.2084:0.4899:0.2258	.	13;13	E9PC84;P24821	.;TENA_HUMAN	I	13	ENSP00000344400:L13I;ENSP00000438152:L13I;ENSP00000344555:L13I;ENSP00000345861:L13I;ENSP00000265131:L13I;ENSP00000339553:L13I;ENSP00000411406:L13I;ENSP00000443478:L13I;ENSP00000442242:L13I;ENSP00000443469:L13I	ENSP00000344400:L13I	L	-	1	0	TNC	116893082	0.079000	0.21365	0.111000	0.21465	0.051000	0.14879	0.120000	0.15647	0.661000	0.30985	0.462000	0.41574	CTT	.	.		0.587	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117853261	G	T	117853261	3	4	29	1	0	0	0	0	1	0	0	0	16285	942	33	3	6676	3	TNC	9	117853261	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	23360023	117853261	23360170	48	3664										
SLC2A6	11182	hgsc.bcm.edu	37	chr9	136340120	136340120	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tgtcgaagatggactgcaggTagaccaggatgggcgtgatg	17	6	0	3			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr9:136340120T>C	ENST00000371899.4	-	6	967	c.890A>G	c.(889-891)tAc>tGc	p.Y297C	SLC2A6_ENST00000371897.4_Missense_Mutation_p.Y297C|SLC2A6_ENST00000485978.1_5'UTR	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	297					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		GGACTGCAGGTAGACCAGGAT	0.711																																					p.Y297C		Atlas-SNP	.											.	SLC2A6	31	.	0			c.A890G						.						28	21	23					9																	136340120		2188	4294	6482	SO:0001583	missense	11182	exon6			TGCAGGTAGACCA	AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"Solute carriers"	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.890A>G	chr9.hg19:g.136340120T>C	ENSP00000360966:p.Tyr297Cys	127.0	0.0		89.0	4.0	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	hg19	CCDS6975.1	.	.	.	.	.	.	.	.	.	.	T	18.96	3.734260	0.69189	.	.	ENSG00000160326	ENST00000371897;ENST00000371899	D;D	0.84070	-1.8;-1.8	5.31	4.15	0.48705	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.93177	0.7827	H	0.97103	3.94	0.51767	D	0.999937	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.92916	0.6351	10	0.87932	D	0	.	9.2422	0.37504	0.2877:0.0:0.0:0.7123	.	297;297	Q9UGQ3-2;Q9UGQ3	.;GTR6_HUMAN	C	297	ENSP00000360964:Y297C;ENSP00000360966:Y297C	ENSP00000360964:Y297C	Y	-	2	0	SLC2A6	135329941	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.495000	0.60353	0.829000	0.34733	0.459000	0.35465	TAC	.	.		0.711	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585		C	136340120	T	C	136340120	3	2	29	1	0	0	0	0	1	0	0	0	14564	1638	57	2	653	2	SLC2A6	9	136340120	Missense_Mutation	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	18486859	136340120	4873311	49	3665										
ARMC4	55130	hgsc.bcm.edu	37	chr10	28228827	28228827	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ctgggagagttcactgcaccTggtaaatggccatggcgcag	14	10	1	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr10:28228827T>C	ENST00000305242.5	-	14	2188	c.2096A>G	c.(2095-2097)cAg>cGg	p.Q699R	ARMC4_ENST00000545014.1_Splice_Site_p.Q224R|ARMC4_ENST00000537576.1_Splice_Site_p.Q391R	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	699					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						TCACTGCACCTGGTAAATGGC	0.473																																					p.Q699R		Atlas-SNP	.											.	ARMC4	177	.	0			c.A2096G						.						87	75	79					10																	28228827		2203	4300	6503	SO:0001630	splice_region_variant	55130	exon14			TGCACCTGGTAAA	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"Armadillo repeat containing"	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2097+1A>G	chr10.hg19:g.28228827T>C		77.0	0.0		72.0	13.0	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	hg19	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.617874	0.46736	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000545014	D;D;D	0.93763	-3.28;-3.28;-3.28	5.62	5.62	0.85841	Armadillo-like helical (1);Armadillo-type fold (1);	0.100059	0.64402	D	0.000001	D	0.86619	0.5976	N	0.08118	0	0.80722	D	1	B;B	0.18310	0.004;0.027	B;B	0.25759	0.005;0.063	T	0.83007	-0.0174	10	0.48119	T	0.1	-24.6254	14.94	0.70986	0.0:0.0:0.0:1.0	.	224;699	B7Z7I1;Q5T2S8	.;ARMC4_HUMAN	R	391;699;224	ENSP00000443208:Q391R;ENSP00000306410:Q699R;ENSP00000441076:Q224R	ENSP00000306410:Q699R	Q	-	2	0	ARMC4	28268833	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	6.444000	0.73452	2.266000	0.75297	0.533000	0.62120	CAG	.	.		0.473	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	Missense_Mutation	C	28228827	T	C	28228827	5	2	29	1	0	0	0	0	0	0	1	0	953	1594	55	2	1066	2	ARMC4	10	28228827	Splice_Site	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10		28228827	107305920	50	3666										
VTI1A	143187	hgsc.bcm.edu	37	chr10	114298012	114298012	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ttttctttttcagagggcacAtctgctcgataacacagaga	8	9	3	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr10:114298012A>T	ENST00000393077.2	+	5	466	c.350A>T	c.(349-351)cAt>cTt	p.H117L	VTI1A_ENST00000432306.1_Missense_Mutation_p.H117L	NM_145206.2	NP_660207.2	Q96AJ9	VTI1A_HUMAN	vesicle transport through interaction with t-SNAREs 1A	117					intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021)	SNAP receptor activity (GO:0005484)		VTI1A/TCF7L2(8)	breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		CAGAGGGCACATCTGCTCGAT	0.428			T	TCF7L2	colorectal																																p.H117L		Atlas-SNP	.		Dom	yes		10	10q25.2	143187	vesicle transport through interaction with t-SNAREs homolog 1A		E	.	VTI1A	15	.	0			c.A350T						.						64	70	68					10																	114298012		2203	4300	6503	SO:0001583	missense	143187	exon5			GGGCACATCTGCT	BC017052	CCDS7575.2	10q25.2	2012-12-10	2012-12-10		ENSG00000151532	ENSG00000151532			17792	protein-coding gene	gene with protein product		614316	"vesicle transport through interaction with t-SNAREs homolog 1A (yeast)"			9446565	Standard	NM_145206		Approved	MVti1, Vti1a, Vti1-rp2	uc001kzz.3	Q96AJ9	OTTHUMG00000019063	ENST00000393077.2:c.350A>T	chr10.hg19:g.114298012A>T	ENSP00000376792:p.His117Leu	485.0	0.0		350.0	53.0	NM_145206	A2A307|B4E137|Q5W0D7	Missense_Mutation	SNP	ENST00000393077.2	hg19	CCDS7575.2	.	.	.	.	.	.	.	.	.	.	A	14.79	2.641967	0.47153	.	.	ENSG00000151532	ENST00000393077;ENST00000432306	.	.	.	5.86	5.86	0.93980	Target SNARE coiled-coil domain (1);	0.000000	0.85682	D	0.000000	T	0.40222	0.1108	N	0.08118	0	0.58432	D	0.999999	B;B	0.09022	0.002;0.001	B;B	0.14578	0.011;0.008	T	0.21075	-1.0256	9	0.34782	T	0.22	-17.2828	16.5602	0.84551	1.0:0.0:0.0:0.0	.	117;117	Q5W0D7;Q96AJ9	.;VTI1A_HUMAN	L	117	.	ENSP00000376792:H117L	H	+	2	0	VTI1A	114288002	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.611000	0.90905	2.367000	0.80283	0.528000	0.53228	CAT	.	.		0.428	VTI1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050397.2			T	114298012	A	T	114298012	3	4	29	1	0	0	0	0	1	0	0	0	17250	217	8	4	368	4	VTI1A	10	114298012	Missense_Mutation	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10	86069185	114298012	21236735	51	3667										
NAV2	89797	hgsc.bcm.edu	37	chr11	20136228	20136228	+	Frame_Shift_Del	DEL	C	C	-													0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gcccacaacagcacgagtggCctcccctgctgcagttacgg							TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr11:20136228delC	ENST00000396087.3	+	40	7327	c.7228delC	c.(7228-7230)cctfs	p.P2411fs	NAV2_ENST00000360655.4_Frame_Shift_Del_p.P2288fs|NAV2_ENST00000349880.4_Frame_Shift_Del_p.P2352fs|NAV2_ENST00000311043.8_Frame_Shift_Del_p.P1416fs|NAV2_ENST00000533917.1_Frame_Shift_Del_p.P1416fs|NAV2_ENST00000396085.1_Frame_Shift_Del_p.P2355fs|NAV2_ENST00000540292.1_Frame_Shift_Del_p.P2342fs|NAV2_ENST00000527559.2_Frame_Shift_Del_p.P2340fs	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2411					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						GCACGAGTGGCCTCCCCTGCT	0.612																																					p.W2409fs		Atlas-INDEL	.											.	NAV2	255	.	0			c.7227delG						.						78	60	66					11																	20136228		2203	4300	6503	SO:0001589	frameshift_variant	89797	exon39			.	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.7228delC	chr11.hg19:g.20136228delC	ENSP00000379396:p.Pro2411fs	66.0	0.0		101.0	11.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Frame_Shift_Del	DEL	ENST00000396087.3	hg19	CCDS58126.1																																																																																			.	.		0.612	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		-	20136228	C	-	20136228	7	5	29	1	0	1	0	1	0	0	0	0	10193	739	26	0	7315	0	NAV2	11	20136228	Frame_Shift_Del	DEL	C	TCGA-5R-AAAM-01A-12D-A40R-10		20136228	114870288	52	3668										
OR5F1	338674	hgsc.bcm.edu	37	chr11	55761610	55761610	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gagtcacagaatgacaagctGctgacatggcttgtgttgac	12	8	1	4			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr11:55761610G>T	ENST00000278409.1	-	1	491	c.492C>A	c.(490-492)agC>agA	p.S164R		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	164					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					ATGACAAGCTGCTGACATGGC	0.473																																					p.S164R		Atlas-SNP	.											.	OR5F1	116	.	0			c.C492A						.						75	71	72					11																	55761610		2201	4296	6497	SO:0001583	missense	338674	exon1			CAAGCTGCTGACA	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"GPCR / Class A : Olfactory receptors"	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.492C>A	chr11.hg19:g.55761610G>T	ENSP00000278409:p.Ser164Arg	142.0	0.0		144.0	38.0	NM_003697	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	hg19	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	G	7.753	0.703698	0.15172	.	.	ENSG00000149133	ENST00000278409	T	0.00164	8.64	3.03	1.97	0.26223	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00412	0.0013	M	0.87456	2.885	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.47959	-0.9076	9	0.87932	D	0	.	2.372	0.04333	0.2559:0.0:0.4899:0.2542	.	164	O95221	OR5F1_HUMAN	R	164	ENSP00000278409:S164R	ENSP00000278409:S164R	S	-	3	2	OR5F1	55518186	0.000000	0.05858	0.082000	0.20525	0.016000	0.09150	0.040000	0.13905	1.422000	0.47177	0.297000	0.19635	AGC	.	.		0.473	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697		T	55761610	G	T	55761610	3	4	29	1	0	0	0	0	1	0	0	0	11167	1310	46	3	455	3	OR5F1	11	55761610	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	35625382	55761610	79244906	53	3669										
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117789435	117789435	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cccggcccggaggtgtcccaGctggagatgcctgggctgga	17	13	0	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr11:117789435G>T	ENST00000430170.2	-	2	227	c.140C>A	c.(139-141)gCt>gAt	p.A47D	TMPRSS13_ENST00000524993.1_Missense_Mutation_p.A47D|TMPRSS13_ENST00000445164.2_Missense_Mutation_p.A47D|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.A47D|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.A47D	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	47	13 X 5 AA repeats of A-S-P-A-[GLQR].|4 X 5 AA repeats of T-P-P-G-R.|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		AGGTGTCCCAGCTGGAGATGC	0.672																																					p.A47D		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.C140A						.						40	47	45					11																	117789435		1886	4105	5991	SO:0001583	missense	84000	exon2			GTCCCAGCTGGAG	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"Serine peptidases / Transmembrane"	29808	protein-coding gene	gene with protein product		610050	"transmembrane protease, serine 11"	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.140C>A	chr11.hg19:g.117789435G>T	ENSP00000387702:p.Ala47Asp	69.0	0.0		95.0	4.0	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	hg19	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.093951	0.36952	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	D;D;D;D;D	0.89050	-2.46;-2.44;-2.44;-2.45;-2.36	2.19	0.0442	0.14224	.	.	.	.	.	T	0.78457	0.4286	L	0.27053	0.805	0.09310	N	1	B;B	0.15141	0.003;0.012	B;B	0.11329	0.006;0.004	T	0.62849	-0.6767	9	0.33940	T	0.23	.	4.476	0.11739	0.1482:0.4707:0.3811:0.0	.	47;47	Q9BYE2-4;E9PRA0	.;.	D	47	ENSP00000435813:A47D;ENSP00000434279:A47D;ENSP00000387702:A47D;ENSP00000394114:A47D;ENSP00000436502:A47D	ENSP00000337113:A47D	A	-	2	0	TMPRSS13	117294645	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.354000	0.07681	0.031000	0.15407	-0.122000	0.15005	GCT	.	.		0.672	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		T	117789435	G	T	117789435	3	4	29	1	0	0	0	0	1	0	0	0	16260	971	34	3	1611	3	TMPRSS13	11	117789435	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	62027825	117789435	17217081	54	3670										
HSPA8	3312	hgsc.bcm.edu	37	chr11	122929825	122929825	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tgaaggtctgtgtctgcttgGtaggaatggtggtattacgc	15	5	2	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr11:122929825G>T	ENST00000532636.1	-	6	1384	c.1265C>A	c.(1264-1266)aCc>aAc	p.T422N	HSPA8_ENST00000453788.2_Missense_Mutation_p.T422N|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000526862.1_5'Flank|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000526110.1_Missense_Mutation_p.T403N|HSPA8_ENST00000533540.1_Missense_Mutation_p.T276N|HSPA8_ENST00000534319.1_Missense_Mutation_p.T186N|HSPA8_ENST00000227378.3_Missense_Mutation_p.T422N|HSPA8_ENST00000534624.1_Missense_Mutation_p.T422N|SNORD14D_ENST00000384390.1_RNA			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	422					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		TGTCTGCTTGGTAGGAATGGT	0.448																																					p.T422N	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.C1265A						.						140	124	129					11																	122929825		2202	4299	6501	SO:0001583	missense	3312	exon6			TGCTTGGTAGGAA	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"Heat shock proteins / HSP70"	5241	protein-coding gene	gene with protein product		600816	"heat shock 70kD protein 8"	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.1265C>A	chr11.hg19:g.122929825G>T	ENSP00000437125:p.Thr422Asn	165.0	0.0		150.0	46.0	NM_006597	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	hg19	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934284	0.73442	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000534319;ENST00000526110;ENST00000524552	T;T;T;T;T;T;T;T	0.04917	3.53;3.53;3.53;3.53;3.53;3.53;3.53;3.53	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.23886	0.0578	H	0.97415	4	0.80722	D	1	B;B;B	0.25105	0.022;0.118;0.022	B;B;B	0.24974	0.057;0.044;0.057	T	0.39014	-0.9634	10	0.87932	D	0	-14.5597	18.3089	0.90192	0.0:0.0:1.0:0.0	.	422;422;422	Q53GZ6;P11142-2;P11142	.;.;HSP7C_HUMAN	N	422;276;422;422;422;186;403;13	ENSP00000437125:T422N;ENSP00000437189:T276N;ENSP00000432083:T422N;ENSP00000404372:T422N;ENSP00000227378:T422N;ENSP00000433316:T186N;ENSP00000433584:T403N;ENSP00000435908:T13N	ENSP00000227378:T422N	T	-	2	0	HSPA8	122435035	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	9.583000	0.98217	2.390000	0.81377	0.561000	0.74099	ACC	.	.		0.448	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			T	122929825	G	T	122929825	3	4	29	1	0	0	0	0	1	0	0	0	7425	1261	44	3	691	3	HSPA8	11	122929825	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	5140390	122929825	12076691	55	3671										
IFLTD1	160492	hgsc.bcm.edu	37	chr12	25679068	25679068	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gcacaggattgttatacaatCaggacttgctctaaacttgt	8	8	2	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr12:25679068C>G	ENST00000282881.6	-	5	849	c.700G>C	c.(700-702)Gat>Cat	p.D234H	IFLTD1_ENST00000458174.2_Missense_Mutation_p.D255H|IFLTD1_ENST00000539744.1_Missense_Mutation_p.D137H|IFLTD1_ENST00000445693.1_Missense_Mutation_p.D171H|IFLTD1_ENST00000413632.2_Intron	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		234	LTD.				cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GTTATACAATCAGGACTTGCT	0.363																																					p.D255H		Atlas-SNP	.											.	IFLTD1	121	.	0			c.G763C						.						115	107	110					12																	25679068		2203	4300	6503	SO:0001583	missense	160492	exon6			TACAATCAGGACT																												ENST00000282881.6:c.700G>C	chr12.hg19:g.25679068C>G	ENSP00000282881:p.Asp234His	66.0	0.0		99.0	32.0	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	hg19	CCDS8704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.50|11.50	1.657786|1.657786	0.29425|0.29425	.|.	.|.	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000545543|ENST00000543629	D;D;D;D;D|.	0.98633|.	-5.04;-5.04;-5.04;-5.04;-5.04|.	5.81|5.81	1.44|1.44	0.22558|0.22558	Intermediate filament, C-terminal (1);|.	.|.	.|.	.|.	.|.	T|.	0.33411|.	0.0862|.	L|L	0.38838|0.38838	1.175|1.175	0.09310|0.09310	N|N	0.999999|0.999999	D;D;D|.	0.60575|.	0.967;0.967;0.988|.	P;P;D|.	0.64237|.	0.562;0.773;0.923|.	T|.	0.24083|.	-1.0170|.	9|.	0.72032|.	D|.	0.01|.	-1.0338|-1.0338	6.7724|6.7724	0.23601|0.23601	0.0:0.5079:0.0:0.4921|0.0:0.5079:0.0:0.4921	.|.	171;255;234|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9|.	.;.;ILFT1_HUMAN|.	H|S	234;137;255;171;64|8	ENSP00000282881:D234H;ENSP00000443132:D137H;ENSP00000407353:D255H;ENSP00000407043:D171H;ENSP00000443596:D64H|.	ENSP00000282881:D234H|.	D|X	-|-	1|2	0|2	IFLTD1|IFLTD1	25570335|25570335	0.002000|0.002000	0.14202|0.14202	0.003000|0.003000	0.11579|0.11579	0.227000|0.227000	0.25037|0.25037	0.582000|0.582000	0.23834|0.23834	0.252000|0.252000	0.21531|0.21531	0.655000|0.655000	0.94253|0.94253	GAT|TGA	.	.		0.363	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1			G	25679068	C	G	25679068	3	3	29	1	0	0	0	0	1	0	0	0	7539	826	29	4	482	4	IFLTD1	12	25679068	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10		25679068	108172827	56	3672										
ANO6	196527	hgsc.bcm.edu	37	chr12	45814873	45814873	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ggccatgatcatagctttcaCgtcggacatgatcccccgcc	9	15	2	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr12:45814873C>T	ENST00000320560.8	+	18	2439	c.2237C>T	c.(2236-2238)aCg>aTg	p.T746M	ANO6_ENST00000435642.1_Missense_Mutation_p.T746M|ANO6_ENST00000441606.2_Missense_Mutation_p.T728M|ANO6_ENST00000423947.3_Missense_Mutation_p.T767M|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000425752.2_Missense_Mutation_p.T746M	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	746					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						ATAGCTTTCACGTCGGACATG	0.488																																					p.T767M		Atlas-SNP	.											.	ANO6	163	.	0			c.C2300T						.						176	153	161					12																	45814873		2203	4300	6503	SO:0001583	missense	196527	exon19			CTTTCACGTCGGA	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.2237C>T	chr12.hg19:g.45814873C>T	ENSP00000320087:p.Thr746Met	146.0	0.0		143.0	34.0	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.937115	0.92458	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.85513	0.5714	H	0.95004	3.61	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.992;0.986;0.979;0.996	D	0.89344	0.3656	10	0.87932	D	0	.	19.2834	0.94061	0.0:1.0:0.0:0.0	.	728;767;746;746	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	M	746;767;746;746;728	ENSP00000391417:T746M;ENSP00000409126:T767M;ENSP00000413840:T746M;ENSP00000320087:T746M;ENSP00000413137:T728M	ENSP00000320087:T746M	T	+	2	0	ANO6	44101140	1.000000	0.71417	0.966000	0.40874	0.994000	0.84299	5.983000	0.70540	2.717000	0.92951	0.650000	0.86243	ACG	.	.		0.488	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743		T	45814873	C	T	45814873	3	4	29	1	0	0	0	0	1	0	0	0	701	536	19	1	2327	1	ANO6	12	45814873	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	20135805	45814873	88037022	57	3673										
RPL21	6144	hgsc.bcm.edu	37	chr13	27830355	27830355	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ccaagagaattaatgtgcgtAttgagcacattaagcactct	8	8	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr13:27830355A>C	ENST00000311549.6	+	5	566	c.277A>C	c.(277-279)Att>Ctt	p.I93L	RPL21_ENST00000272274.4_Missense_Mutation_p.I93L|SNORD102_ENST00000384769.1_RNA|SNORA27_ENST00000384323.1_RNA|RPL21_ENST00000326092.4_Missense_Mutation_p.I93L|RPL21_ENST00000319826.4_Missense_Mutation_p.I93L	NM_000982.3	NP_000973.2	P46778	RL21_HUMAN	ribosomal protein L21	93					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(1)	2		Lung SC(185;0.0156)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0287)|OV - Ovarian serous cystadenocarcinoma(117;0.118)|Epithelial(112;0.139)|GBM - Glioblastoma multiforme(144;0.21)		TAATGTGCGTATTGAGCACAT	0.378																																					p.I93L		Atlas-SNP	.											.	RPL21	12	.	0			c.A277C						.						21	24	23					13																	27830355		2203	4297	6500	SO:0001583	missense	6144	exon5			GTGCGTATTGAGC	AB007176	CCDS9320.1	13q12.2	2008-07-18			ENSG00000122026	ENSG00000122026		"L ribosomal proteins"	10313	protein-coding gene	gene with protein product	"60S ribosomal protein L21"	603636				3459254, 7772601	Standard	NM_000982		Approved	L21, FLJ27458, MGC71252, MGC104274, MGC104275, DKFZp686C06101	uc001ura.3	P46778	OTTHUMG00000016630	ENST00000311549.6:c.277A>C	chr13.hg19:g.27830355A>C	ENSP00000346027:p.Ile93Leu	196.0	0.0		170.0	32.0	NM_000982	Q16699	Missense_Mutation	SNP	ENST00000311549.6	hg19	CCDS9320.1	.	.	.	.	.	.	.	.	.	.	A	15.21	2.766037	0.49574	.	.	ENSG00000122026	ENST00000311549;ENST00000272274;ENST00000319826;ENST00000326092	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	4.83	2.37	0.29283	Translation protein SH3-like (1);	0.059658	0.64402	U	0.000003	T	0.64159	0.2573	M	0.84433	2.695	0.52501	D	0.99995	B;B	0.10296	0.003;0.003	B;B	0.26416	0.069;0.069	T	0.61821	-0.6984	10	0.87932	D	0	.	7.8007	0.29172	0.7662:0.0:0.2338:0.0	.	93;93	P46778;Q6IAX2	RL21_HUMAN;.	L	93	ENSP00000346027:I93L;ENSP00000351021:I93L;ENSP00000370574:I93L;ENSP00000370569:I93L	ENSP00000351021:I93L	I	+	1	0	RPL21	26728355	0.998000	0.40836	0.897000	0.35233	0.843000	0.47879	3.627000	0.54252	0.298000	0.22638	0.459000	0.35465	ATT	.	.		0.378	RPL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044270.1	NM_000982		C	27830355	A	C	27830355	3	2	29	1	0	0	0	0	1	0	0	0	13582	449	16	5	291	5	RPL21	13	27830355	Missense_Mutation	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10		27830355	87339523	58	3674										
FOXO1	2308	hgsc.bcm.edu	37	chr13	41240285	41240285	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tgggcagcggccaggtgcacGagcgcggccggggcagcggc	21	13	0	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr13:41240285G>C	ENST00000379561.5	-	1	449	c.65C>G	c.(64-66)tCg>tGg	p.S22W		NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	22					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		CCAGGTGCACGAGCGCGGCCG	0.761																																					p.S22W		Atlas-SNP	.											.	FOXO1	110	.	0			c.C65G						.						1	2	1					13																	41240285		1143	2568	3711	SO:0001583	missense	2308	exon1			GTGCACGAGCGCG		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"Forkhead boxes"	3819	protein-coding gene	gene with protein product		136533	"forkhead homolog in rhabdomyosarcoma"	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.65C>G	chr13.hg19:g.41240285G>C	ENSP00000368880:p.Ser22Trp	36.0	0.0		27.0	8.0	NM_002015	O43523|Q5VYC7|Q6NSK6	Missense_Mutation	SNP	ENST00000379561.5	hg19	CCDS9371.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.088994	0.55968	.	.	ENSG00000150907	ENST00000379561	D	0.97831	-4.56	4.0	4.0	0.46444	.	0.000000	0.64402	U	0.000006	D	0.98438	0.9480	M	0.80982	2.52	0.80722	D	1	D	0.71674	0.998	D	0.68039	0.955	D	0.99482	1.0948	10	0.87932	D	0	-7.8406	14.673	0.68958	0.0:0.0:1.0:0.0	.	22	Q12778	FOXO1_HUMAN	W	22	ENSP00000368880:S22W	ENSP00000368880:S22W	S	-	2	0	FOXO1	40138285	1.000000	0.71417	0.979000	0.43373	0.044000	0.14063	6.832000	0.75329	1.768000	0.52137	0.514000	0.50259	TCG	.	.		0.761	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015		C	41240285	G	C	41240285	3	2	29	1	0	0	0	0	1	0	0	0	6031	1059	37	4	1910	4	FOXO1	13	41240285	Missense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	13409930	41240285	73929593	59	3675										
RNASE6	6039	hgsc.bcm.edu	37	chr14	21250306	21250306	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ctgtacacttagatagtattCtctaaggcatccactgcatt	6	10	1	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr14:21250306C>G	ENST00000304677.2	+	2	741	c.448C>G	c.(448-450)Ctc>Gtc	p.L150V	RP11-219E7.1_ENST00000556624.1_RNA	NM_005615.4	NP_005606.1	Q93091	RNAS6_HUMAN	ribonuclease, RNase A family, k6	150					defense response (GO:0006952)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			large_intestine(1)	1	all_cancers(95;0.00406)		Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)		AGATAGTATTCTCTAAGGCAT	0.423																																					p.L150V		Atlas-SNP	.											.	RNASE6	7	.	0			c.C448G						.						74	75	75					14																	21250306		2203	4300	6503	SO:0001583	missense	6039	exon2			AGTATTCTCTAAG	U64998	CCDS9558.1	14q11	2008-07-09			ENSG00000169413	ENSG00000169413		"Ribonucleases, RNase A"	10048	protein-coding gene	gene with protein product	"RNase k6"	601981		RNS6		8836175, 9647635	Standard	NM_005615		Approved		uc001vye.4	Q93091	OTTHUMG00000029585	ENST00000304677.2:c.448C>G	chr14.hg19:g.21250306C>G	ENSP00000302046:p.Leu150Val	107.0	0.0		107.0	31.0	NM_005615		Missense_Mutation	SNP	ENST00000304677.2	hg19	CCDS9558.1	.	.	.	.	.	.	.	.	.	.	C	0.018	-1.484530	0.01027	.	.	ENSG00000169413	ENST00000304677	T	0.78126	-1.15	4.94	-1.42	0.08913	Ribonuclease A, domain (2);	1.303180	0.05300	N	0.522833	T	0.49098	0.1537	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43426	-0.9392	10	0.02654	T	1	.	1.3783	0.02225	0.238:0.2673:0.3584:0.1363	.	150	Q93091	RNAS6_HUMAN	V	150	ENSP00000302046:L150V	ENSP00000302046:L150V	L	+	1	0	RNASE6	20320146	0.001000	0.12720	0.008000	0.14137	0.104000	0.19210	-0.888000	0.04148	-0.373000	0.07979	-1.148000	0.01847	CTC	.	.		0.423	RNASE6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073750.2			G	21250306	C	G	21250306	3	3	29	1	0	0	0	0	1	0	0	0	13422	913	32	4	450	4	RNASE6	14	21250306	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10		21250306	86099234	60	3676										
PAPLN	89932	hgsc.bcm.edu	37	chr14	73729359	73729404	+	Frame_Shift_Del	DEL	AAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	AAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	-													0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	acaggggccgcggtgcagagAaagccctggccttctggtgg					rs371499346|rs201201042|rs200348311|rs563152502|rs577625666		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	AAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	AAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr14:73729359_73729404delAAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	ENST00000554301.1	+	18	2710_2755	c.2547_2592delAAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	c.(2545-2592)agaaagccctggccttctggtggtctctggcggcaagaccaacagcctfs	p.RKPWPSGGLWRQDQQP849fs	PAPLN_ENST00000340738.5_Frame_Shift_Del_p.RKPWPSGGLWRQDQQP822fs|PAPLN_ENST00000381166.3_Frame_Shift_Del_p.RKPWPSGGLWRQDQQP849fs|PAPLN_ENST00000555445.1_Frame_Shift_Del_p.RKPWPSGGLWRQDQQP833fs|PAPLN_ENST00000427855.1_Frame_Shift_Del_p.RKPWPSGGLWRQDQQP849fs|PAPLN_ENST00000554314.1_3'UTR			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	849						basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		CGGTGCAGAGAAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCTGGGCCAGGGG	0.679																																					p.822_837del		Pindel	.											.	PAPLN	180	.	0			c.2465_2510del						.																																			SO:0001589	frameshift_variant	89932	exon18			.	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"Immunoglobulin superfamily / I-set domain containing"	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.2547_2592delAAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	chr14.hg19:g.73729359_73729404delAAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	ENSP00000451803:p.Arg849fs	128.0	0.0		126.0	18.0	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Frame_Shift_Del	DEL	ENST00000554301.1	hg19																																																																																				.	.		0.679	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		-	73729404	AAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	-	73729359	7	5	29	1	0	1	0	1	0	0	0	0	11437	243	9	0	2532	0	PAPLN	14	73729359	Frame_Shift_Del	DEL	AAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	TCGA-5R-AAAM-01A-12D-A40R-10	52479053	73729359	33620181	61	3677										
MKRN3	7681	hgsc.bcm.edu	37	chr15	23811290	23811290	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	actgtcgctattcgcacgacCtttctggtcggaagatggcc	11	12	1	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr15:23811290C>G	ENST00000314520.3	+	1	837	c.361C>G	c.(361-363)Ctt>Gtt	p.L121V	RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000568252.1_Intron|MKRN3_ENST00000564592.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	121					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		TTCGCACGACCTTTCTGGTCG	0.602																																					p.L121V		Atlas-SNP	.											.	MKRN3	155	.	0			c.C361G						.						56	58	57					15																	23811290		2203	4300	6503	SO:0001583	missense	7681	exon1			CACGACCTTTCTG	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"RING-type (C3HC4) zinc fingers"	7114	protein-coding gene	gene with protein product	"zinc finger protein 127"	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.361C>G	chr15.hg19:g.23811290C>G	ENSP00000313881:p.Leu121Val	83.0	0.0		106.0	11.0	NM_005664		Missense_Mutation	SNP	ENST00000314520.3	hg19	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	C	19.86	3.904712	0.72868	.	.	ENSG00000179455	ENST00000314520	T	0.34667	1.35	3.94	2.05	0.26809	Zinc finger, CCCH-type (2);	0.280449	0.29451	N	0.012115	T	0.24084	0.0583	L	0.47016	1.485	0.48341	D	0.999631	P	0.37061	0.58	B	0.31245	0.126	T	0.04294	-1.0962	10	0.51188	T	0.08	.	4.7645	0.13125	0.2134:0.6766:0.0:0.1099	.	121	Q13064	MKRN3_HUMAN	V	121	ENSP00000313881:L121V	ENSP00000313881:L121V	L	+	1	0	MKRN3	21362383	0.221000	0.23642	0.010000	0.14722	0.327000	0.28475	1.320000	0.33666	0.631000	0.30412	0.563000	0.77884	CTT	.	.		0.602	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664		G	23811290	C	G	23811290	3	3	29	1	0	0	0	0	1	0	0	0	9617	681	24	4	363	4	MKRN3	15	23811290	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10		23811290	78720102	62	3678										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52635319	52635319	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ggagacaaatataacctgttGgcttgttttaacccttcata	7	8	1	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr15:52635319G>A	ENST00000399231.3	-	31	4278	c.4035C>T	c.(4033-4035)gcC>gcT	p.A1345A	MYO5A_ENST00000356338.6_Intron|MYO5A_ENST00000553916.1_Intron|MYO5A_ENST00000399233.2_Silent_p.A1342A|MYO5A_ENST00000358212.6_Silent_p.A1345A	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1345					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ATAACCTGTTGGCTTGTTTTA	0.388																																					p.A1345A		Atlas-SNP	.											.	MYO5A	145	.	0			c.C4035T						.						98	94	95					15																	52635319		1858	4092	5950	SO:0001819	synonymous_variant	4644	exon31			CCTGTTGGCTTGT		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.4035C>T	chr15.hg19:g.52635319G>A		74.0	0.0		90.0	12.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	hg19	CCDS42037.1																																																																																			.	.		0.388	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		A	52635319	G	A	52635319	2	1	29	1	0	0	0	0	0	0	0	1	10087	1335	47	3		3	MYO5A	15	52635319	Silent	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	28824029	52635319	49896073	63	3679										
USP10	9100	hgsc.bcm.edu	37	chr16	84778402	84778402	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ataacccctgatggtatcacTaaagaagcaagctatggctc	8	10	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr16:84778402T>C	ENST00000219473.7	+	4	428	c.315T>C	c.(313-315)acT>acC	p.T105T	USP10_ENST00000570191.1_Silent_p.T109T|USP10_ENST00000562743.1_3'UTR	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	105					autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						ATGGTATCACTAAAGAAGCAA	0.488																																					p.T109T		Atlas-SNP	.											.	USP10	51	.	0			c.T327C						.						75	73	74					16																	84778402		1846	4086	5932	SO:0001819	synonymous_variant	9100	exon5			TATCACTAAAGAA	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"Ubiquitin-specific peptidases"	12608	protein-coding gene	gene with protein product		609818	"ubiquitin specific protease 10"			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.315T>C	chr16.hg19:g.84778402T>C		142.0	0.0		95.0	29.0	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	hg19	CCDS45537.1																																																																																			.	.		0.488	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1			C	84778402	T	C	84778402	2	2	29	1	0	0	0	0	0	0	0	1	17056	1509	53	2		2	USP10	16	84778402	Silent	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10		84778402	5576351	64	3680										
CCT6B	10693	hgsc.bcm.edu	37	chr17	33267596	33267596	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tttgctctgcgaagagctacTattccatgttttgcaagaga	9	8	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr17:33267596T>G	ENST00000314144.5	-	8	1045	c.930A>C	c.(928-930)atA>atC	p.I310I	CCT6B_ENST00000421975.3_Silent_p.I273I|CCT6B_ENST00000436961.3_Silent_p.I265I	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	310					chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				GAAGAGCTACTATTCCATGTT	0.294																																					p.I310I		Atlas-SNP	.											.	CCT6B	63	.	0			c.A930C						.						68	72	71					17																	33267596		2203	4290	6493	SO:0001819	synonymous_variant	10693	exon8			AGCTACTATTCCA	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"Heat Shock Proteins / Chaperonins"	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.930A>C	chr17.hg19:g.33267596T>G		173.0	0.0		164.0	11.0	NM_006584	B4DX20|B4DYB0|Q8TC34	Silent	SNP	ENST00000314144.5	hg19	CCDS32617.1																																																																																			.	.		0.294	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584		G	33267596	T	G	33267596	2	3	29	1	0	0	0	0	0	0	0	1	2960	1512	53	5		5	CCT6B	17	33267596	Silent	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10		33267596	47927614	65	3681										
C17orf66	256957	hgsc.bcm.edu	37	chr17	34182344	34182344	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	taggtgcctcatatacagagAgaaccttgtttttcagcttg	9	8	2	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr17:34182344A>G	ENST00000311880.2	-	15	1584	c.1436T>C	c.(1435-1437)cTc>cCc	p.L479P	C17orf66_ENST00000592980.1_Missense_Mutation_p.L439P	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		479					hematopoietic progenitor cell differentiation (GO:0002244)			p.L479H(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		ATATACAGAGAGAACCTTGTT	0.438																																					p.L479P		Atlas-SNP	.											C17orf66,NS,carcinoma,0,1	C17orf66	57	.	1	Substitution - Missense(1)	kidney(1)	c.T1436C						.						91	88	89					17																	34182344		2203	4300	6503	SO:0001583	missense	256957	exon15			ACAGAGAGAACCT																												ENST00000311880.2:c.1436T>C	chr17.hg19:g.34182344A>G	ENSP00000309560:p.Leu479Pro	95.0	1.0		96.0	25.0	NM_152781	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Missense_Mutation	SNP	ENST00000311880.2	hg19	CCDS11299.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.034273	0.35893	.	.	ENSG00000172653	ENST00000311880	T	0.55930	0.49	4.08	3.0	0.34707	.	0.960417	0.08546	N	0.929817	T	0.44008	0.1273	N	0.24115	0.695	0.09310	N	0.999998	D;P	0.54207	0.965;0.94	P;B	0.47981	0.563;0.36	T	0.27088	-1.0084	10	0.62326	D	0.03	.	6.2039	0.20591	0.8831:0.0:0.1169:0.0	.	439;479	A2RTY3-3;A2RTY3	.;CQ066_HUMAN	P	479	ENSP00000309560:L479P	ENSP00000309560:L479P	L	-	2	0	C17orf66	31206457	0.360000	0.24964	0.006000	0.13384	0.035000	0.12851	3.807000	0.55591	0.726000	0.32339	0.460000	0.39030	CTC	.	.		0.438	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1			G	34182344	A	G	34182344	3	3	29	1	0	0	0	0	1	0	0	0	1876	304	11	2	280	2	C17orf66	17	34182344	Missense_Mutation	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10	914748	34182344	47012866	66	3682										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8796353	8796353	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	atctgatgcagcaggagctcCggtccttgaagcagaacatt	11	10	1	3	rs369991737		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr18:8796353C>T	ENST00000306329.11	+	7	3091	c.3091C>T	c.(3091-3093)Cgg>Tgg	p.R1031W	SOGA2_ENST00000517570.1_Missense_Mutation_p.R671W|SOGA2_ENST00000359865.3_Missense_Mutation_p.R712W|SOGA2_ENST00000306285.7_Missense_Mutation_p.R27W|SOGA2_ENST00000400050.3_Missense_Mutation_p.R671W|SOGA2_ENST00000518815.1_Missense_Mutation_p.R27W																							GCAGGAGCTCCGGTCCTTGAA	0.517																																					p.R712W		Atlas-SNP	.											.	.	.	.	0			c.C2134T						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	126	118	120		2134	-0.6	0	18		120	0,8600		0,0,4300	no	missense	CCDC165	NM_015210.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	712/1587	8796353	1,13005	2203	4300	6503	SO:0001583	missense	23255	exon9			GAGCTCCGGTCCT																												ENST00000306329.11:c.3091C>T	chr18.hg19:g.8796353C>T	ENSP00000305027:p.Arg1031Trp	150.0	0.0		138.0	7.0	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	hg19		.	.	.	.	.	.	.	.	.	.	C	17.28	3.350425	0.61183	2.27E-4	0.0	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050;ENST00000306285	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	5.91	-0.648	0.11464	.	0.299057	0.24640	N	0.036810	T	0.59046	0.2165	M	0.63843	1.955	0.09310	N	0.999995	D;D	0.89917	0.999;1.0	P;D	0.74023	0.893;0.982	T	0.50197	-0.8856	10	0.87932	D	0	-12.7546	2.3471	0.04274	0.4628:0.2188:0.1851:0.1333	.	1022;712	Q9Y4B5;Q9Y4B5-3	CC165_HUMAN;.	W	733;671;712;671;27	ENSP00000429556:R671W;ENSP00000352927:R712W;ENSP00000382924:R671W;ENSP00000303670:R27W	ENSP00000303670:R27W	R	+	1	2	CCDC165	8786353	0.113000	0.22115	0.030000	0.17652	0.985000	0.73830	-0.144000	0.10280	-0.117000	0.11872	-0.182000	0.12963	CGG	.	.		0.517	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			T	8796353	C	T	8796353	3	4	29	1	0	0	0	0	1	0	0	0	8203	643	23	1	2160	1	KIAA0802	18	8796353	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10		8796353	69280895	67	3683										
INSR	3643	hgsc.bcm.edu	37	chr19	7119538	7119538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	acacctgttcattagacaggCcttggtaaggctgttctgcc	10	11	2	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:7119538C>T	ENST00000302850.5	-	21	3858	c.3716G>A	c.(3715-3717)gGc>gAc	p.G1239D	INSR_ENST00000341500.5_Missense_Mutation_p.G1227D	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	1239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""Insulin(DB00071)|""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	ATTAGACAGGCCTTGGTAAGG	0.463																																					p.G1239D		Atlas-SNP	.											.	INSR	265	.	0			c.G3716A						.						168	138	148					19																	7119538		2203	4300	6503	SO:0001583	missense	3643	exon21			GACAGGCCTTGGT	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"CD molecules", "Fibronectin type III domain containing"	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.3716G>A	chr19.hg19:g.7119538C>T	ENSP00000303830:p.Gly1239Asp	131.0	0.0		116.0	17.0	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	hg19	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.972756	0.92919	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	D;D	0.90133	-2.62;-2.62	5.0	5.0	0.66597	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.46758	D	0.000265	D	0.92374	0.7580	L	0.33137	0.985	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79108	0.986;0.992	D	0.93378	0.6741	10	0.72032	D	0.01	.	15.8435	0.78868	0.0:1.0:0.0:0.0	.	1227;1239	P06213-2;P06213	.;INSR_HUMAN	D	1239;1227	ENSP00000303830:G1239D;ENSP00000342838:G1227D	ENSP00000303830:G1239D	G	-	2	0	INSR	7070538	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.485000	0.81204	2.322000	0.78497	0.449000	0.29647	GGC	.	.		0.463	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			T	7119538	C	T	7119538	3	4	29	1	0	0	0	0	1	0	0	0	7782	739	26	3	440	3	INSR	19	7119538	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10		7119538	52009445	68	3684										
MLL4	9757	hgsc.bcm.edu	37	chr19	36222961	36222961	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cccgttctttttcgggggctCgaatcaaagtgcccaactac	9	13	2	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:36222961C>T	ENST00000222270.7	+	27	5590	c.5590C>T	c.(5590-5592)Cga>Tga	p.R1864*	KMT2B_ENST00000420124.1_Nonsense_Mutation_p.R1864*|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1864					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TTCGGGGGCTCGAATCAAAGT	0.662																																					p.R1864X		Atlas-SNP	.											MLL4,colon,carcinoma,0,3	MLL4	229	.	0			c.C5590T						.						20	22	21					19																	36222961		1889	4099	5988	SO:0001587	stop_gained	8085	exon27			GGGGCTCGAATCA	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5590C>T	chr19.hg19:g.36222961C>T	ENSP00000222270:p.Arg1864*	69.0	0.0		68.0	17.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Nonsense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	44	10.759291	0.99462	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	.	.	.	5.33	4.24	0.50183	.	0.000000	0.36665	N	0.002463	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8877	0.70582	0.1434:0.8566:0.0:0.0	.	.	.	.	X	1864	.	ENSP00000222270:R1864X	R	+	1	2	AD000671.1	40914801	0.998000	0.40836	1.000000	0.80357	0.962000	0.63368	2.373000	0.44266	2.659000	0.90383	0.655000	0.94253	CGA	.	.		0.662	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		T	36222961	C	T	36222961	4	4	29	1	0	0	0	0	0	1	0	0	9632	876	31	1	5696	1	MLL4	19	36222961	Nonsense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	29103423	36222961	22906022	69	3685										
FBXO17	115290	hgsc.bcm.edu	37	chr19	39435635	39435635	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gcagcccctctcagtccactGaaggaccgggtcaggtgagg	14	13	2	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:39435635G>A	ENST00000292852.4	-	5	1008	c.667C>T	c.(667-669)Cag>Tag	p.Q223*	FBXO17_ENST00000595329.1_Nonsense_Mutation_p.Q223*|SARS2_ENST00000448145.2_Nonsense_Mutation_p.Q58*|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.S127L	NM_024907.5	NP_079183.4	Q96EF6	FBX17_HUMAN	F-box protein 17	223	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	7	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			TCAGTCCACTGAAGGACCGGG	0.612																																					p.Q232X		Atlas-SNP	.											.	FBXO17	42	.	0			c.C694T						.						74	68	70					19																	39435635		2203	4300	6503	SO:0001587	stop_gained	115290	exon5			TCCACTGAAGGAC	AF386743	CCDS12526.1	19q13.2	2010-07-02	2004-06-15	2004-06-16		ENSG00000269190		"F-boxes /  "other""	18754	protein-coding gene	gene with protein product	"F-box only protein 26"	609094	"F-box only protein 17"	FBXO26			Standard	NM_148169		Approved	FBG4, FLJ25205, MGC9379, FLJ11798, Fbx17		Q96EF6		ENST00000292852.4:c.667C>T	chr19.hg19:g.39435635G>A	ENSP00000292852:p.Gln223*	106.0	0.0		103.0	10.0	NM_148169	Q96LQ4	Nonsense_Mutation	SNP	ENST00000292852.4	hg19	CCDS12526.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.005405	0.74932	.	.	ENSG00000104835	ENST00000448145;ENST00000392076;ENST00000292852	.	.	.	5.45	4.34	0.51931	.	0.000000	0.53938	D	0.000046	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	10.9866	0.47526	0.0:0.0:0.814:0.186	.	.	.	.	X	58;232;223	.	ENSP00000292852:Q223X	Q	-	1	0	FBXO17	44127475	1.000000	0.71417	1.000000	0.80357	0.140000	0.21249	3.425000	0.52771	2.716000	0.92895	0.467000	0.42956	CAG	.	.		0.612	FBXO17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463273.1	NM_024907		A	39435635	G	A	39435635	4	1	29	1	0	0	0	0	0	1	0	0	5738	1299	45	3	177	3	FBXO17	19	39435635	Nonsense_Mutation	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	3212674	39435635	19693348	70	3686										
PSG9	5678	hgsc.bcm.edu	37	chr19	43766112	43766112	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tactttgtgacaccaaatagAtagagggtcctgttggtttt	10	6	0	3	rs139948336		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:43766112A>T	ENST00000270077.3	-	3	705	c.609T>A	c.(607-609)taT>taA	p.Y203*	PSG9_ENST00000593948.1_Nonsense_Mutation_p.Y203*|PSG9_ENST00000443718.3_Intron|PSG9_ENST00000596730.1_Intron|PSG9_ENST00000291752.5_Intron|PSG9_ENST00000244293.7_Nonsense_Mutation_p.Y203*|PSG9_ENST00000418820.2_Intron	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	203	Ig-like C2-type 1.			Y -> C (in Ref. 1; CAA35612). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				CACCAAATAGATAGAGGGTCC	0.507																																					p.Y203X		Atlas-SNP	.											.	PSG9	77	.	0			c.T609A						.						207	208	208					19																	43766112		2203	4298	6501	SO:0001587	stop_gained	5678	exon3			AAATAGATAGAGG	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.609T>A	chr19.hg19:g.43766112A>T	ENSP00000270077:p.Tyr203*	89.0	0.0		102.0	23.0	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Nonsense_Mutation	SNP	ENST00000270077.3	hg19	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	N	15.14	2.744589	0.49151	.	.	ENSG00000183668	ENST00000270077;ENST00000435220;ENST00000244293	.	.	.	2.12	2.12	0.27331	.	.	.	.	.	.	.	.	.	.	.	0.19300	N	0.999977	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.2622	0.20907	1.0:0.0:0.0:0.0	.	.	.	.	X	203;164;203	.	ENSP00000244293:Y203X	Y	-	3	2	PSG9	48457952	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.773000	0.04689	0.715000	0.32103	0.163000	0.16589	TAT	.	A|0.999;G|0.001		0.507	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784		T	43766112	A	T	43766112	4	4	29	1	0	0	0	0	0	1	0	0	12674	340	12	4	687	4	PSG9	19	43766112	Nonsense_Mutation	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10	4330477	43766112	15362871	71	3687										
IRGQ	126298	hgsc.bcm.edu	37	chr19	44096253	44096253	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tcgagagcctgcagcaggacGccgtgagccgctcggtagcc	15	14	0	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:44096253G>A	ENST00000602269.1	-	2	1982	c.1797C>T	c.(1795-1797)ggC>ggT	p.G599G	L34079.2_ENST00000594374.1_Intron|IRGQ_ENST00000601520.1_Intron|IRGQ_ENST00000422989.1_Silent_p.G599G			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	599	Ala-rich.									endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				GCAGCAGGACGCCGTGAGCCG	0.701																																					p.G599G		Atlas-SNP	.											.	IRGQ	40	.	0			c.C1797T						.						33	40	38					19																	44096253		2192	4277	6469	SO:0001819	synonymous_variant	126298	exon3			CAGGACGCCGTGA	AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"immunity-related GTPase family, Q1"	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.1797C>T	chr19.hg19:g.44096253G>A		146.0	0.0		93.0	9.0	NM_001007561	B2RNP3	Silent	SNP	ENST00000602269.1	hg19	CCDS33040.1																																																																																			.	.		0.701	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561		A	44096253	G	A	44096253	2	1	29	1	0	0	0	0	0	0	0	1	7848	1074	38	1		1	IRGQ	19	44096253	Silent	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	330141	44096253	15032730	72	3688										
LILRA6	79168	hgsc.bcm.edu	37	chr19	54744224	54744224	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	agctgtatgagccgtagcacCtgtaggtccccgcgtgggct	14	12	0	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:54744224C>A	ENST00000396365.2	-	6	1223	c.1184G>T	c.(1183-1185)aGg>aTg	p.R395M	LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000245621.5_Missense_Mutation_p.R395M|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.R395M	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	395	Ig-like C2-type 2.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCCGTAGCACCTGTAGGTCCC	0.602																																					p.R395M		Atlas-SNP	.											.	LILRA6	75	.	0			c.G1184T						.						75	104	94					19																	54744224		2203	4300	6503	SO:0001583	missense	79168	exon6			TAGCACCTGTAGG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15495	protein-coding gene	gene with protein product			"leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.1184G>T	chr19.hg19:g.54744224C>A	ENSP00000379651:p.Arg395Met	239.0	0.0		238.0	18.0	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	hg19	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.808881	0.50421	.	.	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.03301	3.98;3.98;3.98	2.39	1.33	0.21861	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.408932	0.18095	N	0.151861	T	0.28532	0.0706	H	0.99668	4.69	0.80722	D	1	D;B;D	0.89917	1.0;0.148;1.0	D;B;D	0.91635	0.998;0.015;0.999	T	0.10337	-1.0634	10	0.87932	D	0	.	4.3828	0.11302	0.0:0.7999:0.0:0.2001	.	395;395;395	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	M	395	ENSP00000411227:R395M;ENSP00000379651:R395M;ENSP00000245621:R395M	ENSP00000245621:R395M	R	-	2	0	LILRA6	59436036	0.004000	0.15560	0.999000	0.59377	0.235000	0.25334	1.259000	0.32956	1.360000	0.45960	0.195000	0.17529	AGG	.	.		0.602	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		A	54744224	C	A	54744224	3	1	29	1	0	0	0	0	1	0	0	0	8798	681	24	3	273	3	LILRA6	19	54744224	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	10647971	54744224	4384759	73	3689										
TTLL9	164395	hgsc.bcm.edu	37	chr20	30510825	30510825	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gtggagaactatgtggctcaGcgttacattgaaaatcctta	10	7	1	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr20:30510825G>A	ENST00000375938.4	+	8	886	c.633G>A	c.(631-633)caG>caA	p.Q211Q	TTLL9_ENST00000310998.4_Silent_p.Q161Q|TTLL9_ENST00000375934.4_Silent_p.Q193Q|TTLL9_ENST00000535842.1_Silent_p.Q211Q|TTLL9_ENST00000375921.2_Silent_p.Q138Q|TTLL9_ENST00000375922.4_Silent_p.Q138Q			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	211	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			ATGTGGCTCAGCGTTACATTG	0.403																																					p.Q211Q		Atlas-SNP	.											.	TTLL9	95	.	0			c.G633A						.						150	152	151					20																	30510825		2027	4194	6221	SO:0001819	synonymous_variant	164395	exon8			GGCTCAGCGTTAC	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"Tubulin tyrosine ligase-like family"	16118	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 125"	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.633G>A	chr20.hg19:g.30510825G>A		81.0	0.0		103.0	7.0	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Silent	SNP	ENST00000375938.4	hg19	CCDS42863.1																																																																																			.	.		0.403	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409		A	30510825	G	A	30510825	2	1	29	1	0	0	0	0	0	0	0	1	16749	962	34	3		3	TTLL9	20	30510825	Silent	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10		30510825	32514695	74	3690										
EDN3	1908	hgsc.bcm.edu	37	chr20	57876550	57876550	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gccagatctgagggggactgTgaagagactgtggctggccc	17	9	1	4			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr20:57876550T>C	ENST00000337938.2	+	2	524	c.138T>C	c.(136-138)tgT>tgC	p.C46C	EDN3_ENST00000371028.2_Silent_p.C46C|EDN3_ENST00000395654.3_Silent_p.C46C|EDN3_ENST00000371025.3_Silent_p.C46C|EDN3_ENST00000311585.7_Silent_p.C46C	NM_207034.1	NP_996917.1	P14138	EDN3_HUMAN	endothelin 3	46					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inositol phosphate-mediated signaling (GO:0048016)|melanocyte differentiation (GO:0030318)|multicellular organismal development (GO:0007275)|neural crest cell migration (GO:0001755)|neuron differentiation (GO:0030182)|neutrophil chemotaxis (GO:0030593)|peptide hormone secretion (GO:0030072)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|regulation of developmental pigmentation (GO:0048070)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|signal transduction (GO:0007165)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	19	all_lung(29;0.0115)					AGGGGGACTGTGAAGAGACTG	0.672																																					p.C46C		Atlas-SNP	.											.	EDN3	83	.	0			c.T138C						.						28	32	31					20																	57876550		2203	4300	6503	SO:0001819	synonymous_variant	1908	exon2			GGACTGTGAAGAG	X52001	CCDS13477.1, CCDS13478.1, CCDS13479.1	20q13.2-q13.3	2013-02-26			ENSG00000124205	ENSG00000124205		"Endogenous ligands"	3178	protein-coding gene	gene with protein product		131242					Standard	NM_000114		Approved	ET3	uc002yaq.3	P14138	OTTHUMG00000032867	ENST00000337938.2:c.138T>C	chr20.hg19:g.57876550T>C		109.0	0.0		111.0	14.0	NM_207034	E1P5I5|Q03229|Q7Z6D2|Q9UGT7	Silent	SNP	ENST00000337938.2	hg19	CCDS13477.1																																																																																			.	.		0.672	EDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079919.2	NM_000114		C	57876550	T	C	57876550	2	2	29	1	0	0	0	0	0	0	0	1	4920	1702	59	2		2	EDN3	20	57876550	Silent	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	27365725	57876550	5148970	75	3691										
TOP3B	8940	hgsc.bcm.edu	37	chr22	22314746	22314746	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cgaggttggtgggcttgagcCggcgcccgctctccaccgtg	16	14	1	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr22:22314746C>T	ENST00000398793.2	-	14	2035	c.1601G>A	c.(1600-1602)cGg>cAg	p.R534Q	TOP3B_ENST00000357179.5_Missense_Mutation_p.R534Q|TOP3B_ENST00000413067.2_3'UTR	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	534					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		GGGCTTGAGCCGGCGCCCGCT	0.612																																					p.R534Q		Atlas-SNP	.											.	TOP3B	107	.	0			c.G1601A						.						96	77	84					22																	22314746		2203	4300	6503	SO:0001583	missense	8940	exon14			TTGAGCCGGCGCC	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.1601G>A	chr22.hg19:g.22314746C>T	ENSP00000381773:p.Arg534Gln	71.0	0.0		70.0	11.0	NM_003935	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	ENST00000398793.2	hg19	CCDS13797.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.8|22.8	4.334934|4.334934	0.81801|0.81801	.|.	.|.	ENSG00000100038|ENSG00000100038	ENST00000457270|ENST00000357179;ENST00000398793	.|T;T	.|0.21734	.|1.99;1.99	5.69|5.69	5.69|5.69	0.88448|0.88448	.|DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central (1);DNA topoisomerase, type IA, DNA-binding (1);DNA topoisomerase, type IA, central region, subdomain 1 (1);	.|0.151961	.|0.64402	.|D	.|0.000020	T|T	0.31263|0.31263	0.0791|0.0791	L|L	0.58583|0.58583	1.82|1.82	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.43231	.|0.801;0.801;0.763	.|B;B;B	.|0.43658	.|0.426;0.426;0.3	T|T	0.02713|0.02713	-1.1120|-1.1120	5|10	.|0.62326	.|D	.|0.03	.|.	19.8208|19.8208	0.96592|0.96592	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|79;534;534	.|B3KU89;O95985;O95985-2	.|.;TOP3B_HUMAN;.	S|Q	329|534	.|ENSP00000349705:R534Q;ENSP00000381773:R534Q	.|ENSP00000349705:R534Q	G|R	-|-	1|2	0|0	TOP3B|TOP3B	20644746|20644746	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.895000|0.895000	0.52256|0.52256	3.291000|3.291000	0.51764|0.51764	2.688000|2.688000	0.91661|0.91661	0.563000|0.563000	0.77884|0.77884	GGC|CGG	.	.		0.612	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935		T	22314746	C	T	22314746	3	4	29	1	0	0	0	0	1	0	0	0	16383	652	23	1	1007	1	TOP3B	22	22314746	Missense_Mutation	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10		22314746	28989820	76	3692										
TCF20	6942	hgsc.bcm.edu	37	chr22	42610966	42610967	+	Nonsense_Mutation	DNP	GC	GC	AA													0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ctgggggggtccatagctctGcacaggcccagaaggccttc							TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr22:42610966_42610967GC>AA	ENST00000359486.3	-	1	481_482	c.345_346GC>TT	c.(343-348)gtGCag>gtTTag	p.Q116*	TCF20_ENST00000335626.4_Nonsense_Mutation_p.Q116*	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						CCATAGCTCTGCACAGGCCCAG	0.574																																					p.Q116X|p.V115V		Atlas-SNP	.											.	TCF20	164	.	0			c.C346T|c.G345T						.																																			SO:0001587	stop_gained	6942	exon1			AGCTCTGCACAGG|GCTCTGCACAGGC	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.345_346delinsAA	chr22.hg19:g.42610966_42610967delinsAA	ENSP00000352463:p.Gln116*	89.0	0.0		96.0|97.0	40.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Nonsense_Mutation|Silent	SNP	ENST00000359486.3	hg19	CCDS14033.1																																																																																			.	.		0.574	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		AA	42610967	GC	AA	42610966	4	1	29	1	0	0	0	0	0	1	0	0	15705	1328	46	3	5574	3	TCF20	22	42610966	Nonsense_Mutation	DNP	GC	TCGA-5R-AAAM-01A-12D-A40R-10	20296220	42610966	8693600	77	3693										
NHS	4810	hgsc.bcm.edu	37	chrX	17743756	17743756	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	tctcggagccttccccgggaAggtaatagaggtggggatgc	16	9	1	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:17743756A>G	ENST00000380060.3	+	6	1805	c.1467A>G	c.(1465-1467)gaA>gaG	p.E489E	NHS_ENST00000398097.3_Silent_p.E333E	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	510					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TTCCCCGGGAAGGTAATAGAG	0.522																																					p.E489E		Atlas-SNP	.											.	NHS	302	.	0			c.A1467G						.						86	81	82					X																	17743756		2203	4300	6503	SO:0001819	synonymous_variant	4810	exon6			CCGGGAAGGTAAT		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.1467A>G	chrX.hg19:g.17743756A>G		133.0	0.0		129.0	13.0	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Silent	SNP	ENST00000380060.3	hg19	CCDS14181.1																																																																																			.	.		0.522	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		G	17743756	A	G	17743756	2	3	29	1	0	0	0	0	0	0	0	1	10420	69	3	2		2	NHS	23	17743756	Silent	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10		17743756	137526804	78	3694										
CACNA1F	778	hgsc.bcm.edu	37	chrX	49065046	49065046	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	gtccccctgtcatcatcactGggcccaaaggagagtgaatc	10	13	3	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:49065046G>A	ENST00000376265.2	-	43	5146	c.5085C>T	c.(5083-5085)ccC>ccT	p.P1695P	CACNA1F_ENST00000376251.1_Silent_p.P1630P|CACNA1F_ENST00000323022.5_Silent_p.P1684P	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1695					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CATCATCACTGGGCCCAAAGG	0.587																																					p.P1695P		Atlas-SNP	.											.	CACNA1F	218	.	0			c.C5085T						.						67	57	60					X																	49065046		2203	4300	6503	SO:0001819	synonymous_variant	778	exon43			ATCACTGGGCCCA	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1393	protein-coding gene	gene with protein product		300110	"Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.5085C>T	chrX.hg19:g.49065046G>A		160.0	0.0		135.0	18.0	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	hg19	CCDS35253.1																																																																																			.	.		0.587	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		A	49065046	G	A	49065046	2	1	29	1	0	0	0	0	0	0	0	1	2545	1335	47	3		3	CACNA1F	23	49065046	Silent	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	31321290	49065046	106205514	79	3695										
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49126707	49126707	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ttttcgctgccgcccgcgccGggccgtctggagcgcttggg	16	15	1	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:49126707G>T	ENST00000055335.6	+	1	391	c.375G>T	c.(373-375)ccG>ccT	p.P125P	LL0XNC01-7P3.1_ENST00000602455.1_lincRNA|PPP1R3F_ENST00000495799.1_Intron|PPP1R3F_ENST00000466508.1_Intron|PPP1R3F_ENST00000438316.1_Intron	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	125					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CGCCCGCGCCGGGCCGTCTGG	0.746																																					p.P125P		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.G375T						.						3	4	3					X																	49126707		1668	3402	5070	SO:0001819	synonymous_variant	89801	exon1			CGCGCCGGGCCGT		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14944	protein-coding gene	gene with protein product			"protein phosphatase 1, regulatory (inhibitor) subunit 3F"			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.375G>T	chrX.hg19:g.49126707G>T		81.0	0.0		97.0	4.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Silent	SNP	ENST00000055335.6	hg19	CCDS35254.1																																																																																			.	.		0.746	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		T	49126707	G	T	49126707	2	4	29	1	0	0	0	0	0	0	0	1	12387	1103	39	1		1	PPP1R3F	23	49126707	Silent	SNP	G	TCGA-5R-AAAM-01A-12D-A40R-10	61661	49126707	106143853	80	3696										
BRWD3	254065	hgsc.bcm.edu	37	chrX	79971674	79971674	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	accctttgagtagtgtaagaTggctttttcttcttttcaac	7	8	3	2			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:79971674T>C	ENST00000373275.4	-	20	2523	c.2307A>G	c.(2305-2307)ccA>ccG	p.P769P	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	769					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						TAGTGTAAGATGGCTTTTTCT	0.353																																					p.P769P		Atlas-SNP	.											.	BRWD3	251	.	0			c.A2307G						.						176	152	160					X																	79971674		2201	4298	6499	SO:0001819	synonymous_variant	254065	exon20			GTAAGATGGCTTT		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.2307A>G	chrX.hg19:g.79971674T>C		105.0	0.0		84.0	8.0	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Silent	SNP	ENST00000373275.4	hg19	CCDS14447.1																																																																																			.	.		0.353	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		C	79971674	T	C	79971674	2	2	29	1	0	0	0	0	0	0	0	1	1528	1451	51	2		2	BRWD3	23	79971674	Silent	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	30844967	79971674	75298886	81	3697										
TEX13A	56157	hgsc.bcm.edu	37	chrX	104464278	104464278	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	aggggcagccacaacctccaAcatcccctctgctcttcttc	6	18	3	0	rs371523271		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:104464278A>C	ENST00000413579.1	-	4	710	c.599T>G	c.(598-600)gTt>gGt	p.V200G	TEX13A_ENST00000372575.1_Missense_Mutation_p.C200W|IL1RAPL2_ENST00000372582.1_Intron|IL1RAPL2_ENST00000344799.4_Intron|TEX13A_ENST00000372578.3_Missense_Mutation_p.C200W			Q9BXU3	TX13A_HUMAN	testis expressed 13A	200							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						ACAACCTCCAACATCCCCTCT	0.652																																					.		Atlas-SNP	.											.	TEX13A	55	.	0			c.598+1T>G						.						16	19	18					X																	104464278		2040	4059	6099	SO:0001630	splice_region_variant	56157	exon5			CCTCCAACATCCC	AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"testis expressed sequence 13A"			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.600+1T>G	chrX.hg19:g.104464278A>C		0.0	0.0		6.0	4.0	NM_031274	B1B1G8|Q32NB6	Splice_Site	SNP	ENST00000413579.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.024|6.024	0.372734|0.372734	0.11409|0.11409	.|.	.|.	ENSG00000133149|ENSG00000133149	ENST00000372578;ENST00000372575|ENST00000413579	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.22898|0.22898	0.0553|0.0553	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.28964|0.28964	-1.0027|-1.0027	3|3	0.72032|0.23302	D|T	0.01|0.38	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	W|G	200|200	.|.	ENSP00000361656:C200W|ENSP00000399753:V200G	C|V	-|-	3|2	2|0	TEX13A|TEX13A	104350934|104350934	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.099000|0.099000	0.18886|0.18886	-0.302000|-0.302000	0.08221|0.08221	0.000000|0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	TGT|GTT	.	.		0.652	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274	Missense_Mutation	C	104464278	A	C	104464278	5	2	29	1	0	0	0	0	0	0	1	0	15791	41	2	5	635	5	TEX13A	23	104464278	Splice_Site	SNP	A	TCGA-5R-AAAM-01A-12D-A40R-10	24492604	104464278	50806282	82	3698										
LRCH2	57631	hgsc.bcm.edu	37	chrX	114357372	114357372	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	caacagaacgtggccttataTgattggctaaatggcaaaga	10	7	0	3			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:114357372T>C	ENST00000317135.8	-	19	2081	c.2051A>G	c.(2050-2052)cAt>cGt	p.H684R	LRCH2_ENST00000538422.1_Missense_Mutation_p.H667R	NM_020871.3	NP_065922.3	Q5VUJ6	LRCH2_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 2	684	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.									breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	19						TGGCCTTATATGATTGGCTAA	0.373																																					p.H684R		Atlas-SNP	.											.	LRCH2	138	.	0			c.A2051G						.						113	103	106					X																	114357372		1975	4152	6127	SO:0001583	missense	57631	exon19			CTTATATGATTGG	AB040928	CCDS48155.1, CCDS59175.1	Xq24	2008-02-05			ENSG00000130224	ENSG00000130224			29292	protein-coding gene	gene with protein product						10819331	Standard	NM_020871		Approved	KIAA1495	uc010nqe.3	Q5VUJ6	OTTHUMG00000022233	ENST00000317135.8:c.2051A>G	chrX.hg19:g.114357372T>C	ENSP00000325091:p.His684Arg	237.0	0.0		246.0	28.0	NM_020871	F5H2T1|Q08AD5|Q9HA88|Q9P233	Missense_Mutation	SNP	ENST00000317135.8	hg19	CCDS48155.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.720323	0.48728	.	.	ENSG00000130224	ENST00000317135;ENST00000536655;ENST00000538422	D;D	0.94687	-3.49;-3.49	5.39	5.39	0.77823	Calponin homology domain (5);	0.176916	0.48286	D	0.000183	D	0.95796	0.8632	L	0.60957	1.885	0.58432	D	0.999997	D;B	0.61697	0.99;0.361	P;B	0.62491	0.903;0.217	D	0.96106	0.9073	10	0.87932	D	0	-15.544	13.1876	0.59691	0.0:0.0:0.0:1.0	.	684;667	Q5VUJ6;F5H2T1	LRCH2_HUMAN;.	R	684;163;667	ENSP00000325091:H684R;ENSP00000439366:H667R	ENSP00000325091:H684R	H	-	2	0	LRCH2	114263628	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.525000	0.81892	1.995000	0.58328	0.345000	0.21793	CAT	.	.		0.373	LRCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057971.2	NM_020871		C	114357372	T	C	114357372	3	2	29	1	0	0	0	0	1	0	0	0	8942	1464	51	2	258	2	LRCH2	23	114357372	Missense_Mutation	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	9893094	114357372	40913188	83	3699										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123514879	123514879	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	cctctatggtaaaatgtaggTtttccaggtaatgggcatta	10	6	1	0			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:123514879T>C	ENST00000371130.3	-	31	7748	c.7685A>G	c.(7684-7686)aAc>aGc	p.N2562S	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.N2569S	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2562					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AAAATGTAGGTTTTCCAGGTA	0.493																																					p.N2569S		Atlas-SNP	.											.	.	.	.	0			c.A7706G						.						92	80	84					X																	123514879		2203	4300	6503	SO:0001583	missense	10178	exon32			TGTAGGTTTTCCA	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7685A>G	chrX.hg19:g.123514879T>C	ENSP00000360171:p.Asn2562Ser	154.0	0.0		207.0	13.0	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	hg19	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	9.967	1.224370	0.22457	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85484	-1.99;-1.95	5.83	5.83	0.93111	.	0.091536	0.85682	D	0.000000	T	0.81113	0.4755	L	0.46157	1.445	0.37779	D	0.926945	B;B;B	0.24483	0.104;0.049;0.059	B;B;B	0.19148	0.024;0.024;0.021	T	0.78833	-0.2048	10	0.33940	T	0.23	.	15.1686	0.72850	0.0:0.0:0.0:1.0	.	2568;2569;2562	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	S	2562;2569	ENSP00000360171:N2562S;ENSP00000403954:N2569S	ENSP00000360171:N2562S	N	-	2	0	ODZ1	123342560	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.021000	0.49651	1.965000	0.57142	0.486000	0.48141	AAC	.	.		0.493	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	123514879	T	C	123514879	3	2	29	1	0	0	0	0	1	0	0	0	10843	1725	60	2	496	2	ODZ1	23	123514879	Missense_Mutation	SNP	T	TCGA-5R-AAAM-01A-12D-A40R-10	9157507	123514879	31755681	84	3700										
PLXNA3	55558	hgsc.bcm.edu	37	chrX	153689565	153689565	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	1.03338632750397	3.27731092436975	0.509803921568627	1	1	0	ccttcgtgtacttcctgacgCtgcagctggacacccagcag	10	15	0	1			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:153689565C>T	ENST00000369682.3	+	3	896	c.721C>T	c.(721-723)Ctg>Ttg	p.L241L		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	241	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTTCCTGACGCTGCAGCTGGA	0.557																																					p.L241L		Atlas-SNP	.											.	PLXNA3	156	.	0			c.C721T						.						115	90	98					X																	153689565		2203	4300	6503	SO:0001819	synonymous_variant	55558	exon3			CTGACGCTGCAGC	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"Plexins"	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.721C>T	chrX.hg19:g.153689565C>T		131.0	0.0		107.0	14.0	NM_017514	Q5HY36	Silent	SNP	ENST00000369682.3	hg19	CCDS14752.1																																																																																			.	.		0.557	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		T	153689565	C	T	153689565	2	4	29	1	0	0	0	0	0	0	0	1	12130	796	28	3		3	PLXNA3	23	153689565	Silent	SNP	C	TCGA-5R-AAAM-01A-12D-A40R-10	30174686	153689565	1580995	85	3701										
UBE2J2	118424	hgsc.bcm.edu	37	chr1	1190842	1190842	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gtctgctactgagttcgtctTgtgctttctgtttttgttta	9	7	3	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:1190842T>A	ENST00000349431.6	-	7	740	c.521A>T	c.(520-522)cAa>cTa	p.Q174L	UBE2J2_ENST00000491779.1_5'Flank|UBE2J2_ENST00000347370.2_Missense_Mutation_p.Q122L|UBE2J2_ENST00000339385.6_Missense_Mutation_p.Q139L|UBE2J2_ENST00000400930.4_Missense_Mutation_p.Q190L|UBE2J2_ENST00000360466.2_Missense_Mutation_p.Q174L|UBE2J2_ENST00000348298.7_Missense_Mutation_p.Q122L|UBE2J2_ENST00000400929.2_Missense_Mutation_p.Q122L	NM_058167.2	NP_477515.2	Q8N2K1	UB2J2_HUMAN	ubiquitin-conjugating enzyme E2, J2	174					protein ubiquitination (GO:0016567)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			cervix(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.66e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.53e-21)|Colorectal(212;0.00019)|COAD - Colon adenocarcinoma(227;0.000215)|Kidney(185;0.00255)|BRCA - Breast invasive adenocarcinoma(365;0.00266)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0371)|Lung(427;0.205)		GAGTTCGTCTTGTGCTTTCTG	0.542																																					p.Q190L		Atlas-SNP	.											.	UBE2J2	25	.	0			c.A569T						.						108	122	117					1																	1190842		2203	4300	6503	SO:0001583	missense	118424	exon8			TCGTCTTGTGCTT	AF296658	CCDS14.1, CCDS15.1, CCDS16.1	1p36.33	2011-05-19	2011-05-19		ENSG00000160087	ENSG00000160087		"Ubiquitin-conjugating enzymes E2"	19268	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2, J2 (UBC6 homolog, yeast)"			11278356	Standard	NM_058167		Approved	Ubc6p, NCUBE2	uc001ado.3	Q8N2K1	OTTHUMG00000001911	ENST00000349431.6:c.521A>T	chr1.hg19:g.1190842T>A	ENSP00000305826:p.Gln174Leu	243.0	0.0		258.0	70.0	NM_194315	A8MYC7|Q504T9|Q96N26|Q96T84	Missense_Mutation	SNP	ENST00000349431.6	hg19	CCDS14.1	.	.	.	.	.	.	.	.	.	.	T	15.24	2.775239	0.49786	.	.	ENSG00000160087	ENST00000347370;ENST00000349431;ENST00000339385;ENST00000348298;ENST00000400929;ENST00000360466;ENST00000400930;ENST00000435198	T;T;T;T;T;T;T;T	0.72725	0.91;-0.09;0.91;0.91;0.91;-0.09;-0.68;-0.08	5.87	4.75	0.60458	Ubiquitin-conjugating enzyme/RWD-like (1);	0.049900	0.85682	D	0.000000	T	0.59088	0.2168	L	0.40543	1.245	0.80722	D	1	B;B;B;B	0.29253	0.049;0.001;0.0;0.239	B;B;B;B	0.26517	0.014;0.002;0.001;0.07	T	0.53408	-0.8443	10	0.26408	T	0.33	-18.426	10.9167	0.47139	0.0:0.0731:0.0:0.9269	.	122;190;174;207	A6NGS0;A8MYC7;Q8N2K1;B1AME9	.;.;UB2J2_HUMAN;.	L	122;174;139;122;122;174;190;174	ENSP00000344857:Q122L;ENSP00000305826:Q174L;ENSP00000340197:Q139L;ENSP00000342541:Q122L;ENSP00000383718:Q122L;ENSP00000353653:Q174L;ENSP00000383719:Q190L;ENSP00000393301:Q174L	ENSP00000340197:Q139L	Q	-	2	0	UBE2J2	1180705	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	5.912000	0.69948	1.059000	0.40554	0.482000	0.46254	CAA	.	.		0.542	UBE2J2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000005430.1	NM_058167		A	1190842	T	A	1190842	3	1	30	1	0	0	0	0	1	0	0	0	16876	1812	63	4	262	4	UBE2J2	1	1190842	Missense_Mutation	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10		1190842	248059779	1	3702										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32151294	32151294	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ggttcccccttctctccggaTgggccaggcaaggccaccac	11	17	1	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:32151294T>G	ENST00000373672.3	-	29	2478	c.1962A>C	c.(1960-1962)ccA>ccC	p.P654P	COL16A1_ENST00000373668.3_Silent_p.P654P|COL16A1_ENST00000271069.6_Silent_p.P653P	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	654	Triple-helical region 6 (COL6) with 1 imperfection.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TCTCTCCGGATGGGCCAGGCA	0.637																																					p.P654P	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.A1962C						.						102	110	108					1																	32151294		1911	4125	6036	SO:0001819	synonymous_variant	1307	exon29			TCCGGATGGGCCA	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.1962A>C	chr1.hg19:g.32151294T>G		107.0	0.0		162.0	36.0	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.		0.637	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		G	32151294	T	G	32151294	2	3	30	1	0	0	0	0	0	0	0	1	3675	1451	51	5		5	COL16A1	1	32151294	Silent	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	30960452	32151294	217099327	2	3703										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86916353	86916353	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tcaatcactctcccagcataAgcaccccagcccactctatt	3	18	4	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:86916353A>T	ENST00000370565.4	+	12	2254	c.2092A>T	c.(2092-2094)Agc>Tgc	p.S698C	CLCA2_ENST00000498802.1_3'UTR	NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	698					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TCCCAGCATAAGCACCCCAGC	0.398																																					p.S698C	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.A2092T						.						157	147	150					1																	86916353		2203	4300	6503	SO:0001583	missense	9635	exon12			AGCATAAGCACCC		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2092A>T	chr1.hg19:g.86916353A>T	ENSP00000359596:p.Ser698Cys	165.0	0.0		129.0	14.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	A	8.310	0.821970	0.16678	.	.	ENSG00000137975	ENST00000370565	T	0.03242	4.0	5.36	4.23	0.50019	.	0.737030	0.13753	N	0.365105	T	0.02342	0.0072	M	0.71581	2.175	0.09310	N	1	B	0.33739	0.422	B	0.36186	0.219	T	0.42275	-0.9461	10	0.72032	D	0.01	-1.2264	6.6844	0.23136	0.75:0.1709:0.0791:0.0	.	698	Q9UQC9	CLCA2_HUMAN	C	698	ENSP00000359596:S698C	ENSP00000359596:S698C	S	+	1	0	CLCA2	86688941	0.001000	0.12720	0.091000	0.20842	0.016000	0.09150	1.240000	0.32731	0.879000	0.35944	0.528000	0.53228	AGC	.	.		0.398	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		T	86916353	A	T	86916353	3	4	30	1	0	0	0	0	1	0	0	0	3460	72	3	4	2138	4	CLCA2	1	86916353	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	54765059	86916353	162334268	3	3704										
VTCN1	79679	hgsc.bcm.edu	37	chr1	117699311	117699311	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	agccgcaaagaggcattgccAactatcacttgatcagcaaa	8	11	2	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:117699311A>G	ENST00000369458.3	-	3	408	c.330T>C	c.(328-330)gtT>gtC	p.V110V	VTCN1_ENST00000463461.1_5'UTR|VTCN1_ENST00000359008.4_Silent_p.V113V|VTCN1_ENST00000328189.3_Intron|VTCN1_ENST00000539893.1_Silent_p.V15V	NM_024626.3	NP_078902.2			V-set domain containing T cell activation inhibitor 1											large_intestine(7)|lung(4)|upper_aerodigestive_tract(1)	12	Lung SC(450;0.225)	all_cancers(81;6.05e-06)|all_epithelial(167;5.59e-07)|all_lung(203;2.85e-06)|Lung NSC(69;2e-05)		Lung(183;0.0664)|LUSC - Lung squamous cell carcinoma(189;0.214)|Colorectal(144;0.23)		AGGCATTGCCAACTATCACTT	0.468																																					p.V110V		Atlas-SNP	.											.	VTCN1	26	.	0			c.T330C						.						105	99	101					1																	117699311		2203	4300	6503	SO:0001819	synonymous_variant	79679	exon3			ATTGCCAACTATC	BX648021	CCDS894.1, CCDS58019.1, CCDS58020.1	1p12	2013-01-29			ENSG00000134258	ENSG00000134258		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28873	protein-coding gene	gene with protein product	"B7 family member, H4", "B7 superfamily member 1"	608162				12818165, 12818166	Standard	NM_024626		Approved	B7-H4, FLJ22418, B7S1, B7X, B7H4	uc001ehb.3	Q7Z7D3	OTTHUMG00000012118	ENST00000369458.3:c.330T>C	chr1.hg19:g.117699311A>G		115.0	0.0		132.0	38.0	NM_024626		Silent	SNP	ENST00000369458.3	hg19	CCDS894.1																																																																																			.	.		0.468	VTCN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000033500.2	NM_024626		G	117699311	A	G	117699311	2	3	30	1	0	0	0	0	0	0	0	1	17249	117	5	2		2	VTCN1	1	117699311	Silent	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	30782958	117699311	131551310	4	3705										
PGLYRP3	114771	hgsc.bcm.edu	37	chr1	153279733	153279733	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cactccttgcgggagacgatGgtgggagtatctgtagggaa	16	7	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:153279733G>A	ENST00000290722.1	-	2	118	c.66C>T	c.(64-66)acC>acT	p.T22T		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	22					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGGAGACGATGGTGGGAGTAT	0.622																																					p.T22T		Atlas-SNP	.											.	PGLYRP3	55	.	0			c.C66T						.						32	31	32					1																	153279733		2202	4300	6502	SO:0001819	synonymous_variant	114771	exon2			GACGATGGTGGGA	AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I alpha precursor"	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.66C>T	chr1.hg19:g.153279733G>A		39.0	0.0		45.0	18.0	NM_052891	A1A4U8|Q5SY65	Silent	SNP	ENST00000290722.1	hg19	CCDS1035.1																																																																																			.	.		0.622	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891		A	153279733	G	A	153279733	2	1	30	1	0	0	0	0	0	0	0	1	11804	1335	47	3		3	PGLYRP3	1	153279733	Silent	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	35580422	153279733	95970888	5	3706										
NOS1AP	9722	hgsc.bcm.edu	37	chr1	162337003	162337003	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gcagccccttaggtaggcgcGactgcttggtgaagctggag	16	10	0	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:162337003G>T	ENST00000361897.5	+	10	1669	c.1267G>T	c.(1267-1269)Gac>Tac	p.D423Y	NOS1AP_ENST00000454693.1_3'UTR|NOS1AP_ENST00000493151.1_Missense_Mutation_p.D128Y|NOS1AP_ENST00000530878.1_Missense_Mutation_p.D418Y|RP11-565P22.6_ENST00000431696.1_Intron	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	423					regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			AGGTAGGCGCGACTGCTTGGT	0.682																																					p.D423Y		Atlas-SNP	.											.	NOS1AP	139	.	0			c.G1267T						.						51	57	55					1																	162337003		2203	4300	6503	SO:0001583	missense	9722	exon10			AGGCGCGACTGCT	AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"C-terminal PDZ domain ligand of neuronal nitric oxide synthase"	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.1267G>T	chr1.hg19:g.162337003G>T	ENSP00000355133:p.Asp423Tyr	41.0	0.0		43.0	12.0	NM_014697	B7ZLF5|O43564|Q3T551|Q5VU95	Missense_Mutation	SNP	ENST00000361897.5	hg19	CCDS1237.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.136167	0.77662	.	.	ENSG00000198929	ENST00000530878;ENST00000361897;ENST00000464284;ENST00000493151	T;T	0.78246	-1.16;-1.16	4.96	4.96	0.65561	.	0.741680	0.14378	N	0.323360	T	0.69602	0.3129	N	0.14661	0.345	.	.	.	D;D;P	0.62365	0.986;0.991;0.947	P;P;P	0.55824	0.785;0.615;0.511	T	0.76332	-0.2998	9	0.66056	D	0.02	.	17.1256	0.86713	0.0:0.0:1.0:0.0	.	128;418;423	Q3T551;B7ZLF5;O75052	.;.;CAPON_HUMAN	Y	418;423;79;128	ENSP00000431586:D418Y;ENSP00000355133:D423Y	ENSP00000355133:D423Y	D	+	1	0	NOS1AP	160603627	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.219000	0.51200	2.419000	0.82065	0.655000	0.94253	GAC	.	.		0.682	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697		T	162337003	G	T	162337003	3	4	30	1	0	0	0	0	1	0	0	0	10551	1058	37	1	1359	1	NOS1AP	1	162337003	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	9057270	162337003	86913618	6	3707										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200973575	200973575	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aaggcgctgatcacattgccCaaggccagctgtgggagaca	13	11	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:200973575C>A	ENST00000422435.2	-	7	1225	c.909G>T	c.(907-909)ttG>ttT	p.L303F	KIF21B_ENST00000332129.2_Missense_Mutation_p.L303F|KIF21B_ENST00000360529.5_Missense_Mutation_p.L303F|KIF21B_ENST00000461742.2_Missense_Mutation_p.L303F	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	303	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TCACATTGCCCAAGGCCAGCT	0.602																																					p.L303F		Atlas-SNP	.											.	KIF21B	208	.	0			c.G909T						.						67	53	58					1																	200973575		2203	4298	6501	SO:0001583	missense	23046	exon7			ATTGCCCAAGGCC	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.909G>T	chr1.hg19:g.200973575C>A	ENSP00000411831:p.Leu303Phe	59.0	0.0		95.0	23.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	hg19	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	c	25.6	4.652874	0.88056	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38	5.59	5.59	0.84812	Kinesin, motor domain (3);	0.000000	0.64402	D	0.000004	D	0.95258	0.8462	M	0.89601	3.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.997	D	0.95779	0.8815	10	0.87932	D	0	.	14.4547	0.67409	0.1472:0.8528:0.0:0.0	.	303;303;303;303	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	F	303	ENSP00000328494:L303F;ENSP00000353724:L303F;ENSP00000433808:L303F;ENSP00000411831:L303F	ENSP00000328494:L303F	L	-	3	2	KIF21B	199240198	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.129000	0.50500	2.632000	0.89209	0.580000	0.79431	TTG	.	.		0.602	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200973575	C	A	200973575	3	1	30	1	0	0	0	0	1	0	0	0	8298	593	21	3	4077	3	KIF21B	1	200973575	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	38636572	200973575	48277046	7	3708										
ZC3H11A	9877	hgsc.bcm.edu	37	chr1	203816541	203816541	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	caggaagcagagagacaaaaAagcaaaaaggatacaacttg	10	6	0	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:203816541A>C	ENST00000545588.1	+	12	5099	c.1272A>C	c.(1270-1272)aaA>aaC	p.K424N	ZC3H11A_ENST00000332127.4_Missense_Mutation_p.K424N|ZC3H11A_ENST00000367214.1_Missense_Mutation_p.K424N|ZC3H11A_ENST00000367210.1_Missense_Mutation_p.K424N|ZC3H11A_ENST00000367212.3_Missense_Mutation_p.K424N	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	424					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AGAGACAAAAAAGCAAAAAGG	0.423																																					p.K424N		Atlas-SNP	.											.	ZC3H11A	71	.	0			c.A1272C						.						64	68	67					1																	203816541		2203	4300	6503	SO:0001583	missense	9877	exon15			ACAAAAAAGCAAA		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"Zinc fingers, CCCH-type domain containing"	29093	protein-coding gene	gene with protein product		613513	"zinc finger CCCH-type domain containing 11A"	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.1272A>C	chr1.hg19:g.203816541A>C	ENSP00000438527:p.Lys424Asn	167.0	0.0		172.0	37.0	NM_014827	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Missense_Mutation	SNP	ENST00000545588.1	hg19	CCDS30978.1	.	.	.	.	.	.	.	.	.	.	A	13.74	2.326908	0.41197	.	.	ENSG00000058673	ENST00000453771;ENST00000367214;ENST00000537080;ENST00000367212;ENST00000332127;ENST00000545588;ENST00000367210	T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66	5.82	2.25	0.28309	.	0.272209	0.40728	N	0.001034	T	0.34890	0.0913	L	0.43701	1.375	0.33207	D	0.552924	B	0.17667	0.023	B	0.23419	0.046	T	0.30208	-0.9986	10	0.30078	T	0.28	-19.5068	5.597	0.17333	0.6504:0.135:0.2146:0.0	.	424	O75152	ZC11A_HUMAN	N	424;424;370;424;424;424;424	ENSP00000356183:K424N;ENSP00000356181:K424N;ENSP00000333253:K424N;ENSP00000438527:K424N;ENSP00000356179:K424N	ENSP00000333253:K424N	K	+	3	2	ZC3H11A	202083164	0.994000	0.37717	0.977000	0.42913	0.971000	0.66376	3.299000	0.51826	0.137000	0.18759	-0.262000	0.10625	AAA	.	.		0.423	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827		C	203816541	A	C	203816541	3	2	30	1	0	0	0	0	1	0	0	0	17575	11	1	5	1314	5	ZC3H11A	1	203816541	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	2842966	203816541	45434080	8	3709										
USH2A	7399	hgsc.bcm.edu	37	chr1	215916665	215916665	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tgtactccacaggaatttcgGggatgaggatccctttaaag	11	8	0	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:215916665G>A	ENST00000307340.3	-	59	11788	c.11402C>T	c.(11401-11403)cCc>cTc	p.P3801L	USH2A_ENST00000366943.2_Missense_Mutation_p.P3801L	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3801	Fibronectin type-III 23. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AGGAATTTCGGGGATGAGGAT	0.393										HNSCC(13;0.011)																											p.P3801L		Atlas-SNP	.											.	USH2A	1168	.	0			c.C11402T						.						91	86	88					1																	215916665		2203	4300	6503	SO:0001583	missense	7399	exon59			ATTTCGGGGATGA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.11402C>T	chr1.hg19:g.215916665G>A	ENSP00000305941:p.Pro3801Leu	25.0	0.0		37.0	8.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.893444	0.33442	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53857	0.6;0.6	4.94	4.94	0.65067	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.346744	0.21118	N	0.079863	T	0.47377	0.1442	L	0.50919	1.6	0.09310	N	1	P	0.34462	0.454	B	0.38156	0.266	T	0.37384	-0.9708	10	0.25106	T	0.35	.	10.6735	0.45772	0.0952:0.0:0.9048:0.0	.	3801	O75445	USH2A_HUMAN	L	3801	ENSP00000305941:P3801L;ENSP00000355910:P3801L	ENSP00000305941:P3801L	P	-	2	0	USH2A	213983288	0.025000	0.19082	0.025000	0.17156	0.608000	0.37181	1.812000	0.38952	2.706000	0.92434	0.655000	0.94253	CCC	.	.		0.393	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	215916665	G	A	215916665	3	1	30	1	0	0	0	0	1	0	0	0	17051	1232	43	3	4262	3	USH2A	1	215916665	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	12100124	215916665	33333956	9	3710										
USH2A	7399	hgsc.bcm.edu	37	chr1	216062251	216062251	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	actgtgcaattagtgacattTccaggagttctcaagtatag	9	7	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:216062251T>A	ENST00000307340.3	-	41	8126	c.7740A>T	c.(7738-7740)ggA>ggT	p.G2580G	RP5-1111A8.3_ENST00000414995.1_RNA|USH2A_ENST00000366943.2_Silent_p.G2580G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2580	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TAGTGACATTTCCAGGAGTTC	0.418										HNSCC(13;0.011)																											p.G2580G		Atlas-SNP	.											.	USH2A	1168	.	0			c.A7740T						.						149	145	146					1																	216062251		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon41			GACATTTCCAGGA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7740A>T	chr1.hg19:g.216062251T>A		91.0	0.0		108.0	29.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.418	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216062251	T	A	216062251	2	1	30	1	0	0	0	0	0	0	0	1	17051	1770	62	4		4	USH2A	1	216062251	Silent	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	145586	216062251	33188370	10	3711										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227316906	227316908	+	In_Frame_Del	DEL	GCA	GCA	-													0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	accatcaacagttgaatactGcagagcttggacagtctgtg							TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:227316906_227316908delGCA	ENST00000366769.3	-	11	2706_2708	c.1415_1417delTGC	c.(1414-1419)ctgcag>cag	p.L472del	CDC42BPA_ENST00000535525.1_In_Frame_Del_p.L472del|CDC42BPA_ENST00000366766.2_In_Frame_Del_p.L472del|CDC42BPA_ENST00000366767.3_In_Frame_Del_p.L472del|CDC42BPA_ENST00000366764.2_In_Frame_Del_p.L472del|CDC42BPA_ENST00000366765.3_In_Frame_Del_p.L472del|CDC42BPA_ENST00000334218.5_In_Frame_Del_p.L472del	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				GTTGAATACTGCAGAGCTTGGAC	0.271																																					p.472_473del		Atlas-Indel,Pindel	.											.	CDC42BPA	528	.	0			c.1416_1418del						.																																			SO:0001651	inframe_deletion	8476	exon11			.	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.1415_1417delTGC	chr1.hg19:g.227316906_227316908delGCA	ENSP00000355731:p.Leu472del	580.0	0.0		421.0	107.0	NM_003607		In_Frame_Del	DEL	ENST00000366769.3	hg19	CCDS1558.1																																																																																			.	.		0.271	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		-	227316908	GCA	-	227316906	7	5	30	1	0	1	0	1	0	0	0	0	3074	1328	46	0	3846	0	CDC42BPA	1	227316906	In_Frame_Del	DEL	GCA	TCGA-BC-4073-01B-02D-A12Z-10	11254655	227316906	21933715	11	3712										
RYR2	6262	hgsc.bcm.edu	37	chr1	237923107	237923107	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ctacctcaaggagaaaaaggAtgtgggcttctttcagagcc	11	9	3	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:237923107A>C	ENST00000366574.2	+	83	11674	c.11357A>C	c.(11356-11358)gAt>gCt	p.D3786A	RYR2_ENST00000360064.6_Missense_Mutation_p.D3792A|RYR2_ENST00000542537.1_Missense_Mutation_p.D3770A|RYR2_ENST00000609119.1_3'UTR	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3786					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAGAAAAAGGATGTGGGCTTC	0.413																																					p.D3786A		Atlas-SNP	.											.	RYR2	1273	.	0			c.A11357C						.						116	113	114					1																	237923107		1854	4090	5944	SO:0001583	missense	6262	exon83			AAAAGGATGTGGG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.11357A>C	chr1.hg19:g.237923107A>C	ENSP00000355533:p.Asp3786Ala	144.0	0.0		166.0	43.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.020179	0.75275	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.89343	-2.5;-2.5;-2.5	5.81	5.81	0.92471	.	0.000000	0.64402	U	0.000006	D	0.90164	0.6926	M	0.79258	2.445	0.80722	D	1	B;B	0.30146	0.27;0.27	B;B	0.34138	0.176;0.092	D	0.89443	0.3725	10	0.66056	D	0.02	-21.7762	16.1616	0.81721	1.0:0.0:0.0:0.0	.	760;3786	B4DGV4;Q92736	.;RYR2_HUMAN	A	3786;3792;3770;760	ENSP00000355533:D3786A;ENSP00000353174:D3792A;ENSP00000443798:D3770A	ENSP00000353174:D3792A	D	+	2	0	RYR2	235989730	1.000000	0.71417	0.980000	0.43619	0.995000	0.86356	9.279000	0.95777	2.218000	0.71995	0.377000	0.23210	GAT	.	.		0.413	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237923107	A	C	237923107	3	2	30	1	0	0	0	0	1	0	0	0	13784	333	12	5	11687	5	RYR2	1	237923107	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	10606201	237923107	11327514	12	3713										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247582364	247582364	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tttatgagaaagcaaaaagaGatgagccgaagtggggtgag	15	3	0	4			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr1:247582364G>T	ENST00000336119.3	+	1	1014	c.268G>T	c.(268-270)Gat>Tat	p.D90Y	NLRP3_ENST00000366496.2_Missense_Mutation_p.D90Y|NLRP3_ENST00000348069.2_Missense_Mutation_p.D90Y|NLRP3_ENST00000366497.2_Missense_Mutation_p.D90Y|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000391827.2_Missense_Mutation_p.D90Y|NLRP3_ENST00000391828.3_Missense_Mutation_p.D90Y	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	90	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			AGCAAAAAGAGATGAGCCGAA	0.423																																					p.D90Y		Atlas-SNP	.											.	NLRP3	286	.	0			c.G268T						.						56	54	55					1																	247582364		2203	4300	6503	SO:0001583	missense	114548	exon1			AAAAGAGATGAGC	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.268G>T	chr1.hg19:g.247582364G>T	ENSP00000337383:p.Asp90Tyr	16.0	0.0		19.0	10.0	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.209887	0.39003	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	T;T;T;T;T;T	0.58652	0.32;0.32;0.32;0.32;0.32;0.32	4.49	4.49	0.54785	Pyrin (1);DEATH-like (2);	0.631279	0.15000	N	0.286179	T	0.62684	0.2448	L	0.36672	1.1	0.09310	N	0.999999	P;D;D;P;P	0.65815	0.953;0.972;0.995;0.95;0.916	P;P;P;P;B	0.58520	0.507;0.702;0.84;0.492;0.406	T	0.55623	-0.8112	10	0.87932	D	0	.	12.8787	0.58003	0.0:0.0:1.0:0.0	.	90;90;90;90;90	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	Y	90	ENSP00000375704:D90Y;ENSP00000355453:D90Y;ENSP00000337383:D90Y;ENSP00000294752:D90Y;ENSP00000355452:D90Y;ENSP00000375703:D90Y	ENSP00000337383:D90Y	D	+	1	0	NLRP3	245648987	0.363000	0.24989	0.082000	0.20525	0.423000	0.31445	1.668000	0.37481	2.498000	0.84270	0.561000	0.74099	GAT	.	.		0.423	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		T	247582364	G	T	247582364	3	4	30	1	0	0	0	0	1	0	0	0	10487	942	33	3	270	3	NLRP3	1	247582364	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	9659257	247582364	1668257	13	3714										
GTF3C2	2976	hgsc.bcm.edu	37	chr2	27552031	27552031	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cacagtgacaccattgtaggGaagcagccaggccagttctg	12	11	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr2:27552031G>C	ENST00000359541.2	-	14	2425	c.1996C>G	c.(1996-1998)Ccc>Gcc	p.P666A	GTF3C2_ENST00000264720.3_Missense_Mutation_p.P666A			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	666					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCATTGTAGGGAAGCAGCCAG	0.517																																					p.C666G		Atlas-SNP	.											.	GTF3C2	73	.	0			c.T1996G						.						178	181	180					2																	27552031		2203	4300	6503	SO:0001583	missense	2976	exon15			TGTAGGGAAGCAG	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.1996C>G	chr2.hg19:g.27552031G>C	ENSP00000352536:p.Pro666Ala	65.0	0.0		97.0	25.0	NM_001521	D6W557|Q16632|Q9BWI7	Missense_Mutation	SNP	ENST00000359541.2	hg19	CCDS1749.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.68|10.68	1.417812|1.417812	0.25552|0.25552	.|.	.|.	ENSG00000115207|ENSG00000115207	ENST00000454704;ENST00000415683|ENST00000359541;ENST00000264720	.|T;T	.|0.71934	.|-0.61;-0.61	6.03|6.03	6.03|6.03	0.97812|0.97812	.|WD40 repeat-like-containing domain (1);	.|0.277859	.|0.37393	.|N	.|0.002111	T|T	0.55768|0.55768	0.1941|0.1941	N|N	0.24115|0.24115	0.695|0.695	0.40827|0.40827	D|D	0.983556|0.983556	.|P	.|0.38020	.|0.615	.|B	.|0.33196	.|0.159	T|T	0.55438|0.55438	-0.8141|-0.8141	5|10	.|0.13853	.|T	.|0.58	-15.2787|-15.2787	18.0604|18.0604	0.89375|0.89375	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|666	.|Q8WUA4	.|TF3C2_HUMAN	L|A	174;67|666	.|ENSP00000352536:P666A;ENSP00000264720:P666A	.|ENSP00000264720:P666A	F|P	-|-	3|1	2|0	GTF3C2|GTF3C2	27405535|27405535	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	3.796000|3.796000	0.55507|0.55507	2.854000|2.854000	0.98071|0.98071	0.655000|0.655000	0.94253|0.94253	TTC|CCC	.	.		0.517	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			C	27552031	G	C	27552031	3	2	30	1	0	0	0	0	1	0	0	0	6882	1174	41	4	763	4	GTF3C2	2	27552031	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10		27552031	215647342	14	3715										
EIF2B4	8890	hgsc.bcm.edu	37	chr2	27590024	27590024	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tgagctgctagcacaatcttCtcttgcacataccgatcaat	6	12	3	1	rs373520608		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr2:27590024C>T	ENST00000347454.4	-	10	1101	c.930G>A	c.(928-930)gaG>gaA	p.E310E	EIF2B4_ENST00000451130.2_Silent_p.E330E|EIF2B4_ENST00000445933.2_Silent_p.E309E|AC074117.10_ENST00000412749.1_RNA|EIF2B4_ENST00000493344.2_Silent_p.E331E	NM_001034116.1|NM_015636.3	NP_001029288.1|NP_056451.3	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B, subunit 4 delta, 67kDa	310					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation (GO:0045947)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translation (GO:0006417)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(5)|skin(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCACAATCTTCTCTTGCACAT	0.438																																					p.E330E		Atlas-SNP	.											.	EIF2B4	48	.	0			c.G990A						.	C	,,	0,4406		0,0,2203	209	177	188		930,927,990	5.1	1	2		188	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF2B4	NM_001034116.1,NM_015636.3,NM_172195.3	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	310/524,309/523,330/544	27590024	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8890	exon9			AATCTTCTCTTGC	AJ011306	CCDS33164.1, CCDS46244.1, CCDS46245.1	2p23.3	2008-02-05	2002-08-29		ENSG00000115211	ENSG00000115211			3260	protein-coding gene	gene with protein product		606687	"eukaryotic translation initiation factor 2B, subunit 4 (delta, 67kD)"			8929216, 7982969	Standard	NM_172195		Approved	EIF2Bdelta, EIF-2B, DKFZP586J0119, EIF2B	uc002rjz.3	Q9UI10	OTTHUMG00000151927	ENST00000347454.4:c.930G>A	chr2.hg19:g.27590024C>T		79.0	0.0		81.0	22.0	NM_172195	Q53RY7|Q5BJF4|Q9BUV9|Q9UBG4|Q9UIQ9|Q9UJ95	Silent	SNP	ENST00000347454.4	hg19	CCDS33164.1																																																																																			.	.		0.438	EIF2B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324448.1			T	27590024	C	T	27590024	2	4	30	1	0	0	0	0	0	0	0	1	5005	912	32	3		3	EIF2B4	2	27590024	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	37993	27590024	215609349	15	3716										
FAM98A	25940	hgsc.bcm.edu	37	chr2	33810097	33810097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gccaccaccctggtatccacTtcctgtatatgaagaagatg	8	12	0	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr2:33810097T>C	ENST00000238823.8	-	8	1443	c.1303A>G	c.(1303-1305)Agt>Ggt	p.S435G	FAM98A_ENST00000403368.1_3'UTR|FAM98A_ENST00000498340.1_5'Flank|FAM98A_ENST00000441530.2_Missense_Mutation_p.S240G			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	436	Gly-rich.						poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					TGGTATCCACTTCCTGTATAT	0.557																																					p.S435G		Atlas-SNP	.											.	FAM98A	42	.	0			c.A1303G						.						152	138	143					2																	33810097		2203	4300	6503	SO:0001583	missense	25940	exon8			ATCCACTTCCTGT		CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.1303A>G	chr2.hg19:g.33810097T>C	ENSP00000238823:p.Ser435Gly	109.0	0.0		116.0	32.0	NM_015475	B2RNA2|Q9Y3Y6	Missense_Mutation	SNP	ENST00000238823.8	hg19	CCDS33179.1	.	.	.	.	.	.	.	.	.	.	T	9.404	1.078689	0.20227	.	.	ENSG00000119812	ENST00000238823;ENST00000395190;ENST00000441530	T;T	0.51071	0.84;0.72	5.64	5.64	0.86602	.	0.103522	0.64402	D	0.000002	T	0.25082	0.0609	N	0.08118	0	0.46317	D	0.998989	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.14117	-1.0484	10	0.08837	T	0.75	-12.9086	11.7336	0.51752	0.0:0.0705:0.0:0.9295	.	436;266;435;273	Q8NCA5;B4DY25;Q8NCA5-2;B3KTW4	FA98A_HUMAN;.;.;.	G	435;436;240	ENSP00000238823:S435G;ENSP00000408716:S240G	ENSP00000238823:S435G	S	-	1	0	FAM98A	33663601	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.501000	0.45389	2.147000	0.66899	0.533000	0.62120	AGT	.	.		0.557	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475		C	33810097	T	C	33810097	3	2	30	1	0	0	0	0	1	0	0	0	5664	1609	56	2	257	2	FAM98A	2	33810097	Missense_Mutation	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	6220073	33810097	209389276	16	3717										
LY75	4065	hgsc.bcm.edu	37	chr2	160665051	160665051	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	acaaatttattctcatcttcAtcttttatggaaacgatagt	4	7	4	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr2:160665051A>T	ENST00000263636.4	-	33	4758	c.4731T>A	c.(4729-4731)gaT>gaA	p.D1577E	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.D1577E|LY75_ENST00000553424.1_Missense_Mutation_p.D1577E|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.D1577E|LY75_ENST00000554112.1_Missense_Mutation_p.D1577E	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1577	C-type lectin 10. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		TCTCATCTTCATCTTTTATGG	0.343																																					p.D1577E		Atlas-SNP	.											.	LY75	151	.	0			c.T4731A						.						170	167	168					2																	160665051		2202	4299	6501	SO:0001583	missense	4065	exon33			ATCTTCATCTTTT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.4731T>A	chr2.hg19:g.160665051A>T	ENSP00000263636:p.Asp1577Glu	163.0	0.0		140.0	40.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.495988	0.64186	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0	5.55	4.35	0.52113	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.462627	0.16025	U	0.233157	T	0.25865	0.0630	M	0.87971	2.92	0.42835	D	0.994038	P;P;B	0.44946	0.846;0.84;0.433	P;P;B	0.48334	0.557;0.574;0.164	T	0.05971	-1.0853	10	0.56958	D	0.05	-13.1038	11.6348	0.51198	0.8671:0.0:0.0:0.1329	.	1577;1577;1577	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	E	1577	ENSP00000451511:D1577E;ENSP00000451446:D1577E;ENSP00000263636:D1577E;ENSP00000423463:D1577E;ENSP00000421035:D1577E	ENSP00000423463:D1577E	D	-	3	2	LY75;LY75-CD302	160373297	1.000000	0.71417	0.996000	0.52242	0.882000	0.50991	2.724000	0.47285	2.105000	0.64084	0.402000	0.26972	GAT	.	.		0.343	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			T	160665051	A	T	160665051	3	4	30	1	0	0	0	0	1	0	0	0	9108	214	8	4	449	4	LY75	2	160665051	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	126854954	160665051	82534322	17	3718										
DFNB59	494513	hgsc.bcm.edu	37	chr2	179325171	179325171	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gagaaatatcctatttgaaaGaagtatgtttattgaagagt	9	2	0	5			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr2:179325171G>C	ENST00000409117.3	+	6	1120	c.764G>C	c.(763-765)aGa>aCa	p.R255T	DFNB59_ENST00000375129.4_Missense_Mutation_p.R255T	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	255					sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			CTATTTGAAAGAAGTATGTTT	0.353																																					p.R255T		Atlas-SNP	.											.	DFNB59	37	.	0			c.G764C						.						85	81	82					2																	179325171		1833	4085	5918	SO:0001583	missense	494513	exon6			TTGAAAGAAGTAT	BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311			29502	protein-coding gene	gene with protein product		610219				16804542	Standard	NM_001042702		Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.764G>C	chr2.hg19:g.179325171G>C	ENSP00000386647:p.Arg255Thr	126.0	0.0		105.0	20.0	NM_001042702	A0PK14|B9EJE2	Missense_Mutation	SNP	ENST00000409117.3	hg19	CCDS42787.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.803735	0.50315	.	.	ENSG00000204311	ENST00000409117;ENST00000375129	T;T	0.58506	0.33;0.33	5.4	5.4	0.78164	.	0.000000	0.49305	U	0.000141	T	0.44329	0.1288	N	0.22421	0.69	0.49299	D	0.999774	B	0.25441	0.126	B	0.26094	0.066	T	0.32134	-0.9918	10	0.14252	T	0.57	-21.5255	16.9645	0.86282	0.0:0.0:1.0:0.0	.	255	Q0ZLH3	PJVK_HUMAN	T	255	ENSP00000386647:R255T;ENSP00000364271:R255T	ENSP00000364271:R255T	R	+	2	0	DFNB59	179033417	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	4.095000	0.57728	2.538000	0.85594	0.462000	0.41574	AGA	.	.		0.353	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335160.1			C	179325171	G	C	179325171	3	2	30	1	0	0	0	0	1	0	0	0	4458	942	33	4	782	4	DFNB59	2	179325171	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	18660120	179325171	63874202	18	3719										
OSGEPL1	64172	hgsc.bcm.edu	37	chr2	190617632	190617632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gaggaggacacaacaaagtgCactgtgttgcatttgttaaa	11	6	0	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr2:190617632C>T	ENST00000264151.5	-	6	1139	c.1037G>A	c.(1036-1038)tGc>tAc	p.C346Y	Y_RNA_ENST00000411317.1_RNA|OSGEPL1_ENST00000522700.1_Missense_Mutation_p.C346Y|OSGEPL1_ENST00000519810.1_Missense_Mutation_p.C346Y	NM_022353.2	NP_071748.2			O-sialoglycoprotein endopeptidase-like 1											large_intestine(2)|upper_aerodigestive_tract(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0293)|all cancers(119;0.0831)			CAACAAAGTGCACTGTGTTGC	0.403																																					p.C346Y		Atlas-SNP	.											.	OSGEPL1	19	.	0			c.G1037A						.						83	80	81					2																	190617632		1895	4127	6022	SO:0001583	missense	64172	exon6			AAAGTGCACTGTG	AJ295148	CCDS46472.1	2q32	2011-08-12			ENSG00000128694	ENSG00000128694			23075	protein-coding gene	gene with protein product						19578062	Standard	NM_022353		Approved	Qri7	uc002uqz.1	Q9H4B0	OTTHUMG00000164096	ENST00000264151.5:c.1037G>A	chr2.hg19:g.190617632C>T	ENSP00000264151:p.Cys346Tyr	312.0	0.0		271.0	60.0	NM_022353		Missense_Mutation	SNP	ENST00000264151.5	hg19	CCDS46472.1	.	.	.	.	.	.	.	.	.	.	C	2.943	-0.218548	0.06101	.	.	ENSG00000128694	ENST00000264151;ENST00000519810;ENST00000522700	T;T;T	0.41400	1.0;1.0;1.0	5.27	5.27	0.74061	Peptidase M22, glycoprotease (1);	0.179938	0.52532	D	0.000076	T	0.19565	0.0470	N	0.12637	0.245	0.29823	N	0.830666	B	0.18461	0.028	B	0.14578	0.011	T	0.21690	-1.0238	10	0.02654	T	1	-4.9742	8.7283	0.34483	0.2661:0.6021:0.1318:0.0	.	346	Q9H4B0	OSGP2_HUMAN	Y	346	ENSP00000264151:C346Y;ENSP00000428859:C346Y;ENSP00000429697:C346Y	ENSP00000264151:C346Y	C	-	2	0	OSGEPL1	190325877	1.000000	0.71417	0.994000	0.49952	0.917000	0.54804	5.380000	0.66202	2.737000	0.93849	0.563000	0.77884	TGC	.	.		0.403	OSGEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377257.1	NM_022353		T	190617632	C	T	190617632	3	4	30	1	0	0	0	0	1	0	0	0	11297	710	25	3	219	3	OSGEPL1	2	190617632	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	11292461	190617632	52581741	19	3720										
PMS1	5378	hgsc.bcm.edu	37	chr2	190718971	190718971	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	atttgtatttttaggaatctGttttaattgctcttgaaaat	6	3	2	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr2:190718971G>A	ENST00000441310.2	+	9	1206	c.973G>A	c.(973-975)Gtt>Att	p.V325I	PMS1_ENST00000432292.3_Missense_Mutation_p.V149I|PMS1_ENST00000418224.3_Missense_Mutation_p.V149I|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000447232.2_Missense_Mutation_p.V325I|PMS1_ENST00000409823.3_Missense_Mutation_p.V286I	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	325					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			TTAGGAATCTGTTTTAATTGC	0.249			"Mis, N"			"colorectal, endometrial, ovarian"		Direct reversal of damage;Mismatch excision repair (MMR)																													p.V325I		Atlas-SNP	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	.	PMS1	78	.	0			c.G973A						.						26	27	27					2																	190718971		1982	4190	6172	SO:0001583	missense	5378	exon9			GAATCTGTTTTAA		CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"postmeiotic segregation increased (S. cerevisiae) 1"	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.973G>A	chr2.hg19:g.190718971G>A	ENSP00000406490:p.Val325Ile	159.0	0.0		133.0	28.0	NM_001128144	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Missense_Mutation	SNP	ENST00000441310.2	hg19	CCDS2302.1	.	.	.	.	.	.	.	.	.	.	G	12.39	1.924570	0.34002	.	.	ENSG00000064933	ENST00000392338;ENST00000441310;ENST00000418224;ENST00000409823;ENST00000447232;ENST00000432292;ENST00000424307;ENST00000409593	D;D;T;D;D;D;D	0.84944	-1.92;-1.92;-1.42;-1.92;-1.92;-1.92;-1.92	5.29	2.3	0.28687	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.163445	0.53938	N	0.000050	T	0.79353	0.4431	L	0.46614	1.455	0.47778	D	0.999516	B;B;B;B;B;B;B	0.28378	0.06;0.058;0.058;0.209;0.033;0.06;0.06	B;B;B;B;B;B;B	0.34385	0.116;0.181;0.181;0.181;0.181;0.116;0.116	T	0.72459	-0.4287	10	0.37606	T	0.19	-13.062	7.6931	0.28579	0.1397:0.253:0.6073:0.0	.	325;286;286;110;286;325;325	Q4VAL4;B4DMF4;Q5FBZ9;Q5FBZ6;Q5FBZ3;Q5FBZ8;P54277	.;.;.;.;.;.;PMS1_HUMAN	I	149;325;149;286;325;149;264;110	ENSP00000406490:V325I;ENSP00000404492:V149I;ENSP00000387125:V286I;ENSP00000401064:V325I;ENSP00000398378:V149I;ENSP00000389938:V264I;ENSP00000387169:V110I	ENSP00000376149:V149I	V	+	1	0	PMS1	190427216	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.746000	0.38288	0.762000	0.33152	0.557000	0.71058	GTT	.	.		0.249	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2			A	190718971	G	A	190718971	3	1	30	1	0	0	0	0	1	0	0	0	12151	1377	48	3	1003	3	PMS1	2	190718971	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	101339	190718971	52480402	20	3721										
ACCN4	55515	hgsc.bcm.edu	37	chr2	220379823	220379823	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tatcaaccgcttccggcattCggcactcagcgatgccgaca	9	15	2	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr2:220379823C>A	ENST00000347842.3	+	1	772	c.758C>A	c.(757-759)tCg>tAg	p.S253*	ASIC4_ENST00000358078.4_Nonsense_Mutation_p.S253*|AC053503.11_ENST00000429882.1_RNA	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	253					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										TTCCGGCATTCGGCACTCAGC	0.672																																					p.S253X		Atlas-SNP	.											.	.	.	.	0			c.C758A						.						42	38	39					2																	220379823		2203	4300	6503	SO:0001587	stop_gained	55515	exon1			GGCATTCGGCACT	AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"Ion channels / Acid-sensing (proton-gated) ion channels"	21263	protein-coding gene	gene with protein product		606715	"amiloride-sensitive cation channel 4, pituitary", "amiloride-sensitive cation channel family member 4, pituitary"	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.758C>A	chr2.hg19:g.220379823C>A	ENSP00000326627:p.Ser253*	54.0	0.0		77.0	21.0	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Nonsense_Mutation	SNP	ENST00000347842.3	hg19	CCDS2442.1	.	.	.	.	.	.	.	.	.	.	C	37	6.271920	0.97431	.	.	ENSG00000072182	ENST00000347842;ENST00000358078	.	.	.	4.69	4.69	0.59074	.	0.376783	0.23750	N	0.044926	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.7538	17.4292	0.87534	0.0:1.0:0.0:0.0	.	.	.	.	X	253	.	ENSP00000326627:S253X	S	+	2	0	ACCN4	220088067	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.797000	0.69087	2.431000	0.82371	0.655000	0.94253	TCG	.	.		0.672	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674		A	220379823	C	A	220379823	4	1	30	1	0	0	0	0	0	1	0	0	131	893	31	1	760	1	ACCN4	2	220379823	Nonsense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	29660852	220379823	22819550	21	3722										
RBMS3	27303	hgsc.bcm.edu	37	chr3	29781252	29781252	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aacctatacatctcaaatctCcccatttctatggatgagca	4	12	3	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr3:29781252C>G	ENST00000383767.2	+	5	777	c.441C>G	c.(439-441)ctC>ctG	p.L147L	RBMS3_ENST00000273139.9_Silent_p.L147L|RBMS3_ENST00000434693.2_Silent_p.L146L|RBMS3_ENST00000456853.1_Silent_p.L147L|RBMS3_ENST00000396583.3_Silent_p.L147L|RBMS3_ENST00000445033.1_Silent_p.L147L|RBMS3_ENST00000452462.1_Silent_p.L147L|RBMS3_ENST00000383766.2_Silent_p.L146L			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	147	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				TCTCAAATCTCCCCATTTCTA	0.398																																					p.L147L		Atlas-SNP	.											.	RBMS3	62	.	0			c.C441G						.						172	166	168					3																	29781252		2203	4300	6503	SO:0001819	synonymous_variant	27303	exon5			AAATCTCCCCATT	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"RNA binding motif (RRM) containing"	13427	protein-coding gene	gene with protein product	"RNA-binding protein"	605786	"RNA binding motif, single stranded interacting protein"			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.441C>G	chr3.hg19:g.29781252C>G		124.0	0.0		98.0	19.0	NM_001003793	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Silent	SNP	ENST00000383767.2	hg19	CCDS33724.1																																																																																			.	.		0.398	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792		G	29781252	C	G	29781252	2	3	30	1	0	0	0	0	0	0	0	1	13165	842	30	4		4	RBMS3	3	29781252	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10		29781252	168241178	22	3723										
VIPR1	7433	hgsc.bcm.edu	37	chr3	42577594	42577594	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tctcctaggtgcaggcggagCtgaggcggaagtggcggcgc	19	10	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr3:42577594C>T	ENST00000325123.4	+	13	1308	c.1195C>T	c.(1195-1197)Ctg>Ttg	p.L399L	VIPR1_ENST00000543411.1_Silent_p.L351L|VIPR1-AS1_ENST00000610022.1_RNA|VIPR1-AS1_ENST00000608869.1_RNA|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1_ENST00000438259.2_Silent_p.L189L|VIPR1_ENST00000433647.1_Silent_p.L358L	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	399					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		GCAGGCGGAGCTGAGGCGGAA	0.662																																					p.L399L		Atlas-SNP	.											.	VIPR1	45	.	0			c.C1195T						.						11	14	13					3																	42577594		2187	4277	6464	SO:0001819	synonymous_variant	7433	exon13			GCGGAGCTGAGGC	AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12694	protein-coding gene	gene with protein product	"VIP and PACAP receptor 1"	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.1195C>T	chr3.hg19:g.42577594C>T		55.0	0.0		56.0	12.0	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Silent	SNP	ENST00000325123.4	hg19	CCDS2698.1																																																																																			.	.		0.662	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624		T	42577594	C	T	42577594	2	4	30	1	0	0	0	0	0	0	0	1	17184	796	28	3		3	VIPR1	3	42577594	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	12796342	42577594	155444836	23	3724										
SACM1L	22908	hgsc.bcm.edu	37	chr3	45748365	45748365	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	agattttgatgtcctttcttAtaagaagacaatgttgcact	7	6	1	4			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr3:45748365A>G	ENST00000389061.5	+	4	503	c.299A>G	c.(298-300)tAt>tGt	p.Y100C	SACM1L_ENST00000541314.1_Intron|SACM1L_ENST00000418611.1_5'UTR|SACM1L_ENST00000464524.1_3'UTR	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	100					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		GTCCTTTCTTATAAGAAGACA	0.373																																					p.Y100C		Atlas-SNP	.											.	SACM1L	38	.	0			c.A299G						.						90	88	89					3																	45748365		2203	4300	6503	SO:0001583	missense	22908	exon4			TTTCTTATAAGAA	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.299A>G	chr3.hg19:g.45748365A>G	ENSP00000373713:p.Tyr100Cys	240.0	0.0		188.0	52.0	NM_014016	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	hg19	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.424864	0.83667	.	.	ENSG00000211456	ENST00000389061	T	0.56776	0.44	5.52	5.52	0.82312	Synaptojanin, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.60676	0.2287	L	0.33485	1.01	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.55872	-0.8072	10	0.21540	T	0.41	-17.1008	15.6379	0.76970	1.0:0.0:0.0:0.0	.	100	Q9NTJ5	SAC1_HUMAN	C	100	ENSP00000373713:Y100C	ENSP00000373713:Y100C	Y	+	2	0	SACM1L	45723369	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.847000	0.92166	2.094000	0.63399	0.482000	0.46254	TAT	.	.		0.373	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016		G	45748365	A	G	45748365	3	3	30	1	0	0	0	0	1	0	0	0	13818	449	16	2	313	2	SACM1L	3	45748365	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	3170771	45748365	152274065	24	3725										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134920367	134920367	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ttgtgggtatgctcaggggcAtcgctgctggcatgaagtac	15	8	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr3:134920367A>T	ENST00000398015.3	+	12	2552	c.2182A>T	c.(2182-2184)Atc>Ttc	p.I728F	EPHB1_ENST00000493838.1_Missense_Mutation_p.I289F	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	728	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						GCTCAGGGGCATCGCTGCTGG	0.512																																					p.I728F		Atlas-SNP	.											.	EPHB1	519	.	0			c.A2182T						.						237	236	236					3																	134920367		2203	4300	6503	SO:0001583	missense	2047	exon12			AGGGGCATCGCTG	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.2182A>T	chr3.hg19:g.134920367A>T	ENSP00000381097:p.Ile728Phe	133.0	0.0		153.0	32.0	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	hg19	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	A	31	5.063828	0.93898	.	.	ENSG00000154928	ENST00000398015;ENST00000493838	T;T	0.69435	-0.4;-0.4	5.52	5.52	0.82312	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.150822	0.52532	D	0.000078	D	0.87505	0.6194	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91447	0.5178	10	0.87932	D	0	.	15.6001	0.76616	1.0:0.0:0.0:0.0	.	728	P54762	EPHB1_HUMAN	F	728;289	ENSP00000381097:I728F;ENSP00000419574:I289F	ENSP00000381097:I728F	I	+	1	0	EPHB1	136403057	1.000000	0.71417	0.994000	0.49952	0.983000	0.72400	9.263000	0.95617	2.224000	0.72417	0.460000	0.39030	ATC	.	.		0.512	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		T	134920367	A	T	134920367	3	4	30	1	0	0	0	0	1	0	0	0	5176	217	8	4	2228	4	EPHB1	3	134920367	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	89172002	134920367	63102063	25	3726										
AADAC	13	hgsc.bcm.edu	37	chr3	151545693	151545693	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tctgagctggctaaaaaataTccagggttcctagatgtgag	11	7	1	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr3:151545693T>G	ENST00000232892.7	+	5	1059	c.933T>G	c.(931-933)taT>taG	p.Y311*	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	311					positive regulation of triglyceride catabolic process (GO:0010898)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|deacetylase activity (GO:0019213)|lipase activity (GO:0016298)|serine hydrolase activity (GO:0017171)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(5)|skin(2)	19		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			CTAAAAAATATCCAGGGTTCC	0.418																																					p.Y311X	Ovarian(30;839 841 2699 32801 46334)	Atlas-SNP	.											.	AADAC	49	.	0			c.T933G						.						46	46	46					3																	151545693		2203	4300	6503	SO:0001587	stop_gained	13	exon5			AAAATATCCAGGG	L32179	CCDS33877.1	3q25.1	2014-03-18	2012-07-13		ENSG00000114771	ENSG00000114771	3.1.1.3		17	protein-coding gene	gene with protein product		600338	"arylacetamide deacetylase (esterase)"			8063807	Standard	XM_005247103		Approved	DAC, CES5A1	uc003eze.3	P22760	OTTHUMG00000159876	ENST00000232892.7:c.933T>G	chr3.hg19:g.151545693T>G	ENSP00000232892:p.Tyr311*	65.0	0.0		55.0	17.0	NM_001086	A8K3L3|D3DNJ6|Q8N1A9	Nonsense_Mutation	SNP	ENST00000232892.7	hg19	CCDS33877.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.577070	0.86645	.	.	ENSG00000114771	ENST00000232892	.	.	.	4.81	-4.0	0.04057	.	0.581521	0.18265	N	0.146491	.	.	.	.	.	.	0.54753	D	0.999985	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.2852	14.216	0.65792	0.0:0.6926:0.0:0.3074	.	.	.	.	X	311	.	ENSP00000232892:Y311X	Y	+	3	2	AADAC	153028383	0.709000	0.27886	0.084000	0.20598	0.990000	0.78478	-0.243000	0.08915	-0.723000	0.04915	0.482000	0.46254	TAT	.	.		0.418	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086		G	151545693	T	G	151545693	4	3	30	1	0	0	0	0	0	1	0	0	10	1442	50	5	951	5	AADAC	3	151545693	Nonsense_Mutation	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	16625326	151545693	46476737	26	3727										
DGKG	1608	hgsc.bcm.edu	37	chr3	185993350	185993350	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	actcacaagtgcagcacaggCcttgcttgcggacgcccatg	11	14	1	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr3:185993350C>T	ENST00000265022.3	-	10	1435	c.896G>A	c.(895-897)gGc>gAc	p.G299D	DGKG_ENST00000382164.4_Missense_Mutation_p.G299D|DGKG_ENST00000344484.4_Missense_Mutation_p.G299D|DGKG_ENST00000544847.1_Missense_Mutation_p.G299D	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	299					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	GCAGCACAGGCCTTGCTTGCG	0.522																																					p.G299D		Atlas-SNP	.											.	DGKG	98	.	0			c.G896A						.						124	106	112					3																	185993350		2203	4300	6503	SO:0001583	missense	1608	exon10			CACAGGCCTTGCT	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.896G>A	chr3.hg19:g.185993350C>T	ENSP00000265022:p.Gly299Asp	46.0	0.0		54.0	17.0	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	hg19	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.581617	0.86748	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691;ENST00000437018	D;D;D;D;D	0.94687	-3.49;-3.49;-3.49;-3.49;-3.49	5.55	4.63	0.57726	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.058330	0.64402	D	0.000002	D	0.98541	0.9513	H	0.99130	4.44	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;0.999;1.0	D	0.98959	1.0797	10	0.87932	D	0	.	16.0206	0.80486	0.0:0.8655:0.1345:0.0	.	299;299;299;299	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	D	299;299;299;299;302;50	ENSP00000265022:G299D;ENSP00000339777:G299D;ENSP00000371599:G299D;ENSP00000440507:G299D;ENSP00000395526:G50D	ENSP00000265022:G299D	G	-	2	0	DGKG	187476044	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.699000	0.68310	2.761000	0.94854	0.655000	0.94253	GGC	.	.		0.522	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			T	185993350	C	T	185993350	3	4	30	1	0	0	0	0	1	0	0	0	4471	739	26	3	1543	3	DGKG	3	185993350	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	34447657	185993350	12029080	27	3728										
KDR	3791	hgsc.bcm.edu	37	chr4	55955862	55955862	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aaaagaaatgacttacctaaGgaaaatatttcccacagcaa	5	8	0	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr4:55955862G>A	ENST00000263923.4	-	24	3595	c.3300C>T	c.(3298-3300)tcC>tcT	p.S1100S	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	1100	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ACTTACCTAAGGAAAATATTT	0.408			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.S1100S		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.C3300T						.						123	133	130					4																	55955862		2203	4300	6503	SO:0001819	synonymous_variant	3791	exon24			ACCTAAGGAAAAT	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.3300C>T	chr4.hg19:g.55955862G>A		139.0	0.0		120.0	28.0	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	hg19	CCDS3497.1																																																																																			.	.		0.408	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55955862	G	A	55955862	2	1	30	1	0	0	0	0	0	0	0	1	8148	987	35	3		3	KDR	4	55955862	Silent	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10		55955862	135198414	28	3729										
EXOC1	55763	hgsc.bcm.edu	37	chr4	56759928	56759928	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gttttggtgactgtcaaaagGaactttgacaaatgcattgt	10	5	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr4:56759928G>A	ENST00000381295.2	+	15	2283	c.1935G>A	c.(1933-1935)agG>agA	p.R645R	EXOC1_ENST00000349598.6_Silent_p.R630R|EXOC1_ENST00000346134.7_Silent_p.R645R	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	645					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					CTGTCAAAAGGAACTTTGACA	0.333																																					p.R645R		Atlas-SNP	.											.	EXOC1	103	.	0			c.G1935A						.						68	64	65					4																	56759928		2203	4300	6503	SO:0001819	synonymous_variant	55763	exon15			CAAAAGGAACTTT	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"SEC3-like 1 (S. cerevisiae)"	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.1935G>A	chr4.hg19:g.56759928G>A		78.0	0.0		76.0	23.0	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Silent	SNP	ENST00000381295.2	hg19	CCDS3502.1																																																																																			.	.		0.333	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		A	56759928	G	A	56759928	2	1	30	1	0	0	0	0	0	0	0	1	5303	1165	41	3		3	EXOC1	4	56759928	Silent	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	804066	56759928	134394348	29	3730										
AASDH	132949	hgsc.bcm.edu	37	chr4	57204730	57204730	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gattccaagatccacactttCccatcagtagatgctgctgc	7	13	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr4:57204730C>A	ENST00000205214.6	-	15	3315	c.3135G>T	c.(3133-3135)ggG>ggT	p.G1045G	AASDH_ENST00000434343.2_Silent_p.G560G|AASDH_ENST00000513376.1_Silent_p.G945G|AASDH_ENST00000451613.1_3'UTR	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	1045					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TCCACACTTTCCCATCAGTAG	0.433																																					p.G1045G		Atlas-SNP	.											.	AASDH	101	.	0			c.G3135T						.						83	78	80					4																	57204730		2203	4300	6503	SO:0001819	synonymous_variant	132949	exon15			CACTTTCCCATCA	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.3135G>T	chr4.hg19:g.57204730C>A		201.0	0.0		222.0	54.0	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Silent	SNP	ENST00000205214.6	hg19	CCDS3504.1																																																																																			.	.		0.433	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		A	57204730	C	A	57204730	2	1	30	1	0	0	0	0	0	0	0	1	22	842	30	3		3	AASDH	4	57204730	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	444802	57204730	133949546	30	3731										
TMPRSS11F	389208	hgsc.bcm.edu	37	chr4	68934361	68934361	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aaagcagtgagctgctgtgaGcagccatgtgttactgatga	13	7	0	4			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr4:68934361G>T	ENST00000356291.2	-	7	789	c.730C>A	c.(730-732)Ctc>Atc	p.L244I	UBA6-AS1_ENST00000499180.2_RNA|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000511571.1_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	244	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						GCTGCTGTGAGCAGCCATGTG	0.527																																					p.L244I		Atlas-SNP	.											TMPRSS11F,NS,carcinoma,0,1	TMPRSS11F	79	.	0			c.C730A						.						81	71	75					4																	68934361		2203	4300	6503	SO:0001583	missense	389208	exon7			CTGTGAGCAGCCA	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"Serine peptidases / Transmembrane"	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.730C>A	chr4.hg19:g.68934361G>T	ENSP00000348639:p.Leu244Ile	92.0	0.0		148.0	44.0	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	hg19	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.366887	0.41902	.	.	ENSG00000198092	ENST00000356291	D	0.97553	-4.43	5.73	3.91	0.45181	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.133529	0.33631	N	0.004709	D	0.93966	0.8068	L	0.45422	1.42	0.33054	D	0.533191	P	0.38617	0.64	B	0.36567	0.228	D	0.94886	0.8043	10	0.38643	T	0.18	.	11.8022	0.52133	0.0:0.4296:0.5704:0.0	.	244	Q6ZWK6	TM11F_HUMAN	I	244	ENSP00000348639:L244I	ENSP00000348639:L244I	L	-	1	0	TMPRSS11F	68616956	0.998000	0.40836	1.000000	0.80357	0.619000	0.37552	0.779000	0.26746	1.370000	0.46153	0.655000	0.94253	CTC	.	.		0.527	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		T	68934361	G	T	68934361	3	4	30	1	0	0	0	0	1	0	0	0	16258	971	34	3	602	3	TMPRSS11F	4	68934361	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	11729631	68934361	122219915	31	3732										
RASSF6	166824	hgsc.bcm.edu	37	chr4	74451010	74451010	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	agctgcttcactcatggttcTatagagcactggggagtctg	12	9	4	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr4:74451010T>G	ENST00000342081.3	-	6	680	c.550A>C	c.(550-552)Aga>Cga	p.R184R	RASSF6_ENST00000395777.2_Silent_p.R152R|RASSF6_ENST00000307439.5_Silent_p.R152R|RASSF6_ENST00000335049.5_Silent_p.R140R	NM_201431.2	NP_958834.1	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family member 6	184					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)					breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|pancreas(2)|skin(2)	17	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			CTCATGGTTCTATAGAGCACT	0.413																																					p.R184R		Atlas-SNP	.											.	RASSF6	68	.	0			c.A550C						.						153	146	148					4																	74451010		2203	4300	6503	SO:0001819	synonymous_variant	166824	exon6			TGGTTCTATAGAG	AY217664	CCDS3558.1, CCDS3559.1, CCDS58904.1, CCDS58905.1	4q21.1	2008-02-22	2008-02-22		ENSG00000169435	ENSG00000169435			20796	protein-coding gene	gene with protein product		612620					Standard	NM_177532		Approved		uc003hhd.2	Q6ZTQ3	OTTHUMG00000130007	ENST00000342081.3:c.550A>C	chr4.hg19:g.74451010T>G		259.0	0.0		249.0	77.0	NM_201431	Q68DT2|Q6PDA6|Q86WG9|Q86WH0	Silent	SNP	ENST00000342081.3	hg19	CCDS3558.1																																																																																			.	.		0.413	RASSF6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252279.1	NM_177532		G	74451010	T	G	74451010	2	3	30	1	0	0	0	0	0	0	0	1	13105	1530	53	5		5	RASSF6	4	74451010	Silent	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	5516649	74451010	116703266	32	3733										
SLC39A8	64116	hgsc.bcm.edu	37	chr4	103228652	103228652	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cccaatagccagccccacaaAaaaggtcaaaatctttggga	7	12	2	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr4:103228652A>C	ENST00000394833.2	-	3	969	c.493T>G	c.(493-495)Ttt>Gtt	p.F165V	SLC39A8_ENST00000424970.2_Missense_Mutation_p.F165V|SLC39A8_ENST00000510255.1_5'UTR|SLC39A8_ENST00000356736.4_Missense_Mutation_p.F165V	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	165					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		AGCCCCACAAAAAAGGTCAAA	0.368																																					p.F165V		Atlas-SNP	.											.	SLC39A8	24	.	0			c.T493G						.						118	134	129					4																	103228652		2203	4300	6503	SO:0001583	missense	64116	exon3			CCACAAAAAAGGT		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"Solute carriers"	20862	protein-coding gene	gene with protein product		608732	"solute carrier family 39 (metal ion transporter), member 8"			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.493T>G	chr4.hg19:g.103228652A>C	ENSP00000378310:p.Phe165Val	364.0	0.0		294.0	80.0	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Missense_Mutation	SNP	ENST00000394833.2	hg19	CCDS3656.1	.	.	.	.	.	.	.	.	.	.	A	31	5.062340	0.93898	.	.	ENSG00000138821	ENST00000424970;ENST00000356736;ENST00000394833	T;T;T	0.45276	0.9;0.9;0.9	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.64702	0.2622	M	0.75884	2.315	0.80722	D	1	D;D;D	0.76494	0.987;0.999;0.991	D;D;D	0.75484	0.964;0.986;0.915	T	0.68796	-0.5314	10	0.72032	D	0.01	-11.2509	14.8503	0.70292	1.0:0.0:0.0:0.0	.	165;165;98	B4E2H3;Q9C0K1;Q9C0K1-2	.;S39A8_HUMAN;.	V	165	ENSP00000394548:F165V;ENSP00000349174:F165V;ENSP00000378310:F165V	ENSP00000349174:F165V	F	-	1	0	SLC39A8	103447675	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	9.097000	0.94193	2.108000	0.64289	0.533000	0.62120	TTT	.	.		0.368	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154		C	103228652	A	C	103228652	3	2	30	1	0	0	0	0	1	0	0	0	14639	14	1	5	990	5	SLC39A8	4	103228652	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	28777642	103228652	87925624	33	3734										
RBM46	166863	hgsc.bcm.edu	37	chr4	155719022	155719022	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ttgtaggaaaaatacctcgtGatatgtatgaagatgagtta	10	3	0	4			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr4:155719022G>C	ENST00000281722.3	+	3	446	c.211G>C	c.(211-213)Gat>Cat	p.D71H	RBM46_ENST00000514866.1_Missense_Mutation_p.D71H|RBM46_ENST00000510397.1_Missense_Mutation_p.D71H	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	71	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				AATACCTCGTGATATGTATGA	0.373																																					p.D71H		Atlas-SNP	.											.	RBM46	76	.	0			c.G211C						.						122	125	124					4																	155719022		2203	4300	6503	SO:0001583	missense	166863	exon3			CCTCGTGATATGT	BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"RNA binding motif (RRM) containing"	28401	protein-coding gene	gene with protein product	"cancer/testis antigen 68"					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.211G>C	chr4.hg19:g.155719022G>C	ENSP00000281722:p.Asp71His	161.0	0.0		135.0	36.0	NM_144979	B3KWU8|B4DZ27	Missense_Mutation	SNP	ENST00000281722.3	hg19	CCDS3790.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.540670	0.65085	.	.	ENSG00000151962	ENST00000514866;ENST00000281722;ENST00000510397;ENST00000512640	T;T;T;T	0.20200	3.16;2.09;3.16;2.09	5.9	5.9	0.94986	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.045934	0.85682	D	0.000000	T	0.47340	0.1440	M	0.76170	2.325	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.994	D;D;D	0.72075	0.951;0.976;0.964	T	0.42582	-0.9443	10	0.87932	D	0	-29.8799	15.4131	0.74943	0.0681:0.0:0.9319:0.0	.	71;71;71	B4DZ27;B3KWU8;Q8TBY0	.;.;RBM46_HUMAN	H	71	ENSP00000424500:D71H;ENSP00000281722:D71H;ENSP00000422813:D71H;ENSP00000426672:D71H	ENSP00000281722:D71H	D	+	1	0	RBM46	155938472	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.804000	0.85993	2.793000	0.96121	0.563000	0.77884	GAT	.	.		0.373	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979		C	155719022	G	C	155719022	3	2	30	1	0	0	0	0	1	0	0	0	13155	1290	45	4	217	4	RBM46	4	155719022	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	52490370	155719022	35435254	34	3735										
PDZD2	23037	hgsc.bcm.edu	37	chr5	31983740	31983740	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aggtgggaagacggacttccAatcgagtgactgcctggcac	14	10	0	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr5:31983740A>T	ENST00000438447.1	+	3	1344	c.956A>T	c.(955-957)cAa>cTa	p.Q319L	PDZD2_ENST00000282493.3_Missense_Mutation_p.Q319L			O15018	PDZD2_HUMAN	PDZ domain containing 2	319					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						ACGGACTTCCAATCGAGTGAC	0.478																																					p.Q319L		Atlas-SNP	.											.	PDZD2	306	.	0			c.A956T						.						92	97	95					5																	31983740		2202	4300	6502	SO:0001583	missense	23037	exon2			ACTTCCAATCGAG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.956A>T	chr5.hg19:g.31983740A>T	ENSP00000402033:p.Gln319Leu	164.0	0.0		156.0	45.0	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	A	18.70	3.680327	0.68042	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.06687	3.27;3.27	5.68	5.68	0.88126	PDZ/DHR/GLGF (1);	0.000000	0.44902	D	0.000407	T	0.18130	0.0435	L	0.32530	0.975	0.38661	D	0.952077	D;D	0.63880	0.979;0.993	P;D	0.72338	0.747;0.977	T	0.02202	-1.1196	10	0.52906	T	0.07	.	12.3301	0.55035	1.0:0.0:0.0:0.0	.	145;319	B4E3P2;O15018	.;PDZD2_HUMAN	L	319	ENSP00000402033:Q319L;ENSP00000282493:Q319L	ENSP00000282493:Q319L	Q	+	2	0	PDZD2	32019497	0.985000	0.35326	0.899000	0.35326	0.506000	0.33950	3.118000	0.50414	2.167000	0.68274	0.528000	0.53228	CAA	.	.		0.478	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	31983740	A	T	31983740	3	4	30	1	0	0	0	0	1	0	0	0	11710	130	5	4	962	4	PDZD2	5	31983740	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10		31983740	148931520	35	3736										
MCCC2	64087	hgsc.bcm.edu	37	chr5	70936898	70936898	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ttttatggagacacattagtTacaggtataaaggtgaagaa	10	3	0	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr5:70936898T>A	ENST00000340941.6	+	11	1197	c.1068T>A	c.(1066-1068)gtT>gtA	p.V356V	MCCC2_ENST00000323375.8_Silent_p.V318V|MCCC2_ENST00000509358.2_Silent_p.V356V	NM_022132.4	NP_071415.1	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-CoA carboxylase 2 (beta)	356	Acyl-CoA binding. {ECO:0000255}.|Carboxyltransferase.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|coenzyme A metabolic process (GO:0015936)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			endometrium(2)|kidney(15)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	30		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	ACACATTAGTTACAGGTATAA	0.373																																					p.V356V		Atlas-SNP	.											.	MCCC2	47	.	0			c.T1068A						.						106	100	102					5																	70936898		2203	4300	6503	SO:0001819	synonymous_variant	64087	exon11			ATTAGTTACAGGT	AF310971	CCDS34184.1	5q12-q13	2010-04-30	2010-04-30		ENSG00000131844	ENSG00000131844	6.4.1.4		6937	protein-coding gene	gene with protein product		609014	"methylcrotonoyl-Coenzyme A carboxylase 2 (beta)"				Standard	NM_022132		Approved	MCCB	uc003kbs.4	Q9HCC0	OTTHUMG00000162505	ENST00000340941.6:c.1068T>A	chr5.hg19:g.70936898T>A		88.0	0.0		93.0	19.0	NM_022132	A6NIY9|Q96C27|Q9Y4L7	Silent	SNP	ENST00000340941.6	hg19	CCDS34184.1																																																																																			.	.		0.373	MCCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369243.4			A	70936898	T	A	70936898	2	1	30	1	0	0	0	0	0	0	0	1	9384	1741	61	4		4	MCCC2	5	70936898	Silent	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	38953158	70936898	109978362	36	3737										
FBN2	2201	hgsc.bcm.edu	37	chr5	127727761	127727761	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aacccatgttgcattcacatCggtagcttgagacagttggt	10	9	1	1	rs35095480		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr5:127727761C>G	ENST00000508053.1	-	17	2527	c.1553G>C	c.(1552-1554)cGa>cCa	p.R518P	FBN2_ENST00000508989.1_Missense_Mutation_p.R485P|FBN2_ENST00000262464.4_Missense_Mutation_p.R518P			P35556	FBN2_HUMAN	fibrillin 2	518	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GCATTCACATCGGTAGCTTGA	0.348																																					p.R518P		Atlas-SNP	.											.	FBN2	858	.	0			c.G1553C						.						142	133	136					5																	127727761		2203	4300	6503	SO:0001583	missense	2201	exon11			TCACATCGGTAGC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.1553G>C	chr5.hg19:g.127727761C>G	ENSP00000424571:p.Arg518Pro	171.0	0.0		136.0	24.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.253938	0.80135	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.87650	-2.28;-2.28;-2.28	4.14	4.14	0.48551	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.51477	D	0.000087	D	0.94830	0.8330	M	0.92923	3.36	0.58432	D	0.99999	D;D	0.89917	1.0;0.996	D;D	0.72982	0.958;0.979	D	0.95717	0.8763	10	0.62326	D	0.03	.	17.7235	0.88359	0.0:1.0:0.0:0.0	.	485;518	D6RJI3;P35556	.;FBN2_HUMAN	P	518;518;485	ENSP00000262464:R518P;ENSP00000424571:R518P;ENSP00000425596:R485P	ENSP00000262464:R518P	R	-	2	0	FBN2	127755660	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.303000	0.65738	2.592000	0.87571	0.585000	0.79938	CGA	.	.		0.348	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		G	127727761	C	G	127727761	3	3	30	1	0	0	0	0	1	0	0	0	5711	884	31	4	7405	4	FBN2	5	127727761	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	56790863	127727761	53187499	37	3738										
KDM3B	51780	hgsc.bcm.edu	37	chr5	137759953	137759954	+	Missense_Mutation	DNP	GG	GG	TT													0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ctcactcctggctttgtgatGggaggcttctgtgtctccat							TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr5:137759953_137759954GG>TT	ENST00000314358.5	+	16	4362_4363	c.4162_4163GG>TT	c.(4162-4164)GGg>TTg	p.G1388L	KDM3B_ENST00000394866.1_Missense_Mutation_p.G1044L|KDM3B_ENST00000542866.1_Missense_Mutation_p.G420L	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1388					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						GCTTTGTGATGGGAGGCTTCTG	0.49																																					p.G1388W|p.G1388V		Atlas-SNP	.											.	KDM3B	177	.	0			c.G4162T|c.G4163T						.																																			SO:0001583	missense	51780	exon16			TGTGATGGGAGGC|GTGATGGGAGGCT	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	Exception_encountered	chr5.hg19:g.137759953_137759954delinsTT	ENSP00000326563:p.Gly1388Leu	243.0	0.0		260.0|259.0	74.0|73.0	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1																																																																																			.	.		0.49	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		TT	137759954	GG	TT	137759953	3	4	30	1	0	0	0	0	1	0	0	0	8136	1348	47	3	4224	3	KDM3B	5	137759953	Missense_Mutation	DNP	GG	TCGA-BC-4073-01B-02D-A12Z-10	10032192	137759953	43155307	38	3739										
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140176834	140176834	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gcagagggtgtgctctggggAggacccccccaagacggacc	16	13	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr5:140176834A>T	ENST00000526136.1	+	1	2285	c.2285A>T	c.(2284-2286)gAg>gTg	p.E762V	PCDHA2_ENST00000520672.2_Missense_Mutation_p.E762V|PCDHA2_ENST00000378132.1_Missense_Mutation_p.E762V|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	762	5 X 4 AA repeats of P-X-X-P.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTCTGGGGAGGACCCCCCC	0.622																																					p.E762V		Atlas-SNP	.											.	PCDHA2	404	.	0			c.A2285T						.						46	50	49					5																	140176834		2203	4300	6503	SO:0001583	missense	56146	exon1			CTGGGGAGGACCC	AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"Cadherins / Protocadherins : Clustered"	8668	other	complex locus constituent	"KIAA0345-like 12"	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.2285A>T	chr5.hg19:g.140176834A>T	ENSP00000431748:p.Glu762Val	201.0	0.0		225.0	59.0	NM_031495	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	hg19	CCDS54914.1	.	.	.	.	.	.	.	.	.	.	a	16.47	3.132858	0.56828	.	.	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.17213	2.29;2.29;2.29	4.0	4.0	0.46444	.	0.371940	0.19003	U	0.125274	T	0.46658	0.1404	M	0.92880	3.355	0.23341	N	0.997877	D;B;D	0.76494	0.985;0.377;0.999	P;B;D	0.76575	0.891;0.206;0.988	T	0.42699	-0.9436	10	0.62326	D	0.03	.	7.8235	0.29300	0.9027:0.0:0.0973:0.0	.	762;762;762	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	V	762	ENSP00000430584:E762V;ENSP00000367372:E762V;ENSP00000431748:E762V	ENSP00000367372:E762V	E	+	2	0	PCDHA2	140157018	0.999000	0.42202	0.998000	0.56505	0.755000	0.42902	3.253000	0.51469	1.584000	0.49913	0.477000	0.44152	GAG	.	.		0.622	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		T	140176834	A	T	140176834	3	4	30	1	0	0	0	0	1	0	0	0	11533	304	11	4	2287	4	PCDHA2	5	140176834	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	2416881	140176834	40738426	39	3740										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140208267	140208267	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	caaattgggctcttattaaaGaaatccttggacagagagga	10	6	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr5:140208267G>A	ENST00000529310.1	+	1	705	c.591G>A	c.(589-591)aaG>aaA	p.K197K	PCDHA6_ENST00000527624.1_Silent_p.K197K|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	197	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.K197N(2)		NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTATTAAAGAAATCCTTGG	0.433																																					p.K197K		Atlas-SNP	.											PCDHA6_ENST00000529310,colon,carcinoma,0,4	PCDHA6	442	.	2	Substitution - Missense(2)	large_intestine(2)	c.G591A						.						67	72	70					5																	140208267		2203	4300	6503	SO:0001819	synonymous_variant	56142	exon1			ATTAAAGAAATCC	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.591G>A	chr5.hg19:g.140208267G>A		82.0	0.0		74.0	20.0	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	hg19	CCDS47281.1																																																																																			.	.		0.433	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		A	140208267	G	A	140208267	2	1	30	1	0	0	0	0	0	0	0	1	11537	933	33	3		3	PCDHA6	5	140208267	Silent	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	31433	140208267	40706993	40	3741										
KCTD16	57528	hgsc.bcm.edu	37	chr5	143586733	143586733	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	agcgacacaagaatctgcccCccttcctccctgctccctgc	6	20	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr5:143586733C>T	ENST00000507359.3	+	2	1547	c.456C>T	c.(454-456)ccC>ccT	p.P152P	KCTD16_ENST00000512467.1_Silent_p.P152P	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	152					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)				large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			GAATCTGCCCCCCTTCCTCCC	0.547																																					p.P152P		Atlas-SNP	.											.	KCTD16	70	.	0			c.C456T						.						81	87	85					5																	143586733		2203	4300	6503	SO:0001819	synonymous_variant	57528	exon3			CTGCCCCCCTTCC	AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"potassium channel tetramerisation domain containing 16"			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.456C>T	chr5.hg19:g.143586733C>T		72.0	0.0		77.0	21.0	NM_020768	Q9P2M9	Silent	SNP	ENST00000507359.3	hg19	CCDS34260.1																																																																																			.	.		0.547	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368		T	143586733	C	T	143586733	2	4	30	1	0	0	0	0	0	0	0	1	8112	610	22	3		3	KCTD16	5	143586733	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	3378466	143586733	37328527	41	3742										
SLC36A1	206358	hgsc.bcm.edu	37	chr5	150843185	150843185	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cctgggactccctctggcggTgaaaaatgcaggcatcgtgg	14	11	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr5:150843185T>A	ENST00000243389.3	+	3	438	c.215T>A	c.(214-216)gTg>gAg	p.V72E	SLC36A1_ENST00000521351.1_3'UTR|SLC36A1_ENST00000520701.1_Missense_Mutation_p.V72E|SLC36A1_ENST00000521925.1_Missense_Mutation_p.V72E|SLC36A1_ENST00000429484.2_Missense_Mutation_p.V72E	NM_078483.2	NP_510968.2	Q7Z2H8	S36A1_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 1	72				V -> A (in Ref. 7; BAB71435). {ECO:0000305}.	amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen ion transmembrane transporter activity (GO:0015078)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)|symporter activity (GO:0015293)			endometrium(5)|kidney(9)|lung(8)|skin(2)|urinary_tract(1)	25		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Acamprosate(DB00659)|Glycine(DB00145)|Hydroxyproline(DB08847)|L-Alanine(DB00160)|Spaglumic Acid(DB08835)|Vigabatrin(DB01080)	CCTCTGGCGGTGAAAAATGCA	0.463																																					p.V72E	Melanoma(151;1534 1860 12947 32979 37872)	Atlas-SNP	.											.	SLC36A1	50	.	0			c.T215A						.						107	97	101					5																	150843185		2203	4300	6503	SO:0001583	missense	206358	exon3			TGGCGGTGAAAAA	AK057340	CCDS4316.1	5q33.1	2013-05-22			ENSG00000123643	ENSG00000123643		"Solute carriers"	18761	protein-coding gene	gene with protein product		606561				11959859, 11390972	Standard	NM_078483		Approved	LYAAT-1, PAT1, TRAMD3	uc003luc.3	Q7Z2H8	OTTHUMG00000130125	ENST00000243389.3:c.215T>A	chr5.hg19:g.150843185T>A	ENSP00000243389:p.Val72Glu	113.0	0.0		109.0	24.0	NM_078483	C9JI34|Q1LZ56|Q7Z7C0|Q86YK4|Q96M74	Missense_Mutation	SNP	ENST00000243389.3	hg19	CCDS4316.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.924335	0.92319	.	.	ENSG00000123643	ENST00000520111;ENST00000520701;ENST00000429484;ENST00000243389;ENST00000456739;ENST00000521925	T;T;T;T;T	0.02498	4.27;4.27;4.27;4.27;4.27	6.08	6.08	0.98989	.	0.057095	0.64402	D	0.000002	T	0.17152	0.0412	M	0.84683	2.71	0.58432	D	0.999994	P;D	0.53151	0.956;0.958	D;P	0.63283	0.913;0.826	T	0.00083	-1.2103	10	0.72032	D	0.01	.	16.6438	0.85155	0.0:0.0:0.0:1.0	.	72;72	E7EW39;Q7Z2H8	.;S36A1_HUMAN	E	72	ENSP00000429796:V72E;ENSP00000428140:V72E;ENSP00000395640:V72E;ENSP00000243389:V72E;ENSP00000430305:V72E	ENSP00000243389:V72E	V	+	2	0	SLC36A1	150823378	1.000000	0.71417	0.998000	0.56505	0.933000	0.57130	7.859000	0.86982	2.333000	0.79357	0.533000	0.62120	GTG	.	.		0.463	SLC36A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252433.1	NM_078483		A	150843185	T	A	150843185	3	1	30	1	0	0	0	0	1	0	0	0	14608	1696	59	4	221	4	SLC36A1	5	150843185	Missense_Mutation	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	7256452	150843185	30072075	42	3743										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168244433	168244433	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aatccgagagccaggccaggTggcagtcgcagtacaggtgg	16	10	0	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr5:168244433T>A	ENST00000519560.1	-	8	1084	c.665A>T	c.(664-666)cAc>cTc	p.H222L	SLIT3_ENST00000332966.8_Missense_Mutation_p.H222L|SLIT3_ENST00000404867.3_Missense_Mutation_p.H222L	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	222	LRRCT 1.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCAGGCCAGGTGGCAGTCGCA	0.617																																					p.H222L	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.A665T						.						60	56	57					5																	168244433		2203	4300	6503	SO:0001583	missense	6586	exon8			GCCAGGTGGCAGT	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.665A>T	chr5.hg19:g.168244433T>A	ENSP00000430333:p.His222Leu	39.0	0.0		70.0	22.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	hg19	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.497282	0.85069	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.75938	-0.98;-0.98;-0.97	5.53	4.4	0.53042	Cysteine-rich flanking region, C-terminal (1);	0.180128	0.64402	D	0.000013	D	0.84070	0.5391	M	0.93763	3.455	0.80722	D	1	P;P;B	0.45283	0.688;0.855;0.451	B;P;B	0.49953	0.218;0.627;0.341	D	0.87315	0.2314	10	0.87932	D	0	.	10.0534	0.42230	0.0:0.1081:0.0:0.8919	.	222;222;222	O75094-2;O75094-3;O75094	.;.;SLIT3_HUMAN	L	222	ENSP00000430333:H222L;ENSP00000332164:H222L;ENSP00000384890:H222L	ENSP00000332164:H222L	H	-	2	0	SLIT3	168177011	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.520000	0.53465	2.099000	0.63709	0.459000	0.35465	CAC	.	.		0.617	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		A	168244433	T	A	168244433	3	1	30	1	0	0	0	0	1	0	0	0	14756	1696	59	4	4022	4	SLIT3	5	168244433	Missense_Mutation	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	17401248	168244433	12670827	43	3744										
SLC17A1	6568	hgsc.bcm.edu	37	chr6	25811931	25811931	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tcctggtcaggaagaagtctGataactgacctgctaggtta	11	8	2	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr6:25811931G>A	ENST00000244527.4	-	9	1080	c.965C>T	c.(964-966)tCa>tTa	p.S322L	SLC17A1_ENST00000476801.1_Missense_Mutation_p.S322L|SLC17A1_ENST00000468082.1_Missense_Mutation_p.S268L|SLC17A1_ENST00000427328.1_Missense_Mutation_p.S268L	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	322					ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)	p.S322*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						GAAGAAGTCTGATAACTGACC	0.448																																					p.S322L		Atlas-SNP	.											SLC17A1,NS,carcinoma,0,1	SLC17A1	71	.	1	Substitution - Nonsense(1)	lung(1)	c.C965T						.						103	93	96					6																	25811931		2203	4300	6503	SO:0001583	missense	6568	exon9			AAGTCTGATAACT		CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"Solute carriers"	10929	protein-coding gene	gene with protein product		182308	"solute carrier family 17 (sodium phosphate), member 1"	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.965C>T	chr6.hg19:g.25811931G>A	ENSP00000244527:p.Ser322Leu	79.0	0.0		76.0	17.0	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Missense_Mutation	SNP	ENST00000244527.4	hg19	CCDS4565.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.351871	0.24512	.	.	ENSG00000124568	ENST00000244527;ENST00000427328;ENST00000476801;ENST00000468082	T;T;T;T	0.59502	0.26;0.72;0.26;0.72	3.38	3.38	0.38709	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.211340	0.06268	N	0.695074	T	0.43277	0.1240	L	0.50333	1.59	0.09310	N	1	B;B	0.32467	0.321;0.372	B;B	0.39771	0.205;0.309	T	0.48269	-0.9050	10	0.54805	T	0.06	.	10.5584	0.45131	0.0:0.0:1.0:0.0	.	268;322	Q14916-2;Q14916	.;NPT1_HUMAN	L	322;268;322;268	ENSP00000244527:S322L;ENSP00000410549:S268L;ENSP00000420614:S322L;ENSP00000420546:S268L	ENSP00000244527:S322L	S	-	2	0	SLC17A1	25919910	0.981000	0.34729	0.010000	0.14722	0.350000	0.29205	3.678000	0.54627	2.191000	0.70037	0.650000	0.86243	TCA	.	.		0.448	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2			A	25811931	G	A	25811931	3	1	30	1	0	0	0	0	1	0	0	0	14431	1294	45	3	454	3	SLC17A1	6	25811931	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10		25811931	145303136	44	3745										
HIST1H3B	8358	hgsc.bcm.edu	37	chr6	26032209	26032209	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cggtagccggcgcgctcttgCgagcagccttggtagccagc	15	14	1	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr6:26032209C>T	ENST00000244661.2	-	1	79	c.80G>A	c.(79-81)cGc>cAc	p.R27H		NM_003537.3	NP_003528.1	P68431	H31_HUMAN	histone cluster 1, H3b	27					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(10)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	25						CGCGCTCTTGCGAGCAGCCTT	0.612																																					p.R27H		Atlas-SNP	.											.	HIST1H3B	59	.	0			c.G80A						.						67	82	77					6																	26032209		2161	4211	6372	SO:0001583	missense	8358	exon1			CTCTTGCGAGCAG	X00090	CCDS4573.1	6p22.1	2011-01-27	2006-10-11	2003-03-14	ENSG00000124693	ENSG00000274267		"Histones / Replication-dependent"	4776	protein-coding gene	gene with protein product		602819	"H3 histone family, member L", "histone 1, H3b"	H3FL		6647026, 9119399, 12408966	Standard	NM_003537		Approved	H3/l	uc003nfs.1	P68431	OTTHUMG00000014415	ENST00000244661.2:c.80G>A	chr6.hg19:g.26032209C>T	ENSP00000244661:p.Arg27His	22.0	0.0		29.0	10.0	NM_003537	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000244661.2	hg19	CCDS4573.1	.	.	.	.	.	.	.	.	.	.	c	12.66	2.005280	0.35415	.	.	ENSG00000124693	ENST00000244661	T	0.46063	0.88	5.19	5.19	0.71726	.	.	.	.	.	T	0.53029	0.1771	.	.	.	0.43598	D	0.995951	.	.	.	.	.	.	T	0.53208	-0.8471	6	0.51188	T	0.08	.	18.0628	0.89382	0.0:1.0:0.0:0.0	.	.	.	.	H	27	ENSP00000244661:R27H	ENSP00000244661:R27H	R	-	2	0	HIST1H3B	26140188	1.000000	0.71417	0.994000	0.49952	0.013000	0.08279	7.633000	0.83260	2.577000	0.86979	0.561000	0.74099	CGC	.	.		0.612	HIST1H3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040077.1	NM_003537		T	26032209	C	T	26032209	3	4	30	1	0	0	0	0	1	0	0	0	7165	768	27	1	334	1	HIST1H3B	6	26032209	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	220278	26032209	145082858	45	3746										
GSTA4	2941	hgsc.bcm.edu	37	chr6	52858985	52858985	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gcggcagctaaaacccatctCacggactccatccggcctct	8	17	2	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr6:52858985C>A	ENST00000370959.1	-	2	174	c.57G>T	c.(55-57)gtG>gtT	p.V19V	GSTA4_ENST00000541324.1_5'UTR|GSTA4_ENST00000370960.1_5'UTR|RN7SK_ENST00000365328.1_RNA			O15217	GSTA4_HUMAN	glutathione S-transferase alpha 4	19	GST N-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)|skin(2)|urinary_tract(1)	7	Lung NSC(77;0.103)				Glutathione(DB00143)	AAACCCATCTCACGGACTCCA	0.478																																					p.V19V		Atlas-SNP	.											.	GSTA4	20	.	0			c.G57T						.						85	87	86					6																	52858985		2203	4300	6503	SO:0001819	synonymous_variant	2941	exon2			CCATCTCACGGAC	AF020918	CCDS4948.1	6p12.2	2012-06-21	2008-11-26		ENSG00000170899	ENSG00000170899	2.5.1.18	"Glutathione S-transferases / Soluble"	4629	protein-coding gene	gene with protein product		605450	"glutathione S-transferase A4"			9480897	Standard	NM_001512		Approved		uc003pbf.3	O15217	OTTHUMG00000014868	ENST00000370959.1:c.57G>T	chr6.hg19:g.52858985C>A		42.0	0.0		55.0	15.0	NM_001512	B2RD15|Q5T7Q8|Q6P4G1|Q9BX18|Q9H414	Silent	SNP	ENST00000370959.1	hg19	CCDS4948.1																																																																																			.	.		0.478	GSTA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040946.1	NM_001512		A	52858985	C	A	52858985	2	1	30	1	0	0	0	0	0	0	0	1	6842	813	29	3		3	GSTA4	6	52858985	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	26826776	52858985	118256082	46	3747										
IMPG1	3617	hgsc.bcm.edu	37	chr6	76715138	76715138	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ccatggttccatgatagactTcctcactttcaattttgttg	6	10	2	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr6:76715138T>A	ENST00000369950.3	-	10	1190	c.1001A>T	c.(1000-1002)gAa>gTa	p.E334V	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				ATGATAGACTTCCTCACTTTC	0.443																																					p.E334V	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.A1001T						.						181	163	169					6																	76715138		2203	4300	6503	SO:0001583	missense	3617	exon10			TAGACTTCCTCAC	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.1001A>T	chr6.hg19:g.76715138T>A	ENSP00000358966:p.Glu334Val	344.0	0.0		358.0	79.0	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	hg19	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	T	2.784	-0.252760	0.05829	.	.	ENSG00000112706	ENST00000369950	T	0.37752	1.18	5.01	1.07	0.20283	SEA (2);	1.053100	0.07418	N	0.893510	T	0.05547	0.0146	N	0.08118	0	0.20764	N	0.999854	B	0.13145	0.007	B	0.13407	0.009	T	0.38520	-0.9657	10	0.30078	T	0.28	.	3.9146	0.09217	0.1611:0.4147:0.0:0.4242	.	334	Q17R60	IMPG1_HUMAN	V	334	ENSP00000358966:E334V	ENSP00000358966:E334V	E	-	2	0	IMPG1	76771858	0.280000	0.24249	0.040000	0.18447	0.273000	0.26683	0.498000	0.22530	-0.088000	0.12506	-0.472000	0.04984	GAA	.	.		0.443	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76715138	T	A	76715138	3	1	30	1	0	0	0	0	1	0	0	0	7737	1783	62	4	1424	4	IMPG1	6	76715138	Missense_Mutation	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	23856153	76715138	94399929	47	3748										
SLC22A16	85413	hgsc.bcm.edu	37	chr6	110763664	110763664	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tccagtgataaaagttctgaCagtttacaggagcttgccct	9	9	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr6:110763664C>T	ENST00000368919.3	-	4	1032	c.966G>A	c.(964-966)ctG>ctA	p.L322L	RN7SL617P_ENST00000485298.2_RNA|SLC22A16_ENST00000456137.2_3'UTR|SLC22A16_ENST00000439654.1_Silent_p.L322L|SLC22A16_ENST00000330550.4_Silent_p.L288L	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	322					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	AAAGTTCTGACAGTTTACAGG	0.423																																					p.L322L		Atlas-SNP	.											.	SLC22A16	81	.	0			c.G966A						.						104	98	100					6																	110763664		2203	4300	6503	SO:0001819	synonymous_variant	85413	exon4			TTCTGACAGTTTA		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"Solute carriers"	20302	protein-coding gene	gene with protein product		608276	"solute carrier family 22 (organic cation transporter), member 16"			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.966G>A	chr6.hg19:g.110763664C>T		66.0	0.0		76.0	17.0	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Silent	SNP	ENST00000368919.3	hg19	CCDS5084.1																																																																																			.	.		0.423	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125		T	110763664	C	T	110763664	2	4	30	1	0	0	0	0	0	0	0	1	14462	465	17	3		3	SLC22A16	6	110763664	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	34048526	110763664	60351403	48	3749										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48318705	48318705	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tctgatattttggaagaaatTgctgaatttttaacatctgt	7	4	2	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr7:48318705T>A	ENST00000435803.1	+	18	7938	c.7914T>A	c.(7912-7914)atT>atA	p.I2638I		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2638					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TGGAAGAAATTGCTGAATTTT	0.323																																					p.I2638I		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T7914A						.						34	33	33					7																	48318705		1812	4070	5882	SO:0001819	synonymous_variant	154664	exon18			AGAAATTGCTGAA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.7914T>A	chr7.hg19:g.48318705T>A		65.0	0.0		74.0	19.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.323	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48318705	T	A	48318705	2	1	30	1	0	0	0	0	0	0	0	1	31	1800	63	4		4	ABCA13	7	48318705	Silent	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10		48318705	110819958	49	3750										
RNF133	168433	hgsc.bcm.edu	37	chr7	122338762	122338763	+	Frame_Shift_Del	DEL	CT	CT	-													0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tggcactataactcctgccaCtctcttcaaagtggagcttc							TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr7:122338762_122338763delCT	ENST00000340112.2	-	1	447_448	c.210_211delAG	c.(208-213)agagtgfs	p.RV70fs	CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000449022.2_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	70	PA.				protein autoubiquitination (GO:0051865)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21						ACTCCTGCCACTCTCTTCAAAG	0.431																																					p.71_71del	Colon(198;1778 2057 7449 19869 45985)	Atlas-Indel,Pindel	.											.	RNF133	41	.	0			c.211_212del						.																																			SO:0001589	frameshift_variant	168433	exon1			.	AF447589	CCDS5784.1	7q31.33	2013-01-09			ENSG00000188050	ENSG00000188050		"RING-type (C3HC4) zinc fingers"	21154	protein-coding gene	gene with protein product							Standard	NM_139175		Approved		uc003vkj.1	Q8WVZ7	OTTHUMG00000157092	ENST00000340112.2:c.210_211delAG	chr7.hg19:g.122338766_122338767delCT	ENSP00000344489:p.Arg70fs	90.0	0.0		84.0	28.0	NM_139175	A4D0W2|Q8N7G7	Frame_Shift_Del	DEL	ENST00000340112.2	hg19	CCDS5784.1																																																																																			.	.		0.431	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175		-	122338763	CT	-	122338762	7	5	30	1	0	1	0	1	0	0	0	0	13454	565	20	0	923	0	RNF133	7	122338762	Frame_Shift_Del	DEL	CT	TCGA-BC-4073-01B-02D-A12Z-10	74020057	122338762	36799901	50	3751										
SPAM1	6677	hgsc.bcm.edu	37	chr7	123594252	123594252	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ctataaaattgggaaaattaCttcggccaaatcacttgtgg	8	7	1	0	rs376151172		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr7:123594252C>T	ENST00000439500.1	+	4	1241	c.628C>T	c.(628-630)Ctt>Ttt	p.L210F	SPAM1_ENST00000223028.7_Missense_Mutation_p.L210F|SPAM1_ENST00000402183.2_Missense_Mutation_p.L210F|SPAM1_ENST00000460182.1_Missense_Mutation_p.L210F|SPAM1_ENST00000340011.5_Missense_Mutation_p.L210F	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	210					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GGGAAAATTACTTCGGCCAAA	0.383																																					p.L210F		Atlas-SNP	.											.	SPAM1	195	.	0			c.C628T						.						78	83	81					7																	123594252		2203	4299	6502	SO:0001583	missense	6677	exon3			AAATTACTTCGGC	L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.628C>T	chr7.hg19:g.123594252C>T	ENSP00000402123:p.Leu210Phe	142.0	0.0		115.0	31.0	NM_153189	Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	hg19	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	C	12.61	1.990654	0.35131	.	.	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000340011;ENST00000439500;ENST00000223028	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	6.17	3.34	0.38264	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.495783	0.20231	N	0.096470	T	0.36799	0.0980	M	0.88842	2.985	0.09310	N	0.999999	P;P	0.40970	0.734;0.734	B;B	0.38378	0.272;0.272	T	0.42068	-0.9473	9	.	.	.	-26.5249	6.3721	0.21487	0.3469:0.5138:0.0:0.1392	.	210;210	Q8TC30;P38567	.;HYALP_HUMAN	F	210	ENSP00000386028:L210F;ENSP00000417934:L210F;ENSP00000345849:L210F;ENSP00000402123:L210F;ENSP00000223028:L210F	.	L	+	1	0	SPAM1	123381488	0.000000	0.05858	0.023000	0.16930	0.770000	0.43624	-0.053000	0.11846	0.901000	0.36495	0.655000	0.94253	CTT	.	.		0.383	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			T	123594252	C	T	123594252	3	4	30	1	0	0	0	0	1	0	0	0	15001	565	20	3	630	3	SPAM1	7	123594252	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	1255490	123594252	35544411	51	3752										
JHDM1D	80853	hgsc.bcm.edu	37	chr7	139819020	139819020	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ttttctccatctcataacacCtaaatgagtttgaagaaatt	4	8	2	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr7:139819020C>A	ENST00000397560.2	-	9	1237		c.e9-1		JHDM1D_ENST00000006967.5_Splice_Site	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN							histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					CTCATAACACCTAAATGAGTT	0.308																																					.		Atlas-SNP	.											.	JHDM1D	54	.	0			c.1140-1G>T						.						76	73	74					7																	139819020		1783	4055	5838	SO:0001630	splice_region_variant	80853	exon10			TAACACCTAAATG																												ENST00000397560.2:c.1140-1G>T	chr7.hg19:g.139819020C>A		110.0	0.0		81.0	23.0	NM_030647	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Splice_Site	SNP	ENST00000397560.2	hg19	CCDS43658.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.164077	0.78339	.	.	ENSG00000006459	ENST00000397560;ENST00000006967	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3681	0.98887	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	JHDM1D	139465489	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.776000	0.85560	2.890000	0.99128	0.655000	0.94253	.	.	.		0.308	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1		Intron	A	139819020	C	A	139819020	5	1	30	1	0	0	0	0	0	0	1	0	7957	695	24	3	1734	3	JHDM1D	7	139819020	Splice_Site	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	16224768	139819020	19319643	52	3753										
GPR124	25960	hgsc.bcm.edu	37	chr8	37693203	37693203	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cgaaatggccgcctcttccaCagccacagcaacacctcccg	7	19	1	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr8:37693203C>G	ENST00000412232.2	+	13	1978	c.1965C>G	c.(1963-1965)caC>caG	p.H655Q	GPR124_ENST00000315215.7_Intron	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	655					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			GCCTCTTCCACAGCCACAGCA	0.647																																					p.H655Q		Atlas-SNP	.											.	GPR124	85	.	0			c.C1965G						.						57	63	61					8																	37693203		2203	4299	6502	SO:0001583	missense	25960	exon13			CTTCCACAGCCAC	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.1965C>G	chr8.hg19:g.37693203C>G	ENSP00000406367:p.His655Gln	21.0	0.0		53.0	13.0	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	C	14.73	2.621557	0.46736	.	.	ENSG00000020181	ENST00000416514;ENST00000412232	T	0.54279	0.58	5.29	2.02	0.26589	.	0.278824	0.33772	N	0.004561	T	0.25680	0.0625	N	0.08118	0	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.09907	-1.0653	10	0.24483	T	0.36	-27.3241	5.9515	0.19248	0.2893:0.5672:0.0:0.1435	.	655	Q96PE1	GP124_HUMAN	Q	648;655	ENSP00000406367:H655Q	ENSP00000406367:H655Q	H	+	3	2	GPR124	37812361	0.996000	0.38824	1.000000	0.80357	0.901000	0.52897	0.430000	0.21428	1.206000	0.43276	0.655000	0.94253	CAC	.	.		0.647	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			G	37693203	C	G	37693203	3	3	30	1	0	0	0	0	1	0	0	0	6646	477	17	4	1994	4	GPR124	8	37693203	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10		37693203	108670819	53	3754										
POTEA	340441	hgsc.bcm.edu	37	chr8	43152221	43152221	+	RNA	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aagtagtaagtcttctgctgGacagacaatgtcaacttcat	8	8	4	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr8:43152221G>A	ENST00000522175.2	+	0	360							Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A											breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(27)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TCTTCTGCTGGACAGACAATG	0.403																																					p.D120N		Atlas-SNP	.											.	POTEA	87	.	0			c.G358A						.						107	105	106					8																	43152221		2160	4290	6450			340441	exon2			CTGCTGGACAGAC	AY462869		8p11.1	2013-01-11	2008-11-26	2008-11-26	ENSG00000188877	ENSG00000188877		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33893	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 3"	608915	"ANKRD26-like family A, member 1"	A26A1			Standard	NM_001002920		Approved	POTE8, POTE-8, CT104.3	uc003xpz.1	Q6S8J7	OTTHUMG00000164111		chr8.hg19:g.43152221G>A		182.0	0.0		145.0	24.0	NM_001005365	A6ND17|A6ND71|Q6S8J6	Missense_Mutation	SNP	ENST00000522175.2	hg19																																																																																				.	.		0.403	POTEA-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000383492.1	NM_001002920		A	43152221	G	A	43152221	1	1	30	0	1	0	0	0	0	0	0	0	12270	1174	41	3		3	POTEA	8	43152221	RNA	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	5459018	43152221	103211801	54	3755										
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48508456	48508456	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	agttgttgccaaagaagattCagaaaaaacttgtgaagtgt	10	4	1	4			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr8:48508456C>G	ENST00000297423.4	+	9	1565	c.1181C>G	c.(1180-1182)tCa>tGa	p.S394*	SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Nonsense_Mutation_p.S324*|SPIDR_ENST00000518074.1_Nonsense_Mutation_p.S334*	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	394	Necessary for interaction with RAD51.				cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											AAAGAAGATTCAGAAAAAACT	0.378																																					p.S394X		Atlas-SNP	.											.	KIAA0146	64	.	0			c.C1181G						.						101	94	96					8																	48508456		1824	4088	5912	SO:0001587	stop_gained	23514	exon9			AAGATTCAGAAAA	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"KIAA0146"	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.1181C>G	chr8.hg19:g.48508456C>G	ENSP00000297423:p.Ser394*	156.0	0.0		119.0	31.0	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Nonsense_Mutation	SNP	ENST00000297423.4	hg19	CCDS43737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.080166|5.080166	0.94050|0.94050	.|.	.|.	ENSG00000164808|ENSG00000164808	ENST00000519401|ENST00000297423;ENST00000518074;ENST00000541342;ENST00000524006	.|.	.|.	.|.	5.3|5.3	4.43|4.43	0.53597|0.53597	.|.	.|0.513015	.|0.18585	.|N	.|0.136900	T|.	0.52741|.	0.1753|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.61168|.	-0.7117|.	3|.	.|0.27082	.|T	.|0.32	.|.	11.43|11.43	0.50034|0.50034	0.0:0.9141:0.0:0.0859|0.0:0.9141:0.0:0.0859	.|.	.|.	.|.	.|.	E|X	76|394;334;324;83	.|.	.|ENSP00000297423:S394X	Q|S	+|+	1|2	0|0	KIAA0146|KIAA0146	48671009|48671009	0.915000|0.915000	0.31059|0.31059	0.020000|0.020000	0.16555|0.16555	0.257000|0.257000	0.26127|0.26127	1.656000|1.656000	0.37355|0.37355	1.376000|1.376000	0.46267|0.46267	0.655000|0.655000	0.94253|0.94253	CAG|TCA	.	.		0.378	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		G	48508456	C	G	48508456	4	3	30	1	0	0	0	0	0	1	0	0	8166	838	29	4	1215	4	KIAA0146	8	48508456	Nonsense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	5356235	48508456	97855566	55	3756										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72975034	72975034	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tatagaatatgaagagttacCtccactgggtctatttgtgc	9	7	1	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr8:72975034C>A	ENST00000262209.4	-	6	1014	c.807G>T	c.(805-807)gaG>gaT	p.E269D		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	269					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	GAAGAGTTACCTCCACTGGGT	0.358																																					p.E269D		Atlas-SNP	.											.	TRPA1	256	.	0			c.G807T						.						117	109	112					8																	72975034		2203	4300	6503	SO:0001630	splice_region_variant	8989	exon6			AGTTACCTCCACT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.807+1G>T	chr8.hg19:g.72975034C>A		260.0	0.0		243.0	61.0	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.999723	0.35320	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.38887	1.11;2.63	5.62	4.72	0.59763	Ankyrin repeat-containing domain (4);	0.097447	0.64402	D	0.000001	T	0.23846	0.0577	N	0.00468	-1.46	0.49051	D	0.999748	D	0.58268	0.982	P	0.57244	0.816	T	0.46484	-0.9188	9	.	.	.	-25.8627	13.7095	0.62659	0.0:0.9231:0.0:0.0769	.	269	O75762	TRPA1_HUMAN	D	121;269	ENSP00000428151:E121D;ENSP00000262209:E269D	.	E	-	3	2	TRPA1	73137588	1.000000	0.71417	0.989000	0.46669	0.074000	0.17049	5.070000	0.64376	1.301000	0.44836	0.650000	0.86243	GAG	.	.		0.358	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	Missense_Mutation	A	72975034	C	A	72975034	5	1	30	1	0	0	0	0	0	0	1	0	16592	695	24	3	2640	3	TRPA1	8	72975034	Splice_Site	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	24466578	72975034	73388988	56	3757										
TG	7038	hgsc.bcm.edu	37	chr8	133941375	133941375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ggtgatcttcgacgccaatgCtcctgtggctgtcagatcca	11	12	2	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr8:133941375C>T	ENST00000220616.4	+	23	4794	c.4754C>T	c.(4753-4755)gCt>gTt	p.A1585V	TG_ENST00000542445.1_Missense_Mutation_p.A19V|TG_ENST00000377869.1_Missense_Mutation_p.A1528V	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1585					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GACGCCAATGCTCCTGTGGCT	0.463																																					p.A1585V		Atlas-SNP	.											.	TG	416	.	0			c.C4754T						.						142	121	128					8																	133941375		2203	4300	6503	SO:0001583	missense	7038	exon23			CCAATGCTCCTGT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4754C>T	chr8.hg19:g.133941375C>T	ENSP00000220616:p.Ala1585Val	144.0	0.0		177.0	52.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	C	8.043	0.764313	0.15914	.	.	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445	T;T;T	0.62788	0.0;0.0;0.0	5.5	-1.08	0.09936	.	1.845860	0.02581	N	0.098887	T	0.29321	0.0730	N	0.00926	-1.1	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.15093	-1.0449	10	0.24483	T	0.36	.	3.7294	0.08487	0.2064:0.3661:0.0:0.4275	.	19;1585	F5GWW5;P01266	.;THYG_HUMAN	V	1528;391;1585;19	ENSP00000367100:A1528V;ENSP00000220616:A1585V;ENSP00000441693:A19V	ENSP00000220616:A1585V	A	+	2	0	TG	134010557	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.064000	0.14437	0.015000	0.14971	-0.150000	0.13652	GCT	.	.		0.463	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133941375	C	T	133941375	3	4	30	1	0	0	0	0	1	0	0	0	15828	797	28	3	4844	3	TG	8	133941375	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	60966341	133941375	12422647	57	3758										
BNC2	54796	hgsc.bcm.edu	37	chr9	16738381	16738381	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aatttgagatgtatcaacccCacaacatgggaccttgaaat	7	9	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr9:16738381C>A	ENST00000380672.4	-	2	163	c.106G>T	c.(106-108)Ggg>Tgg	p.G36W	BNC2_ENST00000380667.2_Missense_Mutation_p.G36W|BNC2_ENST00000380666.2_Missense_Mutation_p.G36W|BNC2_ENST00000545497.1_Intron	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		GTATCAACCCCACAACATGGG	0.423																																					p.G36W		Atlas-SNP	.											.	BNC2	166	.	0			c.G106T						.						172	143	153					9																	16738381		2203	4300	6503	SO:0001583	missense	54796	exon2			CAACCCCACAACA	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.106G>T	chr9.hg19:g.16738381C>A	ENSP00000370047:p.Gly36Trp	168.0	0.0		176.0	59.0	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	hg19	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	C	10.06	1.247602	0.22880	.	.	ENSG00000173068	ENST00000380672;ENST00000456672;ENST00000436939;ENST00000380667;ENST00000380666;ENST00000540340	T;T;T	0.04156	3.69;3.69;3.69	4.07	-0.347	0.12617	.	1.111260	0.07026	N	0.827613	T	0.05135	0.0137	N	0.08118	0	0.09310	N	1	D;B;P	0.54964	0.969;0.336;0.73	P;B;B	0.53224	0.721;0.052;0.058	T	0.44513	-0.9323	10	0.72032	D	0.01	0.2058	6.6548	0.22981	0.0:0.4942:0.0:0.5058	.	36;36;36	Q06HC4;Q6ZN30-2;Q6ZN30	.;.;BNC2_HUMAN	W	36	ENSP00000370047:G36W;ENSP00000370042:G36W;ENSP00000370041:G36W	ENSP00000370041:G36W	G	-	1	0	BNC2	16728381	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	0.016000	0.13377	-0.062000	0.13088	0.579000	0.79373	GGG	.	.		0.423	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		A	16738381	C	A	16738381	3	1	30	1	0	0	0	0	1	0	0	0	1475	594	21	3	3217	3	BNC2	9	16738381	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10		16738381	124475050	58	3759										
CBWD3	220869	hgsc.bcm.edu	37	chr9	70484455	70484455	+	Frame_Shift_Del	DEL	T	T	-													0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ccttggctgacagctaaggaTttctccagcgcacttcctag							TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr9:70484455delT	ENST00000382405.3	-	3	435	c.258delA	c.(256-258)aaafs	p.K86fs	CBWD5_ENST00000429800.2_Frame_Shift_Del_p.K86fs|CBWD5_ENST00000377395.4_Frame_Shift_Del_p.K86fs|CBWD5_ENST00000430059.2_Frame_Shift_Del_p.K86fs|CBWD5_ENST00000377384.1_Frame_Shift_Del_p.K86fs|CBWD5_ENST00000377392.5_Frame_Shift_Del_p.K50fs			Q5RIA9	CBWD5_HUMAN	COBW domain containing 5	86							ATP binding (GO:0005524)								all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		CAGCTAAGGATTTCTCCAGCG	0.418																																					p.S87fs		Atlas-Indel,Pindel	.											.	CBWD5	1	.	0			c.259delT						.						14	13	13					9																	70484455		2119	4176	6295	SO:0001589	frameshift_variant	220869	exon3			.	BC067803, BC082271	CCDS75841.1, CCDS75843.1, CCDS75844.1	9q13	2005-08-23			ENSG00000147996	ENSG00000147996			24584	protein-coding gene	gene with protein product	"dopamine responsive protein"						Standard	XM_005272748		Approved		uc004ack.3	Q5RIA9	OTTHUMG00000013336	ENST00000382405.3:c.258delA	chr9.hg19:g.70484455delT	ENSP00000371842:p.Lys86fs	3248.0	0.0		3127.0	257.0	NM_001024916	Q8N7U8	Frame_Shift_Del	DEL	ENST00000382405.3	hg19																																																																																				.	.		0.418	CBWD5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000037131.2			-	70484455	T	-	70484455	7	5	30	1	0	1	0	1	0	0	0	0	2716	1490	52	0	981	0	CBWD3	9	70484455	Frame_Shift_Del	DEL	T	TCGA-BC-4073-01B-02D-A12Z-10	53746074	70484455	70728976	59	3760										
CDC14B	8555	hgsc.bcm.edu	37	chr9	99285642	99285642	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gctgctctgtgttgtccattCtcctgcccctttaacttctg	7	14	3	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr9:99285642C>G	ENST00000375241.1	-	11	1597	c.1146G>C	c.(1144-1146)gaG>gaC	p.E382D	CDC14B_ENST00000481149.1_5'Flank|CDC14B_ENST00000375236.1_Missense_Mutation_p.E382D|CDC14B_ENST00000375242.3_Missense_Mutation_p.E345D|CDC14B_ENST00000265659.2_Missense_Mutation_p.E382D|CDC14B_ENST00000375240.3_Missense_Mutation_p.E382D|CDC14B_ENST00000463569.1_Missense_Mutation_p.E382D	NM_003671.3|NM_033331.2	NP_003662.1|NP_201588.1	O60729	CC14B_HUMAN	cell division cycle 14B	382					activation of anaphase-promoting complex activity (GO:0051488)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	15		Acute lymphoblastic leukemia(62;0.0559)				GTTGTCCATTCTCCTGCCCCT	0.453																																					p.E382D		Atlas-SNP	.											.	CDC14B	64	.	0			c.G1146C						.						110	115	113					9																	99285642		2203	4298	6501	SO:0001583	missense	8555	exon11			TCCATTCTCCTGC	AF023158	CCDS6721.1, CCDS6722.1, CCDS43853.1	9q22.3	2013-01-17	2013-01-17		ENSG00000081377	ENSG00000081377		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1719	protein-coding gene	gene with protein product		603505	"CDC14 (cell division cycle 14, S. cerevisiae) homolog B", "CDC14 cell division cycle 14 homolog B (S. cerevisiae)"			9367992	Standard	NM_003671		Approved	Cdc14B1, Cdc14B2, CDC14B3, hCDC14B	uc004awj.3	O60729	OTTHUMG00000020300	ENST00000375241.1:c.1146G>C	chr9.hg19:g.99285642C>G	ENSP00000364389:p.Glu382Asp	230.0	0.0		222.0	57.0	NM_033331	A6N5X8|A8MQ20|B1AL31|B1AL32|O43183|O60730|Q5JU08	Missense_Mutation	SNP	ENST00000375241.1	hg19	CCDS6722.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.245333	0.39697	.	.	ENSG00000081377	ENST00000265659;ENST00000375241;ENST00000375240;ENST00000375242;ENST00000463569;ENST00000375236	D;D;D;D;D;D	0.92199	-2.98;-2.99;-2.99;-2.98;-2.99;-2.99	5.29	4.32	0.51571	.	0.438058	0.24633	N	0.036867	D	0.88894	0.6561	L	0.54323	1.7	0.31311	N	0.687097	B;B;B	0.17465	0.022;0.013;0.013	B;B;B	0.23852	0.049;0.028;0.013	D	0.84695	0.0725	10	0.35671	T	0.21	0.0118	10.6986	0.45913	0.0:0.9011:0.0:0.0989	.	382;382;345	O60729-2;O60729;A8MQ20	.;CC14B_HUMAN;.	D	382;382;382;345;382;382	ENSP00000265659:E382D;ENSP00000364389:E382D;ENSP00000364388:E382D;ENSP00000364390:E345D;ENSP00000420572:E382D;ENSP00000364384:E382D	ENSP00000265659:E382D	E	-	3	2	CDC14B	98325463	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.439000	0.35013	2.759000	0.94783	0.555000	0.69702	GAG	.	.		0.453	CDC14B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053278.2	NM_033331		G	99285642	C	G	99285642	3	3	30	1	0	0	0	0	1	0	0	0	3059	912	32	4	366	4	CDC14B	9	99285642	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	28801187	99285642	41927789	60	3761										
FKBP15	23307	hgsc.bcm.edu	37	chr9	115948581	115948581	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gggtacaaaggccgaacgggCtgcagctgggaggtgacggc	19	9	0	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr9:115948581C>T	ENST00000238256.3	-	15	1563	c.1446G>A	c.(1444-1446)caG>caA	p.Q482Q		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	482					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GCCGAACGGGCTGCAGCTGGG	0.537																																					p.Q482Q		Atlas-SNP	.											.	FKBP15	128	.	0			c.G1446A						.						66	78	74					9																	115948581		2078	4207	6285	SO:0001819	synonymous_variant	23307	exon15			AACGGGCTGCAGC	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23397	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 76", "WASP and FKBP-like protein"		"KIAA0674"	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.1446G>A	chr9.hg19:g.115948581C>T		76.0	0.0		89.0	26.0	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	hg19	CCDS48007.1																																																																																			.	.		0.537	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258		T	115948581	C	T	115948581	2	4	30	1	0	0	0	0	0	0	0	1	5913	796	28	3		3	FKBP15	9	115948581	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	16662939	115948581	25264850	61	3762										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7423775	7423775	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tcctaccagaatcaaggtctCcatttccattagctgagccg	7	13	2	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr10:7423775C>T	ENST00000361972.4	-	2	176	c.86G>A	c.(85-87)gGa>gAa	p.G29E	SFMBT2_ENST00000397167.1_Missense_Mutation_p.G29E|SFMBT2_ENST00000397160.3_Missense_Mutation_p.G29E|SFMBT2_ENST00000379711.2_Missense_Mutation_p.G29E|SFMBT2_ENST00000379713.3_Missense_Mutation_p.G29E	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	29					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						ATCAAGGTCTCCATTTCCATT	0.418																																					p.G29E		Atlas-SNP	.											.	SFMBT2	209	.	0			c.G86A						.						127	119	122					10																	7423775		2203	4300	6503	SO:0001583	missense	57713	exon2			AGGTCTCCATTTC	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.86G>A	chr10.hg19:g.7423775C>T	ENSP00000355109:p.Gly29Glu	86.0	0.0		92.0	24.0	NM_001029880	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	hg19	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.617098	0.28801	.	.	ENSG00000198879	ENST00000361972;ENST00000397167;ENST00000379713;ENST00000379711;ENST00000397160	T;T;T;T;T	0.31510	2.55;2.55;1.89;1.49;1.49	5.41	4.31	0.51392	.	0.351137	0.21051	N	0.080994	T	0.18923	0.0454	L	0.43152	1.355	0.09310	N	1	B;B	0.33694	0.421;0.22	B;B	0.27715	0.082;0.074	T	0.23226	-1.0194	10	0.02654	T	1	.	9.9855	0.41839	0.0:0.8935:0.0:0.1065	.	29;29	Q5T981;Q5VUG0	.;SMBT2_HUMAN	E	29	ENSP00000355109:G29E;ENSP00000380353:G29E;ENSP00000369035:G29E;ENSP00000369033:G29E;ENSP00000380346:G29E	ENSP00000355109:G29E	G	-	2	0	SFMBT2	7463781	0.471000	0.25862	0.305000	0.25099	0.233000	0.25261	2.278000	0.43426	2.553000	0.86117	0.650000	0.86243	GGA	.	.		0.418	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		T	7423775	C	T	7423775	3	4	30	1	0	0	0	0	1	0	0	0	14173	855	30	3	2678	3	SFMBT2	10	7423775	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10		7423775	128110972	62	3763										
SUV39H2	79723	hgsc.bcm.edu	37	chr10	14938885	14938885	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aaaatggaaaggatggccagAttctacaaatacttgggaac	10	6	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr10:14938885A>C	ENST00000354919.6	+	3	218	c.218A>C	c.(217-219)gAt>gCt	p.D73A	SUV39H2_ENST00000313519.5_Missense_Mutation_p.D13A|SUV39H2_ENST00000378325.3_Missense_Mutation_p.D73A	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	73	Chromo. {ECO:0000255|PROSITE- ProRule:PRU00053}.				cell differentiation (GO:0030154)|chromatin assembly or disassembly (GO:0006333)|chromatin remodeling (GO:0006338)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|male meiosis (GO:0007140)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nuclear heterochromatin (GO:0005720)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						GGATGGCCAGATTCTACAAAT	0.328																																					p.D73A		Atlas-SNP	.											.	SUV39H2	72	.	0			c.A218C						.						69	77	74					10																	14938885		2203	4300	6503	SO:0001583	missense	79723	exon3			GGCCAGATTCTAC	AK027067	CCDS7104.1, CCDS53493.1, CCDS53494.1	10p13	2011-07-01			ENSG00000152455	ENSG00000152455		"Chromatin-modifying enzymes / K-methyltransferases"	17287	protein-coding gene	gene with protein product		606503				11094092	Standard	NM_001193424		Approved	FLJ23414, KMT1B	uc021png.1	Q9H5I1	OTTHUMG00000017718	ENST00000354919.6:c.218A>C	chr10.hg19:g.14938885A>C	ENSP00000346997:p.Asp73Ala	68.0	0.0		61.0	12.0	NM_001193426	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Missense_Mutation	SNP	ENST00000354919.6	hg19	CCDS53494.1	.	.	.	.	.	.	.	.	.	.	A	16.25	3.069540	0.55539	.	.	ENSG00000152455	ENST00000433779;ENST00000378325;ENST00000354919;ENST00000313519;ENST00000420416;ENST00000412254	T;T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56;-0.56	5.86	5.86	0.93980	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (2);Chromo domain, conserved site (1);	0.063070	0.64402	D	0.000005	T	0.64681	0.2620	L	0.45470	1.425	0.58432	D	0.999998	B;B	0.25904	0.04;0.137	B;B	0.26969	0.043;0.075	T	0.59958	-0.7356	10	0.20519	T	0.43	.	15.7408	0.77894	1.0:0.0:0.0:0.0	.	73;73	Q9H5I1;Q9H5I1-3	SUV92_HUMAN;.	A	13;73;73;13;13;13	ENSP00000388968:D13A;ENSP00000367576:D73A;ENSP00000346997:D73A;ENSP00000319208:D13A;ENSP00000392201:D13A;ENSP00000388218:D13A	ENSP00000319208:D13A	D	+	2	0	SUV39H2	14978891	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.162000	0.94745	2.367000	0.80283	0.528000	0.53228	GAT	.	.		0.328	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670		C	14938885	A	C	14938885	3	2	30	1	0	0	0	0	1	0	0	0	15428	333	12	5	40	5	SUV39H2	10	14938885	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	7515110	14938885	120595862	63	3764										
PTCHD3	374308	hgsc.bcm.edu	37	chr10	27702131	27702131	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	agatgttcttaatgttggtaAattgatcgagcaaatgggtg	12	3	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr10:27702131A>G	ENST00000438700.3	-	1	1166	c.1049T>C	c.(1048-1050)tTt>tCt	p.F350S		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	350					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						AATGTTGGTAAATTGATCGAG	0.522																																					p.F350S		Atlas-SNP	.											.	PTCHD3	140	.	0			c.T1049C						.						176	187	184					10																	27702131		2203	4300	6503	SO:0001583	missense	374308	exon1			TTGGTAAATTGAT	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1049T>C	chr10.hg19:g.27702131A>G	ENSP00000417658:p.Phe350Ser	109.0	0.0		129.0	37.0	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	hg19	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	A	10.12	1.261729	0.23051	.	.	ENSG00000182077	ENST00000438700	D	0.85258	-1.96	3.98	1.57	0.23409	.	0.331006	0.35151	N	0.003408	T	0.78426	0.4281	L	0.51422	1.61	0.09310	N	1	B	0.16396	0.017	B	0.23150	0.044	T	0.68800	-0.5313	10	0.66056	D	0.02	-3.53	6.1272	0.20186	0.6764:0.0:0.3236:0.0	.	350	Q3KNS1	PTHD3_HUMAN	S	350	ENSP00000417658:F350S	ENSP00000417658:F350S	F	-	2	0	PTCHD3	27742137	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	1.357000	0.34090	0.206000	0.20587	0.459000	0.35465	TTT	.	.		0.522	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		G	27702131	A	G	27702131	3	3	30	1	0	0	0	0	1	0	0	0	12746	14	1	2	1270	2	PTCHD3	10	27702131	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	12763246	27702131	107832616	64	3765										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64967201	64967202	+	Missense_Mutation	DNP	TG	TG	CT													0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tacttctgaaccaccccagcTggaaacactggtagtatcgg							TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr10:64967201_64967202TG>CT	ENST00000399262.2	-	10	4445_4446	c.4227_4228CA>AG	c.(4225-4230)tcCAgc>tcAGgc	p.S1410G	JMJD1C_ENST00000402544.1_Missense_Mutation_p.S1191G|JMJD1C_ENST00000399251.1_Missense_Mutation_p.S1191G|JMJD1C_ENST00000542921.1_Missense_Mutation_p.S1228G	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1410					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					CCACCCCAGCTGGAAACACTGG	0.436																																					p.S1410G|p.S1409S		Atlas-SNP	.											.	JMJD1C	347	.	0			c.A4228G|c.C4227A						.																																			SO:0001583	missense	221037	exon10			CCCAGCTGGAAAC|CCAGCTGGAAACA	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.4227_4228delinsCT	chr10.hg19:g.64967201_64967202delinsCT	ENSP00000382204:p.Ser1410Gly	87.0|89.0	0.0		84.0|86.0	21.0|22.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation|Silent	SNP	ENST00000399262.2	hg19	CCDS41532.1																																																																																			.	.		0.436	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		CT	64967202	TG	CT	64967201	3	2	30	1	0	0	0	0	1	0	0	0	7959	1580	55	2	3462	2	JMJD1C	10	64967201	Missense_Mutation	DNP	TG	TCGA-BC-4073-01B-02D-A12Z-10	37265070	64967201	70567546	65	3766										
MUC2	4583	hgsc.bcm.edu	37	chr11	1078363	1078364	+	Missense_Mutation	DNP	CC	CC	AT													0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ggaggaggtggcccccgcatCctgctccgagcacgtgagtc							TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr11:1078363_1078364CC>AT	ENST00000441003.2	+	5	677_678	c.650_651CC>AT	c.(649-651)tCC>tAT	p.S217Y	MUC2_ENST00000359061.5_Missense_Mutation_p.S217Y	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	217	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCCCCCGCATCCTGCTCCGAGC	0.653																																					p.S217Y|p.S217S		Atlas-SNP	.											.	MUC2	614	.	0			c.C650A|c.C651T						.																																			SO:0001583	missense	4583	exon5			CCGCATCCTGCTC|CGCATCCTGCTCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	Exception_encountered	chr11.hg19:g.1078363_1078364delinsAT	ENSP00000415183:p.Ser217Tyr	52.0|53.0	0.0		83.0|81.0	29.0|28.0	NM_002457	Q14878	Missense_Mutation|Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.		0.653	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		AT	1078364	CC	AT	1078363	3	1	30	1	0	0	0	0	1	0	0	0	9984	855	30	3	668	3	MUC2	11	1078363	Missense_Mutation	DNP	CC	TCGA-BC-4073-01B-02D-A12Z-10		1078363	133928153	66	3767										
OR51G1	79324	hgsc.bcm.edu	37	chr11	4944842	4944842	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cagcacagatatgagagacaCaggtgttgagggctcggagt	15	7	0	4			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr11:4944842C>A	ENST00000321961.2	-	1	795	c.728G>T	c.(727-729)tGt>tTt	p.C243F	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATGAGAGACACAGGTGTTGAG	0.552																																					p.C243F		Atlas-SNP	.											.	OR51G1	74	.	0			c.G728T						.						164	126	139					11																	4944842		2201	4298	6499	SO:0001583	missense	79324	exon1			GAGACACAGGTGT	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"GPCR / Class A : Olfactory receptors"	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.728G>T	chr11.hg19:g.4944842C>A	ENSP00000322546:p.Cys243Phe	118.0	0.0		119.0	22.0	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	hg19	CCDS31366.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.699620	0.48307	.	.	ENSG00000176879	ENST00000321961	T	0.00368	7.75	4.53	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42821	U	0.000656	T	0.01765	0.0056	H	0.96208	3.785	0.50313	D	0.99986	D	0.89917	1.0	D	0.97110	1.0	T	0.31971	-0.9924	10	0.87932	D	0	.	15.9949	0.80232	0.0:1.0:0.0:0.0	.	243	Q8NGK1	O51G1_HUMAN	F	243	ENSP00000322546:C243F	ENSP00000322546:C243F	C	-	2	0	OR51G1	4901418	1.000000	0.71417	0.970000	0.41538	0.156000	0.22039	5.593000	0.67550	2.359000	0.80004	0.557000	0.71058	TGT	.	.		0.552	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237		A	4944842	C	A	4944842	3	1	30	1	0	0	0	0	1	0	0	0	11107	478	17	3	239	3	OR51G1	11	4944842	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	3866479	4944842	130061674	67	3768										
OR1S2	219958	hgsc.bcm.edu	37	chr11	57970715	57970715	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ctattgatgagctttctcagGgcacctttcatatccttatt	6	10	2	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr11:57970715G>A	ENST00000302592.6	-	1	938	c.939C>T	c.(937-939)gcC>gcT	p.A313A		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	313						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				GCTTTCTCAGGGCACCTTTCA	0.423																																					p.A313A		Atlas-SNP	.											.	OR1S2	119	.	0			c.C939T						.						136	138	137					11																	57970715		2201	4294	6495	SO:0001819	synonymous_variant	219958	exon1			TCTCAGGGCACCT	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"GPCR / Class A : Olfactory receptors"	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.939C>T	chr11.hg19:g.57970715G>A		115.0	0.0		101.0	27.0	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	hg19	CCDS31545.1																																																																																			.	.		0.423	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459		A	57970715	G	A	57970715	2	1	30	1	0	0	0	0	0	0	0	1	10982	1219	43	3		3	OR1S2	11	57970715	Silent	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	53025873	57970715	77035801	68	3769										
GLYAT	10249	hgsc.bcm.edu	37	chr11	58477428	58477428	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ccatggagccggtattccggCaaggtgcctgccattctcat	11	13	1	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr11:58477428C>G	ENST00000344743.3	-	6	843	c.702G>C	c.(700-702)ttG>ttC	p.L234F	GLYAT_ENST00000529732.1_Missense_Mutation_p.L234F	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase	234					acyl-CoA metabolic process (GO:0006637)|glycine metabolic process (GO:0006544)|monocarboxylic acid metabolic process (GO:0032787)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)|glycine N-benzoyltransferase activity (GO:0047962)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	GGTATTCCGGCAAGGTGCCTG	0.537																																					p.L234F		Atlas-SNP	.											GLYAT,NS,carcinoma,-1,1	GLYAT	53	.	0			c.G702C						.						63	61	61					11																	58477428		2201	4295	6496	SO:0001583	missense	10249	exon6			TTCCGGCAAGGTG	AF023466	CCDS7970.1, CCDS7971.1	11q12.1	2008-03-11					2.3.1.13		13734	protein-coding gene	gene with protein product		607424					Standard	NM_201648		Approved	GAT, ACGNAT	uc001nnb.3	Q6IB77		ENST00000344743.3:c.702G>C	chr11.hg19:g.58477428C>G	ENSP00000340200:p.Leu234Phe	79.0	0.0		101.0	20.0	NM_201648	O14833|Q96QK7	Missense_Mutation	SNP	ENST00000344743.3	hg19	CCDS7970.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.939572	0.34189	.	.	ENSG00000149124	ENST00000344743;ENST00000529732	T;T	0.20463	2.07;2.07	6.06	1.9	0.25705	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, C-terminal (1);	1.421900	0.04581	N	0.394958	T	0.43077	0.1231	M	0.81802	2.56	0.29804	N	0.832157	D	0.52996	0.957	P	0.59221	0.854	T	0.08827	-1.0703	10	0.54805	T	0.06	0.095	5.1614	0.15064	0.0:0.5944:0.1469:0.2587	.	234	Q6IB77	GLYAT_HUMAN	F	234	ENSP00000340200:L234F;ENSP00000431688:L234F	ENSP00000340200:L234F	L	-	3	2	GLYAT	58234004	0.245000	0.23899	0.234000	0.24042	0.060000	0.15804	-0.077000	0.11394	0.407000	0.25591	0.650000	0.86243	TTG	.	.		0.537	GLYAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394593.1			G	58477428	C	G	58477428	3	3	30	1	0	0	0	0	1	0	0	0	6487	709	25	4	192	4	GLYAT	11	58477428	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	506713	58477428	76529088	69	3770										
TRPT1	83707	hgsc.bcm.edu	37	chr11	63992051	63992051	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gtctccaggcagtcctggggCcaggtgaatgtgcgtccttc	14	12	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr11:63992051C>A	ENST00000317459.6	-	5	634	c.466G>T	c.(466-468)Gcc>Tcc	p.A156S	NUDT22_ENST00000441250.2_5'Flank|NUDT22_ENST00000279206.3_5'Flank|TRPT1_ENST00000394547.3_Missense_Mutation_p.A107S|TRPT1_ENST00000541278.1_Missense_Mutation_p.A156S|TRPT1_ENST00000540472.1_5'Flank|TRPT1_ENST00000546133.1_Missense_Mutation_p.A30S|TRPT1_ENST00000546089.1_Missense_Mutation_p.A107S|TRPT1_ENST00000394546.2_Missense_Mutation_p.A158S			Q86TN4	TRPT1_HUMAN	tRNA phosphotransferase 1	156					regulation of protein kinase activity (GO:0045859)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)		tRNA 2'-phosphotransferase activity (GO:0000215)			lung(2)|skin(1)	3						AGTCCTGGGGCCAGGTGAATG	0.612																																					p.A158S		Atlas-SNP	.											.	TRPT1	14	.	0			c.G472T						.						93	85	88					11																	63992051		2201	4297	6498	SO:0001583	missense	83707	exon5			CTGGGGCCAGGTG		CCDS31595.1, CCDS44639.1, CCDS53652.1, CCDS53653.1	11q13	2012-05-03			ENSG00000149743	ENSG00000149743			20316	protein-coding gene	gene with protein product	"tRNA splicing 2' phosphotransferase 1"	610470				14504659	Standard	NM_001160389		Approved	MGC11134	uc010rnc.2	Q86TN4	OTTHUMG00000167844	ENST00000317459.6:c.466G>T	chr11.hg19:g.63992051C>A	ENSP00000314073:p.Ala156Ser	39.0	0.0		69.0	12.0	NM_001160389	A8MU17|A8MYC9|F5H2B2|Q9BSB9	Missense_Mutation	SNP	ENST00000317459.6	hg19	CCDS31595.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.58|17.58	3.426213|3.426213	0.62733|0.62733	.|.	.|.	ENSG00000149743|ENSG00000149743	ENST00000394547;ENST00000394546;ENST00000541278;ENST00000546133;ENST00000317459;ENST00000546089;ENST00000545812|ENST00000544286	T;T;T;T;T;T;T|.	0.40756|.	1.02;1.02;1.02;1.02;1.02;1.02;1.02|.	4.75|4.75	3.78|3.78	0.43462|0.43462	.|.	0.188584|.	0.44688|.	D|.	0.000432|.	T|T	0.50292|0.50292	0.1607|0.1607	N|N	0.25890|0.25890	0.77|0.77	0.41567|0.41567	D|D	0.988664|0.988664	B;P;P;B|.	0.45986|.	0.059;0.488;0.87;0.335|.	B;B;P;B|.	0.46796|.	0.182;0.305;0.527;0.206|.	T|T	0.43845|0.43845	-0.9366|-0.9366	10|5	0.33940|.	T|.	0.23|.	-12.5052|-12.5052	12.1479|12.1479	0.54034|0.54034	0.2735:0.7265:0.0:0.0|0.2735:0.7265:0.0:0.0	.|.	156;158;107;156|.	F5H2B2;A8MU17;Q86TN4-2;Q86TN4|.	.;.;.;TRPT1_HUMAN|.	S|V	107;158;156;30;156;107;158|19	ENSP00000378051:A107S;ENSP00000378050:A158S;ENSP00000438683:A156S;ENSP00000439586:A30S;ENSP00000314073:A156S;ENSP00000437741:A107S;ENSP00000442066:A158S|.	ENSP00000314073:A156S|.	A|G	-|-	1|2	0|0	TRPT1|TRPT1	63748627|63748627	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.951000|0.951000	0.60555|0.60555	1.936000|1.936000	0.40183|0.40183	2.380000|2.380000	0.81148|0.81148	0.561000|0.561000	0.74099|0.74099	GCC|GGC	.	.		0.612	TRPT1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396579.1	NM_031472		A	63992051	C	A	63992051	3	1	30	1	0	0	0	0	1	0	0	0	16609	739	26	3	314	3	TRPT1	11	63992051	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	5514623	63992051	71014465	70	3771										
PPP2R5B	5526	hgsc.bcm.edu	37	chr11	64695804	64695804	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tagtgaggatccccgggagcGtgagtacctcaagaccatcc	12	12	1	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr11:64695804G>A	ENST00000164133.2	+	6	1251	c.629G>A	c.(628-630)cGt>cAt	p.R210H		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	210					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)	21						CCCCGGGAGCGTGAGTACCTC	0.587																																					p.R210H		Atlas-SNP	.											.	PPP2R5B	47	.	0			c.G629A						.						82	71	74					11																	64695804		2201	4297	6498	SO:0001583	missense	5526	exon6			GGGAGCGTGAGTA	L42374	CCDS8085.1	11q12	2010-06-18	2010-04-14		ENSG00000068971	ENSG00000068971		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9310	protein-coding gene	gene with protein product	"PP2A, B subunit, B' beta isoform", "PP2A, B subunit, B56 beta isoform", "PP2A, B subunit, PR61 beta isoform", "PP2A, B subunit, R5 beta isoform", "serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, beta isoform"	601644	"protein phosphatase 2, regulatory subunit B (B56), beta isoform", "protein phosphatase 2, regulatory subunit B', beta isoform"			7592815	Standard	NM_006244		Approved	FLJ35411, B56B, PR61B	uc001oby.3	Q15173	OTTHUMG00000150043	ENST00000164133.2:c.629G>A	chr11.hg19:g.64695804G>A	ENSP00000164133:p.Arg210His	75.0	0.0		89.0	19.0	NM_006244	Q13853	Missense_Mutation	SNP	ENST00000164133.2	hg19	CCDS8085.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.871173	0.91587	.	.	ENSG00000068971	ENST00000164133;ENST00000359279;ENST00000527441	.	.	.	3.56	3.56	0.40772	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.87168	0.6110	H	0.97707	4.06	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91159	0.4959	9	0.87932	D	0	-9.5765	13.5415	0.61676	0.0:0.0:1.0:0.0	.	210	Q15173	2A5B_HUMAN	H	210;237;210	.	ENSP00000164133:R210H	R	+	2	0	PPP2R5B	64452380	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.137000	0.94496	2.322000	0.78497	0.549000	0.68633	CGT	.	.		0.587	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244		A	64695804	G	A	64695804	3	1	30	1	0	0	0	0	1	0	0	0	12405	1145	40	1	647	1	PPP2R5B	11	64695804	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	703753	64695804	70310712	71	3772										
INPPL1	3636	hgsc.bcm.edu	37	chr11	71948271	71948271	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tccttgaaggggtcccgcacCagctgctgcccccggagcca	12	17	0	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr11:71948271C>T	ENST00000298229.2	+	26	3187	c.2983C>T	c.(2983-2985)Cag>Tag	p.Q995*	INPPL1_ENST00000541756.1_Nonsense_Mutation_p.Q753*|INPPL1_ENST00000538751.1_Nonsense_Mutation_p.Q753*|PHOX2A_ENST00000544057.1_5'Flank	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	995	Pro-rich.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						GGTCCCGCACCAGCTGCTGCC	0.637																																					p.Q995X		Atlas-SNP	.											.	INPPL1	120	.	0			c.C2983T						.						79	95	90					11																	71948271		2200	4293	6493	SO:0001587	stop_gained	3636	exon26			CCGCACCAGCTGC	Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"Sterile alpha motif (SAM) domain containing", "SH2 domain containing"	6080	protein-coding gene	gene with protein product	"51C protein"	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.2983C>T	chr11.hg19:g.71948271C>T	ENSP00000298229:p.Gln995*	30.0	0.0		35.0	10.0	NM_001567	B2RTX5|Q13577|Q13578	Nonsense_Mutation	SNP	ENST00000298229.2	hg19	CCDS8213.1	.	.	.	.	.	.	.	.	.	.	c	36	5.719986	0.96839	.	.	ENSG00000165458	ENST00000298229;ENST00000541756;ENST00000538751;ENST00000541752	.	.	.	5.19	5.19	0.71726	.	0.075721	0.52532	D	0.000063	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	16.1928	0.82004	0.0:1.0:0.0:0.0	.	.	.	.	X	995;753;753;8	.	ENSP00000298229:Q995X	Q	+	1	0	INPPL1	71625919	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.125000	0.77193	2.414000	0.81942	0.462000	0.41574	CAG	.	.		0.637	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		T	71948271	C	T	71948271	4	4	30	1	0	0	0	0	0	1	0	0	7770	595	21	3	3085	3	INPPL1	11	71948271	Nonsense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	7252467	71948271	63058245	72	3773										
GRIK4	2900	hgsc.bcm.edu	37	chr11	120831700	120831700	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tgcagcgcatggatgtgcccAttgagtcagtggatgacctg	14	9	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr11:120831700A>T	ENST00000527524.2	+	17	2244	c.1957A>T	c.(1957-1959)Att>Ttt	p.I653F	GRIK4_ENST00000438375.2_Missense_Mutation_p.I653F	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	653					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		GGATGTGCCCATTGAGTCAGT	0.527																																					p.I653F		Atlas-SNP	.											.	GRIK4	149	.	0			c.A1957T						.						139	110	120					11																	120831700		2203	4299	6502	SO:0001583	missense	2900	exon15			GTGCCCATTGAGT	S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1957A>T	chr11.hg19:g.120831700A>T	ENSP00000435648:p.Ile653Phe	81.0	0.0		76.0	22.0	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	hg19	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	A	33	5.202808	0.94997	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.64085	-0.08;-0.08	5.51	5.51	0.81932	Ionotropic glutamate receptor (2);	0.047918	0.85682	D	0.000000	T	0.77130	0.4085	M	0.73598	2.24	0.80722	D	1	P;D	0.62365	0.949;0.991	P;D	0.63033	0.722;0.91	T	0.80061	-0.1540	10	0.66056	D	0.02	.	15.3185	0.74102	1.0:0.0:0.0:0.0	.	653;653	A6H8K8;Q16099	.;GRIK4_HUMAN	F	653	ENSP00000435648:I653F;ENSP00000404063:I653F	ENSP00000404063:I653F	I	+	1	0	GRIK4	120336910	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.097000	0.63578	0.533000	0.62120	ATT	.	.		0.527	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		T	120831700	A	T	120831700	3	4	30	1	0	0	0	0	1	0	0	0	6785	217	8	4	2015	4	GRIK4	11	120831700	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	48883429	120831700	14174816	73	3774										
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14774139	14774139	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gccaccatgtacgcatcaccGatggtttccacctgtggaaa	9	13	1	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr12:14774139G>T	ENST00000261170.3	-	23	2749	c.2613C>A	c.(2611-2613)atC>atA	p.I871I	RP11-695J4.2_ENST00000545424.1_RNA|RP11-695J4.2_ENST00000542401.1_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	871	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	ACGCATCACCGATGGTTTCCA	0.443																																					p.I871I		Atlas-SNP	.											GUCY2C,NS,carcinoma,0,1	GUCY2C	126	.	0			c.C2613A						.						184	166	172					12																	14774139		2203	4300	6503	SO:0001819	synonymous_variant	2984	exon23			ATCACCGATGGTT		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.2613C>A	chr12.hg19:g.14774139G>T		127.0	1.0		153.0	46.0	NM_004963	B2RMY6	Silent	SNP	ENST00000261170.3	hg19	CCDS8664.1																																																																																			.	.		0.443	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			T	14774139	G	T	14774139	2	4	30	1	0	0	0	0	0	0	0	1	6905	1048	37	1		1	GUCY2C	12	14774139	Silent	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10		14774139	119077756	74	3775										
ACVR1B	91	hgsc.bcm.edu	37	chr12	52374782	52374782	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tctttgtccagcgcacagtgGcccgaaccatcgttttacaa	8	13	1	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr12:52374782G>T	ENST00000257963.4	+	4	687	c.610G>T	c.(610-612)Gcc>Tcc	p.A204S	ACVR1B_ENST00000542485.1_Missense_Mutation_p.A152S|ACVR1B_ENST00000541224.1_Missense_Mutation_p.A204S|ACVR1B_ENST00000415850.2_Missense_Mutation_p.A204S|ACVR1B_ENST00000426655.2_Missense_Mutation_p.A204S	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	204	GS. {ECO:0000255|PROSITE- ProRule:PRU00585}.				activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	GCGCACAGTGGCCCGAACCAT	0.483											OREG0021829	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A204S		Atlas-SNP	.											.	ACVR1B	167	.	0			c.G610T						.						69	67	68					12																	52374782		2203	4300	6503	SO:0001583	missense	91	exon4			ACAGTGGCCCGAA		CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.610G>T	chr12.hg19:g.52374782G>T	ENSP00000257963:p.Ala204Ser	100.0	0.0	984	122.0	34.0	NM_020328	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Missense_Mutation	SNP	ENST00000257963.4	hg19	CCDS8816.1	.	.	.	.	.	.	.	.	.	.	G	33	5.223236	0.95139	.	.	ENSG00000135503	ENST00000257963;ENST00000541224;ENST00000426655;ENST00000415850;ENST00000542485	D;D;D;D;D	0.98585	-5.01;-5.01;-5.01;-5.01;-5.01	4.94	4.94	0.65067	Protein kinase-like domain (1);TGF beta receptor, GS motif (3);	0.000000	0.85682	D	0.000000	D	0.98969	0.9649	M	0.84082	2.675	0.80722	D	1	D;D;P;P	0.89917	0.965;1.0;0.846;0.703	P;D;D;D	0.97110	0.872;1.0;0.91;0.932	D	0.99790	1.1031	10	0.66056	D	0.02	.	18.5621	0.91104	0.0:0.0:1.0:0.0	.	204;204;204;204	P36896-4;P36896;P36896-2;P36896-3	.;ACV1B_HUMAN;.;.	S	204;204;204;204;152	ENSP00000257963:A204S;ENSP00000442656:A204S;ENSP00000390477:A204S;ENSP00000397550:A204S;ENSP00000442885:A152S	ENSP00000257963:A204S	A	+	1	0	ACVR1B	50661049	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.460000	0.83146	0.650000	0.86243	GCC	.	.		0.483	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328		T	52374782	G	T	52374782	3	4	30	1	0	0	0	0	1	0	0	0	221	1203	42	3	624	3	ACVR1B	12	52374782	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	37600643	52374782	81477113	75	3776										
KRT72	140807	hgsc.bcm.edu	37	chr12	52979897	52979897	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gtagctataactgcttgaggCgccaaagcccatgctgaagc	11	11	0	2	rs34119325	byFrequency	TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr12:52979897C>A	ENST00000537672.2	-	9	1415	c.1405G>T	c.(1405-1407)Gcc>Tcc	p.A469S	KRT72_ENST00000354310.4_Missense_Mutation_p.A427S|KRT72_ENST00000398066.3_Missense_Mutation_p.A281S|KRT72_ENST00000293745.2_Missense_Mutation_p.A469S	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	469	Tail.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		CTGCTTGAGGCGCCAAAGCCC	0.577																																					p.A469S		Atlas-SNP	.											KRT72,colon,carcinoma,0,1	KRT72	70	.	0			c.G1405T						.						69	63	65					12																	52979897		2203	4300	6503	SO:0001583	missense	140807	exon9			TTGAGGCGCCAAA	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"-", "Intermediate filaments type II, keratins (basic)"	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.1405G>T	chr12.hg19:g.52979897C>A	ENSP00000441160:p.Ala469Ser	48.0	0.0		71.0	10.0	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	hg19	CCDS8833.1	.	.	.	.	.	.	.	.	.	.	C	0.986	-0.695433	0.03303	.	.	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	T;T;D;T	0.81908	-1.48;-1.48;-1.55;-1.21	4.18	-3.48	0.04739	.	0.883800	0.09298	N	0.821369	T	0.68769	0.3037	N	0.24115	0.695	0.09310	N	1	B;B	0.16166	0.013;0.016	B;B	0.12837	0.004;0.008	T	0.51260	-0.8728	10	0.28530	T	0.3	.	10.3711	0.44055	0.0:0.3612:0.0:0.6388	.	427;469	B4DEI8;Q14CN4	.;K2C72_HUMAN	S	469;469;427;281	ENSP00000441160:A469S;ENSP00000293745:A469S;ENSP00000346269:A427S;ENSP00000446151:A281S	ENSP00000293745:A469S	A	-	1	0	KRT72	51266164	0.000000	0.05858	0.005000	0.12908	0.029000	0.11900	-1.188000	0.03064	-0.683000	0.05190	-1.538000	0.00913	GCC	.	C|0.996;T|0.004		0.577	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747		A	52979897	C	A	52979897	3	1	30	1	0	0	0	0	1	0	0	0	8494	768	27	1	134	1	KRT72	12	52979897	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	605115	52979897	80871998	76	3777										
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105509006	105509006	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ctcttgttttatggagaaggAggtaagtttaaaattccaaa	9	4	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr12:105509006A>T	ENST00000332180.5	+	5	453	c.366A>T	c.(364-366)ggA>ggT	p.G122G		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						ATGGAGAAGGAGGTAAGTTTA	0.259																																					p.G122G		Atlas-SNP	.											.	KIAA1033	83	.	0			c.A366T						.						64	59	61					12																	105509006		1781	4040	5821	SO:0001630	splice_region_variant	23325	exon5			AGAAGGAGGTAAG	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.367+1A>T	chr12.hg19:g.105509006A>T		562.0	1.0		404.0	80.0	NM_015275		Silent	SNP	ENST00000332180.5	hg19	CCDS41826.1																																																																																			.	.		0.259	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275	Silent	T	105509006	A	T	105509006	5	4	30	1	0	0	0	0	0	0	1	0	8215	318	11	4	384	4	KIAA1033	12	105509006	Splice_Site	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	52529109	105509006	28342889	77	3778										
RAD9B	144715	hgsc.bcm.edu	37	chr12	110959986	110959986	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cctattaatacctcaggtcaGatctgattgaaaaaaaggct	7	8	3	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr12:110959986G>A	ENST00000409778.3	+	8	712	c.688G>A	c.(688-690)Gat>Aat	p.D230N	RAD9B_ENST00000409246.1_Missense_Mutation_p.D227N|RAD9B_ENST00000409425.1_Missense_Mutation_p.D227N|RAD9B_ENST00000409300.1_Missense_Mutation_p.D299N|RAD9B_ENST00000392672.4_Missense_Mutation_p.D299N			Q6WBX8	RAD9B_HUMAN	RAD9 homolog B (S. pombe)	296					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	checkpoint clamp complex (GO:0030896)|nucleoplasm (GO:0005654)				endometrium(1)|large_intestine(2)|lung(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	7						CCTCAGGTCAGATCTGATTGA	0.358																																					p.D299N		Atlas-SNP	.											.	RAD9B	50	.	0			c.G895A						.						23	23	23					12																	110959986		2203	4297	6500	SO:0001583	missense	144715	exon10			AGGTCAGATCTGA		CCDS9148.2, CCDS66469.1, CCDS73526.1, CCDS73527.1	12q24.13	2008-12-15	2008-12-15		ENSG00000151164	ENSG00000151164			21700	protein-coding gene	gene with protein product		608368					Standard	NM_152442		Approved	FLJ40346	uc001trf.4	Q6WBX8	OTTHUMG00000152952	ENST00000409778.3:c.688G>A	chr12.hg19:g.110959986G>A	ENSP00000386697:p.Asp230Asn	126.0	0.0		141.0	33.0	NM_152442	Q5U5K0|Q6NVJ1|Q6ZVT7|Q8N7T9|Q96LI8	Missense_Mutation	SNP	ENST00000409778.3	hg19		.	.	.	.	.	.	.	.	.	.	G	11.40	1.626729	0.28978	.	.	ENSG00000151164	ENST00000409246;ENST00000392672;ENST00000409300;ENST00000409425;ENST00000409778	T;T;T;T;T	0.22336	1.96;2.25;2.28;1.96;2.19	5.33	2.22	0.28083	.	0.542931	0.16309	N	0.220078	T	0.16214	0.0390	L	0.29908	0.895	0.24084	N	0.995938	P;B;B	0.40970	0.734;0.006;0.001	B;B;B	0.40329	0.326;0.002;0.0	T	0.11397	-1.0589	10	0.23302	T	0.38	-1.093	12.7805	0.57474	0.0:0.4768:0.5232:0.0	.	230;299;296	B4DYM6;B4DX60;Q6WBX8	.;.;RAD9B_HUMAN	N	227;299;299;227;230	ENSP00000387329:D227N;ENSP00000376440:D299N;ENSP00000386434:D299N;ENSP00000386629:D227N;ENSP00000386697:D230N	ENSP00000376440:D299N	D	+	1	0	RAD9B	109444369	0.995000	0.38212	0.938000	0.37757	0.706000	0.40770	0.801000	0.27055	0.578000	0.29487	0.561000	0.74099	GAT	.	.		0.358	RAD9B-009	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404634.1	NM_152442		A	110959986	G	A	110959986	3	1	30	1	0	0	0	0	1	0	0	0	13011	942	33	3	933	3	RAD9B	12	110959986	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	5450980	110959986	22891909	78	3779										
PCDH9	5101	hgsc.bcm.edu	37	chr13	66878891	66878891	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gtggctgccattgttgaaatGgccttcattggagccatact	11	9	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr13:66878891G>A	ENST00000377865.2	-	4	3744	c.3610C>T	c.(3610-3612)Cat>Tat	p.H1204Y	PCDH9-AS1_ENST00000430861.1_RNA|PCDH9_ENST00000328454.5_Missense_Mutation_p.H1170Y|PCDH9_ENST00000456367.1_Missense_Mutation_p.H1170Y|PCDH9_ENST00000544246.1_Missense_Mutation_p.H1204Y			Q9HC56	PCDH9_HUMAN	protocadherin 9	1204					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		TTGTTGAAATGGCCTTCATTG	0.493																																					p.H1204Y		Atlas-SNP	.											.	PCDH9	252	.	0			c.C3610T						.						164	131	142					13																	66878891		2203	4300	6503	SO:0001583	missense	5101	exon5			TGAAATGGCCTTC	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.3610C>T	chr13.hg19:g.66878891G>A	ENSP00000367096:p.His1204Tyr	345.0	0.0		365.0	82.0	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.181698	0.57800	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454	T;T;T;T	0.56275	0.53;0.53;0.47;0.47	6.05	6.05	0.98169	.	0.000000	0.48767	D	0.000168	T	0.61949	0.2388	N	0.19112	0.55	0.49687	D	0.999814	P;P;P	0.42039	0.659;0.769;0.659	P;P;P	0.61397	0.775;0.888;0.775	T	0.62272	-0.6889	10	0.59425	D	0.04	.	20.6013	0.99457	0.0:0.0:1.0:0.0	.	1162;1170;1204	B7ZM79;Q9HC56-2;Q9HC56	.;.;PCDH9_HUMAN	Y	1204;1204;1170;1170	ENSP00000442186:H1204Y;ENSP00000367096:H1204Y;ENSP00000401699:H1170Y;ENSP00000332060:H1170Y	ENSP00000332060:H1170Y	H	-	1	0	PCDH9	65776892	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.878000	0.98634	0.650000	0.86243	CAT	.	.		0.493	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		A	66878891	G	A	66878891	3	1	30	1	0	0	0	0	1	0	0	0	11527	1348	47	3	107	3	PCDH9	13	66878891	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10		66878891	48290987	79	3780										
PCDH9	5101	hgsc.bcm.edu	37	chr13	67800949	67800949	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cccattgtccctggcagttaCtgtaaaaatgaatcgttctt	7	10	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr13:67800949C>T	ENST00000377865.2	-	1	1758	c.1624G>A	c.(1624-1626)Gta>Ata	p.V542I	PCDH9_ENST00000377861.3_Missense_Mutation_p.V542I|PCDH9_ENST00000328454.5_Missense_Mutation_p.V542I|PCDH9_ENST00000456367.1_Missense_Mutation_p.V542I|PCDH9_ENST00000544246.1_Missense_Mutation_p.V542I			Q9HC56	PCDH9_HUMAN	protocadherin 9	542	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		CTGGCAGTTACTGTAAAAATG	0.458																																					p.V542I		Atlas-SNP	.											.	PCDH9	252	.	0			c.G1624A						.						86	88	87					13																	67800949		2203	4300	6503	SO:0001583	missense	5101	exon2			CAGTTACTGTAAA	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1624G>A	chr13.hg19:g.67800949C>T	ENSP00000367096:p.Val542Ile	165.0	0.0		141.0	39.0	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.536080	0.27475	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74	6.08	6.08	0.98989	Cadherin (5);Cadherin-like (1);	0.058936	0.64402	D	0.000002	T	0.30854	0.0778	L	0.35341	1.055	0.58432	D	0.999999	B;B;B;B	0.31581	0.329;0.01;0.058;0.071	B;B;B;B	0.39738	0.308;0.075;0.065;0.173	T	0.02713	-1.1120	10	0.48119	T	0.1	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	542;542;542;542	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	I	542	ENSP00000442186:V542I;ENSP00000367096:V542I;ENSP00000401699:V542I;ENSP00000332060:V542I;ENSP00000367092:V542I	ENSP00000332060:V542I	V	-	1	0	PCDH9	66698950	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.970000	0.63742	2.894000	0.99253	0.655000	0.94253	GTA	.	.		0.458	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		T	67800949	C	T	67800949	3	4	30	1	0	0	0	0	1	0	0	0	11527	565	20	3	2105	3	PCDH9	13	67800949	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	922058	67800949	47368929	80	3781										
FBXL3	26224	hgsc.bcm.edu	37	chr13	77581424	77581424	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gataggcggccaccacacatCttcacaaactcaacaaaggc	7	14	3	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr13:77581424C>A	ENST00000355619.5	-	5	1467	c.1143G>T	c.(1141-1143)aaG>aaT	p.K381N	FBXL3_ENST00000477982.1_Intron	NM_012158.2	NP_036290.1	Q9UKT7	FBXL3_HUMAN	F-box and leucine-rich repeat protein 3	381					entrainment of circadian clock by photoperiod (GO:0043153)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|urinary_tract(1)	16		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.218)		GBM - Glioblastoma multiforme(99;0.0521)		CACCACACATCTTCACAAACT	0.413																																					p.K381N		Atlas-SNP	.											.	FBXL3	46	.	0			c.G1143T						.						129	121	124					13																	77581424		2203	4300	6503	SO:0001583	missense	26224	exon5			ACACATCTTCACA	AF129532	CCDS9457.1	13q22	2011-06-09	2004-07-20	2004-07-21	ENSG00000005812	ENSG00000005812		"F-boxes / Leucine-rich repeats"	13599	protein-coding gene	gene with protein product		605653	"F-box and leucine-rich repeat protein 3A"	FBXL3A		10531035, 10828603	Standard	NM_012158		Approved	FBL3, FBL3A	uc001vkd.3	Q9UKT7	OTTHUMG00000017099	ENST00000355619.5:c.1143G>T	chr13.hg19:g.77581424C>A	ENSP00000347834:p.Lys381Asn	94.0	0.0		103.0	7.0	NM_012158	B2RB04|Q9P122	Missense_Mutation	SNP	ENST00000355619.5	hg19	CCDS9457.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981810	0.53827	.	.	ENSG00000005812	ENST00000355619	T	0.54866	0.55	5.88	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.66066	0.2752	L	0.54323	1.7	0.58432	D	0.999994	D	0.76494	0.999	D	0.80764	0.994	T	0.65393	-0.6179	10	0.49607	T	0.09	-12.8698	12.7458	0.57280	0.0:0.8667:0.0:0.1333	.	381	Q9UKT7	FBXL3_HUMAN	N	381	ENSP00000347834:K381N	ENSP00000347834:K381N	K	-	3	2	FBXL3	76479425	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.383000	0.34385	0.826000	0.34661	0.655000	0.94253	AAG	.	.		0.413	FBXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045312.3			A	77581424	C	A	77581424	3	1	30	1	0	0	0	0	1	0	0	0	5728	912	32	3	147	3	FBXL3	13	77581424	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	9780475	77581424	37588454	81	3782										
SLC10A2	6555	hgsc.bcm.edu	37	chr13	103701772	103701772	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	agctgcgtgttctgcatcccCgtttcaaaagcaaccgttcg	9	13	2	0	rs201412654		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr13:103701772C>T	ENST00000245312.3	-	5	1382	c.786G>A	c.(784-786)acG>acA	p.T262T		NM_000452.2	NP_000443	Q12908	NTCP2_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 2	262			T -> M (in PBAM; abolishes taurocholate transport; dbSNP:rs72547505). {ECO:0000269|PubMed:9109432}.		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	bile acid:sodium symporter activity (GO:0008508)			breast(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)				Aciclovir(DB00787)|Cyclosporine(DB00091)|Ursodeoxycholic acid(DB01586)|Valaciclovir(DB00577)	TCTGCATCCCCGTTTCAAAAG	0.418																																					p.T262T		Atlas-SNP	.											.	SLC10A2	67	.	0			c.G786A						.						124	94	104					13																	103701772		2203	4300	6503	SO:0001819	synonymous_variant	6555	exon5			CATCCCCGTTTCA	U10417	CCDS9506.1	13q33	2013-07-18	2013-07-18		ENSG00000125255	ENSG00000125255		"Solute carriers"	10906	protein-coding gene	gene with protein product		601295		ASBT, ISBT		8661017	Standard	NM_000452		Approved		uc001vpy.4	Q12908	OTTHUMG00000017313	ENST00000245312.3:c.786G>A	chr13.hg19:g.103701772C>T		90.0	0.0		106.0	28.0	NM_000452	A1L4F4|Q13839	Silent	SNP	ENST00000245312.3	hg19	CCDS9506.1																																																																																			.	.		0.418	SLC10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045716.1			T	103701772	C	T	103701772	2	4	30	1	0	0	0	0	0	0	0	1	14389	639	23	1		1	SLC10A2	13	103701772	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	26120348	103701772	11468106	82	3783										
SLC22A17	51310	hgsc.bcm.edu	37	chr14	23816360	23816360	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aggagggtgctgaggatggcGgcagcttgggaggagaagag	22	4	0	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr14:23816360G>A	ENST00000206544.8	-	8	1614	c.1278C>T	c.(1276-1278)gcC>gcT	p.A426A	SLC22A17_ENST00000354772.3_Silent_p.A408A|SLC22A17_ENST00000474057.1_5'UTR|SLC22A17_ENST00000397260.3_Silent_p.A297A|SLC22A17_ENST00000397267.1_Silent_p.A426A	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	426					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|vacuole (GO:0005773)	transmembrane signaling receptor activity (GO:0004888)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)		TGAGGATGGCGGCAGCTTGGG	0.632																																					p.A426A		Atlas-SNP	.											.	SLC22A17	32	.	0			c.C1278T						.						71	55	60					14																	23816360		2203	4300	6503	SO:0001819	synonymous_variant	51310	exon8			GATGGCGGCAGCT	AJ243653	CCDS9593.1, CCDS9594.2	14q11.2	2013-05-22	2008-01-11		ENSG00000092096	ENSG00000092096		"Solute carriers"	23095	protein-coding gene	gene with protein product	"neutrophil gelatinase-associated lipocalin receptor"	611461				16377569	Standard	NM_016609		Approved	BOCT, BOIT, NGALR	uc001wjl.3	Q8WUG5	OTTHUMG00000028740	ENST00000206544.8:c.1278C>T	chr14.hg19:g.23816360G>A		70.0	0.0		71.0	24.0	NM_020372	A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	Silent	SNP	ENST00000206544.8	hg19	CCDS9593.1																																																																																			.	.		0.632	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157223.3	NM_020372		A	23816360	G	A	23816360	2	1	30	1	0	0	0	0	0	0	0	1	14463	1103	39	1		1	SLC22A17	14	23816360	Silent	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10		23816360	83533180	83	3784										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33293092	33293092	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gttgcctagcacttgaacaaAacggaacagaggaaaatgct	10	8	0	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr14:33293092A>G	ENST00000280979.4	+	13	6243	c.6073A>G	c.(6073-6075)Aac>Gac	p.N2025D	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2025					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		ACTTGAACAAAACGGAACAGA	0.423																																					p.N2025D	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.A6073G						.						89	85	86					14																	33293092		2203	4300	6503	SO:0001583	missense	9472	exon13			GAACAAAACGGAA	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6073A>G	chr14.hg19:g.33293092A>G	ENSP00000280979:p.Asn2025Asp	32.0	0.0		36.0	8.0	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	A	16.30	3.085351	0.55861	.	.	ENSG00000151320	ENST00000280979	T	0.06068	3.35	6.11	6.11	0.99139	.	0.298172	0.35495	N	0.003170	T	0.09158	0.0226	L	0.60455	1.87	0.80722	D	1	P	0.34462	0.454	B	0.27262	0.078	T	0.02294	-1.1181	10	0.72032	D	0.01	-12.7363	15.2732	0.73723	1.0:0.0:0.0:0.0	.	2025	Q13023	AKAP6_HUMAN	D	2025	ENSP00000280979:N2025D	ENSP00000280979:N2025D	N	+	1	0	AKAP6	32362843	0.244000	0.23889	0.920000	0.36463	0.814000	0.46013	2.643000	0.46604	2.343000	0.79666	0.533000	0.62120	AAC	.	.		0.423	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		G	33293092	A	G	33293092	3	3	30	1	0	0	0	0	1	0	0	0	455	14	1	2	6119	2	AKAP6	14	33293092	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	9476732	33293092	74056448	84	3785										
JKAMP	51528	hgsc.bcm.edu	37	chr14	59965466	59965466	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tataccattgtatttatctaTtacgcattctgcttggtatt	5	7	2	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr14:59965466T>G	ENST00000261247.9	+	5	627	c.480T>G	c.(478-480)taT>taG	p.Y160*	RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000356057.5_Nonsense_Mutation_p.Y168*|JKAMP_ENST00000425728.2_Nonsense_Mutation_p.Y154*|JKAMP_ENST00000554271.1_Nonsense_Mutation_p.Y174*	NM_001098625.1|NM_001284203.1|NM_016475.3	NP_001092095.1|NP_001271132.1|NP_057559.2	Q9P055	JKAMP_HUMAN	JNK1/MAPK8-associated membrane protein	175					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(1)|kidney(1)|lung(3)	6						TATTTATCTATTACGCATTCT	0.284																																					p.Y160X		Atlas-SNP	.											.	JKAMP	49	.	0			c.T480G						.						68	60	63					14																	59965466		1810	4074	5884	SO:0001587	stop_gained	51528	exon5			TATCTATTACGCA	AF212245	CCDS45116.1, CCDS45117.1, CCDS61462.1, CCDS61463.1	14q22.3	2014-02-14	2009-08-13	2009-08-13	ENSG00000050130	ENSG00000050130			20184	protein-coding gene	gene with protein product	"Jun N-terminal kinase 1-associated membrane protein"	611176	"chromosome 14 open reading frame 100"	C14orf100		16166642, 19269966	Standard	NM_001284202		Approved	HSPC213, JAMP, HSPC327, CDA06	uc001xef.4	Q9P055	OTTHUMG00000171054	ENST00000261247.9:c.480T>G	chr14.hg19:g.59965466T>G	ENSP00000261247:p.Tyr160*	140.0	0.0		108.0	29.0	NM_016475	B4DP67|Q6FIB6|Q6IAJ2|Q7Z5D4|Q86SY6|Q9H0Q6|Q9H2W0|Q9HAH5|Q9P0R3	Nonsense_Mutation	SNP	ENST00000261247.9	hg19	CCDS45116.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.552834	0.65425	.	.	ENSG00000050130	ENST00000261247;ENST00000425728;ENST00000554271;ENST00000554795;ENST00000356057	.	.	.	5.5	-1.27	0.09347	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-52.5972	10.7707	0.46321	0.0:0.4043:0.0:0.5957	.	.	.	.	X	160;154;174;168;168	.	ENSP00000261247:Y160X	Y	+	3	2	JKAMP	59035219	0.995000	0.38212	0.995000	0.50966	0.988000	0.76386	0.369000	0.20416	-0.137000	0.11455	0.533000	0.62120	TAT	.	.		0.284	JKAMP-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411430.1	NM_001098625		G	59965466	T	G	59965466	4	3	30	1	0	0	0	0	0	1	0	0	7958	1500	52	5	498	5	JKAMP	14	59965466	Nonsense_Mutation	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	26672374	59965466	47384074	85	3786										
C14orf43	91748	hgsc.bcm.edu	37	chr14	74189521	74189521	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ttgtaggtgtagtagaactcCacgcactgggccacggtctt	12	10	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr14:74189521C>T	ENST00000286523.5	-	10	3386	c.2604G>A	c.(2602-2604)gtG>gtA	p.V868V	ELMSAN1_ENST00000394071.2_Silent_p.V868V	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	868	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										AGTAGAACTCCACGCACTGGG	0.527																																					p.V868V		Atlas-SNP	.											.	.	.	.	0			c.G2604A						.						225	204	212					14																	74189521		2203	4300	6503	SO:0001819	synonymous_variant	91748	exon10			GAACTCCACGCAC	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.2604G>A	chr14.hg19:g.74189521C>T		87.0	0.0		116.0	36.0	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Silent	SNP	ENST00000286523.5	hg19	CCDS9819.1																																																																																			.	.		0.527	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		T	74189521	C	T	74189521	2	4	30	1	0	0	0	0	0	0	0	1	1776	581	21	3		3	C14orf43	14	74189521	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	14224055	74189521	33160019	86	3787										
C14orf102	55051	hgsc.bcm.edu	37	chr14	90764607	90764607	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aatgagaggtgacttacctgGgttgatgaccacccagccac	11	11	0	4			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr14:90764607G>T	ENST00000354366.3	-	8	1895	c.1663C>A	c.(1663-1665)Cca>Aca	p.P555T	NRDE2_ENST00000357904.3_Missense_Mutation_p.P324T	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	555																	GACTTACCTGGGTTGATGACC	0.498																																					p.P555T		Atlas-SNP	.											.	.	.	.	0			c.C1663A						.						94	89	91					14																	90764607		2203	4300	6503	SO:0001583	missense	55051	exon8			TACCTGGGTTGAT	AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 102"	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.1663C>A	chr14.hg19:g.90764607G>T	ENSP00000346335:p.Pro555Thr	29.0	0.0		52.0	10.0	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Missense_Mutation	SNP	ENST00000354366.3	hg19	CCDS9890.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.765351	0.31228	.	.	ENSG00000119720	ENST00000354366;ENST00000357904;ENST00000554464	T;T	0.34667	1.35;1.35	5.58	4.68	0.58851	.	0.478879	0.22197	N	0.063287	T	0.30792	0.0776	L	0.45581	1.43	0.35821	D	0.824573	B	0.19445	0.036	B	0.24006	0.05	T	0.29058	-1.0024	10	0.25106	T	0.35	.	9.927	0.41498	0.0722:0.14:0.7878:0.0	.	555	Q9H7Z3	CN102_HUMAN	T	555;324;134	ENSP00000346335:P555T;ENSP00000350579:P324T	ENSP00000346335:P555T	P	-	1	0	C14orf102	89834360	1.000000	0.71417	0.878000	0.34440	0.848000	0.48234	4.195000	0.58400	1.341000	0.45600	0.455000	0.32223	CCA	.	.		0.498	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		T	90764607	G	T	90764607	3	4	30	1	0	0	0	0	1	0	0	0	1737	1232	43	3	1859	3	C14orf102	14	90764607	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	16575086	90764607	16584933	87	3788										
C14orf153	84334	hgsc.bcm.edu	37	chr14	104040498	104040498	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ctaaaggcctgggcctgagaActgaatcaggttagtgtgtt	13	7	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr14:104040498A>G	ENST00000409074.2	+	3	416	c.415A>G	c.(415-417)Act>Gct	p.T139A	RP11-73M18.2_ENST00000472726.2_Missense_Mutation_p.T139A|APOPT1_ENST00000556253.2_Missense_Mutation_p.T126A|AL139300.1_ENST00000583855.1_RNA|APOPT1_ENST00000477116.1_3'UTR|APOPT1_ENST00000247618.4_Missense_Mutation_p.T126A	NM_032374.3	NP_115750.2	Q96IL0	APOP1_HUMAN	apoptogenic 1, mitochondrial	139					intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)	mitochondrion (GO:0005739)											GGGCCTGAGAACTGAATCAGG	0.368																																					p.T139A		Atlas-SNP	.											.	.	.	.	0			c.A415G						.						211	213	212					14																	104040498		2203	4300	6503	SO:0001583	missense	84334	exon3			CTGAGAACTGAAT	BC007412	CCDS9983.2	14q32.33	2012-06-28	2012-06-28	2011-09-07	ENSG00000256053	ENSG00000256053			20492	protein-coding gene	gene with protein product	"apoptogenic protein 1"		"chromosome 14 open reading frame 153", "apoptogenic 1"	C14orf153		16782708, 18977203	Standard	NM_032374		Approved	MGC2562, APOP-1		Q96IL0	OTTHUMG00000153929	ENST00000409074.2:c.415A>G	chr14.hg19:g.104040498A>G	ENSP00000386485:p.Thr139Ala	621.0	0.0		587.0	149.0	NM_032374	Q53G28	Missense_Mutation	SNP	ENST00000409074.2	hg19	CCDS9983.2	.	.	.	.	.	.	.	.	.	.	A	12.01	1.808741	0.31961	.	.	ENSG00000256053;ENSG00000256053;ENSG00000256500;ENSG00000256500	ENST00000409074;ENST00000495778;ENST00000472726;ENST00000247618	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.97	-9.11	0.00711	.	0.408897	0.24889	N	0.034789	T	0.15739	0.0379	L	0.27053	0.805	0.09310	N	0.999995	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.19943	-1.0290	10	0.15066	T	0.55	.	2.2292	0.03992	0.4662:0.0966:0.2414:0.1957	.	139;139	E7EVH7;Q96IL0	.;APOP1_HUMAN	A	139;101;139;126	ENSP00000386485:T139A;ENSP00000451703:T101A;ENSP00000439065:T139A;ENSP00000247618:T126A	ENSP00000247618:T126A	T	+	1	0	C14orf153;RP11-73M18.2	103110251	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-0.557000	0.05985	-2.387000	0.00589	0.533000	0.62120	ACT	.	.		0.368	APOPT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333060.2	NM_032374		G	104040498	A	G	104040498	3	3	30	1	0	0	0	0	1	0	0	0	1755	43	2	2	425	2	C14orf153	14	104040498	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	13275891	104040498	3309042	88	3789										
FMN1	342184	hgsc.bcm.edu	37	chr15	33359250	33359250	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ccttcttcagcacacgaagcCcactgaaaaaagctggaagt	8	12	2	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr15:33359250C>A	ENST00000559047.1	-	3	2043				FMN1_ENST00000334528.9_Missense_Mutation_p.G279V|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000561249.1_Intron|FMN1_ENST00000558197.1_Missense_Mutation_p.G279V			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		CACACGAAGCCCACTGAAAAA	0.468																																					p.G279V		Atlas-SNP	.											.	FMN1	174	.	0			c.G836T						.						59	60	60					15																	33359250		1889	4125	6014	SO:0001627	intron_variant	342184	exon1			CGAAGCCCACTGA	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-1975G>T	chr15.hg19:g.33359250C>A		109.0	0.0		125.0	25.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.00	2.999301	0.54147	.	.	ENSG00000248905	ENST00000334528	T	0.61158	0.13	5.59	4.66	0.58398	.	.	.	.	.	T	0.76884	0.4050	.	.	.	.	.	.	D;D	0.69078	0.997;0.997	D;D	0.71184	0.972;0.963	T	0.82032	-0.0658	7	0.87932	D	0	.	16.3782	0.83418	0.0:0.8679:0.1321:0.0	.	279;279	Q68DA7-3;Q68DA7-5	.;.	V	279	ENSP00000333950:G279V	ENSP00000333950:G279V	G	-	2	0	FMN1	31146542	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	6.983000	0.76180	1.340000	0.45581	0.655000	0.94253	GGG	.	.		0.468	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		A	33359250	C	A	33359250	1	1	30	0	1	0	0	0	0	0	0	0	5957	623	22	3		3	FMN1	15	33359250	Intron	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10		33359250	69172142	89	3790										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91017734	91017734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cagtcaatgctgaggatcctCctatggttgtggtccgaaaa	11	9	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr15:91017734C>T	ENST00000268182.5	+	23	2717	c.2593C>T	c.(2593-2595)Cct>Tct	p.P865S	IQGAP1_ENST00000560020.1_3'UTR|IQGAP1_ENST00000560738.1_Missense_Mutation_p.P293S	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	865					cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TGAGGATCCTCCTATGGTTGT	0.433																																					p.P865S		Atlas-SNP	.											.	IQGAP1	140	.	0			c.C2593T						.						98	98	98					15																	91017734		2198	4298	6496	SO:0001583	missense	8826	exon23			GATCCTCCTATGG	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.2593C>T	chr15.hg19:g.91017734C>T	ENSP00000268182:p.Pro865Ser	92.0	0.0		101.0	28.0	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	hg19	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.601469	0.87055	.	.	ENSG00000140575	ENST00000268182	T	0.02974	4.09	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.12475	0.0303	M	0.63169	1.94	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	T	0.04041	-1.0982	10	0.32370	T	0.25	-15.6881	17.2199	0.86954	0.0:1.0:0.0:0.0	.	865	P46940	IQGA1_HUMAN	S	865	ENSP00000268182:P865S	ENSP00000268182:P865S	P	+	1	0	IQGAP1	88818738	1.000000	0.71417	0.984000	0.44739	0.997000	0.91878	5.781000	0.68964	2.606000	0.88127	0.591000	0.81541	CCT	.	.		0.433	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		T	91017734	C	T	91017734	3	4	30	1	0	0	0	0	1	0	0	0	7823	855	30	3	2683	3	IQGAP1	15	91017734	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	57658484	91017734	11513658	90	3791										
TAT	6898	hgsc.bcm.edu	37	chr16	71606499	71606499	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gtcttgtagagagagaaaccAggtcttggaaccaggatgtt	13	6	2	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr16:71606499A>G	ENST00000355962.4	-	5	634	c.501T>C	c.(499-501)ccT>ccC	p.P167P	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	167					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	GAGAGAAACCAGGTCTTGGAA	0.443																																					p.P167P	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.T501C						.						85	82	83					16																	71606499		2198	4300	6498	SO:0001819	synonymous_variant	6898	exon5			GAAACCAGGTCTT		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.501T>C	chr16.hg19:g.71606499A>G		122.0	0.0		109.0	24.0	NM_000353	B2R8I1|D3DWS2	Silent	SNP	ENST00000355962.4	hg19	CCDS10903.1																																																																																			.	.		0.443	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1			G	71606499	A	G	71606499	2	3	30	1	0	0	0	0	0	0	0	1	15605	175	7	2		2	TAT	16	71606499	Silent	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10		71606499	18748254	91	3792										
SREBF1	6720	hgsc.bcm.edu	37	chr17	17719659	17719659	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gcactcagcgccaggttggtGgcagtgaggtgcccgcctgt	16	12	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr17:17719659G>A	ENST00000261646.5	-	11	2260	c.2076C>T	c.(2074-2076)gcC>gcT	p.A692A	SREBF1_ENST00000395757.1_Silent_p.A438A|SREBF1_ENST00000583732.1_5'Flank|MIR33B_ENST00000385104.1_RNA|SREBF1_ENST00000355815.4_Silent_p.A722A|SREBF1_ENST00000338854.5_Silent_p.A692A	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	692					aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						CCAGGTTGGTGGCAGTGAGGT	0.662																																					p.A722A		Atlas-SNP	.											.	SREBF1	47	.	0			c.C2166T						.						29	18	22					17																	17719659		2192	4297	6489	SO:0001819	synonymous_variant	6720	exon12			GTTGGTGGCAGTG	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"Basic helix-loop-helix proteins"	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.2076C>T	chr17.hg19:g.17719659G>A		15.0	0.0		20.0	11.0	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Silent	SNP	ENST00000261646.5	hg19	CCDS11189.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.658616	0.29515	.	.	ENSG00000072310	ENST00000395751	.	.	.	5.4	1.54	0.23209	.	.	.	.	.	T	0.55481	0.1923	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44605	-0.9317	4	.	.	.	-10.3203	7.9803	0.30179	0.4089:0.0:0.5911:0.0	.	.	.	.	Y	700	.	.	H	-	1	0	SREBF1	17660384	0.748000	0.28294	0.979000	0.43373	0.926000	0.56050	0.563000	0.23547	0.040000	0.15660	0.561000	0.74099	CAC	.	.		0.662	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		A	17719659	G	A	17719659	2	1	30	1	0	0	0	0	0	0	0	1	15156	1335	47	3		3	SREBF1	17	17719659	Silent	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10		17719659	63475551	92	3793										
PROCA1	83871	hgsc.bcm.edu	37	chr17	27038628	27038628	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cacgagcgggccttgggctcGgtcttttccttagtccatct	11	13	2	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr17:27038628G>T	ENST00000395245.3	-	0	1736				PROCA1_ENST00000439862.3_5'Flank|PROCA1_ENST00000581289.1_Silent_p.T17T|PROCA1_ENST00000579650.1_5'Flank|PROCA1_ENST00000301039.2_Silent_p.T17T	NM_001256281.1|NM_031934.5	NP_001243210.1|NP_114140.4	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family						antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					CCTTGGGCTCGGTCTTTTCCT	0.642																																					p.T17T	Pancreas(175;216 2049 29940 32498 41589)	Atlas-SNP	.											.	PROCA1	28	.	0			c.C51A						.						117	99	105					17																	27038628		2203	4300	6503	SO:0001628	intergenic_variant	147011	exon1			GGGCTCGGTCTTT	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"RAB, member RAS oncogene"	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680		chr17.hg19:g.27038628G>T		64.0	0.0		82.0	18.0	NM_152465	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Silent	SNP	ENST00000395245.3	hg19	CCDS11240.1																																																																																			.	.		0.642	RAB34-018	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345906.1	NM_031934		T	27038628	G	T	27038628	1	4	30	0	1	0	0	0	0	0	0	0	12558	1103	39	1		1	PROCA1	17	27038628	IGR	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	9318969	27038628	54156582	93	3794										
CDC27	996	hgsc.bcm.edu	37	chr17	45234594	45234729	+	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-													0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cactagaatataagacacttAcaattgtgtcctggggtgtt					rs149474782|rs113608268|rs370849730|rs78395997|rs76624491|rs370261409|rs75353677|rs368304141|rs376818791|rs372212798|rs375653477|rs374472811|rs76359747|rs147617501|rs374614181|rs78108688|rs142987740|rs143453365|rs75990396|rs144985864|rs367644695|rs202182614|rs139751753|rs11570485|rs372926889|rs140171160|rs368750026|rs201098929|rs199899451|rs75175938|rs200340309|rs537990668	byFrequency	TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr17:45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	ENST00000066544.3	-	6	590_724	c.497_631delAGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG	c.(496-633)cagttcttacggaaacaccccaggacacaattgtaagtgtcttatattctagtgttcaaaatattatgaaaactacaaagaatgatctgaactaaataatatattgtgaatgacttggtagaaattttctgtttcaga>cga	p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	CDC27_ENST00000531206.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000446365.2_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF105fs|CDC27_ENST00000527547.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.T167T(7)|p.T171T(3)|p.V201I(2)|p.E199E(2)|p.T200T(2)|p.L173S(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACTGTCTCAGGCTGTCTGTGAGATAAACTATGATTAGGTACTTGTGTTGTGCAAGAGTTGGGCAGACAGTTGCTAAAGTTCTGTAAAGATGTGAATTTAAATGTTTGGTCAGGATC	0.342																																					p.201_211del		Pindel	.											.	CDC27	337	.	17	Substitution - coding silent(14)|Substitution - Missense(3)	large_intestine(6)|prostate(6)|kidney(4)|NS(1)	c.601_631del						.																																			SO:0001630	splice_region_variant	996	exon6			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.631-104AGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG>-	chr17.hg19:g.45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT		140.0	0.0		153.0	12.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.342	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Frame_Shift_Del	-	45234729	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	45234594	8	5	30	1	0	1	0	1	0	0	1	0	3068	405	14	0	1916	0	CDC27	17	45234594	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	TCGA-BC-4073-01B-02D-A12Z-10	18195966	45234594	35960616	94	3795										
AKAP1	8165	hgsc.bcm.edu	37	chr17	55187484	55187484	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	caggctccaaccctaagaagGtcgacctcatcatctgggag	10	13	3	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr17:55187484G>T	ENST00000337714.3	+	3	2046	c.1813G>T	c.(1813-1815)Gtc>Ttc	p.V605F	AKAP1_ENST00000539273.1_Missense_Mutation_p.V605F|AKAP1_ENST00000571629.1_Missense_Mutation_p.V605F|AKAP1_ENST00000572557.1_Missense_Mutation_p.V605F	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	605					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					CCCTAAGAAGGTCGACCTCAT	0.567																																					p.V605F		Atlas-SNP	.											.	AKAP1	73	.	0			c.G1813T						.						94	91	92					17																	55187484		2203	4300	6503	SO:0001583	missense	8165	exon4			AAGAAGGTCGACC	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Tudor domain containing"	367	protein-coding gene	gene with protein product	"protein kinase anchoring protein 1", "dual specificity A-kinase-anchoring protein 1", "protein phosphatase 1, regulatory subunit 43", "tudor domain containing 17"	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.1813G>T	chr17.hg19:g.55187484G>T	ENSP00000337736:p.Val605Phe	59.0	0.0		60.0	17.0	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	hg19	CCDS11594.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.498453	0.64298	.	.	ENSG00000121057	ENST00000337714;ENST00000427138;ENST00000539273	T;T	0.63255	-0.03;-0.03	5.18	5.18	0.71444	.	0.235917	0.34802	N	0.003673	T	0.60353	0.2262	N	0.19112	0.55	0.80722	D	1	D	0.69078	0.997	P	0.59221	0.854	T	0.63386	-0.6649	10	0.56958	D	0.05	-23.2636	10.6762	0.45787	0.0:0.1414:0.7122:0.1464	.	605	Q92667	AKAP1_HUMAN	F	605;647;605	ENSP00000337736:V605F;ENSP00000443139:V605F	ENSP00000337736:V605F	V	+	1	0	AKAP1	52542483	0.998000	0.40836	1.000000	0.80357	0.970000	0.65996	1.354000	0.34056	2.426000	0.82243	0.655000	0.94253	GTC	.	.		0.567	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1			T	55187484	G	T	55187484	3	4	30	1	0	0	0	0	1	0	0	0	445	1261	44	3	1819	3	AKAP1	17	55187484	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	9952890	55187484	26007726	95	3796										
CACNG4	27092	hgsc.bcm.edu	37	chr17	65026740	65026740	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ctgagaccgtgggcgtcctgGctgtaaacatttacattgag	12	9	0	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr17:65026740G>T	ENST00000262138.3	+	4	606	c.604G>T	c.(604-606)Gct>Tct	p.A202S	RP11-74H8.1_ENST00000579138.1_RNA|AC005544.1_ENST00000375684.1_5'Flank	NM_014405.3	NP_055220.1	Q9UBN1	CCG4_HUMAN	calcium channel, voltage-dependent, gamma subunit 4	202					membrane depolarization (GO:0051899)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(3)	19	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			GGGCGTCCTGGCTGTAAACAT	0.453																																					p.A202S		Atlas-SNP	.											.	CACNG4	44	.	0			c.G604T						.						86	83	84					17																	65026740		2203	4300	6503	SO:0001583	missense	27092	exon4			GTCCTGGCTGTAA	AH008289	CCDS11667.1	17q24	2006-01-23				ENSG00000075461		"Calcium channel subunits"	1408	protein-coding gene	gene with protein product		606404				10613843	Standard	NM_014405		Approved	MGC11138, MGC24983	uc002jft.2	Q9UBN1		ENST00000262138.3:c.604G>T	chr17.hg19:g.65026740G>T	ENSP00000262138:p.Ala202Ser	73.0	0.0		77.0	28.0	NM_014405	B2RCK0	Missense_Mutation	SNP	ENST00000262138.3	hg19	CCDS11667.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.383831	0.61845	.	.	ENSG00000075461	ENST00000262138	D	0.89415	-2.51	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.92328	0.7566	L	0.59436	1.845	0.58432	D	0.999998	D	0.63880	0.993	D	0.75484	0.986	D	0.89747	0.3937	10	0.16420	T	0.52	-1.7597	16.3423	0.83085	0.0:0.0:1.0:0.0	.	202	Q9UBN1	CCG4_HUMAN	S	202	ENSP00000262138:A202S	ENSP00000262138:A202S	A	+	1	0	CACNG4	62457202	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.314000	0.96306	2.285000	0.76669	0.556000	0.70494	GCT	.	.		0.453	CACNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447036.1	NM_014405		T	65026740	G	T	65026740	3	4	30	1	0	0	0	0	1	0	0	0	2561	1203	42	3	618	3	CACNG4	17	65026740	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	9839256	65026740	16168470	96	3797										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3116449	3116450	+	Frame_Shift_Ins	INS	-	-	G													0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tccgcccggagtggactggcINSggcttccactggagaaccag					rs374873325		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr18:3116449_3116450insG	ENST00000356443.4	-	21	3515_3516	c.3182_3183insC	c.(3181-3183)ccgfs	p.P1061fs	MYOM1_ENST00000400569.3_Frame_Shift_Ins_p.P1061fs|MYOM1_ENST00000261606.7_Frame_Shift_Ins_p.P965fs	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1061	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AGTGGACTGGCGGCTTCCACTG	0.55																																					p.P1061fs		Atlas-INDEL	.											.	MYOM1	192	.	0			c.3183_3184insC						.																																			SO:0001589	frameshift_variant	8736	exon21			.	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.3183dupC	chr18.hg19:g.3116451_3116451dupG	ENSP00000348821:p.Pro1061fs	77.0	0.0		90.0	10.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Frame_Shift_Ins	INS	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.55	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		G	3116450	-	G	3116449	7	5	30	1	0	1	1	0	0	0	0	0	10100	755	27	0	1946	0	MYOM1	18	3116449	Frame_Shift_Ins	INS	-	TCGA-BC-4073-01B-02D-A12Z-10		3116449	74960799	97	3798										
ANKRD30B	374860	hgsc.bcm.edu	37	chr18	14850260	14850260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gagaagaaatgtcgatatatTaaaagaaaaaattagacccg	8	4	0	4			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr18:14850260T>C	ENST00000358984.4	+	35	3266	c.3086T>C	c.(3085-3087)tTa>tCa	p.L1029S		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	1029										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						GTCGATATATTAAAAGAAAAA	0.279																																					p.L1029S		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.T3086C						.						50	44	45					18																	14850260		692	1577	2269	SO:0001583	missense	374860	exon35			ATATATTAAAAGA	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"Ankyrin repeat domain containing"	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.3086T>C	chr18.hg19:g.14850260T>C	ENSP00000351875:p.Leu1029Ser	406.0	0.0		348.0	80.0	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	hg19	CCDS54182.1	.	.	.	.	.	.	.	.	.	.	T	7.085	0.570913	0.13623	.	.	ENSG00000180777	ENST00000358984;ENST00000320584;ENST00000277669	T	0.39406	1.08	1.48	1.48	0.22813	.	.	.	.	.	T	0.52108	0.1714	M	0.79258	2.445	0.46241	D	0.998947	D;D	0.69078	0.997;0.995	P;P	0.54889	0.697;0.763	T	0.56414	-0.7983	9	0.87932	D	0	.	7.0503	0.25069	0.0:0.0:0.0:1.0	.	1114;1029	Q9BXX2;F8WAG3	AN30B_HUMAN;.	S	1029;423;449	ENSP00000351875:L1029S	ENSP00000277669:L449S	L	+	2	0	ANKRD30B	14840260	0.031000	0.19500	0.055000	0.19348	0.066000	0.16364	1.168000	0.31859	0.941000	0.37499	0.145000	0.16022	TTA	.	.		0.279	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029		C	14850260	T	C	14850260	3	2	30	1	0	0	0	0	1	0	0	0	659	1764	61	2	3224	2	ANKRD30B	18	14850260	Missense_Mutation	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	11733811	14850260	63226988	98	3799										
SAFB	6294	hgsc.bcm.edu	37	chr19	5653399	5653399	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tctgacaaaagagacagtgaCgggaaaaaggagaagtcgag	14	5	1	4			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr19:5653399C>T	ENST00000292123.5	+	11	1601	c.1494C>T	c.(1492-1494)gaC>gaT	p.D498D	SAFB_ENST00000592224.1_Silent_p.D498D|SAFB_ENST00000433404.1_Silent_p.D328D|SAFB_ENST00000454510.1_Silent_p.D429D|SAFB_ENST00000588852.1_Silent_p.D498D|SAFB_ENST00000538656.1_Silent_p.D341D	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	498					chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GAGACAGTGACGGGAAAAAGG	0.423																																					p.D498D	Colon(88;338 1345 6184 8214 20897)	Atlas-SNP	.											.	SAFB	74	.	0			c.C1494T						.						57	54	55					19																	5653399		2203	4300	6503	SO:0001819	synonymous_variant	6294	exon11			CAGTGACGGGAAA	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"RNA binding motif (RRM) containing"	10520	protein-coding gene	gene with protein product	"Hsp27 ERE-TATA binding protein"	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.1494C>T	chr19.hg19:g.5653399C>T		142.0	0.0		189.0	53.0	NM_002967	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Silent	SNP	ENST00000292123.5	hg19	CCDS12142.1																																																																																			.	.		0.423	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2			T	5653399	C	T	5653399	2	4	30	1	0	0	0	0	0	0	0	1	13821	535	19	1		1	SAFB	19	5653399	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10		5653399	53475584	99	3800										
TNFSF14	8740	hgsc.bcm.edu	37	chr19	6670048	6670048	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	tcggtctgtccatccaccacAaacactgagggccgtacgac	9	15	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr19:6670048A>G	ENST00000599359.1	-	2	414	c.33T>C	c.(31-33)ttT>ttC	p.F11F	TNFSF14_ENST00000245912.3_Silent_p.F11F|TNFSF14_ENST00000326176.9_Silent_p.F11F			O43557	TNF14_HUMAN	tumor necrosis factor (ligand) superfamily, member 14	11					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of T cell chemotaxis (GO:0010820)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|receptor binding (GO:0005102)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18						CATCCACCACAAACACTGAGG	0.602																																					p.F11F		Atlas-SNP	.											.	TNFSF14	40	.	0			c.T33C						.						117	90	99					19																	6670048		2203	4300	6503	SO:0001819	synonymous_variant	8740	exon2			CACCACAAACACT	AF036581	CCDS12171.1, CCDS45939.1	19p13.3	2008-02-05				ENSG00000125735		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11930	protein-coding gene	gene with protein product		604520				9462508	Standard	NM_172014		Approved	LIGHT, LTg, HVEM-L, CD258	uc002mfk.2	O43557		ENST00000599359.1:c.33T>C	chr19.hg19:g.6670048A>G		93.0	0.0		86.0	25.0	NM_003807	A8K7M2|C9J5H4|O75476|Q6FHA1|Q8WVF8|Q96LD2	Silent	SNP	ENST00000599359.1	hg19	CCDS12171.1																																																																																			.	.		0.602	TNFSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457863.1			G	6670048	A	G	6670048	2	3	30	1	0	0	0	0	0	0	0	1	16322	127	5	2		2	TNFSF14	19	6670048	Silent	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	1016649	6670048	52458935	100	3801										
ELAVL1	1994	hgsc.bcm.edu	37	chr19	8038704	8038704	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gggtcatggtccgcgggagcCcgctgatgtacaagttggcg	17	10	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr19:8038704C>A	ENST00000407627.2	-	4	464	c.335G>T	c.(334-336)gGg>gTg	p.G112V	ELAVL1_ENST00000351593.5_Missense_Mutation_p.G139V|ELAVL1_ENST00000593807.1_Missense_Mutation_p.G112V|ELAVL1_ENST00000596459.1_Missense_Mutation_p.G112V	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	112	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CCGCGGGAGCCCGCTGATGTA	0.557																																					p.G112V		Atlas-SNP	.											.	ELAVL1	44	.	0			c.G335T						.						152	117	129					19																	8038704		2203	4300	6503	SO:0001583	missense	1994	exon4			GGGAGCCCGCTGA	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"RNA binding motif (RRM) containing"	3312	protein-coding gene	gene with protein product	"embryonic lethal, abnormal vision, drosophila, homolog-like 1", "Hu antigen R"	603466	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.335G>T	chr19.hg19:g.8038704C>A	ENSP00000385269:p.Gly112Val	120.0	0.0		125.0	38.0	NM_001419	B4DVB8|Q53XN6|Q9BTT1	Missense_Mutation	SNP	ENST00000407627.2	hg19	CCDS12193.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.782162	0.90282	.	.	ENSG00000066044	ENST00000407627;ENST00000351593	T;T	0.08896	3.04;3.04	5.0	5.0	0.66597	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.42787	0.1218	H	0.96015	3.755	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60058	-0.7337	10	0.87932	D	0	.	15.8573	0.78989	0.0:1.0:0.0:0.0	.	112	Q15717	ELAV1_HUMAN	V	112;139	ENSP00000385269:G112V;ENSP00000264073:G139V	ENSP00000264073:G139V	G	-	2	0	ELAVL1	7944704	1.000000	0.71417	0.965000	0.40720	0.925000	0.55904	7.517000	0.81783	2.595000	0.87683	0.655000	0.94253	GGG	.	.		0.557	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419		A	8038704	C	A	8038704	3	1	30	1	0	0	0	0	1	0	0	0	5051	623	22	3	657	3	ELAVL1	19	8038704	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	1368656	8038704	51090279	101	3802										
MAN2B1	4125	hgsc.bcm.edu	37	chr19	12776599	12776599	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	aggtgcacgttcagcatgttCggctgcactgtggggcatgt	15	9	1	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr19:12776599C>G	ENST00000456935.2	-	2	220	c.180G>C	c.(178-180)ccG>ccC	p.P60P	WDR83_ENST00000418543.3_5'Flank|MAN2B1_ENST00000221363.4_Silent_p.P60P|CTD-2192J16.24_ENST00000597961.1_Silent_p.P57P	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	60					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TCAGCATGTTCGGCTGCACTG	0.547																																					p.P60P		Atlas-SNP	.											MAN2B1,colon,carcinoma,0,1	MAN2B1	91	.	0			c.G180C						.						119	91	100					19																	12776599		2203	4300	6503	SO:0001819	synonymous_variant	4125	exon2			CATGTTCGGCTGC		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.180G>C	chr19.hg19:g.12776599C>G		67.0	1.0		100.0	33.0	NM_001173498	G5E928|O15330|Q16680|Q93094|Q9BW13	Silent	SNP	ENST00000456935.2	hg19	CCDS32919.1																																																																																			.	.		0.547	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1			G	12776599	C	G	12776599	2	3	30	1	0	0	0	0	0	0	0	1	9225	871	31	4		4	MAN2B1	19	12776599	Silent	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10	4737895	12776599	46352384	102	3803										
FPR3	2359	hgsc.bcm.edu	37	chr19	52327451	52327451	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	agggtgatgacgggactctgGattttcaccatagtccttac	11	9	2	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr19:52327451G>C	ENST00000339223.4	+	2	629	c.450G>C	c.(448-450)tgG>tgC	p.W150C	FPR3_ENST00000595991.1_Missense_Mutation_p.W150C	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	150					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)			NS(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)	35						CGGGACTCTGGATTTTCACCA	0.478																																					p.W150C		Atlas-SNP	.											.	FPR3	66	.	0			c.G450C						.						103	91	95					19																	52327451		2203	4300	6503	SO:0001583	missense	2359	exon2			ACTCTGGATTTTC		CCDS12841.1	19q13.3-q13.4	2012-08-08	2008-04-17	2008-04-17		ENSG00000187474		"GPCR / Class A : Formyl peptide receptors"	3828	protein-coding gene	gene with protein product		136539	"formyl peptide receptor-like 2"	FPRL2		1612600, 8198572	Standard	NM_002030		Approved	FPRH1, FMLPY, RMLP-R-I	uc002pxt.1	P25089		ENST00000339223.4:c.450G>C	chr19.hg19:g.52327451G>C	ENSP00000341821:p.Trp150Cys	141.0	0.0		162.0	11.0	NM_002030		Missense_Mutation	SNP	ENST00000339223.4	hg19	CCDS12841.1	.	.	.	.	.	.	.	.	.	.	.	13.33	2.206216	0.39003	.	.	ENSG00000187474	ENST00000339223	D	0.88818	-2.43	2.34	2.34	0.29019	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	D	0.96269	0.8783	H	0.98901	4.365	0.48236	D	0.999612	D	0.89917	1.0	D	0.97110	1.0	D	0.95907	0.8920	10	0.87932	D	0	.	10.3497	0.43927	0.0:0.0:1.0:0.0	.	150	P25089	FPR3_HUMAN	C	150	ENSP00000341821:W150C	ENSP00000341821:W150C	W	+	3	0	FPR3	57019263	1.000000	0.71417	0.027000	0.17364	0.052000	0.14988	6.278000	0.72614	1.323000	0.45263	0.467000	0.42956	TGG	.	.		0.478	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030		C	52327451	G	C	52327451	3	2	30	1	0	0	0	0	1	0	0	0	6048	1183	41	4	452	4	FPR3	19	52327451	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	39550852	52327451	6801532	103	3804										
ZNF28	7576	hgsc.bcm.edu	37	chr19	53304147	53304147	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	cctccagtataaattatcttAtgtgtttcaaggtgtgattt	7	6	2	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr19:53304147A>T	ENST00000457749.2	-	4	1070	c.951T>A	c.(949-951)caT>caA	p.H317Q	ZNF28_ENST00000360272.4_Missense_Mutation_p.H264Q|ZNF28_ENST00000438150.2_Missense_Mutation_p.H264Q|ZNF28_ENST00000414252.2_Missense_Mutation_p.H264Q	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	317					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		AAATTATCTTATGTGTTTCAA	0.368																																					p.H317Q		Atlas-SNP	.											.	ZNF28	191	.	0			c.T951A						.						118	120	120					19																	53304147		2203	4300	6503	SO:0001583	missense	7576	exon4			TATCTTATGTGTT	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.951T>A	chr19.hg19:g.53304147A>T	ENSP00000397693:p.His317Gln	112.0	0.0		116.0	27.0	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	hg19	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	12.71	2.020112	0.35606	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	D;D;D;D;D	0.99974	-10.2;-10.2;-10.2;-10.2;-10.2	1.47	0.341	0.15991	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.99972	0.9991	H	0.95504	3.68	0.09310	N	1	D	0.76494	0.999	D	0.74023	0.982	D	0.97983	1.0350	9	0.87932	D	0	.	5.3348	0.15951	0.828:0.0:0.172:0.0	.	317	P17035	ZNF28_HUMAN	Q	264;317;264;264;264	ENSP00000412143:H264Q;ENSP00000397693:H317Q;ENSP00000353410:H264Q;ENSP00000444965:H264Q;ENSP00000375661:H264Q	ENSP00000353410:H264Q	H	-	3	2	ZNF28	57995959	0.002000	0.14202	0.001000	0.08648	0.022000	0.10575	-0.269000	0.08596	-0.119000	0.11830	0.156000	0.16432	CAT	.	.		0.368	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		T	53304147	A	T	53304147	3	4	30	1	0	0	0	0	1	0	0	0	17828	446	16	4	1209	4	ZNF28	19	53304147	Missense_Mutation	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	976696	53304147	5824836	104	3805										
PXMP4	11264	hgsc.bcm.edu	37	chr20	32298387	32298387	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gttgatgttattgttttctcCaaacaccaggatacccccga	7	11	1	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr20:32298387C>A	ENST00000409299.3	-	3	441	c.349G>T	c.(349-351)Gga>Tga	p.G117*	PXMP4_ENST00000217398.3_Missense_Mutation_p.L123F|PXMP4_ENST00000344022.3_Intron	NM_007238.4	NP_009169.3	Q9Y6I8	PXMP4_HUMAN	peroxisomal membrane protein 4, 24kDa	117						integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|large_intestine(2)|lung(8)	13						TTGTTTTCTCCAAACACCAGG	0.577																																					p.G117X		Atlas-SNP	.											.	PXMP4	20	.	0			c.G349T						.						128	116	120					20																	32298387		2203	4300	6503	SO:0001587	stop_gained	11264	exon3			TTTCTCCAAACAC	AF072864	CCDS13225.1, CCDS13226.1	20q11.22	2008-07-02	2002-08-29		ENSG00000101417	ENSG00000101417			15920	protein-coding gene	gene with protein product	"24 kDa peroxisomal intrinsic membrane protein"		"peroxisomal membrane protein 4 (24kD)"			10366717	Standard	NM_183397		Approved	PMP24	uc002wzv.3	Q9Y6I8	OTTHUMG00000032273	ENST00000409299.3:c.349G>T	chr20.hg19:g.32298387C>A	ENSP00000386385:p.Gly117*	161.0	0.0		163.0	40.0	NM_007238	A2A2I7|Q9H0T4	Nonsense_Mutation	SNP	ENST00000409299.3	hg19	CCDS13225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.5|29.5	5.009587|5.009587	0.93346|0.93346	.|.	.|.	ENSG00000101417|ENSG00000101417	ENST00000409299|ENST00000217398	.|.	.|.	.|.	5.15|5.15	1.96|1.96	0.26148|0.26148	.|.	0.217610|.	0.47852|.	D|.	0.000215|.	.|T	.|0.62841	.|0.2461	.|.	.|.	.|.	0.26785|0.26785	N|N	0.969518|0.969518	.|D	.|0.76494	.|0.999	.|D	.|0.66979	.|0.948	.|T	.|0.53436	.|-0.8439	.|7	0.62326|0.66056	D|D	0.03|0.02	0.4395|0.4395	9.2112|9.2112	0.37320|0.37320	0.0:0.7447:0.0:0.2553|0.0:0.7447:0.0:0.2553	.|.	.|123	.|B4DWH1	.|.	X|F	117|123	.|.	ENSP00000386385:G117X|ENSP00000217398:L123F	G|L	-|-	1|3	0|2	PXMP4|PXMP4	31762048|31762048	0.998000|0.998000	0.40836|0.40836	0.785000|0.785000	0.31869|0.31869	0.928000|0.928000	0.56348|0.56348	0.734000|0.734000	0.26101|0.26101	0.127000|0.127000	0.18452|0.18452	0.609000|0.609000	0.83330|0.83330	GGA|TTG	.	.		0.577	PXMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078739.2	NM_007238		A	32298387	C	A	32298387	4	1	30	1	0	0	0	0	0	1	0	0	12866	603	21	3	297	3	PXMP4	20	32298387	Nonsense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10		32298387	30727133	105	3806										
NFATC2	4773	hgsc.bcm.edu	37	chr20	50092056	50092056	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gactttggtgttgcccactaTcttctcatagctggtggtgg	12	9	2	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr20:50092056T>G	ENST00000396009.3	-	4	1693	c.1474A>C	c.(1474-1476)Ata>Cta	p.I492L	NFATC2_ENST00000371564.3_Missense_Mutation_p.I492L|NFATC2_ENST00000610033.1_Missense_Mutation_p.I273L|NFATC2_ENST00000414705.1_Missense_Mutation_p.I472L|NFATC2_ENST00000609943.1_Missense_Mutation_p.I472L|NFATC2_ENST00000609507.1_Missense_Mutation_p.I273L	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	492	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					TTGCCCACTATCTTCTCATAG	0.557																																					p.I492L		Atlas-SNP	.											.	NFATC2	112	.	0			c.A1474C						.						225	223	224					20																	50092056		2203	4300	6503	SO:0001583	missense	4773	exon4			CCACTATCTTCTC	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1474A>C	chr20.hg19:g.50092056T>G	ENSP00000379330:p.Ile492Leu	308.0	0.0		329.0	83.0	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	hg19	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	T	19.60	3.858656	0.71834	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000371567;ENST00000414705	T;T;T	0.41400	1.0;1.0;1.0	5.26	5.26	0.73747	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.195954	0.47093	D	0.000247	T	0.52709	0.1751	N	0.25647	0.755	0.44000	D	0.996704	P;P;B;B	0.42908	0.476;0.793;0.338;0.338	P;D;P;P	0.66497	0.531;0.944;0.531;0.531	T	0.55724	-0.8096	10	0.59425	D	0.04	-8.1108	15.1874	0.73016	0.0:0.0:0.0:1.0	.	472;472;492;492	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	L	492;492;273;472	ENSP00000360619:I492L;ENSP00000379330:I492L;ENSP00000396471:I472L	ENSP00000360619:I492L	I	-	1	0	NFATC2	49525463	1.000000	0.71417	0.979000	0.43373	0.907000	0.53573	1.659000	0.37387	1.983000	0.57843	0.528000	0.53228	ATA	.	.		0.557	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		G	50092056	T	G	50092056	3	3	30	1	0	0	0	0	1	0	0	0	10371	1435	50	5	1379	5	NFATC2	20	50092056	Missense_Mutation	SNP	T	TCGA-BC-4073-01B-02D-A12Z-10	17793669	50092056	12933464	106	3807										
ITSN1	6453	hgsc.bcm.edu	37	chr21	35172168	35172168	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	taaaagtggtgtattaccggGcactgtacccctttgaatcc	9	10	0	1			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr21:35172168G>A	ENST00000381318.3	+	19	2527	c.2239G>A	c.(2239-2241)Gca>Aca	p.A747T	ITSN1_ENST00000399367.3_Missense_Mutation_p.A747T|ITSN1_ENST00000399355.2_Missense_Mutation_p.A747T|ITSN1_ENST00000399326.3_Missense_Mutation_p.A747T|ITSN1_ENST00000381291.4_Missense_Mutation_p.A747T|ITSN1_ENST00000379960.5_Missense_Mutation_p.A747T|ITSN1_ENST00000399349.1_Missense_Mutation_p.A747T|ITSN1_ENST00000399352.1_Missense_Mutation_p.A747T|ITSN1_ENST00000399338.4_Missense_Mutation_p.A747T|ITSN1_ENST00000437442.2_Missense_Mutation_p.A747T|ITSN1_ENST00000381285.4_Missense_Mutation_p.A747T|ITSN1_ENST00000399353.1_Missense_Mutation_p.A710T|AP000304.12_ENST00000429238.1_Intron	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	747	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						GTATTACCGGGCACTGTACCC	0.408																																					p.A747T		Atlas-SNP	.											.	ITSN1	166	.	0			c.G2239A						.						97	96	97					21																	35172168		2203	4300	6503	SO:0001583	missense	6453	exon19			TACCGGGCACTGT	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.2239G>A	chr21.hg19:g.35172168G>A	ENSP00000370719:p.Ala747Thr	44.0	0.0		31.0	8.0	NM_001001132	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	hg19	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.692345	0.88735	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	T;T;T;T;T;T;T;T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42	5.65	5.65	0.86999	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	D	0.84229	0.5426	M	0.83953	2.67	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.997;0.999;1.0;0.999;0.999;0.999;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	0.999;1.0;0.996;0.999;0.999;0.997;0.999;0.999;0.999;1.0	D	0.85856	0.1407	10	0.87932	D	0	.	19.7272	0.96168	0.0:0.0:1.0:0.0	.	710;710;710;747;747;747;747;747;747;710	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	T	710;747;747;747;747;747;747;747;747;747;747;747;747;747	ENSP00000382290:A710T;ENSP00000370719:A747T;ENSP00000370691:A747T;ENSP00000370685:A747T;ENSP00000382301:A747T;ENSP00000382289:A747T;ENSP00000382292:A747T;ENSP00000382286:A747T;ENSP00000382275:A747T;ENSP00000387377:A747T;ENSP00000382265:A747T;ENSP00000369294:A747T	ENSP00000369294:A747T	A	+	1	0	ITSN1	34094038	1.000000	0.71417	0.854000	0.33618	0.680000	0.39746	8.502000	0.90505	2.673000	0.90976	0.557000	0.71058	GCA	.	.		0.408	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		A	35172168	G	A	35172168	3	1	30	1	0	0	0	0	1	0	0	0	7935	1203	42	3	2309	3	ITSN1	21	35172168	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10		35172168	12957727	107	3808										
C21orf57	54059	hgsc.bcm.edu	37	chr21	47711386	47711386	+	Intron	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	acgtcctgactgtaagcgggGatgctgaaatcatataacct	10	9	1	2	rs553720951		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr21:47711386G>C	ENST00000329319.3	+	3	737				YBEY_ENST00000397691.1_Intron|YBEY_ENST00000397694.1_Intron|YBEY_ENST00000397701.4_Intron|YBEY_ENST00000339195.6_Intron|YBEY_ENST00000397692.1_Intron	NM_058181.1	NP_478061.1	P58557	YBEY_HUMAN	ybeY metallopeptidase (putative)						rRNA processing (GO:0006364)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)	9						TGTAAGCGGGGATGCTGAAAT	0.458																																					p.D117H		Atlas-SNP	.											.	YBEY	23	.	0			c.G349C						.						80	78	79					21																	47711386		2203	4300	6503	SO:0001627	intron_variant	54059	exon3			AGCGGGGATGCTG	AK294975	CCDS33591.1	21q22.3	2010-12-08	2010-12-08	2010-12-08	ENSG00000182362	ENSG00000182362			1299	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 57"	C21orf57			Standard	XM_005261155		Approved		uc002ziv.3	P58557	OTTHUMG00000090632	ENST00000329319.3:c.339+10G>C	chr21.hg19:g.47711386G>C		164.0	0.0		147.0	50.0	NM_001006114	B7WPA9|B7WPF7|D3DSN2	Missense_Mutation	SNP	ENST00000329319.3	hg19	CCDS33591.1																																																																																			.	.		0.458	YBEY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207265.1	NM_058181		C	47711386	G	C	47711386	1	2	30	0	1	0	0	0	0	0	0	0	2130	1174	41	4		4	C21orf57	21	47711386	Intron	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	12539218	47711386	418509	108	3809										
KCNJ4	3761	hgsc.bcm.edu	37	chr22	38823337	38823337	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	atgccataaagcgggctgtcCtcgtcgatctcgtggacaat	11	11	1	0			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr22:38823337C>A	ENST00000303592.3	-	2	1059	c.801G>T	c.(799-801)gaG>gaT	p.E267D	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	267					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					GCGGGCTGTCCTCGTCGATCT	0.612																																					p.E267D		Atlas-SNP	.											.	KCNJ4	74	.	0			c.G801T						.						92	76	82					22																	38823337		2203	4300	6503	SO:0001583	missense	3761	exon2			GCTGTCCTCGTCG	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.801G>T	chr22.hg19:g.38823337C>A	ENSP00000306497:p.Glu267Asp	39.0	0.0		62.0	24.0	NM_004981	Q14D44	Missense_Mutation	SNP	ENST00000303592.3	hg19	CCDS13971.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.067975	0.36470	.	.	ENSG00000168135	ENST00000303592	D	0.92595	-3.07	4.94	3.79	0.43588	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.112974	0.64402	D	0.000017	D	0.90256	0.6953	M	0.69523	2.12	0.40481	D	0.980449	B	0.06786	0.001	B	0.12837	0.008	D	0.87653	0.2529	10	0.62326	D	0.03	.	10.6862	0.45843	0.0:0.8325:0.0:0.1675	.	267	P48050	IRK4_HUMAN	D	267	ENSP00000306497:E267D	ENSP00000306497:E267D	E	-	3	2	KCNJ4	37153283	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.255000	0.32909	1.066000	0.40716	0.555000	0.69702	GAG	.	.		0.612	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981		A	38823337	C	A	38823337	3	1	30	1	0	0	0	0	1	0	0	0	8062	680	24	3	540	3	KCNJ4	22	38823337	Missense_Mutation	SNP	C	TCGA-BC-4073-01B-02D-A12Z-10		38823337	12481229	109	3810										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46829366	46829366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gaaccttcggtgccacggtcGttgttgtctcgcctgcatgg	13	12	1	0	rs573686247		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chr22:46829366G>A	ENST00000262738.3	-	5	4534	c.4535C>T	c.(4534-4536)aCg>aTg	p.T1512M		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1512	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TGCCACGGTCGTTGTTGTCTC	0.622													G|||	1	0.000199681	0	0	5008	,	,		16571	0		0.001	False		,,,				2504	0				p.T1512M		Atlas-SNP	.											.	CELSR1	242	.	0			c.C4535T						.						61	50	54					22																	46829366		2203	4300	6503	SO:0001583	missense	9620	exon5			ACGGTCGTTGTTG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.4535C>T	chr22.hg19:g.46829366G>A	ENSP00000262738:p.Thr1512Met	33.0	0.0		33.0	9.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.819755	0.50633	.	.	ENSG00000075275	ENST00000262738	T	0.79845	-1.31	4.62	4.62	0.57501	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.64402	U	0.000001	D	0.89643	0.6774	M	0.78223	2.4	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90785	0.4682	10	0.59425	D	0.04	.	17.4417	0.87566	0.0:0.0:1.0:0.0	.	1512	Q9NYQ6	CELR1_HUMAN	M	1512	ENSP00000262738:T1512M	ENSP00000262738:T1512M	T	-	2	0	CELSR1	45208030	1.000000	0.71417	0.032000	0.17829	0.018000	0.09664	9.015000	0.93640	2.290000	0.77057	0.655000	0.94253	ACG	.	.		0.622	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46829366	G	A	46829366	3	1	30	1	0	0	0	0	1	0	0	0	3223	1145	40	1	4633	1	CELSR1	22	46829366	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	8006029	46829366	4475200	110	3811										
HCCS	3052	hgsc.bcm.edu	37	chrX	11139892	11139892	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	attcactttcggcagtatggGacagaatgaaagtcgcttgg	12	7	1	2			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chrX:11139892G>C	ENST00000321143.4	+	7	971	c.769G>C	c.(769-771)Gac>Cac	p.D257H	HCCS_ENST00000380763.3_Missense_Mutation_p.D257H|ARHGAP6_ENST00000534860.1_Intron|HCCS_ENST00000380762.4_Missense_Mutation_p.D257H	NM_001122608.2|NM_001171991.2|NM_005333.4	NP_001116080.1|NP_001165462.1|NP_005324.3	P53701	CCHL_HUMAN	holocytochrome c synthase	257					organ morphogenesis (GO:0009887)|oxidation-reduction process (GO:0055114)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	holocytochrome-c synthase activity (GO:0004408)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(3)	7						GGCAGTATGGGACAGAATGAA	0.403																																					p.D257H	Ovarian(86;1338 1347 1462 10340 37882)	Atlas-SNP	.											.	HCCS	17	.	0			c.G769C						.						127	99	109					X																	11139892		2203	4300	6503	SO:0001583	missense	3052	exon7			GTATGGGACAGAA		CCDS14139.1	Xp22	2014-01-31	2010-05-11		ENSG00000004961	ENSG00000004961	4.4.1.17		4837	protein-coding gene	gene with protein product	"cytochrome c heme-lyase"	300056	"holocytochrome c synthase (cytochrome c heme-lyase)", "microphthalamia with linear skin defects"	MLS		8364577, 12444108	Standard	NM_001122608		Approved	CCHL	uc004cuj.3	P53701	OTTHUMG00000021128	ENST00000321143.4:c.769G>C	chrX.hg19:g.11139892G>C	ENSP00000326579:p.Asp257His	33.0	0.0		32.0	15.0	NM_001122608	B3KUS1|Q502X8	Missense_Mutation	SNP	ENST00000321143.4	hg19	CCDS14139.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.243512	0.79912	.	.	ENSG00000004961	ENST00000321143;ENST00000380763;ENST00000380762	D;D;D	0.83506	-1.73;-1.73;-1.73	5.84	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.93327	0.7873	H	0.95079	3.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94344	0.7573	10	0.66056	D	0.02	-36.3632	12.9185	0.58218	0.0:0.0:0.8366:0.1634	.	257	P53701	CCHL_HUMAN	H	257	ENSP00000326579:D257H;ENSP00000370140:D257H;ENSP00000370139:D257H	ENSP00000326579:D257H	D	+	1	0	HCCS	11049813	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.239000	0.95389	1.197000	0.43143	0.600000	0.82982	GAC	.	.		0.403	HCCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055742.1			C	11139892	G	C	11139892	3	2	30	1	0	0	0	0	1	0	0	0	6999	1174	41	4	791	4	HCCS	23	11139892	Missense_Mutation	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10		11139892	144130668	111	3812										
PRPS2	5634	hgsc.bcm.edu	37	chrX	12838904	12838904	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	ccgcaagaggacaaaatgaaAcactgcaccaagattcaggt	9	10	1	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chrX:12838904A>G	ENST00000380668.5	+	6	974	c.846A>G	c.(844-846)aaA>aaG	p.K282K	PRPS2_ENST00000398491.2_Silent_p.K285K	NM_001039091.2|NM_002765.4	NP_001034180.1|NP_002756.1	P11908	PRPS2_HUMAN	phosphoribosyl pyrophosphate synthetase 2	282					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|AMP biosynthetic process (GO:0006167)|nucleobase-containing compound metabolic process (GO:0006139)|organ regeneration (GO:0031100)	extracellular vesicular exosome (GO:0070062)|ribose phosphate diphosphokinase complex (GO:0002189)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|carbohydrate binding (GO:0030246)|GDP binding (GO:0019003)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	16						ACAAAATGAAACACTGCACCA	0.448																																					p.K285K		Atlas-SNP	.											.	PRPS2	41	.	0			c.A855G						.						94	76	82					X																	12838904		2203	4300	6503	SO:0001819	synonymous_variant	5634	exon6			AATGAAACACTGC	Y00971	CCDS14150.1, CCDS43918.1	Xp22.2	2012-10-02			ENSG00000101911	ENSG00000101911	2.7.6.1		9465	protein-coding gene	gene with protein product	"PRS II", "ribose-phosphate diphosphokinase 2"	311860				1962753	Standard	NM_002765		Approved		uc004cva.3	P11908	OTTHUMG00000021139	ENST00000380668.5:c.846A>G	chrX.hg19:g.12838904A>G		35.0	0.0		42.0	23.0	NM_001039091	Q0VDH9|Q0VDI0|Q15245|Q2TAK7	Silent	SNP	ENST00000380668.5	hg19	CCDS14150.1																																																																																			.	.		0.448	PRPS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055772.2	NM_002765		G	12838904	A	G	12838904	2	3	30	1	0	0	0	0	0	0	0	1	12592	40	2	2		2	PRPS2	23	12838904	Silent	SNP	A	TCGA-BC-4073-01B-02D-A12Z-10	1699012	12838904	142431656	112	3813										
SLC9A7	84679	hgsc.bcm.edu	37	chrX	46541903	46541903	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707964601769911	8	1	1.21291069619337	2.19256933542648	0.838335334133653	1	1	0	gccctgtcttcctgagtgcaGctgagtgatttgtcacggcc	12	12	2	3			TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	g.chrX:46541903G>A	ENST00000328306.4	-	2	418	c.393C>T	c.(391-393)agC>agT	p.S131S		NM_001257291.1|NM_032591.2	NP_001244220.1|NP_115980.1	Q96T83	SL9A7_HUMAN	solute carrier family 9, subfamily A (NHE7, cation proton antiporter 7), member 7	131					ion transport (GO:0006811)|potassium ion transmembrane transport (GO:0071805)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)	potassium:proton antiporter activity (GO:0015386)|protein homodimerization activity (GO:0042803)|sodium:proton antiporter activity (GO:0015385)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|skin(1)	21						CCTGAGTGCAGCTGAGTGATT	0.488																																					p.S131S	Pancreas(118;454 1696 1930 13865 39976)	Atlas-SNP	.											.	SLC9A7	73	.	0			c.C393T						.						74	56	62					X																	46541903		2203	4300	6503	SO:0001819	synonymous_variant	84679	exon2			AGTGCAGCTGAGT	AF298591	CCDS14269.1, CCDS75967.1	Xp11.3	2013-05-22	2012-03-22		ENSG00000065923	ENSG00000065923		"Solute carriers"	17123	protein-coding gene	gene with protein product		300368	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 7", "solute carrier family 9 (sodium/hydrogen exchanger), member 7"			11279194	Standard	NM_001257291		Approved	NHE7	uc004dgv.2	Q96T83	OTTHUMG00000021428	ENST00000328306.4:c.393C>T	chrX.hg19:g.46541903G>A		51.0	0.0		49.0	26.0	NM_001257291	O75827|Q5JXP9	Silent	SNP	ENST00000328306.4	hg19	CCDS14269.1																																																																																			.	.		0.488	SLC9A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056370.1	NM_032591		A	46541903	G	A	46541903	2	1	30	1	0	0	0	0	0	0	0	1	14734	962	34	3		3	SLC9A7	23	46541903	Silent	SNP	G	TCGA-BC-4073-01B-02D-A12Z-10	33702999	46541903	108728657	113	3814										
DMAP1	55929	hgsc.bcm.edu	37	chr1	44684030	44684030	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	caggagtaccagctttatctCcacgatgatgcttggactaa	9	10	1	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr1:44684030C>T	ENST00000372289.2	+	4	704	c.441C>T	c.(439-441)ctC>ctT	p.L147L	DMAP1_ENST00000315913.5_Silent_p.L147L|DMAP1_ENST00000361745.6_Silent_p.L147L|DMAP1_ENST00000488433.1_3'UTR	NM_019100.4	NP_061973.1	Q9NPF5	DMAP1_HUMAN	DNA methyltransferase 1 associated protein 1	147					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription factor import into nucleus (GO:0042993)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|RNA polymerase II repressing transcription factor binding (GO:0001103)|transcription corepressor activity (GO:0003714)			breast(1)|cervix(1)|endometrium(6)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(166;0.155)					AGCTTTATCTCCACGATGATG	0.537											OREG0013437	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L147L		Atlas-SNP	.											.	DMAP1	35	.	0			c.C441T						.						196	167	176					1																	44684030		2203	4300	6503	SO:0001819	synonymous_variant	55929	exon5			TTATCTCCACGAT	AB037846	CCDS509.1	1p34	2009-07-13			ENSG00000178028	ENSG00000178028			18291	protein-coding gene	gene with protein product		605077				10888872, 10718198	Standard	XM_005271039		Approved	DNMAP1, FLJ11543, KIAA1425, DNMTAP1, EAF2, MEAF2, SWC4	uc001clq.1	Q9NPF5	OTTHUMG00000007577	ENST00000372289.2:c.441C>T	chr1.hg19:g.44684030C>T		306.0	0.0	925	143.0	38.0	NM_001034023	A8K001|D3DPY8|Q0JSM4|Q5TG41|Q7Z3H7|Q9H0S8|Q9P2C2	Silent	SNP	ENST00000372289.2	hg19	CCDS509.1																																																																																			.	.		0.537	DMAP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020027.3	NM_019100		T	44684030	C	T	44684030	2	4	31	1	0	0	0	0	0	0	0	1	4578	842	30	3		3	DMAP1	1	44684030	Silent	SNP	C	TCGA-BC-A10Q-01A-11D-A12Z-10		44684030	204566591	1	3815										
SLC35A3	23443	hgsc.bcm.edu	37	chr1	100483326	100483326	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	ctctttatcgataatattatCaacattgatctcctattttt	2	8	3	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr1:100483326C>T	ENST00000370155.3	+	7	1234	c.842C>T	c.(841-843)tCa>tTa	p.S281L	SLC35A3_ENST00000465289.1_Intron|SLC35A3_ENST00000370153.1_Missense_Mutation_p.S323L|SLC35A3_ENST00000427993.2_Missense_Mutation_p.S281L|SLC35A3_ENST00000370156.3_3'UTR	NM_012243.1	NP_036375.1	Q9Y2D2	S35A3_HUMAN	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3	281					transmembrane transport (GO:0055085)|UDP-N-acetylglucosamine metabolic process (GO:0006047)|UDP-N-acetylglucosamine transport (GO:0015788)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)|UDP-N-acetylglucosamine transmembrane transporter activity (GO:0005462)	p.S281L(1)		biliary_tract(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	11		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.124)|all cancers(265;0.198)|Lung(183;0.199)		ATAATATTATCAACATTGATC	0.303																																					p.S323L	Ovarian(7;298 356 944 2149 6911)	Atlas-SNP	.											SLC35A3,bile_duct,carcinoma,0,1	SLC35A3	25	.	1	Substitution - Missense(1)	biliary_tract(1)	c.C968T						.						62	64	63					1																	100483326		2202	4286	6488	SO:0001583	missense	23443	exon7			TATTATCAACATT	AB021981	CCDS762.1, CCDS60204.1, CCDS60205.1	1p21	2013-05-22			ENSG00000117620	ENSG00000117620		"Solute carriers"	11023	protein-coding gene	gene with protein product		605632	"solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3"			10393322	Standard	NM_001271685		Approved		uc001dsr.2	Q9Y2D2	OTTHUMG00000010805	ENST00000370155.3:c.842C>T	chr1.hg19:g.100483326C>T	ENSP00000359174:p.Ser281Leu	913.0	2.0		495.0	75.0	NM_001271685	A8K3F8|D3DT54|Q68CR2|Q9BSB7	Missense_Mutation	SNP	ENST00000370155.3	hg19	CCDS762.1	.	.	.	.	.	.	.	.	.	.	C	33	5.289102	0.95517	.	.	ENSG00000117620	ENST00000370155;ENST00000427993;ENST00000370153	T;T;T	0.46819	0.86;0.86;0.86	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.74137	0.3677	H	0.96489	3.83	0.80722	D	1	D;P	0.57899	0.981;0.866	P;P	0.60117	0.869;0.619	T	0.83062	-0.0147	10	0.87932	D	0	-28.8252	19.3509	0.94384	0.0:1.0:0.0:0.0	.	322;281	Q9Y2D2-2;Q9Y2D2	.;S35A3_HUMAN	L	281;281;323	ENSP00000359174:S281L;ENSP00000414947:S281L;ENSP00000359172:S323L	ENSP00000359172:S323L	S	+	2	0	SLC35A3	100255914	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.774000	0.85478	2.653000	0.90120	0.655000	0.94253	TCA	.	.		0.303	SLC35A3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000029783.1	NM_012243		T	100483326	C	T	100483326	3	4	31	1	0	0	0	0	1	0	0	0	14587	838	29	3	864	3	SLC35A3	1	100483326	Missense_Mutation	SNP	C	TCGA-BC-A10Q-01A-11D-A12Z-10	55799296	100483326	148767295	2	3816										
HIST2H3D	653604	hgsc.bcm.edu	37	chr1	149784882	149784882	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	gatgtccttgggcatgatggTcacgcgcttggcatggatgg	16	8	1	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr1:149784882T>C	ENST00000331491.1	-	1	354	c.355A>G	c.(355-357)Acc>Gcc	p.T119A	RP11-196G18.21_ENST00000420462.1_RNA|HIST2H2BF_ENST00000469483.1_5'Flank|HIST2H2BF_ENST00000545683.1_5'Flank|HIST2H2BF_ENST00000369167.1_5'Flank|HIST2H2BF_ENST00000427880.2_5'Flank	NM_001123375.2	NP_001116847.1	Q71DI3	H32_HUMAN	histone cluster 2, H3d	119					blood coagulation (GO:0007596)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T119A(1)		biliary_tract(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(3)	7						GGCATGATGGTCACGCGCTTG	0.612																																					p.T119A		Atlas-SNP	.											HIST2H3D,bile_duct,carcinoma,0,1	HIST2H3D	15	.	1	Substitution - Missense(1)	biliary_tract(1)	c.A355G						.						45	47	46					1																	149784882		1568	3581	5149	SO:0001583	missense	653604	exon1			TGATGGTCACGCG	AL591493	CCDS41388.1	1q21.2	2012-03-08	2006-10-11		ENSG00000183598	ENSG00000183598		"Histones / Replication-dependent"	25311	protein-coding gene	gene with protein product			"histone 2, H3d"				Standard	NM_001123375		Approved		uc010pbl.2	Q71DI3	OTTHUMG00000012092	ENST00000331491.1:c.355A>G	chr1.hg19:g.149784882T>C	ENSP00000333277:p.Thr119Ala	277.0	1.0		209.0	62.0	NM_001123375	A2BDF6|A6NFS4|Q6B053	Missense_Mutation	SNP	ENST00000331491.1	hg19	CCDS41388.1	.	.	.	.	.	.	.	.	.	.	T	15.10	2.733815	0.48939	.	.	ENSG00000183598	ENST00000331491	T	0.75367	-0.93	3.81	3.81	0.43845	.	0.000000	0.56097	U	0.000038	T	0.75961	0.3921	.	.	.	0.48632	D	0.999684	.	.	.	.	.	.	T	0.80089	-0.1528	7	0.87932	D	0	.	11.8431	0.52366	0.0:0.0:0.0:1.0	.	.	.	.	A	119	ENSP00000333277:T119A	ENSP00000333277:T119A	T	-	1	0	HIST2H3D	148051506	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	5.428000	0.66489	1.745000	0.51790	0.358000	0.22013	ACC	.	.		0.612	HIST2H3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033452.1	NM_001123375		C	149784882	T	C	149784882	3	2	31	1	0	0	0	0	1	0	0	0	7190	1667	58	2	57	2	HIST2H3D	1	149784882	Missense_Mutation	SNP	T	TCGA-BC-A10Q-01A-11D-A12Z-10	49301556	149784882	99465739	3	3817										
WDR26	80232	hgsc.bcm.edu	37	chr1	224585919	224585919	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	tctgtcttgcaagtcccataAatgaactccctgcaggcaaa	7	12	2	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr1:224585919A>T	ENST00000414423.2	-	12	1847	c.1654T>A	c.(1654-1656)Tta>Ata	p.L552I	WDR26_ENST00000295024.6_Missense_Mutation_p.L405I|WDR26_ENST00000366852.2_3'UTR|WDR26_ENST00000479727.1_5'UTR|MIR4742_ENST00000581069.1_RNA	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	552						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L552I(1)|p.L405I(1)		biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		AAGTCCCATAAATGAACTCCC	0.343																																					p.L552I		Atlas-SNP	.											WDR26_ENST00000414423,bile_duct,carcinoma,0,2	WDR26	104	.	2	Substitution - Missense(2)	biliary_tract(2)	c.T1654A						.						87	86	87					1																	224585919		2203	4300	6503	SO:0001583	missense	80232	exon12			CCCATAAATGAAC	AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"WD repeat domain containing"	21208	protein-coding gene	gene with protein product	"GID complex subunit 7 homolog (S. cerevisiae)"						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.1654T>A	chr1.hg19:g.224585919A>T	ENSP00000408108:p.Leu552Ile	156.0	0.0		95.0	30.0	NM_025160	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Missense_Mutation	SNP	ENST00000414423.2	hg19	CCDS31037.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.0|25.0	4.592110|4.592110	0.86953|0.86953	.|.	.|.	ENSG00000162923|ENSG00000162923	ENST00000480676|ENST00000414423;ENST00000295024	.|D;D	.|0.82433	.|-1.61;-1.61	5.11|5.11	5.11|5.11	0.69529|0.69529	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91229|0.91229	0.7236|0.7236	M|M	0.84326|0.84326	2.69|2.69	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.91799|0.91799	0.5450|0.5450	5|10	.|0.49607	.|T	.|0.09	.|.	15.1926|15.1926	0.73057|0.73057	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|536	.|Q9H7D7-2	.|.	Y|I	185|552;405	.|ENSP00000408108:L552I;ENSP00000295024:L405I	.|ENSP00000295024:L405I	F|L	-|-	2|1	0|2	WDR26|WDR26	222652542|222652542	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.118000|5.118000	0.64673|0.64673	2.053000|2.053000	0.61076|0.61076	0.482000|0.482000	0.46254|0.46254	TTT|TTA	.	.		0.343	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160		T	224585919	A	T	224585919	3	4	31	1	0	0	0	0	1	0	0	0	17298	11	1	4	343	4	WDR26	1	224585919	Missense_Mutation	SNP	A	TCGA-BC-A10Q-01A-11D-A12Z-10	74801037	224585919	24664702	4	3818										
HK2	3099	hgsc.bcm.edu	37	chr2	75104368	75104368	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	gtgaagatggccaaggaggaGctgctctttggggggaagct	18	6	1	2	rs565854734		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr2:75104368G>A	ENST00000290573.2	+	8	1551	c.951G>A	c.(949-951)gaG>gaA	p.E317E	HK2_ENST00000409174.1_Silent_p.E289E	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	317	Hexokinase type-2 1.|Regulatory.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						CCAAGGAGGAGCTGCTCTTTG	0.542																																					p.E317E		Atlas-SNP	.											.	HK2	85	.	0			c.G951A						.						196	197	197					2																	75104368		2203	4300	6503	SO:0001819	synonymous_variant	3099	exon8			GGAGGAGCTGCTC		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.951G>A	chr2.hg19:g.75104368G>A		133.0	0.0		105.0	25.0	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	hg19	CCDS1956.1																																																																																			.	.		0.542	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189		A	75104368	G	A	75104368	2	1	31	1	0	0	0	0	0	0	0	1	7200	962	34	3		3	HK2	2	75104368	Silent	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10		75104368	168095005	5	3819										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109380447	109380447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	acccactttagagacagcaaAcaagaatcatgagacagatg	8	9	1	4			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr2:109380447A>G	ENST00000283195.6	+	20	3578	c.3452A>G	c.(3451-3453)aAc>aGc	p.N1151S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1151					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.N1151S(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GAGACAGCAAACAAGAATCAT	0.433																																					p.N1151S		Atlas-SNP	.											RANBP2_ENST00000283195,bile_duct,carcinoma,0,2	RANBP2	488	.	2	Substitution - Missense(2)	biliary_tract(2)	c.A3452G						.						112	108	110					2																	109380447		2203	4299	6502	SO:0001583	missense	5903	exon20			CAGCAAACAAGAA	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.3452A>G	chr2.hg19:g.109380447A>G	ENSP00000283195:p.Asn1151Ser	165.0	0.0		131.0	71.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	A	1.687	-0.505119	0.04261	.	.	ENSG00000153201	ENST00000283195	T	0.27890	1.64	5.44	-1.4	0.08968	.	.	.	.	.	T	0.19005	0.0456	L	0.31294	0.92	0.22034	N	0.999406	B	0.02656	0.0	B	0.06405	0.002	T	0.20505	-1.0273	9	0.44086	T	0.13	-1.5985	6.1143	0.20117	0.5948:0.1234:0.2817:0.0	.	1151	P49792	RBP2_HUMAN	S	1151	ENSP00000283195:N1151S	ENSP00000283195:N1151S	N	+	2	0	RANBP2	108746879	0.848000	0.29623	0.108000	0.21378	0.011000	0.07611	0.900000	0.28431	-0.502000	0.06596	-0.472000	0.04984	AAC	.	.		0.433	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109380447	A	G	109380447	3	3	31	1	0	0	0	0	1	0	0	0	13043	43	2	2	3530	2	RANBP2	2	109380447	Missense_Mutation	SNP	A	TCGA-BC-A10Q-01A-11D-A12Z-10	34276079	109380447	133818926	6	3820										
TTN	7273	hgsc.bcm.edu	37	chr2	179412302	179412302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	ctgccaagctgttgtacccgAttcacgcttttcaactatgt	7	12	2	0			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr2:179412302A>G	ENST00000591111.1	-	289	89352	c.89128T>C	c.(89128-89130)Tcg>Ccg	p.S29710P	TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S22478P|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S22411P|TTN_ENST00000460472.2_Missense_Mutation_p.S22286P|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S28783P|TTN_ENST00000589042.1_Missense_Mutation_p.S31351P|RP11-65L3.2_ENST00000603415.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29710	Fibronectin type-III 116. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTTGTACCCGATTCACGCTTT	0.433																																					p.S31351P		Atlas-SNP	.											.	TTN	18412	.	0			c.T94051C						.						100	100	100					2																	179412302		1931	4130	6061	SO:0001583	missense	7273	exon339			TACCCGATTCACG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.89128T>C	chr2.hg19:g.179412302A>G	ENSP00000465570:p.Ser29710Pro	246.0	0.0		166.0	31.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.80	3.223076	0.58668	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	5.92	5.92	0.95590	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65974	0.2743	L	0.41124	1.26	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.68554	-0.5378	9	0.87932	D	0	.	16.3526	0.83220	1.0:0.0:0.0:0.0	.	22286;22411;22478;29710	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	28783;22286;22478;22411;22283	ENSP00000343764:S28783P;ENSP00000434586:S22286P;ENSP00000340554:S22478P;ENSP00000352154:S22411P	ENSP00000340554:S22478P	S	-	1	0	TTN	179120548	1.000000	0.71417	0.984000	0.44739	0.913000	0.54294	9.339000	0.96797	2.255000	0.74692	0.533000	0.62120	TCG	.	.		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179412302	A	G	179412302	3	3	31	1	0	0	0	0	1	0	0	0	16750	333	12	2	14024	2	TTN	2	179412302	Missense_Mutation	SNP	A	TCGA-BC-A10Q-01A-11D-A12Z-10	70031855	179412302	63787071	7	3821										
IDH1	3417	hgsc.bcm.edu	37	chr2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	ttgatccccataagcatgacGacctatgatgataggtttta	8	8	0	4	rs121913499		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000345146.2_Missense_Mutation_p.R132C|IDH1_ENST00000446179.1_Missense_Mutation_p.R132C	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																p.R132C	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	IDH1,NS,haematopoietic_neoplasm,0,788	IDH1	6310	.	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)	c.C394T						.						81	74	76					2																	209113113		2203	4300	6503	SO:0001583	missense	3417	exon4			CATGACGACCTAT		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>T	chr2.hg19:g.209113113G>A	ENSP00000390265:p.Arg132Cys	298.0	0.0		189.0	89.0	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	hg19	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT	.	.		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			A	209113113	G	A	209113113	3	1	31	1	0	0	0	0	1	0	0	0	7503	1058	37	1	878	1	IDH1	2	209113113	Missense_Mutation	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10	29700811	209113113	34086260	8	3822										
CXCR7	57007	hgsc.bcm.edu	37	chr2	237489915	237489915	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	gtctgctggctgccctaccaCgtggcggtgctgctggacat	14	13	1	0			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr2:237489915C>T	ENST00000272928.3	+	2	1117	c.807C>T	c.(805-807)caC>caT	p.H269H		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	269					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)										TGCCCTACCACGTGGCGGTGC	0.607																																					p.H269H		Atlas-SNP	.											.	CXCR7	72	.	0			c.C807T						.						163	137	146					2																	237489915		2203	4300	6503	SO:0001819	synonymous_variant	57007	exon2			CTACCACGTGGCG	BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"CD molecules", "GPCR / Class A : Chemokine receptors : Atypical"	23692	protein-coding gene	gene with protein product		610376	"chemokine orphan receptor 1", "chemokine (C-X-C motif) receptor 7"	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.807C>T	chr2.hg19:g.237489915C>T		141.0	0.0		111.0	23.0	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Silent	SNP	ENST00000272928.3	hg19	CCDS2516.1																																																																																			.	.		0.607	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		T	237489915	C	T	237489915	2	4	31	1	0	0	0	0	0	0	0	1	4098	535	19	1		1	CXCR7	2	237489915	Silent	SNP	C	TCGA-BC-A10Q-01A-11D-A12Z-10	28376802	237489915	5709458	9	3823										
RAF1	5894	hgsc.bcm.edu	37	chr3	12645687	12645687	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	tgctgaccatgtggacattaGgtgtggatgtcgacctctgc	13	9	1	1	rs397516828		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr3:12645687G>C	ENST00000251849.4	-	7	1221	c.782C>G	c.(781-783)cCt>cGt	p.P261R	RAF1_ENST00000534997.1_Missense_Mutation_p.P46R|RAF1_ENST00000442415.2_Missense_Mutation_p.P261R|RAF1_ENST00000542177.1_Missense_Mutation_p.P180R	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	261			P -> A (in NS5; shows in vitro greater kinase activity and enhanced MAPK1 activation than wild-type). {ECO:0000269|PubMed:17603482}.|P -> L (in NS5; shows greater kinase activity and enhanced MAPK1 activation than wild-type). {ECO:0000269|PubMed:17603483}.|P -> S (in NS5; shows in vitro greater kinase activity and enhanced MAPK1 activation than wild-type). {ECO:0000269|PubMed:17603482, ECO:0000269|PubMed:17603483, ECO:0000269|PubMed:20683980}.		activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|death-inducing signaling complex assembly (GO:0071550)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intermediate filament cytoskeleton organization (GO:0045104)|ion transmembrane transport (GO:0034220)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein complex assembly (GO:0031333)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of Rho protein signal transduction (GO:0035023)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.P261R(1)	ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)	GTGGACATTAGGTGTGGATGT	0.522			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.P261R		Atlas-SNP	.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	RAF1,bile_duct,carcinoma,0,1	RAF1	66	.	1	Substitution - Missense(1)	biliary_tract(1)	c.C782G	GRCh37	CM073296	RAF1	M		.						153	136	142					3																	12645687		2203	4300	6503	SO:0001583	missense	5894	exon7	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	ACATTAGGTGTGG	X03484	CCDS2612.1	3p25	2014-09-17	2014-06-26		ENSG00000132155	ENSG00000132155			9829	protein-coding gene	gene with protein product	"C-Raf proto-oncogene, serine/threonine kinase"	164760	"v-raf-1 murine leukemia viral oncogene homolog 1"			1611909	Standard	NM_002880		Approved	Raf-1, c-Raf, CRAF	uc003bxf.4	P04049	OTTHUMG00000129789	ENST00000251849.4:c.782C>G	chr3.hg19:g.12645687G>C	ENSP00000251849:p.Pro261Arg	173.0	0.0		126.0	57.0	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	hg19	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.932839	0.73442	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	T;T;T;T;T	0.78707	-1.04;-1.2;-0.99;-0.9;-1.02	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.89375	0.6697	M	0.81802	2.56	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.996	D	0.89645	0.3865	10	0.87932	D	0	.	20.2602	0.98440	0.0:0.0:1.0:0.0	.	180;46;261	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	R	261;261;140;46;180	ENSP00000251849:P261R;ENSP00000401888:P261R;ENSP00000398591:P140R;ENSP00000441186:P46R;ENSP00000443567:P180R	ENSP00000251849:P261R	P	-	2	0	RAF1	12620687	1.000000	0.71417	0.932000	0.37286	0.271000	0.26615	9.807000	0.99171	2.861000	0.98227	0.655000	0.94253	CCT	.	.		0.522	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		C	12645687	G	C	12645687	3	2	31	1	0	0	0	0	1	0	0	0	13017	1000	35	4	1208	4	RAF1	3	12645687	Missense_Mutation	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10		12645687	185376743	10	3824										
BAP1	8314	hgsc.bcm.edu	37	chr3	52440340	52440348	+	In_Frame_Del	DEL	TGCGGTCGG	TGCGGTCGG	-													0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	cctggcctcatacttgatccTgcggtcgggcaccactgcca					rs138180791		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	TGCGGTCGG	TGCGGTCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr3:52440340_52440348delTGCGGTCGG	ENST00000460680.1	-	9	1175_1183	c.704_712delCCGACCGCA	c.(703-714)cccgaccgcagg>cgg	p.PDR235del	BAP1_ENST00000296288.5_Splice_Site	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TACTTGATCCTGCGGTCGGGCACCACTGC	0.632			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.235_238del	GBM(101;493 1458 7992 21037 25532)	Atlas-INDEL	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.705_713del						.																																			SO:0001651	inframe_deletion	8314	exon9			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.704_712delCCGACCGCA	chr3.hg19:g.52440340_52440348delTGCGGTCGG	ENSP00000417132:p.Pro235_Arg237del	111.0	0.0		37.0	16.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	In_Frame_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.632	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52440348	TGCGGTCGG	-	52440340	7	5	31	1	0	1	0	1	0	0	0	0	1311	1579	55	0	1513	0	BAP1	3	52440340	In_Frame_Del	DEL	TGCGGTCGG	TCGA-BC-A10Q-01A-11D-A12Z-10	39794653	52440340	145582090	11	3825										
ECE2	9718	hgsc.bcm.edu	37	chr3	184001717	184001717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	tgccccaggaccagcggcgcGacgaggagaagatctaccac	13	14	1	2	rs370460271		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr3:184001717G>A	ENST00000402825.3	+	8	1315	c.1315G>A	c.(1315-1317)Gac>Aac	p.D439N	ECE2_ENST00000357474.5_Missense_Mutation_p.D367N|ECE2_ENST00000359140.4_Missense_Mutation_p.D292N|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000404464.3_Missense_Mutation_p.D321N	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	439	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CCAGCGGCGCGACGAGGAGAA	0.637																																					p.D439N		Atlas-SNP	.											.	ECE2	303	.	0			c.G1315A						.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	78	66	70		874,1099,961,1315	4.3	0.3	3		70	0,8600		0,0,4300	no	missense,missense,missense,missense	ECE2	NM_001037324.2,NM_001100120.1,NM_001100121.1,NM_014693.3	23,23,23,23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	292/737,367/812,321/766,439/884	184001717	1,13005	2203	4300	6503	SO:0001583	missense	9718	exon8			CGGCGCGACGAGG	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.1315G>A	chr3.hg19:g.184001717G>A	ENSP00000384223:p.Asp439Asn	168.0	0.0		164.0	30.0	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	hg19	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	G	23.3	4.399116	0.83120	2.27E-4	0.0	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	D;D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76;-1.76	4.3	4.3	0.51218	Peptidase M13 (1);	0.051185	0.85682	D	0.000000	D	0.85195	0.5641	L	0.28740	0.885	0.58432	D	0.999993	D;D;D;B;D;D;D	0.89917	1.0;1.0;0.992;0.349;1.0;1.0;1.0	D;D;P;B;D;D;D	0.87578	0.998;0.998;0.759;0.022;0.996;0.996;0.998	D	0.83595	0.0125	10	0.29301	T	0.29	-15.5575	15.4844	0.75555	0.0:0.0:1.0:0.0	.	41;292;310;321;367;292;439	B4DHU4;B4DKF3;B4DF19;O60344-2;O60344-5;O60344-3;O60344	.;.;.;.;.;.;ECE2_HUMAN	N	439;292;321;367;313	ENSP00000384223:D439N;ENSP00000352052:D292N;ENSP00000385846:D321N;ENSP00000350066:D367N;ENSP00000398444:D313N	ENSP00000350066:D367N	D	+	1	0	ECE2	185484411	1.000000	0.71417	0.299000	0.25016	0.943000	0.58893	9.097000	0.94193	2.222000	0.72286	0.650000	0.86243	GAC	.	.		0.637	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693		A	184001717	G	A	184001717	3	1	31	1	0	0	0	0	1	0	0	0	4892	1058	37	1	1909	1	ECE2	3	184001717	Missense_Mutation	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10	131561377	184001717	14020713	12	3826										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72144303	72144303	+	Frame_Shift_Del	DEL	C	C	-													0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	gtcccagtccccagacaccaCcatccagagaaccgtgcaac							TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr5:72144303delC	ENST00000337273.5	+	2	533	c.107delC	c.(106-108)accfs	p.T36fs	TNPO1_ENST00000513944.1_3'UTR|TNPO1_ENST00000523768.1_Frame_Shift_Del_p.T36fs|TNPO1_ENST00000506351.2_Frame_Shift_Del_p.T28fs|TNPO1_ENST00000447967.2_Frame_Shift_Del_p.T28fs|TNPO1_ENST00000454282.1_Frame_Shift_Del_p.T36fs	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	36					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		CCAGACACCACCATCCAGAGA	0.632																																					p.T36fs		Atlas-Indel,Pindel	.											.	TNPO1	90	.	0			c.106delA						.						88	77	81					5																	72144303		2203	4300	6503	SO:0001589	frameshift_variant	3842	exon2			.	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.107delC	chr5.hg19:g.72144303delC	ENSP00000336712:p.Thr36fs	46.0	0.0		67.0	30.0	NM_002270	B4DVC6|Q92957|Q92975	Frame_Shift_Del	DEL	ENST00000337273.5	hg19	CCDS43329.1																																																																																			.	.		0.632	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		-	72144303	C	-	72144303	7	5	31	1	0	1	0	1	0	0	0	0	16350	507	18	0	113	0	TNPO1	5	72144303	Frame_Shift_Del	DEL	C	TCGA-BC-A10Q-01A-11D-A12Z-10		72144303	108770957	13	3827										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48315045	48315045	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	ggcataagatattaccgtttGtcccaccttcaataaatcaa	5	10	2	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr7:48315045G>T	ENST00000435803.1	+	17	5806	c.5782G>T	c.(5782-5784)Gtc>Ttc	p.V1928F		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1928					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATTACCGTTTGTCCCACCTTC	0.368																																					p.V1928F		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G5782T						.						122	123	123					7																	48315045		1828	4089	5917	SO:0001583	missense	154664	exon17			CCGTTTGTCCCAC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.5782G>T	chr7.hg19:g.48315045G>T	ENSP00000411096:p.Val1928Phe	280.0	0.0		222.0	106.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	4.188	0.033512	0.08101	.	.	ENSG00000179869	ENST00000435803	D	0.88277	-2.36	5.73	-2.97	0.05530	.	1.177540	0.06347	N	0.709239	D	0.82935	0.5145	L	0.57536	1.79	0.09310	N	1	B	0.15473	0.013	B	0.12156	0.007	T	0.63607	-0.6599	9	.	.	.	.	2.6635	0.05033	0.3845:0.1063:0.3891:0.1201	.	1928	Q86UQ4	ABCAD_HUMAN	F	1928	ENSP00000411096:V1928F	.	V	+	1	0	ABCA13	48285591	0.000000	0.05858	0.000000	0.03702	0.057000	0.15508	0.347000	0.20014	-0.457000	0.07033	-0.157000	0.13467	GTC	.	.		0.368	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48315045	G	T	48315045	3	4	31	1	0	0	0	0	1	0	0	0	31	1377	48	3	5677	3	ABCA13	7	48315045	Missense_Mutation	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10		48315045	110823618	14	3828										
TPST1	8460	hgsc.bcm.edu	37	chr7	65705902	65705902	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	gtaataaagatccttttgccCtgaaatctttaacttacctt	4	9	1	2			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr7:65705902C>G	ENST00000304842.5	+	2	915	c.490C>G	c.(490-492)Ctg>Gtg	p.L164V	TPST1_ENST00000480281.1_Intron	NM_003596.3	NP_003587.1	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1	164					inflammatory response (GO:0006954)|peptidyl-tyrosine sulfation (GO:0006478)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)	p.L164V(1)		NS(1)|biliary_tract(1)|breast(1)|kidney(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						TCCTTTTGCCCTGAAATCTTT	0.418																																					p.L164V		Atlas-SNP	.											TPST1,bile_duct,carcinoma,0,1	TPST1	25	.	1	Substitution - Missense(1)	biliary_tract(1)	c.C490G						.						57	58	58					7																	65705902		2203	4300	6503	SO:0001583	missense	8460	exon2			TTTGCCCTGAAAT	AF038009	CCDS5533.1	7q11.21	2012-12-13			ENSG00000169902	ENSG00000169902	2.8.2.20	"Sulfotransferases, membrane-bound"	12020	protein-coding gene	gene with protein product	"transport and golgi organization 13 homolog A (Drosophila)"	603125				9501187	Standard	NM_003596		Approved	TANGO13A	uc003tuw.3	O60507	OTTHUMG00000023871	ENST00000304842.5:c.490C>G	chr7.hg19:g.65705902C>G	ENSP00000302413:p.Leu164Val	126.0	0.0		82.0	32.0	NM_003596	A4D2M0|Q6FGM7	Missense_Mutation	SNP	ENST00000304842.5	hg19	CCDS5533.1	.	.	.	.	.	.	.	.	.	.	C	17.31	3.357593	0.61293	.	.	ENSG00000169902	ENST00000304842;ENST00000544114	T	0.51071	0.72	5.75	4.87	0.63330	Sulfotransferase domain (1);	0.000000	0.64402	D	0.000001	T	0.55593	0.1930	M	0.72353	2.195	0.54753	D	0.999989	P;P	0.47677	0.895;0.899	P;P	0.51297	0.567;0.665	T	0.57429	-0.7813	10	0.48119	T	0.1	-11.2355	9.1999	0.37251	0.0:0.7746:0.0:0.2254	.	164;164	F5H7U7;O60507	.;TPST1_HUMAN	V	164	ENSP00000302413:L164V	ENSP00000302413:L164V	L	+	1	2	TPST1	65343337	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.688000	0.37690	1.416000	0.47057	0.585000	0.79938	CTG	.	.		0.418	TPST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251705.2	NM_003596		G	65705902	C	G	65705902	3	3	31	1	0	0	0	0	1	0	0	0	16442	680	24	4	492	4	TPST1	7	65705902	Missense_Mutation	SNP	C	TCGA-BC-A10Q-01A-11D-A12Z-10	17390857	65705902	93432761	15	3829										
STEAP4	79689	hgsc.bcm.edu	37	chr7	87912274	87912274	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	taaacataagggtagattacGtctcttataacacaatagaa	6	6	1	2	rs370475892		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr7:87912274G>C	ENST00000380079.4	-	3	767	c.666C>G	c.(664-666)gaC>gaG	p.D222E	STEAP4_ENST00000301959.5_Intron|AC003991.3_ENST00000447758.1_RNA|AC003991.3_ENST00000595121.1_RNA|AC003991.3_ENST00000434733.1_RNA|STEAP4_ENST00000414498.1_Missense_Mutation_p.D222E|AC003991.3_ENST00000600908.1_RNA	NM_001205315.1|NM_024636.3	NP_001192244.1|NP_078912.2	Q687X5	STEA4_HUMAN	STEAP family member 4	222					copper ion import (GO:0015677)|fat cell differentiation (GO:0045444)|ferric iron import into cell (GO:0097461)|iron ion homeostasis (GO:0055072)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(3)	15	Esophageal squamous(14;0.00802)					GGTAGATTACGTCTCTTATAA	0.373																																					p.D222E		Atlas-SNP	.											STEAP4,colon,carcinoma,0,2	STEAP4	54	.	0			c.C666G						.						88	85	86					7																	87912274		1883	4108	5991	SO:0001583	missense	79689	exon4			GATTACGTCTCTT	AK026806	CCDS43611.1, CCDS56494.1	7q21.13	2014-01-28	2005-06-15	2005-06-15	ENSG00000127954	ENSG00000127954			21923	protein-coding gene	gene with protein product		611098	"tumor necrosis factor, alpha-induced protein 9"	TNFAIP9		11443137, 15897894	Standard	NM_024636		Approved	FLJ23153, TIARP, STAMP2	uc003ujs.3	Q687X5	OTTHUMG00000153853	ENST00000380079.4:c.666C>G	chr7.hg19:g.87912274G>C	ENSP00000369419:p.Asp222Glu	189.0	0.0		103.0	43.0	NM_001205315	Q658Q9|Q687X4|Q8WWB0|Q9H5R1	Missense_Mutation	SNP	ENST00000380079.4	hg19	CCDS43611.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.158991	0.00028	.	.	ENSG00000127954	ENST00000380079;ENST00000414498	T;T	0.10005	3.27;2.92	6.08	-12.2	0.00006	.	0.488014	0.25154	N	0.032740	T	0.04452	0.0122	N	0.25789	0.76	0.22050	N	0.999399	B;B	0.17038	0.02;0.008	B;B	0.17098	0.017;0.017	T	0.70781	-0.4779	10	0.16896	T	0.51	-0.4377	6.9941	0.24772	0.4511:0.1088:0.3663:0.0738	.	222;222	C9JS50;Q687X5	.;STEA4_HUMAN	E	222	ENSP00000369419:D222E;ENSP00000394399:D222E	ENSP00000369419:D222E	D	-	3	2	STEAP4	87750210	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-6.432000	0.00066	-8.793000	0.00000	-2.933000	0.00087	GAC	.	.		0.373	STEAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332712.4	NM_024636		C	87912274	G	C	87912274	3	2	31	1	0	0	0	0	1	0	0	0	15295	1136	40	4	725	4	STEAP4	7	87912274	Missense_Mutation	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10	22206372	87912274	71226389	16	3830										
DIP2C	22982	hgsc.bcm.edu	37	chr10	460026	460026	+	Frame_Shift_Del	DEL	G	G	-													0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	tctgggccccctccggctttGgttggttcggatccggttgt							TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr10:460026delG	ENST00000280886.6	-	8	971	c.884delC	c.(883-885)ccafs	p.P295fs	DIP2C_ENST00000381496.3_Frame_Shift_Del_p.P188fs	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	295						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CTCCGGCTTTGGTTGGTTCGG	0.542																																					p.P295fs		Atlas-Indel,Pindel	.											.	DIP2C	195	.	0			c.885delA						.						40	44	43					10																	460026		2203	4300	6503	SO:0001589	frameshift_variant	22982	exon8			.	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.884delC	chr10.hg19:g.460026delG	ENSP00000280886:p.Pro295fs	57.0	0.0		68.0	24.0	NM_014974	B4DPI5|Q5SS78	Frame_Shift_Del	DEL	ENST00000280886.6	hg19	CCDS7054.1																																																																																			.	.		0.542	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		-	460026	G	-	460026	7	5	31	1	0	1	0	1	0	0	0	0	4531	1348	47	0	3906	0	DIP2C	10	460026	Frame_Shift_Del	DEL	G	TCGA-BC-A10Q-01A-11D-A12Z-10		460026	135074721	17	3831										
ARID5B	84159	hgsc.bcm.edu	37	chr10	63817024	63817024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	ggtggcactttataaatacaTgaaagaaaggaaaacgccga	10	6	0	2			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr10:63817024T>C	ENST00000279873.7	+	6	1405	c.995T>C	c.(994-996)aTg>aCg	p.M332T	ARID5B_ENST00000309334.5_Missense_Mutation_p.M89T	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	332	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					TATAAATACATGAAAGAAAGG	0.373																																					p.M332T		Atlas-SNP	.											.	ARID5B	125	.	0			c.T995C						.						111	120	117					10																	63817024		2203	4300	6503	SO:0001583	missense	84159	exon6			AATACATGAAAGA	M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.995T>C	chr10.hg19:g.63817024T>C	ENSP00000279873:p.Met332Thr	166.0	0.0		72.0	52.0	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	hg19	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.014883	0.75161	.	.	ENSG00000150347	ENST00000279873;ENST00000309334	T;T	0.66460	-0.21;-0.21	5.96	5.96	0.96718	ARID/BRIGHT DNA-binding domain (5);	0.000000	0.85682	D	0.000000	D	0.86201	0.5876	M	0.92122	3.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89446	0.3727	10	0.87932	D	0	-23.0836	16.4484	0.83959	0.0:0.0:0.0:1.0	.	89;332	Q14865-2;Q14865	.;ARI5B_HUMAN	T	332;89	ENSP00000279873:M332T;ENSP00000308862:M89T	ENSP00000279873:M332T	M	+	2	0	ARID5B	63487030	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.285000	0.76669	0.533000	0.62120	ATG	.	.		0.373	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		C	63817024	T	C	63817024	3	2	31	1	0	0	0	0	1	0	0	0	922	1464	51	2	1017	2	ARID5B	10	63817024	Missense_Mutation	SNP	T	TCGA-BC-A10Q-01A-11D-A12Z-10	63356998	63817024	71717723	18	3832										
MLL	4297	hgsc.bcm.edu	37	chr11	118373507	118373507	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	tccagtgcttcagacttggtGtccaagagctcctctttaaa	8	11	2	2			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr11:118373507G>A	ENST00000389506.5	+	27	6891	c.6891G>A	c.(6889-6891)gtG>gtA	p.V2297V	KMT2A_ENST00000534358.1_Silent_p.V2300V|KMT2A_ENST00000354520.4_Silent_p.V2259V			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2297					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CAGACTTGGTGTCCAAGAGCT	0.443																																					p.V2300V		Atlas-SNP	.											.	MLL	548	.	0			c.G6900A						.						68	67	67					11																	118373507		2200	4296	6496	SO:0001819	synonymous_variant	4297	exon27			CTTGGTGTCCAAG	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.6891G>A	chr11.hg19:g.118373507G>A		103.0	0.0		51.0	13.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.443	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118373507	G	A	118373507	2	1	31	1	0	0	0	0	0	0	0	1	9629	1364	48	3		3	MLL	11	118373507	Silent	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10		118373507	16633009	19	3833										
SNX19	399979	hgsc.bcm.edu	37	chr11	130785772	130785772	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	ttccggctactcaacaggttAttgaggtgacagctcgatcc	10	11	1	2			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr11:130785772A>G	ENST00000265909.4	-	1	632	c.63T>C	c.(61-63)aaT>aaC	p.N21N	SNX19_ENST00000530356.1_Intron|SNX19_ENST00000533214.1_Silent_p.N21N|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000533318.1_Intron|SNX19_ENST00000539184.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	21					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		TCAACAGGTTATTGAGGTGAC	0.562																																					p.N21N		Atlas-SNP	.											.	SNX19	84	.	0			c.T63C						.						72	61	65					11																	130785772		2201	4297	6498	SO:0001819	synonymous_variant	399979	exon1			CAGGTTATTGAGG	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.63T>C	chr11.hg19:g.130785772A>G		108.0	0.0		53.0	11.0	NM_014758	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	hg19	CCDS31721.1																																																																																			.	.		0.562	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		G	130785772	A	G	130785772	2	3	31	1	0	0	0	0	0	0	0	1	14905	446	16	2		2	SNX19	11	130785772	Silent	SNP	A	TCGA-BC-A10Q-01A-11D-A12Z-10	12412265	130785772	4220744	20	3834										
C14orf37	145407	hgsc.bcm.edu	37	chr14	58605153	58605153	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	tcccactcatcacttaaggcAgaggcagctggaacagctgt	10	12	2	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr14:58605153A>T	ENST00000267485.7	-	2	1118	c.924T>A	c.(922-924)tcT>tcA	p.S308S	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	308						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						CACTTAAGGCAGAGGCAGCTG	0.512																																					p.S308S		Atlas-SNP	.											.	C14orf37	87	.	0			c.T924A						.						95	98	97					14																	58605153		2203	4300	6503	SO:0001819	synonymous_variant	145407	exon2			TAAGGCAGAGGCA		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.924T>A	chr14.hg19:g.58605153A>T		227.0	0.0		98.0	45.0	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	hg19	CCDS32089.1																																																																																			.	.		0.512	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		T	58605153	A	T	58605153	2	4	31	1	0	0	0	0	0	0	0	1	1773	175	7	4		4	C14orf37	14	58605153	Silent	SNP	A	TCGA-BC-A10Q-01A-11D-A12Z-10		58605153	48744387	21	3835										
TRPV3	162514	hgsc.bcm.edu	37	chr17	3417232	3417232	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	tacaccgaggtttccgggaaTtcctcgacttcttcaaatgc	8	12	2	0			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr17:3417232T>C	ENST00000576742.1	-	18	2673	c.2352A>G	c.(2350-2352)gaA>gaG	p.E784E	SPATA22_ENST00000541913.1_5'Flank|TRPV3_ENST00000301365.4_Silent_p.E785E	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	784					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	TTTCCGGGAATTCCTCGACTT	0.468																																					p.E785E		Atlas-SNP	.											.	TRPV3	85	.	0			c.A2355G						.						124	113	117					17																	3417232		2203	4300	6503	SO:0001819	synonymous_variant	162514	exon18			CGGGAATTCCTCG	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.2352A>G	chr17.hg19:g.3417232T>C		314.0	1.0		217.0	71.0	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Silent	SNP	ENST00000576742.1	hg19	CCDS11029.1																																																																																			.	.		0.468	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		C	3417232	T	C	3417232	2	2	31	1	0	0	0	0	0	0	0	1	16612	1490	52	2		2	TRPV3	17	3417232	Silent	SNP	T	TCGA-BC-A10Q-01A-11D-A12Z-10		3417232	77777978	22	3836										
ANKFY1	51479	hgsc.bcm.edu	37	chr17	4082167	4082167	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	ctcacctgctcagcagccccGgactctcgtttgagaatggc	10	15	3	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr17:4082167G>A	ENST00000341657.4	-	18	2618	c.2583C>T	c.(2581-2583)tcC>tcT	p.S861S	ANKFY1_ENST00000570535.1_Silent_p.S903S|ANKFY1_ENST00000574367.1_Silent_p.S862S|CYB5D2_ENST00000573984.1_Intron	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	861					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CAGCAGCCCCGGACTCTCGTT	0.537																																					p.S903S		Atlas-SNP	.											.	ANKFY1	81	.	0			c.C2709T						.						69	70	69					17																	4082167		1995	4167	6162	SO:0001819	synonymous_variant	51479	exon18			AGCCCCGGACTCT	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"Zinc fingers, FYVE domain containing", "BTB/POZ domain containing", "Ankyrin repeat domain containing"	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.2583C>T	chr17.hg19:g.4082167G>A		135.0	0.0		85.0	20.0	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Silent	SNP	ENST00000341657.4	hg19																																																																																				.	.		0.537	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		A	4082167	G	A	4082167	2	1	31	1	0	0	0	0	0	0	0	1	626	1103	39	1		1	ANKFY1	17	4082167	Silent	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10	664935	4082167	77113043	23	3837										
MYH2	4620	hgsc.bcm.edu	37	chr17	10432777	10432777	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	gtccatgcgaagtttcttttCttgctccaaggacccttcaa	7	12	3	0			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr17:10432777C>A	ENST00000245503.5	-	25	3523	c.3139G>T	c.(3139-3141)Gaa>Taa	p.E1047*	MYH2_ENST00000397183.2_Nonsense_Mutation_p.E1047*|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1047					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						AGTTTCTTTTCTTGCTCCAAG	0.383																																					p.E1047X		Atlas-SNP	.											.	MYH2	390	.	0			c.G3139T						.						120	114	116					17																	10432777		2203	4300	6503	SO:0001587	stop_gained	4620	exon25			TCTTTTCTTGCTC		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.3139G>T	chr17.hg19:g.10432777C>A	ENSP00000245503:p.Glu1047*	246.0	0.0		136.0	15.0	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Nonsense_Mutation	SNP	ENST00000245503.5	hg19	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	C	43	10.488073	0.99414	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	.	.	.	5.24	5.24	0.73138	.	0.000000	0.39985	U	0.001214	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.0151	0.92890	0.0:1.0:0.0:0.0	.	.	.	.	X	1047	.	ENSP00000245503:E1047X	E	-	1	0	MYH2	10373502	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.346000	0.79347	2.718000	0.92993	0.591000	0.81541	GAA	.	.		0.383	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		A	10432777	C	A	10432777	4	1	31	1	0	0	0	0	0	1	0	0	10044	922	32	3	2750	3	MYH2	17	10432777	Nonsense_Mutation	SNP	C	TCGA-BC-A10Q-01A-11D-A12Z-10	6350610	10432777	70762433	24	3838										
TPM4	7171	hgsc.bcm.edu	37	chr19	16186928	16186928	+	5'Flank	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	gagctggataaatattccgaGgacctgaaggacgcgcagga	14	8	0	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr19:16186928G>C	ENST00000300933.4	+	0	0				TPM4_ENST00000344824.6_Missense_Mutation_p.E62D|TPM4_ENST00000538887.1_Missense_Mutation_p.E62D	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4						cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)		TPM4/ALK(12)	breast(1)|large_intestine(3)	4						AATATTCCGAGGACCTGAAGG	0.627			T	ALK	ALCL																																p.E62D		Atlas-SNP	.		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	.	TPM4	28	.	0			c.G186C						.						30	32	31					19																	16186928		1566	3576	5142	SO:0001631	upstream_gene_variant	7171	exon2			TTCCGAGGACCTG		CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"Tropomyosins"	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134		chr19.hg19:g.16186928G>C	Exception_encountered	194.0	0.0		179.0	95.0	NM_001145160	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Missense_Mutation	SNP	ENST00000300933.4	hg19	CCDS12338.1	.	.	.	.	.	.	.	.	.	.	G	9.144	1.014589	0.19355	.	.	ENSG00000167460	ENST00000344824;ENST00000538887	T;T	0.80033	-1.33;-1.33	3.74	1.45	0.22620	.	0.522755	0.15047	N	0.283506	T	0.69133	0.3077	.	.	.	0.24558	N	0.993989	B	0.11235	0.004	B	0.19148	0.024	T	0.61397	-0.7071	9	0.59425	D	0.04	-9.6471	6.5984	0.22687	0.3507:0.0:0.6493:0.0	.	62	P67936-2	.	D	62	ENSP00000345230:E62D;ENSP00000439135:E62D	ENSP00000345230:E62D	E	+	3	2	TPM4	16047928	0.994000	0.37717	0.029000	0.17559	0.004000	0.04260	1.668000	0.37481	0.776000	0.33473	0.591000	0.81541	GAG	.	.		0.627	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290		C	16186928	G	C	16186928	1	2	31	0	1	0	0	0	0	0	0	0	16423	991	35	4		4	TPM4	19	16186928	5'Flank	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10		16186928	42942055	25	3839										
RYR1	6261	hgsc.bcm.edu	37	chr19	39010081	39010081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	atccgctgctcatccgctacGtggacaacaacaggtcagcg	10	14	2	0			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr19:39010081G>A	ENST00000359596.3	+	67	10246	c.10246G>A	c.(10246-10248)Gtg>Atg	p.V3416M	RYR1_ENST00000360985.3_Missense_Mutation_p.V3416M|RYR1_ENST00000355481.4_Missense_Mutation_p.V3416M			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3416					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CATCCGCTACGTGGACAACAA	0.682																																					p.V3416M		Atlas-SNP	.											.	RYR1	708	.	0			c.G10246A						.						44	34	37					19																	39010081		2202	4298	6500	SO:0001583	missense	6261	exon67			CGCTACGTGGACA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.10246G>A	chr19.hg19:g.39010081G>A	ENSP00000352608:p.Val3416Met	62.0	0.0		46.0	17.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.293923	0.40594	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985;ENST00000538206	D;D;D	0.98028	-4.64;-4.67;-4.65	3.71	3.71	0.42584	.	0.091083	0.42294	U	0.000730	D	0.98661	0.9551	M	0.85542	2.76	0.52099	D	0.99994	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.992	D	0.99655	1.0992	10	0.87932	D	0	.	15.3029	0.73969	0.0:0.0:1.0:0.0	.	3416;3416;3416	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	M	3416;3416;3416;336	ENSP00000352608:V3416M;ENSP00000347667:V3416M;ENSP00000354254:V3416M	ENSP00000347667:V3416M	V	+	1	0	RYR1	43701921	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	9.520000	0.98027	1.921000	0.55644	0.555000	0.69702	GTG	.	.		0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	39010081	G	A	39010081	3	1	31	1	0	0	0	0	1	0	0	0	13783	1145	40	1	10512	1	RYR1	19	39010081	Missense_Mutation	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10	22823153	39010081	20118902	26	3840										
ZNF578	147660	hgsc.bcm.edu	37	chr19	53014251	53014251	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	gcctgaaacacatactcctaAtaactatgggaataattttt	5	8	0	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr19:53014251A>C	ENST00000421239.2	+	6	861	c.617A>C	c.(616-618)aAt>aCt	p.N206T	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	206					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		CATACTCCTAATAACTATGGG	0.368																																					p.N206T		Atlas-SNP	.											.	.	.	.	0			c.A617C						.						66	70	69					19																	53014251		2197	4297	6494	SO:0001583	missense	147660	exon6			CTCCTAATAACTA	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.617A>C	chr19.hg19:g.53014251A>C	ENSP00000459216:p.Asn206Thr	398.0	0.0		233.0	14.0	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	hg19	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	12.33	1.906973	0.33628	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.42	1.42	0.22433	.	.	.	.	.	T	0.29749	0.0743	L	0.53671	1.685	0.09310	N	1	P	0.40180	0.705	B	0.38327	0.271	T	0.12889	-1.0530	7	.	.	.	.	5.7141	0.17950	0.486:0.514:0.0:0.0	.	206	G3V4F6	.	T	206	.	.	N	+	2	0	ZNF578	57706063	0.000000	0.05858	0.004000	0.12327	0.279000	0.26890	0.549000	0.23329	0.660000	0.30964	0.113000	0.15668	AAT	.	.		0.368	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		C	53014251	A	C	53014251	3	2	31	1	0	0	0	0	1	0	0	0	18025	101	4	5	627	5	ZNF578	19	53014251	Missense_Mutation	SNP	A	TCGA-BC-A10Q-01A-11D-A12Z-10	14004170	53014251	6114732	27	3841										
U2AF2	11338	hgsc.bcm.edu	37	chr19	56185355	56185355	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	gaaagccatgcagggcctgaCgggccgcaagttcgccaaca	13	13	0	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr19:56185355C>T	ENST00000308924.4	+	12	1389	c.1349C>T	c.(1348-1350)aCg>aTg	p.T450M	EPN1_ENST00000270460.6_5'Flank|U2AF2_ENST00000590551.1_Missense_Mutation_p.T282M|CTD-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.12_ENST00000585940.1_RNA|U2AF2_ENST00000450554.2_Missense_Mutation_p.T446M|CTD-2537I9.13_ENST00000592252.1_RNA|EPN1_ENST00000411543.2_5'Flank|EPN1_ENST00000085079.7_5'Flank			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	450	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T450M(1)		biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CAGGGCCTGACGGGCCGCAAG	0.577																																					p.T450M		Atlas-SNP	.											U2AF2,bile_duct,carcinoma,0,1	U2AF2	62	.	1	Substitution - Missense(1)	biliary_tract(1)	c.C1349T						.						89	84	86					19																	56185355		2203	4300	6503	SO:0001583	missense	11338	exon12			GCCTGACGGGCCG	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"RNA binding motif (RRM) containing"	23156	protein-coding gene	gene with protein product	"U2 small nuclear ribonucleoprotein auxiliary factor (65kD)", "splicing factor U2AF 65 kD subunit", "U2 snRNP auxiliary factor large subunit"	191318	"U2 (RNU2) small nuclear RNA auxiliary factor 2"			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.1349C>T	chr19.hg19:g.56185355C>T	ENSP00000307863:p.Thr450Met	123.0	0.0		106.0	22.0	NM_007279	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	hg19	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373101	0.82573	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	T;T	0.16324	2.35;2.35	4.42	4.42	0.53409	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	U	0.000000	T	0.40619	0.1124	M	0.71871	2.18	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72625	0.978;0.943	T	0.24190	-1.0167	10	0.42905	T	0.14	-22.4265	16.161	0.81712	0.0:1.0:0.0:0.0	.	450;446	P26368;P26368-2	U2AF2_HUMAN;.	M	450;446	ENSP00000307863:T450M;ENSP00000388475:T446M	ENSP00000307863:T450M	T	+	2	0	U2AF2	60877167	1.000000	0.71417	0.951000	0.38953	0.990000	0.78478	5.200000	0.65158	2.173000	0.68751	0.478000	0.44815	ACG	.	.		0.577	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		T	56185355	C	T	56185355	3	4	31	1	0	0	0	0	1	0	0	0	16838	536	19	1	1395	1	U2AF2	19	56185355	Missense_Mutation	SNP	C	TCGA-BC-A10Q-01A-11D-A12Z-10	3171104	56185355	2943628	28	3842										
ZMYND8	23613	hgsc.bcm.edu	37	chr20	45920579	45920579	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	tccattggatggaagatgtaTtccgcatagtcagggtgctg	13	7	1	1			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr20:45920579T>C	ENST00000311275.7	-	6	814	c.561A>G	c.(559-561)gaA>gaG	p.E187E	ZMYND8_ENST00000360911.3_Silent_p.E182E|ZMYND8_ENST00000396281.4_Silent_p.E187E|ZMYND8_ENST00000446994.2_Silent_p.E124E|ZMYND8_ENST00000536340.1_Silent_p.E214E|ZMYND8_ENST00000461685.1_Silent_p.E207E|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000355972.4_Silent_p.E187E|ZMYND8_ENST00000471951.2_Silent_p.E207E|ZMYND8_ENST00000352431.2_Silent_p.E207E|ZMYND8_ENST00000540497.1_Silent_p.E182E|ZMYND8_ENST00000262975.4_Silent_p.E187E|ZMYND8_ENST00000372023.3_Silent_p.E182E|ZMYND8_ENST00000458360.2_Silent_p.E182E	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	187	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			GGAAGATGTATTCCGCATAGT	0.463																																					p.E207E		Atlas-SNP	.											.	ZMYND8	166	.	0			c.A621G						.						125	104	111					20																	45920579		2203	4300	6503	SO:0001819	synonymous_variant	23613	exon6			GATGTATTCCGCA	U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"Zinc fingers, MYND-type", "Zinc fingers, PHD-type"	9397	protein-coding gene	gene with protein product		615713	"protein kinase C binding protein 1"	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.561A>G	chr20.hg19:g.45920579T>C		144.0	0.0		82.0	31.0	NM_183047	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Silent	SNP	ENST00000311275.7	hg19		.	.	.	.	.	.	.	.	.	.	T	10.26	1.299902	0.23650	.	.	ENSG00000101040	ENST00000467200	.	.	.	5.52	-2.29	0.06805	.	.	.	.	.	T	0.57095	0.2030	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52472	-0.8571	4	.	.	.	-26.6872	11.2096	0.48790	0.0:0.3859:0.0:0.6141	.	.	.	.	V	114	.	.	I	-	1	0	ZMYND8	45353986	0.560000	0.26570	0.641000	0.29422	0.970000	0.65996	-0.200000	0.09478	-0.798000	0.04444	-0.256000	0.11100	ATA	.	.		0.463	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047		C	45920579	T	C	45920579	2	2	31	1	0	0	0	0	0	0	0	1	17726	1490	52	2		2	ZMYND8	20	45920579	Silent	SNP	T	TCGA-BC-A10Q-01A-11D-A12Z-10		45920579	17104941	29	3843										
PKNOX1	5316	hgsc.bcm.edu	37	chr21	44450022	44450022	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	gctgttgtcaccatcaccacGcccgtgaacatgaacgtgga	10	13	2	2	rs533645525		TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chr21:44450022G>A	ENST00000291547.5	+	11	1333	c.1122G>A	c.(1120-1122)acG>acA	p.T374T	PKNOX1_ENST00000432907.2_Silent_p.T257T	NM_004571.3	NP_004562.2	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	374					angiogenesis (GO:0001525)|camera-type eye development (GO:0043010)|erythrocyte differentiation (GO:0030218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|prostate(1)	22						CCATCACCACGCCCGTGAACA	0.527													G|||	1	0.000199681	8e-04	0	5008	,	,		17474	0		0	False		,,,				2504	0				p.T374T		Atlas-SNP	.											.	PKNOX1	40	.	0			c.G1122A						.						139	125	130					21																	44450022		2203	4300	6503	SO:0001819	synonymous_variant	5316	exon11			CACCACGCCCGTG		CCDS13692.1, CCDS68211.1	21q22.3	2011-06-20			ENSG00000160199	ENSG00000160199		"Homeoboxes / TALE class"	9022	protein-coding gene	gene with protein product		602100				9479508	Standard	NM_001286258		Approved	PREP1	uc002zcq.1	P55347	OTTHUMG00000086833	ENST00000291547.5:c.1122G>A	chr21.hg19:g.44450022G>A		152.0	0.0		97.0	40.0	NM_004571	O00528|Q8IWT7	Silent	SNP	ENST00000291547.5	hg19	CCDS13692.1																																																																																			.	.		0.527	PKNOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195520.3			A	44450022	G	A	44450022	2	1	31	1	0	0	0	0	0	0	0	1	11991	1074	38	1		1	PKNOX1	21	44450022	Silent	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10		44450022	3679873	30	3844										
PHKA2	5256	hgsc.bcm.edu	37	chrX	18919622	18919622	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	cctgtttcatttcactcctcAgtctgttaatgccactcctc	4	15	4	0			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chrX:18919622A>T	ENST00000379942.4	-	27	3673	c.3008T>A	c.(3007-3009)cTg>cAg	p.L1003Q		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	1003					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.L1003Q(1)		NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					TTCACTCCTCAGTCTGTTAAT	0.552																																					p.L1003Q		Atlas-SNP	.											.	PHKA2	122	.	1	Substitution - Missense(1)	biliary_tract(1)	c.T3008A						.						201	150	167					X																	18919622		2203	4300	6503	SO:0001583	missense	5256	exon27			CTCCTCAGTCTGT		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.3008T>A	chrX.hg19:g.18919622A>T	ENSP00000369274:p.Leu1003Gln	315.0	0.0		210.0	101.0	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	hg19	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	A	19.44	3.828428	0.71143	.	.	ENSG00000044446	ENST00000379942	D	0.92911	-3.13	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.93262	0.7853	M	0.77313	2.365	0.80722	D	1	P	0.51933	0.949	P	0.46885	0.53	D	0.93655	0.6976	10	0.62326	D	0.03	-13.6036	15.4998	0.75687	1.0:0.0:0.0:0.0	.	1003	P46019	KPB2_HUMAN	Q	1003	ENSP00000369274:L1003Q	ENSP00000369274:L1003Q	L	-	2	0	PHKA2	18829543	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	8.854000	0.92228	2.044000	0.60594	0.486000	0.48141	CTG	.	.		0.552	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		T	18919622	A	T	18919622	3	4	31	1	0	0	0	0	1	0	0	0	11853	188	7	4	727	4	PHKA2	23	18919622	Missense_Mutation	SNP	A	TCGA-BC-A10Q-01A-11D-A12Z-10		18919622	136350938	31	3845										
BMP15	9210	hgsc.bcm.edu	37	chrX	50653812	50653812	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	cctcagtattcttagaattcTttttctttgtgaactcgtgc	6	9	4	2			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chrX:50653812T>G	ENST00000252677.3	+	1	29	c.29T>G	c.(28-30)cTt>cGt	p.L10R		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	10					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					CTTAGAATTCTTTTTCTTTGT	0.498																																					p.L10R		Atlas-SNP	.											.	BMP15	62	.	0			c.T29G						.						48	41	43					X																	50653812		2202	4299	6501	SO:0001583	missense	9210	exon1			GAATTCTTTTTCT	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"Bone morphogenetic proteins"	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.29T>G	chrX.hg19:g.50653812T>G	ENSP00000252677:p.Leu10Arg	269.0	0.0		236.0	47.0	NM_005448	Q17RM6|Q5JST1|Q9UMS1	Missense_Mutation	SNP	ENST00000252677.3	hg19	CCDS14334.1	.	.	.	.	.	.	.	.	.	.	t	10.94	1.491958	0.26774	.	.	ENSG00000130385	ENST00000252677	D	0.84070	-1.8	4.48	4.48	0.54585	.	1.158760	0.06236	N	0.689464	D	0.87653	0.6231	L	0.47716	1.5	0.09310	N	1	D	0.64830	0.994	D	0.62955	0.909	T	0.73770	-0.3878	10	0.72032	D	0.01	.	9.7051	0.40211	0.0:0.0:0.0:1.0	.	10	O95972	BMP15_HUMAN	R	10	ENSP00000252677:L10R	ENSP00000252677:L10R	L	+	2	0	BMP15	50670552	0.725000	0.28048	0.024000	0.17045	0.098000	0.18820	2.533000	0.45667	1.750000	0.51863	0.441000	0.28932	CTT	.	.		0.498	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448		G	50653812	T	G	50653812	3	3	31	1	0	0	0	0	1	0	0	0	1458	1609	56	5	31	5	BMP15	23	50653812	Missense_Mutation	SNP	T	TCGA-BC-A10Q-01A-11D-A12Z-10	31734190	50653812	104616748	32	3846										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128315	83128316	+	Frame_Shift_Del	DEL	AG	AG	-													0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	aaattgttcacaaaaagataAgaaagattcaaagaattcca							TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chrX:83128315_83128316delAG	ENST00000329312.4	+	4	636_637	c.599_600delAG	c.(598-600)aagfs	p.K201fs		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	201					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						CAAAAAGATAAGAAAGATTCAA	0.322																																					p.200_200del		Atlas-INDEL	.											.	CYLC1	272	.	0			c.598_599del						.																																			SO:0001589	frameshift_variant	1538	exon4			.	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.599_600delAG	chrX.hg19:g.83128315_83128316delAG	ENSP00000331556:p.Lys201fs	428.0	0.0		250.0	79.0	NM_021118	A0AVQ8|Q5JQQ9	Frame_Shift_Del	DEL	ENST00000329312.4	hg19	CCDS35341.1																																																																																			.	.		0.322	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		-	83128316	AG	-	83128315	7	5	31	1	0	1	0	1	0	0	0	0	4143	72	3	0	613	0	CYLC1	23	83128315	Frame_Shift_Del	DEL	AG	TCGA-BC-A10Q-01A-11D-A12Z-10	32474503	83128315	72142245	33	3847										
HTATSF1	27336	hgsc.bcm.edu	37	chrX	135593729	135593729	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	ttgaagatgacggctctgaaAaagtgttagatgaggaaggc	14	4	1	6			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chrX:135593729A>C	ENST00000218364.4	+	9	1999	c.1825A>C	c.(1825-1827)Aaa>Caa	p.K609Q	HTATSF1_ENST00000535601.1_Missense_Mutation_p.K609Q	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	609	Asp/Glu-rich (acidic).|Mediates interaction with the P-TEFb complex.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K609Q(1)		NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					CGGCTCTGAAAAAGTGTTAGA	0.383																																					p.K609Q		Atlas-SNP	.											.	HTATSF1	66	.	1	Substitution - Missense(1)	biliary_tract(1)	c.A1825C						.						69	74	72					X																	135593729		2202	4295	6497	SO:0001583	missense	27336	exon10			TCTGAAAAAGTGT	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"RNA binding motif (RRM) containing"	5276	protein-coding gene	gene with protein product		300346	"HIV TAT specific factor 1"			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.1825A>C	chrX.hg19:g.135593729A>C	ENSP00000218364:p.Lys609Gln	244.0	0.0		127.0	40.0	NM_001163280	D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	ENST00000218364.4	hg19	CCDS14657.1	.	.	.	.	.	.	.	.	.	.	A	12.22	1.873801	0.33069	.	.	ENSG00000102241	ENST00000535601;ENST00000218364;ENST00000415377	T;T	0.04234	3.67;3.67	4.64	3.48	0.39840	.	0.908123	0.09691	N	0.768412	T	0.03220	0.0094	N	0.08118	0	0.09310	N	1	B	0.30793	0.295	B	0.30029	0.11	T	0.44847	-0.9301	10	0.72032	D	0.01	-12.3679	7.6365	0.28270	0.8971:0.0:0.1029:0.0	.	609	O43719	HTSF1_HUMAN	Q	609	ENSP00000442699:K609Q;ENSP00000218364:K609Q	ENSP00000218364:K609Q	K	+	1	0	HTATSF1	135421395	0.002000	0.14202	0.001000	0.08648	0.964000	0.63967	1.353000	0.34045	0.889000	0.36185	0.425000	0.28330	AAA	.	.		0.383	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		C	135593729	A	C	135593729	3	2	31	1	0	0	0	0	1	0	0	0	7442	15	1	5	1859	5	HTATSF1	23	135593729	Missense_Mutation	SNP	A	TCGA-BC-A10Q-01A-11D-A12Z-10	52465414	135593729	19676831	34	3848										
DUSP9	1852	hgsc.bcm.edu	37	chrX	152914788	152914788	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	1	1	0.433286516853933	0	0.577715355805243	1	1	0	cggtgcccggtccagtgcccGtggtggggttgggcagcctg	19	12	0	0			TCGA-BC-A10Q-01A-11D-A12Z-10	TCGA-BC-A10Q-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f7e9eed5-7a0b-4b2d-bea3-fd8c42a3b90e	454f62ca-7688-48e6-8a59-0149d11f1fe3	g.chrX:152914788G>A	ENST00000342782.3	+	3	740	c.475G>A	c.(475-477)Gtg>Atg	p.V159M	DUSP9_ENST00000370167.4_Missense_Mutation_p.V159M			Q99956	DUS9_HUMAN	dual specificity phosphatase 9	159					inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCCAGTGCCCGTGGTGGGGTT	0.677																																					p.V159M		Atlas-SNP	.											.	DUSP9	41	.	0			c.G475A						.						26	26	26					X																	152914788		2202	4292	6494	SO:0001583	missense	1852	exon3			GTGCCCGTGGTGG	Y08302	CCDS14724.1	Xq28	2011-06-09			ENSG00000130829	ENSG00000130829		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3076	protein-coding gene	gene with protein product	"map kinase phosphatase 4"	300134				9030581, 9286695	Standard	NM_001395		Approved	MKP-4, MKP4	uc004fhx.4	Q99956	OTTHUMG00000024211	ENST00000342782.3:c.475G>A	chrX.hg19:g.152914788G>A	ENSP00000345853:p.Val159Met	117.0	0.0		100.0	12.0	NM_001395	D3DWU5	Missense_Mutation	SNP	ENST00000342782.3	hg19	CCDS14724.1	.	.	.	.	.	.	.	.	.	.	g	14.34	2.505811	0.44558	.	.	ENSG00000130829	ENST00000370167;ENST00000342782	T;T	0.44881	0.91;0.91	5.13	5.13	0.70059	.	0.638340	0.12977	N	0.423652	T	0.48677	0.1513	M	0.70595	2.14	0.48511	D	0.99966	P	0.47677	0.899	B	0.41988	0.372	T	0.57458	-0.7808	10	0.72032	D	0.01	.	16.4389	0.83894	0.0:0.0:1.0:0.0	.	159	Q99956	DUS9_HUMAN	M	159	ENSP00000359186:V159M;ENSP00000345853:V159M	ENSP00000345853:V159M	V	+	1	0	DUSP9	152567982	1.000000	0.71417	0.861000	0.33841	0.024000	0.10985	9.585000	0.98223	2.135000	0.66039	0.529000	0.55759	GTG	.	.		0.677	DUSP9-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061022.3	NM_001395		A	152914788	G	A	152914788	3	1	31	1	0	0	0	0	1	0	0	0	4834	1145	40	1	481	1	DUSP9	23	152914788	Missense_Mutation	SNP	G	TCGA-BC-A10Q-01A-11D-A12Z-10	17321059	152914788	2355772	35	3849										
INADL	10207	hgsc.bcm.edu	37	chr1	62330235	62330235	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	taatgaaccatccgagtctcAagaggcaagaaccgggagga	12	9	1	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr1:62330235A>C	ENST00000371158.2	+	20	2879	c.2765A>C	c.(2764-2766)cAa>cCa	p.Q922P	INADL_ENST00000316485.6_Missense_Mutation_p.Q922P	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	922					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TCCGAGTCTCAAGAGGCAAGA	0.478																																					p.Q922P		Atlas-SNP	.											.	INADL	179	.	0			c.A2765C						.						100	105	103					1																	62330235		2203	4300	6503	SO:0001583	missense	10207	exon20			AGTCTCAAGAGGC	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.2765A>C	chr1.hg19:g.62330235A>C	ENSP00000360200:p.Gln922Pro	83.0	0.0		35.0	19.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	9.052	0.992376	0.18966	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.12984	2.76;2.63	5.18	-4.18	0.03846	.	1.149560	0.06529	N	0.741001	T	0.12603	0.0306	L	0.57536	1.79	0.09310	N	1	B;B;B	0.10296	0.003;0.001;0.003	B;B;B	0.08055	0.003;0.001;0.003	T	0.36601	-0.9741	10	0.30078	T	0.28	.	6.9089	0.24325	0.2472:0.5722:0.0687:0.1119	.	922;922;922	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	P	922	ENSP00000360200:Q922P;ENSP00000326199:Q922P	ENSP00000255202:Q922P	Q	+	2	0	INADL	62102823	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.038000	0.13862	-0.974000	0.03550	-0.501000	0.04562	CAA	.	.		0.478	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		C	62330235	A	C	62330235	3	2	32	1	0	0	0	0	1	0	0	0	7740	130	5	5	2839	5	INADL	1	62330235	Missense_Mutation	SNP	A	TCGA-BC-A10R-01A-11D-A12Z-10		62330235	186920386	1	3850										
PTPN22	26191	hgsc.bcm.edu	37	chr1	114380695	114380695	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tgatttggtccgtgttattgGcacctttgaattaaaatatc	8	6	0	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr1:114380695G>T	ENST00000359785.5	-	13	1462	c.1327C>A	c.(1327-1329)Cca>Aca	p.P443T	PTPN22_ENST00000528414.1_Missense_Mutation_p.P388T|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000420377.2_Missense_Mutation_p.P443T|PTPN22_ENST00000525799.1_Missense_Mutation_p.P316T|PTPN22_ENST00000538253.1_Missense_Mutation_p.P199T	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	443					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CGTGTTATTGGCACCTTTGAA	0.383																																					p.P443T		Atlas-SNP	.											.	PTPN22	90	.	0			c.C1327A						.						82	83	83					1																	114380695		2203	4300	6503	SO:0001583	missense	26191	exon13			TTATTGGCACCTT	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.1327C>A	chr1.hg19:g.114380695G>T	ENSP00000352833:p.Pro443Thr	129.0	0.0		38.0	14.0	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	hg19	CCDS863.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.970819	0.53614	.	.	ENSG00000134242	ENST00000359785;ENST00000528414;ENST00000538253;ENST00000420377;ENST00000525799;ENST00000354605	T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7	5.82	3.91	0.45181	.	0.193747	0.37012	N	0.002281	T	0.30103	0.0754	M	0.71581	2.175	0.19300	N	0.999976	D;D;D;D;D;D	0.89917	1.0;0.999;0.958;0.972;0.99;0.991	D;D;P;P;P;P	0.91635	0.999;0.952;0.776;0.573;0.888;0.856	T	0.11717	-1.0576	10	0.40728	T	0.16	.	8.098	0.30840	0.0803:0.0:0.7616:0.1582	.	199;316;443;388;443;443	F5H2S8;E9PPI1;E9PMT0;E9PLD8;G5E984;Q9Y2R2	.;.;.;.;.;PTN22_HUMAN	T	443;388;199;443;316;443	ENSP00000352833:P443T;ENSP00000435176:P388T;ENSP00000439372:P199T;ENSP00000388229:P443T;ENSP00000432674:P316T	ENSP00000346621:P443T	P	-	1	0	PTPN22	114182218	0.954000	0.32549	0.007000	0.13788	0.852000	0.48524	2.823000	0.48081	0.770000	0.33336	0.655000	0.94253	CCA	.	.		0.383	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		T	114380695	G	T	114380695	3	4	32	1	0	0	0	0	1	0	0	0	12802	1203	42	3	1155	3	PTPN22	1	114380695	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	52050460	114380695	134869926	2	3851										
GJA8	2703	hgsc.bcm.edu	37	chr1	147380863	147380863	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ccattgctgtctcctccatcCagaaagccaagggctatcag	8	14	2	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr1:147380863C>T	ENST00000369235.1	+	1	781	c.781C>T	c.(781-783)Cag>Tag	p.Q261*	GJA8_ENST00000240986.4_Nonsense_Mutation_p.Q261*			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	261					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					CTCCTCCATCCAGAAAGCCAA	0.567																																					p.Q261X	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											.	GJA8	108	.	0			c.C781T						.						50	52	52					1																	147380863		2203	4300	6503	SO:0001587	stop_gained	2703	exon2			TCCATCCAGAAAG	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.781C>T	chr1.hg19:g.147380863C>T	ENSP00000358238:p.Gln261*	74.0	0.0		66.0	31.0	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Nonsense_Mutation	SNP	ENST00000369235.1	hg19	CCDS30834.1	.	.	.	.	.	.	.	.	.	.	c	34	5.391246	0.95988	.	.	ENSG00000121634	ENST00000240986;ENST00000369235	.	.	.	4.4	4.4	0.53042	.	0.501871	0.14206	U	0.334393	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	17.1387	0.86747	0.0:1.0:0.0:0.0	.	.	.	.	X	261	.	ENSP00000240986:Q261X	Q	+	1	0	GJA8	145847487	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.798000	0.69095	2.267000	0.75376	0.313000	0.20887	CAG	.	.		0.567	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		T	147380863	C	T	147380863	4	4	32	1	0	0	0	0	0	1	0	0	6413	595	21	3	783	3	GJA8	1	147380863	Nonsense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	33000168	147380863	101869758	3	3852										
GON4L	54856	hgsc.bcm.edu	37	chr1	155723018	155723018	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	aaacaggcatctctccctttCtggtggtcctgacagtcctg	9	13	2	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr1:155723018C>T	ENST00000368331.1	-	29	5867	c.5819G>A	c.(5818-5820)aGa>aAa	p.R1940K	GON4L_ENST00000271883.5_Missense_Mutation_p.R1940K|GON4L_ENST00000437809.1_Missense_Mutation_p.R1940K	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1940					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					CTCTCCCTTTCTGGTGGTCCT	0.567																																					p.R1940K		Atlas-SNP	.											.	GON4L	392	.	0			c.G5819A						.						89	98	95					1																	155723018		2070	4196	6266	SO:0001583	missense	54856	exon29			CCCTTTCTGGTGG	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.5819G>A	chr1.hg19:g.155723018C>T	ENSP00000357315:p.Arg1940Lys	264.0	0.0		223.0	28.0	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.91	1.780102	0.31502	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883	T;T;T	0.12879	2.64;2.64;2.64	5.32	4.41	0.53225	.	0.374424	0.25708	N	0.028831	T	0.03564	0.0102	L	0.29908	0.895	0.09310	N	1	B;B	0.29988	0.172;0.264	B;B	0.31101	0.058;0.124	T	0.37197	-0.9716	10	0.19147	T	0.46	.	11.8523	0.52417	0.0:0.9191:0.0:0.0809	.	1940;1940	Q3T8J9;Q3T8J9-3	GON4L_HUMAN;.	K	1940	ENSP00000396117:R1940K;ENSP00000357315:R1940K;ENSP00000271883:R1940K	ENSP00000271883:R1940K	R	-	2	0	GON4L	153989642	0.051000	0.20477	0.026000	0.17262	0.260000	0.26232	1.482000	0.35486	1.479000	0.48272	0.650000	0.86243	AGA	.	.		0.567	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		T	155723018	C	T	155723018	3	4	32	1	0	0	0	0	1	0	0	0	6580	913	32	3	919	3	GON4L	1	155723018	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	8342155	155723018	93527603	4	3853										
DUSP10	11221	hgsc.bcm.edu	37	chr1	221912367	221912367	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	atcactcggcttggttcattGgtattctcatcataaactat	6	9	4	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr1:221912367G>A	ENST00000366899.3	-	2	958	c.720C>T	c.(718-720)acC>acT	p.T240T	DUSP10_ENST00000544095.1_5'Flank|DUSP10_ENST00000468085.1_5'Flank|DUSP10_ENST00000323825.3_Intron	NM_007207.4	NP_009138.1	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10	240	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|oligodendrocyte differentiation (GO:0048709)|protein dephosphorylation (GO:0006470)|regulation of adaptive immune response (GO:0002819)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	MAP kinase phosphatase activity (GO:0033549)|MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(131;0.0103)		TTGGTTCATTGGTATTCTCAT	0.458																																					p.T240T		Atlas-SNP	.											.	DUSP10	64	.	0			c.C720T						.						129	134	132					1																	221912367		2203	4300	6503	SO:0001819	synonymous_variant	11221	exon2			TTCATTGGTATTC	AB026436	CCDS1528.1	1q41	2011-06-09			ENSG00000143507	ENSG00000143507		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3065	protein-coding gene	gene with protein product		608867				10391943, 10597297	Standard	NM_007207		Approved	MKP-5, MKP5	uc001hmy.2	Q9Y6W6	OTTHUMG00000037269	ENST00000366899.3:c.720C>T	chr1.hg19:g.221912367G>A		234.0	0.0		156.0	19.0	NM_007207	D3DTB4|Q6GSI4|Q9H9Z5	Silent	SNP	ENST00000366899.3	hg19	CCDS1528.1																																																																																			.	.		0.458	DUSP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090716.1	NM_007207		A	221912367	G	A	221912367	2	1	32	1	0	0	0	0	0	0	0	1	4812	1335	47	3		3	DUSP10	1	221912367	Silent	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	66189349	221912367	27338254	5	3854										
RYR2	6262	hgsc.bcm.edu	37	chr1	237948157	237948157	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tctttcggacatctttggccTggatctgaagagagaaggag	13	7	3	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr1:237948157T>A	ENST00000366574.2	+	90	13462	c.13145T>A	c.(13144-13146)cTg>cAg	p.L4382Q	RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Missense_Mutation_p.L4366Q|RYR2_ENST00000360064.6_Missense_Mutation_p.L4388Q	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4382					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATCTTTGGCCTGGATCTGAAG	0.537																																					p.L4382Q		Atlas-SNP	.											.	RYR2	1273	.	0			c.T13145A						.						43	42	42					1																	237948157		1937	4131	6068	SO:0001583	missense	6262	exon90			TTGGCCTGGATCT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.13145T>A	chr1.hg19:g.237948157T>A	ENSP00000355533:p.Leu4382Gln	84.0	0.0		77.0	23.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	17.27	3.348097	0.61183	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.95001	-3.58;-3.58;-3.58	5.56	5.56	0.83823	Ryanodine Receptor TM 4-6 (1);	0.241031	0.26582	N	0.023565	D	0.95056	0.8399	L	0.29908	0.895	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.69824	0.958;0.966	D	0.95781	0.8817	10	0.66056	D	0.02	-10.7165	15.7141	0.77655	0.0:0.0:0.0:1.0	.	1356;4382	B4DGV4;Q92736	.;RYR2_HUMAN	Q	4382;4388;4366;1356	ENSP00000355533:L4382Q;ENSP00000353174:L4388Q;ENSP00000443798:L4366Q	ENSP00000353174:L4388Q	L	+	2	0	RYR2	236014780	1.000000	0.71417	1.000000	0.80357	0.510000	0.34073	7.842000	0.86851	2.112000	0.64535	0.533000	0.62120	CTG	.	.		0.537	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237948157	T	A	237948157	3	1	32	1	0	0	0	0	1	0	0	0	13784	1580	55	4	13503	4	RYR2	1	237948157	Missense_Mutation	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10	16035790	237948157	11302464	6	3855										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525606	248525606	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gtgtcctcatgctcctcatcCctgtggtgatcatttcaagc	8	13	4	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr1:248525606C>A	ENST00000366475.1	+	1	724	c.724C>A	c.(724-726)Cct>Act	p.P242T		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	242						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCTCCTCATCCCTGTGGTGAT	0.488																																					p.P242T		Atlas-SNP	.											.	OR2T4	126	.	0			c.C724A						.						159	150	153					1																	248525606		2203	4300	6503	SO:0001583	missense	127074	exon1			CTCATCCCTGTGG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.724C>A	chr1.hg19:g.248525606C>A	ENSP00000355431:p.Pro242Thr	1155.0	0.0		1004.0	67.0	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	C	8.392	0.839896	0.16891	.	.	ENSG00000196944	ENST00000366475	T	0.56103	0.48	3.09	2.12	0.27331	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000279	T	0.56187	0.1968	L	0.52759	1.655	0.09310	N	1	D	0.58620	0.983	P	0.58013	0.831	T	0.43343	-0.9397	10	0.87932	D	0	.	7.3606	0.26744	0.0:0.7778:0.0:0.2222	.	242	Q8NH00	OR2T4_HUMAN	T	242	ENSP00000355431:P242T	ENSP00000355431:P242T	P	+	1	0	OR2T4	246592229	0.000000	0.05858	0.028000	0.17463	0.130000	0.20726	-1.205000	0.03014	1.543000	0.49345	0.585000	0.79938	CCT	.	.		0.488	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		A	248525606	C	A	248525606	3	1	32	1	0	0	0	0	1	0	0	0	11036	623	22	3	726	3	OR2T4	1	248525606	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	10577449	248525606	725015	7	3856										
OR2T6	254879	hgsc.bcm.edu	37	chr1	248551626	248551626	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gggaggaagaaggcctttgcCacctgctcttcacacatgat	11	11	2	2	rs148186126		TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr1:248551626C>T	ENST00000355728.2	+	1	717	c.717C>T	c.(715-717)gcC>gcT	p.A239A		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A239A(1)		endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGGCCTTTGCCACCTGCTCTT	0.507																																					p.A239A		Atlas-SNP	.											OR2T6,arm,malignant_melanoma,0,1	OR2T6	101	.	1	Substitution - coding silent(1)	skin(1)	c.C717T						.						271	226	242					1																	248551626		2203	4300	6503	SO:0001819	synonymous_variant	254879	exon1			CTTTGCCACCTGC	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"GPCR / Class A : Olfactory receptors"	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.717C>T	chr1.hg19:g.248551626C>T		307.0	0.0		310.0	86.0	NM_001005471	A6NE36	Silent	SNP	ENST00000355728.2	hg19	CCDS31114.1																																																																																			.	.		0.507	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471		T	248551626	C	T	248551626	2	4	32	1	0	0	0	0	0	0	0	1	11038	581	21	3		3	OR2T6	1	248551626	Silent	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	26020	248551626	698995	8	3857										
OR2G6	391211	hgsc.bcm.edu	37	chr1	248684959	248684959	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gcaggaaaaatggaggaaacCaacaacagctctgaaaaggg	12	7	1	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr1:248684959C>T	ENST00000343414.4	+	1	44	c.12C>T	c.(10-12)acC>acT	p.T4T		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T4T(1)		NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGGAGGAAACCAACAACAGCT	0.398																																					p.T4T		Atlas-SNP	.											OR2G6,NS,carcinoma,0,1	OR2G6	124	.	1	Substitution - coding silent(1)	lung(1)	c.C12T						.						126	119	122					1																	248684959		2203	4300	6503	SO:0001819	synonymous_variant	391211	exon1			GGAAACCAACAAC		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"GPCR / Class A : Olfactory receptors"	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.12C>T	chr1.hg19:g.248684959C>T		250.0	0.0		215.0	74.0	NM_001013355	B2RP33	Silent	SNP	ENST00000343414.4	hg19	CCDS31119.1																																																																																			.	.		0.398	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842		T	248684959	C	T	248684959	2	4	32	1	0	0	0	0	0	0	0	1	11009	581	21	3		3	OR2G6	1	248684959	Silent	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	133333	248684959	565662	9	3858										
OR2T10	127069	hgsc.bcm.edu	37	chr1	248756794	248756794	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gtgccacacccaaggaccgaGatggtcttgtctttggccag	12	12	2	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr1:248756794G>T	ENST00000330500.2	-	1	306	c.276C>A	c.(274-276)atC>atA	p.I92I	Y_RNA_ENST00000364732.1_RNA	NM_001004693.1	NP_001004693.1	Q8NGZ9	O2T10_HUMAN	olfactory receptor, family 2, subfamily T, member 10	92						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(17)|skin(3)|upper_aerodigestive_tract(1)	26	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CAAGGACCGAGATGGTCTTGT	0.502																																					p.I92I		Atlas-SNP	.											.	OR2T10	58	.	0			c.C276A						.						64	75	71					1																	248756794		2040	4235	6275	SO:0001819	synonymous_variant	127069	exon1			GACCGAGATGGTC		CCDS31121.1	1q44	2012-08-09			ENSG00000184022	ENSG00000184022		"GPCR / Class A : Olfactory receptors"	19573	protein-coding gene	gene with protein product							Standard	NM_001004693		Approved		uc010pzn.2	Q8NGZ9	OTTHUMG00000040388	ENST00000330500.2:c.276C>A	chr1.hg19:g.248756794G>T		219.0	0.0		175.0	30.0	NM_001004693	B2RNK7	Silent	SNP	ENST00000330500.2	hg19	CCDS31121.1																																																																																			.	.		0.502	OR2T10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097139.1	NM_001004693		T	248756794	G	T	248756794	2	4	32	1	0	0	0	0	0	0	0	1	11026	932	33	3		3	OR2T10	1	248756794	Silent	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	71835	248756794	493827	10	3859										
SMPD4	55627	hgsc.bcm.edu	37	chr2	130930247	130930247	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	agaatatgtaatactcgaacGgatctgagagcagcgtcagg	12	7	2	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr2:130930247G>T	ENST00000409031.1	-	7	1723	c.575C>A	c.(574-576)cCg>cAg	p.P192Q	SMPD4_ENST00000431183.2_Missense_Mutation_p.P119Q|SMPD4_ENST00000351288.6_Missense_Mutation_p.P192Q|SMPD4_ENST00000473720.1_Intron|SMPD4_ENST00000452225.2_Intron|SMPD4_ENST00000339679.7_Missense_Mutation_p.P79Q|SMPD4_ENST00000426662.2_Intron|SMPD4_ENST00000443958.2_Intron|SMPD4_ENST00000453750.1_Intron	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	153					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	atactcGAACGGATCTGAGAG	0.587																																					p.P192Q		Atlas-SNP	.											.	SMPD4	67	.	0			c.C575A						.						98	104	102					2																	130930247		2203	4300	6503	SO:0001583	missense	55627	exon7			TCGAACGGATCTG	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.575C>A	chr2.hg19:g.130930247G>T	ENSP00000386531:p.Pro192Gln	184.0	0.0		158.0	34.0	NM_017751	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Missense_Mutation	SNP	ENST00000409031.1	hg19	CCDS42751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	14.71|14.71	2.617956|2.617956	0.46736|0.46736	.|.	.|.	ENSG00000136699|ENSG00000136699	ENST00000351288;ENST00000409031;ENST00000431183;ENST00000339679|ENST00000439886	.|.	.|.	.|.	3.5|3.5	3.5|3.5	0.40072|0.40072	.|.	0.199707|.	0.43579|.	D|.	0.000547|.	T|T	0.69593|0.69593	0.3128|0.3128	M|M	0.67953|0.67953	2.075|2.075	0.80722|0.80722	D|D	1|1	D;D;P;P;D|.	0.58268|.	0.982;0.968;0.955;0.915;0.98|.	P;P;P;P;P|.	0.57960|.	0.708;0.77;0.567;0.801;0.83|.	T|T	0.69939|0.69939	-0.5009|-0.5009	9|5	0.56958|.	D|.	0.05|.	.|.	12.5618|12.5618	0.56286|0.56286	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	119;79;153;153;192|.	E7ESA2;B4E0T5;Q9NXE4-2;Q9NXE4;B1PBA3|.	.;.;.;NSMA3_HUMAN;.|.	Q|S	192;192;119;79|21	.|.	ENSP00000339721:P79Q|.	P|R	-|-	2|1	0|0	SMPD4|SMPD4	130646717|130646717	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.921000|0.921000	0.55340|0.55340	6.881000|6.881000	0.75584|0.75584	1.793000|1.793000	0.52555|0.52555	0.455000|0.455000	0.32223|0.32223	CCG|CGT	.	.		0.587	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751		T	130930247	G	T	130930247	3	4	32	1	0	0	0	0	1	0	0	0	14822	1116	39	1	2081	1	SMPD4	2	130930247	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10		130930247	112269126	11	3860										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160807990	160807990	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tttttattgctgcataccaaGtcatatttgcattaattatt	4	6	1	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr2:160807990G>T	ENST00000283243.7	-	24	3607	c.3401C>A	c.(3400-3402)aCt>aAt	p.T1134N	PLA2R1_ENST00000392771.1_Missense_Mutation_p.T1134N	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	1134	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						TGCATACCAAGTCATATTTGC	0.408																																					p.T1134N		Atlas-SNP	.											.	PLA2R1	153	.	0			c.C3401A						.						240	220	227					2																	160807990		2203	4300	6503	SO:0001583	missense	22925	exon24			TACCAAGTCATAT	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.3401C>A	chr2.hg19:g.160807990G>T	ENSP00000283243:p.Thr1134Asn	574.0	0.0		434.0	137.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	hg19	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.951658	0.53186	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.56275	0.47;0.47	5.67	5.67	0.87782	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.057219	0.64402	D	0.000002	T	0.61211	0.2329	L	0.41027	1.25	0.47737	D	0.999507	D;D;D	0.61080	0.989;0.987;0.987	D;P;P	0.68039	0.955;0.843;0.857	T	0.52697	-0.8541	10	0.19147	T	0.46	.	15.2627	0.73637	0.0:0.1399:0.8601:0.0	.	1134;1134;1134	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	N	1134	ENSP00000283243:T1134N;ENSP00000376524:T1134N	ENSP00000283243:T1134N	T	-	2	0	PLA2R1	160516236	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.245000	0.65405	2.680000	0.91292	0.557000	0.71058	ACT	.	.		0.408	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			T	160807990	G	T	160807990	3	4	32	1	0	0	0	0	1	0	0	0	12019	1029	36	3	1026	3	PLA2R1	2	160807990	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	29877743	160807990	82391383	12	3861										
TRAF3IP1	26146	hgsc.bcm.edu	37	chr2	239237694	239237694	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gaaggccaaggagaatggcgGaaacagacacagagaagggg	17	6	0	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr2:239237694G>T	ENST00000373327.4	+	5	848	c.626G>T	c.(625-627)gGa>gTa	p.G209V	TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.G209V|TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.G209V	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	209	Abolishes microtubules-binding when missing.				cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		gagaatggcggaaacagacac	0.527																																					p.G209V		Atlas-SNP	.											.	TRAF3IP1	58	.	0			c.G626T						.						78	63	68					2																	239237694		2043	3941	5984	SO:0001583	missense	26146	exon5			ATGGCGGAAACAG	AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"Intraflagellar transport homologs"	17861	protein-coding gene	gene with protein product	"microtubule interacting protein that associates with TRAF3"	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.626G>T	chr2.hg19:g.239237694G>T	ENSP00000362424:p.Gly209Val	217.0	0.0		203.0	34.0	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	hg19	CCDS33415.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756275	0.49362	.	.	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.13778	2.56;2.56;2.56	4.48	3.6	0.41247	.	0.673120	0.13966	N	0.350493	T	0.08088	0.0202	N	0.14661	0.345	0.28470	N	0.915444	B;B	0.33919	0.378;0.432	B;B	0.34093	0.109;0.175	T	0.26087	-1.0113	10	0.28530	T	0.3	-11.7677	8.465	0.32951	0.1804:0.0:0.8196:0.0	.	209;209	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	V	209	ENSP00000375851:G209V;ENSP00000362424:G209V;ENSP00000375852:G209V	ENSP00000362424:G209V	G	+	2	0	TRAF3IP1	238902433	0.603000	0.26924	0.055000	0.19348	0.349000	0.29174	1.046000	0.30354	1.018000	0.39521	0.655000	0.94253	GGA	.	.		0.527	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650		T	239237694	G	T	239237694	3	4	32	1	0	0	0	0	1	0	0	0	16455	1174	41	3	644	3	TRAF3IP1	2	239237694	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	78429704	239237694	3961679	13	3862										
SEMA3F	6405	hgsc.bcm.edu	37	chr3	50220186	50220186	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gaggcgccgcagagccccgcGgtgtacgcccgcatcgggcg	17	16	0	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr3:50220186G>T	ENST00000002829.3	+	9	1357	c.873G>T	c.(871-873)gcG>gcT	p.A291A	SEMA3F_ENST00000413852.1_Silent_p.A192A|SEMA3F_ENST00000434342.1_Silent_p.A260A	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	291	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		AGAGCCCCGCGGTGTACGCCC	0.607																																					p.A291A		Atlas-SNP	.											.	SEMA3F	62	.	0			c.G873T						.						51	58	56					3																	50220186		2203	4300	6503	SO:0001819	synonymous_variant	6405	exon9			CCCCGCGGTGTAC	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10728	protein-coding gene	gene with protein product	"sema IV"	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.873G>T	chr3.hg19:g.50220186G>T		47.0	0.0		24.0	11.0	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Silent	SNP	ENST00000002829.3	hg19	CCDS2811.1																																																																																			.	.		0.607	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186		T	50220186	G	T	50220186	2	4	32	1	0	0	0	0	0	0	0	1	14044	1103	39	1		1	SEMA3F	3	50220186	Silent	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10		50220186	147802244	14	3863										
BAP1	8314	hgsc.bcm.edu	37	chr3	52436687	52436688	+	Frame_Shift_Ins	INS	-	-	A													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tgggtccttctctggtcatcINSaatctgtaggagagaagaag							TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr3:52436687_52436688insA	ENST00000460680.1	-	16	2457_2458	c.1986_1987insT	c.(1984-1989)attgatfs	p.D663fs	BAP1_ENST00000296288.5_Frame_Shift_Ins_p.D645fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CTCTGGTCATCAATCTGTAGGA	0.53			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.D663_D664delinsX	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	BAP1,bladder,carcinoma,0,1	BAP1	371	.	0			c.1987_1988insT						.																																			SO:0001589	frameshift_variant	8314	exon16			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1987dupT	chr3.hg19:g.52436689_52436689dupA	ENSP00000417132:p.Asp663fs	226.0	0.0		89.0	65.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Ins	INS	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.53	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52436688	-	A	52436687	7	5	32	1	0	1	1	0	0	0	0	0	1311	826	29	0	210	0	BAP1	3	52436687	Frame_Shift_Ins	INS	-	TCGA-BC-A10R-01A-11D-A12Z-10	2216501	52436687	145585743	15	3864										
MRPS22	56945	hgsc.bcm.edu	37	chr3	139062905	139062905	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	caactgtattgctgtggagcCtcttgaggagttctccgggc	13	10	2	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr3:139062905C>T	ENST00000495075.1	+	3	469	c.37C>T	c.(37-39)Ctc>Ttc	p.L13F	MRPS22_ENST00000478464.1_5'Flank|MRPS22_ENST00000310776.4_Missense_Mutation_p.L13F|MRPS22_ENST00000465056.1_Missense_Mutation_p.L13F			P82650	RT22_HUMAN	mitochondrial ribosomal protein S22	13						mitochondrial ribosome (GO:0005761)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12						GCTGTGGAGCCTCTTGAGGAG	0.587																																					p.L13F		Atlas-SNP	.											.	MRPS22	40	.	0			c.C37T						.						52	53	52					3																	139062905		2203	4300	6503	SO:0001583	missense	56945	exon1			TGGAGCCTCTTGA	AF226045	CCDS3107.1	3q23	2012-09-13			ENSG00000175110	ENSG00000175110		"Mitochondrial ribosomal proteins / small subunits"	14508	protein-coding gene	gene with protein product		605810				11175783	Standard	NM_020191		Approved	MRP-S22, GK002, C3orf5, GIBT	uc003etb.3	P82650	OTTHUMG00000159910	ENST00000495075.1:c.37C>T	chr3.hg19:g.139062905C>T	ENSP00000418008:p.Leu13Phe	49.0	0.0		54.0	16.0	NM_020191	Q9H3I1	Missense_Mutation	SNP	ENST00000495075.1	hg19	CCDS3107.1	.	.	.	.	.	.	.	.	.	.	C	7.061	0.566305	0.13560	.	.	ENSG00000175110	ENST00000495075;ENST00000310776;ENST00000465056;ENST00000465373	D;D;D;T	0.83250	-1.7;-1.7;-1.7;-1.12	4.01	-2.38	0.06622	.	1.136100	0.06728	N	0.776041	T	0.65481	0.2695	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.46076	-0.9217	10	0.30078	T	0.28	2.9972	4.8869	0.13708	0.0:0.3398:0.1622:0.4979	.	13;13	G5E9V5;P82650	.;RT22_HUMAN	F	13;13;13;9	ENSP00000418008:L13F;ENSP00000310785:L13F;ENSP00000418233:L13F;ENSP00000419920:L9F	ENSP00000310785:L13F	L	+	1	0	MRPS22	140545595	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.295000	0.02764	-0.680000	0.05211	-0.282000	0.10007	CTC	.	.		0.587	MRPS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358120.1	NM_020191		T	139062905	C	T	139062905	3	4	32	1	0	0	0	0	1	0	0	0	9842	681	24	3	39	3	MRPS22	3	139062905	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	86626218	139062905	58959525	16	3865										
PLS1	5357	hgsc.bcm.edu	37	chr3	142388293	142388293	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gacctgtttaaggaagcaagCcttcctctgcctggctacaa	9	12	1	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr3:142388293C>T	ENST00000337777.3	+	3	345	c.132C>T	c.(130-132)agC>agT	p.S44S	PLS1_ENST00000457734.2_Silent_p.S44S|PLS1_ENST00000497002.1_Silent_p.S44S	NM_002670.2	NP_002661.2	Q14651	PLSI_HUMAN	plastin 1	44	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	27						AGGAAGCAAGCCTTCCTCTGC	0.368																																					p.S44S		Atlas-SNP	.											.	PLS1	71	.	0			c.C132T						.						148	148	148					3																	142388293		2203	4300	6503	SO:0001819	synonymous_variant	5357	exon3			AGCAAGCCTTCCT	L20826	CCDS3125.1	3q23	2013-01-10	2010-02-10		ENSG00000120756	ENSG00000120756		"EF-hand domain containing"	9090	protein-coding gene	gene with protein product		602734	"plastin 1 (I isoform)"			8139549	Standard	NM_002670		Approved	I-plastin, Plastin-1	uc003euz.3	Q14651	OTTHUMG00000159292	ENST00000337777.3:c.132C>T	chr3.hg19:g.142388293C>T		107.0	0.0		79.0	9.0	NM_001172312	A8K2Q1|D3DNG3|Q8NEG6	Silent	SNP	ENST00000337777.3	hg19	CCDS3125.1																																																																																			.	.		0.368	PLS1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354435.1	NM_002670		T	142388293	C	T	142388293	2	4	32	1	0	0	0	0	0	0	0	1	12116	738	26	3		3	PLS1	3	142388293	Silent	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	3325388	142388293	55634137	17	3866										
DHX36	170506	hgsc.bcm.edu	37	chr3	154042059	154042060	+	Frame_Shift_Ins	INS	-	-	C													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gcccgggatgccggcccctgINSccgcctcgaccaccccctcc							TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr3:154042059_154042060insC	ENST00000496811.1	-	1	226_227	c.146_147insG	c.(145-147)ggcfs	p.G49fs	DHX36_ENST00000544526.1_Frame_Shift_Ins_p.G49fs|DHX36_ENST00000329463.5_Frame_Shift_Ins_p.G49fs|DHX36_ENST00000308361.6_Frame_Shift_Ins_p.G49fs	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	49	Gly-rich.|RNA-binding; sufficient and required for recruitment to cytoplasmic stress granules.				ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			GCCGGCCCCTGCCGCCTCGACC	0.678																																					p.G49fs		Atlas-INDEL	.											.	DHX36	98	.	0			c.147_148insG						.																																			SO:0001589	frameshift_variant	170506	exon1			.	AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.147dupG	chr3.hg19:g.154042061_154042061dupC	ENSP00000417078:p.Gly49fs	223.0	0.0		244.0	15.0	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Frame_Shift_Ins	INS	ENST00000496811.1	hg19	CCDS3171.1																																																																																			.	.		0.678	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		C	154042060	-	C	154042059	7	5	32	1	0	1	1	0	0	0	0	0	4511	1306	46	0	2979	0	DHX36	3	154042059	Frame_Shift_Ins	INS	-	TCGA-BC-A10R-01A-11D-A12Z-10	11653766	154042059	43980371	18	3867										
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184039489	184039489	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	catctgaagatctggaaccaGaggtggagtcaagcccagag	13	9	3	4			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr3:184039489G>T	ENST00000346169.2	+	10	1388	c.1117G>T	c.(1117-1119)Gag>Tag	p.E373*	EIF4G1_ENST00000434061.2_Nonsense_Mutation_p.E177*|EIF4G1_ENST00000441154.1_Nonsense_Mutation_p.E209*|EIF4G1_ENST00000382330.3_Nonsense_Mutation_p.E380*|EIF4G1_ENST00000424196.1_Nonsense_Mutation_p.E380*|EIF4G1_ENST00000392537.2_Nonsense_Mutation_p.E286*|EIF4G1_ENST00000352767.3_Nonsense_Mutation_p.E380*|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000411531.1_Nonsense_Mutation_p.E333*|EIF4G1_ENST00000319274.6_Nonsense_Mutation_p.E373*|EIF4G1_ENST00000414031.1_Nonsense_Mutation_p.E333*|EIF4G1_ENST00000350481.5_Nonsense_Mutation_p.E209*|EIF4G1_ENST00000342981.4_Nonsense_Mutation_p.E373*|EIF4G1_ENST00000427845.1_Nonsense_Mutation_p.E286*|EIF4G1_ENST00000435046.2_Nonsense_Mutation_p.E177*	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	373					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCTGGAACCAGAGGTGGAGTC	0.567																																					p.E380X		Atlas-SNP	.											.	EIF4G1	151	.	0			c.G1138T						.						131	138	136					3																	184039489		2203	4300	6503	SO:0001587	stop_gained	1981	exon11			GAACCAGAGGTGG	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1117G>T	chr3.hg19:g.184039489G>T	ENSP00000316879:p.Glu373*	163.0	0.0		135.0	21.0	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Nonsense_Mutation	SNP	ENST00000346169.2	hg19	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.974077	0.74246	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000434061;ENST00000457456;ENST00000435046	.	.	.	5.37	5.37	0.77165	.	0.569134	0.17681	N	0.165603	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-21.7267	12.207	0.54358	0.0:0.171:0.829:0.0	.	.	.	.	X	373;333;286;373;380;380;314;209;380;286;373;373;380;333;209;209;177;177;177	.	ENSP00000323737:E373X	E	+	1	0	EIF4G1	185522183	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.483000	0.66838	2.793000	0.96121	0.563000	0.77884	GAG	.	.		0.567	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		T	184039489	G	T	184039489	4	4	32	1	0	0	0	0	0	1	0	0	5038	943	33	3	1147	3	EIF4G1	3	184039489	Nonsense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	29997430	184039489	13982941	19	3868										
PDE6B	5158	hgsc.bcm.edu	37	chr4	651215	651215	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tgaacaagctggagaaccgcAaggacatcgcacaggacatg	12	10	0	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr4:651215A>G	ENST00000496514.1	+	10	1354	c.1333A>G	c.(1333-1335)Aag>Gag	p.K445E	RP11-1191J2.2_ENST00000468356.1_RNA|PDE6B_ENST00000255622.6_Missense_Mutation_p.K445E|PDE6B_ENST00000429163.2_Missense_Mutation_p.K166E|RP11-1191J2.2_ENST00000489312.1_RNA			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	445					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	GGAGAACCGCAAGGACATCGC	0.597																																					p.K445E	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.A1333G						.						216	132	161					4																	651215		2203	4300	6503	SO:0001583	missense	5158	exon10			AACCGCAAGGACA	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"Phosphodiesterases"	8786	protein-coding gene	gene with protein product	"congenital stationary night blindness 3, autosomal dominant"	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.1333A>G	chr4.hg19:g.651215A>G	ENSP00000420295:p.Lys445Glu	173.0	0.0		192.0	32.0	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	hg19	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.727402	0.89390	.	.	ENSG00000133256	ENST00000255622;ENST00000496514;ENST00000429163	T;T;T	0.69561	-0.41;-0.41;-0.41	4.85	3.62	0.41486	.	0.052152	0.64402	D	0.000001	T	0.81437	0.4822	M	0.88640	2.97	0.53005	D	0.999969	D;D	0.71674	0.997;0.998	P;D	0.68192	0.905;0.956	T	0.81846	-0.0745	10	0.87932	D	0	.	8.9054	0.35521	0.8327:0.0:0.0:0.1673	.	445;445	P35913;P35913-2	PDE6B_HUMAN;.	E	445;445;166	ENSP00000255622:K445E;ENSP00000420295:K445E;ENSP00000406334:K166E	ENSP00000255622:K445E	K	+	1	0	PDE6B	641215	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.695000	0.91298	0.653000	0.30826	0.367000	0.22151	AAG	.	.		0.597	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		G	651215	A	G	651215	3	3	32	1	0	0	0	0	1	0	0	0	11655	131	5	2	1371	2	PDE6B	4	651215	Missense_Mutation	SNP	A	TCGA-BC-A10R-01A-11D-A12Z-10		651215	190503061	20	3869										
OTOP1	133060	hgsc.bcm.edu	37	chr4	4199089	4199090	+	Frame_Shift_Ins	INS	-	-	G													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tggtggcatgtccttgccctINSggggagccacatctctggcc							TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr4:4199089_4199090insG	ENST00000296358.4	-	5	1495_1496	c.1471_1472insC	c.(1471-1473)cagfs	p.Q491fs		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	491					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GTCCTTGCCCTGGGGAGCCACA	0.584																																					p.Q491fs		Atlas-INDEL	.											.	OTOP1	118	.	0			c.1472_1473insC						.																																			SO:0001589	frameshift_variant	133060	exon5			.	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1472dupC	chr4.hg19:g.4199093_4199093dupG	ENSP00000296358:p.Gln491fs	219.0	0.0		157.0	13.0	NM_177998	A1L476	Frame_Shift_Ins	INS	ENST00000296358.4	hg19	CCDS3372.1																																																																																			.	.		0.584	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		G	4199090	-	G	4199089	7	5	32	1	0	1	1	0	0	0	0	0	11314	1580	55	0	374	0	OTOP1	4	4199089	Frame_Shift_Ins	INS	-	TCGA-BC-A10R-01A-11D-A12Z-10	3547874	4199089	186955187	21	3870										
CRMP1	1400	hgsc.bcm.edu	37	chr4	5837733	5837733	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ccacggcaatccgccctttcCttgggtacaggttaaagatc	9	13	0	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr4:5837733C>T	ENST00000397890.2	-	11	1404	c.1190G>A	c.(1189-1191)aGg>aAg	p.R397K	CRMP1_ENST00000512574.1_Missense_Mutation_p.R395K|CRMP1_ENST00000324989.7_Missense_Mutation_p.R511K|CRMP1_ENST00000511535.1_5'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	397					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		CCGCCCTTTCCTTGGGTACAG	0.527																																					p.R511K		Atlas-SNP	.											.	CRMP1	118	.	0			c.G1532A						.						145	133	137					4																	5837733		2203	4300	6503	SO:0001583	missense	1400	exon11			CCTTTCCTTGGGT	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1190G>A	chr4.hg19:g.5837733C>T	ENSP00000380987:p.Arg397Lys	142.0	0.0		91.0	18.0	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	hg19	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.719167	0.89205	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	D;D;D	0.89939	-2.59;-2.59;-2.59	4.33	4.33	0.51752	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.85643	0.5744	N	0.21508	0.67	0.80722	D	1	B;B;B;P	0.42357	0.062;0.214;0.011;0.777	B;B;B;P	0.47346	0.177;0.147;0.042;0.544	D	0.85496	0.1188	10	0.36615	T	0.2	-23.1461	16.3427	0.83092	0.0:1.0:0.0:0.0	.	511;395;397;334	A0EJG6;E9PD68;Q14194;B3KT07	.;.;DPYL1_HUMAN;.	K	511;397;397;395	ENSP00000321606:R511K;ENSP00000380987:R397K;ENSP00000425742:R395K	ENSP00000321606:R511K	R	-	2	0	CRMP1	5888634	0.954000	0.32549	0.972000	0.41901	0.949000	0.60115	7.309000	0.78937	2.418000	0.82041	0.508000	0.49915	AGG	.	.		0.527	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		T	5837733	C	T	5837733	3	4	32	1	0	0	0	0	1	0	0	0	3892	681	24	3	544	3	CRMP1	4	5837733	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	1638644	5837733	185316543	22	3871										
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42580401	42580401	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gtccaaaattactagcgccaCcatctgttgggagaggcagg	12	10	1	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr4:42580401C>T	ENST00000381668.5	-	12	1235	c.1004G>A	c.(1003-1005)gGt>gAt	p.G335D	ATP8A1_ENST00000264449.10_Missense_Mutation_p.G335D	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	335					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	ACTAGCGCCACCATCTGTTGG	0.358																																					p.G335D		Atlas-SNP	.											.	ATP8A1	206	.	0			c.G1004A						.						131	130	131					4																	42580401		2203	4300	6503	SO:0001583	missense	10396	exon12			GCGCCACCATCTG	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1004G>A	chr4.hg19:g.42580401C>T	ENSP00000371084:p.Gly335Asp	117.0	0.0		91.0	14.0	NM_001105529	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	hg19	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	C	2.761	-0.257844	0.05791	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.74947	-0.89;-0.89	5.67	5.67	0.87782	ATPase, P-type, ATPase-associated domain (1);	0.064385	0.64402	D	0.000006	T	0.60599	0.2281	N	0.17764	0.52	0.80722	D	1	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.13407	0.009;0.005;0.002	T	0.55296	-0.8163	10	0.16420	T	0.52	.	16.0524	0.80774	0.0:0.8659:0.1341:0.0	.	335;335;335	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	D	335	ENSP00000371084:G335D;ENSP00000264449:G335D	ENSP00000264449:G335D	G	-	2	0	ATP8A1	42275158	1.000000	0.71417	1.000000	0.80357	0.242000	0.25591	5.687000	0.68219	2.663000	0.90544	0.585000	0.79938	GGT	.	.		0.358	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		T	42580401	C	T	42580401	3	4	32	1	0	0	0	0	1	0	0	0	1192	507	18	3	2594	3	ATP8A1	4	42580401	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	36742668	42580401	148573875	23	3872										
FAM134B	54463	hgsc.bcm.edu	37	chr5	16474884	16474884	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gcagatttgaaaggaaacctGaagacttcttattttgctgt	9	6	1	4			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr5:16474884G>A	ENST00000306320.9	-	9	1546	c.1460C>T	c.(1459-1461)tCa>tTa	p.S487L	FAM134B_ENST00000399793.2_Missense_Mutation_p.S346L	NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	487					sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						AAGGAAACCTGAAGACTTCTT	0.383																																					p.S487L		Atlas-SNP	.											.	FAM134B	72	.	0			c.C1460T						.						123	118	119					5																	16474884		1877	4111	5988	SO:0001583	missense	54463	exon9			AAACCTGAAGACT	BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153			25964	protein-coding gene	gene with protein product		613114				19838196, 24327336	Standard	NM_001034850		Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.1460C>T	chr5.hg19:g.16474884G>A	ENSP00000304642:p.Ser487Leu	135.0	0.0		115.0	54.0	NM_001034850	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	Missense_Mutation	SNP	ENST00000306320.9	hg19	CCDS43304.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.317078	0.60524	.	.	ENSG00000154153	ENST00000399793;ENST00000306320	T;T	0.55052	0.63;0.54	5.82	4.96	0.65561	.	0.319926	0.34046	N	0.004312	T	0.50137	0.1598	L	0.55481	1.735	0.48830	D	0.999713	P;B	0.46395	0.877;0.421	B;B	0.40636	0.335;0.221	T	0.56098	-0.8035	10	0.62326	D	0.03	-1.5733	14.657	0.68841	0.0694:0.0:0.9306:0.0	.	487;346	Q9H6L5;Q9H6L5-2	F134B_HUMAN;.	L	346;487	ENSP00000382691:S346L;ENSP00000304642:S487L	ENSP00000304642:S487L	S	-	2	0	FAM134B	16527884	1.000000	0.71417	0.983000	0.44433	0.990000	0.78478	5.819000	0.69243	1.464000	0.47987	0.655000	0.94253	TCA	.	.		0.383	FAM134B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366090.1	NM_001034850		A	16474884	G	A	16474884	3	1	32	1	0	0	0	0	1	0	0	0	5451	1294	45	3	37	3	FAM134B	5	16474884	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10		16474884	164440376	24	3873										
C5orf22	55322	hgsc.bcm.edu	37	chr5	31534433	31534433	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	agcatcttcctgccagtaatGtaagttttttacatttcgac	6	9	1	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr5:31534433G>C	ENST00000325366.9	+	2	263	c.136G>C	c.(136-138)Gta>Cta	p.V46L	C5orf22_ENST00000355907.3_5'UTR|DROSHA_ENST00000504361.1_5'Flank|DROSHA_ENST00000511367.2_5'Flank|DROSHA_ENST00000513349.1_5'Flank	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	46										kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						TGCCAGTAATGTAAGTTTTTT	0.408																																					p.V46L		Atlas-SNP	.											.	C5orf22	48	.	0			c.G136C						.						168	155	160					5																	31534433		2203	4300	6503	SO:0001583	missense	55322	exon2			AGTAATGTAAGTT	AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.136G>C	chr5.hg19:g.31534433G>C	ENSP00000326879:p.Val46Leu	505.0	0.0		328.0	64.0	NM_018356	Q8ND28|Q8WU61|Q9NUR1	Missense_Mutation	SNP	ENST00000325366.9	hg19	CCDS3895.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.291638	0.59976	.	.	ENSG00000082213	ENST00000325366;ENST00000507818	T;T	0.40756	1.02;1.02	5.41	4.25	0.50352	.	0.046947	0.85682	D	0.000000	T	0.20740	0.0499	N	0.04203	-0.255	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.03863	-1.0997	10	0.23302	T	0.38	-15.2709	11.4383	0.50081	0.9286:0.0:0.0714:0.0	.	46	Q49AR2	CE022_HUMAN	L	46	ENSP00000326879:V46L;ENSP00000430860:V46L	ENSP00000326879:V46L	V	+	1	0	C5orf22	31570190	1.000000	0.71417	0.933000	0.37362	0.873000	0.50193	4.504000	0.60414	0.869000	0.35703	-0.294000	0.09567	GTA	.	.		0.408	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356		C	31534433	G	C	31534433	3	2	32	1	0	0	0	0	1	0	0	0	2287	1377	48	4	142	4	C5orf22	5	31534433	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	15059549	31534433	149380827	25	3874										
TMEM173	340061	hgsc.bcm.edu	37	chr5	138855859	138855859	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ctgggtctcaagagaaatccGtgcggagagggaggggcttt	17	7	1	2	rs370381358		TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr5:138855859G>T	ENST00000330794.4	-	8	1460	c.1127C>A	c.(1126-1128)aCg>aAg	p.T376K	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	376	C-terminal tail (CTT).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGAGAAATCCGTGCGGAGAGG	0.602																																					p.T376K		Atlas-SNP	.											.	TMEM173	19	.	0			c.C1127A						.						43	43	43					5																	138855859		2203	4300	6503	SO:0001583	missense	340061	exon8			AAATCCGTGCGGA		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.1127C>A	chr5.hg19:g.138855859G>T	ENSP00000331288:p.Thr376Lys	116.0	0.0		67.0	31.0	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	hg19	CCDS4215.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.892396	0.33442	.	.	ENSG00000184584	ENST00000330794	T	0.24908	1.83	5.36	4.48	0.54585	.	0.782790	0.11811	N	0.527174	T	0.24470	0.0593	L	0.34521	1.04	0.09310	N	1	P	0.40638	0.725	B	0.40165	0.321	T	0.10776	-1.0615	10	0.72032	D	0.01	-2.6099	13.2827	0.60224	0.0:0.3784:0.6215:0.0	.	376	Q86WV6	TM173_HUMAN	K	376	ENSP00000331288:T376K	ENSP00000331288:T376K	T	-	2	0	TMEM173	138836043	0.031000	0.19500	0.079000	0.20413	0.099000	0.18886	1.556000	0.36288	1.230000	0.43646	0.462000	0.41574	ACG	.	.		0.602	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282		T	138855859	G	T	138855859	3	4	32	1	0	0	0	0	1	0	0	0	16104	1145	40	1	16	1	TMEM173	5	138855859	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	107321426	138855859	42059401	26	3875										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237874	140237874	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	agcgcggtggggagctggtcTtactcgcagcagaggcggca	18	10	1	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr5:140237874T>C	ENST00000307360.5	+	1	2241	c.2241T>C	c.(2239-2241)tcT>tcC	p.S747S	PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	747	6 X 4 AA repeats of P-X-X-P.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGCTGGTCTTACTCGCAGC	0.672																																					p.S747S		Atlas-SNP	.											.	PCDHA10	358	.	0			c.T2241C						.						44	49	47					5																	140237874		1322	2289	3611	SO:0001819	synonymous_variant	56139	exon1			CTGGTCTTACTCG	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.2241T>C	chr5.hg19:g.140237874T>C		285.0	0.0		134.0	29.0	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	hg19	CCDS54921.1																																																																																			.	.		0.672	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		C	140237874	T	C	140237874	2	2	32	1	0	0	0	0	0	0	0	1	11529	1596	56	2		2	PCDHA10	5	140237874	Silent	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10	1382015	140237874	40677386	27	3876										
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140746244	140746244	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	cagacacgctccttagtgaaGagagctgtgagaaaagcgag	13	8	0	4			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr5:140746244G>A	ENST00000518069.1	+	1	2347	c.2347G>A	c.(2347-2349)Gag>Aag	p.E783K	PCDHGA3_ENST00000253812.6_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	783					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTTAGTGAAGAGAGCTGTGA	0.512																																					p.E783K		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.G2347A						.						108	121	117					5																	140746244		2203	4299	6502	SO:0001583	missense	56110	exon1			AGTGAAGAGAGCT	AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.2347G>A	chr5.hg19:g.140746244G>A	ENSP00000429834:p.Glu783Lys	161.0	0.0		81.0	16.0	NM_032054	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	hg19	CCDS54925.1	.	.	.	.	.	.	.	.	.	.	.	14.26	2.481816	0.44147	.	.	ENSG00000253485	ENST00000518069	D	0.94613	-3.47	5.3	3.39	0.38822	.	.	.	.	.	D	0.94159	0.8126	M	0.88181	2.935	0.09310	N	1	B;B	0.22541	0.071;0.042	B;B	0.29663	0.105;0.049	D	0.86697	0.1927	9	0.37606	T	0.19	.	6.673	0.23078	0.0963:0.2763:0.6274:0.0	.	783;783	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	K	783	ENSP00000429834:E783K	ENSP00000429834:E783K	E	+	1	0	PCDHGA5	140726428	0.929000	0.31497	0.431000	0.26735	0.736000	0.42039	1.204000	0.32296	2.630000	0.89119	0.655000	0.94253	GAG	.	.		0.512	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		A	140746244	G	A	140746244	3	1	32	1	0	0	0	0	1	0	0	0	11566	943	33	3	2349	3	PCDHGA5	5	140746244	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	508370	140746244	40169016	28	3877										
HOXA4	3201	hgsc.bcm.edu	37	chr7	27168891	27168891	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ggtgctcgggtgggggtgggGatggaggtgtgggctctgag	25	4	1	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr7:27168891G>A	ENST00000360046.5	-	2	981	c.916C>T	c.(916-918)Ccc>Tcc	p.P306S	HOXA4_ENST00000428284.2_Missense_Mutation_p.P306S|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS2_ENST00000521687.1_RNA|HOXA-AS2_ENST00000517550.1_RNA|HOXA3_ENST00000521401.1_Intron|HOXA3_ENST00000317201.2_5'Flank|HOXA-AS2_ENST00000521159.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA	NM_002141.4	NP_002132.3	Q00056	HXA4_HUMAN	homeobox A4	306					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)	12						tgggggtggggatggaggtgt	0.547																																					p.P306S		Atlas-SNP	.											HOXA4,NS,carcinoma,0,1	HOXA4	21	.	0			c.C916T						.						164	161	162					7																	27168891		2203	4300	6503	SO:0001583	missense	3201	exon2			GGTGGGGATGGAG		CCDS5405.1	7p15.2	2011-06-20	2005-12-22		ENSG00000197576	ENSG00000197576		"Homeoboxes / ANTP class : HOXL subclass"	5105	protein-coding gene	gene with protein product		142953	"homeo box A4"	HOX1D, HOX1		1973146, 1358459	Standard	NM_002141		Approved		uc003sym.4	Q00056	OTTHUMG00000023213	ENST00000360046.5:c.916C>T	chr7.hg19:g.27168891G>A	ENSP00000353151:p.Pro306Ser	321.0	1.0		343.0	56.0	NM_002141	A4D180|O43366	Missense_Mutation	SNP	ENST00000360046.5	hg19	CCDS5405.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.16|10.16	1.274601|1.274601	0.23307|0.23307	.|.	.|.	ENSG00000197576|ENSG00000197576	ENST00000360046;ENST00000428284|ENST00000511914	D;D|.	0.87491|.	-2.26;-2.26|.	5.38|5.38	2.6|2.6	0.31112|0.31112	.|.	0.185824|.	0.26578|.	N|.	0.023592|.	T|T	0.29389|0.29389	0.0732|0.0732	L|L	0.27053|0.27053	0.805|0.805	0.27216|0.27216	N|N	0.959771|0.959771	B|.	0.25719|.	0.132|.	B|.	0.20767|.	0.031|.	T|T	0.21381|0.21381	-1.0247|-1.0247	10|5	0.62326|.	D|.	0.03|.	.|.	6.2652|6.2652	0.20922|0.20922	0.2128:0.1329:0.6543:0.0|0.2128:0.1329:0.6543:0.0	.|.	306|.	Q00056|.	HXA4_HUMAN|.	S|F	306|125	ENSP00000353151:P306S;ENSP00000408845:P306S|.	ENSP00000353151:P306S|.	P|S	-|-	1|2	0|0	HOXA4|HOXA4	27135416|27135416	.|.	.|.	0.953000|0.953000	0.39169|0.39169	0.864000|0.864000	0.49448|0.49448	.|.	.|.	0.271000|0.271000	0.22005|0.22005	-0.484000|-0.484000	0.04775|0.04775	CCC|TCC	.	.		0.547	HOXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059534.4			A	27168891	G	A	27168891	3	1	32	1	0	0	0	0	1	0	0	0	7303	1174	41	3	50	3	HOXA4	7	27168891	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10		27168891	131969772	29	3878										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84666319	84666319	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ctgatgtcagccatgctataCacacaaacagcagagccttt	7	12	1	2	rs143217112		TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr7:84666319C>G	ENST00000284136.6	-	10	1120	c.1077G>C	c.(1075-1077)gtG>gtC	p.V359V	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	359	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CCATGCTATACACACAAACAG	0.398																																					p.V359V	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.G1077C						.						104	93	97					7																	84666319		2203	4300	6503	SO:0001819	synonymous_variant	223117	exon10			GCTATACACACAA	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1077G>C	chr7.hg19:g.84666319C>G		117.0	0.0		66.0	15.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Silent	SNP	ENST00000284136.6	hg19	CCDS34676.1																																																																																			.	C|1.000;T|0.000		0.398	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		G	84666319	C	G	84666319	2	3	32	1	0	0	0	0	0	0	0	1	14042	465	17	4		4	SEMA3D	7	84666319	Silent	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	57497428	84666319	74472344	30	3879										
ZNF498	221785	hgsc.bcm.edu	37	chr7	99227217	99227217	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	cacctgggaaagaggccctaCgtgtgcagcgagtgctggaa	15	10	0	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr7:99227217C>T	ENST00000394152.2	+	8	1536	c.1209C>T	c.(1207-1209)taC>taT	p.Y403Y	ZSCAN25_ENST00000334715.3_Silent_p.Y403Y|ZSCAN25_ENST00000262941.6_Silent_p.Y331Y|ZSCAN25_ENST00000466948.1_Intron	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	403					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AGAGGCCCTACGTGTGCAGCG	0.572																																					p.Y403Y		Atlas-SNP	.											.	.	.	.	0			c.C1209T						.						66	63	64					7																	99227217		2203	4300	6503	SO:0001819	synonymous_variant	221785	exon8			GCCCTACGTGTGC	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"-", "Zinc fingers, C2H2-type"	21961	protein-coding gene	gene with protein product			"zinc finger protein 498"	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.1209C>T	chr7.hg19:g.99227217C>T		77.0	0.0		46.0	11.0	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Silent	SNP	ENST00000394152.2	hg19	CCDS5671.2																																																																																			.	.		0.572	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		T	99227217	C	T	99227217	2	4	32	1	0	0	0	0	0	0	0	1	17962	547	19	1		1	ZNF498	7	99227217	Silent	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	14560898	99227217	59911446	31	3880										
FLNC	2318	hgsc.bcm.edu	37	chr7	128489494	128489494	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	acggtgtccacgccggatggGgcagagctcgatgtggatgt	17	9	0	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr7:128489494G>A	ENST00000325888.8	+	30	5322	c.5061G>A	c.(5059-5061)ggG>ggA	p.G1687G	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.G1687G	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1687					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CGCCGGATGGGGCAGAGCTCG	0.602																																					p.G1687G		Atlas-SNP	.											.	FLNC	339	.	0			c.G5061A						.						93	111	105					7																	128489494		2191	4275	6466	SO:0001819	synonymous_variant	2318	exon30			GGATGGGGCAGAG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.5061G>A	chr7.hg19:g.128489494G>A		94.0	0.0		73.0	10.0	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.602	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128489494	G	A	128489494	2	1	32	1	0	0	0	0	0	0	0	1	5943	1219	43	3		3	FLNC	7	128489494	Silent	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	29262277	128489494	30649169	32	3881										
CNOT4	4850	hgsc.bcm.edu	37	chr7	135107050	135107050	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ttttctcattctttatccttTgcagctcttcctgggagagt	7	10	3	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr7:135107050T>C	ENST00000315544.5	-	3	506	c.227A>G	c.(226-228)cAa>cGa	p.Q76R	CNOT4_ENST00000451834.1_Missense_Mutation_p.Q76R|CNOT4_ENST00000414802.1_Missense_Mutation_p.Q76R|CNOT4_ENST00000428680.2_Missense_Mutation_p.Q76R|CNOT4_ENST00000361528.4_Missense_Mutation_p.Q76R|CNOT4_ENST00000356162.4_Missense_Mutation_p.Q76R|CNOT4_ENST00000541284.1_Missense_Mutation_p.Q76R|CNOT4_ENST00000423368.2_Missense_Mutation_p.Q76R	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	76					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						CTTTATCCTTTGCAGCTCTTC	0.338																																					p.Q76R	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.A227G						.						120	110	113					7																	135107050		1807	4082	5889	SO:0001583	missense	4850	exon3			ATCCTTTGCAGCT	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"RNA binding motif (RRM) containing"	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.227A>G	chr7.hg19:g.135107050T>C	ENSP00000326731:p.Gln76Arg	272.0	0.0		206.0	34.0	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	hg19	CCDS55166.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.305288	0.60305	.	.	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	T;T;T;T;T;T;T;T	0.43688	0.95;0.94;0.95;0.95;0.95;0.95;0.94;0.94	5.97	5.97	0.96955	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.48223	0.1488	N	0.20328	0.56	0.80722	D	1	B;B;B;B;P;P	0.48294	0.038;0.022;0.012;0.021;0.908;0.908	B;B;B;B;P;P	0.61397	0.018;0.041;0.006;0.013;0.888;0.888	T	0.45760	-0.9239	10	0.40728	T	0.16	-5.4292	16.1343	0.81471	0.0:0.0:0.0:1.0	.	76;76;76;76;76;76	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	R	76	ENSP00000445508:Q76R;ENSP00000388491:Q76R;ENSP00000406777:Q76R;ENSP00000354673:Q76R;ENSP00000416532:Q76R;ENSP00000348485:Q76R;ENSP00000399108:Q76R;ENSP00000326731:Q76R	ENSP00000262563:Q76R	Q	-	2	0	CNOT4	134757590	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.288000	0.76882	0.533000	0.62120	CAA	.	.		0.338	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		C	135107050	T	C	135107050	3	2	32	1	0	0	0	0	1	0	0	0	3623	1812	63	2	1833	2	CNOT4	7	135107050	Missense_Mutation	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10	6617556	135107050	24031613	33	3882										
GSTK1	373156	hgsc.bcm.edu	37	chr7	142964755	142964755	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	cagaacaagcccagggacttCtggaaaagatcgcaacgcca	10	12	1	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr7:142964755C>A	ENST00000358406.5	+	6	537	c.466C>A	c.(466-468)Ctg>Atg	p.L156M	AC073342.12_ENST00000427392.1_RNA|GSTK1_ENST00000479303.1_Missense_Mutation_p.L212M|GSTK1_ENST00000409500.3_Missense_Mutation_p.L144M|GSTK1_ENST00000443571.2_Missense_Mutation_p.L113M	NM_015917.2	NP_057001.1	Q9Y2Q3	GSTK1_HUMAN	glutathione S-transferase kappa 1	156					epithelial cell differentiation (GO:0030855)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|peroxisome (GO:0005777)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|protein disulfide oxidoreductase activity (GO:0015035)|receptor binding (GO:0005102)			lung(4)	4	Melanoma(164;0.059)				Glutathione(DB00143)	CCAGGGACTTCTGGAAAAGAT	0.507																																					p.L212M		Atlas-SNP	.											.	GSTK1	36	.	0			c.C634A						.						133	124	127					7																	142964755		2203	4300	6503	SO:0001583	missense	373156	exon5			GGACTTCTGGAAA		CCDS5877.1, CCDS47730.1, CCDS47731.1, CCDS47732.1	7q34	2012-06-21			ENSG00000197448	ENSG00000197448	2.5.1.18	"Glutathione S-transferases / Mitochondrial (kappa)"	16906	protein-coding gene	gene with protein product		602321				12720545, 14742434	Standard	NM_015917		Approved	GST13	uc003wcj.3	Q9Y2Q3	OTTHUMG00000152637	ENST00000358406.5:c.466C>A	chr7.hg19:g.142964755C>A	ENSP00000351181:p.Leu156Met	103.0	0.0		108.0	42.0	NM_001143679	B4DIH1|B4DSY2|Q6P4H0|Q7Z520|Q9P1S4	Missense_Mutation	SNP	ENST00000358406.5	hg19	CCDS5877.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.823752	0.50739	.	.	ENSG00000197448	ENST00000409500;ENST00000443571;ENST00000358406;ENST00000479303	.	.	.	5.28	2.42	0.29668	Protein disulphide isomerase, central domain (1);DSBA-like thioredoxin domain (1);Thioredoxin-like fold (1);	0.140610	0.49305	N	0.000147	T	0.56558	0.1993	M	0.78285	2.405	0.09310	N	0.999999	D;D;D;D	0.89917	0.997;0.999;1.0;0.999	D;D;D;D	0.80764	0.988;0.979;0.994;0.988	T	0.46527	-0.9185	9	0.44086	T	0.13	-10.1516	3.6875	0.08334	0.2986:0.4751:0.1449:0.0813	.	144;113;212;156	Q9Y2Q3-3;Q9Y2Q3-4;Q9Y2Q3-2;Q9Y2Q3	.;.;.;GSTK1_HUMAN	M	144;113;156;212	.	ENSP00000351181:L156M	L	+	1	2	GSTK1	142674877	0.860000	0.29831	0.015000	0.15790	0.090000	0.18270	1.852000	0.39348	0.219000	0.20840	-0.310000	0.09108	CTG	.	.		0.507	GSTK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327091.1	NM_015917		A	142964755	C	A	142964755	3	1	32	1	0	0	0	0	1	0	0	0	6845	912	32	3	652	3	GSTK1	7	142964755	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	7857705	142964755	16173908	34	3883										
CYP7A1	1581	hgsc.bcm.edu	37	chr8	59409293	59409293	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	agtgtcattgagaaacatgcGcaggctgatcagttctgaga	12	7	3	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr8:59409293G>A	ENST00000301645.3	-	3	915	c.778C>T	c.(778-780)Cgc>Tgc	p.R260C		NM_000780.3	NP_000771.2	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A, polypeptide 1	260					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cholesterol catabolic process (GO:0006707)|cholesterol homeostasis (GO:0042632)|regulation of bile acid biosynthetic process (GO:0070857)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	cholesterol 7-alpha-monooxygenase activity (GO:0008123)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(1)|urinary_tract(1)	34		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				AGAAACATGCGCAGGCTGATC	0.527									Neonatal Giant Cell Hepatitis																												p.R260C		Atlas-SNP	.											.	CYP7A1	76	.	0			c.C778T						.						216	217	217					8																	59409293		2203	4300	6503	SO:0001583	missense	1581	exon3	Familial Cancer Database	Neonatal Hemochromatosis	ACATGCGCAGGCT	M89803	CCDS6171.1	8q11-q12	2010-05-04	2003-01-14		ENSG00000167910	ENSG00000167910	1.14.13.17	"Cytochrome P450s"	2651	protein-coding gene	gene with protein product	"cholesterol 7 alpha-monooxygenase"	118455	"cytochrome P450, subfamily VIIA (cholesterol 7 alpha-monooxygenase), polypeptide 1"	CYP7		1358792	Standard	NM_000780		Approved		uc003xtm.4	P22680	OTTHUMG00000164301	ENST00000301645.3:c.778C>T	chr8.hg19:g.59409293G>A	ENSP00000301645:p.Arg260Cys	203.0	0.0		172.0	41.0	NM_000780	P78454|Q3MIL8|Q7KZ19	Missense_Mutation	SNP	ENST00000301645.3	hg19	CCDS6171.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.185375	0.38609	.	.	ENSG00000167910	ENST00000301645	T	0.12361	2.69	4.16	4.16	0.48862	.	0.141832	0.64402	D	0.000007	T	0.41858	0.1177	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.46512	-0.9186	10	0.39692	T	0.17	-10.8183	16.8184	0.85739	0.0:0.0:1.0:0.0	.	260	P22680	CP7A1_HUMAN	C	260	ENSP00000301645:R260C	ENSP00000301645:R260C	R	-	1	0	CYP7A1	59571847	1.000000	0.71417	0.998000	0.56505	0.025000	0.11179	3.613000	0.54152	1.992000	0.58205	0.563000	0.77884	CGC	.	.		0.527	CYP7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378190.1	NM_000780		A	59409293	G	A	59409293	3	1	32	1	0	0	0	0	1	0	0	0	4198	1087	38	1	752	1	CYP7A1	8	59409293	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10		59409293	86954729	35	3884										
FOXH1	8928	hgsc.bcm.edu	37	chr8	145700607	145700607	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tccagccctcgtagtcttccCtgaagaaggggaacacggcc	11	14	1	2	rs150426097		TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr8:145700607C>A	ENST00000377317.4	-	2	790	c.212G>T	c.(211-213)aGg>aTg	p.R71M	FOXH1_ENST00000525197.1_Splice_Site	NM_003923.2	NP_003914.1	O75593	FOXH1_HUMAN	forkhead box H1	71					aorta morphogenesis (GO:0035909)|axial mesoderm development (GO:0048318)|cardiac right ventricle morphogenesis (GO:0003215)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|heart looping (GO:0001947)|negative regulation of androgen receptor activity (GO:2000824)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|secondary heart field specification (GO:0003139)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular trabecula myocardium morphogenesis (GO:0003222)	activin responsive factor complex (GO:0032444)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|bHLH transcription factor binding (GO:0043425)|co-SMAD binding (GO:0070410)|enhancer binding (GO:0035326)|protein domain specific binding (GO:0019904)|R-SMAD binding (GO:0070412)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.76e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GTAGTCTTCCCTGAAGAAGGG	0.677																																					p.R71M		Atlas-SNP	.											.	FOXH1	17	.	0			c.G212T						.						43	42	43					8																	145700607		2202	4299	6501	SO:0001583	missense	8928	exon2			TCTTCCCTGAAGA	AF076292	CCDS6428.1	8q24.3	2014-08-12			ENSG00000160973			"Forkhead boxes"	3814	protein-coding gene	gene with protein product		603621				9702198	Standard	NM_003923		Approved	FAST1	uc003zdc.3	O75593	OTTHUMG00000165172	ENST00000377317.4:c.212G>T	chr8.hg19:g.145700607C>A	ENSP00000366534:p.Arg71Met	59.0	0.0		58.0	13.0	NM_003923	D3DWM4	Missense_Mutation	SNP	ENST00000377317.4	hg19	CCDS6428.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.886553	0.51908	.	.	ENSG00000160973	ENST00000377317;ENST00000292541	D	0.96427	-4.01	5.09	0.612	0.17591	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.239729	0.39985	N	0.001219	D	0.94804	0.8322	M	0.89968	3.075	0.36732	D	0.881752	P	0.38617	0.64	B	0.33620	0.167	D	0.92021	0.5626	10	0.87932	D	0	-22.7546	5.9088	0.19016	0.141:0.5887:0.0:0.2703	.	71	O75593	FOXH1_HUMAN	M	71;98	ENSP00000366534:R71M	ENSP00000292541:R98M	R	-	2	0	FOXH1	145671415	0.326000	0.24669	0.999000	0.59377	0.971000	0.66376	0.255000	0.18333	0.177000	0.19895	0.563000	0.77884	AGG	.	C|1.000;T|0.000		0.677	FOXH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382451.1			A	145700607	C	A	145700607	3	1	32	1	0	0	0	0	1	0	0	0	6016	681	24	3	893	3	FOXH1	8	145700607	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	86291314	145700607	663415	36	3885										
IFNW1	3467	hgsc.bcm.edu	37	chr9	21141286	21141286	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tgttccaggcagcagaggagCgctctgtgtggaagaggctg	17	8	1	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr9:21141286C>A	ENST00000380229.2	-	1	858	c.284G>T	c.(283-285)cGc>cTc	p.R95L		NM_002177.1	NP_002168.1	P05000	IFNW1_HUMAN	interferon, omega 1	95			R -> S (in dbSNP:rs2230055).		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cell cycle arrest (GO:0007050)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|lung(2)|ovary(1)	5				GBM - Glioblastoma multiforme(5;2.35e-185)|Lung(24;2.24e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		AGCAGAGGAGCGCTCTGTGTG	0.557																																					p.R95L		Atlas-SNP	.											.	IFNW1	20	.	0			c.G284T						.						89	86	87					9																	21141286		2203	4300	6503	SO:0001583	missense	3467	exon1			GAGGAGCGCTCTG		CCDS6496.1	9p22	2010-12-10			ENSG00000177047	ENSG00000177047		"Interferons"	5448	protein-coding gene	gene with protein product	"IFN-omega 1, interferon omega-1"	147553				1385305	Standard	NM_002177		Approved		uc003zol.1	P05000	OTTHUMG00000019656	ENST00000380229.2:c.284G>T	chr9.hg19:g.21141286C>A	ENSP00000369578:p.Arg95Leu	113.0	0.0		30.0	9.0	NM_002177	Q13168|Q5U802|Q5VWD0|Q7M4P5	Missense_Mutation	SNP	ENST00000380229.2	hg19	CCDS6496.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.948608	0.34377	.	.	ENSG00000177047	ENST00000380229	T	0.03413	3.94	4.54	-6.97	0.01616	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.767260	0.02616	N	0.102690	T	0.03871	0.0109	L	0.48642	1.525	0.09310	N	1	B	0.27166	0.17	B	0.29716	0.106	T	0.39121	-0.9629	10	0.48119	T	0.1	.	3.0022	0.06017	0.1055:0.1575:0.2256:0.5113	.	95	P05000	IFNW1_HUMAN	L	95	ENSP00000369578:R95L	ENSP00000369578:R95L	R	-	2	0	IFNW1	21131286	0.000000	0.05858	0.000000	0.03702	0.540000	0.34992	-2.191000	0.01246	-1.121000	0.02949	-1.446000	0.01064	CGC	.	.		0.557	IFNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051885.1	NM_002177		A	21141286	C	A	21141286	3	1	32	1	0	0	0	0	1	0	0	0	7561	768	27	1	307	1	IFNW1	9	21141286	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10		21141286	120072145	37	3886										
NOL6	65083	hgsc.bcm.edu	37	chr9	33468831	33468831	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tgtagacacaaggaagacaaCcagcatggagacaaggaacc	11	9	0	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr9:33468831C>G	ENST00000379471.2	-	8	1153	c.1066G>C	c.(1066-1068)Gtt>Ctt	p.V356L	NOL6_ENST00000455041.2_Missense_Mutation_p.V296L|NOL6_ENST00000464829.1_5'UTR			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	356					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		AGGAAGACAACCAGCATGGAG	0.562																																					p.V356L		Atlas-SNP	.											.	NOL6	85	.	0			c.G1066C						.						181	181	181					9																	33468831		2203	4300	6503	SO:0001583	missense	65083	exon8			AGACAACCAGCAT	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"nucleolar protein family 6 (RNA-associated)"			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.1066G>C	chr9.hg19:g.33468831C>G	ENSP00000368784:p.Val356Leu	114.0	0.0		63.0	22.0	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	hg19		.	.	.	.	.	.	.	.	.	.	C	9.620	1.133691	0.21123	.	.	ENSG00000165271	ENST00000353159;ENST00000297990;ENST00000379471;ENST00000325914;ENST00000455041	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	4.88	3.03	0.35002	.	0.354004	0.29579	N	0.011752	T	0.20129	0.0484	L	0.31664	0.95	0.41365	D	0.987458	B;B;B;B;B	0.12013	0.001;0.001;0.001;0.005;0.001	B;B;B;B;B	0.14578	0.011;0.004;0.005;0.011;0.007	T	0.12837	-1.0532	10	0.02654	T	1	.	8.2247	0.31562	0.0:0.751:0.0:0.249	.	296;356;356;356;356	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4-3;Q9H6R4	.;.;.;.;NOL6_HUMAN	L	356;356;356;356;296	ENSP00000313978:V356L;ENSP00000297990:V356L;ENSP00000368784:V356L;ENSP00000395915:V296L	ENSP00000297990:V356L	V	-	1	0	NOL6	33458831	0.999000	0.42202	1.000000	0.80357	0.941000	0.58515	0.690000	0.25451	0.489000	0.27749	-0.258000	0.10820	GTT	.	.		0.562	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		G	33468831	C	G	33468831	3	3	32	1	0	0	0	0	1	0	0	0	10534	507	18	4	2450	4	NOL6	9	33468831	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	12327545	33468831	107744600	38	3887										
LARP4B	23185	hgsc.bcm.edu	37	chr10	858938	858939	+	Frame_Shift_Ins	INS	-	-	C													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tggccgagggcgagggccggINSccccccgccggccgcctctg							TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr10:858938_858939insC	ENST00000316157.3	-	17	2184_2185	c.2144_2145insG	c.(2143-2145)ggcfs	p.G715fs	LARP4B_ENST00000469487.1_5'Flank	NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	715					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						GCGAgggccggccccccgccgg	0.678																																					p.G715fs		Atlas-INDEL	.											.,1	LARP4B	110	.	0			c.2145_2146insG						.																																			SO:0001589	frameshift_variant	23185	exon18			.	D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"La ribonucleoprotein domain containing"	28987	protein-coding gene	gene with protein product			"KIAA0217", "La ribonucleoprotein domain family, member 5"	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.2145dupG	chr10.hg19:g.858944_858944dupC	ENSP00000326128:p.Gly715fs	66.0	0.0		129.0	12.0	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Frame_Shift_Ins	INS	ENST00000316157.3	hg19	CCDS31131.1																																																																																			.	.		0.678	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		C	858939	-	C	858938	7	5	32	1	0	1	1	0	0	0	0	0	8640	1190	42	0	75	0	LARP4B	10	858938	Frame_Shift_Ins	INS	-	TCGA-BC-A10R-01A-11D-A12Z-10		858938	134675809	39	3888										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7285628	7285628	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tttacttggttcaggtcttaGgtcatcaatagtcacttgaa	8	7	5	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr10:7285628G>A	ENST00000361972.4	-	9	1102	c.1012C>T	c.(1012-1014)Cta>Tta	p.L338L	SFMBT2_ENST00000397167.1_Silent_p.L338L	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	338					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						TCAGGTCTTAGGTCATCAATA	0.383																																					p.L338L		Atlas-SNP	.											.	SFMBT2	209	.	0			c.C1012T						.						68	64	65					10																	7285628		2203	4300	6503	SO:0001819	synonymous_variant	57713	exon9			GTCTTAGGTCATC	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.1012C>T	chr10.hg19:g.7285628G>A		93.0	0.0		104.0	11.0	NM_001029880	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	hg19	CCDS31138.1																																																																																			.	.		0.383	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		A	7285628	G	A	7285628	2	1	32	1	0	0	0	0	0	0	0	1	14173	991	35	3		3	SFMBT2	10	7285628	Silent	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	6426690	7285628	128249119	40	3889										
MCM10	55388	hgsc.bcm.edu	37	chr10	13212934	13212934	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tcccctagaggaggaagacaAtctgtctctgctgaccgcac	10	13	2	3	rs571506868		TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr10:13212934A>G	ENST00000484800.2	+	3	123	c.20A>G	c.(19-21)aAt>aGt	p.N7S	MCM10_ENST00000378714.3_Missense_Mutation_p.N7S|MCM10_ENST00000378694.1_Missense_Mutation_p.N7S			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	7	N-terminal domain. {ECO:0000250}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						GAGGAAGACAATCTGTCTCTG	0.453													A|||	1	0.000199681	0	0	5008	,	,		20580	0		0.001	False		,,,				2504	0				p.N7S		Atlas-SNP	.											.	MCM10	76	.	0			c.A20G						.						57	59	58					10																	13212934		2203	4300	6503	SO:0001583	missense	55388	exon3			AAGACAATCTGTC	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.20A>G	chr10.hg19:g.13212934A>G	ENSP00000418268:p.Asn7Ser	168.0	0.0		247.0	127.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	hg19	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	A	15.27	2.784078	0.49997	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.14144	2.53;2.53;2.53	5.91	4.77	0.60923	.	0.140827	0.64402	D	0.000007	T	0.09379	0.0231	N	0.14661	0.345	0.32618	N	0.523713	B;B;B	0.23937	0.094;0.082;0.049	B;B;B	0.21708	0.026;0.036;0.016	T	0.05370	-1.0889	10	0.56958	D	0.05	-0.4625	12.1524	0.54057	0.9332:0.0:0.0668:0.0	.	7;7;7	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	S	7	ENSP00000367986:N7S;ENSP00000418268:N7S;ENSP00000367966:N7S	ENSP00000354945:N7S	N	+	2	0	MCM10	13252940	0.999000	0.42202	0.993000	0.49108	0.943000	0.58893	4.456000	0.60081	1.046000	0.40249	0.533000	0.62120	AAT	.	.		0.453	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		G	13212934	A	G	13212934	3	3	32	1	0	0	0	0	1	0	0	0	9394	101	4	2	26	2	MCM10	10	13212934	Missense_Mutation	SNP	A	TCGA-BC-A10R-01A-11D-A12Z-10	5927306	13212934	122321813	41	3890										
COMMD3	23412	hgsc.bcm.edu	37	chr10	22606865	22606866	+	Frame_Shift_Ins	INS	-	-	G													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ttttaaaacattgtcatgcaINSgcagctgcaacttacatact							TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr10:22606865_22606866insG	ENST00000376836.3	+	2	636_637	c.192_193insG	c.(193-195)gcafs	p.A65fs	COMMD3-BMI1_ENST00000463409.2_3'UTR|COMMD3_ENST00000483684.1_3'UTR|COMMD3-BMI1_ENST00000602390.1_Frame_Shift_Ins_p.A65fs	NM_012071.3	NP_036203.1	Q9UBI1	COMD3_HUMAN	COMM domain containing 3	65										kidney(2)|lung(2)|ovary(1)	5						ATTGTCATGCAGCAGCTGCAAC	0.347																																					p.A64fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.192_193insG						.																																			SO:0001589	frameshift_variant	0	exon2			.	AY542159	CCDS7137.1	10p12.2	2012-09-20	2004-02-13	2004-02-18	ENSG00000148444	ENSG00000148444			23332	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 8"	C10orf8		11042152, 15799966	Standard	NM_012071		Approved	BUP		Q9UBI1	OTTHUMG00000017806	ENST00000376836.3:c.193dupG	chr10.hg19:g.22606866_22606866dupG	ENSP00000366032:p.Ala65fs	305.0	0.0		368.0	63.0	NM_001204062	D3DRU7|Q5T8Y9	Frame_Shift_Ins	INS	ENST00000376836.3	hg19	CCDS7137.1																																																																																			.	.		0.347	COMMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047159.1	NM_012071		G	22606866	-	G	22606865	7	5	32	1	0	1	1	0	0	0	0	0	3719	175	7	0	198	0	COMMD3	10	22606865	Frame_Shift_Ins	INS	-	TCGA-BC-A10R-01A-11D-A12Z-10	9393931	22606865	112927882	42	3891										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37505198	37505198	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	atcactgtgaacaacgtacaGgaaaaatggaacaaatgaaa	8	6	1	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr10:37505198G>C	ENST00000602533.1	+	32	2890	c.2791G>C	c.(2791-2793)Gga>Cga	p.G931R	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.G931R|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.G1050R			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	987					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						ACAACGTACAGGAAAAATGGA	0.333																																					p.G931R		Atlas-SNP	.											ANKRD30A_ENST00000602533,NS,carcinoma,-1,1	ANKRD30A	448	.	0			c.G2791C						.						77	73	74					10																	37505198		1815	4067	5882	SO:0001583	missense	91074	exon32			CGTACAGGAAAAA	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.2791G>C	chr10.hg19:g.37505198G>C	ENSP00000473551:p.Gly931Arg	475.0	0.0		576.0	57.0	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	hg19		.	.	.	.	.	.	.	.	.	.	g	0.052	-1.246677	0.01481	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.05258	3.47;3.47	2.63	1.71	0.24356	.	.	.	.	.	T	0.03564	0.0102	N	0.12961	0.28	0.09310	N	1	B	0.26081	0.141	B	0.20955	0.032	T	0.43245	-0.9403	9	0.41790	T	0.15	.	4.5817	0.12262	0.3205:0.0:0.6795:0.0	.	987	Q9BXX3	AN30A_HUMAN	R	931;1050	ENSP00000354432:G931R;ENSP00000363792:G1050R	ENSP00000354432:G931R	G	+	1	0	ANKRD30A	37545204	0.003000	0.15002	0.002000	0.10522	0.003000	0.03518	0.318000	0.19504	0.297000	0.22615	0.313000	0.20887	GGA	.	.		0.333	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		C	37505198	G	C	37505198	3	2	32	1	0	0	0	0	1	0	0	0	658	1001	35	4	2917	4	ANKRD30A	10	37505198	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	14898333	37505198	98029549	43	3892										
CDHR1	92211	hgsc.bcm.edu	37	chr10	85955343	85955343	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	cctcccagaggacacccctgTaggtgagtagccctggcacc	11	16	0	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr10:85955343T>C	ENST00000372117.3	+	2	252	c.149T>C	c.(148-150)gTa>gCa	p.V50A	CDHR1_ENST00000332904.3_Missense_Mutation_p.V50A	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	50	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						GACACCCCTGTAGGTGAGTAG	0.612																																					p.V50A		Atlas-SNP	.											.	CDHR1	122	.	0			c.T149C						.						99	86	90					10																	85955343		2203	4300	6503	SO:0001583	missense	92211	exon2			CCCCTGTAGGTGA	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.149T>C	chr10.hg19:g.85955343T>C	ENSP00000361189:p.Val50Ala	96.0	0.0		66.0	17.0	NM_001171971	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	hg19	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.359078	0.82353	.	.	ENSG00000148600	ENST00000332904;ENST00000372117	T;T	0.53206	0.63;0.63	4.78	4.78	0.61160	Cadherin (3);Cadherin-like (1);	0.215283	0.39687	N	0.001291	T	0.61362	0.2341	M	0.62154	1.92	0.80722	D	1	D;D	0.69078	0.996;0.997	P;D	0.66497	0.907;0.944	T	0.58601	-0.7608	10	0.24483	T	0.36	-9.5748	13.3093	0.60370	0.0:0.0:0.0:1.0	.	50;50	Q96JP9-2;Q96JP9	.;CDHR1_HUMAN	A	50	ENSP00000331063:V50A;ENSP00000361189:V50A	ENSP00000331063:V50A	V	+	2	0	CDHR1	85945323	1.000000	0.71417	0.946000	0.38457	0.900000	0.52787	6.651000	0.74372	1.782000	0.52362	0.459000	0.35465	GTA	.	.		0.612	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		C	85955343	T	C	85955343	3	2	32	1	0	0	0	0	1	0	0	0	3120	1638	57	2	155	2	CDHR1	10	85955343	Missense_Mutation	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10	48450145	85955343	49579404	44	3893										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135025036	135025036	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ggacttccctcggaacagcgGgctgctggggaagctagagg	17	10	0	1	rs151235501		TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr10:135025036G>T	ENST00000304613.3	+	22	4040	c.4019G>T	c.(4018-4020)gGg>gTg	p.G1340V	KNDC1_ENST00000368572.2_Missense_Mutation_p.G1342V			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1340	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CGGAACAGCGGGCTGCTGGGG	0.667																																					p.G1340V		Atlas-SNP	.											.	KNDC1	155	.	0			c.G4019T						.						88	91	90					10																	135025036		2203	4300	6503	SO:0001583	missense	85442	exon22			ACAGCGGGCTGCT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.4019G>T	chr10.hg19:g.135025036G>T	ENSP00000304437:p.Gly1340Val	74.0	0.0		65.0	23.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	10.99	1.507447	0.27036	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.46451	0.87;0.87	3.96	0.693	0.18056	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.803958	0.11184	U	0.590657	T	0.33089	0.0851	L	0.43152	1.355	0.21147	N	0.999776	P	0.49559	0.925	P	0.44732	0.459	T	0.14282	-1.0478	10	0.33940	T	0.23	-15.4731	4.3895	0.11334	0.229:0.358:0.413:0.0	.	1340	Q76NI1	VKIND_HUMAN	V	1340;1342	ENSP00000304437:G1340V;ENSP00000357561:G1342V	ENSP00000304437:G1340V	G	+	2	0	KNDC1	134875026	0.014000	0.17966	0.080000	0.20451	0.173000	0.22820	0.575000	0.23729	-0.084000	0.12595	0.297000	0.19635	GGG	.	G|1.000;A|0.000		0.667	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		T	135025036	G	T	135025036	3	4	32	1	0	0	0	0	1	0	0	0	8435	1232	43	3	4105	3	KNDC1	10	135025036	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	49069693	135025036	509711	45	3894										
GAB2	9846	hgsc.bcm.edu	37	chr11	77937959	77937960	+	Frame_Shift_Ins	INS	-	-	T													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ctgtattgtgccggctcggcINSttgggaaggctatagaagcc							TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr11:77937959_77937960insT	ENST00000361507.4	-	4	843_844	c.758_759insA	c.(757-759)aagfs	p.K253fs	GAB2_ENST00000340149.2_Frame_Shift_Ins_p.K215fs|GAB2_ENST00000526030.1_5'Flank	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	253					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			GCCGGCTCGGCTTGGGAAGGCT	0.569																																					p.K253fs		Atlas-INDEL	.											.	GAB2	63	.	0			c.759_760insA						.		,	5,4259		0,5,2127					,	3.8	1			75	6,8248		0,6,4121	no	frameshift,frameshift	GAB2	NM_080491.2,NM_012296.3	,	0,11,6248	A1A1,A1R,RR		0.0727,0.1173,0.0879	,	,		11,12507				SO:0001589	frameshift_variant	9846	exon4			.	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"Pleckstrin homology (PH) domain containing"	14458	protein-coding gene	gene with protein product	"Grb2-associated binder 2"	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.759dupA	chr11.hg19:g.77937961_77937961dupT	ENSP00000354952:p.Lys253fs	123.0	0.0		77.0	13.0	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Frame_Shift_Ins	INS	ENST00000361507.4	hg19	CCDS8259.1																																																																																			.	.		0.569	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		T	77937960	-	T	77937959	7	5	32	1	0	1	1	0	0	0	0	0	6157	796	28	0	1299	0	GAB2	11	77937959	Frame_Shift_Ins	INS	-	TCGA-BC-A10R-01A-11D-A12Z-10		77937959	57068557	46	3895										
KCNA5	3741	hgsc.bcm.edu	37	chr12	5154891	5154891	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	aactacttctaccaccgggaAacggatcacgaggagccggc	11	13	2	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr12:5154891A>T	ENST00000252321.3	+	1	1807	c.1578A>T	c.(1576-1578)gaA>gaT	p.E526D		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	526					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	ACCACCGGGAAACGGATCACG	0.632																																					p.E526D		Atlas-SNP	.											.	KCNA5	138	.	0			c.A1578T						.						75	70	71					12																	5154891		2203	4300	6503	SO:0001583	missense	3741	exon1			CCGGGAAACGGAT	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.1578A>T	chr12.hg19:g.5154891A>T	ENSP00000252321:p.Glu526Asp	114.0	0.0		64.0	14.0	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	A	16.63	3.177095	0.57692	.	.	ENSG00000130037	ENST00000252321	D	0.97850	-4.57	4.94	3.13	0.36017	.	0.000000	0.85682	U	0.000000	D	0.97408	0.9152	M	0.90483	3.12	0.51482	D	0.999925	P	0.42161	0.772	B	0.43809	0.432	D	0.96105	0.9072	10	0.87932	D	0	.	8.0911	0.30801	0.2461:0.0:0.7539:0.0	.	526	P22460	KCNA5_HUMAN	D	526	ENSP00000252321:E526D	ENSP00000252321:E526D	E	+	3	2	KCNA5	5025152	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.129000	0.31381	0.682000	0.31407	-0.252000	0.11476	GAA	.	.		0.632	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		T	5154891	A	T	5154891	3	4	32	1	0	0	0	0	1	0	0	0	8015	11	1	4	1580	4	KCNA5	12	5154891	Missense_Mutation	SNP	A	TCGA-BC-A10R-01A-11D-A12Z-10		5154891	128697004	47	3896										
RAPGEF3	10411	hgsc.bcm.edu	37	chr12	48135289	48135289	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	caccctgcctggtccctaccAgctcatgcacttcctgtggg	9	17	1	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr12:48135289A>G	ENST00000449771.2	-	19	2010	c.1922T>C	c.(1921-1923)cTg>cCg	p.L641P	RAPGEF3_ENST00000548919.1_Splice_Site_p.L550P|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000389212.3_Splice_Site_p.L641P|RAPGEF3_ENST00000405493.2_Splice_Site_p.L599P|RAPGEF3_ENST00000171000.4_Splice_Site_p.L599P|RAPGEF3_ENST00000549151.1_Splice_Site_p.L599P			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	641					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		GGTCCCTACCAGCTCATGCAC	0.602																																					p.L641P		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.T1922C						.						80	80	80					12																	48135289		2203	4300	6503	SO:0001630	splice_region_variant	10411	exon19			CCTACCAGCTCAT	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"exchange protein directly activated by cAMP 1"	606057	"RAP guanine-nucleotide-exchange factor (GEF) 3"			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1923+1T>C	chr12.hg19:g.48135289A>G		141.0	0.0		143.0	30.0	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	hg19	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.081437	0.36758	.	.	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919	T;T;T;T;T;T	0.74737	-0.87;-0.86;-0.87;-0.87;-0.86;-0.87	5.13	3.99	0.46301	Ras guanine nucleotide exchange factor, domain (1);	0.091635	0.45867	D	0.000338	T	0.71736	0.3375	L	0.34521	1.04	0.80722	D	1	D	0.55800	0.973	P	0.53689	0.732	T	0.72877	-0.4159	10	0.87932	D	0	.	9.2448	0.37518	0.913:0.0:0.087:0.0	.	641	O95398	RPGF3_HUMAN	P	599;641;288;599;599;599;641;604;550	ENSP00000384521:L599P;ENSP00000395708:L641P;ENSP00000448619:L599P;ENSP00000171000:L599P;ENSP00000373864:L641P;ENSP00000448480:L550P	ENSP00000171000:L599P	L	-	2	0	RAPGEF3	46421556	1.000000	0.71417	0.995000	0.50966	0.001000	0.01503	3.342000	0.52159	0.919000	0.36945	-0.250000	0.11733	CTG	.	.		0.602	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	Missense_Mutation	G	48135289	A	G	48135289	5	3	32	1	0	0	0	0	0	0	1	0	13060	202	7	2	889	2	RAPGEF3	12	48135289	Splice_Site	SNP	A	TCGA-BC-A10R-01A-11D-A12Z-10	42980398	48135289	85716606	48	3897										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80732951	80732951	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	atgtaattactactccagctGgactaatcataaagtggtct	7	8	2	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr12:80732951G>A	ENST00000547103.1	+	42	4900	c.4894G>A	c.(4894-4896)Gga>Aga	p.G1632R	OTOGL_ENST00000458043.2_Missense_Mutation_p.G1644R			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1632	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TACTCCAGCTGGACTAATCAT	0.418																																					p.G1644R		Atlas-SNP	.											.	OTOGL	235	.	0			c.G4930A						.						205	203	204					12																	80732951		1885	4097	5982	SO:0001583	missense	283310	exon42			CCAGCTGGACTAA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.4894G>A	chr12.hg19:g.80732951G>A	ENSP00000447211:p.Gly1632Arg	186.0	0.0		105.0	14.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.34	3.363714	0.61513	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.61859	0.07;0.07	5.72	4.82	0.62117	.	.	.	.	.	T	0.63438	0.2511	L	0.46670	1.46	0.33889	D	0.637099	.	.	.	.	.	.	T	0.72994	-0.4122	7	0.56958	D	0.05	.	14.9976	0.71446	0.0693:0.0:0.9307:0.0	.	.	.	.	R	1632;1644	ENSP00000447211:G1632R;ENSP00000400895:G1644R	ENSP00000400895:G1644R	G	+	1	0	OTOGL	79257082	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.410000	0.66381	2.695000	0.91970	0.650000	0.86243	GGA	.	.		0.418	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		A	80732951	G	A	80732951	3	1	32	1	0	0	0	0	1	0	0	0	1709	1349	47	3	5096	3	C12orf64	12	80732951	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	32597662	80732951	53118944	49	3898										
ACACB	32	hgsc.bcm.edu	37	chr12	109637260	109637260	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gtttgagaaggagaacgatcCtacagtcctgagatccccct	10	11	0	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr12:109637260C>T	ENST00000338432.7	+	18	2800	c.2681C>T	c.(2680-2682)cCt>cTt	p.P894L	ACACB_ENST00000377848.3_Missense_Mutation_p.P894L|ACACB_ENST00000377854.5_Missense_Mutation_p.P894L			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	894	Biotinyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GAGAACGATCCTACAGTCCTG	0.557																																					p.P894L		Atlas-SNP	.											.	ACACB	330	.	0			c.C2681T						.						147	135	139					12																	109637260		2203	4300	6503	SO:0001583	missense	32	exon17			ACGATCCTACAGT	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.2681C>T	chr12.hg19:g.109637260C>T	ENSP00000341044:p.Pro894Leu	91.0	0.0		83.0	15.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.367611	0.61513	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	D;D;D	0.81908	-1.55;-1.55;-1.55	5.42	3.58	0.41010	Single hybrid motif (1);	0.049411	0.85682	D	0.000000	D	0.86121	0.5857	M	0.91510	3.215	0.80722	D	1	B	0.22080	0.064	B	0.27170	0.077	D	0.84232	0.0467	10	0.87932	D	0	.	11.3371	0.49511	0.0:0.8036:0.1266:0.0698	.	894	O00763	ACACB_HUMAN	L	894;894;894;125	ENSP00000341044:P894L;ENSP00000367079:P894L;ENSP00000367085:P894L	ENSP00000341044:P894L	P	+	2	0	ACACB	108121643	1.000000	0.71417	0.028000	0.17463	0.331000	0.28603	4.851000	0.62896	0.765000	0.33221	0.585000	0.79938	CCT	.	.		0.557	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109637260	C	T	109637260	3	4	32	1	0	0	0	0	1	0	0	0	107	681	24	3	2747	3	ACACB	12	109637260	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	28904309	109637260	24214635	50	3899										
HPD	3242	hgsc.bcm.edu	37	chr12	122284995	122284995	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tcttgccaggcgctggctcaTtgatgggcatcttgatggac	13	10	3	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr12:122284995T>C	ENST00000289004.4	-	10	757	c.722A>G	c.(721-723)aAt>aGt	p.N241S	HPD_ENST00000543869.2_5'UTR|HPD_ENST00000543163.1_Missense_Mutation_p.N202S	NM_002150.2	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase	241					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|urinary_tract(1)	18	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	CGCTGGCTCATTGATGGGCAT	0.592																																					p.N241S		Atlas-SNP	.											.	HPD	46	.	0			c.A722G						.						134	129	131					12																	122284995		2203	4300	6503	SO:0001583	missense	3242	exon10			GGCTCATTGATGG	BC014790	CCDS9224.1, CCDS53839.1	12q24.31	2013-09-19			ENSG00000158104	ENSG00000158104	1.13.11.27		5147	protein-coding gene	gene with protein product	"glyoxalase domain containing 3"	609695		PPD			Standard	NM_001171993		Approved	4-HPPD, 4HPPD, GLOD3	uc001ubj.3	P32754	OTTHUMG00000169081	ENST00000289004.4:c.722A>G	chr12.hg19:g.122284995T>C	ENSP00000289004:p.Asn241Ser	125.0	0.0		105.0	14.0	NM_002150	A8K461|B3KQ63|Q13234	Missense_Mutation	SNP	ENST00000289004.4	hg19	CCDS9224.1	.	.	.	.	.	.	.	.	.	.	T	18.82	3.705334	0.68615	.	.	ENSG00000158104	ENST00000289004;ENST00000545969;ENST00000543163	T;T	0.66638	-0.22;-0.22	5.6	4.44	0.53790	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.043491	0.85682	D	0.000000	D	0.85048	0.5608	H	0.94582	3.555	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	D	0.87778	0.2610	10	0.87932	D	0	-39.5295	12.0552	0.53531	0.1292:0.0:0.0:0.8708	.	241	P32754	HPPD_HUMAN	S	241;238;202	ENSP00000289004:N241S;ENSP00000441677:N202S	ENSP00000289004:N241S	N	-	2	0	HPD	120769378	1.000000	0.71417	0.788000	0.31933	0.567000	0.35839	7.676000	0.84012	0.927000	0.37143	0.533000	0.62120	AAT	.	.		0.592	HPD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402184.1	NM_002150		C	122284995	T	C	122284995	3	2	32	1	0	0	0	0	1	0	0	0	7341	1493	52	2	479	2	HPD	12	122284995	Missense_Mutation	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10	12647735	122284995	11566900	51	3900										
CENPJ	55835	hgsc.bcm.edu	37	chr13	25459431	25459431	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	aacctttccatcaggatgacTgatttctccctgtatgtctt	6	11	3	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr13:25459431T>A	ENST00000381884.4	-	13	3645	c.3460A>T	c.(3460-3462)Agt>Tgt	p.S1154C	CENPJ_ENST00000493190.1_5'UTR|CENPJ_ENST00000545981.1_3'UTR	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	1154					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		TCAGGATGACTGATTTCTCCC	0.363																																					p.S1154C		Atlas-SNP	.											.	CENPJ	116	.	0			c.A3460T						.						143	144	144					13																	25459431		2203	4300	6503	SO:0001583	missense	55835	exon13			GATGACTGATTTC	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"centrosomal P4.1-associated protein"	609279	"microcephaly, primary autosomal recessive 6"	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.3460A>T	chr13.hg19:g.25459431T>A	ENSP00000371308:p.Ser1154Cys	258.0	0.0		115.0	31.0	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Missense_Mutation	SNP	ENST00000381884.4	hg19	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	T	15.63	2.891335	0.52014	.	.	ENSG00000151849	ENST00000381884	T	0.37584	1.19	5.74	5.74	0.90152	.	0.573254	0.20095	N	0.099351	T	0.40719	0.1128	L	0.60455	1.87	0.80722	D	1	P	0.48503	0.911	B	0.43225	0.412	T	0.38993	-0.9635	10	0.62326	D	0.03	.	15.3236	0.74141	0.0:0.0:0.0:1.0	.	1154	Q9HC77	CENPJ_HUMAN	C	1154	ENSP00000371308:S1154C	ENSP00000371308:S1154C	S	-	1	0	CENPJ	24357431	1.000000	0.71417	1.000000	0.80357	0.393000	0.30537	4.665000	0.61547	2.317000	0.78254	0.460000	0.39030	AGT	.	.		0.363	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		A	25459431	T	A	25459431	3	1	32	1	0	0	0	0	1	0	0	0	3236	1580	55	4	576	4	CENPJ	13	25459431	Missense_Mutation	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10		25459431	89710447	52	3901										
TTC5	91875	hgsc.bcm.edu	37	chr14	20763925	20763925	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ccagaagttgttgctctcgtTgccggggctctggccaggca	14	12	2	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr14:20763925T>C	ENST00000258821.3	-	7	841	c.785A>G	c.(784-786)cAa>cGa	p.Q262R		NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	262					DNA repair (GO:0006281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		TTGCTCTCGTTGCCGGGGCTC	0.488																																					p.Q262R		Atlas-SNP	.											.	TTC5	34	.	0			c.A785G						.						77	89	85					14																	20763925		2203	4300	6503	SO:0001583	missense	91875	exon7			TCTCGTTGCCGGG	BC008647	CCDS9546.1	14q11.2	2013-01-11			ENSG00000136319	ENSG00000136319		"Tetratricopeptide (TTC) repeat domain containing"	19274	protein-coding gene	gene with protein product						11511361	Standard	NM_138376		Approved	Strap	uc001vwt.3	Q8N0Z6	OTTHUMG00000029506	ENST00000258821.3:c.785A>G	chr14.hg19:g.20763925T>C	ENSP00000258821:p.Gln262Arg	138.0	0.0		106.0	18.0	NM_138376	A8MQ18|Q96HF9	Missense_Mutation	SNP	ENST00000258821.3	hg19	CCDS9546.1	.	.	.	.	.	.	.	.	.	.	T	9.972	1.225632	0.22542	.	.	ENSG00000136319	ENST00000258821	T	0.73469	-0.75	4.83	3.68	0.42216	Tetratricopeptide-like helical (1);	0.386187	0.28290	N	0.015895	T	0.53498	0.1800	N	0.22421	0.69	0.26438	N	0.975829	B	0.09022	0.002	B	0.06405	0.002	T	0.25328	-1.0135	10	0.16420	T	0.52	.	5.6527	0.17625	0.0:0.09:0.1738:0.7361	.	262	Q8N0Z6	TTC5_HUMAN	R	262	ENSP00000258821:Q262R	ENSP00000258821:Q262R	Q	-	2	0	TTC5	19833765	0.929000	0.31497	0.837000	0.33122	0.995000	0.86356	0.992000	0.29667	1.946000	0.56461	0.533000	0.62120	CAA	.	.		0.488	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376		C	20763925	T	C	20763925	3	2	32	1	0	0	0	0	1	0	0	0	16726	1812	63	2	553	2	TTC5	14	20763925	Missense_Mutation	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10		20763925	86585615	53	3902										
MYH6	4624	hgsc.bcm.edu	37	chr14	23851737	23851737	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ccagctcatgctgcaccttgCggaacttggacaggttggtg	13	11	1	0	rs61731171		TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr14:23851737C>A	ENST00000356287.3	-	37	5725	c.5696G>T	c.(5695-5697)cGc>cTc	p.R1899L	MYH6_ENST00000405093.3_Missense_Mutation_p.R1899L			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1899					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)	p.R1899H(1)		breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CTGCACCTTGCGGAACTTGGA	0.582																																					p.R1899L		Atlas-SNP	.											MYH6,NS,carcinoma,0,1	MYH6	274	.	1	Substitution - Missense(1)	stomach(1)	c.G5696T						.						190	160	170					14																	23851737		2203	4300	6503	SO:0001583	missense	4624	exon38			ACCTTGCGGAACT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.5696G>T	chr14.hg19:g.23851737C>A	ENSP00000348634:p.Arg1899Leu	199.0	0.0		132.0	26.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	C	32	5.105714	0.94292	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.85171	-1.95;-1.95	4.05	4.05	0.47172	Myosin tail (1);	.	.	.	.	D	0.95121	0.8419	H	0.97265	3.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97038	0.9755	9	0.87932	D	0	.	16.3671	0.83335	0.0:1.0:0.0:0.0	.	1899	P13533	MYH6_HUMAN	L	1899	ENSP00000386041:R1899L;ENSP00000348634:R1899L	ENSP00000348634:R1899L	R	-	2	0	MYH6	22921577	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.644000	0.83416	2.256000	0.74724	0.561000	0.74099	CGC	.	C|0.986;T|0.014		0.582	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23851737	C	A	23851737	3	1	32	1	0	0	0	0	1	0	0	0	10047	768	27	1	131	1	MYH6	14	23851737	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	3087812	23851737	83497803	54	3903										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94052959	94052959	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	cagcagtaaagaatgataccGaaagaaaattttgctaccaa	7	7	0	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr14:94052959G>A	ENST00000393151.2	+	21	2821	c.2821G>A	c.(2821-2823)Gaa>Aaa	p.E941K	UNC79_ENST00000555664.1_Missense_Mutation_p.E941K|UNC79_ENST00000553484.1_Missense_Mutation_p.E941K|UNC79_ENST00000256339.4_Missense_Mutation_p.E764K			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	941					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						GAATGATACCGAAAGAAAATT	0.338																																					p.E764K		Atlas-SNP	.											UNC79,NS,carcinoma,0,2	UNC79	366	.	0			c.G2290A						.						53	52	53					14																	94052959		2202	4299	6501	SO:0001583	missense	57578	exon21			GATACCGAAAGAA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.2821G>A	chr14.hg19:g.94052959G>A	ENSP00000376858:p.Glu941Lys	208.0	0.0		69.0	19.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	G	20.0	3.930849	0.73327	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.17528	2.27;2.27;2.27;2.27	5.94	5.94	0.96194	.	0.061494	0.64402	D	0.000002	T	0.08268	0.0206	N	0.08118	0	0.49687	D	0.999811	P	0.49253	0.921	B	0.33960	0.173	T	0.34502	-0.9826	10	0.09843	T	0.71	-19.9303	20.3736	0.98901	0.0:0.0:1.0:0.0	.	941	C9JQL1	.	K	764;941;941;941;941	ENSP00000256339:E764K;ENSP00000450868:E941K;ENSP00000451360:E941K;ENSP00000376858:E941K	ENSP00000256339:E764K	E	+	1	0	KIAA1409	93122712	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.198000	0.94994	2.820000	0.97059	0.650000	0.86243	GAA	.	.		0.338	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94052959	G	A	94052959	3	1	32	1	0	0	0	0	1	0	0	0	8239	1059	37	1	2360	1	KIAA1409	14	94052959	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	70201222	94052959	13296581	55	3904										
TDRD9	122402	hgsc.bcm.edu	37	chr14	104488538	104488538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tccaacagagagatttaaaaCccttcctgcagtatatatgg	7	9	0	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr14:104488538C>T	ENST00000409874.4	+	24	2525	c.2477C>T	c.(2476-2478)aCc>aTc	p.T826I	TDRD9_ENST00000339063.5_Missense_Mutation_p.T826I	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	826					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				AGATTTAAAACCCTTCCTGCA	0.363																																					p.T826I		Atlas-SNP	.											.	TDRD9	175	.	0			c.C2477T						.						33	31	31					14																	104488538		2203	4296	6499	SO:0001583	missense	122402	exon24			TTAAAACCCTTCC	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.2477C>T	chr14.hg19:g.104488538C>T	ENSP00000387303:p.Thr826Ile	268.0	0.0		123.0	39.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Missense_Mutation	SNP	ENST00000409874.4	hg19	CCDS9987.2	.	.	.	.	.	.	.	.	.	.	C	7.544	0.661388	0.14645	.	.	ENSG00000156414	ENST00000409874;ENST00000339063	T;T	0.03212	4.02;4.01	5.6	3.78	0.43462	.	0.382936	0.24688	N	0.036418	T	0.03608	0.0103	L	0.38531	1.155	0.23361	N	0.997832	B;B	0.22003	0.063;0.004	B;B	0.19946	0.027;0.003	T	0.36138	-0.9760	10	0.40728	T	0.16	.	7.8325	0.29351	0.0:0.7265:0.0:0.2735	.	826;826	Q8NDG6-2;Q8NDG6	.;TDRD9_HUMAN	I	826	ENSP00000387303:T826I;ENSP00000343545:T826I	ENSP00000343545:T826I	T	+	2	0	TDRD9	103558291	0.018000	0.18449	0.014000	0.15608	0.832000	0.47134	0.971000	0.29396	1.370000	0.46153	0.650000	0.86243	ACC	.	.		0.363	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		T	104488538	C	T	104488538	3	4	32	1	0	0	0	0	1	0	0	0	15751	507	18	3	2571	3	TDRD9	14	104488538	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	10435579	104488538	2861002	56	3905										
GABRA5	2558	hgsc.bcm.edu	37	chr15	27114447	27114447	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tgatcaaaaacctccttctcTtttgtatttccatgaactta	3	10	2	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr15:27114447T>G	ENST00000335625.5	+	3	940	c.52T>G	c.(52-54)Ttt>Gtt	p.F18V	GABRA5_ENST00000355395.5_Missense_Mutation_p.F18V|GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000557449.1_3'UTR|GABRA5_ENST00000400081.3_Missense_Mutation_p.F18V	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	18					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	CCTCCTTCTCTTTTGTATTTC	0.373																																					p.F18V		Atlas-SNP	.											GABRA5,NS,carcinoma,0,1	GABRA5	127	.	0			c.T52G						.						211	204	206					15																	27114447		1890	4111	6001	SO:0001583	missense	2558	exon3			CTTCTCTTTTGTA		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.52T>G	chr15.hg19:g.27114447T>G	ENSP00000335592:p.Phe18Val	409.0	1.0		234.0	48.0	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	hg19	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.611593	0.46631	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000557484;ENST00000400081;ENST00000554038;ENST00000554596;ENST00000554599	T;T;T;T;T;T	0.81415	-0.49;-0.49;-0.49;-1.16;-1.17;-1.49	5.82	3.52	0.40303	.	0.319851	0.30723	N	0.009004	T	0.58424	0.2121	N	0.08118	0	0.30420	N	0.778185	B	0.02656	0.0	B	0.01281	0.0	T	0.53322	-0.8455	10	0.44086	T	0.13	.	4.664	0.12657	0.1681:0.087:0.0:0.7449	.	18	P31644	GBRA5_HUMAN	V	18	ENSP00000335592:F18V;ENSP00000347557:F18V;ENSP00000382953:F18V;ENSP00000451527:F18V;ENSP00000450806:F18V;ENSP00000450717:F18V	ENSP00000335592:F18V	F	+	1	0	GABRA5	24665540	0.996000	0.38824	0.999000	0.59377	0.998000	0.95712	0.989000	0.29629	1.006000	0.39211	0.533000	0.62120	TTT	.	.		0.373	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			G	27114447	T	G	27114447	3	3	32	1	0	0	0	0	1	0	0	0	6172	1609	56	5	54	5	GABRA5	15	27114447	Missense_Mutation	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10		27114447	75416945	57	3906										
TRPM1	4308	hgsc.bcm.edu	37	chr15	31295063	31295063	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ttgatgctgctttgccggagAagatacgttgcctcacattc	10	10	1	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr15:31295063A>C	ENST00000256552.6	-	28	3987	c.3840T>G	c.(3838-3840)ctT>ctG	p.L1280L	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Silent_p.L1258L|TRPM1_ENST00000542188.1_Silent_p.L1297L	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		TTTGCCGGAGAAGATACGTTG	0.468																																					p.L1297L		Atlas-SNP	.											.	TRPM1	183	.	0			c.T3891G						.						93	94	93					15																	31295063		2080	4211	6291	SO:0001819	synonymous_variant	4308	exon27			CCGGAGAAGATAC	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.3840T>G	chr15.hg19:g.31295063A>C		138.0	0.0		82.0	17.0	NM_001252020		Silent	SNP	ENST00000256552.6	hg19	CCDS58346.1																																																																																			.	.		0.468	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		C	31295063	A	C	31295063	2	2	32	1	0	0	0	0	0	0	0	1	16600	233	9	5		5	TRPM1	15	31295063	Silent	SNP	A	TCGA-BC-A10R-01A-11D-A12Z-10	4180616	31295063	71236329	58	3907										
RYR3	6263	hgsc.bcm.edu	37	chr15	34105063	34105063	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tgagtatgcttcaattttcaGtctgatgacccagctgtaaa	8	8	3	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr15:34105063G>C	ENST00000389232.4	+	73	10327		c.e73-1		RYR3_ENST00000415757.3_Splice_Site	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3						calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TCAATTTTCAGTCTGATGACC	0.428																																					.		Atlas-SNP	.											.	RYR3	760	.	0			c.10243-1G>C						.						78	75	76					15																	34105063		1876	4112	5988	SO:0001630	splice_region_variant	6263	exon72			TTTTCAGTCTGAT		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10258-1G>C	chr15.hg19:g.34105063G>C		87.0	0.0		56.0	11.0	NM_001243996	O15175|Q15412	Splice_Site	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.477012	0.84640	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	.	.	.	4.69	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1742	0.89756	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RYR3	31892355	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	9.601000	0.98297	2.581000	0.87130	0.655000	0.94253	.	.	.		0.428	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		Intron	C	34105063	G	C	34105063	5	2	32	1	0	0	0	0	0	0	1	0	13785	1043	36	4	10547	4	RYR3	15	34105063	Splice_Site	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	2810000	34105063	68426329	59	3908										
INO80	54617	hgsc.bcm.edu	37	chr15	41377743	41377743	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ttcttcagaggaaagttcttCatctcttcgtctttttttct	5	9	7	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr15:41377743C>T	ENST00000361937.3	-	7	1121	c.697G>A	c.(697-699)Gaa>Aaa	p.E233K	INO80_ENST00000401393.3_Missense_Mutation_p.E233K			Q9ULG1	INO80_HUMAN	INO80 complex subunit	233	Assembles INO80 complex module consisting of conserved components ACTR8, ACTL6A and YY1.|Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GAAAGTTCTTCATCTCTTCGT	0.443																																					p.E233K		Atlas-SNP	.											.	INO80	122	.	0			c.G697A						.						112	110	111					15																	41377743		2203	4300	6503	SO:0001583	missense	54617	exon7			GTTCTTCATCTCT	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.697G>A	chr15.hg19:g.41377743C>T	ENSP00000355205:p.Glu233Lys	548.0	0.0		315.0	62.0	NM_017553	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	hg19	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.735157	0.89482	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.90563	-2.69;-2.69	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.90669	0.7073	N	0.24115	0.695	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	D	0.84695	0.0725	10	0.05525	T	0.97	.	20.1143	0.97922	0.0:1.0:0.0:0.0	.	233	Q9ULG1	INO80_HUMAN	K	233	ENSP00000355205:E233K;ENSP00000384686:E233K	ENSP00000355205:E233K	E	-	1	0	INO80	39165035	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.765000	0.95021	0.650000	0.86243	GAA	.	.		0.443	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		T	41377743	C	T	41377743	3	4	32	1	0	0	0	0	1	0	0	0	7755	835	29	3	4093	3	INO80	15	41377743	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	7272680	41377743	61153649	60	3909										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75968322	75968322	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tgcttccgtccgggcggcctCggggacactgagcagggcca	16	14	0	1	rs370893364		TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr15:75968322C>T	ENST00000308508.5	-	10	6630	c.6538G>A	c.(6538-6540)Gag>Aag	p.E2180K	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	2180	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CGGGCGGCCTCGGGGACACTG	0.701																																					p.E2180K		Atlas-SNP	.											.	CSPG4	175	.	0			c.G6538A						.	C	LYS/GLU	1,4389		0,1,2194	20	21	21		6538	4.3	0.9	15		21	0,8584		0,0,4292	no	missense	CSPG4	NM_001897.4	56	0,1,6486	TT,TC,CC		0.0,0.0228,0.0077	benign	2180/2323	75968322	1,12973	2195	4292	6487	SO:0001583	missense	1464	exon10			CGGCCTCGGGGAC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.6538G>A	chr15.hg19:g.75968322C>T	ENSP00000312506:p.Glu2180Lys	23.0	0.0		33.0	12.0	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	hg19	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	C	5.218	0.225765	0.09916	2.28E-4	0.0	ENSG00000173546	ENST00000308508;ENST00000537176	T	0.19394	2.15	5.26	4.35	0.52113	.	0.516931	0.18538	N	0.138300	T	0.15609	0.0376	L	0.58101	1.795	0.09310	N	1	P	0.35155	0.487	B	0.16289	0.015	T	0.17561	-1.0365	10	0.25751	T	0.34	.	7.5514	0.27800	0.0:0.7283:0.1811:0.0906	.	2180	Q6UVK1	CSPG4_HUMAN	K	2180;212	ENSP00000312506:E2180K	ENSP00000312506:E2180K	E	-	1	0	CSPG4	73755377	0.015000	0.18098	0.866000	0.34008	0.380000	0.30137	0.295000	0.19065	1.228000	0.43614	0.511000	0.50034	GAG	.	.		0.701	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75968322	C	T	75968322	3	4	32	1	0	0	0	0	1	0	0	0	3962	893	31	1	434	1	CSPG4	15	75968322	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	34590579	75968322	26563070	61	3910										
RPL13	6137	hgsc.bcm.edu	37	chr16	89629361	89629361	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tcaaagccttcgctagtctcCgtatggcccgtgccaacgcc	9	16	2	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr16:89629361C>T	ENST00000393099.3	+	5	796	c.547C>T	c.(547-549)Cgt>Tgt	p.R183C	RPL13_ENST00000567815.1_Missense_Mutation_p.R183C|RPL13_ENST00000311528.5_Missense_Mutation_p.R183C|RPL13_ENST00000452368.3_Missense_Mutation_p.R136C|SNORD68_ENST00000363214.1_RNA	NM_033251.2	NP_150254.1	P26373	RL13_HUMAN	ribosomal protein L13	183					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|cytosolic ribosome (GO:0022626)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			lung(3)|skin(1)|upper_aerodigestive_tract(2)	6		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)		CGCTAGTCTCCGTATGGCCCG	0.488																																					p.R183C		Atlas-SNP	.											.	RPL13	11	.	0			c.C547T						.						38	42	40					16																	89629361		2198	4298	6496	SO:0001583	missense	6137	exon6			AGTCTCCGTATGG	AB007172	CCDS10979.1, CCDS58492.1	16q24.3	2011-04-06			ENSG00000167526	ENSG00000167526		"L ribosomal proteins"	10303	protein-coding gene	gene with protein product		113703				9582194	Standard	NM_000977		Approved	D16S444E, BBC1, L13	uc002fnm.2	P26373	OTTHUMG00000133770	ENST00000393099.3:c.547C>T	chr16.hg19:g.89629361C>T	ENSP00000376811:p.Arg183Cys	165.0	0.0		120.0	13.0	NM_000977	B4DLX3|F5H1S2|Q3KQT8|Q567Q8|Q9BPX0	Missense_Mutation	SNP	ENST00000393099.3	hg19	CCDS10979.1	.	.	.	.	.	.	.	.	.	.	C	14.84	2.656118	0.47467	.	.	ENSG00000167526	ENST00000311528;ENST00000452368;ENST00000393099	T;T;T	0.51071	0.72;0.72;0.72	4.52	3.57	0.40892	.	0.000000	0.85682	U	0.000000	T	0.47377	0.1442	M	0.75447	2.3	0.80722	D	1	B;B	0.32543	0.375;0.027	B;B	0.29785	0.107;0.063	T	0.53158	-0.8478	10	0.62326	D	0.03	-9.6763	12.6145	0.56569	0.0:0.9187:0.0:0.0813	.	136;183	F5H1S2;P26373	.;RL13_HUMAN	C	183;136;183	ENSP00000307889:R183C;ENSP00000438959:R136C;ENSP00000376811:R183C	ENSP00000307889:R183C	R	+	1	0	RPL13	88156862	1.000000	0.71417	0.768000	0.31515	0.452000	0.32318	7.678000	0.84035	1.041000	0.40125	0.462000	0.41574	CGT	.	.		0.488	RPL13-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258294.2	NM_000977		T	89629361	C	T	89629361	3	4	32	1	0	0	0	0	1	0	0	0	13574	652	23	1	565	1	RPL13	16	89629361	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10		89629361	725392	62	3911										
TP53	7157	hgsc.bcm.edu	37	chr17	7578524	7578524	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	agggcaggtcttggccagttGgcaaaacatcttgttgaggg	15	7	2	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr17:7578524G>A	ENST00000269305.4	-	5	595	c.406C>T	c.(406-408)Caa>Taa	p.Q136*	TP53_ENST00000445888.2_Nonsense_Mutation_p.Q136*|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q136*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q136*|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q136*|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q136*|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	136	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Q -> E (in sporadic cancers; somatic mutation).|Q -> H (in sporadic cancers; somatic mutation).|Q -> K (in a sporadic cancer; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q136*(34)|p.0?(8)|p.C135fs*9(3)|p.Q136E(3)|p.N131fs*27(2)|p.F134_T140>S(1)|p.K132_A138delKMFCQLA(1)|p.Q136K(1)|p.S127_Q136del10(1)|p.V73fs*9(1)|p.Q43*(1)|p.Y126fs*11(1)|p.Q4*(1)|p.C3fs*9(1)|p.C42fs*9(1)|p.C135_A138delCQLA(1)|p.Q136_K139delQLAK(1)|p.Q136fs*34(1)|p.C135_T140delCQLAKT(1)|p.Q136fs*13(1)|p.C135_Q136insXXXXXX(1)|p.C135_Q136insX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTGGCCAGTTGGCAAAACATC	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Q136X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,4	TP53	33396	.	67	Substitution - Nonsense(36)|Deletion - Frameshift(10)|Whole gene deletion(8)|Deletion - In frame(5)|Substitution - Missense(4)|Insertion - In frame(2)|Insertion - Frameshift(1)|Complex - deletion inframe(1)	upper_aerodigestive_tract(9)|ovary(9)|urinary_tract(8)|central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(6)|stomach(5)|breast(4)|bone(4)|large_intestine(3)|oesophagus(3)|skin(3)|lung(3)|soft_tissue(1)|endometrium(1)|pancreas(1)	c.C406T	GRCh37	CM971503	TP53	M		.						52	52	52					17																	7578524		2203	4300	6503	SO:0001587	stop_gained	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CCAGTTGGCAAAA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.406C>T	chr17.hg19:g.7578524G>A	ENSP00000269305:p.Gln136*	48.0	0.0		35.0	21.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	34	5.349260	0.95830	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-25.5387	17.2272	0.86973	0.0:0.0:1.0:0.0	.	.	.	.	X	136;136;136;136;136;136;125;43;4;43;4;136	.	ENSP00000269305:Q136X	Q	-	1	0	TP53	7519249	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	9.809000	0.99208	2.733000	0.93635	0.655000	0.94253	CAA	.	.		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578524	G	A	7578524	4	1	32	1	0	0	0	0	0	1	0	0	16396	1357	47	3	892	3	TP53	17	7578524	Nonsense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10		7578524	73616686	63	3912										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12666487	12666487	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	actgctgtcctcaccaagccCtcggcttcctttgaacaagc	7	16	1	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr17:12666487C>T	ENST00000343344.4	+	13	2343	c.2343C>T	c.(2341-2343)ccC>ccT	p.P781P	MYOCD_ENST00000425538.1_Silent_p.P829P|RP11-1090M7.1_ENST00000584772.1_RNA			Q8IZQ8	MYCD_HUMAN	myocardin	781					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		TCACCAAGCCCTCGGCTTCCT	0.493																																					p.P829P		Atlas-SNP	.											.	MYOCD	291	.	0			c.C2487T						.						106	101	103					17																	12666487		2203	4300	6503	SO:0001819	synonymous_variant	93649	exon14			CAAGCCCTCGGCT	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.2343C>T	chr17.hg19:g.12666487C>T		121.0	0.0		56.0	34.0	NM_001146312	Q5UBU5|Q8N7Q1	Silent	SNP	ENST00000343344.4	hg19	CCDS11163.1																																																																																			.	.		0.493	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		T	12666487	C	T	12666487	2	4	32	1	0	0	0	0	0	0	0	1	10096	668	24	3		3	MYOCD	17	12666487	Silent	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	5087963	12666487	68528723	64	3913										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27449219	27449219	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ccctatggaccagccacaccTtctccgtctcattccaggcc	6	19	2	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr17:27449219T>G	ENST00000527372.1	-	3	1232	c.1052A>C	c.(1051-1053)aAg>aCg	p.K351T	MYO18A_ENST00000533112.1_Missense_Mutation_p.K351T|MYO18A_ENST00000354329.4_Missense_Mutation_p.K351T|MYO18A_ENST00000531253.1_Missense_Mutation_p.K351T	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	351	Mediates nucleotide-independent binding to F-actin and interaction with GOLPH3.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CAGCCACACCTTCTCCGTCTC	0.557																																					p.K351T	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.A1052C						.						67	79	75					17																	27449219		2012	4183	6195	SO:0001583	missense	399687	exon3			CACACCTTCTCCG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.1052A>C	chr17.hg19:g.27449219T>G	ENSP00000437073:p.Lys351Thr	262.0	0.0		126.0	74.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.2|27.2	4.808029|4.808029	0.90707|0.90707	.|.	.|.	ENSG00000196535|ENSG00000196535	ENST00000528564|ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000531686	T|D;D;D;D	0.77489|0.88741	-1.1|-2.31;-2.42;-2.31;-2.31	5.11|5.11	5.11|5.11	0.69529|0.69529	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93871|0.93871	0.8039|0.8039	M|M	0.79123|0.79123	2.44|2.44	0.45464|0.45464	D|D	0.998438|0.998438	.|D;D;D;D	.|0.89917	.|0.959;0.999;0.999;1.0	.|P;D;D;D	.|0.87578	.|0.749;0.994;0.994;0.998	D|D	0.93890|0.93890	0.7179|0.7179	7|10	0.48119|0.49607	T|T	0.1|0.09	.|.	14.0293|14.0293	0.64606|0.64606	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|20;351;351;351	.|Q92614-2;Q92614-3;Q92614-4;Q92614	.|.;.;.;MY18A_HUMAN	D|T	56|351;351;351;351;351;31	ENSP00000436660:E56D|ENSP00000346291:K351T;ENSP00000435932:K351T;ENSP00000434228:K351T;ENSP00000437073:K351T	ENSP00000436660:E56D|ENSP00000346291:K351T	E|K	-|-	3|2	2|0	MYO18A|MYO18A	24473345|24473345	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	5.565000|5.565000	0.67365|0.67365	2.145000|2.145000	0.66743|0.66743	0.533000|0.533000	0.62120|0.62120	GAA|AAG	.	.		0.557	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		G	27449219	T	G	27449219	3	3	32	1	0	0	0	0	1	0	0	0	10074	1609	56	5	5272	5	MYO18A	17	27449219	Missense_Mutation	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10	14782732	27449219	53745991	65	3914										
MED24	9862	hgsc.bcm.edu	37	chr17	38189358	38189358	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ccaccagggactgcgtctcgCctgtcaggttcatggtgccc	12	15	3	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr17:38189358C>T	ENST00000394128.2	-	8	854	c.773G>A	c.(772-774)gGc>gAc	p.G258D	MED24_ENST00000356271.3_Missense_Mutation_p.G245D|MED24_ENST00000501516.3_Missense_Mutation_p.G277D|MED24_ENST00000394126.1_Missense_Mutation_p.G283D|MED24_ENST00000394127.2_Missense_Mutation_p.G245D|MED24_ENST00000479829.1_5'Flank	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	258					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CTGCGTCTCGCCTGTCAGGTT	0.637																																					p.G258D		Atlas-SNP	.											.	MED24	89	.	0			c.G773A						.						60	51	54					17																	38189358		2203	4300	6503	SO:0001583	missense	9862	exon8			GTCTCGCCTGTCA	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.773G>A	chr17.hg19:g.38189358C>T	ENSP00000377686:p.Gly258Asp	87.0	0.0		37.0	18.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	hg19	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.567240	0.45694	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000543759;ENST00000535508;ENST00000431269;ENST00000428757	T;T;T	0.47177	0.85;0.85;0.85	5.68	5.68	0.88126	Mediator complex, subunit Med24, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.66752	0.2821	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.99;1.0;0.988;1.0;0.996;0.997;1.0	D;D;D;P;D;D;D;D	0.97110	0.996;0.921;1.0;0.871;0.99;0.953;0.972;0.99	T	0.65269	-0.6209	10	0.52906	T	0.07	-24.9058	19.807	0.96535	0.0:1.0:0.0:0.0	.	245;208;187;208;168;245;258;200	B9TX65;B4DV99;B4DDR8;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;.;.;MED24_HUMAN;.	D	258;258;258;208;245;200;232;232;168;277	ENSP00000377686:G258D;ENSP00000443344:G208D;ENSP00000377685:G245D	ENSP00000348610:G258D	G	-	2	0	MED24	35442884	1.000000	0.71417	0.943000	0.38184	0.601000	0.36947	5.999000	0.70665	2.690000	0.91761	0.655000	0.94253	GGC	.	.		0.637	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		T	38189358	C	T	38189358	3	4	32	1	0	0	0	0	1	0	0	0	9451	739	26	3	2272	3	MED24	17	38189358	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	10740139	38189358	43005852	66	3915										
MTMR4	9110	hgsc.bcm.edu	37	chr17	56582147	56582147	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ttcctctcaatacctccaacGtcctgtaatatgggtccagt	6	13	1	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr17:56582147G>A	ENST00000323456.5	-	12	1416	c.1292C>T	c.(1291-1293)aCg>aTg	p.T431M	MTMR4_ENST00000579925.1_Missense_Mutation_p.T431M	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	431	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TACCTCCAACGTCCTGTAATA	0.552																																					p.T431M		Atlas-SNP	.											.	MTMR4	91	.	0			c.C1292T						.						136	137	137					17																	56582147		2203	4300	6503	SO:0001583	missense	9110	exon12			TCCAACGTCCTGT	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.1292C>T	chr17.hg19:g.56582147G>A	ENSP00000325285:p.Thr431Met	81.0	0.0		47.0	12.0	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Missense_Mutation	SNP	ENST00000323456.5	hg19	CCDS11608.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.962917	0.92791	.	.	ENSG00000108389	ENST00000323456	D	0.96554	-4.05	5.4	5.4	0.78164	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.99174	0.9714	H	0.99764	4.76	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98660	1.0683	10	0.87932	D	0	.	18.5101	0.90913	0.0:0.0:1.0:0.0	.	431	Q9NYA4	MTMR4_HUMAN	M	431	ENSP00000325285:T431M	ENSP00000325285:T431M	T	-	2	0	MTMR4	53937146	1.000000	0.71417	0.961000	0.40146	0.964000	0.63967	9.813000	0.99286	2.688000	0.91661	0.591000	0.81541	ACG	.	.		0.552	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687		A	56582147	G	A	56582147	3	1	32	1	0	0	0	0	1	0	0	0	9955	1145	40	1	2327	1	MTMR4	17	56582147	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	18392789	56582147	24613063	67	3916										
METTL2A	339175	hgsc.bcm.edu	37	chr17	60501620	60501620	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	aagagcaagccgcggcggcgGagagaaaagtccaggagaac	16	9	0	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr17:60501620G>A	ENST00000311506.5	+	2	187	c.151G>A	c.(151-153)Gag>Aag	p.E51K		NM_181725.3	NP_859076.3	Q96IZ6	MET2A_HUMAN	methyltransferase like 2A	51					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(2)|central_nervous_system(1)|endometrium(1)|upper_aerodigestive_tract(2)	6			BRCA - Breast invasive adenocarcinoma(2;1.08e-10)			CGCGGCGGCGGAGAGAAAAGT	0.582											OREG0024635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E51K		Atlas-SNP	.											.	METTL2A	31	.	0			c.G151A						.						66	92	84					17																	60501620		692	1590	2282	SO:0001583	missense	339175	exon2			GCGGCGGAGAGAA	AK000991	CCDS45752.1	17q23.3	2012-12-20		2006-02-10	ENSG00000087995	ENSG00000087995			25755	protein-coding gene	gene with protein product						12477932	Standard	NM_181725		Approved	FLJ12760, METTL2	uc002izv.2	Q96IZ6	OTTHUMG00000164527	ENST00000311506.5:c.151G>A	chr17.hg19:g.60501620G>A	ENSP00000309610:p.Glu51Lys	127.0	0.0	1046	76.0	20.0	NM_181725	A6NNC4|Q9H9G9|Q9NUI8|Q9P0B5	Missense_Mutation	SNP	ENST00000311506.5	hg19	CCDS45752.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.110154	0.37242	.	.	ENSG00000087995	ENST00000311506;ENST00000333483	D	0.82255	-1.59	5.14	3.09	0.35607	.	0.568252	0.21244	N	0.077764	T	0.68705	0.3030	L	0.33189	0.99	0.27932	N	0.937828	B	0.02656	0.0	B	0.08055	0.003	T	0.51387	-0.8712	10	0.14656	T	0.56	-4.2637	5.6823	0.17782	0.1401:0.353:0.5069:0.0	.	51	Q96IZ6	MTL2A_HUMAN	K	51	ENSP00000309610:E51K	ENSP00000309610:E51K	E	+	1	0	METTL2A	57855352	0.698000	0.27777	0.990000	0.47175	0.893000	0.52053	1.356000	0.34079	1.263000	0.44181	0.555000	0.69702	GAG	.	.		0.582	METTL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445130.1	NM_181725		A	60501620	G	A	60501620	3	1	32	1	0	0	0	0	1	0	0	0	9508	1175	41	3	157	3	METTL2A	17	60501620	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	3919473	60501620	20693590	68	3917										
ENPP7	339221	hgsc.bcm.edu	37	chr17	77711821	77711821	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	atgggactgctggggaccgtGattcttctgtctgaggtcgc	15	9	3	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr17:77711821G>A	ENST00000328313.5	+	5	1574	c.1353G>A	c.(1351-1353)gtG>gtA	p.V451V		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			TGGGGACCGTGATTCTTCTGT	0.642																																					p.V451V		Atlas-SNP	.											.	ENPP7	63	.	0			c.G1353A						.						88	80	83					17																	77711821		2203	4300	6503	SO:0001819	synonymous_variant	339221	exon5			GACCGTGATTCTT	AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"alkaline sphingomyelinase"					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.1353G>A	chr17.hg19:g.77711821G>A		43.0	0.0		38.0	16.0	NM_178543		Silent	SNP	ENST00000328313.5	hg19	CCDS11763.1																																																																																			.	.		0.642	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543		A	77711821	G	A	77711821	2	1	32	1	0	0	0	0	0	0	0	1	5137	1277	45	3		3	ENPP7	17	77711821	Silent	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	17210201	77711821	3483389	69	3918										
SOCS6	9306	hgsc.bcm.edu	37	chr18	67992724	67992724	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gtcaggtagaccaggacctaGttgtcgccccagagatcttc	11	12	2	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr18:67992724G>C	ENST00000397942.3	+	2	1136	c.820G>C	c.(820-822)Gtt>Ctt	p.V274L	SOCS6_ENST00000582322.1_Missense_Mutation_p.V274L	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	274					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				CCAGGACCTAGTTGTCGCCCC	0.572																																					p.V274L	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-SNP	.											.	SOCS6	54	.	0			c.G820C						.						161	140	147					18																	67992724		2203	4300	6503	SO:0001583	missense	9306	exon2			GACCTAGTTGTCG	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.820G>C	chr18.hg19:g.67992724G>C	ENSP00000381034:p.Val274Leu	279.0	0.0		164.0	55.0	NM_004232	Q8WUM3	Missense_Mutation	SNP	ENST00000397942.3	hg19	CCDS11998.1	.	.	.	.	.	.	.	.	.	.	G	6.742	0.505609	0.12822	.	.	ENSG00000170677	ENST00000397942	T	0.27104	1.69	5.0	5.0	0.66597	.	0.808617	0.10957	N	0.615438	T	0.24353	0.0590	L	0.29908	0.895	0.39481	D	0.967887	B	0.06786	0.001	B	0.04013	0.001	T	0.06588	-1.0818	10	0.33940	T	0.23	-4.9182	18.3063	0.90182	0.0:0.0:1.0:0.0	.	274	O14544	SOCS6_HUMAN	L	274	ENSP00000381034:V274L	ENSP00000381034:V274L	V	+	1	0	SOCS6	66143704	1.000000	0.71417	0.016000	0.15963	0.209000	0.24338	5.769000	0.68865	2.309000	0.77851	0.561000	0.74099	GTT	.	.		0.572	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			C	67992724	G	C	67992724	3	2	32	1	0	0	0	0	1	0	0	0	14933	1029	36	4	822	4	SOCS6	18	67992724	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10		67992724	10084524	70	3919										
ATP9B	374868	hgsc.bcm.edu	37	chr18	77108133	77108134	+	Splice_Site	INS	-	-	TG													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tgtgggctctctctccaggcINStgtgttttcctcagtcttct							TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr18:77108133_77108134insTG	ENST00000426216.2	+	25	2857_2858	c.2840_2841insTG	c.(2839-2844)gctgtg>gcTGtgtg	p.AV947fs	ATP9B_ENST00000543761.1_Splice_Site_p.AV268fs|ATP9B_ENST00000307671.7_Splice_Site_p.AV947fs	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	947					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		TCTCTCCAGGCTGTGTTTTCCT	0.564																																					p.A947fs		Atlas-Indel,Pindel	.											.	ATP9B	96	.	0			c.2840_2841insTG						.																																			SO:0001630	splice_region_variant	374868	exon25			.	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"ATPases / P-type"	13541	protein-coding gene	gene with protein product		614446	"ATPase, Class II, type 9B"			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.2839-1->TG	chr18.hg19:g.77108136_77108137dupTG		392.0	0.0		242.0	63.0	NM_198531	O60872|Q08AD8|Q08AD9	Frame_Shift_Ins	INS	ENST00000426216.2	hg19	CCDS12014.1																																																																																			.	.		0.564	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	Frame_Shift_Ins	TG	77108134	-	TG	77108133	8	5	32	1	0	1	1	0	0	0	1	0	1199	811	28	0	2938	0	ATP9B	18	77108133	Splice_Site	INS	-	TCGA-BC-A10R-01A-11D-A12Z-10	9115409	77108133	969115	71	3920										
C19orf21	126353	hgsc.bcm.edu	37	chr19	756999	756999	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	catccctcaggcacaccgtgGcaccggcctggtgctggatg	13	15	1	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:756999G>C	ENST00000215582.6	+	2	156	c.53G>C	c.(52-54)gGc>gCc	p.G18A		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	18					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											GCACACCGTGGCACCGGCCTG	0.657																																					p.G18A		Atlas-SNP	.											.	C19orf21	56	.	0			c.G53C						.						25	24	24					19																	756999		2201	4297	6498	SO:0001583	missense	126353	exon2			ACCGTGGCACCGG	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.53G>C	chr19.hg19:g.756999G>C	ENSP00000215582:p.Gly18Ala	113.0	0.0		116.0	15.0	NM_173481		Missense_Mutation	SNP	ENST00000215582.6	hg19	CCDS12042.1	.	.	.	.	.	.	.	.	.	.	G	1.285	-0.609135	0.03690	.	.	ENSG00000099812	ENST00000215582	D	0.91577	-2.87	4.27	0.897	0.19258	.	2.194520	0.02204	N	0.062565	T	0.68824	0.3043	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.71797	-0.4484	10	0.02654	T	1	-3.176	4.1001	0.10010	0.0:0.2111:0.3661:0.4227	.	18	Q8IVT2	CS021_HUMAN	A	18	ENSP00000215582:G18A	ENSP00000215582:G18A	G	+	2	0	C19orf21	707999	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	0.275000	0.18698	0.156000	0.19299	-1.277000	0.01392	GGC	.	.		0.657	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		C	756999	G	C	756999	3	2	32	1	0	0	0	0	1	0	0	0	1915	1203	42	4	55	4	C19orf21	19	756999	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10		756999	58371984	72	3921										
PCSK4	54760	hgsc.bcm.edu	37	chr19	1484101	1484101	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tgcccgtgtgctggtctgtgCacccgtgatgcaggtccgtg	15	12	1	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:1484101C>T	ENST00000300954.5	-	9	1155	c.1094G>A	c.(1093-1095)tGc>tAc	p.C365Y	CTB-25B13.6_ENST00000585643.1_RNA	NM_017573.3	NP_060043.2			proprotein convertase subtilisin/kexin type 4											cervix(2)|endometrium(2)|kidney(1)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGGTCTGTGCACCCGTGATG	0.662																																					p.C365Y		Atlas-SNP	.											.	PCSK4	44	.	0			c.G1094A						.						10	12	11					19																	1484101		2180	4268	6448	SO:0001583	missense	54760	exon9			TCTGTGCACCCGT	AK057235	CCDS12069.2	19p13.3	2008-02-05			ENSG00000115257	ENSG00000115257			8746	protein-coding gene	gene with protein product		600487				7782070	Standard	XM_005259586		Approved	PC4, SPC5, DKFZp434B217, MGC34749	uc002ltb.1	Q6UW60	OTTHUMG00000128541	ENST00000300954.5:c.1094G>A	chr19.hg19:g.1484101C>T	ENSP00000300954:p.Cys365Tyr	68.0	0.0		128.0	71.0	NM_017573		Missense_Mutation	SNP	ENST00000300954.5	hg19	CCDS12069.2	.	.	.	.	.	.	.	.	.	.	-	14.46	2.543283	0.45280	.	.	ENSG00000115257	ENST00000300954;ENST00000441747	T	0.80566	-1.39	2.76	2.76	0.32466	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.552403	0.16865	N	0.196378	D	0.88228	0.6380	M	0.75447	2.3	0.53688	D	0.999977	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	D	0.88770	0.3263	10	0.87932	D	0	.	12.4425	0.55634	0.0:1.0:0.0:0.0	.	365;177	Q6UW60;B3KQ28	PCSK4_HUMAN;.	Y	365;177	ENSP00000300954:C365Y	ENSP00000300954:C365Y	C	-	2	0	PCSK4	1435101	1.000000	0.71417	0.996000	0.52242	0.115000	0.19883	7.590000	0.82653	1.286000	0.44565	0.274000	0.19336	TGC	.	.		0.662	PCSK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449703.1	NM_017573		T	1484101	C	T	1484101	3	4	32	1	0	0	0	0	1	0	0	0	11611	710	25	3	1201	3	PCSK4	19	1484101	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	727102	1484101	57644882	73	3922										
REXO1	57455	hgsc.bcm.edu	37	chr19	1828274	1828275	+	Frame_Shift_Ins	INS	-	-	G													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ctgcccggctcggcaggggcINSggccagtggggtgggctggt					rs545604526		TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:1828274_1828275insG	ENST00000170168.4	-	2	607_608	c.513_514insC	c.(511-516)gccgccfs	p.A172fs	REXO1_ENST00000587524.1_5'UTR	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	172						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGGCAGGGGCGGCCAGTGGGG	0.698																																					p.A172fs		Atlas-INDEL	.											.	REXO1	55	.	0			c.514_515insC						.																																			SO:0001589	frameshift_variant	57455	exon2			.	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"elongin A binding protein 1"	609614	"transcription elongation factor B polypeptide 3 binding protein 1"	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.514dupC	chr19.hg19:g.1828276_1828276dupG	ENSP00000170168:p.Ala172fs	58.0	0.0		51.0	11.0	NM_020695	Q9ULT2	Frame_Shift_Ins	INS	ENST00000170168.4	hg19	CCDS32866.1																																																																																			.	.		0.698	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		G	1828275	-	G	1828274	7	5	32	1	0	1	1	0	0	0	0	0	13256	768	27	0	3211	0	REXO1	19	1828274	Frame_Shift_Ins	INS	-	TCGA-BC-A10R-01A-11D-A12Z-10	344173	1828274	57300709	74	3923										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11143994	11143994	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	agcgcaggaccgagcccaccGcatcgggcagcagaacgagg	15	14	0	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:11143994G>A	ENST00000429416.3	+	27	3856	c.3575G>A	c.(3574-3576)cGc>cAc	p.R1192H	SMARCA4_ENST00000590574.1_Missense_Mutation_p.R1192H|SMARCA4_ENST00000413806.3_Missense_Mutation_p.R1192H|SMARCA4_ENST00000450717.3_Missense_Mutation_p.R1192H|SMARCA4_ENST00000358026.2_Missense_Mutation_p.R1192H|SMARCA4_ENST00000344626.4_Missense_Mutation_p.R1192H|SMARCA4_ENST00000589677.1_Missense_Mutation_p.R1192H|SMARCA4_ENST00000444061.3_Missense_Mutation_p.R1192H|SMARCA4_ENST00000541122.2_Missense_Mutation_p.R1192H	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1192	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CGAGCCCACCGCATCGGGCAG	0.612			"F, N, Mis"		NSCLC																																p.R1192H		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	SMARCA4_ENST00000358026,NS,carcinoma,+1,2	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.G3575A						.						63	62	62					19																	11143994		2203	4300	6503	SO:0001583	missense	6597	exon26			CCCACCGCATCGG	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3575G>A	chr19.hg19:g.11143994G>A	ENSP00000395654:p.Arg1192His	90.0	0.0		77.0	15.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769759	0.90020	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.97850	-4.57;-4.57;-4.57;-4.57;-4.57;-4.57;-4.57	4.74	4.74	0.60224	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99426	0.9797	H	0.99863	4.86	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97804	1.0246	10	0.87932	D	0	-34.1151	16.7067	0.85374	0.0:0.0:1.0:0.0	.	1192;1192;1192;1192;1192;412;1192	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	H	1192;1192;1256;1192;1192;1192;1192;1192	ENSP00000395654:R1192H;ENSP00000350720:R1192H;ENSP00000343896:R1192H;ENSP00000445036:R1192H;ENSP00000392837:R1192H;ENSP00000397783:R1192H;ENSP00000414727:R1192H	ENSP00000343896:R1192H	R	+	2	0	SMARCA4	11004994	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.319000	0.96338	2.488000	0.83962	0.558000	0.71614	CGC	.	.		0.612	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		A	11143994	G	A	11143994	3	1	32	1	0	0	0	0	1	0	0	0	14785	1087	38	1	3673	1	SMARCA4	19	11143994	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	9315720	11143994	47984989	75	3924										
LOC55908	55908	hgsc.bcm.edu	37	chr19	11350899	11350899	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	acagaaggtgctacgggacaGcgtgcagcggctagaagtcc	15	10	0	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:11350899G>T	ENST00000252453.8	+	2	405	c.386G>T	c.(385-387)aGc>aTc	p.S129I	DOCK6_ENST00000294618.7_Intron|DOCK6_ENST00000319867.7_5'Flank|C19orf80_ENST00000591200.1_Missense_Mutation_p.S30I	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	129					cellular lipid metabolic process (GO:0044255)|glucose metabolic process (GO:0006006)|positive regulation of protein processing (GO:0010954)|regulation of lipoprotein metabolic process (GO:0050746)|triglyceride homeostasis (GO:0070328)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|breast(1)|endometrium(2)	4						CTACGGGACAGCGTGCAGCGG	0.597																																					p.S129I		Atlas-SNP	.											.	C19orf80	8	.	0			c.G386T						.						18	25	23					19																	11350899		2042	4195	6237	SO:0001583	missense	55908	exon2			GGGACAGCGTGCA		CCDS54220.1	19p13.2	2014-02-13			ENSG00000130173	ENSG00000130173			24933	protein-coding gene	gene with protein product	"lipasin", "betatrophin"					22809513, 23150577, 24262987	Standard	NM_018687		Approved	TD26, RIFL, ANGPTL8	uc021upg.1	Q6UXH0		ENST00000252453.8:c.386G>T	chr19.hg19:g.11350899G>T	ENSP00000252453:p.Ser129Ile	89.0	0.0		65.0	26.0	NM_018687	Q9NQZ1	Missense_Mutation	SNP	ENST00000252453.8	hg19	CCDS54220.1	.	.	.	.	.	.	.	.	.	.	G	9.127	1.010432	0.19277	.	.	ENSG00000130173	ENST00000397785;ENST00000252453	T	0.32515	1.45	4.42	-2.17	0.07059	.	0.787466	0.11293	N	0.579067	T	0.18759	0.0450	L	0.38175	1.15	0.09310	N	1	B	0.32467	0.372	B	0.30179	0.112	T	0.15206	-1.0445	10	0.52906	T	0.07	-13.0173	4.5847	0.12277	0.3975:0.1551:0.4473:0.0	.	129	Q6UXH0	TD26_HUMAN	I	54;129	ENSP00000252453:S129I	ENSP00000252453:S129I	S	+	2	0	C19orf80	11211899	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.108000	0.10857	-0.493000	0.06678	-0.391000	0.06502	AGC	.	.		0.597	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687		T	11350899	G	T	11350899	3	4	32	1	0	0	0	0	1	0	0	0	8890	971	34	3	392	3	LOC55908	19	11350899	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	206905	11350899	47778084	76	3925										
LGALS14	56891	hgsc.bcm.edu	37	chr19	40196577	40196757	+	Intron	DEL	CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT	CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT	-													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	acccacaggcttcatttgtgCaagtactggggctgtgctgt					rs35970410|rs116895043|rs372314443|rs555819746|rs577451269|rs72480733|rs537596492|rs62121662|rs141242714|rs372371300|rs377187330|rs368365662|rs35541195|rs567124884	byFrequency	TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT	CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:40196577_40196757delCAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT	ENST00000392052.3	+	2	238				LGALS14_ENST00000360675.3_Splice_Site_p.CKYWGCAVSNVCRFWEGRPLPLMIV10fs	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14						apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			TTCATTTGTGCAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCTCAAGTCTTGT	0.444																																					p.10_34del		Pindel	.											.	LGALS14	38	.	0			c.29_102del						.																																			SO:0001627	intron_variant	56891	exon2			.	AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"Lectins, galactoside-binding"	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.16-480CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT>-	chr19.hg19:g.40196577_40196757delCAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT		171.0	0.0		106.0	10.0	NM_203471	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Frame_Shift_Del	DEL	ENST00000392052.3	hg19	CCDS46073.1																																																																																			.	.		0.444	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129		-	40196757	CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT	-	40196577	6	5	32	0	1	1	0	1	0	0	0	0	8750	718	25	0		0	LGALS14	19	40196577	Intron	DEL	CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT	TCGA-BC-A10R-01A-11D-A12Z-10	28845678	40196577	18932406	77	3926										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41073984	41073984	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	caggaggcggcggcctgagcGgcaagagtcagtcgatcaat	16	10	2	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:41073984G>A	ENST00000352632.3	+	31	6838	c.6752G>A	c.(6751-6753)cGg>cAg	p.R2251Q	SPTBN4_ENST00000392025.1_Missense_Mutation_p.R994Q|SPTBN4_ENST00000598249.1_Missense_Mutation_p.R2251Q			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	2251					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CGGCCTGAGCGGCAAGAGTCA	0.746																																					p.R2251Q		Atlas-SNP	.											.	SPTBN4	213	.	0			c.G6752A						.						12	12	12					19																	41073984		2102	4131	6233	SO:0001583	missense	57731	exon31			CTGAGCGGCAAGA	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.6752G>A	chr19.hg19:g.41073984G>A	ENSP00000263373:p.Arg2251Gln	41.0	0.0		50.0	15.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.858181	0.32791	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000392025	T;T	0.77620	-1.11;0.26	4.36	3.32	0.38043	.	0.158713	0.28772	U	0.014193	T	0.55433	0.1920	N	0.14661	0.345	0.21184	N	0.999766	B;B	0.23058	0.079;0.079	B;B	0.10450	0.002;0.005	T	0.40757	-0.9546	10	0.44086	T	0.13	.	4.0106	0.09621	0.2037:0.2073:0.589:0.0	.	994;2251	C9JY79;Q9H254	.;SPTN4_HUMAN	Q	2251;2251;994	ENSP00000263373:R2251Q;ENSP00000375879:R994Q	ENSP00000263373:R2251Q	R	+	2	0	SPTBN4	45765824	0.975000	0.34042	0.935000	0.37517	0.023000	0.10783	3.248000	0.51430	1.955000	0.56771	0.561000	0.74099	CGG	.	.		0.746	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			A	41073984	G	A	41073984	3	1	32	1	0	0	0	0	1	0	0	0	15136	1116	39	1	6964	1	SPTBN4	19	41073984	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	877407	41073984	18054999	78	3927										
PSG11	5680	hgsc.bcm.edu	37	chr19	43529064	43529064	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ggtagaggtccctgatttgcCctttgtaccagatgtagcca	11	10	0	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:43529064C>T	ENST00000401740.1	-	2	312	c.209G>A	c.(208-210)gGg>gAg	p.G70E	PSG11_ENST00000403486.1_Intron|PSG11_ENST00000320078.7_Missense_Mutation_p.G70E|PSG11_ENST00000306322.7_Intron			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	70	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				CCTGATTTGCCCTTTGTACCA	0.438																																					p.G70E		Atlas-SNP	.											.	PSG11	57	.	0			c.G209A						.						130	130	130					19																	43529064		2199	4294	6493	SO:0001583	missense	5680	exon2			ATTTGCCCTTTGT	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9516	protein-coding gene	gene with protein product	"pregnancy specific beta-1-glycoprotein 13"	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.209G>A	chr19.hg19:g.43529064C>T	ENSP00000384995:p.Gly70Glu	250.0	0.0		203.0	27.0	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	hg19	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	c	11.49	1.653235	0.29425	.	.	ENSG00000243130	ENST00000320078;ENST00000401740	T;T	0.01705	4.68;4.68	0.929	0.929	0.19449	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.10594	0.0259	M	0.90870	3.155	0.09310	N	0.999992	D	0.89917	1.0	D	0.97110	1.0	T	0.06320	-1.0833	9	0.87932	D	0	.	5.2086	0.15304	0.0:1.0:0.0:0.0	.	70	Q9UQ72	PSG11_HUMAN	E	70	ENSP00000319140:G70E;ENSP00000384995:G70E	ENSP00000319140:G70E	G	-	2	0	PSG11	48220904	0.121000	0.22262	0.139000	0.22197	0.032000	0.12392	0.542000	0.23222	0.795000	0.33922	0.184000	0.17185	GGG	.	.		0.438	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		T	43529064	C	T	43529064	3	4	32	1	0	0	0	0	1	0	0	0	12666	623	22	3	814	3	PSG11	19	43529064	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	2455080	43529064	15599919	79	3928										
PSG9	5678	hgsc.bcm.edu	37	chr19	43763032	43763032	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ggacatttaggatgactgggTtactgcggaggccaccatat	13	8	0	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:43763032T>G	ENST00000270077.3	-	4	1061	c.965A>C	c.(964-966)aAc>aCc	p.N322T	PSG9_ENST00000244293.7_Intron|PSG9_ENST00000596730.1_Intron|PSG9_ENST00000593948.1_Intron|PSG9_ENST00000443718.3_Missense_Mutation_p.N229T|PSG9_ENST00000418820.2_Missense_Mutation_p.N229T|PSG9_ENST00000291752.5_Intron	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	322	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				GATGACTGGGTTACTGCGGAG	0.493																																					p.N322T		Atlas-SNP	.											.	PSG9	77	.	0			c.A965C						.						105	108	107					19																	43763032		2136	4281	6417	SO:0001583	missense	5678	exon4			ACTGGGTTACTGC	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.965A>C	chr19.hg19:g.43763032T>G	ENSP00000270077:p.Asn322Thr	96.0	0.0		124.0	29.0	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	hg19	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	N	7.137	0.581148	0.13686	.	.	ENSG00000183668	ENST00000270077;ENST00000443718;ENST00000435220	T;T	0.12774	2.65;2.65	1.39	1.39	0.22231	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.10981	0.0268	L	0.39245	1.2	0.09310	N	1	B;B	0.32893	0.389;0.263	B;B	0.41894	0.266;0.369	T	0.32214	-0.9915	9	0.02654	T	1	.	4.833	0.13451	0.0:0.0:0.0:1.0	.	229;322	E7EW65;Q00887	.;PSG9_HUMAN	T	322;229;283	ENSP00000270077:N322T;ENSP00000396753:N229T	ENSP00000270077:N322T	N	-	2	0	PSG9	48454872	0.848000	0.29623	0.036000	0.18154	0.006000	0.05464	1.721000	0.38032	0.620000	0.30215	0.163000	0.16589	AAC	.	.		0.493	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784		G	43763032	T	G	43763032	3	3	32	1	0	0	0	0	1	0	0	0	12674	1725	60	5	327	5	PSG9	19	43763032	Missense_Mutation	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10	233968	43763032	15365951	80	3929										
LMTK3	114783	hgsc.bcm.edu	37	chr19	49013717	49013717	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	atcccctcatgcacctcaccTtgaagccgacatcgccccgt	6	19	2	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:49013717T>G	ENST00000600059.1	-	2	436	c.209A>C	c.(208-210)aAg>aCg	p.K70T	LMTK3_ENST00000270238.3_Splice_Site_p.K99T|CTC-273B12.10_ENST00000598924.1_lincRNA			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	70					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		GCACCTCACCTTGAAGCCGAC	0.592																																					p.K99T		Atlas-SNP	.											.	LMTK3	125	.	0			c.A296C						.						31	40	37					19																	49013717		2050	4197	6247	SO:0001630	splice_region_variant	114783	exon3			CTCACCTTGAAGC	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 101"						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.210+1A>C	chr19.hg19:g.49013717T>G		143.0	0.0		125.0	19.0	NM_001080434	Q4G0U1	Missense_Mutation	SNP	ENST00000600059.1	hg19		.	.	.	.	.	.	.	.	.	.	t	17.24	3.340348	0.60963	.	.	ENSG00000142235	ENST00000270238	T	0.80653	-1.4	3.95	3.95	0.45737	.	0.071329	0.52532	U	0.000063	T	0.77605	0.4155	L	0.47190	1.495	0.41341	D	0.987301	P	0.51791	0.948	P	0.46975	0.533	T	0.80688	-0.1271	10	0.87932	D	0	.	11.1411	0.48402	0.0:0.0:0.0:1.0	.	70	Q96Q04	LMTK3_HUMAN	T	99	ENSP00000270238:K99T	ENSP00000270238:K99T	K	-	2	0	LMTK3	53705529	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	7.232000	0.78116	1.803000	0.52742	0.235000	0.17854	AAG	.	.		0.592	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895	Missense_Mutation	G	49013717	T	G	49013717	5	3	32	1	0	0	0	0	0	0	1	0	8869	1623	56	5	4229	5	LMTK3	19	49013717	Splice_Site	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10	5250685	49013717	10115266	81	3930										
TFPT	29844	hgsc.bcm.edu	37	chr19	54611472	54611472	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gtgcaggagtccttctgggcGgggacagtgtctctttctct	14	10	3	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr19:54611472G>A	ENST00000391759.1	-	5	908	c.503C>T	c.(502-504)cCg>cTg	p.P168L	TFPT_ENST00000391758.1_Missense_Mutation_p.P159L|NDUFA3_ENST00000391764.3_Intron|TFPT_ENST00000391757.1_Missense_Mutation_p.R156C	NM_013342.3	NP_037474.1	P0C1Z6	TFPT_HUMAN	TCF3 (E2A) fusion partner (in childhood Leukemia)	168					apoptotic signaling pathway (GO:0097190)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(2)|lung(2)	4	all_cancers(19;0.004)|all_epithelial(19;0.00195)|all_lung(19;0.0193)|Lung NSC(19;0.0358)|Breast(117;0.137)|Ovarian(34;0.19)					CCTTCTGGGCGGGGACAGTGT	0.701			T	TCF3	pre-B ALL																																p.P168L		Atlas-SNP	.		Dom	yes		19	19q13	29844	TCF3 (E2A) fusion partner (in childhood Leukemia)		L	.	TFPT	17	.	0			c.C503T						.						24	27	26					19																	54611472		2202	4298	6500	SO:0001583	missense	29844	exon5			CTGGGCGGGGACA	AF052052	CCDS12878.1	19q13	2011-07-06			ENSG00000105619	ENSG00000105619		"INO80 complex subunits"	13630	protein-coding gene	gene with protein product	"amida, partner of the E2A", "INO80 complex subunit F"	609519				10644725, 16230350	Standard	NM_013342		Approved	FB1, amida, INO80F	uc010yej.1	P0C1Z6	OTTHUMG00000065906	ENST00000391759.1:c.503C>T	chr19.hg19:g.54611472G>A	ENSP00000375639:p.Pro168Leu	106.0	0.0		93.0	16.0	NM_013342		Missense_Mutation	SNP	ENST00000391759.1	hg19	CCDS12878.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.44|13.44	2.237797|2.237797	0.39598|0.39598	.|.	.|.	ENSG00000105619|ENSG00000105619	ENST00000391759;ENST00000391758|ENST00000391757	.|.	.|.	.|.	5.04|5.04	5.04|5.04	0.67666|0.67666	.|.	0.424346|.	0.24927|.	N|.	0.034489|.	T|T	0.42223|0.42223	0.1193|0.1193	L|L	0.36672|0.36672	1.1|1.1	0.24947|0.24947	N|N	0.991819|0.991819	B|.	0.20459|.	0.045|.	B|.	0.11329|.	0.006|.	T|T	0.37033|0.37033	-0.9723|-0.9723	9|6	0.38643|0.62326	T|D	0.18|0.03	-14.0125|-14.0125	11.1157|11.1157	0.48259|0.48259	0.0867:0.0:0.9133:0.0|0.0867:0.0:0.9133:0.0	.|.	168|.	P0C1Z6|.	TFPT_HUMAN|.	L|C	168;159|156	.|.	ENSP00000375638:P159L|ENSP00000375637:R156C	P|R	-|-	2|1	0|0	TFPT|TFPT	59303284|59303284	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.637000|0.637000	0.38172|0.38172	2.972000|2.972000	0.49256|0.49256	2.512000|2.512000	0.84698|0.84698	0.655000|0.655000	0.94253|0.94253	CCG|CGC	.	.		0.701	TFPT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141215.4	NM_013342		A	54611472	G	A	54611472	3	1	32	1	0	0	0	0	1	0	0	0	15825	1116	39	1	266	1	TFPT	19	54611472	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	5597755	54611472	4517511	82	3931										
SIRPG	55423	hgsc.bcm.edu	37	chr20	1629885	1629885	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	accctggggaagtggccttcTttttgattgtagattaattc	10	7	1	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr20:1629885T>G	ENST00000303415.3	-	2	307	c.243A>C	c.(241-243)aaA>aaC	p.K81N	RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000344103.4_Missense_Mutation_p.K81N|SIRPG_ENST00000216927.4_Missense_Mutation_p.K81N|SIRPG_ENST00000381583.2_Missense_Mutation_p.K81N|SIRPG_ENST00000381580.1_Missense_Mutation_p.K48N	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	81	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						AGTGGCCTTCTTTTTGATTGT	0.527																																					p.K81N		Atlas-SNP	.											.	SIRPG	61	.	0			c.A243C						.						224	198	207					20																	1629885		2203	4300	6503	SO:0001583	missense	55423	exon2			GCCTTCTTTTTGA	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.243A>C	chr20.hg19:g.1629885T>G	ENSP00000305529:p.Lys81Asn	1118.0	2.0		816.0	294.0	NM_001039508	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	hg19	CCDS13020.2	.	.	.	.	.	.	.	.	.	.	.	9.742	1.165088	0.21538	.	.	ENSG00000089012	ENST00000381580;ENST00000344103;ENST00000303415;ENST00000381583;ENST00000216927	T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13	1.93	0.812	0.18744	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65678	0.2714	L	0.60957	1.885	0.09310	N	1	D;B;P	0.61697	0.99;0.288;0.537	P;B;B	0.59288	0.855;0.043;0.113	T	0.53337	-0.8453	9	0.51188	T	0.08	.	3.5695	0.07912	0.0:0.2117:0.0:0.7883	.	81;81;81	Q9P1W8-3;Q9P1W8-4;Q9P1W8	.;.;SIRPG_HUMAN	N	48;81;81;81;81	ENSP00000370992:K48N;ENSP00000342759:K81N;ENSP00000305529:K81N;ENSP00000370995:K81N;ENSP00000216927:K81N	ENSP00000216927:K81N	K	-	3	2	SIRPG	1577885	0.002000	0.14202	0.005000	0.12908	0.188000	0.23474	0.394000	0.20834	0.212000	0.20703	0.164000	0.16699	AAA	.	.		0.527	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		G	1629885	T	G	1629885	3	3	32	1	0	0	0	0	1	0	0	0	14351	1606	56	5	936	5	SIRPG	20	1629885	Missense_Mutation	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10		1629885	61395635	83	3932										
CPXM1	56265	hgsc.bcm.edu	37	chr20	2776314	2776315	+	Frame_Shift_Ins	INS	-	-	G													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gagaagtcctggctgtggcaINSgggtcggcggctggtgtcct							TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr20:2776314_2776315insG	ENST00000380605.2	-	11	1714_1715	c.1650_1651insC	c.(1648-1653)ccctgcfs	p.C551fs		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	551					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						TGGCTGTGGCAGGGTCGGCGGC	0.629																																					p.C551fs		Atlas-INDEL	.											.	CPXM1	107	.	0			c.1651_1652insC						.																																			SO:0001589	frameshift_variant	56265	exon11			.	AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"carboxypeptidase-like protein X1"	609555	"carboxypeptidase X (M14 family)"	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.1651dupC	chr20.hg19:g.2776317_2776317dupG	ENSP00000369979:p.Cys551fs	123.0	0.0		137.0	13.0	NM_019609	Q6P4G8|Q6UW65|Q9NUB5	Frame_Shift_Ins	INS	ENST00000380605.2	hg19	CCDS13033.1																																																																																			.	.		0.629	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		G	2776315	-	G	2776314	7	5	32	1	0	1	1	0	0	0	0	0	3839	188	7	0	569	0	CPXM1	20	2776314	Frame_Shift_Ins	INS	-	TCGA-BC-A10R-01A-11D-A12Z-10	1146429	2776314	60249206	84	3933										
C20orf27	54976	hgsc.bcm.edu	37	chr20	3735113	3735113	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ttcgcaggctagcagtatctCctctttgaggacgccctctt	9	13	3	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr20:3735113C>T	ENST00000379772.3	-	5	1165	c.355G>A	c.(355-357)Gag>Aag	p.E119K	C20orf27_ENST00000217195.8_Missense_Mutation_p.E144K	NM_001258429.1	NP_001245358.1	Q9GZN8	CT027_HUMAN	chromosome 20 open reading frame 27	119										central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)|urinary_tract(1)	7						AGCAGTATCTCCTCTTTGAGG	0.632																																					p.E144K		Atlas-SNP	.											.	C20orf27	17	.	0			c.G430A						.						128	104	112					20																	3735113		2203	4300	6503	SO:0001583	missense	54976	exon5			GTATCTCCTCTTT	AK000557	CCDS33436.1, CCDS58763.1	20p13	2011-01-25			ENSG00000101220	ENSG00000101220			15873	protein-coding gene	gene with protein product	"hypothetical protein LOC54976"					11780052	Standard	NM_001258429		Approved	FLJ20550	uc002wjh.2	Q9GZN8	OTTHUMG00000031753	ENST00000379772.3:c.355G>A	chr20.hg19:g.3735113C>T	ENSP00000369097:p.Glu119Lys	61.0	0.0		83.0	30.0	NM_001039140	A8K4J0|D3DVX8|Q5JX81|Q9NWX3	Missense_Mutation	SNP	ENST00000379772.3	hg19	CCDS58763.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.081242	0.76528	.	.	ENSG00000101220	ENST00000379772;ENST00000217195;ENST00000399672	.	.	.	4.82	4.82	0.62117	.	0.000000	0.64402	U	0.000002	T	0.56016	0.1957	L	0.55103	1.725	0.58432	D	0.999998	B;P	0.37731	0.23;0.607	B;B	0.40375	0.15;0.327	T	0.53851	-0.8380	9	0.29301	T	0.29	-7.2983	15.8093	0.78543	0.0:1.0:0.0:0.0	.	119;144	Q9GZN8;Q9GZN8-2	CT027_HUMAN;.	K	119;144;119	.	ENSP00000217195:E144K	E	-	1	0	C20orf27	3683113	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.276000	0.72601	2.677000	0.91161	0.561000	0.74099	GAG	.	.		0.632	C20orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077750.2	NM_001039140		T	3735113	C	T	3735113	3	4	32	1	0	0	0	0	1	0	0	0	2109	864	30	3	177	3	C20orf27	20	3735113	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10	958799	3735113	59290407	85	3934										
PREX1	57580	hgsc.bcm.edu	37	chr20	47307517	47307518	+	Frame_Shift_Ins	INS	-	-	C													0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ccgctcgcggatgatggcatINSccagccacttctgcttctcc							TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr20:47307517_47307518insC	ENST00000371941.3	-	9	1175_1176	c.1153_1154insG	c.(1153-1155)gatfs	p.D385fs	PREX1_ENST00000396220.1_Frame_Shift_Ins_p.D385fs	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	385	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GATGATGGCATCCAGCCACTTC	0.599																																					p.D385fs		Atlas-INDEL	.											.	PREX1	441	.	0			c.1154_1155insG						.																																			SO:0001589	frameshift_variant	57580	exon9			.	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1154dupG	chr20.hg19:g.47307519_47307519dupC	ENSP00000361009:p.Asp385fs	185.0	0.0		161.0	10.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Frame_Shift_Ins	INS	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.		0.599	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		C	47307518	-	C	47307517	7	5	32	1	0	1	1	0	0	0	0	0	12488	1435	50	0	3953	0	PREX1	20	47307517	Frame_Shift_Ins	INS	-	TCGA-BC-A10R-01A-11D-A12Z-10	43572404	47307517	15718003	86	3935										
C20orf43	51507	hgsc.bcm.edu	37	chr20	55048453	55048453	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	ttgcctgtgaacttggcaggTatggtttttacacttaatca	9	7	1	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr20:55048453T>A	ENST00000023939.4	+	2	271		c.e2+2		RTFDC1_ENST00000395881.3_Splice_Site|snoU13_ENST00000459416.1_RNA|RTFDC1_ENST00000357348.5_Splice_Site	NM_001283035.1|NM_001283036.1|NM_016407.3	NP_001269964.1|NP_001269965.1|NP_057491.2	Q9BY42	RTF2_HUMAN	replication termination factor 2 domain containing 1																		ACTTGGCAGGTATGGTTTTTA	0.373																																					.		Atlas-SNP	.											.	.	.	.	0			c.164+2T>A						.						95	94	94					20																	55048453		2203	4300	6503	SO:0001630	splice_region_variant	51507	exon2			GGCAGGTATGGTT	AF161513	CCDS13453.1, CCDS63316.1, CCDS63317.1	20q13	2012-10-29	2012-10-29	2012-10-29	ENSG00000022277	ENSG00000022277			15890	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 43"	C20orf43			Standard	NM_001283035		Approved	HSPC164, CDAO5	uc002xxt.2	Q9BY42	OTTHUMG00000032801	ENST00000023939.4:c.164+2T>A	chr20.hg19:g.55048453T>A		84.0	0.0		48.0	11.0	NM_016407	E1P5Z9|Q9BYL7|Q9HCV9|Q9NX29|Q9NZZ8|Q9P002|Q9UHW3	Splice_Site	SNP	ENST00000023939.4	hg19	CCDS13453.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.174589	0.78452	.	.	ENSG00000022277	ENST00000023939;ENST00000395881;ENST00000357348;ENST00000449062	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9824	0.71321	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	C20orf43	54481860	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	7.134000	0.77268	2.016000	0.59253	0.477000	0.44152	.	.	.		0.373	RTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079817.2	NM_016407	Intron	A	55048453	T	A	55048453	5	1	32	1	0	0	0	0	0	0	1	0	2114	1652	57	4	172	4	C20orf43	20	55048453	Splice_Site	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10	7740936	55048453	7977067	87	3936										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34022586	34022586	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	caatgctaattttctctaaaCtcatttcttcttccaaattt	1	10	4	0			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr21:34022586C>T	ENST00000322229.7	-	22	2944	c.2945G>A	c.(2944-2946)aGt>aAt	p.S982N	SYNJ1_ENST00000382491.3_Missense_Mutation_p.S977N|SYNJ1_ENST00000357345.3_Missense_Mutation_p.S982N|SYNJ1_ENST00000382499.2_Missense_Mutation_p.S1021N|SYNJ1_ENST00000433931.2_Missense_Mutation_p.S1021N			O43426	SYNJ1_HUMAN	synaptojanin 1	982	Pro-rich.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						TTTCTCTAAACTCATTTCTTC	0.353																																					p.S1021N		Atlas-SNP	.											.	SYNJ1	253	.	0			c.G3062A						.						158	160	160					21																	34022586		2203	4300	6503	SO:0001583	missense	8867	exon23			TCTAAACTCATTT	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.2945G>A	chr21.hg19:g.34022586C>T	ENSP00000322234:p.Ser982Asn	406.0	0.0		237.0	77.0	NM_203446	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	hg19	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	C	10.30	1.313093	0.23908	.	.	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229	D;D;D;D;D	0.93859	-2.42;-3.28;-3.3;-2.49;-2.46	5.65	3.52	0.40303	Domain of unknown function DUF1866 (1);	0.115478	0.85682	D	0.000000	D	0.82898	0.5137	N	0.11201	0.11	0.38489	D	0.947926	B;B;B;B;B	0.12013	0.001;0.001;0.001;0.005;0.0	B;B;B;B;B	0.15484	0.01;0.008;0.002;0.013;0.002	T	0.76085	-0.3088	10	0.13853	T	0.58	.	9.138	0.36886	0.0:0.7065:0.0:0.2935	.	977;1021;982;982;982	B9EGN3;C9JFZ1;O43426-2;O43426;O43426-4	.;.;.;SYNJ1_HUMAN;.	N	977;982;1021;1021;982	ENSP00000371931:S977N;ENSP00000349903:S982N;ENSP00000371939:S1021N;ENSP00000409667:S1021N;ENSP00000322234:S982N	ENSP00000322234:S982N	S	-	2	0	SYNJ1	32944457	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.780000	0.38634	1.400000	0.46741	0.650000	0.86243	AGT	.	.		0.353	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	34022586	C	T	34022586	3	4	32	1	0	0	0	0	1	0	0	0	15467	565	20	3	1841	3	SYNJ1	21	34022586	Missense_Mutation	SNP	C	TCGA-BC-A10R-01A-11D-A12Z-10		34022586	14107309	88	3937										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18358243	18358243	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gagtcggaggagggagaggcGgggcgggcagaggagcggag	26	5	0	2	rs201286172	byFrequency	TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr22:18358243G>A	ENST00000441493.2	-	17	2594				MICAL3_ENST00000429452.1_Silent_p.P825P|MICAL3_ENST00000383094.3_Intron|MICAL3_ENST00000414725.2_Intron|MICAL3_ENST00000585038.1_Silent_p.P825P|MICAL3_ENST00000400561.2_Intron|MICAL3_ENST00000207726.7_Intron|MICAL3_ENST00000444520.1_Intron	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3						actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		AGGGAGAGGCGGGGCGGGCAG	0.557													G|||	2	0.000399361	8e-04	0	5008	,	,		13614	0		0.001	False		,,,				2504	0				p.P825P		Atlas-SNP	.											.	MICAL3	53	.	0			c.C2475T						.						24	34	31					22																	18358243		1561	3562	5123	SO:0001627	intron_variant	57553	exon19			AGAGGCGGGGCGG	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.2242-3454C>T	chr22.hg19:g.18358243G>A		73.0	0.0		59.0	12.0	NM_001136004	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.		0.557	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			A	18358243	G	A	18358243	1	1	32	0	1	0	0	0	0	0	0	0	9580	1103	39	1		1	MICAL3	22	18358243	Intron	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10		18358243	32946323	89	3938										
TCF20	6942	hgsc.bcm.edu	37	chr22	42606748	42606748	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gaaaccctcttgcttcggtgAaatcgtcactgtatcgttct	8	11	3	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chr22:42606748A>T	ENST00000359486.3	-	1	4700	c.4564T>A	c.(4564-4566)Tca>Aca	p.S1522T	TCF20_ENST00000335626.4_Missense_Mutation_p.S1522T|TCF20_ENST00000404876.1_5'Flank	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1522					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						TGCTTCGGTGAAATCGTCACT	0.468																																					p.S1522T		Atlas-SNP	.											.	TCF20	164	.	0			c.T4564A						.						108	93	98					22																	42606748		2203	4300	6503	SO:0001583	missense	6942	exon1			TCGGTGAAATCGT	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.4564T>A	chr22.hg19:g.42606748A>T	ENSP00000352463:p.Ser1522Thr	352.0	0.0		323.0	22.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	A	6.147	0.395309	0.11638	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.59772	0.24;0.24	5.85	5.85	0.93711	.	0.101011	0.44285	D	0.000462	T	0.39655	0.1086	N	0.17082	0.46	0.80722	D	1	B;B	0.12630	0.006;0.003	B;B	0.12156	0.007;0.003	T	0.27331	-1.0077	10	0.29301	T	0.29	-12.5995	10.0749	0.42355	0.7415:0.0:0.0:0.2585	.	1522;1522	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	T	1522	ENSP00000352463:S1522T;ENSP00000335561:S1522T	ENSP00000335561:S1522T	S	-	1	0	TCF20	40936692	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	2.252000	0.43196	2.233000	0.73108	0.533000	0.62120	TCA	.	.		0.468	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		T	42606748	A	T	42606748	3	4	32	1	0	0	0	0	1	0	0	0	15705	246	9	4	1356	4	TCF20	22	42606748	Missense_Mutation	SNP	A	TCGA-BC-A10R-01A-11D-A12Z-10	24248505	42606748	8697818	90	3939										
SCML2	10389	hgsc.bcm.edu	37	chrX	18283818	18283818	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	tcgacttgatctcctgacctGctgtgttggtaatattagag	10	8	1	3			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chrX:18283818G>C	ENST00000251900.4	-	8	994	c.835C>G	c.(835-837)Cag>Gag	p.Q279E	SCML2_ENST00000398048.3_Missense_Mutation_p.Q15E	NM_006089.2	NP_006080.1	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2 (Drosophila)	279					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	36	Hepatocellular(33;0.183)					CTCCTGACCTGCTGTGTTGGT	0.408																																					p.Q279E	Esophageal Squamous(100;1252 1965 19021 35517)	Atlas-SNP	.											.	SCML2	81	.	0			c.C835G						.						162	147	152					X																	18283818		2203	4300	6503	SO:0001583	missense	10389	exon8			TGACCTGCTGTGT	Y18004	CCDS14185.1	Xp22	2013-01-10	2001-11-28		ENSG00000102098	ENSG00000102098		"Sterile alpha motif (SAM) domain containing"	10581	protein-coding gene	gene with protein product		300208	"sex comb on midleg (Drosophila)-like 2"			10331946	Standard	NM_006089		Approved		uc004cyl.2	Q9UQR0	OTTHUMG00000021212	ENST00000251900.4:c.835C>G	chrX.hg19:g.18283818G>C	ENSP00000251900:p.Gln279Glu	461.0	0.0		290.0	62.0	NM_006089	Q5JXE6|Q86U98|Q8IWD0|Q8NDP2|Q9UGC5	Missense_Mutation	SNP	ENST00000251900.4	hg19	CCDS14185.1	.	.	.	.	.	.	.	.	.	.	G	2.142	-0.396585	0.04899	.	.	ENSG00000102098	ENST00000251900;ENST00000398048;ENST00000442000	T;T	0.42513	2.3;0.97	5.5	2.7	0.31948	.	2.455680	0.01472	N	0.016315	T	0.39835	0.1093	L	0.57536	1.79	0.09310	N	1	B;B;B	0.29716	0.01;0.255;0.147	B;B;B	0.27262	0.004;0.078;0.029	T	0.10636	-1.0621	10	0.23891	T	0.37	.	5.0075	0.14295	0.161:0.0:0.54:0.299	.	247;15;279	B4DZR9;B4DRC2;Q9UQR0	.;.;SCML2_HUMAN	E	279;15;247	ENSP00000251900:Q279E;ENSP00000381126:Q15E	ENSP00000251900:Q279E	Q	-	1	0	SCML2	18193739	0.750000	0.28316	0.000000	0.03702	0.070000	0.16714	1.650000	0.37292	0.131000	0.18576	0.468000	0.43344	CAG	.	.		0.408	SCML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055941.1	NM_006089		C	18283818	G	C	18283818	3	2	32	1	0	0	0	0	1	0	0	0	13925	1328	46	4	1299	4	SCML2	23	18283818	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10		18283818	136986742	91	3940										
PHKA2	5256	hgsc.bcm.edu	37	chrX	18972509	18972509	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	cttctgctcatggctggctgAcagcagccccgtgacgggat	13	13	2	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chrX:18972509A>C	ENST00000379942.4	-	2	765	c.100T>G	c.(100-102)Tca>Gca	p.S34A		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	34					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					TGGCTGGCTGACAGCAGCCCC	0.557																																					p.S34A		Atlas-SNP	.											.	PHKA2	122	.	0			c.T100G						.						77	58	64					X																	18972509		2203	4300	6503	SO:0001583	missense	5256	exon2			TGGCTGACAGCAG		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.100T>G	chrX.hg19:g.18972509A>C	ENSP00000369274:p.Ser34Ala	95.0	0.0		60.0	14.0	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	hg19	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.786777	0.49997	.	.	ENSG00000044446	ENST00000379942	D	0.88354	-2.37	5.65	5.65	0.86999	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.058731	0.64402	D	0.000001	D	0.83101	0.5181	L	0.39020	1.185	0.40299	D	0.978581	B	0.18166	0.026	B	0.19666	0.026	T	0.79264	-0.1875	10	0.45353	T	0.12	-8.5786	9.4666	0.38817	0.9205:0.0:0.0795:0.0	.	34	P46019	KPB2_HUMAN	A	34	ENSP00000369274:S34A	ENSP00000369274:S34A	S	-	1	0	PHKA2	18882430	1.000000	0.71417	0.997000	0.53966	0.946000	0.59487	4.211000	0.58507	1.904000	0.55121	0.486000	0.48141	TCA	.	.		0.557	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		C	18972509	A	C	18972509	3	2	32	1	0	0	0	0	1	0	0	0	11853	275	10	5	3735	5	PHKA2	23	18972509	Missense_Mutation	SNP	A	TCGA-BC-A10R-01A-11D-A12Z-10	688691	18972509	136298051	92	3941										
PRICKLE3	4007	hgsc.bcm.edu	37	chrX	49032070	49032070	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	gcctgacgaggcatccctgcGcgagagtccctggggagcga	16	13	0	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chrX:49032070G>A	ENST00000376317.3	-	9	1894	c.1800C>T	c.(1798-1800)cgC>cgT	p.R600R	PRICKLE3_ENST00000540849.1_Silent_p.R532R|PRICKLE3_ENST00000536904.1_Silent_p.R519R|PRICKLE3_ENST00000538114.1_Silent_p.R424R	NM_006150.3	NP_006141.2	O43900	PRIC3_HUMAN	prickle homolog 3 (Drosophila)	600							zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|skin(2)	22						GCATCCCTGCGCGAGAGTCCC	0.602																																					p.R600R		Atlas-SNP	.											.	PRICKLE3	59	.	0			c.C1800T						.						50	48	49					X																	49032070		2203	4300	6503	SO:0001819	synonymous_variant	4007	exon9			CCCTGCGCGAGAG	BC016856	CCDS14320.1	Xp11.23	2008-02-05	2007-09-18	2007-09-18	ENSG00000012211	ENSG00000012211			6645	protein-coding gene	gene with protein product		300111	"LIM domain only 6"	LMO6		9344658	Standard	XM_005272605		Approved		uc004dmy.1	O43900	OTTHUMG00000024134	ENST00000376317.3:c.1800C>T	chrX.hg19:g.49032070G>A		102.0	0.0		94.0	19.0	NM_006150	B7Z8F2|O76007|Q53XR5	Silent	SNP	ENST00000376317.3	hg19	CCDS14320.1	.	.	.	.	.	.	.	.	.	.	-	5.377	0.254793	0.10185	.	.	ENSG00000012211	ENST00000453382	T	0.70399	-0.48	4.44	0.988	0.19796	.	0.826858	0.10174	N	0.706741	T	0.65606	0.2707	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.54735	-0.8249	6	.	.	.	-4.7242	11.6302	0.51168	0.0:0.6556:0.3444:0.0	.	.	.	.	C	613	ENSP00000388599:R613C	.	R	-	1	0	PRICKLE3	48919014	0.029000	0.19370	0.002000	0.10522	0.123000	0.20343	0.358000	0.20216	0.241000	0.21283	0.455000	0.32223	CGC	.	.		0.602	PRICKLE3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060811.1	NM_006150		A	49032070	G	A	49032070	2	1	32	1	0	0	0	0	0	0	0	1	12500	1074	38	1		1	PRICKLE3	23	49032070	Silent	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	30059561	49032070	106238490	93	3942										
SSX7	280658	hgsc.bcm.edu	37	chrX	52677345	52677345	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	atcttctcagaggtacttggTtttcctggagggcacaggtg	13	8	2	1			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chrX:52677345T>C	ENST00000298181.5	-	6	590	c.432A>G	c.(430-432)aaA>aaG	p.K144K		NM_173358.2	NP_775494.1	Q7RTT5	SSX7_HUMAN	synovial sarcoma, X breakpoint 7	144					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|skin(1)	16	Ovarian(276;0.236)					AGGTACTTGGTTTTCCTGGAG	0.507																																					p.K144K		Atlas-SNP	.											.	SSX7	34	.	0			c.A432G						.						199	172	181					X																	52677345		2203	4300	6503	SO:0001819	synonymous_variant	280658	exon6			ACTTGGTTTTCCT	BK000687	CCDS14343.1	Xp11.23	2011-02-10			ENSG00000187754	ENSG00000187754			19653	protein-coding gene	gene with protein product		300542				12216073	Standard	NM_173358		Approved		uc004dqx.1	Q7RTT5	OTTHUMG00000021572	ENST00000298181.5:c.432A>G	chrX.hg19:g.52677345T>C		1399.0	1.0		1049.0	178.0	NM_173358		Silent	SNP	ENST00000298181.5	hg19	CCDS14343.1																																																																																			.	.		0.507	SSX7-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056671.1	NM_173358		C	52677345	T	C	52677345	2	2	32	1	0	0	0	0	0	0	0	1	15224	1722	60	2		2	SSX7	23	52677345	Silent	SNP	T	TCGA-BC-A10R-01A-11D-A12Z-10	3645275	52677345	102593215	94	3943										
KLF8	11279	hgsc.bcm.edu	37	chrX	56291629	56291629	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	taaggtcactgcttctgttcGgaacagagatccccctgaga	10	11	2	2	rs144407506		TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chrX:56291629G>A	ENST00000468660.1	+	3	386	c.98G>A	c.(97-99)cGg>cAg	p.R33Q	KLF8_ENST00000374928.3_Missense_Mutation_p.R33Q	NM_007250.4	NP_009181.2	O95600	KLF8_HUMAN	Kruppel-like factor 8	33					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(4)|large_intestine(6)|lung(5)|ovary(1)	16						GCTTCTGTTCGGAACAGAGAT	0.408																																					p.R33Q		Atlas-SNP	.											.	KLF8	38	.	0			c.G98A						.	G	GLN/ARG,GLN/ARG	0,3835		0,0,1632,571	31	28	29		98,98	-2.2	0	X	dbSNP_134	29	1,6727		0,1,2427,1872	yes	missense,missense	KLF8	NM_001159296.1,NM_007250.4	43,43	0,1,4059,2443	AA,AG,GG,G		0.0149,0.0,0.0095	benign,benign	33/258,33/360	56291629	1,10562	2203	4300	6503	SO:0001583	missense	11279	exon4			CTGTTCGGAACAG	U28282	CCDS14373.1, CCDS55428.1	Xp11.21	2013-01-08			ENSG00000102349	ENSG00000102349		"Zinc fingers, C2H2-type", "Kruppel-like transcription factors"	6351	protein-coding gene	gene with protein product		300286					Standard	NM_007250		Approved	BKLF3, ZNF741, DXS741	uc004dur.3	O95600	OTTHUMG00000021666	ENST00000468660.1:c.98G>A	chrX.hg19:g.56291629G>A	ENSP00000417303:p.Arg33Gln	175.0	0.0		108.0	17.0	NM_001159296	B4DJN3|E7EQQ8|L0R3U8|L0R4U2|Q2M246|Q59GV5|Q5HYQ5|Q5JXP7|Q6MZJ7|Q9UGC4	Missense_Mutation	SNP	ENST00000468660.1	hg19	CCDS14373.1	.	.	.	.	.	.	.	.	.	.	G	2.472	-0.321634	0.05386	0.0	1.49E-4	ENSG00000102349	ENST00000374928;ENST00000468660	T	0.05258	3.47	4.68	-2.22	0.06952	.	0.710568	0.12845	N	0.434498	T	0.01523	0.0049	N	0.01874	-0.695	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43426	-0.9392	10	0.07990	T	0.79	.	1.1714	0.01826	0.4887:0.1919:0.1821:0.1372	.	33;33;33	E7EQQ8;B4DJN3;O95600	.;.;KLF8_HUMAN	Q	33	ENSP00000417303:R33Q	ENSP00000431911:R33Q	R	+	2	0	KLF8	56308354	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	-0.020000	0.12525	-0.482000	0.06782	-1.468000	0.01013	CGG	.	G|1.000;A|0.000		0.408	KLF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056887.2	NM_007250		A	56291629	G	A	56291629	3	1	32	1	0	0	0	0	1	0	0	0	8361	1116	39	1	108	1	KLF8	23	56291629	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	3614284	56291629	98978931	95	3944										
ABCD1	215	hgsc.bcm.edu	37	chrX	153001604	153001604	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0520833333333333	5	1	0.754084967320261	0	0.928104575163399	0.0256410256410257	0.304738562091504	0	aggcagccttggaaaagaagGaggaggagctggtgagcgag	19	5	0	2			TCGA-BC-A10R-01A-11D-A12Z-10	TCGA-BC-A10R-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e98ae9b4-4696-4b17-a6ed-b072d679ba40	a458c859-a526-4bd8-a5ff-ed71b5ce571b	g.chrX:153001604G>C	ENST00000218104.3	+	3	1519	c.1120G>C	c.(1120-1122)Gag>Cag	p.E374Q	U52111.14_ENST00000434284.1_RNA	NM_000033.3	NP_000024.2	P33897	ABCD1_HUMAN	ATP-binding cassette, sub-family D (ALD), member 1	374	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				alpha-linolenic acid metabolic process (GO:0036109)|ATP catabolic process (GO:0006200)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|linoleic acid metabolic process (GO:0043651)|long-chain fatty acid catabolic process (GO:0042758)|peroxisomal long-chain fatty acid import (GO:0015910)|peroxisomal membrane transport (GO:0015919)|peroxisome organization (GO:0007031)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid catabolic process (GO:0042760)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|peroxisomal fatty-acyl-CoA transporter activity (GO:0005325)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(2)	18	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGAAAAGAAGGAGGAGGAGCT	0.617																																					p.E374Q		Atlas-SNP	.											.	ABCD1	59	.	0			c.G1120C						.						102	96	98					X																	153001604		2203	4300	6503	SO:0001583	missense	215	exon3			AAGAAGGAGGAGG	Z21876	CCDS14728.1	Xq28	2012-03-14			ENSG00000101986	ENSG00000101986		"ATP binding cassette transporters / subfamily D"	61	protein-coding gene	gene with protein product		300371		ALD		8441467, 6795626	Standard	NM_000033		Approved	AMN, ALDP, adrenoleukodystrophy	uc004fif.2	P33897	OTTHUMG00000024215	ENST00000218104.3:c.1120G>C	chrX.hg19:g.153001604G>C	ENSP00000218104:p.Glu374Gln	193.0	0.0		129.0	29.0	NM_000033	Q6GTZ2	Missense_Mutation	SNP	ENST00000218104.3	hg19	CCDS14728.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.61|15.61	2.883868|2.883868	0.51908|0.51908	.|.	.|.	ENSG00000101986|ENSG00000101986	ENST00000218104|ENST00000443684	D|.	0.94184|.	-3.37|.	4.85|4.85	3.08|3.08	0.35506|0.35506	.|.	0.221347|.	0.35585|.	N|.	0.003106|.	T|T	0.58595|0.58595	0.2133|0.2133	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	B|.	0.23128|.	0.08|.	B|.	0.20384|.	0.029|.	T|T	0.51403|0.51403	-0.8710|-0.8710	10|5	0.13853|.	T|.	0.58|.	-17.98|-17.98	9.3879|9.3879	0.38354|0.38354	0.1835:0.0:0.8165:0.0|0.1835:0.0:0.8165:0.0	.|.	374|.	P33897|.	ABCD1_HUMAN|.	Q|S	374|41	ENSP00000218104:E374Q|.	ENSP00000218104:E374Q|.	E|R	+|+	1|3	0|2	ABCD1|ABCD1	152654798|152654798	1.000000|1.000000	0.71417|0.71417	0.438000|0.438000	0.26821|0.26821	0.610000|0.610000	0.37248|0.37248	7.600000|7.600000	0.82769|0.82769	0.404000|0.404000	0.25506|0.25506	0.523000|0.523000	0.50628|0.50628	GAG|AGG	.	.		0.617	ABCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061041.1	NM_000033		C	153001604	G	C	153001604	3	2	32	1	0	0	0	0	1	0	0	0	60	1175	41	4	1130	4	ABCD1	23	153001604	Missense_Mutation	SNP	G	TCGA-BC-A10R-01A-11D-A12Z-10	96709975	153001604	2268956	96	3945										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34174693	34174693	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	aatcgatcaattttaccttgAggacatctccttcggagagt	8	9	2	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:34174693A>T	ENST00000373380.1	-	1	411	c.191T>A	c.(190-192)cTc>cAc	p.L64H	CSMD2_ENST00000373381.4_Missense_Mutation_p.L1191H|CSMD2_ENST00000373388.2_5'UTR			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1151	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TTTTACCTTGAGGACATCTCC	0.418																																					p.L1151H		Atlas-SNP	.											.	CSMD2	946	.	0			c.T3452A						.						109	106	107					1																	34174693		2203	4300	6503	SO:0001583	missense	114784	exon22			ACCTTGAGGACAT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.191T>A	chr1.hg19:g.34174693A>T	ENSP00000362478:p.Leu64His	61.0	0.0		190.0	60.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	A	24.5	4.535717	0.85812	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.47869	0.83;0.83	5.49	5.49	0.81192	CUB (5);	0.000000	0.85682	D	0.000000	T	0.80834	0.4699	H	0.98612	4.28	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.995;0.995	D	0.88196	0.2880	10	0.72032	D	0.01	.	14.7747	0.69724	1.0:0.0:0.0:0.0	.	64;1151;1191	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	H	1191;64	ENSP00000362479:L1191H;ENSP00000362478:L64H	ENSP00000241312:L1151H	L	-	2	0	CSMD2	33947280	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.108000	0.94275	2.097000	0.63578	0.459000	0.35465	CTC	.	.		0.418	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		T	34174693	A	T	34174693	3	4	33	1	0	0	0	0	1	0	0	0	3947	304	11	4	7203	4	CSMD2	1	34174693	Missense_Mutation	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10		34174693	215075928	1	3946										
CYP4A22	284541	hgsc.bcm.edu	37	chr1	47603268	47603268	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ctgatcaaggcagctcagctCtacctgcataggcagtggct	11	12	3	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:47603268C>A	ENST00000371891.3	+	1	142	c.111C>A	c.(109-111)ctC>ctA	p.L37L	CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000294337.3_Silent_p.L37L|CYP4A22_ENST00000371890.3_Silent_p.L37L	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	37						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CAGCTCAGCTCTACCTGCATA	0.617																																					p.L37L	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.C111A						.						91	77	82					1																	47603268		2203	4300	6503	SO:0001819	synonymous_variant	284541	exon1			TCAGCTCTACCTG		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"Cytochrome P450s"	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.111C>A	chr1.hg19:g.47603268C>A		66.0	0.0		200.0	54.0	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Silent	SNP	ENST00000371891.3	hg19	CCDS30707.1																																																																																			.	.		0.617	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213		A	47603268	C	A	47603268	2	1	33	1	0	0	0	0	0	0	0	1	4186	900	32	3		3	CYP4A22	1	47603268	Silent	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	13428575	47603268	201647353	2	3947										
FGGY	55277	hgsc.bcm.edu	37	chr1	60223658	60223658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tgtgttcccgagactacaggAtaaaaagtaagtgtgtattt	10	5	0	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:60223658A>G	ENST00000303721.7	+	15	1742	c.1568A>G	c.(1567-1569)gAt>gGt	p.D523G	FGGY_ENST00000371218.4_Missense_Mutation_p.D547G|FGGY_ENST00000371212.1_Missense_Mutation_p.D435G|FGGY_ENST00000371210.1_Missense_Mutation_p.D224G|RP4-782L23.2_ENST00000443012.1_RNA	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	523					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					AGACTACAGGATAAAAAGTAA	0.378																																					p.D547G		Atlas-SNP	.											.	FGGY	99	.	0			c.A1640G						.						99	95	96					1																	60223658		2203	4300	6503	SO:0001583	missense	55277	exon16			TACAGGATAAAAA		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.1568A>G	chr1.hg19:g.60223658A>G	ENSP00000305922:p.Asp523Gly	45.0	0.0		97.0	39.0	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Missense_Mutation	SNP	ENST00000303721.7	hg19	CCDS611.2	.	.	.	.	.	.	.	.	.	.	A	6.236	0.411731	0.11812	.	.	ENSG00000172456	ENST00000371218;ENST00000303721;ENST00000371212;ENST00000371210	D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62	5.09	5.09	0.68999	.	0.342239	0.29034	N	0.013350	D	0.89332	0.6685	M	0.68593	2.085	0.38510	D	0.94844	B;B;B	0.25904	0.137;0.046;0.088	B;B;B	0.31869	0.137;0.045;0.063	D	0.87173	0.2222	9	.	.	.	-14.3042	12.3551	0.55171	1.0:0.0:0.0:0.0	.	547;435;523	Q96C11-3;B1AK94;Q96C11	.;.;FGGY_HUMAN	G	547;523;435;224	ENSP00000360262:D547G;ENSP00000305922:D523G;ENSP00000360256:D435G;ENSP00000360254:D224G	.	D	+	2	0	FGGY	59996246	1.000000	0.71417	0.987000	0.45799	0.128000	0.20619	4.822000	0.62686	2.138000	0.66242	0.460000	0.39030	GAT	.	.		0.378	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411		G	60223658	A	G	60223658	3	3	33	1	0	0	0	0	1	0	0	0	5879	333	12	2	1698	2	FGGY	1	60223658	Missense_Mutation	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10	12620390	60223658	189026963	3	3948										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79385992	79385992	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tgaagaaccagaaggtaaaaAtgcatatggcaagacaaatc	9	6	0	4			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:79385992A>G	ENST00000370742.3	-	10	1400	c.1337T>C	c.(1336-1338)aTt>aCt	p.I446T		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	446					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		GAAGGTAAAAATGCATATGGC	0.308																																					p.I446T		Atlas-SNP	.											.	ELTD1	143	.	0			c.T1337C						.						104	99	101					1																	79385992		1816	4081	5897	SO:0001583	missense	64123	exon10			GTAAAAATGCATA	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1337T>C	chr1.hg19:g.79385992A>G	ENSP00000359778:p.Ile446Thr	40.0	0.0		125.0	50.0	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	A	19.35	3.811657	0.70797	.	.	ENSG00000162618	ENST00000370742	T	0.51574	0.7	5.0	5.0	0.66597	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.67163	0.2864	M	0.91196	3.185	0.80722	D	1	P	0.50943	0.94	P	0.61940	0.896	T	0.75637	-0.3249	9	.	.	.	.	15.0016	0.71476	1.0:0.0:0.0:0.0	.	446	Q9HBW9	ELTD1_HUMAN	T	446	ENSP00000359778:I446T	.	I	-	2	0	ELTD1	79158580	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.255000	0.95524	1.998000	0.58463	0.528000	0.53228	ATT	.	.		0.308	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		G	79385992	A	G	79385992	3	3	33	1	0	0	0	0	1	0	0	0	5086	101	4	2	759	2	ELTD1	1	79385992	Missense_Mutation	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10	19162334	79385992	169864629	4	3949										
ZNHIT6	54680	hgsc.bcm.edu	37	chr1	86173940	86173940	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gtggagacctcccccagactTcccttcattttcagcagcaa	7	15	2	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:86173940T>G	ENST00000370574.3	-	1	161	c.28A>C	c.(28-30)Aag>Cag	p.K10Q	ZNHIT6_ENST00000431532.2_Missense_Mutation_p.K10Q			Q9NWK9	BCD1_HUMAN	zinc finger, HIT-type containing 6	10					box C/D snoRNP assembly (GO:0000492)|ribosome biogenesis (GO:0042254)	extracellular vesicular exosome (GO:0070062)|pre-snoRNP complex (GO:0070761)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(2)|cervix(2)|large_intestine(10)|lung(1)|urinary_tract(1)	17						CCCCCAGACTTCCCTTCATTT	0.567																																					p.K10Q		Atlas-SNP	.											.	ZNHIT6	42	.	0			c.A28C						.						56	59	58					1																	86173940		2203	4300	6503	SO:0001583	missense	54680	exon1			CAGACTTCCCTTC	AL442074	CCDS707.1, CCDS53338.1	1p22.3	2013-01-17	2010-09-15	2008-06-23	ENSG00000117174	ENSG00000117174		"Zinc fingers, HIT-type"	26089	protein-coding gene	gene with protein product	"box C/D snoRNA essential 1 homolog (S. cerevisiae)"		"chromosome 1 open reading frame 181", "zinc finger, HIT type 6"	C1orf181		12747765	Standard	NM_017953		Approved	FLJ20729, NY-BR-75, BCD1	uc001dlh.3	Q9NWK9	OTTHUMG00000010576	ENST00000370574.3:c.28A>C	chr1.hg19:g.86173940T>G	ENSP00000359606:p.Lys10Gln	39.0	0.0		56.0	16.0	NM_017953	B2RBA1|B4DP13|D3DT20|Q9H278|Q9H3X3|Q9NWN0	Missense_Mutation	SNP	ENST00000370574.3	hg19	CCDS707.1	.	.	.	.	.	.	.	.	.	.	T	11.82	1.752754	0.31046	.	.	ENSG00000117174	ENST00000431532;ENST00000370574	T;T	0.45276	0.9;0.91	3.95	0.208	0.15221	.	1.063840	0.07437	N	0.896610	T	0.07007	0.0178	N	0.08118	0	0.09310	N	1	B;B	0.27192	0.079;0.171	B;B	0.15870	0.014;0.014	T	0.29971	-0.9994	10	0.59425	D	0.04	2.826	3.2819	0.06918	0.0:0.2327:0.2119:0.5554	.	10;10	B4DP13;Q9NWK9	.;BCD1_HUMAN	Q	10	ENSP00000414344:K10Q;ENSP00000359606:K10Q	ENSP00000359606:K10Q	K	-	1	0	ZNHIT6	85946528	0.002000	0.14202	0.000000	0.03702	0.094000	0.18550	0.117000	0.15583	-0.052000	0.13311	0.372000	0.22366	AAG	.	.		0.567	ZNHIT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029186.1	NM_017953		G	86173940	T	G	86173940	3	3	33	1	0	0	0	0	1	0	0	0	18224	1792	62	5	1424	5	ZNHIT6	1	86173940	Missense_Mutation	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10	6787948	86173940	163076681	5	3950										
BARHL2	343472	hgsc.bcm.edu	37	chr1	91178035	91178036	+	Frame_Shift_Ins	INS	-	-	C													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gctgtacatggcagcggcagINSccgccgccgccgtagtgctg					rs200824967		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:91178035_91178036insC	ENST00000370445.4	-	3	1038_1039	c.997_998insG	c.(997-999)gctfs	p.A333fs		NM_020063.1	NP_064447.1	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2	333					cell fate determination (GO:0001709)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|positive regulation of translation (GO:0045727)|regulation of axon extension (GO:0030516)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			cervix(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)		GGCAGCGGCAGCCGCCGCCGCC	0.649																																					p.A333fs	GBM(199;3561 4100 22440)	Atlas-INDEL	.											.	BARHL2	62	.	0			c.998_999insG						.																																			SO:0001589	frameshift_variant	343472	exon3			.	AJ251753	CCDS730.1	1p22.2	2011-07-08	2007-07-09		ENSG00000143032	ENSG00000143032		"Homeoboxes / ANTP class : NKL subclass"	954	protein-coding gene	gene with protein product		605212	"BarH (Drosophila)-like 2"				Standard	NM_020063		Approved		uc001dns.3	Q9NY43	OTTHUMG00000010020	ENST00000370445.4:c.998dupG	chr1.hg19:g.91178037_91178037dupC	ENSP00000359474:p.Ala333fs	62.0	0.0		106.0	10.0	NM_020063	A0AVP2|Q7Z4N7	Frame_Shift_Ins	INS	ENST00000370445.4	hg19	CCDS730.1																																																																																			.	.		0.649	BARHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027728.2			C	91178036	-	C	91178035	7	5	33	1	0	1	1	0	0	0	0	0	1314	971	34	0	169	0	BARHL2	1	91178035	Frame_Shift_Ins	INS	-	TCGA-BC-A10T-01A-11D-A12Z-10	5004095	91178035	158072586	6	3951										
CDC7	8317	hgsc.bcm.edu	37	chr1	91977431	91977431	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ttcatcagtttggtattgttCaccgtgatgttaagcccagc	9	9	3	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:91977431C>A	ENST00000428239.1	+	6	782	c.523C>A	c.(523-525)Cac>Aac	p.H175N	CDC7_ENST00000234626.6_Missense_Mutation_p.H175N|CDC7_ENST00000430031.2_Missense_Mutation_p.H147N	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	175	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		TGGTATTGTTCACCGTGATGT	0.318																																					p.H175N		Atlas-SNP	.											.	CDC7	74	.	0			c.C523A						.						84	83	83					1																	91977431		2203	4300	6503	SO:0001583	missense	8317	exon6			ATTGTTCACCGTG	AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1", "CDC7 cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 homolog (S. cerevisiae)"	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.523C>A	chr1.hg19:g.91977431C>A	ENSP00000393139:p.His175Asn	228.0	0.0		465.0	156.0	NM_001134419	D3DT31|O00558|Q5T5U5	Missense_Mutation	SNP	ENST00000428239.1	hg19	CCDS734.1	.	.	.	.	.	.	.	.	.	.	C	32	5.115646	0.94339	.	.	ENSG00000097046	ENST00000430031;ENST00000234626;ENST00000428239	T;T;T	0.50813	0.73;0.73;0.73	5.88	5.88	0.94601	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.83124	0.5186	H	0.99689	4.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90283	0.4316	10	0.87932	D	0	-17.6315	20.2314	0.98350	0.0:1.0:0.0:0.0	.	147;175	B7Z5H7;O00311	.;CDC7_HUMAN	N	147;175;175	ENSP00000407477:H147N;ENSP00000234626:H175N;ENSP00000393139:H175N	ENSP00000234626:H175N	H	+	1	0	CDC7	91750019	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.629000	0.83207	2.789000	0.95967	0.591000	0.81541	CAC	.	.		0.318	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027928.1	NM_003503		A	91977431	C	A	91977431	3	1	33	1	0	0	0	0	1	0	0	0	3086	826	29	3	541	3	CDC7	1	91977431	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	799396	91977431	157273190	7	3952										
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150532349	150532349	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gcggccctccaggaagcgccCctgtaacagccaaccctgca	10	18	0	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:150532349C>T	ENST00000369038.2	+	16	3257	c.3056C>T	c.(3055-3057)cCc>cTc	p.P1019L	ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.P1042L|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.P1019L			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	1019	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			AGGAAGCGCCCCTGTAACAGC	0.612											OREG0013787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P1019L		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.C3056T						.						84	89	87					1																	150532349		2203	4300	6503	SO:0001583	missense	54507	exon18			AGCGCCCCTGTAA	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.3056C>T	chr1.hg19:g.150532349C>T	ENSP00000358034:p.Pro1019Leu	22.0	0.0	1733	50.0	22.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	hg19	CCDS955.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.199905	0.38905	.	.	ENSG00000143382	ENST00000271643;ENST00000369039;ENST00000369038	T;T;T	0.52526	0.66;0.66;0.66	5.5	4.57	0.56435	.	.	.	.	.	T	0.17323	0.0416	L	0.31371	0.925	0.09310	N	0.99999	B;B;B	0.24823	0.112;0.032;0.053	B;B;B	0.31442	0.13;0.062;0.075	T	0.18398	-1.0338	9	0.30078	T	0.28	.	6.9597	0.24590	0.1748:0.7381:0.0:0.0871	.	980;1042;1019	B7ZMJ3;F8WAD0;Q6UY14	.;.;ATL4_HUMAN	L	1019;1042;1019	ENSP00000271643:P1019L;ENSP00000358035:P1042L;ENSP00000358034:P1019L	ENSP00000271643:P1019L	P	+	2	0	ADAMTSL4	148798973	0.000000	0.05858	0.687000	0.30102	0.978000	0.69477	0.775000	0.26689	1.269000	0.44280	0.561000	0.74099	CCC	.	.		0.612	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		T	150532349	C	T	150532349	3	4	33	1	0	0	0	0	1	0	0	0	277	623	22	3	3193	3	ADAMTSL4	1	150532349	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	58554918	150532349	98718272	8	3953										
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200817808	200817808	+	Frame_Shift_Del	DEL	C	C	-													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gattatactgtaagcttggaCtctgacatggatgatgcatc							TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:200817808delC	ENST00000236925.4	+	12	1993	c.1944delC	c.(1942-1944)gacfs	p.D648fs	CAMSAP2_ENST00000358823.2_Frame_Shift_Del_p.D637fs|CAMSAP2_ENST00000413307.2_Frame_Shift_Del_p.D621fs			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	648					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										TAAGCTTGGACTCTGACATGG	0.398																																					p.D637fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1910delA						.						136	135	135					1																	200817808		2203	4300	6503	SO:0001589	frameshift_variant	23271	exon11			.	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.1944delC	chr1.hg19:g.200817808delC	ENSP00000236925:p.Asp648fs	75.0	0.0		253.0	91.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Frame_Shift_Del	DEL	ENST00000236925.4	hg19																																																																																				.	.		0.398	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		-	200817808	C	-	200817808	7	5	33	1	0	1	0	1	0	0	0	0	2614	564	20	0	1953	0	CAMSAP1L1	1	200817808	Frame_Shift_Del	DEL	C	TCGA-BC-A10T-01A-11D-A12Z-10	50285459	200817808	48432813	9	3954										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228462084	228462084	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ttggggctgcgcgcagaggaCgcaggggagtacgtgtgtga	20	7	0	2	rs202200633		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:228462084C>T	ENST00000422127.1	+	19	5666	c.5622C>T	c.(5620-5622)gaC>gaT	p.D1874D	RP5-1139B12.3_ENST00000602529.1_RNA|OBSCN_ENST00000570156.2_Silent_p.D2249D|OBSCN_ENST00000359599.6_Silent_p.D721D|RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000284548.11_Silent_p.D1874D|RP5-1139B12.2_ENST00000602517.1_RNA|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1874	Ig-like 18.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCGCAGAGGACGCAGGGGAGT	0.657																																					p.D2249D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C6747T						.	C	,	0,4342		0,0,2171	45	52	50		5622,5622	-4.5	0.2	1		50	2,8526		0,2,4262	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,2,6433	TT,TC,CC		0.0235,0.0,0.0155	,	1874/7969,1874/6621	228462084	2,12868	2171	4264	6435	SO:0001819	synonymous_variant	84033	exon23			AGAGGACGCAGGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.5622C>T	chr1.hg19:g.228462084C>T		86.0	0.0		127.0	56.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	C|0.996;T|0.004		0.657	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228462084	C	T	228462084	2	4	33	1	0	0	0	0	0	0	0	1	10821	535	19	1		1	OBSCN	1	228462084	Silent	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	27644276	228462084	20788537	10	3955										
OR2B11	127623	hgsc.bcm.edu	37	chr1	247615077	247615077	+	Frame_Shift_Del	DEL	G	G	-													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gcagaggtccaggaaggacaGgtgactgaggaagatgtaca							TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr1:247615077delG	ENST00000318749.6	-	1	231	c.208delC	c.(208-210)ctgfs	p.L70fs		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			AGGAAGGACAGGTGACTGAGG	0.572																																					p.L70fs		Atlas-Indel,Pindel	.											.	OR2B11	102	.	0			c.209delT						.						173	167	169					1																	247615077		2203	4300	6503	SO:0001589	frameshift_variant	127623	exon1			.		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"GPCR / Class A : Olfactory receptors"	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.208delC	chr1.hg19:g.247615077delG	ENSP00000325682:p.Leu70fs	74.0	0.0		215.0	46.0	NM_001004492	B2RP03	Frame_Shift_Del	DEL	ENST00000318749.6	hg19	CCDS31090.1																																																																																			.	.		0.572	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492		-	247615077	G	-	247615077	7	5	33	1	0	1	0	1	0	0	0	0	10997	991	35	0	748	0	OR2B11	1	247615077	Frame_Shift_Del	DEL	G	TCGA-BC-A10T-01A-11D-A12Z-10	19152993	247615077	1635544	11	3956										
MFSD2B	388931	hgsc.bcm.edu	37	chr2	24240356	24240356	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gtggagatggcgggaacactGatgggggccactgtccacgg	18	9	0	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:24240356G>A	ENST00000406420.3	+	6	595	c.579G>A	c.(577-579)ctG>ctA	p.L193L	MFSD2B_ENST00000338315.4_Silent_p.L193L	NM_001080473.1	NP_001073942.1	A6NFX1	MFS2B_HUMAN	major facilitator superfamily domain containing 2B	193					transport (GO:0006810)	integral component of membrane (GO:0016021)				cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10						CGGGAACACTGATGGGGGCCA	0.657																																					p.L193L		Atlas-SNP	.											.	MFSD2B	45	.	0			c.G579A						.						23	27	25					2																	24240356		2049	4184	6233	SO:0001819	synonymous_variant	388931	exon6			AACACTGATGGGG		CCDS46228.1	2p23.3	2010-05-11			ENSG00000205639	ENSG00000205639			37207	protein-coding gene	gene with protein product						18694395	Standard	NM_001080473		Approved		uc002reo.2	A6NFX1	OTTHUMG00000090819	ENST00000406420.3:c.579G>A	chr2.hg19:g.24240356G>A		59.0	0.0		127.0	26.0	NM_001080473	B5MC32	Silent	SNP	ENST00000406420.3	hg19	CCDS46228.1																																																																																			.	.		0.657	MFSD2B-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000324307.1	NM_001080473		A	24240356	G	A	24240356	2	1	33	1	0	0	0	0	0	0	0	1	9540	1277	45	3		3	MFSD2B	2	24240356	Silent	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10		24240356	218959017	12	3957										
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40656836	40656836	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cgcaaatgcttaatcttcctTgtctctccgtcaggcaccac	6	15	3	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:40656836T>G	ENST00000403092.1	-	2	618	c.585A>C	c.(583-585)acA>acC	p.T195T	SLC8A1_ENST00000332839.4_Silent_p.T195T|SLC8A1_ENST00000406391.2_Silent_p.T195T|SLC8A1_ENST00000542756.1_Silent_p.T195T|SLC8A1_ENST00000408028.2_Silent_p.T195T|SLC8A1_ENST00000405901.3_Silent_p.T195T|SLC8A1_ENST00000402441.1_Silent_p.T195T|SLC8A1_ENST00000542024.1_Silent_p.T195T|SLC8A1_ENST00000405269.1_Silent_p.T195T|SLC8A1_ENST00000406785.2_Silent_p.T195T			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	195					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	TAATCTTCCTTGTCTCTCCGT	0.468																																					p.T195T		Atlas-SNP	.											.	SLC8A1	221	.	0			c.A585C						.						80	77	78					2																	40656836		2203	4300	6503	SO:0001819	synonymous_variant	6546	exon1			CTTCCTTGTCTCT		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.585A>C	chr2.hg19:g.40656836T>G		71.0	0.0		189.0	94.0	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Silent	SNP	ENST00000403092.1	hg19	CCDS1806.1																																																																																			.	.		0.468	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		G	40656836	T	G	40656836	2	3	33	1	0	0	0	0	0	0	0	1	14721	1799	63	5		5	SLC8A1	2	40656836	Silent	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10	16416480	40656836	202542537	13	3958										
THADA	63892	hgsc.bcm.edu	37	chr2	43819171	43819171	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	agaagctagatttttcccttCcacatcagcaaaagctatat	5	10	1	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:43819171C>A	ENST00000405006.4	-	3	442	c.91G>T	c.(91-93)Gaa>Taa	p.E31*	THADA_ENST00000415080.2_5'UTR|THADA_ENST00000405975.2_Nonsense_Mutation_p.E31*|THADA_ENST00000403856.1_Nonsense_Mutation_p.E31*|THADA_ENST00000402360.2_Nonsense_Mutation_p.E31*|THADA_ENST00000404790.1_Nonsense_Mutation_p.E31*	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	31										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TTTTTCCCTTCCACATCAGCA	0.308																																					p.E31X		Atlas-SNP	.											.	THADA	131	.	0			c.G91T						.						50	44	46					2																	43819171		1821	4063	5884	SO:0001587	stop_gained	63892	exon3			TCCCTTCCACATC	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.91G>T	chr2.hg19:g.43819171C>A	ENSP00000385995:p.Glu31*	101.0	0.0		297.0	179.0	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Nonsense_Mutation	SNP	ENST00000405006.4	hg19	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	C	38	6.820254	0.97861	.	.	ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	.	.	.	5.04	5.04	0.67666	.	0.173309	0.49916	D	0.000136	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-11.8142	16.7404	0.85457	0.0:1.0:0.0:0.0	.	.	.	.	X	31	.	ENSP00000349464:E31X	E	-	1	0	THADA	43672675	1.000000	0.71417	0.852000	0.33557	0.976000	0.68499	4.557000	0.60782	2.622000	0.88805	0.591000	0.81541	GAA	.	.		0.308	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		A	43819171	C	A	43819171	4	1	33	1	0	0	0	0	0	1	0	0	15855	864	30	3	5914	3	THADA	2	43819171	Nonsense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	3162335	43819171	199380202	14	3959										
USP34	9736	hgsc.bcm.edu	37	chr2	61415443	61415443	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gcttctcaagtcagctaagtCagacagaactgcagagatag	10	9	3	3			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:61415443C>G	ENST00000398571.2	-	80	10511	c.10435G>C	c.(10435-10437)Gac>Cac	p.D3479H	AHSA2_ENST00000394457.3_3'UTR	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3479					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TCAGCTAAGTCAGACAGAACT	0.468																																					p.D3479H		Atlas-SNP	.											.	USP34	334	.	0			c.G10435C						.						74	71	72					2																	61415443		1900	4122	6022	SO:0001583	missense	9736	exon80			CTAAGTCAGACAG	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.10435G>C	chr2.hg19:g.61415443C>G	ENSP00000381577:p.Asp3479His	55.0	0.0		149.0	83.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	17.14|17.14	3.313010|3.313010	0.60414|0.60414	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000436269|ENST00000411912	T|.	0.04049|.	3.72|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.164580|.	0.53938|.	D|.	0.000048|.	T|.	0.56659|.	0.2000|.	N|N	0.24115|0.24115	0.695|0.695	0.45477|0.45477	D|D	0.998447|0.998447	P|.	0.44578|.	0.838|.	B|.	0.35550|.	0.205|.	T|.	0.49762|.	-0.8905|.	10|.	0.72032|.	D|.	0.01|.	.|.	19.8041|19.8041	0.96521|0.96521	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	3479|.	Q70CQ2|.	UBP34_HUMAN|.	H|S	3327;3244;3479;357|1155	ENSP00000381577:D3479H|.	ENSP00000263989:D3327H|.	D|X	-|-	1|2	0|2	USP34|USP34	61268947|61268947	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.105000|4.105000	0.57797|0.57797	2.748000|2.748000	0.94277|0.94277	0.591000|0.591000	0.81541|0.81541	GAC|TGA	.	.		0.468	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			G	61415443	C	G	61415443	3	3	33	1	0	0	0	0	1	0	0	0	17080	826	29	4	209	4	USP34	2	61415443	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	17596272	61415443	181783930	15	3960										
ADD2	119	hgsc.bcm.edu	37	chr2	70923474	70923474	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tgagccgctcccctttggccAggttcagggagtcagctgtg	14	12	2	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:70923474A>T	ENST00000264436.4	-	5	821	c.377T>A	c.(376-378)cTg>cAg	p.L126Q	ADD2_ENST00000430656.1_Missense_Mutation_p.L142Q|ADD2_ENST00000407644.2_Missense_Mutation_p.L126Q|ADD2_ENST00000413157.2_Missense_Mutation_p.L126Q|ADD2_ENST00000355733.3_Missense_Mutation_p.L126Q	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	126					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						CCCTTTGGCCAGGTTCAGGGA	0.592																																					p.L142Q		Atlas-SNP	.											.	ADD2	261	.	0			c.T425A						.						109	85	93					2																	70923474		2203	4300	6503	SO:0001583	missense	119	exon4			TTGGCCAGGTTCA	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.377T>A	chr2.hg19:g.70923474A>T	ENSP00000264436:p.Leu126Gln	56.0	0.0		412.0	111.0	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	hg19	CCDS1906.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.850231	0.91277	.	.	ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000456320;ENST00000355733;ENST00000522886;ENST00000356565;ENST00000517596;ENST00000413157;ENST00000430656;ENST00000415348;ENST00000425976	T;T;T;T;T;T;T;T	0.33438	3.32;3.32;3.16;1.84;3.03;3.02;1.43;1.41	4.98	4.98	0.66077	.	0.062767	0.64402	D	0.000005	T	0.43678	0.1258	L	0.36672	1.1	0.45035	D	0.998053	D;P;D;D;D;D	0.76494	0.982;0.884;0.998;0.994;0.965;0.999	P;P;D;P;P;D	0.68621	0.776;0.615;0.938;0.885;0.658;0.959	T	0.39014	-0.9634	10	0.87932	D	0	-16.043	12.9279	0.58270	1.0:0.0:0.0:0.0	.	142;126;126;126;126;126	B4DM17;P35612-4;E9PAN1;Q05DK5;P35612;P35612-3	.;.;.;.;ADDB_HUMAN;.	Q	126;126;126;126;126;126;126;126;142;126;126	ENSP00000264436:L126Q;ENSP00000384677:L126Q;ENSP00000347972:L126Q;ENSP00000430243:L126Q;ENSP00000388072:L126Q;ENSP00000398112:L142Q;ENSP00000412357:L126Q;ENSP00000412681:L126Q	ENSP00000264436:L126Q	L	-	2	0	ADD2	70776982	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.981000	0.76166	2.213000	0.71641	0.528000	0.53228	CTG	.	.		0.592	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		T	70923474	A	T	70923474	3	4	33	1	0	0	0	0	1	0	0	0	305	188	7	4	2032	4	ADD2	2	70923474	Missense_Mutation	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10	9508031	70923474	172275899	16	3961										
EXOC6B	23233	hgsc.bcm.edu	37	chr2	72727062	72727062	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	agcaaaaagcacaatgaggtTcttcaaatctaacacaaggt	7	8	3	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:72727062T>A	ENST00000272427.6	-	12	1337	c.1207A>T	c.(1207-1209)Aac>Tac	p.N403Y	EXOC6B_ENST00000410104.1_Missense_Mutation_p.N403Y	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	403					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)				breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						ACAATGAGGTTCTTCAAATCT	0.308																																					p.N403Y		Atlas-SNP	.											.	EXOC6B	93	.	0			c.A1207T						.						63	56	59					2																	72727062		1833	4035	5868	SO:0001583	missense	23233	exon12			TGAGGTTCTTCAA	AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036			17085	protein-coding gene	gene with protein product		607880	"SEC15-like 2 (S. cerevisiae)", "SEC15 homolog B (S. cerevisiae)"	SEC15L2, SEC15B		10231032, 11406615	Standard	NM_015189		Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.1207A>T	chr2.hg19:g.72727062T>A	ENSP00000272427:p.Asn403Tyr	223.0	0.0		435.0	128.0	NM_015189	B8ZZY3	Missense_Mutation	SNP	ENST00000272427.6	hg19	CCDS46333.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.160540	0.78226	.	.	ENSG00000144036	ENST00000272427;ENST00000410104;ENST00000290144	T;T	0.34072	1.38;1.38	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.64811	0.2632	M	0.89287	3.02	0.80722	D	1	P;D	0.89917	0.718;1.0	B;D	0.79784	0.168;0.993	T	0.72134	-0.4382	10	0.87932	D	0	.	12.9966	0.58650	0.0:0.0:0.0:1.0	.	403;403	Q9Y2D4;Q9Y2D4-2	EXC6B_HUMAN;.	Y	403	ENSP00000272427:N403Y;ENSP00000386698:N403Y	ENSP00000272427:N403Y	N	-	1	0	EXOC6B	72580570	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.812000	0.69194	2.177000	0.69029	0.533000	0.62120	AAC	.	.		0.308	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327558.1	XM_039570		A	72727062	T	A	72727062	3	1	33	1	0	0	0	0	1	0	0	0	5311	1783	62	4	1272	4	EXOC6B	2	72727062	Missense_Mutation	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10	1803588	72727062	170472311	17	3962										
EIF2AK3	9451	hgsc.bcm.edu	37	chr2	88874831	88874857	+	In_Frame_Del	DEL	CTGAAAAAGACCTGCTTCTTTGTGGTG	CTGAAAAAGACCTGCTTCTTTGTGGTG	-													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ctggtcacaggaaatccctaCtgaaaaagacctgcttcttt					rs55861585|rs201096232|rs574976232		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	CTGAAAAAGACCTGCTTCTTTGTGGTG	CTGAAAAAGACCTGCTTCTTTGTGGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:88874831_88874857delCTGAAAAAGACCTGCTTCTTTGTGGTG	ENST00000303236.3	-	13	2445_2471	c.2144_2170delCACCACAAAGAAGCAGGTCTTTTTCAG	c.(2143-2172)tcaccacaaagaagcaggtctttttcagta>tta	p.715_724SPQRSRSFSV>L	EIF2AK3_ENST00000419748.1_In_Frame_Del_p.564_573SPQRSRSFSV>L|AC104134.2_ENST00000413234.1_RNA|EIF2AK3_ENST00000470706.1_Intron	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	715	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> L. {ECO:0000269|PubMed:17344846}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						GAAATCCCTACTGAAAAAGACCTGCTTCTTTGTGGTGAAGGAGCTAT	0.458																																					p.715_724del	GBM(138;671 1851 16235 39058 45249)	Pindel	.											.	EIF2AK3	160	.	0			c.2145_2171del						.																																			SO:0001651	inframe_deletion	9451	exon13			.	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.2144_2170delCACCACAAAGAAGCAGGTCTTTTTCAG	chr2.hg19:g.88874831_88874857delCTGAAAAAGACCTGCTTCTTTGTGGTG	ENSP00000307235:p.Ser715_Val724delinsLeu	76.0	0.0		189.0	13.0	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	In_Frame_Del	DEL	ENST00000303236.3	hg19	CCDS33241.1																																																																																			.	.		0.458	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		-	88874857	CTGAAAAAGACCTGCTTCTTTGTGGTG	-	88874831	7	5	33	1	0	1	0	1	0	0	0	0	5000	565	20	0	1200	0	EIF2AK3	2	88874831	In_Frame_Del	DEL	CTGAAAAAGACCTGCTTCTTTGTGGTG	TCGA-BC-A10T-01A-11D-A12Z-10	16147769	88874831	154324542	18	3963										
TMEM127	55654	hgsc.bcm.edu	37	chr2	96919804	96919804	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tgctgctgctgggccaagatGagttcagaagcccaataaga	12	9	1	4			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:96919804G>A	ENST00000258439.3	-	4	715	c.459C>T	c.(457-459)ctC>ctT	p.L153L	TMEM127_ENST00000432959.1_Silent_p.L153L|TMEM127_ENST00000435268.1_Silent_p.L69L	NM_001193304.2|NM_017849.3	NP_001180233.1|NP_060319.1	O75204	TM127_HUMAN	transmembrane protein 127	153					negative regulation of cell proliferation (GO:0008285)|negative regulation of TOR signaling (GO:0032007)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	5						GGGCCAAGATGAGTTCAGAAG	0.537																																					p.L153L		Atlas-SNP	.											.	TMEM127	13	.	0			c.C459T						.						103	99	100					2																	96919804		2203	4300	6503	SO:0001819	synonymous_variant	55654	exon4			CAAGATGAGTTCA	AK000514	CCDS2018.1	2q11.2	2014-09-17			ENSG00000135956	ENSG00000135956			26038	protein-coding gene	gene with protein product		613403				10493829	Standard	NM_017849		Approved	FLJ20507, FLJ22257	uc002svr.3	O75204	OTTHUMG00000130454	ENST00000258439.3:c.459C>T	chr2.hg19:g.96919804G>A		55.0	0.0		129.0	11.0	NM_001193304	D3DXH0	Silent	SNP	ENST00000258439.3	hg19	CCDS2018.1																																																																																			.	.		0.537	TMEM127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252845.3	NM_017849		A	96919804	G	A	96919804	2	1	33	1	0	0	0	0	0	0	0	1	16055	1277	45	3		3	TMEM127	2	96919804	Silent	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	8044973	96919804	146279569	19	3964										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141260598	141260598	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	aggacagtcaaagtctccatCacactgccattgagtattta	7	10	3	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:141260598C>T	ENST00000389484.3	-	54	9567	c.8596G>A	c.(8596-8598)Gat>Aat	p.D2866N		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2866	LDL-receptor class A 19. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AAGTCTCCATCACACTGCCAT	0.403										TSP Lung(27;0.18)																											p.D2866N	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G8596A						.						162	147	152					2																	141260598		2203	4300	6503	SO:0001583	missense	53353	exon54			CTCCATCACACTG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8596G>A	chr2.hg19:g.141260598C>T	ENSP00000374135:p.Asp2866Asn	111.0	0.0		289.0	96.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	35	5.479916	0.96307	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.98362	-4.89	5.91	5.91	0.95273	.	0.000000	0.85682	U	0.000000	D	0.98779	0.9589	M	0.68728	2.09	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99023	1.0818	10	0.45353	T	0.12	.	20.3132	0.98646	0.0:1.0:0.0:0.0	.	2866	Q9NZR2	LRP1B_HUMAN	N	2866;2804	ENSP00000374135:D2866N	ENSP00000374135:D2866N	D	-	1	0	LRP1B	140977068	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.729000	0.84864	2.817000	0.96982	0.643000	0.83706	GAT	.	.		0.403	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141260598	C	T	141260598	3	4	33	1	0	0	0	0	1	0	0	0	8964	826	29	3	5355	3	LRP1B	2	141260598	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	44340794	141260598	101938775	20	3965										
PAX3	5077	hgsc.bcm.edu	37	chr2	223163313	223163313	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cggccgcatcatcctgggcaCagcgccggccagcgtggtca	14	16	2	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:223163313C>A	ENST00000350526.4	-	1	158	c.22G>T	c.(22-24)Gtg>Ttg	p.V8L	PAX3_ENST00000392070.2_Missense_Mutation_p.V8L|PAX3_ENST00000392069.2_Missense_Mutation_p.V8L|PAX3_ENST00000409828.3_Missense_Mutation_p.V8L|PAX3_ENST00000336840.6_Missense_Mutation_p.V8L|PAX3_ENST00000409551.3_Missense_Mutation_p.V8L|PAX3_ENST00000258387.5_Missense_Mutation_p.V8L|PAX3_ENST00000344493.4_Missense_Mutation_p.V8L|CCDC140_ENST00000295226.1_Intron	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	8					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATCCTGGGCACAGCGCCGGCC	0.682			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.V8L		Atlas-SNP	.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	PAX3	106	.	0			c.G22T						.						8	10	10					2																	223163313		2188	4279	6467	SO:0001583	missense	5077	exon1			TGGGCACAGCGCC		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.22G>T	chr2.hg19:g.223163313C>A	ENSP00000343052:p.Val8Leu	44.0	0.0		96.0	30.0	NM_181457	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Missense_Mutation	SNP	ENST00000350526.4	hg19	CCDS42826.1	.	.	.	.	.	.	.	.	.	.	C	13.23	2.174503	0.38413	.	.	ENSG00000135903	ENST00000392069;ENST00000344493;ENST00000350526;ENST00000392070;ENST00000336840;ENST00000409551;ENST00000409828;ENST00000258387	D;D;D;D;D;D;D;D	0.99399	-3.42;-3.43;-3.39;-3.38;-3.38;-3.38;-5.82;-5.83	5.37	4.47	0.54385	.	0.188750	0.46758	N	0.000270	D	0.97451	0.9166	N	0.17082	0.46	0.80722	D	1	B;B;B;B;B;B;B	0.16166	0.009;0.007;0.001;0.001;0.004;0.016;0.002	B;B;B;B;B;B;B	0.17098	0.005;0.012;0.004;0.002;0.006;0.017;0.006	D	0.95197	0.8313	10	0.62326	D	0.03	.	14.9316	0.70919	0.1444:0.8556:0.0:0.0	.	8;8;8;8;8;8;8	P23760;P23760-2;P23760-3;Q494Z4;P23760-4;P23760-5;G5E9C1	PAX3_HUMAN;.;.;.;.;.;.	L	8	ENSP00000375921:V8L;ENSP00000342092:V8L;ENSP00000343052:V8L;ENSP00000375922:V8L;ENSP00000338767:V8L;ENSP00000386750:V8L;ENSP00000386817:V8L;ENSP00000258387:V8L	ENSP00000258387:V8L	V	-	1	0	PAX3	222871557	0.999000	0.42202	0.984000	0.44739	0.545000	0.35147	2.787000	0.47798	1.208000	0.43306	0.655000	0.94253	GTG	.	.		0.682	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			A	223163313	C	A	223163313	3	1	33	1	0	0	0	0	1	0	0	0	11489	478	17	3	1664	3	PAX3	2	223163313	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	81902715	223163313	20036060	21	3966										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238263564	238263564	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tagctccggggggtccccttCggccaaagccaccctgtgga	13	15	0	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr2:238263564C>T	ENST00000295550.4	-	24	7057	c.6605G>A	c.(6604-6606)cGa>cAa	p.R2202Q	COL6A3_ENST00000346358.4_Missense_Mutation_p.R2002Q|COL6A3_ENST00000409809.1_Missense_Mutation_p.R1996Q|COL6A3_ENST00000353578.4_Missense_Mutation_p.R1996Q|COL6A3_ENST00000347401.3_Missense_Mutation_p.R2001Q|COL6A3_ENST00000472056.1_Missense_Mutation_p.R1595Q	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2202	Collagen-like 3.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R2202Q(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GGGTCCCCTTCGGCCAAAGCC	0.592																																					p.R2202Q		Atlas-SNP	.											COL6A3,face,carcinoma,0,1	COL6A3	608	.	1	Substitution - Missense(1)	skin(1)	c.G6605A						.						25	26	26					2																	238263564		2203	4300	6503	SO:0001583	missense	1293	exon24			CCCCTTCGGCCAA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.6605G>A	chr2.hg19:g.238263564C>T	ENSP00000295550:p.Arg2202Gln	15.0	0.0		66.0	23.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.927242	0.52759	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.94184	-3.37;-3.37;-3.37;-3.37;-3.37;-3.37	5.51	5.51	0.81932	.	0.000000	0.45126	D	0.000383	D	0.94640	0.8272	L	0.47190	1.495	0.51767	D	0.999937	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.988;0.988;0.995;0.988	D	0.92021	0.5626	10	0.14252	T	0.57	.	16.1839	0.81934	0.0:1.0:0.0:0.0	.	1595;1595;1996;2202	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	Q	2202;2001;1996;1595;1996;2002	ENSP00000295550:R2202Q;ENSP00000315609:R2001Q;ENSP00000315873:R1996Q;ENSP00000418285:R1595Q;ENSP00000386844:R1996Q;ENSP00000295546:R2002Q	ENSP00000295550:R2202Q	R	-	2	0	COL6A3	237928303	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	2.871000	0.48459	2.593000	0.87608	0.655000	0.94253	CGA	.	.		0.592	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238263564	C	T	238263564	3	4	33	1	0	0	0	0	1	0	0	0	3703	884	31	1	3012	1	COL6A3	2	238263564	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	15100251	238263564	4935809	22	3967										
EPHA6	285220	hgsc.bcm.edu	37	chr3	96706230	96706230	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cccattcacacataccaggtAtgtaatgtaatggaaccaaa	6	10	1	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr3:96706230A>T	ENST00000389672.5	+	3	545	c.507A>T	c.(505-507)gtA>gtT	p.V169V	EPHA6_ENST00000470610.2_Silent_p.V169V|EPHA6_ENST00000542517.1_Silent_p.V75V	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	75	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						CATACCAGGTATGTAATGTAA	0.378																																					p.V169V		Atlas-SNP	.											.	EPHA6	439	.	0			c.A507T						.						105	103	104					3																	96706230		1875	4106	5981	SO:0001819	synonymous_variant	285220	exon3			CCAGGTATGTAAT	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.507A>T	chr3.hg19:g.96706230A>T		60.0	0.0		170.0	59.0	NM_001080448	D6RAL5	Silent	SNP	ENST00000389672.5	hg19	CCDS46876.1	.	.	.	.	.	.	.	.	.	.	A	9.136	1.012630	0.19277	.	.	ENSG00000080224	ENST00000506569	.	.	.	5.74	1.85	0.25348	.	.	.	.	.	T	0.43255	0.1239	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21965	-1.0230	4	.	.	.	.	1.8811	0.03228	0.4894:0.2493:0.141:0.1202	.	.	.	.	L	114	.	.	M	+	1	0	EPHA6	98188920	0.071000	0.21146	0.999000	0.59377	0.996000	0.88848	-0.601000	0.05687	0.060000	0.16281	0.533000	0.62120	ATG	.	.		0.378	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		T	96706230	A	T	96706230	2	4	33	1	0	0	0	0	0	0	0	1	5173	436	16	4		4	EPHA6	3	96706230	Silent	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10		96706230	101316200	23	3968										
TM4SF18	116441	hgsc.bcm.edu	37	chr3	149051080	149051080	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	taggaagtttgcccattcggGaaatacaataatatgttcac	8	7	1	0	rs35087723		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr3:149051080G>A	ENST00000296059.2	-	2	355	c.90C>T	c.(88-90)ttC>ttT	p.F30F	TM4SF18_ENST00000470080.1_Silent_p.F30F|RP11-206M11.7_ENST00000489011.1_RNA	NM_138786.3	NP_620141.1	Q96CE8	T4S18_HUMAN	transmembrane 4 L six family member 18	30						integral component of membrane (GO:0016021)				lung(1)|ovary(1)|prostate(1)	3			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			GCCCATTCGGGAAATACAATA	0.428																																					p.F30F		Atlas-SNP	.											.	TM4SF18	12	.	0			c.C90T						.						96	91	93					3																	149051080		2203	4300	6503	SO:0001819	synonymous_variant	116441	exon1			ATTCGGGAAATAC	BC014339	CCDS3142.1	3q25.1	2005-08-09			ENSG00000163762	ENSG00000163762			25181	protein-coding gene	gene with protein product						10975581	Standard	NM_001184723		Approved	L6D	uc021xfl.1	Q96CE8	OTTHUMG00000159582	ENST00000296059.2:c.90C>T	chr3.hg19:g.149051080G>A		87.0	0.0		375.0	107.0	NM_001184723	B2R8K0|D3DNH5	Silent	SNP	ENST00000296059.2	hg19	CCDS3142.1																																																																																			.	.		0.428	TM4SF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356326.1	NM_138786		A	149051080	G	A	149051080	2	1	33	1	0	0	0	0	0	0	0	1	15982	1165	41	3		3	TM4SF18	3	149051080	Silent	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	52344850	149051080	48971350	24	3969										
SEC24B	10427	hgsc.bcm.edu	37	chr4	110447421	110447421	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tcacggtaacttctttgtccGttctactgatttgttatccc	6	11	3	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr4:110447421G>A	ENST00000265175.5	+	17	2886	c.2831G>A	c.(2830-2832)cGt>cAt	p.R944H	SEC24B_ENST00000504968.2_Missense_Mutation_p.R974H|SEC24B_ENST00000399100.2_Missense_Mutation_p.R909H	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	944					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)	p.R944H(1)|p.R909H(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		TTCTTTGTCCGTTCTACTGAT	0.358																																					p.R944H		Atlas-SNP	.											SEC24B_ENST00000265175,NS,carcinoma,0,2	SEC24B	186	.	2	Substitution - Missense(2)	prostate(2)	c.G2831A						.						205	186	192					4																	110447421		1856	4094	5950	SO:0001583	missense	10427	exon17			TTGTCCGTTCTAC	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.2831G>A	chr4.hg19:g.110447421G>A	ENSP00000265175:p.Arg944His	162.0	0.0		276.0	19.0	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	hg19	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.870183	0.91587	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;T;T	0.27256	1.68;1.68;1.68	5.21	4.35	0.52113	Sec23/Sec24 beta-sandwich (1);	0.054311	0.85682	D	0.000000	T	0.51466	0.1676	M	0.77616	2.38	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.78314	0.979;0.986;0.991;0.984;0.979	T	0.56523	-0.7965	10	0.87932	D	0	-16.5841	14.7926	0.69854	0.0735:0.0:0.9265:0.0	.	858;543;974;909;944	B4DTM6;B4E2E1;B7ZKM8;O95487-2;O95487	.;.;.;.;SC24B_HUMAN	H	974;909;944	ENSP00000428564:R974H;ENSP00000382051:R909H;ENSP00000265175:R944H	ENSP00000265175:R944H	R	+	2	0	SEC24B	110666870	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.013000	0.88655	2.596000	0.87737	0.591000	0.81541	CGT	.	.		0.358	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			A	110447421	G	A	110447421	3	1	33	1	0	0	0	0	1	0	0	0	14010	1145	40	1	2897	1	SEC24B	4	110447421	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10		110447421	80706855	25	3970										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55247872	55247872	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gcttcgtttttccctactttTtttgtccgaacagtaggtcc	7	11	0	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr5:55247872T>C	ENST00000381298.2	-	13	1896	c.1584A>G	c.(1582-1584)aaA>aaG	p.K528K	IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000336909.5_Silent_p.K528K|IL6ST_ENST00000381294.3_Silent_p.K467K|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000502326.3_Silent_p.K528K|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000522633.2_3'UTR	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	528	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				TCCCTACTTTTTTTGTCCGAA	0.343			O		hepatocellular ca																																p.K528K		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.A1584G						.						73	64	67					5																	55247872		2203	4300	6503	SO:0001819	synonymous_variant	3572	exon13			TACTTTTTTTGTC	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.1584A>G	chr5.hg19:g.55247872T>C		123.0	0.0		389.0	122.0	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Silent	SNP	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.		0.343	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		C	55247872	T	C	55247872	2	2	33	1	0	0	0	0	0	0	0	1	7712	1838	64	2		2	IL6ST	5	55247872	Silent	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10		55247872	125667388	26	3971										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128977592	128977592	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	atggtgcaaggtagaaggtgAgaaagaatgcagaaccaagc	14	5	0	4			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr5:128977592A>T	ENST00000274487.4	+	11	1938	c.1793A>T	c.(1792-1794)gAg>gTg	p.E598V	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	598	Disintegrin.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GTAGAAGGTGAGAAAGAATGC	0.393																																					p.E598V		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.A1793T						.						233	193	206					5																	128977592		2203	4300	6503	SO:0001583	missense	171019	exon11			AAGGTGAGAAAGA	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1793A>T	chr5.hg19:g.128977592A>T	ENSP00000274487:p.Glu598Val	110.0	0.0		324.0	94.0	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.671827	0.47781	.	.	ENSG00000145808	ENST00000274487	T	0.63417	-0.04	4.02	4.02	0.46733	.	0.175049	0.35838	N	0.002951	T	0.53254	0.1785	L	0.48877	1.53	0.58432	D	0.99999	B	0.24368	0.102	B	0.20767	0.031	T	0.51036	-0.8756	9	.	.	.	.	14.01	0.64490	1.0:0.0:0.0:0.0	.	598	Q8TE59	ATS19_HUMAN	V	598	ENSP00000274487:E598V	.	E	+	2	0	ADAMTS19	129005491	1.000000	0.71417	0.924000	0.36721	0.976000	0.68499	6.834000	0.75339	2.039000	0.60335	0.482000	0.46254	GAG	.	.		0.393	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		T	128977592	A	T	128977592	3	4	33	1	0	0	0	0	1	0	0	0	264	304	11	4	1835	4	ADAMTS19	5	128977592	Missense_Mutation	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10	73729720	128977592	51937668	27	3972										
FAT2	2196	hgsc.bcm.edu	37	chr5	150886943	150886944	+	Frame_Shift_Ins	INS	-	-	T													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	agctcgatggcaggcatggcINSttgggtgtcaacaccaacac							TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr5:150886943_150886944insT	ENST00000261800.5	-	22	12300_12301	c.12288_12289insA	c.(12286-12291)caagccfs	p.A4097fs	CTC-251D13.1_ENST00000606930.1_RNA	NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	4097					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCAGGCATGGCTTGGGTGTCAA	0.579																																					p.A4097fs		Atlas-INDEL	.											.	FAT2	465	.	0			c.12289_12290insA						.																																			SO:0001589	frameshift_variant	2196	exon22			.	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.12289dupA	chr5.hg19:g.150886945_150886945dupT	ENSP00000261800:p.Ala4097fs	110.0	0.0		361.0	25.0	NM_001447	O75091|Q9NSR7	Frame_Shift_Ins	INS	ENST00000261800.5	hg19	CCDS4317.1																																																																																			.	.		0.579	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150886944	-	T	150886943	7	5	33	1	0	1	1	0	0	0	0	0	5698	797	28	0	768	0	FAT2	5	150886943	Frame_Shift_Ins	INS	-	TCGA-BC-A10T-01A-11D-A12Z-10	21909351	150886943	30028317	28	3973										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152676100	152676100	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gcctgcccctctgcacagtgTacctgtagctcctgcagaga	10	15	1	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr6:152676100T>C	ENST00000367255.5	-	67	11221	c.10620A>G	c.(10618-10620)gtA>gtG	p.V3540V	SYNE1_ENST00000265368.4_Silent_p.V3540V|SYNE1_ENST00000423061.1_Silent_p.V3547V|SYNE1_ENST00000341594.5_Silent_p.V3511V|SYNE1_ENST00000448038.1_Silent_p.V3547V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3540					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTGCACAGTGTACCTGTAGCT	0.527										HNSCC(10;0.0054)																											p.V3547V		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A10641G						.						88	91	90					6																	152676100		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon67			ACAGTGTACCTGT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.10620A>G	chr6.hg19:g.152676100T>C		26.0	0.0		73.0	31.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.527	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152676100	T	C	152676100	2	2	33	1	0	0	0	0	0	0	0	1	15460	1625	57	2		2	SYNE1	6	152676100	Silent	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10		152676100	18438967	29	3974										
MYCT1	80177	hgsc.bcm.edu	37	chr6	153043057	153043058	+	Frame_Shift_Ins	INS	-	-	C													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ctcaacagaactggattttaINSccgccacagtggctgtgaac					rs529302802|rs74502972		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr6:153043057_153043058insC	ENST00000367245.5	+	2	385_386	c.377_378insC	c.(376-381)taccgcfs	p.R127fs	MYCT1_ENST00000529453.1_Intron	NM_025107.2	NP_079383.2	Q8N699	MYCT1_HUMAN	myc target 1	127			R -> G (in dbSNP:rs17852097). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	20		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		ACTGGATTTTACCGCCACAGTG	0.515																																					p.Y126fs		Atlas-INDEL	.											.	MYCT1	48	.	0			c.377_378insC						.																																			SO:0001589	frameshift_variant	80177	exon2			.	AF527367	CCDS5239.1	6q25.1	2008-02-05			ENSG00000120279	ENSG00000120279			23172	protein-coding gene	gene with protein product						12477932	Standard	NM_025107		Approved	MTLC, FLJ21269	uc003qpc.4	Q8N699	OTTHUMG00000015850	ENST00000367245.5:c.379dupC	chr6.hg19:g.153043059_153043059dupC	ENSP00000356214:p.Arg127fs	131.0	0.0		342.0	21.0	NM_025107	Q8N396|Q8TBE8|Q9H763	Frame_Shift_Ins	INS	ENST00000367245.5	hg19	CCDS5239.1																																																																																			.	.		0.515	MYCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042750.2	NM_025107		C	153043058	-	C	153043057	7	5	33	1	0	1	1	0	0	0	0	0	10031	391	14	0	383	0	MYCT1	6	153043057	Frame_Shift_Ins	INS	-	TCGA-BC-A10T-01A-11D-A12Z-10	366957	153043057	18072010	30	3975										
OPRM1	4988	hgsc.bcm.edu	37	chr6	154331688	154331688	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cagcaccaaagctgggaagcCctccaggttcatttggaaga	11	11	1	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr6:154331688C>T	ENST00000518759.1	+	1	53	c.41C>T	c.(40-42)cCc>cTc	p.P14L	OPRM1_ENST00000434900.2_5'UTR|OPRM1_ENST00000520708.1_5'UTR	NM_001145281.1	NP_001138753.1	P35372	OPRM_HUMAN	opioid receptor, mu 1	0					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	GCTGGGAAGCCCTCCAGGTTC	0.413																																					p.P14L		Atlas-SNP	.											.	OPRM1	241	.	0			c.C41T						.						128	108	114					6																	154331688		692	1591	2283	SO:0001583	missense	4988	exon1			GGAAGCCCTCCAG	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000518759.1:c.41C>T	chr6.hg19:g.154331688C>T	ENSP00000430260:p.Pro14Leu	47.0	0.0		115.0	31.0	NM_001145281	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000518759.1	hg19	CCDS55068.1	.	.	.	.	.	.	.	.	.	.	C	10.33	1.320709	0.23994	.	.	ENSG00000112038	ENST00000518759	T	0.71934	-0.61	5.5	0.435	0.16544	.	.	.	.	.	T	0.33556	0.0867	.	.	.	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.27434	-1.0074	8	0.51188	T	0.08	.	4.4125	0.11439	0.1448:0.5267:0.0:0.3285	.	14	B8Q1L9	.	L	14	ENSP00000430260:P14L	ENSP00000430260:P14L	P	+	2	0	OPRM1	154373381	0.016000	0.18221	0.281000	0.24762	0.649000	0.38597	-0.136000	0.10405	0.034000	0.15491	-0.142000	0.14014	CCC	.	.		0.413	OPRM1-006	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375911.1	NM_000914		T	154331688	C	T	154331688	3	4	33	1	0	0	0	0	1	0	0	0	10896	623	22	3	43	3	OPRM1	6	154331688	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	1288631	154331688	16783379	31	3976										
C7orf27	221927	hgsc.bcm.edu	37	chr7	2579479	2579479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	agccgggggtcttgggtgagCtcaggagccacctgagcgtg	18	10	2	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr7:2579479C>T	ENST00000340611.4	-	11	1695	c.1439G>A	c.(1438-1440)aGc>aAc	p.S480N	BRAT1_ENST00000473879.1_5'UTR	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	480					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						CTTGGGTGAGCTCAGGAGCCA	0.657																																					p.S480N		Atlas-SNP	.											.	BRAT1	57	.	0			c.G1439A						.						28	31	30					7																	2579479		2199	4299	6498	SO:0001583	missense	221927	exon11			GGTGAGCTCAGGA	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"BRCA1-associated protein required for ATM activation protein 1"	614506	"chromosome 7 open reading frame 27"	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.1439G>A	chr7.hg19:g.2579479C>T	ENSP00000339637:p.Ser480Asn	17.0	0.0		90.0	33.0	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	hg19	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	C	6.015	0.371237	0.11409	.	.	ENSG00000106009	ENST00000340611	T	0.31510	1.49	5.2	3.37	0.38596	Armadillo-like helical (1);Armadillo-type fold (1);	0.513015	0.22022	N	0.065704	T	0.18718	0.0449	L	0.38838	1.175	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.28332	-1.0047	10	0.12430	T	0.62	-5.923	5.3229	0.15891	0.1353:0.5819:0.0:0.2828	.	480	Q6PJG6	BRAT1_HUMAN	N	480	ENSP00000339637:S480N	ENSP00000339637:S480N	S	-	2	0	BRAT1	2546005	0.000000	0.05858	0.002000	0.10522	0.091000	0.18340	-0.084000	0.11268	0.567000	0.29293	0.462000	0.41574	AGC	.	.		0.657	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		T	2579479	C	T	2579479	3	4	33	1	0	0	0	0	1	0	0	0	2384	797	28	3	1042	3	C7orf27	7	2579479	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10		2579479	156559184	32	3977										
SDK1	221935	hgsc.bcm.edu	37	chr7	4009044	4009044	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ccctgaatgcatcggccacgCtcactgtgtggagtaaggag	13	11	1	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr7:4009044C>T	ENST00000404826.2	+	11	1841	c.1702C>T	c.(1702-1704)Ctc>Ttc	p.L568F	SDK1_ENST00000389531.3_Missense_Mutation_p.L568F	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	568	Ig-like C2-type 5.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		ATCGGCCACGCTCACTGTGTG	0.587																																					p.L568F		Atlas-SNP	.											.	SDK1	361	.	0			c.C1702T						.						75	75	75					7																	4009044		2203	4300	6503	SO:0001583	missense	221935	exon11			GCCACGCTCACTG	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1702C>T	chr7.hg19:g.4009044C>T	ENSP00000385899:p.Leu568Phe	30.0	0.0		74.0	31.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.840180	0.51057	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	D;D	0.98602	-5.02;-5.02	5.63	5.63	0.86233	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000025	D	0.99180	0.9716	M	0.93328	3.405	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.99087	1.0839	10	0.87932	D	0	.	14.8485	0.70277	0.1436:0.8563:0.0:0.0	.	568	Q7Z5N4	SDK1_HUMAN	F	568	ENSP00000385899:L568F;ENSP00000374182:L568F	ENSP00000374182:L568F	L	+	1	0	SDK1	3975570	1.000000	0.71417	0.337000	0.25536	0.004000	0.04260	4.351000	0.59398	2.826000	0.97356	0.655000	0.94253	CTC	.	.		0.587	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4009044	C	T	4009044	3	4	33	1	0	0	0	0	1	0	0	0	13983	797	28	3	1744	3	SDK1	7	4009044	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	1429565	4009044	155129619	33	3978										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87179344	87179344	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	agaaaccttacatttatggtCctaatatcctgtccatcaac	4	11	1	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr7:87179344C>T	ENST00000265724.3	-	14	1794	c.1377G>A	c.(1375-1377)agG>agA	p.R459R	ABCB1_ENST00000543898.1_Silent_p.R395R	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	459	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CATTTATGGTCCTAATATCCT	0.408																																					p.R459R		Atlas-SNP	.											.	ABCB1	263	.	0			c.G1377A						.						121	110	113					7																	87179344		2203	4300	6503	SO:0001819	synonymous_variant	5243	exon14			TATGGTCCTAATA	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.1377G>A	chr7.hg19:g.87179344C>T		46.0	0.0		193.0	44.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Silent	SNP	ENST00000265724.3	hg19	CCDS5608.1																																																																																			.	.		0.408	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		T	87179344	C	T	87179344	2	4	33	1	0	0	0	0	0	0	0	1	40	854	30	3		3	ABCB1	7	87179344	Silent	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	83170300	87179344	71959319	34	3979										
C7orf63	79846	hgsc.bcm.edu	37	chr7	89938655	89938655	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	aaaatgcaatatttcaccaaAcacatattaaaggccttaac	3	9	1	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr7:89938655A>G	ENST00000389297.4	+	22	2880	c.2629A>G	c.(2629-2631)Aca>Gca	p.T877A	C7orf63_ENST00000497910.1_Missense_Mutation_p.T859A|C7orf63_ENST00000316089.8_Missense_Mutation_p.T831A	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		877										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						ATTTCACCAAACACATATTAA	0.313																																					p.T877A		Atlas-SNP	.											.	C7orf63	158	.	0			c.A2629G						.						120	113	115					7																	89938655		1810	4073	5883	SO:0001583	missense	79846	exon22			CACCAAACACATA																												ENST00000389297.4:c.2629A>G	chr7.hg19:g.89938655A>G	ENSP00000373948:p.Thr877Ala	290.0	0.0		440.0	167.0	NM_001039706	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	hg19	CCDS43613.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.47|15.47	2.842236|2.842236	0.51057|0.51057	.|.	.|.	ENSG00000105792|ENSG00000105792	ENST00000412839|ENST00000389297;ENST00000316089;ENST00000497910;ENST00000449577	.|T;T;T;T	.|0.27720	.|2.18;2.19;2.2;1.65	5.48|5.48	5.48|5.48	0.80851|0.80851	.|.	.|0.128766	.|0.52532	.|D	.|0.000061	T|T	0.54111|0.54111	0.1838|0.1838	M|M	0.77103|0.77103	2.36|2.36	0.43982|0.43982	D|D	0.996675|0.996675	.|D;D	.|0.69078	.|0.984;0.997	.|P;P	.|0.61800	.|0.785;0.894	T|T	0.58470|0.58470	-0.7631|-0.7631	5|10	.|0.54805	.|T	.|0.06	-19.0344|-19.0344	15.627|15.627	0.76867|0.76867	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|859;877	.|A5D8W1-5;A5D8W1	.|.;CG063_HUMAN	S|A	105|877;831;859;414	.|ENSP00000373948:T877A;ENSP00000321753:T831A;ENSP00000419549:T859A;ENSP00000391571:T414A	.|ENSP00000321753:T831A	N|T	+|+	2|1	0|0	C7orf63|C7orf63	89776591|89776591	1.000000|1.000000	0.71417|0.71417	0.786000|0.786000	0.31890|0.31890	0.132000|0.132000	0.20833|0.20833	7.075000|7.075000	0.76798|0.76798	2.102000|2.102000	0.63906|0.63906	0.477000|0.477000	0.44152|0.44152	AAC|ACA	.	.		0.313	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			G	89938655	A	G	89938655	3	3	33	1	0	0	0	0	1	0	0	0	2411	43	2	2	2715	2	C7orf63	7	89938655	Missense_Mutation	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10	2759311	89938655	69200008	35	3980										
NAA38	84316	hgsc.bcm.edu	37	chr7	117828373	117828373	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cagaccattaatttgattttGgatgaaagccatgaacgagt	9	6	0	4			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr7:117828373G>T	ENST00000249299.2	+	3	306	c.114G>T	c.(112-114)ttG>ttT	p.L38F	NAA38_ENST00000422760.1_Missense_Mutation_p.L17F|NAA38_ENST00000424702.1_Missense_Mutation_p.L38F	NM_016200.4	NP_057284.1	Q9BRA0	LSMD1_HUMAN	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	78					negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	8						ATTTGATTTTGGATGAAAGCC	0.353																																					p.L38F		Atlas-SNP	.											.	NAA38	16	.	0			c.G114T						.						91	92	92					7																	117828373		2203	4300	6503	SO:0001583	missense	51691	exon3			GATTTTGGATGAA		CCDS11122.1	17p13.1	2014-01-21	2014-01-21	2014-01-21		ENSG00000183011		"N(alpha)-acetyltransferase subunits"	28212	protein-coding gene	gene with protein product			"LSM domain containing 1"	LSMD1		16484612, 19398576	Standard	NM_032356		Approved	MGC14151, PFAAP2	uc002gja.3	Q9BRA0		ENST00000249299.2:c.114G>T	chr7.hg19:g.117828373G>T	ENSP00000249299:p.Leu38Phe	99.0	0.0		161.0	53.0	NM_016200	Q8N4M0	Missense_Mutation	SNP	ENST00000249299.2	hg19	CCDS5775.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.965706	0.92855	.	.	ENSG00000128534	ENST00000249299;ENST00000424702;ENST00000422760;ENST00000411938	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	5.69	5.69	0.88448	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.000000	0.64402	D	0.000001	T	0.81522	0.4840	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82563	-0.0395	9	0.62326	D	0.03	-9.8012	19.8148	0.96562	0.0:0.0:1.0:0.0	.	38	O95777	NAA38_HUMAN	F	38;38;17;49	ENSP00000249299:L38F;ENSP00000395263:L38F;ENSP00000403811:L17F;ENSP00000408267:L49F	ENSP00000249299:L38F	L	+	3	2	NAA38	117615609	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.753000	0.68736	2.687000	0.91594	0.650000	0.86243	TTG	.	.		0.353	NAA38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346774.2	NM_032356		T	117828373	G	T	117828373	3	4	33	1	0	0	0	0	1	0	0	0	10133	1339	47	3	124	3	NAA38	7	117828373	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	27889718	117828373	41310290	36	3981										
C7orf49	78996	hgsc.bcm.edu	37	chr7	134852549	134852550	+	Missense_Mutation	DNP	TC	TC	AA													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	catgcagtacacagtccttgTcgcagggagtctgaaaaaaa							TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr7:134852549_134852550TC>AA	ENST00000393114.3	-	3	328_329	c.147_148GA>TT	c.(145-150)gcGAca>gcTTca	p.T50S	C7orf49_ENST00000424142.1_5'UTR|C7orf49_ENST00000459937.1_Intron|C7orf49_ENST00000430372.1_Missense_Mutation_p.T49S|RP11-134L10.1_ENST00000608819.1_RNA|C7orf49_ENST00000483029.2_5'UTR			Q9BWK5	MRI_HUMAN	chromosome 7 open reading frame 49	50						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(4)|lung(1)|ovary(1)	7						ACAGTCCTTGTCGCAGGGAGTC	0.48																																					p.D62V|p.D62Y		Atlas-SNP	.											.	C7orf49	24	.	0			c.A185T|c.G184T						.																																			SO:0001583	missense	78996	exon3			TCCTTGTCGCAGG|CCTTGTCGCAGGG	BC000168	CCDS5838.2, CCDS59082.1, CCDS75663.1	7q33	2011-12-09			ENSG00000122783	ENSG00000122783			22432	protein-coding gene	gene with protein product	"modulator of retrovirus infection"					17043244	Standard	NM_001243755		Approved	MGC5242, FLJ27285, FLJ22450, MRI	uc003vsh.3	Q9BWK5	OTTHUMG00000155447	ENST00000393114.3:c.147_148delinsAA	chr7.hg19:g.134852549_134852550delinsAA	ENSP00000376823:p.Thr50Ser	66.0|67.0	0.0		125.0|122.0	47.0|45.0	NM_001243749	Q6NWZ4|Q6ZNR5	Missense_Mutation	SNP	ENST00000393114.3	hg19	CCDS5838.2																																																																																			.	.		0.48	C7orf49-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340145.1	NM_024033		AA	134852550	TC	AA	134852549	3	1	33	1	0	0	0	0	1	0	0	0	2400	1667	58	4	333	4	C7orf49	7	134852549	Missense_Mutation	DNP	TC	TCGA-BC-A10T-01A-11D-A12Z-10	17024176	134852549	24286114	37	3982										
MLL3	58508	hgsc.bcm.edu	37	chr7	151833918	151833918	+	Nonstop_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	agctagcaaggaatgcatttCagttcatccacttccggcag	9	11	2	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr7:151833918C>A	ENST00000262189.6	-	59	14953	c.14735G>T	c.(14734-14736)tGa>tTa	p.*4912L	KMT2C_ENST00000485655.2_Nonstop_Mutation_p.*117L|KMT2C_ENST00000355193.2_Nonstop_Mutation_p.*4969L	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	0					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GAATGCATTTCAGTTCATCCA	0.473																																					p.X4912L		Atlas-SNP	.											.	MLL3	1564	.	0			c.G14735T						.						92	79	84					7																	151833918		2203	4300	6503	SO:0001578	stop_lost	58508	exon59			GCATTTCAGTTCA	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.14735G>T	chr7.hg19:g.151833918C>A		13.0	0.0		55.0	15.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.244925	0.59103	.	.	ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000485655;ENST00000424877	.	.	.	5.19	2.98	0.34508	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.247	0.10675	0.0:0.5256:0.0:0.4744	.	.	.	.	L	4912;4969;117;1525	.	.	X	-	2	2	MLL3	151464851	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	3.187000	0.50950	1.308000	0.44962	0.655000	0.94253	TGA	.	.		0.473	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151833918	C	A	151833918	4	1	33	1	0	0	0	0	0	0	0	0	9631	837	29	3	4	3	MLL3	7	151833918	Nonstop_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	16981369	151833918	7304745	38	3983										
CHRNB3	1142	hgsc.bcm.edu	37	chr8	42587132	42587132	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cctttatcacgtattccttcGtcctgagacgcctgccttta	6	14	1	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr8:42587132G>A	ENST00000289957.2	+	5	810	c.682G>A	c.(682-684)Gtc>Atc	p.V228I		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	228					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	GTATTCCTTCGTCCTGAGACG	0.478																																					p.V228I		Atlas-SNP	.											CHRNB3,right_upper_lobe,carcinoma,0,2	CHRNB3	74	.	0			c.G682A						.						89	92	91					8																	42587132		2203	4300	6503	SO:0001583	missense	1142	exon5			TCCTTCGTCCTGA	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.682G>A	chr8.hg19:g.42587132G>A	ENSP00000289957:p.Val228Ile	131.0	0.0		211.0	73.0	NM_000749	Q15827	Missense_Mutation	SNP	ENST00000289957.2	hg19	CCDS6134.1	.	.	.	.	.	.	.	.	.	.	g	2.895	-0.228696	0.06022	.	.	ENSG00000147432	ENST00000289957	T	0.79033	-1.23	5.46	5.46	0.80206	Neurotransmitter-gated ion-channel ligand-binding (3);	0.052626	0.85682	D	0.000000	T	0.58452	0.2123	N	0.05414	-0.055	0.41498	D	0.988266	B	0.26512	0.151	B	0.28305	0.088	T	0.57323	-0.7831	10	0.10377	T	0.69	.	14.127	0.65228	0.0:0.0:0.8128:0.1872	.	228	Q05901	ACHB3_HUMAN	I	228	ENSP00000289957:V228I	ENSP00000289957:V228I	V	+	1	0	CHRNB3	42706289	0.929000	0.31497	0.109000	0.21407	0.265000	0.26407	2.384000	0.44362	2.568000	0.86640	0.558000	0.71614	GTC	.	.		0.478	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			A	42587132	G	A	42587132	3	1	33	1	0	0	0	0	1	0	0	0	3394	1145	40	1	700	1	CHRNB3	8	42587132	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10		42587132	103776890	39	3984										
ZNF572	137209	hgsc.bcm.edu	37	chr8	125987939	125987939	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	aacagctttatggagagggaGagtttgaaaagccctttcac	11	7	1	3			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr8:125987939G>A	ENST00000319286.5	+	2	211	c.57G>A	c.(55-57)gaG>gaA	p.E19E		NM_152412.2	NP_689625.2	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	19					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	31	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TGGAGAGGGAGAGTTTGAAAA	0.413										HNSCC(60;0.17)																											p.E19E		Atlas-SNP	.											.	ZNF572	82	.	0			c.G57A						.						116	112	114					8																	125987939		2203	4300	6503	SO:0001819	synonymous_variant	137209	exon2			GAGGGAGAGTTTG	BX537876	CCDS6354.1	8q24.13	2013-09-20			ENSG00000180938	ENSG00000180938		"Zinc fingers, C2H2-type"	26758	protein-coding gene	gene with protein product							Standard	NM_152412		Approved	FLJ38002	uc003yrr.3	Q7Z3I7	OTTHUMG00000164988	ENST00000319286.5:c.57G>A	chr8.hg19:g.125987939G>A		108.0	0.0		278.0	64.0	NM_152412	A1L4F1|Q8N1Q0	Silent	SNP	ENST00000319286.5	hg19	CCDS6354.1																																																																																			.	.		0.413	ZNF572-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381359.1	NM_152412		A	125987939	G	A	125987939	2	1	33	1	0	0	0	0	0	0	0	1	18019	933	33	3		3	ZNF572	8	125987939	Silent	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	83400807	125987939	20376083	40	3985										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139895383	139895384	+	Frame_Shift_Ins	INS	-	-	C													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gcagcagcatccagaggaggINSccagccacagcgttccctcg							TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr8:139895383_139895384insC	ENST00000303045.6	-	2	478_479	c.32_33insG	c.(31-33)ggcfs	p.G11fs	COL22A1_ENST00000435777.1_Frame_Shift_Ins_p.G11fs	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	11					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.G11D(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TCCAGAGGAGGCCAGCCACAGC	0.663										HNSCC(7;0.00092)																											p.G11fs		Atlas-INDEL	.											.	COL22A1	390	.	1	Substitution - Missense(1)	endometrium(1)	c.33_34insG						.																																			SO:0001589	frameshift_variant	169044	exon2			.	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.33dupG	chr8.hg19:g.139895385_139895385dupC	ENSP00000303153:p.Gly11fs	38.0	0.0		88.0	10.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Frame_Shift_Ins	INS	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.663	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		C	139895384	-	C	139895383	7	5	33	1	0	1	1	0	0	0	0	0	3683	1190	42	0	5103	0	COL22A1	8	139895383	Frame_Shift_Ins	INS	-	TCGA-BC-A10T-01A-11D-A12Z-10	13907444	139895383	6468639	41	3986										
MELK	9833	hgsc.bcm.edu	37	chr9	36630338	36630338	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	agtggctctctcccagtagcAttctgcttcttcaacaaatg	7	12	4	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr9:36630338A>G	ENST00000298048.2	+	9	893	c.709A>G	c.(709-711)Att>Gtt	p.I237V	MELK_ENST00000538311.1_Missense_Mutation_p.I43V|MELK_ENST00000536987.1_Missense_Mutation_p.I106V|MELK_ENST00000487398.1_3'UTR|MELK_ENST00000543751.1_Missense_Mutation_p.I205V|MELK_ENST00000536860.1_Missense_Mutation_p.I189V|MELK_ENST00000545008.1_Missense_Mutation_p.I166V|MELK_ENST00000541717.1_Missense_Mutation_p.I237V|MELK_ENST00000536329.1_Missense_Mutation_p.I166V	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	237	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			TCCCAGTAGCATTCTGCTTCT	0.348																																					p.I237V	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.A709G						.						196	206	203					9																	36630338		2203	4300	6503	SO:0001583	missense	9833	exon9			AGTAGCATTCTGC	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.709A>G	chr9.hg19:g.36630338A>G	ENSP00000298048:p.Ile237Val	56.0	0.0		118.0	41.0	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	hg19	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	A	6.913	0.538062	0.13188	.	.	ENSG00000165304	ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751	T;T;T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	5.41	-1.06	0.10002	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.423208	0.29451	N	0.012116	T	0.34337	0.0894	N	0.11789	0.175	0.09310	N	0.999999	B;B;B;B;B;B;B	0.10296	0.001;0.003;0.0;0.0;0.001;0.003;0.0	B;B;B;B;B;B;B	0.20577	0.03;0.003;0.001;0.001;0.004;0.006;0.004	T	0.31752	-0.9932	10	0.02654	T	1	-1.4603	10.5173	0.44898	0.5641:0.0:0.4359:0.0	.	157;166;189;237;166;205;237	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680	.;.;.;.;.;.;MELK_HUMAN	V	237;43;106;166;189;166;237;205	ENSP00000298048:I237V;ENSP00000438226:I43V;ENSP00000439184:I106V;ENSP00000445452:I166V;ENSP00000439792:I189V;ENSP00000443550:I166V;ENSP00000437804:I237V;ENSP00000441596:I205V	ENSP00000298048:I237V	I	+	1	0	MELK	36620338	0.005000	0.15991	0.383000	0.26132	0.985000	0.73830	0.932000	0.28884	-0.456000	0.07043	-0.250000	0.11733	ATT	.	.		0.348	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		G	36630338	A	G	36630338	3	3	33	1	0	0	0	0	1	0	0	0	9479	217	8	2	739	2	MELK	9	36630338	Missense_Mutation	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10		36630338	104583093	42	3987										
FAM75A6	389730	hgsc.bcm.edu	37	chr9	43630592	43630592	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ggagtaataggaagaagaacCccagggcaaacaccaaggtg	13	8	0	2	rs543743372		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr9:43630592C>T	ENST00000332857.6	-	1	138	c.110G>A	c.(109-111)gGg>gAg	p.G37E	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	37					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GAAGAAGAACCCCAGGGCAAA	0.498																																					p.G37E		Atlas-SNP	.											FAM75A6,NS,carcinoma,0,1	.	.	.	0			c.G110A						.																																			SO:0001583	missense	389730	exon1			AAGAACCCCAGGG		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"family with sequence similarity 75, member A6"	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.110G>A	chr9.hg19:g.43630592C>T	ENSP00000329825:p.Gly37Glu	17.0	0.0		30.0	11.0	NM_001145196		Missense_Mutation	SNP	ENST00000332857.6	hg19	CCDS47973.1	.	.	.	.	.	.	.	.	.	.	C	7.383	0.629230	0.14257	.	.	ENSG00000185775	ENST00000332857	T	0.18657	2.2	1.96	0.992	0.19819	.	0.379536	0.19422	N	0.114662	T	0.10423	0.0255	N	0.16903	0.455	0.09310	N	1	B	0.10296	0.003	B	0.14023	0.01	T	0.24799	-1.0150	10	0.30854	T	0.27	-5.6059	5.5217	0.16936	0.328:0.672:0.0:0.0	.	37	Q5VVP1	F75A6_HUMAN	E	37	ENSP00000329825:G37E	ENSP00000329825:G37E	G	-	2	0	FAM75A6	43570588	0.001000	0.12720	0.233000	0.24025	0.393000	0.30537	0.147000	0.16202	0.360000	0.24265	0.184000	0.17185	GGG	.	.		0.498	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196		T	43630592	C	T	43630592	3	4	33	1	0	0	0	0	1	0	0	0	5630	623	22	3	3937	3	FAM75A6	9	43630592	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	7000254	43630592	97582839	43	3988										
DFNB31	25861	hgsc.bcm.edu	37	chr9	117168768	117168769	+	Frame_Shift_Ins	INS	-	-	C													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gtgatgggggcagaaggcagINScccccagccactgtggcctc							TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr9:117168768_117168769insC	ENST00000362057.3	-	9	2270_2271	c.2102_2103insG	c.(2101-2103)ggcfs	p.G701fs	DFNB31_ENST00000265134.6_Frame_Shift_Ins_p.G318fs|DFNB31_ENST00000374059.3_Frame_Shift_Ins_p.G350fs	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	701	Pro-rich.				inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCAGAAGGCAGCCCCCAGCCAC	0.658																																					p.G701fs		Atlas-INDEL	.											.	DFNB31	100	.	0			c.2103_2104insG						.																																			SO:0001589	frameshift_variant	25861	exon9			.	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"whirlin"	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.2103dupG	chr9.hg19:g.117168773_117168773dupC	ENSP00000354623:p.Gly701fs	55.0	0.0		108.0	10.0	NM_001173425	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Frame_Shift_Ins	INS	ENST00000362057.3	hg19	CCDS6806.1																																																																																			.	.		0.658	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404		C	117168769	-	C	117168768	7	5	33	1	0	1	1	0	0	0	0	0	4457	958	34	0	636	0	DFNB31	9	117168768	Frame_Shift_Ins	INS	-	TCGA-BC-A10T-01A-11D-A12Z-10	73538176	117168768	24044663	44	3989										
MPP7	143098	hgsc.bcm.edu	37	chr10	28420525	28420525	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ttgaccagacggattattttTactgagtcttcctcatcgtc	7	10	2	3			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr10:28420525T>C	ENST00000375732.1	-	6	670	c.411A>G	c.(409-411)gtA>gtG	p.V137V	MPP7_ENST00000540098.1_Silent_p.V137V|MPP7_ENST00000337532.5_Silent_p.V137V|MPP7_ENST00000375719.3_Silent_p.V137V|MPP7_ENST00000481244.1_5'UTR|MPP7_ENST00000445954.2_Silent_p.V12V			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	137					establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						GGATTATTTTTACTGAGTCTT	0.433																																					p.V137V		Atlas-SNP	.											.	MPP7	60	.	0			c.A411G						.						134	122	126					10																	28420525		2203	4300	6503	SO:0001819	synonymous_variant	143098	exon8			TATTTTTACTGAG	BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.411A>G	chr10.hg19:g.28420525T>C		73.0	0.0		225.0	82.0	NM_173496	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Silent	SNP	ENST00000375732.1	hg19	CCDS7158.1																																																																																			.	.		0.433	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		C	28420525	T	C	28420525	2	2	33	1	0	0	0	0	0	0	0	1	9748	1741	61	2		2	MPP7	10	28420525	Silent	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10		28420525	107114222	45	3990										
OPALIN	93377	hgsc.bcm.edu	37	chr10	98108095	98108095	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ctgaaatttcacatggtctgTcactttcctaaattggaaaa	6	8	3	1	rs113141694		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr10:98108095T>C	ENST00000371172.3	-	5	605	c.200A>G	c.(199-201)gAc>gGc	p.D67G	OPALIN_ENST00000419479.1_Missense_Mutation_p.D57G|OPALIN_ENST00000536387.1_Missense_Mutation_p.D57G|OPALIN_ENST00000393870.2_Missense_Mutation_p.D56G|OPALIN_ENST00000393871.1_Missense_Mutation_p.D44G	NM_001284326.1|NM_001284327.1|NM_033207.3	NP_001271255.1|NP_001271256.1|NP_149984.1	Q96PE5	OPALI_HUMAN	oligodendrocytic myelin paranodal and inner loop protein	67						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(5)|prostate(2)	9						ACATGGTCTGTCACTTTCCTA	0.318																																					p.D67G		Atlas-SNP	.											.	OPALIN	31	.	0			c.A200G						.						66	67	66					10																	98108095		2202	4299	6501	SO:0001583	missense	93377	exon5			GGTCTGTCACTTT	AF367761	CCDS7448.1, CCDS41556.1, CCDS44466.1, CCDS60602.1, CCDS73172.1, CCDS73173.1	10q23-q24	2010-11-23	2008-05-01	2008-05-01	ENSG00000197430	ENSG00000197430			20707	protein-coding gene	gene with protein product			"transmembrane protein 10"	TMEM10		11814680, 17442045	Standard	NM_001284324		Approved	TMP10, HTMP10	uc001kmj.3	Q96PE5	OTTHUMG00000018831	ENST00000371172.3:c.200A>G	chr10.hg19:g.98108095T>C	ENSP00000360214:p.Asp67Gly	37.0	0.0		93.0	23.0	NM_033207	A8MX69|A8MYG4|B4DK96|B4DKH0|Q5W102	Missense_Mutation	SNP	ENST00000371172.3	hg19	CCDS7448.1	.	.	.	.	.	.	.	.	.	.	T	13.96	2.392535	0.42410	.	.	ENSG00000197430	ENST00000371172;ENST00000393871;ENST00000419479;ENST00000393870;ENST00000536387	.	.	.	4.92	4.92	0.64577	.	0.494915	0.18727	N	0.132852	T	0.19846	0.0477	N	0.08118	0	0.22412	N	0.999123	B;B;B	0.30281	0.13;0.13;0.275	B;B;B	0.26416	0.051;0.051;0.069	T	0.16778	-1.0391	9	0.66056	D	0.02	-5.1212	11.1806	0.48625	0.0:0.0:0.0:1.0	.	44;67;57	A8MYG4;Q96PE5;B4DK96	.;OPALI_HUMAN;.	G	67;44;57;56;57	.	ENSP00000360214:D67G	D	-	2	0	OPALIN	98098085	0.914000	0.31030	0.983000	0.44433	0.866000	0.49608	3.167000	0.50793	2.198000	0.70561	0.456000	0.33151	GAC	.	T|0.500;C|0.500		0.318	OPALIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049606.1	NM_033207		C	98108095	T	C	98108095	3	2	33	1	0	0	0	0	1	0	0	0	10882	1667	58	2	233	2	OPALIN	10	98108095	Missense_Mutation	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10	69687570	98108095	37426652	46	3991										
HPS6	79803	hgsc.bcm.edu	37	chr10	103825804	103825804	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ctgcaccactgccctgccttCgggctgctggcctcctgcag	11	18	0	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr10:103825804C>T	ENST00000299238.5	+	1	658	c.573C>T	c.(571-573)ttC>ttT	p.F191F		NM_024747.5	NP_079023.2	Q86YV9	HPS6_HUMAN	Hermansky-Pudlak syndrome 6	191					blood coagulation (GO:0007596)|melanocyte differentiation (GO:0030318)|organelle organization (GO:0006996)|protein localization to membrane (GO:0072657)	BLOC-2 complex (GO:0031084)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|Rab GTPase binding (GO:0017137)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)	11		Colorectal(252;0.122)		Epithelial(162;5.93e-08)|all cancers(201;1.03e-06)		GCCCTGCCTTCGGGCTGCTGG	0.662									Hermansky-Pudlak syndrome																												p.F191F		Atlas-SNP	.											.	HPS6	38	.	0			c.C573T						.						25	27	26					10																	103825804		2203	4298	6501	SO:0001819	synonymous_variant	79803	exon1	Familial Cancer Database	HPS, HPS1-8	TGCCTTCGGGCTG	BC009258	CCDS7527.1	10q24.32	2014-06-18			ENSG00000166189	ENSG00000166189			18817	protein-coding gene	gene with protein product		607522				12548288	Standard	NM_024747		Approved	FLJ22501	uc001kuj.3	Q86YV9	OTTHUMG00000018945	ENST00000299238.5:c.573C>T	chr10.hg19:g.103825804C>T		18.0	0.0		28.0	9.0	NM_024747	Q5VV69|Q9H685	Silent	SNP	ENST00000299238.5	hg19	CCDS7527.1																																																																																			.	.		0.662	HPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050018.2	NM_024747		T	103825804	C	T	103825804	2	4	33	1	0	0	0	0	0	0	0	1	7352	883	31	1		1	HPS6	10	103825804	Silent	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	5717709	103825804	31708943	47	3992										
OR8I2	120586	hgsc.bcm.edu	37	chr11	55861148	55861148	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gggatcaatggcctacaatcGctacatagcaatctgcaatc	8	11	2	0	rs148027692		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr11:55861148G>T	ENST00000302124.2	+	1	396	c.365G>T	c.(364-366)cGc>cTc	p.R122L		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R122H(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					GCCTACAATCGCTACATAGCA	0.438																																					p.R122L		Atlas-SNP	.											OR8I2,NS,malignant_melanoma,+1,1	OR8I2	119	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G365T						.						155	138	144					11																	55861148		2201	4296	6497	SO:0001583	missense	120586	exon1			ACAATCGCTACAT	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.365G>T	chr11.hg19:g.55861148G>T	ENSP00000303864:p.Arg122Leu	80.0	1.0		175.0	58.0	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	hg19	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.604242	0.46423	.	.	ENSG00000172154	ENST00000302124	T	0.77358	-1.09	4.5	3.58	0.41010	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40728	U	0.001035	D	0.84727	0.5536	H	0.96489	3.83	0.38452	D	0.946974	P	0.47106	0.89	B	0.43155	0.41	D	0.89065	0.3465	10	0.87932	D	0	-8.8288	12.1049	0.53807	0.0861:0.0:0.9139:0.0	.	122	Q8N0Y5	OR8I2_HUMAN	L	122	ENSP00000303864:R122L	ENSP00000303864:R122L	R	+	2	0	OR8I2	55617724	0.962000	0.33011	0.343000	0.25615	0.002000	0.02628	4.874000	0.63064	1.019000	0.39547	0.440000	0.28878	CGC	.	G|1.000;A|0.000		0.438	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		T	55861148	G	T	55861148	3	4	33	1	0	0	0	0	1	0	0	0	11249	1087	38	1	367	1	OR8I2	11	55861148	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10		55861148	79145368	48	3993										
MRPL11	65003	hgsc.bcm.edu	37	chr11	66206166	66206166	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cctgcccgcacgatcgcccgGatcacaccgccgacctcggg	11	20	1	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr11:66206166G>T	ENST00000310999.7	-	1	153	c.60C>A	c.(58-60)atC>atA	p.I20I	MRPL11_ENST00000430466.2_Intron|MRPL11_ENST00000329819.4_Silent_p.I20I|MRPL11_ENST00000524576.1_Intron	NM_016050.3	NP_057134.1	Q9Y3B7	RM11_HUMAN	mitochondrial ribosomal protein L11	20					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|prostate(1)	7						CGATCGCCCGGATCACACCGC	0.721																																					p.I20I		Atlas-SNP	.											.	MRPL11	25	.	0			c.C60A						.						9	12	11					11																	66206166		2073	4192	6265	SO:0001819	synonymous_variant	65003	exon1			CGCCCGGATCACA	AB051338	CCDS8139.1, CCDS8140.1, CCDS44655.1	11q13.2	2012-11-14			ENSG00000174547	ENSG00000174547		"Mitochondrial ribosomal proteins / large subunits"	14042	protein-coding gene	gene with protein product		611826					Standard	XR_247672		Approved		uc001ohz.4	Q9Y3B7	OTTHUMG00000167097	ENST00000310999.7:c.60C>A	chr11.hg19:g.66206166G>T		67.0	0.0		81.0	24.0	NM_170739	A6NLT0|A8K219|Q32P46|Q96Q73	Silent	SNP	ENST00000310999.7	hg19	CCDS8139.1																																																																																			.	.		0.721	MRPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393098.2	NM_016050		T	66206166	G	T	66206166	2	4	33	1	0	0	0	0	0	0	0	1	9785	1164	41	3		3	MRPL11	11	66206166	Silent	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	10345018	66206166	68800350	49	3994										
CABP4	57010	hgsc.bcm.edu	37	chr11	67223230	67223230	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gacgctgctcagaggacataCgggcccctgctcaatcgagt	12	13	2	1	rs369080675		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr11:67223230C>T	ENST00000325656.5	+	1	413	c.336C>T	c.(334-336)taC>taT	p.Y112Y	CABP4_ENST00000542025.2_3'UTR|CABP4_ENST00000438189.2_5'UTR	NM_145200.3	NP_660201.1	P57796	CABP4_HUMAN	calcium binding protein 4	112					photoreceptor cell morphogenesis (GO:0008594)|phototransduction (GO:0007602)|retinal bipolar neuron differentiation (GO:0060040)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytosol (GO:0005829)|extracellular region (GO:0005576)|synapse (GO:0045202)|terminal bouton (GO:0043195)	calcium ion binding (GO:0005509)			central_nervous_system(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)	11			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			AGAGGACATACGGGCCCCTGC	0.682													C|||	1	0.000199681	8e-04	0	5008	,	,		16360	0		0	False		,,,				2504	0				p.Y112Y		Atlas-SNP	.											.	CABP4	33	.	0			c.C336T						.	C		1,4327		0,1,2163	7	9	8		336	-3	0.3	11		8	0,8510		0,0,4255	no	coding-synonymous	CABP4	NM_145200.3		0,1,6418	TT,TC,CC		0.0,0.0231,0.0078		112/276	67223230	1,12837	2164	4255	6419	SO:0001819	synonymous_variant	57010	exon1			GACATACGGGCCC	AC005849	CCDS8166.1, CCDS73333.1	11q13.2	2013-09-20			ENSG00000175544	ENSG00000175544		"EF-hand domain containing"	1386	protein-coding gene	gene with protein product		608965				10625670, 16960802	Standard	NM_145200		Approved	CSNB2B	uc001olo.3	P57796	OTTHUMG00000168033	ENST00000325656.5:c.336C>T	chr11.hg19:g.67223230C>T		38.0	0.0		75.0	33.0	NM_145200	Q8N4Z2|Q8WWY5	Silent	SNP	ENST00000325656.5	hg19	CCDS8166.1																																																																																			.	.		0.682	CABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397624.2			T	67223230	C	T	67223230	2	4	33	1	0	0	0	0	0	0	0	1	2535	547	19	1		1	CABP4	11	67223230	Silent	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	1017064	67223230	67783286	50	3995										
MAML2	84441	hgsc.bcm.edu	37	chr11	95825206	95825206	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ggctgagaagatggttgttgCtgctgctgctgctgctgttg	16	7	0	2	rs547023702|rs149006316	byFrequency	TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr11:95825206C>T	ENST00000524717.1	-	2	3273	c.1989G>A	c.(1987-1989)caG>caA	p.Q663Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	663					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				atggttgttgctgctgctgct	0.517			T	"MECT1, CRTC3"	salivary gland mucoepidermoid								C|||	2	0.000399361	0	0	5008	,	,		18052	0		0	False		,,,				2504	0.002				p.Q663Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.G1989A						.						44	50	48					11																	95825206		2191	4282	6473	SO:0001819	synonymous_variant	84441	exon2			TTGTTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1989G>A	chr11.hg19:g.95825206C>T		103.0	0.0		328.0	34.0	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.		0.517	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825206	C	T	95825206	2	4	33	1	0	0	0	0	0	0	0	1	9215	796	28	3		3	MAML2	11	95825206	Silent	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	28601976	95825206	39181310	51	3996										
PDGFD	80310	hgsc.bcm.edu	37	chr11	103797732	103797732	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	atttcctccacagcgctgcaCgaggaggcaacgtggaaaga	12	11	0	1	rs371743652		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr11:103797732C>T	ENST00000393158.2	-	6	1074	c.895G>A	c.(895-897)Gtg>Atg	p.V299M	PDGFD_ENST00000302251.5_Missense_Mutation_p.V293M			Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D	299					cellular response to amino acid stimulus (GO:0071230)|multicellular organismal development (GO:0007275)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		CAGCGCTGCACGAGGAGGCAA	0.483													C|||	1	0.000199681	0	0	5008	,	,		21537	0		0	False		,,,				2504	0.001				p.V299M		Atlas-SNP	.											.	PDGFD	125	.	0			c.G895A						.						147	121	130					11																	103797732		2202	4299	6501	SO:0001583	missense	80310	exon6			GCTGCACGAGGAG	AF113216	CCDS8326.1, CCDS41703.1	11q22.3	2008-02-05			ENSG00000170962	ENSG00000170962			30620	protein-coding gene	gene with protein product	"spinal cord derived growth factor B"	609673				11162582, 11980634	Standard	NM_033135		Approved	SCDGF-B, MSTP036, IEGF	uc001phq.3	Q9GZP0	OTTHUMG00000165953	ENST00000393158.2:c.895G>A	chr11.hg19:g.103797732C>T	ENSP00000376865:p.Val299Met	61.0	0.0		137.0	51.0	NM_025208	A8K9T6|Q9BWV5	Missense_Mutation	SNP	ENST00000393158.2	hg19	CCDS41703.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.643067	0.87859	.	.	ENSG00000170962	ENST00000393158;ENST00000302251	T;T	0.46451	0.87;0.87	5.87	5.87	0.94306	Platelet-derived growth factor (PDGF) (3);	0.059149	0.64402	D	0.000002	T	0.62720	0.2451	M	0.69823	2.125	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.957	T	0.64824	-0.6316	10	0.87932	D	0	-13.9236	13.4113	0.60944	0.0:0.9285:0.0:0.0715	.	299;293	Q9GZP0;Q9GZP0-2	PDGFD_HUMAN;.	M	299;293	ENSP00000376865:V299M;ENSP00000302193:V293M	ENSP00000302193:V293M	V	-	1	0	PDGFD	103302942	1.000000	0.71417	0.965000	0.40720	0.977000	0.68977	5.757000	0.68766	2.774000	0.95407	0.650000	0.86243	GTG	.	.		0.483	PDGFD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387231.2	NM_025208		T	103797732	C	T	103797732	3	4	33	1	0	0	0	0	1	0	0	0	11669	536	19	1	225	1	PDGFD	11	103797732	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	7972526	103797732	31208784	52	3997										
PKNOX2	63876	hgsc.bcm.edu	37	chr11	125237753	125237753	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tctctgcagatgacggcaacCgcccagccaccctccaaggc	9	18	1	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr11:125237753C>T	ENST00000298282.9	+	5	370	c.99C>T	c.(97-99)acC>acT	p.T33T	PKNOX2_ENST00000542175.1_Intron|PKNOX2_ENST00000530517.1_3'UTR	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	33					regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		TGACGGCAACCGCCCAGCCAC	0.662																																					p.T33T		Atlas-SNP	.											.	PKNOX2	60	.	0			c.C99T						.						53	65	61					11																	125237753		2090	4203	6293	SO:0001819	synonymous_variant	63876	exon5			GGCAACCGCCCAG	AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"Homeoboxes / TALE class"	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.99C>T	chr11.hg19:g.125237753C>T		73.0	0.0		156.0	53.0	NM_022062	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Silent	SNP	ENST00000298282.9	hg19	CCDS41730.1																																																																																			.	.		0.662	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3			T	125237753	C	T	125237753	2	4	33	1	0	0	0	0	0	0	0	1	11992	639	23	1		1	PKNOX2	11	125237753	Silent	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	21440021	125237753	9768763	53	3998										
A2M	2	hgsc.bcm.edu	37	chr12	9244021	9244021	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tcctacctcagccacacctgCtgagctggagaggagtgtaa	11	12	1	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr12:9244021C>A	ENST00000318602.7	-	19	2552	c.2245G>T	c.(2245-2247)Gca>Tca	p.A749S		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	749					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	GCCACACCTGCTGAGCTGGAG	0.488																																					p.A749S		Atlas-SNP	.											.	A2M	180	.	0			c.G2245T						.						59	58	59					12																	9244021		2203	4300	6503	SO:0001583	missense	2	exon19			CACCTGCTGAGCT	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.2245G>T	chr12.hg19:g.9244021C>A	ENSP00000323929:p.Ala749Ser	44.0	0.0		161.0	9.0	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	hg19	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	c	0.731	-0.779979	0.02929	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.24350	1.86	5.28	-2.05	0.07321	Alpha-2-macroglobulin (1);	1.090690	0.07002	N	0.823420	T	0.04861	0.0131	N	0.00237	-1.79	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.39761	-0.9598	10	0.02654	T	1	.	7.283	0.26322	0.3883:0.3427:0.0:0.2691	.	749	P01023	A2MG_HUMAN	S	749;764	ENSP00000323929:A749S	ENSP00000323929:A749S	A	-	1	0	A2M	9135288	0.000000	0.05858	0.049000	0.19019	0.004000	0.04260	-1.398000	0.02509	-0.239000	0.09710	-1.679000	0.00737	GCA	.	.		0.488	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		A	9244021	C	A	9244021	3	1	33	1	0	0	0	0	1	0	0	0	4	797	28	3	2251	3	A2M	12	9244021	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10		9244021	124607874	54	3999										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20833113	20833113	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	accagacccctcagtcgcacTcttcagaacagatccaggct	7	16	3	3			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr12:20833113T>A	ENST00000359062.3	+	16	3374	c.3334T>A	c.(3334-3336)Tct>Act	p.S1112T	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	1112					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	TCAGTCGCACTCTTCAGAACA	0.483																																					p.S1112T		Atlas-SNP	.											.	PDE3A	184	.	0			c.T3334A						.						100	98	99					12																	20833113		2203	4300	6503	SO:0001583	missense	5139	exon16			TCGCACTCTTCAG		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.3334T>A	chr12.hg19:g.20833113T>A	ENSP00000351957:p.Ser1112Thr	203.0	0.0		402.0	87.0	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	T	6.231	0.410840	0.11812	.	.	ENSG00000172572	ENST00000359062	T	0.61980	0.06	5.72	-6.01	0.02199	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	2.019320	0.01443	N	0.015176	T	0.43964	0.1271	L	0.28274	0.84	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25433	-1.0132	10	0.14656	T	0.56	.	8.267	0.31819	0.1151:0.4918:0.0:0.3931	.	1112	Q14432	PDE3A_HUMAN	T	1112	ENSP00000351957:S1112T	ENSP00000351957:S1112T	S	+	1	0	PDE3A	20724380	0.000000	0.05858	0.003000	0.11579	0.360000	0.29518	-2.237000	0.01200	-1.136000	0.02892	0.533000	0.62120	TCT	.	.		0.483	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			A	20833113	T	A	20833113	3	1	33	1	0	0	0	0	1	0	0	0	11646	1551	54	4	3396	4	PDE3A	12	20833113	Missense_Mutation	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10	11589092	20833113	113018782	55	4000										
ITGA7	3679	hgsc.bcm.edu	37	chr12	56087102	56087102	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gactggccttggttggaaacCtgtgggaaaaagagagtatg	15	5	0	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr12:56087102C>T	ENST00000555728.1	-	21	2696		c.e21-1		ITGA7_ENST00000257880.7_Splice_Site|ITGA7_ENST00000257879.6_Splice_Site|ITGA7_ENST00000394229.2_Splice_Site|ITGA7_ENST00000394230.2_Splice_Site|ITGA7_ENST00000452168.2_Splice_Site|ITGA7_ENST00000347027.6_Splice_Site|ITGA7_ENST00000553804.1_Splice_Site			Q13683	ITA7_HUMAN	integrin, alpha 7						blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GGTTGGAAACCTGTGGGAAAA	0.453																																					.		Atlas-SNP	.											.	ITGA7	194	.	0			c.2548-1G>A						.						52	53	52					12																	56087102		2203	4300	6503	SO:0001630	splice_region_variant	3679	exon21			GGAAACCTGTGGG		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.2668-1G>A	chr12.hg19:g.56087102C>T		29.0	0.0		101.0	24.0	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Splice_Site	SNP	ENST00000555728.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.50	3.404770	0.62288	.	.	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000353687;ENST00000555728	.	.	.	4.83	4.83	0.62350	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8526	0.78943	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ITGA7	54373369	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	7.253000	0.78320	2.400000	0.81607	0.485000	0.47835	.	.	.		0.453	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	Intron	T	56087102	C	T	56087102	5	4	33	1	0	0	0	0	0	0	1	0	7890	695	24	3	902	3	ITGA7	12	56087102	Splice_Site	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	35253989	56087102	77764793	56	4001										
DGKA	1606	hgsc.bcm.edu	37	chr12	56332338	56332338	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gacagaaatgggatcctggaCagctcagtgagttggggacc	15	8	1	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr12:56332338C>T	ENST00000331886.5	+	6	847	c.393C>T	c.(391-393)gaC>gaT	p.D131D	DGKA_ENST00000549079.2_3'UTR|DGKA_ENST00000394147.1_Silent_p.D131D|DGKA_ENST00000551156.1_Silent_p.D131D	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	131	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	GGATCCTGGACAGCTCAGTGA	0.507																																					p.D131D		Atlas-SNP	.											.	DGKA	70	.	0			c.C393T						.						181	166	171					12																	56332338		2203	4300	6503	SO:0001819	synonymous_variant	1606	exon6			CCTGGACAGCTCA	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"EF-hand domain containing"	2849	protein-coding gene	gene with protein product		125855	"diacylglycerol kinase, alpha (80kD)"	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.393C>T	chr12.hg19:g.56332338C>T		133.0	0.0		413.0	106.0	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Silent	SNP	ENST00000331886.5	hg19	CCDS8896.1																																																																																			.	.		0.507	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1			T	56332338	C	T	56332338	2	4	33	1	0	0	0	0	0	0	0	1	4467	477	17	3		3	DGKA	12	56332338	Silent	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	245236	56332338	77519557	57	4002										
C12orf50	160419	hgsc.bcm.edu	37	chr12	88420359	88420359	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	caaccaagaggctgagtttcCcagaagcatgaaatgctgca	10	10	0	4			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr12:88420359C>A	ENST00000298699.2	-	3	219	c.39G>T	c.(37-39)tgG>tgT	p.W13C	C12orf50_ENST00000546547.1_5'Flank|C12orf50_ENST00000550553.1_Missense_Mutation_p.W13C	NM_152589.1	NP_689802.1	Q8NA57	CL050_HUMAN	chromosome 12 open reading frame 50	13										NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|urinary_tract(2)	34						GCTGAGTTTCCCAGAAGCATG	0.378																																					p.W13C		Atlas-SNP	.											.	C12orf50	70	.	0			c.G39T						.						95	92	93					12																	88420359		2203	4300	6503	SO:0001583	missense	160419	exon3			AGTTTCCCAGAAG	AK093140	CCDS9031.1	12q21.32	2006-02-03				ENSG00000165805			26665	protein-coding gene	gene with protein product						12477932	Standard	NM_152589		Approved	FLJ35821	uc001tam.1	Q8NA57	OTTHUMG00000169869	ENST00000298699.2:c.39G>T	chr12.hg19:g.88420359C>A	ENSP00000298699:p.Trp13Cys	51.0	0.0		177.0	10.0	NM_152589	Q6P674	Missense_Mutation	SNP	ENST00000298699.2	hg19	CCDS9031.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.329690	0.60743	.	.	ENSG00000165805	ENST00000298699;ENST00000550553;ENST00000551944;ENST00000551163	T;T	0.74632	-0.86;-0.76	5.83	4.95	0.65309	.	0.000000	0.64402	D	0.000008	D	0.84768	0.5545	M	0.72353	2.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86499	0.1802	10	0.87932	D	0	.	13.7749	0.63048	0.1541:0.8459:0.0:0.0	.	67;13	G3V208;Q8NA57	.;CL050_HUMAN	C	13;13;67;13	ENSP00000298699:W13C;ENSP00000448344:W13C	ENSP00000298699:W13C	W	-	3	0	C12orf50	86944490	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	3.675000	0.54605	1.481000	0.48307	-0.224000	0.12420	TGG	.	.		0.378	C12orf50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406328.1	NM_152589		A	88420359	C	A	88420359	3	1	33	1	0	0	0	0	1	0	0	0	1697	624	22	3	1249	3	C12orf50	12	88420359	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	32088021	88420359	45431536	58	4003										
CCDC41	51134	hgsc.bcm.edu	37	chr12	94706794	94706794	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ttttcatgaagagattttctCtaaaaagagaaatatgaaca	6	4	2	4			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr12:94706794C>T	ENST00000397809.5	-	15	2257		c.e15-1		CCDC41_ENST00000339839.5_Splice_Site	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN							cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						GAGATTTTCTCTAAAAAGAGA	0.274																																					.		Atlas-SNP	.											.	CCDC41	59	.	0			c.1708-1G>A						.						73	64	67					12																	94706794		1781	4053	5834	SO:0001630	splice_region_variant	51134	exon16			TTTTCTCTAAAAA																												ENST00000397809.5:c.1708-1G>A	chr12.hg19:g.94706794C>T		104.0	0.0		289.0	151.0	NM_016122	A4FVB1|Q08AP1	Splice_Site	SNP	ENST00000397809.5	hg19	CCDS41820.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.109054	0.56398	.	.	ENSG00000173588	ENST00000552632;ENST00000339839;ENST00000397809	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4499	0.90700	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CCDC41	93230925	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	5.743000	0.68655	2.359000	0.80004	0.557000	0.71058	.	.	.		0.274	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3		Intron	T	94706794	C	T	94706794	5	4	33	1	0	0	0	0	0	0	1	0	2815	927	32	3	410	3	CCDC41	12	94706794	Splice_Site	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	6286435	94706794	39145101	59	4004										
NT5DC3	51559	hgsc.bcm.edu	37	chr12	104208729	104208729	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tcttacccggtgttcattgaTgagaaggtcccgtgcagcat	11	10	2	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr12:104208729T>C	ENST00000392876.3	-	2	419	c.379A>G	c.(379-381)Atc>Gtc	p.I127V		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	127						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						TGTTCATTGATGAGAAGGTCC	0.463																																					p.I127V		Atlas-SNP	.											.	NT5DC3	113	.	0			c.A379G						.						164	155	158					12																	104208729		2203	4300	6503	SO:0001583	missense	51559	exon2			CATTGATGAGAAG	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.379A>G	chr12.hg19:g.104208729T>C	ENSP00000376615:p.Ile127Val	158.0	0.0		530.0	288.0	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Missense_Mutation	SNP	ENST00000392876.3	hg19	CCDS41824.1	.	.	.	.	.	.	.	.	.	.	T	9.834	1.189300	0.21954	.	.	ENSG00000111696	ENST00000392876	T	0.16457	2.34	5.87	5.87	0.94306	HAD-like domain (1);	0.043669	0.85682	D	0.000000	T	0.10252	0.0251	N	0.20357	0.565	0.47584	D	0.99946	B	0.10296	0.003	B	0.17722	0.019	T	0.11036	-1.0604	10	0.06757	T	0.87	-43.6022	11.6025	0.51012	0.0:0.069:0.0:0.931	.	127	Q86UY8	NT5D3_HUMAN	V	127	ENSP00000376615:I127V	ENSP00000376615:I127V	I	-	1	0	NT5DC3	102732859	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.166000	0.50785	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.463	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575		C	104208729	T	C	104208729	3	2	33	1	0	0	0	0	1	0	0	0	10701	1464	51	2	1319	2	NT5DC3	12	104208729	Missense_Mutation	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10	9501935	104208729	29643166	60	4005										
UNG	7374	hgsc.bcm.edu	37	chr12	109540669	109540669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	agaacatttataaagagttgTctacagacatagaggatttt	8	4	1	4			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr12:109540669T>C	ENST00000242576.2	+	5	665	c.559T>C	c.(559-561)Tct>Cct	p.S187P	UNG_ENST00000336865.2_Missense_Mutation_p.S178P	NM_080911.2	NP_550433.1			uracil-DNA glycosylase											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						TAAAGAGTTGTCTACAGACAT	0.363								Base excision repair (BER), DNA glycosylases	Immune Deficiency with Hyper-IgM																												p.S187P		Atlas-SNP	.											.	UNG	30	.	0			c.T559C						.						67	70	69					12																	109540669		2203	4300	6503	SO:0001583	missense	7374	exon5	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	GAGTTGTCTACAG	A64377	CCDS9124.1, CCDS9125.1	12q23-q24.1	2014-09-17			ENSG00000076248	ENSG00000076248	3.2.2.27		12572	protein-coding gene	gene with protein product	"uracil-DNA glycosylase 1, uracil-DNA glycosylase 2"	191525		DGU		1923798, 17101234	Standard	NM_080911		Approved	UDG, UNG1, UNG2, HIGM4	uc001tnz.2	P13051	OTTHUMG00000169247	ENST00000242576.2:c.559T>C	chr12.hg19:g.109540669T>C	ENSP00000242576:p.Ser187Pro	59.0	0.0		188.0	49.0	NM_080911		Missense_Mutation	SNP	ENST00000242576.2	hg19	CCDS9124.1	.	.	.	.	.	.	.	.	.	.	T	17.34	3.363887	0.61513	.	.	ENSG00000076248	ENST00000242576;ENST00000336865;ENST00000537518	T;T	0.77098	-1.07;-1.07	5.26	5.26	0.73747	Uracil-DNA glycosylase-like (3);	0.187321	0.46442	D	0.000289	T	0.81616	0.4860	M	0.85197	2.74	0.41372	D	0.987493	P;P	0.49447	0.866;0.924	P;P	0.46479	0.518;0.518	D	0.84016	0.0351	10	0.51188	T	0.08	-20.3511	10.7753	0.46346	0.0:0.0:0.1588:0.8412	.	178;187	E5KTA6;P13051	.;UNG_HUMAN	P	187;178;144	ENSP00000242576:S187P;ENSP00000337398:S178P	ENSP00000242576:S187P	S	+	1	0	UNG	108025052	0.998000	0.40836	1.000000	0.80357	0.916000	0.54674	1.900000	0.39828	2.123000	0.65237	0.528000	0.53228	TCT	.	.		0.363	UNG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403067.1	NM_080911		C	109540669	T	C	109540669	3	2	33	1	0	0	0	0	1	0	0	0	17014	1667	58	2	682	2	UNG	12	109540669	Missense_Mutation	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10	5331940	109540669	24311226	61	4006										
FAM48A	55578	hgsc.bcm.edu	37	chr13	37599542	37599542	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tgaccggacatttggcttcaTtctggactaattcttggtac	9	9	3	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr13:37599542T>C	ENST00000350612.6	-	17	1464	c.1244A>G	c.(1243-1245)aAt>aGt	p.N415S	SUPT20H_ENST00000356185.3_Missense_Mutation_p.N416S|SUPT20H_ENST00000475892.1_Missense_Mutation_p.N415S|SUPT20H_ENST00000360252.4_Missense_Mutation_p.N416S|SUPT20H_ENST00000464744.1_Missense_Mutation_p.N416S|SUPT20H_ENST00000542180.1_Missense_Mutation_p.N379S	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	415					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										TTTGGCTTCATTCTGGACTAA	0.383																																					p.N416S		Atlas-SNP	.											.	.	.	.	0			c.A1247G						.						122	106	111					13																	37599542		2203	4300	6503	SO:0001583	missense	55578	exon17			GCTTCATTCTGGA	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.1244A>G	chr13.hg19:g.37599542T>C	ENSP00000218894:p.Asn415Ser	121.0	0.0		265.0	83.0	NM_017569	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	hg19	CCDS31959.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.17|10.17	1.277928|1.277928	0.23307|0.23307	.|.	.|.	ENSG00000102710|ENSG00000102710	ENST00000469488|ENST00000360252;ENST00000475892;ENST00000350612;ENST00000356185;ENST00000536874;ENST00000464744;ENST00000542180	.|T;T;T;T;T;T	.|0.40476	.|1.03;1.03;1.61;1.03;1.03;1.05	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	.|0.154235	.|0.64402	.|D	.|0.000014	T|T	0.19248|0.19248	0.0462|0.0462	N|N	0.10874|0.10874	0.06|0.06	0.30065|0.30065	N|N	0.810589|0.810589	.|B;B;B;B;B;B	.|0.09022	.|0.0;0.001;0.002;0.001;0.002;0.001	.|B;B;B;B;B;B	.|0.09377	.|0.002;0.002;0.004;0.002;0.004;0.003	T|T	0.22521|0.22521	-1.0214|-1.0214	5|10	.|0.07813	.|T	.|0.8	-12.5689|-12.5689	6.8917|6.8917	0.24232|0.24232	0.1338:0.0725:0.0:0.7937|0.1338:0.0725:0.0:0.7937	.|.	.|379;415;415;416;416;415	.|B4E2D5;B3KNI1;E7ER46;A8K8L1;Q8NEM7-2;Q8NEM7	.|.;.;.;.;.;FA48A_HUMAN	V|S	23|416;415;415;416;415;416;379	.|ENSP00000353388:N416S;ENSP00000417510:N415S;ENSP00000218894:N415S;ENSP00000348512:N416S;ENSP00000419754:N416S;ENSP00000439000:N379S	.|ENSP00000218894:N415S	M|N	-|-	1|2	0|0	FAM48A|FAM48A	36497542|36497542	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.834000|0.834000	0.47266|0.47266	1.791000|1.791000	0.38744|0.38744	2.126000|2.126000	0.65437|0.65437	0.482000|0.482000	0.46254|0.46254	ATG|AAT	.	.		0.383	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		C	37599542	T	C	37599542	3	2	33	1	0	0	0	0	1	0	0	0	5580	1493	52	2	1135	2	FAM48A	13	37599542	Missense_Mutation	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10		37599542	77570336	62	4007										
ADCY4	196883	hgsc.bcm.edu	37	chr14	24787938	24787939	+	Frame_Shift_Ins	INS	-	-	T													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cccaaatgtcatattgcggcINSttctgggccccaataactcc							TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr14:24787938_24787939insT	ENST00000310677.4	-	25	3115_3116	c.3002_3003insA	c.(3001-3003)aagfs	p.K1001fs	ADCY4_ENST00000418030.2_Frame_Shift_Ins_p.K1001fs|ADCY4_ENST00000554068.2_Frame_Shift_Ins_p.K1001fs	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	1001					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		CATATTGCGGCTTCTGGGCCCC	0.53																																					p.K1001fs		Atlas-INDEL	.											.	ADCY4	86	.	0			c.3003_3004insA						.																																			SO:0001589	frameshift_variant	196883	exon25			.	AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"Adenylate cyclases"	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.3003dupA	chr14.hg19:g.24787940_24787940dupT	ENSP00000312126:p.Lys1001fs	81.0	0.0		273.0	17.0	NM_139247	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Frame_Shift_Ins	INS	ENST00000310677.4	hg19	CCDS9627.1																																																																																			.	.		0.53	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			T	24787939	-	T	24787938	7	5	33	1	0	1	1	0	0	0	0	0	296	796	28	0	238	0	ADCY4	14	24787938	Frame_Shift_Ins	INS	-	TCGA-BC-A10T-01A-11D-A12Z-10		24787938	82561602	63	4008										
TDRD9	122402	hgsc.bcm.edu	37	chr14	104472995	104472996	+	Frame_Shift_Ins	INS	-	-	T													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tggttagcggcagctctttcINStttgaagaatttttttgcaa					rs79907994		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr14:104472995_104472996insT	ENST00000409874.4	+	17	1940_1941	c.1892_1893insT	c.(1891-1896)tctttgfs	p.L632fs	TDRD9_ENST00000339063.5_Frame_Shift_Ins_p.L632fs	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	632					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				GCAGCTCTTTCTTTGAAGAATT	0.332																																					p.S631fs		Atlas-INDEL	.											.	TDRD9	175	.	0			c.1892_1893insT						.																																			SO:0001589	frameshift_variant	122402	exon17			.	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1895dupT	chr14.hg19:g.104472998_104472998dupT	ENSP00000387303:p.Leu632fs	177.0	0.0		240.0	15.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Frame_Shift_Ins	INS	ENST00000409874.4	hg19	CCDS9987.2																																																																																			.	.		0.332	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		T	104472996	-	T	104472995	7	5	33	1	0	1	1	0	0	0	0	0	15751	913	32	0	1958	0	TDRD9	14	104472995	Frame_Shift_Ins	INS	-	TCGA-BC-A10T-01A-11D-A12Z-10	79685057	104472995	2876545	64	4009										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48057214	48057214	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tcctttctctttgaacgacaGcgtattactggaagagattg	9	8	1	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr15:48057214G>T	ENST00000316364.5	+	13	1827	c.1388G>T	c.(1387-1389)aGc>aTc	p.S463I	SEMA6D_ENST00000354744.4_Missense_Mutation_p.S463I|SEMA6D_ENST00000558014.1_Missense_Mutation_p.S463I|SEMA6D_ENST00000389425.3_Missense_Mutation_p.S463I|SEMA6D_ENST00000389432.2_Missense_Mutation_p.S463I|SEMA6D_ENST00000389433.2_Missense_Mutation_p.S463I|SEMA6D_ENST00000358066.4_Missense_Mutation_p.S463I|SEMA6D_ENST00000389428.3_Missense_Mutation_p.S463I|SEMA6D_ENST00000537942.1_Missense_Mutation_p.S463I|SEMA6D_ENST00000558816.1_Missense_Mutation_p.S463I|SEMA6D_ENST00000355997.3_Missense_Mutation_p.S463I|SEMA6D_ENST00000536845.2_Missense_Mutation_p.S463I	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	463	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TTGAACGACAGCGTATTACTG	0.448																																					p.S463I		Atlas-SNP	.											.	SEMA6D	322	.	0			c.G1388T						.						132	116	122					15																	48057214		2198	4297	6495	SO:0001583	missense	80031	exon13			ACGACAGCGTATT	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1388G>T	chr15.hg19:g.48057214G>T	ENSP00000324857:p.Ser463Ile	46.0	0.0		109.0	30.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	G	32	5.142822	0.94560	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77	5.79	5.79	0.91817	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.34861	0.0912	M	0.65677	2.01	0.80722	D	1	D;D;D;D;D	0.71674	0.998;0.994;0.998;0.998;0.998	D;D;D;D;D	0.79108	0.925;0.919;0.925;0.992;0.925	T	0.01488	-1.1342	10	0.87932	D	0	.	20.04	0.97581	0.0:0.0:1.0:0.0	.	463;463;463;463;463	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	I	463	ENSP00000442040:S463I;ENSP00000446152:S463I;ENSP00000324857:S463I;ENSP00000374084:S463I;ENSP00000374083:S463I;ENSP00000346786:S463I;ENSP00000350770:S463I;ENSP00000374079:S463I;ENSP00000348276:S463I;ENSP00000374076:S463I	ENSP00000324857:S463I	S	+	2	0	SEMA6D	45844506	1.000000	0.71417	0.995000	0.50966	0.976000	0.68499	7.912000	0.87465	2.733000	0.93635	0.655000	0.94253	AGC	.	.		0.448	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		T	48057214	G	T	48057214	3	4	33	1	0	0	0	0	1	0	0	0	14057	971	34	3	1434	3	SEMA6D	15	48057214	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10		48057214	54474178	65	4010										
MAPK6	5597	hgsc.bcm.edu	37	chr15	52357196	52357196	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cattctgaaacatctgaactAaaacactcagcagacattta	4	10	3	3			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr15:52357196A>G	ENST00000261845.5	+	6	2972	c.2165A>G	c.(2164-2166)tAa>tGa	p.*722*	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	0					cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		CATCTGAACTAAAACACTCAG	0.338																																					p.X722X		Atlas-SNP	.											.	MAPK6	70	.	0			c.A2165G						.						36	38	38					15																	52357196		2135	4102	6237	SO:0001819	synonymous_variant	5597	exon6			TGAACTAAAACAC	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"Mitogen-activated protein kinase cascade / Kinases"	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.2165A>G	chr15.hg19:g.52357196A>G		170.0	0.0		279.0	110.0	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Silent	SNP	ENST00000261845.5	hg19	CCDS10147.1																																																																																			.	.		0.338	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748		G	52357196	A	G	52357196	2	3	33	1	0	0	0	0	0	0	0	1	9290	369	13	2		2	MAPK6	15	52357196	Silent	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10	4299982	52357196	50174196	66	4011										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54435882	54435882	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gcactccaggtgtgtggtggGtaagtaccttcatacctttc	11	10	1	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr15:54435882G>A	ENST00000260323.11	+	3	3071		c.e3+1		UNC13C_ENST00000537900.1_Splice_Site|UNC13C_ENST00000545554.1_Splice_Site	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)						exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TGTGTGGTGGGTAAGTACCTT	0.383																																					.		Atlas-SNP	.											.	UNC13C	674	.	0			c.3071+1G>A						.						150	141	144					15																	54435882		1894	4124	6018	SO:0001630	splice_region_variant	440279	exon3			TGGTGGGTAAGTA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.3071+1G>A	chr15.hg19:g.54435882G>A		72.0	0.0		224.0	67.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Splice_Site	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.634978	0.67130	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5373	0.91015	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UNC13C	52223174	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	6.636000	0.74299	2.636000	0.89361	0.484000	0.47621	.	.	.		0.383	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	Intron	A	54435882	G	A	54435882	5	1	33	1	0	0	0	0	0	0	1	0	17001	1275	44	3	3082	3	UNC13C	15	54435882	Splice_Site	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	2078686	54435882	48095510	67	4012										
SCAPER	49855	hgsc.bcm.edu	37	chr15	77087747	77087747	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ccaactgacacctgtgggagCcagacgaggagctggcactg	14	12	0	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr15:77087747C>T	ENST00000563290.1	-	8	741	c.646G>A	c.(646-648)Gct>Act	p.A216T	SCAPER_ENST00000538941.2_5'UTR|SCAPER_ENST00000324767.7_Missense_Mutation_p.A216T|SCAPER_ENST00000562890.1_5'UTR			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	216						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						CCTGTGGGAGCCAGACGAGGA	0.423																																					p.A216T		Atlas-SNP	.											.	SCAPER	160	.	0			c.G646A						.						68	66	67					15																	77087747		1868	4096	5964	SO:0001583	missense	49855	exon7			TGGGAGCCAGACG	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.646G>A	chr15.hg19:g.77087747C>T	ENSP00000454973:p.Ala216Thr	87.0	0.0		113.0	34.0	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	hg19	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.868777	0.51588	.	.	ENSG00000140386	ENST00000324767;ENST00000303521	T	0.25250	1.81	5.66	5.66	0.87406	.	0.103099	0.64402	D	0.000002	T	0.21921	0.0528	L	0.39898	1.24	0.46279	D	0.998962	B;B	0.18610	0.014;0.029	B;B	0.16289	0.013;0.015	T	0.02860	-1.1101	10	0.28530	T	0.3	.	13.0138	0.58745	0.0:0.9263:0.0:0.0737	.	216;231	Q6NSF1;Q9BY12-2	.;.	T	216;232	ENSP00000326924:A216T	ENSP00000303560:A232T	A	-	1	0	SCAPER	74874802	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.781000	0.47750	2.681000	0.91329	0.585000	0.79938	GCT	.	.		0.423	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		T	77087747	C	T	77087747	3	4	33	1	0	0	0	0	1	0	0	0	13893	739	26	3	3694	3	SCAPER	15	77087747	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	22651865	77087747	25443645	68	4013										
MFGE8	4240	hgsc.bcm.edu	37	chr15	89450543	89450543	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cccaagaaggtcacacgcacAgacgaggcggcgatctgtga	13	12	2	3			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr15:89450543A>C	ENST00000566497.1	-	3	331	c.270T>G	c.(268-270)tcT>tcG	p.S90S	MFGE8_ENST00000559997.1_5'UTR|MFGE8_ENST00000268151.7_Silent_p.S90S|MFGE8_ENST00000542878.1_Silent_p.S46S|MFGE8_ENST00000268150.8_Silent_p.S90S|MFGE8_ENST00000539437.1_Silent_p.S82S			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	90	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					TCACACGCACAGACGAGGCGG	0.617																																					p.S90S		Atlas-SNP	.											.	MFGE8	60	.	0			c.T270G						.						133	92	106					15																	89450543		2200	4299	6499	SO:0001819	synonymous_variant	4240	exon3			ACGCACAGACGAG	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"sperm surface protein hP47"	602281	"sperm associated antigen 10"	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.270T>G	chr15.hg19:g.89450543A>C		93.0	0.0		186.0	56.0	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Silent	SNP	ENST00000566497.1	hg19	CCDS10347.1																																																																																			.	.		0.617	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928		C	89450543	A	C	89450543	2	2	33	1	0	0	0	0	0	0	0	1	9529	175	7	5		5	MFGE8	15	89450543	Silent	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10	12362796	89450543	13080849	69	4014										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101592005	101592005	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cagcctgggcccagcacacgGaccccagtgagaaatcagag	12	14	1	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr15:101592005G>A	ENST00000388948.3	+	24	3888	c.3529G>A	c.(3529-3531)Gac>Aac	p.D1177N	RP11-505E24.2_ENST00000559857.1_RNA|RP11-505E24.3_ENST00000558979.1_RNA|LRRK1_ENST00000284395.5_Missense_Mutation_p.D1174N	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CCAGCACACGGACCCCAGTGA	0.607																																					p.D1177N		Atlas-SNP	.											.	LRRK1	310	.	0			c.G3529A						.						63	74	71					15																	101592005		2142	4237	6379	SO:0001583	missense	79705	exon24			CACACGGACCCCA	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.3529G>A	chr15.hg19:g.101592005G>A	ENSP00000373600:p.Asp1177Asn	74.0	0.0		200.0	12.0	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	G	8.773	0.926329	0.18056	.	.	ENSG00000154237	ENST00000388948;ENST00000284395	T;T	0.72835	-0.67;-0.69	5.41	4.5	0.54988	.	0.538297	0.19751	N	0.106883	T	0.49830	0.1580	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30208	-0.9986	10	0.21014	T	0.42	.	8.7802	0.34787	0.2268:0.0:0.7732:0.0	.	1177	Q38SD2	LRRK1_HUMAN	N	1177;1174	ENSP00000373600:D1177N;ENSP00000284395:D1174N	ENSP00000284395:D1174N	D	+	1	0	LRRK1	99409528	0.059000	0.20769	0.011000	0.14972	0.051000	0.14879	0.870000	0.28010	1.289000	0.44618	0.655000	0.94253	GAC	.	.		0.607	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101592005	G	A	101592005	3	1	33	1	0	0	0	0	1	0	0	0	9041	1174	41	3	3619	3	LRRK1	15	101592005	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	12141462	101592005	939387	70	4015										
MINK1	50488	hgsc.bcm.edu	37	chr17	4796728	4796728	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tcacgtggctcctccctgcaGgactttgtgttgctgaaaga	11	11	1	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr17:4796728G>A	ENST00000355280.6	+	21	2596		c.e21-1		MINK1_ENST00000453408.3_Splice_Site|MINK1_ENST00000347992.7_Splice_Site	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						CCTCCCTGCAGGACTTTGTGT	0.652																																					.		Atlas-SNP	.											.	MINK1	110	.	0			c.2401-1G>A						.						54	60	58					17																	4796728		2006	4168	6174	SO:0001630	splice_region_variant	50488	exon21			CCTGCAGGACTTT	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"misshapen/NIK-related kinase"	609426	"misshapen-like kinase 1 (zebrafish)"			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.2401-1G>A	chr17.hg19:g.4796728G>A		70.0	0.0		125.0	8.0	NM_153827		Splice_Site	SNP	ENST00000355280.6	hg19	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	G	16.18	3.051393	0.55218	.	.	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4054	0.74874	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MINK1	4737504	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	6.225000	0.72271	2.497000	0.84241	0.561000	0.74099	.	.	.		0.652	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	Intron	A	4796728	G	A	4796728	5	1	33	1	0	0	0	0	0	0	1	0	9596	1014	35	3	2249	3	MINK1	17	4796728	Splice_Site	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10		4796728	76398482	71	4016										
PHF23	79142	hgsc.bcm.edu	37	chr17	7139869	7139869	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gcttcatcttctcaagcaagGtagcactgtcgggggcctgc	12	12	3	0	rs564325710		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr17:7139869G>C	ENST00000320316.3	-	4	603	c.377C>G	c.(376-378)aCc>aGc	p.T126S	PHF23_ENST00000576955.1_5'UTR|PHF23_ENST00000571362.1_Missense_Mutation_p.T59S|DVL2_ENST00000005340.5_5'Flank|PHF23_ENST00000570753.1_5'Flank|DVL2_ENST00000575458.1_5'Flank|PHF23_ENST00000454255.2_Missense_Mutation_p.T122S	NM_001284518.1|NM_024297.2	NP_001271447.1|NP_077273.2	Q9BUL5	PHF23_HUMAN	PHD finger protein 23	126							zinc ion binding (GO:0008270)			breast(4)|kidney(2)|large_intestine(6)|lung(3)	15						CTCAAGCAAGGTAGCACTGTC	0.562																																					p.T126S		Atlas-SNP	.											.	PHF23	38	.	0			c.C377G						.						86	95	92					17																	7139869		1964	4149	6113	SO:0001583	missense	79142	exon4			AGCAAGGTAGCAC	AK122791	CCDS42250.1, CCDS67143.1, CCDS67144.1	17p13.1	2014-08-13			ENSG00000040633	ENSG00000040633		"Zinc fingers, PHD-type"	28428	protein-coding gene	gene with protein product		612910					Standard	NM_024297		Approved	MGC2941, FLJ16355	uc002gfa.3	Q9BUL5	OTTHUMG00000177972	ENST00000320316.3:c.377C>G	chr17.hg19:g.7139869G>C	ENSP00000322579:p.Thr126Ser	66.0	0.0		137.0	37.0	NM_024297	A1DZ74|B3KVH8|B4DLK6|D3DTN4|Q8IZK0|Q96HG7|Q9H5X0	Missense_Mutation	SNP	ENST00000320316.3	hg19	CCDS42250.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.973698	0.34848	.	.	ENSG00000040633	ENST00000320316;ENST00000454255;ENST00000043410	T;T	0.37584	1.2;1.19	4.81	3.83	0.44106	.	0.200803	0.42682	N	0.000678	T	0.23766	0.0575	N	0.19112	0.55	0.32888	D	0.511521	B;B	0.29162	0.012;0.235	B;B	0.29077	0.007;0.098	T	0.30119	-0.9989	10	0.41790	T	0.15	-4.8691	11.055	0.47913	0.0:0.1868:0.8132:0.0	.	59;126	B4DLK6;Q9BUL5	.;PHF23_HUMAN	S	126;122;126	ENSP00000322579:T126S;ENSP00000414607:T122S	ENSP00000043410:T126S	T	-	2	0	PHF23	7080593	0.992000	0.36948	0.691000	0.30163	0.812000	0.45895	3.015000	0.49599	1.214000	0.43395	0.563000	0.77884	ACC	.	.		0.562	PHF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440047.1	NM_024297		C	7139869	G	C	7139869	3	2	33	1	0	0	0	0	1	0	0	0	11844	1261	44	4	842	4	PHF23	17	7139869	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	2343141	7139869	74055341	72	4017										
APPBP2	10513	hgsc.bcm.edu	37	chr17	58539193	58539193	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gataaattgcaacagactgaCagatattatctacattgagt	7	6	1	4			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr17:58539193C>A	ENST00000083182.3	-	8	1201	c.914G>T	c.(913-915)tGt>tTt	p.C305F	APPBP2_ENST00000592995.1_5'UTR	NM_001282476.1|NM_006380.2	NP_001269405.1|NP_006371.2	Q92624	APBP2_HUMAN	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	305					intracellular protein transport (GO:0006886)|intracellular transport (GO:0046907)|metabolic process (GO:0008152)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	microtubule motor activity (GO:0003777)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(17)|pancreas(1)|urinary_tract(1)	25	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			AACAGACTGACAGATATTATC	0.338																																					p.C305F		Atlas-SNP	.											.	APPBP2	48	.	0			c.G914T						.						100	109	106					17																	58539193		2203	4299	6502	SO:0001583	missense	10513	exon8			GACTGACAGATAT	AF017782	CCDS32699.1	17q23.2	2012-09-20	2001-11-28		ENSG00000062725	ENSG00000062725			622	protein-coding gene	gene with protein product	"protein interacting with APP tail 1"	605324	"amyloid beta precursor protein (cytoplasmic tail)-binding protein 2"			9843960	Standard	NM_006380		Approved	KIAA0228, Hs.84084, PAT1	uc002iys.1	Q92624		ENST00000083182.3:c.914G>T	chr17.hg19:g.58539193C>A	ENSP00000083182:p.Cys305Phe	162.0	0.0		312.0	124.0	NM_006380	A8K862|O95095|Q8WVC9	Missense_Mutation	SNP	ENST00000083182.3	hg19	CCDS32699.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.270510	0.23221	.	.	ENSG00000062725	ENST00000083182	T	0.75260	-0.92	5.3	5.3	0.74995	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.67116	0.2859	N	0.05078	-0.115	0.80722	D	1	P	0.45531	0.86	P	0.52309	0.695	T	0.67696	-0.5604	10	0.23891	T	0.37	-15.6009	18.9711	0.92715	0.0:1.0:0.0:0.0	.	305	Q92624	APBP2_HUMAN	F	305	ENSP00000083182:C305F	ENSP00000083182:C305F	C	-	2	0	APPBP2	55893975	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.456000	0.80751	2.502000	0.84385	0.460000	0.39030	TGT	.	.		0.338	APPBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449465.1	NM_006380		A	58539193	C	A	58539193	3	1	33	1	0	0	0	0	1	0	0	0	816	478	17	3	867	3	APPBP2	17	58539193	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	51399324	58539193	22656017	73	4018										
BPTF	2186	hgsc.bcm.edu	37	chr17	65889635	65889635	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tactccaccaattcatttgcTttgaataagcaccagcacag	5	12	1	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr17:65889635T>G	ENST00000321892.4	+	8	2644	c.2583T>G	c.(2581-2583)gcT>gcG	p.A861A	BPTF_ENST00000424123.3_Silent_p.A722A|BPTF_ENST00000335221.5_Silent_p.A861A|BPTF_ENST00000306378.6_Silent_p.A735A			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	861	Interaction with MAZ.				anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			ATTCATTTGCTTTGAATAAGC	0.403																																					p.A861A		Atlas-SNP	.											.	BPTF	415	.	0			c.T2583G						.						108	98	101					17																	65889635		2203	4300	6503	SO:0001819	synonymous_variant	2186	exon8			ATTTGCTTTGAAT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.2583T>G	chr17.hg19:g.65889635T>G		454.0	0.0		852.0	331.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	hg19																																																																																				.	.		0.403	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65889635	T	G	65889635	2	3	33	1	0	0	0	0	0	0	0	1	1497	1596	56	5		5	BPTF	17	65889635	Silent	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10	7350442	65889635	15305575	74	4019										
UBE2O	63893	hgsc.bcm.edu	37	chr17	74387574	74387574	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gcaccagctgggtcatggacTgcaccacgcggatcagcgcc	13	15	2	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr17:74387574T>A	ENST00000319380.7	-	18	3393	c.3329A>T	c.(3328-3330)cAg>cTg	p.Q1110L		NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	1110					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						GGTCATGGACTGCACCACGCG	0.592																																					p.Q1110L		Atlas-SNP	.											.	UBE2O	207	.	0			c.A3329T						.						92	88	90					17																	74387574		2203	4300	6503	SO:0001583	missense	63893	exon18			ATGGACTGCACCA	AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.3329A>T	chr17.hg19:g.74387574T>A	ENSP00000323687:p.Gln1110Leu	82.0	0.0		178.0	40.0	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Missense_Mutation	SNP	ENST00000319380.7	hg19	CCDS32742.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.370436	0.82573	.	.	ENSG00000175931	ENST00000319380	T	0.71222	-0.55	4.49	4.49	0.54785	Ubiquitin-conjugating enzyme/RWD-like (1);	0.000000	0.64402	D	0.000001	T	0.79441	0.4446	L	0.57536	1.79	0.58432	D	0.999999	D	0.57899	0.981	D	0.67231	0.95	T	0.80353	-0.1418	10	0.52906	T	0.07	-22.5804	12.5171	0.56038	0.0:0.0:0.0:1.0	.	1110	Q9C0C9	UBE2O_HUMAN	L	1110	ENSP00000323687:Q1110L	ENSP00000323687:Q1110L	Q	-	2	0	UBE2O	71899169	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	7.509000	0.81698	1.889000	0.54706	0.533000	0.62120	CAG	.	.		0.592	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		A	74387574	T	A	74387574	3	1	33	1	0	0	0	0	1	0	0	0	16883	1580	55	4	553	4	UBE2O	17	74387574	Missense_Mutation	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10	8497939	74387574	6807636	75	4020										
RNF213	57674	hgsc.bcm.edu	37	chr17	78328292	78328292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cagtgtctttttaaagaagcAagaagagagccagtttcacc	9	8	2	3			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr17:78328292A>G	ENST00000582970.1	+	36	10921	c.10778A>G	c.(10777-10779)cAa>cGa	p.Q3593R	RNF213_ENST00000508628.2_Missense_Mutation_p.Q3642R|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.Q1666R|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3593					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TTAAAGAAGCAAGAAGAGAGC	0.532																																					p.Q3593R		Atlas-SNP	.											.	RNF213	766	.	0			c.A10778G						.						83	78	79					17																	78328292		2203	4300	6503	SO:0001583	missense	57674	exon36			AGAAGCAAGAAGA	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.10778A>G	chr17.hg19:g.78328292A>G	ENSP00000464087:p.Gln3593Arg	27.0	0.0		90.0	22.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	A	9.693	1.152391	0.21371	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.22134	1.97	4.93	4.93	0.64822	.	0.216684	0.42294	D	0.000726	T	0.26666	0.0652	M	0.72576	2.205	0.25911	N	0.98323	P;B	0.50528	0.936;0.287	B;B	0.42555	0.391;0.078	T	0.23119	-1.0197	10	0.30078	T	0.28	.	14.5981	0.68422	1.0:0.0:0.0:0.0	.	3642;1666	C9JCP4;Q63HN8	.;RN213_HUMAN	R	3593;3642;1666	ENSP00000338218:Q1666R	ENSP00000338218:Q1666R	Q	+	2	0	RNF213	75942887	0.997000	0.39634	0.973000	0.42090	0.236000	0.25371	4.122000	0.57910	1.856000	0.53863	0.528000	0.53228	CAA	.	.		0.532	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78328292	A	G	78328292	3	3	33	1	0	0	0	0	1	0	0	0	13492	130	5	2	11235	2	RNF213	17	78328292	Missense_Mutation	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10	3940718	78328292	2866918	76	4021										
ZNF532	55205	hgsc.bcm.edu	37	chr18	56651549	56651549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	aggagaacaaacccagccacGaggatgaatcccctgatggc	11	12	0	3			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr18:56651549G>A	ENST00000336078.4	+	11	4533	c.3757G>A	c.(3757-3759)Gag>Aag	p.E1253K	ZNF532_ENST00000589288.1_Missense_Mutation_p.E1253K|ZNF532_ENST00000591083.1_Missense_Mutation_p.E1253K|ZNF532_ENST00000588956.1_3'UTR|ZNF532_ENST00000591230.1_Missense_Mutation_p.E1253K|ZNF532_ENST00000591808.1_Missense_Mutation_p.E1253K	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	1253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						ACCCAGCCACGAGGATGAATC	0.493																																					p.E1253K		Atlas-SNP	.											.	ZNF532	108	.	0			c.G3757A						.						35	38	37					18																	56651549		2203	4300	6503	SO:0001583	missense	55205	exon11			AGCCACGAGGATG	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.3757G>A	chr18.hg19:g.56651549G>A	ENSP00000338217:p.Glu1253Lys	125.0	0.0		232.0	84.0	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	hg19	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	g	18.26	3.583653	0.65992	.	.	ENSG00000074657	ENST00000336078	T	0.01548	4.78	5.79	5.79	0.91817	.	0.217202	0.45867	D	0.000329	T	0.02047	0.0064	N	0.22421	0.69	0.42356	D	0.992399	B;B	0.31040	0.082;0.305	B;B	0.18263	0.007;0.021	T	0.64114	-0.6483	10	0.51188	T	0.08	-24.7636	19.7038	0.96066	0.0:0.0:1.0:0.0	.	1253;1253	B3KXW2;Q9HCE3	.;ZN532_HUMAN	K	1253	ENSP00000338217:E1253K	ENSP00000338217:E1253K	E	+	1	0	ZNF532	54802529	1.000000	0.71417	0.955000	0.39395	0.649000	0.38597	4.408000	0.59761	2.762000	0.94881	0.550000	0.68814	GAG	.	.		0.493	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		A	56651549	G	A	56651549	3	1	33	1	0	0	0	0	1	0	0	0	17987	1059	37	1	3787	1	ZNF532	18	56651549	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10		56651549	21425699	77	4022										
CDH7	1005	hgsc.bcm.edu	37	chr18	63511096	63511096	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	acacgctacggatagaagctGcaaataaagatgccgaccct	9	11	0	2			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr18:63511096G>T	ENST00000397968.2	+	7	1456	c.1030G>T	c.(1030-1032)Gca>Tca	p.A344S	CDH7_ENST00000536984.2_Missense_Mutation_p.A344S|CDH7_ENST00000323011.3_Missense_Mutation_p.A344S	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	344	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				GATAGAAGCTGCAAATAAAGA	0.433																																					p.A344S		Atlas-SNP	.											.	CDH7	362	.	0			c.G1030T						.						120	111	114					18																	63511096		2203	4300	6503	SO:0001583	missense	1005	exon7			GAAGCTGCAAATA	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1030G>T	chr18.hg19:g.63511096G>T	ENSP00000381058:p.Ala344Ser	99.0	0.0		249.0	97.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	hg19	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	G	8.737	0.918083	0.17982	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.48836	0.8;0.8;0.8	5.04	4.15	0.48705	Cadherin (5);Cadherin-like (1);	0.312090	0.35291	N	0.003305	T	0.16300	0.0392	N	0.00801	-1.175	0.36919	D	0.891312	B;B	0.06786	0.001;0.0	B;B	0.11329	0.004;0.006	T	0.24621	-1.0155	10	0.05833	T	0.94	.	12.948	0.58384	0.0:0.0:0.7051:0.2949	.	344;344	F5H5X9;Q9ULB5	.;CADH7_HUMAN	S	344	ENSP00000319166:A344S;ENSP00000443030:A344S;ENSP00000381058:A344S	ENSP00000319166:A344S	A	+	1	0	CDH7	61662076	1.000000	0.71417	0.993000	0.49108	0.967000	0.64934	3.093000	0.50217	1.437000	0.47472	0.655000	0.94253	GCA	.	.		0.433	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		T	63511096	G	T	63511096	3	4	33	1	0	0	0	0	1	0	0	0	3117	1319	46	3	1052	3	CDH7	18	63511096	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	6859547	63511096	14566152	78	4023										
ZNF799	90576	hgsc.bcm.edu	37	chr19	12502155	12502155	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gtgagttctttcatgactttTcagtgaactaggacaatcaa	8	7	4	3	rs201335235		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr19:12502155T>G	ENST00000430385.3	-	4	1257	c.1057A>C	c.(1057-1059)Aaa>Caa	p.K353Q	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Missense_Mutation_p.K321Q	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	353					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						TCATGACTTTTCAGTGAACTA	0.413																																					p.K353Q		Atlas-SNP	.											.	ZNF799	111	.	0			c.A1057C						.						160	156	157					19																	12502155		2203	4300	6503	SO:0001583	missense	90576	exon4			GACTTTTCAGTGA	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"Zinc fingers, C2H2-type", "-"	28071	protein-coding gene	gene with protein product			"zinc finger protein 842"	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1057A>C	chr19.hg19:g.12502155T>G	ENSP00000411084:p.Lys353Gln	90.0	0.0		226.0	11.0	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	hg19	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.323810	0.01309	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.04406	3.63;3.63	1.31	-1.61	0.08399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.12527	0.23	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49041	-0.8980	9	0.14252	T	0.57	.	6.8386	0.23951	0.0:0.0:0.2963:0.7037	.	353	Q96GE5	ZN799_HUMAN	Q	321;353	ENSP00000415278:K321Q;ENSP00000411084:K353Q	ENSP00000415278:K321Q	K	-	1	0	ZNF799	12363155	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.687000	0.05156	-0.936000	0.03723	-1.919000	0.00516	AAA	.	.		0.413	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		G	12502155	T	G	12502155	3	3	33	1	0	0	0	0	1	0	0	0	18181	1792	62	5	878	5	ZNF799	19	12502155	Missense_Mutation	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10		12502155	46626828	79	4024										
ELMO2	63916	hgsc.bcm.edu	37	chr20	44997586	44997586	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	atcagggtcatacaggatggAgaaggccaattccaacacct	10	10	2	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr20:44997586A>T	ENST00000290246.6	-	21	2100	c.1906T>A	c.(1906-1908)Tcc>Acc	p.S636T	ELMO2_ENST00000372176.1_Missense_Mutation_p.S548T|ELMO2_ENST00000396391.1_Missense_Mutation_p.S636T|ELMO2_ENST00000439931.2_Missense_Mutation_p.S648T|ELMO2_ENST00000445496.2_Missense_Mutation_p.S453T|ELMO2_ENST00000454865.2_Missense_Mutation_p.S368T|ELMO2_ENST00000352077.2_Missense_Mutation_p.S634T	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	636	PH.				apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				TACAGGATGGAGAAGGCCAAT	0.468																																					p.S636T		Atlas-SNP	.											.	ELMO2	51	.	0			c.T1906A						.						167	156	160					20																	44997586		2203	4300	6503	SO:0001583	missense	63916	exon20			GGATGGAGAAGGC	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"Engulfment and cell motility proteins"	17233	protein-coding gene	gene with protein product		606421	"engulfment and cell motility 2 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.1906T>A	chr20.hg19:g.44997586A>T	ENSP00000290246:p.Ser636Thr	63.0	0.0		149.0	49.0	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Missense_Mutation	SNP	ENST00000290246.6	hg19	CCDS13398.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.843744	0.91197	.	.	ENSG00000062598	ENST00000290246;ENST00000372176;ENST00000452857;ENST00000396391;ENST00000439931;ENST00000445496;ENST00000454865;ENST00000352077	T;T;T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38	5.26	5.26	0.73747	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.75737	0.3890	M	0.86420	2.815	0.80722	D	1	P;D;D	0.89917	0.865;1.0;0.982	B;D;P	0.83275	0.418;0.996;0.835	T	0.80739	-0.1248	10	0.87932	D	0	-22.6458	14.5233	0.67870	1.0:0.0:0.0:0.0	.	648;368;636	B4DRL5;B4DZ20;Q96JJ3	.;.;ELMO2_HUMAN	T	636;548;199;636;648;453;368;634	ENSP00000290246:S636T;ENSP00000361249:S548T;ENSP00000414329:S199T;ENSP00000379673:S636T;ENSP00000396519:S648T;ENSP00000409920:S453T;ENSP00000415641:S368T;ENSP00000326172:S634T	ENSP00000290246:S636T	S	-	1	0	ELMO2	44430993	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.139000	0.94554	2.207000	0.71202	0.533000	0.62120	TCC	.	.		0.468	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086		T	44997586	A	T	44997586	3	4	33	1	0	0	0	0	1	0	0	0	5068	304	11	4	264	4	ELMO2	20	44997586	Missense_Mutation	SNP	A	TCGA-BC-A10T-01A-11D-A12Z-10		44997586	18027934	80	4025										
TH1L	51497	hgsc.bcm.edu	37	chr20	57561177	57561177	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gattctggagaaggagaggaTgatgcggaggttcagcaaga	17	4	2	4			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr20:57561177T>A	ENST00000344018.3	+	2	144	c.117T>A	c.(115-117)gaT>gaA	p.D39E	NELFCD_ENST00000602795.1_Missense_Mutation_p.D48E			Q8IXH7	NELFD_HUMAN	negative elongation factor complex member C/D	39					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	membrane (GO:0016020)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)											AAGGAGAGGATGATGCGGAGG	0.423																																					p.D48E		Atlas-SNP	.											.	.	.	.	0			c.T144A						.						113	118	116					20																	57561177		2203	4300	6503	SO:0001583	missense	51497	exon2			AGAGGATGATGCG	AF161479	CCDS13473.1, CCDS13473.2	20q13	2013-01-31	2013-01-31	2013-01-31	ENSG00000101158	ENSG00000101158			15934	protein-coding gene	gene with protein product	"trihydrophobin 1"	605297	"TH1-like (Drosophila homolog)", "TH1-like (Drosophila)"	TH1L		11030415, 11042152	Standard	NM_198976		Approved	HSPC130, TH1, NELF-C, NELF-D	uc002yag.4	Q8IXH7	OTTHUMG00000032861	ENST00000344018.3:c.117T>A	chr20.hg19:g.57561177T>A	ENSP00000342300:p.Asp39Glu	78.0	0.0		135.0	63.0	NM_198976	B4DE06|Q9BYL2|Q9H405|Q9H888|Q9H8T3|Q9NVX5|Q9P029|Q9UGN1|Q9UGN2|Q9UGN3	Missense_Mutation	SNP	ENST00000344018.3	hg19		.	.	.	.	.	.	.	.	.	.	T	14.05	2.419627	0.42918	.	.	ENSG00000101158	ENST00000344018	.	.	.	5.43	-2.54	0.06307	.	0.206028	0.43416	D	0.000566	T	0.18964	0.0455	N	0.03608	-0.345	0.38649	D	0.951805	P;B;B	0.38280	0.625;0.164;0.071	B;B;B	0.35182	0.197;0.062;0.042	T	0.11108	-1.0601	9	0.15952	T	0.53	-25.7774	12.7703	0.57417	0.0:0.5094:0.0:0.4906	.	39;48;39	B4E2K1;E1P5H4;Q8IXH7	.;.;NELFD_HUMAN	E	39	.	ENSP00000342300:D39E	D	+	3	2	TH1L	56994572	0.820000	0.29190	0.499000	0.27577	0.870000	0.49936	-0.174000	0.09839	-0.839000	0.04212	0.533000	0.62120	GAT	.	.		0.423	NELFCD-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198976		A	57561177	T	A	57561177	3	1	33	1	0	0	0	0	1	0	0	0	15854	1461	51	4	123	4	TH1L	20	57561177	Missense_Mutation	SNP	T	TCGA-BC-A10T-01A-11D-A12Z-10	12563591	57561177	5464343	81	4026										
SRMS	6725	hgsc.bcm.edu	37	chr20	62178615	62178615	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	gcggcggacactcagctcccCgccacaccgcgccgtgaagt	12	18	1	1	rs149894938		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr20:62178615C>T	ENST00000217188.1	-	1	242	c.202G>A	c.(202-204)Ggg>Agg	p.G68R		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	68	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.G68W(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			CTCAGCTCCCCGCCACACCGC	0.697																																					p.G68R		Atlas-SNP	.											.	SRMS	48	.	1	Substitution - Missense(1)	lung(1)	c.G202A						.	C	ARG/GLY	1,4341		0,1,2170	135	138	137		202	4.1	0	20	dbSNP_134	137	0,8464		0,0,4232	no	missense	SRMS	NM_080823.2	125	0,1,6402	TT,TC,CC		0.0,0.023,0.0078	benign	68/489	62178615	1,12805	2171	4232	6403	SO:0001583	missense	6725	exon1			GCTCCCCGCCACA		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"SH2 domain containing"	11298	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 148"	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.202G>A	chr20.hg19:g.62178615C>T	ENSP00000217188:p.Gly68Arg	34.0	0.0		49.0	18.0	NM_080823		Missense_Mutation	SNP	ENST00000217188.1	hg19	CCDS13525.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.466318	0.26335	2.3E-4	0.0	ENSG00000125508	ENST00000217188	T	0.49720	0.77	4.09	4.09	0.47781	Src homology-3 domain (3);	1.198130	0.06232	N	0.688818	T	0.40119	0.1104	L	0.44542	1.39	0.09310	N	1	P	0.39964	0.697	B	0.21917	0.037	T	0.43782	-0.9370	10	0.44086	T	0.13	.	15.9068	0.79436	0.0:1.0:0.0:0.0	.	68	Q9H3Y6	SRMS_HUMAN	R	68	ENSP00000217188:G68R	ENSP00000217188:G68R	G	-	1	0	SRMS	61649059	0.119000	0.22226	0.002000	0.10522	0.006000	0.05464	4.328000	0.59253	1.820000	0.53075	0.491000	0.48974	GGG	.	C|1.000;T|0.000		0.697	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823		T	62178615	C	T	62178615	3	4	33	1	0	0	0	0	1	0	0	0	15167	652	23	1	1296	1	SRMS	20	62178615	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10	4617438	62178615	846905	82	4027										
HUNK	30811	hgsc.bcm.edu	37	chr21	33340695	33340695	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tgtaatgtcacctatcccaaCaggtaatttcgtgcacccag	7	12	1	0			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr21:33340695C>A	ENST00000270112.2	+	6	1368	c.1008C>A	c.(1006-1008)aaC>aaA	p.N336K		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	336					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						CCTATCCCAACAGGTAATTTC	0.532																																					p.N336K		Atlas-SNP	.											.	HUNK	74	.	0			c.C1008A						.						79	76	77					21																	33340695		2203	4300	6503	SO:0001583	missense	30811	exon6			TCCCAACAGGTAA	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"hormonally upregulated Neu-associated kinase"			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.1008C>A	chr21.hg19:g.33340695C>A	ENSP00000270112:p.Asn336Lys	56.0	0.0		90.0	28.0	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	hg19	CCDS13610.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.812700	0.90707	.	.	ENSG00000142149	ENST00000270112	T	0.69175	-0.38	5.37	5.37	0.77165	Protein kinase-like domain (1);	0.114105	0.56097	D	0.000026	T	0.68137	0.2968	L	0.36672	1.1	0.80722	D	1	P	0.51057	0.941	P	0.52823	0.71	T	0.60984	-0.7154	10	0.18276	T	0.48	-29.8074	19.3056	0.94161	0.0:1.0:0.0:0.0	.	336	P57058	HUNK_HUMAN	K	336	ENSP00000270112:N336K	ENSP00000270112:N336K	N	+	3	2	HUNK	32262566	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	6.525000	0.73795	2.783000	0.95769	0.637000	0.83480	AAC	.	.		0.532	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		A	33340695	C	A	33340695	3	1	33	1	0	0	0	0	1	0	0	0	7467	477	17	3	1030	3	HUNK	21	33340695	Missense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10		33340695	14789200	83	4028										
POFUT2	23275	hgsc.bcm.edu	37	chr21	46707671	46707671	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tttaccgtctgcgggaagccGcccccgacagaatatcggcc	11	15	1	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr21:46707671G>A	ENST00000349485.5	-	1	142	c.116C>T	c.(115-117)gCg>gTg	p.A39V	BX322557.10_ENST00000454115.2_RNA|POFUT2_ENST00000331343.7_Missense_Mutation_p.A39V	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	39					fucose metabolic process (GO:0006004)|mesoderm formation (GO:0001707)|protein O-linked fucosylation (GO:0036066)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of gene expression (GO:0010468)|regulation of secretion (GO:0051046)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	20				Colorectal(79;0.243)		GCGGGAAGCCGCCCCCGACAG	0.697																																					p.A39V		Atlas-SNP	.											.	POFUT2	77	.	0			c.C116T						.						8	11	10					21																	46707671		2093	4124	6217	SO:0001583	missense	23275	exon1			GAAGCCGCCCCCG	AJ203079	CCDS13719.1, CCDS13721.1	21q22.3	2013-03-06	2004-06-07	2004-06-09	ENSG00000186866	ENSG00000186866	2.4.1.221	"Fucosyltransferases"	14683	protein-coding gene	gene with protein product	"peptide-O-fucosyltransferase", "GDP-fucose protein O-fucosyltransferase 2"	610249	"chromosome 21 open reading frame 80"	C21orf80			Standard	NM_133635		Approved	KIAA0958, FUT13	uc002zhc.3	Q9Y2G5	OTTHUMG00000084874	ENST00000349485.5:c.116C>T	chr21.hg19:g.46707671G>A	ENSP00000339613:p.Ala39Val	30.0	0.0		54.0	21.0	NM_015227	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Missense_Mutation	SNP	ENST00000349485.5	hg19	CCDS13719.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.186937	0.38609	.	.	ENSG00000186866	ENST00000331343;ENST00000349485	.	.	.	2.89	1.98	0.26296	.	0.461733	0.19783	N	0.106164	T	0.23649	0.0572	N	0.19112	0.55	0.36415	D	0.863997	P;B;B	0.35011	0.48;0.006;0.002	B;B;B	0.20577	0.03;0.005;0.001	T	0.17684	-1.0361	9	0.25106	T	0.35	-12.3452	7.8696	0.29558	0.0:0.2566:0.7434:0.0	.	39;39;39	B4DH78;Q9Y2G5-1;Q9Y2G5	.;.;OFUT2_HUMAN	V	39	.	ENSP00000329682:A39V	A	-	2	0	POFUT2	45532099	0.000000	0.05858	0.987000	0.45799	0.868000	0.49771	-0.448000	0.06820	0.766000	0.33244	0.650000	0.86243	GCG	.	.		0.697	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227		A	46707671	G	A	46707671	3	1	33	1	0	0	0	0	1	0	0	0	12193	1087	38	1	1348	1	POFUT2	21	46707671	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	13366976	46707671	1422224	84	4029										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32188763	32188763	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	aaataaaccgagcctcaattCgacaggatcacaaggggaga	10	9	2	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr22:32188763C>T	ENST00000382112.3	+	11	797	c.727C>T	c.(727-729)Cga>Tga	p.R243*	DEPDC5_ENST00000536766.1_Nonsense_Mutation_p.R215*|DEPDC5_ENST00000400249.2_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000400246.1_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000266091.3_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000382111.2_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000535622.1_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000400242.3_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000382105.2_Nonsense_Mutation_p.R243*|DEPDC5_ENST00000400248.2_Nonsense_Mutation_p.R243*	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	243					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)	p.R243*(1)		breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						AGCCTCAATTCGACAGGATCA	0.353																																					p.R243X		Atlas-SNP	.											DEPDC5_ENST00000535622,colon,carcinoma,0,3	DEPDC5	266	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C727T						.						130	122	124					22																	32188763		1804	4082	5886	SO:0001587	stop_gained	9681	exon12			TCAATTCGACAGG	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.727C>T	chr22.hg19:g.32188763C>T	ENSP00000371546:p.Arg243*	81.0	0.0		125.0	64.0	NM_001242897	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Nonsense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	-	38	6.701398	0.97772	.	.	ENSG00000100150	ENST00000535622;ENST00000536766;ENST00000400242;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	.	.	.	5.29	1.87	0.25490	.	0.117813	0.53938	D	0.000050	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	.	13.4713	0.61283	0.6194:0.3806:0.0:0.0	.	.	.	.	X	243;215;243;243;243;243;243;243;243;243;243	.	ENSP00000266091:R243X	R	+	1	2	DEPDC5	30518763	1.000000	0.71417	0.999000	0.59377	0.913000	0.54294	1.746000	0.38288	0.154000	0.19237	0.567000	0.79289	CGA	.	.		0.353	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		T	32188763	C	T	32188763	4	4	33	1	0	0	0	0	0	1	0	0	4444	876	31	1	769	1	DEPDC5	22	32188763	Nonsense_Mutation	SNP	C	TCGA-BC-A10T-01A-11D-A12Z-10		32188763	19115803	85	4030										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46931320	46931320	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	ccgcctgaatgtgcaccacgGggtagcccaggggcacattc	13	14	0	1			TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chr22:46931320G>T	ENST00000262738.3	-	1	1747	c.1748C>A	c.(1747-1749)cCc>cAc	p.P583H	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Missense_Mutation_p.P583H	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	583	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GTGCACCACGGGGTAGCCCAG	0.642																																					p.P583H		Atlas-SNP	.											.	CELSR1	242	.	0			c.C1748A						.						40	40	40					22																	46931320		2203	4300	6503	SO:0001583	missense	9620	exon1			ACCACGGGGTAGC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.1748C>A	chr22.hg19:g.46931320G>T	ENSP00000262738:p.Pro583His	35.0	0.0		21.0	14.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.884833	0.51908	.	.	ENSG00000075275	ENST00000262738;ENST00000395964	T;T	0.52526	0.66;0.66	4.92	4.92	0.64577	Cadherin (3);Cadherin-like (1);	0.088018	0.47455	U	0.000228	T	0.34658	0.0905	N	0.16790	0.44	0.29125	N	0.879973	B	0.30146	0.27	B	0.26202	0.067	T	0.36625	-0.9740	10	0.52906	T	0.07	.	17.747	0.88423	0.0:0.0:1.0:0.0	.	583	Q9NYQ6	CELR1_HUMAN	H	583	ENSP00000262738:P583H;ENSP00000379293:P583H	ENSP00000262738:P583H	P	-	2	0	CELSR1	45309984	1.000000	0.71417	0.970000	0.41538	0.362000	0.29581	7.492000	0.81482	2.281000	0.76405	0.462000	0.41574	CCC	.	.		0.642	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46931320	G	T	46931320	3	4	33	1	0	0	0	0	1	0	0	0	3223	1232	43	3	7436	3	CELSR1	22	46931320	Missense_Mutation	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	14742557	46931320	4373246	86	4031										
AWAT1	158833	hgsc.bcm.edu	37	chrX	69459750	69459751	+	Frame_Shift_Ins	INS	-	-	C													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tctgtcaaggctccactgggINSctcctgccatactccaggcc							TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chrX:69459750_69459751insC	ENST00000374521.3	+	6	839_840	c.798_799insC	c.(799-801)ctcfs	p.L267fs		NM_001013579.2	NP_001013597.1	Q58HT5	AWAT1_HUMAN	acyl-CoA wax alcohol acyltransferase 1	267					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(3)|ovary(4)|skin(1)	15						GCTCCACTGGGCTCCTGCCATA	0.545																																					p.G266fs		Atlas-INDEL	.											.	AWAT1	74	.	0			c.798_799insC						.																																			SO:0001589	frameshift_variant	158833	exon6			.	BC039181	CCDS35321.1	Xq13.1	2010-01-25	2009-02-23	2009-02-23	ENSG00000204195	ENSG00000204195			23252	protein-coding gene	gene with protein product		300924	"diacylglycerol O-acyltransferase 2-like 3"	DGAT2L3		14970677, 15671038	Standard	NM_001013579		Approved		uc004dxy.3	Q58HT5	OTTHUMG00000021773	ENST00000374521.3:c.799dupC	chrX.hg19:g.69459751_69459751dupC	ENSP00000363645:p.Leu267fs	64.0	0.0		149.0	11.0	NM_001013579	Q5JT21|Q6IEE4	Frame_Shift_Ins	INS	ENST00000374521.3	hg19	CCDS35321.1																																																																																			.	.		0.545	AWAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057066.3	NM_001013579		C	69459751	-	C	69459750	7	5	33	1	0	1	1	0	0	0	0	0	1234	1190	42	0	820	0	AWAT1	23	69459750	Frame_Shift_Ins	INS	-	TCGA-BC-A10T-01A-11D-A12Z-10		69459750	85810810	87	4032										
ARMCX6	54470	hgsc.bcm.edu	37	chrX	100871412	100871412	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	cccatcctcagtccagggccGagccatagtttcaaaatcaa	7	14	3	0	rs138992392		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chrX:100871412G>T	ENST00000361910.4	-	3	543	c.199C>A	c.(199-201)Cgg>Agg	p.R67R	ARMCX6_ENST00000497931.1_Intron|ARMCX6_ENST00000538627.1_Silent_p.R67R|ARMCX6_ENST00000539247.1_Silent_p.R67R	NM_019007.3	NP_061880.2	Q7L4S7	ARMX6_HUMAN	armadillo repeat containing, X-linked 6	67						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|liver(2)|lung(3)	9						GTCCAGGGCCGAGCCATAGTT	0.592																																					p.R67R		Atlas-SNP	.											.	ARMCX6	21	.	0			c.C199A						.						76	70	72					X																	100871412		2203	4300	6503	SO:0001819	synonymous_variant	54470	exon4			AGGGCCGAGCCAT	BC007677	CCDS14488.1	Xq21.33-q22.3	2014-03-21			ENSG00000198960	ENSG00000198960		"Armadillo repeat containing"	26094	protein-coding gene	gene with protein product						16221301, 22569362	Standard	NM_001184768		Approved	FLJ20811, GASP10	uc004ehy.3	Q7L4S7	OTTHUMG00000022034	ENST00000361910.4:c.199C>A	chrX.hg19:g.100871412G>T		61.0	0.0		124.0	102.0	NM_001184768	Q9NWJ3	Silent	SNP	ENST00000361910.4	hg19	CCDS14488.1																																																																																			.	G|1.000;A|0.000		0.592	ARMCX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057562.1	NM_019007		T	100871412	G	T	100871412	2	4	33	1	0	0	0	0	0	0	0	1	963	1057	37	1		1	ARMCX6	23	100871412	Silent	SNP	G	TCGA-BC-A10T-01A-11D-A12Z-10	31411662	100871412	54399148	88	4033										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140993903	140993905	+	In_Frame_Del	DEL	GCC	GCC	-													0.0674157303370786	6	1	1.26870474658085	3.48893805309735	1.12546388809592	0.131221719457014	0.709357990687916	0	tcctctccagattcctgtgaGcccctcctcctcctccactt					rs140031379|rs176040	byFrequency	TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	GCC	GCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	g.chrX:140993903_140993905delGCC	ENST00000285879.4	+	4	999_1001	c.713_715delGCC	c.(712-717)agcccc>acc	p.238_239SP>T	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	238				P -> S (in Ref. 1 and 2). {ECO:0000305}.				p.P239S(2)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					ATTCCTGTGAGCCCCTCCTCCTC	0.473										HNSCC(15;0.026)																											p.238_238del		Atlas-INDEL	.											.	MAGEC1	317	.	2	Substitution - Missense(2)	stomach(2)	c.712_714del						.																																			SO:0001651	inframe_deletion	9947	exon4			.	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.713_715delGCC	chrX.hg19:g.140993903_140993905delGCC	ENSP00000285879:p.Ser238_Pro239delinsThr	110.0	0.0		236.0	24.0	NM_005462	A0PK03|O75451|Q8TCV4	In_Frame_Del	DEL	ENST00000285879.4	hg19	CCDS35417.1																																																																																			.	.		0.473	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		-	140993905	GCC	-	140993903	7	5	33	1	0	1	0	1	0	0	0	0	9189	971	34	0	719	0	MAGEC1	23	140993903	In_Frame_Del	DEL	GCC	TCGA-BC-A10T-01A-11D-A12Z-10	40122491	140993903	14276657	89	4034										
ZNF436	80818	hgsc.bcm.edu	37	chr1	23689653	23689653	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ctttcagatgtagtcccaaaTtgtacatcttcactaatctc	4	11	4	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:23689653T>C	ENST00000314011.4	-	4	358	c.222A>G	c.(220-222)caA>caG	p.Q74Q	ZNF436_ENST00000374608.3_Silent_p.Q74Q	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	74	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		TAGTCCCAAATTGTACATCTT	0.393																																					p.Q74Q		Atlas-SNP	.											.	ZNF436	49	.	0			c.A222G						.						123	124	124					1																	23689653		2203	4300	6503	SO:0001819	synonymous_variant	80818	exon4			CCCAAATTGTACA	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"Zinc fingers, C2H2-type", "-"	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.222A>G	chr1.hg19:g.23689653T>C		120.0	0.0		279.0	121.0	NM_001077195	Q658I9	Silent	SNP	ENST00000314011.4	hg19	CCDS233.1																																																																																			.	.		0.393	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		C	23689653	T	C	23689653	2	2	34	1	0	0	0	0	0	0	0	1	17924	1490	52	2		2	ZNF436	1	23689653	Silent	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10		23689653	225560968	1	4035										
SFPQ	6421	hgsc.bcm.edu	37	chr1	35654866	35654867	+	Frame_Shift_Ins	INS	-	-	T													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tgtcttttgcatctttcatgINStttttttcaacttgttccct							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:35654866_35654867insT	ENST00000357214.5	-	5	1630_1631	c.1532_1533insA	c.(1531-1533)aacfs	p.N511fs		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	511					alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)		SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				CATCTTTCATGTTTTTTTCAAC	0.406			T	TFE3	papillary renal cell																																p.N511fs		Atlas-Indel,Pindel	.		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ	51	.	0			c.1533_1534insA						.																																			SO:0001589	frameshift_variant	6421	exon5			.	X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"RNA binding motif (RRM) containing"	10774	protein-coding gene	gene with protein product	"polypyrimidine tract binding protein associated", "protein phosphatase 1, regulatory subunit 140"	605199	"splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.1533dupA	chr1.hg19:g.35654873_35654873dupT	ENSP00000349748:p.Asn511fs	262.0	0.0		711.0	262.0	NM_005066	P30808|Q5SZ71	Frame_Shift_Ins	INS	ENST00000357214.5	hg19	CCDS388.1																																																																																			.	.		0.406	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		T	35654867	-	T	35654866	7	5	34	1	0	1	1	0	0	0	0	0	14175	1368	48	0	614	0	SFPQ	1	35654866	Frame_Shift_Ins	INS	-	TCGA-BC-A10U-01A-11D-A12Z-10	11965213	35654866	213595755	2	4036										
SLC1A7	6512	hgsc.bcm.edu	37	chr1	53555552	53555552	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agcacgatgaccatggtgacGaggccggcctgggggatgcc	17	11	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:53555552G>C	ENST00000371494.4	-	9	1408	c.1281C>G	c.(1279-1281)ctC>ctG	p.L427L	SLC1A7_ENST00000488036.1_5'UTR	NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7	427					dicarboxylic acid transport (GO:0006835)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.L427L(1)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Colorectal(1306;0.234)		CCATGGTGACGAGGCCGGCCT	0.627																																					p.L427L	NSCLC(128;80 1811 21245 38490 51715)	Atlas-SNP	.											SLC1A7,NS,carcinoma,0,1	SLC1A7	65	.	1	Substitution - coding silent(1)	lung(1)	c.C1281G						.						81	72	75					1																	53555552		2203	4300	6503	SO:0001819	synonymous_variant	6512	exon9			GGTGACGAGGCCG	U76362	CCDS574.1, CCDS72796.1, CCDS72797.1, CCDS72798.1	1p32.3	2013-05-22			ENSG00000162383	ENSG00000162383		"Solute carriers"	10945	protein-coding gene	gene with protein product		604471				9108121	Standard	NM_001287597		Approved	EAAT5	uc001cuy.3	O00341	OTTHUMG00000008937	ENST00000371494.4:c.1281C>G	chr1.hg19:g.53555552G>C		90.0	0.0		173.0	76.0	NM_006671	Q5VVZ0|Q969Z8|Q9BW45	Silent	SNP	ENST00000371494.4	hg19	CCDS574.1																																																																																			.	.		0.627	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1	NM_006671		C	53555552	G	C	53555552	2	2	34	1	0	0	0	0	0	0	0	1	14452	1045	37	4		4	SLC1A7	1	53555552	Silent	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	17900686	53555552	195695069	3	4037										
KANK4	163782	hgsc.bcm.edu	37	chr1	62718788	62718789	+	Frame_Shift_Ins	INS	-	-	C													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tcttaagagcttccagacaaINScagccatgtcttcattggtc							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:62718788_62718789insC	ENST00000371153.4	-	8	3010_3011	c.2632_2633insG	c.(2632-2634)gttfs	p.V878fs	KANK4_ENST00000317477.4_Frame_Shift_Ins_p.V16fs|KANK4_ENST00000371150.1_Frame_Shift_Ins_p.V234fs|KANK4_ENST00000354381.3_Frame_Shift_Ins_p.V250fs	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	878						cytoplasm (GO:0005737)		p.V878I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						CTTCCAGACAACAGCCATGTCT	0.5																																					p.V878fs		Atlas-INDEL	.											.	KANK4	135	.	1	Substitution - Missense(1)	lung(1)	c.2633_2634insG						.																																			SO:0001589	frameshift_variant	163782	exon8			.	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	27263	protein-coding gene	gene with protein product		614612	"ankyrin repeat domain 38"	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.2633dupG	chr1.hg19:g.62718789_62718789dupC	ENSP00000360195:p.Val878fs	55.0	0.0		154.0	10.0	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Frame_Shift_Ins	INS	ENST00000371153.4	hg19	CCDS620.1																																																																																			.	.		0.5	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		C	62718789	-	C	62718788	7	5	34	1	0	1	1	0	0	0	0	0	7988	43	2	0	366	0	KANK4	1	62718788	Frame_Shift_Ins	INS	-	TCGA-BC-A10U-01A-11D-A12Z-10	9163236	62718788	186531833	4	4038										
NTNG1	22854	hgsc.bcm.edu	37	chr1	107937923	107937923	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agtccaggctcctatctcccCatccccaaaggcactgcaaa	6	17	1	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:107937923C>T	ENST00000370068.1	+	4	1881	c.1035C>T	c.(1033-1035)ccC>ccT	p.P345P	NTNG1_ENST00000370071.2_Silent_p.P345P|NTNG1_ENST00000370072.3_Silent_p.P345P|NTNG1_ENST00000370061.3_Silent_p.P345P|NTNG1_ENST00000370065.1_Silent_p.P345P|NTNG1_ENST00000370074.4_Silent_p.P345P|NTNG1_ENST00000370067.1_Silent_p.P345P|NTNG1_ENST00000370073.2_Silent_p.P345P|NTNG1_ENST00000370070.2_Silent_p.P345P|NTNG1_ENST00000542803.1_Silent_p.P345P|NTNG1_ENST00000370066.1_Silent_p.P345P			Q9Y2I2	NTNG1_HUMAN	netrin G1	345	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		CCTATCTCCCCATCCCCAAAG	0.458																																					p.P345P		Atlas-SNP	.											.	NTNG1	274	.	0			c.C1035T						.						156	155	155					1																	107937923		2203	4300	6503	SO:0001819	synonymous_variant	22854	exon4			TCTCCCCATCCCC	AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"Netrins"	23319	protein-coding gene	gene with protein product	"netrin G1f", "Netrin-G1"	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.1035C>T	chr1.hg19:g.107937923C>T		48.0	0.0		125.0	54.0	NM_014917	Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Silent	SNP	ENST00000370068.1	hg19	CCDS44180.1																																																																																			.	.		0.458	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917		T	107937923	C	T	107937923	2	4	34	1	0	0	0	0	0	0	0	1	10713	581	21	3		3	NTNG1	1	107937923	Silent	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	45219135	107937923	141312698	5	4039										
FCRL2	79368	hgsc.bcm.edu	37	chr1	157739786	157739786	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agctccggagagctgctccaGcctgaccccaggacctggtt	12	15	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:157739786G>A	ENST00000361516.3	-	4	513	c.465C>T	c.(463-465)ggC>ggT	p.G155G	FCRL2_ENST00000469986.1_5'Flank|FCRL2_ENST00000368181.4_Intron|FCRL2_ENST00000392274.3_Silent_p.G155G	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	155	Ig-like C2-type 2.				cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGCTGCTCCAGCCTGACCCCA	0.542																																					p.G155G		Atlas-SNP	.											.	FCRL2	104	.	0			c.C465T						.						56	62	60					1																	157739786		2203	4300	6503	SO:0001819	synonymous_variant	79368	exon4			GCTCCAGCCTGAC	AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14875	protein-coding gene	gene with protein product		606509	"SH2 domain-containing phosphatase anchor protein 1"	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.465C>T	chr1.hg19:g.157739786G>A		94.0	0.0		393.0	223.0	NM_030764	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Silent	SNP	ENST00000361516.3	hg19	CCDS1168.1																																																																																			.	.		0.542	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764		A	157739786	G	A	157739786	2	1	34	1	0	0	0	0	0	0	0	1	5803	958	34	3		3	FCRL2	1	157739786	Silent	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	49801863	157739786	91510835	6	4040										
DCAF6	55827	hgsc.bcm.edu	37	chr1	168014320	168014320	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	atgaaaataacaccaatcctGagcctcagttccaaacagaa	5	11	1	3			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:168014320G>C	ENST00000312263.6	+	14	2086	c.1882G>C	c.(1882-1884)Gag>Cag	p.E628Q	DCAF6_ENST00000367843.3_Missense_Mutation_p.E648Q|DCAF6_ENST00000367840.3_Missense_Mutation_p.E705Q|DCAF6_ENST00000432587.2_Missense_Mutation_p.E674Q	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	628					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						CACCAATCCTGAGCCTCAGTT	0.473																																					p.E705Q		Atlas-SNP	.											.	DCAF6	99	.	0			c.G2113C						.						66	67	67					1																	168014320		2203	4300	6503	SO:0001583	missense	55827	exon16			AATCCTGAGCCTC	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.1882G>C	chr1.hg19:g.168014320G>C	ENSP00000311949:p.Glu628Gln	134.0	0.0		389.0	225.0	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	hg19	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	G	13.03	2.116445	0.37339	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.31	4.38	0.52667	WD40 repeat-like-containing domain (1);	0.171751	0.51477	N	0.000084	T	0.31199	0.0789	L	0.50333	1.59	0.31299	N	0.6884669999999999	B;B;P;D	0.62365	0.321;0.385;0.568;0.991	B;B;B;P	0.59703	0.084;0.387;0.216;0.862	T	0.07751	-1.0756	9	0.33141	T	0.24	.	14.1999	0.65696	0.0:0.1495:0.8505:0.0	.	674;705;628;648	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	Q	648;674;628;705	ENSP00000356817:E648Q;ENSP00000396238:E674Q;ENSP00000311949:E628Q;ENSP00000356814:E705Q	ENSP00000311949:E628Q	E	+	1	0	DCAF6	166280944	0.995000	0.38212	0.099000	0.21106	0.794000	0.44872	3.386000	0.52492	1.207000	0.43291	0.467000	0.42956	GAG	.	.		0.473	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		C	168014320	G	C	168014320	3	2	34	1	0	0	0	0	1	0	0	0	4276	1291	45	4	2000	4	DCAF6	1	168014320	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	10274534	168014320	81236301	7	4041										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183093943	183093943	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ctataacactgctggcttctAttgtgaccggtgcaaagacg	10	10	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:183093943A>G	ENST00000258341.4	+	14	2836	c.2579A>G	c.(2578-2580)tAt>tGt	p.Y860C		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	860	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GCTGGCTTCTATTGTGACCGG	0.478																																					p.Y860C		Atlas-SNP	.											.	LAMC1	176	.	0			c.A2579G						.						90	80	83					1																	183093943		2203	4300	6503	SO:0001583	missense	3915	exon14			GCTTCTATTGTGA	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.2579A>G	chr1.hg19:g.183093943A>G	ENSP00000258341:p.Tyr860Cys	77.0	0.0		221.0	48.0	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	A	18.52	3.642132	0.67244	.	.	ENSG00000135862	ENST00000258341	T	0.61392	0.11	5.51	5.51	0.81932	EGF-like, laminin (4);	0.054008	0.85682	D	0.000000	T	0.76572	0.4006	M	0.80332	2.49	0.58432	D	0.999994	D	0.89917	1.0	D	0.71414	0.973	T	0.80082	-0.1531	10	0.66056	D	0.02	.	15.2812	0.73787	1.0:0.0:0.0:0.0	.	860	P11047	LAMC1_HUMAN	C	860	ENSP00000258341:Y860C	ENSP00000258341:Y860C	Y	+	2	0	LAMC1	181360566	1.000000	0.71417	0.980000	0.43619	0.978000	0.69477	4.890000	0.63178	2.091000	0.63221	0.528000	0.53228	TAT	.	.		0.478	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		G	183093943	A	G	183093943	3	3	34	1	0	0	0	0	1	0	0	0	8623	449	16	2	2633	2	LAMC1	1	183093943	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	15079623	183093943	66156678	8	4042										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228529240	228529240	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gcaagtacctgctgcaggcaCggacagccattatcaagagc	11	12	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:228529240C>T	ENST00000422127.1	+	74	18003	c.17959C>T	c.(17959-17961)Cgg>Tgg	p.R5987W	OBSCN_ENST00000366709.4_Missense_Mutation_p.R3106W|OBSCN_ENST00000570156.2_Missense_Mutation_p.R6944W|OBSCN_ENST00000366707.4_Missense_Mutation_p.R3621W|OBSCN_ENST00000284548.11_Missense_Mutation_p.R5987W	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5987	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTGCAGGCACGGACAGCCAT	0.647																																					p.R6944W		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C20830T						.						45	57	53					1																	228529240		2177	4267	6444	SO:0001583	missense	84033	exon85			CAGGCACGGACAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.17959C>T	chr1.hg19:g.228529240C>T	ENSP00000409493:p.Arg5987Trp	33.0	0.0		84.0	25.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.1|21.1	4.093970|4.093970	0.76870|0.76870	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709|ENST00000441106	T;T;T;T|.	0.12465|.	2.68;2.68;2.68;2.68|.	5.48|5.48	4.57|4.57	0.56435|0.56435	Pleckstrin homology-type (1);Pleckstrin homology domain (2);|.	0.081715|.	0.50627|.	D|.	0.000112|.	T|T	0.70692|0.70692	0.3253|0.3253	M|M	0.76002|0.76002	2.32|2.32	0.48696|0.48696	D|D	0.999697|0.999697	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.75020|.	0.967;0.985|.	T|T	0.70824|0.70824	-0.4767|-0.4767	10|5	0.87932|.	D|.	0|.	.|.	9.9133|9.9133	0.41419|0.41419	0.1384:0.7894:0.0:0.0722|0.1384:0.7894:0.0:0.0722	.|.	5987;5987|.	Q5VST9;Q5VST9-3|.	OBSCN_HUMAN;.|.	W|M	5987;5987;3621;3106|603	ENSP00000284548:R5987W;ENSP00000409493:R5987W;ENSP00000355668:R3621W;ENSP00000355670:R3106W|.	ENSP00000284548:R5987W|.	R|T	+|+	1|2	2|0	OBSCN|OBSCN	226595863|226595863	0.998000|0.998000	0.40836|0.40836	0.200000|0.200000	0.23457|0.23457	0.471000|0.471000	0.32888|0.32888	3.764000|3.764000	0.55264|0.55264	1.326000|1.326000	0.45319|0.45319	0.563000|0.563000	0.77884|0.77884	CGG|ACG	.	.		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228529240	C	T	228529240	3	4	34	1	0	0	0	0	1	0	0	0	10821	527	19	1	18249	1	OBSCN	1	228529240	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	45435297	228529240	20721381	9	4043										
OR2L13	284521	hgsc.bcm.edu	37	chr1	248262994	248262994	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	aagcttcttcttcctgaccaTggcgtgttctgaaggcttac	9	11	3	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:248262994T>C	ENST00000358120.2	+	2	462	c.317T>C	c.(316-318)aTg>aCg	p.M106T	OR2L13_ENST00000366478.2_Missense_Mutation_p.M106T			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	106						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			TTCCTGACCATGGCGTGTTCT	0.517																																					p.M106T		Atlas-SNP	.											.	OR2L13	261	.	0			c.T317C						.						253	230	238					1																	248262994		2203	4300	6503	SO:0001583	missense	284521	exon3			TGACCATGGCGTG	BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"GPCR / Class A : Olfactory receptors"	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.317T>C	chr1.hg19:g.248262994T>C	ENSP00000350836:p.Met106Thr	91.0	0.0		312.0	169.0	NM_175911	Q5VUR5	Missense_Mutation	SNP	ENST00000358120.2	hg19	CCDS1637.1	.	.	.	.	.	.	.	.	.	.	T	3.812	-0.039461	0.07497	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	T;T	0.00342	8.03;8.03	3.74	3.74	0.42951	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000035	T	0.00178	0.0005	N	0.16066	0.365	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.43360	-0.9396	10	0.87932	D	0	.	7.5649	0.27872	0.0:0.0998:0.0:0.9002	.	106	Q8N349	OR2LD_HUMAN	T	106	ENSP00000355434:M106T;ENSP00000350836:M106T	ENSP00000350836:M106T	M	+	2	0	OR2L13	246329617	0.657000	0.27393	0.243000	0.24186	0.134000	0.20937	3.389000	0.52516	1.688000	0.51068	0.528000	0.53228	ATG	.	.		0.517	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911		C	248262994	T	C	248262994	3	2	34	1	0	0	0	0	1	0	0	0	11015	1464	51	2	319	2	OR2L13	1	248262994	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	19733754	248262994	987627	10	4044										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525893	248525893	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggggctctgaagaaaatgttAacagtggaacctgcctttca	11	8	2	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:248525893A>G	ENST00000366475.1	+	1	1011	c.1011A>G	c.(1009-1011)ttA>ttG	p.L337L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	337						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGAAAATGTTAACAGTGGAAC	0.393																																					p.L337L		Atlas-SNP	.											.	OR2T4	126	.	0			c.A1011G						.						103	108	107					1																	248525893		2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			AATGTTAACAGTG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.1011A>G	chr1.hg19:g.248525893A>G		257.0	0.0		689.0	225.0	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	hg19	CCDS31113.1																																																																																			.	.		0.393	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		G	248525893	A	G	248525893	2	3	34	1	0	0	0	0	0	0	0	1	11036	359	13	2		2	OR2T4	1	248525893	Silent	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	262899	248525893	724728	11	4045										
OR2T27	403239	hgsc.bcm.edu	37	chr1	248813316	248813316	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	acatccttgttcctaaggctGtaaatgagtggattgagcat	10	7	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr1:248813316G>T	ENST00000344889.3	-	1	869	c.870C>A	c.(868-870)taC>taA	p.Y290*		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCTAAGGCTGTAAATGAGTG	0.478																																					p.Y290X		Atlas-SNP	.											.	OR2T27	52	.	0			c.C870A						.						75	76	75					1																	248813316		2174	4269	6443	SO:0001587	stop_gained	403239	exon1			AAGGCTGTAAATG		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"GPCR / Class A : Olfactory receptors"	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.870C>A	chr1.hg19:g.248813316G>T	ENSP00000342008:p.Tyr290*	197.0	0.0		573.0	83.0	NM_001001824		Nonsense_Mutation	SNP	ENST00000344889.3	hg19	CCDS31124.1	.	.	.	.	.	.	.	.	.	.	.	6.679	0.493898	0.12702	.	.	ENSG00000187701	ENST00000344889	.	.	.	3.3	-0.96	0.10340	.	0.000000	0.36002	N	0.002857	.	.	.	.	.	.	0.52501	D	0.99995	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6348	0.45558	0.3614:0.0:0.6386:0.0	.	.	.	.	X	290	.	ENSP00000342008:Y290X	Y	-	3	2	OR2T27	246879939	0.003000	0.15002	0.093000	0.20910	0.008000	0.06430	-0.342000	0.07801	-0.331000	0.08501	-1.478000	0.00992	TAC	.	.		0.478	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824		T	248813316	G	T	248813316	4	4	34	1	0	0	0	0	0	1	0	0	11030	1372	48	3	86	3	OR2T27	1	248813316	Nonsense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	287423	248813316	437305	12	4046										
SH3YL1	26751	hgsc.bcm.edu	37	chr2	218860	218860	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	aaatgccagtttgacctcgaAgttttccttcccaccaatca	5	13	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr2:218860A>C	ENST00000405430.1	-	12	1356	c.980T>G	c.(979-981)cTt>cGt	p.L327R	SH3YL1_ENST00000415006.2_Missense_Mutation_p.L231R|SH3YL1_ENST00000403658.1_Missense_Mutation_p.L212R|SH3YL1_ENST00000403712.2_Missense_Mutation_p.L308R|SH3YL1_ENST00000356150.5_Missense_Mutation_p.L327R|SH3YL1_ENST00000403657.1_Missense_Mutation_p.L212R|SH3YL1_ENST00000468321.1_5'UTR			Q96HL8	SH3Y1_HUMAN	SH3 and SYLF domain containing 1	327	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				phosphatidylinositol biosynthetic process (GO:0006661)|regulation of ruffle assembly (GO:1900027)	ruffle membrane (GO:0032587)	phosphatase binding (GO:0019902)|phosphatidylinositol binding (GO:0035091)			large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)		TTGACCTCGAAGTTTTCCTTC	0.353																																					p.L327R		Atlas-SNP	.											.	SH3YL1	49	.	0			c.T980G						.						128	119	122					2																	218860		1854	4093	5947	SO:0001583	missense	26751	exon10			CCTCGAAGTTTTC		CCDS42646.1, CCDS42646.2, CCDS54332.1, CCDS62841.1	2p25.3	2013-10-18	2013-10-18		ENSG00000035115	ENSG00000035115			29546	protein-coding gene	gene with protein product			"SH3 domain containing, Ysc84-like 1 (S. cerevisiae)"			21624956	Standard	NM_001282687		Approved	Ray, DKFZP586F1318	uc002qvx.3	Q96HL8	OTTHUMG00000151359	ENST00000405430.1:c.980T>G	chr2.hg19:g.218860A>C	ENSP00000384269:p.Leu327Arg	48.0	0.0		152.0	75.0	NM_015677	A8K8E7|B7WNJ4|B7WPL6|Q8NEL2|Q9H5X4|Q9Y3V5	Missense_Mutation	SNP	ENST00000405430.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.5	4.157471	0.78114	.	.	ENSG00000035115	ENST00000415006;ENST00000403712;ENST00000403657;ENST00000405430;ENST00000356150;ENST00000403658;ENST00000451005	T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69	6.03	6.03	0.97812	Src homology-3 domain (5);	0.000000	0.64402	D	0.000001	T	0.67221	0.2870	M	0.71581	2.175	0.80722	D	1	D;D;D;D	0.76494	0.998;0.991;0.999;0.999	D;P;D;D	0.70716	0.97;0.891;0.969;0.948	T	0.70353	-0.4895	10	0.72032	D	0.01	-12.012	14.5176	0.67830	1.0:0.0:0.0:0.0	.	212;308;327;231	Q96HL8-4;Q96HL8-2;Q96HL8;Q96HL8-3	.;.;SH3Y1_HUMAN;.	R	231;308;212;327;327;212;240	ENSP00000404143:L231R;ENSP00000384276:L308R;ENSP00000385668:L212R;ENSP00000384269:L327R;ENSP00000348471:L327R;ENSP00000383928:L212R;ENSP00000416312:L240R	ENSP00000348471:L327R	L	-	2	0	SH3YL1	208860	1.000000	0.71417	0.948000	0.38648	0.965000	0.64279	5.939000	0.70179	2.302000	0.77476	0.533000	0.62120	CTT	.	.		0.353	SH3YL1-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322352.1	NM_015677		C	218860	A	C	218860	3	2	34	1	0	0	0	0	1	0	0	0	14278	72	3	5	52	5	SH3YL1	2	218860	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10		218860	242980513	13	4047										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73717941	73717941	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ccattctccccttcctcaagGtcaggattctatagcttcag	6	14	5	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr2:73717941G>C	ENST00000264448.6	+	10	8963	c.8852G>C	c.(8851-8853)gGt>gCt	p.G2951A	AC096546.1_ENST00000408160.1_RNA|ALMS1_ENST00000409009.1_Missense_Mutation_p.G2909A	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2951					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CTTCCTCAAGGTCAGGATTCT	0.418																																					p.G2951A		Atlas-SNP	.											.	ALMS1	384	.	0			c.G8852C						.						164	152	156					2																	73717941		1883	4104	5987	SO:0001583	missense	7840	exon10			CTCAAGGTCAGGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.8852G>C	chr2.hg19:g.73717941G>C	ENSP00000264448:p.Gly2951Ala	62.0	0.0		86.0	33.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	g	3.883	-0.025554	0.07589	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.05855	3.39;3.38	4.78	3.9	0.45041	.	0.496401	0.19006	N	0.125204	T	0.06462	0.0166	L	0.48642	1.525	0.38002	D	0.934273	P;P;P	0.46064	0.872;0.793;0.573	B;B;B	0.41510	0.359;0.164;0.164	T	0.43972	-0.9358	10	0.15499	T	0.54	.	9.0041	0.36100	0.098:0.0:0.902:0.0	.	2951;2909;2951	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	A	2909;2951	ENSP00000386627:G2909A;ENSP00000264448:G2951A	ENSP00000264448:G2951A	G	+	2	0	ALMS1	73571449	0.743000	0.28239	0.456000	0.27044	0.216000	0.24613	1.882000	0.39648	1.612000	0.50221	0.650000	0.86243	GGT	.	.		0.418	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73717941	G	C	73717941	3	2	34	1	0	0	0	0	1	0	0	0	535	1261	44	4	8890	4	ALMS1	2	73717941	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	73499081	73717941	169481432	14	4048										
KCMF1	56888	hgsc.bcm.edu	37	chr2	85255054	85255054	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	aaaaggaaattttcgaggtcGcagatataagtgtttaattt	9	3	0	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr2:85255054G>A	ENST00000409785.4	+	2	418	c.59G>A	c.(58-60)cGc>cAc	p.R20H		NM_020122.4	NP_064507.3	Q9P0J7	KCMF1_HUMAN	potassium channel modulatory factor 1	20							ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						TTTCGAGGTCGCAGATATAAG	0.363																																					p.R20H		Atlas-SNP	.											.	KCMF1	38	.	0			c.G59A						.						110	99	103					2																	85255054		1903	4150	6053	SO:0001583	missense	56888	exon2			GAGGTCGCAGATA	AF155652	CCDS46350.1	2p11.2	2010-11-23			ENSG00000176407	ENSG00000176407		"Zinc fingers, ZZ-type"	20589	protein-coding gene	gene with protein product		614719					Standard	NM_020122		Approved	DEBT91, PCMF, DKFZP434L1021, ZZZ1	uc002sox.4	Q9P0J7	OTTHUMG00000153004	ENST00000409785.4:c.59G>A	chr2.hg19:g.85255054G>A	ENSP00000386738:p.Arg20His	166.0	0.0		258.0	103.0	NM_020122	Q4ZG04|Q53SC7|Q9BWK2|Q9H8P5|Q9UFE8	Missense_Mutation	SNP	ENST00000409785.4	hg19	CCDS46350.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.469646	0.84533	.	.	ENSG00000176407	ENST00000409785	D	0.91295	-2.82	5.46	4.59	0.56863	Zinc finger, ZZ-type (4);	0.052611	0.85682	D	0.000000	D	0.92001	0.7466	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.88933	0.3374	10	0.15499	T	0.54	-5.9955	12.0886	0.53713	0.0842:0.0:0.9158:0.0	.	20	Q9P0J7	KCMF1_HUMAN	H	20	ENSP00000386738:R20H	ENSP00000386738:R20H	R	+	2	0	KCMF1	85108565	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.869000	0.99810	1.309000	0.44985	0.591000	0.81541	CGC	.	.		0.363	KCMF1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328942.4	NM_020122		A	85255054	G	A	85255054	3	1	34	1	0	0	0	0	1	0	0	0	8009	1087	38	1	65	1	KCMF1	2	85255054	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	11537113	85255054	157944319	15	4049										
ZNF2	7549	hgsc.bcm.edu	37	chr2	95847630	95847630	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agtgtggcaaagctttctttGaccgctcatcccttacacag	8	12	2	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr2:95847630G>T	ENST00000340539.5	+	5	1519	c.1057G>T	c.(1057-1059)Gac>Tac	p.D353Y	ZNF2_ENST00000453539.2_Missense_Mutation_p.D366Y|ZNF2_ENST00000425369.1_Missense_Mutation_p.D273Y|ZNF2_ENST00000295210.6_Missense_Mutation_p.D315Y|ZNF2_ENST00000398107.2_Missense_Mutation_p.D311Y	NM_021088.2	NP_066574	Q9BSG1	ZNF2_HUMAN	zinc finger protein 2	353					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	12		Ovarian(717;0.00768)		READ - Rectum adenocarcinoma(193;0.0222)		AGCTTTCTTTGACCGCTCATC	0.517																																					p.D353Y		Atlas-SNP	.											.	ZNF2	21	.	0			c.G1057T						.						89	97	95					2																	95847630		2129	4277	6406	SO:0001583	missense	7549	exon5			TTCTTTGACCGCT	X60152	CCDS42712.1, CCDS42713.1, CCDS62957.1	2q11.1	2013-09-24	2005-02-07		ENSG00000163067	ENSG00000275111		"Zinc fingers, C2H2-type", "-"	12991	protein-coding gene	gene with protein product		194500	"zinc finger protein 2 (A1-5)"			8183940, 1945843	Standard	NM_021088		Approved	A1-5, ZNF661, Zfp661	uc002suf.3	Q9BSG1	OTTHUMG00000155150	ENST00000340539.5:c.1057G>T	chr2.hg19:g.95847630G>T	ENSP00000345392:p.Asp353Tyr	54.0	0.0		119.0	54.0	NM_021088	A8MWV7|B4DIR4|Q4ZFY6|Q96G44|Q9UMC5	Missense_Mutation	SNP	ENST00000340539.5	hg19	CCDS42712.1	.	.	.	.	.	.	.	.	.	.	G	4.727	0.135240	0.09032	.	.	ENSG00000163067	ENST00000398107;ENST00000340539;ENST00000425369;ENST00000295210;ENST00000453539	T;T;T;T;T	0.55052	0.54;2.48;3.3;0.54;2.48	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.138238	0.33670	N	0.004673	T	0.50514	0.1620	N	0.05554	-0.025	0.42318	D	0.992242	D;P;D	0.89917	1.0;0.887;1.0	D;B;D	0.91635	0.969;0.261;0.999	T	0.44375	-0.9332	10	0.10636	T	0.68	-17.8972	16.2332	0.82358	0.0:0.0:1.0:0.0	.	315;311;352	B4DIR4;A8MWV7;Q9BSG1	.;.;ZNF2_HUMAN	Y	311;353;273;315;366	ENSP00000381178:D311Y;ENSP00000345392:D353Y;ENSP00000406017:D273Y;ENSP00000295210:D315Y;ENSP00000411051:D366Y	ENSP00000295210:D315Y	D	+	1	0	ZNF2	95211357	0.000000	0.05858	1.000000	0.80357	0.661000	0.39034	-0.622000	0.05553	2.697000	0.92050	0.563000	0.77884	GAC	.	.		0.517	ZNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338595.2	NM_021088		T	95847630	G	T	95847630	3	4	34	1	0	0	0	0	1	0	0	0	17775	1290	45	3	1071	3	ZNF2	2	95847630	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	10592576	95847630	147351743	16	4050										
STK39	27347	hgsc.bcm.edu	37	chr2	169018309	169018309	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agctttacctgctatttgtaCtgaaccatcctcacccagaa	5	13	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr2:169018309C>A	ENST00000355999.4	-	5	1321	c.616G>T	c.(616-618)Gta>Tta	p.V206L		NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	206	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						GCTATTTGTACTGAACCATCC	0.303																																					p.V206L		Atlas-SNP	.											.	STK39	95	.	0			c.G616T						.						81	74	76					2																	169018309		1796	4058	5854	SO:0001583	missense	27347	exon5			TTTGTACTGAACC	AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648			17717	protein-coding gene	gene with protein product	"STE20/SPS1 homolog (yeast)"	607648				10980603	Standard	NM_013233		Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.616G>T	chr2.hg19:g.169018309C>A	ENSP00000348278:p.Val206Leu	195.0	0.0		348.0	126.0	NM_013233	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	Missense_Mutation	SNP	ENST00000355999.4	hg19	CCDS42770.1	.	.	.	.	.	.	.	.	.	.	C	32	5.174476	0.94807	.	.	ENSG00000198648	ENST00000355999	T	0.22743	1.94	6.17	6.17	0.99709	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.39682	0.1087	L	0.44542	1.39	0.80722	D	1	P	0.52842	0.956	P	0.59643	0.861	T	0.02064	-1.1220	10	0.87932	D	0	-10.3885	20.8794	0.99867	0.0:1.0:0.0:0.0	.	206	Q9UEW8	STK39_HUMAN	L	206	ENSP00000348278:V206L	ENSP00000348278:V206L	V	-	1	0	STK39	168726555	1.000000	0.71417	0.971000	0.41717	0.959000	0.62525	6.875000	0.75551	2.941000	0.99782	0.655000	0.94253	GTA	.	.		0.303	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258112.2	NM_013233		A	169018309	C	A	169018309	3	1	34	1	0	0	0	0	1	0	0	0	15320	565	20	3	1077	3	STK39	2	169018309	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	73170679	169018309	74181064	17	4051										
ZNF142	7701	hgsc.bcm.edu	37	chr2	219509578	219509579	+	Frame_Shift_Ins	INS	-	-	GG													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cagcacagcctgcttgtggcINSggctctggtaactgcagtag					rs200389237		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr2:219509578_219509579insGG	ENST00000449707.1	-	8	2081_2082	c.1660_1661insCC	c.(1660-1662)cgcfs	p.R554fs	ZNF142_ENST00000411696.2_Frame_Shift_Ins_p.R554fs	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	554					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CTGCTTGTGGCGGCTCTGGTAA	0.594																																					p.R554fs	Colon(170;867 1942 8995 15834 18053)	Atlas-INDEL	.											.	ZNF142	190	.	0			c.1661_1662insCC						.																																			SO:0001589	frameshift_variant	7701	exon8			.	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.1659_1660dupCC	chr2.hg19:g.219509579_219509580dupGG	ENSP00000408643:p.Arg554fs	119.0	0.0		231.0	19.0	NM_001105537	Q92510	Frame_Shift_Ins	INS	ENST00000449707.1	hg19	CCDS42817.1																																																																																			.	.		0.594	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		GG	219509579	-	GG	219509578	7	5	34	1	0	1	1	0	0	0	0	0	17746	768	27	0	3414	0	ZNF142	2	219509578	Frame_Shift_Ins	INS	-	TCGA-BC-A10U-01A-11D-A12Z-10	50491269	219509578	23689795	18	4052										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38835301	38835301	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agttctgctgggagctcaccAtagaacttgggcagctggtt	13	9	2	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr3:38835301A>G	ENST00000449082.2	-	1	200	c.201T>C	c.(199-201)taT>taC	p.Y67Y		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	67					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GGAGCTCACCATAGAACTTGG	0.547																																					p.Y67Y		Atlas-SNP	.											.	SCN10A	359	.	0			c.T201C						.						137	144	142					3																	38835301		2203	4300	6503	SO:0001819	synonymous_variant	6336	exon1			CTCACCATAGAAC	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.201T>C	chr3.hg19:g.38835301A>G		122.0	0.0		335.0	149.0	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.		0.547	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		G	38835301	A	G	38835301	2	3	34	1	0	0	0	0	0	0	0	1	13927	224	8	2		2	SCN10A	3	38835301	Silent	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10		38835301	159187129	19	4053										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266132	41266133	+	Frame_Shift_Ins	INS	-	-	C													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ctggtgccactaccacagctINSccttctctgagtggtaaagg							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr3:41266132_41266133insC	ENST00000349496.5	+	3	409_410	c.129_130insC	c.(130-132)cctfs	p.P44fs	CTNNB1_ENST00000453024.1_Frame_Shift_Ins_p.P37fs|CTNNB1_ENST00000396183.3_Frame_Shift_Ins_p.P44fs|CTNNB1_ENST00000396185.3_Frame_Shift_Ins_p.P44fs|CTNNB1_ENST00000405570.1_Frame_Shift_Ins_p.P44fs	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	44					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.P44A(5)|p.?(4)|p.P44S(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.A43del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.P44del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTACCACAGCTCCTTCTCTGAG	0.505		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.A43fs	Colon(6;3 56 14213 18255)	Atlas-INDEL	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+1,1	CTNNB1	4904	.	133	Deletion - In frame(99)|Complex - deletion inframe(18)|Substitution - Missense(9)|Unknown(7)	liver(90)|large_intestine(18)|stomach(7)|thyroid(4)|kidney(4)|adrenal_gland(3)|soft_tissue(2)|small_intestine(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	c.129_130insC						.																																			SO:0001589	frameshift_variant	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	.	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.131dupC	chr3.hg19:g.41266134_41266134dupC	ENSP00000344456:p.Pro44fs	102.0	0.0		229.0	29.0	NM_001098210	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Frame_Shift_Ins	INS	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.505	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266133	-	C	41266132	7	5	34	1	0	1	1	0	0	0	0	0	4018	1538	54	0	135	0	CTNNB1	3	41266132	Frame_Shift_Ins	INS	-	TCGA-BC-A10U-01A-11D-A12Z-10	2430831	41266132	156756298	20	4054	14	3								
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266135	41266135	+	Silent	SNP	T	T	C													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggtgccactaccacagctccTtctctgagtggtaaaggcaa							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr3:41266135T>C	ENST00000349496.5	+	3	412	c.132T>C	c.(130-132)ccT>ccC	p.P44P	CTNNB1_ENST00000453024.1_Silent_p.P37P|CTNNB1_ENST00000396183.3_Silent_p.P44P|CTNNB1_ENST00000396185.3_Silent_p.P44P|CTNNB1_ENST00000405570.1_Silent_p.P44P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	44					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_S45insAP(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S45del(1)|p.H24_M131del(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.P44del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CCACAGCTCCTTCTCTGAGTG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.P44P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+2,1	CTNNB1	4904	.	124	Deletion - In frame(98)|Complex - deletion inframe(18)|Unknown(7)|Insertion - In frame(1)	liver(88)|large_intestine(17)|stomach(7)|adrenal_gland(3)|soft_tissue(2)|small_intestine(2)|skin(2)|kidney(2)|haematopoietic_and_lymphoid_tissue(1)	c.T132C						.						85	75	78					3																	41266135		2203	4300	6503	SO:0001819	synonymous_variant	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	AGCTCCTTCTCTG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.132T>C	chr3.hg19:g.41266135T>C		105.0	0.0		231.0	72.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266135	T	C	41266135	2	2	34	1	0	0	0	0	0	0	0	1	4018	1596	56	2		2	CTNNB1	3	41266135	Silent	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	3	41266135	156756295	21	4055	14	3								
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266137	41266138	+	Missense_Mutation	DNP	CT	CT	TC													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tgccactaccacagctccttCtctgagtggtaaaggcaatc					rs121913409		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr3:41266137_41266138CT>TC	ENST00000349496.5	+	3	414_415	c.134_135CT>TC	c.(133-135)tCT>tTC	p.S45F	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45F(384)|p.S45del(53)|p.A5_A80del(53)|p.S45C(19)|p.S45Y(17)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.S45fs*2(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.S45S(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACAGCTCCTTCTCTGAGTGGTA	0.5	S45F(HCC15_LUNG)|S45F(LS180_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45F|p.S45S	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+1,2|CTNNB1,NS,carcinoma,+2,4	CTNNB1	4904	.	602	Substitution - Missense(421)|Deletion - In frame(152)|Complex - deletion inframe(20)|Unknown(7)|Deletion - Frameshift(1)|Substitution - coding silent(1)	soft_tissue(233)|liver(141)|large_intestine(85)|kidney(74)|endometrium(16)|skin(11)|adrenal_gland(9)|stomach(7)|biliary_tract(5)|ovary(5)|lung(3)|central_nervous_system(2)|cervix(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(1)|pituitary(1)|prostate(1)|bone(1)|pancreas(1)	c.C134T|c.T135C						.																																			SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTCCTTCTCTGAG|TCCTTCTCTGAGT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	Exception_encountered	chr3.hg19:g.41266137_41266138delinsTC	ENSP00000344456:p.Ser45Phe	106.0|103.0	1.0|0.0		232.0|227.0	62.0|93.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation|Silent	SNP	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.5	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		TC	41266138	CT	TC	41266137	3	4	34	1	0	0	0	0	1	0	0	0	4018	913	32	3	140	3	CTNNB1	3	41266137	Missense_Mutation	DNP	CT	TCGA-BC-A10U-01A-11D-A12Z-10	2	41266137	156756293	22	4056	14	3								
CADPS	8618	hgsc.bcm.edu	37	chr3	62739120	62739120	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gcgagaaacaccttacctggCaggcattgtaaaggagctga	12	9	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr3:62739120C>G	ENST00000383710.4	-	3	1233	c.884G>C	c.(883-885)tGc>tCc	p.C295S	CADPS_ENST00000283269.9_Missense_Mutation_p.C295S|CADPS_ENST00000490353.2_Missense_Mutation_p.C295S|CADPS_ENST00000357948.3_Missense_Mutation_p.C295S	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	295					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		CCTTACCTGGCAGGCATTGTA	0.448																																					p.C295S		Atlas-SNP	.											.	CADPS	387	.	0			c.G884C						.						67	64	65					3																	62739120		2203	4300	6503	SO:0001583	missense	8618	exon3			ACCTGGCAGGCAT	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.884G>C	chr3.hg19:g.62739120C>G	ENSP00000373215:p.Cys295Ser	34.0	0.0		93.0	45.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.913566	0.92178	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000490353	D;D;D;D	0.85013	-1.93;-1.93;-1.93;-1.93	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.92251	0.7542	M	0.71581	2.175	0.80722	D	1	P;D;P	0.58970	0.837;0.984;0.651	P;D;B	0.71656	0.457;0.974;0.214	D	0.92186	0.5755	10	0.87932	D	0	.	20.2228	0.98330	0.0:1.0:0.0:0.0	.	295;295;295	Q9ULU8-2;Q9ULU8-3;Q9ULU8	.;.;CAPS1_HUMAN	S	295	ENSP00000373215:C295S;ENSP00000350632:C295S;ENSP00000283269:C295S;ENSP00000418736:C295S	ENSP00000283269:C295S	C	-	2	0	CADPS	62714160	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.789000	0.95967	0.655000	0.94253	TGC	.	.		0.448	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		G	62739120	C	G	62739120	3	3	34	1	0	0	0	0	1	0	0	0	2572	710	25	4	3362	4	CADPS	3	62739120	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	21472983	62739120	135283310	23	4057										
ABHD10	55347	hgsc.bcm.edu	37	chr3	111710276	111710279	+	Frame_Shift_Del	DEL	CTGA	CTGA	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gagcatgccatcaaaatactCtgaagaaggagtttataacg							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	CTGA	CTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr3:111710276_111710279delCTGA	ENST00000273359.3	+	5	656_659	c.629_632delCTGA	c.(628-633)tctgaafs	p.SE210fs	ABHD10_ENST00000494817.1_3'UTR|ABHD10_ENST00000534857.1_Frame_Shift_Del_p.SE53fs	NM_018394.2	NP_060864.1	Q9NUJ1	ABHDA_HUMAN	abhydrolase domain containing 10	210					glucuronoside catabolic process (GO:0019391)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			large_intestine(2)|lung(7)|skin(1)	10						TCAAAATACTCTGAAGAAGGAGTT	0.368																																					p.210_211del		Atlas-Indel,Pindel	.											.	ABHD10	20	.	0			c.628_631del						.																																			SO:0001589	frameshift_variant	55347	exon5			.	AL713726	CCDS2963.1, CCDS63718.1	3q13.2	2012-03-26			ENSG00000144827	ENSG00000144827		"Abhydrolase domain containing"	25656	protein-coding gene	gene with protein product						22294686	Standard	NM_018394		Approved	FLJ11342	uc003dyk.5	Q9NUJ1	OTTHUMG00000159280	ENST00000273359.3:c.629_632delCTGA	chr3.hg19:g.111710276_111710279delCTGA	ENSP00000273359:p.Ser210fs	96.0	0.0		208.0	83.0	NM_018394	B7Z6A8|C9IZX5|D3DN63|Q8TCF9	Frame_Shift_Del	DEL	ENST00000273359.3	hg19	CCDS2963.1																																																																																			.	.		0.368	ABHD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354326.1	NM_018394		-	111710279	CTGA	-	111710276	7	5	34	1	0	1	0	1	0	0	0	0	74	913	32	0	647	0	ABHD10	3	111710276	Frame_Shift_Del	DEL	CTGA	TCGA-BC-A10U-01A-11D-A12Z-10	48971156	111710276	86312154	24	4058										
CCDC14	64770	hgsc.bcm.edu	37	chr3	123650008	123650008	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tgacgtaatgttatccccaaTatctggttttccttttcagc	6	10	2	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr3:123650008T>C	ENST00000488653.2	-	12	1953	c.1863A>G	c.(1861-1863)atA>atG	p.I621M	CCDC14_ENST00000489746.1_Missense_Mutation_p.I421M|CCDC14_ENST00000433542.2_Missense_Mutation_p.I580M|CCDC14_ENST00000485727.1_Missense_Mutation_p.I421M|CCDC14_ENST00000310351.4_Missense_Mutation_p.I461M|CCDC14_ENST00000483247.1_Intron			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	621					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		TTATCCCCAATATCTGGTTTT	0.373																																					p.I580M		Atlas-SNP	.											.	CCDC14	97	.	0			c.A1740G						.						80	79	79					3																	123650008		2203	4300	6503	SO:0001583	missense	64770	exon11			CCCCAATATCTGG	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.1863A>G	chr3.hg19:g.123650008T>C	ENSP00000420180:p.Ile621Met	217.0	0.0		340.0	125.0	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Missense_Mutation	SNP	ENST00000488653.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.94|16.94	3.260091|3.260091	0.59321|0.59321	.|.	.|.	ENSG00000175455|ENSG00000175455	ENST00000488653;ENST00000310351;ENST00000485727;ENST00000489746;ENST00000433542;ENST00000409697;ENST00000419247|ENST00000479903	T;T;T;T;T;T;T|.	0.62788|.	0.0;0.0;0.0;0.0;0.0;0.0;0.0|.	5.17|5.17	2.74|2.74	0.32292|0.32292	.|.	0.137208|.	0.49916|.	D|.	0.000129|.	T|T	0.46756|0.46756	0.1409|0.1409	L|L	0.59436|0.59436	1.845|1.845	0.30968|0.30968	N|N	0.722921|0.722921	D;D;D;D|.	0.63046|.	0.992;0.992;0.992;0.992|.	D;D;P;P|.	0.64321|.	0.924;0.924;0.862;0.895|.	T|T	0.50759|0.50759	-0.8790|-0.8790	10|5	0.48119|.	T|.	0.1|.	.|.	5.0782|5.0782	0.14642|0.14642	0.3723:0.0:0.1524:0.4753|0.3723:0.0:0.1524:0.4753	.|.	621;580;421;462|.	Q49A88;Q49A88-6;Q49A88-4;Q49A88-5|.	CCD14_HUMAN;.;.;.|.	M|C	621;461;421;421;580;602;262|203	ENSP00000420180:I621M;ENSP00000312031:I461M;ENSP00000418002:I421M;ENSP00000418403:I421M;ENSP00000395706:I580M;ENSP00000386866:I602M;ENSP00000400957:I262M|.	ENSP00000312031:I461M|.	I|Y	-|-	3|2	3|0	CCDC14|CCDC14	125132698|125132698	0.939000|0.939000	0.31865|0.31865	0.996000|0.996000	0.52242|0.52242	0.983000|0.983000	0.72400|0.72400	-0.081000|-0.081000	0.11321|0.11321	0.974000|0.974000	0.38366|0.38366	0.460000|0.460000	0.39030|0.39030	ATA|TAT	.	.		0.373	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757		C	123650008	T	C	123650008	3	2	34	1	0	0	0	0	1	0	0	0	2775	1396	49	2	1006	2	CCDC14	3	123650008	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	11939732	123650008	74372422	25	4059										
NEK11	28990	hgsc.bcm.edu	37	chr3	130748574	130748574	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tgctgaaattccaagaggcaGctaagtgtgtgagtggatca	13	6	1	3			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr3:130748574G>T	ENST00000264992.3	-	0	0				NEK11_ENST00000429253.2_Missense_Mutation_p.A8S|NEK11_ENST00000383366.4_Missense_Mutation_p.A8S|NEK11_ENST00000507910.1_Missense_Mutation_p.A8S|NEK11_ENST00000412440.2_5'UTR|NEK11_ENST00000508196.1_Missense_Mutation_p.A8S|NEK11_ENST00000511262.1_Missense_Mutation_p.A8S|NEK11_ENST00000356918.4_Missense_Mutation_p.A8S|ASTE1_ENST00000514044.1_5'Flank|NEK11_ENST00000510688.1_Missense_Mutation_p.A8S|NEK11_ENST00000510769.1_Missense_Mutation_p.A8S	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)						DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						CCAAGAGGCAGCTAAGTGTGT	0.393																																					p.A8S		Atlas-SNP	.											.	NEK11	76	.	0			c.G22T						.						119	111	114					3																	130748574		2203	4300	6503	SO:0001631	upstream_gene_variant	79858	exon3			GAGGCAGCTAAGT	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644		chr3.hg19:g.130748574G>T	Exception_encountered	79.0	0.0		188.0	89.0	NM_024800	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Missense_Mutation	SNP	ENST00000264992.3	hg19	CCDS3068.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.582576	0.46006	.	.	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000356918;ENST00000510688;ENST00000511262;ENST00000383366;ENST00000507910;ENST00000508196	T;T;T;T;T;T;T;T	0.70869	-0.52;-0.39;-0.51;-0.45;-0.5;-0.39;-0.51;-0.39	5.83	4.01	0.46588	.	0.255712	0.27388	N	0.019586	T	0.55970	0.1954	N	0.19112	0.55	0.80722	D	1	P;P;P;P;P	0.42692	0.649;0.787;0.775;0.666;0.775	B;B;B;B;B	0.41412	0.273;0.273;0.356;0.115;0.23	T	0.55774	-0.8088	10	0.49607	T	0.09	.	9.9423	0.41587	0.0723:0.1385:0.7893:0.0	.	8;8;8;8;8	Q8NG66-3;E9PHI8;Q8NG66-4;Q8NG66;Q8NG66-2	.;.;.;NEK11_HUMAN;.	S	8	ENSP00000421549:A8S;ENSP00000397180:A8S;ENSP00000349389:A8S;ENSP00000423458:A8S;ENSP00000425114:A8S;ENSP00000372857:A8S;ENSP00000426662:A8S;ENSP00000421851:A8S	ENSP00000349389:A8S	A	+	1	0	NEK11	132231264	0.567000	0.26626	0.839000	0.33178	0.510000	0.34073	0.511000	0.22739	0.798000	0.33994	0.650000	0.86243	GCT	.	.		0.393	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		T	130748574	G	T	130748574	1	4	34	0	1	0	0	0	0	0	0	0	10332	971	34	3		3	NEK11	3	130748574	5'Flank	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	7098566	130748574	67273856	26	4060										
C3orf72	401089	hgsc.bcm.edu	37	chr3	138669225	138669225	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agcgcttcgctagaaccactCagctcgtcccgcgccgccgc	10	19	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr3:138669225C>T	ENST00000383165.3	+	3	470	c.339C>T	c.(337-339)ctC>ctT	p.L113L		NM_001040061.2	NP_001035150.1	Q6ZUU3	FOXNB_HUMAN		113										large_intestine(1)|lung(3)	4						TAGAACCACTCAGCTCGTCCC	0.716																																					p.L113L		Atlas-SNP	.											.	C3orf72	13	.	0			c.C339T						.						13	19	17					3																	138669225		1829	4081	5910	SO:0001819	synonymous_variant	401089	exon3			ACCACTCAGCTCG																												ENST00000383165.3:c.339C>T	chr3.hg19:g.138669225C>T		34.0	0.0		26.0	9.0	NM_001040061	A6NGX0	Silent	SNP	ENST00000383165.3	hg19	CCDS43155.1																																																																																			.	.		0.716	C3orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357986.1			T	138669225	C	T	138669225	2	4	34	1	0	0	0	0	0	0	0	1	2246	813	29	3		3	C3orf72	3	138669225	Silent	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	7920651	138669225	59353205	27	4061										
WDR49	151790	hgsc.bcm.edu	37	chr3	167246878	167246878	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	caaccatccatcaagatctcCtgtggtaaggtatcgattca	7	11	3	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr3:167246878C>T	ENST00000308378.3	-	10	1617	c.1312G>A	c.(1312-1314)Gga>Aga	p.G438R	WDR49_ENST00000479765.1_Intron|WDR49_ENST00000476376.1_Missense_Mutation_p.G263R|WDR49_ENST00000453925.2_Missense_Mutation_p.G502R	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	438										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						TCAAGATCTCCTGTGGTAAGG	0.348																																					p.G438R		Atlas-SNP	.											.	WDR49	188	.	0			c.G1312A						.						87	84	85					3																	167246878		2203	4300	6503	SO:0001583	missense	151790	exon10			GATCTCCTGTGGT	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.1312G>A	chr3.hg19:g.167246878C>T	ENSP00000311343:p.Gly438Arg	140.0	0.0		273.0	93.0	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	hg19	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.083773	0.55861	.	.	ENSG00000174776	ENST00000308378;ENST00000476376;ENST00000453925	T;T;T	0.47869	1.07;0.83;1.8	5.52	5.52	0.82312	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.109048	0.64402	D	0.000009	T	0.80132	0.4567	H	0.96576	3.845	0.43540	D	0.995836	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	D	0.86822	0.2005	10	0.87932	D	0	.	18.2233	0.89909	0.0:1.0:0.0:0.0	.	502;438	E7EQK3;Q8IV35	.;WDR49_HUMAN	R	438;263;502	ENSP00000311343:G438R;ENSP00000420508:G263R;ENSP00000410863:G502R	ENSP00000311343:G438R	G	-	1	0	WDR49	168729572	1.000000	0.71417	1.000000	0.80357	0.206000	0.24218	4.951000	0.63610	2.599000	0.87857	0.563000	0.77884	GGA	.	.		0.348	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		T	167246878	C	T	167246878	3	4	34	1	0	0	0	0	1	0	0	0	17317	690	24	3	805	3	WDR49	3	167246878	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	28577653	167246878	30775552	28	4062										
ZCCHC4	29063	hgsc.bcm.edu	37	chr4	25353268	25353268	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cccctatttttttgaatcccGaatttgtcagttttttccaa	4	10	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr4:25353268G>T	ENST00000302874.4	+	8	992	c.968G>T	c.(967-969)cGa>cTa	p.R323L	AC108218.1_ENST00000580712.1_RNA|ZCCHC4_ENST00000505451.1_3'UTR	NM_024936.2	NP_079212.2	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	323							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)	9		Breast(46;0.0503)				TTTGAATCCCGAATTTGTCAG	0.348																																					p.R323L		Atlas-SNP	.											.	ZCCHC4	34	.	0			c.G968T						.						129	120	123					4																	25353268		1792	4064	5856	SO:0001583	missense	29063	exon8			AATCCCGAATTTG	AF161537	CCDS43218.1	4p15.31	2014-02-18			ENSG00000168228	ENSG00000168228		"Zinc fingers, CCHC domain containing"	22917	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 4"	611792				11042152	Standard	NM_024936		Approved	HSPC052, FLJ23024, ZGRF4	uc003grl.4	Q9H5U6	OTTHUMG00000160563	ENST00000302874.4:c.968G>T	chr4.hg19:g.25353268G>T	ENSP00000303468:p.Arg323Leu	123.0	0.0		343.0	134.0	NM_024936	B2RXF6|B4DRD8|B7ZW20|Q5IW78|Q96AN7	Missense_Mutation	SNP	ENST00000302874.4	hg19	CCDS43218.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.956075	0.92726	.	.	ENSG00000168228	ENST00000302874	T	0.32515	1.45	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.48677	0.1513	M	0.77103	2.36	0.58432	D	0.999996	D	0.53745	0.962	P	0.50162	0.633	T	0.44697	-0.9311	10	0.44086	T	0.13	-16.3091	19.1733	0.93590	0.0:0.0:1.0:0.0	.	323	Q9H5U6	ZCHC4_HUMAN	L	323	ENSP00000303468:R323L	ENSP00000303468:R323L	R	+	2	0	ZCCHC4	24962366	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.011000	0.76359	2.815000	0.96918	0.650000	0.86243	CGA	.	.		0.348	ZCCHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361151.1			T	25353268	G	T	25353268	3	4	34	1	0	0	0	0	1	0	0	0	17605	1058	37	1	998	1	ZCCHC4	4	25353268	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10		25353268	165801008	29	4063										
RFC1	5981	hgsc.bcm.edu	37	chr4	39322038	39322038	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agaacttttggttttcttagGagtttttgtctctcctttca	7	7	3	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr4:39322038G>C	ENST00000381897.1	-	9	1193	c.1060C>G	c.(1060-1062)Cct>Gct	p.P354A	RFC1_ENST00000349703.2_Missense_Mutation_p.P354A|RFC1_ENST00000418436.1_5'Flank	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	354					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						GTTTTCTTAGGAGTTTTTGTC	0.313																																					p.P354A	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.C1060G						.						36	36	36					4																	39322038		2201	4300	6501	SO:0001583	missense	5981	exon9			TCTTAGGAGTTTT	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.1060C>G	chr4.hg19:g.39322038G>C	ENSP00000371321:p.Pro354Ala	166.0	0.0		267.0	108.0	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	hg19	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.418820	0.62622	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.54071	0.59;0.59	5.72	5.72	0.89469	.	0.274572	0.42294	D	0.000729	T	0.70378	0.3217	M	0.70275	2.135	0.80722	D	1	B;D	0.67145	0.326;0.996	B;D	0.63877	0.105;0.919	T	0.66736	-0.5848	10	0.33141	T	0.24	-10.5685	18.876	0.92337	0.0:0.0:1.0:0.0	.	354;354	P35251;P35251-2	RFC1_HUMAN;.	A	354	ENSP00000371321:P354A;ENSP00000261424:P354A	ENSP00000261424:P354A	P	-	1	0	RFC1	38998433	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.941000	0.63540	2.693000	0.91896	0.655000	0.94253	CCT	.	.		0.313	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		C	39322038	G	C	39322038	3	2	34	1	0	0	0	0	1	0	0	0	13259	1174	41	4	2451	4	RFC1	4	39322038	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	13968770	39322038	151832238	30	4064										
KCTD8	386617	hgsc.bcm.edu	37	chr4	44449751	44449751	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gtagaagcgggacgtgtactTctccggctgccggtcggggt	17	10	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr4:44449751T>A	ENST00000360029.3	-	1	1073	c.790A>T	c.(790-792)Aag>Tag	p.K264*	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	264					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						GACGTGTACTTCTCCGGCTGC	0.652										HNSCC(17;0.042)																											p.K264X		Atlas-SNP	.											.	KCTD8	96	.	0			c.A790T						.						45	40	42					4																	44449751		2203	4300	6503	SO:0001587	stop_gained	386617	exon1			TGTACTTCTCCGG	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.790A>T	chr4.hg19:g.44449751T>A	ENSP00000353129:p.Lys264*	53.0	0.0		55.0	16.0	NM_198353	A2RU39	Nonsense_Mutation	SNP	ENST00000360029.3	hg19	CCDS3467.1	.	.	.	.	.	.	.	.	.	.	T	39	7.791863	0.98492	.	.	ENSG00000183783	ENST00000360029	.	.	.	4.19	4.19	0.49359	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	.	12.5991	0.56487	0.0:0.0:0.0:1.0	.	.	.	.	X	264	.	ENSP00000353129:K264X	K	-	1	0	KCTD8	44144508	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.451000	0.44952	1.765000	0.52091	0.477000	0.44152	AAG	.	.		0.652	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			A	44449751	T	A	44449751	4	1	34	1	0	0	0	0	0	1	0	0	8124	1792	62	4	639	4	KCTD8	4	44449751	Nonsense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	5127713	44449751	146704525	31	4065										
C4orf21	55345	hgsc.bcm.edu	37	chr4	113510881	113510881	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gcaatgtggtaacgactaccCtccaagttgagaaaatgaag	10	8	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr4:113510881C>G	ENST00000505019.1	-	11	3251	c.3126G>C	c.(3124-3126)gaG>gaC	p.E1042D	C4orf21_ENST00000309071.5_Missense_Mutation_p.E1042D	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		1042						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		AACGACTACCCTCCAAGTTGA	0.338																																					p.E1042D		Atlas-SNP	.											.	C4orf21	223	.	0			c.G3126C						.						100	102	101					4																	113510881		2203	4300	6503	SO:0001630	splice_region_variant	55345	exon11			ACTACCCTCCAAG																												ENST00000505019.1:c.3127+1G>C	chr4.hg19:g.113510881C>G		151.0	0.0		150.0	107.0	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	hg19		.	.	.	.	.	.	.	.	.	.	C	4.785	0.145885	0.09134	.	.	ENSG00000138658	ENST00000505019;ENST00000309071	D;T	0.82433	-1.61;1.78	3.12	-6.25	0.02039	.	.	.	.	.	T	0.54822	0.1882	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.49041	-0.8980	9	0.12103	T	0.63	.	1.5577	0.02588	0.1413:0.1855:0.1416:0.5316	.	1042;1042	Q86YA3;G5EA02	CD021_HUMAN;.	D	1042	ENSP00000424737:E1042D;ENSP00000309095:E1042D	ENSP00000309095:E1042D	E	-	3	2	C4orf21	113730330	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-1.438000	0.02416	-1.868000	0.01142	0.460000	0.39030	GAG	.	.		0.338	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		Missense_Mutation	G	113510881	C	G	113510881	5	3	34	1	0	0	0	0	0	0	1	0	2256	695	24	4	3260	4	C4orf21	4	113510881	Splice_Site	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	69061130	113510881	77643395	32	4066										
TNIP3	79931	hgsc.bcm.edu	37	chr4	122085259	122085259	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tgcggcaatcattctagatgTgccctgtacaaaatgtgcca	9	10	2	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr4:122085259T>C	ENST00000509841.1	-	4	331	c.253A>G	c.(253-255)Aca>Gca	p.T85A	TNIP3_ENST00000057513.3_Missense_Mutation_p.T8A|TNIP3_ENST00000454328.1_Missense_Mutation_p.T8A|TNIP3_ENST00000507879.1_Missense_Mutation_p.T78A	NM_001244764.1	NP_001231693.1			TNFAIP3 interacting protein 3											NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2)	24						ATTCTAGATGTGCCCTGTACA	0.403																																					p.T85A		Atlas-SNP	.											.	TNIP3	58	.	0			c.A253G						.						121	113	116					4																	122085259		2203	4300	6503	SO:0001583	missense	79931	exon4			TAGATGTGCCCTG	AJ320534	CCDS3718.1, CCDS58925.1, CCDS58926.1	4q27	2008-02-05			ENSG00000050730	ENSG00000050730			19315	protein-coding gene	gene with protein product		608019				11345586	Standard	NM_024873		Approved	LIND, FLJ21162, ABIN-3	uc021xrj.1	Q96KP6	OTTHUMG00000132969	ENST00000509841.1:c.253A>G	chr4.hg19:g.122085259T>C	ENSP00000426613:p.Thr85Ala	66.0	0.0		162.0	55.0	NM_001244764		Missense_Mutation	SNP	ENST00000509841.1	hg19	CCDS58926.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.020591	0.54576	.	.	ENSG00000050730	ENST00000057513;ENST00000454328;ENST00000507879;ENST00000509841	T;T;T;T	0.51071	0.94;0.94;0.73;0.72	5.44	-5.44	0.02624	.	0.337042	0.22233	N	0.062785	T	0.27594	0.0678	L	0.51422	1.61	0.09310	N	1	B;B;B	0.20052	0.041;0.041;0.041	B;B;B	0.17722	0.011;0.019;0.011	T	0.12785	-1.0534	10	0.25751	T	0.34	-0.8549	1.2525	0.01985	0.2434:0.1499:0.3748:0.2318	.	78;8;8	B4DVF5;A5HU65;Q96KP6	.;.;TNIP3_HUMAN	A	8;8;78;85	ENSP00000057513:T8A;ENSP00000411817:T8A;ENSP00000427106:T78A;ENSP00000426613:T85A	ENSP00000057513:T8A	T	-	1	0	TNIP3	122304709	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.027000	0.12371	-0.705000	0.05035	-0.321000	0.08615	ACA	.	.		0.403	TNIP3-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364000.4	NM_024873		C	122085259	T	C	122085259	3	2	34	1	0	0	0	0	1	0	0	0	16331	1696	59	2	999	2	TNIP3	4	122085259	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	8574378	122085259	69069017	33	4067										
PCDH10	57575	hgsc.bcm.edu	37	chr4	134071720	134071720	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cacgccaggcactcgcttccCcttggagagcgcattcgacc	10	17	0	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr4:134071720C>A	ENST00000264360.5	+	1	1251	c.425C>A	c.(424-426)cCc>cAc	p.P142H	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	142	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		ACTCGCTTCCCCTTGGAGAGC	0.612																																					p.P142H		Atlas-SNP	.											.	PCDH10	290	.	0			c.C425A						.						57	60	59					4																	134071720		2203	4300	6503	SO:0001583	missense	57575	exon1			GCTTCCCCTTGGA	AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.425C>A	chr4.hg19:g.134071720C>A	ENSP00000264360:p.Pro142His	32.0	0.0		51.0	22.0	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	hg19	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.770027	0.69992	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.20200	2.09	4.78	4.78	0.61160	Cadherin (2);Cadherin-like (1);	0.000000	0.44902	D	0.000414	T	0.51686	0.1689	M	0.86028	2.79	0.80722	D	1	D;P	0.89917	1.0;0.559	D;P	0.91635	0.999;0.566	T	0.56129	-0.8030	10	0.45353	T	0.12	.	17.5675	0.87924	0.0:1.0:0.0:0.0	.	142;142	Q9P2E7;Q96SF0	PCD10_HUMAN;.	H	142	ENSP00000264360:P142H	ENSP00000264360:P142H	P	+	2	0	PCDH10	134291170	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.651000	0.83577	2.467000	0.83353	0.555000	0.69702	CCC	.	.		0.612	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		A	134071720	C	A	134071720	3	1	34	1	0	0	0	0	1	0	0	0	11516	623	22	3	427	3	PCDH10	4	134071720	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	11986461	134071720	57082556	34	4068										
IRF2	3660	hgsc.bcm.edu	37	chr4	185340688	185340688	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	catcccacccatgtctagccGcatgcatccaggggatctga	9	15	2	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr4:185340688G>A	ENST00000393593.3	-	3	329	c.122C>T	c.(121-123)gCg>gTg	p.A41V	IRF2_ENST00000512020.1_5'UTR	NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	41					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A41V(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		ATGTCTAGCCGCATGCATCCA	0.423																																					p.A41V		Atlas-SNP	.											IRF2,colon,carcinoma,0,1	IRF2	53	.	1	Substitution - Missense(1)	large_intestine(1)	c.C122T						.						108	109	109					4																	185340688		2203	4300	6503	SO:0001583	missense	3660	exon3			CTAGCCGCATGCA		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.122C>T	chr4.hg19:g.185340688G>A	ENSP00000377218:p.Ala41Val	33.0	0.0		61.0	12.0	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Missense_Mutation	SNP	ENST00000393593.3	hg19	CCDS3835.1	.	.	.	.	.	.	.	.	.	.	G	32	5.135806	0.94517	.	.	ENSG00000168310	ENST00000393593;ENST00000507523;ENST00000510814;ENST00000506230;ENST00000505316	D;D;D;D	0.98044	-4.68;-4.68;-4.68;-4.68	4.99	4.99	0.66335	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.98855	0.9613	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99785	1.1029	10	0.87932	D	0	-9.6502	18.4742	0.90786	0.0:0.0:1.0:0.0	.	41	P14316	IRF2_HUMAN	V	41	ENSP00000377218:A41V;ENSP00000427204:A41V;ENSP00000424552:A41V;ENSP00000422860:A41V	ENSP00000377218:A41V	A	-	2	0	IRF2	185577682	1.000000	0.71417	0.957000	0.39632	0.942000	0.58702	9.645000	0.98471	2.581000	0.87130	0.655000	0.94253	GCG	.	.		0.423	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1			A	185340688	G	A	185340688	3	1	34	1	0	0	0	0	1	0	0	0	7837	1087	38	1	955	1	IRF2	4	185340688	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	51268968	185340688	5813588	35	4069										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	140645	140645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	caggtccaggagctgcagggCggactcttcccaggagatct	14	12	2	1	rs369792305		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr5:140645C>T	ENST00000283426.6	+	1	273	c.223C>T	c.(223-225)Cgg>Tgg	p.R75W	CTD-2231H16.1_ENST00000512035.1_lincRNA	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	75							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		AGCTGCAGGGCGGACTCTTCC	0.662																																					p.R75W		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.C223T						.		TRP/ARG	0,4338		0,0,2169	16	21	19		223	1.4	0	5		19	1,8549		0,1,4274	no	missense	PLEKHG4B	NM_052909.3	101	0,1,6443	TT,TC,CC		0.0117,0.0,0.0078	possibly-damaging	75/1272	140645	1,12887	2169	4275	6444	SO:0001583	missense	153478	exon1			GCAGGGCGGACTC	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.223C>T	chr5.hg19:g.140645C>T	ENSP00000283426:p.Arg75Trp	100.0	0.0		153.0	67.0	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	hg19	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	.	12.80	2.047131	0.36085	0.0	1.17E-4	ENSG00000153404	ENST00000283426	T	0.25579	1.79	2.59	1.37	0.22104	.	.	.	.	.	T	0.12860	0.0312	N	0.19112	0.55	0.09310	N	1	P	0.50066	0.931	B	0.36766	0.232	T	0.14671	-1.0464	9	0.87932	D	0	.	5.4782	0.16708	0.6837:0.3163:0.0:0.0	.	75	Q96PX9	PKH4B_HUMAN	W	75	ENSP00000283426:R75W	ENSP00000283426:R75W	R	+	1	2	PLEKHG4B	193645	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.714000	0.25808	-0.022000	0.13986	0.298000	0.19748	CGG	.	.		0.662	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		T	140645	C	T	140645	3	4	34	1	0	0	0	0	1	0	0	0	12081	759	27	1	225	1	PLEKHG4B	5	140645	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10		140645	180774615	36	4070										
ZNF608	57507	hgsc.bcm.edu	37	chr5	123982848	123982848	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	atactggccataataaagtgActgagccagggcaggatgtc	12	8	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr5:123982848A>T	ENST00000306315.5	-	4	3664	c.3229T>A	c.(3229-3231)Tca>Aca	p.S1077T	ZNF608_ENST00000504926.1_Missense_Mutation_p.S650T|ZNF608_ENST00000513985.1_5'Flank	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1077							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		TAATAAAGTGACTGAGCCAGG	0.483																																					p.S1077T		Atlas-SNP	.											.	ZNF608	117	.	0			c.T3229A						.						72	68	69					5																	123982848		2203	4300	6503	SO:0001583	missense	57507	exon4			AAAGTGACTGAGC	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.3229T>A	chr5.hg19:g.123982848A>T	ENSP00000307746:p.Ser1077Thr	148.0	0.0		291.0	111.0	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	hg19	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	A	17.16	3.319352	0.60524	.	.	ENSG00000168916	ENST00000504926;ENST00000306315	T;T	0.51071	0.73;0.72	5.57	5.57	0.84162	.	0.064020	0.64402	D	0.000004	T	0.64461	0.2600	M	0.66939	2.045	0.49389	D	0.999785	D	0.76494	0.999	D	0.66602	0.945	T	0.61207	-0.7109	10	0.26408	T	0.33	-13.2497	16.0213	0.80499	1.0:0.0:0.0:0.0	.	1077	Q9ULD9	ZN608_HUMAN	T	650;1077	ENSP00000427657:S650T;ENSP00000307746:S1077T	ENSP00000307746:S1077T	S	-	1	0	ZNF608	124010747	1.000000	0.71417	0.998000	0.56505	0.962000	0.63368	5.253000	0.65452	2.239000	0.73571	0.523000	0.50628	TCA	.	.		0.483	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		T	123982848	A	T	123982848	3	4	34	1	0	0	0	0	1	0	0	0	18049	275	10	4	1333	4	ZNF608	5	123982848	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	123842203	123982848	56932412	37	4071										
H2AFY	9555	hgsc.bcm.edu	37	chr5	134724771	134724771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggtggacttcttcttcccacCgcggctcgacatggcggtgg	14	13	2	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr5:134724771C>T	ENST00000511689.1	-	2	606	c.13G>A	c.(13-15)Ggt>Agt	p.G5S	H2AFY_ENST00000312469.4_Missense_Mutation_p.G5S|H2AFY_ENST00000510038.1_Missense_Mutation_p.G5S|H2AFY_ENST00000304332.4_Missense_Mutation_p.G5S|H2AFY_ENST00000423969.2_Missense_Mutation_p.G5S	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	5	Histone H2A.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTCTTCCCACCGCGGCTCGAC	0.622																																					p.G5S		Atlas-SNP	.											.	H2AFY	61	.	0			c.G13A						.						83	69	74					5																	134724771		2203	4300	6503	SO:0001583	missense	9555	exon2			TCCCACCGCGGCT	AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"Histones / Replication-independent"	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.13G>A	chr5.hg19:g.134724771C>T	ENSP00000423563:p.Gly5Ser	24.0	0.0		52.0	21.0	NM_138610	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Missense_Mutation	SNP	ENST00000511689.1	hg19	CCDS4185.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.909180	0.72868	.	.	ENSG00000113648	ENST00000511689;ENST00000304332;ENST00000312469;ENST00000423969;ENST00000510038	T;T;T;D;T	0.84442	1.58;1.6;1.59;-1.85;1.58	5.11	5.11	0.69529	Histone-fold (1);Histone H2A (1);	0.052671	0.85682	N	0.000000	D	0.89643	0.6774	L	0.44542	1.39	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.987;0.999;0.999;0.997	D	0.88148	0.2849	10	0.36615	T	0.2	.	18.7267	0.91716	0.0:1.0:0.0:0.0	.	5;5;5;5	B4DJC3;O75367-3;O75367-2;O75367	.;.;.;H2AY_HUMAN	S	5	ENSP00000423563:G5S;ENSP00000302572:G5S;ENSP00000310169:G5S;ENSP00000415121:G5S;ENSP00000424971:G5S	ENSP00000302572:G5S	G	-	1	0	H2AFY	134752670	1.000000	0.71417	0.990000	0.47175	0.921000	0.55340	7.644000	0.83416	2.665000	0.90641	0.573000	0.79308	GGT	.	.		0.622	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893		T	134724771	C	T	134724771	3	4	34	1	0	0	0	0	1	0	0	0	6938	652	23	1	1232	1	H2AFY	5	134724771	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	10741923	134724771	46190489	38	4072										
SPOCK1	6695	hgsc.bcm.edu	37	chr5	136314376	136314376	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ccgacctcatcctctttgtcAtcatcctcatcctcatcatc	2	18	7	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr5:136314376A>G	ENST00000394945.1	-	11	1456	c.1287T>C	c.(1285-1287)gaT>gaC	p.D429D	SPOCK1_ENST00000282223.7_Silent_p.D429D|SPOCK1_ENST00000509978.1_5'Flank	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	429					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCTCTTTGTCATCATCCTCAT	0.483																																					p.D429D		Atlas-SNP	.											.	SPOCK1	58	.	0			c.T1287C						.						293	230	251					5																	136314376		2203	4300	6503	SO:0001819	synonymous_variant	6695	exon11			TTTGTCATCATCC	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.1287T>C	chr5.hg19:g.136314376A>G		123.0	0.0		304.0	131.0	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Silent	SNP	ENST00000394945.1	hg19	CCDS4191.1																																																																																			.	.		0.483	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		G	136314376	A	G	136314376	2	3	34	1	0	0	0	0	0	0	0	1	15094	214	8	2		2	SPOCK1	5	136314376	Silent	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	1589605	136314376	44600884	39	4073										
PCYOX1L	78991	hgsc.bcm.edu	37	chr5	148745666	148745666	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tattgatgatgtcgtttctgCtgtcctgcgggccagctatg	12	9	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr5:148745666C>G	ENST00000274569.4	+	4	694	c.632C>G	c.(631-633)gCt>gGt	p.A211G	PCYOX1L_ENST00000514349.1_Missense_Mutation_p.A121G	NM_024028.3	NP_076933.3	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like	211					prenylcysteine catabolic process (GO:0030328)	extracellular region (GO:0005576)|membrane (GO:0016020)	prenylcysteine oxidase activity (GO:0001735)			breast(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCGTTTCTGCTGTCCTGCGG	0.612																																					p.A211G	Ovarian(62;1136 1477 27277 27495)	Atlas-SNP	.											.	PCYOX1L	32	.	0			c.C632G						.						48	46	47					5																	148745666		2203	4300	6503	SO:0001583	missense	78991	exon4			TTTCTGCTGTCCT		CCDS4296.1	5q33.1	2008-02-05			ENSG00000145882	ENSG00000145882			28477	protein-coding gene	gene with protein product						12477932	Standard	NM_024028		Approved	MGC3265	uc003lqk.2	Q8NBM8	OTTHUMG00000130052	ENST00000274569.4:c.632C>G	chr5.hg19:g.148745666C>G	ENSP00000274569:p.Ala211Gly	31.0	0.0		73.0	28.0	NM_024028	Q7Z4S2|Q8NCY5|Q8NF69|Q9BTE8|Q9BWS3	Missense_Mutation	SNP	ENST00000274569.4	hg19	CCDS4296.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737902	0.69304	.	.	ENSG00000145882	ENST00000274569;ENST00000514349	T;T	0.16743	3.01;2.32	5.18	5.18	0.71444	Prenylcysteine lyase (1);	0.059356	0.64402	D	0.000002	T	0.25827	0.0629	L	0.57536	1.79	0.80722	D	1	P;P	0.43857	0.62;0.819	P;P	0.44860	0.462;0.451	T	0.01045	-1.1470	10	0.33141	T	0.24	-16.972	19.0548	0.93059	0.0:1.0:0.0:0.0	.	121;211	E7EVZ5;Q8NBM8	.;PCYXL_HUMAN	G	211;121	ENSP00000274569:A211G;ENSP00000428512:A121G	ENSP00000274569:A211G	A	+	2	0	PCYOX1L	148725859	1.000000	0.71417	0.324000	0.25361	0.681000	0.39784	7.750000	0.85110	2.593000	0.87608	0.561000	0.74099	GCT	.	.		0.612	PCYOX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252331.2	NM_024028		G	148745666	C	G	148745666	3	3	34	1	0	0	0	0	1	0	0	0	11618	797	28	4	646	4	PCYOX1L	5	148745666	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	12431290	148745666	32169594	40	4074										
EIF4E1B	253314	hgsc.bcm.edu	37	chr5	176070173	176070173	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cgcccacaggagaaaagtctCcaaactctcccaggactttg	8	14	2	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr5:176070173C>A	ENST00000318682.6	+	4	690	c.106C>A	c.(106-108)Cca>Aca	p.P36T	EIF4E1B_ENST00000504597.1_Missense_Mutation_p.P36T	NM_001099408.1	NP_001092878.1	A6NMX2	I4E1B_HUMAN	eukaryotic translation initiation factor 4E family member 1B	36					regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)	translation initiation factor activity (GO:0003743)			breast(1)|large_intestine(1)|lung(2)|pancreas(1)	5	all_cancers(89;0.00185)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGAAAAGTCTCCAAACTCTCC	0.602																																					p.P36T		Atlas-SNP	.											.	EIF4E1B	24	.	0			c.C106A						.						47	57	54					5																	176070173		1961	4145	6106	SO:0001583	missense	253314	exon4			AAGTCTCCAAACT		CCDS47345.1	5q35.2	2008-06-12			ENSG00000175766	ENSG00000175766			33179	protein-coding gene	gene with protein product						16191198	Standard	NM_001099408		Approved	FLJ36951	uc010jkf.1	A6NMX2	OTTHUMG00000163227	ENST00000318682.6:c.106C>A	chr5.hg19:g.176070173C>A	ENSP00000323714:p.Pro36Thr	113.0	0.0		185.0	72.0	NM_001099408		Missense_Mutation	SNP	ENST00000318682.6	hg19	CCDS47345.1	.	.	.	.	.	.	.	.	.	.	C	8.682	0.905479	0.17760	.	.	ENSG00000175766	ENST00000318682;ENST00000510660;ENST00000504597	T;T	0.41400	1.0;1.0	4.14	-0.355	0.12587	Translation Initiation factor eIF- 4e-like  domain (1);	.	.	.	.	T	0.18923	0.0454	N	0.14661	0.345	0.09310	N	1	B	0.29432	0.244	B	0.26864	0.074	T	0.20075	-1.0286	9	0.19147	T	0.46	.	2.9823	0.05957	0.3898:0.3842:0.0:0.226	.	36	A6NMX2	I4E1B_HUMAN	T	36	ENSP00000323714:P36T;ENSP00000427633:P36T	ENSP00000323714:P36T	P	+	1	0	EIF4E1B	176002779	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.939000	0.03933	0.097000	0.17492	0.561000	0.74099	CCA	.	.		0.602	EIF4E1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372187.1	NM_001099408		A	176070173	C	A	176070173	3	1	34	1	0	0	0	0	1	0	0	0	5031	855	30	3	112	3	EIF4E1B	5	176070173	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	27324507	176070173	4845087	41	4075										
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12162108	12162108	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	atgtctgtggactaccctgaGtcagaagaaattctgagaag	11	7	3	4			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr6:12162108G>T	ENST00000379388.2	+	8	7256	c.6924G>T	c.(6922-6924)gaG>gaT	p.E2308D	HIVEP1_ENST00000541134.1_Missense_Mutation_p.E173D	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2308					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				ACTACCCTGAGTCAGAAGAAA	0.448																																					p.E2308D		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G6924T						.						87	86	87					6																	12162108		1922	4148	6070	SO:0001583	missense	3096	exon8			CCCTGAGTCAGAA	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.6924G>T	chr6.hg19:g.12162108G>T	ENSP00000368698:p.Glu2308Asp	85.0	0.0		346.0	81.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	hg19	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.738734	0.30774	.	.	ENSG00000095951	ENST00000379388;ENST00000442081;ENST00000541134;ENST00000542327	T;T	0.25250	3.17;1.81	5.76	-4.43	0.03568	.	0.643086	0.12906	N	0.429327	T	0.01870	0.0059	N	0.12569	0.235	0.23923	N	0.996456	B	0.06786	0.001	B	0.04013	0.001	T	0.39981	-0.9587	10	0.05959	T	0.93	-15.0873	1.0466	0.01571	0.2636:0.2011:0.3367:0.1987	.	2308	P15822	ZEP1_HUMAN	D	2308;235;173;290	ENSP00000368698:E2308D;ENSP00000445617:E173D	ENSP00000368698:E2308D	E	+	3	2	HIVEP1	12270094	0.000000	0.05858	0.004000	0.12327	0.817000	0.46193	-0.512000	0.06313	-0.394000	0.07727	-0.290000	0.09829	GAG	.	.		0.448	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		T	12162108	G	T	12162108	3	4	34	1	0	0	0	0	1	0	0	0	7195	1020	36	3	6950	3	HIVEP1	6	12162108	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10		12162108	158952959	42	4076										
KDM1B	221656	hgsc.bcm.edu	37	chr6	18215297	18215297	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gctgtcgcatccgtgaggacCctggatgacaaacaggtgct	13	11	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr6:18215297C>A	ENST00000297792.5	+	16	1650	c.1473C>A	c.(1471-1473)acC>acA	p.T491T	KDM1B_ENST00000546309.2_Silent_p.T14T|KDM1B_ENST00000388870.2_Silent_p.T724T|KDM1B_ENST00000397244.1_Silent_p.T492T			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	723					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						CCGTGAGGACCCTGGATGACA	0.582																																					p.T491T		Atlas-SNP	.											.	KDM1B	58	.	0			c.C1473A						.						78	72	74					6																	18215297		2203	4300	6503	SO:0001819	synonymous_variant	221656	exon16			GAGGACCCTGGAT	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"Chromatin-modifying enzymes / K-demethylases"	21577	protein-coding gene	gene with protein product		613081	"amine oxidase, flavin containing 1", "chromosome 6 open reading frame 193", "amine oxidase (flavin containing) domain 1"	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.1473C>A	chr6.hg19:g.18215297C>A		51.0	0.0		141.0	30.0	NM_153042	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Silent	SNP	ENST00000297792.5	hg19	CCDS34343.1	.	.	.	.	.	.	.	.	.	.	C	6.645	0.487486	0.12641	.	.	ENSG00000165097	ENST00000449850	.	.	.	5.99	5.12	0.69794	.	.	.	.	.	T	0.45736	0.1357	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50136	-0.8863	4	.	.	.	-11.1785	7.8068	0.29206	0.0:0.7137:0.135:0.1513	.	.	.	.	H	541	.	.	P	+	2	0	KDM1B	18323276	0.995000	0.38212	0.888000	0.34837	0.532000	0.34746	0.490000	0.22403	1.518000	0.48934	0.650000	0.86243	CCC	.	.		0.582	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042		A	18215297	C	A	18215297	2	1	34	1	0	0	0	0	0	0	0	1	8132	610	22	3		3	KDM1B	6	18215297	Silent	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	6053189	18215297	152899770	43	4077										
HIST1H4G	8369	hgsc.bcm.edu	37	chr6	26246995	26246995	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggcgtgctccgtgttggtcaCggcgtaccagatcacatttt	12	11	2	1	rs140916075		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr6:26246995C>T	ENST00000244537.4	-	1	264	c.211G>A	c.(211-213)Gtg>Atg	p.V71M		NM_003547.2	NP_003538.1	Q99525	H4G_HUMAN	histone cluster 1, H4g	71						nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				GTGTTGGTCACGGCGTACCAG	0.592																																					p.V71M		Atlas-SNP	.											.	HIST1H4G	18	.	0			c.G211A						.	C	MET/VAL	0,4406		0,0,2203	78	67	71		211	2.3	0.7	6	dbSNP_134	71	1,8599		0,1,4299	no	missense	HIST1H4G	NM_003547.2	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	71/99	26246995	1,13005	2203	4300	6503	SO:0001583	missense	8369	exon1			TGGTCACGGCGTA	Z80788	CCDS4599.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124578	ENSG00000275663		"Histones / Replication-dependent"	4792	protein-coding gene	gene with protein product		602832	"H4 histone family, member L", "histone 1, H4g"	H4FL		9119399, 12408966	Standard	NM_003547		Approved	H4/l	uc003nhf.3	Q99525	OTTHUMG00000014444	ENST00000244537.4:c.211G>A	chr6.hg19:g.26246995C>T	ENSP00000244537:p.Val71Met	82.0	0.0		223.0	120.0	NM_003547		Missense_Mutation	SNP	ENST00000244537.4	hg19	CCDS4599.1	.	.	.	.	.	.	.	.	.	.	.	9.134	1.012034	0.19277	0.0	1.16E-4	ENSG00000124578	ENST00000244537	T	0.68903	-0.36	3.2	2.32	0.28847	Histone-fold (2);Histone core (1);	.	.	.	.	T	0.72637	0.3485	.	.	.	0.33596	D	0.601659	D	0.89917	1.0	D	0.85130	0.997	T	0.73792	-0.3871	8	0.87932	D	0	.	10.1053	0.42530	0.0:0.8946:0.0:0.1054	.	71	Q99525	H4G_HUMAN	M	71	ENSP00000244537:V71M	ENSP00000244537:V71M	V	-	1	0	HIST1H4G	26354974	1.000000	0.71417	0.697000	0.30258	0.011000	0.07611	6.913000	0.75759	0.663000	0.31027	-0.539000	0.04255	GTG	.	C|1.000;T|0.000		0.592	HIST1H4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040107.1	NM_003547		T	26246995	C	T	26246995	3	4	34	1	0	0	0	0	1	0	0	0	7180	536	19	1	89	1	HIST1H4G	6	26246995	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	8031698	26246995	144868072	44	4078										
OR2H2	7932	hgsc.bcm.edu	37	chr6	29556264	29556264	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tttgtctgtgaggtcccagcTctaattcgactctcctgtga	9	11	3	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr6:29556264T>C	ENST00000383640.2	+	1	582	c.543T>C	c.(541-543)gcT>gcC	p.A181A	GABBR1_ENST00000355973.3_Intron	NM_007160.3	NP_009091.3	O95918	OR2H2_HUMAN	olfactory receptor, family 2, subfamily H, member 2	181					defense response (GO:0006952)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|mating (GO:0007618)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	14						AGGTCCCAGCTCTAATTCGAC	0.542																																					p.A181A		Atlas-SNP	.											.	OR2H2	29	.	0			c.T543C						.						117	115	115					6																	29556264		1511	2708	4219	SO:0001819	synonymous_variant	7932	exon1			CCCAGCTCTAATT		CCDS34365.1	6p22.2-p21.31	2012-08-09				ENSG00000204657		"GPCR / Class A : Olfactory receptors"	8253	protein-coding gene	gene with protein product		600578					Standard	XM_005249407		Approved	hs6M1-12	uc003nmr.1	O95918		ENST00000383640.2:c.543T>C	chr6.hg19:g.29556264T>C		114.0	0.0		467.0	24.0	NM_007160	Q15062|Q2M1Y3|Q5STL8|Q5SUK1|Q6IFN7|Q6NTB7|Q96R14	Silent	SNP	ENST00000383640.2	hg19	CCDS34365.1																																																																																			.	.		0.542	OR2H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076057.2			C	29556264	T	C	29556264	2	2	34	1	0	0	0	0	0	0	0	1	11011	1538	54	2		2	OR2H2	6	29556264	Silent	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	3309269	29556264	141558803	45	4079										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30917879	30917879	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cctacagaaaatagagaaagGacagccaatgagaagaccac	9	9	0	4			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr6:30917879G>A	ENST00000462446.1	+	2	1666	c.1638G>A	c.(1636-1638)agG>agA	p.R546R	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	291						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						ATAGAGAAAGGACAGCCAATG	0.527																																					p.R546R		Atlas-SNP	.											.	DPCR1	99	.	0			c.G1638A						.						57	67	64					6																	30917879		692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			AGAAAGGACAGCC	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.1638G>A	chr6.hg19:g.30917879G>A		303.0	0.0		894.0	58.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	hg19	CCDS4692.2																																																																																			.	.		0.527	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		A	30917879	G	A	30917879	2	1	34	1	0	0	0	0	0	0	0	1	4714	1165	41	3		3	DPCR1	6	30917879	Silent	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	1361615	30917879	140197188	46	4080										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38810541	38810541	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tgtcctctactggaaatgatGaccaataaggccatgaaaca	8	9	1	3			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr6:38810541G>A	ENST00000359357.3	+	33	4310	c.4056G>A	c.(4054-4056)atG>atA	p.M1352I	DNAH8_ENST00000441566.1_Missense_Mutation_p.M1352I|DNAH8_ENST00000449981.2_Missense_Mutation_p.M1569I			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1352					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGGAAATGATGACCAATAAGG	0.383																																					p.M1569I		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G4707A						.						120	113	115					6																	38810541		2203	4300	6503	SO:0001583	missense	1769	exon35			AATGATGACCAAT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.4056G>A	chr6.hg19:g.38810541G>A	ENSP00000352312:p.Met1352Ile	84.0	0.0		319.0	67.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	G	29.7	5.029218	0.93518	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.60171	0.21;0.21;0.21	5.46	5.46	0.80206	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	T	0.67477	0.2897	M	0.81112	2.525	0.80722	D	1	P	0.50156	0.932	P	0.52758	0.708	T	0.70425	-0.4875	10	0.54805	T	0.06	.	19.6693	0.95905	0.0:0.0:1.0:0.0	.	1352	Q96JB1	DYH8_HUMAN	I	1557;1557;1352;1352	ENSP00000333363:M1557I;ENSP00000352312:M1352I;ENSP00000402294:M1352I	ENSP00000333363:M1557I	M	+	3	0	DNAH8	38918519	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.943000	0.87716	2.711000	0.92665	0.650000	0.86243	ATG	.	.		0.383	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38810541	G	A	38810541	3	1	34	1	0	0	0	0	1	0	0	0	4609	1290	45	3	4178	3	DNAH8	6	38810541	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	7892662	38810541	132304526	47	4081										
COL19A1	1310	hgsc.bcm.edu	37	chr6	70852682	70852682	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cagcaaggatctgcaggctcCatgggacccagaggaccgcc	13	14	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr6:70852682C>T	ENST00000322773.4	+	23	1698	c.1596C>T	c.(1594-1596)tcC>tcT	p.S532S	COL19A1_ENST00000393344.1_Silent_p.S154S	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	532	Triple-helical region 3 (COL3).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						CTGCAGGCTCCATGGGACCCA	0.353																																					p.S532S		Atlas-SNP	.											.	COL19A1	232	.	0			c.C1596T						.						105	110	108					6																	70852682		2203	4300	6503	SO:0001819	synonymous_variant	1310	exon23			AGGCTCCATGGGA		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.1596C>T	chr6.hg19:g.70852682C>T		54.0	0.0		78.0	30.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Silent	SNP	ENST00000322773.4	hg19	CCDS4970.1																																																																																			.	.		0.353	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			T	70852682	C	T	70852682	2	4	34	1	0	0	0	0	0	0	0	1	3678	581	21	3		3	COL19A1	6	70852682	Silent	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	32042141	70852682	100262385	48	4082										
LPA	4018	hgsc.bcm.edu	37	chr6	161006134	161006134	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tgtggtgtcatagacgaccaAgactgacatgttcttcctgt	10	9	2	3			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr6:161006134A>C	ENST00000316300.5	-	26	4277	c.4233T>G	c.(4231-4233)tcT>tcG	p.S1411S	LPA_ENST00000447678.1_Silent_p.S1411S			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3919	Kringle 13. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TAGACGACCAAGACTGACATG	0.458																																					p.S1411S		Atlas-SNP	.											.	LPA	237	.	0			c.T4233G						.						225	226	225					6																	161006134		2190	4295	6485	SO:0001819	synonymous_variant	4018	exon27			CGACCAAGACTGA	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4233T>G	chr6.hg19:g.161006134A>C		91.0	0.0		216.0	66.0	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	hg19	CCDS43523.1																																																																																			.	.		0.458	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		C	161006134	A	C	161006134	2	2	34	1	0	0	0	0	0	0	0	1	8912	59	3	5		5	LPA	6	161006134	Silent	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	90153452	161006134	10108933	49	4083										
C6orf118	168090	hgsc.bcm.edu	37	chr6	165715292	165715292	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggcagccggagttcttccctCctgcgccatccaggagggcc	13	16	1	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr6:165715292C>A	ENST00000230301.8	-	2	539	c.519G>T	c.(517-519)agG>agT	p.R173S	C6orf118_ENST00000543069.1_Missense_Mutation_p.R69S	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	173										breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		GTTCTTCCCTCCTGCGCCATC	0.617																																					p.R173S		Atlas-SNP	.											.	C6orf118	116	.	0			c.G519T						.						37	43	41					6																	165715292		2203	4300	6503	SO:0001583	missense	168090	exon2			TTCCCTCCTGCGC		CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.519G>T	chr6.hg19:g.165715292C>A	ENSP00000230301:p.Arg173Ser	27.0	0.0		42.0	19.0	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	hg19	CCDS5288.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530253	0.45073	.	.	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.14391	2.51;2.51	4.47	1.51	0.23008	.	2.239880	0.01455	N	0.015640	T	0.06554	0.0168	L	0.50333	1.59	0.09310	N	1	P	0.52316	0.952	P	0.46659	0.523	T	0.15983	-1.0418	10	0.27082	T	0.32	-1.3071	5.227	0.15399	0.0:0.4852:0.3277:0.1871	.	173	Q5T5N4	CF118_HUMAN	S	173;69	ENSP00000230301:R173S;ENSP00000439288:R69S	ENSP00000230301:R173S	R	-	3	2	C6orf118	165635282	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.572000	0.23684	0.162000	0.19483	0.655000	0.94253	AGG	.	.		0.617	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980		A	165715292	C	A	165715292	3	1	34	1	0	0	0	0	1	0	0	0	2325	854	30	3	922	3	C6orf118	6	165715292	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	4709158	165715292	5399775	50	4084										
SNX13	23161	hgsc.bcm.edu	37	chr7	17908059	17908059	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gacatactgattaatataatCaggatcactgagttgattta	7	5	2	3			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr7:17908059C>G	ENST00000409389.1	-	9	980	c.808G>C	c.(808-810)Gat>Cat	p.D270H	SNX13_ENST00000428135.3_Missense_Mutation_p.D270H			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	270	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					TTAATATAATCAGGATCACTG	0.269																																					p.D270H		Atlas-SNP	.											.	SNX13	113	.	0			c.G808C						.						35	35	35					7																	17908059		1787	4033	5820	SO:0001583	missense	23161	exon9			TATAATCAGGATC	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"Sorting nexins"	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.808G>C	chr7.hg19:g.17908059C>G	ENSP00000386705:p.Asp270His	124.0	0.0		347.0	110.0	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	hg19		.	.	.	.	.	.	.	.	.	.	C	21.5	4.165450	0.78339	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	T;T	0.33865	1.39;1.65	5.22	4.34	0.51931	Phox-associated domain (2);PX-associated, sorting nexin 13 (1);	0.000000	0.85682	D	0.000000	T	0.62332	0.2419	M	0.83774	2.66	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;1.0;0.998	T	0.68258	-0.5456	10	0.72032	D	0.01	-6.7173	13.5344	0.61639	0.0:0.9233:0.0:0.0767	.	67;270;270;270	B3KN60;Q9Y5W8;B8ZZT9;Q9Y5W8-2	.;SNX13_HUMAN;.;.	H	270;270;318	ENSP00000386705:D270H;ENSP00000398789:D270H	ENSP00000242044:D318H	D	-	1	0	SNX13	17874584	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.229000	0.78088	1.187000	0.43000	0.650000	0.86243	GAT	.	.		0.269	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132		G	17908059	C	G	17908059	3	3	34	1	0	0	0	0	1	0	0	0	14899	826	29	4	2137	4	SNX13	7	17908059	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10		17908059	141230604	51	4085										
MACC1	346389	hgsc.bcm.edu	37	chr7	20199410	20199410	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	aattgtattcaaatcaaggcAggagcgggccagctggcgtt	13	8	2	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr7:20199410A>T	ENST00000400331.5	-	5	882	c.574T>A	c.(574-576)Tgc>Agc	p.C192S	MACC1_ENST00000332878.4_Missense_Mutation_p.C192S|MACC1_ENST00000589011.1_Missense_Mutation_p.C192S	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	192					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						AAATCAAGGCAGGAGCGGGCC	0.483																																					p.C192S		Atlas-SNP	.											.	MACC1	99	.	0			c.T574A						.						54	53	54					7																	20199410		2203	4300	6503	SO:0001583	missense	346389	exon5			CAAGGCAGGAGCG		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.574T>A	chr7.hg19:g.20199410A>T	ENSP00000383185:p.Cys192Ser	93.0	0.0		175.0	41.0	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	hg19	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	A	18.89	3.718563	0.68844	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.29397	1.57;1.57	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.57242	0.2040	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.61691	-0.7011	10	0.87932	D	0	-9.7184	15.9795	0.80097	1.0:0.0:0.0:0.0	.	192	Q6ZN28	MACC1_HUMAN	S	192	ENSP00000383185:C192S;ENSP00000328410:C192S	ENSP00000328410:C192S	C	-	1	0	MACC1	20165935	1.000000	0.71417	0.998000	0.56505	0.713000	0.41058	9.339000	0.96797	2.168000	0.68352	0.477000	0.44152	TGC	.	.		0.483	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		T	20199410	A	T	20199410	3	4	34	1	0	0	0	0	1	0	0	0	9152	188	7	4	1996	4	MACC1	7	20199410	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	2291351	20199410	138939253	52	4086										
ZNF679	168417	hgsc.bcm.edu	37	chr7	63726562	63726562	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	acatactggaaagaaacattTcaaatgtaaaaaatatggca	6	5	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr7:63726562T>G	ENST00000421025.1	+	5	820	c.551T>G	c.(550-552)tTc>tGc	p.F184C	ZNF679_ENST00000255746.4_Missense_Mutation_p.F184C	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	184					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						AAGAAACATTTCAAATGTAAA	0.318																																					p.F184C		Atlas-SNP	.											.	ZNF679	80	.	0			c.T551G						.						66	58	61					7																	63726562		692	1591	2283	SO:0001583	missense	168417	exon5			AACATTTCAAATG	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"Zinc fingers, C2H2-type", "-"	28650	protein-coding gene	gene with protein product	"hypothetical protein MGC42415"					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.551T>G	chr7.hg19:g.63726562T>G	ENSP00000416809:p.Phe184Cys	196.0	0.0		428.0	230.0	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	hg19	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	T	10.27	1.304053	0.23736	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.33654	1.4;1.4	1.12	-2.23	0.06930	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41673	0.1169	M	0.71871	2.18	0.09310	N	0.999999	D	0.64830	0.994	P	0.52710	0.707	T	0.31138	-0.9954	9	0.56958	D	0.05	.	4.0757	0.09902	0.4393:0.0:0.0:0.5607	.	184	Q8IYX0	ZN679_HUMAN	C	184	ENSP00000416809:F184C;ENSP00000255746:F184C	ENSP00000255746:F184C	F	+	2	0	ZNF679	63363997	0.000000	0.05858	0.006000	0.13384	0.107000	0.19398	-0.540000	0.06106	-0.659000	0.05359	0.163000	0.16589	TTC	.	.		0.318	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		G	63726562	T	G	63726562	3	3	34	1	0	0	0	0	1	0	0	0	18101	1783	62	5	565	5	ZNF679	7	63726562	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	43527152	63726562	95412101	53	4087										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98506458	98506458	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cttcgccaagaacatcgacgAtgagtccctgcccagcagca	9	15	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr7:98506458A>G	ENST00000359863.4	+	14	1432	c.1223A>G	c.(1222-1224)gAt>gGt	p.D408G	TRRAP_ENST00000446306.3_Missense_Mutation_p.D408G|TRRAP_ENST00000355540.3_Missense_Mutation_p.D408G	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	408					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AACATCGACGATGAGTCCCTG	0.632																																					p.D408G		Atlas-SNP	.											.	TRRAP	863	.	0			c.A1223G						.						94	66	76					7																	98506458		2203	4300	6503	SO:0001583	missense	8295	exon14			TCGACGATGAGTC	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.1223A>G	chr7.hg19:g.98506458A>G	ENSP00000352925:p.Asp408Gly	45.0	0.0		132.0	38.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.94|18.94	3.729672|3.729672	0.69074|0.69074	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306|ENST00000456197	T;T|.	0.73575|.	3.18;-0.76|.	5.84|5.84	5.84|5.84	0.93424|0.93424	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77631|0.77631	0.4159|0.4159	M|M	0.80332|0.80332	2.49|2.49	0.80722|0.80722	D|D	1|1	D;D;D|.	0.67145|.	0.996;0.993;0.993|.	D;D;D|.	0.73708|.	0.981;0.956;0.956|.	T|T	0.78773|0.78773	-0.2073|-0.2073	10|5	0.72032|.	D|.	0.01|.	.|.	16.2302|16.2302	0.82332|0.82332	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	408;122;408|.	Q9Y4A5-2;Q59FH1;Q9Y4A5|.	.;.;TRRAP_HUMAN|.	G|V	408|123	ENSP00000352925:D408G;ENSP00000347733:D408G|.	ENSP00000347733:D408G|.	D|M	+|+	2|1	0|0	TRRAP|TRRAP	98344394|98344394	1.000000|1.000000	0.71417|0.71417	0.525000|0.525000	0.27900|0.27900	0.714000|0.714000	0.41099|0.41099	9.109000|9.109000	0.94291|0.94291	2.228000|2.228000	0.72767|0.72767	0.533000|0.533000	0.62120|0.62120	GAT|ATG	.	.		0.632	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		G	98506458	A	G	98506458	3	3	34	1	0	0	0	0	1	0	0	0	16616	333	12	2	1273	2	TRRAP	7	98506458	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	34779896	98506458	60632205	54	4088										
COPS6	10980	hgsc.bcm.edu	37	chr7	99686935	99686935	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gtccccagcgtgatggcctgCggagtgactgggagtgtttc	16	10	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr7:99686935C>T	ENST00000303904.3	+	2	136	c.99C>T	c.(97-99)tgC>tgT	p.C33C	COPS6_ENST00000418625.1_Silent_p.C32C	NM_006833.4	NP_006824.2	Q7L5N1	CSN6_HUMAN	COP9 signalosome subunit 6	33					cullin deneddylation (GO:0010388)|viral process (GO:0016032)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|stomach(1)	12	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			TGATGGCCTGCGGAGTGACTG	0.632																																					p.C33C		Atlas-SNP	.											.	COPS6	31	.	0			c.C99T						.						127	119	121					7																	99686935		2203	4300	6503	SO:0001819	synonymous_variant	10980	exon2			GGCCTGCGGAGTG	BC002520	CCDS5682.1	7q22.1	2013-03-14	2013-03-14		ENSG00000168090	ENSG00000168090			21749	protein-coding gene	gene with protein product	"COP9 subunit 6 (MOV34 homolog, 34 kD)"	614729	"COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)"			12477932	Standard	NM_006833		Approved	MOV34-34KD, CSN6	uc003usu.3	Q7L5N1	OTTHUMG00000154632	ENST00000303904.3:c.99C>T	chr7.hg19:g.99686935C>T		34.0	0.0		157.0	50.0	NM_006833	A4D2A3|O15387	Silent	SNP	ENST00000303904.3	hg19	CCDS5682.1																																																																																			.	.		0.632	COPS6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336412.3	NM_006833		T	99686935	C	T	99686935	2	4	34	1	0	0	0	0	0	0	0	1	3739	776	27	1		1	COPS6	7	99686935	Silent	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	1180477	99686935	59451728	55	4089										
C7orf61	402573	hgsc.bcm.edu	37	chr7	100054424	100054425	+	Frame_Shift_Ins	INS	-	-	G													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggactgagccgggttgggtcINSggggggcagcatggcatcgg							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr7:100054424_100054425insG	ENST00000332375.3	-	3	816_817	c.571_572insC	c.(571-573)cgafs	p.R191fs		NM_001004323.1	NP_001004323.1	Q8IZ16	CG061_HUMAN	chromosome 7 open reading frame 61	191						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|prostate(1)|skin(1)	4						CGGGTTGGGTCGGGGGGCAGCA	0.644																																					p.R191fs		Atlas-Indel,Pindel	.											.	C7orf61	12	.	0			c.572_573insC						.																																			SO:0001589	frameshift_variant	402573	exon3			.		CCDS47661.1	7q22.1	2013-10-11			ENSG00000185955	ENSG00000185955			22135	protein-coding gene	gene with protein product						12690205	Standard	NM_001004323		Approved	IMAGE:4839025	uc003uuz.1	Q8IZ16	OTTHUMG00000150234	ENST00000332375.3:c.572dupC	chr7.hg19:g.100054430_100054430dupG	ENSP00000327732:p.Arg191fs	29.0	0.0		96.0	19.0	NM_001004323		Frame_Shift_Ins	INS	ENST00000332375.3	hg19	CCDS47661.1																																																																																			.	.		0.644	C7orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316976.2	NM_001004323		G	100054425	-	G	100054424	7	5	34	1	0	1	1	0	0	0	0	0	2410	884	31	0	52	0	C7orf61	7	100054424	Frame_Shift_Ins	INS	-	TCGA-BC-A10U-01A-11D-A12Z-10	367489	100054424	59084239	56	4090										
MLL3	58508	hgsc.bcm.edu	37	chr7	151884488	151884488	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cattgtgtcattttctccttCcacagtgggagctgatgatg	10	9	2	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr7:151884488C>A	ENST00000262189.6	-	33	5085	c.4867G>T	c.(4867-4869)Gaa>Taa	p.E1623*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.E1623*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1623					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTTTCTCCTTCCACAGTGGGA	0.433																																					p.E1623X		Atlas-SNP	.											.	MLL3	1564	.	0			c.G4867T						.						180	181	181					7																	151884488		2203	4300	6503	SO:0001587	stop_gained	58508	exon33			CTCCTTCCACAGT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.4867G>T	chr7.hg19:g.151884488C>A	ENSP00000262189:p.Glu1623*	94.0	0.0		212.0	112.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Nonsense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	47	13.290567	0.99732	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	.	.	.	5.47	5.47	0.80525	.	0.000000	0.44483	U	0.000447	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	19.6994	0.96047	0.0:1.0:0.0:0.0	.	.	.	.	X	1623	.	ENSP00000262189:E1623X	E	-	1	0	MLL3	151515421	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	7.776000	0.85560	2.718000	0.92993	0.579000	0.79373	GAA	.	.		0.433	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151884488	C	A	151884488	4	1	34	1	0	0	0	0	0	1	0	0	9631	864	30	3	9976	3	MLL3	7	151884488	Nonsense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	51830064	151884488	7254175	57	4091										
ANK1	286	hgsc.bcm.edu	37	chr8	41573290	41573290	+	Frame_Shift_Del	DEL	G	G	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gtggtggccaggttggggttGgcgttattttccagcaggag							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr8:41573290delG	ENST00000347528.4	-	14	1565	c.1482delC	c.(1480-1482)gccfs	p.A494fs	ANK1_ENST00000379758.2_Frame_Shift_Del_p.A494fs|ANK1_ENST00000396945.1_Frame_Shift_Del_p.A494fs|ANK1_ENST00000352337.4_Frame_Shift_Del_p.A494fs|ANK1_ENST00000289734.7_Frame_Shift_Del_p.A494fs|ANK1_ENST00000265709.8_Frame_Shift_Del_p.A527fs|ANK1_ENST00000396942.1_Frame_Shift_Del_p.A494fs	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	494	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GGTTGGGGTTGGCGTTATTTT	0.587																																					p.N528fs		Atlas-Indel,Pindel	.											.	ANK1	497	.	0			c.1582delA						.						121	107	112					8																	41573290		2203	4300	6503	SO:0001589	frameshift_variant	286	exon14			.	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.1482delC	chr8.hg19:g.41573290delG	ENSP00000339620:p.Ala494fs	69.0	0.0		144.0	68.0	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Frame_Shift_Del	DEL	ENST00000347528.4	hg19	CCDS6119.1																																																																																			.	.		0.587	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		-	41573290	G	-	41573290	7	5	34	1	0	1	0	1	0	0	0	0	620	1335	47	0	4633	0	ANK1	8	41573290	Frame_Shift_Del	DEL	G	TCGA-BC-A10U-01A-11D-A12Z-10		41573290	104790732	58	4092										
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885237	88885246	+	Frame_Shift_Del	DEL	ATGCACGGGT	ATGCACGGGT	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	actccttcttcttcgttcacAtgcacgggtaggtaggcgga					rs143361209	byFrequency	TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	ATGCACGGGT	ATGCACGGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr8:88885237_88885246delATGCACGGGT	ENST00000319675.3	-	1	1050_1059	c.954_963delACCCGTGCAT	c.(952-963)ctacccgtgcatfs	p.LPVH318fs		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	318										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						CTTCGTTCACATGCACGGGTAGGTAGGCGG	0.543																																					p.319_322del		Pindel	.											.	DCAF4L2	187	.	0			c.955_964del						.																																			SO:0001589	frameshift_variant	138009	exon1			.	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.954_963delACCCGTGCAT	chr8.hg19:g.88885237_88885246delATGCACGGGT	ENSP00000316496:p.Leu318fs	111.0	0.0		209.0	22.0	NM_152418		Frame_Shift_Del	DEL	ENST00000319675.3	hg19	CCDS6245.1																																																																																			.	.		0.543	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		-	88885246	ATGCACGGGT	-	88885237	7	5	34	1	0	1	0	1	0	0	0	0	4274	214	8	0	228	0	DCAF4L2	8	88885237	Frame_Shift_Del	DEL	ATGCACGGGT	TCGA-BC-A10U-01A-11D-A12Z-10	47311947	88885237	57478785	59	4093	15	3								
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885240	88885242	+	In_Frame_Del	DEL	CAC	CAC	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ccttcttcttcgttcacatgCacgggtaggtaggcggagtt							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr8:88885240_88885242delCAC	ENST00000319675.3	-	1	1054_1056	c.958_960delGTG	c.(958-960)gtgdel	p.V320del		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	320										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						CGTTCACATGCACGGGTAGGTAG	0.537																																					p.320_321del		Atlas-INDEL	.											.	DCAF4L2	187	.	0			c.959_961del						.																																			SO:0001651	inframe_deletion	138009	exon1			.	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.958_960delGTG	chr8.hg19:g.88885240_88885242delCAC	ENSP00000316496:p.Val320del	110.0	0.0		198.0	26.0	NM_152418		In_Frame_Del	DEL	ENST00000319675.3	hg19	CCDS6245.1																																																																																			.	.		0.537	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		-	88885242	CAC	-	88885240	7	5	34	1	0	1	0	1	0	0	0	0	4274	697	25	0	231	0	DCAF4L2	8	88885240	In_Frame_Del	DEL	CAC	TCGA-BC-A10U-01A-11D-A12Z-10	3	88885240	57478782	60	4094	15	3								
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885245	88885246	+	Frame_Shift_Del	DEL	GT	GT	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ttcttcgttcacatgcacggGtaggtaggcggagttattca							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr8:88885245_88885246delGT	ENST00000319675.3	-	1	1050_1051	c.954_955delAC	c.(952-957)ctacccfs	p.P319fs		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	319										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						ACATGCACGGGTAGGTAGGCGG	0.535																																					p.319_319del		Atlas-INDEL	.											.	DCAF4L2	187	.	0			c.955_956del						.																																			SO:0001589	frameshift_variant	138009	exon1			.	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.954_955delAC	chr8.hg19:g.88885245_88885246delGT	ENSP00000316496:p.Pro319fs	113.0	0.0		213.0	27.0	NM_152418		Frame_Shift_Del	DEL	ENST00000319675.3	hg19	CCDS6245.1																																																																																			.	.		0.535	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		-	88885246	GT	-	88885245	7	5	34	1	0	1	0	1	0	0	0	0	4274	1261	44	0	236	0	DCAF4L2	8	88885245	Frame_Shift_Del	DEL	GT	TCGA-BC-A10U-01A-11D-A12Z-10	5	88885245	57478777	61	4095	15	3								
EIF3E	3646	hgsc.bcm.edu	37	chr8	109229595	109229595	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tttaactagatcttttagaaCctgccgacgttttcgaacat	6	9	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr8:109229595C>A	ENST00000220849.5	-	8	879	c.817G>T	c.(817-819)Gtt>Ttt	p.V273F	EIF3E_ENST00000519030.1_Missense_Mutation_p.V180F|EIF3E_ENST00000519517.1_5'UTR	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E										EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			TCTTTTAGAACCTGCCGACGT	0.308																																					p.V273F	GBM(15;360 410 8460 34179 52246)	Atlas-SNP	.											.	EIF3E	73	.	0			c.G817T						.						58	54	55					8																	109229595		2198	4298	6496	SO:0001583	missense	3646	exon8			TTAGAACCTGCCG	U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"eukaryotic translation initiation factor 3, subunit 6 48kDa"	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.817G>T	chr8.hg19:g.109229595C>A	ENSP00000220849:p.Val273Phe	18.0	0.0		47.0	12.0	NM_001568		Missense_Mutation	SNP	ENST00000220849.5	hg19	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.955073	0.34471	.	.	ENSG00000104408	ENST00000220849;ENST00000519030;ENST00000519627	T;T;T	0.42900	0.96;0.96;0.96	5.29	5.29	0.74685	.	0.060765	0.64402	D	0.000004	T	0.47544	0.1451	M	0.71581	2.175	0.80722	D	1	B;P	0.43973	0.087;0.823	B;B	0.41510	0.036;0.359	T	0.44832	-0.9302	10	0.27082	T	0.32	-16.7748	19.294	0.94115	0.0:1.0:0.0:0.0	.	273;273	B2R806;P60228	.;EIF3E_HUMAN	F	273;180;146	ENSP00000220849:V273F;ENSP00000428796:V180F;ENSP00000430839:V146F	ENSP00000220849:V273F	V	-	1	0	EIF3E	109298771	1.000000	0.71417	1.000000	0.80357	0.349000	0.29174	7.776000	0.85560	2.640000	0.89533	0.655000	0.94253	GTT	.	.		0.308	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		A	109229595	C	A	109229595	3	1	34	1	0	0	0	0	1	0	0	0	5017	507	18	3	544	3	EIF3E	8	109229595	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	20344350	109229595	37134427	62	4096										
TG	7038	hgsc.bcm.edu	37	chr8	133925494	133925494	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ttgacaagtgaggccagtcaGgacggactgggatgcggtag	17	7	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr8:133925494G>C	ENST00000220616.4	+	20	4402	c.4362G>C	c.(4360-4362)caG>caC	p.Q1454H	TG_ENST00000377869.1_Missense_Mutation_p.Q1454H	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1454					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AGGCCAGTCAGGACGGACTGG	0.572																																					p.Q1454H		Atlas-SNP	.											.	TG	416	.	0			c.G4362C						.						87	72	77					8																	133925494		2203	4300	6503	SO:0001583	missense	7038	exon20			CAGTCAGGACGGA	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4362G>C	chr8.hg19:g.133925494G>C	ENSP00000220616:p.Gln1454His	52.0	0.0		148.0	53.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	11.79	1.744127	0.30865	.	.	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;D	0.97480	-0.11;-4.4	5.45	2.71	0.32032	.	2.229260	0.01478	N	0.016568	D	0.96269	0.8783	M	0.68317	2.08	0.09310	N	1	P	0.45283	0.855	B	0.41510	0.359	D	0.86702	0.1930	10	0.87932	D	0	.	7.4202	0.27067	0.2669:0.0:0.7331:0.0	.	1454	P01266	THYG_HUMAN	H	1454;260;1454	ENSP00000367100:Q1454H;ENSP00000220616:Q1454H	ENSP00000220616:Q1454H	Q	+	3	2	TG	133994676	0.823000	0.29233	0.011000	0.14972	0.089000	0.18198	1.312000	0.33574	0.282000	0.22254	-0.145000	0.13849	CAG	.	.		0.572	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	133925494	G	C	133925494	3	2	34	1	0	0	0	0	1	0	0	0	15828	991	35	4	4440	4	TG	8	133925494	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	24695899	133925494	12438528	63	4097										
TTLL11	158135	hgsc.bcm.edu	37	chr9	124855337	124855337	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	caccgtctccgctgtggcctCggcctcagctttggccgccg	12	18	2	0	rs201124286		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr9:124855337C>T	ENST00000373776.3	-	1	548	c.361G>A	c.(361-363)Gag>Aag	p.E121K	TTLL11_ENST00000321582.5_Missense_Mutation_p.E121K|TTLL11_ENST00000474723.1_5'UTR	NM_194252.2	NP_919228.2	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	121					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						gctgtggcctcggcctcagct	0.751																																					p.E121K		Atlas-SNP	.											.	TTLL11	67	.	0			c.G361A						.						2	2	2					9																	124855337		1346	2941	4287	SO:0001583	missense	158135	exon1			TGGCCTCGGCCTC	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"Tubulin tyrosine ligase-like family"	18113	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 20"	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000373776.3:c.361G>A	chr9.hg19:g.124855337C>T	ENSP00000362881:p.Glu121Lys	11.0	0.0		5.0	4.0	NM_001139442		Missense_Mutation	SNP	ENST00000373776.3	hg19	CCDS6834.2	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687198	0.29962	.	.	ENSG00000175764	ENST00000321582;ENST00000373776	T;T	0.05855	3.52;3.38	2.1	1.14	0.20703	.	2.107800	0.03051	U	0.154530	T	0.02929	0.0087	N	0.08118	0	0.09310	N	1	P;B	0.35656	0.514;0.38	B;B	0.19666	0.026;0.012	T	0.35798	-0.9774	9	.	.	.	.	4.4339	0.11542	0.0:0.7822:0.0:0.2178	.	121;121	F8W6M1;Q8NHH1	.;TTL11_HUMAN	K	121	ENSP00000321346:E121K;ENSP00000362881:E121K	.	E	-	1	0	TTLL11	123895158	0.000000	0.05858	0.006000	0.13384	0.418000	0.31294	-0.595000	0.05727	0.057000	0.16193	0.462000	0.41574	GAG	.	.		0.751	TTLL11-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053907.1	XM_088486		T	124855337	C	T	124855337	3	4	34	1	0	0	0	0	1	0	0	0	16739	893	31	1	2155	1	TTLL11	9	124855337	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10		124855337	16358094	64	4098										
STXBP1	6812	hgsc.bcm.edu	37	chr9	130442485	130442485	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	acactacccttatatctctaCccgttcctctgcctccttca	2	18	3	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr9:130442485C>T	ENST00000373299.1	+	17	1626	c.1511C>T	c.(1510-1512)aCc>aTc	p.T504I	STXBP1_ENST00000481942.1_Intron|STXBP1_ENST00000373302.3_Missense_Mutation_p.T504I	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	504					axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)			breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						TATATCTCTACCCGTTCCTCT	0.502																																					p.T504I		Atlas-SNP	.											.	STXBP1	99	.	0			c.C1511T						.						247	213	224					9																	130442485		2203	4300	6503	SO:0001583	missense	6812	exon17			TCTCTACCCGTTC	AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"syntaxin-binding protein 1"	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.1511C>T	chr9.hg19:g.130442485C>T	ENSP00000362396:p.Thr504Ile	35.0	0.0		47.0	36.0	NM_001032221	B1AM97|Q28208|Q62759|Q64320|Q96TG8	Missense_Mutation	SNP	ENST00000373299.1	hg19	CCDS35146.1	.	.	.	.	.	.	.	.	.	.	C	13.03	2.114720	0.37339	.	.	ENSG00000136854	ENST00000535154;ENST00000373302;ENST00000541198;ENST00000373299	T;T	0.80653	-1.4;-1.4	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.75481	0.3855	L	0.38175	1.15	0.80722	D	1	B;B	0.31174	0.311;0.265	B;B	0.32342	0.144;0.089	T	0.74343	-0.3696	10	0.52906	T	0.07	-26.234	17.5557	0.87889	0.0:1.0:0.0:0.0	.	504;504	P61764;P61764-2	STXB1_HUMAN;.	I	458;504;336;504	ENSP00000362399:T504I;ENSP00000362396:T504I	ENSP00000362396:T504I	T	+	2	0	STXBP1	129482306	1.000000	0.71417	1.000000	0.80357	0.089000	0.18198	7.366000	0.79548	2.826000	0.97356	0.561000	0.74099	ACC	.	.		0.502	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165		T	130442485	C	T	130442485	3	4	34	1	0	0	0	0	1	0	0	0	15367	507	18	3	1577	3	STXBP1	9	130442485	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	5587148	130442485	10770946	65	4099										
ITIH2	3698	hgsc.bcm.edu	37	chr10	7773850	7773850	+	Frame_Shift_Del	DEL	T	T	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ccatacatcagtcacggacgTcactcaaaacaatttccata							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr10:7773850delT	ENST00000358415.4	+	13	1704	c.1538delT	c.(1537-1539)gtcfs	p.V513fs	ITIH2_ENST00000379587.4_Frame_Shift_Del_p.V502fs	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	513					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						GTCACGGACGTCACTCAAAAC	0.433																																					p.V513fs		Atlas-Indel,Pindel	.											.	ITIH2	144	.	0			c.1537delG						.						172	165	167					10																	7773850		2203	4300	6503	SO:0001589	frameshift_variant	3698	exon13			.	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1538delT	chr10.hg19:g.7773850delT	ENSP00000351190:p.Val513fs	53.0	0.0		81.0	39.0	NM_002216	Q14659|Q15484|Q5T986	Frame_Shift_Del	DEL	ENST00000358415.4	hg19	CCDS31141.1																																																																																			.	.		0.433	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		-	7773850	T	-	7773850	7	5	34	1	0	1	0	1	0	0	0	0	7913	1667	58	0	1588	0	ITIH2	10	7773850	Frame_Shift_Del	DEL	T	TCGA-BC-A10U-01A-11D-A12Z-10		7773850	127760897	66	4100										
FAM188A	80013	hgsc.bcm.edu	37	chr10	15858832	15858832	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	aaaaatcctgctataagcatAccttggcaaaaaatacggtg	7	8	0	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr10:15858832A>G	ENST00000277632.3	-	10	1103		c.e10+1		FAM188A_ENST00000378036.1_Splice_Site|FAM188A_ENST00000477891.1_Splice_Site	NM_024948.2	NP_079224.1	Q9H8M7	F188A_HUMAN	family with sequence similarity 188, member A						apoptotic process (GO:0006915)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	22						CTATAAGCATACCTTGGCAAA	0.353																																					.	Pancreas(159;946 1953 2111 4475 22008)	Atlas-SNP	.											.	FAM188A	44	.	0			c.882+2T>C						.						65	66	66					10																	15858832		2203	4300	6503	SO:0001630	splice_region_variant	80013	exon11			AAGCATACCTTGG	AK023459	CCDS7110.1	10p13	2009-07-14	2009-07-14	2009-07-14	ENSG00000148481	ENSG00000148481			23578	protein-coding gene	gene with protein product	"caspase recruitment domain containing pro-apoptotic protein", "CARD-containing protein"	611649	"chromosome 10 open reading frame 97"	C10orf97		12054670, 17652099	Standard	XM_005252600		Approved	FLJ13397, CARP, my042, DERP5	uc001iod.1	Q9H8M7	OTTHUMG00000017734	ENST00000277632.3:c.882+1T>C	chr10.hg19:g.15858832A>G		87.0	0.0		162.0	57.0	NM_024948	Q5SZ68|Q5SZ69|Q5SZ70|Q6IA40|Q6P7P0|Q7Z2S1|Q8WUF1|Q9H3I4	Splice_Site	SNP	ENST00000277632.3	hg19	CCDS7110.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.452530	0.63290	.	.	ENSG00000148481	ENST00000277632;ENST00000418767;ENST00000436829	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4223	0.67193	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAM188A	15898838	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.467000	0.73547	2.100000	0.63781	0.533000	0.62120	.	.	.		0.353	FAM188A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046990.2	NM_024948	Intron	G	15858832	A	G	15858832	5	3	34	1	0	0	0	0	0	0	1	0	5519	405	14	2	477	2	FAM188A	10	15858832	Splice_Site	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	8084982	15858832	119675915	67	4101										
VIM	7431	hgsc.bcm.edu	37	chr10	17277290	17277291	+	Frame_Shift_Ins	INS	-	-	C													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	atatgaaggaggaaatggctINScgtcaccttcgtgaatacca					rs201530534		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr10:17277290_17277291insC	ENST00000224237.5	+	6	1276_1277	c.1131_1132insC	c.(1132-1134)cgtfs	p.R378fs	VIM_ENST00000544301.1_Frame_Shift_Ins_p.R378fs|RP11-124N14.3_ENST00000456355.1_RNA			P08670	VIME_HUMAN	vimentin	378	Coil 2.|Rod.				apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)	p.A377A(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						AGGAAATGGCTCGTCACCTTCG	0.49																																					p.A377fs		Atlas-INDEL	.											VIM,NS,carcinoma,0,1	VIM	71	.	1	Substitution - coding silent(1)	endometrium(1)	c.1131_1132insC						.																																			SO:0001589	frameshift_variant	7431	exon7			.	M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.1132dupC	chr10.hg19:g.17277291_17277291dupC	ENSP00000224237:p.Arg378fs	63.0	0.0		127.0	10.0	NM_003380	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Frame_Shift_Ins	INS	ENST00000224237.5	hg19	CCDS7120.1																																																																																			.	.		0.49	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		C	17277291	-	C	17277290	7	5	34	1	0	1	1	0	0	0	0	0	17181	1538	54	0	1153	0	VIM	10	17277290	Frame_Shift_Ins	INS	-	TCGA-BC-A10U-01A-11D-A12Z-10	1418458	17277290	118257457	68	4102										
BMI1	648	hgsc.bcm.edu	37	chr10	22618024	22618024	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ttaaaggattattatacactAatggatattgcctacattta	5	5	0	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr10:22618024A>G	ENST00000376663.3	+	9	1123	c.618A>G	c.(616-618)ctA>ctG	p.L206L	COMMD3-BMI1_ENST00000602390.1_Silent_p.L349L	NM_005180.8	NP_005171.4	P35226	BMI1_HUMAN	BMI1 proto-oncogene, polycomb ring finger	206	Interaction with E4F1.				chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|regulation of gene expression (GO:0010468)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|ubiquitin ligase complex (GO:0000151)	RING-like zinc finger domain binding (GO:0071535)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|urinary_tract(1)	12						ATTATACACTAATGGATATTG	0.264																																					p.L349L		Atlas-SNP	.											.	.	.	.	0			c.A1047G						.						112	133	126					10																	22618024		2198	4284	6482	SO:0001819	synonymous_variant	0	exon13			TACACTAATGGAT	BC011652	CCDS7138.1	10p13	2014-06-26	2014-06-26	2006-04-26	ENSG00000168283	ENSG00000168283		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	1066	protein-coding gene	gene with protein product		164831	"polycomb group ring finger 4", "B lymphoma Mo-MLV insertion region 1 homolog (mouse)"	PCGF4		8268912	Standard	NM_005180		Approved	RNF51		P35226	OTTHUMG00000017807	ENST00000376663.3:c.618A>G	chr10.hg19:g.22618024A>G		115.0	0.0		172.0	56.0	NM_001204062	Q16030|Q5T8Z3|Q96F37	Silent	SNP	ENST00000376663.3	hg19	CCDS7138.1																																																																																			.	.		0.264	BMI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047176.1	NM_005180		G	22618024	A	G	22618024	2	3	34	1	0	0	0	0	0	0	0	1	1455	349	13	2		2	BMI1	10	22618024	Silent	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	5340734	22618024	112916723	69	4103										
CHAT	1103	hgsc.bcm.edu	37	chr10	50827803	50827803	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ctgcccgtgcccccgctgcaGcagaccctggccacgtacct	10	20	0	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr10:50827803G>C	ENST00000337653.2	+	3	573	c.420G>C	c.(418-420)caG>caC	p.Q140H	CHAT_ENST00000339797.1_Missense_Mutation_p.Q22H|CHAT_ENST00000455728.2_Missense_Mutation_p.Q22H|CHAT_ENST00000395559.2_Missense_Mutation_p.Q22H|CHAT_ENST00000351556.3_Missense_Mutation_p.Q22H|CHAT_ENST00000395562.2_Missense_Mutation_p.Q58H|CHAT_ENST00000460699.1_3'UTR	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	140					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	CCCCGCTGCAGCAGACCCTGG	0.612																																					p.Q140H		Atlas-SNP	.											.	CHAT	162	.	0			c.G420C						.						53	43	47					10																	50827803		2203	4300	6503	SO:0001583	missense	1103	exon3			GCTGCAGCAGACC	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.420G>C	chr10.hg19:g.50827803G>C	ENSP00000337103:p.Gln140His	27.0	0.0		31.0	13.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	hg19	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	G	8.314	0.822684	0.16678	.	.	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	T;T;T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47;-1.47;-1.47	5.09	3.08	0.35506	.	0.254877	0.38897	N	0.001523	T	0.73289	0.3568	L	0.60957	1.885	0.26170	N	0.979882	B;P	0.39920	0.091;0.695	B;B	0.36092	0.074;0.217	T	0.66783	-0.5836	10	0.72032	D	0.01	-5.7437	7.6624	0.28410	0.3642:0.0:0.6358:0.0	.	22;140	F8W8I2;P28329	.;CLAT_HUMAN	H	22;22;22;140;58;22	ENSP00000343486:Q22H;ENSP00000345878:Q22H;ENSP00000378926:Q22H;ENSP00000337103:Q140H;ENSP00000378929:Q58H;ENSP00000390521:Q22H	ENSP00000337103:Q140H	Q	+	3	2	CHAT	50497809	0.996000	0.38824	0.998000	0.56505	0.028000	0.11728	0.356000	0.20181	0.475000	0.27415	0.462000	0.41574	CAG	.	.		0.612	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		C	50827803	G	C	50827803	3	2	34	1	0	0	0	0	1	0	0	0	3315	962	34	4	474	4	CHAT	10	50827803	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	28209779	50827803	84706944	70	4104										
ALDH18A1	5832	hgsc.bcm.edu	37	chr10	97402774	97402774	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	caacaatagatgccaagcgcCccagggccaggccacattca	9	15	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr10:97402774C>T	ENST00000371224.2	-	3	415	c.278G>A	c.(277-279)gGg>gAg	p.G93E	ALDH18A1_ENST00000371221.3_Missense_Mutation_p.G93E|ALDH18A1_ENST00000483788.1_5'UTR	NM_002860.3	NP_002851.2	P54886	P5CS_HUMAN	aldehyde dehydrogenase 18 family, member A1	93	Glutamate 5-kinase.				cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|glutamate metabolic process (GO:0006536)|L-proline biosynthetic process (GO:0055129)|ornithine biosynthetic process (GO:0006592)|proline biosynthetic process (GO:0006561)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glutamate 5-kinase activity (GO:0004349)|glutamate-5-semialdehyde dehydrogenase activity (GO:0004350)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(9)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)		TGCCAAGCGCCCCAGGGCCAG	0.507																																					p.G93E		Atlas-SNP	.											.	ALDH18A1	63	.	0			c.G278A						.						74	57	63					10																	97402774		2203	4300	6503	SO:0001583	missense	5832	exon3			AAGCGCCCCAGGG	X94453	CCDS7443.1, CCDS31257.1	10q24.3-q24.6	2004-08-12	2004-08-12	2004-08-12	ENSG00000059573	ENSG00000059573		"Aldehyde dehydrogenases"	9722	protein-coding gene	gene with protein product		138250	"pyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase)"	GSAS, PYCS		8921385	Standard	XM_006717933		Approved	P5CS	uc001kkz.3	P54886	OTTHUMG00000018815	ENST00000371224.2:c.278G>A	chr10.hg19:g.97402774C>T	ENSP00000360268:p.Gly93Glu	41.0	0.0		73.0	32.0	NM_001017423	B2R5Q4|B7Z350|B7Z5X8|B7ZLP1|D3DR44|O95952|Q3KQU2|Q5T566|Q5T567|Q9UM72	Missense_Mutation	SNP	ENST00000371224.2	hg19	CCDS7443.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.853867	0.71719	.	.	ENSG00000059573	ENST00000371224;ENST00000371221	T;T	0.70516	-0.49;-0.49	5.45	4.53	0.55603	Aspartate/glutamate/uridylate kinase (3);	0.049282	0.85682	D	0.000000	T	0.78181	0.4243	L	0.41027	1.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80600	-0.1310	10	0.87932	D	0	-17.4333	14.3078	0.66395	0.0:0.8501:0.1499:0.0	.	93;93	P54886;P54886-2	P5CS_HUMAN;.	E	93	ENSP00000360268:G93E;ENSP00000360265:G93E	ENSP00000360265:G93E	G	-	2	0	ALDH18A1	97392764	1.000000	0.71417	0.998000	0.56505	0.624000	0.37722	7.330000	0.79181	1.406000	0.46857	-0.176000	0.13171	GGG	.	.		0.507	ALDH18A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049552.1	NM_002860		T	97402774	C	T	97402774	3	4	34	1	0	0	0	0	1	0	0	0	489	623	22	3	2173	3	ALDH18A1	10	97402774	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	46574971	97402774	38131973	71	4105										
FAM160B1	57700	hgsc.bcm.edu	37	chr10	116595358	116595359	+	Frame_Shift_Ins	INS	-	-	C													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	aacttctgggaagaatccggINScagccactacttccacacat					rs202149779	byFrequency	TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr10:116595358_116595359insC	ENST00000369248.4	+	4	692_693	c.357_358insC	c.(358-360)cagfs	p.Q120fs	FAM160B1_ENST00000369250.3_Frame_Shift_Ins_p.Q120fs	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	120				Q -> R (in Ref. 1; CAI45992). {ECO:0000305}.						NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						GAAGAATCCGGCAGCCACTACT	0.406																																					p.R119fs		Atlas-INDEL	.											.	FAM160B1	107	.	0			c.357_358insC						.																																			SO:0001589	frameshift_variant	57700	exon4			.	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"KIAA1600"	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.358dupC	chr10.hg19:g.116595359_116595359dupC	ENSP00000358251:p.Gln120fs	53.0	0.0		91.0	10.0	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Frame_Shift_Ins	INS	ENST00000369248.4	hg19	CCDS31290.1																																																																																			.	.		0.406	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351		C	116595359	-	C	116595358	7	5	34	1	0	1	1	0	0	0	0	0	5475	1190	42	0	371	0	FAM160B1	10	116595358	Frame_Shift_Ins	INS	-	TCGA-BC-A10U-01A-11D-A12Z-10	19192584	116595358	18939389	72	4106										
FANK1	92565	hgsc.bcm.edu	37	chr10	127684064	127684064	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gctggtccgaatacttcaagGagggtgagagaactctgtca	13	8	3	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr10:127684064G>C	ENST00000368693.1	+	4	499	c.395G>C	c.(394-396)gGa>gCa	p.G132A	FANK1_ENST00000368695.1_Missense_Mutation_p.G126A|FANK1_ENST00000368689.1_Missense_Mutation_p.G132A			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	132						cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				ATACTTCAAGGAGGGTGAGAG	0.428																																					p.G132A		Atlas-SNP	.											.	FANK1	46	.	0			c.G395C						.						168	152	157					10																	127684064		2203	4300	6503	SO:0001583	missense	92565	exon4			TTCAAGGAGGGTG	BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	23527	protein-coding gene	gene with protein product		611640	"fibronectin type 3 and ankyrin repeat domains 1"			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.395G>C	chr10.hg19:g.127684064G>C	ENSP00000357682:p.Gly132Ala	254.0	0.0		521.0	210.0	NM_145235	Q6UXY9|Q6X7T6	Missense_Mutation	SNP	ENST00000368693.1	hg19	CCDS31309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.21|11.21	1.570538|1.570538	0.28003|0.28003	.|.	.|.	ENSG00000203780|ENSG00000203780	ENST00000456942|ENST00000368695;ENST00000368693;ENST00000445510;ENST00000368691;ENST00000368689;ENST00000368692	.|T;T;T;T;T	.|0.61859	.|0.07;0.07;1.6;0.07;1.6	4.21|4.21	3.29|3.29	0.37713|0.37713	.|Ankyrin repeat-containing domain (4);	.|0.411523	.|0.21885	.|N	.|0.067666	T|T	0.36635|0.36635	0.0974|0.0974	N|N	0.00894|0.00894	-1.105|-1.105	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.67145	.|0.996;0.99;0.978	.|P;P;P	.|0.61940	.|0.896;0.861;0.622	T|T	0.41161|0.41161	-0.9524|-0.9524	5|10	.|0.02654	.|T	.|1	-16.2468|-16.2468	10.2657|10.2657	0.43453|0.43453	0.0:0.2005:0.7995:0.0|0.0:0.2005:0.7995:0.0	.|.	.|158;132;132	.|Q8TC84-3;Q8TC84-2;Q8TC84	.|.;.;FANK1_HUMAN	Q|A	27|126;132;132;132;132;158	.|ENSP00000357684:G126A;ENSP00000357682:G132A;ENSP00000415719:G132A;ENSP00000357680:G132A;ENSP00000357678:G132A	.|ENSP00000357678:G132A	E|G	+|+	1|2	0|0	FANK1|FANK1	127674054|127674054	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.993000|0.993000	0.82548|0.82548	2.833000|2.833000	0.48159|0.48159	1.099000|1.099000	0.41499|0.41499	0.557000|0.557000	0.71058|0.71058	GAG|GGA	.	.		0.428	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145235		C	127684064	G	C	127684064	3	2	34	1	0	0	0	0	1	0	0	0	5680	1174	41	4	409	4	FANK1	10	127684064	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	11088706	127684064	7850683	73	4107										
C10orf90	118611	hgsc.bcm.edu	37	chr10	128193357	128193357	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggccgtgatggtgatggatgCaaaccctctgcgggggcccc	16	12	1	2	rs199676174		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr10:128193357C>A	ENST00000284694.7	-	3	532	c.412G>T	c.(412-414)Gca>Tca	p.A138S	C10orf90_ENST00000356858.3_Missense_Mutation_p.A91S|C10orf90_ENST00000392694.1_Missense_Mutation_p.A91S|C10orf90_ENST00000544758.1_Missense_Mutation_p.A235S|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000454341.1_Missense_Mutation_p.A138S	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	138	Required for interaction with HDAC1. {ECO:0000250}.				mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		GTGATGGATGCAAACCCTCTG	0.677											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A138S		Atlas-SNP	.											.	C10orf90	121	.	0			c.G412T						.						28	34	32					10																	128193357		2191	4290	6481	SO:0001583	missense	118611	exon3			TGGATGCAAACCC	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.412G>T	chr10.hg19:g.128193357C>A	ENSP00000284694:p.Ala138Ser	36.0	0.0	1563	55.0	21.0	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	hg19	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	C	13.36	2.214460	0.39102	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.25579	2.17;2.15;2.16;2.17;1.79	4.97	1.66	0.24008	.	0.382729	0.22732	N	0.056306	T	0.26048	0.0635	L	0.38175	1.15	0.09310	N	1	P;B;B;B;B	0.36683	0.565;0.364;0.353;0.065;0.312	P;B;B;B;B	0.44990	0.466;0.121;0.181;0.041;0.332	T	0.16424	-1.0403	10	0.27082	T	0.32	-11.7681	13.1454	0.59459	0.5211:0.4789:0.0:0.0	.	235;235;91;138;138	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	S	91;138;138;235;138;91;91	ENSP00000284694:A138S;ENSP00000398786:A138S;ENSP00000444369:A235S;ENSP00000405995:A138S;ENSP00000376459:A91S	ENSP00000284694:A138S	A	-	1	0	C10orf90	128183347	0.323000	0.24643	0.013000	0.15412	0.620000	0.37586	0.007000	0.13174	0.609000	0.30018	0.561000	0.74099	GCA	.	C|1.000;G|0.000		0.677	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		A	128193357	C	A	128193357	3	1	34	1	0	0	0	0	1	0	0	0	1625	710	25	3	1715	3	C10orf90	10	128193357	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	509293	128193357	7341390	74	4108										
KNDC1	85442	hgsc.bcm.edu	37	chr10	134981785	134981785	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tgagggtgccttcgttccccCcgagttcgacgtgaccggga	14	13	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr10:134981785C>A	ENST00000304613.3	+	3	350	c.329C>A	c.(328-330)cCc>cAc	p.P110H	KNDC1_ENST00000368571.2_Missense_Mutation_p.P45H|KNDC1_ENST00000368572.2_Missense_Mutation_p.P110H|KNDC1_ENST00000530127.1_3'UTR			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	110	KIND 1. {ECO:0000255|PROSITE- ProRule:PRU00709}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TTCGTTCCCCCCGAGTTCGAC	0.577																																					p.P110H		Atlas-SNP	.											.	KNDC1	155	.	0			c.C329A						.						119	114	116					10																	134981785		2203	4300	6503	SO:0001583	missense	85442	exon3			TTCCCCCCGAGTT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.329C>A	chr10.hg19:g.134981785C>A	ENSP00000304437:p.Pro110His	27.0	0.0		43.0	13.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.775382	0.49786	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	D;D;T	0.91945	-2.94;-2.94;-0.59	4.14	4.14	0.48551	KIND (2);	0.000000	0.64402	D	0.000008	D	0.95589	0.8566	M	0.78049	2.395	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.96124	0.9087	10	0.87932	D	0	-17.5516	14.3225	0.66496	0.0:1.0:0.0:0.0	.	45;110	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	H	110;110;45	ENSP00000304437:P110H;ENSP00000357561:P110H;ENSP00000357560:P45H	ENSP00000304437:P110H	P	+	2	0	KNDC1	134831775	1.000000	0.71417	0.993000	0.49108	0.027000	0.11550	6.552000	0.73914	2.052000	0.61016	0.485000	0.47835	CCC	.	.		0.577	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	134981785	C	A	134981785	3	1	34	1	0	0	0	0	1	0	0	0	8435	623	22	3	339	3	KNDC1	10	134981785	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	6788428	134981785	552962	75	4109										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1280240	1280240	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ctctctggggacacccaggaCccaacggtgcaatgtcagga	12	13	2	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:1280240C>A	ENST00000529681.1	+	44	16720	c.16662C>A	c.(16660-16662)gaC>gaA	p.D5554E	MUC5B_ENST00000447027.1_Missense_Mutation_p.D5557E	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5554	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACACCCAGGACCCAACGGTGC	0.652																																					p.D5554E		Atlas-SNP	.											.	MUC5B	473	.	0			c.C16662A						.						42	50	48					11																	1280240		1953	4100	6053	SO:0001583	missense	727897	exon44			CCAGGACCCAACG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16662C>A	chr11.hg19:g.1280240C>A	ENSP00000436812:p.Asp5554Glu	25.0	0.0		30.0	10.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	11.96	1.794947	0.31777	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844;ENST00000526859	T;T	0.15603	2.41;2.6	4.8	-4.99	0.03010	.	.	.	.	.	T	0.07143	0.0181	N	0.11560	0.145	0.09310	N	1	B;B	0.25563	0.049;0.129	B;B	0.26517	0.07;0.07	T	0.34378	-0.9831	9	0.87932	D	0	.	3.0599	0.06196	0.1821:0.2209:0.4387:0.1583	.	5891;5557	A7Y9J9;E9PBJ0	.;.	E	5554;5557;5498;453;5266;99	ENSP00000436812:D5554E;ENSP00000415793:D5557E	ENSP00000343037:D5498E	D	+	3	2	MUC5B	1236816	0.000000	0.05858	0.000000	0.03702	0.270000	0.26580	-2.809000	0.00756	-1.355000	0.02186	-0.254000	0.11334	GAC	.	.		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1280240	C	A	1280240	3	1	34	1	0	0	0	0	1	0	0	0	9988	506	18	3	16845	3	MUC5B	11	1280240	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10		1280240	133726276	76	4110										
OR51L1	119682	hgsc.bcm.edu	37	chr11	5020988	5020988	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cttctttgtgccagttattgGggtgtcaatggtccatcgct	11	9	2	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:5020988G>A	ENST00000321543.1	+	1	776	c.776G>A	c.(775-777)gGg>gAg	p.G259E		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CCAGTTATTGGGGTGTCAATG	0.473																																					p.G259E		Atlas-SNP	.											.	OR51L1	60	.	0			c.G776A						.						211	183	192					11																	5020988		2201	4298	6499	SO:0001583	missense	119682	exon1			TTATTGGGGTGTC	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"GPCR / Class A : Olfactory receptors"	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.776G>A	chr11.hg19:g.5020988G>A	ENSP00000322156:p.Gly259Glu	162.0	0.0		361.0	162.0	NM_001004755	Q6IFE5	Missense_Mutation	SNP	ENST00000321543.1	hg19	CCDS31369.1	.	.	.	.	.	.	.	.	.	.	G	18.66	3.672481	0.67928	.	.	ENSG00000176798	ENST00000321543	T	0.00115	8.71	5.43	5.43	0.79202	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43260	D	0.000588	T	0.00580	0.0019	M	0.91872	3.25	0.26485	N	0.975031	D	0.89917	1.0	D	0.97110	1.0	T	0.33033	-0.9884	10	0.87932	D	0	.	11.6263	0.51147	0.0:0.0:0.8229:0.1771	.	259	Q8NGJ5	O51L1_HUMAN	E	259	ENSP00000322156:G259E	ENSP00000322156:G259E	G	+	2	0	OR51L1	4977564	0.003000	0.15002	1.000000	0.80357	0.981000	0.71138	0.388000	0.20735	2.822000	0.97130	0.650000	0.86243	GGG	.	.		0.473	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755		A	5020988	G	A	5020988	3	1	34	1	0	0	0	0	1	0	0	0	11111	1232	43	3	778	3	OR51L1	11	5020988	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	3740748	5020988	129985528	77	4111										
OR52E2	119678	hgsc.bcm.edu	37	chr11	5079905	5079905	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	acctcgtatgtattaggtacTcttccttttccattccttgt	5	11	1	0	rs547180704		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:5079905T>A	ENST00000321522.2	-	1	952	c.953A>T	c.(952-954)gAg>gTg	p.E318V		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	318						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(13)|ovary(2)|skin(3)	20		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.03e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.191)		TATTAGGTACTCTTCCTTTTC	0.338																																					p.E318V		Atlas-SNP	.											.	OR52E2	63	.	0			c.A953T						.						58	59	59					11																	5079905		2201	4298	6499	SO:0001583	missense	119678	exon1			AGGTACTCTTCCT	AB065800	CCDS31371.1	11p15.4	2012-08-09			ENSG00000176787	ENSG00000176787		"GPCR / Class A : Olfactory receptors"	14769	protein-coding gene	gene with protein product							Standard	NM_001005164		Approved		uc010qyw.2	Q8NGJ4	OTTHUMG00000066608	ENST00000321522.2:c.953A>T	chr11.hg19:g.5079905T>A	ENSP00000322088:p.Glu318Val	66.0	0.0		121.0	34.0	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	hg19	CCDS31371.1	.	.	.	.	.	.	.	.	.	.	T	4.051	0.007160	0.07866	.	.	ENSG00000176787	ENST00000321522	T	0.00004	9.81	3.56	2.48	0.30137	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.01608	-1.1313	9	0.42905	T	0.14	.	4.199	0.10457	0.0:0.3364:0.0:0.6636	.	318	Q8NGJ4	O52E2_HUMAN	V	318	ENSP00000322088:E318V	ENSP00000322088:E318V	E	-	2	0	OR52E2	5036481	0.004000	0.15560	0.001000	0.08648	0.021000	0.10359	0.903000	0.28475	0.826000	0.34661	0.477000	0.44152	GAG	.	.		0.338	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164		A	5079905	T	A	5079905	3	1	34	1	0	0	0	0	1	0	0	0	11124	1551	54	4	27	4	OR52E2	11	5079905	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	58917	5079905	129926611	78	4112										
OR52H1	390067	hgsc.bcm.edu	37	chr11	5566529	5566529	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gacaagatgaggtcagtcatGgccagcatggagagaaagaa	14	6	2	4			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:5566529G>T	ENST00000322653.4	-	1	250	c.225C>A	c.(223-225)gcC>gcA	p.A75A	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	75						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGTCAGTCATGGCCAGCATGG	0.478																																					p.A75A		Atlas-SNP	.											.	OR52H1	46	.	0			c.C225A						.						89	78	81					11																	5566529		2201	4297	6498	SO:0001819	synonymous_variant	390067	exon1			AGTCATGGCCAGC	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"GPCR / Class A : Olfactory receptors"	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.225C>A	chr11.hg19:g.5566529G>T		93.0	0.0		212.0	80.0	NM_001005289	B9EH26|Q6IF79	Silent	SNP	ENST00000322653.4	hg19	CCDS31386.1																																																																																			.	.		0.478	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289		T	5566529	G	T	5566529	2	4	34	1	0	0	0	0	0	0	0	1	11128	1335	47	3		3	OR52H1	11	5566529	Silent	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	486624	5566529	129439987	79	4113										
USP47	55031	hgsc.bcm.edu	37	chr11	11964527	11964527	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	aagggaaaaaagaaacatggGatacagcagaagaagactct	11	5	1	4			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:11964527G>T	ENST00000399455.2	+	21	3139	c.3019G>T	c.(3019-3021)Gat>Tat	p.D1007Y	USP47_ENST00000339865.5_Missense_Mutation_p.D919Y|USP47_ENST00000527733.1_Missense_Mutation_p.D987Y|USP47_ENST00000539466.1_5'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1007					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		AGAAACATGGGATACAGCAGA	0.413																																					p.D919Y		Atlas-SNP	.											.	USP47	91	.	0			c.G2755T						.						156	147	150					11																	11964527		1933	4133	6066	SO:0001583	missense	55031	exon19			ACATGGGATACAG	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.3019G>T	chr11.hg19:g.11964527G>T	ENSP00000382382:p.Asp1007Tyr	88.0	0.0		152.0	62.0	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.45|17.45	3.393869|3.393869	0.62066|0.62066	.|.	.|.	ENSG00000170242|ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455|ENST00000540365	T;T;T|.	0.05717|.	3.42;3.41;3.4|.	6.02|6.02	5.11|5.11	0.69529|0.69529	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.55721|0.55721	0.1938|0.1938	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	D;P;P|.	0.76494|.	0.999;0.799;0.873|.	D;P;P|.	0.80764|.	0.994;0.554;0.74|.	T|T	0.61681|0.61681	-0.7013|-0.7013	10|6	0.87932|0.87932	D|D	0|0	.|.	15.1392|15.1392	0.72599|0.72599	0.0684:0.0:0.9316:0.0|0.0684:0.0:0.9316:0.0	.|.	1007;987;919|.	Q96K76;E9PM46;Q96K76-2|.	UBP47_HUMAN;.;.|.	Y|V	919;987;1007|203	ENSP00000339957:D919Y;ENSP00000433146:D987Y;ENSP00000382382:D1007Y|.	ENSP00000339957:D919Y|ENSP00000445548:G203V	D|G	+|+	1|2	0|0	USP47|USP47	11921103|11921103	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.694000|0.694000	0.40290|0.40290	9.476000|9.476000	0.97823|0.97823	1.556000|1.556000	0.49512|0.49512	0.591000|0.591000	0.81541|0.81541	GAT|GGA	.	.		0.413	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		T	11964527	G	T	11964527	3	4	34	1	0	0	0	0	1	0	0	0	17093	1174	41	3	2829	3	USP47	11	11964527	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	6397998	11964527	123041989	80	4114										
F2	2147	hgsc.bcm.edu	37	chr11	46747715	46747715	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ctttgggtactgcgacctcaActattgtggtgagctgcctg	12	10	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:46747715A>G	ENST00000311907.5	+	7	922	c.866A>G	c.(865-867)aAc>aGc	p.N289S	F2_ENST00000530231.1_Missense_Mutation_p.N289S	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	289	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell surface receptor signaling pathway (GO:0007166)|cellular protein metabolic process (GO:0044267)|cytosolic calcium ion homeostasis (GO:0051480)|fibrinolysis (GO:0042730)|leukocyte migration (GO:0050900)|multicellular organismal development (GO:0007275)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|negative regulation of proteolysis (GO:0045861)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900738)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of blood coagulation (GO:0030193)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|thrombospondin receptor activity (GO:0070053)			endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	27		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|ART-123(DB05777)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Dabigatran etexilate(DB06695)|Drotrecogin alfa(DB00055)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Suramin(DB04786)|Ximelagatran(DB04898)	TGCGACCTCAACTATTGTGGT	0.577																																					p.N289S	Esophageal Squamous(147;1147 1808 2148 38609 51144)	Atlas-SNP	.											.	F2	75	.	0			c.A866G						.						52	61	58					11																	46747715		2201	4299	6500	SO:0001583	missense	2147	exon7			ACCTCAACTATTG	M33031	CCDS31476.1	11p11.2	2013-02-28			ENSG00000180210	ENSG00000180210	3.4.21.5	"Endogenous ligands"	3535	protein-coding gene	gene with protein product	"prepro-coagulation factor II"	176930					Standard	NM_000506		Approved		uc001ndf.4	P00734	OTTHUMG00000150344	ENST00000311907.5:c.866A>G	chr11.hg19:g.46747715A>G	ENSP00000308541:p.Asn289Ser	24.0	0.0		27.0	12.0	NM_000506	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Missense_Mutation	SNP	ENST00000311907.5	hg19	CCDS31476.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.069530	0.36470	.	.	ENSG00000180210	ENST00000311907;ENST00000530231;ENST00000442468	T;T;T	0.79940	-1.32;-1.32;-1.32	5.27	2.58	0.30949	Kringle (4);Kringle-like fold (1);	0.736545	0.14306	N	0.327987	T	0.68339	0.2990	N	0.20685	0.6	0.27658	N	0.947178	B	0.29862	0.259	B	0.34590	0.186	T	0.64892	-0.6300	10	0.87932	D	0	.	8.2886	0.31943	0.7341:0.1358:0.0:0.1302	.	289	P00734	THRB_HUMAN	S	289;289;279	ENSP00000308541:N289S;ENSP00000433907:N289S;ENSP00000387413:N279S	ENSP00000308541:N289S	N	+	2	0	F2	46704291	0.694000	0.27738	0.985000	0.45067	0.667000	0.39255	2.536000	0.45693	1.985000	0.57927	0.460000	0.39030	AAC	.	.		0.577	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1			G	46747715	A	G	46747715	3	3	34	1	0	0	0	0	1	0	0	0	5344	43	2	2	892	2	F2	11	46747715	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	34783188	46747715	88258801	81	4115										
SLC22A8	9376	hgsc.bcm.edu	37	chr11	62761284	62761284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cacttgtgtagaggaagaggCagctgaaggagctggatagg	17	5	0	3			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:62761284C>T	ENST00000336232.2	-	9	1418	c.1283G>A	c.(1282-1284)tGc>tAc	p.C428Y	SLC22A8_ENST00000545207.1_Missense_Mutation_p.C337Y|SLC22A8_ENST00000311438.8_Missense_Mutation_p.C428Y|SLC22A8_ENST00000535878.1_Missense_Mutation_p.C305Y|SLC22A8_ENST00000542795.1_5'Flank|SLC22A8_ENST00000430500.2_Missense_Mutation_p.C428Y	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8	428					glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GAGGAAGAGGCAGCTGAAGGA	0.562																																					p.C428Y		Atlas-SNP	.											.	SLC22A8	60	.	0			c.G1283A						.						103	92	96					11																	62761284		2201	4298	6499	SO:0001583	missense	9376	exon9			AAGAGGCAGCTGA	AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"Solute carriers"	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.1283G>A	chr11.hg19:g.62761284C>T	ENSP00000337335:p.Cys428Tyr	89.0	0.0		145.0	68.0	NM_001184732	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Missense_Mutation	SNP	ENST00000336232.2	hg19	CCDS8042.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.881186	0.72294	.	.	ENSG00000149452	ENST00000336232;ENST00000540631;ENST00000545207;ENST00000535878;ENST00000311438;ENST00000430500	T;T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91;-0.91	5.89	5.89	0.94794	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.89315	0.6680	M	0.91768	3.24	0.42859	D	0.994103	D;D	0.89917	1.0;1.0	D;D	0.81914	0.994;0.995	D	0.91167	0.4965	10	0.87932	D	0	.	17.7556	0.88447	0.0:1.0:0.0:0.0	.	428;428	Q8TCC7-2;Q8TCC7	.;S22A8_HUMAN	Y	428;414;337;305;428;428	ENSP00000337335:C428Y;ENSP00000441658:C337Y;ENSP00000443368:C305Y;ENSP00000311463:C428Y;ENSP00000398548:C428Y	ENSP00000311463:C428Y	C	-	2	0	SLC22A8	62517860	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.683000	0.46943	2.793000	0.96121	0.655000	0.94253	TGC	.	.		0.562	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254		T	62761284	C	T	62761284	3	4	34	1	0	0	0	0	1	0	0	0	14475	710	25	3	357	3	SLC22A8	11	62761284	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	16013569	62761284	72245232	82	4116										
MACROD1	28992	hgsc.bcm.edu	37	chr11	63918758	63918758	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gcttggtgatgtcgctgcggAgcagggagattttctcattg	15	7	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:63918758A>G	ENST00000255681.6	-	3	536	c.470T>C	c.(469-471)cTc>cCc	p.L157P	MACROD1_ENST00000538595.1_5'UTR	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1	157	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						GTCGCTGCGGAGCAGGGAGAT	0.602																																					p.L157P		Atlas-SNP	.											.	MACROD1	17	.	0			c.T470C						.						181	148	159					11																	63918758		2201	4297	6498	SO:0001583	missense	28992	exon3			CTGCGGAGCAGGG	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.470T>C	chr11.hg19:g.63918758A>G	ENSP00000255681:p.Leu157Pro	63.0	0.0		116.0	44.0	NM_014067	Q9UH96	Missense_Mutation	SNP	ENST00000255681.6	hg19	CCDS8056.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.594495	0.46214	.	.	ENSG00000133315	ENST00000255681	T	0.23348	1.91	3.86	2.69	0.31865	Appr-1-p processing (2);	0.361143	0.27754	N	0.017981	T	0.28863	0.0716	L	0.58810	1.83	0.43874	D	0.996487	P	0.36990	0.577	B	0.42343	0.384	T	0.04537	-1.0944	10	0.72032	D	0.01	-5.7312	8.94	0.35725	0.8338:0.0:0.0:0.1662	.	157	Q9BQ69	MACD1_HUMAN	P	157	ENSP00000255681:L157P	ENSP00000255681:L157P	L	-	2	0	MACROD1	63675334	1.000000	0.71417	0.974000	0.42286	0.615000	0.37417	3.573000	0.53856	0.456000	0.26937	0.379000	0.24179	CTC	.	.		0.602	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		G	63918758	A	G	63918758	3	3	34	1	0	0	0	0	1	0	0	0	9154	304	11	2	539	2	MACROD1	11	63918758	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	1157474	63918758	71087758	83	4117										
GAL3ST3	89792	hgsc.bcm.edu	37	chr11	65810799	65810799	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gtagtagctgaagagcgactCgaacatggcggccggctcgc	15	11	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:65810799C>A	ENST00000312006.4	-	3	756	c.475G>T	c.(475-477)Gag>Tag	p.E159*	GAL3ST3_ENST00000527878.1_Nonsense_Mutation_p.E159*	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	159					monosaccharide metabolic process (GO:0005996)|oligosaccharide metabolic process (GO:0009311)|poly-N-acetyllactosamine metabolic process (GO:0030309)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|carbohydrate binding (GO:0030246)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			kidney(1)|lung(9)|ovary(2)|skin(2)	14						AAGAGCGACTCGAACATGGCG	0.682																																					p.E159X		Atlas-SNP	.											.	GAL3ST3	40	.	0			c.G475T						.						32	34	34					11																	65810799		2199	4293	6492	SO:0001587	stop_gained	89792	exon3			GCGACTCGAACAT	AY026481	CCDS8128.1	11q13.1	2014-08-12			ENSG00000175229	ENSG00000175229		"Sulfotransferases, membrane-bound"	24144	protein-coding gene	gene with protein product		608234				11323440, 11356829	Standard	NM_033036		Approved	GAL3ST2	uc001ogw.3	Q96A11	OTTHUMG00000166667	ENST00000312006.4:c.475G>T	chr11.hg19:g.65810799C>A	ENSP00000308591:p.Glu159*	43.0	0.0		34.0	9.0	NM_033036	Q14D05	Nonsense_Mutation	SNP	ENST00000312006.4	hg19	CCDS8128.1	.	.	.	.	.	.	.	.	.	.	C	35	5.586885	0.96578	.	.	ENSG00000175229	ENST00000312006;ENST00000527878	.	.	.	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-21.8951	15.4161	0.74970	0.0:1.0:0.0:0.0	.	.	.	.	X	159	.	ENSP00000308591:E159X	E	-	1	0	GAL3ST3	65567375	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.758000	0.85224	2.304000	0.77564	0.561000	0.74099	GAG	.	.		0.682	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391052.1	NM_033036		A	65810799	C	A	65810799	4	1	34	1	0	0	0	0	0	1	0	0	6207	893	31	1	824	1	GAL3ST3	11	65810799	Nonsense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	1892041	65810799	69195717	84	4118										
NPAS4	266743	hgsc.bcm.edu	37	chr11	66191452	66191452	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cagcactaacccactcttcaCcgcagcactgggggctccca	8	18	2	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:66191452C>T	ENST00000311034.2	+	7	1267	c.1091C>T	c.(1090-1092)aCc>aTc	p.T364I		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	364					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						CCACTCTTCACCGCAGCACTG	0.567																																					p.T364I		Atlas-SNP	.											.	NPAS4	133	.	0			c.C1091T						.						142	148	146					11																	66191452		2200	4295	6495	SO:0001583	missense	266743	exon7			TCTTCACCGCAGC	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"Basic helix-loop-helix proteins"	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.1091C>T	chr11.hg19:g.66191452C>T	ENSP00000311196:p.Thr364Ile	35.0	0.0		58.0	24.0	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	hg19	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.691579	0.30052	.	.	ENSG00000174576	ENST00000311034	T	0.48836	0.8	4.45	3.53	0.40419	.	0.393717	0.21716	N	0.070200	T	0.35998	0.0951	L	0.29908	0.895	0.46061	D	0.998845	B	0.15141	0.012	B	0.13407	0.009	T	0.21449	-1.0245	10	0.62326	D	0.03	-1.4082	11.4897	0.50373	0.1812:0.8188:0.0:0.0	.	364	Q8IUM7	NPAS4_HUMAN	I	364	ENSP00000311196:T364I	ENSP00000311196:T364I	T	+	2	0	NPAS4	65948028	0.404000	0.25328	0.607000	0.28956	0.844000	0.47949	1.186000	0.32078	1.080000	0.41073	0.563000	0.77884	ACC	.	.		0.567	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		T	66191452	C	T	66191452	3	4	34	1	0	0	0	0	1	0	0	0	10574	507	18	3	1117	3	NPAS4	11	66191452	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	380653	66191452	68815064	85	4119										
SYT12	91683	hgsc.bcm.edu	37	chr11	66807406	66807406	+	Frame_Shift_Del	DEL	G	G	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gcctctggagctgatgggccGggagttggacctggccccct							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:66807406delG	ENST00000393946.2	+	7	1515	c.353delG	c.(352-354)cggfs	p.R118fs	SYT12_ENST00000527043.1_Frame_Shift_Del_p.R118fs|SYT12_ENST00000526281.1_3'UTR|SYT12_ENST00000525457.1_Frame_Shift_Del_p.R118fs			Q8IV01	SYT12_HUMAN	synaptotagmin XII	118						cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|synapse (GO:0045202)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	20						CTGATGGGCCGGGAGTTGGAC	0.637																																					p.R118fs	Ovarian(65;2862 3307)	Atlas-INDEL	.											SYT12,NS,carcinoma,0,1	SYT12	60	.	0			c.352delC						.						67	71	70					11																	66807406		2200	4295	6495	SO:0001589	frameshift_variant	91683	exon4			.	AK024280	CCDS8154.1	11q13.2	2014-07-02			ENSG00000173227	ENSG00000173227		"Synaptotagmins"	18381	protein-coding gene	gene with protein product		606436				8987811	Standard	NM_177963		Approved	SRG1	uc001oju.3	Q8IV01	OTTHUMG00000167101	ENST00000393946.2:c.353delG	chr11.hg19:g.66807406delG	ENSP00000377520:p.Arg118fs	46.0	0.0		66.0	21.0	NM_177963		Frame_Shift_Del	DEL	ENST00000393946.2	hg19	CCDS8154.1																																																																																			.	.		0.637	SYT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393129.1	NM_177963		-	66807406	G	-	66807406	7	5	34	1	0	1	0	1	0	0	0	0	15483	1116	39	0	363	0	SYT12	11	66807406	Frame_Shift_Del	DEL	G	TCGA-BC-A10U-01A-11D-A12Z-10	615954	66807406	68199110	86	4120	16	3								
SYT12	91683	hgsc.bcm.edu	37	chr11	66807407	66807409	+	In_Frame_Del	DEL	GGA	GGA	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cctctggagctgatgggccgGgagttggacctggcccccta					rs572041584|rs556621897		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:66807407_66807409delGGA	ENST00000393946.2	+	7	1516_1518	c.354_356delGGA	c.(352-357)cgggag>cgg	p.E119del	SYT12_ENST00000527043.1_In_Frame_Del_p.E119del|SYT12_ENST00000526281.1_3'UTR|SYT12_ENST00000525457.1_In_Frame_Del_p.E119del			Q8IV01	SYT12_HUMAN	synaptotagmin XII	119						cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|synapse (GO:0045202)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	20						TGATGGGCCGGGAGTTGGACCTG	0.631																																					p.118_119del	Ovarian(65;2862 3307)	Pindel	.											.	SYT12	60	.	0			c.353_355del						.																																			SO:0001651	inframe_deletion	91683	exon4			.	AK024280	CCDS8154.1	11q13.2	2014-07-02			ENSG00000173227	ENSG00000173227		"Synaptotagmins"	18381	protein-coding gene	gene with protein product		606436				8987811	Standard	NM_177963		Approved	SRG1	uc001oju.3	Q8IV01	OTTHUMG00000167101	ENST00000393946.2:c.354_356delGGA	chr11.hg19:g.66807407_66807409delGGA	ENSP00000377520:p.Glu119del	47.0	0.0		70.0	20.0	NM_177963		In_Frame_Del	DEL	ENST00000393946.2	hg19	CCDS8154.1																																																																																			.	.		0.631	SYT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393129.1	NM_177963		-	66807409	GGA	-	66807407	7	5	34	1	0	1	0	1	0	0	0	0	15483	1219	43	0	364	0	SYT12	11	66807407	In_Frame_Del	DEL	GGA	TCGA-BC-A10U-01A-11D-A12Z-10	1	66807407	68199109	87	4121	16	3								
SYT12	91683	hgsc.bcm.edu	37	chr11	66807408	66807409	+	Missense_Mutation	DNP	GA	GA	TC													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ctctggagctgatgggccggGagttggacctggccccctat					rs556621897		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:66807408_66807409GA>TC	ENST00000393946.2	+	7	1517_1518	c.355_356GA>TC	c.(355-357)GAg>TCg	p.E119S	SYT12_ENST00000527043.1_Missense_Mutation_p.E119S|SYT12_ENST00000526281.1_3'UTR|SYT12_ENST00000525457.1_Missense_Mutation_p.E119S			Q8IV01	SYT12_HUMAN	synaptotagmin XII	119						cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|synapse (GO:0045202)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	20						GATGGGCCGGGAGTTGGACCTG	0.629																																					p.E119X|p.E119A	Ovarian(65;2862 3307)	Atlas-SNP	.											.	SYT12	60	.	0			c.G355T|c.A356C						.																																			SO:0001583	missense	91683	exon4			GGCCGGGAGTTGG|GCCGGGAGTTGGA	AK024280	CCDS8154.1	11q13.2	2014-07-02			ENSG00000173227	ENSG00000173227		"Synaptotagmins"	18381	protein-coding gene	gene with protein product		606436				8987811	Standard	NM_177963		Approved	SRG1	uc001oju.3	Q8IV01	OTTHUMG00000167101	Exception_encountered	chr11.hg19:g.66807408_66807409delinsTC	ENSP00000377520:p.Glu119Ser	47.0	0.0		69.0|73.0	24.0	NM_001177880		Nonsense_Mutation|Missense_Mutation	SNP	ENST00000393946.2	hg19	CCDS8154.1																																																																																			.	.		0.629	SYT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393129.1	NM_177963		TC	66807409	GA	TC	66807408	3	4	34	1	0	0	0	0	1	0	0	0	15483	1175	41	3	365	3	SYT12	11	66807408	Missense_Mutation	DNP	GA	TCGA-BC-A10U-01A-11D-A12Z-10	1	66807408	68199108	88	4122	16	3								
NAALAD2	10003	hgsc.bcm.edu	37	chr11	89924847	89924847	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gtttggcctggaaagaagtaAagaaacatatttctattgca	9	5	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:89924847A>G	ENST00000534061.1	+	19	2385	c.2155A>G	c.(2155-2157)Aag>Gag	p.K719E	NAALAD2_ENST00000321955.4_Missense_Mutation_p.K686E|NAALAD2_ENST00000375944.3_Silent_p.*306*	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	719					neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GAAAGAAGTAAAGAAACATAT	0.368																																					p.K719E		Atlas-SNP	.											.	NAALAD2	113	.	0			c.A2155G						.						84	87	86					11																	89924847		2201	4298	6499	SO:0001583	missense	10003	exon19			GAAGTAAAGAAAC	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.2155A>G	chr11.hg19:g.89924847A>G	ENSP00000432481:p.Lys719Glu	48.0	0.0		109.0	39.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Missense_Mutation	SNP	ENST00000534061.1	hg19	CCDS8288.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.461601	0.84317	.	.	ENSG00000077616	ENST00000534061;ENST00000321955	T;T	0.58506	0.33;0.33	5.08	5.08	0.68730	Transferrin receptor-like, dimerisation domain (3);	0.074850	0.53938	D	0.000043	T	0.66839	0.2830	M	0.62154	1.92	0.80722	D	1	P	0.51057	0.941	P	0.54100	0.742	T	0.67409	-0.5678	9	.	.	.	-11.4098	15.1983	0.73112	1.0:0.0:0.0:0.0	.	719	Q9Y3Q0	NALD2_HUMAN	E	719;686	ENSP00000432481:K719E;ENSP00000320083:K686E	.	K	+	1	0	NAALAD2	89564495	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.333000	0.90026	2.050000	0.60909	0.373000	0.22412	AAG	.	.		0.368	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		G	89924847	A	G	89924847	3	3	34	1	0	0	0	0	1	0	0	0	10137	15	1	2	2229	2	NAALAD2	11	89924847	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	23117439	89924847	45081669	89	4123										
FAT3	120114	hgsc.bcm.edu	37	chr11	92616349	92616349	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cctacacaccctgcttccagAgtgactccaggagcaacctg	8	16	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr11:92616349A>G	ENST00000298047.6	+	23	12744	c.12727A>G	c.(12727-12729)Agt>Ggt	p.S4243G	FAT3_ENST00000409404.2_Missense_Mutation_p.S4243G|FAT3_ENST00000533797.1_Missense_Mutation_p.S578G|FAT3_ENST00000525166.1_Missense_Mutation_p.S4093G			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4243					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CTGCTTCCAGAGTGACTCCAG	0.667										TCGA Ovarian(4;0.039)																											p.S4243G		Atlas-SNP	.											.	FAT3	1822	.	0			c.A12727G						.						71	86	81					11																	92616349		2079	4190	6269	SO:0001583	missense	120114	exon23			TTCCAGAGTGACT	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12727A>G	chr11.hg19:g.92616349A>G	ENSP00000298047:p.Ser4243Gly	23.0	0.0		26.0	17.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	A	11.26	1.586430	0.28268	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;D	0.86297	-0.85;-0.95;-0.86;-2.1	5.85	3.56	0.40772	.	.	.	.	.	T	0.80003	0.4544	L	0.36672	1.1	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.70536	-0.4845	9	0.34782	T	0.22	.	10.1404	0.42732	0.8656:0.0:0.1344:0.0	.	4243;4243	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	G	4243;4243;4093;578	ENSP00000298047:S4243G;ENSP00000387040:S4243G;ENSP00000432586:S4093G;ENSP00000436399:S578G	ENSP00000298047:S4243G	S	+	1	0	FAT3	92255997	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.087000	0.50167	0.488000	0.27723	0.533000	0.62120	AGT	.	.		0.667	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		G	92616349	A	G	92616349	3	3	34	1	0	0	0	0	1	0	0	0	5699	304	11	2	12817	2	FAT3	11	92616349	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	2691502	92616349	42390167	90	4124										
PARP11	57097	hgsc.bcm.edu	37	chr12	3939168	3939168	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ttttagaaaataattcttctGctttgtgaaacatctcctga	5	7	3	3			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr12:3939168G>C	ENST00000228820.4	-	2	179	c.35C>G	c.(34-36)gCa>gGa	p.A12G	PARP11_ENST00000447133.3_5'UTR|PARP11_ENST00000397096.2_Missense_Mutation_p.A5G|PARP11_ENST00000427057.2_5'UTR	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	5							NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	17			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			TAATTCTTCTGCTTTGTGAAA	0.368																																					p.A12G		Atlas-SNP	.											.	PARP11	39	.	0			c.C35G						.						107	98	101					12																	3939168		2203	4300	6503	SO:0001583	missense	57097	exon2			TCTTCTGCTTTGT	AF263540	CCDS8523.2, CCDS66281.1	12p13.3	2014-01-28	2004-08-25	2004-08-26	ENSG00000111224	ENSG00000111224		"Poly (ADP-ribose) polymerases"	1186	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 6"	C12orf6		15273990	Standard	NM_001286522		Approved		uc001qml.2	Q9NR21	OTTHUMG00000156442	ENST00000228820.4:c.35C>G	chr12.hg19:g.3939168G>C	ENSP00000228820:p.Ala12Gly	126.0	0.0		178.0	77.0	NM_020367	B4DRQ0|Q68DS1|Q8N5Y9	Missense_Mutation	SNP	ENST00000228820.4	hg19	CCDS8523.2	.	.	.	.	.	.	.	.	.	.	G	10.80	1.451925	0.26074	.	.	ENSG00000111224	ENST00000397096;ENST00000228820	T;T	0.31769	1.48;2.69	5.52	5.52	0.82312	.	0.796683	0.12037	N	0.505442	T	0.21022	0.0506	N	0.19112	0.55	0.80722	D	1	B;B	0.19817	0.039;0.023	B;B	0.18871	0.023;0.01	T	0.05616	-1.0874	10	0.32370	T	0.25	.	10.2001	0.43077	0.0872:0.0:0.9128:0.0	.	12;5	Q9NR21-4;Q9NR21	.;PAR11_HUMAN	G	5;12	ENSP00000380284:A5G;ENSP00000228820:A12G	ENSP00000228820:A12G	A	-	2	0	PARP11	3809429	0.161000	0.22892	0.998000	0.56505	0.425000	0.31504	2.197000	0.42696	2.873000	0.98535	0.563000	0.77884	GCA	.	.		0.368	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1			C	3939168	G	C	3939168	3	2	34	1	0	0	0	0	1	0	0	0	11465	1319	46	4	1009	4	PARP11	12	3939168	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10		3939168	129912727	91	4125										
CHD4	1108	hgsc.bcm.edu	37	chr12	6710565	6710565	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ccacagctaccgctgctgctGccgcagctgccactgatgcc	10	18	0	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr12:6710565G>A	ENST00000357008.2	-	6	852	c.689C>T	c.(688-690)gCa>gTa	p.A230V	CHD4_ENST00000544040.1_Missense_Mutation_p.A223V|CHD4_ENST00000309577.6_Missense_Mutation_p.A230V|CHD4_ENST00000544484.1_Missense_Mutation_p.A227V	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	230	Poly-Ala.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						CGCTGCTGCTGCCGCAGCTGC	0.577																																					p.A230V	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.C689T						.						86	97	93					12																	6710565		2203	4300	6503	SO:0001583	missense	1108	exon6			GCTGCTGCCGCAG	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.689C>T	chr12.hg19:g.6710565G>A	ENSP00000349508:p.Ala230Val	53.0	0.0		74.0	25.0	NM_001273	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	hg19	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.735652	0.30774	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464;ENST00000545942	D;D;D;D;T	0.90504	-2.67;-2.68;-2.67;-2.68;0.81	5.87	5.87	0.94306	.	0.160296	0.47093	D	0.000249	D	0.88858	0.6551	L	0.37800	1.135	0.47621	D	0.999479	P;B;P	0.36535	0.557;0.193;0.557	B;B;B	0.41764	0.366;0.036;0.366	D	0.85496	0.1188	10	0.22109	T	0.4	-1.1386	20.2084	0.98285	0.0:0.0:1.0:0.0	.	230;230;223	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	V	227;223;230;230;204;230	ENSP00000440392:A227V;ENSP00000440542:A223V;ENSP00000312419:A230V;ENSP00000349508:A230V;ENSP00000437506:A230V	ENSP00000312419:A230V	A	-	2	0	CHD4	6580826	1.000000	0.71417	0.578000	0.28575	0.613000	0.37349	4.419000	0.59835	2.774000	0.95407	0.650000	0.86243	GCA	.	.		0.577	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6710565	G	A	6710565	3	1	34	1	0	0	0	0	1	0	0	0	3329	1319	46	3	5189	3	CHD4	12	6710565	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	2771397	6710565	127141330	92	4126										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22606893	22606893	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	atgtaggagacaacagcattCcctcctaatgcagcaacatg	8	11	0	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr12:22606893C>G	ENST00000333957.4	-	24	3063	c.2808G>C	c.(2806-2808)ggG>ggC	p.G936G	C2CD5_ENST00000542676.1_Silent_p.G987G|C2CD5_ENST00000545552.1_Silent_p.G990G|C2CD5_ENST00000396028.2_Silent_p.G978G|C2CD5_ENST00000536386.1_Silent_p.G989G|C2CD5_ENST00000446597.1_Silent_p.G987G|C2CD5_ENST00000544930.1_Silent_p.G792G	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	936					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CAACAGCATTCCCTCCTAATG	0.418																																					p.G936G		Atlas-SNP	.											.	.	.	.	0			c.G2808C						.						155	140	145					12																	22606893		2203	4300	6503	SO:0001819	synonymous_variant	9847	exon24			AGCATTCCCTCCT	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.2808G>C	chr12.hg19:g.22606893C>G		91.0	0.0		220.0	83.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	C	8.314	0.822710	0.16678	.	.	ENSG00000111731	ENST00000539615	.	.	.	5.41	1.24	0.21308	.	0.000000	0.85682	D	0.000000	T	0.70640	0.3247	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72581	-0.4250	6	0.56958	D	0.05	-10.6763	13.3155	0.60405	0.0:0.3971:0.5369:0.066	.	.	.	.	A	237	.	ENSP00000437935:G237A	G	-	2	0	KIAA0528	22498160	0.980000	0.34600	1.000000	0.80357	0.971000	0.66376	0.123000	0.15708	0.242000	0.21303	0.561000	0.74099	GGA	.	.		0.418	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		G	22606893	C	G	22606893	2	3	34	1	0	0	0	0	0	0	0	1	8191	842	30	4		4	KIAA0528	12	22606893	Silent	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	15896328	22606893	111245002	93	4127										
CCDC65	85478	hgsc.bcm.edu	37	chr12	49312509	49312509	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggcaagatcatgatacacagCcgtgagagtgaagatgagaa	13	6	1	6			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr12:49312509C>A	ENST00000320516.4	+	6	1037	c.849C>A	c.(847-849)agC>agA	p.S283R	CCDC65_ENST00000266984.5_Missense_Mutation_p.S283R|RP11-302B13.5_ENST00000398092.4_Intron	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	283										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						TGATACACAGCCGTGAGAGTG	0.458																																					p.S283R		Atlas-SNP	.											.	CCDC65	41	.	0			c.C849A						.						103	93	96					12																	49312509		2203	4300	6503	SO:0001583	missense	85478	exon6			ACACAGCCGTGAG		CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.849C>A	chr12.hg19:g.49312509C>A	ENSP00000312706:p.Ser283Arg	93.0	0.0		104.0	45.0	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Missense_Mutation	SNP	ENST00000320516.4	hg19	CCDS8772.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.117650	0.56505	.	.	ENSG00000139537	ENST00000266984;ENST00000552942;ENST00000320516	T;T;T	0.45668	1.49;0.89;1.5	4.72	2.9	0.33743	.	0.520042	0.21941	N	0.066862	T	0.44603	0.1301	L	0.52364	1.645	0.38630	D	0.951349	D	0.63880	0.993	P	0.57776	0.827	T	0.42050	-0.9474	10	0.17369	T	0.5	-3.3456	5.9072	0.19008	0.1545:0.6762:0.0:0.1694	.	283	Q8IXS2	CCD65_HUMAN	R	283;180;283	ENSP00000266984:S283R;ENSP00000446569:S180R;ENSP00000312706:S283R	ENSP00000266984:S283R	S	+	3	2	CCDC65	47598776	0.018000	0.18449	0.991000	0.47740	0.991000	0.79684	0.035000	0.13797	0.737000	0.32582	0.655000	0.94253	AGC	.	.		0.458	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124		A	49312509	C	A	49312509	3	1	34	1	0	0	0	0	1	0	0	0	2839	738	26	3	871	3	CCDC65	12	49312509	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	26705616	49312509	84539386	94	4128										
MLL2	8085	hgsc.bcm.edu	37	chr12	49449093	49449100	+	Frame_Shift_Del	DEL	CTTCTGGC	CTTCTGGC	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tctttatcctcaccagccagCttctggctgtccatccctct							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	CTTCTGGC	CTTCTGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr12:49449093_49449100delCTTCTGGC	ENST00000301067.7	-	1	7_14	c.8_15delGCCAGAAG	c.(7-15)agccagaagfs	p.SQK3fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CACCAGCCAGCTTCTGGCTGTCCATCCC	0.49																																					p.3_6del		Atlas-INDEL	.											.	MLL2	1173	.	0			c.9_16del						.																																			SO:0001589	frameshift_variant	8085	exon1			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.8_15delGCCAGAAG	chr12.hg19:g.49449093_49449100delCTTCTGGC	ENSP00000301067:p.Ser3fs	93.0	0.0		80.0	26.0	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.49	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49449100	CTTCTGGC	-	49449093	7	5	34	1	0	1	0	1	0	0	0	0	9630	796	28	0	16814	0	MLL2	12	49449093	Frame_Shift_Del	DEL	CTTCTGGC	TCGA-BC-A10U-01A-11D-A12Z-10	136584	49449093	84402802	95	4129										
MFSD5	84975	hgsc.bcm.edu	37	chr12	53647509	53647509	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agccagcctgcttggctcttCcctgtaccgtatcgccacct	8	17	1	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr12:53647509C>A	ENST00000329548.4	+	2	1081	c.890C>A	c.(889-891)tCc>tAc	p.S297Y	MFSD5_ENST00000534842.1_Missense_Mutation_p.S404Y	NM_032889.4	NP_116278.3	Q6N075	MFSD5_HUMAN	major facilitator superfamily domain containing 5	297					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(3)|urinary_tract(1)	16						CTTGGCTCTTCCCTGTACCGT	0.562																																					p.S404Y		Atlas-SNP	.											.	MFSD5	40	.	0			c.C1211A						.						94	80	85					12																	53647509		2203	4300	6503	SO:0001583	missense	84975	exon2			GCTCTTCCCTGTA	AK097576	CCDS8851.1, CCDS53796.1	12q13.13	2012-03-09			ENSG00000182544	ENSG00000182544			28156	protein-coding gene	gene with protein product							Standard	NM_032889		Approved	MGC11308	uc001sch.2	Q6N075	OTTHUMG00000170028	ENST00000329548.4:c.890C>A	chr12.hg19:g.53647509C>A	ENSP00000332624:p.Ser297Tyr	62.0	0.0		141.0	52.0	NM_001170790	G3V1N7|Q6NW04|Q8N7W8|Q8NCK0|Q96IA5	Missense_Mutation	SNP	ENST00000329548.4	hg19	CCDS8851.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.863953	0.51482	.	.	ENSG00000182544	ENST00000551660;ENST00000534842;ENST00000328704;ENST00000329548	.	.	.	5.04	4.15	0.48705	Major facilitator superfamily domain, general substrate transporter (1);	0.442010	0.22915	N	0.054086	T	0.64461	0.2600	M	0.66439	2.03	0.48762	D	0.999702	D;D	0.64830	0.991;0.994	P;P	0.53102	0.703;0.718	T	0.62798	-0.6778	9	0.31617	T	0.26	-17.4767	12.2428	0.54553	0.0:0.9158:0.0:0.0842	.	297;404	Q6N075;G3V1N7	MFSD5_HUMAN;.	Y	404;404;404;297	.	ENSP00000331231:S404Y	S	+	2	0	MFSD5	51933776	1.000000	0.71417	0.997000	0.53966	0.844000	0.47949	2.985000	0.49362	1.130000	0.42092	0.561000	0.74099	TCC	.	.		0.562	MFSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406896.1	NM_032889		A	53647509	C	A	53647509	3	1	34	1	0	0	0	0	1	0	0	0	9543	855	30	3	1217	3	MFSD5	12	53647509	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	4198416	53647509	80204386	96	4130										
PTPRR	5801	hgsc.bcm.edu	37	chr12	71139795	71139795	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tgtaatgtgatgggcgatagGtggatctcctggtttttctc	13	6	2	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr12:71139795G>A	ENST00000283228.2	-	6	1262	c.810C>T	c.(808-810)caC>caT	p.H270H	PTPRR_ENST00000342084.4_Silent_p.H158H|PTPRR_ENST00000549308.1_Silent_p.H25H|PTPRR_ENST00000440835.2_Silent_p.H25H|PTPRR_ENST00000378778.1_Silent_p.H64H	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	270					ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		TGGGCGATAGGTGGATCTCCT	0.438																																					p.H270H		Atlas-SNP	.											.	PTPRR	109	.	0			c.C810T						.						198	168	178					12																	71139795		2203	4300	6503	SO:0001819	synonymous_variant	5801	exon6			CGATAGGTGGATC	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.810C>T	chr12.hg19:g.71139795G>A		302.0	0.0		697.0	276.0	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Silent	SNP	ENST00000283228.2	hg19	CCDS8998.1																																																																																			.	.		0.438	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		A	71139795	G	A	71139795	2	1	34	1	0	0	0	0	0	0	0	1	12825	1252	44	3		3	PTPRR	12	71139795	Silent	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	17492286	71139795	62712100	97	4131										
PLEKHG7	440107	hgsc.bcm.edu	37	chr12	93148009	93148009	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gctgagaaaatcatgatctaCtccatcaaggaaaaggtgga	10	7	3	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr12:93148009C>G	ENST00000344636.3	+	6	643	c.459C>G	c.(457-459)taC>taG	p.Y153*		NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	153	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						TCATGATCTACTCCATCAAGG	0.468																																					p.Y153X		Atlas-SNP	.											.	PLEKHG7	38	.	0			c.C459G						.						96	86	89					12																	93148009		2203	4300	6503	SO:0001587	stop_gained	440107	exon6			GATCTACTCCATC	AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"Pleckstrin homology (PH) domain containing"	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.459C>G	chr12.hg19:g.93148009C>G	ENSP00000344961:p.Tyr153*	63.0	0.0		111.0	40.0	NM_001004330	B2RNR7	Nonsense_Mutation	SNP	ENST00000344636.3	hg19	CCDS31873.1	.	.	.	.	.	.	.	.	.	.	C	35	5.457813	0.96240	.	.	ENSG00000187510	ENST00000344636	.	.	.	5.4	1.6	0.23607	.	0.238813	0.44097	D	0.000499	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-17.2431	6.5086	0.22208	0.0:0.5426:0.1156:0.3418	.	.	.	.	X	153	.	ENSP00000344961:Y153X	Y	+	3	2	PLEKHG7	91672140	0.022000	0.18835	0.991000	0.47740	0.940000	0.58332	-0.046000	0.11983	0.029000	0.15352	-1.430000	0.01095	TAC	.	.		0.468	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330		G	93148009	C	G	93148009	4	3	34	1	0	0	0	0	0	1	0	0	12084	576	20	4	477	4	PLEKHG7	12	93148009	Nonsense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	22008214	93148009	40703886	98	4132										
TMPO	7112	hgsc.bcm.edu	37	chr12	98938128	98938128	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gaagaactccaaggaaaaggGtgatgcaaggcttattcctt	11	7	0	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr12:98938128G>C	ENST00000556029.1	+	5	1139		c.e5+1		TMPO_ENST00000343315.5_Intron|TMPO_ENST00000548223.1_Splice_Site|TMPO_ENST00000393053.2_Intron	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						AAGGAAAAGGGTGATGCAAGG	0.378																																					.		Atlas-SNP	.											.	TMPO	111	.	0			c.783+1G>C						.						87	90	89					12																	98938128		2203	4300	6503	SO:0001630	splice_region_variant	7112	exon5			AAAAGGGTGATGC		CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.783+1G>C	chr12.hg19:g.98938128G>C		65.0	0.0		140.0	51.0	NM_001032283	A2T926|Q14861	Splice_Site	SNP	ENST00000556029.1	hg19	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.332546	0.60853	.	.	ENSG00000120802	ENST00000556029	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9478	0.97189	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMPO	97462259	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.473000	0.73572	2.712000	0.92718	0.591000	0.81541	.	.	.		0.378	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276	Intron	C	98938128	G	C	98938128	5	2	34	1	0	0	0	0	0	0	1	0	16252	1275	44	4	2326	4	TMPO	12	98938128	Splice_Site	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	5790119	98938128	34913767	99	4133										
VPS33A	65082	hgsc.bcm.edu	37	chr12	122745969	122745969	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cacaaacagaatatgaaaatCtctcgttgggcctcgtctat	7	10	2	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr12:122745969C>G	ENST00000267199.4	-	4	434	c.322G>C	c.(322-324)Gat>Cat	p.D108H	RP11-512M8.5_ENST00000535844.1_Missense_Mutation_p.D108H|VPS33A_ENST00000451053.2_Missense_Mutation_p.D108H|VPS33A_ENST00000542310.1_5'UTR	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	108					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of developmental pigmentation (GO:0048070)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	28	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		ATATGAAAATCTCTCGTTGGG	0.463																																					p.D108H		Atlas-SNP	.											.	VPS33A	61	.	0			c.G322C						.						85	73	77					12																	122745969		2203	4300	6503	SO:0001583	missense	65082	exon4			GAAAATCTCTCGT	AK026048	CCDS9231.1	12q24.31	2008-06-23	2006-04-04		ENSG00000139719	ENSG00000139719			18179	protein-coding gene	gene with protein product		610034	"vacuolar protein sorting 33A (yeast)"			11250079	Standard	NM_022916		Approved		uc001ucd.3	Q96AX1	OTTHUMG00000168920	ENST00000267199.4:c.322G>C	chr12.hg19:g.122745969C>G	ENSP00000267199:p.Asp108His	61.0	0.0		127.0	43.0	NM_022916	Q547V4|Q9H5Q0	Missense_Mutation	SNP	ENST00000267199.4	hg19	CCDS9231.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650784	0.87958	.	.	ENSG00000139719	ENST00000267199;ENST00000451053	T;T	0.76709	-1.04;-1.04	5.11	5.11	0.69529	.	0.153560	0.56097	D	0.000022	T	0.81635	0.4864	L	0.43152	1.355	0.80722	D	1	P;P	0.49783	0.928;0.858	P;P	0.54312	0.748;0.726	D	0.83545	0.0098	10	0.72032	D	0.01	-13.7253	18.8821	0.92360	0.0:1.0:0.0:0.0	.	108;108	F5H6Y0;Q96AX1	.;VP33A_HUMAN	H	108	ENSP00000267199:D108H;ENSP00000442951:D108H	ENSP00000446319:D108H	D	-	1	0	VPS33A	121311922	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	7.709000	0.84645	2.544000	0.85801	0.561000	0.74099	GAT	.	.		0.463	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401607.2			G	122745969	C	G	122745969	3	3	34	1	0	0	0	0	1	0	0	0	17216	913	32	4	1508	4	VPS33A	12	122745969	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	23807841	122745969	11105926	100	4134										
SACS	26278	hgsc.bcm.edu	37	chr13	23905027	23905027	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ccatttcaaatacaaccgccTaataatcttttttcgttccg	3	12	2	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr13:23905027T>C	ENST00000382292.3	-	9	13261	c.12988A>G	c.(12988-12990)Agg>Ggg	p.R4330G	SACS_ENST00000402364.1_Missense_Mutation_p.R3580G|SACS_ENST00000382298.3_Missense_Mutation_p.R4330G			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4330	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TACAACCGCCTAATAATCTTT	0.358																																					p.R4330G		Atlas-SNP	.											.	SACS	871	.	0			c.A12988G						.						112	122	118					13																	23905027		2203	4299	6502	SO:0001583	missense	26278	exon10			ACCGCCTAATAAT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.12988A>G	chr13.hg19:g.23905027T>C	ENSP00000371729:p.Arg4330Gly	139.0	0.0		271.0	14.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	18.55	3.648155	0.67358	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.86432	-2.12;-2.12;-2.12	5.83	4.62	0.57501	Heat shock protein DnaJ, N-terminal (4);	0.000000	0.85682	D	0.000000	D	0.94338	0.8180	M	0.91406	3.205	0.52501	D	0.999958	D	0.76494	0.999	D	0.78314	0.991	D	0.94762	0.7937	10	0.87932	D	0	.	12.9845	0.58583	0.0:0.0:0.1351:0.8649	.	4330	Q9NZJ4	SACS_HUMAN	G	4330;3580;4330	ENSP00000371729:R4330G;ENSP00000385844:R3580G;ENSP00000371735:R4330G	ENSP00000371729:R4330G	R	-	1	2	SACS	22803027	1.000000	0.71417	0.992000	0.48379	0.996000	0.88848	2.150000	0.42254	0.990000	0.38787	0.460000	0.39030	AGG	.	.		0.358	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23905027	T	C	23905027	3	2	34	1	0	0	0	0	1	0	0	0	13819	1521	53	2	755	2	SACS	13	23905027	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10		23905027	91264851	101	4135										
SOHLH2	54937	hgsc.bcm.edu	37	chr13	36776092	36776092	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gagaaccatgttgaatatgcAatcatccaaaagcgctgctg	9	9	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr13:36776092A>G	ENST00000379881.3	-	2	275	c.187T>C	c.(187-189)Tgc>Cgc	p.C63R	CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.C140R|SOHLH2_ENST00000554962.1_Missense_Mutation_p.C140R|SOHLH2_ENST00000317764.6_Missense_Mutation_p.C63R	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	63					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		TTGAATATGCAATCATCCAAA	0.453																																					p.C140R		Atlas-SNP	.											.	.	.	.	0			c.T418C						.						148	119	129					13																	36776092		2203	4300	6503	SO:0001583	missense	100526761	exon7			ATATGCAATCATC	AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"Basic helix-loop-helix proteins"	26026	protein-coding gene	gene with protein product	"spermatogenesis associated 28"					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.187T>C	chr13.hg19:g.36776092A>G	ENSP00000369210:p.Cys63Arg	56.0	0.0		130.0	49.0	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Missense_Mutation	SNP	ENST00000379881.3	hg19	CCDS9355.1	.	.	.	.	.	.	.	.	.	.	A	7.782	0.709683	0.15239	.	.	ENSG00000120669;ENSG00000120669;ENSG00000120669;ENSG00000250709	ENST00000379881;ENST00000554962;ENST00000317764;ENST00000511166	T;T;T;T	0.41758	1.59;1.59;0.99;1.59	5.54	-0.183	0.13284	.	0.588548	0.16395	N	0.216309	T	0.22003	0.0530	N	0.24115	0.695	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.11203	-1.0597	10	0.41790	T	0.15	-0.0896	2.4207	0.04447	0.4127:0.356:0.0859:0.1454	.	140;63	B4DX90;Q9NX45	.;SOLH2_HUMAN	R	63;140;63;140	ENSP00000369210:C63R;ENSP00000451542:C140R;ENSP00000326838:C63R;ENSP00000421868:C140R	ENSP00000421868:C140R	C	-	1	0	CCDC169-SOHLH2;SOHLH2	35674092	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.217000	0.17603	-0.253000	0.09514	-0.313000	0.08912	TGC	.	.		0.453	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826		G	36776092	A	G	36776092	3	3	34	1	0	0	0	0	1	0	0	0	14939	130	5	2	1130	2	SOHLH2	13	36776092	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	12871065	36776092	78393786	102	4136										
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21543017	21543017	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggtacccctcggagaacaggCaaaggaaacagaagaaagaa	12	8	0	4			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr14:21543017C>G	ENST00000298694.4	+	3	1255	c.1128C>G	c.(1126-1128)ggC>ggG	p.G376G	ARHGEF40_ENST00000298693.3_Silent_p.G376G			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	376	Gly-rich.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						GGAGAACAGGCAAAGGAAACA	0.632																																					p.G376G		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.C1128G						.						65	54	58					14																	21543017		2203	4300	6503	SO:0001819	synonymous_variant	55701	exon3			AACAGGCAAAGGA		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"Rho guanine nucleotide exchange factors"	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.1128C>G	chr14.hg19:g.21543017C>G		34.0	0.0		33.0	20.0	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	hg19	CCDS32041.1																																																																																			.	.		0.632	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			G	21543017	C	G	21543017	2	3	34	1	0	0	0	0	0	0	0	1	5934	697	25	4		4	FLJ10357	14	21543017	Silent	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10		21543017	85806523	103	4137										
NID2	22795	hgsc.bcm.edu	37	chr14	52509060	52509060	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cactttcccattcactcggtGaggtgcccctaaaagacagc	8	14	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr14:52509060G>T	ENST00000216286.5	-	7	1587	c.1588C>A	c.(1588-1590)Cac>Aac	p.H530N	NID2_ENST00000541773.1_Missense_Mutation_p.H477N	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	530	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					TTCACTCGGTGAGGTGCCCCT	0.512																																					p.H530N		Atlas-SNP	.											.	NID2	201	.	0			c.C1588A						.						106	108	107					14																	52509060		2203	4300	6503	SO:0001583	missense	22795	exon7			CTCGGTGAGGTGC	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1588C>A	chr14.hg19:g.52509060G>T	ENSP00000216286:p.His530Asn	23.0	0.0		68.0	34.0	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.848874	0.51164	.	.	ENSG00000087303	ENST00000216286;ENST00000541773;ENST00000395707	T;T	0.29655	1.56;1.56	6.16	5.25	0.73442	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.189121	0.56097	N	0.000022	T	0.49762	0.1576	M	0.72479	2.2	0.43036	D	0.99461	P;D;P	0.53462	0.546;0.96;0.607	B;P;B	0.54965	0.376;0.765;0.395	T	0.56001	-0.8051	10	0.72032	D	0.01	.	16.3625	0.83273	0.0:0.0:0.867:0.133	.	477;532;530	Q14112-2;Q5CZI2;Q14112	.;.;NID2_HUMAN	N	530;477;532	ENSP00000216286:H530N;ENSP00000443730:H477N	ENSP00000216286:H530N	H	-	1	0	NID2	51578810	1.000000	0.71417	0.997000	0.53966	0.638000	0.38207	5.317000	0.65822	1.557000	0.49525	0.650000	0.86243	CAC	.	.		0.512	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			T	52509060	G	T	52509060	3	4	34	1	0	0	0	0	1	0	0	0	10424	1290	45	3	2603	3	NID2	14	52509060	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	30966043	52509060	54840480	104	4138										
STON2	85439	hgsc.bcm.edu	37	chr14	81862242	81862242	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cttcctacctcctcacctgtCtcagctgtttcctgatgagg	7	15	2	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr14:81862242C>G	ENST00000267540.2	-	2	569	c.369G>C	c.(367-369)gaG>gaC	p.E123D	STON2_ENST00000555447.1_Missense_Mutation_p.E123D	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	123					hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		CCTCACCTGTCTCAGCTGTTT	0.567																																					p.E123D		Atlas-SNP	.											.	STON2	94	.	0			c.G369C						.						79	80	80					14																	81862242		2203	4300	6503	SO:0001583	missense	85439	exon4			ACCTGTCTCAGCT	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"stoned B homolog 2 (Drosophila)"	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.369G>C	chr14.hg19:g.81862242C>G	ENSP00000267540:p.Glu123Asp	51.0	0.0		118.0	50.0	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	hg19	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.293747	0.23564	.	.	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.54866	0.55;0.55	5.82	5.82	0.92795	Stonin-2, N-terminal (1);	1.323900	0.05364	N	0.534288	T	0.50411	0.1614	L	0.29908	0.895	0.09310	N	0.999995	B;B;B	0.23185	0.033;0.081;0.027	B;B;B	0.30943	0.113;0.122;0.069	T	0.41342	-0.9514	10	0.29301	T	0.29	-0.2313	15.6141	0.76750	0.0:1.0:0.0:0.0	.	123;123;123	Q8WXE9;Q17R23;G3V2T7	STON2_HUMAN;.;.	D	123;135;123	ENSP00000450857:E123D;ENSP00000267540:E123D	ENSP00000267540:E123D	E	-	3	2	STON2	80931995	0.154000	0.22792	0.047000	0.18901	0.717000	0.41224	3.968000	0.56809	2.751000	0.94390	0.655000	0.94253	GAG	.	.		0.567	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104		G	81862242	C	G	81862242	3	3	34	1	0	0	0	0	1	0	0	0	15333	912	32	4	2362	4	STON2	14	81862242	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	29353182	81862242	25487298	105	4139										
NUDT14	256281	hgsc.bcm.edu	37	chr14	105643003	105643004	+	Frame_Shift_Ins	INS	-	-	C													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggcacacagctcaactgtcaINScccccgctgagccgggcagg							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr14:105643003_105643004insC	ENST00000392568.2	-	4	388_389	c.295_296insG	c.(295-297)gtgfs	p.V99fs	NUDT14_ENST00000550912.1_5'Flank|RP11-44N21.4_ENST00000548203.1_RNA	NM_177533.4	NP_803877.2	O95848	NUD14_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 14	99	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ADP-ribose diphosphatase activity (GO:0047631)|metal ion binding (GO:0046872)|UDP-sugar diphosphatase activity (GO:0008768)			cervix(2)|endometrium(1)|lung(3)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	14		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		CTCAACTGTCACCCCCGCTGAG	0.673										HNSCC(42;0.11)																											p.V99fs		Atlas-Indel,Pindel	.											.	NUDT14	24	.	0			c.296_297insG						.																																			SO:0001589	frameshift_variant	256281	exon4			.	AB087802	CCDS10000.1	14q32.33	2013-02-15			ENSG00000183828	ENSG00000183828		"Nudix motif containing"	20141	protein-coding gene	gene with protein product		609219				12429023	Standard	NM_177533		Approved	UGPP	uc010tyn.3	O95848	OTTHUMG00000170372	ENST00000392568.2:c.296dupG	chr14.hg19:g.105643008_105643008dupC	ENSP00000376349:p.Val99fs	48.0	0.0		48.0	18.0	NM_177533	Q86SJ8	Frame_Shift_Ins	INS	ENST00000392568.2	hg19	CCDS10000.1																																																																																			.	.		0.673	NUDT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074544.4	NM_177533		C	105643004	-	C	105643003	7	5	34	1	0	1	1	0	0	0	0	0	10739	159	6	0	380	0	NUDT14	14	105643003	Frame_Shift_Ins	INS	-	TCGA-BC-A10U-01A-11D-A12Z-10	23780761	105643003	1706537	106	4140										
GNB5	10681	hgsc.bcm.edu	37	chr15	52418147	52418147	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tctgaaataaaatcttaccaCtgagggagaagtccacgctg	9	9	2	3			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr15:52418147C>A	ENST00000261837.7	-	11	1072	c.1007G>T	c.(1006-1008)aGt>aTt	p.S336I	GNB5_ENST00000396335.4_Missense_Mutation_p.S224I|CTD-2184D3.7_ENST00000557898.1_RNA|GNB5_ENST00000559348.1_5'UTR|GNB5_ENST00000358784.7_Missense_Mutation_p.S294I	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	336					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		AATCTTACCACTGAGGGAGAA	0.478																																					p.S336I		Atlas-SNP	.											.	GNB5	28	.	0			c.G1007T						.						66	58	61					15																	52418147		2195	4292	6487	SO:0001583	missense	10681	exon11			TTACCACTGAGGG	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"WD repeat domain containing"	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.1007G>T	chr15.hg19:g.52418147C>A	ENSP00000261837:p.Ser336Ile	76.0	0.0		213.0	79.0	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Missense_Mutation	SNP	ENST00000261837.7	hg19	CCDS10149.1	.	.	.	.	.	.	.	.	.	.	C	34	5.386658	0.95967	.	.	ENSG00000069966	ENST00000261837;ENST00000396335;ENST00000544480;ENST00000358784	T	0.01406	4.93	6.08	6.08	0.98989	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.15262	0.0368	M	0.93462	3.42	0.80722	D	1	D;D	0.89917	1.0;0.961	D;D	0.85130	0.997;0.935	T	0.00548	-1.1677	10	0.87932	D	0	-31.5859	20.6634	0.99662	0.0:1.0:0.0:0.0	.	336;224	O14775;O14775-3	GBB5_HUMAN;.	I	336;294;134;224	ENSP00000261837:S336I	ENSP00000261837:S336I	S	-	2	0	GNB5	50205439	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.539000	0.82063	2.894000	0.99253	0.655000	0.94253	AGT	.	.		0.478	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			A	52418147	C	A	52418147	3	1	34	1	0	0	0	0	1	0	0	0	6529	565	20	3	192	3	GNB5	15	52418147	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10		52418147	50113245	107	4141										
ATF7IP2	80063	hgsc.bcm.edu	37	chr16	10574815	10574815	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	accccattggcacaaaatgcAgtccaggtactgaatcaaag	8	11	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr16:10574815A>G	ENST00000396560.2	+	11	1856	c.1629A>G	c.(1627-1629)gcA>gcG	p.A543A	ATF7IP2_ENST00000543967.1_Silent_p.A87A|ATF7IP2_ENST00000396559.1_Missense_Mutation_p.Q521R|ATF7IP2_ENST00000324570.5_Missense_Mutation_p.Q521R|ATF7IP2_ENST00000356427.2_Silent_p.A543A	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	543			A -> T (in dbSNP:rs9931441).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						CACAAAATGCAGTCCAGGTAC	0.413																																					p.Q521R		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.A1562G						.						95	96	96					16																	10574815		2197	4300	6497	SO:0001819	synonymous_variant	80063	exon11			AAATGCAGTCCAG	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.1629A>G	chr16.hg19:g.10574815A>G		52.0	0.0		77.0	27.0	NM_001256160	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	hg19	CCDS10540.1	.	.	.	.	.	.	.	.	.	.	A	4.595	0.110580	0.08780	.	.	ENSG00000166669	ENST00000396559;ENST00000324570	.	.	.	4.7	4.7	0.59300	.	.	.	.	.	T	0.47764	0.1463	.	.	.	0.09310	N	1	D	0.54207	0.965	P	0.50049	0.629	T	0.42361	-0.9456	7	0.87932	D	0	-1.4743	10.8381	0.46698	1.0:0.0:0.0:0.0	.	521	Q5U623-2	.	R	521	.	ENSP00000322811:Q521R	Q	+	2	0	ATF7IP2	10482316	0.976000	0.34144	0.076000	0.20297	0.011000	0.07611	1.677000	0.37576	1.882000	0.54519	0.460000	0.39030	CAG	.	.		0.413	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997		G	10574815	A	G	10574815	2	3	34	1	0	0	0	0	0	0	0	1	1088	175	7	2		2	ATF7IP2	16	10574815	Silent	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10		10574815	79779938	108	4142										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30724538	30724538	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tgatccctcagggctggaccAagcccaatgcctttcatgtg	10	13	2	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr16:30724538A>T	ENST00000262518.4	+	15	2525	c.2140A>T	c.(2140-2142)Aag>Tag	p.K714*	SRCAP_ENST00000395059.2_Nonsense_Mutation_p.K714*|SNORA30_ENST00000384028.1_RNA|SRCAP_ENST00000344771.4_Nonsense_Mutation_p.K714*	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	714	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GGGCTGGACCAAGCCCAATGC	0.488																																					p.K714X		Atlas-SNP	.											.	SRCAP	298	.	0			c.A2140T						.						125	116	119					16																	30724538		2197	4300	6497	SO:0001587	stop_gained	10847	exon15			TGGACCAAGCCCA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.2140A>T	chr16.hg19:g.30724538A>T	ENSP00000262518:p.Lys714*	51.0	0.0		123.0	47.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Nonsense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	A	38	6.920643	0.97936	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	.	.	.	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.2524	9.081	0.36552	0.9178:0.0:0.0822:0.0	.	.	.	.	X	714	.	ENSP00000262518:K714X	K	+	1	0	SRCAP	30632039	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.896000	0.56266	2.272000	0.75746	0.460000	0.39030	AAG	.	.		0.488	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30724538	A	T	30724538	4	4	34	1	0	0	0	0	0	1	0	0	15150	131	5	4	2190	4	SRCAP	16	30724538	Nonsense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	20149723	30724538	59630215	109	4143										
TP53	7157	hgsc.bcm.edu	37	chr17	7578211	7578211	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agggcaccaccacactatgtCgaaaagtgtttctgtcatcc	8	12	2	0	rs587778720		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr17:7578211C>T	ENST00000269305.4	-	6	827	c.638G>A	c.(637-639)cGa>cAa	p.R213Q	TP53_ENST00000574684.1_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R213Q|TP53_ENST00000455263.2_Missense_Mutation_p.R213Q|TP53_ENST00000359597.4_Missense_Mutation_p.R213Q|TP53_ENST00000445888.2_Missense_Mutation_p.R213Q|TP53_ENST00000413465.2_Missense_Mutation_p.R213Q	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	213	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R213L(38)|p.R213Q(29)|p.0?(8)|p.R213P(5)|p.?(5)|p.R120L(4)|p.R81L(4)|p.R120Q(2)|p.R81Q(2)|p.D208_V216delDRNTFRHSV(1)|p.D207_R213delDDRNTFR(1)|p.T211_S215delTFRHS(1)|p.D208fs*1(1)|p.R213>L(1)|p.R209_R213delRNTFR(1)|p.R213fs*2(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213fs*32(1)|p.R209fs*6(1)|p.R213W(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CACACTATGTCGAAAAGTGTT	0.532		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R213Q	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,-1,1	TP53	33396	.	110	Substitution - Missense(85)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(5)|Unknown(5)|Complex - deletion inframe(1)|Complex - compound substitution(1)	prostate(15)|large_intestine(14)|urinary_tract(9)|liver(9)|haematopoietic_and_lymphoid_tissue(8)|biliary_tract(6)|stomach(6)|oesophagus(6)|kidney(5)|lung(5)|central_nervous_system(4)|ovary(4)|pancreas(4)|bone(4)|upper_aerodigestive_tract(3)|soft_tissue(2)|eye(2)|vulva(1)|endometrium(1)|skin(1)|breast(1)	c.G638A	GRCh37	CM004906|CM022474	TP53	M		.						132	118	122					17																	7578211		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CTATGTCGAAAAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.638G>A	chr17.hg19:g.7578211C>T	ENSP00000269305:p.Arg213Gln	76.0	0.0		90.0	57.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	37	6.233765	0.97399	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	5.28	4.32	0.51571	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.057335	0.64402	N	0.000003	D	0.99871	0.9939	M	0.92507	3.315	0.50039	D	0.999845	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.993;0.996;1.0;0.995;0.994;0.999	D	0.96662	0.9490	10	0.87932	D	0	-7.5444	11.7807	0.52013	0.0:0.9141:0.0:0.0859	.	174;213;213;120;213;213;213	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	Q	213;213;213;213;213;213;202;120;81;120;81	ENSP00000410739:R213Q;ENSP00000352610:R213Q;ENSP00000269305:R213Q;ENSP00000398846:R213Q;ENSP00000391127:R213Q;ENSP00000391478:R213Q;ENSP00000425104:R81Q;ENSP00000423862:R120Q	ENSP00000269305:R213Q	R	-	2	0	TP53	7518936	0.996000	0.38824	0.185000	0.23176	0.961000	0.63080	7.775000	0.85489	1.367000	0.46095	0.563000	0.77884	CGA	.	.		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578211	C	T	7578211	3	4	34	1	0	0	0	0	1	0	0	0	16396	884	31	1	656	1	TP53	17	7578211	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10		7578211	73616999	110	4144										
TBC1D26	353149	hgsc.bcm.edu	37	chr17	15642108	15642108	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	agatgtcagccacaccctgcAgaaacacatgatgttcatac	7	12	2	3			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr17:15642108A>G	ENST00000437605.2	+	8	711	c.461A>G	c.(460-462)cAg>cGg	p.Q154R	TBC1D26_ENST00000579428.1_Missense_Mutation_p.Q154R|ZNF286A_ENST00000413242.2_3'UTR|AC005324.6_ENST00000433873.1_RNA|AC005324.6_ENST00000434017.1_RNA|AC005324.6_ENST00000580194.1_RNA	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	154	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		CACACCCTGCAGAAACACATG	0.532																																					p.Q154R		Atlas-SNP	.											.	TBC1D26	16	.	0			c.A461G						.						111	102	105					17																	15642108		2136	4226	6362	SO:0001583	missense	353149	exon8			CCCTGCAGAAACA		CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.461A>G	chr17.hg19:g.15642108A>G	ENSP00000410111:p.Gln154Arg	189.0	0.0		215.0	111.0	NM_178571	A8K929|Q4G172	Missense_Mutation	SNP	ENST00000437605.2	hg19	CCDS42265.1	.	.	.	.	.	.	.	.	.	.	a	0.915	-0.717755	0.03182	.	.	ENSG00000214946	ENST00000437605	T	0.03717	3.83	1.44	-2.89	0.05665	Rab-GAP/TBC domain (4);	0.142512	0.46145	N	0.000318	T	0.00936	0.0031	N	0.01219	-0.95	0.09310	N	1	B;B	0.18741	0.03;0.012	B;B	0.26614	0.071;0.023	T	0.35375	-0.9791	10	0.02654	T	1	.	2.8292	0.05495	0.2353:0.2885:0.4763:0.0	.	154;154	Q86UD7;Q86UD7-2	TBC26_HUMAN;.	R	154	ENSP00000410111:Q154R	ENSP00000410111:Q154R	Q	+	2	0	TBC1D26	15582833	0.525000	0.26290	0.000000	0.03702	0.002000	0.02628	1.230000	0.32612	-1.068000	0.03156	-0.811000	0.03165	CAG	.	.		0.532	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571		G	15642108	A	G	15642108	3	3	34	1	0	0	0	0	1	0	0	0	15631	188	7	2	483	2	TBC1D26	17	15642108	Missense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	8063897	15642108	65553102	111	4145										
ATAD5	79915	hgsc.bcm.edu	37	chr17	29162318	29162318	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gacagcaatttatgaaagcaTttaggcagccagcatcagat	9	8	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr17:29162318T>C	ENST00000321990.4	+	2	1597	c.1219T>C	c.(1219-1221)Ttt>Ctt	p.F407L	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	407					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TATGAAAGCATTTAGGCAGCC	0.368																																					p.F407L		Atlas-SNP	.											.	ATAD5	150	.	0			c.T1219C						.						66	71	69					17																	29162318		2201	4299	6500	SO:0001583	missense	79915	exon2			AAAGCATTTAGGC		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.1219T>C	chr17.hg19:g.29162318T>C	ENSP00000313171:p.Phe407Leu	103.0	0.0		152.0	55.0	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.556173	0.45487	.	.	ENSG00000176208	ENST00000321990	T	0.38401	1.14	5.91	5.91	0.95273	.	0.114300	0.64402	D	0.000004	T	0.60663	0.2286	M	0.70275	2.135	0.48511	D	0.999666	D;D	0.71674	0.998;0.997	D;D	0.80764	0.994;0.985	T	0.63721	-0.6573	10	0.72032	D	0.01	.	16.3436	0.83110	0.0:0.0:0.0:1.0	.	407;407	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	L	407	ENSP00000313171:F407L	ENSP00000313171:F407L	F	+	1	0	ATAD5	26186444	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.431000	0.73395	2.269000	0.75478	0.533000	0.62120	TTT	.	.		0.368	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		C	29162318	T	C	29162318	3	2	34	1	0	0	0	0	1	0	0	0	1076	1493	52	2	1225	2	ATAD5	17	29162318	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	13520210	29162318	52032892	112	4146										
IGFBP4	3487	hgsc.bcm.edu	37	chr17	38600272	38600272	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	cccctgcacacactgatgcaCgggcaaggcgtgtgcatgga	13	13	0	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr17:38600272C>A	ENST00000269593.4	+	1	560	c.285C>A	c.(283-285)caC>caA	p.H95Q	IGFBP4_ENST00000542955.1_Intron	NM_001552.2	NP_001543.2	P22692	IBP4_HUMAN	insulin-like growth factor binding protein 4	95	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|DNA metabolic process (GO:0006259)|inflammatory response (GO:0006954)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			CACTGATGCACGGGCAAGGCG	0.672																																					p.H95Q	GBM(160;940 3581 26177)	Atlas-SNP	.											.	IGFBP4	17	.	0			c.C285A						.						18	12	14					17																	38600272		2144	4202	6346	SO:0001583	missense	3487	exon1			GATGCACGGGCAA	M38177	CCDS11367.1	17q21.2	2014-09-16	2001-11-28		ENSG00000141753	ENSG00000141753			5473	protein-coding gene	gene with protein product	"IGF-binding protein 4"	146733	"insulin-like growth factor-binding protein 4"			1707125, 1704481	Standard	NM_001552		Approved	IBP4, BP-4, HT29-IGFBP, IGFBP-4	uc002hus.3	P22692	OTTHUMG00000133326	ENST00000269593.4:c.285C>A	chr17.hg19:g.38600272C>A	ENSP00000269593:p.His95Gln	17.0	0.0		22.0	8.0	NM_001552	A0N9W2|B4E351|Q5U012|Q9UCL6	Missense_Mutation	SNP	ENST00000269593.4	hg19	CCDS11367.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.705853	0.68615	.	.	ENSG00000141753	ENST00000269593	T	0.62639	0.01	5.16	-3.05	0.05396	Insulin-like growth factor-binding protein, IGFBP (2);Growth factor, receptor (1);	0.449529	0.24343	N	0.039353	T	0.45034	0.1322	N	0.12663	0.25	0.80722	D	1	D	0.71674	0.998	P	0.59703	0.862	T	0.51996	-0.8634	10	0.16420	T	0.52	-11.3722	2.9448	0.05842	0.1073:0.4315:0.2129:0.2483	.	95	P22692	IBP4_HUMAN	Q	95	ENSP00000269593:H95Q	ENSP00000269593:H95Q	H	+	3	2	IGFBP4	35853798	0.000000	0.05858	0.867000	0.34043	0.993000	0.82548	-1.859000	0.01657	-0.385000	0.07833	0.591000	0.81541	CAC	.	.		0.672	IGFBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257134.1	NM_001552		A	38600272	C	A	38600272	3	1	34	1	0	0	0	0	1	0	0	0	7590	535	19	1	287	1	IGFBP4	17	38600272	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	9437954	38600272	42594938	113	4147										
ADAM11	4185	hgsc.bcm.edu	37	chr17	42855379	42855379	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tggacaggcaaagactgcagTatccataaccccctgcccac	8	15	0	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr17:42855379T>A	ENST00000200557.6	+	24	2299	c.2130T>A	c.(2128-2130)agT>agA	p.S710R	ADAM11_ENST00000535346.1_Missense_Mutation_p.S510R	NM_002390.4	NP_002381.2	O75078	ADA11_HUMAN	ADAM metallopeptidase domain 11	710					integrin-mediated signaling pathway (GO:0007229)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Prostate(33;0.0959)				AAGACTGCAGTATCCATAACC	0.617																																					p.S710R		Atlas-SNP	.											.	ADAM11	118	.	0			c.T2130A						.						106	107	107					17																	42855379		2203	4300	6503	SO:0001583	missense	4185	exon24			CTGCAGTATCCAT	D17390	CCDS11486.1	17q21.3	2014-08-12	2005-08-18		ENSG00000073670			"ADAM metallopeptidase domain containing"	189	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, cysteine-rich protein"	155120	"a disintegrin and metalloproteinase domain 11"	MDC		8252040	Standard	XM_005257373		Approved		uc002ihh.3	O75078	OTTHUMG00000179038	ENST00000200557.6:c.2130T>A	chr17.hg19:g.42855379T>A	ENSP00000200557:p.Ser710Arg	40.0	0.0		62.0	29.0	NM_002390	Q14808|Q14809|Q14810	Missense_Mutation	SNP	ENST00000200557.6	hg19	CCDS11486.1	.	.	.	.	.	.	.	.	.	.	T	18.63	3.665086	0.67700	.	.	ENSG00000073670	ENST00000200557;ENST00000535346	T;T	0.41758	3.14;0.99	4.3	-5.76	0.02376	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.102842	0.64402	D	0.000003	T	0.50086	0.1595	L	0.48986	1.54	0.58432	D	0.999999	D;D	0.71674	0.991;0.998	D;D	0.68353	0.924;0.957	T	0.56408	-0.7984	10	0.52906	T	0.07	.	14.7285	0.69362	0.0:0.1995:0.0:0.8005	.	510;710	B4DKD2;O75078	.;ADA11_HUMAN	R	710;510	ENSP00000200557:S710R;ENSP00000443773:S510R	ENSP00000200557:S710R	S	+	3	2	ADAM11	40210905	0.000000	0.05858	0.931000	0.37212	0.987000	0.75469	-1.938000	0.01546	-1.060000	0.03189	-0.366000	0.07423	AGT	.	.		0.617	ADAM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444531.1	NM_002390		A	42855379	T	A	42855379	3	1	34	1	0	0	0	0	1	0	0	0	235	1635	57	4	2224	4	ADAM11	17	42855379	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	4255107	42855379	38339831	114	4148										
FAM38B	63895	hgsc.bcm.edu	37	chr18	10696431	10696440	+	Frame_Shift_Del	DEL	CAGTGTCAGC	CAGTGTCAGC	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gacaatgatgatgaagtccaCagtgtcagccaggaacatga							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	CAGTGTCAGC	CAGTGTCAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr18:10696431_10696440delCAGTGTCAGC	ENST00000503781.3	-	42	6585_6594	c.6586_6595delGCTGACACTG	c.(6586-6597)gctgacactgtgfs	p.ADTV2196fs	PIEZO2_ENST00000580640.1_Frame_Shift_Del_p.ADTV2221fs|PIEZO2_ENST00000285141.4_Frame_Shift_Del_p.ADTV51fs|PIEZO2_ENST00000302079.6_Frame_Shift_Del_p.ADTV2196fs|PIEZO2_ENST00000538948.1_Frame_Shift_Del_p.ADTV153fs	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2196					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)	p.T2198I(1)|p.T53I(1)									ATGAAGTCCACAGTGTCAGCCAGGAACATG	0.552																																					p.2196_2199del		Atlas-Indel,Pindel	.											.	.	.	.	2	Substitution - Missense(2)	lung(2)	c.6587_6596del						.																																			SO:0001589	frameshift_variant	63895	exon42			.	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"chromosome 18 open reading frame 30", "chromosome 18 open reading frame 58", "family with sequence similarity 38, member B"	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.6586_6595delGCTGACACTG	chr18.hg19:g.10696431_10696440delCAGTGTCAGC	ENSP00000421377:p.Ala2196fs	67.0	0.0		96.0	19.0	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Frame_Shift_Del	DEL	ENST00000503781.3	hg19																																																																																				.	.		0.552	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		-	10696440	CAGTGTCAGC	-	10696431	7	5	34	1	0	1	0	1	0	0	0	0	5563	478	17	0	1707	0	FAM38B	18	10696431	Frame_Shift_Del	DEL	CAGTGTCAGC	TCGA-BC-A10U-01A-11D-A12Z-10		10696431	67380817	115	4149										
POTEC	388468	hgsc.bcm.edu	37	chr18	14542729	14542729	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gctctgtggagcttgtccagAtcttctcgacggacgtggta	13	10	3	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr18:14542729A>G	ENST00000358970.5	-	1	416	c.417T>C	c.(415-417)gaT>gaC	p.D139D	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	139										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GCTTGTCCAGATCTTCTCGAC	0.597																																					p.D139D		Atlas-SNP	.											.	POTEC	129	.	0			c.T417C						.						65	73	71					18																	14542729		692	1584	2276	SO:0001819	synonymous_variant	388468	exon1			GTCCAGATCTTCT	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33894	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 6"		"ANKRD26-like family B, member 2"	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.417T>C	chr18.hg19:g.14542729A>G		327.0	0.0		906.0	360.0	NM_001137671		Silent	SNP	ENST00000358970.5	hg19	CCDS45835.1																																																																																			.	.		0.597	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		G	14542729	A	G	14542729	2	3	34	1	0	0	0	0	0	0	0	1	12271	330	12	2		2	POTEC	18	14542729	Silent	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	3846298	14542729	63534519	116	4150										
NEDD4L	23327	hgsc.bcm.edu	37	chr18	55996342	55996342	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tggagcccgagccctcggagGgcggggatgtccccgaggta	18	12	0	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr18:55996342G>C	ENST00000400345.3	+	10	1079	c.796G>C	c.(796-798)Ggc>Cgc	p.G266R	NEDD4L_ENST00000356462.6_Missense_Mutation_p.G266R|NEDD4L_ENST00000456986.1_Missense_Mutation_p.G145R|NEDD4L_ENST00000256832.7_Missense_Mutation_p.G145R|NEDD4L_ENST00000431212.2_Missense_Mutation_p.G145R|NEDD4L_ENST00000382850.4_Missense_Mutation_p.G266R|NEDD4L_ENST00000435432.2_Missense_Mutation_p.G145R|NEDD4L_ENST00000456173.2_Missense_Mutation_p.G145R|NEDD4L_ENST00000586263.1_Missense_Mutation_p.G258R|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000256830.9_Missense_Mutation_p.G266R|NEDD4L_ENST00000357895.5_Missense_Mutation_p.G258R	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	266					cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						GCCCTCGGAGGGCGGGGATGT	0.567																																					p.G266R		Atlas-SNP	.											.	NEDD4L	126	.	0			c.G796C						.						26	31	29					18																	55996342		2024	4169	6193	SO:0001583	missense	23327	exon10			TCGGAGGGCGGGG	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.796G>C	chr18.hg19:g.55996342G>C	ENSP00000383199:p.Gly266Arg	57.0	0.0		63.0	28.0	NM_015277	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	hg19	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	G	10.23	1.293134	0.23564	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	T;T;T;T;T;T;T;T;T;T	0.32988	1.46;1.47;1.43;1.45;1.94;1.92;1.86;1.94;1.94;1.92	5.97	5.11	0.69529	.	0.441226	0.28365	N	0.015616	T	0.24314	0.0589	L	0.36672	1.1	0.36379	D	0.861814	B;B;B;B;B;B;B	0.27791	0.189;0.116;0.145;0.036;0.045;0.0;0.145	B;B;B;B;B;B;B	0.33254	0.16;0.06;0.063;0.047;0.063;0.001;0.063	T	0.20605	-1.0270	10	0.16420	T	0.52	.	9.5568	0.39343	0.1971:0.0:0.8029:0.0	.	266;258;258;145;266;266;266	Q96PU5-3;Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;.;.;NED4L_HUMAN;.	R	266;266;266;266;145;145;258;145;145;145	ENSP00000383199:G266R;ENSP00000372301:G266R;ENSP00000348847:G266R;ENSP00000256830:G266R;ENSP00000256832:G145R;ENSP00000411947:G145R;ENSP00000350569:G258R;ENSP00000393395:G145R;ENSP00000405440:G145R;ENSP00000389406:G145R	ENSP00000256830:G266R	G	+	1	0	NEDD4L	54147322	0.998000	0.40836	0.870000	0.34147	0.066000	0.16364	2.582000	0.46085	1.540000	0.49301	0.655000	0.94253	GGC	.	.		0.567	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			C	55996342	G	C	55996342	3	2	34	1	0	0	0	0	1	0	0	0	10320	1232	43	4	862	4	NEDD4L	18	55996342	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	41453613	55996342	22080906	117	4151										
XAB2	56949	hgsc.bcm.edu	37	chr19	7687527	7687527	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tcaaagtactcggcccggcgGgcaggcagcgccgtggcctt	15	14	1	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr19:7687527G>A	ENST00000358368.4	-	11	1429	c.1392C>T	c.(1390-1392)gcC>gcT	p.A464A	XAB2_ENST00000534844.1_Silent_p.A461A	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	464					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CGGCCCGGCGGGCAGGCAGCG	0.677								Direct reversal of damage;Nucleotide excision repair (NER)																													p.A464A		Atlas-SNP	.											.	XAB2	69	.	0			c.C1392T						.						33	35	34					19																	7687527		2203	4299	6502	SO:0001819	synonymous_variant	56949	exon11			CCGGCGGGCAGGC	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"SYF1 homolog, RNA splicing factor (S. cerevisiae)", "SYF1 pre-mRNA-splicing factor"	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.1392C>T	chr19.hg19:g.7687527G>A		16.0	0.0		17.0	8.0	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	hg19	CCDS32892.1																																																																																			.	.		0.677	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		A	7687527	G	A	7687527	2	1	34	1	0	0	0	0	0	0	0	1	17433	1219	43	3		3	XAB2	19	7687527	Silent	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10		7687527	51441456	118	4152										
ZNF700	90592	hgsc.bcm.edu	37	chr19	12059506	12059506	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	acagtggggatggaacttatAaatgtaaattttgtgggaaa	12	2	0	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr19:12059506A>T	ENST00000254321.5	+	4	810	c.667A>T	c.(667-669)Aaa>Taa	p.K223*	ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000538752.1_Intron|ZNF700_ENST00000482090.1_Nonsense_Mutation_p.K205*|ZNF763_ENST00000590798.1_Intron|CTD-2006C1.12_ENST00000586394.1_RNA	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						TGGAACTTATAAATGTAAATT	0.368																																					p.K226X		Atlas-SNP	.											.	ZNF700	81	.	0			c.A676T						.						79	85	83					19																	12059506		2203	4300	6503	SO:0001587	stop_gained	90592	exon4			ACTTATAAATGTA	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"Zinc fingers, C2H2-type", "-"	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.667A>T	chr19.hg19:g.12059506A>T	ENSP00000254321:p.Lys223*	106.0	0.0		189.0	79.0	NM_001271848	B9EGU4	Nonsense_Mutation	SNP	ENST00000254321.5	hg19	CCDS32915.1	.	.	.	.	.	.	.	.	.	.	a	16.06	3.014522	0.54468	.	.	ENSG00000196757	ENST00000254321	.	.	.	0.732	-0.667	0.11395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.5805	0.02633	0.3076:0.0:0.3686:0.3237	.	.	.	.	X	223	.	ENSP00000254321:K223X	K	+	1	0	ZNF700	11920506	0.000000	0.05858	0.039000	0.18376	0.151000	0.21798	-4.230000	0.00270	-0.246000	0.09611	0.254000	0.18369	AAA	.	.		0.368	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		T	12059506	A	T	12059506	4	4	34	1	0	0	0	0	0	1	0	0	18119	363	13	4	681	4	ZNF700	19	12059506	Nonsense_Mutation	SNP	A	TCGA-BC-A10U-01A-11D-A12Z-10	4371979	12059506	47069477	119	4153										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22156136	22156136	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ttttcttatgataactaaggGttgaggaccacttataggct	9	6	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr19:22156136G>T	ENST00000397126.4	-	4	1848	c.1700C>A	c.(1699-1701)aCc>aAc	p.T567N	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	567					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				ATAACTAAGGGTTGAGGACCA	0.343																																					p.T567N		Atlas-SNP	.											.	ZNF208	817	.	0			c.C1700A						.						24	24	24					19																	22156136		1924	4104	6028	SO:0001583	missense	7757	exon4			CTAAGGGTTGAGG	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1700C>A	chr19.hg19:g.22156136G>T	ENSP00000380315:p.Thr567Asn	22.0	0.0		56.0	20.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	G	0.206	-1.040222	0.02013	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.07800	3.16	2.82	-5.63	0.02474	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02848	0.0085	.	.	.	0.09310	N	1	B	0.23377	0.084	B	0.26614	0.071	T	0.35226	-0.9797	8	0.06891	T	0.86	.	2.7578	0.05298	0.1287:0.3034:0.3969:0.171	.	467	O43345	ZN208_HUMAN	N	567;467	ENSP00000380315:T567N	ENSP00000380315:T567N	T	-	2	0	ZNF208	21947976	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.956000	0.00675	-3.152000	0.00230	-2.155000	0.00331	ACC	.	.		0.343	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22156136	G	T	22156136	3	4	34	1	0	0	0	0	1	0	0	0	17781	1261	44	3	2146	3	ZNF208	19	22156136	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	10096630	22156136	36972847	120	4154										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30936253	30936254	+	Frame_Shift_Ins	INS	-	-	AAGT													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggcagccagagagacctgccINSaagtaagctcgaccctttag							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr19:30936253_30936254insAAGT	ENST00000355537.3	+	2	1931_1932	c.1784_1785insAAGT	c.(1783-1788)ccaagtfs	p.-597fs		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536						negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					AGAGACCTGCCAAGTAAGCTCG	0.52																																					p.P595fs		Atlas-Indel,Pindel	.											.	ZNF536	424	.	0			c.1784_1785insAAGT						.																																			SO:0001589	frameshift_variant	9745	exon2			.		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.1785_1788dupAAGT	chr19.hg19:g.30936254_30936257dupAAGT	ENSP00000347730:p.Lys597fs	52.0	0.0		70.0	12.0	NM_014717	A2RU18	Frame_Shift_Ins	INS	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.		0.52	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		AAGT	30936254	-	AAGT	30936253	7	5	34	1	0	1	1	0	0	0	0	0	17989	594	21	0	1786	0	ZNF536	19	30936253	Frame_Shift_Ins	INS	-	TCGA-BC-A10U-01A-11D-A12Z-10	8780117	30936253	28192730	121	4155										
SHKBP1	92799	hgsc.bcm.edu	37	chr19	41089323	41089323	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ggtccaggaggtgcagcccaTcaccagttatgacgcggcag	14	12	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr19:41089323T>A	ENST00000291842.5	+	11	1029	c.980T>A	c.(979-981)aTc>aAc	p.I327N	SHKBP1_ENST00000600733.1_Missense_Mutation_p.I302N	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	327					protein homooligomerization (GO:0051260)					breast(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(3)|urinary_tract(1)	29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GTGCAGCCCATCACCAGTTAT	0.647																																					p.I327N		Atlas-SNP	.											.	SHKBP1	68	.	0			c.T980A						.						32	28	30					19																	41089323		2203	4298	6501	SO:0001583	missense	92799	exon11			AGCCCATCACCAG	AF258553	CCDS12560.1	19q13.2	2013-01-10				ENSG00000160410		"WD repeat domain containing"	19214	protein-coding gene	gene with protein product						11152963	Standard	NM_138392		Approved	PP203, Sb1	uc002oob.3	Q8TBC3		ENST00000291842.5:c.980T>A	chr19.hg19:g.41089323T>A	ENSP00000291842:p.Ile327Asn	34.0	0.0		50.0	20.0	NM_138392	Q8N2I6|Q8WY93|Q96IB8	Missense_Mutation	SNP	ENST00000291842.5	hg19	CCDS12560.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.845362	0.51164	.	.	ENSG00000160410	ENST00000291842;ENST00000446701	T	0.09817	2.94	5.27	4.24	0.50183	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.32852	0.0843	M	0.81942	2.565	0.80722	D	1	D;D;D;B;D;B	0.89917	1.0;1.0;0.997;0.22;0.999;0.141	D;D;D;B;D;B	0.83275	0.996;0.991;0.994;0.062;0.996;0.028	T	0.04607	-1.0939	10	0.87932	D	0	-20.1167	10.6089	0.45410	0.1443:0.0:0.0:0.8557	.	205;164;250;164;327;327	B4DLI0;B4DUW2;B4DUV2;B3KVX8;B2R6W9;Q8TBC3	.;.;.;.;.;SHKB1_HUMAN	N	327;164	ENSP00000291842:I327N	ENSP00000291842:I327N	I	+	2	0	SHKBP1	45781163	1.000000	0.71417	0.998000	0.56505	0.289000	0.27227	7.495000	0.81514	0.832000	0.34804	-0.509000	0.04479	ATC	.	.		0.647	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462613.2	NM_138392		A	41089323	T	A	41089323	3	1	34	1	0	0	0	0	1	0	0	0	14299	1435	50	4	1022	4	SHKBP1	19	41089323	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	10153070	41089323	18039660	122	4156										
CYP2A6	1548	hgsc.bcm.edu	37	chr19	41354534	41354534	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ctcaccgccagtgccccggaGggcgtcgatgaggaagcccg	15	15	1	1	rs60563539		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr19:41354534G>T	ENST00000301141.5	-	3	498	c.478C>A	c.(478-480)Ctc>Atc	p.L160I	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	160			L -> H (in allele CYP2A6*2; unable to catalyze 7-hydroxylation of coumarin; causes switching from coumarin 7- hydroxylation to 3-hydroxylation; dbSNP:rs1801272). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2322567, ECO:0000269|PubMed:2748347, ECO:0000269|Ref.6}.		coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GTGCCCCGGAGGGCGTCGATG	0.706																																					p.L160I		Atlas-SNP	.											.	CYP2A6	69	.	0			c.C478A						.						35	39	37					19																	41354534		2203	4299	6502	SO:0001583	missense	1548	exon3			CCCGGAGGGCGTC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.478C>A	chr19.hg19:g.41354534G>T	ENSP00000301141:p.Leu160Ile	56.0	0.0		63.0	7.0	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	hg19	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	7.661	0.684983	0.14973	.	.	ENSG00000255974	ENST00000301141	T	0.72282	-0.64	2.95	-5.91	0.02269	.	0.336308	0.29676	U	0.011482	T	0.46814	0.1412	L	0.28649	0.875	0.09310	N	1	B	0.02656	0.0	B	0.25506	0.061	T	0.25187	-1.0139	10	0.49607	T	0.09	.	0.9801	0.01434	0.4696:0.1142:0.2033:0.2128	rs60563539	160	P11509	CP2A6_HUMAN	I	160	ENSP00000301141:L160I	ENSP00000301141:L160I	L	-	1	0	CYP2A6	46046374	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.497000	0.00969	-2.055000	0.00899	-1.602000	0.00811	CTC	.	.		0.706	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		T	41354534	G	T	41354534	3	4	34	1	0	0	0	0	1	0	0	0	4164	1000	35	3	1034	3	CYP2A6	19	41354534	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	265211	41354534	17774449	123	4157										
ZNF28	7576	hgsc.bcm.edu	37	chr19	53303182	53303182	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gactgaaggtcttgccacacTcattacacttgtaaggtttc	8	10	2	1	rs142391659		TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr19:53303182T>C	ENST00000457749.2	-	4	2035	c.1916A>G	c.(1915-1917)gAg>gGg	p.E639G	ZNF28_ENST00000414252.2_Missense_Mutation_p.E586G|ZNF28_ENST00000438150.2_Missense_Mutation_p.E586G|ZNF28_ENST00000360272.4_Missense_Mutation_p.E586G	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	639					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		CTTGCCACACTCATTACACTT	0.428																																					p.E639G		Atlas-SNP	.											.	ZNF28	191	.	0			c.A1916G						.						193	181	185					19																	53303182		2203	4300	6503	SO:0001583	missense	7576	exon4			CCACACTCATTAC	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.1916A>G	chr19.hg19:g.53303182T>C	ENSP00000397693:p.Glu639Gly	99.0	0.0		249.0	11.0	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	hg19	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	10.84	1.465403	0.26335	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252	T;T;T;T	0.35789	1.29;1.29;1.29;1.29	1.81	0.634	0.17718	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40546	0.1121	L	0.47716	1.5	0.09310	N	1	D	0.60575	0.988	P	0.55615	0.78	T	0.22695	-1.0209	9	0.72032	D	0.01	.	5.8153	0.18490	0.2376:0.0:0.0:0.7624	.	639	P17035	ZNF28_HUMAN	G	586;639;586;586	ENSP00000412143:E586G;ENSP00000397693:E639G;ENSP00000353410:E586G;ENSP00000444965:E586G	ENSP00000353410:E586G	E	-	2	0	ZNF28	57994994	0.000000	0.05858	0.024000	0.17045	0.568000	0.35870	-0.093000	0.11111	-0.035000	0.13691	0.248000	0.18094	GAG	.	.		0.428	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		C	53303182	T	C	53303182	3	2	34	1	0	0	0	0	1	0	0	0	17828	1551	54	2	244	2	ZNF28	19	53303182	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	11948648	53303182	5825801	124	4158										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53856410	53856410	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ataaggcaattcatagtggaGagaaaccttacaagtgtaat	9	5	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr19:53856410G>A	ENST00000595091.1	+	5	2701	c.2482G>A	c.(2482-2484)Gag>Aag	p.E828K	ZNF845_ENST00000458035.1_Missense_Mutation_p.E828K			Q96IR2	ZN845_HUMAN	zinc finger protein 845	828					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TCATAGTGGAGAGAAACCTTA	0.398																																					p.E828K		Atlas-SNP	.											.	ZNF845	101	.	0			c.G2482A						.						46	44	44					19																	53856410		692	1591	2283	SO:0001583	missense	91664	exon4			AGTGGAGAGAAAC	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2482G>A	chr19.hg19:g.53856410G>A	ENSP00000470005:p.Glu828Lys	109.0	0.0		197.0	96.0	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	hg19	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.052672	0.36181	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.24350	1.86	1.95	0.783	0.18572	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35364	0.0929	L	0.56280	1.765	0.24756	N	0.992955	P	0.43633	0.813	P	0.53760	0.734	T	0.18304	-1.0341	9	0.46703	T	0.11	.	9.0555	0.36403	0.0:0.2296:0.7703:0.0	.	828	Q96IR2	ZN845_HUMAN	K	828;744	ENSP00000388311:E828K	ENSP00000412086:E744K	E	+	1	0	ZNF845	58548222	0.068000	0.21057	0.001000	0.08648	0.007000	0.05969	2.180000	0.42537	0.132000	0.18615	0.454000	0.30748	GAG	.	.		0.398	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		A	53856410	G	A	53856410	3	1	34	1	0	0	0	0	1	0	0	0	18206	943	33	3	2492	3	ZNF845	19	53856410	Missense_Mutation	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	553228	53856410	5272573	125	4159										
CST11	140880	hgsc.bcm.edu	37	chr20	23431159	23431159	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	acacctagtcactgctgcagCttttgttcaaaattttgtac	6	10	2	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr20:23431159C>G	ENST00000377009.3	-	3	434	c.401G>C	c.(400-402)aGc>aCc	p.S134T	CST11_ENST00000377007.3_Missense_Mutation_p.S99T	NM_130794.1	NP_570612.1	Q9H112	CST11_HUMAN	cystatin 11	134					defense response to bacterium (GO:0042742)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			kidney(2)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	14	Colorectal(13;0.0431)|Lung NSC(19;0.235)					ACTGCTGCAGCTTTTGTTCAA	0.393																																					p.S134T		Atlas-SNP	.											.	CST11	27	.	0			c.G401C						.						113	96	102					20																	23431159		2203	4300	6503	SO:0001583	missense	140880	exon3			CTGCAGCTTTTGT	AL096677	CCDS13154.1, CCDS13155.1	20p11.21	2012-08-14			ENSG00000125831	ENSG00000125831			15959	protein-coding gene	gene with protein product		609731		CST8L		20565543	Standard	NM_080830		Approved	dJ322G13.6, CTES2	uc002wtf.1	Q9H112	OTTHUMG00000032060	ENST00000377009.3:c.401G>C	chr20.hg19:g.23431159C>G	ENSP00000366208:p.Ser134Thr	91.0	0.0		148.0	64.0	NM_130794	Q0VAF2|Q0VAF3|Q8WXU5|Q8WXU6|Q9H113	Missense_Mutation	SNP	ENST00000377009.3	hg19	CCDS13155.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.682908	0.00745	.	.	ENSG00000125831	ENST00000377009;ENST00000377007	T;T	0.16196	2.71;2.36	3.86	1.59	0.23543	Proteinase inhibitor I25, cystatin (1);	0.621839	0.16746	N	0.201255	T	0.07007	0.0178	N	0.10685	0.025	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31280	-0.9949	10	0.36615	T	0.2	-7.6746	3.4946	0.07650	0.0:0.2151:0.2044:0.5805	.	99;134	Q9H112-2;Q9H112	.;CST11_HUMAN	T	134;99	ENSP00000366208:S134T;ENSP00000366206:S99T	ENSP00000366206:S99T	S	-	2	0	CST11	23379159	0.530000	0.26330	0.290000	0.24890	0.002000	0.02628	0.301000	0.19174	0.021000	0.15133	-2.587000	0.00166	AGC	.	.		0.393	CST11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078314.1	NM_130794		G	23431159	C	G	23431159	3	3	34	1	0	0	0	0	1	0	0	0	3973	797	28	4	19	4	CST11	20	23431159	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10		23431159	39594361	126	4160										
MYBL2	4605	hgsc.bcm.edu	37	chr20	42331511	42331511	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gcctcacgcccaagagcacaCctgttaagaccctgcccttc	7	18	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr20:42331511C>G	ENST00000217026.4	+	8	1460	c.1333C>G	c.(1333-1335)Cct>Gct	p.P445A	MYBL2_ENST00000396863.4_Missense_Mutation_p.P421A	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	445					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CAAGAGCACACCTGTTAAGAC	0.592																																					p.P445A		Atlas-SNP	.											.	MYBL2	82	.	0			c.C1333G						.						132	108	116					20																	42331511		2203	4300	6503	SO:0001583	missense	4605	exon8			AGCACACCTGTTA		CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.1333C>G	chr20.hg19:g.42331511C>G	ENSP00000217026:p.Pro445Ala	70.0	0.0		124.0	39.0	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	hg19	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.326144	0.60743	.	.	ENSG00000101057	ENST00000396863;ENST00000217026	T;T	0.51325	0.71;0.75	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.51058	0.1652	L	0.32530	0.975	0.80722	D	1	D;P	0.56968	0.978;0.539	P;B	0.52793	0.709;0.124	T	0.54583	-0.8272	10	0.62326	D	0.03	-15.5247	17.4343	0.87547	0.0:1.0:0.0:0.0	.	421;445	F8W6N6;P10244	.;MYBB_HUMAN	A	421;445	ENSP00000380072:P421A;ENSP00000217026:P445A	ENSP00000217026:P445A	P	+	1	0	MYBL2	41764925	1.000000	0.71417	0.929000	0.37066	0.839000	0.47603	7.269000	0.78482	2.488000	0.83962	0.462000	0.41574	CCT	.	.		0.592	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		G	42331511	C	G	42331511	3	3	34	1	0	0	0	0	1	0	0	0	10019	507	18	4	1363	4	MYBL2	20	42331511	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	18900352	42331511	20694009	127	4161										
PMEPA1	56937	hgsc.bcm.edu	37	chr20	56227217	56227217	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gtcccctccagcaaggagggCggcccactgctctgctggtg	14	15	1	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chr20:56227217C>A	ENST00000341744.3	-	4	1075	c.756G>T	c.(754-756)ccG>ccT	p.P252P	PMEPA1_ENST00000395816.3_Silent_p.P202P|PMEPA1_ENST00000395814.1_Silent_p.P202P|PMEPA1_ENST00000347215.4_Silent_p.P217P|PMEPA1_ENST00000265626.4_Silent_p.P202P	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	252					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						GCAAGGAGGGCGGCCCACTGC	0.667																																					p.P252P		Atlas-SNP	.											.	PMEPA1	29	.	0			c.G756T						.						19	20	20					20																	56227217		2197	4291	6488	SO:0001819	synonymous_variant	56937	exon4			GGAGGGCGGCCCA	AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"solid tumor-associated 1"	606564	"transmembrane, prostate androgen induced RNA"	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.756G>T	chr20.hg19:g.56227217C>A		43.0	0.0		46.0	20.0	NM_020182	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Silent	SNP	ENST00000341744.3	hg19	CCDS13463.1																																																																																			.	.		0.667	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182		A	56227217	C	A	56227217	2	1	34	1	0	0	0	0	0	0	0	1	12141	755	27	1		1	PMEPA1	20	56227217	Silent	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	13895706	56227217	6798303	128	4162										
ZFX	7543	hgsc.bcm.edu	37	chrX	24227055	24227104	+	Frame_Shift_Del	DEL	GCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGC	GCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGC	-													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	ttgaaaaccggaatggcactGcaagtgccctcttgcacata							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	GCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGC	GCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chrX:24227055_24227104delGCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGC	ENST00000379177.1	+	10	1559_1608	c.1132_1181delGCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGC	c.(1132-1182)gcaagtgccctcttgcacatagatgagtctgctggcctcggcagactggctfs	p.ASALLHIDESAGLGRLA378fs	ZFX_ENST00000379188.3_Frame_Shift_Del_p.ASALLHIDESAGLGRLA378fs|ZFX_ENST00000304543.5_Frame_Shift_Del_p.ASALLHIDESAGLGRLA378fs|ZFX_ENST00000459724.1_3'UTR|ZFX_ENST00000338565.3_Frame_Shift_Del_p.ASALLHIDESAGLGRLA328fs|ZFX_ENST00000539115.1_Frame_Shift_Del_p.ASALLHIDESAGLGRLA149fs|ZFX_ENST00000540034.1_Frame_Shift_Del_p.ASALLHIDESAGLGRLA417fs	NM_001178085.1|NM_003410.3	NP_001171556.1|NP_003401.2	P17010	ZFX_HUMAN	zinc finger protein, X-linked	378					death (GO:0016265)|fertilization (GO:0009566)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|parental behavior (GO:0060746)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|prostate(1)	24						GAATGGCACTGCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGCTAAACAAAAA	0.424																																					p.377_394del	Esophageal Squamous(20;306 562 7346 32868 37983)	Atlas-Indel,Pindel	.											.	ZFX	61	.	0			c.1131_1180del						.																																			SO:0001589	frameshift_variant	7543	exon9			.		CCDS14211.1, CCDS55390.1	Xp22.1-p21.3	2013-01-08			ENSG00000005889	ENSG00000005889		"Zinc fingers, C2H2-type"	12869	protein-coding gene	gene with protein product		314980					Standard	NM_003410		Approved	ZNF926	uc022bua.1	P17010	OTTHUMG00000021264	ENST00000379177.1:c.1132_1181delGCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGC	chrX.hg19:g.24227055_24227104delGCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGC	ENSP00000368475:p.Ala378fs	106.0	0.0		45.0	18.0	NM_003410	B9EG97|O43668|Q8WYJ8	Frame_Shift_Del	DEL	ENST00000379177.1	hg19	CCDS14211.1																																																																																			.	.		0.424	ZFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056084.1	NM_003410		-	24227104	GCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGC	-	24227055	7	5	34	1	0	1	0	1	0	0	0	0	17676	1319	46	0	1154	0	ZFX	23	24227055	Frame_Shift_Del	DEL	GCAAGTGCCCTCTTGCACATAGATGAGTCTGCTGGCCTCGGCAGACTGGC	TCGA-BC-A10U-01A-11D-A12Z-10		24227055	131043505	129	4163										
CXorf59	286464	hgsc.bcm.edu	37	chrX	36122659	36122659	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gccatactgcagcaataataTgccccccatatgtgtgcaaa	7	12	0	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chrX:36122659T>C	ENST00000313548.4	+	8	1082	c.896T>C	c.(895-897)aTg>aCg	p.M299T		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	299						integral component of membrane (GO:0016021)											AGCAATAATATGCCCCCCATA	0.353																																					p.M299T		Atlas-SNP	.											.	.	.	.	0			c.T896C						.						125	107	113					X																	36122659		2202	4300	6502	SO:0001583	missense	286464	exon8			ATAATATGCCCCC	AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"chromosome X open reading frame 59"	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.896T>C	chrX.hg19:g.36122659T>C	ENSP00000324767:p.Met299Thr	231.0	0.0		473.0	21.0	NM_173695		Missense_Mutation	SNP	ENST00000313548.4	hg19	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	T	9.757	1.169143	0.21621	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	.	.	.	5.53	0.0558	0.14316	.	1.589030	0.03720	N	0.251685	T	0.23492	0.0568	L	0.29908	0.895	0.09310	N	1	B	0.29341	0.242	B	0.26094	0.066	T	0.13255	-1.0516	9	0.34782	T	0.22	-0.148	1.2548	0.01989	0.1474:0.1735:0.1497:0.5294	.	299	Q8N9S7	CX059_HUMAN	T	299	.	ENSP00000324767:M299T	M	+	2	0	CXorf59	36032580	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	0.051000	0.14141	-0.034000	0.13713	0.486000	0.48141	ATG	.	.		0.353	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695		C	36122659	T	C	36122659	3	2	34	1	0	0	0	0	1	0	0	0	4117	1464	51	2	922	2	CXorf59	23	36122659	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	11895604	36122659	119147901	130	4164										
ACRC	93953	hgsc.bcm.edu	37	chrX	70824010	70824010	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gcagtgatgattcggaagctTccgacgacagcagtgatgat	13	8	0	4			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chrX:70824010T>C	ENST00000373695.1	+	7	1420	c.883T>C	c.(883-885)Tcc>Ccc	p.S295P	ACRC_ENST00000373696.3_Missense_Mutation_p.S295P			Q96QF7	ACRC_HUMAN	acidic repeat containing	295	Asp/Ser-rich.					nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1)	54	Renal(35;0.156)					TTCGGAAGCTTCCGACGACAG	0.527																																					p.S295P		Atlas-SNP	.											.	ACRC	110	.	0			c.T883C						.						132	124	127					X																	70824010		2203	4300	6503	SO:0001583	missense	93953	exon8			GAAGCTTCCGACG	AJ311392	CCDS35326.1	Xq13.1	2010-08-05			ENSG00000147174	ENSG00000147174			15805	protein-coding gene	gene with protein product		300369					Standard	NM_052957		Approved		uc004eae.2	Q96QF7	OTTHUMG00000033327	ENST00000373695.1:c.883T>C	chrX.hg19:g.70824010T>C	ENSP00000362799:p.Ser295Pro	35.0	0.0		168.0	14.0	NM_052957	B9EG62	Missense_Mutation	SNP	ENST00000373695.1	hg19	CCDS35326.1	.	.	.	.	.	.	.	.	.	.	T	2.597	-0.293877	0.05568	.	.	ENSG00000147174	ENST00000373696;ENST00000373695	T;T	0.29397	1.57;1.57	0.14	-0.28	0.12886	.	.	.	.	.	T	0.09642	0.0237	N	0.01874	-0.695	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.30268	-0.9984	9	0.20519	T	0.43	.	4.4172	0.11463	0.0:0.6635:0.0:0.3365	.	295	Q96QF7	ACRC_HUMAN	P	295	ENSP00000362800:S295P;ENSP00000362799:S295P	ENSP00000362799:S295P	S	+	1	0	ACRC	70740735	0.000000	0.05858	0.009000	0.14445	0.009000	0.06853	-1.504000	0.02275	-1.219000	0.02597	-1.215000	0.01618	TCC	.	.		0.527	ACRC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081856.1			C	70824010	T	C	70824010	3	2	34	1	0	0	0	0	1	0	0	0	171	1783	62	2	909	2	ACRC	23	70824010	Missense_Mutation	SNP	T	TCGA-BC-A10U-01A-11D-A12Z-10	34701351	70824010	84446550	131	4165										
PHKA1	5255	hgsc.bcm.edu	37	chrX	71800935	71800936	+	Frame_Shift_Ins	INS	-	-	C													0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	aggtaggtcatggtgccaaaINScctgccactgggtgcactgt							TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chrX:71800935_71800936insC	ENST00000373542.4	-	32	3747_3748	c.3588_3589insG	c.(3586-3591)aggtttfs	p.F1197fs	PHKA1_ENST00000541944.1_Frame_Shift_Ins_p.F1125fs|PHKA1_ENST00000373539.3_Frame_Shift_Ins_p.F1214fs|PHKA1_ENST00000373545.3_Frame_Shift_Ins_p.F1155fs|PHKA1_ENST00000339490.3_Frame_Shift_Ins_p.F1184fs	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	1197					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					ATGGTGCCAAACCTGCCACTGG	0.55																																					p.F1197fs		Atlas-INDEL	.											.	PHKA1	129	.	0			c.3589_3590insG						.																																			SO:0001589	frameshift_variant	5255	exon32			.		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.3589dupG	chrX.hg19:g.71800937_71800937dupC	ENSP00000362643:p.Phe1197fs	57.0	0.0		263.0	26.0	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Frame_Shift_Ins	INS	ENST00000373542.4	hg19	CCDS14421.1																																																																																			.	.		0.55	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			C	71800936	-	C	71800935	7	5	34	1	0	1	1	0	0	0	0	0	11852	43	2	0	86	0	PHKA1	23	71800935	Frame_Shift_Ins	INS	-	TCGA-BC-A10U-01A-11D-A12Z-10	976925	71800935	83469625	132	4166										
DRP2	1821	hgsc.bcm.edu	37	chrX	100513348	100513348	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	gtggcagcatgaggaggcagCtgaggcacccagtctggctg	17	10	1	2			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chrX:100513348C>G	ENST00000395209.3	+	22	2968	c.2441C>G	c.(2440-2442)gCt>gGt	p.A814G	DRP2_ENST00000541709.1_Missense_Mutation_p.A736G|DRP2_ENST00000402866.1_Missense_Mutation_p.A814G|DRP2_ENST00000538510.1_Missense_Mutation_p.A814G	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	814					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						GAGGAGGCAGCTGAGGCACCC	0.597																																					p.A814G		Atlas-SNP	.											.	DRP2	98	.	0			c.C2441G						.						29	28	29					X																	100513348		2199	4290	6489	SO:0001583	missense	1821	exon22			AGGCAGCTGAGGC	U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.2441C>G	chrX.hg19:g.100513348C>G	ENSP00000378635:p.Ala814Gly	51.0	0.0		221.0	135.0	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	hg19	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	C	0.089	-1.170240	0.01660	.	.	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	T;T;T;T	0.05081	3.62;3.62;3.5;3.62	4.48	1.63	0.23807	.	0.505563	0.21254	N	0.077586	T	0.01765	0.0056	N	0.02665	-0.54	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.46527	-0.9185	10	0.02654	T	1	-0.35	4.3961	0.11363	0.0:0.4408:0.1631:0.3961	.	814	Q13474	DRP2_HUMAN	G	814;814;736;814	ENSP00000385038:A814G;ENSP00000378635:A814G;ENSP00000444752:A736G;ENSP00000441051:A814G	ENSP00000378635:A814G	A	+	2	0	DRP2	100400004	0.047000	0.20315	0.069000	0.20011	0.354000	0.29330	0.522000	0.22909	0.334000	0.23590	0.422000	0.28245	GCT	.	.		0.597	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		G	100513348	C	G	100513348	3	3	34	1	0	0	0	0	1	0	0	0	4766	797	28	4	2519	4	DRP2	23	100513348	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	28712413	100513348	54757212	133	4167										
ACTRT1	139741	hgsc.bcm.edu	37	chrX	127185963	127185963	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tcctgttaccagtccacgctCaatggggtagtgcaaatgta	10	10	1	0			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chrX:127185963C>T	ENST00000371124.3	-	1	419	c.223G>A	c.(223-225)Gag>Aag	p.E75K		NM_138289.3	NP_612146.1	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	75						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	34						AGTCCACGCTCAATGGGGTAG	0.463																																					p.E75K		Atlas-SNP	.											.	ACTRT1	92	.	0			c.G223A						.						165	153	157					X																	127185963		2203	4300	6503	SO:0001583	missense	139741	exon1			CACGCTCAATGGG	AF440739	CCDS14611.1	Xq25	2008-02-05	2005-11-22		ENSG00000123165	ENSG00000123165			24027	protein-coding gene	gene with protein product		300487				12243744	Standard	NM_138289		Approved	AIP1, KIAA0705, ARIP1, Arp-T1	uc004eum.3	Q8TDG2	OTTHUMG00000022359	ENST00000371124.3:c.223G>A	chrX.hg19:g.127185963C>T	ENSP00000360165:p.Glu75Lys	56.0	0.0		322.0	215.0	NM_138289	Q6X7C1|Q96L10	Missense_Mutation	SNP	ENST00000371124.3	hg19	CCDS14611.1	.	.	.	.	.	.	.	.	.	.	C	8.882	0.951787	0.18431	.	.	ENSG00000123165	ENST00000371124	D	0.97328	-4.34	3.76	1.98	0.26296	.	0.090484	0.45867	D	0.000339	D	0.95290	0.8472	L	0.48362	1.52	0.34742	D	0.73087	P	0.41366	0.747	P	0.48334	0.574	D	0.94629	0.7820	10	0.87932	D	0	.	6.4851	0.22085	0.0:0.7073:0.1816:0.111	.	75	Q8TDG2	ACTT1_HUMAN	K	75	ENSP00000360165:E75K	ENSP00000360165:E75K	E	-	1	0	ACTRT1	127013644	1.000000	0.71417	0.003000	0.11579	0.022000	0.10575	3.404000	0.52623	0.406000	0.25560	-1.268000	0.01426	GAG	.	.		0.463	ACTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058192.1	NM_138289		T	127185963	C	T	127185963	3	4	34	1	0	0	0	0	1	0	0	0	218	835	29	3	911	3	ACTRT1	23	127185963	Missense_Mutation	SNP	C	TCGA-BC-A10U-01A-11D-A12Z-10	26672615	127185963	28084597	134	4168										
BRCC3	79184	hgsc.bcm.edu	37	chrX	154299926	154299926	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.062015503875969	8	1	1.23432825899089	1.37459283387622	1.12003860538062	1	1	0	tggggctgtgcataggggagGtgagtaggtctgttagcctg	19	5	1	1			TCGA-BC-A10U-01A-11D-A12Z-10	TCGA-BC-A10U-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a85cabff-e8dc-440a-90f5-4fca51c33dd9	33582c29-22ba-4b6d-b59e-89d662e0486d	g.chrX:154299926G>A	ENST00000369462.1	+	1	148		c.e1+1		BRCC3_ENST00000340647.4_Splice_Site|MTCP1_ENST00000362018.2_Intron|MTCP1_ENST00000369476.3_5'Flank|BRCC3_ENST00000330045.7_Splice_Site|BRCC3_ENST00000369459.2_Splice_Site|CMC4_ENST00000369484.3_5'Flank|MTCP1_ENST00000482244.1_5'Flank|BRCC3_ENST00000399042.1_Missense_Mutation_p.V42M	NM_024332.3	NP_077308.1	P46736	BRCC3_HUMAN	BRCA1/BRCA2-containing complex, subunit 3						double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|regulation of catalytic activity (GO:0050790)|response to ionizing radiation (GO:0010212)|response to X-ray (GO:0010165)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|nuclear ubiquitin ligase complex (GO:0000152)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	enzyme regulator activity (GO:0030234)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|polyubiquitin binding (GO:0031593)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|skin(1)	22	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CATAGGGGAGGTGAGTAGGTC	0.612																																					.		Atlas-SNP	.											.	BRCC3	44	.	0			c.123+1G>A						.						36	46	43					X																	154299926		2103	4201	6304	SO:0001630	splice_region_variant	79184	exon1			GGGGAGGTGAGTA	X64643	CCDS56610.1, CCDS56611.1, CCDS56612.1	Xq28	2013-05-29	2005-11-21	2005-11-21	ENSG00000185515	ENSG00000185515			24185	protein-coding gene	gene with protein product	"Lys-63-specific deubiquitinase"	300617	"chromosome X open reading frame 53"	CXorf53		1303175, 14636569	Standard	NM_024332		Approved	C6.1A, BRCC36	uc004fna.3	P46736	OTTHUMG00000022658	ENST00000369462.1:c.123+1G>A	chrX.hg19:g.154299926G>A		18.0	0.0		146.0	42.0	NM_001018055	A6QRF8|A6QRF9|A8MUX5|A8MWH0|A9Z1Y0|A9Z1Y5|B1B062|B4DQN7|Q16107|Q53YX5|Q9BTZ6	Splice_Site	SNP	ENST00000369462.1	hg19	CCDS56611.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.97|15.97	2.989290|2.989290	0.53934|0.53934	.|.	.|.	ENSG00000185515|ENSG00000185515	ENST00000340647;ENST00000330045;ENST00000369459;ENST00000369462;ENST00000411985|ENST00000399042;ENST00000457026	.|T	.|0.56275	.|0.47	4.09|4.09	4.09|4.09	0.47781|0.47781	.|.	.|1.413030	.|0.05247	.|N	.|0.513239	.|T	.|0.62816	.|0.2459	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.52155	.|-0.8613	.|7	.|0.54805	.|T	.|0.06	.|.	11.407|11.407	0.49904|0.49904	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	.|M	-1|42	.|ENSP00000381998:V42M	.|ENSP00000381998:V42M	.|V	+|+	.|1	.|0	BRCC3|BRCC3	153953120|153953120	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.640000|0.640000	0.38277|0.38277	8.004000|8.004000	0.88535|0.88535	1.968000|1.968000	0.57251|0.57251	0.600000|0.600000	0.82982|0.82982	.|GTG	.	.		0.612	BRCC3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058788.4	NM_024332	Intron	A	154299926	G	A	154299926	5	1	34	1	0	0	0	0	0	0	1	0	1502	1275	44	3	126	3	BRCC3	23	154299926	Splice_Site	SNP	G	TCGA-BC-A10U-01A-11D-A12Z-10	27113963	154299926	970634	135	4169										
UBE2J2	118424	hgsc.bcm.edu	37	chr1	1192490	1192490	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tccacgtgtccgggtggaaaTccgtgatagaaagacacagc	12	10	0	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:1192490T>C	ENST00000349431.6	-	5	515	c.296A>G	c.(295-297)gAt>gGt	p.D99G	UBE2J2_ENST00000400929.2_Missense_Mutation_p.D47G|UBE2J2_ENST00000348298.7_Missense_Mutation_p.D47G|UBE2J2_ENST00000491779.1_5'UTR|UBE2J2_ENST00000339385.6_Missense_Mutation_p.D64G|UBE2J2_ENST00000400930.4_Missense_Mutation_p.D115G|UBE2J2_ENST00000360466.2_Missense_Mutation_p.D99G|UBE2J2_ENST00000347370.2_Missense_Mutation_p.D47G	NM_058167.2	NP_477515.2	Q8N2K1	UB2J2_HUMAN	ubiquitin-conjugating enzyme E2, J2	99					protein ubiquitination (GO:0016567)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			cervix(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.66e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.53e-21)|Colorectal(212;0.00019)|COAD - Colon adenocarcinoma(227;0.000215)|Kidney(185;0.00255)|BRCA - Breast invasive adenocarcinoma(365;0.00266)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0371)|Lung(427;0.205)		CGGGTGGAAATCCGTGATAGA	0.632																																					p.D115G		Atlas-SNP	.											.	UBE2J2	25	.	0			c.A344G						.						79	91	86					1																	1192490		2203	4300	6503	SO:0001583	missense	118424	exon6			TGGAAATCCGTGA	AF296658	CCDS14.1, CCDS15.1, CCDS16.1	1p36.33	2011-05-19	2011-05-19		ENSG00000160087	ENSG00000160087		"Ubiquitin-conjugating enzymes E2"	19268	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2, J2 (UBC6 homolog, yeast)"			11278356	Standard	NM_058167		Approved	Ubc6p, NCUBE2	uc001ado.3	Q8N2K1	OTTHUMG00000001911	ENST00000349431.6:c.296A>G	chr1.hg19:g.1192490T>C	ENSP00000305826:p.Asp99Gly	93.0	0.0		48.0	4.0	NM_194315	A8MYC7|Q504T9|Q96N26|Q96T84	Missense_Mutation	SNP	ENST00000349431.6	hg19	CCDS14.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.509712	0.85282	.	.	ENSG00000160087	ENST00000347370;ENST00000349431;ENST00000339385;ENST00000348298;ENST00000400929;ENST00000360466;ENST00000400930;ENST00000435198	T;T;T;T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03	5.52	4.38	0.52667	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.042296	0.85682	D	0.000000	T	0.56292	0.1975	L	0.56280	1.765	0.80722	D	1	D;B;D;D	0.89917	1.0;0.218;0.997;1.0	D;B;D;D	0.97110	1.0;0.199;0.992;0.989	T	0.50608	-0.8808	10	0.27785	T	0.31	-17.1661	11.9834	0.53133	0.0:0.0:0.1452:0.8548	.	47;115;99;132	A6NGS0;A8MYC7;Q8N2K1;B1AME9	.;.;UB2J2_HUMAN;.	G	47;99;64;47;47;99;115;99	ENSP00000344857:D47G;ENSP00000305826:D99G;ENSP00000340197:D64G;ENSP00000342541:D47G;ENSP00000383718:D47G;ENSP00000353653:D99G;ENSP00000383719:D115G;ENSP00000393301:D99G	ENSP00000340197:D64G	D	-	2	0	UBE2J2	1182353	1.000000	0.71417	0.890000	0.34922	0.928000	0.56348	7.613000	0.82986	0.914000	0.36822	-0.328000	0.08392	GAT	.	.		0.632	UBE2J2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000005430.1	NM_058167		C	1192490	T	C	1192490	3	2	35	1	0	0	0	0	1	0	0	0	16876	1435	50	2	495	2	UBE2J2	1	1192490	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10		1192490	248058131	1	4170										
PRKCZ	5590	hgsc.bcm.edu	37	chr1	2105426	2105426	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	catcatcaccgacaacccggAcatgaacacagaggactacc	7	15	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:2105426A>G	ENST00000400921.2	+	11	1510	c.827A>G	c.(826-828)gAc>gGc	p.D276G	PRKCZ_ENST00000400920.1_Missense_Mutation_p.D276G|PRKCZ_ENST00000479263.1_3'UTR	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta	459	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	GACAACCCGGACATGAACACA	0.592											OREG0013007	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D459G		Atlas-SNP	.											.	PRKCZ	84	.	0			c.A1376G						.						136	116	122					1																	2105426		2203	4300	6503	SO:0001583	missense	5590	exon14			ACCCGGACATGAA	BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.827A>G	chr1.hg19:g.2105426A>G	ENSP00000383712:p.Asp276Gly	198.0	0.0	601	100.0	4.0	NM_002744	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Missense_Mutation	SNP	ENST00000400921.2	hg19	CCDS41229.1	.	.	.	.	.	.	.	.	.	.	A	18.43	3.622554	0.66787	.	.	ENSG00000067606	ENST00000378567;ENST00000400921;ENST00000461106;ENST00000400920	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	4.93	4.93	0.64822	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.097591	0.64402	D	0.000002	T	0.25901	0.0631	N	0.10916	0.065	0.58432	D	0.999999	P;D;P;D	0.58970	0.956;0.962;0.956;0.984	D;D;D;D	0.68039	0.955;0.919;0.955;0.925	T	0.20107	-1.0285	10	0.87932	D	0	.	12.8492	0.57848	1.0:0.0:0.0:0.0	.	355;283;355;459	E9PCW2;B3KUN5;B7Z2J7;Q05513	.;.;.;KPCZ_HUMAN	G	459;276;355;276	ENSP00000367830:D459G;ENSP00000383712:D276G;ENSP00000426412:D355G;ENSP00000383711:D276G	ENSP00000367830:D459G	D	+	2	0	PRKCZ	2095286	1.000000	0.71417	0.961000	0.40146	0.024000	0.10985	8.187000	0.89708	1.986000	0.57962	0.477000	0.44152	GAC	.	.		0.592	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		G	2105426	A	G	2105426	3	3	35	1	0	0	0	0	1	0	0	0	12529	275	10	2	1430	2	PRKCZ	1	2105426	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	912936	2105426	247145195	2	4171										
NPHP4	261734	hgsc.bcm.edu	37	chr1	5934637	5934637	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gggccaggctgccacgcaggTggaacatgtcctcctccacc	12	16	0	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:5934637T>C	ENST00000378156.4	-	22	3390	c.3125A>G	c.(3124-3126)cAc>cGc	p.H1042R	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	1042					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GCCACGCAGGTGGAACATGTC	0.657																																					p.H1042R		Atlas-SNP	.											.	NPHP4	119	.	0			c.A3125G						.						25	28	27					1																	5934637		2151	4241	6392	SO:0001583	missense	261734	exon22			CGCAGGTGGAACA	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.3125A>G	chr1.hg19:g.5934637T>C	ENSP00000367398:p.His1042Arg	144.0	0.0		85.0	7.0	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	hg19	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	T	13.19	2.163444	0.38217	.	.	ENSG00000131697	ENST00000378156	T	0.72835	-0.69	5.38	-1.55	0.08558	.	0.272597	0.33895	N	0.004443	T	0.60945	0.2308	L	0.55834	1.745	0.33568	D	0.598298	B	0.22080	0.064	B	0.21917	0.037	T	0.56438	-0.7979	10	0.52906	T	0.07	.	10.085	0.42412	0.0:0.3804:0.0:0.6196	.	1042	O75161	NPHP4_HUMAN	R	1042	ENSP00000367398:H1042R	ENSP00000367398:H1042R	H	-	2	0	NPHP4	5857224	1.000000	0.71417	0.247000	0.24249	0.651000	0.38670	3.233000	0.51311	-0.562000	0.06086	0.528000	0.53228	CAC	.	.		0.657	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			C	5934637	T	C	5934637	3	2	35	1	0	0	0	0	1	0	0	0	10590	1696	59	2	1191	2	NPHP4	1	5934637	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	3829211	5934637	243315984	3	4172										
CHD5	26038	hgsc.bcm.edu	37	chr1	6188597	6188597	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gcttcttctttgcactggcgGccaagttcccccctttggag	10	14	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:6188597G>A	ENST00000262450.3	-	24	3791	c.3692C>T	c.(3691-3693)gCc>gTc	p.A1231V	CHD5_ENST00000378021.1_Missense_Mutation_p.A88V	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TGCACTGGCGGCCAAGTTCCC	0.627																																					p.A1231V		Atlas-SNP	.											.	CHD5	267	.	0			c.C3692T						.						58	61	60					1																	6188597		2203	4300	6503	SO:0001583	missense	26038	exon24			CTGGCGGCCAAGT	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.3692C>T	chr1.hg19:g.6188597G>A	ENSP00000262450:p.Ala1231Val	153.0	0.0		79.0	4.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	hg19	CCDS57.1	.	.	.	.	.	.	.	.	.	.	G	16.61	3.172138	0.57584	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000378021;ENST00000536802;ENST00000538279;ENST00000377999	D;T	0.90620	-2.7;2.27	4.48	4.48	0.54585	.	1.006430	0.07998	N	0.988353	D	0.83940	0.5363	N	0.19112	0.55	0.19300	N	0.99997	B;B	0.15719	0.014;0.008	B;B	0.14023	0.01;0.004	T	0.64651	-0.6357	10	0.11182	T	0.66	-1.0944	14.289	0.66265	0.0:0.0:1.0:0.0	.	1231;88	Q8TDI0;Q5TG85	CHD5_HUMAN;.	V	1231;747;88;639;639;88	ENSP00000262450:A1231V;ENSP00000367260:A88V	ENSP00000262450:A1231V	A	-	2	0	CHD5	6111184	0.950000	0.32346	0.760000	0.31359	0.688000	0.40055	5.667000	0.68067	2.045000	0.60652	0.313000	0.20887	GCC	.	.		0.627	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		A	6188597	G	A	6188597	3	1	35	1	0	0	0	0	1	0	0	0	3330	1203	42	3	2244	3	CHD5	1	6188597	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	253960	6188597	243062024	4	4173										
NOL9	79707	hgsc.bcm.edu	37	chr1	6589090	6589090	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	acagattggagtctgggcaaGcaggatgggcccattcgtgt	15	8	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:6589090G>A	ENST00000377705.5	-	10	1821	c.1789C>T	c.(1789-1791)Ctt>Ttt	p.L597F		NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	597					maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		GTCTGGGCAAGCAGGATGGGC	0.483																																					p.L597F		Atlas-SNP	.											.	NOL9	49	.	0			c.C1789T						.						115	102	107					1																	6589090		2203	4300	6503	SO:0001583	missense	79707	exon10			GGGCAAGCAGGAT	AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408			26265	protein-coding gene	gene with protein product	"polynucleotide 5'-kinase"					21063389	Standard	NM_024654		Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.1789C>T	chr1.hg19:g.6589090G>A	ENSP00000366934:p.Leu597Phe	176.0	0.0		95.0	4.0	NM_024654	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	Missense_Mutation	SNP	ENST00000377705.5	hg19	CCDS80.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.361468	0.82353	.	.	ENSG00000162408	ENST00000377705	T	0.47528	0.84	5.77	5.77	0.91146	Pre-mRNA cleavage complex II Clp1 (1);	0.000000	0.64402	D	0.000002	T	0.63486	0.2515	M	0.73962	2.25	0.46749	D	0.999189	D	0.89917	1.0	D	0.91635	0.999	T	0.59521	-0.7439	10	0.13108	T	0.6	-25.1663	10.8478	0.46753	0.0848:0.0:0.9152:0.0	.	597	Q5SY16	NOL9_HUMAN	F	597	ENSP00000366934:L597F	ENSP00000366934:L597F	L	-	1	0	NOL9	6511677	1.000000	0.71417	0.969000	0.41365	0.983000	0.72400	6.374000	0.73132	2.724000	0.93272	0.561000	0.74099	CTT	.	.		0.483	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002625.1	NM_024654		A	6589090	G	A	6589090	3	1	35	1	0	0	0	0	1	0	0	0	10537	971	34	3	331	3	NOL9	1	6589090	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	400493	6589090	242661531	5	4174										
ENO1	2023	hgsc.bcm.edu	37	chr1	8930511	8930511	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tatcaggaggcaggtcctacCttgctaaccagggcaggcgc	13	12	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:8930511C>T	ENST00000234590.4	-	4	359	c.240G>A	c.(238-240)aaG>aaA	p.K80K		NM_001428.3	NP_001419.1	P06733	ENOA_HUMAN	enolase 1, (alpha)	80					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphopyruvate hydratase complex (GO:0000015)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	10	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.42e-07)|COAD - Colon adenocarcinoma(227;2.78e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		CAGGTCCTACCTTGCTAACCA	0.458																																					p.K80K	Esophageal Squamous(21;302 608 19946 22210 33560)	Atlas-SNP	.											.	ENO1	38	.	0			c.G240A						.						96	82	87					1																	8930511		2203	4300	6503	SO:0001630	splice_region_variant	2023	exon4			TCCTACCTTGCTA	BC022545	CCDS97.1	1p36.2	2010-03-11			ENSG00000074800	ENSG00000074800	4.2.1.11		3350	protein-coding gene	gene with protein product		172430		ENO1L1, MPB1		9653645, 9691177	Standard	NM_001428		Approved	PPH, MBP-1	uc001apj.2	P06733	OTTHUMG00000001773	ENST00000234590.4:c.240+1G>A	chr1.hg19:g.8930511C>T		85.0	0.0		54.0	4.0	NM_001428	B2RD59|P22712|Q16704|Q4TUS4|Q53FT9|Q53HR3|Q658M5|Q6GMP2|Q71V37|Q7Z3V6|Q8WU71|Q96GV1|Q9BT62|Q9UCH6|Q9UM55	Silent	SNP	ENST00000234590.4	hg19	CCDS97.1																																																																																			.	.		0.458	ENO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004945.1	NM_001428	Silent	T	8930511	C	T	8930511	5	4	35	1	0	0	0	0	0	0	1	0	5123	695	24	3	1100	3	ENO1	1	8930511	Splice_Site	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	2341421	8930511	240320110	6	4175										
HNRNPCL1	343069	hgsc.bcm.edu	37	chr1	12908011	12908011	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cccttatgaacagagcagccCgcaattttgccatacttgga	8	12	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:12908011C>T	ENST00000317869.6	-	2	357	c.132G>A	c.(130-132)gcG>gcA	p.A44A		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	44	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.					nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A44A(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						CAGAGCAGCCCGCAATTTTGC	0.478																																					p.A44A		Atlas-SNP	.											.	HNRNPCL1	68	.	1	Substitution - coding silent(1)	lung(1)	c.G132A						.						117	112	114					1																	12908011		2203	4300	6503	SO:0001819	synonymous_variant	343069	exon2			GCAGCCCGCAATT	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"RNA binding motif (RRM) containing"	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.132G>A	chr1.hg19:g.12908011C>T		495.0	0.0		301.0	60.0	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	hg19	CCDS30591.1																																																																																			.	.		0.478	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631		T	12908011	C	T	12908011	2	4	35	1	0	0	0	0	0	0	0	1	7272	639	23	1		1	HNRNPCL1	1	12908011	Silent	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	3977500	12908011	236342610	7	4176										
CLCNKB	1188	hgsc.bcm.edu	37	chr1	16377074	16377074	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	atcacctacccacccagcgcCggccgcttcctagcttctcg	7	20	2	0	rs375017657		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:16377074C>T	ENST00000375679.4	+	11	1143	c.1032C>T	c.(1030-1032)gcC>gcT	p.A344A	CLCNKB_ENST00000375667.3_Silent_p.A175A	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	344					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CACCCAGCGCCGGCCGCTTCC	0.627																																					p.A344A		Atlas-SNP	.											.	CLCNKB	50	.	0			c.C1032T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	106	93	97		1032,525	0.8	0.1	1		97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CLCNKB	NM_000085.3,NM_001165945.1	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	344/688,175/519	16377074	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1188	exon11			CAGCGCCGGCCGC	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"Ion channels / Chloride channels : Voltage-sensitive"	2027	protein-coding gene	gene with protein product		602023	"chloride channel Kb"				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1032C>T	chr1.hg19:g.16377074C>T		102.0	0.0		74.0	4.0	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Silent	SNP	ENST00000375679.4	hg19	CCDS168.1																																																																																			.	.		0.627	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085		T	16377074	C	T	16377074	2	4	35	1	0	0	0	0	0	0	0	1	3472	639	23	1		1	CLCNKB	1	16377074	Silent	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	3469063	16377074	232873547	8	4177										
UBR4	23352	hgsc.bcm.edu	37	chr1	19446726	19446726	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ccagcgcaccgaggaagaatTggactctaacaggaaacaac	10	11	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:19446726T>C	ENST00000375254.3	-	69	10285	c.10258A>G	c.(10258-10260)Aat>Gat	p.N3420D	UBR4_ENST00000375267.2_Missense_Mutation_p.N3420D|UBR4_ENST00000375226.2_Missense_Mutation_p.N3396D|UBR4_ENST00000375218.3_5'Flank|UBR4_ENST00000375217.2_Missense_Mutation_p.N3413D	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3420					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GAGGAAGAATTGGACTCTAAC	0.552																																					p.N3420D		Atlas-SNP	.											.	UBR4	415	.	0			c.A10258G						.						125	110	115					1																	19446726		2203	4300	6503	SO:0001583	missense	23352	exon69			AAGAATTGGACTC	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.10258A>G	chr1.hg19:g.19446726T>C	ENSP00000364403:p.Asn3420Asp	136.0	0.0		62.0	4.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.216399	0.79352	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.78136	0.4236	M	0.79258	2.445	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.80890	-0.1180	10	0.72032	D	0.01	.	14.586	0.68326	0.0:0.0:0.0:1.0	.	3420	Q5T4S7	UBR4_HUMAN	D	3420;3420;3413;3396	ENSP00000364403:N3420D;ENSP00000364416:N3420D;ENSP00000364365:N3413D;ENSP00000364374:N3396D	ENSP00000364365:N3413D	N	-	1	0	UBR4	19319313	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.525000	0.81892	2.302000	0.77476	0.533000	0.62120	AAT	.	.		0.552	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19446726	T	C	19446726	3	2	35	1	0	0	0	0	1	0	0	0	16919	1812	63	2	5445	2	UBR4	1	19446726	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	3069652	19446726	229803895	9	4178										
UBR4	23352	hgsc.bcm.edu	37	chr1	19518865	19518865	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cacccagcaattggaaattcTgatagtgctgttgtgaaagg	11	7	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:19518865T>C	ENST00000375254.3	-	11	1238	c.1211A>G	c.(1210-1212)cAg>cGg	p.Q404R	UBR4_ENST00000375267.2_Missense_Mutation_p.Q404R|UBR4_ENST00000375226.2_Missense_Mutation_p.Q404R|UBR4_ENST00000375217.2_Missense_Mutation_p.Q404R	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	404					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TTGGAAATTCTGATAGTGCTG	0.413																																					p.Q404R		Atlas-SNP	.											.	UBR4	415	.	0			c.A1211G						.						75	77	76					1																	19518865		2203	4300	6503	SO:0001583	missense	23352	exon11			AAATTCTGATAGT	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.1211A>G	chr1.hg19:g.19518865T>C	ENSP00000364403:p.Gln404Arg	114.0	0.0		64.0	4.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.337165	0.81911	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.34072	1.41;1.41;1.39;1.38	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.49830	0.1580	L	0.50333	1.59	0.80722	D	1	P	0.45126	0.851	P	0.55391	0.775	T	0.50890	-0.8774	10	0.87932	D	0	.	14.6068	0.68486	0.0:0.0:0.0:1.0	.	404	Q5T4S7	UBR4_HUMAN	R	404	ENSP00000364403:Q404R;ENSP00000364416:Q404R;ENSP00000364365:Q404R;ENSP00000364374:Q404R	ENSP00000364365:Q404R	Q	-	2	0	UBR4	19391452	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	7.649000	0.83500	2.125000	0.65367	0.482000	0.46254	CAG	.	.		0.413	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19518865	T	C	19518865	3	2	35	1	0	0	0	0	1	0	0	0	16919	1580	55	2	14724	2	UBR4	1	19518865	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	72139	19518865	229731756	10	4179										
RAP1GAP	5909	hgsc.bcm.edu	37	chr1	21936087	21936087	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ccttcctgaacacagcggggTccgggagggggggtccaaag	17	11	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:21936087T>C	ENST00000374765.4	-	15	1252	c.1052A>G	c.(1051-1053)gAc>gGc	p.D351G	RAP1GAP_ENST00000374761.2_Missense_Mutation_p.D382G|RAP1GAP_ENST00000290101.4_Missense_Mutation_p.D415G|RAP1GAP_ENST00000374763.2_Missense_Mutation_p.D351G|RAP1GAP_ENST00000542643.2_Missense_Mutation_p.D351G	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	351	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		CACAGCGGGGTCCGGGAGGGG	0.622																																					p.D415G		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.A1244G						.						66	72	70					1																	21936087		2203	4300	6503	SO:0001583	missense	5909	exon15			GCGGGGTCCGGGA	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"RAP1, GTPase activating protein 1"	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1052A>G	chr1.hg19:g.21936087T>C	ENSP00000363897:p.Asp351Gly	145.0	0.0		88.0	5.0	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Missense_Mutation	SNP	ENST00000374765.4	hg19	CCDS218.1	.	.	.	.	.	.	.	.	.	.	T	12.18	1.861278	0.32884	.	.	ENSG00000076864	ENST00000290101;ENST00000374761;ENST00000542643;ENST00000374765;ENST00000374763;ENST00000374758	D;D;D;D	0.94931	-3.56;-3.56;-3.56;-3.56	5.71	4.57	0.56435	Rap/ran-GAP (2);	0.201409	0.46758	D	0.000261	D	0.91050	0.7184	L	0.41236	1.265	0.38914	D	0.957595	B;B;B;B	0.26002	0.002;0.139;0.02;0.139	B;B;B;B	0.29598	0.006;0.104;0.049;0.104	D	0.88131	0.2838	10	0.49607	T	0.09	-34.6276	11.2196	0.48846	0.0:0.0:0.1539:0.8461	.	351;351;381;351	P47736-2;P47736;P47736-3;Q7Z5S8	.;RPGP1_HUMAN;.;.	G	415;382;351;351;381;351	ENSP00000290101:D415G;ENSP00000363893:D382G;ENSP00000441661:D351G;ENSP00000363897:D351G	ENSP00000290101:D415G	D	-	2	0	RAP1GAP	21808674	1.000000	0.71417	0.979000	0.43373	0.129000	0.20672	5.853000	0.69496	0.982000	0.38575	-0.316000	0.08728	GAC	.	.		0.622	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885		C	21936087	T	C	21936087	3	2	35	1	0	0	0	0	1	0	0	0	13052	1667	58	2	1061	2	RAP1GAP	1	21936087	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	2417222	21936087	227314534	11	4180										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22191789	22191789	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gccccttacctctcggaacaTgatctcgtagctcctcctct	6	17	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:22191789T>C	ENST00000374695.3	-	35	4463	c.4384A>G	c.(4384-4386)Atg>Gtg	p.M1462V		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1462	Laminin IV type A 3. {ECO:0000255|PROSITE-ProRule:PRU00458}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TCTCGGAACATGATCTCGTAG	0.602																																					p.M1462V		Atlas-SNP	.											.	HSPG2	311	.	0			c.A4384G						.						119	110	113					1																	22191789		2203	4300	6503	SO:0001583	missense	3339	exon35			GGAACATGATCTC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.4384A>G	chr1.hg19:g.22191789T>C	ENSP00000363827:p.Met1462Val	165.0	0.0		95.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.987245	0.00443	.	.	ENSG00000142798	ENST00000374695	T	0.34859	1.34	5.57	-9.5	0.00584	Laminin B type IV (2);Laminin B, subgroup (1);	1.020000	0.07886	N	0.970325	T	0.09247	0.0228	N	0.01219	-0.95	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41106	-0.9527	10	0.02654	T	1	.	12.5266	0.56089	0.0:0.2321:0.0824:0.6855	.	1462	P98160	PGBM_HUMAN	V	1462	ENSP00000363827:M1462V	ENSP00000363827:M1462V	M	-	1	0	HSPG2	22064376	0.000000	0.05858	0.053000	0.19242	0.005000	0.04900	-2.593000	0.00897	-1.971000	0.01002	-1.840000	0.00586	ATG	.	.		0.602	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		C	22191789	T	C	22191789	3	2	35	1	0	0	0	0	1	0	0	0	7439	1464	51	2	9043	2	HSPG2	1	22191789	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	255702	22191789	227058832	12	4181										
KDM1A	23028	hgsc.bcm.edu	37	chr1	23409728	23409728	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	atccgtaactacccagccacAgtgcatggtgctctgctgag	10	13	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:23409728A>G	ENST00000356634.3	+	19	2579	c.2430A>G	c.(2428-2430)acA>acG	p.T810T	KDM1A_ENST00000400181.4_Silent_p.T834T|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000542151.1_Silent_p.T834T	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	810	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						ACCCAGCCACAGTGCATGGTG	0.532																																					p.T834T		Atlas-SNP	.											.	KDM1A	49	.	0			c.A2502G						.						94	82	86					1																	23409728		2203	4300	6503	SO:0001819	synonymous_variant	23028	exon21			AGCCACAGTGCAT	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.2430A>G	chr1.hg19:g.23409728A>G		199.0	0.0		84.0	5.0	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	hg19	CCDS30627.1																																																																																			.	.		0.532	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		G	23409728	A	G	23409728	2	3	35	1	0	0	0	0	0	0	0	1	8131	175	7	2		2	KDM1A	1	23409728	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	1217939	23409728	225840893	13	4182										
CNKSR1	10256	hgsc.bcm.edu	37	chr1	26514760	26514760	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cattacctgcatctccaagtAccagtctccaggccgggccc	8	17	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:26514760A>G	ENST00000374253.5	+	17	1550	c.1511A>G	c.(1510-1512)tAc>tGc	p.Y504C	CATSPER4_ENST00000456354.2_5'Flank|CNKSR1_ENST00000531191.1_Missense_Mutation_p.Y239C|CNKSR1_ENST00000361530.6_Missense_Mutation_p.Y497C	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	504					Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		ATCTCCAAGTACCAGTCTCCA	0.607																																					p.Y497C	NSCLC(180;1396 2109 28270 30756 34275)	Atlas-SNP	.											.	CNKSR1	66	.	0			c.A1490G						.						85	83	84					1																	26514760		2203	4300	6503	SO:0001583	missense	10256	exon17			CCAAGTACCAGTC	AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.1511A>G	chr1.hg19:g.26514760A>G	ENSP00000363371:p.Tyr504Cys	118.0	0.0		78.0	42.0	NM_006314	B1AMW9|O95381	Missense_Mutation	SNP	ENST00000374253.5	hg19		.	.	.	.	.	.	.	.	.	.	A	21.0	4.078803	0.76528	.	.	ENSG00000142675	ENST00000361530;ENST00000374253;ENST00000531191	T;T;T	0.16597	2.36;2.37;2.33	5.82	4.7	0.59300	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.119371	0.56097	D	0.000021	T	0.36276	0.0961	M	0.63428	1.95	0.39724	D	0.971518	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.98	T	0.16394	-1.0404	10	0.72032	D	0.01	-21.9064	10.4071	0.44266	0.9263:0.0:0.0737:0.0	.	504;497	Q969H4;Q53GM7	CNKR1_HUMAN;.	C	497;504;239	ENSP00000354609:Y497C;ENSP00000363371:Y504C;ENSP00000431817:Y239C	ENSP00000354609:Y497C	Y	+	2	0	CNKSR1	26387347	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.837000	0.55820	1.041000	0.40125	0.533000	0.62120	TAC	.	.		0.607	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314		G	26514760	A	G	26514760	3	3	35	1	0	0	0	0	1	0	0	0	3608	391	14	2	1556	2	CNKSR1	1	26514760	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	3105032	26514760	222735861	14	4183										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27056354	27056354	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggcctctcttatacacagcaGgtagatggtgattgtgatta	11	7	1	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:27056354G>A	ENST00000324856.7	+	2	1721	c.1350G>A	c.(1348-1350)caG>caA	p.Q450Q	ARID1A_ENST00000374152.2_Splice_Site_p.Q67Q|ARID1A_ENST00000457599.2_Splice_Site_p.Q450Q	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	450					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		ATACACAGCAGGTAGATGGTG	0.552			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Q450Q		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.G1350A						.						32	35	34					1																	27056354		2203	4300	6503	SO:0001630	splice_region_variant	8289	exon2			ACAGCAGGTAGAT	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1350+1G>A	chr1.hg19:g.27056354G>A		315.0	1.0		223.0	129.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Silent	SNP	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.552	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	Silent	A	27056354	G	A	27056354	5	1	35	1	0	0	0	0	0	0	1	0	913	1014	35	3	1356	3	ARID1A	1	27056354	Splice_Site	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	541594	27056354	222194267	15	4184										
SLC9A1	6548	hgsc.bcm.edu	37	chr1	27429041	27429041	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tcacatatttcttattaaacCggttgagcctggtgggagga	11	7	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:27429041C>T	ENST00000263980.3	-	8	2230	c.1655G>A	c.(1654-1656)cGg>cAg	p.R552Q	SLC9A1_ENST00000490329.1_5'Flank|SLC9A1_ENST00000545949.1_Missense_Mutation_p.R213Q	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	552					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	CTTATTAAACCGGTTGAGCCT	0.592											OREG0013277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R552Q		Atlas-SNP	.											SLC9A1,NS,carcinoma,0,1	SLC9A1	68	.	0			c.G1655A						.						69	76	74					1																	27429041		2203	4300	6503	SO:0001583	missense	6548	exon8			TTAAACCGGTTGA	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.1655G>A	chr1.hg19:g.27429041C>T	ENSP00000263980:p.Arg552Gln	42.0	0.0	794	18.0	2.0	NM_003047	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	ENST00000263980.3	hg19	CCDS295.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.854202	0.91355	.	.	ENSG00000090020	ENST00000263980;ENST00000374089;ENST00000545949	T;T	0.45668	0.89;1.5	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.32823	0.0842	L	0.41492	1.28	0.80722	D	1	P	0.38223	0.623	B	0.24848	0.056	T	0.21280	-1.0250	10	0.44086	T	0.13	.	18.1634	0.89717	0.0:1.0:0.0:0.0	.	552	P19634	SL9A1_HUMAN	Q	552;56;213	ENSP00000263980:R552Q;ENSP00000445520:R213Q	ENSP00000263980:R552Q	R	-	2	0	SLC9A1	27301628	0.987000	0.35691	1.000000	0.80357	0.961000	0.63080	2.509000	0.45459	2.623000	0.88846	0.561000	0.74099	CGG	.	.		0.592	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		T	27429041	C	T	27429041	3	4	35	1	0	0	0	0	1	0	0	0	14724	652	23	1	812	1	SLC9A1	1	27429041	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	372687	27429041	221821580	16	4185										
PTPRU	10076	hgsc.bcm.edu	37	chr1	29641992	29641992	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgtgtgaagactctctgctcCcggcgtgtcaacatgatcca	10	12	2	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:29641992C>T	ENST00000345512.3	+	24	3495	c.3366C>T	c.(3364-3366)tcC>tcT	p.S1122S	PTPRU_ENST00000428026.2_Silent_p.S1109S|PTPRU_ENST00000356870.3_Silent_p.S1118S|PTPRU_ENST00000460170.2_Silent_p.S1118S|PTPRU_ENST00000373779.3_Silent_p.S1112S|PTPRU_ENST00000323874.8_Silent_p.S1118S	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	1122	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		CTCTCTGCTCCCGGCGTGTCA	0.562																																					p.S1122S		Atlas-SNP	.											.	PTPRU	374	.	0			c.C3366T						.						132	122	126					1																	29641992		2203	4300	6503	SO:0001819	synonymous_variant	10076	exon24			CTGCTCCCGGCGT	U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.3366C>T	chr1.hg19:g.29641992C>T		161.0	0.0		82.0	48.0	NM_005704	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Silent	SNP	ENST00000345512.3	hg19	CCDS334.1																																																																																			.	.		0.562	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			T	29641992	C	T	29641992	2	4	35	1	0	0	0	0	0	0	0	1	12828	610	22	3		3	PTPRU	1	29641992	Silent	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	2212951	29641992	219608629	17	4186										
NKAIN1	79570	hgsc.bcm.edu	37	chr1	31656794	31656794	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaacaggtgtcaccaggcagCctggcccattctccatccac	9	16	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:31656794C>A	ENST00000373736.2	-	4	347	c.341G>T	c.(340-342)gGc>gTc	p.G114V	NKAIN1_ENST00000528449.1_5'Flank|NKAIN1_ENST00000263693.1_Missense_Mutation_p.G70V|NKAIN1_ENST00000398657.2_Missense_Mutation_p.G43V	NM_024522.2	NP_078798.2	Q4KMZ8	NKAI1_HUMAN	Na+/K+ transporting ATPase interacting 1	114						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|ovary(1)|prostate(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|Breast(348;0.141)|all_neural(195;0.146)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0184)|READ - Rectum adenocarcinoma(331;0.148)		CACCAGGCAGCCTGGCCCATT	0.592											OREG0004725	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G114V		Atlas-SNP	.											.	NKAIN1	21	.	0			c.G341T						.						101	75	83					1																	31656794		2203	4300	6503	SO:0001583	missense	79570	exon4			AGGCAGCCTGGCC	AK022712	CCDS339.1, CCDS339.2	1p35.2	2010-06-25	2007-10-04	2007-10-04	ENSG00000084628	ENSG00000084628		"Na+/K+ transporting ATPase interacting"	25743	protein-coding gene	gene with protein product		612871	"family with sequence similarity 77, member C"	FAM77C		17606467	Standard	NM_024522		Approved	FLJ12650	uc010ogd.2	Q4KMZ8	OTTHUMG00000003788	ENST00000373736.2:c.341G>T	chr1.hg19:g.31656794C>A	ENSP00000362841:p.Gly114Val	112.0	0.0	826	88.0	4.0	NM_024522	A2VDJ3|B7Z5F5|B7Z5W9|Q9H9M7	Missense_Mutation	SNP	ENST00000373736.2	hg19	CCDS339.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.16|19.16	3.773464|3.773464	0.69992|0.69992	.|.	.|.	ENSG00000084628|ENSG00000084628	ENST00000526106|ENST00000373736;ENST00000263693;ENST00000398657	.|T;T;T	.|0.38722	.|1.12;1.12;1.12	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.72211|0.72211	0.3432|0.3432	M|M	0.88450|0.88450	2.955|2.955	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	T|T	0.77525|0.77525	-0.2555|-0.2555	5|10	.|0.87932	.|D	.|0	-10.5819|-10.5819	19.5743|19.5743	0.95436|0.95436	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|114;43	.|Q4KMZ8;B7Z5F5	.|NKAI1_HUMAN;.	S|V	58|114;70;43	.|ENSP00000362841:G114V;ENSP00000263693:G70V;ENSP00000381650:G43V	.|ENSP00000263693:G70V	A|G	-|-	1|2	0|0	NKAIN1|NKAIN1	31429381|31429381	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.281000|0.281000	0.26958|0.26958	7.487000|7.487000	0.81328|0.81328	2.611000|2.611000	0.88343|0.88343	0.655000|0.655000	0.94253|0.94253	GCT|GGC	.	.		0.592	NKAIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010655.2	NM_024522		A	31656794	C	A	31656794	3	1	35	1	0	0	0	0	1	0	0	0	10444	739	26	3	298	3	NKAIN1	1	31656794	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	2014802	31656794	217593827	18	4187										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32149600	32149600	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaactcctggtagaccgggtTggccctaaaaggcataaggt	13	9	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:32149600T>C	ENST00000373672.3	-	33	2804	c.2288A>G	c.(2287-2289)cAa>cGa	p.Q763R	COL16A1_ENST00000373668.3_Missense_Mutation_p.Q763R|COL16A1_ENST00000271069.6_Missense_Mutation_p.Q762R	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	763	Triple-helical region 5 (COL5) with 3 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TAGACCGGGTTGGCCCTAAAA	0.647																																					p.Q763R	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.A2288G						.						46	51	50					1																	32149600		1966	4130	6096	SO:0001583	missense	1307	exon33			CCGGGTTGGCCCT	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.2288A>G	chr1.hg19:g.32149600T>C	ENSP00000362776:p.Gln763Arg	164.0	0.0		105.0	5.0	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	T	16.21	3.059818	0.55325	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668	D;D;D	0.93547	-3.24;-3.24;-3.24	4.92	4.92	0.64577	.	0.222271	0.37906	N	0.001885	D	0.87912	0.6297	L	0.28014	0.82	0.33396	D	0.576764	B;B;B	0.23650	0.089;0.043;0.073	B;B;B	0.29077	0.098;0.01;0.022	D	0.86160	0.1593	10	0.17369	T	0.5	.	12.7489	0.57298	0.0:0.0:0.0:1.0	.	763;763;763	A6NCT7;Q07092;Q07092-2	.;COGA1_HUMAN;.	R	763;762;763	ENSP00000362776:Q763R;ENSP00000271069:Q762R;ENSP00000362772:Q763R	ENSP00000271069:Q762R	Q	-	2	0	COL16A1	31922187	0.996000	0.38824	1.000000	0.80357	0.958000	0.62258	1.164000	0.31810	2.152000	0.67230	0.402000	0.26972	CAA	.	.		0.647	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		C	32149600	T	C	32149600	3	2	35	1	0	0	0	0	1	0	0	0	3675	1812	63	2	2682	2	COL16A1	1	32149600	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	492806	32149600	217101021	19	4188										
SPOCD1	90853	hgsc.bcm.edu	37	chr1	32280899	32280899	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggactgagcacagggtctccTgtgctggggccttctacgtc	14	12	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:32280899T>C	ENST00000360482.2	-	2	165	c.36A>G	c.(34-36)acA>acG	p.T12T	SPOCD1_ENST00000373648.2_Silent_p.T12T|SPOCD1_ENST00000533231.1_Silent_p.T12T|SPOCD1_ENST00000257100.3_Intron	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	12					negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		CAGGGTCTCCTGTGCTGGGGC	0.592																																					p.T12T		Atlas-SNP	.											.	SPOCD1	109	.	0			c.A36G						.						38	41	40					1																	32280899		2203	4300	6503	SO:0001819	synonymous_variant	90853	exon2			GTCTCCTGTGCTG	AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 146"					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.36A>G	chr1.hg19:g.32280899T>C		102.0	0.0		59.0	4.0	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Silent	SNP	ENST00000360482.2	hg19	CCDS347.1																																																																																			.	.		0.592	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		C	32280899	T	C	32280899	2	2	35	1	0	0	0	0	0	0	0	1	15093	1567	55	2		2	SPOCD1	1	32280899	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	131299	32280899	216969722	20	4189										
KPNA6	23633	hgsc.bcm.edu	37	chr1	32631794	32631794	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaaggaagcttgctggactaTttcaaatattactgctggca	10	7	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:32631794T>C	ENST00000373625.3	+	11	1172	c.1079T>C	c.(1078-1080)aTt>aCt	p.I360T	KPNA6_ENST00000545542.1_Missense_Mutation_p.I365T|KPNA6_ENST00000537234.1_Missense_Mutation_p.I357T	NM_012316.4	NP_036448.1	O60684	IMA7_HUMAN	karyopherin alpha 6 (importin alpha 7)	360	NLS binding site (minor). {ECO:0000250}.				maternal process involved in female pregnancy (GO:0060135)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			large_intestine(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TGCTGGACTATTTCAAATATT	0.473																																					p.I360T		Atlas-SNP	.											.	KPNA6	34	.	0			c.T1079C						.						95	89	91					1																	32631794		2203	4300	6503	SO:0001583	missense	23633	exon11			GGACTATTTCAAA	AF060543	CCDS352.1	1p35.1	2013-02-14			ENSG00000025800	ENSG00000025800		"Importins", "Armadillo repeat containing"	6399	protein-coding gene	gene with protein product		610563				10523667	Standard	NM_012316		Approved	IPOA7, KPNA7, MGC17918, FLJ11249	uc001bug.3	O60684	OTTHUMG00000004333	ENST00000373625.3:c.1079T>C	chr1.hg19:g.32631794T>C	ENSP00000362728:p.Ile360Thr	142.0	0.0		91.0	4.0	NM_012316	B2RDC7|D3DPP5|Q5VVU3	Missense_Mutation	SNP	ENST00000373625.3	hg19	CCDS352.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.893297	0.91889	.	.	ENSG00000025800	ENST00000373625;ENST00000373617;ENST00000537234;ENST00000545542;ENST00000446515	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	5.11	5.11	0.69529	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.89588	0.6758	H	0.98199	4.17	0.80722	D	1	D;D;D	0.58970	0.98;0.984;0.96	P;D;D	0.66979	0.897;0.938;0.948	D	0.93410	0.6768	10	0.87932	D	0	-10.365	15.6231	0.76824	0.0:0.0:0.0:1.0	.	365;365;360	F5GYL8;B4DWX3;O60684	.;.;IMA7_HUMAN	T	360;290;357;365;267	ENSP00000362728:I360T;ENSP00000444930:I357T;ENSP00000440609:I365T;ENSP00000415677:I267T	ENSP00000362719:I290T	I	+	2	0	KPNA6	32404381	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.993000	0.88291	2.234000	0.73211	0.528000	0.53228	ATT	.	.		0.473	KPNA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000012527.4	NM_012316		C	32631794	T	C	32631794	3	2	35	1	0	0	0	0	1	0	0	0	8443	1493	52	2	1121	2	KPNA6	1	32631794	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	350895	32631794	216618827	21	4190										
IQCC	55721	hgsc.bcm.edu	37	chr1	32673299	32673299	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cattgtcccaggaagtccagGacacagctgtctgcactcta	9	13	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:32673299G>A	ENST00000291358.6	+	5	1038	c.1017G>A	c.(1015-1017)agG>agA	p.R339R	RP4-622L5.7_ENST00000373604.4_RNA|RP4-622L5.7_ENST00000421616.1_RNA|DCDC2B_ENST00000409358.1_5'Flank|IQCC_ENST00000537469.1_Silent_p.R419R	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	339										endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GGAAGTCCAGGACACAGCTGT	0.507																																					p.R419R		Atlas-SNP	.											.	IQCC	46	.	0			c.G1257A						.						66	74	71					1																	32673299		2203	4300	6503	SO:0001819	synonymous_variant	55721	exon5			GTCCAGGACACAG	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.1017G>A	chr1.hg19:g.32673299G>A		139.0	0.0		72.0	4.0	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Silent	SNP	ENST00000291358.6	hg19	CCDS355.1																																																																																			.	.		0.507	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134		A	32673299	G	A	32673299	2	1	35	1	0	0	0	0	0	0	0	1	7813	1165	41	3		3	IQCC	1	32673299	Silent	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	41505	32673299	216577322	22	4191										
AK2	204	hgsc.bcm.edu	37	chr1	33478978	33478978	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ccttttcattatcatctgatCgacggatcaagggttccccg	8	12	4	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:33478978C>T	ENST00000373449.2	-	6	565	c.524G>A	c.(523-525)cGa>cAa	p.R175Q	AK2_ENST00000548033.1_Missense_Mutation_p.R133Q|AK2_ENST00000480134.1_3'UTR|AK2_ENST00000467905.1_Missense_Mutation_p.R175Q|AK2_ENST00000491241.1_5'Flank|RP1-117O3.2_ENST00000427524.1_RNA|AK2_ENST00000354858.6_Missense_Mutation_p.R175Q	NM_001199199.1|NM_013411.4	NP_001186128.1|NP_037543.1			adenylate kinase 2											kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				ATCATCTGATCGACGGATCAA	0.488																																					p.R175Q		Atlas-SNP	.											.	AK2	27	.	0			c.G524A						.						69	65	66					1																	33478978		2203	4300	6503	SO:0001583	missense	204	exon6			TCTGATCGACGGA	U84371	CCDS373.1, CCDS374.1	1p35.1	2014-09-17			ENSG00000004455	ENSG00000004455	2.7.4.3	"Adenylate kinases"	362	protein-coding gene	gene with protein product		103020				8843353, 6961883	Standard	NM_013411		Approved		uc001bwp.2	P54819	OTTHUMG00000004131	ENST00000373449.2:c.524G>A	chr1.hg19:g.33478978C>T	ENSP00000362548:p.Arg175Gln	161.0	0.0		109.0	44.0	NM_013411		Missense_Mutation	SNP	ENST00000373449.2	hg19	CCDS373.1	.	.	.	.	.	.	.	.	.	.	C	33	5.260021	0.95368	.	.	ENSG00000004455	ENST00000373449;ENST00000548033;ENST00000467905;ENST00000354858;ENST00000398192	D;D;D;D	0.96716	-4.1;-4.1;-4.1;-4.1	5.17	4.26	0.50523	Adenylate kinase, active site lid domain (1);	0.000000	0.85682	D	0.000000	D	0.98732	0.9574	H	0.96889	3.9	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.998	D	0.99655	1.0992	10	0.87932	D	0	-7.9968	14.7526	0.69536	0.0:0.929:0.0:0.071	.	167;133;175;175	P54819-5;F8VY04;P54819;P54819-2	.;.;KAD2_HUMAN;.	Q	175;133;175;175;175	ENSP00000362548:R175Q;ENSP00000449003:R133Q;ENSP00000447082:R175Q;ENSP00000346921:R175Q	ENSP00000346921:R175Q	R	-	2	0	AK2	33251565	1.000000	0.71417	0.974000	0.42286	0.976000	0.68499	7.786000	0.85741	1.504000	0.48704	0.563000	0.77884	CGA	.	.		0.488	AK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011884.1	NM_001625		T	33478978	C	T	33478978	3	4	35	1	0	0	0	0	1	0	0	0	440	884	31	1	208	1	AK2	1	33478978	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	805679	33478978	215771643	23	4192										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34035040	34035040	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctcacgcaccctggagcccaCcagtgtgtatccggaattgc	10	15	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:34035040C>T	ENST00000373381.4	-	52	8241	c.8065G>A	c.(8065-8067)Gtg>Atg	p.V2689M		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2691	Sushi 17. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CTGGAGCCCACCAGTGTGTAT	0.597																																					p.V2691M		Atlas-SNP	.											.	CSMD2	946	.	0			c.G8071A						.						92	82	85					1																	34035040		2203	4300	6503	SO:0001583	missense	114784	exon53			AGCCCACCAGTGT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.8065G>A	chr1.hg19:g.34035040C>T	ENSP00000362479:p.Val2689Met	98.0	0.0		77.0	4.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	C	18.31	3.595133	0.66219	.	.	ENSG00000121904	ENST00000373381	T	0.65364	-0.15	5.47	5.47	0.80525	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.78916	0.4359	M	0.71871	2.18	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.984	T	0.78314	-0.2252	10	0.45353	T	0.12	.	18.3184	0.90229	0.0:1.0:0.0:0.0	.	2691;2689	Q7Z408;E7EUA6	CSMD2_HUMAN;.	M	2689	ENSP00000362479:V2689M	ENSP00000241312:V2691M	V	-	1	0	CSMD2	33807627	1.000000	0.71417	0.998000	0.56505	0.024000	0.10985	7.818000	0.86416	2.566000	0.86566	0.655000	0.94253	GTG	.	.		0.597	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34035040	C	T	34035040	3	4	35	1	0	0	0	0	1	0	0	0	3947	507	18	3	2460	3	CSMD2	1	34035040	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	556062	34035040	215215581	24	4193										
STK40	83931	hgsc.bcm.edu	37	chr1	36814304	36814304	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctggcacacacacgtaccgcTgagcacgtcgggactgatgt	12	13	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:36814304T>C	ENST00000373129.3	-	8	1142	c.736A>G	c.(736-738)Agc>Ggc	p.S246G	STK40_ENST00000373132.3_Missense_Mutation_p.S246G|STK40_ENST00000373130.3_Missense_Mutation_p.S251G|STK40_ENST00000359297.2_Missense_Mutation_p.S246G	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	246	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				CACGTACCGCTGAGCACGTCG	0.587																																					p.S246G		Atlas-SNP	.											.	STK40	53	.	0			c.A736G						.						97	74	81					1																	36814304		2203	4300	6503	SO:0001583	missense	83931	exon8			TACCGCTGAGCAC	BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.736A>G	chr1.hg19:g.36814304T>C	ENSP00000362221:p.Ser246Gly	94.0	0.0		92.0	4.0	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Missense_Mutation	SNP	ENST00000373129.3	hg19	CCDS407.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.179122	0.57800	.	.	ENSG00000196182	ENST00000373129;ENST00000359297;ENST00000373130;ENST00000373132	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.24	5.24	0.73138	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.113452	0.85682	D	0.000000	T	0.51329	0.1668	L	0.28740	0.885	0.58432	D	0.999996	B;B;B	0.16603	0.018;0.005;0.007	B;B;B	0.15052	0.011;0.007;0.012	T	0.48747	-0.9008	10	0.48119	T	0.1	.	14.3227	0.66496	0.0:0.0:0.0:1.0	.	246;251;246	Q8N2I9-3;Q8N2I9-4;Q8N2I9	.;.;STK40_HUMAN	G	246;246;251;246	ENSP00000362221:S246G;ENSP00000352245:S246G;ENSP00000362222:S251G;ENSP00000362224:S246G	ENSP00000352245:S246G	S	-	1	0	STK40	36586891	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	7.662000	0.83803	1.969000	0.57287	0.533000	0.62120	AGC	.	.		0.587	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017		C	36814304	T	C	36814304	3	2	35	1	0	0	0	0	1	0	0	0	15322	1580	55	2	591	2	STK40	1	36814304	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	2779264	36814304	212436317	25	4194										
EPHA10	284656	hgsc.bcm.edu	37	chr1	38186511	38186511	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctcggtgacaatcatcaaggTgcttcctgtgcccagggatg	12	11	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:38186511T>C	ENST00000373048.4	-	12	2151	c.2152A>G	c.(2152-2154)Acc>Gcc	p.T718A	EPHA10_ENST00000540011.1_3'UTR|EPHA10_ENST00000330210.7_Missense_Mutation_p.T213A|EPHA10_ENST00000427468.2_Missense_Mutation_p.T718A|EPHA10_ENST00000446149.2_5'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	718	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ATCATCAAGGTGCTTCCTGTG	0.582																																					p.T718A		Atlas-SNP	.											.	EPHA10	120	.	0			c.A2152G						.						72	80	77					1																	38186511		2047	4189	6236	SO:0001583	missense	284656	exon12			TCAAGGTGCTTCC	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2152A>G	chr1.hg19:g.38186511T>C	ENSP00000362139:p.Thr718Ala	94.0	0.0		84.0	5.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	hg19	CCDS41305.1	.	.	.	.	.	.	.	.	.	.	T	12.47	1.947019	0.34377	.	.	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000373048	D;D;D	0.82255	-1.59;-1.59;-1.59	4.57	0.998	0.19857	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.373991	0.16770	N	0.200224	T	0.72382	0.3453	N	0.13327	0.33	0.80722	D	1	B	0.21381	0.055	B	0.29942	0.109	T	0.64613	-0.6366	10	0.66056	D	0.02	.	14.1443	0.65339	0.0:0.0:0.695:0.305	.	718	Q5JZY3	EPHAA_HUMAN	A	213;718;718	ENSP00000330379:T213A;ENSP00000397746:T718A;ENSP00000362139:T718A	ENSP00000330379:T213A	T	-	1	0	EPHA10	37959098	1.000000	0.71417	0.948000	0.38648	0.651000	0.38670	1.168000	0.31859	-0.003000	0.14444	-0.435000	0.05868	ACC	.	.		0.582	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		C	38186511	T	C	38186511	3	2	35	1	0	0	0	0	1	0	0	0	5168	1696	59	2	898	2	EPHA10	1	38186511	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	1372207	38186511	211064110	26	4195										
MTF1	4520	hgsc.bcm.edu	37	chr1	38281033	38281033	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gacccgggaacaggggctgaAgagaaagtctgcgctgggag	18	8	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:38281033A>G	ENST00000373036.4	-	11	2177	c.2037T>C	c.(2035-2037)tcT>tcC	p.S679S		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	679					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CAGGGGCTGAAGAGAAAGTCT	0.607																																					p.S679S		Atlas-SNP	.											.	MTF1	67	.	0			c.T2037C						.						70	75	73					1																	38281033		2203	4300	6503	SO:0001819	synonymous_variant	4520	exon11			GGCTGAAGAGAAA	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.2037T>C	chr1.hg19:g.38281033A>G		126.0	0.0		97.0	4.0	NM_005955	B2RAK6|Q96CB1	Silent	SNP	ENST00000373036.4	hg19	CCDS30676.1																																																																																			.	.		0.607	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955		G	38281033	A	G	38281033	2	3	35	1	0	0	0	0	0	0	0	1	9931	59	3	2		2	MTF1	1	38281033	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	94522	38281033	210969588	27	4196										
FHL3	2275	hgsc.bcm.edu	37	chr1	38463119	38463119	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ccctggcagagcacttggtcTccatccggtacgaagccctg	11	15	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:38463119T>C	ENST00000373016.3	-	6	969	c.801A>G	c.(799-801)ggA>ggG	p.G267G	FHL3_ENST00000485803.1_5'UTR	NM_001243878.1|NM_004468.4	NP_001230807.1|NP_004459.2	Q13643	FHL3_HUMAN	four and a half LIM domains 3	267	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|muscle organ development (GO:0007517)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)|Z disc (GO:0030018)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GCACTTGGTCTCCATCCGGTA	0.627																																					p.G267G		Atlas-SNP	.											.	FHL3	9	.	0			c.A801G						.						71	74	73					1																	38463119		2203	4300	6503	SO:0001819	synonymous_variant	2275	exon6			TTGGTCTCCATCC	BC011697	CCDS30678.1	1p34.3	2008-02-05			ENSG00000183386	ENSG00000183386			3704	protein-coding gene	gene with protein product		602790				8753811, 10226657	Standard	NM_004468		Approved	SLIM2	uc001cck.3	Q13643	OTTHUMG00000004434	ENST00000373016.3:c.801A>G	chr1.hg19:g.38463119T>C		86.0	0.0		76.0	4.0	NM_004468	D3DPT6|Q6I9T0|Q9BVA2	Silent	SNP	ENST00000373016.3	hg19	CCDS30678.1																																																																																			.	.		0.627	FHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012958.1	NM_004468		C	38463119	T	C	38463119	2	2	35	1	0	0	0	0	0	0	0	1	5888	1538	54	2		2	FHL3	1	38463119	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	182086	38463119	210787502	28	4197										
SCMH1	22955	hgsc.bcm.edu	37	chr1	41493981	41493981	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gcagcagcagcagggccttgCcatcgatctcctggggggtg	16	12	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:41493981C>A	ENST00000326197.7	-	15	2167	c.1868G>T	c.(1867-1869)gGc>gTc	p.G623V	SCMH1_ENST00000472037.1_5'UTR|SCMH1_ENST00000402904.2_Missense_Mutation_p.G623V|SCMH1_ENST00000361705.3_Missense_Mutation_p.G554V|SCMH1_ENST00000456518.2_Missense_Mutation_p.G443V|SCMH1_ENST00000397174.2_Missense_Mutation_p.G581V|SCMH1_ENST00000372596.1_Missense_Mutation_p.G540V|SCMH1_ENST00000372597.1_Missense_Mutation_p.G554V|SCMH1_ENST00000361191.5_Missense_Mutation_p.G540V|SCMH1_ENST00000397171.2_Missense_Mutation_p.G540V|SCMH1_ENST00000337495.5_Missense_Mutation_p.G611V|SCMH1_ENST00000372595.1_Missense_Mutation_p.G562V					sex comb on midleg homolog 1 (Drosophila)											breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				CAGGGCCTTGCCATCGATCTC	0.587																																					p.G623V		Atlas-SNP	.											.	SCMH1	120	.	0			c.G1868T						.						47	45	46					1																	41493981		2203	4300	6503	SO:0001583	missense	22955	exon16			GCCTTGCCATCGA	AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"Sterile alpha motif (SAM) domain containing"	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.1868G>T	chr1.hg19:g.41493981C>A	ENSP00000318094:p.Gly623Val	145.0	0.0		94.0	4.0	NM_001031694		Missense_Mutation	SNP	ENST00000326197.7	hg19	CCDS30688.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.404886	0.83230	.	.	ENSG00000010803	ENST00000361705;ENST00000456518;ENST00000402904;ENST00000397174;ENST00000397171;ENST00000361191;ENST00000372597;ENST00000372596;ENST00000337495;ENST00000372595;ENST00000326197	D;D;D;D;D;D;D;D;D;D;D	0.90004	-2.6;-2.6;-2.6;-2.6;-2.6;-2.6;-2.6;-2.6;-2.6;-2.6;-2.6	4.97	4.97	0.65823	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.063082	0.64402	D	0.000007	D	0.96987	0.9016	H	0.98818	4.34	0.80722	D	1	P;P;D;D	0.89917	0.904;0.603;1.0;1.0	P;B;D;D	0.97110	0.757;0.352;0.999;1.0	D	0.98561	1.0641	10	0.87932	D	0	.	16.9727	0.86304	0.0:1.0:0.0:0.0	.	443;611;554;623	B4DRQ8;Q96GD3-2;Q96GD3-4;Q96GD3	.;.;.;SCMH1_HUMAN	V	554;443;623;581;540;540;554;540;611;562;623	ENSP00000354996:G554V;ENSP00000403974:G443V;ENSP00000386079:G623V;ENSP00000380359:G581V;ENSP00000380356:G540V;ENSP00000354656:G540V;ENSP00000361678:G554V;ENSP00000361677:G540V;ENSP00000337352:G611V;ENSP00000361676:G562V;ENSP00000318094:G623V	ENSP00000318094:G623V	G	-	2	0	SCMH1	41266568	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	7.151000	0.77411	2.575000	0.86900	0.563000	0.77884	GGC	.	.		0.587	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1			A	41493981	C	A	41493981	3	1	35	1	0	0	0	0	1	0	0	0	13923	739	26	3	118	3	SCMH1	1	41493981	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	3030862	41493981	207756640	29	4198										
TTC4	7268	hgsc.bcm.edu	37	chr1	55194027	55194027	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tttcatttttagcgaattgaAcagagggatgtgaggaaagc	12	4	1	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:55194027A>G	ENST00000371281.3	+	6	690	c.603A>G	c.(601-603)gaA>gaG	p.E201E	TTC4_ENST00000371284.5_3'UTR|MROH7-TTC4_ENST00000414150.2_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	201										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						AGCGAATTGAACAGAGGGATG	0.418																																					p.E201E		Atlas-SNP	.											.	TTC4	21	.	0			c.A603G						.						96	97	97					1																	55194027		2203	4300	6503	SO:0001819	synonymous_variant	7268	exon6			AATTGAACAGAGG		CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"Tetratricopeptide (TTC) repeat domain containing"	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.603A>G	chr1.hg19:g.55194027A>G		72.0	0.0		165.0	7.0	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Silent	SNP	ENST00000371281.3	hg19	CCDS596.1																																																																																			.	.		0.418	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623		G	55194027	A	G	55194027	2	3	35	1	0	0	0	0	0	0	0	1	16725	40	2	2		2	TTC4	1	55194027	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	13700046	55194027	194056594	30	4199										
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77334294	77334294	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cccgcagcagcagcagcagcAgcagcaacagcagcagcagg	13	15	0	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:77334294A>G	ENST00000477717.1	+	2	363	c.128A>G	c.(127-129)cAg>cGg	p.Q43R	ST6GALNAC5_ENST00000496845.1_3'UTR	NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	43	Poly-Gln.				glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						cagcagcagcagcagcaacag	0.711																																					p.Q43R		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.A128G						.						13	13	13					1																	77334294		2070	3983	6053	SO:0001583	missense	81849	exon2			AGCAGCAGCAGCA		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.128A>G	chr1.hg19:g.77334294A>G	ENSP00000417583:p.Gln43Arg	62.0	0.0		190.0	8.0	NM_030965	B1AK82	Missense_Mutation	SNP	ENST00000477717.1	hg19	CCDS673.1	.	.	.	.	.	.	.	.	.	.	A	8.625	0.892423	0.17613	.	.	ENSG00000117069	ENST00000477717	T	0.24723	1.84	3.99	1.48	0.22813	.	0.692175	0.11394	U	0.568467	T	0.03651	0.0104	N	0.14661	0.345	0.30364	N	0.783559	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.45948	-0.9226	10	0.16420	T	0.52	.	5.3205	0.15879	0.7257:0.1772:0.0971:0.0	.	43;43	B4DV27;Q9BVH7	.;SIA7E_HUMAN	R	43	ENSP00000417583:Q43R	ENSP00000436263:Q43R	Q	+	2	0	ST6GALNAC5	77106882	0.539000	0.26402	0.983000	0.44433	0.222000	0.24845	0.577000	0.23758	0.070000	0.16634	0.334000	0.21626	CAG	.	.		0.711	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		G	77334294	A	G	77334294	3	3	35	1	0	0	0	0	1	0	0	0	15242	188	7	2	134	2	ST6GALNAC5	1	77334294	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	22140267	77334294	171916327	31	4200										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103364262	103364262	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaagaccttctggaccaggcTttcctgcaggtccctgagga	12	12	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:103364262T>A	ENST00000370096.3	-	56	4520	c.4208A>T	c.(4207-4209)aAg>aTg	p.K1403M	COL11A1_ENST00000512756.1_Missense_Mutation_p.K1287M|COL11A1_ENST00000353414.4_Missense_Mutation_p.K1364M|COL11A1_ENST00000358392.2_Missense_Mutation_p.K1415M	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1403	Collagen-like 6.|Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TGGACCAGGCTTTCCTGCAGG	0.458																																					p.K1415M		Atlas-SNP	.											.	COL11A1	972	.	0			c.A4244T						.						45	48	47					1																	103364262		2203	4300	6503	SO:0001583	missense	1301	exon56			CCAGGCTTTCCTG	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.4208A>T	chr1.hg19:g.103364262T>A	ENSP00000359114:p.Lys1403Met	202.0	0.0		421.0	63.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.160808	0.78226	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.94376	-3.41;-3.41;-3.41;-3.41	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.93012	0.7776	N	0.21448	0.665	0.80722	D	1	D;D;B;D;D	0.89917	1.0;1.0;0.126;1.0;1.0	D;D;P;D;D	0.91635	0.999;0.998;0.766;0.999;0.998	D	0.94853	0.8015	10	0.72032	D	0.01	.	16.6245	0.84952	0.0:0.0:0.0:1.0	.	1287;1364;1415;1403;623	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	M	1403;1415;1364;623;1287	ENSP00000359114:K1403M;ENSP00000351163:K1415M;ENSP00000302551:K1364M;ENSP00000426533:K1287M	ENSP00000302551:K1364M	K	-	2	0	COL11A1	103136850	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.968000	0.87980	2.323000	0.78572	0.528000	0.53228	AAG	.	.		0.458	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103364262	T	A	103364262	3	1	35	1	0	0	0	0	1	0	0	0	3669	1609	56	4	1260	4	COL11A1	1	103364262	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	26029968	103364262	145886359	32	4201										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120461034	120461034	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gcctttcatccctaccatggTcatccactgcattcacatcc	4	17	3	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:120461034T>C	ENST00000256646.2	-	32	6143	c.5924A>G	c.(5923-5925)gAc>gGc	p.D1975G		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1975					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.D1975G(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCTACCATGGTCATCCACTGC	0.527			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.D1975G		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	NOTCH2,colon,carcinoma,0,1	NOTCH2	348	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5924G						.						136	109	118					1																	120461034		2203	4300	6503	SO:0001583	missense	4853	exon32	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CCATGGTCATCCA	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.5924A>G	chr1.hg19:g.120461034T>C	ENSP00000256646:p.Asp1975Gly	100.0	0.0		181.0	9.0	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	hg19	CCDS908.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.852764	0.91355	.	.	ENSG00000134250	ENST00000256646	T	0.64991	-0.13	5.76	5.76	0.90799	Ankyrin repeat-containing domain (4);	0.000000	0.39985	U	0.001214	T	0.63094	0.2482	L	0.31926	0.97	0.80722	D	1	D	0.67145	0.996	D	0.70935	0.971	T	0.68565	-0.5375	10	0.62326	D	0.03	.	15.2578	0.73599	0.0:0.0:0.0:1.0	.	1975	Q04721	NOTC2_HUMAN	G	1975	ENSP00000256646:D1975G	ENSP00000256646:D1975G	D	-	2	0	NOTCH2	120262557	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.698000	0.84413	2.202000	0.70862	0.533000	0.62120	GAC	.	.		0.527	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		C	120461034	T	C	120461034	3	2	35	1	0	0	0	0	1	0	0	0	10557	1667	58	2	1503	2	NOTCH2	1	120461034	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	17096772	120461034	128789587	33	4202										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120539927	120539927	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tttgcacagggatgagacagGcaggcatccgtccattggca	13	10	0	1	rs587603360		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:120539927G>A	ENST00000256646.2	-	4	663	c.444C>T	c.(442-444)tgC>tgT	p.C148C	NOTCH2_ENST00000602566.1_Silent_p.C109C	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	148	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GATGAGACAGGCAGGCATCCG	0.502			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome				G|||	1	0.000199681	8e-04	0	5008	,	,		27585	0		0	False		,,,				2504	0				p.C148C		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C444T						.						124	98	107					1																	120539927		2201	4299	6500	SO:0001819	synonymous_variant	4853	exon4	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AGACAGGCAGGCA	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.444C>T	chr1.hg19:g.120539927G>A		317.0	1.0		614.0	406.0	NM_001200001	Q5T3X7|Q99734|Q9H240	Silent	SNP	ENST00000256646.2	hg19	CCDS908.1																																																																																			.	.		0.502	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		A	120539927	G	A	120539927	2	1	35	1	0	0	0	0	0	0	0	1	10557	1195	42	3		3	NOTCH2	1	120539927	Silent	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	78893	120539927	128710694	34	4203										
LIX1L	128077	hgsc.bcm.edu	37	chr1	145497479	145497479	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aacaagggcaaatcaatgttGgagttccaggtactttccca	9	9	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:145497479G>A	ENST00000369308.3	+	4	758	c.684G>A	c.(682-684)ttG>ttA	p.L228L	RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA	NM_153713.1	NP_714924.1	Q8IVB5	LIX1L_HUMAN	Lix1 homolog (chicken) like	228										large_intestine(4)|lung(6)|ovary(2)|skin(1)	13	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AATCAATGTTGGAGTTCCAGG	0.453																																					p.L228L		Atlas-SNP	.											.	LIX1L	28	.	0			c.G684A						.						81	66	71					1																	145497479		2203	4300	6503	SO:0001819	synonymous_variant	128077	exon4			AATGTTGGAGTTC	AK128733	CCDS72873.1	1q21.1	2014-07-15	2014-07-15		ENSG00000152022	ENSG00000271601			28715	protein-coding gene	gene with protein product			"Lix1 homolog (mouse) like", "Lix1 homolog (chicken)-like"			12477932	Standard	NM_153713		Approved	MGC46719	uc001enr.3	Q8IVB5	OTTHUMG00000013741	ENST00000369308.3:c.684G>A	chr1.hg19:g.145497479G>A		205.0	0.0		537.0	73.0	NM_153713	Q6AI36	Silent	SNP	ENST00000369308.3	hg19	CCDS915.1																																																																																			.	.		0.453	LIX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038513.1	NM_153713		A	145497479	G	A	145497479	2	1	35	1	0	0	0	0	0	0	0	1	8841	1339	47	3		3	LIX1L	1	145497479	Silent	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	24957552	145497479	103753142	35	4204										
ITGA10	8515	hgsc.bcm.edu	37	chr1	145530929	145530929	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tacatgagtggtccctgggaGatttccgaacgaaggaagaa	13	7	0	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:145530929G>T	ENST00000369304.3	+	7	836	c.661G>T	c.(661-663)Gat>Tat	p.D221Y	ITGA10_ENST00000538811.1_Missense_Mutation_p.D90Y|ITGA10_ENST00000539363.1_Missense_Mutation_p.D78Y	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	221	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GTCCCTGGGAGATTTCCGAAC	0.522																																					p.D221Y		Atlas-SNP	.											ITGA10,NS,carcinoma,0,1	ITGA10	131	.	0			c.G661T						.						102	98	99					1																	145530929		2203	4300	6503	SO:0001583	missense	8515	exon7			CTGGGAGATTTCC	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.661G>T	chr1.hg19:g.145530929G>T	ENSP00000358310:p.Asp221Tyr	175.0	0.0		482.0	23.0	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.984862	0.74474	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	D;D;D	0.85013	-1.93;-1.93;-1.93	5.4	5.4	0.78164	von Willebrand factor, type A (3);	0.068341	0.56097	D	0.000039	D	0.90655	0.7069	M	0.81802	2.56	0.50171	D	0.999856	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.85130	0.993;0.993;0.986;0.997	D	0.91702	0.5374	10	0.87932	D	0	.	12.4144	0.55486	0.0:0.1691:0.8308:0.0	.	187;90;78;221	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	Y	221;187;78;90	ENSP00000358310:D221Y;ENSP00000439894:D78Y;ENSP00000440011:D90Y	ENSP00000358310:D221Y	D	+	1	0	ITGA10	144242286	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.758000	0.62220	2.539000	0.85634	0.655000	0.94253	GAT	.	.		0.522	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		T	145530929	G	T	145530929	3	4	35	1	0	0	0	0	1	0	0	0	7882	942	33	3	687	3	ITGA10	1	145530929	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	33450	145530929	103719692	36	4205										
CTSK	1513	hgsc.bcm.edu	37	chr1	150778691	150778691	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ccaaattaaacgccgagagaTttcatccacctaaacaaagc	5	12	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:150778691T>C	ENST00000271651.3	-	3	240	c.130A>G	c.(130-132)Atc>Gtc	p.I44V	CTSK_ENST00000480670.1_Intron	NM_000396.3	NP_000387.1	P43235	CATK_HUMAN	cathepsin K	44					bone resorption (GO:0045453)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|intramembranous ossification (GO:0001957)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|proteoglycan binding (GO:0043394)			cervix(1)|endometrium(1)|lung(4)|skin(1)	7	all_cancers(9;2.32e-51)|all_epithelial(9;3.89e-42)|all_lung(15;4.59e-35)|Lung NSC(24;1.7e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Colorectal(459;0.171)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			CGCCGAGAGATTTCATCCACC	0.368																																					p.I44V		Atlas-SNP	.											.	CTSK	27	.	0			c.A130G						.						51	52	52					1																	150778691		2203	4300	6503	SO:0001583	missense	1513	exon3			GAGAGATTTCATC	BC016058	CCDS969.1	1q21	2008-02-05	2006-12-05		ENSG00000143387	ENSG00000143387		"Cathepsins"	2536	protein-coding gene	gene with protein product		601105	"cathepsin K (pycnodysostosis)"	CTSO2, CTSO, PYCD		7818555	Standard	NM_000396		Approved	PKND	uc001evp.2	P43235	OTTHUMG00000035008	ENST00000271651.3:c.130A>G	chr1.hg19:g.150778691T>C	ENSP00000271651:p.Ile44Val	133.0	1.0		341.0	258.0	NM_000396	Q6FHS6	Missense_Mutation	SNP	ENST00000271651.3	hg19	CCDS969.1	.	.	.	.	.	.	.	.	.	.	T	7.890	0.732120	0.15507	.	.	ENSG00000143387	ENST00000271651;ENST00000443913	D;D	0.85339	-1.97;-1.97	5.57	3.21	0.36854	Proteinase inhibitor I29, cathepsin propeptide (2);	0.596147	0.18243	N	0.147179	T	0.38852	0.1056	N	0.02142	-0.665	0.33544	D	0.595303	B	0.02656	0.0	B	0.01281	0.0	T	0.03202	-1.1061	10	0.14656	T	0.56	.	6.2491	0.20835	0.0:0.0804:0.3058:0.6137	.	44	P43235	CATK_HUMAN	V	44;103	ENSP00000271651:I44V;ENSP00000405083:I103V	ENSP00000271651:I44V	I	-	1	0	CTSK	149045315	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	0.138000	0.16016	0.382000	0.24878	0.459000	0.35465	ATC	.	.		0.368	CTSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084732.1	NM_000396		C	150778691	T	C	150778691	3	2	35	1	0	0	0	0	1	0	0	0	4039	1493	52	2	883	2	CTSK	1	150778691	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	5247762	150778691	98471930	37	4206										
LCE1F	353137	hgsc.bcm.edu	37	chr1	152748869	152748869	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgtcttgccagcagagccagCagcagtgccagccccctccc	10	18	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:152748869C>A	ENST00000334371.2	+	1	22	c.22C>A	c.(22-24)Cag>Aag	p.Q8K		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	8					keratinization (GO:0031424)					kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCAGAGCCAGCAGCAGTGCCA	0.617																																					p.Q8K		Atlas-SNP	.											.	LCE1F	42	.	0			c.C22A						.						60	60	60					1																	152748869		2203	4300	6503	SO:0001583	missense	353137	exon1			AGCCAGCAGCAGT		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"Late cornified envelopes"	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	ENST00000334371.2:c.22C>A	chr1.hg19:g.152748869C>A	ENSP00000334187:p.Gln8Lys	260.0	0.0		841.0	640.0	NM_178354		Missense_Mutation	SNP	ENST00000334371.2	hg19	CCDS1023.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049933	0.36181	.	.	ENSG00000240386	ENST00000334371	T	0.04194	3.68	4.28	4.28	0.50868	.	0.000000	0.33534	N	0.004804	T	0.10078	0.0247	M	0.70595	2.14	0.26403	N	0.976398	P	0.52577	0.954	D	0.65140	0.932	T	0.00867	-1.1534	10	0.87932	D	0	.	12.392	0.55364	0.0:1.0:0.0:0.0	.	8	Q5T754	LCE1F_HUMAN	K	8	ENSP00000334187:Q8K	ENSP00000334187:Q8K	Q	+	1	0	LCE1F	151015493	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.596000	0.54024	2.356000	0.79943	0.563000	0.77884	CAG	.	.		0.617	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354		A	152748869	C	A	152748869	3	1	35	1	0	0	0	0	1	0	0	0	8673	711	25	3	24	3	LCE1F	1	152748869	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	1970178	152748869	96501752	38	4207										
UBQLN4	56893	hgsc.bcm.edu	37	chr1	156011369	156011371	+	In_Frame_Del	DEL	CGT	CGT	-													0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gttggagaagatgtggctggCgtggctggtgaggaagtggg					rs371953742		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	CGT	CGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:156011369_156011371delCGT	ENST00000368309.3	-	10	1650_1652	c.1558_1560delACG	c.(1558-1560)acgdel	p.T520del		NM_020131.3	NP_064516.2	Q9NRR5	UBQL4_HUMAN	ubiquilin 4	520					regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|polyubiquitin binding (GO:0031593)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)	16	Hepatocellular(266;0.133)|all_neural(408;0.195)					ATGTGGCTGGCGTGGCTGGTGAG	0.606																																					p.520_521del		Atlas-INDEL	.											.	UBQLN4	47	.	0			c.1559_1561del						.																																			SO:0001651	inframe_deletion	56893	exon10			.	BC018403	CCDS1127.1	1q21	2013-02-12	2004-11-05	2004-11-06	ENSG00000160803	ENSG00000160803		"Ubiquilin family"	1237	protein-coding gene	gene with protein product	"ataxin-1 ubiquitin-like interacting protein"	605440	"chromosome 1 open reading frame 6"	C1orf6		10575211, 11001934	Standard	NM_020131		Approved	A1U, UBIN	uc001fna.3	Q9NRR5	OTTHUMG00000017461	ENST00000368309.3:c.1558_1560delACG	chr1.hg19:g.156011369_156011371delCGT	ENSP00000357292:p.Thr520del	152.0	0.0		403.0	45.0	NM_020131	A6ND44|B2RAY7|Q5VYA0|Q5VYA1|Q9BR98|Q9UHX4	In_Frame_Del	DEL	ENST00000368309.3	hg19	CCDS1127.1																																																																																			.	.		0.606	UBQLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046193.1	NM_020131		-	156011371	CGT	-	156011369	7	5	35	1	0	1	0	1	0	0	0	0	16914	755	27	0	253	0	UBQLN4	1	156011369	In_Frame_Del	DEL	CGT	TCGA-BC-A10W-01A-11D-A12Z-10	3262500	156011369	93239252	39	4208										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156909536	156909536	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agctgggtgttgtccccttcAcccccagggggtgcttgccc	13	15	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:156909536A>G	ENST00000361409.2	-	36	4522	c.3780T>C	c.(3778-3780)ggT>ggC	p.G1260G	ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000315174.8_Silent_p.G676G|ARHGEF11_ENST00000368194.3_Silent_p.G1300G	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1260					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TGTCCCCTTCACCCCCAGGGG	0.642																																					p.G1300G		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.T3900C						.						44	48	47					1																	156909536		2203	4300	6503	SO:0001819	synonymous_variant	9826	exon37			CCCTTCACCCCCA	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.3780T>C	chr1.hg19:g.156909536A>G		71.0	0.0		164.0	7.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Silent	SNP	ENST00000361409.2	hg19	CCDS1162.1																																																																																			.	.		0.642	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		G	156909536	A	G	156909536	2	3	35	1	0	0	0	0	0	0	0	1	896	146	6	2		2	ARHGEF11	1	156909536	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	898167	156909536	92341085	40	4209										
KLHDC9	126823	hgsc.bcm.edu	37	chr1	161068368	161068368	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gtcgggccgcaggctcaggcTgggcctggaggccagtggcg	20	12	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:161068368T>C	ENST00000368011.4	+	1	185	c.43T>C	c.(43-45)Tgg>Cgg	p.W15R	PFDN2_ENST00000468311.1_5'Flank|KLHDC9_ENST00000392192.2_Missense_Mutation_p.W15R|KLHDC9_ENST00000490724.2_Intron	NM_152366.4	NP_689579.3	Q8NEP7	KLDC9_HUMAN	kelch domain containing 9	15										lung(5)|upper_aerodigestive_tract(1)	6	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			AGGCTCAGGCTGGGCCTGGAG	0.692																																					p.W15R		Atlas-SNP	.											.	KLHDC9	16	.	0			c.T43C						.						12	13	13					1																	161068368		2193	4282	6475	SO:0001583	missense	126823	exon1			TCAGGCTGGGCCT	BC022077	CCDS30919.1, CCDS41425.1	1q23.3	2008-02-05			ENSG00000162755	ENSG00000162755			28489	protein-coding gene	gene with protein product	"kelch/ankyrin repeat containing cyclin A1 interacting protein"					15159402	Standard	NM_152366		Approved	KARCA1	uc001fxr.3	Q8NEP7	OTTHUMG00000031479	ENST00000368011.4:c.43T>C	chr1.hg19:g.161068368T>C	ENSP00000356990:p.Trp15Arg	79.0	0.0		345.0	17.0	NM_001007255	Q5SY56|Q6NXT9|Q6PKN4|Q8N5E1|Q8NA16	Missense_Mutation	SNP	ENST00000368011.4	hg19	CCDS30919.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.310336	0.60414	.	.	ENSG00000162755	ENST00000368011;ENST00000392192	T;T	0.55413	1.57;0.52	3.99	3.99	0.46301	.	0.000000	0.49916	D	0.000129	T	0.50548	0.1622	L	0.32530	0.975	0.42632	D	0.993383	D;D	0.76494	0.999;0.998	D;D	0.85130	0.997;0.993	T	0.57871	-0.7736	10	0.87932	D	0	-12.1303	11.1743	0.48590	0.0:0.0:0.0:1.0	.	15;15	Q8NEP7-2;Q8NEP7	.;KLDC9_HUMAN	R	15	ENSP00000356990:W15R;ENSP00000376030:W15R	ENSP00000356990:W15R	W	+	1	0	KLHDC9	159334992	1.000000	0.71417	0.961000	0.40146	0.662000	0.39071	4.381000	0.59587	1.787000	0.52448	0.260000	0.18958	TGG	.	.		0.692	KLHDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077092.1	NM_152366		C	161068368	T	C	161068368	3	2	35	1	0	0	0	0	1	0	0	0	8373	1580	55	2	45	2	KLHDC9	1	161068368	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	4158832	161068368	88182253	41	4210										
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173526509	173526509	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	acttccacttttcgttcagcGagattataaacatcaggagc	7	10	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:173526509G>A	ENST00000367714.3	-	10	1607	c.1185C>T	c.(1183-1185)ctC>ctT	p.L395L	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Silent_p.L293L|RP3-436N22.3_ENST00000431459.1_RNA	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	395					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.L395L(2)									TTCGTTCAGCGAGATTATAAA	0.348																																					p.L395L		Atlas-SNP	.											SLC9A11,NS,carcinoma,0,1	.	.	.	2	Substitution - coding silent(2)	lung(2)	c.C1185T						.						107	118	114					1																	173526509		2203	4300	6503	SO:0001819	synonymous_variant	284525	exon10			TTCAGCGAGATTA	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1185C>T	chr1.hg19:g.173526509G>A		366.0	1.0		1002.0	105.0	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	hg19	CCDS1308.1																																																																																			.	.		0.348	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		A	173526509	G	A	173526509	2	1	35	1	0	0	0	0	0	0	0	1	14726	1045	37	1		1	SLC9A11	1	173526509	Silent	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	12458141	173526509	75724112	42	4211										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176668293	176668293	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	acaggcctggagccctgaggTccacctgtaccacatgaaca	10	14	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:176668293T>C	ENST00000367662.3	+	8	3968	c.2804T>C	c.(2803-2805)gTc>gCc	p.V935A		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	935					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						AGCCCTGAGGTCCACCTGTAC	0.587																																					p.V935A		Atlas-SNP	.											.	PAPPA2	665	.	0			c.T2804C						.						87	87	87					1																	176668293		1958	4130	6088	SO:0001583	missense	60676	exon8			CTGAGGTCCACCT	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.2804T>C	chr1.hg19:g.176668293T>C	ENSP00000356634:p.Val935Ala	68.0	0.0		196.0	9.0	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	hg19	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.565586	0.45694	.	.	ENSG00000116183	ENST00000367662	T	0.01505	4.82	5.14	5.14	0.70334	Fibronectin, type III (2);	0.144286	0.51477	D	0.000086	T	0.01489	0.0048	N	0.11064	0.09	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.64232	-0.6456	10	0.30078	T	0.28	-15.6357	14.7864	0.69806	0.0:0.0:0.0:1.0	.	935	Q9BXP8	PAPP2_HUMAN	A	935	ENSP00000356634:V935A	ENSP00000356634:V935A	V	+	2	0	PAPPA2	174934916	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.656000	0.67988	2.141000	0.66446	0.533000	0.62120	GTC	.	.		0.587	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			C	176668293	T	C	176668293	3	2	35	1	0	0	0	0	1	0	0	0	11442	1667	58	2	2883	2	PAPPA2	1	176668293	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	3141784	176668293	72582328	43	4212										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186064493	186064493	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cccagtatggcctggcttagAgatggccagcctctggggct	14	12	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:186064493A>G	ENST00000271588.4	+	68	10642	c.10413A>G	c.(10411-10413)agA>agG	p.R3471R	HMCN1_ENST00000367492.2_Silent_p.R3471R	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3471	Ig-like C2-type 33.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CCTGGCTTAGAGATGGCCAGC	0.517																																					p.R3471R		Atlas-SNP	.											.	HMCN1	797	.	0			c.A10413G						.						61	57	59					1																	186064493		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon68			GCTTAGAGATGGC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.10413A>G	chr1.hg19:g.186064493A>G		78.0	0.0		168.0	7.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.517	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186064493	A	G	186064493	2	3	35	1	0	0	0	0	0	0	0	1	7229	301	11	2		2	HMCN1	1	186064493	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	9396200	186064493	63186128	44	4213										
CFH	3075	hgsc.bcm.edu	37	chr1	196705955	196705955	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tatttttaatattttttagtGgcacaaatacaattatgccc	4	6	0	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:196705955G>T	ENST00000367429.4	+	16	2655	c.2415G>T	c.(2413-2415)atG>atT	p.M805I		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	805	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						attttttaGTGGCACAAATAC	0.234																																					p.M805I		Atlas-SNP	.											.	CFH	251	.	0			c.G2415T						.						23	22	22					1																	196705955		2202	4296	6498	SO:0001630	splice_region_variant	3075	exon16			TTTAGTGGCACAA	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2414-1G>T	chr1.hg19:g.196705955G>T		59.0	0.0		105.0	6.0	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	hg19	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	G	9.135	1.012351	0.19277	.	.	ENSG00000000971	ENST00000367429	T	0.28454	1.61	5.12	-1.88	0.07713	Sushi/SCR/CCP (1);	.	.	.	.	T	0.15955	0.0384	N	0.22421	0.69	0.09310	N	1	B	0.26547	0.152	B	0.24701	0.055	T	0.23297	-1.0192	9	0.33940	T	0.23	.	3.6277	0.08119	0.3475:0.0:0.2456:0.4069	.	805	P08603	CFAH_HUMAN	I	805	ENSP00000356399:M805I	ENSP00000356399:M805I	M	+	3	0	CFH	194972578	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	0.150000	0.16263	-0.418000	0.07450	-1.069000	0.02264	ATG	.	.		0.234	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	Missense_Mutation	T	196705955	G	T	196705955	5	4	35	1	0	0	0	0	0	0	1	0	3285	1362	47	3	2495	3	CFH	1	196705955	Splice_Site	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	10641462	196705955	52544666	45	4214										
TMEM206	55248	hgsc.bcm.edu	37	chr1	212558758	212558758	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	actgggcctgaccggggtacAaggcaatacctgggggcaca	15	11	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:212558758A>G	ENST00000261455.4	-	4	490	c.353T>C	c.(352-354)tTg>tCg	p.L118S	TMEM206_ENST00000471937.1_5'UTR|TMEM206_ENST00000535273.1_Missense_Mutation_p.L179S	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	118						cell surface (GO:0009986)|integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		ACCGGGGTACAAGGCAATACC	0.532																																					p.L179S		Atlas-SNP	.											TMEM206,NS,carcinoma,0,1	TMEM206	41	.	0			c.T536C						.						78	73	75					1																	212558758		2203	4300	6503	SO:0001583	missense	55248	exon5			GGGTACAAGGCAA	AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 75"	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.353T>C	chr1.hg19:g.212558758A>G	ENSP00000261455:p.Leu118Ser	132.0	0.0		74.0	3.0	NM_001198862	B7Z4D6|Q6IA87|Q9NV85	Missense_Mutation	SNP	ENST00000261455.4	hg19	CCDS1504.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.174854	0.78564	.	.	ENSG00000065600	ENST00000261455;ENST00000535273	.	.	.	5.43	5.43	0.79202	.	0.148190	0.46442	D	0.000294	T	0.65544	0.2701	L	0.32530	0.975	0.44447	D	0.997379	D;P	0.67145	0.996;0.912	D;P	0.64410	0.925;0.678	T	0.69533	-0.5120	9	0.87932	D	0	-15.2815	15.4672	0.75409	1.0:0.0:0.0:0.0	.	179;118	B7Z4D6;Q9H813	.;TM206_HUMAN	S	118;179	.	ENSP00000261455:L118S	L	-	2	0	TMEM206	210625381	1.000000	0.71417	0.995000	0.50966	0.618000	0.37518	8.248000	0.89832	2.047000	0.60756	0.533000	0.62120	TTG	.	.		0.532	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252		G	212558758	A	G	212558758	3	3	35	1	0	0	0	0	1	0	0	0	16146	131	5	2	719	2	TMEM206	1	212558758	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	15852803	212558758	36691863	46	4215										
PROX1	5629	hgsc.bcm.edu	37	chr1	214171377	214171377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tcagagcccattaggtgctcCctccggctccttctctggaa	9	15	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:214171377C>T	ENST00000366958.4	+	2	2107	c.1499C>T	c.(1498-1500)cCc>cTc	p.P500L	PROX1_ENST00000435016.1_Missense_Mutation_p.P500L|PROX1_ENST00000261454.4_Missense_Mutation_p.P500L|PROX1_ENST00000498508.2_Missense_Mutation_p.P500L	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	500					aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		TTAGGTGCTCCCTCCGGCTCC	0.562																																					p.P500L		Atlas-SNP	.											.	PROX1	124	.	0			c.C1499T						.						76	84	81					1																	214171377		2203	4300	6503	SO:0001583	missense	5629	exon2			GTGCTCCCTCCGG	U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"Homeoboxes / PROS class"	9459	protein-coding gene	gene with protein product		601546	"prospero-related homeobox 1"			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.1499C>T	chr1.hg19:g.214171377C>T	ENSP00000355925:p.Pro500Leu	86.0	0.0		61.0	4.0	NM_001270616	A6NK29|A8K2B1|Q5SW76|Q8TB91	Missense_Mutation	SNP	ENST00000366958.4	hg19	CCDS31021.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.615348	0.46631	.	.	ENSG00000117707	ENST00000541470;ENST00000498508;ENST00000366958;ENST00000435016;ENST00000261454	T;T;T;T	0.44083	0.95;0.93;0.95;0.95	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.48943	0.1528	L	0.41632	1.29	0.80722	D	1	D	0.56746	0.977	P	0.57057	0.812	T	0.22487	-1.0215	10	0.07482	T	0.82	-4.6478	19.8546	0.96752	0.0:1.0:0.0:0.0	.	500	Q92786	PROX1_HUMAN	L	72;500;500;500;500	ENSP00000420283:P500L;ENSP00000355925:P500L;ENSP00000400694:P500L;ENSP00000261454:P500L	ENSP00000261454:P500L	P	+	2	0	PROX1	212238000	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.963000	0.70372	2.697000	0.92050	0.655000	0.94253	CCC	.	.		0.562	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		T	214171377	C	T	214171377	3	4	35	1	0	0	0	0	1	0	0	0	12572	623	22	3	1501	3	PROX1	1	214171377	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	1612619	214171377	35079244	47	4216										
USH2A	7399	hgsc.bcm.edu	37	chr1	216373309	216373309	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gagtctgagccaataggaatGatataacttaaagtcaagtt	9	5	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:216373309G>T	ENST00000307340.3	-	17	3857	c.3471C>A	c.(3469-3471)atC>atA	p.I1157I	USH2A_ENST00000366942.3_Silent_p.I1157I|RP5-1099E6.3_ENST00000420867.1_RNA|USH2A_ENST00000366943.2_Silent_p.I1157I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1157	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CAATAGGAATGATATAACTTA	0.438										HNSCC(13;0.011)																											p.I1157I		Atlas-SNP	.											.	USH2A	1168	.	0			c.C3471A						.						106	105	106					1																	216373309		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon17			AGGAATGATATAA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.3471C>A	chr1.hg19:g.216373309G>T		189.0	0.0		116.0	5.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.438	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216373309	G	T	216373309	2	4	35	1	0	0	0	0	0	0	0	1	17051	1280	45	3		3	USH2A	1	216373309	Silent	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	2201932	216373309	32877312	48	4217										
SPATA17	128153	hgsc.bcm.edu	37	chr1	217947703	217947703	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaatatacaattcacccttcAgaaaagagcctgatccatgg	7	10	2	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:217947703A>G	ENST00000366933.4	+	7	602	c.547A>G	c.(547-549)Aga>Gga	p.R183G		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	183						cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		TTCACCCTTCAGAAAAGAGCC	0.378																																					p.R183G		Atlas-SNP	.											.	SPATA17	59	.	0			c.A547G						.						83	81	82					1																	217947703		2203	4300	6503	SO:0001583	missense	128153	exon7			CCCTTCAGAAAAG	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"IQ motif containing H"	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.547A>G	chr1.hg19:g.217947703A>G	ENSP00000355900:p.Arg183Gly	94.0	0.0		90.0	4.0	NM_138796	A5D6N2	Missense_Mutation	SNP	ENST00000366933.4	hg19	CCDS1519.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.190224	0.78789	.	.	ENSG00000162814	ENST00000366933	T	0.46819	0.86	5.45	4.3	0.51218	.	0.048454	0.85682	D	0.000000	T	0.65606	0.2707	M	0.78916	2.43	0.38615	D	0.951005	D	0.69078	0.997	D	0.63033	0.91	T	0.71892	-0.4455	10	0.66056	D	0.02	-11.2255	12.556	0.56254	0.8559:0.1441:0.0:0.0	.	183	Q96L03	SPT17_HUMAN	G	183	ENSP00000355900:R183G	ENSP00000355900:R183G	R	+	1	2	SPATA17	216014326	1.000000	0.71417	0.913000	0.36048	0.983000	0.72400	2.377000	0.44300	0.983000	0.38602	0.460000	0.39030	AGA	.	.		0.378	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796		G	217947703	A	G	217947703	3	3	35	1	0	0	0	0	1	0	0	0	15017	180	7	2	573	2	SPATA17	1	217947703	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	1574394	217947703	31302918	49	4218										
TGFB2	7042	hgsc.bcm.edu	37	chr1	218578636	218578636	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tctttcgtttgcagaacccaAaagccagagtgcctgaacaa	8	11	1	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:218578636A>G	ENST00000366930.4	+	2	939	c.472A>G	c.(472-474)Aaa>Gaa	p.K158E	TGFB2_ENST00000366929.4_Missense_Mutation_p.K186E	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	158					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		GCAGAACCCAAAAGCCAGAGT	0.408																																					p.K186E		Atlas-SNP	.											.	TGFB2	102	.	0			c.A556G						.						189	182	185					1																	218578636		2203	4300	6503	SO:0001583	missense	7042	exon3			AACCCAAAAGCCA	M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.472A>G	chr1.hg19:g.218578636A>G	ENSP00000355897:p.Lys158Glu	135.0	0.0		61.0	4.0	NM_001135599	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	hg19	CCDS1521.1	.	.	.	.	.	.	.	.	.	.	A	13.34	2.209081	0.39003	.	.	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.63913	-0.07;-0.07	5.09	5.09	0.68999	Transforming growth factor-beta, N-terminal (1);	0.239182	0.42964	D	0.000631	T	0.60327	0.2260	L	0.28556	0.865	0.44807	D	0.997815	B;B;D	0.59357	0.217;0.042;0.985	B;B;P	0.58013	0.138;0.103;0.831	T	0.56637	-0.7946	10	0.05721	T	0.95	.	14.9051	0.70711	1.0:0.0:0.0:0.0	.	186;158;187	P61812-2;P61812;Q59EG9	.;TGFB2_HUMAN;.	E	158;186	ENSP00000355897:K158E;ENSP00000355896:K186E	ENSP00000355896:K186E	K	+	1	0	TGFB2	216645259	1.000000	0.71417	0.802000	0.32245	0.960000	0.62799	4.886000	0.63149	1.916000	0.55485	0.528000	0.53228	AAA	.	.		0.408	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		G	218578636	A	G	218578636	3	3	35	1	0	0	0	0	1	0	0	0	15833	15	1	2	566	2	TGFB2	1	218578636	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	630933	218578636	30671985	50	4219										
ACTA1	58	hgsc.bcm.edu	37	chr1	229568488	229568488	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaagctcgttgtagaaggtgTggtgccagatcttctccatg	13	8	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:229568488T>C	ENST00000366684.3	-	3	371	c.269A>G	c.(268-270)cAc>cGc	p.H90R	ACTA1_ENST00000366683.2_Missense_Mutation_p.H90R	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	90					cell growth (GO:0016049)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to extracellular stimulus (GO:0009991)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to steroid hormone (GO:0048545)|skeletal muscle fiber adaptation (GO:0043503)|skeletal muscle fiber development (GO:0048741)|skeletal muscle thin filament assembly (GO:0030240)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|striated muscle thin filament (GO:0005865)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|myosin binding (GO:0017022)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|large_intestine(4)|lung(18)|prostate(1)|urinary_tract(1)	28	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)				GTAGAAGGTGTGGTGCCAGAT	0.602																																					p.H90R		Atlas-SNP	.											.	ACTA1	65	.	0			c.A269G						.						93	90	91					1																	229568488		2203	4300	6503	SO:0001583	missense	58	exon3			AAGGTGTGGTGCC	J00068	CCDS1578.1	1q42.13	2014-09-17			ENSG00000143632	ENSG00000143632			129	protein-coding gene	gene with protein product	"nemaline myopathy type 3"	102610		ACTA		10072583, 6865942	Standard	NM_001100		Approved	NEM3	uc001htm.3	P68133	OTTHUMG00000038006	ENST00000366684.3:c.269A>G	chr1.hg19:g.229568488T>C	ENSP00000355645:p.His90Arg	132.0	0.0		100.0	4.0	NM_001100	P02568|P99020|Q5T8M9	Missense_Mutation	SNP	ENST00000366684.3	hg19	CCDS1578.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.870248	0.51588	.	.	ENSG00000143632	ENST00000366684;ENST00000308794;ENST00000366683;ENST00000342787	D;D	0.97404	-4.37;-3.43	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	D	0.98899	0.9627	H	0.96633	3.855	0.39113	D	0.961516	D	0.53619	0.961	D	0.71414	0.973	D	0.99915	1.1222	10	0.62326	D	0.03	.	13.7356	0.62815	0.0:0.0:0.0:1.0	.	90	P68133	ACTS_HUMAN	R	90	ENSP00000355645:H90R;ENSP00000355644:H90R	ENSP00000312351:H90R	H	-	2	0	ACTA1	227635111	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.861000	0.87004	1.913000	0.55393	0.460000	0.39030	CAC	.	.		0.602	ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	NM_001100		C	229568488	T	C	229568488	3	2	35	1	0	0	0	0	1	0	0	0	191	1696	59	2	884	2	ACTA1	1	229568488	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	10989852	229568488	19682133	51	4220										
ABCB10	23456	hgsc.bcm.edu	37	chr1	229666086	229666086	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgggcacctctgggcgagctGgataggcaaaatgcacgttc	14	10	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:229666086G>A	ENST00000344517.4	-	8	1547	c.1505C>T	c.(1504-1506)cCa>cTa	p.P502L		NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	502	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				TGGGCGAGCTGGATAGGCAAA	0.448																																					p.P502L		Atlas-SNP	.											.	ABCB10	71	.	0			c.C1505T						.						134	134	134					1																	229666086		2203	4300	6503	SO:0001583	missense	23456	exon8			CGAGCTGGATAGG	U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"ATP binding cassette transporters / subfamily B"	41	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family B member 10, mitochondrial", "ATP-binding cassette transporter 10", "ABC transporter 10 protein", "mitochondrial ATP-binding cassette 2"	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.1505C>T	chr1.hg19:g.229666086G>A	ENSP00000355637:p.Pro502Leu	119.0	0.0		90.0	5.0	NM_012089	Q13040|Q6P1Q8|Q9H3V0	Missense_Mutation	SNP	ENST00000344517.4	hg19	CCDS1580.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.761626	0.89932	.	.	ENSG00000135776	ENST00000344517	D	0.91124	-2.79	5.83	5.83	0.93111	ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.94918	0.8357	M	0.62209	1.925	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94792	0.7963	10	0.87932	D	0	-27.3017	20.1082	0.97900	0.0:0.0:1.0:0.0	.	502	Q9NRK6	ABCBA_HUMAN	L	502	ENSP00000355637:P502L	ENSP00000355637:P502L	P	-	2	0	ABCB10	227732709	1.000000	0.71417	0.437000	0.26809	0.788000	0.44548	8.643000	0.91040	2.745000	0.94114	0.563000	0.77884	CCA	.	.		0.448	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089		A	229666086	G	A	229666086	3	1	35	1	0	0	0	0	1	0	0	0	41	1348	47	3	735	3	ABCB10	1	229666086	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	97598	229666086	19584535	52	4221										
PGBD5	79605	hgsc.bcm.edu	37	chr1	230492867	230492867	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggactcgcagtgggagatgcTggtggagatcatgtagccca	16	8	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:230492867T>C	ENST00000525115.1	-	2	348	c.325A>G	c.(325-327)Agc>Ggc	p.S109G	PGBD5_ENST00000391860.1_Missense_Mutation_p.S63G|PGBD5_ENST00000321327.2_Missense_Mutation_p.S208G			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	109						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		TGGGAGATGCTGGTGGAGATC	0.612																																					p.S178G		Atlas-SNP	.											.	PGBD5	73	.	0			c.A532G						.						126	100	109					1																	230492867		2203	4300	6503	SO:0001583	missense	79605	exon2			AGATGCTGGTGGA	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.325A>G	chr1.hg19:g.230492867T>C	ENSP00000431404:p.Ser109Gly	123.0	0.0		69.0	4.0	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Missense_Mutation	SNP	ENST00000525115.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.74	1.728776	0.30593	.	.	ENSG00000177614	ENST00000391860;ENST00000321327;ENST00000525115	T;T;T	0.10005	2.92;2.92;2.92	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.09686	0.0238	N	0.19112	0.55	0.58432	D	0.999992	P	0.44429	0.835	P	0.46685	0.524	T	0.05007	-1.0912	10	0.02654	T	1	-44.9623	16.1303	0.81428	0.0:0.0:0.0:1.0	.	109	Q8N414	PGBD5_HUMAN	G	63;208;109	ENSP00000375733:S63G;ENSP00000322530:S208G;ENSP00000431404:S109G	ENSP00000322530:S208G	S	-	1	0	PGBD5	228559490	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.268000	0.72552	2.218000	0.71995	0.533000	0.62120	AGC	.	.		0.612	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		C	230492867	T	C	230492867	3	2	35	1	0	0	0	0	1	0	0	0	11793	1580	55	2	1066	2	PGBD5	1	230492867	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	826781	230492867	18757754	53	4222										
C1orf198	84886	hgsc.bcm.edu	37	chr1	230979276	230979276	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gttgggaagaggacgctgctCctgacggagggtgctgggcc	19	9	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:230979276C>A	ENST00000366663.5	-	3	891	c.751G>T	c.(751-753)Gag>Tag	p.E251*	C1orf198_ENST00000427697.2_Nonsense_Mutation_p.E34*|C1orf198_ENST00000470540.1_Nonsense_Mutation_p.E213*|C1orf198_ENST00000523410.1_Nonsense_Mutation_p.E121*	NM_032800.2	NP_116189.1	Q9H425	CA198_HUMAN	chromosome 1 open reading frame 198	251						cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	17	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GGACGCTGCTCCTGACGGAGG	0.647																																					p.E251X		Atlas-SNP	.											C1orf198,NS,carcinoma,0,1	C1orf198	29	.	0			c.G751T						.						55	53	54					1																	230979276		2203	4300	6503	SO:0001587	stop_gained	84886	exon3			GCTGCTCCTGACG	BC066649	CCDS1587.1, CCDS44330.1, CCDS44331.1	1q42.2	2008-02-05			ENSG00000119280	ENSG00000119280			25900	protein-coding gene	gene with protein product							Standard	NM_032800		Approved	FLJ14525, MGC10710, FLJ16283, DKFZp667D152, FLJ38847	uc001hub.3	Q9H425	OTTHUMG00000037790	ENST00000366663.5:c.751G>T	chr1.hg19:g.230979276C>A	ENSP00000355623:p.Glu251*	84.0	0.0		48.0	2.0	NM_032800	A8K8R8|B3KTW1|G5EA08	Nonsense_Mutation	SNP	ENST00000366663.5	hg19	CCDS1587.1	.	.	.	.	.	.	.	.	.	.	C	33	5.205788	0.95033	.	.	ENSG00000119280	ENST00000366663;ENST00000470540;ENST00000427697;ENST00000523410	.	.	.	4.46	4.46	0.54185	.	0.133192	0.50627	D	0.000115	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	-25.1385	10.7508	0.46209	0.0:0.9118:0.0:0.0882	.	.	.	.	X	251;213;34;121	.	ENSP00000355623:E251X	E	-	1	0	C1orf198	229045899	1.000000	0.71417	0.914000	0.36105	0.819000	0.46315	3.152000	0.50677	2.017000	0.59298	0.462000	0.41574	GAG	.	.		0.647	C1orf198-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092236.2	NM_032800		A	230979276	C	A	230979276	4	1	35	1	0	0	0	0	0	1	0	0	2028	864	30	3	240	3	C1orf198	1	230979276	Nonsense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	486409	230979276	18271345	54	4223										
C1orf198	84886	hgsc.bcm.edu	37	chr1	231004122	231004122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tctcgcggatcttctccttgTcctgcatgatcttcctggcc	8	15	4	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:231004122T>C	ENST00000366663.5	-	1	277	c.137A>G	c.(136-138)gAc>gGc	p.D46G	C1orf198_ENST00000427697.2_Intron|C1orf198_ENST00000470540.1_Missense_Mutation_p.D8G	NM_032800.2	NP_116189.1	Q9H425	CA198_HUMAN	chromosome 1 open reading frame 198	46						cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	17	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				CTTCTCCTTGTCCTGCATGAT	0.677																																					p.D46G		Atlas-SNP	.											.	C1orf198	29	.	0			c.A137G						.						24	28	27					1																	231004122		2203	4300	6503	SO:0001583	missense	84886	exon1			TCCTTGTCCTGCA	BC066649	CCDS1587.1, CCDS44330.1, CCDS44331.1	1q42.2	2008-02-05			ENSG00000119280	ENSG00000119280			25900	protein-coding gene	gene with protein product							Standard	NM_032800		Approved	FLJ14525, MGC10710, FLJ16283, DKFZp667D152, FLJ38847	uc001hub.3	Q9H425	OTTHUMG00000037790	ENST00000366663.5:c.137A>G	chr1.hg19:g.231004122T>C	ENSP00000355623:p.Asp46Gly	110.0	0.0		108.0	5.0	NM_032800	A8K8R8|B3KTW1|G5EA08	Missense_Mutation	SNP	ENST00000366663.5	hg19	CCDS1587.1	.	.	.	.	.	.	.	.	.	.	t	32	5.154254	0.94645	.	.	ENSG00000119280	ENST00000366663;ENST00000470540;ENST00000522201	T;T	0.38401	1.14;1.24	3.71	3.71	0.42584	.	0.068933	0.56097	U	0.000025	T	0.50718	0.1632	M	0.65975	2.015	0.80722	D	1	D	0.58268	0.982	P	0.57425	0.82	T	0.56282	-0.8005	10	0.72032	D	0.01	.	12.2062	0.54353	0.0:0.0:0.0:1.0	.	46	Q9H425	CA198_HUMAN	G	46;8;3	ENSP00000355623:D46G;ENSP00000428172:D8G	ENSP00000355623:D46G	D	-	2	0	C1orf198	229070745	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.745000	0.62125	1.526000	0.49068	0.375000	0.23000	GAC	.	.		0.677	C1orf198-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092236.2	NM_032800		C	231004122	T	C	231004122	3	2	35	1	0	0	0	0	1	0	0	0	2028	1667	58	2	862	2	C1orf198	1	231004122	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	24846	231004122	18246499	55	4224										
LYST	1130	hgsc.bcm.edu	37	chr1	235922305	235922305	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cagttcggttgtaatttggcTcataaccaagagaataggca	10	7	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:235922305T>C	ENST00000389794.3	-	23	7022	c.6848A>G	c.(6847-6849)gAg>gGg	p.E2283G	LYST_ENST00000389793.2_Missense_Mutation_p.E2283G			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2283					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GTAATTTGGCTCATAACCAAG	0.418																																					p.E2283G		Atlas-SNP	.											.	LYST	370	.	0			c.A6848G						.						79	72	75					1																	235922305		2203	4300	6503	SO:0001583	missense	1130	exon23			TTTGGCTCATAAC	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.6848A>G	chr1.hg19:g.235922305T>C	ENSP00000374444:p.Glu2283Gly	126.0	0.0		85.0	5.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.640388	0.47153	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.65364	-0.15;-0.15	4.93	2.58	0.30949	.	1.094320	0.06799	N	0.788353	T	0.53465	0.1798	L	0.36672	1.1	0.80722	D	1	B	0.16166	0.016	B	0.12837	0.008	T	0.46205	-0.9208	10	0.66056	D	0.02	.	8.822	0.35032	0.0:0.1556:0.0:0.8444	.	2283	Q99698	LYST_HUMAN	G	2283	ENSP00000374444:E2283G;ENSP00000374443:E2283G	ENSP00000374443:E2283G	E	-	2	0	LYST	233988928	0.996000	0.38824	0.631000	0.29282	0.969000	0.65631	3.596000	0.54024	0.839000	0.34971	0.456000	0.33151	GAG	.	.		0.418	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			C	235922305	T	C	235922305	3	2	35	1	0	0	0	0	1	0	0	0	9137	1551	54	2	4681	2	LYST	1	235922305	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	4918183	235922305	13328316	56	4225										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370245	240370245	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gccagtggtcatcaagggctTgagaatggagtgacagcctc	14	9	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:240370245T>C	ENST00000319653.9	+	5	2363	c.2133T>C	c.(2131-2133)ctT>ctC	p.L711L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	711					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ATCAAGGGCTTGAGAATGGAG	0.488																																					p.L711L		Atlas-SNP	.											.	FMN2	451	.	0			c.T2133C						.						73	72	73					1																	240370245		2203	4300	6503	SO:0001819	synonymous_variant	56776	exon5			AGGGCTTGAGAAT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2133T>C	chr1.hg19:g.240370245T>C		142.0	0.0		73.0	4.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	hg19	CCDS31069.2																																																																																			.	.		0.488	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		C	240370245	T	C	240370245	2	2	35	1	0	0	0	0	0	0	0	1	5958	1799	63	2		2	FMN2	1	240370245	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	4447940	240370245	8880376	57	4226										
ZNF238	10472	hgsc.bcm.edu	37	chr1	244218512	244218512	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaagccgcacgcctgcaagtGgtgcgagcgcaggttcacgc	15	13	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:244218512G>A	ENST00000358704.4	+	2	1585	c.1436G>A	c.(1435-1437)tGg>tAg	p.W479*		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	470					cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCCTGCAAGTGGTGCGAGCGC	0.602																																					p.W479X		Atlas-SNP	.											.	.	.	.	0			c.G1436A						.						62	62	62					1																	244218512		2203	4300	6503	SO:0001587	stop_gained	10472	exon2			GCAAGTGGTGCGA	U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13030	protein-coding gene	gene with protein product		608433	"zinc finger protein 238"	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.1436G>A	chr1.hg19:g.244218512G>A	ENSP00000351539:p.Trp479*	105.0	0.0		76.0	4.0	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Nonsense_Mutation	SNP	ENST00000358704.4	hg19	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	G	37	6.512571	0.97629	.	.	ENSG00000179456	ENST00000358704	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0124	0.97464	0.0:0.0:1.0:0.0	.	.	.	.	X	479	.	ENSP00000351539:W479X	W	+	2	0	ZNF238	242285135	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.863000	0.87023	2.749000	0.94314	0.655000	0.94253	TGG	.	.		0.602	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768		A	244218512	G	A	244218512	4	1	35	1	0	0	0	0	0	1	0	0	17805	1357	47	3	1442	3	ZNF238	1	244218512	Nonsense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	3848267	244218512	5032109	58	4227										
TFB2M	64216	hgsc.bcm.edu	37	chr1	246727677	246727677	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tggaataaaagttttgtcacTttcgagcgcaaccactttgg	9	8	1	0	rs567380020	byFrequency	TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:246727677T>C	ENST00000366514.4	-	2	558	c.373A>G	c.(373-375)Agt>Ggt	p.S125G	CNST_ENST00000366513.4_5'Flank|TFB2M_ENST00000544618.1_Missense_Mutation_p.S125G|CNST_ENST00000366512.3_5'Flank	NM_022366.2	NP_071761.1	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	125					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(1)|kidney(12)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)			GTTTTGTCACTTTCGAGCGCA	0.373													T|||	13	0.00259585	0	0	5008	,	,		19545	0		0	False		,,,				2504	0.0133				p.S125G		Atlas-SNP	.											.	TFB2M	46	.	0			c.A373G						.						86	80	82					1																	246727677		2203	4300	6503	SO:0001583	missense	64216	exon2			TGTCACTTTCGAG	AK026835	CCDS1627.1	1q44	2008-02-05			ENSG00000162851	ENSG00000162851			18559	protein-coding gene	gene with protein product		607055					Standard	NM_022366		Approved	FLJ23182, FLJ22661, Hkp1	uc001ibn.3	Q9H5Q4	OTTHUMG00000040091	ENST00000366514.4:c.373A>G	chr1.hg19:g.246727677T>C	ENSP00000355471:p.Ser125Gly	128.0	0.0		90.0	4.0	NM_022366	Q9H626	Missense_Mutation	SNP	ENST00000366514.4	hg19	CCDS1627.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.812315	0.70912	.	.	ENSG00000162851	ENST00000366514;ENST00000544618	T;T	0.30182	1.54;1.54	5.73	4.6	0.57074	.	0.107611	0.64402	D	0.000004	T	0.34919	0.0914	L	0.58669	1.825	0.47374	D	0.9994	P	0.48294	0.908	P	0.46917	0.531	T	0.05370	-1.0889	10	0.30854	T	0.27	-16.0732	11.2522	0.49032	0.137:0.0:0.0:0.863	.	125	Q9H5Q4	TFB2M_HUMAN	G	125	ENSP00000355471:S125G;ENSP00000442426:S125G	ENSP00000355471:S125G	S	-	1	0	TFB2M	244794300	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	3.176000	0.50863	0.987000	0.38709	0.533000	0.62120	AGT	.	.		0.373	TFB2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096673.1	NM_022366		C	246727677	T	C	246727677	3	2	35	1	0	0	0	0	1	0	0	0	15809	1609	56	2	845	2	TFB2M	1	246727677	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	2509165	246727677	2522944	59	4228										
OR6F1	343169	hgsc.bcm.edu	37	chr1	247875175	247875175	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cagagtctctcttacttcctTattacgaagcgtatagatga	7	9	2	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr1:247875175T>A	ENST00000302084.2	-	1	930	c.883A>T	c.(883-885)Aag>Tag	p.K295*	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			CTTACTTCCTTATTACGAAGC	0.428																																					p.K295X		Atlas-SNP	.											.	OR6F1	88	.	0			c.A883T						.						123	122	122					1																	247875175		2203	4300	6503	SO:0001587	stop_gained	343169	exon1			CTTCCTTATTACG	BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"GPCR / Class A : Olfactory receptors"	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.883A>T	chr1.hg19:g.247875175T>A	ENSP00000305640:p.Lys295*	166.0	0.0		84.0	4.0	NM_001005286	B2RNV6|Q6IF02|Q96R39	Nonsense_Mutation	SNP	ENST00000302084.2	hg19	CCDS31095.1	.	.	.	.	.	.	.	.	.	.	T	15.97	2.990218	0.54041	.	.	ENSG00000169214	ENST00000302084	.	.	.	3.49	0.938	0.19500	.	0.000000	0.45606	D	0.000343	.	.	.	.	.	.	0.47905	D	0.999546	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.0213	11.2106	0.48795	0.0:0.0:0.6421:0.3579	.	.	.	.	X	295	.	ENSP00000305640:K295X	K	-	1	0	OR6F1	245941798	0.001000	0.12720	0.055000	0.19348	0.012000	0.07955	0.311000	0.19380	0.055000	0.16094	0.482000	0.46254	AAG	.	.		0.428	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286		A	247875175	T	A	247875175	4	1	35	1	0	0	0	0	0	1	0	0	11210	1763	61	4	47	4	OR6F1	1	247875175	Nonsense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	1147498	247875175	1375446	60	4229										
PXDN	7837	hgsc.bcm.edu	37	chr2	1652432	1652432	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agcgtcctcatgcccacctcCcccaggatcttcgggagcca	9	18	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:1652432C>T	ENST00000252804.4	-	17	3170	c.3120G>A	c.(3118-3120)ggG>ggA	p.G1040G		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1040					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TGCCCACCTCCCCCAGGATCT	0.622																																					p.G1040G		Atlas-SNP	.											.	PXDN	255	.	0			c.G3120A						.						35	41	39					2																	1652432		2191	4277	6468	SO:0001819	synonymous_variant	7837	exon17			CACCTCCCCCAGG	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.3120G>A	chr2.hg19:g.1652432C>T		96.0	0.0		80.0	4.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	hg19	CCDS46221.1																																																																																			.	.		0.622	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1652432	C	T	1652432	2	4	35	1	0	0	0	0	0	0	0	1	12862	610	22	3		3	PXDN	2	1652432	Silent	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10		1652432	241546941	61	4230										
ASAP2	8853	hgsc.bcm.edu	37	chr2	9541497	9541497	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cgagggggatgtgatcatcgTggacggggaggaggaccagg	21	6	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:9541497T>C	ENST00000281419.3	+	27	3258	c.2918T>C	c.(2917-2919)gTg>gCg	p.V973A	ASAP2_ENST00000315273.4_Missense_Mutation_p.V928A	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	973	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						GTGATCATCGTGGACGGGGAG	0.622																																					p.V973A		Atlas-SNP	.											.	ASAP2	91	.	0			c.T2918C						.						74	80	78					2																	9541497		2198	4297	6495	SO:0001583	missense	8853	exon27			TCATCGTGGACGG	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2918T>C	chr2.hg19:g.9541497T>C	ENSP00000281419:p.Val973Ala	138.0	0.0		148.0	7.0	NM_003887	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	hg19	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	T	32	5.158533	0.94686	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.59906	0.23;0.23	5.66	5.66	0.87406	Src homology-3 domain (4);	0.057951	0.64402	D	0.000002	D	0.82577	0.5067	H	0.94542	3.55	0.58432	D	0.999998	D;P	0.67145	0.996;0.881	D;P	0.76071	0.987;0.777	D	0.87726	0.2576	10	0.87932	D	0	.	15.8923	0.79309	0.0:0.0:0.0:1.0	.	928;973	O43150-2;O43150	.;ASAP2_HUMAN	A	973;928	ENSP00000281419:V973A;ENSP00000316404:V928A	ENSP00000281419:V973A	V	+	2	0	ASAP2	9458948	1.000000	0.71417	0.998000	0.56505	0.892000	0.51952	7.679000	0.84048	2.157000	0.67596	0.533000	0.62120	GTG	.	.		0.622	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		C	9541497	T	C	9541497	3	2	35	1	0	0	0	0	1	0	0	0	1011	1696	59	2	3024	2	ASAP2	2	9541497	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	7889065	9541497	233657876	62	4231										
E2F6	1876	hgsc.bcm.edu	37	chr2	11587894	11587894	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gctccttatgtgcactgtgaTagagtcctagcaaaggacac	10	10	0	2	rs371114161		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:11587894T>C	ENST00000381525.3	-	6	927	c.658A>G	c.(658-660)Atc>Gtc	p.I220V	E2F6_ENST00000546212.1_Missense_Mutation_p.I145V|E2F6_ENST00000362009.4_Silent_p.L129L|E2F6_ENST00000542100.1_Missense_Mutation_p.I145V|E2F6_ENST00000307236.4_Missense_Mutation_p.I188V	NM_198256.2	NP_937987.2	O75461	E2F6_HUMAN	E2F transcription factor 6	220	Dimerization. {ECO:0000255}.|Transcription repression.			I -> V (in Ref. 10; AAC14694). {ECO:0000305}.	negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|kidney(1)|lung(3)|prostate(1)|skin(2)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.114)|OV - Ovarian serous cystadenocarcinoma(76;0.168)		TGCACTGTGATAGAGTCCTAG	0.413																																					p.I220V		Atlas-SNP	.											.	E2F6	17	.	0			c.A658G						.	T	VAL/ILE	1,3783		0,1,1891	59	52	54		658	4.1	0.6	2		54	0,8254		0,0,4127	no	missense	E2F6	NM_198256.2	29	0,1,6018	CC,CT,TT		0.0,0.0264,0.0083	benign	220/282	11587894	1,12037	1892	4127	6019	SO:0001583	missense	1876	exon6			CTGTGATAGAGTC	AF041381	CCDS1680.2, CCDS62858.1, CCDS62859.1	2p25.1	2008-02-05			ENSG00000169016	ENSG00000169016			3120	protein-coding gene	gene with protein product		602944				9501179	Standard	NM_198256		Approved	E2F-6	uc002rbh.4	O75461	OTTHUMG00000090565	ENST00000381525.3:c.658A>G	chr2.hg19:g.11587894T>C	ENSP00000370936:p.Ile220Val	265.0	0.0		141.0	55.0	NM_198256	A8K2Z8|G5E936|O60544|Q53QY9|Q6Q9Z6|Q7Z2H6	Missense_Mutation	SNP	ENST00000381525.3	hg19	CCDS1680.2	.	.	.	.	.	.	.	.	.	.	T	12.81	2.050901	0.36181	2.64E-4	0.0	ENSG00000169016	ENST00000381525;ENST00000307236;ENST00000542100;ENST00000546212	D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13	5.21	4.05	0.47172	.	0.092120	0.64402	N	0.000001	D	0.82765	0.5108	M	0.62723	1.935	0.80722	D	1	B;B	0.21452	0.004;0.056	B;B	0.17722	0.006;0.019	T	0.75434	-0.3319	10	0.24483	T	0.36	-33.8571	9.0229	0.36211	0.0:0.0941:0.0:0.9059	.	220;188	O75461;G5E936	E2F6_HUMAN;.	V	220;188;145;145	ENSP00000370936:I220V;ENSP00000302159:I188V;ENSP00000446315:I145V;ENSP00000438864:I145V	ENSP00000302159:I188V	I	-	1	0	E2F6	11505345	0.963000	0.33076	0.622000	0.29159	0.904000	0.53231	1.662000	0.37418	0.923000	0.37045	0.533000	0.62120	ATC	.	.		0.413	E2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207101.2	NM_001952		C	11587894	T	C	11587894	3	2	35	1	0	0	0	0	1	0	0	0	4873	1406	49	2	195	2	E2F6	2	11587894	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	2046397	11587894	231611479	63	4232										
NBAS	51594	hgsc.bcm.edu	37	chr2	15514800	15514800	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cttggataagatctagctccTcttgaatggcagggggtctg	13	8	3	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:15514800T>C	ENST00000281513.5	-	31	3660	c.3635A>G	c.(3634-3636)gAg>gGg	p.E1212G	NBAS_ENST00000441750.1_Missense_Mutation_p.E1092G	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1212					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						ATCTAGCTCCTCTTGAATGGC	0.383																																					p.E1212G		Atlas-SNP	.											.	NBAS	246	.	0			c.A3635G						.						137	144	142					2																	15514800		2203	4300	6503	SO:0001583	missense	51594	exon31			AGCTCCTCTTGAA	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.3635A>G	chr2.hg19:g.15514800T>C	ENSP00000281513:p.Glu1212Gly	100.0	0.0		119.0	5.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.2|28.2	4.901282|4.901282	0.92035|0.92035	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000441750;ENST00000281513;ENST00000441755|ENST00000442506	T;T;T|.	0.20069|.	2.1;2.1;2.1|.	5.73|5.73	5.73|5.73	0.89815|0.89815	Secretory pathway Sec39 (1);|.	0.045450|.	0.85682|.	D|.	0.000000|.	T|T	0.74230|0.74230	0.3689|0.3689	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.992;0.999|.	D;D|.	0.77004|.	0.921;0.989|.	T|T	0.74203|0.74203	-0.3741|-0.3741	10|5	0.87932|.	D|.	0|.	.|.	16.0173|16.0173	0.80450|0.80450	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1092;1212|.	A2RRP1-2;A2RRP1|.	.;NBAS_HUMAN|.	G|G	1092;1212;259|260	ENSP00000413201:E1092G;ENSP00000281513:E1212G;ENSP00000396501:E259G|.	ENSP00000281513:E1212G|.	E|R	-|-	2|1	0|2	NBAS|NBAS	15432251|15432251	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.629000|6.629000	0.74267|0.74267	2.181000|2.181000	0.69327|0.69327	0.533000|0.533000	0.62120|0.62120	GAG|AGG	.	.		0.383	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		C	15514800	T	C	15514800	3	2	35	1	0	0	0	0	1	0	0	0	10195	1551	54	2	3568	2	NBAS	2	15514800	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	3926906	15514800	227684573	64	4233										
NBAS	51594	hgsc.bcm.edu	37	chr2	15534402	15534402	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tcagcttgcgtgcctcttctGagctagattgagtgttttta	10	8	3	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:15534402G>T	ENST00000281513.5	-	28	3231	c.3206C>A	c.(3205-3207)tCa>tAa	p.S1069*	NBAS_ENST00000441750.1_Nonsense_Mutation_p.S949*	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1069					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TGCCTCTTCTGAGCTAGATTG	0.338																																					p.S1069X		Atlas-SNP	.											.	NBAS	246	.	0			c.C3206A						.						57	55	56					2																	15534402		2203	4298	6501	SO:0001587	stop_gained	51594	exon28			TCTTCTGAGCTAG	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.3206C>A	chr2.hg19:g.15534402G>T	ENSP00000281513:p.Ser1069*	143.0	0.0		130.0	6.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Nonsense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.211634|6.211634	0.97380|0.97380	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000442506|ENST00000441750;ENST00000281513;ENST00000441755	.|.	.|.	.|.	5.48|5.48	3.69|3.69	0.42338|0.42338	.|.	.|0.618852	.|0.17033	.|N	.|0.189625	T|.	0.66046|.	0.2750|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.75280|.	-0.3373|.	3|.	.|0.87932	.|D	.|0	.|.	11.3888|11.3888	0.49802|0.49802	0.1293:0.0:0.8707:0.0|0.1293:0.0:0.8707:0.0	.|.	.|.	.|.	.|.	K|X	117|949;1069;116	.|.	.|ENSP00000281513:S1069X	Q|S	-|-	1|2	0|0	NBAS|NBAS	15451853|15451853	0.031000|0.031000	0.19500|0.19500	0.024000|0.024000	0.17045|0.17045	0.598000|0.598000	0.36846|0.36846	2.190000|2.190000	0.42630|0.42630	0.688000|0.688000	0.31529|0.31529	0.655000|0.655000	0.94253|0.94253	CAG|TCA	.	.		0.338	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15534402	G	T	15534402	4	4	35	1	0	0	0	0	0	1	0	0	10195	1294	45	3	4009	3	NBAS	2	15534402	Nonsense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	19602	15534402	227664971	65	4234										
OTOF	9381	hgsc.bcm.edu	37	chr2	26693459	26693459	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctcaccctacccgaggtctcAcctccttcatggtgtcaatg	7	16	4	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:26693459A>G	ENST00000272371.2	-	32	4150		c.e32+1		OTOF_ENST00000338581.6_Splice_Site|OTOF_ENST00000403946.3_Splice_Site|OTOF_ENST00000402415.3_Splice_Site|OTOF_ENST00000339598.3_Splice_Site	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin						membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCGAGGTCTCACCTCCTTCAT	0.602																																					.	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.4023+2T>C						.						226	193	204					2																	26693459		2203	4300	6503	SO:0001630	splice_region_variant	9381	exon33			GGTCTCACCTCCT	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.4023+1T>C	chr2.hg19:g.26693459A>G		131.0	0.0		97.0	4.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Splice_Site	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.610958	0.87258	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7917	0.78369	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	OTOF	26546963	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.404000	0.79996	2.218000	0.71995	0.533000	0.62120	.	.	.		0.602	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		Intron	G	26693459	A	G	26693459	5	3	35	1	0	0	0	0	0	0	1	0	11312	173	6	2	2213	2	OTOF	2	26693459	Splice_Site	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	11159057	26693459	216505914	66	4235										
C2orf16	84226	hgsc.bcm.edu	37	chr2	27803857	27803857	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ccaaactgcctcagtggggcAgcctctgagaactgttcaaa	10	12	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:27803857A>G	ENST00000408964.2	+	1	4469	c.4418A>G	c.(4417-4419)cAg>cGg	p.Q1473R	ZNF512_ENST00000355467.4_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000416005.2_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1473						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TCAGTGGGGCAGCCTCTGAGA	0.473																																					p.Q1473R		Atlas-SNP	.											.	C2orf16	357	.	0			c.A4418G						.						99	101	100					2																	27803857		1860	4106	5966	SO:0001583	missense	84226	exon1			TGGGGCAGCCTCT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4418A>G	chr2.hg19:g.27803857A>G	ENSP00000386190:p.Gln1473Arg	78.0	0.0		74.0	5.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	hg19	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	A	12.15	1.852837	0.32699	.	.	ENSG00000221843	ENST00000408964	T	0.59364	0.27	4.13	0.24	0.15489	.	.	.	.	.	T	0.42063	0.1186	N	0.24115	0.695	0.09310	N	1	D	0.58268	0.982	P	0.47573	0.55	T	0.25606	-1.0127	9	0.28530	T	0.3	.	4.7413	0.13013	0.5099:0.3846:0.1055:0.0	.	1473	Q68DN1	CB016_HUMAN	R	1473	ENSP00000386190:Q1473R	ENSP00000386190:Q1473R	Q	+	2	0	C2orf16	27657361	0.009000	0.17119	0.000000	0.03702	0.010000	0.07245	1.739000	0.38217	-0.039000	0.13602	0.379000	0.24179	CAG	.	.		0.473	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		G	27803857	A	G	27803857	3	3	35	1	0	0	0	0	1	0	0	0	2159	188	7	2	4420	2	C2orf16	2	27803857	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	1110398	27803857	215395516	67	4236										
FOSL2	2355	hgsc.bcm.edu	37	chr2	28627206	28627206	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cattggcaccaccgtgggccGcaggaggagagatgagcagg	17	10	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:28627206G>A	ENST00000264716.4	+	2	1198	c.335G>A	c.(334-336)cGc>cAc	p.R112H	FOSL2_ENST00000379619.1_Missense_Mutation_p.R87H|FOSL2_ENST00000460736.1_3'UTR|FOSL2_ENST00000545753.1_Missense_Mutation_p.R73H	NM_005253.3	NP_005244.1	P15408	FOSL2_HUMAN	FOS-like antigen 2	112					cell death (GO:0008219)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R112H(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)					ACCGTGGGCCGCAGGAGGAGA	0.627																																					p.R112H		Atlas-SNP	.											FOSL2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	FOSL2	39	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G335A						.						68	73	72					2																	28627206		2203	4300	6503	SO:0001583	missense	2355	exon2			TGGGCCGCAGGAG		CCDS1766.1	2p23.3	2013-01-10			ENSG00000075426	ENSG00000075426		"basic leucine zipper proteins"	3798	protein-coding gene	gene with protein product		601575					Standard	NM_005253		Approved	FRA2, FLJ23306	uc002rma.3	P15408	OTTHUMG00000097832	ENST00000264716.4:c.335G>A	chr2.hg19:g.28627206G>A	ENSP00000264716:p.Arg112His	67.0	0.0		70.0	3.0	NM_005253	B2RD58|B3KP27|B4DYV4|Q6FG46	Missense_Mutation	SNP	ENST00000264716.4	hg19	CCDS1766.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.774822	0.90108	.	.	ENSG00000075426	ENST00000379619;ENST00000264716;ENST00000436647;ENST00000545753	T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.84120	0.5402	M	0.80183	2.485	0.80722	D	1	D	0.76494	0.999	P	0.61800	0.894	D	0.86203	0.1620	10	0.87932	D	0	-21.3146	19.3052	0.94158	0.0:0.0:1.0:0.0	.	112	P15408	FOSL2_HUMAN	H	87;112;73;73	ENSP00000368939:R87H;ENSP00000264716:R112H;ENSP00000396497:R73H;ENSP00000439303:R73H	ENSP00000264716:R112H	R	+	2	0	FOSL2	28480710	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	5.953000	0.70290	2.555000	0.86185	0.563000	0.77884	CGC	.	.		0.627	FOSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215116.2	NM_005253		A	28627206	G	A	28627206	3	1	35	1	0	0	0	0	1	0	0	0	5996	1087	38	1	341	1	FOSL2	2	28627206	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	823349	28627206	214572167	68	4237										
THADA	63892	hgsc.bcm.edu	37	chr2	43519292	43519292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gatcaagaactcctttggggTcagatggacacagtgctccg	12	10	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:43519292T>C	ENST00000405006.4	-	33	5239	c.4888A>G	c.(4888-4890)Acc>Gcc	p.T1630A	THADA_ENST00000405975.2_Missense_Mutation_p.T1630A|THADA_ENST00000330266.7_Intron|THADA_ENST00000415080.2_Missense_Mutation_p.T1311A	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1630										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TCCTTTGGGGTCAGATGGACA	0.488																																					p.T1630A		Atlas-SNP	.											.	THADA	131	.	0			c.A4888G						.						55	58	57					2																	43519292		1949	4137	6086	SO:0001583	missense	63892	exon33			TTGGGGTCAGATG	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.4888A>G	chr2.hg19:g.43519292T>C	ENSP00000385995:p.Thr1630Ala	120.0	0.0		104.0	5.0	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	hg19	CCDS46268.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.43|14.43	2.532561|2.532561	0.45073|0.45073	.|.	.|.	ENSG00000115970|ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006|ENST00000407351	T;T;T|.	0.11930|.	2.91;2.73;2.91|.	5.18|5.18	3.99|3.99	0.46301|0.46301	.|.	0.527792|.	0.19381|.	N|.	0.115658|.	T|.	0.32315|.	0.0825|.	L|L	0.27053|0.27053	0.805|0.805	0.22896|0.22896	N|N	0.998592|0.998592	P;B|.	0.35844|.	0.524;0.104|.	B;B|.	0.37091|.	0.241;0.023|.	T|.	0.18871|.	-1.0323|.	10|.	0.09843|.	T|.	0.71|.	.|.	8.9455|8.9455	0.35756|0.35756	0.1718:0.0:0.0:0.8282|0.1718:0.0:0.0:0.8282	.|.	1557;1630|.	B6ZDQ0;Q6YHU6|.	.;THADA_HUMAN|.	A|W	1630;1557;1311;1630|869	ENSP00000386088:T1630A;ENSP00000416048:T1311A;ENSP00000385995:T1630A|.	ENSP00000349464:T1557A|.	T|X	-|-	1|3	0|0	THADA|THADA	43372796|43372796	0.993000|0.993000	0.37304|0.37304	0.828000|0.828000	0.32881|0.32881	0.870000|0.870000	0.49936|0.49936	2.704000|2.704000	0.47118|0.47118	0.778000|0.778000	0.33520|0.33520	0.524000|0.524000	0.50904|0.50904	ACC|TGA	.	.		0.488	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		C	43519292	T	C	43519292	3	2	35	1	0	0	0	0	1	0	0	0	15855	1667	58	2	997	2	THADA	2	43519292	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	14892086	43519292	199680081	69	4238										
FBXO11	80204	hgsc.bcm.edu	37	chr2	48037548	48037548	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttgagcattcctgaaaatatCattttcttcaaggagaccta	6	8	3	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:48037548C>A	ENST00000403359.3	-	19	2317	c.2245G>T	c.(2245-2247)Gat>Tat	p.D749Y	FBXO11_ENST00000434523.2_Missense_Mutation_p.D173Y|FBXO11_ENST00000402508.1_Missense_Mutation_p.D665Y|FBXO11_ENST00000316377.4_Missense_Mutation_p.D665Y|FBXO11_ENST00000405808.1_5'Flank	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	749					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTGAAAATATCATTTTCTTCA	0.333			"Mis, F, D"		DLBCL																																p.D749Y		Atlas-SNP	.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11	127	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.G2245T						.						61	62	62					2																	48037548		2203	4300	6503	SO:0001583	missense	80204	exon19			AAATATCATTTTC	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"Ubiquitin protein ligase E3 component n-recognins", "F-boxes /  "other""	13590	protein-coding gene	gene with protein product	"ubiquitin protein ligase E3 component n-recognin 6"	607871	"F-box only protein 11"			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.2245G>T	chr2.hg19:g.48037548C>A	ENSP00000384823:p.Asp749Tyr	99.0	0.0		85.0	4.0	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	hg19	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.826362	0.90955	.	.	ENSG00000138081	ENST00000402508;ENST00000403359;ENST00000316377;ENST00000434523	T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	D	0.88328	0.6407	L	0.49126	1.545	0.80722	D	1	D	0.60160	0.987	D	0.79108	0.992	D	0.87734	0.2581	10	0.87932	D	0	-0.5037	20.8598	0.99761	0.0:1.0:0.0:0.0	.	173	B3KUR1	.	Y	665;749;665;173	ENSP00000385398:D665Y;ENSP00000384823:D749Y;ENSP00000323822:D665Y;ENSP00000397359:D173Y	ENSP00000323822:D665Y	D	-	1	0	FBXO11	47891052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.792000	0.85828	2.937000	0.99478	0.650000	0.86243	GAT	.	.		0.333	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		A	48037548	C	A	48037548	3	1	35	1	0	0	0	0	1	0	0	0	5735	826	29	3	558	3	FBXO11	2	48037548	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	4518256	48037548	195161825	70	4239										
PSME4	23198	hgsc.bcm.edu	37	chr2	54122147	54122147	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgaaatggaatgcttacctcTgtcatatcctccctgcttct	6	12	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:54122147T>C	ENST00000404125.1	-	34	3964	c.3909A>G	c.(3907-3909)acA>acG	p.T1303T	PSME4_ENST00000421748.2_Silent_p.T447T	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1303					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			TGCTTACCTCTGTCATATCCT	0.388																																					p.T1303T		Atlas-SNP	.											.	PSME4	247	.	0			c.A3909G						.						202	176	185					2																	54122147		2203	4300	6503	SO:0001819	synonymous_variant	23198	exon34			TACCTCTGTCATA	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.3909A>G	chr2.hg19:g.54122147T>C		95.0	0.0		95.0	4.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	hg19	CCDS33197.2																																																																																			.	.		0.388	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		C	54122147	T	C	54122147	2	2	35	1	0	0	0	0	0	0	0	1	12721	1567	55	2		2	PSME4	2	54122147	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	6084599	54122147	189077226	71	4240										
PUS10	150962	hgsc.bcm.edu	37	chr2	61175283	61175283	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cagccaggggccttcggtgaAggacgcgcaaaggtgttttc	15	10	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:61175283A>G	ENST00000316752.6	-	16	1607	c.1346T>C	c.(1345-1347)cTt>cCt	p.L449P	PUS10_ENST00000407787.1_Missense_Mutation_p.L449P	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	449	RNA binding thumb loop. {ECO:0000255}.				pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			CCTTCGGTGAAGGACGCGCAA	0.527																																					p.L449P		Atlas-SNP	.											.	PUS10	49	.	0			c.T1346C						.						171	171	171					2																	61175283		2203	4300	6503	SO:0001583	missense	150962	exon16			CGGTGAAGGACGC	AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"coiled-coil domain containing 139"	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.1346T>C	chr2.hg19:g.61175283A>G	ENSP00000326003:p.Leu449Pro	152.0	0.0		123.0	5.0	NM_144709	Q5JPJ5|Q96MI8	Missense_Mutation	SNP	ENST00000316752.6	hg19	CCDS1865.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.713327	0.89112	.	.	ENSG00000162927	ENST00000316752;ENST00000407787	D;D	0.89123	-2.47;-2.47	6.16	6.16	0.99307	Pseudouridine synthase, catalytic domain (1);	0.065114	0.64402	D	0.000006	D	0.95411	0.8510	M	0.89414	3.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.95812	0.8842	10	0.66056	D	0.02	-2.398	16.8061	0.85666	1.0:0.0:0.0:0.0	.	449;449	A8K6R4;Q3MIT2	.;PUS10_HUMAN	P	449	ENSP00000326003:L449P;ENSP00000386074:L449P	ENSP00000326003:L449P	L	-	2	0	PUS10	61028787	1.000000	0.71417	0.986000	0.45419	0.906000	0.53458	8.962000	0.93254	2.367000	0.80283	0.528000	0.53228	CTT	.	.		0.527	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709		G	61175283	A	G	61175283	3	3	35	1	0	0	0	0	1	0	0	0	12846	72	3	2	255	2	PUS10	2	61175283	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	7053136	61175283	182024090	72	4241										
XPO1	7514	hgsc.bcm.edu	37	chr2	61706090	61706090	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aacaaatcagaagtgtcttcAcctgcaaattcctgtgaaaa	6	9	3	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:61706090A>C	ENST00000401558.2	-	25	3808	c.3081T>G	c.(3079-3081)ggT>ggG	p.G1027G	RP11-355B11.2_ENST00000603199.1_RNA|RP11-355B11.2_ENST00000603028.1_RNA|RP11-355B11.2_ENST00000578974.2_RNA|RP11-355B11.2_ENST00000603652.1_RNA|XPO1_ENST00000406957.1_Silent_p.G1027G|XPO1_ENST00000404992.2_Silent_p.G1027G	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	1027					gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			AAGTGTCTTCACCTGCAAATT	0.373			Mis		CLL																																p.G1027G		Atlas-SNP	.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1	108	.	0			c.T3081G						.						114	110	111					2																	61706090		2203	4300	6503	SO:0001819	synonymous_variant	7514	exon25			GTCTTCACCTGCA	Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.3081T>G	chr2.hg19:g.61706090A>C		241.0	0.0		189.0	59.0	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Silent	SNP	ENST00000401558.2	hg19	CCDS33205.1																																																																																			.	.		0.373	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		C	61706090	A	C	61706090	2	2	35	1	0	0	0	0	0	0	0	1	17460	146	6	5		5	XPO1	2	61706090	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	530807	61706090	181493283	73	4242										
ARHGAP25	9938	hgsc.bcm.edu	37	chr2	69053300	69053300	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tcaaggaatttgtcaaatccAtgaaggaacccaagaccgag	9	9	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:69053300A>G	ENST00000295381.3	+	11	2331	c.1912A>G	c.(1912-1914)Atg>Gtg	p.M638V	ARHGAP25_ENST00000409202.3_Missense_Mutation_p.M639V|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.M599V|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.M631V|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.M332V|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.M632V	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	638					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						TGTCAAATCCATGAAGGAACC	0.547																																					p.M639V		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.A1915G						.						76	80	79					2																	69053300		2203	4300	6503	SO:0001583	missense	9938	exon11			AAATCCATGAAGG	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1912A>G	chr2.hg19:g.69053300A>G	ENSP00000295381:p.Met638Val	102.0	0.0		67.0	4.0	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	hg19		.	.	.	.	.	.	.	.	.	.	A	11.11	1.542141	0.27563	.	.	ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000543533;ENST00000479844	T;T;T;T;T;T	0.16457	2.93;2.93;2.67;2.93;2.93;2.34	5.95	-2.02	0.07388	.	0.321333	0.30649	N	0.009176	T	0.05914	0.0154	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.0;0.0;0.0;0.0;0.002	T	0.17837	-1.0356	10	0.52906	T	0.07	.	2.262	0.04069	0.5152:0.116:0.2572:0.1116	.	599;639;632;631;638	E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331	.;.;.;.;RHG25_HUMAN	V	638;639;599;631;632;623;332	ENSP00000295381:M638V;ENSP00000386911:M639V;ENSP00000420583:M599V;ENSP00000386863:M631V;ENSP00000386241:M632V;ENSP00000417467:M332V	ENSP00000295381:M638V	M	+	1	0	ARHGAP25	68906804	0.003000	0.15002	0.023000	0.16930	0.823000	0.46562	0.493000	0.22451	-0.324000	0.08589	-0.250000	0.11733	ATG	.	.		0.547	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882		G	69053300	A	G	69053300	3	3	35	1	0	0	0	0	1	0	0	0	874	217	8	2	1997	2	ARHGAP25	2	69053300	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	7347210	69053300	174146073	74	4243										
ADD2	119	hgsc.bcm.edu	37	chr2	70919547	70919547	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ccactcaccgctgctgtggcCggtgtgtgcaggtggatgat	15	11	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:70919547C>T	ENST00000264436.4	-	7	1137	c.693G>A	c.(691-693)ccG>ccA	p.P231P	ADD2_ENST00000355733.3_Silent_p.P231P|ADD2_ENST00000413157.2_Silent_p.P231P|AC007395.3_ENST00000457851.1_RNA|ADD2_ENST00000407644.2_Silent_p.P231P|ADD2_ENST00000430656.1_Silent_p.P247P	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	231					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						CTGCTGTGGCCGGTGTGTGCA	0.582																																					p.P247P		Atlas-SNP	.											.	ADD2	261	.	0			c.G741A						.						55	51	52					2																	70919547		2203	4300	6503	SO:0001819	synonymous_variant	119	exon6			TGTGGCCGGTGTG	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.693G>A	chr2.hg19:g.70919547C>T		78.0	0.0		92.0	4.0	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Silent	SNP	ENST00000264436.4	hg19	CCDS1906.1																																																																																			.	.		0.582	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		T	70919547	C	T	70919547	2	4	35	1	0	0	0	0	0	0	0	1	305	639	23	1		1	ADD2	2	70919547	Silent	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	1866247	70919547	172279826	75	4244										
LOXL3	84695	hgsc.bcm.edu	37	chr2	74763252	74763252	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tcctgtccagagcagcgaacTtcactcaggtggatagcacc	10	13	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:74763252T>C	ENST00000264094.3	-	7	1190	c.1119A>G	c.(1117-1119)gaA>gaG	p.E373E	LOXL3_ENST00000409249.1_Intron|LOXL3_ENST00000409986.1_Silent_p.E228E|LOXL3_ENST00000393937.2_Silent_p.E228E|LOXL3_ENST00000409549.1_Silent_p.E373E	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	373	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						AGCAGCGAACTTCACTCAGGT	0.542																																					p.E373E		Atlas-SNP	.											.	LOXL3	73	.	0			c.A1119G						.						81	83	82					2																	74763252		2203	4300	6503	SO:0001819	synonymous_variant	84695	exon7			GCGAACTTCACTC	AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.1119A>G	chr2.hg19:g.74763252T>C		73.0	0.0		61.0	4.0	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Silent	SNP	ENST00000264094.3	hg19	CCDS1953.1	.	.	.	.	.	.	.	.	.	.	T	6.948	0.544686	0.13312	.	.	ENSG00000115318	ENST00000420535	.	.	.	5.09	-2.87	0.05700	.	.	.	.	.	T	0.50718	0.1632	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47032	-0.9148	4	.	.	.	.	7.337	0.26615	0.0:0.5076:0.1569:0.3355	.	.	.	.	G	100	.	.	S	-	1	0	LOXL3	74616760	0.998000	0.40836	0.909000	0.35828	0.986000	0.74619	0.600000	0.24104	-0.339000	0.08401	0.450000	0.29827	AGT	.	.		0.542	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		C	74763252	T	C	74763252	2	2	35	1	0	0	0	0	0	0	0	1	8910	1606	56	2		2	LOXL3	2	74763252	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	3843705	74763252	168436121	76	4245										
HK2	3099	hgsc.bcm.edu	37	chr2	75113635	75113635	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aggcacgggcagcaatgcctGctacatggaggagatgcgca	15	10	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:75113635G>T	ENST00000290573.2	+	15	2654	c.2054G>T	c.(2053-2055)tGc>tTc	p.C685F	HK2_ENST00000409174.1_Missense_Mutation_p.C657F	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	685	Catalytic.|Hexokinase type-2 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						AGCAATGCCTGCTACATGGAG	0.587																																					p.C685F		Atlas-SNP	.											.	HK2	85	.	0			c.G2054T						.						105	98	101					2																	75113635		2203	4300	6503	SO:0001583	missense	3099	exon15			ATGCCTGCTACAT		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.2054G>T	chr2.hg19:g.75113635G>T	ENSP00000290573:p.Cys685Phe	143.0	0.0		129.0	50.0	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	hg19	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.571500	0.86542	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.98701	-5.08;-5.08	5.49	5.49	0.81192	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99507	0.9824	H	0.97806	4.08	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98130	1.0430	10	0.87932	D	0	-25.4229	16.9239	0.86170	0.0:0.0:1.0:0.0	.	685	P52789	HXK2_HUMAN	F	685;685;657	ENSP00000290573:C685F;ENSP00000387140:C657F	ENSP00000290573:C685F	C	+	2	0	HK2	74967143	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.584000	0.98220	2.865000	0.98341	0.655000	0.94253	TGC	.	.		0.587	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189		T	75113635	G	T	75113635	3	4	35	1	0	0	0	0	1	0	0	0	7200	1319	46	3	2112	3	HK2	2	75113635	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	350383	75113635	168085738	77	4246										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84949784	84949784	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	attaaaaccaggctggaagaAgcagagtccactgagcagat	11	8	0	4			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:84949784A>G	ENST00000237449.6	+	59	9836	c.9828A>G	c.(9826-9828)gaA>gaG	p.E3276E	DNAH6_ENST00000389394.3_Silent_p.E3276E			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3276					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GGCTGGAAGAAGCAGAGTCCA	0.443																																					p.E3276E		Atlas-SNP	.											.	DNAH6	194	.	0			c.A9828G						.						94	85	87					2																	84949784		692	1591	2283	SO:0001819	synonymous_variant	1768	exon60			GGAAGAAGCAGAG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.9828A>G	chr2.hg19:g.84949784A>G		112.0	0.0		97.0	4.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.443	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84949784	A	G	84949784	2	3	35	1	0	0	0	0	0	0	0	1	4607	69	3	2		2	DNAH6	2	84949784	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	9836149	84949784	158249589	78	4247										
CD8A	925	hgsc.bcm.edu	37	chr2	87013062	87013062	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gttagacgtatctcgccgaaAggctgggcttgtctcccgat	12	11	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:87013062A>G	ENST00000409511.2	-	9	1719	c.689T>C	c.(688-690)cTt>cCt	p.L230P	CD8A_ENST00000456996.2_Missense_Mutation_p.L193P|CD8A_ENST00000409781.1_Missense_Mutation_p.L193P|CD8A_ENST00000352580.3_Missense_Mutation_p.L193P|CD8A_ENST00000538832.1_Missense_Mutation_p.L271P|CD8A_ENST00000283635.3_Missense_Mutation_p.L230P	NM_001145873.1	NP_001139345.1	P01732	CD8A_HUMAN	CD8a molecule	230					antigen processing and presentation (GO:0019882)|cytotoxic T cell differentiation (GO:0045065)|defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of calcium-mediated signaling (GO:0050850)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|T cell mediated immunity (GO:0002456)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|MHC class I protein binding (GO:0042288)			lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	8						TCTCGCCGAAAGGCTGGGCTT	0.512																																					p.L230P		Atlas-SNP	.											.	CD8A	28	.	0			c.T689C						.						188	184	185					2																	87013062		2203	4300	6503	SO:0001583	missense	925	exon9			GCCGAAAGGCTGG		CCDS1992.1, CCDS1993.1	2p12	2014-09-17	2006-03-28		ENSG00000153563	ENSG00000153563		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1706	protein-coding gene	gene with protein product		186910	"CD8 antigen, alpha polypeptide (p32)", "T-cell surface glycoprotein CD8 alpha chain"	CD8		1541829	Standard	NM_171827		Approved		uc002sru.3	P01732	OTTHUMG00000130265	ENST00000409511.2:c.689T>C	chr2.hg19:g.87013062A>G	ENSP00000386559:p.Leu230Pro	105.0	0.0		107.0	5.0	NM_001145873	B4DT80|D6W5M8|Q13970|Q4ZG17	Missense_Mutation	SNP	ENST00000409511.2	hg19	CCDS1992.1	.	.	.	.	.	.	.	.	.	.	A	8.538	0.872529	0.17322	.	.	ENSG00000153563	ENST00000456996;ENST00000352580;ENST00000283635;ENST00000409511;ENST00000442577;ENST00000538832;ENST00000409781	T;T;T;T;T;T	0.77620	-0.94;-0.94;-1.02;-1.02;-1.11;-1.07	4.03	-2.39	0.06602	.	1.967440	0.02026	N	0.048205	T	0.47266	0.1436	N	0.00985	-1.075	0.09310	N	0.999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.39781	-0.9597	10	0.37606	T	0.19	4.5251	3.0785	0.06254	0.4029:0.0:0.2808:0.3163	.	271;193;230	B4DT80;P01732-2;P01732	.;.;CD8A_HUMAN	P	193;193;230;230;215;271;193	ENSP00000398868:L193P;ENSP00000321631:L193P;ENSP00000283635:L230P;ENSP00000386559:L230P;ENSP00000438371:L271P;ENSP00000387314:L193P	ENSP00000283635:L230P	L	-	2	0	CD8A	86866573	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.464000	0.06688	-0.536000	0.06298	-1.252000	0.01501	CTT	.	.		0.512	CD8A-006	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330784.3	NM_001768		G	87013062	A	G	87013062	3	3	35	1	0	0	0	0	1	0	0	0	3046	72	3	2	22	2	CD8A	2	87013062	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	2063278	87013062	156186311	79	4248										
NCAPH	23397	hgsc.bcm.edu	37	chr2	97009872	97009872	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctactgaaatgggaacaaccAaaaaggctgtaaagccaaag	9	8	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:97009872A>G	ENST00000240423.4	+	6	668	c.625A>G	c.(625-627)Aaa>Gaa	p.K209E	NCAPH_ENST00000455200.1_Missense_Mutation_p.K198E|NCAPH_ENST00000427946.1_Missense_Mutation_p.K73E	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	209					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				GGGAACAACCAAAAAGGCTGT	0.418																																					p.K209E		Atlas-SNP	.											.	NCAPH	67	.	0			c.A625G						.						98	89	92					2																	97009872		2203	4300	6503	SO:0001583	missense	23397	exon6			ACAACCAAAAAGG	BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"barren (Drosophila) homolog", "barren homolog (Drosophila)", "barren homolog 1 (Drosophila)"	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	ENST00000240423.4:c.625A>G	chr2.hg19:g.97009872A>G	ENSP00000240423:p.Lys209Glu	101.0	0.0		97.0	4.0	NM_015341	B4E189|Q8TB87	Missense_Mutation	SNP	ENST00000240423.4	hg19	CCDS2021.1	.	.	.	.	.	.	.	.	.	.	A	10.38	1.333114	0.24167	.	.	ENSG00000121152	ENST00000240423;ENST00000427946;ENST00000435975;ENST00000455200	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.17	2.71	0.32032	.	0.569443	0.19541	N	0.111803	T	0.29556	0.0737	L	0.45698	1.435	0.26974	N	0.965517	B;B;P;B	0.36837	0.234;0.234;0.571;0.234	B;B;B;B	0.34038	0.158;0.158;0.174;0.158	T	0.17592	-1.0364	10	0.07325	T	0.83	-9.6048	10.8058	0.46516	0.6971:0.3029:0.0:0.0	.	185;198;198;209	B4DRG7;E9PHA2;C9J470;Q15003	.;.;.;CND2_HUMAN	E	209;73;198;198	ENSP00000240423:K209E;ENSP00000400774:K73E;ENSP00000405237:K198E;ENSP00000407308:K198E	ENSP00000240423:K209E	K	+	1	0	NCAPH	96373599	1.000000	0.71417	0.901000	0.35422	0.853000	0.48598	4.128000	0.57951	0.353000	0.24079	-0.328000	0.08392	AAA	.	.		0.418	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341		G	97009872	A	G	97009872	3	3	35	1	0	0	0	0	1	0	0	0	10218	131	5	2	647	2	NCAPH	2	97009872	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	9996810	97009872	146189501	80	4249										
TMEM131	23505	hgsc.bcm.edu	37	chr2	98410005	98410005	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aggctgttccaatgaccaaaAgaaacagtgcactgcagggg	12	9	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:98410005A>G	ENST00000186436.5	-	30	3626	c.3398T>C	c.(3397-3399)cTt>cCt	p.L1133P		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1133						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						AATGACCAAAAGAAACAGTGC	0.438																																					p.L1133P		Atlas-SNP	.											.	TMEM131	258	.	0			c.T3398C						.						34	34	34					2																	98410005		1830	4079	5909	SO:0001583	missense	23505	exon30			ACCAAAAGAAACA	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.3398T>C	chr2.hg19:g.98410005A>G	ENSP00000186436:p.Leu1133Pro	107.0	0.0		104.0	7.0	NM_015348		Missense_Mutation	SNP	ENST00000186436.5	hg19	CCDS46368.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.440541	0.83993	.	.	ENSG00000075568	ENST00000186436;ENST00000409721	T	0.39229	1.09	5.77	5.77	0.91146	.	0.061214	0.64402	D	0.000002	T	0.61813	0.2377	M	0.61703	1.905	0.80722	D	1	D	0.76494	0.999	D	0.67231	0.95	T	0.64668	-0.6353	10	0.87932	D	0	-14.6149	16.3948	0.83586	1.0:0.0:0.0:0.0	.	1133	Q92545	TM131_HUMAN	P	1133;50	ENSP00000186436:L1133P	ENSP00000186436:L1133P	L	-	2	0	TMEM131	97776437	1.000000	0.71417	0.938000	0.37757	0.993000	0.82548	8.678000	0.91211	2.326000	0.78906	0.533000	0.62120	CTT	.	.		0.438	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		G	98410005	A	G	98410005	3	3	35	1	0	0	0	0	1	0	0	0	16059	72	3	2	2301	2	TMEM131	2	98410005	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	1400133	98410005	144789368	81	4250										
VWA3B	200403	hgsc.bcm.edu	37	chr2	98750292	98750292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctcttcacgtttcagattccAcgcatttgccgagagaacag	8	12	3	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:98750292A>G	ENST00000477737.1	+	7	1082	c.878A>G	c.(877-879)cAc>cGc	p.H293R	VWA3B_ENST00000451075.2_Missense_Mutation_p.H143R|VWA3B_ENST00000435344.1_Missense_Mutation_p.H293R	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	293										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TTCAGATTCCACGCATTTGCC	0.473																																					p.H293R		Atlas-SNP	.											.	VWA3B	138	.	0			c.A878G						.						284	269	274					2																	98750292		2100	4230	6330	SO:0001583	missense	200403	exon7			GATTCCACGCATT	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.878A>G	chr2.hg19:g.98750292A>G	ENSP00000417955:p.His293Arg	89.0	0.0		78.0	4.0	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.704507	0.48412	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.49720	7.42;7.42;0.77	5.66	5.66	0.87406	.	0.088339	0.48767	D	0.000172	T	0.69700	0.3140	M	0.80982	2.52	0.35522	D	0.801546	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.988;0.959;0.996	T	0.80384	-0.1405	10	0.87932	D	0	.	13.4291	0.61044	1.0:0.0:0.0:0.0	.	143;293;293	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	R	293;293;143	ENSP00000401959:H293R;ENSP00000417955:H293R;ENSP00000389463:H143R	ENSP00000411168:H293R	H	+	2	0	VWA3B	98116724	0.999000	0.42202	0.921000	0.36526	0.045000	0.14185	5.314000	0.65804	2.154000	0.67381	0.533000	0.62120	CAC	.	.		0.473	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		G	98750292	A	G	98750292	3	3	35	1	0	0	0	0	1	0	0	0	17256	159	6	2	900	2	VWA3B	2	98750292	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	340287	98750292	144449081	82	4251										
AFF3	3899	hgsc.bcm.edu	37	chr2	100343586	100343586	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctctctggctctgcatcaccTttctcttaaaaaggaagcag	7	12	4	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:100343586T>C	ENST00000409236.2	-	9	1156	c.1044A>G	c.(1042-1044)aaA>aaG	p.K348K	AFF3_ENST00000356421.2_Silent_p.K373K|AFF3_ENST00000317233.4_Silent_p.K348K|AFF3_ENST00000409579.1_Silent_p.K373K			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	348					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						CTGCATCACCTTTCTCTTAAA	0.348																																					p.K373K		Atlas-SNP	.											.	AFF3	164	.	0			c.A1119G						.						74	74	74					2																	100343586		2203	4300	6503	SO:0001819	synonymous_variant	3899	exon10			ATCACCTTTCTCT	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1044A>G	chr2.hg19:g.100343586T>C		83.0	0.0		80.0	4.0	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	hg19	CCDS42723.1																																																																																			.	.		0.348	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		C	100343586	T	C	100343586	2	2	35	1	0	0	0	0	0	0	0	1	358	1606	56	2		2	AFF3	2	100343586	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	1593294	100343586	142855787	83	4252										
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105885829	105885829	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ccctcatggcccccatcaggAatgggcagaggagctgcact	12	14	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:105885829A>G	ENST00000393359.2	-	11	2732	c.2306T>C	c.(2305-2307)tTc>tCc	p.F769S	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.F769S			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	769					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						CCCCATCAGGAATGGGCAGAG	0.602																																					p.F769S	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.T2306C						.						38	38	38					2																	105885829		2203	4300	6503	SO:0001583	missense	9392	exon11			ATCAGGAATGGGC	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.2306T>C	chr2.hg19:g.105885829A>G	ENSP00000377027:p.Phe769Ser	123.0	0.0		119.0	5.0	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	hg19	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	A	19.87	3.906747	0.72868	.	.	ENSG00000135966	ENST00000393359;ENST00000258449;ENST00000543724	T;T	0.58060	0.36;0.36	5.36	5.36	0.76844	Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.77651	0.4162	M	0.89715	3.055	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.82694	-0.0330	10	0.66056	D	0.02	-31.4532	15.6465	0.77061	1.0:0.0:0.0:0.0	.	224;769	B3KMM9;Q8WUH2	.;TGFA1_HUMAN	S	769;769;224	ENSP00000377027:F769S;ENSP00000258449:F769S	ENSP00000258449:F769S	F	-	2	0	TGFBRAP1	105252261	1.000000	0.71417	1.000000	0.80357	0.383000	0.30230	8.910000	0.92685	2.164000	0.68074	0.459000	0.35465	TTC	.	.		0.602	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		G	105885829	A	G	105885829	3	3	35	1	0	0	0	0	1	0	0	0	15839	246	9	2	284	2	TGFBRAP1	2	105885829	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	5542243	105885829	137313544	84	4253										
ST6GAL2	84620	hgsc.bcm.edu	37	chr2	107459744	107459744	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cgcaccccgtgcttgttggcGgtcaggtaatccttcatcgc	11	14	2	0	rs144265287		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:107459744G>A	ENST00000409382.3	-	2	1300	c.690C>T	c.(688-690)acC>acT	p.T230T	AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000361686.4_Silent_p.T230T|ST6GAL2_ENST00000409087.3_Silent_p.T230T	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	230					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						GCTTGTTGGCGGTCAGGTAAT	0.672																																					p.T230T		Atlas-SNP	.											.	ST6GAL2	159	.	0			c.C690T						.						27	28	28					2																	107459744		2202	4300	6502	SO:0001819	synonymous_variant	84620	exon2			GTTGGCGGTCAGG	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"sialyltransferase 2 (monosialoganglioside sialyltransferase)"	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.690C>T	chr2.hg19:g.107459744G>A		31.0	0.0		51.0	4.0	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	hg19	CCDS2073.1																																																																																			.	G|1.000;C|0.000		0.672	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		A	107459744	G	A	107459744	2	1	35	1	0	0	0	0	0	0	0	1	15237	1103	39	1		1	ST6GAL2	2	107459744	Silent	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	1573915	107459744	135739629	85	4254										
NPHP1	4867	hgsc.bcm.edu	37	chr2	110881571	110881571	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaatgggggtaggcgtgtggAgtggagaagtgggagcacgc	22	4	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:110881571A>G	ENST00000393272.3	-	20	2093	c.1996T>C	c.(1996-1998)Tcc>Ccc	p.S666P	NPHP1_ENST00000417665.1_Missense_Mutation_p.S645P|NPHP1_ENST00000316534.4_Missense_Mutation_p.S667P|NPHP1_ENST00000445609.2_Missense_Mutation_p.S611P|AC013268.1_ENST00000390802.1_RNA|NPHP1_ENST00000355301.4_Missense_Mutation_p.S548P	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	666					actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						AGGCGTGTGGAGTGGAGAAGT	0.498																																					p.S667P		Atlas-SNP	.											.	NPHP1	68	.	0			c.T1999C						.						119	119	119					2																	110881571		2203	4300	6503	SO:0001583	missense	4867	exon20			GTGTGGAGTGGAG	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"nephrocystin-1"	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.1996T>C	chr2.hg19:g.110881571A>G	ENSP00000376953:p.Ser666Pro	105.0	0.0		66.0	4.0	NM_000272	O14837	Missense_Mutation	SNP	ENST00000393272.3	hg19	CCDS46385.1	.	.	.	.	.	.	.	.	.	.	A	15.66	2.899515	0.52227	.	.	ENSG00000144061	ENST00000316534;ENST00000445609;ENST00000393272;ENST00000355301;ENST00000417665	T;T;T;T;T	0.69926	-0.06;-0.05;-0.06;-0.04;-0.44	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.82167	0.4978	M	0.79805	2.47	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.999;0.999	D	0.84741	0.0751	10	0.72032	D	0.01	-14.5899	14.4178	0.67163	1.0:0.0:0.0:0.0	.	610;548;666;611;667	B4DQY0;O15259-3;O15259;O15259-2;O15259-4	.;.;NPHP1_HUMAN;.;.	P	667;611;666;548;645	ENSP00000313169:S667P;ENSP00000389879:S611P;ENSP00000376953:S666P;ENSP00000347452:S548P;ENSP00000402176:S645P	ENSP00000313169:S667P	S	-	1	0	NPHP1	110238860	0.987000	0.35691	0.074000	0.20217	0.159000	0.22180	2.865000	0.48412	2.086000	0.62901	0.379000	0.24179	TCC	.	.		0.498	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272		G	110881571	A	G	110881571	3	3	35	1	0	0	0	0	1	0	0	0	10588	304	11	2	206	2	NPHP1	2	110881571	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	3421827	110881571	132317802	86	4255										
PSD4	23550	hgsc.bcm.edu	37	chr2	113958938	113958938	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aaggtgaagcgcaacatctcAgagcgcagaacctaccggaa	11	11	1	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:113958938A>G	ENST00000245796.6	+	17	3312	c.3117A>G	c.(3115-3117)tcA>tcG	p.S1039S	PSD4_ENST00000441564.3_Silent_p.S1010S	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	1039					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GCAACATCTCAGAGCGCAGAA	0.607																																					p.S1039S		Atlas-SNP	.											.	PSD4	74	.	0			c.A3117G						.						106	93	98					2																	113958938		2203	4300	6503	SO:0001819	synonymous_variant	23550	exon17			CATCTCAGAGCGC	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"Pleckstrin homology (PH) domain containing"	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.3117A>G	chr2.hg19:g.113958938A>G		70.0	0.0		69.0	4.0	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Silent	SNP	ENST00000245796.6	hg19	CCDS33276.1																																																																																			.	.		0.607	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455		G	113958938	A	G	113958938	2	3	35	1	0	0	0	0	0	0	0	1	12661	175	7	2		2	PSD4	2	113958938	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	3077367	113958938	129240435	87	4256										
CLASP1	23332	hgsc.bcm.edu	37	chr2	122227423	122227423	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggtggatgaaccaagccggcGggtggttcccattccaacgt	14	11	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:122227423G>A	ENST00000263710.4	-	9	1215	c.826C>T	c.(826-828)Cgc>Tgc	p.R276C	CLASP1_ENST00000430234.1_5'UTR|CLASP1_ENST00000455322.2_Missense_Mutation_p.R276C|CLASP1_ENST00000409078.3_Missense_Mutation_p.R276C|CLASP1_ENST00000397587.3_Missense_Mutation_p.R276C|CLASP1_ENST00000541859.1_Missense_Mutation_p.R45C|CLASP1_ENST00000541377.1_Missense_Mutation_p.R276C|CLASP1_ENST00000545861.1_Missense_Mutation_p.R44C	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	276					axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					CCAAGCCGGCGGGTGGTTCCC	0.517																																					p.R276C		Atlas-SNP	.											.	CLASP1	135	.	0			c.C826T						.						68	70	69					2																	122227423		1904	4138	6042	SO:0001583	missense	23332	exon9			GCCGGCGGGTGGT	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"multiple asters 1"	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.826C>T	chr2.hg19:g.122227423G>A	ENSP00000263710:p.Arg276Cys	96.0	0.0		108.0	6.0	NM_001207051	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	hg19		.	.	.	.	.	.	.	.	.	.	G	21.4	4.140626	0.77775	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861;ENST00000418989;ENST00000449975	T;T;T;T;T;T;T;T	0.50813	1.99;2.01;2.0;2.02;0.73;2.01;0.73;0.75	4.75	4.75	0.60458	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67183	0.2866	M	0.61703	1.905	0.58432	D	0.999995	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.993;0.997;0.995;0.997	T	0.70044	-0.4980	10	0.59425	D	0.04	-19.0472	18.1235	0.89579	0.0:0.0:1.0:0.0	.	276;276;276;276	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	C	276;276;276;276;45;276;44;45;45	ENSP00000263710:R276C;ENSP00000389372:R276C;ENSP00000380717:R276C;ENSP00000441625:R276C;ENSP00000441770:R45C;ENSP00000386442:R276C;ENSP00000392886:R45C;ENSP00000402101:R45C	ENSP00000263710:R276C	R	-	1	0	CLASP1	121943893	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	3.889000	0.56212	2.363000	0.80096	0.460000	0.39030	CGC	.	.		0.517	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		A	122227423	G	A	122227423	3	1	35	1	0	0	0	0	1	0	0	0	3456	1116	39	1	3970	1	CLASP1	2	122227423	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	8268485	122227423	120971950	88	4257										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125204453	125204453	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gcaggtgaacttcacggtggAcaagcacacacagcacttcc	10	13	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:125204453A>G	ENST00000431078.1	+	6	1221	c.857A>G	c.(856-858)gAc>gGc	p.D286G		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	286	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		TTCACGGTGGACAAGCACACA	0.602																																					p.D286G		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.A857G						.						114	116	115					2																	125204453		2172	4281	6453	SO:0001583	missense	129684	exon6			CGGTGGACAAGCA	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.857A>G	chr2.hg19:g.125204453A>G	ENSP00000399013:p.Asp286Gly	182.0	0.0		149.0	6.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.959204	0.92726	.	.	ENSG00000155052	ENST00000431078	D	0.88354	-2.37	5.78	5.78	0.91487	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.53938	D	0.000052	D	0.95906	0.8667	M	0.93808	3.46	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96862	0.9633	10	0.87932	D	0	.	15.5785	0.76414	1.0:0.0:0.0:0.0	.	286	Q8WYK1	CNTP5_HUMAN	G	286	ENSP00000399013:D286G	ENSP00000399013:D286G	D	+	2	0	CNTNAP5	124920923	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.153000	0.94687	2.333000	0.79357	0.533000	0.62120	GAC	.	.		0.602	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			G	125204453	A	G	125204453	3	3	35	1	0	0	0	0	1	0	0	0	3652	275	10	2	879	2	CNTNAP5	2	125204453	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	2977030	125204453	117994920	89	4258										
CYP27C1	339761	hgsc.bcm.edu	37	chr2	127958787	127958787	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	atctggggatggcgcctgcaTacatggaggtcttgaacatg	14	8	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:127958787T>G	ENST00000335247.7	-	3	429	c.299A>C	c.(298-300)tAt>tCt	p.Y100S	CYP27C1_ENST00000409327.1_Missense_Mutation_p.Y100S	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	100						membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		GGCGCCTGCATACATGGAGGT	0.537																																					p.Y100S		Atlas-SNP	.											.	CYP27C1	52	.	0			c.A299C						.						116	117	116					2																	127958787		2203	4300	6503	SO:0001583	missense	339761	exon3			CCTGCATACATGG	AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684		"Cytochrome P450s"	33480	protein-coding gene	gene with protein product							Standard	NM_001001665		Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.299A>C	chr2.hg19:g.127958787T>G	ENSP00000334128:p.Tyr100Ser	94.0	0.0		88.0	31.0	NM_001001665	Q6ZNI7	Missense_Mutation	SNP	ENST00000335247.7	hg19	CCDS33285.1	.	.	.	.	.	.	.	.	.	.	T	17.01	3.280568	0.59758	.	.	ENSG00000186684	ENST00000335247;ENST00000409327	T;T	0.67171	-0.25;-0.25	4.04	2.82	0.32997	.	0.072732	0.56097	D	0.000023	T	0.61999	0.2392	L	0.35487	1.065	0.44719	D	0.99771	P	0.51240	0.943	P	0.52109	0.69	T	0.59241	-0.7491	10	0.51188	T	0.08	-10.4256	8.4863	0.33074	0.0:0.1022:0.0:0.8978	.	100	Q4G0S4	C27C1_HUMAN	S	100	ENSP00000334128:Y100S;ENSP00000387198:Y100S	ENSP00000334128:Y100S	Y	-	2	0	CYP27C1	127675257	1.000000	0.71417	0.529000	0.27951	0.866000	0.49608	2.923000	0.48868	0.394000	0.25230	-0.366000	0.07423	TAT	.	.		0.537	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665		G	127958787	T	G	127958787	3	3	35	1	0	0	0	0	1	0	0	0	4162	1406	49	5	843	5	CYP27C1	2	127958787	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	2754334	127958787	115240586	90	4259										
PROC	5624	hgsc.bcm.edu	37	chr2	128186428	128186428	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gggctgtgggctccttcacaActacggcgtttacaccaaag	11	12	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:128186428A>G	ENST00000234071.3	+	9	1379	c.1292A>G	c.(1291-1293)aAc>aGc	p.N431S	PROC_ENST00000422777.3_Missense_Mutation_p.N431S|PROC_ENST00000453608.2_Missense_Mutation_p.N486S|PROC_ENST00000409048.1_Missense_Mutation_p.N465S	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	431	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood coagulation (GO:0030195)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	CTCCTTCACAACTACGGCGTT	0.637																																					p.N431S		Atlas-SNP	.											.	PROC	31	.	0			c.A1292G						.						90	96	94					2																	128186428		2203	4300	6503	SO:0001583	missense	5624	exon9			TTCACAACTACGG	X02750	CCDS2145.1	2q13-q14	2014-01-30			ENSG00000115718	ENSG00000115718		"Endogenous ligands"	9451	protein-coding gene	gene with protein product	"prepro-protein C"	612283				2991887, 2437584	Standard	NM_000312		Approved		uc002tok.3	P04070	OTTHUMG00000131528	ENST00000234071.3:c.1292A>G	chr2.hg19:g.128186428A>G	ENSP00000234071:p.Asn431Ser	63.0	0.0		73.0	4.0	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Missense_Mutation	SNP	ENST00000234071.3	hg19	CCDS2145.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.46|17.46	3.394261|3.394261	0.62066|0.62066	.|.	.|.	ENSG00000115718|ENSG00000115718	ENST00000234071;ENST00000537436;ENST00000453608;ENST00000409048;ENST00000422777|ENST00000402125	D;D;D;D|.	0.88431|.	-2.38;-2.38;-2.38;-2.38|.	5.16|5.16	3.95|3.95	0.45737|0.45737	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);|.	0.000000|.	0.47852|.	D|.	0.000203|.	T|T	0.31575|0.31575	0.0801|0.0801	N|N	0.03891|0.03891	-0.335|-0.335	0.43719|0.43719	D|D	0.996194|0.996194	P;P;B;P|.	0.51537|.	0.946;0.87;0.017;0.939|.	P;P;B;P|.	0.61003|.	0.882;0.728;0.126;0.8|.	T|T	0.15607|0.15607	-1.0431|-1.0431	10|5	0.38643|.	T|.	0.18|.	.|.	12.2975|12.2975	0.54857|0.54857	0.859:0.141:0.0:0.0|0.859:0.141:0.0:0.0	.|.	486;487;465;431|.	B4DPQ7;B4DPQ3;E7END6;P04070|.	.;.;.;PROC_HUMAN|.	S|A	431;390;486;465;431|206	ENSP00000234071:N431S;ENSP00000404030:N486S;ENSP00000386679:N465S;ENSP00000409543:N431S|.	ENSP00000234071:N431S|.	N|T	+|+	2|1	0|0	PROC|PROC	127902898|127902898	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.960000|0.960000	0.62799|0.62799	5.935000|5.935000	0.70145|0.70145	2.177000|2.177000	0.69029|0.69029	0.533000|0.533000	0.62120|0.62120	AAC|ACT	.	.		0.637	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312		G	128186428	A	G	128186428	3	3	35	1	0	0	0	0	1	0	0	0	12557	43	2	2	1322	2	PROC	2	128186428	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	227641	128186428	115012945	91	4260										
MYO7B	4648	hgsc.bcm.edu	37	chr2	128338357	128338357	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cctggacgcctcagacgtgaTggagacgcccgcctttccca	11	16	1	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:128338357T>C	ENST00000409816.2	+	9	1072	c.1040T>C	c.(1039-1041)aTg>aCg	p.M347T	MYO7B_ENST00000428314.1_Missense_Mutation_p.M347T|MYO7B_ENST00000389524.4_Missense_Mutation_p.M347T			Q6PIF6	MYO7B_HUMAN	myosin VIIB	347	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		TCAGACGTGATGGAGACGCCC	0.597																																					p.M347T		Atlas-SNP	.											.	MYO7B	359	.	0			c.T1040C						.						55	57	57					2																	128338357		1985	4163	6148	SO:0001583	missense	4648	exon10			ACGTGATGGAGAC		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.1040T>C	chr2.hg19:g.128338357T>C	ENSP00000386461:p.Met347Thr	93.0	0.0		83.0	4.0	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	T	0.350	-0.945258	0.02304	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.86627	-2.15;-2.15;-2.15	5.27	2.84	0.33178	Myosin head, motor domain (2);	0.403000	0.27622	N	0.018543	T	0.65995	0.2745	N	0.02736	-0.51	0.30694	N	0.750989	P	0.37573	0.6	B	0.37091	0.241	T	0.64241	-0.6454	10	0.14656	T	0.56	.	6.4617	0.21960	0.0:0.0803:0.1571:0.7625	.	347	Q6PIF6	MYO7B_HUMAN	T	347	ENSP00000374175:M347T;ENSP00000415090:M347T;ENSP00000386461:M347T	ENSP00000374175:M347T	M	+	2	0	MYO7B	128054827	1.000000	0.71417	1.000000	0.80357	0.103000	0.19146	1.729000	0.38115	0.392000	0.25172	-0.376000	0.06991	ATG	.	.		0.597	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		C	128338357	T	C	128338357	3	2	35	1	0	0	0	0	1	0	0	0	10092	1464	51	2	1074	2	MYO7B	2	128338357	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	151929	128338357	114861016	92	4261										
WDR33	55339	hgsc.bcm.edu	37	chr2	128522284	128522336	+	Intron	DEL	GTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	GTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	-													0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aaaaatattgtgtttataggGtgcagaaagtttcccagaaa					rs200736326|rs369619546	byFrequency	TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	GTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	GTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:128522284_128522336delGTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	ENST00000322313.4	-	6	785				WDR33_ENST00000409658.3_Frame_Shift_Del_p.ILGAEMHGLCQFLGNFLH231fs|WDR33_ENST00000393006.1_Intron	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33						mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TGTTTATAGGGTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAATACACTTAGA	0.403																																					p.231_249del		Atlas-Indel,Pindel	.											.	WDR33	136	.	0			c.693_745del						.																																			SO:0001627	intron_variant	55339	exon6			.		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.626+65TTCTGGGTGCAGAGATGCATGGGCTCTGTCAGTTTCTGGGAAACTTTCTGCAC>-	chr2.hg19:g.128522284_128522336delGTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA		271.0	0.0		155.0	16.0	NM_001006622	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Frame_Shift_Del	DEL	ENST00000322313.4	hg19	CCDS2150.1																																																																																			.	.		0.403	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		-	128522336	GTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	-	128522284	6	5	35	0	1	1	0	1	0	0	0	0	17302	1252	44	0		0	WDR33	2	128522284	Intron	DEL	GTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	TCGA-BC-A10W-01A-11D-A12Z-10	183927	128522284	114677089	93	4262										
GPR148	344561	hgsc.bcm.edu	37	chr2	131487061	131487061	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tctcctccagcagcctgggtGgctgggagctgggccgcatg	16	13	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:131487061G>A	ENST00000309926.4	+	1	419	c.337G>A	c.(337-339)Ggc>Agc	p.G113S		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					CAGCCTGGGTGGCTGGGAGCT	0.622																																					p.G113S		Atlas-SNP	.											.	GPR148	54	.	0			c.G337A						.						53	58	56					2																	131487061		2203	4300	6503	SO:0001583	missense	344561	exon1			CTGGGTGGCTGGG	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"GPCR / Class A : Orphans"	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.337G>A	chr2.hg19:g.131487061G>A	ENSP00000308908:p.Gly113Ser	166.0	0.0		140.0	7.0	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	hg19	CCDS2163.1	.	.	.	.	.	.	.	.	.	.	.	3.436	-0.115181	0.06881	.	.	ENSG00000173302	ENST00000309926	T	0.36340	1.26	3.15	-0.467	0.12150	GPCR, rhodopsin-like superfamily (1);	0.226724	0.26995	N	0.021450	T	0.17874	0.0429	N	0.19112	0.55	0.09310	N	1	B	0.23937	0.094	B	0.31614	0.133	T	0.13845	-1.0494	10	0.22109	T	0.4	-0.2022	2.1136	0.03708	0.1305:0.3404:0.3565:0.1726	.	113	Q8TDV2	GP148_HUMAN	S	113	ENSP00000308908:G113S	ENSP00000308908:G113S	G	+	1	0	GPR148	131203531	0.006000	0.16342	0.532000	0.27989	0.166000	0.22503	0.010000	0.13242	-0.176000	0.10707	0.462000	0.41574	GGC	.	.		0.622	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092		A	131487061	G	A	131487061	3	1	35	1	0	0	0	0	1	0	0	0	6661	1348	47	3	339	3	GPR148	2	131487061	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	2964777	131487061	111712312	94	4263										
R3HDM1	23518	hgsc.bcm.edu	37	chr2	136481779	136481779	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agaatgcactgaagaaacaaAttaactcagttaacaagttt	6	6	1	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:136481779A>G	ENST00000264160.4	+	26	3587	c.3217A>G	c.(3217-3219)Att>Gtt	p.I1073V	R3HDM1_ENST00000409478.1_Missense_Mutation_p.I945V|R3HDM1_ENST00000329971.3_Missense_Mutation_p.I944V|R3HDM1_ENST00000409606.1_Missense_Mutation_p.I1074V|R3HDM1_ENST00000410054.1_Missense_Mutation_p.I1018V	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	1073							poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		GAAGAAACAAATTAACTCAGT	0.458																																					p.I1073V		Atlas-SNP	.											.	R3HDM1	84	.	0			c.A3217G						.						71	67	68					2																	136481779		2203	4300	6503	SO:0001583	missense	23518	exon26			AAACAAATTAACT	D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing"	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.3217A>G	chr2.hg19:g.136481779A>G	ENSP00000264160:p.Ile1073Val	124.0	0.0		87.0	4.0	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	hg19	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.581|1.581	-0.531644|-0.531644	0.04112|0.04112	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000409478;ENST00000264160;ENST00000329971;ENST00000410054;ENST00000409606|ENST00000429703	T;T;T;T;T|.	0.28454|.	1.61;1.62;1.61;1.61;1.62|.	5.74|5.74	4.58|4.58	0.56647|0.56647	.|.	0.181695|.	0.45867|.	N|.	0.000334|.	T|T	0.47451|0.47451	0.1446|0.1446	L|L	0.44542|0.44542	1.39|1.39	0.30052|0.30052	N|N	0.811708|0.811708	B;B;B;B|.	0.17667|.	0.023;0.003;0.0;0.003|.	B;B;B;B|.	0.12837|.	0.008;0.002;0.0;0.003|.	T|T	0.46527|0.46527	-0.9185|-0.9185	10|5	0.45353|.	T|.	0.12|.	-8.0449|-8.0449	12.1509|12.1509	0.54050|0.54050	0.9327:0.0:0.0673:0.0|0.9327:0.0:0.0673:0.0	.|.	945;1074;1018;1073|.	G5E9G8;E9PBB4;E9PG42;Q15032|.	.;.;.;R3HD1_HUMAN|.	V|S	945;1073;944;1018;1074|796	ENSP00000386457:I945V;ENSP00000264160:I1073V;ENSP00000331396:I944V;ENSP00000386877:I1018V;ENSP00000387010:I1074V|.	ENSP00000264160:I1073V|.	I|N	+|+	1|2	0|0	R3HDM1|R3HDM1	136198249|136198249	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.985000|0.985000	0.73830|0.73830	4.709000|4.709000	0.61867|0.61867	1.097000|1.097000	0.41459|0.41459	0.459000|0.459000	0.35465|0.35465	ATT|AAT	.	.		0.458	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		G	136481779	A	G	136481779	3	3	35	1	0	0	0	0	1	0	0	0	12902	101	4	2	3311	2	R3HDM1	2	136481779	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	4994718	136481779	106717594	95	4264										
CXCR4	7852	hgsc.bcm.edu	37	chr2	136872711	136872711	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gatttccaggaggatgaaggAgtcgatgctgatcccaatgt	13	7	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:136872711A>G	ENST00000241393.3	-	2	891	c.787T>C	c.(787-789)Tcc>Ccc	p.S263P	CXCR4_ENST00000409817.1_Missense_Mutation_p.S267P|CXCR4_ENST00000466288.1_5'UTR	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	263					activation of MAPK activity (GO:0000187)|ameboidal cell migration (GO:0001667)|apoptotic process (GO:0006915)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular response to cytokine stimulus (GO:0071345)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|inflammatory response (GO:0006954)|motor neuron axon guidance (GO:0008045)|myelin maintenance (GO:0043217)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|neutrophil activation (GO:0042119)|patterning of blood vessels (GO:0001569)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of chemotaxis (GO:0050920)|response to hypoxia (GO:0001666)|response to virus (GO:0009615)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)|myosin light chain binding (GO:0032027)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)|Plerixafor(DB06809)	AGGATGAAGGAGTCGATGCTG	0.522																																					p.S267P		Atlas-SNP	.											.	CXCR4	51	.	0			c.T799C						.						226	214	218					2																	136872711		2203	4300	6503	SO:0001583	missense	7852	exon1			TGAAGGAGTCGAT	AF005058	CCDS33295.1, CCDS46420.1	2q21	2014-09-17	2002-08-22		ENSG00000121966	ENSG00000121966		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	2561	protein-coding gene	gene with protein product		162643	"chemokine (C-X-C motif), receptor 4 (fusin)"			9599023, 9379028	Standard	NM_001008540		Approved	LESTR, NPY3R, HM89, NPYY3R, D2S201E, fusin, HSY3RR, NPYR, CD184	uc002tuz.3	P61073	OTTHUMG00000153583	ENST00000241393.3:c.787T>C	chr2.hg19:g.136872711A>G	ENSP00000241393:p.Ser263Pro	109.0	0.0		80.0	4.0	NM_001008540	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Missense_Mutation	SNP	ENST00000241393.3	hg19	CCDS46420.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.567435	0.45694	.	.	ENSG00000121966	ENST00000409817;ENST00000241393;ENST00000537957	T;T	0.37752	1.18;1.18	6.17	3.69	0.42338	GPCR, rhodopsin-like superfamily (1);	0.137085	0.64402	D	0.000003	T	0.36663	0.0975	L	0.35249	1.045	0.45194	D	0.9982	D;P	0.58268	0.982;0.878	P;B	0.55455	0.776;0.092	T	0.20140	-1.0284	10	0.87932	D	0	.	5.7662	0.18227	0.5395:0.1107:0.0:0.3498	.	263;267	P61073;P61073-2	CXCR4_HUMAN;.	P	267;263;133	ENSP00000386884:S267P;ENSP00000241393:S263P	ENSP00000241393:S263P	S	-	1	0	CXCR4	136589181	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.818000	0.55678	1.137000	0.42214	0.533000	0.62120	TCC	.	.		0.522	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1			G	136872711	A	G	136872711	3	3	35	1	0	0	0	0	1	0	0	0	4095	304	11	2	275	2	CXCR4	2	136872711	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	390932	136872711	106326662	96	4265										
FIGN	55137	hgsc.bcm.edu	37	chr2	164466794	164466794	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aggatgctccgaggtaaggcCgtcagtccactgaacgcgtc	13	12	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:164466794C>A	ENST00000333129.3	-	3	1862	c.1548G>T	c.(1546-1548)acG>acT	p.T516T	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	516					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						GAGGTAAGGCCGTCAGTCCAC	0.507																																					p.T516T		Atlas-SNP	.											.	FIGN	106	.	0			c.G1548T						.						96	90	92					2																	164466794		1995	4167	6162	SO:0001819	synonymous_variant	55137	exon3			TAAGGCCGTCAGT	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"ATPases / AAA-type"	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.1548G>T	chr2.hg19:g.164466794C>A		175.0	0.0		148.0	55.0	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Silent	SNP	ENST00000333129.3	hg19	CCDS2221.2																																																																																			.	.		0.507	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		A	164466794	C	A	164466794	2	1	35	1	0	0	0	0	0	0	0	1	5899	639	23	1		1	FIGN	2	164466794	Silent	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	27594083	164466794	78732579	97	4266										
COBLL1	22837	hgsc.bcm.edu	37	chr2	165552127	165552127	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tcttttctgcactgggttgaTtcagtttttgatctggtact	9	7	4	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:165552127T>C	ENST00000392717.2	-	13	2007	c.2003A>G	c.(2002-2004)aAt>aGt	p.N668S	COBLL1_ENST00000194871.6_Missense_Mutation_p.N697S|COBLL1_ENST00000409184.3_Missense_Mutation_p.N630S|COBLL1_ENST00000342193.4_Missense_Mutation_p.N630S|COBLL1_ENST00000375458.2_Missense_Mutation_p.N592S			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	668						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						ACTGGGTTGATTCAGTTTTTG	0.398																																					p.N630S		Atlas-SNP	.											.	COBLL1	122	.	0			c.A1889G						.						304	298	300					2																	165552127		2203	4300	6503	SO:0001583	missense	22837	exon12			GGTTGATTCAGTT	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.2003A>G	chr2.hg19:g.165552127T>C	ENSP00000376478:p.Asn668Ser	668.0	0.0		654.0	232.0	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	hg19		.	.	.	.	.	.	.	.	.	.	T	5.660	0.306376	0.10733	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	6.06	0.816	0.18768	.	0.379490	0.28290	N	0.015888	T	0.26666	0.0652	L	0.44542	1.39	0.09310	N	1	B;B;B	0.20671	0.028;0.028;0.047	B;B;B	0.22152	0.017;0.019;0.038	T	0.24048	-1.0171	9	0.09338	T	0.73	-10.2753	5.9997	0.19513	0.1127:0.2637:0.0:0.6236	.	668;697;630	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	S	592;630;630;668;697	.	ENSP00000194871:N697S	N	-	2	0	COBLL1	165260373	0.920000	0.31207	0.789000	0.31954	0.744000	0.42396	0.644000	0.24766	0.148000	0.19059	0.533000	0.62120	AAT	.	.		0.398	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		C	165552127	T	C	165552127	3	2	35	1	0	0	0	0	1	0	0	0	3656	1493	52	2	1623	2	COBLL1	2	165552127	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	1085333	165552127	77647246	98	4267										
LRP2	4036	hgsc.bcm.edu	37	chr2	170031784	170031784	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctgcgggctggtgcagttgcCgtcactgcactggaactgtc	14	12	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:170031784C>T	ENST00000263816.3	-	55	10972	c.10687G>A	c.(10687-10689)Ggc>Agc	p.G3563S	LRP2_ENST00000461418.1_5'Flank	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3563	LDL-receptor class A 27. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GTGCAGTTGCCGTCACTGCAC	0.527																																					p.G3563S		Atlas-SNP	.											.	LRP2	751	.	0			c.G10687A						.						81	80	80					2																	170031784		2203	4300	6503	SO:0001583	missense	4036	exon55			AGTTGCCGTCACT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.10687G>A	chr2.hg19:g.170031784C>T	ENSP00000263816:p.Gly3563Ser	213.0	0.0		200.0	88.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.352685	0.61293	.	.	ENSG00000081479	ENST00000263816;ENST00000536293	D	0.92595	-3.07	5.71	3.9	0.45041	.	0.050715	0.85682	D	0.000000	D	0.95503	0.8539	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93670	0.6989	10	0.25751	T	0.34	.	11.4275	0.50020	0.0:0.8052:0.1269:0.0679	.	3563	P98164	LRP2_HUMAN	S	3563;258	ENSP00000263816:G3563S	ENSP00000263816:G3563S	G	-	1	0	LRP2	169740030	1.000000	0.71417	0.861000	0.33841	0.116000	0.19942	6.089000	0.71384	0.746000	0.32786	-0.300000	0.09419	GGC	.	.		0.527	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170031784	C	T	170031784	3	4	35	1	0	0	0	0	1	0	0	0	8965	652	23	1	3380	1	LRP2	2	170031784	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	4479657	170031784	73167589	99	4268										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171323061	171323061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aaatggtggttggacagcccCactttgtgcgctgcattaaa	11	9	0	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:171323061C>T	ENST00000408978.4	+	25	2997	c.2854C>T	c.(2854-2856)Cac>Tac	p.H952Y	MYO3B_ENST00000602629.1_Intron|MYO3B_ENST00000409044.3_Missense_Mutation_p.H952Y|MYO3B_ENST00000334231.6_Missense_Mutation_p.H961Y	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	952	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TGGACAGCCCCACTTTGTGCG	0.527																																					p.H952Y		Atlas-SNP	.											.	MYO3B	320	.	0			c.C2854T						.						97	100	99					2																	171323061		1931	4134	6065	SO:0001583	missense	140469	exon25			CAGCCCCACTTTG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2854C>T	chr2.hg19:g.171323061C>T	ENSP00000386213:p.His952Tyr	71.0	0.0		75.0	4.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	hg19	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.800726	0.90538	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85	5.03	5.03	0.67393	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.87071	0.6086	M	0.80508	2.5	0.80722	D	1	D;P;D	0.89917	0.999;0.929;1.0	D;P;D	0.81914	0.979;0.729;0.995	D	0.89015	0.3431	10	0.87932	D	0	.	18.3721	0.90411	0.0:1.0:0.0:0.0	.	952;952;952	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	Y	952;952;951;961;961	ENSP00000386497:H952Y;ENSP00000386213:H952Y;ENSP00000446237:H961Y;ENSP00000335100:H961Y	ENSP00000314213:H951Y	H	+	1	0	MYO3B	171031307	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.731000	0.84895	2.348000	0.79779	0.563000	0.77884	CAC	.	.		0.527	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			T	171323061	C	T	171323061	3	4	35	1	0	0	0	0	1	0	0	0	10086	594	21	3	2952	3	MYO3B	2	171323061	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	1291277	171323061	71876312	100	4269										
GAD1	2571	hgsc.bcm.edu	37	chr2	171710458	171710458	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agcagtatgatgtctcctacGacaccggggacaaggcaatt	11	10	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:171710458G>A	ENST00000358196.3	+	14	1889	c.1339G>A	c.(1339-1341)Gac>Aac	p.D447N		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	447					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						TGTCTCCTACGACACCGGGGA	0.478																																					p.D447N		Atlas-SNP	.											.	GAD1	79	.	0			c.G1339A						.						154	141	145					2																	171710458		2203	4300	6503	SO:0001583	missense	2571	exon14			TCCTACGACACCG		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1339G>A	chr2.hg19:g.171710458G>A	ENSP00000350928:p.Asp447Asn	134.0	0.0		99.0	5.0	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	hg19	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	G	35	5.533135	0.96460	.	.	ENSG00000128683	ENST00000358196	T	0.57273	0.41	5.5	5.5	0.81552	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.043255	0.85682	D	0.000000	T	0.71375	0.3332	L	0.58510	1.815	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72666	-0.4224	10	0.87932	D	0	-25.3619	19.7739	0.96383	0.0:0.0:1.0:0.0	.	447	Q99259	DCE1_HUMAN	N	447	ENSP00000350928:D447N	ENSP00000350928:D447N	D	+	1	0	GAD1	171418704	1.000000	0.71417	0.957000	0.39632	0.965000	0.64279	9.420000	0.97426	2.744000	0.94065	0.655000	0.94253	GAC	.	.		0.478	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			A	171710458	G	A	171710458	3	1	35	1	0	0	0	0	1	0	0	0	6187	1058	37	1	1430	1	GAD1	2	171710458	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	387397	171710458	71488915	101	4270										
OLA1	29789	hgsc.bcm.edu	37	chr2	174945976	174945976	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttaatgatctttggcaaagcActgaaatcaaatgaaacaaa	6	6	2	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:174945976A>G	ENST00000409546.1	-	9	1560	c.930T>C	c.(928-930)agT>agC	p.S310S	OLA1_ENST00000284719.3_Splice_Site_p.S290S|OLA1_ENST00000428402.2_Intron|OLA1_ENST00000392560.2_5'UTR|OLA1_ENST00000344357.5_Splice_Site_p.S132S					Obg-like ATPase 1											breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						TTGGCAAAGCACTGAAATCAA	0.388																																					p.S290S		Atlas-SNP	.											.	OLA1	37	.	0			c.T870C						.						63	56	58					2																	174945976		2203	4299	6502	SO:0001630	splice_region_variant	29789	exon9			CAAAGCACTGAAA		CCDS2255.1, CCDS42779.1	2q31.1	2014-06-24	2007-07-27	2007-07-27	ENSG00000138430	ENSG00000138430			28833	protein-coding gene	gene with protein product		611175	"GTP-binding protein 9 (putative)"	GTPBP9		17430889, 24486488	Standard	NM_013341		Approved	PTD004	uc002uih.3	Q9NTK5	OTTHUMG00000132335	ENST00000409546.1:c.930-1T>C	chr2.hg19:g.174945976A>G		97.0	0.0		112.0	5.0	NM_013341		Silent	SNP	ENST00000409546.1	hg19																																																																																				.	.		0.388	OLA1-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333877.1	NM_013341	Silent	G	174945976	A	G	174945976	5	3	35	1	0	0	0	0	0	0	1	0	10859	173	6	2	332	2	OLA1	2	174945976	Splice_Site	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	3235518	174945976	68253397	102	4271										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196750867	196750867	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaaggcaacggaccttacctCaagcaaagagtaagtttctc	9	10	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:196750867C>T	ENST00000312428.6	-	34	5636	c.5536G>A	c.(5536-5538)Gag>Aag	p.E1846K		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1846					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GACCTTACCTCAAGCAAAGAG	0.408																																					p.E1846K		Atlas-SNP	.											.	DNAH7	512	.	0			c.G5536A						.						153	153	153					2																	196750867		1880	4120	6000	SO:0001583	missense	56171	exon34			TTACCTCAAGCAA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.5536G>A	chr2.hg19:g.196750867C>T	ENSP00000311273:p.Glu1846Lys	100.0	0.0		88.0	4.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.866593	0.72065	.	.	ENSG00000118997	ENST00000312428	T	0.26067	1.76	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.55832	0.1945	M	0.85099	2.735	0.80722	D	1	D	0.64830	0.994	D	0.70227	0.968	T	0.61667	-0.7016	10	0.49607	T	0.09	.	17.8593	0.88776	0.0:1.0:0.0:0.0	.	1846	Q8WXX0	DYH7_HUMAN	K	1846	ENSP00000311273:E1846K	ENSP00000311273:E1846K	E	-	1	0	DNAH7	196459112	1.000000	0.71417	0.986000	0.45419	0.360000	0.29518	6.944000	0.75940	2.377000	0.81083	0.557000	0.71058	GAG	.	.		0.408	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196750867	C	T	196750867	3	4	35	1	0	0	0	0	1	0	0	0	4608	835	29	3	6666	3	DNAH7	2	196750867	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	21804891	196750867	46448506	103	4272										
CCDC150	284992	hgsc.bcm.edu	37	chr2	197521794	197521794	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctgagagctgtaaaagaggaAgaagacaaggcacaagatga	13	5	0	6			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:197521794A>G	ENST00000389175.4	+	4	645	c.510A>G	c.(508-510)gaA>gaG	p.E170E	CCDC150_ENST00000423093.2_Intron|CCDC150_ENST00000272831.7_Intron|CCDC150_ENST00000472405.2_Silent_p.E67E	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	170										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						TAAAAGAGGAAGAAGACAAGG	0.443																																					p.E170E		Atlas-SNP	.											.	CCDC150	96	.	0			c.A510G						.						92	94	94					2																	197521794		1999	4172	6171	SO:0001819	synonymous_variant	284992	exon4			AGAGGAAGAAGAC		CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.510A>G	chr2.hg19:g.197521794A>G		148.0	0.0		98.0	4.0	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Silent	SNP	ENST00000389175.4	hg19	CCDS46478.1																																																																																			.	.		0.443	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539		G	197521794	A	G	197521794	2	3	35	1	0	0	0	0	0	0	0	1	2787	69	3	2		2	CCDC150	2	197521794	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	770927	197521794	45677579	104	4273										
GTF3C3	9330	hgsc.bcm.edu	37	chr2	197664292	197664292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cgaactcctcaaaggagattTtcccttccaagtagtcgatg	8	11	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:197664292T>C	ENST00000263956.3	-	1	133	c.44A>G	c.(43-45)aAa>aGa	p.K15R	GTF3C3_ENST00000409364.3_Missense_Mutation_p.K15R	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	15					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						AAAGGAGATTTTCCCTTCCAA	0.542																																					p.K15R		Atlas-SNP	.											.	GTF3C3	96	.	0			c.A44G						.						121	129	126					2																	197664292		2203	4300	6503	SO:0001583	missense	9330	exon1			GAGATTTTCCCTT	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.44A>G	chr2.hg19:g.197664292T>C	ENSP00000263956:p.Lys15Arg	102.0	0.0		94.0	4.0	NM_001206774	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	hg19	CCDS2316.1	.	.	.	.	.	.	.	.	.	.	T	15.69	2.908198	0.52333	.	.	ENSG00000119041	ENST00000263956;ENST00000409364	T;T	0.44881	0.91;0.98	5.36	5.36	0.76844	.	0.054636	0.64402	D	0.000001	T	0.32793	0.0841	N	0.25647	0.755	0.43467	D	0.995674	B;B	0.27625	0.183;0.006	B;B	0.28011	0.085;0.014	T	0.09596	-1.0667	10	0.34782	T	0.22	-26.2667	15.1834	0.72978	0.0:0.0:0.0:1.0	.	15;15	Q9Y5Q9-2;Q9Y5Q9	.;TF3C3_HUMAN	R	15	ENSP00000263956:K15R;ENSP00000386465:K15R	ENSP00000263956:K15R	K	-	2	0	GTF3C3	197372537	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.575000	0.53870	2.250000	0.74265	0.477000	0.44152	AAA	.	.		0.542	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			C	197664292	T	C	197664292	3	2	35	1	0	0	0	0	1	0	0	0	6883	1841	64	2	2688	2	GTF3C3	2	197664292	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	142498	197664292	45535081	105	4274										
CASP8	841	hgsc.bcm.edu	37	chr2	202134252	202134252	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggttccacttctgccgcatgAgctgggctgaagcaaacagc	12	12	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:202134252A>G	ENST00000432109.2	+	4	494				CASP8_ENST00000358485.4_Intron|CASP8_ENST00000323492.7_Intron|CASP8_ENST00000264274.9_Intron|CASP8_ENST00000392259.2_Intron|CASP8_ENST00000392266.3_Intron|CASP8_ENST00000392258.3_Intron|CASP8_ENST00000264275.5_Missense_Mutation_p.S109G	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase						activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						CTGCCGCATGAGCTGGGCTGA	0.502										HNSCC(4;0.00038)																											p.S109G	Melanoma(82;831 1348 20716 36952 40159)	Atlas-SNP	.											.	CASP8	272	.	0			c.A325G						.						65	67	66					2																	202134252		1908	4128	6036	SO:0001627	intron_variant	841	exon4			CGCATGAGCTGGG	U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"Caspases"	1509	protein-coding gene	gene with protein product		601763	"caspase 8, apoptosis-related cysteine protease"			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	ENST00000432109.2:c.306-1987A>G	chr2.hg19:g.202134252A>G		98.0	0.0		98.0	6.0	NM_001228	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Missense_Mutation	SNP	ENST00000432109.2	hg19	CCDS2342.1	.	.	.	.	.	.	.	.	.	.	A	8.347	0.830110	0.16749	.	.	ENSG00000064012	ENST00000264275	D	0.83250	-1.7	2.54	-3.27	0.05048	.	.	.	.	.	T	0.66117	0.2757	.	.	.	0.09310	N	0.999998	B	0.06786	0.001	B	0.08055	0.003	T	0.47328	-0.9126	8	0.27785	T	0.31	.	3.8432	0.08923	0.363:0.3948:0.2421:0.0	.	109	Q14790-4	.	G	109	ENSP00000264275:S109G	ENSP00000264275:S109G	S	+	1	0	CASP8	201842497	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	-0.279000	0.08479	-0.772000	0.04602	0.421000	0.28195	AGC	.	.		0.502	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228		G	202134252	A	G	202134252	1	3	35	0	1	0	0	0	0	0	0	0	2679	304	11	2		2	CASP8	2	202134252	Intron	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	4469960	202134252	41065121	106	4275										
GPR1	2825	hgsc.bcm.edu	37	chr2	207041288	207041288	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttcttcaccttgaagatgagAcacaagtagcaaatactcat	6	9	3	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:207041288A>G	ENST00000407325.2	-	3	1046	c.684T>C	c.(682-684)tgT>tgC	p.C228C	GPR1_ENST00000437420.1_Silent_p.C228C	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	228					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.C228C(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		TGAAGATGAGACACAAGTAGC	0.443																																					p.C228C		Atlas-SNP	.											GPR1,NS,carcinoma,0,1	GPR1	38	.	1	Substitution - coding silent(1)	kidney(1)	c.T684C						.						106	105	105					2																	207041288		2203	4300	6503	SO:0001819	synonymous_variant	2825	exon3			GATGAGACACAAG		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"GPCR / Class A : Orphans"	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.684T>C	chr2.hg19:g.207041288A>G		102.0	0.0		75.0	3.0	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Silent	SNP	ENST00000407325.2	hg19	CCDS2368.1																																																																																			.	.		0.443	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199		G	207041288	A	G	207041288	2	3	35	1	0	0	0	0	0	0	0	1	6629	273	10	2		2	GPR1	2	207041288	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	4907036	207041288	36158085	107	4276										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209217489	209217490	+	Missense_Mutation	DNP	GG	GG	TC													0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tcatggaaaatcttttctacGggagaaagatggcacaggta					rs191717036		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:209217489_209217490GG>TC	ENST00000264380.4	+	39	5985_5986	c.5827_5828GG>TC	c.(5827-5829)GGg>TCg	p.G1943S		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1943	Catalytic.|PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TCTTTTCTACGGGAGAAAGATG	0.376																																					p.G1943W|p.G1943A		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.G5827T|c.G5828C						.																																			SO:0001583	missense	200576	exon39			TTCTACGGGAGAA|TCTACGGGAGAAA	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	Exception_encountered	chr2.hg19:g.209217489_209217490delinsTC	ENSP00000264380:p.Gly1943Ser	67.0	0.0		53.0|54.0	15.0	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	hg19	CCDS2382.1																																																																																			.	G|1.000;A|0.000|.		0.376	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		TC	209217490	GG	TC	209217489	3	4	35	1	0	0	0	0	1	0	0	0	11933	1116	39	1	5988	1	PIKFYVE	2	209217489	Missense_Mutation	DNP	GG	TCGA-BC-A10W-01A-11D-A12Z-10	2176201	209217489	33981884	108	4277										
MAP2	4133	hgsc.bcm.edu	37	chr2	210558811	210558811	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	caagaagcagggtacagcacTctcgcacagagttatccatc	9	12	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:210558811T>C	ENST00000360351.4	+	7	2423	c.1917T>C	c.(1915-1917)acT>acC	p.T639T	MAP2_ENST00000447185.1_Silent_p.T635T|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	639					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	GGTACAGCACTCTCGCACAGA	0.443																																					p.T639T	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.T1917C						.						60	59	59					2																	210558811		2203	4300	6503	SO:0001819	synonymous_variant	4133	exon7			CAGCACTCTCGCA		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.1917T>C	chr2.hg19:g.210558811T>C		114.0	0.0		94.0	4.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.		0.443	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		C	210558811	T	C	210558811	2	2	35	1	0	0	0	0	0	0	0	1	9244	1538	54	2		2	MAP2	2	210558811	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	1341322	210558811	32640562	109	4278										
MAP2	4133	hgsc.bcm.edu	37	chr2	210570348	210570348	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aagcgctcttctctcccaagAccttcctccattctccctcc	3	20	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:210570348A>G	ENST00000360351.4	+	11	5135	c.4629A>G	c.(4627-4629)agA>agG	p.R1543R	MAP2_ENST00000447185.1_Silent_p.R1539R|MAP2_ENST00000392194.1_Silent_p.R187R|MAP2_ENST00000475600.1_3'UTR|MAP2_ENST00000361559.4_Silent_p.R187R|MAP2_ENST00000199940.6_Silent_p.R244R	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1543					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.R1543R(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	CTCTCCCAAGACCTTCCTCCA	0.468																																					p.R1543R	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											MAP2_ENST00000199940,caecum,carcinoma,0,3	MAP2	372	.	1	Substitution - coding silent(1)	ovary(1)	c.A4629G						.						121	123	123					2																	210570348		2203	4300	6503	SO:0001819	synonymous_variant	4133	exon11			CCCAAGACCTTCC		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.4629A>G	chr2.hg19:g.210570348A>G		105.0	0.0		91.0	5.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.		0.468	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		G	210570348	A	G	210570348	2	3	35	1	0	0	0	0	0	0	0	1	9244	272	10	2		2	MAP2	2	210570348	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	11537	210570348	32629025	110	4279										
CPS1	1373	hgsc.bcm.edu	37	chr2	211523405	211523405	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	atttcttgtcaaaggaaatgAtgtcttggtaagaaatgcca	9	5	3	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:211523405A>G	ENST00000233072.5	+	31	3945	c.3749A>G	c.(3748-3750)gAt>gGt	p.D1250G	CPS1_ENST00000430249.2_Missense_Mutation_p.D1256G|CPS1_ENST00000451903.2_Missense_Mutation_p.D799G	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1250	ATP-grasp 2.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	AAAGGAAATGATGTCTTGGTA	0.438																																					p.D1256G		Atlas-SNP	.											.	CPS1	485	.	0			c.A3767G						.						101	93	95					2																	211523405		2203	4300	6503	SO:0001583	missense	1373	exon32			GAAATGATGTCTT	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3749A>G	chr2.hg19:g.211523405A>G	ENSP00000233072:p.Asp1250Gly	121.0	0.0		91.0	4.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	A	16.49	3.139075	0.56936	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.97303	-4.33;-4.33;-4.33	5.76	4.6	0.57074	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.145114	0.64402	D	0.000011	D	0.97077	0.9045	M	0.85945	2.785	0.43267	D	0.995213	B;B	0.33883	0.43;0.43	B;B	0.40982	0.345;0.345	D	0.96161	0.9115	10	0.87932	D	0	-14.2383	11.5602	0.50772	0.9302:0.0:0.0698:0.0	.	1260;1250	Q59HF8;P31327	.;CPSM_HUMAN	G	1256;1258;1250;799	ENSP00000402608:D1256G;ENSP00000233072:D1250G;ENSP00000406136:D799G	ENSP00000233072:D1250G	D	+	2	0	CPS1	211231650	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	8.625000	0.90965	0.995000	0.38917	0.460000	0.39030	GAT	.	.		0.438	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			G	211523405	A	G	211523405	3	3	35	1	0	0	0	0	1	0	0	0	3825	333	12	2	3893	2	CPS1	2	211523405	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	953057	211523405	31675968	111	4280										
PECR	55825	hgsc.bcm.edu	37	chr2	216904018	216904018	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tcagagcttagctttctcctTaaaggtctccttcatctttt	5	11	5	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:216904018T>C	ENST00000265322.7	-	8	966	c.892A>G	c.(892-894)Aag>Gag	p.K298E		NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	298					fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	GCTTTCTCCTTAAAGGTCTCC	0.453																																					p.K298E		Atlas-SNP	.											.	PECR	22	.	0			c.A892G						.						151	148	149					2																	216904018		2203	4300	6503	SO:0001583	missense	55825	exon8			TCTCCTTAAAGGT	AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18281	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 29C, member 1"	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.892A>G	chr2.hg19:g.216904018T>C	ENSP00000265322:p.Lys298Glu	89.0	0.0		100.0	4.0	NM_018441	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	Missense_Mutation	SNP	ENST00000265322.7	hg19	CCDS33375.1	.	.	.	.	.	.	.	.	.	.	T	12.74	2.028975	0.35797	.	.	ENSG00000115425	ENST00000265322	D	0.83755	-1.76	4.59	3.46	0.39613	.	0.592548	0.18550	N	0.137922	T	0.65709	0.2717	N	0.17082	0.46	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.10450	0.002;0.005	T	0.47275	-0.9130	10	0.18276	T	0.48	.	6.2887	0.21047	0.0:0.1097:0.0:0.8903	.	298;152	Q9BY49;Q9BY49-2	PECR_HUMAN;.	E	298	ENSP00000265322:K298E	ENSP00000265322:K298E	K	-	1	0	PECR	216612263	0.018000	0.18449	0.008000	0.14137	0.008000	0.06430	1.175000	0.31944	2.061000	0.61500	0.459000	0.35465	AAG	.	.		0.453	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441		C	216904018	T	C	216904018	3	2	35	1	0	0	0	0	1	0	0	0	11726	1763	61	2	23	2	PECR	2	216904018	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	5380613	216904018	26295355	112	4281										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220506390	220506390	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cagctggactcggaagatgcTgaaccaaacttcgatgagga	12	9	0	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:220506390T>C	ENST00000358055.3	+	23	4151	c.3639T>C	c.(3637-3639)gcT>gcC	p.A1213A	SLC4A3_ENST00000273063.6_Silent_p.A1240A|SLC4A3_ENST00000373762.3_Silent_p.A1240A|SLC4A3_ENST00000373760.2_Silent_p.A1213A|SLC4A3_ENST00000317151.3_Silent_p.A1213A			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	1213	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CGGAAGATGCTGAACCAAACT	0.567																																					p.A1240A		Atlas-SNP	.											.	SLC4A3	144	.	0			c.T3720C						.						178	130	146					2																	220506390		2203	4300	6503	SO:0001819	synonymous_variant	6508	exon23			AGATGCTGAACCA		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.3639T>C	chr2.hg19:g.220506390T>C		129.0	0.0		115.0	5.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Silent	SNP	ENST00000358055.3	hg19	CCDS2445.1																																																																																			.	.		0.567	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		C	220506390	T	C	220506390	2	2	35	1	0	0	0	0	0	0	0	1	14670	1567	55	2		2	SLC4A3	2	220506390	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	3602372	220506390	22692983	113	4282										
WDFY1	57590	hgsc.bcm.edu	37	chr2	224746759	224746759	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cttgctgctgcacttcccgcAgacagcctgcccgcatttcc	8	18	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:224746759A>G	ENST00000233055.4	-	10	1066	c.964T>C	c.(964-966)Tgc>Cgc	p.C322R		NM_020830.3	NP_065881.1	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1	322						cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)	18		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)		CACTTCCCGCAGACAGCCTGC	0.502																																					p.C322R		Atlas-SNP	.											.	WDFY1	46	.	0			c.T964C						.						184	188	187					2																	224746759		2203	4300	6503	SO:0001583	missense	57590	exon10			TCCCGCAGACAGC	AB037856	CCDS33387.1	2q36.2	2013-01-09	2003-03-13		ENSG00000085449	ENSG00000085449		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20451	protein-coding gene	gene with protein product			"WD40 and FYVE domain containing 1"			11739631	Standard	NM_020830		Approved	KIAA1435, FENS-1, WDF1, ZFYVE17	uc002vnq.3	Q8IWB7	OTTHUMG00000153370	ENST00000233055.4:c.964T>C	chr2.hg19:g.224746759A>G	ENSP00000233055:p.Cys322Arg	58.0	0.0		72.0	4.0	NM_020830	Q53S17|Q9H9D5|Q9P2B3	Missense_Mutation	SNP	ENST00000233055.4	hg19	CCDS33387.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.698483	0.88830	.	.	ENSG00000085449	ENST00000233055	D	0.93076	-3.16	5.9	5.9	0.94986	Zinc finger, RING/FYVE/PHD-type (1);WD40 repeat-like-containing domain (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.98194	0.9403	H	0.99475	4.585	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.99929	1.1307	10	0.17369	T	0.5	-20.6731	16.3322	0.83039	1.0:0.0:0.0:0.0	.	322	Q8IWB7	WDFY1_HUMAN	R	322	ENSP00000233055:C322R	ENSP00000233055:C322R	C	-	1	0	WDFY1	224455003	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.958000	0.93099	2.251000	0.74343	0.528000	0.53228	TGC	.	.		0.502	WDFY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330908.1	NM_020830		G	224746759	A	G	224746759	3	3	35	1	0	0	0	0	1	0	0	0	17283	188	7	2	280	2	WDFY1	2	224746759	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	4240369	224746759	18452614	114	4283										
GPR55	9290	hgsc.bcm.edu	37	chr2	231775064	231775064	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggcggcccagcaggatgtggAtgctcctggagcagcagaag	17	10	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:231775064A>G	ENST00000392040.1	-	2	806	c.614T>C	c.(613-615)aTc>aCc	p.I205T	GPR55_ENST00000392039.2_Missense_Mutation_p.I205T|AC012507.4_ENST00000454890.1_RNA	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	205					activation of phospholipase C activity (GO:0007202)|bone resorption (GO:0045453)|cannabinoid signaling pathway (GO:0038171)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho protein signal transduction (GO:0035025)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|G-protein coupled receptor activity (GO:0004930)			endometrium(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)		CAGGATGTGGATGCTCCTGGA	0.602																																					p.I205T		Atlas-SNP	.											.	GPR55	46	.	0			c.T614C						.						76	82	80					2																	231775064		2203	4300	6503	SO:0001583	missense	9290	exon2			ATGTGGATGCTCC	AF096786	CCDS2480.1	2q37	2012-08-21			ENSG00000135898	ENSG00000135898		"GPCR / Class A : Orphans"	4511	protein-coding gene	gene with protein product		604107				9931487	Standard	NM_005683		Approved		uc002vrg.3	Q9Y2T6	OTTHUMG00000133224	ENST00000392040.1:c.614T>C	chr2.hg19:g.231775064A>G	ENSP00000375894:p.Ile205Thr	96.0	0.0		92.0	5.0	NM_005683	Q8N580	Missense_Mutation	SNP	ENST00000392040.1	hg19	CCDS2480.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.163116	0.78226	.	.	ENSG00000135898	ENST00000392040;ENST00000392039;ENST00000438398	T;T;T	0.40225	1.04;1.04;1.04	5.38	5.38	0.77491	GPCR, rhodopsin-like superfamily (1);	0.049335	0.85682	D	0.000000	T	0.60805	0.2297	M	0.78344	2.41	0.44635	D	0.997614	D	0.59357	0.985	P	0.60345	0.873	T	0.63225	-0.6685	10	0.44086	T	0.13	-29.4351	13.3386	0.60533	1.0:0.0:0.0:0.0	.	205	Q9Y2T6	GPR55_HUMAN	T	205	ENSP00000375894:I205T;ENSP00000375893:I205T;ENSP00000412768:I205T	ENSP00000375893:I205T	I	-	2	0	GPR55	231483308	1.000000	0.71417	0.233000	0.24025	0.955000	0.61496	7.414000	0.80117	2.025000	0.59659	0.459000	0.35465	ATC	.	.		0.602	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683		G	231775064	A	G	231775064	3	3	35	1	0	0	0	0	1	0	0	0	6707	333	12	2	349	2	GPR55	2	231775064	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	7028305	231775064	11424309	115	4284										
NMUR1	10316	hgsc.bcm.edu	37	chr2	232392897	232392897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gagcctgcaggtgtatctggAcctggctgctgcagagcccc	14	13	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:232392897A>G	ENST00000305141.4	-	2	968	c.835T>C	c.(835-837)Tcc>Ccc	p.S279P		NM_006056.4	NP_006047.3	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	279					activation of phospholipase C activity (GO:0007202)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|chloride transport (GO:0006821)|G-protein coupled receptor signaling pathway (GO:0007186)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|smooth muscle contraction (GO:0006939)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuromedin U receptor activity (GO:0001607)|neuropeptide receptor activity (GO:0008188)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(12)|pancreas(1)|skin(1)	24		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;8.37e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GTGTATCTGGACCTGGCTGCT	0.637																																					p.S279P		Atlas-SNP	.											.	NMUR1	46	.	0			c.T835C						.						46	46	46					2																	232392897		2203	4300	6503	SO:0001583	missense	10316	exon2			ATCTGGACCTGGC	AF044600	CCDS2486.1	2q37.1	2012-08-08	2004-05-27	2004-05-28	ENSG00000171596	ENSG00000171596		"GPCR / Class A : Neuromedin U receptors"	4518	protein-coding gene	gene with protein product		604153	"G protein-coupled receptor 66"	GPR66		9782091	Standard	NM_006056		Approved	GPC-R, FM-3, NMU1R	uc002vry.4	Q9HB89	OTTHUMG00000133225	ENST00000305141.4:c.835T>C	chr2.hg19:g.232392897A>G	ENSP00000305877:p.Ser279Pro	86.0	0.0		74.0	5.0	NM_006056	O43664|Q7LDP6|Q8NE20	Missense_Mutation	SNP	ENST00000305141.4	hg19	CCDS2486.1	.	.	.	.	.	.	.	.	.	.	A	8.663	0.901073	0.17760	.	.	ENSG00000171596	ENST00000305141	T	0.38401	1.14	2.75	-5.33	0.02713	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.20740	0.0499	L	0.45581	1.43	0.09310	N	1	P	0.39157	0.662	B	0.33392	0.163	T	0.09465	-1.0673	9	0.30078	T	0.28	.	3.6817	0.08313	0.5167:0.2307:0.0:0.2525	.	279	Q9HB89	NMUR1_HUMAN	P	279	ENSP00000305877:S279P	ENSP00000305877:S279P	S	-	1	0	NMUR1	232101141	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.048000	0.03517	-1.146000	0.02854	0.374000	0.22700	TCC	.	.		0.637	NMUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256961.1	NM_006056		G	232392897	A	G	232392897	3	3	35	1	0	0	0	0	1	0	0	0	10515	275	10	2	453	2	NMUR1	2	232392897	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	617833	232392897	10806476	116	4285										
C2orf57	165100	hgsc.bcm.edu	37	chr2	232458839	232458839	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gccaggcccaggctgaccccAactatgattagagccctgca	10	15	0	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:232458839A>G	ENST00000313965.2	+	1	1265	c.1177A>G	c.(1177-1179)Aac>Gac	p.N393D		NM_152614.2	NP_689827.2	Q53QW1	CB057_HUMAN	chromosome 2 open reading frame 57	393										endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	19		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)		GGCTGACCCCAACTATGATTA	0.647																																					p.N393D		Atlas-SNP	.											.	C2orf57	35	.	0			c.A1177G						.						26	25	26					2																	232458839		2201	4299	6500	SO:0001583	missense	165100	exon1			GACCCCAACTATG	BC034405	CCDS2487.1	2q37.1	2008-02-05			ENSG00000177673	ENSG00000177673			28563	protein-coding gene	gene with protein product						12477932	Standard	NM_152614		Approved	MGC35154	uc002vrz.3	Q53QW1	OTTHUMG00000133226	ENST00000313965.2:c.1177A>G	chr2.hg19:g.232458839A>G	ENSP00000315557:p.Asn393Asp	84.0	0.0		100.0	4.0	NM_152614	Q8N4F2	Missense_Mutation	SNP	ENST00000313965.2	hg19	CCDS2487.1	.	.	.	.	.	.	.	.	.	.	A	12.56	1.975392	0.34848	.	.	ENSG00000177673	ENST00000313965	T	0.19938	2.11	4.92	-0.295	0.12828	.	.	.	.	.	T	0.12603	0.0306	L	0.29908	0.895	0.09310	N	1	B	0.31459	0.324	B	0.30179	0.112	T	0.25950	-1.0117	9	0.54805	T	0.06	.	3.5746	0.07930	0.5646:0.0:0.2752:0.1602	.	393	Q53QW1	CB057_HUMAN	D	393	ENSP00000315557:N393D	ENSP00000315557:N393D	N	+	1	0	C2orf57	232167083	0.000000	0.05858	0.001000	0.08648	0.163000	0.22366	-0.022000	0.12480	0.056000	0.16144	0.455000	0.32223	AAC	.	.		0.647	C2orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256962.1	NM_152614		G	232458839	A	G	232458839	3	3	35	1	0	0	0	0	1	0	0	0	2180	130	5	2	1179	2	C2orf57	2	232458839	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	65942	232458839	10740534	117	4286										
ECEL1	9427	hgsc.bcm.edu	37	chr2	233344956	233344956	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tcaaactgggacacactgccCagcaccctggggtggggaga	14	12	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:233344956C>A	ENST00000304546.1	-	18	2445	c.2235G>T	c.(2233-2235)ctG>ctT	p.L745L	ECEL1_ENST00000409941.1_Silent_p.L743L	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	745					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		ACACACTGCCCAGCACCCTGG	0.617																																					p.L745L		Atlas-SNP	.											.	ECEL1	73	.	0			c.G2235T						.						74	61	65					2																	233344956		2203	4300	6503	SO:0001819	synonymous_variant	9427	exon18			ACTGCCCAGCACC	Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.2235G>T	chr2.hg19:g.233344956C>A		143.0	0.0		102.0	49.0	NM_004826	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Silent	SNP	ENST00000304546.1	hg19	CCDS2493.1																																																																																			.	.		0.617	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		A	233344956	C	A	233344956	2	1	35	1	0	0	0	0	0	0	0	1	4893	581	21	3		3	ECEL1	2	233344956	Silent	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	886117	233344956	9854417	118	4287										
NEU2	4759	hgsc.bcm.edu	37	chr2	233898881	233898881	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggatggccaccggtccatgaAcccatgccccttgtatgacg	11	14	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:233898881A>G	ENST00000233840.3	+	2	257	c.257A>G	c.(256-258)aAc>aGc	p.N86S		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	86					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	CGGTCCATGAACCCATGCCCC	0.612																																					p.N86S		Atlas-SNP	.											.	NEU2	42	.	0			c.A257G						.						120	101	108					2																	233898881		2203	4300	6503	SO:0001583	missense	4759	exon2			CCATGAACCCATG	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"N-acetyl-alpha-neuraminidase 2"	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.257A>G	chr2.hg19:g.233898881A>G	ENSP00000233840:p.Asn86Ser	119.0	0.0		107.0	5.0	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	hg19	CCDS2501.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.999122	0.54147	.	.	ENSG00000115488	ENST00000233840	D	0.92397	-3.03	4.88	3.74	0.42951	Neuraminidase (2);	0.083507	0.51477	D	0.000096	D	0.93070	0.7794	L	0.55103	1.725	0.44736	D	0.997735	D	0.58970	0.984	P	0.62089	0.898	D	0.92618	0.6105	10	0.59425	D	0.04	-48.0065	9.1916	0.37202	0.9143:0.0:0.0857:0.0	.	86	Q9Y3R4	NEUR2_HUMAN	S	86	ENSP00000233840:N86S	ENSP00000233840:N86S	N	+	2	0	NEU2	233607125	1.000000	0.71417	1.000000	0.80357	0.239000	0.25481	5.054000	0.64275	1.821000	0.53095	0.459000	0.35465	AAC	.	.		0.612	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383		G	233898881	A	G	233898881	3	3	35	1	0	0	0	0	1	0	0	0	10351	43	2	2	263	2	NEU2	2	233898881	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	553925	233898881	9300492	119	4288										
HJURP	55355	hgsc.bcm.edu	37	chr2	234756078	234756078	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aactgactcttcctggtctgAcgtggcatcgacctcaccgc	9	15	3	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr2:234756078A>G	ENST00000411486.2	-	5	432	c.367T>C	c.(367-369)Tca>Cca	p.S123P	HJURP_ENST00000432087.1_Intron|HJURP_ENST00000434039.1_5'Flank|HJURP_ENST00000441687.1_Intron	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	123					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		TCCTGGTCTGACGTGGCATCG	0.478																																					p.S123P		Atlas-SNP	.											.	HJURP	72	.	0			c.T367C						.						117	100	106					2																	234756078		2203	4300	6503	SO:0001583	missense	55355	exon5			GGTCTGACGTGGC		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.367T>C	chr2.hg19:g.234756078A>G	ENSP00000414109:p.Ser123Pro	164.0	0.0		134.0	6.0	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	hg19	CCDS33406.1	.	.	.	.	.	.	.	.	.	.	A	5.107	0.205451	0.09704	.	.	ENSG00000123485	ENST00000411486;ENST00000454020	T;T	0.32988	3.21;1.43	3.14	-2.97	0.05530	.	5.373250	0.00166	N	0.000013	T	0.22475	0.0542	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07328	-1.0778	10	0.28530	T	0.3	5.0109	1.6263	0.02724	0.2501:0.4445:0.1342:0.1712	.	123	Q8NCD3	HJURP_HUMAN	P	123;82	ENSP00000414109:S123P;ENSP00000414051:S82P	ENSP00000414109:S123P	S	-	1	0	HJURP	234420817	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.274000	0.08537	-0.587000	0.05890	0.533000	0.62120	TCA	.	.		0.478	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410		G	234756078	A	G	234756078	3	3	35	1	0	0	0	0	1	0	0	0	7198	275	10	2	1899	2	HJURP	2	234756078	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	857197	234756078	8443295	120	4289										
BHLHE40	8553	hgsc.bcm.edu	37	chr3	5025019	5025019	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aaaaaagaaccggatgcagcTttcggatgatgaaggccatt	11	7	0	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:5025019T>C	ENST00000256495.3	+	5	1484	c.881T>C	c.(880-882)cTt>cCt	p.L294P		NM_003670.2	NP_003661.1	O14503	BHE40_HUMAN	basic helix-loop-helix family, member e40	294					circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|MRF binding (GO:0043426)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)	12						CGGATGCAGCTTTCGGATGAT	0.547																																					p.L294P		Atlas-SNP	.											.	BHLHE40	35	.	0			c.T881C						.						103	97	99					3																	5025019		2203	4300	6503	SO:0001583	missense	8553	exon5			TGCAGCTTTCGGA	AB004066	CCDS2565.1	3p26	2009-01-12	2009-01-12	2009-01-12	ENSG00000134107	ENSG00000134107		"Basic helix-loop-helix proteins"	1046	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 1", " differentiated embryo chondrocyte expressed gene 1"	604256	"basic helix-loop-helix domain containing, class B, 2"	STRA13, BHLHB2		9240428, 10449910, 18557763	Standard	NM_003670		Approved	DEC1, bHLHe40	uc003bqf.3	O14503	OTTHUMG00000119035	ENST00000256495.3:c.881T>C	chr3.hg19:g.5025019T>C	ENSP00000256495:p.Leu294Pro	95.0	0.0		83.0	5.0	NM_003670	Q96TD3	Missense_Mutation	SNP	ENST00000256495.3	hg19	CCDS2565.1	.	.	.	.	.	.	.	.	.	.	T	2.778	-0.254100	0.05829	.	.	ENSG00000134107	ENST00000256495	T	0.42131	0.98	5.62	3.09	0.35607	.	2.530130	0.02512	N	0.091610	T	0.31606	0.0802	N	0.22421	0.69	0.20403	N	0.99991	B	0.06786	0.001	B	0.06405	0.002	T	0.16958	-1.0385	10	0.36615	T	0.2	-10.7409	5.6528	0.17627	0.0:0.2083:0.1334:0.6584	.	294	O14503	BHE40_HUMAN	P	294	ENSP00000256495:L294P	ENSP00000256495:L294P	L	+	2	0	BHLHE40	5000019	0.511000	0.26179	0.379000	0.26080	0.163000	0.22366	2.540000	0.45727	0.354000	0.24105	0.533000	0.62120	CTT	.	.		0.547	BHLHE40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239244.2	NM_003670		C	5025019	T	C	5025019	3	2	35	1	0	0	0	0	1	0	0	0	1423	1609	56	2	899	2	BHLHE40	3	5025019	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10		5025019	192997411	121	4290										
SETD5	55209	hgsc.bcm.edu	37	chr3	9517690	9517690	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttccaattcacagcactaccCacaccgtgggagtgggggtg	12	12	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:9517690C>G	ENST00000406341.1	+	22	4434	c.4244C>G	c.(4243-4245)cCa>cGa	p.P1415R	SETD5_ENST00000407969.1_Missense_Mutation_p.P1434R|SETD5_ENST00000402198.1_Missense_Mutation_p.P1415R|SETD5_ENST00000402466.1_Missense_Mutation_p.P1317R|SETD5_ENST00000302463.6_Missense_Mutation_p.P1317R			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1415								p.P1415Q(1)|p.P1317Q(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		CAGCACTACCCACACCGTGGG	0.572																																					p.P1415R		Atlas-SNP	.											.	SETD5	210	.	2	Substitution - Missense(2)	lung(2)	c.C4244G						.						44	43	44					3																	9517690		1970	4158	6128	SO:0001583	missense	55209	exon23			ACTACCCACACCG	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.4244C>G	chr3.hg19:g.9517690C>G	ENSP00000383939:p.Pro1415Arg	123.0	0.0		92.0	4.0	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	hg19	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319176	0.60524	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	D;D;D;D;D	0.92965	-2.81;-3.14;-2.81;-2.79;-3.14	4.96	4.96	0.65561	.	0.000000	0.64402	D	0.000002	D	0.92473	0.7610	N	0.14661	0.345	0.51482	D	0.999923	D;D;D	0.76494	0.999;0.999;0.994	D;D;P	0.83275	0.983;0.996;0.755	D	0.94247	0.7490	10	0.72032	D	0.01	-8.8772	18.5784	0.91163	0.0:1.0:0.0:0.0	.	1084;1317;1415	B3KXG4;Q9C0A6-3;Q9C0A6	.;.;SETD5_HUMAN	R	1415;1317;1415;1434;1317	ENSP00000385852:P1415R;ENSP00000384429:P1317R;ENSP00000383939:P1415R;ENSP00000384114:P1434R;ENSP00000302028:P1317R	ENSP00000302028:P1317R	P	+	2	0	SETD5	9492690	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	3.323000	0.52014	2.448000	0.82819	0.467000	0.42956	CCA	.	.		0.572	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		G	9517690	C	G	9517690	3	3	35	1	0	0	0	0	1	0	0	0	14149	594	21	4	4326	4	SETD5	3	9517690	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	4492671	9517690	188504740	122	4291										
IL17RE	132014	hgsc.bcm.edu	37	chr3	9944675	9944675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cctcctcatagtcatcgaccTctctgactctgctgggattg	8	14	4	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:9944675T>C	ENST00000383814.3	+	1	164	c.59T>C	c.(58-60)cTc>cCc	p.L20P	IL17RE_ENST00000295980.3_Missense_Mutation_p.L20P|IL17RE_ENST00000421412.1_Missense_Mutation_p.L53P|IL17RE_ENST00000454190.2_Missense_Mutation_p.L20P	NM_153480.1	NP_705613.1	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E	20					inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(11)|skin(1)	21				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		GTCATCGACCTCTCTGACTCT	0.617																																					p.L60P		Atlas-SNP	.											.	IL17RE	62	.	0			c.T179C						.						84	75	78					3																	9944675		2203	4300	6503	SO:0001583	missense	132014	exon2			TCGACCTCTCTGA	AF458069	CCDS2589.1, CCDS54552.1	3p25.3	2008-02-05			ENSG00000163701	ENSG00000163701		"Interleukins and interleukin receptors"	18439	protein-coding gene	gene with protein product		614995					Standard	NM_153480		Approved	FLJ23658	uc003btu.3	Q8NFR9	OTTHUMG00000128649	ENST00000383814.3:c.59T>C	chr3.hg19:g.9944675T>C	ENSP00000373325:p.Leu20Pro	136.0	0.0		160.0	7.0	NM_153483	B2RB34|B2RNR1|B9EH65|Q6P532|Q8N8H7|Q8N8H8|Q8TEC2	Missense_Mutation	SNP	ENST00000383814.3	hg19	CCDS2589.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.660295	0.67586	.	.	ENSG00000163701	ENST00000421412;ENST00000295980;ENST00000383814;ENST00000454190;ENST00000454992	T;T;T;T	0.41065	1.05;1.09;1.09;1.01	5.17	5.17	0.71159	.	0.296788	0.23056	N	0.052422	T	0.57917	0.2086	L	0.59436	1.845	0.21841	N	0.999519	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.68765	0.943;0.943;0.96	T	0.53194	-0.8473	10	0.87932	D	0	-6.324	11.3942	0.49832	0.0:0.0:0.0:1.0	.	20;20;20	Q8NFR9-3;Q8NFR9-5;Q8NFR9	.;.;I17RE_HUMAN	P	53;20;20;20;20	ENSP00000404916:L53P;ENSP00000295980:L20P;ENSP00000373325:L20P;ENSP00000388086:L20P	ENSP00000295980:L20P	L	+	2	0	IL17RE	9919675	0.071000	0.21146	0.008000	0.14137	0.028000	0.11728	2.249000	0.43169	1.948000	0.56530	0.533000	0.62120	CTC	.	.		0.617	IL17RE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250529.1	NM_153480		C	9944675	T	C	9944675	3	2	35	1	0	0	0	0	1	0	0	0	7652	1551	54	2	61	2	IL17RE	3	9944675	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	426985	9944675	188077755	123	4292										
C3orf20	84077	hgsc.bcm.edu	37	chr3	14724660	14724660	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gtccatccacctgctgacggAgctcctcagactgaagatga	10	13	1	5			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:14724660A>G	ENST00000253697.3	+	3	892	c.440A>G	c.(439-441)gAg>gGg	p.E147G	C3orf20_ENST00000412910.1_Missense_Mutation_p.E25G|C3orf20_ENST00000435614.1_Missense_Mutation_p.E25G	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	147						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CTGCTGACGGAGCTCCTCAGA	0.602																																					p.E147G		Atlas-SNP	.											.	C3orf20	109	.	0			c.A440G						.						92	85	88					3																	14724660		2203	4300	6503	SO:0001583	missense	84077	exon3			TGACGGAGCTCCT	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.440A>G	chr3.hg19:g.14724660A>G	ENSP00000253697:p.Glu147Gly	109.0	0.0		118.0	5.0	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	hg19	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.094674	0.76870	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.19669	2.43;2.13;2.13	4.93	4.93	0.64822	.	0.000000	0.44902	D	0.000408	T	0.35307	0.0927	L	0.36672	1.1	0.39811	D	0.972704	D	0.89917	1.0	D	0.87578	0.998	T	0.20042	-1.0287	10	0.87932	D	0	-33.9103	12.1238	0.53905	1.0:0.0:0.0:0.0	.	147	Q8ND61	CC020_HUMAN	G	147;25;25	ENSP00000253697:E147G;ENSP00000402933:E25G;ENSP00000396081:E25G	ENSP00000253697:E147G	E	+	2	0	C3orf20	14699664	1.000000	0.71417	0.857000	0.33713	0.913000	0.54294	4.731000	0.62022	1.858000	0.53909	0.482000	0.46254	GAG	.	.		0.602	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		G	14724660	A	G	14724660	3	3	35	1	0	0	0	0	1	0	0	0	2215	304	11	2	442	2	C3orf20	3	14724660	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	4779985	14724660	183297770	124	4293										
FGD5	152273	hgsc.bcm.edu	37	chr3	14862587	14862587	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaagacggagaacaaattgcAtgtggatgtgaacgtgtctt	13	5	1	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:14862587A>G	ENST00000285046.5	+	1	2119	c.2009A>G	c.(2008-2010)cAt>cGt	p.H670R	FGD5_ENST00000543601.1_Missense_Mutation_p.H429R	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	670					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						AACAAATTGCATGTGGATGTG	0.512																																					p.H670R		Atlas-SNP	.											.	FGD5	248	.	0			c.A2009G						.						79	78	78					3																	14862587		1976	4174	6150	SO:0001583	missense	152273	exon1			AATTGCATGTGGA	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.2009A>G	chr3.hg19:g.14862587A>G	ENSP00000285046:p.His670Arg	148.0	0.0		123.0	5.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	A	4.077	0.012113	0.07912	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.76448	-1.02;-0.83	5.32	4.15	0.48705	.	0.000000	0.64402	D	0.000013	T	0.68513	0.3009	L	0.55481	1.735	0.23611	N	0.99729	P;P	0.40834	0.553;0.73	B;B	0.32533	0.109;0.147	T	0.59085	-0.7520	10	0.36615	T	0.2	-24.7629	11.6535	0.51304	0.8671:0.0:0.0:0.1329	.	429;670	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	R	670;429	ENSP00000285046:H670R;ENSP00000445949:H429R	ENSP00000285046:H670R	H	+	2	0	FGD5	14837591	0.969000	0.33509	0.054000	0.19295	0.001000	0.01503	3.642000	0.54367	0.842000	0.35045	-0.327000	0.08410	CAT	.	.		0.512	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		G	14862587	A	G	14862587	3	3	35	1	0	0	0	0	1	0	0	0	5844	217	8	2	2011	2	FGD5	3	14862587	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	137927	14862587	183159843	125	4294										
CNOT10	25904	hgsc.bcm.edu	37	chr3	32811404	32811404	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttcaatgatccatcctaaagAggtgccccctgaggccatct	8	13	2	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:32811404A>G	ENST00000328834.5	+	18	2346	c.2030A>G	c.(2029-2031)gAg>gGg	p.E677G	CNOT10_ENST00000331889.6_Missense_Mutation_p.E650G|CNOT10_ENST00000454516.2_Missense_Mutation_p.E737G	NM_015442.2	NP_056257.1	Q9H9A5	CNO10_HUMAN	CCR4-NOT transcription complex, subunit 10	677					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(3)	23						CATCCTAAAGAGGTGCCCCCT	0.453																																					p.E737G		Atlas-SNP	.											.	CNOT10	57	.	0			c.A2210G						.						126	127	127					3																	32811404		2203	4300	6503	SO:0001583	missense	25904	exon18			CTAAAGAGGTGCC	BC002928	CCDS2655.1, CCDS58821.1, CCDS58822.1	3p23	2013-01-10			ENSG00000182973	ENSG00000182973		"Tetratricopeptide (TTC) repeat domain containing"	23817	protein-coding gene	gene with protein product							Standard	NR_046352		Approved	FLJ12890, FLJ13165	uc011axj.2	Q9H9A5	OTTHUMG00000130748	ENST00000328834.5:c.2030A>G	chr3.hg19:g.32811404A>G	ENSP00000330060:p.Glu677Gly	93.0	0.0		82.0	4.0	NM_001256742	B7Z7L1|F8WAF2|Q9BU30|Q9H5J7|Q9H8X1|Q9H9W0|Q9HAH3|Q9UFJ2	Missense_Mutation	SNP	ENST00000328834.5	hg19	CCDS2655.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.985415	0.93044	.	.	ENSG00000182973	ENST00000331889;ENST00000328834;ENST00000454516;ENST00000430408	T;T;T	0.29397	1.57;1.57;1.57	5.52	5.52	0.82312	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.48333	0.1494	L	0.53249	1.67	0.80722	D	1	D;D;D;D	0.63880	0.98;0.974;0.993;0.979	P;P;D;P	0.63033	0.718;0.736;0.91;0.628	T	0.38308	-0.9667	10	0.39692	T	0.17	-22.7079	15.6346	0.76941	1.0:0.0:0.0:0.0	.	737;650;676;677	F8WAF2;Q9H9A5-3;Q9H9A5-2;Q9H9A5	.;.;.;CNOTA_HUMAN	G	650;677;737;212	ENSP00000329376:E650G;ENSP00000330060:E677G;ENSP00000399862:E737G	ENSP00000330060:E677G	E	+	2	0	CNOT10	32786408	1.000000	0.71417	0.982000	0.44146	0.996000	0.88848	9.339000	0.96797	2.093000	0.63338	0.460000	0.39030	GAG	.	.		0.453	CNOT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253248.2	NM_015442		G	32811404	A	G	32811404	3	3	35	1	0	0	0	0	1	0	0	0	3620	304	11	2	2100	2	CNOT10	3	32811404	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	17948817	32811404	165211026	126	4295										
TRANK1	9881	hgsc.bcm.edu	37	chr3	36874860	36874860	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctcaggctcggcctcacactGgctggctgcttcgtagagtg	13	13	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:36874860G>C	ENST00000429976.2	-	21	6329	c.6082C>G	c.(6082-6084)Cag>Gag	p.Q2028E	TRANK1_ENST00000301807.6_Missense_Mutation_p.Q1478E|TRANK1_ENST00000428977.2_Missense_Mutation_p.Q1478E	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2028							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						GCCTCACACTGGCTGGCTGCT	0.547																																					p.Q2028E		Atlas-SNP	.											.	TRANK1	398	.	0			c.C6082G						.						27	27	27					3																	36874860		1941	4150	6091	SO:0001583	missense	9881	exon21			CACACTGGCTGGC	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.6082C>G	chr3.hg19:g.36874860G>C	ENSP00000416168:p.Gln2028Glu	87.0	0.0		99.0	4.0	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	G	6.513	0.462928	0.12402	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.28895	1.59;2.01;1.59	4.5	4.5	0.54988	.	0.906562	0.09217	N	0.832386	T	0.17023	0.0409	N	0.08118	0	0.09310	N	1	B	0.18166	0.026	B	0.14023	0.01	T	0.05289	-1.0894	10	0.36615	T	0.2	.	8.6352	0.33943	0.1027:0.0:0.8973:0.0	.	2028	O15050	TRNK1_HUMAN	E	1478;2028;1478	ENSP00000416826:Q1478E;ENSP00000416168:Q2028E;ENSP00000301807:Q1478E	ENSP00000301807:Q1478E	Q	-	1	0	TRANK1	36849864	0.010000	0.17322	0.549000	0.28204	0.801000	0.45260	1.711000	0.37930	2.496000	0.84212	0.555000	0.69702	CAG	.	.		0.547	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		C	36874860	G	C	36874860	3	2	35	1	0	0	0	0	1	0	0	0	16469	1357	47	4	2707	4	TRANK1	3	36874860	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	4063456	36874860	161147570	127	4296										
MLH1	4292	hgsc.bcm.edu	37	chr3	37053518	37053518	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tcagcaaggagagacagtagCtgatgttaggacactaccca	11	9	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:37053518C>G	ENST00000231790.2	+	8	821	c.605C>G	c.(604-606)gCt>gGt	p.A202G	MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000435176.1_Missense_Mutation_p.A104G	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	202					ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						GAGACAGTAGCTGATGTTAGG	0.408		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.A202G		Atlas-SNP	.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	.	MLH1	226	.	1	Whole gene deletion(1)	ovary(1)	c.C605G						.						144	130	135					3																	37053518		2203	4300	6503	SO:0001583	missense	4292	exon8	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CAGTAGCTGATGT	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.605C>G	chr3.hg19:g.37053518C>G	ENSP00000231790:p.Ala202Gly	209.0	0.0		178.0	56.0	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	hg19	CCDS2663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.54|19.54	3.846296|3.846296	0.71603|0.71603	.|.	.|.	ENSG00000076242|ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176|ENST00000456676	T;T|.	0.81247|.	-1.47;-1.47|.	5.76|5.76	5.76|5.76	0.90799|0.90799	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (2);|.	0.173869|.	0.49305|.	D|.	0.000145|.	T|T	0.78799|0.78799	0.4340|0.4340	M|M	0.78049|0.78049	2.395|2.395	0.80722|0.80722	D|D	1|1	P;B;B|.	0.38455|.	0.632;0.275;0.151|.	B;B;B|.	0.41946|.	0.371;0.24;0.185|.	T|T	0.77656|0.77656	-0.2506|-0.2506	10|5	0.25751|.	T|.	0.34|.	-7.6496|-7.6496	19.9576|19.9576	0.97228|0.97228	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	104;202;202|.	E9PCU2;Q53GX1;P40692|.	.;.;MLH1_HUMAN|.	G|V	202;168;168;66;104|194	ENSP00000231790:A202G;ENSP00000402564:A104G|.	ENSP00000231790:A202G|.	A|L	+|+	2|1	0|2	MLH1|MLH1	37028522|37028522	1.000000|1.000000	0.71417|0.71417	0.437000|0.437000	0.26809|0.26809	0.769000|0.769000	0.43574|0.43574	7.417000|7.417000	0.80156|0.80156	2.736000|2.736000	0.93811|0.93811	0.655000|0.655000	0.94253|0.94253	GCT|CTG	.	.		0.408	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		G	37053518	C	G	37053518	3	3	35	1	0	0	0	0	1	0	0	0	9626	797	28	4	635	4	MLH1	3	37053518	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	178658	37053518	160968912	128	4297										
PLCD1	5333	hgsc.bcm.edu	37	chr3	38049787	38049787	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cggctcacgccatggatctcCactgtcactttggggtccac	10	15	3	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:38049787C>A	ENST00000334661.4	-	13	2196	c.1974G>T	c.(1972-1974)gtG>gtT	p.V658V	PLCD1_ENST00000479619.1_5'Flank|PLCD1_ENST00000463876.1_Silent_p.V679V	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	658	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CATGGATCTCCACTGTCACTT	0.557																																					p.V679V		Atlas-SNP	.											.	PLCD1	87	.	0			c.G2037T						.						93	98	96					3																	38049787		2203	4300	6503	SO:0001819	synonymous_variant	5333	exon13			GATCTCCACTGTC		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"EF-hand domain containing"	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.1974G>T	chr3.hg19:g.38049787C>A		133.0	0.0		79.0	4.0	NM_001130964	B3KR14|Q86VN8	Silent	SNP	ENST00000334661.4	hg19	CCDS2671.1																																																																																			.	.		0.557	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2			A	38049787	C	A	38049787	2	1	35	1	0	0	0	0	0	0	0	1	12040	581	21	3		3	PLCD1	3	38049787	Silent	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	996269	38049787	159972643	129	4298										
SCN5A	6331	hgsc.bcm.edu	37	chr3	38640487	38640487	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctcctcgaagccatctacacAcggagcctgggaggtcagca	11	14	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:38640487A>G	ENST00000333535.4	-	13	2094	c.1945T>C	c.(1945-1947)Tgt>Cgt	p.C649R	SCN5A_ENST00000449557.2_Missense_Mutation_p.C649R|SCN5A_ENST00000443581.1_Missense_Mutation_p.C649R|SCN5A_ENST00000414099.2_Missense_Mutation_p.C649R|SCN5A_ENST00000425664.1_Missense_Mutation_p.C649R|SCN5A_ENST00000450102.2_Missense_Mutation_p.C649R|SCN5A_ENST00000451551.2_Missense_Mutation_p.C649R|SCN5A_ENST00000413689.1_Missense_Mutation_p.C649R|SCN5A_ENST00000423572.2_Missense_Mutation_p.C649R|SCN5A_ENST00000455624.2_Missense_Mutation_p.C649R			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	649					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CCATCTACACACGGAGCCTGG	0.632																																					p.C649R		Atlas-SNP	.											.	SCN5A	634	.	0			c.T1945C						.						33	40	38					3																	38640487		2186	4284	6470	SO:0001583	missense	6331	exon13			CTACACACGGAGC	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1945T>C	chr3.hg19:g.38640487A>G	ENSP00000328968:p.Cys649Arg	78.0	0.0		84.0	4.0	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	hg19	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	A	7.281	0.609018	0.14066	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62;-2.62	3.97	1.32	0.21799	Domain of unknown function DUF3451 (1);	0.665356	0.14237	N	0.332336	D	0.83510	0.5270	N	0.22421	0.69	0.28086	N	0.932019	B;B;B;B;B;B;B	0.33477	0.023;0.116;0.144;0.18;0.174;0.413;0.09	B;B;B;B;B;B;B	0.35073	0.079;0.113;0.146;0.079;0.175;0.195;0.048	T	0.75187	-0.3406	10	0.66056	D	0.02	.	10.1617	0.42855	0.6777:0.3223:0.0:0.0	.	649;649;649;649;649;649;649	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	R	649	ENSP00000398962:C649R;ENSP00000398266:C649R;ENSP00000410257:C649R;ENSP00000388797:C649R;ENSP00000397915:C649R;ENSP00000416634:C649R;ENSP00000328968:C649R;ENSP00000399524:C649R;ENSP00000403355:C649R;ENSP00000413996:C649R	ENSP00000328968:C649R	C	-	1	0	SCN5A	38615491	0.706000	0.27856	0.013000	0.15412	0.008000	0.06430	2.290000	0.43531	0.085000	0.17107	0.459000	0.35465	TGT	.	.		0.632	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		G	38640487	A	G	38640487	3	3	35	1	0	0	0	0	1	0	0	0	13937	159	6	2	4169	2	SCN5A	3	38640487	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	590700	38640487	159381943	130	4299										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38812863	38812863	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctcttgccagtatctttatcAaggcttcaaaggtgtaaatg	8	8	4	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:38812863A>G	ENST00000449082.2	-	4	505	c.506T>C	c.(505-507)tTg>tCg	p.L169S		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	169					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TATCTTTATCAAGGCTTCAAA	0.453																																					p.L169S		Atlas-SNP	.											.	SCN10A	359	.	0			c.T506C						.						125	123	124					3																	38812863		2203	4300	6503	SO:0001583	missense	6336	exon4			TTTATCAAGGCTT	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.506T>C	chr3.hg19:g.38812863A>G	ENSP00000390600:p.Leu169Ser	103.0	0.0		90.0	5.0	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	hg19	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.163203	0.38217	.	.	ENSG00000185313	ENST00000449082	D	0.98901	-5.22	5.15	4.0	0.46444	Ion transport (1);	0.186924	0.23656	N	0.045865	D	0.97990	0.9338	M	0.87328	2.875	0.19945	N	0.999949	B	0.20368	0.044	B	0.24701	0.055	D	0.95523	0.8596	10	0.72032	D	0.01	.	10.782	0.46384	0.9249:0.0:0.0751:0.0	.	169	Q9Y5Y9	SCNAA_HUMAN	S	169	ENSP00000390600:L169S	ENSP00000390600:L169S	L	-	2	0	SCN10A	38787867	0.402000	0.25311	0.977000	0.42913	0.919000	0.55068	3.116000	0.50399	0.970000	0.38263	-0.274000	0.10170	TTG	.	.		0.453	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		G	38812863	A	G	38812863	3	3	35	1	0	0	0	0	1	0	0	0	13927	131	5	2	5460	2	SCN10A	3	38812863	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	172376	38812863	159209567	131	4300										
USP19	10869	hgsc.bcm.edu	37	chr3	49149789	49149789	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cctccgactgttgcttccgcTggcaggctgcacacttggag	12	14	0	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:49149789T>C	ENST00000398888.2	-	18	2702	c.2384A>G	c.(2383-2385)cAg>cGg	p.Q795R	USP19_ENST00000398896.1_Missense_Mutation_p.Q603R|USP19_ENST00000417901.1_Missense_Mutation_p.Q898R|USP19_ENST00000453664.1_Missense_Mutation_p.Q886R|USP19_ENST00000434032.2_Missense_Mutation_p.Q896R|USP19_ENST00000398898.2_Missense_Mutation_p.Q835R|USP19_ENST00000398892.3_Missense_Mutation_p.Q835R	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	795	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TTGCTTCCGCTGGCAGGCTGC	0.637																																					p.Q898R		Atlas-SNP	.											.	USP19	158	.	0			c.A2693G						.						48	55	53					3																	49149789		2062	4206	6268	SO:0001583	missense	10869	exon19			TTCCGCTGGCAGG	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"Zinc fingers, MYND-type", "Ubiquitin-specific peptidases"	12617	protein-coding gene	gene with protein product		614471	"ubiquitin specific protease 19"			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.2384A>G	chr3.hg19:g.49149789T>C	ENSP00000381863:p.Gln795Arg	109.0	0.0		119.0	5.0	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	hg19	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.603235	0.66445	.	.	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.20332	2.11;2.08;2.18;2.18;2.08;2.21;2.18	5.8	5.8	0.92144	Zinc finger, MYND-type (3);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.177194	0.51477	D	0.000086	T	0.35393	0.0930	L	0.33485	1.01	0.43018	D	0.994561	D;D;D;D;D	0.76494	0.999;0.999;0.997;0.994;0.995	D;D;D;D;P	0.76575	0.967;0.967;0.95;0.988;0.874	T	0.04522	-1.0945	10	0.33141	T	0.24	-23.4359	15.8026	0.78468	0.0:0.0:0.0:1.0	.	896;886;795;835;603	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	R	603;835;898;886;835;795;896	ENSP00000381870:Q603R;ENSP00000381872:Q835R;ENSP00000395260:Q898R;ENSP00000400090:Q886R;ENSP00000381867:Q835R;ENSP00000381863:Q795R;ENSP00000401197:Q896R	ENSP00000381863:Q795R	Q	-	2	0	USP19	49124793	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.585000	0.46111	2.211000	0.71520	0.459000	0.35465	CAG	.	.		0.637	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		C	49149789	T	C	49149789	3	2	35	1	0	0	0	0	1	0	0	0	17065	1580	55	2	1608	2	USP19	3	49149789	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	10336926	49149789	148872641	132	4301										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49169091	49169091	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cagtcataggagaaatatcgGtacacatgccaggtgcggcc	12	10	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:49169091G>A	ENST00000418109.1	-	6	689	c.525C>T	c.(523-525)taC>taT	p.Y175Y	LAMB2_ENST00000305544.4_Silent_p.Y175Y	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	175	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGAAATATCGGTACACATGCC	0.582																																					p.Y175Y		Atlas-SNP	.											.	LAMB2	156	.	0			c.C525T						.						87	91	90					3																	49169091		2203	4300	6503	SO:0001819	synonymous_variant	3913	exon5			ATATCGGTACACA		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.525C>T	chr3.hg19:g.49169091G>A		68.0	0.0		92.0	5.0	NM_002292	Q16321	Silent	SNP	ENST00000418109.1	hg19	CCDS2789.1																																																																																			.	.		0.582	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		A	49169091	G	A	49169091	2	1	35	1	0	0	0	0	0	0	0	1	8620	1256	44	3		3	LAMB2	3	49169091	Silent	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	19302	49169091	148853339	133	4302										
IP6K1	9807	hgsc.bcm.edu	37	chr3	49775655	49775655	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tacctcttacctctcagaggTctcaagggacaggctggctt	10	12	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:49775655T>C	ENST00000321599.4	-	3	725	c.424A>G	c.(424-426)Acc>Gcc	p.T142A	IP6K1_ENST00000468463.1_Missense_Mutation_p.T142A|IP6K1_ENST00000460540.1_5'UTR|IP6K1_ENST00000395238.1_5'UTR	NM_001242829.1|NM_153273.3	NP_001229758.1|NP_695005.1	Q92551	IP6K1_HUMAN	inositol hexakisphosphate kinase 1	142					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|skin(2)	15						CTCTCAGAGGTCTCAAGGGAC	0.577																																					p.T142A		Atlas-SNP	.											.	IP6K1	41	.	0			c.A424G						.						127	105	112					3																	49775655		2203	4300	6503	SO:0001583	missense	9807	exon3			CAGAGGTCTCAAG	D87452	CCDS33760.1, CCDS43092.1	3p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000176095	ENSG00000176095			18360	protein-coding gene	gene with protein product		606991	"inositol hexaphosphate kinase 1"	IHPK1			Standard	NM_001242829		Approved	KIAA0263	uc003cxm.1	Q92551	OTTHUMG00000158197	ENST00000321599.4:c.424A>G	chr3.hg19:g.49775655T>C	ENSP00000323780:p.Thr142Ala	118.0	0.0		120.0	5.0	NM_153273	A8K157|A8MUX4|Q7L3I7|Q96E38	Missense_Mutation	SNP	ENST00000321599.4	hg19	CCDS33760.1	.	.	.	.	.	.	.	.	.	.	T	5.005	0.186671	0.09547	.	.	ENSG00000176095	ENST00000321599;ENST00000468463	T;T	0.61392	0.11;0.11	5.93	0.582	0.17412	.	0.463132	0.24291	N	0.039815	T	0.32164	0.0820	L	0.29908	0.895	0.34560	D	0.712236	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18967	-1.0320	10	0.07813	T	0.8	-5.7755	1.9413	0.03347	0.1195:0.1404:0.2483:0.4917	.	142;142	C9JNA8;Q92551	.;IP6K1_HUMAN	A	142	ENSP00000323780:T142A;ENSP00000420467:T142A	ENSP00000323780:T142A	T	-	1	0	IP6K1	49750659	0.409000	0.25368	0.210000	0.23637	0.843000	0.47879	-0.020000	0.12525	-0.112000	0.11979	0.460000	0.39030	ACC	.	.		0.577	IP6K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350380.1	NM_153273		C	49775655	T	C	49775655	3	2	35	1	0	0	0	0	1	0	0	0	7797	1667	58	2	917	2	IP6K1	3	49775655	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	606564	49775655	148246775	134	4303										
RASSF1	11334	hgsc.bcm.edu	37	chr3	50368106	50368106	+	5'Flank	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggaggtgctcctcctcctccCgctgcaggatacgtaggaag	13	13	0	0	rs142957899		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:50368106C>G	ENST00000232496.4	-	0	0				RASSF1_ENST00000357043.2_Missense_Mutation_p.R314P|RASSF1_ENST00000395126.3_Missense_Mutation_p.R159P|RASSF1_ENST00000359365.4_Missense_Mutation_p.R310P|TUSC2_ENST00000462137.1_5'Flank|RASSF1_ENST00000327761.3_Missense_Mutation_p.R240P	NM_007275.1	NP_009206.1	O75896	TUSC2_HUMAN	tumor suppressor candidate 2						cell cycle (GO:0007049)|cell maturation (GO:0048469)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|chemokine (C-C motif) ligand 5 production (GO:0071609)|inflammatory response (GO:0006954)|interleukin-15 production (GO:0032618)|natural killer cell differentiation (GO:0001779)|negative regulation of interleukin-17 production (GO:0032700)|neutrophil mediated killing of gram-negative bacterium (GO:0070945)|phagocytosis (GO:0006909)|positive regulation of interleukin-10 production (GO:0032733)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to defense-related host reactive oxygen species production (GO:0052567)	mitochondrion (GO:0005739)				lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CTCCTCCTCCCGCTGCAGGAT	0.587																																					p.R314P		Atlas-SNP	.											.	RASSF1	46	.	0			c.G941C						.						103	92	95					3																	50368106		2203	4300	6503	SO:0001631	upstream_gene_variant	11186	exon6			TCCTCCCGCTGCA	AF055479	CCDS2819.1	3p21.3	2010-09-21	2004-01-20	2004-01-21	ENSG00000114383	ENSG00000114383			17034	protein-coding gene	gene with protein product		607052	"PDGFA associated protein 2"	PDAP2		8780057, 11593436	Standard	NM_007275		Approved	FUS1, PAP, C3orf11	uc003czy.1	O75896	OTTHUMG00000156877		chr3.hg19:g.50368106C>G	Exception_encountered	79.0	0.0		60.0	12.0	NM_170714	B2R4Y9	Missense_Mutation	SNP	ENST00000232496.4	hg19	CCDS2819.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.613182	0.87359	.	.	ENSG00000068028	ENST00000327761;ENST00000395126;ENST00000357043;ENST00000359365	T;T;T;T	0.77750	2.65;2.18;-1.12;-1.12	5.49	5.49	0.81192	SARAH (1);	0.000000	0.85682	D	0.000000	D	0.87822	0.6274	M	0.70595	2.14	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.995	D;D;P	0.97110	0.987;1.0;0.905	D	0.88382	0.3002	10	0.72032	D	0.01	-30.2568	18.3174	0.90226	0.0:1.0:0.0:0.0	.	310;314;240	Q9NS23-2;Q9NS23;Q5TZT2	.;RASF1_HUMAN;.	P	240;159;314;310	ENSP00000333327:R240P;ENSP00000378558:R159P;ENSP00000349547:R314P;ENSP00000352323:R310P	ENSP00000333327:R240P	R	-	2	0	RASSF1	50343110	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	3.852000	0.55934	2.735000	0.93741	0.563000	0.77884	CGG	.	C|1.000;T|0.000		0.587	TUSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346399.1	NM_007275		G	50368106	C	G	50368106	1	3	35	0	1	0	0	0	0	0	0	0	13099	652	23	4		4	RASSF1	3	50368106	5'Flank	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	592451	50368106	147654324	135	4304										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52429610	52429610	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agctccatagagaggggcaaAtgggtcttcttccagaactg	12	9	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:52429610A>G	ENST00000420323.2	+	70	11436	c.11175A>G	c.(11173-11175)aaA>aaG	p.K3725K		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3790	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGAGGGGCAAATGGGTCTTCT	0.637																																					p.K3725K		Atlas-SNP	.											.	DNAH1	534	.	0			c.A11175G						.						57	64	61					3																	52429610		2073	4242	6315	SO:0001819	synonymous_variant	25981	exon70			GGGCAAATGGGTC	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.11175A>G	chr3.hg19:g.52429610A>G		126.0	0.0		93.0	4.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	hg19	CCDS46842.1																																																																																			.	.		0.637	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52429610	A	G	52429610	2	3	35	1	0	0	0	0	0	0	0	1	4599	98	4	2		2	DNAH1	3	52429610	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	2061504	52429610	145592820	136	4305										
CACNA1D	776	hgsc.bcm.edu	37	chr3	53839136	53839136	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gtttgctatgattcacggagAtctccaaggagacgcctact	10	10	2	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:53839136A>G	ENST00000350061.5	+	45	6223	c.5712A>G	c.(5710-5712)agA>agG	p.R1904R	CACNA1D_ENST00000422281.2_Silent_p.R1880R|CACNA1D_ENST00000544977.1_Silent_p.R283R|CACNA1D_ENST00000288139.4_Silent_p.R1924R	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	1904					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ATTCACGGAGATCTCCAAGGA	0.562																																					p.R1924R		Atlas-SNP	.											.	CACNA1D	324	.	0			c.A5772G						.						95	93	93					3																	53839136		2203	4300	6503	SO:0001819	synonymous_variant	776	exon46			ACGGAGATCTCCA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.5712A>G	chr3.hg19:g.53839136A>G		41.0	0.0		29.0	4.0	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Silent	SNP	ENST00000350061.5	hg19	CCDS46848.1																																																																																			.	.		0.562	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		G	53839136	A	G	53839136	2	3	35	1	0	0	0	0	0	0	0	1	2543	330	12	2		2	CACNA1D	3	53839136	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	1409526	53839136	144183294	137	4306										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64138962	64138962	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgtagcgctggccgcccagcActgtctcacactcgaagcag	11	15	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:64138962A>G	ENST00000295902.6	-	6	1268	c.683T>C	c.(682-684)gTg>gCg	p.V228A	PRICKLE2_ENST00000564377.1_Missense_Mutation_p.V284A	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	228	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		GCCGCCCAGCACTGTCTCACA	0.522																																					p.V228A		Atlas-SNP	.											.	PRICKLE2	88	.	0			c.T683C						.						172	151	158					3																	64138962		2203	4300	6503	SO:0001583	missense	166336	exon6			CCCAGCACTGTCT	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.683T>C	chr3.hg19:g.64138962A>G	ENSP00000295902:p.Val228Ala	73.0	0.0		98.0	4.0	NM_198859	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	hg19	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.731365	0.48939	.	.	ENSG00000163637	ENST00000295902	D	0.86865	-2.18	5.56	5.56	0.83823	Zinc finger, LIM-type (5);	0.000000	0.64402	D	0.000007	D	0.85022	0.5602	L	0.49513	1.565	0.80722	D	1	B	0.21071	0.051	B	0.26094	0.066	T	0.81215	-0.1034	10	0.38643	T	0.18	-42.7799	15.9994	0.80280	1.0:0.0:0.0:0.0	.	228	Q7Z3G6	PRIC2_HUMAN	A	228	ENSP00000295902:V228A	ENSP00000295902:V228A	V	-	2	0	PRICKLE2	64114002	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.526000	0.81920	2.241000	0.73720	0.533000	0.62120	GTG	.	.		0.522	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		G	64138962	A	G	64138962	3	3	35	1	0	0	0	0	1	0	0	0	12499	159	6	2	1863	2	PRICKLE2	3	64138962	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	10299826	64138962	133883468	138	4307										
VGLL3	389136	hgsc.bcm.edu	37	chr3	87027732	87027732	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aaatggcagattctggatggAgggtgatggcttggcccaaa	15	6	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:87027732A>G	ENST00000398399.2	-	2	710	c.347T>C	c.(346-348)cTc>cCc	p.L116P	VGLL3_ENST00000383698.3_Missense_Mutation_p.L116P	NM_016206.2	NP_057290.2			vestigial-like family member 3											NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(11)	19	all_cancers(8;0.109)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		TTCTGGATGGAGGGTGATGGC	0.473																																					p.L116P		Atlas-SNP	.											.	VGLL3	62	.	0			c.T347C						.						124	121	122					3																	87027732		1973	4181	6154	SO:0001583	missense	389136	exon2			GGATGGAGGGTGA	AF099505	CCDS43110.1	3p12.1	2014-03-03	2014-03-03		ENSG00000206538	ENSG00000206538			24327	protein-coding gene	gene with protein product		609980	"vestigial like 3 (Drosophila)"			12376544	Standard	NM_016206		Approved	VGL-3	uc003dqn.3	A8MV65	OTTHUMG00000158984	ENST00000398399.2:c.347T>C	chr3.hg19:g.87027732A>G	ENSP00000381436:p.Leu116Pro	68.0	0.0		117.0	6.0	NM_016206		Missense_Mutation	SNP	ENST00000398399.2	hg19	CCDS43110.1	.	.	.	.	.	.	.	.	.	.	A	17.27	3.347752	0.61183	.	.	ENSG00000206538	ENST00000398399;ENST00000383698	T;T	0.47528	0.84;0.84	5.41	5.41	0.78517	.	0.063714	0.64402	D	0.000010	T	0.42223	0.1193	L	0.44542	1.39	0.52099	D	0.999948	B	0.11235	0.004	B	0.11329	0.006	T	0.21586	-1.0241	10	0.32370	T	0.25	-4.1992	15.4467	0.75235	1.0:0.0:0.0:0.0	.	116	A8MV65	VGLL3_HUMAN	P	116	ENSP00000381436:L116P;ENSP00000373199:L116P	ENSP00000373199:L116P	L	-	2	0	VGLL3	87110422	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.452000	0.52971	2.048000	0.60808	0.533000	0.62120	CTC	.	.		0.473	VGLL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352805.1	NM_016206		G	87027732	A	G	87027732	3	3	35	1	0	0	0	0	1	0	0	0	17175	304	11	2	645	2	VGLL3	3	87027732	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	22888770	87027732	110994698	139	4308										
IFT57	55081	hgsc.bcm.edu	37	chr3	107940994	107940994	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggttgctcttccggaggaacTcctcctcgtagcggagcagc	13	13	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:107940994T>C	ENST00000264538.3	-	1	423	c.176A>G	c.(175-177)gAg>gGg	p.E59G		NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	59					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			CCGGAGGAACTCCTCCTCGTA	0.677																																					p.E59G		Atlas-SNP	.											.	IFT57	44	.	0			c.A176G						.						25	27	26					3																	107940994		2202	4300	6502	SO:0001583	missense	55081	exon1			AGGAACTCCTCCT	AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"Intraflagellar transport homologs"	17367	protein-coding gene	gene with protein product		606621	"estrogen-related receptor beta like 1", "intraflagellar transport 57 homolog (Chlamydomonas)"	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.176A>G	chr3.hg19:g.107940994T>C	ENSP00000264538:p.Glu59Gly	114.0	0.0		95.0	5.0	NM_018010	Q96DA9	Missense_Mutation	SNP	ENST00000264538.3	hg19	CCDS2951.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.256450	0.59321	.	.	ENSG00000114446	ENST00000264538;ENST00000492106	.	.	.	5.45	4.3	0.51218	.	0.371791	0.32518	N	0.005982	T	0.45637	0.1352	L	0.37750	1.13	0.42558	D	0.993138	B	0.11235	0.004	B	0.04013	0.001	T	0.31475	-0.9942	9	0.30078	T	0.28	.	11.2919	0.49256	0.0:0.0715:0.0:0.9285	.	59	Q9NWB7	IFT57_HUMAN	G	59	.	ENSP00000264538:E59G	E	-	2	0	IFT57	109423684	1.000000	0.71417	0.910000	0.35882	0.972000	0.66771	4.432000	0.59922	1.015000	0.39444	0.455000	0.32223	GAG	.	.		0.677	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010		C	107940994	T	C	107940994	3	2	35	1	0	0	0	0	1	0	0	0	7571	1551	54	2	1157	2	IFT57	3	107940994	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	20913262	107940994	90081436	140	4309										
RETNLB	84666	hgsc.bcm.edu	37	chr3	108475432	108475432	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgcttataggagagggactgTactctgagtaggaaagaaga	14	4	1	4			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:108475432T>C	ENST00000295755.6	-	2	329	c.131A>G	c.(130-132)tAc>tGc	p.Y44C	RETNLB_ENST00000482939.1_5'UTR	NM_032579.2	NP_115968.1	Q9BQ08	RETNB_HUMAN	resistin like beta	44					cell proliferation (GO:0008283)	extracellular region (GO:0005576)				endometrium(1)|kidney(3)|lung(10)|prostate(1)|skin(1)	16						AGAGGGACTGTACTCTGAGTA	0.507																																					p.Y44C		Atlas-SNP	.											.	RETNLB	38	.	0			c.A131G						.						152	123	133					3																	108475432		2203	4300	6503	SO:0001583	missense	84666	exon2			GGACTGTACTCTG	AF290873	CCDS2953.1	3q13.1	2008-02-05			ENSG00000163515	ENSG00000163515			20388	protein-coding gene	gene with protein product		605645				10921885, 12574343	Standard	NM_032579		Approved	HXCP2, FIZZ2, RELMb	uc003dxh.2	Q9BQ08	OTTHUMG00000159393	ENST00000295755.6:c.131A>G	chr3.hg19:g.108475432T>C	ENSP00000295755:p.Tyr44Cys	113.0	0.0		81.0	4.0	NM_032579	Q14D27	Missense_Mutation	SNP	ENST00000295755.6	hg19	CCDS2953.1	.	.	.	.	.	.	.	.	.	.	T	7.813	0.716107	0.15306	.	.	ENSG00000163515	ENST00000295755	T	0.42513	0.97	3.96	-5.23	0.02798	.	1.318770	0.05653	N	0.585484	T	0.22166	0.0534	N	0.22421	0.69	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.18808	-1.0325	10	0.39692	T	0.17	.	1.7816	0.03033	0.5548:0.1178:0.119:0.2083	.	44	Q9BQ08	RETNB_HUMAN	C	44	ENSP00000295755:Y44C	ENSP00000295755:Y44C	Y	-	2	0	RETNLB	109958122	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.130000	0.03241	-0.516000	0.06470	0.523000	0.50628	TAC	.	.		0.507	RETNLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355093.1			C	108475432	T	C	108475432	3	2	35	1	0	0	0	0	1	0	0	0	13252	1638	57	2	212	2	RETNLB	3	108475432	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	534438	108475432	89546998	141	4310										
DPPA2	151871	hgsc.bcm.edu	37	chr3	109028179	109028179	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tttgtttgaagtagatgaccTaagacaagaatggaaccaaa	9	5	0	5			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:109028179T>C	ENST00000478945.1	-	4	428		c.e4-2			NM_138815.3	NP_620170.3	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2						lung-associated mesenchyme development (GO:0060484)|positive regulation of stem cell proliferation (GO:2000648)|regulation of histone methylation (GO:0031060)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GTAGATGACCTAAGACAAGAA	0.393																																					.		Atlas-SNP	.											.	DPPA2	52	.	0			c.182-2A>G						.						89	88	88					3																	109028179		2203	4300	6503	SO:0001630	splice_region_variant	151871	exon5			ATGACCTAAGACA	AY283672	CCDS2956.1	3q13.13	2010-05-04			ENSG00000163530	ENSG00000163530			19197	protein-coding gene	gene with protein product	"cancer/testis antigen 100"	614445				15583978	Standard	NM_138815		Approved	PESCRG1, CT100	uc003dxo.3	Q7Z7J5	OTTHUMG00000159227	ENST00000478945.1:c.182-2A>G	chr3.hg19:g.109028179T>C		210.0	0.0		124.0	5.0	NM_138815	Q8WVF0	Splice_Site	SNP	ENST00000478945.1	hg19	CCDS2956.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.455084	0.26161	.	.	ENSG00000163530	ENST00000478945	.	.	.	4.97	1.23	0.21249	.	.	.	.	.	.	.	.	.	.	.	0.29211	N	0.874552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.9406	0.09325	0.0:0.1895:0.1832:0.6273	.	.	.	.	.	-1	.	.	.	-	.	.	DPPA2	110510869	0.003000	0.15002	0.003000	0.11579	0.379000	0.30106	-0.024000	0.12435	0.130000	0.18549	0.459000	0.35465	.	.	.		0.393	DPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353938.1	NM_138815	Intron	C	109028179	T	C	109028179	5	2	35	1	0	0	0	0	0	0	1	0	4736	1536	53	2	736	2	DPPA2	3	109028179	Splice_Site	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	552747	109028179	88994251	142	4311										
WDR5B	54554	hgsc.bcm.edu	37	chr3	122133628	122133628	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	atatttctcattcttatgacCagtgtatgttttcaggcacc	6	9	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:122133628C>T	ENST00000330689.4	-	1	1254	c.748G>A	c.(748-750)Ggt>Agt	p.G250S	RP11-299J3.8_ENST00000608465.1_RNA|RP11-299J3.8_ENST00000608346.1_RNA|RP11-299J3.8_ENST00000608015.1_RNA|RP11-299J3.8_ENST00000608756.1_RNA|RP11-299J3.8_ENST00000609469.1_RNA	NM_019069.3	NP_061942.2	Q86VZ2	WDR5B_HUMAN	WD repeat domain 5B	250										kidney(2)|large_intestine(4)|lung(2)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.0704)		TTCTTATGACCAGTGTATGTT	0.373																																					p.G250S		Atlas-SNP	.											.	WDR5B	36	.	0			c.G748A						.						107	110	109					3																	122133628		2203	4300	6503	SO:0001583	missense	54554	exon1			TATGACCAGTGTA	AK002149	CCDS3012.1	3q21.1	2013-01-09			ENSG00000196981	ENSG00000196981		"WD repeat domain containing"	17826	protein-coding gene	gene with protein product						10369878	Standard	NM_019069		Approved	FLJ11287	uc003efa.1	Q86VZ2	OTTHUMG00000159489	ENST00000330689.4:c.748G>A	chr3.hg19:g.122133628C>T	ENSP00000330381:p.Gly250Ser	169.0	0.0		114.0	5.0	NM_019069	B2RCM9|Q9NUL4	Missense_Mutation	SNP	ENST00000330689.4	hg19	CCDS3012.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152237	0.57259	.	.	ENSG00000196981	ENST00000330689	T	0.70045	-0.45	4.77	4.77	0.60923	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.048353	0.85682	D	0.000000	T	0.65144	0.2663	M	0.74389	2.26	0.80722	D	1	P	0.43431	0.807	B	0.39805	0.31	T	0.71334	-0.4624	10	0.72032	D	0.01	.	10.7016	0.45931	0.1903:0.8097:0.0:0.0	.	250	Q86VZ2	WDR5B_HUMAN	S	250	ENSP00000330381:G250S	ENSP00000330381:G250S	G	-	1	0	WDR5B	123616318	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	4.797000	0.62503	2.644000	0.89710	0.561000	0.74099	GGT	.	.		0.373	WDR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355753.1	NM_019069		T	122133628	C	T	122133628	3	4	35	1	0	0	0	0	1	0	0	0	17324	594	21	3	248	3	WDR5B	3	122133628	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	13105449	122133628	75888802	143	4312										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126739124	126739124	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	atccccttccttgactaccgGacatatgccatgcgggtgct	9	14	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:126739124G>T	ENST00000393409.2	+	20	3975	c.3975G>T	c.(3973-3975)cgG>cgT	p.R1325R	PLXNA1_ENST00000251772.4_Silent_p.R1302R	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1325					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		TTGACTACCGGACATATGCCA	0.607																																					p.R1325R		Atlas-SNP	.											.	PLXNA1	185	.	0			c.G3975T						.						102	83	89					3																	126739124		2203	4300	6503	SO:0001819	synonymous_variant	5361	exon20			CTACCGGACATAT	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.3975G>T	chr3.hg19:g.126739124G>T		106.0	0.0		87.0	4.0	NM_032242		Silent	SNP	ENST00000393409.2	hg19	CCDS33847.2																																																																																			.	.		0.607	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		T	126739124	G	T	126739124	2	4	35	1	0	0	0	0	0	0	0	1	12128	1161	41	3		3	PLXNA1	3	126739124	Silent	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	4605496	126739124	71283306	144	4313										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130285737	130285737	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	acttggaatttgagatcaatAaatactccaacaagcaggat	7	7	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:130285737A>G	ENST00000358511.6	+	4	1505	c.1474A>G	c.(1474-1476)Aaa>Gaa	p.K492E	COL6A6_ENST00000453409.2_Missense_Mutation_p.K492E	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	492	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TGAGATCAATAAATACTCCAA	0.488																																					p.K492E		Atlas-SNP	.											.	COL6A6	497	.	0			c.A1474G						.						114	116	115					3																	130285737		1909	4116	6025	SO:0001583	missense	131873	exon4			ATCAATAAATACT	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1474A>G	chr3.hg19:g.130285737A>G	ENSP00000351310:p.Lys492Glu	148.0	0.0		123.0	5.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	A	3.309	-0.141255	0.06669	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.77098	-1.07;-1.07	5.18	4.0	0.46444	von Willebrand factor, type A (3);	0.185922	0.37955	N	0.001874	T	0.54127	0.1839	N	0.16066	0.365	0.09310	N	1	B	0.22909	0.077	B	0.24848	0.056	T	0.44267	-0.9339	10	0.02654	T	1	.	6.5047	0.22188	0.6208:0.3012:0.0781:0.0	.	492	A6NMZ7	CO6A6_HUMAN	E	492	ENSP00000351310:K492E;ENSP00000399236:K492E	ENSP00000351310:K492E	K	+	1	0	COL6A6	131768427	0.000000	0.05858	0.073000	0.20177	0.867000	0.49689	0.386000	0.20702	0.794000	0.33899	0.459000	0.35465	AAA	.	.		0.488	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		G	130285737	A	G	130285737	3	3	35	1	0	0	0	0	1	0	0	0	3705	363	13	2	1488	2	COL6A6	3	130285737	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	3546613	130285737	67736693	145	4314										
PIK3R4	30849	hgsc.bcm.edu	37	chr3	130435261	130435261	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgtgagagcaacttcttcagAagctgtgctatggcaggatc	12	8	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:130435261A>G	ENST00000356763.3	-	9	2867	c.2310T>C	c.(2308-2310)ctT>ctC	p.L770L		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	770					innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L770L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						ACTTCTTCAGAAGCTGTGCTA	0.398																																					p.L770L		Atlas-SNP	.											PIK3R4,NS,carcinoma,0,1	PIK3R4	145	.	1	Substitution - coding silent(1)	lung(1)	c.T2310C						.						90	95	93					3																	130435261		2203	4300	6503	SO:0001819	synonymous_variant	30849	exon9			CTTCAGAAGCTGT	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.2310T>C	chr3.hg19:g.130435261A>G		134.0	0.0		113.0	6.0	NM_014602	Q2TBF4	Silent	SNP	ENST00000356763.3	hg19	CCDS3067.1																																																																																			.	.		0.398	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		G	130435261	A	G	130435261	2	3	35	1	0	0	0	0	0	0	0	1	11930	233	9	2		2	PIK3R4	3	130435261	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	149524	130435261	67587169	146	4315										
RAB6B	51560	hgsc.bcm.edu	37	chr3	133560224	133560224	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaccagctgtgtcccagagcTgcagtcgcacctgtctcagg	12	14	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:133560224T>C	ENST00000285208.4	-	4	543	c.194A>G	c.(193-195)cAg>cGg	p.Q65R	RAB6B_ENST00000469959.1_Intron|RAB6B_ENST00000486858.1_Missense_Mutation_p.Q52R|RAB6B_ENST00000543906.1_Missense_Mutation_p.Q65R	NM_016577.3	NP_057661.3	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family	65					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	11						GTCCCAGAGCTGCAGTCGCAC	0.652																																					p.Q65R		Atlas-SNP	.											.	RAB6B	36	.	0			c.A194G						.						89	77	81					3																	133560224		2203	4300	6503	SO:0001583	missense	51560	exon4			CAGAGCTGCAGTC	AF166492	CCDS3082.1	3q22.1	2008-05-15			ENSG00000154917	ENSG00000154917		"RAB, member RAS oncogene"	14902	protein-coding gene	gene with protein product		615852					Standard	NM_016577		Approved		uc003epy.3	Q9NRW1	OTTHUMG00000159749	ENST00000285208.4:c.194A>G	chr3.hg19:g.133560224T>C	ENSP00000285208:p.Gln65Arg	83.0	0.0		84.0	4.0	NM_016577	B2R5Z9|B7Z337|D3DND3|Q92929	Missense_Mutation	SNP	ENST00000285208.4	hg19	CCDS3082.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.543305	0.65198	.	.	ENSG00000154917	ENST00000285208;ENST00000543906;ENST00000486858;ENST00000477759;ENST00000460865;ENST00000488969	T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	4.7	4.7	0.59300	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.88220	0.6378	M	0.84156	2.68	0.80722	D	1	P;P	0.36048	0.534;0.491	B;P	0.58577	0.417;0.841	D	0.88946	0.3383	10	0.59425	D	0.04	-5.2834	13.444	0.61129	0.0:0.0:0.0:1.0	.	52;65	B7Z337;Q9NRW1	.;RAB6B_HUMAN	R	65;65;52;32;11;32	ENSP00000285208:Q65R;ENSP00000437797:Q65R;ENSP00000419381:Q52R;ENSP00000419941:Q32R;ENSP00000419526:Q11R;ENSP00000417433:Q32R	ENSP00000285208:Q65R	Q	-	2	0	RAB6B	135042914	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.339000	0.79282	1.868000	0.54150	0.379000	0.24179	CAG	.	.		0.652	RAB6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357152.1			C	133560224	T	C	133560224	3	2	35	1	0	0	0	0	1	0	0	0	12967	1580	55	2	452	2	RAB6B	3	133560224	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	3124963	133560224	64462206	147	4316										
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135721457	135721457	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tacaatccattccaaacaacTccacaaattccttatataac	0	13	0	0	rs148236440		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:135721457T>C	ENST00000264977.3	+	2	1734	c.1117T>C	c.(1117-1119)Tcc>Ccc	p.S373P	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	373					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TCCAAACAACTCCACAAATTC	0.373																																					p.S373P		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T1117C						.						63	64	63					3																	135721457		2203	4298	6501	SO:0001583	missense	5523	exon2			AACAACTCCACAA	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.1117T>C	chr3.hg19:g.135721457T>C	ENSP00000264977:p.Ser373Pro	135.0	0.0		119.0	5.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	hg19	CCDS3087.1	.	.	.	.	.	.	.	.	.	.	T	5.003	0.186191	0.09495	.	.	ENSG00000073711	ENST00000264977	T	0.06068	3.35	4.95	1.25	0.21368	.	0.275476	0.35615	N	0.003083	T	0.03263	0.0095	L	0.31664	0.95	0.35027	D	0.758389	P	0.37864	0.61	B	0.29440	0.102	T	0.50065	-0.8871	10	0.28530	T	0.3	.	4.2532	0.10705	0.1628:0.1525:0.0:0.6847	.	373	Q06190	P2R3A_HUMAN	P	373	ENSP00000264977:S373P	ENSP00000264977:S373P	S	+	1	0	PPP2R3A	137204147	0.650000	0.27331	0.129000	0.21949	0.584000	0.36387	1.367000	0.34204	0.681000	0.31386	0.533000	0.62120	TCC	.	T|1.000;G|0.000		0.373	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		C	135721457	T	C	135721457	3	2	35	1	0	0	0	0	1	0	0	0	12400	1551	54	2	1119	2	PPP2R3A	3	135721457	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	2161233	135721457	62300973	148	4317										
DBR1	51163	hgsc.bcm.edu	37	chr3	137880850	137880850	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cctcttcaatggcaccttggTtaagtcctctccattccctg	6	15	3	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:137880850T>A	ENST00000260803.4	-	8	1669	c.1516A>T	c.(1516-1518)Acc>Tcc	p.T506S	DBR1_ENST00000505015.2_Missense_Mutation_p.T272S	NM_016216.3	NP_057300.2	Q9UK59	DBR1_HUMAN	debranching RNA lariats 1	506					mRNA splicing, via spliceosome (GO:0000398)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA lariat debranching enzyme activity (GO:0008419)			NS(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						GGCACCTTGGTTAAGTCCTCT	0.448																																					p.T506S		Atlas-SNP	.											.	DBR1	45	.	0			c.A1516T						.						208	195	200					3																	137880850		2203	4300	6503	SO:0001583	missense	51163	exon8			CCTTGGTTAAGTC	AF180919	CCDS33863.1	3q22.3	2013-05-01	2013-05-01		ENSG00000138231	ENSG00000138231			15594	protein-coding gene	gene with protein product		607024	"debranching enzyme (S. Cerevisiae) homolog 1", "debranching enzyme homolog 1 (S. cerevisiae)"			10982890	Standard	NM_016216		Approved		uc003erv.3	Q9UK59	OTTHUMG00000159824	ENST00000260803.4:c.1516A>T	chr3.hg19:g.137880850T>A	ENSP00000260803:p.Thr506Ser	602.0	0.0		540.0	194.0	NM_016216	Q96GH0|Q9NXQ6	Missense_Mutation	SNP	ENST00000260803.4	hg19	CCDS33863.1	.	.	.	.	.	.	.	.	.	.	T	1.206	-0.631146	0.03584	.	.	ENSG00000138231	ENST00000260803;ENST00000505015	T	0.42513	0.97	5.59	1.79	0.24919	.	1.023440	0.07748	N	0.948007	T	0.23611	0.0571	N	0.25647	0.755	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.28235	-1.0050	10	0.08381	T	0.77	-8.8053	2.2824	0.04118	0.148:0.084:0.3067:0.4612	.	506;274	Q9UK59;Q9UK59-2	DBR1_HUMAN;.	S	506;272	ENSP00000260803:T506S	ENSP00000260803:T506S	T	-	1	0	DBR1	139363540	0.000000	0.05858	0.009000	0.14445	0.497000	0.33675	0.240000	0.18042	0.063000	0.16370	0.533000	0.62120	ACC	.	.		0.448	DBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357585.1			A	137880850	T	A	137880850	3	1	35	1	0	0	0	0	1	0	0	0	4259	1725	60	4	122	4	DBR1	3	137880850	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	2159393	137880850	60141580	149	4318										
PLOD2	5352	hgsc.bcm.edu	37	chr3	145795696	145795696	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttccggagtaggggagtcttTttccctttgtaaagtctaaa	10	7	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:145795696T>C	ENST00000360060.3	-	14	1678				PLOD2_ENST00000461497.1_Missense_Mutation_p.K166E|RP11-274H2.2_ENST00000480247.1_RNA|PLOD2_ENST00000494950.1_Missense_Mutation_p.K451E|PLOD2_ENST00000282903.5_Missense_Mutation_p.K506E	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2						cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	GGGGAGTCTTTTTCCCTTTGT	0.343																																					p.K506E		Atlas-SNP	.											.	PLOD2	81	.	0			c.A1516G						.						105	118	113					3																	145795696		2203	4299	6502	SO:0001627	intron_variant	5352	exon14			AGTCTTTTTCCCT	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"lysyl hydroxlase 2"	601865	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.1501-1014A>G	chr3.hg19:g.145795696T>C		41.0	0.0		57.0	4.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	hg19	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	t	14.42	2.529067	0.44969	.	.	ENSG00000152952	ENST00000461497;ENST00000282903;ENST00000494950	D;T;T	0.90504	-2.68;-0.06;-0.05	6.0	6.0	0.97389	.	0.185560	0.38058	N	0.001838	D	0.84575	0.5502	N	0.14661	0.345	0.37782	D	0.927046	P;D;P	0.55605	0.877;0.972;0.877	B;P;B	0.47162	0.339;0.54;0.265	D	0.83788	0.0229	10	0.09843	T	0.71	-32.0152	16.537	0.84375	0.0:0.0:0.0:1.0	.	451;506;166	E7ETU9;O00469-2;B3KWS3	.;.;.	E	166;506;451	ENSP00000419354:K166E;ENSP00000282903:K506E;ENSP00000420094:K451E	ENSP00000282903:K506E	K	-	1	0	PLOD2	147278386	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.590000	0.82653	2.296000	0.77279	0.524000	0.50904	AAA	.	.		0.343	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		C	145795696	T	C	145795696	1	2	35	0	1	0	0	0	0	0	0	0	12111	1850	64	2		2	PLOD2	3	145795696	Intron	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	7914846	145795696	52226734	150	4319										
MED12L	116931	hgsc.bcm.edu	37	chr3	150874118	150874118	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tagcatttcacatgttccagGtaaccttttgaagacatgca	7	9	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:150874118G>A	ENST00000474524.1	+	5	764		c.e5+1		MED12L_ENST00000273432.4_Splice_Site|MED12L_ENST00000422248.2_Splice_Site|MED12L_ENST00000309237.4_Splice_Site	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.?(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CATGTTCCAGGTAACCTTTTG	0.453																																					.		Atlas-SNP	.											MED12L,NS,carcinoma,0,1	MED12L	271	.	1	Unknown(1)	kidney(1)	c.726+1G>A						.						128	118	121					3																	150874118		2203	4300	6503	SO:0001630	splice_region_variant	116931	exon5			TTCCAGGTAACCT	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.726+1G>A	chr3.hg19:g.150874118G>A		99.0	0.0		71.0	3.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Splice_Site	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.663821	0.88251	.	.	ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4315	0.90627	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MED12L	152356808	1.000000	0.71417	0.992000	0.48379	0.971000	0.66376	9.250000	0.95477	2.515000	0.84797	0.557000	0.71058	.	.	.		0.453	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	Intron	A	150874118	G	A	150874118	5	1	35	1	0	0	0	0	0	0	1	0	9438	1275	44	3	745	3	MED12L	3	150874118	Splice_Site	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	5078422	150874118	47148312	151	4320										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151154684	151154684	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	catgtgatttctggcttgggAactcccaaggccacacagtg	11	11	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:151154684A>G	ENST00000282466.3	-	6	7664	c.7665T>C	c.(7663-7665)gtT>gtC	p.V2555V	IGSF10_ENST00000495443.1_5'UTR|MED12L_ENST00000474524.1_3'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2555	Ig-like C2-type 12.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CTGGCTTGGGAACTCCCAAGG	0.522																																					p.V2555V		Atlas-SNP	.											.	IGSF10	279	.	0			c.T7665C						.						72	66	68					3																	151154684		2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			CTTGGGAACTCCC	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.7665T>C	chr3.hg19:g.151154684A>G		170.0	0.0		144.0	6.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	hg19	CCDS3160.1																																																																																			.	.		0.522	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		G	151154684	A	G	151154684	2	3	35	1	0	0	0	0	0	0	0	1	7606	233	9	2		2	IGSF10	3	151154684	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	280566	151154684	46867746	152	4321										
LEKR1	389170	hgsc.bcm.edu	37	chr3	156763334	156763334	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agagagaagccttgcaagacTgaactctgaaaaaggaatcc	10	8	1	5			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:156763334T>C	ENST00000470811.1	+	14	2297	c.962T>C	c.(961-963)cTg>cCg	p.L321P	LEKR1_ENST00000356539.4_Missense_Mutation_p.L625P			Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1	321										breast(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	11			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CTTGCAAGACTGAACTCTGAA	0.522																																					p.L625P		Atlas-SNP	.											.	LEKR1	66	.	0			c.T1874C						.						84	90	88					3																	156763334		2203	4300	6503	SO:0001583	missense	389170	exon13			CAAGACTGAACTC	AK131473	CCDS54660.1	3q25.31	2014-02-12	2008-02-21		ENSG00000197980	ENSG00000197980			33765	protein-coding gene	gene with protein product		613536					Standard	NM_001004316		Approved	FLJ16641	uc021xgh.1	Q6ZMV7	OTTHUMG00000160130	ENST00000470811.1:c.962T>C	chr3.hg19:g.156763334T>C	ENSP00000418214:p.Leu321Pro	103.0	0.0		92.0	4.0	NM_001004316		Missense_Mutation	SNP	ENST00000470811.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.90	1.777115	0.31411	.	.	ENSG00000178110	ENST00000470811;ENST00000356539	T;T	0.50277	0.75;0.75	4.94	-0.8	0.10897	.	1.367640	0.04888	N	0.448914	T	0.32675	0.0837	L	0.31294	0.92	0.09310	N	0.999999	B	0.09022	0.002	B	0.08055	0.003	T	0.15435	-1.0437	10	0.27082	T	0.32	0.9376	4.9006	0.13773	0.1453:0.3366:0.0:0.5181	.	321	Q6ZMV7	LEKR1_HUMAN	P	321;625	ENSP00000418214:L321P;ENSP00000348936:L625P	ENSP00000348936:L625P	L	+	2	0	LEKR1	158246028	0.000000	0.05858	0.001000	0.08648	0.586000	0.36452	-0.777000	0.04669	-0.043000	0.13513	0.533000	0.62120	CTG	.	.		0.522	LEKR1-010	KNOWN	upstream_ATG|basic	protein_coding	protein_coding	OTTHUMT00000351625.3	NM_001004316		C	156763334	T	C	156763334	3	2	35	1	0	0	0	0	1	0	0	0	8726	1580	55	2	1920	2	LEKR1	3	156763334	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	5608650	156763334	41259096	153	4322										
FNDC3B	64778	hgsc.bcm.edu	37	chr3	171965470	171965470	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cacattttattcataactcaCacacggcttactacccacct	2	15	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:171965470C>T	ENST00000336824.4	+	5	511	c.412C>T	c.(412-414)Cac>Tac	p.H138Y	FNDC3B_ENST00000415807.2_Missense_Mutation_p.H138Y|FNDC3B_ENST00000416957.1_Missense_Mutation_p.H138Y	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	138					cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.H138Y(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		TCATAACTCACACACGGCTTA	0.502																																					p.H138Y		Atlas-SNP	.											FNDC3B,NS,carcinoma,0,1	FNDC3B	118	.	1	Substitution - Missense(1)	lung(1)	c.C412T						.						248	212	224					3																	171965470		2203	4300	6503	SO:0001583	missense	64778	exon5			AACTCACACACGG	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.412C>T	chr3.hg19:g.171965470C>T	ENSP00000338523:p.His138Tyr	289.0	0.0		263.0	101.0	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	hg19	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	C	31	5.082043	0.94050	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957;ENST00000443501	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.58	5.58	0.84498	.	0.046445	0.85682	D	0.000000	T	0.53514	0.1801	L	0.57536	1.79	0.80722	D	1	D;B	0.67145	0.996;0.409	D;B	0.78314	0.991;0.119	T	0.41466	-0.9507	10	0.34782	T	0.22	-16.8634	19.5677	0.95401	0.0:1.0:0.0:0.0	.	138;138	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	Y	138;138;138;111	ENSP00000411242:H138Y;ENSP00000338523:H138Y;ENSP00000389094:H138Y;ENSP00000389064:H111Y	ENSP00000338523:H138Y	H	+	1	0	FNDC3B	173448164	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.339000	0.65953	2.617000	0.88574	0.655000	0.94253	CAC	.	.		0.502	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		T	171965470	C	T	171965470	3	4	35	1	0	0	0	0	1	0	0	0	5978	478	17	3	426	3	FNDC3B	3	171965470	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	15202136	171965470	26056960	154	4323										
GHSR	2693	hgsc.bcm.edu	37	chr3	172163000	172163000	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cccgagaactttcatctttcAgagtggagagctttctctgg	10	10	4	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:172163000A>G	ENST00000241256.2	-	2	1094	c.1052T>C	c.(1051-1053)cTg>cCg	p.L351P		NM_198407.2	NP_940799.1	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor	351					actin polymerization or depolymerization (GO:0008154)|adult feeding behavior (GO:0008343)|cellular response to insulin stimulus (GO:0032869)|decidualization (GO:0046697)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone secretion (GO:0030252)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin secretion (GO:0046676)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of appetite (GO:0032100)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of hindgut contraction (GO:0043134)|regulation of synapse assembly (GO:0051963)|response to food (GO:0032094)|response to hormone (GO:0009725)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|growth hormone secretagogue receptor activity (GO:0001616)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	33	Ovarian(172;0.00143)|Breast(254;0.197)		Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			TTCATCTTTCAGAGTGGAGAG	0.463																																					p.L351P	Esophageal Squamous(93;641 1401 20883 29581 34638)	Atlas-SNP	.											.	GHSR	104	.	0			c.T1052C						.						87	98	94					3																	172163000		2203	4300	6503	SO:0001583	missense	2693	exon2			TCTTTCAGAGTGG	AY429112	CCDS3218.1, CCDS46959.1	3q26.31	2012-08-08			ENSG00000121853	ENSG00000121853		"GPCR / Class A : Ghrelin receptors"	4267	protein-coding gene	gene with protein product		601898				8688086	Standard	NM_198407		Approved		uc003fib.2	Q92847	OTTHUMG00000156946	ENST00000241256.2:c.1052T>C	chr3.hg19:g.172163000A>G	ENSP00000241256:p.Leu351Pro	84.0	0.0		78.0	4.0	NM_198407	Q14D12|Q6ISR8|Q92848|Q96RJ7	Missense_Mutation	SNP	ENST00000241256.2	hg19	CCDS3218.1	.	.	.	.	.	.	.	.	.	.	A	12.61	1.989569	0.35131	.	.	ENSG00000121853	ENST00000241256	T	0.69175	-0.38	5.91	5.91	0.95273	.	0.515542	0.19252	N	0.118895	T	0.48205	0.1487	N	0.22421	0.69	0.80722	D	1	B	0.31193	0.312	B	0.31290	0.127	T	0.49652	-0.8917	10	0.34782	T	0.22	-8.276	4.4458	0.11597	0.6547:0.1727:0.1726:0.0	.	351	Q92847	GHSR_HUMAN	P	351	ENSP00000241256:L351P	ENSP00000241256:L351P	L	-	2	0	GHSR	173645694	1.000000	0.71417	1.000000	0.80357	0.695000	0.40330	3.789000	0.55454	2.252000	0.74401	0.528000	0.53228	CTG	.	.		0.463	GHSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346728.1	NM_004122		G	172163000	A	G	172163000	3	3	35	1	0	0	0	0	1	0	0	0	6383	188	7	2	52	2	GHSR	3	172163000	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	197530	172163000	25859430	155	4324										
DCUN1D1	54165	hgsc.bcm.edu	37	chr3	182665120	182665120	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggtattgatcgtttatgatgTtcctatttaaaaaacaaaaa	6	4	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:182665120T>C	ENST00000292782.4	-	6	759	c.606A>G	c.(604-606)gaA>gaG	p.E202E	DCUN1D1_ENST00000469954.1_Silent_p.E187E	NM_020640.2	NP_065691.2	Q96GG9	DCNL1_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 1	202	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.					ubiquitin ligase complex (GO:0000151)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			GTTTATGATGTTCCTATTTAA	0.294																																					p.E202E		Atlas-SNP	.											.	DCUN1D1	27	.	0			c.A606G						.						114	109	111					3																	182665120		2200	4298	6498	SO:0001819	synonymous_variant	54165	exon6			ATGATGTTCCTAT	AF292100, AK056335	CCDS3240.1	3q26.3	2013-06-10	2013-06-10		ENSG00000043093	ENSG00000043093			18184	protein-coding gene	gene with protein product	"squamous cell carcinoma related oncogene"	605905	"DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)"			10777668, 15988528	Standard	NM_020640		Approved	RP42, SCRO, DCUN1L1, Tes3, SCCRO	uc003fld.1	Q96GG9	OTTHUMG00000158314	ENST00000292782.4:c.606A>G	chr3.hg19:g.182665120T>C		107.0	0.0		90.0	4.0	NM_020640	B2RB37|Q7L3G9|Q8TEX7|Q9H6M1|Q9HCT3	Silent	SNP	ENST00000292782.4	hg19	CCDS3240.1																																																																																			.	.		0.294	DCUN1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350658.1	NM_020640		C	182665120	T	C	182665120	2	2	35	1	0	0	0	0	0	0	0	1	4315	1722	60	2		2	DCUN1D1	3	182665120	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	10502120	182665120	15357310	156	4325										
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184049876	184049876	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	accttagaacagcctcccagTaagagccaggccatggggac	11	13	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:184049876T>A	ENST00000346169.2	+	32	4889		c.e32+2		EIF4G1_ENST00000427845.1_Splice_Site|EIF4G1_ENST00000434061.2_Splice_Site|EIF4G1_ENST00000414031.1_Splice_Site|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000392537.2_Splice_Site|EIF4G1_ENST00000441154.1_Splice_Site|EIF4G1_ENST00000411531.1_Splice_Site|EIF4G1_ENST00000350481.5_Splice_Site|EIF4G1_ENST00000424196.1_Splice_Site|EIF4G1_ENST00000435046.2_Splice_Site|EIF4G1_ENST00000342981.4_Splice_Site|EIF4G1_ENST00000382330.3_Splice_Site|EIF4G1_ENST00000319274.6_Splice_Site|EIF4G1_ENST00000352767.3_Splice_Site	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1						cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGCCTCCCAGTAAGAGCCAGG	0.572																																					.		Atlas-SNP	.											.	EIF4G1	151	.	0			c.4639+2T>A						.						39	39	39					3																	184049876		2203	4300	6503	SO:0001630	splice_region_variant	1981	exon33			TCCCAGTAAGAGC	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.4618+2T>A	chr3.hg19:g.184049876T>A		88.0	0.0		65.0	4.0	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Splice_Site	SNP	ENST00000346169.2	hg19	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.941711	0.73557	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000382330;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000441154;ENST00000434061;ENST00000435046	.	.	.	4.35	4.35	0.52113	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2405	0.59994	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF4G1	185532570	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	7.502000	0.81614	1.588000	0.49971	0.369000	0.22263	.	.	.		0.572	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	Intron	A	184049876	T	A	184049876	5	1	35	1	0	0	0	0	0	0	1	0	5038	1652	57	4	4738	4	EIF4G1	3	184049876	Splice_Site	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	1384756	184049876	13972554	157	4326										
MAP3K13	9175	hgsc.bcm.edu	37	chr3	185191353	185191353	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	acagtatgggtccttagacaTaccctctgctgagccagtgg	11	11	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr3:185191353T>C	ENST00000265026.3	+	11	2568	c.2234T>C	c.(2233-2235)aTa>aCa	p.I745T	MAP3K13_ENST00000535426.1_Missense_Mutation_p.I601T|MAP3K13_ENST00000446828.1_Missense_Mutation_p.I538T|MAP3K13_ENST00000443863.1_Missense_Mutation_p.I601T|MAP3K13_ENST00000424227.1_Missense_Mutation_p.I745T	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13									p.P746fs*4(1)		NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			TCCTTAGACATACCCTCTGCT	0.562																																					p.I745T		Atlas-SNP	.											.,1	MAP3K13	209	.	1	Insertion - Frameshift(1)	breast(1)	c.T2234C						.						90	93	92					3																	185191353		2203	4300	6503	SO:0001583	missense	9175	exon11			TAGACATACCCTC	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.2234T>C	chr3.hg19:g.185191353T>C	ENSP00000265026:p.Ile745Thr	60.0	0.0		54.0	3.0	NM_004721		Missense_Mutation	SNP	ENST00000265026.3	hg19	CCDS3270.1	.	.	.	.	.	.	.	.	.	.	T	7.644	0.681444	0.14907	.	.	ENSG00000073803	ENST00000446828;ENST00000424227;ENST00000443863;ENST00000535426;ENST00000265026	T;T;T;T;T	0.14022	2.54;2.54;2.54;2.54;2.54	6.08	-12.2	0.00006	.	2.989660	0.00855	N	0.001866	T	0.03695	0.0105	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.31447	-0.9943	10	0.13108	T	0.6	.	2.3442	0.04267	0.1543:0.3369:0.2354:0.2734	.	601;538;745	O43283-4;O43283-5;O43283	.;.;M3K13_HUMAN	T	538;745;601;601;745	ENSP00000411483:I538T;ENSP00000399910:I745T;ENSP00000409325:I601T;ENSP00000439257:I601T;ENSP00000265026:I745T	ENSP00000265026:I745T	I	+	2	0	MAP3K13	186674047	0.000000	0.05858	0.000000	0.03702	0.593000	0.36681	-0.563000	0.05943	-1.687000	0.01437	-0.290000	0.09829	ATA	.	.		0.562	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		C	185191353	T	C	185191353	3	2	35	1	0	0	0	0	1	0	0	0	9256	1406	49	2	2272	2	MAP3K13	3	185191353	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	1141477	185191353	12831077	158	4327										
FGFR3	2261	hgsc.bcm.edu	37	chr4	1805419	1805419	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gctctgctctctctttgtagAcggcgggcgctaacaccacc	10	15	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:1805419A>G	ENST00000260795.2	+	7	1033	c.931A>G	c.(931-933)Acg>Gcg	p.T311A	FGFR3_ENST00000352904.1_Intron|FGFR3_ENST00000481110.2_Splice_Site_p.T311A|FGFR3_ENST00000340107.4_Intron|FGFR3_ENST00000440486.2_Splice_Site_p.T311A|FGFR3_ENST00000412135.2_Intron			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	311	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	CTCTTTGTAGACGGCGGGCGC	0.632		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.T311A		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3	3320	.	0			c.A931G						.						54	52	52					4																	1805419		2200	4300	6500	SO:0001630	splice_region_variant	2261	exon8	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	TTGTAGACGGCGG	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.931-1A>G	chr4.hg19:g.1805419A>G		127.0	0.0		68.0	5.0	NM_000142	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	hg19	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	a	14.77	2.633238	0.47049	.	.	ENSG00000068078	ENST00000481110;ENST00000440486;ENST00000260795;ENST00000507588	T;T;T;T	0.78246	-0.19;-0.19;-0.19;-1.16	4.29	4.29	0.51040	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.320176	0.32444	N	0.006093	T	0.66426	0.2788	L	0.33753	1.03	0.80722	D	1	B;B;B;B	0.25772	0.134;0.068;0.005;0.002	B;B;B;B	0.30029	0.11;0.107;0.021;0.011	T	0.60865	-0.7178	9	.	.	.	.	9.9822	0.41819	0.8297:0.1703:0.0:0.0	.	274;311;311;311	Q8NI15;P22607-4;P22607;F8W9L4	.;.;FGFR3_HUMAN;.	A	311;311;311;97	ENSP00000420533:T311A;ENSP00000414914:T311A;ENSP00000260795:T311A;ENSP00000427289:T97A	.	T	+	1	0	FGFR3	1775217	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.079000	0.76829	1.690000	0.51089	0.459000	0.35465	ACG	.	.		0.632	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	Missense_Mutation	G	1805419	A	G	1805419	5	3	35	1	0	0	0	0	0	0	1	0	5875	289	10	2	1112	2	FGFR3	4	1805419	Splice_Site	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10		1805419	189348857	159	4328										
LETM1	3954	hgsc.bcm.edu	37	chr4	1843301	1843301	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gtccttcaaggacttgagggActtctctactaccgagtcat	9	11	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:1843301A>G	ENST00000302787.2	-	3	663	c.367T>C	c.(367-369)Tcc>Ccc	p.S123P		NM_012318.2	NP_036450.1	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane protein 1	123					cristae formation (GO:0042407)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(2)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	13			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)			GACTTGAGGGACTTCTCTACT	0.607																																					p.S123P		Atlas-SNP	.											LETM1,caecum,carcinoma,0,1	LETM1	48	.	0			c.T367C						.						70	72	72					4																	1843301		2203	4300	6503	SO:0001583	missense	3954	exon3			TGAGGGACTTCTC	AF061025	CCDS3355.1	4p16.3	2013-01-10			ENSG00000168924	ENSG00000168924		"EF-hand domain containing"	6556	protein-coding gene	gene with protein product	"Mdm38 homolog (yeast)"	604407				10486213	Standard	NM_012318		Approved		uc003gdv.3	O95202	OTTHUMG00000121149	ENST00000302787.2:c.367T>C	chr4.hg19:g.1843301A>G	ENSP00000305653:p.Ser123Pro	73.0	0.0		52.0	4.0	NM_012318	B4DED2|Q9UF65	Missense_Mutation	SNP	ENST00000302787.2	hg19	CCDS3355.1	.	.	.	.	.	.	.	.	.	.	A	17.41	3.382222	0.61845	.	.	ENSG00000168924	ENST00000302787;ENST00000417150	.	.	.	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.77525	0.4143	M	0.70275	2.135	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.994	T	0.80527	-0.1343	9	0.72032	D	0.01	-24.0072	14.4179	0.67163	1.0:0.0:0.0:0.0	.	123;123	O95202-3;O95202	.;LETM1_HUMAN	P	123;83	.	ENSP00000305653:S123P	S	-	1	0	LETM1	1813099	1.000000	0.71417	1.000000	0.80357	0.737000	0.42083	8.353000	0.90077	2.004000	0.58718	0.460000	0.39030	TCC	.	.		0.607	LETM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241634.1			G	1843301	A	G	1843301	3	3	35	1	0	0	0	0	1	0	0	0	8743	275	10	2	1900	2	LETM1	4	1843301	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	37882	1843301	189310975	160	4329										
POLN	353497	hgsc.bcm.edu	37	chr4	2210196	2210196	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agaacctcttgatgtctgacTtcttaaagatttaagatcct	6	8	3	5			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:2210196T>C	ENST00000511885.2	-	5	585	c.232A>G	c.(232-234)Agt>Ggt	p.S78G	POLN_ENST00000515357.1_5'UTR|POLN_ENST00000382865.1_Missense_Mutation_p.S78G			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	78					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			GATGTCTGACTTCTTAAAGAT	0.378								DNA polymerases (catalytic subunits)																													p.S78G		Atlas-SNP	.											.	POLN	82	.	0			c.A232G						.						45	47	46					4																	2210196		2202	4300	6502	SO:0001583	missense	353497	exon3			TCTGACTTCTTAA	AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"DNA polymerases"	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.232A>G	chr4.hg19:g.2210196T>C	ENSP00000435506:p.Ser78Gly	78.0	0.0		59.0	4.0	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	hg19	CCDS3360.1	.	.	.	.	.	.	.	.	.	.	T	8.282	0.815687	0.16607	.	.	ENSG00000130997	ENST00000511885;ENST00000382865	T;T	0.46819	0.86;0.86	5.26	1.56	0.23342	.	3.085710	0.00575	N	0.000310	T	0.33381	0.0861	L	0.29908	0.895	0.09310	N	1	P;B	0.39782	0.688;0.435	B;B	0.28849	0.095;0.057	T	0.32851	-0.9891	10	0.62326	D	0.03	-3.4331	5.763	0.18211	0.0:0.4072:0.0:0.5928	.	78;78	E7ERY2;Q7Z5Q5	.;DPOLN_HUMAN	G	78	ENSP00000435506:S78G;ENSP00000372316:S78G	ENSP00000372316:S78G	S	-	1	0	POLN	2179994	0.000000	0.05858	0.068000	0.19968	0.175000	0.22909	0.385000	0.20685	0.326000	0.23384	0.454000	0.30748	AGT	.	.		0.378	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808		C	2210196	T	C	2210196	3	2	35	1	0	0	0	0	1	0	0	0	12216	1609	56	2	2558	2	POLN	4	2210196	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	366895	2210196	188944080	161	4330										
SH3BP2	6452	hgsc.bcm.edu	37	chr4	2824742	2824742	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctgcctccccgcagggcgccTtctccctgagtggctataac	10	17	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:2824742T>C	ENST00000356331.5	+	3	478	c.217T>C	c.(217-219)Ttc>Ctc	p.F73L	SH3BP2_ENST00000389838.2_Missense_Mutation_p.F73L|SH3BP2_ENST00000435136.2_Missense_Mutation_p.F73L|SH3BP2_ENST00000503393.2_Missense_Mutation_p.F130L|SH3BP2_ENST00000511747.1_Missense_Mutation_p.F73L|SH3BP2_ENST00000442312.2_Missense_Mutation_p.F101L|SH3BP2_ENST00000452765.2_Missense_Mutation_p.F73L	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	73	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		GCAGGGCGCCTTCTCCCTGAG	0.657									Cherubism																												p.F130L		Atlas-SNP	.											.	SH3BP2	43	.	0			c.T388C						.						58	53	54					4																	2824742		2203	4300	6503	SO:0001583	missense	6452	exon3	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	GGCGCCTTCTCCC	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	10825	protein-coding gene	gene with protein product		602104	"Cherubism"			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.217T>C	chr4.hg19:g.2824742T>C	ENSP00000348685:p.Phe73Leu	128.0	0.0		95.0	4.0	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Missense_Mutation	SNP	ENST00000356331.5	hg19	CCDS33944.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962250	0.53400	.	.	ENSG00000087266	ENST00000452765;ENST00000389838;ENST00000503219;ENST00000504294;ENST00000508385;ENST00000512014;ENST00000513095;ENST00000442312;ENST00000502260;ENST00000435136;ENST00000511747;ENST00000503393;ENST00000356331	T;T;T;T;T;T;T;T;T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85	4.18	2.95	0.34219	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.74465	0.3720	L	0.49778	1.585	0.46654	D	0.999144	P;D;B;P	0.53619	0.722;0.961;0.435;0.625	B;P;B;B	0.53224	0.338;0.721;0.084;0.266	T	0.75482	-0.3302	10	0.56958	D	0.05	-8.6345	9.4275	0.38590	0.0:0.0905:0.0:0.9095	.	101;101;130;73	B4DT04;B7Z9B6;D6R919;P78314	.;.;.;3BP2_HUMAN	L	73;73;73;73;73;73;73;101;73;73;73;130;73	ENSP00000409746:F73L;ENSP00000374488:F73L;ENSP00000422796:F73L;ENSP00000423275:F73L;ENSP00000424917:F73L;ENSP00000424105:F73L;ENSP00000423823:F73L;ENSP00000388152:F101L;ENSP00000425537:F73L;ENSP00000403231:F73L;ENSP00000424846:F73L;ENSP00000422168:F130L;ENSP00000348685:F73L	ENSP00000348685:F73L	F	+	1	0	SH3BP2	2794540	1.000000	0.71417	1.000000	0.80357	0.622000	0.37654	5.228000	0.65310	1.538000	0.49270	0.402000	0.26972	TTC	.	.		0.657	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023		C	2824742	T	C	2824742	3	2	35	1	0	0	0	0	1	0	0	0	14260	1609	56	2	482	2	SH3BP2	4	2824742	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	614546	2824742	188329534	162	4331										
LAP3	51056	hgsc.bcm.edu	37	chr4	17586728	17586728	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttattgagaagaatctcaaaAgtgctagtagtaaaaccgag	9	5	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:17586728A>G	ENST00000226299.4	+	6	947	c.673A>G	c.(673-675)Agt>Ggt	p.S225G	AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000606142.1_Missense_Mutation_p.S194G	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	225					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						GAATCTCAAAAGTGCTAGTAG	0.453																																					p.S225G		Atlas-SNP	.											.	LAP3	50	.	0			c.A673G						.						98	99	99					4																	17586728		2203	4300	6503	SO:0001583	missense	51056	exon6			CTCAAAAGTGCTA	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"peptidase S"	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.673A>G	chr4.hg19:g.17586728A>G	ENSP00000226299:p.Ser225Gly	110.0	0.0		99.0	4.0	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	hg19	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	A	8.928	0.962686	0.18583	.	.	ENSG00000002549	ENST00000226299;ENST00000513105	T;T	0.44881	0.91;0.99	5.14	1.31	0.21738	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.713801	0.15548	N	0.256569	T	0.17534	0.0421	N	0.02802	-0.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20538	-1.0272	10	0.30854	T	0.27	-0.4062	8.5401	0.33388	0.7614:0.0:0.2386:0.0	.	225	P28838	AMPL_HUMAN	G	225;59	ENSP00000226299:S225G;ENSP00000424724:S59G	ENSP00000226299:S225G	S	+	1	0	LAP3	17195826	0.000000	0.05858	0.002000	0.10522	0.946000	0.59487	0.039000	0.13884	0.061000	0.16311	0.459000	0.35465	AGT	.	.		0.453	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			G	17586728	A	G	17586728	3	3	35	1	0	0	0	0	1	0	0	0	8632	72	3	2	695	2	LAP3	4	17586728	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	14761986	17586728	173567548	163	4332										
TLR6	10333	hgsc.bcm.edu	37	chr4	38830367	38830367	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttgaacctctggtgagttctGataaaaatttaatgaaaact	7	5	2	4			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:38830367G>A	ENST00000381950.1	-	1	793	c.728C>T	c.(727-729)tCa>tTa	p.S243L	TLR6_ENST00000436693.2_Missense_Mutation_p.S243L			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	243					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGTGAGTTCTGATAAAAATTT	0.353																																					p.S243L		Atlas-SNP	.											.	TLR6	67	.	0			c.C728T						.						49	54	52					4																	38830367		2203	4300	6503	SO:0001583	missense	10333	exon2			AGTTCTGATAAAA		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"CD molecules"	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.728C>T	chr4.hg19:g.38830367G>A	ENSP00000371376:p.Ser243Leu	132.0	0.0		86.0	4.0	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	hg19	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	G	0.708	-0.788184	0.02884	.	.	ENSG00000174130	ENST00000436693;ENST00000381950;ENST00000508542	T;T	0.25579	1.79;1.79	5.56	1.98	0.26296	.	0.333724	0.25383	N	0.031061	T	0.11707	0.0285	N	0.12182	0.205	0.18873	N	0.999982	B	0.02656	0.0	B	0.08055	0.003	T	0.35649	-0.9780	10	0.08837	T	0.75	.	10.1964	0.43056	0.323:0.0:0.677:0.0	.	243	Q9Y2C9	TLR6_HUMAN	L	243	ENSP00000389600:S243L;ENSP00000371376:S243L	ENSP00000371376:S243L	S	-	2	0	TLR6	38506762	0.000000	0.05858	0.929000	0.37066	0.044000	0.14063	-0.709000	0.05030	0.050000	0.15949	-0.663000	0.03849	TCA	.	.		0.353	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			A	38830367	G	A	38830367	3	1	35	1	0	0	0	0	1	0	0	0	15970	1294	45	3	1666	3	TLR6	4	38830367	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	21243639	38830367	152323909	164	4333										
PHOX2B	8929	hgsc.bcm.edu	37	chr4	41750513	41750513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gttatactggaagccactggCctggctgcaggaactgaagt	13	9	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:41750513C>T	ENST00000226382.2	-	1	474	c.115G>A	c.(115-117)Gcc>Acc	p.A39T	RP11-227F19.1_ENST00000508038.1_RNA|RP11-227F19.2_ENST00000510602.1_lincRNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	39					autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						AAGCCACTGGCCTGGCTGCAG	0.587			"Mis, F"		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.A39T		Atlas-SNP	.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B	53	.	0			c.G115A						.						35	36	36					4																	41750513		2203	4300	6503	SO:0001583	missense	8929	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CACTGGCCTGGCT	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"Homeoboxes / PRD class"	9143	protein-coding gene	gene with protein product		603851	"paired mesoderm homeobox 2b"	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.115G>A	chr4.hg19:g.41750513C>T	ENSP00000226382:p.Ala39Thr	66.0	0.0		70.0	4.0	NM_003924	Q6PJD9	Missense_Mutation	SNP	ENST00000226382.2	hg19	CCDS3463.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.839351	0.51057	.	.	ENSG00000109132	ENST00000226382	D	0.90732	-2.72	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.81365	0.4807	N	0.03608	-0.345	0.80722	D	1	B	0.26483	0.15	B	0.23419	0.046	T	0.77675	-0.2499	10	0.42905	T	0.14	.	19.4899	0.95046	0.0:1.0:0.0:0.0	.	39	Q99453	PHX2B_HUMAN	T	39	ENSP00000226382:A39T	ENSP00000226382:A39T	A	-	1	0	PHOX2B	41445270	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.582000	0.67477	2.611000	0.88343	0.555000	0.69702	GCC	.	.		0.587	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2			T	41750513	C	T	41750513	3	4	35	1	0	0	0	0	1	0	0	0	11868	739	26	3	841	3	PHOX2B	4	41750513	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	2920146	41750513	149403763	165	4334										
TMPRSS11B	132724	hgsc.bcm.edu	37	chr4	69097023	69097023	+	Frame_Shift_Del	DEL	G	G	-													0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgctggcctgccatggccatGccccctccagggagcttttt							TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:69097023delG	ENST00000332644.5	-	7	745	c.584delC	c.(583-585)gcafs	p.A195fs		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	195	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.A195E(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						CCATGGCCATGCCCCCTCCAG	0.493																																					p.A195fs		Atlas-Indel,Pindel	.											.	TMPRSS11B	66	.	1	Substitution - Missense(1)	skin(1)	c.585delA						.						81	81	81					4																	69097023		2203	4300	6503	SO:0001589	frameshift_variant	132724	exon7			.	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"Serine peptidases / Transmembrane"	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.584delC	chr4.hg19:g.69097023delG	ENSP00000330475:p.Ala195fs	187.0	0.0		241.0	76.0	NM_182502	A8K4D9	Frame_Shift_Del	DEL	ENST00000332644.5	hg19	CCDS3521.1																																																																																			.	.		0.493	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502		-	69097023	G	-	69097023	7	5	35	1	0	1	0	1	0	0	0	0	16255	1319	46	0	682	0	TMPRSS11B	4	69097023	Frame_Shift_Del	DEL	G	TCGA-BC-A10W-01A-11D-A12Z-10	27346510	69097023	122057253	166	4335										
ART3	419	hgsc.bcm.edu	37	chr4	77018798	77018798	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctttatctttgtgtttcaggActaaaaaccgaaaactgtat	6	7	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:77018798A>G	ENST00000355810.4	+	4	902	c.783A>G	c.(781-783)ggA>ggG	p.G261G	ART3_ENST00000341029.5_Splice_Site_p.G261G|ART3_ENST00000349321.3_Splice_Site_p.G261G|AC112719.1_ENST00000582318.1_RNA|ART3_ENST00000513494.1_3'UTR	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	261					protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|stomach(1)	16			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GTGTTTCAGGACTAAAAACCG	0.323																																					p.G261G		Atlas-SNP	.											.	ART3	34	.	0			c.A783G						.						89	101	97					4																	77018798		2203	4299	6502	SO:0001630	splice_region_variant	419	exon4			TTCAGGACTAAAA	X95827	CCDS3575.1, CCDS47079.1, CCDS47080.1	4q21.1	2008-05-15			ENSG00000156219	ENSG00000156219			725	protein-coding gene	gene with protein product		603086				9119374	Standard	NM_001130017		Approved		uc003hjo.3	Q13508	OTTHUMG00000130110	ENST00000355810.4:c.782-1A>G	chr4.hg19:g.77018798A>G		139.0	0.0		97.0	4.0	NM_001130017	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Silent	SNP	ENST00000355810.4	hg19	CCDS47079.1																																																																																			.	.		0.323	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179	Silent	G	77018798	A	G	77018798	5	3	35	1	0	0	0	0	0	0	1	0	998	289	10	2	793	2	ART3	4	77018798	Splice_Site	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	7921775	77018798	114135478	167	4336										
AFF1	4299	hgsc.bcm.edu	37	chr4	88035706	88035706	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agatcctccccctaaaagctCcagcaaagccccccgggccc	7	20	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:88035706C>A	ENST00000307808.6	+	11	2120	c.1700C>A	c.(1699-1701)tCc>tAc	p.S567Y	AFF1_ENST00000544085.1_Missense_Mutation_p.S205Y|AFF1_ENST00000395146.4_Missense_Mutation_p.S574Y	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	567					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		CCTAAAAGCTCCAGCAAAGCC	0.632																																					p.S574Y		Atlas-SNP	.											.	AFF1	102	.	0			c.C1721A						.						9	13	12					4																	88035706		2182	4278	6460	SO:0001583	missense	4299	exon12			AAAGCTCCAGCAA	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.1700C>A	chr4.hg19:g.88035706C>A	ENSP00000305689:p.Ser567Tyr	76.0	0.0		62.0	17.0	NM_001166693	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	hg19	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.983544	0.35036	.	.	ENSG00000172493	ENST00000395146;ENST00000541943;ENST00000307808;ENST00000544085	T;T;T	0.66995	-0.24;-0.24;-0.24	6.04	5.18	0.71444	.	0.319347	0.31636	N	0.007315	T	0.77177	0.4092	M	0.66939	2.045	0.43583	D	0.995929	D;D;D	0.58970	0.984;0.984;0.984	P;P;P	0.62184	0.899;0.865;0.899	T	0.79369	-0.1832	10	0.72032	D	0.01	-8.2015	11.7338	0.51752	0.1392:0.727:0.1338:0.0	.	574;567;567	E9PBM3;Q14C88;P51825	.;.;AFF1_HUMAN	Y	574;226;567;205	ENSP00000378578:S574Y;ENSP00000305689:S567Y;ENSP00000440843:S205Y	ENSP00000305689:S567Y	S	+	2	0	AFF1	88254730	0.343000	0.24818	0.986000	0.45419	0.133000	0.20885	1.907000	0.39897	1.528000	0.49103	0.561000	0.74099	TCC	.	.		0.632	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		A	88035706	C	A	88035706	3	1	35	1	0	0	0	0	1	0	0	0	356	855	30	3	1784	3	AFF1	4	88035706	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	11016908	88035706	103118570	168	4337										
GRID2	2895	hgsc.bcm.edu	37	chr4	94006348	94006348	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	actctctcagttcgcccaccTgtctacttgcatgatgttat	6	13	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:94006348T>G	ENST00000282020.4	+	3	705	c.447T>G	c.(445-447)ccT>ccG	p.P149P	GRID2_ENST00000510992.1_Intron|GRID2_ENST00000505687.1_3'UTR	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	149					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		TTCGCCCACCTGTCTACTTGC	0.458																																					p.P149P		Atlas-SNP	.											.	GRID2	233	.	0			c.T447G						.						107	103	105					4																	94006348		2203	4300	6503	SO:0001819	synonymous_variant	2895	exon3			CCCACCTGTCTAC	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.447T>G	chr4.hg19:g.94006348T>G		193.0	0.0		136.0	53.0	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Silent	SNP	ENST00000282020.4	hg19	CCDS3637.1																																																																																			.	.		0.458	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			G	94006348	T	G	94006348	2	3	35	1	0	0	0	0	0	0	0	1	6781	1567	55	5		5	GRID2	4	94006348	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	5970642	94006348	97147928	169	4338										
PDHA2	5161	hgsc.bcm.edu	37	chr4	96761829	96761829	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cccctgggcgctggcattgcTctggcctgtaaatataaagg	12	11	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:96761829T>C	ENST00000295266.4	+	1	591	c.528T>C	c.(526-528)gcT>gcC	p.A176A		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	176					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		CTGGCATTGCTCTGGCCTGTA	0.502																																					p.A176A		Atlas-SNP	.											.	PDHA2	118	.	0			c.T528C						.						62	66	65					4																	96761829		2203	4300	6503	SO:0001819	synonymous_variant	5161	exon1			CATTGCTCTGGCC		CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.528T>C	chr4.hg19:g.96761829T>C		72.0	0.0		75.0	4.0	NM_005390	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Silent	SNP	ENST00000295266.4	hg19	CCDS3644.1																																																																																			.	.		0.502	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1			C	96761829	T	C	96761829	2	2	35	1	0	0	0	0	0	0	0	1	11674	1538	54	2		2	PDHA2	4	96761829	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	2755481	96761829	94392447	170	4339										
CENPE	1062	hgsc.bcm.edu	37	chr4	104053878	104053878	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgttattaaagaagttattcActtgacaaatcctatcattt	4	6	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:104053878A>T	ENST00000265148.3	-	42	6985	c.6896T>A	c.(6895-6897)gTg>gAg	p.V2299E	CENPE_ENST00000380026.3_Missense_Mutation_p.V2178E	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2299	Kinetochore-binding domain.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		GAAGTTATTCACTTGACAAAT	0.289																																					p.V2299E		Atlas-SNP	.											.	CENPE	253	.	0			c.T6896A						.						71	75	74					4																	104053878		2201	4295	6496	SO:0001583	missense	1062	exon42			TTATTCACTTGAC	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.6896T>A	chr4.hg19:g.104053878A>T	ENSP00000265148:p.Val2299Glu	348.0	0.0		236.0	92.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.016421	0.75161	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.76578	-1.03;-0.98	5.36	5.36	0.76844	.	.	.	.	.	D	0.85340	0.5674	L	0.56769	1.78	0.23537	N	0.997464	D;D	0.89917	1.0;0.998	D;P	0.87578	0.998;0.905	T	0.77086	-0.2718	9	0.66056	D	0.02	.	12.0565	0.53538	1.0:0.0:0.0:0.0	.	2178;2299	Q02224-3;Q02224	.;CENPE_HUMAN	E	2299;2263;2178	ENSP00000265148:V2299E;ENSP00000369365:V2178E	ENSP00000265148:V2299E	V	-	2	0	CENPE	104273327	1.000000	0.71417	0.995000	0.50966	0.925000	0.55904	4.702000	0.61817	2.158000	0.67659	0.523000	0.50628	GTG	.	.		0.289	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	104053878	A	T	104053878	3	4	35	1	0	0	0	0	1	0	0	0	3232	159	6	4	1241	4	CENPE	4	104053878	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	7292049	104053878	87100398	171	4340										
ANK2	287	hgsc.bcm.edu	37	chr4	114274414	114274414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgctgaggaagagccaggagAgccttttgaaatcgttgaaa	13	6	0	5			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:114274414A>G	ENST00000357077.4	+	38	4693	c.4640A>G	c.(4639-4641)gAg>gGg	p.E1547G	ANK2_ENST00000394537.3_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.E1514G|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1547					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GAGCCAGGAGAGCCTTTTGAA	0.448																																					p.E1547G		Atlas-SNP	.											.	ANK2	576	.	0			c.A4640G						.						55	57	56					4																	114274414		2203	4300	6503	SO:0001583	missense	287	exon38			CAGGAGAGCCTTT	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.4640A>G	chr4.hg19:g.114274414A>G	ENSP00000349588:p.Glu1547Gly	121.0	0.0		106.0	5.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.392949	0.62066	.	.	ENSG00000145362	ENST00000503423;ENST00000504454;ENST00000357077;ENST00000264366	T;T;T;T	0.77750	-0.57;-0.74;-1.12;-1.03	5.35	5.35	0.76521	.	0.000000	0.56097	D	0.000036	D	0.87366	0.6159	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.996;0.999	D	0.87899	0.2689	10	0.49607	T	0.09	.	15.3528	0.74402	1.0:0.0:0.0:0.0	.	1514;1547	Q01484;Q01484-4	ANK2_HUMAN;.	G	1460;1562;1547;1514	ENSP00000421011:E1460G;ENSP00000424722:E1562G;ENSP00000349588:E1547G;ENSP00000264366:E1514G	ENSP00000264366:E1514G	E	+	2	0	ANK2	114493863	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.157000	0.94714	2.024000	0.59613	0.528000	0.53228	GAG	.	.		0.448	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114274414	A	G	114274414	3	3	35	1	0	0	0	0	1	0	0	0	621	304	11	2	4855	2	ANK2	4	114274414	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	10220536	114274414	76879862	172	4341										
PDE5A	8654	hgsc.bcm.edu	37	chr4	120549709	120549709	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aacaaagtatgagaaggtaaAgtcccagtgatcgtccagcc	10	9	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:120549709A>G	ENST00000354960.3	-	1	437	c.118T>C	c.(118-120)Ttt>Ctt	p.F40L	PDE5A_ENST00000264805.5_5'Flank|PDE5A_ENST00000394439.1_5'Flank	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	40					blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	GAGAAGGTAAAGTCCCAGTGA	0.562											OREG0016307	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F40L		Atlas-SNP	.											.	PDE5A	83	.	0			c.T118C						.						111	98	103					4																	120549709		2203	4300	6503	SO:0001583	missense	8654	exon1			AGGTAAAGTCCCA	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.118T>C	chr4.hg19:g.120549709A>G	ENSP00000347046:p.Phe40Leu	76.0	0.0	1504	75.0	5.0	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	hg19	CCDS3713.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.097894	0.76870	.	.	ENSG00000138735	ENST00000354960	T	0.71341	-0.56	5.98	5.98	0.97165	.	0.408709	0.28641	N	0.014626	T	0.60843	0.2300	L	0.38692	1.165	0.80722	D	1	B	0.13594	0.008	B	0.06405	0.002	T	0.56080	-0.8038	10	0.16896	T	0.51	.	15.4404	0.75178	1.0:0.0:0.0:0.0	.	40	O76074	PDE5A_HUMAN	L	40	ENSP00000347046:F40L	ENSP00000347046:F40L	F	-	1	0	PDE5A	120769157	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.149000	0.64863	2.288000	0.76882	0.482000	0.46254	TTT	.	.		0.562	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		G	120549709	A	G	120549709	3	3	35	1	0	0	0	0	1	0	0	0	11653	72	3	2	2623	2	PDE5A	4	120549709	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	6275295	120549709	70604567	173	4342										
LARP1B	55132	hgsc.bcm.edu	37	chr4	129127685	129127685	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaagaaaccaaaaaagactaCgaatctggtaacaataacat	6	7	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:129127685C>A	ENST00000326639.6	+	18	2623	c.2412C>A	c.(2410-2412)taC>taA	p.Y804*	LARP1B_ENST00000264584.5_Nonsense_Mutation_p.Y745*|LARP1B_ENST00000354456.3_Nonsense_Mutation_p.Y223*|LARP1B_ENST00000441387.1_Intron|LARP1B_ENST00000506199.1_3'UTR	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	804						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						AAAAAGACTACGAATCTGGTA	0.333																																					p.Y804X		Atlas-SNP	.											.	LARP1B	120	.	0			c.C2412A						.						42	48	46					4																	129127685		2202	4296	6498	SO:0001587	stop_gained	55132	exon18			AGACTACGAATCT		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.2412C>A	chr4.hg19:g.129127685C>A	ENSP00000321997:p.Tyr804*	103.0	0.0		76.0	4.0	NM_018078	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Nonsense_Mutation	SNP	ENST00000326639.6	hg19	CCDS3738.1	.	.	.	.	.	.	.	.	.	.	C	38	6.689746	0.97764	.	.	ENSG00000138709	ENST00000326639;ENST00000264584;ENST00000354456	.	.	.	4.97	-1.63	0.08345	.	0.062930	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.3942	0.49832	0.0:0.3263:0.0:0.6737	.	.	.	.	X	804;745;223	.	ENSP00000264584:Y745X	Y	+	3	2	LARP1B	129347135	0.949000	0.32298	0.992000	0.48379	0.981000	0.71138	0.012000	0.13287	-0.252000	0.09528	-0.367000	0.07326	TAC	.	.		0.333	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		A	129127685	C	A	129127685	4	1	35	1	0	0	0	0	0	1	0	0	8638	547	19	1	2608	1	LARP1B	4	129127685	Nonsense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	8577976	129127685	62026591	174	4343										
GAB1	2549	hgsc.bcm.edu	37	chr4	144378870	144378870	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttaagactcaaaccccatggTttagagcgaactgattcaca	7	10	2	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:144378870T>C	ENST00000262994.4	+	7	1887				GAB1_ENST00000262995.4_Silent_p.G541G|GAB1_ENST00000505913.1_Intron	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1						activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					AACCCCATGGTTTAGAGCGAA	0.348																																					p.G541G		Atlas-SNP	.											.	GAB1	80	.	0			c.T1623C						.						53	48	50					4																	144378870		2203	4300	6503	SO:0001627	intron_variant	2549	exon7			CCATGGTTTAGAG	U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"Pleckstrin homology (PH) domain containing"	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.1586-1668T>C	chr4.hg19:g.144378870T>C		107.0	0.0		94.0	5.0	NM_207123	A8K152|Q4W5G2|Q6P1W2	Silent	SNP	ENST00000262994.4	hg19	CCDS3759.1																																																																																			.	.		0.348	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039		C	144378870	T	C	144378870	1	2	35	0	1	0	0	0	0	0	0	0	6156	1712	60	2		2	GAB1	4	144378870	Intron	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	15251185	144378870	46775406	175	4344										
PRMT10	90826	hgsc.bcm.edu	37	chr4	148563937	148563937	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	acttctcctctagacacttaCctgaaactggttaataaaag	5	10	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:148563937C>T	ENST00000322396.6	-	10	2442		c.e10+1		PRMT10_ENST00000541232.1_Splice_Site|TMEM184C_ENST00000508208.1_Intron	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN								cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						TAGACACTTACCTGAAACTGG	0.408																																					.		Atlas-SNP	.											.	PRMT10	68	.	0			c.2199+1G>A						.						97	98	98					4																	148563937		2203	4300	6503	SO:0001630	splice_region_variant	90826	exon11			CACTTACCTGAAA																												ENST00000322396.6:c.2199+1G>A	chr4.hg19:g.148563937C>T		128.0	0.0		78.0	4.0	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Splice_Site	SNP	ENST00000322396.6	hg19	CCDS3771.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.911053	0.92178	.	.	ENSG00000164169	ENST00000322396;ENST00000541232	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1731	0.98165	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRMT10	148783387	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	6.817000	0.75252	2.768000	0.95171	0.655000	0.94253	.	.	.		0.408	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		Intron	T	148563937	C	T	148563937	5	4	35	1	0	0	0	0	0	0	1	0	12548	521	18	3	349	3	PRMT10	4	148563937	Splice_Site	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	4185067	148563937	42590339	176	4345										
NR3C2	4306	hgsc.bcm.edu	37	chr4	149073680	149073680	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgttcgtatgtttgtacgatCtccagctcaaggcaaatgat	9	8	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:149073680C>A	ENST00000358102.3	-	6	2812	c.2450G>T	c.(2449-2451)aGa>aTa	p.R817I	NR3C2_ENST00000511528.1_Missense_Mutation_p.R821I|NR3C2_ENST00000355292.3_Missense_Mutation_p.R821I|NR3C2_ENST00000503313.1_5'UTR|RP11-76G10.1_ENST00000514843.1_RNA|NR3C2_ENST00000512865.1_Missense_Mutation_p.R700I|NR3C2_ENST00000344721.4_Missense_Mutation_p.R817I	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	817	Steroid-binding.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	TTTGTACGATCTCCAGCTCAA	0.363																																					p.R817I	Melanoma(27;428 957 40335 51025 51111)	Atlas-SNP	.											.	NR3C2	94	.	0			c.G2450T						.						133	131	132					4																	149073680		2203	4300	6503	SO:0001583	missense	4306	exon6			TACGATCTCCAGC	M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.2450G>T	chr4.hg19:g.149073680C>A	ENSP00000350815:p.Arg817Ile	308.0	0.0		234.0	78.0	NM_000901	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Missense_Mutation	SNP	ENST00000358102.3	hg19	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	C	31	5.080490	0.94050	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000511528	D;D;D;D;D	0.96334	-3.98;-3.98;-3.98;-3.98;-3.98	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.98717	0.9569	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99293	1.0899	9	.	.	.	.	19.7686	0.96352	0.0:1.0:0.0:0.0	.	700;817	B0ZBF5;B0ZBF6	.;.	I	817;821;817;700;821	ENSP00000341390:R817I;ENSP00000347441:R821I;ENSP00000350815:R817I;ENSP00000423510:R700I;ENSP00000421481:R821I	.	R	-	2	0	NR3C2	149293130	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.665000	0.90641	0.591000	0.81541	AGA	.	.		0.363	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			A	149073680	C	A	149073680	3	1	35	1	0	0	0	0	1	0	0	0	10640	913	32	3	520	3	NR3C2	4	149073680	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	509743	149073680	42080596	177	4346										
RBM46	166863	hgsc.bcm.edu	37	chr4	155719149	155719149	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gatgtacactacaaaagaagAagcccaattagccatcagaa	7	9	1	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:155719149A>G	ENST00000281722.3	+	3	573	c.338A>G	c.(337-339)gAa>gGa	p.E113G	RBM46_ENST00000514866.1_Missense_Mutation_p.E113G|RBM46_ENST00000510397.1_Missense_Mutation_p.E113G	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	113	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				ACAAAAGAAGAAGCCCAATTA	0.338																																					p.E113G		Atlas-SNP	.											.	RBM46	76	.	0			c.A338G						.						100	107	105					4																	155719149		2203	4300	6503	SO:0001583	missense	166863	exon3			AAGAAGAAGCCCA	BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"RNA binding motif (RRM) containing"	28401	protein-coding gene	gene with protein product	"cancer/testis antigen 68"					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.338A>G	chr4.hg19:g.155719149A>G	ENSP00000281722:p.Glu113Gly	159.0	0.0		100.0	4.0	NM_144979	B3KWU8|B4DZ27	Missense_Mutation	SNP	ENST00000281722.3	hg19	CCDS3790.1	.	.	.	.	.	.	.	.	.	.	A	11.87	1.766891	0.31320	.	.	ENSG00000151962	ENST00000514866;ENST00000281722;ENST00000510397;ENST00000512640	T;T;T;T	0.46819	2.33;0.86;2.33;0.86	5.9	4.65	0.58169	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.202982	0.51477	D	0.000088	T	0.37183	0.0994	L	0.31065	0.9	0.42403	D	0.992578	B;B;B	0.14805	0.011;0.001;0.007	B;B;B	0.19666	0.026;0.016;0.026	T	0.24657	-1.0154	10	0.49607	T	0.09	-21.5981	12.8283	0.57733	0.8639:0.1361:0.0:0.0	.	113;113;113	B4DZ27;B3KWU8;Q8TBY0	.;.;RBM46_HUMAN	G	113	ENSP00000424500:E113G;ENSP00000281722:E113G;ENSP00000422813:E113G;ENSP00000426672:E113G	ENSP00000281722:E113G	E	+	2	0	RBM46	155938599	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.341000	0.52151	2.254000	0.74563	0.460000	0.39030	GAA	.	.		0.338	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979		G	155719149	A	G	155719149	3	3	35	1	0	0	0	0	1	0	0	0	13155	246	9	2	344	2	RBM46	4	155719149	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	6645469	155719149	35435127	178	4347										
GALNTL6	442117	hgsc.bcm.edu	37	chr4	173730521	173730521	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttcctacctagaacacctgaAggataaattggaagaataca	7	8	0	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:173730521A>G	ENST00000506823.1	+	6	1220	c.563A>G	c.(562-564)aAg>aGg	p.K188R	GALNTL6_ENST00000508122.1_Missense_Mutation_p.K171R	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	188	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						GAACACCTGAAGGATAAATTG	0.433																																					p.K188R		Atlas-SNP	.											.	GALNTL6	102	.	0			c.A563G						.						92	90	91					4																	173730521		2203	4300	6503	SO:0001583	missense	442117	exon6			ACCTGAAGGATAA		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.563A>G	chr4.hg19:g.173730521A>G	ENSP00000423313:p.Lys188Arg	171.0	0.0		97.0	4.0	NM_001034845	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	hg19	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	A	10.47	1.359869	0.24598	.	.	ENSG00000174473	ENST00000506823;ENST00000404275;ENST00000508122	T;T	0.61859	0.07;0.07	5.45	5.45	0.79879	Glycosyl transferase, family 2 (1);	0.160836	0.42294	N	0.000734	T	0.53642	0.1809	M	0.64080	1.96	0.53688	D	0.999972	B	0.12013	0.005	B	0.12156	0.007	T	0.54234	-0.8324	10	0.52906	T	0.07	.	10.2026	0.43094	0.9255:0.0:0.0745:0.0	.	188	Q49A17	GLTL6_HUMAN	R	188;188;171	ENSP00000423313:K188R;ENSP00000423827:K171R	ENSP00000385382:K188R	K	+	2	0	GALNTL6	173967096	1.000000	0.71417	0.997000	0.53966	0.138000	0.21146	6.279000	0.72620	2.196000	0.70406	0.402000	0.26972	AAG	.	.		0.433	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		G	173730521	A	G	173730521	3	3	35	1	0	0	0	0	1	0	0	0	6233	72	3	2	581	2	GALNTL6	4	173730521	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	18011372	173730521	17423755	179	4348										
NEIL3	55247	hgsc.bcm.edu	37	chr4	178257425	178257425	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tattgcctggagtagggaacAtcatcaaaaatgaagctctc	9	8	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:178257425A>G	ENST00000264596.3	+	4	695	c.577A>G	c.(577-579)Atc>Gtc	p.I193V		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	193					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		AGTAGGGAACATCATCAAAAA	0.373								Base excision repair (BER), DNA glycosylases																													p.I193V		Atlas-SNP	.											.	NEIL3	89	.	0			c.A577G						.						146	148	147					4																	178257425		2203	4300	6503	SO:0001583	missense	55247	exon4			GGGAACATCATCA	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 3"	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.577A>G	chr4.hg19:g.178257425A>G	ENSP00000264596:p.Ile193Val	174.0	0.0		94.0	4.0	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	hg19	CCDS3828.1	.	.	.	.	.	.	.	.	.	.	A	18.59	3.657674	0.67586	.	.	ENSG00000109674	ENST00000264596	T	0.20200	2.09	4.93	4.93	0.64822	DNA glycosylase/AP lyase, H2TH DNA-binding (1);Ribosomal protein S13-like, H2TH (1);	0.000000	0.85682	D	0.000000	T	0.41166	0.1147	L	0.52823	1.66	0.58432	D	0.999997	D	0.89917	1.0	D	0.81914	0.995	T	0.21586	-1.0241	10	0.59425	D	0.04	-19.4282	14.22	0.65820	1.0:0.0:0.0:0.0	.	193	Q8TAT5	NEIL3_HUMAN	V	193	ENSP00000264596:I193V	ENSP00000264596:I193V	I	+	1	0	NEIL3	178494419	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.484000	0.90445	2.191000	0.70037	0.533000	0.62120	ATC	.	.		0.373	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		G	178257425	A	G	178257425	3	3	35	1	0	0	0	0	1	0	0	0	10329	217	8	2	591	2	NEIL3	4	178257425	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	4526904	178257425	12896851	180	4349										
WWC2	80014	hgsc.bcm.edu	37	chr4	184169911	184169911	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tttcatttggatcagaacatTggcagatctgagccagattt	9	7	3	4			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:184169911T>C	ENST00000403733.3	+	7	976	c.777T>C	c.(775-777)atT>atC	p.I259I	WWC2_ENST00000448232.2_Silent_p.I259I|WWC2_ENST00000504005.1_Intron|WWC2_ENST00000378925.3_Silent_p.I161I|WWC2_ENST00000513834.1_Silent_p.I259I	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	259					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		ATCAGAACATTGGCAGATCTG	0.433																																					p.I259I		Atlas-SNP	.											.	WWC2	78	.	0			c.T777C						.						91	86	87					4																	184169911		2203	4300	6503	SO:0001819	synonymous_variant	80014	exon7			GAACATTGGCAGA	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.777T>C	chr4.hg19:g.184169911T>C		116.0	0.0		97.0	5.0	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Silent	SNP	ENST00000403733.3	hg19	CCDS34109.2																																																																																			.	.		0.433	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		C	184169911	T	C	184169911	2	2	35	1	0	0	0	0	0	0	0	1	17427	1800	63	2		2	WWC2	4	184169911	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	5912486	184169911	6984365	181	4350										
UFSP2	55325	hgsc.bcm.edu	37	chr4	186336995	186336995	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agggaggttgacatttccagCataagatctatatttactat	8	6	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:186336995C>T	ENST00000264689.6	-	5	476	c.360G>A	c.(358-360)atG>atA	p.M120I	Y_RNA_ENST00000384502.1_RNA|UFSP2_ENST00000502282.1_Intron	NM_018359.3	NP_060829.2	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2	120						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	small conjugating protein-specific protease activity (GO:0019783)|thiolester hydrolase activity (GO:0016790)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;3.4e-25)|Epithelial(43;2.23e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;8.1e-05)|GBM - Glioblastoma multiforme(59;0.000148)|STAD - Stomach adenocarcinoma(60;0.000782)|LUSC - Lung squamous cell carcinoma(40;0.00939)|COAD - Colon adenocarcinoma(29;0.0108)|READ - Rectum adenocarcinoma(43;0.166)		ACATTTCCAGCATAAGATCTA	0.348																																					p.M120I		Atlas-SNP	.											.	UFSP2	33	.	0			c.G360A						.						76	69	71					4																	186336995		2203	4300	6503	SO:0001583	missense	55325	exon5			TTCCAGCATAAGA	AK002062	CCDS3842.1	4q35.1	2008-03-25	2008-03-25	2008-03-25	ENSG00000109775	ENSG00000109775			25640	protein-coding gene	gene with protein product		611482	"chromosome 4 open reading frame 20"	C4orf20		17182609	Standard	NM_018359		Approved	FLJ11200	uc003ixo.2	Q9NUQ7	OTTHUMG00000160441	ENST00000264689.6:c.360G>A	chr4.hg19:g.186336995C>T	ENSP00000264689:p.Met120Ile	126.0	0.0		79.0	4.0	NM_018359	Q6IA77|Q96FS3	Missense_Mutation	SNP	ENST00000264689.6	hg19	CCDS3842.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.76|16.76	3.211299|3.211299	0.58343|0.58343	.|.	.|.	ENSG00000109775|ENSG00000109775	ENST00000511485|ENST00000264689;ENST00000505357	.|T;T	.|0.52754	.|1.56;0.65	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	.|0.043790	.|0.85682	.|D	.|0.000000	T|T	0.41581|0.41581	0.1165|0.1165	L|L	0.59436|0.59436	1.845|1.845	0.39946|0.39946	D|D	0.974478|0.974478	.|P;B	.|0.35844	.|0.524;0.162	.|B;B	.|0.27887	.|0.084;0.03	T|T	0.50013|0.50013	-0.8877|-0.8877	5|10	.|0.66056	.|D	.|0.02	-17.3221|-17.3221	12.4411|12.4411	0.55625|0.55625	0.0:0.9219:0.0:0.0781|0.0:0.9219:0.0:0.0781	.|.	.|120;20	.|Q9NUQ7;B3KRI4	.|UFSP2_HUMAN;.	T|I	34|120;114	.|ENSP00000264689:M120I;ENSP00000423108:M114I	.|ENSP00000264689:M120I	A|M	-|-	1|3	0|0	UFSP2|UFSP2	186573989|186573989	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.729000|3.729000	0.54999|0.54999	2.665000|2.665000	0.90641|0.90641	0.655000|0.655000	0.94253|0.94253	GCT|ATG	.	.		0.348	UFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360589.2	NM_018359		T	186336995	C	T	186336995	3	4	35	1	0	0	0	0	1	0	0	0	16953	710	25	3	1081	3	UFSP2	4	186336995	Missense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	2167084	186336995	4817281	182	4351										
FAT1	2195	hgsc.bcm.edu	37	chr4	187541014	187541014	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gccgggtgggcctcaaagtcCagaggagctatgacattgat	14	9	1	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr4:187541014C>T	ENST00000441802.2	-	10	6935	c.6726G>A	c.(6724-6726)ctG>ctA	p.L2242L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2242	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CCTCAAAGTCCAGAGGAGCTA	0.488										HNSCC(5;0.00058)																											p.L2242L	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G6726A						.						145	151	149					4																	187541014		2037	4215	6252	SO:0001819	synonymous_variant	2195	exon10			AAAGTCCAGAGGA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.6726G>A	chr4.hg19:g.187541014C>T		168.0	0.0		76.0	4.0	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.488	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187541014	C	T	187541014	2	4	35	1	0	0	0	0	0	0	0	1	5697	581	21	3		3	FAT1	4	187541014	Silent	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	1204019	187541014	3613262	183	4352										
SLC9A3	6550	hgsc.bcm.edu	37	chr5	488453	488453	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cggtgactgcgtcgttcagcAgcgactccccgaagacgatg	13	13	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:488453A>G	ENST00000264938.3	-	3	662	c.653T>C	c.(652-654)cTg>cCg	p.L218P	SLC9A3_ENST00000514375.1_Missense_Mutation_p.L218P	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	218					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			GTCGTTCAGCAGCGACTCCCC	0.672																																					p.L218P		Atlas-SNP	.											.	SLC9A3	89	.	0			c.T653C						.						69	63	65					5																	488453		2202	4300	6502	SO:0001583	missense	6550	exon3			TTCAGCAGCGACT		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.653T>C	chr5.hg19:g.488453A>G	ENSP00000264938:p.Leu218Pro	84.0	0.0		89.0	4.0	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	hg19	CCDS3855.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.706543	0.89018	.	.	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.19669	2.13;2.13	4.64	4.64	0.57946	Cation/H+ exchanger (1);	0.000000	0.64402	D	0.000001	T	0.55065	0.1897	M	0.93016	3.37	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.79784	0.993;0.955	T	0.67757	-0.5588	10	0.87932	D	0	.	14.0411	0.64676	1.0:0.0:0.0:0.0	.	218;218	E9PF67;P48764	.;SL9A3_HUMAN	P	218	ENSP00000264938:L218P;ENSP00000422983:L218P	ENSP00000264938:L218P	L	-	2	0	SLC9A3	541453	1.000000	0.71417	0.970000	0.41538	0.869000	0.49853	8.952000	0.93031	1.851000	0.53745	0.459000	0.35465	CTG	.	.		0.672	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		G	488453	A	G	488453	3	3	35	1	0	0	0	0	1	0	0	0	14728	188	7	2	1911	2	SLC9A3	5	488453	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10		488453	180426807	184	4353										
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9119234	9119234	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gcagggagaccacgaggtccAgggagtccagcctccgttcc	14	14	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:9119234A>G	ENST00000382496.5	-	15	2466	c.1801T>C	c.(1801-1803)Tgg>Cgg	p.W601R		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	601	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						CACGAGGTCCAGGGAGTCCAG	0.647																																					p.W601R		Atlas-SNP	.											.	SEMA5A	236	.	0			c.T1801C						.						54	49	51					5																	9119234		2203	4300	6503	SO:0001583	missense	9037	exon15			AGGTCCAGGGAGT	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1801T>C	chr5.hg19:g.9119234A>G	ENSP00000371936:p.Trp601Arg	122.0	0.0		140.0	7.0	NM_003966	D3DTC6|O60408|Q1RLL9	Missense_Mutation	SNP	ENST00000382496.5	hg19	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.649576	0.67358	.	.	ENSG00000112902	ENST00000382496	T	0.64085	-0.08	5.35	4.18	0.49190	.	0.000000	0.85682	D	0.000000	D	0.85483	0.5707	H	0.98426	4.23	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.87282	0.2293	10	0.87932	D	0	.	9.4575	0.38764	0.9152:0.0:0.0848:0.0	.	601	Q13591	SEM5A_HUMAN	R	601	ENSP00000371936:W601R	ENSP00000371936:W601R	W	-	1	0	SEMA5A	9172234	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	8.969000	0.93411	0.868000	0.35678	0.455000	0.32223	TGG	.	.		0.647	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			G	9119234	A	G	9119234	3	3	35	1	0	0	0	0	1	0	0	0	14052	188	7	2	1459	2	SEMA5A	5	9119234	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	8630781	9119234	171796026	185	4354										
TRIO	7204	hgsc.bcm.edu	37	chr5	14474101	14474101	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tatcataactgtttaattgtAgggctacatggcacttatga	8	6	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:14474101A>G	ENST00000344204.4	+	40	6003		c.e40-1		TRIO_ENST00000537187.1_Splice_Site	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor						apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					GTTTAATTGTAGGGCTACATG	0.383																																					.		Atlas-SNP	.											.	TRIO	305	.	0			c.5980-2A>G						.						136	116	123					5																	14474101		2203	4300	6503	SO:0001630	splice_region_variant	7204	exon40			AATTGTAGGGCTA	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.5980-1A>G	chr5.hg19:g.14474101A>G		110.0	0.0		92.0	4.0	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Splice_Site	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	A	17.85	3.491429	0.64074	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206;ENST00000541447	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4933	0.75629	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TRIO	14527101	1.000000	0.71417	0.911000	0.35937	0.885000	0.51271	9.221000	0.95188	2.064000	0.61679	0.460000	0.39030	.	.	.		0.383	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	Intron	G	14474101	A	G	14474101	5	3	35	1	0	0	0	0	0	0	1	0	16567	434	15	2	6136	2	TRIO	5	14474101	Splice_Site	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	5354867	14474101	166441159	186	4355										
TRIO	7204	hgsc.bcm.edu	37	chr5	14502746	14502746	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	aactttgactccttctacagTgaagtggctgagcttggcag	11	9	1	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:14502746T>C	ENST00000344204.4	+	54	8415	c.8391T>C	c.(8389-8391)agT>agC	p.S2797S	TRIO_ENST00000537187.1_Silent_p.S2621S|TRIO_ENST00000344135.5_Silent_p.S296S	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2797	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CCTTCTACAGTGAAGTGGCTG	0.522																																					p.S2797S		Atlas-SNP	.											.	TRIO	305	.	0			c.T8391C						.						141	112	122					5																	14502746		2203	4300	6503	SO:0001819	synonymous_variant	7204	exon54			CTACAGTGAAGTG	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.8391T>C	chr5.hg19:g.14502746T>C		60.0	0.0		69.0	5.0	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	hg19	CCDS3883.1																																																																																			.	.		0.522	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		C	14502746	T	C	14502746	2	2	35	1	0	0	0	0	0	0	0	1	16567	1693	59	2		2	TRIO	5	14502746	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	28645	14502746	166412514	187	4356										
TRIO	7204	hgsc.bcm.edu	37	chr5	14508302	14508302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctttaaaggagtgagccagaAggccaaggagttcgtgtgct	14	7	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:14508302A>G	ENST00000344204.4	+	57	9089	c.9065A>G	c.(9064-9066)aAg>aGg	p.K3022R	TRIO_ENST00000537187.1_Missense_Mutation_p.K2846R|TRIO_ENST00000344135.5_Missense_Mutation_p.K521R	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	3022	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					GTGAGCCAGAAGGCCAAGGAG	0.602																																					p.K3022R		Atlas-SNP	.											.	TRIO	305	.	0			c.A9065G						.						88	95	92					5																	14508302		2203	4300	6503	SO:0001583	missense	7204	exon57			GCCAGAAGGCCAA	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.9065A>G	chr5.hg19:g.14508302A>G	ENSP00000339299:p.Lys3022Arg	90.0	0.0		64.0	4.0	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.668093	0.29604	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000344135	T;T;T	0.65549	-0.16;-0.16;-0.16	5.72	1.93	0.25924	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.184175	0.48286	N	0.000198	T	0.42607	0.1210	N	0.17312	0.475	0.20307	N	0.999912	B	0.30236	0.274	B	0.37304	0.246	T	0.30822	-0.9965	10	0.16896	T	0.51	.	6.4663	0.21983	0.7261:0.1315:0.1424:0.0	.	3022	O75962	TRIO_HUMAN	R	3022;2846;521	ENSP00000339299:K3022R;ENSP00000446348:K2846R;ENSP00000339291:K521R	ENSP00000339291:K521R	K	+	2	0	TRIO	14561302	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	1.885000	0.39678	0.085000	0.17107	-0.256000	0.11100	AAG	.	.		0.602	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		G	14508302	A	G	14508302	3	3	35	1	0	0	0	0	1	0	0	0	16567	72	3	2	9291	2	TRIO	5	14508302	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	5556	14508302	166406958	188	4357										
ZFR	51663	hgsc.bcm.edu	37	chr5	32444759	32444759	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gaaactacagggcatatgggAatcatgggctcgggctgctg	15	8	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:32444759A>C	ENST00000265069.8	-	1	108	c.6T>G	c.(4-6)atT>atG	p.I2M		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	2					multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		GGCATATGGGAATCATGGGCT	0.672																																					p.I2M		Atlas-SNP	.											.	ZFR	98	.	0			c.T6G						.						79	79	79					5																	32444759		2195	4290	6485	SO:0001583	missense	51663	exon1			TATGGGAATCATG	AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.6T>G	chr5.hg19:g.32444759A>C	ENSP00000265069:p.Ile2Met	223.0	0.0		326.0	36.0	NM_016107	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	hg19	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.397754	0.62177	.	.	ENSG00000056097	ENST00000265069;ENST00000416900	T	0.07021	3.23	4.59	4.59	0.56863	.	0.064020	0.64402	D	0.000009	T	0.08537	0.0212	N	0.22421	0.69	0.52099	D	0.999945	P;B	0.38565	0.637;0.232	B;B	0.41813	0.367;0.147	T	0.19031	-1.0318	10	0.87932	D	0	.	12.5026	0.55964	1.0:0.0:0.0:0.0	.	2;2	B2RNR6;Q96KR1	.;ZFR_HUMAN	M	2	ENSP00000265069:I2M	ENSP00000265069:I2M	I	-	3	3	ZFR	32480516	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.867000	0.75511	1.822000	0.53115	0.454000	0.30748	ATT	.	.		0.672	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			C	32444759	A	C	32444759	3	2	35	1	0	0	0	0	1	0	0	0	17674	242	9	5	3298	5	ZFR	5	32444759	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	17936457	32444759	148470501	189	4358										
RICTOR	253260	hgsc.bcm.edu	37	chr5	38978735	38978735	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tgtctgtagtgaaaatcagtAtagggtgctaaaattctcta	9	5	3	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:38978735A>T	ENST00000357387.3	-	9	801	c.771T>A	c.(769-771)taT>taA	p.Y257*	RICTOR_ENST00000296782.5_Nonsense_Mutation_p.Y257*	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					GAAAATCAGTATAGGGTGCTA	0.289																																					p.Y257X		Atlas-SNP	.											.	RICTOR	182	.	0			c.T771A						.						52	56	54					5																	38978735		2203	4296	6499	SO:0001587	stop_gained	253260	exon9			ATCAGTATAGGGT		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.771T>A	chr5.hg19:g.38978735A>T	ENSP00000349959:p.Tyr257*	92.0	0.0		99.0	4.0	NM_152756		Nonsense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	A	34	5.338480	0.95783	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	.	.	.	5.69	3.25	0.37280	.	0.055706	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.8045	7.6001	0.28071	0.6406:0.0:0.3594:0.0	.	.	.	.	X	257	.	ENSP00000296782:Y257X	Y	-	3	2	RICTOR	39014492	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.739000	0.47409	0.410000	0.25675	0.377000	0.23210	TAT	.	.		0.289	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		T	38978735	A	T	38978735	4	4	35	1	0	0	0	0	0	1	0	0	13373	456	16	4	4475	4	RICTOR	5	38978735	Nonsense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	6533976	38978735	141936525	190	4359										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54674959	54674959	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ttttctttctttttaggtaaAgaatgaaggagatgactttg	9	3	2	4			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:54674959A>G	ENST00000230640.5	+	18	2242	c.1988A>G	c.(1987-1989)aAg>aGg	p.K663R	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.K562R	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	663					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TTTTAGGTAAAGAATGAAGGA	0.313																																					p.K663R	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.A1988G						.						45	50	48					5																	54674959		2203	4298	6501	SO:0001583	missense	23517	exon18			AGGTAAAGAATGA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.1988A>G	chr5.hg19:g.54674959A>G	ENSP00000230640:p.Lys663Arg	32.0	0.0		36.0	4.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	hg19	CCDS3967.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.082615	0.36758	.	.	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.30448	1.53;1.53	5.61	5.61	0.85477	.	0.048228	0.85682	D	0.000000	T	0.20495	0.0493	N	0.16833	0.445	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.004	T	0.07385	-1.0775	10	0.17369	T	0.5	-17.457	15.4537	0.75297	1.0:0.0:0.0:0.0	.	562;663	F5H7E2;P42285	.;SK2L2_HUMAN	R	663;562	ENSP00000230640:K663R;ENSP00000442583:K562R	ENSP00000230640:K663R	K	+	2	0	SKIV2L2	54710716	1.000000	0.71417	0.992000	0.48379	0.916000	0.54674	8.015000	0.88690	2.134000	0.65973	0.528000	0.53228	AAG	.	.		0.313	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			G	54674959	A	G	54674959	3	3	35	1	0	0	0	0	1	0	0	0	14375	72	3	2	2058	2	SKIV2L2	5	54674959	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	15696224	54674959	126240301	191	4360										
RGS7BP	401190	hgsc.bcm.edu	37	chr5	63802520	63802520	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cgctcctcgatcttccagatCagcaagcccccgctgcagag	9	17	2	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:63802520C>A	ENST00000334025.2	+	1	395	c.69C>A	c.(67-69)atC>atA	p.I23I	RGS7BP_ENST00000508162.1_3'UTR	NM_001029875.1|NM_001271890.1|NM_001271891.1	NP_001025046.1|NP_001258819.1|NP_001258820.1	Q6MZT1	R7BP_HUMAN	regulator of G-protein signaling 7 binding protein	23					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|stomach(1)	11		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)		TCTTCCAGATCAGCAAGCCCC	0.637																																					p.I23I		Atlas-SNP	.											.	RGS7BP	32	.	0			c.C69A						.						29	39	35					5																	63802520		2203	4300	6503	SO:0001819	synonymous_variant	401190	exon1			CCAGATCAGCAAG	BX640900	CCDS34170.1	5q12.3	2008-02-05	2007-08-14		ENSG00000186479	ENSG00000186479			23271	protein-coding gene	gene with protein product		610890	"regulator of G-protein signalling 7 binding protein"			15632198	Standard	NM_001271890		Approved	R7BP	uc003jtj.4	Q6MZT1	OTTHUMG00000162293	ENST00000334025.2:c.69C>A	chr5.hg19:g.63802520C>A		84.0	0.0		115.0	5.0	NM_001029875	B7Z3X1	Silent	SNP	ENST00000334025.2	hg19	CCDS34170.1																																																																																			.	.		0.637	RGS7BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368464.1	NM_001029875		A	63802520	C	A	63802520	2	1	35	1	0	0	0	0	0	0	0	1	13326	816	29	3		3	RGS7BP	5	63802520	Silent	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	9127561	63802520	117112740	192	4361										
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64558682	64558682	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cttagggatgaggagacgccTcccccgcaggtcctgctgca	13	14	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:64558682T>C								ADAMTS6 (64090 upstream) : ADAMTS6 (34352 downstream)																							AGGAGACGCCTCCCCCGCAGG	0.537																																					p.G576G		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.A1728G						.						49	42	44					5																	64558682		2203	4300	6503	SO:0001628	intergenic_variant	11174	exon13			GACGCCTCCCCCG																													chr5.hg19:g.64558682T>C		53.0	0.0		88.0	4.0	NM_197941		Silent	SNP		hg19																																																																																				.	.	0	0.537									C	64558682	T	C	64558682	1	2	35	0	1	0	0	0	0	0	0	0	270	1538	54	2		2	ADAMTS6	5	64558682	IGR	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	756162	64558682	116356578	193	4362										
CCNB1	891	hgsc.bcm.edu	37	chr5	68467214	68467214	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	atgatgtggatgcagaagatGgagctgatccaaacctttgt	12	6	0	4			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:68467214G>A	ENST00000256442.5	+	4	734	c.481G>A	c.(481-483)Gga>Aga	p.G161R		NM_031966.3	NP_114172.1	P14635	CCNB1_HUMAN	cyclin B1	161					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to iron(III) ion (GO:0071283)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle checkpoint (GO:0071174)|mitotic spindle stabilization (GO:0043148)|negative regulation of gene expression (GO:0010629)|negative regulation of protein phosphorylation (GO:0001933)|oocyte maturation (GO:0001556)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of chromosome condensation (GO:0060623)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to DDT (GO:0046680)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|spermatogenesis (GO:0007283)|tissue regeneration (GO:0042246)|ventricular cardiac muscle cell development (GO:0055015)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase activity (GO:0016301)|patched binding (GO:0005113)|protein kinase binding (GO:0019901)			large_intestine(2)|lung(5)|skin(1)	8		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TGCAGAAGATGGAGCTGATCC	0.388																																					p.G161R		Atlas-SNP	.											.	CCNB1	36	.	0			c.G481A						.						145	143	143					5																	68467214		2203	4300	6503	SO:0001583	missense	891	exon4			GAAGATGGAGCTG	U22364	CCDS3997.1	5q12	2008-07-18			ENSG00000134057	ENSG00000134057			1579	protein-coding gene	gene with protein product	"G2/mitotic-specific cyclin B1"	123836		CCNB		1386342	Standard	NM_031966		Approved		uc003jvm.3	P14635	OTTHUMG00000097817	ENST00000256442.5:c.481G>A	chr5.hg19:g.68467214G>A	ENSP00000256442:p.Gly161Arg	237.0	0.0		286.0	88.0	NM_031966	A8K066|Q5TZP9	Missense_Mutation	SNP	ENST00000256442.5	hg19	CCDS3997.1	.	.	.	.	.	.	.	.	.	.	G	11.31	1.601127	0.28534	.	.	ENSG00000134057	ENST00000256442;ENST00000506572;ENST00000508407;ENST00000505500	T;T;T;T	0.31510	2.78;2.78;1.49;2.56	5.62	4.56	0.56223	Cyclin-like (1);	0.330907	0.32301	N	0.006291	T	0.29256	0.0728	L	0.56769	1.78	0.32326	N	0.56171	P;B;B	0.41475	0.751;0.01;0.001	B;B;B	0.41723	0.365;0.007;0.007	T	0.28427	-1.0044	10	0.24483	T	0.36	.	9.1402	0.36899	0.0875:0.0:0.7618:0.1507	.	161;161;161	E9PC90;Q5TZP9;P14635	.;.;CCNB1_HUMAN	R	161	ENSP00000256442:G161R;ENSP00000423387:G161R;ENSP00000426092:G161R;ENSP00000424588:G161R	ENSP00000256442:G161R	G	+	1	0	CCNB1	68502970	0.140000	0.22579	1.000000	0.80357	0.892000	0.51952	1.519000	0.35888	2.640000	0.89533	0.591000	0.81541	GGA	.	.		0.388	CCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215084.1	NM_031966		A	68467214	G	A	68467214	3	1	35	1	0	0	0	0	1	0	0	0	2913	1349	47	3	495	3	CCNB1	5	68467214	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	3908532	68467214	112448046	194	4363										
VCAN	1462	hgsc.bcm.edu	37	chr5	82807955	82807955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cctcactgtccccagtaaatTcaccttcgaggaggctgcaa	8	14	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:82807955T>C	ENST00000265077.3	+	6	1347	c.782T>C	c.(781-783)tTc>tCc	p.F261S	VCAN_ENST00000512590.2_Missense_Mutation_p.F213S|VCAN_ENST00000342785.4_Missense_Mutation_p.F261S|VCAN_ENST00000513984.1_Missense_Mutation_p.F261S|VCAN_ENST00000343200.5_Missense_Mutation_p.F261S|VCAN_ENST00000502527.2_Missense_Mutation_p.F261S	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	261	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CCCAGTAAATTCACCTTCGAG	0.473																																					p.F261S		Atlas-SNP	.											.	VCAN	498	.	0			c.T782C						.						57	55	55					5																	82807955		2203	4300	6503	SO:0001583	missense	1462	exon6			GTAAATTCACCTT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.782T>C	chr5.hg19:g.82807955T>C	ENSP00000265077:p.Phe261Ser	59.0	0.0		65.0	5.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470943	0.63625	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000513960;ENST00000513984;ENST00000502527	T;T;T;T;T;T;T	0.09163	3.01;3.01;3.01;3.01;3.01;3.01;3.01	5.49	5.49	0.81192	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.189449	0.31697	N	0.007216	T	0.31857	0.0810	M	0.67569	2.06	0.42692	D	0.993584	D;B;D;D;P	0.76494	0.995;0.145;0.999;0.993;0.7	D;B;D;D;P	0.75020	0.942;0.164;0.943;0.985;0.532	T	0.03898	-1.0994	10	0.87932	D	0	.	15.5685	0.76313	0.0:0.0:0.0:1.0	.	261;261;261;261;261	P13611-3;P13611-4;P13611-2;P13611;Q86W61	.;.;.;CSPG2_HUMAN;.	S	261;261;261;213;261;261;261	ENSP00000265077:F261S;ENSP00000340062:F261S;ENSP00000342768:F261S;ENSP00000425959:F213S;ENSP00000426251:F261S;ENSP00000426715:F261S;ENSP00000421362:F261S	ENSP00000265077:F261S	F	+	2	0	VCAN	82843711	0.999000	0.42202	0.976000	0.42696	0.035000	0.12851	7.992000	0.88273	2.078000	0.62432	0.460000	0.39030	TTC	.	.		0.473	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		C	82807955	T	C	82807955	3	2	35	1	0	0	0	0	1	0	0	0	17153	1783	62	2	800	2	VCAN	5	82807955	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	14340741	82807955	98107305	195	4364										
MCTP1	79772	hgsc.bcm.edu	37	chr5	94224673	94224673	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggttgtgaaatatcctcaatGggctctgaaagaccccaaca	9	10	2	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:94224673G>A	ENST00000515393.1	-	12	1843	c.1844C>T	c.(1843-1845)cCa>cTa	p.P615L	MCTP1_ENST00000429576.2_Missense_Mutation_p.P348L|MCTP1_ENST00000312216.8_Missense_Mutation_p.P394L|MCTP1_ENST00000505208.1_Missense_Mutation_p.P394L|MCTP1_ENST00000505078.1_Missense_Mutation_p.P131L	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	615	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		TATCCTCAATGGGCTCTGAAA	0.428																																					p.P615L		Atlas-SNP	.											.	MCTP1	110	.	0			c.C1844T						.						75	78	77					5																	94224673		2203	4300	6503	SO:0001583	missense	79772	exon12			CTCAATGGGCTCT		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.1844C>T	chr5.hg19:g.94224673G>A	ENSP00000424126:p.Pro615Leu	91.0	0.0		108.0	5.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Missense_Mutation	SNP	ENST00000515393.1	hg19	CCDS34203.1	.	.	.	.	.	.	.	.	.	.	G	6.028	0.373600	0.11409	.	.	ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000505078;ENST00000312216;ENST00000508509;ENST00000512425;ENST00000505208;ENST00000506568	T;T;T;T;T;T;T;T	0.78126	-1.15;-0.85;-0.13;-1.02;-0.84;-0.96;-1.13;-0.76	5.65	5.65	0.86999	.	0.064498	0.64402	D	0.000008	T	0.41880	0.1178	N	0.00642	-1.3	0.48040	D	0.999578	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.09377	0.003;0.004;0.001	T	0.53005	-0.8499	10	0.07030	T	0.85	-10.2496	8.0979	0.30840	0.1905:0.0:0.8095:0.0	.	615;348;394	Q6DN14;Q6DN14-3;Q6DN14-2	MCTP1_HUMAN;.;.	L	615;348;131;394;335;276;394;216	ENSP00000424126:P615L;ENSP00000391639:P348L;ENSP00000426417:P131L;ENSP00000308957:P394L;ENSP00000423410:P335L;ENSP00000431075:P276L;ENSP00000426438:P394L;ENSP00000426294:P216L	ENSP00000308957:P394L	P	-	2	0	MCTP1	94250429	1.000000	0.71417	0.987000	0.45799	0.933000	0.57130	4.022000	0.57203	2.824000	0.97209	0.655000	0.94253	CCA	.	.		0.428	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		A	94224673	G	A	94224673	3	1	35	1	0	0	0	0	1	0	0	0	9409	1348	47	3	1203	3	MCTP1	5	94224673	Missense_Mutation	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	11416718	94224673	86690587	196	4365										
FTMT	94033	hgsc.bcm.edu	37	chr5	121187671	121187671	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gcggcgctatgctgtcctgcTtcaggctcctctccaggcac	11	16	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:121187671T>C	ENST00000321339.1	+	1	22	c.13T>C	c.(13-15)Ttc>Ctc	p.F5L		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	5					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		GCTGTCCTGCTTCAGGCTCCT	0.692																																					p.F5L		Atlas-SNP	.											.	FTMT	71	.	0			c.T13C						.						31	35	34					5																	121187671		2201	4297	6498	SO:0001583	missense	94033	exon1			TCCTGCTTCAGGC	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.13T>C	chr5.hg19:g.121187671T>C	ENSP00000313691:p.Phe5Leu	60.0	0.0		76.0	4.0	NM_177478		Missense_Mutation	SNP	ENST00000321339.1	hg19	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.282230	0.40394	.	.	ENSG00000181867	ENST00000321339	T	0.67865	-0.29	3.1	1.94	0.25998	.	.	.	.	.	T	0.46889	0.1416	L	0.27053	0.805	0.09310	N	1	B	0.29037	0.231	B	0.19391	0.025	T	0.32771	-0.9894	9	0.44086	T	0.13	.	4.7468	0.13042	0.0:0.1469:0.0:0.8531	.	5	Q8N4E7	FTMT_HUMAN	L	5	ENSP00000313691:F5L	ENSP00000313691:F5L	F	+	1	0	FTMT	121215570	0.001000	0.12720	0.017000	0.16124	0.113000	0.19764	0.358000	0.20216	0.577000	0.29470	0.528000	0.53228	TTC	.	.		0.692	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		C	121187671	T	C	121187671	3	2	35	1	0	0	0	0	1	0	0	0	6093	1609	56	2	15	2	FTMT	5	121187671	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	26962998	121187671	59727589	197	4366										
LEAP2	116842	hgsc.bcm.edu	37	chr5	132209684	132209685	+	Frame_Shift_Ins	INS	-	-	G													0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agtgagttcggcaaagagaaINSggccacggagaatgacccca					rs377649330		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:132209684_132209685insG	ENST00000296877.2	+	2	1473_1474	c.100_101insG	c.(100-102)aggfs	p.R34fs	LEAP2_ENST00000485457.1_3'UTR	NM_052971.2	NP_443203.1	Q969E1	LEAP2_HUMAN	liver expressed antimicrobial peptide 2	34					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				NS(1)|endometrium(1)	2		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGCAAAGAGAAGGCCACGGAGA	0.51																																					p.R34fs		Atlas-Indel,Pindel	.											.	LEAP2	6	.	0			c.100_101insG						.																																			SO:0001589	frameshift_variant	116842	exon2			.	AJ409065, BX443829	CCDS4163.1	5q31.1	2008-02-05			ENSG00000164406	ENSG00000164406			29571	protein-coding gene	gene with protein product		611373				12493837	Standard	NM_052971		Approved	LEAP-2	uc003kyc.3	Q969E1	OTTHUMG00000059837	ENST00000296877.2:c.102dupG	chr5.hg19:g.132209686_132209686dupG	ENSP00000296877:p.Arg34fs	137.0	0.0		136.0	64.0	NM_052971	D3DQ91	Frame_Shift_Ins	INS	ENST00000296877.2	hg19	CCDS4163.1																																																																																			.	.		0.51	LEAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133046.1	NM_052971		G	132209685	-	G	132209684	7	5	35	1	0	1	1	0	0	0	0	0	8720	63	3	0	106	0	LEAP2	5	132209684	Frame_Shift_Ins	INS	-	TCGA-BC-A10W-01A-11D-A12Z-10	11022013	132209684	48705576	198	4367										
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138260967	138260967	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	atgccacgttttactgagcaAgtagaagcagccgtggaagc	12	9	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:138260967A>G	ENST00000302763.7	+	13	1860	c.1770A>G	c.(1768-1770)caA>caG	p.Q590Q	CTNNA1_ENST00000518825.1_Silent_p.Q590Q|CTNNA1_ENST00000540387.1_Silent_p.Q220Q|CTNNA1_ENST00000355078.5_Silent_p.Q487Q	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	590					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTACTGAGCAAGTAGAAGCAG	0.557																																					p.Q590Q		Atlas-SNP	.											.	CTNNA1	114	.	0			c.A1770G						.						79	71	74					5																	138260967		2203	4300	6503	SO:0001819	synonymous_variant	1495	exon13			TGAGCAAGTAGAA	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.1770A>G	chr5.hg19:g.138260967A>G		75.0	0.0		97.0	5.0	NM_001903	Q12795|Q8N1C0	Silent	SNP	ENST00000302763.7	hg19	CCDS34243.1																																																																																			.	.		0.557	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		G	138260967	A	G	138260967	2	3	35	1	0	0	0	0	0	0	0	1	4014	69	3	2		2	CTNNA1	5	138260967	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	6051283	138260967	42654293	199	4368										
DND1	373863	hgsc.bcm.edu	37	chr5	140052972	140052972	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gattcaccctctcacaccacAgctgagagggaaaggaaggt	11	11	2	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:140052972A>G	ENST00000542735.1	-	2	69	c.26T>C	c.(25-27)cTg>cCg	p.L9P	HARS_ENST00000504156.1_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	9					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCACACCACAGCTGAGAGGG	0.647																																					p.L9P		Atlas-SNP	.											.	DND1	15	.	0			c.T26C						.						53	53	53					5																	140052972		2203	4300	6503	SO:0001630	splice_region_variant	373863	exon2			CACCACAGCTGAG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"RNA binding motif (RRM) containing"	23799	protein-coding gene	gene with protein product		609385	"dead end homolog 1 (zebrafish)"			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.25-1T>C	chr5.hg19:g.140052972A>G		97.0	0.0		122.0	6.0	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	hg19	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	A	12.15	1.852215	0.32699	.	.	ENSG00000256453	ENST00000542735	T	0.33865	1.39	4.7	3.52	0.40303	.	0.299359	0.22494	N	0.059325	T	0.16300	0.0392	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.05750	-1.0866	10	0.30854	T	0.27	-2.1486	5.2348	0.15441	0.4857:0.125:0.0:0.3893	.	9	Q8IYX4	DND1_HUMAN	P	9	ENSP00000445366:L9P	ENSP00000445366:L9P	L	-	2	0	DND1	140033156	0.193000	0.23313	0.998000	0.56505	0.705000	0.40729	1.105000	0.31086	0.790000	0.33803	0.379000	0.24179	CTG	.	.		0.647	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	Missense_Mutation	G	140052972	A	G	140052972	5	3	35	1	0	0	0	0	0	0	1	0	4668	202	7	2	1047	2	DND1	5	140052972	Splice_Site	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	1792005	140052972	40862288	200	4369										
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140515856	140515856	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	tatgggagtgtagcctatgcTctattccaaggcgatgaagt	12	7	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:140515856T>C	ENST00000231134.5	+	1	1057	c.840T>C	c.(838-840)gcT>gcC	p.A280A		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	280	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TAGCCTATGCTCTATTCCAAG	0.463																																					p.A280A		Atlas-SNP	.											.	PCDHB5	184	.	0			c.T840C						.						119	121	120					5																	140515856		2203	4300	6503	SO:0001819	synonymous_variant	26167	exon1			CTATGCTCTATTC	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.840T>C	chr5.hg19:g.140515856T>C		100.0	0.0		99.0	4.0	NM_015669	Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	hg19	CCDS4247.1																																																																																			.	.		0.463	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		C	140515856	T	C	140515856	2	2	35	1	0	0	0	0	0	0	0	1	11554	1538	54	2		2	PCDHB5	5	140515856	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	462884	140515856	40399404	201	4370										
PCDHB6	56130	hgsc.bcm.edu	37	chr5	140530199	140530199	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	agttttttcaggcttccttgCgagtcagagatataaatgac	9	7	2	2	rs144886449		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:140530199C>T	ENST00000231136.1	+	1	361	c.361C>T	c.(361-363)Cga>Tga	p.R121*	PCDHB6_ENST00000543635.1_5'UTR	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	121	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCTTCCTTGCGAGTCAGAGA	0.468																																					p.R121X		Atlas-SNP	.											.	PCDHB6	161	.	0			c.C361T						.						53	58	56					5																	140530199		2203	4300	6503	SO:0001587	stop_gained	56130	exon1			TCCTTGCGAGTCA	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.361C>T	chr5.hg19:g.140530199C>T	ENSP00000231136:p.Arg121*	89.0	0.0		93.0	4.0	NM_018939	B2R8R9	Nonsense_Mutation	SNP	ENST00000231136.1	hg19	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.621023	0.46736	.	.	ENSG00000113211	ENST00000231136	.	.	.	4.97	-6.87	0.01671	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	2.4032	0.04407	0.4866:0.1269:0.2371:0.1494	.	.	.	.	X	121	.	ENSP00000231136:R121X	R	+	1	2	PCDHB6	140510383	0.000000	0.05858	0.000000	0.03702	0.953000	0.61014	-4.537000	0.00219	-0.893000	0.03930	-0.224000	0.12420	CGA	.	C|1.000;A|0.000		0.468	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		T	140530199	C	T	140530199	4	4	35	1	0	0	0	0	0	1	0	0	11555	760	27	1	363	1	PCDHB6	5	140530199	Nonsense_Mutation	SNP	C	TCGA-BC-A10W-01A-11D-A12Z-10	14343	140530199	40385061	202	4371										
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140856091	140856091	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gacaacaatcctgctttcccTacccaggaaatgaaattgga	7	11	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:140856091T>C	ENST00000308177.3	+	1	512	c.408T>C	c.(406-408)ccT>ccC	p.P136P	PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB1_ENST00000523390.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	136	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGCTTTCCCTACCCAGGAAA	0.557																																					p.P136P		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.T408C						.						75	76	75					5																	140856091		2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			TTTCCCTACCCAG	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.408T>C	chr5.hg19:g.140856091T>C		120.0	0.0		119.0	5.0	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	hg19	CCDS4261.1																																																																																			.	.		0.557	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		C	140856091	T	C	140856091	2	2	35	1	0	0	0	0	0	0	0	1	11578	1509	53	2		2	PCDHGC3	5	140856091	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	325892	140856091	40059169	203	4372										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148407517	148407517	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ccagcagggcacctgcctttTccaacagggcggagccttta	11	14	0	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:148407517T>C	ENST00000515425.1	-	11	1879	c.1778A>G	c.(1777-1779)gAa>gGa	p.E593G	SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000538184.1_Missense_Mutation_p.E140G|SH3TC2_ENST00000394358.2_Missense_Mutation_p.E478G|SH3TC2_ENST00000512049.1_Missense_Mutation_p.E586G	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	593					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCTGCCTTTTCCAACAGGGC	0.572																																					p.E593G		Atlas-SNP	.											.	SH3TC2	178	.	0			c.A1778G						.						64	62	63					5																	148407517		2203	4300	6503	SO:0001583	missense	79628	exon11			GCCTTTTCCAACA	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.1778A>G	chr5.hg19:g.148407517T>C	ENSP00000423660:p.Glu593Gly	81.0	0.0		81.0	4.0	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	T	8.646	0.897215	0.17686	.	.	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049;ENST00000394358	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	6.04	4.9	0.64082	Tetratricopeptide-like helical (1);	0.059425	0.64402	D	0.000004	T	0.53546	0.1803	L	0.41632	1.29	0.50313	D	0.999869	B;B;B;B	0.18013	0.025;0.008;0.008;0.008	B;B;B;B	0.18561	0.022;0.009;0.015;0.009	T	0.51687	-0.8674	10	0.35671	T	0.21	.	7.3318	0.26586	0.0:0.1557:0.0:0.8443	.	478;586;593;593	C9JLC3;Q14CC0;E9PDF1;Q8TF17	.;.;.;S3TC2_HUMAN	G	140;593;586;478	ENSP00000441427:E140G;ENSP00000423660:E593G;ENSP00000421860:E586G;ENSP00000377886:E478G	ENSP00000377886:E478G	E	-	2	0	SH3TC2	148387710	1.000000	0.71417	0.998000	0.56505	0.370000	0.29829	4.899000	0.63245	2.317000	0.78254	0.460000	0.39030	GAA	.	.		0.572	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		C	148407517	T	C	148407517	3	2	35	1	0	0	0	0	1	0	0	0	14277	1783	62	2	2116	2	SH3TC2	5	148407517	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	7551426	148407517	32507743	204	4373										
ARHGEF37	389337	hgsc.bcm.edu	37	chr5	148980772	148980772	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	caggagacagcctccaaggaAgaggaacaagtgcagctagt	13	9	0	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:148980772A>G	ENST00000333677.6	+	3	451	c.288A>G	c.(286-288)gaA>gaG	p.E96E		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	96	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						CCTCCAAGGAAGAGGAACAAG	0.463																																					p.E96E		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.A288G						.						81	83	83					5																	148980772		1988	4174	6162	SO:0001819	synonymous_variant	389337	exon3			CAAGGAAGAGGAA	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"Rho guanine nucleotide exchange factors"	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.288A>G	chr5.hg19:g.148980772A>G		86.0	0.0		100.0	4.0	NM_001001669	Q6ZW51	Silent	SNP	ENST00000333677.6	hg19	CCDS43385.1																																																																																			.	.		0.463	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669		G	148980772	A	G	148980772	2	3	35	1	0	0	0	0	0	0	0	1	906	69	3	2		2	ARHGEF37	5	148980772	Silent	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	573255	148980772	31934488	205	4374										
TNIP1	10318	hgsc.bcm.edu	37	chr5	150436496	150436496	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gcagcatcaggttgccgtccTcacggggcagggggcccagc	16	14	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:150436496T>C	ENST00000389378.2	-	6	1046	c.458A>G	c.(457-459)gAg>gGg	p.E153G	TNIP1_ENST00000522226.1_Missense_Mutation_p.E153G|TNIP1_ENST00000518977.1_Missense_Mutation_p.E153G|TNIP1_ENST00000315050.7_Missense_Mutation_p.E153G|TNIP1_ENST00000524280.1_Missense_Mutation_p.E153G|TNIP1_ENST00000521591.1_Missense_Mutation_p.E153G|TNIP1_ENST00000523338.1_Missense_Mutation_p.E153G|TNIP1_ENST00000520931.1_Missense_Mutation_p.E100G|TNIP1_ENST00000523200.1_Missense_Mutation_p.E153G	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	153	Interacts with Nef.				defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTTGCCGTCCTCACGGGGCAG	0.682																																					p.E153G		Atlas-SNP	.											.	TNIP1	51	.	0			c.A458G						.						24	25	25					5																	150436496		2203	4298	6501	SO:0001583	missense	10318	exon6			CCGTCCTCACGGG	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"virion-associated nuclear-shuttling protein", "Nef-associated factor 1 SNP"	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.458A>G	chr5.hg19:g.150436496T>C	ENSP00000374029:p.Glu153Gly	38.0	0.0		61.0	5.0	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Missense_Mutation	SNP	ENST00000389378.2	hg19	CCDS34280.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.494990	0.44352	.	.	ENSG00000145901	ENST00000520931;ENST00000389378;ENST00000315050;ENST00000523338;ENST00000544828;ENST00000417127;ENST00000539213;ENST00000522226;ENST00000521591;ENST00000518977;ENST00000524280;ENST00000523200;ENST00000545840;ENST00000522100	T;T;T;T;T;T;T;T;T;T	0.25749	1.96;2.03;2.03;2.04;2.03;2.03;2.04;2.08;2.08;1.78	5.03	3.87	0.44632	.	0.052153	0.85682	D	0.000000	T	0.33818	0.0876	M	0.77103	2.36	0.51482	D	0.999926	B;B;B;B;B;B;B	0.27192	0.011;0.068;0.02;0.068;0.068;0.171;0.171	B;B;B;B;B;B;B	0.33521	0.016;0.059;0.016;0.059;0.064;0.165;0.165	T	0.19582	-1.0301	10	0.87932	D	0	-17.8083	10.6611	0.45702	0.0:0.076:0.0:0.924	.	153;107;107;153;153;153;153	B7Z8K2;A4F1X9;A4F1X7;E7EPY1;E7ET96;A4F1W9;Q15025	.;.;.;.;.;.;TNIP1_HUMAN	G	100;153;153;153;110;110;115;153;153;153;153;153;110;100	ENSP00000429891:E100G;ENSP00000374029:E153G;ENSP00000317891:E153G;ENSP00000428243:E153G;ENSP00000428187:E153G;ENSP00000430760:E153G;ENSP00000430971:E153G;ENSP00000429912:E153G;ENSP00000431105:E153G;ENSP00000428487:E100G	ENSP00000317891:E153G	E	-	2	0	TNIP1	150416689	1.000000	0.71417	0.952000	0.39060	0.412000	0.31113	5.169000	0.64984	0.872000	0.35775	0.533000	0.62120	GAG	.	.		0.682	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		C	150436496	T	C	150436496	3	2	35	1	0	0	0	0	1	0	0	0	16329	1551	54	2	1504	2	TNIP1	5	150436496	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	1455724	150436496	30478764	206	4375										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160063301	160063301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggtgttcttcaaaggtcccaTtccagatgctgtgacctgag	11	10	2	3			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:160063301T>C	ENST00000327245.5	-	11	1862	c.1016A>G	c.(1015-1017)aAt>aGt	p.N339S	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	339					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AAAGGTCCCATTCCAGATGCT	0.498																																					p.N339S		Atlas-SNP	.											.	ATP10B	201	.	0			c.A1016G						.						91	90	90					5																	160063301		1957	4154	6111	SO:0001583	missense	23120	exon11			GTCCCATTCCAGA	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.1016A>G	chr5.hg19:g.160063301T>C	ENSP00000313600:p.Asn339Ser	65.0	0.0		85.0	4.0	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	hg19	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	T	11.78	1.740137	0.30865	.	.	ENSG00000118322	ENST00000327245	D	0.88354	-2.37	5.18	4.02	0.46733	ATPase, P-type, ATPase-associated domain (1);	0.391334	0.28510	N	0.015087	T	0.75459	0.3852	N	0.10945	0.07	0.26882	N	0.967521	B;B;B;B	0.22683	0.073;0.002;0.008;0.023	B;B;B;B	0.25987	0.065;0.022;0.006;0.033	T	0.61530	-0.7044	9	.	.	.	.	6.6745	0.23085	0.0:0.0824:0.2552:0.6624	.	383;339;311;339	B4DHG1;O94823-2;O94823-3;O94823	.;.;.;AT10B_HUMAN	S	339	ENSP00000313600:N339S	.	N	-	2	0	ATP10B	159995879	0.997000	0.39634	0.791000	0.31998	0.864000	0.49448	2.903000	0.48711	0.920000	0.36970	-0.389000	0.06534	AAT	.	.		0.498	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		C	160063301	T	C	160063301	3	2	35	1	0	0	0	0	1	0	0	0	1117	1493	52	2	3433	2	ATP10B	5	160063301	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	9626805	160063301	20851959	207	4376										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161576259	161576259	+	Frame_Shift_Del	DEL	G	G	-													0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ctggtggagtatggcaccttGcattattttgtcagcaaccg							TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:161576259delG	ENST00000361925.4	+	8	1288	c.1068delG	c.(1066-1068)ttgfs	p.L356fs	GABRG2_ENST00000393933.4_Frame_Shift_Del_p.L261fs|GABRG2_ENST00000356592.3_Frame_Shift_Del_p.L356fs|GABRG2_ENST00000414552.2_Frame_Shift_Del_p.L396fs			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	356					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ATGGCACCTTGCATTATTTTG	0.408																																					p.L396fs		Atlas-Indel,Pindel	.											.	GABRG2	142	.	0			c.1187delT						.						192	162	172					5																	161576259		2203	4300	6503	SO:0001589	frameshift_variant	2566	exon9			.		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1068delG	chr5.hg19:g.161576259delG	ENSP00000354651:p.Leu356fs	807.0	0.0		915.0	222.0	NM_198903	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Frame_Shift_Del	DEL	ENST00000361925.4	hg19	CCDS4358.1																																																																																			.	.		0.408	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			-	161576259	G	-	161576259	7	5	35	1	0	1	0	1	0	0	0	0	6180	1310	46	0	1222	0	GABRG2	5	161576259	Frame_Shift_Del	DEL	G	TCGA-BC-A10W-01A-11D-A12Z-10	1512958	161576259	19339001	208	4377										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161580269	161580269	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	ggagcttggagacatgggagGatacatatccgcattgccaa	13	8	0	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:161580269G>A	ENST00000361925.4	+	9	1519	c.1299G>A	c.(1297-1299)agG>agA	p.R433R	GABRG2_ENST00000393933.4_Silent_p.R338R|GABRG2_ENST00000356592.3_Silent_p.R441R|GABRG2_ENST00000414552.2_Silent_p.R481R			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	433	Interaction with GABARAP. {ECO:0000255}.				adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GACATGGGAGGATACATATCC	0.488																																					p.R481R		Atlas-SNP	.											.	GABRG2	142	.	0			c.G1443A						.						252	246	248					5																	161580269		2203	4300	6503	SO:0001819	synonymous_variant	2566	exon11			TGGGAGGATACAT		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1299G>A	chr5.hg19:g.161580269G>A		589.0	0.0		716.0	200.0	NM_198903	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Silent	SNP	ENST00000361925.4	hg19	CCDS4358.1																																																																																			.	.		0.488	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			A	161580269	G	A	161580269	2	1	35	1	0	0	0	0	0	0	0	1	6180	1165	41	3		3	GABRG2	5	161580269	Silent	SNP	G	TCGA-BC-A10W-01A-11D-A12Z-10	4010	161580269	19334991	209	4378										
FAM193B	54540	hgsc.bcm.edu	37	chr5	176951436	176951436	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gcctcagcacagctgcctacTttgggaagctctaggaccct	10	14	2	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:176951436T>C	ENST00000514747.1	-	6	2094	c.2046A>G	c.(2044-2046)aaA>aaG	p.K682K	FAM193B_ENST00000329540.5_Silent_p.K308K|FAM193B_ENST00000508298.1_5'Flank|FAM193B_ENST00000443375.2_Silent_p.K649K	NM_001190946.1	NP_001177875.1	Q96PV7	F193B_HUMAN	family with sequence similarity 193, member B	762						cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)	4						AGCTGCCTACTTTGGGAAGCT	0.677																																					p.K682K		Atlas-SNP	.											.	FAM193B	28	.	0			c.A2046G						.						13	14	14					5																	176951436		1872	4088	5960	SO:0001819	synonymous_variant	54540	exon6			GCCTACTTTGGGA		CCDS54954.1	5q35	2010-02-17			ENSG00000146067	ENSG00000146067			25524	protein-coding gene	gene with protein product		615813				11572484	Standard	NR_024019		Approved	KIAA1931, FLJ10404	uc003mhu.3	Q96PV7	OTTHUMG00000163396	ENST00000514747.1:c.2046A>G	chr5.hg19:g.176951436T>C		129.0	0.0		99.0	5.0	NM_001190946	E9PET5|Q9NW00	Silent	SNP	ENST00000514747.1	hg19	CCDS54954.1	.	.	.	.	.	.	.	.	.	.	T	6.885	0.532741	0.13127	.	.	ENSG00000146067	ENST00000524677	.	.	.	4.98	-3.55	0.04639	.	.	.	.	.	T	0.28764	0.0713	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.35822	-0.9773	4	.	.	.	-1.2745	7.7099	0.28671	0.0:0.4714:0.1289:0.3997	.	.	.	.	G	368	.	.	S	-	1	0	FAM193B	176884042	0.084000	0.21492	0.015000	0.15790	0.935000	0.57460	0.155000	0.16362	-0.458000	0.07023	0.454000	0.30748	AGT	.	.		0.677	FAM193B-003	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373121.1	NM_019057		C	176951436	T	C	176951436	2	2	35	1	0	0	0	0	0	0	0	1	5530	1606	56	2		2	FAM193B	5	176951436	Silent	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	15371167	176951436	3963824	210	4379										
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179320450	179320450	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cagacgcgttatgtccacccActgcaccacgaggctcactg	9	16	1	1			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:179320450A>G	ENST00000356834.3	-	5	632	c.595T>C	c.(595-597)Tgg>Cgg	p.W199R	TBC1D9B_ENST00000355235.3_Missense_Mutation_p.W199R	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	199	GRAM 1.					integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATGTCCACCCACTGCACCACG	0.607																																					p.W199R		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.T595C						.						92	75	81					5																	179320450		2203	4300	6503	SO:0001583	missense	23061	exon5			CCACCCACTGCAC	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"EF-hand domain containing"	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.595T>C	chr5.hg19:g.179320450A>G	ENSP00000349291:p.Trp199Arg	64.0	0.0		72.0	4.0	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Missense_Mutation	SNP	ENST00000356834.3	hg19	CCDS43408.1	.	.	.	.	.	.	.	.	.	.	A	18.76	3.693004	0.68271	.	.	ENSG00000197226	ENST00000356834;ENST00000355235	D;D	0.87029	-2.2;-2.2	4.36	4.36	0.52297	GRAM (2);	0.000000	0.85682	D	0.000000	D	0.94584	0.8255	M	0.92923	3.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95692	0.8741	10	0.87932	D	0	-11.1939	13.7011	0.62608	1.0:0.0:0.0:0.0	.	199;199;199	A1L3A9;Q66K14-2;Q66K14	.;.;TBC9B_HUMAN	R	199	ENSP00000349291:W199R;ENSP00000347375:W199R	ENSP00000347375:W199R	W	-	1	0	TBC1D9B	179253056	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	9.047000	0.93823	1.841000	0.53522	0.260000	0.18958	TGG	.	.		0.607	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		G	179320450	A	G	179320450	3	3	35	1	0	0	0	0	1	0	0	0	15643	159	6	2	3229	2	TBC1D9B	5	179320450	Missense_Mutation	SNP	A	TCGA-BC-A10W-01A-11D-A12Z-10	2369014	179320450	1594810	211	4380										
MGAT1	4245	hgsc.bcm.edu	37	chr5	180218962	180218962	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	gctgggtgaagtgcacaaacTgctggttcagcttgataaac	12	8	1	2			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr5:180218962T>C	ENST00000446023.2	-	3	1760	c.1010A>G	c.(1009-1011)cAg>cGg	p.Q337R	MGAT1_ENST00000393340.3_Missense_Mutation_p.Q337R|MGAT1_ENST00000333055.3_Missense_Mutation_p.Q337R|MGAT1_ENST00000427865.2_Missense_Mutation_p.Q337R|MGAT1_ENST00000307826.4_Missense_Mutation_p.Q337R	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	337					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTGCACAAACTGCTGGTTCAG	0.572																																					p.Q337R		Atlas-SNP	.											.	MGAT1	48	.	0			c.A1010G						.																																			SO:0001583	missense	4245	exon3			ACAAACTGCTGGT	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.1010A>G	chr5.hg19:g.180218962T>C	ENSP00000404718:p.Gln337Arg	88.0	0.0		89.0	4.0	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	hg19	CCDS4458.1	.	.	.	.	.	.	.	.	.	.	T	9.329	1.060068	0.19987	.	.	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865	D;D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82;-1.82	4.52	3.38	0.38709	.	0.470122	0.21631	N	0.071499	T	0.72293	0.3442	N	0.20986	0.625	0.28281	N	0.923964	B	0.02656	0.0	B	0.04013	0.001	T	0.60326	-0.7285	10	0.28530	T	0.3	-8.6443	8.1092	0.30905	0.0:0.0994:0.0:0.9006	.	337	P26572	MGAT1_HUMAN	R	337;337;337;337;194;337	ENSP00000332073:Q337R;ENSP00000311888:Q337R;ENSP00000404718:Q337R;ENSP00000377010:Q337R;ENSP00000402838:Q337R	ENSP00000311888:Q337R	Q	-	2	0	MGAT1	180151568	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.002000	0.57053	2.030000	0.59900	0.533000	0.62120	CAG	.	.		0.572	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618		C	180218962	T	C	180218962	3	2	35	1	0	0	0	0	1	0	0	0	9551	1580	55	2	331	2	MGAT1	5	180218962	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10	898512	180218962	696298	212	4381										
SLC22A23	63027	hgsc.bcm.edu	37	chr6	3290023	3290023	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.00938967136150235	2	1	0.337871096754346	0	0.37165820642978	0.466666666666667	1	0	cacacacaggaccacaatgtTcttccacaggttccgtgtcc	7	15	1	0			TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	g.chr6:3290023T>C	ENST00000406686.3	-	6	1287	c.1288A>G	c.(1288-1290)Aac>Gac	p.N430D	SLC22A23_ENST00000380302.4_Missense_Mutation_p.N149D|SLC22A23_ENST00000436008.2_Missense_Mutation_p.N430D|SLC22A23_ENST00000490273.1_Missense_Mutation_p.N149D|PSMG4_ENST00000451246.2_Intron	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	430					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				ACCACAATGTTCTTCCACAGG	0.582																																					p.N430D		Atlas-SNP	.											.	SLC22A23	89	.	0			c.A1288G						.						165	125	138					6																	3290023		2203	4300	6503	SO:0001583	missense	63027	exon6			CAATGTTCTTCCA	AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"Solute carriers"	21106	protein-coding gene	gene with protein product		611697	"chromosome 6 open reading frame 85"	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.1288A>G	chr6.hg19:g.3290023T>C	ENSP00000385028:p.Asn430Asp	88.0	0.0		84.0	4.0	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Missense_Mutation	SNP	ENST00000406686.3	hg19	CCDS47363.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.613979	0.87359	.	.	ENSG00000137266	ENST00000436008;ENST00000406686;ENST00000380302;ENST00000490273;ENST00000485307;ENST00000467177	T;T;T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8;-0.8;-0.8	4.33	4.33	0.51752	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.045545	0.85682	D	0.000000	T	0.71467	0.3343	L	0.43923	1.385	0.80722	D	1	D;D	0.63046	0.992;0.992	P;P	0.60286	0.872;0.872	T	0.71224	-0.4656	10	0.34782	T	0.22	-35.1252	13.9461	0.64086	0.0:0.0:0.0:1.0	.	430;430	C9J4Z0;A1A5C7	.;S22AN_HUMAN	D	430;430;149;149;258;256	ENSP00000410245:N430D;ENSP00000385028:N430D;ENSP00000369657:N149D;ENSP00000419463:N149D;ENSP00000418134:N258D;ENSP00000418985:N256D	ENSP00000369657:N149D	N	-	1	0	SLC22A23	3235022	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.353000	0.79414	1.942000	0.56320	0.459000	0.35465	AAC	.	.		0.582	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945		C	3290023	T	C	3290023	3	2	35	1	0	0	0	0	1	0	0	0	14467	1783	62	2	792	2	SLC22A23	6	3290023	Missense_Mutation	SNP	T	TCGA-BC-A10W-01A-11D-A12Z-10		3290023	167825044	213	4382										
OR10K1	391109	hgsc.bcm.edu	37	chr1	158435869	158435869	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	NA	NA	NA	1	1	0	gcccttccactcctccaaccAgctccatcacttcttctgtg	4	19	3	0			TCGA-BC-A10X-01A-11D-A12Z-10	TCGA-BC-A10X-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36938443-c826-4abe-aaf6-dd7217b07f51	4285989b-f8d8-4ced-99a1-894ff2b37cf3	g.chr1:158435869A>G	ENST00000289451.2	+	1	598	c.518A>G	c.(517-519)cAg>cGg	p.Q173R		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, member 1	173						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					TCCTCCAACCAGCTCCATCAC	0.527																																					p.Q173R		Atlas-SNP	.											.	OR10K1	80	.	0			c.A518G						.						213	210	211					1																	158435869		2203	4300	6503	SO:0001583	missense	391109	exon1			CCAACCAGCTCCA	AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"GPCR / Class A : Olfactory receptors"	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.518A>G	chr1.hg19:g.158435869A>G	ENSP00000289451:p.Gln173Arg	538.0	0.0		447.0	18.0	NM_001004473	Q6IFS2	Missense_Mutation	SNP	ENST00000289451.2	hg19	CCDS30897.1	.	.	.	.	.	.	.	.	.	.	a	0.048	-1.260420	0.01445	.	.	ENSG00000173285	ENST00000289451	T	0.00099	8.73	4.24	3.1	0.35709	GPCR, rhodopsin-like superfamily (1);	0.371038	0.19467	N	0.113545	T	0.00039	0.0001	N	0.25789	0.76	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.36261	-0.9755	10	0.22109	T	0.4	.	4.4059	0.11409	0.7292:0.0:0.0972:0.1736	.	173	Q8NGX5	O10K1_HUMAN	R	173	ENSP00000289451:Q173R	ENSP00000289451:Q173R	Q	+	2	0	OR10K1	156702493	0.000000	0.05858	0.091000	0.20842	0.665000	0.39181	-0.476000	0.06591	0.651000	0.30788	0.455000	0.32223	CAG	.	.		0.527	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1			G	158435869	A	G	158435869	3	3	36	1	0	0	0	0	1	0	0	0	10922	188	7	2	520	2	OR10K1	1	158435869	Missense_Mutation	SNP	A	TCGA-BC-A10X-01A-11D-A12Z-10		158435869	90814752	1	4383										
OR2C3	81472	hgsc.bcm.edu	37	chr1	247694952	247694952	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	NA	NA	NA	1	1	0	cctcagggtgtaaataagtgGgttcagcgcaggagtgacta	14	7	2	1	rs201468915		TCGA-BC-A10X-01A-11D-A12Z-10	TCGA-BC-A10X-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36938443-c826-4abe-aaf6-dd7217b07f51	4285989b-f8d8-4ced-99a1-894ff2b37cf3	g.chr1:247694952G>T	ENST00000366487.3	-	2	1223	c.862C>A	c.(862-864)Cca>Aca	p.P288T	GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000531662.1_Intron|GCSAML_ENST00000366489.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	288						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			TAAATAAGTGGGTTCAGCGCA	0.532																																					p.P288T		Atlas-SNP	.											.	OR2C3	92	.	0			c.C862A						.						98	85	89					1																	247694952		2203	4300	6503	SO:0001583	missense	81472	exon2			TAAGTGGGTTCAG	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"GPCR / Class A : Olfactory receptors"	15005	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily C, member 4"	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.862C>A	chr1.hg19:g.247694952G>T	ENSP00000355443:p.Pro288Thr	145.0	0.0		147.0	7.0	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Missense_Mutation	SNP	ENST00000366487.3	hg19	CCDS1634.2	.	.	.	.	.	.	.	.	.	.	G	13.89	2.373063	0.42105	.	.	ENSG00000196242	ENST00000366487	T	0.63913	-0.07	3.91	3.91	0.45181	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35585	U	0.003103	T	0.76601	0.4010	M	0.83012	2.62	0.33934	D	0.642374	D	0.67145	0.996	P	0.59643	0.861	D	0.86056	0.1529	10	0.87932	D	0	.	13.8211	0.63320	0.0:0.0:1.0:0.0	.	288	Q8N628	OR2C3_HUMAN	T	288	ENSP00000355443:P288T	ENSP00000355443:P288T	P	-	1	0	OR2C3	245761575	1.000000	0.71417	0.196000	0.23383	0.007000	0.05969	6.081000	0.71309	2.157000	0.67596	0.655000	0.94253	CCA	.	G|1.000;A|0.000		0.532	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074		T	247694952	G	T	247694952	3	4	36	1	0	0	0	0	1	0	0	0	11002	1232	43	3	104	3	OR2C3	1	247694952	Missense_Mutation	SNP	G	TCGA-BC-A10X-01A-11D-A12Z-10	89259083	247694952	1555669	2	4384										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32162651	32162651	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	atctcaatgagctcattgctCtgggtgtcccggcgggcctt	12	12	3	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr1:32162651C>G	ENST00000373672.3	-	8	1293	c.777G>C	c.(775-777)caG>caC	p.Q259H	COL16A1_ENST00000271069.6_Missense_Mutation_p.Q259H|COL16A1_ENST00000373668.3_Missense_Mutation_p.Q259H	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	259	Nonhelical region 10 (NC10).				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		GCTCATTGCTCTGGGTGTCCC	0.602																																					p.Q259H	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.G777C						.						113	125	121					1																	32162651		1986	4145	6131	SO:0001583	missense	1307	exon8			ATTGCTCTGGGTG	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.777G>C	chr1.hg19:g.32162651C>G	ENSP00000362776:p.Gln259His	273.0	0.0		305.0	136.0	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	C	14.55	2.569750	0.45798	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668	T;T;T	0.71934	-0.61;-0.61;-0.61	4.87	2.97	0.34412	.	0.195831	0.35495	N	0.003162	T	0.74230	0.3689	L	0.40543	1.245	0.33708	D	0.615411	D;D;D	0.69078	0.993;0.995;0.997	P;P;D	0.67548	0.903;0.897;0.952	T	0.80663	-0.1282	10	0.87932	D	0	.	9.755	0.40498	0.0:0.8279:0.0:0.1721	.	259;259;259	A6NCT7;Q07092;Q07092-2	.;COGA1_HUMAN;.	H	259	ENSP00000362776:Q259H;ENSP00000271069:Q259H;ENSP00000362772:Q259H	ENSP00000271069:Q259H	Q	-	3	2	COL16A1	31935238	0.986000	0.35501	1.000000	0.80357	0.884000	0.51177	0.422000	0.21296	1.182000	0.42928	0.655000	0.94253	CAG	.	.		0.602	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		G	32162651	C	G	32162651	3	3	37	1	0	0	0	0	1	0	0	0	3675	912	32	4	4293	4	COL16A1	1	32162651	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10		32162651	217087970	1	4385										
BAI2	576	hgsc.bcm.edu	37	chr1	32196897	32196897	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tattcccaggcagtggtgagAagctgaggctgccctcaggg	15	10	1	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr1:32196897A>T	ENST00000373658.3	-	29	4225	c.3884T>A	c.(3883-3885)tTc>tAc	p.F1295Y	BAI2_ENST00000398538.1_Missense_Mutation_p.F1283Y|BAI2_ENST00000398556.3_Missense_Mutation_p.F1210Y|BAI2_ENST00000398547.1_Missense_Mutation_p.F1228Y|BAI2_ENST00000373655.2_Missense_Mutation_p.F1295Y|BAI2_ENST00000398542.1_Missense_Mutation_p.F1195Y|BAI2_ENST00000527361.1_Missense_Mutation_p.F1262Y|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000440175.2_Missense_Mutation_p.F904Y|BAI2_ENST00000257070.4_Missense_Mutation_p.F1262Y	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1295					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		CAGTGGTGAGAAGCTGAGGCT	0.647																																					p.F1295Y		Atlas-SNP	.											.	BAI2	128	.	0			c.T3884A						.						31	26	28					1																	32196897		2203	4300	6503	SO:0001583	missense	576	exon29			GGTGAGAAGCTGA	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.3884T>A	chr1.hg19:g.32196897A>T	ENSP00000362762:p.Phe1295Tyr	163.0	0.0		175.0	85.0	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	hg19	CCDS346.2	.	.	.	.	.	.	.	.	.	.	A	16.50	3.141251	0.57044	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538	T;T;T;T;T;T;T;T;T	0.57107	1.13;1.3;0.42;0.42;1.56;0.46;0.46;1.2;0.49	5.16	5.16	0.70880	.	0.000000	0.45126	D	0.000394	T	0.53158	0.1779	L	0.40543	1.245	0.43152	D	0.994923	B;P;P;P;B;P;P	0.49447	0.082;0.924;0.709;0.876;0.161;0.876;0.468	B;P;B;P;B;P;B	0.51266	0.219;0.664;0.217;0.463;0.279;0.463;0.348	T	0.47736	-0.9094	10	0.21540	T	0.41	.	14.9679	0.71208	1.0:0.0:0.0:0.0	.	1262;1283;904;1210;1295;1295;1283	O60241-4;O60241-3;B4DKC3;A2A3C6;O60241-2;O60241;A2A3C2	.;.;.;.;.;BAI2_HUMAN;.	Y	1210;1228;1295;1295;1195;1262;1262;904;1283	ENSP00000381564:F1210Y;ENSP00000381555:F1228Y;ENSP00000362762:F1295Y;ENSP00000362759:F1295Y;ENSP00000381550:F1195Y;ENSP00000257070:F1262Y;ENSP00000435397:F1262Y;ENSP00000391071:F904Y;ENSP00000381548:F1283Y	ENSP00000257070:F1262Y	F	-	2	0	BAI2	31969484	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.306000	0.59117	2.074000	0.62210	0.459000	0.35465	TTC	.	.		0.647	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		T	32196897	A	T	32196897	3	4	37	1	0	0	0	0	1	0	0	0	1299	246	9	4	893	4	BAI2	1	32196897	Missense_Mutation	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10	34246	32196897	217053724	2	4386										
LHX8	431707	hgsc.bcm.edu	37	chr1	75602325	75602325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	agaggagtgcgggcggactaCagccctggcggccgggagga	20	10	0	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr1:75602325C>T	ENST00000294638.5	+	3	720	c.56C>T	c.(55-57)aCa>aTa	p.T19I	LHX8_ENST00000356261.3_Missense_Mutation_p.T9I	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8	19					female gonad development (GO:0008585)|forebrain neuron development (GO:0021884)|learning or memory (GO:0007611)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	female germ cell nucleus (GO:0001674)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(18)|ovary(3)|urinary_tract(1)	30						GGGCGGACTACAGCCCTGGCG	0.667																																					p.T19I		Atlas-SNP	.											.	LHX8	73	.	0			c.C56T						.						21	22	22					1																	75602325		1790	3354	5144	SO:0001583	missense	431707	exon3			GGACTACAGCCCT	AB050476	CCDS30756.1, CCDS58008.1	1p31.1	2011-06-20			ENSG00000162624	ENSG00000162624		"Homeoboxes / LIM class"	28838	protein-coding gene	gene with protein product		604425				9598319	Standard	NM_001256114		Approved	Lhx7	uc031pmx.1	Q68G74	OTTHUMG00000009692	ENST00000294638.5:c.56C>T	chr1.hg19:g.75602325C>T	ENSP00000294638:p.Thr19Ile	74.0	0.0		73.0	34.0	NM_001001933	E9PGE3	Missense_Mutation	SNP	ENST00000294638.5	hg19	CCDS30756.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.076522	0.55753	.	.	ENSG00000162624	ENST00000294638;ENST00000356261	D;D	0.86297	-2.1;-2.09	3.58	3.58	0.41010	.	0.925878	0.08939	N	0.871821	T	0.64713	0.2623	N	0.08118	0	0.27613	N	0.948593	B	0.15473	0.013	B	0.04013	0.001	T	0.62348	-0.6873	10	0.72032	D	0.01	.	14.7861	0.69806	0.0:1.0:0.0:0.0	.	19	Q68G74	LHX8_HUMAN	I	19;9	ENSP00000294638:T19I;ENSP00000348597:T9I	ENSP00000294638:T19I	T	+	2	0	LHX8	75374913	0.992000	0.36948	0.998000	0.56505	0.955000	0.61496	2.339000	0.43965	1.533000	0.49186	0.313000	0.20887	ACA	.	.		0.667	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	NM_001001933		T	75602325	C	T	75602325	3	4	37	1	0	0	0	0	1	0	0	0	8785	478	17	3	62	3	LHX8	1	75602325	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	43405428	75602325	173648296	3	4387										
POGZ	23126	hgsc.bcm.edu	37	chr1	151414583	151414583	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tagttttatccactgaattaTaatcttcaactacagagtcc	4	9	2	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr1:151414583T>C	ENST00000271715.2	-	2	412	c.98A>G	c.(97-99)tAt>tGt	p.Y33C	POGZ_ENST00000368863.2_Missense_Mutation_p.Y33C|POGZ_ENST00000409503.1_Missense_Mutation_p.Y33C|POGZ_ENST00000540984.1_5'UTR|POGZ_ENST00000491586.1_Missense_Mutation_p.Y33C|POGZ_ENST00000361398.3_Missense_Mutation_p.Y33C|POGZ_ENST00000531094.1_Missense_Mutation_p.Y33C|POGZ_ENST00000392723.1_Missense_Mutation_p.Y33C	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	33					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CACTGAATTATAATCTTCAAC	0.388																																					p.Y33C		Atlas-SNP	.											.	POGZ	211	.	0			c.A98G						.						95	92	93					1																	151414583		2203	4300	6503	SO:0001583	missense	23126	exon2			GAATTATAATCTT	AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.98A>G	chr1.hg19:g.151414583T>C	ENSP00000271715:p.Tyr33Cys	207.0	0.0		265.0	87.0	NM_145796	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	hg19	CCDS997.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.954328	0.73902	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000491586;ENST00000437847;ENST00000533461;ENST00000533351;ENST00000450842	T;T;T;T;T;T;T	0.01185	5.64;5.86;5.64;5.75;5.84;5.72;5.21	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000020	T	0.01523	0.0049	N	0.14661	0.345	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0;0.999;0.999	D;D;D;D;D;D;D	0.83275	0.945;0.962;0.996;0.964;0.983;0.975;0.924	T	0.74621	-0.3604	10	0.62326	D	0.03	-14.65	15.3964	0.74798	0.0:0.0:0.0:1.0	.	33;33;33;33;33;33;33	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-4;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;.;POGZ_HUMAN	C	33	ENSP00000376484:Y33C;ENSP00000271715:Y33C;ENSP00000354467:Y33C;ENSP00000357856:Y33C;ENSP00000386836:Y33C;ENSP00000431259:Y33C;ENSP00000418408:Y33C	ENSP00000271715:Y33C	Y	-	2	0	POGZ	149681207	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.129000	0.64739	2.313000	0.78055	0.455000	0.32223	TAT	.	.		0.388	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		C	151414583	T	C	151414583	3	2	37	1	0	0	0	0	1	0	0	0	12195	1406	49	2	4220	2	POGZ	1	151414583	Missense_Mutation	SNP	T	TCGA-BC-A10Y-01A-11D-A12Z-10	75812258	151414583	97836038	4	4388										
USH2A	7399	hgsc.bcm.edu	37	chr1	216496858	216496858	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ccactgcataatatctgtgtCtgaggttaacagcagtctca	8	10	3	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr1:216496858C>T	ENST00000307340.3	-	8	1894	c.1508G>A	c.(1507-1509)aGa>aAa	p.R503K	USH2A_ENST00000366943.2_Missense_Mutation_p.R503K|USH2A_ENST00000366942.3_Missense_Mutation_p.R503K	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	503	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATATCTGTGTCTGAGGTTAAC	0.368										HNSCC(13;0.011)																											p.R503K		Atlas-SNP	.											USH2A,NS,carcinoma,0,1	USH2A	1168	.	0			c.G1508A						.						149	146	147					1																	216496858		2203	4300	6503	SO:0001583	missense	7399	exon8			CTGTGTCTGAGGT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.1508G>A	chr1.hg19:g.216496858C>T	ENSP00000305941:p.Arg503Lys	217.0	1.0		359.0	104.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049535	0.36181	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.20738	2.44;2.43;2.05	5.5	4.59	0.56863	Laminin, N-terminal (3);	0.000000	0.49305	D	0.000150	T	0.22166	0.0534	M	0.68728	2.09	0.41999	D	0.990888	B;P	0.42785	0.164;0.79	B;B	0.34242	0.098;0.178	T	0.05649	-1.0872	10	0.41790	T	0.15	.	14.2176	0.65805	0.0:0.9281:0.0:0.0719	.	503;503	O75445-2;O75445	.;USH2A_HUMAN	K	503	ENSP00000305941:R503K;ENSP00000355910:R503K;ENSP00000355909:R503K	ENSP00000305941:R503K	R	-	2	0	USH2A	214563481	0.058000	0.20735	0.759000	0.31340	0.645000	0.38454	2.330000	0.43885	1.301000	0.44836	0.655000	0.94253	AGA	.	.		0.368	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216496858	C	T	216496858	3	4	37	1	0	0	0	0	1	0	0	0	17051	913	32	3	14374	3	USH2A	1	216496858	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	65082275	216496858	32753763	5	4389										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1079315	1079315	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	agaaacaagatgttgtctgtGtgggcggaagccaccagggc	15	8	1	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr2:1079315G>T	ENST00000308624.5	+	2	313	c.184G>T	c.(184-186)Gtg>Ttg	p.V62L	SNTG2_ENST00000407292.1_Missense_Mutation_p.V62L	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	62					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		TGTTGTCTGTGTGGGCGGAAG	0.488																																					p.V62L		Atlas-SNP	.											.	SNTG2	125	.	0			c.G184T						.						114	113	113					2																	1079315		1996	4168	6164	SO:0001583	missense	54221	exon2			GTCTGTGTGGGCG	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.184G>T	chr2.hg19:g.1079315G>T	ENSP00000311837:p.Val62Leu	110.0	0.0		90.0	36.0	NM_018968	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	hg19	CCDS46220.1	.	.	.	.	.	.	.	.	.	.	G	3.107	-0.183483	0.06340	.	.	ENSG00000172554	ENST00000308624;ENST00000407292	T;T	0.54071	1.15;0.59	4.23	1.06	0.20224	PDZ/DHR/GLGF (1);	0.574520	0.17993	N	0.155145	T	0.37210	0.0995	L	0.45137	1.4	0.19300	N	0.999975	B;B	0.22276	0.046;0.067	B;B	0.24541	0.054;0.035	T	0.28902	-1.0029	10	0.09843	T	0.71	.	7.5428	0.27748	0.3238:0.0:0.6762:0.0	.	62;62	Q9NY99-2;Q9NY99	.;SNTG2_HUMAN	L	62	ENSP00000311837:V62L;ENSP00000385020:V62L	ENSP00000311837:V62L	V	+	1	0	SNTG2	1069315	0.838000	0.29461	0.027000	0.17364	0.061000	0.15899	0.319000	0.19522	-0.124000	0.11724	0.591000	0.81541	GTG	.	.		0.488	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		T	1079315	G	T	1079315	3	4	37	1	0	0	0	0	1	0	0	0	14890	1377	48	3	190	3	SNTG2	2	1079315	Missense_Mutation	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10		1079315	242120058	6	4390										
PIGF	5281	hgsc.bcm.edu	37	chr2	46839477	46839477	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gcaaataaaaatgtttccaaTgccaacctagaaaaaaaaaa	4	7	0	1	rs1824050	byFrequency	TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr2:46839477T>A	ENST00000281382.6	-	4	497	c.327A>T	c.(325-327)gcA>gcT	p.A109A	PIGF_ENST00000306465.4_Silent_p.A109A|PIGF_ENST00000495933.1_5'UTR	NM_002643.3	NP_002634.1	Q07326	PIGF_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class F	109					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ethanolaminephosphotransferase activity (GO:0004307)			breast(1)|endometrium(1)|lung(1)|stomach(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			ATGTTTCCAATGCCAACCTAG	0.274																																					p.A109A		Atlas-SNP	.											.	PIGF	9	.	0			c.A327T						.						23	21	22					2																	46839477		2180	4280	6460	SO:0001819	synonymous_variant	5281	exon4			TTCCAATGCCAAC		CCDS1827.1, CCDS1828.1	2p21-p16	2013-02-26	2006-06-28		ENSG00000151665	ENSG00000151665		"Phosphatidylinositol glycan anchor biosynthesis"	8962	protein-coding gene	gene with protein product		600153	"phosphatidylinositol glycan, class F"			8575782, 8463218	Standard	NM_173074		Approved		uc002rvd.3	Q07326	OTTHUMG00000128816	ENST00000281382.6:c.327A>T	chr2.hg19:g.46839477T>A		502.0	2.0		323.0	152.0	NM_002643	Q8WW20	Silent	SNP	ENST00000281382.6	hg19	CCDS1827.1																																																																																			.	T|0.798;C|0.202		0.274	PIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250749.2	NM_173074		A	46839477	T	A	46839477	2	1	37	1	0	0	0	0	0	0	0	1	11896	1451	51	4		4	PIGF	2	46839477	Silent	SNP	T	TCGA-BC-A10Y-01A-11D-A12Z-10	45760162	46839477	196359896	7	4391										
VRK2	7444	hgsc.bcm.edu	37	chr2	58373591	58373591	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gagaaactgattggattgatGaacaatgaagcagctcaggt	12	5	1	5			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr2:58373591G>C	ENST00000435505.2	+	15	1909	c.1164G>C	c.(1162-1164)atG>atC	p.M388I	VRK2_ENST00000340157.4_Missense_Mutation_p.M388I|VRK2_ENST00000440705.2_Missense_Mutation_p.M365I|VRK2_ENST00000412104.2_Missense_Mutation_p.M388I|VRK2_ENST00000417641.2_Missense_Mutation_p.M388I			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	388					cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						TTGGATTGATGAACAATGAAG	0.378																																					p.M388I		Atlas-SNP	.											.	VRK2	46	.	0			c.G1164C						.						213	230	224					2																	58373591		2203	4300	6503	SO:0001583	missense	7444	exon12			ATTGATGAACAAT	AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.1164G>C	chr2.hg19:g.58373591G>C	ENSP00000408002:p.Met388Ile	402.0	0.0		343.0	145.0	NM_001130480	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Missense_Mutation	SNP	ENST00000435505.2	hg19	CCDS1859.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.269199	0.40095	.	.	ENSG00000028116	ENST00000435505;ENST00000417641;ENST00000412104;ENST00000340157;ENST00000394539;ENST00000440705	T;T;T;T;T	0.04809	3.55;3.81;3.81;3.55;3.56	5.61	-7.56	0.01322	.	1.800900	0.02598	N	0.100790	T	0.02688	0.0081	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41770	-0.9490	10	0.37606	T	0.19	7.6974	4.3483	0.11143	0.0696:0.301:0.1975:0.4319	.	388;388;388	Q86Y07-2;Q86Y07-5;Q86Y07	.;.;VRK2_HUMAN	I	388;388;388;388;388;365	ENSP00000408002:M388I;ENSP00000402375:M388I;ENSP00000404156:M388I;ENSP00000342381:M388I;ENSP00000398323:M365I	ENSP00000342381:M388I	M	+	3	0	VRK2	58227095	0.000000	0.05858	0.000000	0.03702	0.850000	0.48378	-0.280000	0.08468	-1.183000	0.02723	0.650000	0.86243	ATG	.	.		0.378	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296		C	58373591	G	C	58373591	3	2	37	1	0	0	0	0	1	0	0	0	17235	1290	45	4	1206	4	VRK2	2	58373591	Missense_Mutation	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10	11534114	58373591	184825782	8	4392										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80085161	80085161	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gagacgatgcggatcgcctcCtccgagtttgcagatgaccc	12	13	0	3			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr2:80085161C>T	ENST00000402739.4	+	3	326	c.321C>T	c.(319-321)tcC>tcT	p.S107S	CTNNA2_ENST00000541047.1_Silent_p.S107S|CTNNA2_ENST00000466387.1_Silent_p.S107S|CTNNA2_ENST00000361291.4_Silent_p.S141S|CTNNA2_ENST00000496558.1_Silent_p.S107S|CTNNA2_ENST00000540488.1_Silent_p.S107S	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	107					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GGATCGCCTCCTCCGAGTTTG	0.582																																					p.S107S		Atlas-SNP	.											.	CTNNA2	462	.	0			c.C321T						.						97	94	95					2																	80085161		2054	4194	6248	SO:0001819	synonymous_variant	1496	exon4			CGCCTCCTCCGAG		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.321C>T	chr2.hg19:g.80085161C>T		136.0	0.0		128.0	52.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	hg19																																																																																				.	.		0.582	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		T	80085161	C	T	80085161	2	4	37	1	0	0	0	0	0	0	0	1	4015	668	24	3		3	CTNNA2	2	80085161	Silent	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	21711570	80085161	163114212	9	4393										
DPP10	57628	hgsc.bcm.edu	37	chr2	116510776	116510776	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ctatatcactatggttaaatGggtaagcaataccaagactg	8	7	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr2:116510776G>T	ENST00000410059.1	+	11	1457	c.977G>T	c.(976-978)tGg>tTg	p.W326L	DPP10_ENST00000393147.2_Missense_Mutation_p.W330L|DPP10_ENST00000310323.8_Missense_Mutation_p.W319L|DPP10_ENST00000409163.1_Missense_Mutation_p.W276L	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	326						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						ATGGTTAAATGGGTAAGCAAT	0.378																																					p.W330L		Atlas-SNP	.											.	DPP10	415	.	0			c.G989T						.						104	92	96					2																	116510776		2203	4300	6503	SO:0001583	missense	57628	exon11			TTAAATGGGTAAG	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.977G>T	chr2.hg19:g.116510776G>T	ENSP00000386565:p.Trp326Leu	299.0	0.0		196.0	73.0	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.730807	0.89390	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	5.1	5.1	0.69264	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.81763	0.4891	H	0.96142	3.775	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	D	0.87568	0.2476	10	0.87932	D	0	-28.5782	17.6852	0.88255	0.0:0.0:1.0:0.0	.	319;330;322;326	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	L	326;276;330;319;276	ENSP00000386565:W326L;ENSP00000387038:W276L;ENSP00000376855:W330L;ENSP00000309066:W319L	ENSP00000309066:W319L	W	+	2	0	DPP10	116227246	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.236000	0.95360	2.660000	0.90430	0.650000	0.86243	TGG	.	.		0.378	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		T	116510776	G	T	116510776	3	4	37	1	0	0	0	0	1	0	0	0	4729	1357	47	3	1190	3	DPP10	2	116510776	Missense_Mutation	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10	36425615	116510776	126688597	10	4394										
ZNF445	353274	hgsc.bcm.edu	37	chr3	44489484	44489484	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tcttcttagcatgggtttctCggtgcagacggtaggctgac	13	9	3	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr3:44489484C>A	ENST00000396077.2	-	8	2026	c.1679G>T	c.(1678-1680)cGa>cTa	p.R560L	ZNF445_ENST00000425708.2_Missense_Mutation_p.R560L	NM_181489.5	NP_852466.1	P59923	ZN445_HUMAN	zinc finger protein 445	560					transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|skin(3)	31				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		ATGGGTTTCTCGGTGCAGACG	0.463																																					p.R560L		Atlas-SNP	.											.	ZNF445	91	.	0			c.G1679T						.						111	113	112					3																	44489484		2203	4300	6503	SO:0001583	missense	353274	exon8			GTTTCTCGGTGCA	AY262260	CCDS2713.1	3p21.32	2013-01-09	2003-10-07		ENSG00000185219	ENSG00000185219		"Zinc fingers, C2H2-type", "-", "-", "-"	21018	protein-coding gene	gene with protein product			"zinc finger protein 168"	ZNF168		7814019	Standard	NM_181489		Approved	ZKSCAN15, ZSCAN47	uc003cnf.2	P59923	OTTHUMG00000133042	ENST00000396077.2:c.1679G>T	chr3.hg19:g.44489484C>A	ENSP00000379387:p.Arg560Leu	114.0	0.0		92.0	12.0	NM_181489	Q3MJD1	Missense_Mutation	SNP	ENST00000396077.2	hg19	CCDS2713.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.662061	0.29515	.	.	ENSG00000185219	ENST00000425708;ENST00000396077	T;T	0.59083	0.29;0.29	3.61	0.854	0.19007	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.499968	0.17093	N	0.187319	T	0.33527	0.0866	N	0.16567	0.415	0.22511	N	0.999038	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17992	-1.0351	10	0.59425	D	0.04	.	2.4045	0.04409	0.2079:0.2355:0.0:0.5566	.	548;560	B7ZKX2;P59923	.;ZN445_HUMAN	L	560	ENSP00000413073:R560L;ENSP00000379387:R560L	ENSP00000379387:R560L	R	-	2	0	ZNF445	44464488	0.004000	0.15560	0.986000	0.45419	0.910000	0.53928	0.614000	0.24314	0.220000	0.20860	-0.423000	0.05987	CGA	.	.		0.463	ZNF445-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256647.2	NM_181489		A	44489484	C	A	44489484	3	1	37	1	0	0	0	0	1	0	0	0	17933	884	31	1	1420	1	ZNF445	3	44489484	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10		44489484	153532946	11	4395										
CSPG5	10675	hgsc.bcm.edu	37	chr3	47618408	47618409	+	Frame_Shift_Ins	INS	-	-	G													0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	aggtcgcacactgaccggcaINSggagccgttatgccgcacaa							TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr3:47618408_47618409insG	ENST00000383738.2	-	2	3205_3206	c.1107_1108insC	c.(1105-1110)tcctgcfs	p.C370fs	CSPG5_ENST00000465441.1_5'Flank|CSPG5_ENST00000264723.4_Frame_Shift_Ins_p.C370fs|CSPG5_ENST00000456150.1_Frame_Shift_Ins_p.C232fs	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	370					axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)	p.C370R(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		ACTGACCGGCAGGAGCCGTTAT	0.619																																					p.C370fs		Atlas-INDEL	.											CSPG5,NS,carcinoma,0,1	CSPG5	46	.	1	Substitution - Missense(1)	prostate(1)	c.1108_1109insC						.																																			SO:0001589	frameshift_variant	10675	exon2			.	AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.1108dupC	chr3.hg19:g.47618410_47618410dupG	ENSP00000373244:p.Cys370fs	130.0	0.0		159.0	10.0	NM_001206944	Q71M39|Q71M40	Frame_Shift_Ins	INS	ENST00000383738.2	hg19	CCDS56253.1																																																																																			.	.		0.619	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574		G	47618409	-	G	47618408	7	5	37	1	0	1	1	0	0	0	0	0	3963	188	7	0	527	0	CSPG5	3	47618408	Frame_Shift_Ins	INS	-	TCGA-BC-A10Y-01A-11D-A12Z-10	3128924	47618408	150404022	12	4396										
UPK1B	7348	hgsc.bcm.edu	37	chr3	118909118	118909118	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	attctgatgtttatagtataTgcctttgaagtggcatcttg	9	5	2	2	rs113148509		TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr3:118909118T>A	ENST00000264234.3	+	4	446	c.297T>A	c.(295-297)taT>taA	p.Y99*	UPK1B_ENST00000497685.1_Nonsense_Mutation_p.Y19*|UPK1B_ENST00000460625.1_Nonsense_Mutation_p.Y99*	NM_006952.3	NP_008883.2	O75841	UPK1B_HUMAN	uroplakin 1B	99					epithelial cell differentiation (GO:0030855)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	structural molecule activity (GO:0005198)			breast(1)|endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)	14				GBM - Glioblastoma multiforme(114;0.222)		TTATAGTATATGCCTTTGAAG	0.313																																					p.Y99X		Atlas-SNP	.											.	UPK1B	27	.	0			c.T297A						.						148	149	149					3																	118909118		2203	4300	6503	SO:0001587	stop_gained	7348	exon4			AGTATATGCCTTT	AF082888	CCDS2985.1	3q13.32	2013-02-14			ENSG00000114638	ENSG00000114638		"Tetraspanins"	12578	protein-coding gene	gene with protein product		602380		UPK1		9935153, 9846985	Standard	NM_006952		Approved	TSPAN20	uc003ecc.3	O75841	OTTHUMG00000159354	ENST00000264234.3:c.297T>A	chr3.hg19:g.118909118T>A	ENSP00000264234:p.Tyr99*	523.0	0.0		443.0	178.0	NM_006952	O60753|Q9UIM2|Q9UNX6	Nonsense_Mutation	SNP	ENST00000264234.3	hg19	CCDS2985.1	.	.	.	.	.	.	.	.	.	.	T	35	5.447698	0.96205	.	.	ENSG00000114638	ENST00000497685;ENST00000264234;ENST00000479520;ENST00000494855;ENST00000460625	.	.	.	4.57	-0.897	0.10553	.	0.079382	0.52532	D	0.000062	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-10.4254	8.7815	0.34794	0.0:0.3214:0.0:0.6786	.	.	.	.	X	19;99;99;99;99	.	ENSP00000264234:Y99X	Y	+	3	2	UPK1B	120391808	0.864000	0.29904	0.942000	0.38095	0.995000	0.86356	-0.303000	0.08210	-0.309000	0.08779	0.460000	0.39030	TAT	.	T|0.500;C|0.500		0.313	UPK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354883.2			A	118909118	T	A	118909118	4	1	37	1	0	0	0	0	0	1	0	0	17023	1471	51	4	307	4	UPK1B	3	118909118	Nonsense_Mutation	SNP	T	TCGA-BC-A10Y-01A-11D-A12Z-10	71290710	118909118	79113312	13	4397										
RHO	6010	hgsc.bcm.edu	37	chr3	129252455	129252455	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gcctcttgccttccagttccGgaactgcatgctcaccacca	7	17	2	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr3:129252455G>A	ENST00000296271.3	+	5	1035	c.941G>A	c.(940-942)cGg>cAg	p.R314Q		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	314					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)			breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	TTCCAGTTCCGGAACTGCATG	0.622																																					p.R314Q	Esophageal Squamous(118;214 1623 30842 43234 46940)	Atlas-SNP	.											.	RHO	57	.	0			c.G941A						.						153	134	140					3																	129252455		2203	4300	6503	SO:0001583	missense	6010	exon5			AGTTCCGGAACTG	AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"GPCR / Class A : Opsin receptors"	10012	protein-coding gene	gene with protein product	"opsin 2, rod pigment"	180380	"retinitis pigmentosa 4, autosomal dominant"	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.941G>A	chr3.hg19:g.129252455G>A	ENSP00000296271:p.Arg314Gln	33.0	0.0		68.0	33.0	NM_000539	Q16414|Q2M249	Missense_Mutation	SNP	ENST00000296271.3	hg19	CCDS3063.1	.	.	.	.	.	.	.	.	.	.	G	35	5.479852	0.96307	.	.	ENSG00000163914	ENST00000296271	T	0.57273	0.41	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.72439	0.3460	M	0.70275	2.135	0.80722	D	1	D	0.76494	0.999	D	0.71870	0.975	T	0.75909	-0.3151	10	0.87932	D	0	.	18.7559	0.91832	0.0:0.0:1.0:0.0	.	314	P08100	OPSD_HUMAN	Q	314	ENSP00000296271:R314Q	ENSP00000296271:R314Q	R	+	2	0	RHO	130735145	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.383000	0.97214	2.428000	0.82296	0.655000	0.94253	CGG	.	.		0.622	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539		A	129252455	G	A	129252455	3	1	37	1	0	0	0	0	1	0	0	0	13345	1116	39	1	959	1	RHO	3	129252455	Missense_Mutation	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10	10343337	129252455	68769975	14	4398										
UGT2B15	7366	hgsc.bcm.edu	37	chr4	69535667	69535667	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	cagatcataaatttgaaaccAaaagtcaaaataaagcatat	4	6	2	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr4:69535667A>G	ENST00000338206.5	-	1	679	c.670T>C	c.(670-672)Tgg>Cgg	p.W224R		NM_001076.3	NP_001067.2	P54855	UDB15_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B15	224					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)									Acetaminophen(DB00316)|Dabigatran etexilate(DB06695)|Ezetimibe(DB00973)|Lorazepam(DB00186)|Morphine(DB00295)|Oxazepam(DB00842)|Valproic Acid(DB00313)	ATTTGAAACCAAAAGTCAAAA	0.328																																					p.W224R		Atlas-SNP	.											.	UGT2B15	48	.	0			c.T670C						.						100	111	107					4																	69535667		2203	4296	6499	SO:0001583	missense	7366	exon1			GAAACCAAAAGTC	AF180322	CCDS3524.1	4q13	2008-02-05	2005-07-20		ENSG00000196620	ENSG00000196620		"UDP glucuronosyltransferases"	12546	protein-coding gene	gene with protein product		600069	"UDP glycosyltransferase 2 family, polypeptide B15"			7835904	Standard	NM_001076		Approved	UGT2B8	uc021xow.1	P54855	OTTHUMG00000161507	ENST00000338206.5:c.670T>C	chr4.hg19:g.69535667A>G	ENSP00000341045:p.Trp224Arg	429.0	2.0		184.0	147.0	NM_001076	A6NDX0|A6NNJ4|A8K054|P23765|Q9UK63	Missense_Mutation	SNP	ENST00000338206.5	hg19	CCDS3524.1	.	.	.	.	.	.	.	.	.	.	a	6.602	0.479446	0.12581	.	.	ENSG00000196620	ENST00000338206	T	0.60424	0.19	2.79	2.79	0.32731	.	0.376195	0.20935	U	0.083027	T	0.50956	0.1646	M	0.64567	1.98	0.23192	N	0.998149	B	0.15473	0.013	B	0.23852	0.049	T	0.50363	-0.8837	10	0.59425	D	0.04	.	5.9768	0.19385	0.7309:0.2691:0.0:0.0	.	224	P54855	UDB15_HUMAN	R	224	ENSP00000341045:W224R	ENSP00000341045:W224R	W	-	1	0	UGT2B15	69218262	0.010000	0.17322	1.000000	0.80357	0.578000	0.36192	1.985000	0.40668	1.259000	0.44117	0.363000	0.22086	TGG	.	.		0.328	UGT2B15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365172.1	NM_001076		G	69535667	A	G	69535667	3	3	37	1	0	0	0	0	1	0	0	0	16973	130	5	2	2563	2	UGT2B15	4	69535667	Missense_Mutation	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10		69535667	121618609	15	4399										
NR3C2	4306	hgsc.bcm.edu	37	chr4	149075987	149075988	+	Frame_Shift_Ins	INS	-	-	C													0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ggtgggggtgggggtgggggINSctgctgctgctgtggctgct							TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr4:149075987_149075988insC	ENST00000358102.3	-	5	2441_2442	c.2079_2080insG	c.(2077-2082)cagcccfs	p.P694fs	NR3C2_ENST00000344721.4_Frame_Shift_Ins_p.P694fs|NR3C2_ENST00000512865.1_Intron|NR3C2_ENST00000511528.1_Frame_Shift_Ins_p.P698fs|NR3C2_ENST00000503313.1_5'UTR|NR3C2_ENST00000355292.3_Frame_Shift_Ins_p.P698fs|RP11-76G10.1_ENST00000514843.1_RNA	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	694	Hinge.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	gggggtgggggCTGCTGCTGCT	0.515																																					p.P694fs	Melanoma(27;428 957 40335 51025 51111)	Atlas-INDEL	.											.	NR3C2	94	.	0			c.2080_2081insG						.																																			SO:0001589	frameshift_variant	4306	exon5			.	M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.2080dupG	chr4.hg19:g.149075988_149075988dupC	ENSP00000350815:p.Pro694fs	106.0	0.0		146.0	10.0	NM_000901	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Frame_Shift_Ins	INS	ENST00000358102.3	hg19	CCDS3772.1																																																																																			.	.		0.515	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			C	149075988	-	C	149075987	7	5	37	1	0	1	1	0	0	0	0	0	10640	1203	42	0	894	0	NR3C2	4	149075987	Frame_Shift_Ins	INS	-	TCGA-BC-A10Y-01A-11D-A12Z-10	79540320	149075987	42078289	16	4400										
PCDHGC5	56097	hgsc.bcm.edu	37	chr5	140869331	140869332	+	Frame_Shift_Ins	INS	-	-	C													0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ttttacactctaagccccaaINScagccacttctctctgaatg					rs145669059		TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr5:140869331_140869332insC	ENST00000252087.1	+	1	524_525	c.524_525insC	c.(523-528)aacagcfs	p.S176fs	PCDHGA3_ENST00000253812.6_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	176	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTAAGCCCCAACAGCCACTTCT	0.535																																					p.N175fs		Atlas-INDEL	.											.	PCDHGC5	199	.	0			c.524_525insC						.																																			SO:0001589	frameshift_variant	56097	exon1			.	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"Cadherins / Protocadherins : Clustered"	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.525dupC	chr5.hg19:g.140869332_140869332dupC	ENSP00000252087:p.Ser176fs	86.0	0.0		122.0	11.0	NM_018929	Q9Y5C2	Frame_Shift_Ins	INS	ENST00000252087.1	hg19	CCDS4263.1																																																																																			.	.		0.535	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929		C	140869332	-	C	140869331	7	5	37	1	0	1	1	0	0	0	0	0	11580	43	2	0	526	0	PCDHGC5	5	140869331	Frame_Shift_Ins	INS	-	TCGA-BC-A10Y-01A-11D-A12Z-10		140869331	40045929	17	4401										
NIPAL4	348938	hgsc.bcm.edu	37	chr5	156899886	156899886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tgttattagactggaagacaAgaacgtccttgtggacaata	10	6	0	3	rs536139990		TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr5:156899886A>G	ENST00000311946.7	+	6	1435	c.1319A>G	c.(1318-1320)aAg>aGg	p.K440R	NIPAL4_ENST00000435489.2_Missense_Mutation_p.K421R|ADAM19_ENST00000430702.2_Intron	NM_001099287.1	NP_001092757.1	Q0D2K0	NIPA4_HUMAN	NIPA-like domain containing 4	440						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(3)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|skin(1)	22						CTGGAAGACAAGAACGTCCTT	0.483																																					p.K440R		Atlas-SNP	.											.	NIPAL4	48	.	0			c.A1319G						.						45	44	45					5																	156899886		1897	4129	6026	SO:0001583	missense	348938	exon6			AAGACAAGAACGT	AK026158	CCDS47328.1, CCDS54944.1	5q33.3	2009-03-24	2009-03-24		ENSG00000172548	ENSG00000172548			28018	protein-coding gene	gene with protein product	"ichthyin"	609383	"NIPA-like 4"			8619474, 9110174, 15317751	Standard	NM_001099287		Approved	ICHYN	uc003lwx.4	Q0D2K0	OTTHUMG00000163497	ENST00000311946.7:c.1319A>G	chr5.hg19:g.156899886A>G	ENSP00000311687:p.Lys440Arg	80.0	0.0		82.0	34.0	NM_001099287	A8S6F1|A8S6F5|A8S6F8|B4DLF3|Q0D2J8|Q0D2J9	Missense_Mutation	SNP	ENST00000311946.7	hg19	CCDS47328.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.518720	0.64634	.	.	ENSG00000172548	ENST00000435489;ENST00000311946	D;D	0.91521	-2.73;-2.86	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.91630	0.7355	N	0.24115	0.695	0.58432	D	0.999991	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	D	0.91331	0.5090	10	0.35671	T	0.21	-30.6807	16.3829	0.83481	1.0:0.0:0.0:0.0	.	421;440	Q0D2K0-2;Q0D2K0	.;NIPA4_HUMAN	R	421;440	ENSP00000406456:K421R;ENSP00000311687:K440R	ENSP00000311687:K440R	K	+	2	0	NIPAL4	156832464	1.000000	0.71417	1.000000	0.80357	0.409000	0.31022	5.975000	0.70475	2.271000	0.75665	0.459000	0.35465	AAG	.	.		0.483	NIPAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373789.1	NM_001099287		G	156899886	A	G	156899886	3	3	37	1	0	0	0	0	1	0	0	0	10436	72	3	2	1341	2	NIPAL4	5	156899886	Missense_Mutation	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10	16030555	156899886	24015374	18	4402										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168119629	168119629	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tacctgaatcctttgtccagGgggatgcacttggcctcatg	11	11	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr5:168119629G>A	ENST00000519560.1	-	29	3578	c.3159C>T	c.(3157-3159)ccC>ccT	p.P1053P	SLIT3_ENST00000332966.8_Silent_p.P1060P|SLIT3_ENST00000404867.3_Silent_p.P1053P	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1053	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTTTGTCCAGGGGGATGCACT	0.542																																					p.P1060P	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C3180T						.						112	85	94					5																	168119629		2203	4300	6503	SO:0001819	synonymous_variant	6586	exon29			GTCCAGGGGGATG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.3159C>T	chr5.hg19:g.168119629G>A		73.0	0.0		90.0	9.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.542	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		A	168119629	G	A	168119629	2	1	37	1	0	0	0	0	0	0	0	1	14756	1219	43	3		3	SLIT3	5	168119629	Silent	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10	11219743	168119629	12795631	19	4403										
PDGFA	5154	hgsc.bcm.edu	37	chr7	550578	550578	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gacgtggggtcgacctgactCcgaggaatctcgtaaatgac	13	10	1	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr7:550578C>T	ENST00000354513.5	-	4	713	c.321G>A	c.(319-321)cgG>cgA	p.R107R	PDGFA_ENST00000402802.3_Silent_p.R107R|PDGFA_ENST00000426681.2_5'Flank	NM_002607.5	NP_002598.4	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha polypeptide	107					actin cytoskeleton organization (GO:0030036)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell activation (GO:0001775)|cell projection assembly (GO:0030031)|cell-cell signaling (GO:0007267)|embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|negative chemotaxis (GO:0050919)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling (GO:0060683)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of smooth muscle cell migration (GO:0014910)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|microvillus (GO:0005902)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|growth factor activity (GO:0008083)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		CGACCTGACTCCGAGGAATCT	0.647																																					p.R107R		Atlas-SNP	.											.	PDGFA	34	.	0			c.G321A						.						72	57	62					7																	550578		2202	4300	6502	SO:0001819	synonymous_variant	5154	exon4			CTGACTCCGAGGA		CCDS34578.1, CCDS47524.1	7p22	2008-07-18			ENSG00000197461	ENSG00000197461			8799	protein-coding gene	gene with protein product	"PDGF A-chain", "platelet-derived growth factor alpha chain"	173430				1505216, 2536956	Standard	NM_002607		Approved	PDGF1, PDGF-A	uc003sir.3	P04085	OTTHUMG00000151412	ENST00000354513.5:c.321G>A	chr7.hg19:g.550578C>T		93.0	0.0		137.0	63.0	NM_002607	B5BU73	Silent	SNP	ENST00000354513.5	hg19	CCDS34578.1	.	.	.	.	.	.	.	.	.	.	c	3.113	-0.182242	0.06340	.	.	ENSG00000197461	ENST00000400761	.	.	.	4.69	1.76	0.24704	.	.	.	.	.	T	0.45538	0.1347	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27739	-1.0065	4	.	.	.	-15.6095	3.0708	0.06230	0.143:0.5642:0.1386:0.1542	.	.	.	.	K	114	.	.	E	-	1	0	PDGFA	517104	0.985000	0.35326	1.000000	0.80357	0.113000	0.19764	0.340000	0.19892	0.420000	0.25954	-0.251000	0.11542	GAG	.	.		0.647	PDGFA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322534.1			T	550578	C	T	550578	2	4	37	1	0	0	0	0	0	0	0	1	11666	842	30	3		3	PDGFA	7	550578	Silent	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10		550578	158588085	20	4404										
PCLO	27445	hgsc.bcm.edu	37	chr7	82464992	82464992	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	aacaactctaccttgcattcTggacaaccatgacttgactg	6	12	2	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr7:82464992T>C	ENST00000333891.9	-	16	14577	c.14240A>G	c.(14239-14241)cAg>cGg	p.Q4747R	PCLO_ENST00000426442.2_Intron|PCLO_ENST00000423517.2_Missense_Mutation_p.Q4747R	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CCTTGCATTCTGGACAACCAT	0.388																																					p.Q4747R		Atlas-SNP	.											.	PCLO	1506	.	0			c.A14240G						.						59	58	58					7																	82464992		1889	4129	6018	SO:0001583	missense	27445	exon16			GCATTCTGGACAA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14240A>G	chr7.hg19:g.82464992T>C	ENSP00000334319:p.Gln4747Arg	162.0	0.0		180.0	84.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	15.84	2.952682	0.53293	.	.	ENSG00000186472	ENST00000333891;ENST00000423517	T;T	0.40756	1.02;1.02	5.88	5.88	0.94601	.	.	.	.	.	T	0.53302	0.1788	N	0.25890	0.77	0.80722	D	1	D;D	0.65815	0.995;0.995	D;D	0.85130	0.997;0.997	T	0.57619	-0.7780	9	0.87932	D	0	.	15.958	0.79902	0.0:0.0:0.0:1.0	.	4747;4747	Q9Y6V0-5;Q9Y6V0-6	.;.	R	4747	ENSP00000334319:Q4747R;ENSP00000388393:Q4747R	ENSP00000334319:Q4747R	Q	-	2	0	PCLO	82302928	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.816000	0.86201	2.243000	0.73865	0.528000	0.53228	CAG	.	.		0.388	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82464992	T	C	82464992	3	2	37	1	0	0	0	0	1	0	0	0	11592	1580	55	2	1245	2	PCLO	7	82464992	Missense_Mutation	SNP	T	TCGA-BC-A10Y-01A-11D-A12Z-10	81914414	82464992	76673671	21	4405										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107688358	107688358	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	agagaagatatttacctgatTtttcaacccacgaacctgtt	6	9	1	3			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr7:107688358T>C	ENST00000388781.3	-	28	4404	c.4321A>G	c.(4321-4323)Aat>Gat	p.N1441D	LAMB4_ENST00000205386.4_Missense_Mutation_p.N1441D|LAMB4_ENST00000388780.3_Missense_Mutation_p.N1441D	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1441	Domain I.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						TTTACCTGATTTTTCAACCCA	0.383																																					p.N1441D		Atlas-SNP	.											.	LAMB4	253	.	0			c.A4321G						.						62	66	65					7																	107688358		2203	4300	6503	SO:0001583	missense	22798	exon28			CCTGATTTTTCAA	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.4321A>G	chr7.hg19:g.107688358T>C	ENSP00000373433:p.Asn1441Asp	374.0	0.0		354.0	168.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	hg19	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.687673	0.29962	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000422975;ENST00000388780	T;T;T;T	0.31510	1.49;1.49;1.9;1.51	4.69	4.69	0.59074	.	0.114976	0.38436	N	0.001692	T	0.26593	0.0650	L	0.27053	0.805	0.80722	D	1	B;P	0.46784	0.03;0.884	B;P	0.46419	0.012;0.516	T	0.02294	-1.1181	10	0.18710	T	0.47	.	13.9803	0.64301	0.0:0.0:0.0:1.0	.	1441;1441	A4D0S4-3;A4D0S4	.;LAMB4_HUMAN	D	1441;1441;467;1441	ENSP00000205386:N1441D;ENSP00000373433:N1441D;ENSP00000416562:N467D;ENSP00000373432:N1441D	ENSP00000205386:N1441D	N	-	1	0	LAMB4	107475594	1.000000	0.71417	0.769000	0.31535	0.189000	0.23516	2.397000	0.44477	1.972000	0.57404	0.482000	0.46254	AAT	.	.		0.383	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		C	107688358	T	C	107688358	3	2	37	1	0	0	0	0	1	0	0	0	8622	1841	64	2	992	2	LAMB4	7	107688358	Missense_Mutation	SNP	T	TCGA-BC-A10Y-01A-11D-A12Z-10	25223366	107688358	51450305	22	4406										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107866734	107866734	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gcataacagatatagtcttcGcgggtgtcctctgggaggac	13	9	2	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr7:107866734G>A	ENST00000425651.2	-	6	638	c.639C>T	c.(637-639)cgC>cgT	p.R213R	NRCAM_ENST00000351718.4_Silent_p.R207R|NRCAM_ENST00000413765.2_Silent_p.R213R|NRCAM_ENST00000379028.3_Silent_p.R213R|NRCAM_ENST00000379024.4_Silent_p.R213R|NRCAM_ENST00000379022.4_Silent_p.R213R	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	213	Ig-like 2.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						TATAGTCTTCGCGGGTGTCCT	0.428																																					p.R213R		Atlas-SNP	.											.	NRCAM	267	.	0			c.C639T						.						127	134	132					7																	107866734		2203	4300	6503	SO:0001819	synonymous_variant	4897	exon6			GTCTTCGCGGGTG		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.639C>T	chr7.hg19:g.107866734G>A		62.0	0.0		47.0	21.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	hg19	CCDS47686.1																																																																																			.	.		0.428	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		A	107866734	G	A	107866734	2	1	37	1	0	0	0	0	0	0	0	1	10653	1074	38	1		1	NRCAM	7	107866734	Silent	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10	178376	107866734	51271929	23	4407										
MLL3	58508	hgsc.bcm.edu	37	chr7	151873592	151873592	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	acctgcacaccctgagaaaaAacatggtttaccctagagac	7	12	0	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr7:151873592A>C	ENST00000262189.6	-	38	9164	c.8946T>G	c.(8944-8946)gtT>gtG	p.V2982V	KMT2C_ENST00000355193.2_Silent_p.V2982V	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2982					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CCTGAGAAAAAACATGGTTTA	0.473																																					p.V2982V		Atlas-SNP	.											.	MLL3	1564	.	0			c.T8946G						.						55	53	54					7																	151873592		2203	4300	6503	SO:0001819	synonymous_variant	58508	exon38			AGAAAAAACATGG	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8946T>G	chr7.hg19:g.151873592A>C		191.0	0.0		187.0	76.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	A	5.855	0.341872	0.11069	.	.	ENSG00000055609	ENST00000360104	.	.	.	5.47	0.266	0.15617	.	.	.	.	.	T	0.44973	0.1319	.	.	.	0.52099	D	0.999947	.	.	.	.	.	.	T	0.22452	-1.0216	4	.	.	.	.	3.6374	0.08154	0.4698:0.0:0.2762:0.254	.	.	.	.	V	488	.	.	F	-	1	0	MLL3	151504525	0.682000	0.27624	0.829000	0.32907	0.966000	0.64601	0.648000	0.24828	-0.182000	0.10602	-0.256000	0.11100	TTT	.	.		0.473	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151873592	A	C	151873592	2	2	37	1	0	0	0	0	0	0	0	1	9631	1	1	5		5	MLL3	7	151873592	Silent	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10	44006858	151873592	7265071	24	4408										
ZHX2	22882	hgsc.bcm.edu	37	chr8	123965265	123965265	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gtccacatcaccagcgaatcCcttgccaaagaccagttggc	8	15	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr8:123965265C>A	ENST00000314393.4	+	3	2350	c.1515C>A	c.(1513-1515)tcC>tcA	p.S505S		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	505					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CCAGCGAATCCCTTGCCAAAG	0.562																																					p.S505S	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.C1515A						.						83	67	72					8																	123965265		2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CGAATCCCTTGCC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1515C>A	chr8.hg19:g.123965265C>A		31.0	0.0		40.0	17.0	NM_014943		Silent	SNP	ENST00000314393.4	hg19	CCDS6336.1																																																																																			.	.		0.562	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		A	123965265	C	A	123965265	2	1	37	1	0	0	0	0	0	0	0	1	17691	610	22	3		3	ZHX2	8	123965265	Silent	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10		123965265	22398757	25	4409										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77416900	77416900	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	attgcccggtagaggatacaCgcaatcacggctttaaccgt	10	11	1	1	rs372508531		TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr9:77416900C>T	ENST00000360774.1	-	16	2160	c.1923G>A	c.(1921-1923)gcG>gcA	p.A641A	TRPM6_ENST00000451710.3_Silent_p.A641A|TRPM6_ENST00000361255.3_Silent_p.A636A|TRPM6_ENST00000376864.4_Silent_p.A641A|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000376871.3_Intron|RN7SKP47_ENST00000365347.1_RNA|TRPM6_ENST00000449912.2_Silent_p.A636A	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	641					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						AGAGGATACACGCAATCACGG	0.493																																					p.A641A		Atlas-SNP	.											.	TRPM6	377	.	0			c.G1923A						.	C	,,	0,4406		0,0,2203	146	122	130		1908,1908,1923	-6.3	0.1	9		130	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	636/2018,636/2018,641/2023	77416900	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon16			GATACACGCAATC	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.1923G>A	chr9.hg19:g.77416900C>T		168.0	0.0		192.0	84.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	hg19	CCDS6647.1																																																																																			.	.		0.493	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		T	77416900	C	T	77416900	2	4	37	1	0	0	0	0	0	0	0	1	16605	523	19	1		1	TRPM6	9	77416900	Silent	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10		77416900	63796531	26	4410										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98268744	98268744	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ttcgctgcttttaatcccacCgcgaaggccccaaatatgag	8	13	0	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr9:98268744C>A	ENST00000331920.6	-	2	638	c.339G>T	c.(337-339)gcG>gcT	p.A113A	PTCH1_ENST00000437951.1_Silent_p.A47A|PTCH1_ENST00000418258.1_5'UTR|PTCH1_ENST00000421141.1_5'UTR|PTCH1_ENST00000430669.2_Silent_p.A47A|RP11-435O5.5_ENST00000604104.1_RNA|PTCH1_ENST00000429896.2_5'UTR|PTCH1_ENST00000468211.2_Silent_p.A47A|PTCH1_ENST00000375274.2_Silent_p.A112A	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	113					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TTAATCCCACCGCGAAGGCCC	0.577																																					p.A113A		Atlas-SNP	.											.	PTCH1	1850	.	0			c.G339T						.						61	60	60					9																	98268744		2203	4300	6503	SO:0001819	synonymous_variant	5727	exon2			TCCCACCGCGAAG	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.339G>T	chr9.hg19:g.98268744C>A		181.0	0.0		200.0	90.0	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	hg19	CCDS6714.1																																																																																			.	.		0.577	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		A	98268744	C	A	98268744	2	1	37	1	0	0	0	0	0	0	0	1	12742	639	23	1		1	PTCH1	9	98268744	Silent	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	20851844	98268744	42944687	27	4411										
GPSM1	26086	hgsc.bcm.edu	37	chr9	139234260	139234260	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ttcgccaagaagcacctgcaGatctcccaggaggtgagcca	11	13	1	3			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr9:139234260G>A	ENST00000440944.1	+	8	1291	c.1071G>A	c.(1069-1071)caG>caA	p.Q357Q	GPSM1_ENST00000392945.3_Silent_p.Q357Q	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	357	Mediates association with membranes. {ECO:0000250}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		AGCACCTGCAGATCTCCCAGG	0.711																																					p.Q357Q		Atlas-SNP	.											.	GPSM1	50	.	0			c.G1071A						.						28	29	29					9																	139234260		1829	3503	5332	SO:0001819	synonymous_variant	26086	exon8			CCTGCAGATCTCC	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"Tetratricopeptide (TTC) repeat domain containing"	17858	protein-coding gene	gene with protein product	"AGS3 homolog (C. elegans)"	609491	"G-protein signalling modulator 1 (AGS3-like, C. elegans)"			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1071G>A	chr9.hg19:g.139234260G>A		86.0	0.0		105.0	30.0	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Silent	SNP	ENST00000440944.1	hg19	CCDS48055.1																																																																																			.	.		0.711	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		A	139234260	G	A	139234260	2	1	37	1	0	0	0	0	0	0	0	1	6743	933	33	3		3	GPSM1	9	139234260	Silent	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10	40965516	139234260	1979171	28	4412										
C9orf86	55684	hgsc.bcm.edu	37	chr9	139732077	139732077	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	atcatctctaggctgtttggGacgtcacctgccaccgaggc	11	13	3	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr9:139732077G>A	ENST00000311502.7	+	9	1325	c.1089G>A	c.(1087-1089)ggG>ggA	p.G363G	RABL6_ENST00000432842.2_Silent_p.G325G|RABL6_ENST00000371675.3_Silent_p.G248G|RABL6_ENST00000357466.2_Intron|RABL6_ENST00000371663.4_Silent_p.G364G			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	363	Pro-rich.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										GGCTGTTTGGGACGTCACCTG	0.697																																					p.G364G		Atlas-SNP	.											.	.	.	.	0			c.G1092A						.						9	10	9					9																	139732077		1893	4086	5979	SO:0001819	synonymous_variant	55684	exon9			GTTTGGGACGTCA	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"Rab-like protein 1", "partner of ARF"	610615	"chromosome 9 open reading frame 86"	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1089G>A	chr9.hg19:g.139732077G>A		32.0	0.0		82.0	24.0	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Silent	SNP	ENST00000311502.7	hg19	CCDS48058.1																																																																																			.	.		0.697	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718		A	139732077	G	A	139732077	2	1	37	1	0	0	0	0	0	0	0	1	2504	1161	41	3		3	C9orf86	9	139732077	Silent	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10	497817	139732077	1481354	29	4413										
MAN1B1	11253	hgsc.bcm.edu	37	chr9	140001761	140001761	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ggcgtctaccacggcctgccCgccagccacatggagctggc	13	17	1	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr9:140001761C>T	ENST00000371589.4	+	11	1699	c.1626C>T	c.(1624-1626)ccC>ccT	p.P542P	MAN1B1_ENST00000540391.1_3'UTR|MAN1B1_ENST00000474902.1_Silent_p.P245P	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	542					cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		ACGGCCTGCCCGCCAGCCACA	0.632																																					p.P542P		Atlas-SNP	.											.	MAN1B1	40	.	0			c.C1626T						.						47	52	50					9																	140001761		2202	4300	6502	SO:0001819	synonymous_variant	11253	exon11			CCTGCCCGCCAGC	AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239			6823	protein-coding gene	gene with protein product	"endoplasmic reticulum alpha-mannosidase 1", "alpha 1,2-mannosidase", "endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1", "ER alpha 1,2-mannosidase", "Man9GlcNAc2-specific processing alpha-mannosidase"	604346				10409699, 10521544	Standard	NM_016219		Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.1626C>T	chr9.hg19:g.140001761C>T		162.0	0.0		264.0	89.0	NM_016219	Q5VSG3|Q9BRS9|Q9Y5K7	Silent	SNP	ENST00000371589.4	hg19	CCDS7029.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.802124	0.00075	.	.	ENSG00000177239	ENST00000535144;ENST00000475449	.	.	.	4.47	-8.94	0.00768	.	.	.	.	.	T	0.14960	0.0361	.	.	.	0.26598	N	0.973067	.	.	.	.	.	.	T	0.08371	-1.0725	4	.	.	.	.	1.0599	0.01598	0.2887:0.0969:0.2715:0.343	.	.	.	.	C	516;16	.	.	R	+	1	0	MAN1B1	139121582	0.000000	0.05858	0.001000	0.08648	0.253000	0.25986	-5.232000	0.00139	-3.577000	0.00138	-1.319000	0.01295	CGC	.	.		0.632	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055294.2	NM_016219		T	140001761	C	T	140001761	2	4	37	1	0	0	0	0	0	0	0	1	9221	639	23	1		1	MAN1B1	9	140001761	Silent	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	269684	140001761	1211670	30	4414										
GRIN1	2902	hgsc.bcm.edu	37	chr9	140057425	140057425	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gaagcacaactacgagagtgCggcggaggccatccaggccg	15	12	0	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr9:140057425C>G	ENST00000371561.3	+	15	3238	c.2141C>G	c.(2140-2142)gCg>gGg	p.A714G	GRIN1_ENST00000315048.3_Missense_Mutation_p.A714G|GRIN1_ENST00000371553.3_Missense_Mutation_p.A735G|GRIN1_ENST00000471122.1_3'UTR|GRIN1_ENST00000350902.5_Missense_Mutation_p.A714G|GRIN1_ENST00000371559.4_Missense_Mutation_p.A714G|GRIN1_ENST00000371560.3_Missense_Mutation_p.A735G|GRIN1_ENST00000371555.4_Missense_Mutation_p.A735G|GRIN1_ENST00000371546.4_Missense_Mutation_p.A735G|GRIN1_ENST00000371550.4_Missense_Mutation_p.A714G	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	714					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TACGAGAGTGCGGCGGAGGCC	0.677																																					p.A735G	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											.	GRIN1	51	.	0			c.C2204G						.						24	21	22					9																	140057425		2198	4296	6494	SO:0001583	missense	2902	exon16			AGAGTGCGGCGGA		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4584	protein-coding gene	gene with protein product		138249	"N-methyl-D-aspartate receptor subunit NR1"	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.2141C>G	chr9.hg19:g.140057425C>G	ENSP00000360616:p.Ala714Gly	37.0	0.0		46.0	9.0	NM_001185091	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Missense_Mutation	SNP	ENST00000371561.3	hg19	CCDS7031.1	.	.	.	.	.	.	.	.	.	.	c	26.8	4.771107	0.90108	.	.	ENSG00000176884	ENST00000371561;ENST00000315048;ENST00000350902;ENST00000371550;ENST00000371546;ENST00000371555;ENST00000371553;ENST00000371559;ENST00000371560	T;T;T;T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81;1.81;1.81;1.81	4.83	4.83	0.62350	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.50616	0.1626	M	0.71581	2.175	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;1.0;0.999	D;D;D;D;D;D	0.78314	0.982;0.984;0.969;0.969;0.982;0.991	T	0.52548	-0.8561	10	0.52906	T	0.07	.	16.5012	0.84257	0.0:1.0:0.0:0.0	.	735;735;714;714;714;714	Q5VSF4;Q5VSF5;Q05586-2;Q05586-3;Q05586;A2AVK2	.;.;.;.;NMDZ1_HUMAN;.	G	714;714;714;714;735;735;735;714;735	ENSP00000360616:A714G;ENSP00000316696:A714G;ENSP00000316915:A714G;ENSP00000360605:A714G;ENSP00000360601:A735G;ENSP00000360610:A735G;ENSP00000360608:A735G;ENSP00000360614:A714G;ENSP00000360615:A735G	ENSP00000316696:A714G	A	+	2	0	GRIN1	139177246	1.000000	0.71417	0.518000	0.27811	0.964000	0.63967	5.527000	0.67123	2.247000	0.74100	0.450000	0.29827	GCG	.	.		0.677	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327		G	140057425	C	G	140057425	3	3	37	1	0	0	0	0	1	0	0	0	6787	768	27	4	2266	4	GRIN1	9	140057425	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	55664	140057425	1156006	31	4415										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64952867	64952867	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tgctgctgagactcaggcatGcacagagaaattttattact	9	8	1	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr10:64952867G>A	ENST00000399262.2	-	16	6125	c.5907C>T	c.(5905-5907)tgC>tgT	p.C1969C	JMJD1C_ENST00000402544.1_Intron|JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000542921.1_Silent_p.C1787C	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1969					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					ACTCAGGCATGCACAGAGAAA	0.368																																					p.C1969C		Atlas-SNP	.											.	JMJD1C	347	.	0			c.C5907T						.						89	80	83					10																	64952867		1870	4124	5994	SO:0001819	synonymous_variant	221037	exon16			AGGCATGCACAGA	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.5907C>T	chr10.hg19:g.64952867G>A		165.0	0.0		144.0	63.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Silent	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	G	9.178	1.022904	0.19433	.	.	ENSG00000171988	ENST00000327520	.	.	.	5.67	4.63	0.57726	.	.	.	.	.	T	0.59404	0.2191	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56553	-0.7960	4	.	.	.	-1.7841	8.8589	0.35245	0.1963:0.0:0.8037:0.0	.	.	.	.	V	516	.	.	A	-	2	0	JMJD1C	64622873	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.388000	0.34442	1.141000	0.42275	0.650000	0.86243	GCA	.	.		0.368	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		A	64952867	G	A	64952867	2	1	37	1	0	0	0	0	0	0	0	1	7959	1311	46	3		3	JMJD1C	10	64952867	Silent	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10		64952867	70581880	32	4416										
PHRF1	57661	hgsc.bcm.edu	37	chr11	608299	608299	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ggatgaggaggatggggcgtCttgcagcaccttctttggct	16	8	2	1	rs200183606		TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr11:608299C>T	ENST00000264555.5	+	14	2971	c.2843C>T	c.(2842-2844)tCt>tTt	p.S948F	PHRF1_ENST00000413872.2_Missense_Mutation_p.S946F|PHRF1_ENST00000416188.2_Missense_Mutation_p.S947F|PHRF1_ENST00000533464.1_Missense_Mutation_p.S944F	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	948					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GATGGGGCGTCTTGCAGCACC	0.687																																					p.S947F		Atlas-SNP	.											.	PHRF1	188	.	0			c.C2840T						.	C	PHE/SER	0,4022		0,0,2011	17	23	21		2840	2.5	0	11		21	2,8286		0,2,4142	yes	missense	PHRF1	NM_020901.2	155	0,2,6153	TT,TC,CC		0.0241,0.0,0.0162	benign	947/1649	608299	2,12308	2011	4144	6155	SO:0001583	missense	57661	exon14			GGGCGTCTTGCAG	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.2843C>T	chr11.hg19:g.608299C>T	ENSP00000264555:p.Ser948Phe	21.0	0.0		34.0	14.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	C	10.04	1.240978	0.22711	0.0	2.41E-4	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	4.35	2.48	0.30137	.	0.915450	0.08977	N	0.866320	T	0.65647	0.2711	N	0.19112	0.55	0.09310	N	1	P;P;P;P	0.39157	0.531;0.662;0.662;0.531	B;B;B;B	0.33196	0.076;0.159;0.159;0.076	T	0.54470	-0.8289	10	0.56958	D	0.05	-4.1525	8.2573	0.31765	0.0:0.5833:0.3026:0.1141	.	944;946;947;948	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	F	948;946;947;944	ENSP00000264555:S948F;ENSP00000388589:S946F;ENSP00000410626:S947F;ENSP00000431870:S944F	ENSP00000264555:S948F	S	+	2	0	PHRF1	598299	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	1.261000	0.32980	0.473000	0.27368	0.555000	0.69702	TCT	.	C|0.996;T|0.004		0.687	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		T	608299	C	T	608299	3	4	37	1	0	0	0	0	1	0	0	0	11870	913	32	3	2890	3	PHRF1	11	608299	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10		608299	134398217	33	4417										
PRB3	5544	hgsc.bcm.edu	37	chr12	11420457	11420583	+	Frame_Shift_Del	DEL	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	-													0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ggtccttctggctttcctggAcgaggtgggggaccttgagg					rs367917023|rs552923329|rs12811806|rs200902635|rs570697251|rs113884749|rs11054203|rs370173277|rs28435564|rs112526960|rs375731986|rs12368171|rs200117404|rs12811811|rs539718896|rs550913655	byFrequency	TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr12:11420457_11420583delGAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	ENST00000279573.7	-	3	735_861	c.600_726delGTCCAGGAAAGCCAGAAGGACCACCCCCACAAGGAGGAAACCAGTCCCAAGGTCCCCCACCTCGTCCAGGAAAGCCAGAAGGACCACCTTCACAAGGAGGCAACAAACCTCAAGGTCCCCCACCCTC	c.(598-726)cggtccaggaaagccagaaggaccacccccacaaggaggaaaccagtcccaaggtcccccacctcgtccaggaaagccagaaggaccaccttcacaaggaggcaacaaacctcaaggtcccccaccctcfs	p.RSRKARRTTPTRRKPVPRSPTSSRKARRTTFTRRQQTSRSPTL200fs	PRB3_ENST00000538488.1_Splice_Site_p.RSRKARRTTPTRRKPVPRSPTSSR179fs|PRB3_ENST00000440870.3_Intron|PRB3_ENST00000381842.3_Splice_Site_p.RSR200fs			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	200	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.		Missing (in allele S).		defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)		p.Q193K(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			GCTTTCCTGGACGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCCGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCCGGACGAGGTGGGG	0.618																																					p.242_242del		Pindel	.											PRB3_ENST00000538488,caecum,carcinoma,0,2	PRB3	84	.	1	Substitution - Missense(1)	endometrium(1)	c.725_725del						.																																			SO:0001589	frameshift_variant	5544	exon4			.			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.600_726delGTCCAGGAAAGCCAGAAGGACCACCCCCACAAGGAGGAAACCAGTCCCAAGGTCCCCCACCTCGTCCAGGAAAGCCAGAAGGACCACCTTCACAAGGAGGCAACAAACCTCAAGGTCCCCCACCCTC	chr12.hg19:g.11420457_11420583delGAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	ENSP00000279573:p.Arg200fs	139.0	0.0		79.0	15.0	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Frame_Shift_Del	DEL	ENST00000279573.7	hg19																																																																																				.	.		0.618	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249		-	11420583	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	-	11420457	7	5	37	1	0	1	0	1	0	0	0	0	12456	289	10	0	211	0	PRB3	12	11420457	Frame_Shift_Del	DEL	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	TCGA-BC-A10Y-01A-11D-A12Z-10		11420457	122431438	34	4418										
ATP5B	506	hgsc.bcm.edu	37	chr12	57032145	57032145	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	agccagcttatcagcttttgCcacagcttcttcaatgggtc	8	12	3	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr12:57032145C>T	ENST00000262030.3	-	10	1602	c.1552G>A	c.(1552-1554)Gca>Aca	p.A518T	BAZ2A_ENST00000179765.5_5'Flank|BAZ2A_ENST00000551812.1_5'Flank|ATP5B_ENST00000550162.1_5'Flank|BAZ2A_ENST00000379441.3_5'Flank|ATP5B_ENST00000552919.1_Missense_Mutation_p.A507T	NM_001686.3	NP_001677.2	P06576	ATPB_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide	518					angiogenesis (GO:0001525)|ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|osteoblast differentiation (GO:0001649)|proton transport (GO:0015992)|regulation of intracellular pH (GO:0051453)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial nucleoid (GO:0042645)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase, catalytic core (GO:0005754)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TCAGCTTTTGCCACAGCTTCT	0.453																																					p.A518T		Atlas-SNP	.											.	ATP5B	48	.	0			c.G1552A						.						180	170	174					12																	57032145		2203	4300	6503	SO:0001583	missense	506	exon10			CTTTTGCCACAGC	M27132	CCDS8924.1	12p13.3	2012-10-12			ENSG00000110955	ENSG00000110955	3.6.3.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	830	protein-coding gene	gene with protein product		102910		ATPSB		2687158	Standard	NM_001686		Approved		uc001slr.3	P06576	OTTHUMG00000170291	ENST00000262030.3:c.1552G>A	chr12.hg19:g.57032145C>T	ENSP00000262030:p.Ala518Thr	147.0	0.0		146.0	55.0	NM_001686	A8K4X0|Q14283	Missense_Mutation	SNP	ENST00000262030.3	hg19	CCDS8924.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.943984	0.53079	.	.	ENSG00000110955	ENST00000262030;ENST00000552919	T;T	0.77877	-1.13;-1.13	5.37	3.19	0.36642	ATPase, F1/V1/A1 complex, alpha/beta subunit, C-terminal (2);ATPase, F1 complex beta subunit/V1 complex, C-terminal (1);	0.306615	0.35739	N	0.003014	T	0.70176	0.3194	L	0.54323	1.7	0.28680	N	0.905134	B	0.02656	0.0	B	0.04013	0.001	T	0.63892	-0.6534	10	0.42905	T	0.14	-4.2747	9.6137	0.39679	0.0:0.7446:0.0:0.2554	.	518	P06576	ATPB_HUMAN	T	518;507	ENSP00000262030:A518T;ENSP00000450297:A507T	ENSP00000262030:A518T	A	-	1	0	ATP5B	55318412	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.730000	0.47335	1.261000	0.44149	0.561000	0.74099	GCA	.	.		0.453	ATP5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408380.1	NM_001686		T	57032145	C	T	57032145	3	4	37	1	0	0	0	0	1	0	0	0	1148	739	26	3	41	3	ATP5B	12	57032145	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	45611688	57032145	76819750	35	4419										
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26153014	26153014	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tatggaggaaacattatgccAtctggaatactttgccacgg	10	8	1	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr13:26153014A>G	ENST00000381655.2	+	21	1986	c.1844A>G	c.(1843-1845)cAt>cGt	p.H615R	ATP8A2_ENST00000255283.8_Missense_Mutation_p.H575R|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	575					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		ACATTATGCCATCTGGAATAC	0.388																																					p.H615R		Atlas-SNP	.											.	ATP8A2	181	.	0			c.A1844G						.						136	130	132					13																	26153014		1883	4114	5997	SO:0001583	missense	51761	exon21			TATGCCATCTGGA	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.1844A>G	chr13.hg19:g.26153014A>G	ENSP00000371070:p.His615Arg	111.0	0.0		89.0	38.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	hg19	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.336979	0.81801	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	T;T	0.67865	-0.29;-0.29	5.61	5.61	0.85477	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.048152	0.85682	D	0.000000	D	0.84174	0.5414	M	0.88241	2.94	0.80722	D	1	D;D;D	0.58620	0.983;0.979;0.983	D;D;D	0.68483	0.958;0.947;0.958	D	0.87335	0.2327	10	0.87932	D	0	.	16.1054	0.81216	1.0:0.0:0.0:0.0	.	575;395;575	B7Z880;F5GZN5;Q9NTI2	.;.;AT8A2_HUMAN	R	615;575;395	ENSP00000371070:H615R;ENSP00000255283:H575R	ENSP00000255283:H575R	H	+	2	0	ATP8A2	25051014	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.847000	0.92166	2.266000	0.75297	0.533000	0.62120	CAT	.	.		0.388	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		G	26153014	A	G	26153014	3	3	37	1	0	0	0	0	1	0	0	0	1193	217	8	2	1926	2	ATP8A2	13	26153014	Missense_Mutation	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10		26153014	89016864	36	4420										
BRCA2	675	hgsc.bcm.edu	37	chr13	32914712	32914712	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ccattttagaaagttccttaCacaaagttaagggagtgtta	8	6	0	1	rs34309943|rs276174867	byFrequency	TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr13:32914712C>G	ENST00000380152.3	+	11	6453	c.6220C>G	c.(6220-6222)Cac>Gac	p.H2074D	BRCA2_ENST00000544455.1_Missense_Mutation_p.H2074D			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2074			H -> N (in dbSNP:rs34309943).		brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AAGTTCCTTACACAAAGTTAA	0.343			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.H2074D	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2	812	.	0			c.C6220G	GRCh37	CM012589	BRCA2	M	rs34309943	.						62	64	64					13																	32914712		2203	4297	6500	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TCCTTACACAAAG	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.6220C>G	chr13.hg19:g.32914712C>G	ENSP00000369497:p.His2074Asp	127.0	0.0		94.0	38.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	9.633	1.136989	0.21123	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.73897	-0.79;-0.79	5.77	-4.11	0.03928	.	0.987072	0.08269	N	0.971792	T	0.51058	0.1652	N	0.19112	0.55	0.09310	N	1	B	0.27416	0.178	B	0.28385	0.089	T	0.37314	-0.9711	10	0.21540	T	0.41	.	3.5294	0.07771	0.5141:0.2527:0.1001:0.1331	.	2074	P51587	BRCA2_HUMAN	D	2074	ENSP00000369497:H2074D;ENSP00000439902:H2074D	ENSP00000369497:H2074D	H	+	1	0	BRCA2	31812712	0.833000	0.29383	0.091000	0.20842	0.550000	0.35303	0.382000	0.20635	-0.334000	0.08463	0.591000	0.81541	CAC	.	C|0.998;A|0.002		0.343	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32914712	C	G	32914712	3	3	37	1	0	0	0	0	1	0	0	0	1501	478	17	4	6258	4	BRCA2	13	32914712	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	6761698	32914712	82255166	37	4421										
MAB21L1	4081	hgsc.bcm.edu	37	chr13	36049710	36049710	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ccggccaggggatgtggggaAgtggccagtgggcagcactc	19	10	0	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr13:36049710A>G	ENST00000379919.4	-	1	1122	c.566T>C	c.(565-567)cTt>cCt	p.L189P	NBEA_ENST00000310336.4_Intron|NBEA_ENST00000540320.1_Intron|NBEA_ENST00000379939.2_Intron|NBEA_ENST00000400445.3_Intron|NBEA_ENST00000537702.1_5'Flank	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)	189					anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		GATGTGGGGAAGTGGCCAGTG	0.607																																					p.L189P		Atlas-SNP	.											.	MAB21L1	52	.	0			c.T566C						.						45	52	50					13																	36049710		2203	4300	6503	SO:0001583	missense	4081	exon1			TGGGGAAGTGGCC	BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"mab-21 (C. elegans)-like 1"			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.566T>C	chr13.hg19:g.36049710A>G	ENSP00000369251:p.Leu189Pro	96.0	0.0		55.0	23.0	NM_005584	Q6I9T5	Missense_Mutation	SNP	ENST00000379919.4	hg19	CCDS9353.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.570144	0.45798	.	.	ENSG00000180660	ENST00000379919	T	0.07908	3.15	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.14614	0.0353	L	0.40543	1.245	0.80722	D	1	B	0.29955	0.263	B	0.43990	0.438	T	0.17258	-1.0375	10	0.27785	T	0.31	-8.1728	15.8843	0.79232	1.0:0.0:0.0:0.0	.	189	Q13394	MB211_HUMAN	P	189	ENSP00000369251:L189P	ENSP00000369251:L189P	L	-	2	0	MAB21L1	34947710	1.000000	0.71417	0.955000	0.39395	0.987000	0.75469	9.339000	0.96797	2.164000	0.68074	0.533000	0.62120	CTT	.	.		0.607	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584		G	36049710	A	G	36049710	3	3	37	1	0	0	0	0	1	0	0	0	9150	72	3	2	517	2	MAB21L1	13	36049710	Missense_Mutation	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10	3134998	36049710	79120168	38	4422										
DCLK1	9201	hgsc.bcm.edu	37	chr13	36385025	36385025	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gttggggtgccacagactgtGtacagggggccgtctacaat	15	9	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr13:36385025G>T	ENST00000360631.3	-	12	1846	c.1635C>A	c.(1633-1635)taC>taA	p.Y545*	DCLK1_ENST00000379893.1_Nonsense_Mutation_p.Y238*|DCLK1_ENST00000255448.4_Nonsense_Mutation_p.Y545*			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	545	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		CACAGACTGTGTACAGGGGGC	0.463																																					p.Y545X		Atlas-SNP	.											DCLK1_ENST00000379893,NS,carcinoma,0,3	DCLK1	350	.	0			c.C1635A						.						171	165	167					13																	36385025		2203	4300	6503	SO:0001587	stop_gained	9201	exon12			GACTGTGTACAGG	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1635C>A	chr13.hg19:g.36385025G>T	ENSP00000353846:p.Tyr545*	202.0	0.0		252.0	111.0	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Nonsense_Mutation	SNP	ENST00000360631.3	hg19		.	.	.	.	.	.	.	.	.	.	G	39	7.667052	0.98422	.	.	ENSG00000133083	ENST00000399319;ENST00000255448;ENST00000360631;ENST00000379893;ENST00000539451	.	.	.	5.18	1.52	0.23074	.	0.059652	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1631	0.42864	0.3398:0.0:0.6602:0.0	.	.	.	.	X	237;545;545;238;527	.	ENSP00000255448:Y545X	Y	-	3	2	DCLK1	35283025	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	1.537000	0.36083	0.036000	0.15547	-0.136000	0.14681	TAC	.	.		0.463	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		T	36385025	G	T	36385025	4	4	37	1	0	0	0	0	0	1	0	0	4293	1372	48	3	582	3	DCLK1	13	36385025	Nonsense_Mutation	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10	335315	36385025	78784853	39	4423										
OR4M1	441670	hgsc.bcm.edu	37	chr14	20249191	20249191	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ctcaggtgagaataccaacaGggccatgtccacctgctatt	9	12	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr14:20249191G>A	ENST00000315957.4	+	1	791	c.710G>A	c.(709-711)aGg>aAg	p.R237K		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		AATACCAACAGGGCCATGTCC	0.463																																					p.R237K		Atlas-SNP	.											.	OR4M1	104	.	0			c.G710A						.						298	258	272					14																	20249191		2203	4300	6503	SO:0001583	missense	441670	exon1			CCAACAGGGCCAT		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"GPCR / Class A : Olfactory receptors"	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.710G>A	chr14.hg19:g.20249191G>A	ENSP00000319654:p.Arg237Lys	701.0	0.0		693.0	279.0	NM_001005500	B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	hg19	CCDS32021.1	.	.	.	.	.	.	.	.	.	.	.	4.405	0.074809	0.08485	.	.	ENSG00000176299	ENST00000315957	T	0.00007	9.64	4.42	3.52	0.40303	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000127	T	0.00012	0.0000	N	0.00063	-2.32	0.31973	N	0.606841	B	0.17268	0.021	B	0.15484	0.013	T	0.06232	-1.0838	10	0.02654	T	1	-9.6388	6.0147	0.19596	0.2032:0.0:0.7968:0.0	.	237	Q8NGD0	OR4M1_HUMAN	K	237	ENSP00000319654:R237K	ENSP00000319654:R237K	R	+	2	0	OR4M1	19319031	1.000000	0.71417	0.982000	0.44146	0.951000	0.60555	3.858000	0.55979	2.468000	0.83385	0.506000	0.49869	AGG	.	.		0.463	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1			A	20249191	G	A	20249191	3	1	37	1	0	0	0	0	1	0	0	0	11084	1000	35	3	712	3	OR4M1	14	20249191	Missense_Mutation	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10		20249191	87100349	40	4424										
POLE2	5427	hgsc.bcm.edu	37	chr14	50140883	50140883	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tcacgaaacatctctgctttAtctcttggtgttccaaataa	5	10	3	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr14:50140883A>G	ENST00000216367.5	-	5	474	c.375T>C	c.(373-375)gaT>gaC	p.D125D	POLE2_ENST00000554396.1_Silent_p.D125D|POLE2_ENST00000556584.1_5'UTR|POLE2_ENST00000539565.2_Silent_p.D99D	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	125					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	TCTCTGCTTTATCTCTTGGTG	0.413																																					p.D125D		Atlas-SNP	.											.	POLE2	36	.	0			c.T375C						.						248	252	251					14																	50140883		2203	4300	6503	SO:0001819	synonymous_variant	5427	exon5			TGCTTTATCTCTT	AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479		"DNA polymerases"	9178	protein-coding gene	gene with protein product	"DNA polymerase epsilon subunit B"	602670	"polymerase (DNA directed), epsilon 2 (p59 subunit)"			9405441, 9443964	Standard	NM_002692		Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.375T>C	chr14.hg19:g.50140883A>G		182.0	0.0		167.0	78.0	NM_001197331	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	Silent	SNP	ENST00000216367.5	hg19	CCDS32073.1																																																																																			.	.		0.413	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410512.1	NM_002692		G	50140883	A	G	50140883	2	3	37	1	0	0	0	0	0	0	0	1	12206	446	16	2		2	POLE2	14	50140883	Silent	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10	29891692	50140883	57208657	41	4425										
GPHN	10243	hgsc.bcm.edu	37	chr14	67646366	67646366	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ctaacttggcatcaccaagaAccactaccttgggcacagag	8	13	1	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr14:67646366A>T	ENST00000315266.5	+	21	3173	c.2052A>T	c.(2050-2052)gaA>gaT	p.E684D	GPHN_ENST00000305960.9_Missense_Mutation_p.E653D|GPHN_ENST00000478722.1_Missense_Mutation_p.E717D|GPHN_ENST00000543237.1_Missense_Mutation_p.E730D|GPHN_ENST00000544752.2_3'UTR	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	684	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		ATCACCAAGAACCACTACCTT	0.363			T	MLL	AL																																p.E717D		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.A2151T						.						130	107	115					14																	67646366		2203	4300	6503	SO:0001583	missense	10243	exon22			CCAAGAACCACTA	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.2052A>T	chr14.hg19:g.67646366A>T	ENSP00000312771:p.Glu684Asp	329.0	0.0		300.0	139.0	NM_020806	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	hg19	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	A	8.510	0.866181	0.17250	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000305960	.	.	.	5.79	2.24	0.28232	MoeA, C-terminal, domain IV (3);	0.000000	0.85682	D	0.000000	T	0.28797	0.0714	N	0.12502	0.225	0.58432	D	0.999999	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.10450	0.003;0.005;0.004;0.004	T	0.04333	-1.0959	9	0.16420	T	0.52	-10.9275	8.3167	0.32104	0.7147:0.0:0.2853:0.0	.	653;730;684;717	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2	.;.;GEPH_HUMAN;.	D	684;717;730;653	.	ENSP00000303019:E653D	E	+	3	2	GPHN	66716119	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.607000	0.46300	0.468000	0.27243	-0.256000	0.11100	GAA	.	.		0.363	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		T	67646366	A	T	67646366	3	4	37	1	0	0	0	0	1	0	0	0	6618	40	2	4	2237	4	GPHN	14	67646366	Missense_Mutation	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10	17505483	67646366	39703174	42	4426										
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91770248	91770248	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tcgttctccgtctccttggcCgtgtggtggttctgcagcag	13	12	3	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr14:91770248C>T	ENST00000389857.6	-	20	3518	c.3432G>A	c.(3430-3432)acG>acA	p.T1144T		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1144					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				TCTCCTTGGCCGTGTGGTGGT	0.657																																					p.T1144T		Atlas-SNP	.											.	CCDC88C	192	.	0			c.G3432A						.						75	82	80					14																	91770248		2150	4255	6405	SO:0001819	synonymous_variant	440193	exon20			CTTGGCCGTGTGG		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"Dvl-associating protein with a high frequency of leucine residues", "spinocerebellar ataxia 40"	611204	"KIAA1509"	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.3432G>A	chr14.hg19:g.91770248C>T		100.0	0.0		130.0	51.0	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	hg19	CCDS45151.1																																																																																			.	.		0.657	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		T	91770248	C	T	91770248	2	4	37	1	0	0	0	0	0	0	0	1	2867	639	23	1		1	CCDC88C	14	91770248	Silent	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	24123882	91770248	15579292	43	4427										
APBA2	321	hgsc.bcm.edu	37	chr15	29346830	29346830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	catcaccagcgccagtgaggCcagccccgagcatgggcctg	13	16	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr15:29346830C>T	ENST00000558402.1	+	5	1342	c.743C>T	c.(742-744)gCc>gTc	p.A248V	APBA2_ENST00000558330.1_Missense_Mutation_p.A248V|APBA2_ENST00000561069.1_Missense_Mutation_p.A248V|APBA2_ENST00000558259.1_Missense_Mutation_p.A248V|APBA2_ENST00000411764.1_Missense_Mutation_p.A248V			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	248	STXBP1-binding.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)	p.A248D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		GCCAGTGAGGCCAGCCCCGAG	0.652																																					p.A248V		Atlas-SNP	.											.	APBA2	132	.	1	Substitution - Missense(1)	lung(1)	c.C743T						.						50	43	45					15																	29346830		2203	4300	6503	SO:0001583	missense	321	exon3			GTGAGGCCAGCCC	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.743C>T	chr15.hg19:g.29346830C>T	ENSP00000453293:p.Ala248Val	126.0	0.0		134.0	60.0	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	hg19	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.455267	0.43634	.	.	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.46451	0.87	4.96	3.93	0.45458	.	0.364621	0.28135	N	0.016475	T	0.32675	0.0837	L	0.51422	1.61	0.28731	N	0.902478	B;B;B	0.29481	0.245;0.129;0.062	B;B;B	0.30646	0.118;0.058;0.058	T	0.12243	-1.0555	10	0.23891	T	0.37	.	6.6082	0.22737	0.0:0.7989:0.0:0.2011	.	248;248;248	Q5XKC0;E9PGI4;Q99767	.;.;APBA2_HUMAN	V	248	ENSP00000409312:A248V	ENSP00000219865:A248V	A	+	2	0	APBA2	27134122	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	2.864000	0.48404	2.280000	0.76307	0.650000	0.86243	GCC	.	.		0.652	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		T	29346830	C	T	29346830	3	4	37	1	0	0	0	0	1	0	0	0	757	739	26	3	745	3	APBA2	15	29346830	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10		29346830	73184562	44	4428										
ACSBG1	23205	hgsc.bcm.edu	37	chr15	78472115	78472136	+	Splice_Site	DEL	TCAGGTCGCTGGTGGGAGAGGG	TCAGGTCGCTGGTGGGAGAGGG	-													0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	cagtctggttgtgaagggctTcaggtcgctggtgggagagg					rs199505466|rs144974698	byFrequency	TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	TCAGGTCGCTGGTGGGAGAGGG	TCAGGTCGCTGGTGGGAGAGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr15:78472115_78472136delTCAGGTCGCTGGTGGGAGAGGG	ENST00000258873.4	-	10	1459_1466	c.1254_1261delCCCTCTCCCACCAGCGACCTGA	c.(1252-1263)agccctctccca>agca	p.PLP419fs	ACSBG1_ENST00000541759.1_Splice_Site_p.PLP177fs|ACSBG1_ENST00000560817.1_Splice_Site_p.PLP177fs	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	419					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						GTGAAGGGCTTCAGGTCGCTGGTGGGAGAGGGAGAATGGTTC	0.514																																					p.418_421del		Atlas-INDEL	.											.	ACSBG1	79	.	0			c.1254_1262del						.																																			SO:0001630	splice_region_variant	23205	exon10			.	AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"Acyl-CoA synthetase family"	29567	protein-coding gene	gene with protein product	"bubblegum", "very long-chain acyl-CoA synthetase", "lipidosin"	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.1254-1CCCTCTCCCACCAGCGACCTGA>-	chr15.hg19:g.78472115_78472136delTCAGGTCGCTGGTGGGAGAGGG		125.0	0.0		152.0	14.0	NM_015162	B2RB61|O75126|Q76N27|Q9HC26	In_Frame_Del	DEL	ENST00000258873.4	hg19	CCDS10298.1																																																																																			.	.		0.514	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162	Frame_Shift_Del	-	78472136	TCAGGTCGCTGGTGGGAGAGGG	-	78472115	8	5	37	1	0	1	0	1	0	0	1	0	173	1792	62	0	933	0	ACSBG1	15	78472115	Splice_Site	DEL	TCAGGTCGCTGGTGGGAGAGGG	TCGA-BC-A10Y-01A-11D-A12Z-10	49125285	78472115	24059277	45	4429										
ST8SIA2	8128	hgsc.bcm.edu	37	chr15	93007604	93007604	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tgactgtcggccagtgcgatGgggccacgtagggtgggcac	18	10	0	1	rs149476731		TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr15:93007604G>T	ENST00000268164.3	+	6	1354	c.1117G>T	c.(1117-1119)Ggg>Tgg	p.G373W	ST8SIA2_ENST00000539113.1_Missense_Mutation_p.G352W	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	373					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			CCAGTGCGATGGGGCCACGTA	0.597																																					p.G373W		Atlas-SNP	.											.	ST8SIA2	41	.	0			c.G1117T						.	G	TRP/GLY	1,4395		0,1,2197	71	68	69		1117	5.6	1	15	dbSNP_134	69	0,8596		0,0,4298	no	missense	ST8SIA2	NM_006011.3	184	0,1,6495	TT,TG,GG		0.0,0.0227,0.0077	possibly-damaging	373/376	93007604	1,12991	2198	4298	6496	SO:0001583	missense	8128	exon6			TGCGATGGGGCCA	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.1117G>T	chr15.hg19:g.93007604G>T	ENSP00000268164:p.Gly373Trp	45.0	0.0		86.0	26.0	NM_006011	Q4VAZ0|Q92470|Q92746	Missense_Mutation	SNP	ENST00000268164.3	hg19	CCDS10372.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.078754	0.76528	2.27E-4	0.0	ENSG00000140557	ENST00000268164;ENST00000539113;ENST00000555434	T;T;T	0.23552	2.2;2.44;1.9	5.6	5.6	0.85130	.	0.241297	0.40144	N	0.001174	T	0.33904	0.0879	L	0.29908	0.895	0.50632	D	0.999883	D;D	0.60575	0.988;0.988	P;P	0.53006	0.715;0.715	T	0.05733	-1.0867	10	0.72032	D	0.01	-17.3051	19.6223	0.95663	0.0:0.0:1.0:0.0	.	352;373	C6G488;Q92186	.;SIA8B_HUMAN	W	373;352;330	ENSP00000268164:G373W;ENSP00000437382:G352W;ENSP00000450851:G330W	ENSP00000268164:G373W	G	+	1	0	ST8SIA2	90808608	1.000000	0.71417	0.980000	0.43619	0.925000	0.55904	6.156000	0.71840	2.635000	0.89317	0.650000	0.86243	GGG	.	G|1.000;T|0.000		0.597	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		T	93007604	G	T	93007604	3	4	37	1	0	0	0	0	1	0	0	0	15247	1348	47	3	1139	3	ST8SIA2	15	93007604	Missense_Mutation	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10	14535489	93007604	9523788	46	4430										
LOC81691	81691	hgsc.bcm.edu	37	chr16	20826252	20826252	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gtttgatttcttggcagctgGtgccagctttttcatcaaaa	9	8	3	1	rs201728796		TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr16:20826252G>T	ENST00000261377.6	+	4	464	c.255G>T	c.(253-255)tgG>tgT	p.W85C	AC004381.6_ENST00000348433.6_Missense_Mutation_p.W85C|AC004381.6_ENST00000564274.1_Missense_Mutation_p.W85C|AC004381.6_ENST00000567297.1_3'UTR|ERI2_ENST00000564349.1_Intron	NM_001199053.1|NM_030941.2	NP_001185982.1|NP_112203.2																					TTGGCAGCTGGTGCCAGCTTT	0.433																																					p.W85C		Atlas-SNP	.											.	LOC81691	41	.	0			c.G255T						.						101	89	93					16																	20826252		2201	4300	6501	SO:0001583	missense	0	exon4			CAGCTGGTGCCAG																												ENST00000261377.6:c.255G>T	chr16.hg19:g.20826252G>T	ENSP00000261377:p.Trp85Cys	211.0	0.0		184.0	76.0	NM_030941		Missense_Mutation	SNP	ENST00000261377.6	hg19	CCDS10591.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.581324	0.65992	.	.	ENSG00000005189	ENST00000348433;ENST00000261377	T;T	0.72051	-0.62;-0.4	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.82384	0.5025	M	0.65498	2.005	0.80722	D	1	D;P	0.89917	1.0;0.459	D;B	0.91635	0.999;0.403	D	0.83665	0.0163	10	0.66056	D	0.02	-10.6428	14.8209	0.70070	0.0:0.0:1.0:0.0	.	85;85	Q96IC2-2;Q96IC2	.;REXON_HUMAN	C	85	ENSP00000261378:W85C;ENSP00000261377:W85C	ENSP00000261377:W85C	W	+	3	0	AC004381.6	20733753	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	5.476000	0.66793	2.557000	0.86248	0.561000	0.74099	TGG	.	G|1.000;A|0.000		0.433	AC004381.6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254418.2			T	20826252	G	T	20826252	3	4	37	1	0	0	0	0	1	0	0	0	8899	1270	44	3	265	3	LOC81691	16	20826252	Missense_Mutation	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10		20826252	69528501	47	4431										
METTL9	51108	hgsc.bcm.edu	37	chr16	21636425	21636425	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tgtcctcccctttcatccctAtgtggaaaacggtaagtgtg	9	11	1	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr16:21636425A>G	ENST00000358154.3	+	4	998	c.740A>G	c.(739-741)tAt>tGt	p.Y247C	METTL9_ENST00000396014.4_Missense_Mutation_p.Y247C|CTB-31N19.3_ENST00000564271.1_RNA	NM_001077180.1|NM_016025.3	NP_001070648.1|NP_057109.3	Q9H1A3	METL9_HUMAN	methyltransferase like 9	247										endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)	7				GBM - Glioblastoma multiforme(48;0.0759)		TTTCATCCCTATGTGGAAAAC	0.443																																					p.Y247C		Atlas-SNP	.											.	METTL9	18	.	0			c.A740G						.						102	91	95					16																	21636425		2199	4300	6499	SO:0001583	missense	51108	exon4			ATCCCTATGTGGA	NM_016025, AF151839	CCDS10598.2, CCDS45440.1	16p12.2	2008-11-06			ENSG00000197006	ENSG00000197006			24586	protein-coding gene	gene with protein product	"DORA reverse strand protein 1"	609388				10810093, 11132146	Standard	NM_001077180		Approved	DREV1	uc002dje.3	Q9H1A3	OTTHUMG00000131584	ENST00000358154.3:c.740A>G	chr16.hg19:g.21636425A>G	ENSP00000350874:p.Tyr247Cys	169.0	0.0		139.0	46.0	NM_016025	Q8NBT8|Q9BWJ7|Q9H1A2|Q9Y390	Missense_Mutation	SNP	ENST00000358154.3	hg19	CCDS10598.2	.	.	.	.	.	.	.	.	.	.	A	16.29	3.081694	0.55753	.	.	ENSG00000197006	ENST00000358154;ENST00000396014;ENST00000540294	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.75184	0.3815	L	0.54323	1.7	0.80722	D	1	D;B	0.89917	1.0;0.241	D;B	0.85130	0.997;0.111	T	0.75508	-0.3293	9	0.51188	T	0.08	-14.1756	14.7743	0.69713	1.0:0.0:0.0:0.0	.	247;247	Q9H1A3-2;Q9H1A3	.;METL9_HUMAN	C	247;247;211	.	ENSP00000350874:Y247C	Y	+	2	0	METTL9	21543926	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.148000	0.71788	2.371000	0.80710	0.533000	0.62120	TAT	.	.		0.443	METTL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254465.1	NM_016025		G	21636425	A	G	21636425	3	3	37	1	0	0	0	0	1	0	0	0	9517	449	16	2	754	2	METTL9	16	21636425	Missense_Mutation	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10	810173	21636425	68718328	48	4432										
MAZ	4150	hgsc.bcm.edu	37	chr16	29820038	29820038	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	tgcacagccagggtcctcacCatgtctgtgagctctgcaac	10	14	3	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr16:29820038C>T	ENST00000322945.6	+	4	1420	c.1255C>T	c.(1255-1257)Cat>Tat	p.H419Y	AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000569978.1_Missense_Mutation_p.H20Y|MAZ_ENST00000219782.6_Missense_Mutation_p.H419Y|AC009133.14_ENST00000563806.1_RNA|AC009133.20_ENST00000569039.1_RNA|MAZ_ENST00000566906.2_Intron|AC009133.14_ENST00000569981.1_RNA|MAZ_ENST00000563402.1_Intron|MAZ_ENST00000568282.1_Missense_Mutation_p.H20Y|MAZ_ENST00000568544.1_Missense_Mutation_p.H20Y|MAZ_ENST00000545521.1_Missense_Mutation_p.H396Y|MAZ_ENST00000562337.1_Missense_Mutation_p.H114Y	NM_002383.2	NP_002374.2	P56270	MAZ_HUMAN	MYC-associated zinc finger protein (purine-binding transcription factor)	419					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|termination of RNA polymerase II transcription (GO:0006369)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						GGGTCCTCACCATGTCTGTGA	0.607																																					p.H419Y	Colon(72;875 1167 15364 30899 37091)	Atlas-SNP	.											.	MAZ	48	.	0			c.C1255T						.						43	45	44					16																	29820038		2112	4225	6337	SO:0001583	missense	4150	exon4			CCTCACCATGTCT	M93339	CCDS42143.1, CCDS42144.1, CCDS61902.1, CCDS61903.1	16p11.2	2013-01-08			ENSG00000103495	ENSG00000103495		"Zinc fingers, C2H2-type"	6914	protein-coding gene	gene with protein product		600999				1567856, 1502157	Standard	NM_001276275		Approved	ZF87, Pur-1, Zif87, ZNF801	uc002dtx.4	P56270	OTTHUMG00000132119	ENST00000322945.6:c.1255C>T	chr16.hg19:g.29820038C>T	ENSP00000313362:p.His419Tyr	104.0	0.0		85.0	36.0	NM_002383	A8QJL9|C6G496|G5E927|H3BQD6|Q15703|Q8NFN7|Q99443	Missense_Mutation	SNP	ENST00000322945.6	hg19	CCDS42143.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.748142	0.49257	.	.	ENSG00000103495	ENST00000545521;ENST00000322945;ENST00000219782;ENST00000544343	T;T;T	0.11604	2.76;2.76;5.07	5.3	4.35	0.52113	.	0.058153	0.64402	D	0.000002	T	0.03783	0.0107	N	0.04508	-0.205	0.33481	D	0.587416	P;B;B;B	0.35507	0.506;0.067;0.23;0.383	B;B;B;B	0.29716	0.083;0.054;0.053;0.106	T	0.21415	-1.0246	10	0.02654	T	1	-2.0738	11.944	0.52918	0.0:0.9143:0.0:0.0857	.	396;194;419;419	C6G496;F5H7A6;P56270;G5E927	.;.;MAZ_HUMAN;.	Y	396;419;419;194	ENSP00000443956:H396Y;ENSP00000313362:H419Y;ENSP00000219782:H419Y	ENSP00000219782:H419Y	H	+	1	0	MAZ	29727539	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.434000	0.44802	1.364000	0.46038	0.655000	0.94253	CAT	.	.		0.607	MAZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435536.1	NM_002383		T	29820038	C	T	29820038	3	4	37	1	0	0	0	0	1	0	0	0	9349	594	21	3	1269	3	MAZ	16	29820038	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	8183613	29820038	60534715	49	4433										
ZNF785	146540	hgsc.bcm.edu	37	chr16	30594358	30594358	+	Frame_Shift_Del	DEL	C	C	-													0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ttctccccggtgtgagcccgCctgtggatagccagggaacc							TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr16:30594358delC	ENST00000395216.2	-	3	900	c.741delG	c.(739-741)aggfs	p.R248fs	AC002310.7_ENST00000486926.1_RNA|ZNF785_ENST00000470110.1_Frame_Shift_Del_p.R233fs|AC002310.7_ENST00000492040.1_RNA|RP11-146F11.5_ENST00000563540.1_RNA	NM_152458.6	NP_689671.2	A8K8V0	ZN785_HUMAN	zinc finger protein 785	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	9						TGTGAGCCCGCCTGTGGATAG	0.657																																					p.R248fs		Atlas-Indel,Pindel	.											.	ZNF785	30	.	0			c.742delC						.						36	35	35					16																	30594358		2197	4300	6497	SO:0001589	frameshift_variant	146540	exon3			.	BC040642	CCDS10685.1	16p11.2	2013-01-08			ENSG00000197162	ENSG00000197162		"Zinc fingers, C2H2-type", "-"	26496	protein-coding gene	gene with protein product						10493829	Standard	NM_152458		Approved	FLJ32130	uc002dyu.3	A8K8V0	OTTHUMG00000132398	ENST00000395216.2:c.741delG	chr16.hg19:g.30594358delC	ENSP00000378642:p.Arg248fs	68.0	0.0		68.0	31.0	NM_152458	O75701|Q8IW91|Q8WV14|Q96MN0	Frame_Shift_Del	DEL	ENST00000395216.2	hg19	CCDS10685.1																																																																																			.	.		0.657	ZNF785-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255529.2	NM_152458		-	30594358	C	-	30594358	7	5	37	1	0	1	0	1	0	0	0	0	18172	738	26	0	480	0	ZNF785	16	30594358	Frame_Shift_Del	DEL	C	TCGA-BC-A10Y-01A-11D-A12Z-10	774320	30594358	59760395	50	4434										
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84486812	84486812	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	aggaggtggacagcgtggagAagggcgagctggccgaccgc	20	9	0	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr16:84486812A>T	ENST00000262429.4	+	19	1989	c.1900A>T	c.(1900-1902)Aag>Tag	p.K634*	ATP2C2_ENST00000420010.2_3'UTR|ATP2C2_ENST00000416219.2_Nonsense_Mutation_p.K634*	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	634					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						CAGCGTGGAGAAGGGCGAGCT	0.617																																					p.K634X		Atlas-SNP	.											.	ATP2C2	75	.	0			c.A1900T						.						60	68	66					16																	84486812		2061	4190	6251	SO:0001587	stop_gained	9914	exon19			GTGGAGAAGGGCG	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"ATPases / P-type"	29103	protein-coding gene	gene with protein product	"secretory pathway calcium ATPase 2"	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.1900A>T	chr16.hg19:g.84486812A>T	ENSP00000262429:p.Lys634*	111.0	0.0		115.0	49.0	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Nonsense_Mutation	SNP	ENST00000262429.4	hg19	CCDS42207.1	.	.	.	.	.	.	.	.	.	.	A	39	7.849860	0.98525	.	.	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	.	.	.	5.22	3.07	0.35406	.	0.586522	0.17025	N	0.189949	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	6.5657	0.22511	0.2928:0.5234:0.1837:0.0	.	.	.	.	X	634;634;483	.	ENSP00000262429:K634X	K	+	1	0	ATP2C2	83044313	0.991000	0.36638	0.393000	0.26258	0.035000	0.12851	0.592000	0.23984	0.452000	0.26830	0.459000	0.35465	AAG	.	.		0.617	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		T	84486812	A	T	84486812	4	4	37	1	0	0	0	0	0	1	0	0	1144	247	9	4	1974	4	ATP2C2	16	84486812	Nonsense_Mutation	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10	53892454	84486812	5867941	51	4435										
COTL1	23406	hgsc.bcm.edu	37	chr16	84623756	84623756	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ttgtccgtcccggttttggcGcgctgcagcccgctgacgtt	13	14	0	1	rs376530038		TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr16:84623756G>A	ENST00000262428.4	-	3	435	c.273C>T	c.(271-273)cgC>cgT	p.R91R	COTL1_ENST00000564057.1_Silent_p.R22R	NM_021149.2	NP_066972.1	Q14019	COTL1_HUMAN	coactosin-like F-actin binding protein 1	91	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				defense response to fungus (GO:0050832)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)			endometrium(1)|large_intestine(1)|liver(1)|lung(2)|skin(1)	6						CGGTTTTGGCGCGCTGCAGCC	0.592																																					p.R91R		Atlas-SNP	.											.	COTL1	17	.	0			c.C273T						.						101	76	85					16																	84623756		2199	4300	6499	SO:0001819	synonymous_variant	23406	exon3			TTTGGCGCGCTGC	L54057	CCDS10947.1	16q24.1	2014-03-05	2014-03-05	2002-08-01	ENSG00000103187	ENSG00000103187			18304	protein-coding gene	gene with protein product		606748	"coactosin-like 1 (Dictyostelium)"			10051563, 9326934, 16924104	Standard	NM_021149		Approved	CLP	uc002fid.3	Q14019	OTTHUMG00000137634	ENST00000262428.4:c.273C>T	chr16.hg19:g.84623756G>A		120.0	0.0		139.0	67.0	NM_021149	B2RDU3|D3DUL9|Q86XM5	Silent	SNP	ENST00000262428.4	hg19	CCDS10947.1																																																																																			.	.		0.592	COTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269075.1	NM_021149		A	84623756	G	A	84623756	2	1	37	1	0	0	0	0	0	0	0	1	3763	1074	38	1		1	COTL1	16	84623756	Silent	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10	136944	84623756	5730997	52	4436										
MED24	9862	hgsc.bcm.edu	37	chr17	38185119	38185120	+	Frame_Shift_Ins	INS	-	-	GGGG													0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gatttcagctttccagtggcINSggcggcggcagccagcagca					rs142237214|rs150608790	byFrequency	TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr17:38185119_38185120insGGGG	ENST00000394128.2	-	14	1449_1450	c.1368_1369insCCCC	c.(1366-1371)gccgccfs	p.A457fs	MED24_ENST00000394127.2_Frame_Shift_Ins_p.A444fs|MED24_ENST00000394126.1_Frame_Shift_Ins_p.A482fs|MED24_ENST00000501516.3_Frame_Shift_Ins_p.A476fs|SNORD124_ENST00000459577.1_RNA|MED24_ENST00000356271.3_Frame_Shift_Ins_p.A444fs	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	457					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					TTTCCAGTGGCGGCGGCGGCAG	0.634																																					p.A457fs		Atlas-INDEL	.											MED24,colon,carcinoma,0,1	MED24	89	.	0			c.1369_1370insCCCC						.																																			SO:0001589	frameshift_variant	9862	exon14			.	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1368_1369insCCCC	chr17.hg19:g.38185119_38185120insGGGG	ENSP00000377686:p.Ala457fs	102.0	0.0		72.0	12.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Frame_Shift_Ins	INS	ENST00000394128.2	hg19	CCDS11359.1																																																																																			.	.		0.634	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		GGGG	38185120	-	GGGG	38185119	7	5	37	1	0	1	1	0	0	0	0	0	9451	768	27	0	1652	0	MED24	17	38185119	Frame_Shift_Ins	INS	-	TCGA-BC-A10Y-01A-11D-A12Z-10		38185119	43010091	53	4437										
G6PC	2538	hgsc.bcm.edu	37	chr17	41063222	41063222	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gcatgtacagggagagctgcAaggggaaactcagcaagtgg	16	7	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr17:41063222A>G	ENST00000253801.2	+	5	932	c.853A>G	c.(853-855)Aag>Gag	p.K285E	G6PC_ENST00000592383.1_3'UTR|G6PC_ENST00000585489.1_3'UTR	NM_000151.3	NP_000142.2	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit	285					carbohydrate metabolic process (GO:0005975)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|hexose transport (GO:0008645)|multicellular organism growth (GO:0035264)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)|urate metabolic process (GO:0046415)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)|phosphate ion binding (GO:0042301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GGAGAGCTGCAAGGGGAAACT	0.577																																					p.K285E		Atlas-SNP	.											.	G6PC	48	.	0			c.A853G						.						94	88	90					17																	41063222		2203	4300	6503	SO:0001583	missense	2538	exon5			AGCTGCAAGGGGA	U01120	CCDS11446.1, CCDS59291.1	17q21	2014-09-17	2006-06-28			ENSG00000131482	3.1.3.9		4056	protein-coding gene	gene with protein product	"glycogen storage disease type I, von Gierke disease"	613742	"glucose-6-phosphatase, catalytic (glycogen storage disease type I, von Gierke disease)"	G6PT		7774924	Standard	NM_000151		Approved	GSD1a	uc002icb.2	P35575		ENST00000253801.2:c.853A>G	chr17.hg19:g.41063222A>G	ENSP00000253801:p.Lys285Glu	155.0	0.0		177.0	74.0	NM_000151	A1L4C0|B4E1C3|K7EL82	Missense_Mutation	SNP	ENST00000253801.2	hg19	CCDS11446.1	.	.	.	.	.	.	.	.	.	.	A	11.76	1.735432	0.30774	.	.	ENSG00000131482	ENST00000253801	T	0.76968	-1.06	4.94	2.7	0.31948	.	0.500148	0.21229	N	0.078016	T	0.64940	0.2644	L	0.40543	1.245	0.80722	D	1	B	0.28713	0.22	B	0.22386	0.039	T	0.57171	-0.7857	10	0.42905	T	0.14	.	7.4228	0.27081	0.6356:0.2889:0.0755:0.0	.	285	P35575	G6PC_HUMAN	E	285	ENSP00000253801:K285E	ENSP00000253801:K285E	K	+	1	0	G6PC	38316748	0.978000	0.34361	0.669000	0.29828	0.561000	0.35649	1.281000	0.33214	0.364000	0.24374	0.445000	0.29226	AAG	.	.		0.577	G6PC-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452451.1	NM_000151		G	41063222	A	G	41063222	3	3	37	1	0	0	0	0	1	0	0	0	6151	131	5	2	871	2	G6PC	17	41063222	Missense_Mutation	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10	2878103	41063222	40131988	54	4438										
GH1	2688	hgsc.bcm.edu	37	chr17	61994712	61994712	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	cagagcggcactgcacgatgCgcaggaatgtctcgaccttg	13	12	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr17:61994712C>T	ENST00000323322.5	-	5	653	c.611G>A	c.(610-612)cGc>cAc	p.R204H	GH1_ENST00000342364.4_Missense_Mutation_p.R109H|GH1_ENST00000351388.4_Missense_Mutation_p.R164H|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000458650.2_Missense_Mutation_p.R189H	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	204					bone maturation (GO:0070977)|glucose transport (GO:0015758)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|growth hormone receptor binding (GO:0005131)|metal ion binding (GO:0046872)|prolactin receptor binding (GO:0005148)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	19						CTGCACGATGCGCAGGAATGT	0.582																																					p.R204H		Atlas-SNP	.											.	GH1	39	.	0			c.G611A						.						159	123	135					17																	61994712		2203	4297	6500	SO:0001583	missense	2688	exon5			ACGATGCGCAGGA	M13438	CCDS11653.1, CCDS11654.1, CCDS45760.1	17q22-q24	2014-01-30				ENSG00000259384		"Endogenous ligands"	4261	protein-coding gene	gene with protein product	"pituitary growth hormone", "somatotropin"	139250				6306568	Standard	XM_005257218		Approved	GH-N, GHN, GH, hGH-N	uc002jdj.3	P01241		ENST00000323322.5:c.611G>A	chr17.hg19:g.61994712C>T	ENSP00000312673:p.Arg204His	413.0	1.0		610.0	163.0	NM_000515	A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Missense_Mutation	SNP	ENST00000323322.5	hg19	CCDS11653.1	.	.	.	.	.	.	.	.	.	.	c	12.36	1.913401	0.33815	.	.	ENSG00000204414	ENST00000323322;ENST00000458650;ENST00000351388;ENST00000342364	D;T;D;D	0.91464	-2.85;0.79;-2.85;-2.85	2.62	2.62	0.31277	Somatotropin hormone, conserved site (1);Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	4.792870	0.00622	N	0.000451	D	0.88966	0.6581	M	0.79123	2.44	0.31505	N	0.664319	P;B;B;B	0.41102	0.738;0.241;0.164;0.164	B;B;B;B	0.32928	0.155;0.12;0.061;0.061	T	0.81415	-0.0943	10	0.56958	D	0.05	.	4.6175	0.12433	0.0:0.7127:0.0:0.2873	.	109;164;204;189	B1A4G9;A6NEF6;P01241;B1A4G7	.;.;SOMA_HUMAN;.	H	204;189;164;109	ENSP00000312673:R204H;ENSP00000408486:R189H;ENSP00000343791:R164H;ENSP00000339278:R109H	ENSP00000312673:R204H	R	-	2	0	GH1	59348444	1.000000	0.71417	0.994000	0.49952	0.824000	0.46624	3.326000	0.52037	1.470000	0.48102	0.298000	0.19748	CGC	.	.		0.582	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515		T	61994712	C	T	61994712	3	4	37	1	0	0	0	0	1	0	0	0	6375	768	27	1	46	1	GH1	17	61994712	Missense_Mutation	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	20931490	61994712	19200498	55	4439										
ICAM1	3383	hgsc.bcm.edu	37	chr19	10385686	10385686	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	atgggcagtcaacagctaaaAccttcctcaccgtgtactgt	8	12	2	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr19:10385686A>G	ENST00000264832.3	+	2	638	c.313A>G	c.(313-315)Acc>Gcc	p.T105A	CTD-2369P2.5_ENST00000592893.1_RNA|ICAM1_ENST00000423829.2_Intron	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	105					adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	AACAGCTAAAACCTTCCTCAC	0.562																																					p.T105A		Atlas-SNP	.											.	ICAM1	32	.	0			c.A313G						.						105	105	105					19																	10385686		2202	4299	6501	SO:0001583	missense	3383	exon2			GCTAAAACCTTCC		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	5344	protein-coding gene	gene with protein product	"human rhinovirus receptor"	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.313A>G	chr19.hg19:g.10385686A>G	ENSP00000264832:p.Thr105Ala	77.0	0.0		55.0	31.0	NM_000201	B2R6M3|Q5NKV7|Q96B50	Missense_Mutation	SNP	ENST00000264832.3	hg19	CCDS12231.1	.	.	.	.	.	.	.	.	.	.	A	2.259	-0.369764	0.05069	.	.	ENSG00000090339	ENST00000264832	T	0.26518	1.73	4.46	-7.41	0.01392	Intercellular adhesion molecule, N-terminal (1);Immunoglobulin-like fold (1);	1.154360	0.06315	N	0.703431	T	0.11965	0.0291	N	0.10760	0.04	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.39583	-0.9607	10	0.15499	T	0.54	-0.4045	14.6977	0.69134	0.1734:0.0:0.8266:0.0	.	105	P05362	ICAM1_HUMAN	A	105	ENSP00000264832:T105A	ENSP00000264832:T105A	T	+	1	0	ICAM1	10246686	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.788000	0.04614	-1.333000	0.02247	-0.408000	0.06270	ACC	.	.		0.562	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1			G	10385686	A	G	10385686	3	3	37	1	0	0	0	0	1	0	0	0	7488	43	2	2	319	2	ICAM1	19	10385686	Missense_Mutation	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10		10385686	48743297	56	4440										
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19756558	19756558	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gaaactgccagactccacacCaggggcttgttctcgggcag	12	13	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr19:19756558C>T	ENST00000357324.6	-	25	3428	c.3402G>A	c.(3400-3402)ctG>ctA	p.L1134L	ATP13A1_ENST00000291503.5_Silent_p.L1016L|GMIP_ENST00000445806.2_5'Flank|GMIP_ENST00000203556.4_5'Flank|GMIP_ENST00000587238.1_5'Flank	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	1134						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GACTCCACACCAGGGGCTTGT	0.627																																					p.L1134L	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.G3402A						.						29	32	31					19																	19756558		2203	4297	6500	SO:0001819	synonymous_variant	57130	exon25			CCACACCAGGGGC	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"ATPases / P-type"	24215	protein-coding gene	gene with protein product	"cation transporting ATPase"		"ATPase type 13A"	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.3402G>A	chr19.hg19:g.19756558C>T		81.0	0.0		85.0	53.0	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Silent	SNP	ENST00000357324.6	hg19	CCDS32970.2																																																																																			.	.		0.627	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		T	19756558	C	T	19756558	2	4	37	1	0	0	0	0	0	0	0	1	1123	581	21	3		3	ATP13A1	19	19756558	Silent	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10	9370872	19756558	39372425	57	4441										
RRBP1	6238	hgsc.bcm.edu	37	chr20	17596122	17596122	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ctgaagactctagggggccgGctgtgcggagcttctccaat	14	11	2	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr20:17596122G>A	ENST00000377813.1	-	23	4307	c.4004C>T	c.(4003-4005)gCc>gTc	p.A1335V	RRBP1_ENST00000470422.1_5'UTR|RRBP1_ENST00000246043.4_Missense_Mutation_p.A1335V|RRBP1_ENST00000377807.2_Missense_Mutation_p.A902V|RRBP1_ENST00000360807.4_Missense_Mutation_p.A902V|RRBP1_ENST00000455029.2_Missense_Mutation_p.A676V			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1335					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						TAGGGGGCCGGCTGTGCGGAG	0.617																																					p.A902V		Atlas-SNP	.											.	RRBP1	157	.	0			c.C2705T						.						52	54	53					20																	17596122		2203	4300	6503	SO:0001583	missense	6238	exon23			GGGCCGGCTGTGC	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"ribosome binding protein 1 (dog 180kD homolog)", "ribosome binding protein 1 homolog 180kDa (dog)"			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.4004C>T	chr20.hg19:g.17596122G>A	ENSP00000367044:p.Ala1335Val	97.0	0.0		100.0	44.0	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Missense_Mutation	SNP	ENST00000377813.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.11	2.138467	0.37728	.	.	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000455029	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.13	-0.565	0.11771	.	2.631350	0.01755	N	0.030204	T	0.23611	0.0571	L	0.36672	1.1	0.09310	N	1	B;B	0.24132	0.098;0.015	B;B	0.26770	0.073;0.01	T	0.08700	-1.0709	10	0.29301	T	0.29	6.4995	2.7014	0.05149	0.1518:0.2642:0.4465:0.1375	.	902;1335	Q9P2E9-3;Q9P2E9	.;RRBP1_HUMAN	V	902;1335;902;1335;676	ENSP00000354045:A902V;ENSP00000367044:A1335V;ENSP00000367038:A902V;ENSP00000246043:A1335V;ENSP00000401206:A676V	ENSP00000246043:A1335V	A	-	2	0	RRBP1	17544122	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.966000	0.29331	-0.348000	0.08286	0.556000	0.70494	GCC	.	.		0.617	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576		A	17596122	G	A	17596122	3	1	37	1	0	0	0	0	1	0	0	0	13693	1203	42	3	240	3	RRBP1	20	17596122	Missense_Mutation	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10		17596122	45429398	58	4442										
RRP1B	23076	hgsc.bcm.edu	37	chr21	45092191	45092191	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ccaaccccgcctctgcaggaAgagctcgccaacaccattgc	8	18	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chr21:45092191A>G	ENST00000340648.4	+	3	333	c.216A>G	c.(214-216)gaA>gaG	p.E72E		NM_015056.2	NP_055871.1	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1B	72					negative regulation of phosphatase activity (GO:0010923)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome, small subunit precursor (GO:0030688)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(1)	21				STAD - Stomach adenocarcinoma(101;0.178)		CTCTGCAGGAAGAGCTCGCCA	0.557																																					p.E72E		Atlas-SNP	.											.	RRP1B	51	.	0			c.A216G						.						170	142	151					21																	45092191		2203	4300	6503	SO:0001819	synonymous_variant	23076	exon3			GCAGGAAGAGCTC	AK124620	CCDS33577.1	21q22.3	2014-06-13	2013-07-02	2007-03-26	ENSG00000160208	ENSG00000160208			23818	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 136"	610654	"KIAA0179", "ribosomal RNA processing 1 homolog B (S. cerevisiae)"	KIAA0179			Standard	NM_015056		Approved	Nnp1, RRP1, PPP1R136	uc002zdk.3	Q14684	OTTHUMG00000086872	ENST00000340648.4:c.216A>G	chr21.hg19:g.45092191A>G		139.0	0.0		118.0	54.0	NM_015056	Q8TBZ4	Silent	SNP	ENST00000340648.4	hg19	CCDS33577.1																																																																																			.	.		0.557	RRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195651.1	NM_015056		G	45092191	A	G	45092191	2	3	37	1	0	0	0	0	0	0	0	1	13703	69	3	2		2	RRP1B	21	45092191	Silent	SNP	A	TCGA-BC-A10Y-01A-11D-A12Z-10		45092191	3037704	59	4443										
MAP3K15	389840	hgsc.bcm.edu	37	chrX	19410152	19410152	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	ctgtgcaggggttcacacccGcaagacgtttcgaggttcca	12	12	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chrX:19410152G>A	ENST00000338883.4	-	18	2398	c.2399C>T	c.(2398-2400)gCg>gTg	p.A800V	MAP3K15_ENST00000359173.3_Missense_Mutation_p.A235V|MAP3K15_ENST00000469203.2_Missense_Mutation_p.A632V|MAP3K15_ENST00000518578.1_5'UTR	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	800	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					GTTCACACCCGCAAGACGTTT	0.502																																					p.A800V		Atlas-SNP	.											.	MAP3K15	108	.	0			c.C2399T						.						77	73	75					X																	19410152		2203	4300	6503	SO:0001583	missense	389840	exon18			ACACCCGCAAGAC	AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.2399C>T	chrX.hg19:g.19410152G>A	ENSP00000345629:p.Ala800Val	36.0	0.0		49.0	44.0	NM_001001671	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Missense_Mutation	SNP	ENST00000338883.4	hg19		.	.	.	.	.	.	.	.	.	.	G	14.46	2.543327	0.45280	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	T;T;T	0.65732	-0.17;-0.17;-0.17	5.09	4.2	0.49525	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.39036	0.1063	N	0.16166	0.38	0.80722	D	1	P;P	0.51537	0.946;0.853	B;B	0.31101	0.124;0.066	T	0.46830	-0.9163	10	0.72032	D	0.01	.	14.2245	0.65850	0.0:0.0:0.8495:0.1505	.	275;800	Q6ZN16-3;Q6ZN16	.;M3K15_HUMAN	V	800;235;632	ENSP00000345629:A800V;ENSP00000352093:A235V;ENSP00000428356:A632V	ENSP00000345629:A800V	A	-	2	0	MAP3K15	19320073	1.000000	0.71417	0.862000	0.33874	0.325000	0.28411	6.300000	0.72776	1.006000	0.39211	0.513000	0.50165	GCG	.	.		0.502	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671		A	19410152	G	A	19410152	3	1	37	1	0	0	0	0	1	0	0	0	9258	1087	38	1	1590	1	MAP3K15	23	19410152	Missense_Mutation	SNP	G	TCGA-BC-A10Y-01A-11D-A12Z-10		19410152	135860408	60	4444										
EIF2S3	1968	hgsc.bcm.edu	37	chrX	24084190	24084190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	aggtgtagctggtggtagtaTcctaaaaggagtattaaagg	14	3	0	0			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chrX:24084190T>C	ENST00000253039.4	+	8	1101	c.848T>C	c.(847-849)aTc>aCc	p.I283T		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	283					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						GGTGGTAGTATCCTAAAAGGA	0.323																																					p.I283T		Atlas-SNP	.											.	EIF2S3	31	.	0			c.T848C						.						166	153	158					X																	24084190		2203	4299	6502	SO:0001583	missense	1968	exon8			GTAGTATCCTAAA	L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741			3267	protein-coding gene	gene with protein product	"eukaryotic translation initiation factor 2G"	300161	"eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)"	EIF2G		8106381, 9736774	Standard	NM_001415		Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.848T>C	chrX.hg19:g.24084190T>C	ENSP00000253039:p.Ile283Thr	479.0	0.0		387.0	347.0	NM_001415	B5BTZ4	Missense_Mutation	SNP	ENST00000253039.4	hg19	CCDS14210.1	.	.	.	.	.	.	.	.	.	.	t	20.9	4.073711	0.76415	.	.	ENSG00000130741	ENST00000253039	T	0.71817	-0.6	5.49	5.49	0.81192	Translation elongation factor EFTu/EF1A, domain 2 (1);Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	D	0.89770	0.6811	H	0.98089	4.145	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	D	0.93420	0.6776	10	0.87932	D	0	.	14.804	0.69938	0.0:0.0:0.0:1.0	.	283	P41091	IF2G_HUMAN	T	283	ENSP00000253039:I283T	ENSP00000253039:I283T	I	+	2	0	EIF2S3	23994111	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.553000	0.82203	1.946000	0.56461	0.438000	0.28831	ATC	.	.		0.323	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415		C	24084190	T	C	24084190	3	2	37	1	0	0	0	0	1	0	0	0	5013	1435	50	2	878	2	EIF2S3	23	24084190	Missense_Mutation	SNP	T	TCGA-BC-A10Y-01A-11D-A12Z-10	4674038	24084190	131186370	61	4445										
AFF2	2334	hgsc.bcm.edu	37	chrX	147744245	147744245	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	gaaaacccagtgcagccagtTcaaagactaaactgccaaag	8	11	1	1			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chrX:147744245T>A	ENST00000370460.2	+	3	1476	c.997T>A	c.(997-999)Tca>Aca	p.S333T	AFF2_ENST00000342251.3_Missense_Mutation_p.S329T|AFF2_ENST00000370457.5_Missense_Mutation_p.S329T|AFF2_ENST00000370458.1_Missense_Mutation_p.S329T	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	333					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					TGCAGCCAGTTCAAAGACTAA	0.378																																					p.S333T		Atlas-SNP	.											.	AFF2	679	.	0			c.T997A						.						44	41	42					X																	147744245		2203	4299	6502	SO:0001583	missense	2334	exon3			GCCAGTTCAAAGA	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.997T>A	chrX.hg19:g.147744245T>A	ENSP00000359489:p.Ser333Thr	357.0	1.0		309.0	288.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	hg19	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	T	2.028	-0.423185	0.04734	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000370458	T;T;T;T	0.66638	0.03;-0.22;-0.22;1.01	5.92	-2.34	0.06704	.	0.486350	0.21455	N	0.074274	T	0.43545	0.1252	N	0.25890	0.77	0.80722	D	1	B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B	0.12156	0.003;0.003;0.003;0.003;0.004;0.007	T	0.08106	-1.0738	10	0.16896	T	0.51	.	7.0505	0.25071	0.4558:0.0:0.2588:0.2855	.	333;329;329;329;333;329	P51816-6;P51816-3;P51816-2;P51816-5;P51816;P51816-4	.;.;.;.;AFF2_HUMAN;.	T	333;329;329;329	ENSP00000359489:S333T;ENSP00000359486:S329T;ENSP00000345459:S329T;ENSP00000359487:S329T	ENSP00000345459:S329T	S	+	1	0	AFF2	147551937	0.994000	0.37717	0.990000	0.47175	0.995000	0.86356	0.113000	0.15499	-0.385000	0.07833	0.486000	0.48141	TCA	.	.		0.378	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		A	147744245	T	A	147744245	3	1	37	1	0	0	0	0	1	0	0	0	357	1783	62	4	1007	4	AFF2	23	147744245	Missense_Mutation	SNP	T	TCGA-BC-A10Y-01A-11D-A12Z-10	123660055	147744245	7526315	62	4446										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	4925278	4925278	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	5	1	1.5429085303186	4.32014388489209	1.08003597122302	1	1	0	atcccaagggatgagcattgCttttatgaagtggaggttgc	13	6	0	2			TCGA-BC-A10Y-01A-11D-A12Z-10	TCGA-BC-A10Y-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	54f8357c-9dd7-4e08-bd47-a1ebedb30b62	5589b608-e6ae-4953-8a37-484d4116179b	g.chrY:4925278C>T	ENST00000333703.4	+	4	894	c.381C>T	c.(379-381)tgC>tgT	p.C127C	PCDH11Y_ENST00000362095.5_Silent_p.C138C|PCDH11Y_ENST00000215473.6_Silent_p.C138C	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	138	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						ATGAGCATTGCTTTTATGAAG	0.408																																					p.C138C		Atlas-SNP	.											.	PCDH11Y	163	.	0			c.C414T						.																																			SO:0001819	synonymous_variant	83259	exon1			GCATTGCTTTTAT	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000333703.4:c.381C>T	chrY.hg19:g.4925278C>T		736.0	1.0		684.0	496.0	NM_032972	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Silent	SNP	ENST00000333703.4	hg19	CCDS14776.1																																																																																			.	.		0.408	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	NM_032973		T	4925278	C	T	4925278	2	4	37	1	0	0	0	0	0	0	0	1	11518	805	28	3		3	PCDH11Y	24	4925278	Silent	SNP	C	TCGA-BC-A10Y-01A-11D-A12Z-10		4925278	54448288	63	4447										
MXRA8	54587	hgsc.bcm.edu	37	chr1	1289296	1289296	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccgccctctccttcaggatgTtgtttttgtaatctgtggga	10	10	3	0	rs532502120		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr1:1289296T>A	ENST00000309212.6	-	9	1265	c.1235A>T	c.(1234-1236)aAc>aTc	p.N412I	MXRA8_ENST00000477278.2_Missense_Mutation_p.N403I|MXRA8_ENST00000342753.4_Missense_Mutation_p.N311I|MXRA8_ENST00000445648.2_Missense_Mutation_p.N418I	NM_001282582.1|NM_032348.2	NP_001269511.1|NP_115724.1	Q9BRK3	MXRA8_HUMAN	matrix-remodelling associated 8	412					establishment of glial blood-brain barrier (GO:0060857)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CTTCAGGATGTTGTTTTTGTA	0.647																																					p.N412I		Atlas-SNP	.											.	MXRA8	28	.	0			c.A1235T						.						36	35	35					1																	1289296		2199	4296	6495	SO:0001583	missense	54587	exon9			AGGATGTTGTTTT	BC006213	CCDS24.1, CCDS59950.1, CCDS59951.1, CCDS59952.1	1p36.33	2013-01-11			ENSG00000162576	ENSG00000162576		"Immunoglobulin superfamily / V-set domain containing"	7542	protein-coding gene	gene with protein product	"limitrin"					14603461	Standard	XM_005244758		Approved	DKFZp586E2023	uc001aew.3	Q9BRK3	OTTHUMG00000002973	ENST00000309212.6:c.1235A>T	chr1.hg19:g.1289296T>A	ENSP00000307887:p.Asn412Ile	80.0	0.0		83.0	43.0	NM_032348	B3KTR6|B4DE34|Q5TA39|Q96KC3	Missense_Mutation	SNP	ENST00000309212.6	hg19	CCDS24.1	.	.	.	.	.	.	.	.	.	.	.	16.80	3.221887	0.58560	.	.	ENSG00000162576	ENST00000309212;ENST00000378864;ENST00000342753;ENST00000445648	T;T;T	0.30182	1.58;1.72;1.54	3.85	3.85	0.44370	.	0.112986	0.64402	U	0.000018	T	0.53594	0.1806	M	0.74881	2.28	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.998;0.999;0.997	T	0.59096	-0.7518	10	0.87932	D	0	-20.6303	12.1349	0.53966	0.0:0.0:0.0:1.0	.	403;311;418;412	B3KTR6;B4DE34;Q9BRK3-2;Q9BRK3	.;.;.;MXRA8_HUMAN	I	412;403;311;418	ENSP00000307887:N412I;ENSP00000344998:N311I;ENSP00000399229:N418I	ENSP00000307887:N412I	N	-	2	0	MXRA8	1279159	1.000000	0.71417	1.000000	0.80357	0.597000	0.36814	3.913000	0.56394	1.520000	0.48965	0.459000	0.35465	AAC	.	.		0.647	MXRA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008282.2	NM_032348		A	1289296	T	A	1289296	3	1	38	1	0	0	0	0	1	0	0	0	10014	1725	60	4	101	4	MXRA8	1	1289296	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10		1289296	247961325	1	4448										
ARHGEF10L	55160	hgsc.bcm.edu	37	chr1	17991069	17991069	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccctgggtcactgtcctggaAgccaccaccctgcagcctca	9	18	2	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr1:17991069A>C	ENST00000361221.3	+	26	3147	c.2988A>C	c.(2986-2988)gaA>gaC	p.E996D	ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.E991D|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.E957D|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.E769D|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.E957D|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.E699D	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	996						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		CTGTCCTGGAAGCCACCACCC	0.647																																					p.E996D		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.A2988C						.						50	46	47					1																	17991069		2203	4300	6503	SO:0001583	missense	55160	exon26			CCTGGAAGCCACC	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.2988A>C	chr1.hg19:g.17991069A>C	ENSP00000355060:p.Glu996Asp	62.0	0.0		60.0	28.0	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	hg19	CCDS182.1	.	.	.	.	.	.	.	.	.	.	A	0.565	-0.843565	0.02671	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415;ENST00000375408;ENST00000457829;ENST00000167825	T;T;T;T;T;T	0.49432	2.04;2.04;0.78;2.04;2.04;2.04	4.22	-2.71	0.05986	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.248271	0.38005	N	0.001848	T	0.12050	0.0293	N	0.02960	-0.455	0.20821	N	0.999841	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.001;0.001;0.0;0.0;0.001;0.001	T	0.20371	-1.0277	10	0.02654	T	1	-10.507	0.3757	0.00387	0.2841:0.263:0.135:0.3179	.	769;991;699;757;952;957;996	Q5VXI4;Q9HCE6-5;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;.;ARGAL_HUMAN	D	996;957;991;957;769;769;699	ENSP00000355060:E996D;ENSP00000399401:E957D;ENSP00000394621:E991D;ENSP00000364564:E957D;ENSP00000364557:E769D;ENSP00000167825:E699D	ENSP00000167825:E699D	E	+	3	2	ARHGEF10L	17863656	0.060000	0.20803	0.979000	0.43373	0.608000	0.37181	-1.115000	0.03289	-0.487000	0.06735	-0.695000	0.03696	GAA	.	.		0.647	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		C	17991069	A	C	17991069	3	2	38	1	0	0	0	0	1	0	0	0	895	69	3	5	3086	5	ARHGEF10L	1	17991069	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	16701773	17991069	231259552	2	4449										
MAST2	23139	hgsc.bcm.edu	37	chr1	46500283	46500283	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccagccggctctgggcacacAcggcccagctccctccacgg	11	20	1	0	rs139679191	byFrequency	TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr1:46500283A>G	ENST00000361297.2	+	29	4225	c.3942A>G	c.(3940-3942)acA>acG	p.T1314T	MAST2_ENST00000372009.2_Intron	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CTGGGCACACACGGCCCAGCT	0.637																																					p.T1314T		Atlas-SNP	.											.	MAST2	136	.	0			c.A3942G						.						60	69	66					1																	46500283		2168	4252	6420	SO:0001819	synonymous_variant	23139	exon29			GCACACACGGCCC	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.3942A>G	chr1.hg19:g.46500283A>G		193.0	0.0		300.0	20.0	NM_015112		Silent	SNP	ENST00000361297.2	hg19	CCDS41326.1																																																																																			.	A|0.999;T|0.001		0.637	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		G	46500283	A	G	46500283	2	3	38	1	0	0	0	0	0	0	0	1	9334	146	6	2		2	MAST2	1	46500283	Silent	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	28509214	46500283	202750338	3	4450										
TTC39A	22996	hgsc.bcm.edu	37	chr1	51761791	51761791	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gtccccgaacggcttgtggtCctccttcccaaacatgctga	9	15	0	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr1:51761791C>A	ENST00000447632.2	-	13	1261	c.1213G>T	c.(1213-1215)Gac>Tac	p.D405Y	TTC39A_ENST00000413473.2_Missense_Mutation_p.D373Y|TTC39A_ENST00000371750.5_Missense_Mutation_p.D370Y|TTC39A_ENST00000371747.3_Missense_Mutation_p.D404Y|TTC39A_ENST00000530004.1_Missense_Mutation_p.D13Y|TTC39A_ENST00000534098.1_Intron|TTC39A_ENST00000451380.1_Missense_Mutation_p.D369Y|TTC39A_ENST00000262675.7_Missense_Mutation_p.D342Y			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	405								p.0?(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(2)|prostate(2)|skin(3)|urinary_tract(1)	17						GGCTTGTGGTCCTCCTTCCCA	0.592																																					p.D373Y		Atlas-SNP	.											.	TTC39A	40	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.G1117T						.						50	58	56					1																	51761791		2042	4180	6222	SO:0001583	missense	22996	exon13			TGTGGTCCTCCTT	AB007921	CCDS44143.1, CCDS44144.1, CCDS72789.1, CCDS72790.1	1p32.3	2013-01-11	2008-06-23	2008-06-23	ENSG00000085831	ENSG00000085831		"Tetratricopeptide (TTC) repeat domain containing"	18657	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 34"	C1orf34		9455484, 9461476	Standard	XM_005270643		Approved	KIAA0452, DEME-6	uc010onf.2	Q5SRH9	OTTHUMG00000008193	ENST00000447632.2:c.1213G>T	chr1.hg19:g.51761791C>A	ENSP00000393952:p.Asp405Tyr	41.0	0.0		60.0	19.0	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Missense_Mutation	SNP	ENST00000447632.2	hg19		.	.	.	.	.	.	.	.	.	.	C	23.1	4.373576	0.82573	.	.	ENSG00000085831	ENST00000530004;ENST00000447632;ENST00000413473;ENST00000262675;ENST00000451380;ENST00000371750;ENST00000525906;ENST00000371747	T;T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.09	5.09	0.68999	.	0.182539	0.56097	D	0.000021	T	0.67401	0.2889	M	0.64404	1.975	0.53688	D	0.999977	B;P;D;D;B;D	0.89917	0.211;0.828;1.0;1.0;0.251;0.995	B;P;D;D;B;D	0.76071	0.246;0.579;0.987;0.987;0.361;0.947	T	0.70085	-0.4969	10	0.62326	D	0.03	-22.6578	18.4872	0.90834	0.0:1.0:0.0:0.0	.	373;369;342;369;405;370	Q5SRH9-4;E7EQY9;D3DQ30;B7Z782;Q5SRH9;G3XAF8	.;.;.;.;TT39A_HUMAN;.	Y	13;405;373;342;369;370;13;404	ENSP00000431228:D13Y;ENSP00000393952:D405Y;ENSP00000406144:D373Y;ENSP00000262675:D342Y;ENSP00000397207:D369Y;ENSP00000360815:D370Y;ENSP00000436659:D13Y;ENSP00000360812:D404Y	ENSP00000262675:D342Y	D	-	1	0	TTC39A	51534379	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	7.393000	0.79851	2.344000	0.79699	0.563000	0.77884	GAC	.	.		0.592	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2			A	51761791	C	A	51761791	3	1	38	1	0	0	0	0	1	0	0	0	16722	855	30	3	652	3	TTC39A	1	51761791	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	5261508	51761791	197488830	4	4451										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79412048	79412048	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	acatacaataataacttcctTctgtgttagtgcaattagca	5	8	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr1:79412048T>C	ENST00000370742.3	-	3	299	c.236A>G	c.(235-237)gAa>gGa	p.E79G		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	79	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		ATAACTTCCTTCTGTGTTAGT	0.353																																					p.E79G		Atlas-SNP	.											.	ELTD1	143	.	0			c.A236G						.						88	83	84					1																	79412048		1887	4120	6007	SO:0001583	missense	64123	exon3			CTTCCTTCTGTGT	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.236A>G	chr1.hg19:g.79412048T>C	ENSP00000359778:p.Glu79Gly	443.0	0.0		400.0	197.0	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.258033	0.39896	.	.	ENSG00000162618	ENST00000370742	D	0.92348	-3.02	5.03	0.966	0.19667	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.662208	0.15084	N	0.281499	T	0.81945	0.4930	L	0.52364	1.645	0.27218	N	0.959743	B	0.33883	0.43	B	0.37198	0.243	T	0.71925	-0.4445	9	.	.	.	.	11.0916	0.48119	0.5071:0.0:0.0:0.4929	.	79	Q9HBW9	ELTD1_HUMAN	G	79	ENSP00000359778:E79G	.	E	-	2	0	ELTD1	79184636	0.958000	0.32768	0.934000	0.37439	0.969000	0.65631	0.475000	0.22164	0.211000	0.20683	0.528000	0.53228	GAA	.	.		0.353	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		C	79412048	T	C	79412048	3	2	38	1	0	0	0	0	1	0	0	0	5086	1783	62	2	1888	2	ELTD1	1	79412048	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	27650257	79412048	169838573	5	4452										
ZNF326	284695	hgsc.bcm.edu	37	chr1	90486427	90486427	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agtgtttatatccctgctttAcatagttcagttcagcagca	7	9	2	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr1:90486427A>G	ENST00000340281.4	+	10	1394	c.1251A>G	c.(1249-1251)ttA>ttG	p.L417L	ZNF326_ENST00000370447.3_Silent_p.L328L|ZNF326_ENST00000455342.2_Silent_p.L211L	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	417					mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		TCCCTGCTTTACATAGTTCAG	0.363																																					p.L417L		Atlas-SNP	.											.	ZNF326	60	.	0			c.A1251G						.						132	129	130					1																	90486427		2203	4300	6503	SO:0001819	synonymous_variant	284695	exon10			TGCTTTACATAGT	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1251A>G	chr1.hg19:g.90486427A>G		601.0	0.0		501.0	221.0	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Silent	SNP	ENST00000340281.4	hg19	CCDS727.1																																																																																			.	.		0.363	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		G	90486427	A	G	90486427	2	3	38	1	0	0	0	0	0	0	0	1	17861	388	14	2		2	ZNF326	1	90486427	Silent	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	11074379	90486427	158764194	6	4453										
FAM102B	284611	hgsc.bcm.edu	37	chr1	109148855	109148855	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tctttggcaggaattaaaagGtggaaaagcttatgcaaagg	12	4	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr1:109148855G>C	ENST00000370035.3	+	3	609	c.269G>C	c.(268-270)gGt>gCt	p.G90A	FAM102B_ENST00000405454.1_Missense_Mutation_p.G90A	NM_001010883.2	NP_001010883.2	Q5T8I3	F102B_HUMAN	family with sequence similarity 102, member B	90										autonomic_ganglia(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	5		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		GAATTAAAAGGTGGAAAAGCT	0.264																																					p.G90A		Atlas-SNP	.											.	FAM102B	49	.	0			c.G269C						.						93	95	94					1																	109148855		2203	4298	6501	SO:0001583	missense	284611	exon3			TAAAAGGTGGAAA	CR749397	CCDS30786.2	1p13.3	2012-11-05			ENSG00000162636	ENSG00000162636			27637	protein-coding gene	gene with protein product	"sym-3 homolog B (C. elegans)"						Standard	NM_001010883		Approved	DKFZp779B126, SYM-3B	uc010ouy.2	Q5T8I3	OTTHUMG00000010967	ENST00000370035.3:c.269G>C	chr1.hg19:g.109148855G>C	ENSP00000359052:p.Gly90Ala	361.0	0.0		283.0	121.0	NM_001010883	A1L1A1|B0QZ46|B0QZ47|Q68DH7	Missense_Mutation	SNP	ENST00000370035.3	hg19	CCDS30786.2	.	.	.	.	.	.	.	.	.	.	G	27.5	4.836359	0.91117	.	.	ENSG00000162636	ENST00000370035;ENST00000405454;ENST00000437902	T;T	0.41758	0.99;0.99	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.69663	0.3136	M	0.91140	3.18	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73930	-0.3827	10	0.54805	T	0.06	-20.0134	19.8512	0.96741	0.0:0.0:1.0:0.0	.	90	Q5T8I3	F102B_HUMAN	A	90	ENSP00000359052:G90A;ENSP00000386084:G90A	ENSP00000359052:G90A	G	+	2	0	FAM102B	108950378	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.061000	0.93913	2.797000	0.96272	0.563000	0.77884	GGT	.	.		0.264	FAM102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030188.3	NM_001010883		C	109148855	G	C	109148855	3	2	38	1	0	0	0	0	1	0	0	0	5388	1261	44	4	279	4	FAM102B	1	109148855	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	18662428	109148855	140101766	7	4454										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201046155	201046155	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gagctgcatgcccaggagggCgaagatgacgatgaagagga	17	7	0	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr1:201046155C>T	ENST00000362061.3	-	12	1946	c.1720G>A	c.(1720-1722)Gcc>Acc	p.A574T	CACNA1S_ENST00000367338.3_Missense_Mutation_p.A574T	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	574				A -> R (in Ref. 1; AAA51902 and 2; AAB37235). {ECO:0000305}.	axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCCAGGAGGGCGAAGATGACG	0.562																																					p.A574T		Atlas-SNP	.											.	CACNA1S	249	.	0			c.G1720A						.						155	137	143					1																	201046155		2203	4300	6503	SO:0001583	missense	779	exon12			GGAGGGCGAAGAT	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.1720G>A	chr1.hg19:g.201046155C>T	ENSP00000355192:p.Ala574Thr	420.0	1.0		646.0	400.0	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.425577	0.62733	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.98400	-4.91;-4.91	4.45	3.45	0.39498	Ion transport (1);	0.176123	0.49305	D	0.000152	D	0.97823	0.9285	M	0.87180	2.865	0.43010	D	0.994549	P	0.43662	0.814	B	0.44315	0.446	D	0.98423	1.0578	10	0.87932	D	0	.	11.5339	0.50626	0.3126:0.6874:0.0:0.0	.	574	Q13698	CAC1S_HUMAN	T	574	ENSP00000355192:A574T;ENSP00000356307:A574T	ENSP00000355192:A574T	A	-	1	0	CACNA1S	199312778	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	2.632000	0.46511	2.189000	0.69895	0.549000	0.68633	GCC	.	.		0.562	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		T	201046155	C	T	201046155	3	4	38	1	0	0	0	0	1	0	0	0	2549	768	27	1	4033	1	CACNA1S	1	201046155	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	91897300	201046155	48204466	8	4455										
CR1	1378	hgsc.bcm.edu	37	chr1	207760833	207760833	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tttgaattatgaatgccgtcCtgggtattttgggaaaatgt	11	4	0	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr1:207760833C>T	ENST00000367049.4	+	34	5633	c.5633C>T	c.(5632-5634)cCt>cTt	p.P1878L	CR1_ENST00000400960.2_Missense_Mutation_p.P1428L|RP11-78B10.2_ENST00000597497.1_RNA|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367052.1_Missense_Mutation_p.P1428L|CR1_ENST00000367053.1_Missense_Mutation_p.P1428L|CR1_ENST00000367051.1_Missense_Mutation_p.P1428L	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1428	Sushi 29. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						GAATGCCGTCCTGGGTATTTT	0.453																																					p.P1878L		Atlas-SNP	.											.	CR1	354	.	0			c.C5633T						.						143	131	135					1																	207760833		1835	4087	5922	SO:0001583	missense	1378	exon34			GCCGTCCTGGGTA	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.5633C>T	chr1.hg19:g.207760833C>T	ENSP00000356016:p.Pro1878Leu	647.0	1.0		534.0	241.0	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	hg19	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.817015	0.32145	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;-0.19	3.11	2.19	0.27852	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.80428	0.4621	M	0.93720	3.45	0.37949	D	0.932606	P;D;D	0.89917	0.594;1.0;1.0	B;D;D	0.91635	0.094;0.998;0.999	T	0.80879	-0.1185	9	0.62326	D	0.03	.	6.2079	0.20613	0.0:0.8601:0.0:0.1399	.	1428;1428;1878	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	L	1428;1428;1428;1428;978;1878	ENSP00000356019:P1428L;ENSP00000356018:P1428L;ENSP00000356020:P1428L;ENSP00000383744:P1428L;ENSP00000436139:P978L;ENSP00000356016:P1878L	ENSP00000356016:P1878L	P	+	2	0	CR1	205827456	0.984000	0.35163	0.876000	0.34364	0.186000	0.23388	0.968000	0.29357	0.852000	0.35287	0.655000	0.94253	CCT	.	.		0.453	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		T	207760833	C	T	207760833	3	4	38	1	0	0	0	0	1	0	0	0	3842	681	24	3	5767	3	CR1	1	207760833	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	6714678	207760833	41489788	9	4456										
ACTN2	88	hgsc.bcm.edu	37	chr1	236881238	236881238	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gaggaagacttcaggaatggCcttaagctcatgctgctttt	11	8	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr1:236881238C>A	ENST00000366578.4	+	2	373	c.207C>A	c.(205-207)ggC>ggA	p.G69G	ACTN2_ENST00000492634.1_3'UTR|ACTN2_ENST00000542672.1_Silent_p.G69G	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	69	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			TCAGGAATGGCCTTAAGCTCA	0.443																																					p.G69G		Atlas-SNP	.											.	ACTN2	191	.	0			c.C207A						.						181	157	165					1																	236881238		2203	4300	6503	SO:0001819	synonymous_variant	88	exon2			GAATGGCCTTAAG	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.207C>A	chr1.hg19:g.236881238C>A		392.0	0.0		345.0	155.0	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Silent	SNP	ENST00000366578.4	hg19	CCDS1613.1																																																																																			.	.		0.443	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		A	236881238	C	A	236881238	2	1	38	1	0	0	0	0	0	0	0	1	205	726	26	3		3	ACTN2	1	236881238	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	29120405	236881238	12369383	10	4457										
ACP1	52	hgsc.bcm.edu	37	chr2	277266	277266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agacggtgtaccagcagtgtGtcaggtgctgcagagcgttc	15	9	1	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:277266G>A	ENST00000272065.5	+	6	532	c.439G>A	c.(439-441)Gtc>Atc	p.V147I	ACP1_ENST00000272067.6_Missense_Mutation_p.V147I|ACP1_ENST00000484464.1_3'UTR	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble	147						cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	CCAGCAGTGTGTCAGGTGCTG	0.517																																					p.V147I		Atlas-SNP	.											.	ACP1	42	.	0			c.G439A						.						147	140	142					2																	277266		2203	4300	6503	SO:0001583	missense	52	exon6			CAGTGTGTCAGGT	M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"Protein tyrosine phosphatases / Class II Cys-based PTPs"	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.439G>A	chr2.hg19:g.277266G>A	ENSP00000272065:p.Val147Ile	400.0	0.0		365.0	30.0	NM_007099	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Missense_Mutation	SNP	ENST00000272065.5	hg19	CCDS1639.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.835149	0.50951	.	.	ENSG00000143727	ENST00000272067;ENST00000272065	T;T	0.30182	1.54;1.54	5.62	-6.39	0.01951	Phosphotyrosine protein phosphatase I superfamily (3);	0.749136	0.12667	N	0.449134	T	0.24236	0.0587	L	0.58925	1.835	0.25308	N	0.989222	B;B	0.02656	0.0;0.0	B;B	0.12156	0.005;0.007	T	0.15150	-1.0447	10	0.30854	T	0.27	-1.1228	11.0838	0.48074	0.2473:0.558:0.1947:0.0	.	147;147	P24666-2;P24666	.;PPAC_HUMAN	I	147	ENSP00000272067:V147I;ENSP00000272065:V147I	ENSP00000272065:V147I	V	+	1	0	ACP1	267266	0.003000	0.15002	0.001000	0.08648	0.989000	0.77384	-1.320000	0.02700	-1.433000	0.01977	0.655000	0.94253	GTC	.	.		0.517	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3			A	277266	G	A	277266	3	1	38	1	0	0	0	0	1	0	0	0	162	1377	48	3	616	3	ACP1	2	277266	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10		277266	242922107	11	4458										
APOB	338	hgsc.bcm.edu	37	chr2	21228142	21228157	+	Frame_Shift_Del	DEL	GGAGGGAATCTCAATG	GGAGGGAATCTCAATG	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gcaggtacagagaacttaatGgagggaatctcaatggtctg					rs553934960		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	GGAGGGAATCTCAATG	GGAGGGAATCTCAATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:21228142_21228157delGGAGGGAATCTCAATG	ENST00000233242.1	-	26	11710_11725	c.11583_11598delCATTGAGATTCCCTCC	c.(11581-11598)accattgagattccctccfs	p.TIEIPS3861fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3861					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAACTTAATGGAGGGAATCTCAATGGTCTGCTCAG	0.468																																					p.3862_3867del		Atlas-Indel,Pindel	.											.	APOB	761	.	0			c.11584_11599del						.																																			SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.11583_11598delCATTGAGATTCCCTCC	chr2.hg19:g.21228142_21228157delGGAGGGAATCTCAATG	ENSP00000233242:p.Thr3861fs	242.0	0.0		145.0	33.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.468	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21228157	GGAGGGAATCTCAATG	-	21228142	7	5	38	1	0	1	0	1	0	0	0	0	785	1335	47	0	2109	0	APOB	2	21228142	Frame_Shift_Del	DEL	GGAGGGAATCTCAATG	TCGA-BC-A10Z-01A-11D-A12Z-10	20950876	21228142	221971231	12	4459										
ALK	238	hgsc.bcm.edu	37	chr2	29443612	29443612	+	Frame_Shift_Del	DEL	C	C	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggaggaaggacttgaggtctCcccccgccatgagctccagc							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:29443612delC	ENST00000389048.3	-	23	4511	c.3605delG	c.(3604-3606)ggafs	p.G1202fs	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1202	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CTTGAGGTCTCCCCCCGCCAT	0.587			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.G1202fs		Pindel	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	ALK,NS,carcinoma,0,1	ALK	533	.	0			c.3606delA						.						46	47	47					2																	29443612		2203	4300	6503	SO:0001589	frameshift_variant	238	exon23	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	.	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.3605delG	chr2.hg19:g.29443612delC	ENSP00000373700:p.Gly1202fs	90.0	0.0		118.0	29.0	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Frame_Shift_Del	DEL	ENST00000389048.3	hg19	CCDS33172.1																																																																																			.	.		0.587	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		-	29443612	C	-	29443612	7	5	38	1	0	1	0	1	0	0	0	0	525	855	30	0	1285	0	ALK	2	29443612	Frame_Shift_Del	DEL	C	TCGA-BC-A10Z-01A-11D-A12Z-10	8215470	29443612	213755761	13	4460										
THADA	63892	hgsc.bcm.edu	37	chr2	43813540	43813540	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgccaacatatagcacttgcCtattttcttccaggatttca	5	11	2	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:43813540C>A	ENST00000405006.4	-	7	884	c.533G>T	c.(532-534)aGa>aTa	p.R178I	THADA_ENST00000405975.2_Splice_Site_p.R178I|THADA_ENST00000402360.2_Splice_Site_p.R178I|THADA_ENST00000403856.1_Splice_Site_p.R178I|THADA_ENST00000415080.2_5'UTR|THADA_ENST00000404790.1_Splice_Site_p.R178I	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	178										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TAGCACTTGCCTATTTTCTTC	0.313																																					p.R178I		Atlas-SNP	.											.	THADA	131	.	0			c.G533T						.						63	56	58					2																	43813540		1811	4072	5883	SO:0001630	splice_region_variant	63892	exon7			ACTTGCCTATTTT	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.533+1G>T	chr2.hg19:g.43813540C>A		513.0	1.0		475.0	258.0	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	hg19	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.477815	0.63849	.	.	ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	T;T;T;T;T	0.34859	2.79;2.79;1.38;1.37;1.34	5.35	5.35	0.76521	.	0.061993	0.64402	D	0.000009	T	0.55033	0.1895	L	0.56769	1.78	0.80722	D	1	D;P;P;D	0.76494	0.978;0.956;0.939;0.999	P;P;P;D	0.66196	0.731;0.742;0.745;0.942	T	0.51284	-0.8725	9	.	.	.	.	16.8609	0.86018	0.0:1.0:0.0:0.0	.	178;178;178;178	B5MC89;Q8IY32;Q6YHU6-5;Q6YHU6	.;.;.;THADA_HUMAN	I	178	ENSP00000386088:R178I;ENSP00000385995:R178I;ENSP00000385441:R178I;ENSP00000384266:R178I;ENSP00000385469:R178I	.	R	-	2	0	THADA	43667044	1.000000	0.71417	1.000000	0.80357	0.317000	0.28152	4.341000	0.59335	2.493000	0.84123	0.655000	0.94253	AGA	.	.		0.313	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	Missense_Mutation	A	43813540	C	A	43813540	5	1	38	1	0	0	0	0	0	0	1	0	15855	695	24	3	5456	3	THADA	2	43813540	Splice_Site	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	14369928	43813540	199385833	14	4461										
EHBP1	23301	hgsc.bcm.edu	37	chr2	63092103	63092103	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aactgaagaagaagaattggAtgagtaagtacatttcattt	9	3	1	5			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:63092103A>T	ENST00000263991.5	+	10	1582	c.1100A>T	c.(1099-1101)gAt>gTt	p.D367V	EHBP1_ENST00000354487.3_Missense_Mutation_p.D332V|EHBP1_ENST00000405015.3_Missense_Mutation_p.D332V|EHBP1_ENST00000405289.1_Missense_Mutation_p.D332V|EHBP1_ENST00000431489.1_Missense_Mutation_p.D332V	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	367						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			GAAGAATTGGATGAGTAAGTA	0.343																																					p.D367V		Atlas-SNP	.											.	EHBP1	127	.	0			c.A1100T						.						66	65	65					2																	63092103		2203	4298	6501	SO:0001583	missense	23301	exon10			AATTGGATGAGTA	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.1100A>T	chr2.hg19:g.63092103A>T	ENSP00000263991:p.Asp367Val	138.0	0.0		86.0	36.0	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	hg19	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.549318	0.86127	.	.	ENSG00000115504	ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T	0.78003	-1.14;-1.14;-1.06;-1.11;-1.11	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.86343	0.5910	M	0.61703	1.905	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.87873	0.2672	10	0.87932	D	0	.	15.4926	0.75619	1.0:0.0:0.0:0.0	.	332;332;367	Q8NDI1-2;Q8NDI1-3;Q8NDI1	.;.;EHBP1_HUMAN	V	332;332;367;332;332	ENSP00000384143:D332V;ENSP00000403783:D332V;ENSP00000263991:D367V;ENSP00000346482:D332V;ENSP00000385524:D332V	ENSP00000263991:D367V	D	+	2	0	EHBP1	62945607	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.254000	0.89844	2.114000	0.64651	0.455000	0.32223	GAT	.	.		0.343	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		T	63092103	A	T	63092103	3	4	38	1	0	0	0	0	1	0	0	0	4977	333	12	4	1134	4	EHBP1	2	63092103	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	19278563	63092103	180107270	15	4462										
RGPD4	285190	hgsc.bcm.edu	37	chr2	108487515	108487515	+	Frame_Shift_Del	DEL	G	G	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccaataaagcaaacacttccGgtgactttgagaaagatgat							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:108487515delG	ENST00000408999.3	+	20	3132	c.3055delG	c.(3055-3057)ggtfs	p.G1019fs	RGPD4_ENST00000354986.4_Frame_Shift_Del_p.G1019fs	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1019					protein targeting to Golgi (GO:0000042)			p.G1019S(1)		breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						AAACACTTCCGGTGACTTTGA	0.388																																					p.S1018fs		Atlas-INDEL	.											.	RGPD4	112	.	1	Substitution - Missense(1)	endometrium(1)	c.3054delC						.						1	2	2					2																	108487515		250	756	1006	SO:0001589	frameshift_variant	285190	exon20			.	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.3055delG	chr2.hg19:g.108487515delG	ENSP00000386810:p.Gly1019fs	398.0	0.0		311.0	121.0	NM_182588	B9A029	Frame_Shift_Del	DEL	ENST00000408999.3	hg19	CCDS46381.1																																																																																			.	.		0.388	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		-	108487515	G	-	108487515	7	5	38	1	0	1	0	1	0	0	0	0	13303	1116	39	0	3133	0	RGPD4	2	108487515	Frame_Shift_Del	DEL	G	TCGA-BC-A10Z-01A-11D-A12Z-10	45395412	108487515	134711858	16	4463										
IL1F8	27177	hgsc.bcm.edu	37	chr2	113788640	113788640	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctcaccaggcttaatgctgcGgctaagaggagctgctatta	11	10	1	1	rs34754959	byFrequency	TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:113788640G>T	ENST00000259213.4	-	3	213	c.106C>A	c.(106-108)Cgc>Agc	p.R36S	IL36B_ENST00000327407.2_Missense_Mutation_p.R36S	NM_014438.3	NP_055253.2	Q9NZH7	IL36B_HUMAN	interleukin 36, beta	36			R -> C (in dbSNP:rs34754959). {ECO:0000269|Ref.4}.		immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-1 receptor binding (GO:0005149)			kidney(1)|ovary(1)|pancreas(1)	3						TTAATGCTGCGGCTAAGAGGA	0.512																																					p.R36S		Atlas-SNP	.											.	IL36B	69	.	0			c.C106A						.						105	93	97					2																	113788640		2203	4300	6503	SO:0001583	missense	27177	exon3			TGCTGCGGCTAAG	AF201833	CCDS2109.1, CCDS2110.1	2q14	2011-07-14	2011-06-06	2011-06-06	ENSG00000136696	ENSG00000136696		"Interleukins and interleukin receptors"	15564	protein-coding gene	gene with protein product		605508	"interleukin 1 family, member 8 (eta)"	IL1F8		10625660, 10512743, 16646978	Standard	NM_173178		Approved	FIL1, IL-1H2, IL-1F8, FILI-(ETA), IL1-ETA, IL1H2, MGC126880, MGC126882	uc002tiq.1	Q9NZH7	OTTHUMG00000131338	ENST00000259213.4:c.106C>A	chr2.hg19:g.113788640G>T	ENSP00000259213:p.Arg36Ser	134.0	0.0		129.0	64.0	NM_173178	Q3MIH0|Q53SR6|Q7RTZ7|Q9UHA5	Missense_Mutation	SNP	ENST00000259213.4	hg19	CCDS2109.1	.	.	.	.	.	.	.	.	.	.	g	3.130	-0.178604	0.06380	.	.	ENSG00000136696	ENST00000259213;ENST00000327407	T;T	0.16196	2.36;2.36	3.04	0.651	0.17817	.	1.093160	0.07044	N	0.830755	T	0.05914	0.0154	N	0.02916	-0.46	0.09310	N	1	B;B	0.25850	0.001;0.136	B;B	0.23852	0.005;0.049	T	0.40384	-0.9566	10	0.17369	T	0.5	.	2.9288	0.05793	0.0:0.1474:0.2715:0.5811	.	36;36	Q9NZH7-2;Q9NZH7	.;IL36B_HUMAN	S	36	ENSP00000259213:R36S;ENSP00000328420:R36S	ENSP00000259213:R36S	R	-	1	0	IL36B	113505111	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.027000	0.12371	0.401000	0.25424	-0.459000	0.05422	CGC	.	G|0.989;A|0.011		0.512	IL36B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254110.1	NM_014438		T	113788640	G	T	113788640	3	4	38	1	0	0	0	0	1	0	0	0	7665	1116	39	1	621	1	IL1F8	2	113788640	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	5301125	113788640	129410733	17	4464										
LRP1B	53353	hgsc.bcm.edu	37	chr2	142567848	142567848	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	atgagaacctttctactcacAggtatctaaagactcgtctg	7	10	4	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:142567848A>T	ENST00000389484.3	-	2	1176	c.205T>A	c.(205-207)Tgt>Agt	p.C69S	LRP1B_ENST00000486364.1_5'UTR	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	69	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TTCTACTCACAGGTATCTAAA	0.438										TSP Lung(27;0.18)																											p.C69S	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T205A						.						58	55	56					2																	142567848		2203	4300	6503	SO:0001630	splice_region_variant	53353	exon2			ACTCACAGGTATC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.205+1T>A	chr2.hg19:g.142567848A>T		554.0	0.0		385.0	171.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.0|22.0	4.227139|4.227139	0.79576|0.79576	.|.	.|.	ENSG00000168702|ENSG00000168702	ENST00000389484|ENST00000434794	D|D	0.99919|0.91011	-8.0|-2.77	5.62|5.62	5.62|5.62	0.85841|0.85841	Low-density lipoprotein (LDL) receptor class A, conserved site (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.92851|0.92851	0.7726|0.7726	M|M	0.93638|0.93638	3.44|3.44	0.58432|0.58432	D|D	0.999999|0.999999	D|B	0.62365|0.13145	0.991|0.007	D|B	0.78314|0.10450	0.991|0.005	D|D	0.90607|0.90607	0.4549|0.4549	9|8	.|.	.|.	.|.	.|.	15.4882|15.4882	0.75584|0.75584	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	69|107	Q9NZR2|Q96NT6	LRP1B_HUMAN|.	S|T	69|69	ENSP00000374135:C69S|ENSP00000413239:S69T	.|.	C|S	-|-	1|1	0|0	LRP1B|LRP1B	142284318|142284318	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.287000|8.287000	0.89918|0.89918	2.141000|2.141000	0.66446|0.66446	0.528000|0.528000	0.53228|0.53228	TGT|TCC	.	.		0.438	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Missense_Mutation	T	142567848	A	T	142567848	5	4	38	1	0	0	0	0	0	0	1	0	8964	202	7	4	13954	4	LRP1B	2	142567848	Splice_Site	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	28779208	142567848	100631525	18	4465										
EPC2	26122	hgsc.bcm.edu	37	chr2	149519486	149519486	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tattgcacttaaccttagaaGttgtggagaaaaggtaacat	9	5	0	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:149519486G>T	ENST00000258484.6	+	5	836	c.802G>T	c.(802-804)Gtt>Ttt	p.V268F		NM_015630.3	NP_056445.3	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2 (Drosophila)	268					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0516)		AACCTTAGAAGTTGTGGAGAA	0.353																																					p.V268F		Atlas-SNP	.											.	EPC2	57	.	0			c.G802T						.						78	73	74					2																	149519486		1836	4075	5911	SO:0001583	missense	26122	exon5			TTAGAAGTTGTGG	AF286904	CCDS46422.1	2q23	2008-02-05			ENSG00000135999	ENSG00000135999			24543	protein-coding gene	gene with protein product		611000					Standard	NM_015630		Approved	DKFZP566F2124	uc010zbt.2	Q52LR7	OTTHUMG00000153739	ENST00000258484.6:c.802G>T	chr2.hg19:g.149519486G>T	ENSP00000258484:p.Val268Phe	538.0	0.0		347.0	143.0	NM_015630	B3KWT7|D3DP89|Q7L9J1|Q96RR7|Q9NUT8|Q9NVR1|Q9UFM9	Missense_Mutation	SNP	ENST00000258484.6	hg19	CCDS46422.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.958703	0.74016	.	.	ENSG00000135999	ENST00000258484	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.81983	0.4938	M	0.81802	2.56	0.80722	D	1	D	0.62365	0.991	P	0.60949	0.881	D	0.84109	0.0400	9	0.87932	D	0	-3.4451	19.5983	0.95549	0.0:0.0:1.0:0.0	.	268	Q52LR7	EPC2_HUMAN	F	268	.	ENSP00000258484:V268F	V	+	1	0	EPC2	149235956	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.401000	0.66326	2.640000	0.89533	0.585000	0.79938	GTT	.	.		0.353	EPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332278.1	NM_015630		T	149519486	G	T	149519486	3	4	38	1	0	0	0	0	1	0	0	0	5163	1029	36	3	820	3	EPC2	2	149519486	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	6951638	149519486	93679887	19	4466										
TTN	7273	hgsc.bcm.edu	37	chr2	179463285	179463285	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	attcaacgatgtatccagttActttggatccaccatctttt	5	10	2	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:179463285A>T	ENST00000591111.1	-	242	52360	c.52136T>A	c.(52135-52137)gTa>gAa	p.V17379E	TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V19020E|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V16452E|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V10080E|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V9955E|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V10147E|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17379	Fibronectin type-III 26. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTATCCAGTTACTTTGGATCC	0.413																																					p.V19020E		Atlas-SNP	.											.	TTN	18412	.	0			c.T57059A						.						93	88	89					2																	179463285		1837	4090	5927	SO:0001583	missense	7273	exon292			CCAGTTACTTTGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.52136T>A	chr2.hg19:g.179463285A>T	ENSP00000465570:p.Val17379Glu	408.0	0.0		380.0	156.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.07	2.724730	0.48833	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59772	0.24;0.24;0.24;0.24	5.91	5.91	0.95273	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.77505	0.4140	M	0.90705	3.14	0.35177	D	0.772089	P;P;P;P	0.39311	0.667;0.667;0.667;0.667	P;P;P;P	0.51945	0.529;0.529;0.685;0.685	D	0.86183	0.1607	9	0.87932	D	0	.	16.3364	0.83064	1.0:0.0:0.0:0.0	.	9955;10080;10147;17379	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	16452;9955;10147;10080;9953	ENSP00000343764:V16452E;ENSP00000434586:V9955E;ENSP00000340554:V10147E;ENSP00000352154:V10080E	ENSP00000340554:V10147E	V	-	2	0	TTN	179171530	1.000000	0.71417	0.996000	0.52242	0.999000	0.98932	9.326000	0.96389	2.252000	0.74401	0.528000	0.53228	GTA	.	.		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179463285	A	T	179463285	3	4	38	1	0	0	0	0	1	0	0	0	16750	391	14	4	50918	4	TTN	2	179463285	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	29943799	179463285	63736088	20	4467										
TTN	7273	hgsc.bcm.edu	37	chr2	179470150	179470150	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agattccgcaccttcatcatCttgtatgactacattaagag	6	10	3	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:179470150C>T	ENST00000591111.1	-	229	49173	c.48949G>A	c.(48949-48951)Gat>Aat	p.D16317N	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D17958N|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D15390N|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D9018N|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D8893N|TTN_ENST00000342175.6_Missense_Mutation_p.D9085N|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16317	Fibronectin type-III 18. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTTCATCATCTTGTATGACT	0.333																																					p.D17958N		Atlas-SNP	.											.	TTN	18412	.	0			c.G53872A						.						72	67	68					2																	179470150		1847	4091	5938	SO:0001583	missense	7273	exon279			CATCATCTTGTAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48949G>A	chr2.hg19:g.179470150C>T	ENSP00000465570:p.Asp16317Asn	245.0	0.0		181.0	88.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.55	3.154827	0.57259	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	5.74	5.74	0.90152	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.71600	0.3359	L	0.58354	1.805	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.72564	-0.4255	9	0.87932	D	0	.	19.9346	0.97133	0.0:1.0:0.0:0.0	.	8893;9018;9085;16317	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	15390;8893;9085;9018;8893	ENSP00000343764:D15390N;ENSP00000434586:D8893N;ENSP00000340554:D9085N;ENSP00000352154:D9018N	ENSP00000340554:D9085N	D	-	1	0	TTN	179178395	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.710000	0.84655	2.712000	0.92718	0.563000	0.77884	GAT	.	.		0.333	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179470150	C	T	179470150	3	4	38	1	0	0	0	0	1	0	0	0	16750	913	32	3	54157	3	TTN	2	179470150	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	6865	179470150	63729223	21	4468										
MAP2	4133	hgsc.bcm.edu	37	chr2	210559239	210559239	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tggagaagaaagtactcaagCggagatatcatgtgagtctc	12	6	3	4	rs184529696	byFrequency	TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:210559239C>A	ENST00000360351.4	+	7	2851	c.2345C>A	c.(2344-2346)gCg>gAg	p.A782E	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.A778E|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	782					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AGTACTCAAGCGGAGATATCA	0.448																																					p.A782E	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.C2345A						.						91	91	91					2																	210559239		2203	4300	6503	SO:0001583	missense	4133	exon7			CTCAAGCGGAGAT		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.2345C>A	chr2.hg19:g.210559239C>A	ENSP00000353508:p.Ala782Glu	110.0	0.0		87.0	45.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	hg19	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	c	6.755	0.508134	0.12883	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.18960	2.18;2.18	5.79	2.14	0.27477	MAP2/Tau projection (1);	0.753411	0.12103	N	0.499317	T	0.15262	0.0368	N	0.14661	0.345	0.09310	N	1	P;P	0.35821	0.467;0.523	B;B	0.40444	0.221;0.329	T	0.23547	-1.0185	10	0.87932	D	0	-1.3603	9.134	0.36863	0.0:0.3339:0.0:0.6661	.	778;782	P11137-3;P11137	.;MAP2_HUMAN	E	782;778	ENSP00000353508:A782E;ENSP00000392164:A778E	ENSP00000353508:A782E	A	+	2	0	MAP2	210267484	0.531000	0.26338	0.004000	0.12327	0.411000	0.31082	1.419000	0.34793	0.144000	0.18951	-0.295000	0.09555	GCG	.	C|0.994;T|0.006		0.448	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		A	210559239	C	A	210559239	3	1	38	1	0	0	0	0	1	0	0	0	9244	768	27	1	2359	1	MAP2	2	210559239	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	31089089	210559239	32640134	22	4469										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220432912	220432913	+	Frame_Shift_Ins	INS	-	-	G													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	atctgctcgtacttgcggcaINSgggcagcagccgctggtcct							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:220432912_220432913insG	ENST00000404537.1	-	2	1202_1203	c.1146_1147insC	c.(1144-1149)ccctgcfs	p.C383fs	OBSL1_ENST00000265318.4_Frame_Shift_Ins_p.C383fs|OBSL1_ENST00000289656.3_5'UTR|OBSL1_ENST00000603926.1_Frame_Shift_Ins_p.C383fs|OBSL1_ENST00000373876.1_Frame_Shift_Ins_p.C383fs|OBSL1_ENST00000491370.1_5'Flank|OBSL1_ENST00000373873.4_Frame_Shift_Ins_p.C383fs	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	383	Ig-like 4.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		TACTTGCGGCAGGGCAGCAGCC	0.624											OREG0003988	type=REGULATORY REGION|Gene=OBSL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.C383fs		Atlas-INDEL	.											.	OBSL1	120	.	0			c.1147_1148insC						.																																			SO:0001589	frameshift_variant	23363	exon2			.	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.1147dupC	chr2.hg19:g.220432915_220432915dupG	ENSP00000385636:p.Cys383fs	148.0	0.0	2266	163.0	10.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Frame_Shift_Ins	INS	ENST00000404537.1	hg19	CCDS46520.1																																																																																			.	.		0.624	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			G	220432913	-	G	220432912	7	5	38	1	0	1	1	0	0	0	0	0	10822	188	7	0	4775	0	OBSL1	2	220432912	Frame_Shift_Ins	INS	-	TCGA-BC-A10Z-01A-11D-A12Z-10	9873673	220432912	22766461	23	4470										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222347238	222347238	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ttctgctgtggggtgtagtgGaccccacttccacagggtcg	14	11	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:222347238G>T	ENST00000281821.2	-	5	1193	c.1152C>A	c.(1150-1152)gtC>gtA	p.V384V	EPHA4_ENST00000392071.4_Silent_p.V333V|EPHA4_ENST00000409854.1_Silent_p.V384V|EPHA4_ENST00000409938.1_Silent_p.V384V	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	384	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GGGTGTAGTGGACCCCACTTC	0.512																																					p.V384V		Atlas-SNP	.											.	EPHA4	263	.	0			c.C1152A						.						240	247	245					2																	222347238		2203	4300	6503	SO:0001819	synonymous_variant	2043	exon5			GTAGTGGACCCCA	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.1152C>A	chr2.hg19:g.222347238G>T		363.0	0.0		293.0	133.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Silent	SNP	ENST00000281821.2	hg19	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	G	8.141	0.785290	0.16189	.	.	ENSG00000116106	ENST00000441679	.	.	.	6.06	3.1	0.35709	.	.	.	.	.	T	0.47116	0.1428	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35968	-0.9767	4	.	.	.	.	3.8226	0.08842	0.0722:0.2114:0.3317:0.3847	.	.	.	.	Y	121	.	.	S	-	2	0	EPHA4	222055482	0.995000	0.38212	1.000000	0.80357	0.822000	0.46500	0.301000	0.19174	0.860000	0.35481	0.655000	0.94253	TCC	.	.		0.512	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222347238	G	T	222347238	2	4	38	1	0	0	0	0	0	0	0	1	5171	1161	41	3		3	EPHA4	2	222347238	Silent	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	1914326	222347238	20852135	24	4471										
SP110	3431	hgsc.bcm.edu	37	chr2	231079722	231079722	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	atattcacgcaggttaatttGactgaacaatgtcaccagaa	7	8	2	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr2:231079722G>C	ENST00000358662.4	-	3	337	c.259C>G	c.(259-261)Caa>Gaa	p.Q87E	SP110_ENST00000258382.5_Missense_Mutation_p.Q87E|SP110_ENST00000338556.3_5'UTR|SP110_ENST00000392048.3_Missense_Mutation_p.Q87E|SP110_ENST00000486146.2_5'Flank|SP110_ENST00000540870.1_Missense_Mutation_p.Q93E|SP110_ENST00000258381.6_Missense_Mutation_p.Q87E	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	87	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		AGGTTAATTTGACTGAACAAT	0.408																																					p.Q93E		Atlas-SNP	.											.	SP110	105	.	0			c.C277G						.						100	99	99					2																	231079722		2203	4300	6503	SO:0001583	missense	3431	exon4			TAATTTGACTGAA	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"interferon-induced protein 41, 30kD"	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.259C>G	chr2.hg19:g.231079722G>C	ENSP00000351488:p.Gln87Glu	233.0	0.0		232.0	102.0	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	hg19	CCDS2474.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.758235	0.00657	.	.	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000409815;ENST00000455674;ENST00000416610	D;D;D;D;D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27	4.2	2.31	0.28768	Sp100 (2);	1.304430	0.05488	N	0.556123	D	0.84257	0.5432	N	0.04880	-0.145	0.40754	D	0.982946	B;B;B;B	0.30563	0.009;0.009;0.285;0.004	B;B;B;B	0.31495	0.005;0.005;0.131;0.016	T	0.72127	-0.4384	10	0.19590	T	0.45	.	6.8514	0.24016	0.0:0.1867:0.6028:0.2104	.	87;93;87;87	G5E9C0;F5H1M1;Q9HB58;Q9HB58-6	.;.;SP110_HUMAN;.	E	87;87;87;87;93;87;41;87	ENSP00000258381:Q87E;ENSP00000351488:Q87E;ENSP00000375902:Q87E;ENSP00000258382:Q87E;ENSP00000439558:Q93E;ENSP00000387172:Q87E;ENSP00000393992:Q41E;ENSP00000399978:Q87E	ENSP00000258381:Q87E	Q	-	1	0	SP110	230787966	0.797000	0.28877	0.502000	0.27614	0.263000	0.26337	0.900000	0.28431	0.650000	0.30769	-0.165000	0.13383	CAA	.	.		0.408	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424		C	231079722	G	C	231079722	3	2	38	1	0	0	0	0	1	0	0	0	14976	1299	45	4	2014	4	SP110	2	231079722	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	8732484	231079722	12119651	25	4472										
CHL1	10752	hgsc.bcm.edu	37	chr3	430967	430967	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	atggagcagaatggaccaggCctagagtacagagtgacctg	14	8	0	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr3:430967C>G	ENST00000256509.2	+	20	2922	c.2280C>G	c.(2278-2280)ggC>ggG	p.G760G	CHL1_ENST00000397491.2_Silent_p.G744G	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		atggaccaggcctagagtaca	0.498																																					p.G760G		Atlas-SNP	.											.	CHL1	242	.	0			c.C2280G						.						81	74	76					3																	430967		2203	4300	6503	SO:0001819	synonymous_variant	10752	exon18			ACCAGGCCTAGAG	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.2280C>G	chr3.hg19:g.430967C>G		187.0	0.0		159.0	69.0	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000256509.2	hg19	CCDS2556.1																																																																																			.	.		0.498	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		G	430967	C	G	430967	2	3	38	1	0	0	0	0	0	0	0	1	3351	726	26	4		4	CHL1	3	430967	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10		430967	197591463	26	4473										
GADL1	339896	hgsc.bcm.edu	37	chr3	30827849	30827849	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aattatgcaatcacttacttCcatcagtaacttgaatcctt	3	10	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr3:30827849C>A	ENST00000282538.5	-	13	1450	c.1300G>T	c.(1300-1302)Gaa>Taa	p.E434*		NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	434					carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						TCACTTACTTCCATCAGTAAC	0.299																																					p.E434X		Atlas-SNP	.											.	GADL1	91	.	0			c.G1300T						.						167	152	157					3																	30827849		2196	4300	6496	SO:0001587	stop_gained	339896	exon13			TTACTTCCATCAG	AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644			27949	protein-coding gene	gene with protein product		615601					Standard	NM_207359		Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.1300G>T	chr3.hg19:g.30827849C>A	ENSP00000282538:p.Glu434*	313.0	0.0		292.0	127.0	NM_207359		Nonsense_Mutation	SNP	ENST00000282538.5	hg19	CCDS2649.2	.	.	.	.	.	.	.	.	.	.	C	39	7.560775	0.98358	.	.	ENSG00000144644	ENST00000282538	.	.	.	5.96	5.96	0.96718	.	0.053589	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-4.7869	18.1922	0.89810	0.0:1.0:0.0:0.0	.	.	.	.	X	434	.	ENSP00000282538:E434X	E	-	1	0	GADL1	30802853	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.187000	0.65087	2.831000	0.97527	0.650000	0.86243	GAA	.	.		0.299	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359		A	30827849	C	A	30827849	4	1	38	1	0	0	0	0	0	1	0	0	6193	864	30	3	277	3	GADL1	3	30827849	Nonsense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	30396882	30827849	167194581	27	4474										
KIF9	64147	hgsc.bcm.edu	37	chr3	47307360	47307360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tggcttccttcaggacttggCcctcagactacaaagcaaag	9	12	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr3:47307360C>T	ENST00000265529.3	-	9	1456	c.776G>A	c.(775-777)gGc>gAc	p.G259D	KIF9_ENST00000352910.4_Missense_Mutation_p.G166D|KIF9_ENST00000444589.2_Missense_Mutation_p.G259D|KIF9_ENST00000487440.1_5'UTR|KIF9_ENST00000452770.2_Missense_Mutation_p.G259D|KIF9_ENST00000335044.2_Missense_Mutation_p.G259D			Q9HAQ2	KIF9_HUMAN	kinesin family member 9	259	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle disassembly (GO:1903008)|regulation of podosome assembly (GO:0071801)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|podosome (GO:0002102)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein dimerization activity (GO:0046983)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(15)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)	34		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CAGGACTTGGCCCTCAGACTA	0.502																																					p.G259D	Colon(44;962 1147 15977 24541)	Atlas-SNP	.											KIF9,NS,adenoma,0,1	KIF9	59	.	0			c.G776A						.						159	141	147					3																	47307360		2203	4300	6503	SO:0001583	missense	64147	exon8			ACTTGGCCCTCAG	AF311212	CCDS2751.1, CCDS2752.1	3p21.31	2008-03-03			ENSG00000088727	ENSG00000088727		"Kinesins"	16666	protein-coding gene	gene with protein product		607910				11483511	Standard	NM_022342		Approved	MGC104186	uc003cqx.3	Q9HAQ2	OTTHUMG00000133512	ENST00000265529.3:c.776G>A	chr3.hg19:g.47307360C>T	ENSP00000265529:p.Gly259Asp	192.0	1.0		144.0	66.0	NM_182902	Q86Z28|Q9H8A4	Missense_Mutation	SNP	ENST00000265529.3	hg19	CCDS2752.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.760356	0.89932	.	.	ENSG00000088727	ENST00000335044;ENST00000265529;ENST00000444589;ENST00000452770;ENST00000352910	T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07	5.0	5.0	0.66597	Kinesin, motor domain (4);	0.060422	0.64402	D	0.000005	D	0.86053	0.5841	M	0.78285	2.405	0.51482	D	0.999922	D;D	0.71674	0.988;0.998	P;D	0.69479	0.861;0.964	D	0.87064	0.2155	10	0.87932	D	0	.	10.5916	0.45312	0.0:0.9117:0.0:0.0883	.	259;259	Q9HAQ2-2;Q9HAQ2	.;KIF9_HUMAN	D	259;259;259;259;166	ENSP00000333942:G259D;ENSP00000265529:G259D;ENSP00000414987:G259D;ENSP00000391100:G259D;ENSP00000292334:G166D	ENSP00000265529:G259D	G	-	2	0	KIF9	47282364	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	4.380000	0.59581	2.615000	0.88500	0.650000	0.86243	GGC	.	.		0.502	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257475.2			T	47307360	C	T	47307360	3	4	38	1	0	0	0	0	1	0	0	0	8319	739	26	3	1652	3	KIF9	3	47307360	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	16479511	47307360	150715070	28	4475										
EPHA6	285220	hgsc.bcm.edu	37	chr3	96706423	96706423	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	atgagtcccacggaattaaaTtcaagccaaaccagtataca	6	10	1	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr3:96706423T>G	ENST00000389672.5	+	3	738	c.700T>G	c.(700-702)Ttc>Gtc	p.F234V	EPHA6_ENST00000542517.1_Missense_Mutation_p.F140V|EPHA6_ENST00000470610.2_Missense_Mutation_p.F234V	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	140						integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						CGGAATTAAATTCAAGCCAAA	0.408																																					p.F234V		Atlas-SNP	.											.	EPHA6	439	.	0			c.T700G						.						155	158	157					3																	96706423		1872	4125	5997	SO:0001583	missense	285220	exon3			ATTAAATTCAAGC	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.700T>G	chr3.hg19:g.96706423T>G	ENSP00000374323:p.Phe234Val	190.0	0.0		153.0	80.0	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	hg19	CCDS46876.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.06|16.06	3.016963|3.016963	0.54576|0.54576	.|.	.|.	ENSG00000080224|ENSG00000080224	ENST00000470610;ENST00000389672;ENST00000542517|ENST00000506569	T;T;T|.	0.03386|.	3.95;3.95;3.95|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.719649|.	0.12467|.	U|.	0.466381|.	T|T	0.75989|0.75989	0.3925|0.3925	M|M	0.77820|0.77820	2.39|2.39	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.999|.	T|T	0.76969|0.76969	-0.2762|-0.2762	10|5	0.40728|.	T|.	0.16|.	.|.	15.2298|15.2298	0.73378|0.73378	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	234;234|.	B3KS12;E7EU71|.	.;.|.	V|S	234;234;140|178	ENSP00000420598:F234V;ENSP00000374323:F234V;ENSP00000439758:F140V|.	ENSP00000374323:F234V|.	F|I	+|+	1|2	0|0	EPHA6|EPHA6	98189113|98189113	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	8.040000|8.040000	0.89188|0.89188	2.183000|2.183000	0.69458|0.69458	0.533000|0.533000	0.62120|0.62120	TTC|ATT	.	.		0.408	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		G	96706423	T	G	96706423	3	3	38	1	0	0	0	0	1	0	0	0	5173	1493	52	5	710	5	EPHA6	3	96706423	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	49399063	96706423	101316007	29	4476										
POLQ	10721	hgsc.bcm.edu	37	chr3	121251856	121251856	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccttcacttgtagcatgggcTcaaattccctcacaagtttc	6	13	3	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr3:121251856T>C	ENST00000264233.5	-	6	1069	c.941A>G	c.(940-942)gAg>gGg	p.E314G	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	314					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TAGCATGGGCTCAAATTCCCT	0.358								DNA polymerases (catalytic subunits)																													p.E314G	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A941G						.						70	74	72					3																	121251856		2203	4300	6503	SO:0001583	missense	10721	exon6			ATGGGCTCAAATT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.941A>G	chr3.hg19:g.121251856T>C	ENSP00000264233:p.Glu314Gly	523.0	0.0		495.0	229.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	T	10.29	1.309163	0.23821	.	.	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.71461	-0.57	5.29	5.29	0.74685	.	0.506627	0.21426	N	0.074729	T	0.65913	0.2737	L	0.46157	1.445	0.27916	N	0.938442	B	0.19200	0.034	B	0.22386	0.039	T	0.58532	-0.7620	10	0.35671	T	0.21	.	15.5172	0.75833	0.0:0.0:0.0:1.0	.	314	O75417	DPOLQ_HUMAN	G	314;449	ENSP00000264233:E314G	ENSP00000264233:E314G	E	-	2	0	POLQ	122734546	1.000000	0.71417	0.994000	0.49952	0.505000	0.33919	4.620000	0.61226	2.126000	0.65437	0.377000	0.23210	GAG	.	.		0.358	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		C	121251856	T	C	121251856	3	2	38	1	0	0	0	0	1	0	0	0	12217	1551	54	2	6931	2	POLQ	3	121251856	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	24545433	121251856	76770574	30	4477										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173993239	173993239	+	Frame_Shift_Del	DEL	G	G	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gaatcactgtttttggatctGgtgctgggggttcatgtgtc							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr3:173993239delG	ENST00000457714.1	+	5	1210	c.781delG	c.(781-783)ggtfs	p.G261fs	NLGN1_ENST00000361589.4_Frame_Shift_Del_p.G261fs|NLGN1_ENST00000401917.3_Frame_Shift_Del_p.G301fs|NLGN1_ENST00000545397.1_Frame_Shift_Del_p.G261fs|NLGN1_ENST00000466350.1_3'UTR	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	278					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TTTTGGATCTGGTGCTGGGGG	0.413																																					p.S260fs		Atlas-INDEL	.											.	NLGN1	209	.	0			c.780delT						.						95	92	93					3																	173993239		2203	4299	6502	SO:0001589	frameshift_variant	22871	exon5			.	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.781delG	chr3.hg19:g.173993239delG	ENSP00000392500:p.Gly261fs	264.0	0.0		316.0	96.0	NM_014932	Q9UPT2	Frame_Shift_Del	DEL	ENST00000457714.1	hg19	CCDS3222.1																																																																																			.	.		0.413	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		-	173993239	G	-	173993239	7	5	38	1	0	1	0	1	0	0	0	0	10470	1348	47	0	791	0	NLGN1	3	173993239	Frame_Shift_Del	DEL	G	TCGA-BC-A10Z-01A-11D-A12Z-10	52741383	173993239	24029191	31	4478										
PDS5A	23244	hgsc.bcm.edu	37	chr4	39928476	39928476	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgtctggtaataaacaaaaaTatgtcctgttaaaaaaaaaa	5	4	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr4:39928476T>C	ENST00000303538.8	-	4	887	c.348A>G	c.(346-348)atA>atG	p.I116M	PDS5A_ENST00000503396.1_Missense_Mutation_p.I116M	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						TAAACAAAAATATGTCCTGTT	0.239																																					p.I116M		Atlas-SNP	.											.	PDS5A	114	.	0			c.A348G						.						19	19	19					4																	39928476		1235	2808	4043	SO:0001583	missense	23244	exon4			CAAAAATATGTCC	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.348A>G	chr4.hg19:g.39928476T>C	ENSP00000303427:p.Ile116Met	278.0	0.0		180.0	79.0	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.221376	0.58560	.	.	ENSG00000121892	ENST00000303538;ENST00000503396	T;T	0.70399	-0.37;-0.48	5.73	4.48	0.54585	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80105	0.4562	M	0.69823	2.125	0.54753	D	0.999985	D;D	0.76494	0.997;0.999	D;D	0.91635	0.946;0.999	T	0.79841	-0.1633	9	.	.	.	-22.3401	7.9066	0.29765	0.1358:0.0:0.1418:0.7223	.	116;116	Q29RF7-3;Q29RF7	.;PDS5A_HUMAN	M	116	ENSP00000303427:I116M;ENSP00000426749:I116M	.	I	-	3	3	PDS5A	39604871	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.915000	0.28638	2.187000	0.69744	0.533000	0.62120	ATA	.	.		0.239	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		C	39928476	T	C	39928476	3	2	38	1	0	0	0	0	1	0	0	0	11700	1396	49	2	3818	2	PDS5A	4	39928476	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10		39928476	151225800	32	4479										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46060339	46060339	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggtctgaatagtgaaatatcCcattcttctgctcaggtcaa	8	9	5	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr4:46060339C>A	ENST00000295452.4	-	7	978	c.811G>T	c.(811-813)Gga>Tga	p.G271*		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	271					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GTGAAATATCCCATTCTTCTG	0.333																																					p.G271X		Atlas-SNP	.											.	GABRG1	172	.	0			c.G811T						.						107	109	108					4																	46060339		2203	4300	6503	SO:0001587	stop_gained	2565	exon7			AATATCCCATTCT	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.811G>T	chr4.hg19:g.46060339C>A	ENSP00000295452:p.Gly271*	645.0	1.0		445.0	192.0	NM_173536	Q5H9T8	Nonsense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	C	38	7.231907	0.98150	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.1446	0.93459	0.0:1.0:0.0:0.0	.	.	.	.	X	271	.	ENSP00000295452:G271X	G	-	1	0	GABRG1	45755096	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.705000	0.84606	2.771000	0.95319	0.644000	0.83932	GGA	.	.		0.333	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		A	46060339	C	A	46060339	4	1	38	1	0	0	0	0	0	1	0	0	6179	632	22	3	598	3	GABRG1	4	46060339	Nonsense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	6131863	46060339	145093937	33	4480										
CENPE	1062	hgsc.bcm.edu	37	chr4	104079539	104079539	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cttcctcagaaattttcgatTttagtgtattaattgtttct	5	6	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr4:104079539T>A	ENST00000265148.3	-	24	3040	c.2951A>T	c.(2950-2952)aAa>aTa	p.K984I	CENPE_ENST00000380026.3_Missense_Mutation_p.K959I	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	984					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		AATTTTCGATTTTAGTGTATT	0.294																																					p.K984I		Atlas-SNP	.											.	CENPE	253	.	0			c.A2951T						.						58	58	58					4																	104079539		2201	4291	6492	SO:0001583	missense	1062	exon24			TTCGATTTTAGTG	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.2951A>T	chr4.hg19:g.104079539T>A	ENSP00000265148:p.Lys984Ile	279.0	0.0		90.0	77.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	T	8.551	0.875574	0.17395	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	T;T;T	0.72167	-0.63;-0.61;-0.16	4.15	1.71	0.24356	.	.	.	.	.	T	0.72415	0.3457	M	0.61703	1.905	0.09310	N	1	D;P	0.55385	0.971;0.926	P;P	0.52481	0.7;0.459	T	0.61407	-0.7069	9	0.66056	D	0.02	.	6.5698	0.22533	0.0:0.2044:0.0:0.7956	.	959;984	Q02224-3;Q02224	.;CENPE_HUMAN	I	984;984;959;984	ENSP00000265148:K984I;ENSP00000369365:K959I;ENSP00000423981:K984I	ENSP00000265148:K984I	K	-	2	0	CENPE	104298988	0.140000	0.22579	0.012000	0.15200	0.014000	0.08584	1.350000	0.34010	0.247000	0.21414	0.528000	0.53228	AAA	.	.		0.294	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104079539	T	A	104079539	3	1	38	1	0	0	0	0	1	0	0	0	3232	1841	64	4	5258	4	CENPE	4	104079539	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	58019200	104079539	87074737	34	4481										
C4orf45	152940	hgsc.bcm.edu	37	chr4	159894436	159894437	+	Missense_Mutation	DNP	GG	GG	TT													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aggtgtgctgatgaattttgGgtaaataatcctttatgtag							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr4:159894436_159894437GG>TT	ENST00000434826.2	-	2	175_176	c.91_92CC>AA	c.(91-93)CCc>AAc	p.P31N	C4orf45_ENST00000508011.1_5'UTR	NM_152543.2	NP_689756.2	Q96LM5	CD045_HUMAN	chromosome 4 open reading frame 45	31										large_intestine(2)|lung(3)	5						ATGAATTTTGGGTAAATAATCC	0.356																																					p.P31H|p.P31T		Atlas-SNP	.											.	C4orf45	8	.	0			c.C92A|c.C91A						.																																			SO:0001583	missense	152940	exon2			ATTTTGGGTAAAT|TTTTGGGTAAATA		CCDS47156.1	4q32.1	2012-03-02			ENSG00000164123	ENSG00000164123			26342	protein-coding gene	gene with protein product							Standard	NM_152543		Approved	FLJ25371	uc003iqf.1	Q96LM5	OTTHUMG00000161988	ENST00000434826.2:c.91_92delinsTT	chr4.hg19:g.159894436_159894437delinsTT	ENSP00000412215:p.Pro31Asn	270.0|263.0	0.0		223.0|221.0	100.0|98.0	NM_152543	A8MPU3|C9J0T8	Missense_Mutation	SNP	ENST00000434826.2	hg19	CCDS47156.1																																																																																			.	.		0.356	C4orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366636.1	NM_152543		TT	159894437	GG	TT	159894436	3	4	38	1	0	0	0	0	1	0	0	0	2275	1232	43	3	484	3	C4orf45	4	159894436	Missense_Mutation	DNP	GG	TCGA-BC-A10Z-01A-11D-A12Z-10	55814897	159894436	31259840	35	4482										
ANKH	56172	hgsc.bcm.edu	37	chr5	14716830	14716832	+	In_Frame_Del	DEL	AGG	AGG	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tttacctggaactgggaagaAggagaagatccgcaaaggaa					rs121908406		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:14716830_14716832delAGG	ENST00000284268.6	-	9	1454_1456	c.1124_1126delCCT	c.(1123-1128)tccttc>ttc	p.S375del	ANKH_ENST00000535119.1_In_Frame_Del_p.S177del	NM_054027.4	NP_473368.1	Q9HCJ1	ANKH_HUMAN	ANKH inorganic pyrophosphate transport regulator	375			Missing (in CMDD). {ECO:0000269|PubMed:11326272, ECO:0000269|PubMed:11326338}.		locomotory behavior (GO:0007626)|regulation of bone mineralization (GO:0030500)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	inorganic diphosphate transmembrane transporter activity (GO:0030504)|inorganic phosphate transmembrane transporter activity (GO:0005315)|phosphate ion transmembrane transporter activity (GO:0015114)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						ACTGGGAAGAAGGAGAAGATCCG	0.399																																					p.375_376del		Atlas-Indel,Pindel	.											.	ANKH	64	.	0			c.1125_1127del	GRCh37	CD011582	ANKH	D		.																																			SO:0001651	inframe_deletion	56172	exon9			.	AF274753	CCDS3885.1	5p15.2	2013-06-19	2013-06-19		ENSG00000154122	ENSG00000154122			15492	protein-coding gene	gene with protein product		605145	"ankylosis, progressive (mouse) homolog", "craniometaphyseal dysplasia, Jackson type (dominant)", "ankylosis, progressive homolog (mouse)"	CCAL2, CMDJ		10894769, 12297989, 11326338	Standard	NM_054027		Approved	HANK, ANK, CPPDD	uc003jfm.4	Q9HCJ1	OTTHUMG00000090539	ENST00000284268.6:c.1124_1126delCCT	chr5.hg19:g.14716830_14716832delAGG	ENSP00000284268:p.Ser375del	137.0	0.0		149.0	41.0	NM_054027	B2RCA7|B3KMG4|D3DTD4|Q9NQW2	In_Frame_Del	DEL	ENST00000284268.6	hg19	CCDS3885.1																																																																																			.	.		0.399	ANKH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207063.1	NM_054027		-	14716832	AGG	-	14716830	7	5	38	1	0	1	0	1	0	0	0	0	627	72	3	0	368	0	ANKH	5	14716830	In_Frame_Del	DEL	AGG	TCGA-BC-A10Z-01A-11D-A12Z-10		14716830	166198430	36	4483										
WDR41	55255	hgsc.bcm.edu	37	chr5	76785371	76785371	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tagggattctgggtttgttcTtcacctattgtctgtaaagg	11	6	4	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:76785371T>A	ENST00000296679.4	-	2	453	c.78A>T	c.(76-78)gaA>gaT	p.E26D	WDR41_ENST00000414719.2_De_novo_Start_OutOfFrame|WDR41_ENST00000507029.1_Intron	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	26						lysosomal membrane (GO:0005765)				NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		GGGTTTGTTCTTCACCTATTG	0.323																																					p.E26D		Atlas-SNP	.											.	WDR41	29	.	0			c.A78T						.						209	199	202					5																	76785371		2203	4300	6503	SO:0001583	missense	55255	exon2			TTGTTCTTCACCT	AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"WD repeat domain containing"	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.78A>T	chr5.hg19:g.76785371T>A	ENSP00000296679:p.Glu26Asp	378.0	0.0		350.0	164.0	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Missense_Mutation	SNP	ENST00000296679.4	hg19	CCDS4038.1	.	.	.	.	.	.	.	.	.	.	T	18.49	3.636011	0.67130	.	.	ENSG00000164253	ENST00000296679;ENST00000515253;ENST00000514559;ENST00000511036;ENST00000504895;ENST00000509971	T;T;T;T;T;T	0.64085	0.63;0.66;0.4;0.4;-0.08;0.13	5.97	2.88	0.33553	.	0.044935	0.85682	D	0.000000	T	0.62853	0.2462	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.56092	-0.8036	10	0.13108	T	0.6	-27.1156	9.9787	0.41800	0.0:0.1955:0.0:0.8045	.	26	Q9HAD4	WDR41_HUMAN	D	26;19;26;21;18;23	ENSP00000296679:E26D;ENSP00000426499:E19D;ENSP00000426937:E26D;ENSP00000422510:E21D;ENSP00000426141:E18D;ENSP00000422922:E23D	ENSP00000296679:E26D	E	-	3	2	WDR41	76821127	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.825000	0.27393	0.878000	0.35920	0.523000	0.50628	GAA	.	.		0.323	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268		A	76785371	T	A	76785371	3	1	38	1	0	0	0	0	1	0	0	0	17309	1606	56	4	1349	4	WDR41	5	76785371	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	62068541	76785371	104129889	37	4484										
POU5F2	134187	hgsc.bcm.edu	37	chr5	93076516	93076516	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gaaccaaactcgaaccacatCcttctgcagctggaggcacc	8	15	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:93076516C>G	ENST00000510627.4	-	1	827	c.754G>C	c.(754-756)Gat>Cat	p.D252H	FAM172A_ENST00000395965.3_Intron|RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000505869.1_Intron|POU5F2_ENST00000606183.1_5'UTR	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	252					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		CGAACCACATCCTTCTGCAGC	0.572																																					p.D252H		Atlas-SNP	.											.	POU5F2	10	.	0			c.G754C						.						48	50	49					5																	93076516		2012	4178	6190	SO:0001583	missense	134187	exon1			CCACATCCTTCTG		CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.754G>C	chr5.hg19:g.93076516C>G	ENSP00000464890:p.Asp252His	257.0	0.0		251.0	117.0	NM_153216	Q15169|Q6MZL7|Q8N748	Missense_Mutation	SNP	ENST00000510627.4	hg19	CCDS59489.1																																																																																			.	.		0.572	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		G	93076516	C	G	93076516	3	3	38	1	0	0	0	0	1	0	0	0	12292	855	30	4	236	4	POU5F2	5	93076516	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	16291145	93076516	87838744	38	4485										
LNPEP	4012	hgsc.bcm.edu	37	chr5	96332096	96332096	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgttttctctccccccagtgGtttggcaatctggtaacaat	8	11	2	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:96332096G>T	ENST00000231368.5	+	7	2102	c.1410G>T	c.(1408-1410)tgG>tgT	p.W470C	LNPEP_ENST00000395770.3_Missense_Mutation_p.W456C	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	470					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		CCCCCCAGTGGTTTGGCAATC	0.358																																					p.W470C		Atlas-SNP	.											.	LNPEP	80	.	0			c.G1410T						.						106	104	105					5																	96332096		2203	4300	6503	SO:0001583	missense	4012	exon7			CCAGTGGTTTGGC	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"cystinyl aminopeptidase", "placental leucine aminopeptidase"	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.1410G>T	chr5.hg19:g.96332096G>T	ENSP00000231368:p.Trp470Cys	456.0	0.0		345.0	178.0	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	hg19	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.132835	0.77662	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.47528	0.84;0.84	5.24	5.24	0.73138	Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.82426	0.5034	H	0.99042	4.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89791	0.3968	10	0.87932	D	0	.	18.7851	0.91951	0.0:0.0:1.0:0.0	.	470	Q9UIQ6	LCAP_HUMAN	C	470;456	ENSP00000231368:W470C;ENSP00000379117:W456C	ENSP00000231368:W470C	W	+	3	0	LNPEP	96357852	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	9.729000	0.98795	2.598000	0.87819	0.563000	0.77884	TGG	.	.		0.358	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		T	96332096	G	T	96332096	3	4	38	1	0	0	0	0	1	0	0	0	8873	1270	44	3	1436	3	LNPEP	5	96332096	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	3255580	96332096	84583164	39	4486										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101816070	101816070	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cttttccaatgccaacttctCaatggttttcagttgatatt	5	9	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:101816070C>G	ENST00000506729.1	-	2	598	c.427G>C	c.(427-429)Gag>Cag	p.E143Q	SLCO6A1_ENST00000514551.1_5'UTR|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.E143Q|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.E143Q|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.E143Q|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.E143Q			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		GCCAACTTCTCAATGGTTTTC	0.348																																					p.E143Q		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.G427C						.						115	116	116					5																	101816070		2203	4300	6503	SO:0001583	missense	133482	exon2			ACTTCTCAATGGT	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.427G>C	chr5.hg19:g.101816070C>G	ENSP00000421339:p.Glu143Gln	486.0	0.0		368.0	169.0	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	hg19	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	C	11.47	1.648681	0.29336	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34;-1.34	4.56	-1.87	0.07737	Major facilitator superfamily domain, general substrate transporter (1);	1.362850	0.04600	N	0.398418	T	0.79257	0.4415	L	0.39566	1.225	0.09310	N	1	P;B;P	0.45569	0.859;0.011;0.861	P;B;P	0.60682	0.759;0.018;0.878	T	0.64635	-0.6361	10	0.16420	T	0.52	.	0.8792	0.01230	0.153:0.2692:0.2995:0.2782	.	143;143;143	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	Q	143	ENSP00000421339:E143Q;ENSP00000369135:E143Q;ENSP00000373671:E143Q;ENSP00000421990:E143Q;ENSP00000369138:E143Q	ENSP00000369135:E143Q	E	-	1	0	SLCO6A1	101843969	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.482000	0.06544	-0.257000	0.09459	-1.045000	0.02358	GAG	.	.		0.348	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		G	101816070	C	G	101816070	3	3	38	1	0	0	0	0	1	0	0	0	14747	835	29	4	1780	4	SLCO6A1	5	101816070	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	5483974	101816070	79099190	40	4487										
APC	324	hgsc.bcm.edu	37	chr5	112177044	112177044	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agctattgcaaagcagccaaTaaatcgaggtcagcctaaac	8	10	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:112177044T>C	ENST00000457016.1	+	16	6133	c.5753T>C	c.(5752-5754)aTa>aCa	p.I1918T	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.I1918T|APC_ENST00000257430.4_Missense_Mutation_p.I1918T			P25054	APC_HUMAN	adenomatous polyposis coli	1918	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAGCAGCCAATAAATCGAGGT	0.418		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.I1918T	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	1	Unknown(1)	skin(1)	c.T5753C						.						103	97	99					5																	112177044		2202	4300	6502	SO:0001583	missense	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AGCCAATAAATCG	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5753T>C	chr5.hg19:g.112177044T>C	ENSP00000413133:p.Ile1918Thr	254.0	0.0		267.0	134.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.530597	0.00951	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89485	-2.52;-2.52;-2.52	5.91	0.891	0.19224	.	1.124860	0.06222	N	0.686948	T	0.75309	0.3832	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.61272	-0.7096	9	.	.	.	-0.0728	5.6114	0.17408	0.1243:0.3416:0.0:0.5341	.	1920;1918	Q4LE70;P25054	.;APC_HUMAN	T	1918	ENSP00000413133:I1918T;ENSP00000257430:I1918T;ENSP00000427089:I1918T	.	I	+	2	0	APC	112204943	0.000000	0.05858	0.082000	0.20525	0.252000	0.25951	0.603000	0.24149	0.463000	0.27118	0.528000	0.53228	ATA	.	.		0.418	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112177044	T	C	112177044	3	2	38	1	0	0	0	0	1	0	0	0	763	1406	49	2	5811	2	APC	5	112177044	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	10360974	112177044	68738216	41	4488										
PRR16	51334	hgsc.bcm.edu	37	chr5	120022379	120022380	+	Missense_Mutation	DNP	GG	GG	TT													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	accacagaagacgatcttgaGgaagtcaaccactacaaccg							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:120022379_120022380GG>TT	ENST00000407149.2	+	2	1099_1100	c.890_891GG>TT	c.(889-891)aGG>aTT	p.R297I	PRR16_ENST00000505123.1_Missense_Mutation_p.R227I|PRR16_ENST00000446965.1_Missense_Mutation_p.R227I|PRR16_ENST00000379551.2_Missense_Mutation_p.R274I			Q569H4	LARGN_HUMAN	proline rich 16	297					positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		ACGATCTTGAGGAAGTCAACCA	0.396																																					p.R274M|p.R274S		Atlas-SNP	.											.|PRR16,NS,carcinoma,0,1	PRR16	71	.	0			c.G821T|c.G822T						.																																			SO:0001583	missense	51334	exon3			TCTTGAGGAAGTC|CTTGAGGAAGTCA	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	Exception_encountered	chr5.hg19:g.120022379_120022380delinsTT	ENSP00000385118:p.Arg297Ile	20.0	0.0		25.0	15.0	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Missense_Mutation	SNP	ENST00000407149.2	hg19																																																																																				.	.		0.396	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644		TT	120022380	GG	TT	120022379	3	4	38	1	0	0	0	0	1	0	0	0	12601	1000	35	3	827	3	PRR16	5	120022379	Missense_Mutation	DNP	GG	TCGA-BC-A10Z-01A-11D-A12Z-10	7845335	120022379	60892881	42	4489										
PSD2	84249	hgsc.bcm.edu	37	chr5	139189077	139189077	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctgaggaaggcgatgccaccCgtgaccccggtccagagcct	13	15	0	3	rs146689892		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:139189077C>T	ENST00000274710.3	+	2	257	c.52C>T	c.(52-54)Cgt>Tgt	p.R18C		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	18					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGATGCCACCCGTGACCCCGG	0.642																																					p.R18C		Atlas-SNP	.											.	PSD2	88	.	0			c.C52T						.	C	CYS/ARG	0,4406		0,0,2203	19	22	21		52	-5	0	5	dbSNP_134	21	2,8598		0,2,4298	no	missense	PSD2	NM_032289.2	180	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	18/772	139189077	2,13004	2203	4300	6503	SO:0001583	missense	84249	exon2			GCCACCCGTGACC	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.52C>T	chr5.hg19:g.139189077C>T	ENSP00000274710:p.Arg18Cys	122.0	0.0		139.0	63.0	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.709654	0.30322	0.0	2.33E-4	ENSG00000146005	ENST00000274710	T	0.12569	2.67	4.45	-5.02	0.02982	.	2.275110	0.01786	N	0.032041	T	0.08935	0.0221	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37865	-0.9687	10	0.52906	T	0.07	.	9.6634	0.39969	0.0:0.637:0.1532:0.2098	.	18	Q9BQI7	PSD2_HUMAN	C	18	ENSP00000274710:R18C	ENSP00000274710:R18C	R	+	1	0	PSD2	139169261	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.938000	0.03938	-0.907000	0.03862	-0.367000	0.07326	CGT	.	C|1.000;T|0.000		0.642	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139189077	C	T	139189077	3	4	38	1	0	0	0	0	1	0	0	0	12659	652	23	1	54	1	PSD2	5	139189077	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	19166698	139189077	41726183	43	4490										
SPINK5	11005	hgsc.bcm.edu	37	chr5	147503432	147503432	+	Frame_Shift_Del	DEL	G	G	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ttcgaagcatgcagagaaatGgaaagcttatctgcaccaga							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:147503432delG	ENST00000256084.7	+	27	2617	c.2575delG	c.(2575-2577)ggafs	p.G859fs	SPINK5_ENST00000359874.3_Frame_Shift_Del_p.G859fs|SPINK5_ENST00000398454.1_Frame_Shift_Del_p.G859fs	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	859	Kazal-like 13. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGAGAAATGGAAAGCTTAT	0.398																																					p.N858fs		Atlas-Indel,Pindel	.											.	SPINK5	245	.	0			c.2574delT						.						109	107	108					5																	147503432		1895	4126	6021	SO:0001589	frameshift_variant	11005	exon27			.	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.2575delG	chr5.hg19:g.147503432delG	ENSP00000256084:p.Gly859fs	189.0	0.0		170.0	93.0	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Frame_Shift_Del	DEL	ENST00000256084.7	hg19	CCDS43382.1																																																																																			.	.		0.398	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		-	147503432	G	-	147503432	7	5	38	1	0	1	0	1	0	0	0	0	15077	1349	47	0	2681	0	SPINK5	5	147503432	Frame_Shift_Del	DEL	G	TCGA-BC-A10Z-01A-11D-A12Z-10	8314355	147503432	33411828	44	4491										
RNF145	153830	hgsc.bcm.edu	37	chr5	158603765	158603766	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	attgatgataacaattgtctCcaaaggaacaaggcagagtc							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:158603765_158603766CC>AA	ENST00000424310.2	-	5	854_855	c.495_496GG>TT	c.(493-498)ttGGag>ttTTag	p.165_166LE>F*	RNF145_ENST00000521606.2_Nonsense_Mutation_p.182_183LE>F*|RNF145_ENST00000519865.1_Nonsense_Mutation_p.165_166LE>F*|RNF145_ENST00000274542.2_Nonsense_Mutation_p.193_194LE>F*|RNF145_ENST00000518802.1_Nonsense_Mutation_p.195_196LE>F*|RNF145_ENST00000520638.1_Nonsense_Mutation_p.179_180LE>F*	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	165						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACAATTGTCTCCAAAGGAACAA	0.381																																					p.E196X|p.L195F		Atlas-SNP	.											.	RNF145	110	.	0			c.G586T|c.G585T						.																																			SO:0001587	stop_gained	153830	exon5			TTGTCTCCAAAGG|TGTCTCCAAAGGA	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"RING-type (C3HC4) zinc fingers"	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.495_496delinsAA	chr5.hg19:g.158603765_158603766delinsAA	ENSP00000409064:p.L165_E166delinsF*	873.0|868.0	1.0|2.0		788.0|785.0	317.0	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000424310.2	hg19	CCDS56390.1																																																																																			.	.		0.381	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		AA	158603766	CC	AA	158603765	4	1	38	1	0	0	0	0	0	1	0	0	13462	864	30	3	1523	3	RNF145	5	158603765	Nonsense_Mutation	DNP	CC	TCGA-BC-A10Z-01A-11D-A12Z-10	11100333	158603765	22311495	45	4492										
GNB2L1	10399	hgsc.bcm.edu	37	chr5	180666567	180666567	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gcggacacaagacacccactCtgagtggctctcatcctaca	8	15	2	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr5:180666567C>G	ENST00000512805.1	-	4	853	c.445G>C	c.(445-447)Gag>Cag	p.E149Q	GNB2L1_ENST00000376817.4_Missense_Mutation_p.E105Q|GNB2L1_ENST00000505461.1_5'Flank|SNORD96A_ENST00000606577.1_RNA|GNB2L1_ENST00000511900.1_Missense_Mutation_p.E101Q|GNB2L1_ENST00000504726.1_Intron|GNB2L1_ENST00000511566.1_Missense_Mutation_p.E149Q|GNB2L1_ENST00000514455.1_5'Flank	NM_006098.4	NP_006089.1	P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1	149					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cell cycle (GO:0007049)|gastrulation (GO:0007369)|negative regulation of cell growth (GO:0030308)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron death (GO:1903208)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of translation (GO:0017148)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of cell migration (GO:0030335)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of gastrulation (GO:2000543)|positive regulation of GTPase activity (GO:0043547)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein phosphorylation (GO:0001934)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein localization (GO:0032880)|rhythmic process (GO:0048511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|small ribosomal subunit (GO:0015935)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|ion channel inhibitor activity (GO:0008200)|poly(A) RNA binding (GO:0044822)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase inhibitor activity (GO:0030292)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)			lung(3)|skin(2)	5	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)		GACACCCACTCTGAGTGGCTC	0.537																																					p.E149Q		Atlas-SNP	.											.	GNB2L1	22	.	0			c.G445C						.						104	103	103					5																	180666567		2203	4300	6503	SO:0001583	missense	10399	exon4			CCCACTCTGAGTG	M24194	CCDS34324.1	5q35.3	2013-01-10				ENSG00000204628		"WD repeat domain containing"	4399	protein-coding gene	gene with protein product	"Receptor for Activated C Kinase 1"	176981				8302854, 2499885	Standard	NM_006098		Approved	Gnb2-rs1, RACK1, H12.3	uc003mni.1	P63244		ENST00000512805.1:c.445G>C	chr5.hg19:g.180666567C>G	ENSP00000426909:p.Glu149Gln	106.0	0.0		94.0	43.0	NM_006098	B3KTJ0|D3DWS0|P25388|P99049|Q53HU2|Q5J8M6|Q5VLR4|Q6FH47	Missense_Mutation	SNP	ENST00000512805.1	hg19	CCDS34324.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	34|34|34	5.358137|5.358137|5.358137	0.95854|0.95854|0.95854	.|.|.	.|.|.	ENSG00000204628|ENSG00000204628|ENSG00000204628	ENST00000511566;ENST00000376817;ENST00000512805;ENST00000511900;ENST00000512968;ENST00000510199;ENST00000502844;ENST00000507000;ENST00000503081;ENST00000513027|ENST00000507756;ENST00000509535|ENST00000502905;ENST00000504128	T;T;T;T;T;T;T;T;T;T|.|.	0.81163|.|.	0.22;-1.46;0.22;-1.46;-1.46;0.22;0.22;0.22;0.22;-1.45|.|.	5.9|5.9|5.9	5.9|5.9|5.9	0.94986|0.94986|0.94986	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.54886|0.54886|0.54886	0.1886|0.1886|0.1886	N|N|N	0.21097|0.21097|0.21097	0.63|0.63|0.63	0.80722|0.80722|0.80722	D|D|D	1|1|1	D;B;P;P;P|.|.	0.53745|.|.	0.962;0.324;0.6;0.936;0.6|.|.	P;B;P;P;P|.|.	0.59643|.|.	0.861;0.421;0.647;0.799;0.647|.|.	T|T|T	0.47573|0.47573|0.47573	-0.9107|-0.9107|-0.9107	10|5|5	0.66056|.|.	D|.|.	0.02|.|.	-32.7101|-32.7101|-32.7101	17.7642|17.7642|17.7642	0.88473|0.88473|0.88473	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	120;197;149;101;149|.|.	B4DVD2;D6R9L0;E9KL35;D6RAC2;P63244|.|.	.;.;.;.;GBLP_HUMAN|.|.	Q|H|T	149;105;149;101;167;197;135;108;125;189|79;6|66;55	ENSP00000426101:E149Q;ENSP00000366013:E105Q;ENSP00000426909:E149Q;ENSP00000422768:E101Q;ENSP00000425008:E167Q;ENSP00000423569:E197Q;ENSP00000422029:E135Q;ENSP00000421416:E108Q;ENSP00000424237:E125Q;ENSP00000421356:E189Q|.|.	ENSP00000366013:E105Q|.|.	E|Q|R	-|-|-	1|3|2	0|2|0	GNB2L1|GNB2L1|GNB2L1	180599173|180599173|180599173	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.973000|0.973000|0.973000	0.42090|0.42090|0.42090	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	5.977000|5.977000|5.977000	0.70492|0.70492|0.70492	2.793000|2.793000|2.793000	0.96121|0.96121|0.96121	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GAG|CAG|AGA	.	.		0.537	GNB2L1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372943.2	NM_006098		G	180666567	C	G	180666567	3	3	38	1	0	0	0	0	1	0	0	0	6526	922	32	4	528	4	GNB2L1	5	180666567	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	22062802	180666567	248693	46	4493										
BAT5	7920	hgsc.bcm.edu	37	chr6	31657365	31657366	+	Frame_Shift_Ins	INS	-	-	C													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggaggctggtaccagtgaagINSccgccgatggaccaggcgta							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr6:31657365_31657366insC	ENST00000395952.3	-	12	1235_1236	c.1073_1074insG	c.(1072-1074)ggcfs	p.G358fs	ABHD16A_ENST00000375842.4_Frame_Shift_Ins_p.G139fs|ABHD16A_ENST00000471644.1_5'UTR|ABHD16A_ENST00000440843.2_Frame_Shift_Ins_p.G325fs|XXbac-BPG32J3.20_ENST00000461287.1_3'UTR	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	358						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						TACCAGTGAAGCCGCCGATGGA	0.609																																					p.G358fs		Atlas-INDEL	.											.	ABHD16A	34	.	0			c.1074_1075insG						.																																			SO:0001589	frameshift_variant	7920	exon12			.	AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"Abhydrolase domain containing"	13921	protein-coding gene	gene with protein product		142620	"HLA-B associated transcript 5"	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.1074dupG	chr6.hg19:g.31657367_31657367dupC	ENSP00000379282:p.Gly358fs	57.0	0.0		97.0	10.0	NM_021160	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Frame_Shift_Ins	INS	ENST00000395952.3	hg19	CCDS4713.1																																																																																			.	.		0.609	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4			C	31657366	-	C	31657365	7	5	38	1	0	1	1	0	0	0	0	0	1324	958	34	0	638	0	BAT5	6	31657365	Frame_Shift_Ins	INS	-	TCGA-BC-A10Z-01A-11D-A12Z-10		31657365	139457702	47	4494										
XPO5	57510	hgsc.bcm.edu	37	chr6	43517661	43517661	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	caacagtttcaaaagtgacaGatgaaaatagctaagggaga	10	5	1	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr6:43517661G>A	ENST00000265351.7	-	16	1949	c.1739C>T	c.(1738-1740)tCt>tTt	p.S580F	XPO5_ENST00000424378.2_5'Flank	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	580	Necessary for interaction with ILF3.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			AAAAGTGACAGATGAAAATAG	0.348																																					p.S580F		Atlas-SNP	.											.	XPO5	79	.	0			c.C1739T						.						126	119	121					6																	43517661		1854	4090	5944	SO:0001583	missense	57510	exon16			GTGACAGATGAAA	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.1739C>T	chr6.hg19:g.43517661G>A	ENSP00000265351:p.Ser580Phe	181.0	0.0		264.0	160.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Missense_Mutation	SNP	ENST00000265351.7	hg19	CCDS47430.1	.	.	.	.	.	.	.	.	.	.	G	16.07	3.019143	0.54576	.	.	ENSG00000124571	ENST00000265351;ENST00000436943;ENST00000372252;ENST00000372258;ENST00000439465	T	0.66815	-0.23	5.82	4.94	0.65067	Armadillo-like helical (1);Armadillo-type fold (1);	0.324438	0.33980	N	0.004372	T	0.34978	0.0916	L	0.39397	1.21	0.42107	D	0.991368	B	0.06786	0.001	B	0.04013	0.001	T	0.27606	-1.0069	10	0.09084	T	0.74	-6.9371	12.0098	0.53280	0.0818:0.0:0.9182:0.0	.	580	Q9HAV4	XPO5_HUMAN	F	580;285;120;120;208	ENSP00000265351:S580F	ENSP00000265351:S580F	S	-	2	0	XPO5	43625639	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.063000	0.71162	1.443000	0.47586	0.655000	0.94253	TCT	.	.		0.348	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		A	43517661	G	A	43517661	3	1	38	1	0	0	0	0	1	0	0	0	17462	942	33	3	1943	3	XPO5	6	43517661	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	11860296	43517661	127597406	48	4495										
RFX6	222546	hgsc.bcm.edu	37	chr6	117198538	117198538	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	actgctgtgtgcagctcctgGgcaagggcttgctagtctat	13	10	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr6:117198538G>A	ENST00000332958.2	+	1	116	c.100G>A	c.(100-102)Ggc>Agc	p.G34S		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	34					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						GCAGCTCCTGGGCAAGGGCTT	0.667																																					p.G34S		Atlas-SNP	.											.	RFX6	141	.	0			c.G100A						.						21	23	23					6																	117198538		2203	4299	6502	SO:0001583	missense	222546	exon1			CTCCTGGGCAAGG	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.100G>A	chr6.hg19:g.117198538G>A	ENSP00000332208:p.Gly34Ser	63.0	0.0		108.0	49.0	NM_173560	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	hg19	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.680894	0.47886	.	.	ENSG00000185002	ENST00000332958	T	0.57595	0.39	5.03	2.0	0.26442	.	1.875720	0.02080	N	0.052237	T	0.21022	0.0506	N	0.19112	0.55	0.32374	N	0.55548	B	0.06786	0.001	B	0.06405	0.002	T	0.01062	-1.1464	10	0.66056	D	0.02	-2.8757	8.4723	0.32993	0.265:0.0:0.735:0.0	.	34	Q8HWS3	RFX6_HUMAN	S	34	ENSP00000332208:G34S	ENSP00000332208:G34S	G	+	1	0	RFX6	117305231	1.000000	0.71417	0.997000	0.53966	0.873000	0.50193	0.765000	0.26546	0.214000	0.20742	0.591000	0.81541	GGC	.	.		0.667	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		A	117198538	G	A	117198538	3	1	38	1	0	0	0	0	1	0	0	0	13282	1232	43	3	102	3	RFX6	6	117198538	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	73680877	117198538	53916529	49	4496										
IYD	389434	hgsc.bcm.edu	37	chr6	150713484	150713493	+	Frame_Shift_Del	DEL	CAGCCCCGAG	CAGCCCCGAG	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aatggaatgggtgacaggaaCagccccgagtggggctcaca					rs151181823|rs372196319	byFrequency	TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	CAGCCCCGAG	CAGCCCCGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr6:150713484_150713493delCAGCCCCGAG	ENST00000344419.3	+	3	514_523	c.374_383delCAGCCCCGAG	c.(373-384)acagccccgagtfs	p.TAPS125fs	IYD_ENST00000229447.5_Frame_Shift_Del_p.TAPS125fs|IYD_ENST00000500320.3_Frame_Shift_Del_p.TAPS125fs|IYD_ENST00000425615.3_Frame_Shift_Del_p.TAPS70fs|IYD_ENST00000392256.2_Frame_Shift_Del_p.TAPS125fs|IYD_ENST00000392255.3_Frame_Shift_Del_p.TAPS125fs	NM_203395.2	NP_981932.1	Q6PHW0	IYD1_HUMAN	iodotyrosine deiodinase	125					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	iodide peroxidase activity (GO:0004447)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	15		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.215)	OV - Ovarian serous cystadenocarcinoma(155;4.16e-12)		GTGACAGGAACAGCCCCGAGTGGGGCTCAC	0.486																																					p.125_128del		Atlas-Indel,Pindel	.											.	IYD	106	.	0			c.373_382del						.																																			SO:0001589	frameshift_variant	389434	exon3			.	AK129950	CCDS5227.1, CCDS55066.1, CCDS55067.1	6q25.1	2006-08-24	2006-08-24	2006-08-24	ENSG00000009765	ENSG00000009765			21071	protein-coding gene	gene with protein product		612025	"chromosome 6 open reading frame 71"	C6orf71		16316988, 15289438	Standard	NM_001164694		Approved	dJ422F24.1, DEHAL1	uc003qnx.2	Q6PHW0	OTTHUMG00000016347	ENST00000344419.3:c.374_383delCAGCCCCGAG	chr6.hg19:g.150713484_150713493delCAGCCCCGAG	ENSP00000343763:p.Thr125fs	65.0	0.0		46.0	12.0	NM_203395	C9JFW2|Q2VPW0|Q2VPW1|Q5F1L5|Q5F1L6|Q5THM4|Q6ZP69|Q7Z7D7|Q7Z7D8	Frame_Shift_Del	DEL	ENST00000344419.3	hg19	CCDS5227.1																																																																																			.	.		0.486	IYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043754.3	NM_203395		-	150713493	CAGCCCCGAG	-	150713484	7	5	38	1	0	1	0	1	0	0	0	0	7941	478	17	0	384	0	IYD	6	150713484	Frame_Shift_Del	DEL	CAGCCCCGAG	TCGA-BC-A10Z-01A-11D-A12Z-10	33514946	150713484	20401583	50	4497										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152765606	152765606	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tcagtatccaagatcttctcAgcttgttcctggacttcttt	6	11	4	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr6:152765606A>T	ENST00000367255.5	-	30	4378	c.3777T>A	c.(3775-3777)gcT>gcA	p.A1259A	SYNE1_ENST00000367253.4_Silent_p.A1259A|SYNE1_ENST00000341594.5_Silent_p.A1325A|SYNE1_ENST00000265368.4_Silent_p.A1259A|SYNE1_ENST00000423061.1_Silent_p.A1266A|SYNE1_ENST00000448038.1_Silent_p.A1266A|SYNE1_ENST00000367248.3_Silent_p.A1249A|SYNE1_ENST00000413186.2_Silent_p.A1259A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1259					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGATCTTCTCAGCTTGTTCCT	0.368										HNSCC(10;0.0054)																											p.A1266A		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T3798A						.						126	124	124					6																	152765606		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon30			CTTCTCAGCTTGT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.3777T>A	chr6.hg19:g.152765606A>T		310.0	0.0		253.0	120.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.368	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152765606	A	T	152765606	2	4	38	1	0	0	0	0	0	0	0	1	15460	175	7	4		4	SYNE1	6	152765606	Silent	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	2052122	152765606	18349461	51	4498										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152765624	152765624	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tcagcttgttcctggacttcTttagagccagaaattaattc	7	9	2	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr6:152765624T>G	ENST00000367255.5	-	30	4360	c.3759A>C	c.(3757-3759)aaA>aaC	p.K1253N	SYNE1_ENST00000367253.4_Missense_Mutation_p.K1253N|SYNE1_ENST00000341594.5_Missense_Mutation_p.K1319N|SYNE1_ENST00000265368.4_Missense_Mutation_p.K1253N|SYNE1_ENST00000423061.1_Missense_Mutation_p.K1260N|SYNE1_ENST00000448038.1_Missense_Mutation_p.K1260N|SYNE1_ENST00000367248.3_Missense_Mutation_p.K1243N|SYNE1_ENST00000413186.2_Missense_Mutation_p.K1253N	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1253					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CCTGGACTTCTTTAGAGCCAG	0.368										HNSCC(10;0.0054)																											p.K1260N		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A3780C						.						107	106	106					6																	152765624		2203	4300	6503	SO:0001583	missense	23345	exon30			GACTTCTTTAGAG	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.3759A>C	chr6.hg19:g.152765624T>G	ENSP00000356224:p.Lys1253Asn	329.0	0.0		255.0	115.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	19.07	3.756884	0.69648	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186	T;T;T;T;T;D;D;D	0.89050	0.48;0.48;0.39;0.48;0.54;-2.35;-2.46;-2.46	5.96	-0.955	0.10356	.	0.371038	0.25663	N	0.029121	T	0.80644	0.4662	L	0.55481	1.735	0.80722	D	1	B;P;P;P;P;P	0.52463	0.418;0.756;0.817;0.953;0.756;0.842	B;B;P;P;B;P	0.49226	0.074;0.398;0.474;0.597;0.398;0.603	T	0.77115	-0.2707	10	0.20519	T	0.43	.	11.813	0.52194	0.0:0.4208:0.0:0.5791	.	1236;1253;1243;1253;1253;1260	B3W695;Q8NF91;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.	N	1253;1260;1253;1260;1319;1253;1243;1253	ENSP00000356224:K1253N;ENSP00000396024:K1260N;ENSP00000265368:K1253N;ENSP00000390975:K1260N;ENSP00000341887:K1319N;ENSP00000356222:K1253N;ENSP00000356217:K1243N;ENSP00000414510:K1253N	ENSP00000265368:K1253N	K	-	3	2	SYNE1	152807317	0.996000	0.38824	0.960000	0.40013	0.991000	0.79684	0.283000	0.18846	-0.377000	0.07930	0.533000	0.62120	AAA	.	.		0.368	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152765624	T	G	152765624	3	3	38	1	0	0	0	0	1	0	0	0	15460	1606	56	5	23175	5	SYNE1	6	152765624	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	18	152765624	18349443	52	4499										
CARD11	84433	hgsc.bcm.edu	37	chr7	2979547	2979547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctccatcttattcaaccggtGctttagctgatcgatctgaa	7	11	3	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr7:2979547G>A	ENST00000396946.4	-	6	1103	c.700C>T	c.(700-702)Cac>Tac	p.H234Y		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	234					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.K226_H227>N(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TTCAACCGGTGCTTTAGCTGA	0.498			Mis		DLBCL																																p.H234Y		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	1	Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(1)	c.C700T						.						130	119	123					7																	2979547		2203	4300	6503	SO:0001583	missense	84433	exon6			ACCGGTGCTTTAG	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.700C>T	chr7.hg19:g.2979547G>A	ENSP00000380150:p.His234Tyr	422.0	0.0		350.0	169.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	18.16	3.561707	0.65538	.	.	ENSG00000198286	ENST00000396946	T	0.34072	1.38	5.67	5.67	0.87782	.	0.098627	0.64402	D	0.000001	T	0.45034	0.1322	M	0.64404	1.975	0.58432	D	0.999999	D	0.57257	0.979	P	0.51079	0.658	T	0.38156	-0.9674	10	0.05436	T	0.98	-32.5575	19.836	0.96658	0.0:0.0:1.0:0.0	.	234	Q9BXL7	CAR11_HUMAN	Y	234	ENSP00000380150:H234Y	ENSP00000380150:H234Y	H	-	1	0	CARD11	2946073	1.000000	0.71417	0.990000	0.47175	0.981000	0.71138	9.146000	0.94640	2.690000	0.91761	0.579000	0.79373	CAC	.	.		0.498	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2979547	G	A	2979547	3	1	38	1	0	0	0	0	1	0	0	0	2647	1319	46	3	2844	3	CARD11	7	2979547	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10		2979547	156159116	53	4500										
WIPF3	644150	hgsc.bcm.edu	37	chr7	29923639	29923639	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	acgtgcctgccccgccccctCccaccccaccccctccgcct	5	28	0	0	rs555650905	byFrequency	TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr7:29923639C>G	ENST00000409290.1	+	4	529	c.529C>G	c.(529-531)Ccc>Gcc	p.P177A	WIPF3_ENST00000409123.1_Missense_Mutation_p.P177A|WIPF3_ENST00000242140.5_Missense_Mutation_p.P177A	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	177	Poly-Pro.				cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						cccgccccctcccaccccacc	0.701																																					p.P177A		Atlas-SNP	.											.	WIPF3	46	.	0			c.C529G						.						1	1	1					7																	29923639		395	1206	1601	SO:0001583	missense	644150	exon5			CCCCCTCCCACCC	AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.529C>G	chr7.hg19:g.29923639C>G	ENSP00000386878:p.Pro177Ala	13.0	0.0		31.0	14.0	NM_001080529	B8ZZV2	Missense_Mutation	SNP	ENST00000409290.1	hg19	CCDS56472.1	.	.	.	.	.	.	.	.	.	.	C	1.589	-0.529668	0.04112	.	.	ENSG00000122574	ENST00000409123;ENST00000409290;ENST00000242140	T;T;T	0.48522	0.81;0.81;0.81	3.58	2.67	0.31697	.	0.471112	0.19178	N	0.120779	T	0.31606	0.0802	L	0.47716	1.5	0.09310	N	1	P	0.40970	0.734	B	0.32090	0.14	T	0.11155	-1.0599	10	0.18710	T	0.47	.	8.4137	0.32659	0.2322:0.7678:0.0:0.0	.	177	A6NGB9	WIPF3_HUMAN	A	177	ENSP00000386790:P177A;ENSP00000386878:P177A;ENSP00000242140:P177A	ENSP00000242140:P177A	P	+	1	0	WIPF3	29890164	0.020000	0.18652	0.002000	0.10522	0.007000	0.05969	1.247000	0.32815	0.811000	0.34303	0.542000	0.68232	CCC	.	.		0.701	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1			G	29923639	C	G	29923639	3	3	38	1	0	0	0	0	1	0	0	0	17384	855	30	4	543	4	WIPF3	7	29923639	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	26944092	29923639	129215024	54	4501										
CCDC129	223075	hgsc.bcm.edu	37	chr7	31683115	31683115	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gctccaggtctgtaatgaccCagatgtcctccagcctggtg	11	13	1	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr7:31683115C>A	ENST00000407970.3	+	11	2169	c.2131C>A	c.(2131-2133)Cag>Aag	p.Q711K	CCDC129_ENST00000319386.3_Missense_Mutation_p.Q563K|CCDC129_ENST00000451887.2_Missense_Mutation_p.Q737K|CCDC129_ENST00000409210.1_Missense_Mutation_p.Q619K	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	711										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TGTAATGACCCAGATGTCCTC	0.522																																					p.Q737K		Atlas-SNP	.											.	CCDC129	127	.	0			c.C2209A						.						64	67	66					7																	31683115		2203	4300	6503	SO:0001583	missense	223075	exon11			ATGACCCAGATGT	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.2131C>A	chr7.hg19:g.31683115C>A	ENSP00000384416:p.Gln711Lys	190.0	0.0		189.0	93.0	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	hg19	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	C	19.80	3.895603	0.72639	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.32753	1.44;1.79;1.78;1.5	5.9	5.9	0.94986	.	0.611986	0.15036	N	0.284192	T	0.50565	0.1623	M	0.66939	2.045	0.32531	N	0.535011	D;P;P;D	0.63880	0.99;0.908;0.908;0.993	P;P;P;P	0.60789	0.864;0.492;0.492;0.879	T	0.52808	-0.8526	10	0.27082	T	0.32	0.7037	15.7701	0.78162	0.0:1.0:0.0:0.0	.	737;721;711;563	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	K	563;711;737;721;619	ENSP00000313062:Q563K;ENSP00000384416:Q711K;ENSP00000395835:Q737K;ENSP00000387214:Q619K	ENSP00000313062:Q563K	Q	+	1	0	CCDC129	31649640	0.995000	0.38212	0.953000	0.39169	0.528000	0.34623	3.798000	0.55522	2.804000	0.96469	0.655000	0.94253	CAG	.	.		0.522	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		A	31683115	C	A	31683115	3	1	38	1	0	0	0	0	1	0	0	0	2766	595	21	3	2169	3	CCDC129	7	31683115	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	1759476	31683115	127455548	55	4502										
GPR141	353345	hgsc.bcm.edu	37	chr7	37780403	37780403	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctgcatgctgtggctgccagTgctggcatgtggacgctggt	16	10	0	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr7:37780403T>C	ENST00000447769.1	+	4	697	c.408T>C	c.(406-408)agT>agC	p.S136S	GPR141_ENST00000461610.1_Intron|GPR141_ENST00000334425.1_Silent_p.S136S|EPDR1_ENST00000476620.1_Intron			Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(13)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGGCTGCCAGTGCTGGCATGT	0.463																																					p.S136S		Atlas-SNP	.											.	GPR141	79	.	0			c.T408C						.						151	147	149					7																	37780403		2203	4300	6503	SO:0001819	synonymous_variant	353345	exon1			TGCCAGTGCTGGC	AY288420	CCDS5451.1	7p14.1	2012-08-21			ENSG00000187037	ENSG00000187037		"GPCR / Class A : Orphans"	19997	protein-coding gene	gene with protein product		609045				12679517, 14623098	Standard	NM_181791		Approved	PGR13	uc003tfm.1	Q7Z602	OTTHUMG00000102105	ENST00000447769.1:c.408T>C	chr7.hg19:g.37780403T>C		314.0	1.0		258.0	108.0	NM_181791	A4D1X7|Q0VAR5|Q86SP3	Silent	SNP	ENST00000447769.1	hg19	CCDS5451.1																																																																																			.	.		0.463	GPR141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219943.2	NM_181791		C	37780403	T	C	37780403	2	2	38	1	0	0	0	0	0	0	0	1	6657	1693	59	2		2	GPR141	7	37780403	Silent	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	6097288	37780403	121358260	56	4503										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44579861	44579861	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agtgtcatgaggcttccagaCagctctgggttcttcccaca	10	12	3	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr7:44579861C>T	ENST00000289547.4	-	2	190	c.135G>A	c.(133-135)ctG>ctA	p.L45L	NPC1L1_ENST00000546276.1_Silent_p.L45L|NPC1L1_ENST00000381160.3_Silent_p.L45L|NPC1L1_ENST00000423141.1_Silent_p.L45L	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	45					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	GGCTTCCAGACAGCTCTGGGT	0.557																																					p.L45L		Atlas-SNP	.											.	NPC1L1	141	.	0			c.G135A						.						85	80	82					7																	44579861		2203	4300	6503	SO:0001819	synonymous_variant	29881	exon2			TCCAGACAGCTCT		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.135G>A	chr7.hg19:g.44579861C>T		115.0	0.0		122.0	49.0	NM_001101648	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	hg19	CCDS5491.1																																																																																			.	.		0.557	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		T	44579861	C	T	44579861	2	4	38	1	0	0	0	0	0	0	0	1	10580	465	17	3		3	NPC1L1	7	44579861	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	6799458	44579861	114558802	57	4504										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	71130478	71130478	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gaagaagaagccatataataGcaacattggcttctacacca	7	9	1	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr7:71130478G>T	ENST00000333538.5	+	7	1797	c.1163G>T	c.(1162-1164)aGc>aTc	p.S388I	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	388					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CCATATAATAGCAACATTGGC	0.517																																					p.S388I		Atlas-SNP	.											.	WBSCR17	208	.	0			c.G1163T						.						116	105	109					7																	71130478		2203	4300	6503	SO:0001583	missense	64409	exon7			ATAATAGCAACAT	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1163G>T	chr7.hg19:g.71130478G>T	ENSP00000329654:p.Ser388Ile	137.0	0.0		188.0	96.0	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	hg19	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.920181	0.33908	.	.	ENSG00000185274	ENST00000333538	T	0.57752	0.38	5.85	4.87	0.63330	.	0.088641	0.85682	D	0.000000	T	0.48132	0.1483	L	0.49455	1.56	0.44899	D	0.997917	P	0.35944	0.529	B	0.42771	0.397	T	0.33574	-0.9863	10	0.22706	T	0.39	.	7.9303	0.29899	0.1594:0.0:0.8406:0.0	.	388	Q6IS24	GLTL3_HUMAN	I	388	ENSP00000329654:S388I	ENSP00000329654:S388I	S	+	2	0	WBSCR17	70768414	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	2.966000	0.49208	2.770000	0.95276	0.563000	0.77884	AGC	.	.		0.517	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		T	71130478	G	T	71130478	3	4	38	1	0	0	0	0	1	0	0	0	17279	971	34	3	1189	3	WBSCR17	7	71130478	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	26550617	71130478	88008185	58	4505										
ZKSCAN1	7586	hgsc.bcm.edu	37	chr7	99621227	99621227	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gaaggtggaagaggaagatgAggaagaccacatgtgggggc	19	4	0	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr7:99621227A>T	ENST00000324306.6	+	2	332	c.98A>T	c.(97-99)gAg>gTg	p.E33V	ZKSCAN1_ENST00000426572.1_De_novo_Start_OutOfFrame|ZKSCAN1_ENST00000535170.1_Intron	NM_003439.1	NP_003430.1	P17029	ZKSC1_HUMAN	zinc finger with KRAB and SCAN domains 1	33					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			GAGGAAGATGAGGAAGACCAC	0.547																																					p.E33V		Atlas-SNP	.											.	ZKSCAN1	59	.	0			c.A98T						.						95	85	89					7																	99621227		2203	4300	6503	SO:0001583	missense	7586	exon2			AAGATGAGGAAGA	X52349	CCDS34698.1, CCDS69349.1, CCDS75640.1	7q22	2013-01-09	2004-11-16	2004-11-17	ENSG00000106261	ENSG00000106261		"Zinc fingers, C2H2-type", "-", "-", "-"	13101	protein-coding gene	gene with protein product		601260	"zinc finger protein 36 (KOX 18)"	ZNF139, ZNF36			Standard	NM_001287055		Approved	KOX18, PHZ-37, ZSCAN33	uc003usk.1	P17029	OTTHUMG00000156534	ENST00000324306.6:c.98A>T	chr7.hg19:g.99621227A>T	ENSP00000323148:p.Glu33Val	117.0	0.0		96.0	36.0	NM_003439	A4D294|P52745|Q2M1U1|Q8TBW5|Q8TEK7	Missense_Mutation	SNP	ENST00000324306.6	hg19	CCDS34698.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893772	0.72639	.	.	ENSG00000106261	ENST00000324306;ENST00000432317	T;T	0.07114	3.22;3.85	4.63	4.63	0.57726	.	0.000000	0.51477	D	0.000087	T	0.20495	0.0493	L	0.50333	1.59	0.80722	D	1	D	0.71674	0.998	D	0.73708	0.981	T	0.00792	-1.1564	10	0.34782	T	0.22	.	12.0381	0.53438	1.0:0.0:0.0:0.0	.	33	P17029	ZKSC1_HUMAN	V	33	ENSP00000323148:E33V;ENSP00000394445:E33V	ENSP00000323148:E33V	E	+	2	0	ZKSCAN1	99459163	0.900000	0.30661	0.999000	0.59377	0.843000	0.47879	1.287000	0.33284	1.942000	0.56320	0.397000	0.26171	GAG	.	.		0.547	ZKSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344550.2	NM_003439		T	99621227	A	T	99621227	3	4	38	1	0	0	0	0	1	0	0	0	17701	304	11	4	100	4	ZKSCAN1	7	99621227	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	28490749	99621227	59517436	59	4506										
DUS4L	11062	hgsc.bcm.edu	37	chr7	107216972	107216972	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aaatatgtctatacctgtaaTtgctaatggagacatcagaa	7	6	2	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr7:107216972T>C	ENST00000265720.3	+	7	1003	c.641T>C	c.(640-642)aTt>aCt	p.I214T	DUS4L_ENST00000402620.1_Missense_Mutation_p.I93T	NM_001270419.1|NM_181581.2	NP_001257348.1|NP_853559.1	O95620	DUS4L_HUMAN	dihydrouridine synthase 4-like (S. cerevisiae)	214							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	8						ATACCTGTAATTGCTAATGGA	0.378																																					p.I214T		Atlas-SNP	.											.	DUS4L	27	.	0			c.T641C						.						61	63	62					7																	107216972		2203	4300	6503	SO:0001583	missense	11062	exon7			CTGTAATTGCTAA	U62767	CCDS5745.1	7q22-q31	2007-12-04			ENSG00000105865	ENSG00000105865			21517	protein-coding gene	gene with protein product	"protein similar to E.coli yhdg and R. capsulatus nifR3"						Standard	NM_181581		Approved	PP35, DUS4	uc031syv.1	O95620	OTTHUMG00000154763	ENST00000265720.3:c.641T>C	chr7.hg19:g.107216972T>C	ENSP00000265720:p.Ile214Thr	246.0	0.0		179.0	81.0	NM_001270419	B4DLX0|Q2NKK1	Missense_Mutation	SNP	ENST00000265720.3	hg19	CCDS5745.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.496590	0.85069	.	.	ENSG00000105865	ENST00000265720;ENST00000402620	T;T	0.29917	1.55;1.55	6.01	6.01	0.97437	Aldolase-type TIM barrel (1);	0.291974	0.39759	N	0.001266	T	0.54532	0.1864	M	0.86268	2.805	0.53005	D	0.999962	P;P	0.36909	0.573;0.573	P;P	0.49012	0.598;0.598	T	0.59059	-0.7525	10	0.87932	D	0	.	16.5285	0.84344	0.0:0.0:0.0:1.0	.	214;214	A4D0R5;O95620	.;DUS4L_HUMAN	T	214;93	ENSP00000265720:I214T;ENSP00000385274:I93T	ENSP00000265720:I214T	I	+	2	0	DUS4L	107004208	1.000000	0.71417	0.986000	0.45419	0.992000	0.81027	7.606000	0.82863	2.307000	0.77673	0.528000	0.53228	ATT	.	.		0.378	DUS4L-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336967.2	NM_181581		C	107216972	T	C	107216972	3	2	38	1	0	0	0	0	1	0	0	0	4810	1493	52	2	659	2	DUS4L	7	107216972	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	7595745	107216972	51921691	60	4507										
CHRM2	1129	hgsc.bcm.edu	37	chr7	136699983	136699983	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cagctttgacaggtacttctGtgtcacaaaacctctgacct	7	12	3	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr7:136699983G>T	ENST00000445907.2	+	3	899	c.371G>T	c.(370-372)tGt>tTt	p.C124F	hsa-mir-490_ENST00000592183.1_RNA|hsa-mir-490_ENST00000439694.1_RNA|CHRM2_ENST00000453373.1_Missense_Mutation_p.C124F|hsa-mir-490_ENST00000597642.1_RNA|CHRM2_ENST00000401861.1_Missense_Mutation_p.C124F|CHRM2_ENST00000397608.3_Missense_Mutation_p.C124F|CHRM2_ENST00000402486.3_Missense_Mutation_p.C124F|CHRM2_ENST00000320658.5_Missense_Mutation_p.C124F|hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000586239.1_RNA|hsa-mir-490_ENST00000593789.1_RNA|hsa-mir-490_ENST00000598184.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	124					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	AGGTACTTCTGTGTCACAAAA	0.507																																					p.C124F		Atlas-SNP	.											.	CHRM2	167	.	0			c.G371T						.						116	110	112					7																	136699983		2203	4300	6503	SO:0001583	missense	1129	exon3			ACTTCTGTGTCAC		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.371G>T	chr7.hg19:g.136699983G>T	ENSP00000399745:p.Cys124Phe	389.0	1.0		315.0	160.0	NM_001006632	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	hg19	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559013	0.65538	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	T;T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23;1.23	5.61	5.61	0.85477	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.65709	0.2717	M	0.83118	2.625	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.69840	-0.5036	10	0.87932	D	0	-14.1208	19.7047	0.96068	0.0:0.0:1.0:0.0	.	124	P08172	ACM2_HUMAN	F	124	ENSP00000399745:C124F;ENSP00000415386:C124F;ENSP00000319984:C124F;ENSP00000380733:C124F;ENSP00000384937:C124F;ENSP00000384401:C124F	ENSP00000319984:C124F	C	+	2	0	CHRM2	136350523	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.817000	0.86213	2.655000	0.90218	0.650000	0.86243	TGT	.	.		0.507	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			T	136699983	G	T	136699983	3	4	38	1	0	0	0	0	1	0	0	0	3379	1377	48	3	373	3	CHRM2	7	136699983	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	29483011	136699983	22438680	61	4508										
MGAM	8972	hgsc.bcm.edu	37	chr7	141731507	141731507	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctggacaaactgtgtttcctGattataccaatcccaactgt	6	11	0	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr7:141731507G>T	ENST00000549489.2	+	13	1593	c.1498G>T	c.(1498-1500)Gat>Tat	p.D500Y	MGAM_ENST00000475668.2_Missense_Mutation_p.D500Y	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	500	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGTGTTTCCTGATTATACCAA	0.363																																					p.D500Y		Atlas-SNP	.											.	MGAM	767	.	0			c.G1498T						.						162	149	153					7																	141731507		1833	4092	5925	SO:0001583	missense	8972	exon13			TTTCCTGATTATA	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.1498G>T	chr7.hg19:g.141731507G>T	ENSP00000447378:p.Asp500Tyr	463.0	0.0		396.0	171.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.651125	0.88056	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.97850	-4.57	5.14	5.14	0.70334	Glycoside hydrolase, superfamily (1);	0.000000	0.64402	D	0.000011	D	0.99345	0.9770	H	0.98980	4.39	0.49915	D	0.999836	D	0.89917	1.0	D	0.97110	1.0	D	0.98376	1.0556	10	0.87932	D	0	.	17.8981	0.88895	0.0:0.0:1.0:0.0	.	500	O43451	MGA_HUMAN	Y	500;500;377	ENSP00000447378:D500Y	ENSP00000316431:D377Y	D	+	1	0	MGAM	141377976	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.748000	0.91615	2.837000	0.97791	0.655000	0.94253	GAT	.	.		0.363	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141731507	G	T	141731507	3	4	38	1	0	0	0	0	1	0	0	0	9550	1290	45	3	1544	3	MGAM	7	141731507	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	5031524	141731507	17407156	62	4509										
DEFA4	1669	hgsc.bcm.edu	37	chr8	6793612	6793612	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agttcccaacacgaagttctGttcgccggcagaatactaat	8	11	1	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:6793612G>C	ENST00000297435.2	-	3	348	c.224C>G	c.(223-225)aCa>aGa	p.T75R		NM_001925.1	NP_001916.1	P12838	DEF4_HUMAN	defensin, alpha 4, corticostatin	75					antibacterial humoral response (GO:0019731)|defense response to fungus (GO:0050832)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	10				COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		ACGAAGTTCTGTTCGCCGGCA	0.507																																					p.T75R		Atlas-SNP	.											.	DEFA4	19	.	0			c.C224G						.						120	103	109					8																	6793612		2203	4300	6503	SO:0001583	missense	1669	exon3			AGTTCTGTTCGCC	X65977	CCDS5961.1	8p23.1	2007-02-20			ENSG00000164821	ENSG00000164821		"Defensins, alpha"	2763	protein-coding gene	gene with protein product		601157		DEF4		8469233	Standard	NM_001925		Approved	HP-4	uc003wqu.1	P12838	OTTHUMG00000090382	ENST00000297435.2:c.224C>G	chr8.hg19:g.6793612G>C	ENSP00000297435:p.Thr75Arg	67.0	0.0		102.0	45.0	NM_001925	Q6EZF8	Missense_Mutation	SNP	ENST00000297435.2	hg19	CCDS5961.1	.	.	.	.	.	.	.	.	.	.	.	0.273	-0.991689	0.02162	.	.	ENSG00000164821	ENST00000297435	T	0.36699	1.24	1.54	-3.08	0.05347	Beta defensin/Neutrophil defensin (1);Mammalian defensins (2);	.	.	.	.	T	0.22975	0.0555	.	.	.	0.09310	N	1	P	0.48589	0.912	P	0.46850	0.529	T	0.07102	-1.0790	8	0.19590	T	0.45	.	0.5216	0.00613	0.1813:0.3034:0.202:0.3134	.	75	P12838	DEF4_HUMAN	R	75	ENSP00000297435:T75R	ENSP00000297435:T75R	T	-	2	0	DEFA4	6781022	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.742000	0.04850	-1.929000	0.01057	-0.502000	0.04539	ACA	.	.		0.507	DEFA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206754.1	NM_001925		C	6793612	G	C	6793612	3	2	38	1	0	0	0	0	1	0	0	0	4393	1377	48	4	73	4	DEFA4	8	6793612	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10		6793612	139570410	63	4510										
SGK223	157285	hgsc.bcm.edu	37	chr8	8185737	8185737	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gagattcgtcgtggacgttgGtttccgagtggcttaggttc	15	7	0	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:8185737G>T	ENST00000520004.1	-	5	2819	c.2555C>A	c.(2554-2556)aCc>aAc	p.T852N	SGK223_ENST00000330777.4_Missense_Mutation_p.T852N			Q86YV5	SG223_HUMAN		854							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GTGGACGTTGGTTTCCGAGTG	0.572																																					p.T852N	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C2555A						.						169	181	177					8																	8185737		2009	4157	6166	SO:0001583	missense	0	exon4			ACGTTGGTTTCCG																												ENST00000520004.1:c.2555C>A	chr8.hg19:g.8185737G>T	ENSP00000428054:p.Thr852Asn	72.0	0.0		88.0	43.0	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	hg19	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.635444	0.29068	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.57107	0.42;0.42	4.97	3.16	0.36331	.	0.470089	0.20037	N	0.100589	T	0.33265	0.0857	L	0.38531	1.155	0.34078	D	0.659273	B	0.23316	0.083	B	0.16289	0.015	T	0.26916	-1.0089	10	0.10902	T	0.67	.	4.4414	0.11575	0.0822:0.3041:0.4735:0.1402	.	852	Q86YV5	SG223_HUMAN	N	852	ENSP00000330930:T852N;ENSP00000428054:T852N	ENSP00000330930:T852N	T	-	2	0	AC068353.1	8223147	1.000000	0.71417	0.998000	0.56505	0.943000	0.58893	2.129000	0.42055	0.793000	0.33875	0.563000	0.77884	ACC	.	.		0.572	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			T	8185737	G	T	8185737	3	4	38	1	0	0	0	0	1	0	0	0	14225	1261	44	3	1661	3	SGK223	8	8185737	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	1392125	8185737	138178285	64	4511										
PCM1	5108	hgsc.bcm.edu	37	chr8	17794745	17794745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	taaccaatgatatttctccgGagtcgtcaccaggagttgga	10	9	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:17794745G>A	ENST00000519253.1	+	4	450	c.199G>A	c.(199-201)Gag>Aag	p.E67K	PCM1_ENST00000518537.1_Missense_Mutation_p.E67K|PCM1_ENST00000518936.1_3'UTR|PCM1_ENST00000524226.1_Missense_Mutation_p.E67K|PCM1_ENST00000325083.8_Missense_Mutation_p.E67K			Q15154	PCM1_HUMAN	pericentriolar material 1	67					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TATTTCTCCGGAGTCGTCACC	0.423			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.E67K		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.G199A						.						55	56	55					8																	17794745		2048	4175	6223	SO:0001583	missense	5108	exon4			TCTCCGGAGTCGT		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.199G>A	chr8.hg19:g.17794745G>A	ENSP00000431099:p.Glu67Lys	345.0	0.0		281.0	130.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.862437	0.97036	.	.	ENSG00000078674	ENST00000325083;ENST00000325126;ENST00000517730;ENST00000518537;ENST00000523055;ENST00000519253;ENST00000524226	T;T;T;T;T;T	0.28454	3.29;2.44;1.62;1.61;3.29;3.05	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.46964	0.1420	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.76494	0.999;0.992;0.999;0.999	D;D;D;D	0.74674	0.973;0.984;0.973;0.973	T	0.43702	-0.9375	10	0.87932	D	0	-17.6915	20.0691	0.97712	0.0:0.0:1.0:0.0	.	67;67;67;67	E7ETA6;E7EV93;E7EV56;Q15154	.;.;.;PCM1_HUMAN	K	67	ENSP00000327077:E67K;ENSP00000428131:E67K;ENSP00000428123:E67K;ENSP00000429941:E67K;ENSP00000431099:E67K;ENSP00000430521:E67K	ENSP00000327077:E67K	E	+	1	0	PCM1	17839025	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.847000	0.99503	2.819000	0.97034	0.585000	0.79938	GAG	.	.		0.423	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		A	17794745	G	A	17794745	3	1	38	1	0	0	0	0	1	0	0	0	11593	1175	41	3	205	3	PCM1	8	17794745	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	9609008	17794745	128569277	65	4512										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36691164	36691173	+	Frame_Shift_Del	DEL	TGAGGCGAGT	TGAGGCGAGT	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgcaatgaagtgggaggatcTgaggcgagttgcggtaagat					rs369258362		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	TGAGGCGAGT	TGAGGCGAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:36691164_36691173delTGAGGCGAGT	ENST00000399881.3	+	11	1236_1245	c.1199_1208delTGAGGCGAGT	c.(1198-1209)ctgaggcgagttfs	p.LRRV400fs		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	400	RCK N-terminal.				multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TGGGAGGATCTGAGGCGAGTTGCGGTAAGA	0.371																																					p.400_403del		Atlas-Indel,Pindel	.											.	KCNU1	359	.	0			c.1198_1207del						.																																			SO:0001589	frameshift_variant	157855	exon11			.	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1199_1208delTGAGGCGAGT	chr8.hg19:g.36691164_36691173delTGAGGCGAGT	ENSP00000382770:p.Leu400fs	688.0	0.0		391.0	116.0	NM_001031836		Frame_Shift_Del	DEL	ENST00000399881.3	hg19	CCDS55220.1																																																																																			.	.		0.371	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		-	36691173	TGAGGCGAGT	-	36691164	7	5	38	1	0	1	0	1	0	0	0	0	8102	1580	55	0	1241	0	KCNU1	8	36691164	Frame_Shift_Del	DEL	TGAGGCGAGT	TCGA-BC-A10Z-01A-11D-A12Z-10	18896419	36691164	109672858	66	4513										
BAG4	9530	hgsc.bcm.edu	37	chr8	38067967	38067967	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccagaaaagaggctgtttgtAagattcaggccatactggaa	11	7	1	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:38067967A>C	ENST00000287322.4	+	5	1601	c.1330A>C	c.(1330-1332)Aag>Cag	p.K444Q	BAG4_ENST00000432471.2_Missense_Mutation_p.K408Q	NM_004874.3	NP_004865.1	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	444	BAG. {ECO:0000255|PROSITE- ProRule:PRU00369}.				cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to tumor necrosis factor (GO:0071356)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA modification (GO:0090367)|negative regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:2001145)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein localization to plasma membrane (GO:0072659)|ruffle assembly (GO:0097178)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	11	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				GGCTGTTTGTAAGATTCAGGC	0.408																																					p.K444Q		Atlas-SNP	.											.	BAG4	32	.	0			c.A1330C						.						31	34	33					8																	38067967		2201	4295	6496	SO:0001583	missense	9530	exon5			GTTTGTAAGATTC	AF095194	CCDS6104.1, CCDS56533.1	8p11.23	2008-08-07			ENSG00000156735	ENSG00000156735			940	protein-coding gene	gene with protein product	"silencer of death domains"	603884				9873016, 9915703	Standard	NM_004874		Approved	SODD	uc003xky.2	O95429	OTTHUMG00000164064	ENST00000287322.4:c.1330A>C	chr8.hg19:g.38067967A>C	ENSP00000287322:p.Lys444Gln	168.0	0.0		135.0	54.0	NM_004874	B4E217|O95818	Missense_Mutation	SNP	ENST00000287322.4	hg19	CCDS6104.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.877832	0.33162	.	.	ENSG00000156735	ENST00000432471;ENST00000287322	D;D	0.89123	-2.47;-2.47	5.27	4.12	0.48240	BAG domain (3);	0.055372	0.64402	D	0.000002	D	0.90160	0.6925	L	0.47716	1.5	0.40867	D	0.983889	D;D	0.64830	0.989;0.994	P;P	0.59643	0.701;0.861	D	0.90105	0.4187	10	0.66056	D	0.02	-15.6272	10.5295	0.44969	0.9239:0.0:0.0761:0.0	.	408;444	B4E217;O95429	.;BAG4_HUMAN	Q	408;444	ENSP00000393298:K408Q;ENSP00000287322:K444Q	ENSP00000287322:K444Q	K	+	1	0	BAG4	38187124	1.000000	0.71417	1.000000	0.80357	0.001000	0.01503	5.619000	0.67729	0.966000	0.38159	-0.394000	0.06481	AAG	.	.		0.408	BAG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377038.2	NM_004874		C	38067967	A	C	38067967	3	2	38	1	0	0	0	0	1	0	0	0	1289	363	13	5	1348	5	BAG4	8	38067967	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	1376803	38067967	108296055	67	4514										
AP3M2	10947	hgsc.bcm.edu	37	chr8	42022613	42022614	+	Frame_Shift_Ins	INS	-	-	G													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	acaattactgctgagatccaINSgggggtgattgatgcctgtg							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:42022613_42022614insG	ENST00000518421.1	+	6	899_900	c.608_609insG	c.(607-612)caggggfs	p.QG203fs	AP3M2_ENST00000396926.3_Frame_Shift_Ins_p.QG203fs|AP3M2_ENST00000174653.3_Frame_Shift_Ins_p.QG203fs|AP3M2_ENST00000517922.1_Frame_Shift_Ins_p.QG203fs|AP3M2_ENST00000520685.1_Intron	NM_001134296.1	NP_001127768.1	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	203	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|stomach(1)	17	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)			GCTGAGATCCAGGGGGTGATTG	0.446																																					p.Q203fs		Atlas-Indel,Pindel	.											.	AP3M2	41	.	0			c.608_609insG						.																																			SO:0001589	frameshift_variant	10947	exon6			.	D38293	CCDS6125.1	8p11.2	2008-07-07			ENSG00000070718	ENSG00000070718			570	protein-coding gene	gene with protein product		610469				7601449	Standard	NM_006803		Approved	CLA20, AP47B	uc003xoo.3	P53677	OTTHUMG00000164060	ENST00000518421.1:c.613dupG	chr8.hg19:g.42022618_42022618dupG	ENSP00000428787:p.Gln203fs	299.0	0.0		310.0	140.0	NM_001134296	B2RCR0|D3DSY2|Q7Z472	Frame_Shift_Ins	INS	ENST00000518421.1	hg19	CCDS6125.1																																																																																			.	.		0.446	AP3M2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376996.1			G	42022614	-	G	42022613	7	5	38	1	0	1	1	0	0	0	0	0	748	188	7	0	622	0	AP3M2	8	42022613	Frame_Shift_Ins	INS	-	TCGA-BC-A10Z-01A-11D-A12Z-10	3954646	42022613	104341409	68	4515										
CSPP1	79848	hgsc.bcm.edu	37	chr8	68105731	68105731	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cctaatgtagcaccagatggTctctctctaaaatctatatc	5	11	3	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:68105731T>G	ENST00000262210.5	+	28	3379	c.3348T>G	c.(3346-3348)ggT>ggG	p.G1116G	CSPP1_ENST00000412460.1_Silent_p.G771G|CSPP1_ENST00000521168.1_Intron|ARFGEF1_ENST00000520381.1_Intron	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	1151					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			CACCAGATGGTCTCTCTCTAA	0.358																																					p.G1116G		Atlas-SNP	.											.	CSPP1	129	.	0			c.T3348G						.						141	135	137					8																	68105731		1877	4102	5979	SO:0001819	synonymous_variant	79848	exon28			AGATGGTCTCTCT	AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.3348T>G	chr8.hg19:g.68105731T>G		221.0	0.0		213.0	98.0	NM_024790	A6ND63|Q70F00|Q8TBC1	Silent	SNP	ENST00000262210.5	hg19	CCDS43744.1																																																																																			.	.		0.358	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		G	68105731	T	G	68105731	2	3	38	1	0	0	0	0	0	0	0	1	3964	1654	58	5		5	CSPP1	8	68105731	Silent	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	26083118	68105731	78258291	69	4516										
NECAB1	64168	hgsc.bcm.edu	37	chr8	91946573	91946573	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gaagaagaaattattgaaggGaatactaaatctgtaagtat	9	2	1	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:91946573G>C	ENST00000417640.2	+	9	1072	c.735G>C	c.(733-735)ggG>ggC	p.G245G		NM_022351.4	NP_071746.1	Q8N987	NECA1_HUMAN	N-terminal EF-hand calcium binding protein 1	245						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)	12			BRCA - Breast invasive adenocarcinoma(11;0.0499)			TTATTGAAGGGAATACTAAAT	0.244																																					p.G245G		Atlas-SNP	.											.	NECAB1	31	.	0			c.G735C						.						17	16	16					8																	91946573		1479	3337	4816	SO:0001819	synonymous_variant	64168	exon9			TGAAGGGAATACT	AF414126	CCDS47889.1	8q21.3	2013-01-10	2007-12-06	2007-12-06	ENSG00000123119	ENSG00000123119		"N-terminal EF-hand calcium binding proteins", "EF-hand domain containing"	20983	protein-coding gene	gene with protein product			"EF-hand calcium binding protein 1"	EFCBP1			Standard	NM_022351		Approved		uc011lgg.2	Q8N987	OTTHUMG00000164009	ENST00000417640.2:c.735G>C	chr8.hg19:g.91946573G>C		581.0	0.0		341.0	126.0	NM_022351	Q6NUS7|Q96AZ7|Q9HBW8	Silent	SNP	ENST00000417640.2	hg19	CCDS47889.1																																																																																			.	.		0.244	NECAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376728.1	NM_022351		C	91946573	G	C	91946573	2	2	38	1	0	0	0	0	0	0	0	1	10313	1161	41	4		4	NECAB1	8	91946573	Silent	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	23840842	91946573	54417449	70	4517										
ANKRD46	157567	hgsc.bcm.edu	37	chr8	101540171	101540171	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aaagattccagcaatcggatGacatctttatttactcctct	5	10	2	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:101540171G>A	ENST00000520552.1	-	4	533	c.372C>T	c.(370-372)gtC>gtT	p.V124V	ANKRD46_ENST00000335659.3_Silent_p.V124V|ANKRD46_ENST00000519316.1_Intron|ANKRD46_ENST00000520311.1_Silent_p.V124V|ANKRD46_ENST00000519597.1_Silent_p.V124V	NM_001270379.1	NP_001257308.1	Q86W74	ANR46_HUMAN	ankyrin repeat domain 46	124						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(4)	7	all_cancers(14;5.07e-05)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000353)|all_lung(17;0.000998)		Epithelial(11;2.61e-11)|all cancers(13;5.03e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.49e-06)|STAD - Stomach adenocarcinoma(118;0.0957)			GCAATCGGATGACATCTTTAT	0.378																																					p.V124V		Atlas-SNP	.											.	ANKRD46	13	.	0			c.C372T						.						133	131	132					8																	101540171		2203	4300	6503	SO:0001819	synonymous_variant	157567	exon4			TCGGATGACATCT	AB077205	CCDS6287.1, CCDS59109.1	8q22.3	2013-01-10						"Ankyrin repeat domain containing"	27229	protein-coding gene	gene with protein product							Standard	NM_001270377		Approved		uc003yjm.4	Q86W74		ENST00000520552.1:c.372C>T	chr8.hg19:g.101540171G>A		374.0	1.0		270.0	112.0	NM_001270378	Q6P9B7	Silent	SNP	ENST00000520552.1	hg19	CCDS59109.1																																																																																			.	.		0.378	ANKRD46-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379899.1	NM_198401		A	101540171	G	A	101540171	2	1	38	1	0	0	0	0	0	0	0	1	674	1277	45	3		3	ANKRD46	8	101540171	Silent	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	9593598	101540171	44823851	71	4518										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113519006	113519006	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgcggatatggatgagggaaGtttggtgaaagaataaagcc	15	3	0	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:113519006G>T	ENST00000297405.5	-	29	5053	c.4809C>A	c.(4807-4809)aaC>aaA	p.N1603K	CSMD3_ENST00000343508.3_Missense_Mutation_p.N1563K|CSMD3_ENST00000352409.3_Missense_Mutation_p.N1603K|CSMD3_ENST00000455883.2_Missense_Mutation_p.N1499K	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1603	CUB 9. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GATGAGGGAAGTTTGGTGAAA	0.373										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.N1603K		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C4809A						.						121	114	116					8																	113519006		2203	4300	6503	SO:0001583	missense	114788	exon29			AGGGAAGTTTGGT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4809C>A	chr8.hg19:g.113519006G>T	ENSP00000297405:p.Asn1603Lys	290.0	0.0		280.0	112.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.416390	0.62511	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.25085	1.82;1.82;1.82;1.82;1.82	4.99	1.17	0.20885	CUB (5);	0.000000	0.85682	D	0.000000	T	0.51415	0.1673	M	0.90309	3.105	0.29106	N	0.881177	D;D;P	0.67145	0.995;0.996;0.938	D;D;P	0.69307	0.938;0.963;0.794	T	0.51888	-0.8648	10	0.44086	T	0.13	.	10.2855	0.43564	0.2528:0.0:0.7472:0.0	.	1499;1603;1563	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	K	1563;1603;943;1499;1603	ENSP00000345799:N1563K;ENSP00000297405:N1603K;ENSP00000341558:N943K;ENSP00000412263:N1499K;ENSP00000343124:N1603K	ENSP00000297405:N1603K	N	-	3	2	CSMD3	113588182	1.000000	0.71417	0.998000	0.56505	0.925000	0.55904	2.365000	0.44196	0.031000	0.15407	0.557000	0.71058	AAC	.	.		0.373	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113519006	G	T	113519006	3	4	38	1	0	0	0	0	1	0	0	0	3948	1020	36	3	6486	3	CSMD3	8	113519006	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	11978835	113519006	32845016	72	4519										
MYC	4609	hgsc.bcm.edu	37	chr8	128751001	128751001	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	acagcggcagcccgaaccccGcccgcggccacagcgtctgc	12	20	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:128751001G>A	ENST00000259523.6	+	2	1698	c.493G>A	c.(493-495)Gcc>Acc	p.A165T	MYC_ENST00000377970.2_Missense_Mutation_p.A180T|MYC_ENST00000524013.1_Missense_Mutation_p.A179T			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	165					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular iron ion homeostasis (GO:0006879)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|chromosome organization (GO:0051276)|energy reserve metabolic process (GO:0006112)|fibroblast apoptotic process (GO:0044346)|gene expression (GO:0010467)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell division (GO:0051782)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|oxygen transport (GO:0015671)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric cap mesenchymal cell proliferation (GO:0090096)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of telomere maintenance (GO:0032204)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to growth factor (GO:0070848)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein complex binding (GO:0032403)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	all_cancers(1;6.19e-134)|all_epithelial(1;1.75e-119)|all_lung(1;5.66e-51)|Breast(1;1.08e-22)|all_neural(1;4.45e-21)|Medulloblastoma(1;1.88e-20)|Colorectal(1;1.92e-09)|Lung SC(1;4.52e-07)|Ovarian(5;0.000122)|Esophageal squamous(12;0.000995)|Renal(1;0.0921)|Hepatocellular(40;0.108)|Myeloproliferative disorder(2;0.135)|Melanoma(291;0.185)	Myeloproliferative disorder(644;0.0255)|Ovarian(118;0.0654)|Breast(495;0.212)|Acute lymphoblastic leukemia(644;0.22)	Epithelial(1;1.63e-94)|all cancers(1;5.82e-87)|OV - Ovarian serous cystadenocarcinoma(1;2.12e-71)|BRCA - Breast invasive adenocarcinoma(1;4.3e-14)|Lung(2;0.000381)|Colorectal(2;0.0102)|LUAD - Lung adenocarcinoma(14;0.0172)|READ - Rectum adenocarcinoma(2;0.0723)|LUSC - Lung squamous cell carcinoma(258;0.151)	KIRC - Kidney renal clear cell carcinoma(542;0.248)	Nadroparin(DB08813)	CCCGAACCCCGCCCGCGGCCA	0.677		3	"A, T"	"IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@"	"Burkitt lymphoma,  amplified in other cancers, B-CLL"						OREG0018982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A180T		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	.	MYC	168	.	0			c.G538A						.						19	22	21					8																	128751001		2202	4297	6499	SO:0001583	missense	4609	exon2			AACCCCGCCCGCG		CCDS6359.2	8q24	2013-07-09	2013-07-09		ENSG00000136997	ENSG00000136997		"Basic helix-loop-helix proteins"	7553	protein-coding gene	gene with protein product		190080					Standard	NM_002467		Approved	c-Myc, bHLHe39, MYCC	uc003ysi.3	P01106	OTTHUMG00000128475	ENST00000259523.6:c.493G>A	chr8.hg19:g.128751001G>A	ENSP00000259523:p.Ala165Thr	29.0	0.0	1567	44.0	27.0	NM_002467	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	ENST00000259523.6	hg19		.	.	.	.	.	.	.	.	.	.	G	15.88	2.963005	0.53507	.	.	ENSG00000136997	ENST00000259523;ENST00000517291;ENST00000377970;ENST00000524013;ENST00000454617	T;T;T;T	0.18657	2.2;2.23;2.2;2.2	4.78	3.9	0.45041	Transcription regulator Myc, N-terminal (1);	0.382752	0.26321	N	0.025050	T	0.37489	0.1005	L	0.49640	1.575	0.26174	N	0.97982	D	0.89917	1.0	D	0.79108	0.992	T	0.10314	-1.0635	10	0.40728	T	0.16	-26.6013	11.9855	0.53145	0.0861:0.0:0.9138:0.0	.	165	P01106	MYC_HUMAN	T	165;179;180;179;146	ENSP00000259523:A165T;ENSP00000429441:A179T;ENSP00000367207:A180T;ENSP00000430235:A179T	ENSP00000259523:A165T	A	+	1	0	MYC	128820183	0.000000	0.05858	1.000000	0.80357	0.840000	0.47671	0.291000	0.18994	1.127000	0.42034	0.561000	0.74099	GCC	.	.		0.677	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			A	128751001	G	A	128751001	3	1	38	1	0	0	0	0	1	0	0	0	10025	1087	38	1	544	1	MYC	8	128751001	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	15231995	128751001	17613021	73	4520										
C8orf31	286122	hgsc.bcm.edu	37	chr8	144124680	144124680	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gggagtccacaacggcacttGtaagtttcagcagggggaat	14	8	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:144124680G>A	ENST00000395172.1	+	3	538		c.e3+1		C8orf31_ENST00000517653.1_Splice_Site	NM_173687.2	NP_775958.1	Q8N9H6	CH031_HUMAN	chromosome 8 open reading frame 31											breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10	all_cancers(97;1.89e-10)|all_epithelial(106;8.73e-09)|Lung NSC(106;0.000161)|all_lung(105;0.000447)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					AACGGCACTTGTAAGTTTCAG	0.612																																					.		Atlas-SNP	.											.	C8orf31	18	.	0			c.186+1G>A						.						29	31	30					8																	144124680		2203	4300	6503	SO:0001630	splice_region_variant	286122	exon3			GCACTTGTAAGTT		CCDS6395.1	8q24.3	2012-04-11			ENSG00000177335	ENSG00000177335			26731	protein-coding gene	gene with protein product							Standard	NM_173687		Approved	FLJ37131	uc003yxp.1	Q8N9H6	OTTHUMG00000164771	ENST00000395172.1:c.186+1G>A	chr8.hg19:g.144124680G>A		27.0	0.0		29.0	11.0	NM_173687	Q6GMU7	Splice_Site	SNP	ENST00000395172.1	hg19	CCDS6395.1	.	.	.	.	.	.	.	.	.	.	G	0.036	-1.304949	0.01353	.	.	ENSG00000177335	ENST00000395172	.	.	.	1.85	-3.7	0.04437	.	.	.	.	.	.	.	.	.	.	.	0.21064	N	0.999794	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.0882	0.00037	0.2694:0.2595:0.1974:0.2737	.	.	.	.	.	-1	.	.	.	+	.	.	C8orf31	144196055	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.393000	0.02521	-1.955000	0.01023	0.391000	0.25812	.	.	.		0.612	C8orf31-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380167.1	NM_173687	Intron	A	144124680	G	A	144124680	5	1	38	1	0	0	0	0	0	0	1	0	2422	1391	48	3	193	3	C8orf31	8	144124680	Splice_Site	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	15373679	144124680	2239342	74	4521										
RHPN1	114822	hgsc.bcm.edu	37	chr8	144460480	144460480	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggagaggacggcgcctcctaCgaggcagaaatcagggagct	16	10	1	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:144460480C>T	ENST00000289013.6	+	5	524	c.423C>T	c.(421-423)taC>taT	p.Y141Y		NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	141	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)		small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(1)|lung(7)	9	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)			GCGCCTCCTACGAGGCAGAAA	0.652																																					p.Y141Y		Atlas-SNP	.											.	RHPN1	76	.	0			c.C423T						.						32	38	36					8																	144460480		1969	4132	6101	SO:0001819	synonymous_variant	114822	exon5			CTCCTACGAGGCA	AB067516	CCDS47927.1	8q24.3	2003-02-06			ENSG00000158106	ENSG00000158106			19973	protein-coding gene	gene with protein product		601031				11572484	Standard	NM_052924		Approved	KIAA1929, RHPN, ODF5	uc003yyb.3	Q8TCX5	OTTHUMG00000165006	ENST00000289013.6:c.423C>T	chr8.hg19:g.144460480C>T		59.0	0.0		77.0	37.0	NM_052924	Q8TAV1|Q96PV9	Silent	SNP	ENST00000289013.6	hg19	CCDS47927.1																																																																																			.	.		0.652	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1			T	144460480	C	T	144460480	2	4	38	1	0	0	0	0	0	0	0	1	13365	547	19	1		1	RHPN1	8	144460480	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	335800	144460480	1903542	75	4522										
GSDMD	79792	hgsc.bcm.edu	37	chr8	144644198	144644198	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggcagaggtggagaccatctCcaaggaactggagcttttgg	15	8	1	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr8:144644198C>G	ENST00000526406.1	+	11	1776	c.893C>G	c.(892-894)tCc>tGc	p.S298C	GSDMD_ENST00000533063.1_Missense_Mutation_p.S346C|GSDMD_ENST00000262580.4_Missense_Mutation_p.S298C	NM_001166237.1	NP_001159709.1	P57764	GSDMD_HUMAN	gasdermin D	298					cellular response to extracellular stimulus (GO:0031668)					breast(1)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	12						GAGACCATCTCCAAGGAACTG	0.652																																					p.S298C		Atlas-SNP	.											.	GSDMD	28	.	0			c.C893G						.						55	57	56					8																	144644198		2202	4300	6502	SO:0001583	missense	79792	exon11			CCATCTCCAAGGA	AK096216	CCDS34956.1	8q24.3	2008-07-31	2008-07-31	2008-07-31		ENSG00000104518			25697	protein-coding gene	gene with protein product			"gasdermin domain containing 1"	GSDMDC1		15289881, 17350798	Standard	NM_024736		Approved	FLJ12150, DF5L	uc003yyg.3	P57764		ENST00000526406.1:c.893C>G	chr8.hg19:g.144644198C>G	ENSP00000433209:p.Ser298Cys	26.0	0.0		35.0	17.0	NM_001166237	D3DWJ9|Q96Q98	Missense_Mutation	SNP	ENST00000526406.1	hg19	CCDS34956.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.122698	0.37436	.	.	ENSG00000104518	ENST00000526406;ENST00000533063;ENST00000262580	T;T;T	0.22539	1.95;1.95;1.95	4.39	0.448	0.16614	.	1.726280	0.02499	N	0.090281	T	0.38081	0.1027	L	0.60455	1.87	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.998	P;P;P	0.62740	0.905;0.905;0.906	T	0.09207	-1.0685	10	0.46703	T	0.11	-7.8434	5.0637	0.14570	0.0:0.4856:0.3268:0.1876	.	298;298;346	A8K702;P57764;G3V1A6	.;GSDMD_HUMAN;.	C	298;346;298	ENSP00000433209:S298C;ENSP00000433958:S346C;ENSP00000262580:S298C	ENSP00000262580:S298C	S	+	2	0	GSDMD	144715341	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.152000	0.16302	0.066000	0.16515	0.549000	0.68633	TCC	.	.		0.652	GSDMD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382046.3	NM_024736		G	144644198	C	G	144644198	3	3	38	1	0	0	0	0	1	0	0	0	6828	855	30	4	919	4	GSDMD	8	144644198	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	183718	144644198	1719824	76	4523										
FREM1	158326	hgsc.bcm.edu	37	chr9	14816837	14816837	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgacctccaagagtaggtcaTcctgaagaacttcagttcca	8	11	2	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr9:14816837T>C	ENST00000380880.3	-	15	3362	c.2579A>G	c.(2578-2580)gAt>gGt	p.D860G	FREM1_ENST00000380881.4_Missense_Mutation_p.D861G|FREM1_ENST00000422223.2_Missense_Mutation_p.D860G			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	860					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		gagtaggtcatcctgaagaac	0.418																																					p.D860G		Atlas-SNP	.											.	FREM1	261	.	0			c.A2579G						.						66	69	69					9																	14816837		1871	4095	5966	SO:0001583	missense	158326	exon16			AGGTCATCCTGAA	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.2579A>G	chr9.hg19:g.14816837T>C	ENSP00000370262:p.Asp860Gly	63.0	0.0		69.0	20.0	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	hg19	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.051220	0.75960	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.51817	0.69;0.69;0.69	5.65	5.65	0.86999	.	0.085714	0.85682	D	0.000000	T	0.74794	0.3763	M	0.93550	3.43	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.79640	-0.1719	10	0.48119	T	0.1	-20.9429	12.1892	0.54261	0.0:0.0:0.0:1.0	.	860	Q5H8C1	FREM1_HUMAN	G	861;860;860	ENSP00000370263:D861G;ENSP00000412940:D860G;ENSP00000370262:D860G	ENSP00000370257:D863G	D	-	2	0	FREM1	14806837	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	5.150000	0.64869	2.371000	0.80710	0.533000	0.62120	GAT	.	.		0.418	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		C	14816837	T	C	14816837	3	2	38	1	0	0	0	0	1	0	0	0	6052	1435	50	2	4102	2	FREM1	9	14816837	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10		14816837	126396594	77	4524										
TLN1	7094	hgsc.bcm.edu	37	chr9	35697837	35697837	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gaaacttgtactgctgctgcCggatctgggccagtttcttc	11	11	2	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr9:35697837C>T	ENST00000314888.9	-	57	7930	c.7577G>A	c.(7576-7578)cGg>cAg	p.R2526Q	TLN1_ENST00000540444.1_Missense_Mutation_p.R2414Q	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2526	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CTGCTGCTGCCGGATCTGGGC	0.542											OREG0019174	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R2526Q		Atlas-SNP	.											.	TLN1	185	.	0			c.G7577A						.						95	90	92					9																	35697837		2203	4300	6503	SO:0001583	missense	7094	exon57			TGCTGCCGGATCT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.7577G>A	chr9.hg19:g.35697837C>T	ENSP00000316029:p.Arg2526Gln	426.0	0.0	857	550.0	187.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	32	5.140189	0.94560	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.68331	-0.32;-0.32	5.09	5.09	0.68999	I/LWEQ (4);	0.065800	0.64402	D	0.000007	D	0.86867	0.6036	M	0.93720	3.45	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90160	0.4227	10	0.87932	D	0	-11.3857	18.6738	0.91521	0.0:1.0:0.0:0.0	.	2526	Q9Y490	TLN1_HUMAN	Q	2526;2414	ENSP00000316029:R2526Q;ENSP00000442981:R2414Q	ENSP00000316029:R2526Q	R	-	2	0	TLN1	35687837	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.587000	0.82613	2.633000	0.89246	0.563000	0.77884	CGG	.	.		0.542	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		T	35697837	C	T	35697837	3	4	38	1	0	0	0	0	1	0	0	0	15962	652	23	1	52	1	TLN1	9	35697837	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	20881000	35697837	105515594	78	4525										
ZNF510	22869	hgsc.bcm.edu	37	chr9	99522164	99522164	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	acagttgacttctcaaaggaTttcccacattgattaagatg	7	8	1	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr9:99522164T>C	ENST00000375231.1	-	6	1598	c.948A>G	c.(946-948)aaA>aaG	p.K316K	ZNF510_ENST00000223428.4_Silent_p.K316K			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	316					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				TCTCAAAGGATTTCCCACATT	0.338																																					p.K316K		Atlas-SNP	.											.	ZNF510	59	.	0			c.A948G						.						94	99	98					9																	99522164		2203	4300	6503	SO:0001819	synonymous_variant	22869	exon6			AAAGGATTTCCCA	AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"Zinc fingers, C2H2-type", "-"	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.948A>G	chr9.hg19:g.99522164T>C		297.0	0.0		215.0	110.0	NM_014930	Q5SZP5	Silent	SNP	ENST00000375231.1	hg19	CCDS35074.1																																																																																			.	.		0.338	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930		C	99522164	T	C	99522164	2	2	38	1	0	0	0	0	0	0	0	1	17969	1490	52	2		2	ZNF510	9	99522164	Silent	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	63824327	99522164	41691267	79	4526										
ABCA1	19	hgsc.bcm.edu	37	chr9	107584777	107584777	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gaaccacaccctcttcttacAtggtggtcgtcttccccgct	7	16	3	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr9:107584777A>G	ENST00000374736.3	-	19	3222	c.2828T>C	c.(2827-2829)aTg>aCg	p.M943T		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	943	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CTCTTCTTACATGGTGGTCGT	0.527																																					p.M943T		Atlas-SNP	.											.	ABCA1	244	.	0			c.T2828C						.						126	117	120					9																	107584777		2203	4300	6503	SO:0001630	splice_region_variant	19	exon19			TCTTACATGGTGG	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.2828+1T>C	chr9.hg19:g.107584777A>G		107.0	0.0		86.0	43.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.401775	0.83120	.	.	ENSG00000165029	ENST00000374736	T	0.80738	-1.41	5.79	5.79	0.91817	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.035406	0.85682	D	0.000000	D	0.87892	0.6292	M	0.72479	2.2	0.80722	D	1	D	0.54964	0.969	P	0.62089	0.898	D	0.87747	0.2589	9	.	.	.	.	16.1224	0.81369	1.0:0.0:0.0:0.0	.	943	O95477	ABCA1_HUMAN	T	943	ENSP00000363868:M943T	.	M	-	2	0	ABCA1	106624598	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	9.339000	0.96797	2.208000	0.71279	0.533000	0.62120	ATG	.	.		0.527	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	Missense_Mutation	G	107584777	A	G	107584777	5	3	38	1	0	0	0	0	0	0	1	0	28	231	8	2	4085	2	ABCA1	9	107584777	Splice_Site	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	8062613	107584777	33628654	80	4527										
PTPN3	5774	hgsc.bcm.edu	37	chr9	112185130	112185130	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgcaatattggttatttaccGacctgaaaaaccagatgcag	8	8	0	2	rs376647767		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr9:112185130G>A	ENST00000374541.2	-	13	1108	c.1004C>T	c.(1003-1005)tCg>tTg	p.S335L	PTPN3_ENST00000446349.1_Intron|PTPN3_ENST00000412145.1_Missense_Mutation_p.S204L|PTPN3_ENST00000262539.3_Intron	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	335					negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						GTTATTTACCGACCTGAAAAA	0.443																																					p.S335L		Atlas-SNP	.											.	PTPN3	106	.	0			c.C1004T						.	G	,LEU/SER,,LEU/SER,,LEU/SER	0,4406		0,0,2203	190	175	180		,611,,143,,1004	4.5	1	9		180	1,8599	2.2+/-6.3	0,1,4299	no	intron,missense,intron,missense,intron,missense	PTPN3	NM_001145368.1,NM_001145369.1,NM_001145370.1,NM_001145371.1,NM_001145372.1,NM_002829.3	,145,,145,,145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,benign,,benign,,benign	,204/783,,48/627,,335/914	112185130	1,13005	2203	4300	6503	SO:0001583	missense	5774	exon13			TTTACCGACCTGA		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.1004C>T	chr9.hg19:g.112185130G>A	ENSP00000363667:p.Ser335Leu	193.0	0.0		169.0	54.0	NM_002829	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	hg19	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.555894	0.65425	0.0	1.16E-4	ENSG00000070159	ENST00000394831;ENST00000412145;ENST00000374541	D;D	0.82526	-1.62;-1.62	5.43	4.52	0.55395	.	0.200478	0.42172	D	0.000752	T	0.76126	0.3944	L	0.38531	1.155	0.80722	D	1	B	0.29253	0.239	B	0.24394	0.053	T	0.74300	-0.3710	10	0.52906	T	0.07	.	15.3342	0.74238	0.0:0.0:0.8591:0.1409	.	335	P26045	PTN3_HUMAN	L	335;204;335	ENSP00000416654:S204L;ENSP00000363667:S335L	ENSP00000363667:S335L	S	-	2	0	PTPN3	111224951	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.033000	0.76504	1.266000	0.44231	0.650000	0.86243	TCG	.	.		0.443	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			A	112185130	G	A	112185130	3	1	38	1	0	0	0	0	1	0	0	0	12804	1059	37	1	1793	1	PTPN3	9	112185130	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	4600353	112185130	29028301	81	4528										
OR1L8	138881	hgsc.bcm.edu	37	chr9	125329852	125329852	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	atctcttgctcataagcttcCtcaggccctgtttcaggtct	7	13	5	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr9:125329852C>A	ENST00000304865.2	-	1	986	c.905G>T	c.(904-906)aGg>aTg	p.R302M		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						CATAAGCTTCCTCAGGCCCTG	0.443																																					p.R302M		Atlas-SNP	.											.	OR1L8	90	.	0			c.G905T						.						89	90	89					9																	125329852		2203	4300	6503	SO:0001583	missense	138881	exon1			AGCTTCCTCAGGC		CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"GPCR / Class A : Olfactory receptors"	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.905G>T	chr9.hg19:g.125329852C>A	ENSP00000306607:p.Arg302Met	156.0	0.0		102.0	46.0	NM_001004454	A3KFM3|B9EIR6|Q6IF15|Q96R79	Missense_Mutation	SNP	ENST00000304865.2	hg19	CCDS35124.1	.	.	.	.	.	.	.	.	.	.	C	9.087	1.000885	0.19121	.	.	ENSG00000171496	ENST00000304865	T	0.39997	1.05	4.64	1.77	0.24775	.	0.642146	0.13432	N	0.388371	T	0.40546	0.1121	M	0.74546	2.27	0.09310	N	1	B	0.25563	0.129	B	0.23018	0.043	T	0.34800	-0.9814	10	0.49607	T	0.09	-0.2245	7.7336	0.28802	0.0:0.6556:0.0:0.3444	.	302	Q8NGR8	OR1L8_HUMAN	M	302	ENSP00000306607:R302M	ENSP00000306607:R302M	R	-	2	0	OR1L8	124369673	0.000000	0.05858	0.008000	0.14137	0.876000	0.50452	-1.066000	0.03454	0.311000	0.23014	0.449000	0.29647	AGG	.	.		0.443	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1			A	125329852	C	A	125329852	3	1	38	1	0	0	0	0	1	0	0	0	10976	681	24	3	28	3	OR1L8	9	125329852	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	13144722	125329852	15883579	82	4529										
ABCA2	20	hgsc.bcm.edu	37	chr9	139904510	139904510	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tcccgggccgtgagctcgtcGaacagcgcgtcacactgcgg	14	15	1	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr9:139904510G>A	ENST00000371605.3	-	41	6564	c.6417C>T	c.(6415-6417)ttC>ttT	p.F2139F	ABCA2_ENST00000341511.6_Silent_p.F2140F|ABCA2_ENST00000265662.5_Silent_p.F2140F			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	2139	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		TGAGCTCGTCGAACAGCGCGT	0.692																																					p.F2170F		Atlas-SNP	.											.	ABCA2	113	.	0			c.C6510T						.						11	15	14					9																	139904510		2124	4199	6323	SO:0001819	synonymous_variant	20	exon42			CTCGTCGAACAGC	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.6417C>T	chr9.hg19:g.139904510G>A		37.0	0.0		39.0	19.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	hg19																																																																																				.	.		0.692	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		A	139904510	G	A	139904510	2	1	38	1	0	0	0	0	0	0	0	1	32	1049	37	1		1	ABCA2	9	139904510	Silent	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	14574658	139904510	1308921	83	4530										
PRKG1	5592	hgsc.bcm.edu	37	chr10	54048601	54048601	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctgctaatttaattaaaaaaCtatgcaggtaagtatttcaa	5	5	1	0	rs541150590		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr10:54048601C>T	ENST00000401604.2	+	15	1974	c.1780C>T	c.(1780-1782)Cta>Tta	p.L594L	PRKG1_ENST00000373975.2_Silent_p.L312L|PRKG1-AS1_ENST00000452247.2_RNA|PRKG1-AS1_ENST00000426785.2_RNA|PRKG1_ENST00000373985.1_Silent_p.L582L|PRKG1_ENST00000373980.4_Silent_p.L609L			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	594	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		AATTAAAAAACTATGCAGGTA	0.279													C|||	1	0.000199681	0	0	5008	,	,		16677	0		0	False		,,,				2504	0.001				p.L609L		Atlas-SNP	.											PRKG1_ENST00000401604,colon,carcinoma,0,2	PRKG1	167	.	0			c.C1825T						.						50	53	52					10																	54048601		2201	4300	6501	SO:0001819	synonymous_variant	5592	exon15			AAAAAACTATGCA		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.1780C>T	chr10.hg19:g.54048601C>T		229.0	0.0		135.0	64.0	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Silent	SNP	ENST00000401604.2	hg19	CCDS44399.1																																																																																			.	.		0.279	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	54048601	C	T	54048601	2	4	38	1	0	0	0	0	0	0	0	1	12534	564	20	3		3	PRKG1	10	54048601	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10		54048601	81486146	84	4531										
SLC16A9	220963	hgsc.bcm.edu	37	chr10	61413875	61413875	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aaaagggctgaaaatactttGtttttaaaaagagccacagt	8	5	0	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr10:61413875G>T	ENST00000395348.3	-	5	1545	c.909C>A	c.(907-909)aaC>aaA	p.N303K	SLC16A9_ENST00000395347.1_Missense_Mutation_p.N303K	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	303					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						AAAATACTTTGTTTTTAAAAA	0.373																																					p.N303K		Atlas-SNP	.											.	SLC16A9	58	.	0			c.C909A						.						66	67	67					10																	61413875		2203	4300	6503	SO:0001583	missense	220963	exon5			TACTTTGTTTTTA	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.909C>A	chr10.hg19:g.61413875G>T	ENSP00000378757:p.Asn303Lys	268.0	0.0		191.0	90.0	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	hg19	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.337746	0.60963	.	.	ENSG00000165449	ENST00000395348;ENST00000395347	D;D	0.82344	-1.6;-1.6	4.92	3.79	0.43588	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.089669	0.85682	D	0.000000	D	0.88687	0.6504	M	0.69823	2.125	0.50632	D	0.999886	D	0.64830	0.994	D	0.63793	0.918	D	0.89026	0.3438	10	0.49607	T	0.09	.	14.0905	0.64987	0.0872:0.0:0.9128:0.0	.	303	Q7RTY1	MOT9_HUMAN	K	303	ENSP00000378757:N303K;ENSP00000378756:N303K	ENSP00000378756:N303K	N	-	3	2	SLC16A9	61083881	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.900000	0.56295	2.261000	0.74972	0.591000	0.81541	AAC	.	.		0.373	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		T	61413875	G	T	61413875	3	4	38	1	0	0	0	0	1	0	0	0	14430	1368	48	3	628	3	SLC16A9	10	61413875	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	7365274	61413875	74120872	85	4532										
HK1	3098	hgsc.bcm.edu	37	chr10	71136836	71136836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	taacaccagtgatgtgtcagCcatcgaaaagtaggtaccat	9	9	1	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr10:71136836C>T	ENST00000359426.6	+	8	1126	c.1022C>T	c.(1021-1023)gCc>gTc	p.A341V	HK1_ENST00000494253.1_3'UTR|HK1_ENST00000360289.2_Missense_Mutation_p.A329V|HK1_ENST00000298649.3_Missense_Mutation_p.A340V|HK1_ENST00000404387.2_Missense_Mutation_p.A345V|HK1_ENST00000448642.2_Missense_Mutation_p.A376V	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	341	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GATGTGTCAGCCATCGAAAAG	0.527																																					p.A345V		Atlas-SNP	.											.	HK1	170	.	0			c.C1034T						.						108	102	104					10																	71136836		2203	4300	6503	SO:0001583	missense	3098	exon11			TGTCAGCCATCGA	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.1022C>T	chr10.hg19:g.71136836C>T	ENSP00000352398:p.Ala341Val	127.0	0.0		95.0	36.0	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	hg19	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.497760	0.85069	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	D;D;D;D;D	0.96427	-4.01;-4.01;-4.01;-4.01;-4.01	4.87	4.87	0.63330	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96071	0.8720	M	0.64997	1.995	0.80722	D	1	P;P;P;P;P;B	0.46912	0.885;0.886;0.505;0.704;0.458;0.268	P;B;B;B;B;B	0.46659	0.523;0.328;0.226;0.26;0.121;0.026	D	0.96480	0.9355	10	0.59425	D	0.04	-12.4398	18.0069	0.89212	0.0:1.0:0.0:0.0	.	341;341;340;376;345;329	A8K7J7;P19367;P19367-2;E7ENR4;P19367-3;P19367-4	.;HXK1_HUMAN;.;.;.;.	V	329;376;345;340;341;341	ENSP00000353433:A329V;ENSP00000402103:A376V;ENSP00000384774:A345V;ENSP00000298649:A340V;ENSP00000352398:A341V	ENSP00000298649:A340V	A	+	2	0	HK1	70806842	1.000000	0.71417	0.997000	0.53966	0.924000	0.55760	7.782000	0.85680	2.252000	0.74401	0.585000	0.79938	GCC	.	.		0.527	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		T	71136836	C	T	71136836	3	4	38	1	0	0	0	0	1	0	0	0	7199	739	26	3	1230	3	HK1	10	71136836	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	9722961	71136836	64397911	86	4533										
TIAL1	7073	hgsc.bcm.edu	37	chr10	121337034	121337034	+	Frame_Shift_Del	DEL	T	T	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccaaatggtgagaatgtctgTctcataagctgatctataaa							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr10:121337034delT	ENST00000436547.2	-	9	710	c.666delA	c.(664-666)agafs	p.R222fs	TIAL1_ENST00000369093.2_Frame_Shift_Del_p.R239fs|TIAL1_ENST00000463089.2_5'Flank|TIAL1_ENST00000369092.4_Frame_Shift_Del_p.R99fs	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	222	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		AGAATGTCTGTCTCATAAGCT	0.328																																					p.Q240fs		Atlas-Indel,Pindel	.											.	TIAL1	47	.	0			c.718delC						.						85	84	84					10																	121337034		2202	4300	6502	SO:0001589	frameshift_variant	7073	exon9			.	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"RNA binding motif (RRM) containing"	11804	protein-coding gene	gene with protein product		603413	"TIA1 cytotoxic granule-associated RNA-binding protein-like 1"			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.666delA	chr10.hg19:g.121337034delT	ENSP00000394902:p.Arg222fs	153.0	0.0		153.0	65.0	NM_001033925	A8K3T0|A8K4L9	Frame_Shift_Del	DEL	ENST00000436547.2	hg19	CCDS7613.1																																																																																			.	.		0.328	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252		-	121337034	T	-	121337034	7	5	38	1	0	1	0	1	0	0	0	0	15904	1664	58	0	477	0	TIAL1	10	121337034	Frame_Shift_Del	DEL	T	TCGA-BC-A10Z-01A-11D-A12Z-10	50200198	121337034	14197713	87	4534										
ADAM12	8038	hgsc.bcm.edu	37	chr10	127708372	127708372	+	Frame_Shift_Del	DEL	G	G	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctgcaggcagaggcttctgaGgggggtttggcttacaggtc							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr10:127708372delG	ENST00000368679.4	-	22	2870	c.2561delC	c.(2560-2562)cctfs	p.P854fs		NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	854					cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		AGGCTTCTGAGGGGGGTTTGG	0.612																																					p.P854fs		Atlas-Indel,Pindel	.											.	ADAM12	388	.	0			c.2562delT						.						37	38	38					10																	127708372		2203	4300	6503	SO:0001589	frameshift_variant	8038	exon22			.	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.2561delC	chr10.hg19:g.127708372delG	ENSP00000357668:p.Pro854fs	105.0	0.0		91.0	37.0	NM_003474	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Frame_Shift_Del	DEL	ENST00000368679.4	hg19	CCDS7653.1																																																																																			.	.		0.612	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			-	127708372	G	-	127708372	7	5	38	1	0	1	0	1	0	0	0	0	236	1000	35	0	176	0	ADAM12	10	127708372	Frame_Shift_Del	DEL	G	TCGA-BC-A10Z-01A-11D-A12Z-10	6371338	127708372	7826375	88	4535										
OR51V1	283111	hgsc.bcm.edu	37	chr11	5221902	5221902	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgctggtgctagggcttactGaagtaatcattctggaactg	12	7	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr11:5221902G>A	ENST00000321255.1	-	1	28	c.29C>T	c.(28-30)tCa>tTa	p.S10L		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	10					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGGGCTTACTGAAGTAATCAT	0.388																																					p.S10L		Atlas-SNP	.											.	OR51V1	77	.	0			c.C29T						.						76	75	76					11																	5221902		2201	4298	6499	SO:0001583	missense	283111	exon1			CTTACTGAAGTAA	BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"GPCR / Class A : Olfactory receptors"	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.29C>T	chr11.hg19:g.5221902G>A	ENSP00000321729:p.Ser10Leu	164.0	0.0		121.0	54.0	NM_001004760		Missense_Mutation	SNP	ENST00000321255.1	hg19	CCDS31375.1	.	.	.	.	.	.	.	.	.	.	G	10.38	1.335556	0.24253	.	.	ENSG00000176742	ENST00000321255	T	0.00566	6.55	3.73	0.695	0.18070	.	12.234700	0.02867	U	0.131040	T	0.00468	0.0015	L	0.31526	0.94	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.50524	-0.8818	10	0.09843	T	0.71	.	5.9734	0.19365	0.3661:0.0:0.6339:0.0	.	10	Q9H2C8	O51V1_HUMAN	L	10	ENSP00000321729:S10L	ENSP00000321729:S10L	S	-	2	0	OR51V1	5178478	0.009000	0.17119	0.001000	0.08648	0.013000	0.08279	-0.514000	0.06298	0.280000	0.22209	0.585000	0.79938	TCA	.	.		0.388	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760		A	5221902	G	A	5221902	3	1	38	1	0	0	0	0	1	0	0	0	11116	1294	45	3	939	3	OR51V1	11	5221902	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10		5221902	129784614	89	4536										
TRIM3	10612	hgsc.bcm.edu	37	chr11	6477958	6477958	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gctggcccactagcgcctggCgcaggccctctcccgtggcc	13	19	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr11:6477958C>A	ENST00000525074.1	-	6	1392	c.998G>T	c.(997-999)cGc>cTc	p.R333L	TRIM3_ENST00000536344.1_Missense_Mutation_p.R214L|TRIM3_ENST00000529058.1_5'UTR|TRIM3_ENST00000359518.3_Missense_Mutation_p.R333L|TRIM3_ENST00000345851.3_Missense_Mutation_p.R333L|TRIM3_ENST00000537602.1_Missense_Mutation_p.R255L	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	333					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TAGCGCCTGGCGCAGGCCCTC	0.662																																					p.R333L	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.G998T						.						39	41	40					11																	6477958		2188	4282	6470	SO:0001583	missense	10612	exon6			GCCTGGCGCAGGC	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10064	protein-coding gene	gene with protein product	"ring finger protein 22", "brain expressed ring finger", "tripartite motif protein TRIM3"	605493	"tripartite motif-containing 3"	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.998G>T	chr11.hg19:g.6477958C>A	ENSP00000433102:p.Arg333Leu	56.0	0.0		76.0	29.0	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Missense_Mutation	SNP	ENST00000525074.1	hg19	CCDS7764.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070042	0.76301	.	.	ENSG00000110171	ENST00000530899;ENST00000525074;ENST00000545029;ENST00000345851;ENST00000336043;ENST00000537602;ENST00000359518;ENST00000536344	D;D;D;D;D	0.84873	-1.91;-1.91;-1.91;-1.91;-1.91	5.27	3.35	0.38373	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.160727	0.56097	D	0.000031	D	0.87474	0.6186	M	0.62154	1.92	0.49213	D	0.999761	P;P;P	0.51147	0.485;0.942;0.677	B;P;P	0.55545	0.299;0.778;0.624	D	0.85024	0.0913	10	0.40728	T	0.16	-19.0968	10.9691	0.47428	0.1466:0.7124:0.141:0.0	.	214;214;333	F5H2Q8;D3DQT4;O75382	.;.;TRIM3_HUMAN	L	333;333;333;333;322;255;333;214	ENSP00000433102:R333L;ENSP00000340797:R333L;ENSP00000441091:R255L;ENSP00000352508:R333L;ENSP00000445460:R214L	ENSP00000337094:R322L	R	-	2	0	TRIM3	6434534	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.682000	0.61671	0.572000	0.29383	0.563000	0.77884	CGC	.	.		0.662	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458		A	6477958	C	A	6477958	3	1	38	1	0	0	0	0	1	0	0	0	16519	768	27	1	1264	1	TRIM3	11	6477958	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	1256056	6477958	128528558	90	4537										
MRVI1	10335	hgsc.bcm.edu	37	chr11	10651167	10651167	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctcaccaacttggcttcttcCagcagcgccaggtttttctt	7	14	3	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr11:10651167C>A	ENST00000436272.1	-	4	543	c.465G>T	c.(463-465)ctG>ctT	p.L155L	MRVI1_ENST00000423302.2_Silent_p.L164L|MRVI1_ENST00000421747.1_Silent_p.L155L|MRVI1_ENST00000545852.1_5'UTR|MRVI1_ENST00000532037.1_5'Flank|MRVI1_ENST00000531107.1_Silent_p.L155L|MRVI1_ENST00000541483.1_Silent_p.L164L|MRVI1_ENST00000547195.1_Silent_p.L73L|MRVI1_ENST00000552103.1_Silent_p.L73L|MRVI1_ENST00000534266.2_5'UTR|MRVI1_ENST00000527509.2_Silent_p.L73L|MRVI1_ENST00000558540.1_5'UTR|MRVI1_ENST00000424001.1_5'UTR			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	155	Interaction with PRKG1. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		TGGCTTCTTCCAGCAGCGCCA	0.587																																					p.L164L		Atlas-SNP	.											.	MRVI1	113	.	0			c.G492T						.						77	83	81					11																	10651167		2057	4186	6243	SO:0001819	synonymous_variant	10335	exon5			TTCTTCCAGCAGC	AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"inositol 1,4,5-triphosphate-associated cGMP kinase substrate", "IP3R-associated cGMP kinase substrate"	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.465G>T	chr11.hg19:g.10651167C>A		353.0	0.0		340.0	158.0	NM_001206880	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Silent	SNP	ENST00000436272.1	hg19																																																																																				.	.		0.587	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		A	10651167	C	A	10651167	2	1	38	1	0	0	0	0	0	0	0	1	9862	581	21	3		3	MRVI1	11	10651167	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	4173209	10651167	124355349	91	4538										
LRP4	4038	hgsc.bcm.edu	37	chr11	46896621	46896621	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gaggcaagcagaggtgggagCagccgccatttctcgagccg	16	11	1	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr11:46896621C>T	ENST00000378623.1	-	28	4201	c.3959G>A	c.(3958-3960)tGc>tAc	p.C1320Y	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1320					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GAGGTGGGAGCAGCCGCCATT	0.547																																					p.C1320Y		Atlas-SNP	.											.	LRP4	160	.	0			c.G3959A						.						30	33	32					11																	46896621		2201	4299	6500	SO:0001583	missense	4038	exon28			TGGGAGCAGCCGC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.3959G>A	chr11.hg19:g.46896621C>T	ENSP00000367888:p.Cys1320Tyr	51.0	0.0		51.0	16.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.309071	0.81247	.	.	ENSG00000134569	ENST00000378623	D	0.99818	-6.92	5.67	5.67	0.87782	Epidermal growth factor-like (1);	0.096722	0.64402	D	0.000001	D	0.99896	0.9950	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96485	0.9359	10	0.87932	D	0	.	17.9629	0.89091	0.0:1.0:0.0:0.0	.	1320	O75096	LRP4_HUMAN	Y	1320	ENSP00000367888:C1320Y	ENSP00000367888:C1320Y	C	-	2	0	LRP4	46853197	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	7.805000	0.86005	2.677000	0.91161	0.561000	0.74099	TGC	.	.		0.547	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		T	46896621	C	T	46896621	3	4	38	1	0	0	0	0	1	0	0	0	8968	710	25	3	1802	3	LRP4	11	46896621	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	36245454	46896621	88109895	92	4539										
OR4C3	256144	hgsc.bcm.edu	37	chr11	48346884	48346884	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tcagctctttggagctcattTtttgggaggtgttgagatca	12	6	4	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr11:48346884T>G	ENST00000319856.4	+	1	413	c.392T>G	c.(391-393)tTt>tGt	p.F131C		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						GGAGCTCATTTTTTGGGAGGT	0.463																																					p.F131C		Atlas-SNP	.											.	OR4C3	75	.	0			c.T392G						.						262	249	253					11																	48346884		2201	4298	6499	SO:0001583	missense	256144	exon1			CTCATTTTTTGGG	AB065567	CCDS31489.1	11p11.2	2012-08-09				ENSG00000176547		"GPCR / Class A : Olfactory receptors"	14697	protein-coding gene	gene with protein product							Standard	NM_001004702		Approved		uc010rhv.2	Q8NH37	OTTHUMG00000166579	ENST00000319856.4:c.392T>G	chr11.hg19:g.48346884T>G	ENSP00000321419:p.Phe131Cys	992.0	1.0		857.0	163.0	NM_001004702	B2RNF2|Q6IFB3	Missense_Mutation	SNP	ENST00000319856.4	hg19	CCDS31489.1	.	.	.	.	.	.	.	.	.	.	T	19.30	3.801430	0.70682	.	.	ENSG00000176547	ENST00000319856	T	0.00902	5.56	5.78	5.78	0.91487	GPCR, rhodopsin-like superfamily (1);	0.510284	0.18247	N	0.147075	T	0.05090	0.0136	M	0.80183	2.485	0.30797	N	0.740272	D	0.58970	0.984	P	0.60345	0.873	T	0.00893	-1.1524	10	0.87932	D	0	.	14.2031	0.65716	0.0:0.0:0.0:1.0	.	104	Q8NH37	OR4C3_HUMAN	C	131	ENSP00000321419:F131C	ENSP00000321419:F131C	F	+	2	0	OR4C3	48303460	0.001000	0.12720	0.944000	0.38274	0.965000	0.64279	1.072000	0.30678	2.245000	0.73994	0.391000	0.25812	TTT	.	.		0.463	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702		G	48346884	T	G	48346884	3	3	38	1	0	0	0	0	1	0	0	0	11059	1841	64	5	394	5	OR4C3	11	48346884	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	1450263	48346884	86659632	93	4540										
OR4A5	81318	hgsc.bcm.edu	37	chr11	51412172	51412172	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctacaattaacttgggagaaAtggtagtggaatatgcagca	11	5	0	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr11:51412172A>G	ENST00000319760.6	-	1	276	c.224T>C	c.(223-225)aTt>aCt	p.I75T		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	75						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				CTTGGGAGAAATGGTAGTGGA	0.423																																					p.I75T		Atlas-SNP	.											.	OR4A5	116	.	0			c.T224C						.						58	59	59					11																	51412172		2201	4296	6497	SO:0001583	missense	81318	exon1			GGAGAAATGGTAG	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"GPCR / Class A : Olfactory receptors"	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.224T>C	chr11.hg19:g.51412172A>G	ENSP00000367664:p.Ile75Thr	482.0	0.0		430.0	188.0	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	hg19	CCDS31497.1	.	.	.	.	.	.	.	.	.	.	.	0.032	-1.327600	0.01309	.	.	ENSG00000221840	ENST00000319760	T	0.01139	5.28	1.93	1.93	0.25924	GPCR, rhodopsin-like superfamily (1);	1.173960	0.06502	N	0.736428	T	0.00784	0.0026	N	0.05050	-0.12	0.09310	N	1	B	0.16802	0.019	B	0.21151	0.033	T	0.42085	-0.9472	10	0.10636	T	0.68	.	7.8263	0.29318	1.0:0.0:0.0:0.0	.	75	Q8NH83	OR4A5_HUMAN	T	75	ENSP00000367664:I75T	ENSP00000367664:I75T	I	-	2	0	OR4A5	51268748	0.000000	0.05858	0.589000	0.28718	0.032000	0.12392	-0.025000	0.12413	1.143000	0.42306	0.136000	0.15936	ATT	.	.		0.423	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		G	51412172	A	G	51412172	3	3	38	1	0	0	0	0	1	0	0	0	11052	101	4	2	727	2	OR4A5	11	51412172	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	3065288	51412172	83594344	94	4541										
OR5B17	219965	hgsc.bcm.edu	37	chr11	58125852	58125852	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agataaaggcttctggtatcCcttacctgtgtgcctcttaa	8	10	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr11:58125852C>G	ENST00000357377.3	-	1	690	c.691G>C	c.(691-693)Gga>Cga	p.G231R		NM_001005489.1	NP_001005489.1	Q8NGF7	OR5BH_HUMAN	olfactory receptor, family 5, subfamily B, member 17	231						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TTCTGGTATCCCTTACCTGTG	0.358																																					p.G231R		Atlas-SNP	.											OR5B17,NS,adenoma,0,1	OR5B17	64	.	0			c.G691C						.						99	95	96					11																	58125852		2201	4295	6496	SO:0001583	missense	219965	exon1			GGTATCCCTTACC	AB065849	CCDS31548.1	11q12.1	2012-08-09			ENSG00000197786	ENSG00000197786		"GPCR / Class A : Olfactory receptors"	15267	protein-coding gene	gene with protein product				OR5B20P			Standard	NM_001005489		Approved		uc010rke.2	Q8NGF7	OTTHUMG00000167465	ENST00000357377.3:c.691G>C	chr11.hg19:g.58125852C>G	ENSP00000349945:p.Gly231Arg	147.0	0.0		91.0	43.0	NM_001005489	Q6IEX1	Missense_Mutation	SNP	ENST00000357377.3	hg19	CCDS31548.1	.	.	.	.	.	.	.	.	.	.	c	13.45	2.241382	0.39598	.	.	ENSG00000197786	ENST00000357377	T	0.00295	8.25	3.27	3.27	0.37495	GPCR, rhodopsin-like superfamily (1);	0.210963	0.23587	N	0.046588	T	0.00637	0.0021	M	0.83012	2.62	0.22330	N	0.999195	D	0.65815	0.995	D	0.63877	0.919	T	0.34976	-0.9807	10	0.87932	D	0	-0.8625	13.3041	0.60342	0.0:1.0:0.0:0.0	.	231	Q8NGF7	OR5BH_HUMAN	R	231	ENSP00000349945:G231R	ENSP00000349945:G231R	G	-	1	0	OR5B17	57882428	0.000000	0.05858	0.013000	0.15412	0.008000	0.06430	0.301000	0.19174	1.667000	0.50832	0.461000	0.40582	GGA	.	.		0.358	OR5B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394708.2	NM_001005489		G	58125852	C	G	58125852	3	3	38	1	0	0	0	0	1	0	0	0	11158	632	22	4	255	4	OR5B17	11	58125852	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	6713680	58125852	76880664	95	4542										
TYR	7299	hgsc.bcm.edu	37	chr11	88911272	88911272	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gtccctgtggccagctttcaGgcagaggttcctgtcagaat	12	11	2	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr11:88911272G>A	ENST00000263321.5	+	1	653	c.151G>A	c.(151-153)Ggc>Agc	p.G51S	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	51					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G51S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	CCAGCTTTCAGGCAGAGGTTC	0.562																																					p.G51S		Atlas-SNP	.											TYR,NS,carcinoma,-1,1	TYR	130	.	1	Substitution - Missense(1)	lung(1)	c.G151A	GRCh37	HM070075	TYR	M		.						61	52	55					11																	88911272		2201	4299	6500	SO:0001583	missense	7299	exon1			CTTTCAGGCAGAG	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"oculocutaneous albinism IA"	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.151G>A	chr11.hg19:g.88911272G>A	ENSP00000263321:p.Gly51Ser	112.0	0.0		98.0	32.0	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	hg19	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.364750	0.61513	.	.	ENSG00000077498	ENST00000263321	D	0.99454	-5.92	6.07	6.07	0.98685	.	0.095612	0.64402	D	0.000001	D	0.98887	0.9623	M	0.90870	3.155	0.53688	D	0.99997	P	0.35307	0.494	B	0.27608	0.081	D	0.98012	1.0366	9	.	.	.	.	14.2203	0.65823	0.0761:0.0:0.9239:0.0	.	51	P14679	TYRO_HUMAN	S	51	ENSP00000263321:G51S	.	G	+	1	0	TYR	88550920	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	5.945000	0.70226	2.885000	0.99019	0.655000	0.94253	GGC	.	.		0.562	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		A	88911272	G	A	88911272	3	1	38	1	0	0	0	0	1	0	0	0	16828	1000	35	3	153	3	TYR	11	88911272	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	30785420	88911272	46095244	96	4543										
ST14	6768	hgsc.bcm.edu	37	chr11	130058534	130058534	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	actgagtttgtaagcctggcCagcaaggtgaaggacgcggt	15	8	0	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr11:130058534C>T	ENST00000278742.5	+	3	769	c.351C>T	c.(349-351)gcC>gcT	p.A117A		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	117	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	TAAGCCTGGCCAGCAAGGTGA	0.572																																					p.A117A		Atlas-SNP	.											.	ST14	82	.	0			c.C351T						.						99	89	92					11																	130058534		2201	4297	6498	SO:0001819	synonymous_variant	6768	exon3			CCTGGCCAGCAAG	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"Serine peptidases / Transmembrane"	11344	protein-coding gene	gene with protein product	"epithin", "matriptase"	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.351C>T	chr11.hg19:g.130058534C>T		62.0	0.0		89.0	37.0	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Silent	SNP	ENST00000278742.5	hg19	CCDS8487.1																																																																																			.	.		0.572	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1			T	130058534	C	T	130058534	2	4	38	1	0	0	0	0	0	0	0	1	15226	581	21	3		3	ST14	11	130058534	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	41147262	130058534	4947982	97	4544										
TMPRSS12	283471	hgsc.bcm.edu	37	chr12	51237659	51237659	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccgcttaaggatgtgttgcaAgggtctcggattataggggg	16	6	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:51237659A>G	ENST00000398458.3	+	2	254	c.222A>G	c.(220-222)caA>caG	p.Q74Q	RN7SL519P_ENST00000497925.2_RNA|TMPRSS12_ENST00000551456.1_Silent_p.Q74Q	NM_182559.2	NP_872365	Q86WS5	TMPSC_HUMAN	transmembrane (C-terminal) protease, serine 12	74						integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	18						ATGTGTTGCAAGGGTCTCGGA	0.443																																					p.Q74Q		Atlas-SNP	.											.	TMPRSS12	33	.	0			c.A222G						.						44	43	44					12																	51237659		1956	4134	6090	SO:0001819	synonymous_variant	283471	exon2			GTTGCAAGGGTCT	BC048112	CCDS44881.1	12q13.12	2014-08-12	2010-04-21		ENSG00000186452	ENSG00000186452		"Serine peptidases / Transmembrane"	28779	protein-coding gene	gene with protein product			"transmembrane protease, serine 12"				Standard	NM_182559		Approved	MGC57341, CT151	uc001rwx.4	Q86WS5	OTTHUMG00000169483	ENST00000398458.3:c.222A>G	chr12.hg19:g.51237659A>G		153.0	0.0		132.0	63.0	NM_182559	B9ZVX2	Silent	SNP	ENST00000398458.3	hg19	CCDS44881.1																																																																																			.	.		0.443	TMPRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404289.1	NM_182559		G	51237659	A	G	51237659	2	3	38	1	0	0	0	0	0	0	0	1	16259	69	3	2		2	TMPRSS12	12	51237659	Silent	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10		51237659	82614236	98	4545										
KRT75	9119	hgsc.bcm.edu	37	chr12	52822123	52822123	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	atgttcatcagctcctggtaCtcacgcaggagccgagccat	10	13	3	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:52822123C>A	ENST00000252245.5	-	7	1519	c.1299G>T	c.(1297-1299)gaG>gaT	p.E433D	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	433	Coil 2.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		GCTCCTGGTACTCACGCAGGA	0.622																																					p.E433D		Atlas-SNP	.											.	KRT75	75	.	0			c.G1299T						.						60	48	52					12																	52822123		2203	4300	6503	SO:0001583	missense	9119	exon7			CTGGTACTCACGC	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"-", "Intermediate filaments type II, keratins (basic)"	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.1299G>T	chr12.hg19:g.52822123C>A	ENSP00000252245:p.Glu433Asp	108.0	0.0		104.0	50.0	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	hg19	CCDS8827.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.149869	0.57151	.	.	ENSG00000170454	ENST00000252245	D	0.92805	-3.11	5.63	3.8	0.43715	Filament (1);	0.000000	0.53938	D	0.000042	D	0.89406	0.6706	L	0.38733	1.17	0.39639	D	0.97029	B	0.31705	0.336	P	0.44921	0.464	D	0.86838	0.2015	10	0.46703	T	0.11	.	6.1396	0.20253	0.1305:0.6619:0.0:0.2076	.	433	O95678	K2C75_HUMAN	D	433	ENSP00000252245:E433D	ENSP00000252245:E433D	E	-	3	2	KRT75	51108390	0.934000	0.31675	1.000000	0.80357	0.988000	0.76386	0.132000	0.15891	1.382000	0.46385	0.561000	0.74099	GAG	.	.		0.622	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693		A	52822123	C	A	52822123	3	1	38	1	0	0	0	0	1	0	0	0	8497	564	20	3	368	3	KRT75	12	52822123	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	1584464	52822123	81029772	99	4546										
KRT6B	3854	hgsc.bcm.edu	37	chr12	52841356	52841356	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tccaacgccttcgccattcaGcctgtggagaggaacacagg	11	13	1	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:52841356G>A	ENST00000252252.3	-	8	1473	c.1426C>T	c.(1426-1428)Ctg>Ttg	p.L476L		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	476	Tail.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		TCGCCATTCAGCCTGTGGAGA	0.557																																					p.L476L		Atlas-SNP	.											.	KRT6B	90	.	0			c.C1426T						.						126	101	109					12																	52841356		2203	4300	6503	SO:0001630	splice_region_variant	3854	exon8			CATTCAGCCTGTG	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"-", "Intermediate filaments type II, keratins (basic)"	6444	protein-coding gene	gene with protein product		148042	"keratin-like 1 (a type II keratin sequence)"	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.1425-1C>T	chr12.hg19:g.52841356G>A		219.0	0.0		205.0	90.0	NM_005555	P48669	Silent	SNP	ENST00000252252.3	hg19	CCDS8828.1																																																																																			.	.		0.557	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	Silent	A	52841356	G	A	52841356	5	1	38	1	0	0	0	0	0	0	1	0	8490	985	34	3	276	3	KRT6B	12	52841356	Splice_Site	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	19233	52841356	81010539	100	4547										
AMHR2	269	hgsc.bcm.edu	37	chr12	53823987	53823987	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agaactgggcaatacccctaCctctgatgagctatgggcct	10	12	1	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:53823987C>A	ENST00000257863.4	+	10	1426	c.1346C>A	c.(1345-1347)aCc>aAc	p.T449N	AMHR2_ENST00000379791.3_Intron|AMHR2_ENST00000550311.1_Missense_Mutation_p.P448T	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	449	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Missing (in PMDS2). {ECO:0000269|PubMed:8872466}.		Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	AATACCCCTACCTCTGATGAG	0.587																																					p.T449N		Atlas-SNP	.											.	AMHR2	61	.	0			c.C1346A						.						246	210	222					12																	53823987		2203	4300	6503	SO:0001583	missense	269	exon10			CCCCTACCTCTGA	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"Muellerian inhibiting substance type II receptor"	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.1346C>A	chr12.hg19:g.53823987C>A	ENSP00000257863:p.Thr449Asn	219.0	0.0		218.0	110.0	NM_020547	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Missense_Mutation	SNP	ENST00000257863.4	hg19	CCDS8858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.028|8.028	0.761140|0.761140	0.15914|0.15914	.|.	.|.	ENSG00000135409|ENSG00000135409	ENST00000550311|ENST00000257863	D|D	0.93019|0.93488	-3.15|-3.23	5.09|5.09	3.1|3.1	0.35709|0.35709	.|Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.384005	.|0.19286	.|N	.|0.118025	D|D	0.91945|0.91945	0.7449|0.7449	L|L	0.43598|0.43598	1.365|1.365	0.80722|0.80722	D|D	1|1	B|P	0.30281|0.47484	0.275|0.896	B|P	0.28232|0.48270	0.087|0.572	D|D	0.91121|0.91121	0.4930|0.4930	9|10	0.72032|0.87932	D|D	0.01|0	.|.	13.1494|13.1494	0.59480|0.59480	0.0:0.599:0.401:0.0|0.0:0.599:0.401:0.0	.|.	448|449	F8W1D2|Q16671	.|AMHR2_HUMAN	T|N	448|449	ENSP00000446661:P448T|ENSP00000257863:T449N	ENSP00000446661:P448T|ENSP00000257863:T449N	P|T	+|+	1|2	0|0	AMHR2|AMHR2	52110254|52110254	0.234000|0.234000	0.23783|0.23783	0.272000|0.272000	0.24630|0.24630	0.478000|0.478000	0.33099|0.33099	0.589000|0.589000	0.23939|0.23939	0.708000|0.708000	0.31955|0.31955	0.557000|0.557000	0.71058|0.71058	CCT|ACC	.	.		0.587	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547		A	53823987	C	A	53823987	3	1	38	1	0	0	0	0	1	0	0	0	573	507	18	3	1384	3	AMHR2	12	53823987	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	982631	53823987	80027908	101	4548										
HOXC10	3226	hgsc.bcm.edu	37	chr12	54382961	54382961	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tatttttaacagaggagataAaggcagaaaacaccacagga	9	6	0	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:54382961A>G	ENST00000303460.4	+	2	834	c.760A>G	c.(760-762)Aag>Gag	p.K254E	MIR196A2_ENST00000385189.1_RNA|HOXC10_ENST00000511575.1_3'UTR|RP11-834C11.12_ENST00000513209.1_Intron	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	254					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|neuromuscular process (GO:0050905)|positive regulation of cell proliferation (GO:0008284)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(3)|lung(14)|pancreas(1)	20						AGAGGAGATAAAGGCAGAAAA	0.468											OREG0021882	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K254E		Atlas-SNP	.											.	HOXC10	42	.	0			c.A760G						.						55	53	54					12																	54382961		2203	4300	6503	SO:0001583	missense	3226	exon2			GAGATAAAGGCAG		CCDS8868.1	12q13.13	2011-06-20	2005-12-22		ENSG00000180818	ENSG00000180818		"Homeoboxes / ANTP class : HOXL subclass"	5122	protein-coding gene	gene with protein product		605560	"homeo box C10"	HOX3I		1358459	Standard	NM_017409		Approved		uc001sen.3	Q9NYD6	OTTHUMG00000160031	ENST00000303460.4:c.760A>G	chr12.hg19:g.54382961A>G	ENSP00000307321:p.Lys254Glu	174.0	0.0	999	127.0	61.0	NM_017409	O15219|O15220|Q9BVD5	Missense_Mutation	SNP	ENST00000303460.4	hg19	CCDS8868.1	.	.	.	.	.	.	.	.	.	.	A	14.30	2.494829	0.44352	.	.	ENSG00000180818	ENST00000303460	D	0.92199	-2.99	3.97	3.97	0.46021	Homeodomain-like (1);	0.055946	0.64402	D	0.000002	D	0.91855	0.7422	M	0.81497	2.545	0.80722	D	1	B	0.22276	0.067	B	0.27076	0.076	D	0.91285	0.5054	10	0.87932	D	0	.	12.5235	0.56073	1.0:0.0:0.0:0.0	.	254	Q9NYD6	HXC10_HUMAN	E	254	ENSP00000307321:K254E	ENSP00000307321:K254E	K	+	1	0	HOXC10	52669228	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.434000	0.59935	1.743000	0.51761	0.374000	0.22700	AAG	.	.		0.468	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2			G	54382961	A	G	54382961	3	3	38	1	0	0	0	0	1	0	0	0	7318	15	1	2	766	2	HOXC10	12	54382961	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	558974	54382961	79468934	102	4549										
CCDC59	29080	hgsc.bcm.edu	37	chr12	82752141	82752141	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggccgccacttcgcggaccgCctcaccggcgccattgcagc	12	19	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:82752141C>A	ENST00000256151.7	-	1	426	c.15G>T	c.(13-15)agG>agT	p.R5S	CCDC59_ENST00000548126.1_Intron|METTL25_ENST00000248306.3_5'Flank	NM_014167.4	NP_054886.2	Q9P031	TAP26_HUMAN	coiled-coil domain containing 59	5					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)	5						TCGCGGACCGCCTCACCGGCG	0.577											OREG0022008	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R5S		Atlas-SNP	.											.	CCDC59	17	.	0			c.G15T						.						33	34	34					12																	82752141		2203	4300	6503	SO:0001583	missense	29080	exon1			GGACCGCCTCACC	AF213377	CCDS9023.1	12q21.31	2007-10-17				ENSG00000133773			25005	protein-coding gene	gene with protein product						16630564, 12882447	Standard	NM_014167		Approved	HSPC128, TAP26, BR22	uc001szp.4	Q9P031		ENST00000256151.7:c.15G>T	chr12.hg19:g.82752141C>A	ENSP00000256151:p.Arg5Ser	38.0	0.0	1216	53.0	24.0	NM_014167	Q9H2V5|Q9NW62	Missense_Mutation	SNP	ENST00000256151.7	hg19	CCDS9023.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.528422	0.44969	.	.	ENSG00000133773	ENST00000552377;ENST00000256151	.	.	.	5.13	2.25	0.28309	.	0.509953	0.19603	N	0.110325	T	0.27866	0.0686	L	0.34521	1.04	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.16453	-1.0402	9	0.38643	T	0.18	-1.7965	6.1651	0.20386	0.0:0.6759:0.1534:0.1707	.	5	Q9P031	TAP26_HUMAN	S	5	.	ENSP00000256151:R5S	R	-	3	2	CCDC59	81276272	0.000000	0.05858	0.033000	0.17914	0.154000	0.21943	-0.066000	0.11598	0.174000	0.19809	-0.225000	0.12378	AGG	.	.		0.577	CCDC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408186.1	NM_014167		A	82752141	C	A	82752141	3	1	38	1	0	0	0	0	1	0	0	0	2831	738	26	3	726	3	CCDC59	12	82752141	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	28369180	82752141	51099754	103	4550										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85546125	85546125	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ttcacaaacactgcttctttCaaaccagctgcattggccaa	5	13	3	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:85546125C>A	ENST00000393217.2	+	20	4458	c.4397C>A	c.(4396-4398)tCa>tAa	p.S1466*		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1466										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		CTGCTTCTTTCAAACCAGCTG	0.383																																					p.S1466X		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.C4397A						.						132	126	128					12																	85546125		1892	4114	6006	SO:0001587	stop_gained	84125	exon20			TTCTTTCAAACCA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.4397C>A	chr12.hg19:g.85546125C>A	ENSP00000376910:p.Ser1466*	253.0	0.0		225.0	102.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Nonsense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	C	43	10.329874	0.99384	.	.	ENSG00000133640	ENST00000393217	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8375	0.92168	0.0:1.0:0.0:0.0	.	.	.	.	X	1466	.	ENSP00000376910:S1466X	S	+	2	0	LRRIQ1	84070256	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	6.010000	0.70753	2.471000	0.83476	0.586000	0.80456	TCA	.	.		0.383	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		A	85546125	C	A	85546125	4	1	38	1	0	0	0	0	0	1	0	0	9038	838	29	3	4475	3	LRRIQ1	12	85546125	Nonsense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	2793984	85546125	48305770	104	4551										
DUSP6	1848	hgsc.bcm.edu	37	chr12	89744457	89744457	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgtatttaaactctcctgcgTtctcaaagagattcggcaaa	7	9	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:89744457T>C	ENST00000279488.7	-	2	1977	c.746A>G	c.(745-747)aAc>aGc	p.N249S	DUSP6_ENST00000547140.1_5'UTR|DUSP6_ENST00000308385.6_Intron|DUSP6_ENST00000547291.1_Missense_Mutation_p.N124S	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6	249	Tyrosine-protein phosphatase.				cell differentiation (GO:0030154)|dorsal/ventral pattern formation (GO:0009953)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|regulation of endodermal cell fate specification (GO:0042663)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of heart growth (GO:0060420)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			large_intestine(5)|lung(8)|skin(2)|urinary_tract(1)	16						CTCTCCTGCGTTCTCAAAGAG	0.478																																					p.N249S	Colon(132;3456 5224)	Atlas-SNP	.											.	DUSP6	30	.	0			c.A746G						.						155	165	161					12																	89744457		2203	4300	6503	SO:0001583	missense	1848	exon2			CCTGCGTTCTCAA	BC037236	CCDS9033.1, CCDS9034.1	12q22-q23	2011-06-09				ENSG00000139318		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3072	protein-coding gene	gene with protein product		602748				8626780, 9205128	Standard	NM_001946		Approved	MKP-3, PYST1	uc001tay.3	Q16828		ENST00000279488.7:c.746A>G	chr12.hg19:g.89744457T>C	ENSP00000279488:p.Asn249Ser	206.0	0.0		165.0	72.0	NM_001946	O75109|Q53Y75|Q9BSH6	Missense_Mutation	SNP	ENST00000279488.7	hg19	CCDS9033.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.148449	0.37923	.	.	ENSG00000139318	ENST00000279488;ENST00000547291	T;T	0.59638	0.25;0.25	5.64	5.64	0.86602	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	T	0.39600	0.1084	N	0.15975	0.35	0.80722	D	1	B	0.09022	0.002	B	0.11329	0.006	T	0.30297	-0.9983	10	0.09338	T	0.73	.	15.8683	0.79084	0.0:0.0:0.0:1.0	.	249	Q16828	DUS6_HUMAN	S	249;124	ENSP00000279488:N249S;ENSP00000449838:N124S	ENSP00000279488:N249S	N	-	2	0	DUSP6	88268588	1.000000	0.71417	0.996000	0.52242	0.923000	0.55619	7.970000	0.88000	2.148000	0.66965	0.533000	0.62120	AAC	.	.		0.478	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	NM_001946, NM_022652		C	89744457	T	C	89744457	3	2	38	1	0	0	0	0	1	0	0	0	4831	1725	60	2	407	2	DUSP6	12	89744457	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	4198332	89744457	44107438	105	4552										
ANO4	121601	hgsc.bcm.edu	37	chr12	101491695	101491695	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	taatggtgctaaagcagaccTggaataatttcatggaactt	9	6	1	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:101491695T>A	ENST00000392977.3	+	21	2188	c.1978T>A	c.(1978-1980)Tgg>Agg	p.W660R	ANO4_ENST00000550015.1_Missense_Mutation_p.W180R|ANO4_ENST00000299222.9_Missense_Mutation_p.W180R|ANO4_ENST00000392979.3_Missense_Mutation_p.W625R			Q32M45	ANO4_HUMAN	anoctamin 4	660					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						aaagcagacctggaataattt	0.413										HNSCC(74;0.22)																											p.W625R		Atlas-SNP	.											.	ANO4	183	.	0			c.T1873A						.						167	153	158					12																	101491695		2203	4300	6503	SO:0001583	missense	121601	exon20			CAGACCTGGAATA	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.1978T>A	chr12.hg19:g.101491695T>A	ENSP00000376703:p.Trp660Arg	316.0	0.0		231.0	112.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	hg19		.	.	.	.	.	.	.	.	.	.	T	23.0	4.367818	0.82463	.	.	ENSG00000151572	ENST00000392979;ENST00000299222;ENST00000392977;ENST00000550015	T;T;T;T	0.62498	0.02;0.02;0.02;0.02	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.76877	0.4049	M	0.65498	2.005	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.91635	0.999;0.999;0.999	T	0.74481	-0.3651	10	0.29301	T	0.29	.	16.0993	0.81158	0.0:0.0:0.0:1.0	.	180;660;625	Q32M45-3;Q32M45;Q32M45-2	.;ANO4_HUMAN;.	R	625;180;660;180	ENSP00000376705:W625R;ENSP00000299222:W180R;ENSP00000376703:W660R;ENSP00000450192:W180R	ENSP00000299222:W180R	W	+	1	0	ANO4	100015826	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.846000	0.86887	2.207000	0.71202	0.459000	0.35465	TGG	.	.		0.413	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		A	101491695	T	A	101491695	3	1	38	1	0	0	0	0	1	0	0	0	699	1580	55	4	1947	4	ANO4	12	101491695	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	11747238	101491695	32360200	106	4553										
ACACB	32	hgsc.bcm.edu	37	chr12	109637346	109637347	+	Missense_Mutation	DNP	GC	GC	CT													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ttgaggctgggagcagctacGctgagatggaggtgactgca							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:109637346_109637347GC>CT	ENST00000338432.7	+	18	2886_2887	c.2767_2768GC>CT	c.(2767-2769)GCt>CTt	p.A923L	ACACB_ENST00000377854.5_Missense_Mutation_p.A923L|ACACB_ENST00000377848.3_Missense_Mutation_p.A923L			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	923	Biotinyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GAGCAGCTACGCTGAGATGGAG	0.584																																					p.A923P|p.A923V		Atlas-SNP	.											.	ACACB	330	.	0			c.G2767C|c.C2768T						.																																			SO:0001583	missense	32	exon17			AGCTACGCTGAGA|GCTACGCTGAGAT	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	Exception_encountered	chr12.hg19:g.109637346_109637347delinsCT	ENSP00000341044:p.Ala923Leu	54.0|53.0	0.0		31.0	26.0|24.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1																																																																																			.	.		0.584	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		CT	109637347	GC	CT	109637346	3	2	38	1	0	0	0	0	1	0	0	0	107	1087	38	4	2833	4	ACACB	12	109637346	Missense_Mutation	DNP	GC	TCGA-BC-A10Z-01A-11D-A12Z-10	8145651	109637346	24214549	107	4554										
NAA25	80018	hgsc.bcm.edu	37	chr12	112499100	112499100	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gtcagctgcaccacacacaaAtgttgctgcagagctctgat	9	12	2	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:112499100A>T	ENST00000261745.4	-	12	1490	c.1242T>A	c.(1240-1242)caT>caA	p.H414Q	RP1-267L14.3_ENST00000551125.1_RNA	NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	414						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						CCACACACAAATGTTGCTGCA	0.448																																					p.H414Q		Atlas-SNP	.											.	NAA25	105	.	0			c.T1242A						.						112	102	106					12																	112499100		2203	4300	6503	SO:0001583	missense	80018	exon12			ACACAAATGTTGC	AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"N(alpha)-acetyltransferase subunits"	25783	protein-coding gene	gene with protein product		612755	"chromosome 12 open reading frame 30"	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.1242T>A	chr12.hg19:g.112499100A>T	ENSP00000261745:p.His414Gln	163.0	0.0		202.0	95.0	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	hg19	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.123296	0.77436	.	.	ENSG00000111300	ENST00000261745	T	0.44083	0.93	5.84	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.63414	0.2509	M	0.84585	2.705	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.64706	-0.6344	10	0.38643	T	0.18	-17.2825	8.4538	0.32886	0.7962:0.0:0.2038:0.0	.	414;414	A8K8X0;Q14CX7	.;NAA25_HUMAN	Q	414	ENSP00000261745:H414Q	ENSP00000261745:H414Q	H	-	3	2	NAA25	110983483	0.987000	0.35691	1.000000	0.80357	0.996000	0.88848	0.911000	0.28584	2.234000	0.73211	0.528000	0.53228	CAT	.	.		0.448	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		T	112499100	A	T	112499100	3	4	38	1	0	0	0	0	1	0	0	0	10130	98	4	4	1728	4	NAA25	12	112499100	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	2861754	112499100	21352795	108	4555										
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123474487	123474487	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gggggtatggctgagcgcatCgggggcctctgagaagcaag	19	8	1	2	rs563437854		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:123474487C>A	ENST00000542749.1	-	16	2641	c.2578G>T	c.(2578-2580)Gat>Tat	p.D860Y	PITPNM2_ENST00000280562.5_Intron|PITPNM2_ENST00000320201.4_Missense_Mutation_p.D860Y|PITPNM2_ENST00000392428.1_Missense_Mutation_p.D581Y			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	860	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CTGAGCGCATCGGGGGCCTCT	0.701																																					p.D860Y		Atlas-SNP	.											.	PITPNM2	105	.	0			c.G2578T						.						4	4	4					12																	123474487		1755	3485	5240	SO:0001583	missense	57605	exon17			GCGCATCGGGGGC	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.2578G>T	chr12.hg19:g.123474487C>A	ENSP00000437611:p.Asp860Tyr	15.0	0.0		20.0	9.0	NM_020845	Q9P271	Missense_Mutation	SNP	ENST00000542749.1	hg19	CCDS9242.1	.	.	.	.	.	.	.	.	.	.	c	5.685	0.310961	0.10733	.	.	ENSG00000090975	ENST00000320201;ENST00000392428;ENST00000542749	T;T;T	0.42900	1.29;0.96;1.29	4.66	-2.26	0.06867	DDHD (2);	2.637130	0.01909	U	0.039711	T	0.18341	0.0440	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.07139	-1.0788	10	0.15066	T	0.55	0.0	0.3664	0.00372	0.3334:0.2117:0.1245:0.3303	.	860	Q9BZ72	PITM2_HUMAN	Y	860;581;860	ENSP00000322218:D860Y;ENSP00000376223:D581Y;ENSP00000437611:D860Y	ENSP00000322218:D860Y	D	-	1	0	PITPNM2	122040440	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.318000	0.02705	-0.080000	0.12685	-0.370000	0.07254	GAT	.	.		0.701	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		A	123474487	C	A	123474487	3	1	38	1	0	0	0	0	1	0	0	0	11960	884	31	1	1507	1	PITPNM2	12	123474487	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	10975387	123474487	10377408	109	4556										
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123497236	123497236	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccagcatcagttttataaaaGgtttcaatgtcgatggagaa	9	6	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr12:123497236G>A	ENST00000542749.1	-	3	402	c.339C>T	c.(337-339)acC>acT	p.T113T	PITPNM2_ENST00000280562.5_Silent_p.T113T|PITPNM2_ENST00000451868.2_5'UTR|MIR4304_ENST00000580964.1_RNA|PITPNM2_ENST00000546049.1_Silent_p.T113T|PITPNM2_ENST00000320201.4_Silent_p.T113T|PITPNM2_ENST00000392428.1_Intron			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	113					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)	p.T113T(1)		NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		TTTTATAAAAGGTTTCAATGT	0.507																																					p.T113T		Atlas-SNP	.											PITPNM2,NS,carcinoma,0,1	PITPNM2	105	.	1	Substitution - coding silent(1)	ovary(1)	c.C339T						.						154	166	162					12																	123497236		2203	4300	6503	SO:0001819	synonymous_variant	57605	exon4			ATAAAAGGTTTCA	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.339C>T	chr12.hg19:g.123497236G>A		145.0	0.0		116.0	48.0	NM_020845	Q9P271	Silent	SNP	ENST00000542749.1	hg19	CCDS9242.1																																																																																			.	.		0.507	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		A	123497236	G	A	123497236	2	1	38	1	0	0	0	0	0	0	0	1	11960	987	35	3		3	PITPNM2	12	123497236	Silent	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	22749	123497236	10354659	110	4557										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24797411	24797411	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccggaaaatgggatcctttaAgaaactgaagtcctcagtcc	9	10	1	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr13:24797411A>T	ENST00000382095.4	+	2	185				SPATA13_ENST00000424834.2_Missense_Mutation_p.K115M|SPATA13_ENST00000382108.3_Missense_Mutation_p.K115M|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.K115M	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		GGATCCTTTAAGAAACTGAAG	0.577																																					p.K115M		Atlas-SNP	.											.	SPATA13	92	.	0			c.A344T						.						29	33	32					13																	24797411		692	1591	2283	SO:0001627	intron_variant	221178	exon2			CCTTTAAGAAACT	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.-222-26204A>T	chr13.hg19:g.24797411A>T		45.0	0.0		58.0	27.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	hg19	CCDS9305.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.86|18.86	3.713979|3.713979	0.68730|0.68730	.|.	.|.	ENSG00000182957|ENSG00000182957	ENST00000382108|ENST00000424834	D|.	0.86097|.	-2.07|.	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	0.000000|.	0.39544|.	U|.	0.001339|.	T|.	0.62134|.	0.2403|.	L|L	0.47190|0.47190	1.495|1.495	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.59799|.	-0.7386|.	8|.	0.87932|.	D|.	0|.	.|.	14.6861|14.6861	0.69049|0.69049	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	M|Y	115|152	ENSP00000371542:K115M|.	ENSP00000371542:K115M|.	K|X	+|+	2|3	0|2	SPATA13|SPATA13	23695411|23695411	1.000000|1.000000	0.71417|0.71417	0.069000|0.069000	0.20011|0.20011	0.637000|0.637000	0.38172|0.38172	7.857000|7.857000	0.86963|0.86963	2.136000|2.136000	0.66102|0.66102	0.392000|0.392000	0.25879|0.25879	AAG|TAA	.	.		0.577	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		T	24797411	A	T	24797411	1	4	38	0	1	0	0	0	0	0	0	0	15015	72	3	4		4	SPATA13	13	24797411	Intron	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10		24797411	90372467	111	4558										
N4BP2L2	10443	hgsc.bcm.edu	37	chr13	33017687	33017687	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	atgggttcatgtgagagattTttatctactatttctctctt	7	6	4	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr13:33017687T>C	ENST00000504114.1	-	6	1033	c.942A>G	c.(940-942)aaA>aaG	p.K314K	N4BP2L2_ENST00000446957.2_Intron|N4BP2L2_ENST00000380121.3_5'UTR|N4BP2L2_ENST00000399396.3_Silent_p.K329K|N4BP2L2_ENST00000357505.6_Silent_p.K314K			Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	0					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		GTGAGAGATTTTTATCTACTA	0.348																																					p.K329K		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.A987G						.						47	44	45					13																	33017687		1826	4074	5900	SO:0001819	synonymous_variant	10443	exon7			GAGATTTTTATCT	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"phosphonoformate immuno-associated protein 5"	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000504114.1:c.942A>G	chr13.hg19:g.33017687T>C		379.0	0.0		331.0	175.0	NM_033111	A3KME8	Silent	SNP	ENST00000504114.1	hg19																																																																																				.	.		0.348	N4BP2L2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000361380.1	NM_014887		C	33017687	T	C	33017687	2	2	38	1	0	0	0	0	0	0	0	1	10121	1838	64	2		2	N4BP2L2	13	33017687	Silent	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	8220276	33017687	82152191	112	4559										
POSTN	10631	hgsc.bcm.edu	37	chr13	38164531	38164531	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aatccaagttgtcccaagccTcattactcggtgcaaagtaa	7	11	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr13:38164531T>A	ENST00000379747.4	-	4	536	c.419A>T	c.(418-420)gAg>gTg	p.E140V	POSTN_ENST00000379749.4_Missense_Mutation_p.E140V|POSTN_ENST00000541481.1_Missense_Mutation_p.E140V|POSTN_ENST00000541179.1_Missense_Mutation_p.E140V|POSTN_ENST00000379742.4_Missense_Mutation_p.E140V|POSTN_ENST00000379743.4_Missense_Mutation_p.E140V	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	140	FAS1 1. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		GTCCCAAGCCTCATTACTCGG	0.388																																					p.E140V		Atlas-SNP	.											.	POSTN	161	.	0			c.A419T						.						100	84	89					13																	38164531		2203	4300	6503	SO:0001583	missense	10631	exon4			CAAGCCTCATTAC	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.419A>T	chr13.hg19:g.38164531T>A	ENSP00000369071:p.Glu140Val	93.0	0.0		57.0	23.0	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	hg19	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.577221	0.86645	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481;ENST00000538347	D;D;D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11;-3.11;-3.11	5.36	5.36	0.76844	FAS1 domain (5);	0.261736	0.43579	D	0.000555	D	0.96519	0.8864	M	0.90369	3.11	0.58432	D	0.999997	D;D;D;D;D;D;D	0.76494	0.994;0.987;0.996;0.987;0.999;0.999;0.999	D;P;D;P;D;D;D	0.68621	0.91;0.854;0.93;0.854;0.911;0.953;0.959	D	0.97283	0.9919	10	0.72032	D	0.01	-4.8692	15.3597	0.74460	0.0:0.0:0.0:1.0	.	140;140;140;140;140;140;140	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	V	140;140;140;140;140;140;57	ENSP00000437959:E140V;ENSP00000369073:E140V;ENSP00000369071:E140V;ENSP00000369067:E140V;ENSP00000369066:E140V;ENSP00000437953:E140V	ENSP00000369066:E140V	E	-	2	0	POSTN	37062531	1.000000	0.71417	0.981000	0.43875	0.970000	0.65996	7.698000	0.84413	2.036000	0.60181	0.528000	0.53228	GAG	.	.		0.388	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		A	38164531	T	A	38164531	3	1	38	1	0	0	0	0	1	0	0	0	12268	1551	54	4	2171	4	POSTN	13	38164531	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	5146844	38164531	77005347	113	4560										
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42293771	42293771	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggctttgctccgataggtatCccgtatttgtgtaaagtgtt	11	7	0	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr13:42293771C>A	ENST00000379310.3	-	26	3140	c.3072G>T	c.(3070-3072)ggG>ggT	p.G1024G	VWA8_ENST00000281496.6_Silent_p.G1024G	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1024						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										CGATAGGTATCCCGTATTTGT	0.403																																					p.G1024G		Atlas-SNP	.											.	.	.	.	0			c.G3072T						.						190	163	172					13																	42293771		2203	4300	6503	SO:0001819	synonymous_variant	23078	exon26			AGGTATCCCGTAT	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.3072G>T	chr13.hg19:g.42293771C>A		307.0	0.0		312.0	120.0	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Silent	SNP	ENST00000379310.3	hg19	CCDS41881.1																																																																																			.	.		0.403	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		A	42293771	C	A	42293771	2	1	38	1	0	0	0	0	0	0	0	1	8194	842	30	3		3	KIAA0564	13	42293771	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	4129240	42293771	72876107	114	4561										
JPH4	84502	hgsc.bcm.edu	37	chr14	24040535	24040535	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggcagggggtcgccagggttGgcgggaggaggcaggactgc	23	8	0	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr14:24040535G>A	ENST00000397118.3	-	6	2307	c.1405C>T	c.(1405-1407)Caa>Taa	p.Q469*	JPH4_ENST00000356300.4_Nonsense_Mutation_p.Q469*|JPH4_ENST00000544177.1_Nonsense_Mutation_p.Q134*	NM_032452.2	NP_115828.2	Q96JJ6	JPH4_HUMAN	junctophilin 4	469					calcium ion transport into cytosol (GO:0060402)|learning (GO:0007612)|neuromuscular process controlling balance (GO:0050885)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic plasticity (GO:0048167)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)				endometrium(1)|large_intestine(2)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		CGCCAGGGTTGGCGGGAGGAG	0.687																																					p.Q469X		Atlas-SNP	.											.	JPH4	64	.	0			c.C1405T						.						34	38	37					14																	24040535		2203	4300	6503	SO:0001587	stop_gained	84502	exon5			AGGGTTGGCGGGA	AB058734	CCDS9603.1	14q11	2004-05-28	2004-05-28	2004-05-28	ENSG00000092051	ENSG00000092051			20156	protein-coding gene	gene with protein product			"junctophilin like 1"	JPHL1		11347906	Standard	NM_032452		Approved	KIAA1831	uc001wkr.2	Q96JJ6	OTTHUMG00000028769	ENST00000397118.3:c.1405C>T	chr14.hg19:g.24040535G>A	ENSP00000380307:p.Gln469*	51.0	0.0		48.0	21.0	NM_001146028	D3DS53|Q8ND44|Q96DQ0	Nonsense_Mutation	SNP	ENST00000397118.3	hg19	CCDS9603.1	.	.	.	.	.	.	.	.	.	.	G	40	8.115515	0.98662	.	.	ENSG00000092051	ENST00000356300;ENST00000397118;ENST00000543864;ENST00000267407;ENST00000544177	.	.	.	5.17	4.22	0.49857	.	0.000000	0.29073	U	0.013231	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	10.4703	0.44633	0.0:0.0:0.8061:0.1939	.	.	.	.	X	469;469;469;470;134	.	ENSP00000267407:Q470X	Q	-	1	0	JPH4	23110375	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.703000	0.54808	2.575000	0.86900	0.655000	0.94253	CAA	.	.		0.687	JPH4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413853.1	NM_032452		A	24040535	G	A	24040535	4	1	38	1	0	0	0	0	0	1	0	0	7972	1357	47	3	489	3	JPH4	14	24040535	Nonsense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10		24040535	83309005	115	4562										
CLEC14A	161198	hgsc.bcm.edu	37	chr14	38724364	38724365	+	Missense_Mutation	DNP	GG	GG	AT													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gtcggctgtccttccccactGgtcacacaagagcggccgtc							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr14:38724364_38724365GG>AT	ENST00000342213.2	-	1	1209_1210	c.863_864CC>AT	c.(862-864)aCC>aAT	p.T288N		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	288						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		CTTCCCCACTGGTCACACAAGA	0.653																																					p.T288T|p.T288N		Atlas-SNP	.											.	CLEC14A	83	.	0			c.C864T|c.C863A						.																																			SO:0001583	missense	161198	exon1			CCCACTGGTCACA|CCACTGGTCACAC		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"C-type lectin domain containing"	19832	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 27"	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.863_864delinsAT	chr14.hg19:g.38724364_38724365delinsAT	ENSP00000353013:p.Thr288Asn	35.0|33.0	0.0		35.0	9.0	NM_175060	Q695G9|Q6PWT6|Q8N5V5	Silent|Missense_Mutation	SNP	ENST00000342213.2	hg19	CCDS9667.1																																																																																			.	.		0.653	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		AT	38724365	GG	AT	38724364	3	1	38	1	0	0	0	0	1	0	0	0	3501	1335	47	3	612	3	CLEC14A	14	38724364	Missense_Mutation	DNP	GG	TCGA-BC-A10Z-01A-11D-A12Z-10	14683829	38724364	68625176	116	4563										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68274384	68274384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cagggggcaccgaatcagggCcctgcaaagcccgcaatgcc	13	15	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr14:68274384C>T	ENST00000347230.4	-	5	755	c.617G>A	c.(616-618)gGc>gAc	p.G206D	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.G206D	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	206					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CGAATCAGGGCCCTGCAAAGC	0.602																																					p.G206D		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.G617A						.						72	72	72					14																	68274384		2203	4300	6503	SO:0001583	missense	23503	exon5			TCAGGGCCCTGCA	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.617G>A	chr14.hg19:g.68274384C>T	ENSP00000251119:p.Gly206Asp	40.0	0.0		19.0	13.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	C	1.532	-0.544116	0.04024	.	.	ENSG00000072121	ENST00000347230;ENST00000555452	T;T	0.26518	1.87;1.73	5.69	0.697	0.18081	.	0.542263	0.20668	N	0.087890	T	0.15003	0.0362	L	0.35723	1.085	0.09310	N	1	B;B;B	0.14438	0.01;0.002;0.0	B;B;B	0.13407	0.009;0.004;0.001	T	0.37197	-0.9716	10	0.05959	T	0.93	-2.7155	9.5295	0.39185	0.0:0.4255:0.0:0.5745	.	206;206;206	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	D	206	ENSP00000251119:G206D;ENSP00000450603:G206D	ENSP00000251119:G206D	G	-	2	0	ZFYVE26	67344137	0.066000	0.20996	0.233000	0.24025	0.272000	0.26649	0.584000	0.23864	0.052000	0.16007	0.491000	0.48974	GGC	.	.		0.602	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		T	68274384	C	T	68274384	3	4	38	1	0	0	0	0	1	0	0	0	17683	739	26	3	7154	3	ZFYVE26	14	68274384	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	29550020	68274384	39075156	117	4564										
ACTN1	87	hgsc.bcm.edu	37	chr14	69350972	69350972	+	Missense_Mutation	SNP	C	C	A													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ttgttgaagggtgcagcccgCttggcatactccaagtacag							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr14:69350972C>A	ENST00000193403.6	-	14	1931	c.1548G>T	c.(1546-1548)aaG>aaT	p.K516N	ACTN1_ENST00000376839.3_Missense_Mutation_p.K451N|ACTN1_ENST00000438964.2_Missense_Mutation_p.K516N|ACTN1_ENST00000538545.2_Missense_Mutation_p.K516N|ACTN1_ENST00000394419.4_Missense_Mutation_p.K516N	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	516	Interaction with DDN.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GTGCAGCCCGCTTGGCATACT	0.552																																					p.K516N		Atlas-SNP	.											.	ACTN1	77	.	0			c.G1548T						.						115	94	101					14																	69350972		2203	4300	6503	SO:0001583	missense	87	exon14			AGCCCGCTTGGCA	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"EF-hand domain containing"	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.1548G>T	chr14.hg19:g.69350972C>A	ENSP00000193403:p.Lys516Asn	251.0	1.0		122.0	111.0	NM_001102	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	hg19	CCDS9792.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.989389|3.989389	0.74589|0.74589	.|.	.|.	ENSG00000072110|ENSG00000072110	ENST00000553290|ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545;ENST00000544964	.|T;T;T;T;T;T	.|0.68624	.|-0.34;-0.34;-0.34;-0.34;-0.34;-0.34	4.68|4.68	4.68|4.68	0.58851|0.58851	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.83968|0.83968	0.5369|0.5369	M|M	0.89785|0.89785	3.06|3.06	0.80722|0.80722	D|D	1|1	.|D;D;D;P;D	.|0.71674	.|0.998;0.981;0.972;0.946;0.958	.|D;D;P;D;D	.|0.85130	.|0.997;0.962;0.891;0.935;0.914	D|D	0.86937|0.86937	0.2077|0.2077	5|10	.|0.87932	.|D	.|0	.|.	13.5873|13.5873	0.61940|0.61940	0.0:0.9223:0.0:0.0777|0.0:0.9223:0.0:0.0777	.|.	.|147;516;516;516;163	.|B7Z2W3;P12814-2;Q1HE25;P12814;B4DFY0	.|.;.;.;ACTN1_HUMAN;.	S|N	17|516;516;516;451;516;106	.|ENSP00000193403:K516N;ENSP00000377941:K516N;ENSP00000414272:K516N;ENSP00000366035:K451N;ENSP00000439828:K516N;ENSP00000444422:K106N	.|ENSP00000193403:K516N	A|K	-|-	1|3	0|2	ACTN1|ACTN1	68420725|68420725	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.869000|0.869000	0.49853|0.49853	1.358000|1.358000	0.34102|0.34102	2.597000|2.597000	0.87782|0.87782	0.655000|0.655000	0.94253|0.94253	GCG|AAG	.	.		0.552	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		A	69350972	C	A	69350972	3	1	38	1	0	0	0	0	1	0	0	0	204	796	28	3	1232	3	ACTN1	14	69350972	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	1076588	69350972	37998568	118	4565	17	2								
ACTN1	87	hgsc.bcm.edu	37	chr14	69350974	69350974	+	Missense_Mutation	SNP	T	T	C													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gttgaagggtgcagcccgctTggcatactccaagtacagct							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr14:69350974T>C	ENST00000193403.6	-	14	1929	c.1546A>G	c.(1546-1548)Aag>Gag	p.K516E	ACTN1_ENST00000376839.3_Missense_Mutation_p.K451E|ACTN1_ENST00000438964.2_Missense_Mutation_p.K516E|ACTN1_ENST00000538545.2_Missense_Mutation_p.K516E|ACTN1_ENST00000394419.4_Missense_Mutation_p.K516E	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	516	Interaction with DDN.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GCAGCCCGCTTGGCATACTCC	0.552																																					p.K516E		Atlas-SNP	.											.	ACTN1	77	.	0			c.A1546G						.						115	95	102					14																	69350974		2203	4300	6503	SO:0001583	missense	87	exon14			CCCGCTTGGCATA	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"EF-hand domain containing"	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.1546A>G	chr14.hg19:g.69350974T>C	ENSP00000193403:p.Lys516Glu	260.0	0.0		122.0	110.0	NM_001102	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	hg19	CCDS9792.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.1|28.1	4.894292|4.894292	0.91889|0.91889	.|.	.|.	ENSG00000072110|ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545;ENST00000544964|ENST00000553290	T;T;T;T;T;T|.	0.68025|.	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3|.	4.68|4.68	4.68|4.68	0.58851|0.58851	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77968|0.77968	0.4210|0.4210	M|M	0.84683|0.84683	2.71|2.71	0.80722|0.80722	D|D	1|1	D;P;P;B;B|.	0.63880|.	0.993;0.687;0.547;0.383;0.448|.	D;P;B;B;B|.	0.75484|.	0.986;0.78;0.365;0.403;0.428|.	T|T	0.81040|0.81040	-0.1113|-0.1113	10|5	0.87932|.	D|.	0|.	.|.	14.5916|14.5916	0.68368|0.68368	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	147;516;516;516;163|.	B7Z2W3;P12814-2;Q1HE25;P12814;B4DFY0|.	.;.;.;ACTN1_HUMAN;.|.	E|R	516;516;516;451;516;106|16	ENSP00000193403:K516E;ENSP00000377941:K516E;ENSP00000414272:K516E;ENSP00000366035:K451E;ENSP00000439828:K516E;ENSP00000444422:K106E|.	ENSP00000193403:K516E|.	K|Q	-|-	1|2	0|0	ACTN1|ACTN1	68420727|68420727	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.914000|0.914000	0.54420|0.54420	7.825000|7.825000	0.86693|0.86693	2.100000|2.100000	0.63781|0.63781	0.533000|0.533000	0.62120|0.62120	AAG|CAA	.	.		0.552	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		C	69350974	T	C	69350974	3	2	38	1	0	0	0	0	1	0	0	0	204	1821	63	2	1234	2	ACTN1	14	69350974	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	2	69350974	37998566	119	4566	17	2								
ACOT2	10965	hgsc.bcm.edu	37	chr14	74036182	74036182	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gccgctgctgctgggacgaaCcggtgcgaatcgccgtgcgc	16	14	0	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr14:74036182C>A	ENST00000238651.5	+	1	420	c.238C>A	c.(238-240)Ccg>Acg	p.P80T	ACOT2_ENST00000538782.1_Intron	NM_006821.5	NP_006812.3	P49753	ACOT2_HUMAN	acyl-CoA thioesterase 2	80					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(234;0.0033)|OV - Ovarian serous cystadenocarcinoma(108;0.0639)		CTGGGACGAACCGGTGCGAAT	0.701																																					p.P80T		Atlas-SNP	.											.	ACOT2	24	.	0			c.C238A						.						43	37	39					14																	74036182		2203	4299	6502	SO:0001583	missense	10965	exon1			GACGAACCGGTGC	AY005822, AK001939	CCDS9816.1	14q24.3	2013-09-20			ENSG00000119673	ENSG00000119673		"Acyl CoA thioesterases"	18431	protein-coding gene	gene with protein product	"mitochondrial acyl-CoA thioesterase 1"	609972				16103133, 16940157	Standard	NM_006821		Approved	Mte1, ZAP128	uc001xon.5	P49753	OTTHUMG00000171608	ENST00000238651.5:c.238C>A	chr14.hg19:g.74036182C>A	ENSP00000238651:p.Pro80Thr	61.0	0.0		47.0	41.0	NM_006821	Q3I5F8|Q53EK4|Q9NUX4	Missense_Mutation	SNP	ENST00000238651.5	hg19	CCDS9816.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.605985	0.46527	.	.	ENSG00000119673	ENST00000238651	T	0.70869	-0.52	3.81	2.91	0.33838	Acyl-CoA thioester hydrolase/bile acid-CoA amino acid N-acetyltransferase (1);	0.064498	0.64402	D	0.000008	D	0.86497	0.5947	H	0.94264	3.515	0.49582	D	0.999806	D	0.69078	0.997	D	0.70487	0.969	D	0.88288	0.2941	10	0.87932	D	0	-20.5873	11.4465	0.50127	0.0:0.9096:0.0:0.0904	.	80	P49753	ACOT2_HUMAN	T	80	ENSP00000238651:P80T	ENSP00000238651:P80T	P	+	1	0	ACOT2	73105935	1.000000	0.71417	0.348000	0.25681	0.012000	0.07955	2.796000	0.47869	0.705000	0.31890	0.467000	0.42956	CCG	.	.		0.701	ACOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414435.1	NM_006821		A	74036182	C	A	74036182	3	1	38	1	0	0	0	0	1	0	0	0	152	507	18	3	240	3	ACOT2	14	74036182	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	4685208	74036182	33313358	120	4567										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102478246	102478246	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tcagatcacccagatcaatcAtggcctgatgatggtggggc	12	10	4	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr14:102478246A>T	ENST00000360184.4	+	33	6817	c.6653A>T	c.(6652-6654)cAt>cTt	p.H2218L		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2218	AAA 2. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						CAGATCAATCATGGCCTGATG	0.602																																					p.H2218L		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A6653T						.						92	77	82					14																	102478246		2203	4300	6503	SO:0001583	missense	1778	exon33			TCAATCATGGCCT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.6653A>T	chr14.hg19:g.102478246A>T	ENSP00000348965:p.His2218Leu	131.0	0.0		118.0	61.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	A	34	5.332562	0.95733	.	.	ENSG00000197102	ENST00000360184	T	0.39406	1.08	5.8	5.8	0.92144	ATPase, AAA+ type, core (1);	0.044125	0.85682	D	0.000000	T	0.77525	0.4143	H	0.97635	4.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85982	0.1483	10	0.87932	D	0	.	16.1547	0.81649	1.0:0.0:0.0:0.0	.	2218	Q14204	DYHC1_HUMAN	L	2218	ENSP00000348965:H2218L	ENSP00000348965:H2218L	H	+	2	0	DYNC1H1	101547999	1.000000	0.71417	0.937000	0.37676	0.957000	0.61999	9.281000	0.95811	2.221000	0.72209	0.528000	0.53228	CAT	.	.		0.602	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102478246	A	T	102478246	3	4	38	1	0	0	0	0	1	0	0	0	4843	217	8	4	6783	4	DYNC1H1	14	102478246	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	28442064	102478246	4871294	121	4568										
ZFP106	64397	hgsc.bcm.edu	37	chr15	42734378	42734378	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gctcttgtttaatctgaactGatgagtctggagcagggaca	12	7	3	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr15:42734378G>A	ENST00000263805.4	-	7	3913	c.3587C>T	c.(3586-3588)tCa>tTa	p.S1196L	ZNF106_ENST00000565380.1_Missense_Mutation_p.S424L|ZNF106_ENST00000565611.1_Missense_Mutation_p.S381L	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	1196					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										AATCTGAACTGATGAGTCTGG	0.493																																					p.S1196L		Atlas-SNP	.											.	ZFP106	117	.	0			c.C3587T						.						153	141	145					15																	42734378		2203	4299	6502	SO:0001583	missense	64397	exon7			TGAACTGATGAGT	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"Zinc fingers, C2H2-type"	12886	protein-coding gene	gene with protein product	"SH3-domain binding protein 3"		"zinc finger protein 106 homolog (mouse)"	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.3587C>T	chr15.hg19:g.42734378G>A	ENSP00000263805:p.Ser1196Leu	262.0	0.0		241.0	116.0	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	hg19	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.701669	0.88924	.	.	ENSG00000103994	ENST00000263805;ENST00000434903	T	0.67698	-0.28	5.44	5.44	0.79542	.	0.162012	0.43260	D	0.000589	T	0.80396	0.4615	L	0.56769	1.78	0.53005	D	0.999967	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.986;0.994;0.986	T	0.81097	-0.1087	10	0.87932	D	0	-11.187	19.441	0.94821	0.0:0.0:1.0:0.0	.	424;1196;424	E9PE29;Q9H2Y7;B4DZ40	.;ZF106_HUMAN;.	L	1196;424	ENSP00000263805:S1196L	ENSP00000263805:S1196L	S	-	2	0	ZFP106	40521670	1.000000	0.71417	0.960000	0.40013	0.933000	0.57130	6.516000	0.73755	2.831000	0.97527	0.655000	0.94253	TCA	.	.		0.493	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		A	42734378	G	A	42734378	3	1	38	1	0	0	0	0	1	0	0	0	17652	1294	45	3	2116	3	ZFP106	15	42734378	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10		42734378	59797014	122	4569										
SPATA5L1	79029	hgsc.bcm.edu	37	chr15	45713263	45713263	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgctttgctggctctgcaagAaaatggactagacgcaacta	10	9	1	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr15:45713263A>G	ENST00000305560.6	+	8	2216	c.2117A>G	c.(2116-2118)gAa>gGa	p.E706G	SPATA5L1_ENST00000533841.1_3'UTR	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	706						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		GCTCTGCAAGAAAATGGACTA	0.373																																					p.E706G		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.A2117G						.						59	60	59					15																	45713263		2198	4298	6496	SO:0001583	missense	79029	exon8			TGCAAGAAAATGG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"ATPases / AAA-type"	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.2117A>G	chr15.hg19:g.45713263A>G	ENSP00000305494:p.Glu706Gly	99.0	0.0		84.0	41.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	hg19	CCDS10123.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.0|25.0	4.589728|4.589728	0.86851|0.86851	.|.	.|.	ENSG00000171763|ENSG00000171763	ENST00000305560|ENST00000531624	D|.	0.95482|.	-3.72|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	0.056632|.	0.64402|.	D|.	0.000001|.	T|T	0.60805|0.60805	0.2297|0.2297	L|L	0.43757|0.43757	1.38|1.38	0.80722|0.80722	D|D	1|1	P|.	0.36282|.	0.546|.	B|.	0.37387|.	0.248|.	T|T	0.57963|0.57963	-0.7720|-0.7720	10|5	0.87932|.	D|.	0|.	-28.6605|-28.6605	14.603|14.603	0.68456|0.68456	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	706|.	Q9BVQ7|.	SPA5L_HUMAN|.	G|E	706|211	ENSP00000305494:E706G|.	ENSP00000305494:E706G|.	E|K	+|+	2|1	0|0	SPATA5L1|SPATA5L1	43500555|43500555	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.849000|0.849000	0.48306|0.48306	7.021000|7.021000	0.76425|0.76425	2.127000|2.127000	0.65507|0.65507	0.459000|0.459000	0.35465|0.35465	GAA|AAA	.	.		0.373	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		G	45713263	A	G	45713263	3	3	38	1	0	0	0	0	1	0	0	0	15027	246	9	2	2147	2	SPATA5L1	15	45713263	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	2978885	45713263	56818129	123	4570										
FBN1	2200	hgsc.bcm.edu	37	chr15	48796007	48796007	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aattctgtgcaggacacggcTggcaaggttccccaaatgca	11	11	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr15:48796007T>G	ENST00000316623.5	-	17	2545	c.2090A>C	c.(2089-2091)cAg>cCg	p.Q697P		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	697	TB 3.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		AGGACACGGCTGGCAAGGTTC	0.493																																					p.Q697P		Atlas-SNP	.											.	FBN1	310	.	0			c.A2090C						.						151	128	136					15																	48796007		2197	4296	6493	SO:0001583	missense	2200	exon17			CACGGCTGGCAAG	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.2090A>C	chr15.hg19:g.48796007T>G	ENSP00000325527:p.Gln697Pro	259.0	1.0		223.0	96.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.539958	0.85917	.	.	ENSG00000166147	ENST00000316623	D	0.93307	-3.2	6.06	6.06	0.98353	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.85682	D	0.000000	D	0.95806	0.8635	M	0.79805	2.47	0.80722	D	1	D	0.61697	0.99	P	0.56343	0.796	D	0.95878	0.8896	10	0.59425	D	0.04	.	15.4333	0.75121	0.0:0.0:0.0:1.0	.	697	P35555	FBN1_HUMAN	P	697	ENSP00000325527:Q697P	ENSP00000325527:Q697P	Q	-	2	0	FBN1	46583299	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.139000	0.71728	2.324000	0.78689	0.533000	0.62120	CAG	.	.		0.493	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			G	48796007	T	G	48796007	3	3	38	1	0	0	0	0	1	0	0	0	5710	1580	55	5	6725	5	FBN1	15	48796007	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	3082744	48796007	53735385	124	4571										
ISL2	64843	hgsc.bcm.edu	37	chr15	76632729	76632729	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cagctgcacactctgcggacCtgctacgccgccaacccgcg	10	19	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr15:76632729C>G	ENST00000290759.4	+	4	784	c.624C>G	c.(622-624)acC>acG	p.T208T	RP11-685G9.2_ENST00000559539.1_RNA	NM_145805.1	NP_665804.1	Q96A47	ISL2_HUMAN	ISL LIM homeobox 2	208					negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|peripheral nervous system neuron development (GO:0048935)|regulation of transcription, DNA-templated (GO:0006355)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord motor neuron cell fate specification (GO:0021520)|visceral motor neuron differentiation (GO:0021524)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6						CTCTGCGGACCTGCTACGCCG	0.677																																					p.T208T	GBM(97;953 1391 16164 31496 36951)	Atlas-SNP	.											.	ISL2	20	.	0			c.C624G						.						41	44	43					15																	76632729		2197	4292	6489	SO:0001819	synonymous_variant	64843	exon4			GCGGACCTGCTAC	AK001022	CCDS10290.1	15q24.3	2012-03-09	2007-07-13		ENSG00000159556	ENSG00000159556		"Homeoboxes / LIM class"	18524	protein-coding gene	gene with protein product		609481	"ISL2 transcription factor, LIM/homeodomain, (islet-2)"				Standard	NM_145805		Approved	FLJ10160	uc002bbw.1	Q96A47	OTTHUMG00000143723	ENST00000290759.4:c.624C>G	chr15.hg19:g.76632729C>G		77.0	0.0		125.0	28.0	NM_145805	B3KM37	Silent	SNP	ENST00000290759.4	hg19	CCDS10290.1																																																																																			.	.		0.677	ISL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289779.1			G	76632729	C	G	76632729	2	3	38	1	0	0	0	0	0	0	0	1	7866	668	24	4		4	ISL2	15	76632729	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	27836722	76632729	25898663	125	4572										
BTBD1	53339	hgsc.bcm.edu	37	chr15	83687553	83687553	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgttagctgtcccatcacaaCtaaagccggtatcattctgt	7	11	3	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr15:83687553C>T	ENST00000261721.4	-	7	1398	c.1196G>A	c.(1195-1197)aGt>aAt	p.S399N	RP11-382A20.7_ENST00000570202.1_RNA|RP11-382A20.5_ENST00000566841.1_RNA|BTBD1_ENST00000379403.2_Missense_Mutation_p.V370I	NM_001011885.1|NM_025238.3	NP_001011885.1|NP_079514.1	Q9H0C5	BTBD1_HUMAN	BTB (POZ) domain containing 1	399					protein ubiquitination (GO:0016567)|regulation of protein binding (GO:0043393)	cytoplasmic mRNA processing body (GO:0000932)|protein complex (GO:0043234)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	10				all cancers(203;0.000186)		CCCATCACAACTAAAGCCGGT	0.393																																					p.S399N		Atlas-SNP	.											.	BTBD1	32	.	0			c.G1196A						.						175	144	154					15																	83687553		2203	4300	6503	SO:0001583	missense	53339	exon7			TCACAACTAAAGC	AF355402	CCDS10322.1, CCDS32313.1	15q24	2013-01-08			ENSG00000064726	ENSG00000064726		"BTB/POZ domain containing"	1120	protein-coding gene	gene with protein product		608530					Standard	XM_006720573		Approved		uc002bjn.3	Q9H0C5	OTTHUMG00000147364	ENST00000261721.4:c.1196G>A	chr15.hg19:g.83687553C>T	ENSP00000261721:p.Ser399Asn	388.0	0.0		332.0	166.0	NM_025238	A6NMI8|Q9BX71|Q9NWN4	Missense_Mutation	SNP	ENST00000261721.4	hg19	CCDS10322.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.32|18.32	3.598166|3.598166	0.66332|0.66332	.|.	.|.	ENSG00000064726|ENSG00000064726	ENST00000261721|ENST00000379403	T|T	0.77489|0.75589	-1.1|-0.95	5.23|5.23	5.23|5.23	0.72850|0.72850	PHR (1);|.	0.044312|.	0.85682|.	D|.	0.000000|.	T|T	0.70868|0.70868	0.3273|0.3273	L|L	0.48877|0.48877	1.53|1.53	0.28154|0.28154	N|N	0.929289|0.929289	B|B	0.06786|0.30741	0.001|0.293	B|B	0.12156|0.25140	0.007|0.058	T|T	0.68462|0.68462	-0.5402|-0.5402	10|9	0.27785|0.87932	T|D	0.31|0	-19.6963|-19.6963	18.8027|18.8027	0.92025|0.92025	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	399|370	Q9H0C5|A6NMI8	BTBD1_HUMAN|.	N|I	399|370	ENSP00000261721:S399N|ENSP00000368713:V370I	ENSP00000261721:S399N|ENSP00000368713:V370I	S|V	-|-	2|1	0|0	BTBD1|BTBD1	81478557|81478557	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	6.020000|6.020000	0.70826|0.70826	2.450000|2.450000	0.82876|0.82876	0.563000|0.563000	0.77884|0.77884	AGT|GTT	.	.		0.393	BTBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304008.1			T	83687553	C	T	83687553	3	4	38	1	0	0	0	0	1	0	0	0	1539	565	20	3	260	3	BTBD1	15	83687553	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	7054824	83687553	18843839	126	4573										
CDIPT	10423	hgsc.bcm.edu	37	chr16	29873915	29873915	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggtgtctgtcaccttgattaAgagcgcgagcagcgtgtcca	13	10	2	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr16:29873915A>G	ENST00000219789.6	-	2	1048	c.170T>C	c.(169-171)cTt>cCt	p.L57P	CDIPT_ENST00000561555.1_5'Flank|CDIPT_ENST00000569956.1_Missense_Mutation_p.L57P|CDIPT_ENST00000563415.1_Missense_Mutation_p.L57P|CDIPT-AS1_ENST00000398859.3_RNA|CDIPT_ENST00000566113.1_Intron|CDIPT_ENST00000570016.1_Missense_Mutation_p.L57P|CDIPT-AS1_ENST00000565014.1_RNA	NM_006319.3	NP_006310.1	O14735	CDIPT_HUMAN	CDP-diacylglycerol--inositol 3-phosphatidyltransferase	57					CDP-diacylglycerol metabolic process (GO:0046341)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alcohol binding (GO:0043178)|carbohydrate binding (GO:0030246)|CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity (GO:0003881)|diacylglycerol binding (GO:0019992)|manganese ion binding (GO:0030145)			endometrium(1)|lung(3)	4						ACCTTGATTAAGAGCGCGAGC	0.602																																					p.L57P		Atlas-SNP	.											.	CDIPT	15	.	0			c.T170C						.						37	39	39					16																	29873915		2186	4288	6474	SO:0001583	missense	10423	exon2			TGATTAAGAGCGC	AF014807	CCDS10657.1, CCDS67002.1	16p11.2	2012-11-19	2010-04-29		ENSG00000103502	ENSG00000103502	2.7.8.11		1769	protein-coding gene	gene with protein product	"phosphatidylinositol synthase"	605893	"CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)"			9407135	Standard	NM_006319		Approved	PIS1, PIS	uc002dum.3	O14735	OTTHUMG00000177144	ENST00000219789.6:c.170T>C	chr16.hg19:g.29873915A>G	ENSP00000219789:p.Leu57Pro	124.0	0.0		138.0	63.0	NM_006319	B4DUV0|H3BTV1|Q6FGU1|Q6ZN70	Missense_Mutation	SNP	ENST00000219789.6	hg19	CCDS10657.1	.	.	.	.	.	.	.	.	.	.	A	31	5.067577	0.93898	.	.	ENSG00000103502	ENST00000219789;ENST00000403894	T	0.47528	0.84	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.77177	0.4092	H	0.95574	3.69	0.80722	D	1	D	0.60160	0.987	D	0.70016	0.967	D	0.84012	0.0349	10	0.72032	D	0.01	-11.135	14.2679	0.66133	1.0:0.0:0.0:0.0	.	57	O14735	CDIPT_HUMAN	P	57;110	ENSP00000219789:L57P	ENSP00000219789:L57P	L	-	2	0	CDIPT	29781416	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.651000	0.83577	2.254000	0.74563	0.533000	0.62120	CTT	.	.		0.602	CDIPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255147.3	NM_006319		G	29873915	A	G	29873915	3	3	38	1	0	0	0	0	1	0	0	0	3125	72	3	2	491	2	CDIPT	16	29873915	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10		29873915	60480838	127	4574										
CHD9	80205	hgsc.bcm.edu	37	chr16	53352155	53352156	+	Frame_Shift_Ins	INS	-	-	AAAAAGAC													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	catgagggaagacccaaacaINSaaaaagacaccgttgcagaa							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr16:53352155_53352156insAAAAAGAC	ENST00000398510.3	+	36	7703_7704	c.7616_7617insAAAAAGAC	c.(7615-7620)caaaaafs	p.-2540fs	CHD9_ENST00000566029.1_Frame_Shift_Ins_p.-2524fs|CHD9_ENST00000564845.1_Frame_Shift_Ins_p.-2524fs|CHD9_ENST00000447540.1_Frame_Shift_Ins_p.-2525fs			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9						cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				AGACCCAAACAAAAAAGACACC	0.327																																					p.Q2523fs		Atlas-Indel,Pindel	.											.	CHD9	203	.	0			c.7568_7569insAAAAAGAC						.																																			SO:0001589	frameshift_variant	80205	exon37			.	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.7617_7624dupAAAAAGAC	chr16.hg19:g.53352156_53352163dupAAAAAGAC	ENSP00000381522:p.Lys2540fs	370.0	0.0		64.0	25.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Frame_Shift_Ins	INS	ENST00000398510.3	hg19																																																																																				.	.		0.327	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		AAAAAGAC	53352156	-	AAAAAGAC	53352155	7	5	38	1	0	1	1	0	0	0	0	0	3334	130	5	0	7710	0	CHD9	16	53352155	Frame_Shift_Ins	INS	-	TCGA-BC-A10Z-01A-11D-A12Z-10	23478240	53352155	37002598	128	4575										
SLC6A2	6530	hgsc.bcm.edu	37	chr16	55736246	55736246	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tctctgcagttgcaacactgGctggccatctgagcctgcct	10	14	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr16:55736246G>T	ENST00000379906.2	+	14	2097	c.1842G>T	c.(1840-1842)tgG>tgT	p.W614C	SLC6A2_ENST00000219833.8_Intron|SLC6A2_ENST00000566163.1_Missense_Mutation_p.W569C|SLC6A2_ENST00000561820.1_Intron|SLC6A2_ENST00000567238.1_Missense_Mutation_p.W509C|SLC6A2_ENST00000414754.3_Missense_Mutation_p.W558C|SLC6A2_ENST00000568943.1_Missense_Mutation_p.W614C	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	614					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	TGCAACACTGGCTGGCCATCT	0.607											OREG0023807	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W614C		Atlas-SNP	.											.	SLC6A2	189	.	0			c.G1842T						.						86	77	80					16																	55736246		2198	4300	6498	SO:0001583	missense	6530	exon15			ACACTGGCTGGCC		CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"Solute carriers"	11048	protein-coding gene	gene with protein product	"norepinephrine transporter"	163970	"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.1842G>T	chr16.hg19:g.55736246G>T	ENSP00000369237:p.Trp614Cys	298.0	1.0	1010	150.0	141.0	NM_001172501	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	hg19	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.676340	0.47886	.	.	ENSG00000103546	ENST00000414754;ENST00000537705;ENST00000379906	T	0.74737	-0.87	5.38	5.38	0.77491	.	.	.	.	.	T	0.77811	0.4186	N	0.24115	0.695	0.80722	D	1	D;D;D	0.89917	1.0;0.991;0.967	D;P;P	0.74023	0.982;0.855;0.779	T	0.80446	-0.1379	9	0.87932	D	0	.	14.9917	0.71393	0.0:0.0:1.0:0.0	.	328;509;614	F5H0T4;B4DX48;P23975	.;.;SC6A2_HUMAN	C	614;328;614	ENSP00000369237:W614C	ENSP00000369237:W614C	W	+	3	0	SLC6A2	54293747	1.000000	0.71417	1.000000	0.80357	0.286000	0.27126	6.299000	0.72770	2.677000	0.91161	0.563000	0.77884	TGG	.	.		0.607	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			T	55736246	G	T	55736246	3	4	38	1	0	0	0	0	1	0	0	0	14698	1212	42	3	1987	3	SLC6A2	16	55736246	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	2384091	55736246	34618507	129	4576										
NCOR1	9611	hgsc.bcm.edu	37	chr17	15973499	15973499	+	Frame_Shift_Del	DEL	A	A	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	catcagaagttctgttcatcAtgggtgagcctctggacatg							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:15973499delA	ENST00000268712.3	-	31	4750	c.4493delT	c.(4492-4494)atgfs	p.M1499fs	NCOR1_ENST00000395857.3_Frame_Shift_Del_p.M83fs|NCOR1_ENST00000395851.1_Frame_Shift_Del_p.M1515fs	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1499	Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TCTGTTCATCATGGGTGAGCC	0.398																																					p.M1514fs		Atlas-INDEL	.											.	NCOR1	240	.	0			c.4542delG						.						204	198	200					17																	15973499		2203	4300	6503	SO:0001589	frameshift_variant	9611	exon30			.	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.4493delT	chr17.hg19:g.15973499delA	ENSP00000268712:p.Met1499fs	150.0	0.0		82.0	69.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Frame_Shift_Del	DEL	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.		0.398	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		-	15973499	A	-	15973499	7	5	38	1	0	1	0	1	0	0	0	0	10244	217	8	0	2893	0	NCOR1	17	15973499	Frame_Shift_Del	DEL	A	TCGA-BC-A10Z-01A-11D-A12Z-10		15973499	65221711	130	4577	18	3								
NCOR1	9611	hgsc.bcm.edu	37	chr17	15973501	15973501	+	Silent	SNP	G	G	T													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tcagaagttctgttcatcatGggtgagcctctggacatggt							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:15973501G>T	ENST00000268712.3	-	31	4748	c.4491C>A	c.(4489-4491)ccC>ccA	p.P1497P	NCOR1_ENST00000395857.3_Silent_p.P81P|NCOR1_ENST00000395851.1_Silent_p.P1513P	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1497	Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TGTTCATCATGGGTGAGCCTC	0.398																																					p.P1513P		Atlas-SNP	.											.	NCOR1	240	.	0			c.C4539A						.						207	202	203					17																	15973501		2203	4300	6503	SO:0001819	synonymous_variant	9611	exon30			CATCATGGGTGAG	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.4491C>A	chr17.hg19:g.15973501G>T		154.0	0.0		84.0	68.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.		0.398	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		T	15973501	G	T	15973501	2	4	38	1	0	0	0	0	0	0	0	1	10244	1335	47	3		3	NCOR1	17	15973501	Silent	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	2	15973501	65221709	131	4578	18	3								
NCOR1	9611	hgsc.bcm.edu	37	chr17	15973503	15973503	+	Frame_Shift_Del	DEL	G	G	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agaagttctgttcatcatggGtgagcctctggacatggtgt							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:15973503delG	ENST00000268712.3	-	31	4746	c.4489delC	c.(4489-4491)cccfs	p.P1497fs	NCOR1_ENST00000395857.3_Frame_Shift_Del_p.P81fs|NCOR1_ENST00000395851.1_Frame_Shift_Del_p.P1513fs	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1497	Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TTCATCATGGGTGAGCCTCTG	0.408																																					p.P1513fs		Pindel	.											.	NCOR1	240	.	0			c.4538delC						.						211	205	207					17																	15973503		2203	4300	6503	SO:0001589	frameshift_variant	9611	exon30			.	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.4489delC	chr17.hg19:g.15973503delG	ENSP00000268712:p.Pro1497fs	160.0	0.0		86.0	43.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Frame_Shift_Del	DEL	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.		0.408	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		-	15973503	G	-	15973503	7	5	38	1	0	1	0	1	0	0	0	0	10244	1261	44	0	2897	0	NCOR1	17	15973503	Frame_Shift_Del	DEL	G	TCGA-BC-A10Z-01A-11D-A12Z-10	2	15973503	65221707	132	4579	18	3								
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28295950	28295950	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgaactgaaatcaaagccagAgcacacatggaagaaaaacc	8	9	1	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:28295950A>G	ENST00000394835.3	+	4	524	c.332A>G	c.(331-333)gAg>gGg	p.E111G	EFCAB5_ENST00000534836.2_Intron|EFCAB5_ENST00000541045.1_Intron|EFCAB5_ENST00000378738.3_Missense_Mutation_p.E111G|EFCAB5_ENST00000394832.2_Missense_Mutation_p.E111G|EFCAB5_ENST00000536908.2_Missense_Mutation_p.E55G|EFCAB5_ENST00000320856.5_Missense_Mutation_p.E111G	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	111							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TCAAAGCCAGAGCACACATGG	0.353																																					p.E111G		Atlas-SNP	.											.	EFCAB5	122	.	0			c.A332G						.						28	26	26					17																	28295950		1831	4093	5924	SO:0001583	missense	374786	exon4			AGCCAGAGCACAC	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.332A>G	chr17.hg19:g.28295950A>G	ENSP00000378312:p.Glu111Gly	242.0	1.0		213.0	113.0	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	hg19	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	A	11.99	1.804495	0.31869	.	.	ENSG00000176927	ENST00000448319;ENST00000536908;ENST00000421238;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598	T;T;T;T;T	0.27402	1.72;2.71;2.7;2.0;1.67	5.43	3.05	0.35203	.	.	.	.	.	T	0.22666	0.0547	L	0.40543	1.245	0.09310	N	1	P;P	0.42908	0.793;0.617	B;B	0.36666	0.23;0.173	T	0.11518	-1.0584	9	0.72032	D	0.01	-5.1217	7.5505	0.27793	0.5174:0.3584:0.0:0.1242	.	55;111	F5GYL2;A4FU69	.;EFCB5_HUMAN	G	55;55;55;111;111;111;111;55	ENSP00000440619:E55G;ENSP00000378312:E111G;ENSP00000322003:E111G;ENSP00000378309:E111G;ENSP00000368012:E111G	ENSP00000322003:E111G	E	+	2	0	EFCAB5	25320076	0.020000	0.18652	0.020000	0.16555	0.129000	0.20672	2.523000	0.45580	0.978000	0.38470	-0.313000	0.08912	GAG	.	.		0.353	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		G	28295950	A	G	28295950	3	3	38	1	0	0	0	0	1	0	0	0	4940	304	11	2	346	2	EFCAB5	17	28295950	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	12322447	28295950	52899260	133	4580										
TMEM132E	124842	hgsc.bcm.edu	37	chr17	32959819	32959819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gctacgacgtcctcaatgctCccctggaaatgacagtctgg	10	13	2	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:32959819C>T	ENST00000321639.5	+	7	1637	c.1309C>T	c.(1309-1311)Ccc>Tcc	p.P437S		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	437						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		CCTCAATGCTCCCCTGGAAAT	0.577																																					p.P437S		Atlas-SNP	.											TMEM132E,NS,carcinoma,0,1	TMEM132E	122	.	0			c.C1309T						.						202	173	183					17																	32959819		2203	4300	6503	SO:0001583	missense	124842	exon7			AATGCTCCCCTGG	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1309C>T	chr17.hg19:g.32959819C>T	ENSP00000316532:p.Pro437Ser	190.0	0.0		262.0	74.0	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	hg19	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.962487	0.74016	.	.	ENSG00000181291	ENST00000321639	T	0.19105	2.17	4.61	4.61	0.57282	.	0.108387	0.64402	D	0.000005	T	0.22513	0.0543	L	0.39245	1.2	0.80722	D	1	P	0.46142	0.873	P	0.47299	0.543	T	0.01879	-1.1255	10	0.08599	T	0.76	-27.8359	16.6219	0.84932	0.0:1.0:0.0:0.0	.	437	Q6IEE7	T132E_HUMAN	S	437	ENSP00000316532:P437S	ENSP00000316532:P437S	P	+	1	0	TMEM132E	29983932	0.985000	0.35326	0.997000	0.53966	0.959000	0.62525	3.235000	0.51328	2.388000	0.81334	0.551000	0.68910	CCC	.	.		0.577	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		T	32959819	C	T	32959819	3	4	38	1	0	0	0	0	1	0	0	0	16063	855	30	3	1335	3	TMEM132E	17	32959819	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	4663869	32959819	48235391	134	4581										
LYZL6	57151	hgsc.bcm.edu	37	chr17	34261843	34261843	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gccagtagaagagtggccggCctgaacagtgcaacctccat	12	12	0	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:34261843C>A	ENST00000585556.1	-	5	738	c.404G>T	c.(403-405)gGc>gTc	p.G135V	LYZL6_ENST00000492340.2_5'Flank|LYZL6_ENST00000394523.3_Missense_Mutation_p.G135V|LYZL6_ENST00000293274.4_Missense_Mutation_p.G135V			O75951	LYZL6_HUMAN	lysozyme-like 6	135					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	12				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GAGTGGCCGGCCTGAACAGTG	0.537																																					p.G135V		Atlas-SNP	.											.	LYZL6	18	.	0			c.G404T						.						90	83	85					17																	34261843		2203	4300	6503	SO:0001583	missense	57151	exon4			GGCCGGCCTGAAC	AF088219, AY742214	CCDS11302.1	17q11.2	2014-04-10			ENSG00000161572	ENSG00000275722			29614	protein-coding gene	gene with protein product		612751				10213461	Standard	NM_020426		Approved	LYC1, PRO1485, TKAL754	uc002hkj.2	O75951	OTTHUMG00000188400	ENST00000585556.1:c.404G>T	chr17.hg19:g.34261843C>A	ENSP00000468094:p.Gly135Val	65.0	0.0		115.0	69.0	NM_020426	Q6UW30	Missense_Mutation	SNP	ENST00000585556.1	hg19	CCDS11302.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.469314	0.43839	.	.	ENSG00000161572	ENST00000293274;ENST00000394523	T;T	0.54071	0.59;0.59	4.65	3.68	0.42216	Lysozyme-like domain (1);	0.000000	0.64402	D	0.000004	T	0.72534	0.3472	H	0.94808	3.585	0.58432	D	0.999997	D	0.57257	0.979	P	0.56088	0.791	T	0.78254	-0.2275	10	0.72032	D	0.01	-0.303	9.362	0.38201	0.0:0.8977:0.0:0.1023	.	135	O75951	LYZL6_HUMAN	V	135	ENSP00000293274:G135V;ENSP00000378031:G135V	ENSP00000293274:G135V	G	-	2	0	LYZL6	31285956	0.054000	0.20591	0.933000	0.37362	0.105000	0.19272	0.852000	0.27764	1.272000	0.44329	0.563000	0.77884	GGC	.	.		0.537	LYZL6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256578.2	NM_020426		A	34261843	C	A	34261843	3	1	38	1	0	0	0	0	1	0	0	0	9143	739	26	3	46	3	LYZL6	17	34261843	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	1302024	34261843	46933367	135	4582										
SYNRG	11276	hgsc.bcm.edu	37	chr17	35880688	35880688	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gcacactccacaggcaagctCctgagcatttttaatcccag	7	14	0	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:35880688C>G	ENST00000339208.6	-	20	3870	c.3730G>C	c.(3730-3732)Gag>Cag	p.E1244Q	SYNRG_ENST00000394378.2_Missense_Mutation_p.E1189Q|SYNRG_ENST00000346661.4_Missense_Mutation_p.E1244Q|SYNRG_ENST00000345615.4_Missense_Mutation_p.E1166Q|SYNRG_ENST00000591288.1_Missense_Mutation_p.E1038Q|SYNRG_ENST00000585472.1_Missense_Mutation_p.E1165Q|SYNRG_ENST00000502449.2_Missense_Mutation_p.E1121Q	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	1244					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CAGGCAAGCTCCTGAGCATTT	0.512																																					p.E1244Q		Atlas-SNP	.											.	SYNRG	101	.	0			c.G3730C						.						80	81	80					17																	35880688		2203	4300	6503	SO:0001583	missense	11276	exon20			CAAGCTCCTGAGC	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"gamma-synergin", "adaptor-related protein complex 1 gamma subunit-binding protein 1"	607291	"AP1 gamma subunit binding protein 1"	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.3730G>C	chr17.hg19:g.35880688C>G	ENSP00000343610:p.Glu1244Gln	158.0	0.0		208.0	71.0	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	hg19	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.915251	0.92178	.	.	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378	T;T	0.48836	1.4;0.8	5.56	5.56	0.83823	.	0.109912	0.64402	D	0.000010	T	0.65460	0.2693	M	0.61703	1.905	0.58432	D	0.999999	P;D;D;B;D;D	0.63880	0.742;0.993;0.993;0.309;0.986;0.986	B;D;D;B;P;P	0.63703	0.363;0.917;0.917;0.149;0.87;0.87	T	0.60821	-0.7187	10	0.33940	T	0.23	-14.4844	19.5168	0.95168	0.0:1.0:0.0:0.0	.	1038;1166;1189;1166;1244;1244	B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;SYNRG_HUMAN	Q	1244;1038;1244;1166;1189	ENSP00000005279:E1244Q;ENSP00000377903:E1189Q	ENSP00000343610:E1038Q	E	-	1	0	SYNRG	32954801	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	4.894000	0.63206	2.621000	0.88768	0.591000	0.81541	GAG	.	.		0.512	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247		G	35880688	C	G	35880688	3	3	38	1	0	0	0	0	1	0	0	0	15475	864	30	4	226	4	SYNRG	17	35880688	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	1618845	35880688	45314522	136	4583										
FBXO47	494188	hgsc.bcm.edu	37	chr17	37093476	37093476	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aaatacaggacctccttatgGaagttagcctgagcatgtac	9	9	0	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:37093476G>T	ENST00000378079.2	-	11	1510	c.1311C>A	c.(1309-1311)ttC>ttA	p.F437L		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	437										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						CCTCCTTATGGAAGTTAGCCT	0.413																																					p.F437L		Atlas-SNP	.											.	FBXO47	34	.	0			c.C1311A						.						131	113	119					17																	37093476		2203	4300	6503	SO:0001583	missense	494188	exon11			CTTATGGAAGTTA		CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"F-boxes /  "other""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.1311C>A	chr17.hg19:g.37093476G>T	ENSP00000367319:p.Phe437Leu	183.0	0.0		278.0	165.0	NM_001008777	B2RTZ4	Missense_Mutation	SNP	ENST00000378079.2	hg19	CCDS32639.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015781	0.75161	.	.	ENSG00000204952	ENST00000378079	T	0.59224	0.28	5.88	2.85	0.33270	.	0.096875	0.64402	D	0.000001	T	0.61009	0.2313	L	0.29908	0.895	0.41365	D	0.987454	D	0.69078	0.997	D	0.70716	0.97	T	0.62982	-0.6738	10	0.87932	D	0	-2.3123	9.711	0.40245	0.225:0.0:0.775:0.0	.	437	Q5MNV8	FBX47_HUMAN	L	437	ENSP00000367319:F437L	ENSP00000367319:F437L	F	-	3	2	FBXO47	34347002	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	1.909000	0.39917	0.832000	0.34804	0.650000	0.86243	TTC	.	.		0.413	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777		T	37093476	G	T	37093476	3	4	38	1	0	0	0	0	1	0	0	0	5764	1165	41	3	51	3	FBXO47	17	37093476	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	1212788	37093476	44101734	137	4584										
STARD3	10948	hgsc.bcm.edu	37	chr17	37814042	37814042	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	caccaggtcctggccttcttCcgcttctctggactgctcct	8	17	2	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:37814042C>T	ENST00000336308.5	+	4	530	c.312C>T	c.(310-312)ttC>ttT	p.F104F	STARD3_ENST00000394250.4_Silent_p.F104F|STARD3_ENST00000578232.1_3'UTR|STARD3_ENST00000580611.1_Silent_p.F78F|STARD3_ENST00000544210.2_Silent_p.F104F	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	104	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.				cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TGGCCTTCTTCCGCTTCTCTG	0.657																																					p.F104F		Atlas-SNP	.											.	STARD3	33	.	0			c.C312T						.						105	112	110					17																	37814042		2203	4300	6503	SO:0001819	synonymous_variant	10948	exon4			CTTCTTCCGCTTC		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"StAR-related lipid transfer (START) domain containing"	17579	protein-coding gene	gene with protein product		607048	"START domain containing 3"				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.312C>T	chr17.hg19:g.37814042C>T		284.0	0.0		427.0	254.0	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Silent	SNP	ENST00000336308.5	hg19	CCDS11341.1																																																																																			.	.		0.657	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1			T	37814042	C	T	37814042	2	4	38	1	0	0	0	0	0	0	0	1	15272	854	30	3		3	STARD3	17	37814042	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	720566	37814042	43381168	138	4585										
KRT34	3885	hgsc.bcm.edu	37	chr17	39534380	39534380	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccactagcattggtggtggcGcatgggttgcaggggagcct	17	9	0	0	rs138365209	byFrequency	TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:39534380G>T	ENST00000394001.1	-	7	1272	c.1242C>A	c.(1240-1242)tgC>tgA	p.C414*		NM_021013.3	NP_066293.2	O76011	KRT34_HUMAN	keratin 34	414	Tail.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Breast(137;0.000496)				TGGTGGTGGCGCATGGGTTGC	0.478																																					p.C414X		Atlas-SNP	.											.	KRT34	71	.	0			c.C1242A						.						108	103	105					17																	39534380		2203	4300	6503	SO:0001587	stop_gained	3885	exon7			GGTGGCGCATGGG	Y16790	CCDS11390.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131737	ENSG00000131737		"-", "Intermediate filaments type I, keratins (acidic)"	6452	protein-coding gene	gene with protein product	"hard keratin type I 4"	602763	"keratin, hair, acidic, 4"	KRTHA4		2431943, 9756910, 16831889	Standard	NM_021013		Approved	Ha-4	uc002hwm.3	O76011	OTTHUMG00000133436	ENST00000394001.1:c.1242C>A	chr17.hg19:g.39534380G>T	ENSP00000377570:p.Cys414*	114.0	0.0		175.0	60.0	NM_021013	Q8IUT8|Q8N4W2	Nonsense_Mutation	SNP	ENST00000394001.1	hg19	CCDS11390.1	.	.	.	.	.	.	.	.	.	.	-	25.1	4.600806	0.87055	.	.	ENSG00000131737	ENST00000394001;ENST00000251648	.	.	.	5.54	1.95	0.26073	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.48511	D	0.999668	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.6019	0.28081	0.7444:0.0:0.2556:0.0	.	.	.	.	X	372;414	.	ENSP00000251648:C414X	C	-	3	2	KRT34	36787906	0.907000	0.30839	0.993000	0.49108	0.912000	0.54170	-0.267000	0.08619	0.059000	0.16252	-0.331000	0.08364	TGC	.	G|0.999;A|0.001		0.478	KRT34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257304.3	NM_021013		T	39534380	G	T	39534380	4	4	38	1	0	0	0	0	0	1	0	0	8480	1079	38	1	72	1	KRT34	17	39534380	Nonsense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	1720338	39534380	41660830	139	4586										
ARSG	22901	hgsc.bcm.edu	37	chr17	66303755	66303755	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agaagccaaactttgtgattAttttggccgatgacatgggg	12	6	0	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:66303755A>G	ENST00000448504.2	+	2	917	c.121A>G	c.(121-123)Att>Gtt	p.I41V	ARSG_ENST00000452479.2_Intron	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	41					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			CTTTGTGATTATTTTGGCCGA	0.478																																					p.I41V		Atlas-SNP	.											.	ARSG	55	.	0			c.A121G						.						98	96	96					17																	66303755		2203	4300	6503	SO:0001583	missense	22901	exon2			GTGATTATTTTGG	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"Arylsulfatase family"	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.121A>G	chr17.hg19:g.66303755A>G	ENSP00000407193:p.Ile41Val	519.0	0.0		753.0	241.0	NM_001267727	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	hg19	CCDS11676.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.498412	0.64298	.	.	ENSG00000141337	ENST00000452479	.	.	.	5.59	4.52	0.55395	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	T	0.63283	0.2498	M	0.68593	2.085	0.80722	D	1	P	0.49862	0.929	P	0.52309	0.695	T	0.66208	-0.5981	9	0.56958	D	0.05	.	9.0431	0.36329	0.9143:0.0:0.0857:0.0	.	41	Q96EG1	ARSG_HUMAN	V	41	.	ENSP00000413953:I41V	I	+	1	0	ARSG	63815350	1.000000	0.71417	1.000000	0.80357	0.616000	0.37450	2.653000	0.46691	2.120000	0.65058	0.460000	0.39030	ATT	.	.		0.478	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960		G	66303755	A	G	66303755	3	3	38	1	0	0	0	0	1	0	0	0	992	449	16	2	123	2	ARSG	17	66303755	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	26769375	66303755	14891455	140	4587										
KIF19	124602	hgsc.bcm.edu	37	chr17	72345442	72345442	+	Frame_Shift_Del	DEL	C	C	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gatgagcagactgggcggggCcaggcccggggccggcagga							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:72345442delC	ENST00000389916.4	+	10	1305	c.1167delC	c.(1165-1167)ggcfs	p.G389fs		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	389					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						CTGGGCGGGGCCAGGCCCGGG	0.662																																					p.G389fs		Atlas-Indel,Pindel	.											.	KIF19	102	.	0			c.1166delG						.						32	31	31					17																	72345442		2202	4300	6502	SO:0001589	frameshift_variant	124602	exon10			.	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.1167delC	chr17.hg19:g.72345442delC	ENSP00000374566:p.Gly389fs	127.0	0.0		166.0	96.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Frame_Shift_Del	DEL	ENST00000389916.4	hg19	CCDS32718.2																																																																																			.	.		0.662	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		-	72345442	C	-	72345442	7	5	38	1	0	1	0	1	0	0	0	0	8291	726	26	0	1205	0	KIF19	17	72345442	Frame_Shift_Del	DEL	C	TCGA-BC-A10Z-01A-11D-A12Z-10	6041687	72345442	8849768	141	4588										
C17orf28	283987	hgsc.bcm.edu	37	chr17	72949120	72949120	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cccactctggcgttgggctcCactgcccactggctgatgag	12	15	1	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:72949120C>T	ENST00000425042.2	-	16	2110	c.2033G>A	c.(2032-2034)tGg>tAg	p.W678*		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	678					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)											CGTTGGGCTCCACTGCCCACT	0.692																																					p.W678X		Atlas-SNP	.											.	.	.	.	0			c.G2033A						.						26	22	23					17																	72949120		2202	4296	6498	SO:0001587	stop_gained	283987	exon16			GGGCTCCACTGCC		CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"downregulated in multiple cancer 1"	605752	"chromosome 17 open reading frame 28"	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.2033G>A	chr17.hg19:g.72949120C>T	ENSP00000413520:p.Trp678*	124.0	0.0		256.0	83.0	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Nonsense_Mutation	SNP	ENST00000425042.2	hg19	CCDS32726.1	.	.	.	.	.	.	.	.	.	.	C	36	5.968936	0.97156	.	.	ENSG00000167861	ENST00000525426;ENST00000425042;ENST00000318565	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.9882	18.4895	0.90842	0.0:1.0:0.0:0.0	.	.	.	.	X	450;678;450	.	ENSP00000317795:W450X	W	-	2	0	C17orf28	70460715	1.000000	0.71417	1.000000	0.80357	0.092000	0.18411	6.156000	0.71840	2.372000	0.80975	0.561000	0.74099	TGG	.	.		0.692	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630		T	72949120	C	T	72949120	4	4	38	1	0	0	0	0	0	1	0	0	1855	595	21	3	349	3	C17orf28	17	72949120	Nonsense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	603678	72949120	8246090	142	4589										
TEX19	400629	hgsc.bcm.edu	37	chr17	80320463	80320463	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgactggacccagggtcttcCctggagatttgaggagcttc	13	10	1	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr17:80320463C>G	ENST00000333437.4	+	2	747	c.437C>G	c.(436-438)cCc>cGc	p.P146R		NM_207459.3	NP_997342.1	Q8NA77	TEX19_HUMAN	testis expressed 19	146					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6						CAGGGTCTTCCCTGGAGATTT	0.602																																					p.P146R		Atlas-SNP	.											.	TEX19	17	.	0			c.C437G						.						52	52	52					17																	80320463		2203	4297	6500	SO:0001583	missense	400629	exon2			GTCTTCCCTGGAG	BC016939	CCDS11809.1	17q25.3	2009-04-14			ENSG00000182459	ENSG00000182459			33802	protein-coding gene	gene with protein product		615647					Standard	NM_207459		Approved	FLJ35767	uc002keq.3	Q8NA77	OTTHUMG00000132857	ENST00000333437.4:c.437C>G	chr17.hg19:g.80320463C>G	ENSP00000331500:p.Pro146Arg	160.0	0.0		215.0	68.0	NM_207459		Missense_Mutation	SNP	ENST00000333437.4	hg19	CCDS11809.1	.	.	.	.	.	.	.	.	.	.	C	12.69	2.012124	0.35511	.	.	ENSG00000182459	ENST00000333437	.	.	.	3.55	3.55	0.40652	.	.	.	.	.	T	0.63861	0.2547	L	0.34521	1.04	0.38363	D	0.944661	D	0.89917	1.0	D	0.91635	0.999	T	0.68648	-0.5353	8	0.87932	D	0	-18.5464	10.8916	0.46998	0.0:1.0:0.0:0.0	.	146	Q8NA77	TEX19_HUMAN	R	146	.	ENSP00000331500:P146R	P	+	2	0	TEX19	77913752	0.963000	0.33076	0.992000	0.48379	0.044000	0.14063	1.568000	0.36418	2.265000	0.75225	0.563000	0.77884	CCC	.	.		0.602	TEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256331.1	NM_207459		G	80320463	C	G	80320463	3	3	38	1	0	0	0	0	1	0	0	0	15795	623	22	4	439	4	TEX19	17	80320463	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	7371343	80320463	874747	143	4590										
SPIRE1	56907	hgsc.bcm.edu	37	chr18	12453128	12453128	+	Frame_Shift_Del	DEL	A	A	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aaacctcctggttcggcaacAaaagcagagctaaaaaatac							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr18:12453128delA	ENST00000409402.4	-	14	2053	c.1786delT	c.(1786-1788)tgtfs	p.C597fs	SPIRE1_ENST00000453447.2_Frame_Shift_Del_p.C463fs|SPIRE1_ENST00000464481.1_5'UTR|SPIRE1_ENST00000383356.2_Frame_Shift_Del_p.C424fs|SPIRE1_ENST00000309836.5_Frame_Shift_Del_p.C386fs|SPIRE1_ENST00000410092.3_Frame_Shift_Del_p.C583fs	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1											breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						GTTCGGCAACAAAAGCAGAGC	0.313																																					p.C596fs		Atlas-Indel,Pindel	.											.	SPIRE1	120	.	0			c.1787delG						.						51	54	53					18																	12453128		2202	4300	6502	SO:0001589	frameshift_variant	56907	exon14			.	AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"spire homolog 1 (Drosophila)", "spire family actin nucleation factor 1"			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.1786delT	chr18.hg19:g.12453128delA	ENSP00000387266:p.Cys597fs	281.0	0.0		225.0	22.0	NM_001128626		Frame_Shift_Del	DEL	ENST00000409402.4	hg19	CCDS45829.1																																																																																			.	.		0.313	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818		-	12453128	A	-	12453128	7	5	38	1	0	1	0	1	0	0	0	0	15086	130	5	0	500	0	SPIRE1	18	12453128	Frame_Shift_Del	DEL	A	TCGA-BC-A10Z-01A-11D-A12Z-10		12453128	65624120	144	4591										
CCBE1	147372	hgsc.bcm.edu	37	chr18	57364549	57364549	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gctggcccctggcagctcctCcccggctcggaggcggcggc	16	18	0	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr18:57364549C>A	ENST00000439986.4	-	1	63	c.26G>T	c.(25-27)gGa>gTa	p.G9V	RP11-2N1.2_ENST00000588946.1_RNA	NM_133459.3	NP_597716.1	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	9					lymphangiogenesis (GO:0001946)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of protein processing (GO:0010954)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|positive regulation vascular endothelial growth factor production (GO:0010575)|sprouting angiogenesis (GO:0002040)|venous blood vessel morphogenesis (GO:0048845)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|protease binding (GO:0002020)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(3)	24		Colorectal(73;0.175)				GGCAGCTCCTCCCCGGCTCGG	0.731											OREG0025022	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G9V	NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)	Atlas-SNP	.											.	CCBE1	59	.	0			c.G26T						.						6	7	7					18																	57364549		2015	4006	6021	SO:0001583	missense	147372	exon1			GCTCCTCCCCGGC	AB075863	CCDS32838.1	18q21.32	2005-01-18				ENSG00000183287			29426	protein-coding gene	gene with protein product		612753				11853319, 12975309	Standard	NM_133459		Approved	FLJ30681, KIAA1983	uc002lib.3	Q6UXH8		ENST00000439986.4:c.26G>T	chr18.hg19:g.57364549C>A	ENSP00000404464:p.Gly9Val	32.0	0.0	1022	52.0	25.0	NM_133459	Q6MZX5|Q86SS2|Q8TF19	Missense_Mutation	SNP	ENST00000439986.4	hg19	CCDS32838.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.045007	0.36085	.	.	ENSG00000183287	ENST00000439986	D	0.86497	-2.13	4.14	1.15	0.20763	.	0.969120	0.08413	U	0.949473	T	0.73361	0.3577	N	0.08118	0	0.80722	D	1	B	0.20052	0.041	B	0.17098	0.017	T	0.61033	-0.7144	10	0.87932	D	0	-0.1761	5.7568	0.18178	0.0:0.5021:0.387:0.1109	.	9	Q6UXH8	CCBE1_HUMAN	V	9	ENSP00000404464:G9V	ENSP00000404464:G9V	G	-	2	0	CCBE1	55515529	1.000000	0.71417	0.672000	0.29872	0.952000	0.60782	1.467000	0.35321	0.027000	0.15297	0.655000	0.94253	GGA	.	.		0.731	CCBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449685.2	NM_133459		A	57364549	C	A	57364549	3	1	38	1	0	0	0	0	1	0	0	0	2733	855	30	3	1238	3	CCBE1	18	57364549	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	44911421	57364549	20712699	145	4592										
DOT1L	84444	hgsc.bcm.edu	37	chr19	2217053	2217053	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccgcggcccctgtcccctggGgccttgcagcttgctggaga	14	16	0	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:2217053G>A	ENST00000398665.3	+	21	2544	c.2508G>A	c.(2506-2508)ggG>ggA	p.G836G	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	836					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGTCCCCTGGGGCCTTGCAGC	0.682																																					p.G836G		Atlas-SNP	.											.	DOT1L	205	.	0			c.G2508A						.						25	28	27					19																	2217053		1978	4154	6132	SO:0001819	synonymous_variant	84444	exon21			CCCTGGGGCCTTG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.2508G>A	chr19.hg19:g.2217053G>A		39.0	0.0		43.0	17.0	NM_032482	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	G	0.674	-0.800634	0.02841	.	.	ENSG00000104885	ENST00000440640	T	0.39406	1.08	5.32	1.81	0.25067	.	0.933118	0.09169	N	0.839146	T	0.17916	0.0430	.	.	.	0.18873	N	0.999981	.	.	.	.	.	.	T	0.23833	-1.0177	7	0.07030	T	0.85	-5.3005	6.27	0.20949	0.1634:0.0:0.6881:0.1486	.	.	.	.	E	623	ENSP00000388276:G623E	ENSP00000388276:G623E	G	+	2	0	DOT1L	2168053	0.001000	0.12720	0.004000	0.12327	0.098000	0.18820	-0.027000	0.12371	0.604000	0.29930	-0.258000	0.10820	GGG	.	.		0.682	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		A	2217053	G	A	2217053	2	1	38	1	0	0	0	0	0	0	0	1	4711	1219	43	3		3	DOT1L	19	2217053	Silent	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10		2217053	56911930	146	4593										
TLE6	79816	hgsc.bcm.edu	37	chr19	2989558	2989558	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tggggccttcctgcgcacctGcctgctgtcctcaaacagca	10	16	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:2989558G>A	ENST00000246112.4	+	13	1220	c.1019G>A	c.(1018-1020)tGc>tAc	p.C340Y	TLE6_ENST00000452088.1_Missense_Mutation_p.C217Y|TLE6_ENST00000478073.2_3'UTR	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	340					regulation of transcription, DNA-templated (GO:0006355)	cell cortex (GO:0005938)|nucleus (GO:0005634)|protein complex (GO:0043234)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGCGCACCTGCCTGCTGTCC	0.657																																					p.C340Y		Atlas-SNP	.											.	TLE6	68	.	0			c.G1019A						.						23	25	24					19																	2989558		2202	4296	6498	SO:0001583	missense	79816	exon13			GCACCTGCCTGCT	AK024071	CCDS12100.1, CCDS45910.1	19p13.3	2014-03-07	2014-03-07		ENSG00000104953	ENSG00000104953		"WD repeat domain containing"	30788	protein-coding gene	gene with protein product		612399	"transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)"			11486032	Standard	NM_024760		Approved	FLJ14009, GRG6	uc002lwt.2	Q9H808	OTTHUMG00000156793	ENST00000246112.4:c.1019G>A	chr19.hg19:g.2989558G>A	ENSP00000246112:p.Cys340Tyr	67.0	0.0		49.0	15.0	NM_001143986	J3KMZ1	Missense_Mutation	SNP	ENST00000246112.4	hg19	CCDS45910.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.522465	0.44866	.	.	ENSG00000104953	ENST00000447920;ENST00000246112;ENST00000452088;ENST00000441927	T;T	0.11385	2.78;2.78	3.15	3.15	0.36227	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.31009	0.0783	M	0.82716	2.605	0.58432	D	0.999998	D;D;D;D	0.71674	0.998;0.995;0.993;0.993	D;D;D;D	0.66847	0.947;0.914;0.911;0.911	T	0.08554	-1.0716	9	0.87932	D	0	.	10.0139	0.42003	0.0:0.0:1.0:0.0	.	340;198;217;217	C9JGZ7;Q9Y6S1;Q9H808;Q6PJM9	.;.;TLE6_HUMAN;.	Y	340;340;217;217	ENSP00000246112:C340Y;ENSP00000406893:C217Y	ENSP00000246112:C340Y	C	+	2	0	TLE6	2940558	1.000000	0.71417	1.000000	0.80357	0.180000	0.23129	7.561000	0.82288	2.083000	0.62718	0.505000	0.49811	TGC	.	.		0.657	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760		A	2989558	G	A	2989558	3	1	38	1	0	0	0	0	1	0	0	0	15957	1319	46	3	1065	3	TLE6	19	2989558	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	772505	2989558	56139425	147	4594										
TIMM44	10469	hgsc.bcm.edu	37	chr19	7996055	7996055	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccagtctttgagaatgtcaaGctctccagaaatcatggcct	8	11	4	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:7996055G>C	ENST00000270538.3	-	10	1274	c.1006C>G	c.(1006-1008)Ctt>Gtt	p.L336V	TIMM44_ENST00000598968.1_5'UTR	NM_006351.3	NP_006342.2	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44 homolog (yeast)	336					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			NS(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	17						AGAATGTCAAGCTCTCCAGAA	0.433																																					p.L336V		Atlas-SNP	.											.	TIMM44	47	.	0			c.C1006G						.						110	106	108					19																	7996055		2203	4300	6503	SO:0001583	missense	10469	exon10			TGTCAAGCTCTCC	AF026030	CCDS12192.1	19p13.3-p13.2	2008-07-04				ENSG00000104980			17316	protein-coding gene	gene with protein product		605058				10848612, 10339406	Standard	NM_006351		Approved	TIM44	uc002miz.3	O43615		ENST00000270538.3:c.1006C>G	chr19.hg19:g.7996055G>C	ENSP00000270538:p.Leu336Val	370.0	1.0		271.0	89.0	NM_006351	A8K0R9|D6W664|Q8N193	Missense_Mutation	SNP	ENST00000270538.3	hg19	CCDS12192.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.992637	0.74703	.	.	ENSG00000104980	ENST00000270538	T	0.78364	-1.17	4.5	4.5	0.54988	.	0.000000	0.85682	D	0.000000	T	0.78541	0.4299	L	0.39397	1.21	0.80722	D	1	P	0.48230	0.907	P	0.55871	0.786	T	0.73940	-0.3824	10	0.16896	T	0.51	-10.2862	14.7762	0.69734	0.0:0.0:1.0:0.0	.	336	O43615	TIM44_HUMAN	V	336	ENSP00000270538:L336V	ENSP00000270538:L336V	L	-	1	0	TIMM44	7902055	1.000000	0.71417	0.989000	0.46669	0.990000	0.78478	5.978000	0.70501	2.084000	0.62774	0.556000	0.70494	CTT	.	.		0.433	TIMM44-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461596.3			C	7996055	G	C	7996055	3	2	38	1	0	0	0	0	1	0	0	0	15927	971	34	4	368	4	TIMM44	19	7996055	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	5006497	7996055	51132928	148	4595										
ELAVL1	1994	hgsc.bcm.edu	37	chr19	8028565	8028565	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ccaaacggcccaaacatctgCcagaggatcccctcgtcggc	9	17	1	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:8028565C>A	ENST00000407627.2	-	6	912	c.783G>T	c.(781-783)tgG>tgT	p.W261C	ELAVL1_ENST00000351593.5_Missense_Mutation_p.W288C|ELAVL1_ENST00000593807.1_3'UTR|ELAVL1_ENST00000596459.1_Missense_Mutation_p.W261C	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	261	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CAAACATCTGCCAGAGGATCC	0.557																																					p.W261C		Atlas-SNP	.											.	ELAVL1	44	.	0			c.G783T						.						112	96	101					19																	8028565		2203	4300	6503	SO:0001583	missense	1994	exon6			CATCTGCCAGAGG	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"RNA binding motif (RRM) containing"	3312	protein-coding gene	gene with protein product	"embryonic lethal, abnormal vision, drosophila, homolog-like 1", "Hu antigen R"	603466	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.783G>T	chr19.hg19:g.8028565C>A	ENSP00000385269:p.Trp261Cys	247.0	0.0		194.0	105.0	NM_001419	B4DVB8|Q53XN6|Q9BTT1	Missense_Mutation	SNP	ENST00000407627.2	hg19	CCDS12193.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.513873	0.64522	.	.	ENSG00000066044	ENST00000407627;ENST00000351593	T;T	0.15952	2.38;2.38	5.66	5.66	0.87406	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.28532	0.0706	N	0.17345	0.48	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.08827	-1.0703	10	0.87932	D	0	.	17.2498	0.87039	0.0:1.0:0.0:0.0	.	261	Q15717	ELAV1_HUMAN	C	261;288	ENSP00000385269:W261C;ENSP00000264073:W288C	ENSP00000264073:W288C	W	-	3	0	ELAVL1	7934565	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.665000	0.90641	0.655000	0.94253	TGG	.	.		0.557	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419		A	8028565	C	A	8028565	3	1	38	1	0	0	0	0	1	0	0	0	5051	740	26	3	201	3	ELAVL1	19	8028565	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	32510	8028565	51100418	149	4596										
MUC16	94025	hgsc.bcm.edu	37	chr19	9045850	9045853	+	Frame_Shift_Del	DEL	AGTT	AGTT	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aattctgggggtccaactgaAgttacagatggtgaggtttc					rs577410182		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	AGTT	AGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:9045850_9045853delAGTT	ENST00000397910.4	-	5	35981_35984	c.35778_35781delAACT	c.(35776-35781)gtaactfs	p.VT11926fs		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11928	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCCAACTGAAGTTACAGATGGTG	0.49																																					p.11927_11928del		Atlas-Indel,Pindel	.											.	MUC16	4315	.	0			c.35779_35782del						.																																			SO:0001589	frameshift_variant	94025	exon5			.	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.35778_35781delAACT	chr19.hg19:g.9045850_9045853delAGTT	ENSP00000381008:p.Val11926fs	317.0	0.0		236.0	89.0	NM_024690	Q6ZQW5|Q96RK2	Frame_Shift_Del	DEL	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.49	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		-	9045853	AGTT	-	9045850	7	5	38	1	0	1	0	1	0	0	0	0	9982	59	3	0	8062	0	MUC16	19	9045850	Frame_Shift_Del	DEL	AGTT	TCGA-BC-A10Z-01A-11D-A12Z-10	1017285	9045850	50083133	150	4597										
FDX1L	112812	hgsc.bcm.edu	37	chr19	10426560	10426560	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	actttctggttgtccccagcGccaccccctcccccgacccg	7	22	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:10426560G>A	ENST00000393708.3	-	1	131	c.113C>T	c.(112-114)gCg>gTg	p.A38V	FDX1L_ENST00000494368.1_Intron|CTD-2369P2.10_ENST00000452032.2_Missense_Mutation_p.A38V|FDX1L_ENST00000492239.1_5'Flank|CTD-2369P2.12_ENST00000586529.1_Intron|FDX1L_ENST00000541276.1_Missense_Mutation_p.A41V	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like	38					oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			NS(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(20;9.5e-10)|Epithelial(33;2.11e-06)|all cancers(31;5.06e-06)			TGTCCCCAGCGCCACCCCCTC	0.706																																					p.A38V		Atlas-SNP	.											.	FDX1L	21	.	0			c.C113T						.						18	22	21					19																	10426560		2193	4292	6485	SO:0001583	missense	112812	exon1			CCCAGCGCCACCC	AK097022	CCDS32905.1	19p13.2	2012-10-09			ENSG00000267673	ENSG00000267673			30546	protein-coding gene	gene with protein product		614585				12477932	Standard	NM_001031734		Approved	MGC19604	uc002mny.1	Q6P4F2	OTTHUMG00000141299	ENST00000393708.3:c.113C>T	chr19.hg19:g.10426560G>A	ENSP00000377311:p.Ala38Val	79.0	0.0		71.0	28.0	NM_001031734	Q8N8B8	Missense_Mutation	SNP	ENST00000393708.3	hg19	CCDS32905.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.289113	0.40494	.	.	ENSG00000167807	ENST00000541276;ENST00000393708	.	.	.	4.59	2.46	0.29980	.	0.900133	0.09629	N	0.776469	T	0.28366	0.0701	N	0.24115	0.695	0.19300	N	0.999972	B	0.06786	0.001	B	0.01281	0.0	T	0.25257	-1.0137	9	0.66056	D	0.02	-16.7108	6.2373	0.20770	0.2326:0.0:0.7674:0.0	.	38	Q6P4F2	ADXL_HUMAN	V	41;38	.	ENSP00000341665:A38V	A	-	2	0	FDX1L	10287560	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	0.136000	0.15974	0.547000	0.28938	0.455000	0.32223	GCG	.	.		0.706	FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2			A	10426560	G	A	10426560	3	1	38	1	0	0	0	0	1	0	0	0	5813	1087	38	1	458	1	FDX1L	19	10426560	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	1380710	10426560	48702423	151	4598										
CALR	811	hgsc.bcm.edu	37	chr19	13054680	13054680	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aggatgaggaggacaaggagGaagatgaggaggaagatgtc	19	2	0	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:13054680G>T	ENST00000316448.5	+	9	1280	c.1207G>T	c.(1207-1209)Gaa>Taa	p.E403*	RAD23A_ENST00000541222.1_5'Flank|CTC-425F1.4_ENST00000589120.1_RNA|RAD23A_ENST00000586534.1_5'Flank|RAD23A_ENST00000316856.3_5'Flank|RAD23A_ENST00000592268.1_5'Flank	NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	403	Asp/Glu/Lys-rich.|C-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	ggacaaggaggaagatgagga	0.587																																					p.E403X		Atlas-SNP	.											CALR,NS,lymphoid_neoplasm,0,1	CALR	31	.	0			c.G1207T						.						251	193	213					19																	13054680		2203	4300	6503	SO:0001587	stop_gained	811	exon9			AAGGAGGAAGATG	M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"Sicca syndrome antigen A (autoantigen Ro; calreticulin)", "autoantigen Ro"	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.1207G>T	chr19.hg19:g.13054680G>T	ENSP00000320866:p.Glu403*	424.0	1.0		388.0	193.0	NM_004343	Q6IAT4|Q9UDG2	Nonsense_Mutation	SNP	ENST00000316448.5	hg19	CCDS12288.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.808459	0.70797	.	.	ENSG00000179218	ENST00000316448;ENST00000539083	.	.	.	5.4	5.4	0.78164	.	0.251665	0.36409	N	0.002611	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-20.8665	12.1195	0.53883	0.0833:0.0:0.9167:0.0	.	.	.	.	X	403;282	.	ENSP00000320866:E403X	E	+	1	0	CALR	12915680	1.000000	0.71417	0.122000	0.21767	0.183000	0.23260	5.663000	0.68038	2.526000	0.85167	0.555000	0.69702	GAA	.	.		0.587	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343		T	13054680	G	T	13054680	4	4	38	1	0	0	0	0	0	1	0	0	2594	1175	41	3	1241	3	CALR	19	13054680	Nonsense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	2628120	13054680	46074303	152	4599										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14038069	14038069	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	atagcatgtgaggtccgggaGatccttgaggtgagaggtgg	18	5	0	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:14038069G>A	ENST00000318003.7	+	22	2548	c.2307G>A	c.(2305-2307)gaG>gaA	p.E769E	CC2D1A_ENST00000589606.1_Silent_p.E769E	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	769					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			AGGTCCGGGAGATCCTTGAGG	0.537																																					p.E769E		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G2307A						.						102	123	116					19																	14038069		2163	4252	6415	SO:0001819	synonymous_variant	54862	exon22			CCGGGAGATCCTT	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.2307G>A	chr19.hg19:g.14038069G>A		217.0	0.0		221.0	9.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Silent	SNP	ENST00000318003.7	hg19	CCDS42512.1																																																																																			.	.		0.537	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		A	14038069	G	A	14038069	2	1	38	1	0	0	0	0	0	0	0	1	2728	933	33	3		3	CC2D1A	19	14038069	Silent	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	983389	14038069	45090914	153	4600										
ZNF486	90649	hgsc.bcm.edu	37	chr19	20308237	20308237	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctagagagaaaccctacaaaTgtgaagaatgtggcaaagtc	10	7	0	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:20308237T>C	ENST00000335117.8	+	4	775	c.718T>C	c.(718-720)Tgt>Cgt	p.C240R	CTC-260E6.6_ENST00000593655.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000586657.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	240					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						ACCCTACAAATGTGAAGAATG	0.378																																					p.C240R		Atlas-SNP	.											.	ZNF486	74	.	0			c.T718C						.						37	40	39					19																	20308237		2146	4271	6417	SO:0001583	missense	90649	exon4			TACAAATGTGAAG	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"Zinc fingers, C2H2-type", "-"	20807	protein-coding gene	gene with protein product			"KRAB domain only 2"	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.718T>C	chr19.hg19:g.20308237T>C	ENSP00000335042:p.Cys240Arg	94.0	0.0		93.0	52.0	NM_052852	Q0VG00	Missense_Mutation	SNP	ENST00000335117.8	hg19	CCDS46029.1	.	.	.	.	.	.	.	.	.	.	t	11.26	1.585708	0.28268	.	.	ENSG00000256229	ENST00000545779;ENST00000335117	D	0.85258	-1.96	0.85	0.85	0.18980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.91147	0.7212	H	0.99026	4.405	0.43588	D	0.995934	P	0.36483	0.555	B	0.43754	0.43	D	0.88072	0.2801	9	0.72032	D	0.01	.	5.4501	0.16560	0.0:0.0:0.0:1.0	.	240	Q96H40	ZN486_HUMAN	R	279;240	ENSP00000335042:C240R	ENSP00000335042:C240R	C	+	1	0	ZNF486	20169237	1.000000	0.71417	0.029000	0.17559	0.029000	0.11900	5.474000	0.66781	0.166000	0.19597	0.164000	0.16699	TGT	.	.		0.378	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852		C	20308237	T	C	20308237	3	2	38	1	0	0	0	0	1	0	0	0	17954	1464	51	2	732	2	ZNF486	19	20308237	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	6270168	20308237	38820746	154	4601										
ZNF429	353088	hgsc.bcm.edu	37	chr19	21720692	21720692	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	caagacttactcaacataagAaaattcatactagagagaaa	5	7	2	4			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:21720692A>T	ENST00000358491.4	+	4	2045	c.1837A>T	c.(1837-1839)Aaa>Taa	p.K613*	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	613					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						TCAACATAAGAAAATTCATAC	0.363																																					p.K613X		Atlas-SNP	.											.	ZNF429	338	.	0			c.A1837T						.						59	64	62					19																	21720692		2070	4242	6312	SO:0001587	stop_gained	353088	exon4			CATAAGAAAATTC	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1837A>T	chr19.hg19:g.21720692A>T	ENSP00000351280:p.Lys613*	90.0	0.0		102.0	45.0	NM_001001415	A6NLV7|Q9BZE6	Nonsense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	33	5.282575	0.95489	.	.	ENSG00000197013	ENST00000358491	.	.	.	1.09	1.09	0.20402	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	7.1337	0.25517	1.0:0.0:0.0:0.0	.	.	.	.	X	613	.	ENSP00000351280:K613X	K	+	1	0	ZNF429	21512532	0.000000	0.05858	0.006000	0.13384	0.356000	0.29392	-0.226000	0.09139	0.464000	0.27142	0.248000	0.18094	AAA	.	.		0.363	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		T	21720692	A	T	21720692	4	4	38	1	0	0	0	0	0	1	0	0	17917	247	9	4	1851	4	ZNF429	19	21720692	Nonsense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	1412455	21720692	37408291	155	4602										
IL29	282618	hgsc.bcm.edu	37	chr19	39787118	39787119	+	Frame_Shift_Ins	INS	-	-	G													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgctaggcttggccgtggcaINSggccctgtccccacttccaa							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:39787118_39787119insG	ENST00000333625.2	+	1	154_155	c.57_58insG	c.(58-60)ggcfs	p.G20fs		NM_172140.1	NP_742152.1	Q8IU54	IFNL1_HUMAN	interferon, lambda 1	20					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of cell proliferation (GO:0008285)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of memory T cell differentiation (GO:0043381)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of immune response (GO:0050778)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-28 receptor complex (GO:0032002)	interleukin-28 receptor binding (GO:0032003)|receptor binding (GO:0005102)										TGGCCGTGGCAGGCCCTGTCCC	0.584																																					p.A19fs		Atlas-INDEL	.											.	.	.	.	0			c.57_58insG						.																																			SO:0001589	frameshift_variant	282618	exon1			.	AY129150	CCDS12531.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000182393	ENSG00000182393		"Interferons"	18363	protein-coding gene	gene with protein product		607403	"interleukin 29", "interleukin 29 (interferon, lambda 1)"	IL29			Standard	NM_172140		Approved	IL-29	uc002okv.3	Q8IU54		ENST00000333625.2:c.59dupG	chr19.hg19:g.39787120_39787120dupG	ENSP00000329991:p.Gly20fs	124.0	0.0		111.0	10.0	NM_172140	A0AV25|Q17R34	Frame_Shift_Ins	INS	ENST00000333625.2	hg19	CCDS12531.1																																																																																			.	.		0.584	IFNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463834.1	NM_172140		G	39787119	-	G	39787118	7	5	38	1	0	1	1	0	0	0	0	0	7694	175	7	0	59	0	IL29	19	39787118	Frame_Shift_Ins	INS	-	TCGA-BC-A10Z-01A-11D-A12Z-10	18066426	39787118	19341865	156	4603										
SERTAD1	29950	hgsc.bcm.edu	37	chr19	40929016	40929016	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cccaggctgggcgctgctccCccgatgctacggcctggtgg	15	16	0	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:40929016C>A	ENST00000357949.4	-	2	596	c.438G>T	c.(436-438)ggG>ggT	p.G146G		NM_013376.3	NP_037508.2	Q9UHV2	SRTD1_HUMAN	SERTA domain containing 1	146					positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription, DNA-templated (GO:0006351)					endometrium(2)|lung(1)|prostate(1)|skin(1)	5			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCGCTGCTCCCCCGATGCTAC	0.652																																					p.G146G		Atlas-SNP	.											.	SERTAD1	18	.	0			c.G438T						.						15	14	14					19																	40929016		2193	4297	6490	SO:0001819	synonymous_variant	29950	exon2			TGCTCCCCCGATG	AF117959	CCDS12557.1	19q13.1-q13.2	2008-02-05				ENSG00000197019			17932	protein-coding gene	gene with protein product	"CDK4-binding protein p34SEI", "transcriptional regulator interacting with the PHD-bromodomain 1"					6434876, 10580009	Standard	NM_013376		Approved	SEI1, TRIP-Br1	uc002ont.4	Q9UHV2		ENST00000357949.4:c.438G>T	chr19.hg19:g.40929016C>A		56.0	0.0		40.0	19.0	NM_013376	Q9BUE7	Silent	SNP	ENST00000357949.4	hg19	CCDS12557.1																																																																																			.	.		0.652	SERTAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462571.1	NM_013376		A	40929016	C	A	40929016	2	1	38	1	0	0	0	0	0	0	0	1	14135	610	22	3		3	SERTAD1	19	40929016	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	1141898	40929016	18199967	157	4604										
POU2F2	5452	hgsc.bcm.edu	37	chr19	42636560	42636560	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	agcccccatgctggagtgaaCcatgctgcccgccccgccag	11	18	0	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:42636560C>A	ENST00000526816.2	-	1	19	c.4G>T	c.(4-6)Gtt>Ttt	p.V2F	CTC-378H22.1_ENST00000527895.1_RNA|POU2F2_ENST00000529067.1_Missense_Mutation_p.V2F|POU2F2_ENST00000560398.1_Missense_Mutation_p.V2F|POU2F2_ENST00000389341.5_Missense_Mutation_p.V2F|POU2F2_ENST00000342301.4_Missense_Mutation_p.V2F|CTC-378H22.1_ENST00000531517.1_RNA|POU2F2_ENST00000529952.1_Missense_Mutation_p.V2F|POU2F2_ENST00000533720.1_Missense_Mutation_p.V2F|POU2F2_ENST00000560558.1_Missense_Mutation_p.V2F|MIR4323_ENST00000582929.1_RNA|POU2F2_ENST00000524801.2_Intron			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	2					cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	CTGGAGTGAACCATGCTGCCC	0.657																																					p.V2F		Atlas-SNP	.											.	POU2F2	106	.	0			c.G4T						.						37	36	36					19																	42636560		2203	4300	6503	SO:0001583	missense	5452	exon1			AGTGAACCATGCT		CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9213	protein-coding gene	gene with protein product		164176	"POU domain class 2, transcription factor 2"	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.4G>T	chr19.hg19:g.42636560C>A	ENSP00000431603:p.Val2Phe	69.0	0.0		92.0	42.0	NM_002698	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	hg19	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.542156	0.65198	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952	D;D;D;D;D	0.83755	-1.69;-1.74;-1.76;-1.5;-1.67	4.09	4.09	0.47781	.	4.384240	0.00780	N	0.001278	T	0.81805	0.4900	N	0.08118	0	0.29510	N	0.854286	B;P;B	0.50156	0.087;0.932;0.213	B;P;B	0.55391	0.086;0.775;0.141	T	0.74990	-0.3475	10	0.59425	D	0.04	.	12.011	0.53286	0.0:1.0:0.0:0.0	.	2;2;2	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	F	2;2;2;2;1;2;2	ENSP00000373992:V2F;ENSP00000339369:V2F;ENSP00000437221:V2F;ENSP00000437224:V2F;ENSP00000436988:V2F	ENSP00000292077:V2F	V	-	1	0	POU2F2	47328400	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.610000	0.46325	2.296000	0.77279	0.313000	0.20887	GTT	.	.		0.657	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			A	42636560	C	A	42636560	3	1	38	1	0	0	0	0	1	0	0	0	12281	507	18	3	1443	3	POU2F2	19	42636560	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	1707544	42636560	16492423	158	4605										
ZNF285	26974	hgsc.bcm.edu	37	chr19	44890851	44890851	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ctgaattccggctgaagcctTtaccacactcatcacattta	5	13	2	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:44890851T>G	ENST00000330997.4	-	4	1620	c.1556A>C	c.(1555-1557)aAa>aCa	p.K519T	ZNF285_ENST00000591679.1_Missense_Mutation_p.K526T|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Missense_Mutation_p.K519T	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	519					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						GCTGAAGCCTTTACCACACTC	0.413																																					p.K519T		Atlas-SNP	.											.	ZNF285	86	.	0			c.A1556C						.						90	92	91					19																	44890851		2203	4300	6503	SO:0001583	missense	26974	exon4			AAGCCTTTACCAC	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1556A>C	chr19.hg19:g.44890851T>G	ENSP00000333595:p.Lys519Thr	501.0	0.0		422.0	204.0	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	hg19	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.152482	0.57259	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.07908	3.15	3.6	2.56	0.30785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23249	0.0562	M	0.94101	3.495	0.23515	N	0.997514	D;D	0.56968	0.978;0.978	P;P	0.48488	0.579;0.579	T	0.17715	-1.0360	9	0.87932	D	0	.	8.1482	0.31124	0.0:0.103:0.0:0.897	.	543;519	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	T	542;519	ENSP00000333595:K519T	ENSP00000333595:K519T	K	-	2	0	ZNF285	49582691	0.999000	0.42202	0.972000	0.41901	0.983000	0.72400	5.705000	0.68355	0.389000	0.25086	0.373000	0.22412	AAA	.	.		0.413	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		G	44890851	T	G	44890851	3	3	38	1	0	0	0	0	1	0	0	0	17837	1841	64	5	220	5	ZNF285	19	44890851	Missense_Mutation	SNP	T	TCGA-BC-A10Z-01A-11D-A12Z-10	2254291	44890851	14238132	159	4606										
IZUMO1	284359	hgsc.bcm.edu	37	chr19	49248991	49248991	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tgcttcgcatccaggtggccAggcaggtaatctttctccag	11	12	2	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:49248991A>G	ENST00000332955.2	-	2	673	c.126T>C	c.(124-126)ccT>ccC	p.P42P		NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	42					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		CCAGGTGGCCAGGCAGGTAAT	0.547																																					p.P42P		Atlas-SNP	.											.	IZUMO1	30	.	0			c.T126C						.						143	139	140					19																	49248991		2203	4300	6503	SO:0001819	synonymous_variant	284359	exon2			GTGGCCAGGCAGG	BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"-"	28539	protein-coding gene	gene with protein product	"oocyte binding/fusion factor"	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.126T>C	chr19.hg19:g.49248991A>G		378.0	0.0		356.0	161.0	NM_182575	Q6Q8P6|Q6Q8P7	Silent	SNP	ENST00000332955.2	hg19	CCDS12732.1																																																																																			.	.		0.547	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575		G	49248991	A	G	49248991	2	3	38	1	0	0	0	0	0	0	0	1	7942	175	7	2		2	IZUMO1	19	49248991	Silent	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	4358140	49248991	9879992	160	4607										
IL4I1	259307	hgsc.bcm.edu	37	chr19	50393089	50393089	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gcgtgcccctcggggctggcCgtgtccgatgcaggcccctt	15	16	0	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:50393089C>T	ENST00000391826.2	-	8	1684	c.1542G>A	c.(1540-1542)acG>acA	p.T514T	MIR4750_ENST00000584564.1_RNA|IL4I1_ENST00000595948.1_Silent_p.T536T|IL4I1_ENST00000341114.3_Silent_p.T536T	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	514						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	CGGGGCTGGCCGTGTCCGATG	0.687																																					p.T536T		Atlas-SNP	.											.	IL4I1	50	.	0			c.G1608A						.						46	46	46					19																	50393089		2202	4299	6501	SO:0001819	synonymous_variant	259307	exon10			GCTGGCCGTGTCC	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.1542G>A	chr19.hg19:g.50393089C>T		155.0	0.0		147.0	6.0	NM_172374	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Silent	SNP	ENST00000391826.2	hg19	CCDS12787.1																																																																																			.	.		0.687	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			T	50393089	C	T	50393089	2	4	38	1	0	0	0	0	0	0	0	1	7706	639	23	1		1	IL4I1	19	50393089	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	1144098	50393089	8735894	161	4608										
KLK6	5653	hgsc.bcm.edu	37	chr19	51465087	51465087	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	taggcatgctcacactcctcAcgggacaccaggtggatgta	11	12	2	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:51465087A>T	ENST00000376851.3	-	5	934	c.495T>A	c.(493-495)cgT>cgA	p.R165R	KLK6_ENST00000594641.1_Silent_p.R165R|KLK6_ENST00000391808.1_Silent_p.R58R|KLK6_ENST00000310157.2_Silent_p.R165R|KLK6_ENST00000456750.2_Silent_p.R58R|CTB-147C22.8_ENST00000601506.1_RNA|KLK6_ENST00000376853.4_Intron	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	165	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		CACACTCCTCACGGGACACCA	0.582																																					p.R165R		Atlas-SNP	.											.	KLK6	35	.	0			c.T495A						.						161	124	136					19																	51465087		2203	4300	6503	SO:0001819	synonymous_variant	5653	exon5			CTCCTCACGGGAC	U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"Kallikreins", "Serine peptidases / Serine peptidases"	6367	protein-coding gene	gene with protein product		602652	"protease, serine, 18", "kallikrein 6 (neurosin, zyme)"	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.495T>A	chr19.hg19:g.51465087A>T		121.0	0.0		149.0	65.0	NM_001012964	A6NJA1|A8MW09|Q6H301	Silent	SNP	ENST00000376851.3	hg19	CCDS12811.1																																																																																			.	.		0.582	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774		T	51465087	A	T	51465087	2	4	38	1	0	0	0	0	0	0	0	1	8417	146	6	4		4	KLK6	19	51465087	Silent	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10	1071998	51465087	7663896	162	4609										
KLK8	11202	hgsc.bcm.edu	37	chr19	51503358	51503358	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	actttggaccccagggatgcCtggtcacgcagttgaagaag	13	10	1	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:51503358C>T	ENST00000600767.1	-	5	876	c.387G>A	c.(385-387)caG>caA	p.Q129Q	KLK8_ENST00000320838.5_Intron|KLK8_ENST00000291726.7_Silent_p.Q129Q|CTB-147C22.9_ENST00000594512.1_RNA|KLK8_ENST00000347619.4_Intron|KLK8_ENST00000391806.2_Silent_p.Q174Q|KLK8_ENST00000593490.1_Intron|KLK8_ENST00000598195.1_5'Flank			O60259	KLK8_HUMAN	kallikrein-related peptidase 8	129	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell death (GO:0008219)|keratinocyte proliferation (GO:0043616)|memory (GO:0007613)|negative regulation of axon regeneration (GO:0048681)|negative regulation of myelination (GO:0031642)|neuron projection morphogenesis (GO:0048812)|regulation of synapse organization (GO:0050807)|response to wounding (GO:0009611)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(8)|prostate(1)	15		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.0033)|GBM - Glioblastoma multiforme(134;0.00888)		CCAGGGATGCCTGGTCACGCA	0.567																																					p.Q174Q		Atlas-SNP	.											.	KLK8	46	.	0			c.G522A						.						136	124	128					19																	51503358		2203	4300	6503	SO:0001819	synonymous_variant	11202	exon4			GGATGCCTGGTCA	AB008390	CCDS12813.1, CCDS12814.1, CCDS12815.1, CCDS42600.1, CCDS74433.1	19q13	2011-09-07	2006-10-27			ENSG00000129455		"Kallikreins", "Serine peptidases / Serine peptidases"	6369	protein-coding gene	gene with protein product		605644	"kallikrein 8 (neuropsin/ovasin)"	PRSS19		10102990, 9714609, 16800724, 16800723	Standard	NM_144505		Approved	HNP, TADG14, neuropsin, ovasin	uc002pur.1	O60259		ENST00000600767.1:c.387G>A	chr19.hg19:g.51503358C>T		108.0	0.0		97.0	53.0	NM_144505	Q5V9X1|Q5V9X2|Q8IW69|Q9HCB3|Q9NR68|Q9NR69|Q9UIL9|Q9UQ47	Silent	SNP	ENST00000600767.1	hg19	CCDS12813.1																																																																																			.	.		0.567	KLK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465032.2	NM_007196		T	51503358	C	T	51503358	2	4	38	1	0	0	0	0	0	0	0	1	8419	680	24	3		3	KLK8	19	51503358	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	38271	51503358	7625625	163	4610										
ZNF835	90485	hgsc.bcm.edu	37	chr19	57176266	57176266	+	Frame_Shift_Del	DEL	C	C	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cttggggcctccacctctctCccgctggcggctgtcaggat							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr19:57176266delC	ENST00000537055.2	-	2	532	c.301delG	c.(301-303)gagfs	p.E101fs		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	101					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CCACCTCTCTCCCGCTGGCGG	0.637																																					p.E101fs		Atlas-Indel,Pindel	.											.	ZNF835	106	.	0			c.302delA						.						46	55	52					19																	57176266		2139	4263	6402	SO:0001589	frameshift_variant	90485	exon2			.	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.301delG	chr19.hg19:g.57176266delC	ENSP00000444747:p.Glu101fs	81.0	0.0		80.0	38.0	NM_001005850	B7Z5Y0|G3V1S0	Frame_Shift_Del	DEL	ENST00000537055.2	hg19	CCDS56105.1																																																																																			.	.		0.637	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		-	57176266	C	-	57176266	7	5	38	1	0	1	0	1	0	0	0	0	18201	864	30	0	1314	0	ZNF835	19	57176266	Frame_Shift_Del	DEL	C	TCGA-BC-A10Z-01A-11D-A12Z-10	5672908	57176266	1952717	164	4611										
ZFP64	55734	hgsc.bcm.edu	37	chr20	50701265	50701265	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	atctcagagagtcatccctgAcgaaggaggcgccgcaggtc	13	12	2	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr20:50701265A>C	ENST00000361387.2	-	9	1829	c.1769T>G	c.(1768-1770)gTc>gGc	p.V590G	ZFP64_ENST00000371523.4_Missense_Mutation_p.V371G|ZFP64_ENST00000371518.2_Intron	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	435					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						GTCATCCCTGACGAAGGAGGC	0.602																																					p.V590G		Atlas-SNP	.											.	ZFP64	240	.	0			c.T1769G						.						56	49	51					20																	50701265		2203	4300	6503	SO:0001583	missense	55734	exon9			TCCCTGACGAAGG	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000361387.2:c.1769T>G	chr20.hg19:g.50701265A>C	ENSP00000355179:p.Val590Gly	75.0	0.0		93.0	52.0	NM_199427	Q9NTS7|Q9NVH4	Missense_Mutation	SNP	ENST00000361387.2	hg19	CCDS13439.1	.	.	.	.	.	.	.	.	.	.	A	14.24	2.476129	0.44044	.	.	ENSG00000020256	ENST00000371523;ENST00000361387	T;T	0.70516	-0.49;-0.49	4.4	3.26	0.37387	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57213	0.2038	L	0.28694	0.88	0.80722	D	1	B;B	0.25441	0.092;0.126	B;B	0.27715	0.036;0.082	T	0.50591	-0.8810	9	0.33940	T	0.23	.	10.3403	0.43873	0.9204:0.0:0.0796:0.0	.	590;371	Q9NTW7;Q9NTW7-2	ZF64B_HUMAN;.	G	371;590	ENSP00000360578:V371G;ENSP00000355179:V590G	ENSP00000355179:V590G	V	-	2	0	ZFP64	50134672	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.096000	0.76960	0.778000	0.33520	0.533000	0.62120	GTC	.	.		0.602	ZFP64-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079743.2	NM_018197		C	50701265	A	C	50701265	3	2	38	1	0	0	0	0	1	0	0	0	17667	275	10	5	172	5	ZFP64	20	50701265	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10		50701265	12324255	165	4612										
PMEPA1	56937	hgsc.bcm.edu	37	chr20	56227370	56227370	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggggggcaggggccgcccagCctggcactatccatcaggtc	16	14	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr20:56227370C>T	ENST00000341744.3	-	4	922	c.603G>A	c.(601-603)agG>agA	p.R201R	PMEPA1_ENST00000265626.4_Silent_p.R151R|PMEPA1_ENST00000395814.1_Silent_p.R151R|PMEPA1_ENST00000347215.4_Silent_p.R166R|PMEPA1_ENST00000395816.3_Silent_p.R151R	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	201					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						GGCCGCCCAGCCTGGCACTAT	0.687																																					p.R201R		Atlas-SNP	.											.	PMEPA1	29	.	0			c.G603A						.						33	37	36					20																	56227370		2203	4300	6503	SO:0001819	synonymous_variant	56937	exon4			GCCCAGCCTGGCA	AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"solid tumor-associated 1"	606564	"transmembrane, prostate androgen induced RNA"	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.603G>A	chr20.hg19:g.56227370C>T		17.0	0.0		34.0	20.0	NM_020182	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Silent	SNP	ENST00000341744.3	hg19	CCDS13463.1																																																																																			.	.		0.687	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182		T	56227370	C	T	56227370	2	4	38	1	0	0	0	0	0	0	0	1	12141	738	26	3		3	PMEPA1	20	56227370	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	5526105	56227370	6798150	166	4613										
SS18L1	26039	hgsc.bcm.edu	37	chr20	60747838	60747838	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cccagccagcagagctacccCgggcagcagcagggctacgg	14	16	0	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr20:60747838C>T	ENST00000331758.3	+	9	1043	c.1017C>T	c.(1015-1017)ccC>ccT	p.P339P	SS18L1_ENST00000421564.1_Silent_p.P339P|SS18L1_ENST00000370848.4_Silent_p.P342P	NM_198935.1	NP_945173.1	O75177	CREST_HUMAN	synovial sarcoma translocation gene on chromosome 18-like 1	339	Gln-rich.|Necessary for nuclear localization. {ECO:0000250}.				chromatin modification (GO:0016568)|dendrite development (GO:0016358)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of dendrite development (GO:0050773)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)|kinetochore (GO:0000776)|nuclear body (GO:0016604)|nucleus (GO:0005634)			SS18L1/SSX1(2)	ovary(2)|skin(1)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			AGAGCTACCCCGGGCAGCAGC	0.687			T	SSX1	synovial sarcoma																																p.P339P		Atlas-SNP	.		Dom	yes		20	20q13.3	26039	synovial sarcoma translocation gene on chromosome 18-like 1		M	SS18L1_ENST00000331758,right_upper_lobe,carcinoma,0,1	SS18L1	37	.	0			c.C1017T						.						40	45	43					20																	60747838		2203	4300	6503	SO:0001819	synonymous_variant	26039	exon9			CTACCCCGGGCAG	AB014593	CCDS13491.1	20q13.3	2008-07-28			ENSG00000184402	ENSG00000184402			15592	protein-coding gene	gene with protein product		606472					Standard	XM_005260389		Approved	KIAA0693	uc002ycb.3	O75177	OTTHUMG00000032902	ENST00000331758.3:c.1017C>T	chr20.hg19:g.60747838C>T		78.0	0.0		94.0	4.0	NM_198935	A6NNE3|A8K620|B3KWR8|E1P5H7|Q5JXJ3|Q6MZV9|Q6NTH3|Q6XYD9|Q8NE69|Q9BR55|Q9H4K6	Silent	SNP	ENST00000331758.3	hg19	CCDS13491.1																																																																																			.	.		0.687	SS18L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080004.2			T	60747838	C	T	60747838	2	4	38	1	0	0	0	0	0	0	0	1	15191	639	23	1		1	SS18L1	20	60747838	Silent	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	4520468	60747838	2277682	167	4614										
MYT1	4661	hgsc.bcm.edu	37	chr20	62839764	62839764	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ggctgcccgcctgccgagcaGagccagctgggcctgggaga	17	14	0	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr20:62839764G>T	ENST00000328439.1	+	7	1579	c.1215G>T	c.(1213-1215)caG>caT	p.Q405H	MYT1_ENST00000536311.1_Missense_Mutation_p.Q405H|MYT1_ENST00000360149.4_Intron	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	Interaction with PIN1.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					CTGCCGAGCAGAGCCAGCTGG	0.662																																					p.Q405H	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.G1215T						.						21	23	22					20																	62839764		2202	4294	6496	SO:0001583	missense	4661	exon7			CGAGCAGAGCCAG	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.1215G>T	chr20.hg19:g.62839764G>T	ENSP00000327465:p.Gln405His	53.0	0.0		63.0	25.0	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	hg19	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	g	0.398	-0.919828	0.02396	.	.	ENSG00000196132	ENST00000328439;ENST00000536311	T;T	0.42513	0.97;0.97	4.03	-1.15	0.09709	.	0.738237	0.12756	N	0.441789	T	0.24005	0.0581	L	0.40543	1.245	0.09310	N	0.999994	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.0	T	0.17289	-1.0374	10	0.25751	T	0.34	-2.8734	0.0439	0.00009	0.3183:0.2156:0.1788:0.2872	.	405;405	F5H7M8;Q01538	.;MYT1_HUMAN	H	405	ENSP00000327465:Q405H;ENSP00000442412:Q405H	ENSP00000327465:Q405H	Q	+	3	2	MYT1	62310208	0.015000	0.18098	0.423000	0.26634	0.187000	0.23431	-0.972000	0.03802	0.176000	0.19873	0.450000	0.29827	CAG	.	.		0.662	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		T	62839764	G	T	62839764	3	4	38	1	0	0	0	0	1	0	0	0	10115	933	33	3	1233	3	MYT1	20	62839764	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	2091926	62839764	185756	168	4615										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41505791	41505791	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cgtctctcaccatcctctttGgtccgggtgaagatctgctc	9	14	4	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr21:41505791G>T	ENST00000400454.1	-	19	4029	c.3552C>A	c.(3550-3552)acC>acA	p.T1184T		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1184	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CATCCTCTTTGGTCCGGGTGA	0.602																																					p.T1184T	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C3552A						.						78	83	81					21																	41505791		2055	4220	6275	SO:0001819	synonymous_variant	1826	exon19			CTCTTTGGTCCGG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.3552C>A	chr21.hg19:g.41505791G>T		159.0	0.0		146.0	59.0	NM_001271534	O60468	Silent	SNP	ENST00000400454.1	hg19	CCDS42929.1																																																																																			.	.		0.602	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		T	41505791	G	T	41505791	2	4	38	1	0	0	0	0	0	0	0	1	4770	1335	47	3		3	DSCAM	21	41505791	Silent	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10		41505791	6624104	169	4616										
CABIN1	23523	hgsc.bcm.edu	37	chr22	24472172	24472172	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	catgctgctgaacacagcccAcgagtatttgggcagaaggt	12	10	0	2			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr22:24472172A>T	ENST00000398319.2	+	19	3072	c.2687A>T	c.(2686-2688)cAc>cTc	p.H896L	CABIN1_ENST00000405822.2_Missense_Mutation_p.H846L|CABIN1_ENST00000263119.5_Missense_Mutation_p.H896L	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	896					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AACACAGCCCACGAGTATTTG	0.572																																					p.H896L		Atlas-SNP	.											.	CABIN1	153	.	0			c.A2687T						.						124	94	104					22																	24472172		2203	4300	6503	SO:0001583	missense	23523	exon19			CAGCCCACGAGTA	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.2687A>T	chr22.hg19:g.24472172A>T	ENSP00000381364:p.His896Leu	270.0	0.0		297.0	147.0	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	hg19	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.885211	0.91814	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.51071	0.72;0.72;0.72	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.68559	0.3014	M	0.77313	2.365	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.986	T	0.73655	-0.3914	10	0.87932	D	0	.	14.0721	0.64865	1.0:0.0:0.0:0.0	.	846;896	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	L	896;846;896	ENSP00000263119:H896L;ENSP00000384694:H846L;ENSP00000381364:H896L	ENSP00000263119:H896L	H	+	2	0	CABIN1	22802172	1.000000	0.71417	0.988000	0.46212	0.988000	0.76386	9.334000	0.96470	1.988000	0.58038	0.529000	0.55759	CAC	.	.		0.572	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		T	24472172	A	T	24472172	3	4	38	1	0	0	0	0	1	0	0	0	2530	159	6	4	2757	4	CABIN1	22	24472172	Missense_Mutation	SNP	A	TCGA-BC-A10Z-01A-11D-A12Z-10		24472172	26832394	170	4617										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26423432	26423432	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	ttttgaagaagagcccggagCccaaggaggatcccgctcac	12	12	1	3			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr22:26423432C>T	ENST00000407587.2	+	43	7664	c.7495C>T	c.(7495-7497)Ccc>Tcc	p.P2499S	MYO18B_ENST00000335473.7_Missense_Mutation_p.P2498S|MYO18B_ENST00000536101.1_Missense_Mutation_p.P2498S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2498						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GAGCCCGGAGCCCAAGGAGGA	0.537																																					p.P2498S		Atlas-SNP	.											.	MYO18B	322	.	0			c.C7492T						.						62	65	64					22																	26423432		2009	4151	6160	SO:0001583	missense	84700	exon43			CCGGAGCCCAAGG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7495C>T	chr22.hg19:g.26423432C>T	ENSP00000386096:p.Pro2499Ser	68.0	0.0		66.0	33.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	7.796	0.712680	0.15306	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86030	-2.04;-2.04;-2.06	5.17	-6.48	0.01896	.	0.923307	0.09057	N	0.854978	T	0.47060	0.1425	N	0.00677	-1.265	0.09310	N	1	B;B;B;B;B	0.09022	0.002;0.001;0.001;0.001;0.001	B;B;B;B;B	0.08055	0.003;0.001;0.001;0.002;0.002	T	0.54002	-0.8358	10	0.07030	T	0.85	.	2.2834	0.04120	0.1081:0.1833:0.321:0.3877	.	2011;2500;2498;2499;2498	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	S	2498;2498;2499	ENSP00000441229:P2498S;ENSP00000334563:P2498S;ENSP00000386096:P2499S	ENSP00000334563:P2498S	P	+	1	0	MYO18B	24753432	0.000000	0.05858	0.026000	0.17262	0.775000	0.43874	-1.064000	0.03461	-1.266000	0.02446	0.561000	0.74099	CCC	.	.		0.537	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26423432	C	T	26423432	3	4	38	1	0	0	0	0	1	0	0	0	10075	739	26	3	7658	3	MYO18B	22	26423432	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	1951260	26423432	24881134	171	4618										
SMTN	6525	hgsc.bcm.edu	37	chr22	31487025	31487025	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	tcgtgtccacaagttcacatCtgattctcctatggctgcta	7	12	3	1			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chr22:31487025C>G	ENST00000347557.2	+	10	1234	c.1016C>G	c.(1015-1017)tCt>tGt	p.S339C	SMTN_ENST00000404574.1_5'Flank|SMTN_ENST00000333137.7_Missense_Mutation_p.S339C|SMTN_ENST00000358743.1_Missense_Mutation_p.S339C	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	339					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						AAGTTCACATCTGATTCTCCT	0.632																																					p.S395C		Atlas-SNP	.											.	SMTN	219	.	0			c.C1184G						.						119	112	115					22																	31487025		2203	4300	6503	SO:0001583	missense	6525	exon9			TCACATCTGATTC	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.1016C>G	chr22.hg19:g.31487025C>G	ENSP00000328635:p.Ser339Cys	247.0	0.0		261.0	109.0	NM_001207018	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	hg19	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.983413	0.35036	.	.	ENSG00000183963	ENST00000358743;ENST00000347557;ENST00000333137;ENST00000329852;ENST00000404496	T;T;T	0.71341	-0.13;-0.56;-0.56	5.22	3.12	0.35913	.	0.000000	0.33496	N	0.004859	T	0.78585	0.4306	L	0.54323	1.7	0.49389	D	0.999786	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;0.999;1.0	D;D;D;D;D;D	0.79784	0.993;0.985;0.993;0.96;0.993;0.98	T	0.78460	-0.2195	10	0.72032	D	0.01	-4.3699	10.7585	0.46251	0.0:0.8412:0.0:0.1588	.	395;393;331;339;339;339	E7ETT8;B4E229;B5MC56;E7EWD0;P53814;P53814-5	.;.;.;.;SMTN_HUMAN;.	C	339;339;339;339;331	ENSP00000351593:S339C;ENSP00000328635:S339C;ENSP00000329532:S339C	ENSP00000329393:S339C	S	+	2	0	SMTN	29817025	0.623000	0.27094	0.016000	0.15963	0.152000	0.21847	1.474000	0.35398	0.710000	0.31997	-0.339000	0.08088	TCT	.	.		0.632	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		G	31487025	C	G	31487025	3	3	38	1	0	0	0	0	1	0	0	0	14829	913	32	4	1050	4	SMTN	22	31487025	Missense_Mutation	SNP	C	TCGA-BC-A10Z-01A-11D-A12Z-10	5063593	31487025	19817541	172	4619										
NHS	4810	hgsc.bcm.edu	37	chrX	17710579	17710579	+	Frame_Shift_Del	DEL	C	C	-													0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	cgtgagtttaaggaccgtcaCtttttaacggtaagtttggt							TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chrX:17710579delC	ENST00000380060.3	+	3	1181	c.843delC	c.(841-843)cacfs	p.H281fs	NHS_ENST00000398097.3_Frame_Shift_Del_p.H104fs	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	281					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					AGGACCGTCACTTTTTAACGG	0.557																																					p.H281fs		Atlas-Indel,Pindel	.											.	NHS	302	.	0			c.842delA						.						97	76	83					X																	17710579		2203	4300	6503	SO:0001589	frameshift_variant	4810	exon3			.		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.843delC	chrX.hg19:g.17710579delC	ENSP00000369400:p.His281fs	267.0	0.0		191.0	88.0	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Frame_Shift_Del	DEL	ENST00000380060.3	hg19	CCDS14181.1																																																																																			.	.		0.557	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		-	17710579	C	-	17710579	7	5	38	1	0	1	0	1	0	0	0	0	10420	564	20	0	891	0	NHS	23	17710579	Frame_Shift_Del	DEL	C	TCGA-BC-A10Z-01A-11D-A12Z-10		17710579	137559981	173	4620										
CNKSR2	22866	hgsc.bcm.edu	37	chrX	21627708	21627708	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	aggaggaggaggaaggggagGcagcaggggaaaacatagga	21	3	0	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chrX:21627708G>T	ENST00000379510.3	+	20	2701	c.2665G>T	c.(2665-2667)Gca>Tca	p.A889S	CNKSR2_ENST00000425654.2_Missense_Mutation_p.A859S|CNKSR2_ENST00000279451.4_Missense_Mutation_p.A889S|CNKSR2_ENST00000543067.1_Missense_Mutation_p.A840S	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	889					regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						ggaaggggaggCAGCAGGGGA	0.483																																					p.A889S		Atlas-SNP	.											.	CNKSR2	158	.	0			c.G2665T						.						30	22	24					X																	21627708		2198	4286	6484	SO:0001583	missense	22866	exon20			GGGGAGGCAGCAG	AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.2665G>T	chrX.hg19:g.21627708G>T	ENSP00000368824:p.Ala889Ser	22.0	0.0		29.0	21.0	NM_014927	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Missense_Mutation	SNP	ENST00000379510.3	hg19	CCDS14198.1	.	.	.	.	.	.	.	.	.	.	G	9.358	1.067308	0.20067	.	.	ENSG00000149970	ENST00000425654;ENST00000543067;ENST00000279451;ENST00000379510	T;T;T;T	0.18338	2.52;2.22;2.22;2.52	5.38	5.38	0.77491	.	0.466636	0.22677	N	0.056985	T	0.07728	0.0194	N	0.03608	-0.345	0.32442	N	0.546594	B;B;B;B	0.10296	0.001;0.003;0.003;0.001	B;B;B;B	0.06405	0.001;0.001;0.002;0.001	T	0.14924	-1.0455	10	0.12103	T	0.63	-24.7324	13.3527	0.60611	0.0:0.0:0.8425:0.1575	.	859;840;481;889	B7ZLJ1;B4DGR4;B3KPN2;Q8WXI2	.;.;.;CNKR2_HUMAN	S	859;840;889;889	ENSP00000397906:A859S;ENSP00000444633:A840S;ENSP00000279451:A889S;ENSP00000368824:A889S	ENSP00000279451:A889S	A	+	1	0	CNKSR2	21537629	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.914000	0.63348	2.365000	0.80145	0.513000	0.50165	GCA	.	.		0.483	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927		T	21627708	G	T	21627708	3	4	38	1	0	0	0	0	1	0	0	0	3609	1203	42	3	2743	3	CNKSR2	23	21627708	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	3917129	21627708	133642852	174	4621										
AR	367	hgsc.bcm.edu	37	chrX	66766453	66766453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0581395348837209	10	1	1.29237288135593	1.90625	1.06395348837209	0.688167990308251	1	0	gctacactcggccccctcagGggctggcgggccaggaaagc	15	15	1	0			TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	g.chrX:66766453G>A	ENST00000374690.3	+	1	1989	c.1465G>A	c.(1465-1467)Ggg>Agg	p.G489R	AR_ENST00000513847.1_3'UTR|AR_ENST00000504326.1_Missense_Mutation_p.G489R|AR_ENST00000396044.3_Missense_Mutation_p.G489R	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	488	Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	GCCCCCTCAGGGGCTGGCGGG	0.731									Androgen Insensitivity Syndrome																												p.G489R		Atlas-SNP	.											.	AR	249	.	0			c.G1465A						.						20	16	17					X																	66766453		2190	4266	6456	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CCTCAGGGGCTGG	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.1465G>A	chrX.hg19:g.66766453G>A	ENSP00000363822:p.Gly489Arg	48.0	0.0		53.0	22.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	g	24.7	4.561604	0.86335	.	.	ENSG00000169083	ENST00000544984;ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	D;D;D	0.93712	-2.55;-3.27;-2.75	5.06	5.06	0.68205	.	0.400730	0.25503	N	0.030237	D	0.96318	0.8799	M	0.78916	2.43	0.39176	D	0.962693	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.96683	0.9505	10	0.48119	T	0.1	.	14.701	0.69157	0.0:0.0:1.0:0.0	.	489;489;488	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	R	299;489;489;489;481	ENSP00000363822:G489R;ENSP00000421155:G489R;ENSP00000379359:G489R	ENSP00000363822:G489R	G	+	1	0	AR	66683178	1.000000	0.71417	0.996000	0.52242	0.877000	0.50540	4.056000	0.57448	2.349000	0.79799	0.509000	0.49947	GGG	.	.		0.731	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		A	66766453	G	A	66766453	3	1	38	1	0	0	0	0	1	0	0	0	836	1232	43	3	1467	3	AR	23	66766453	Missense_Mutation	SNP	G	TCGA-BC-A10Z-01A-11D-A12Z-10	45138745	66766453	88504107	175	4622										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158651408	158651408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	actggtcacccttctccaggGtcagctctaacagcaggtcc	9	15	4	0			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr1:158651408G>A	ENST00000368147.4	-	4	620	c.440C>T	c.(439-441)aCc>aTc	p.T147I		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	147					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CTTCTCCAGGGTCAGCTCTAA	0.547																																					p.T147I		Atlas-SNP	.											.	SPTA1	720	.	0			c.C440T						.						132	135	134					1																	158651408		2011	4166	6177	SO:0001583	missense	6708	exon4			TCCAGGGTCAGCT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.440C>T	chr1.hg19:g.158651408G>A	ENSP00000357129:p.Thr147Ile	281.0	0.0		224.0	16.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	9.380	1.072843	0.20147	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48836	0.8;0.8	5.15	3.25	0.37280	.	.	.	.	.	T	0.24470	0.0593	M	0.65677	2.01	0.35854	D	0.826973	B	0.10296	0.003	B	0.18561	0.022	T	0.06881	-1.0802	9	0.23302	T	0.38	.	6.9641	0.24613	0.3221:0.0:0.6779:0.0	.	147	P02549	SPTA1_HUMAN	I	147	ENSP00000357130:T147I;ENSP00000357129:T147I	ENSP00000357129:T147I	T	-	2	0	SPTA1	156918032	0.999000	0.42202	0.960000	0.40013	0.347000	0.29111	3.240000	0.51368	1.401000	0.46761	0.563000	0.77884	ACC	.	.		0.547	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158651408	G	A	158651408	3	1	39	1	0	0	0	0	1	0	0	0	15131	1261	44	3	7015	3	SPTA1	1	158651408	Missense_Mutation	SNP	G	TCGA-BC-A110-01A-11D-A12Z-10		158651408	90599213	1	4623										
PKP1	5317	hgsc.bcm.edu	37	chr1	201293599	201293600	+	Frame_Shift_Ins	INS	-	-	C													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	attgggctgaaggaaaagggINScctgccacaaattgcccgcc							TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr1:201293599_201293600insC	ENST00000352845.3	+	11	1787_1788	c.1787_1788insC	c.(1786-1791)ggcctgfs	p.L597fs	PKP1_ENST00000367324.3_Frame_Shift_Ins_p.L576fs|PKP1_ENST00000263946.3_Frame_Shift_Ins_p.L597fs			Q13835	PKP1_HUMAN	plakophilin 1	597					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						AAGGAAAAGGGCCTGCCACAAA	0.579																																					p.G596fs		Atlas-INDEL	.											.,2	PKP1	127	.	0			c.1787_1788insC						.																																			SO:0001589	frameshift_variant	5317	exon11			.	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"Armadillo repeat containing"	9023	protein-coding gene	gene with protein product	"ectodermal dysplasia/skin fragility syndrome"	601975	"plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.1789dupC	chr1.hg19:g.201293601_201293601dupC	ENSP00000295597:p.Leu597fs	106.0	0.0		78.0	10.0	NM_000299	O00645|Q14CA0|Q15152	Frame_Shift_Ins	INS	ENST00000352845.3	hg19	CCDS30966.1																																																																																			.	.		0.579	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		C	201293600	-	C	201293599	7	5	39	1	0	1	1	0	0	0	0	0	11993	1203	42	0	1829	0	PKP1	1	201293599	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10	42642191	201293599	47957022	2	4624										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214557735	214557735	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	ggtgcctctcccgcatctccGgttggctgtacaccagatcc	10	16	2	1	rs144475962		TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr1:214557735G>T	ENST00000366956.5	-	13	1657	c.1463C>A	c.(1462-1464)cCg>cAg	p.P488Q	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	488					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CCGCATCTCCGGTTGGCTGTA	0.537																																					p.P488Q	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											PTPN14,NS,malignant_melanoma,0,1	PTPN14	168	.	0			c.C1463A						.						149	158	155					1																	214557735		2203	4300	6503	SO:0001583	missense	5784	exon13			ATCTCCGGTTGGC	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.1463C>A	chr1.hg19:g.214557735G>T	ENSP00000355923:p.Pro488Gln	392.0	1.0		329.0	23.0	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.290951	0.80914	.	.	ENSG00000152104	ENST00000366956	T	0.75704	-0.96	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.86234	0.5884	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86783	0.1980	10	0.62326	D	0.03	.	19.3634	0.94451	0.0:0.0:1.0:0.0	.	488	Q15678	PTN14_HUMAN	Q	488	ENSP00000355923:P488Q	ENSP00000355923:P488Q	P	-	2	0	PTPN14	212624358	1.000000	0.71417	0.962000	0.40283	0.912000	0.54170	9.666000	0.98612	2.583000	0.87209	0.650000	0.86243	CCG	.	G|0.999;A|0.001		0.537	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		T	214557735	G	T	214557735	3	4	39	1	0	0	0	0	1	0	0	0	12796	1116	39	1	2128	1	PTPN14	1	214557735	Missense_Mutation	SNP	G	TCGA-BC-A110-01A-11D-A12Z-10	13264136	214557735	34692886	3	4625										
C1orf65	164127	hgsc.bcm.edu	37	chr1	223568584	223568584	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	ttccaggagttccagaagctCcctcaggcctccaggagaga	11	13	1	2			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr1:223568584C>T	ENST00000366875.3	+	1	1870	c.1767C>T	c.(1765-1767)ctC>ctT	p.L589L		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		589										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		TCCAGAAGCTCCCTCAGGCCT	0.557																																					p.L589L		Atlas-SNP	.											.	C1orf65	71	.	0			c.C1767T						.						65	64	64					1																	223568584		2203	4300	6503	SO:0001819	synonymous_variant	164127	exon1			GAAGCTCCCTCAG																												ENST00000366875.3:c.1767C>T	chr1.hg19:g.223568584C>T		138.0	0.0		115.0	9.0	NM_152610	Q8N746|Q8NA93	Silent	SNP	ENST00000366875.3	hg19	CCDS1537.1																																																																																			.	.		0.557	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			T	223568584	C	T	223568584	2	4	39	1	0	0	0	0	0	0	0	1	2057	842	30	3		3	C1orf65	1	223568584	Silent	SNP	C	TCGA-BC-A110-01A-11D-A12Z-10	9010849	223568584	25682037	4	4626										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228495849	228495849	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	gtacgggggctggttgatgcGgaggtgacggccgatgagga	21	6	0	3	rs562134549		TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr1:228495849G>T	ENST00000422127.1	+	47	12548	c.12504G>T	c.(12502-12504)gcG>gcT	p.A4168A	OBSCN_ENST00000366707.4_Silent_p.A1802A|OBSCN_ENST00000284548.11_Silent_p.A4168A|OBSCN_ENST00000570156.2_Silent_p.A5125A|OBSCN_ENST00000366709.4_Silent_p.A1287A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4168					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGGTTGATGCGGAGGTGACGG	0.602																																					p.A5125A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G15375T						.						88	101	97					1																	228495849		2160	4257	6417	SO:0001819	synonymous_variant	84033	exon58			TGATGCGGAGGTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.12504G>T	chr1.hg19:g.228495849G>T		168.0	0.0		129.0	9.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.602	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228495849	G	T	228495849	2	4	39	1	0	0	0	0	0	0	0	1	10821	1103	39	1		1	OBSCN	1	228495849	Silent	SNP	G	TCGA-BC-A110-01A-11D-A12Z-10	4927265	228495849	20754772	5	4627										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71658550	71658550	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	caaatcagtggcgtctgatgTccctgagggtaaagttaaaa	11	7	2	2	rs201989581		TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr2:71658550T>G	ENST00000409544.1	+	26	6374	c.5744T>G	c.(5743-5745)gTc>gGc	p.V1915G	ZNF638_ENST00000264447.4_Missense_Mutation_p.V1915G|ZNF638_ENST00000355812.3_3'UTR|ZNF638_ENST00000409407.1_Missense_Mutation_p.V855G	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1915					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GCGTCTGATGTCCCTGAGGGT	0.443																																					p.V1915G		Atlas-SNP	.											.	ZNF638	179	.	0			c.T5744G						.						48	47	47					2																	71658550		2203	4300	6503	SO:0001583	missense	27332	exon26			CTGATGTCCCTGA	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5744T>G	chr2.hg19:g.71658550T>G	ENSP00000386433:p.Val1915Gly	404.0	0.0		292.0	12.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	T	15.04	2.714121	0.48622	.	.	ENSG00000075292	ENST00000264447;ENST00000409544;ENST00000409407	T;T;T	0.34072	1.38;1.38;1.78	4.87	2.38	0.29361	.	0.747498	0.11444	N	0.563489	T	0.34395	0.0896	L	0.29908	0.895	0.33958	D	0.645225	P;P	0.49783	0.928;0.546	P;B	0.50659	0.647;0.205	T	0.45131	-0.9282	10	0.66056	D	0.02	0.1063	7.1578	0.25647	0.0:0.189:0.0:0.811	.	1915;1915	Q14966-3;Q14966	.;ZN638_HUMAN	G	1915;1915;855	ENSP00000264447:V1915G;ENSP00000386433:V1915G;ENSP00000386813:V855G	ENSP00000264447:V1915G	V	+	2	0	ZNF638	71512058	0.550000	0.26489	0.722000	0.30670	0.991000	0.79684	0.518000	0.22847	0.390000	0.25115	0.392000	0.25879	GTC	.	T|0.999;C|0.001		0.443	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		G	71658550	T	G	71658550	3	3	39	1	0	0	0	0	1	0	0	0	18070	1667	58	5	5842	5	ZNF638	2	71658550	Missense_Mutation	SNP	T	TCGA-BC-A110-01A-11D-A12Z-10		71658550	171540823	6	4628										
NCL	4691	hgsc.bcm.edu	37	chr2	232325420	232325420	+	Missense_Mutation	SNP	A	A	T													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	tcctcctcatcatcttcatcAtcatcatcttcatcatcttc					rs527711138|rs371359723	byFrequency	TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr2:232325420A>T	ENST00000322723.4	-	4	1011	c.771T>A	c.(769-771)gaT>gaA	p.D257E	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	257	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		catcttcatcatcatcatctt	0.433																																					p.D257E		Atlas-SNP	.											.	NCL	80	.	0			c.T771A						.						231	195	207					2																	232325420		2203	4300	6503	SO:0001583	missense	4691	exon4			TTCATCATCATCA		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.771T>A	chr2.hg19:g.232325420A>T	ENSP00000318195:p.Asp257Glu	258.0	0.0		322.0	41.0	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	hg19	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	A	0.113	-1.136367	0.01742	.	.	ENSG00000115053	ENST00000322723;ENST00000392033	T	0.12147	2.71	4.93	-9.86	0.00473	.	1.236740	0.05337	N	0.529361	T	0.03651	0.0104	N	0.01800	-0.715	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.20974	-1.0259	10	0.02654	T	1	0.6458	10.0345	0.42120	0.1491:0.5688:0.1562:0.1259	.	257	P19338	NUCL_HUMAN	E	257;149	ENSP00000318195:D257E	ENSP00000318195:D257E	D	-	3	2	NCL	232033664	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-13.503000	0.00001	-5.449000	0.00014	-3.075000	0.00066	GAT	.	.		0.433	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		T	232325420	A	T	232325420	3	4	39	1	0	0	0	0	1	0	0	0	10235	214	8	4	1405	4	NCL	2	232325420	Missense_Mutation	SNP	A	TCGA-BC-A110-01A-11D-A12Z-10	160666870	232325420	10873953	7	4629	19	2								
NCL	4691	hgsc.bcm.edu	37	chr2	232325423	232325423	+	Missense_Mutation	SNP	A	A	T													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	tcctcatcatcttcatcatcAtcatcttcatcatcttcgtc					rs375194579		TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr2:232325423A>T	ENST00000322723.4	-	4	1008	c.768T>A	c.(766-768)gaT>gaA	p.D256E	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	256	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		cttcatcatcatcatcttcat	0.433																																					p.D256E		Atlas-SNP	.											.	NCL	80	.	0			c.T768A						.						238	199	212					2																	232325423		2203	4300	6503	SO:0001583	missense	4691	exon4			ATCATCATCATCT		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.768T>A	chr2.hg19:g.232325423A>T	ENSP00000318195:p.Asp256Glu	473.0	0.0		384.0	36.0	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	hg19	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	A	0.085	-1.176650	0.01646	.	.	ENSG00000115053	ENST00000322723;ENST00000392033	T	0.41400	1.0	4.86	-9.72	0.00515	.	1.228550	0.05655	N	0.585809	T	0.09379	0.0231	N	0.01109	-1.01	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.05500	-1.0881	10	0.06365	T	0.9	0.1898	3.4755	0.07583	0.235:0.3943:0.2326:0.1382	.	256	P19338	NUCL_HUMAN	E	256;148	ENSP00000318195:D256E	ENSP00000318195:D256E	D	-	3	2	NCL	232033667	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.904000	0.00091	-3.318000	0.00188	-2.212000	0.00299	GAT	.	.		0.433	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		T	232325423	A	T	232325423	3	4	39	1	0	0	0	0	1	0	0	0	10235	214	8	4	1408	4	NCL	2	232325423	Missense_Mutation	SNP	A	TCGA-BC-A110-01A-11D-A12Z-10	3	232325423	10873950	8	4630	19	2								
USP40	55230	hgsc.bcm.edu	37	chr2	234394446	234394446	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	ggaagccactcgaacttttcGggaaagtatttggcaatttc	10	8	0	0	rs542793420		TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr2:234394446G>A	ENST00000427112.2	-	28	3407	c.3372C>T	c.(3370-3372)ccC>ccT	p.P1124P	USP40_ENST00000496298.1_5'UTR|USP40_ENST00000251722.6_Silent_p.P1124P|USP40_ENST00000450966.1_Silent_p.P1136P			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1124					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CGAACTTTTCGGGAAAGTATT	0.512													G|||	1	0.000199681	0	0	5008	,	,		18876	0.001		0	False		,,,				2504	0				p.P1136P		Atlas-SNP	.											.	USP40	174	.	0			c.C3408T						.						24	27	26					2																	234394446		1875	4098	5973	SO:0001819	synonymous_variant	55230	exon28			CTTTTCGGGAAAG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3372C>T	chr2.hg19:g.234394446G>A		438.0	0.0		335.0	21.0	NM_018218	Q6NX38|Q70EL0	Silent	SNP	ENST00000427112.2	hg19	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312564	0.23908	.	.	ENSG00000085982	ENST00000454354	T	0.34072	1.38	5.75	-2.8	0.05823	.	0.636347	0.17268	N	0.180514	T	0.36853	0.0982	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33574	-0.9863	7	0.62326	D	0.03	.	4.7274	0.12948	0.4326:0.0:0.3385:0.2289	.	.	.	.	L	92	ENSP00000394133:P92L	ENSP00000394133:P92L	P	-	2	0	USP40	234059185	0.357000	0.24938	0.954000	0.39281	0.965000	0.64279	-0.372000	0.07504	-0.444000	0.07170	-1.000000	0.02509	CCG	.	.		0.512	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		A	234394446	G	A	234394446	2	1	39	1	0	0	0	0	0	0	0	1	17087	1103	39	1		1	USP40	2	234394446	Silent	SNP	G	TCGA-BC-A110-01A-11D-A12Z-10	2069023	234394446	8804927	9	4631										
SMARCC1	6599	hgsc.bcm.edu	37	chr3	47629720	47629721	+	Frame_Shift_Ins	INS	-	-	G													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	aaggagcagctgaggctggcINSgggccaggagcaggaggcgg					rs35867350		TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr3:47629720_47629721insG	ENST00000254480.5	-	28	3415_3416	c.3296_3297insC	c.(3295-3297)ccgfs	p.P1099fs	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	1099	Pro-rich.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		CTGAGGCTGGCGGGCCAGGAGC	0.604																																					p.P1099fs		Atlas-INDEL	.											.	SMARCC1	85	.	0			c.3297_3298insC						.																																			SO:0001589	frameshift_variant	6599	exon28			.	U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.3297dupC	chr3.hg19:g.47629723_47629723dupG	ENSP00000254480:p.Pro1099fs	151.0	0.0		116.0	11.0	NM_003074	Q17RS0|Q6P172|Q8IWH2	Frame_Shift_Ins	INS	ENST00000254480.5	hg19	CCDS2758.1																																																																																			.	.		0.604	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1			G	47629721	-	G	47629720	7	5	39	1	0	1	1	0	0	0	0	0	14790	755	27	0	24	0	SMARCC1	3	47629720	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10		47629720	150392710	10	4632										
IFT57	55081	hgsc.bcm.edu	37	chr3	107937444	107937444	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	aagcaatcaagaacatagcaTacatgttctccataacctga	5	10	2	2			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr3:107937444T>C	ENST00000264538.3	-	3	679	c.432A>G	c.(430-432)gtA>gtG	p.V144V		NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	144					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			GAACATAGCATACATGTTCTC	0.338																																					p.V144V		Atlas-SNP	.											.	IFT57	44	.	0			c.A432G						.						69	70	69					3																	107937444		2203	4300	6503	SO:0001819	synonymous_variant	55081	exon3			ATAGCATACATGT	AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"Intraflagellar transport homologs"	17367	protein-coding gene	gene with protein product		606621	"estrogen-related receptor beta like 1", "intraflagellar transport 57 homolog (Chlamydomonas)"	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.432A>G	chr3.hg19:g.107937444T>C		393.0	0.0		307.0	13.0	NM_018010	Q96DA9	Silent	SNP	ENST00000264538.3	hg19	CCDS2951.1																																																																																			.	.		0.338	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010		C	107937444	T	C	107937444	2	2	39	1	0	0	0	0	0	0	0	1	7571	1393	49	2		2	IFT57	3	107937444	Silent	SNP	T	TCGA-BC-A110-01A-11D-A12Z-10	60307724	107937444	90084986	11	4633										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148886196	148886196	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	aagcggcagcccagaatctcGtgttaatgcgatccatttct	9	11	2	1			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr4:148886196G>A	ENST00000336498.3	+	17	1711	c.1472G>A	c.(1471-1473)cGt>cAt	p.R491H	ARHGAP10_ENST00000414545.2_Missense_Mutation_p.R140H	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	1254					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		CCAGAATCTCGTGTTAATGCG	0.308																																					p.R491H		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.G1472A						.						78	76	77					4																	148886196		2203	4300	6503	SO:0001583	missense	79658	exon17			AATCTCGTGTTAA	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.1472G>A	chr4.hg19:g.148886196G>A	ENSP00000336923:p.Arg491His	561.0	0.0		466.0	23.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.634973	0.67130	.	.	ENSG00000071205	ENST00000336498;ENST00000414545	T;T	0.22743	1.94;1.94	5.55	5.55	0.83447	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.64907	0.2641	H	0.97465	4.01	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.991;0.996	T	0.78548	-0.2162	10	0.87932	D	0	.	19.5156	0.95162	0.0:0.0:1.0:0.0	.	72;140;491	Q86T21;E7EUW5;A1A4S6	.;.;RHG10_HUMAN	H	491;140	ENSP00000336923:R491H;ENSP00000406624:R140H	ENSP00000336923:R491H	R	+	2	0	ARHGAP10	149105646	1.000000	0.71417	0.961000	0.40146	0.122000	0.20287	9.059000	0.93902	2.611000	0.88343	0.561000	0.74099	CGT	.	.		0.308	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		A	148886196	G	A	148886196	3	1	39	1	0	0	0	0	1	0	0	0	862	1145	40	1	1538	1	ARHGAP10	4	148886196	Missense_Mutation	SNP	G	TCGA-BC-A110-01A-11D-A12Z-10		148886196	42268080	12	4634										
SGTB	54557	hgsc.bcm.edu	37	chr5	64976616	64976616	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	atttattcaaggcagtgaggGccagcctgaagggaatagaa	13	6	1	3			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr5:64976616G>A	ENST00000381007.4	-	7	720	c.485C>T	c.(484-486)gCc>gTc	p.A162V		NM_019072.2	NP_061945.1	Q96EQ0	SGTB_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, beta	162										large_intestine(3)|lung(3)|skin(3)	9		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)		GGCAGTGAGGGCCAGCCTGAA	0.353																																					p.A162V		Atlas-SNP	.											.	SGTB	22	.	0			c.C485T						.						71	69	70					5																	64976616		2203	4300	6503	SO:0001583	missense	54557	exon7			GTGAGGGCCAGCC	AK096321	CCDS3988.1	5q12.3	2013-01-10			ENSG00000197860	ENSG00000197860		"Tetratricopeptide (TTC) repeat domain containing"	23567	protein-coding gene	gene with protein product						12477932	Standard	XM_005248548		Approved	Sgt2, FLJ39002	uc003jud.3	Q96EQ0	OTTHUMG00000097801	ENST00000381007.4:c.485C>T	chr5.hg19:g.64976616G>A	ENSP00000370395:p.Ala162Val	182.0	0.0		136.0	9.0	NM_019072		Missense_Mutation	SNP	ENST00000381007.4	hg19	CCDS3988.1	.	.	.	.	.	.	.	.	.	.	G	34	5.356958	0.95854	.	.	ENSG00000197860	ENST00000381007;ENST00000506816	T;T	0.67171	-0.25;-0.25	5.31	5.31	0.75309	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.114435	0.64402	D	0.000014	D	0.82504	0.5051	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.83842	0.0258	10	0.56958	D	0.05	-26.1574	18.9824	0.92760	0.0:0.0:1.0:0.0	.	162	Q96EQ0	SGTB_HUMAN	V	162	ENSP00000370395:A162V;ENSP00000421447:A162V	ENSP00000370395:A162V	A	-	2	0	SGTB	65012372	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.444000	0.97578	2.496000	0.84212	0.557000	0.71058	GCC	.	.		0.353	SGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215057.2	NM_019072		A	64976616	G	A	64976616	3	1	39	1	0	0	0	0	1	0	0	0	14241	1203	42	3	449	3	SGTB	5	64976616	Missense_Mutation	SNP	G	TCGA-BC-A110-01A-11D-A12Z-10		64976616	115938644	13	4635										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167645298	167645299	+	Frame_Shift_Ins	INS	-	-	T													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	tgactactcactcagcaaacINStagccattcactctgccctg							TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr5:167645298_167645299insT	ENST00000518659.1	+	23	4441_4442	c.4402_4403insT	c.(4402-4404)ctafs	p.L1468fs	TENM2_ENST00000520394.1_Frame_Shift_Ins_p.L1229fs|TENM2_ENST00000545108.1_Frame_Shift_Ins_p.L1467fs|TENM2_ENST00000519204.1_Frame_Shift_Ins_p.L1347fs|TENM2_ENST00000403607.2_Frame_Shift_Ins_p.L1292fs	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1468					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										ACTCAGCAAACTAGCCATTCAC	0.51																																					p.L1459fs		Atlas-INDEL	.											.	.	.	.	0			c.4375_4376insT						.																																			SO:0001589	frameshift_variant	57451	exon23			.	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.4403dupT	chr5.hg19:g.167645299_167645299dupT	ENSP00000429430:p.Leu1468fs	174.0	0.0		115.0	12.0	NM_001122679	Q9ULU2	Frame_Shift_Ins	INS	ENST00000518659.1	hg19																																																																																				.	.		0.51	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	167645299	-	T	167645298	7	5	39	1	0	1	1	0	0	0	0	0	10844	564	20	0	4465	0	ODZ2	5	167645298	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10	102668682	167645298	13269962	14	4636										
MSH5	4439	hgsc.bcm.edu	37	chr6	31729664	31729665	+	Frame_Shift_Ins	INS	-	-	C													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	ttgcgaaggtgttgcgaaggINSccagccatgcctcccacaca							TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr6:31729664_31729665insC	ENST00000375755.3	+	23	2537_2538	c.2251_2252insC	c.(2251-2253)gccfs	p.A751fs	SAPCD1_ENST00000415669.2_5'Flank|MSH5_ENST00000375750.3_Frame_Shift_Ins_p.A751fs|MSH5_ENST00000375742.3_Frame_Shift_Ins_p.A768fs|MSH5_ENST00000375740.3_Intron|MSH5-SAPCD1_ENST00000491552.1_Intron|MSH5_ENST00000375703.3_Frame_Shift_Ins_p.A752fs|SAPCD1-AS1_ENST00000419679.1_RNA|SAPCD1_ENST00000425424.1_5'Flank|MSH5_ENST00000431848.2_Frame_Shift_Ins_p.A450fs|MSH5_ENST00000534153.4_Frame_Shift_Ins_p.A768fs|MSH5-SAPCD1_ENST00000493662.2_Frame_Shift_Ins_p.A768fs|MSH5_ENST00000395853.1_Frame_Shift_Ins_p.A425fs	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	751					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						TGTTGCGAAGGCCAGCCATGCC	0.515								Direct reversal of damage;Mismatch excision repair (MMR)																													p.A752fs		Atlas-INDEL	.											.	MSH5	108	.	0			c.2254_2255insC						.																																			SO:0001589	frameshift_variant	4439	exon23			.	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"mutS (E. coli) homolog 5", "mutS homolog 5 (E. coli)"			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.2253dupC	chr6.hg19:g.31729666_31729666dupC	ENSP00000364908:p.Ala751fs	224.0	0.0		169.0	11.0	NM_172165	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Frame_Shift_Ins	INS	ENST00000375755.3	hg19	CCDS4720.1																																																																																			.	.		0.515	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4			C	31729665	-	C	31729664	7	5	39	1	0	1	1	0	0	0	0	0	9882	1203	42	0	2391	0	MSH5	6	31729664	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10		31729664	139385403	15	4637										
C6orf106	64771	hgsc.bcm.edu	37	chr6	34574641	34574641	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	agctgctgcgttactcctaaAagtccacccacctccacact	5	17	0	0			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr6:34574641A>C	ENST00000374023.3	-	4	795	c.552T>G	c.(550-552)ctT>ctG	p.L184L	C6orf106_ENST00000374026.3_Silent_p.L118L|C6orf106_ENST00000374021.1_Silent_p.L110L	NM_024294.2	NP_077270.1	Q9H6K1	CF106_HUMAN	chromosome 6 open reading frame 106	184										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10						TTACTCCTAAAAGTCCACCCA	0.468																																					p.L184L		Atlas-SNP	.											.	C6orf106	29	.	0			c.T552G						.						73	65	68					6																	34574641		2203	4300	6503	SO:0001819	synonymous_variant	64771	exon4			TCCTAAAAGTCCA	AF052106	CCDS4795.1, CCDS4796.1	6p21.31	2012-01-27			ENSG00000196821	ENSG00000196821			21215	protein-coding gene	gene with protein product		612217					Standard	XM_005249298		Approved	FLJ22195, dJ391O22.4	uc003ojr.2	Q9H6K1	OTTHUMG00000014553	ENST00000374023.3:c.552T>G	chr6.hg19:g.34574641A>C		91.0	0.0		67.0	8.0	NM_024294	B2R8K7|Q5VV77|Q96MG5|Q9BUR9	Silent	SNP	ENST00000374023.3	hg19	CCDS4796.1																																																																																			.	.		0.468	C6orf106-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040251.1	NM_022758		C	34574641	A	C	34574641	2	2	39	1	0	0	0	0	0	0	0	1	2321	1	1	5		5	C6orf106	6	34574641	Silent	SNP	A	TCGA-BC-A110-01A-11D-A12Z-10	2844977	34574641	136540426	16	4638										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76018525	76018526	+	Frame_Shift_Ins	INS	-	-	C													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	cagatttcctgctcctggggINSctgccactactggctttcct							TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr6:76018525_76018526insC	ENST00000237172.7	-	6	3853_3854	c.3523_3524insG	c.(3523-3525)gccfs	p.A1175fs	FILIP1_ENST00000393004.2_Intron|FILIP1_ENST00000370020.1_Frame_Shift_Ins_p.A1076fs|FILIP1_ENST00000498523.1_5'UTR	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1175										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						TGCTCCTGGGGCTGCCACTACT	0.52																																					p.A1175fs		Atlas-INDEL	.											.	FILIP1	173	.	0			c.3524_3525insG						.																																			SO:0001589	frameshift_variant	27145	exon6			.	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.3524dupG	chr6.hg19:g.76018526_76018526dupC	ENSP00000237172:p.Ala1175fs	455.0	0.0		214.0	17.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Frame_Shift_Ins	INS	ENST00000237172.7	hg19	CCDS4984.1																																																																																			.	.		0.52	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		C	76018526	-	C	76018525	7	5	39	1	0	1	1	0	0	0	0	0	5902	1203	42	0	121	0	FILIP1	6	76018525	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10	41443884	76018525	95096542	17	4639										
GJB7	375519	hgsc.bcm.edu	37	chr6	87994213	87994213	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	atatagcttataaaataaaaCaaggaagccaatttcaaaac	4	6	1	0	rs568580095|rs373942790	byFrequency	TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr6:87994213C>T	ENST00000525899.1	-	3	763	c.418G>A	c.(418-420)Gtt>Att	p.V140I	GJB7_ENST00000296882.3_Missense_Mutation_p.V140I	NM_198568.2	NP_940970.1	Q6PEY0	CXB7_HUMAN	gap junction protein, beta 7, 25kDa	140					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)	5		all_cancers(76;1.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;7.38e-10)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00323)		BRCA - Breast invasive adenocarcinoma(108;0.0167)		TAAAATAAAACAAGGAAGCCA	0.403																																					p.V140I		Atlas-SNP	.											.	GJB7	28	.	0			c.G418A						.																																			SO:0001583	missense	375519	exon3			ATAAAACAAGGAA	AJ414563	CCDS5008.1	6q15	2008-02-05	2007-11-06			ENSG00000164411		"Ion channels / Gap junction proteins (connexins)"	16690	protein-coding gene	gene with protein product	"connexin 25"	611921	"gap junction protein, beta 7"				Standard	NM_198568		Approved	CX25, bA136M9.1	uc003plo.2	Q6PEY0		ENST00000525899.1:c.418G>A	chr6.hg19:g.87994213C>T	ENSP00000435355:p.Val140Ile	99.0	0.0		79.0	16.0	NM_198568	B3KXL0|Q96KP0	Missense_Mutation	SNP	ENST00000525899.1	hg19	CCDS5008.1	.	.	.	.	.	.	.	.	.	.	C	3.485	-0.105081	0.06967	.	.	ENSG00000164411	ENST00000525899;ENST00000296882;ENST00000369576	D;D;D	0.95788	-3.81;-3.81;-3.81	4.98	1.07	0.20283	Gap junction protein, cysteine-rich domain (1);	0.205176	0.31199	U	0.008077	D	0.83133	0.5188	L	0.41124	1.26	0.09310	N	1	B	0.20368	0.044	B	0.25987	0.065	T	0.74025	-0.3797	10	0.22706	T	0.39	.	5.8059	0.18440	0.1334:0.6349:0.0:0.2317	.	140	Q6PEY0	CXB7_HUMAN	I	140	ENSP00000435355:V140I;ENSP00000296882:V140I;ENSP00000358589:V140I	ENSP00000296882:V140I	V	-	1	0	GJB7	88050932	0.009000	0.17119	0.983000	0.44433	0.056000	0.15407	0.695000	0.25527	0.145000	0.18977	-0.314000	0.08810	GTT	.	.		0.403	GJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394780.1			T	87994213	C	T	87994213	3	4	39	1	0	0	0	0	1	0	0	0	6421	478	17	3	257	3	GJB7	6	87994213	Missense_Mutation	SNP	C	TCGA-BC-A110-01A-11D-A12Z-10	11975688	87994213	83120854	18	4640										
SUMF2	25870	hgsc.bcm.edu	37	chr7	56144554	56144555	+	Frame_Shift_Ins	INS	-	-	C													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	tacccatgggggaactggttINSccagccaaaccgcaccaacc					rs541718189		TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr7:56144554_56144555insC	ENST00000413756.1	+	6	586_587	c.563_564insC	c.(562-567)ttccagfs	p.Q189fs	SUMF2_ENST00000395435.2_Intron|SUMF2_ENST00000395436.2_Frame_Shift_Ins_p.Q193fs|SUMF2_ENST00000434526.2_Frame_Shift_Ins_p.Q208fs|SUMF2_ENST00000275607.9_Frame_Shift_Ins_p.Q101fs|SUMF2_ENST00000342190.6_Frame_Shift_Ins_p.Q208fs|SUMF2_ENST00000437307.2_Intron			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	189					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GGGAACTGGTTCCAGCCAAACC	0.54																																					p.F207fs		Atlas-INDEL	.											.	SUMF2	56	.	0			c.620_621insC						.																																			SO:0001589	frameshift_variant	25870	exon6			.	AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103			20415	protein-coding gene	gene with protein product		607940				12757706	Standard	NM_015411		Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.565dupC	chr7.hg19:g.56144556_56144556dupC	ENSP00000406445:p.Gln189fs	207.0	0.0		140.0	10.0	NM_015411	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Frame_Shift_Ins	INS	ENST00000413756.1	hg19																																																																																				.	.		0.54	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411		C	56144555	-	C	56144554	7	5	39	1	0	1	1	0	0	0	0	0	15401	1783	62	0	642	0	SUMF2	7	56144554	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10		56144554	102994109	19	4641										
GUSB	2990	hgsc.bcm.edu	37	chr7	65440043	65440043	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	cacaggccccagtgacgtctGtgcagtcagctgcacctatg	11	14	2	1			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr7:65440043G>A	ENST00000304895.4	-	6	1058	c.928C>T	c.(928-930)Cag>Tag	p.Q310*	GUSB_ENST00000421103.1_Nonsense_Mutation_p.Q164*|GUSB_ENST00000345660.6_Intron|GUSB_ENST00000476486.1_5'UTR	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	310					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						AGTGACGTCTGTGCAGTCAGC	0.607																																					p.Q310X		Atlas-SNP	.											.	GUSB	52	.	0			c.C928T						.						70	64	66					7																	65440043		2203	4300	6503	SO:0001587	stop_gained	2990	exon6			ACGTCTGTGCAGT	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.928C>T	chr7.hg19:g.65440043G>A	ENSP00000302728:p.Gln310*	80.0	0.0		68.0	9.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Nonsense_Mutation	SNP	ENST00000304895.4	hg19	CCDS5530.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376815	0.82682	.	.	ENSG00000169919	ENST00000304895;ENST00000421103	.	.	.	4.99	1.04	0.20106	.	0.888310	0.09996	N	0.729024	.	.	.	.	.	.	0.38947	D	0.958264	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	9.8986	0.41334	0.0:0.3697:0.3767:0.2536	.	.	.	.	X	310;164	.	ENSP00000302728:Q310X	Q	-	1	0	GUSB	65077478	0.937000	0.31787	0.003000	0.11579	0.219000	0.24729	1.931000	0.40134	0.005000	0.14708	0.511000	0.50034	CAG	.	.		0.607	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		A	65440043	G	A	65440043	4	1	39	1	0	0	0	0	0	1	0	0	6911	1386	48	3	1055	3	GUSB	7	65440043	Nonsense_Mutation	SNP	G	TCGA-BC-A110-01A-11D-A12Z-10	9295489	65440043	93698620	20	4642										
LRRCC1	85444	hgsc.bcm.edu	37	chr8	86057622	86057622	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	taaaatttacatgtcgatttAggtccatcaaattgaaaaag	6	5	1	1			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr8:86057622A>T	ENST00000360375.3	+	19	3125		c.e19-1		LRRCC1_ENST00000414626.2_Splice_Site	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1						mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.?(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						ATGTCGATTTAGGTCCATCAA	0.264																																					.		Atlas-SNP	.											LRRCC1_ENST00000414626,NS,carcinoma,0,2	LRRCC1	212	.	2	Unknown(2)	lung(2)	c.2977-2A>T						.						37	34	35					8																	86057622		1785	4056	5841	SO:0001630	splice_region_variant	85444	exon19			CGATTTAGGTCCA	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.2977-1A>T	chr8.hg19:g.86057622A>T		463.0	2.0		438.0	27.0	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Splice_Site	SNP	ENST00000360375.3	hg19	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	A	10.56	1.384971	0.25031	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9715	0.71238	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LRRCC1	86244874	1.000000	0.71417	0.972000	0.41901	0.023000	0.10783	7.483000	0.81158	2.112000	0.64535	0.459000	0.35465	.	.	.		0.264	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	Intron	T	86057622	A	T	86057622	5	4	39	1	0	0	0	0	0	0	1	0	9035	434	15	4	3049	4	LRRCC1	8	86057622	Splice_Site	SNP	A	TCGA-BC-A110-01A-11D-A12Z-10		86057622	60306400	21	4643										
CTHRC1	115908	hgsc.bcm.edu	37	chr8	104388131	104388131	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	aggagtcctggacacccaacTacaagcagtgttcatggagt	11	10	1	0			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr8:104388131T>A	ENST00000330295.5	+	2	458	c.316T>A	c.(316-318)Tac>Aac	p.Y106N	CTHRC1_ENST00000520880.1_5'Flank|CTHRC1_ENST00000520337.1_Missense_Mutation_p.Y92N|CTHRC1_ENST00000415886.2_Missense_Mutation_p.Y106N	NM_138455.3	NP_612464.1	Q96CG8	CTHR1_HUMAN	collagen triple helix repeat containing 1	106					cell migration (GO:0016477)|cochlea morphogenesis (GO:0090103)|establishment of planar polarity involved in neural tube closure (GO:0090177)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|ossification involved in bone remodeling (GO:0043932)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein binding (GO:0032092)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)				endometrium(1)|large_intestine(5)|lung(4)|ovary(1)|urinary_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)			GACACCCAACTACAAGCAGTG	0.433																																					p.Y106N		Atlas-SNP	.											.	CTHRC1	29	.	0			c.T316A						.						65	62	63					8																	104388131		2203	4300	6503	SO:0001583	missense	115908	exon2			CCCAACTACAAGC	BC014245	CCDS6299.1, CCDS59110.1	8q22.3	2008-08-07			ENSG00000164932	ENSG00000164932			18831	protein-coding gene	gene with protein product		610635				15618538	Standard	NM_138455		Approved		uc003ylk.4	Q96CG8	OTTHUMG00000164887	ENST00000330295.5:c.316T>A	chr8.hg19:g.104388131T>A	ENSP00000330523:p.Tyr106Asn	147.0	0.0		143.0	8.0	NM_138455	G3V141|Q6UW91|Q8IX63	Missense_Mutation	SNP	ENST00000330295.5	hg19	CCDS6299.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.717135	0.68844	.	.	ENSG00000164932	ENST00000330295;ENST00000415886;ENST00000520337;ENST00000297577	T;D;T	0.97066	-0.09;-4.23;0.93	5.69	5.69	0.88448	.	0.113131	0.64402	D	0.000007	D	0.96996	0.9019	L	0.36672	1.1	0.80722	D	1	D;P	0.76494	0.999;0.734	P;B	0.62014	0.897;0.133	D	0.97670	1.0166	10	0.59425	D	0.04	-13.2529	15.9482	0.79809	0.0:0.0:0.0:1.0	.	106;106	E7EVQ5;Q96CG8	.;CTHR1_HUMAN	N	106;106;92;92	ENSP00000330523:Y106N;ENSP00000416045:Y106N;ENSP00000430550:Y92N	ENSP00000297577:Y92N	Y	+	1	0	CTHRC1	104457307	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.166000	0.68216	0.477000	0.44152	TAC	.	.		0.433	CTHRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380792.1	NM_138455		A	104388131	T	A	104388131	3	1	39	1	0	0	0	0	1	0	0	0	4012	1522	53	4	322	4	CTHRC1	8	104388131	Missense_Mutation	SNP	T	TCGA-BC-A110-01A-11D-A12Z-10	18330509	104388131	41975891	22	4644										
ABRA	137735	hgsc.bcm.edu	37	chr8	107782232	107782232	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	agggggtgtgattggtttagGagcttgaggtgagtcctggg	20	3	0	3			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr8:107782232G>C	ENST00000311955.3	-	1	241	c.187C>G	c.(187-189)Cct>Gct	p.P63A		NM_139166.4	NP_631905.1			actin-binding Rho activating protein									p.P63T(1)		breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			ATTGGTTTAGGAGCTTGAGGT	0.607																																					p.P63A		Atlas-SNP	.											ABRA,NS,carcinoma,0,1	ABRA	57	.	1	Substitution - Missense(1)	ovary(1)	c.C187G						.						89	90	90					8																	107782232		2203	4300	6503	SO:0001583	missense	137735	exon1			GTTTAGGAGCTTG	AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"striated muscle activator of Rho-dependent signaling"	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.187C>G	chr8.hg19:g.107782232G>C	ENSP00000311436:p.Pro63Ala	573.0	0.0		354.0	32.0	NM_139166		Missense_Mutation	SNP	ENST00000311955.3	hg19	CCDS6305.1	.	.	.	.	.	.	.	.	.	.	G	1.608	-0.524884	0.04141	.	.	ENSG00000174429	ENST00000311955	D	0.92446	-3.04	5.66	0.368	0.16146	.	0.804396	0.11835	N	0.524850	D	0.85124	0.5625	L	0.50333	1.59	0.09310	N	1	B	0.27068	0.167	B	0.24269	0.052	T	0.71269	-0.4643	10	0.31617	T	0.26	0.172	0.8137	0.01098	0.3794:0.1161:0.2683:0.2362	.	63	Q8N0Z2	ABRA_HUMAN	A	63	ENSP00000311436:P63A	ENSP00000311436:P63A	P	-	1	0	ABRA	107851408	0.000000	0.05858	0.008000	0.14137	0.330000	0.28571	0.103000	0.15292	0.030000	0.15379	-0.150000	0.13652	CCT	.	.		0.607	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166		C	107782232	G	C	107782232	3	2	39	1	0	0	0	0	1	0	0	0	100	1174	41	4	966	4	ABRA	8	107782232	Missense_Mutation	SNP	G	TCGA-BC-A110-01A-11D-A12Z-10	3394101	107782232	38581790	23	4645										
TLN1	7094	hgsc.bcm.edu	37	chr9	35725253	35725254	+	Frame_Shift_Ins	INS	-	-	C													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	atgtagtagtccaaagctttINScccagcctccagccatatac							TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr9:35725253_35725254insC	ENST00000314888.9	-	3	548_549	c.195_196insG	c.(193-198)gggaaafs	p.K66fs	TLN1_ENST00000540444.1_Frame_Shift_Ins_p.K66fs	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	66					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCCAAAGCTTTCCCAGCCTCCA	0.485																																					p.K66fs		Atlas-INDEL	.											.	TLN1	185	.	0			c.196_197insG						.																																			SO:0001589	frameshift_variant	7094	exon3			.	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.196dupG	chr9.hg19:g.35725256_35725256dupC	ENSP00000316029:p.Lys66fs	175.0	0.0		136.0	12.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Frame_Shift_Ins	INS	ENST00000314888.9	hg19	CCDS35009.1																																																																																			.	.		0.485	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		C	35725254	-	C	35725253	7	5	39	1	0	1	1	0	0	0	0	0	15962	1792	62	0	7649	0	TLN1	9	35725253	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10		35725253	105488178	24	4646										
OLFML2A	169611	hgsc.bcm.edu	37	chr9	127561615	127561615	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	aggtggtgaaggacagcgtgCgccacctcagtgagcagttg	16	9	1	2	rs533587628	byFrequency	TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr9:127561615C>A	ENST00000373580.3	+	4	514	c.514C>A	c.(514-516)Cgc>Agc	p.R172S	OLFML2A_ENST00000288815.5_5'Flank	NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	172					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						GGACAGCGTGCGCCACCTCAG	0.597																																					p.R172S		Atlas-SNP	.											.	OLFML2A	61	.	0			c.C514A						.						45	51	49					9																	127561615		2157	4275	6432	SO:0001583	missense	169611	exon4			AGCGTGCGCCACC	AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.514C>A	chr9.hg19:g.127561615C>A	ENSP00000362682:p.Arg172Ser	159.0	0.0		125.0	10.0	NM_182487	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Missense_Mutation	SNP	ENST00000373580.3	hg19	CCDS6857.2	.	.	.	.	.	.	.	.	.	.	C	12.18	1.861208	0.32884	.	.	ENSG00000185585	ENST00000331715;ENST00000425732;ENST00000373580	T;T	0.44083	0.93;0.93	5.67	3.76	0.43208	.	0.489979	0.22803	N	0.055449	T	0.31009	0.0783	L	0.44542	1.39	0.80722	D	1	P;B	0.36392	0.551;0.395	B;B	0.34489	0.184;0.062	T	0.03202	-1.1061	10	0.19147	T	0.46	.	10.8651	0.46851	0.1204:0.661:0.2186:0.0	.	136;172	Q5JTM7;Q68BL7	.;OLM2A_HUMAN	S	136;136;172	ENSP00000336425:R136S;ENSP00000362682:R172S	ENSP00000336425:R136S	R	+	1	0	OLFML2A	126601436	0.683000	0.27633	1.000000	0.80357	0.691000	0.40173	1.032000	0.30178	2.681000	0.91329	0.655000	0.94253	CGC	.	.		0.597	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487		A	127561615	C	A	127561615	3	1	39	1	0	0	0	0	1	0	0	0	10866	768	27	1	528	1	OLFML2A	9	127561615	Missense_Mutation	SNP	C	TCGA-BC-A110-01A-11D-A12Z-10	91836362	127561615	13651816	25	4647										
COL17A1	1308	hgsc.bcm.edu	37	chr10	105837253	105837254	+	Frame_Shift_Ins	INS	-	-	G													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	tccctccaccaagagaggctINSgttttagcatagccattgct					rs374753420		TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr10:105837253_105837254insG	ENST00000353479.5	-	4	418_419	c.128_129insC	c.(127-129)acafs	p.T43fs	COL17A1_ENST00000393211.3_Frame_Shift_Ins_p.T43fs|COL17A1_ENST00000369733.3_Frame_Shift_Ins_p.T43fs	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	43	Nonhelical region (NC16).				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CAAGAGAGGCTGTTTTAGCATA	0.559																																					p.T43fs		Atlas-INDEL	.											.	COL17A1	149	.	0			c.129_130insC						.																																			SO:0001589	frameshift_variant	1308	exon4			.	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.129dupC	chr10.hg19:g.105837254_105837254dupG	ENSP00000340937:p.Thr43fs	144.0	0.0		101.0	10.0	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Frame_Shift_Ins	INS	ENST00000353479.5	hg19	CCDS7554.1																																																																																			.	.		0.559	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		G	105837254	-	G	105837253	7	5	39	1	0	1	1	0	0	0	0	0	3676	1567	55	0	4576	0	COL17A1	10	105837253	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10		105837253	29697494	26	4648										
ARFGAP2	84364	hgsc.bcm.edu	37	chr11	47187860	47187861	+	Frame_Shift_Ins	INS	-	-	C													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	ttggccagcacagccattttINScccagccacagacttgacac							TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr11:47187860_47187861insC	ENST00000524782.1	-	15	1731_1732	c.1503_1504insG	c.(1501-1506)gggaaafs	p.K502fs	RP11-390K5.6_ENST00000524412.1_RNA|ARFGAP2_ENST00000419701.2_Frame_Shift_Ins_p.K395fs|ARFGAP2_ENST00000395449.3_5'UTR|ARFGAP2_ENST00000426335.2_Frame_Shift_Ins_p.K366fs|ARFGAP2_ENST00000319543.6_Frame_Shift_Ins_p.K233fs	NM_001242832.1|NM_032389.4	NP_001229761.1|NP_115765.2	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating protein 2	502	Required for interaction with coatomer.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						ACAGCCATTTTCCCAGCCACAG	0.545																																					p.K502fs		Atlas-INDEL	.											.	ARFGAP2	43	.	0			c.1504_1505insG						.																																			SO:0001589	frameshift_variant	84364	exon15			.	AK027482	CCDS7926.1, CCDS73283.1	11p11.2-p11.12	2012-10-05	2008-01-09	2008-01-09	ENSG00000149182	ENSG00000149182		"ADP-ribosylation factor GTPase activating proteins"	13504	protein-coding gene	gene with protein product		606908	"zinc finger protein 289, ID1 regulated"	ZNF289		11278321, 14690497	Standard	NM_032389		Approved	IRZ, Zfp289, FLJ14576	uc001ndt.3	Q8N6H7	OTTHUMG00000166773	ENST00000524782.1:c.1504dupG	chr11.hg19:g.47187863_47187863dupC	ENSP00000434442:p.Lys502fs	210.0	0.0		121.0	16.0	NM_032389	B4DX29|B7Z9M7|D3DQQ9|Q3LIF2|Q8N3I1|Q96SX7	Frame_Shift_Ins	INS	ENST00000524782.1	hg19	CCDS7926.1																																																																																			.	.		0.545	ARFGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391425.1	NM_032389		C	47187861	-	C	47187860	7	5	39	1	0	1	1	0	0	0	0	0	850	1792	62	0	69	0	ARFGAP2	11	47187860	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10		47187860	87818656	27	4649										
IFT88	8100	hgsc.bcm.edu	37	chr13	21219024	21219025	+	Frame_Shift_Ins	INS	-	-	T													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	tattgaagtcattgagtggcINSttggagcctattacattgac							TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr13:21219024_21219025insT	ENST00000319980.6	+	22	2230_2231	c.1903_1904insT	c.(1903-1905)cttfs	p.L635fs	IFT88_ENST00000351808.5_Frame_Shift_Ins_p.L626fs|IFT88_ENST00000382778.4_Frame_Shift_Ins_p.L635fs|IFT88_ENST00000537103.1_Frame_Shift_Ins_p.L607fs	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	635					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		CATTGAGTGGCTTGGAGCCTAT	0.302																																					p.L635fs		Atlas-INDEL	.											.	IFT88	83	.	0			c.1903_1904insT						.																																			SO:0001589	frameshift_variant	8100	exon22			.	AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	20606	protein-coding gene	gene with protein product	"polaris homolog"	600595	"tetratricopeptide repeat domain 10", "intraflagellar transport 88 homolog (Chlamydomonas)"	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.1905dupT	chr13.hg19:g.21219026_21219026dupT	ENSP00000323580:p.Leu635fs	300.0	0.0		279.0	17.0	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Frame_Shift_Ins	INS	ENST00000319980.6	hg19	CCDS31944.1																																																																																			.	.		0.302	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		T	21219025	-	T	21219024	7	5	39	1	0	1	1	0	0	0	0	0	7575	797	28	0	1981	0	IFT88	13	21219024	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10		21219024	93950854	28	4650										
HIF1A	3091	hgsc.bcm.edu	37	chr14	62207716	62207716	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	caaaagaccgtatggaagacAttaaaatattgattgcatct	7	6	1	3			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr14:62207716A>T	ENST00000337138.4	+	12	2168	c.1903A>T	c.(1903-1905)Att>Ttt	p.I635F	HIF1A_ENST00000323441.6_Missense_Mutation_p.I635F|RP11-618G20.1_ENST00000555937.1_RNA|HIF1A_ENST00000557538.1_Missense_Mutation_p.I576F|HIF1A_ENST00000394997.1_Missense_Mutation_p.I636F|HIF1A_ENST00000539097.1_Missense_Mutation_p.I659F|HIF1A-AS2_ENST00000554254.1_lincRNA	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	635	ID.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	TATGGAAGACATTAAAATATT	0.408																																					p.I659F		Atlas-SNP	.											.	HIF1A	120	.	0			c.A1975T						.						108	100	103					14																	62207716		2203	4300	6503	SO:0001583	missense	3091	exon12			GAAGACATTAAAA	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.1903A>T	chr14.hg19:g.62207716A>T	ENSP00000338018:p.Ile635Phe	235.0	0.0		159.0	9.0	NM_001243084	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Missense_Mutation	SNP	ENST00000337138.4	hg19	CCDS9753.1	.	.	.	.	.	.	.	.	.	.	A	8.810	0.935036	0.18206	.	.	ENSG00000100644	ENST00000539494;ENST00000394988;ENST00000337138;ENST00000394997;ENST00000323441;ENST00000557538;ENST00000539097	T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65	5.72	2.13	0.27403	.	3.176880	0.00628	N	0.000473	T	0.30916	0.0780	N	0.19112	0.55	0.30200	N	0.798702	B;B;B	0.26809	0.16;0.16;0.16	B;B;B	0.26693	0.072;0.072;0.072	T	0.21381	-1.0247	10	0.15952	T	0.53	.	2.0923	0.03660	0.4959:0.1201:0.2679:0.1161	.	636;635;635	A8MYV6;D0VY79;Q16665	.;.;HIF1A_HUMAN	F	386;576;635;636;635;576;659	ENSP00000338018:I635F;ENSP00000378446:I636F;ENSP00000323326:I635F;ENSP00000451696:I576F;ENSP00000437955:I659F	ENSP00000323326:I635F	I	+	1	0	HIF1A	61277469	0.902000	0.30710	0.996000	0.52242	0.898000	0.52572	0.814000	0.27239	0.187000	0.20147	-0.256000	0.11100	ATT	.	.		0.408	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		T	62207716	A	T	62207716	3	4	39	1	0	0	0	0	1	0	0	0	7112	217	8	4	1949	4	HIF1A	14	62207716	Missense_Mutation	SNP	A	TCGA-BC-A110-01A-11D-A12Z-10		62207716	45141824	29	4651										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105419292	105419292	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	ttgaacttgggcattttgaaCttgctgtctttggcagtcac	10	8	2	2			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr14:105419292C>A	ENST00000333244.5	-	7	2615	c.2496G>T	c.(2494-2496)aaG>aaT	p.K832N	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	832						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCATTTTGAACTTGCTGTCTT	0.622																																					p.K832N		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G2496T						.						236	259	252					14																	105419292		1956	4145	6101	SO:0001583	missense	113146	exon7			TTTGAACTTGCTG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.2496G>T	chr14.hg19:g.105419292C>A	ENSP00000353114:p.Lys832Asn	323.0	0.0		228.0	13.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	8.580	0.882016	0.17467	.	.	ENSG00000185567	ENST00000333244	T	0.01871	4.59	4.02	2.13	0.27403	.	.	.	.	.	T	0.11367	0.0277	M	0.87328	2.875	0.21184	N	0.999764	D	0.76494	0.999	D	0.81914	0.995	T	0.16512	-1.0400	9	0.20519	T	0.43	.	9.0866	0.36586	0.0:0.7193:0.0:0.2807	.	832	Q8IVF2	AHNK2_HUMAN	N	832	ENSP00000353114:K832N	ENSP00000353114:K832N	K	-	3	2	AHNAK2	104490337	0.000000	0.05858	0.558000	0.28319	0.017000	0.09413	-0.608000	0.05641	0.187000	0.20147	-1.579000	0.00862	AAG	.	.		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105419292	C	A	105419292	3	1	39	1	0	0	0	0	1	0	0	0	415	564	20	3	14895	3	AHNAK2	14	105419292	Missense_Mutation	SNP	C	TCGA-BC-A110-01A-11D-A12Z-10	43211576	105419292	1930248	30	4652										
C19orf2	8725	hgsc.bcm.edu	37	chr19	30476164	30476164	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	atgactataatgcccttcgaGaaagactcagcaccttgcct	7	12	1	3			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr19:30476164G>A	ENST00000542441.2	+	3	484	c.187G>A	c.(187-189)Gaa>Aaa	p.E63K	URI1_ENST00000392271.1_5'UTR|URI1_ENST00000312051.6_Missense_Mutation_p.E23K|URI1_ENST00000360605.4_Missense_Mutation_p.E45K			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	63					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)										TGCCCTTCGAGAAAGACTCAG	0.279																																					p.E63K		Atlas-SNP	.											.	.	.	.	0			c.G187A						.						188	196	193					19																	30476164		2203	4300	6503	SO:0001583	missense	8725	exon3			CTTCGAGAAAGAC	AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.187G>A	chr19.hg19:g.30476164G>A	ENSP00000442436:p.Glu63Lys	359.0	0.0		263.0	15.0	NM_003796	A8K805|H7BY42|Q8TC23|Q9UNU3	Missense_Mutation	SNP	ENST00000542441.2	hg19	CCDS12420.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.035399	0.93630	.	.	ENSG00000105176	ENST00000360605;ENST00000542441;ENST00000312051	T;T	0.46451	0.87;0.87	4.8	4.8	0.61643	Prefoldin (1);Prefoldin subunit (1);	0.049109	0.85682	D	0.000000	T	0.55465	0.1922	L	0.43152	1.355	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.69824	0.96;0.958;0.966	T	0.53041	-0.8494	10	0.38643	T	0.18	-19.7679	16.0247	0.80536	0.0:0.0:1.0:0.0	.	23;63;61	F8W9T0;O94763;Q8TC23	.;RMP_HUMAN;.	K	61;63;23	ENSP00000442436:E63K;ENSP00000312530:E23K	ENSP00000312530:E23K	E	+	1	0	C19orf2	35168004	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.082000	0.76851	2.230000	0.72887	0.563000	0.77884	GAA	.	.		0.279	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		A	30476164	G	A	30476164	3	1	39	1	0	0	0	0	1	0	0	0	1913	943	33	3	197	3	C19orf2	19	30476164	Missense_Mutation	SNP	G	TCGA-BC-A110-01A-11D-A12Z-10		30476164	28652819	31	4653										
KRTAP19-8	728299	hgsc.bcm.edu	37	chr21	32410712	32410713	+	Frame_Shift_Ins	INS	-	-	C													0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	catagccccagccaccaaagINScctccatagccatagcccag							TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr21:32410712_32410713insC	ENST00000382822.2	-	1	82_83	c.50_51insG	c.(49-51)ggcfs	p.G17fs		NM_001099219.1	NP_001092689.1	Q3LI54	KR198_HUMAN	keratin associated protein 19-8	17						intermediate filament (GO:0005882)				endometrium(2)|upper_aerodigestive_tract(1)	3						AGCCACCAAAGCCTCCATAGCC	0.545																																					p.G17fs		Atlas-INDEL	.											.	KRTAP19-8	9	.	0			c.51_52insG						.																																			SO:0001589	frameshift_variant	728299	exon1			.	AB096964	CCDS42917.1	21q22.11	2007-11-23			ENSG00000206102	ENSG00000206102		"Keratin associated proteins"	33898	protein-coding gene	gene with protein product							Standard	NM_001099219		Approved		uc010glt.3	Q3LI54	OTTHUMG00000057787	ENST00000382822.2:c.51dupG	chr21.hg19:g.32410714_32410714dupC	ENSP00000372272:p.Gly17fs	216.0	0.0		134.0	10.0	NM_001099219		Frame_Shift_Ins	INS	ENST00000382822.2	hg19	CCDS42917.1																																																																																			.	.		0.545	KRTAP19-8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000128239.3	NM_001099219		C	32410713	-	C	32410712	7	5	39	1	0	1	1	0	0	0	0	0	8544	958	34	0	144	0	KRTAP19-8	21	32410712	Frame_Shift_Ins	INS	-	TCGA-BC-A110-01A-11D-A12Z-10		32410712	15719183	32	4654										
SON	6651	hgsc.bcm.edu	37	chr21	34925206	34925206	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	caaagtgagatttcggagccTtcagcagtgcctactgatta	10	9	1	2			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chr21:34925206T>A	ENST00000356577.4	+	3	4144	c.3669T>A	c.(3667-3669)ccT>ccA	p.P1223P	SON_ENST00000381679.4_Silent_p.P1223P|SON_ENST00000290239.6_Silent_p.P1223P|SON_ENST00000300278.4_Silent_p.P1223P|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1223					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						TTTCGGAGCCTTCAGCAGTGC	0.493																																					p.P1223P		Atlas-SNP	.											.	SON	343	.	0			c.T3669A						.						153	156	155					21																	34925206		2203	4300	6503	SO:0001819	synonymous_variant	6651	exon3			GGAGCCTTCAGCA	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.3669T>A	chr21.hg19:g.34925206T>A		282.0	0.0		237.0	14.0	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	hg19	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	5.392	0.257602	0.10239	.	.	ENSG00000159140	ENST00000436227	.	.	.	5.42	4.25	0.50352	.	.	.	.	.	T	0.55016	0.1894	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51044	-0.8755	4	.	.	.	.	5.6107	0.17404	0.0:0.0869:0.1746:0.7385	.	.	.	.	H	218	.	.	L	+	2	0	SON	33847076	0.879000	0.30193	0.882000	0.34594	0.509000	0.34042	1.139000	0.31504	0.875000	0.35847	0.460000	0.39030	CTT	.	.		0.493	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		A	34925206	T	A	34925206	2	1	39	1	0	0	0	0	0	0	0	1	14941	1596	56	4		4	SON	21	34925206	Silent	SNP	T	TCGA-BC-A110-01A-11D-A12Z-10	2514494	34925206	13204689	33	4655										
HMGB3	3149	hgsc.bcm.edu	37	chrX	150155724	150155724	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	1	1	0.770244821092279	0	0.866525423728814	1	1	0	aataatttaaatgacagtgaAaagcagccttacatcactaa	5	7	1	2			TCGA-BC-A110-01A-11D-A12Z-10	TCGA-BC-A110-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7df1cd46-d00e-474c-9815-b41edb5ccf20	10045d1f-6bbd-4855-878e-90705d76e6f8	g.chrX:150155724A>T	ENST00000325307.7	+	4	510	c.414A>T	c.(412-414)gaA>gaT	p.E138D	HMGB3_ENST00000448905.2_Missense_Mutation_p.E138D	NM_005342.2	NP_005333.2	O15347	HMGB3_HUMAN	high mobility group box 3	138					DNA recombination (GO:0006310)|multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(2)|lung(2)|skin(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					ATGACAGTGAAAAGCAGCCTT	0.488																																					p.E138D		Atlas-SNP	.											.	HMGB3	27	.	0			c.A414T						.						47	45	46					X																	150155724		2203	4297	6500	SO:0001583	missense	3149	exon4			CAGTGAAAAGCAG	AF274572	CCDS35428.1	Xq28	2011-07-01	2011-04-05	2002-08-16	ENSG00000029993	ENSG00000029993		"High-mobility group / Canonical"	5004	protein-coding gene	gene with protein product	"non-histone chromosomal protein"	300193	"high-mobility group (nonhistone chromosomal) protein 4", "high-mobility group box 3"	HMG4		9598312	Standard	XM_005274665		Approved	HMG2A, MGC90319	uc004fep.3	O15347	OTTHUMG00000024162	ENST00000325307.7:c.414A>T	chrX.hg19:g.150155724A>T	ENSP00000359393:p.Glu138Asp	219.0	0.0		158.0	11.0	NM_005342	O95556|Q6NS40	Missense_Mutation	SNP	ENST00000325307.7	hg19	CCDS35428.1	.	.	.	.	.	.	.	.	.	.	a	5.724	0.318006	0.10845	.	.	ENSG00000029993	ENST00000419110;ENST00000325307;ENST00000455596;ENST00000448905;ENST00000430118	D;D;D;D;D	0.95342	-3.68;-3.68;-3.68;-3.68;-3.68	5.05	-3.08	0.05347	High mobility group, HMG1/HMG2, subgroup (1);High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.127237	0.52532	D	0.000079	T	0.81341	0.4802	N	0.02192	-0.645	0.41426	D	0.987836	B	0.19200	0.034	B	0.24848	0.056	T	0.66763	-0.5841	10	0.02654	T	1	.	15.3324	0.74223	0.2667:0.0:0.7333:0.0	.	138	O15347	HMGB3_HUMAN	D	138	ENSP00000410354:E138D;ENSP00000359393:E138D;ENSP00000405601:E138D;ENSP00000442758:E138D;ENSP00000417027:E138D	ENSP00000359393:E138D	E	+	3	2	HMGB3	149906382	0.619000	0.27059	0.765000	0.31456	0.990000	0.78478	-0.130000	0.10498	-0.793000	0.04475	0.430000	0.28490	GAA	.	.		0.488	HMGB3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060867.1	NM_005342		T	150155724	A	T	150155724	3	4	39	1	0	0	0	0	1	0	0	0	7236	11	1	4	424	4	HMGB3	23	150155724	Missense_Mutation	SNP	A	TCGA-BC-A110-01A-11D-A12Z-10		150155724	5114836	34	4656										
PANK4	55229	hgsc.bcm.edu	37	chr1	2452651	2452651	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggtctttgatgaagtccaggCaggcttcgatgtaggtattc	13	7	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:2452651C>G	ENST00000378466.3	-	3	323	c.311G>C	c.(310-312)tGc>tCc	p.C104S	PANK4_ENST00000435556.3_Missense_Mutation_p.C104S|PANK4_ENST00000491212.1_5'Flank	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	104					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		GAAGTCCAGGCAGGCTTCGAT	0.498																																					p.C104S		.	.											.	PANK4	.	.	0			c.G311C						.						149	148	148					1																	2452651		2203	4300	6503	SO:0001583	missense	55229	exon3			TCCAGGCAGGCTT	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.311G>C	1.37:g.2452651C>G	ENSP00000367727:p.Cys104Ser	299.0	0.0		312.0	54.0	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.755702	0.89843	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	D;D	0.99541	-6.12;-4.21	4.74	4.74	0.60224	.	0.057435	0.64402	D	0.000001	D	0.99351	0.9772	M	0.76838	2.35	0.80722	D	1	P;P	0.46277	0.875;0.875	P;P	0.51895	0.683;0.683	D	0.98829	1.0750	10	0.54805	T	0.06	-35.3018	16.6921	0.85324	0.0:1.0:0.0:0.0	.	104;104	E9PHT6;Q9NVE7	.;PANK4_HUMAN	S	104	ENSP00000367727:C104S;ENSP00000421433:C104S	ENSP00000367727:C104S	C	-	2	0	PANK4	2442511	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.132000	0.77251	2.177000	0.69029	0.462000	0.41574	TGC	.	.		0.498	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1			G	2452651	C	G	2452651	3	3	40	1	0	0	0	0	1	0	0	0	11428	710	25	4	2078	4	PANK4	1	2452651	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10		2452651	246797970	1	4657										
MTOR	2475	hgsc.bcm.edu	37	chr1	11303173	11303173	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cataacagaggtgcttacttAtgggcgaagtcctttggggg	14	7	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:11303173A>G	ENST00000361445.4	-	9	1486	c.1410T>C	c.(1408-1410)caT>caC	p.H470H		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	470	Interaction with NBN.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	GTGCTTACTTATGGGCGAAGT	0.512																																					p.H470H		.	.											.	MTOR	.	.	0			c.T1410C						.						63	67	66					1																	11303173		2203	4300	6503	SO:0001819	synonymous_variant	2475	exon9			TTACTTATGGGCG	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.1410T>C	1.37:g.11303173A>G		67.0	0.0		40.0	24.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			.	.		0.512	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		G	11303173	A	G	11303173	2	3	40	1	0	0	0	0	0	0	0	1	9963	446	16	2		2	MTOR	1	11303173	Silent	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	8850522	11303173	237947448	2	4658										
WDTC1	23038	hgsc.bcm.edu	37	chr1	27622887	27622888	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cctagaaaatgccactcctcINSggggggtaagttctccctta					rs267598533		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:27622887_27622888insG	ENST00000319394.3	+	10	1479_1480	c.944_945insG	c.(943-948)tcggggfs	p.SG315fs	WDTC1_ENST00000361771.3_Frame_Shift_Ins_p.SG315fs	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	315					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		TGCCACTCCTCGGGGGGTAAGT	0.52																																					p.S315fs		.	.											.	WDTC1	.	.	0			c.944_945insG						.																																			SO:0001589	frameshift_variant	23038	exon10			.	AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"DDB1 and CUL4 associated factors", "WD repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29175	protein-coding gene	gene with protein product	"adipose homolog (Drosophila)", "DDB1 and CUL4 associated factor 9"					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.949dupG	1.37:g.27622893_27622893dupG	ENSP00000317971:p.Ser315fs	415.0	0.0		237.0	17.0	NM_015023	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Frame_Shift_Ins	INS	ENST00000319394.3	37																																																																																				.	.		0.52	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023		G	27622888	-	G	27622887	7	5	40	1	0	1	1	0	0	0	0	0	17357	893	31	0	978	0	WDTC1	1	27622887	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	16319714	27622887	221627734	3	4659										
THRAP3	9967	hgsc.bcm.edu	37	chr1	36755000	36755001	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctaaagtcataggtgcaaacINSaaaaaccaggaggaggagaa					rs374538181		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:36755000_36755001insA	ENST00000354618.5	+	5	1604_1605	c.1380_1381insA	c.(1381-1383)aaafs	p.K461fs	THRAP3_ENST00000469141.2_Frame_Shift_Ins_p.K461fs	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	461	Required for mRNA decay activity.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TAGGTGCAAACAAAAACCAGGA	0.455			T	USP6	aneurysmal bone cysts																																p.N460fs	Pancreas(129;785 1795 20938 23278 32581)	.	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	THRAP3	.	.	0			c.1380_1381insA						.																																			SO:0001589	frameshift_variant	9967	exon5			.	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.1385dupA	1.37:g.36755005_36755005dupA	ENSP00000346634:p.Lys461fs	126.0	0.0		128.0	10.0	NM_005119	D3DPS5|Q5VTK6	Frame_Shift_Ins	INS	ENST00000354618.5	37	CCDS405.1																																																																																			.	.		0.455	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		A	36755001	-	A	36755000	7	5	40	1	0	1	1	0	0	0	0	0	15889	477	17	0	1390	0	THRAP3	1	36755000	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	9132113	36755000	212495621	4	4660										
RIMS3	9783	hgsc.bcm.edu	37	chr1	41092203	41092203	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	acatccttaagagcatgaggGgctggtggcactctccaggg	14	10	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:41092203G>A	ENST00000372684.3	-	8	1382	c.913C>T	c.(913-915)Ccc>Tcc	p.P305S	RIMS3_ENST00000372683.1_Missense_Mutation_p.P305S	NM_014747.2	NP_055562.2	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3	305					calcium ion-dependent exocytosis (GO:0017156)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			GAGCATGAGGGGCTGGTGGCA	0.607																																					p.P305S		.	.											.	RIMS3	.	.	0			c.C913T						.						36	35	35					1																	41092203		2202	4300	6502	SO:0001583	missense	9783	exon8			ATGAGGGGCTGGT	BC003103	CCDS30687.1	1p34.2	2013-09-19			ENSG00000117016	ENSG00000117016			21292	protein-coding gene	gene with protein product		611600				12620390, 10748113	Standard	NM_014747		Approved	RIM3, NIM3	uc001cfu.1	Q9UJD0	OTTHUMG00000007453	ENST00000372684.3:c.913C>T	1.37:g.41092203G>A	ENSP00000361769:p.Pro305Ser	82.0	0.0		51.0	9.0	NM_014747	D3DPV8|Q92511|X5D7U7	Missense_Mutation	SNP	ENST00000372684.3	37	CCDS30687.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.507400	0.85282	.	.	ENSG00000117016	ENST00000372684;ENST00000372683	T;T	0.51574	0.7;0.7	4.59	4.59	0.56863	.	0.000000	0.85682	D	0.000000	T	0.67515	0.2901	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.71672	-0.4522	10	0.66056	D	0.02	-23.1161	14.9393	0.70980	0.0:0.0:1.0:0.0	.	305	Q9UJD0	RIMS3_HUMAN	S	305	ENSP00000361769:P305S;ENSP00000361768:P305S	ENSP00000361768:P305S	P	-	1	0	RIMS3	40864790	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.737000	0.84957	2.381000	0.81170	0.561000	0.74099	CCC	.	.		0.607	RIMS3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019585.1	NM_014747		A	41092203	G	A	41092203	3	1	40	1	0	0	0	0	1	0	0	0	13384	1232	43	3	17	3	RIMS3	1	41092203	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	4337203	41092203	208158418	5	4661										
ERMAP	114625	hgsc.bcm.edu	37	chr1	43304572	43304573	+	Splice_Site	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctctctttctggtttttaggINSaaaactccataaagctgtca							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:43304572_43304573insA	ENST00000372517.2	+	8	861_862	c.617_618insA	c.(616-621)ggaaaa>ggAaaaa	p.GK206fs	ERMAP_ENST00000328249.3_Splice_Site_p.GK116fs|RP11-342M1.3_ENST00000416809.2_RNA|RP11-342M1.3_ENST00000425076.1_RNA|RP11-342M1.3_ENST00000444563.1_RNA|RP11-342M1.3_ENST00000414798.1_RNA|ERMAP_ENST00000487556.1_3'UTR|ERMAP_ENST00000372514.3_Splice_Site_p.GK206fs	NM_001017922.1	NP_001017922.1	Q96PL5	ERMAP_HUMAN	erythroblast membrane-associated protein (Scianna blood group)	206			Missing (in Sc-3 allele).			cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TGGTTTTTAGGAAAACTCCATA	0.45																																					p.G206fs		.	.											.	ERMAP	.	.	0			c.617_618insA						.																																			SO:0001630	splice_region_variant	114625	exon7			.	AF311284	CCDS475.1	1p34	2014-07-19	2006-02-23		ENSG00000164010	ENSG00000164010		"Blood group antigens", "Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	15743	protein-coding gene	gene with protein product		609017	"Radin blood group", "Scianna blood group", "erythroblast membrane-associated protein", "erythroblast membrane-associated protein (RD and SC blood groups)"	RD, SC		11549310	Standard	XM_005270415		Approved	BTN5	uc001cie.1	Q96PL5	OTTHUMG00000007619	ENST00000372517.2:c.617-1->A	1.37:g.43304576_43304576dupA		186.0	0.0		182.0	11.0	NM_018538	D3DPW8|Q5VV53|Q6DUE0|Q7Z3X0|Q8NCV8|Q8NCW2|Q8NCW3|Q96PL6	Frame_Shift_Ins	INS	ENST00000372517.2	37	CCDS475.1																																																																																			.	.		0.45	ERMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020180.1	NM_018538	Frame_Shift_Ins	A	43304573	-	A	43304572	8	5	40	1	0	1	1	0	0	0	1	0	5236	1188	41	0	639	0	ERMAP	1	43304572	Splice_Site	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	2212369	43304572	205946049	6	4662										
ORC1L	4998	hgsc.bcm.edu	37	chr1	52859445	52859445	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aatccaaggaggcacatgaaGtctgctgggacatctgaggg	14	8	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:52859445G>T	ENST00000371568.3	-	6	970	c.752C>A	c.(751-753)aCt>aAt	p.T251N	ORC1_ENST00000371566.1_Missense_Mutation_p.T251N	NM_001190818.1|NM_001190819.1|NM_004153.3	NP_001177747.1|NP_001177748.1|NP_004144.2	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	251					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear origin of replication recognition complex (GO:0005664)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GGCACATGAAGTCTGCTGGGA	0.418																																					p.T251N		.	.											.	ORC1	.	.	0			c.C752A						.						52	49	50					1																	52859445		2203	4300	6503	SO:0001583	missense	4998	exon6			CATGAAGTCTGCT		CCDS566.1	1p32	2010-10-12	2010-10-12	2010-10-12	ENSG00000085840	ENSG00000085840		"ATPases / AAA-type"	8487	protein-coding gene	gene with protein product	"origin recognition complex, subunit 1, S. cerevisiae, homolog-like", "origin recognition complex 1", "replication control protein 1"	601902	"origin recognition complex, subunit 1 (yeast homolog)-like", "origin recognition complex, subunit 1-like (yeast)", "origin recognition complex, subunit 1 homolog (S. cerevisiae)"	ORC1L		8884289	Standard	NM_004153		Approved	HSORC1, PARC1	uc001ctu.3	Q13415	OTTHUMG00000008104	ENST00000371568.3:c.752C>A	1.37:g.52859445G>T	ENSP00000360623:p.Thr251Asn	70.0	0.0		104.0	39.0	NM_004153	D3DQ34|Q13471|Q5T0F5	Missense_Mutation	SNP	ENST00000371568.3	37	CCDS566.1	.	.	.	.	.	.	.	.	.	.	G	0.143	-1.100376	0.01843	.	.	ENSG00000085840	ENST00000371568;ENST00000371566	T;T	0.40225	1.04;1.04	4.94	-4.95	0.03048	.	1.308390	0.04413	N	0.366392	T	0.16171	0.0389	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10730	-1.0617	10	0.12766	T	0.61	0.0307	0.8723	0.01217	0.322:0.1064:0.1711:0.4005	.	251;251	B7Z8H0;Q13415	.;ORC1_HUMAN	N	251	ENSP00000360623:T251N;ENSP00000360621:T251N	ENSP00000360621:T251N	T	-	2	0	ORC1	52632033	0.004000	0.15560	0.000000	0.03702	0.005000	0.04900	-0.259000	0.08721	-0.837000	0.04223	-0.181000	0.13052	ACT	.	.		0.418	ORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022202.1	NM_004153		T	52859445	G	T	52859445	3	4	40	1	0	0	0	0	1	0	0	0	11270	1029	36	3	1881	3	ORC1L	1	52859445	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	9554873	52859445	196391176	7	4663										
AK5	26289	hgsc.bcm.edu	37	chr1	77763544	77763544	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aacaattacagagataaagcAaaaattgatgcaaatacctg	6	6	0	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:77763544A>G	ENST00000354567.2	+	5	874	c.611A>G	c.(610-612)cAa>cGa	p.Q204R	AK5_ENST00000317704.4_3'UTR|AK5_ENST00000344720.5_Missense_Mutation_p.Q178R	NM_174858.2	NP_777283.1	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5	204	Adenylate kinase 1.				ADP biosynthetic process (GO:0006172)|ATP metabolic process (GO:0046034)|dADP biosynthetic process (GO:0006173)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|pyrimidine ribonucleotide biosynthetic process (GO:0009220)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule organizing center (GO:0005815)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside kinase activity (GO:0019206)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|prostate(1)|skin(2)|stomach(1)	40						GAGATAAAGCAAAAATTGATG	0.338																																					p.Q204R		.	.											.	AK5	.	.	0			c.A611G						.						91	92	92					1																	77763544		2203	4300	6503	SO:0001583	missense	26289	exon5			TAAAGCAAAAATT	AF062595	CCDS675.1, CCDS676.1	1p31	2008-02-05			ENSG00000154027	ENSG00000154027		"Adenylate kinases"	365	protein-coding gene	gene with protein product		608009				10215863	Standard	NM_012093		Approved		uc001dhn.3	Q9Y6K8	OTTHUMG00000009796	ENST00000354567.2:c.611A>G	1.37:g.77763544A>G	ENSP00000346577:p.Gln204Arg	156.0	0.0		154.0	51.0	NM_174858	Q5U622|Q6FH66|Q7Z4T5|Q86YS0|Q8N464|Q96EC9	Missense_Mutation	SNP	ENST00000354567.2	37	CCDS675.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.720961	0.89205	.	.	ENSG00000154027	ENST00000354567;ENST00000344720	T;T	0.76839	-1.05;-1.05	5.51	5.51	0.81932	.	0.061471	0.64402	D	0.000002	T	0.77538	0.4145	L	0.33245	0.995	0.80722	D	1	P;D	0.64830	0.858;0.994	P;D	0.76575	0.462;0.988	T	0.77362	-0.2616	10	0.34782	T	0.22	-7.6916	15.9245	0.79606	1.0:0.0:0.0:0.0	.	204;180	Q9Y6K8;Q8N291	KAD5_HUMAN;.	R	204;178	ENSP00000346577:Q204R;ENSP00000341430:Q178R	ENSP00000341430:Q178R	Q	+	2	0	AK5	77536132	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.664000	0.91139	2.236000	0.73375	0.528000	0.53228	CAA	.	.		0.338	AK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026993.4	NM_174858		G	77763544	A	G	77763544	3	3	40	1	0	0	0	0	1	0	0	0	443	130	5	2	629	2	AK5	1	77763544	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	24904099	77763544	171487077	8	4664										
FUBP1	8880	hgsc.bcm.edu	37	chr1	78429797	78429797	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttctgcagcatgttgacatcGgtctggaggtcctgttattt	11	8	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:78429797G>A	ENST00000370768.2	-	12	1072	c.991C>T	c.(991-993)Cga>Tga	p.R331*	FUBP1_ENST00000436586.2_Nonsense_Mutation_p.R352*|FUBP1_ENST00000370767.1_Nonsense_Mutation_p.R331*	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	331	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						TGTTGACATCGGTCTGGAGGT	0.323			"F, N"		oligodendroglioma																																p.R331X		.	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1	.	.	0			c.C991T						.						234	227	229					1																	78429797		2203	4300	6503	SO:0001587	stop_gained	8880	exon12			GACATCGGTCTGG	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.991C>T	1.37:g.78429797G>A	ENSP00000359804:p.Arg331*	645.0	0.0		602.0	221.0	NM_003902	Q12828	Nonsense_Mutation	SNP	ENST00000370768.2	37	CCDS683.1	.	.	.	.	.	.	.	.	.	.	G	32	5.135069	0.94517	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586	.	.	.	5.81	0.557	0.17260	.	0.052464	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-14.5785	16.917	0.86154	0.0:0.0:0.1913:0.8087	.	.	.	.	X	330;331;331;330;352	.	ENSP00000294623:R330X	R	-	1	2	FUBP1	78202385	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	0.942000	0.29017	0.025000	0.15241	0.650000	0.86243	CGA	.	.		0.323	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		A	78429797	G	A	78429797	4	1	40	1	0	0	0	0	0	1	0	0	6100	1124	39	1	979	1	FUBP1	1	78429797	Nonsense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	666253	78429797	170820824	9	4665										
HFM1	164045	hgsc.bcm.edu	37	chr1	91742600	91742600	+	Frame_Shift_Del	DEL	T	T	-													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttgcattctcggttcccaggTtttttgctggcagtcgttcc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:91742600delT	ENST00000370425.3	-	31	3509	c.3411delA	c.(3409-3411)aaafs	p.K1137fs	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Frame_Shift_Del_p.K816fs|HFM1_ENST00000294696.5_Frame_Shift_Del_p.K369fs	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1137					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		GGTTCCCAGGTTTTTTGCTGG	0.284																																					p.P1138fs		.	.											.	HFM1	.	.	0			c.3412delC						.						114	113	113					1																	91742600		2203	4299	6502	SO:0001589	frameshift_variant	164045	exon31			.	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.3411delA	1.37:g.91742600delT	ENSP00000359454:p.Lys1137fs	313.0	0.0		310.0	77.0	NM_001017975	B1B0B6|Q8N9Q0	Frame_Shift_Del	DEL	ENST00000370425.3	37	CCDS30769.2																																																																																			.	.		0.284	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		-	91742600	T	-	91742600	7	5	40	1	0	1	0	1	0	0	0	0	7092	1722	60	0	932	0	HFM1	1	91742600	Frame_Shift_Del	DEL	T	TCGA-BC-A112-01A-11D-A12Z-10	13312803	91742600	157508021	10	4666	20	3								
HFM1	164045	hgsc.bcm.edu	37	chr1	91742605	91742605	+	Missense_Mutation	SNP	T	T	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttctcggttcccaggtttttTgctggcagtcgttcctaaat							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:91742605T>G	ENST00000370425.3	-	31	3504	c.3406A>C	c.(3406-3408)Aaa>Caa	p.K1136Q	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Missense_Mutation_p.K815Q|HFM1_ENST00000294696.5_Missense_Mutation_p.K368Q	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1136					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		CCAGGTTTTTTGCTGGCAGTC	0.289																																					p.K1136Q		.	.											.	HFM1	.	.	0			c.A3406C						.						110	109	109					1																	91742605		2203	4299	6502	SO:0001583	missense	164045	exon31			GTTTTTTGCTGGC	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.3406A>C	1.37:g.91742605T>G	ENSP00000359454:p.Lys1136Gln	300.0	0.0		296.0	13.0	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	11.88	1.769468	0.31320	.	.	ENSG00000162669	ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	T;T;T	0.64438	0.27;0.64;-0.1	5.71	5.71	0.89125	.	0.217537	0.31772	N	0.007085	T	0.41282	0.1152	L	0.53249	1.67	0.34985	D	0.754507	B;B;B	0.32010	0.351;0.242;0.201	B;B;B	0.28465	0.09;0.074;0.05	T	0.46582	-0.9181	10	0.31617	T	0.26	.	13.4861	0.61366	0.0:0.0:0.0:1.0	.	815;347;1136	A6NGI5;B1B0B5;A2PYH4	.;.;HFM1_HUMAN	Q	1136;368;815;820	ENSP00000359454:K1136Q;ENSP00000294696:K368Q;ENSP00000359453:K815Q	ENSP00000294696:K368Q	K	-	1	0	HFM1	91515193	1.000000	0.71417	0.983000	0.44433	0.577000	0.36160	5.255000	0.65462	2.178000	0.69098	0.477000	0.44152	AAA	.	.		0.289	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		G	91742605	T	G	91742605	3	3	40	1	0	0	0	0	1	0	0	0	7092	1821	63	5	937	5	HFM1	1	91742605	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	5	91742605	157508016	11	4667	20	3								
HFM1	164045	hgsc.bcm.edu	37	chr1	91742607	91742607	+	Missense_Mutation	SNP	C	C	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctcggttcccaggttttttgCtggcagtcgttcctaaatta							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:91742607C>G	ENST00000370425.3	-	31	3502	c.3404G>C	c.(3403-3405)aGc>aCc	p.S1135T	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Missense_Mutation_p.S814T|HFM1_ENST00000294696.5_Missense_Mutation_p.S367T	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1135					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AGGTTTTTTGCTGGCAGTCGT	0.299																																					p.S1135T		.	.											.	HFM1	.	.	0			c.G3404C						.						109	107	108					1																	91742607		2203	4299	6502	SO:0001583	missense	164045	exon31			TTTTTGCTGGCAG	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.3404G>C	1.37:g.91742607C>G	ENSP00000359454:p.Ser1135Thr	294.0	0.0		292.0	91.0	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.104|0.104	-1.148444|-1.148444	0.01714|0.01714	.|.	.|.	ENSG00000162669|ENSG00000162669	ENST00000430465|ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	.|T;T;T	.|0.63096	.|0.35;0.71;-0.02	5.71|5.71	2.75|2.75	0.32379|0.32379	.|.	.|0.325149	.|0.26911	.|N	.|0.021877	T|T	0.15652|0.15652	0.0377|0.0377	N|N	0.14661|0.14661	0.345|0.345	0.20764|0.20764	N|N	0.999856|0.999856	.|B;B;B	.|0.09022	.|0.002;0.001;0.002	.|B;B;B	.|0.09377	.|0.004;0.003;0.001	T|T	0.28964|0.28964	-1.0027|-1.0027	5|10	.|0.13470	.|T	.|0.59	.|.	5.4308|5.4308	0.16452|0.16452	0.0:0.6141:0.1458:0.2401|0.0:0.6141:0.1458:0.2401	.|.	.|814;346;1135	.|A6NGI5;B1B0B5;A2PYH4	.|.;.;HFM1_HUMAN	P|T	347|1135;367;814;819	.|ENSP00000359454:S1135T;ENSP00000294696:S367T;ENSP00000359453:S814T	.|ENSP00000294696:S367T	A|S	-|-	1|2	0|0	HFM1|HFM1	91515195|91515195	0.171000|0.171000	0.23029|0.23029	0.595000|0.595000	0.28798|0.28798	0.539000|0.539000	0.34962|0.34962	0.179000|0.179000	0.16840|0.16840	0.315000|0.315000	0.23110|0.23110	0.585000|0.585000	0.79938|0.79938	GCA|AGC	.	.		0.299	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		G	91742607	C	G	91742607	3	3	40	1	0	0	0	0	1	0	0	0	7092	797	28	4	939	4	HFM1	1	91742607	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	2	91742607	157508014	12	4668	20	3								
GPSM2	29899	hgsc.bcm.edu	37	chr1	109465168	109465168	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atacagcttcaacaacaactTcttccactccccctaaaatg	2	15	2	0	rs374875864|rs35029887|rs201481482	byFrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:109465168T>A	ENST00000406462.2	+	14	2343	c.1570T>A	c.(1570-1572)Tct>Act	p.S524T	AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_Missense_Mutation_p.S524T			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	524					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		AACAACAACTTCTTCCACTCC	0.373																																					p.S524T		.	.											.	GPSM2	.	.	0			c.T1570A						.						79	117	104					1																	109465168		2190	4293	6483	SO:0001583	missense	29899	exon13			ACAACTTCTTCCA	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"Tetratricopeptide (TTC) repeat domain containing"	29501	protein-coding gene	gene with protein product		609245	"G-protein signalling modulator 2 (AGS3-like, C. elegans)", "deafness, autosomal recessive 82"	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.1570T>A	1.37:g.109465168T>A	ENSP00000385510:p.Ser524Thr	5.0	0.0		62.0	20.0	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	37	CCDS792.2	.	.	.	.	.	.	.	.	.	.	T	7.387	0.629929	0.14257	.	.	ENSG00000121957	ENST00000406462;ENST00000264126	D;D	0.93712	-3.27;-3.27	6.17	-6.6	0.01824	.	0.546439	0.21807	N	0.068824	T	0.62563	0.2438	N	0.08118	0	0.09310	N	0.999996	B	0.11235	0.004	B	0.06405	0.002	T	0.64601	-0.6369	10	0.15499	T	0.54	-3.6969	9.2309	0.37437	0.0:0.2789:0.4599:0.2613	.	524	P81274	GPSM2_HUMAN	T	524	ENSP00000385510:S524T;ENSP00000264126:S524T	ENSP00000264126:S524T	S	+	1	0	GPSM2	109266691	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.350000	0.07721	-1.555000	0.01697	-0.250000	0.11733	TCT	.	.		0.373	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296		A	109465168	T	A	109465168	3	1	40	1	0	0	0	0	1	0	0	0	6744	1783	62	4	1616	4	GPSM2	1	109465168	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	17722561	109465168	139785453	13	4669										
AHCYL1	10768	hgsc.bcm.edu	37	chr1	110561690	110561690	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cagggtcgtctactcaatttGagctgctccacagttcccac	8	14	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:110561690G>C	ENST00000369799.5	+	14	1702	c.1335G>C	c.(1333-1335)ttG>ttC	p.L445F	AHCYL1_ENST00000393614.4_Missense_Mutation_p.L398F|AHCYL1_ENST00000359172.3_Missense_Mutation_p.L398F	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	445	NAD binding. {ECO:0000250}.				mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		TACTCAATTTGAGCTGCTCCA	0.502																																					p.L445F		.	.											.	AHCYL1	.	.	0			c.G1335C						.						150	129	136					1																	110561690		2203	4300	6503	SO:0001583	missense	10768	exon14			CAATTTGAGCTGC	U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"inositol 1,4,5-trisphosphate receptor-binding protein", "protein phosphatase 1, regulatory subunit 78"	607826	"S-adenosylhomocysteine hydrolase-like 1"			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.1335G>C	1.37:g.110561690G>C	ENSP00000358814:p.Leu445Phe	176.0	0.0		154.0	71.0	NM_006621	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Missense_Mutation	SNP	ENST00000369799.5	37	CCDS818.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.169422	0.78452	.	.	ENSG00000168710	ENST00000369799;ENST00000359172;ENST00000393614	D;D;D	0.82803	-1.65;-1.62;-1.62	5.95	5.95	0.96441	S-adenosyl-L-homocysteine hydrolase, NAD binding (1);	0.000000	0.85682	D	0.000000	D	0.90532	0.7033	H	0.96970	3.915	0.80722	D	1	P	0.44260	0.83	P	0.52710	0.707	D	0.92447	0.5967	10	0.87932	D	0	-27.4656	10.6537	0.45663	0.0691:0.1329:0.798:0.0	.	445	O43865	SAHH2_HUMAN	F	445;398;398	ENSP00000358814:L445F;ENSP00000352092:L398F;ENSP00000377238:L398F	ENSP00000352092:L398F	L	+	3	2	AHCYL1	110363213	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.098000	0.50259	2.824000	0.97209	0.655000	0.94253	TTG	.	.		0.502	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1			C	110561690	G	C	110561690	3	2	40	1	0	0	0	0	1	0	0	0	410	1281	45	4	1389	4	AHCYL1	1	110561690	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	1096522	110561690	138688931	14	4670										
ADORA3	140	hgsc.bcm.edu	37	chr1	112042806	112042806	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atagataaaggcagccatgaCagagcaaacaagaaaagaac	9	7	0	5			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:112042806C>T	ENST00000241356.4	-	2	1128	c.723G>A	c.(721-723)ctG>ctA	p.L241L	ADORA3_ENST00000369717.4_Intron|ADORA3_ENST00000486342.1_5'Flank|ADORA3_ENST00000369716.4_Intron	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	241					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	GCAGCCATGACAGAGCAAACA	0.448																																					p.L241L		.	.											.	ADORA3	.	.	0			c.G723A						.						120	116	118					1																	112042806		2203	4300	6503	SO:0001819	synonymous_variant	140	exon2			CCATGACAGAGCA	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"GPCR / Class A : Adenosine receptors", "Immunoglobulin superfamily / V-set domain containing"	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.723G>A	1.37:g.112042806C>T		223.0	0.0		212.0	58.0	NM_000677	A2A3P4|Q6UWU0|Q9BYZ1	Silent	SNP	ENST00000241356.4	37	CCDS839.1																																																																																			.	.		0.448	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683		T	112042806	C	T	112042806	2	4	40	1	0	0	0	0	0	0	0	1	329	465	17	3		3	ADORA3	1	112042806	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1481116	112042806	137207815	15	4671										
NGF	4803	hgsc.bcm.edu	37	chr1	115829018	115829018	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctgacactgtcacacaccgaGaattcgcccctgtggaagat	9	13	1	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:115829018G>A	ENST00000369512.2	-	3	567	c.399C>T	c.(397-399)ttC>ttT	p.F133F	RP4-663N10.1_ENST00000425449.1_RNA	NM_002506.2	NP_002497.2	P01138	NGF_HUMAN	nerve growth factor (beta polypeptide)	133					activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|adult locomotory behavior (GO:0008344)|apoptotic signaling pathway (GO:0097190)|circadian rhythm (GO:0007623)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|inflammatory response (GO:0006954)|memory (GO:0007613)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|nerve growth factor processing (GO:0032455)|neuron apoptotic process (GO:0051402)|neuron projection morphogenesis (GO:0048812)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axon extension (GO:0045773)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotrophin TRK receptor signaling pathway (GO:0051388)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|Ras protein signal transduction (GO:0007265)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of neurotransmitter secretion (GO:0046928)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to nicotine (GO:0035094)|response to ozone (GO:0010193)|response to peptide hormone (GO:0043434)|response to radiation (GO:0009314)|sensory perception of pain (GO:0019233)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)	nerve growth factor receptor binding (GO:0005163)|receptor signaling protein activity (GO:0005057)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13	Lung SC(450;0.211)	all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)	Clenbuterol(DB01407)	CACACACCGAGAATTCGCCCC	0.562																																					p.F133F		.	.											.	NGF	.	.	0			c.C399T						.						92	78	83					1																	115829018		2203	4300	6503	SO:0001819	synonymous_variant	4803	exon3			CACCGAGAATTCG		CCDS882.1	1p13.1	2014-09-17	2008-02-07	2008-02-07	ENSG00000134259	ENSG00000134259		"Endogenous ligands"	7808	protein-coding gene	gene with protein product		162030		NGFB			Standard	XM_006710663		Approved		uc001efu.1	P01138	OTTHUMG00000011880	ENST00000369512.2:c.399C>T	1.37:g.115829018G>A		158.0	0.0		143.0	60.0	NM_002506	A1A4E5|Q6FHA0|Q96P60|Q9P2Q8|Q9UKL8	Silent	SNP	ENST00000369512.2	37	CCDS882.1																																																																																			.	.		0.562	NGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032832.1	NM_002506		A	115829018	G	A	115829018	2	1	40	1	0	0	0	0	0	0	0	1	10404	933	33	3		3	NGF	1	115829018	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	3786212	115829018	133421603	16	4672										
NUDT17	200035	hgsc.bcm.edu	37	chr1	145587383	145587384	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aggtcctgggggagaagtccINSgggtgtctctgtcccatcct					rs139528449|rs139789829	byFrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:145587383_145587384insG	ENST00000334513.5	-	6	707_708	c.696_697insC	c.(694-699)cccggafs	p.G233fs	NUDT17_ENST00000444015.2_5'UTR	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	233	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.						hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(2)	9	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGGAGAAGTCCGGGTGTCTCTG	0.545																																					p.G233fs		.	.											.	NUDT17	.	.	0			c.697_698insC						.																																			SO:0001589	frameshift_variant	200035	exon6			.	BC046352	CCDS72865.1	1q21.1	2008-02-05			ENSG00000186364	ENSG00000186364		"Nudix motif containing"	26618	protein-coding gene	gene with protein product						12477932	Standard	NM_001012758		Approved	FLJ34433	uc001eoe.3	P0C025	OTTHUMG00000013752	ENST00000334513.5:c.697dupC	1.37:g.145587386_145587386dupG	ENSP00000334437:p.Gly233fs	97.0	0.0		127.0	10.0	NM_001012758		Frame_Shift_Ins	INS	ENST00000334513.5	37	CCDS30830.1																																																																																			.	.		0.545	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395		G	145587384	-	G	145587383	7	5	40	1	0	1	1	0	0	0	0	0	10743	661	23	0	301	0	NUDT17	1	145587383	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	29758365	145587383	103663238	17	4673										
LCE1D	353134	hgsc.bcm.edu	37	chr1	152770450	152770451	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcggctgtggctccaactctINSgggggctgctgcagctctgg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:152770450_152770451insG	ENST00000326233.6	+	2	223_224	c.180_181insG	c.(181-183)gggfs	p.G61fs		NM_178352.2	NP_848129.1	Q5T752	LCE1D_HUMAN	late cornified envelope 1D	61	Cys-rich.				cellular response to calcium ion (GO:0071277)|cognition (GO:0050890)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(1)	1	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTCCAACTCTGGGGGCTGCTG	0.663																																					p.S60fs		.	.											.	LCE1D	.	.	0			c.180_181insG						.																																			SO:0001589	frameshift_variant	353134	exon2			.		CCDS1025.1	1q21.3	2008-02-05			ENSG00000172155	ENSG00000172155		"Late cornified envelopes"	29465	protein-coding gene	gene with protein product		612606				11698679	Standard	NM_178352		Approved	LEP4	uc009wnp.3	Q5T752	OTTHUMG00000012444	ENST00000326233.6:c.185dupG	1.37:g.152770455_152770455dupG	ENSP00000316737:p.Gly61fs	131.0	0.0		128.0	11.0	NM_178352		Frame_Shift_Ins	INS	ENST00000326233.6	37	CCDS1025.1																																																																																			.	.		0.663	LCE1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034657.2	NM_178352		G	152770451	-	G	152770450	7	5	40	1	0	1	1	0	0	0	0	0	8671	1567	55	0	182	0	LCE1D	1	152770450	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	7183067	152770450	96480171	18	4674										
LCE1C	353133	hgsc.bcm.edu	37	chr1	152777757	152777758	+	Frame_Shift_Ins	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctcccccagaactgcagcatINScccccagagctggagccaca					rs565723067|rs534849272	byFrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:152777757_152777758insC	ENST00000607093.1	-	1	196_197	c.197_198insG	c.(196-198)ggafs	p.G66fs	LCE1C_ENST00000368768.1_Frame_Shift_Ins_p.G66fs			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	66	Gly-rich.				keratinization (GO:0031424)			p.G66E(1)		NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1)	9	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AACTGCAGCATCCCCCAGAGCT	0.668																																					p.G66fs		.	.											.	LCE1C	.	.	1	Substitution - Missense(1)	lung(1)	c.198_199insG						.																																			SO:0001589	frameshift_variant	353133	exon2			.		CCDS1026.1	1q21.3	2008-02-05			ENSG00000197084	ENSG00000197084		"Late cornified envelopes"	29464	protein-coding gene	gene with protein product		612605				11698679	Standard	NM_001276331		Approved	LEP3	uc001fap.1	Q5T751	OTTHUMG00000012445	ENST00000607093.1:c.198dupG	1.37:g.152777762_152777762dupC	ENSP00000475270:p.Gly66fs	150.0	0.0		161.0	10.0	NM_178351		Frame_Shift_Ins	INS	ENST00000607093.1	37	CCDS1026.1																																																																																			.	.		0.668	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351		C	152777758	-	C	152777757	7	5	40	1	0	1	1	0	0	0	0	0	8670	1422	50	0	162	0	LCE1C	1	152777757	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	7307	152777757	96472864	19	4675										
IL6R	3570	hgsc.bcm.edu	37	chr1	154437759	154437760	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccggtgtcccccagcagcctINSggggtctgacaatacctcga							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:154437759_154437760insG	ENST00000368485.3	+	10	1747_1748	c.1310_1311insG	c.(1309-1314)ctggggfs	p.LG437fs	IL6R_ENST00000507256.1_3'UTR|IL6R_ENST00000344086.4_3'UTR	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	437					acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)		IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	CCCAGCAGCCTGGGGTCTGACA	0.604																																					p.L437fs		.	.											.	IL6R	.	.	0			c.1310_1311insG						.																																			SO:0001589	frameshift_variant	3570	exon10			.	X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.1314dupG	1.37:g.154437763_154437763dupG	ENSP00000357470:p.Leu437fs	158.0	0.0		172.0	11.0	NM_000565	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Frame_Shift_Ins	INS	ENST00000368485.3	37	CCDS1067.1																																																																																			.	.		0.604	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565		G	154437760	-	G	154437759	7	5	40	1	0	1	1	0	0	0	0	0	7711	1580	55	0	1348	0	IL6R	1	154437759	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	1660002	154437759	94812862	20	4676										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842187	154842188	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gagttgggcgagctgagacaINSggggatgcggtggctgctgc					rs372000131		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:154842187_154842188insG	ENST00000271915.4	-	1	568_569	c.253_254insC	c.(253-255)ctgfs	p.L85fs	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	90	Gln-rich.		Missing.		potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	GAGCTGAGACAGGGGATGCGGT	0.693																																					p.L85fs		.	.											.	KCNN3	.	.	0			c.254_255insC						.																																			SO:0001589	frameshift_variant	3782	exon1			.	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.254dupC	1.37:g.154842191_154842191dupG	ENSP00000271915:p.Leu85fs	66.0	0.0		149.0	10.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Frame_Shift_Ins	INS	ENST00000271915.4	37	CCDS30880.1																																																																																			.	.		0.693	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		G	154842188	-	G	154842187	7	5	40	1	0	1	1	0	0	0	0	0	8089	188	7	0	1995	0	KCNN3	1	154842187	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	404428	154842187	94408434	21	4677										
ADAM15	8751	hgsc.bcm.edu	37	chr1	155029712	155029713	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcagccgacgggccctggagINSaaagccctcctggatggaat							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:155029712_155029713insA	ENST00000356955.2	+	12	1298_1299	c.1197_1198insA	c.(1198-1200)aaafs	p.K400fs	ADAM15_ENST00000447332.3_Frame_Shift_Ins_p.K384fs|ADAM15_ENST00000271836.6_Frame_Shift_Ins_p.K400fs|ADAM15_ENST00000360674.4_Frame_Shift_Ins_p.K400fs|ADAM15_ENST00000368413.1_Frame_Shift_Ins_p.K106fs|ADAM15_ENST00000368412.3_Frame_Shift_Ins_p.K400fs|ADAM15_ENST00000531455.1_Frame_Shift_Ins_p.K410fs|ADAM15_ENST00000355956.2_Frame_Shift_Ins_p.K400fs|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000368410.2_Frame_Shift_Ins_p.K106fs|ADAM15_ENST00000359280.4_Frame_Shift_Ins_p.K400fs|ADAM15_ENST00000449910.2_Frame_Shift_Ins_p.K400fs	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	400	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			GGGCCCTGGAGAAAGCCCTCCT	0.634																																					p.E409fs		.	.											.	ADAM15	.	.	0			c.1227_1228insA						.																																			SO:0001589	frameshift_variant	8751	exon12			.	U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"ADAM metallopeptidase domain containing"	193	protein-coding gene	gene with protein product	"metargidin"	605548	"a disintegrin and metalloproteinase domain 15 (metargidin)"			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.1200dupA	1.37:g.155029715_155029715dupA	ENSP00000349436:p.Lys400fs	76.0	0.0		157.0	11.0	NM_001261464	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Frame_Shift_Ins	INS	ENST00000356955.2	37	CCDS1087.1																																																																																			.	.		0.634	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815		A	155029713	-	A	155029712	7	5	40	1	0	1	1	0	0	0	0	0	237	933	33	0	1243	0	ADAM15	1	155029712	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	187525	155029712	94220909	22	4678										
HCN3	57657	hgsc.bcm.edu	37	chr1	155255629	155255629	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgcgctttgaggtcttccagCcgggggatctcgtggtgcgt	16	10	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:155255629C>A	ENST00000368358.3	+	6	1359	c.1351C>A	c.(1351-1353)Ccg>Acg	p.P451T	HCN3_ENST00000496230.1_3'UTR	NM_020897.2	NP_065948.1	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 3	451					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGTCTTCCAGCCGGGGGATCT	0.657																																					p.P451T		.	.											.	HCN3	.	.	0			c.C1351A						.						74	70	71					1																	155255629		2203	4300	6503	SO:0001583	missense	57657	exon6			TTCCAGCCGGGGG	AB040968	CCDS1108.1	1q21.2	2011-07-05			ENSG00000143630	ENSG00000143630		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	19183	protein-coding gene	gene with protein product		609973				16382102	Standard	NM_020897		Approved	KIAA1535	uc001fjz.2	Q9P1Z3	OTTHUMG00000035872	ENST00000368358.3:c.1351C>A	1.37:g.155255629C>A	ENSP00000357342:p.Pro451Thr	184.0	0.0		401.0	36.0	NM_020897	D3DV90|Q4VX12|Q8N6W6|Q9BWQ2	Missense_Mutation	SNP	ENST00000368358.3	37	CCDS1108.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.973201	0.92919	.	.	ENSG00000143630	ENST00000368358	D	0.97505	-4.41	5.46	5.46	0.80206	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.51477	D	0.000099	D	0.98448	0.9483	M	0.84846	2.72	0.80722	D	1	D;P	0.62365	0.991;0.685	D;P	0.74674	0.984;0.709	D	0.99360	1.0917	10	0.87932	D	0	.	17.154	0.86785	0.0:1.0:0.0:0.0	.	146;451	B7Z5R8;Q9P1Z3	.;HCN3_HUMAN	T	451	ENSP00000357342:P451T	ENSP00000357342:P451T	P	+	1	0	HCN3	153522253	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.776000	0.85560	2.724000	0.93272	0.561000	0.74099	CCG	.	.		0.657	HCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087388.1	NM_020897		A	155255629	C	A	155255629	3	1	40	1	0	0	0	0	1	0	0	0	7007	739	26	3	1373	3	HCN3	1	155255629	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	225917	155255629	93994992	23	4679										
RXFP4	339403	hgsc.bcm.edu	37	chr1	155912224	155912225	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	acggcggcggcaggacagcaINSgggtcgtggcccgctctgtc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:155912224_155912225insG	ENST00000368318.3	+	1	745_746	c.724_725insG	c.(724-726)aggfs	p.R242fs		NM_181885.2	NP_871001.1	Q8TDU9	RL3R2_HUMAN	relaxin/insulin-like family peptide receptor 4	242						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)			endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	13	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GCAGGACAGCAGGGTCGTGGCC	0.634																																					p.R242fs		.	.											.	RXFP4	.	.	0			c.724_725insG						.																																			SO:0001589	frameshift_variant	339403	exon1			.	AB065617	CCDS1124.1	1q22	2012-08-08	2006-05-09	2006-03-15	ENSG00000173080	ENSG00000173080		"GPCR / Class A : Relaxin family peptide receptors"	14666	protein-coding gene	gene with protein product		609043	"G protein-coupled receptor 100", "relaxin 3 receptor 2", "relaxin family peptide receptor 4"	GPR100, RLN3R2		15956688, 16507880	Standard	NM_181885		Approved	GPCR142, RXFPR4	uc010pgs.2	Q8TDU9	OTTHUMG00000017463	ENST00000368318.3:c.727dupG	1.37:g.155912227_155912227dupG	ENSP00000357301:p.Arg242fs	149.0	0.0		158.0	10.0	NM_181885	B0M0L4|Q3MJB1|Q8NGZ8	Frame_Shift_Ins	INS	ENST00000368318.3	37	CCDS1124.1																																																																																			.	.		0.634	RXFP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046203.1	NM_181885		G	155912225	-	G	155912224	7	5	40	1	0	1	1	0	0	0	0	0	13777	179	7	0	726	0	RXFP4	1	155912224	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	656595	155912224	93338397	24	4680										
ETV3L	440695	hgsc.bcm.edu	37	chr1	157067713	157067714	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agaggtctctggtggccctcINSggggggtctgctgtcctgtc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:157067713_157067714insG	ENST00000454449.2	-	4	837_838	c.553_554insC	c.(553-555)cgafs	p.R185fs		NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	185					cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Hepatocellular(266;0.158)	Prostate(1639;0.184)				TGGTGGCCCTCGGGGGGTCTGC	0.619																																					p.R185fs		.	.											.	ETV3L	.	.	0			c.554_555insC						.																																			SO:0001589	frameshift_variant	440695	exon4			.	AK131392	CCDS30893.1	1q23.1	2013-09-24	2008-09-12		ENSG00000253831	ENSG00000253831			33834	protein-coding gene	gene with protein product			"ets variant gene 3-like"				Standard	NM_001004341		Approved	FLJ16478	uc001fqq.2	Q6ZN32	OTTHUMG00000041325	ENST00000454449.2:c.554dupC	1.37:g.157067719_157067719dupG	ENSP00000430271:p.Arg185fs	169.0	0.0		184.0	12.0	NM_001004341		Frame_Shift_Ins	INS	ENST00000454449.2	37	CCDS30893.1																																																																																			.	.		0.619	ETV3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099024.2	NM_001004341		G	157067714	-	G	157067713	7	5	40	1	0	1	1	0	0	0	0	0	5282	884	31	0	539	0	ETV3L	1	157067713	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	1155489	157067713	92182908	25	4681										
B4GALT3	8703	hgsc.bcm.edu	37	chr1	161143503	161143504	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgagactcctccgaagtactINSgggggtacgggaggctaggg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:161143503_161143504insG	ENST00000319769.5	-	6	916_917	c.694_695insC	c.(694-696)cagfs	p.Q232fs	PPOX_ENST00000535223.1_Intron|B4GALT3_ENST00000470882.1_5'UTR|PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000367998.1_Frame_Shift_Ins_p.Q232fs|PPOX_ENST00000495483.1_Intron	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	232					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	TCCGAAGTACTGGGGGTACGGG	0.554																																					p.Q232fs		.	.											.	B4GALT3	.	.	0			c.695_696insC						.																																			SO:0001589	frameshift_variant	8703	exon6			.	BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"Beta 4-glycosyltransferases"	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.695dupC	1.37:g.161143508_161143508dupG	ENSP00000320965:p.Gln232fs	130.0	0.0		147.0	11.0	NM_003779	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Frame_Shift_Ins	INS	ENST00000319769.5	37	CCDS1222.1																																																																																			.	.		0.554	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779		G	161143504	-	G	161143503	7	5	40	1	0	1	1	0	0	0	0	0	1272	1580	55	0	498	0	B4GALT3	1	161143503	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	4075790	161143503	88107118	26	4682										
RGS4	5999	hgsc.bcm.edu	37	chr1	163039295	163039295	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atgtgcaaagggcttgcaggTctgccggcttcttgcttgag	14	9	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:163039295T>A	ENST00000367909.6	+	1	361	c.21T>A	c.(19-21)ggT>ggA	p.G7G	RGS4_ENST00000531057.1_Silent_p.G7G|RGS4_ENST00000527809.1_Intron|RGS4_ENST00000491263.1_3'UTR|RGS4_ENST00000367906.3_5'Flank|RGS4_ENST00000367908.4_Silent_p.G7G|RGS4_ENST00000421743.2_Silent_p.G104G	NM_001113380.1|NM_005613.5	NP_001106851.1|NP_005604.1	P49798	RGS4_HUMAN	regulator of G-protein signaling 4	7					inactivation of MAPK activity (GO:0000188)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)	21						GGCTTGCAGGTCTGCCGGCTT	0.438											OREG0013952	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G104G	Ovarian(76;1257 1738 3039 6086)	.	.											.	RGS4	.	.	0			c.T312A						.						67	63	65					1																	163039295		2203	4300	6503	SO:0001819	synonymous_variant	5999	exon2			TGCAGGTCTGCCG	BC051869	CCDS1243.1, CCDS44270.1, CCDS44271.1, CCDS44272.1	1q23.3	2008-05-14	2007-08-14		ENSG00000117152	ENSG00000117152		"Regulators of G-protein signaling"	10000	protein-coding gene	gene with protein product		602516	"regulator of G-protein signalling 4", "schizophrenia disorder 9"	SCZD9		8602223, 8756726	Standard	NM_001102445		Approved		uc001gcl.4	P49798	OTTHUMG00000034417	ENST00000367909.6:c.21T>A	1.37:g.163039295T>A		140.0	0.0	1828	146.0	23.0	NM_001102445	A7XA56|A7XA58|A7XA59|A7YVV7|B1APZ3	Silent	SNP	ENST00000367909.6	37	CCDS1243.1																																																																																			.	.		0.438	RGS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083197.2	NM_005613		A	163039295	T	A	163039295	2	1	40	1	0	0	0	0	0	0	0	1	13322	1654	58	4		4	RGS4	1	163039295	Silent	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	1895792	163039295	86211326	27	4683										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179437688	179437689	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agaatggcaggaaatagatgINSaaaaaattaatgaaatgaaa							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:179437688_179437689insA	ENST00000367618.3	+	17	2296_2297	c.1909_1910insA	c.(1909-1911)gaafs	p.E637fs	AXDND1_ENST00000457238.2_3'UTR|AXDND1_ENST00000461179.2_3'UTR	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	637										NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						GGAAATAGATGAAAAAATTAAT	0.351																																					p.E637fs		.	.											.	AXDND1	.	.	0			c.1909_1910insA						.																																			SO:0001589	frameshift_variant	126859	exon17			.	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.1915dupA	1.37:g.179437694_179437694dupA	ENSP00000356590:p.Glu637fs	149.0	0.0		221.0	15.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Frame_Shift_Ins	INS	ENST00000367618.3	37	CCDS30948.1																																																																																			.	.		0.351	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		A	179437689	-	A	179437688	7	5	40	1	0	1	1	0	0	0	0	0	1995	1291	45	0	1971	0	C1orf125	1	179437688	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	16398393	179437688	69812933	28	4684										
C4BPA	722	hgsc.bcm.edu	37	chr1	207318042	207318042	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gagacagcgcaagacaatccActttggataaagaactataa	8	8	0	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:207318042A>T	ENST00000367070.3	+	12	1968	c.1774A>T	c.(1774-1776)Act>Tct	p.T592S		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	592					complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						AAGACAATCCACTTTGGATAA	0.413																																					p.T592S		.	.											.	C4BPA	.	.	0			c.A1774T						.						39	39	39					1																	207318042		2203	4300	6503	SO:0001583	missense	722	exon12			CAATCCACTTTGG	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.1774A>T	1.37:g.207318042A>T	ENSP00000356037:p.Thr592Ser	84.0	0.0		150.0	17.0	NM_000715	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	.	.	.	.	.	.	.	.	.	.	A	3.375	-0.127570	0.06753	.	.	ENSG00000123838	ENST00000367070	T	0.29917	1.55	4.07	-4.11	0.03928	.	2.128780	0.01768	N	0.030972	T	0.13329	0.0323	N	0.12182	0.205	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.10109	-1.0644	10	0.11485	T	0.65	.	1.5392	0.02551	0.3172:0.1575:0.3709:0.1544	.	592	P04003	C4BPA_HUMAN	S	592	ENSP00000356037:T592S	ENSP00000356037:T592S	T	+	1	0	C4BPA	205384665	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.214000	0.09292	-0.932000	0.03742	-0.250000	0.11733	ACT	.	.		0.413	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			T	207318042	A	T	207318042	3	4	40	1	0	0	0	0	1	0	0	0	2251	159	6	4	1816	4	C4BPA	1	207318042	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	27880354	207318042	41932579	29	4685										
ACTN2	88	hgsc.bcm.edu	37	chr1	236891012	236891012	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttggactctgtgccctcatcCaccgacaccggcctgacctc	8	18	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:236891012C>A	ENST00000366578.4	+	6	737	c.571C>A	c.(571-573)Cac>Aac	p.H191N	ACTN2_ENST00000492634.1_3'UTR|ACTN2_ENST00000542672.1_Missense_Mutation_p.H191N	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	191	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			TGCCCTCATCCACCGACACCG	0.547																																					p.H191N		.	.											.	ACTN2	.	.	0			c.C571A						.						179	145	156					1																	236891012		2203	4300	6503	SO:0001583	missense	88	exon6			CTCATCCACCGAC	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.571C>A	1.37:g.236891012C>A	ENSP00000355537:p.His191Asn	111.0	0.0		163.0	27.0	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	37	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.005920	0.93287	.	.	ENSG00000077522	ENST00000542672;ENST00000366578	D;D	0.95035	-3.59;-3.59	5.2	5.2	0.72013	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.97729	0.9255	M	0.89214	3.015	0.80722	D	1	D;P	0.89917	1.0;0.884	D;D	0.87578	0.998;0.981	D	0.98588	1.0653	10	0.87932	D	0	.	18.7382	0.91764	0.0:1.0:0.0:0.0	.	191;191	B2RCS5;P35609	.;ACTN2_HUMAN	N	191	ENSP00000443495:H191N;ENSP00000355537:H191N	ENSP00000355537:H191N	H	+	1	0	ACTN2	234957635	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.411000	0.81874	0.462000	0.41574	CAC	.	.		0.547	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		A	236891012	C	A	236891012	3	1	40	1	0	0	0	0	1	0	0	0	205	594	21	3	593	3	ACTN2	1	236891012	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	29572970	236891012	12359609	30	4686										
ZP4	57829	hgsc.bcm.edu	37	chr1	238053180	238053180	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cctttacctagaagatccatAggacacttgagcagcttcct	7	12	0	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:238053180A>G	ENST00000366570.4	-	3	545	c.387T>C	c.(385-387)ccT>ccC	p.P129P	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	129					acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GAAGATCCATAGGACACTTGA	0.552																																					p.P129P	NSCLC(166;160 2029 11600 18754 19936)	.	.											.	ZP4	.	.	0			c.T387C						.						225	228	227					1																	238053180		2203	4300	6503	SO:0001819	synonymous_variant	57829	exon3			ATCCATAGGACAC	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"Zona pellucida glycoproteins"	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.387T>C	1.37:g.238053180A>G		141.0	0.0		174.0	40.0	NM_021186	B2RAE1	Silent	SNP	ENST00000366570.4	37	CCDS1615.1																																																																																			.	.		0.552	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			G	238053180	A	G	238053180	2	3	40	1	0	0	0	0	0	0	0	1	18233	407	15	2		2	ZP4	1	238053180	Silent	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	1162168	238053180	11197441	31	4687										
RGS7	6000	hgsc.bcm.edu	37	chr1	240976967	240976967	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atcggacagccatgggttagAagggtcaggtggcaaaagaa	15	6	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:240976967A>C	ENST00000407727.1	-	12	906	c.907T>G	c.(907-909)Tct>Gct	p.S303A	RGS7_ENST00000366562.4_Missense_Mutation_p.S303A|RGS7_ENST00000401882.1_Missense_Mutation_p.S250A|RGS7_ENST00000446183.2_Missense_Mutation_p.S219A|RGS7_ENST00000366563.1_Missense_Mutation_p.S303A|RGS7_ENST00000348120.2_Missense_Mutation_p.S250A|RGS7_ENST00000366564.1_Missense_Mutation_p.S303A|RGS7_ENST00000331110.7_Missense_Mutation_p.S277A|RGS7_ENST00000366565.1_Missense_Mutation_p.S303A			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	303	G protein gamma.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			CATGGGTTAGAAGGGTCAGGT	0.423																																					p.S303A		.	.											.	RGS7	.	.	0			c.T907G						.						114	107	110					1																	240976967		2203	4300	6503	SO:0001583	missense	6000	exon13			GGTTAGAAGGGTC	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"Regulators of G-protein signaling"	10003	protein-coding gene	gene with protein product		602517	"regulator of G-protein signalling 7"			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.907T>G	1.37:g.240976967A>C	ENSP00000384428:p.Ser303Ala	105.0	0.0		148.0	72.0	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	37		.	.	.	.	.	.	.	.	.	.	A	17.02	3.281245	0.59758	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000440928;ENST00000348120;ENST00000446183;ENST00000366562;ENST00000407727;ENST00000401882	T;T;T;T;T;T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85	5.5	4.34	0.51931	G-protein gamma domain (4);	0.059407	0.64402	N	0.000001	T	0.42314	0.1197	M	0.90425	3.115	0.44110	D	0.99688	B;B;B;B;B;P;B	0.34800	0.091;0.041;0.296;0.064;0.033;0.469;0.041	B;B;B;B;B;B;B	0.40506	0.097;0.074;0.124;0.149;0.075;0.331;0.122	T	0.44112	-0.9349	10	0.62326	D	0.03	-11.572	11.7489	0.51837	0.8523:0.1477:0.0:0.0	.	219;277;250;303;303;303;303	B7Z223;B7Z257;P49802-4;P49802-2;P49802-5;P49802-3;P49802	.;.;.;.;.;.;RGS7_HUMAN	A	277;303;303;303;134;250;219;303;303;250	ENSP00000331485:S277A;ENSP00000355523:S303A;ENSP00000355522:S303A;ENSP00000355521:S303A;ENSP00000404399:S134A;ENSP00000341242:S250A;ENSP00000390138:S219A;ENSP00000355520:S303A;ENSP00000384428:S303A;ENSP00000385508:S250A	ENSP00000331485:S277A	S	-	1	0	RGS7	239043590	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.453000	0.80700	0.871000	0.35750	0.533000	0.62120	TCT	.	.		0.423	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		C	240976967	A	C	240976967	3	2	40	1	0	0	0	0	1	0	0	0	13325	246	9	5	580	5	RGS7	1	240976967	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	2923787	240976967	8273654	32	4688										
OR2B11	127623	hgsc.bcm.edu	37	chr1	247614658	247614658	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gccaggggcaccaacacgaaGaaggccaccagcacagccag	12	15	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:247614658G>T	ENST00000318749.6	-	1	650	c.627C>A	c.(625-627)ttC>ttA	p.F209L		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	209						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CCAACACGAAGAAGGCCACCA	0.562																																					p.F209L		.	.											.	OR2B11	.	.	0			c.C627A						.						65	68	67					1																	247614658		2203	4300	6503	SO:0001583	missense	127623	exon1			CACGAAGAAGGCC		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"GPCR / Class A : Olfactory receptors"	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.627C>A	1.37:g.247614658G>T	ENSP00000325682:p.Phe209Leu	93.0	0.0		111.0	34.0	NM_001004492	B2RP03	Missense_Mutation	SNP	ENST00000318749.6	37	CCDS31090.1	.	.	.	.	.	.	.	.	.	.	G	1.854	-0.464310	0.04476	.	.	ENSG00000177535	ENST00000318749	T	0.34667	1.35	5.09	4.18	0.49190	GPCR, rhodopsin-like superfamily (1);	0.460023	0.20562	N	0.089897	T	0.14657	0.0354	N	0.02708	-0.52	0.30174	N	0.800983	B	0.26775	0.159	B	0.27887	0.084	T	0.15549	-1.0433	10	0.07813	T	0.8	.	11.4177	0.49962	0.0873:0.0:0.9127:0.0	.	209	Q5JQS5	OR2BB_HUMAN	L	209	ENSP00000325682:F209L	ENSP00000325682:F209L	F	-	3	2	OR2B11	245681281	0.000000	0.05858	1.000000	0.80357	0.554000	0.35429	0.216000	0.17585	1.524000	0.49035	0.643000	0.83706	TTC	.	.		0.562	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492		T	247614658	G	T	247614658	3	4	40	1	0	0	0	0	1	0	0	0	10997	933	33	3	329	3	OR2B11	1	247614658	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	6637691	247614658	1635963	33	4689										
OR2W5	441932	hgsc.bcm.edu	37	chr1	247655276	247655276	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctcttctacaccatcgtcatTcccagcatcaaccccctcat	2	19	5	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr1:247655276T>C	ENST00000522351.1	+	0	907							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CCATCGTCATTCCCAGCATCA	0.527																																					p.S283P		.	.											.	OR2W5	.	.	0			c.T847C						.						113	103	106					1																	247655276		2203	4300	6503			441932	exon1			CGTCATTCCCAGC			1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"GPCR / Class A : Olfactory receptors"	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		1.37:g.247655276T>C		224.0	0.0		291.0	12.0	NM_001004698	B9EH85	Missense_Mutation	SNP	ENST00000522351.1	37																																																																																				.	.		0.527	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698		C	247655276	T	C	247655276	1	2	40	0	1	0	0	0	0	0	0	0	11043	1783	62	2		2	OR2W5	1	247655276	RNA	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	40618	247655276	1595345	34	4690										
NBAS	51594	hgsc.bcm.edu	37	chr2	15519748	15519748	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggctagatccatgcagctatCagtgaggttggtagaagaat	13	6	1	4			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:15519748C>A	ENST00000281513.5	-	30	3593	c.3568G>T	c.(3568-3570)Gat>Tat	p.D1190Y	NBAS_ENST00000441750.1_Missense_Mutation_p.D1070Y	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1190					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						ATGCAGCTATCAGTGAGGTTG	0.423																																					p.D1190Y		.	.											.	NBAS	.	.	0			c.G3568T						.						98	96	97					2																	15519748		2203	4300	6503	SO:0001583	missense	51594	exon30			AGCTATCAGTGAG	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.3568G>T	2.37:g.15519748C>A	ENSP00000281513:p.Asp1190Tyr	337.0	0.0		334.0	45.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631951	0.87660	.	.	ENSG00000151779	ENST00000441750;ENST00000281513;ENST00000441755	T;T;T	0.19105	2.17;2.17;2.17	5.79	5.79	0.91817	Secretory pathway Sec39 (1);	0.000000	0.85682	D	0.000000	T	0.51635	0.1686	M	0.77820	2.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.52351	-0.8587	10	0.87932	D	0	.	20.0361	0.97558	0.0:1.0:0.0:0.0	.	1070;1190	A2RRP1-2;A2RRP1	.;NBAS_HUMAN	Y	1070;1190;237	ENSP00000413201:D1070Y;ENSP00000281513:D1190Y;ENSP00000396501:D237Y	ENSP00000281513:D1190Y	D	-	1	0	NBAS	15437199	1.000000	0.71417	0.946000	0.38457	0.941000	0.58515	6.917000	0.75782	2.740000	0.93945	0.563000	0.77884	GAT	.	.		0.423	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		A	15519748	C	A	15519748	3	1	40	1	0	0	0	0	1	0	0	0	10195	826	29	3	3639	3	NBAS	2	15519748	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10		15519748	227679625	35	4691										
RDH14	57665	hgsc.bcm.edu	37	chr2	18736770	18736770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	catttgtgccttctaagcggCgggctagttccctggtaaaa	11	10	1	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:18736770C>T	ENST00000381249.3	-	2	805	c.698G>A	c.(697-699)cGc>cAc	p.R233H	RDH14_ENST00000468071.1_5'UTR	NM_020905.3	NP_065956.1	Q9HBH5	RDH14_HUMAN	retinol dehydrogenase 14 (all-trans/9-cis/11-cis)	233					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)				Vitamin A(DB00162)	TTCTAAGCGGCGGGCTAGTTC	0.428																																					p.R547H		.	.											.	.	.	.	0			c.G1640A						.						119	116	117					2																	18736770		2203	4300	6503	SO:0001583	missense	100526794	exon9			AAGCGGCGGGCTA	AF237952	CCDS1693.1	2p24.2	2011-09-14	2006-05-09		ENSG00000240857	ENSG00000240857	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	19979	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 4"		"retinol dehydrogenase 14 (all-trans and 9-cis)"			12226107, 19027726	Standard	NM_020905		Approved	PAN2, SDR7C4		Q9HBH5	OTTHUMG00000090705	ENST00000381249.3:c.698G>A	2.37:g.18736770C>T	ENSP00000370648:p.Arg233His	146.0	0.0		187.0	33.0	NM_001199103		Missense_Mutation	SNP	ENST00000381249.3	37	CCDS1693.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.669703	0.47677	.	.	ENSG00000240857	ENST00000381249	D	0.96041	-3.89	5.67	2.86	0.33363	NAD(P)-binding domain (1);	.	.	.	.	D	0.94542	0.8242	M	0.85945	2.785	0.39580	D	0.969427	B	0.21753	0.06	B	0.14023	0.01	D	0.92443	0.5963	9	0.49607	T	0.09	.	10.6185	0.45465	0.0:0.7369:0.0:0.2631	.	233	Q9HBH5	RDH14_HUMAN	H	233	ENSP00000370648:R233H	ENSP00000370648:R233H	R	-	2	0	RDH14	18600251	0.924000	0.31332	1.000000	0.80357	1.000000	0.99986	0.978000	0.29488	0.746000	0.32786	0.655000	0.94253	CGC	.	.		0.428	RDH14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207394.1			T	18736770	C	T	18736770	3	4	40	1	0	0	0	0	1	0	0	0	13208	768	27	1	316	1	RDH14	2	18736770	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	3217022	18736770	224462603	36	4692										
NCOA1	8648	hgsc.bcm.edu	37	chr2	24991260	24991260	+	Nonstop_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cagcagctactgactgaataAccacttttaaaggaatgtga	8	8	0	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:24991260A>T	ENST00000406961.1	+	23	4978	c.4326A>T	c.(4324-4326)taA>taT	p.*1442Y	NCOA1_ENST00000395856.3_Nonstop_Mutation_p.*1441Y|NCOA1_ENST00000405141.1_3'UTR|NCOA1_ENST00000348332.3_Nonstop_Mutation_p.*1442Y|NCOA1_ENST00000288599.5_3'UTR|NCOA1_ENST00000407230.1_3'UTR			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	0					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGACTGAATAACCACTTTTAA	0.413			T	PAX3	alveolar rhadomyosarcoma																																p.X1442Y		.	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	.	.	0			c.A4326T						.						42	48	46					2																	24991260		2203	4300	6503	SO:0001578	stop_lost	8648	exon21			TGAATAACCACTT	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.4326A>T	2.37:g.24991260A>T	ENSP00000385216:p.*1442Tyrext*9	102.0	0.0		81.0	18.0	NM_003743	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	A	16.51	3.143497	0.57044	.	.	ENSG00000084676	ENST00000406961;ENST00000348332;ENST00000395856	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.6128	0.28139	0.8423:0.0:0.1577:0.0	.	.	.	.	Y	1442;1442;1441	.	.	X	+	3	2	NCOA1	24844764	1.000000	0.71417	0.999000	0.59377	0.967000	0.64934	4.331000	0.59273	2.219000	0.72066	0.460000	0.39030	TAA	.	.		0.413	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		T	24991260	A	T	24991260	4	4	40	1	0	0	0	0	0	0	0	0	10237	50	2	4	4449	4	NCOA1	2	24991260	Nonstop_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	6254490	24991260	218208113	37	4693										
TTC27	55622	hgsc.bcm.edu	37	chr2	33012108	33012108	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgtaactatgaacactggcaGatttgggaaaactacatcct	8	8	0	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:33012108G>T	ENST00000317907.4	+	16	2121	c.1890G>T	c.(1888-1890)caG>caT	p.Q630H		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	630										breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						AACACTGGCAGATTTGGGAAA	0.378																																					p.Q630H		.	.											.	TTC27	.	.	0			c.G1890T						.						86	83	84					2																	33012108		2203	4300	6503	SO:0001583	missense	55622	exon16			CTGGCAGATTTGG	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1890G>T	2.37:g.33012108G>T	ENSP00000313953:p.Gln630His	187.0	0.0		153.0	24.0	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.301712	0.40694	.	.	ENSG00000018699	ENST00000317907	T	0.38077	1.16	4.94	-2.28	0.06826	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.45498	0.1345	L	0.39898	1.24	0.47276	D	0.999376	D	0.89917	1.0	D	0.73380	0.98	T	0.36138	-0.9760	10	0.52906	T	0.07	-10.2774	14.2328	0.65906	0.3619:0.0:0.6381:0.0	.	630	Q6P3X3	TTC27_HUMAN	H	630	ENSP00000313953:Q630H	ENSP00000313953:Q630H	Q	+	3	2	TTC27	32865612	1.000000	0.71417	0.991000	0.47740	0.966000	0.64601	1.556000	0.36288	-0.364000	0.08088	-0.946000	0.02672	CAG	.	.		0.378	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		T	33012108	G	T	33012108	3	4	40	1	0	0	0	0	1	0	0	0	16710	933	33	3	1952	3	TTC27	2	33012108	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	8020848	33012108	210187265	38	4694										
STON1	11037	hgsc.bcm.edu	37	chr2	48809580	48809581	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atgaaccgccgagcatgtctINSggggagtttacaggaacttg					rs199917756		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:48809580_48809581insG	ENST00000406226.1	+	3	2003_2004	c.1808_1809insG	c.(1807-1812)ctggggfs	p.LG603fs	STON1_ENST00000404752.1_Frame_Shift_Ins_p.LG603fs|STON1-GTF2A1L_ENST00000394754.1_Frame_Shift_Ins_p.LG603fs|STON1-GTF2A1L_ENST00000309827.2_Frame_Shift_Ins_p.LG603fs|STON1-GTF2A1L_ENST00000402114.2_Frame_Shift_Ins_p.LG603fs|STON1-GTF2A1L_ENST00000394751.3_Frame_Shift_Ins_p.LG603fs|STON1-GTF2A1L_ENST00000405008.1_Frame_Shift_Ins_p.LG603fs|STON1_ENST00000309835.3_Frame_Shift_Ins_p.LG603fs	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	603	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CGAGCATGTCTGGGGAGTTTAC	0.485																																					p.L603fs		.	.											.	STON1	.	.	0			c.1808_1809insG						.																																			SO:0001589	frameshift_variant	11037	exon3			.	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1812dupG	2.37:g.48809584_48809584dupG	ENSP00000384615:p.Leu603fs	151.0	0.0		164.0	11.0	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Frame_Shift_Ins	INS	ENST00000406226.1	37	CCDS1841.1																																																																																			.	.		0.485	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		G	48809581	-	G	48809580	7	5	40	1	0	1	1	0	0	0	0	0	15331	1580	55	0	1810	0	STON1	2	48809580	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	15797472	48809580	194389793	39	4695										
C2orf42	54980	hgsc.bcm.edu	37	chr2	70408519	70408519	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atgtatgcaaataccccaaaCtgtgcttctggcttgccttg	8	11	1	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:70408519C>T	ENST00000264434.2	-	3	978	c.599G>A	c.(598-600)aGt>aAt	p.S200N	C2orf42_ENST00000420306.1_Missense_Mutation_p.S200N|C2orf42_ENST00000470096.1_5'Flank	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	200										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						ATACCCCAAACTGTGCTTCTG	0.498																																					p.S200N		.	.											.	C2orf42	.	.	0			c.G599A						.						119	117	118					2																	70408519		2203	4300	6503	SO:0001583	missense	54980	exon3			CCCAAACTGTGCT	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.599G>A	2.37:g.70408519C>T	ENSP00000264434:p.Ser200Asn	150.0	0.0		123.0	20.0	NM_017880	D6W5G3|Q9H629	Missense_Mutation	SNP	ENST00000264434.2	37	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.772148	0.31411	.	.	ENSG00000115998	ENST00000264434;ENST00000420306	T;T	0.44482	0.92;0.92	4.96	4.07	0.47477	.	0.138843	0.64402	N	0.000003	T	0.26810	0.0656	N	0.19112	0.55	0.34079	D	0.659377	B	0.02656	0.0	B	0.04013	0.001	T	0.27739	-1.0065	10	0.26408	T	0.33	-18.7241	11.3326	0.49485	0.0:0.9096:0.0:0.0904	.	200	Q9NWW7	CB042_HUMAN	N	200	ENSP00000264434:S200N;ENSP00000404515:S200N	ENSP00000264434:S200N	S	-	2	0	C2orf42	70262023	1.000000	0.71417	0.989000	0.46669	0.984000	0.73092	4.717000	0.61923	1.286000	0.44565	0.485000	0.47835	AGT	.	.		0.498	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880		T	70408519	C	T	70408519	3	4	40	1	0	0	0	0	1	0	0	0	2168	565	20	3	1157	3	C2orf42	2	70408519	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	21598939	70408519	172790854	40	4696										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84774640	84774640	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cagaacgcctaggagaatttCgaaatgaggcaaaatatgta	10	6	0	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:84774640C>T	ENST00000237449.6	+	6	1098	c.1090C>T	c.(1090-1092)Cga>Tga	p.R364*	DNAH6_ENST00000389394.3_Nonsense_Mutation_p.R364*|DNAH6_ENST00000398278.2_Nonsense_Mutation_p.R364*			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	364	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R364G(1)		NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						AGGAGAATTTCGAAATGAGGC	0.388																																					p.R364X		.	.											.	DNAH6	.	.	1	Substitution - Missense(1)	breast(1)	c.C1090T						.						239	205	215					2																	84774640		692	1591	2283	SO:0001587	stop_gained	1768	exon7			GAATTTCGAAATG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.1090C>T	2.37:g.84774640C>T	ENSP00000237449:p.Arg364*	353.0	1.0		359.0	149.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Nonsense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	C	33	5.247637	0.95305	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	.	.	.	5.35	0.848	0.18966	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0192	0.64543	0.5216:0.4783:0.0:0.0	.	.	.	.	X	364	.	ENSP00000237449:R364X	R	+	1	2	DNAH6	84628151	1.000000	0.71417	0.346000	0.25655	0.764000	0.43329	0.979000	0.29500	0.568000	0.29311	0.591000	0.81541	CGA	.	.		0.388	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84774640	C	T	84774640	4	4	40	1	0	0	0	0	0	1	0	0	4607	876	31	1	1112	1	DNAH6	2	84774640	Nonsense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	14366121	84774640	158424733	41	4697										
GLI2	2736	hgsc.bcm.edu	37	chr2	121726367	121726367	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccatctccccactctcagacGccagcctggacctgcagcgg	9	19	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:121726367G>A	ENST00000452319.1	+	6	781	c.721G>A	c.(721-723)Gcc>Acc	p.A241T	GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_5'UTR|GLI2_ENST00000361492.4_Missense_Mutation_p.A241T					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				ACTCTCAGACGCCAGCCTGGA	0.647																																					p.A241T		.	.											.	GLI2	.	.	0			c.G721A						.						80	73	76					2																	121726367		2203	4300	6503	SO:0001583	missense	2736	exon5			TCAGACGCCAGCC		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.721G>A	2.37:g.121726367G>A	ENSP00000390436:p.Ala241Thr	132.0	0.0		94.0	14.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.404358|5.404358	0.96051|0.96051	.|.	.|.	ENSG00000074047|ENSG00000074047	ENST00000452319;ENST00000361492|ENST00000440937;ENST00000360874	T;T|.	0.71579|.	-0.58;-0.58|.	4.91|4.91	4.91|4.91	0.64330|0.64330	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72724|0.72724	0.3496|0.3496	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	D;D|D	0.89917|0.69078	1.0;1.0|0.997	D;D|P	0.70935|0.53861	0.971;0.949|0.736	T|T	0.77172|0.77172	-0.2685|-0.2685	10|8	0.15066|0.87932	T|D	0.55|0	.|.	18.2868|18.2868	0.90117|0.90117	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	241;241|111	P10070;Q0VGA0|F5H4D9	GLI2_HUMAN;.|.	T|H	241|111;103	ENSP00000390436:A241T;ENSP00000354586:A241T|.	ENSP00000354586:A241T|ENSP00000441454:R103H	A|R	+|+	1|2	0|0	GLI2|GLI2	121442837|121442837	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.982000|0.982000	0.71751|0.71751	7.807000|7.807000	0.86032|0.86032	2.557000|2.557000	0.86248|0.86248	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.		0.647	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		A	121726367	G	A	121726367	3	1	40	1	0	0	0	0	1	0	0	0	6446	1087	38	1	739	1	GLI2	2	121726367	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	36951727	121726367	121473006	42	4698										
ZEB2	9839	hgsc.bcm.edu	37	chr2	145187479	145187479	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	actcatggttgggcacactaGctggactcgtctcctggtcc	11	13	2	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:145187479G>C	ENST00000558170.2	-	3	1372	c.188C>G	c.(187-189)gCt>gGt	p.A63G	ZEB2_ENST00000303660.4_Missense_Mutation_p.A63G|ZEB2_ENST00000409487.3_Missense_Mutation_p.A63G|ZEB2_ENST00000539609.3_Missense_Mutation_p.A63G	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	63					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		GGGCACACTAGCTGGACTCGT	0.522																																					p.A63G	Melanoma(33;1235 1264 5755 16332)	.	.											.	ZEB2	.	.	0			c.C188G						.						142	116	125					2																	145187479		2203	4300	6503	SO:0001583	missense	9839	exon3			ACACTAGCTGGAC	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.188C>G	2.37:g.145187479G>C	ENSP00000454157:p.Ala63Gly	282.0	0.0		252.0	97.0	NM_001171653	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	37	CCDS2186.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.42|12.42	1.933168|1.933168	0.34096|0.34096	.|.	.|.	ENSG00000169554|ENSG00000169554	ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861;ENST00000409211;ENST00000435831;ENST00000444559|ENST00000419938;ENST00000431672;ENST00000440875	D;D;D;D;D;D;D;D|.	0.89270|.	-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49|.	5.7|5.7	1.98|1.98	0.26296|0.26296	.|.	0.053490|.	0.85682|.	D|.	0.000000|.	T|T	0.35335|0.35335	0.0928|0.0928	N|N	0.12746|0.12746	0.255|0.255	0.52501|0.52501	D|D	0.999953|0.999953	D;P;P;B;B|.	0.71674|.	0.998;0.489;0.923;0.093;0.093|.	D;B;P;B;B|.	0.65684|.	0.937;0.149;0.514;0.033;0.033|.	T|T	0.04281|0.04281	-1.0963|-1.0963	10|5	0.62326|.	D|.	0.03|.	-0.0034|-0.0034	10.1847|10.1847	0.42991|0.42991	0.2644:0.0:0.7356:0.0|0.2644:0.0:0.7356:0.0	.|.	63;63;63;63;63|.	F5H814;B7Z2P2;E7ESP8;A0JP08;O60315|.	.;.;.;.;ZEB2_HUMAN|.	G|V	58;63;63;63;63;63;63;63;63|39;53;50	ENSP00000443792:A63G;ENSP00000302501:A63G;ENSP00000386854:A63G;ENSP00000395496:A63G;ENSP00000376601:A63G;ENSP00000387256:A63G;ENSP00000400993:A63G;ENSP00000399451:A63G|.	ENSP00000302501:A63G|.	A|L	-|-	2|1	0|2	ZEB2|ZEB2	144903949|144903949	1.000000|1.000000	0.71417|0.71417	0.744000|0.744000	0.31058|0.31058	0.321000|0.321000	0.28281|0.28281	3.555000|3.555000	0.53727|0.53727	0.092000|0.092000	0.17331|0.17331	-0.781000|-0.781000	0.03364|0.03364	GCT|CTA	.	.		0.522	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		C	145187479	G	C	145187479	3	2	40	1	0	0	0	0	1	0	0	0	17639	971	34	4	3488	4	ZEB2	2	145187479	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	23461112	145187479	98011894	43	4699										
PRPF40A	55660	hgsc.bcm.edu	37	chr2	153529052	153529052	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cttagcctctttgtactttgAtcttgcttcttctttttctt	4	10	5	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:153529052A>T	ENST00000410080.1	-	13	1832	c.1291T>A	c.(1291-1293)Tca>Aca	p.S431T		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	458	FF 1.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|mRNA processing (GO:0006397)|regulation of cell shape (GO:0008360)|regulation of cytokinesis (GO:0032465)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|urinary_tract(1)	21						TTGTACTTTGATCTTGCTTCT	0.323																																					p.S431T		.	.											.	PRPF40A	.	.	0			c.T1291A						.						117	112	114					2																	153529052		1828	4079	5907	SO:0001583	missense	55660	exon13			ACTTTGATCTTGC	AF049523	CCDS46430.1	2q23.3	2010-01-25	2007-01-12	2006-01-13	ENSG00000196504	ENSG00000196504			16463	protein-coding gene	gene with protein product		612941	"formin-binding protein 3", "formin binding protein 3", "PRP40 pre-mRNA processing factor 40 homolog A (yeast)"	FNBP3		9724750, 12460579	Standard	NM_017892		Approved	FLJ20585, FBP11, HYPA, NY-REN-6, HIP10, FBP-11, FLAF1, Prp40	uc002tyh.4	O75400	OTTHUMG00000154031	ENST00000410080.1:c.1291T>A	2.37:g.153529052A>T	ENSP00000386458:p.Ser431Thr	247.0	0.0		259.0	90.0	NM_017892	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	Missense_Mutation	SNP	ENST00000410080.1	37	CCDS46430.1	.	.	.	.	.	.	.	.	.	.	A	16.29	3.082583	0.55861	.	.	ENSG00000196504	ENST00000410080;ENST00000356402;ENST00000440252;ENST00000359961	T	0.30981	1.51	5.48	5.48	0.80851	FF domain (1);	0.130731	0.51477	D	0.000090	T	0.22003	0.0530	L	0.35854	1.095	0.34891	D	0.745513	B;B	0.32620	0.378;0.132	B;B	0.27500	0.073;0.08	T	0.31308	-0.9948	10	0.31617	T	0.26	-9.5398	10.2647	0.43447	0.9262:0.0:0.0738:0.0	.	458;431	O75400;E9PFS0	PR40A_HUMAN;.	T	431;440;327;378	ENSP00000386458:S431T	ENSP00000348770:S440T	S	-	1	0	PRPF40A	153237298	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.891000	0.63185	2.206000	0.71126	0.533000	0.62120	TCA	.	.		0.323	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575		T	153529052	A	T	153529052	3	4	40	1	0	0	0	0	1	0	0	0	12583	333	12	4	1557	4	PRPF40A	2	153529052	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	8341573	153529052	89670321	44	4700										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168104502	168104503	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	attctaataaggatataaagINSaaaaagaatataaaccttca							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:168104502_168104503insA	ENST00000409195.1	+	9	6689_6690	c.6600_6601insA	c.(6601-6603)aaafs	p.K2201fs	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Frame_Shift_Ins_p.K1979fs|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000295237.9_Frame_Shift_Ins_p.K2201fs|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2026	Pro-rich.				actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGGATATAAAGAAAAAGAATAT	0.366																																					p.K2200fs		.	.											.	XIRP2	.	.	0			c.6600_6601insA						.																																			SO:0001589	frameshift_variant	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6605dupA	2.37:g.168104507_168104507dupA	ENSP00000386840:p.Lys2201fs	153.0	0.0		172.0	11.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Ins	INS	ENST00000409195.1	37	CCDS42769.1																																																																																			.	.		0.366	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168104503	-	A	168104502	7	5	40	1	0	1	1	0	0	0	0	0	17445	933	33	0	6630	0	XIRP2	2	168104502	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	14575450	168104502	75094871	45	4701										
CCDC141	285025	hgsc.bcm.edu	37	chr2	179702272	179702272	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgtcagatggtgcaagagggGactcagggcttcctgggaga	17	7	2	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:179702272G>A	ENST00000420890.2	-	23	3791	c.3674C>T	c.(3673-3675)tCc>tTc	p.S1225F	CCDC141_ENST00000295723.5_Missense_Mutation_p.S650F|CCDC141_ENST00000480419.1_5'UTR	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	1225										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TGCAAGAGGGGACTCAGGGCT	0.577																																					p.S1225F		.	.											.	CCDC141	.	.	0			c.C3674T						.						68	67	67					2																	179702272		2203	4300	6503	SO:0001583	missense	285025	exon23			AGAGGGGACTCAG	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.3674C>T	2.37:g.179702272G>A	ENSP00000395995:p.Ser1225Phe	111.0	0.0		103.0	14.0	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	37		.	.	.	.	.	.	.	.	.	.	G	15.59	2.879578	0.51801	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723	T;T;T	0.61040	0.14;0.7;0.71	5.81	4.93	0.64822	.	0.000000	0.53938	D	0.000041	T	0.72170	0.3427	L	0.59436	1.845	0.39513	D	0.968384	D;D	0.71674	0.991;0.998	P;D	0.66084	0.904;0.941	T	0.77199	-0.2675	10	0.87932	D	0	-9.1397	17.0548	0.86530	0.0:0.1271:0.8729:0.0	.	650;650	Q6ZP82;Q6ZP82-2	CC141_HUMAN;.	F	1225;669;650	ENSP00000395995:S1225F;ENSP00000344627:S669F;ENSP00000295723:S650F	ENSP00000295723:S650F	S	-	2	0	CCDC141	179410517	1.000000	0.71417	0.455000	0.27031	0.367000	0.29736	4.901000	0.63259	1.444000	0.47605	-0.156000	0.13503	TCC	.	.		0.577	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		A	179702272	G	A	179702272	3	1	40	1	0	0	0	0	1	0	0	0	2777	1174	41	3	682	3	CCDC141	2	179702272	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	11597770	179702272	63497101	46	4702										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186673386	186673387	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atacaaatacagcctttcctINSaaaaaagtggctagtttaat							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:186673386_186673387insA	ENST00000424728.1	+	17	19353_19354	c.19353_19354insA	c.(19354-19356)aaafs	p.K6452fs	FSIP2_ENST00000343098.5_Frame_Shift_Ins_p.K6541fs			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6452										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						CAGCCTTTCCTAAAAAAGTGGC	0.317																																					p.P6540fs		.	.											.	FSIP2	.	.	0			c.19620_19621insA						.																																			SO:0001589	frameshift_variant	401024	exon17			.	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.19359dupA	2.37:g.186673392_186673392dupA	ENSP00000401306:p.Lys6452fs	132.0	0.0		167.0	11.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Frame_Shift_Ins	INS	ENST00000424728.1	37																																																																																				.	.		0.317	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		A	186673387	-	A	186673386	7	5	40	1	0	1	1	0	0	0	0	0	6083	1509	53	0	19686	0	FSIP2	2	186673386	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	6971114	186673386	56525987	47	4703										
ITGAV	3685	hgsc.bcm.edu	37	chr2	187540361	187540361	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttgctcagtgcttgaagattGtctgccaagttgggagatta	12	6	2	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:187540361G>T	ENST00000261023.3	+	27	3011	c.2737G>T	c.(2737-2739)Gtc>Ttc	p.V913F	AC017101.10_ENST00000453665.1_RNA|ITGAV_ENST00000374907.3_Missense_Mutation_p.V877F|ITGAV_ENST00000433736.2_Missense_Mutation_p.V867F	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	913					angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	CTTGAAGATTGTCTGCCAAGT	0.388																																					p.V913F	Melanoma(58;108 1995 6081)	.	.											.	ITGAV	.	.	0			c.G2737T						.						125	117	120					2																	187540361		2203	4300	6503	SO:0001583	missense	3685	exon27			AAGATTGTCTGCC		CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"CD molecules", "Integrins"	6150	protein-coding gene	gene with protein product		193210	"antigen identified by monoclonal antibody L230", "vitronectin receptor", "integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.2737G>T	2.37:g.187540361G>T	ENSP00000261023:p.Val913Phe	253.0	0.0		291.0	88.0	NM_002210	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Missense_Mutation	SNP	ENST00000261023.3	37	CCDS2292.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.75|15.75	2.926836|2.926836	0.52759|0.52759	.|.	.|.	ENSG00000138448|ENSG00000138448	ENST00000430709|ENST00000261023;ENST00000374907;ENST00000433736	.|T;T;T	.|0.46819	.|0.86;0.86;0.86	5.4|5.4	3.24|3.24	0.37175|0.37175	.|Integrin alpha-2 (1);	.|0.474754	.|0.22860	.|N	.|0.054758	T|T	0.31606|0.31606	0.0802|0.0802	N|N	0.22421|0.22421	0.69|0.69	0.27546|0.27546	N|N	0.950647|0.950647	.|P;B;P	.|0.35155	.|0.487;0.069;0.487	.|B;B;B	.|0.33392	.|0.104;0.091;0.163	T|T	0.16188|0.16188	-1.0411|-1.0411	5|10	.|0.56958	.|D	.|0.05	.|.	9.6868|9.6868	0.40103|0.40103	0.1986:0.0:0.8014:0.0|0.1986:0.0:0.8014:0.0	.|.	.|867;877;913	.|E7EWZ6;P06756-2;P06756	.|.;.;ITAV_HUMAN	F|F	63|913;877;867	.|ENSP00000261023:V913F;ENSP00000364042:V877F;ENSP00000404291:V867F	.|ENSP00000261023:V913F	L|V	+|+	3|1	2|0	ITGAV|ITGAV	187248606|187248606	0.948000|0.948000	0.32251|0.32251	0.992000|0.992000	0.48379|0.48379	0.921000|0.921000	0.55340|0.55340	1.442000|1.442000	0.35046|0.35046	0.560000|0.560000	0.29169|0.29169	-0.244000|-0.244000	0.11960|0.11960	TTG|GTC	.	.		0.388	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		T	187540361	G	T	187540361	3	4	40	1	0	0	0	0	1	0	0	0	7897	1377	48	3	2894	3	ITGAV	2	187540361	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	866975	187540361	55659012	48	4704										
HECW2	57520	hgsc.bcm.edu	37	chr2	197183465	197183465	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttctgcccctggcccttcatCctccccactgggcacctgta	7	19	2	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:197183465C>G	ENST00000260983.3	-	9	2331	c.2149G>C	c.(2149-2151)Gat>Cat	p.D717H	HECW2_ENST00000409111.1_Missense_Mutation_p.D361H	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	717					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						GGCCCTTCATCCTCCCCACTG	0.657																																					p.D717H		.	.											.	HECW2	.	.	0			c.G2149C						.						30	32	31					2																	197183465		2203	4300	6503	SO:0001583	missense	57520	exon9			CTTCATCCTCCCC	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.2149G>C	2.37:g.197183465C>G	ENSP00000260983:p.Asp717His	163.0	0.0		127.0	9.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.287536	0.40494	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	T;T	0.32023	1.47;1.47	4.91	4.91	0.64330	.	2.075770	0.01897	N	0.038942	T	0.26810	0.0656	N	0.08118	0	0.22479	N	0.999065	B	0.22480	0.07	B	0.23018	0.043	T	0.44832	-0.9302	10	0.51188	T	0.08	.	18.2942	0.90139	0.0:1.0:0.0:0.0	.	717	Q9P2P5	HECW2_HUMAN	H	361;717	ENSP00000386775:D361H;ENSP00000260983:D717H	ENSP00000260983:D717H	D	-	1	0	HECW2	196891710	0.976000	0.34144	0.982000	0.44146	0.982000	0.71751	3.304000	0.51866	2.558000	0.86282	0.462000	0.41574	GAT	.	.		0.657	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		G	197183465	C	G	197183465	3	3	40	1	0	0	0	0	1	0	0	0	7052	855	30	4	2653	4	HECW2	2	197183465	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	9643104	197183465	46015908	49	4705										
BMPR2	659	hgsc.bcm.edu	37	chr2	203420129	203420130	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cacacctttgactataggggINSaaaaaaaccgaaattcaatt							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:203420129_203420130insA	ENST00000374580.4	+	12	2280_2281	c.1741_1742insA	c.(1741-1743)gaafs	p.E581fs	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	581					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						GACTATAGGGGAAAAAAACCGA	0.441																																					p.E581fs		.	.											.	BMPR2	.	.	0			c.1741_1742insA						.																																			SO:0001589	frameshift_variant	659	exon12			.	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.1748dupA	2.37:g.203420136_203420136dupA	ENSP00000363708:p.Glu581fs	178.0	0.0		184.0	12.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Frame_Shift_Ins	INS	ENST00000374580.4	37	CCDS33361.1																																																																																			.	.		0.441	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204		A	203420130	-	A	203420129	7	5	40	1	0	1	1	0	0	0	0	0	1471	1175	41	0	1787	0	BMPR2	2	203420129	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	6236664	203420129	39779244	50	4706										
MFF	56947	hgsc.bcm.edu	37	chr2	228220420	228220420	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atttcaaatatagatacaacCattgaaggaacgtcagatga	7	6	2	4			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr2:228220420C>T	ENST00000353339.3	+	10	1281	c.840C>T	c.(838-840)acC>acT	p.T280T	MFF_ENST00000349901.7_Silent_p.T176T|MFF_ENST00000524634.1_Silent_p.T27T|MFF_ENST00000476924.1_3'UTR|MFF_ENST00000409616.1_Silent_p.T176T|MFF_ENST00000354503.6_Silent_p.T156T|MFF_ENST00000304593.9_Silent_p.T229T|MFF_ENST00000392059.1_Silent_p.T280T|MFF_ENST00000409565.1_Silent_p.T156T|MFF_ENST00000337110.7_Silent_p.T181T	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	280					mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)			breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						TAGATACAACCATTGAAGGAA	0.358																																					p.T280T		.	.											.	MFF	.	.	0			c.C840T						.						157	158	158					2																	228220420		2203	4300	6503	SO:0001819	synonymous_variant	56947	exon10			TACAACCATTGAA	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"chromosome 2 open reading frame 33"	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.840C>T	2.37:g.228220420C>T		350.0	0.0		372.0	127.0	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Silent	SNP	ENST00000353339.3	37	CCDS2465.1																																																																																			.	.		0.358	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194		T	228220420	C	T	228220420	2	4	40	1	0	0	0	0	0	0	0	1	9528	581	21	3		3	MFF	2	228220420	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	24800291	228220420	14978953	51	4707										
CAND2	23066	hgsc.bcm.edu	37	chr3	12854821	12854821	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	acataaaacacgaccccaacTacaactacgacagtgatgag	6	12	0	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:12854821T>G	ENST00000456430.2	+	7	981	c.940T>G	c.(940-942)Tac>Gac	p.Y314D	CAND2_ENST00000295989.5_Missense_Mutation_p.Y221D	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	314					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CGACCCCAACTACAACTACGA	0.537																																					p.Y314D	GBM(43;676 868 1633 6395 37496)	.	.											.	CAND2	.	.	0			c.T940G						.						113	118	116					3																	12854821		2072	4216	6288	SO:0001583	missense	23066	exon7			CCCAACTACAACT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.940T>G	3.37:g.12854821T>G	ENSP00000387641:p.Tyr314Asp	250.0	0.0		171.0	66.0	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	T	15.53	2.862040	0.51482	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.63255	-0.03;-0.03	4.55	4.55	0.56014	Armadillo-type fold (1);	0.000000	0.64402	D	0.000003	D	0.83170	0.5196	H	0.94264	3.515	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.80764	0.963;0.994	D	0.87125	0.2193	10	0.72032	D	0.01	-38.8703	11.8714	0.52523	0.0:0.0:0.0:1.0	.	314;221	O75155;O75155-2	CAND2_HUMAN;.	D	221;314	ENSP00000295989:Y221D;ENSP00000387641:Y314D	ENSP00000295989:Y221D	Y	+	1	0	CAND2	12829821	1.000000	0.71417	0.952000	0.39060	0.133000	0.20885	7.902000	0.87389	1.682000	0.51000	0.379000	0.24179	TAC	.	.		0.537	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		G	12854821	T	G	12854821	3	3	40	1	0	0	0	0	1	0	0	0	2618	1522	53	5	966	5	CAND2	3	12854821	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10		12854821	185167609	52	4708										
ZFYVE20	64145	hgsc.bcm.edu	37	chr3	15126258	15126258	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctacttgccaagggaaggctGatgagctccatacacttctt	9	11	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:15126258G>A	ENST00000253699.3	-	8	1195	c.582C>T	c.(580-582)atC>atT	p.I194I	ZFYVE20_ENST00000435849.3_Silent_p.I194I|ZFYVE20_ENST00000449964.2_5'UTR|ZFYVE20_ENST00000476527.2_Silent_p.I194I	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	194	Necessary for the correct targeting to endosomes.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						AGGGAAGGCTGATGAGCTCCA	0.537																																					p.I194I		.	.											.	ZFYVE20	.	.	0			c.C582T						.						81	87	85					3																	15126258		2203	4300	6503	SO:0001819	synonymous_variant	64145	exon8			AAGGCTGATGAGC	AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"Zinc fingers, FYVE domain containing"	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.582C>T	3.37:g.15126258G>A		142.0	0.0		125.0	66.0	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Silent	SNP	ENST00000253699.3	37	CCDS2623.1																																																																																			.	.		0.537	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		A	15126258	G	A	15126258	2	1	40	1	0	0	0	0	0	0	0	1	17681	1280	45	3		3	ZFYVE20	3	15126258	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	2271437	15126258	182896172	53	4709										
SCAP	22937	hgsc.bcm.edu	37	chr3	47476584	47476584	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cttcacaggggtggtgaattCcacaggtcctgttcctggca	12	11	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:47476584C>A	ENST00000265565.5	-	3	578	c.166G>T	c.(166-168)Gaa>Taa	p.E56*	SCAP_ENST00000441517.2_5'UTR|SCAP_ENST00000545718.1_5'UTR	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	56					aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		GTGGTGAATTCCACAGGTCCT	0.532																																					p.E56X	Pancreas(149;978 1908 29304 37806 46700)	.	.											.	SCAP	.	.	0			c.G166T						.						99	94	96					3																	47476584		2203	4300	6503	SO:0001587	stop_gained	22937	exon3			TGAATTCCACAGG	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.166G>T	3.37:g.47476584C>A	ENSP00000265565:p.Glu56*	167.0	0.0		108.0	25.0	NM_012235	Q8N2E0|Q8WUA1	Nonsense_Mutation	SNP	ENST00000265565.5	37	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	C	34	5.345937	0.95807	.	.	ENSG00000114650	ENST00000339815;ENST00000265565;ENST00000416847;ENST00000495603;ENST00000448217	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-15.2104	18.3633	0.90382	0.0:1.0:0.0:0.0	.	.	.	.	X	56	.	ENSP00000265565:E56X	E	-	1	0	SCAP	47451588	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.281000	0.78621	2.672000	0.90937	0.462000	0.41574	GAA	.	.		0.532	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		A	47476584	C	A	47476584	4	1	40	1	0	0	0	0	0	1	0	0	13892	864	30	3	3757	3	SCAP	3	47476584	Nonsense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	32350326	47476584	150545846	54	4710										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48608550	48608550	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttaccttcacacctggagggCcaggaggcccaggggagccc	14	14	1	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:48608550C>T	ENST00000328333.8	-	93	7255	c.7148G>A	c.(7147-7149)gGc>gAc	p.G2383D	COL7A1_ENST00000454817.1_Missense_Mutation_p.G2351D	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2383	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACCTGGAGGGCCAGGAGGCCC	0.632																																					p.G2383D		.	.											.	COL7A1	.	.	0			c.G7148A						.						33	42	39					3																	48608550		2203	4299	6502	SO:0001583	missense	1294	exon93			GGAGGGCCAGGAG	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.7148G>A	3.37:g.48608550C>T	ENSP00000332371:p.Gly2383Asp	125.0	0.0		99.0	25.0	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	9.446	1.089401	0.20390	.	.	ENSG00000114270	ENST00000328333;ENST00000454817;ENST00000422991	D;D;D	0.99353	-5.77;-5.77;-5.14	4.91	3.99	0.46301	.	0.000000	0.46442	D	0.000297	D	0.99588	0.9851	H	0.97214	3.96	0.41532	D	0.988466	D	0.89917	1.0	D	0.83275	0.996	D	0.97707	1.0188	10	0.72032	D	0.01	.	12.3656	0.55226	0.167:0.833:0.0:0.0	.	2383	Q02388	CO7A1_HUMAN	D	2383;2351;48	ENSP00000332371:G2383D;ENSP00000412569:G2351D;ENSP00000391608:G48D	ENSP00000332371:G2383D	G	-	2	0	COL7A1	48583554	1.000000	0.71417	0.997000	0.53966	0.213000	0.24496	2.719000	0.47244	2.439000	0.82584	0.655000	0.94253	GGC	.	.		0.632	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		T	48608550	C	T	48608550	3	4	40	1	0	0	0	0	1	0	0	0	3706	739	26	3	1790	3	COL7A1	3	48608550	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1131966	48608550	149413880	55	4711										
EBLN2	55096	hgsc.bcm.edu	37	chr3	73111508	73111509	+	Frame_Shift_Ins	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atccactggatgcattggaaINSccccaacccagcattgggga							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:73111508_73111509insC	ENST00000533473.1	+	1	699_700	c.276_277insC	c.(277-279)cccfs	p.P93fs	PPP4R2_ENST00000394284.3_Intron|PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000356692.5_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	93										endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						ATGCATTGGAACCCCAACCCAG	0.48																																					p.E92fs		.	.											.	.	.	.	0			c.276_277insC						.																																			SO:0001589	frameshift_variant	55096	exon1			.		CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"endogenous Borna-like N element 2"	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.280dupC	3.37:g.73111512_73111512dupC	ENSP00000432104:p.Pro93fs	151.0	0.0		148.0	10.0	NM_018029	Q8WWH3|Q9NW89	Frame_Shift_Ins	INS	ENST00000533473.1	37	CCDS54608.1																																																																																			.	.		0.48	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029		C	73111509	-	C	73111508	7	5	40	1	0	1	1	0	0	0	0	0	4886	40	2	0	278	0	EBLN2	3	73111508	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	24502958	73111508	124910922	56	4712										
EBLN2	55096	hgsc.bcm.edu	37	chr3	73111541	73111542	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttggggatattaaggacattINSaaaaaagcagccaagtctat							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:73111541_73111542insA	ENST00000533473.1	+	1	732_733	c.309_310insA	c.(310-312)aaafs	p.K104fs	PPP4R2_ENST00000394284.3_Intron|PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000356692.5_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	104										endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						TTAAGGACATTAAAAAAGCAGC	0.426																																					p.I103fs		.	.											.	.	.	.	0			c.309_310insA						.																																			SO:0001589	frameshift_variant	55096	exon1			.		CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"endogenous Borna-like N element 2"	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.315dupA	3.37:g.73111547_73111547dupA	ENSP00000432104:p.Lys104fs	231.0	0.0		195.0	13.0	NM_018029	Q8WWH3|Q9NW89	Frame_Shift_Ins	INS	ENST00000533473.1	37	CCDS54608.1																																																																																			.	.		0.426	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029		A	73111542	-	A	73111541	7	5	40	1	0	1	1	0	0	0	0	0	4886	1742	61	0	311	0	EBLN2	3	73111541	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	33	73111541	124910889	57	4713										
FILIP1L	11259	hgsc.bcm.edu	37	chr3	99568989	99568990	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttatcttcagttttctttaaINStttttcactcattgttttcc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:99568989_99568990insT	ENST00000354552.3	-	5	2000_2001	c.1530_1531insA	c.(1528-1533)aaattafs	p.L511fs	FILIP1L_ENST00000383694.2_Frame_Shift_Ins_p.L271fs|FILIP1L_ENST00000471562.1_Frame_Shift_Ins_p.L271fs|FILIP1L_ENST00000476723.1_Intron|CMSS1_ENST00000496116.1_Intron|CMSS1_ENST00000421999.2_Intron|FILIP1L_ENST00000331335.5_Frame_Shift_Ins_p.L511fs|FILIP1L_ENST00000487087.1_Frame_Shift_Ins_p.L87fs	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	511						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						GTTTTCTTTAATTTTTCACTCA	0.322																																					p.L511fs		.	.											.	FILIP1L	.	.	0			c.1531_1532insA						.																																			SO:0001589	frameshift_variant	11259	exon5			.		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"downregulated in ovarian cancer 1", "GPBP-interacting protein of 130 kDa"	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.1531dupA	3.37:g.99568994_99568994dupT	ENSP00000346560:p.Leu511fs	276.0	0.0		232.0	15.0	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Frame_Shift_Ins	INS	ENST00000354552.3	37	CCDS43117.1																																																																																			.	.		0.322	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890		T	99568990	-	T	99568989	7	5	40	1	0	1	1	0	0	0	0	0	5903	98	4	0	1905	0	FILIP1L	3	99568989	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	26457448	99568989	98453441	58	4714										
CCDC37	348807	hgsc.bcm.edu	37	chr3	126142435	126142435	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tccagaacagccaggagacgGagaagaccctggaggagctg	15	10	0	4	rs140223152|rs398102320|rs35657615|rs200815085	byFrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:126142435G>A	ENST00000352312.1	+	13	1333	c.1234G>A	c.(1234-1236)Gag>Aag	p.E412K	CCDC37_ENST00000505024.1_Missense_Mutation_p.E413K|CCDC37_ENST00000393425.1_Missense_Mutation_p.E413K	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	412				Missing (in Ref. 3; AAI01370/AAI01368). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		CCAGGAGACGGAGAAGACCCT	0.612													G|||	1	0.000199681	0	0.0014	5008	,	,		17029	0		0	False		,,,				2504	0				p.E412K		.	.											.	CCDC37	.	.	0			c.G1234A						.						109	83	92					3																	126142435		2200	4257	6457	SO:0001583	missense	348807	exon13			GAGACGGAGAAGA	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1234G>A	3.37:g.126142435G>A	ENSP00000344749:p.Glu412Lys	0.0	0.0		9.0	8.0	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Missense_Mutation	SNP	ENST00000352312.1	37	CCDS3037.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.295376	0.81025	.	.	ENSG00000163885	ENST00000352312;ENST00000393425;ENST00000505024	T;T;T	0.41400	1.0;1.0;1.0	4.93	4.93	0.64822	.	0.159668	0.53938	D	0.000054	T	0.66015	0.2747	M	0.83384	2.64	0.58432	D	0.999999	D;D	0.69078	0.997;0.996	D;P	0.66716	0.946;0.884	T	0.71137	-0.4680	10	0.56958	D	0.05	-35.5644	15.657	0.77144	0.0:0.0:1.0:0.0	.	413;412	Q494V2-2;Q494V2	.;CCD37_HUMAN	K	412;413;413	ENSP00000344749:E412K;ENSP00000377076:E413K;ENSP00000423046:E413K	ENSP00000344749:E412K	E	+	1	0	CCDC37	127625125	1.000000	0.71417	1.000000	0.80357	0.523000	0.34469	6.860000	0.75473	2.284000	0.76573	0.491000	0.48974	GAG	.	.		0.612	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		A	126142435	G	A	126142435	3	1	40	1	0	0	0	0	1	0	0	0	2811	1175	41	3	1280	3	CCDC37	3	126142435	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	26573446	126142435	71879995	59	4715										
SOX14	8403	hgsc.bcm.edu	37	chr3	137483875	137483875	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	taccgacctcggcgcaagccCaagaacctgctcaagaagga	10	14	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:137483875C>G	ENST00000306087.1	+	1	297	c.249C>G	c.(247-249)ccC>ccG	p.P83P		NM_004189.3	NP_004180.1	O95416	SOX14_HUMAN	SRY (sex determining region Y)-box 14	83					entrainment of circadian clock (GO:0009649)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|regulation of neuron migration (GO:2001222)|visual perception (GO:0007601)	nuclear transcription factor complex (GO:0044798)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			large_intestine(2)|lung(12)	14						GGCGCAAGCCCAAGAACCTGC	0.642																																					p.P83P		.	.											.	SOX14	.	.	0			c.C249G						.						140	151	148					3																	137483875		2203	4300	6503	SO:0001819	synonymous_variant	8403	exon1			CAAGCCCAAGAAC	AJ006230	CCDS3094.1	3q22-q23	2008-07-18			ENSG00000168875	ENSG00000168875		"SRY (sex determining region Y)-boxes"	11193	protein-coding gene	gene with protein product	"HMG box transcription factor SOX-14", "SRY-box 14"	604747				9925951	Standard	NM_004189		Approved	SOX28	uc003erm.2	O95416	OTTHUMG00000159757	ENST00000306087.1:c.249C>G	3.37:g.137483875C>G		159.0	0.0		131.0	9.0	NM_004189	B2RAC0|Q3KPH7	Silent	SNP	ENST00000306087.1	37	CCDS3094.1																																																																																			.	.		0.642	SOX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357182.1	NM_004189		G	137483875	C	G	137483875	2	3	40	1	0	0	0	0	0	0	0	1	14960	581	21	4		4	SOX14	3	137483875	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	11341440	137483875	60538555	60	4716										
PLCH1	23007	hgsc.bcm.edu	37	chr3	155200477	155200478	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gacgcttcctgacaagatgcINSttttcccttccacaaagtcc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:155200477_155200478insT	ENST00000340059.7	-	23	3360_3361	c.3361_3362insA	c.(3361-3363)agcfs	p.S1121fs	PLCH1_ENST00000414191.1_Frame_Shift_Ins_p.S1083fs|PLCH1_ENST00000334686.6_Frame_Shift_Ins_p.S1083fs|PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000460012.1_Frame_Shift_Ins_p.S1083fs	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1121					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TGACAAGATGCTTTTCCCTTCC	0.46																																					p.S1121fs		.	.											.	PLCH1	.	.	0			c.3362_3363insA						.																																			SO:0001589	frameshift_variant	23007	exon23			.	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.3362dupA	3.37:g.155200481_155200481dupT	ENSP00000345988:p.Ser1121fs	210.0	0.0		183.0	11.0	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Frame_Shift_Ins	INS	ENST00000340059.7	37	CCDS46939.1																																																																																			.	.		0.46	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		T	155200478	-	T	155200477	7	5	40	1	0	1	1	0	0	0	0	0	12046	797	28	0	1723	0	PLCH1	3	155200477	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	17716602	155200477	42821953	61	4717										
SHOX2	6474	hgsc.bcm.edu	37	chr3	157823590	157823590	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctcctcctcctacacctcctCcgcctcctccgccgccgcct	4	26	0	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:157823590C>A	ENST00000425436.3	-	1	249	c.224G>T	c.(223-225)gGa>gTa	p.G75V	SHOX2_ENST00000554685.1_5'UTR|SHOX2_ENST00000389589.4_Missense_Mutation_p.G75V|SHOX2_ENST00000441443.2_5'UTR|RSRC1_ENST00000480820.1_5'Flank|SHOX2_ENST00000490689.2_5'Flank|SHOX2_ENST00000483851.2_Missense_Mutation_p.G75V	NM_001163678.1|NM_006884.3	NP_001157150.1|NP_006875.2	O60902	SHOX2_HUMAN	short stature homeobox 2	75	Poly-Gly.				cardiac atrium morphogenesis (GO:0003209)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte development (GO:0002063)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|heart development (GO:0007507)|heart valve development (GO:0003170)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of axonogenesis (GO:0050772)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of chondrocyte differentiation (GO:0032330)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(10)|skin(3)|upper_aerodigestive_tract(1)	20			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)			tacacctcctccgcctcctcc	0.781																																					p.G75V		.	.											.	SHOX2	.	.	0			c.G224T						.						4	7	6					3																	157823590		1502	3313	4815	SO:0001583	missense	6474	exon1			CCTCCTCCGCCTC	AJ002368	CCDS33884.1, CCDS43164.1, CCDS33884.2, CCDS54664.1	3q25.32	2011-06-20			ENSG00000168779	ENSG00000168779		"Homeoboxes / PRD class"	10854	protein-coding gene	gene with protein product		602504				9482898, 9466998	Standard	NM_006884		Approved	SHOT, OG12X, OG12	uc003fbs.3	O60902	OTTHUMG00000158755	ENST00000425436.3:c.224G>T	3.37:g.157823590C>A	ENSP00000398704:p.Gly75Val	21.0	0.0		19.0	13.0	NM_003030	O60465|O60467|O60903	Missense_Mutation	SNP	ENST00000425436.3	37	CCDS43164.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.291661	0.23564	.	.	ENSG00000168779;ENSG00000168779;ENSG00000258518	ENST00000425436;ENST00000389589;ENST00000483851	D;D;D	0.95622	-3.76;-3.76;-3.76	2.23	1.32	0.21799	.	0.241563	0.26601	N	0.023468	D	0.93239	0.7846	N	0.14661	0.345	0.80722	D	1	B;D;D	0.89917	0.186;1.0;0.999	B;D;D	0.87578	0.033;0.998;0.972	D	0.89183	0.3545	10	0.29301	T	0.29	.	8.0787	0.30731	0.0:0.4998:0.5002:0.0	.	75;75;75	O60902-2;O60902-3;O60902	.;.;SHOX2_HUMAN	V	75	ENSP00000398704:G75V;ENSP00000374240:G75V;ENSP00000419362:G75V	ENSP00000374240:G75V	G	-	2	0	SHOX2;AC112502.1	159306284	0.595000	0.26857	1.000000	0.80357	0.995000	0.86356	-0.336000	0.07863	0.475000	0.27415	0.462000	0.41574	GGA	.	.		0.781	SHOX2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352057.2			A	157823590	C	A	157823590	3	1	40	1	0	0	0	0	1	0	0	0	14304	855	30	3	867	3	SHOX2	3	157823590	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	2623113	157823590	40198840	62	4718										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173998709	173998709	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aacatcttggcctttgcagcCctgtactacaaaaaggataa	7	10	1	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:173998709C>T	ENST00000457714.1	+	7	2517	c.2088C>T	c.(2086-2088)gcC>gcT	p.A696A	NLGN1_ENST00000401917.3_Silent_p.A736A|NLGN1_ENST00000545397.1_Silent_p.A696A|NLGN1_ENST00000361589.4_Silent_p.A696A	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	713					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			CCTTTGCAGCCCTGTACTACA	0.463																																					p.A696A		.	.											.	NLGN1	.	.	0			c.C2088T						.						89	89	89					3																	173998709		2203	4300	6503	SO:0001819	synonymous_variant	22871	exon7			TGCAGCCCTGTAC	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.2088C>T	3.37:g.173998709C>T		142.0	0.0		121.0	56.0	NM_014932	Q9UPT2	Silent	SNP	ENST00000457714.1	37	CCDS3222.1																																																																																			.	.		0.463	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		T	173998709	C	T	173998709	2	4	40	1	0	0	0	0	0	0	0	1	10470	610	22	3		3	NLGN1	3	173998709	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	16175119	173998709	24023721	63	4719										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atcctctctctgaaatcactGagcaggagaaagattttcta	7	9	4	4	rs104886003		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E545K	Colon(199;1504 1750 3362 26421 31210 32040)	.	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA,bladder,carcinoma,0	PIK3CA	.	.	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)	c.G1633A						.						61	60	60					3																	178936091		1813	4072	5885	SO:0001583	missense	5290	exon10			ATCACTGAGCAGG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	3.37:g.178936091G>A	ENSP00000263967:p.Glu545Lys	497.0	1.0		460.0	90.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG	.	.		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178936091	G	A	178936091	3	1	40	1	0	0	0	0	1	0	0	0	11922	1291	45	3	1667	3	PIK3CA	3	178936091	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	4937382	178936091	19086339	64	4720										
DGKG	1608	hgsc.bcm.edu	37	chr3	185969660	185969660	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggtccagcatcaccaaggggCtctgctcaatgtctttcagg	11	12	5	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr3:185969660C>T	ENST00000265022.3	-	19	2188	c.1649G>A	c.(1648-1650)aGc>aAc	p.S550N	DGKG_ENST00000382164.4_Missense_Mutation_p.S511N|DGKG_ENST00000544847.1_Missense_Mutation_p.S491N|DGKG_ENST00000344484.4_Missense_Mutation_p.S525N	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	550	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	CACCAAGGGGCTCTGCTCAAT	0.512																																					p.S550N		.	.											.	DGKG	.	.	0			c.G1649A						.						157	150	152					3																	185969660		2203	4300	6503	SO:0001583	missense	1608	exon19			AAGGGGCTCTGCT	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.1649G>A	3.37:g.185969660C>T	ENSP00000265022:p.Ser550Asn	220.0	0.0		145.0	28.0	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	37	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305227	0.81247	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.06	5.06	0.68205	Diacylglycerol kinase, catalytic domain (3);	0.000000	0.85682	D	0.000000	T	0.63236	0.2494	M	0.75615	2.305	0.58432	D	0.999999	D;D;D;D	0.89917	0.998;0.998;1.0;0.999	D;D;D;D	0.76575	0.988;0.988;0.976;0.986	T	0.66432	-0.5925	10	0.87932	D	0	.	13.1306	0.59380	0.0:0.8388:0.1612:0.0	.	491;525;511;550	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	N	550;525;511;491;514	ENSP00000265022:S550N;ENSP00000339777:S525N;ENSP00000371599:S511N;ENSP00000440507:S491N	ENSP00000265022:S550N	S	-	2	0	DGKG	187452354	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.579000	0.82511	2.645000	0.89757	0.467000	0.42956	AGC	.	.		0.512	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			T	185969660	C	T	185969660	3	4	40	1	0	0	0	0	1	0	0	0	4471	797	28	3	754	3	DGKG	3	185969660	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	7033569	185969660	12052770	65	4721										
ZBTB49	166793	hgsc.bcm.edu	37	chr4	4303971	4303971	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgtaatagtacattgtctctAcaaagcaccctgaccccaga	6	12	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr4:4303971A>G	ENST00000337872.4	+	3	529	c.408A>G	c.(406-408)ctA>ctG	p.L136L	ZBTB49_ENST00000538529.1_5'UTR|ZBTB49_ENST00000355834.3_Silent_p.L136L	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	28						CATTGTCTCTACAAAGCACCC	0.438																																					p.L136L		.	.											.	ZBTB49	.	.	0			c.A408G						.						129	122	125					4																	4303971		2203	4300	6503	SO:0001819	synonymous_variant	166793	exon3			GTCTCTACAAAGC	AK095878	CCDS3375.1	4p16.2	2013-01-08	2010-01-26	2010-01-26	ENSG00000168826	ENSG00000168826		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	19883	protein-coding gene	gene with protein product			"zinc finger protein 509"	ZNF509		12477932	Standard	NM_145291		Approved	FLJ38559	uc003ghu.3	Q6ZSB9	OTTHUMG00000090325	ENST00000337872.4:c.408A>G	4.37:g.4303971A>G		114.0	0.0		98.0	48.0	NM_145291	Q59FJ4|Q5EBN0|Q8TB80	Silent	SNP	ENST00000337872.4	37	CCDS3375.1																																																																																			.	.		0.438	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291		G	4303971	A	G	4303971	2	3	40	1	0	0	0	0	0	0	0	1	17565	378	14	2		2	ZBTB49	4	4303971	Silent	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10		4303971	186850305	66	4722										
DRD5	1816	hgsc.bcm.edu	37	chr4	9784569	9784569	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cggtgatcatgggggtcttcGtgtgttgctggctgcccttc	15	10	2	1	rs572964780		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr4:9784569G>A	ENST00000304374.2	+	1	1312	c.916G>A	c.(916-918)Gtg>Atg	p.V306M		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	306					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	GGGGGTCTTCGTGTGTTGCTG	0.627																																					p.V306M		.	.											.	DRD5	.	.	0			c.G916A						.						62	60	61					4																	9784569		2203	4299	6502	SO:0001583	missense	1816	exon1			GTCTTCGTGTGTT	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"GPCR / Class A : Dopamine receptors"	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.916G>A	4.37:g.9784569G>A	ENSP00000306129:p.Val306Met	66.0	0.0		49.0	8.0	NM_000798	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	g	21.4	4.141049	0.77775	.	.	ENSG00000169676	ENST00000304374	T	0.74526	-0.85	4.73	4.73	0.59995	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.87120	0.6098	M	0.83118	2.625	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.89208	0.3562	10	0.87932	D	0	.	16.9019	0.86116	0.0:0.0:1.0:0.0	.	306	P21918	DRD5_HUMAN	M	306	ENSP00000306129:V306M	ENSP00000306129:V306M	V	+	1	0	DRD5	9393667	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.202000	0.95026	2.457000	0.83068	0.460000	0.39030	GTG	.	.		0.627	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			A	9784569	G	A	9784569	3	1	40	1	0	0	0	0	1	0	0	0	4762	1145	40	1	918	1	DRD5	4	9784569	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	5480598	9784569	181369707	67	4723										
GUF1	60558	hgsc.bcm.edu	37	chr4	44692732	44692732	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgctgatttttctaatttttAggaacatagagaaaaagaaa	7	3	1	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr4:44692732A>T	ENST00000281543.5	+	12	1529		c.e12-1		GUF1_ENST00000506793.1_Splice_Site	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						TCTAATTTTTAGGAACATAGA	0.279																																					.		.	.											.	GUF1	.	.	0			c.1336-2A>T						.						30	31	31					4																	44692732		2197	4291	6488	SO:0001630	splice_region_variant	60558	exon12			ATTTTTAGGAACA		CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.1336-1A>T	4.37:g.44692732A>T		248.0	0.0		239.0	104.0	NM_021927		Splice_Site	SNP	ENST00000281543.5	37	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	A	19.22	3.785991	0.70337	.	.	ENSG00000151806	ENST00000281543	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0983	0.72253	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GUF1	44387489	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	8.854000	0.92228	2.216000	0.71823	0.533000	0.62120	.	.	.		0.279	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927	Intron	T	44692732	A	T	44692732	5	4	40	1	0	0	0	0	0	0	1	0	6908	434	15	4	1380	4	GUF1	4	44692732	Splice_Site	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	34908163	44692732	146461544	68	4724										
KDR	3791	hgsc.bcm.edu	37	chr4	55976873	55976873	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cttcgcagggattctgacacGctcccccaccgtggcttcca	9	17	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr4:55976873G>A	ENST00000263923.4	-	8	1334	c.1039C>T	c.(1039-1041)Cgt>Tgt	p.R347C		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	347	Ig-like C2-type 4.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATTCTGACACGCTCCCCCACC	0.418			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.R347C		.	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	.	.	0			c.C1039T						.						75	83	81					4																	55976873		2203	4300	6503	SO:0001583	missense	3791	exon8			TGACACGCTCCCC	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.1039C>T	4.37:g.55976873G>A	ENSP00000263923:p.Arg347Cys	333.0	0.0		267.0	116.0	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	G	12.52	1.962291	0.34659	.	.	ENSG00000128052	ENST00000263923	T	0.68181	-0.31	5.65	3.92	0.45320	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.765736	0.13043	N	0.418394	T	0.65801	0.2726	M	0.83483	2.645	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.06405	0.002;0.002	T	0.60732	-0.7205	10	0.54805	T	0.06	.	5.0904	0.14706	0.0715:0.1265:0.5409:0.261	.	347;347	P35968-2;P35968	.;VGFR2_HUMAN	C	347	ENSP00000263923:R347C	ENSP00000263923:R347C	R	-	1	0	KDR	55671630	0.004000	0.15560	0.001000	0.08648	0.968000	0.65278	1.439000	0.35013	0.732000	0.32470	0.563000	0.77884	CGT	.	.		0.418	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55976873	G	A	55976873	3	1	40	1	0	0	0	0	1	0	0	0	8148	1087	38	1	3123	1	KDR	4	55976873	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	11284141	55976873	135177403	69	4725										
ADH1A	124	hgsc.bcm.edu	37	chr4	100205756	100205757	+	Frame_Shift_Ins	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctggtgccatcctgcagggtINScccctgaggattgcttacac							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr4:100205756_100205757insC	ENST00000209668.2	-	5	479_480	c.366_367insG	c.(364-369)gggaccfs	p.T123fs	RP11-696N14.1_ENST00000500358.2_RNA|ADH1A_ENST00000511656.1_5'Flank	NM_000667.3	NP_000658.1	P07327	ADH1A_HUMAN	alcohol dehydrogenase 1A (class I), alpha polypeptide	123					alcohol metabolic process (GO:0006066)|drug metabolic process (GO:0017144)|ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)	25				OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Ethanol(DB00898)|Fomepizole(DB01213)	TCCTGCAGGGTCCCCTGAGGAT	0.515																																					p.T123fs		.	.											.	ADH1A	.	.	0			c.367_368insG						.																																			SO:0001589	frameshift_variant	124	exon5			.	M12963	CCDS3648.1	4q23	2009-12-04			ENSG00000187758	ENSG00000187758	1.1.1.1	"Alcohol dehydrogenases"	249	protein-coding gene	gene with protein product		103700		ADH1		3006456	Standard	NM_000667		Approved		uc003hur.2	P07327	OTTHUMG00000131026	ENST00000209668.2:c.367dupG	4.37:g.100205760_100205760dupC	ENSP00000209668:p.Thr123fs	210.0	0.0		181.0	11.0	NM_000667	A8K3E3|Q17R68	Frame_Shift_Ins	INS	ENST00000209668.2	37	CCDS3648.1																																																																																			.	.		0.515	ADH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253669.1	NM_000667		C	100205757	-	C	100205756	7	5	40	1	0	1	1	0	0	0	0	0	307	1667	58	0	780	0	ADH1A	4	100205756	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	44228883	100205756	90948520	70	4726										
LARP7	51574	hgsc.bcm.edu	37	chr4	113568542	113568542	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgctcaaagaaaaagaaaaaAcgggacagagttgaagcatc	10	6	1	4			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr4:113568542A>T	ENST00000344442.5	+	7	1112	c.834A>T	c.(832-834)aaA>aaT	p.K278N	MIR302C_ENST00000362232.1_RNA|MIR302B_ENST00000362188.1_RNA|LARP7_ENST00000324052.6_Missense_Mutation_p.K278N|LARP7_ENST00000509061.1_Missense_Mutation_p.K285N|MIR302D_ENST00000362275.1_RNA|MIR302B_ENST00000509938.1_RNA|MIR302B_ENST00000505215.1_RNA|MIR302A_ENST00000385192.1_RNA|MIR302B_ENST00000510655.1_RNA|MIR367_ENST00000362299.1_RNA	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	278	Lys-rich.				RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		AAAAGAAAAAACGGGACAGAG	0.463																																					p.K285N		.	.											.	LARP7	.	.	0			c.A855T						.						102	101	101					4																	113568542		1854	4106	5960	SO:0001583	missense	51574	exon9			GAAAAAACGGGAC	AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	24912	protein-coding gene	gene with protein product	"P-TEFb-interaction protein for 7SK stability"	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.834A>T	4.37:g.113568542A>T	ENSP00000344950:p.Lys278Asn	273.0	0.0		248.0	121.0	NM_001267039	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Missense_Mutation	SNP	ENST00000344442.5	37	CCDS3701.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.18|14.18	2.457685|2.457685	0.43634|0.43634	.|.	.|.	ENSG00000174720|ENSG00000174720	ENST00000344442;ENST00000509061;ENST00000505034;ENST00000324052|ENST00000511529	T;T;T;T|.	0.41400|.	1.0;1.0;2.14;1.0|.	5.86|5.86	-5.36|-5.36	0.02689|0.02689	.|.	0.142951|.	0.64402|.	N|.	0.000011|.	T|T	0.51770|0.51770	0.1694|0.1694	M|M	0.76002|0.76002	2.32|2.32	0.20307|0.20307	N|N	0.999914|0.999914	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.87578|.	0.994;0.998|.	T|T	0.54918|0.54918	-0.8221|-0.8221	10|5	0.35671|.	T|.	0.21|.	-25.4983|-25.4983	10.7858|10.7858	0.46405|0.46405	0.4306:0.0:0.4769:0.0926|0.4306:0.0:0.4769:0.0926	.|.	278;278|.	D6RFF0;Q4G0J3|.	.;LARP7_HUMAN|.	N|I	278;285;278;278|59	ENSP00000344950:K278N;ENSP00000422626:K285N;ENSP00000421541:K278N;ENSP00000314311:K278N|.	ENSP00000314311:K278N|.	K|N	+|+	3|2	2|0	LARP7|LARP7	113787991|113787991	0.045000|0.045000	0.20229|0.20229	0.042000|0.042000	0.18584|0.18584	0.155000|0.155000	0.21991|0.21991	0.331000|0.331000	0.19733|0.19733	-1.441000|-1.441000	0.01958|0.01958	-1.450000|-1.450000	0.01041|0.01041	AAA|AAC	.	.		0.463	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648		T	113568542	A	T	113568542	3	4	40	1	0	0	0	0	1	0	0	0	8642	40	2	4	856	4	LARP7	4	113568542	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	13362786	113568542	77585734	71	4727										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155157446	155157447	+	Frame_Shift_Del	DEL	AG	AG	-													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcatttatagagcatatggtAgaggaaataggcagattttc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr4:155157446_155157447delAG	ENST00000357232.4	-	25	6991_6992	c.6992_6993delCT	c.(6991-6993)tctfs	p.S2331fs		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2331	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AGCATATGGTAGAGGAAATAGG	0.411																																					p.2331_2332del		.	.											.	DCHS2	.	.	0			c.6993_6994del						.																																			SO:0001589	frameshift_variant	54798	exon25			.	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6992_6993delCT	4.37:g.155157448_155157449delAG	ENSP00000349768:p.Ser2331fs	191.0	0.0		225.0	74.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Frame_Shift_Del	DEL	ENST00000357232.4	37	CCDS3785.1																																																																																			.	.		0.411	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		-	155157447	AG	-	155157446	7	5	40	1	0	1	0	1	0	0	0	0	4290	407	15	0	1761	0	DCHS2	4	155157446	Frame_Shift_Del	DEL	AG	TCGA-BC-A112-01A-11D-A12Z-10	41588904	155157446	35996830	72	4728										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13727745	13727745	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttatcaaaccaaattttccaCattttctcatttctcgatat	1	10	3	0	rs377633103		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:13727745C>T	ENST00000265104.4	-	70	12008	c.11904G>A	c.(11902-11904)atG>atA	p.M3968I		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3968					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AAATTTTCCACATTTTCTCAT	0.373									Kartagener syndrome																												p.M3968I		.	.											.	DNAH5	.	.	0			c.G11904A						.	C	ILE/MET	0,4406		0,0,2203	95	96	96		11904	4.6	1	5		96	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH5	NM_001369.2	10	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	3968/4625	13727745	1,13005	2203	4300	6503	SO:0001583	missense	1767	exon70	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TTTCCACATTTTC	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.11904G>A	5.37:g.13727745C>T	ENSP00000265104:p.Met3968Ile	320.0	0.0		354.0	119.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.262348	0.39995	0.0	1.16E-4	ENSG00000039139	ENST00000265104	T	0.08193	3.12	5.49	4.62	0.57501	Dynein heavy chain (1);	0.558290	0.20333	N	0.094397	T	0.04724	0.0128	N	0.04880	-0.145	0.33289	D	0.563269	B	0.06786	0.001	B	0.16722	0.016	T	0.14504	-1.0470	10	0.38643	T	0.18	.	10.3593	0.43982	0.0:0.8504:0.0:0.1496	.	3968	Q8TE73	DYH5_HUMAN	I	3968	ENSP00000265104:M3968I	ENSP00000265104:M3968I	M	-	3	0	DNAH5	13780745	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.671000	0.25172	1.320000	0.45209	0.650000	0.86243	ATG	.	.		0.373	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13727745	C	T	13727745	3	4	40	1	0	0	0	0	1	0	0	0	4606	478	17	3	2010	3	DNAH5	5	13727745	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10		13727745	167187515	73	4729										
MYO10	4651	hgsc.bcm.edu	37	chr5	16701663	16701663	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	acacactcgtcgatctcgtcGaaattgagggactcgaggaa	11	10	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:16701663G>A	ENST00000513610.1	-	25	3295	c.2841C>T	c.(2839-2841)ttC>ttT	p.F947F	MYO10_ENST00000505695.1_Silent_p.F286F|MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000515803.1_Silent_p.F286F|MYO10_ENST00000427430.2_Silent_p.F304F|MYO10_ENST00000274203.9_Silent_p.F304F	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	947					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.F947F(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CGATCTCGTCGAAATTGAGGG	0.632																																					p.F947F		.	.											.	MYO10	.	.	1	Substitution - coding silent(1)	kidney(1)	c.C2841T						.						38	44	42					5																	16701663		2150	4273	6423	SO:0001819	synonymous_variant	4651	exon25			CTCGTCGAAATTG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2841C>T	5.37:g.16701663G>A		114.0	0.0		83.0	33.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			.	.		0.632	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16701663	G	A	16701663	2	1	40	1	0	0	0	0	0	0	0	1	10071	1049	37	1		1	MYO10	5	16701663	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	2973918	16701663	164213597	74	4730										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32058103	32058104	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccccgaacttcaataccagtINSgggggagcctcagcgggagg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:32058103_32058104insG	ENST00000438447.1	+	12	2482_2483	c.2094_2095insG	c.(2095-2097)gggfs	p.G699fs	PDZD2_ENST00000282493.3_Frame_Shift_Ins_p.G699fs			O15018	PDZD2_HUMAN	PDZ domain containing 2	699					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						TCAATACCAGTGGGGGAGCCTC	0.569																																					p.S698fs		.	.											.	PDZD2	.	.	0			c.2094_2095insG						.																																			SO:0001589	frameshift_variant	23037	exon11			.	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.2099dupG	5.37:g.32058108_32058108dupG	ENSP00000402033:p.Gly699fs	223.0	0.0		201.0	13.0	NM_178140	Q9BXD4	Frame_Shift_Ins	INS	ENST00000438447.1	37	CCDS34137.1																																																																																			.	.		0.569	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			G	32058104	-	G	32058103	7	5	40	1	0	1	1	0	0	0	0	0	11710	1693	59	0	2136	0	PDZD2	5	32058103	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	15356440	32058103	148857157	75	4731										
RXFP3	51289	hgsc.bcm.edu	37	chr5	33937720	33937720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gtgctacctgctgctggtgcGcttcatcgccgaccgccgcg	13	16	1	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:33937720G>A	ENST00000330120.3	+	1	1230	c.875G>A	c.(874-876)cGc>cAc	p.R292H		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	292					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)			endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						CTGCTGGTGCGCTTCATCGCC	0.682																																					p.R292H		.	.											.	RXFP3	.	.	0			c.G875A						.						36	27	30					5																	33937720		2190	4274	6464	SO:0001583	missense	51289	exon1			TGGTGCGCTTCAT	D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"GPCR / Class A : Relaxin family peptide receptors"	24883	protein-coding gene	gene with protein product		609445	"relaxin 3 receptor 1", "relaxin family peptide receptor 3"	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.875G>A	5.37:g.33937720G>A	ENSP00000328708:p.Arg292His	117.0	0.0		151.0	67.0	NM_016568	Q14DA5	Missense_Mutation	SNP	ENST00000330120.3	37	CCDS3900.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360728	0.95877	.	.	ENSG00000182631	ENST00000330120	T	0.39592	1.07	5.74	5.74	0.90152	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.72078	0.3416	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.76152	-0.3064	10	0.62326	D	0.03	-36.9412	19.9295	0.97114	0.0:0.0:1.0:0.0	.	292	Q9NSD7	RL3R1_HUMAN	H	292	ENSP00000328708:R292H	ENSP00000328708:R292H	R	+	2	0	RXFP3	33973477	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.801000	0.99128	2.695000	0.91970	0.655000	0.94253	CGC	.	.		0.682	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568		A	33937720	G	A	33937720	3	1	40	1	0	0	0	0	1	0	0	0	13776	1087	38	1	877	1	RXFP3	5	33937720	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	1879617	33937720	146977540	76	4732										
SPEF2	79925	hgsc.bcm.edu	37	chr5	35807028	35807028	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccaatagatttgccagccacCtaaagatagagaacatttat	6	9	0	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:35807028C>A	ENST00000356031.3	+	35	5384	c.5230C>A	c.(5230-5232)Cta>Ata	p.L1744I	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000440995.2_Missense_Mutation_p.L1739I|SPEF2_ENST00000303129.4_Missense_Mutation_p.L541I	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1744					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGCCAGCCACCTAAAGATAGA	0.363																																					p.L1744I		.	.											.	SPEF2	.	.	0			c.C5230A						.						64	61	62					5																	35807028		1845	4079	5924	SO:0001583	missense	79925	exon35			AGCCACCTAAAGA	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.5230C>A	5.37:g.35807028C>A	ENSP00000348314:p.Leu1744Ile	369.0	0.0		325.0	119.0	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	.	.	.	.	.	.	.	.	.	.	C	4.718	0.133489	0.09032	.	.	ENSG00000152582	ENST00000356031;ENST00000440995;ENST00000303129	T;T;T	0.46819	3.32;3.31;0.86	5.85	3.95	0.45737	HAT dimerisation (1);	0.302945	0.23043	N	0.052584	T	0.31606	0.0802	L	0.51422	1.61	0.09310	N	1	P;B;B	0.43352	0.804;0.176;0.211	B;B;B	0.28465	0.09;0.054;0.09	T	0.27971	-1.0058	10	0.36615	T	0.2	.	7.0868	0.25261	0.1239:0.6647:0.1361:0.0753	.	541;1739;1744	Q9C093-4;Q9C093-2;Q9C093	.;.;SPEF2_HUMAN	I	1744;1739;541	ENSP00000348314:L1744I;ENSP00000412125:L1739I;ENSP00000303843:L541I	ENSP00000303843:L541I	L	+	1	2	SPEF2	35842785	0.007000	0.16637	0.009000	0.14445	0.042000	0.13812	2.127000	0.42035	1.454000	0.47793	0.655000	0.94253	CTA	.	.		0.363	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		A	35807028	C	A	35807028	3	1	40	1	0	0	0	0	1	0	0	0	15050	680	24	3	5389	3	SPEF2	5	35807028	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1869308	35807028	145108232	77	4733										
RGNEF	64283	hgsc.bcm.edu	37	chr5	73153515	73153515	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aatgggataaatacatcataCctgccaaatcagagtctgaa	7	8	3	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:73153515C>A	ENST00000426542.2	+	14	1845	c.1825C>A	c.(1825-1827)Cct>Act	p.P609T	ARHGEF28_ENST00000287898.5_Missense_Mutation_p.P609T|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.P609T|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.P296T|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.P609T|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.P609T|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.P609T			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	609					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										ATACATCATACCTGCCAAATC	0.353																																					p.P609T		.	.											.	.	.	.	0			c.C1825A						.						65	66	66					5																	73153515		1872	4094	5966	SO:0001583	missense	64283	exon15			ATCATACCTGCCA		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.1825C>A	5.37:g.73153515C>A	ENSP00000412175:p.Pro609Thr	300.0	0.0		340.0	113.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519472	0.85495	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.17691	2.46;2.43;2.44;2.3;2.43;2.44;2.26	5.51	5.51	0.81932	.	.	.	.	.	T	0.34193	0.0889	L	0.32530	0.975	0.53005	D	0.999963	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	1.0;1.0;0.972;0.987	T	0.04551	-1.0943	9	0.72032	D	0.01	.	19.0039	0.92843	0.0:1.0:0.0:0.0	.	296;609;609;609	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	T	609;609;609;609;609;609;296	ENSP00000296794:P609T;ENSP00000441913:P609T;ENSP00000441436:P609T;ENSP00000287898:P609T;ENSP00000411459:P609T;ENSP00000412175:P609T;ENSP00000296799:P296T	ENSP00000287898:P609T	P	+	1	0	RP11-428C6.1	73189271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.199000	0.77831	2.615000	0.88500	0.650000	0.86243	CCT	.	.		0.353	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			A	73153515	C	A	73153515	3	1	40	1	0	0	0	0	1	0	0	0	13298	507	18	3	1879	3	RGNEF	5	73153515	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	37346487	73153515	107761745	78	4734										
AP3B1	8546	hgsc.bcm.edu	37	chr5	77412060	77412060	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctggggtccattcttttgccTgtttaaacaaataaagtaaa	7	7	1	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:77412060T>C	ENST00000255194.6	-	18	2144		c.e18-2		AP3B1_ENST00000519295.1_Splice_Site	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit						anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		TTCTTTTGCCTGTTTAAACAA	0.343									Hermansky-Pudlak syndrome																												.		.	.											.	AP3B1	.	.	0			c.1969-2A>G						.						64	66	65					5																	77412060		2203	4300	6503	SO:0001630	splice_region_variant	8546	exon19	Familial Cancer Database	HPS, HPS1-8	TTTGCCTGTTTAA	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1969-2A>G	5.37:g.77412060T>C		155.0	0.0		208.0	22.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Splice_Site	SNP	ENST00000255194.6	37	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	T	17.27	3.347203	0.61183	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760	.	.	.	5.99	5.99	0.97316	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4413	0.67321	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	AP3B1	77447816	1.000000	0.71417	0.978000	0.43139	0.896000	0.52359	4.721000	0.61951	2.296000	0.77279	0.533000	0.62120	.	.	.		0.343	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		Intron	C	77412060	T	C	77412060	5	2	40	1	0	0	0	0	0	0	1	0	744	1594	55	2	1357	2	AP3B1	5	77412060	Splice_Site	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	4258545	77412060	103503200	79	4735										
ERAP1	51752	hgsc.bcm.edu	37	chr5	96132948	96132949	+	In_Frame_Ins	INS	-	-	TCATCTTCA													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gaaggccaccagataggtgcINStcatcttcacagtgacatca							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:96132948_96132949insTCATCTTCA	ENST00000443439.2	-	4	793_794	c.727_728insTGAAGATGA	c.(727-729)agc>aTGAAGATGAgc	p.242_243insMKM	ERAP1_ENST00000296754.3_In_Frame_Ins_p.242_243insMKM	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	242					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		CAGATAGGTGCTCATCTTCACA	0.401																																					p.S243delinsMKMS		.	.											.	ERAP1	.	.	0			c.728_729insTGAAGATGA						.																																			SO:0001652	inframe_insertion	51752	exon4			.	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.719_727dupTGAAGATGA	5.37:g.96132949_96132957dupTCATCTTCA	ENSP00000406304:p.Met242_Ser243insMetLysMet	281.0	0.0		239.0	20.0	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	In_Frame_Ins	INS	ENST00000443439.2	37	CCDS47250.1																																																																																			.	.		0.401	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		TCATCTTCA	96132949	-	TCATCTTCA	96132948	7	5	40	1	0	1	1	0	0	0	0	0	5205	797	28	0	2194	0	ERAP1	5	96132948	In_Frame_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	18720888	96132948	84782312	80	4736										
AQPEP	206338	hgsc.bcm.edu	37	chr5	115298764	115298764	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctgctgctgcatagcctcttCcaggactgcgagcgcgccga	12	15	1	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:115298764C>G	ENST00000357872.4	+	1	574	c.450C>G	c.(448-450)ttC>ttG	p.F150L	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		150						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										ATAGCCTCTTCCAGGACTGCG	0.697																																					p.F150L		.	.											.	.	.	.	0			c.C450G						.						40	43	42					5																	115298764		2202	4299	6501	SO:0001583	missense	0	exon1			CCTCTTCCAGGAC																												ENST00000357872.4:c.450C>G	5.37:g.115298764C>G	ENSP00000350541:p.Phe150Leu	53.0	0.0		71.0	16.0	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	C	1.095	-0.662916	0.03454	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.04119	3.7	4.64	-0.977	0.10282	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	1.099670	0.06968	N	0.817619	T	0.02727	0.0082	N	0.17082	0.46	0.26840	N	0.96841	B	0.06786	0.001	B	0.06405	0.002	T	0.47761	-0.9092	10	0.30078	T	0.28	.	0.6167	0.00771	0.172:0.3271:0.1685:0.3325	.	150	Q6Q4G3	AMPQ_HUMAN	L	150	ENSP00000350541:F150L	ENSP00000350541:F150L	F	+	3	2	AC010282.1	115326663	0.000000	0.05858	0.488000	0.27440	0.140000	0.21249	-0.627000	0.05521	-0.203000	0.10251	-0.225000	0.12378	TTC	.	.		0.697	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			G	115298764	C	G	115298764	3	3	40	1	0	0	0	0	1	0	0	0	834	854	30	4	452	4	AQPEP	5	115298764	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	19165816	115298764	65616496	81	4737										
RAD50	10111	hgsc.bcm.edu	37	chr5	131924503	131924503	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggaccattcagtgaaagacaGattaaaaattttcacaaact	6	7	2	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:131924503G>T	ENST00000265335.6	+	8	1563	c.1176G>T	c.(1174-1176)caG>caT	p.Q392H	RAD50_ENST00000378823.3_Missense_Mutation_p.Q253H			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	392					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTGAAAGACAGATTAAAAATT	0.383								Homologous recombination																													p.Q392H		.	.											.	RAD50	.	.	0			c.G1176T						.						89	88	88					5																	131924503		2203	4300	6503	SO:0001583	missense	10111	exon8			AAGACAGATTAAA	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.1176G>T	5.37:g.131924503G>T	ENSP00000265335:p.Gln392His	400.0	0.0		524.0	47.0	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.215788	0.39102	.	.	ENSG00000113522	ENST00000378823;ENST00000265335;ENST00000453394	T;T;T	0.08458	3.4;3.09;3.09	5.97	2.61	0.31194	.	0.106596	0.64402	N	0.000003	T	0.09335	0.0230	M	0.69823	2.125	0.48975	D	0.99973	B	0.12013	0.005	B	0.11329	0.006	T	0.12708	-1.0537	10	0.52906	T	0.07	-5.6091	3.1478	0.06478	0.2277:0.1203:0.519:0.1331	.	392	Q92878	RAD50_HUMAN	H	253;392;392	ENSP00000368100:Q253H;ENSP00000265335:Q392H;ENSP00000400049:Q392H	ENSP00000265335:Q392H	Q	+	3	2	RAD50	131952402	0.996000	0.38824	1.000000	0.80357	0.993000	0.82548	0.385000	0.20685	0.757000	0.33036	-0.345000	0.07892	CAG	.	.		0.383	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		T	131924503	G	T	131924503	3	4	40	1	0	0	0	0	1	0	0	0	12999	933	33	3	1206	3	RAD50	5	131924503	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	16625739	131924503	48990757	82	4738										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140793274	140793274	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgcagagctatcagctcagcCccaataagcacttctcccta	6	15	3	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:140793274C>T	ENST00000398610.2	+	1	532	c.532C>T	c.(532-534)Ccc>Tcc	p.P178S	PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	178	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAGCTCAGCCCCAATAAGCA	0.532																																					p.P178S		.	.											.	.	.	.	0			c.C532T						.						33	35	34					5																	140793274		1950	4141	6091	SO:0001583	missense	56106	exon1			CTCAGCCCCAATA		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.532C>T	5.37:g.140793274C>T	ENSP00000381611:p.Pro178Ser	72.0	0.0		72.0	13.0	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	37	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	c	3.205	-0.162954	0.06502	.	.	ENSG00000253846	ENST00000398610	T	0.18174	2.23	5.49	2.57	0.30868	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.09598	0.0236	N	0.25890	0.77	0.09310	N	1	B;B	0.12013	0.004;0.005	B;B	0.21360	0.02;0.034	T	0.41734	-0.9492	9	0.16420	T	0.52	.	2.3261	0.04223	0.1124:0.4548:0.2091:0.2238	.	178;178	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	S	178	ENSP00000381611:P178S	ENSP00000381611:P178S	P	+	1	0	PCDHGA10	140773458	0.000000	0.05858	0.951000	0.38953	0.657000	0.38888	-0.837000	0.04377	0.214000	0.20742	0.557000	0.71058	CCC	.	.		0.532	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		T	140793274	C	T	140793274	3	4	40	1	0	0	0	0	1	0	0	0	11560	623	22	3	534	3	PCDHGA10	5	140793274	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	8868771	140793274	40121986	83	4739										
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140855947	140855947	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gagaccggagagatgtttgtGaacgaccgtctggatcgaga	15	7	1	4			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:140855947G>C	ENST00000308177.3	+	1	368	c.264G>C	c.(262-264)gtG>gtC	p.V88V	PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB1_ENST00000523390.1_Intron|RN7SL68P_ENST00000488078.2_RNA	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	88	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGATGTTTGTGAACGACCGTC	0.577																																					p.V88V		.	.											.	PCDHGC3	.	.	0			c.G264C						.						135	139	138					5																	140855947		2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			GTTTGTGAACGAC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.264G>C	5.37:g.140855947G>C		168.0	0.0		175.0	27.0	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	37	CCDS4261.1																																																																																			.	.		0.577	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		C	140855947	G	C	140855947	2	2	40	1	0	0	0	0	0	0	0	1	11578	1277	45	4		4	PCDHGC3	5	140855947	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	62673	140855947	40059313	84	4740										
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156714055	156714055	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttgacacaaactttgaggacAggaatgcatttgtcacgggc	11	8	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:156714055A>G	ENST00000521420.1	+	3	236	c.145A>G	c.(145-147)Agg>Ggg	p.R49G	CYFIP2_ENST00000318218.6_Missense_Mutation_p.R49G|CYFIP2_ENST00000541131.1_Intron|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000347377.6_Missense_Mutation_p.R49G|CYFIP2_ENST00000522463.1_Missense_Mutation_p.R49G|CYFIP2_ENST00000377576.3_Missense_Mutation_p.R49G					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTTGAGGACAGGAATGCATT	0.488																																					p.R49G		.	.											.	CYFIP2	.	.	0			c.A145G						.						83	81	82					5																	156714055		2040	4207	6247	SO:0001583	missense	26999	exon3			GAGGACAGGAATG	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.145A>G	5.37:g.156714055A>G	ENSP00000430904:p.Arg49Gly	102.0	0.0		183.0	108.0	NM_001037332		Missense_Mutation	SNP	ENST00000521420.1	37		.	.	.	.	.	.	.	.	.	.	A	17.56	3.420124	0.62622	.	.	ENSG00000055163	ENST00000318218;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576	T;T;T;T;T	0.42900	0.96;1.69;1.84;0.96;0.96	5.49	2.89	0.33648	.	0.000000	0.85682	D	0.000000	T	0.62441	0.2428	M	0.85945	2.785	0.80722	D	1	P;D;D;D;P	0.59357	0.462;0.985;0.976;0.969;0.717	P;P;P;P;P	0.59357	0.478;0.633;0.7;0.856;0.478	T	0.69150	-0.5221	10	0.56958	D	0.05	-27.8786	13.3997	0.60876	0.6366:0.3634:0.0:0.0	.	49;49;49;49;49	E7EW33;E7EVJ5;E7EVF4;Q96F07-2;Q96F07	.;.;.;.;CYFP2_HUMAN	G	49	ENSP00000325817:R49G;ENSP00000428009:R49G;ENSP00000430904:R49G;ENSP00000313567:R49G;ENSP00000366799:R49G	ENSP00000325817:R49G	R	+	1	2	CYFIP2	156646633	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	2.419000	0.44671	0.891000	0.36235	0.459000	0.35465	AGG	.	.		0.488	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		G	156714055	A	G	156714055	3	3	40	1	0	0	0	0	1	0	0	0	4140	179	7	2	151	2	CYFIP2	5	156714055	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	15858108	156714055	24201205	85	4741										
ADRA1B	147	hgsc.bcm.edu	37	chr5	159398905	159398905	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggctccttgttctccaccctGaagccccccgacgccgtgtt	9	18	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:159398905G>A	ENST00000306675.3	+	2	1092	c.969G>A	c.(967-969)ctG>ctA	p.L323L		NM_000679.3	NP_000670.1	P35368	ADA1B_HUMAN	adrenoceptor alpha 1B	323					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|adult heart development (GO:0007512)|behavioral response to cocaine (GO:0048148)|blood vessel remodeling (GO:0001974)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|multicellular organismal development (GO:0007275)|negative regulation of glycogen catabolic process (GO:0045818)|organ growth (GO:0035265)|positive regulation of glycogen catabolic process (GO:0045819)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of the force of heart contraction by epinephrine-norepinephrine (GO:0001997)|regulation of cardiac muscle contraction (GO:0055117)|regulation of vasoconstriction (GO:0019229)|response to amphetamine (GO:0001975)|response to morphine (GO:0043278)|vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure (GO:0001987)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)|protein heterodimerization activity (GO:0046982)			endometrium(3)|large_intestine(6)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acepromazine(DB01614)|Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Dapiprazole(DB00298)|Desipramine(DB01151)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Ziprasidone(DB00246)	TCTCCACCCTGAAGCCCCCCG	0.582																																					p.L323L		.	.											.	ADRA1B	.	.	0			c.G969A						.						30	34	33					5																	159398905		2187	4261	6448	SO:0001819	synonymous_variant	147	exon2			CACCCTGAAGCCC	L31773	CCDS4347.1	5q33.3	2012-08-08	2012-05-09		ENSG00000170214	ENSG00000170214		"GPCR / Class A : Adrenoceptors : alpha"	278	protein-coding gene	gene with protein product		104220	"adrenergic, alpha-1B-, receptor"				Standard	XM_005265818		Approved		uc003lxt.1	P35368	OTTHUMG00000130327	ENST00000306675.3:c.969G>A	5.37:g.159398905G>A		238.0	1.0		249.0	131.0	NM_000679	B0LPE1	Silent	SNP	ENST00000306675.3	37	CCDS4347.1																																																																																			.	.		0.582	ADRA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252676.1			A	159398905	G	A	159398905	2	1	40	1	0	0	0	0	0	0	0	1	335	1277	45	3		3	ADRA1B	5	159398905	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	2684850	159398905	21516355	86	4742										
TTC1	7265	hgsc.bcm.edu	37	chr5	159437629	159437629	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aagccgagtgtgctggccctCcagttcctgatcccaaaaat	9	13	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:159437629C>G	ENST00000231238.5	+	2	204	c.94C>G	c.(94-96)Cca>Gca	p.P32A	TTC1_ENST00000522793.1_Missense_Mutation_p.P32A|Y_RNA_ENST00000362528.1_RNA	NM_001282500.1|NM_003314.1	NP_001269429.1|NP_003305.1	Q99614	TTC1_HUMAN	tetratricopeptide repeat domain 1	32					protein folding (GO:0006457)	peroxisomal membrane (GO:0005778)	unfolded protein binding (GO:0051082)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|prostate(1)|skin(1)	12	Renal(175;0.00196)	all_hematologic(541;0.00014)|Breast(839;0.0101)|all_neural(177;0.0281)|Medulloblastoma(196;0.0425)|Lung NSC(249;0.119)|all_lung(500;0.163)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Epithelial(171;8.37e-05)|all cancers(165;0.000694)|OV - Ovarian serous cystadenocarcinoma(192;0.0402)		TGCTGGCCCTCCAGTTCCTGA	0.522																																					p.P32A		.	.											.	TTC1	.	.	0			c.C94G						.						57	59	59					5																	159437629		2203	4300	6503	SO:0001583	missense	7265	exon2			GGCCCTCCAGTTC	U46570	CCDS4348.1	5q32-q33.2	2013-01-10			ENSG00000113312	ENSG00000113312		"Tetratricopeptide (TTC) repeat domain containing"	12391	protein-coding gene	gene with protein product		601963				8836031	Standard	NM_003314		Approved	TPR1	uc003lxu.3	Q99614	OTTHUMG00000130326	ENST00000231238.5:c.94C>G	5.37:g.159437629C>G	ENSP00000231238:p.Pro32Ala	87.0	0.0		97.0	38.0	NM_003314	B2RCT2|D3DQJ8|Q9BVT3	Missense_Mutation	SNP	ENST00000231238.5	37	CCDS4348.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.426001	0.00186	.	.	ENSG00000113312	ENST00000231238;ENST00000522793	T;T	0.16324	2.35;2.35	5.09	-2.61	0.06171	.	1.602510	0.03083	N	0.158727	T	0.10981	0.0268	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19063	-1.0317	10	0.06625	T	0.88	-14.1256	1.3757	0.02220	0.1235:0.3545:0.1941:0.328	.	32	Q99614	TTC1_HUMAN	A	32	ENSP00000231238:P32A;ENSP00000429225:P32A	ENSP00000231238:P32A	P	+	1	0	TTC1	159370207	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-1.185000	0.03073	-0.696000	0.05098	-0.300000	0.09419	CCA	.	.		0.522	TTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252675.3	NM_003314		G	159437629	C	G	159437629	3	3	40	1	0	0	0	0	1	0	0	0	16693	855	30	4	96	4	TTC1	5	159437629	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	38724	159437629	21477631	87	4743										
RNF44	22838	hgsc.bcm.edu	37	chr5	175957958	175957958	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcaggatgtagtggtcactgGagatgaggtgggggtaggcc	20	5	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:175957958G>T	ENST00000274811.4	-	5	1054	c.530C>A	c.(529-531)tCc>tAc	p.S177Y	RNF44_ENST00000509404.1_5'Flank|RNF44_ENST00000537487.1_Missense_Mutation_p.S96Y	NM_014901.4	NP_055716.1	Q7L0R7	RNF44_HUMAN	ring finger protein 44	177	Pro-rich.						zinc ion binding (GO:0008270)			endometrium(2)|lung(3)|prostate(1)|skin(1)|stomach(1)	8	all_cancers(89;0.0029)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTGGTCACTGGAGATGAGGTG	0.657																																					p.S177Y		.	.											.	RNF44	.	.	0			c.C530A						.						18	20	19					5																	175957958		2180	4269	6449	SO:0001583	missense	22838	exon5			TCACTGGAGATGA	AB029023	CCDS4404.1	5q35.3	2013-01-09			ENSG00000146083	ENSG00000146083		"RING-type (C3HC4) zinc fingers"	19180	protein-coding gene	gene with protein product						10470851	Standard	NM_014901		Approved	KIAA1100	uc003mek.1	Q7L0R7	OTTHUMG00000130664	ENST00000274811.4:c.530C>A	5.37:g.175957958G>T	ENSP00000274811:p.Ser177Tyr	70.0	0.0		76.0	20.0	NM_014901	B4DYE0|Q8ND05|Q9UPQ2	Missense_Mutation	SNP	ENST00000274811.4	37	CCDS4404.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.020586	0.93462	.	.	ENSG00000146083	ENST00000274811;ENST00000537487	T;T	0.47177	0.85;0.85	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.68467	0.3004	M	0.65498	2.005	0.53688	D	0.999971	D	0.89917	1.0	D	0.74023	0.982	T	0.71031	-0.4710	10	0.72032	D	0.01	-40.9803	19.0753	0.93159	0.0:0.0:1.0:0.0	.	177	Q7L0R7	RNF44_HUMAN	Y	177;96	ENSP00000274811:S177Y;ENSP00000440352:S96Y	ENSP00000274811:S177Y	S	-	2	0	RNF44	175890564	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.324000	0.96373	2.526000	0.85167	0.549000	0.68633	TCC	.	.		0.657	RNF44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253156.2			T	175957958	G	T	175957958	3	4	40	1	0	0	0	0	1	0	0	0	13511	1174	41	3	796	3	RNF44	5	175957958	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	16520329	175957958	4957302	88	4744										
TMED9	54732	hgsc.bcm.edu	37	chr5	177019352	177019354	+	In_Frame_Del	DEL	AGA	AGA	-													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctttcacatcggagagacggAgaagaagtgctttattgagg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:177019352_177019354delAGA	ENST00000332598.6	+	1	194_196	c.137_139delAGA	c.(136-141)gagaag>gag	p.K48del		NM_017510.4	NP_059980.2	Q9BVK6	TMED9_HUMAN	transmembrane emp24 protein transport domain containing 9	48	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				COPI coating of Golgi vesicle (GO:0048205)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network transport vesicle (GO:0030140)	syntaxin binding (GO:0019905)			endometrium(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(2)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGAGAGACGGAGAAGAAGTGCTT	0.64																																					p.46_46del		.	.											.	TMED9	.	.	0			c.136_138del						.																																			SO:0001651	inframe_deletion	54732	exon1			.	AF441399	CCDS4428.1	5q35.3	2008-02-05			ENSG00000184840	ENSG00000184840			24878	protein-coding gene	gene with protein product						12477932	Standard	NM_017510		Approved	HSGP25L2G	uc003mhx.3	Q9BVK6	OTTHUMG00000130859	ENST00000332598.6:c.137_139delAGA	5.37:g.177019355_177019357delAGA	ENSP00000330945:p.Lys48del	280.0	0.0		246.0	34.0	NM_017510	Q14437|Q8WZ61	In_Frame_Del	DEL	ENST00000332598.6	37	CCDS4428.1																																																																																			.	.		0.64	TMED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253433.1	NM_017510		-	177019354	AGA	-	177019352	7	5	40	1	0	1	0	1	0	0	0	0	16027	304	11	0	139	0	TMED9	5	177019352	In_Frame_Del	DEL	AGA	TCGA-BC-A112-01A-11D-A12Z-10	1061394	177019352	3895908	89	4745										
AGXT2L2	85007	hgsc.bcm.edu	37	chr5	177642304	177642305	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cccgacgatgggatgtttgaINSttttttgctgcccgaggagc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr5:177642304_177642305insT	ENST00000308158.5	-	9	1288_1289	c.1054_1055insA	c.(1054-1056)atcfs	p.I352fs	PHYKPL_ENST00000481811.1_5'UTR	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase	352						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	GGGATGTTTGATTTTTTGCTGC	0.574																																					p.I352fs		.	.											.	AGXT2L2	.	.	0			c.1055_1056insA						.																																			SO:0001589	frameshift_variant	85007	exon9			.	BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892	ENST00000308158.5:c.1055dupA	5.37:g.177642310_177642310dupT	ENSP00000310978:p.Ile352fs	215.0	0.0		246.0	16.0	NM_153373	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Frame_Shift_Ins	INS	ENST00000308158.5	37	CCDS4434.1																																																																																			.	.		0.574	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		T	177642305	-	T	177642304	7	5	40	1	0	1	1	0	0	0	0	0	407	333	12	0	313	0	AGXT2L2	5	177642304	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	622952	177642304	3272956	90	4746										
F13A1	2162	hgsc.bcm.edu	37	chr6	6145912	6145912	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccatacacatgtctcagggaGtcactgctcatgctggctat	9	12	3	0	rs200672690		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:6145912G>A	ENST00000264870.3	-	15	2404	c.2139C>T	c.(2137-2139)gaC>gaT	p.D713D		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	713					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	GTCTCAGGGAGTCACTGCTCA	0.557																																					p.D713D		.	.											.	F13A1	.	.	0			c.C2139T						.						144	126	132					6																	6145912		2203	4300	6503	SO:0001819	synonymous_variant	2162	exon15			CAGGGAGTCACTG	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"Transglutaminases"	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.2139C>T	6.37:g.6145912G>A		171.0	0.0		144.0	61.0	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Silent	SNP	ENST00000264870.3	37	CCDS4496.1																																																																																			G|0.999;A|0.001	.		0.557	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129		A	6145912	G	A	6145912	2	1	40	1	0	0	0	0	0	0	0	1	5342	1020	36	3		3	F13A1	6	6145912	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10		6145912	164969155	91	4747										
RANBP9	10048	hgsc.bcm.edu	37	chr6	13657454	13657454	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aaggttgtccagttccagaaGaacaaaacgaatgtccatca	8	9	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:13657454G>C	ENST00000011619.3	-	4	849	c.791C>G	c.(790-792)tCt>tGt	p.S264C	RANBP9_ENST00000539980.1_Missense_Mutation_p.S35C	NM_005493.2	NP_005484.2	Q96S59	RANB9_HUMAN	RAN binding protein 9	264	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				axon guidance (GO:0007411)|microtubule nucleation (GO:0007020)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	16	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			AGTTCCAGAAGAACAAAACGA	0.393																																					p.S264C		.	.											.	RANBP9	.	.	0			c.C791G						.						170	132	145					6																	13657454		2203	4300	6503	SO:0001583	missense	10048	exon4			CCAGAAGAACAAA	AB008515	CCDS4529.1	6p23	2010-05-25			ENSG00000010017	ENSG00000010017			13727	protein-coding gene	gene with protein product	"Ran Binding Protein in the Microtubule organizing center"	603854				9817760	Standard	NM_005493		Approved	RanBPM	uc003nbb.3	Q96S59	OTTHUMG00000015642	ENST00000011619.3:c.791C>G	6.37:g.13657454G>C	ENSP00000011619:p.Ser264Cys	223.0	0.0		211.0	23.0	NM_005493	A0PJA2|B2R8E1|O94764|Q6P3T7|Q7LBR2|Q7Z7F9	Missense_Mutation	SNP	ENST00000011619.3	37	CCDS4529.1	.	.	.	.	.	.	.	.	.	.	G	31	5.077381	0.94000	.	.	ENSG00000010017	ENST00000011619;ENST00000539980;ENST00000283152	T;T	0.69926	-0.44;-0.44	5.86	5.86	0.93980	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.72614	0.3482	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.73360	-0.4007	10	0.59425	D	0.04	-16.2831	20.1823	0.98208	0.0:0.0:1.0:0.0	.	264	Q96S59	RANB9_HUMAN	C	264;35;264	ENSP00000011619:S264C;ENSP00000438162:S35C	ENSP00000011619:S264C	S	-	2	0	RANBP9	13765433	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.869000	0.99810	2.771000	0.95319	0.650000	0.86243	TCT	.	.		0.393	RANBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042373.1			C	13657454	G	C	13657454	3	2	40	1	0	0	0	0	1	0	0	0	13047	942	33	4	1442	4	RANBP9	6	13657454	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	7511542	13657454	157457613	92	4748										
C6orf62	81688	hgsc.bcm.edu	37	chr6	24706479	24706480	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	acttgaagattgtagctttgINSttttttggagtctggaaggg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:24706479_24706480insT	ENST00000378119.4	-	5	2742_2743	c.575_576insA	c.(574-576)aacfs	p.N192fs	RP1-30M3.6_ENST00000606921.1_RNA|C6orf62_ENST00000540769.1_Frame_Shift_Ins_p.N134fs|C6orf62_ENST00000378102.3_Frame_Shift_Ins_p.N163fs	NM_030939.4	NP_112201.1	Q9GZU0	CF062_HUMAN	chromosome 6 open reading frame 62	192						intracellular (GO:0005622)				endometrium(2)|kidney(3)|large_intestine(2)|lung(3)	10						TTGTAGCTTTGTTTTTTGGAGT	0.406																																					p.N192fs		.	.											.	C6orf62	.	.	0			c.576_577insA						.																																			SO:0001589	frameshift_variant	81688	exon5			.	AL136632	CCDS4559.1	6p22.1	2011-12-13			ENSG00000112308	ENSG00000112308			20998	protein-coding gene	gene with protein product	"HBV X-transactivated protein 12"					11230166	Standard	NM_030939		Approved	FLJ12619, DKFZP564G182, XTP12	uc003nel.3	Q9GZU0	OTTHUMG00000014361	ENST00000378119.4:c.576dupA	6.37:g.24706485_24706485dupT	ENSP00000367359:p.Asn192fs	129.0	0.0		179.0	11.0	NM_030939	Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2	Frame_Shift_Ins	INS	ENST00000378119.4	37	CCDS4559.1																																																																																			.	.		0.406	C6orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040017.1	NM_030939		T	24706480	-	T	24706479	7	5	40	1	0	1	1	0	0	0	0	0	2370	1368	48	0	117	0	C6orf62	6	24706479	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	11049025	24706479	146408588	93	4749										
HIST1H4D	8360	hgsc.bcm.edu	37	chr6	26189253	26189253	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	acgcaataccttacggtgacGcttggcgccacccttaccta	8	15	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:26189253G>A	ENST00000340756.2	-	1	51	c.52C>T	c.(52-54)Cgt>Tgt	p.R18C		NM_003539.3	NP_003530.1	P62805	H4_HUMAN	histone cluster 1, H4d	18					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|large_intestine(2)|lung(1)|prostate(1)	8		all_hematologic(11;0.196)				TTACGGTGACGCTTGGCGCCA	0.572																																					p.R18C		.	.											.	HIST1H4D	.	.	0			c.C52T						.						55	60	58					6																	26189253		2203	4300	6503	SO:0001583	missense	8360	exon1			GGTGACGCTTGGC	X60482	CCDS4589.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000188987	ENSG00000277157		"Histones / Replication-dependent"	4782	protein-coding gene	gene with protein product		602823	"H4 histone family, member B", "histone 1, H4d"	H4FB		9119399, 12408966	Standard	NM_003539		Approved	H4/b	uc003ngu.3	P62805	OTTHUMG00000014423	ENST00000340756.2:c.52C>T	6.37:g.26189253G>A	ENSP00000343282:p.Arg18Cys	64.0	0.0		75.0	32.0	NM_003539	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000340756.2	37	CCDS4589.1	.	.	.	.	.	.	.	.	.	.	.	16.34	3.094365	0.56075	.	.	ENSG00000188987	ENST00000340756	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.72431	0.3459	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.75297	-0.3367	6	0.62326	D	0.03	.	17.9848	0.89153	0.0:0.0:1.0:0.0	.	.	.	.	C	18	.	ENSP00000343282:R18C	R	-	1	0	HIST1H4D	26297232	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	9.370000	0.97159	2.494000	0.84150	0.650000	0.86243	CGT	.	.		0.572	HIST1H4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040085.1	NM_003539		A	26189253	G	A	26189253	3	1	40	1	0	0	0	0	1	0	0	0	7177	1087	38	1	263	1	HIST1H4D	6	26189253	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	1482774	26189253	144925814	94	4750										
HIST1H2BM	8342	hgsc.bcm.edu	37	chr6	27782957	27782957	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctgtgtatgtgtacaaggtgCtgaagcaggtccaccccgac	12	11	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:27782957C>G	ENST00000359465.4	+	1	136	c.136C>G	c.(136-138)Ctg>Gtg	p.L46V	HIST1H2AJ_ENST00000333151.3_5'Flank	NM_003521.2	NP_003512.1	Q99879	H2B1M_HUMAN	histone cluster 1, H2bm	46					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	12						GTACAAGGTGCTGAAGCAGGT	0.522																																					p.L46V		.	.											.	HIST1H2BM	.	.	0			c.C136G						.						199	189	192					6																	27782957		2203	4300	6503	SO:0001583	missense	8342	exon1			AAGGTGCTGAAGC	Z83738	CCDS4629.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196374	ENSG00000273703		"Histones / Replication-dependent"	4750	protein-coding gene	gene with protein product		602802	"H2B histone family, member E", "histone 1, H2bm"	H2BFE		9439656, 12408966	Standard	NM_003521		Approved	H2B/e, dJ160A22.3	uc003njo.3	Q99879	OTTHUMG00000014489	ENST00000359465.4:c.136C>G	6.37:g.27782957C>G	ENSP00000352442:p.Leu46Val	266.0	0.0		192.0	76.0	NM_003521	Q6NWQ3	Missense_Mutation	SNP	ENST00000359465.4	37	CCDS4629.1	.	.	.	.	.	.	.	.	.	.	.	8.916	0.959835	0.18507	.	.	ENSG00000196374	ENST00000359465	T	0.65916	-0.18	4.29	4.29	0.51040	Histone-fold (2);Histone core (1);	0.000000	0.45867	U	0.000324	D	0.85932	0.5812	H	0.99689	4.705	0.48762	D	0.999708	P	0.49447	0.924	P	0.60068	0.868	D	0.91878	0.5513	10	0.87932	D	0	.	16.2598	0.82535	0.0:1.0:0.0:0.0	.	46	Q99879	H2B1M_HUMAN	V	46	ENSP00000352442:L46V	ENSP00000352442:L46V	L	+	1	2	HIST1H2BM	27890936	1.000000	0.71417	1.000000	0.80357	0.033000	0.12548	1.624000	0.37018	2.373000	0.80994	0.563000	0.77884	CTG	.	.		0.522	HIST1H2BM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040157.1	NM_003521		G	27782957	C	G	27782957	3	3	40	1	0	0	0	0	1	0	0	0	7161	796	28	4	138	4	HIST1H2BM	6	27782957	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1593704	27782957	143332110	95	4751										
RDBP	7936	hgsc.bcm.edu	37	chr6	31921602	31921602	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tacagactccacctgggtccCgttgagctgaagcagaagag	12	11	0	5			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:31921602C>G	ENST00000375429.3	-	10	1175	c.949G>C	c.(949-951)Ggg>Cgg	p.G317R	NELFE_ENST00000444811.2_Missense_Mutation_p.G287R|NELFE_ENST00000375425.5_Missense_Mutation_p.G324R	NM_002904.5	NP_002895.3	P18615	NELFE_HUMAN	negative elongation factor complex member E	317	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										ACCTGGGTCCCGTTGAGCTGA	0.522																																					p.G317R		.	.											.	.	.	.	0			c.G949C						.						81	81	81					6																	31921602		1511	2708	4219	SO:0001583	missense	7936	exon10			GGGTCCCGTTGAG	M33230	CCDS4730.1	6p21.3	2013-02-12	2013-01-31	2013-01-31	ENSG00000204356	ENSG00000204356		"RNA binding motif (RRM) containing"	13974	protein-coding gene	gene with protein product		154040	"RD RNA-binding protein", "RD RNA binding protein"	RDBP			Standard	XM_006715205		Approved	RD, D6S45, NELF-E, RDP	uc003nyk.3	P18615	OTTHUMG00000031046	ENST00000375429.3:c.949G>C	6.37:g.31921602C>G	ENSP00000364578:p.Gly317Arg	251.0	0.0		327.0	65.0	NM_002904	A2BE08|B4DUN1|B4DYX9|Q5JP74|Q5JP75|Q96F56|Q9NPK2	Missense_Mutation	SNP	ENST00000375429.3	37	CCDS4730.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.603820	0.46423	.	.	ENSG00000204356	ENST00000375429;ENST00000375425;ENST00000444811;ENST00000441998	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	6.07	6.07	0.98685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.172834	0.50627	D	0.000119	T	0.49115	0.1538	M	0.87758	2.905	0.58432	D	0.999995	P;P;P	0.39964	0.697;0.697;0.697	B;B;B	0.37833	0.259;0.259;0.259	T	0.62115	-0.6922	10	0.87932	D	0	-25.8007	12.7035	0.57046	0.0:0.9243:0.0:0.0757	.	287;312;317	B4DUN1;E9PCL7;P18615	.;.;NELFE_HUMAN	R	317;324;287;312	ENSP00000364578:G317R;ENSP00000364574:G324R;ENSP00000388400:G287R;ENSP00000397914:G312R	ENSP00000364574:G324R	G	-	1	0	RDBP	32029581	1.000000	0.71417	0.992000	0.48379	0.758000	0.43043	4.402000	0.59722	2.884000	0.98904	0.655000	0.94253	GGG	.	.		0.522	NELFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076047.4			G	31921602	C	G	31921602	3	3	40	1	0	0	0	0	1	0	0	0	13203	652	23	4	201	4	RDBP	6	31921602	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	4138645	31921602	139193465	96	4752										
BRD2	6046	hgsc.bcm.edu	37	chr6	32948467	32948467	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctcttcctcgtcgtcgtcttCagacaccagtgattcagact	7	14	4	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:32948467C>A	ENST00000374825.4	+	13	4079	c.2378C>A	c.(2377-2379)tCa>tAa	p.S793*	BRD2_ENST00000443797.2_Nonsense_Mutation_p.S673*|BRD2_ENST00000395287.1_Nonsense_Mutation_p.S828*|BRD2_ENST00000395289.2_Nonsense_Mutation_p.S828*|BRD2_ENST00000374831.4_Nonsense_Mutation_p.S793*|BRD2_ENST00000449085.2_Nonsense_Mutation_p.S746*	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	793	Poly-Ser.|Ser-rich.				chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						TCGTCGTCTTCAGACACCAGT	0.597																																					p.S828X		.	.											.	BRD2	.	.	0			c.C2483A						.						102	88	93					6																	32948467		1510	2708	4218	SO:0001587	stop_gained	6046	exon13			CGTCTTCAGACAC	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"bromodomain-containing 2"			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.2378C>A	6.37:g.32948467C>A	ENSP00000363958:p.Ser793*	136.0	0.0		93.0	27.0	NM_001199455	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Nonsense_Mutation	SNP	ENST00000374825.4	37	CCDS4762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	52|52	19.282057|19.282057	0.99917|0.99917	.|.	.|.	ENSG00000204256|ENSG00000204256	ENST00000449025|ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085	.|.	.|.	.|.	6.15|6.15	6.15|6.15	0.99193|0.99193	.|.	.|0.000000	.|0.37012	.|N	.|0.002289	T|.	0.31734|.	0.0806|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.17198|.	-1.0377|.	4|.	.|0.06099	.|T	.|0.92	-13.3034|-13.3034	16.3388|16.3388	0.83075|0.83075	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	K|X	799|793;793;828;673;828;746	.|.	.|ENSP00000363958:S793X	Q|S	+|+	1|2	0|0	BRD2|BRD2	33056445|33056445	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.856000|0.856000	0.48823|0.48823	4.969000|4.969000	0.63735|0.63735	2.932000|2.932000	0.99384|0.99384	0.643000|0.643000	0.83706|0.83706	CAG|TCA	.	.		0.597	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			A	32948467	C	A	32948467	4	1	40	1	0	0	0	0	0	1	0	0	1504	838	29	3	2424	3	BRD2	6	32948467	Nonsense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1026865	32948467	138166600	97	4753										
RING1	6015	hgsc.bcm.edu	37	chr6	33177781	33177781	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgatgccctgatctctaagaTctatcctagccgggaggaat	10	10	2	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:33177781T>G	ENST00000374656.4	+	4	537	c.329T>G	c.(328-330)aTc>aGc	p.I110S	MIR219-1_ENST00000362166.1_RNA|RING1_ENST00000478431.1_3'UTR	NM_002931.3	NP_002922.2	Q06587	RING1_HUMAN	ring finger protein 1	110	Necessary for transcriptional repression. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|histone H2A monoubiquitination (GO:0035518)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I110S(1)		endometrium(5)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|skin(4)	17						ATCTCTAAGATCTATCCTAGC	0.567																																					p.I110S		.	.											RING1,NS,carcinoma,0	RING1	.	.	1	Substitution - Missense(1)	ovary(1)	c.T329G						.						70	63	66					6																	33177781		2203	4300	6503	SO:0001583	missense	6015	exon4			CTAAGATCTATCC		CCDS34424.1	6p21.3	2013-01-09			ENSG00000204227	ENSG00000204227		"RING-type (C3HC4) zinc fingers"	10018	protein-coding gene	gene with protein product		602045				1906426	Standard	NM_002931		Approved	RNF1	uc003odk.3	Q06587	OTTHUMG00000031278	ENST00000374656.4:c.329T>G	6.37:g.33177781T>G	ENSP00000363787:p.Ile110Ser	102.0	0.0		132.0	39.0	NM_002931	A8JZZ0|Q5JP96|Q5SQW2|Q86V19	Missense_Mutation	SNP	ENST00000374656.4	37	CCDS34424.1	.	.	.	.	.	.	.	.	.	.	T	19.25	3.791731	0.70452	.	.	ENSG00000204227	ENST00000374656	D	0.85702	-2.02	4.23	4.23	0.50019	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.64402	D	0.000001	D	0.89206	0.6649	M	0.73598	2.24	0.58432	D	0.999997	D	0.71674	0.998	D	0.83275	0.996	D	0.90554	0.4511	10	0.87932	D	0	-27.3229	11.3179	0.49403	0.0:0.0:0.0:1.0	.	110	Q06587	RING1_HUMAN	S	110	ENSP00000363787:I110S	ENSP00000363787:I110S	I	+	2	0	RING1	33285759	1.000000	0.71417	0.997000	0.53966	0.918000	0.54935	7.463000	0.80869	1.767000	0.52121	0.443000	0.29094	ATC	.	.		0.567	RING1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076609.2			G	33177781	T	G	33177781	3	3	40	1	0	0	0	0	1	0	0	0	13389	1435	50	5	339	5	RING1	6	33177781	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	229314	33177781	137937286	98	4754										
RPL10A	4736	hgsc.bcm.edu	37	chr6	35437288	35437288	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aaaaactcaacaagaataaaAaactggtcaagaagctgggt	8	6	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:35437288A>C	ENST00000322203.6	+	4	319	c.292A>C	c.(292-294)Aaa>Caa	p.K98Q	RPL10A_ENST00000467020.1_3'UTR	NM_007104.4	NP_009035.3	P62906	RL10A_HUMAN	ribosomal protein L10a	98					anatomical structure morphogenesis (GO:0009653)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|large_intestine(2)|ovary(1)	4						CAAGAATAAAAAACTGGTCAA	0.512																																					p.K98Q		.	.											.	RPL10A	.	.	0			c.A292C						.						41	42	42					6																	35437288		2203	4300	6503	SO:0001583	missense	4736	exon4			AATAAAAAACTGG	U12404	CCDS4806.1	6p21.31	2011-04-06			ENSG00000198755	ENSG00000198755		"L ribosomal proteins"	10299	protein-coding gene	gene with protein product		615660		NEDD6		7609734, 9647638	Standard	NM_007104		Approved	Csa-19, L10A	uc003okp.1	P62906	OTTHUMG00000014566	ENST00000322203.6:c.292A>C	6.37:g.35437288A>C	ENSP00000363018:p.Lys98Gln	71.0	0.0		72.0	26.0	NM_007104	B2R801|P52859|P53025|Q5TZT6|Q8J013	Missense_Mutation	SNP	ENST00000322203.6	37	CCDS4806.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.913719	0.72983	.	.	ENSG00000198755	ENST00000322203	T	0.50001	0.76	4.61	4.61	0.57282	Ribosomal protein L1, 3-layer alpha/beta-sandwich (1);Ribosomal protein L1, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.70971	0.3285	H	0.95402	3.665	0.80722	D	1	D	0.57899	0.981	D	0.71414	0.973	T	0.80643	-0.1291	10	0.87932	D	0	.	12.8579	0.57897	1.0:0.0:0.0:0.0	.	98	P62906	RL10A_HUMAN	Q	98	ENSP00000363018:K98Q	ENSP00000363018:K98Q	K	+	1	0	RPL10A	35545266	1.000000	0.71417	0.994000	0.49952	0.653000	0.38743	9.266000	0.95659	1.717000	0.51406	0.374000	0.22700	AAA	.	.		0.512	RPL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040283.1	NM_007104		C	35437288	A	C	35437288	3	2	40	1	0	0	0	0	1	0	0	0	13570	15	1	5	306	5	RPL10A	6	35437288	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	2259507	35437288	135677779	99	4755										
CPNE5	57699	hgsc.bcm.edu	37	chr6	36710124	36710124	+	Frame_Shift_Del	DEL	G	G	-													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agtgggttggtgctgcgggtGggggacgcgggcgaatgccc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:36710124delG	ENST00000244751.2	-	21	2327	c.1703delC	c.(1702-1704)ccafs	p.P569fs	CPNE5_ENST00000459703.1_5'UTR|CPNE5_ENST00000393189.2_Frame_Shift_Del_p.P277fs	NM_020939.1	NP_065990.1	Q9HCH3	CPNE5_HUMAN	copine V	569						extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(4)|liver(1)|lung(9)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						TGCTGCGGGTGGGGGACGCGG	0.682																																					p.P568fs		.	.											.	CPNE5	.	.	0			c.1704delA						.						79	73	75					6																	36710124		2203	4300	6503	SO:0001589	frameshift_variant	57699	exon21			.	H09181	CCDS4825.1	6p21.2	2010-05-28			ENSG00000124772	ENSG00000124772			2318	protein-coding gene	gene with protein product		604209				9430674	Standard	NM_020939		Approved	CPN5, COPN5, KIAA1599	uc003omr.1	Q9HCH3	OTTHUMG00000014602	ENST00000244751.2:c.1703delC	6.37:g.36710124delG	ENSP00000244751:p.Pro569fs	110.0	0.0		91.0	23.0	NM_020939	Q7Z6C8	Frame_Shift_Del	DEL	ENST00000244751.2	37	CCDS4825.1																																																																																			.	.		0.682	CPNE5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040351.1	NM_020939		-	36710124	G	-	36710124	7	5	40	1	0	1	0	1	0	0	0	0	3817	1348	47	0	82	0	CPNE5	6	36710124	Frame_Shift_Del	DEL	G	TCGA-BC-A112-01A-11D-A12Z-10	1272836	36710124	134404943	100	4756										
DLK2	65989	hgsc.bcm.edu	37	chr6	43418412	43418413	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cagggtagcaacagggtccaINSggggggcagacaccccggcg					rs200290716		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:43418412_43418413insG	ENST00000357338.3	-	6	1716_1717	c.1016_1017insC	c.(1015-1017)cctfs	p.P339fs	DLK2_ENST00000414245.1_Frame_Shift_Ins_p.P333fs|DLK2_ENST00000372488.3_Frame_Shift_Ins_p.P339fs|DLK2_ENST00000372485.1_Frame_Shift_Ins_p.P333fs	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	339					negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			AACAGGGTCCAGGGGGGCAGAC	0.658																																					p.P339fs		.	.											.	DLK2	.	.	0			c.1017_1018insC						.																																			SO:0001589	frameshift_variant	65989	exon6			.	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"EGF-like-domain, multiple 9"	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.1017dupC	6.37:g.43418418_43418418dupG	ENSP00000349893:p.Pro339fs	182.0	0.0		143.0	12.0	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Frame_Shift_Ins	INS	ENST00000357338.3	37	CCDS4897.1																																																																																			.	.		0.658	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932		G	43418413	-	G	43418412	7	5	40	1	0	1	1	0	0	0	0	0	4567	175	7	0	138	0	DLK2	6	43418412	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	6708288	43418412	127696655	101	4757										
SENP6	26054	hgsc.bcm.edu	37	chr6	76386875	76386875	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	caatttttttgcgaaaattcCctttgaagaagctaatggca	7	7	0	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:76386875C>G	ENST00000447266.2	+	14	2229	c.1751C>G	c.(1750-1752)cCc>cGc	p.P584R	SENP6_ENST00000370014.3_Missense_Mutation_p.P584R|SENP6_ENST00000327284.8_Missense_Mutation_p.P577R|SENP6_ENST00000370010.2_Missense_Mutation_p.P577R|SENP6_ENST00000541192.1_Missense_Mutation_p.P180R	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	584					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				GCGAAAATTCCCTTTGAAGAA	0.343																																					p.P584R		.	.											.	SENP6	.	.	0			c.C1751G						.						37	36	36					6																	76386875		1811	4070	5881	SO:0001583	missense	26054	exon14			AAATTCCCTTTGA		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.1751C>G	6.37:g.76386875C>G	ENSP00000402527:p.Pro584Arg	399.0	1.0		514.0	165.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	37	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	C	10.14	1.267921	0.23136	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000327284;ENST00000447266;ENST00000424947;ENST00000541192	T;T;T;T;T;T	0.32515	2.71;2.71;1.45;2.71;1.45;1.48	5.26	1.46	0.22682	.	0.751883	0.13601	N	0.375823	T	0.14485	0.0350	L	0.46157	1.445	0.20764	N	0.999852	B;B;P	0.43633	0.355;0.242;0.813	B;B;P	0.45071	0.279;0.144;0.468	T	0.11470	-1.0586	10	0.33141	T	0.24	0.3653	10.3264	0.43796	0.0:0.7303:0.0:0.2697	.	577;584;577	Q9GZR1-2;Q9GZR1;F8W6D9	.;SENP6_HUMAN;.	R	577;584;577;584;474;180	ENSP00000359027:P577R;ENSP00000359031:P584R;ENSP00000321820:P577R;ENSP00000402527:P584R;ENSP00000391426:P474R;ENSP00000441715:P180R	ENSP00000321820:P577R	P	+	2	0	SENP6	76443595	0.995000	0.38212	0.993000	0.49108	0.310000	0.27922	1.710000	0.37920	-0.015000	0.14150	-0.459000	0.05422	CCC	.	.		0.343	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		G	76386875	C	G	76386875	3	3	40	1	0	0	0	0	1	0	0	0	14065	623	22	4	1805	4	SENP6	6	76386875	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	32968463	76386875	94728192	102	4758										
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83847672	83847673	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cctaaagtaaaacttgccagINSaaaaaaggatgatgacaaga							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:83847672_83847673insA	ENST00000349129.2	+	21	4171_4172	c.3911_3912insA	c.(3910-3915)agaaaafs	p.RK1304fs	DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000237163.5_Frame_Shift_Ins_p.RK1285fs|DOPEY1_ENST00000369739.3_Frame_Shift_Ins_p.RK1295fs	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	1304					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		AAACTTGCCAGAAAAAAGGATG	0.347																																					p.R1304fs		.	.											.	DOPEY1	.	.	0			c.3911_3912insA						.																																			SO:0001589	frameshift_variant	23033	exon21			.	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.3917dupA	6.37:g.83847678_83847678dupA	ENSP00000195654:p.Arg1304fs	132.0	0.0		144.0	11.0	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Frame_Shift_Ins	INS	ENST00000349129.2	37	CCDS4996.1																																																																																			.	.		0.347	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		A	83847673	-	A	83847672	7	5	40	1	0	1	1	0	0	0	0	0	4709	942	33	0	3985	0	DOPEY1	6	83847672	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	7460797	83847672	87267395	103	4759										
ANKRD6	22881	hgsc.bcm.edu	37	chr6	90333665	90333665	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aagaacctgcatgctcataaTcaccctaaaaagaggaacag	7	10	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:90333665T>G	ENST00000522441.1	+	12	1748	c.1107T>G	c.(1105-1107)aaT>aaG	p.N369K	ANKRD6_ENST00000339746.4_Missense_Mutation_p.N369K|ANKRD6_ENST00000369408.5_Missense_Mutation_p.N334K|ANKRD6_ENST00000520793.1_Missense_Mutation_p.N310K|ANKRD6_ENST00000447838.2_Missense_Mutation_p.N369K|LYRM2_ENST00000520441.1_Intron	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	369					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		ATGCTCATAATCACCCTAAAA	0.547																																					p.N369K		.	.											.	ANKRD6	.	.	0			c.T1107G						.						105	111	109					6																	90333665		2088	4227	6315	SO:0001583	missense	22881	exon12			TCATAATCACCCT	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"Ankyrin repeat domain containing"	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.1107T>G	6.37:g.90333665T>G	ENSP00000430985:p.Asn369Lys	226.0	0.0		175.0	19.0	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Missense_Mutation	SNP	ENST00000522441.1	37	CCDS56441.1	.	.	.	.	.	.	.	.	.	.	T	10.01	1.233653	0.22626	.	.	ENSG00000135299	ENST00000369408;ENST00000339746;ENST00000447838;ENST00000522441;ENST00000518150;ENST00000520793	T;T;T;T;T	0.68025	1.18;1.22;1.21;1.22;-0.3	6.02	-2.04	0.07343	.	0.919996	0.09193	N	0.835739	T	0.31263	0.0791	N	0.24115	0.695	0.34961	D	0.7522	B;B;B;B	0.26845	0.1;0.025;0.161;0.032	B;B;B;B	0.24394	0.024;0.02;0.053;0.013	T	0.07829	-1.0752	10	0.44086	T	0.13	0.5272	11.0166	0.47693	0.0:0.5636:0.0:0.4364	.	310;369;334;369	B3KUC3;Q9Y2G4;Q9Y2G4-1;C9JJE8	.;ANKR6_HUMAN;.;.	K	334;369;369;369;110;310	ENSP00000358416:N334K;ENSP00000345767:N369K;ENSP00000396771:N369K;ENSP00000430985:N369K;ENSP00000429782:N310K	ENSP00000345767:N369K	N	+	3	2	ANKRD6	90390386	0.005000	0.15991	0.028000	0.17463	0.778000	0.44026	-0.070000	0.11523	-0.320000	0.08640	-0.250000	0.11733	AAT	.	.		0.547	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1			G	90333665	T	G	90333665	3	3	40	1	0	0	0	0	1	0	0	0	685	1432	50	5	1149	5	ANKRD6	6	90333665	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	6485993	90333665	80781402	104	4760										
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90577003	90577004	+	RNA	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cagcagtgttaactgtactgINSaaaaaagtgagtgggagtta							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:90577003_90577004insA	ENST00000551025.1	+	0	5431_5432									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		TAACTGTACTGAAAAAAGTGAG	0.396																																					p.E1332fs	Colon(187;1656 2025 17045 31481 39901)	.	.											.	CASP8AP2	.	.	0			c.3994_3995insA						.																																					9994	exon8			.	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90577009_90577009dupA		145.0	0.0		168.0	10.0	NM_001137667		Frame_Shift_Ins	INS	ENST00000551025.1	37																																																																																				.	.		0.396	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		A	90577004	-	A	90577003	6	5	40	0	1	1	1	0	0	0	0	0	2680	1291	45	0		0	CASP8AP2	6	90577003	RNA	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	243338	90577003	80538064	105	4761										
C6orf204	387119	hgsc.bcm.edu	37	chr6	118886846	118886847	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccttacggaaggctgaatggINSgaactccacctactgcctgt							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:118886846_118886847insA	ENST00000368491.3	-	3	1486_1487	c.865_866insT	c.(865-867)cccfs	p.P289fs	CEP85L_ENST00000360290.3_Frame_Shift_Ins_p.P187fs|CEP85L_ENST00000368488.5_Frame_Shift_Ins_p.P292fs|CEP85L_ENST00000392500.3_Frame_Shift_Ins_p.P292fs|CEP85L_ENST00000419517.2_Frame_Shift_Ins_p.P289fs|CEP85L_ENST00000472713.1_5'UTR	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	289						centrosome (GO:0005813)|cytoplasm (GO:0005737)											AGGCTGAATGGGAACTCCACCT	0.446																																					p.P292fs		.	.											.	.	.	.	0			c.875_876insT						.																																			SO:0001589	frameshift_variant	387119	exon4			.	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 204"	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.865_866insT	6.37:g.118886846_118886847insA	ENSP00000357477:p.Pro289fs	287.0	0.0		300.0	27.0	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Frame_Shift_Ins	INS	ENST00000368491.3	37	CCDS43498.1																																																																																			.	.		0.446	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		A	118886847	-	A	118886846	7	5	40	1	0	1	1	0	0	0	0	0	2355	1232	43	0	1649	0	C6orf204	6	118886846	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	28309843	118886846	52228221	106	4762										
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143094744	143094745	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gatggctcagaatcttgtccINSttttttctctgacagtctta							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:143094744_143094745insT	ENST00000367604.1	-	4	1770_1771	c.1131_1132insA	c.(1129-1134)aaaggafs	p.G378fs	HIVEP2_ENST00000367603.2_Frame_Shift_Ins_p.G378fs|HIVEP2_ENST00000012134.2_Frame_Shift_Ins_p.G378fs			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GAATCTTGTCCTTTTTTCTCTG	0.431																																					p.G378fs	Esophageal Squamous(107;843 1510 13293 16805 42198)	.	.											.	HIVEP2	.	.	0			c.1132_1133insA						.																																			SO:0001589	frameshift_variant	3097	exon5			.	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.1132dupA	6.37:g.143094750_143094750dupT	ENSP00000356576:p.Gly378fs	284.0	0.0		299.0	18.0	NM_006734	Q02646|Q5THT5|Q9NS05	Frame_Shift_Ins	INS	ENST00000367604.1	37	CCDS43510.1																																																																																			.	.		0.431	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			T	143094745	-	T	143094744	7	5	40	1	0	1	1	0	0	0	0	0	7196	690	24	0	6232	0	HIVEP2	6	143094744	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	24207898	143094744	28020323	107	4763										
LRP11	84918	hgsc.bcm.edu	37	chr6	150174142	150174142	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gtgacaacatgcgttaccttCatgtccactgacgggtcccc	9	14	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:150174142C>T	ENST00000239367.2	-	2	773	c.768G>A	c.(766-768)atG>atA	p.M256I	LRP11_ENST00000546019.1_Start_Codon_SNP_p.M1I|LRP11_ENST00000367368.2_Missense_Mutation_p.M256I|RP11-350J20.12_ENST00000472053.2_RNA	NM_032832.5	NP_116221.3	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein 11	256	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.					integral component of membrane (GO:0016021)		p.M256I(1)		cervix(1)|kidney(5)|large_intestine(1)|lung(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		GCGTTACCTTCATGTCCACTG	0.527																																					p.M256I		.	.											.	LRP11	.	.	1	Substitution - Missense(1)	kidney(1)	c.G768A						.						88	79	82					6																	150174142		2203	4300	6503	SO:0001583	missense	84918	exon2			TACCTTCATGTCC	AK027641	CCDS5220.1	6q24.3	2013-02-27			ENSG00000120256	ENSG00000120256		"Low density lipoprotein receptors"	16936	protein-coding gene	gene with protein product							Standard	NM_032832		Approved	bA350J20.3, MANSC3	uc003qng.2	Q86VZ4	OTTHUMG00000015801	ENST00000239367.2:c.768G>A	6.37:g.150174142C>T	ENSP00000239367:p.Met256Ile	199.0	0.0		146.0	57.0	NM_032832	Q5VYC0|Q96SN6	Missense_Mutation	SNP	ENST00000239367.2	37	CCDS5220.1	.	.	.	.	.	.	.	.	.	.	C	35	5.536507	0.96460	.	.	ENSG00000120256	ENST00000239367;ENST00000546019;ENST00000367368	T;D;T	0.97066	3.57;-4.23;2.86	5.45	5.45	0.79879	PKD/Chitinase domain (1);PKD domain (3);	0.077012	0.85682	D	0.000000	D	0.96056	0.8715	L	0.35644	1.08	0.80722	D	1	D;D	0.65815	0.995;0.984	P;P	0.59115	0.852;0.724	D	0.95362	0.8456	10	0.36615	T	0.2	-14.4133	16.2004	0.82067	0.0:1.0:0.0:0.0	.	256;256	Q5VYB9;Q86VZ4	.;LRP11_HUMAN	I	256;1;256	ENSP00000239367:M256I;ENSP00000440196:M1I;ENSP00000356338:M256I	ENSP00000239367:M256I	M	-	3	0	LRP11	150215835	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.146000	0.58072	2.562000	0.86427	0.591000	0.81541	ATG	.	.		0.527	LRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042664.1	NM_032832		T	150174142	C	T	150174142	3	4	40	1	0	0	0	0	1	0	0	0	8962	826	29	3	758	3	LRP11	6	150174142	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	7079398	150174142	20940925	108	4764										
TCP10	6953	hgsc.bcm.edu	37	chr6	167790069	167790070	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	accccccgtctttctgcaccINSgggagtcggccttccagtgg					rs75579977	byFrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr6:167790069_167790070insG	ENST00000397829.4	-	5	707_708	c.540_541insC	c.(538-543)cccggtfs	p.G181fs	TCP10_ENST00000366827.2_Frame_Shift_Ins_p.G181fs	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	208						cytosol (GO:0005829)		p.G181S(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(6)	18		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		CTTTCTGCACCGGGAGTCGGCC	0.53																																					p.G181fs		.	.											.	TCP10	.	.	2	Substitution - Missense(2)	NS(1)|endometrium(1)	c.541_542insC						.																																			SO:0001589	frameshift_variant	6953	exon5			.	U03399	CCDS43527.1	6q27	2012-09-20	2012-09-20		ENSG00000203690	ENSG00000203690			11656	protein-coding gene	gene with protein product		187020	"t-complex 10 (a murine tcp homolog)", "t-complex 10 (mouse)", "t-complex 10 homolog (mouse)"			8111376	Standard	NM_004610		Approved		uc003qvv.1	Q12799	OTTHUMG00000016026	ENST00000397829.4:c.541dupC	6.37:g.167790072_167790072dupG	ENSP00000380929:p.Gly181fs	294.0	0.0		336.0	22.0	NM_004610	Q5JR60|Q6P4F4	Frame_Shift_Ins	INS	ENST00000397829.4	37	CCDS43527.1																																																																																			.	.		0.53	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1	NM_004610		G	167790070	-	G	167790069	7	5	40	1	0	1	1	0	0	0	0	0	15725	652	23	0	455	0	TCP10	6	167790069	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	17615927	167790069	3324998	109	4765										
NXPH1	30010	hgsc.bcm.edu	37	chr7	8791057	8791057	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tatttcaggcataattcaacTggtcaagggaatgtatctgt	9	6	4	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:8791057T>A	ENST00000405863.1	+	3	1385	c.474T>A	c.(472-474)acT>acA	p.T158T	NXPH1_ENST00000497400.1_3'UTR|NXPH1_ENST00000602349.1_Silent_p.T41T	NM_152745.2	NP_689958.1	P58417	NXPH1_HUMAN	neurexophilin 1	158	III.					extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|ovary(1)	17		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		ATAATTCAACTGGTCAAGGGA	0.398																																					p.T158T		.	.											.	NXPH1	.	.	0			c.T474A						.						83	83	83					7																	8791057		1877	4116	5993	SO:0001819	synonymous_variant	30010	exon3			TTCAACTGGTCAA	AB047362	CCDS47540.1	7p22	2003-03-20			ENSG00000122584	ENSG00000122584			20693	protein-coding gene	gene with protein product		604639				9570794	Standard	NM_152745		Approved		uc003srv.3	P58417	OTTHUMG00000151941	ENST00000405863.1:c.474T>A	7.37:g.8791057T>A		128.0	0.0		144.0	42.0	NM_152745	Q8NB31	Silent	SNP	ENST00000405863.1	37	CCDS47540.1																																																																																			.	.		0.398	NXPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324591.1	NM_152745		A	8791057	T	A	8791057	2	1	40	1	0	0	0	0	0	0	0	1	10799	1567	55	4		4	NXPH1	7	8791057	Silent	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10		8791057	150347606	110	4766										
SCIN	85477	hgsc.bcm.edu	37	chr7	12666376	12666376	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aaattacacagttctccgcaGatggcagcccagcacaatat	7	12	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:12666376G>T	ENST00000297029.5	+	8	1250	c.1149G>T	c.(1147-1149)caG>caT	p.Q383H	SCIN_ENST00000519209.1_Missense_Mutation_p.Q136H|SCIN_ENST00000445618.2_Missense_Mutation_p.Q136H|SCIN_ENST00000473722.1_3'UTR	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	383	Ca(2+)-dependent actin binding.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		GTTCTCCGCAGATGGCAGCCC	0.418																																					p.Q383H		.	.											.	SCIN	.	.	0			c.G1149T						.						61	62	62					7																	12666376		1945	4135	6080	SO:0001583	missense	85477	exon8			TCCGCAGATGGCA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.1149G>T	7.37:g.12666376G>T	ENSP00000297029:p.Gln383His	269.0	0.0		296.0	105.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	G	9.425	1.084134	0.20309	.	.	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.29917	1.55;1.55;1.55	5.78	3.72	0.42706	.	0.114869	0.64402	D	0.000012	T	0.26882	0.0658	L	0.50333	1.59	0.47341	D	0.999392	B	0.02656	0.0	B	0.08055	0.003	T	0.05500	-1.0881	10	0.62326	D	0.03	-6.8698	8.3504	0.32299	0.3363:0.0:0.6637:0.0	.	383	Q9Y6U3	ADSV_HUMAN	H	383;136;136	ENSP00000297029:Q383H;ENSP00000430997:Q136H;ENSP00000390189:Q136H	ENSP00000297029:Q383H	Q	+	3	2	SCIN	12632901	1.000000	0.71417	0.981000	0.43875	0.266000	0.26442	2.089000	0.41672	0.539000	0.28788	0.557000	0.71058	CAG	.	.		0.418	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		T	12666376	G	T	12666376	3	4	40	1	0	0	0	0	1	0	0	0	13920	933	33	3	1179	3	SCIN	7	12666376	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	3875319	12666376	146472287	111	4767										
NPSR1	387129	hgsc.bcm.edu	37	chr7	34888201	34888201	+	Missense_Mutation	SNP	C	C	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcctctgtgatcattcagaaCctgccagcattgaatagtgc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:34888201C>A	ENST00000360581.1	+	8	1079	c.951C>A	c.(949-951)aaC>aaA	p.N317K	NPSR1_ENST00000359791.1_Missense_Mutation_p.N317K|NPSR1_ENST00000381542.1_Missense_Mutation_p.N251K|NPSR1_ENST00000531252.1_Missense_Mutation_p.N306K|NPSR1_ENST00000381539.3_Missense_Mutation_p.N317K	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	317						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	TCATTCAGAACCTGCCAGCAT	0.498																																					p.N317K		.	.											.	NPSR1	.	.	0			c.C951A						.						231	219	223					7																	34888201		2203	4300	6503	SO:0001583	missense	387129	exon8			TCAGAACCTGCCA	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"GPCR / Class A : Neuropeptide receptors : S"	23631	protein-coding gene	gene with protein product		608595	"G protein-coupled receptor 154"	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.951C>A	7.37:g.34888201C>A	ENSP00000353788:p.Asn317Lys	265.0	0.0		225.0	86.0	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	37	CCDS5444.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.767081	0.69878	.	.	ENSG00000187258	ENST00000360581;ENST00000381542;ENST00000359791;ENST00000531252;ENST00000381539;ENST00000334481	T;T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59;-0.59	5.37	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.72590	0.3479	L	0.34521	1.04	0.44098	D	0.996867	D;D;D;P;D;P	0.64830	0.994;0.99;0.993;0.887;0.99;0.775	D;P;P;P;P;P	0.64506	0.926;0.797;0.879;0.669;0.797;0.697	T	0.72161	-0.4374	10	0.44086	T	0.13	-41.3813	9.8026	0.40773	0.0:0.8456:0.0:0.1544	.	251;306;251;317;317;317	B7ZMA2;Q6W5P4-5;Q6W5P4-2;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;.;.;NPSR1_HUMAN	K	317;251;317;306;317;120	ENSP00000353788:N317K;ENSP00000370953:N251K;ENSP00000352839:N317K;ENSP00000433258:N306K;ENSP00000370950:N317K	ENSP00000334093:N120K	N	+	3	2	NPSR1	34854726	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.086000	0.30853	1.513000	0.48852	-0.126000	0.14955	AAC	.	.		0.498	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173		A	34888201	C	A	34888201	3	1	40	1	0	0	0	0	1	0	0	0	10609	506	18	3	981	3	NPSR1	7	34888201	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	22221825	34888201	124250462	112	4768	21	2								
NPSR1	387129	hgsc.bcm.edu	37	chr7	34888202	34888202	+	Missense_Mutation	SNP	C	C	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cctctgtgatcattcagaacCtgccagcattgaatagtgcc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:34888202C>A	ENST00000360581.1	+	8	1080	c.952C>A	c.(952-954)Ctg>Atg	p.L318M	NPSR1_ENST00000359791.1_Missense_Mutation_p.L318M|NPSR1_ENST00000381542.1_Missense_Mutation_p.L252M|NPSR1_ENST00000531252.1_Missense_Mutation_p.L307M|NPSR1_ENST00000381539.3_Missense_Mutation_p.L318M	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	318						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	CATTCAGAACCTGCCAGCATT	0.498																																					p.L318M		.	.											.	NPSR1	.	.	0			c.C952A						.						230	218	222					7																	34888202		2203	4300	6503	SO:0001583	missense	387129	exon8			CAGAACCTGCCAG	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"GPCR / Class A : Neuropeptide receptors : S"	23631	protein-coding gene	gene with protein product		608595	"G protein-coupled receptor 154"	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.952C>A	7.37:g.34888202C>A	ENSP00000353788:p.Leu318Met	263.0	0.0		223.0	81.0	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	37	CCDS5444.1	.	.	.	.	.	.	.	.	.	.	C	18.03	3.533024	0.64972	.	.	ENSG00000187258	ENST00000360581;ENST00000381542;ENST00000359791;ENST00000531252;ENST00000381539;ENST00000334481	T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72	5.37	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47455	D	0.000240	T	0.67906	0.2943	M	0.83603	2.65	0.47659	D	0.999486	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.997;1.0;0.998	D;D;D;D;D;D	0.91635	0.999;0.999;0.998;0.966;0.999;0.974	T	0.71397	-0.4605	10	0.66056	D	0.02	-12.4707	9.491	0.38960	0.0:0.8415:0.0:0.1585	.	252;307;252;318;318;318	B7ZMA2;Q6W5P4-5;Q6W5P4-2;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;.;.;NPSR1_HUMAN	M	318;252;318;307;318;121	ENSP00000353788:L318M;ENSP00000370953:L252M;ENSP00000352839:L318M;ENSP00000433258:L307M;ENSP00000370950:L318M	ENSP00000334093:L121M	L	+	1	2	NPSR1	34854727	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.780000	0.47742	1.493000	0.48517	0.655000	0.94253	CTG	.	.		0.498	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173		A	34888202	C	A	34888202	3	1	40	1	0	0	0	0	1	0	0	0	10609	680	24	3	982	3	NPSR1	7	34888202	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1	34888202	124250461	113	4769	21	2								
DPY19L1	23333	hgsc.bcm.edu	37	chr7	35050986	35050986	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gtccttctcctctggtaaccGtccaacatatcttggtttga	7	12	3	1	rs569347879		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:35050986G>A	ENST00000310974.4	-	5	551	c.407C>T	c.(406-408)aCg>aTg	p.T136M		NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	136						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						TCTGGTAACCGTCCAACATAT	0.348													G|||	1	0.000199681	8e-04	0	5008	,	,		18556	0		0	False		,,,				2504	0				p.T136M		.	.											.	DPY19L1	.	.	0			c.C407T						.						95	87	89					7																	35050986		1831	4084	5915	SO:0001583	missense	23333	exon5			GTAACCGTCCAAC	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.407C>T	7.37:g.35050986G>A	ENSP00000308695:p.Thr136Met	364.0	0.0		368.0	69.0	NM_015283	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	37	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.982340	0.74474	.	.	ENSG00000173852	ENST00000310974	T	0.60040	0.22	5.21	4.33	0.51752	.	0.053328	0.64402	D	0.000001	T	0.70868	0.3273	L	0.56769	1.78	0.48571	D	0.999673	D	0.89917	1.0	D	0.77004	0.989	T	0.72516	-0.4269	10	0.56958	D	0.05	-19.4131	13.0619	0.59012	0.0775:0.0:0.9225:0.0	.	136	Q2PZI1	D19L1_HUMAN	M	136	ENSP00000308695:T136M	ENSP00000308695:T136M	T	-	2	0	DPY19L1	35017511	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	7.712000	0.84684	1.200000	0.43188	-0.143000	0.13931	ACG	.	.		0.348	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			A	35050986	G	A	35050986	3	1	40	1	0	0	0	0	1	0	0	0	4742	1145	40	1	1692	1	DPY19L1	7	35050986	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	162784	35050986	124087677	114	4770										
AUTS2	26053	hgsc.bcm.edu	37	chr7	70255627	70255627	+	Frame_Shift_Del	DEL	A	A	-													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gtctgtggaccctcggcgggAgcacgagcggggaggccacc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:70255627delA	ENST00000342771.4	+	19	3746	c.3425delA	c.(3424-3426)gagfs	p.E1142fs	AUTS2_ENST00000406775.2_Frame_Shift_Del_p.E1118fs	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1142	His-rich.									breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CCTCGGCGGGAGCACGAGCGG	0.682																																					p.E1142fs		.	.											.	AUTS2	.	.	0			c.3424delG						.						18	19	19					7																	70255627		2197	4290	6487	SO:0001589	frameshift_variant	26053	exon19			.	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.3425delA	7.37:g.70255627delA	ENSP00000344087:p.Glu1142fs	64.0	0.0		58.0	13.0	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Frame_Shift_Del	DEL	ENST00000342771.4	37	CCDS5539.1																																																																																			.	.		0.682	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			-	70255627	A	-	70255627	7	5	40	1	0	1	0	1	0	0	0	0	1225	304	11	0	3644	0	AUTS2	7	70255627	Frame_Shift_Del	DEL	A	TCGA-BC-A112-01A-11D-A12Z-10	35204641	70255627	88883036	115	4771										
ELN	2006	hgsc.bcm.edu	37	chr7	73459566	73459566	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cggcaggagctcggttccccGgtgtgggggtgctccctgga	18	12	0	0	rs139718810		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:73459566G>T	ENST00000252034.7	+	10	883	c.484G>T	c.(484-486)Ggt>Tgt	p.G162C	ELN_ENST00000380576.5_Missense_Mutation_p.G162C|ELN_ENST00000320492.7_Missense_Mutation_p.G150C|ELN_ENST00000458204.1_Missense_Mutation_p.G152C|ELN_ENST00000357036.5_Missense_Mutation_p.G167C|ELN_ENST00000320399.6_Missense_Mutation_p.G162C|ELN_ENST00000380584.4_Missense_Mutation_p.G162C|ELN_ENST00000429192.1_Missense_Mutation_p.G167C|ELN_ENST00000414324.1_Missense_Mutation_p.G157C|ELN_ENST00000445912.1_Missense_Mutation_p.G162C|ELN_ENST00000358929.4_Missense_Mutation_p.G162C|ELN_ENST00000380553.4_Intron|ELN_ENST00000380575.4_Missense_Mutation_p.G152C|ELN_ENST00000380562.4_Missense_Mutation_p.G162C	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	162					blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				TCGGTTCCCCGGTGTGGGGGT	0.657			T	PAX5	B-ALL		"Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"																														p.G167C		.	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN	.	.	0			c.G499T						.						48	51	50					7																	73459566		2203	4300	6503	SO:0001583	missense	2006	exon10			TTCCCCGGTGTGG		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"tropoelastin", "supravalvular aortic stenosis", "Williams-Beuren syndrome"	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.484G>T	7.37:g.73459566G>T	ENSP00000252034:p.Gly162Cys	48.0	0.0		59.0	23.0	NM_001081753	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Missense_Mutation	SNP	ENST00000252034.7	37	CCDS5562.2	.	.	.	.	.	.	.	.	.	.	G	14.38	2.517070	0.44763	.	.	ENSG00000049540	ENST00000445912;ENST00000252034;ENST00000358929;ENST00000431562;ENST00000320492;ENST00000438906;ENST00000414324;ENST00000380562;ENST00000380575;ENST00000380584;ENST00000458204;ENST00000357036;ENST00000429192;ENST00000442462;ENST00000380576;ENST00000320399	D;D;D;T;T;T;D;D;D;D;D;D;D;D;D	0.96232	-3.95;-3.95;-3.95;0.91;0.91;0.91;-3.95;-3.95;-3.95;-3.95;-3.95;-3.95;-3.95;-3.95;-3.95	3.75	3.75	0.43078	.	.	.	.	.	D	0.97473	0.9173	M	0.74881	2.28	0.47009	D	0.999284	D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97392	0.9990	9	0.66056	D	0.02	-3.2704	11.2593	0.49074	0.0:0.0:1.0:0.0	.	162;131;150;157;152;162;152;167;167;162;162;162	E7ENM0;E9PBM4;G5E950;G3V0G6;E7EN65;P15502-1;P15502-7;P15502-12;P15502-5;P15502-13;P15502-8;P15502-2	.;.;.;.;.;.;.;.;.;.;.;.	C	162;162;162;140;150;150;157;162;152;162;152;167;167;131;162;162	ENSP00000389857:G162C;ENSP00000252034:G162C;ENSP00000351807:G162C;ENSP00000394549:G140C;ENSP00000315607:G150C;ENSP00000406949:G150C;ENSP00000392575:G157C;ENSP00000369936:G162C;ENSP00000369949:G152C;ENSP00000369958:G162C;ENSP00000403162:G152C;ENSP00000349540:G167C;ENSP00000391129:G167C;ENSP00000369950:G162C;ENSP00000313565:G162C	ENSP00000252034:G162C	G	+	1	0	ELN	73097502	0.999000	0.42202	0.984000	0.44739	0.877000	0.50540	4.954000	0.63631	2.103000	0.63969	0.467000	0.42956	GGT	G|1.000;A|0.000	.		0.657	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501		T	73459566	G	T	73459566	3	4	40	1	0	0	0	0	1	0	0	0	5073	1116	39	1	537	1	ELN	7	73459566	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	3203939	73459566	85679097	116	4772										
SRCRB4D	136853	hgsc.bcm.edu	37	chr7	76029631	76029631	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aggacagccacatcctcgtaGtgaaagcaattgtggacgcc	11	11	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:76029631G>C	ENST00000275560.3	-	4	794	c.447C>G	c.(445-447)caC>caG	p.H149Q	ZP3_ENST00000336517.4_Intron	NM_080744.1	NP_542782.1														autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(9)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21						CATCCTCGTAGTGAAAGCAAT	0.637																																					p.H149Q		.	.											.	SRCRB4D	.	.	0			c.C447G						.						39	41	40					7																	76029631		2203	4299	6502	SO:0001583	missense	136853	exon4			CTCGTAGTGAAAG																												ENST00000275560.3:c.447C>G	7.37:g.76029631G>C	ENSP00000275560:p.His149Gln	184.0	0.0		147.0	51.0	NM_080744		Missense_Mutation	SNP	ENST00000275560.3	37	CCDS5585.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.634900	0.87760	.	.	ENSG00000146700	ENST00000275560	T	0.52526	0.66	5.45	5.45	0.79879	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.102960	0.64402	D	0.000003	T	0.77698	0.4169	M	0.93763	3.455	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.82497	-0.0428	10	0.56958	D	0.05	.	18.644	0.91405	0.0:0.0:1.0:0.0	.	149	Q8WTU2	SRB4D_HUMAN	Q	149	ENSP00000275560:H149Q	ENSP00000275560:H149Q	H	-	3	2	SRCRB4D	75867567	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.800000	0.62524	2.722000	0.93159	0.563000	0.77884	CAC	.	.		0.637	SRCRB4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253001.3			C	76029631	G	C	76029631	3	2	40	1	0	0	0	0	1	0	0	0	15152	1020	36	4	1312	4	SRCRB4D	7	76029631	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	2570065	76029631	83109032	117	4773										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107763585	107763585	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	caaatactcaccaaggtgcaAaaaaagggtcagttgaaatt	8	7	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:107763585A>G	ENST00000388781.3	-	2	108	c.25T>C	c.(25-27)Ttg>Ctg	p.L9L	LAMB4_ENST00000388780.3_Silent_p.L9L|LAMB4_ENST00000418464.1_Silent_p.L9L|LAMB4_ENST00000414450.2_Silent_p.L9L|LAMB4_ENST00000205386.4_Silent_p.L9L	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	9					cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						CCAAGGTGCAAAAAAAGGGTC	0.308																																					p.L9L		.	.											.	LAMB4	.	.	0			c.T25C						.						100	103	102					7																	107763585		2203	4300	6503	SO:0001819	synonymous_variant	22798	exon2			GGTGCAAAAAAAG	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.25T>C	7.37:g.107763585A>G		146.0	0.0		146.0	60.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			.	.		0.308	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		G	107763585	A	G	107763585	2	3	40	1	0	0	0	0	0	0	0	1	8622	11	1	2		2	LAMB4	7	107763585	Silent	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	31733954	107763585	51375078	118	4774										
POT1	25913	hgsc.bcm.edu	37	chr7	124464094	124464094	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gttccatttgtgacattgtaTgacttgatgaagcattccaa	8	7	0	4			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:124464094T>C	ENST00000357628.3	-	19	2425	c.1827A>G	c.(1825-1827)tcA>tcG	p.S609S	POT1_ENST00000393329.1_Silent_p.S478S	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	609					DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47						TGACATTGTATGACTTGATGA	0.308																																					p.S609S	Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)	.	.											.	POT1	.	.	0			c.A1827G						.						168	144	152					7																	124464094		2202	4300	6502	SO:0001819	synonymous_variant	25913	exon19			ATTGTATGACTTG	AK022580	CCDS5793.1	7q31.33	2013-01-21	2013-01-21		ENSG00000128513	ENSG00000128513			17284	protein-coding gene	gene with protein product		606478	"protection of telomeres 1 homolog (S. pombe)"			11349150, 12391173	Standard	NR_003102		Approved	hPot1, DKFZp586D211	uc003vlm.3	Q9NUX5	OTTHUMG00000157194	ENST00000357628.3:c.1827A>G	7.37:g.124464094T>C		262.0	0.0		304.0	115.0	NM_015450	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Silent	SNP	ENST00000357628.3	37	CCDS5793.1	.	.	.	.	.	.	.	.	.	.	T	10.89	1.479418	0.26511	.	.	ENSG00000128513	ENST00000436534	.	.	.	5.95	-5.93	0.02254	.	.	.	.	.	T	0.35508	0.0934	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41556	-0.9502	4	.	.	.	-15.3249	1.4427	0.02357	0.2143:0.0863:0.1816:0.5178	.	.	.	.	V	108	.	.	I	-	1	0	POT1	124251330	0.342000	0.24809	0.954000	0.39281	0.984000	0.73092	-0.808000	0.04515	-0.717000	0.04955	0.533000	0.62120	ATA	.	.		0.308	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1			C	124464094	T	C	124464094	2	2	40	1	0	0	0	0	0	0	0	1	12269	1451	51	2		2	POT1	7	124464094	Silent	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	16700509	124464094	34674569	119	4775										
KIAA1147	57189	hgsc.bcm.edu	37	chr7	141362636	141362636	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gtctgaaatatccggttgttTtgttctaggaaaaacctgca	9	7	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:141362636T>G	ENST00000536163.1	-	9	1187	c.1188A>C	c.(1186-1188)caA>caC	p.Q396H	RP5-894A10.6_ENST00000602609.1_RNA|KIAA1147_ENST00000482493.1_Missense_Mutation_p.Q292H	NM_001080392.1	NP_001073861.1	A4D1U4	LCHN_HUMAN	KIAA1147	396										breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|ovary(1)|skin(1)	12	Melanoma(164;0.0171)					TCCGGTTGTTTTGTTCTAGGA	0.488																																					p.Q396H		.	.											.	KIAA1147	.	.	0			c.A1188C						.						29	29	29					7																	141362636		1846	4086	5932	SO:0001583	missense	57189	exon9			GTTGTTTTGTTCT	AB032973	CCDS47726.1	7q34	2012-10-04			ENSG00000257093	ENSG00000257093			29472	protein-coding gene	gene with protein product							Standard	NM_001080392		Approved	LCHN	uc003vwk.3	A4D1U4	OTTHUMG00000157539	ENST00000536163.1:c.1188A>C	7.37:g.141362636T>G	ENSP00000445768:p.Gln396His	99.0	0.0		118.0	39.0	NM_001080392	Q9ULS3	Missense_Mutation	SNP	ENST00000536163.1	37	CCDS47726.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.414595	0.42817	.	.	ENSG00000257093	ENST00000536163;ENST00000482493	.	.	.	5.3	-7.49	0.01355	.	0.063133	0.64402	D	0.000005	T	0.58235	0.2108	L	0.59436	1.845	0.41751	D	0.989669	B	0.09022	0.002	B	0.08055	0.003	T	0.19257	-1.0311	9	0.51188	T	0.08	-7.8517	18.9371	0.92590	0.0:0.7327:0.0:0.2673	.	396	A4D1U4	LCHN_HUMAN	H	396;292	.	ENSP00000297761:Q396H	Q	-	3	2	KIAA1147	141009105	0.170000	0.23016	0.858000	0.33744	0.970000	0.65996	-0.471000	0.06631	-1.425000	0.01997	-0.326000	0.08463	CAA	.	.		0.488	KIAA1147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349104.1			G	141362636	T	G	141362636	3	3	40	1	0	0	0	0	1	0	0	0	8219	1838	64	5	183	5	KIAA1147	7	141362636	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	16898542	141362636	17776027	120	4776										
OR2A12	346525	hgsc.bcm.edu	37	chr7	143792820	143792821	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggttctgcgttcatcttagtINSggggccgctctgcctggtgc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:143792820_143792821insG	ENST00000408949.2	+	1	680_681	c.620_621insG	c.(619-624)gtggggfs	p.VG207fs		NM_001004135.1	NP_001004135.1	Q8NGT7	O2A12_HUMAN	olfactory receptor, family 2, subfamily A, member 12	207						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)	25	Melanoma(164;0.0783)					TTCATCTTAGTGGGGCCGCTCT	0.54																																					p.V207fs		.	.											.	OR2A12	.	.	0			c.620_621insG						.																																			SO:0001589	frameshift_variant	346525	exon1			.		CCDS43670.1	7q35	2013-09-20	2002-11-13	2002-11-13	ENSG00000221858	ENSG00000221858		"GPCR / Class A : Olfactory receptors"	15082	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 12 pseudogene"	OR2A12P			Standard	NM_001004135		Approved		uc011kty.2	Q8NGT7	OTTHUMG00000157996	ENST00000408949.2:c.624dupG	7.37:g.143792824_143792824dupG	ENSP00000386174:p.Val207fs	133.0	0.0		143.0	10.0	NM_001004135	Q6IF43	Frame_Shift_Ins	INS	ENST00000408949.2	37	CCDS43670.1																																																																																			.	.		0.54	OR2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349969.1			G	143792821	-	G	143792820	7	5	40	1	0	1	1	0	0	0	0	0	10984	1696	59	0	622	0	OR2A12	7	143792820	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	2430184	143792820	15345843	121	4777										
KCNH2	3757	hgsc.bcm.edu	37	chr7	150671893	150671893	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcgcggcgctgcgtgcgcggCccgtgcaggaagtcgcaggt	19	13	0	0	rs529607739		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr7:150671893C>A	ENST00000262186.5	-	2	614	c.213G>T	c.(211-213)ggG>ggT	p.G71G	KCNH2_ENST00000430723.3_Silent_p.G71G	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	71					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GCGTGCGCGGCCCGTGCAGGA	0.672													C|||	1	0.000199681	8e-04	0	5008	,	,		8692	0		0	False		,,,				2504	0				p.G71G	GBM(137;110 1844 13671 20123 45161)	.	.											.	KCNH2	.	.	0			c.G213T						.						16	15	15					7																	150671893		2195	4289	6484	SO:0001819	synonymous_variant	3757	exon2			GCGCGGCCCGTGC	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.213G>T	7.37:g.150671893C>A		21.0	0.0		61.0	17.0	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	37	CCDS5910.1																																																																																			.	.		0.672	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		A	150671893	C	A	150671893	2	1	40	1	0	0	0	0	0	0	0	1	8041	726	26	3		3	KCNH2	7	150671893	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	6879073	150671893	8466770	122	4778										
PDLIM2	64236	hgsc.bcm.edu	37	chr8	22438952	22438952	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctggagacataatcgtggccAtcaacggggaaagcgcggag	15	9	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr8:22438952A>G	ENST00000397760.4	+	3	554	c.154A>G	c.(154-156)Atc>Gtc	p.I52V	PDLIM2_ENST00000397761.2_Missense_Mutation_p.I52V|PDLIM2_ENST00000409417.1_Missense_Mutation_p.I52V|PDLIM2_ENST00000409141.1_Missense_Mutation_p.I52V|PDLIM2_ENST00000339162.7_Missense_Mutation_p.I52V|PDLIM2_ENST00000308354.7_Missense_Mutation_p.I302V|PDLIM2_ENST00000265810.4_Missense_Mutation_p.I52V			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)	52	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		AATCGTGGCCATCAACGGGGA	0.672																																					p.I302V		.	.											.	PDLIM2	.	.	0			c.A904G						.						99	84	89					8																	22438952		2203	4300	6503	SO:0001583	missense	64236	exon3			GTGGCCATCAACG	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270	ENST00000397760.4:c.154A>G	8.37:g.22438952A>G	ENSP00000380867:p.Ile52Val	261.0	0.0		82.0	25.0	NM_021630	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	37		.	.	.	.	.	.	.	.	.	.	A	18.80	3.700131	0.68501	.	.	ENSG00000120913	ENST00000456545;ENST00000308354;ENST00000452226;ENST00000397760;ENST00000339162;ENST00000381194;ENST00000397761;ENST00000436754;ENST00000426493;ENST00000429812;ENST00000409141;ENST00000265810;ENST00000409417	T;T;T;T;T;T;T;T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74	4.99	4.99	0.66335	PDZ/DHR/GLGF (4);	0.133176	0.48286	D	0.000191	T	0.37758	0.1015	L	0.31207	0.915	0.46478	D	0.999061	D;D;D;D	0.63046	0.967;0.967;0.992;0.973	P;P;D;P	0.79108	0.718;0.718;0.992;0.815	T	0.23154	-1.0196	10	0.87932	D	0	-24.5238	12.2156	0.54404	1.0:0.0:0.0:0.0	.	52;52;52;52	Q96JY6-3;Q96JY6-4;Q96JY6;C9JS55	.;.;PDLI2_HUMAN;.	V	52;302;52;52;52;52;52;52;52;52;52;52;52	ENSP00000401992:I52V;ENSP00000312634:I302V;ENSP00000394376:I52V;ENSP00000380867:I52V;ENSP00000342035:I52V;ENSP00000380868:I52V;ENSP00000397738:I52V;ENSP00000392920:I52V;ENSP00000407643:I52V;ENSP00000386868:I52V;ENSP00000265810:I52V;ENSP00000387084:I52V	ENSP00000265810:I52V	I	+	1	0	PDLIM2	22494897	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	4.472000	0.60189	1.868000	0.54150	0.533000	0.62120	ATC	.	.		0.672	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1			G	22438952	A	G	22438952	3	3	40	1	0	0	0	0	1	0	0	0	11689	217	8	2	160	2	PDLIM2	8	22438952	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10		22438952	123925070	123	4779										
ST18	9705	hgsc.bcm.edu	37	chr8	53092714	53092714	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gaccatgtgtttccaaggggCcatcgtcctctgtcctgtca	10	13	2	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr8:53092714C>A	ENST00000276480.7	-	9	928	c.245G>T	c.(244-246)gGc>gTc	p.G82V		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	82					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TTCCAAGGGGCCATCGTCCTC	0.527																																					p.G82V		.	.											.	ST18	.	.	0			c.G245T						.						312	250	271					8																	53092714		2203	4300	6503	SO:0001583	missense	9705	exon9			AAGGGGCCATCGT	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.245G>T	8.37:g.53092714C>A	ENSP00000276480:p.Gly82Val	355.0	0.0		260.0	47.0	NM_014682	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	37	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.806814	0.31961	.	.	ENSG00000147488	ENST00000276480;ENST00000517580	T;T	0.43688	0.95;0.94	5.53	4.65	0.58169	.	0.492703	0.23789	N	0.044546	T	0.31358	0.0794	L	0.47716	1.5	0.20489	N	0.999897	B	0.20671	0.047	B	0.16289	0.015	T	0.17167	-1.0378	10	0.22706	T	0.39	-0.7385	6.5156	0.22246	0.1466:0.7057:0.0:0.1477	.	82	O60284	ST18_HUMAN	V	82	ENSP00000276480:G82V;ENSP00000428521:G82V	ENSP00000276480:G82V	G	-	2	0	ST18	53255267	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.110000	0.15437	1.346000	0.45694	0.655000	0.94253	GGC	.	.		0.527	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			A	53092714	C	A	53092714	3	1	40	1	0	0	0	0	1	0	0	0	15227	739	26	3	2970	3	ST18	8	53092714	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	30653762	53092714	93271308	124	4780										
RP1	6101	hgsc.bcm.edu	37	chr8	55542461	55542462	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gatgggtaaaagaagaaaacINSaaaaaagaattaacttcttg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr8:55542461_55542462insA	ENST00000220676.1	+	4	6167_6168	c.6019_6020insA	c.(6019-6021)caafs	p.Q2007fs		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	2007					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AAGAAGAAAACAAAAAAGAATT	0.302																																					p.Q2007fs	Colon(91;1014 1389 7634 14542 40420)	.	.											.	RP1	.	.	0			c.6019_6020insA						.																																			SO:0001589	frameshift_variant	6101	exon4			.	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.6025dupA	8.37:g.55542467_55542467dupA	ENSP00000220676:p.Gln2007fs	208.0	0.0		188.0	13.0	NM_006269		Frame_Shift_Ins	INS	ENST00000220676.1	37	CCDS6160.1																																																																																			.	.		0.302	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		A	55542462	-	A	55542461	7	5	40	1	0	1	1	0	0	0	0	0	13547	479	17	0	6029	0	RP1	8	55542461	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	2449747	55542461	90821561	125	4781										
TERF1	7013	hgsc.bcm.edu	37	chr8	73951354	73951355	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atttttctacttttaggtacINSaaaaaagaaaaaagaaagca							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr8:73951354_73951355insA	ENST00000276603.5	+	9	1066_1067	c.1043_1044insA	c.(1042-1047)acaaaafs	p.TK348fs	TERF1_ENST00000276602.6_Frame_Shift_Ins_p.TK328fs	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	348	Interaction with RLIM.				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			CTTTTAGGTACAAAAAAGAAAA	0.297																																					p.T348fs		.	.											.	TERF1	.	.	0			c.1043_1044insA						.																																			SO:0001589	frameshift_variant	7013	exon9			.	U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.1049dupA	8.37:g.73951360_73951360dupA	ENSP00000276603:p.Thr348fs	102.0	0.0		135.0	11.0	NM_017489	A7XP29|Q15553|Q8NHT6|Q93029	Frame_Shift_Ins	INS	ENST00000276603.5	37	CCDS6211.1																																																																																			.	.		0.297	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		A	73951355	-	A	73951354	7	5	40	1	0	1	1	0	0	0	0	0	15776	478	17	0	1077	0	TERF1	8	73951354	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	18408893	73951354	72412668	126	4782										
POP1	10940	hgsc.bcm.edu	37	chr8	99148886	99148887	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gagaaaatgctaaaccaattINSaaaaaaattatcggtgatgg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr8:99148886_99148887insA	ENST00000401707.2	+	8	1269_1270	c.1188_1189insA	c.(1189-1191)aaafs	p.K397fs	POP1_ENST00000349693.3_Frame_Shift_Ins_p.K397fs	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	397					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			CTAAACCAATTAAAAAAATTAT	0.371																																					p.I396fs		.	.											.	POP1	.	.	0			c.1188_1189insA						.																																			SO:0001589	frameshift_variant	10940	exon8			.	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"processing of precursors 1"	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.1195dupA	8.37:g.99148893_99148893dupA	ENSP00000385787:p.Lys397fs	139.0	0.0		149.0	12.0	NM_001145860	A8K5W9|Q15037	Frame_Shift_Ins	INS	ENST00000401707.2	37	CCDS6277.1																																																																																			.	.		0.371	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		A	99148887	-	A	99148886	7	5	40	1	0	1	1	0	0	0	0	0	12260	1742	61	0	1214	0	POP1	8	99148886	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	25197532	99148886	47215136	127	4783										
LRP12	29967	hgsc.bcm.edu	37	chr8	105509428	105509429	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atggaaatttcctggttggcINSaaaaaaagcagtttttttca					rs35928649		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr8:105509428_105509429insA	ENST00000276654.5	-	5	1459_1460	c.1351_1352insT	c.(1351-1353)tgcfs	p.C451fs	LRP12_ENST00000424843.2_Frame_Shift_Ins_p.C432fs|LRP12_ENST00000518375.1_5'Flank	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	451	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			TCCTGGTTGGCAAAAAAAGCAG	0.406																																					p.C451fs		.	.											.	LRP12	.	.	0			c.1352_1353insT						.																																			SO:0001589	frameshift_variant	29967	exon5			.	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.1352dupT	8.37:g.105509435_105509435dupA	ENSP00000276654:p.Cys451fs	208.0	0.0		156.0	12.0	NM_013437	A8K137|B4DRQ2	Frame_Shift_Ins	INS	ENST00000276654.5	37	CCDS6303.1																																																																																			.	.		0.406	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		A	105509429	-	A	105509428	7	5	40	1	0	1	1	0	0	0	0	0	8963	710	25	0	1239	0	LRP12	8	105509428	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	6360542	105509428	40854594	128	4784										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121326235	121326235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gggtccacctggacctcaagGaccaagtggtctgtccattc	11	13	2	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr8:121326235G>A	ENST00000297848.3	+	38	4790	c.4520G>A	c.(4519-4521)gGa>gAa	p.G1507E	COL14A1_ENST00000309791.4_Missense_Mutation_p.G1507E|COL14A1_ENST00000247781.3_Missense_Mutation_p.G1412E	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			GGACCTCAAGGACCAAGTGGT	0.473																																					p.G1507E		.	.											.	COL14A1	.	.	0			c.G4520A						.						139	131	133					8																	121326235		2203	4300	6503	SO:0001583	missense	7373	exon38			CTCAAGGACCAAG		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4520G>A	8.37:g.121326235G>A	ENSP00000297848:p.Gly1507Glu	263.0	1.0		204.0	86.0	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.920711	0.92249	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781	D;D;D	0.99353	-5.77;-5.77;-5.77	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.99616	0.9860	H	0.94542	3.55	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.98147	1.0439	10	0.87932	D	0	.	19.1953	0.93686	0.0:0.0:1.0:0.0	.	1507	Q05707	COEA1_HUMAN	E	1507;1507;1412	ENSP00000311809:G1507E;ENSP00000297848:G1507E;ENSP00000247781:G1412E	ENSP00000247781:G1412E	G	+	2	0	COL14A1	121395416	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.536000	0.82023	2.834000	0.97654	0.650000	0.86243	GGA	.	.		0.473	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121326235	G	A	121326235	3	1	40	1	0	0	0	0	1	0	0	0	3673	1174	41	3	4666	3	COL14A1	8	121326235	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	15816807	121326235	25037787	129	4785										
CDC37L1	55664	hgsc.bcm.edu	37	chr9	4706065	4706065	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctctctgcagcttaaactcgGtggtacataaagaagatgat	9	8	1	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr9:4706065G>A	ENST00000381854.3	+	7	1169	c.967G>A	c.(967-969)Gtg>Atg	p.V323M		NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	323	Interaction with Hsp70.|Required for interaction with STIP1.					cytoplasm (GO:0005737)				breast(1)|kidney(1)|lung(2)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		CTTAAACTCGGTGGTACATAA	0.393																																					p.V323M		.	.											.	CDC37L1	.	.	0			c.G967A						.						128	112	117					9																	4706065		2203	4300	6503	SO:0001583	missense	55664	exon7			AACTCGGTGGTAC	AK000497	CCDS6454.1	9p24.1	2013-01-17	2013-01-17		ENSG00000106993	ENSG00000106993			17179	protein-coding gene	gene with protein product		610346	"CDC37 cell division cycle 37 homolog (S. cerevisiae)-like 1", "cell division cycle 37 homolog (S. cerevisiae)-like 1"				Standard	NM_017913		Approved	HARC, FLJ20639, CDC37B	uc003zio.3	Q7L3B6	OTTHUMG00000019465	ENST00000381854.3:c.967G>A	9.37:g.4706065G>A	ENSP00000371278:p.Val323Met	291.0	0.0		269.0	58.0	NM_017913	B1AL70|Q9NWS3|Q9NX16	Missense_Mutation	SNP	ENST00000381854.3	37	CCDS6454.1	.	.	.	.	.	.	.	.	.	.	G	7.721	0.697169	0.15106	.	.	ENSG00000106993	ENST00000381854	T	0.53857	0.6	5.47	4.57	0.56435	.	0.272398	0.35436	N	0.003214	T	0.25382	0.0617	N	0.03608	-0.345	0.26256	N	0.978657	B	0.12013	0.005	B	0.11329	0.006	T	0.09509	-1.0671	10	0.21540	T	0.41	-18.2187	8.0743	0.30708	0.2277:0.0:0.7723:0.0	.	323	Q7L3B6	CD37L_HUMAN	M	323	ENSP00000371278:V323M	ENSP00000371278:V323M	V	+	1	0	CDC37L1	4696065	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.791000	0.38744	2.558000	0.86282	0.655000	0.94253	GTG	.	.		0.393	CDC37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051564.1	NM_017913		A	4706065	G	A	4706065	3	1	40	1	0	0	0	0	1	0	0	0	3071	1261	44	3	993	3	CDC37L1	9	4706065	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10		4706065	136507366	130	4786										
JAK2	3717	hgsc.bcm.edu	37	chr9	5069192	5069193	+	Frame_Shift_Ins	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tccagtttactaaatgctgtINScccccaaagccaaaaggtaa							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr9:5069192_5069193insC	ENST00000381652.3	+	11	1991_1992	c.1497_1498insC	c.(1498-1500)cccfs	p.P500fs	JAK2_ENST00000544510.1_Frame_Shift_Ins_p.P351fs|JAK2_ENST00000539801.1_Frame_Shift_Ins_p.P500fs	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	500					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CTAAATGCTGTCCCCCAAAGCC	0.337		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.C499fs		.	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	.	.	0			c.1497_1498insC						.																																			SO:0001589	frameshift_variant	3717	exon11	Familial Cancer Database		.		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1502dupC	9.37:g.5069197_5069197dupC	ENSP00000371067:p.Pro500fs	195.0	0.0		178.0	12.0	NM_004972	O14636|O75297	Frame_Shift_Ins	INS	ENST00000381652.3	37	CCDS6457.1																																																																																			.	.		0.337	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			C	5069193	-	C	5069192	7	5	40	1	0	1	1	0	0	0	0	0	7947	1673	58	0	1531	0	JAK2	9	5069192	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	363127	5069192	136144239	131	4787										
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88247814	88247815	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agtttcaactccagtgcagcINSaaagcttccctagctgaact							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr9:88247814_88247815insA	ENST00000357081.3	-	14	1921_1922	c.1777_1778insT	c.(1777-1779)tgcfs	p.C593fs	AGTPBP1_ENST00000376109.3_Frame_Shift_Ins_p.C605fs|AGTPBP1_ENST00000376083.3_Frame_Shift_Ins_p.C553fs|AGTPBP1_ENST00000432218.1_Frame_Shift_Ins_p.C431fs|AGTPBP1_ENST00000337006.4_3'UTR			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	593					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						TCCAGTGCAGCAAAGCTTCCCT	0.446																																					p.C553fs		.	.											.	AGTPBP1	.	.	0			c.1658_1659insT						.																																			SO:0001589	frameshift_variant	23287	exon14			.	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.1778dupT	9.37:g.88247817_88247817dupA	ENSP00000349592:p.Cys593fs	199.0	0.0		163.0	12.0	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Frame_Shift_Ins	INS	ENST00000357081.3	37																																																																																				.	.		0.446	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		A	88247815	-	A	88247814	7	5	40	1	0	1	1	0	0	0	0	0	400	710	25	0	1954	0	AGTPBP1	9	88247814	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	83178622	88247814	52965617	132	4788										
FGD3	89846	hgsc.bcm.edu	37	chr9	95796931	95796931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccgccatccccatgtcagatCcccaggtgctgcacctgcag	9	18	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr9:95796931C>T	ENST00000375482.3	+	17	2390	c.1894C>T	c.(1894-1896)Ccc>Tcc	p.P632S	FGD3_ENST00000416701.2_Missense_Mutation_p.P631S|FGD3_ENST00000337352.6_Missense_Mutation_p.P632S|FGD3_ENST00000538555.1_Missense_Mutation_p.P235S	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	632	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						CATGTCAGATCCCCAGGTGCT	0.701																																					p.P632S		.	.											.	FGD3	.	.	0			c.C1894T						.						32	40	38					9																	95796931		2057	4196	6253	SO:0001583	missense	89846	exon17			TCAGATCCCCAGG	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16027	protein-coding gene	gene with protein product			"FGD1 family, member 3"			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.1894C>T	9.37:g.95796931C>T	ENSP00000364631:p.Pro632Ser	112.0	0.0		73.0	22.0	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Missense_Mutation	SNP	ENST00000375482.3	37	CCDS43849.1	.	.	.	.	.	.	.	.	.	.	C	9.537	1.112404	0.20795	.	.	ENSG00000127084	ENST00000375482;ENST00000416701;ENST00000337352;ENST00000538555	T;T;T;T	0.73363	-0.68;-0.69;-0.68;-0.74	4.43	0.192	0.15134	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.423808	0.17658	N	0.166421	T	0.63034	0.2477	L	0.48877	1.53	0.35437	D	0.7945	B;B	0.19200	0.034;0.013	B;B	0.25987	0.056;0.065	T	0.58364	-0.7649	10	0.66056	D	0.02	.	4.2856	0.10853	0.3105:0.5031:0.0:0.1864	.	631;632	F8W7P2;Q5JSP0	.;FGD3_HUMAN	S	632;631;632;235	ENSP00000364631:P632S;ENSP00000413833:P631S;ENSP00000336914:P632S;ENSP00000442560:P235S	ENSP00000336914:P632S	P	+	1	0	FGD3	94836752	0.160000	0.22878	0.066000	0.19879	0.229000	0.25112	0.961000	0.29267	-0.052000	0.13311	0.561000	0.74099	CCC	.	.		0.701	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086		T	95796931	C	T	95796931	3	4	40	1	0	0	0	0	1	0	0	0	5842	855	30	3	1952	3	FGD3	9	95796931	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	7549117	95796931	45416500	133	4789										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767323	105767324	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gaatcagaattaaaacaaggINSaaaaaaagattcaaagaaag							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr9:105767323_105767324insA	ENST00000374798.3	+	5	480_481	c.410_411insA	c.(409-414)ggaaaafs	p.GK137fs	CYLC2_ENST00000487798.1_Frame_Shift_Ins_p.GK137fs	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	137	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				TTAaaacaaggaaaaaaagatt	0.332																																					p.G137fs		.	.											.	CYLC2	.	.	0			c.410_411insA						.																																			SO:0001589	frameshift_variant	1539	exon5			.	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.417dupA	9.37:g.105767330_105767330dupA	ENSP00000420256:p.Gly137fs	244.0	0.0		208.0	13.0	NM_001340	B2R8F4|Q5VVJ9	Frame_Shift_Ins	INS	ENST00000374798.3	37	CCDS35085.1																																																																																			.	.		0.332	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		A	105767324	-	A	105767323	7	5	40	1	0	1	1	0	0	0	0	0	4144	1174	41	0	428	0	CYLC2	9	105767323	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	9970392	105767323	35446108	134	4790										
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134501450	134501451	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atagcagcaaagggcgcgtaINSggggacggatgggatcgggg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr9:134501450_134501451insG	ENST00000372189.3	-	10	1632_1633	c.1509_1510insC	c.(1507-1512)ccctacfs	p.Y504fs	RAPGEF1_ENST00000372195.1_Frame_Shift_Ins_p.Y521fs|RAPGEF1_ENST00000481260.1_5'Flank|RAPGEF1_ENST00000372190.3_Frame_Shift_Ins_p.Y522fs	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	504					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		AAGGGCGCGTAGGGGACGGATG	0.594																																					p.Y522fs		.	.											.	RAPGEF1	.	.	0			c.1564_1565insC						.																																			SO:0001589	frameshift_variant	2889	exon10			.	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1510dupC	9.37:g.134501454_134501454dupG	ENSP00000361263:p.Tyr504fs	199.0	0.0		157.0	10.0	NM_198679	Q5JUE4|Q8IV73	Frame_Shift_Ins	INS	ENST00000372189.3	37	CCDS48047.1																																																																																			.	.		0.594	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		G	134501451	-	G	134501450	7	5	40	1	0	1	1	0	0	0	0	0	13058	420	15	0	1783	0	RAPGEF1	9	134501450	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	28734127	134501450	6711981	135	4791										
TTF1	7270	hgsc.bcm.edu	37	chr9	135277201	135277202	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cctggtgattggactttttcINSttttttttcttagacttgtt							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr9:135277201_135277202insT	ENST00000334270.2	-	2	1046_1047	c.1007_1008insA	c.(1006-1008)aagfs	p.K336fs		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	336	Poly-Lys.				chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		TGGACTTTTTCTTTTTTTTCTT	0.51																																					p.K336fs		.	.											.	TTF1	.	.	0			c.1008_1009insA						.																																			SO:0001589	frameshift_variant	7270	exon2			.	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.1008dupA	9.37:g.135277209_135277209dupT	ENSP00000333920:p.Lys336fs	164.0	0.0		151.0	10.0	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Frame_Shift_Ins	INS	ENST00000334270.2	37	CCDS6948.1																																																																																			.	.		0.51	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344		T	135277202	-	T	135277201	7	5	40	1	0	1	1	0	0	0	0	0	16733	912	32	0	1749	0	TTF1	9	135277201	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	775751	135277201	5936230	136	4792										
FAM107B	83641	hgsc.bcm.edu	37	chr10	14563197	14563197	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgcagcctcagcctaggactCctgggcttgggcgacttctt	12	13	2	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:14563197C>A	ENST00000378470.1	-	4	674	c.388G>T	c.(388-390)Gag>Tag	p.E130*	FAM107B_ENST00000378467.4_Nonsense_Mutation_p.E130*|FAM107B_ENST00000496330.1_Nonsense_Mutation_p.E130*|FAM107B_ENST00000479731.1_Nonsense_Mutation_p.E130*|FAM107B_ENST00000378458.2_Nonsense_Mutation_p.E130*|FAM107B_ENST00000478076.1_Nonsense_Mutation_p.E130*|FAM107B_ENST00000378465.3_Nonsense_Mutation_p.E130*|FAM107B_ENST00000181796.2_Nonsense_Mutation_p.E305*|FAM107B_ENST00000378462.1_Nonsense_Mutation_p.E130*|FAM107B_ENST00000468747.1_Nonsense_Mutation_p.E130*	NM_001282695.1|NM_001282696.1|NM_001282697.1|NM_001282698.1|NM_001282700.1|NM_001282701.1|NM_001282702.1|NM_001282703.1	NP_001269624.1|NP_001269625.1|NP_001269626.1|NP_001269627.1|NP_001269629.1|NP_001269630.1|NP_001269631.1|NP_001269632.1	Q9H098	F107B_HUMAN	family with sequence similarity 107, member B	130					sensory perception of sound (GO:0007605)					breast(7)|kidney(1)|large_intestine(4)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GCCTAGGACTCCTGGGCTTGG	0.527																																					p.E305X		.	.											.	FAM107B	.	.	0			c.G913T						.						157	142	147					10																	14563197		2203	4300	6503	SO:0001587	stop_gained	83641	exon5			AGGACTCCTGGGC	AK127413	CCDS7102.1, CCDS60486.1	10p14	2006-01-17	2006-01-17	2005-11-20	ENSG00000065809	ENSG00000065809			23726	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 45"	C10orf45		11230166	Standard	XM_005252616		Approved	FLJ45505, MGC11034	uc001ina.1	Q9H098	OTTHUMG00000017709	ENST00000378470.1:c.388G>T	10.37:g.14563197C>A	ENSP00000367731:p.Glu130*	200.0	0.0		140.0	30.0	NM_031453	A8K1P4|D3DRT2|Q5T9K7|Q5T9K8|Q6ZSI4	Nonsense_Mutation	SNP	ENST00000378470.1	37		.	.	.	.	.	.	.	.	.	.	C	36	5.790557	0.96945	.	.	ENSG00000065809	ENST00000378470;ENST00000181796;ENST00000468747;ENST00000378467;ENST00000378465;ENST00000378458;ENST00000478076;ENST00000378462;ENST00000378461;ENST00000496330;ENST00000479731;ENST00000468492	.	.	.	5.62	5.62	0.85841	.	0.280557	0.39909	N	0.001232	.	.	.	.	.	.	0.43522	D	0.995794	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-12.8842	11.6661	0.51374	0.0:0.9184:0.0:0.0816	.	.	.	.	X	130;305;130;130;130;130;130;130;130;130;130;130	.	ENSP00000181796:E305X	E	-	1	0	FAM107B	14603203	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.803000	0.38863	2.642000	0.89623	0.563000	0.77884	GAG	.	.		0.527	FAM107B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046899.1	NM_031453		A	14563197	C	A	14563197	4	1	40	1	0	0	0	0	0	1	0	0	5395	864	30	3	11	3	FAM107B	10	14563197	Nonsense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10		14563197	120971550	137	4793										
CUBN	8029	hgsc.bcm.edu	37	chr10	17169924	17169924	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tcttctttgtttttctggatCtaattttagaaaaagaagaa	6	4	4	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:17169924C>G	ENST00000377833.4	-	3	318		c.e3-1		CUBN_ENST00000377823.1_Splice_Site	NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)						cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTTTCTGGATCTAATTTTAGA	0.274																																					.		.	.											.	CUBN	.	.	0			c.253-1G>C						.						114	115	115					10																	17169924		2202	4300	6502	SO:0001630	splice_region_variant	8029	exon4			CTGGATCTAATTT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.253-1G>C	10.37:g.17169924C>G		104.0	0.0		104.0	23.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Splice_Site	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.416664	0.62511	.	.	ENSG00000107611	ENST00000377833;ENST00000377823	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.293	0.90136	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CUBN	17209930	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.321000	0.65846	2.699000	0.92147	0.650000	0.86243	.	.	.		0.274	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	Intron	G	17169924	C	G	17169924	5	3	40	1	0	0	0	0	0	0	1	0	4053	927	32	4	10879	4	CUBN	10	17169924	Splice_Site	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	2606727	17169924	118364823	138	4794										
ST8SIA6	338596	hgsc.bcm.edu	37	chr10	17365101	17365101	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tggatttatagtcacaagatTtgttttactgccaacatctt	6	7	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:17365101T>A	ENST00000377602.4	-	7	765	c.691A>T	c.(691-693)Aat>Tat	p.N231Y		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	231					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						GTCACAAGATTTGTTTTACTG	0.338																																					p.N231Y		.	.											.	ST8SIA6	.	.	0			c.A691T						.						201	181	188					10																	17365101		2203	4300	6503	SO:0001583	missense	338596	exon7			CAAGATTTGTTTT		CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.691A>T	10.37:g.17365101T>A	ENSP00000366827:p.Asn231Tyr	354.0	0.0		266.0	62.0	NM_001004470	B0YJ97|B9EH72|Q5VZH4	Missense_Mutation	SNP	ENST00000377602.4	37	CCDS31158.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.61|16.61	3.169972|3.169972	0.57584|0.57584	.|.	.|.	ENSG00000148488|ENSG00000148488	ENST00000440449|ENST00000377610;ENST00000377602	.|T	.|0.32023	.|1.47	5.12|5.12	3.99|3.99	0.46301|0.46301	.|.	.|0.132733	.|0.64402	.|D	.|0.000002	T|T	0.59128|0.59128	0.2171|0.2171	M|M	0.91354|0.91354	3.2|3.2	0.46376|0.46376	D|D	0.999017|0.999017	.|D	.|0.67145	.|0.996	.|D	.|0.64877	.|0.93	T|T	0.67233|0.67233	-0.5722|-0.5722	5|10	.|0.87932	.|D	.|0	-9.9539|-9.9539	11.0133|11.0133	0.47675|0.47675	0.0:0.073:0.0:0.927|0.0:0.073:0.0:0.927	.|.	.|231	.|P61647	.|SIA8F_HUMAN	I|Y	51|61;231	.|ENSP00000366827:N231Y	.|ENSP00000366827:N231Y	K|N	-|-	2|1	0|0	ST8SIA6|ST8SIA6	17405107|17405107	0.900000|0.900000	0.30661|0.30661	0.950000|0.950000	0.38849|0.38849	0.947000|0.947000	0.59692|0.59692	1.385000|1.385000	0.34408|0.34408	1.086000|1.086000	0.41228|0.41228	0.460000|0.460000	0.39030|0.39030	AAA|AAT	.	.		0.338	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		A	17365101	T	A	17365101	3	1	40	1	0	0	0	0	1	0	0	0	15251	1841	64	4	513	4	ST8SIA6	10	17365101	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	195177	17365101	118169646	139	4795										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27324037	27324038	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	taacttgttcattttgatacINSttttgttccatttccttcat							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:27324037_27324038insT	ENST00000376087.4	-	24	3506_3507	c.3341_3342insA	c.(3340-3342)aagfs	p.K1114fs	ANKRD26_ENST00000436985.2_Frame_Shift_Ins_p.K1130fs|ANKRD26_ENST00000376070.3_Frame_Shift_Ins_p.K671fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1113					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CATTTTGATACTTTTGTTCCAT	0.391																																					p.K1114fs		.	.											.	ANKRD26	.	.	0			c.3342_3343insA						.																																			SO:0001589	frameshift_variant	22852	exon24			.	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3342dupA	10.37:g.27324041_27324041dupT	ENSP00000365255:p.Lys1114fs	159.0	0.0		178.0	12.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Ins	INS	ENST00000376087.4	37	CCDS41499.1																																																																																			.	.		0.391	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			T	27324038	-	T	27324037	7	5	40	1	0	1	1	0	0	0	0	0	654	564	20	0	1834	0	ANKRD26	10	27324037	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	9958936	27324037	108210710	140	4796										
PARD3	56288	hgsc.bcm.edu	37	chr10	34400172	34400172	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	acctgagaaggggaggggggCacatcttgccggaagggccc	18	10	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:34400172C>T	ENST00000374789.3	-	25	4321	c.3996G>A	c.(3994-3996)gtG>gtA	p.V1332V	PARD3_ENST00000545260.1_Silent_p.V1242V|PARD3_ENST00000374794.3_Silent_p.V1220V|PARD3_ENST00000374788.3_Silent_p.V1329V|PARD3_ENST00000350537.4_Silent_p.V1286V|PARD3_ENST00000346874.4_Silent_p.V1295V|PARD3_ENST00000545693.1_Silent_p.V1316V|PARD3_ENST00000374790.3_Silent_p.V1272V	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	1332					apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				GGGAGGGGGGCACATCTTGCC	0.572																																					p.V1332V		.	.											.	PARD3	.	.	0			c.G3996A						.						47	50	49					10																	34400172		2203	4300	6503	SO:0001819	synonymous_variant	56288	exon25			GGGGGGCACATCT	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"atypical PKC isotype-specific interacting protein", "par-3 family cell polarity regulator alpha", "protein phosphatase 1, regulatory subunit 118"	606745	"par-3 (partitioning defective 3, C.elegans) homolog", "par-3 partitioning defective 3 homolog (C. elegans)"			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.3996G>A	10.37:g.34400172C>T		150.0	0.0		101.0	53.0	NM_019619	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Silent	SNP	ENST00000374789.3	37	CCDS7178.1																																																																																			.	.		0.572	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619		T	34400172	C	T	34400172	2	4	40	1	0	0	0	0	0	0	0	1	11452	697	25	3		3	PARD3	10	34400172	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	7076135	34400172	101134575	141	4797										
PCDH15	65217	hgsc.bcm.edu	37	chr10	56128943	56128943	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gagttgtcattcctgtctctCaccactattcgcacttcatg	6	13	4	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:56128943C>T	ENST00000320301.6	-	5	805	c.411G>A	c.(409-411)gtG>gtA	p.V137V	PCDH15_ENST00000395445.1_Silent_p.V137V|PCDH15_ENST00000437009.1_Silent_p.V137V|PCDH15_ENST00000395438.1_Silent_p.V137V|PCDH15_ENST00000395433.1_Silent_p.V115V|PCDH15_ENST00000373957.3_Silent_p.V115V|PCDH15_ENST00000414778.1_Silent_p.V142V|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000361849.3_Silent_p.V137V|PCDH15_ENST00000395446.1_Silent_p.V137V|PCDH15_ENST00000395430.1_Silent_p.V137V|PCDH15_ENST00000373965.2_Silent_p.V137V|PCDH15_ENST00000395432.2_Silent_p.V137V|PCDH15_ENST00000395440.1_Silent_p.V137V|PCDH15_ENST00000373955.1_Silent_p.V137V|PCDH15_ENST00000395442.1_Silent_p.V137V	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	137	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TCCTGTCTCTCACCACTATTC	0.443										HNSCC(58;0.16)																											p.V142V		.	.											.	PCDH15	.	.	0			c.G426A						.						170	128	142					10																	56128943		2203	4300	6503	SO:0001819	synonymous_variant	65217	exon6			GTCTCTCACCACT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.411G>A	10.37:g.56128943C>T		162.0	0.0		136.0	24.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			.	.		0.443	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	56128943	C	T	56128943	2	4	40	1	0	0	0	0	0	0	0	1	11520	813	29	3		3	PCDH15	10	56128943	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	21728771	56128943	79405804	142	4798										
MYPN	84665	hgsc.bcm.edu	37	chr10	69881741	69881741	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cgtgcctgcaaaaaccacaaGagtaaactggaatctcaaaa	7	10	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:69881741G>T	ENST00000358913.5	+	2	1034	c.546G>T	c.(544-546)aaG>aaT	p.K182N	MYPN_ENST00000354393.2_Intron|MYPN_ENST00000373675.3_Missense_Mutation_p.K182N|MYPN_ENST00000540630.1_Missense_Mutation_p.K182N	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	182	Interaction with CARP.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						AAAACCACAAGAGTAAACTGG	0.418																																					p.K182N		.	.											.	MYPN	.	.	0			c.G546T						.						47	48	48					10																	69881741		2203	4300	6503	SO:0001583	missense	84665	exon2			CCACAAGAGTAAA	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.546G>T	10.37:g.69881741G>T	ENSP00000351790:p.Lys182Asn	111.0	0.0		85.0	22.0	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.675451	0.47781	.	.	ENSG00000138347	ENST00000358913;ENST00000540630;ENST00000373675	T;T;T	0.63417	-0.04;-0.04;-0.04	5.91	5.0	0.66597	.	0.099314	0.64402	D	0.000002	T	0.57533	0.2060	L	0.51422	1.61	0.37573	D	0.919524	P;P	0.41848	0.763;0.501	B;B	0.41894	0.369;0.203	T	0.61412	-0.7068	9	.	.	.	.	12.7089	0.57078	0.1294:0.0:0.8706:0.0	.	182;182	Q86TC9-3;Q86TC9	.;MYPN_HUMAN	N	182	ENSP00000351790:K182N;ENSP00000441668:K182N;ENSP00000362779:K182N	.	K	+	3	2	MYPN	69551747	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.702000	0.47102	2.791000	0.96007	0.655000	0.94253	AAG	.	.		0.418	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		T	69881741	G	T	69881741	3	4	40	1	0	0	0	0	1	0	0	0	10107	933	33	3	548	3	MYPN	10	69881741	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	13752798	69881741	65653006	143	4799										
MYST4	23522	hgsc.bcm.edu	37	chr10	76735587	76735588	+	Frame_Shift_Ins	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttcttcacttccacccccaaINScccccatctccggtcagagc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:76735587_76735588insC	ENST00000287239.4	+	8	1981_1982	c.1492_1493insC	c.(1492-1494)accfs	p.T498fs	KAT6B_ENST00000372711.1_Intron|KAT6B_ENST00000372714.1_Intron|KAT6B_ENST00000372724.1_Intron|KAT6B_ENST00000372725.1_Intron	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	498	Negatively regulates HAT activity.|Ser-rich.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										TCCACCCCCAACCCCCATCTCC	0.535																																					p.T498fs		.	.											.	.	.	.	0			c.1492_1493insC						.																																			SO:0001589	frameshift_variant	23522	exon8			.	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.1497dupC	10.37:g.76735592_76735592dupC	ENSP00000287239:p.Thr498fs	130.0	0.0		118.0	10.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Frame_Shift_Ins	INS	ENST00000287239.4	37	CCDS7345.1																																																																																			.	.		0.535	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		C	76735588	-	C	76735587	7	5	40	1	0	1	1	0	0	0	0	0	10114	43	2	0	1514	0	MYST4	10	76735587	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	6853846	76735587	58799160	144	4800										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720665	89720666	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tttaggacaaaatgtttcacINSttttgggtaaatacattctt							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:89720665_89720666insT	ENST00000371953.3	+	8	2173_2174	c.816_817insT	c.(817-819)tttfs	p.F273fs	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	273	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		AAATGTTTCACTTTTGGGTAAA	0.262		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.H272fs		.	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,NS,carcinoma,+2	PTEN	.	.	49	Whole gene deletion(37)|Deletion - Frameshift(9)|Unknown(2)|Deletion - In frame(1)	prostate(16)|central_nervous_system(11)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	c.816_817insT						.																																			SO:0001589	frameshift_variant	5728	exon8	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.820dupT	10.37:g.89720669_89720669dupT	ENSP00000361021:p.Phe273fs	139.0	0.0		218.0	15.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Ins	INS	ENST00000371953.3	37	CCDS31238.1																																																																																			.	.		0.262	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89720666	-	T	89720665	7	5	40	1	0	1	1	0	0	0	0	0	12750	564	20	0	846	0	PTEN	10	89720665	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	12985078	89720665	45814082	145	4801										
CPEB3	22849	hgsc.bcm.edu	37	chr10	93999727	93999727	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atggtcccgttgactggggtGatcccctggaagaagctgtc	14	10	0	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:93999727G>A	ENST00000265997.4	-	2	553	c.381C>T	c.(379-381)atC>atT	p.I127I	CPEB3_ENST00000412050.4_Silent_p.I127I	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	127	Pro-rich.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				TGACTGGGGTGATCCCCTGGA	0.662																																					p.I127I		.	.											.	CPEB3	.	.	0			c.C381T						.						54	48	50					10																	93999727		2203	4300	6503	SO:0001819	synonymous_variant	22849	exon2			TGGGGTGATCCCC	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.381C>T	10.37:g.93999727G>A		76.0	0.0		71.0	18.0	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Silent	SNP	ENST00000265997.4	37	CCDS31246.1																																																																																			.	.		0.662	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		A	93999727	G	A	93999727	2	1	40	1	0	0	0	0	0	0	0	1	3804	1280	45	3		3	CPEB3	10	93999727	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	4279062	93999727	41535020	146	4802										
HELLS	3070	hgsc.bcm.edu	37	chr10	96322576	96322577	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttttttttatagttatgaggINSaaaaaaagaggaagagaaga							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:96322576_96322577insA	ENST00000348459.5	+	6	483_484	c.378_379insA	c.(379-381)aaafs	p.K127fs	HELLS_ENST00000371332.4_Frame_Shift_Ins_p.K127fs|HELLS_ENST00000462057.1_3'UTR|HELLS_ENST00000394036.1_Intron|HELLS_ENST00000394045.1_Frame_Shift_Ins_p.K127fs|HELLS_ENST00000239026.6_3'UTR|HELLS_ENST00000394044.1_Frame_Shift_Ins_p.K127fs	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		taGTTATGAGGAAAAAAAGAGG	0.282																																					p.R126fs		.	.											.	HELLS	.	.	0			c.378_379insA						.																																			SO:0001589	frameshift_variant	3070	exon6			.	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6", "proliferation-associated SNF2-like protein"	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.385dupA	10.37:g.96322583_96322583dupA	ENSP00000239027:p.Lys127fs	240.0	0.0		271.0	19.0	NM_018063		Frame_Shift_Ins	INS	ENST00000348459.5	37	CCDS7434.1																																																																																			.	.		0.282	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		A	96322577	-	A	96322576	7	5	40	1	0	1	1	0	0	0	0	0	7055	1165	41	0	400	0	HELLS	10	96322576	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	2322849	96322576	39212171	147	4803										
RRP12	23223	hgsc.bcm.edu	37	chr10	99116875	99116876	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gtcgacgatcctttctgcggINStttttgtgtcccacctggga							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:99116875_99116876insT	ENST00000370992.4	-	34	3980_3981	c.3869_3870insA	c.(3868-3870)aacfs	p.N1290fs	RRP12_ENST00000536831.1_Frame_Shift_Ins_p.N1008fs|RRP12_ENST00000414986.1_Frame_Shift_Ins_p.N1229fs|RRP12_ENST00000315563.6_Frame_Shift_Ins_p.N1190fs|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1290						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.N1290S(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CCTTTCTGCGGTTTTTGTGTCC	0.639																																					p.N1290fs		.	.											.	RRP12	.	.	1	Substitution - Missense(1)	kidney(1)	c.3870_3871insA						.																																			SO:0001589	frameshift_variant	23223	exon34			.		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"KIAA0690"	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3870dupA	10.37:g.99116880_99116880dupT	ENSP00000360031:p.Asn1290fs	104.0	0.0		118.0	10.0	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Frame_Shift_Ins	INS	ENST00000370992.4	37	CCDS7457.1																																																																																			.	.		0.639	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		T	99116876	-	T	99116875	7	5	40	1	0	1	1	0	0	0	0	0	13701	1252	44	0	27	0	RRP12	10	99116875	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	2794299	99116875	36417872	148	4804										
SMNDC1	10285	hgsc.bcm.edu	37	chr10	112053908	112053908	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aaatccaacagtttttctgaTtattgaggcatcaaatgcct	6	8	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:112053908T>C	ENST00000369603.5	-	6	920	c.717A>G	c.(715-717)taA>taG	p.*239*	SMNDC1_ENST00000369592.1_Silent_p.*239*	NM_005871.3	NP_005862.1	O75940	SPF30_HUMAN	survival motor neuron domain containing 1	0					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	4		Breast(234;0.174)		Epithelial(162;6.86e-05)|all cancers(201;0.00149)|BRCA - Breast invasive adenocarcinoma(275;0.119)		GTTTTTCTGATTATTGAGGCA	0.338																																					p.X239X		.	.											.	SMNDC1	.	.	0			c.A717G						.						116	117	117					10																	112053908		2203	4300	6503	SO:0001819	synonymous_variant	10285	exon6			TTCTGATTATTGA	AF083385	CCDS7565.1	10q23	2013-01-23			ENSG00000119953	ENSG00000119953		"Tudor domain containing"	16900	protein-coding gene	gene with protein product	"splicing factor 30, survival of motor neuron-related", "tudor domain containing 16C"	603519				9731529, 9817934	Standard	NM_005871		Approved	SPF30, SMNR, TDRD16C	uc001kzc.4	O75940	OTTHUMG00000019036	ENST00000369603.5:c.717A>G	10.37:g.112053908T>C		159.0	0.0		132.0	54.0	NM_005871	B2RA27|D3DRB1|Q5T3K6	Silent	SNP	ENST00000369603.5	37	CCDS7565.1																																																																																			.	.		0.338	SMNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050325.2	NM_005871		C	112053908	T	C	112053908	2	2	40	1	0	0	0	0	0	0	0	1	14814	1500	52	2		2	SMNDC1	10	112053908	Silent	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	12937033	112053908	23480839	149	4805										
AFAP1L2	84632	hgsc.bcm.edu	37	chr10	116060312	116060312	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttgtccaggcaggacaacgtCggggaggaggcctgggcctg	18	10	0	0	rs367606214		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr10:116060312C>A	ENST00000304129.4	-	14	1709	c.1680G>T	c.(1678-1680)ccG>ccT	p.P560P	AFAP1L2_ENST00000369271.3_Silent_p.P560P|AFAP1L2_ENST00000491814.1_5'UTR|AFAP1L2_ENST00000545353.1_Silent_p.P613P			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	560					inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		AGGACAACGTCGGGGAGGAGG	0.602																																					p.P560P		.	.											.	AFAP1L2	.	.	0			c.G1680T						.						79	76	77					10																	116060312		2203	4300	6503	SO:0001819	synonymous_variant	84632	exon14			CAACGTCGGGGAG	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"Pleckstrin homology (PH) domain containing"	25901	protein-coding gene	gene with protein product		612420	"KIAA1914"	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.1680G>T	10.37:g.116060312C>A		126.0	0.0		88.0	43.0	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																			.	.		0.602	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550		A	116060312	C	A	116060312	2	1	40	1	0	0	0	0	0	0	0	1	355	871	31	1		1	AFAP1L2	10	116060312	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	4006404	116060312	19474435	150	4806										
PSMD13	5719	hgsc.bcm.edu	37	chr11	244104	244105	+	Intron	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tctcatccgtttttcactttINSgaaaatgagtgcattgatgc					rs373900649		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:244104_244105insG	ENST00000532097.1	+	3	713				PSMD13_ENST00000431206.2_Frame_Shift_Ins_p.E54fs|PSMD13_ENST00000352303.5_Intron	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		TTTTTCACTTTGAAAATGAGTG	0.401																																					p.F53fs		.	.											.	PSMD13	.	.	0			c.159_160insG						.																																			SO:0001627	intron_variant	5719	exon2			.	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"Proteasome (prosome, macropain) subunits"	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.209+29->G	11.37:g.244105_244105dupG		180.0	0.0		154.0	10.0	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Frame_Shift_Ins	INS	ENST00000532097.1	37	CCDS7692.1																																																																																			.	.		0.401	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817		G	244105	-	G	244104	6	5	40	0	1	1	1	0	0	0	0	0	12708	1809	63	0		0	PSMD13	11	244104	Intron	INS	-	TCGA-BC-A112-01A-11D-A12Z-10		244104	134762412	151	4807										
KRTAP5-1	387264	hgsc.bcm.edu	37	chr11	1605983	1605984	+	Frame_Shift_Ins	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcccccacaagaaccacaggINScccccttggagcacccacag					rs59007122		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:1605983_1605984insC	ENST00000382171.2	-	1	529_530	c.496_497insG	c.(496-498)gccfs	p.A166fs	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	166	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AGAACCACAGGCCCCCTTGGAG	0.658																																					p.A166fs		.	.											.	KRTAP5-1	.	.	0			c.497_498insG						.																																			SO:0001589	frameshift_variant	387264	exon1			.	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"Keratin associated proteins"	23596	protein-coding gene	gene with protein product		148022	"keratin, cuticle, ultrahigh sulphur 1-like"	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.497dupG	11.37:g.1605988_1605988dupC	ENSP00000371606:p.Ala166fs	248.0	0.0		135.0	10.0	NM_001005922		Frame_Shift_Ins	INS	ENST00000382171.2	37	CCDS31330.1																																																																																			.	.		0.658	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922		C	1605984	-	C	1605983	7	5	40	1	0	1	1	0	0	0	0	0	8567	1203	42	0	343	0	KRTAP5-1	11	1605983	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	1361879	1605983	133400533	152	4808										
FAM160A2	84067	hgsc.bcm.edu	37	chr11	6238840	6238841	+	Frame_Shift_Ins	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggagatgccctctagcagttINSccccagctccctcctttggc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:6238840_6238841insC	ENST00000449352.2	-	9	2238_2239	c.1975_1976insG	c.(1975-1977)gaafs	p.E659fs	FAM160A2_ENST00000265978.4_Frame_Shift_Ins_p.E673fs|FAM160A2_ENST00000524416.1_Frame_Shift_Ins_p.E659fs|FAM160A2_ENST00000529360.1_5'Flank			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	659					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CTCTAGCAGTTCCCCAGCTCCC	0.634																																					p.E673fs		.	.											.	FAM160A2	.	.	0			c.2018_2019insG						.																																			SO:0001589	frameshift_variant	84067	exon9			.		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 56"	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.1976dupG	11.37:g.6238844_6238844dupC	ENSP00000416918:p.Glu659fs	297.0	0.0		157.0	11.0	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Frame_Shift_Ins	INS	ENST00000449352.2	37	CCDS44530.1																																																																																			.	.		0.634	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127		C	6238841	-	C	6238840	7	5	40	1	0	1	1	0	0	0	0	0	5474	1783	62	0	958	0	FAM160A2	11	6238840	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	4632857	6238840	128767676	153	4809										
APBB1	322	hgsc.bcm.edu	37	chr11	6423899	6423900	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctgccacactgctgcgtccaINSggggccagctcctcctcggt							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:6423899_6423900insG	ENST00000609360.1	-	7	1259_1260	c.1160_1161insC	c.(1159-1161)cctfs	p.P387fs	APBB1_ENST00000389906.2_Frame_Shift_Ins_p.P387fs|APBB1_ENST00000311051.3_Frame_Shift_Ins_p.P387fs|APBB1_ENST00000608645.1_Frame_Shift_Ins_p.P128fs|APBB1_ENST00000609331.1_Frame_Shift_Ins_p.P152fs|APBB1_ENST00000608655.1_Frame_Shift_Ins_p.P167fs|APBB1_ENST00000608704.1_Frame_Shift_Ins_p.P128fs|APBB1_ENST00000529519.1_Intron|APBB1_ENST00000299402.6_Frame_Shift_Ins_p.P387fs|APBB1_ENST00000530885.1_Frame_Shift_Ins_p.P167fs|APBB1_ENST00000608394.1_Frame_Shift_Ins_p.P128fs	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	387	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		TGCTGCGTCCAGGGGCCAGCTC	0.579																																					p.P387fs	GBM(147;1810 2556 5672 39622)	.	.											.	APBB1	.	.	0			c.1161_1162insC						.																																			SO:0001589	frameshift_variant	322	exon7			.	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.1161dupC	11.37:g.6423903_6423903dupG	ENSP00000477213:p.Pro387fs	275.0	0.0		185.0	11.0	NM_001164	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Frame_Shift_Ins	INS	ENST00000609360.1	37																																																																																				.	.		0.579	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164		G	6423900	-	G	6423899	7	5	40	1	0	1	1	0	0	0	0	0	759	175	7	0	1003	0	APBB1	11	6423899	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	185059	6423899	128582617	154	4810										
OR10A2	341276	hgsc.bcm.edu	37	chr11	6891840	6891840	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctgagaaataacgaggtgaaGaatgccctcagcaggacggt	13	8	1	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:6891840G>T	ENST00000307322.4	+	1	917	c.855G>T	c.(853-855)aaG>aaT	p.K285N		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	285						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K285N(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		ACGAGGTGAAGAATGCCCTCA	0.453																																					p.K285N		.	.											.	OR10A2	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G855T						.						103	100	101					11																	6891840		2201	4296	6497	SO:0001583	missense	341276	exon1			GGTGAAGAATGCC	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"GPCR / Class A : Olfactory receptors"	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.855G>T	11.37:g.6891840G>T	ENSP00000303862:p.Lys285Asn	202.0	0.0		127.0	49.0	NM_001004460	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	37	CCDS31415.1	.	.	.	.	.	.	.	.	.	.	g	12.29	1.893894	0.33442	.	.	ENSG00000170790	ENST00000307322	T	0.40756	1.02	4.18	-1.12	0.09808	.	0.000000	0.64402	D	0.000008	T	0.55257	0.1909	M	0.70787	2.145	0.30214	N	0.797439	D	0.89917	1.0	D	0.77557	0.99	T	0.54860	-0.8230	10	0.62326	D	0.03	.	8.0966	0.30833	0.5882:0.0:0.4118:0.0	.	285	Q9H208	O10A2_HUMAN	N	285	ENSP00000303862:K285N	ENSP00000303862:K285N	K	+	3	2	OR10A2	6848416	0.001000	0.12720	0.997000	0.53966	0.347000	0.29111	0.159000	0.16442	-0.063000	0.13065	-0.141000	0.14075	AAG	.	.		0.453	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460		T	6891840	G	T	6891840	3	4	40	1	0	0	0	0	1	0	0	0	10899	933	33	3	857	3	OR10A2	11	6891840	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	467941	6891840	128114676	155	4811										
IPO7	10527	hgsc.bcm.edu	37	chr11	9463685	9463693	+	In_Frame_Del	DEL	AACAAAGAA	AACAAAGAA	-													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gactcacggtcttaatgaagAacaaagaaaacagttacagg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AACAAAGAA	AACAAAGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:9463685_9463693delAACAAAGAA	ENST00000379719.3	+	24	3102_3110	c.2960_2968delAACAAAGAA	c.(2959-2970)gaacaaagaaaa>gaa	p.QRK988del		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	988					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		CTTAATGAAGAACAAAGAAAACAGTTACA	0.354																																					p.987_989del		.	.											.	IPO7	.	.	0			c.2959_2967del						.																																			SO:0001651	inframe_deletion	10527	exon24			.	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.2960_2968delAACAAAGAA	11.37:g.9463685_9463693delAACAAAGAA	ENSP00000369042:p.Gln988_Lys990del	361.0	0.0		311.0	21.0	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	In_Frame_Del	DEL	ENST00000379719.3	37	CCDS31425.1																																																																																			.	.		0.354	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		-	9463693	AACAAAGAA	-	9463685	7	5	40	1	0	1	0	1	0	0	0	0	7806	246	9	0	3054	0	IPO7	11	9463685	In_Frame_Del	DEL	AACAAAGAA	TCGA-BC-A112-01A-11D-A12Z-10	2571845	9463685	125542831	156	4812										
SWAP70	23075	hgsc.bcm.edu	37	chr11	9769515	9769515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcaggagttggagaatcagcGtgtcctgaaggaacaggccc	15	9	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:9769515G>A	ENST00000318950.6	+	10	1569	c.1466G>A	c.(1465-1467)cGt>cAt	p.R489H	SWAP70_ENST00000447399.2_Missense_Mutation_p.R431H	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	489					isotype switching (GO:0045190)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	11				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		GAGAATCAGCGTGTCCTGAAG	0.542																																					p.R489H		.	.											.	SWAP70	.	.	0			c.G1466A						.						105	95	98					11																	9769515		2201	4294	6495	SO:0001583	missense	23075	exon10			ATCAGCGTGTCCT	AB014540	CCDS31426.1, CCDS73257.1	11p15	2013-01-10			ENSG00000133789	ENSG00000133789		"Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	17070	protein-coding gene	gene with protein product		604762				9734811, 10681448	Standard	XM_005252829		Approved	KIAA0640, SWAP-70	uc001mhw.3	Q9UH65	OTTHUMG00000165865	ENST00000318950.6:c.1466G>A	11.37:g.9769515G>A	ENSP00000315630:p.Arg489His	125.0	0.0		96.0	17.0	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	37	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.996842	0.74818	.	.	ENSG00000133789	ENST00000447399;ENST00000318950	T;T	0.24538	1.85;1.85	5.84	4.93	0.64822	.	0.048575	0.85682	D	0.000000	T	0.42517	0.1206	L	0.53249	1.67	0.54753	D	0.999982	D;D	0.64830	0.994;0.987	P;P	0.59012	0.85;0.719	T	0.36744	-0.9735	10	0.66056	D	0.02	-9.208	15.2006	0.73132	0.0673:0.0:0.9327:0.0	.	431;489	E7EMB1;Q9UH65	.;SWP70_HUMAN	H	431;489	ENSP00000399056:R431H;ENSP00000315630:R489H	ENSP00000315630:R489H	R	+	2	0	SWAP70	9726091	1.000000	0.71417	0.845000	0.33349	0.613000	0.37349	5.120000	0.64685	1.493000	0.48517	-0.119000	0.15052	CGT	.	.		0.542	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055		A	9769515	G	A	9769515	3	1	40	1	0	0	0	0	1	0	0	0	15440	1145	40	1	1504	1	SWAP70	11	9769515	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	305830	9769515	125237001	157	4813										
SPTY2D1	144108	hgsc.bcm.edu	37	chr11	18637172	18637173	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agttttccatctgtctcaagINStttttttctcctatgctttc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:18637172_18637173insT	ENST00000336349.5	-	3	883_884	c.648_649insA	c.(646-651)aaacttfs	p.L217fs	SPTY2D1_ENST00000543776.1_5'Flank	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	217								p.K216fs*254(1)		breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						TCTGTCTCAAGTTTTTTTCTCC	0.446																																					p.L217fs		.	.											.	SPTY2D1	.	.	1	Deletion - Frameshift(1)	lung(1)	c.649_650insA						.																																			SO:0001589	frameshift_variant	144108	exon3			.	BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.649dupA	11.37:g.18637179_18637179dupT	ENSP00000337991:p.Leu217fs	294.0	0.0		253.0	16.0	NM_194285	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Frame_Shift_Ins	INS	ENST00000336349.5	37	CCDS31441.1																																																																																			.	.		0.446	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285		T	18637173	-	T	18637172	7	5	40	1	0	1	1	0	0	0	0	0	15141	1029	36	0	1424	0	SPTY2D1	11	18637172	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	8867657	18637172	116369344	158	4814										
OR5D13	390142	hgsc.bcm.edu	37	chr11	55541187	55541187	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agaacttggttgtggaatacAgaaccatctctttctctggt	9	8	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:55541187A>T	ENST00000361760.1	+	1	274	c.274A>T	c.(274-276)Aga>Tga	p.R92*		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	92						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				TGTGGAATACAGAACCATCTC	0.393																																					p.R92X		.	.											.	OR5D13	.	.	0			c.A274T						.						188	179	182					11																	55541187		2200	4296	6496	SO:0001587	stop_gained	390142	exon1			GAATACAGAACCA	BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"GPCR / Class A : Olfactory receptors"	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.274A>T	11.37:g.55541187A>T	ENSP00000354800:p.Arg92*	637.0	0.0		525.0	111.0	NM_001001967	Q6IF68|Q6IFC9	Nonsense_Mutation	SNP	ENST00000361760.1	37	CCDS31507.1	.	.	.	.	.	.	.	.	.	.	A	8.603	0.887303	0.17540	.	.	ENSG00000198877	ENST00000361760	.	.	.	3.52	3.52	0.40303	.	0.000000	0.37178	U	0.002220	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-9.0487	6.57	0.22533	0.8857:0.0:0.1143:0.0	.	.	.	.	X	92	.	ENSP00000354800:R92X	R	+	1	2	OR5D13	55297763	0.000000	0.05858	0.357000	0.25798	0.015000	0.08874	1.189000	0.32114	1.626000	0.50381	0.398000	0.26397	AGA	.	.		0.393	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967		T	55541187	A	T	55541187	4	4	40	1	0	0	0	0	0	1	0	0	11163	180	7	4	276	4	OR5D13	11	55541187	Nonsense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	36904015	55541187	79465329	159	4815										
OR5D16	390144	hgsc.bcm.edu	37	chr11	55606431	55606431	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tattttttcctcaaccacctCtcctttgtggatttctgcta	4	12	3	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:55606431C>A	ENST00000378396.1	+	1	204	c.204C>A	c.(202-204)ctC>ctA	p.L68L		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	68						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				TCAACCACCTCTCCTTTGTGG	0.433																																					p.L68L		.	.											.	OR5D16	.	.	0			c.C204A						.						193	189	190					11																	55606431		2201	4296	6497	SO:0001819	synonymous_variant	390144	exon1			CCACCTCTCCTTT	AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"GPCR / Class A : Olfactory receptors"	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.204C>A	11.37:g.55606431C>A		511.0	0.0		407.0	90.0	NM_001005496	Q6IF65|Q96RB4	Silent	SNP	ENST00000378396.1	37	CCDS31512.1																																																																																			.	.		0.433	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496		A	55606431	C	A	55606431	2	1	40	1	0	0	0	0	0	0	0	1	11165	900	32	3		3	OR5D16	11	55606431	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	65244	55606431	79400085	160	4816										
PYGM	5837	hgsc.bcm.edu	37	chr11	64517976	64517976	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atggtcagagccccgttgagCatgaacttcatgttgccggt	12	10	2	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:64517976C>T	ENST00000164139.3	-	17	2447	c.2049G>A	c.(2047-2049)atG>atA	p.M683I	PYGM_ENST00000377432.3_Missense_Mutation_p.M595I|PYGM_ENST00000462303.1_5'Flank	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	683					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CCCCGTTGAGCATGAACTTCA	0.597																																					p.M683I		.	.											.	PYGM	.	.	0			c.G2049A						.						140	125	130					11																	64517976		2201	4297	6498	SO:0001583	missense	5837	exon17			GTTGAGCATGAAC		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.2049G>A	11.37:g.64517976C>T	ENSP00000164139:p.Met683Ile	177.0	0.0		138.0	24.0	NM_005609	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	37	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996298	0.74818	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.94232	-3.11;-3.38	4.91	4.91	0.64330	.	0.000000	0.64402	D	0.000007	D	0.95683	0.8596	M	0.93375	3.41	0.80722	D	1	B;B	0.28971	0.229;0.137	B;B	0.37780	0.228;0.258	D	0.95288	0.8392	10	0.49607	T	0.09	-42.4242	15.638	0.76970	0.0:1.0:0.0:0.0	.	595;683	A6NDY6;P11217	.;PYGM_HUMAN	I	595;683;664	ENSP00000366650:M595I;ENSP00000164139:M683I	ENSP00000164139:M683I	M	-	3	0	PYGM	64274552	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.616000	0.83018	2.564000	0.86499	0.555000	0.69702	ATG	.	.		0.597	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		T	64517976	C	T	64517976	3	4	40	1	0	0	0	0	1	0	0	0	12877	710	25	3	495	3	PYGM	11	64517976	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	8911545	64517976	70488540	161	4817										
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93822053	93822053	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gataagaactttttacatcgCcgctgaagaagtagaatggg	11	6	0	4			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:93822053C>A	ENST00000315765.9	+	12	2221	c.2213C>A	c.(2212-2214)gCc>gAc	p.A738D		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	738	Plastocyanin-like 5.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TTTTACATCGCCGCTGAAGAA	0.537																																					p.A738D		.	.											.	HEPHL1	.	.	0			c.C2213A						.						95	97	97					11																	93822053		1945	4152	6097	SO:0001583	missense	341208	exon12			ACATCGCCGCTGA	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.2213C>A	11.37:g.93822053C>A	ENSP00000313699:p.Ala738Asp	106.0	0.0		83.0	17.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240220	0.79912	.	.	ENSG00000181333	ENST00000315765	D	0.99080	-5.4	5.66	5.66	0.87406	Cupredoxin (2);	0.147481	0.64402	D	0.000010	D	0.99468	0.9811	M	0.92784	3.345	0.37580	D	0.91978	D	0.76494	0.999	D	0.71414	0.973	D	0.99895	1.1146	10	0.56958	D	0.05	.	19.7508	0.96268	0.0:1.0:0.0:0.0	.	738	Q6MZM0	HPHL1_HUMAN	D	738	ENSP00000313699:A738D	ENSP00000313699:A738D	A	+	2	0	HEPHL1	93461701	0.983000	0.35010	0.994000	0.49952	0.969000	0.65631	2.039000	0.41193	2.671000	0.90904	0.555000	0.69702	GCC	.	.		0.537	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		A	93822053	C	A	93822053	3	1	40	1	0	0	0	0	1	0	0	0	7064	739	26	3	2259	3	HEPHL1	11	93822053	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	29304077	93822053	41184463	162	4818										
GUCY1A2	2977	hgsc.bcm.edu	37	chr11	106810544	106810544	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	taagacagctacaattgcctGggtttgaaacatcagagcat	9	8	1	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:106810544G>T	ENST00000526355.2	-	4	1316	c.848C>A	c.(847-849)cCa>cAa	p.P283Q	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.P283Q|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.P283Q	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	283					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	ACAATTGCCTGGGTTTGAAAC	0.443																																					p.P283Q		.	.											.	GUCY1A2	.	.	0			c.C848A						.						112	110	111					11																	106810544		2201	4298	6499	SO:0001583	missense	2977	exon4			TTGCCTGGGTTTG	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.848C>A	11.37:g.106810544G>T	ENSP00000431245:p.Pro283Gln	118.0	0.0		94.0	22.0	NM_000855	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	37	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	G	11.57	1.677897	0.29783	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.86627	-1.81;-2.15;-1.8	5.45	5.45	0.79879	NO signalling/Golgi transport  ligand-binding domain (1);	0.000000	0.44902	U	0.000408	D	0.87034	0.6077	L	0.27053	0.805	0.49483	D	0.999799	D;D;D	0.71674	0.998;0.987;0.974	P;P;P	0.59761	0.855;0.863;0.497	T	0.83134	-0.0112	10	0.12766	T	0.61	.	18.2758	0.90083	0.0:0.0:1.0:0.0	.	283;283;283	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	Q	283	ENSP00000431245:P283Q;ENSP00000282249:P283Q;ENSP00000344874:P283Q	ENSP00000282249:P283Q	P	-	2	0	GUCY1A2	106315754	1.000000	0.71417	1.000000	0.80357	0.370000	0.29829	5.565000	0.67365	2.553000	0.86117	0.591000	0.81541	CCA	.	.		0.443	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			T	106810544	G	T	106810544	3	4	40	1	0	0	0	0	1	0	0	0	6902	1348	47	3	1370	3	GUCY1A2	11	106810544	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	12988491	106810544	28195972	163	4819										
HSPB2	3316	hgsc.bcm.edu	37	chr11	111784239	111784239	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggcctcgggccgccccagctGgggagggcagcagggcaggg	21	13	0	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:111784239G>A	ENST00000304298.3	+	2	757	c.169G>A	c.(169-171)Ggg>Agg	p.G57R	CRYAB_ENST00000533280.1_5'Flank|CRYAB_ENST00000527950.1_Intron|CRYAB_ENST00000227251.3_5'Flank|CRYAB_ENST00000531198.1_5'Flank|CRYAB_ENST00000533475.1_Intron|CRYAB_ENST00000526180.1_5'Flank|CRYAB_ENST00000533971.1_5'Flank|HSPB2_ENST00000537382.1_Missense_Mutation_p.G57R|HSPB2-C11orf52_ENST00000534100.1_Intron|CRYAB_ENST00000525823.1_5'Flank	NM_001541.3	NP_001532.1	Q16082	HSPB2_HUMAN	heat shock 27kDa protein 2	57					positive regulation of catalytic activity (GO:0043085)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)			large_intestine(2)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_cancers(61;3.75e-11)|all_epithelial(67;2.33e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;3.57e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.57e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.051)		CGCCCCAGCTGGGGAGGGCAG	0.617																																					p.G57R		.	.											.	HSPB2	.	.	0			c.G169A						.						104	114	110					11																	111784239		2201	4297	6498	SO:0001583	missense	3316	exon2			CCAGCTGGGGAGG	U75898	CCDS8352.1	11q22-q23	2011-09-02	2002-08-29			ENSG00000170276		"Heat shock proteins / HSPB"	5247	protein-coding gene	gene with protein product		602179	"heat shock 27kD protein 2"			9344664, 9490724	Standard	NM_001541		Approved	Hs.78846, MKBP	uc001pmg.2	Q16082		ENST00000304298.3:c.169G>A	11.37:g.111784239G>A	ENSP00000302476:p.Gly57Arg	54.0	0.0		50.0	10.0	NM_001541	Q6I9U7	Missense_Mutation	SNP	ENST00000304298.3	37	CCDS8352.1	.	.	.	.	.	.	.	.	.	.	G	9.050	0.991858	0.18966	.	.	ENSG00000170276	ENST00000304298;ENST00000537382	D;D	0.89552	-2.53;-2.53	4.99	3.1	0.35709	HSP20-like chaperone (1);	0.750468	0.12883	N	0.431238	T	0.79902	0.4526	N	0.08118	0	0.30018	N	0.81462	P	0.50156	0.932	P	0.50590	0.645	T	0.71656	-0.4527	10	0.14252	T	0.57	-17.9801	6.1967	0.20553	0.0937:0.0:0.7223:0.1839	.	57	Q16082	HSPB2_HUMAN	R	57	ENSP00000302476:G57R;ENSP00000445585:G57R	ENSP00000302476:G57R	G	+	1	0	HSPB2	111289449	0.999000	0.42202	0.903000	0.35520	0.993000	0.82548	2.715000	0.47210	0.797000	0.33971	0.650000	0.86243	GGG	.	.		0.617	HSPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391669.1			A	111784239	G	A	111784239	3	1	40	1	0	0	0	0	1	0	0	0	7429	1348	47	3	175	3	HSPB2	11	111784239	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	4973695	111784239	23222277	164	4820										
C11orf57	55216	hgsc.bcm.edu	37	chr11	111953315	111953316	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agcagaaaaaaaggtcacacINSaaaaaacagaagaaaagcaa							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:111953315_111953316insA	ENST00000280352.9	+	6	1134_1135	c.498_499insA	c.(499-501)aaafs	p.K167fs	C11orf57_ENST00000532163.1_Frame_Shift_Ins_p.K139fs|TIMM8B_ENST00000507614.1_5'Flank|C11orf57_ENST00000420986.2_Frame_Shift_Ins_p.K167fs|C11orf57_ENST00000393047.3_Frame_Shift_Ins_p.K168fs	NM_001082970.1|NM_018195.3	NP_001076439.1|NP_060665.3	Q6ZUT1	CK057_HUMAN	chromosome 11 open reading frame 57	167	Lys-rich.									autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12		all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521)		AAAGGTCACACAAAAAACAGAA	0.411																																					p.H167fs		.	.											.	C11orf57	.	.	0			c.501_502insA						.																																			SO:0001589	frameshift_variant	55216	exon6			.	BX538107	CCDS8356.2, CCDS41715.1, CCDS73383.1	11q23.1	2006-03-09			ENSG00000150776	ENSG00000150776			25569	protein-coding gene	gene with protein product						12477932	Standard	NM_001082970		Approved	FLJ10726	uc001pmw.4	Q6ZUT1	OTTHUMG00000150213	ENST00000280352.9:c.504dupA	11.37:g.111953321_111953321dupA	ENSP00000339076:p.Lys167fs	305.0	0.0		242.0	15.0	NM_001082969	Q5RL41|Q6IN53|Q7Z357|Q8N2T3	Frame_Shift_Ins	INS	ENST00000280352.9	37	CCDS41715.1																																																																																			.	.		0.411	C11orf57-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316852.1	NM_018195		A	111953316	-	A	111953315	7	5	40	1	0	1	1	0	0	0	0	0	1652	477	17	0	519	0	C11orf57	11	111953315	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	169076	111953315	23053201	165	4821										
TMPRSS4	56649	hgsc.bcm.edu	37	chr11	117979580	117979580	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctgtcttccaggccctgtctCtcaggctccctggtctccct	8	18	4	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:117979580C>T	ENST00000437212.3	+	7	766	c.552C>T	c.(550-552)ctC>ctT	p.L184L	TMPRSS4_ENST00000523251.1_Silent_p.L144L|TMPRSS4_ENST00000534111.1_Silent_p.L182L|TMPRSS4_ENST00000522824.1_Silent_p.L179L|TMPRSS4_ENST00000522307.1_Silent_p.L37L			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	184	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		GGCCCTGTCTCTCAGGCTCCC	0.577																																					p.L184L		.	.											.	TMPRSS4	.	.	0			c.C552T						.						117	97	103					11																	117979580		2200	4296	6496	SO:0001819	synonymous_variant	56649	exon7			CTGTCTCTCAGGC	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"Serine peptidases / Transmembrane"	11878	protein-coding gene	gene with protein product	"transmembrane serine protease 3", "membrane-type serine protease 2", "type II membrane serine protease"	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.552C>T	11.37:g.117979580C>T		107.0	0.0		76.0	40.0	NM_019894	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Silent	SNP	ENST00000437212.3	37	CCDS31684.1																																																																																			.	.		0.577	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894		T	117979580	C	T	117979580	2	4	40	1	0	0	0	0	0	0	0	1	16264	900	32	3		3	TMPRSS4	11	117979580	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	6026265	117979580	17026936	166	4822										
RNF26	79102	hgsc.bcm.edu	37	chr11	119206969	119206969	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gagcaagaggagcggaagaaGtgtgtcatctgccaggacca	15	8	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:119206969G>C	ENST00000311413.4	+	1	1733	c.1137G>C	c.(1135-1137)aaG>aaC	p.K379N	C1QTNF5_ENST00000525657.1_5'Flank|RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	379						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.8e-05)		AGCGGAAGAAGTGTGTCATCT	0.602																																					p.K379N		.	.											.	RNF26	.	.	0			c.G1137C						.						116	98	104					11																	119206969		2199	4295	6494	SO:0001583	missense	79102	exon1			GAAGAAGTGTGTC	AB055622	CCDS8419.1	11q23	2008-07-21				ENSG00000173456		"RING-type (C3HC4) zinc fingers"	14646	protein-coding gene	gene with protein product	"ring finger protein with leucine zipper"	606130				11352657	Standard	NM_032015		Approved	MGC2642	uc001pwh.3	Q9BY78		ENST00000311413.4:c.1137G>C	11.37:g.119206969G>C	ENSP00000312439:p.Lys379Asn	82.0	0.0		61.0	9.0	NM_032015	Q542Y8	Missense_Mutation	SNP	ENST00000311413.4	37	CCDS8419.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.417352	0.42918	.	.	ENSG00000173456	ENST00000311413	T	0.78595	-1.19	5.05	4.06	0.47325	Zinc finger, RING/FYVE/PHD-type (1);	0.071335	0.53938	D	0.000053	T	0.71550	0.3353	N	0.24115	0.695	0.50313	D	0.999866	P	0.51537	0.946	P	0.56127	0.792	T	0.71755	-0.4497	10	0.56958	D	0.05	-12.6746	4.6837	0.12747	0.2563:0.0:0.7437:0.0	.	379	Q9BY78	RNF26_HUMAN	N	379	ENSP00000312439:K379N	ENSP00000312439:K379N	K	+	3	2	RNF26	118712179	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.774000	0.38573	2.619000	0.88677	0.491000	0.48974	AAG	.	.		0.602	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015		C	119206969	G	C	119206969	3	2	40	1	0	0	0	0	1	0	0	0	13501	1020	36	4	1139	4	RNF26	11	119206969	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	1227389	119206969	15799547	167	4823										
OR6X1	390260	hgsc.bcm.edu	37	chr11	123624382	123624383	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ataaataaagggattcagaaINSggggggtgaggatagtattt					rs187417785		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:123624382_123624383insG	ENST00000327930.2	-	1	870_871	c.844_845insC	c.(844-846)cttfs	p.L282fs		NM_001005188.1	NP_001005188.1	Q8NH79	OR6X1_HUMAN	olfactory receptor, family 6, subfamily X, member 1	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)	23		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GGGATTCAGAAGGGGGGTGAGG	0.436																																					p.L282fs		.	.											.	OR6X1	.	.	0			c.845_846insC						.																																			SO:0001589	frameshift_variant	390260	exon1			.	AB065510	CCDS31695.1	11q24.1	2012-08-09			ENSG00000221931	ENSG00000221931		"GPCR / Class A : Olfactory receptors"	14737	protein-coding gene	gene with protein product							Standard	NM_001005188		Approved		uc010rzy.2	Q8NH79	OTTHUMG00000166011	ENST00000327930.2:c.845dupC	11.37:g.123624388_123624388dupG	ENSP00000333724:p.Leu282fs	168.0	0.0		144.0	10.0	NM_001005188	B9EGW9|Q6IFA0	Frame_Shift_Ins	INS	ENST00000327930.2	37	CCDS31695.1																																																																																			.	.		0.436	OR6X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387436.1	NM_001005188		G	123624383	-	G	123624382	7	5	40	1	0	1	1	0	0	0	0	0	11221	72	3	0	95	0	OR6X1	11	123624382	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	4417413	123624382	11382134	168	4824										
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128842442	128842443	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctgggaaggcggagggggaaINSggggacgattagttctgtgc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr11:128842442_128842443insG	ENST00000310343.9	-	21	3915_3916	c.3916_3917insC	c.(3916-3918)cttfs	p.L1306fs	ARHGAP32_ENST00000392657.3_Frame_Shift_Ins_p.L957fs|ARHGAP32_ENST00000527272.1_Frame_Shift_Ins_p.L957fs|ARHGAP32_ENST00000524655.1_3'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1306	Poly-Pro.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						CGGAGGGGGAAGGGGACGATTA	0.53																																					p.L1306fs		.	.											.	ARHGAP32	.	.	0			c.3917_3918insC						.																																			SO:0001589	frameshift_variant	9743	exon21			.	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.3917dupC	11.37:g.128842446_128842446dupG	ENSP00000310561:p.Leu1306fs	227.0	0.0		169.0	10.0	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Frame_Shift_Ins	INS	ENST00000310343.9	37	CCDS44769.1																																																																																			.	.		0.53	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		G	128842443	-	G	128842442	7	5	40	1	0	1	1	0	0	0	0	0	881	72	3	0	2354	0	ARHGAP32	11	128842442	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	5218060	128842442	6164074	169	4825										
RAD52	5893	hgsc.bcm.edu	37	chr12	1023279	1023279	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccacttttcagagttgtcttCaagagtctctacagaggtca	8	10	5	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:1023279C>G	ENST00000358495.3	-	11	1114	c.976G>C	c.(976-978)Gaa>Caa	p.E326Q	RAD52_ENST00000539046.1_Missense_Mutation_p.E249Q|RAD52_ENST00000430095.2_Missense_Mutation_p.E326Q|RAD52_ENST00000535376.1_5'UTR	NM_134424.2	NP_602296.2	P43351	RAD52_HUMAN	RAD52 homolog (S. cerevisiae)	326					DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)			GAGTTGTCTTCAAGAGTCTCT	0.493								Homologous recombination																													p.E326Q		.	.											.	RAD52	.	.	0			c.G976C						.						67	62	63					12																	1023279		1885	4122	6007	SO:0001583	missense	5893	exon11			TGTCTTCAAGAGT		CCDS8507.2	12p13-p12.2	2008-08-05	2001-11-28		ENSG00000002016	ENSG00000002016			9824	protein-coding gene	gene with protein product		600392	"RAD52 (S. cerevisiae) homolog"			7774919, 18313388	Standard	XM_005253721		Approved		uc001qis.1	P43351	OTTHUMG00000090361	ENST00000358495.3:c.976G>C	12.37:g.1023279C>G	ENSP00000351284:p.Glu326Gln	144.0	0.0		125.0	19.0	NM_134424	Q13205|Q9Y5T7|Q9Y5T8|Q9Y5T9	Missense_Mutation	SNP	ENST00000358495.3	37	CCDS8507.2	.	.	.	.	.	.	.	.	.	.	C	9.081	0.999376	0.19121	.	.	ENSG00000002016	ENST00000358495;ENST00000430095;ENST00000539046	T;T;T	0.35048	1.75;1.75;1.33	4.87	1.67	0.24075	.	0.611865	0.15390	N	0.264861	T	0.24509	0.0594	L	0.46157	1.445	0.18873	N	0.999987	P	0.40144	0.704	B	0.35353	0.201	T	0.10497	-1.0627	10	0.17369	T	0.5	-8.9029	7.4817	0.27408	0.0:0.663:0.0:0.337	.	326	P43351	RAD52_HUMAN	Q	326;326;249	ENSP00000351284:E326Q;ENSP00000387901:E326Q;ENSP00000445245:E249Q	ENSP00000351284:E326Q	E	-	1	0	RAD52	893540	0.004000	0.15560	0.728000	0.30774	0.531000	0.34715	-0.092000	0.11129	0.582000	0.29556	0.561000	0.74099	GAA	.	.		0.493	RAD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206733.2	NM_134424		G	1023279	C	G	1023279	3	3	40	1	0	0	0	0	1	0	0	0	13006	835	29	4	288	4	RAD52	12	1023279	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10		1023279	132828616	170	4826										
CLECL1	160365	hgsc.bcm.edu	37	chr12	9885713	9885713	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	caaagaaacttctgataagtAaattgagatggcaaatttcc	7	6	1	3	rs200639830		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:9885713A>T	ENST00000327839.3	-	1	182	c.148T>A	c.(148-150)Tac>Aac	p.Y50N		NM_172004.3	NP_742001.1	Q8IZS7	CLCL1_HUMAN	C-type lectin-like 1	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|kidney(1)|large_intestine(4)|lung(3)	9						TCTGATAAGTAAATTGAGATG	0.403																																					p.Y50N		.	.											.	CLECL1	.	.	0			c.T148A						.						77	80	79					12																	9885713		2203	4300	6503	SO:0001583	missense	160365	exon1			ATAAGTAAATTGA	AF518873	CCDS8603.1, CCDS73441.1	12p13.31	2007-06-21				ENSG00000184293			24462	protein-coding gene	gene with protein product	"dendritic cell associated lectin 1"	607467				12421943	Standard	NM_172004		Approved	DCAL1	uc001qwi.3	Q8IZS7		ENST00000327839.3:c.148T>A	12.37:g.9885713A>T	ENSP00000331766:p.Tyr50Asn	145.0	0.0		144.0	7.0	NM_001267701		Missense_Mutation	SNP	ENST00000327839.3	37	CCDS8603.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.915|6.915	0.538458|0.538458	0.13250|0.13250	.|.	.|.	ENSG00000184293|ENSG00000184293	ENST00000542530|ENST00000327839	.|T	.|0.56275	.|0.47	1.86|1.86	0.666|0.666	0.17901|0.17901	.|.	.|.	.|.	.|.	.|.	T|T	0.21590|0.21590	0.0520|0.0520	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	.|P	.|0.51147	.|0.942	.|B	.|0.39217	.|0.294	T|T	0.08027|0.08027	-1.0742|-1.0742	5|8	.|.	.|.	.|.	.|.	3.7406|3.7406	0.08528|0.08528	0.7983:0.0:0.2017:0.0|0.7983:0.0:0.2017:0.0	.|.	.|50	.|Q8IZS7	.|CLCL1_HUMAN	L|N	1|50	.|ENSP00000331766:Y50N	.|.	F|Y	-|-	3|1	2|0	CLECL1|CLECL1	9776980|9776980	0.002000|0.002000	0.14202|0.14202	0.001000|0.001000	0.08648|0.08648	0.004000|0.004000	0.04260|0.04260	1.812000|1.812000	0.38952|0.38952	0.170000|0.170000	0.19704|0.19704	-0.463000|-0.463000	0.05309|0.05309	TTT|TAC	.	.		0.403	CLECL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399815.1	NM_172004		T	9885713	A	T	9885713	3	4	40	1	0	0	0	0	1	0	0	0	3525	362	13	4	363	4	CLECL1	12	9885713	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	8862434	9885713	123966182	171	4827										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19427544	19427545	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	accagagatccaaaacaatcINSaaaaaaacaaggaaatgagc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:19427544_19427545insA	ENST00000299275.6	+	10	928_929	c.922_923insA	c.(922-924)caafs	p.Q308fs	PLEKHA5_ENST00000309364.4_Frame_Shift_Ins_p.Q308fs|PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000359180.3_Frame_Shift_Ins_p.Q308fs|PLEKHA5_ENST00000355397.3_Frame_Shift_Ins_p.Q308fs|PLEKHA5_ENST00000317589.4_Frame_Shift_Ins_p.Q308fs|PLEKHA5_ENST00000543806.1_Frame_Shift_Ins_p.Q200fs|PLEKHA5_ENST00000538714.1_Frame_Shift_Ins_p.Q308fs|PLEKHA5_ENST00000539256.1_Frame_Shift_Ins_p.Q66fs|PLEKHA5_ENST00000424268.1_Frame_Shift_Ins_p.Q200fs|PLEKHA5_ENST00000429027.2_Frame_Shift_Ins_p.Q314fs	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	308					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					CCAAAACAATCAAAAAAACAAG	0.327																																					p.Q314fs	Pancreas(196;329 2193 11246 14234 19524)	.	.											.	PLEKHA5	.	.	0			c.940_941insA						.																																			SO:0001589	frameshift_variant	54477	exon11			.	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.929dupA	12.37:g.19427551_19427551dupA	ENSP00000299275:p.Gln308fs	133.0	0.0		145.0	10.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Frame_Shift_Ins	INS	ENST00000299275.6	37	CCDS8682.1																																																																																			.	.		0.327	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		A	19427545	-	A	19427544	7	5	40	1	0	1	1	0	0	0	0	0	12068	827	29	0	960	0	PLEKHA5	12	19427544	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	9541831	19427544	114424351	172	4828										
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21329794	21329794	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgtttaattaatcaaattttAtcactcaatagagcatcacc	3	8	4	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:21329794A>G	ENST00000256958.2	+	5	540	c.444A>G	c.(442-444)ttA>ttG	p.L148L		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	148					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	ATCAAATTTTATCACTCAATA	0.279																																					p.L148L		.	.											.	SLCO1B1	.	.	0			c.A444G						.						76	77	76					12																	21329794		2203	4288	6491	SO:0001819	synonymous_variant	10599	exon5			AATTTTATCACTC		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.444A>G	12.37:g.21329794A>G		274.0	0.0		266.0	80.0	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Silent	SNP	ENST00000256958.2	37	CCDS8685.1																																																																																			.	.		0.279	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		G	21329794	A	G	21329794	2	3	40	1	0	0	0	0	0	0	0	1	14738	446	16	2		2	SLCO1B1	12	21329794	Silent	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	1902250	21329794	112522101	173	4829										
SLCO1A2	6579	hgsc.bcm.edu	37	chr12	21453394	21453395	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cctttggaagtgtgttgggcINSaaaaagaaaaaaggaatggc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:21453394_21453395insA	ENST00000307378.6	-	9	1517_1518	c.797_798insT	c.(796-798)ttgfs	p.L266fs	SLCO1A2_ENST00000458504.1_Frame_Shift_Ins_p.L134fs|SLCO1A2_ENST00000537524.1_Frame_Shift_Ins_p.L134fs|SLCO1A2_ENST00000390670.3_Frame_Shift_Ins_p.L264fs|SLCO1A2_ENST00000452078.1_Frame_Shift_Ins_p.L266fs	NM_134431.3	NP_602307.1	P46721	SO1A2_HUMAN	solute carrier organic anion transporter family, member 1A2	266					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(6)|upper_aerodigestive_tract(1)	48					Aminohippurate(DB00345)|Atorvastatin(DB01076)|Bumetanide(DB00887)|Chlorambucil(DB00291)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Enalapril(DB00584)|Erythromycin(DB00199)|Estradiol(DB00783)|Estriol(DB04573)|Estrone(DB00655)|Fexofenadine(DB00950)|Glyburide(DB01016)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Indinavir(DB00224)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Mirabegron(DB08893)|Naloxone(DB01183)|Naproxen(DB00788)|Nelfinavir(DB00220)|Ouabain(DB01092)|Pravastatin(DB00175)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rocuronium(DB00728)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Simvastatin(DB00641)|Spironolactone(DB00421)|Sumatriptan(DB00669)|Tauroursodeoxycholic acid(DB08834)|Testosterone(DB00624)|Tolbutamide(DB01124)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)	GTGTGTTGGGCAAAAAGAAAAA	0.406																																					p.L266fs		.	.											.	SLCO1A2	.	.	0			c.798_799insT						.																																			SO:0001589	frameshift_variant	6579	exon9			.		CCDS8686.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000084453	ENSG00000084453		"Solute carriers"	10956	protein-coding gene	gene with protein product		602883	"solute carrier family 21 (organic anion transporter), member 3"	SLC21A3		9007731	Standard	NM_134431		Approved	OATP, OATP1A2, OATP-A	uc001rer.3	P46721	OTTHUMG00000156259	ENST00000307378.6:c.798dupT	12.37:g.21453399_21453399dupA	ENSP00000305974:p.Leu266fs	188.0	0.0		214.0	13.0	NM_134431	Q9UGP7|Q9UL38	Frame_Shift_Ins	INS	ENST00000307378.6	37	CCDS8686.1																																																																																			.	.		0.406	SLCO1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343648.3	NM_021094		A	21453395	-	A	21453394	7	5	40	1	0	1	1	0	0	0	0	0	14737	709	25	0	1246	0	SLCO1A2	12	21453394	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	123600	21453394	112398501	174	4830										
BICD1	636	hgsc.bcm.edu	37	chr12	32490708	32490708	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cctgcatagtcagggcccacAgacacccaacattcgggtca	9	15	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:32490708A>T	ENST00000281474.5	+	7	2631	c.2528A>T	c.(2527-2529)cAg>cTg	p.Q843L	BICD1_ENST00000548411.1_Intron	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	843					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			CAGGGCCCACAGACACCCAAC	0.512																																					p.Q843L		.	.											.	BICD1	.	.	0			c.A2528T						.						113	105	108					12																	32490708		2203	4300	6503	SO:0001583	missense	636	exon7			GCCCACAGACACC	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.2528A>T	12.37:g.32490708A>T	ENSP00000281474:p.Gln843Leu	98.0	0.0		105.0	18.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	37	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.981936	0.34942	.	.	ENSG00000151746	ENST00000281474	T	0.46063	0.88	4.9	4.9	0.64082	.	0.454037	0.21742	N	0.069815	T	0.21631	0.0521	N	0.08118	0	0.80722	D	1	P	0.43477	0.808	B	0.36464	0.225	T	0.06570	-1.0819	9	.	.	.	.	13.2645	0.60125	1.0:0.0:0.0:0.0	.	843	Q96G01	BICD1_HUMAN	L	843	ENSP00000281474:Q843L	.	Q	+	2	0	BICD1	32381975	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.136000	0.58004	2.060000	0.61445	0.482000	0.46254	CAG	.	.		0.512	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		T	32490708	A	T	32490708	3	4	40	1	0	0	0	0	1	0	0	0	1428	188	7	4	2554	4	BICD1	12	32490708	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	11037314	32490708	101361187	175	4831										
FGD4	121512	hgsc.bcm.edu	37	chr12	32760995	32760995	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aaggactatctaaggaaattGcctcctgattccctggactg	9	10	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:32760995G>A	ENST00000427716.2	+	8	1522	c.1098G>A	c.(1096-1098)ttG>ttA	p.L366L	FGD4_ENST00000534526.2_Silent_p.L503L|FGD4_ENST00000381025.3_Silent_p.L118L|FGD4_ENST00000266482.3_Silent_p.L118L|FGD4_ENST00000525053.1_Silent_p.L478L|FGD4_ENST00000531134.1_Silent_p.L451L|FGD4_ENST00000546442.1_Silent_p.L273L	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	366	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					TAAGGAAATTGCCTCCTGATT	0.418																																					p.L366L		.	.											.	FGD4	.	.	0			c.G1098A						.						165	163	164					12																	32760995		2203	4300	6503	SO:0001819	synonymous_variant	121512	exon8			GAAATTGCCTCCT	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.1098G>A	12.37:g.32760995G>A		344.0	0.0		328.0	109.0	NM_139241	Q6ULS2|Q8TCP6	Silent	SNP	ENST00000427716.2	37	CCDS8727.1																																																																																			.	.		0.418	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		A	32760995	G	A	32760995	2	1	40	1	0	0	0	0	0	0	0	1	5843	1310	46	3		3	FGD4	12	32760995	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	270287	32760995	101090900	176	4832										
ABCD2	225	hgsc.bcm.edu	37	chr12	40013265	40013266	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggtaagctgctgcttttttcINSttcccgtggccagattgctt							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:40013265_40013266insT	ENST00000308666.3	-	1	287_288	c.152_153insA	c.(151-153)aagfs	p.K51fs		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	51	Interaction with PEX19.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						CTGCTTTTTTCTTCCCGTGGCC	0.5																																					p.K51fs		.	.											.	ABCD2	.	.	0			c.153_154insA						.																																			SO:0001589	frameshift_variant	225	exon1			.	U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.153dupA	12.37:g.40013267_40013267dupT	ENSP00000310688:p.Lys51fs	163.0	0.0		166.0	10.0	NM_005164	B2RAM3|Q13210|Q2M3H9	Frame_Shift_Ins	INS	ENST00000308666.3	37	CCDS8734.1																																																																																			.	.		0.5	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164		T	40013266	-	T	40013265	7	5	40	1	0	1	1	0	0	0	0	0	61	912	32	0	2109	0	ABCD2	12	40013265	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	7252270	40013265	93838630	177	4833										
PLEKHA9	51054	hgsc.bcm.edu	37	chr12	45567240	45567241	+	RNA	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccccatttttcacttctgtcINSaaaaatcccttcaaaaattt							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:45567240_45567241insA	ENST00000256692.5	-	0	1444_1445					NR_037144.1		O95397	PKHA9_HUMAN	pleckstrin homology domain containing, family A member 8 pseudogene 1							cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TCACTTCTGTCAAAAATCCCTT	0.485																																					.		.	.											.	PLEKHA8P1	.	.	0			.						.																																					51054	.			.	AF103731		12q12	2010-11-24	2010-11-24	2010-11-24	ENSG00000134297	ENSG00000134297			30222	pseudogene	pseudogene	"putative glycolipid transfer protein"		"pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 9"	PLEKHA9		12477932	Standard	NR_037144		Approved	FLJ14156	uc001rom.2	O95397			12.37:g.45567245_45567245dupA		180.0	0.0		163.0	10.0	.		RNA	INS	ENST00000256692.5	37																																																																																				.	.		0.485	PLEKHA8P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000404814.1	NR_037144		A	45567241	-	A	45567240	6	5	40	0	1	1	1	0	0	0	0	0	12072	825	29	0		0	PLEKHA9	12	45567240	RNA	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	5553975	45567240	88284655	178	4834										
ARID2	196528	hgsc.bcm.edu	37	chr12	46246025	46246026	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gagatggttctcatttaagcINSaaaaacattccaaatcataa							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:46246025_46246026insA	ENST00000334344.6	+	15	4291_4292	c.4119_4120insA	c.(4120-4122)aaafs	p.K1374fs	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000422737.1_Frame_Shift_Ins_p.K1225fs|ARID2_ENST00000444670.1_Frame_Shift_Ins_p.K984fs	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1374					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CTCATTTAAGCAAAAACATTCC	0.351			"N, S, F"		hepatocellular carcinoma																																p.S1373fs		.	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	.	.	0			c.4119_4120insA						.																																			SO:0001589	frameshift_variant	196528	exon15			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4124dupA	12.37:g.46246030_46246030dupA	ENSP00000335044:p.Lys1374fs	165.0	0.0		198.0	12.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Ins	INS	ENST00000334344.6	37	CCDS31783.1																																																																																			.	.		0.351	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46246026	-	A	46246025	7	5	40	1	0	1	1	0	0	0	0	0	915	709	25	0	4177	0	ARID2	12	46246025	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	678785	46246025	87605870	179	4835										
MLL2	8085	hgsc.bcm.edu	37	chr12	49425625	49425626	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tcctggtggggcagggagccINSggggtgggccctgaggtcga					rs576644174|rs542331667	byFrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:49425625_49425626insG	ENST00000301067.7	-	39	12861_12862	c.12862_12863insC	c.(12862-12864)cggfs	p.R4288fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4288	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GGCAGGGAGCCGGGGTGGGCCC	0.658																																					p.R4288fs		.	.											.	MLL2	.	.	0			c.12863_12864insC						.																																			SO:0001589	frameshift_variant	8085	exon39			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.12863dupC	12.37:g.49425629_49425629dupG	ENSP00000301067:p.Arg4288fs	239.0	0.0		165.0	11.0	NM_003482	O14687	Frame_Shift_Ins	INS	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.		0.658	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49425626	-	G	49425625	7	5	40	1	0	1	1	0	0	0	0	0	9630	652	23	0	3814	0	MLL2	12	49425625	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	3179600	49425625	84426270	180	4836										
HOXC10	3226	hgsc.bcm.edu	37	chr12	54382990	54382990	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aacaccacaggaaattggctGacagcaaagagcggaaggaa	12	8	0	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:54382990G>A	ENST00000303460.4	+	2	863	c.789G>A	c.(787-789)ctG>ctA	p.L263L	RP11-834C11.12_ENST00000513209.1_Intron|HOXC10_ENST00000511575.1_3'UTR|MIR196A2_ENST00000385189.1_RNA	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	263					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|neuromuscular process (GO:0050905)|positive regulation of cell proliferation (GO:0008284)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(3)|lung(14)|pancreas(1)	20						GAAATTGGCTGACAGCAAAGA	0.428											OREG0021882	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L263L		.	.											.	HOXC10	.	.	0			c.G789A						.						65	63	63					12																	54382990		2203	4300	6503	SO:0001819	synonymous_variant	3226	exon2			TTGGCTGACAGCA		CCDS8868.1	12q13.13	2011-06-20	2005-12-22		ENSG00000180818	ENSG00000180818		"Homeoboxes / ANTP class : HOXL subclass"	5122	protein-coding gene	gene with protein product		605560	"homeo box C10"	HOX3I		1358459	Standard	NM_017409		Approved		uc001sen.3	Q9NYD6	OTTHUMG00000160031	ENST00000303460.4:c.789G>A	12.37:g.54382990G>A		220.0	0.0	999	200.0	25.0	NM_017409	O15219|O15220|Q9BVD5	Silent	SNP	ENST00000303460.4	37	CCDS8868.1																																																																																			.	.		0.428	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2			A	54382990	G	A	54382990	2	1	40	1	0	0	0	0	0	0	0	1	7318	1277	45	3		3	HOXC10	12	54382990	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	4957365	54382990	79468905	181	4837										
HOXC8	3224	hgsc.bcm.edu	37	chr12	54404963	54404963	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctttaatccttatttgacacGaaaacgtcggattgaagtct	7	8	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:54404963G>C	ENST00000040584.4	+	2	764	c.527G>C	c.(526-528)cGa>cCa	p.R176P	RP11-834C11.12_ENST00000513209.1_Intron	NM_022658.3	NP_073149.1	P31273	HXC8_HUMAN	homeobox C8	176					anterior/posterior pattern specification (GO:0009952)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	8						TATTTGACACGAAAACGTCGG	0.488																																					p.R176P	GBM(197;701 2226 7002 18822 41696)	.	.											.	HOXC8	.	.	0			c.G527C						.						101	96	98					12																	54404963		2203	4300	6503	SO:0001583	missense	3224	exon2			TGACACGAAAACG	X99680	CCDS8870.1	12q13.13	2011-06-20	2005-12-22			ENSG00000037965		"Homeoboxes / ANTP class : HOXL subclass"	5129	protein-coding gene	gene with protein product		142970	"homeo box C8"	HOX3, HOX3A		1973146, 1358459	Standard	NM_022658		Approved		uc001ser.3	P31273		ENST00000040584.4:c.527G>C	12.37:g.54404963G>C	ENSP00000040584:p.Arg176Pro	105.0	0.0		116.0	20.0	NM_022658	A8K4J4|O15221|O15362	Missense_Mutation	SNP	ENST00000040584.4	37	CCDS8870.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531925	0.64972	.	.	ENSG00000037965	ENST00000040584	D	0.96334	-3.98	5.31	3.49	0.39957	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000002	D	0.97173	0.9076	M	0.63428	1.95	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96782	0.9576	10	0.87932	D	0	.	11.0126	0.47671	0.1547:0.0:0.8453:0.0	.	176	P31273	HXC8_HUMAN	P	176	ENSP00000040584:R176P	ENSP00000040584:R176P	R	+	2	0	HOXC8	52691230	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.030000	0.88816	0.750000	0.32877	0.655000	0.94253	CGA	.	.		0.488	HOXC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358957.2			C	54404963	G	C	54404963	3	2	40	1	0	0	0	0	1	0	0	0	7325	1058	37	4	533	4	HOXC8	12	54404963	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	21973	54404963	79446932	182	4838										
OR6C4	341418	hgsc.bcm.edu	37	chr12	55945306	55945307	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gctggctgcttgactcagtaINStttttttgctatatttcttg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:55945306_55945307insT	ENST00000394256.2	+	1	324_325	c.296_297insT	c.(295-300)tattttfs	p.YF99fs	RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	11						TTGACTCAGTATTTTTTTGCTA	0.401																																					p.Y99fs		.	.											.	OR6C4	.	.	0			c.296_297insT						.																																			SO:0001589	frameshift_variant	341418	exon1			.	BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"GPCR / Class A : Olfactory receptors"	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.303dupT	12.37:g.55945313_55945313dupT	ENSP00000377799:p.Tyr99fs	206.0	0.0		218.0	18.0	NM_001005494	A8MZG7|B2RNN2|Q6IFK1	Frame_Shift_Ins	INS	ENST00000394256.2	37	CCDS31827.1																																																																																			.	.		0.401	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1			T	55945307	-	T	55945306	7	5	40	1	0	1	1	0	0	0	0	0	11202	449	16	0	298	0	OR6C4	12	55945306	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	1540343	55945306	77906589	183	4839										
ZBTB39	9880	hgsc.bcm.edu	37	chr12	57397205	57397205	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gagatgccgagatgggacagCgtgtgccacatgaggctgca	16	9	0	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:57397205C>T	ENST00000300101.2	-	2	1582	c.1497G>A	c.(1495-1497)acG>acA	p.T499T		NM_014830.2	NP_055645.1	O15060	ZBT39_HUMAN	zinc finger and BTB domain containing 39	499					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|prostate(1)	16						GATGGGACAGCGTGTGCCACA	0.557																																					p.T499T		.	.											.	ZBTB39	.	.	0			c.G1497A						.						62	52	56					12																	57397205		2203	4300	6503	SO:0001819	synonymous_variant	9880	exon2			GGACAGCGTGTGC	AB002350	CCDS31839.1	12q13.3	2013-01-09				ENSG00000166860		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	29014	protein-coding gene	gene with protein product						9205841	Standard	NM_014830		Approved	KIAA0352, ZNF922	uc001sml.2	O15060		ENST00000300101.2:c.1497G>A	12.37:g.57397205C>T		63.0	0.0		63.0	14.0	NM_014830	A7MD38|Q9UD98	Silent	SNP	ENST00000300101.2	37	CCDS31839.1																																																																																			.	.		0.557	ZBTB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411214.1	NM_014830		T	57397205	C	T	57397205	2	4	40	1	0	0	0	0	0	0	0	1	17555	755	27	1		1	ZBTB39	12	57397205	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1451899	57397205	76454690	184	4840										
SLC25A3	5250	hgsc.bcm.edu	37	chr12	98991699	98991699	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	acacttaaagaggatggtgtTcgtggtttggctaaaggatg	14	4	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:98991699T>C	ENST00000228318.3	+	4	468	c.348T>C	c.(346-348)gtT>gtC	p.V116V	SLC25A3_ENST00000551917.1_Silent_p.V116V|SLC25A3_ENST00000547534.1_Silent_p.V115V|SLC25A3_ENST00000548847.1_Silent_p.V115V|SLC25A3_ENST00000552981.1_Silent_p.V115V|SNORA53_ENST00000391141.1_RNA|SLC25A3_ENST00000188376.5_Silent_p.V115V|SLC25A3_ENST00000549338.1_Silent_p.V115V|SLC25A3_ENST00000401722.3_Silent_p.V115V	NM_005888.3	NP_005879.1	Q00325	MPCP_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3	116					generation of precursor metabolites and energy (GO:0006091)|phosphate ion transmembrane transport (GO:0035435)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	phosphate ion carrier activity (GO:0015320)|protein complex binding (GO:0032403)|symporter activity (GO:0015293)			breast(1)|endometrium(2)|large_intestine(4)|lung(8)|prostate(1)	16		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		AGGATGGTGTTCGTGGTTTGG	0.393																																					p.V116V		.	.											.	SLC25A3	.	.	0			c.T348C						.						163	148	153					12																	98991699		2203	4300	6503	SO:0001819	synonymous_variant	5250	exon4			TGGTGTTCGTGGT		CCDS9065.1, CCDS9066.1	12q23.1	2013-05-22			ENSG00000075415	ENSG00000075415		"Solute carriers"	10989	protein-coding gene	gene with protein product		600370		PHC		8168843	Standard	NM_213611		Approved		uc001tfo.3	Q00325	OTTHUMG00000170212	ENST00000228318.3:c.348T>C	12.37:g.98991699T>C		410.0	0.0		459.0	173.0	NM_005888	B3KS34|Q7Z7N7|Q96A03	Silent	SNP	ENST00000228318.3	37	CCDS9066.1																																																																																			.	.		0.393	SLC25A3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407989.1	NM_005888		C	98991699	T	C	98991699	2	2	40	1	0	0	0	0	0	0	0	1	14508	1770	62	2		2	SLC25A3	12	98991699	Silent	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	41594494	98991699	34860196	185	4841										
UTP20	27340	hgsc.bcm.edu	37	chr12	101711355	101711355	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gaaatcgaagaggaacctgcCgcaggagatgatgaagagtt	14	6	0	5			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:101711355C>T	ENST00000261637.4	+	22	2826	c.2652C>T	c.(2650-2652)gcC>gcT	p.A884A		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	884					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						AGGAACCTGCCGCAGGAGATG	0.498																																					p.A884A		.	.											.	UTP20	.	.	0			c.C2652T						.						89	86	87					12																	101711355		2203	4300	6503	SO:0001819	synonymous_variant	27340	exon22			ACCTGCCGCAGGA	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.2652C>T	12.37:g.101711355C>T		138.0	0.0		141.0	34.0	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			.	.		0.498	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101711355	C	T	101711355	2	4	40	1	0	0	0	0	0	0	0	1	17114	639	23	1		1	UTP20	12	101711355	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	2719656	101711355	32140540	186	4842										
HSP90B1	7184	hgsc.bcm.edu	37	chr12	104341190	104341190	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atggatgtgggaacagatgaAgaagaagaaacagcaaaggt	14	3	0	5	rs5800607|rs201427769	byFrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:104341190A>T	ENST00000299767.5	+	17	2546	c.2364A>T	c.(2362-2364)gaA>gaT	p.E788D	C12orf73_ENST00000543740.2_5'Flank	NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	788					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	gaacagatgaagaagaagaaA	0.418																																					p.E788D		.	.											.	HSP90B1	.	.	0			c.A2364T						.						217	207	210					12																	104341190		2203	4300	6503	SO:0001583	missense	7184	exon17			AGATGAAGAAGAA	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.2364A>T	12.37:g.104341190A>T	ENSP00000299767:p.Glu788Asp	186.0	0.0		264.0	13.0	NM_003299	Q96A97	Missense_Mutation	SNP	ENST00000299767.5	37	CCDS9094.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.29|11.29	1.595812|1.595812	0.28445|0.28445	.|.	.|.	ENSG00000166598|ENSG00000166598	ENST00000299767;ENST00000421266|ENST00000550595	T|.	0.10099|.	2.91|.	4.76|4.76	-7.53|-7.53	0.01336|0.01336	.|.	1.243000|.	0.05329|.	N|.	0.527908|.	T|T	0.30727|0.30727	0.0774|0.0774	L|L	0.27053|0.27053	0.805|0.805	0.38952|0.38952	D|D	0.958377|0.958377	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.31998|0.31998	-0.9923|-0.9923	10|5	0.22109|.	T|.	0.4|.	.|.	2.0253|2.0253	0.03517|0.03517	0.2288:0.2713:0.0769:0.423|0.2288:0.2713:0.0769:0.423	.|.	788|.	P14625|.	ENPL_HUMAN|.	D|M	788;538|139	ENSP00000299767:E788D|.	ENSP00000299767:E788D|.	E|K	+|+	3|2	2|0	HSP90B1|HSP90B1	102865320|102865320	0.067000|0.067000	0.21026|0.21026	0.613000|0.613000	0.29037|0.29037	0.540000|0.540000	0.34992|0.34992	-1.814000|-1.814000	0.01723|0.01723	-1.394000|-1.394000	0.02077|0.02077	-0.336000|-0.336000	0.08194|0.08194	GAA|AAG	.	.		0.418	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		T	104341190	A	T	104341190	3	4	40	1	0	0	0	0	1	0	0	0	7412	69	3	4	2430	4	HSP90B1	12	104341190	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	2629835	104341190	29510705	187	4843										
ACACB	32	hgsc.bcm.edu	37	chr12	109617830	109617830	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tggagctgaatcctcgcttgCaggtggaacatccctgcaca	11	12	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:109617830C>T	ENST00000338432.7	+	11	1875	c.1756C>T	c.(1756-1758)Cag>Tag	p.Q586*	ACACB_ENST00000377854.5_Nonsense_Mutation_p.Q586*|ACACB_ENST00000377848.3_Nonsense_Mutation_p.Q586*|ACACB_ENST00000543080.1_3'UTR			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	586	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TCCTCGCTTGCAGGTGGAACA	0.562																																					p.Q586X		.	.											.	ACACB	.	.	0			c.C1756T						.						105	91	96					12																	109617830		2203	4300	6503	SO:0001587	stop_gained	32	exon10			CGCTTGCAGGTGG	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.1756C>T	12.37:g.109617830C>T	ENSP00000341044:p.Gln586*	152.0	0.0		157.0	54.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Nonsense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	C	37	6.111445	0.97291	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	.	.	.	4.89	3.98	0.46160	.	0.053750	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.3778	0.66889	0.1492:0.8508:0.0:0.0	.	.	.	.	X	586	.	ENSP00000341044:Q586X	Q	+	1	0	ACACB	108102213	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	7.710000	0.84655	1.026000	0.39733	0.655000	0.94253	CAG	.	.		0.562	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109617830	C	T	109617830	4	4	40	1	0	0	0	0	0	1	0	0	107	711	25	3	1794	3	ACACB	12	109617830	Nonsense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	5276640	109617830	24234065	188	4844										
KNTC1	9735	hgsc.bcm.edu	37	chr12	123097712	123097712	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agaactcgagctcttcagtgTctcttctatttggctgacaa	8	10	4	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:123097712T>G	ENST00000333479.7	+	54	5853	c.5676T>G	c.(5674-5676)tgT>tgG	p.C1892W	KNTC1_ENST00000537348.1_Missense_Mutation_p.C317W|KNTC1_ENST00000436959.3_5'UTR|KNTC1_ENST00000450485.2_Missense_Mutation_p.C817W	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	1892					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		CTCTTCAGTGTCTCTTCTATT	0.348																																					p.C1892W		.	.											.	KNTC1	.	.	0			c.T5676G						.						177	170	172					12																	123097712		1831	4085	5916	SO:0001583	missense	9735	exon54			TCAGTGTCTCTTC		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.5676T>G	12.37:g.123097712T>G	ENSP00000328236:p.Cys1892Trp	158.0	0.0		177.0	63.0	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	T	18.04	3.533662	0.64972	.	.	ENSG00000184445	ENST00000450485;ENST00000333479;ENST00000537348;ENST00000546125	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.46	-0.867	0.10655	RZZ complex, subunit KNTC1/ROD, C-terminal (1);	0.039449	0.85682	D	0.000000	T	0.47838	0.1467	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.45877	-0.9231	10	0.87932	D	0	-16.1272	10.7332	0.46109	0.0:0.3956:0.0:0.6044	.	817;1892	E7ES84;P50748	.;KNTC1_HUMAN	W	817;1892;317;79	ENSP00000397992:C817W;ENSP00000328236:C1892W;ENSP00000443622:C317W;ENSP00000439119:C79W	ENSP00000328236:C1892W	C	+	3	2	KNTC1	121663665	0.999000	0.42202	0.997000	0.53966	0.989000	0.77384	0.380000	0.20602	-0.149000	0.11215	0.533000	0.62120	TGT	.	.		0.348	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			G	123097712	T	G	123097712	3	3	40	1	0	0	0	0	1	0	0	0	8437	1673	58	5	5886	5	KNTC1	12	123097712	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	13479882	123097712	10754183	189	4845										
SFRS8	6433	hgsc.bcm.edu	37	chr12	132204080	132204080	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gagcgtcccgtctgacgtggAgttggtatgtgtcctgcatg	15	9	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr12:132204080A>T	ENST00000261674.4	+	4	743	c.602A>T	c.(601-603)gAg>gTg	p.E201V	SFSWAP_ENST00000541286.1_Missense_Mutation_p.E201V	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	201					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						TCTGACGTGGAGTTGGTATGT	0.398																																					p.E201V		.	.											.	SFSWAP	.	.	0			c.A602T						.						128	118	121					12																	132204080		2203	4300	6503	SO:0001583	missense	6433	exon4			ACGTGGAGTTGGT	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)", "splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)", "splicing factor, suppressor of white-apricot homolog (Drosophila)"	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.602A>T	12.37:g.132204080A>T	ENSP00000261674:p.Glu201Val	215.0	0.0		362.0	81.0	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	37	CCDS9273.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.989197	0.74589	.	.	ENSG00000061936	ENST00000261674;ENST00000544623;ENST00000541286	T;T	0.11712	2.75;2.75	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.23451	0.0567	L	0.34521	1.04	0.80722	D	1	P;B;D	0.89917	0.508;0.374;1.0	P;B;D	0.87578	0.463;0.273;0.998	T	0.00984	-1.1491	10	0.41790	T	0.15	-39.0219	15.9586	0.79910	1.0:0.0:0.0:0.0	.	201;201;138	F5H6B8;Q12872;F5H525	.;SFSWA_HUMAN;.	V	201;138;201	ENSP00000261674:E201V;ENSP00000437738:E201V	ENSP00000261674:E201V	E	+	2	0	SFSWAP	130770033	1.000000	0.71417	1.000000	0.80357	0.480000	0.33159	8.502000	0.90505	2.234000	0.73211	0.459000	0.35465	GAG	.	.		0.398	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592		T	132204080	A	T	132204080	3	4	40	1	0	0	0	0	1	0	0	0	14198	304	11	4	616	4	SFRS8	12	132204080	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	9106368	132204080	1647815	190	4846										
TUBA3C	7278	hgsc.bcm.edu	37	chr13	19751669	19751669	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgagagccgctccatgagcaGagatgcgaacccagagccag	13	12	0	4			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr13:19751669G>C	ENST00000400113.3	-	4	558	c.454C>G	c.(454-456)Ctg>Gtg	p.L152V		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	152					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		TCCATGAGCAGAGATGCGAAC	0.582																																					p.L152V		.	.											.	TUBA3C	.	.	0			c.C454G						.						74	77	76					13																	19751669		2203	4300	6503	SO:0001583	missense	7278	exon4			TGAGCAGAGATGC	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"Tubulins"	12408	protein-coding gene	gene with protein product		602528	"tubulin, alpha 2"	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.454C>G	13.37:g.19751669G>C	ENSP00000382982:p.Leu152Val	570.0	0.0		358.0	78.0	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000400113.3	37	CCDS9284.1	.	.	.	.	.	.	.	.	.	.	g	5.266	0.234455	0.09969	.	.	ENSG00000198033	ENST00000400113;ENST00000360801	T	0.68903	-0.36	1.19	0.282	0.15692	.	0.000000	0.38548	U	0.001649	T	0.66167	0.2762	.	.	.	0.35405	D	0.791932	.	.	.	.	.	.	T	0.68769	-0.5321	7	0.87932	D	0	.	5.2966	0.15756	0.2219:0.0:0.7781:0.0	.	.	.	.	V	152	ENSP00000382982:L152V	ENSP00000354037:L152V	L	-	1	2	TUBA3C	18649669	1.000000	0.71417	0.996000	0.52242	0.189000	0.23516	4.940000	0.63533	0.075000	0.16796	0.162000	0.16502	CTG	.	.		0.582	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001		C	19751669	G	C	19751669	3	2	40	1	0	0	0	0	1	0	0	0	16761	933	33	4	906	4	TUBA3C	13	19751669	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10		19751669	95418209	191	4847										
ELF1	1997	hgsc.bcm.edu	37	chr13	41507921	41507922	+	Frame_Shift_Ins	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cctgctgaacctgggcagggINScccaagacaattgaaggagg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr13:41507921_41507922insC	ENST00000239882.3	-	9	1813_1814	c.1499_1500insG	c.(1498-1500)ggcfs	p.G500fs	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Frame_Shift_Ins_p.G476fs	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	500					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		CCTGGGCAGGGCCCAAGACAAT	0.495																																					p.G500fs		.	.											.	ELF1	.	.	0			c.1500_1501insG						.																																			SO:0001589	frameshift_variant	1997	exon9			.	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.1500dupG	13.37:g.41507924_41507924dupC	ENSP00000239882:p.Gly500fs	207.0	0.0		179.0	11.0	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Frame_Shift_Ins	INS	ENST00000239882.3	37	CCDS9374.1																																																																																			.	.		0.495	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373		C	41507922	-	C	41507921	7	5	40	1	0	1	1	0	0	0	0	0	5055	1190	42	0	363	0	ELF1	13	41507921	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	21756252	41507921	73661957	192	4848										
KCTD4	386618	hgsc.bcm.edu	37	chr13	45768382	45768383	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cttcttgtgcaagaagttgaINSttttctcgaaacccttcggg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr13:45768382_45768383insT	ENST00000379108.1	-	1	469_470	c.320_321insA	c.(319-321)aatfs	p.N107fs	KCTD4_ENST00000405872.1_Frame_Shift_Ins_p.N107fs|GTF2F2_ENST00000340473.6_Intron			Q8WVF5	KCTD4_HUMAN	potassium channel tetramerization domain containing 4	107	BTB.				protein homooligomerization (GO:0051260)					breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8		Lung NSC(96;6.55e-05)|Breast(139;0.00378)|Prostate(109;0.00438)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000249)|BRCA - Breast invasive adenocarcinoma(63;0.207)		CAAGAAGTTGATTTTCTCGAAA	0.45																																					p.N107fs		.	.											.	KCTD4	.	.	0			c.321_322insA						.																																			SO:0001589	frameshift_variant	386618	exon2			.	BC018063	CCDS9396.1	13q14.12-q14.13	2013-06-20	2013-06-20		ENSG00000180332	ENSG00000180332			23227	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 4"				Standard	NM_198404		Approved	bA321C24.3	uc001uzx.4	Q8WVF5	OTTHUMG00000016844	ENST00000379108.1:c.321dupA	13.37:g.45768386_45768386dupT	ENSP00000368402:p.Asn107fs	241.0	0.0		175.0	11.0	NM_198404	Q5W0P9	Frame_Shift_Ins	INS	ENST00000379108.1	37	CCDS9396.1																																																																																			.	.		0.45	KCTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044757.1			T	45768383	-	T	45768382	7	5	40	1	0	1	1	0	0	0	0	0	8120	330	12	0	462	0	KCTD4	13	45768382	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	4260461	45768382	69401496	193	4849										
POTEM	641455	hgsc.bcm.edu	37	chr14	20019862	20019863	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gctgtcgtcgtagtctccccINSaggggcccactttgctcttg					rs564173388		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:20019862_20019863insA	ENST00000551509.1	-	1	409_410	c.358_359insT	c.(358-360)tggfs	p.W120fs		NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN	POTE ankyrin domain family, member M	120										endometrium(4)|kidney(1)|lung(4)	9						GTAGTCTCCCCAGGGGCCCACT	0.609																																					p.W120fs		.	.											.	.	.	.	0			c.359_360insT						.																																			SO:0001589	frameshift_variant	641455	exon1			.		CCDS73609.1	14q11.2	2013-01-10			ENSG00000187537	ENSG00000187537		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	37096	protein-coding gene	gene with protein product	"prostate-specific P704P"					16364570	Standard	NM_001145442		Approved	POTE14beta, P704P, ACT	uc001vwc.3	A6NI47		ENST00000551509.1:c.359dupT	14.37:g.20019863_20019863dupA	ENSP00000452296:p.Trp120fs	138.0	0.0		119.0	22.0	NM_001145442		Frame_Shift_Ins	INS	ENST00000551509.1	37	CCDS45076.1																																																																																			.	.		0.609	POTEM-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409490.3	NM_001145442		A	20019863	-	A	20019862	7	5	40	1	0	1	1	0	0	0	0	0	12277	595	21	0	1207	0	POTEM	14	20019862	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10		20019862	87329678	194	4850										
APEX1	328	hgsc.bcm.edu	37	chr14	20925388	20925389	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttcgcaaccccaaggggaacINSaaaaagaatgctggcttcac					rs538008341		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:20925388_20925389insA	ENST00000216714.3	+	5	946_947	c.678_679insA	c.(679-681)aaafs	p.K227fs	APEX1_ENST00000557365.1_3'UTR|APEX1_ENST00000398030.4_Frame_Shift_Ins_p.K227fs|APEX1_ENST00000555414.1_Frame_Shift_Ins_p.K227fs|OSGEP_ENST00000206542.4_5'Flank|OSGEP_ENST00000556252.1_5'Flank|APEX1_ENST00000557054.1_3'UTR	NM_001244249.1|NM_001641.3	NP_001231178.1|NP_001632.2	P27695	APEX1_HUMAN	APEX nuclease (multifunctional DNA repair enzyme) 1	227					aging (GO:0007568)|base-excision repair (GO:0006284)|cell redox homeostasis (GO:0045454)|cellular response to cAMP (GO:0071320)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to peptide hormone stimulus (GO:0071375)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA demethylation (GO:0080111)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|negative regulation of smooth muscle cell migration (GO:0014912)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oxidation-reduction process (GO:0055114)|positive regulation of DNA repair (GO:0045739)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribosome (GO:0005840)|transcription factor complex (GO:0005667)	3'-5' exonuclease activity (GO:0008408)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|phosphodiesterase I activity (GO:0004528)|phosphoric diester hydrolase activity (GO:0008081)|poly(A) RNA binding (GO:0044822)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|uracil DNA N-glycosylase activity (GO:0004844)			breast(2)|endometrium(1)|large_intestine(4)|ovary(2)	9	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)	Lucanthone(DB04967)	CCAAGGGGAACAAAAAGAATGC	0.554								Other BER factors																													p.N226fs		.	.											.	APEX1	.	.	0			c.678_679insA						.																																			SO:0001589	frameshift_variant	328	exon5			.	X59764	CCDS9550.1	14q11.2	2008-02-05	2002-09-11	2002-09-13	ENSG00000100823	ENSG00000100823	4.2.99.18		587	protein-coding gene	gene with protein product		107748	"APEX nuclease (multifunctional DNA repair enzyme)"	APEX			Standard	NM_001641		Approved	APE, REF1, HAP1, APX, APEN, REF-1, APE-1	uc021rnr.1	P27695	OTTHUMG00000029544	ENST00000216714.3:c.683dupA	14.37:g.20925393_20925393dupA	ENSP00000216714:p.Lys227fs	206.0	0.0		169.0	12.0	NM_080648	Q969L5|Q99775	Frame_Shift_Ins	INS	ENST00000216714.3	37	CCDS9550.1																																																																																			.	.		0.554	APEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073641.3	NM_001641		A	20925389	-	A	20925388	7	5	40	1	0	1	1	0	0	0	0	0	769	477	17	0	692	0	APEX1	14	20925388	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	905526	20925388	86424152	195	4851										
RABGGTA	5875	hgsc.bcm.edu	37	chr14	24738189	24738189	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgcaggcagcgcagtgcatcCtgggggtcagctgcggggag	19	10	1	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:24738189C>T	ENST00000399409.3	-	7	1209	c.726G>A	c.(724-726)caG>caA	p.Q242Q	RABGGTA_ENST00000559586.1_5'Flank|RABGGTA_ENST00000560777.1_5'UTR|RABGGTA_ENST00000216840.6_Silent_p.Q242Q	NM_004581.5	NP_004572.3	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase, alpha subunit	242					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)	12				GBM - Glioblastoma multiforme(265;0.0184)		GCAGTGCATCCTGGGGGTCAG	0.562																																					p.Q242Q		.	.											.	.	.	.	0			c.G726A						.						44	55	51					14																	24738189		2122	4251	6373	SO:0001819	synonymous_variant	5875	exon7			TGCATCCTGGGGG		CCDS45088.1	14q11.2	2011-06-27				ENSG00000100949		"Prenyltransferase alpha subunit repeat containing"	9795	protein-coding gene	gene with protein product	"protein prenyltransferase alpha subunit repeat containing 3"	601905				8954794	Standard	NM_182836		Approved	PTAR3	uc001wog.4	Q92696		ENST00000399409.3:c.726G>A	14.37:g.24738189C>T		150.0	0.0		128.0	29.0	NM_004581	A8K5N2|D3DS69	Silent	SNP	ENST00000399409.3	37	CCDS45088.1																																																																																			.	.		0.562	RABGGTA-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415308.5	NM_182836		T	24738189	C	T	24738189	2	4	40	1	0	0	0	0	0	0	0	1	12982	680	24	3		3	RABGGTA	14	24738189	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	3812801	24738189	82611351	196	4852										
PRPF39	55015	hgsc.bcm.edu	37	chr14	45564691	45564692	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tccctccagaatatgaaaaaINSttttggaaaactgtagaaaa							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:45564691_45564692insT	ENST00000355765.6	+	2	419_420	c.249_250insT	c.(250-252)tttfs	p.F84fs		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	84					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						AATATGAAAAATTTTGGAAAAC	0.371																																					p.K83fs		.	.											.	PRPF39	.	.	0			c.249_250insT						.																																			SO:0001589	frameshift_variant	55015	exon2			.	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"PRP39 pre-mRNA processing factor 39 homolog (yeast)", "PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.253dupT	14.37:g.45564695_45564695dupT	ENSP00000348010:p.Phe84fs	176.0	0.0		166.0	10.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Frame_Shift_Ins	INS	ENST00000355765.6	37	CCDS9682.2																																																																																			.	.		0.371	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			T	45564692	-	T	45564691	7	5	40	1	0	1	1	0	0	0	0	0	12581	98	4	0	251	0	PRPF39	14	45564691	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	20826502	45564691	61784849	197	4853										
ATP6V1D	51382	hgsc.bcm.edu	37	chr14	67819690	67819691	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cgaagagttaaggcatcagaINSttttttcttcaggaggtttc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:67819690_67819691insT	ENST00000216442.7	-	2	658_659	c.108_109insA	c.(106-111)aaatctfs	p.S37fs	ATP6V1D_ENST00000555431.1_Intron|ATP6V1D_ENST00000554236.1_Frame_Shift_Ins_p.S37fs|ATP6V1D_ENST00000555474.1_Frame_Shift_Ins_p.S37fs	NM_015994.3	NP_057078.1	Q9Y5K8	VATD_HUMAN	ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D	37					cellular iron ion homeostasis (GO:0006879)|cilium assembly (GO:0042384)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|protein localization to cilium (GO:0061512)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			lung(3)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	7				all cancers(60;0.000739)|OV - Ovarian serous cystadenocarcinoma(108;0.00597)|BRCA - Breast invasive adenocarcinoma(234;0.00957)		AAGGCATCAGATTTTTTCTTCA	0.347																																					p.S37fs		.	.											.	ATP6V1D	.	.	0			c.109_110insA						.																																			SO:0001589	frameshift_variant	51382	exon2			.	AF145316	CCDS9780.1	14q23-q24.2	2010-04-21	2002-08-29	2002-05-10	ENSG00000100554	ENSG00000100554		"ATPases / V-type"	13527	protein-coding gene	gene with protein product		609398	"ATPase, H+ transporting, lysosomal (vacuolar proton pump)"	ATP6M		9442887	Standard	NM_015994		Approved	VATD, VMA8	uc001xjf.3	Q9Y5K8		ENST00000216442.7:c.109dupA	14.37:g.67819696_67819696dupT	ENSP00000216442:p.Ser37fs	202.0	0.0		184.0	11.0	NM_015994	B2RE33|Q9Y688	Frame_Shift_Ins	INS	ENST00000216442.7	37	CCDS9780.1																																																																																			.	.		0.347	ATP6V1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412511.1	NM_015994		T	67819691	-	T	67819690	7	5	40	1	0	1	1	0	0	0	0	0	1182	333	12	0	666	0	ATP6V1D	14	67819690	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	22254999	67819690	39529850	198	4854										
DCAF5	8816	hgsc.bcm.edu	37	chr14	69584924	69584924	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctgaggaactggcaaaaatgTtgtcattcactgggctcaca	10	9	3	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:69584924T>C	ENST00000341516.5	-	4	614	c.467A>G	c.(466-468)aAc>aGc	p.N156S	DCAF5_ENST00000553293.1_5'Flank|DCAF5_ENST00000556847.1_Missense_Mutation_p.N74S|DCAF5_ENST00000557386.1_Missense_Mutation_p.N155S|DCAF5_ENST00000389997.6_Missense_Mutation_p.N156S|DCAF5_ENST00000554215.1_Missense_Mutation_p.N74S	NM_001284206.1|NM_001284207.1|NM_003861.2	NP_001271135.1|NP_001271136.1|NP_003852.1	Q96JK2	DCAF5_HUMAN	DDB1 and CUL4 associated factor 5	156					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|upper_aerodigestive_tract(2)	29						GGCAAAAATGTTGTCATTCAC	0.498																																					p.N156S		.	.											.	DCAF5	.	.	0			c.A467G						.						124	101	109					14																	69584924		2203	4300	6503	SO:0001583	missense	8816	exon4			AAAATGTTGTCAT	AB058727	CCDS32106.1, CCDS61480.1, CCDS61481.1, CCDS73646.1	14q23-q24.1	2013-01-09	2009-07-17	2009-07-17				"WD repeat domain containing", "DDB1 and CUL4 associated factors"	20224	protein-coding gene	gene with protein product		603812	"WD repeat domain 22"	WDR22		9740667, 9521877	Standard	NM_003861		Approved	BCRP2, D14S1461E, BCRG2, KIAA1824	uc001xkp.3	Q96JK2		ENST00000341516.5:c.467A>G	14.37:g.69584924T>C	ENSP00000341351:p.Asn156Ser	125.0	0.0		90.0	16.0	NM_003861	B2RN31|G3V4J7|O60559|Q8N3V3|Q8N3V5	Missense_Mutation	SNP	ENST00000341516.5	37	CCDS32106.1	.	.	.	.	.	.	.	.	.	.	T	19.50	3.840109	0.71488	.	.	ENSG00000139990	ENST00000341516;ENST00000554215;ENST00000556847;ENST00000557386;ENST00000389997;ENST00000554681	T;T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21;0.21	5.68	5.68	0.88126	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63379	0.2506	N	0.20304	0.555	0.58432	D	0.999999	D;P;P	0.76494	0.999;0.48;0.716	D;B;B	0.79108	0.992;0.184;0.376	T	0.66139	-0.5998	10	0.46703	T	0.11	-22.5015	15.9389	0.79739	0.0:0.0:0.0:1.0	.	156;155;156	Q8TBB7;G3V4J7;Q96JK2	.;.;DCAF5_HUMAN	S	156;74;74;155;156;73	ENSP00000341351:N156S;ENSP00000451551:N74S;ENSP00000452052:N74S;ENSP00000451845:N155S;ENSP00000374647:N156S;ENSP00000451394:N73S	ENSP00000341351:N156S	N	-	2	0	DCAF5	68654677	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.959000	0.70339	2.160000	0.67779	0.533000	0.62120	AAC	.	.		0.498	DCAF5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414806.2	NM_003861		C	69584924	T	C	69584924	3	2	40	1	0	0	0	0	1	0	0	0	4275	1725	60	2	2385	2	DCAF5	14	69584924	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	1765234	69584924	37764616	199	4855										
C14orf174	161394	hgsc.bcm.edu	37	chr14	77844867	77844868	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gagataagaaagtcaaatgaINSgaaaaaaaatccacagccac					rs111283439		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:77844867_77844868insG	ENST00000216471.4	+	1	1392_1393	c.1106_1107insG	c.(1105-1110)gagaaafs	p.K370fs	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	370			K -> E (in dbSNP:rs4903576).							breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						AAGTCAAATGAGAAAAAAAATC	0.386																																					p.E369fs		.	.											.	SAMD15	.	.	0			c.1106_1107insG						.																																			SO:0001589	frameshift_variant	161394	exon1			.	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"Sterile alpha motif (SAM) domain containing"	18631	protein-coding gene	gene with protein product			"family with sequence similarity 15, member A", "chromosome 14 open reading frame 174"	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.1107dupG	14.37:g.77844868_77844868dupG	ENSP00000216471:p.Lys370fs	222.0	0.0		215.0	17.0	NM_001010860	Q2M3P3	Frame_Shift_Ins	INS	ENST00000216471.4	37	CCDS32126.1																																																																																			.	.		0.386	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		G	77844868	-	G	77844867	7	5	40	1	0	1	1	0	0	0	0	0	1761	304	11	0	1108	0	C14orf174	14	77844867	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	8259943	77844867	29504673	200	4856										
TSHR	7253	hgsc.bcm.edu	37	chr14	81609512	81609513	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttggttttggccaggagctcINSaaaaacccccaggaagagac							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:81609512_81609513insA	ENST00000541158.2	+	11	1432_1433	c.1110_1111insA	c.(1111-1113)aaafs	p.K371fs	TSHR_ENST00000298171.2_Frame_Shift_Ins_p.K371fs|RP11-114N19.3_ENST00000557775.1_RNA			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	371					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)			breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	GCCAGGAGCTCAAAAACCCCCA	0.446			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																														p.L370fs		.	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	.	TSHR	.	.	0			c.1110_1111insA						.																																			SO:0001589	frameshift_variant	7253	exon10			.	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"GPCR / Class A : Gonadotropin and TSH receptors"	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.1115dupA	14.37:g.81609517_81609517dupA	ENSP00000441235:p.Lys371fs	213.0	0.0		188.0	12.0	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Frame_Shift_Ins	INS	ENST00000541158.2	37	CCDS9872.1																																																																																			.	.		0.446	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		A	81609513	-	A	81609512	7	5	40	1	0	1	1	0	0	0	0	0	16637	813	29	0	1285	0	TSHR	14	81609512	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	3764645	81609512	25740028	201	4857										
PTPN21	11099	hgsc.bcm.edu	37	chr14	88938677	88938677	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	atcataaggaagaacatcttGgaatcgatttctttctgcat	7	7	4	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:88938677G>A	ENST00000556564.1	-	15	3066	c.2782C>T	c.(2782-2784)Caa>Taa	p.Q928*	PTPN21_ENST00000328736.3_Nonsense_Mutation_p.Q928*	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	928	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						AGAACATCTTGGAATCGATTT	0.403																																					p.Q928X		.	.											.	PTPN21	.	.	0			c.C2782T						.						196	171	180					14																	88938677		2203	4300	6503	SO:0001587	stop_gained	11099	exon15			CATCTTGGAATCG	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.2782C>T	14.37:g.88938677G>A	ENSP00000452414:p.Gln928*	358.0	0.0		284.0	51.0	NM_007039		Nonsense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	G	43	10.348499	0.99388	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	.	.	.	5.86	5.86	0.93980	.	0.119510	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	.	20.2019	0.98263	0.0:0.0:1.0:0.0	.	.	.	.	X	928	.	ENSP00000330276:Q928X	Q	-	1	0	PTPN21	88008430	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.567000	0.67378	2.776000	0.95493	0.655000	0.94253	CAA	.	.		0.403	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			A	88938677	G	A	88938677	4	1	40	1	0	0	0	0	0	1	0	0	12801	1357	47	3	762	3	PTPN21	14	88938677	Nonsense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	7329165	88938677	18410863	202	4858										
ATXN3	4287	hgsc.bcm.edu	37	chr14	92548653	92548653	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aatgtctttaccttgcatacTtagctgaatagccctgcgga	8	10	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:92548653T>G	ENST00000532032.1	-	8	775	c.766A>C	c.(766-768)Agt>Cgt	p.S256R	ATXN3_ENST00000502250.1_Missense_Mutation_p.S77R|ATXN3_ENST00000503767.1_Missense_Mutation_p.S241R|ATXN3_ENST00000393287.5_Missense_Mutation_p.S256R|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000545170.1_Missense_Mutation_p.S256R|ATXN3_ENST00000429774.2_Missense_Mutation_p.S241R|ATXN3_ENST00000340660.6_Missense_Mutation_p.S201R			P54252	ATX3_HUMAN	ataxin 3	256					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		CCTTGCATACTTAGCTGAATA	0.413																																					p.S256R	Esophageal Squamous(190;752 2094 29897 44875 49530)	.	.											.	ATXN3	.	.	0			c.A766C						.						163	140	148					14																	92548653		2203	4300	6503	SO:0001583	missense	4287	exon8			GCATACTTAGCTG	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"Ataxins"	7106	protein-coding gene	gene with protein product		607047	"Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.766A>C	14.37:g.92548653T>G	ENSP00000437157:p.Ser256Arg	169.0	0.0		149.0	28.0	NM_004993	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	37		.	.	.	.	.	.	.	.	.	.	T	26.9	4.777368	0.90195	.	.	ENSG00000066427	ENST00000545278;ENST00000539555;ENST00000537884;ENST00000545170;ENST00000447800;ENST00000359819;ENST00000393289;ENST00000429774;ENST00000539454;ENST00000393287;ENST00000502250;ENST00000503767;ENST00000340660;ENST00000532032;ENST00000555381;ENST00000557311;ENST00000554592;ENST00000554672;ENST00000553491;ENST00000556220;ENST00000506466	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.56103	1.67;1.59;1.82;0.82;1.72;1.37;1.49;0.96;0.6;1.4;0.95;0.69;0.78;0.48	5.29	5.29	0.74685	Ubiquitin interacting motif (3);	0.000000	0.85682	D	0.000000	T	0.71626	0.3362	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;0.991	T	0.75566	-0.3273	10	0.87932	D	0	.	15.2672	0.73672	0.0:0.0:0.0:1.0	.	256;241;256;201;256	P54252;E9PB63;F5H096;P54252-3;P54252-2	ATX3_HUMAN;.;.;.;.	R	256;256;256;256;256;256;256;241;255;256;77;241;201;256;186;77;255;158;205;150;190	ENSP00000445618:S256R;ENSP00000389376:S241R;ENSP00000376965:S256R;ENSP00000425322:S77R;ENSP00000426697:S241R;ENSP00000339110:S201R;ENSP00000437157:S256R;ENSP00000451001:S186R;ENSP00000450642:S77R;ENSP00000451385:S255R;ENSP00000451417:S158R;ENSP00000451996:S205R;ENSP00000450641:S150R;ENSP00000435571:S190R	ENSP00000339110:S201R	S	-	1	0	ATXN3	91618406	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.528000	0.81941	2.014000	0.59158	0.397000	0.26171	AGT	.	.		0.413	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993		G	92548653	T	G	92548653	3	3	40	1	0	0	0	0	1	0	0	0	1213	1609	56	5	335	5	ATXN3	14	92548653	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	3609976	92548653	14800887	203	4859										
WARS	7453	hgsc.bcm.edu	37	chr14	100808872	100808873	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggtttaggatagccgatcctINSgggggcgacgtcccttgtca							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:100808872_100808873insG	ENST00000355338.2	-	9	1593_1594	c.975_976insC	c.(973-978)cccaggfs	p.R326fs	WARS_ENST00000556645.1_Frame_Shift_Ins_p.R285fs|WARS_ENST00000358655.4_Frame_Shift_Ins_p.R285fs|WARS_ENST00000557135.1_Frame_Shift_Ins_p.R326fs|RP11-638I2.9_ENST00000556212.1_RNA|WARS_ENST00000392882.2_Frame_Shift_Ins_p.R326fs|RP11-638I2.8_ENST00000557226.1_RNA|WARS_ENST00000344102.5_Frame_Shift_Ins_p.R285fs	NM_173701.1	NP_776049.1	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase	326					angiogenesis (GO:0001525)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|regulation of angiogenesis (GO:0045765)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)			breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	TAGCCGATCCTGGGGGCGACGT	0.579																																					p.R326fs		.	.											.	WARS	.	.	0			c.976_977insC						.																																			SO:0001589	frameshift_variant	7453	exon9			.	M61715	CCDS9960.1, CCDS9961.1	14q32.2	2014-03-19			ENSG00000140105	ENSG00000140105	6.1.1.2	"Aminoacyl tRNA synthetases / Class I"	12729	protein-coding gene	gene with protein product	"tryptophan tRNA ligase 1, cytoplasmic"	191050		IFI53		1537332, 1763065	Standard	NM_004184		Approved	IFP53	uc001yhl.1	P23381	OTTHUMG00000171572	ENST00000355338.2:c.976dupC	14.37:g.100808877_100808877dupG	ENSP00000347495:p.Arg326fs	249.0	0.0		208.0	15.0	NM_004184	A6NGN1|A6NID3|P78535|Q502Y0|Q53XB6|Q9UDI5|Q9UDL3	Frame_Shift_Ins	INS	ENST00000355338.2	37	CCDS9960.1																																																																																			.	.		0.579	WARS-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414236.1	NM_004184		G	100808873	-	G	100808872	7	5	40	1	0	1	1	0	0	0	0	0	17264	1579	55	0	451	0	WARS	14	100808872	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	8260219	100808872	6540668	204	4860										
JAG2	3714	hgsc.bcm.edu	37	chr14	105609430	105609430	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccgctctttcctgcgcttgcGtgtccaccacacgcacagga	9	17	1	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr14:105609430G>A	ENST00000331782.3	-	26	3722	c.3319C>T	c.(3319-3321)Cgc>Tgc	p.R1107C	JAG2_ENST00000347004.2_Missense_Mutation_p.R1069C	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	1107					auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		CTGCGCTTGCGTGTCCACCAC	0.682																																					p.R1107C		.	.											.	JAG2	.	.	0			c.C3319T						.						20	27	24					14																	105609430		2194	4292	6486	SO:0001583	missense	3714	exon26			GCTTGCGTGTCCA	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.3319C>T	14.37:g.105609430G>A	ENSP00000328169:p.Arg1107Cys	27.0	0.0		14.0	7.0	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	37	CCDS9998.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.440212	0.83993	.	.	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.88046	-2.32;-2.33	4.09	4.09	0.47781	.	0.070739	0.64402	D	0.000016	D	0.92260	0.7545	M	0.67397	2.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.93322	0.6693	10	0.87932	D	0	.	15.4312	0.75102	0.0:0.0:1.0:0.0	.	1069;1107	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	C	1107;1069	ENSP00000328169:R1107C;ENSP00000328566:R1069C	ENSP00000328169:R1107C	R	-	1	0	JAG2	104680475	1.000000	0.71417	0.535000	0.28026	0.909000	0.53808	4.675000	0.61619	2.111000	0.64477	0.491000	0.48974	CGC	.	.		0.682	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			A	105609430	G	A	105609430	3	1	40	1	0	0	0	0	1	0	0	0	7944	1145	40	1	401	1	JAG2	14	105609430	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	4800558	105609430	1740110	205	4861										
RAD51	5888	hgsc.bcm.edu	37	chr15	41022163	41022164	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aatatcatcgcccatgcatcINSaacaaccaggtaaggtgttg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr15:41022163_41022164insA	ENST00000267868.3	+	9	1155_1156	c.887_888insA	c.(886-891)tcaacafs	p.T297fs	RAD51_ENST00000557850.1_Frame_Shift_Ins_p.T200fs|RAD51_ENST00000530766.1_Intron|RAD51_ENST00000382643.3_Frame_Shift_Ins_p.T298fs|RAD51_ENST00000532743.1_Frame_Shift_Ins_p.T298fs|RAD51_ENST00000423169.2_Intron	NM_002875.4	NP_002866.2	Q06609	RAD51_HUMAN	RAD51 recombinase	297					ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA unwinding involved in DNA replication (GO:0006268)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|mitotic recombination (GO:0006312)|positive regulation of DNA ligation (GO:0051106)|protein homooligomerization (GO:0051260)|reciprocal meiotic recombination (GO:0007131)|regulation of double-strand break repair via homologous recombination (GO:0010569)	condensed chromosome (GO:0000793)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|lateral element (GO:0000800)|mitochondrion (GO:0005739)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|PML body (GO:0016605)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA polymerase binding (GO:0070182)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|single-stranded DNA binding (GO:0003697)|single-stranded DNA-dependent ATPase activity (GO:0043142)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)	9		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)		GCCCATGCATCAACAACCAGGT	0.406								Homologous recombination																													p.S297fs		.	.											.	RAD51	.	.	0			c.890_891insA						.																																			SO:0001589	frameshift_variant	5888	exon9			.	D13804	CCDS10062.1, CCDS53931.1, CCDS53932.1	15q15.1	2014-06-12	2013-07-02		ENSG00000051180	ENSG00000051180			9817	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 5"	179617	"RAD51 (S. cerevisiae) homolog (E coli RecA homolog)", "RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)", "RAD51 homolog (S. cerevisiae)"	RAD51A, RECA		8358431, 8479919	Standard	NM_002875		Approved	HsRad51, HsT16930, BRCC5	uc010bbx.3	Q06609	OTTHUMG00000130067	ENST00000267868.3:c.889dupA	15.37:g.41022165_41022165dupA	ENSP00000267868:p.Thr297fs	185.0	0.0		164.0	10.0	NM_133487	B0FXP0|B2R8T6|Q6FHX9|Q6ZNA8|Q9BV60	Frame_Shift_Ins	INS	ENST00000267868.3	37	CCDS10062.1																																																																																			.	.		0.406	RAD51-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252358.1	NM_002875, NM_133487		A	41022164	-	A	41022163	7	5	40	1	0	1	1	0	0	0	0	0	13000	838	29	0	1042	0	RAD51	15	41022163	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10		41022163	61509229	206	4862										
CAPN3	825	hgsc.bcm.edu	37	chr15	42703132	42703132	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tcattaccatgcggtacgcaGacaaacacatgaacatcgac	7	12	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr15:42703132G>A	ENST00000397163.3	+	22	2533	c.2314G>A	c.(2314-2316)Gac>Aac	p.D772N	CAPN3_ENST00000349748.3_Missense_Mutation_p.D680N|CAPN3_ENST00000562199.1_3'UTR|CAPN3_ENST00000569136.1_Missense_Mutation_p.D107N|CAPN3_ENST00000561817.1_Missense_Mutation_p.D107N|CAPN3_ENST00000357568.3_Missense_Mutation_p.D766N|CAPN3_ENST00000397204.4_Missense_Mutation_p.D107N|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000337571.4_Missense_Mutation_p.D107N|CAPN3_ENST00000356316.3_Missense_Mutation_p.D679N|CAPN3_ENST00000397200.4_Missense_Mutation_p.D260N|CAPN3_ENST00000318023.7_Missense_Mutation_p.D766N	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	772	Domain IV.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		GCGGTACGCAGACAAACACAT	0.542																																					p.D772N		.	.											.	CAPN3	.	.	0			c.G2314A	GRCh37	CD951643	CAPN3	D		.						234	186	203					15																	42703132		2203	4299	6502	SO:0001583	missense	825	exon22			TACGCAGACAAAC	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"EF-hand domain containing"	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.2314G>A	15.37:g.42703132G>A	ENSP00000380349:p.Asp772Asn	240.0	0.0		204.0	51.0	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Missense_Mutation	SNP	ENST00000397163.3	37	CCDS45245.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.362995	0.61403	.	.	ENSG00000092529	ENST00000356316;ENST00000337522;ENST00000397163;ENST00000357568;ENST00000349748;ENST00000318023;ENST00000397200;ENST00000337571;ENST00000397204	D;D;D;D;D;D;D;D	0.94966	-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57	5.4	5.4	0.78164	EF-hand-like domain (1);	0.065340	0.64402	U	0.000007	D	0.90827	0.7119	L	0.28344	0.845	0.46521	D	0.99908	B;B;B;B;B;B;B	0.31519	0.09;0.09;0.004;0.03;0.327;0.219;0.098	B;B;B;B;B;B;B	0.38020	0.047;0.101;0.008;0.035;0.263;0.255;0.144	D	0.88741	0.3243	10	0.44086	T	0.13	.	12.6478	0.56744	0.0749:0.0:0.9251:0.0	.	637;685;107;680;766;772;679	C6EVS4;C6EVS3;A4FTZ9;P20807-2;P20807-3;P20807;Q762C8	.;.;.;.;.;CAN3_HUMAN;.	N	679;260;772;766;680;766;260;107;107	ENSP00000348667:D679N;ENSP00000380349:D772N;ENSP00000350181:D766N;ENSP00000183936:D680N;ENSP00000326281:D766N;ENSP00000380384:D260N;ENSP00000336840:D107N;ENSP00000380387:D107N	ENSP00000326281:D766N	D	+	1	0	CAPN3	40490424	1.000000	0.71417	0.996000	0.52242	0.986000	0.74619	5.011000	0.64011	2.818000	0.97014	0.655000	0.94253	GAC	.	.		0.542	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1			A	42703132	G	A	42703132	3	1	40	1	0	0	0	0	1	0	0	0	2630	942	33	3	2452	3	CAPN3	15	42703132	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	1680969	42703132	59828260	207	4863										
MSLN	10232	hgsc.bcm.edu	37	chr16	812697	812697	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gaccatggccttgccaacggCtcgacccctgttggggtcct	12	15	0	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:812697C>G	ENST00000382862.3	+	2	112	c.17C>G	c.(16-18)gCt>gGt	p.A6G	MSLN_ENST00000563941.1_Missense_Mutation_p.A6G|MSLN_ENST00000545450.2_Missense_Mutation_p.A6G|MSLN_ENST00000566549.1_Missense_Mutation_p.A6G	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	6				PTARPLLG -> QRLDPCW (in Ref. 2; AAC50348). {ECO:0000305}.	cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				TTGCCAACGGCTCGACCCCTG	0.677																																					p.A6G		.	.											.	MSLN	.	.	0			c.C17G						.						105	111	109					16																	812697		2200	4296	6496	SO:0001583	missense	10232	exon3			CAACGGCTCGACC	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.17C>G	16.37:g.812697C>G	ENSP00000372313:p.Ala6Gly	131.0	0.0		159.0	29.0	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.354659	0.41700	.	.	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.18016	2.24;2.24	2.75	2.75	0.32379	.	154.510000	0.00567	U	0.000283	T	0.35740	0.0942	L	0.51422	1.61	0.09310	N	1	D;D;D;D	0.65815	0.994;0.995;0.994;0.994	P;P;P;P	0.61722	0.828;0.893;0.828;0.828	T	0.21518	-1.0243	10	0.87932	D	0	.	9.1818	0.37146	0.0:1.0:0.0:0.0	.	6;6;6;6	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	G	6	ENSP00000442965:A6G;ENSP00000372313:A6G	ENSP00000372313:A6G	A	+	2	0	MSLN	752698	0.012000	0.17670	0.033000	0.17914	0.001000	0.01503	2.173000	0.42472	1.886000	0.54624	0.561000	0.74099	GCT	.	.		0.677	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2			G	812697	C	G	812697	3	3	40	1	0	0	0	0	1	0	0	0	9890	797	28	4	19	4	MSLN	16	812697	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10		812697	89542056	208	4864										
UNKL	64718	hgsc.bcm.edu	37	chr16	1417771	1417772	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gacttgcactcgaagaggatINSggggggccggcactcaggat							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:1417771_1417772insG	ENST00000389221.4	-	13	1663_1664	c.1664_1665insC	c.(1663-1665)ccafs	p.P555fs	UNKL_ENST00000508903.2_Frame_Shift_Ins_p.P558fs|UNKL_ENST00000391893.2_Frame_Shift_Ins_p.P54fs|UNKL_ENST00000397464.1_Frame_Shift_Ins_p.P57fs|UNKL_ENST00000248104.7_Frame_Shift_Ins_p.P54fs|UNKL_ENST00000402641.2_Frame_Shift_Ins_p.P57fs|UNKL_ENST00000403703.1_Frame_Shift_Ins_p.P57fs	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	555	Ser-rich.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Hepatocellular(780;0.0893)				TCGAAGAGGATGGGGGGCCGGC	0.644																																					p.P558fs		.	.											.	UNKL	.	.	0			c.1674_1675insC						.																																			SO:0001589	frameshift_variant	64718	exon13			.	BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145		"Zinc fingers, CCCH-type domain containing"	14184	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 28", "unkempt homolog (Drosophila)-like"	C16orf28		20148946	Standard	NM_001193389		Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000389221.4:c.1665dupC	16.37:g.1417777_1417777dupG	ENSP00000373873:p.Pro555fs	196.0	0.0		185.0	11.0	NM_001193388	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Frame_Shift_Ins	INS	ENST00000389221.4	37	CCDS53981.1																																																																																			.	.		0.644	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125		G	1417772	-	G	1417771	7	5	40	1	0	1	1	0	0	0	0	0	17016	1451	51	0	539	0	UNKL	16	1417771	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	605074	1417771	88936982	209	4865										
OR2C1	4993	hgsc.bcm.edu	37	chr16	3406154	3406154	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	acctctcctccttggaccttGctttcgctactagttcagtc	6	15	2	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:3406154G>A	ENST00000304936.2	+	1	266	c.214G>A	c.(214-216)Gct>Act	p.A72T		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	72					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)	cell cortex (GO:0005938)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						CTTGGACCTTGCTTTCGCTAC	0.522																																					p.A72T		.	.											.	OR2C1	.	.	0			c.G214A						.						147	126	133					16																	3406154		2197	4300	6497	SO:0001583	missense	4993	exon1			GACCTTGCTTTCG	AF098664	CCDS10502.1	16p13.3	2012-08-09			ENSG00000168158	ENSG00000168158		"GPCR / Class A : Olfactory receptors"	8242	protein-coding gene	gene with protein product				OR2C2P		9847080	Standard	NM_012368		Approved	OLFmf3	uc002cuw.1	O95371	OTTHUMG00000090505	ENST00000304936.2:c.214G>A	16.37:g.3406154G>A	ENSP00000307726:p.Ala72Thr	292.0	0.0		520.0	34.0	NM_012368	A0AVA4|Q6IF34|Q6IF55	Missense_Mutation	SNP	ENST00000304936.2	37	CCDS10502.1	.	.	.	.	.	.	.	.	.	.	g	9.692	1.152102	0.21371	.	.	ENSG00000168158	ENST00000304936	T	0.01347	4.99	4.35	3.4	0.38934	GPCR, rhodopsin-like superfamily (1);	0.181464	0.26605	N	0.023454	T	0.01189	0.0039	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.47275	-0.9130	10	0.72032	D	0.01	.	10.0324	0.42109	0.0996:0.0:0.9004:0.0	.	72	O95371	OR2C1_HUMAN	T	72	ENSP00000307726:A72T	ENSP00000307726:A72T	A	+	1	0	OR2C1	3346155	0.000000	0.05858	0.712000	0.30502	0.580000	0.36256	0.088000	0.14979	1.046000	0.40249	0.401000	0.26515	GCT	.	.		0.522	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3			A	3406154	G	A	3406154	3	1	40	1	0	0	0	0	1	0	0	0	11001	1319	46	3	216	3	OR2C1	16	3406154	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	1988383	3406154	86948599	210	4866										
SRL	6345	hgsc.bcm.edu	37	chr16	4242512	4242512	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgaagaaggtcattttgtccTtgtaagtctgcaggtagcgg	13	6	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:4242512T>A	ENST00000399609.3	-	6	1076	c.1064A>T	c.(1063-1065)aAg>aTg	p.K355M	SRL_ENST00000537996.1_Missense_Mutation_p.K313M	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	814	Acidic domain, probably binds calcium. {ECO:0000250}.					sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						CATTTTGTCCTTGTAAGTCTG	0.502																																					p.K355M		.	.											.	SRL	.	.	0			c.A1064T						.						113	118	116					16																	4242512		2086	4223	6309	SO:0001583	missense	6345	exon6			TTGTCCTTGTAAG	AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739			11295	protein-coding gene	gene with protein product		604992				2762314	Standard	NM_001098814		Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.1064A>T	16.37:g.4242512T>A	ENSP00000382518:p.Lys355Met	233.0	0.0		263.0	44.0	NM_001098814		Missense_Mutation	SNP	ENST00000399609.3	37	CCDS42113.1	.	.	.	.	.	.	.	.	.	.	T	16.72	3.202141	0.58234	.	.	ENSG00000185739	ENST00000399609;ENST00000330063;ENST00000537996	T;T	0.33654	1.4;1.4	5.83	2.4	0.29515	.	0.000000	0.85682	U	0.000000	T	0.45975	0.1369	M	0.71581	2.175	0.53688	D	0.999979	P	0.52692	0.955	P	0.52758	0.708	T	0.31194	-0.9952	10	0.45353	T	0.12	-16.3634	9.35	0.38131	0.0:0.2682:0.0:0.7318	.	355	Q86TD4-2	.	M	355;813;313	ENSP00000382518:K355M;ENSP00000440350:K313M	ENSP00000333285:K813M	K	-	2	0	SRL	4182513	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	3.959000	0.56744	0.130000	0.18549	-0.274000	0.10170	AAG	.	.		0.502	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152		A	4242512	T	A	4242512	3	1	40	1	0	0	0	0	1	0	0	0	15165	1609	56	4	361	4	SRL	16	4242512	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	836358	4242512	86112241	211	4867										
TMEM186	25880	hgsc.bcm.edu	37	chr16	8890210	8890210	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tggcaaagctaccactgtcaGggcagtctgtgccaacttca	10	12	3	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:8890210G>C	ENST00000333050.6	-	2	274	c.241C>G	c.(241-243)Ctg>Gtg	p.L81V	PMM2_ENST00000569958.1_5'Flank|TMEM186_ENST00000564869.1_Intron|PMM2_ENST00000566983.1_Intron|PMM2_ENST00000268261.4_5'Flank|PMM2_ENST00000539622.1_5'Flank|PMM2_ENST00000537352.1_5'Flank	NM_015421.3	NP_056236.2	Q96B77	TM186_HUMAN	transmembrane protein 186	81						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9						ACCACTGTCAGGGCAGTCTGT	0.517																																					p.L81V		.	.											.	TMEM186	.	.	0			c.C241G						.						118	104	109					16																	8890210		2197	4300	6497	SO:0001583	missense	25880	exon2			CTGTCAGGGCAGT	BC015912	CCDS10535.1	16p13.2	2008-02-05	2007-02-08	2007-02-08	ENSG00000184857	ENSG00000184857			24530	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 51"	C16orf51		11230166	Standard	NM_015421		Approved	DKFZP564K2062	uc002cze.3	Q96B77	OTTHUMG00000129696	ENST00000333050.6:c.241C>G	16.37:g.8890210G>C	ENSP00000331640:p.Leu81Val	129.0	0.0		123.0	8.0	NM_015421	B2RAY0|Q9Y4T4	Missense_Mutation	SNP	ENST00000333050.6	37	CCDS10535.1	.	.	.	.	.	.	.	.	.	.	G	9.564	1.119318	0.20877	.	.	ENSG00000184857	ENST00000333050	.	.	.	5.36	1.76	0.24704	.	0.848519	0.09714	N	0.765361	T	0.44603	0.1301	L	0.31578	0.945	0.58432	D	0.999993	B	0.23249	0.082	B	0.28916	0.096	T	0.13710	-1.0499	9	0.15066	T	0.55	-8.0658	10.2021	0.43089	0.0:0.1133:0.5867:0.2999	.	81	Q96B77	TM186_HUMAN	V	81	.	ENSP00000331640:L81V	L	-	1	2	TMEM186	8797711	0.002000	0.14202	0.988000	0.46212	0.859000	0.49053	-0.365000	0.07573	0.579000	0.29504	0.561000	0.74099	CTG	.	.		0.517	TMEM186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251903.1	NM_015421		C	8890210	G	C	8890210	3	2	40	1	0	0	0	0	1	0	0	0	16123	991	35	4	404	4	TMEM186	16	8890210	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	4647698	8890210	81464543	212	4868										
ERI2	112479	hgsc.bcm.edu	37	chr16	20809480	20809481	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tcatgaatagtgaagggttgINStttttttgctggtgggaaag							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:20809480_20809481insT	ENST00000357967.4	-	9	1683_1684	c.1641_1642insA	c.(1639-1644)aaacaafs	p.Q548fs	ERI2_ENST00000389345.5_Frame_Shift_Ins_p.Q283fs|ERI2_ENST00000300005.3_Intron|ERI2_ENST00000569729.1_Frame_Shift_Ins_p.N262fs|ERI2_ENST00000564349.1_Frame_Shift_Ins_p.Q455fs|ERI2_ENST00000563117.1_Frame_Shift_Ins_p.Q455fs	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	548							exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(2)	11						GTGAAGGGTTGTTTTTTTGCTG	0.431																																					p.Q548fs		.	.											.	ERI2	.	.	0			c.1642_1643insA						.																																			SO:0001589	frameshift_variant	112479	exon9			.	BC010503	CCDS10590.1, CCDS45436.1	16p12.3	2014-02-18	2009-10-07	2008-12-16	ENSG00000196678	ENSG00000196678		"Enhanced RNAi three prime mRNA exonucleases"	30541	protein-coding gene	gene with protein product	"enhanced RNAi three prime mRNA exonuclease homolog 2 (C.elegans)", "exoribonuclease 2", "zinc finger, GRF-type containing 5"		"exonuclease domain containing 1"	EXOD1		10819331	Standard	NM_080663		Approved	KIAA1504, MGC16943, ZGRF5	uc010vbb.1	A8K979	OTTHUMG00000131557	ENST00000357967.4:c.1642dupA	16.37:g.20809487_20809487dupT	ENSP00000350651:p.Gln548fs	114.0	0.0		155.0	10.0	NM_001142725	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Frame_Shift_Ins	INS	ENST00000357967.4	37	CCDS45436.1																																																																																			.	.		0.431	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663		T	20809481	-	T	20809480	7	5	40	1	0	1	1	0	0	0	0	0	5230	1386	48	0	704	0	ERI2	16	20809480	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	11919270	20809480	69545273	213	4869										
ERI2	112479	hgsc.bcm.edu	37	chr16	20810230	20810230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tataggagaatttgcacaaaTtgacttcatttgaacttttt	6	5	1	3	rs557835094		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:20810230T>C	ENST00000357967.4	-	9	934	c.892A>G	c.(892-894)Att>Gtt	p.I298V	ERI2_ENST00000389345.5_Missense_Mutation_p.I33V|ERI2_ENST00000300005.3_Intron|ERI2_ENST00000569729.1_Intron|ERI2_ENST00000564349.1_Missense_Mutation_p.I205V|ERI2_ENST00000563117.1_Missense_Mutation_p.I205V	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	298							exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(2)	11						TTTGCACAAATTGACTTCATT	0.323																																					p.I298V		.	.											.	ERI2	.	.	0			c.A892G						.						82	67	72					16																	20810230		692	1591	2283	SO:0001583	missense	112479	exon9			CACAAATTGACTT	BC010503	CCDS10590.1, CCDS45436.1	16p12.3	2014-02-18	2009-10-07	2008-12-16	ENSG00000196678	ENSG00000196678		"Enhanced RNAi three prime mRNA exonucleases"	30541	protein-coding gene	gene with protein product	"enhanced RNAi three prime mRNA exonuclease homolog 2 (C.elegans)", "exoribonuclease 2", "zinc finger, GRF-type containing 5"		"exonuclease domain containing 1"	EXOD1		10819331	Standard	NM_080663		Approved	KIAA1504, MGC16943, ZGRF5	uc010vbb.1	A8K979	OTTHUMG00000131557	ENST00000357967.4:c.892A>G	16.37:g.20810230T>C	ENSP00000350651:p.Ile298Val	427.0	0.0		605.0	190.0	NM_001142725	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Missense_Mutation	SNP	ENST00000357967.4	37	CCDS45436.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.974842	0.00047	.	.	ENSG00000196678	ENST00000357967;ENST00000389345	T;T	0.15952	2.38;2.39	6.17	1.14	0.20703	.	1.346770	0.04751	N	0.424586	T	0.03651	0.0104	N	0.00170	-1.935	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35895	-0.9770	10	0.02654	T	1	-0.1205	9.9626	0.41706	0.0:0.5853:0.0:0.4147	.	298	A8K979	ERI2_HUMAN	V	298;33	ENSP00000350651:I298V;ENSP00000373996:I33V	ENSP00000350651:I298V	I	-	1	0	ERI2	20717731	0.000000	0.05858	0.001000	0.08648	0.107000	0.19398	0.187000	0.16998	0.425000	0.26087	-0.993000	0.02533	ATT	.	.		0.323	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663		C	20810230	T	C	20810230	3	2	40	1	0	0	0	0	1	0	0	0	5230	1493	52	2	1454	2	ERI2	16	20810230	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	750	20810230	69544523	214	4870										
USP31	57478	hgsc.bcm.edu	37	chr16	23093878	23093878	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccaggcatcatcgggggcaaGctgaaaacagaagcatgact	12	10	1	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:23093878G>C	ENST00000219689.7	-	12	1830	c.1831C>G	c.(1831-1833)Ctt>Gtt	p.L611V		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	262	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		TCGGGGGCAAGCTGAAAACAG	0.498																																					p.L611V		.	.											.	USP31	.	.	0			c.C1831G						.						74	63	67					16																	23093878		2197	4300	6497	SO:0001630	splice_region_variant	57478	exon12			GGGCAAGCTGAAA	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.1831-1C>G	16.37:g.23093878G>C		133.0	0.0		168.0	30.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171238	0.78452	.	.	ENSG00000103404	ENST00000219689	T	0.03745	3.82	4.9	4.9	0.64082	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.081669	0.49916	D	0.000121	T	0.18257	0.0438	M	0.84846	2.72	0.80722	D	1	P	0.49447	0.924	P	0.56823	0.807	T	0.00593	-1.1654	10	0.87932	D	0	-11.7004	17.4507	0.87591	0.0:0.0:1.0:0.0	.	611	Q70CQ4	UBP31_HUMAN	V	611	ENSP00000219689:L611V	ENSP00000219689:L611V	L	-	1	0	USP31	23001379	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.203000	0.77864	2.410000	0.81850	0.650000	0.86243	CTT	.	.		0.498	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	Missense_Mutation	C	23093878	G	C	23093878	5	2	40	1	0	0	0	0	0	0	1	0	17077	985	34	4	2247	4	USP31	16	23093878	Splice_Site	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	2283648	23093878	67260875	215	4871										
RBL2	5934	hgsc.bcm.edu	37	chr16	53513829	53513830	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gttttgataaaagggaaaagINSaaaaagaagaaattctggca							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:53513829_53513830insA	ENST00000262133.6	+	19	2944_2945	c.2807_2808insA	c.(2806-2811)agaaaafs	p.RK936fs	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Intron	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	936	Domain B.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						AAAGGGAAAAGAAAAAGAAGAA	0.376																																					p.R936fs		.	.											.	RBL2	.	.	0			c.2807_2808insA						.																																			SO:0001589	frameshift_variant	5934	exon19			.	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2812dupA	16.37:g.53513834_53513834dupA	ENSP00000262133:p.Arg936fs	269.0	0.0		151.0	10.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Frame_Shift_Ins	INS	ENST00000262133.6	37	CCDS10748.1																																																																																			.	.		0.376	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		A	53513830	-	A	53513829	7	5	40	1	0	1	1	0	0	0	0	0	13125	942	33	0	2881	0	RBL2	16	53513829	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	30419951	53513829	36840924	216	4872										
CMTM1	113540	hgsc.bcm.edu	37	chr16	66600574	66600575	+	Intron	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aagaccgcaccccggaagcaINSccccgcagtctcaattcgca							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:66600574_66600575insC	ENST00000457188.2	+	1	202				CMTM1_ENST00000528324.1_Intron|CKLF-CMTM1_ENST00000527729.1_Intron|CMTM1_ENST00000535705.1_Intron|CMTM1_ENST00000533666.1_Intron|CMTM1_ENST00000529506.1_Intron|CMTM1_ENST00000332695.7_Intron|CMTM1_ENST00000328020.6_Frame_Shift_Ins_p.HP53fs|CMTM1_ENST00000531885.1_Intron|CMTM1_ENST00000336328.6_Intron|CMTM1_ENST00000379500.2_Frame_Shift_Ins_p.HP53fs|CMTM1_ENST00000533953.1_Frame_Shift_Ins_p.HP53fs	NM_181269.2	NP_851786.1	Q8IZ96	CKLF1_HUMAN	CKLF-like MARVEL transmembrane domain containing 1						chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0702)|Epithelial(162;0.222)		CCCCGGAAGCACCCCGCAGTCT	0.658																																					p.H53fs		.	.											.	CMTM1	.	.	0			c.158_159insC						.																																			SO:0001627	intron_variant	113540	exon1			.	AF278577	CCDS10810.1, CCDS10811.1, CCDS10812.2, CCDS45503.1, CCDS45504.1, CCDS54019.1, CCDS54020.1, CCDS54021.1	16q22.1	2009-10-06	2005-11-08	2005-11-08	ENSG00000089505	ENSG00000089505			19172	protein-coding gene	gene with protein product		607884	"chemokine-like factor super family 1", "chemokine-like factor superfamily 1"	CKLFSF1		12782130	Standard	NM_181268		Approved	CKLFH1a, CKLFH	uc002epr.4	Q8IZ96	OTTHUMG00000137502	ENST00000457188.2:c.81+77->C	16.37:g.66600578_66600578dupC		209.0	0.0		139.0	10.0	NM_181268	Q2PPY5|Q6PEV5|Q8IU76|Q8IU83|Q8IU86|Q8IU93|Q8IZ87|Q8IZ88|Q8IZ89|Q8IZ90|Q8IZ91|Q8IZ92|Q8IZ93|Q8IZ94|Q8IZ95|Q96JC2|Q96JC3	Frame_Shift_Ins	INS	ENST00000457188.2	37	CCDS45503.1																																																																																			.	.		0.658	CMTM1-015	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390261.2	NM_052999		C	66600575	-	C	66600574	6	5	40	0	1	1	1	0	0	0	0	0	3584	159	6	0		0	CMTM1	16	66600574	Intron	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	13086745	66600574	23754179	217	4873										
NFATC3	4775	hgsc.bcm.edu	37	chr16	68224766	68224766	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agacccagaggccttcctctGattcagggtgttcacatgac	10	12	3	4			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:68224766G>C	ENST00000346183.3	+	9	2218	c.2194G>C	c.(2194-2196)Gat>Cat	p.D732H	SNORA48_ENST00000391143.1_RNA|NFATC3_ENST00000575270.1_Missense_Mutation_p.D732H|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000329524.4_Missense_Mutation_p.D732H|NFATC3_ENST00000349223.5_Missense_Mutation_p.D732H	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	732					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		GCCTTCCTCTGATTCAGGGTG	0.468																																					p.D732H		.	.											.	NFATC3	.	.	0			c.G2194C						.						100	87	91					16																	68224766		2198	4300	6498	SO:0001583	missense	4775	exon9			TCCTCTGATTCAG	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"Nuclear factor of activated T-cells"	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.2194G>C	16.37:g.68224766G>C	ENSP00000300659:p.Asp732His	217.0	0.0		185.0	15.0	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	37	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.107591	0.37145	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524;ENST00000535127	T;T;T	0.09350	2.99;3.0;2.99	5.55	5.55	0.83447	.	1.042500	0.07468	N	0.901830	T	0.16896	0.0406	L	0.29908	0.895	0.39968	D	0.974755	P;P;P;P	0.42337	0.612;0.776;0.612;0.612	B;P;B;B	0.47528	0.417;0.549;0.417;0.417	T	0.03017	-1.1082	10	0.59425	D	0.04	-4.9679	14.359	0.66757	0.0:0.0:0.852:0.148	.	732;732;732;732	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	H	732;732;732;253	ENSP00000264008:D732H;ENSP00000300659:D732H;ENSP00000331324:D732H	ENSP00000331324:D732H	D	+	1	0	NFATC3	66782267	1.000000	0.71417	1.000000	0.80357	0.378000	0.30076	7.026000	0.76455	2.617000	0.88574	0.557000	0.71058	GAT	.	.		0.468	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		C	68224766	G	C	68224766	3	2	40	1	0	0	0	0	1	0	0	0	10373	1290	45	4	2228	4	NFATC3	16	68224766	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	1624192	68224766	22129987	218	4874										
CMIP	80790	hgsc.bcm.edu	37	chr16	81736275	81736275	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cactgccctccaagtccacaGtgagttggtttggttctctt	9	12	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:81736275G>A	ENST00000537098.3	+	17	2016		c.e17+1		CMIP_ENST00000539778.2_Splice_Site|CMIP_ENST00000398040.4_Splice_Site|CMIP_ENST00000566513.1_Splice_Site	NM_198390.2	NP_938204.2	Q8IY22	CMIP_HUMAN	c-Maf inducing protein							cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(5)|kidney(1)|lung(7)	13						CAAGTCCACAGTGAGTTGGTT	0.542																																					.		.	.											.	.	.	.	0			c.1944+1G>A						.						156	154	155					16																	81736275		1992	4167	6159	SO:0001630	splice_region_variant	80790	exon17			TCCACAGTGAGTT	AB051481	CCDS54044.1, CCDS54045.1	16q23	2011-08-04			ENSG00000153815	ENSG00000153815			24319	protein-coding gene	gene with protein product		610112				11214970, 12939343	Standard	NM_030629		Approved		uc002fgp.3	Q8IY22		ENST00000537098.3:c.1944+1G>A	16.37:g.81736275G>A		934.0	2.0		724.0	376.0	NM_198390	Q9C0G9	Splice_Site	SNP	ENST00000537098.3	37	CCDS54044.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165130	0.78339	.	.	ENSG00000153815	ENST00000537098;ENST00000539778;ENST00000398040;ENST00000542097	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.258	0.93955	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CMIP	80293776	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	9.096000	0.94182	2.554000	0.86153	0.655000	0.94253	.	.	.		0.542	CMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432399.2	NM_030629	Intron	A	81736275	G	A	81736275	5	1	40	1	0	0	0	0	0	0	1	0	3580	1043	36	3	2033	3	CMIP	16	81736275	Splice_Site	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	13511509	81736275	8618478	219	4875										
IL17C	27189	hgsc.bcm.edu	37	chr16	88705412	88705412	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctccccggcctcctgtttctGacctggctgcacacatgcct	8	18	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:88705412G>A	ENST00000244241.4	+	2	79	c.30G>A	c.(28-30)ctG>ctA	p.L10L		NM_013278.3	NP_037410.1	Q9P0M4	IL17C_HUMAN	interleukin 17C	10					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|neutrophil differentiation (GO:0030223)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)			large_intestine(1)|lung(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0477)		TCCTGTTTCTGACCTGGCTGC	0.647																																					p.L10L		.	.											.	IL17C	.	.	0			c.G30A						.						87	99	95					16																	88705412		1993	4161	6154	SO:0001819	synonymous_variant	27189	exon2			GTTTCTGACCTGG	AF152099	CCDS42217.1	16q24	2011-07-14			ENSG00000124391	ENSG00000124391		"Interleukins and interleukin receptors"	5983	protein-coding gene	gene with protein product		604628				10639155	Standard	NM_013278		Approved	IL-17C, CX2, IL-21, MGC126884, MGC138401	uc002fla.3	Q9P0M4		ENST00000244241.4:c.30G>A	16.37:g.88705412G>A		185.0	0.0		142.0	23.0	NM_013278	Q3MIG8|Q9HC75	Silent	SNP	ENST00000244241.4	37	CCDS42217.1																																																																																			.	.		0.647	IL17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422575.1	NM_013278		A	88705412	G	A	88705412	2	1	40	1	0	0	0	0	0	0	0	1	7645	1277	45	3		3	IL17C	16	88705412	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	6969137	88705412	1649341	220	4876										
RNF166	115992	hgsc.bcm.edu	37	chr16	88766049	88766049	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tggggataggctgtgatgtgGgcaccacggggacgaacttg	18	7	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:88766049G>T	ENST00000312838.4	-	3	499	c.404C>A	c.(403-405)cCc>cAc	p.P135H	RNF166_ENST00000562499.1_5'Flank|RNF166_ENST00000567844.1_Missense_Mutation_p.P54H|RNF166_ENST00000568683.1_Missense_Mutation_p.P26H|RNF166_ENST00000537718.2_Missense_Mutation_p.P26H|RNF166_ENST00000541206.2_Missense_Mutation_p.P26H|RP5-1142A6.5_ENST00000561699.1_RNA	NM_178841.3	NP_849163.1	Q96A37	RN166_HUMAN	ring finger protein 166	135							zinc ion binding (GO:0008270)			endometrium(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0476)		CTGTGATGTGGGCACCACGGG	0.617																																					p.P135H		.	.											.	RNF166	.	.	0			c.C404A						.						117	92	100					16																	88766049		2196	4299	6495	SO:0001583	missense	115992	exon3			GATGTGGGCACCA	AK057106	CCDS10969.1, CCDS54056.1, CCDS54057.1	16q24.3	2013-01-09			ENSG00000158717	ENSG00000158717		"RING-type (C3HC4) zinc fingers"	28856	protein-coding gene	gene with protein product						12477932	Standard	NM_178841		Approved	MGC2647, MGC14381	uc002flk.3	Q96A37	OTTHUMG00000137863	ENST00000312838.4:c.404C>A	16.37:g.88766049G>T	ENSP00000326095:p.Pro135His	135.0	0.0		94.0	53.0	NM_178841	B3KQ03|D3DX75|H3BTU8|Q96DM0	Missense_Mutation	SNP	ENST00000312838.4	37	CCDS10969.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.061536	0.76187	.	.	ENSG00000158717	ENST00000312838;ENST00000537718;ENST00000541206	T	0.15834	2.39	4.57	3.61	0.41365	.	0.115488	0.64402	D	0.000014	T	0.24470	0.0593	L	0.36672	1.1	0.58432	D	0.999999	D	0.76494	0.999	P	0.59703	0.862	T	0.01848	-1.1261	10	0.13853	T	0.58	-14.3429	14.3952	0.67005	0.0:0.1488:0.8512:0.0	.	135	Q96A37	RN166_HUMAN	H	135;54;26	ENSP00000326095:P135H	ENSP00000326095:P135H	P	-	2	0	RNF166	87293550	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	8.580000	0.90784	0.924000	0.37069	0.313000	0.20887	CCC	.	.		0.617	RNF166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269544.1	NM_178841		T	88766049	G	T	88766049	3	4	40	1	0	0	0	0	1	0	0	0	13472	1232	43	3	325	3	RNF166	16	88766049	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	60637	88766049	1588704	221	4877										
SPATA2L	124044	hgsc.bcm.edu	37	chr16	89764069	89764069	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gccaggtccccaggcctactCagctcacggcgcagagagag	13	15	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr16:89764069C>G	ENST00000289805.5	-	3	1016	c.948G>C	c.(946-948)ctG>ctC	p.L316L	SPATA2L_ENST00000335360.7_Intron	NM_152339.3	NP_689552.2	Q8IUW3	SPA2L_HUMAN	spermatogenesis associated 2-like	316										breast(1)|cervix(1)|endometrium(1)|lung(2)|skin(1)	6		Lung NSC(15;0.00043)|all_lung(18;0.000665)|all_hematologic(23;0.0355)		BRCA - Breast invasive adenocarcinoma(80;0.0272)		CAGGCCTACTCAGCTCACGGC	0.652																																					p.L316L		.	.											.	SPATA2L	.	.	0			c.G948C						.						30	33	32					16																	89764069		2197	4300	6497	SO:0001819	synonymous_variant	124044	exon3			CCTACTCAGCTCA	AF070574	CCDS10985.1	16q24.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000158792	ENSG00000158792			28393	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 76"	C16orf76		8619474	Standard	NM_152339		Approved	MGC26885, tamo	uc002foj.3	Q8IUW3	OTTHUMG00000138047	ENST00000289805.5:c.948G>C	16.37:g.89764069C>G		65.0	0.0		91.0	18.0	NM_152339	D3DX85|Q8NHV3	Silent	SNP	ENST00000289805.5	37	CCDS10985.1																																																																																			.	.		0.652	SPATA2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269923.1	NM_152339		G	89764069	C	G	89764069	2	3	40	1	0	0	0	0	0	0	0	1	15024	813	29	4		4	SPATA2L	16	89764069	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	998020	89764069	590684	222	4878										
NLRP1	22861	hgsc.bcm.edu	37	chr17	5462267	5462268	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	catctggactgaaaagggtcINStttttttgccagatgccctc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:5462267_5462268insT	ENST00000572272.1	-	4	1747_1748	c.1748_1749insA	c.(1747-1749)aagfs	p.K583fs	NLRP1_ENST00000269280.4_Frame_Shift_Ins_p.K583fs|NLRP1_ENST00000345221.3_Frame_Shift_Ins_p.K583fs|NLRP1_ENST00000262467.5_Frame_Shift_Ins_p.K583fs|NLRP1_ENST00000577119.1_Frame_Shift_Ins_p.K583fs|NLRP1_ENST00000354411.3_Frame_Shift_Ins_p.K583fs|NLRP1_ENST00000571307.1_5'UTR			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	583	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				TGAAAAGGGTCTTTTTTTGCCA	0.535																																					p.K583fs		.	.											.	NLRP1	.	.	0			c.1749_1750insA						.																																			SO:0001589	frameshift_variant	22861	exon4			.	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.1749dupA	17.37:g.5462274_5462274dupT	ENSP00000460475:p.Lys583fs	219.0	0.0		158.0	10.0	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Frame_Shift_Ins	INS	ENST00000572272.1	37	CCDS42246.1																																																																																			.	.		0.535	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		T	5462268	-	T	5462267	7	5	40	1	0	1	1	0	0	0	0	0	10480	912	32	0	2803	0	NLRP1	17	5462267	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10		5462267	75732943	223	4879										
SENP3	26168	hgsc.bcm.edu	37	chr17	7470288	7470288	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tatgataaactccgtaccaaAgggttatgatggggtgaaaa	11	5	0	3	rs76586164		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:7470288A>G	ENST00000429205.2	+	8	1356	c.1307A>G	c.(1306-1308)aAg>aGg	p.K436R	SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000321337.7_Splice_Site|SENP3_ENST00000578868.1_3'UTR			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	436	Protease.					cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				TCCGTACCAAAGGGTTATGAT	0.398																																					p.K436R		.	.											.	SENP3	.	.	0			c.A1307G						.						193	199	197					17																	7470288		989	2111	3100	SO:0001630	splice_region_variant	26168	exon8			TACCAAAGGGTTA	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"SUMO1/sentrin/SMT3 specific protease 3"			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.1306-1A>G	17.37:g.7470288A>G		405.0	0.0		209.0	23.0	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Missense_Mutation	SNP	ENST00000429205.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.4|20.4	3.977344|3.977344	0.74360|0.74360	.|.	.|.	ENSG00000161956|ENSG00000161956	ENST00000321337|ENST00000429205	.|T	.|0.28895	.|1.59	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	.|.	.|.	.|.	.|.	.|T	.|0.54902	.|0.1887	.|.	.|.	.|.	0.58432|0.58432	D|D	0.999999|0.999999	.|D	.|0.69078	.|0.997	.|D	.|0.77004	.|0.989	.|T	.|0.55755	.|-0.8091	.|8	.|0.45353	.|T	.|0.12	.|-15.252	13.941|13.941	0.64054|0.64054	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|436	.|Q9H4L4	.|SENP3_HUMAN	.|R	-1|436	.|ENSP00000403712:K436R	.|ENSP00000403712:K436R	.|K	+|+	.|2	.|0	SENP3|SENP3	7411012|7411012	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	0.000000|0.000000	0.12993|0.12993	2.179000|2.179000	0.69175|0.69175	0.421000|0.421000	0.28195|0.28195	.|AAG	A|0.500;G|0.500	.		0.398	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	Missense_Mutation	G	7470288	A	G	7470288	5	3	40	1	0	0	0	0	0	0	1	0	14063	69	3	2	1330	2	SENP3	17	7470288	Splice_Site	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	2008021	7470288	73724922	224	4880										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7701533	7701533	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aacatgctcctggtgggtatCgggggcagcggacgccagag	17	10	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:7701533C>T	ENST00000572933.1	+	54	9749	c.8289C>T	c.(8287-8289)atC>atT	p.I2763I	DNAH2_ENST00000389173.2_Silent_p.I2763I			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2763	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TGGTGGGTATCGGGGGCAGCG	0.607																																					p.I2763I		.	.											.	DNAH2	.	.	0			c.C8289T						.						64	64	64					17																	7701533		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon53			GGGTATCGGGGGC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.8289C>T	17.37:g.7701533C>T		86.0	0.0		46.0	30.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			.	.		0.607	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7701533	C	T	7701533	2	4	40	1	0	0	0	0	0	0	0	1	4604	874	31	1		1	DNAH2	17	7701533	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	231245	7701533	73493677	225	4881										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27001353	27001353	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	caggatgagcaaggcaacttGaaaggctttatcaatgacga	11	7	1	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:27001353G>T	ENST00000314616.6	+	3	445	c.162G>T	c.(160-162)ttG>ttT	p.L54F	SUPT6H_ENST00000347486.4_Missense_Mutation_p.L54F|AC010761.13_ENST00000578819.1_RNA	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	54	Asp/Glu-rich.|Interaction with IWS1. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					AAGGCAACTTGAAAGGCTTTA	0.468																																					p.L54F		.	.											.	SUPT6H	.	.	0			c.G162T						.						160	122	135					17																	27001353		2203	4300	6503	SO:0001583	missense	6830	exon3			CAACTTGAAAGGC	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.162G>T	17.37:g.27001353G>T	ENSP00000319104:p.Leu54Phe	192.0	0.0		284.0	31.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.469003	0.43839	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.92	-0.0841	0.13691	.	0.000000	0.64402	D	0.000001	T	0.36138	0.0956	N	0.08118	0	0.58432	D	0.999991	D	0.65815	0.995	D	0.70487	0.969	T	0.29941	-0.9995	9	0.10377	T	0.69	-11.5806	6.4959	0.22142	0.222:0.2314:0.5466:0.0	.	54	Q7KZ85	SPT6H_HUMAN	F	54	.	ENSP00000319104:L54F	L	+	3	2	SUPT6H	24025480	0.985000	0.35326	0.990000	0.47175	0.988000	0.76386	0.138000	0.16016	-0.202000	0.10268	-0.176000	0.13171	TTG	.	.		0.468	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27001353	G	T	27001353	3	4	40	1	0	0	0	0	1	0	0	0	15415	1281	45	3	168	3	SUPT6H	17	27001353	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	19299820	27001353	54193857	226	4882										
CDK12	51755	hgsc.bcm.edu	37	chr17	37627327	37627327	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gctgctgctgctgcagcaaaGatggatggaaaggagtccaa	14	8	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:37627327G>C	ENST00000447079.4	+	2	1275	c.1242G>C	c.(1240-1242)aaG>aaC	p.K414N	CDK12_ENST00000430627.2_Missense_Mutation_p.K414N	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	414					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CTGCAGCAAAGATGGATGGAA	0.448			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																											p.K414N		.	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	.	.	0			c.G1242C						.						55	55	55					17																	37627327		2203	4300	6503	SO:0001583	missense	51755	exon2			AGCAAAGATGGAT	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"Cyclin-dependent kinases"	24224	protein-coding gene	gene with protein product	"CDC2 related protein kinase 7"	615514	"Cdc2-related kinase, arginine/serine-rich"	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.1242G>C	17.37:g.37627327G>C	ENSP00000398880:p.Lys414Asn	119.0	0.0		174.0	26.0	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.009093	0.35415	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.44083	0.93;0.93	6.16	3.97	0.46021	.	0.000000	0.52532	D	0.000068	T	0.45617	0.1351	L	0.27053	0.805	0.33757	D	0.621339	D;D;D	0.76494	0.999;0.999;0.999	P;D;D	0.68943	0.879;0.915;0.961	T	0.58020	-0.7710	10	0.56958	D	0.05	-14.1497	7.6919	0.28573	0.7771:0.0:0.2229:0.0	.	413;414;414	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	N	414	ENSP00000407720:K414N;ENSP00000398880:K414N	ENSP00000407720:K414N	K	+	3	2	CDK12	34880853	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.519000	0.35888	1.159000	0.42565	-0.247000	0.11927	AAG	.	.		0.448	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		C	37627327	G	C	37627327	3	2	40	1	0	0	0	0	1	0	0	0	3130	933	33	4	1248	4	CDK12	17	37627327	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	10625974	37627327	43567883	227	4883										
CDK12	51755	hgsc.bcm.edu	37	chr17	37687306	37687306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttccaggggaccaggacctcCgttttgccagggtcccctta	11	14	0	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:37687306C>T	ENST00000447079.4	+	14	4243	c.4210C>T	c.(4210-4212)Cgt>Tgt	p.R1404C	CDK12_ENST00000430627.2_Missense_Mutation_p.R1395C	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1404					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CCAGGACCTCCGTTTTGCCAG	0.572			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																											p.R1404C		.	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	.	.	0			c.C4210T						.						73	76	75					17																	37687306		2203	4300	6503	SO:0001583	missense	51755	exon14			GACCTCCGTTTTG	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"Cyclin-dependent kinases"	24224	protein-coding gene	gene with protein product	"CDC2 related protein kinase 7"	615514	"Cdc2-related kinase, arginine/serine-rich"	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.4210C>T	17.37:g.37687306C>T	ENSP00000398880:p.Arg1404Cys	138.0	0.0		112.0	14.0	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.286037	0.40394	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	D;D	0.84298	-1.62;-1.83	5.34	5.34	0.76211	.	0.000000	0.49305	D	0.000145	D	0.88373	0.6419	L	0.38175	1.15	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	D	0.88897	0.3350	10	0.87932	D	0	-8.5279	13.7736	0.63039	0.1535:0.8465:0.0:0.0	.	1404;1395	Q9NYV4;Q9NYV4-2	CDK12_HUMAN;.	C	1395;1404	ENSP00000407720:R1395C;ENSP00000398880:R1404C	ENSP00000407720:R1395C	R	+	1	0	CDK12	34940832	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.412000	0.52679	2.775000	0.95449	0.650000	0.86243	CGT	.	.		0.572	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		T	37687306	C	T	37687306	3	4	40	1	0	0	0	0	1	0	0	0	3130	652	23	1	4264	1	CDK12	17	37687306	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	59979	37687306	43507904	228	4884										
KLHL10	317719	hgsc.bcm.edu	37	chr17	40004434	40004434	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gtatataccgcagtgctctgAgctgctgtgtagtaccaggg	13	9	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:40004434A>C	ENST00000293303.4	+	5	1855	c.1702A>C	c.(1702-1704)Agc>Cgc	p.S568R	RP11-156E6.1_ENST00000560400.1_RNA	NM_152467.3	NP_689680.2	Q6JEL2	KLH10_HUMAN	kelch-like family member 10	568					cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia morphogenesis (GO:0048808)|male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26		Breast(137;0.000162)				CAGTGCTCTGAGCTGCTGTGT	0.448																																					p.S568R		.	.											.	KLHL10	.	.	0			c.A1702C						.						122	121	121					17																	40004434		2007	4186	6193	SO:0001583	missense	317719	exon5			GCTCTGAGCTGCT	AK057224	CCDS42340.1	17q21.2	2013-01-30	2013-01-30		ENSG00000161594	ENSG00000161594		"Kelch-like", "BTB/POZ domain containing"	18829	protein-coding gene	gene with protein product		608778	"kelch-like 10 (Drosophila)"				Standard	NM_152467		Approved	FLJ32662	uc010cxr.3	Q6JEL2	OTTHUMG00000152510	ENST00000293303.4:c.1702A>C	17.37:g.40004434A>C	ENSP00000293303:p.Ser568Arg	270.0	0.0		387.0	201.0	NM_152467	Q6NW28|Q96MC0	Missense_Mutation	SNP	ENST00000293303.4	37	CCDS42340.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.376683	0.82682	.	.	ENSG00000161594	ENST00000293303	T	0.68765	-0.35	6.17	6.17	0.99709	Galactose oxidase, beta-propeller (1);	0.037755	0.85682	N	0.000000	T	0.73768	0.3629	L	0.32530	0.975	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.71955	-0.4436	9	.	.	.	.	15.6462	0.77055	1.0:0.0:0.0:0.0	.	568	Q6JEL2	KLH10_HUMAN	R	568	ENSP00000293303:S568R	.	S	+	1	0	KLHL10	37257960	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.020000	0.76419	2.371000	0.80710	0.533000	0.62120	AGC	.	.		0.448	KLHL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326535.1	NM_152467		C	40004434	A	C	40004434	3	2	40	1	0	0	0	0	1	0	0	0	8375	304	11	5	1720	5	KLHL10	17	40004434	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	2317128	40004434	41190776	229	4885										
KLHL11	55175	hgsc.bcm.edu	37	chr17	40010740	40010740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	caggactaaagttgccatgtCctccaatgctatagagcttc	8	11	0	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:40010740C>T	ENST00000319121.3	-	2	1439	c.1379G>A	c.(1378-1380)gGa>gAa	p.G460E		NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	460										NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				GTTGCCATGTCCTCCAATGCT	0.388																																					p.G460E		.	.											.	KLHL11	.	.	0			c.G1379A						.						123	126	125					17																	40010740		2203	4300	6503	SO:0001583	missense	55175	exon2			CCATGTCCTCCAA		CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"Kelch-like", "BTB/POZ domain containing"	19008	protein-coding gene	gene with protein product			"kelch-like 11 (Drosophila)"				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.1379G>A	17.37:g.40010740C>T	ENSP00000314608:p.Gly460Glu	350.0	0.0		498.0	45.0	NM_018143		Missense_Mutation	SNP	ENST00000319121.3	37	CCDS11411.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.692021	0.68271	.	.	ENSG00000178502	ENST00000319121;ENST00000540254	D	0.99494	-6.01	4.73	4.73	0.59995	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.99739	0.9897	H	0.97214	3.96	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97090	0.9790	10	0.87932	D	0	9.2103	18.2506	0.90002	0.0:1.0:0.0:0.0	.	460	Q9NVR0	KLH11_HUMAN	E	460;323	ENSP00000314608:G460E	ENSP00000314608:G460E	G	-	2	0	KLHL11	37264266	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	7.185000	0.77714	2.606000	0.88127	0.585000	0.79938	GGA	.	.		0.388	KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143		T	40010740	C	T	40010740	3	4	40	1	0	0	0	0	1	0	0	0	8376	855	30	3	751	3	KLHL11	17	40010740	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	6306	40010740	41184470	230	4886										
EZH1	2145	hgsc.bcm.edu	37	chr17	40871173	40871173	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tcagggaacattgaggcaatTgcactgaagatcatgtcatt	10	7	3	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:40871173T>C	ENST00000428826.2	-	8	838	c.717A>G	c.(715-717)gcA>gcG	p.A239A	EZH1_ENST00000585893.1_Silent_p.A199A|EZH1_ENST00000435174.1_Silent_p.A100A|EZH1_ENST00000415827.2_Silent_p.A230A|EZH1_ENST00000590078.1_Silent_p.A169A|EZH1_ENST00000592743.1_Silent_p.A239A			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	239					anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)			breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		TTGAGGCAATTGCACTGAAGA	0.443																																					p.A239A		.	.											.	EZH1	.	.	0			c.A717G						.						318	277	291					17																	40871173		2203	4300	6503	SO:0001819	synonymous_variant	2145	exon8			GGCAATTGCACTG		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.717A>G	17.37:g.40871173T>C		266.0	0.0		325.0	45.0	NM_001991	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Silent	SNP	ENST00000428826.2	37	CCDS32659.1																																																																																			.	.		0.443	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		C	40871173	T	C	40871173	2	2	40	1	0	0	0	0	0	0	0	1	5335	1799	63	2		2	EZH1	17	40871173	Silent	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	860433	40871173	40324037	231	4887										
BRCA1	672	hgsc.bcm.edu	37	chr17	41223109	41223109	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tggactctgggcagattctgCaactttcaattggggaactt	11	8	3	1	rs80359888|rs397507238		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:41223109C>T	ENST00000357654.3	-	15	4940	c.4822G>A	c.(4822-4824)Gca>Aca	p.A1608T	BRCA1_ENST00000309486.4_Missense_Mutation_p.A1312T|BRCA1_ENST00000471181.2_Missense_Mutation_p.A1629T|BRCA1_ENST00000346315.3_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.A1561T|BRCA1_ENST00000591534.1_Missense_Mutation_p.A99T|BRCA1_ENST00000491747.2_Missense_Mutation_p.A504T|BRCA1_ENST00000351666.3_Missense_Mutation_p.A425T|BRCA1_ENST00000468300.1_Missense_Mutation_p.A504T|BRCA1_ENST00000352993.3_Missense_Mutation_p.A466T|BRCA1_ENST00000354071.3_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1608					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GCAGATTCTGCAACTTTCAAT	0.483			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.A1629T		.	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	.	.	0			c.G4885A						.						142	136	138					17																	41223109		2203	4300	6503	SO:0001583	missense	672	exon16	Familial Cancer Database		ATTCTGCAACTTT	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.4822G>A	17.37:g.41223109C>T	ENSP00000350283:p.Ala1608Thr	195.0	0.0		262.0	41.0	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.719755	0.30503	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000352993;ENST00000351666;ENST00000309486;ENST00000468300;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747;ENST00000478531;ENST00000484087;ENST00000493919	D;D;D;D;D;D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16;-2.16;-2.16;-2.16;-2.16;-2.16	4.65	2.62	0.31277	BRCT (1);	0.726285	0.12356	N	0.476100	T	0.80025	0.4548	N	0.24115	0.695	0.09310	N	1	P;P;B;P;B;P;B;P	0.40731	0.608;0.501;0.281;0.688;0.281;0.608;0.031;0.728	B;B;B;B;B;B;B;P	0.44359	0.193;0.081;0.112;0.218;0.112;0.261;0.006;0.447	T	0.70375	-0.4889	10	0.56958	D	0.05	.	5.7699	0.18247	0.0:0.6954:0.2002:0.1044	.	504;457;503;505;504;1630;1608;1608	E7EUM2;B4DES0;E7ETR2;P38398-3;Q6IN79;E9PFC7;P38398;P38398-2	.;.;.;.;.;.;BRCA1_HUMAN;.	T	1608;1629;466;425;1312;504;457;1630;1561;503;504;379;458	ENSP00000350283:A1608T;ENSP00000312236:A466T;ENSP00000338007:A425T;ENSP00000310938:A1312T;ENSP00000417148:A504T;ENSP00000377294:A457T;ENSP00000418775:A1561T;ENSP00000420412:A504T;ENSP00000419481:A379T;ENSP00000418819:A458T	ENSP00000310938:A1312T	A	-	1	0	BRCA1	38476635	0.001000	0.12720	0.176000	0.23000	0.096000	0.18686	0.191000	0.17076	1.272000	0.44329	0.563000	0.77884	GCA	.	.		0.483	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		T	41223109	C	T	41223109	3	4	40	1	0	0	0	0	1	0	0	0	1500	710	25	3	805	3	BRCA1	17	41223109	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	351936	41223109	39972101	232	4888										
NBR1	4077	hgsc.bcm.edu	37	chr17	41352494	41352495	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggcaggaaccagctgaggctINSggggaaagactccctggagg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:41352494_41352495insG	ENST00000422280.1	+	17	2796_2797	c.2337_2338insG	c.(2338-2340)gggfs	p.G780fs	NBR1_ENST00000589872.1_Frame_Shift_Ins_p.G780fs|NBR1_ENST00000590996.1_Frame_Shift_Ins_p.G780fs|NBR1_ENST00000542611.1_Frame_Shift_Ins_p.G759fs|NBR1_ENST00000389312.4_Frame_Shift_Ins_p.G780fs|NBR1_ENST00000341165.6_Frame_Shift_Ins_p.G780fs	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	780					macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		CAGCTGAGGCTGGGGAAAGACT	0.594																																					p.A779fs		.	.											.	NBR1	.	.	0			c.2337_2338insG						.																																			SO:0001589	frameshift_variant	4077	exon17			.	X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.2341dupG	17.37:g.41352498_41352498dupG	ENSP00000411250:p.Gly780fs	76.0	0.0		93.0	10.0	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Frame_Shift_Ins	INS	ENST00000422280.1	37	CCDS45694.1																																																																																			.	.		0.594	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		G	41352495	-	G	41352494	7	5	40	1	0	1	1	0	0	0	0	0	10209	1567	55	0	2399	0	NBR1	17	41352494	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	129385	41352494	39842716	233	4889										
MYL4	4635	hgsc.bcm.edu	37	chr17	45299202	45299202	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gtcatgggtgctgagcttcgGcacgtccttgccaccctggg	14	13	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:45299202G>C	ENST00000354968.1	+	5	596	c.468G>C	c.(466-468)cgG>cgC	p.R156R	MYL4_ENST00000572316.1_Silent_p.R156R|MYL4_ENST00000393450.1_Silent_p.R156R|snoU13_ENST00000516279.1_RNA	NM_001002841.1	NP_001002841.1	P12829	MYL4_HUMAN	myosin, light chain 4, alkali; atrial, embryonic	156	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cardiac muscle contraction (GO:0060048)|muscle filament sliding (GO:0030049)|positive regulation of ATPase activity (GO:0032781)|regulation of the force of heart contraction (GO:0002026)	A band (GO:0031672)|cytosol (GO:0005829)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|calcium ion binding (GO:0005509)|myosin II heavy chain binding (GO:0032038)			endometrium(2)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)	11						CTGAGCTTCGGCACGTCCTTG	0.592																																					p.R156R		.	.											.	MYL4	.	.	0			c.G468C						.						97	73	81					17																	45299202		2203	4300	6503	SO:0001819	synonymous_variant	4635	exon5			GCTTCGGCACGTC		CCDS11510.1	17q21.32	2013-09-19	2006-09-29		ENSG00000198336	ENSG00000198336		"Myosins / Light chain", "EF-hand domain containing"	7585	protein-coding gene	gene with protein product	"myosin, atrial/fetal muscle, light chain"	160770	"myosin, light polypeptide 4, alkali; atrial, embryonic"			3417683	Standard	NM_002476		Approved	ALC1, AMLC, GT1, PRO1957	uc002ilg.3	P12829	OTTHUMG00000178232	ENST00000354968.1:c.468G>C	17.37:g.45299202G>C		144.0	0.0		167.0	83.0	NM_001002841	D3DXJ7|P11783	Silent	SNP	ENST00000354968.1	37	CCDS11510.1																																																																																			.	.		0.592	MYL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441059.1	NM_001002841		C	45299202	G	C	45299202	2	2	40	1	0	0	0	0	0	0	0	1	10058	1190	42	4		4	MYL4	17	45299202	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	3946708	45299202	35896008	234	4890										
SPAG9	9043	hgsc.bcm.edu	37	chr17	49075937	49075937	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gattaacaggtggttcaggcTtcttagtcgtgttacttgag	12	6	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:49075937T>G	ENST00000262013.7	-	15	1914	c.1706A>C	c.(1705-1707)aAg>aCg	p.K569T	SPAG9_ENST00000357122.4_Missense_Mutation_p.K555T|SPAG9_ENST00000505279.1_Missense_Mutation_p.K559T|SPAG9_ENST00000510283.1_Missense_Mutation_p.K412T	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	569					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			TGGTTCAGGCTTCTTAGTCGT	0.438																																					p.K569T		.	.											.	SPAG9	.	.	0			c.A1706C						.						164	138	147					17																	49075937		2203	4300	6503	SO:0001583	missense	9043	exon15			TCAGGCTTCTTAG	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.1706A>C	17.37:g.49075937T>G	ENSP00000262013:p.Lys569Thr	288.0	0.0		386.0	47.0	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.515151	0.85389	.	.	ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	T;T;D;T	0.89810	2.14;2.14;-2.57;2.14	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.89567	0.6752	L	0.47716	1.5	0.51233	D	0.999919	D;P;B;B;P;P	0.54207	0.965;0.766;0.067;0.04;0.878;0.575	P;B;B;B;B;B	0.52481	0.7;0.406;0.103;0.029;0.441;0.219	D	0.88074	0.2802	10	0.30078	T	0.28	-18.587	15.9886	0.80183	0.0:0.0:0.0:1.0	.	555;569;559;569;555;412	O60271-5;O60271-3;O60271-2;O60271;O60271-4;E7ENU2	.;.;.;JIP4_HUMAN;.;.	T	569;325;315;412;559;555;167	ENSP00000262013:K569T;ENSP00000423165:K412T;ENSP00000426900:K559T;ENSP00000349636:K555T	ENSP00000262013:K569T	K	-	2	0	SPAG9	46430936	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.243000	0.72384	2.178000	0.69098	0.482000	0.46254	AAG	.	.		0.438	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		G	49075937	T	G	49075937	3	3	40	1	0	0	0	0	1	0	0	0	15000	1609	56	5	2323	5	SPAG9	17	49075937	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	3776735	49075937	32119273	235	4891										
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56389687	56389687	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccccaggccccagggcctgtCgcagctccccattcacacag	9	20	1	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:56389687C>T	ENST00000343736.4	-	17	2658	c.2495G>A	c.(2494-2496)cGa>cAa	p.R832Q	BZRAP1_ENST00000355701.3_Missense_Mutation_p.R832Q|BZRAP1_ENST00000268893.6_Missense_Mutation_p.R772Q			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	832	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CAGGGCCTGTCGCAGCTCCCC	0.667																																					p.R832Q		.	.											.	BZRAP1	.	.	0			c.G2495A						.						20	22	21					17																	56389687		2202	4298	6500	SO:0001583	missense	9256	exon17			GCCTGTCGCAGCT	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.2495G>A	17.37:g.56389687C>T	ENSP00000345824:p.Arg832Gln	92.0	0.0		85.0	15.0	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.603024	0.46423	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.10960	2.84;2.84;2.82	4.86	-0.621	0.11564	Fibronectin, type III (2);	0.181808	0.50627	N	0.000115	T	0.22244	0.0536	M	0.80183	2.485	0.45194	D	0.9982	B;D;D	0.69078	0.272;0.997;0.985	B;P;P	0.56865	0.022;0.808;0.784	T	0.05131	-1.0904	10	0.29301	T	0.29	.	9.6507	0.39895	0.0:0.6227:0.0:0.3773	.	832;772;832	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	Q	832;832;772	ENSP00000347929:R832Q;ENSP00000345824:R832Q;ENSP00000268893:R772Q	ENSP00000268893:R772Q	R	-	2	0	BZRAP1	53744686	0.130000	0.22417	0.230000	0.23976	0.133000	0.20885	0.749000	0.26320	-0.011000	0.14247	-0.368000	0.07277	CGA	.	.		0.667	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		T	56389687	C	T	56389687	3	4	40	1	0	0	0	0	1	0	0	0	1579	884	31	1	3138	1	BZRAP1	17	56389687	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	7313750	56389687	24805523	236	4892										
CBX4	8535	hgsc.bcm.edu	37	chr17	77808830	77808831	+	Frame_Shift_Ins	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cgcccccaggtagcctttggINScccccgcaccttgcgcccac							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:77808830_77808831insC	ENST00000269397.4	-	5	787_788	c.610_611insG	c.(610-612)gccfs	p.A204fs		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	204	Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GTAGCCTTTGGCCCCCGCACCT	0.738											OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A204fs		.	.											.	CBX4	.	.	0			c.611_612insG						.																																			SO:0001589	frameshift_variant	8535	exon5			.	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"NS5ATP1-binding protein 16", "Pc class 2 homolog (Drosophila)"	603079	"chromobox homolog 4 (Drosophila Pc class)"			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.611dupG	17.37:g.77808835_77808835dupC	ENSP00000269397:p.Ala204fs	78.0	0.0	1178	206.0	12.0	NM_003655	B1PJR7|Q6TPI8|Q96C04	Frame_Shift_Ins	INS	ENST00000269397.4	37	CCDS32758.1																																																																																			.	.		0.738	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655		C	77808831	-	C	77808830	7	5	40	1	0	1	1	0	0	0	0	0	2722	1203	42	0	1075	0	CBX4	17	77808830	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	21419143	77808830	3386380	237	4893										
SLC38A10	124565	hgsc.bcm.edu	37	chr17	79226065	79226066	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcggcggtccccccttggccINSttttcccctccacccaccgc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr17:79226065_79226066insT	ENST00000374759.3	-	13	2257_2258	c.1874_1875insA	c.(1873-1875)aagfs	p.K625fs	SLC38A10_ENST00000288439.5_Frame_Shift_Ins_p.K625fs	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	625					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCCCCTTGGCCTTTTCCCCTCC	0.708																																					p.K625fs		.	.											.	SLC38A10	.	.	0			c.1875_1876insA						.																																			SO:0001589	frameshift_variant	124565	exon13			.	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.1875dupA	17.37:g.79226069_79226069dupT	ENSP00000363891:p.Lys625fs	114.0	0.0		132.0	11.0	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Frame_Shift_Ins	INS	ENST00000374759.3	37	CCDS42397.1																																																																																			.	.		0.708	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		T	79226066	-	T	79226065	7	5	40	1	0	1	1	0	0	0	0	0	14617	680	24	0	1778	0	SLC38A10	17	79226065	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	1417235	79226065	1969145	238	4894										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9255075	9255076	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aaaatcttgtaagcataaggINSaaaaaagcaaacatcagaaa							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr18:9255075_9255076insA	ENST00000262126.4	+	9	2050_2051	c.1810_1811insA	c.(1810-1812)gaafs	p.E604fs	ANKRD12_ENST00000400020.3_Frame_Shift_Ins_p.E581fs|ANKRD12_ENST00000383440.2_Frame_Shift_Ins_p.E581fs	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	604				E -> K (in Ref. 5; CAH56382). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						TAAGCATAAGGAAAAAAGCAAA	0.317																																					p.E604fs		.	.											.	ANKRD12	.	.	0			c.1810_1811insA						.																																			SO:0001589	frameshift_variant	23253	exon9			.	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.1816dupA	18.37:g.9255081_9255081dupA	ENSP00000262126:p.Glu604fs	280.0	0.0		198.0	14.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Frame_Shift_Ins	INS	ENST00000262126.4	37	CCDS11843.1																																																																																			.	.		0.317	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		A	9255076	-	A	9255075	7	5	40	1	0	1	1	0	0	0	0	0	640	1175	41	0	1840	0	ANKRD12	18	9255075	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10		9255075	68822173	239	4895										
ESCO1	114799	hgsc.bcm.edu	37	chr18	19112484	19112484	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttcttccgacgcatcatgctGaatacccatattcgactgat	6	12	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr18:19112484G>A	ENST00000269214.5	-	11	3262	c.2325C>T	c.(2323-2325)ttC>ttT	p.F775F		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	775					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)			breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						GCATCATGCTGAATACCCATA	0.413																																					p.F775F		.	.											.	ESCO1	.	.	0			c.C2325T						.						154	144	148					18																	19112484		2203	4300	6503	SO:0001819	synonymous_variant	114799	exon11			CATGCTGAATACC	AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.2325C>T	18.37:g.19112484G>A		285.0	0.0		229.0	155.0	NM_052911	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Silent	SNP	ENST00000269214.5	37	CCDS32800.1																																																																																			.	.		0.413	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		A	19112484	G	A	19112484	2	1	40	1	0	0	0	0	0	0	0	1	5250	1281	45	3		3	ESCO1	18	19112484	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	9857409	19112484	58964764	240	4896										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21331052	21331052	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gatccaactgtcactcggcgGgtgagtagtcagagcatttg	13	9	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr18:21331052G>T	ENST00000313654.9	+	5	1096	c.855G>T	c.(853-855)cgG>cgT	p.R285R	LAMA3_ENST00000399516.3_Splice_Site_p.R285R	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	285	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TCACTCGGCGGGTGAGTAGTC	0.403																																					p.R285R		.	.											.	LAMA3	.	.	0			c.G855T						.						84	83	83					18																	21331052		1861	4108	5969	SO:0001630	splice_region_variant	3909	exon5			TCGGCGGGTGAGT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.855+1G>T	18.37:g.21331052G>T		161.0	0.0		111.0	28.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			.	.		0.403	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	Silent	T	21331052	G	T	21331052	5	4	40	1	0	0	0	0	0	0	1	0	8616	1246	43	3	873	3	LAMA3	18	21331052	Splice_Site	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	2218568	21331052	56746196	241	4897										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22804595	22804595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cgctcttactgagattcacgCagccggcacacagaccatat	8	14	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr18:22804595C>T	ENST00000361524.3	-	4	3435	c.3287G>A	c.(3286-3288)tGc>tAc	p.C1096Y	ZNF521_ENST00000584787.1_Missense_Mutation_p.C876Y|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Missense_Mutation_p.C1096Y	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1096					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GAGATTCACGCAGCCGGCACA	0.517			T	PAX5	ALL																																p.C1096Y		.	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	.	.	0			c.G3287A						.						88	81	83					18																	22804595		2203	4300	6503	SO:0001583	missense	25925	exon4			TTCACGCAGCCGG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3287G>A	18.37:g.22804595C>T	ENSP00000354794:p.Cys1096Tyr	135.0	0.0		104.0	75.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.775366	0.31411	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.28895	2.37;1.59	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.47911	0.1471	L	0.32530	0.975	0.58432	D	0.999996	D	0.76494	0.999	D	0.70487	0.969	T	0.42965	-0.9420	10	0.87932	D	0	-20.51	20.1996	0.98256	0.0:1.0:0.0:0.0	.	1096	Q96K83	ZN521_HUMAN	Y	1096;1130;1096	ENSP00000354794:C1096Y;ENSP00000382352:C1096Y	ENSP00000354794:C1096Y	C	-	2	0	ZNF521	21058593	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.482000	0.81143	2.776000	0.95493	0.650000	0.86243	TGC	.	.		0.517	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		T	22804595	C	T	22804595	3	4	40	1	0	0	0	0	1	0	0	0	17980	710	25	3	668	3	ZNF521	18	22804595	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1473543	22804595	55272653	242	4898										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43458391	43458391	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggcttaaagagctgaatgatTactgaatgtagggatttcag	12	4	1	4			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr18:43458391T>C	ENST00000282041.5	-	34	5926	c.5892A>G	c.(5890-5892)gtA>gtG	p.V1964V	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1964					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						GCTGAATGATTACTGAATGTA	0.323																																					p.V1964V		.	.											.	EPG5	.	.	0			c.A5892G						.						78	71	73					18																	43458391		1815	4068	5883	SO:0001819	synonymous_variant	57724	exon34			AATGATTACTGAA	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.5892A>G	18.37:g.43458391T>C		80.0	0.0		113.0	12.0	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	37	CCDS11926.2																																																																																			.	.		0.323	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43458391	T	C	43458391	2	2	40	1	0	0	0	0	0	0	0	1	8258	1741	61	2		2	KIAA1632	18	43458391	Silent	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	20653796	43458391	34618857	243	4899										
RTTN	25914	hgsc.bcm.edu	37	chr18	67794863	67794863	+	Missense_Mutation	SNP	C	C	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gtgacagcagccctaacttcCctgtgggttgcagcctgaac							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr18:67794863C>A	ENST00000255674.6	-	25	3544	c.3258G>T	c.(3256-3258)agG>agT	p.R1086S	RTTN_ENST00000454359.1_3'UTR|RTTN_ENST00000437017.1_Missense_Mutation_p.R1086S	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1086					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CCCTAACTTCCCTGTGGGTTG	0.483																																					p.R1086S		.	.											.	RTTN	.	.	0			c.G3258T						.						66	65	65					18																	67794863		1931	4135	6066	SO:0001583	missense	25914	exon25			AACTTCCCTGTGG	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.3258G>T	18.37:g.67794863C>A	ENSP00000255674:p.Arg1086Ser	93.0	0.0		71.0	55.0	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	C	10.90	1.481072	0.26598	.	.	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.19806	2.12;2.12	5.37	3.48	0.39840	.	0.326303	0.35235	N	0.003348	T	0.14270	0.0345	L	0.39633	1.23	0.80722	D	1	B	0.30824	0.296	B	0.22753	0.041	T	0.07501	-1.0769	10	0.16896	T	0.51	.	10.6687	0.45745	0.0:0.7959:0.132:0.0721	.	1086	Q86VV8	RTTN_HUMAN	S	1086	ENSP00000255674:R1086S;ENSP00000399520:R1086S	ENSP00000255674:R1086S	R	-	3	2	RTTN	65945843	0.993000	0.37304	1.000000	0.80357	0.977000	0.68977	0.196000	0.17176	1.266000	0.44231	-0.143000	0.13931	AGG	.	.		0.483	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		A	67794863	C	A	67794863	3	1	40	1	0	0	0	0	1	0	0	0	13752	622	22	3	3522	3	RTTN	18	67794863	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	24336472	67794863	10282385	244	4900	22	2								
RTTN	25914	hgsc.bcm.edu	37	chr18	67794864	67794864	+	Missense_Mutation	SNP	C	C	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgacagcagccctaacttccCtgtgggttgcagcctgaaca					rs199762299		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr18:67794864C>A	ENST00000255674.6	-	25	3543	c.3257G>T	c.(3256-3258)aGg>aTg	p.R1086M	RTTN_ENST00000454359.1_3'UTR|RTTN_ENST00000437017.1_Missense_Mutation_p.R1086M	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1086					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CCTAACTTCCCTGTGGGTTGC	0.483																																					p.R1086M		.	.											.	RTTN	.	.	0			c.G3257T						.						66	65	65					18																	67794864		1930	4135	6065	SO:0001583	missense	25914	exon25			ACTTCCCTGTGGG	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.3257G>T	18.37:g.67794864C>A	ENSP00000255674:p.Arg1086Met	94.0	0.0		71.0	55.0	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.097593	0.76870	.	.	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.21734	1.99;1.99	5.37	4.3	0.51218	.	0.326303	0.35235	N	0.003348	T	0.36331	0.0963	L	0.56769	1.78	0.80722	D	1	D	0.65815	0.995	P	0.56823	0.807	T	0.09707	-1.0662	10	0.54805	T	0.06	.	14.9358	0.70954	0.0:0.919:0.0:0.081	.	1086	Q86VV8	RTTN_HUMAN	M	1086	ENSP00000255674:R1086M;ENSP00000399520:R1086M	ENSP00000255674:R1086M	R	-	2	0	RTTN	65945844	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.412000	0.52679	2.511000	0.84671	0.650000	0.86243	AGG	C|0.999;G|0.000	.		0.483	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		A	67794864	C	A	67794864	3	1	40	1	0	0	0	0	1	0	0	0	13752	681	24	3	3523	3	RTTN	18	67794864	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1	67794864	10282384	245	4901	22	2								
DOT1L	84444	hgsc.bcm.edu	37	chr19	2202716	2202716	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cagtgttatatttgtgaataAttttgcctttggtcctgagg	10	5	0	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:2202716A>G	ENST00000398665.3	+	9	761	c.725A>G	c.(724-726)aAt>aGt	p.N242S		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	242	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTTGTGAATAATTTTGCCTTT	0.537																																					p.N242S		.	.											.	DOT1L	.	.	0			c.A725G						.						184	191	189					19																	2202716		1996	4163	6159	SO:0001583	missense	84444	exon9			TGAATAATTTTGC	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.725A>G	19.37:g.2202716A>G	ENSP00000381657:p.Asn242Ser	346.0	0.0		287.0	203.0	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.3|23.3	4.401898|4.401898	0.83120|0.83120	.|.	.|.	ENSG00000104885|ENSG00000104885	ENST00000440640|ENST00000398665;ENST00000221482	.|T	.|0.23754	.|1.89	4.49|4.49	4.49|4.49	0.54785|0.54785	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.59865|0.59865	0.2225|0.2225	M|M	0.93978|0.93978	3.48|3.48	0.58432|0.58432	D|D	0.999995|0.999995	.|D	.|0.76494	.|0.999	.|D	.|0.79108	.|0.992	T|T	0.71424|0.71424	-0.4597|-0.4597	5|10	.|0.87932	.|D	.|0	-37.1699|-37.1699	12.9757|12.9757	0.58537|0.58537	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|242	.|Q8TEK3-2	.|.	V|S	29|242	.|ENSP00000381657:N242S	.|ENSP00000221482:N242S	I|N	+|+	1|2	0|0	DOT1L|DOT1L	2153716|2153716	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	8.830000|8.830000	0.92063|0.92063	1.662000|1.662000	0.50781|0.50781	0.379000|0.379000	0.24179|0.24179	ATT|AAT	.	.		0.537	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		G	2202716	A	G	2202716	3	3	40	1	0	0	0	0	1	0	0	0	4711	101	4	2	759	2	DOT1L	19	2202716	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10		2202716	56926267	246	4902										
PIAS4	51588	hgsc.bcm.edu	37	chr19	4037690	4037690	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctgggcagcacgggtggcggCggcccggtgggcagcatgga	21	11	0	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:4037690C>T	ENST00000262971.2	+	11	1465	c.1350C>T	c.(1348-1350)ggC>ggT	p.G450G		NM_015897.2	NP_056981.2	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	450					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(3)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGGTGGCGGCGGCCCGGTGG	0.706																																					p.G450G		.	.											.	PIAS4	.	.	0			c.C1350T						.																																			SO:0001819	synonymous_variant	51588	exon11			TGGCGGCGGCCCG	AF077952	CCDS12118.1	19p13.3	2011-10-11						"Zinc fingers, MIZ-type"	17002	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 6"	605989				9724754	Standard	NM_015897		Approved	Piasg, PIASY, FLJ12419, ZMIZ6	uc002lzg.3	Q8N2W9		ENST00000262971.2:c.1350C>T	19.37:g.4037690C>T		33.0	0.0		68.0	37.0	NM_015897	O75926|Q96G19|Q9UN16	Silent	SNP	ENST00000262971.2	37	CCDS12118.1																																																																																			.	.		0.706	PIAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457496.1	NM_015897		T	4037690	C	T	4037690	2	4	40	1	0	0	0	0	0	0	0	1	11887	755	27	1		1	PIAS4	19	4037690	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1834974	4037690	55091293	247	4903										
ZNF20	7568	hgsc.bcm.edu	37	chr19	12243428	12243428	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	attaatggtatgagttctttCatgttctcgacatgaactgg	9	6	3	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:12243428C>G	ENST00000334213.5	-	4	1797	c.1573G>C	c.(1573-1575)Gaa>Caa	p.E525Q	ZNF20_ENST00000600335.1_Intron|ZNF625-ZNF20_ENST00000430024.1_3'UTR|ZNF20_ENST00000485451.1_5'Flank	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	525					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|lung(6)	8						TGAGTTCTTTCATGTTCTCGA	0.403																																					p.E525Q		.	.											.	ZNF20	.	.	0			c.G1573C						.						146	156	153					19																	12243428		2160	4285	6445	SO:0001583	missense	7568	exon4			TTCTTTCATGTTC	X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"Zinc fingers, C2H2-type", "-"	12992	protein-coding gene	gene with protein product		194557	"zinc finger protein 20 (KOX 13)"				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.1573G>C	19.37:g.12243428C>G	ENSP00000335437:p.Glu525Gln	145.0	0.0		192.0	67.0	NM_021143	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	37	CCDS45986.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.039|9.039	0.989099|0.989099	0.18966|0.18966	.|.	.|.	ENSG00000132010|ENSG00000132010	ENST00000334213|ENST00000292241	T|.	0.01484|.	4.84|.	0.94|0.94	-0.173|-0.173	0.13322|0.13322	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	.|.	.|.	.|.	.|.	T|T	0.21347|0.21347	0.0514|0.0514	N|N	0.17345|0.17345	0.48|0.48	0.19775|0.19775	N|N	0.99996|0.99996	P|.	0.43477|.	0.808|.	B|.	0.39027|.	0.288|.	T|T	0.25779|0.25779	-1.0122|-1.0122	9|6	0.02654|0.87932	T|D	1|0	.|.	3.1081|3.1081	0.06348|0.06348	0.0:0.6655:0.0:0.3345|0.0:0.6655:0.0:0.3345	.|.	525|.	P17024|.	ZNF20_HUMAN|.	Q|I	525|524	ENSP00000335437:E525Q|.	ENSP00000335437:E525Q|ENSP00000292241:M524I	E|M	-|-	1|3	0|0	ZNF20|ZNF20	12104428|12104428	0.000000|0.000000	0.05858|0.05858	0.040000|0.040000	0.18447|0.18447	0.791000|0.791000	0.44710|0.44710	-1.527000|-1.527000	0.02227|0.02227	-0.041000|-0.041000	0.13558|0.13558	0.313000|0.313000	0.20887|0.20887	GAA|ATG	.	.		0.403	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143		G	12243428	C	G	12243428	3	3	40	1	0	0	0	0	1	0	0	0	17776	835	29	4	29	4	ZNF20	19	12243428	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	8205738	12243428	46885555	248	4904										
PRDX2	7001	hgsc.bcm.edu	37	chr19	12911099	12911100	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcccaagcctccctctttccINSggggggtgttgatcctggga					rs369634820|rs541050535		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:12911099_12911100insG	ENST00000301522.2	-	4	399_400	c.271_272insC	c.(271-273)cggfs	p.R91fs	CTD-2659N19.10_ENST00000585496.1_RNA|PRDX2_ENST00000334482.5_Frame_Shift_Ins_p.R91fs	NM_005809.4	NP_005800.3	P32119	PRDX2_HUMAN	peroxiredoxin 2	91	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular response to oxidative stress (GO:0034599)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of apoptotic process (GO:0042981)|removal of superoxide radicals (GO:0019430)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)|thioredoxin peroxidase activity (GO:0008379)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4						TCCCTCTTTCCGGGGGGTGTTG	0.599																																					p.I91fs		.	.											.	PRDX2	.	.	0			c.272_273insC						.																																			SO:0001589	frameshift_variant	7001	exon4			.		CCDS12281.1	19p13.2	2008-07-17			ENSG00000167815	ENSG00000167815			9353	protein-coding gene	gene with protein product	"thioredoxin-dependent peroxide reductase 1", "thiol-specific antioxidant 1", "natural killer-enhancing factor B", "thioredoxin peroxidase 1", "torin"	600538		TDPX1		7607688	Standard	NM_005809		Approved	PRP, NKEFB, TSA, PRXII, PRX2, MGC4104	uc002mvd.4	P32119	OTTHUMG00000134285	ENST00000301522.2:c.272dupC	19.37:g.12911105_12911105dupG	ENSP00000301522:p.Arg91fs	212.0	0.0		184.0	11.0	NM_005809	A8K0C0|P31945|P32118|P35701|Q6FHG4|Q92763|Q9UC23	Frame_Shift_Ins	INS	ENST00000301522.2	37	CCDS12281.1																																																																																			.	.		0.599	PRDX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258950.2	NM_005809		G	12911100	-	G	12911099	7	5	40	1	0	1	1	0	0	0	0	0	12477	652	23	0	336	0	PRDX2	19	12911099	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	667671	12911099	46217884	249	4905										
ZNF714	148206	hgsc.bcm.edu	37	chr19	21299774	21299774	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gtaaggtgtacaaaaaaggtTatgaactaaaccagtgtttg	10	4	0	1	rs36125838|rs57999210	byFrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:21299774T>A	ENST00000596143.1	+	5	629	c.304T>A	c.(304-306)Tat>Aat	p.Y102N	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	102				Y -> YN (in Ref. 1; BAB71072, 2; CAD39077 and 4; AAH50468). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						CAAAAAAGGTTATGAACTAAA	0.323																																					p.Y102N		.	.											.	ZNF714	.	.	0			c.T304A						.						42	41	41					19																	21299774		2187	4289	6476	SO:0001583	missense	148206	exon5			AAAGGTTATGAAC	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.304T>A	19.37:g.21299774T>A	ENSP00000472368:p.Tyr102Asn	286.0	0.0		278.0	14.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	8.069	0.769843	0.15983	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.601	0.601	0.17529	.	.	.	.	.	T	0.53562	0.1804	M	0.67517	2.055	0.09310	N	1	P;D	0.71674	0.923;0.998	P;D	0.80764	0.504;0.994	T	0.36962	-0.9726	8	0.51188	T	0.08	.	2.6817	0.05095	0.0:0.3485:0.0:0.6515	.	102;102	Q96N38-2;A6NEM4	.;.	N	102	.	ENSP00000291770:Y102N	Y	+	1	0	ZNF714	21091614	0.002000	0.14202	0.002000	0.10522	0.005000	0.04900	-0.137000	0.10389	0.506000	0.28125	0.374000	0.22700	TAT	.	.		0.323	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		A	21299774	T	A	21299774	3	1	40	1	0	0	0	0	1	0	0	0	18133	1754	61	4	314	4	ZNF714	19	21299774	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	8388675	21299774	37829209	250	4906										
ZNF675	171392	hgsc.bcm.edu	37	chr19	23836432	23836432	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ttcagtaagttttgaggatcGgttaaaagctttgccacatt	9	6	1	1	rs199957959		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:23836432G>A	ENST00000359788.4	-	4	1471	c.1303C>T	c.(1303-1305)Cga>Tga	p.R435*	ZNF675_ENST00000600313.1_Intron|ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	435					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTTGAGGATCGGTTAAAAGCT	0.378																																					p.R435X		.	.											.	ZNF675	.	.	0			c.C1303T						.						52	55	54					19																	23836432		2202	4300	6502	SO:0001587	stop_gained	171392	exon4			AGGATCGGTTAAA		CCDS32981.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	30768	protein-coding gene	gene with protein product	"TRAF6 inhibitory zinc finger"					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.1303C>T	19.37:g.23836432G>A	ENSP00000352836:p.Arg435*	82.0	0.0		70.0	6.0	NM_138330	Q8N211	Nonsense_Mutation	SNP	ENST00000359788.4	37	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	14.11	2.436250	0.43224	.	.	ENSG00000197372	ENST00000359788	.	.	.	0.876	-1.75	0.08031	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	3.7084	0.08410	0.0:0.2017:0.47:0.3283	.	.	.	.	X	435	.	ENSP00000352836:R435X	R	-	1	2	ZNF675	23628272	0.000000	0.05858	0.008000	0.14137	0.008000	0.06430	-0.308000	0.08156	-0.892000	0.03935	-0.901000	0.02856	CGA	G|0.999;A|0.001	.		0.378	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330		A	23836432	G	A	23836432	4	1	40	1	0	0	0	0	0	1	0	0	18097	1124	39	1	407	1	ZNF675	19	23836432	Nonsense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	2536658	23836432	35292551	251	4907										
C19orf46	163183	hgsc.bcm.edu	37	chr19	36496296	36496296	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agcgtttctggtggccgaggCcagactccagcatgtcctgt	13	12	1	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:36496296C>T	ENST00000324444.3	-	6	1022	c.911G>A	c.(910-912)gGc>gAc	p.G304D	SYNE4_ENST00000340477.5_Missense_Mutation_p.G191D	NM_001039876.1	NP_001034965.1	Q8N205	SYNE4_HUMAN	spectrin repeat containing, nuclear envelope family member 4	304					establishment of epithelial cell apical/basal polarity (GO:0045198)	integral component of nuclear outer membrane (GO:0031309)											GTGGCCGAGGCCAGACTCCAG	0.567																																					p.G304D		.	.											.	.	.	.	0			c.G911A						.						85	90	88					19																	36496296		2076	4218	6294	SO:0001583	missense	163183	exon6			CCGAGGCCAGACT	BC038360	CCDS42553.1	19q13.12	2014-01-28	2012-05-31	2012-05-31	ENSG00000181392	ENSG00000181392			26703	protein-coding gene	gene with protein product		615535	"chromosome 19 open reading frame 46", "deafness, autosomal recessive 76"	C19orf46, DFNB76		23348741	Standard	XM_005258597		Approved	FLJ36445, Nesprin-4, Nesp4	uc002ocq.1	Q8N205	OTTHUMG00000048135	ENST00000324444.3:c.911G>A	19.37:g.36496296C>T	ENSP00000316130:p.Gly304Asp	172.0	0.0		197.0	33.0	NM_001039876	A8MRS0|A8MYE3|Q7Z7L3	Missense_Mutation	SNP	ENST00000324444.3	37	CCDS42553.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.30|13.30	2.197423|2.197423	0.38806|0.38806	.|.	.|.	ENSG00000181392|ENSG00000181392	ENST00000397428;ENST00000340477;ENST00000324444|ENST00000490730	T;T|.	0.58210|.	0.48;0.35|.	3.99|3.99	2.94|2.94	0.34122|0.34122	.|.	.|.	.|.	.|.	.|.	T|.	0.33789|.	0.0875|.	L|L	0.32530|0.32530	0.975|0.975	0.26468|0.26468	N|N	0.975332|0.975332	B;B|.	0.29531|.	0.247;0.037|.	B;B|.	0.32583|.	0.148;0.029|.	T|.	0.18681|.	-1.0329|.	9|.	0.87932|.	D|.	0|.	-4.2898|-4.2898	8.0888|8.0888	0.30788|0.30788	0.0:0.8888:0.0:0.1112|0.0:0.8888:0.0:0.1112	.|.	191;304|.	Q8N205-2;Q8N205|.	.;SYNE4_HUMAN|.	D|X	28;191;304|244	ENSP00000343152:G191D;ENSP00000316130:G304D|.	ENSP00000316130:G304D|.	G|W	-|-	2|3	0|0	C19orf46|C19orf46	41188136|41188136	0.587000|0.587000	0.26791|0.26791	0.639000|0.639000	0.29394|0.29394	0.023000|0.023000	0.10783|0.10783	1.023000|1.023000	0.30065|0.30065	1.264000|1.264000	0.44198|0.44198	0.591000|0.591000	0.81541|0.81541	GGC|TGG	.	.		0.567	SYNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109525.3	NM_001039876		T	36496296	C	T	36496296	3	4	40	1	0	0	0	0	1	0	0	0	1931	739	26	3	315	3	C19orf46	19	36496296	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	12659864	36496296	22632687	252	4908										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40400622	40400623	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gggaagacctggtcattgttINSggggttgcggtccatgttac							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:40400622_40400623insG	ENST00000221347.6	-	12	5473_5474	c.5466_5467insC	c.(5464-5469)cccaacfs	p.N1823fs		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1823	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TGGTCATTGTTGGGGTTGCGGT	0.619																																					p.N1823fs		.	.											.	FCGBP	.	.	0			c.5467_5468insC						.																																			SO:0001589	frameshift_variant	8857	exon12			.	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.5467dupC	19.37:g.40400626_40400626dupG	ENSP00000221347:p.Asn1823fs	256.0	0.0		226.0	14.0	NM_003890	O95784	Frame_Shift_Ins	INS	ENST00000221347.6	37	CCDS12546.1																																																																																			.	.		0.619	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		G	40400623	-	G	40400622	7	5	40	1	0	1	1	0	0	0	0	0	5786	1812	63	0	10850	0	FCGBP	19	40400622	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	3904326	40400622	18728361	253	4909										
CYP2A7	1549	hgsc.bcm.edu	37	chr19	41387943	41387943	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tgccttgggacaccttcatgAtggagtcacatatgtgctct	10	10	3	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:41387943A>G	ENST00000301146.4	-	1	714	c.173T>C	c.(172-174)aTc>aCc	p.I58T	CYP2A7_ENST00000291764.3_Missense_Mutation_p.I58T|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	58						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CACCTTCATGATGGAGTCACA	0.592																																					p.I58T		.	.											.	CYP2A7	.	.	0			c.T173C						.						84	63	70					19																	41387943		2203	4300	6503	SO:0001583	missense	1549	exon1			TTCATGATGGAGT	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"Cytochrome P450s"	2611	protein-coding gene	gene with protein product		608054	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.173T>C	19.37:g.41387943A>G	ENSP00000301146:p.Ile58Thr	409.0	1.0		375.0	180.0	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	.	.	.	.	.	.	.	.	.	.	A	11.61	1.688721	0.29962	.	.	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.69040	-0.37;2.62	2.33	2.33	0.28932	.	0.210173	0.30473	U	0.009552	T	0.66015	0.2747	L	0.42245	1.32	0.20489	N	0.999895	B;B	0.28512	0.214;0.154	B;P	0.44447	0.239;0.45	T	0.63959	-0.6519	10	0.87932	D	0	.	9.3499	0.38131	1.0:0.0:0.0:0.0	.	58;58	F8W816;P20853	.;CP2A7_HUMAN	T	58	ENSP00000301146:I58T;ENSP00000291764:I58T	ENSP00000291764:I58T	I	-	2	0	CYP2A7	46079783	0.631000	0.27164	0.018000	0.16275	0.051000	0.14879	4.464000	0.60134	1.072000	0.40860	0.155000	0.16302	ATC	.	.		0.592	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589		G	41387943	A	G	41387943	3	3	40	1	0	0	0	0	1	0	0	0	4165	333	12	2	1357	2	CYP2A7	19	41387943	Missense_Mutation	SNP	A	TCGA-BC-A112-01A-11D-A12Z-10	987321	41387943	17741040	254	4910										
NAPA	8775	hgsc.bcm.edu	37	chr19	47995348	47995349	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tttggcgctgtacttgaggaINSgggggctgtccatggcattg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:47995348_47995349insG	ENST00000263354.3	-	8	888_889	c.589_590insC	c.(589-591)ctcfs	p.L197fs	NAPA_ENST00000595227.1_Frame_Shift_Ins_p.L158fs|NAPA-AS1_ENST00000593284.1_RNA|NAPA-AS1_ENST00000594367.1_RNA	NM_003827.3	NP_003818.2	P54920	SNAA_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, alpha	197					apical protein localization (GO:0045176)|brain development (GO:0007420)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron differentiation (GO:0030182)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)	11		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000466)|all cancers(93;0.000739)|Epithelial(262;0.0168)|GBM - Glioblastoma multiforme(486;0.049)		GTACTTGAGGAGGGGGCTGTCC	0.614																																					p.L197fs	Ovarian(185;1135 2042 27703 31345 42493)	.	.											.	NAPA	.	.	0			c.590_591insC						.																																			SO:0001589	frameshift_variant	8775	exon8			.	U39412	CCDS12702.1	19q13.33	2012-08-16			ENSG00000105402	ENSG00000105402			7641	protein-coding gene	gene with protein product	"alpha SNAP"	603215				9269766	Standard	NM_003827		Approved		uc002pha.2	P54920		ENST00000263354.3:c.590dupC	19.37:g.47995353_47995353dupG	ENSP00000263354:p.Leu197fs	145.0	0.0		158.0	13.0	NM_003827	A8K879|Q96IK3|Q9BVJ3	Frame_Shift_Ins	INS	ENST00000263354.3	37	CCDS12702.1																																																																																			.	.		0.614	NAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466048.2	NM_003827		G	47995349	-	G	47995348	7	5	40	1	0	1	1	0	0	0	0	0	10170	304	11	0	313	0	NAPA	19	47995348	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	6607405	47995348	11133635	255	4911										
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305271	48305272	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tcggggctctgaggccataaINSgggggctggggctgggagtg					rs149923413|rs139632837	byFrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:48305271_48305272insG	ENST00000322175.3	-	2	1151_1152	c.996_997insC	c.(994-999)cccttafs	p.PL332fs	TPRX1_ENST00000535759.1_Frame_Shift_Ins_p.PL429fs|TPRX1_ENST00000543508.1_Frame_Shift_Ins_p.PL322fs	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	332						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		TGAGGCCATAAGggggctgggg	0.624																																					p.L333fs	Esophageal Squamous(123;175 2281 3051 32395)	.	.											.	TPRX1	.	.	0			c.997_998insC						.																																			SO:0001589	frameshift_variant	284355	exon2			.		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"Homeoboxes / PRD class"	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.997dupC	19.37:g.48305276_48305276dupG	ENSP00000323455:p.Pro332fs	122.0	0.0		160.0	10.0	NM_198479	A5D8Y3|B2RPL5	Frame_Shift_Ins	INS	ENST00000322175.3	37	CCDS33066.1																																																																																			.	.		0.624	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		G	48305272	-	G	48305271	7	5	40	1	0	1	1	0	0	0	0	0	16437	69	3	0	242	0	TPRX1	19	48305271	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	309923	48305271	10823712	256	4912										
PLEKHA4	57664	hgsc.bcm.edu	37	chr19	49364948	49364948	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agagacggagccccgagctgTcctggggagagagatgggag	19	8	0	3			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:49364948T>C	ENST00000263265.6	-	4	749	c.194A>G	c.(193-195)gAc>gGc	p.D65G	PLEKHA4_ENST00000596713.1_5'Flank|PLEKHA4_ENST00000355496.5_Splice_Site_p.D65G	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	65	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		CCCCGAGCTGTCCTGGGGAGA	0.577																																					p.D65G		.	.											.	PLEKHA4	.	.	0			c.A194G						.						23	25	24					19																	49364948		2203	4298	6501	SO:0001630	splice_region_variant	57664	exon4			GAGCTGTCCTGGG	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"Pleckstrin homology (PH) domain containing"	14339	protein-coding gene	gene with protein product		607769	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.193-1A>G	19.37:g.49364948T>C		68.0	0.0		77.0	29.0	NM_001161354	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	t	21.5	4.154062	0.78114	.	.	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.08458	3.09;3.09	4.38	4.38	0.52667	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.067384	0.56097	D	0.000038	T	0.10208	0.0250	N	0.12961	0.28	0.48762	D	0.999708	P;B	0.45957	0.869;0.01	P;B	0.53450	0.726;0.059	T	0.21999	-1.0229	10	0.48119	T	0.1	.	11.8829	0.52586	0.0:0.0:0.0:1.0	.	65;65	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	G	65	ENSP00000263265:D65G;ENSP00000347683:D65G	ENSP00000263265:D65G	D	-	2	0	PLEKHA4	54056760	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	5.592000	0.67543	1.986000	0.57962	0.375000	0.23000	GAC	.	.		0.577	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		Missense_Mutation	C	49364948	T	C	49364948	5	2	40	1	0	0	0	0	0	0	1	0	12067	1681	58	2	2213	2	PLEKHA4	19	49364948	Splice_Site	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10	1059677	49364948	9764035	257	4913										
HRC	3270	hgsc.bcm.edu	37	chr19	49657886	49657886	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ccatactcagtggaggcctcCtcttcctcctcctcctcctc	5	20	2	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:49657886C>T	ENST00000252825.4	-	1	795	c.609G>A	c.(607-609)gaG>gaA	p.E203E	HRC_ENST00000595625.1_Silent_p.E203E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	203	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		TGGAGGcctcctcttcctcct	0.572																																					p.E203E	Melanoma(37;75 1097 24567 25669 30645)	.	.											.	HRC	.	.	0			c.G609A						.						123	91	102					19																	49657886		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			GGCCTCCTCTTCC		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.609G>A	19.37:g.49657886C>T		258.0	0.0		234.0	10.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			.	.		0.572	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		T	49657886	C	T	49657886	2	4	40	1	0	0	0	0	0	0	0	1	7361	680	24	3		3	HRC	19	49657886	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	292938	49657886	9471097	258	4914										
ACPT	93650	hgsc.bcm.edu	37	chr19	51298214	51298214	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ggcccctatgaggctgccatCcccccaggtgacagtcctct	10	17	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:51298214C>T	ENST00000270593.1	+	10	1158	c.1158C>T	c.(1156-1158)atC>atT	p.I386I	CTD-2568A17.8_ENST00000594114.1_RNA|ACPT_ENST00000270594.3_Silent_p.I293I	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	386						integral component of membrane (GO:0016021)	acid phosphatase activity (GO:0003993)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(3)	11		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		AGGCTGCCATCCCCCCAGGTG	0.697																																					p.I386I		.	.											.	ACPT	.	.	0			c.C1158T						.						33	41	38					19																	51298214		2201	4299	6500	SO:0001819	synonymous_variant	93650	exon10			TGCCATCCCCCCA	AF321918	CCDS12802.1	19q13.33	2012-10-02			ENSG00000142513	ENSG00000142513			14376	protein-coding gene	gene with protein product		606362				11414767	Standard	NM_033068		Approved		uc002pta.1	Q9BZG2		ENST00000270593.1:c.1158C>T	19.37:g.51298214C>T		178.0	0.0		163.0	18.0	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Silent	SNP	ENST00000270593.1	37	CCDS12802.1																																																																																			.	.		0.697	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068		T	51298214	C	T	51298214	2	4	40	1	0	0	0	0	0	0	0	1	168	845	30	3		3	ACPT	19	51298214	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	1640328	51298214	7830769	259	4915										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55508705	55508705	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gttgtggggatgttccatccCtccgttcagttgtgaagacc	12	10	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:55508705C>G	ENST00000543010.1	+	12	3043	c.2900C>G	c.(2899-2901)cCt>cGt	p.P967R	NLRP2_ENST00000339757.7_Missense_Mutation_p.P945R|NLRP2_ENST00000537859.1_Missense_Mutation_p.P945R|NLRP2_ENST00000427260.2_Missense_Mutation_p.P944R|NLRP2_ENST00000538819.1_Missense_Mutation_p.P943R|NLRP2_ENST00000391721.4_Missense_Mutation_p.P943R|NLRP2_ENST00000263437.6_Missense_Mutation_p.P964R|NLRP2_ENST00000448584.2_Missense_Mutation_p.P967R	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	967					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TGTTCCATCCCTCCGTTCAGT	0.567																																					p.P967R		.	.											.	NLRP2	.	.	0			c.C2900G						.						168	139	149					19																	55508705		2203	4300	6503	SO:0001583	missense	55655	exon12			CCATCCCTCCGTT	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.2900C>G	19.37:g.55508705C>G	ENSP00000445135:p.Pro967Arg	313.0	0.0		320.0	96.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	37	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	C	12.51	1.959608	0.34565	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	3.2	0.425	0.16473	.	.	.	.	.	T	0.29355	0.0731	N	0.02225	-0.63	0.09310	N	1	P;P;P;P;P	0.46859	0.885;0.877;0.883;0.877;0.804	B;P;P;P;P	0.53224	0.333;0.721;0.46;0.721;0.53	T	0.11916	-1.0568	9	0.87932	D	0	.	3.2623	0.06853	0.2393:0.5711:0.0:0.1896	.	944;945;964;943;967	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	R	967;943;945;967;945;944;943;964	ENSP00000445135:P967R;ENSP00000375601:P943R;ENSP00000344074:P945R;ENSP00000409370:P967R;ENSP00000440601:P945R;ENSP00000402474:P944R;ENSP00000441133:P943R;ENSP00000263437:P964R	ENSP00000263437:P964R	P	+	2	0	NLRP2	60200517	0.001000	0.12720	0.002000	0.10522	0.083000	0.17756	1.070000	0.30653	0.052000	0.16007	0.561000	0.74099	CCT	.	.		0.567	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		G	55508705	C	G	55508705	3	3	40	1	0	0	0	0	1	0	0	0	10486	681	24	4	2942	4	NLRP2	19	55508705	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	4210491	55508705	3620278	260	4916										
GP6	51206	hgsc.bcm.edu	37	chr19	55539031	55539040	+	Frame_Shift_Del	DEL	GCTGTGGGCG	GCTGTGGGCG	-													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctgtagcatcggtaggttccGctgtgggcggcggtcaccgt					rs387906919|rs367907292		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GCTGTGGGCG	GCTGTGGGCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr19:55539031_55539040delGCTGTGGGCG	ENST00000417454.1	-	4	543_552	c.516_525delCGCCCACAGC	c.(514-525)gccgcccacagcfs	p.AAHS172fs	CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000310373.3_Frame_Shift_Del_p.AAHS172fs|CTC-550B14.7_ENST00000586845.1_RNA|CTC-550B14.7_ENST00000586961.1_RNA|CTC-550B14.6_ENST00000585492.1_RNA|GP6_ENST00000333884.2_Frame_Shift_Del_p.AAHS172fs	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	172	Ig-like C2-type 2.				blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		GGTAGGTTCCGCTGTGGGCGGCGGTCACCG	0.59																																					p.173_176del		.	.											.	GP6	.	.	0			c.517_526del						.																																			SO:0001589	frameshift_variant	51206	exon4			.	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.516_525delCGCCCACAGC	19.37:g.55539031_55539040delGCTGTGGGCG	ENSP00000394922:p.Ala172fs	108.0	0.0		82.0	11.0	NM_016363	Q9HCN7|Q9UIF2	Frame_Shift_Del	DEL	ENST00000417454.1	37	CCDS46184.1																																																																																			.	.		0.59	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1			-	55539040	GCTGTGGGCG	-	55539031	7	5	40	1	0	1	0	1	0	0	0	0	6592	1078	38	0	1357	0	GP6	19	55539031	Frame_Shift_Del	DEL	GCTGTGGGCG	TCGA-BC-A112-01A-11D-A12Z-10	30326	55539031	3589952	261	4917										
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36869926	36869927	+	Frame_Shift_Ins	INS	-	-	C													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	agtgcctctaatggaaggggINScccccaggcttggcagaggg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr20:36869926_36869927insC	ENST00000279024.4	-	3	877_878	c.606_607insG	c.(604-609)gggcccfs	p.P203fs		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	203										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AATGGAAGGGGCCCCCAGGCTT	0.574																																					p.P203fs		.	.											.	KIAA1755	.	.	0			c.607_608insG						.																																			SO:0001589	frameshift_variant	85449	exon3			.	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.607dupG	20.37:g.36869931_36869931dupC	ENSP00000279024:p.Pro203fs	198.0	0.0		181.0	12.0	NM_001029864	Q9C0A8	Frame_Shift_Ins	INS	ENST00000279024.4	37	CCDS33467.1																																																																																			.	.		0.574	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		C	36869927	-	C	36869926	7	5	40	1	0	1	1	0	0	0	0	0	8266	1203	42	0	3043	0	KIAA1755	20	36869926	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10		36869926	26155594	262	4918										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39794969	39794969	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	taccagcaggtgcccctgcgCtgtaatgagtttgagatgcg	13	10	0	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr20:39794969C>T	ENST00000373271.1	+	17	2340	c.1935C>T	c.(1933-1935)cgC>cgT	p.R645R	PLCG1_ENST00000244007.3_Silent_p.R645R|PLCG1_ENST00000373272.2_Silent_p.R645R	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	645	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				TGCCCCTGCGCTGTAATGAGT	0.587																																					p.R645R		.	.											.	PLCG1	.	.	0			c.C1935T						.						89	83	85					20																	39794969		2203	4300	6503	SO:0001819	synonymous_variant	5335	exon17			CCTGCGCTGTAAT	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.1935C>T	20.37:g.39794969C>T		119.0	0.0		95.0	18.0	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Silent	SNP	ENST00000373271.1	37	CCDS13314.1																																																																																			.	.		0.587	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		T	39794969	C	T	39794969	2	4	40	1	0	0	0	0	0	0	0	1	12044	784	28	3		3	PLCG1	20	39794969	Silent	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	2925043	39794969	23230551	263	4919										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52199201	52199202	+	Frame_Shift_Ins	INS	-	-	T													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	acccctcgatttggatgacaINStttttttcttgtgtagctcg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr20:52199201_52199202insT	ENST00000371471.2	-	2	589_590	c.164_165insA	c.(163-165)aatfs	p.N55fs	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Frame_Shift_Ins_p.N55fs			O75362	ZN217_HUMAN	zinc finger protein 217	55					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			TTTGGATGACATTTTTTTCTTG	0.46																																					p.N55fs		.	.											.	ZNF217	.	.	0			c.165_166insA						.																																			SO:0001589	frameshift_variant	7764	exon1			.	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.165dupA	20.37:g.52199208_52199208dupT	ENSP00000360526:p.Asn55fs	151.0	0.0		155.0	10.0	NM_006526	E1P5Y6|Q14DB8	Frame_Shift_Ins	INS	ENST00000371471.2	37	CCDS13443.1																																																																																			.	.		0.46	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		T	52199202	-	T	52199201	7	5	40	1	0	1	1	0	0	0	0	0	17787	214	8	0	2997	0	ZNF217	20	52199201	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	12404232	52199201	10826319	264	4920										
DNAJC28	54943	hgsc.bcm.edu	37	chr21	34860757	34860757	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tcaggatgggaacaattaaaTtaaaatcattaattcgcttg	7	5	2	0			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr21:34860757T>A	ENST00000314399.3	-	2	1382	c.944A>T	c.(943-945)aAt>aTt	p.N315I	DNAJC28_ENST00000402202.1_Missense_Mutation_p.N315I|DNAJC28_ENST00000381947.3_Missense_Mutation_p.N315I	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	315										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						AACAATTAAATTAAAATCATT	0.348																																					p.N315I		.	.											.	DNAJC28	.	.	0			c.A944T						.						83	79	80					21																	34860757		2203	4300	6503	SO:0001583	missense	54943	exon2			ATTAAATTAAAAT	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"Heat shock proteins / DNAJ (HSP40)"	1297	protein-coding gene	gene with protein product	"Orf28"		"chromosome 21 open reading frame 55"	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.944A>T	21.37:g.34860757T>A	ENSP00000320303:p.Asn315Ile	470.0	0.0		347.0	32.0	NM_001040192	D3DSF2	Missense_Mutation	SNP	ENST00000314399.3	37	CCDS13626.1	.	.	.	.	.	.	.	.	.	.	T	19.95	3.921477	0.73213	.	.	ENSG00000177692	ENST00000381947;ENST00000314399;ENST00000402202	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.79816	0.4511	M	0.80183	2.485	0.53688	D	0.999979	D	0.89917	1.0	D	0.87578	0.998	T	0.83136	-0.0111	9	0.87932	D	0	-25.7443	14.8401	0.70217	0.0:0.0:0.0:1.0	.	315	Q9NX36	DJC28_HUMAN	I	315	.	ENSP00000320303:N315I	N	-	2	0	DNAJC28	33782627	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.094000	0.76944	2.050000	0.60909	0.528000	0.53228	AAT	.	.		0.348	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3			A	34860757	T	A	34860757	3	1	40	1	0	0	0	0	1	0	0	0	4648	1493	52	4	226	4	DNAJC28	21	34860757	Missense_Mutation	SNP	T	TCGA-BC-A112-01A-11D-A12Z-10		34860757	13269138	265	4921										
PCNT	5116	hgsc.bcm.edu	37	chr21	47819683	47819684	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aggaagaagtggaaaaacagINSaaaaacatcgtgaaagggct							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr21:47819683_47819684insA	ENST00000359568.5	+	25	4871_4872	c.4764_4765insA	c.(4765-4767)aaafs	p.K1589fs	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1589					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TGGAAAAACAGAAAAACATCGT	0.49																																					p.Q1588fs		.	.											.	PCNT	.	.	0			c.4764_4765insA						.																																			SO:0001589	frameshift_variant	5116	exon25			.	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.4769dupA	21.37:g.47819688_47819688dupA	ENSP00000352572:p.Lys1589fs	237.0	0.0		207.0	13.0	NM_006031	O43152|Q7Z7C9	Frame_Shift_Ins	INS	ENST00000359568.5	37	CCDS33592.1																																																																																			.	.		0.49	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		A	47819684	-	A	47819683	7	5	40	1	0	1	1	0	0	0	0	0	11599	933	33	0	4862	0	PCNT	21	47819683	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	12958926	47819683	310212	266	4922										
AP1B1	162	hgsc.bcm.edu	37	chr22	29736737	29736737	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gctcactggggggccgaggtCcaggttgaggaggtcaccca	17	11	2	1			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr22:29736737C>G	ENST00000405198.1	-	13	1937	c.1906G>C	c.(1906-1908)Gac>Cac	p.D636H	AP1B1_ENST00000415447.1_Missense_Mutation_p.D636H|AP1B1_ENST00000432560.2_Missense_Mutation_p.D636H|AP1B1_ENST00000357586.2_Missense_Mutation_p.D636H|AP1B1_ENST00000472057.1_5'UTR|AP1B1_ENST00000356015.2_Missense_Mutation_p.D636H|AP1B1_ENST00000317368.7_Missense_Mutation_p.D636H|AP1B1_ENST00000402502.1_Missense_Mutation_p.D636H			Q10567	AP1B1_HUMAN	adaptor-related protein complex 1, beta 1 subunit	636	Pro-rich (stalk region).				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGGCCGAGGTCCAGGTTGAGG	0.672																																					p.D636H		.	.											.	AP1B1	.	.	0			c.G1906C						.						20	21	21					22																	29736737		2198	4296	6494	SO:0001583	missense	162	exon14			CGAGGTCCAGGTT	L13939	CCDS13855.1, CCDS13856.1, CCDS13856.2, CCDS54515.1	22q12.2	2010-06-18			ENSG00000100280	ENSG00000100280			554	protein-coding gene	gene with protein product		600157		ADTB1, CLAPB2		7987321, 8812422	Standard	NM_145730		Approved	BAM22, AP105A	uc003afj.3	Q10567	OTTHUMG00000151109	ENST00000405198.1:c.1906G>C	22.37:g.29736737C>G	ENSP00000384194:p.Asp636His	92.0	0.0		97.0	11.0	NM_001127	C9JRD1|F8WDL0|P78436|Q20WL3|Q86X54	Missense_Mutation	SNP	ENST00000405198.1	37	CCDS13855.1	.	.	.	.	.	.	.	.	.	.	C	32	5.126483	0.94429	.	.	ENSG00000100280	ENST00000357586;ENST00000356015;ENST00000432560;ENST00000405198;ENST00000317368;ENST00000402502;ENST00000415447	T;T;T;T;T;T;T	0.37915	1.25;1.22;1.17;1.25;1.24;1.17;1.17	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.65471	0.2694	M	0.83774	2.66	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.996;0.997;0.997	T	0.66988	-0.5784	10	0.49607	T	0.09	-37.5738	19.1697	0.93572	0.0:1.0:0.0:0.0	.	189;636;636;636;636	B4DS79;F8WDL0;Q10567-2;Q10567;Q10567-3	.;.;.;AP1B1_HUMAN;.	H	636	ENSP00000350199:D636H;ENSP00000348297:D636H;ENSP00000400065:D636H;ENSP00000384194:D636H;ENSP00000319361:D636H;ENSP00000386071:D636H;ENSP00000387612:D636H	ENSP00000319361:D636H	D	-	1	0	AP1B1	28066737	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.768000	0.85345	2.638000	0.89438	0.655000	0.94253	GAC	.	.		0.672	AP1B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321374.1	NM_001127		G	29736737	C	G	29736737	3	3	40	1	0	0	0	0	1	0	0	0	731	855	30	4	983	4	AP1B1	22	29736737	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10		29736737	21567829	267	4923										
SSTR3	6753	hgsc.bcm.edu	37	chr22	37602710	37602710	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	gcccgctggtgccaggctgcGtgatctggctgacccggccg	16	15	1	2	rs371635196		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr22:37602710G>A	ENST00000328544.3	-	2	1666	c.1133C>T	c.(1132-1134)aCg>aTg	p.T378M	SSTR3_ENST00000402501.1_Missense_Mutation_p.T378M	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	378					cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	GCCAGGCTGCGTGATCTGGCT	0.667																																					p.T378M		.	.											.	SSTR3	.	.	0			c.C1133T						.	G	MET/THR	0,4406		0,0,2203	47	44	45		1133	3.2	0.3	22		45	2,8598	2.2+/-6.3	0,2,4298	no	missense	SSTR3	NM_001051.2	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	378/419	37602710	2,13004	2203	4300	6503	SO:0001583	missense	6753	exon2			GGCTGCGTGATCT		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"GPCR / Class A : Somatostatin receptors"	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.1133C>T	22.37:g.37602710G>A	ENSP00000330138:p.Thr378Met	104.0	0.0		82.0	5.0	NM_001051	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	37	CCDS13944.1	.	.	.	.	.	.	.	.	.	.	G	8.607	0.888145	0.17540	0.0	2.33E-4	ENSG00000183473	ENST00000328544;ENST00000402501	T;T	0.72394	-0.65;-0.65	5.51	3.24	0.37175	.	0.793886	0.11124	N	0.597147	T	0.60586	0.2280	L	0.54323	1.7	0.09310	N	1	P	0.43662	0.814	B	0.33454	0.164	T	0.53464	-0.8435	10	0.49607	T	0.09	.	9.2651	0.37636	0.1449:0.1324:0.7227:0.0	.	378	P32745	SSR3_HUMAN	M	378	ENSP00000330138:T378M;ENSP00000384904:T378M	ENSP00000330138:T378M	T	-	2	0	SSTR3	35932656	0.870000	0.30015	0.299000	0.25016	0.384000	0.30261	3.543000	0.53633	1.325000	0.45301	0.591000	0.81541	ACG	.	.		0.667	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1			A	37602710	G	A	37602710	3	1	40	1	0	0	0	0	1	0	0	0	15214	1145	40	1	127	1	SSTR3	22	37602710	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	7865973	37602710	13701856	268	4924										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46930690	46930691	+	Frame_Shift_Ins	INS	-	-	G													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	actgacactcactgtgtaatINSgggagctctgaaagacaggc							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chr22:46930690_46930691insG	ENST00000262738.3	-	1	2376_2377	c.2377_2378insC	c.(2377-2379)catfs	p.H793fs	CELSR1_ENST00000395964.1_Frame_Shift_Ins_p.H793fs|CELSR1_ENST00000497509.1_5'Flank	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	793	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CACTGTGTAATGGGAGCTCTGA	0.579																																					p.H793fs		.	.											.	CELSR1	.	.	0			c.2378_2379insC						.																																			SO:0001589	frameshift_variant	9620	exon1			.	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.2378dupC	22.37:g.46930693_46930693dupG	ENSP00000262738:p.His793fs	139.0	0.0		167.0	10.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Frame_Shift_Ins	INS	ENST00000262738.3	37	CCDS14076.1																																																																																			.	.		0.579	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		G	46930691	-	G	46930690	7	5	40	1	0	1	1	0	0	0	0	0	3223	1464	51	0	6806	0	CELSR1	22	46930690	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	9327980	46930690	4373876	269	4925										
VCX	26609	hgsc.bcm.edu	37	chrX	7811709	7811709	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cctcagcacgagctgccgccGgaggagccagtgagcgaggg	17	13	1	1	rs139507263	byFrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chrX:7811709G>C	ENST00000381059.3	+	3	492	c.273G>C	c.(271-273)ccG>ccC	p.P91P	VCX_ENST00000341408.4_Silent_p.P91P	NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	91	Glu-rich.				chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.P91P(1)		NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				AGCTGCCGCCGGAGGAGCCAG	0.701																																					p.P91P		.	.											.	VCX	.	.	1	Substitution - coding silent(1)	endometrium(1)	c.G273C						.						23	31	28					X																	7811709		2089	4025	6114	SO:0001819	synonymous_variant	26609	exon3			GCCGCCGGAGGAG	AF167081	CCDS14128.1	Xp22.31	2008-02-05	2003-09-12		ENSG00000182583	ENSG00000182583			12667	protein-coding gene	gene with protein product		300229	"variable charge, X chromosome"			10607842, 10903929	Standard	NM_013452		Approved	VCX1, VCX10R, VCX-10r, VCX-B1	uc004crz.3	Q9H320	OTTHUMG00000028608	ENST00000381059.3:c.273G>C	X.37:g.7811709G>C		81.0	0.0		83.0	28.0	NM_013452	A0JNS5|Q4V774|Q9P0H3	Silent	SNP	ENST00000381059.3	37	CCDS14128.1																																																																																			G|0.999;A|0.001	.		0.701	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071474.1	NM_013452		C	7811709	G	C	7811709	2	2	40	1	0	0	0	0	0	0	0	1	17157	1103	39	4		4	VCX	23	7811709	Silent	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10		7811709	147458851	270	4926										
DDX3X	1654	hgsc.bcm.edu	37	chrX	41205635	41205636	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	cttcaccagttccgctcaggINSaaaaagcccaattttagtgg							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chrX:41205635_41205636insA	ENST00000399959.2	+	13	2324_2325	c.1469_1470insA	c.(1468-1473)ggaaaafs	p.GK490fs	RN7SL15P_ENST00000582825.1_RNA|DDX3X_ENST00000542215.1_3'UTR|DDX3X_ENST00000441189.2_Intron|DDX3X_ENST00000457138.2_Frame_Shift_Ins_p.GK474fs|DDX3X_ENST00000478993.1_3'UTR	NM_001193416.1|NM_001193417.1|NM_001356.3	NP_001180345.1|NP_001180346.1|NP_001347.3	O00571	DDX3X_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked	490	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with GSK3B.|Necessary for interaction with XPO1.				ATP catabolic process (GO:0006200)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to osmotic stress (GO:0071470)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|mature ribosome assembly (GO:0042256)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell growth (GO:0030307)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|stress granule assembly (GO:0034063)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 5'-UTR binding (GO:0048027)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|transcription factor binding (GO:0008134)|translation initiation factor binding (GO:0031369)			NS(3)|breast(8)|central_nervous_system(36)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84						TTCCGCTCAGGAAAAAGCCCAA	0.411										HNSCC(61;0.18)																											p.G490fs		.	.											.	DDX3X	.	.	0			c.1469_1470insA						.																																			SO:0001589	frameshift_variant	1654	exon13			.	U50553	CCDS43931.1, CCDS55404.1	Xp11.3-p11.23	2013-07-16	2013-07-16	2003-06-20	ENSG00000215301	ENSG00000215301		"DEAD-boxes"	2745	protein-coding gene	gene with protein product		300160	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked"	DDX3		9381176, 9730595	Standard	NM_001193416		Approved	DBX, HLP2, DDX14	uc004dfe.3	O00571	OTTHUMG00000021369	ENST00000399959.2:c.1474dupA	X.37:g.41205640_41205640dupA	ENSP00000382840:p.Gly490fs	153.0	0.0		177.0	11.0	NM_001193416	A8K538|B4E3E8|O15536	Frame_Shift_Ins	INS	ENST00000399959.2	37	CCDS43931.1																																																																																			.	.		0.411	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005		A	41205636	-	A	41205635	7	5	40	1	0	1	1	0	0	0	0	0	4360	1174	41	0	1519	0	DDX3X	23	41205635	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	33393926	41205635	114064925	271	4927										
PJA1	64219	hgsc.bcm.edu	37	chrX	68382256	68382257	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tcgtcatcatcatcagtatcINSaaaaaaaatttttggtttca							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chrX:68382256_68382257insA	ENST00000361478.1	-	2	1202_1203	c.825_826insT	c.(823-828)tttgatfs	p.D276fs	PJA1_ENST00000374584.3_Intron|PJA1_ENST00000477231.1_5'UTR|PJA1_ENST00000374583.1_Frame_Shift_Ins_p.D276fs|PJA1_ENST00000374571.4_Frame_Shift_Ins_p.D221fs	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	276	Poly-Asp.				protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						TCATCAGTATCAAAAAAAATTT	0.495																																					p.D276_T277delinsX		.	.											.	PJA1	.	.	0			c.826_827insT						.																																			SO:0001589	frameshift_variant	64219	exon2			.	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"RING-type (C3HC4) zinc fingers"	16648	protein-coding gene	gene with protein product		300420	"praja 1", "praja ring finger 1"			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.826dupT	X.37:g.68382264_68382264dupA	ENSP00000355014:p.Asp276fs	127.0	0.0		152.0	10.0	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Frame_Shift_Ins	INS	ENST00000361478.1	37	CCDS14393.1																																																																																			.	.		0.495	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119		A	68382257	-	A	68382256	7	5	40	1	0	1	1	0	0	0	0	0	11970	826	29	0	1109	0	PJA1	23	68382256	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	27176621	68382256	86888304	272	4928										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128980	83128981	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aaaggagagtcagaaagatgINSaaaaaaaggataaaaaagat							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chrX:83128980_83128981insA	ENST00000329312.4	+	4	1301_1302	c.1264_1265insA	c.(1264-1266)gaafs	p.E422fs		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	422					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.E421K(1)|p.K423fs*69(1)		NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						TCAGAAAGATGAAAAAAAGGAT	0.342																																					p.E422fs		.	.											CYLC1,NS,malignant_melanoma,0	CYLC1	.	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	lung(1)|skin(1)	c.1264_1265insA						.																																			SO:0001589	frameshift_variant	1538	exon4			.	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1271dupA	X.37:g.83128987_83128987dupA	ENSP00000331556:p.Glu422fs	136.0	0.0		149.0	10.0	NM_021118	A0AVQ8|Q5JQQ9	Frame_Shift_Ins	INS	ENST00000329312.4	37	CCDS35341.1																																																																																			.	.		0.342	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		A	83128981	-	A	83128980	7	5	40	1	0	1	1	0	0	0	0	0	4143	1291	45	0	1278	0	CYLC1	23	83128980	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	14746724	83128980	72141580	273	4929										
RPL36A	6173	hgsc.bcm.edu	37	chrX	100646804	100646805	+	Frame_Shift_Ins	INS	-	-	A													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	aaactaagccgattttccggINSaaaaaggtgagtggtagtta							TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chrX:100646804_100646805insA	ENST00000553110.3	+	3	255_256	c.171_172insA	c.(172-174)aaafs	p.K58fs	RPL36A_ENST00000471855.1_5'UTR|RPL36A_ENST00000427805.2_Frame_Shift_Ins_p.K94fs|RPL36A-HNRNPH2_ENST00000409170.3_Frame_Shift_Ins_p.GK68fs			P83881	RL36A_HUMAN	ribosomal protein L36a	58					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			liver(4)|lung(1)|prostate(1)	6						CGATTTTCCGGAAAAAGGTGAG	0.421																																					p.R93fs		.	.											.	.	.	.	0			c.279_280insA						.																																			SO:0001589	frameshift_variant	0	exon3			.	BC001781	CCDS14483.1, CCDS14483.2	Xq22.1	2011-04-06	2002-01-15	2002-01-18	ENSG00000241343	ENSG00000241343		"L ribosomal proteins"	10359	protein-coding gene	gene with protein product		300902	"ribosomal protein L44"	RPL44		3461443	Standard	NM_021029		Approved	L36A		P83881	OTTHUMG00000022027	ENST00000553110.3:c.176dupA	X.37:g.100646809_100646809dupA	ENSP00000446503:p.Lys58fs	196.0	0.0		153.0	10.0	NM_001199973	P09896|P10661|Q08ES5|Q5J9I6	Frame_Shift_Ins	INS	ENST00000553110.3	37																																																																																				.	.		0.421	RPL36A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021029		A	100646805	-	A	100646804	7	5	40	1	0	1	1	0	0	0	0	0	13602	1161	41	0	181	0	RPL36A	23	100646804	Frame_Shift_Ins	INS	-	TCGA-BC-A112-01A-11D-A12Z-10	17517824	100646804	54623756	274	4930										
GLA	2717	hgsc.bcm.edu	37	chrX	100655664	100655678	+	In_Frame_Del	DEL	GGCCACATATAAAGA	GGCCACATATAAAGA	-													0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	actatctcaccttttgaaagGgccacatataaagaggccac					rs372416832		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GGCCACATATAAAGA	GGCCACATATAAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chrX:100655664_100655678delGGCCACATATAAAGA	ENST00000218516.3	-	4	636_650	c.615_629delTCTTTATATGTGGCC	c.(613-630)cctctttatatgtggccc>ccc	p.205_210PLYMWP>P	GLA_ENST00000479445.1_5'Flank|RPL36A-HNRNPH2_ENST00000409170.3_Intron	NM_000169.2	NP_000160.1	P06280	AGAL_HUMAN	galactosidase, alpha	205	Substrate binding.		Missing (in FD). {ECO:0000269|PubMed:9100224}.|P -> T (in FD). {ECO:0000269|PubMed:8807334, ECO:0000269|PubMed:8875188}.		glycoside catabolic process (GO:0016139)|glycosphingolipid catabolic process (GO:0046479)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide catabolic process (GO:0046477)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|oligosaccharide metabolic process (GO:0009311)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|catalytic activity (GO:0003824)|galactoside binding (GO:0016936)|hydrolase activity (GO:0016787)|protein homodimerization activity (GO:0042803)|raffinose alpha-galactosidase activity (GO:0052692)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						CTTTTGAAAGGGCCACATATAAAGAGGCCACTCAC	0.428																																					p.206_210del	Colon(193;776 2816 31189 44474)	.	.											.	GLA	.	.	0			c.616_630del	GRCh37	CD033537|CD972786|CI082255|CM023794|CX023866	GLA	D|I|M|X		.																																			SO:0001651	inframe_deletion	2717	exon4			.	X16889	CCDS14484.1	Xq21.3-q22	2014-09-17			ENSG00000102393	ENSG00000102393	3.2.1.22		4296	protein-coding gene	gene with protein product		300644					Standard	NM_000169		Approved	GALA	uc004ehl.1	P06280	OTTHUMG00000022026	ENST00000218516.3:c.615_629delTCTTTATATGTGGCC	X.37:g.100655664_100655678delGGCCACATATAAAGA	ENSP00000218516:p.Pro205_Trp209del	115.0	0.0		110.0	11.0	NM_000169	Q6LER7	In_Frame_Del	DEL	ENST00000218516.3	37	CCDS14484.1																																																																																			.	.		0.428	GLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057540.1			-	100655678	GGCCACATATAAAGA	-	100655664	7	5	40	1	0	1	0	1	0	0	0	0	6434	1232	43	0	676	0	GLA	23	100655664	In_Frame_Del	DEL	GGCCACATATAAAGA	TCGA-BC-A112-01A-11D-A12Z-10	8860	100655664	54614896	275	4931										
WDR44	54521	hgsc.bcm.edu	37	chrX	117528110	117528110	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	ctcagccttctcttgatttgGcaagtgctaccagtggagat	10	10	2	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chrX:117528110G>T	ENST00000254029.3	+	5	1314	c.919G>T	c.(919-921)Gca>Tca	p.A307S	WDR44_ENST00000371825.3_Missense_Mutation_p.A307S|WDR44_ENST00000371822.5_Missense_Mutation_p.A282S	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	307						endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						TCTTGATTTGGCAAGTGCTAC	0.438																																					p.A307S		.	.											.	WDR44	.	.	0			c.G919T						.						132	128	130					X																	117528110		2203	4300	6503	SO:0001583	missense	54521	exon5			GATTTGGCAAGTG	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"WD repeat domain containing"	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.919G>T	X.37:g.117528110G>T	ENSP00000254029:p.Ala307Ser	190.0	0.0		148.0	108.0	NM_001184965	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Missense_Mutation	SNP	ENST00000254029.3	37	CCDS14572.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.254332|5.254332	0.95336|0.95336	.|.	.|.	ENSG00000131725|ENSG00000131725	ENST00000371822;ENST00000254029;ENST00000371825|ENST00000371848	T;T;T|.	0.76448|.	-1.02;-0.4;-0.27|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59542|0.59542	0.2201|0.2201	L|L	0.32530|0.32530	0.975|0.975	0.58432|0.58432	D|D	0.999996|0.999996	D;D;D;D|.	0.76494|.	0.992;0.996;0.999;0.986|.	P;P;D;P|.	0.69142|.	0.845;0.831;0.962;0.784|.	T|T	0.54860|0.54860	-0.8230|-0.8230	10|5	0.17369|.	T|.	0.5|.	-11.7317|-11.7317	18.4537|18.4537	0.90713|0.90713	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	282;307;307;307|.	F8W913;E9PCI7;Q5JSH3-2;Q5JSH3|.	.;.;.;WDR44_HUMAN|.	S|V	282;307;307|206	ENSP00000360887:A282S;ENSP00000254029:A307S;ENSP00000360890:A307S|.	ENSP00000254029:A307S|.	A|G	+|+	1|2	0|0	WDR44|WDR44	117412138|117412138	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	9.230000|9.230000	0.95299|0.95299	2.300000|2.300000	0.77407|0.77407	0.600000|0.600000	0.82982|0.82982	GCA|GGC	.	.		0.438	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045		T	117528110	G	T	117528110	3	4	40	1	0	0	0	0	1	0	0	0	17311	1203	42	3	937	3	WDR44	23	117528110	Missense_Mutation	SNP	G	TCGA-BC-A112-01A-11D-A12Z-10	16872446	117528110	37742450	276	4932										
F8	2157	hgsc.bcm.edu	37	chrX	154158684	154158684	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0805860805860806	22	1	1.63828800337339	2.30849673202614	1.31914098972922	0.792808399497203	1	0	tttccatgagtcctttgtatCcaccttgctgattctggcaa	7	11	1	2			TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	g.chrX:154158684C>G	ENST00000360256.4	-	14	3581	c.3381G>C	c.(3379-3381)tgG>tgC	p.W1127C		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1127	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TCCTTTGTATCCACCTTGCTG	0.443																																					p.W1127C		.	.											.	F8	.	.	0			c.G3381C	GRCh37	CM012943	F8	M		.						65	64	64					X																	154158684		2203	4298	6501	SO:0001583	missense	2157	exon14			TTGTATCCACCTT	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3381G>C	X.37:g.154158684C>G	ENSP00000353393:p.Trp1127Cys	149.0	0.0		165.0	28.0	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	c	5.085	0.201423	0.09652	.	.	ENSG00000185010	ENST00000360256	D	0.99282	-5.68	4.94	3.0	0.34707	.	1.026450	0.07723	N	0.943986	D	0.98223	0.9412	M	0.64997	1.995	0.18873	N	0.999982	D	0.60575	0.988	P	0.46975	0.533	D	0.95268	0.8375	10	0.52906	T	0.07	0.3189	4.3522	0.11160	0.2434:0.637:0.0:0.1196	.	1127	P00451	FA8_HUMAN	C	1127	ENSP00000353393:W1127C	ENSP00000353393:W1127C	W	-	3	0	F8	153811878	0.000000	0.05858	0.001000	0.08648	0.050000	0.14768	0.732000	0.26072	1.084000	0.41184	0.597000	0.82753	TGG	.	.		0.443	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			G	154158684	C	G	154158684	3	3	40	1	0	0	0	0	1	0	0	0	5352	856	30	4	3754	4	F8	23	154158684	Missense_Mutation	SNP	C	TCGA-BC-A112-01A-11D-A12Z-10	36630574	154158684	1111876	277	4933										
SERINC2	347735	hgsc.bcm.edu	37	chr1	31907019	31907019	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tggaccctggtagccccactCctcctgcgcaaccgcgactt	9	18	0	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr1:31907019C>A	ENST00000373709.3	+	10	1491	c.1341C>A	c.(1339-1341)ctC>ctA	p.L447L	SERINC2_ENST00000536859.1_Silent_p.L451L|SERINC2_ENST00000373710.1_Silent_p.L456L|SERINC2_ENST00000491976.1_3'UTR|SERINC2_ENST00000536384.1_Silent_p.L451L	NM_178865.4	NP_849196.2	Q96SA4	SERC2_HUMAN	serine incorporator 2	447					phosphatidylserine metabolic process (GO:0006658)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	L-serine transmembrane transporter activity (GO:0015194)			cervix(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	12		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151)		TAGCCCCACTCCTCCTGCGCA	0.647																																					p.L456L		Atlas-SNP	.											.	SERINC2	44	.	0			c.C1368A						.						173	166	168					1																	31907019		2203	4300	6503	SO:0001819	synonymous_variant	347735	exon11			CCCACTCCTCCTG	AY094595	CCDS30662.1, CCDS55583.1, CCDS55584.1, CCDS55585.1	1p35.1	2008-02-05	2005-11-01	2005-11-01	ENSG00000168528	ENSG00000168528			23231	protein-coding gene	gene with protein product		614549	"tumor differentially expressed 2-like"	TDE2L		12949800	Standard	NM_178865		Approved	FKSG84, PRO0899, TDE2	uc010ogh.2	Q96SA4	OTTHUMG00000003796	ENST00000373709.3:c.1341C>A	chr1.hg19:g.31907019C>A		54.0	0.0		35.0	29.0	NM_001199038	A0AVB4|B4DJK5|B7Z567|B7ZAP2|E7EUZ9|Q86Y23	Silent	SNP	ENST00000373709.3	hg19	CCDS30662.1																																																																																			.	.		0.647	SERINC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010680.1	NM_018565		A	31907019	C	A	31907019	2	1	41	1	0	0	0	0	0	0	0	1	14095	842	30	3		3	SERINC2	1	31907019	Silent	SNP	C	TCGA-BC-A216-01A-11D-A152-10		31907019	217343602	1	4934										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79403615	79403615	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tctcctatgattcacagataActtgtcccaaactacaaatg	4	11	2	2			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr1:79403615A>T	ENST00000370742.3	-	6	700	c.637T>A	c.(637-639)Tta>Ata	p.L213I		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	213					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		TTCACAGATAACTTGTCCCAA	0.343																																					p.L213I		Atlas-SNP	.											.	ELTD1	143	.	0			c.T637A						.						159	145	149					1																	79403615		1843	4096	5939	SO:0001583	missense	64123	exon6			CAGATAACTTGTC	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.637T>A	chr1.hg19:g.79403615A>T	ENSP00000359778:p.Leu213Ile	296.0	0.0		371.0	114.0	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	A	13.66	2.303610	0.40795	.	.	ENSG00000162618	ENST00000370742	T	0.12361	2.69	5.79	2.33	0.28932	Domain of unknown function DUF3497 (1);	0.109877	0.64402	D	0.000017	T	0.03434	0.0099	L	0.44542	1.39	0.22620	N	0.998922	B	0.20368	0.044	B	0.28709	0.093	T	0.38156	-0.9674	9	.	.	.	.	3.3665	0.07206	0.5024:0.0:0.3272:0.1704	.	213	Q9HBW9	ELTD1_HUMAN	I	213	ENSP00000359778:L213I	.	L	-	1	2	ELTD1	79176203	0.963000	0.33076	0.600000	0.28864	0.953000	0.61014	2.053000	0.41326	1.021000	0.39600	0.455000	0.32223	TTA	.	.		0.343	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		T	79403615	A	T	79403615	3	4	41	1	0	0	0	0	1	0	0	0	5086	40	2	4	1475	4	ELTD1	1	79403615	Missense_Mutation	SNP	A	TCGA-BC-A216-01A-11D-A152-10	47496596	79403615	169847006	2	4935										
ITGA10	8515	hgsc.bcm.edu	37	chr1	145532146	145532146	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tcagtcagtcccatgggggcCgacccgaggctgccaggcta	14	14	2	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr1:145532146C>T	ENST00000369304.3	+	8	965	c.790C>T	c.(790-792)Cga>Tga	p.R264*	ITGA10_ENST00000538811.1_Nonsense_Mutation_p.R133*|ITGA10_ENST00000539363.1_Nonsense_Mutation_p.R121*|ITGA10_ENST00000481236.1_3'UTR	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	264	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCATGGGGGCCGACCCGAGGC	0.547																																					p.R264X		Atlas-SNP	.											.	ITGA10	131	.	0			c.C790T						.						90	91	90					1																	145532146		2203	4300	6503	SO:0001587	stop_gained	8515	exon8			GGGGGCCGACCCG	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.790C>T	chr1.hg19:g.145532146C>T	ENSP00000358310:p.Arg264*	51.0	0.0		62.0	14.0	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Nonsense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.712684	0.89112	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	.	.	.	5.2	4.28	0.50868	.	0.174265	0.37715	N	0.001963	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.3139	0.49379	0.3285:0.6714:0.0:0.0	.	.	.	.	X	264;230;121;133	.	ENSP00000358310:R264X	R	+	1	2	ITGA10	144243503	0.041000	0.20044	0.998000	0.56505	0.993000	0.82548	0.402000	0.20965	1.325000	0.45301	0.511000	0.50034	CGA	.	.		0.547	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		T	145532146	C	T	145532146	4	4	41	1	0	0	0	0	0	1	0	0	7882	644	23	1	820	1	ITGA10	1	145532146	Nonsense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10	66128531	145532146	103718475	3	4936										
RNASEL	6041	hgsc.bcm.edu	37	chr1	182551358	182551360	+	In_Frame_Del	DEL	CTT	CTT	-													0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tcctcaaatgagatgcttccCttctttaccacatagaggac							TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr1:182551358_182551360delCTT	ENST00000367559.3	-	4	1853_1855	c.1600_1602delAAG	c.(1600-1602)aagdel	p.K534del	RNASEL_ENST00000444138.1_In_Frame_Del_p.K534del|RNASEL_ENST00000539397.1_In_Frame_Del_p.K534del	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	534	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						AGATGCTTCCCTTCTTTACCACA	0.443																																					p.534_535del		Atlas-Indel,Pindel	.											.	RNASEL	83	.	0			c.1601_1603del						.																																			SO:0001651	inframe_deletion	6041	exon4			.	L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"Ankyrin repeat domain containing"	10050	protein-coding gene	gene with protein product		180435	"prostate cancer 1"	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.1600_1602delAAG	chr1.hg19:g.182551361_182551363delCTT	ENSP00000356530:p.Lys534del	143.0	0.0		219.0	15.0	NM_021133	Q5W0L2|Q6AI46	In_Frame_Del	DEL	ENST00000367559.3	hg19	CCDS1347.1																																																																																			.	.		0.443	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085189.1	NM_021133		-	182551360	CTT	-	182551358	7	5	41	1	0	1	0	1	0	0	0	0	13431	680	24	0	639	0	RNASEL	1	182551358	In_Frame_Del	DEL	CTT	TCGA-BC-A216-01A-11D-A152-10	37019212	182551358	66699263	4	4937										
TP53BP2	7159	hgsc.bcm.edu	37	chr1	224002032	224002032	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	ttgaagaacatcaaacattcGctcattatccgcaactggac	6	11	2	2			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr1:224002032G>A	ENST00000343537.7	-	3	490	c.199C>T	c.(199-201)Cga>Tga	p.R67*	TP53BP2_ENST00000391878.2_5'UTR	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	61					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		TCAAACATTCGCTCATTATCC	0.413																																					p.R67X		Atlas-SNP	.											.	TP53BP2	144	.	0			c.C199T						.						119	118	118					1																	224002032		1914	4130	6044	SO:0001587	stop_gained	7159	exon3			ACATTCGCTCATT	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.199C>T	chr1.hg19:g.224002032G>A	ENSP00000341957:p.Arg67*	30.0	0.0		60.0	9.0	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Nonsense_Mutation	SNP	ENST00000343537.7	hg19	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	G	40	8.038094	0.98621	.	.	ENSG00000143514	ENST00000343537	.	.	.	5.61	2.26	0.28386	.	0.110648	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8993	0.79359	0.0:0.0:0.6418:0.3582	.	.	.	.	X	67	.	ENSP00000341957:R67X	R	-	1	2	TP53BP2	222068655	1.000000	0.71417	0.882000	0.34594	0.997000	0.91878	3.453000	0.52978	0.684000	0.31448	0.563000	0.77884	CGA	.	.		0.413	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		A	224002032	G	A	224002032	4	1	41	1	0	0	0	0	0	1	0	0	16399	1095	38	1	3269	1	TP53BP2	1	224002032	Nonsense_Mutation	SNP	G	TCGA-BC-A216-01A-11D-A152-10	41450674	224002032	25248589	5	4938										
DTNB	1838	hgsc.bcm.edu	37	chr2	25611083	25611083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	aaactcaccttgtgcgaaggCctcctgcacgtctcccccga	8	17	2	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr2:25611083C>T	ENST00000406818.3	-	17	1972	c.1723G>A	c.(1723-1725)Gcc>Acc	p.A575T	DTNB_ENST00000407661.3_Missense_Mutation_p.A575T|DTNB_ENST00000496972.2_Missense_Mutation_p.A511T|DTNB_ENST00000405222.1_Missense_Mutation_p.A538T|DTNB_ENST00000404103.3_Missense_Mutation_p.A575T|DTNB_ENST00000545439.1_Missense_Mutation_p.A364T|DTNB_ENST00000407186.1_Missense_Mutation_p.A538T|DTNB_ENST00000407038.3_Missense_Mutation_p.A545T|DTNB_ENST00000288642.8_Missense_Mutation_p.A575T	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	575						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTGCGAAGGCCTCCTGCACG	0.607																																					p.A575T		Atlas-SNP	.											DTNB,colon,carcinoma,0,1	DTNB	43	.	0			c.G1723A						.						18	23	21					2																	25611083		2017	4183	6200	SO:0001583	missense	1838	exon17			CGAAGGCCTCCTG	AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.1723G>A	chr2.hg19:g.25611083C>T	ENSP00000384084:p.Ala575Thr	33.0	1.0		22.0	12.0	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Missense_Mutation	SNP	ENST00000406818.3	hg19	CCDS46237.1	.	.	.	.	.	.	.	.	.	.	C	36	5.819810	0.96982	.	.	ENSG00000138101	ENST00000496972;ENST00000406818;ENST00000404103;ENST00000407661;ENST00000407038;ENST00000405222;ENST00000407186;ENST00000288642;ENST00000545439	T;T;T;T;T;T;T;T;T	0.57107	1.71;1.69;2.12;1.69;2.13;2.12;1.71;2.12;0.42	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.72170	0.3427	M	0.79258	2.445	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D	0.71674	0.998;0.997;0.998;0.988;0.996;0.991;0.993;0.996;0.996;0.997;0.998;0.996	D;D;D;P;P;P;D;D;D;D;D;P	0.73708	0.928;0.913;0.928;0.821;0.821;0.881;0.956;0.981;0.981;0.913;0.928;0.821	T	0.70432	-0.4873	10	0.32370	T	0.25	-16.4453	16.7312	0.85435	0.0:1.0:0.0:0.0	.	364;511;568;568;511;538;538;545;575;575;575;575	B7Z202;F5GZG4;B7Z6A9;Q1I0L3;B7Z733;E9PEY4;Q96AW0;O60941-2;O60941-4;G5E9F6;O60941;Q86VR4	.;.;.;.;.;.;.;.;.;.;DTNB_HUMAN;.	T	511;575;575;575;545;538;538;575;364	ENSP00000444463:A511T;ENSP00000384084:A575T;ENSP00000385482:A575T;ENSP00000385193:A575T;ENSP00000384767:A545T;ENSP00000384787:A538T;ENSP00000385784:A538T;ENSP00000288642:A575T;ENSP00000444961:A364T	ENSP00000288642:A575T	A	-	1	0	DTNB	25464587	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.628000	0.83189	2.551000	0.86045	0.561000	0.74099	GCC	.	.		0.607	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147		T	25611083	C	T	25611083	3	4	41	1	0	0	0	0	1	0	0	0	4791	739	26	3	176	3	DTNB	2	25611083	Missense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10		25611083	217588290	6	4939										
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85536399	85536400	+	In_Frame_Ins	INS	-	-	GCA													0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	ccttcctgtcggctaaggctINSgcagcctcctcctctgggca							TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr2:85536399_85536400insGCA	ENST00000282111.3	+	12	1856_1857	c.1581_1582insGCA	c.(1582-1584)gca>GCAgca	p.528_528A>AA		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	528					anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CGGCTAAGGCTGCAGCCTCCTC	0.688																																					p.A527delinsAA		Atlas-INDEL	.											.	TCF7L1	44	.	0			c.1581_1582insGCA						.																																			SO:0001652	inframe_insertion	83439	exon12			.	X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.1582_1584dupGCA	chr2.hg19:g.85536400_85536402dupGCA	ENSP00000282111:p.Ala529dup	71.0	0.0		66.0	19.0	NM_031283	Q53R97|Q6PD70|Q9NP00	In_Frame_Ins	INS	ENST00000282111.3	hg19	CCDS1971.1																																																																																			.	.		0.688	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		GCA	85536400	-	GCA	85536399	7	5	41	1	0	1	1	0	0	0	0	0	15712	1567	55	0	1627	0	TCF7L1	2	85536399	In_Frame_Ins	INS	-	TCGA-BC-A216-01A-11D-A152-10	59925316	85536399	157662974	7	4940										
TGOLN2	10618	hgsc.bcm.edu	37	chr2	85552051	85552051	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tccttaccttctggtccaaaCgttggtagtcactggccttt	8	12	2	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr2:85552051C>T	ENST00000409232.3	-	3	1356	c.1295G>A	c.(1294-1296)cGt>cAt	p.R432H	TGOLN2_ENST00000409015.1_Missense_Mutation_p.R432H|TGOLN2_ENST00000377386.3_Missense_Mutation_p.R432H|TGOLN2_ENST00000444342.2_Missense_Mutation_p.R432H|TGOLN2_ENST00000282120.2_Missense_Mutation_p.R276H|TGOLN2_ENST00000398263.2_Missense_Mutation_p.R374H			O43493	TGON2_HUMAN	trans-golgi network protein 2	432						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											CTGGTCCAAACGTTGGTAGTC	0.493																																					p.R432H		Atlas-SNP	.											.	TGOLN2	32	.	0			c.G1295A						.						80	83	82					2																	85552051		1928	4094	6022	SO:0001583	missense	10618	exon3			TCCAAACGTTGGT	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"trans-Golgi network protein (46, 48, 51kD isoforms)"	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.1295G>A	chr2.hg19:g.85552051C>T	ENSP00000386443:p.Arg432His	99.0	0.0		114.0	35.0	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Missense_Mutation	SNP	ENST00000409232.3	hg19	CCDS56126.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.418580	0.83559	.	.	ENSG00000152291	ENST00000377386;ENST00000282120;ENST00000398263;ENST00000409232;ENST00000409015;ENST00000444342	T;T;T;T;T;T	0.33438	1.52;1.68;1.41;1.57;1.5;1.58	5.46	4.57	0.56435	.	.	.	.	.	T	0.51227	0.1662	L	0.59436	1.845	0.35098	D	0.764987	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.995;0.992;0.993;0.996	T	0.65689	-0.6107	9	0.87932	D	0	-12.8409	13.6679	0.62407	0.1558:0.8442:0.0:0.0	.	432;432;374;432	O43493;O43493-5;O43493-4;O43493-2	TGON2_HUMAN;.;.;.	H	432;276;374;432;432;432	ENSP00000366603:R432H;ENSP00000282120:R276H;ENSP00000381312:R374H;ENSP00000386443:R432H;ENSP00000387035:R432H;ENSP00000391190:R432H	ENSP00000282120:R276H	R	-	2	0	TGOLN2	85405562	0.991000	0.36638	1.000000	0.80357	0.996000	0.88848	3.085000	0.50151	1.406000	0.46857	0.555000	0.69702	CGT	.	.		0.493	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464		T	85552051	C	T	85552051	3	4	41	1	0	0	0	0	1	0	0	0	15851	536	19	1	26	1	TGOLN2	2	85552051	Missense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10	15652	85552051	157647322	8	4941										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131521437	131521437	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	ggactggcacactgtccaggGatgcctctcgagaggaagag	15	10	1	2			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr2:131521437G>A	ENST00000423981.1	+	2	1902	c.1792G>A	c.(1792-1794)Gat>Aat	p.D598N	AMER3_ENST00000321420.4_Missense_Mutation_p.D598N	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	598					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										ACTGTCCAGGGATGCCTCTCG	0.592																																					p.D598N		Atlas-SNP	.											.	.	.	.	0			c.G1792A						.						65	70	68					2																	131521437		2203	4300	6503	SO:0001583	missense	205147	exon2			TCCAGGGATGCCT	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.1792G>A	chr2.hg19:g.131521437G>A	ENSP00000392700:p.Asp598Asn	65.0	0.0		47.0	21.0	NM_152698	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	hg19	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	G	13.92	2.380921	0.42207	.	.	ENSG00000178171	ENST00000321420;ENST00000423981	T;T	0.48201	0.82;0.82	4.84	3.03	0.35002	.	0.651836	0.12750	N	0.442236	T	0.30262	0.0759	L	0.27053	0.805	0.09310	N	1	B	0.33694	0.421	B	0.30495	0.116	T	0.12066	-1.0562	10	0.27082	T	0.32	.	6.9945	0.24774	0.0959:0.175:0.7292:0.0	.	598	Q8N944	F123C_HUMAN	N	598	ENSP00000314914:D598N;ENSP00000392700:D598N	ENSP00000314914:D598N	D	+	1	0	FAM123C	131237907	0.009000	0.17119	0.013000	0.15412	0.102000	0.19082	1.019000	0.30014	0.567000	0.29293	-0.304000	0.09214	GAT	.	.		0.592	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		A	131521437	G	A	131521437	3	1	41	1	0	0	0	0	1	0	0	0	5429	1174	41	3	1794	3	FAM123C	2	131521437	Missense_Mutation	SNP	G	TCGA-BC-A216-01A-11D-A152-10	45969386	131521437	111677936	9	4942										
CDCA7	83879	hgsc.bcm.edu	37	chr2	174224139	174224139	+	Intron	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	caaggccagatgtcactaacGaactggccggtatttttcat	9	10	2	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr2:174224139G>A	ENST00000347703.3	+	2	291				CDCA7_ENST00000410101.3_Missense_Mutation_p.E58K|CDCA7_ENST00000410019.3_Intron|CDCA7_ENST00000306721.3_Missense_Mutation_p.E102K|CDCA7_ENST00000392567.2_Intron	NM_145810.2	NP_665809.1	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7						apoptotic process (GO:0006915)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E102K(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.116)			TGTCACTAACGAACTGGCCGG	0.423																																					p.E102K		Atlas-SNP	.											CDCA7,NS,carcinoma,0,2	CDCA7	48	.	1	Substitution - Missense(1)	large_intestine(1)	c.G304A						.						101	101	101					2																	174224139		2203	4300	6503	SO:0001627	intron_variant	83879	exon3			ACTAACGAACTGG	BG354580	CCDS2252.1, CCDS2253.1	2q31.1	2008-02-05			ENSG00000144354	ENSG00000144354			14628	protein-coding gene	gene with protein product		609937				11598121, 12188893	Standard	NM_145810		Approved	FLJ14736, JPO1	uc002uic.1	Q9BWT1	OTTHUMG00000132296	ENST00000347703.3:c.147+574G>A	chr2.hg19:g.174224139G>A		177.0	1.0		210.0	64.0	NM_031942	B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	Missense_Mutation	SNP	ENST00000347703.3	hg19	CCDS2253.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.078203	0.76528	.	.	ENSG00000144354	ENST00000306721;ENST00000410101	T;T	0.53857	0.6;0.73	6.06	5.19	0.71726	.	0.064355	0.64402	N	0.000012	T	0.65091	0.2658	M	0.65975	2.015	0.80722	D	1	D;D	0.76494	0.997;0.999	P;P	0.59825	0.735;0.864	T	0.63980	-0.6514	10	0.30854	T	0.27	-11.606	13.3714	0.60715	0.0732:0.0:0.9268:0.0	.	58;102	B4DV66;Q9BWT1-2	.;.	K	102;58	ENSP00000306968:E102K;ENSP00000386656:E58K	ENSP00000306968:E102K	E	+	1	0	CDCA7	173932385	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	2.376000	0.44292	1.575000	0.49775	0.650000	0.86243	GAA	.	.		0.423	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255400.1	NM_031942		A	174224139	G	A	174224139	1	1	41	0	1	0	0	0	0	0	0	0	3092	1059	37	1		1	CDCA7	2	174224139	Intron	SNP	G	TCGA-BC-A216-01A-11D-A152-10	42702702	174224139	68975234	10	4943										
IL17RD	54756	hgsc.bcm.edu	37	chr3	57154328	57154328	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	acagcccactgtttctgctgGctggccccactccctgtggg	11	16	1	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr3:57154328G>A	ENST00000296318.7	-	2	228	c.140C>T	c.(139-141)gCc>gTc	p.A47V	IL17RD_ENST00000427856.2_Missense_Mutation_p.A23V|IL17RD_ENST00000463523.1_5'UTR|IL17RD_ENST00000479825.1_5'UTR|IL17RD_ENST00000320057.5_5'UTR	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	47					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		GTTTCTGCTGGCTGGCCCCAC	0.468																																					p.A47V		Atlas-SNP	.											.	IL17RD	93	.	0			c.C140T						.						99	95	96					3																	57154328		1991	4177	6168	SO:0001583	missense	54756	exon2			CTGCTGGCTGGCC	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.140C>T	chr3.hg19:g.57154328G>A	ENSP00000296318:p.Ala47Val	85.0	0.0		95.0	31.0	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Missense_Mutation	SNP	ENST00000296318.7	hg19	CCDS2880.2	.	.	.	.	.	.	.	.	.	.	G	10.67	1.416150	0.25552	.	.	ENSG00000144730	ENST00000296318;ENST00000427856	T;T	0.09723	2.96;2.95	6.06	5.01	0.66863	.	0.313090	0.30742	N	0.008975	T	0.03390	0.0098	N	0.02539	-0.55	0.31469	N	0.66865	B;B	0.11235	0.002;0.004	B;B	0.11329	0.005;0.006	T	0.35025	-0.9805	10	0.07813	T	0.8	3.8493	7.0422	0.25027	0.2312:0.0:0.7687:0.0	.	47;23	Q8NFM7;Q8NFM7-3	I17RD_HUMAN;.	V	47;23	ENSP00000296318:A47V;ENSP00000399209:A23V	ENSP00000296318:A47V	A	-	2	0	IL17RD	57129368	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	2.734000	0.47368	2.882000	0.98803	0.655000	0.94253	GCC	.	.		0.468	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		A	57154328	G	A	57154328	3	1	41	1	0	0	0	0	1	0	0	0	7651	1203	42	3	2127	3	IL17RD	3	57154328	Missense_Mutation	SNP	G	TCGA-BC-A216-01A-11D-A152-10		57154328	140868102	11	4944										
POLQ	10721	hgsc.bcm.edu	37	chr3	121158902	121158903	+	Frame_Shift_Del	DEL	GG	GG	-													0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tatctacgccttcccaaaatGgtctgaacaaatccgtctct							TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr3:121158902_121158903delGG	ENST00000264233.5	-	27	7453_7454	c.7325_7326delCC	c.(7324-7326)accfs	p.T2442fs		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2442					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TTCCCAAAATGGTCTGAACAAA	0.322								DNA polymerases (catalytic subunits)																													p.2442_2443del	Pancreas(152;907 1925 26081 31236 36904)	Atlas-Indel,Pindel	.											.	POLQ	273	.	0			c.7326_7327del						.																																			SO:0001589	frameshift_variant	10721	exon27			.	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.7325_7326delCC	chr3.hg19:g.121158902_121158903delGG	ENSP00000264233:p.Thr2442fs	64.0	0.0		61.0	23.0	NM_199420	O95160|Q6VMB5	Frame_Shift_Del	DEL	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.322	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		-	121158903	GG	-	121158902	7	5	41	1	0	1	0	1	0	0	0	0	12217	1335	47	0	462	0	POLQ	3	121158902	Frame_Shift_Del	DEL	GG	TCGA-BC-A216-01A-11D-A152-10	64004574	121158902	76863528	12	4945										
ACAD11	84129	hgsc.bcm.edu	37	chr3	132349391	132349391	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tattgaaatcagttcttccaTtgatggtatccctataaaaa	5	7	2	2			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr3:132349391T>A	ENST00000264990.6	-	7	1824	c.853A>T	c.(853-855)Atg>Ttg	p.M285L	ACAD11_ENST00000355458.3_Missense_Mutation_p.M285L|ACAD11_ENST00000545291.1_5'UTR|ACAD11_ENST00000489991.1_5'UTR|ACAD11_ENST00000481970.2_Missense_Mutation_p.M285L	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	285					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)			breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						AGTTCTTCCATTGATGGTATC	0.328																																					p.M285L		Atlas-SNP	.											.	ACAD11	78	.	0			c.A853T						.						50	53	52					3																	132349391		2202	4300	6502	SO:0001583	missense	84129	exon7			CTTCCATTGATGG	BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"acyl-Coenzyme A dehydrogenase family, member 11"				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.853A>T	chr3.hg19:g.132349391T>A	ENSP00000264990:p.Met285Leu	132.0	0.0		125.0	22.0	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Missense_Mutation	SNP	ENST00000264990.6	hg19	CCDS3074.1	.	.	.	.	.	.	.	.	.	.	T	5.919	0.353669	0.11182	.	.	ENSG00000240303	ENST00000355458;ENST00000264990;ENST00000481970	T;T;T	0.26957	1.7;1.7;1.7	5.57	-4.41	0.03590	Protein kinase-like domain (1);	.	.	.	.	T	0.10852	0.0265	L	0.28608	0.87	0.25836	N	0.98412	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39941	-0.9589	9	0.08381	T	0.77	.	0.5992	0.00742	0.4183:0.188:0.1812:0.2125	.	285;285	D6RDI8;Q709F0	.;ACD11_HUMAN	L	285	ENSP00000347636:M285L;ENSP00000264990:M285L;ENSP00000420907:M285L	ENSP00000264990:M285L	M	-	1	0	ACAD11	133832081	0.003000	0.15002	0.190000	0.23270	0.935000	0.57460	-0.906000	0.04071	-0.510000	0.06523	-0.274000	0.10170	ATG	.	.		0.328	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169		A	132349391	T	A	132349391	3	1	41	1	0	0	0	0	1	0	0	0	109	1493	52	4	1545	4	ACAD11	3	132349391	Missense_Mutation	SNP	T	TCGA-BC-A216-01A-11D-A152-10	11190489	132349391	65673039	13	4946										
EHHADH	1962	hgsc.bcm.edu	37	chr3	184911175	184911175	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	aagacagaggttatcatcttGtttgcagttgctagctggtt	11	6	2	2			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr3:184911175G>T	ENST00000231887.3	-	7	1086	c.1011C>A	c.(1009-1011)aaC>aaA	p.N337K	EHHADH-AS1_ENST00000417720.1_RNA|EHHADH_ENST00000456310.1_Missense_Mutation_p.N241K	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	337	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			TTATCATCTTGTTTGCAGTTG	0.483																																					p.N337K		Atlas-SNP	.											.	EHHADH	73	.	0			c.C1011A						.						128	130	129					3																	184911175		2203	4300	6503	SO:0001583	missense	1962	exon7			CATCTTGTTTGCA	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1011C>A	chr3.hg19:g.184911175G>T	ENSP00000231887:p.Asn337Lys	166.0	0.0		108.0	33.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	G	0.480	-0.880108	0.02530	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.76448	-1.02;-1.02	6.08	1.87	0.25490	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.584920	0.20110	N	0.099023	T	0.28400	0.0702	N	0.00064	-2.31	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42865	-0.9426	10	0.15952	T	0.53	-3.1336	0.7779	0.01035	0.1966:0.2589:0.3155:0.229	.	337	Q08426	ECHP_HUMAN	K	337;337;241	ENSP00000231887:N337K;ENSP00000387746:N241K	ENSP00000231887:N337K	N	-	3	2	EHHADH	186393869	0.000000	0.05858	0.002000	0.10522	0.988000	0.76386	0.752000	0.26362	0.855000	0.35359	0.591000	0.81541	AAC	.	.		0.483	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			T	184911175	G	T	184911175	3	4	41	1	0	0	0	0	1	0	0	0	4984	1368	48	3	1164	3	EHHADH	3	184911175	Missense_Mutation	SNP	G	TCGA-BC-A216-01A-11D-A152-10	52561784	184911175	13111255	14	4947										
RTP1	132112	hgsc.bcm.edu	37	chr3	186917604	186917604	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	accgcatccacgtggccagcCgccaggacaaccggcggcac	12	18	0	0	rs372732386		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr3:186917604C>T	ENST00000312295.4	+	2	568	c.538C>T	c.(538-540)Cgc>Tgc	p.R180C	RP11-208N14.4_ENST00000356133.3_RNA	NM_153708.2	NP_714919.2	P59025	RTP1_HUMAN	receptor (chemosensory) transporter protein 1	180					protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)			breast(2)|endometrium(4)|large_intestine(5)|lung(6)|ovary(3)|skin(2)	22	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		CGTGGCCAGCCGCCAGGACAA	0.682																																					p.R180C		Atlas-SNP	.											.	RTP1	51	.	0			c.C538T						.	C	CYS/ARG	0,4400		0,0,2200	24	25	25		538	4.8	1	3		25	1,8583		0,1,4291	no	missense	RTP1	NM_153708.2	180	0,1,6491	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	180/264	186917604	1,12983	2200	4292	6492	SO:0001583	missense	132112	exon2			GCCAGCCGCCAGG	BC034744	CCDS3287.2	3q27.3	2014-02-20	2006-11-21		ENSG00000175077	ENSG00000175077		"Receptor transporter proteins"	28580	protein-coding gene	gene with protein product	"receptor transporting protein 1", "zinc finger, 3CxxC-type 1"	609137	"receptor transporter protein 1"			16271481, 15550249, 16720576	Standard	NM_153708		Approved	MGC35450, Z3CXXC1	uc003frg.3	P59025	OTTHUMG00000149886	ENST00000312295.4:c.538C>T	chr3.hg19:g.186917604C>T	ENSP00000311712:p.Arg180Cys	29.0	0.0		32.0	18.0	NM_153708		Missense_Mutation	SNP	ENST00000312295.4	hg19	CCDS3287.2	.	.	.	.	.	.	.	.	.	.	C	19.02	3.746024	0.69418	0.0	1.16E-4	ENSG00000175077	ENST00000312295	T	0.23950	1.88	5.7	4.82	0.62117	.	0.381494	0.30649	N	0.009169	T	0.33731	0.0873	L	0.44542	1.39	0.39746	D	0.97181	D	0.61697	0.99	P	0.54060	0.741	T	0.12192	-1.0557	10	0.52906	T	0.07	.	12.2521	0.54603	0.1691:0.8309:0.0:0.0	.	180	P59025	RTP1_HUMAN	C	180	ENSP00000311712:R180C	ENSP00000311712:R180C	R	+	1	0	RTP1	188400298	0.604000	0.26932	1.000000	0.80357	0.963000	0.63663	0.710000	0.25748	1.403000	0.46800	0.561000	0.74099	CGC	.	.		0.682	RTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313731.2	NM_153708		T	186917604	C	T	186917604	3	4	41	1	0	0	0	0	1	0	0	0	13748	652	23	1	544	1	RTP1	3	186917604	Missense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10	2006429	186917604	11104826	15	4948										
IBSP	3381	hgsc.bcm.edu	37	chr4	88732600	88732600	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	gaaggaaatgaaaacgaagaAagcgaagcagaagtggatga	14	3	0	4			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr4:88732600A>T	ENST00000226284.5	+	7	559	c.492A>T	c.(490-492)gaA>gaT	p.E164D		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	164	Asp/Glu-rich (acidic).				biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		aaaacgaagaaagcgaagcag	0.458																																					p.E164D		Atlas-SNP	.											.	IBSP	53	.	0			c.A492T						.						136	125	129					4																	88732600		2203	4300	6503	SO:0001583	missense	3381	exon7			CGAAGAAAGCGAA		CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"bone sialoprotein", "bone sialoprotein II"	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.492A>T	chr4.hg19:g.88732600A>T	ENSP00000226284:p.Glu164Asp	197.0	0.0		151.0	53.0	NM_004967		Missense_Mutation	SNP	ENST00000226284.5	hg19	CCDS3624.1	.	.	.	.	.	.	.	.	.	.	A	14.96	2.691079	0.48097	.	.	ENSG00000029559	ENST00000226284	T	0.14391	2.51	4.92	0.699	0.18093	.	0.691694	0.13979	N	0.349626	T	0.14917	0.0360	L	0.46157	1.445	0.29739	N	0.837225	P	0.47253	0.892	P	0.49421	0.61	T	0.11542	-1.0583	10	0.39692	T	0.17	.	4.1592	0.10275	0.5304:0.1873:0.2823:0.0	.	164	P21815	SIAL_HUMAN	D	164	ENSP00000226284:E164D	ENSP00000226284:E164D	E	+	3	2	IBSP	88951624	0.505000	0.26131	0.976000	0.42696	0.858000	0.48976	-0.084000	0.11268	0.299000	0.22661	0.482000	0.46254	GAA	.	.		0.458	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2			T	88732600	A	T	88732600	3	4	41	1	0	0	0	0	1	0	0	0	7484	11	1	4	514	4	IBSP	4	88732600	Missense_Mutation	SNP	A	TCGA-BC-A216-01A-11D-A152-10		88732600	102421676	16	4949										
MTNR1A	4543	hgsc.bcm.edu	37	chr4	187455191	187455191	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	acaaacatggtgacaaaattCctgaagtcctgtggtttcag	9	8	1	2			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr4:187455191C>T	ENST00000307161.5	-	2	906	c.705G>A	c.(703-705)agG>agA	p.R235R	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	235					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	TGACAAAATTCCTGAAGTCCT	0.502																																					p.R235R		Atlas-SNP	.											.	MTNR1A	46	.	0			c.G705A						.						133	143	139					4																	187455191		2203	4300	6503	SO:0001819	synonymous_variant	4543	exon2			AAAATTCCTGAAG		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"GPCR / Class A : Melatonin receptors"	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.705G>A	chr4.hg19:g.187455191C>T		162.0	0.0		192.0	47.0	NM_005958	A0AVC5|B0M0L2	Silent	SNP	ENST00000307161.5	hg19	CCDS3848.1																																																																																			.	.		0.502	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1			T	187455191	C	T	187455191	2	4	41	1	0	0	0	0	0	0	0	1	9960	854	30	3		3	MTNR1A	4	187455191	Silent	SNP	C	TCGA-BC-A216-01A-11D-A152-10	98722591	187455191	3699085	17	4950										
DSP	1832	hgsc.bcm.edu	37	chr6	7583427	7583427	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tgaggaagaaggtgacagcaAtgcagctctatgagtgtcag	14	6	2	4			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr6:7583427A>G	ENST00000379802.3	+	24	6273	c.5932A>G	c.(5932-5934)Atg>Gtg	p.M1978V	DSP_ENST00000418664.2_Missense_Mutation_p.M1379V	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1978	4.5 X 38 AA tandem repeats (Domain A).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GGTGACAGCAATGCAGCTCTA	0.502																																					p.M1978V		Atlas-SNP	.											DSP,NS,carcinoma,0,1	DSP	306	.	0			c.A5932G						.						101	101	101					6																	7583427		2203	4300	6503	SO:0001583	missense	1832	exon24			ACAGCAATGCAGC	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.5932A>G	chr6.hg19:g.7583427A>G	ENSP00000369129:p.Met1978Val	132.0	1.0		126.0	56.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	A	10.78	1.447587	0.26074	.	.	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.66815	-0.23;-0.23	5.48	4.31	0.51392	.	0.000000	0.85682	D	0.000000	T	0.30355	0.0762	L	0.34521	1.04	0.09310	N	0.999999	B;B	0.16802	0.019;0.0	B;B	0.12156	0.007;0.001	T	0.13602	-1.0503	10	0.30078	T	0.28	.	6.9741	0.24664	0.6415:0.2862:0.0723:0.0	.	1426;1978	Q4LE79;P15924	.;DESP_HUMAN	V	1978;1379	ENSP00000369129:M1978V;ENSP00000396591:M1379V	ENSP00000369129:M1978V	M	+	1	0	DSP	7528426	0.931000	0.31567	0.750000	0.31169	0.921000	0.55340	2.156000	0.42310	0.893000	0.36288	0.533000	0.62120	ATG	.	.		0.502	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		G	7583427	A	G	7583427	3	3	41	1	0	0	0	0	1	0	0	0	4783	101	4	2	6026	2	DSP	6	7583427	Missense_Mutation	SNP	A	TCGA-BC-A216-01A-11D-A152-10		7583427	163531640	18	4951										
HIST1H2AG	8969	hgsc.bcm.edu	37	chr6	27101166	27101166	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	gcaaagtcaccatcgcacagGgcggtgtcctgcccaacatt	10	14	1	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr6:27101166G>T	ENST00000359193.2	+	1	335	c.316G>T	c.(316-318)Ggc>Tgc	p.G106C	HIST1H2BJ_ENST00000607124.1_5'Flank|HIST1H2BJ_ENST00000339812.2_5'Flank|HIST1H2BJ_ENST00000541790.1_5'Flank	NM_021064.4	NP_066408.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ag	106						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	17						CATCGCACAGGGCGGTGTCCT	0.562																																					p.G106C		Atlas-SNP	.											.	HIST1H2AG	37	.	0			c.G316T						.						109	102	105					6																	27101166		2203	4300	6503	SO:0001583	missense	8969	exon1			GCACAGGGCGGTG	L19778	CCDS4619.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000196787	ENSG00000196787		"Histones / Replication-dependent"	4737	protein-coding gene	gene with protein product		615012	"H2A histone family, member P", "histone 1, H2ag"	H2AFP		8179821, 12408966	Standard	NM_021064		Approved	pH2A/f, H2A/p, H2A.1b	uc003niw.3	P0C0S8	OTTHUMG00000014469	ENST00000359193.2:c.316G>T	chr6.hg19:g.27101166G>T	ENSP00000352119:p.Gly106Cys	186.0	0.0		134.0	53.0	NM_021064	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000359193.2	hg19	CCDS4619.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.704086	0.68615	.	.	ENSG00000196787	ENST00000359193	T	0.47869	0.83	4.08	4.08	0.47627	Histone-fold (2);Histone H2A (2);	0.000000	0.41001	D	0.000968	T	0.62588	0.2440	.	.	.	0.43977	D	0.996666	D	0.89917	1.0	D	0.91635	0.999	T	0.68827	-0.5306	9	0.87932	D	0	.	14.6102	0.68510	0.0:0.0:1.0:0.0	.	106	P0C0S8	H2A1_HUMAN	C	106	ENSP00000352119:G106C	ENSP00000352119:G106C	G	+	1	0	HIST1H2AG	27209145	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.086000	0.76885	2.217000	0.71921	0.655000	0.94253	GGC	.	.		0.562	HIST1H2AG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040137.1	NM_021064		T	27101166	G	T	27101166	3	4	41	1	0	0	0	0	1	0	0	0	7142	1232	43	3	318	3	HIST1H2AG	6	27101166	Missense_Mutation	SNP	G	TCGA-BC-A216-01A-11D-A152-10	19517739	27101166	144013901	19	4952										
HMGCLL1	54511	hgsc.bcm.edu	37	chr6	55360266	55360266	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	cttgtccgtatgtgtcatgaCagtgaacagcaagagcacct	10	10	1	3			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr6:55360266C>G	ENST00000398661.2	-	8	967	c.836G>C	c.(835-837)tGt>tCt	p.C279S	HMGCLL1_ENST00000370850.2_Missense_Mutation_p.C146S|HMGCLL1_ENST00000274901.4_Missense_Mutation_p.C249S|HMGCLL1_ENST00000508459.1_Intron|HMGCLL1_ENST00000308161.4_Missense_Mutation_p.C217S	NM_019036.2	NP_061909.2	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1	279					ketone body biosynthetic process (GO:0046951)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|metal ion binding (GO:0046872)	p.C279Y(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)			TGTGTCATGACAGTGAACAGC	0.428																																					p.C279S	Ovarian(35;840 893 7837 15538 42887)	Atlas-SNP	.											HMGCLL1,NS,carcinoma,0,1	HMGCLL1	70	.	1	Substitution - Missense(1)	prostate(1)	c.G836C						.						145	130	135					6																	55360266		1903	4119	6022	SO:0001583	missense	54511	exon8			TCATGACAGTGAA	AK055075	CCDS43474.1, CCDS43475.1, CCDS75472.1, CCDS75473.1	6p12.1	2010-04-30	2010-04-30		ENSG00000146151	ENSG00000146151			21359	protein-coding gene	gene with protein product			"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1"			8619474, 9110174	Standard	NM_001042406		Approved	DKFZP434G1411, bA418P12.1	uc003pcn.3	Q8TB92	OTTHUMG00000014902	ENST00000398661.2:c.836G>C	chr6.hg19:g.55360266C>G	ENSP00000381654:p.Cys279Ser	203.0	0.0		160.0	64.0	NM_019036	B1AQ42|B3KNV0|B7Z1S7|F8W793|Q6ZSA9	Missense_Mutation	SNP	ENST00000398661.2	hg19	CCDS43475.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.400326	0.83120	.	.	ENSG00000146151	ENST00000274901;ENST00000398661;ENST00000370850;ENST00000308161	D;D;D;D	0.98313	-4.86;-4.86;-4.86;-4.86	5.62	5.62	0.85841	Aldolase-type TIM barrel (1);Pyruvate carboxyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.99242	0.9736	M	0.91459	3.21	0.80722	D	1	D;D;D;D	0.89917	0.998;0.995;0.998;1.0	D;D;D;D	0.97110	0.999;0.975;0.996;1.0	D	0.99425	1.0934	10	0.87932	D	0	-16.0907	19.6685	0.95901	0.0:1.0:0.0:0.0	.	146;217;249;279	B7Z212;F8W793;Q8TB92-2;Q8TB92	.;.;.;HMGC2_HUMAN	S	249;279;146;217	ENSP00000274901:C249S;ENSP00000381654:C279S;ENSP00000359887:C146S;ENSP00000309737:C217S	ENSP00000274901:C249S	C	-	2	0	HMGCLL1	55468225	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	6.070000	0.71220	2.639000	0.89480	0.655000	0.94253	TGT	.	.		0.428	HMGCLL1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360290.1	XM_166383		G	55360266	C	G	55360266	3	3	41	1	0	0	0	0	1	0	0	0	7239	478	17	4	288	4	HMGCLL1	6	55360266	Missense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10	28259100	55360266	115754801	20	4953										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152651593	152651593	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tggctgccaaggctgacctgTgctgcgaaaaccttcttttt	10	11	1	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr6:152651593T>G	ENST00000367255.5	-	78	14828	c.14227A>C	c.(14227-14229)Aca>Cca	p.T4743P	SYNE1_ENST00000423061.1_Missense_Mutation_p.T4672P|SYNE1_ENST00000341594.5_Missense_Mutation_p.T4490P|SYNE1_ENST00000448038.1_Missense_Mutation_p.T4672P|SYNE1_ENST00000265368.4_Missense_Mutation_p.T4743P	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4743					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GGCTGACCTGTGCTGCGAAAA	0.512										HNSCC(10;0.0054)																											p.T4743P		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A14227C						.						88	93	91					6																	152651593		2203	4300	6503	SO:0001583	missense	23345	exon78			GACCTGTGCTGCG	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.14227A>C	chr6.hg19:g.152651593T>G	ENSP00000356224:p.Thr4743Pro	69.0	0.0		49.0	25.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	16.66	3.183698	0.57800	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000006	T	0.51415	0.1673	L	0.52573	1.65	0.80722	D	1	D;D;D;D	0.60575	0.988;0.98;0.98;0.988	P;B;B;P	0.61397	0.888;0.439;0.439;0.759	T	0.50110	-0.8866	10	0.41790	T	0.15	.	16.2087	0.82144	0.0:0.0:0.0:1.0	.	4743;4743;4743;4672	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	P	4743;4672;4743;4672;4490	ENSP00000356224:T4743P;ENSP00000396024:T4672P;ENSP00000265368:T4743P;ENSP00000390975:T4672P;ENSP00000341887:T4490P	ENSP00000265368:T4743P	T	-	1	0	SYNE1	152693286	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.233000	0.73108	0.482000	0.46254	ACA	.	.		0.512	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152651593	T	G	152651593	3	3	41	1	0	0	0	0	1	0	0	0	15460	1696	59	5	12515	5	SYNE1	6	152651593	Missense_Mutation	SNP	T	TCGA-BC-A216-01A-11D-A152-10	97291327	152651593	18463474	21	4954										
TWISTNB	221830	hgsc.bcm.edu	37	chr7	19738145	19738145	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tttctttggctcctcctcccAgatgccattcgcattattag	6	13	1	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr7:19738145A>G	ENST00000222567.5	-	4	881	c.811T>C	c.(811-813)Tgg>Cgg	p.W271R		NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	271	Lys-rich.				transcription from RNA polymerase I promoter (GO:0006360)	DNA-directed RNA polymerase I complex (GO:0005736)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	20						TCCTCCTCCCAGATGCCATTC	0.468																																					p.W271R		Atlas-SNP	.											.	TWISTNB	63	.	0			c.T811C						.						289	312	305					7																	19738145		2203	4300	6503	SO:0001583	missense	221830	exon4			CCTCCCAGATGCC	AK090846	CCDS34606.1	7p21.1	2010-08-05			ENSG00000105849	ENSG00000105849			18027	protein-coding gene	gene with protein product		608312				12438708	Standard	NM_001002926		Approved		uc003sup.1	Q3B726	OTTHUMG00000152497	ENST00000222567.5:c.811T>C	chr7.hg19:g.19738145A>G	ENSP00000222567:p.Trp271Arg	192.0	0.0		158.0	59.0	NM_001002926	A0PJ45|B7Z724	Missense_Mutation	SNP	ENST00000222567.5	hg19	CCDS34606.1	.	.	.	.	.	.	.	.	.	.	A	9.776	1.174034	0.21704	.	.	ENSG00000105849	ENST00000222567	.	.	.	5.54	-1.33	0.09172	.	1.477610	0.03093	N	0.160111	T	0.31263	0.0791	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06006	-1.0851	9	0.25106	T	0.35	12.4601	2.3197	0.04207	0.5795:0.1174:0.1905:0.1126	.	271	Q3B726	RPA43_HUMAN	R	271	.	ENSP00000222567:W271R	W	-	1	0	TWISTNB	19704670	0.000000	0.05858	0.002000	0.10522	0.372000	0.29890	0.404000	0.20999	-0.371000	0.08004	-0.755000	0.03482	TGG	.	.		0.468	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1			G	19738145	A	G	19738145	3	3	41	1	0	0	0	0	1	0	0	0	16799	188	7	2	209	2	TWISTNB	7	19738145	Missense_Mutation	SNP	A	TCGA-BC-A216-01A-11D-A152-10		19738145	139400518	22	4955										
AUTS2	26053	hgsc.bcm.edu	37	chr7	70252291	70252291	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	gctgcaccgaacgcctccgtCgttcccgacccctccgccct	8	22	0	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr7:70252291C>T	ENST00000342771.4	+	18	2726	c.2405C>T	c.(2404-2406)tCg>tTg	p.S802L	AUTS2_ENST00000406775.2_Missense_Mutation_p.S778L	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	802										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		ACGCCTCCGTCGTTCCCGACC	0.602																																					p.S802L		Atlas-SNP	.											.	AUTS2	173	.	0			c.C2405T						.						45	40	42					7																	70252291		2203	4300	6503	SO:0001583	missense	26053	exon18			CTCCGTCGTTCCC	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.2405C>T	chr7.hg19:g.70252291C>T	ENSP00000344087:p.Ser802Leu	81.0	0.0		73.0	31.0	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	hg19	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.022037	0.93462	.	.	ENSG00000158321	ENST00000406775;ENST00000342771;ENST00000418686	T;T	0.50813	0.76;0.73	4.88	4.88	0.63580	.	0.186688	0.48767	D	0.000169	T	0.61937	0.2387	M	0.66939	2.045	0.80722	D	1	D;D;D	0.67145	0.991;0.996;0.996	P;P;P	0.55965	0.508;0.788;0.788	T	0.63773	-0.6561	9	.	.	.	-16.1247	18.0311	0.89285	0.0:1.0:0.0:0.0	.	254;778;802	B4DLG0;Q8WXX7-2;Q8WXX7	.;.;AUTS2_HUMAN	L	778;802;82	ENSP00000385263:S778L;ENSP00000344087:S802L	.	S	+	2	0	AUTS2	69890227	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.280000	0.78610	2.251000	0.74343	0.655000	0.94253	TCG	.	.		0.602	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			T	70252291	C	T	70252291	3	4	41	1	0	0	0	0	1	0	0	0	1225	893	31	1	2620	1	AUTS2	7	70252291	Missense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10	50514146	70252291	88886372	23	4956										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113421218	113421218	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	ccatcatacacctcaacaacAtcgtggagtgatgtctggaa	8	11	3	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr8:113421218A>T	ENST00000297405.5	-	33	5683	c.5439T>A	c.(5437-5439)gaT>gaA	p.D1813E	CSMD3_ENST00000352409.3_Intron|CSMD3_ENST00000343508.3_Missense_Mutation_p.D1773E|CSMD3_ENST00000455883.2_Missense_Mutation_p.D1709E	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1813	CUB 10. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CCTCAACAACATCGTGGAGTG	0.443										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.D1813E		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T5439A						.						170	158	162					8																	113421218		2203	4300	6503	SO:0001583	missense	114788	exon33			AACAACATCGTGG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.5439T>A	chr8.hg19:g.113421218A>T	ENSP00000297405:p.Asp1813Glu	160.0	0.0		134.0	58.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.452061	0.63290	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883	T;T;T	0.29917	1.55;1.55;1.55	5.07	3.9	0.45041	CUB (5);	0.000000	0.64402	D	0.000001	T	0.64929	0.2643	H	0.96691	3.865	0.80722	D	1	D;D;D	0.89917	0.998;0.999;1.0	D;D;D	0.91635	0.997;0.996;0.999	T	0.69986	-0.4996	10	0.59425	D	0.04	.	8.2404	0.31656	0.8457:0.0:0.1543:0.0	.	1709;1813;1773	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	E	1773;1813;1709	ENSP00000345799:D1773E;ENSP00000297405:D1813E;ENSP00000412263:D1709E	ENSP00000297405:D1813E	D	-	3	2	CSMD3	113490394	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.178000	0.42519	0.948000	0.37687	0.482000	0.46254	GAT	.	.		0.443	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113421218	A	T	113421218	3	4	41	1	0	0	0	0	1	0	0	0	3948	214	8	4	5840	4	CSMD3	8	113421218	Missense_Mutation	SNP	A	TCGA-BC-A216-01A-11D-A152-10		113421218	32942804	24	4957										
RAB18	22931	hgsc.bcm.edu	37	chr10	27826828	27826828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	caagtgcaaaaacctgtgatGgtgtacaatgtgcctttgaa	10	7	0	2			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr10:27826828G>A	ENST00000356940.6	+	7	571	c.469G>A	c.(469-471)Ggt>Agt	p.G157S	RAB18_ENST00000375802.3_Missense_Mutation_p.G112S|RAB18_ENST00000465772.1_3'UTR|RAB18_ENST00000535776.1_Missense_Mutation_p.G93S	NM_001256410.1|NM_001256415.1|NM_021252.4	NP_001243339.1|NP_001243344.1|NP_067075.1	Q9NP72	RAB18_HUMAN	RAB18, member RAS oncogene family	157					brain development (GO:0007420)|endoplasmic reticulum tubular network organization (GO:0071786)|eye development (GO:0001654)|GTP catabolic process (GO:0006184)|lipid particle organization (GO:0034389)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|large_intestine(1)|lung(1)	3						AACCTGTGATGGTGTACAATG	0.398																																					p.G186S		Atlas-SNP	.											.	RAB18	18	.	0			c.G556A						.						99	96	97					10																	27826828		2203	4300	6503	SO:0001583	missense	22931	exon8			TGTGATGGTGTAC	AJ277145	CCDS7155.1, CCDS58073.1, CCDS73080.1, CCDS73081.1	10p12	2011-03-07			ENSG00000099246	ENSG00000099246		"RAB, member RAS oncogene"	14244	protein-coding gene	gene with protein product		602207				10648831	Standard	NM_021252		Approved		uc001itw.4	Q9NP72	OTTHUMG00000017861	ENST00000356940.6:c.469G>A	chr10.hg19:g.27826828G>A	ENSP00000349415:p.Gly157Ser	96.0	0.0		81.0	31.0	NM_001256410	B3KMC7|B7Z333|D3DRW1|Q53FX8|Q56UN9|Q6FIH1	Missense_Mutation	SNP	ENST00000356940.6	hg19	CCDS7155.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.6|29.6	5.022809|5.022809	0.93462|0.93462	.|.	.|.	ENSG00000099246|ENSG00000099246	ENST00000356940;ENST00000535776;ENST00000540268;ENST00000375802|ENST00000423465	T;D;T|.	0.82433|.	-0.41;-1.61;-0.41|.	6.02|6.02	6.02|6.02	0.97574|0.97574	Small GTP-binding protein domain (1);|.	.|.	.|.	.|.	.|.	T|.	0.71134|.	0.3304|.	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.993;1.0;0.998|.	P;D;D|.	0.87578|.	0.877;0.998;0.98|.	T|.	0.65315|.	-0.6198|.	9|.	0.72032|.	D|.	0.01|.	.|.	19.5352|19.5352	0.95251|0.95251	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	93;186;157|.	B7Z333;Q56UN9;Q9NP72|.	.;.;RAB18_HUMAN|.	S|X	157;93;135;112|269	ENSP00000349415:G157S;ENSP00000439321:G93S;ENSP00000364960:G112S|.	ENSP00000349415:G157S|.	G|W	+|+	1|2	0|0	RAB18|RAB18	27866834|27866834	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.776000|9.776000	0.99001|0.99001	2.850000|2.850000	0.98022|0.98022	0.650000|0.650000	0.86243|0.86243	GGT|TGG	.	.		0.398	RAB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047326.2	NM_021252		A	27826828	G	A	27826828	3	1	41	1	0	0	0	0	1	0	0	0	12918	1348	47	3	495	3	RAB18	10	27826828	Missense_Mutation	SNP	G	TCGA-BC-A216-01A-11D-A152-10		27826828	107707919	25	4958										
C10orf137	26098	hgsc.bcm.edu	37	chr10	127426555	127426555	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	cttgtgcttagctatgttctAgaggtaagtttaagtttagt	10	4	1	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr10:127426555A>G	ENST00000356792.4	+	14	2059	c.1827A>G	c.(1825-1827)ctA>ctG	p.L609L	C10orf137_ENST00000337623.3_Silent_p.L575L	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		609					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.L575L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GCTATGTTCTAGAGGTAAGTT	0.338																																					p.L609L		Atlas-SNP	.											C10orf137_ENST00000356792,NS,adenocarcinoma,0,4	C10orf137	153	.	1	Substitution - coding silent(1)	lung(1)	c.A1827G						.						180	171	174					10																	127426555		2203	4300	6503	SO:0001819	synonymous_variant	26098	exon14			TGTTCTAGAGGTA																												ENST00000356792.4:c.1827A>G	chr10.hg19:g.127426555A>G		284.0	0.0		246.0	87.0	NM_001202438	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Silent	SNP	ENST00000356792.4	hg19	CCDS55733.1																																																																																			.	.		0.338	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			G	127426555	A	G	127426555	2	3	41	1	0	0	0	0	0	0	0	1	1596	407	15	2		2	C10orf137	10	127426555	Silent	SNP	A	TCGA-BC-A216-01A-11D-A152-10	99599727	127426555	8108192	26	4959										
GRIN2B	2904	hgsc.bcm.edu	37	chr12	13716219	13716219	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tcaggcttacgctgcgcgggGccagggcggcttcttccttc	14	14	2	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr12:13716219G>C	ENST00000609686.1	-	13	4162	c.3953C>G	c.(3952-3954)gCc>gGc	p.A1318G		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	1318					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTGCGCGGGGCCAGGGCGGC	0.592																																					p.A1318G		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C3953G						.						67	76	73					12																	13716219		2203	4300	6503	SO:0001583	missense	2904	exon13			CGCGGGGCCAGGG		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.3953C>G	chr12.hg19:g.13716219G>C	ENSP00000477455:p.Ala1318Gly	184.0	0.0		186.0	93.0	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	hg19	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.480261	0.44044	.	.	ENSG00000150086	ENST00000279593	T	0.10477	2.87	4.7	4.7	0.59300	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.057069	0.64402	D	0.000001	T	0.10937	0.0267	N	0.14661	0.345	0.53688	D	0.999979	P	0.36086	0.536	B	0.42738	0.396	T	0.32428	-0.9907	10	0.36615	T	0.2	.	18.2005	0.89836	0.0:0.0:1.0:0.0	.	1318	Q13224	NMDE2_HUMAN	G	1318	ENSP00000279593:A1318G	ENSP00000279593:A1318G	A	-	2	0	GRIN2B	13607486	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	9.202000	0.95026	2.579000	0.87056	0.563000	0.77884	GCC	.	.		0.592	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			C	13716219	G	C	13716219	3	2	41	1	0	0	0	0	1	0	0	0	6789	1203	42	4	505	4	GRIN2B	12	13716219	Missense_Mutation	SNP	G	TCGA-BC-A216-01A-11D-A152-10		13716219	120135676	27	4960										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41410483	41410483	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	aatcttttaatttctatttaGcctttgtcaagagaatacca	4	7	3	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr12:41410483G>A	ENST00000551295.2	+	19	2301		c.e19-1		CNTN1_ENST00000348761.2_Splice_Site|CNTN1_ENST00000550305.1_Splice_Site|CNTN1_ENST00000347616.1_Splice_Site	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TTTCTATTTAGCCTTTGTCAA	0.368																																					.		Atlas-SNP	.											.	CNTN1	207	.	0			c.2185-1G>A						.						53	50	51					12																	41410483		2203	4300	6503	SO:0001630	splice_region_variant	1272	exon19			TATTTAGCCTTTG	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.2185-1G>A	chr12.hg19:g.41410483G>A		126.0	0.0		125.0	57.0	NM_001843	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Splice_Site	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.558606	0.65538	.	.	ENSG00000018236	ENST00000551295;ENST00000347616;ENST00000348761	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7385	0.96217	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNTN1	39696750	1.000000	0.71417	0.998000	0.56505	0.676000	0.39594	4.105000	0.57797	2.838000	0.97847	0.655000	0.94253	.	.	.		0.368	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843	Intron	A	41410483	G	A	41410483	5	1	41	1	0	0	0	0	0	0	1	0	3642	985	34	3	2254	3	CNTN1	12	41410483	Splice_Site	SNP	G	TCGA-BC-A216-01A-11D-A152-10	27694264	41410483	92441412	28	4961										
RBMS2	5939	hgsc.bcm.edu	37	chr12	56975266	56975266	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	gaaaatttgtgcaaaatggaCgggcttggccaaggaatgca	13	6	0	0	rs376730098		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr12:56975266C>T	ENST00000262031.5	+	7	801	c.706C>T	c.(706-708)Cgg>Tgg	p.R236W	RBMS2_ENST00000542360.1_Missense_Mutation_p.R91W|RBMS2_ENST00000550726.1_Missense_Mutation_p.R111W|RBMS2_ENST00000552247.2_Missense_Mutation_p.R236W	NM_002898.3	NP_002889.1	Q15434	RBMS2_HUMAN	RNA binding motif, single stranded interacting protein 2	236					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(3)|skin(2)|urinary_tract(1)	18						GCAAAATGGACGGGCTTGGCC	0.488																																					p.R236W		Atlas-SNP	.											.	RBMS2	29	.	0			c.C706T						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	59	52	55		706	3.3	1	12		55	0,8600		0,0,4300	no	missense	RBMS2	NM_002898.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	236/408	56975266	1,13005	2203	4300	6503	SO:0001583	missense	5939	exon7			AATGGACGGGCTT	D28483	CCDS8923.1	12q13.13	2013-02-12			ENSG00000076067	ENSG00000076067		"RNA binding motif (RRM) containing"	9909	protein-coding gene	gene with protein product		602387				8041632	Standard	NM_002898		Approved	SCR3	uc001sln.2	Q15434	OTTHUMG00000170488	ENST00000262031.5:c.706C>T	chr12.hg19:g.56975266C>T	ENSP00000262031:p.Arg236Trp	39.0	0.0		45.0	21.0	NM_002898		Missense_Mutation	SNP	ENST00000262031.5	hg19	CCDS8923.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.051563	0.55218	2.27E-4	0.0	ENSG00000076067	ENST00000262031;ENST00000552247;ENST00000550726;ENST00000542360	T;T;T	0.75704	2.56;-0.96;-0.96	5.21	3.35	0.38373	.	0.000000	0.85682	D	0.000000	T	0.71904	0.3395	M	0.67700	2.07	0.80722	D	1	P;P	0.48589	0.912;0.592	B;B	0.43728	0.429;0.189	T	0.72663	-0.4225	10	0.87932	D	0	.	9.2655	0.37639	0.1451:0.7777:0.0:0.0772	.	91;236	F5H5C8;Q15434	.;RBMS2_HUMAN	W	236;236;111;91	ENSP00000262031:R236W;ENSP00000447426:R236W;ENSP00000449678:R111W	ENSP00000262031:R236W	R	+	1	2	RBMS2	55261533	0.454000	0.25728	0.998000	0.56505	0.996000	0.88848	0.927000	0.28818	0.680000	0.31366	0.655000	0.94253	CGG	.	.		0.488	RBMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409366.2	NM_002898		T	56975266	C	T	56975266	3	4	41	1	0	0	0	0	1	0	0	0	13164	527	19	1	732	1	RBMS2	12	56975266	Missense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10	15564783	56975266	76876629	29	4962										
SLC16A7	9194	hgsc.bcm.edu	37	chr12	60169055	60169056	+	Frame_Shift_Ins	INS	-	-	GTCACCTCTTGTGCCCACTGGCACAGGACTA													0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	aatcatgttcaatggagtgtINSgtcacctcttgtgcccactg							TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr12:60169055_60169056insGTCACCTCTTGTGCCCACTGGCACAGGACTA	ENST00000261187.4	+	4	1143_1144	c.979_980insGTCACCTCTTGTGCCCACTGGCACAGGACTA	c.(979-981)tgtfs	p.-327fs	SLC16A7_ENST00000547379.1_Frame_Shift_Ins_p.-327fs|SLC16A7_ENST00000552024.1_Frame_Shift_Ins_p.-327fs|SLC16A7_ENST00000543448.1_Frame_Shift_Ins_p.-228fs|SLC16A7_ENST00000552432.1_Frame_Shift_Ins_p.-327fs	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7						lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	CAATGGAGTGTGTCACCTCTTG	0.411																																					p.C327_H328delinsCHLLCPLAQDX		Pindel	.											.	SLC16A7	82	.	0			c.979_980insGTCACCTCTTGTGCCCACTGGCACAGGACTA						.																																			SO:0001589	frameshift_variant	9194	exon5			.	AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"Solute carriers"	10928	protein-coding gene	gene with protein product		603654	"solute carrier family 16 (monocarboxylic acid transporters), member 7"			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000261187.4:c.980_1010dupGTCACCTCTTGTGCCCACTGGCACAGGACTA	chr12.hg19:g.60169055_60169056insGTCACCTCTTGTGCCCACTGGCACAGGACTA	ENSP00000261187:p.Cys327fs	238.0	0.0		172.0	19.0	NM_001270623	Q8NEM3|Q9UPB3	Frame_Shift_Ins	INS	ENST00000261187.4	hg19	CCDS8961.1																																																																																			.	.		0.411	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731		GTCACCTCTTGTGCCCACTGGCACAGGACTA	60169056	-	GTCACCTCTTGTGCCCACTGGCACAGGACTA	60169055	7	5	41	1	0	1	1	0	0	0	0	0	14428	1696	59	0	989	0	SLC16A7	12	60169055	Frame_Shift_Ins	INS	-	TCGA-BC-A216-01A-11D-A152-10	3193789	60169055	73682840	30	4963										
USP15	9958	hgsc.bcm.edu	37	chr12	62775287	62775287	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	gcagtgtttgagcaacacacCtccacttactgagtatttcc	7	12	0	2			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr12:62775287C>T	ENST00000280377.5	+	9	990	c.932C>T	c.(931-933)cCt>cTt	p.P311L	USP15_ENST00000393654.3_Missense_Mutation_p.P286L|USP15_ENST00000353364.3_Missense_Mutation_p.P282L	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	311	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		AGCAACACACCTCCACTTACT	0.294																																					p.P311L	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.C932T						.						105	98	100					12																	62775287		2203	4300	6503	SO:0001583	missense	9958	exon9			ACACACCTCCACT	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.932C>T	chr12.hg19:g.62775287C>T	ENSP00000280377:p.Pro311Leu	79.0	0.0		71.0	31.0	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Missense_Mutation	SNP	ENST00000280377.5	hg19	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.561086	0.86335	.	.	ENSG00000135655	ENST00000353364;ENST00000280377;ENST00000393654	T;T;T	0.35973	1.28;1.28;1.28	5.09	5.09	0.68999	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.110987	0.64402	D	0.000006	T	0.51398	0.1672	L	0.42245	1.32	0.80722	D	1	D;P	0.63880	0.993;0.575	D;B	0.64410	0.925;0.288	T	0.38866	-0.9641	9	.	.	.	-10.5756	18.6711	0.91512	0.0:1.0:0.0:0.0	.	311;282	Q9Y4E8;Q9Y4E8-2	UBP15_HUMAN;.	L	282;311;286	ENSP00000258123:P282L;ENSP00000280377:P311L;ENSP00000377264:P286L	.	P	+	2	0	USP15	61061554	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.648000	0.89879	0.585000	0.79938	CCT	.	.		0.294	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		T	62775287	C	T	62775287	3	4	41	1	0	0	0	0	1	0	0	0	17061	681	24	3	875	3	USP15	12	62775287	Missense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10	2606232	62775287	71076608	31	4964										
PIWIL1	9271	hgsc.bcm.edu	37	chr12	130834407	130834407	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	caactgatccctaggtataaCaataagacatacagagtgga	8	8	0	3			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr12:130834407C>T	ENST00000245255.3	+	9	1211	c.939C>T	c.(937-939)aaC>aaT	p.N313N		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	313	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		CTAGGTATAACAATAAGACAT	0.378																																					p.N313N		Atlas-SNP	.											.	PIWIL1	157	.	0			c.C939T						.						78	79	79					12																	130834407		2203	4300	6503	SO:0001819	synonymous_variant	9271	exon9			GTATAACAATAAG	AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.939C>T	chr12.hg19:g.130834407C>T		101.0	0.0		66.0	33.0	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Silent	SNP	ENST00000245255.3	hg19	CCDS9268.1																																																																																			.	.		0.378	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			T	130834407	C	T	130834407	2	4	41	1	0	0	0	0	0	0	0	1	11966	477	17	3		3	PIWIL1	12	130834407	Silent	SNP	C	TCGA-BC-A216-01A-11D-A152-10	68059120	130834407	3017488	32	4965										
GPR12	2835	hgsc.bcm.edu	37	chr13	27332981	27332981	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tacacatcactgggcgagcgCgctctctgggcgagactgga	14	12	2	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr13:27332981C>T	ENST00000381436.2	-	1	1446	c.984G>A	c.(982-984)gcG>gcA	p.A328A	GPR12_ENST00000405846.3_Silent_p.A328A			P47775	GPR12_HUMAN	G protein-coupled receptor 12	328					cellular calcium ion homeostasis (GO:0006874)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			endometrium(7)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		TGGGCGAGCGCGCTCTCTGGG	0.537																																					p.A328A		Atlas-SNP	.											.	GPR12	67	.	0			c.G984A						.						65	67	66					13																	27332981		2203	4300	6503	SO:0001819	synonymous_variant	2835	exon2			CGAGCGCGCTCTC	U18548	CCDS9319.1	13q12	2014-06-12			ENSG00000132975	ENSG00000132975		"GPCR / Class A : Orphans"	4466	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 84"	600752				8262253, 8530049	Standard	NM_005288		Approved	GPCR21, PPP1R84	uc010aal.3	P47775	OTTHUMG00000016620	ENST00000381436.2:c.984G>A	chr13.hg19:g.27332981C>T		107.0	0.0		86.0	30.0	NM_005288	Q5T8P3	Silent	SNP	ENST00000381436.2	hg19	CCDS9319.1																																																																																			.	.		0.537	GPR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044257.2			T	27332981	C	T	27332981	2	4	41	1	0	0	0	0	0	0	0	1	6643	755	27	1		1	GPR12	13	27332981	Silent	SNP	C	TCGA-BC-A216-01A-11D-A152-10		27332981	87836897	33	4966										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31597908	31597908	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	gttgttcgtggcattagtccGtgctatgtttgccactctcc	10	11	1	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr14:31597908G>A	ENST00000399332.1	-	25	5157	c.4669C>T	c.(4669-4671)Cgg>Tgg	p.R1557W	HECTD1_ENST00000553700.1_Missense_Mutation_p.R1557W	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1557	Ser-rich.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		GCATTAGTCCGTGCTATGTTT	0.468																																					p.R1557W		Atlas-SNP	.											.	HECTD1	159	.	0			c.C4669T						.						151	138	143					14																	31597908		2025	4185	6210	SO:0001583	missense	25831	exon25			TAGTCCGTGCTAT	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.4669C>T	chr14.hg19:g.31597908G>A	ENSP00000382269:p.Arg1557Trp	276.0	1.0		234.0	97.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.059759	0.55325	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957	T;T;T	0.43688	0.94;0.94;3.07	6.16	6.16	0.99307	.	0.000000	0.64402	U	0.000007	T	0.50326	0.1609	N	0.19112	0.55	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.982	T	0.52283	-0.8596	10	0.87932	D	0	-7.4753	15.5636	0.76269	0.0:0.0:0.8622:0.1378	.	1557;1557	D3DS86;Q9ULT8	.;HECD1_HUMAN	W	1557;1559;1557;984	ENSP00000450697:R1557W;ENSP00000382269:R1557W;ENSP00000451860:R984W	ENSP00000261312:R1559W	R	-	1	2	HECTD1	30667659	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.183000	0.65065	2.937000	0.99478	0.650000	0.86243	CGG	.	.		0.468	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			A	31597908	G	A	31597908	3	1	41	1	0	0	0	0	1	0	0	0	7048	1144	40	1	3239	1	HECTD1	14	31597908	Missense_Mutation	SNP	G	TCGA-BC-A216-01A-11D-A152-10		31597908	75751632	34	4967										
MYO1E	4643	hgsc.bcm.edu	37	chr15	59450529	59450529	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	actgggtagttggcattttgAgtcccactggaataacctgt	11	8	0	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr15:59450529A>C	ENST00000288235.4	-	25	3234	c.2835T>G	c.(2833-2835)acT>acG	p.T945T		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	945					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		TGGCATTTTGAGTCCCACTGG	0.463																																					p.T945T		Atlas-SNP	.											.	MYO1E	99	.	0			c.T2835G						.						157	119	132					15																	59450529		2191	4290	6481	SO:0001819	synonymous_variant	4643	exon25			ATTTTGAGTCCCA	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.2835T>G	chr15.hg19:g.59450529A>C		209.0	0.0		165.0	81.0	NM_004998	Q14778	Silent	SNP	ENST00000288235.4	hg19	CCDS32254.1																																																																																			.	.		0.463	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		C	59450529	A	C	59450529	2	2	41	1	0	0	0	0	0	0	0	1	10081	291	11	5		5	MYO1E	15	59450529	Silent	SNP	A	TCGA-BC-A216-01A-11D-A152-10		59450529	43080863	35	4968										
TP53	7157	hgsc.bcm.edu	37	chr17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	gatggtgaggatgggcctccGgttcatgccgcccatgcagg	16	11	1	1	rs397516437|rs121912651		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W|TP53_ENST00000413465.2_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGGCCTCCGGTTCATGCCG	0.577	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R248W	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,+1,16	TP53	33396	.	617	Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2)	large_intestine(156)|breast(72)|ovary(42)|endometrium(38)|oesophagus(38)|skin(37)|haematopoietic_and_lymphoid_tissue(37)|central_nervous_system(35)|stomach(27)|lung(26)|upper_aerodigestive_tract(25)|urinary_tract(19)|biliary_tract(17)|pancreas(12)|prostate(10)|soft_tissue(6)|bone(6)|thyroid(4)|liver(4)|penis(2)|peritoneum(1)|vulva(1)|kidney(1)|cervix(1)	c.C742T	GRCh37	CM010465|CM900211	TP53	M	rs121912651	.						151	112	125					17																	7577539		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GCCTCCGGTTCAT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.742C>T	chr17.hg19:g.7577539G>A	ENSP00000269305:p.Arg248Trp	114.0	1.0		46.0	31.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710019	0.68730	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.62	2.56	0.30785	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92507	3.315	0.58432	A	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	9	0.87932	D	0	-9.5643	7.568	0.27890	0.0893:0.0:0.7471:0.1636	.	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	W	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W	ENSP00000269305:R248W	R	-	1	2	TP53	7518264	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.447000	0.35101	0.644000	0.30656	0.462000	0.41574	CGG	.	.		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577539	G	A	7577539	3	1	41	1	0	0	0	0	1	0	0	0	16396	1115	39	1	548	1	TP53	17	7577539	Missense_Mutation	SNP	G	TCGA-BC-A216-01A-11D-A152-10		7577539	73617671	36	4969										
MYH1	4619	hgsc.bcm.edu	37	chr17	10404040	10404040	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	atttcactcagttgatcttcTagagcgcggcacatcttttc	7	11	5	2			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr17:10404040T>C	ENST00000226207.5	-	28	3862	c.3768A>G	c.(3766-3768)ctA>ctG	p.L1256L	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1256					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						GTTGATCTTCTAGAGCGCGGC	0.458																																					p.L1256L		Atlas-SNP	.											.	MYH1	403	.	0			c.A3768G						.						155	136	142					17																	10404040		2203	4300	6503	SO:0001819	synonymous_variant	4619	exon28			ATCTTCTAGAGCG		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3768A>G	chr17.hg19:g.10404040T>C		114.0	0.0		108.0	25.0	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	hg19	CCDS11155.1																																																																																			.	.		0.458	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		C	10404040	T	C	10404040	2	2	41	1	0	0	0	0	0	0	0	1	10038	1509	53	2		2	MYH1	17	10404040	Silent	SNP	T	TCGA-BC-A216-01A-11D-A152-10	2826501	10404040	70791170	37	4970										
MAPT	4137	hgsc.bcm.edu	37	chr17	44051811	44051811	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	gcaggctgccgcgcagccccAcacggagatcccagaaggaa	13	15	0	2			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr17:44051811A>G	ENST00000571987.1	+	3	281	c.281A>G	c.(280-282)cAc>cGc	p.H94R	MAPT_ENST00000446361.3_Intron|MAPT_ENST00000576518.1_5'UTR|MAPT_ENST00000535772.1_Missense_Mutation_p.H94R|MAPT_ENST00000431008.3_Missense_Mutation_p.H94R|MAPT_ENST00000262410.5_Missense_Mutation_p.H94R|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000351559.5_Missense_Mutation_p.H94R|MAPT_ENST00000344290.5_Missense_Mutation_p.H94R|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.H94R|MAPT_ENST00000574436.1_Missense_Mutation_p.H94R			P10636	TAU_HUMAN	microtubule-associated protein tau	94					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GCGCAGCCCCACACGGAGATC	0.627																																					p.H94R		Atlas-SNP	.											.	MAPT	135	.	0			c.A281G						.						26	23	24					17																	44051811		2200	4299	6499	SO:0001583	missense	4137	exon4			AGCCCCACACGGA	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.281A>G	chr17.hg19:g.44051811A>G	ENSP00000458742:p.His94Arg	43.0	0.0		38.0	19.0	NM_005910	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	hg19	CCDS11501.1	.	.	.	.	.	.	.	.	.	.	A	9.268	1.044903	0.19748	.	.	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000351559;ENST00000535772;ENST00000415613	T;T;T;T;T	0.17370	2.89;2.89;2.28;2.54;2.89	5.22	-4.86	0.03132	.	1.044480	0.07579	N	0.920002	T	0.11537	0.0281	L	0.40543	1.245	0.19575	N	0.999968	B;B;B	0.18166	0.009;0.026;0.001	B;B;B	0.20384	0.015;0.029;0.004	T	0.40942	-0.9536	10	0.16420	T	0.52	0.1525	7.7441	0.28858	0.2822:0.4972:0.2205:0.0	.	94;94;94	P10636-9;P10636-8;P10636	.;.;TAU_HUMAN	R	94	ENSP00000340820:H94R;ENSP00000262410:H94R;ENSP00000303214:H94R;ENSP00000443028:H94R;ENSP00000410838:H94R	ENSP00000262410:H94R	H	+	2	0	MAPT	41407647	0.007000	0.16637	0.011000	0.14972	0.630000	0.37929	-0.062000	0.11674	-1.084000	0.03092	-0.441000	0.05720	CAC	.	.		0.627	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		G	44051811	A	G	44051811	3	3	41	1	0	0	0	0	1	0	0	0	9306	159	6	2	291	2	MAPT	17	44051811	Missense_Mutation	SNP	A	TCGA-BC-A216-01A-11D-A152-10	33647771	44051811	37143399	38	4971										
IGF2BP1	10642	hgsc.bcm.edu	37	chr17	47117454	47117454	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	gaggctaaggacaccaaaacGtaagtctccagcttttcttg	9	10	2	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr17:47117454G>A	ENST00000290341.3	+	7	1152		c.e7+1		IGF2BP1_ENST00000431824.2_Intron	NM_006546.3	NP_006537.3	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding protein 1						CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of mRNA stability involved in response to stress (GO:0010610)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						ACACCAAAACGTAAGTCTCCA	0.453																																					.	Esophageal Squamous(198;1041 2123 8248 37119 38268)	Atlas-SNP	.											.	IGF2BP1	80	.	0			c.818+1G>A						.						136	120	125					17																	47117454		2203	4300	6503	SO:0001630	splice_region_variant	10642	exon7			CAAAACGTAAGTC	AF198254	CCDS11543.1, CCDS54138.1	17q21.32	2013-02-12			ENSG00000159217	ENSG00000159217		"RNA binding motif (RRM) containing"	28866	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 1"	608288				9891060, 11992722	Standard	NM_001160423		Approved	IMP-1	uc002iom.3	Q9NZI8	OTTHUMG00000161173	ENST00000290341.3:c.818+1G>A	chr17.hg19:g.47117454G>A		85.0	0.0		61.0	24.0	NM_006546	C9JT33	Splice_Site	SNP	ENST00000290341.3	hg19	CCDS11543.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.683950	0.88639	.	.	ENSG00000159217	ENST00000290341	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.512	0.90920	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IGF2BP1	44472453	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	9.866000	0.99616	2.655000	0.90218	0.655000	0.94253	.	.	.		0.453	IGF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364046.1	NM_006546	Intron	A	47117454	G	A	47117454	5	1	41	1	0	0	0	0	0	0	1	0	7582	1159	40	1	845	1	IGF2BP1	17	47117454	Splice_Site	SNP	G	TCGA-BC-A216-01A-11D-A152-10	3065643	47117454	34077756	39	4972										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22364341	22364341	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	cattttttggaaagaatcttCtatgccttgctctggccaaa	7	9	3	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr19:22364341C>G	ENST00000397121.2	-	3	495	c.178G>C	c.(178-180)Gaa>Caa	p.E60Q		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	60					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				AAAGAATCTTCTATGCCTTGC	0.299																																					p.E60Q		Atlas-SNP	.											.	ZNF676	146	.	0			c.G178C						.						48	43	45					19																	22364341		1887	4137	6024	SO:0001583	missense	163223	exon3			AATCTTCTATGCC	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.178G>C	chr19.hg19:g.22364341C>G	ENSP00000380310:p.Glu60Gln	122.0	0.0		115.0	54.0	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	hg19	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	2.906	-0.226528	0.06022	.	.	ENSG00000196109	ENST00000397121	T	0.08102	3.13	0.814	-0.526	0.11913	.	.	.	.	.	T	0.07143	0.0181	N	0.13168	0.305	0.09310	N	1	P	0.51653	0.947	P	0.53490	0.727	T	0.29912	-0.9996	9	0.40728	T	0.16	.	2.6619	0.05029	0.0:0.5266:0.0:0.4734	.	60	Q8N7Q3	ZN676_HUMAN	Q	60	ENSP00000380310:E60Q	ENSP00000380310:E60Q	E	-	1	0	ZNF676	22156181	0.000000	0.05858	0.100000	0.21137	0.100000	0.18952	-0.520000	0.06252	0.183000	0.20059	0.186000	0.17326	GAA	.	.		0.299	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		G	22364341	C	G	22364341	3	3	41	1	0	0	0	0	1	0	0	0	18098	922	32	4	1592	4	ZNF676	19	22364341	Missense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10		22364341	36764642	40	4973										
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39330868	39330869	+	In_Frame_Ins	INS	-	-	GGG													0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	cgggtggtgggggagggggtINSggggggtgcccatactgggg							TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr19:39330868_39330869insGGG	ENST00000221419.5	-	8	1466_1467	c.1100_1101insCCC	c.(1099-1101)cca>ccCCCa	p.367_367P>PP	HNRNPL_ENST00000600873.1_In_Frame_Ins_p.234_234P>PP|AC104534.3_ENST00000594769.1_5'Flank	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	367	Pro-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)	p.P367P(1)|p.P234P(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			GGGGAGGGGGTGGGGGGTGCCC	0.644																																					p.P367delinsPP		Atlas-INDEL	.											HNRPL,right_upper_lobe,carcinoma,0,6	HNRNPL	67	.	2	Substitution - coding silent(2)	central_nervous_system(2)	c.1101_1102insCCC						.																																			SO:0001652	inframe_insertion	3191	exon8			.	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1098_1100dupCCC	chr19.hg19:g.39330872_39330874dupGGG	ENSP00000221419:p.Pro373dup	86.0	0.0		64.0	14.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	In_Frame_Ins	INS	ENST00000221419.5	hg19	CCDS33015.1																																																																																			.	.		0.644	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			GGG	39330869	-	GGG	39330868	7	5	41	1	0	1	1	0	0	0	0	0	7279	1683	59	0	692	0	HNRNPL	19	39330868	In_Frame_Ins	INS	-	TCGA-BC-A216-01A-11D-A152-10	16966527	39330868	19798115	41	4974										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40360958	40360959	+	Missense_Mutation	DNP	GC	GC	TT													0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	cactcacagccctcaaaacaGcgggtggtgcagcccgtgag					rs371263426		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr19:40360958_40360959GC>TT	ENST00000221347.6	-	33	15456_15457	c.15449_15450GC>AA	c.(15448-15450)cGC>cAA	p.R5150Q		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	5150	Cys-rich.|TIL 12.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCTCAAAACAGCGGGTGGTGCA	0.629																																					p.R5150R|p.R5150H		Atlas-SNP	.											.	FCGBP	416	.	0			c.C15450A|c.G15449A						.																																			SO:0001583	missense	8857	exon33			AAAACAGCGGGTG|AAACAGCGGGTGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.15449_15450delinsTT	chr19.hg19:g.40360958_40360959delinsTT	ENSP00000221347:p.Arg5150Gln	69.0|68.0	0.0		47.0	19.0|18.0	NM_003890	O95784	Silent|Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.		0.629	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		TT	40360959	GC	TT	40360958	3	4	41	1	0	0	0	0	1	0	0	0	5786	958	34	3	783	3	FCGBP	19	40360958	Missense_Mutation	DNP	GC	TCGA-BC-A216-01A-11D-A152-10	1030090	40360958	18768025	42	4975										
KLK12	43849	hgsc.bcm.edu	37	chr19	51535232	51535232	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	ggttgaacgctgctggttacGcggacgggcaggcgcagccg	18	11	0	1	rs371203521		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr19:51535232G>A	ENST00000525263.1	-	3	476	c.357C>T	c.(355-357)cgC>cgT	p.R119R	KLK12_ENST00000250351.4_Silent_p.R119R|CTC-518B2.9_ENST00000594910.1_RNA|KLK12_ENST00000319590.4_Silent_p.R119R|KLK12_ENST00000250352.11_Intron|KLK12_ENST00000529888.1_Intron			Q9UKR0	KLK12_HUMAN	kallikrein-related peptidase 12	119	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	12		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)		TGCTGGTTACGCGGACGGGCA	0.682																																					p.R119R		Atlas-SNP	.											.	KLK12	30	.	0			c.C357T						.	G	,,	0,4406		0,0,2203	39	39	39		357,357,	0.7	0	19		39	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous,intron	KLK12	NM_019598.2,NM_145894.1,NM_145895.1	,,	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	,,	119/255,119/249,	51535232	1,13001	2203	4298	6501	SO:0001819	synonymous_variant	43849	exon4			GGTTACGCGGACG		CCDS12820.1, CCDS12821.1, CCDS54298.1	19q13.33	2008-02-05	2006-10-27		ENSG00000186474	ENSG00000186474		"Kallikreins"	6360	protein-coding gene	gene with protein product		605539	"kallikrein 12"			16800724, 16800723	Standard	NM_019598		Approved	KLK-L5	uc002pvh.1	Q9UKR0	OTTHUMG00000165806	ENST00000525263.1:c.357C>T	chr19.hg19:g.51535232G>A		15.0	0.0		32.0	15.0	NM_019598	Q9UKR1|Q9UKR2	Silent	SNP	ENST00000525263.1	hg19	CCDS12821.1																																																																																			.	.		0.682	KLK12-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386288.1	NM_019598		A	51535232	G	A	51535232	2	1	41	1	0	0	0	0	0	0	0	1	8409	1074	38	1		1	KLK12	19	51535232	Silent	SNP	G	TCGA-BC-A216-01A-11D-A152-10	11174274	51535232	7593751	43	4976										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31023622	31023622	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	ggacaaggatgagaaacccaAttggaaccaatctgccccac	9	12	1	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr20:31023622A>G	ENST00000375687.4	+	13	3531	c.3107A>G	c.(3106-3108)aAt>aGt	p.N1036S	ASXL1_ENST00000306058.5_Missense_Mutation_p.N1031S	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1036					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						GAGAAACCCAATTGGAACCAA	0.522			"F, N, Mis"		"MDS, CMML"																																p.N1036S		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.A3107G						.						224	186	199					20																	31023622		2203	4300	6503	SO:0001583	missense	171023	exon12			AACCCAATTGGAA	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3107A>G	chr20.hg19:g.31023622A>G	ENSP00000364839:p.Asn1036Ser	53.0	0.0		49.0	21.0	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	hg19	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.827394	0.00071	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.21031	2.03;2.03	4.32	-8.64	0.00874	.	1.688650	0.02613	N	0.102362	T	0.08935	0.0221	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19910	-1.0291	10	0.16896	T	0.51	3.4374	11.7114	0.51626	0.3067:0.1743:0.5191:0.0	.	1031;1036	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	S	1036;1036;1036;957;1031	ENSP00000364839:N1036S;ENSP00000305119:N1031S	ENSP00000305119:N1031S	N	+	2	0	ASXL1	30487283	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.819000	0.01716	-2.367000	0.00605	-2.262000	0.00279	AAT	.	.		0.522	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		G	31023622	A	G	31023622	3	3	41	1	0	0	0	0	1	0	0	0	1066	101	4	2	3163	2	ASXL1	20	31023622	Missense_Mutation	SNP	A	TCGA-BC-A216-01A-11D-A152-10		31023622	32001898	44	4977										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61528282	61528282	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tgcccaccgcggagcctggaGgggctgttttctttgaggct	15	11	1	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr20:61528282G>A	ENST00000266070.4	-	7	1980	c.1655C>T	c.(1654-1656)cCt>cTt	p.P552L	DIDO1_ENST00000395335.2_Missense_Mutation_p.P552L|DIDO1_ENST00000395340.1_Missense_Mutation_p.P552L|DIDO1_ENST00000395343.1_Missense_Mutation_p.P552L	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	552					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GGAGCCTGGAGGGGCTGTTTT	0.552																																					p.P552L	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C1655T						.						30	33	32					20																	61528282		2203	4300	6503	SO:0001583	missense	11083	exon7			CCTGGAGGGGCTG	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.1655C>T	chr20.hg19:g.61528282G>A	ENSP00000266070:p.Pro552Leu	93.0	0.0		84.0	29.0	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.686740	0.29962	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.13196	2.99;2.99;2.61;2.61	5.51	-1.2	0.09554	.	0.553042	0.15080	N	0.281682	T	0.10423	0.0255	L	0.56769	1.78	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.30534	-0.9975	10	0.30078	T	0.28	-1.8123	2.462	0.04544	0.3955:0.1133:0.3752:0.1159	.	552;552	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	L	552	ENSP00000266070:P552L;ENSP00000378752:P552L;ENSP00000378749:P552L;ENSP00000378744:P552L	ENSP00000266070:P552L	P	-	2	0	DIDO1	60998727	0.001000	0.12720	0.000000	0.03702	0.370000	0.29829	0.494000	0.22467	-0.472000	0.06881	-0.251000	0.11542	CCT	.	.		0.552	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		A	61528282	G	A	61528282	3	1	41	1	0	0	0	0	1	0	0	0	4524	1000	35	3	5136	3	DIDO1	20	61528282	Missense_Mutation	SNP	G	TCGA-BC-A216-01A-11D-A152-10	30504660	61528282	1497238	45	4978										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26294307	26294307	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	aaagtgcttatgacggggccAagaagatggctcaccaactg	12	9	1	3			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chr22:26294307A>G	ENST00000407587.2	+	29	4874	c.4705A>G	c.(4705-4707)Aag>Gag	p.K1569E	CTA-125H2.2_ENST00000594856.1_RNA|CTA-125H2.2_ENST00000608921.1_RNA|CTA-125H2.2_ENST00000596813.1_RNA|CTA-125H2.2_ENST00000608507.1_RNA|CTA-125H2.2_ENST00000600903.1_RNA|CTA-125H2.2_ENST00000609823.1_RNA|CTA-125H2.2_ENST00000608115.1_RNA|CTA-125H2.2_ENST00000594542.1_RNA|MYO18B_ENST00000335473.7_Missense_Mutation_p.K1568E|CTA-125H2.2_ENST00000600269.1_RNA|CTA-125H2.2_ENST00000595093.1_RNA|CTA-125H2.2_ENST00000609820.1_RNA|CTA-125H2.2_ENST00000608257.1_RNA|CTA-125H2.2_ENST00000599080.1_RNA|MYO18B_ENST00000536101.1_Missense_Mutation_p.K1568E|CTA-125H2.2_ENST00000595102.1_RNA|CTA-125H2.2_ENST00000597548.1_RNA|CTA-125H2.2_ENST00000609809.1_RNA|CTA-125H2.2_ENST00000593715.1_RNA|CTA-125H2.2_ENST00000609889.1_RNA|CTA-125H2.2_ENST00000597284.1_RNA|CTA-125H2.2_ENST00000594585.1_RNA|CTA-125H2.2_ENST00000609570.1_RNA|CTA-125H2.2_ENST00000607895.1_RNA|CTA-125H2.2_ENST00000609275.1_RNA|CTA-125H2.2_ENST00000609157.1_RNA|CTA-125H2.2_ENST00000597614.2_RNA|CTA-125H2.2_ENST00000453457.3_RNA|CTA-125H2.2_ENST00000599792.1_RNA|CTA-125H2.2_ENST00000600211.1_RNA			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1568	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TGACGGGGCCAAGAAGATGGC	0.473																																					p.K1568E		Atlas-SNP	.											.	MYO18B	322	.	0			c.A4702G						.						108	110	110					22																	26294307		1981	4166	6147	SO:0001583	missense	84700	exon29			GGGGCCAAGAAGA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.4705A>G	chr22.hg19:g.26294307A>G	ENSP00000386096:p.Lys1569Glu	77.0	0.0		78.0	34.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	A	11.20	1.569254	0.28003	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;T	0.86497	-2.13;-2.13;-1.05	5.9	3.71	0.42584	.	0.277591	0.32175	N	0.006475	D	0.82384	0.5025	L	0.54323	1.7	0.28415	N	0.918008	P;B;P;P	0.36789	0.57;0.434;0.51;0.57	B;B;B;B	0.32864	0.154;0.074;0.107;0.154	T	0.74765	-0.3554	10	0.56958	D	0.05	.	11.3383	0.49518	0.7108:0.2892:0.0:0.0	.	1081;1568;1569;1568	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	E	1568;1568;1569	ENSP00000441229:K1568E;ENSP00000334563:K1568E;ENSP00000386096:K1569E	ENSP00000334563:K1568E	K	+	1	0	MYO18B	24624307	1.000000	0.71417	0.984000	0.44739	0.468000	0.32798	1.825000	0.39081	0.443000	0.26582	0.533000	0.62120	AAG	.	.		0.473	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26294307	A	G	26294307	3	3	41	1	0	0	0	0	1	0	0	0	10075	131	5	2	4812	2	MYO18B	22	26294307	Missense_Mutation	SNP	A	TCGA-BC-A216-01A-11D-A152-10		26294307	25010259	46	4979										
ARX	170302	hgsc.bcm.edu	37	chrX	25033826	25033826	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	tgcactcgggcctctcggagCagccctcctcctggtactga	11	16	1	1			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chrX:25033826C>G	ENST00000379044.4	-	1	239	c.29G>C	c.(28-30)tGc>tCc	p.C10S		NM_139058.2	NP_620689.1	Q96QS3	ARX_HUMAN	aristaless related homeobox	10					axon guidance (GO:0007411)|cell proliferation in forebrain (GO:0021846)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex tangential migration (GO:0021800)|embryonic olfactory bulb interneuron precursor migration (GO:0021831)|epithelial cell fate commitment (GO:0072148)|globus pallidus development (GO:0021759)|lipid digestion (GO:0044241)|positive regulation of organ growth (GO:0046622)|regulation of cell proliferation (GO:0042127)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			kidney(1)|large_intestine(2)|lung(1)	4						CCTCTCGGAGCAGCCCTCCTC	0.612																																					p.C10S		Atlas-SNP	.											.	ARX	19	.	0			c.G29C						.						40	34	36					X																	25033826		2201	4297	6498	SO:0001583	missense	170302	exon1			TCGGAGCAGCCCT	AY038071	CCDS14215.1	Xp21.3	2011-06-20			ENSG00000004848	ENSG00000004848		"Homeoboxes / PRD class"	18060	protein-coding gene	gene with protein product	"cancer/testis antigen 121"	300382	"mental retardation, X-linked 54", "mental retardation, X-linked 43", "mental retardation, X-linked 36", "mental retardation, X-linked 29", "mental retardation, X-linked 32", "mental retardation, X-linked 33", "mental retardation, X-linked 38", "mental retardation, X-linked 87", "mental retardation, X-linked 76"	MRXS1, PRTS, MRX76, MRX54, MRX43, MRX36, MRX29, MRX32, MRX33, MRX38, MRX87		11889467, 15850492, 17480217	Standard	NM_139058		Approved	ISSX, CT121, EIEE1	uc004dbp.4	Q96QS3	OTTHUMG00000021275	ENST00000379044.4:c.29G>C	chrX.hg19:g.25033826C>G	ENSP00000368332:p.Cys10Ser	341.0	0.0		361.0	83.0	NM_139058		Missense_Mutation	SNP	ENST00000379044.4	hg19	CCDS14215.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.964084	0.53507	.	.	ENSG00000004848	ENST00000379044	D	0.89552	-2.53	5.3	5.3	0.74995	.	0.465752	0.21298	U	0.076847	D	0.85978	0.5823	L	0.38531	1.155	0.37897	D	0.930911	P	0.52842	0.956	B	0.44224	0.444	D	0.89127	0.3507	10	0.66056	D	0.02	.	15.7804	0.78255	0.0:1.0:0.0:0.0	.	10	Q96QS3	ARX_HUMAN	S	10	ENSP00000368332:C10S	ENSP00000368332:C10S	C	-	2	0	ARX	24943747	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.810000	0.38932	2.194000	0.70268	0.600000	0.82982	TGC	.	.		0.612	ARX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056109.1			G	25033826	C	G	25033826	3	3	41	1	0	0	0	0	1	0	0	0	1004	710	25	4	1679	4	ARX	23	25033826	Missense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10		25033826	130236734	47	4980										
NXF3	56000	hgsc.bcm.edu	37	chrX	102335094	102335094	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.339428571428571	2.12142857142857	0	1	1	0	accttacaggttggtaacctCttgtgggcttcagtaccaca	9	11	2	0			TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	g.chrX:102335094C>A	ENST00000395065.3	-	11	1079	c.978G>T	c.(976-978)aaG>aaT	p.K326N	NXF3_ENST00000425644.1_Missense_Mutation_p.R17I	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	326					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)			NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						TTGGTAACCTCTTGTGGGCTT	0.547																																					p.K326N		Atlas-SNP	.											.	NXF3	81	.	0			c.G978T						.						195	172	180					X																	102335094		2203	4300	6503	SO:0001583	missense	56000	exon11			TAACCTCTTGTGG	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.978G>T	chrX.hg19:g.102335094C>A	ENSP00000378504:p.Lys326Asn	76.0	0.0		88.0	37.0	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Missense_Mutation	SNP	ENST00000395065.3	hg19	CCDS14503.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	9.801|9.801|9.801	1.180415|1.180415|1.180415	0.21787|0.21787|0.21787	.|.|.	.|.|.	ENSG00000147206|ENSG00000147206|ENSG00000147206	ENST00000427570|ENST00000395065|ENST00000425644	.|T|.	.|0.47177|.	.|0.85|.	4.44|4.44|4.44	3.56|3.56|3.56	0.40772|0.40772|0.40772	.|.|.	.|0.105018|.	.|0.64402|.	.|D|.	.|0.000006|.	.|T|T	.|0.44932|0.44932	.|0.1317|0.1317	L|L|L	0.54323|0.54323|0.54323	1.7|1.7|1.7	0.19775|0.19775|0.19775	N|N|N	0.999958|0.999958|0.999958	.|P;B|.	.|0.48503|.	.|0.911;0.207|.	.|P;B|.	.|0.44623|.	.|0.455;0.106|.	.|T|T	.|0.28554|0.28554	.|-1.0040|-1.0040	.|10|6	.|0.16420|0.37606	.|T|T	.|0.52|0.19	-20.0199|-20.0199|-20.0199	10.0461|10.0461|10.0461	0.42188|0.42188|0.42188	0.0:0.7989:0.2011:0.0|0.0:0.7989:0.2011:0.0|0.0:0.7989:0.2011:0.0	.|.|.	.|222;326|.	.|E9PEY7;Q9H4D5|.	.|.;NXF3_HUMAN|.	X|N|I	203|326|17	.|ENSP00000378504:K326N|.	.|ENSP00000378504:K326N|ENSP00000401026:R17I	E|K|R	-|-|-	1|3|2	0|2|0	NXF3|NXF3|NXF3	102221750|102221750|102221750	0.005000|0.005000|0.005000	0.15991|0.15991|0.15991	0.005000|0.005000|0.005000	0.12908|0.12908|0.12908	0.002000|0.002000|0.002000	0.02628|0.02628|0.02628	-0.130000|-0.130000|-0.130000	0.10498|0.10498|0.10498	0.958000|0.958000|0.958000	0.37956|0.37956|0.37956	0.600000|0.600000|0.600000	0.82982|0.82982|0.82982	GAG|AAG|AGA	.	.		0.547	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		A	102335094	C	A	102335094	3	1	41	1	0	0	0	0	1	0	0	0	10794	912	32	3	653	3	NXF3	23	102335094	Missense_Mutation	SNP	C	TCGA-BC-A216-01A-11D-A152-10	77301268	102335094	52935466	48	4981										
SLC44A5	204962	hgsc.bcm.edu	37	chr1	75805298	75805298	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	aggccccttgaaatctgggtCatatgtccttggatcacctg	10	11	3	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr1:75805298C>A	ENST00000370855.5	-	4	183	c.70G>T	c.(70-72)Gac>Tac	p.D24Y	SLC44A5_ENST00000535611.1_5'UTR|SLC44A5_ENST00000370859.3_Missense_Mutation_p.D24Y|SLC44A5_ENST00000469525.1_5'UTR	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	24					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						AAATCTGGGTCATATGTCCTT	0.343																																					p.D24Y		Atlas-SNP	.											.	SLC44A5	231	.	0			c.G70T						.						198	218	211					1																	75805298		2203	4300	6503	SO:0001583	missense	204962	exon4			CTGGGTCATATGT	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.70G>T	chr1.hg19:g.75805298C>A	ENSP00000359892:p.Asp24Tyr	74.0	0.0		65.0	14.0	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Missense_Mutation	SNP	ENST00000370855.5	hg19	CCDS667.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.083835	0.36758	.	.	ENSG00000137968	ENST00000370859;ENST00000536707;ENST00000370855;ENST00000535790	T;T	0.44482	0.92;0.92	5.54	4.62	0.57501	.	0.221145	0.44688	D	0.000432	T	0.57548	0.2061	M	0.85197	2.74	0.54753	D	0.99998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.996;0.993;0.992;0.997	T	0.66031	-0.6024	10	0.87932	D	0	-4.9098	10.5386	0.45020	0.0:0.9103:0.0:0.0897	.	18;63;24;24	B7Z5Y4;B7Z470;Q8NCS7;Q8NCS7-2	.;.;CTL5_HUMAN;.	Y	24;63;24;17	ENSP00000359896:D24Y;ENSP00000359892:D24Y	ENSP00000359892:D24Y	D	-	1	0	SLC44A5	75577886	0.872000	0.30054	0.058000	0.19502	0.574000	0.36063	1.692000	0.37731	1.468000	0.48064	0.650000	0.86243	GAC	.	.		0.343	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		A	75805298	C	A	75805298	3	1	42	1	0	0	0	0	1	0	0	0	14654	826	29	3	2284	3	SLC44A5	1	75805298	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10		75805298	173445323	1	4982										
KCNC4	3749	hgsc.bcm.edu	37	chr1	110775555	110775555	+	3'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	acctgccaagacgccctctcGtccaactatgcccaggctga	8	17	1	2	rs374236746		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr1:110775555G>A	ENST00000369787.3	+	0	2559				KCNC4_ENST00000438661.2_Silent_p.S614S|KCNC4_ENST00000413138.3_3'UTR|KCNC4_ENST00000412512.2_Intron	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4						potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(2)	32		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		ACGCCCTCTCGTCCAACTATG	0.562													G|||	1	0.000199681	0	0	5008	,	,		19127	0		0	False		,,,				2504	0.001				p.S614S		Atlas-SNP	.											KCNC4_ENST00000438661,NS,carcinoma,0,1	KCNC4	113	.	0			c.G1842A						.	G	,	0,3982		0,0,1991	60	63	62		1842,	2.4	1	1		62	1,8313		0,1,4156	no	coding-synonymous,utr-3	KCNC4	NM_001039574.2,NM_004978.4	,	0,1,6147	AA,AG,GG		0.012,0.0,0.0081	,	614/627,	110775555	1,12295	1991	4157	6148	SO:0001624	3_prime_UTR_variant	3749	exon4			CCTCTCGTCCAAC	BC101769	CCDS821.1, CCDS44193.1	1p21	2012-07-05			ENSG00000116396	ENSG00000116396		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6236	protein-coding gene	gene with protein product		176265	"chromosome 1 open reading frame 30"	C1orf30		1920536, 1740329, 16382104	Standard	NM_004978		Approved	Kv3.4, HKSHIIIC	uc001dzh.3	Q03721	OTTHUMG00000011037	ENST00000369787.3:c.*624G>A	chr1.hg19:g.110775555G>A		69.0	0.0		37.0	25.0	NM_001039574	Q3MIM4|Q5TBI6	Silent	SNP	ENST00000369787.3	hg19	CCDS821.1																																																																																			.	.		0.562	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		A	110775555	G	A	110775555	1	1	42	0	1	0	0	0	0	0	0	0	8026	1132	40	1		1	KCNC4	1	110775555	3'UTR	SNP	G	TCGA-BC-A217-01A-11D-A152-10	34970257	110775555	138475066	2	4983										
PLEKHO1	51177	hgsc.bcm.edu	37	chr1	150131276	150131276	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ggcacccaagaagttgacgcCcacagagaaaggccgctgcg	13	13	0	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr1:150131276C>T	ENST00000369124.4	+	6	1066	c.788C>T	c.(787-789)cCc>cTc	p.P263L	PLEKHO1_ENST00000025469.6_Missense_Mutation_p.P229L|PLEKHO1_ENST00000369126.1_Missense_Mutation_p.P80L	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	263	Interaction with ATM, CKIP, IFP35 and NMI.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			AAGTTGACGCCCACAGAGAAA	0.642																																					p.P263L		Atlas-SNP	.											.	PLEKHO1	37	.	0			c.C788T						.						32	38	36					1																	150131276		2203	4300	6503	SO:0001583	missense	51177	exon6			TGACGCCCACAGA	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.788C>T	chr1.hg19:g.150131276C>T	ENSP00000358120:p.Pro263Leu	117.0	0.0		303.0	15.0	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Missense_Mutation	SNP	ENST00000369124.4	hg19	CCDS945.1	.	.	.	.	.	.	.	.	.	.	C	3.672	-0.067277	0.07273	.	.	ENSG00000023902	ENST00000369126;ENST00000025469;ENST00000369124;ENST00000441340	T;T	0.40476	1.03;1.04	4.97	4.04	0.47022	.	0.833567	0.11286	N	0.579801	T	0.13713	0.0332	L	0.36672	1.1	0.09310	N	0.999999	B	0.13594	0.008	B	0.14578	0.011	T	0.20140	-1.0284	10	0.24483	T	0.36	-8.0699	7.7059	0.28650	0.2855:0.5641:0.1504:0.0	.	263	Q53GL0	PKHO1_HUMAN	L	80;229;263;143	ENSP00000025469:P229L;ENSP00000358120:P263L	ENSP00000025469:P229L	P	+	2	0	PLEKHO1	148397900	0.011000	0.17503	0.074000	0.20217	0.636000	0.38137	1.493000	0.35605	1.275000	0.44379	0.655000	0.94253	CCC	.	.		0.642	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		T	150131276	C	T	150131276	3	4	42	1	0	0	0	0	1	0	0	0	12093	623	22	3	810	3	PLEKHO1	1	150131276	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	39355721	150131276	99119345	3	4984										
PLEKHO1	51177	hgsc.bcm.edu	37	chr1	150131673	150131673	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	cagaccccggactcccacctCagacagaccaccccgcacag	7	21	1	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr1:150131673C>G	ENST00000369124.4	+	6	1463	c.1185C>G	c.(1183-1185)ctC>ctG	p.L395L	PLEKHO1_ENST00000025469.6_Silent_p.L361L|PLEKHO1_ENST00000369126.1_Silent_p.L212L	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	395	Negative regulator of AP-1 activity.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			ACTCCCACCTCAGACAGACCA	0.587																																					p.L395L		Atlas-SNP	.											PLEKHO1,bladder,carcinoma,0,1	PLEKHO1	37	.	0			c.C1185G						.						27	30	29					1																	150131673		2203	4300	6503	SO:0001819	synonymous_variant	51177	exon6			CCACCTCAGACAG	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.1185C>G	chr1.hg19:g.150131673C>G		165.0	0.0		390.0	16.0	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Silent	SNP	ENST00000369124.4	hg19	CCDS945.1																																																																																			.	.		0.587	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		G	150131673	C	G	150131673	2	3	42	1	0	0	0	0	0	0	0	1	12093	813	29	4		4	PLEKHO1	1	150131673	Silent	SNP	C	TCGA-BC-A217-01A-11D-A152-10	397	150131673	99118948	4	4985										
DHX9	1660	hgsc.bcm.edu	37	chr1	182823304	182823304	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gtacacccaagtgggtcctgAtcacaacaggtttgcttgtt	10	10	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr1:182823304A>G	ENST00000367549.3	+	6	727	c.617A>G	c.(616-618)gAt>gGt	p.D206G		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	206	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.|Interaction with CREBBP.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						GTGGGTCCTGATCACAACAGG	0.363																																					p.D206G	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.A617G						.						72	71	71					1																	182823304		1845	4085	5930	SO:0001583	missense	1660	exon6			GTCCTGATCACAA	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.617A>G	chr1.hg19:g.182823304A>G	ENSP00000356520:p.Asp206Gly	223.0	0.0		166.0	100.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.703563	0.88924	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	T	0.77098	-1.07	5.39	5.39	0.77823	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.90215	0.6941	M	0.92219	3.285	0.80722	D	1	P	0.46952	0.887	D	0.64042	0.921	D	0.92387	0.5918	10	0.87932	D	0	.	15.0812	0.72117	1.0:0.0:0.0:0.0	.	206	Q08211	DHX9_HUMAN	G	206	ENSP00000356520:D206G	ENSP00000356520:D206G	D	+	2	0	DHX9	181089927	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.661000	0.91125	2.045000	0.60652	0.533000	0.62120	GAT	.	.		0.363	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		G	182823304	A	G	182823304	3	3	42	1	0	0	0	0	1	0	0	0	4518	333	12	2	635	2	DHX9	1	182823304	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10	32691631	182823304	66427317	5	4986										
TRIM54	57159	hgsc.bcm.edu	37	chr2	27528584	27528584	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	agaagctgcagcgcgtccgcGgcctcatccgtcagtatggc	13	14	2	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:27528584G>C	ENST00000380075.2	+	5	1082	c.742G>C	c.(742-744)Ggc>Cgc	p.G248R	TRIM54_ENST00000296098.4_Missense_Mutation_p.G290R	NM_187841.2	NP_912730.2	Q9BYV2	TRI54_HUMAN	tripartite motif containing 54	248					cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|negative regulation of microtubule depolymerization (GO:0007026)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCGCGTCCGCGGCCTCATCCG	0.632																																					p.G290R		Atlas-SNP	.											.	TRIM54	35	.	0			c.G868C						.						34	32	33					2																	27528584		2202	4300	6502	SO:0001583	missense	57159	exon6			GTCCGCGGCCTCA	AJ291714	CCDS1745.2, CCDS1746.2	2p23.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000138100	ENSG00000138100		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16008	protein-coding gene	gene with protein product		606474	"ring finger protein 30", "tripartite motif-containing 54"	RNF30		11243782	Standard	NM_032546		Approved	MURF, MURF-3	uc002rjn.3	Q9BYV2	OTTHUMG00000097078	ENST00000380075.2:c.742G>C	chr2.hg19:g.27528584G>C	ENSP00000369415:p.Gly248Arg	100.0	0.0		79.0	33.0	NM_032546	A5D8T7|Q53SY4|Q9BYV3	Missense_Mutation	SNP	ENST00000380075.2	hg19	CCDS1746.2	.	.	.	.	.	.	.	.	.	.	G	15.64	2.894559	0.52121	.	.	ENSG00000138100	ENST00000380075;ENST00000380073;ENST00000296098	T;T	0.40225	1.24;1.04	4.85	3.04	0.35103	.	0.386929	0.26867	N	0.022083	T	0.43478	0.1249	L	0.46157	1.445	0.18873	N	0.999989	P;P	0.41366	0.488;0.747	B;P	0.52823	0.357;0.71	T	0.20438	-1.0275	10	0.33141	T	0.24	-14.4805	4.6928	0.12788	0.1859:0.0:0.6429:0.1711	.	248;290	Q9BYV2;Q9BYV2-2	TRI54_HUMAN;.	R	248;69;290	ENSP00000369415:G248R;ENSP00000296098:G290R	ENSP00000296098:G290R	G	+	1	0	TRIM54	27382088	0.002000	0.14202	0.852000	0.33557	0.858000	0.48976	0.624000	0.24462	0.461000	0.27071	-0.291000	0.09656	GGC	.	.		0.632	TRIM54-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214199.2	NM_187841		C	27528584	G	C	27528584	3	2	42	1	0	0	0	0	1	0	0	0	16543	1116	39	4	890	4	TRIM54	2	27528584	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10		27528584	215670789	6	4987										
LOC728819	130271	hgsc.bcm.edu	37	chr2	43903342	43903342	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ggacgaaggtgatggtgctcGtggtcttgagtttgacctct	15	7	2	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:43903342G>A	ENST00000282406.4	+	3	233					NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2						negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GATGGTGCTCGTGGTCTTGAG	0.403																																					p.H40H		Atlas-SNP	.											.	.	.	.	0			c.C120T						.						74	72	73					2																	43903342		2032	4180	6212	SO:0001627	intron_variant	0	exon1			GTGCTCGTGGTCT	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.124-2660G>A	chr2.hg19:g.43903342G>A		448.0	0.0		377.0	173.0	NM_001101330	Q5JPJ6|Q6P4Q1|Q8N3Q3	Silent	SNP	ENST00000282406.4	hg19	CCDS1812.1																																																																																			.	.		0.403	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		A	43903342	G	A	43903342	1	1	42	0	1	0	0	0	0	0	0	0	8896	1136	40	1		1	LOC728819	2	43903342	Intron	SNP	G	TCGA-BC-A217-01A-11D-A152-10	16374758	43903342	199296031	7	4988										
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85361140	85361140	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ctttgtgtctcctccgcaggCggagaggcgcccgcagcccg	14	16	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:85361140C>A	ENST00000282111.3	+	2	526	c.251C>A	c.(250-252)gCg>gAg	p.A84E		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	84					anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CCTCCGCAGGCGGAGAGGCGC	0.692																																					p.A84E		Atlas-SNP	.											.	TCF7L1	44	.	0			c.C251A						.						18	24	22					2																	85361140		2201	4299	6500	SO:0001630	splice_region_variant	83439	exon2			CGCAGGCGGAGAG	X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.250-1C>A	chr2.hg19:g.85361140C>A		80.0	0.0		41.0	24.0	NM_031283	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000282111.3	hg19	CCDS1971.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671724	0.67928	.	.	ENSG00000152284	ENST00000282111	D	0.98777	-5.13	4.11	3.2	0.36748	CTNNB1 binding, N-teminal (1);	0.222293	0.37669	N	0.001996	D	0.97235	0.9096	M	0.68317	2.08	0.32570	N	0.529866	P	0.43169	0.8	P	0.45881	0.496	D	0.95871	0.8891	10	0.33141	T	0.24	.	4.9863	0.14190	0.2109:0.677:0.0:0.112	.	84	Q9HCS4	TF7L1_HUMAN	E	84	ENSP00000282111:A84E	ENSP00000282111:A84E	A	+	2	0	TCF7L1	85214651	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.685000	0.61693	0.665000	0.31066	0.462000	0.41574	GCG	.	.		0.692	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283	Missense_Mutation	A	85361140	C	A	85361140	5	1	42	1	0	0	0	0	0	0	1	0	15712	782	27	1	257	1	TCF7L1	2	85361140	Splice_Site	SNP	C	TCGA-BC-A217-01A-11D-A152-10	41457798	85361140	157838233	8	4989										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109381074	109381074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gtcttggtggcattgtaacaGctgctcattaaagaatgctt	10	7	2	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:109381074G>A	ENST00000283195.6	+	20	4205	c.4079G>A	c.(4078-4080)aGc>aAc	p.S1360N		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1360					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CATTGTAACAGCTGCTCATTA	0.388																																					p.S1360N		Atlas-SNP	.											.	RANBP2	488	.	0			c.G4079A						.						88	89	89					2																	109381074		2203	4300	6503	SO:0001583	missense	5903	exon20			GTAACAGCTGCTC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.4079G>A	chr2.hg19:g.109381074G>A	ENSP00000283195:p.Ser1360Asn	157.0	0.0		112.0	53.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	G	5.864	0.343570	0.11126	.	.	ENSG00000153201	ENST00000283195	T	0.57595	0.39	5.48	5.48	0.80851	Zinc finger, RanBP2-type (4);	.	.	.	.	T	0.46737	0.1408	L	0.47716	1.5	0.20196	N	0.999923	B	0.32010	0.351	B	0.34038	0.174	T	0.37174	-0.9717	9	0.29301	T	0.29	-5.1313	11.2651	0.49106	0.0:0.1352:0.7251:0.1397	.	1360	P49792	RBP2_HUMAN	N	1360	ENSP00000283195:S1360N	ENSP00000283195:S1360N	S	+	2	0	RANBP2	108747506	0.890000	0.30428	0.998000	0.56505	0.992000	0.81027	1.266000	0.33039	2.554000	0.86153	0.655000	0.94253	AGC	.	.		0.388	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		A	109381074	G	A	109381074	3	1	42	1	0	0	0	0	1	0	0	0	13043	971	34	3	4157	3	RANBP2	2	109381074	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	24019934	109381074	133818299	9	4990										
KCNJ3	3760	hgsc.bcm.edu	37	chr2	155555841	155555841	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ctgcatgttcatcaagatgtCccagcccaagaagcgcgccg	10	14	2	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:155555841C>A	ENST00000295101.2	+	1	1031	c.554C>A	c.(553-555)tCc>tAc	p.S185Y	KCNJ3_ENST00000544049.1_Missense_Mutation_p.S185Y|AC061961.2_ENST00000443901.1_RNA	NM_001260509.1|NM_002239.3	NP_001247438.1|NP_002230.1	P48549	KCNJ3_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 3	185					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to electrical stimulus (GO:0051602)|synaptic transmission (GO:0007268)	external side of plasma membrane (GO:0009897)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)			breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(30)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	54					Halothane(DB01159)	ATCAAGATGTCCCAGCCCAAG	0.587																																					p.S185Y		Atlas-SNP	.											.	KCNJ3	126	.	0			c.C554A						.						77	67	70					2																	155555841		2203	4300	6503	SO:0001583	missense	3760	exon1			AGATGTCCCAGCC	U50964	CCDS2200.1, CCDS58733.1	2q24.1	2011-07-05			ENSG00000162989	ENSG00000162989		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6264	protein-coding gene	gene with protein product		601534				8088798, 16382105	Standard	NM_002239		Approved	Kir3.1, GIRK1, KGA	uc002tyv.2	P48549	OTTHUMG00000131937	ENST00000295101.2:c.554C>A	chr2.hg19:g.155555841C>A	ENSP00000295101:p.Ser185Tyr	87.0	0.0		79.0	17.0	NM_001260509	B4DEW7|Q8TBI0	Missense_Mutation	SNP	ENST00000295101.2	hg19	CCDS2200.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.105048	0.77096	.	.	ENSG00000162989	ENST00000295101;ENST00000544049	D;D	0.94793	-3.52;-3.52	5.41	5.41	0.78517	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.98185	0.9400	H	0.95437	3.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99391	1.0925	10	0.87932	D	0	.	17.7563	0.88450	0.0:1.0:0.0:0.0	.	185;185	B4DEW7;P48549	.;IRK3_HUMAN	Y	185	ENSP00000295101:S185Y;ENSP00000438410:S185Y	ENSP00000295101:S185Y	S	+	2	0	KCNJ3	155264087	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.035000	0.70940	2.537000	0.85549	0.561000	0.74099	TCC	.	.		0.587	KCNJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254890.2	NM_002239		A	155555841	C	A	155555841	3	1	42	1	0	0	0	0	1	0	0	0	8061	855	30	3	556	3	KCNJ3	2	155555841	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	46174767	155555841	87643532	10	4991										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168100239	168100239	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	atgtttgaaacacagccgttGgacacaattaacaaagatat	7	7	0	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:168100239G>T	ENST00000409195.1	+	9	2426	c.2337G>T	c.(2335-2337)ttG>ttT	p.L779F	XIRP2_ENST00000295237.9_Missense_Mutation_p.L779F|XIRP2_ENST00000409273.1_Missense_Mutation_p.L557F|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	604					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CACAGCCGTTGGACACAATTA	0.408																																					p.L779F		Atlas-SNP	.											.	XIRP2	914	.	0			c.G2337T						.						70	66	67					2																	168100239		1860	4098	5958	SO:0001583	missense	129446	exon9			GCCGTTGGACACA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2337G>T	chr2.hg19:g.168100239G>T	ENSP00000386840:p.Leu779Phe	305.0	0.0		230.0	114.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.718542	0.30503	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.57907	0.37;0.37;0.37	5.92	-0.957	0.10350	.	0.000000	0.64402	D	0.000001	T	0.63510	0.2517	M	0.77486	2.375	0.49389	D	0.999786	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.59847	-0.7377	10	0.87932	D	0	-4.3371	2.694	0.05129	0.413:0.1095:0.366:0.1114	.	604;604;557	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	F	779;779;557	ENSP00000386840:L779F;ENSP00000295237:L779F;ENSP00000387255:L557F	ENSP00000295237:L779F	L	+	3	2	XIRP2	167808485	0.566000	0.26618	0.346000	0.25655	0.605000	0.37080	-0.080000	0.11339	-0.499000	0.06623	-0.355000	0.07637	TTG	.	.		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168100239	G	T	168100239	3	4	42	1	0	0	0	0	1	0	0	0	17445	1339	47	3	2367	3	XIRP2	2	168100239	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	12544398	168100239	75099134	11	4992										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179170928	179170928	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	agcgatgagttcagatgagaAgggcatttcccctgctcata	11	9	2	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:179170928A>G	ENST00000190611.4	+	3	393	c.17A>G	c.(16-18)aAg>aGg	p.K6R	OSBPL6_ENST00000357080.4_Missense_Mutation_p.K6R|OSBPL6_ENST00000409045.3_Missense_Mutation_p.K6R|OSBPL6_ENST00000409631.1_Missense_Mutation_p.K6R|OSBPL6_ENST00000392505.2_Missense_Mutation_p.K6R|OSBPL6_ENST00000359685.3_Missense_Mutation_p.K6R	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	6					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TCAGATGAGAAGGGCATTTCC	0.438																																					p.K6R		Atlas-SNP	.											.	OSBPL6	178	.	0			c.A17G						.						155	132	140					2																	179170928		2203	4300	6503	SO:0001583	missense	114880	exon3			ATGAGAAGGGCAT	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.17A>G	chr2.hg19:g.179170928A>G	ENSP00000190611:p.Lys6Arg	110.0	0.0		83.0	46.0	NM_001201482	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	hg19	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	A	17.32	3.359892	0.61403	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631	T;T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61;0.61	5.87	4.72	0.59763	.	0.176314	0.34986	U	0.003537	T	0.27933	0.0688	N	0.05510	-0.035	0.39990	D	0.975022	B;B;B;B;B	0.17667	0.008;0.004;0.021;0.005;0.023	B;B;B;B;B	0.15484	0.009;0.004;0.013;0.004;0.006	T	0.07102	-1.0790	10	0.45353	T	0.12	-15.2766	11.0392	0.47820	0.9264:0.0:0.0736:0.0	.	6;6;6;6;6	Q9BZF3-4;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;OSBL6_HUMAN;.	R	6	ENSP00000376293:K6R;ENSP00000352713:K6R;ENSP00000349591:K6R;ENSP00000387248:K6R;ENSP00000190611:K6R;ENSP00000386885:K6R	ENSP00000190611:K6R	K	+	2	0	OSBPL6	178879174	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.699000	0.61796	1.160000	0.42584	0.533000	0.62120	AAG	.	.		0.438	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		G	179170928	A	G	179170928	3	3	42	1	0	0	0	0	1	0	0	0	11290	72	3	2	19	2	OSBPL6	2	179170928	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10	11070689	179170928	64028445	12	4993										
HIBCH	26275	hgsc.bcm.edu	37	chr2	191155206	191155206	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ttttgccttttcagcttccgAgatcactaggaaggaaagat	9	8	2	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:191155206A>C	ENST00000359678.5	-	5	604	c.310T>G	c.(310-312)Tcg>Gcg	p.S104A	HIBCH_ENST00000392332.3_Missense_Mutation_p.S104A	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	104					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			TCAGCTTCCGAGATCACTAGG	0.323																																					p.S104A		Atlas-SNP	.											.	HIBCH	28	.	0			c.T310G						.						72	68	70					2																	191155206		2203	4300	6503	SO:0001583	missense	26275	exon5			CTTCCGAGATCAC	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"3-hydroxyisobutyryl-Coenzyme A hydrolase"			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.310T>G	chr2.hg19:g.191155206A>C	ENSP00000352706:p.Ser104Ala	136.0	0.0		135.0	58.0	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Missense_Mutation	SNP	ENST00000359678.5	hg19	CCDS2304.1	.	.	.	.	.	.	.	.	.	.	A	0.017	-1.494319	0.01009	.	.	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000409934	T;T;T	0.70282	-0.14;-0.47;-0.14	5.42	-0.0735	0.13735	Crotonase, core (1);	.	.	.	.	T	0.33381	0.0861	N	0.01289	-0.905	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.38564	-0.9655	9	0.05620	T	0.96	0.7649	9.0984	0.36653	0.3045:0.5681:0.0:0.1274	.	104;104	Q6NVY1-2;Q6NVY1	.;HIBCH_HUMAN	A	104;104;158	ENSP00000376144:S104A;ENSP00000352706:S104A;ENSP00000387247:S158A	ENSP00000352706:S104A	S	-	1	0	HIBCH	190863451	0.985000	0.35326	0.903000	0.35520	0.007000	0.05969	0.560000	0.23500	0.111000	0.17947	-0.461000	0.05368	TCG	.	.		0.323	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1			C	191155206	A	C	191155206	3	2	42	1	0	0	0	0	1	0	0	0	7109	304	11	5	890	5	HIBCH	2	191155206	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10	11984278	191155206	52044167	13	4994										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196825086	196825086	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gaatttcatcaactgatgccAaaataaatgtcccagtttct	5	9	3	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:196825086A>G	ENST00000312428.6	-	18	2889	c.2789T>C	c.(2788-2790)tTg>tCg	p.L930S		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	930	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AACTGATGCCAAAATAAATGT	0.348																																					p.L930S		Atlas-SNP	.											.	DNAH7	512	.	0			c.T2789C						.						117	116	116					2																	196825086		1856	4101	5957	SO:0001583	missense	56171	exon18			GATGCCAAAATAA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.2789T>C	chr2.hg19:g.196825086A>G	ENSP00000311273:p.Leu930Ser	108.0	0.0		98.0	44.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018893	0.75275	.	.	ENSG00000118997	ENST00000312428	T	0.69561	-0.41	5.64	5.64	0.86602	Dynein heavy chain, domain-2 (1);	0.000000	0.35151	U	0.003404	D	0.89441	0.6716	H	0.99090	4.425	0.80722	D	1	D	0.56287	0.975	D	0.68483	0.958	D	0.93764	0.7069	10	0.87932	D	0	.	15.8646	0.79055	1.0:0.0:0.0:0.0	.	930	Q8WXX0	DYH7_HUMAN	S	930	ENSP00000311273:L930S	ENSP00000311273:L930S	L	-	2	0	DNAH7	196533331	1.000000	0.71417	0.805000	0.32314	0.845000	0.48019	7.403000	0.79983	2.149000	0.67028	0.477000	0.44152	TTG	.	.		0.348	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		G	196825086	A	G	196825086	3	3	42	1	0	0	0	0	1	0	0	0	4608	131	5	2	9477	2	DNAH7	2	196825086	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10	5669880	196825086	46374287	14	4995										
SGOL2	151246	hgsc.bcm.edu	37	chr2	201400832	201400832	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gctctcatgaacaataacttGataactgcaattgaaatgag	7	7	1	4			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:201400832G>C	ENST00000357799.4	+	4	452	c.354G>C	c.(352-354)ttG>ttC	p.L118F	SGOL2_ENST00000409203.3_Missense_Mutation_p.L118F|SGOL2_ENST00000469840.1_3'UTR	NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	118					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						ACAATAACTTGATAACTGCAA	0.294																																					p.L118F		Atlas-SNP	.											SGOL2,bladder,carcinoma,0,1	SGOL2	126	.	0			c.G354C						.						131	131	131					2																	201400832		1813	4058	5871	SO:0001583	missense	151246	exon4			TAACTTGATAACT	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.354G>C	chr2.hg19:g.201400832G>C	ENSP00000350447:p.Leu118Phe	101.0	0.0		97.0	40.0	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	hg19	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	G	16.77	3.216060	0.58452	.	.	ENSG00000163535	ENST00000357799;ENST00000409203	T;T	0.65178	-0.14;-0.14	5.34	3.48	0.39840	.	0.000000	0.43110	D	0.000604	T	0.70037	0.3178	M	0.66939	2.045	0.31308	N	0.687501	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.73380	0.98;0.98;0.98;0.974	T	0.70547	-0.4842	10	0.72032	D	0.01	-1.3662	2.0135	0.03493	0.172:0.1518:0.52:0.1561	.	118;118;118;118	B7Z7S9;Q562F6-2;Q562F6;Q562F6-3	.;.;SGOL2_HUMAN;.	F	118	ENSP00000350447:L118F;ENSP00000386249:L118F	ENSP00000350447:L118F	L	+	3	2	SGOL2	201109077	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	0.877000	0.28106	0.766000	0.33244	0.655000	0.94253	TTG	.	.		0.294	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		C	201400832	G	C	201400832	3	2	42	1	0	0	0	0	1	0	0	0	14232	1281	45	4	364	4	SGOL2	2	201400832	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	4575746	201400832	41798541	15	4996										
ABI2	10152	hgsc.bcm.edu	37	chr2	204193320	204193320	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	cagctacacaaatctggaacGggtggccgattactgcgaga	12	10	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:204193320G>T	ENST00000422511.2	+	1	114	c.83G>T	c.(82-84)cGg>cTg	p.R28L	ABI2_ENST00000261017.5_Missense_Mutation_p.R28L|ABI2_ENST00000295851.5_Missense_Mutation_p.R28L|RP11-363J17.1_ENST00000469747.2_RNA|ABI2_ENST00000430418.1_Missense_Mutation_p.R28L|ABI2_ENST00000261016.6_5'UTR|ABI2_ENST00000424558.1_Missense_Mutation_p.R28L			Q9NYB9	ABI2_HUMAN	abl-interactor 2	28					actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						AATCTGGAACGGGTGGCCGAT	0.672																																					p.R28L		Atlas-SNP	.											.	ABI2	44	.	0			c.G83T						.						39	46	44					2																	204193320		2203	4300	6503	SO:0001583	missense	10152	exon1			TGGAACGGGTGGC	AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443			24011	protein-coding gene	gene with protein product		606442				7590236, 10964520	Standard	XM_005246217		Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.83G>T	chr2.hg19:g.204193320G>T	ENSP00000396249:p.Arg28Leu	104.0	0.0		80.0	34.0	NM_005759	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	Missense_Mutation	SNP	ENST00000422511.2	hg19		.	.	.	.	.	.	.	.	.	.	G	32	5.121756	0.94385	.	.	ENSG00000138443	ENST00000295851;ENST00000261017;ENST00000430418;ENST00000424558;ENST00000417864;ENST00000422511	D;D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51;-1.51	3.77	3.77	0.43336	.	0.132117	0.47093	D	0.000245	T	0.81049	0.4742	M	0.76838	2.35	0.80722	D	1	B;B;B	0.17268	0.021;0.002;0.0	B;B;B	0.14578	0.011;0.001;0.005	T	0.81992	-0.0678	10	0.87932	D	0	-0.6104	15.7751	0.78207	0.0:0.0:1.0:0.0	.	28;28;28	Q9NYB9-4;Q9NYB9;Q9NYB9-2	.;ABI2_HUMAN;.	L	28	ENSP00000295851:R28L;ENSP00000261017:R28L;ENSP00000408898:R28L;ENSP00000391433:R28L;ENSP00000414703:R28L;ENSP00000396249:R28L	ENSP00000261017:R28L	R	+	2	0	ABI2	203901565	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	8.342000	0.90049	1.923000	0.55706	0.305000	0.20034	CGG	.	.		0.672	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000336179.2	NM_005759		T	204193320	G	T	204193320	3	4	42	1	0	0	0	0	1	0	0	0	89	1116	39	1	85	1	ABI2	2	204193320	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	2792488	204193320	39006053	16	4997										
DYTN	391475	hgsc.bcm.edu	37	chr2	207530732	207530732	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tgcaacttgtctttgtattgGtttaactgttttttaaggag	9	4	1	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr2:207530732G>T	ENST00000452335.2	-	10	1118	c.1002C>A	c.(1000-1002)aaC>aaA	p.N334K		NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	334						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		CTTTGTATTGGTTTAACTGTT	0.403																																					p.N334K		Atlas-SNP	.											.	DYTN	168	.	0			c.C1002A						.						174	154	161					2																	207530732		1826	4080	5906	SO:0001583	missense	391475	exon10			GTATTGGTTTAAC	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.1002C>A	chr2.hg19:g.207530732G>T	ENSP00000396593:p.Asn334Lys	364.0	1.0		283.0	131.0	NM_001093730		Missense_Mutation	SNP	ENST00000452335.2	hg19	CCDS46502.1	.	.	.	.	.	.	.	.	.	.	G	8.469	0.857115	0.17106	.	.	ENSG00000232125	ENST00000452335	T	0.15718	2.4	4.89	0.962	0.19643	.	.	.	.	.	T	0.07548	0.0190	N	0.24115	0.695	0.09310	N	1	P	0.39282	0.666	B	0.33339	0.162	T	0.24119	-1.0169	9	0.22109	T	0.4	-1.6294	1.7438	0.02958	0.1824:0.162:0.4882:0.1675	.	334	A2CJ06	DYTN_HUMAN	K	334	ENSP00000396593:N334K	ENSP00000396593:N334K	N	-	3	2	DYTN	207238977	0.026000	0.19158	0.013000	0.15412	0.517000	0.34286	-0.050000	0.11904	0.061000	0.16311	0.561000	0.74099	AAC	.	.		0.403	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			T	207530732	G	T	207530732	3	4	42	1	0	0	0	0	1	0	0	0	4863	1252	44	3	746	3	DYTN	2	207530732	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	3337412	207530732	35668641	17	4998										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47030821	47030821	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gccctacatgctctgcttctCtgcgagggcctctttgaccc	9	16	3	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr3:47030821C>G	ENST00000450053.3	+	5	602	c.423C>G	c.(421-423)ctC>ctG	p.L141L	NBEAL2_ENST00000292309.5_Silent_p.L141L|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	141					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CTCTGCTTCTCTGCGAGGGCC	0.632																																					p.L141L		Atlas-SNP	.											.	NBEAL2	267	.	0			c.C423G						.						32	38	36					3																	47030821		2066	4181	6247	SO:0001819	synonymous_variant	23218	exon5			GCTTCTCTGCGAG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.423C>G	chr3.hg19:g.47030821C>G		91.0	0.0		74.0	29.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	hg19	CCDS46817.1																																																																																			.	.		0.632	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		G	47030821	C	G	47030821	2	3	42	1	0	0	0	0	0	0	0	1	10198	900	32	4		4	NBEAL2	3	47030821	Silent	SNP	C	TCGA-BC-A217-01A-11D-A152-10		47030821	150991609	18	4999										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77629195	77629195	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tggattattcccaggtattcAataccgggtagaggttgcag	12	7	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr3:77629195A>C	ENST00000461745.1	+	16	3326	c.2426A>C	c.(2425-2427)cAa>cCa	p.Q809P	ROBO2_ENST00000332191.8_Missense_Mutation_p.Q809P|ROBO2_ENST00000487694.3_Missense_Mutation_p.Q825P	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	809	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CCAGGTATTCAATACCGGGTA	0.448																																					p.Q809P		Atlas-SNP	.											.	ROBO2	527	.	0			c.A2426C						.						124	122	122					3																	77629195		1888	4118	6006	SO:0001583	missense	6092	exon16			GTATTCAATACCG	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.2426A>C	chr3.hg19:g.77629195A>C	ENSP00000417164:p.Gln809Pro	206.0	0.0		98.0	86.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.790591	0.31685	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.57436	0.4;0.4;0.4	5.53	5.53	0.82687	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.38492	U	0.001662	T	0.43500	0.1250	L	0.35414	1.06	0.42344	D	0.992343	B;B;B	0.11235	0.002;0.004;0.002	B;B;B	0.16289	0.007;0.015;0.007	T	0.48115	-0.9063	9	0.30078	T	0.28	.	15.3169	0.74089	1.0:0.0:0.0:0.0	.	825;809;809	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	P	825;825;829;809;809;530	ENSP00000417335:Q825P;ENSP00000417164:Q809P;ENSP00000327536:Q809P	ENSP00000327536:Q809P	Q	+	2	0	ROBO2	77711885	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	3.750000	0.55157	2.095000	0.63458	0.460000	0.39030	CAA	.	.		0.448	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		C	77629195	A	C	77629195	3	2	42	1	0	0	0	0	1	0	0	0	13529	130	5	5	2490	5	ROBO2	3	77629195	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10	30598374	77629195	120393235	19	5000										
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113737618	113737618	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tccaggcccgcaggaccttcAgctgaatcttccagtcagac	9	15	3	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr3:113737618A>T	ENST00000295878.3	-	8	1216	c.1070T>A	c.(1069-1071)cTg>cAg	p.L357Q	KIAA1407_ENST00000545063.1_Missense_Mutation_p.L188Q	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	357										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						CAGGACCTTCAGCTGAATCTT	0.488																																					p.L357Q		Atlas-SNP	.											.	KIAA1407	80	.	0			c.T1070A						.						209	218	215					3																	113737618		2203	4300	6503	SO:0001583	missense	57577	exon8			ACCTTCAGCTGAA	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.1070T>A	chr3.hg19:g.113737618A>T	ENSP00000295878:p.Leu357Gln	86.0	0.0		74.0	16.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.588477	0.66105	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000	T;T;T	0.68181	0.82;-0.31;0.26	5.76	5.76	0.90799	.	0.160773	0.42964	D	0.000623	T	0.73393	0.3581	L	0.58810	1.83	0.80722	D	1	P;D;D	0.60575	0.952;0.988;0.988	P;P;P	0.56398	0.678;0.797;0.797	T	0.74572	-0.3621	10	0.48119	T	0.1	.	12.3312	0.55041	0.8737:0.0:0.0:0.1263	.	344;233;357	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	Q	357;188;344	ENSP00000295878:L357Q;ENSP00000446381:L188Q;ENSP00000418099:L344Q	ENSP00000295878:L357Q	L	-	2	0	KIAA1407	115220308	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.828000	0.55753	2.201000	0.70794	0.533000	0.62120	CTG	.	.		0.488	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		T	113737618	A	T	113737618	3	4	42	1	0	0	0	0	1	0	0	0	8238	188	7	4	1780	4	KIAA1407	3	113737618	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10	36108423	113737618	84284812	20	5001										
HGD	3081	hgsc.bcm.edu	37	chr3	120365198	120365198	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ctcctcaaagacatctatgcTgaaccgcattcctctctgga	6	14	3	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr3:120365198T>A	ENST00000283871.5	-	9	1024	c.565A>T	c.(565-567)Agc>Tgc	p.S189C		NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	189			S -> I (in AKU). {ECO:0000269|PubMed:9529363}.		cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	homogentisate 1,2-dioxygenase activity (GO:0004411)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25				GBM - Glioblastoma multiforme(114;0.158)		ACATCTATGCTGAACCGCATT	0.478																																					p.S189C		Atlas-SNP	.											.	HGD	65	.	0			c.A565T						.						109	101	104					3																	120365198		2203	4300	6503	SO:0001583	missense	3081	exon9			CTATGCTGAACCG		CCDS3000.1	3q	2010-04-27	2010-04-27		ENSG00000113924	ENSG00000113924	1.13.11.5		4892	protein-coding gene	gene with protein product	"homogentisate oxidase"	607474	"homogentisate 1,2-dioxygenase (homogentisate oxidase)"	AKU		8188241	Standard	NM_000187		Approved	HGO	uc003edw.3	Q93099	OTTHUMG00000159441	ENST00000283871.5:c.565A>T	chr3.hg19:g.120365198T>A	ENSP00000283871:p.Ser189Cys	45.0	0.0		41.0	20.0	NM_000187	A8K417|B2R8Z0	Missense_Mutation	SNP	ENST00000283871.5	hg19	CCDS3000.1	.	.	.	.	.	.	.	.	.	.	T	17.82	3.483529	0.63962	.	.	ENSG00000113924	ENST00000283871	D	0.99042	-5.36	5.91	5.91	0.95273	Cupin, RmlC-type (1);	0.078065	0.85682	D	0.000000	D	0.98359	0.9455	L	0.61036	1.89	0.80722	D	1	P	0.38800	0.648	P	0.45138	0.471	D	0.99019	1.0817	10	0.66056	D	0.02	-20.7815	14.2973	0.66321	0.0:0.0:0.0:1.0	.	189	Q93099	HGD_HUMAN	C	189	ENSP00000283871:S189C	ENSP00000283871:S189C	S	-	1	0	HGD	121847888	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.173000	0.77612	2.261000	0.74972	0.533000	0.62120	AGC	.	.		0.478	HGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355410.1			A	120365198	T	A	120365198	3	1	42	1	0	0	0	0	1	0	0	0	7093	1580	55	4	796	4	HGD	3	120365198	Missense_Mutation	SNP	T	TCGA-BC-A217-01A-11D-A152-10	6627580	120365198	77657232	21	5002										
MYLK	4638	hgsc.bcm.edu	37	chr3	123411616	123411616	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tggcaggagcactccgcctgGccagcgtcattcttggctac	12	14	2	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr3:123411616G>A	ENST00000475616.1	-	16	3530	c.3531C>T	c.(3529-3531)ggC>ggT	p.G1177G	MYLK_ENST00000360304.3_Silent_p.G1177G|MYLK_ENST00000346322.5_Silent_p.G1108G|MYLK_ENST00000360772.3_Silent_p.G1177G|MYLK_ENST00000354792.5_5'Flank|MYLK_ENST00000359169.1_Silent_p.G1177G|MYLK_ENST00000510775.1_5'UTR|MYLK-AS2_ENST00000510827.1_RNA|MYLK-AS2_ENST00000515464.1_RNA			Q15746	MYLK_HUMAN	myosin light chain kinase	1177	Actin-binding (calcium/calmodulin- insensitive). {ECO:0000250}.|Ig-like C2-type 7.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		ACTCCGCCTGGCCAGCGTCAT	0.597																																					p.G1177G		Atlas-SNP	.											.	MYLK	224	.	0			c.C3531T						.						91	70	77					3																	123411616		2203	4300	6503	SO:0001819	synonymous_variant	4638	exon19			CGCCTGGCCAGCG	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7590	protein-coding gene	gene with protein product	"smooth muscle myosin light chain kinase"	600922	"myosin, light polypeptide kinase"			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.3531C>T	chr3.hg19:g.123411616G>A		81.0	0.0		48.0	24.0	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Silent	SNP	ENST00000475616.1	hg19	CCDS46896.1																																																																																			.	.		0.597	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		A	123411616	G	A	123411616	2	1	42	1	0	0	0	0	0	0	0	1	10065	1190	42	3		3	MYLK	3	123411616	Silent	SNP	G	TCGA-BC-A217-01A-11D-A152-10	3046418	123411616	74610814	22	5003										
SHOX2	6474	hgsc.bcm.edu	37	chr3	157820591	157820591	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gttccagggtgaaattggtcCgacttcgcctctgcttgatt	11	10	1	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr3:157820591C>T	ENST00000425436.3	-	2	456	c.431G>A	c.(430-432)cGg>cAg	p.R144Q	SHOX2_ENST00000490689.2_Missense_Mutation_p.R15Q|SHOX2_ENST00000483851.2_Missense_Mutation_p.R144Q|SHOX2_ENST00000389589.4_Missense_Mutation_p.R168Q|SHOX2_ENST00000441443.2_Missense_Mutation_p.R15Q|SHOX2_ENST00000554685.1_5'UTR	NM_001163678.1|NM_006884.3	NP_001157150.1|NP_006875.2	O60902	SHOX2_HUMAN	short stature homeobox 2	144					cardiac atrium morphogenesis (GO:0003209)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte development (GO:0002063)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|heart development (GO:0007507)|heart valve development (GO:0003170)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of axonogenesis (GO:0050772)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of chondrocyte differentiation (GO:0032330)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(10)|skin(3)|upper_aerodigestive_tract(1)	20			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)			GAAATTGGTCCGACTTCGCCT	0.567																																					p.R168Q		Atlas-SNP	.											.	SHOX2	84	.	0			c.G503A						.						185	150	162					3																	157820591		2203	4300	6503	SO:0001583	missense	6474	exon3			TTGGTCCGACTTC	AJ002368	CCDS33884.1, CCDS43164.1, CCDS33884.2, CCDS54664.1	3q25.32	2011-06-20			ENSG00000168779	ENSG00000168779		"Homeoboxes / PRD class"	10854	protein-coding gene	gene with protein product		602504				9482898, 9466998	Standard	NM_006884		Approved	SHOT, OG12X, OG12	uc003fbs.3	O60902	OTTHUMG00000158755	ENST00000425436.3:c.431G>A	chr3.hg19:g.157820591C>T	ENSP00000398704:p.Arg144Gln	264.0	1.0		202.0	95.0	NM_003030	O60465|O60467|O60903	Missense_Mutation	SNP	ENST00000425436.3	hg19	CCDS43164.1	.	.	.	.	.	.	.	.	.	.	C	36	5.790320	0.96945	.	.	ENSG00000168779;ENSG00000168779;ENSG00000168779;ENSG00000168779;ENSG00000168779;ENSG00000258518	ENST00000425436;ENST00000490689;ENST00000389589;ENST00000313019;ENST00000441443;ENST00000483851	D;D;D;D;D	0.99150	-5.49;-5.49;-5.49;-5.49;-5.49	5.49	5.49	0.81192	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000001	D	0.99664	0.9875	H	0.98833	4.345	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.97110	0.986;0.999;1.0	D	0.97355	0.9966	10	0.87932	D	0	.	19.3594	0.94431	0.0:1.0:0.0:0.0	.	144;168;144	O60902-2;O60902-3;O60902	.;.;SHOX2_HUMAN	Q	168;15;144;15;15;144	ENSP00000398704:R168Q;ENSP00000451888:R15Q;ENSP00000374240:R144Q;ENSP00000397099:R15Q;ENSP00000419362:R144Q	ENSP00000327294:R15Q	R	-	2	0	SHOX2;AC112502.1	159303285	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.576000	0.86940	0.655000	0.94253	CGG	.	.		0.567	SHOX2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352057.2			T	157820591	C	T	157820591	3	4	42	1	0	0	0	0	1	0	0	0	14304	652	23	1	580	1	SHOX2	3	157820591	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	34408975	157820591	40201839	23	5004										
TMEM175	84286	hgsc.bcm.edu	37	chr4	944240	944240	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	aagtgtacagaggcttctggCaacacggattgccgtctacc	11	11	2	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr4:944240C>A	ENST00000264771.4	+	4	409	c.224C>A	c.(223-225)gCa>gAa	p.A75E	TMEM175_ENST00000508204.1_5'UTR|TMEM175_ENST00000515740.1_5'UTR|TMEM175_ENST00000504180.1_3'UTR	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	75						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			AGGCTTCTGGCAACACGGATT	0.577																																					p.A75E		Atlas-SNP	.											.	TMEM175	44	.	0			c.C224A						.						130	113	119					4																	944240		2203	4300	6503	SO:0001583	missense	84286	exon4			TTCTGGCAACACG	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.224C>A	chr4.hg19:g.944240C>A	ENSP00000264771:p.Ala75Glu	182.0	0.0		111.0	44.0	NM_032326	D3DVN4|Q8ND13	Missense_Mutation	SNP	ENST00000264771.4	hg19	CCDS3341.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.418695	0.42918	.	.	ENSG00000127419	ENST00000507319;ENST00000264771;ENST00000514453;ENST00000514546	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.9	4.9	0.64082	.	0.331079	0.28252	N	0.016034	T	0.50548	0.1622	L	0.46157	1.445	0.80722	D	1	D	0.64830	0.994	P	0.61658	0.892	T	0.35051	-0.9804	10	0.15066	T	0.55	-22.9253	13.6304	0.62191	0.0:1.0:0.0:0.0	.	75	Q9BSA9	TM175_HUMAN	E	74;75;62;75	ENSP00000424746:A74E;ENSP00000264771:A75E;ENSP00000425181:A62E;ENSP00000425763:A75E	ENSP00000264771:A75E	A	+	2	0	TMEM175	934240	0.998000	0.40836	0.929000	0.37066	0.014000	0.08584	3.836000	0.55813	2.290000	0.77057	0.549000	0.68633	GCA	.	.		0.577	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326		A	944240	C	A	944240	3	1	42	1	0	0	0	0	1	0	0	0	16106	710	25	3	234	3	TMEM175	4	944240	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10		944240	190210036	24	5005										
TBC1D14	57533	hgsc.bcm.edu	37	chr4	7026792	7026792	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	cctgtcgtatctgggacgtgTtctgtcgcgatggggaagag	16	8	2	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr4:7026792T>C	ENST00000409757.4	+	13	1943	c.1819T>C	c.(1819-1821)Ttc>Ctc	p.F607L	TBC1D14_ENST00000410031.1_Missense_Mutation_p.F379L|TBC1D14_ENST00000446947.2_Missense_Mutation_p.F254L|TBC1D14_ENST00000448507.1_Missense_Mutation_p.F607L|TBC1D14_ENST00000451522.2_Missense_Mutation_p.F327L	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	607	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						CTGGGACGTGTTCTGTCGCGA	0.498																																					p.F607L		Atlas-SNP	.											TBC1D14_ENST00000409757,colon,carcinoma,0,2	TBC1D14	110	.	0			c.T1819C						.						174	159	164					4																	7026792		2203	4300	6503	SO:0001583	missense	57533	exon13			GACGTGTTCTGTC	AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405			29246	protein-coding gene	gene with protein product		614855				10718198	Standard	NM_020773		Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.1819T>C	chr4.hg19:g.7026792T>C	ENSP00000386921:p.Phe607Leu	276.0	1.0		203.0	47.0	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	hg19	CCDS3394.2	.	.	.	.	.	.	.	.	.	.	T	22.4	4.280978	0.80692	.	.	ENSG00000132405	ENST00000448507;ENST00000409757;ENST00000410031;ENST00000451522;ENST00000446947	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	5.15	5.15	0.70609	Rab-GAP/TBC domain (4);	0.049635	0.85682	D	0.000000	T	0.27278	0.0669	L	0.42632	1.34	0.80722	D	1	P;B;B	0.42375	0.778;0.357;0.226	B;B;P	0.47528	0.399;0.219;0.549	T	0.01496	-1.1340	10	0.45353	T	0.12	-24.8858	14.1839	0.65592	0.0:0.0:0.0:1.0	.	254;327;607	F5GXK4;Q9P2M4-2;Q9P2M4	.;.;TBC14_HUMAN	L	607;607;379;327;254	ENSP00000404041:F607L;ENSP00000386921:F607L;ENSP00000386343:F379L;ENSP00000388886:F327L;ENSP00000405875:F254L	ENSP00000386921:F607L	F	+	1	0	TBC1D14	7077693	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.658000	0.83755	1.953000	0.56701	0.459000	0.35465	TTC	.	.		0.498	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773		C	7026792	T	C	7026792	3	2	42	1	0	0	0	0	1	0	0	0	15618	1725	60	2	1872	2	TBC1D14	4	7026792	Missense_Mutation	SNP	T	TCGA-BC-A217-01A-11D-A152-10	6082552	7026792	184127484	25	5006										
C4orf23	152992	hgsc.bcm.edu	37	chr4	8469838	8469838	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	caagctctggacgccagggtCgggtgtgtaaccagggcctg	16	11	1	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr4:8469838C>T	ENST00000389737.4	+	9	1692	c.1692C>T	c.(1690-1692)gtC>gtT	p.V564V	TRMT44_ENST00000513449.2_Silent_p.V323V	NM_152544.2	NP_689757.2	Q8IYL2	TRM44_HUMAN	tRNA methyltransferase 44 homolog (S. cerevisiae)	564					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										ACGCCAGGGTCGGGTGTGTAA	0.632																																					p.V564V		Atlas-SNP	.											.	TRMT44	7	.	0			c.C1692T						.						36	34	35					4																	8469838		2203	4300	6503	SO:0001819	synonymous_variant	152992	exon9			CAGGGTCGGGTGT	AK093044	CCDS3402.1, CCDS3402.2	4p16.1	2012-06-12	2012-06-12	2012-06-12	ENSG00000155275	ENSG00000155275			26653	protein-coding gene	gene with protein product	"tRNA methyltransferase 44 homolog (S. cerevisiae)"	614309	"chromosome 4 open reading frame 23", "methyltransferase like 19"	C4orf23, METTL19		21658913	Standard	NM_152544		Approved	FLJ35725, TRM44	uc003glg.2	Q8IYL2	OTTHUMG00000160935	ENST00000389737.4:c.1692C>T	chr4.hg19:g.8469838C>T		155.0	0.0		123.0	5.0	NM_152544	Q8NA95	Silent	SNP	ENST00000389737.4	hg19	CCDS3402.2																																																																																			.	.		0.632	TRMT44-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359197.2	NM_152544		T	8469838	C	T	8469838	2	4	42	1	0	0	0	0	0	0	0	1	2258	871	31	1		1	C4orf23	4	8469838	Silent	SNP	C	TCGA-BC-A217-01A-11D-A152-10	1443046	8469838	182684438	26	5007										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30724910	30724910	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	atccccgtgctgcagggcagCactacggtgattgtgcaggt	14	11	0	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr4:30724910C>A	ENST00000361762.2	+	1	2874	c.1866C>A	c.(1864-1866)agC>agA	p.S622R	PCDH7_ENST00000543491.1_Missense_Mutation_p.S622R	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	622	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						TGCAGGGCAGCACTACGGTGA	0.488																																					p.S622R		Atlas-SNP	.											.	PCDH7	215	.	0			c.C1866A						.						92	97	95					4																	30724910		2203	4300	6503	SO:0001583	missense	5099	exon1			GGGCAGCACTACG	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1866C>A	chr4.hg19:g.30724910C>A	ENSP00000355243:p.Ser622Arg	68.0	0.0		89.0	36.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.82|13.82	2.352629|2.352629	0.41700|0.41700	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000511884|ENST00000361762;ENST00000543491;ENST00000333135	.|T;T	.|0.50813	.|0.73;0.73	5.37|5.37	3.65|3.65	0.41850|0.41850	.|Cadherin (5);Cadherin-like (1);	.|.	.|.	.|.	.|.	T|T	0.45054|0.45054	0.1323|0.1323	N|N	0.25957|0.25957	0.775|0.775	0.48975|0.48975	D|D	0.99973|0.99973	.|D;D;P	.|0.55800	.|0.973;0.973;0.872	.|P;P;P	.|0.55871	.|0.786;0.786;0.756	T|T	0.41342|0.41342	-0.9514|-0.9514	5|9	.|0.72032	.|D	.|0.01	.|.	6.8325|6.8325	0.23917|0.23917	0.1414:0.7145:0.0:0.1441|0.1414:0.7145:0.0:0.1441	.|.	.|622;575;622	.|F5GWJ1;O60245-3;O60245	.|.;.;PCDH7_HUMAN	N|R	312|622;622;575	.|ENSP00000355243:S622R;ENSP00000441802:S622R	.|ENSP00000330302:S575R	H|S	+|+	1|3	0|2	PCDH7|PCDH7	30334008|30334008	0.845000|0.845000	0.29573|0.29573	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	-0.058000|-0.058000	0.11750|0.11750	0.839000|0.839000	0.34971|0.34971	0.655000|0.655000	0.94253|0.94253	CAC|AGC	.	.		0.488	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		A	30724910	C	A	30724910	3	1	42	1	0	0	0	0	1	0	0	0	11525	709	25	3	1868	3	PCDH7	4	30724910	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	22255072	30724910	160429366	27	5008										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30725405	30725405	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tacagcattgtgggaggaaaTcccttcaagctgtttgaaat	10	7	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr4:30725405T>A	ENST00000361762.2	+	1	3369	c.2361T>A	c.(2359-2361)aaT>aaA	p.N787K	PCDH7_ENST00000543491.1_Missense_Mutation_p.N787K	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	787	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						TGGGAGGAAATCCCTTCAAGC	0.468																																					p.N787K		Atlas-SNP	.											.	PCDH7	215	.	0			c.T2361A						.						54	53	54					4																	30725405		2203	4300	6503	SO:0001583	missense	5099	exon1			AGGAAATCCCTTC	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.2361T>A	chr4.hg19:g.30725405T>A	ENSP00000355243:p.Asn787Lys	104.0	0.0		89.0	38.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.57|14.57	2.575956|2.575956	0.45902|0.45902	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000361762;ENST00000543491;ENST00000333135|ENST00000511884	T;T|.	0.53857|.	0.6;0.6|.	4.96|4.96	3.79|3.79	0.43588|0.43588	Cadherin (4);Cadherin-like (1);|.	.|.	.|.	.|.	.|.	T|T	0.65217|0.65217	0.2670|0.2670	M|M	0.77616|0.77616	2.38|2.38	0.48288|0.48288	D|D	0.99962|0.99962	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.999;0.999;1.0|.	T|T	0.63677|0.63677	-0.6583|-0.6583	9|5	0.87932|.	D|.	0|.	.|.	6.7845|6.7845	0.23665|0.23665	0.0:0.2297:0.0:0.7703|0.0:0.2297:0.0:0.7703	.|.	787;740;787|.	F5GWJ1;O60245-3;O60245|.	.;.;PCDH7_HUMAN|.	K|T	787;787;740|477	ENSP00000355243:N787K;ENSP00000441802:N787K|.	ENSP00000330302:N740K|.	N|S	+|+	3|1	2|0	PCDH7|PCDH7	30334503|30334503	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	0.940000|0.940000	0.28992|0.28992	0.930000|0.930000	0.37217|0.37217	0.533000|0.533000	0.62120|0.62120	AAT|TCC	.	.		0.468	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		A	30725405	T	A	30725405	3	1	42	1	0	0	0	0	1	0	0	0	11525	1432	50	4	2363	4	PCDH7	4	30725405	Missense_Mutation	SNP	T	TCGA-BC-A217-01A-11D-A152-10	495	30725405	160428871	28	5009										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62936605	62936605	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ggaagttcaaaaggaccggcTcatttggtcactagtctata	10	8	4	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr4:62936605T>C	ENST00000514591.1	+	25	4718	c.4389T>C	c.(4387-4389)gcT>gcC	p.A1463A	RP11-84A1.3_ENST00000506704.1_RNA|LPHN3_ENST00000506700.1_3'UTR|LPHN3_ENST00000507164.1_3'UTR|LPHN3_ENST00000508693.1_3'UTR|LPHN3_ENST00000504896.1_3'UTR|LPHN3_ENST00000511324.1_3'UTR|RP11-84A1.3_ENST00000509461.1_RNA|LPHN3_ENST00000508946.1_Silent_p.A1506A|LPHN3_ENST00000507625.1_Silent_p.A1522A|LPHN3_ENST00000514996.1_Silent_p.A1497A|LPHN3_ENST00000506720.1_Silent_p.A1574A|LPHN3_ENST00000514157.1_3'UTR|RP11-84A1.3_ENST00000504135.1_RNA|LPHN3_ENST00000512091.2_3'UTR|LPHN3_ENST00000506746.1_Silent_p.A1565A|LPHN3_ENST00000509896.1_3'UTR|LPHN3_ENST00000545650.1_Silent_p.A1463A			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1441					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						AAGGACCGGCTCATTTGGTCA	0.443																																					p.A1463A		Atlas-SNP	.											.	LPHN3	800	.	0			c.T4389C						.						51	52	52					4																	62936605		692	1591	2283	SO:0001819	synonymous_variant	23284	exon23			ACCGGCTCATTTG	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.4389T>C	chr4.hg19:g.62936605T>C		69.0	0.0		86.0	56.0	NM_015236	E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	hg19	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	T	4.504	0.093563	0.08632	.	.	ENSG00000150471	ENST00000502815	.	.	.	5.5	1.47	0.22746	.	.	.	.	.	T	0.55752	0.1940	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48103	-0.9064	4	.	.	.	.	8.4372	0.32795	0.122:0.0:0.4432:0.4348	.	.	.	.	P	912	.	.	S	+	1	0	LPHN3	62619200	0.950000	0.32346	0.998000	0.56505	0.994000	0.84299	-0.010000	0.12743	0.373000	0.24621	0.482000	0.46254	TCA	.	.		0.443	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			C	62936605	T	C	62936605	2	2	42	1	0	0	0	0	0	0	0	1	8926	1538	54	2		2	LPHN3	4	62936605	Silent	SNP	T	TCGA-BC-A217-01A-11D-A152-10	32211200	62936605	128217671	29	5010										
NPY5R	4889	hgsc.bcm.edu	37	chr4	164272591	164272591	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gccactacaccttttccatgTggtaactgattttaatgaca	6	10	0	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr4:164272591T>A	ENST00000515560.1	+	4	2688	c.1166T>A	c.(1165-1167)gTg>gAg	p.V389E	NPY5R_ENST00000338566.3_Missense_Mutation_p.V389E|NPY5R_ENST00000506953.1_Missense_Mutation_p.V389E			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	389					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				CTTTTCCATGTGGTAACTGAT	0.348																																					p.V389E	Melanoma(139;1287 1774 9781 19750 25599)	Atlas-SNP	.											.	NPY5R	101	.	0			c.T1166A						.						160	152	155					4																	164272591		2203	4300	6503	SO:0001583	missense	4889	exon4			TCCATGTGGTAAC	BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"GPCR / Class A : Neuropeptide receptors : Y"	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.1166T>A	chr4.hg19:g.164272591T>A	ENSP00000423917:p.Val389Glu	207.0	0.0		154.0	86.0	NM_006174	Q6GTR7|Q92916	Missense_Mutation	SNP	ENST00000515560.1	hg19	CCDS3804.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.453285	0.63290	.	.	ENSG00000164129	ENST00000338566;ENST00000515560;ENST00000506953	T;T;T	0.55930	0.49;0.49;0.49	4.9	3.7	0.42460	GPCR, rhodopsin-like superfamily (1);	0.283599	0.24294	N	0.039799	T	0.63331	0.2502	M	0.68317	2.08	0.35343	D	0.786634	D	0.61080	0.989	P	0.58172	0.834	T	0.74349	-0.3694	10	0.62326	D	0.03	.	11.1021	0.48182	0.0:0.0772:0.0:0.9228	.	389	Q15761	NPY5R_HUMAN	E	389	ENSP00000339377:V389E;ENSP00000423917:V389E;ENSP00000423474:V389E	ENSP00000339377:V389E	V	+	2	0	NPY5R	164492041	1.000000	0.71417	0.999000	0.59377	0.854000	0.48673	5.294000	0.65687	1.966000	0.57179	0.377000	0.23210	GTG	.	.		0.348	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174		A	164272591	T	A	164272591	3	1	42	1	0	0	0	0	1	0	0	0	10619	1696	59	4	1168	4	NPY5R	4	164272591	Missense_Mutation	SNP	T	TCGA-BC-A217-01A-11D-A152-10	101335986	164272591	26881685	30	5011										
DDX60	55601	hgsc.bcm.edu	37	chr4	169201507	169201507	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ttcttcacttcggcaatgttCtttccaggctttcaagcaag	7	11	4	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr4:169201507C>G	ENST00000393743.3	-	14	2248	c.1957G>C	c.(1957-1959)Gaa>Caa	p.E653Q		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	653					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		CGGCAATGTTCTTTCCAGGCT	0.358																																					p.E653Q		Atlas-SNP	.											.	DDX60	304	.	0			c.G1957C						.						89	83	85					4																	169201507		2203	4300	6503	SO:0001583	missense	55601	exon14			AATGTTCTTTCCA	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.1957G>C	chr4.hg19:g.169201507C>G	ENSP00000377344:p.Glu653Gln	307.0	0.0		247.0	144.0	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	hg19	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.873492	0.33069	.	.	ENSG00000137628	ENST00000393743	T	0.19532	2.14	5.48	4.64	0.57946	.	0.302034	0.30210	N	0.010142	T	0.35480	0.0933	M	0.75264	2.295	0.32678	N	0.515851	D	0.65815	0.995	P	0.53062	0.717	T	0.52711	-0.8539	10	0.40728	T	0.16	.	11.3079	0.49347	0.0:0.849:0.0:0.151	.	653	Q8IY21	DDX60_HUMAN	Q	653	ENSP00000377344:E653Q	ENSP00000377344:E653Q	E	-	1	0	DDX60	169438082	0.657000	0.27393	0.794000	0.32065	0.056000	0.15407	1.215000	0.32431	1.326000	0.45319	0.563000	0.77884	GAA	.	.		0.358	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		G	169201507	C	G	169201507	3	3	42	1	0	0	0	0	1	0	0	0	4380	922	32	4	3281	4	DDX60	4	169201507	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	4928916	169201507	21952769	31	5012										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169382958	169382958	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	acaacattgactttcattccCcaggaatgtatgattaggaa	7	8	1	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr4:169382958C>T	ENST00000511577.1	-	5	745	c.498G>A	c.(496-498)tgG>tgA	p.W166*	DDX60L_ENST00000505890.1_Nonsense_Mutation_p.W166*|DDX60L_ENST00000260184.7_Nonsense_Mutation_p.W166*			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	166							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CTTTCATTCCCCAGGAATGTA	0.368																																					p.W166X		Atlas-SNP	.											.	DDX60L	116	.	0			c.G498A						.						56	50	52					4																	169382958		1838	4094	5932	SO:0001587	stop_gained	91351	exon5			CATTCCCCAGGAA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.498G>A	chr4.hg19:g.169382958C>T	ENSP00000422423:p.Trp166*	114.0	0.0		89.0	30.0	NM_001012967	Q96ND6	Nonsense_Mutation	SNP	ENST00000511577.1	hg19		.	.	.	.	.	.	.	.	.	.	C	20.1	3.934346	0.73442	.	.	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890	.	.	.	3.43	3.43	0.39272	.	0.227351	0.22562	U	0.058453	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	14.7903	0.69837	0.0:1.0:0.0:0.0	.	.	.	.	X	166	.	ENSP00000260184:W166X	W	-	3	0	DDX60L	169619533	0.228000	0.23718	0.006000	0.13384	0.063000	0.16089	3.164000	0.50770	1.604000	0.50143	0.467000	0.42956	TGG	.	.		0.368	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		T	169382958	C	T	169382958	4	4	42	1	0	0	0	0	0	1	0	0	4381	624	22	3	4758	3	DDX60L	4	169382958	Nonsense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	181451	169382958	21771318	32	5013										
IRX1	79192	hgsc.bcm.edu	37	chr5	3599577	3599577	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	catcaccaagatgaccctcaCgcaggtctccacctggttcg	8	16	3	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr5:3599577C>A	ENST00000302006.3	+	2	567	c.515C>A	c.(514-516)aCg>aAg	p.T172K	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	172					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						ATGACCCTCACGCAGGTCTCC	0.617																																					p.T172K		Atlas-SNP	.											.	IRX1	106	.	0			c.C515A						.						154	119	131					5																	3599577		2203	4300	6503	SO:0001583	missense	79192	exon2			CCCTCACGCAGGT	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.515C>A	chr5.hg19:g.3599577C>A	ENSP00000305244:p.Thr172Lys	236.0	0.0		227.0	116.0	NM_024337	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	hg19	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.936665	0.92458	.	.	ENSG00000170549	ENST00000302006	D	0.90324	-2.65	4.81	4.81	0.61882	Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1);Homeobox, conserved site (1);	0.049539	0.85682	D	0.000000	D	0.92280	0.7551	L	0.36672	1.1	0.80722	D	1	D	0.54964	0.969	P	0.62560	0.904	D	0.93527	0.6866	10	0.87932	D	0	-25.1634	17.5082	0.87753	0.0:1.0:0.0:0.0	.	172	P78414	IRX1_HUMAN	K	172	ENSP00000305244:T172K	ENSP00000305244:T172K	T	+	2	0	IRX1	3652577	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.547000	0.82146	2.173000	0.68751	0.655000	0.94253	ACG	.	.		0.617	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		A	3599577	C	A	3599577	3	1	42	1	0	0	0	0	1	0	0	0	7852	536	19	1	521	1	IRX1	5	3599577	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10		3599577	177315683	33	5014										
CTNND2	1501	hgsc.bcm.edu	37	chr5	10992757	10992757	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tccctctcgatggttgaagaCgaggctacaaagtggtattg	12	8	1	2	rs531016201		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr5:10992757C>A	ENST00000304623.8	-	19	3306	c.3117G>T	c.(3115-3117)tcG>tcT	p.S1039S	CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000359640.2_Silent_p.S981S|CTNND2_ENST00000458100.2_Silent_p.S606S|CTNND2_ENST00000503622.1_Silent_p.S702S|CTNND2_ENST00000511377.1_Silent_p.S948S	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	1039					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						TGGTTGAAGACGAGGCTACAA	0.542																																					p.S1039S		Atlas-SNP	.											.	CTNND2	289	.	0			c.G3117T						.						143	130	134					5																	10992757		2203	4300	6503	SO:0001819	synonymous_variant	1501	exon19			TGAAGACGAGGCT	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.3117G>T	chr5.hg19:g.10992757C>A		159.0	0.0		123.0	60.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Silent	SNP	ENST00000304623.8	hg19	CCDS3881.1																																																																																			.	.		0.542	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	10992757	C	A	10992757	2	1	42	1	0	0	0	0	0	0	0	1	4022	523	19	1		1	CTNND2	5	10992757	Silent	SNP	C	TCGA-BC-A217-01A-11D-A152-10	7393180	10992757	169922503	34	5015										
FSTL4	23105	hgsc.bcm.edu	37	chr5	132534838	132534838	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	cccccctttatacctgacacCtcacaccgcagcgtgttttg	6	17	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr5:132534838C>G	ENST00000265342.7	-	16	2727	c.2478G>C	c.(2476-2478)gaG>gaC	p.E826D	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	826						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TACCTGACACCTCACACCGCA	0.577																																					p.E826D		Atlas-SNP	.											.	FSTL4	74	.	0			c.G2478C						.						68	65	66					5																	132534838		2203	4300	6503	SO:0001583	missense	23105	exon16			TGACACCTCACAC	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.2478G>C	chr5.hg19:g.132534838C>G	ENSP00000265342:p.Glu826Asp	86.0	0.0		66.0	25.0	NM_015082	Q8TBU0|Q9UPU1	Missense_Mutation	SNP	ENST00000265342.7	hg19	CCDS34238.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.455853	0.63401	.	.	ENSG00000053108	ENST00000265342;ENST00000360575	T	0.62364	0.03	5.24	5.24	0.73138	Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.75867	0.3908	M	0.82323	2.585	0.80722	D	1	D;D	0.63046	0.962;0.992	P;P	0.53224	0.611;0.721	T	0.80817	-0.1213	10	0.72032	D	0.01	-33.8418	17.4006	0.87459	0.0:1.0:0.0:0.0	.	826;475	Q6MZW2;B3KPF3	FSTL4_HUMAN;.	D	826;657	ENSP00000265342:E826D	ENSP00000265342:E826D	E	-	3	2	FSTL4	132562737	1.000000	0.71417	1.000000	0.80357	0.224000	0.24922	4.688000	0.61715	2.446000	0.82766	0.650000	0.86243	GAG	.	.		0.577	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786		G	132534838	C	G	132534838	3	3	42	1	0	0	0	0	1	0	0	0	6087	680	24	4	54	4	FSTL4	5	132534838	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	121542081	132534838	48380422	35	5016										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140209550	140209550	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tcgcttcccgtttcgcgtggGgctgtacacgggcgagatca	14	12	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr5:140209550G>A	ENST00000529310.1	+	1	1988	c.1874G>A	c.(1873-1875)gGg>gAg	p.G625E	PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	625	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCGCGTGGGGCTGTACACG	0.667																																					p.G625E		Atlas-SNP	.											.	PCDHA6	442	.	0			c.G1874A						.						72	77	75					5																	140209550		2203	4300	6503	SO:0001583	missense	56142	exon1			GCGTGGGGCTGTA	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1874G>A	chr5.hg19:g.140209550G>A	ENSP00000433378:p.Gly625Glu	131.0	0.0		118.0	49.0	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	hg19	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	G	10.67	1.416124	0.25552	.	.	ENSG00000081842	ENST00000529310	T	0.37752	1.18	3.98	2.09	0.27110	Cadherin (4);Cadherin-like (1);	0.443885	0.16053	U	0.231876	T	0.54663	0.1872	M	0.61703	1.905	0.80722	D	1	D;D	0.71674	0.994;0.998	D;D	0.70716	0.924;0.97	T	0.53906	-0.8372	10	0.51188	T	0.08	.	13.7146	0.62689	0.0:0.2959:0.7041:0.0	.	625;625	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	E	625	ENSP00000433378:G625E	ENSP00000433378:G625E	G	+	2	0	PCDHA6	140189734	0.914000	0.31030	0.974000	0.42286	0.181000	0.23173	1.727000	0.38095	0.410000	0.25675	0.306000	0.20318	GGG	.	.		0.667	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		A	140209550	G	A	140209550	3	1	42	1	0	0	0	0	1	0	0	0	11537	1232	43	3	1876	3	PCDHA6	5	140209550	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	7674712	140209550	40705710	36	5017										
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140347607	140347607	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gaatggctttggaaactcctAtacactggtggtgagcggcc	13	9	0	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr5:140347607A>G	ENST00000289269.5	+	1	1788	c.1256A>G	c.(1255-1257)tAt>tGt	p.Y419C	PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	419	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAAACTCCTATACACTGGTG	0.577																																					p.Y419C	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.A1256G						.						90	89	89					5																	140347607		2203	4300	6503	SO:0001583	missense	56134	exon1			ACTCCTATACACT	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"Cadherins / Protocadherins : Clustered"	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1256A>G	chr5.hg19:g.140347607A>G	ENSP00000289269:p.Tyr419Cys	61.0	0.0		92.0	49.0	NM_031883	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	hg19	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	A	10.47	1.358951	0.24598	.	.	ENSG00000243232	ENST00000289269	T	0.68181	-0.31	5.82	5.82	0.92795	Cadherin (4);Cadherin-like (1);	0.000000	0.38164	N	0.001799	D	0.88115	0.6350	H	0.97077	3.935	0.58432	D	0.999995	D;D	0.89917	0.999;1.0	D;D	0.97110	0.97;1.0	D	0.92032	0.5634	10	0.87932	D	0	.	16.1728	0.81831	1.0:0.0:0.0:0.0	.	419;419	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	C	419	ENSP00000289269:Y419C	ENSP00000289269:Y419C	Y	+	2	0	PCDHAC2	140327791	1.000000	0.71417	0.978000	0.43139	0.029000	0.11900	5.199000	0.65152	2.228000	0.72767	0.533000	0.62120	TAT	.	.		0.577	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		G	140347607	A	G	140347607	3	3	42	1	0	0	0	0	1	0	0	0	11542	449	16	2	1258	2	PCDHAC2	5	140347607	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10	138057	140347607	40567653	37	5018										
PCDHB7	56129	hgsc.bcm.edu	37	chr5	140554546	140554546	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ctcctgttcgtggcggtgcgGctgtgcaggaggagcagggc	19	10	0	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr5:140554546G>A	ENST00000231137.3	+	1	2304	c.2130G>A	c.(2128-2130)cgG>cgA	p.R710R	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	710					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGCGGTGCGGCTGTGCAGGA	0.682																																					p.R710R		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G2130A						.						72	122	105					5																	140554546		2197	4285	6482	SO:0001819	synonymous_variant	56129	exon1			GGTGCGGCTGTGC	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.2130G>A	chr5.hg19:g.140554546G>A		198.0	0.0		177.0	28.0	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	hg19	CCDS4249.1																																																																																			.	.		0.682	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		A	140554546	G	A	140554546	2	1	42	1	0	0	0	0	0	0	0	1	11556	1190	42	3		3	PCDHB7	5	140554546	Silent	SNP	G	TCGA-BC-A217-01A-11D-A152-10	206939	140554546	40360714	38	5019										
GPR151	134391	hgsc.bcm.edu	37	chr5	145895523	145895523	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	aatcacacacaggtttcccaCgaagcccaccaggcagacag	8	15	1	1	rs181265546	byFrequency	TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr5:145895523C>T	ENST00000311104.2	-	1	230	c.154G>A	c.(154-156)Gtg>Atg	p.V52M		NM_194251.2	NP_919227.2	Q8TDV0	GP151_HUMAN	G protein-coupled receptor 151	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(2)	14			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGTTTCCCACGAAGCCCACC	0.552													C|||	3	0.000599042	0	0	5008	,	,		19817	0		0	False		,,,				2504	0.0031				p.V52M	Pancreas(78;420 1386 18535 37114 49710)	Atlas-SNP	.											.	GPR151	35	.	0			c.G154A						.						105	104	104					5																	145895523		2203	4300	6503	SO:0001583	missense	134391	exon1			TTCCCACGAAGCC	AY255557	CCDS34266.1	5q32	2012-08-21						"GPCR / Class A : Orphans"	23624	protein-coding gene	gene with protein product	"galanin receptor 4"					12679517	Standard	NM_194251		Approved	PGR7, GALR4	uc003lod.1	Q8TDV0		ENST00000311104.2:c.154G>A	chr5.hg19:g.145895523C>T	ENSP00000308733:p.Val52Met	134.0	0.0		105.0	17.0	NM_194251	Q86SN8|Q8NGV2	Missense_Mutation	SNP	ENST00000311104.2	hg19	CCDS34266.1	.	.	.	.	.	.	.	.	.	.	C	11.11	1.542848	0.27563	.	.	ENSG00000173250	ENST00000311104	T	0.40225	1.04	5.99	0.66	0.17868	.	0.400813	0.25798	N	0.028236	T	0.31482	0.0798	L	0.54323	1.7	0.27329	N	0.956834	B	0.23806	0.091	B	0.17098	0.017	T	0.15983	-1.0418	10	0.37606	T	0.19	.	6.1039	0.20063	0.0:0.5202:0.2451:0.2347	.	52	Q8TDV0	GP151_HUMAN	M	52	ENSP00000308733:V52M	ENSP00000308733:V52M	V	-	1	0	GPR151	145875716	0.897000	0.30589	0.995000	0.50966	0.984000	0.73092	0.005000	0.13129	0.031000	0.15407	-0.345000	0.07892	GTG	.	C|1.000;G|0.000		0.552	GPR151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373457.1	NM_194251		T	145895523	C	T	145895523	3	4	42	1	0	0	0	0	1	0	0	0	6665	536	19	1	1109	1	GPR151	5	145895523	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	5340977	145895523	35019737	39	5020										
CLK4	57396	hgsc.bcm.edu	37	chr5	178040784	178040784	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	aatacttggatttctgaacgAgctgcttcacggtaacggcc	10	10	2	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr5:178040784A>T	ENST00000316308.4	-	6	771	c.603T>A	c.(601-603)gcT>gcA	p.A201A		NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	201	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		TTTCTGAACGAGCTGCTTCAC	0.338																																					p.A201A		Atlas-SNP	.											.	CLK4	103	.	0			c.T603A						.						133	132	133					5																	178040784		2203	4300	6503	SO:0001819	synonymous_variant	57396	exon6			TGAACGAGCTGCT	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.603T>A	chr5.hg19:g.178040784A>T		231.0	0.0		173.0	65.0	NM_020666		Silent	SNP	ENST00000316308.4	hg19	CCDS4437.1																																																																																			.	.		0.338	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			T	178040784	A	T	178040784	2	4	42	1	0	0	0	0	0	0	0	1	3541	291	11	4		4	CLK4	5	178040784	Silent	SNP	A	TCGA-BC-A217-01A-11D-A152-10	32145261	178040784	2874476	40	5021										
HIST1H3F	8968	hgsc.bcm.edu	37	chr6	26250628	26250628	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	cgatctcacgtaccagacgcTggaatggtagcttgcgaatc	11	11	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr6:26250628T>C	ENST00000446824.2	-	1	207	c.206A>G	c.(205-207)cAg>cGg	p.Q69R	HIST1H2BH_ENST00000356350.2_5'Flank	NM_021018.2	NP_066298.1	P68431	H31_HUMAN	histone cluster 1, H3f	69					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			lung(6)|urinary_tract(1)	7						TACCAGACGCTGGAATGGTAG	0.597											OREG0017241	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q69R		Atlas-SNP	.											.	HIST1H3F	16	.	0			c.A206G						.						124	123	123					6																	26250628		2203	4300	6503	SO:0001583	missense	8968	exon1			AGACGCTGGAATG	Z80786	CCDS4600.1	6p22.1	2011-01-27	2006-10-11	2003-03-14	ENSG00000256316	ENSG00000277775		"Histones / Replication-dependent"	4773	protein-coding gene	gene with protein product		602816	"H3 histone family, member I", "histone 1, H3f"	H3FI		9119399, 12408966	Standard	NM_021018		Approved	H3/i	uc003nhg.1	P68431	OTTHUMG00000014435	ENST00000446824.2:c.206A>G	chr6.hg19:g.26250628T>C	ENSP00000444823:p.Gln69Arg	191.0	1.0	785	194.0	104.0	NM_021018	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000446824.2	hg19	CCDS4600.1	.	.	.	.	.	.	.	.	.	.	.	15.60	2.880807	0.51801	.	.	ENSG00000256316	ENST00000446824	T	0.67171	-0.25	4.82	4.82	0.62117	.	.	.	.	.	T	0.71273	0.3320	.	.	.	0.39988	D	0.975005	.	.	.	.	.	.	T	0.76639	-0.2885	6	0.87932	D	0	.	14.2481	0.66001	0.0:0.0:0.0:1.0	.	.	.	.	R	69	ENSP00000444823:Q69R	ENSP00000444823:Q69R	Q	-	2	0	HIST1H3F	26358607	1.000000	0.71417	1.000000	0.80357	0.299000	0.27559	6.007000	0.70731	2.103000	0.63969	0.459000	0.35465	CAG	.	.		0.597	HIST1H3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040098.1	NM_021018		C	26250628	T	C	26250628	3	2	42	1	0	0	0	0	1	0	0	0	7169	1580	55	2	208	2	HIST1H3F	6	26250628	Missense_Mutation	SNP	T	TCGA-BC-A217-01A-11D-A152-10		26250628	144864439	41	5022										
HSPA1L	3305	hgsc.bcm.edu	37	chr6	31777908	31777908	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gcaggcccagtgcatcctccTtggtagagttttgtgatgat	12	9	0	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr6:31777908T>C	ENST00000375654.4	-	2	2031	c.1842A>G	c.(1840-1842)caA>caG	p.Q614Q	HSPA1L_ENST00000417199.3_Silent_p.Q614Q	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	614					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						TGCATCCTCCTTGGTAGAGTT	0.473																																					p.Q614Q		Atlas-SNP	.											.	HSPA1L	185	.	0			c.A1842G						.						114	104	107					6																	31777908		2203	4300	6503	SO:0001819	synonymous_variant	3305	exon2			TCCTCCTTGGTAG	D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"Heat shock proteins / HSP70"	5234	protein-coding gene	gene with protein product		140559	"heat shock 70kD protein-like 1"			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.1842A>G	chr6.hg19:g.31777908T>C		217.0	0.0		413.0	120.0	NM_005527	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Silent	SNP	ENST00000375654.4	hg19	CCDS34413.1																																																																																			.	.		0.473	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			C	31777908	T	C	31777908	2	2	42	1	0	0	0	0	0	0	0	1	7419	1606	56	2		2	HSPA1L	6	31777908	Silent	SNP	T	TCGA-BC-A217-01A-11D-A152-10	5527280	31777908	139337159	42	5023										
CPNE5	57699	hgsc.bcm.edu	37	chr6	36712088	36712088	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ccgacgataatgatggacatGgggagcttggcagcctggga	16	8	0	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr6:36712088G>T	ENST00000244751.2	-	19	2070	c.1446C>A	c.(1444-1446)ccC>ccA	p.P482P	CPNE5_ENST00000393189.2_Silent_p.P190P|CPNE5_ENST00000459703.1_5'UTR	NM_020939.1	NP_065990.1	Q9HCH3	CPNE5_HUMAN	copine V	482	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(4)|liver(1)|lung(9)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						TGATGGACATGGGGAGCTTGG	0.597																																					p.P482P		Atlas-SNP	.											.	CPNE5	56	.	0			c.C1446A						.						62	43	50					6																	36712088		2198	4296	6494	SO:0001819	synonymous_variant	57699	exon19			GGACATGGGGAGC	H09181	CCDS4825.1	6p21.2	2010-05-28			ENSG00000124772	ENSG00000124772			2318	protein-coding gene	gene with protein product		604209				9430674	Standard	NM_020939		Approved	CPN5, COPN5, KIAA1599	uc003omr.1	Q9HCH3	OTTHUMG00000014602	ENST00000244751.2:c.1446C>A	chr6.hg19:g.36712088G>T		119.0	0.0		80.0	40.0	NM_020939	Q7Z6C8	Silent	SNP	ENST00000244751.2	hg19	CCDS4825.1																																																																																			.	.		0.597	CPNE5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040351.1	NM_020939		T	36712088	G	T	36712088	2	4	42	1	0	0	0	0	0	0	0	1	3817	1335	47	3		3	CPNE5	6	36712088	Silent	SNP	G	TCGA-BC-A217-01A-11D-A152-10	4934180	36712088	134402979	43	5024										
DST	667	hgsc.bcm.edu	37	chr6	56480865	56480865	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tccgatcaaccaaatttctaCgggaggcttttagtacagag	9	9	2	1	rs200851382		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr6:56480865C>T	ENST00000370765.6	-	24	7507	c.7400G>A	c.(7399-7401)cGt>cAt	p.R2467H	DST_ENST00000446842.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370788.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1763					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CAAATTTCTACGGGAGGCTTT	0.498																																					p.R2467H		Atlas-SNP	.											.	DST	1427	.	0			c.G7400A						.						61	66	64					6																	56480865		2203	4300	6503	SO:0001583	missense	667	exon24			TTTCTACGGGAGG	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.7400G>A	chr6.hg19:g.56480865C>T	ENSP00000359801:p.Arg2467His	112.0	0.0		122.0	30.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	hg19	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	9.092	1.001920	0.19121	.	.	ENSG00000151914	ENST00000370765	T	0.69685	-0.42	5.94	5.94	0.96194	.	.	.	.	.	T	0.30665	0.0772	.	.	.	0.18873	N	0.999989	P	0.41929	0.765	B	0.35727	0.209	T	0.50320	-0.8842	7	0.02654	T	1	.	20.3593	0.98849	0.0:1.0:0.0:0.0	.	2467	Q03001-3	.	H	2467	ENSP00000359801:R2467H	ENSP00000359801:R2467H	R	-	2	0	DST	56588824	1.000000	0.71417	0.967000	0.41034	0.948000	0.59901	5.745000	0.68672	2.822000	0.97130	0.557000	0.71058	CGT	.	C|0.999;T|0.001		0.498	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		T	56480865	C	T	56480865	3	4	42	1	0	0	0	0	1	0	0	0	4785	536	19	1	12999	1	DST	6	56480865	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	19768777	56480865	114634202	44	5025										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72968729	72968729	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	caacaagaaggtcacgttctCcaaccagacaccatgatgcc	7	14	2	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr6:72968729C>A	ENST00000521978.1	+	18	2968	c.2968C>A	c.(2968-2970)Cca>Aca	p.P990T	RIMS1_ENST00000401910.3_Missense_Mutation_p.P463T|RIMS1_ENST00000522291.1_Missense_Mutation_p.P989T|RIMS1_ENST00000264839.7_Missense_Mutation_p.P990T|RIMS1_ENST00000425662.2_Missense_Mutation_p.P383T|RIMS1_ENST00000523963.1_Missense_Mutation_p.P464T|RIMS1_ENST00000538414.1_5'UTR|RIMS1_ENST00000348717.5_Missense_Mutation_p.P989T|RIMS1_ENST00000517960.1_Missense_Mutation_p.P989T|RIMS1_ENST00000520567.1_Missense_Mutation_p.P989T|RIMS1_ENST00000518273.1_Missense_Mutation_p.P990T|RIMS1_ENST00000491071.2_Missense_Mutation_p.P990T|RIMS1_ENST00000517827.1_Missense_Mutation_p.P449T	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	990					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GTCACGTTCTCCAACCAGACA	0.378																																					p.P990T		Atlas-SNP	.											.	RIMS1	278	.	0			c.C2968A						.						137	137	137					6																	72968729		1944	4129	6073	SO:0001583	missense	22999	exon18			CGTTCTCCAACCA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2968C>A	chr6.hg19:g.72968729C>A	ENSP00000428417:p.Pro990Thr	98.0	0.0		104.0	41.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.53|14.53	2.561642|2.561642	0.45590|0.45590	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420|ENST00000517433	T;T;T;T;T;T;T;T;T;T;T;T;T;T|T	0.17370|0.15952	2.56;2.7;2.57;2.7;2.7;2.72;2.65;2.54;2.7;2.74;2.68;2.49;2.68;2.28|2.38	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.000000|.	0.64402|.	D|.	0.000005|.	T|T	0.27169|0.27169	0.0666|0.0666	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	B;D;D;P;B;B;B;B;D;B;D;D|.	0.89917|.	0.012;0.998;1.0;0.584;0.021;0.434;0.001;0.069;0.999;0.063;1.0;0.999|.	B;D;D;B;B;B;B;B;D;B;D;D|.	0.87578|.	0.005;0.981;0.998;0.113;0.015;0.417;0.001;0.032;0.991;0.05;0.998;0.993|.	T|T	0.00837|0.00837	-1.1546|-1.1546	10|7	0.15066|0.87932	T|D	0.55|0	-15.6514|-15.6514	19.5526|19.5526	0.95328|0.95328	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	449;464;990;449;463;989;242;990;989;243;990;990|.	B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5|.	.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN|.	T|Y	990;990;990;989;990;989;990;989;990;989;989;990;463;464;383;383;449;215|563	ENSP00000430101:P990T;ENSP00000275037:P989T;ENSP00000264839:P990T;ENSP00000429959:P989T;ENSP00000430408:P990T;ENSP00000430502:P989T;ENSP00000430932:P989T;ENSP00000428417:P990T;ENSP00000385649:P463T;ENSP00000428328:P464T;ENSP00000411235:P383T;ENSP00000389503:P383T;ENSP00000428367:P449T;ENSP00000359448:P215T|ENSP00000430359:S563Y	ENSP00000264839:P990T|ENSP00000430359:S563Y	P|S	+|+	1|2	0|0	RIMS1|RIMS1	73025450|73025450	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.610000|5.610000	0.67668|0.67668	2.701000|2.701000	0.92244|0.92244	0.563000|0.563000	0.77884|0.77884	CCA|TCC	.	.		0.378	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			A	72968729	C	A	72968729	3	1	42	1	0	0	0	0	1	0	0	0	13382	855	30	3	3201	3	RIMS1	6	72968729	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	16487864	72968729	98146338	45	5026										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152583243	152583243	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	attcttgatgtaggctttccCatttcattctcatctggtct	6	10	5	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr6:152583243C>A	ENST00000367255.5	-	101	19497	c.18896G>T	c.(18895-18897)tGg>tTg	p.W6299L	SYNE1_ENST00000448038.1_Missense_Mutation_p.W6228L|SYNE1_ENST00000341594.5_Missense_Mutation_p.W5911L|SYNE1_ENST00000265368.4_Missense_Mutation_p.W6299L|SYNE1_ENST00000423061.1_Missense_Mutation_p.W6228L|SYNE1_ENST00000356820.4_Missense_Mutation_p.W823L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6299					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TAGGCTTTCCCATTTCATTCT	0.373										HNSCC(10;0.0054)																											p.W6299L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G18896T						.						157	144	148					6																	152583243		2203	4300	6503	SO:0001583	missense	23345	exon101			CTTTCCCATTTCA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.18896G>T	chr6.hg19:g.152583243C>A	ENSP00000356224:p.Trp6299Leu	238.0	0.0		212.0	49.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	29.2	4.982397	0.93044	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	D;D;D;D;D;T	0.86865	-2.09;-2.12;-2.18;-2.1;-1.56;0.05	5.96	5.96	0.96718	.	0.000000	0.56097	D	0.000035	D	0.92198	0.7526	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.89072	0.3470	10	0.32370	T	0.25	.	20.4192	0.99033	0.0:1.0:0.0:0.0	.	6299;6299;6228	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	L	6299;6228;6299;6228;5911;823	ENSP00000356224:W6299L;ENSP00000396024:W6228L;ENSP00000265368:W6299L;ENSP00000390975:W6228L;ENSP00000341887:W5911L;ENSP00000349276:W823L	ENSP00000265368:W6299L	W	-	2	0	SYNE1	152624936	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.439000	0.73430	2.831000	0.97527	0.650000	0.86243	TGG	.	.		0.373	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152583243	C	A	152583243	3	1	42	1	0	0	0	0	1	0	0	0	15460	595	21	3	7754	3	SYNE1	6	152583243	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	79614514	152583243	18531824	46	5027										
HGF	3082	hgsc.bcm.edu	37	chr7	81339555	81339556	+	Missense_Mutation	DNP	GG	GG	TT													0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gttttggcacaagatattacGggatctgaaacaggaccaaa					rs375872396		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr7:81339555_81339556GG>TT	ENST00000222390.5	-	13	1674_1675	c.1448_1449CC>AA	c.(1447-1449)cCC>cAA	p.P483Q	HGF_ENST00000457544.2_Missense_Mutation_p.P478Q	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	483					activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						AAGATATTACGGGATCTGAAAC	0.317																																					p.P483P|p.P483H		Atlas-SNP	.											.	HGF	171	.	0			c.C1449A|c.C1448A						.																																			SO:0001583	missense	3082	exon13			TATTACGGGATCT|ATTACGGGATCTG		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.1448_1449delinsTT	chr7.hg19:g.81339555_81339556delinsTT	ENSP00000222390:p.Pro483Gln	197.0|194.0	0.0		126.0|124.0	58.0|59.0	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Silent|Missense_Mutation	SNP	ENST00000222390.5	hg19	CCDS5597.1																																																																																			.	.		0.317	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		TT	81339556	GG	TT	81339555	3	4	42	1	0	0	0	0	1	0	0	0	7094	1103	39	1	761	1	HGF	7	81339555	Missense_Mutation	DNP	GG	TCGA-BC-A217-01A-11D-A152-10		81339555	77799108	47	5028										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131912231	131912231	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	attctctgtgatgatccgggGcacctccttggctgcagggg	14	11	1	2	rs533775501		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr7:131912231G>A	ENST00000359827.3	-	7	2823	c.1861C>T	c.(1861-1863)Ccc>Tcc	p.P621S	PLXNA4_ENST00000321063.4_Missense_Mutation_p.P621S			Q9HCM2	PLXA4_HUMAN	plexin A4	621					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						ATGATCCGGGGCACCTCCTTG	0.582																																					p.P621S		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C1861T						.						64	68	66					7																	131912231		2078	4217	6295	SO:0001583	missense	91584	exon7			TCCGGGGCACCTC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.1861C>T	chr7.hg19:g.131912231G>A	ENSP00000352882:p.Pro621Ser	115.0	0.0		46.0	21.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.211224	0.79240	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.01192	5.2;5.2	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.02571	0.0078	L	0.56340	1.77	0.80722	D	1	B	0.29212	0.237	B	0.32149	0.141	T	0.55927	-0.8063	10	0.66056	D	0.02	.	19.9025	0.96993	0.0:0.0:1.0:0.0	.	621	Q9HCM2	PLXA4_HUMAN	S	621	ENSP00000323194:P621S;ENSP00000352882:P621S	ENSP00000323194:P621S	P	-	1	0	PLXNA4	131562771	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	6.351000	0.73022	2.722000	0.93159	0.655000	0.94253	CCC	.	.		0.582	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	131912231	G	A	131912231	3	1	42	1	0	0	0	0	1	0	0	0	12131	1203	42	3	3927	3	PLXNA4	7	131912231	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	50572676	131912231	27226432	48	5029										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10467732	10467732	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tcttgcactgtgttttcagcTaactgctccaggttcgagct	9	11	2	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr8:10467732T>A	ENST00000382483.3	-	4	4099	c.3876A>T	c.(3874-3876)ttA>ttT	p.L1292F		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1292	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGTTTTCAGCTAACTGCTCCA	0.512																																					p.L1292F		Atlas-SNP	.											.	RP1L1	453	.	0			c.A3876T						.						174	170	171					8																	10467732		2043	4197	6240	SO:0001583	missense	94137	exon4			TTCAGCTAACTGC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3876A>T	chr8.hg19:g.10467732T>A	ENSP00000371923:p.Leu1292Phe	132.0	0.0		49.0	26.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	T	5.704	0.314484	0.10789	.	.	ENSG00000183638	ENST00000382483	T	0.04406	3.63	4.08	-8.17	0.01057	.	1.971510	0.03439	N	0.209094	T	0.02230	0.0069	N	0.08118	0	0.09310	N	1	B	0.18461	0.028	B	0.14023	0.01	T	0.42766	-0.9432	10	0.52906	T	0.07	6.4955	2.7625	0.05311	0.1113:0.3826:0.2254:0.2808	.	1292	A6NKC6	.	F	1292	ENSP00000371923:L1292F	ENSP00000371923:L1292F	L	-	3	2	RP1L1	10505142	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.375000	0.02563	-1.498000	0.01824	-1.144000	0.01866	TTA	.	.		0.512	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10467732	T	A	10467732	3	1	42	1	0	0	0	0	1	0	0	0	13548	1519	53	4	3330	4	RP1L1	8	10467732	Missense_Mutation	SNP	T	TCGA-BC-A217-01A-11D-A152-10		10467732	135896290	49	5030										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77618337	77618337	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	agaaacaccctgagccgggtGgctcttgtgtttattgtaag	12	8	1	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr8:77618337G>A	ENST00000521891.2	+	2	2462	c.2014G>A	c.(2014-2016)Ggc>Agc	p.G672S	ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000518282.1_Missense_Mutation_p.G672S|ZFHX4_ENST00000050961.6_Missense_Mutation_p.G672S|ZFHX4_ENST00000455469.2_Missense_Mutation_p.G672S	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	672					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.G672C(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TGAGCCGGGTGGCTCTTGTGT	0.498										HNSCC(33;0.089)																											p.G672S		Atlas-SNP	.											ZFHX4,NS,carcinoma,0,1	ZFHX4	878	.	1	Substitution - Missense(1)	lung(1)	c.G2014A						.						49	54	52					8																	77618337		1998	4193	6191	SO:0001583	missense	79776	exon2			CCGGGTGGCTCTT		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.2014G>A	chr8.hg19:g.77618337G>A	ENSP00000430497:p.Gly672Ser	96.0	0.0		52.0	8.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	18.19	3.570096	0.65765	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.50813	0.73;0.8;0.77;0.76	5.3	5.3	0.74995	.	0.000000	0.45361	U	0.000367	T	0.58133	0.2101	L	0.41236	1.265	0.80722	D	1	D;D;D;B	0.69078	0.996;0.997;0.997;0.328	P;D;D;B	0.68353	0.907;0.957;0.957;0.413	T	0.45175	-0.9279	10	0.12430	T	0.62	.	19.15	0.93483	0.0:0.0:1.0:0.0	.	672;672;672;672	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	S	672	ENSP00000430497:G672S;ENSP00000399605:G672S;ENSP00000050961:G672S;ENSP00000430848:G672S	ENSP00000050961:G672S	G	+	1	0	ZFHX4	77780892	1.000000	0.71417	0.968000	0.41197	0.996000	0.88848	9.657000	0.98554	2.750000	0.94351	0.655000	0.94253	GGC	.	.		0.498	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77618337	G	A	77618337	3	1	42	1	0	0	0	0	1	0	0	0	17650	1348	47	3	2016	3	ZFHX4	8	77618337	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	67150605	77618337	68745685	50	5031										
ANXA13	312	hgsc.bcm.edu	37	chr8	124701110	124701112	+	Splice_Site	DEL	CCG	CCG	-													0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gctctcctaactttactttaCcgagagttaaataggccttc					rs367655009		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr8:124701110_124701112delCCG	ENST00000419625.1	-	9	789_791	c.717_719delCGG	c.(715-720)ctcggg>ctg	p.G240del	ANXA13_ENST00000262219.6_Splice_Site_p.G281del	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	240					cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			CTTTACTTTACCGAGAGTTAAAT	0.448																																					p.281_281del		Atlas-INDEL	.											.	ANXA13	38	.	0			c.841_841del						.																																			SO:0001630	splice_region_variant	312	exon10			.	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"Annexins"	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.718+1CGG>-	chr8.hg19:g.124701110_124701112delCCG		184.0	0.0		114.0	16.0	NM_001003954	Q9BQR5	Frame_Shift_Del	DEL	ENST00000419625.1	hg19	CCDS47917.1																																																																																			.	.		0.448	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306	In_Frame_Del	-	124701112	CCG	-	124701110	8	5	42	1	0	1	0	1	0	0	1	0	717	521	18	0	243	0	ANXA13	8	124701110	Splice_Site	DEL	CCG	TCGA-BC-A217-01A-11D-A152-10	47082773	124701110	21662912	51	5032										
GSDMC	56169	hgsc.bcm.edu	37	chr8	130777987	130777987	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tgtcaccacgtacaggttgtCccctctcctccggcactcct	7	18	2	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr8:130777987C>G	ENST00000276708.4	-	4	1338	c.457G>C	c.(457-459)Gac>Cac	p.D153H		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	153						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						TACAGGTTGTCCCCTCTCCTC	0.468																																					p.D153H		Atlas-SNP	.											.	GSDMC	71	.	0			c.G457C						.						96	88	91					8																	130777987		2203	4300	6503	SO:0001583	missense	56169	exon4			GGTTGTCCCCTCT	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"melanoma-derived leucine zipper, extra-nuclear factor"	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.457G>C	chr8.hg19:g.130777987C>G	ENSP00000276708:p.Asp153His	110.0	0.0		53.0	18.0	NM_031415	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	hg19	CCDS6360.1	.	.	.	.	.	.	.	.	.	.	C	9.544	1.114025	0.20795	.	.	ENSG00000147697	ENST00000276708	T	0.26660	1.72	4.51	0.607	0.17564	.	1.441670	0.04076	N	0.308803	T	0.22936	0.0554	L	0.39147	1.195	0.09310	N	1	B	0.30068	0.267	B	0.30646	0.118	T	0.27938	-1.0059	10	0.46703	T	0.11	.	6.3838	0.21550	0.0:0.5506:0.0:0.4494	.	153	Q9BYG8	GSDMC_HUMAN	H	153	ENSP00000276708:D153H	ENSP00000276708:D153H	D	-	1	0	GSDMC	130847169	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.393000	0.07305	-0.071000	0.12886	0.591000	0.81541	GAC	.	.		0.468	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1			G	130777987	C	G	130777987	3	3	42	1	0	0	0	0	1	0	0	0	6827	855	30	4	1113	4	GSDMC	8	130777987	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	6076877	130777987	15586035	52	5033										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79824389	79824389	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ttgcagaaaaattagttacaCagatcataaaaaatcttcag	5	6	3	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr9:79824389C>T	ENST00000360280.3	+	6	696	c.436C>T	c.(436-438)Cag>Tag	p.Q146*	VPS13A_ENST00000357409.5_Nonsense_Mutation_p.Q146*|VPS13A_ENST00000376634.4_Nonsense_Mutation_p.Q146*|VPS13A_ENST00000376636.3_Nonsense_Mutation_p.Q146*	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	146					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						ATTAGTTACACAGATCATAAA	0.254																																					p.Q146X		Atlas-SNP	.											.	VPS13A	735	.	0			c.C436T						.						38	40	39					9																	79824389		2203	4290	6493	SO:0001587	stop_gained	23230	exon6			GTTACACAGATCA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.436C>T	chr9.hg19:g.79824389C>T	ENSP00000353422:p.Gln146*	332.0	0.0		233.0	127.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Nonsense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	C	38	6.912853	0.97928	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4521	0.94872	0.0:1.0:0.0:0.0	.	.	.	.	X	146	.	ENSP00000349985:Q146X	Q	+	1	0	VPS13A	79014209	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.182000	0.77689	2.703000	0.92315	0.655000	0.94253	CAG	.	.		0.254	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		T	79824389	C	T	79824389	4	4	42	1	0	0	0	0	0	1	0	0	17204	479	17	3	458	3	VPS13A	9	79824389	Nonsense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10		79824389	61389042	53	5034										
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104449365	104449365	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gaagtcggtgatgttccagtCttcctggcacagcaacaagc	11	11	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr9:104449365C>A	ENST00000361820.3	-	2	1417	c.817G>T	c.(817-819)Gac>Tac	p.D273Y		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	273					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	ATGTTCCAGTCTTCCTGGCAC	0.448																																					p.D273Y		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G817T						.						134	122	126					9																	104449365		2203	4300	6503	SO:0001583	missense	116443	exon2			TCCAGTCTTCCTG		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.817G>T	chr9.hg19:g.104449365C>A	ENSP00000355155:p.Asp273Tyr	258.0	0.0		212.0	77.0	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.670461	0.67814	.	.	ENSG00000198785	ENST00000361820	D	0.88896	-2.44	5.82	5.82	0.92795	.	0.350421	0.31821	N	0.007002	D	0.84897	0.5574	L	0.44542	1.39	0.58432	D	0.999999	P	0.34780	0.468	B	0.32864	0.154	T	0.81693	-0.0817	10	0.11182	T	0.66	.	20.1178	0.97943	0.0:1.0:0.0:0.0	.	273	Q8TCU5	NMD3A_HUMAN	Y	273	ENSP00000355155:D273Y	ENSP00000355155:D273Y	D	-	1	0	GRIN3A	103489186	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.495000	0.66912	2.759000	0.94783	0.557000	0.71058	GAC	.	.		0.448	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			A	104449365	C	A	104449365	3	1	42	1	0	0	0	0	1	0	0	0	6792	913	32	3	2562	3	GRIN3A	9	104449365	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	24624976	104449365	36764066	54	5035										
ADAMTSL2	9719	hgsc.bcm.edu	37	chr9	136402628	136402628	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gcgtgttcccgcagttgcggGggtggggtgacatcccagga	18	10	0	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr9:136402628G>A	ENST00000354484.4	+	3	749	c.192G>A	c.(190-192)ggG>ggA	p.G64G	ADAMTSL2_ENST00000393060.1_Silent_p.G64G|ADAMTSL2_ENST00000393061.3_Silent_p.G173G	NM_001145320.1	NP_001138792.1	Q86TH1	ATL2_HUMAN	ADAMTS-like 2	64	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(145;9.31e-08)|Epithelial(140;6.62e-07)|all cancers(34;7.74e-06)		GCAGTTGCGGGGGTGGGGTGA	0.677																																					p.G64G		Atlas-SNP	.											.	ADAMTSL2	40	.	0			c.G192A						.						33	38	37					9																	136402628		2201	4298	6499	SO:0001819	synonymous_variant	9719	exon3			TTGCGGGGGTGGG	AB011177	CCDS6976.1	9q34.3	2005-01-12			ENSG00000197859	ENSG00000197859			14631	protein-coding gene	gene with protein product		612277				9628581, 14667842	Standard	NM_014694		Approved	KIAA0605	uc004cei.3	Q86TH1	OTTHUMG00000131706	ENST00000354484.4:c.192G>A	chr9.hg19:g.136402628G>A		115.0	0.0		60.0	25.0	NM_014694	B1B0D5|O60345	Silent	SNP	ENST00000354484.4	hg19	CCDS6976.1																																																																																			.	.		0.677	ADAMTSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254619.1	NM_014694		A	136402628	G	A	136402628	2	1	42	1	0	0	0	0	0	0	0	1	275	1219	43	3		3	ADAMTSL2	9	136402628	Silent	SNP	G	TCGA-BC-A217-01A-11D-A152-10	31953263	136402628	4810803	55	5036										
AKR1C1	1645	hgsc.bcm.edu	37	chr10	5009199	5009199	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	aatcttcaattggattatgtTgacctctaccttattcattt	4	8	4	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr10:5009199T>C	ENST00000380872.4	+	3	525	c.333T>C	c.(331-333)gtT>gtC	p.V111V	AKR1C1_ENST00000380859.1_Silent_p.V113V|AKR1C1_ENST00000434459.2_Silent_p.V111V|AKR1C1_ENST00000477661.1_3'UTR	NM_001353.5	NP_001344.2	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	111					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|cholesterol homeostasis (GO:0042632)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|intestinal cholesterol absorption (GO:0030299)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|progesterone metabolic process (GO:0042448)|protein homooligomerization (GO:0051260)|response to organophosphorus (GO:0046683)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase (B-specific) activity (GO:0047042)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|indanol dehydrogenase activity (GO:0047718)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(2)|ovary(3)|prostate(1)	13					Acetylsalicylic acid(DB00945)|Salicylic acid(DB00936)	TGGATTATGTTGACCTCTACC	0.398																																					p.V111V	Colon(130;2054 2316 13360 15380)	Atlas-SNP	.											.	AKR1C1	39	.	0			c.T333C						.						125	115	118					10																	5009199		2203	4300	6503	SO:0001819	synonymous_variant	1645	exon3			TTATGTTGACCTC	D26124	CCDS7061.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000187134	ENSG00000187134	1.3.1.20, 1.1.1.149, 1.1.1.112	"Aldo-keto reductases"	384	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase"	600449	"aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)"	DDH1		8011662	Standard	NM_001353		Approved	DDH, MBAB, DD1, HAKRC		Q04828	OTTHUMG00000017580	ENST00000380872.4:c.333T>C	chr10.hg19:g.5009199T>C		347.0	0.0		311.0	137.0	NM_001353	P52896|Q5SR15|Q7M4N2|Q9UCX2	Silent	SNP	ENST00000380872.4	hg19	CCDS7061.1	.	.	.	.	.	.	.	.	.	.	T	3.685	-0.064794	0.07273	.	.	ENSG00000187134	ENST00000442997	.	.	.	2.95	-5.91	0.02269	.	.	.	.	.	T	0.37019	0.0988	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37502	-0.9703	4	.	.	.	.	2.0885	0.03651	0.3674:0.0969:0.3694:0.1663	.	.	.	.	S	78	.	.	L	+	2	0	AKR1C1	4999199	0.349000	0.24870	0.022000	0.16811	0.029000	0.11900	-0.852000	0.04308	-2.566000	0.00470	0.254000	0.18369	TTG	.	.		0.398	AKR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046523.2	NM_001353		C	5009199	T	C	5009199	2	2	42	1	0	0	0	0	0	0	0	1	469	1799	63	2		2	AKR1C1	10	5009199	Silent	SNP	T	TCGA-BC-A217-01A-11D-A152-10		5009199	130525548	56	5037										
ARMC3	219681	hgsc.bcm.edu	37	chr10	23297251	23297251	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	aatcagatgttggttatggaCgaagtatttcttcttcatct	8	6	5	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr10:23297251C>A	ENST00000298032.5	+	15	1960	c.1876C>A	c.(1876-1878)Cga>Aga	p.R626R	ARMC3_ENST00000376528.4_Silent_p.R363R|ARMC3_ENST00000409049.3_Silent_p.R626R|ARMC3_ENST00000409983.3_Silent_p.R626R	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	626			R -> Q (in dbSNP:rs10828395). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TGGTTATGGACGAAGTATTTC	0.279																																					p.R626R		Atlas-SNP	.											.	ARMC3	102	.	0			c.C1876A						.						35	32	33					10																	23297251		2191	4269	6460	SO:0001819	synonymous_variant	219681	exon15			TATGGACGAAGTA	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"Armadillo repeat containing"	30964	protein-coding gene	gene with protein product	"cancer/testis antigen 81"	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1876C>A	chr10.hg19:g.23297251C>A		151.0	0.0		138.0	21.0	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Silent	SNP	ENST00000298032.5	hg19	CCDS7142.1																																																																																			.	.		0.279	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		A	23297251	C	A	23297251	2	1	42	1	0	0	0	0	0	0	0	1	952	528	19	1		1	ARMC3	10	23297251	Silent	SNP	C	TCGA-BC-A217-01A-11D-A152-10	18288052	23297251	112237496	57	5038										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26462898	26462898	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	aaagtggagaaagaggaagcTatgatccagagttactatca	11	5	1	4			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr10:26462898T>C	ENST00000265944.5	+	30	3871	c.3705T>C	c.(3703-3705)gcT>gcC	p.A1235A	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1235					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AAGAGGAAGCTATGATCCAGA	0.438																																					p.A1235A		Atlas-SNP	.											.	MYO3A	371	.	0			c.T3705C						.						110	112	111					10																	26462898		2203	4300	6503	SO:0001819	synonymous_variant	53904	exon30			GGAAGCTATGATC	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3705T>C	chr10.hg19:g.26462898T>C		156.0	0.0		136.0	61.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	hg19	CCDS7148.1																																																																																			.	.		0.438	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		C	26462898	T	C	26462898	2	2	42	1	0	0	0	0	0	0	0	1	10085	1509	53	2		2	MYO3A	10	26462898	Silent	SNP	T	TCGA-BC-A217-01A-11D-A152-10	3165647	26462898	109071849	58	5039										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88206050	88206050	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ctccttcttatgtttctcttCtgtaccatcagtcttttcag	4	12	6	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr10:88206050C>T	ENST00000298767.5	-	16	3743	c.3271G>A	c.(3271-3273)Gaa>Aaa	p.E1091K	WAPAL_ENST00000372075.1_Missense_Mutation_p.E303K|WAPAL_ENST00000263070.7_Missense_Mutation_p.E303K|WAPAL_ENST00000484070.1_5'Flank	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	1091	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						TGTTTCTCTTCTGTACCATCA	0.388																																					p.E1091K		Atlas-SNP	.											.	WAPAL	81	.	0			c.G3271A						.						186	185	186					10																	88206050		2203	4300	6503	SO:0001583	missense	23063	exon16			TCTCTTCTGTACC	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.3271G>A	chr10.hg19:g.88206050C>T	ENSP00000298767:p.Glu1091Lys	261.0	0.0		180.0	104.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.300015	0.60195	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076;ENST00000372075;ENST00000263070	T;T;T	0.36520	1.25;1.25;1.25	5.51	5.51	0.81932	Armadillo-type fold (1);	0.269247	0.36628	N	0.002493	T	0.37489	0.1005	L	0.48642	1.525	0.54753	D	0.999989	P;B;P;B	0.37864	0.61;0.06;0.61;0.447	B;B;B;B	0.40982	0.345;0.018;0.345;0.168	T	0.06899	-1.0801	10	0.13853	T	0.58	.	19.4394	0.94811	0.0:1.0:0.0:0.0	.	1085;1129;1091;1128	B2RTX8;E9PH12;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	K	1176;1091;1176;303;303	ENSP00000298767:E1091K;ENSP00000361145:E303K;ENSP00000263070:E303K	ENSP00000263070:E303K	E	-	1	0	WAPAL	88196030	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	3.385000	0.52485	2.581000	0.87130	0.655000	0.94253	GAA	.	.		0.388	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		T	88206050	C	T	88206050	3	4	42	1	0	0	0	0	1	0	0	0	17263	922	32	3	317	3	WAPAL	10	88206050	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	61743152	88206050	47328697	59	5040										
IDE	3416	hgsc.bcm.edu	37	chr10	94225544	94225544	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	catgtctgtttggtagtataTctcgatgccacagttattgt	9	7	2	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr10:94225544T>C	ENST00000265986.6	-	20	2433	c.2377A>G	c.(2377-2379)Ata>Gta	p.I793V	IDE_ENST00000496903.1_5'UTR|IDE_ENST00000371581.5_Missense_Mutation_p.I238V	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	793					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TGGTAGTATATCTCGATGCCA	0.408																																					p.I793V		Atlas-SNP	.											.	IDE	77	.	0			c.A2377G						.						184	168	174					10																	94225544		2203	4300	6503	SO:0001583	missense	3416	exon20			AGTATATCTCGAT	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.2377A>G	chr10.hg19:g.94225544T>C	ENSP00000265986:p.Ile793Val	282.0	0.0		186.0	53.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	2.951	-0.216720	0.06101	.	.	ENSG00000119912	ENST00000265986;ENST00000371581	T;T	0.08193	3.12;3.12	6.02	6.02	0.97574	Peptidase M16, C-terminal (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.03959	0.0111	N	0.02247	-0.625	0.80722	D	1	B;B	0.18013	0.008;0.025	B;B	0.25987	0.015;0.065	T	0.29088	-1.0023	10	0.02654	T	1	-16.6034	16.5494	0.84464	0.0:0.0:0.0:1.0	.	793;238	P14735;B3KSB8	IDE_HUMAN;.	V	793;238	ENSP00000265986:I793V;ENSP00000360637:I238V	ENSP00000265986:I793V	I	-	1	0	IDE	94215524	1.000000	0.71417	0.985000	0.45067	0.187000	0.23431	7.803000	0.85983	2.299000	0.77371	0.528000	0.53228	ATA	.	.		0.408	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		C	94225544	T	C	94225544	3	2	42	1	0	0	0	0	1	0	0	0	7502	1435	50	2	706	2	IDE	10	94225544	Missense_Mutation	SNP	T	TCGA-BC-A217-01A-11D-A152-10	6019494	94225544	41309203	60	5041										
SAA2	6289	hgsc.bcm.edu	37	chr11	18267513	18267513	+	Frame_Shift_Del	DEL	C	C	-													0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	cttttggcagcatcatagttCccccgagcatggaagtattt							TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr11:18267513delC	ENST00000526900.1	-	3	357	c.174delG	c.(172-174)gggfs	p.G58fs	SAA2-SAA4_ENST00000524555.1_RNA|SAA2_ENST00000256733.4_Frame_Shift_Del_p.G58fs|SAA2_ENST00000528349.1_Frame_Shift_Del_p.G58fs|SAA2_ENST00000414546.2_Frame_Shift_Del_p.G58fs|SAA2_ENST00000529528.1_Frame_Shift_Del_p.G58fs|SAA2_ENST00000530400.1_Frame_Shift_Del_p.G58fs|RNA5SP333_ENST00000363466.1_RNA			P0DJI9	SAA2_HUMAN	serum amyloid A2	58					acute-phase response (GO:0006953)	extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(1)	6						CATCATAGTTCCCCCGAGCAT	0.552																																					p.N59fs		Atlas-Indel,Pindel	.											.	SAA2	22	.	0			c.175delA						.						76	72	74					11																	18267513		2199	4290	6489	SO:0001589	frameshift_variant	6289	exon3			.	M26152	CCDS7833.1, CCDS44548.1	11p15.1-p14	2008-07-21			ENSG00000134339	ENSG00000134339			10514	protein-coding gene	gene with protein product		104751				7686132	Standard	NM_030754		Approved			P0DJI9	OTTHUMG00000166484	ENST00000526900.1:c.174delG	chr11.hg19:g.18267513delC	ENSP00000436126:p.Gly58fs	428.0	0.0		366.0	60.0	NM_030754	G3XAK9|P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Frame_Shift_Del	DEL	ENST00000526900.1	hg19	CCDS7833.1																																																																																			.	.		0.552	SAA2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389983.1	NM_030754		-	18267513	C	-	18267513	7	5	42	1	0	1	0	1	0	0	0	0	13814	842	30	0	228	0	SAA2	11	18267513	Frame_Shift_Del	DEL	C	TCGA-BC-A217-01A-11D-A152-10		18267513	116739003	61	5042										
SAA1	6288	hgsc.bcm.edu	37	chr11	18290820	18290820	+	Frame_Shift_Del	DEL	G	G	-													0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	agacaaatacttccatgctcGggggaactatgatgctgcca							TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr11:18290820delG	ENST00000405158.2	+	3	354	c.170delG	c.(169-171)cggfs	p.R57fs	SAA1_ENST00000356524.4_Frame_Shift_Del_p.R57fs|RNA5SP334_ENST00000364825.1_RNA|SAA1_ENST00000532858.1_Frame_Shift_Del_p.R57fs	NM_000331.4	NP_000322	P0DJI8	SAA1_HUMAN	serum amyloid A1	57					acute-phase response (GO:0006953)|innate immune response (GO:0045087)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of inflammatory response (GO:0050728)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of interleukin-1 secretion (GO:0050716)|regulation of protein secretion (GO:0050708)	endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	G-protein coupled receptor binding (GO:0001664)|heparin binding (GO:0008201)			endometrium(1)|large_intestine(3)|lung(2)|stomach(3)	9					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	TTCCATGCTCGGGGGAACTAT	0.557																																					p.R57fs		Atlas-Indel,Pindel	.											.	SAA1	14	.	0			c.169delC						.						25	26	26					11																	18290820		2196	4270	6466	SO:0001589	frameshift_variant	6288	exon3			.	M10906	CCDS7835.1	11p15.1	2014-01-30			ENSG00000173432	ENSG00000173432		"Endogenous ligands"	10513	protein-coding gene	gene with protein product		104750		SAA		2595451, 9305847	Standard	NM_199161		Approved	PIG4, TP53I4	uc021qeo.1	P0DJI8	OTTHUMG00000166147	ENST00000405158.2:c.170delG	chr11.hg19:g.18290820delG	ENSP00000384906:p.Arg57fs	217.0	0.0		208.0	60.0	NM_199161	P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Frame_Shift_Del	DEL	ENST00000405158.2	hg19	CCDS7835.1																																																																																			.	.		0.557	SAA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395864.1	NM_199161		-	18290820	G	-	18290820	7	5	42	1	0	1	0	1	0	0	0	0	13813	1116	39	0	176	0	SAA1	11	18290820	Frame_Shift_Del	DEL	G	TCGA-BC-A217-01A-11D-A152-10	23307	18290820	116715696	62	5043										
SLC39A13	91252	hgsc.bcm.edu	37	chr11	47436693	47436693	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	aacgtgctccctgacctcttGgaagaagaggacccgtggtg	13	11	1	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr11:47436693G>T	ENST00000362021.4	+	9	1065	c.1023G>T	c.(1021-1023)ttG>ttT	p.L341F	SLC39A13_ENST00000524928.1_3'UTR|SLC39A13_ENST00000354884.4_Missense_Mutation_p.L334F|SLC39A13_ENST00000533076.1_3'UTR	NM_001128225.2	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter), member 13	341					cellular zinc ion homeostasis (GO:0006882)|connective tissue development (GO:0061448)|zinc ion transmembrane transport (GO:0071577)	Golgi apparatus (GO:0005794)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|kidney(1)|lung(1)|prostate(1)	4				Lung(87;0.0936)		CTGACCTCTTGGAAGAAGAGG	0.632																																					p.L341F		Atlas-SNP	.											.	SLC39A13	18	.	0			c.G1023T						.						43	40	41					11																	47436693		2201	4297	6498	SO:0001583	missense	91252	exon9			CCTCTTGGAAGAA		CCDS7934.1, CCDS44592.1	11p11.2	2013-05-22			ENSG00000165915	ENSG00000165915		"Solute carriers"	20859	protein-coding gene	gene with protein product		608735	"solute carrier family 39 (metal ion transporter), member 13"			12659941	Standard	NM_001128225		Approved	FLJ25785	uc009ylq.3	Q96H72	OTTHUMG00000166890	ENST00000362021.4:c.1023G>T	chr11.hg19:g.47436693G>T	ENSP00000354689:p.Leu341Phe	136.0	0.0		127.0	48.0	NM_001128225	D3DQR6|D3DQR7|E9PLY1|E9PQV3|Q659D9|Q8N7C9|Q8WV10	Missense_Mutation	SNP	ENST00000362021.4	hg19	CCDS44592.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.691759	0.68271	.	.	ENSG00000165915	ENST00000362021;ENST00000354884	T;T	0.51574	0.7;0.7	5.46	4.55	0.56014	.	0.072955	0.56097	D	0.000022	T	0.69296	0.3095	M	0.89478	3.035	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.981	T	0.71341	-0.4622	10	0.45353	T	0.12	-16.5436	8.6848	0.34232	0.2285:0.0:0.7715:0.0	.	341;334	Q96H72;Q96H72-2	S39AD_HUMAN;.	F	341;334	ENSP00000354689:L341F;ENSP00000346956:L334F	ENSP00000346956:L334F	L	+	3	2	SLC39A13	47393269	0.998000	0.40836	1.000000	0.80357	0.968000	0.65278	0.471000	0.22100	1.303000	0.44873	0.462000	0.41574	TTG	.	.		0.632	SLC39A13-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395652.1	NM_152264		T	47436693	G	T	47436693	3	4	42	1	0	0	0	0	1	0	0	0	14631	1339	47	3	1053	3	SLC39A13	11	47436693	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	29145873	47436693	87569823	63	5044										
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120317715	120317715	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	agctgactaaacttgatgcaGagcgagacaaggaccgattg	12	8	0	4			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr11:120317715G>C	ENST00000397843.2	+	18	1676	c.1510G>C	c.(1510-1512)Gag>Cag	p.E504Q	ARHGEF12_ENST00000532993.1_Missense_Mutation_p.E401Q|ARHGEF12_ENST00000356641.3_Missense_Mutation_p.E485Q	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	504	RGSL.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		ACTTGATGCAGAGCGAGACAA	0.428			T	MLL	AML																																p.E504Q		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.G1510C						.						127	119	121					11																	120317715		1976	4177	6153	SO:0001583	missense	23365	exon18			GATGCAGAGCGAG	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.1510G>C	chr11.hg19:g.120317715G>C	ENSP00000380942:p.Glu504Gln	217.0	0.0		143.0	42.0	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	hg19	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	G	33	5.252150	0.95336	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	D;D;D	0.85013	-1.93;-1.93;-1.93	5.3	5.3	0.74995	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.000000	0.46758	D	0.000263	D	0.92011	0.7469	M	0.70595	2.14	0.58432	D	0.999995	D;D;D	0.89917	0.994;0.999;1.0	D;D;D	0.79108	0.95;0.979;0.992	D	0.91908	0.5537	10	0.54805	T	0.06	-19.1516	19.3235	0.94252	0.0:0.0:1.0:0.0	.	401;485;504	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	Q	504;485;401	ENSP00000380942:E504Q;ENSP00000349056:E485Q;ENSP00000432984:E401Q	ENSP00000349056:E485Q	E	+	1	0	ARHGEF12	119822925	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.314000	0.96306	2.627000	0.88993	0.650000	0.86243	GAG	.	.		0.428	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		C	120317715	G	C	120317715	3	2	42	1	0	0	0	0	1	0	0	0	897	943	33	4	1580	4	ARHGEF12	11	120317715	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	72881022	120317715	14688801	64	5045										
RECQL	5965	hgsc.bcm.edu	37	chr12	21643210	21643210	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	taacaagaaatacctcctttCcagccattgttacgttaata	4	10	0	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr12:21643210C>G	ENST00000444129.2	-	4	785	c.317G>C	c.(316-318)gGa>gCa	p.G106A	RECQL_ENST00000421138.2_Missense_Mutation_p.G106A	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	106	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)	membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						TACCTCCTTTCCAGCCATTGT	0.348								Other identified genes with known or suspected DNA repair function																													p.G106A		Atlas-SNP	.											.	RECQL	45	.	0			c.G317C						.						120	121	120					12																	21643210		2203	4300	6503	SO:0001583	missense	5965	exon5			TCCTTTCCAGCCA	D37984	CCDS31756.1	12p12.1	2014-03-07	2014-03-07	2014-03-07	ENSG00000004700	ENSG00000004700			9948	protein-coding gene	gene with protein product	"DNA helicase Q1-like"	600537	"RecQ protein-like (DNA helicase Q1-like)"			7527136, 7961977	Standard	NM_002907		Approved	RecQ1, RecQL1	uc001rex.3	P46063	OTTHUMG00000169131	ENST00000444129.2:c.317G>C	chr12.hg19:g.21643210C>G	ENSP00000416739:p.Gly106Ala	175.0	0.0		94.0	88.0	NM_032941	A8K6G2	Missense_Mutation	SNP	ENST00000444129.2	hg19	CCDS31756.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708568	0.89018	.	.	ENSG00000004700	ENST00000444129;ENST00000421138;ENST00000396093;ENST00000314748;ENST00000542432;ENST00000536240	T;T;T;T;T;T	0.76968	-0.97;-0.97;-0.53;-0.53;-0.53;-1.06	5.29	5.29	0.74685	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.117022	0.64402	D	0.000017	D	0.84790	0.5550	M	0.91038	3.17	0.58432	D	0.999992	P	0.48407	0.91	B	0.43575	0.424	D	0.88762	0.3258	10	0.66056	D	0.02	-1.1318	19.2899	0.94095	0.0:1.0:0.0:0.0	.	106	P46063	RECQ1_HUMAN	A	106	ENSP00000416739:G106A;ENSP00000395449:G106A;ENSP00000379400:G106A;ENSP00000318727:G106A;ENSP00000445555:G106A;ENSP00000439069:G106A	ENSP00000318727:G106A	G	-	2	0	RECQL	21534477	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.570000	0.82390	2.615000	0.88500	0.650000	0.86243	GGA	.	.		0.348	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907		G	21643210	C	G	21643210	3	3	42	1	0	0	0	0	1	0	0	0	13216	855	30	4	1680	4	RECQL	12	21643210	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10		21643210	112208685	65	5046										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41967431	41967431	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gaggagagaaagcagcacctGgttagggccaaagagcagcg	16	8	0	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr12:41967431G>T	ENST00000402685.2	+	10	2858	c.2850G>T	c.(2848-2850)ctG>ctT	p.L950L	PDZRN4_ENST00000539469.2_Silent_p.L692L|PDZRN4_ENST00000298919.7_Silent_p.L690L	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	950							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				AGCAGCACCTGGTTAGGGCCA	0.562																																					p.L950L		Atlas-SNP	.											.	PDZRN4	346	.	0			c.G2850T						.						94	87	89					12																	41967431		2203	4300	6503	SO:0001819	synonymous_variant	29951	exon10			GCACCTGGTTAGG	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2850G>T	chr12.hg19:g.41967431G>T		91.0	0.0		60.0	14.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	hg19	CCDS53777.1																																																																																			.	.		0.562	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		T	41967431	G	T	41967431	2	4	42	1	0	0	0	0	0	0	0	1	11719	1335	47	3		3	PDZRN4	12	41967431	Silent	SNP	G	TCGA-BC-A217-01A-11D-A152-10	20324221	41967431	91884464	66	5047										
HOXC4	3221	hgsc.bcm.edu	37	chr12	54447739	54447739	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tcgtatttgatggactctaaCtacatcgatccgaaatttcc	6	10	1	1	rs377491433		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr12:54447739C>A	ENST00000430889.2	+	1	79	c.33C>A	c.(31-33)aaC>aaA	p.N11K	HOXC4_ENST00000609810.1_Missense_Mutation_p.N11K|HOXC4_ENST00000303406.4_Missense_Mutation_p.N11K	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	11					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						TGGACTCTAACTACATCGATC	0.423																																					p.N11K		Atlas-SNP	.											.	HOXC4	29	.	0			c.C33A						.						97	96	96					12																	54447739		2203	4300	6503	SO:0001583	missense	3221	exon3			CTCTAACTACATC		CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"Homeoboxes / ANTP class : HOXL subclass"	5126	protein-coding gene	gene with protein product		142974	"homeo box C4"	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.33C>A	chr12.hg19:g.54447739C>A	ENSP00000399808:p.Asn11Lys	112.0	0.0		87.0	20.0	NM_014620		Missense_Mutation	SNP	ENST00000430889.2	hg19	CCDS8873.1	.	.	.	.	.	.	.	.	.	.	C	12.51	1.960162	0.34565	.	.	ENSG00000198353	ENST00000303406;ENST00000430889	T;T	0.55234	0.53;0.53	3.41	3.41	0.39046	.	0.055508	0.64402	D	0.000002	T	0.62368	0.2422	L	0.46819	1.47	0.80722	D	1	D	0.63880	0.993	D	0.70227	0.968	T	0.57929	-0.7726	10	0.23302	T	0.38	.	14.7795	0.69754	0.0:1.0:0.0:0.0	.	11	P09017	HXC4_HUMAN	K	11	ENSP00000305973:N11K;ENSP00000399808:N11K	ENSP00000305973:N11K	N	+	3	2	HOXC4	52734006	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.319000	0.43788	2.187000	0.69744	0.462000	0.41574	AAC	.	.		0.423	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1			A	54447739	C	A	54447739	3	1	42	1	0	0	0	0	1	0	0	0	7322	564	20	3	35	3	HOXC4	12	54447739	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	12480308	54447739	79404156	67	5048										
WIF1	11197	hgsc.bcm.edu	37	chr12	65448938	65448938	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tgccaaccttcttgacattgGcatttgttgggttcatggca	10	9	2	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr12:65448938G>C	ENST00000286574.4	-	9	1352	c.978C>G	c.(976-978)tgC>tgG	p.C326W		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	326	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		CTTGACATTGGCATTTGTTGG	0.393			T	HMGA2	pleomorphic salivary gland adenoma																																p.C326W	Esophageal Squamous(148;1595 1816 48559 49439 49664)	Atlas-SNP	.		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	WIF1	96	.	0			c.C978G						.						92	87	89					12																	65448938		2203	4300	6503	SO:0001583	missense	11197	exon9			ACATTGGCATTTG	AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.978C>G	chr12.hg19:g.65448938G>C	ENSP00000286574:p.Cys326Trp	149.0	0.0		95.0	24.0	NM_007191	Q6UXI1|Q8WVG4	Missense_Mutation	SNP	ENST00000286574.4	hg19	CCDS8971.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.851565	0.51270	.	.	ENSG00000156076	ENST00000286574;ENST00000543094	D;D	0.99984	-11.36;-6.54	5.71	3.89	0.44902	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99986	0.9997	H	0.95611	3.695	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.96261	0.9191	9	.	.	.	.	9.9417	0.41585	0.2071:0.0:0.7929:0.0	.	326	Q9Y5W5	WIF1_HUMAN	W	326;75	ENSP00000286574:C326W;ENSP00000439024:C75W	.	C	-	3	2	WIF1	63735205	1.000000	0.71417	0.998000	0.56505	0.601000	0.36947	3.540000	0.53611	0.887000	0.36136	0.655000	0.94253	TGC	.	.		0.393	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2			C	65448938	G	C	65448938	3	2	42	1	0	0	0	0	1	0	0	0	17381	1195	42	4	169	4	WIF1	12	65448938	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	11001199	65448938	68402957	68	5049										
FREM2	341640	hgsc.bcm.edu	37	chr13	39357273	39357273	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tgttggtgagctgttcattcCcatcaggaggagcggagatg	15	7	2	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr13:39357273C>T	ENST00000280481.7	+	5	5924	c.5708C>T	c.(5707-5709)cCc>cTc	p.P1903L		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1903	Calx-beta 2.				cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CTGTTCATTCCCATCAGGAGG	0.438																																					p.P1903L		Atlas-SNP	.											.	FREM2	385	.	0			c.C5708T						.						208	192	198					13																	39357273		2203	4300	6503	SO:0001583	missense	341640	exon5			TCATTCCCATCAG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.5708C>T	chr13.hg19:g.39357273C>T	ENSP00000280481:p.Pro1903Leu	189.0	0.0		182.0	120.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.954021	0.73902	.	.	ENSG00000150893	ENST00000280481	T	0.27557	1.66	5.84	5.84	0.93424	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.60676	0.2287	M	0.78916	2.43	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.62539	-0.6833	10	0.87932	D	0	.	20.1336	0.98010	0.0:1.0:0.0:0.0	.	1903	Q5SZK8	FREM2_HUMAN	L	1903	ENSP00000280481:P1903L	ENSP00000280481:P1903L	P	+	2	0	FREM2	38255273	1.000000	0.71417	1.000000	0.80357	0.043000	0.13939	7.811000	0.86092	2.751000	0.94390	0.514000	0.50259	CCC	.	.		0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39357273	C	T	39357273	3	4	42	1	0	0	0	0	1	0	0	0	6053	623	22	3	5726	3	FREM2	13	39357273	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10		39357273	75812605	69	5050										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64518635	64518635	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	aaccaaagcatgattgccttGaccactgacctccaggctac	7	14	0	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr14:64518635G>T	ENST00000344113.4	+	48	8216	c.8004G>T	c.(8002-8004)ttG>ttT	p.L2668F	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.L2701F|SYNE2_ENST00000358025.3_Missense_Mutation_p.L2668F	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2668					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGATTGCCTTGACCACTGACC	0.453																																					p.L2668F		Atlas-SNP	.											.	SYNE2	577	.	0			c.G8004T						.						102	103	103					14																	64518635		1970	4153	6123	SO:0001583	missense	23224	exon48			TGCCTTGACCACT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.8004G>T	chr14.hg19:g.64518635G>T	ENSP00000341781:p.Leu2668Phe	291.0	0.0		252.0	126.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	4.015	0.000139	0.07819	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.59224	0.65;0.66;0.28	5.68	2.39	0.29439	.	0.797647	0.10644	N	0.650623	T	0.51398	0.1672	L	0.27053	0.805	0.18873	N	0.999986	P;P	0.50272	0.933;0.919	P;P	0.48704	0.462;0.587	T	0.40776	-0.9545	10	0.62326	D	0.03	.	9.9368	0.41556	0.2556:0.0:0.7444:0.0	.	2668;2668	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	F	2668;2668;2701;2701	ENSP00000350719:L2668F;ENSP00000341781:L2668F;ENSP00000452570:L2701F	ENSP00000261678:L2701F	L	+	3	2	SYNE2	63588388	0.058000	0.20735	0.032000	0.17829	0.036000	0.12997	1.632000	0.37102	0.730000	0.32425	0.563000	0.77884	TTG	.	.		0.453	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64518635	G	T	64518635	3	4	42	1	0	0	0	0	1	0	0	0	15461	1281	45	3	8190	3	SYNE2	14	64518635	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10		64518635	42830905	70	5051										
TYRO3	7301	hgsc.bcm.edu	37	chr15	41865515	41865515	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gccccttgtaggctggcagaGgacatgacagtgtgtgtggc	16	9	0	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr15:41865515G>A	ENST00000263798.3	+	17	2219	c.1995G>A	c.(1993-1995)gaG>gaA	p.E665E	TYRO3_ENST00000559066.1_Silent_p.E620E	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	665	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GGCTGGCAGAGGACATGACAG	0.557																																					p.E665E		Atlas-SNP	.											.	TYRO3	169	.	0			c.G1995A						.						211	212	212					15																	41865515		2203	4300	6503	SO:0001819	synonymous_variant	7301	exon17			GGCAGAGGACATG	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.1995G>A	chr15.hg19:g.41865515G>A		115.0	0.0		62.0	12.0	NM_006293	O14953|Q86VR3	Silent	SNP	ENST00000263798.3	hg19	CCDS10080.1																																																																																			.	.		0.557	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2			A	41865515	G	A	41865515	2	1	42	1	0	0	0	0	0	0	0	1	16829	991	35	3		3	TYRO3	15	41865515	Silent	SNP	G	TCGA-BC-A217-01A-11D-A152-10		41865515	60665877	71	5052										
SHC4	399694	hgsc.bcm.edu	37	chr15	49148299	49148299	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	atcttctctctcctcggcatGgctatcaatatgcacctcct	5	15	4	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr15:49148299G>A	ENST00000332408.4	-	8	1521	c.1093C>T	c.(1093-1095)Cat>Tat	p.H365Y	SHC4_ENST00000396535.3_Missense_Mutation_p.H122Y|SHC4_ENST00000537958.1_Missense_Mutation_p.H79Y	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	365	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		TCCTCGGCATGGCTATCAATA	0.448																																					p.H365Y		Atlas-SNP	.											.	SHC4	70	.	0			c.C1093T						.						137	129	132					15																	49148299		2197	4294	6491	SO:0001583	missense	399694	exon8			CGGCATGGCTATC	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"SH2 domain containing"	16743	protein-coding gene	gene with protein product	"rai-like protein"						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.1093C>T	chr15.hg19:g.49148299G>A	ENSP00000329668:p.His365Tyr	163.0	0.0		123.0	37.0	NM_203349	Q6UXQ3|Q8IYW3	Missense_Mutation	SNP	ENST00000332408.4	hg19	CCDS10130.1	.	.	.	.	.	.	.	.	.	.	G	4.357	0.065842	0.08388	.	.	ENSG00000185634	ENST00000332408;ENST00000396535;ENST00000537958	T;T;T	0.30182	3.55;1.54;1.55	5.14	0.673	0.17941	.	1.508310	0.03699	N	0.248252	T	0.15089	0.0364	N	0.08118	0	0.09310	N	1	B;B	0.30709	0.291;0.035	B;B	0.25884	0.064;0.009	T	0.18366	-1.0339	10	0.62326	D	0.03	-6.9214	2.2079	0.03940	0.1485:0.1126:0.3831:0.3559	.	122;365	Q6S5L8-2;Q6S5L8	.;SHC4_HUMAN	Y	365;122;79	ENSP00000329668:H365Y;ENSP00000379786:H122Y;ENSP00000443300:H79Y	ENSP00000329668:H365Y	H	-	1	0	SHC4	46935591	0.003000	0.15002	0.002000	0.10522	0.041000	0.13682	0.523000	0.22925	0.010000	0.14839	0.655000	0.94253	CAT	.	.		0.448	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349		A	49148299	G	A	49148299	3	1	42	1	0	0	0	0	1	0	0	0	14288	1348	47	3	819	3	SHC4	15	49148299	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	7282784	49148299	53383093	72	5053										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94901825	94901825	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gaaaggacaacaaaaagcatGaggaacgtctgggcacgtga	13	7	1	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr15:94901825G>C	ENST00000357742.4	+	9	1285	c.1285G>C	c.(1285-1287)Gag>Cag	p.E429Q	MCTP2_ENST00000331706.4_Missense_Mutation_p.E17Q|MCTP2_ENST00000557742.1_Missense_Mutation_p.E17Q|MCTP2_ENST00000451018.3_Missense_Mutation_p.E429Q|MCTP2_ENST00000543482.1_3'UTR	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	429	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			CAAAAAGCATGAGGAACGTCT	0.507																																					p.E429Q		Atlas-SNP	.											.	MCTP2	122	.	0			c.G1285C						.						114	99	104					15																	94901825		2197	4298	6495	SO:0001583	missense	55784	exon9			AAGCATGAGGAAC	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.1285G>C	chr15.hg19:g.94901825G>C	ENSP00000350377:p.Glu429Gln	182.0	0.0		176.0	95.0	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	hg19	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.593492	0.66219	.	.	ENSG00000140563	ENST00000451018;ENST00000331706;ENST00000357742	T;T;T	0.71579	2.97;-0.58;2.97	5.87	4.95	0.65309	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.093845	0.64402	N	0.000001	T	0.69691	0.3139	L	0.48362	1.52	0.58432	D	0.999997	B;B;B	0.32188	0.023;0.332;0.359	B;B;B	0.39503	0.073;0.135;0.301	T	0.67565	-0.5638	10	0.36615	T	0.2	.	16.6123	0.84886	0.0:0.1405:0.8595:0.0	.	429;17;429	Q6DN12-2;Q6DN12-4;Q6DN12	.;.;MCTP2_HUMAN	Q	429;17;429	ENSP00000395109:E429Q;ENSP00000329646:E17Q;ENSP00000350377:E429Q	ENSP00000329646:E17Q	E	+	1	0	MCTP2	92702829	1.000000	0.71417	0.990000	0.47175	0.914000	0.54420	6.074000	0.71253	1.454000	0.47793	0.650000	0.86243	GAG	.	.		0.507	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		C	94901825	G	C	94901825	3	2	42	1	0	0	0	0	1	0	0	0	9410	1291	45	4	1319	4	MCTP2	15	94901825	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	45753526	94901825	7629567	73	5054										
CHTF18	63922	hgsc.bcm.edu	37	chr16	845334	845334	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	cagccacacacccaggatcaCcttccccagcagccagcagg	8	19	1	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr16:845334C>A	ENST00000262315.9	+	16	2216	c.2153C>A	c.(2152-2154)aCc>aAc	p.T718N	CHTF18_ENST00000455171.2_Missense_Mutation_p.T746N|CHTF18_ENST00000317063.6_Missense_Mutation_p.T927N	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	718					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				CCCAGGATCACCTTCCCCAGC	0.697																																					p.T718N		Atlas-SNP	.											.	CHTF18	52	.	0			c.C2153A						.						32	40	37					16																	845334		1767	3449	5216	SO:0001583	missense	63922	exon16			GGATCACCTTCCC	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"ATPases / AAA-type"	18435	protein-coding gene	gene with protein product		613201	"chromosome 16 open reading frame 41"	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.2153C>A	chr16.hg19:g.845334C>A	ENSP00000262315:p.Thr718Asn	48.0	0.0		52.0	27.0	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	hg19	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	C	1.879	-0.458342	0.04508	.	.	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.09817	2.94;2.98;2.98	4.61	2.61	0.31194	.	0.946639	0.08884	N	0.879632	T	0.06142	0.0159	N	0.14661	0.345	0.09310	N	0.999999	B;B	0.29988	0.264;0.083	B;B	0.23275	0.045;0.02	T	0.44050	-0.9353	10	0.19147	T	0.46	-4.3262	8.652	0.34040	0.0:0.7607:0.1531:0.0862	.	746;718	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	N	927;746;718	ENSP00000313029:T927N;ENSP00000406252:T746N;ENSP00000262315:T718N	ENSP00000262315:T718N	T	+	2	0	CHTF18	785335	0.322000	0.24634	0.143000	0.22291	0.579000	0.36224	1.157000	0.31724	0.379000	0.24794	-0.502000	0.04539	ACC	.	.		0.697	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		A	845334	C	A	845334	3	1	42	1	0	0	0	0	1	0	0	0	3416	507	18	3	2215	3	CHTF18	16	845334	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10		845334	89509419	74	5055										
TELO2	9894	hgsc.bcm.edu	37	chr16	1551758	1551758	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	aagcacagctggcgggctctGactcggacctggacaggtag	15	11	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr16:1551758G>C	ENST00000262319.6	+	11	1735	c.1456G>C	c.(1456-1458)Gac>Cac	p.D486H	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	486					regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				GGCGGGCTCTGACTCGGACCT	0.697																																					p.D486H		Atlas-SNP	.											.	TELO2	44	.	0			c.G1456C						.						31	37	35					16																	1551758		2197	4299	6496	SO:0001583	missense	9894	exon11			GGCTCTGACTCGG	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"TEL2, telomere maintenance 2, homolog (S. cerevisiae)"			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.1456G>C	chr16.hg19:g.1551758G>C	ENSP00000262319:p.Asp486His	49.0	0.0		37.0	12.0	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	hg19	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.167598	0.38315	.	.	ENSG00000100726	ENST00000437914;ENST00000262319	T	0.19806	2.12	5.08	3.09	0.35607	.	0.182951	0.56097	D	0.000023	T	0.38639	0.1048	M	0.74258	2.255	0.09310	N	0.999997	D	0.76494	0.999	D	0.65443	0.935	T	0.08106	-1.0738	10	0.48119	T	0.1	-10.842	7.215	0.25955	0.1996:0.0:0.8004:0.0	.	486	Q9Y4R8	TELO2_HUMAN	H	100;486	ENSP00000262319:D486H	ENSP00000262319:D486H	D	+	1	0	TELO2	1491759	0.363000	0.24989	0.032000	0.17829	0.211000	0.24417	3.391000	0.52530	1.283000	0.44513	0.655000	0.94253	GAC	.	.		0.697	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111		C	1551758	G	C	1551758	3	2	42	1	0	0	0	0	1	0	0	0	15772	1290	45	4	1494	4	TELO2	16	1551758	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	706424	1551758	88802995	75	5056										
ITGAX	3687	hgsc.bcm.edu	37	chr16	31372494	31372494	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gactttgatgctctgaaagaTattcaaaaccaactgaagga	8	7	2	4			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr16:31372494T>C	ENST00000268296.4	+	9	1093	c.972T>C	c.(970-972)gaT>gaC	p.D324D	ITGAX_ENST00000562522.1_Silent_p.D324D	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	324	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CTCTGAAAGATATTCAAAACC	0.418																																					p.D324D		Atlas-SNP	.											.	ITGAX	198	.	0			c.T972C						.						125	134	131					16																	31372494		2197	4300	6497	SO:0001819	synonymous_variant	3687	exon9			GAAAGATATTCAA	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.972T>C	chr16.hg19:g.31372494T>C		128.0	0.0		96.0	65.0	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	hg19	CCDS10711.1																																																																																			.	.		0.418	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		C	31372494	T	C	31372494	2	2	42	1	0	0	0	0	0	0	0	1	7898	1403	49	2		2	ITGAX	16	31372494	Silent	SNP	T	TCGA-BC-A217-01A-11D-A152-10	29820736	31372494	58982259	76	5057										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11775087	11775087	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ggacagaacttggaggccctAcctgagccagctgaaagtac	12	11	0	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr17:11775087A>T	ENST00000262442.4	+	52	10294	c.10226A>T	c.(10225-10227)tAc>tTc	p.Y3409F	DNAH9_ENST00000454412.2_Missense_Mutation_p.Y3409F	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3409					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TGGAGGCCCTACCTGAGCCAG	0.488																																					p.Y3409F		Atlas-SNP	.											.	DNAH9	695	.	0			c.A10226T						.						95	104	101					17																	11775087		2203	4300	6503	SO:0001583	missense	1770	exon52			GGCCCTACCTGAG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10226A>T	chr17.hg19:g.11775087A>T	ENSP00000262442:p.Tyr3409Phe	154.0	0.0		77.0	66.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	4.653	0.121327	0.08881	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.75589	-0.95;-0.95	4.82	3.72	0.42706	Dynein heavy chain, coiled coil stalk (1);	0.145258	0.48767	D	0.000178	T	0.43010	0.1228	N	0.01656	-0.775	0.80722	D	1	B	0.06786	0.001	B	0.13407	0.009	T	0.34354	-0.9832	10	0.07482	T	0.82	.	11.1169	0.48266	0.8614:0.0:0.0:0.1386	.	3409	Q9NYC9	DYH9_HUMAN	F	3409;3409;1991	ENSP00000262442:Y3409F;ENSP00000414874:Y3409F	ENSP00000262442:Y3409F	Y	+	2	0	DNAH9	11715812	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	5.868000	0.69605	0.939000	0.37446	0.523000	0.50628	TAC	.	.		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11775087	A	T	11775087	3	4	42	1	0	0	0	0	1	0	0	0	4610	391	14	4	10432	4	DNAH9	17	11775087	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10		11775087	69420123	77	5058										
SLFN12	55106	hgsc.bcm.edu	37	chr17	33749277	33749277	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	atttctctttctaagtcatcGaggtcactcatctctgcttt	5	11	6	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr17:33749277G>T	ENST00000394562.1	-	4	1294	c.771C>A	c.(769-771)ctC>ctA	p.L257L	SLFN12_ENST00000304905.5_Silent_p.L257L|SLFN12_ENST00000452764.3_Silent_p.L257L|SLFN12_ENST00000460530.1_5'Flank			Q8IYM2	SLN12_HUMAN	schlafen family member 12	257							ATP binding (GO:0005524)			breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTAAGTCATCGAGGTCACTCA	0.338																																					p.L257L		Atlas-SNP	.											.	SLFN12	56	.	0			c.C771A						.						84	89	87					17																	33749277		2203	4300	6503	SO:0001819	synonymous_variant	55106	exon2			GTCATCGAGGTCA	AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.771C>A	chr17.hg19:g.33749277G>T		122.0	0.0		167.0	60.0	NM_018042	A8K711|Q9NP47	Silent	SNP	ENST00000394562.1	hg19	CCDS11295.1																																																																																			.	.		0.338	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042		T	33749277	G	T	33749277	2	4	42	1	0	0	0	0	0	0	0	1	14749	1045	37	1		1	SLFN12	17	33749277	Silent	SNP	G	TCGA-BC-A217-01A-11D-A152-10	21974190	33749277	47445933	78	5059										
NBR1	4077	hgsc.bcm.edu	37	chr17	41345518	41345518	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	cttcccattggcgtctttctCacaaaggccagcaatttggg	9	12	2	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr17:41345518C>T	ENST00000422280.1	+	12	1846	c.1387C>T	c.(1387-1389)Cac>Tac	p.H463Y	NBR1_ENST00000341165.6_Missense_Mutation_p.H463Y|NBR1_ENST00000590996.1_Missense_Mutation_p.H463Y|NBR1_ENST00000589872.1_Missense_Mutation_p.H463Y|NBR1_ENST00000542611.1_Missense_Mutation_p.H442Y|NBR1_ENST00000389312.4_Missense_Mutation_p.H463Y	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	463					macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		GCGTCTTTCTCACAAAGGCCA	0.522																																					p.H463Y		Atlas-SNP	.											.	NBR1	55	.	0			c.C1387T						.						70	68	69					17																	41345518		1904	4120	6024	SO:0001583	missense	4077	exon12			CTTTCTCACAAAG	X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.1387C>T	chr17.hg19:g.41345518C>T	ENSP00000411250:p.His463Tyr	181.0	0.0		227.0	32.0	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	hg19	CCDS45694.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.039340	0.93630	.	.	ENSG00000188554	ENST00000422280;ENST00000542611;ENST00000341165;ENST00000389312;ENST00000389311	T;T;T;T	0.48836	1.39;0.8;1.39;1.38	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.70245	0.3202	M	0.74881	2.28	0.80722	D	1	D;D;D;P	0.62365	0.972;0.972;0.991;0.939	P;P;D;P	0.64506	0.703;0.703;0.926;0.703	T	0.70008	-0.4990	10	0.72032	D	0.01	-4.6646	20.8794	0.99867	0.0:1.0:0.0:0.0	.	463;442;463;463	A8K1U0;B7Z5R6;Q14596-2;Q14596	.;.;.;NBR1_HUMAN	Y	463;442;463;463;463	ENSP00000411250:H463Y;ENSP00000437545:H442Y;ENSP00000343479:H463Y;ENSP00000373963:H463Y	ENSP00000343479:H463Y	H	+	1	0	NBR1	38599044	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	CAC	.	.		0.522	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		T	41345518	C	T	41345518	3	4	42	1	0	0	0	0	1	0	0	0	10209	826	29	3	1429	3	NBR1	17	41345518	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	7596241	41345518	39849692	79	5060										
SPATA20	64847	hgsc.bcm.edu	37	chr17	48629417	48629417	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gaggcctcacaggagagtgcGtggctcgagtgggctctgcg	18	10	2	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr17:48629417G>A	ENST00000356488.4	+	13	1868	c.1785G>A	c.(1783-1785)gcG>gcA	p.A595A	SPATA20_ENST00000006658.6_Silent_p.A611A|SPATA20_ENST00000393244.3_Silent_p.A551A|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	595					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			AGGAGAGTGCGTGGCTCGAGT	0.657																																					p.A611A		Atlas-SNP	.											.	SPATA20	59	.	0			c.G1833A						.						31	35	33					17																	48629417		2202	4299	6501	SO:0001819	synonymous_variant	64847	exon14			GAGTGCGTGGCTC		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1785G>A	chr17.hg19:g.48629417G>A		223.0	0.0		248.0	81.0	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Silent	SNP	ENST00000356488.4	hg19	CCDS58563.1																																																																																			.	.		0.657	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48629417	G	A	48629417	2	1	42	1	0	0	0	0	0	0	0	1	15021	1132	40	1		1	SPATA20	17	48629417	Silent	SNP	G	TCGA-BC-A217-01A-11D-A152-10	7283899	48629417	32565793	80	5061										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9182491	9182491	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	attctgacagtgacagcaatAtggtagagaaaccatatgga	10	6	1	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr18:9182491A>G	ENST00000262126.4	+	2	301	c.61A>G	c.(61-63)Atg>Gtg	p.M21V	ANKRD12_ENST00000400020.3_Missense_Mutation_p.M21V|ANKRD12_ENST00000540578.2_3'UTR|ANKRD12_ENST00000383440.2_Missense_Mutation_p.M21V|RP11-21J18.1_ENST00000579126.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	21						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						TGACAGCAATATGGTAGAGAA	0.343																																					p.M21V		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A61G						.						70	71	70					18																	9182491		2203	4299	6502	SO:0001583	missense	23253	exon2			AGCAATATGGTAG	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.61A>G	chr18.hg19:g.9182491A>G	ENSP00000262126:p.Met21Val	81.0	0.0		53.0	35.0	NM_001083625	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.708582	0.48517	.	.	ENSG00000101745	ENST00000383440;ENST00000546007;ENST00000262126;ENST00000540578	T;T;T	0.76316	-1.01;0.87;3.49	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.86024	0.5834	M	0.68952	2.095	0.53688	D	0.999978	P;D;P	0.58268	0.865;0.982;0.865	P;D;P	0.68943	0.824;0.961;0.824	D	0.87480	0.2420	10	0.87932	D	0	-1.5897	14.079	0.64909	1.0:0.0:0.0:0.0	.	21;21;21	Q6PG48;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	V	21	ENSP00000372932:M21V;ENSP00000441510:M21V;ENSP00000262126:M21V	ENSP00000262126:M21V	M	+	1	0	ANKRD12	9172491	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.674000	0.68117	2.203000	0.70933	0.482000	0.46254	ATG	.	.		0.343	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		G	9182491	A	G	9182491	3	3	42	1	0	0	0	0	1	0	0	0	640	449	16	2	63	2	ANKRD12	18	9182491	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10		9182491	68894757	81	5062										
HRH4	59340	hgsc.bcm.edu	37	chr18	22057509	22057509	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ctctaccatcacaacacagtCggtcagtatcttcttaaaga	5	12	5	1	rs115905515	byFrequency	TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr18:22057509C>A	ENST00000256906.4	+	3	1256	c.1156C>A	c.(1156-1158)Cgg>Agg	p.R386R	HRH4_ENST00000426880.2_Silent_p.R298R	NM_001160166.1|NM_021624.3	NP_001153638.1|NP_067637.2	Q9H3N8	HRH4_HUMAN	histamine receptor H4	386					inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of MAPK cascade (GO:0043408)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Amitriptyline(DB00321)|Amoxapine(DB00543)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Mianserin(DB06148)|Olanzapine(DB00334)	ACAACACAGTCGGTCAGTATC	0.358																																					p.R386R		Atlas-SNP	.											.	HRH4	46	.	0			c.C1156A						.						48	49	48					18																	22057509		2203	4298	6501	SO:0001819	synonymous_variant	59340	exon3			CACAGTCGGTCAG	AF312230	CCDS11887.1, CCDS45841.1	18q11.2	2012-08-08			ENSG00000134489	ENSG00000134489		"GPCR / Class A : Histamine receptors"	17383	protein-coding gene	gene with protein product		606792				11118334, 10973974	Standard	NM_021624		Approved	H4R, HH4R, AXOR35, GPCR105, GPRv53	uc002kvi.3	Q9H3N8	OTTHUMG00000131945	ENST00000256906.4:c.1156C>A	chr18.hg19:g.22057509C>A		83.0	0.0		80.0	30.0	NM_021624	B0YJ19|B2KJ48|Q4G0I6|Q9GZQ0	Silent	SNP	ENST00000256906.4	hg19	CCDS11887.1																																																																																			.	C|0.998;T|0.002		0.358	HRH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254904.1			A	22057509	C	A	22057509	2	1	42	1	0	0	0	0	0	0	0	1	7367	875	31	1		1	HRH4	18	22057509	Silent	SNP	C	TCGA-BC-A217-01A-11D-A152-10	12875018	22057509	56019739	82	5063										
DSC2	1824	hgsc.bcm.edu	37	chr18	28650707	28650707	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	cttaccactttgtcatctccAggagcttctgtgtttgatac	7	11	3	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr18:28650707A>T	ENST00000280904.6	-	14	2678	c.2235T>A	c.(2233-2235)ccT>ccA	p.P745P	DSC2_ENST00000251081.6_Silent_p.P745P|snoU13_ENST00000459603.1_RNA	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	745					bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			TGTCATCTCCAGGAGCTTCTG	0.383																																					p.P745P		Atlas-SNP	.											.	DSC2	168	.	0			c.T2235A						.						115	119	117					18																	28650707		2203	4300	6503	SO:0001819	synonymous_variant	1824	exon14			ATCTCCAGGAGCT	X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"Cadherins / Major cadherins"	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.2235T>A	chr18.hg19:g.28650707A>T		166.0	0.0		114.0	73.0	NM_024422		Silent	SNP	ENST00000280904.6	hg19	CCDS11892.1																																																																																			.	.		0.383	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		T	28650707	A	T	28650707	2	4	42	1	0	0	0	0	0	0	0	1	4768	175	7	4		4	DSC2	18	28650707	Silent	SNP	A	TCGA-BC-A217-01A-11D-A152-10	6593198	28650707	49426541	83	5064										
FAM59A	64762	hgsc.bcm.edu	37	chr18	29890226	29890226	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ccttagccacctcctccacaCtgttgaaatattgcactggc	6	15	0	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr18:29890226C>A	ENST00000269209.6	-	3	326	c.323G>T	c.(322-324)aGt>aTt	p.S108I	GAREM_ENST00000578619.1_5'UTR|GAREM_ENST00000399218.4_Missense_Mutation_p.S108I			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	108	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										CTCCTCCACACTGTTGAAATA	0.418																																					p.S108I		Atlas-SNP	.											FAM59A,NS,adenocarcinoma,0,1	.	.	.	0			c.G323T						.						244	210	221					18																	29890226		2203	4300	6503	SO:0001583	missense	64762	exon3			TCCACACTGTTGA	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.323G>T	chr18.hg19:g.29890226C>A	ENSP00000269209:p.Ser108Ile	275.0	0.0		179.0	50.0	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	hg19	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	C	33	5.224369	0.95139	.	.	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.20332	2.08;2.08	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.51568	0.1682	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.996	T	0.52480	-0.8570	10	0.87932	D	0	-16.913	19.9625	0.97256	0.0:1.0:0.0:0.0	.	108;108	Q9H706;Q9H706-3	FA59A_HUMAN;.	I	108	ENSP00000382165:S108I;ENSP00000269209:S108I	ENSP00000269209:S108I	S	-	2	0	FAM59A	28144224	1.000000	0.71417	0.982000	0.44146	0.991000	0.79684	7.420000	0.80191	2.726000	0.93360	0.655000	0.94253	AGT	.	.		0.418	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		A	29890226	C	A	29890226	3	1	42	1	0	0	0	0	1	0	0	0	5600	565	20	3	2320	3	FAM59A	18	29890226	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	1239519	29890226	48187022	84	5065										
DTNA	1837	hgsc.bcm.edu	37	chr18	32438291	32438291	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	agacttcggctagagcatgaAcaagcttctcagcccacgcc	9	14	1	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr18:32438291A>G	ENST00000399113.3	+	15	1494	c.1494A>G	c.(1492-1494)gaA>gaG	p.E498E	DTNA_ENST00000556414.3_Silent_p.E150E|DTNA_ENST00000591182.1_Silent_p.E146E|DTNA_ENST00000399121.5_Silent_p.E438E|DTNA_ENST00000595022.1_Silent_p.E438E|DTNA_ENST00000269191.6_Silent_p.E498E|DTNA_ENST00000597674.1_Silent_p.E120E|DTNA_ENST00000348997.5_Silent_p.E495E|DTNA_ENST00000597599.1_Silent_p.E438E|DTNA_ENST00000399097.3_Silent_p.E146E|DTNA_ENST00000596745.1_Silent_p.E248E|DTNA_ENST00000283365.9_Silent_p.E441E|DTNA_ENST00000598334.1_Silent_p.E438E|DTNA_ENST00000598774.1_Silent_p.E441E|DTNA_ENST00000269192.7_Silent_p.E207E|DTNA_ENST00000269190.7_Silent_p.E499E|DTNA_ENST00000601125.1_Silent_p.E120E|DTNA_ENST00000598142.1_Silent_p.E441E|DTNA_ENST00000599844.1_Silent_p.E120E|DTNA_ENST00000444659.1_Silent_p.E498E			Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	498					neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						TAGAGCATGAACAAGCTTCTC	0.522																																					p.E498E		Atlas-SNP	.											.	DTNA	321	.	0			c.A1494G						.						66	64	65					18																	32438291		2203	4300	6503	SO:0001819	synonymous_variant	1837	exon15			GCATGAACAAGCT	U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769			3057	protein-coding gene	gene with protein product	"dystrophin-related protein 3"	601239				8081380, 15834686	Standard	NM_001390		Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399113.3:c.1494A>G	chr18.hg19:g.32438291A>G		113.0	0.0		74.0	42.0	NM_001390	A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	Silent	SNP	ENST00000399113.3	hg19	CCDS59311.1																																																																																			.	.		0.522	DTNA-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255422.2	NM_001390		G	32438291	A	G	32438291	2	3	42	1	0	0	0	0	0	0	0	1	4790	40	2	2		2	DTNA	18	32438291	Silent	SNP	A	TCGA-BC-A217-01A-11D-A152-10	2548065	32438291	45638957	85	5066										
MALT1	10892	hgsc.bcm.edu	37	chr18	56401614	56401614	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	attgtgtttggatatgccacGtaagaacatttgatgtttac	9	5	0	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr18:56401614G>A	ENST00000348428.3	+	12	1733		c.e12+1		MALT1_ENST00000345724.3_Splice_Site|RP11-126O1.4_ENST00000588835.1_RNA	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1						activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						GATATGCCACGTAAGAACATT	0.413			T	BIRC3	MALT																																.		Atlas-SNP	.		Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	.	MALT1	55	.	0			c.1475+1G>A						.						134	114	121					18																	56401614		2203	4300	6503	SO:0001630	splice_region_variant	10892	exon12			TGCCACGTAAGAA		CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6819	protein-coding gene	gene with protein product	"paracaspase"	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.1475+1G>A	chr18.hg19:g.56401614G>A		198.0	0.0		117.0	73.0	NM_006785	Q9NTB7|Q9ULX4	Splice_Site	SNP	ENST00000348428.3	hg19	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.852421	0.91355	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0095	0.92867	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MALT1	54552594	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.476000	0.97823	2.779000	0.95612	0.650000	0.86243	.	.	.		0.413	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2		Intron	A	56401614	G	A	56401614	5	1	42	1	0	0	0	0	0	0	1	0	9211	1159	40	1	1522	1	MALT1	18	56401614	Splice_Site	SNP	G	TCGA-BC-A217-01A-11D-A152-10	23963323	56401614	21675634	86	5067										
PIGN	23556	hgsc.bcm.edu	37	chr18	59768329	59768329	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	taatgttgcccagctaataaTttgattcatgagaggcagtc	9	7	1	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr18:59768329T>C	ENST00000357637.5	-	22	2471	c.2056A>G	c.(2056-2058)Att>Gtt	p.I686V	PIGN_ENST00000400334.3_Missense_Mutation_p.I686V	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	686					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				CAGCTAATAATTTGATTCATG	0.398																																					p.I686V		Atlas-SNP	.											.	PIGN	62	.	0			c.A2056G						.						94	88	90					18																	59768329		1895	4119	6014	SO:0001583	missense	23556	exon22			TAATAATTTGATT	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.2056A>G	chr18.hg19:g.59768329T>C	ENSP00000350263:p.Ile686Val	81.0	0.0		56.0	37.0	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Missense_Mutation	SNP	ENST00000357637.5	hg19	CCDS45879.1	.	.	.	.	.	.	.	.	.	.	T	7.451	0.642660	0.14451	.	.	ENSG00000197563	ENST00000357637;ENST00000400334	T;T	0.53640	0.61;0.61	5.57	3.2	0.36748	GPI ethanolamine phosphate transferase 1, C-terminal (1);	0.407110	0.26971	N	0.021573	T	0.29716	0.0742	L	0.28504	0.86	0.38908	D	0.957467	B;B	0.15473	0.013;0.013	B;B	0.20955	0.032;0.032	T	0.10847	-1.0612	10	0.05959	T	0.93	-8.9591	9.6172	0.39698	0.0:0.1423:0.0:0.8577	.	686;686	B2RCI8;O95427	.;PIGN_HUMAN	V	686	ENSP00000350263:I686V;ENSP00000383188:I686V	ENSP00000350263:I686V	I	-	1	0	PIGN	57919309	0.993000	0.37304	0.796000	0.32109	0.887000	0.51463	0.908000	0.28545	0.928000	0.37168	0.477000	0.44152	ATT	.	.		0.398	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		C	59768329	T	C	59768329	3	2	42	1	0	0	0	0	1	0	0	0	11902	1493	52	2	779	2	PIGN	18	59768329	Missense_Mutation	SNP	T	TCGA-BC-A217-01A-11D-A152-10	3366715	59768329	18308919	87	5068										
ZNF229	7772	hgsc.bcm.edu	37	chr19	44934591	44934591	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ttccttgcagatttactctaCagtcttggctcccaggtaat	7	11	2	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr19:44934591C>G	ENST00000588931.1	-	6	798	c.365G>C	c.(364-366)tGt>tCt	p.C122S	ZNF229_ENST00000591289.1_Intron|ZNF229_ENST00000291187.4_Missense_Mutation_p.C116S|CTC-512J12.4_ENST00000588655.1_RNA	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	122					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				ATTTACTCTACAGTCTTGGCT	0.443																																					p.C122S		Atlas-SNP	.											.	ZNF229	123	.	0			c.G365C						.						80	78	79					19																	44934591		1874	4089	5963	SO:0001583	missense	7772	exon6			ACTCTACAGTCTT	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"Zinc fingers, C2H2-type", "-"	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.365G>C	chr19.hg19:g.44934591C>G	ENSP00000466519:p.Cys122Ser	169.0	0.0		106.0	25.0	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	hg19	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	C	0.308	-0.969550	0.02232	.	.	ENSG00000167383	ENST00000291187	.	.	.	3.33	-6.65	0.01795	.	.	.	.	.	T	0.14141	0.0342	N	0.12746	0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08889	-1.0700	8	0.21014	T	0.42	.	3.3636	0.07196	0.0871:0.4048:0.2242:0.284	.	122	Q9UJW7	ZN229_HUMAN	S	122	.	ENSP00000291187:C122S	C	-	2	0	ZNF229	49626431	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.896000	0.00172	-3.665000	0.00124	-0.198000	0.12761	TGT	.	.		0.443	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		G	44934591	C	G	44934591	3	3	42	1	0	0	0	0	1	0	0	0	17797	478	17	4	2116	4	ZNF229	19	44934591	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10		44934591	14194392	88	5069										
SYT3	84258	hgsc.bcm.edu	37	chr19	51133064	51133064	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ggtctgaaactttttcttgcGgtcaggcagcaggtagatct	12	8	4	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr19:51133064G>T	ENST00000338916.4	-	3	1672	c.1039C>A	c.(1039-1041)Cgc>Agc	p.R347S	SYT3_ENST00000600079.1_Missense_Mutation_p.R347S|SYT3_ENST00000544769.1_Missense_Mutation_p.R347S|SYT3_ENST00000593901.1_Missense_Mutation_p.R347S	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	347	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		TTTTTCTTGCGGTCAGGCAGC	0.622																																					p.R347S		Atlas-SNP	.											.	SYT3	85	.	0			c.C1039A						.						61	61	61					19																	51133064		2203	4300	6503	SO:0001583	missense	84258	exon3			TCTTGCGGTCAGG	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.1039C>A	chr19.hg19:g.51133064G>T	ENSP00000340914:p.Arg347Ser	91.0	0.0		35.0	7.0	NM_032298	Q8N5Z1|Q8N640	Missense_Mutation	SNP	ENST00000338916.4	hg19	CCDS12798.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.783077	0.70222	.	.	ENSG00000213023	ENST00000338916;ENST00000544769	T;T	0.08546	3.08;3.08	4.67	4.67	0.58626	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	U	0.000011	T	0.19644	0.0472	L	0.38692	1.165	0.58432	D	0.999997	D	0.76494	0.999	D	0.66602	0.945	T	0.00978	-1.1493	10	0.87932	D	0	.	16.7093	0.85381	0.0:0.0:1.0:0.0	.	347	Q9BQG1	SYT3_HUMAN	S	347	ENSP00000340914:R347S;ENSP00000438883:R347S	ENSP00000340914:R347S	R	-	1	0	SYT3	55824876	1.000000	0.71417	0.998000	0.56505	0.783000	0.44284	2.641000	0.46587	2.301000	0.77427	0.655000	0.94253	CGC	.	.		0.622	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		T	51133064	G	T	51133064	3	4	42	1	0	0	0	0	1	0	0	0	15490	1116	39	1	757	1	SYT3	19	51133064	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	6198473	51133064	7995919	89	5070										
LILRA5	353514	hgsc.bcm.edu	37	chr19	54823336	54823336	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tattcctgggcctccagggtCccctgacaccggatggtcac	11	15	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr19:54823336C>A	ENST00000301219.3	-	4	326	c.207G>T	c.(205-207)ggG>ggT	p.G69G	LILRA5_ENST00000432233.3_Silent_p.G69G|LILRA5_ENST00000346508.3_Silent_p.G57G|LILRA5_ENST00000446712.3_Silent_p.G57G|AC008984.2_ENST00000507363.1_RNA	NM_021250.2	NP_067073.1	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5	69	Ig-like C2-type 1.				innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCTCCAGGGTCCCCTGACACC	0.587																																					p.G69G		Atlas-SNP	.											.	LILRA5	49	.	0			c.G207T						.						160	148	152					19																	54823336		2203	4300	6503	SO:0001819	synonymous_variant	353514	exon4			CAGGGTCCCCTGA	AF212842	CCDS12888.1, CCDS12889.1	19q13.4	2013-01-11	2005-05-13	2005-05-13	ENSG00000187116	ENSG00000187116		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16309	protein-coding gene	gene with protein product		606047		LILRB7		10941842	Standard	NM_181986		Approved	ILT11, LIR9, CD85, CD85f	uc002qfe.3	A6NI73	OTTHUMG00000065357	ENST00000301219.3:c.207G>T	chr19.hg19:g.54823336C>A		297.0	1.0		204.0	122.0	NM_181879	A6NHI3	Silent	SNP	ENST00000301219.3	hg19	CCDS12888.1																																																																																			.	.		0.587	LILRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140231.1	NM_181985		A	54823336	C	A	54823336	2	1	42	1	0	0	0	0	0	0	0	1	8797	842	30	3		3	LILRA5	19	54823336	Silent	SNP	C	TCGA-BC-A217-01A-11D-A152-10	3690272	54823336	4305647	90	5071										
LILRA1	11024	hgsc.bcm.edu	37	chr19	55111991	55111991	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tctcaggagcagctaacaccCtcagcccatcacaaaacaag	6	15	3	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr19:55111991C>A	ENST00000251372.3	+	9	1509	c.1327C>A	c.(1327-1329)Ctc>Atc	p.L443I	LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRA1_ENST00000453777.1_Missense_Mutation_p.L243I|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	443					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		AGCTAACACCCTCAGCCCATC	0.537																																					p.L443I		Atlas-SNP	.											.	LILRA1	105	.	0			c.C1327A						.						96	96	96					19																	55111991		2203	4300	6503	SO:0001583	missense	11024	exon9			AACACCCTCAGCC	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.1327C>A	chr19.hg19:g.55111991C>A	ENSP00000251372:p.Leu443Ile	103.0	0.0		62.0	15.0	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	hg19	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	C	2.191	-0.385190	0.04966	.	.	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.00531	6.76;6.89	1.75	-3.5	0.04710	.	.	.	.	.	T	0.00356	0.0011	L	0.43152	1.355	0.09310	N	1	B	0.31519	0.327	B	0.19148	0.024	T	0.34254	-0.9836	9	0.20046	T	0.44	.	7.8519	0.29459	0.2912:0.7088:0.0:0.0	.	443	O75019	LIRA1_HUMAN	I	443;243	ENSP00000251372:L443I;ENSP00000413715:L243I	ENSP00000251372:L443I	L	+	1	0	LILRA1	59803803	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.580000	0.02121	-0.674000	0.05253	0.195000	0.17529	CTC	.	.		0.537	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863		A	55111991	C	A	55111991	3	1	42	1	0	0	0	0	1	0	0	0	8793	681	24	3	1357	3	LILRA1	19	55111991	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10	288655	55111991	4016992	91	5072										
ERGIC3	51614	hgsc.bcm.edu	37	chr20	34130635	34130635	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	gatgtggaacacaacctgttCaagcaacgactagataaaga	9	8	1	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr20:34130635C>A	ENST00000348547.2	+	4	389	c.312C>A	c.(310-312)ttC>ttA	p.F104L	ERGIC3_ENST00000357394.4_Missense_Mutation_p.F104L|ERGIC3_ENST00000447986.1_Missense_Mutation_p.F104L|ERGIC3_ENST00000279052.6_Missense_Mutation_p.F104L	NM_015966.2	NP_057050.1	Q9Y282	ERGI3_HUMAN	ERGIC and golgi 3	104					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)	16	Lung NSC(9;0.00489)|all_lung(11;0.00729)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			ACAACCTGTTCAAGCAACGAC	0.547																																					p.F104L		Atlas-SNP	.											.	ERGIC3	41	.	0			c.C312A						.						147	112	124					20																	34130635		2203	4300	6503	SO:0001583	missense	51614	exon4			CCTGTTCAAGCAA	AF077030	CCDS13257.1, CCDS13258.1	20q11.22	2013-09-19	2006-01-19	2006-01-19	ENSG00000125991	ENSG00000125991			15927	protein-coding gene	gene with protein product			"serologically defined breast cancer antigen 84", "chromosome 20 open reading frame 47"	SDBCAG84, C20orf47		10810093	Standard	NM_015966		Approved	CGI-54, PRO0989, NY-BR-84, Erv46	uc002xcs.3	Q9Y282	OTTHUMG00000032346	ENST00000348547.2:c.312C>A	chr20.hg19:g.34130635C>A	ENSP00000341358:p.Phe104Leu	150.0	0.0		140.0	53.0	NM_015966	Q5JWS3|Q6ZWP7|Q9H276|Q9P1L3	Missense_Mutation	SNP	ENST00000348547.2	hg19	CCDS13257.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	15.41|15.41|15.41	2.824972|2.824972|2.824972	0.50739|0.50739|0.50739	.|.|.	.|.|.	ENSG00000125991|ENSG00000125991|ENSG00000125991	ENST00000348547;ENST00000357394;ENST00000447986;ENST00000279052;ENST00000411577|ENST00000413587|ENST00000416206	T;T;T;T;T|.|.	0.42513|.|.	0.98;0.99;0.97;0.98;0.97|.|.	5.25|5.25|5.25	1.22|1.22|1.22	0.21188|0.21188|0.21188	.|.|.	0.050723|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|.	0.53769|0.53769|.	0.1817|0.1817|.	L|L|L	0.45422|0.45422|0.45422	1.42|1.42|1.42	0.80722|0.80722|0.80722	D|D|D	1|1|1	B;B;B;B;B;B|.|.	0.09022|.|.	0.002;0.002;0.001;0.001;0.001;0.001|.|.	B;B;B;B;B;B|.|.	0.19148|.|.	0.008;0.024;0.003;0.006;0.008;0.003|.|.	T|T|.	0.41822|0.41822|.	-0.9487|-0.9487|.	10|5|.	0.17369|.|.	T|.|.	0.5|.|.	-18.1001|-18.1001|-18.1001	9.7158|9.7158|9.7158	0.40274|0.40274|0.40274	0.0:0.6255:0.0:0.3745|0.0:0.6255:0.0:0.3745|0.0:0.6255:0.0:0.3745	.|.|.	104;104;104;104;104;104|.|.	B4DV36;E9PFA8;Q9Y282;Q9Y282-3;Q9Y282-2;A2TJK5|.|.	.;.;ERGI3_HUMAN;.;.;.|.|.	L|K|X	104;104;104;104;98|106|103	ENSP00000341358:F104L;ENSP00000349970:F104L;ENSP00000392341:F104L;ENSP00000279052:F104L;ENSP00000414490:F98L|.|.	ENSP00000279052:F104L|.|.	F|Q|S	+|+|+	3|1|2	2|0|0	ERGIC3|ERGIC3|ERGIC3	33594049|33594049|33594049	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.902000|0.902000|0.902000	0.53008|0.53008|0.53008	0.774000|0.774000|0.774000	0.26675|0.26675|0.26675	0.098000|0.098000|0.098000	0.17522|0.17522|0.17522	-0.680000|-0.680000|-0.680000	0.03767|0.03767|0.03767	TTC|CAA|TCA	.	.		0.547	ERGIC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078880.2	NM_015966		A	34130635	C	A	34130635	3	1	42	1	0	0	0	0	1	0	0	0	5227	825	29	3	326	3	ERGIC3	20	34130635	Missense_Mutation	SNP	C	TCGA-BC-A217-01A-11D-A152-10		34130635	28894885	92	5073										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44686186	44686186	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	cgaggtcctcacagagcaccTggaccgggtgatgctggtcc	14	13	1	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr20:44686186T>G	ENST00000454036.2	+	26	3411	c.3362T>G	c.(3361-3363)cTg>cGg	p.L1121R	SLC12A5_ENST00000243964.3_Missense_Mutation_p.L1098R	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	1121					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	ACAGAGCACCTGGACCGGGTG	0.677																																					p.L1121R		Atlas-SNP	.											.	SLC12A5	181	.	0			c.T3362G						.						49	54	52					20																	44686186		2203	4300	6503	SO:0001583	missense	57468	exon26			AGCACCTGGACCG	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.3362T>G	chr20.hg19:g.44686186T>G	ENSP00000387694:p.Leu1121Arg	204.0	0.0		174.0	67.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	hg19	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.941138	0.73557	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	T;T	0.60672	0.17;0.17	4.24	4.24	0.50183	.	0.175663	0.38720	N	0.001585	T	0.80199	0.4579	M	0.92507	3.315	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.87578	0.947;0.998	D	0.85025	0.0914	10	0.87932	D	0	.	12.6986	0.57018	0.0:0.0:0.0:1.0	.	1121;1098	Q9H2X9;Q9H2X9-2	S12A5_HUMAN;.	R	1121;1098	ENSP00000387694:L1121R;ENSP00000243964:L1098R	ENSP00000243964:L1098R	L	+	2	0	SLC12A5	44119593	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.637000	0.67854	1.778000	0.52293	0.454000	0.30748	CTG	.	.		0.677	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			G	44686186	T	G	44686186	3	3	42	1	0	0	0	0	1	0	0	0	14401	1580	55	5	3520	5	SLC12A5	20	44686186	Missense_Mutation	SNP	T	TCGA-BC-A217-01A-11D-A152-10	10555551	44686186	18339334	93	5074										
CDH22	64405	hgsc.bcm.edu	37	chr20	44856179	44856179	+	Frame_Shift_Del	DEL	C	C	-													0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ccacggtgaagtggtgctcgCcgtccagcacgctgtacacc							TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr20:44856179delC	ENST00000372262.3	-	3	1038	c.638delG	c.(637-639)ggcfs	p.G213fs	CDH22_ENST00000537909.1_Frame_Shift_Del_p.G213fs	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	213	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				GTGGTGCTCGCCGTCCAGCAC	0.741																																					p.G213fs		Atlas-Indel,Pindel	.											.	CDH22	112	.	0			c.639delC						.						27	23	24					20																	44856179		2203	4299	6502	SO:0001589	frameshift_variant	64405	exon4			.	AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"Cadherins / Major cadherins"	13251	protein-coding gene	gene with protein product		609920	"cadherin-like 22"	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.638delG	chr20.hg19:g.44856179delC	ENSP00000361336:p.Gly213fs	62.0	0.0		54.0	30.0	NM_021248	B9EGK7|O43205	Frame_Shift_Del	DEL	ENST00000372262.3	hg19	CCDS13395.1																																																																																			.	.		0.741	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		-	44856179	C	-	44856179	7	5	42	1	0	1	0	1	0	0	0	0	3109	739	26	0	1884	0	CDH22	20	44856179	Frame_Shift_Del	DEL	C	TCGA-BC-A217-01A-11D-A152-10	169993	44856179	18169341	94	5075										
BACE2	25825	hgsc.bcm.edu	37	chr21	42622762	42622762	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	acaccttggtcttacttcccTaaaatctccatctacctgag	4	14	3	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr21:42622762T>A	ENST00000330333.6	+	7	1531	c.1068T>A	c.(1066-1068)ccT>ccA	p.P356P	BACE2_ENST00000466122.1_3'UTR|BACE2_ENST00000328735.6_Silent_p.P356P|BACE2_ENST00000347667.5_Intron	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2	356					membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				CTTACTTCCCTAAAATCTCCA	0.458																																					p.P356P		Atlas-SNP	.											.	BACE2	45	.	0			c.T1068A						.						125	107	113					21																	42622762		2203	4300	6503	SO:0001819	synonymous_variant	25825	exon7			CTTCCCTAAAATC	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.1068T>A	chr21.hg19:g.42622762T>A		218.0	0.0		209.0	96.0	NM_138992	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Silent	SNP	ENST00000330333.6	hg19	CCDS13668.1																																																																																			.	.		0.458	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			A	42622762	T	A	42622762	2	1	42	1	0	0	0	0	0	0	0	1	1282	1509	53	4		4	BACE2	21	42622762	Silent	SNP	T	TCGA-BC-A217-01A-11D-A152-10		42622762	5507133	95	5076										
CECR1	51816	hgsc.bcm.edu	37	chr22	17662466	17662466	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ctctccaacagggtactgtaCctgcaggaagaggaggagcc	13	11	1	1			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr22:17662466C>A	ENST00000399839.1	-	10	1713	c.1443G>T	c.(1441-1443)aaG>aaT	p.K481N	CECR1_ENST00000330232.4_Splice_Site_p.K240N|CECR1_ENST00000449907.2_Splice_Site_p.K439N|CECR1_ENST00000262607.3_Splice_Site_p.K481N|CECR1_ENST00000399837.2_Splice_Site_p.K481N	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	481					adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				GGGTACTGTACCTGCAGGAAG	0.532																																					p.K481N		Atlas-SNP	.											.	CECR1	77	.	0			c.G1443T						.						129	131	130					22																	17662466		2203	4300	6503	SO:0001630	splice_region_variant	51816	exon9			ACTGTACCTGCAG	AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.1443-1G>T	chr22.hg19:g.17662466C>A		164.0	0.0		121.0	62.0	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Missense_Mutation	SNP	ENST00000399839.1	hg19	CCDS13742.1	.	.	.	.	.	.	.	.	.	.	C	6.453	0.451754	0.12223	.	.	ENSG00000093072	ENST00000399839;ENST00000330232;ENST00000262607;ENST00000449907;ENST00000399837	D;D;D;D;D	0.95622	-3.76;-3.76;-3.76;-3.76;-3.76	3.62	0.0265	0.14150	Adenosine/AMP deaminase (1);	0.338897	0.33670	N	0.004670	D	0.92051	0.7481	L	0.61387	1.9	0.25253	N	0.989652	B;B	0.30605	0.287;0.01	B;B	0.28991	0.097;0.026	D	0.84961	0.0877	10	0.48119	T	0.1	.	8.2936	0.31971	0.0:0.5987:0.0:0.4013	.	481;240	Q9NZK5;Q9NZK5-2	CECR1_HUMAN;.	N	481;240;481;439;481	ENSP00000382733:K481N;ENSP00000332871:K240N;ENSP00000262607:K481N;ENSP00000406443:K439N;ENSP00000382731:K481N	ENSP00000262607:K481N	K	-	3	2	CECR1	16042466	1.000000	0.71417	0.194000	0.23346	0.038000	0.13279	1.327000	0.33746	0.061000	0.16311	0.655000	0.94253	AAG	.	.		0.532	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1		Missense_Mutation	A	17662466	C	A	17662466	5	1	42	1	0	0	0	0	0	0	1	0	3207	521	18	3	96	3	CECR1	22	17662466	Splice_Site	SNP	C	TCGA-BC-A217-01A-11D-A152-10		17662466	33642100	96	5077										
PLA2G3	50487	hgsc.bcm.edu	37	chr22	31533849	31533849	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ccccttccgaaggtgctgctTctgtcgaggcttgggagggg	16	11	1	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr22:31533849T>A	ENST00000215885.3	-	4	1165	c.913A>T	c.(913-915)Aag>Tag	p.K305*		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	305					acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						AGGTGCTGCTTCTGTCGAGGC	0.652																																					p.K305X		Atlas-SNP	.											.	PLA2G3	85	.	0			c.A913T						.						82	94	90					22																	31533849		2203	4300	6503	SO:0001587	stop_gained	50487	exon4			GCTGCTTCTGTCG	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.913A>T	chr22.hg19:g.31533849T>A	ENSP00000215885:p.Lys305*	304.0	0.0		189.0	101.0	NM_015715	O95768	Nonsense_Mutation	SNP	ENST00000215885.3	hg19	CCDS13889.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.612473	0.87258	.	.	ENSG00000100078	ENST00000215885	.	.	.	3.68	1.48	0.22813	.	0.904173	0.09678	N	0.770218	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.9249	4.5179	0.11945	0.0:0.1107:0.3999:0.4894	.	.	.	.	X	305	.	ENSP00000215885:K305X	K	-	1	0	PLA2G3	29863849	0.001000	0.12720	0.006000	0.13384	0.023000	0.10783	0.169000	0.16641	0.257000	0.21650	0.533000	0.62120	AAG	.	.		0.652	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715		A	31533849	T	A	31533849	4	1	42	1	0	0	0	0	0	1	0	0	12009	1792	62	4	632	4	PLA2G3	22	31533849	Nonsense_Mutation	SNP	T	TCGA-BC-A217-01A-11D-A152-10	13871383	31533849	19770717	97	5078										
TOM1	10043	hgsc.bcm.edu	37	chr22	35717981	35717981	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	tgccctccgagcagtaaagaAgagaatcgtggggaataaga	13	7	0	3			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chr22:35717981A>G	ENST00000449058.2	+	3	292	c.167A>G	c.(166-168)aAg>aGg	p.K56R	TOM1_ENST00000447733.1_Missense_Mutation_p.K23R|TOM1_ENST00000425375.1_Missense_Mutation_p.K56R|TOM1_ENST00000436462.2_Intron|TOM1_ENST00000382034.5_5'UTR|TOM1_ENST00000411850.1_Missense_Mutation_p.K56R	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	56	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	clathrin binding (GO:0030276)			NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						GCAGTAAAGAAGAGAATCGTG	0.527																																					p.K56R		Atlas-SNP	.											.	TOM1	43	.	0			c.A167G						.						128	113	118					22																	35717981		2203	4300	6503	SO:0001583	missense	10043	exon3			TAAAGAAGAGAAT	AJ006973	CCDS13913.1, CCDS46696.1, CCDS46697.1, CCDS46698.1	22q13.1	2011-01-31	2001-11-28		ENSG00000100284	ENSG00000100284			11982	protein-coding gene	gene with protein product		604700	"target of myb1 (chicken) homolog"			10329004, 15047686	Standard	NM_005488		Approved		uc003anp.3	O60784	OTTHUMG00000150958	ENST00000449058.2:c.167A>G	chr22.hg19:g.35717981A>G	ENSP00000394466:p.Lys56Arg	104.0	0.0		71.0	24.0	NM_001135732	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Missense_Mutation	SNP	ENST00000449058.2	hg19	CCDS13913.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.772105	0.90108	.	.	ENSG00000100284	ENST00000447733;ENST00000456128;ENST00000449058;ENST00000411850;ENST00000425375;ENST00000450839;ENST00000451197;ENST00000443206	T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6	5.03	5.03	0.67393	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.046850	0.85682	D	0.000000	T	0.34424	0.0897	L	0.35341	1.055	0.80722	D	1	P;P;P;D	0.56035	0.834;0.888;0.823;0.974	B;P;B;P	0.51516	0.188;0.624;0.298;0.672	T	0.06162	-1.0842	10	0.42905	T	0.14	-30.0149	14.7793	0.69754	1.0:0.0:0.0:0.0	.	56;56;56;56	O60784-3;B4DKQ5;O60784-2;O60784	.;.;.;TOM1_HUMAN	R	23;56;56;56;56;56;56;23	ENSP00000398876:K23R;ENSP00000393714:K56R;ENSP00000394466:K56R;ENSP00000413697:K56R;ENSP00000394924:K56R;ENSP00000389789:K23R	ENSP00000338422:K56R	K	+	2	0	TOM1	34047981	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.389000	0.79806	1.895000	0.54865	0.459000	0.35465	AAG	.	.		0.527	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488		G	35717981	A	G	35717981	3	3	42	1	0	0	0	0	1	0	0	0	16366	72	3	2	177	2	TOM1	22	35717981	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10	4184132	35717981	15586585	98	5079										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	105011223	105011223	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	agggatccaaaagcagcaaaTtaaattctaagttttggaag	9	5	1	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chrX:105011223T>C	ENST00000372582.1	+	11	2386	c.1630T>C	c.(1630-1632)Tta>Cta	p.L544L	IL1RAPL2_ENST00000344799.4_Silent_p.L544L	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	544	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AAGCAGCAAATTAAATTCTAA	0.408																																					p.L544L		Atlas-SNP	.											.	IL1RAPL2	105	.	0			c.T1630C						.						102	110	107					X																	105011223		2203	4300	6503	SO:0001819	synonymous_variant	26280	exon11			AGCAAATTAAATT	AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1630T>C	chrX.hg19:g.105011223T>C		246.0	0.0		210.0	109.0	NM_017416	Q2M3U3|Q9NZN0	Silent	SNP	ENST00000372582.1	hg19	CCDS14517.1																																																																																			.	.		0.408	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		C	105011223	T	C	105011223	2	2	42	1	0	0	0	0	0	0	0	1	7671	1490	52	2		2	IL1RAPL2	23	105011223	Silent	SNP	T	TCGA-BC-A217-01A-11D-A152-10		105011223	50259337	99	5080										
CUL4B	8450	hgsc.bcm.edu	37	chrX	119669737	119669737	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	ctagggttgactgccactgaAgtttcctgccactatgtttg	10	10	0	2			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chrX:119669737A>C	ENST00000404115.3	-	18	2563	c.2162T>G	c.(2161-2163)cTt>cGt	p.L721R	CUL4B_ENST00000371322.5_Missense_Mutation_p.L703R|CUL4B_ENST00000336592.6_Missense_Mutation_p.L708R	NM_003588.3	NP_003579.3	Q13620	CUL4B_HUMAN	cullin 4B	721					cell cycle (GO:0007049)|histone H2A monoubiquitination (GO:0035518)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of protein catabolic process (GO:0045732)|ubiquitin-dependent protein catabolic process (GO:0006511)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CTGCCACTGAAGTTTCCTGCC	0.338																																					p.L721R		Atlas-SNP	.											.	CUL4B	181	.	0			c.T2162G						.						136	139	138					X																	119669737		2203	4300	6503	SO:0001583	missense	8450	exon18			CACTGAAGTTTCC	U58091	CCDS35379.1, CCDS43987.1	Xq23	2011-05-24			ENSG00000158290	ENSG00000158290			2555	protein-coding gene	gene with protein product		300304				8681378	Standard	NM_003588		Approved		uc004esw.3	Q13620	OTTHUMG00000022302	ENST00000404115.3:c.2162T>G	chrX.hg19:g.119669737A>C	ENSP00000384109:p.Leu721Arg	574.0	0.0		573.0	136.0	NM_003588	B1APK5|B3KVX4|B7Z5K8|Q6PIE4|Q6UP07|Q7Z673|Q9BY37|Q9UEB7|Q9UED7	Missense_Mutation	SNP	ENST00000404115.3	hg19	CCDS35379.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.003165	0.74932	.	.	ENSG00000158290	ENST00000371322;ENST00000336592;ENST00000404115	D;D;D	0.90197	-2.63;-2.63;-2.63	5.79	4.61	0.57282	Cullin, N-terminal (1);Cullin homology (3);	0.000000	0.85682	D	0.000000	D	0.97040	0.9033	H	0.98466	4.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.96750	0.9553	9	.	.	.	-5.702	11.4747	0.50291	0.8516:0.1484:0.0:0.0	.	525;721;703	Q13620-3;Q13620;Q13620-1	.;CUL4B_HUMAN;.	R	703;708;721	ENSP00000360373:L703R;ENSP00000338919:L708R;ENSP00000384109:L721R	.	L	-	2	0	CUL4B	119553765	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.168000	0.94781	0.795000	0.33922	0.472000	0.43445	CTT	.	.		0.338	CUL4B-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058103.1	NM_003588		C	119669737	A	C	119669737	3	2	42	1	0	0	0	0	1	0	0	0	4060	72	3	5	599	5	CUL4B	23	119669737	Missense_Mutation	SNP	A	TCGA-BC-A217-01A-11D-A152-10	14658514	119669737	35600823	100	5081										
IDH3G	3421	hgsc.bcm.edu	37	chrX	153055245	153055245	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.629565376187	3.60732848232848	0.558277027027027	0.0968421052631578	0.617038875103394	0	atcagcattggaactcacgtGcacctcttcaaagtccactg	7	13	4	0			TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	g.chrX:153055245G>A	ENST00000217901.5	-	5	464	c.268C>T	c.(268-270)Cac>Tac	p.H90Y	IDH3G_ENST00000497043.1_5'UTR|IDH3G_ENST00000427365.2_Missense_Mutation_p.H32Y|IDH3G_ENST00000370092.3_Missense_Mutation_p.H90Y|IDH3G_ENST00000370093.1_Missense_Mutation_p.H90Y	NM_004135.3	NP_004126.1	P51553	IDH3G_HUMAN	isocitrate dehydrogenase 3 (NAD+) gamma	90					carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)	17	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					GAACTCACGTGCACCTCTTCA	0.647																																					p.H90Y		Atlas-SNP	.											.	IDH3G	36	.	0			c.C268T						.						86	59	68					X																	153055245		2202	4298	6500	SO:0001583	missense	3421	exon5			TCACGTGCACCTC		CCDS14730.1, CCDS44019.1	Xq28	2008-02-05			ENSG00000067829	ENSG00000067829	1.1.1.41		5386	protein-coding gene	gene with protein product		300089				9286695	Standard	NM_004135		Approved		uc004fip.4	P51553	OTTHUMG00000024219	ENST00000217901.5:c.268C>T	chrX.hg19:g.153055245G>A	ENSP00000217901:p.His90Tyr	66.0	0.0		38.0	12.0	NM_004135	E9PDD5|Q9BUU5	Missense_Mutation	SNP	ENST00000217901.5	hg19	CCDS14730.1	.	.	.	.	.	.	.	.	.	.	G	17.42	3.384208	0.61845	.	.	ENSG00000067829	ENST00000370092;ENST00000217901;ENST00000370093;ENST00000427365;ENST00000444450;ENST00000444338	T;T;T;T;T;T	0.66280	0.64;0.64;0.64;0.64;0.64;-0.2	5.34	5.34	0.76211	Isopropylmalate dehydrogenase-like domain (2);	0.281987	0.39020	N	0.001489	T	0.38825	0.1055	N	0.12569	0.235	0.26986	N	0.965255	P;B	0.34800	0.469;0.137	B;B	0.27380	0.079;0.035	T	0.25882	-1.0119	10	0.21014	T	0.42	.	12.0109	0.53286	0.0:0.0:0.8271:0.1729	.	90;90	E9PDD5;P51553	.;IDH3G_HUMAN	Y	90;90;90;32;67;1	ENSP00000359110:H90Y;ENSP00000217901:H90Y;ENSP00000359111:H90Y;ENSP00000408529:H32Y;ENSP00000401862:H67Y;ENSP00000402747:H1Y	ENSP00000217901:H90Y	H	-	1	0	IDH3G	152708439	0.965000	0.33210	1.000000	0.80357	0.955000	0.61496	3.048000	0.49862	2.238000	0.73509	0.529000	0.55759	CAC	.	.		0.647	IDH3G-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061084.27			A	153055245	G	A	153055245	3	1	42	1	0	0	0	0	1	0	0	0	7507	1319	46	3	1012	3	IDH3G	23	153055245	Missense_Mutation	SNP	G	TCGA-BC-A217-01A-11D-A152-10	33385508	153055245	2215315	101	5082										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7151365	7151365	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttttattcttctgtttcaggAaattgcagcttatttaataa	5	5	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:7151365A>G	ENST00000303635.7	+	4	443	c.236A>G	c.(235-237)gAa>gGa	p.E79G	CAMTA1_ENST00000439411.2_Splice_Site_p.E79G	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	79					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CTGTTTCAGGAAATTGCAGCT	0.363			T	WWTR1	epitheliod hemangioendothelioma																																p.E79G		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.A236G						.						100	96	97					1																	7151365		2203	4300	6503	SO:0001630	splice_region_variant	23261	exon4			TTCAGGAAATTGC	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.235-1A>G	chr1.hg19:g.7151365A>G		78.0	0.0		96.0	4.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	hg19	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.220641	0.79464	.	.	ENSG00000171735	ENST00000303635;ENST00000439411	T;T	0.38560	1.13;1.14	5.35	5.35	0.76521	CG-1 (2);	0.092388	0.42172	D	0.000755	T	0.69024	0.3065	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.75587	-0.3266	10	0.87932	D	0	-12.2974	14.812	0.70003	1.0:0.0:0.0:0.0	.	79	Q9Y6Y1	CMTA1_HUMAN	G	79	ENSP00000306522:E79G;ENSP00000402561:E79G	ENSP00000306522:E79G	E	+	2	0	CAMTA1	7073952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.239000	0.89811	2.149000	0.67028	0.533000	0.62120	GAA	.	.		0.363	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	Missense_Mutation	G	7151365	A	G	7151365	5	3	43	1	0	0	0	0	0	0	1	0	2615	260	9	2	250	2	CAMTA1	1	7151365	Splice_Site	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10		7151365	242099256	1	5083										
PER3	8863	hgsc.bcm.edu	37	chr1	7887204	7887204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctacttccaagcagacgcggTcggccggctgcaggaaaggg	15	12	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:7887204T>C	ENST00000361923.2	+	17	2366	c.2191T>C	c.(2191-2193)Tcg>Ccg	p.S731P	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.S739P	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	731	CSNK1E binding domain. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGACGCGGTCGGCCGGCTG	0.552																																					p.S731P		Atlas-SNP	.											.	PER3	95	.	0			c.T2191C						.						14	18	17					1																	7887204		2081	4140	6221	SO:0001583	missense	8863	exon17			ACGCGGTCGGCCG	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2191T>C	chr1.hg19:g.7887204T>C	ENSP00000355031:p.Ser731Pro	60.0	0.0		95.0	4.0	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	hg19	CCDS89.1	.	.	.	.	.	.	.	.	.	.	T	10.43	1.348940	0.24426	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.10960	2.84;2.82	4.52	2.22	0.28083	.	71.754500	0.00166	N	0.000000	T	0.22859	0.0552	L	0.49126	1.545	0.09310	N	1	D;B;B;D	0.71674	0.998;0.152;0.236;0.998	P;B;B;P	0.59115	0.852;0.032;0.07;0.852	T	0.07102	-1.0790	10	0.30854	T	0.27	.	5.9575	0.19281	0.0:0.3271:0.0:0.6729	.	731;739;739;731	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	P	739;731	ENSP00000366755:S739P;ENSP00000355031:S731P	ENSP00000355031:S731P	S	+	1	0	PER3	7809791	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.421000	0.07053	0.284000	0.22305	0.459000	0.35465	TCG	.	.		0.552	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		C	7887204	T	C	7887204	3	2	43	1	0	0	0	0	1	0	0	0	11740	1667	58	2	2257	2	PER3	1	7887204	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	735839	7887204	241363417	2	5084										
SPEN	23013	hgsc.bcm.edu	37	chr1	16174601	16174601	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catctctgggtgggcaacttAcccgagaacgtgcgggaaga	14	10	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:16174601A>G	ENST00000375759.3	+	1	243	c.39A>G	c.(37-39)ttA>ttG	p.L13L	RP11-169K16.9_ENST00000317122.1_RNA	NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	13	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TGGGCAACTTACCCGAGAACG	0.692																																					p.L13L		Atlas-SNP	.											.	SPEN	374	.	0			c.A39G						.						35	32	33					1																	16174601		2195	4291	6486	SO:0001819	synonymous_variant	23013	exon1			CAACTTACCCGAG		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.39A>G	chr1.hg19:g.16174601A>G		100.0	0.0		97.0	4.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	hg19	CCDS164.1																																																																																			.	.		0.692	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16174601	A	G	16174601	2	3	43	1	0	0	0	0	0	0	0	1	15053	388	14	2		2	SPEN	1	16174601	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	8287397	16174601	233076020	3	5085										
SERINC2	347735	hgsc.bcm.edu	37	chr1	31905905	31905906	+	Missense_Mutation	DNP	GT	GT	CA													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccacacagcagcagcagcagGtggcagcctgtgagggccgg					rs375057852		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:31905905_31905906GT>CA	ENST00000373709.3	+	9	1255_1256	c.1105_1106GT>CA	c.(1105-1107)GTg>CAg	p.V369Q	SERINC2_ENST00000491976.1_3'UTR|SERINC2_ENST00000536384.1_Missense_Mutation_p.V373Q|SERINC2_ENST00000536859.1_Missense_Mutation_p.V373Q|SERINC2_ENST00000373710.1_Missense_Mutation_p.V378Q	NM_178865.4	NP_849196.2	Q96SA4	SERC2_HUMAN	serine incorporator 2	369					phosphatidylserine metabolic process (GO:0006658)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	L-serine transmembrane transporter activity (GO:0015194)			cervix(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	12		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151)		GCAGCAGCAGGTGGCAGCCTGT	0.634																																					p.V378L|p.V378E		Atlas-SNP	.											.	SERINC2	44	.	0			c.G1132C|c.T1133A						.																																			SO:0001583	missense	347735	exon10			CAGCAGGTGGCAG|AGCAGGTGGCAGC	AY094595	CCDS30662.1, CCDS55583.1, CCDS55584.1, CCDS55585.1	1p35.1	2008-02-05	2005-11-01	2005-11-01	ENSG00000168528	ENSG00000168528			23231	protein-coding gene	gene with protein product		614549	"tumor differentially expressed 2-like"	TDE2L		12949800	Standard	NM_178865		Approved	FKSG84, PRO0899, TDE2	uc010ogh.2	Q96SA4	OTTHUMG00000003796	Exception_encountered	chr1.hg19:g.31905905_31905906delinsCA	ENSP00000362813:p.Val369Gln	82.0	0.0		117.0	7.0|6.0	NM_001199038	A0AVB4|B4DJK5|B7Z567|B7ZAP2|E7EUZ9|Q86Y23	Missense_Mutation	SNP	ENST00000373709.3	hg19	CCDS30662.1																																																																																			.	.		0.634	SERINC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010680.1	NM_018565		CA	31905906	GT	CA	31905905	3	2	43	1	0	0	0	0	1	0	0	0	14095	1261	44	4	1139	4	SERINC2	1	31905905	Missense_Mutation	DNP	GT	TCGA-BC-A3KF-01A-11D-A20W-10	15731304	31905905	217344716	4	5086										
TRIM62	55223	hgsc.bcm.edu	37	chr1	33646996	33646996	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cctggtagatgctcaggcagAtggagcacagcagctcgtcc	13	12	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:33646996A>G	ENST00000291416.5	-	1	271	c.38T>C	c.(37-39)aTc>aCc	p.I13T	TRIM62_ENST00000485148.1_5'UTR	NM_018207.2	NP_060677.2	Q9BVG3	TRI62_HUMAN	tripartite motif containing 62	13					innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)				GCTCAGGCAGATGGAGCACAG	0.711																																					p.I13T		Atlas-SNP	.											.	TRIM62	26	.	0			c.T38C						.						7	9	9					1																	33646996		2075	4114	6189	SO:0001583	missense	55223	exon1			AGGCAGATGGAGC	BC007999	CCDS376.1	1p35.1	2013-10-11	2011-01-25		ENSG00000116525	ENSG00000116525		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	25574	protein-coding gene	gene with protein product	"ductal epithelium-associated RING Chromosome 1"		"tripartite motif-containing 62"			19536326	Standard	NM_018207		Approved	FLJ10759, DEAR1	uc001bxb.3	Q9BVG3	OTTHUMG00000004132	ENST00000291416.5:c.38T>C	chr1.hg19:g.33646996A>G	ENSP00000291416:p.Ile13Thr	24.0	0.0		43.0	4.0	NM_018207	B3KVH5|B4DTE4|D3DPR1|Q9NVG0	Missense_Mutation	SNP	ENST00000291416.5	hg19	CCDS376.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.197937	0.58126	.	.	ENSG00000116525	ENST00000291416;ENST00000373432;ENST00000373430	D	0.89270	-2.49	4.74	4.74	0.60224	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.96100	0.8729	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96914	0.9669	10	0.87932	D	0	.	12.1608	0.54103	1.0:0.0:0.0:0.0	.	13	Q9BVG3	TRI62_HUMAN	T	13	ENSP00000291416:I13T	ENSP00000291416:I13T	I	-	2	0	TRIM62	33419583	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	9.080000	0.94040	1.740000	0.51718	0.402000	0.26972	ATC	.	.		0.711	TRIM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011890.1	NM_018207		G	33646996	A	G	33646996	3	3	43	1	0	0	0	0	1	0	0	0	16552	333	12	2	1409	2	TRIM62	1	33646996	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1741091	33646996	215603625	5	5087										
GRIK3	2899	hgsc.bcm.edu	37	chr1	37282833	37282833	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcgtgaagaaccaccagatgCcaccaatgatgcgtgtggac	12	11	0	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:37282833C>A	ENST00000373091.3	-	13	1935	c.1919G>T	c.(1918-1920)gGc>gTc	p.G640V	GRIK3_ENST00000373093.4_Missense_Mutation_p.G640V	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	640					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CCACCAGATGCCACCAATGAT	0.552																																					p.G640V		Atlas-SNP	.											.	GRIK3	195	.	0			c.G1919T						.						164	143	150					1																	37282833		2203	4300	6503	SO:0001583	missense	2899	exon13			CAGATGCCACCAA	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.1919G>T	chr1.hg19:g.37282833C>A	ENSP00000362183:p.Gly640Val	127.0	0.0		188.0	72.0	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	hg19	CCDS416.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.029633	0.93518	.	.	ENSG00000163873	ENST00000373091;ENST00000373093	D;D	0.96913	-4.17;-4.17	5.74	5.74	0.90152	Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	D	0.98143	0.9387	M	0.78285	2.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98686	1.0694	10	0.87932	D	0	.	19.9326	0.97124	0.0:1.0:0.0:0.0	.	640;640	A9Z1Z8;Q13003	.;GRIK3_HUMAN	V	640	ENSP00000362183:G640V;ENSP00000362185:G640V	ENSP00000362183:G640V	G	-	2	0	GRIK3	37055420	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.818000	0.86416	2.720000	0.93068	0.650000	0.86243	GGC	.	.		0.552	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		A	37282833	C	A	37282833	3	1	43	1	0	0	0	0	1	0	0	0	6784	739	26	3	856	3	GRIK3	1	37282833	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	3635837	37282833	211967788	6	5088										
NRD1	4898	hgsc.bcm.edu	37	chr1	52306057	52306057	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atttcagctccagaatcttcAtcatcatcttcttcttcttc	2	13	9	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:52306057A>T	ENST00000354831.7	-	2	660	c.471T>A	c.(469-471)gaT>gaA	p.D157E	NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000352171.7_Missense_Mutation_p.D157E|NRD1_ENST00000544028.1_Missense_Mutation_p.D25E|NRD1_ENST00000539524.1_Missense_Mutation_p.D25E	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						CAGAAtcttcatcatcatctt	0.373																																					p.D157E		Atlas-SNP	.											.	NRD1	89	.	0			c.T471A						.						195	158	171					1																	52306057		2203	4300	6503	SO:0001583	missense	4898	exon2			ATCTTCATCATCA	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.471T>A	chr1.hg19:g.52306057A>T	ENSP00000346890:p.Asp157Glu	220.0	0.0		263.0	11.0	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	A	8.848	0.943971	0.18281	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.52754	1.49;3.25;0.65;1.57	5.22	2.89	0.33648	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.397003	0.22061	N	0.065179	T	0.22475	0.0542	.	.	.	0.26633	N	0.972435	B;B;B	0.13145	0.007;0.004;0.004	B;B;B	0.12156	0.007;0.003;0.003	T	0.25813	-1.0121	9	0.02654	T	1	-2.3898	11.1792	0.48618	0.9192:0.0:0.0808:0.0	.	157;156;157	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	E	157;157;25;157;25	ENSP00000262679:D157E;ENSP00000346890:D157E;ENSP00000444416:D25E;ENSP00000442262:D25E	ENSP00000262679:D157E	D	-	3	2	NRD1	52078645	0.996000	0.38824	1.000000	0.80357	0.777000	0.43975	1.218000	0.32467	0.313000	0.23062	-1.236000	0.01555	GAT	.	.		0.373	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		T	52306057	A	T	52306057	3	4	43	1	0	0	0	0	1	0	0	0	10654	214	8	4	3316	4	NRD1	1	52306057	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	15023224	52306057	196944564	7	5089										
NRD1	4898	hgsc.bcm.edu	37	chr1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catcatcttcttcttcttccTccacctcctcttcttcttca	0	18	9	0	rs62648104		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:52306079T>A	ENST00000354831.7	-	2	638	c.449A>T	c.(448-450)gAg>gTg	p.E150V	NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000352171.7_Missense_Mutation_p.E150V|NRD1_ENST00000544028.1_Missense_Mutation_p.E18V|NRD1_ENST00000539524.1_Missense_Mutation_p.E18V	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).|Poly-Glu.				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcttcttcctccacctcctc	0.378																																					p.E150V		Atlas-SNP	.											.	NRD1	89	.	0			c.A449T						.						163	138	146					1																	52306079		2203	4300	6503	SO:0001583	missense	4898	exon2			TCTTCCTCCACCT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.449A>T	chr1.hg19:g.52306079T>A	ENSP00000346890:p.Glu150Val	164.0	0.0		177.0	14.0	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	3.056	-0.194350	0.06259	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.38240	1.31;3.15;1.15;1.22	5.25	2.92	0.33932	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.525899	0.19688	N	0.108344	T	0.18341	0.0440	N	0.14661	0.345	0.09310	N	1	B;B;B	0.23650	0.062;0.089;0.01	B;B;B	0.17098	0.017;0.007;0.007	T	0.14755	-1.0461	10	0.38643	T	0.18	-0.0317	5.1939	0.15225	0.0:0.1704:0.2022:0.6274	rs62648104	150;150;150	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	V	150;150;18;150;18	ENSP00000262679:E150V;ENSP00000346890:E150V;ENSP00000444416:E18V;ENSP00000442262:E18V	ENSP00000262679:E150V	E	-	2	0	NRD1	52078667	0.129000	0.22400	0.012000	0.15200	0.145000	0.21501	0.870000	0.28010	0.317000	0.23160	0.454000	0.30748	GAG	.	T|0.024;A|0.976		0.378	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		A	52306079	T	A	52306079	3	1	43	1	0	0	0	0	1	0	0	0	10654	1551	54	4	3338	4	NRD1	1	52306079	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	22	52306079	196944542	8	5090										
DAB1	1600	hgsc.bcm.edu	37	chr1	57480890	57480890	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gctggcaaaggcataacagtTtgtgtgggcatgaaggcggc	16	7	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:57480890T>C	ENST00000371231.1	-	13	1243	c.1209A>G	c.(1207-1209)caA>caG	p.Q403Q	DAB1_ENST00000485760.1_5'UTR|DAB1_ENST00000371236.2_Silent_p.Q370Q|DAB1_ENST00000439789.2_Silent_p.Q284Q|DAB1_ENST00000414851.2_Silent_p.Q352Q|DAB1_ENST00000420954.2_Silent_p.Q368Q|DAB1_ENST00000371234.4_Silent_p.Q370Q			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	403					adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						GCATAACAGTTTGTGTGGGCA	0.637																																					p.Q370Q		Atlas-SNP	.											.	DAB1	129	.	0			c.A1110G						.						86	74	78					1																	57480890		2203	4300	6503	SO:0001819	synonymous_variant	1600	exon14			AACAGTTTGTGTG	BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406			2661	protein-coding gene	gene with protein product		603448	"disabled (Drosophila) homolog 1", "disabled homolog 1 (Drosophila)", "Dab, reelin signal transducer, homolog 1 (Drosophila)", "Dab reelin signal transducer 1"			9790777	Standard	NM_021080		Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000371231.1:c.1209A>G	chr1.hg19:g.57480890T>C		41.0	0.0		64.0	5.0	NM_021080	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Silent	SNP	ENST00000371231.1	hg19																																																																																				.	.		0.637	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1	NM_021080		C	57480890	T	C	57480890	2	2	43	1	0	0	0	0	0	0	0	1	4219	1838	64	2		2	DAB1	1	57480890	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5174811	57480890	191769731	9	5091										
INADL	10207	hgsc.bcm.edu	37	chr1	62593700	62593700	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggaagaggaagtcccttaggAgatatccccgtatttattgc	11	8	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:62593700A>G	ENST00000371158.2	+	40	5214	c.5100A>G	c.(5098-5100)ggA>ggG	p.G1700G	INADL_ENST00000472512.1_3'UTR	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1700	PDZ 10. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GTCCCTTAGGAGATATCCCCG	0.413																																					p.G1700G		Atlas-SNP	.											.	INADL	179	.	0			c.A5100G						.						96	92	93					1																	62593700		1894	4125	6019	SO:0001819	synonymous_variant	10207	exon40			CTTAGGAGATATC	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.5100A>G	chr1.hg19:g.62593700A>G		62.0	0.0		86.0	4.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	hg19	CCDS617.2																																																																																			.	.		0.413	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62593700	A	G	62593700	2	3	43	1	0	0	0	0	0	0	0	1	7740	291	11	2		2	INADL	1	62593700	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	5112810	62593700	186656921	10	5092										
RAVER2	55225	hgsc.bcm.edu	37	chr1	65255125	65255125	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caaatccagtacaaattatgAaaagtttaaacaaccctgcc	4	10	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:65255125A>G	ENST00000294428.3	+	5	1111	c.1033A>G	c.(1033-1035)Aaa>Gaa	p.K345E	RAVER2_ENST00000430964.2_Missense_Mutation_p.K51E|RAVER2_ENST00000371072.4_Missense_Mutation_p.K345E			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	345						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						ACAAATTATGAAAAGTTTAAA	0.373																																					p.K345E		Atlas-SNP	.											.	RAVER2	56	.	0			c.A1033G						.						99	91	94					1																	65255125		1849	4092	5941	SO:0001583	missense	55225	exon5			ATTATGAAAAGTT	AB046799	CCDS41345.1	1p31.3	2013-02-12			ENSG00000162437	ENSG00000162437		"RNA binding motif (RRM) containing"	25577	protein-coding gene	gene with protein product		609953				16051233	Standard	NM_018211		Approved	KIAA1579, FLJ10770	uc001dbs.2	Q9HCJ3	OTTHUMG00000009102	ENST00000294428.3:c.1033A>G	chr1.hg19:g.65255125A>G	ENSP00000294428:p.Lys345Glu	82.0	0.0		80.0	27.0	NM_018211	Q6P141|Q9NPV7	Missense_Mutation	SNP	ENST00000294428.3	hg19		.	.	.	.	.	.	.	.	.	.	A	16.29	3.081993	0.55861	.	.	ENSG00000162437	ENST00000371072;ENST00000294428;ENST00000430964	T;T	0.32753	1.44;1.45	4.9	4.9	0.64082	.	0.204244	0.50627	D	0.000116	T	0.13713	0.0332	L	0.46157	1.445	0.27606	N	0.94882	P;P	0.50943	0.9;0.94	B;B	0.43754	0.248;0.43	T	0.06232	-1.0838	10	0.23302	T	0.38	-33.0872	10.399	0.44218	0.8359:0.1641:0.0:0.0	.	345;345	Q9HCJ3;Q9HCJ3-2	RAVR2_HUMAN;.	E	345;345;51	ENSP00000360112:K345E;ENSP00000294428:K345E	ENSP00000294428:K345E	K	+	1	0	RAVER2	65027713	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	5.683000	0.68189	1.835000	0.53391	0.482000	0.46254	AAA	.	.		0.373	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211		G	65255125	A	G	65255125	3	3	43	1	0	0	0	0	1	0	0	0	13110	247	9	2	1051	2	RAVER2	1	65255125	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	2661425	65255125	183995496	11	5093										
FAM73A	374986	hgsc.bcm.edu	37	chr1	78245387	78245387	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catcagctgggaagctggcgTgggcaggccagctgtacctg	16	11	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:78245387T>C	ENST00000370791.3	+	1	79	c.47T>C	c.(46-48)gTg>gCg	p.V16A	RNA5SP21_ENST00000410917.1_RNA|FAM73A_ENST00000443751.2_Missense_Mutation_p.V16A	NM_001270384.1|NM_198549.3	NP_001257313.1|NP_940951.1	Q8NAN2	FA73A_HUMAN	family with sequence similarity 73, member A	16						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	19				Colorectal(170;0.226)		GAAGCTGGCGTGGGCAGGCCA	0.672																																					p.V16A		Atlas-SNP	.											.	FAM73A	56	.	0			c.T47C						.						7	7	7					1																	78245387		2175	4250	6425	SO:0001583	missense	374986	exon1			CTGGCGTGGGCAG		CCDS681.1, CCDS72809.1	1p31.1	2008-02-05			ENSG00000180488	ENSG00000180488			24741	protein-coding gene	gene with protein product							Standard	NM_001270384		Approved	FLJ35093	uc010ork.3	Q8NAN2	OTTHUMG00000009766	ENST00000370791.3:c.47T>C	chr1.hg19:g.78245387T>C	ENSP00000359827:p.Val16Ala	49.0	0.0		90.0	4.0	NM_001270384	Q6MZG0	Missense_Mutation	SNP	ENST00000370791.3	hg19	CCDS681.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.345644	0.41498	.	.	ENSG00000180488	ENST00000370791;ENST00000443751	T;T	0.31769	1.96;1.48	4.33	-2.21	0.06973	.	1.377560	0.05336	N	0.529266	T	0.04272	0.0118	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.35624	-0.9781	10	0.87932	D	0	-8.5736	0.8207	0.01111	0.1575:0.2444:0.1618:0.4362	.	16;16;16	F8W7S1;B7ZLZ8;Q8NAN2	.;.;FA73A_HUMAN	A	16	ENSP00000359827:V16A;ENSP00000393675:V16A	ENSP00000359827:V16A	V	+	2	0	FAM73A	78017975	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	-1.357000	0.02607	-0.363000	0.08101	-0.321000	0.08615	GTG	.	.		0.672	FAM73A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026931.1	NM_198549		C	78245387	T	C	78245387	3	2	43	1	0	0	0	0	1	0	0	0	5625	1696	59	2	49	2	FAM73A	1	78245387	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	12990262	78245387	171005234	12	5094										
CLCA4	22802	hgsc.bcm.edu	37	chr1	87025972	87025972	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	agttcacagaatgtggagagAaaggcgaatacattcacttc	10	7	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:87025972A>G	ENST00000370563.3	+	3	421	c.379A>G	c.(379-381)Aaa>Gaa	p.K127E	CLCA4_ENST00000263723.5_5'UTR	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	127	Metalloprotease domain. {ECO:0000250|UniProtKB:A8K7I4}.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		ATGTGGAGAGAAAGGCGAATA	0.388																																					p.K127E		Atlas-SNP	.											.	CLCA4	131	.	0			c.A379G						.						141	123	128					1																	87025972		1886	4128	6014	SO:0001583	missense	22802	exon3			GGAGAGAAAGGCG	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"chloride channel, calcium activated, family member 4", "chloride channel regulator 4"			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.379A>G	chr1.hg19:g.87025972A>G	ENSP00000359594:p.Lys127Glu	52.0	0.0		91.0	4.0	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Missense_Mutation	SNP	ENST00000370563.3	hg19	CCDS41355.1	.	.	.	.	.	.	.	.	.	.	A	16.63	3.175595	0.57692	.	.	ENSG00000016602	ENST00000370563	T	0.12672	2.66	5.75	3.25	0.37280	Chloride channel calcium-activated (1);	0.388829	0.28257	N	0.016019	T	0.12646	0.0307	L	0.53617	1.68	0.80722	D	1	P	0.42649	0.786	P	0.51945	0.685	T	0.03068	-1.1076	10	0.28530	T	0.3	-22.0051	12.9577	0.58441	0.5335:0.4665:0.0:0.0	.	127	Q14CN2	CLCA4_HUMAN	E	127	ENSP00000359594:K127E	ENSP00000359594:K127E	K	+	1	0	CLCA4	86798560	0.356000	0.24930	0.890000	0.34922	0.995000	0.86356	0.995000	0.29706	0.961000	0.38030	0.533000	0.62120	AAA	.	.		0.388	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128		G	87025972	A	G	87025972	3	3	43	1	0	0	0	0	1	0	0	0	3461	247	9	2	389	2	CLCA4	1	87025972	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	8780585	87025972	162224649	13	5095										
CLCA4	22802	hgsc.bcm.edu	37	chr1	87038340	87038340	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gatgaagctcagaacaatggCctcattgatgcttttggggc	12	8	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:87038340C>T	ENST00000370563.3	+	9	1446	c.1404C>T	c.(1402-1404)ggC>ggT	p.G468G	CLCA4_ENST00000496322.1_3'UTR|CLCA4_ENST00000263723.5_Silent_p.G181G|RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	468	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		AGAACAATGGCCTCATTGATG	0.363																																					p.G468G		Atlas-SNP	.											.	CLCA4	131	.	0			c.C1404T						.						106	110	109					1																	87038340		2184	4296	6480	SO:0001819	synonymous_variant	22802	exon9			CAATGGCCTCATT	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"chloride channel, calcium activated, family member 4", "chloride channel regulator 4"			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.1404C>T	chr1.hg19:g.87038340C>T		109.0	0.0		98.0	4.0	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Silent	SNP	ENST00000370563.3	hg19	CCDS41355.1																																																																																			.	.		0.363	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128		T	87038340	C	T	87038340	2	4	43	1	0	0	0	0	0	0	0	1	3461	726	26	3		3	CLCA4	1	87038340	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	12368	87038340	162212281	14	5096										
PKN2	5586	hgsc.bcm.edu	37	chr1	89299097	89299097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggaagaggagcaggaaatgtTcagagattttgactacattg	13	4	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:89299097T>C	ENST00000370521.3	+	22	3280	c.2921T>C	c.(2920-2922)tTc>tCc	p.F974S	PKN2_ENST00000370513.5_Missense_Mutation_p.F926S|PKN2_ENST00000495119.1_3'UTR|PKN2_ENST00000370505.3_Missense_Mutation_p.F817S|PKN2_ENST00000544045.1_Missense_Mutation_p.F648S	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	974	AGC-kinase C-terminal.|Necessary for the catalytic activity.				apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		CAGGAAATGTTCAGAGATTTT	0.403																																					p.F974S		Atlas-SNP	.											.	PKN2	109	.	0			c.T2921C						.						84	84	84					1																	89299097		1985	4158	6143	SO:0001583	missense	5586	exon22			AAATGTTCAGAGA	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"cardiolipin-activated protein kinase Pak2"	602549	"protein kinase C-like 2"	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.2921T>C	chr1.hg19:g.89299097T>C	ENSP00000359552:p.Phe974Ser	69.0	0.0		70.0	4.0	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	hg19	CCDS714.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.553933	0.86231	.	.	ENSG00000065243	ENST00000370521;ENST00000370505;ENST00000370513;ENST00000544045	D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87	5.84	5.84	0.93424	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.47455	U	0.000226	D	0.97473	0.9173	H	0.99299	4.505	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99338	1.0911	10	0.87932	D	0	.	16.2055	0.82126	0.0:0.0:0.0:1.0	.	958;926;974	B4DTP5;E7ESL7;Q16513	.;.;PKN2_HUMAN	S	974;817;926;648	ENSP00000359552:F974S;ENSP00000359536:F817S;ENSP00000359544:F926S;ENSP00000439643:F648S	ENSP00000359536:F817S	F	+	2	0	PKN2	89071685	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.698000	0.84413	2.226000	0.72624	0.482000	0.46254	TTC	.	.		0.403	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		C	89299097	T	C	89299097	3	2	43	1	0	0	0	0	1	0	0	0	11989	1783	62	2	3007	2	PKN2	1	89299097	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2260757	89299097	159951524	15	5097										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103481268	103481268	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aggaccaggtagaccatcagCccctggtaagccaggacgtc	12	13	1	1	rs150428394		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:103481268C>A	ENST00000370096.3	-	12	1756	c.1444G>T	c.(1444-1446)Gct>Tct	p.A482S	COL11A1_ENST00000358392.2_Missense_Mutation_p.A494S|COL11A1_ENST00000512756.1_Missense_Mutation_p.A366S|COL11A1_ENST00000353414.4_Missense_Mutation_p.A443S	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	482	Collagen-like 1.|Triple-helical region (interrupted).				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		AGACCATCAGCCCCTGGTAAG	0.353																																					p.A494S		Atlas-SNP	.											.	COL11A1	972	.	0			c.G1480T						.						37	36	36					1																	103481268		2203	4299	6502	SO:0001583	missense	1301	exon12			CATCAGCCCCTGG	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1444G>T	chr1.hg19:g.103481268C>A	ENSP00000359114:p.Ala482Ser	134.0	0.0		129.0	45.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.531033	0.45073	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239	D;D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42;-3.42	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.91157	0.7215	L	0.40543	1.245	0.80722	D	1	P;P;P;P	0.45348	0.77;0.827;0.827;0.856	B;B;P;P	0.48454	0.376;0.442;0.52;0.578	D	0.89616	0.3845	10	0.16896	T	0.51	.	18.675	0.91525	0.0:1.0:0.0:0.0	.	366;443;494;482	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	S	482;494;443;366;494	ENSP00000359114:A482S;ENSP00000351163:A494S;ENSP00000302551:A443S;ENSP00000426533:A366S;ENSP00000408640:A494S	ENSP00000302551:A443S	A	-	1	0	COL11A1	103253856	1.000000	0.71417	0.997000	0.53966	0.907000	0.53573	5.552000	0.67281	2.510000	0.84645	0.585000	0.79938	GCT	.	C|1.000;T|0.000		0.353	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103481268	C	A	103481268	3	1	43	1	0	0	0	0	1	0	0	0	3669	739	26	3	4200	3	COL11A1	1	103481268	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	14182171	103481268	145769353	16	5098										
GPSM2	29899	hgsc.bcm.edu	37	chr1	109465168	109465168	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atacagcttcaacaacaactTcttccactccccctaaaatg	2	15	2	0	rs374875864|rs35029887|rs201481482	byFrequency	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:109465168T>A	ENST00000406462.2	+	14	2343	c.1570T>A	c.(1570-1572)Tct>Act	p.S524T	GPSM2_ENST00000264126.3_Missense_Mutation_p.S524T|AKNAD1_ENST00000357393.4_Intron			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	524					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		AACAACAACTTCTTCCACTCC	0.373																																					p.S524T		Atlas-SNP	.											.	GPSM2	56	.	0			c.T1570A						.						79	117	104					1																	109465168		2190	4293	6483	SO:0001583	missense	29899	exon13			ACAACTTCTTCCA	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"Tetratricopeptide (TTC) repeat domain containing"	29501	protein-coding gene	gene with protein product		609245	"G-protein signalling modulator 2 (AGS3-like, C. elegans)", "deafness, autosomal recessive 82"	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.1570T>A	chr1.hg19:g.109465168T>A	ENSP00000385510:p.Ser524Thr	53.0	0.0		80.0	5.0	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	hg19	CCDS792.2	.	.	.	.	.	.	.	.	.	.	T	7.387	0.629929	0.14257	.	.	ENSG00000121957	ENST00000406462;ENST00000264126	D;D	0.93712	-3.27;-3.27	6.17	-6.6	0.01824	.	0.546439	0.21807	N	0.068824	T	0.62563	0.2438	N	0.08118	0	0.09310	N	0.999996	B	0.11235	0.004	B	0.06405	0.002	T	0.64601	-0.6369	10	0.15499	T	0.54	-3.6969	9.2309	0.37437	0.0:0.2789:0.4599:0.2613	.	524	P81274	GPSM2_HUMAN	T	524	ENSP00000385510:S524T;ENSP00000264126:S524T	ENSP00000264126:S524T	S	+	1	0	GPSM2	109266691	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.350000	0.07721	-1.555000	0.01697	-0.250000	0.11733	TCT	.	.		0.373	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296		A	109465168	T	A	109465168	3	1	43	1	0	0	0	0	1	0	0	0	6744	1783	62	4	1616	4	GPSM2	1	109465168	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5983900	109465168	139785453	17	5099										
HIPK1	204851	hgsc.bcm.edu	37	chr1	114500750	114500750	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctttctctggctaattcagaTgtctcactactaaactacca	4	12	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:114500750T>C	ENST00000369558.1	+	8	2050	c.1818T>C	c.(1816-1818)gaT>gaC	p.D606D	HIPK1_ENST00000369553.1_Silent_p.D212D|HIPK1_ENST00000406344.1_Silent_p.D212D|HIPK1_ENST00000369554.2_Silent_p.D606D|HIPK1_ENST00000340480.4_Silent_p.D232D|HIPK1_ENST00000369555.2_Silent_p.D606D|HIPK1_ENST00000426820.2_Silent_p.D606D|HIPK1_ENST00000369559.4_Silent_p.D606D|HIPK1_ENST00000369561.4_Silent_p.D572D			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	606					anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTAATTCAGATGTCTCACTAC	0.458																																					p.D606D		Atlas-SNP	.											.	HIPK1	195	.	0			c.T1818C						.						134	132	133					1																	114500750		2203	4300	6503	SO:0001819	synonymous_variant	204851	exon8			TTCAGATGTCTCA	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.1818T>C	chr1.hg19:g.114500750T>C		112.0	0.0		136.0	50.0	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Silent	SNP	ENST00000369558.1	hg19	CCDS867.1																																																																																			.	.		0.458	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		C	114500750	T	C	114500750	2	2	43	1	0	0	0	0	0	0	0	1	7125	1461	51	2		2	HIPK1	1	114500750	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5035582	114500750	134749871	18	5100										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153907287	153907287	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgacacctgctcctgctgctGctgctgctgctgctgctgtt	11	14	0	1	rs3835302|rs199597671		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:153907287G>C	ENST00000361217.4	-	18	3140	c.2722C>G	c.(2722-2724)Cag>Gag	p.Q908E	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	908	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tcctgctgctgctgctgctgc	0.632																																					p.Q908E		Atlas-SNP	.											.	DENND4B	210	.	0			c.C2722G						.						23	27	26					1																	153907287		2184	4281	6465	SO:0001583	missense	9909	exon18			GCTGCTGCTGCTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2722C>G	chr1.hg19:g.153907287G>C	ENSP00000354597:p.Gln908Glu	46.0	0.0		80.0	9.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	1.785	-0.481073	0.04383	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06294	3.33;3.32	2.67	0.673	0.17941	.	5.053470	0.00166	N	0.000001	T	0.00815	0.0027	N	0.14661	0.345	0.19300	N	0.999977	B	0.02656	0.0	B	0.04013	0.001	T	0.26573	-1.0099	10	0.02654	T	1	-2.4288	3.3651	0.07201	0.1454:0.0:0.5849:0.2697	.	908	O75064	DEN4B_HUMAN	E	908;919	ENSP00000354597:Q908E;ENSP00000357635:Q919E	ENSP00000354597:Q908E	Q	-	1	0	DENND4B	152173911	0.943000	0.32029	0.986000	0.45419	0.760000	0.43138	0.537000	0.23144	0.194000	0.20326	0.271000	0.19318	CAG	.	.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153907287	G	C	153907287	3	2	43	1	0	0	0	0	1	0	0	0	4436	1328	46	4	1812	4	DENND4B	1	153907287	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	39406537	153907287	95343334	19	5101										
HAX1	10456	hgsc.bcm.edu	37	chr1	154247645	154247645	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tccagatcttgattcccaggTttcccaggagggtcttggcc	11	12	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:154247645T>C	ENST00000328703.7	+	5	785	c.572T>C	c.(571-573)gTt>gCt	p.V191A	HAX1_ENST00000457918.2_Missense_Mutation_p.V143A|HAX1_ENST00000532105.1_Missense_Mutation_p.V63A|HAX1_ENST00000483970.2_Missense_Mutation_p.V199A	NM_006118.3	NP_006109.2	O00165	HAX1_HUMAN	HCLS1 associated protein X-1	191	Involved in CASP9 binding.|Involved in GNA13 binding.|Involved in HCLS1 binding.|Involved in PKD2 binding.|Required for localization in sarcoplasmic reticulum. {ECO:0000250}.				cellular response to cytokine stimulus (GO:0071345)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin filament polymerization (GO:0030833)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein targeting to mitochondrion (GO:1903214)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|lamellipodium (GO:0030027)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|sarcoplasmic reticulum (GO:0016529)|transcription factor complex (GO:0005667)	interleukin-1 binding (GO:0019966)|protein N-terminus binding (GO:0047485)			cervix(1)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	15	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GATTCCCAGGTTTCCCAGGAG	0.483									Kostmann syndrome																												p.V191A		Atlas-SNP	.											.	HAX1	25	.	0			c.T572C						.						62	63	63					1																	154247645		2203	4300	6503	SO:0001583	missense	10456	exon5	Familial Cancer Database	Kostmann Infantile Agranulocytosis, Severe Congenital Neutropenia, Congenital Agranulocytosis	CCCAGGTTTCCCA	U68566	CCDS1064.1, CCDS44230.1	1q21.3	2014-09-17			ENSG00000143575	ENSG00000143575			16915	protein-coding gene	gene with protein product	"HCLS1 (and PKD2) associated protein"	605998				9058808, 10760273	Standard	NM_006118		Approved	HS1BP1, HCLSBP1	uc001fes.3	O00165	OTTHUMG00000035978	ENST00000328703.7:c.572T>C	chr1.hg19:g.154247645T>C	ENSP00000329002:p.Val191Ala	93.0	0.0		91.0	4.0	NM_006118	A8W4W9|A8W4X0|B4DUJ7|Q5VYD5|Q5VYD7|Q96AU4|Q9BS80	Missense_Mutation	SNP	ENST00000328703.7	hg19	CCDS1064.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.040682	0.75732	.	.	ENSG00000143575	ENST00000328703;ENST00000457918;ENST00000483970;ENST00000435087;ENST00000532105	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;-0.69	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.81697	0.4877	M	0.82630	2.6	0.58432	D	0.999992	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.87578	0.993;0.995;0.998;0.995	D	0.85121	0.0969	10	0.87932	D	0	-16.2253	13.3471	0.60580	0.0:0.0:0.0:1.0	.	199;165;143;191	O00165-2;O00165-3;O00165-5;O00165	.;.;.;HAX1_HUMAN	A	191;143;199;195;63	ENSP00000329002:V191A;ENSP00000411448:V143A;ENSP00000435088:V199A;ENSP00000394920:V195A;ENSP00000433951:V63A	ENSP00000329002:V191A	V	+	2	0	HAX1	152514269	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	5.600000	0.67599	2.168000	0.68352	0.460000	0.39030	GTT	.	.		0.483	HAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087650.1	NM_006118		C	154247645	T	C	154247645	3	2	43	1	0	0	0	0	1	0	0	0	6984	1725	60	2	590	2	HAX1	1	154247645	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	340358	154247645	95002976	20	5102										
EFNA3	1944	hgsc.bcm.edu	37	chr1	155057654	155057654	+	Silent	SNP	C	C	A													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tacaacagctcgggggtgggCcccggggcgggaccggggcc					rs199552063	byFrequency	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:155057654C>A	ENST00000368408.3	+	2	286	c.216C>A	c.(214-216)ggC>ggA	p.G72G	EFNA3_ENST00000505139.1_Silent_p.G67G|EFNA3_ENST00000418360.2_Silent_p.G72G|EFNA3_ENST00000556931.1_Silent_p.G67G	NM_004952.4	NP_004943.1	P52797	EFNA3_HUMAN	ephrin-A3	72	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.			Missing (in Ref. 2; AAA52368). {ECO:0000305}.	axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|transmembrane-ephrin receptor activity (GO:0005005)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		all cancers(21;5.67e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000284)|LUSC - Lung squamous cell carcinoma(543;0.193)			CGGGGGTgggccccggggcgg	0.662																																					p.G72G		Atlas-SNP	.											.	EFNA3	15	.	0			c.C216A						.						21	26	24					1																	155057654		2181	4259	6440	SO:0001819	synonymous_variant	1944	exon2			GGTGGGCCCCGGG	BC017722	CCDS1090.1	1q21-q22	2011-03-09			ENSG00000143590	ENSG00000143590		"Ephrins"	3223	protein-coding gene	gene with protein product		601381		EPLG3		8660976	Standard	NM_004952		Approved	LERK3, Ehk1-L	uc001fhf.3	P52797	OTTHUMG00000035313	ENST00000368408.3:c.216C>A	chr1.hg19:g.155057654C>A		30.0	0.0		68.0	10.0	NM_004952	B7ZAD3|D3DV85|Q0VGC9|Q5SR70	Silent	SNP	ENST00000368408.3	hg19	CCDS1090.1																																																																																			.	.		0.662	EFNA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085429.1	NM_004952		A	155057654	C	A	155057654	2	1	43	1	0	0	0	0	0	0	0	1	4954	726	26	3		3	EFNA3	1	155057654	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	810009	155057654	94192967	21	5103	23	2								
EFNA3	1944	hgsc.bcm.edu	37	chr1	155057657	155057657	+	Silent	SNP	C	C	G													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aacagctcgggggtgggcccCggggcgggaccggggcccgg					rs199552063	byFrequency	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:155057657C>G	ENST00000368408.3	+	2	289	c.219C>G	c.(217-219)ccC>ccG	p.P73P	EFNA3_ENST00000505139.1_Silent_p.P68P|EFNA3_ENST00000418360.2_Silent_p.P73P|EFNA3_ENST00000556931.1_Silent_p.P68P	NM_004952.4	NP_004943.1	P52797	EFNA3_HUMAN	ephrin-A3	73	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.			Missing (in Ref. 2; AAA52368). {ECO:0000305}.	axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|transmembrane-ephrin receptor activity (GO:0005005)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		all cancers(21;5.67e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000284)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGGTgggccccggggcgggac	0.662																																					p.P73P		Atlas-SNP	.											.	EFNA3	15	.	0			c.C219G						.						19	25	23					1																	155057657		2168	4252	6420	SO:0001819	synonymous_variant	1944	exon2			GGGCCCCGGGGCG	BC017722	CCDS1090.1	1q21-q22	2011-03-09			ENSG00000143590	ENSG00000143590		"Ephrins"	3223	protein-coding gene	gene with protein product		601381		EPLG3		8660976	Standard	NM_004952		Approved	LERK3, Ehk1-L	uc001fhf.3	P52797	OTTHUMG00000035313	ENST00000368408.3:c.219C>G	chr1.hg19:g.155057657C>G		30.0	0.0		72.0	10.0	NM_004952	B7ZAD3|D3DV85|Q0VGC9|Q5SR70	Silent	SNP	ENST00000368408.3	hg19	CCDS1090.1																																																																																			.	.		0.662	EFNA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085429.1	NM_004952		G	155057657	C	G	155057657	2	3	43	1	0	0	0	0	0	0	0	1	4954	639	23	4		4	EFNA3	1	155057657	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	3	155057657	94192964	22	5104	23	2								
MTX1	4580	hgsc.bcm.edu	37	chr1	155180142	155180142	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cttccttccctgcagacctaTgccagatttactggtgctcc	7	15	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:155180142T>C	ENST00000368376.3	+	2	640	c.534T>C	c.(532-534)taT>taC	p.Y178Y	MTX1_ENST00000609421.1_Silent_p.Y29Y|THBS3_ENST00000541990.1_5'Flank|THBS3_ENST00000457183.2_5'Flank|THBS3_ENST00000368378.3_5'Flank|THBS3_ENST00000486260.1_5'Flank|MTX1_ENST00000316721.4_Silent_p.Y178Y|RP11-263K19.6_ENST00000455788.1_RNA	NM_002455.3	NP_002446.2	Q13505	MTX1_HUMAN	metaxin 1	178					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGCAGACCTATGCCAGATTTA	0.502																																					p.Y178Y		Atlas-SNP	.											.	MTX1	17	.	0			c.T534C						.						121	111	115					1																	155180142		2203	4300	6503	SO:0001819	synonymous_variant	4580	exon2			GACCTATGCCAGA		CCDS1100.1, CCDS1101.1	1q21	2008-07-18			ENSG00000173171	ENSG00000173171			7504	protein-coding gene	gene with protein product		600605		MTX		7753840	Standard	XM_006711338		Approved	MTXN	uc001fjb.3	Q13505	OTTHUMG00000035708	ENST00000368376.3:c.534T>C	chr1.hg19:g.155180142T>C		106.0	0.0		119.0	51.0	NM_198883	B1AVR9|B1AVS0|B2R9P4|Q9BUU3	Silent	SNP	ENST00000368376.3	hg19	CCDS1100.1	.	.	.	.	.	.	.	.	.	.	T	11.84	1.759243	0.31137	.	.	ENSG00000173171	ENST00000424959	.	.	.	5.87	3.58	0.41010	.	.	.	.	.	T	0.41949	0.1181	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38908	-0.9639	4	.	.	.	-29.5015	6.5199	0.22269	0.0:0.2489:0.0:0.7511	.	.	.	.	T	34	.	.	M	+	2	0	MTX1	153446766	0.994000	0.37717	1.000000	0.80357	0.927000	0.56198	0.182000	0.16900	1.166000	0.42689	0.533000	0.62120	ATG	.	.		0.502	MTX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086844.1	NM_198883		C	155180142	T	C	155180142	2	2	43	1	0	0	0	0	0	0	0	1	9976	1471	51	2		2	MTX1	1	155180142	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	122485	155180142	94070479	23	5105										
BCAN	63827	hgsc.bcm.edu	37	chr1	156622302	156622302	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtcctgcagcctggtgcatcAccacttcctgatggagagtc	11	13	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:156622302A>G	ENST00000329117.5	+	8	1896	c.1560A>G	c.(1558-1560)tcA>tcG	p.S520S	RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Silent_p.S520S	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	520	O-glycosylated at two sites.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTGGTGCATCACCACTTCCTG	0.642																																					p.S520S		Atlas-SNP	.											.	BCAN	174	.	0			c.A1560G						.						24	23	23					1																	156622302		2203	4299	6502	SO:0001819	synonymous_variant	63827	exon8			TGCATCACCACTT	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1560A>G	chr1.hg19:g.156622302A>G		48.0	0.0		78.0	4.0	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Silent	SNP	ENST00000329117.5	hg19	CCDS1149.1																																																																																			.	.		0.642	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		G	156622302	A	G	156622302	2	3	43	1	0	0	0	0	0	0	0	1	1345	146	6	2		2	BCAN	1	156622302	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1442160	156622302	92628319	24	5106										
CD48	962	hgsc.bcm.edu	37	chr1	160648863	160648863	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caggtaagtaacaggccaagAatggtgggcaccgtgaccac	13	10	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:160648863A>G	ENST00000368046.3	-	4	798	c.711T>C	c.(709-711)atT>atC	p.I237I	RP11-404F10.2_ENST00000443928.2_RNA|RP11-404F10.2_ENST00000588034.1_RNA|RP11-404F10.2_ENST00000598917.2_RNA	NM_001778.3	NP_001769.2	P09326	CD48_HUMAN	CD48 molecule	237					blood coagulation (GO:0007596)|defense response (GO:0006952)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|stomach(1)	10	all_cancers(52;2.18e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			ACAGGCCAAGAATGGTGGGCA	0.473																																					p.I237I		Atlas-SNP	.											.	CD48	31	.	0			c.T711C						.						117	109	112					1																	160648863		2203	4300	6503	SO:0001819	synonymous_variant	962	exon4			GCCAAGAATGGTG	BC016182	CCDS1208.1, CCDS72955.1	1q21.3-q22	2013-01-29	2006-03-31		ENSG00000117091	ENSG00000117091		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1683	protein-coding gene	gene with protein product		109530	"CD48 antigen (B-cell membrane protein)", "CD48 molecule "	BCM1		2828034	Standard	NM_001256030		Approved	BLAST, mCD48, hCD48, SLAMF2	uc001fwo.2	P09326	OTTHUMG00000024009	ENST00000368046.3:c.711T>C	chr1.hg19:g.160648863A>G		63.0	0.0		85.0	4.0	NM_001778	Q5U055|Q8MGR0	Silent	SNP	ENST00000368046.3	hg19	CCDS1208.1																																																																																			.	.		0.473	CD48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060471.1	NM_001778		G	160648863	A	G	160648863	2	3	43	1	0	0	0	0	0	0	0	1	3022	242	9	2		2	CD48	1	160648863	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	4026561	160648863	88601758	25	5107										
FMO3	2328	hgsc.bcm.edu	37	chr1	171061807	171061807	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgcacaggttaccatggggaAgaaagtggccatcattggag	14	7	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:171061807A>G	ENST00000367755.4	+	2	119	c.8A>G	c.(7-9)aAg>aGg	p.K3R	FMO3_ENST00000392085.2_Missense_Mutation_p.K3R|FMO3_ENST00000542847.1_5'UTR|FMO3_ENST00000534514.1_3'UTR|FMO3_ENST00000538429.1_Missense_Mutation_p.K3R	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	3					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	ACCATGGGGAAGAAAGTGGCC	0.458																																					p.K3R		Atlas-SNP	.											.	FMO3	73	.	0			c.A8G						.						91	89	90					1																	171061807		2203	4300	6503	SO:0001583	missense	2328	exon2			TGGGGAAGAAAGT	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.8A>G	chr1.hg19:g.171061807A>G	ENSP00000356729:p.Lys3Arg	87.0	0.0		98.0	4.0	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	hg19	CCDS1292.1	.	.	.	.	.	.	.	.	.	.	A	12.41	1.930519	0.34096	.	.	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000538429	T;T;T	0.61392	0.11;0.11;0.22	4.56	2.15	0.27550	.	0.441677	0.21716	N	0.070196	T	0.31638	0.0803	L	0.46741	1.465	0.20196	N	0.999922	B;B	0.24368	0.022;0.102	B;B	0.34385	0.018;0.181	T	0.36065	-0.9763	10	0.46703	T	0.11	-7.0076	8.3035	0.32027	0.8307:0.0:0.1693:0.0	.	3;3	F5H261;P31513	.;FMO3_HUMAN	R	3	ENSP00000356729:K3R;ENSP00000375935:K3R;ENSP00000439500:K3R	ENSP00000356729:K3R	K	+	2	0	FMO3	169328431	0.042000	0.20092	0.258000	0.24420	0.981000	0.71138	1.404000	0.34623	0.122000	0.18314	0.460000	0.39030	AAG	.	.		0.458	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		G	171061807	A	G	171061807	3	3	43	1	0	0	0	0	1	0	0	0	5964	72	3	2	10	2	FMO3	1	171061807	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	10412944	171061807	78188814	26	5108										
PRG4	10216	hgsc.bcm.edu	37	chr1	186276411	186276411	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccttcacccaccactcccaaGgagcctgcacccaccaccac	4	23	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:186276411G>A	ENST00000445192.2	+	7	1605	c.1560G>A	c.(1558-1560)aaG>aaA	p.K520K	PRG4_ENST00000367483.4_Silent_p.K479K|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Silent_p.K477K|PRG4_ENST00000367485.4_Silent_p.K427K	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	520	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCACTCCCAAGGAGCCTGCAC	0.632																																					p.K520K		Atlas-SNP	.											PRG4,NS,malignant_melanoma,0,1	PRG4	259	.	0			c.G1560A						.						129	118	122					1																	186276411		2203	4299	6502	SO:0001819	synonymous_variant	10216	exon7			TCCCAAGGAGCCT	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1560G>A	chr1.hg19:g.186276411G>A		79.0	2.0		91.0	4.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	hg19	CCDS1369.1																																																																																			.	.		0.632	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		A	186276411	G	A	186276411	2	1	43	1	0	0	0	0	0	0	0	1	12493	991	35	3		3	PRG4	1	186276411	Silent	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	15214604	186276411	62974210	27	5109										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196451495	196451495	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aaggtagacttctgttcaccCaaaagatatgagacctataa	7	8	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:196451495C>G	ENST00000294725.9	-	4	1205	c.290G>C	c.(289-291)tGg>tCg	p.W97S	KCNT2_ENST00000609185.1_Missense_Mutation_p.W97S|KCNT2_ENST00000367431.4_Missense_Mutation_p.W97S|KCNT2_ENST00000367433.5_Missense_Mutation_p.W97S|KCNT2_ENST00000451324.2_5'UTR			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	97					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						TCTGTTCACCCAAAAGATATG	0.274																																					p.W97S		Atlas-SNP	.											.	KCNT2	243	.	0			c.G290C						.						50	47	48					1																	196451495		2202	4299	6501	SO:0001583	missense	343450	exon4			TTCACCCAAAAGA	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.290G>C	chr1.hg19:g.196451495C>G	ENSP00000294725:p.Trp97Ser	59.0	0.0		52.0	19.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	hg19	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.105261	0.77096	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.19532	2.14;2.19;2.38	5.44	5.44	0.79542	.	0.000000	0.56097	D	0.000028	T	0.54287	0.1849	M	0.86953	2.85	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.993;0.999;0.999;0.993	T	0.60712	-0.7209	10	0.72032	D	0.01	-10.332	18.4088	0.90543	0.0:1.0:0.0:0.0	.	97;97;97;97	A9LNM6;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;KCNT2_HUMAN	S	97	ENSP00000356403:W97S;ENSP00000356401:W97S;ENSP00000294725:W97S	ENSP00000294725:W97S	W	-	2	0	KCNT2	194718118	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.374000	0.73132	2.703000	0.92315	0.655000	0.94253	TGG	.	.		0.274	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		G	196451495	C	G	196451495	3	3	43	1	0	0	0	0	1	0	0	0	8101	595	21	4	3217	4	KCNT2	1	196451495	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	10175084	196451495	52799126	28	5110										
SOX13	9580	hgsc.bcm.edu	37	chr1	204092852	204092852	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaggcccatgaacgccttcaTggtgtgggccaaggatgagc	15	10	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:204092852T>C	ENST00000367204.1	+	12	1404	c.1295T>C	c.(1294-1296)aTg>aCg	p.M432T		NM_005686.2	NP_005677.2	Q9UN79	SOX13_HUMAN	SRY (sex determining region Y)-box 13	432					anatomical structure morphogenesis (GO:0009653)|regulation of gamma-delta T cell differentiation (GO:0045586)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	13	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			AACGCCTTCATGGTGTGGGCC	0.597											OREG0014126	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M432T		Atlas-SNP	.											.	SOX13	38	.	0			c.T1295C						.						58	62	61					1																	204092852		2194	4299	6493	SO:0001583	missense	9580	exon12			CCTTCATGGTGTG		CCDS44299.1	1q32	2008-07-18			ENSG00000143842	ENSG00000143842		"SRY (sex determining region Y)-boxes"	11192	protein-coding gene	gene with protein product	"islet cell antibody 12", "SRY-related HMG-box gene 13", "type 1 diabetes autoantigen", "SRY-box 13"	604748				10198172	Standard	NM_005686		Approved	Sox-13, ICA12, MGC117216	uc001ham.3	Q9UN79	OTTHUMG00000036050	ENST00000367204.1:c.1295T>C	chr1.hg19:g.204092852T>C	ENSP00000356172:p.Met432Thr	44.0	0.0	2142	74.0	4.0	NM_005686	B4E2B0|O95275|O95826|Q3KQV7|Q5SXX1|Q9UHW7	Missense_Mutation	SNP	ENST00000367204.1	hg19	CCDS44299.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.742257	0.89573	.	.	ENSG00000143842	ENST00000367204	D	0.98249	-4.82	5.69	5.69	0.88448	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	D	0.99260	0.9742	H	0.95745	3.715	0.80722	D	1	D;D;D	0.64830	0.994;0.994;0.994	D;D;D	0.75020	0.985;0.985;0.985	D	0.98914	1.0781	10	0.87932	D	0	.	15.6035	0.76642	0.0:0.0:0.0:1.0	.	299;299;432	B4DX26;B4E3N9;Q9UN79	.;.;SOX13_HUMAN	T	432	ENSP00000356172:M432T	ENSP00000356172:M432T	M	+	2	0	SOX13	202359475	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.162000	0.67917	0.533000	0.62120	ATG	.	.		0.597	SOX13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087881.2	NM_005686		C	204092852	T	C	204092852	3	2	43	1	0	0	0	0	1	0	0	0	14959	1464	51	2	1337	2	SOX13	1	204092852	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	7641357	204092852	45157769	29	5111										
IARS2	55699	hgsc.bcm.edu	37	chr1	220276069	220276069	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	attttggtctggaccacacaAccttggacgattccagccaa	8	12	1	0	rs112842443		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:220276069A>G	ENST00000302637.5	+	7	1004	c.900A>G	c.(898-900)caA>caG	p.Q300Q	IARS2_ENST00000366922.1_Silent_p.Q228Q	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	300					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	GGACCACACAACCTTGGACGA	0.343																																					p.Q300Q		Atlas-SNP	.											.	IARS2	106	.	0			c.A900G						.						111	107	108					1																	220276069		2203	4300	6503	SO:0001819	synonymous_variant	55699	exon7			CACACAACCTTGG	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.900A>G	chr1.hg19:g.220276069A>G		65.0	0.0		76.0	4.0	NM_018060	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Silent	SNP	ENST00000302637.5	hg19	CCDS1523.1																																																																																			.	A|0.500;G|0.500		0.343	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		G	220276069	A	G	220276069	2	3	43	1	0	0	0	0	0	0	0	1	7483	40	2	2		2	IARS2	1	220276069	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	16183217	220276069	28974552	30	5112										
EPHX1	2052	hgsc.bcm.edu	37	chr1	226016567	226016567	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtccgcagccagggaggacgAcagcatccgccctttcaagg	13	14	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:226016567A>G	ENST00000366837.4	+	2	333	c.137A>G	c.(136-138)gAc>gGc	p.D46G	EPHX1_ENST00000467015.1_3'UTR|EPHX1_ENST00000272167.5_Missense_Mutation_p.D46G	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	46					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					AGGGAGGACGACAGCATCCGC	0.602																																					p.D46G		Atlas-SNP	.											.	EPHX1	57	.	0			c.A137G						.						43	38	40					1																	226016567		2203	4300	6503	SO:0001583	missense	2052	exon2			AGGACGACAGCAT	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.137A>G	chr1.hg19:g.226016567A>G	ENSP00000355802:p.Asp46Gly	84.0	0.0		99.0	5.0	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Missense_Mutation	SNP	ENST00000366837.4	hg19	CCDS1547.1	.	.	.	.	.	.	.	.	.	.	A	8.638	0.895363	0.17613	.	.	ENSG00000143819	ENST00000445856;ENST00000272167;ENST00000448202;ENST00000366837	T;T;T;T	0.03831	3.79;3.79;3.79;3.79	5.0	3.85	0.44370	.	0.319521	0.30949	N	0.008543	T	0.04003	0.0112	N	0.19112	0.55	0.23232	N	0.998072	B	0.18013	0.025	B	0.20184	0.028	T	0.39292	-0.9621	10	0.33940	T	0.23	0.0749	11.7659	0.51930	0.6484:0.3516:0.0:0.0	.	46	P07099	HYEP_HUMAN	G	46	ENSP00000398491:D46G;ENSP00000272167:D46G;ENSP00000408469:D46G;ENSP00000355802:D46G	ENSP00000272167:D46G	D	+	2	0	EPHX1	224083190	0.856000	0.29760	0.988000	0.46212	0.303000	0.27691	1.829000	0.39121	0.726000	0.32339	0.379000	0.24179	GAC	.	.		0.602	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120		G	226016567	A	G	226016567	3	3	43	1	0	0	0	0	1	0	0	0	5181	275	10	2	139	2	EPHX1	1	226016567	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	5740498	226016567	23234054	31	5113										
LIN9	286826	hgsc.bcm.edu	37	chr1	226420805	226420805	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctaacgaattacctgatattAgaagcgtctattgtactctt	6	8	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:226420805A>G	ENST00000328205.5	-	14	2108	c.1563T>C	c.(1561-1563)tcT>tcC	p.S521S	LIN9_ENST00000481685.1_Silent_p.S486S|LIN9_ENST00000366801.1_Silent_p.S470S	NM_173083.3	NP_775106.2	Q5TKA1	LIN9_HUMAN	lin-9 DREAM MuvB core complex component	505					DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|transcriptional repressor complex (GO:0017053)				breast(3)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		ACCTGATATTAGAAGCGTCTA	0.323																																					p.S521S	Ovarian(197;1696 2974 11248 14117)	Atlas-SNP	.											.	LIN9	57	.	0			c.T1563C						.						68	75	73					1																	226420805		2203	4291	6494	SO:0001819	synonymous_variant	286826	exon14			GATATTAGAAGCG	AY166858	CCDS1553.1	1q42	2014-07-17	2014-07-17		ENSG00000183814	ENSG00000183814			30830	protein-coding gene	gene with protein product	"TUDOR gene similar", "rb related pathway actor"	609375	"lin-9 homolog (C. elegans)"			15538385, 23667535	Standard	NM_173083		Approved	TGS	uc001hqa.3	Q5TKA1	OTTHUMG00000037557	ENST00000328205.5:c.1563T>C	chr1.hg19:g.226420805A>G		59.0	0.0		90.0	4.0	NM_173083	Q5U5L8|Q5U7E1|Q6PI55|Q6ZTV4|Q7Z3J1	Silent	SNP	ENST00000328205.5	hg19	CCDS1553.1																																																																																			.	.		0.323	LIN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091523.2	NM_173083		G	226420805	A	G	226420805	2	3	43	1	0	0	0	0	0	0	0	1	8822	407	15	2		2	LIN9	1	226420805	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	404238	226420805	22829816	32	5114										
ADSS	159	hgsc.bcm.edu	37	chr1	244574699	244574699	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgttccatcctgggagagtcTtatattgaacttcaacttta	7	8	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:244574699T>C	ENST00000366535.3	-	12	1524	c.1208A>G	c.(1207-1209)aAg>aGg	p.K403R	RP11-518L10.5_ENST00000417765.1_RNA	NM_001126.3	NP_001117.2			adenylosuccinate synthase											endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(71;2.17e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)	all_cancers(173;0.0896)|all_epithelial(177;0.172)	all cancers(7;9.71e-08)|GBM - Glioblastoma multiforme(7;1.28e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.0014)			TGGGAGAGTCTTATATTGAAC	0.343																																					p.K403R		Atlas-SNP	.											.	ADSS	49	.	0			c.A1208G						.						130	129	130					1																	244574699		2203	4300	6503	SO:0001583	missense	159	exon12			AGAGTCTTATATT	BC012356	CCDS1624.1	1q44	2008-02-05			ENSG00000035687	ENSG00000035687	6.3.4.4		292	protein-coding gene	gene with protein product		103060				2004783, 1592113	Standard	NM_001126		Approved		uc001iaj.3	P30520	OTTHUMG00000040102	ENST00000366535.3:c.1208A>G	chr1.hg19:g.244574699T>C	ENSP00000355493:p.Lys403Arg	78.0	0.0		89.0	4.0	NM_001126		Missense_Mutation	SNP	ENST00000366535.3	hg19	CCDS1624.1	.	.	.	.	.	.	.	.	.	.	T	17.26	3.345552	0.61073	.	.	ENSG00000035687	ENST00000366535;ENST00000449326	T	0.45668	0.89	5.81	4.68	0.58851	.	0.088135	0.85682	D	0.000000	T	0.31199	0.0789	L	0.27975	0.815	0.41124	D	0.985835	B	0.06786	0.001	B	0.06405	0.002	T	0.07233	-1.0783	10	0.59425	D	0.04	-11.5745	11.9233	0.52803	0.0:0.068:0.0:0.932	.	403	P30520	PURA2_HUMAN	R	403;382	ENSP00000355493:K403R	ENSP00000355493:K403R	K	-	2	0	ADSS	242641322	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.999000	0.70665	1.014000	0.39417	0.528000	0.53228	AAG	.	.		0.343	ADSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096697.1	NM_001126		C	244574699	T	C	244574699	3	2	43	1	0	0	0	0	1	0	0	0	347	1609	56	2	170	2	ADSS	1	244574699	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	18153894	244574699	4675922	33	5115										
CNST	163882	hgsc.bcm.edu	37	chr1	246754974	246754974	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctgtctgccttctgcatcagAtgaaaatgaaaatcagcttg	8	9	4	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr1:246754974A>T	ENST00000366513.4	+	2	379	c.110A>T	c.(109-111)gAt>gTt	p.D37V	CNST_ENST00000366512.3_Missense_Mutation_p.D37V|CNST_ENST00000483271.1_3'UTR	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	37					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						TCTGCATCAGATGAAAATGAA	0.493																																					p.D37V		Atlas-SNP	.											.	CNST	73	.	0			c.A110T						.						144	127	133					1																	246754974		2203	4300	6503	SO:0001583	missense	163882	exon2			CATCAGATGAAAA	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	26486	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 64"	613439	"chromosome 1 open reading frame 71"	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.110A>T	chr1.hg19:g.246754974A>T	ENSP00000355470:p.Asp37Val	119.0	0.0		143.0	45.0	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	hg19	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443183	0.83993	.	.	ENSG00000162852	ENST00000366513;ENST00000366512;ENST00000366511	T;T;T	0.26223	1.75;1.75;1.75	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.52125	0.1715	M	0.76002	2.32	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.55010	-0.8207	10	0.87932	D	0	-10.1254	14.5632	0.68156	1.0:0.0:0.0:0.0	.	37;37	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	V	37	ENSP00000355470:D37V;ENSP00000355469:D37V;ENSP00000355468:D37V	ENSP00000355468:D37V	D	+	2	0	CNST	244821597	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	5.987000	0.70571	2.371000	0.80710	0.533000	0.62120	GAT	.	.		0.493	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		T	246754974	A	T	246754974	3	4	43	1	0	0	0	0	1	0	0	0	3636	333	12	4	112	4	CNST	1	246754974	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	2180275	246754974	2495647	34	5116										
WDR35	57539	hgsc.bcm.edu	37	chr2	20169327	20169327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acctccttcccaagatagtgCagatatttcctttccaggaa	6	12	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:20169327C>T	ENST00000345530.3	-	9	1037	c.922G>A	c.(922-924)Gca>Aca	p.A308T	WDR35_ENST00000281405.4_Missense_Mutation_p.A308T|WDR35_ENST00000416055.2_5'UTR	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	308					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)		p.A308T(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAGATAGTGCAGATATTTCC	0.323																																					p.A308T		Atlas-SNP	.											WDR35,rectum,carcinoma,0,1	WDR35	92	.	1	Substitution - Missense(1)	large_intestine(1)	c.G922A						.						78	80	79					2																	20169327		2203	4300	6503	SO:0001583	missense	57539	exon9			ATAGTGCAGATAT	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"WD repeat domain containing", "Intraflagellar transport homologs"	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.922G>A	chr2.hg19:g.20169327C>T	ENSP00000314444:p.Ala308Thr	46.0	0.0		47.0	2.0	NM_020779	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	hg19	CCDS33152.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.100893	0.56183	.	.	ENSG00000118965	ENST00000345530;ENST00000281405	T;T	0.63096	-0.02;-0.02	4.58	3.67	0.42095	.	0.116795	0.56097	D	0.000027	T	0.59418	0.2192	M	0.69823	2.125	0.80722	D	1	B;B	0.26483	0.15;0.034	B;B	0.34779	0.189;0.081	T	0.51466	-0.8702	10	0.06494	T	0.89	-8.2294	12.0686	0.53603	0.3201:0.6799:0.0:0.0	.	308;308	Q9P2L0-2;Q9P2L0	.;WDR35_HUMAN	T	308	ENSP00000314444:A308T;ENSP00000281405:A308T	ENSP00000281405:A308T	A	-	1	0	WDR35	20032808	1.000000	0.71417	0.963000	0.40424	0.976000	0.68499	4.954000	0.63631	0.846000	0.35142	0.460000	0.39030	GCA	.	.		0.323	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779		T	20169327	C	T	20169327	3	4	43	1	0	0	0	0	1	0	0	0	17304	710	25	3	2703	3	WDR35	2	20169327	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10		20169327	223030046	35	5117										
NRBP1	29959	hgsc.bcm.edu	37	chr2	27656637	27656637	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaatgaggtacagttctctgAacgcaagaactacaagctgc	10	9	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:27656637A>G	ENST00000233557.3	+	4	1140	c.308A>G	c.(307-309)gAa>gGa	p.E103G	NRBP1_ENST00000379852.3_Missense_Mutation_p.E103G|NRBP1_ENST00000379863.3_Missense_Mutation_p.E103G			Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein 1	103	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ER to Golgi vesicle-mediated transport (GO:0006888)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell projection (GO:0042995)|endomembrane system (GO:0012505)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					CAGTTCTCTGAACGCAAGAAC	0.483																																					p.E103G		Atlas-SNP	.											.	NRBP1	40	.	0			c.A308G						.						116	113	114					2																	27656637		2203	4300	6503	SO:0001583	missense	29959	exon3			TCTCTGAACGCAA	AF113249	CCDS1753.1	2p23	2008-02-05	2005-12-22	2005-12-22	ENSG00000115216	ENSG00000115216			7993	protein-coding gene	gene with protein product		606010	"nuclear receptor binding protein"	NRBP		10843813, 11956649	Standard	NM_013392		Approved	BCON3, MUDPNP, MADM	uc002rkp.3	Q9UHY1	OTTHUMG00000097789	ENST00000233557.3:c.308A>G	chr2.hg19:g.27656637A>G	ENSP00000233557:p.Glu103Gly	74.0	0.0		81.0	4.0	NM_013392	B3KV40|D6W558|Q53FZ5|Q96SU3	Missense_Mutation	SNP	ENST00000233557.3	hg19	CCDS1753.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.029826	0.93575	.	.	ENSG00000115216	ENST00000233557;ENST00000421823;ENST00000379852;ENST00000379863;ENST00000419281	T;T;T	0.67171	-0.25;-0.25;-0.25	5.26	5.26	0.73747	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77955	0.4208	M	0.64080	1.96	0.80722	D	1	D;D	0.60575	0.984;0.988	D;D	0.66716	0.91;0.946	T	0.78677	-0.2111	10	0.48119	T	0.1	-12.8784	13.9748	0.64265	1.0:0.0:0.0:0.0	.	103;103	F8W6G1;Q9UHY1	.;NRBP_HUMAN	G	103;83;103;103;103	ENSP00000233557:E103G;ENSP00000369181:E103G;ENSP00000369192:E103G	ENSP00000233557:E103G	E	+	2	0	NRBP1	27510141	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.847000	0.92166	1.988000	0.58038	0.459000	0.35465	GAA	.	.		0.483	NRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215033.1	NM_013392		G	27656637	A	G	27656637	3	3	43	1	0	0	0	0	1	0	0	0	10651	246	9	2	314	2	NRBP1	2	27656637	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	7487310	27656637	215542736	36	5118										
FAM98A	25940	hgsc.bcm.edu	37	chr2	33811687	33811687	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catccaaacgttttattagcAgctttctccggacttcatat	5	11	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:33811687A>G	ENST00000238823.8	-	6	802	c.662T>C	c.(661-663)cTg>cCg	p.L221P	FAM98A_ENST00000403368.1_Missense_Mutation_p.L221P|FAM98A_ENST00000498340.1_5'Flank|FAM98A_ENST00000441530.2_Missense_Mutation_p.L26P			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	222							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					TTTTATTAGCAGCTTTCTCCG	0.348																																					p.L221P		Atlas-SNP	.											.	FAM98A	42	.	0			c.T662C						.						144	140	141					2																	33811687		2203	4300	6503	SO:0001583	missense	25940	exon6			ATTAGCAGCTTTC		CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.662T>C	chr2.hg19:g.33811687A>G	ENSP00000238823:p.Leu221Pro	84.0	0.0		87.0	4.0	NM_015475	B2RNA2|Q9Y3Y6	Missense_Mutation	SNP	ENST00000238823.8	hg19	CCDS33179.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.252846	0.80135	.	.	ENSG00000119812	ENST00000238823;ENST00000395190;ENST00000403368;ENST00000441530	T;T;T	0.48836	0.8;0.8;0.8	5.76	4.59	0.56863	.	0.061993	0.64402	D	0.000014	T	0.63058	0.2479	L	0.52905	1.665	0.80722	D	1	D;D;P	0.71674	0.995;0.998;0.936	P;D;B	0.75484	0.879;0.986;0.367	T	0.65615	-0.6125	10	0.87932	D	0	-5.4484	13.2866	0.60247	0.8677:0.1323:0.0:0.0	.	222;52;221	Q8NCA5;B4DY25;Q8NCA5-2	FA98A_HUMAN;.;.	P	221;222;221;26	ENSP00000238823:L221P;ENSP00000384711:L221P;ENSP00000408716:L26P	ENSP00000238823:L221P	L	-	2	0	FAM98A	33665191	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.415000	0.80131	1.090000	0.41315	0.528000	0.53228	CTG	.	.		0.348	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475		G	33811687	A	G	33811687	3	3	43	1	0	0	0	0	1	0	0	0	5664	188	7	2	906	2	FAM98A	2	33811687	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	6155050	33811687	209387686	37	5119										
FAM82A1	151393	hgsc.bcm.edu	37	chr2	38218373	38218373	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cttttttcaggaacatctagAtatagcaatcaaacttttac	4	8	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:38218373A>G	ENST00000406384.1	+	7	1072	c.878A>G	c.(877-879)gAt>gGt	p.D293G	RMDN2_ENST00000417700.2_Missense_Mutation_p.D148G|RMDN2_ENST00000234195.3_Missense_Mutation_p.D471G|RMDN2_ENST00000354545.2_Missense_Mutation_p.D293G|RMDN2_ENST00000407257.1_Missense_Mutation_p.D471G|RMDN2-AS1_ENST00000414365.2_RNA	NM_001170792.1	NP_001164263.1	Q96LZ7	RMD2_HUMAN	regulator of microtubule dynamics 2	293						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)											GAACATCTAGATATAGCAATC	0.343																																					p.D471G		Atlas-SNP	.											.	.	.	.	0			c.A1412G						.						90	92	91					2																	38218373		2203	4300	6503	SO:0001583	missense	151393	exon7			ATCTAGATATAGC	AK057516	CCDS1792.1, CCDS54351.1, CCDS54352.1	2p22.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000115841	ENSG00000115841			26567	protein-coding gene	gene with protein product		611872	"family with sequence similarity 82, member A1"	FAM82A, FAM82A1		12477932	Standard	XM_005264161		Approved	FLJ32954, RMD2	uc002rqn.2	Q96LZ7	OTTHUMG00000128487	ENST00000406384.1:c.878A>G	chr2.hg19:g.38218373A>G	ENSP00000386004:p.Asp293Gly	47.0	0.0		64.0	4.0	NM_144713	A9UMZ7|A9UN00|Q4ZG33|Q6UXN4|Q8N657|Q8N9A2|Q8NCV6|Q8NHM0	Missense_Mutation	SNP	ENST00000406384.1	hg19	CCDS54351.1	.	.	.	.	.	.	.	.	.	.	A	15.18	2.758402	0.49468	.	.	ENSG00000115841	ENST00000354545;ENST00000406384;ENST00000407257;ENST00000417700;ENST00000234195;ENST00000442857	T;T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59;0.59	5.63	4.4	0.53042	Tetratricopeptide-like helical (1);	0.347273	0.30455	N	0.009598	T	0.64057	0.2564	M	0.84082	2.675	0.44985	D	0.998004	B;P;P;P	0.50943	0.39;0.94;0.94;0.894	B;P;P;P	0.51742	0.341;0.678;0.678;0.678	T	0.69946	-0.5007	10	0.72032	D	0.01	.	10.0512	0.42216	0.8492:0.0:0.0:0.1508	.	471;148;293;148	Q96LZ7-2;Q96LZ7-4;Q96LZ7;Q96LZ7-3	.;.;RMD2_HUMAN;.	G	293;293;471;148;471;148	ENSP00000346549:D293G;ENSP00000386004:D293G;ENSP00000385049:D471G;ENSP00000392977:D148G;ENSP00000234195:D471G;ENSP00000416367:D148G	ENSP00000234195:D471G	D	+	2	0	FAM82A1	38071877	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.193000	0.58385	2.271000	0.75665	0.533000	0.62120	GAT	.	.		0.343	RMDN2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325577.1	NM_144713		G	38218373	A	G	38218373	3	3	43	1	0	0	0	0	1	0	0	0	5638	333	12	2	1894	2	FAM82A1	2	38218373	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	4406686	38218373	204981000	38	5120										
DYNC2LI1	51626	hgsc.bcm.edu	37	chr2	44032355	44032355	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cctcagtatgctgaaaatgaAgtcgatgagatgagaattca	10	6	2	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:44032355A>G	ENST00000260605.8	+	12	1063	c.963A>G	c.(961-963)gaA>gaG	p.E321E	DYNC2LI1_ENST00000605786.1_Silent_p.E322E|DYNC2LI1_ENST00000443170.3_Silent_p.E195E	NM_001193464.1|NM_016008.3	NP_001180393.1|NP_057092.2	Q8TCX1	DC2L1_HUMAN	dynein, cytoplasmic 2, light intermediate chain 1	321					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)	apical part of cell (GO:0045177)|axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytosol (GO:0005829)|intraciliary transport particle (GO:0030990)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|primary cilium (GO:0072372)	motor activity (GO:0003774)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|skin(1)	26		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CTGAAAATGAAGTCGATGAGA	0.373																																					p.E322E		Atlas-SNP	.											.	DYNC2LI1	46	.	0			c.A966G						.						88	93	91					2																	44032355		2203	4300	6503	SO:0001819	synonymous_variant	51626	exon12			AAATGAAGTCGAT		CCDS1813.1, CCDS46270.1, CCDS62903.1	2p25.1-p24.1	2008-02-05			ENSG00000138036	ENSG00000138036		"Cytoplasmic dyneins"	24595	protein-coding gene	gene with protein product						10810093, 11907264	Standard	NM_016008		Approved	D2LIC, LIC3, CGI-60, DKFZP564A033	uc002rtl.3	Q8TCX1	OTTHUMG00000128656	ENST00000260605.8:c.963A>G	chr2.hg19:g.44032355A>G		99.0	0.0		119.0	6.0	NM_001193464	A8MVJ5|Q53F57|Q6PDB2|Q8IWA3|Q96B03|Q96J00|Q9Y370|Q9Y3S9	Silent	SNP	ENST00000260605.8	hg19	CCDS1813.1	.	.	.	.	.	.	.	.	.	.	A	7.232	0.599551	0.13939	.	.	ENSG00000138036	ENST00000378587	.	.	.	4.88	3.68	0.42216	.	.	.	.	.	T	0.62575	0.2439	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60094	-0.7330	4	.	.	.	-29.5592	11.8498	0.52405	0.8534:0.1466:0.0:0.0	.	.	.	.	R	305	.	.	K	+	2	0	DYNC2LI1	43885859	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	1.350000	0.34010	0.948000	0.37687	0.533000	0.62120	AAG	.	.		0.373	DYNC2LI1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250536.2	NM_016008		G	44032355	A	G	44032355	2	3	43	1	0	0	0	0	0	0	0	1	4849	69	3	2		2	DYNC2LI1	2	44032355	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	5813982	44032355	199167018	39	5121										
RTN4	57142	hgsc.bcm.edu	37	chr2	55254181	55254181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttcatcctctttaaccaattTagtaagagctgtaggtaact	6	8	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:55254181T>C	ENST00000337526.6	-	3	1297	c.1054A>G	c.(1054-1056)Aaa>Gaa	p.K352E	RTN4_ENST00000357732.4_Intron|RTN4_ENST00000404909.1_Missense_Mutation_p.K146E|RTN4_ENST00000354474.6_Missense_Mutation_p.K120E|RTN4_ENST00000394611.2_Missense_Mutation_p.K146E|RTN4_ENST00000405240.1_Missense_Mutation_p.K146E|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357376.3_Missense_Mutation_p.K146E	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	352					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						TTAACCAATTTAGTAAGAGCT	0.348																																					p.K352E		Atlas-SNP	.											.	RTN4	189	.	0			c.A1054G						.						109	111	110					2																	55254181		2203	4298	6501	SO:0001583	missense	57142	exon3			CCAATTTAGTAAG	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.1054A>G	chr2.hg19:g.55254181T>C	ENSP00000337838:p.Lys352Glu	84.0	0.0		66.0	30.0	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	hg19	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	T	0.033	-1.319899	0.01320	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.18810	2.19;2.19;2.29;2.19;2.19;2.2	5.83	-6.08	0.02151	.	7739.210000	0.00166	N	0.000000	T	0.10165	0.0249	N	0.17082	0.46	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.16600	-1.0397	10	0.18276	T	0.48	0.2994	3.1864	0.06602	0.0972:0.3614:0.193:0.3484	.	352	Q9NQC3	RTN4_HUMAN	E	146;146;352;146;146;120	ENSP00000384471:K146E;ENSP00000349944:K146E;ENSP00000337838:K352E;ENSP00000378109:K146E;ENSP00000385650:K146E;ENSP00000346465:K120E	ENSP00000337838:K352E	K	-	1	0	RTN4	55107685	0.000000	0.05858	0.000000	0.03702	0.183000	0.23260	-0.582000	0.05814	-1.296000	0.02353	0.528000	0.53228	AAA	.	.		0.348	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			C	55254181	T	C	55254181	3	2	43	1	0	0	0	0	1	0	0	0	13743	1763	61	2	2590	2	RTN4	2	55254181	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	11221826	55254181	187945192	40	5122										
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55562103	55562103	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tctcctttttctttataatgTtccaattcttttttaatttg	2	7	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:55562103T>C	ENST00000436346.1	-	15	2695	c.1854A>G	c.(1852-1854)gaA>gaG	p.E618E	AC012358.8_ENST00000608103.1_RNA|AC012358.8_ENST00000599475.1_RNA|AC012358.8_ENST00000599352.1_RNA|AC012358.8_ENST00000600219.1_RNA|AC012358.8_ENST00000594078.1_RNA|CCDC88A_ENST00000336838.6_Silent_p.E618E|CCDC88A_ENST00000413716.2_Silent_p.E618E|CCDC88A_ENST00000263630.8_Silent_p.E618E	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	618					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						CTTTATAATGTTCCAATTCTT	0.244																																					p.E618E		Atlas-SNP	.											.	CCDC88A	336	.	0			c.A1854G						.						28	27	27					2																	55562103		2199	4294	6493	SO:0001819	synonymous_variant	55704	exon15			ATAATGTTCCAAT	AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.1854A>G	chr2.hg19:g.55562103T>C		83.0	0.0		99.0	4.0	NM_018084	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Silent	SNP	ENST00000436346.1	hg19																																																																																				.	.		0.244	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		C	55562103	T	C	55562103	2	2	43	1	0	0	0	0	0	0	0	1	2865	1722	60	2		2	CCDC88A	2	55562103	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	307922	55562103	187637270	41	5123										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73799567	73799567	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttcagcatcatccagacaaAcatagagaacacatgtgtct	6	10	3	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:73799567A>G	ENST00000264448.6	+	16	10671	c.10560A>G	c.(10558-10560)aaA>aaG	p.K3520K	ALMS1_ENST00000409009.1_Silent_p.K3478K	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3520					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						ATCCAGACAAACATAGAGAAC	0.373																																					p.K3520K		Atlas-SNP	.											.	ALMS1	384	.	0			c.A10560G						.						86	79	81					2																	73799567		1879	4118	5997	SO:0001819	synonymous_variant	7840	exon16			AGACAAACATAGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.10560A>G	chr2.hg19:g.73799567A>G		83.0	0.0		96.0	4.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.373	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		G	73799567	A	G	73799567	2	3	43	1	0	0	0	0	0	0	0	1	535	40	2	2		2	ALMS1	2	73799567	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	18237464	73799567	169399806	42	5124										
EIF2AK3	9451	hgsc.bcm.edu	37	chr2	88879055	88879055	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cctattggggagacggatccTcttgatagcataattgcagt	11	8	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:88879055T>C	ENST00000303236.3	-	11	2168	c.1867A>G	c.(1867-1869)Agg>Ggg	p.R623G	EIF2AK3_ENST00000419748.1_Missense_Mutation_p.R472G	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	623	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						AGACGGATCCTCTTGATAGCA	0.403																																					p.R623G	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.A1867G						.						167	160	162					2																	88879055		2203	4300	6503	SO:0001583	missense	9451	exon11			GGATCCTCTTGAT	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.1867A>G	chr2.hg19:g.88879055T>C	ENSP00000307235:p.Arg623Gly	107.0	0.0		90.0	5.0	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Missense_Mutation	SNP	ENST00000303236.3	hg19	CCDS33241.1	.	.	.	.	.	.	.	.	.	.	T	16.26	3.072809	0.55646	.	.	ENSG00000172071	ENST00000419748;ENST00000303236;ENST00000535951;ENST00000415570	T;T;T	0.21361	2.01;2.01;2.01	6.06	6.06	0.98353	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043020	0.85682	D	0.000000	T	0.32852	0.0843	M	0.84219	2.685	0.80722	D	1	B	0.25235	0.121	B	0.26416	0.069	T	0.12785	-1.0534	10	0.87932	D	0	-24.0879	15.1804	0.72952	0.0:0.0:0.0:1.0	.	623	Q9NZJ5	E2AK3_HUMAN	G	472;623;472;502	ENSP00000408325:R472G;ENSP00000307235:R623G;ENSP00000412076:R502G	ENSP00000307235:R623G	R	-	1	2	EIF2AK3	88660170	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.170000	0.71920	2.324000	0.78689	0.533000	0.62120	AGG	.	.		0.403	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		C	88879055	T	C	88879055	3	2	43	1	0	0	0	0	1	0	0	0	5000	1550	54	2	1511	2	EIF2AK3	2	88879055	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	15079488	88879055	154320318	43	5125										
PSD4	23550	hgsc.bcm.edu	37	chr2	113950141	113950141	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tggagggcttccggaagtctGaagtggctgcctacctgcag	15	10	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:113950141G>A	ENST00000245796.6	+	6	2008	c.1813G>A	c.(1813-1815)Gaa>Aaa	p.E605K	PSD4_ENST00000441564.3_Missense_Mutation_p.E577K	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	605	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCGGAAGTCTGAAGTGGCTGC	0.597																																					p.E605K		Atlas-SNP	.											.	PSD4	74	.	0			c.G1813A						.						71	74	73					2																	113950141		2203	4300	6503	SO:0001583	missense	23550	exon6			AAGTCTGAAGTGG	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"Pleckstrin homology (PH) domain containing"	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.1813G>A	chr2.hg19:g.113950141G>A	ENSP00000245796:p.Glu605Lys	47.0	0.0		33.0	20.0	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	hg19	CCDS33276.1	.	.	.	.	.	.	.	.	.	.	g	26.9	4.781639	0.90282	.	.	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.51817	0.69;0.69	5.68	5.68	0.88126	SEC7-like (4);	0.161385	0.53938	D	0.000043	T	0.42921	0.1224	N	0.20483	0.58	0.80722	D	1	P;P;B	0.49783	0.766;0.928;0.333	P;P;P	0.49708	0.561;0.62;0.536	T	0.42932	-0.9422	10	0.87932	D	0	.	12.9495	0.58391	0.0:0.1627:0.8373:0.0	.	263;577;605	Q59HG0;Q8NDX1-2;Q8NDX1	.;.;PSD4_HUMAN	K	605;577	ENSP00000245796:E605K;ENSP00000413997:E577K	ENSP00000245796:E605K	E	+	1	0	PSD4	113666612	1.000000	0.71417	0.988000	0.46212	0.996000	0.88848	3.299000	0.51826	2.692000	0.91855	0.651000	0.88453	GAA	.	.		0.597	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455		A	113950141	G	A	113950141	3	1	43	1	0	0	0	0	1	0	0	0	12661	1291	45	3	1831	3	PSD4	2	113950141	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	25071086	113950141	129249232	44	5126										
NMI	9111	hgsc.bcm.edu	37	chr2	152127280	152127280	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctacttctccacctccattcTttgcccgttgaaagtgaatg	6	13	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:152127280T>C	ENST00000243346.5	-	8	1321	c.851A>G	c.(850-852)aAg>aGg	p.K284R		NM_004688.2	NP_004679.2	Q13287	NMI_HUMAN	N-myc (and STAT) interactor	284					inflammatory response (GO:0006954)|JAK-STAT cascade (GO:0007259)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription cofactor activity (GO:0003712)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.0571)		ACCTCCATTCTTTGCCCGTTG	0.393																																					p.K284R		Atlas-SNP	.											.	NMI	21	.	0			c.A851G						.						182	171	175					2																	152127280		2203	4300	6503	SO:0001583	missense	9111	exon8			CCATTCTTTGCCC	U32849	CCDS2192.1	2q23	2008-05-23			ENSG00000123609	ENSG00000123609			7854	protein-coding gene	gene with protein product		603525				8668343, 9989503	Standard	NM_004688		Approved		uc002txi.2	Q13287	OTTHUMG00000131867	ENST00000243346.5:c.851A>G	chr2.hg19:g.152127280T>C	ENSP00000243346:p.Lys284Arg	102.0	0.0		94.0	4.0	NM_004688	B5BU69|Q53TI8|Q9BVE5	Missense_Mutation	SNP	ENST00000243346.5	hg19	CCDS2192.1	.	.	.	.	.	.	.	.	.	.	T	9.898	1.206042	0.22205	.	.	ENSG00000123609	ENST00000243346	T	0.38240	1.15	5.26	1.42	0.22433	Nmi/IFP 35 (1);	0.373716	0.30126	N	0.010349	T	0.17492	0.0420	N	0.17312	0.475	0.09310	N	1	B	0.18741	0.03	B	0.20184	0.028	T	0.14755	-1.0461	10	0.20519	T	0.43	-11.8808	5.2342	0.15437	0.0:0.1:0.3929:0.5072	.	284	Q13287	NMI_HUMAN	R	284	ENSP00000243346:K284R	ENSP00000243346:K284R	K	-	2	0	NMI	151835526	0.163000	0.22920	0.951000	0.38953	0.907000	0.53573	0.194000	0.17135	0.818000	0.34468	0.482000	0.46254	AAG	.	.		0.393	NMI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254817.2	NM_004688		C	152127280	T	C	152127280	3	2	43	1	0	0	0	0	1	0	0	0	10506	1609	56	2	76	2	NMI	2	152127280	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	38177139	152127280	91072093	45	5127										
NMI	9111	hgsc.bcm.edu	37	chr2	152128184	152128184	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgtgtatggagaaacagtaaCtctatggcaggtttgattta	11	4	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:152128184C>A	ENST00000243346.5	-	7	1167	c.697G>T	c.(697-699)Gtt>Ttt	p.V233F		NM_004688.2	NP_004679.2	Q13287	NMI_HUMAN	N-myc (and STAT) interactor	233					inflammatory response (GO:0006954)|JAK-STAT cascade (GO:0007259)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription cofactor activity (GO:0003712)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.0571)		GAAACAGTAACTCTATGGCAG	0.343																																					p.V233F		Atlas-SNP	.											.	NMI	21	.	0			c.G697T						.						148	161	156					2																	152128184		2203	4300	6503	SO:0001583	missense	9111	exon7			CAGTAACTCTATG	U32849	CCDS2192.1	2q23	2008-05-23			ENSG00000123609	ENSG00000123609			7854	protein-coding gene	gene with protein product		603525				8668343, 9989503	Standard	NM_004688		Approved		uc002txi.2	Q13287	OTTHUMG00000131867	ENST00000243346.5:c.697G>T	chr2.hg19:g.152128184C>A	ENSP00000243346:p.Val233Phe	60.0	0.0		22.0	14.0	NM_004688	B5BU69|Q53TI8|Q9BVE5	Missense_Mutation	SNP	ENST00000243346.5	hg19	CCDS2192.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.041873	0.55003	.	.	ENSG00000123609	ENST00000243346	T	0.59906	0.23	5.92	5.92	0.95590	Nmi/IFP 35 (1);	0.114299	0.64402	D	0.000013	T	0.78654	0.4317	M	0.85542	2.76	0.38913	D	0.957577	D	0.89917	1.0	D	0.79784	0.993	T	0.82287	-0.0532	10	0.72032	D	0.01	-21.175	15.8301	0.78743	0.0:1.0:0.0:0.0	.	233	Q13287	NMI_HUMAN	F	233	ENSP00000243346:V233F	ENSP00000243346:V233F	V	-	1	0	NMI	151836430	0.883000	0.30277	0.199000	0.23439	0.361000	0.29550	2.276000	0.43408	2.810000	0.96702	0.585000	0.79938	GTT	.	.		0.343	NMI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254817.2	NM_004688		A	152128184	C	A	152128184	3	1	43	1	0	0	0	0	1	0	0	0	10506	565	20	3	234	3	NMI	2	152128184	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	904	152128184	91071189	46	5128										
ACVR1C	130399	hgsc.bcm.edu	37	chr2	158390463	158390463	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcttctttgacacaaagttgAgatatagtcttcttaatacg	6	7	4	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:158390463A>G	ENST00000243349.8	-	9	1809	c.1449T>C	c.(1447-1449)tcT>tcC	p.S483S	ACVR1C_ENST00000409680.3_Silent_p.S433S|ACVR1C_ENST00000335450.7_Silent_p.S403S|ACVR1C_ENST00000348328.5_Silent_p.S326S	NM_001111032.1|NM_145259.2	NP_001104502.1|NP_660302.2			activin A receptor, type IC											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	42						CACAAAGTTGAGATATAGTCT	0.403																																					p.S483S		Atlas-SNP	.											ACVR1C,right_upper_lobe,carcinoma,0,1	ACVR1C	85	.	0			c.T1449C						.						96	105	102					2																	158390463		2203	4300	6503	SO:0001819	synonymous_variant	130399	exon9			AAGTTGAGATATA	BC022530	CCDS2205.1, CCDS46432.1, CCDS46433.1, CCDS46434.1	2q24.2	2008-02-05			ENSG00000123612	ENSG00000123612			18123	protein-coding gene	gene with protein product		608981					Standard	NM_145259		Approved	ALK7, ACVRLK7	uc002tzk.4	Q8NER5	OTTHUMG00000131964	ENST00000243349.8:c.1449T>C	chr2.hg19:g.158390463A>G		47.0	0.0		37.0	2.0	NM_145259		Silent	SNP	ENST00000243349.8	hg19	CCDS2205.1																																																																																			.	.		0.403	ACVR1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254924.2	NM_145259		G	158390463	A	G	158390463	2	3	43	1	0	0	0	0	0	0	0	1	222	291	11	2		2	ACVR1C	2	158390463	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	6262279	158390463	84808910	47	5129										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160879270	160879270	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgacaagaacgcagagcctcAtgccaggtcttttcttcttt	8	11	4	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:160879270A>G	ENST00000283243.7	-	7	1406	c.1200T>C	c.(1198-1200)caT>caC	p.H400H	PLA2R1_ENST00000392771.1_Silent_p.H400H	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	400	C-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						GCAGAGCCTCATGCCAGGTCT	0.438																																					p.H400H		Atlas-SNP	.											.	PLA2R1	153	.	0			c.T1200C						.						150	141	144					2																	160879270		2203	4300	6503	SO:0001819	synonymous_variant	22925	exon7			AGCCTCATGCCAG	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.1200T>C	chr2.hg19:g.160879270A>G		133.0	0.0		81.0	4.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	hg19	CCDS33309.1																																																																																			.	.		0.438	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			G	160879270	A	G	160879270	2	3	43	1	0	0	0	0	0	0	0	1	12019	214	8	2		2	PLA2R1	2	160879270	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	2488807	160879270	82320103	48	5130										
TTC21B	79809	hgsc.bcm.edu	37	chr2	166788360	166788360	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcccaagttttccagcttggTggaagcctaaaacaaaagga	9	9	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:166788360T>C	ENST00000243344.7	-	8	939	c.802A>G	c.(802-804)Acc>Gcc	p.T268A	AC010127.5_ENST00000443032.1_RNA|AC010127.5_ENST00000440322.1_RNA	NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	268					forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)		p.T268S(1)		breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						TCCAGCTTGGTGGAAGCCTAA	0.368																																					p.T268A		Atlas-SNP	.											TTC21B,NS,carcinoma,0,1	TTC21B	130	.	1	Substitution - Missense(1)	lung(1)	c.A802G						.						115	105	108					2																	166788360		2203	4300	6503	SO:0001583	missense	79809	exon8			GCTTGGTGGAAGC	AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"Tetratricopeptide (TTC) repeat domain containing", "Intraflagellar transport homologs"	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.802A>G	chr2.hg19:g.166788360T>C	ENSP00000243344:p.Thr268Ala	59.0	0.0		55.0	3.0	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	hg19	CCDS33315.1	.	.	.	.	.	.	.	.	.	.	T	1.929	-0.446471	0.04604	.	.	ENSG00000123607	ENST00000243344	T	0.49139	0.79	5.48	-2.46	0.06461	Tetratricopeptide-like helical (1);	0.808960	0.11771	N	0.531104	T	0.19167	0.0460	N	0.11201	0.11	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.26883	-1.0090	10	0.07990	T	0.79	-0.3644	4.5639	0.12173	0.2916:0.3352:0.0:0.3732	.	268;268	Q7Z4L5-2;Q7Z4L5	.;TT21B_HUMAN	A	268	ENSP00000243344:T268A	ENSP00000243344:T268A	T	-	1	0	TTC21B	166496606	0.028000	0.19301	0.088000	0.20740	0.085000	0.17905	-0.318000	0.08050	-0.405000	0.07599	-0.256000	0.11100	ACC	.	.		0.368	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753		C	166788360	T	C	166788360	3	2	43	1	0	0	0	0	1	0	0	0	16703	1696	59	2	3236	2	TTC21B	2	166788360	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5909090	166788360	76411013	49	5131										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167142891	167142891	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcatgtgctcgcctatgcccTtcgacaccaaggtggaaact	9	13	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:167142891T>C	ENST00000409435.1	-	10	1556	c.1557A>G	c.(1555-1557)gaA>gaG	p.E519E	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.E520E|SCN9A_ENST00000409672.1_Silent_p.E519E|SCN9A_ENST00000375387.4_Silent_p.E520E			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	519			E -> K (in dbSNP:rs187453572). {ECO:0000269|PubMed:19763161}.		behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GCCTATGCCCTTCGACACCAA	0.458																																					p.E519E		Atlas-SNP	.											.	SCN9A	296	.	0			c.A1557G						.						255	239	244					2																	167142891		1930	4137	6067	SO:0001819	synonymous_variant	6335	exon11			ATGCCCTTCGACA	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1557A>G	chr2.hg19:g.167142891T>C		127.0	0.0		92.0	4.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	hg19	CCDS46441.1																																																																																			.	.		0.458	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		C	167142891	T	C	167142891	2	2	43	1	0	0	0	0	0	0	0	1	13940	1606	56	2		2	SCN9A	2	167142891	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	354531	167142891	76056482	50	5132										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167297978	167297978	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tggcctgcaacctccatacaGtcccacaaggtctctaccca	6	17	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:167297978G>A	ENST00000409855.1	-	14	2211	c.2085C>T	c.(2083-2085)gaC>gaT	p.D695D		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	695					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	CCTCCATACAGTCCCACAAGG	0.433																																					p.D695D		Atlas-SNP	.											.	SCN7A	410	.	0			c.C2085T						.						66	69	68					2																	167297978		2203	4300	6503	SO:0001819	synonymous_variant	6332	exon14			CATACAGTCCCAC	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.2085C>T	chr2.hg19:g.167297978G>A		146.0	0.0		82.0	57.0	NM_002976		Silent	SNP	ENST00000409855.1	hg19	CCDS46442.1																																																																																			.	.		0.433	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			A	167297978	G	A	167297978	2	1	43	1	0	0	0	0	0	0	0	1	13938	1020	36	3		3	SCN7A	2	167297978	Silent	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	155087	167297978	75901395	51	5133										
LASS6	253782	hgsc.bcm.edu	37	chr2	169626076	169626076	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcagatgaggaggactcagaAcctccgggaaagaatcccca	11	11	2	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:169626076A>G	ENST00000305747.6	+	10	1646	c.1059A>G	c.(1057-1059)gaA>gaG	p.E353E	CERS6_ENST00000392687.4_Silent_p.E361E|CERS6-AS1_ENST00000425636.2_RNA	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	353					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AGGACTCAGAACCTCCGGGAA	0.498																																					p.E361E		Atlas-SNP	.											.	.	.	.	0			c.A1083G						.						109	104	106					2																	169626076		2203	4300	6503	SO:0001819	synonymous_variant	253782	exon11			CTCAGAACCTCCG	BX393696	CCDS2228.1, CCDS58734.1	2q31	2011-07-11	2011-07-08	2011-07-08	ENSG00000172292	ENSG00000172292		"Homeoboxes / CERS class"	23826	protein-coding gene	gene with protein product		615336	"LAG1 longevity assurance homolog 6 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 6"	LASS6			Standard	NM_203463		Approved		uc002uec.2	Q6ZMG9	OTTHUMG00000132183	ENST00000305747.6:c.1059A>G	chr2.hg19:g.169626076A>G		59.0	0.0		86.0	4.0	NM_001256126	Q32M63|Q8N617	Silent	SNP	ENST00000305747.6	hg19	CCDS2228.1																																																																																			.	.		0.498	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463		G	169626076	A	G	169626076	2	3	43	1	0	0	0	0	0	0	0	1	8652	40	2	2		2	LASS6	2	169626076	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	2328098	169626076	73573297	52	5134										
LRP2	4036	hgsc.bcm.edu	37	chr2	170048456	170048456	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cagtacaatccacatcgccaTcacagacccaagactgggga	8	14	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:170048456T>C	ENST00000263816.3	-	48	9203	c.8918A>G	c.(8917-8919)gAt>gGt	p.D2973G		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2973	LDL-receptor class A 22. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CACATCGCCATCACAGACCCA	0.478																																					p.D2973G		Atlas-SNP	.											.	LRP2	751	.	0			c.A8918G						.						98	91	93					2																	170048456		2203	4300	6503	SO:0001583	missense	4036	exon48			TCGCCATCACAGA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.8918A>G	chr2.hg19:g.170048456T>C	ENSP00000263816:p.Asp2973Gly	78.0	0.0		69.0	4.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.740147	0.89573	.	.	ENSG00000081479	ENST00000263816	D	0.98732	-5.1	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.99527	0.9831	H	0.98682	4.3	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97869	1.0285	10	0.87932	D	0	.	16.0014	0.80294	0.0:0.0:0.0:1.0	.	2973	P98164	LRP2_HUMAN	G	2973	ENSP00000263816:D2973G	ENSP00000263816:D2973G	D	-	2	0	LRP2	169756702	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	7.841000	0.86834	2.181000	0.69327	0.528000	0.53228	GAT	.	.		0.478	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		C	170048456	T	C	170048456	3	2	43	1	0	0	0	0	1	0	0	0	8965	1435	50	2	5177	2	LRP2	2	170048456	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	422380	170048456	73150917	53	5135										
CHN1	1123	hgsc.bcm.edu	37	chr2	175673733	175673733	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccagtgataatgttgatatcTtcatacatgttcacagaaat	6	7	3	3	rs376051698		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:175673733T>C	ENST00000409900.3	-	11	1315	c.1002A>G	c.(1000-1002)gaA>gaG	p.E334E	CHN1_ENST00000409597.1_Silent_p.E150E|CHN1_ENST00000488080.1_5'UTR|CHN1_ENST00000409156.3_Silent_p.E308E|CHN1_ENST00000295497.7_Silent_p.E209E	NM_001822.5	NP_001813.1	P15882	CHIN_HUMAN	chimerin 1	334	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				ephrin receptor signaling pathway (GO:0048013)|motor neuron axon guidance (GO:0008045)|positive regulation of signal transduction (GO:0009967)|regulation of axonogenesis (GO:0050770)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.226)			TGTTGATATCTTCATACATGT	0.343			T	TAF15	extraskeletal myxoid chondrosarcoma																																p.E334E		Atlas-SNP	.		Dom	yes		2	2q31-q32.1	1123	chimerin (chimaerin) 1		M	.	CHN1	67	.	0			c.A1002G						.	T	,,	1,3743		0,1,1871	181	174	176		924,627,1002	3.7	1	2		176	3,8215		0,3,4106	no	coding-synonymous,coding-synonymous,coding-synonymous	CHN1	NM_001025201.3,NM_001206602.1,NM_001822.5	,,	0,4,5977	CC,CT,TT		0.0365,0.0267,0.0334	,,	308/434,209/335,334/460	175673733	4,11958	1872	4109	5981	SO:0001819	synonymous_variant	1123	exon11			GATATCTTCATAC		CCDS46454.1, CCDS46455.1, CCDS56147.1	2q31-q32.1	2013-02-14	2012-10-17		ENSG00000128656	ENSG00000128656		"Rho GTPase activating proteins", "SH2 domain containing"	1943	protein-coding gene	gene with protein product	"Chimerin 1 (GTPase-activating protein, rho, 2)", "chimaerin 1"	118423	"Duane retraction syndrome 2", "chimerin (chimaerin) 1"	CHN, DURS2		2299665, 15013773, 18653847	Standard	NM_001822		Approved	RhoGAP2, ARHGAP2, n-chimerin	uc002uji.3	P15882	OTTHUMG00000154225	ENST00000409900.3:c.1002A>G	chr2.hg19:g.175673733T>C		129.0	0.0		93.0	4.0	NM_001822	A8K1M6|B3KNU6|B4DV19|Q53SD6|Q53SH5|Q96FB0	Silent	SNP	ENST00000409900.3	hg19	CCDS46455.1																																																																																			.	.		0.343	CHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334453.1	NM_001822		C	175673733	T	C	175673733	2	2	43	1	0	0	0	0	0	0	0	1	3364	1606	56	2		2	CHN1	2	175673733	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5625277	175673733	67525640	54	5136										
TTN	7273	hgsc.bcm.edu	37	chr2	179577610	179577610	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttgaaccagctaacactgaAaggaggtgttccttttacga	9	8	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:179577610A>T	ENST00000591111.1	-	92	26415	c.26191T>A	c.(26191-26193)Ttc>Atc	p.F8731I	TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.F9048I|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.F7804I|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	12884	Ig-like 70.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTAACACTGAAAGGAGGTGTT	0.428																																					p.F9048I		Atlas-SNP	.											.	TTN	18412	.	0			c.T27142A						.						59	55	56					2																	179577610		1929	4130	6059	SO:0001583	missense	7273	exon94			CACTGAAAGGAGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.26191T>A	chr2.hg19:g.179577610A>T	ENSP00000465570:p.Phe8731Ile	78.0	0.0		95.0	35.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.09	2.132850	0.37630	.	.	ENSG00000155657	ENST00000342992	T	0.65916	-0.18	5.48	5.48	0.80851	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50548	0.1622	L	0.31065	0.9	0.80722	D	1	B	0.21071	0.051	B	0.17433	0.018	T	0.51482	-0.8700	9	0.87932	D	0	.	11.7623	0.51910	0.9291:0.0:0.0709:0.0	.	8731	Q8WZ42	TITIN_HUMAN	I	7804	ENSP00000343764:F7804I	ENSP00000343764:F7804I	F	-	1	0	TTN	179285855	0.816000	0.29132	0.998000	0.56505	0.996000	0.88848	1.358000	0.34102	2.198000	0.70561	0.533000	0.62120	TTC	.	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179577610	A	T	179577610	3	4	43	1	0	0	0	0	1	0	0	0	16750	14	1	4	77463	4	TTN	2	179577610	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	3903877	179577610	63621763	55	5137										
CCDC150	284992	hgsc.bcm.edu	37	chr2	197540964	197540964	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgaactacagactgttcagaAtgagaaaacccaactccagg	8	10	1	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:197540964A>G	ENST00000389175.4	+	11	1370	c.1235A>G	c.(1234-1236)aAt>aGt	p.N412S	CCDC150_ENST00000423093.2_Missense_Mutation_p.N80S|CCDC150_ENST00000272831.7_Missense_Mutation_p.N80S|CCDC150_ENST00000472405.2_3'UTR	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	412										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						ACTGTTCAGAATGAGAAAACC	0.403																																					p.N412S		Atlas-SNP	.											.	CCDC150	96	.	0			c.A1235G						.						170	169	169					2																	197540964		1905	4124	6029	SO:0001583	missense	284992	exon11			TTCAGAATGAGAA		CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.1235A>G	chr2.hg19:g.197540964A>G	ENSP00000373827:p.Asn412Ser	120.0	0.0		100.0	4.0	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Missense_Mutation	SNP	ENST00000389175.4	hg19	CCDS46478.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.026094	0.35701	.	.	ENSG00000144395	ENST00000272831;ENST00000389175;ENST00000423093	T	0.53857	0.6	5.26	4.08	0.47627	.	0.275149	0.28290	N	0.015898	T	0.48059	0.1479	L	0.60455	1.87	0.23712	N	0.997048	P;P	0.44139	0.728;0.827	B;B	0.41510	0.197;0.359	T	0.38650	-0.9651	10	0.36615	T	0.2	.	10.1163	0.42593	0.8317:0.1683:0.0:0.0	.	80;412	B4DZ03;Q8NCX0	.;CC150_HUMAN	S	80;412;80	ENSP00000373827:N412S	ENSP00000272831:N80S	N	+	2	0	CCDC150	197249209	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	3.635000	0.54309	0.973000	0.38340	0.455000	0.32223	AAT	.	.		0.403	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539		G	197540964	A	G	197540964	3	3	43	1	0	0	0	0	1	0	0	0	2787	101	4	2	1277	2	CCDC150	2	197540964	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	17963354	197540964	45658409	56	5138										
ALS2CR8	79800	hgsc.bcm.edu	37	chr2	203834662	203834662	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gatttacattaaaaaggtacAgaagtttcctgaatatagag	8	4	0	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:203834662A>G	ENST00000402905.3	+	10	1295	c.974A>G	c.(973-975)cAg>cGg	p.Q325R	CARF_ENST00000414439.1_Missense_Mutation_p.Q223R|CARF_ENST00000545262.1_Missense_Mutation_p.Q249R|CARF_ENST00000320443.8_Missense_Mutation_p.Q325R|CARF_ENST00000428585.1_Missense_Mutation_p.Q249R|WDR12_ENST00000477723.1_Intron|CARF_ENST00000545253.1_Missense_Mutation_p.Q237R|CARF_ENST00000456821.2_3'UTR|CARF_ENST00000438828.2_Missense_Mutation_p.Q325R	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	325					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AAAAAGGTACAGAAGTTTCCT	0.299																																					p.Q325R		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.A974G						.						59	53	54					2																	203834662		1786	4059	5845	SO:0001583	missense	79800	exon11			AGGTACAGAAGTT	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.974A>G	chr2.hg19:g.203834662A>G	ENSP00000384006:p.Gln325Arg	112.0	0.0		72.0	4.0	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	hg19	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	A	12.26	1.884843	0.33255	.	.	ENSG00000138380	ENST00000402905;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000320443;ENST00000438828	.	.	.	5.12	5.12	0.69794	.	0.078378	0.53938	D	0.000054	T	0.27134	0.0665	N	0.08118	0	0.33720	D	0.616834	B;B;B	0.30455	0.118;0.118;0.28	B;B;B	0.31442	0.13;0.09;0.09	T	0.33828	-0.9853	9	0.10636	T	0.68	-5.8278	14.0921	0.64998	1.0:0.0:0.0:0.0	.	237;249;325	B4DIA7;G3V1K7;Q8N187	.;.;AL2S8_HUMAN	R	325;223;249;237;249;325;325	.	ENSP00000316224:Q325R	Q	+	2	0	ALS2CR8	203542907	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.588000	0.60999	1.915000	0.55452	0.528000	0.53228	CAG	.	.		0.299	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		G	203834662	A	G	203834662	3	3	43	1	0	0	0	0	1	0	0	0	555	188	7	2	1004	2	ALS2CR8	2	203834662	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	6293698	203834662	39364711	57	5139										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207174473	207174473	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atagagatctagaagtgagcTgtgaaccggatggttttgag	14	4	1	5			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:207174473T>C	ENST00000374423.3	+	5	5607	c.5221T>C	c.(5221-5223)Tgt>Cgt	p.C1741R		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1741							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGAAGTGAGCTGTGAACCGGA	0.433																																					p.C1741R		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T5221C						.						71	71	71					2																	207174473		1867	4099	5966	SO:0001583	missense	57683	exon5			GTGAGCTGTGAAC	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5221T>C	chr2.hg19:g.207174473T>C	ENSP00000363545:p.Cys1741Arg	91.0	0.0		72.0	4.0	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	T	5.271	0.235353	0.10023	.	.	ENSG00000204186	ENST00000374423	T	0.49720	0.77	4.11	-2.77	0.05877	.	.	.	.	.	T	0.22704	0.0548	N	0.16478	0.41	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.15492	-1.0435	9	0.29301	T	0.29	.	0.8665	0.01205	0.1567:0.1963:0.322:0.325	.	1741	Q9HCK1	ZDBF2_HUMAN	R	1741	ENSP00000363545:C1741R	ENSP00000363545:C1741R	C	+	1	0	ZDBF2	206882718	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.076000	0.14712	-0.486000	0.06744	-0.280000	0.10049	TGT	.	.		0.433	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		C	207174473	T	C	207174473	3	2	43	1	0	0	0	0	1	0	0	0	17614	1580	55	2	5231	2	ZDBF2	2	207174473	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3339811	207174473	36024900	58	5140										
FN1	2335	hgsc.bcm.edu	37	chr2	216264012	216264012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcttggagcaggcgtccatgTgatcacaatggtggtctcag	13	9	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:216264012T>C	ENST00000359671.1	-	21	3581	c.3316A>G	c.(3316-3318)Aca>Gca	p.T1106A	FN1_ENST00000354785.4_Missense_Mutation_p.T1106A|FN1_ENST00000323926.6_Missense_Mutation_p.T1106A|FN1_ENST00000432072.2_Missense_Mutation_p.T1106A|FN1_ENST00000336916.4_Missense_Mutation_p.T1106A|FN1_ENST00000346544.3_Missense_Mutation_p.T1106A|FN1_ENST00000357009.2_Missense_Mutation_p.T1106A|FN1_ENST00000421182.1_Missense_Mutation_p.T1106A|FN1_ENST00000345488.5_Missense_Mutation_p.T1106A|FN1_ENST00000446046.1_Missense_Mutation_p.T1106A|FN1_ENST00000357867.4_Missense_Mutation_p.T1106A|FN1_ENST00000443816.1_Missense_Mutation_p.T1106A|FN1_ENST00000356005.4_Missense_Mutation_p.T1106A			P02751	FINC_HUMAN	fibronectin 1	1106	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	GGCGTCCATGTGATCACAATG	0.468																																					p.T1106A		Atlas-SNP	.											.	FN1	521	.	0			c.A3316G						.						172	164	166					2																	216264012		2203	4300	6503	SO:0001583	missense	2335	exon21			TCCATGTGATCAC		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.3316A>G	chr2.hg19:g.216264012T>C	ENSP00000352696:p.Thr1106Ala	78.0	0.0		84.0	4.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	T	22.9	4.348521	0.82132	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36	5.75	5.75	0.90469	.	0.000000	0.64402	D	0.000001	T	0.67306	0.2879	L	0.47716	1.5	0.54753	D	0.999989	D;D;D;D;D;P;D;D;D;D	0.71674	0.994;0.987;0.957;0.994;0.99;0.863;0.998;0.988;0.994;0.987	D;P;D;D;D;P;D;D;D;D	0.85130	0.992;0.891;0.936;0.992;0.996;0.729;0.997;0.992;0.992;0.992	T	0.69401	-0.5155	10	0.66056	D	0.02	.	16.0707	0.80928	0.0:0.0:0.0:1.0	.	1106;1106;1106;1106;1106;1106;1106;1106;1106;1106	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	A	1106	ENSP00000394423:T1106A;ENSP00000323534:T1106A;ENSP00000338200:T1106A;ENSP00000350534:T1106A;ENSP00000346839:T1106A;ENSP00000352696:T1106A;ENSP00000265312:T1106A;ENSP00000273049:T1106A;ENSP00000349509:T1106A;ENSP00000410422:T1106A;ENSP00000415018:T1106A;ENSP00000399538:T1106A;ENSP00000348285:T1106A	ENSP00000265313:T1106A	T	-	1	0	FN1	215972257	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	3.912000	0.56386	2.194000	0.70268	0.533000	0.62120	ACA	.	.		0.468	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		C	216264012	T	C	216264012	3	2	43	1	0	0	0	0	1	0	0	0	5970	1696	59	2	4221	2	FN1	2	216264012	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	9089539	216264012	26935361	59	5141										
CTDSP1	58190	hgsc.bcm.edu	37	chr2	219266306	219266306	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggtgaccagaagtcagcagcTtcccagaagccccgaagccg	12	14	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:219266306T>C	ENST00000273062.2	+	2	423	c.87T>C	c.(85-87)gcT>gcC	p.A29A	MIR26B_ENST00000362251.2_RNA|RP11-378A13.2_ENST00000608367.1_RNA|CTDSP1_ENST00000488627.1_3'UTR|CTDSP1_ENST00000443891.1_Silent_p.A29A	NM_021198.2|NM_182642.2	NP_067021.1|NP_872580.1	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	29					negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|protein dephosphorylation (GO:0006470)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			NS(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	8		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGTCAGCAGCTTCCCAGAAGC	0.637																																					p.A29A		Atlas-SNP	.											.	CTDSP1	19	.	0			c.T87C						.						59	64	62					2																	219266306		2203	4300	6503	SO:0001819	synonymous_variant	58190	exon2			AGCAGCTTCCCAG	AF229162	CCDS2416.1, CCDS56166.1	2q35	2010-06-21			ENSG00000144579	ENSG00000144579		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	21614	protein-coding gene	gene with protein product	"nuclear LIM interactor-interacting factor", "small CTD phosphatase 1"	605323				11950066, 12721286	Standard	NM_021198		Approved	NLIIF, SCP1	uc021vwv.1	Q9GZU7	OTTHUMG00000133109	ENST00000273062.2:c.87T>C	chr2.hg19:g.219266306T>C		125.0	0.0		87.0	4.0	NM_001206878	C9IYG0|Q7Z5Q3|Q7Z5Q4	Silent	SNP	ENST00000273062.2	hg19	CCDS2416.1	.	.	.	.	.	.	.	.	.	.	T	11.22	1.573427	0.28092	.	.	ENSG00000144579	ENST00000452977;ENST00000428361;ENST00000431127	.	.	.	5.08	1.42	0.22433	.	.	.	.	.	T	0.55909	0.1950	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47799	-0.9089	4	.	.	.	-5.8045	8.5109	0.33217	0.0:0.2295:0.0:0.7705	.	.	.	.	P	15;31;99	.	.	L	+	2	0	CTDSP1	218974550	1.000000	0.71417	0.993000	0.49108	0.897000	0.52465	1.831000	0.39141	0.277000	0.22141	-0.290000	0.09829	CTT	.	.		0.637	CTDSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256774.1	NM_182642, NM_021198		C	219266306	T	C	219266306	2	2	43	1	0	0	0	0	0	0	0	1	4005	1596	56	2		2	CTDSP1	2	219266306	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3002294	219266306	23933067	60	5142										
MOGAT1	116255	hgsc.bcm.edu	37	chr2	223559205	223559205	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gctcatcctggaaagttcacTctgttcatccgccagcggaa	9	13	4	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr2:223559205T>C	ENST00000446656.3	+	4	603	c.603T>C	c.(601-603)acT>acC	p.T201T		NM_058165.2	NP_477513.2	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1	201					diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)			breast(1)|cervix(1)|endometrium(1)|lung(5)|urinary_tract(1)	9		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)		GAAAGTTCACTCTGTTCATCC	0.443																																					p.T201T	Ovarian(93;205 1446 2385 11581 25911)	Atlas-SNP	.											.	MOGAT1	47	.	0			c.T603C						.						86	86	86					2																	223559205		1898	4123	6021	SO:0001819	synonymous_variant	116255	exon4			GTTCACTCTGTTC	AF384163	CCDS46524.1	2q36.2	2006-10-06	2004-05-28	2004-05-28	ENSG00000124003	ENSG00000124003			18210	protein-coding gene	gene with protein product		610268	"diacylglycerol O-acyltransferase 2 like 1"	DGAT2L1		14970677	Standard	NM_058165		Approved	DGAT2L, MGAT1	uc010fws.1	Q96PD6	OTTHUMG00000153394	ENST00000446656.3:c.603T>C	chr2.hg19:g.223559205T>C		93.0	0.0		57.0	4.0	NM_058165	Q6IEE5	Silent	SNP	ENST00000446656.3	hg19	CCDS46524.1																																																																																			.	.		0.443	MOGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331010.3	NM_058165		C	223559205	T	C	223559205	2	2	43	1	0	0	0	0	0	0	0	1	9703	1538	54	2		2	MOGAT1	2	223559205	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	4292899	223559205	19640168	61	5143										
LMCD1	29995	hgsc.bcm.edu	37	chr3	8607167	8607167	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcctgacagccccgtggtctActcggacagggcaggctaca	12	14	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:8607167A>T	ENST00000157600.3	+	5	1005	c.773A>T	c.(772-774)tAc>tTc	p.Y258F	LMCD1-AS1_ENST00000439407.1_RNA|LMCD1_ENST00000454244.1_Missense_Mutation_p.Y185F|LMCD1_ENST00000397386.3_Missense_Mutation_p.Y146F	NM_014583.2	NP_055398.1	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1	258	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|regulation of cardiac muscle hypertrophy (GO:0010611)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)	16				OV - Ovarian serous cystadenocarcinoma(96;0.124)		CCCGTGGTCTACTCGGACAGG	0.602																																					p.Y258F		Atlas-SNP	.											.	LMCD1	38	.	0			c.A773T						.						99	107	104					3																	8607167		2203	4300	6503	SO:0001583	missense	29995	exon5			TGGTCTACTCGGA	AF169284	CCDS33688.1, CCDS63533.1, CCDS63534.1	3p26-p24	2008-07-18			ENSG00000071282	ENSG00000071282			6633	protein-coding gene	gene with protein product	"dyxin"	604859				10662546	Standard	NM_001278233		Approved		uc003bqq.4	Q9NZU5	OTTHUMG00000154971	ENST00000157600.3:c.773A>T	chr3.hg19:g.8607167A>T	ENSP00000157600:p.Tyr258Phe	90.0	0.0		125.0	51.0	NM_014583	B4DG80	Missense_Mutation	SNP	ENST00000157600.3	hg19	CCDS33688.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.173647	0.78452	.	.	ENSG00000071282	ENST00000157600;ENST00000454244;ENST00000397386	T;T;T	0.49720	0.8;0.8;0.77	5.27	5.27	0.74061	Zinc finger, LIM-type (4);	0.000000	0.64402	D	0.000020	T	0.34513	0.0900	N	0.10629	0.01	0.54753	D	0.999984	P;P	0.49090	0.84;0.919	B;P	0.51974	0.405;0.686	T	0.22243	-1.0222	10	0.02654	T	1	-28.9704	14.0186	0.64539	1.0:0.0:0.0:0.0	.	146;258	B4DEY6;Q9NZU5	.;LMCD1_HUMAN	F	258;185;146	ENSP00000157600:Y258F;ENSP00000396515:Y185F;ENSP00000380542:Y146F	ENSP00000157600:Y258F	Y	+	2	0	LMCD1	8582167	1.000000	0.71417	0.960000	0.40013	0.967000	0.64934	7.111000	0.77077	1.996000	0.58369	0.482000	0.46254	TAC	.	.		0.602	LMCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337854.1	NM_014583		T	8607167	A	T	8607167	3	4	43	1	0	0	0	0	1	0	0	0	8853	391	14	4	791	4	LMCD1	3	8607167	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10		8607167	189415263	62	5144										
IQSEC1	9922	hgsc.bcm.edu	37	chr3	12942853	12942853	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cggtgggtgggggggtggccAgggctggggctgagggcagg	27	6	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:12942853A>G	ENST00000273221.4	-	13	3064					NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1						actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GGGGGTGGCCAGGGCTGGGGC	0.692																																					p.L992P		Atlas-SNP	.											.	IQSEC1	88	.	0			c.T2975C						.						2	2	2					3																	12942853		587	1389	1976	SO:0001627	intron_variant	9922	exon14			GTGGCCAGGGCTG	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"brefeldin A-resistant ARF-GEF2"	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.2847+1419T>C	chr3.hg19:g.12942853A>G		25.0	0.0		42.0	5.0	NM_001134382	O94863|Q96D85	Missense_Mutation	SNP	ENST00000273221.4	hg19	CCDS33703.1	.	.	.	.	.	.	.	.	.	.	a	0.309	-0.968904	0.02232	.	.	ENSG00000144711	ENST00000435445;ENST00000429247	T	0.50277	0.75	3.83	-3.76	0.04359	.	.	.	.	.	T	0.17662	0.0424	.	.	.	0.21579	N	0.999639	B	0.02656	0.0	B	0.01281	0.0	T	0.26360	-1.0105	8	0.07644	T	0.81	.	3.0466	0.06155	0.1077:0.1748:0.4542:0.2633	.	992	E9PG60	.	P	992	ENSP00000402299:L992P	ENSP00000402299:L992P	L	-	2	0	IQSEC1	12917853	0.803000	0.28956	0.000000	0.03702	0.044000	0.14063	0.719000	0.25881	-0.633000	0.05545	-0.246000	0.11932	CTG	.	.		0.692	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869		G	12942853	A	G	12942853	1	3	43	0	1	0	0	0	0	0	0	0	7826	188	7	2		2	IQSEC1	3	12942853	Intron	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	4335686	12942853	185079577	63	5145										
WNT7A	7476	hgsc.bcm.edu	37	chr3	13896149	13896149	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cggatgtcggcagagcagccAccccacttccagccctcgtc	10	18	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:13896149A>G	ENST00000285018.4	-	3	754	c.450T>C	c.(448-450)ggT>ggC	p.G150G		NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	150					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						CAGAGCAGCCACCCCACTTCC	0.607																																					p.G150G		Atlas-SNP	.											.	WNT7A	70	.	0			c.T450C						.						115	109	111					3																	13896149		2203	4300	6503	SO:0001819	synonymous_variant	7476	exon3			GCAGCCACCCCAC	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"Wingless-type MMTV integration sites"	12786	protein-coding gene	gene with protein product	"proto-oncogene Wnt7a protein"	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.450T>C	chr3.hg19:g.13896149A>G		49.0	0.0		63.0	5.0	NM_004625	Q96H90|Q9Y560	Silent	SNP	ENST00000285018.4	hg19	CCDS2616.1																																																																																			.	.		0.607	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625		G	13896149	A	G	13896149	2	3	43	1	0	0	0	0	0	0	0	1	17409	146	6	2		2	WNT7A	3	13896149	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	953296	13896149	184126281	64	5146										
METTL6	131965	hgsc.bcm.edu	37	chr3	15467900	15467900	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gatcccaatttttctgagccTcttgttccaatttctgctgt	6	11	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:15467900T>C	ENST00000443029.1	-	2	359	c.119A>G	c.(118-120)gAg>gGg	p.E40G	METTL6_ENST00000383790.3_Missense_Mutation_p.E40G|METTL6_ENST00000450816.2_Missense_Mutation_p.E40G|METTL6_ENST00000383789.5_Missense_Mutation_p.E40G|EAF1_ENST00000396842.2_5'Flank|EAF1_ENST00000432764.2_5'Flank			Q8TCB7	METL6_HUMAN	methyltransferase like 6	40							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(9)|lung(3)|prostate(1)	15						TTTCTGAGCCTCTTGTTCCAA	0.398																																					p.E40G		Atlas-SNP	.											.	METTL6	27	.	0			c.A119G						.						127	118	121					3																	15467900		1824	4075	5899	SO:0001583	missense	131965	exon2			TGAGCCTCTTGTT	AK057791	CCDS43056.1	3p25.1	2005-11-02			ENSG00000206562	ENSG00000206562			28343	protein-coding gene	gene with protein product						12477932	Standard	NM_152396		Approved	MGC24132	uc003bzs.1	Q8TCB7	OTTHUMG00000156431	ENST00000443029.1:c.119A>G	chr3.hg19:g.15467900T>C	ENSP00000407613:p.Glu40Gly	84.0	0.0		113.0	5.0	NM_152396	Q96LU4	Missense_Mutation	SNP	ENST00000443029.1	hg19	CCDS43056.1	.	.	.	.	.	.	.	.	.	.	T	16.30	3.083044	0.55861	.	.	ENSG00000206562	ENST00000383790;ENST00000450816;ENST00000383789	T;T;T	0.69306	-0.39;-0.39;-0.39	5.68	5.68	0.88126	.	0.092095	0.85682	D	0.000000	T	0.73590	0.3606	M	0.73598	2.24	0.58432	D	0.999999	P;P;B	0.38535	0.635;0.503;0.204	P;B;B	0.44811	0.461;0.43;0.126	T	0.77040	-0.2735	10	0.72032	D	0.01	-13.8455	15.6013	0.76628	0.0:0.0:0.0:1.0	.	40;40;40	B4DDX3;Q8TCB7-2;Q8TCB7	.;.;METL6_HUMAN	G	40	ENSP00000373300:E40G;ENSP00000410726:E40G;ENSP00000373299:E40G	ENSP00000373299:E40G	E	-	2	0	METTL6	15442904	1.000000	0.71417	1.000000	0.80357	0.427000	0.31564	8.040000	0.89188	2.164000	0.68074	0.528000	0.53228	GAG	.	.		0.398	METTL6-007	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346373.1	NM_152396		C	15467900	T	C	15467900	3	2	43	1	0	0	0	0	1	0	0	0	9513	1551	54	2	755	2	METTL6	3	15467900	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1571751	15467900	182554530	65	5147										
TOP2B	7155	hgsc.bcm.edu	37	chr3	25670532	25670532	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aatgcaaagagtacctttacAataggagtaatgaactcttc	7	7	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:25670532A>T	ENST00000264331.4	-	14	1793	c.1794T>A	c.(1792-1794)atT>atA	p.I598I	TOP2B_ENST00000435706.2_Silent_p.I593I	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	598					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	GTACCTTTACAATAGGAGTAA	0.294																																					p.I593I		Atlas-SNP	.											.	TOP2B	98	.	0			c.T1779A						.						95	90	92					3																	25670532		1796	4060	5856	SO:0001819	synonymous_variant	7155	exon14			CTTTACAATAGGA	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.1794T>A	chr3.hg19:g.25670532A>T		40.0	0.0		46.0	23.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Silent	SNP	ENST00000264331.4	hg19																																																																																				.	.		0.294	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				T	25670532	A	T	25670532	2	4	43	1	0	0	0	0	0	0	0	1	16381	126	5	4		4	TOP2B	3	25670532	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	10202632	25670532	172351898	66	5148										
MYRIP	25924	hgsc.bcm.edu	37	chr3	40211580	40211580	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctaccgtgctcccgctgcccTctgggtgagtccccaagcag	11	17	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:40211580T>C	ENST00000302541.6	+	8	1211	c.869T>C	c.(868-870)cTc>cCc	p.L290P	MYRIP_ENST00000396217.3_Missense_Mutation_p.L201P|MYRIP_ENST00000459828.1_3'UTR|MYRIP_ENST00000444716.1_Missense_Mutation_p.L290P|MYRIP_ENST00000425621.1_Missense_Mutation_p.L290P|MYRIP_ENST00000539167.1_Missense_Mutation_p.L103P	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	290	Myosin-binding.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		CCCGCTGCCCTCTGGGTGAGT	0.607																																					p.L290P		Atlas-SNP	.											.	MYRIP	98	.	0			c.T869C						.						70	63	66					3																	40211580		2203	4300	6503	SO:0001583	missense	25924	exon8			CTGCCCTCTGGGT	AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"A-kinase anchor proteins"	19156	protein-coding gene	gene with protein product	"synaptotagmin-like protein homologue lacking C2 domains-c", "rab effector MYRIP", "Slp homologue lacking C2 domains"	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.869T>C	chr3.hg19:g.40211580T>C	ENSP00000301972:p.Leu290Pro	58.0	0.0		96.0	4.0	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	hg19	CCDS2689.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.111257	0.37242	.	.	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.71	2.23	0.28157	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.278895	0.29126	N	0.013067	T	0.50222	0.1603	L	0.52573	1.65	0.49299	D	0.99977	D;D;D	0.89917	1.0;0.997;0.998	D;D;D	0.79784	0.993;0.944;0.967	T	0.41197	-0.9522	9	.	.	.	.	4.9851	0.14185	0.0:0.0988:0.1855:0.7156	.	201;290;290	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	P	290;290;290;201;103	ENSP00000398665:L290P;ENSP00000301972:L290P;ENSP00000389323:L290P;ENSP00000379519:L201P;ENSP00000438297:L103P	.	L	+	2	0	MYRIP	40186584	0.686000	0.27661	0.684000	0.30055	0.317000	0.28152	1.423000	0.34837	0.246000	0.21394	0.459000	0.35465	CTC	.	.		0.607	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460		C	40211580	T	C	40211580	3	2	43	1	0	0	0	0	1	0	0	0	10109	1551	54	2	895	2	MYRIP	3	40211580	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	14541048	40211580	157810850	67	5149										
SNRK	54861	hgsc.bcm.edu	37	chr3	43388906	43388906	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gccactcctttgtcccacgcGactgtccctcagtctcctgc	7	19	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:43388906G>A	ENST00000296088.7	+	7	1459	c.1155G>A	c.(1153-1155)gcG>gcA	p.A385A	RP11-188P20.3_ENST00000607513.1_RNA|SNRK_ENST00000454177.1_Silent_p.A385A|SNRK_ENST00000429705.2_Silent_p.A385A|SNRK_ENST00000437827.1_Silent_p.A179A|SNRK-AS1_ENST00000422681.1_RNA	NM_017719.4	NP_060189.3			SNF related kinase											breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(5)|prostate(1)|skin(2)|stomach(1)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)		TGTCCCACGCGACTGTCCCTC	0.547																																					p.A385A		Atlas-SNP	.											.	SNRK	118	.	0			c.G1155A						.						70	75	74					3																	43388906		2039	4193	6232	SO:0001819	synonymous_variant	54861	exon7			CCACGCGACTGTC	D43636	CCDS43075.1	3p22.1	2005-08-09			ENSG00000163788	ENSG00000163788			30598	protein-coding gene	gene with protein product		612760				8654423, 7788527	Standard	NM_017719		Approved	FLJ20224, HSNFRK, KIAA0096	uc003cmt.4	Q9NRH2	OTTHUMG00000156491	ENST00000296088.7:c.1155G>A	chr3.hg19:g.43388906G>A		22.0	0.0		47.0	19.0	NM_017719		Silent	SNP	ENST00000296088.7	hg19	CCDS43075.1																																																																																			.	.		0.547	SNRK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344325.1	NM_017719		A	43388906	G	A	43388906	2	1	43	1	0	0	0	0	0	0	0	1	14866	1045	37	1		1	SNRK	3	43388906	Silent	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	3177326	43388906	154633524	68	5150										
KIF15	56992	hgsc.bcm.edu	37	chr3	44816758	44816758	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtctttagtaatgaaggtgaTgccatcaaagtttttgtgcg	11	5	2	2	rs34893204		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:44816758T>C	ENST00000326047.4	+	3	224	c.75T>C	c.(73-75)gaT>gaC	p.D25D		NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	25					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		ATGAAGGTGATGCCATCAAAG	0.388																																					p.D25D		Atlas-SNP	.											.	KIF15	103	.	0			c.T75C						.						142	130	134					3																	44816758		2203	4300	6503	SO:0001819	synonymous_variant	56992	exon3			AGGTGATGCCATC	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.75T>C	chr3.hg19:g.44816758T>C		83.0	0.0		98.0	4.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Silent	SNP	ENST00000326047.4	hg19	CCDS33744.1																																																																																			.	T|0.987;A|0.013		0.388	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			C	44816758	T	C	44816758	2	2	43	1	0	0	0	0	0	0	0	1	8286	1461	51	2		2	KIF15	3	44816758	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1427852	44816758	153205672	69	5151										
CDHR4	389118	hgsc.bcm.edu	37	chr3	49832387	49832387	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tggggctgggcacctcaaggActctgtcataaaggcagagg	15	9	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:49832387A>G	ENST00000412678.2	-	9	1186	c.1178T>C	c.(1177-1179)gTc>gCc	p.V393A	CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	393	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						CACCTCAAGGACTCTGTCATA	0.622																																					p.V393A		Atlas-SNP	.											.	CDHR4	37	.	0			c.T1178C						.						47	53	51					3																	49832387		692	1591	2283	SO:0001583	missense	389118	exon9			TCAAGGACTCTGT		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"Cadherins / Cadherin-related"	34527	protein-coding gene	gene with protein product			"cadherin-like 29"	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.1178T>C	chr3.hg19:g.49832387A>G	ENSP00000391409:p.Val393Ala	60.0	0.0		73.0	5.0	NM_001007540	Q6UXT0	Missense_Mutation	SNP	ENST00000412678.2	hg19	CCDS46829.1	.	.	.	.	.	.	.	.	.	.	A	9.067	0.996049	0.19043	.	.	ENSG00000187492	ENST00000412678	T	0.68624	-0.34	4.75	-4.5	0.03493	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.34890	0.0913	N	0.08118	0	0.25389	N	0.988542	B	0.02656	0.0	B	0.04013	0.001	T	0.31223	-0.9951	9	0.08179	T	0.78	.	5.9065	0.19004	0.4414:0.0:0.4237:0.1349	.	393	A6H8M9	CDHR4_HUMAN	A	393	ENSP00000391409:V393A	ENSP00000391409:V393A	V	-	2	0	CDHR4	49807391	0.000000	0.05858	0.029000	0.17559	0.537000	0.34900	-1.076000	0.03420	-0.906000	0.03866	-0.421000	0.06004	GTC	.	.		0.622	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540		G	49832387	A	G	49832387	3	3	43	1	0	0	0	0	1	0	0	0	3123	275	10	2	1232	2	CDHR4	3	49832387	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	5015629	49832387	148190043	70	5152										
NT5DC2	64943	hgsc.bcm.edu	37	chr3	52558487	52558487	+	Nonstop_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccagacaataaaggtgccctCagcggatgtgggccatgtca	12	11	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:52558487C>A	ENST00000307076.4	-	14	1962	c.1562G>T	c.(1561-1563)tGa>tTa	p.*521L	NT5DC2_ENST00000307092.4_Nonstop_Mutation_p.*462L|NT5DC2_ENST00000422318.2_Nonstop_Mutation_p.*558L|NT5DC2_ENST00000459839.1_Nonstop_Mutation_p.*533L|STAB1_ENST00000321725.6_3'UTR	NM_022908.2	NP_075059.1	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2	0							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(1)|lung(3)|prostate(1)|stomach(1)	6				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)		AAGGTGCCCTCAGCGGATGTG	0.612																																					p.X558L		Atlas-SNP	.											NT5DC2,bladder,carcinoma,0,1	NT5DC2	35	.	0			c.G1673T						.						82	93	89					3																	52558487		2203	4299	6502	SO:0001578	stop_lost	64943	exon14			TGCCCTCAGCGGA	AF131781	CCDS2858.1, CCDS46843.1	3p21.1	2006-02-03			ENSG00000168268	ENSG00000168268			25717	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_022908		Approved	FLJ12442	uc003den.3	Q9H857	OTTHUMG00000158626	ENST00000307076.4:c.1562G>T	chr3.hg19:g.52558487C>A		47.0	0.0		55.0	3.0	NM_001134231	C9JTZ6|E9PAL9|O95888|Q96C80|Q9H9Z8	Missense_Mutation	SNP	ENST00000307076.4	hg19	CCDS2858.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.321470	0.81580	.	.	ENSG00000168268	ENST00000307092;ENST00000463947;ENST00000307076;ENST00000422318;ENST00000459839	.	.	.	5.76	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8637	0.52480	0.0:0.8599:0.0:0.1401	.	.	.	.	L	462;195;521;558;533	.	.	X	-	2	2	NT5DC2	52533527	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	1.449000	0.35123	1.453000	0.47775	-0.140000	0.14226	TGA	.	.		0.612	NT5DC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000351509.1	NM_022908		A	52558487	C	A	52558487	4	1	43	1	0	0	0	0	0	0	0	0	10700	837	29	3	4	3	NT5DC2	3	52558487	Nonstop_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	2726100	52558487	145463943	71	5153										
RPP14	11102	hgsc.bcm.edu	37	chr3	58302307	58302307	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	accttgtcagccatcttgagAatatgtagcaggtatgacag	10	8	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:58302307A>G	ENST00000445193.3	+	4	639	c.228A>G	c.(226-228)agA>agG	p.R76R	RPP14_ENST00000528153.1_5'Flank|RPP14_ENST00000477305.1_3'UTR|RPP14_ENST00000466547.1_Silent_p.R76R|RPP14_ENST00000295959.5_Silent_p.R76R	NM_001098783.2	NP_001092253.1	O95059	RPP14_HUMAN	ribonuclease P/MRP 14kDa subunit	76					tRNA processing (GO:0008033)	nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)|RNA binding (GO:0003723)			large_intestine(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.000187)|KIRC - Kidney renal clear cell carcinoma(10;0.0102)|Kidney(10;0.0118)|OV - Ovarian serous cystadenocarcinoma(275;0.191)		CCATCTTGAGAATATGTAGCA	0.413																																					p.R76R		Atlas-SNP	.											.	RPP14	6	.	0			c.A228G						.						148	139	142					3																	58302307		2203	4300	6503	SO:0001819	synonymous_variant	11102	exon4			CTTGAGAATATGT	AF001175	CCDS2888.1	3p21.2	2012-05-21	2007-06-26		ENSG00000163684	ENSG00000163684			30327	protein-coding gene	gene with protein product		606112	"ribonuclease P 14kDa subunit"			10024167, 11929972	Standard	NM_001098783		Approved	P14	uc031sah.1	O95059	OTTHUMG00000159152	ENST00000445193.3:c.228A>G	chr3.hg19:g.58302307A>G		83.0	0.0		103.0	5.0	NM_007042	Q53X97	Silent	SNP	ENST00000445193.3	hg19	CCDS2888.1																																																																																			.	.		0.413	RPP14-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353527.2	NM_007042		G	58302307	A	G	58302307	2	3	43	1	0	0	0	0	0	0	0	1	13624	243	9	2		2	RPP14	3	58302307	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	5743820	58302307	139720123	72	5154										
CADPS	8618	hgsc.bcm.edu	37	chr3	62385129	62385129	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctgtccttcatgctgatgccCtgcagtcccccaccttcact	6	18	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:62385129C>T	ENST00000383710.4	-	30	4363	c.4014G>A	c.(4012-4014)caG>caA	p.Q1338Q	CADPS_ENST00000357948.3_Silent_p.Q1259Q|CADPS_ENST00000283269.9_Silent_p.Q1299Q	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1338	Mediates targeting and association with DCVs. {ECO:0000250}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TGCTGATGCCCTGCAGTCCCC	0.522																																					p.Q1338Q		Atlas-SNP	.											.	CADPS	387	.	0			c.G4014A						.						217	189	198					3																	62385129		2203	4300	6503	SO:0001819	synonymous_variant	8618	exon30			GATGCCCTGCAGT	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.4014G>A	chr3.hg19:g.62385129C>T		132.0	0.0		119.0	45.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	C	4.156	0.027463	0.08054	.	.	ENSG00000163618	ENST00000473635	.	.	.	5.86	3.1	0.35709	.	.	.	.	.	T	0.59622	0.2207	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55263	-0.8168	4	.	.	.	.	10.0739	0.42349	0.0:0.7833:0.0:0.2167	.	.	.	.	K	330	.	.	R	-	2	0	CADPS	62360169	0.996000	0.38824	1.000000	0.80357	0.902000	0.53008	0.512000	0.22755	0.809000	0.34255	-0.140000	0.14226	AGG	.	.		0.522	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		T	62385129	C	T	62385129	2	4	43	1	0	0	0	0	0	0	0	1	2572	680	24	3		3	CADPS	3	62385129	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	4082822	62385129	135637301	73	5155										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64617541	64617541	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcatgaagaattatcgccacCacaaaccccacatttatctc	4	14	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:64617541C>G	ENST00000498707.1	-	15	2578	c.2236G>C	c.(2236-2238)Ggt>Cgt	p.G746R	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.G718R	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	746	Cys-rich.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		TTATCGCCACCACAAACCCCA	0.358																																					p.G746R		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G2236C						.						119	118	118					3																	64617541		2202	4300	6502	SO:0001583	missense	56999	exon15			CGCCACCACAAAC	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.2236G>C	chr3.hg19:g.64617541C>G	ENSP00000418735:p.Gly746Arg	104.0	0.0		122.0	46.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	C	33	5.265563	0.95399	.	.	ENSG00000163638	ENST00000295903;ENST00000498707	T;T	0.68025	-0.3;-0.3	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.81545	0.4845	M	0.63169	1.94	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;P	0.97110	0.997;1.0;1.0;0.882	T	0.80567	-0.1325	10	0.59425	D	0.04	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	718;746;746;746	B7ZVX9;Q9P2N4-2;Q9P2N4-1;Q9P2N4	.;.;.;ATS9_HUMAN	R	718;746	ENSP00000295903:G718R;ENSP00000418735:G746R	ENSP00000295903:G718R	G	-	1	0	ADAMTS9	64592581	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.487000	0.81328	2.857000	0.98124	0.650000	0.86243	GGT	.	.		0.358	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			G	64617541	C	G	64617541	3	3	43	1	0	0	0	0	1	0	0	0	273	594	21	4	3671	4	ADAMTS9	3	64617541	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	2232412	64617541	133404889	74	5156										
EBLN2	55096	hgsc.bcm.edu	37	chr3	73111481	73111481	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttgagctatctgggaaaaaCagacagtatccactggatgc	10	8	1	2	rs3832186|rs201649088	byFrequency	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:73111481C>A	ENST00000533473.1	+	1	672	c.249C>A	c.(247-249)aaC>aaA	p.N83K	PPP4R2_ENST00000394284.3_Intron|PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000356692.5_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	83										endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						CTGGGAAAAACAGACAGTATC	0.478																																					p.N83K		Atlas-SNP	.											.	EBLN2	18	.	0			c.C249A						.						34	34	34					3																	73111481		1942	4138	6080	SO:0001583	missense	55096	exon1			GAAAAACAGACAG		CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"endogenous Borna-like N element 2"	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.249C>A	chr3.hg19:g.73111481C>A	ENSP00000432104:p.Asn83Lys	64.0	0.0		76.0	5.0	NM_018029	Q8WWH3|Q9NW89	Missense_Mutation	SNP	ENST00000533473.1	hg19	CCDS54608.1	.	.	.	.	.	.	.	.	.	.	C	4.916	0.170168	0.09339	.	.	ENSG00000255423	ENST00000533473	.	.	.	0.458	0.458	0.16670	P40 nucleoprotein, subdomain 1, Borna disease virus (1);	.	.	.	.	T	0.16854	0.0405	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.13407	0.009	T	0.23368	-1.0190	7	0.31617	T	0.26	.	.	.	.	.	83	Q6P2I7	EBLN2_HUMAN	K	83	.	ENSP00000432104:N83K	N	+	3	2	EBLN2	73194171	0.047000	0.20315	0.005000	0.12908	0.005000	0.04900	0.305000	0.19254	0.482000	0.27582	0.484000	0.47621	AAC	.	.		0.478	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029		A	73111481	C	A	73111481	3	1	43	1	0	0	0	0	1	0	0	0	4886	477	17	3	251	3	EBLN2	3	73111481	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	8493940	73111481	124910949	75	5157										
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73434932	73434932	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catcatccatccagccctcaTccagctgcaggcaagagcag	8	16	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:73434932T>C	ENST00000263666.4	-	9	1637	c.1523A>G	c.(1522-1524)gAt>gGt	p.D508G	PDZRN3_ENST00000466348.1_5'UTR|PDZRN3_ENST00000462146.2_Missense_Mutation_p.D165G|PDZRN3_ENST00000535920.1_Missense_Mutation_p.D230G|PDZRN3_ENST00000466780.1_Missense_Mutation_p.D165G|PDZRN3_ENST00000479530.1_Missense_Mutation_p.D225G	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	508					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		CCAGCCCTCATCCAGCTGCAG	0.463																																					p.D508G		Atlas-SNP	.											.	PDZRN3	196	.	0			c.A1523G						.						163	132	143					3																	73434932		2203	4300	6503	SO:0001583	missense	23024	exon9			CCCTCATCCAGCT	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.1523A>G	chr3.hg19:g.73434932T>C	ENSP00000263666:p.Asp508Gly	43.0	0.0		78.0	5.0	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	hg19	CCDS33789.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.5|24.5	4.537290|4.537290	0.85812|0.85812	.|.	.|.	ENSG00000121440|ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530;ENST00000416926;ENST00000492909|ENST00000494559	T;T;T;T;T;T|.	0.11063|.	2.81;3.51;3.41;3.41;3.52;3.52|.	5.44|5.44	5.44|5.44	0.79542|0.79542	PDZ/DHR/GLGF (1);|.	0.097121|.	0.64402|.	N|.	0.000002|.	T|T	0.72260|0.72260	0.3438|0.3438	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	B;D;D;D|.	0.89917|.	0.006;1.0;0.972;0.991|.	B;D;D;D|.	0.91635|.	0.122;0.999;0.938;0.996|.	T|T	0.72020|0.72020	-0.4416|-0.4416	10|5	0.49607|.	T|.	0.09|.	.|.	15.1433|15.1433	0.72626|0.72626	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	230;225;225;508|.	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7|.	.;.;.;PZRN3_HUMAN|.	G|V	508;230;165;165;225;508;206|105	ENSP00000263666:D508G;ENSP00000442026:D230G;ENSP00000418168:D165G;ENSP00000418484:D165G;ENSP00000418624:D225G;ENSP00000419250:D206G|.	ENSP00000263666:D508G|.	D|M	-|-	2|1	0|0	PDZRN3|PDZRN3	73517622|73517622	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	7.852000|7.852000	0.86927|0.86927	2.053000|2.053000	0.61076|0.61076	0.533000|0.533000	0.62120|0.62120	GAT|ATG	.	.		0.463	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		C	73434932	T	C	73434932	3	2	43	1	0	0	0	0	1	0	0	0	11718	1435	50	2	1685	2	PDZRN3	3	73434932	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	323451	73434932	124587498	76	5158										
SLC35A5	55032	hgsc.bcm.edu	37	chr3	112299917	112299917	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgtaactgcattccagggccTttcagtggctttcattctga	9	10	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:112299917T>C	ENST00000492406.1	+	6	1236	c.953T>C	c.(952-954)cTt>cCt	p.L318P	SLC35A5_ENST00000460713.1_3'UTR	NM_017945.2	NP_060415.1	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5	318					nucleotide-sugar transport (GO:0015780)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)|sugar:proton symporter activity (GO:0005351)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|skin(1)	11						TTCCAGGGCCTTTCAGTGGCT	0.428																																					p.L318P		Atlas-SNP	.											.	SLC35A5	40	.	0			c.T953C						.						78	75	76					3																	112299917		2203	4299	6502	SO:0001583	missense	55032	exon6			AGGGCCTTTCAGT	AK000737	CCDS2967.1	3q13.13	2013-05-22			ENSG00000138459	ENSG00000138459		"Solute carriers"	20792	protein-coding gene	gene with protein product							Standard	NM_017945		Approved	FLJ20730	uc003dze.4	Q9BS91	OTTHUMG00000159263	ENST00000492406.1:c.953T>C	chr3.hg19:g.112299917T>C	ENSP00000417654:p.Leu318Pro	69.0	0.0		90.0	4.0	NM_017945	D3DN66|Q69YY6|Q6ZMD6|Q9NWM9	Missense_Mutation	SNP	ENST00000492406.1	hg19	CCDS2967.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.169361	0.78339	.	.	ENSG00000138459	ENST00000492406	T	0.61040	0.14	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.81269	0.4787	M	0.90922	3.16	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85399	0.1130	9	.	.	.	-19.211	16.2076	0.82138	0.0:0.0:0.0:1.0	.	318	Q9BS91	S35A5_HUMAN	P	318	ENSP00000417654:L318P	.	L	+	2	0	SLC35A5	113782607	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.554000	0.82212	2.285000	0.76669	0.477000	0.44152	CTT	.	.		0.428	SLC35A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354184.1	NM_017945		C	112299917	T	C	112299917	3	2	43	1	0	0	0	0	1	0	0	0	14589	1609	56	2	971	2	SLC35A5	3	112299917	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	38864985	112299917	85722513	77	5159										
GRAMD1C	54762	hgsc.bcm.edu	37	chr3	113601662	113601662	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtatctttaggttgtggcagAatgtattattagataaggta	11	2	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:113601662A>G	ENST00000358160.4	+	6	1015	c.523A>G	c.(523-525)Aat>Gat	p.N175D	GRAMD1C_ENST00000479212.1_3'UTR|GRAMD1C_ENST00000452134.2_5'UTR	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	175						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						GTTGTGGCAGAATGTATTATT	0.348																																					p.N175D		Atlas-SNP	.											.	GRAMD1C	71	.	0			c.A523G						.						165	167	167					3																	113601662		2203	4300	6503	SO:0001583	missense	54762	exon6			TGGCAGAATGTAT		CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.523A>G	chr3.hg19:g.113601662A>G	ENSP00000350881:p.Asn175Asp	92.0	0.0		87.0	4.0	NM_017577	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Missense_Mutation	SNP	ENST00000358160.4	hg19	CCDS33826.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.360984	0.82353	.	.	ENSG00000178075	ENST00000358160	T	0.36699	1.24	5.2	5.2	0.72013	.	0.481200	0.24260	N	0.040096	T	0.62466	0.2430	M	0.85197	2.74	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.65635	-0.6120	10	0.42905	T	0.14	.	13.0454	0.58922	1.0:0.0:0.0:0.0	.	175	Q8IYS0	GRM1C_HUMAN	D	175	ENSP00000350881:N175D	ENSP00000350881:N175D	N	+	1	0	GRAMD1C	115084352	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.682000	0.91232	1.955000	0.56771	0.523000	0.50628	AAT	.	.		0.348	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577		G	113601662	A	G	113601662	3	3	43	1	0	0	0	0	1	0	0	0	6758	246	9	2	545	2	GRAMD1C	3	113601662	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1301745	113601662	84420768	78	5160										
POLQ	10721	hgsc.bcm.edu	37	chr3	121158914	121158914	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cccaaaatggtctgaacaaaTccgtctcttttacaattctt	4	11	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:121158914T>C	ENST00000264233.5	-	27	7442	c.7314A>G	c.(7312-7314)ggA>ggG	p.G2438G		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2438					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TCTGAACAAATCCGTCTCTTT	0.338								DNA polymerases (catalytic subunits)																													p.G2438G	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A7314G						.						117	115	116					3																	121158914		2201	4300	6501	SO:0001819	synonymous_variant	10721	exon27			AACAAATCCGTCT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.7314A>G	chr3.hg19:g.121158914T>C		18.0	0.0		30.0	4.0	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.338	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		C	121158914	T	C	121158914	2	2	43	1	0	0	0	0	0	0	0	1	12217	1422	50	2		2	POLQ	3	121158914	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	7557252	121158914	76863516	79	5161										
MBD4	8930	hgsc.bcm.edu	37	chr3	129151369	129151369	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cttccactcattgacacaaaAaattcggtaagagtcgttgc	7	10	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:129151369A>G	ENST00000249910.1	-	7	1817	c.1642T>C	c.(1642-1644)Ttt>Ctt	p.F548L	MBD4_ENST00000429544.2_Missense_Mutation_p.F542L|MBD4_ENST00000503197.1_Intron|MBD4_ENST00000509587.1_5'Flank|MBD4_ENST00000393278.2_Missense_Mutation_p.F230L|MBD4_ENST00000507208.1_Missense_Mutation_p.F548L	NM_003925.1	NP_003916.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	548					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						TTGACACAAAAAATTCGGTAA	0.413								Base excision repair (BER), DNA glycosylases																													p.F548L		Atlas-SNP	.											.	MBD4	53	.	0			c.T1642C						.						184	170	175					3																	129151369		2203	4300	6503	SO:0001583	missense	8930	exon7			CACAAAAAATTCG	AF072250	CCDS3058.1, CCDS63766.1, CCDS63767.1, CCDS63768.1, CCDS63769.1	3q21.3	2004-03-02			ENSG00000129071	ENSG00000129071			6919	protein-coding gene	gene with protein product		603574				9774669, 10097147	Standard	NM_003925		Approved	MED1	uc003emh.2	O95243	OTTHUMG00000159463	ENST00000249910.1:c.1642T>C	chr3.hg19:g.129151369A>G	ENSP00000249910:p.Phe548Leu	111.0	0.0		94.0	4.0	NM_003925	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000249910.1	hg19	CCDS3058.1	.	.	.	.	.	.	.	.	.	.	A	35	5.437390	0.96168	.	.	ENSG00000129071	ENST00000429544;ENST00000249910;ENST00000393278;ENST00000507208	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.84	5.84	0.93424	DNA glycosylase (2);	0.051405	0.85682	D	0.000000	T	0.69878	0.3160	M	0.87827	2.91	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.75912	-0.3150	10	0.87932	D	0	-23.3192	15.9385	0.79736	1.0:0.0:0.0:0.0	.	548;230;542;548	E9PEE4;Q2MD36;O95243-2;O95243	.;.;.;MBD4_HUMAN	L	542;548;230;548	ENSP00000394080:F542L;ENSP00000249910:F548L;ENSP00000376959:F230L;ENSP00000422327:F548L	ENSP00000249910:F548L	F	-	1	0	MBD4	130634059	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	8.720000	0.91442	2.241000	0.73720	0.529000	0.55759	TTT	.	.		0.413	MBD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355529.1	NM_003925		G	129151369	A	G	129151369	3	3	43	1	0	0	0	0	1	0	0	0	9355	14	1	2	108	2	MBD4	3	129151369	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	7992455	129151369	68871061	80	5162										
STAG1	10274	hgsc.bcm.edu	37	chr3	136085882	136085882	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caagtagattccttcttttaTgtaaggcctcaattttatta	5	7	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:136085882T>C	ENST00000383202.2	-	25	2844	c.2588A>G	c.(2587-2589)cAt>cGt	p.H863R	STAG1_ENST00000536929.1_Missense_Mutation_p.H447R|STAG1_ENST00000236698.5_Missense_Mutation_p.H863R|STAG1_ENST00000434713.2_Missense_Mutation_p.H637R	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	863					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						CCTTCTTTTATGTAAGGCCTC	0.353																																					p.H863R		Atlas-SNP	.											.	STAG1	135	.	0			c.A2588G						.						213	203	206					3																	136085882		2202	4299	6501	SO:0001583	missense	10274	exon25			CTTTTATGTAAGG	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.2588A>G	chr3.hg19:g.136085882T>C	ENSP00000372689:p.His863Arg	121.0	0.0		149.0	61.0	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	hg19	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.517726	0.85495	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.36340	1.69;1.7;1.83;1.26	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.67088	0.2856	M	0.88377	2.95	0.80722	D	1	D;D	0.89917	1.0;0.991	D;D	0.85130	0.997;0.957	T	0.74051	-0.3789	10	0.72032	D	0.01	.	16.1354	0.81481	0.0:0.0:0.0:1.0	.	863;863	Q6P275;Q8WVM7	.;STAG1_HUMAN	R	863;863;637;447	ENSP00000372689:H863R;ENSP00000236698:H863R;ENSP00000404396:H637R;ENSP00000445787:H447R	ENSP00000236698:H863R	H	-	2	0	STAG1	137568572	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.040000	0.89188	2.207000	0.71202	0.533000	0.62120	CAT	.	.		0.353	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		C	136085882	T	C	136085882	3	2	43	1	0	0	0	0	1	0	0	0	15257	1464	51	2	1228	2	STAG1	3	136085882	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	6934513	136085882	61936548	81	5163										
ARMC8	25852	hgsc.bcm.edu	37	chr3	137960687	137960687	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctagaggagagagttgaaggAgctgagacacttgcctatct	13	7	1	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:137960687A>G	ENST00000469044.1	+	11	1171	c.900A>G	c.(898-900)ggA>ggG	p.G300G	ARMC8_ENST00000485396.1_Silent_p.G227G|ARMC8_ENST00000491704.1_Silent_p.G258G|ARMC8_ENST00000471453.1_Silent_p.G286G|ARMC8_ENST00000538260.1_Silent_p.G269G|ARMC8_ENST00000489213.1_Silent_p.G258G|ARMC8_ENST00000481646.1_Silent_p.G286G|ARMC8_ENST00000358441.2_Silent_p.G286G|ARMC8_ENST00000393058.3_Silent_p.G290G|ARMC8_ENST00000461822.1_Intron|ARMC8_ENST00000470821.1_Silent_p.G300G	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	300										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						GAGTTGAAGGAGCTGAGACAC	0.398																																					p.G286G		Atlas-SNP	.											.	ARMC8	79	.	0			c.A858G						.						155	139	144					3																	137960687		2203	4300	6503	SO:0001819	synonymous_variant	25852	exon12			TGAAGGAGCTGAG		CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"Armadillo repeat containing"	24999	protein-coding gene	gene with protein product	"GID complex subunit 5, VID28 homolog (S. cerevisiae)"					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.900A>G	chr3.hg19:g.137960687A>G		76.0	0.0		93.0	4.0	NM_213654	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Silent	SNP	ENST00000469044.1	hg19																																																																																				.	.		0.398	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396		G	137960687	A	G	137960687	2	3	43	1	0	0	0	0	0	0	0	1	957	291	11	2		2	ARMC8	3	137960687	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1874805	137960687	60061743	82	5164										
SLC9A9	285195	hgsc.bcm.edu	37	chr3	143550901	143550901	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cttgatgaggattgatgttgTgctgacttatttctcttttg	10	5	1	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:143550901T>C	ENST00000316549.6	-	2	546	c.338A>G	c.(337-339)cAc>cGc	p.H113R		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	113					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)			breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						ATTGATGTTGTGCTGACTTAT	0.303																																					p.H113R		Atlas-SNP	.											.	SLC9A9	117	.	0			c.A338G						.						148	140	143					3																	143550901		2203	4299	6502	SO:0001583	missense	285195	exon2			ATGTTGTGCTGAC	AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"Solute carriers"	20653	protein-coding gene	gene with protein product		608396	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 9", "solute carrier family 9 (sodium/hydrogen exchanger), member 9"			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.338A>G	chr3.hg19:g.143550901T>C	ENSP00000320246:p.His113Arg	46.0	0.0		68.0	4.0	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Missense_Mutation	SNP	ENST00000316549.6	hg19	CCDS33872.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.441778	0.25900	.	.	ENSG00000181804	ENST00000316549;ENST00000474151	T;T	0.21932	1.98;1.98	5.14	5.14	0.70334	Cation/H+ exchanger (1);	0.144593	0.49305	D	0.000159	T	0.10680	0.0261	N	0.01048	-1.04	0.44899	D	0.997915	P	0.37914	0.611	P	0.48598	0.583	T	0.41592	-0.9500	10	0.16420	T	0.52	.	9.851	0.41057	0.0:0.0762:0.0:0.9238	.	113	Q8IVB4	SL9A9_HUMAN	R	113	ENSP00000320246:H113R;ENSP00000418627:H113R	ENSP00000320246:H113R	H	-	2	0	SLC9A9	145033591	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.570000	0.53834	2.285000	0.76669	0.533000	0.62120	CAC	.	.		0.303	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653		C	143550901	T	C	143550901	3	2	43	1	0	0	0	0	1	0	0	0	14736	1696	59	2	1659	2	SLC9A9	3	143550901	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5590214	143550901	54471529	83	5165										
ZIC1	7545	hgsc.bcm.edu	37	chr3	147128660	147128660	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caccatgcacgagctagttaCgcacgtcaccgtggagcacg	11	14	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:147128660C>A	ENST00000282928.4	+	1	1490	c.761C>A	c.(760-762)aCg>aAg	p.T254K		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	254					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						GAGCTAGTTACGCACGTCACC	0.557																																					p.T254K		Atlas-SNP	.											.	ZIC1	141	.	0			c.C761A						.						103	95	98					3																	147128660		2203	4300	6503	SO:0001583	missense	7545	exon1			TAGTTACGCACGT	D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"Zinc fingers, C2H2-type"	12872	protein-coding gene	gene with protein product		600470	"Zic family member 1 (odd-paired Drosophila homolog)", "Zic family member 1 (odd-paired homolog, Drosophila)"			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.761C>A	chr3.hg19:g.147128660C>A	ENSP00000282928:p.Thr254Lys	103.0	0.0		181.0	69.0	NM_003412	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	hg19	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.253887	0.80135	.	.	ENSG00000152977	ENST00000282928	D	0.91124	-2.79	4.01	4.01	0.46588	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	D	0.95076	0.8405	M	0.81179	2.53	0.80722	D	1	D	0.65815	0.995	D	0.71184	0.972	D	0.95992	0.8986	10	0.87932	D	0	.	16.467	0.84081	0.0:1.0:0.0:0.0	.	254	Q15915	ZIC1_HUMAN	K	254	ENSP00000282928:T254K	ENSP00000282928:T254K	T	+	2	0	ZIC1	148611350	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.870000	0.69620	1.930000	0.55929	0.561000	0.74099	ACG	.	.		0.557	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		A	147128660	C	A	147128660	3	1	43	1	0	0	0	0	1	0	0	0	17693	536	19	1	763	1	ZIC1	3	147128660	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	3577759	147128660	50893770	84	5166										
IL12A	3592	hgsc.bcm.edu	37	chr3	159711260	159711260	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgagagttgcctaaattccaGagagacctctttcataactg	8	9	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:159711260G>C	ENST00000305579.2	+	4	708	c.401G>C	c.(400-402)aGa>aCa	p.R134T	IL12A-AS1_ENST00000497452.1_RNA|IL12A_ENST00000466512.1_Intron|IL12A_ENST00000480787.1_Missense_Mutation_p.R96T	NM_000882.3	NP_000873.2	P29459	IL12A_HUMAN	interleukin 12A	100					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cell adhesion (GO:0045785)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|response to lipopolysaccharide (GO:0032496)|response to UV-B (GO:0010224)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)	interleukin-12 beta subunit binding (GO:0042163)|interleukin-12 receptor binding (GO:0005143)|interleukin-27 binding (GO:0045513)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)	9			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CTAAATTCCAGAGAGACCTCT	0.308																																					p.R134T		Atlas-SNP	.											.	IL12A	23	.	0			c.G401C						.						59	60	59					3																	159711260		2203	4300	6503	SO:0001583	missense	3592	exon4			ATTCCAGAGAGAC	M65271	CCDS3187.1	3q25.33	2014-04-04	2014-04-04		ENSG00000168811	ENSG00000168811		"Interleukins and interleukin receptors"	5969	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor 1, 35 kD subunit", "cytotoxic lymphocyte maturation factor 1, p35", "interleukin 12, p35", "IL-12, subunit p35", "NF cell stimulatory factor chain 1", "interleukin-12 alpha chain", "IL35 subunit"	161560	"interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35)"	NKSF1		1673147	Standard	NM_000882		Approved	CLMF, IL-12A, p35, NFSK	uc003fcx.3	P29459	OTTHUMG00000158942	ENST00000305579.2:c.401G>C	chr3.hg19:g.159711260G>C	ENSP00000303231:p.Arg134Thr	115.0	0.0		112.0	45.0	NM_000882	Q96QZ1	Missense_Mutation	SNP	ENST00000305579.2	hg19	CCDS3187.1	.	.	.	.	.	.	.	.	.	.	G	1.493	-0.554082	0.03996	.	.	ENSG00000168811	ENST00000305579;ENST00000480787	.	.	.	3.8	0.996	0.19844	.	0.851921	0.10463	N	0.671752	T	0.48589	0.1508	L	0.55103	1.725	0.58432	D	0.999991	P	0.43231	0.801	B	0.43990	0.438	T	0.44205	-0.9343	9	0.51188	T	0.08	-0.4938	6.1096	0.20094	0.3345:0.0:0.6655:0.0	.	134	O60595	.	T	134;96	.	ENSP00000303231:R134T	R	+	2	0	IL12A	161193954	0.178000	0.23122	0.868000	0.34077	0.150000	0.21749	0.030000	0.13688	0.207000	0.20607	-0.142000	0.14014	AGA	.	.		0.308	IL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352602.2	NM_000882		C	159711260	G	C	159711260	3	2	43	1	0	0	0	0	1	0	0	0	7633	942	33	4	415	4	IL12A	3	159711260	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	12582600	159711260	38311170	85	5167										
SI	6476	hgsc.bcm.edu	37	chr3	164764772	164764772	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcgggtaagaatgaagcttcTcttattaggaaaaacttttt	9	5	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:164764772T>C	ENST00000264382.3	-	16	1806	c.1744A>G	c.(1744-1746)Aga>Gga	p.R582G		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	582	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	ATGAAGCTTCTCTTATTAGGA	0.313										HNSCC(35;0.089)																											p.R582G		Atlas-SNP	.											.	SI	500	.	0			c.A1744G						.						53	52	52					3																	164764772		2203	4300	6503	SO:0001583	missense	6476	exon16			AGCTTCTCTTATT	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.1744A>G	chr3.hg19:g.164764772T>C	ENSP00000264382:p.Arg582Gly	126.0	0.0		142.0	6.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	hg19	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.238316	0.58886	.	.	ENSG00000090402	ENST00000264382	D	0.94330	-3.4	5.36	4.18	0.49190	Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.97983	0.9336	H	0.99011	4.4	0.48511	D	0.999663	D	0.89917	1.0	D	0.97110	1.0	D	0.97757	1.0218	10	0.87932	D	0	.	11.6805	0.51455	0.0:0.0:0.1485:0.8515	.	582	P14410	SUIS_HUMAN	G	582	ENSP00000264382:R582G	ENSP00000264382:R582G	R	-	1	2	SI	166247466	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	1.665000	0.37449	0.856000	0.35383	0.383000	0.25322	AGA	.	.		0.313	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		C	164764772	T	C	164764772	3	2	43	1	0	0	0	0	1	0	0	0	14312	1559	54	2	3871	2	SI	3	164764772	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5053512	164764772	33257658	86	5168										
PLD1	5337	hgsc.bcm.edu	37	chr3	171406587	171406587	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tccctcccacaaaggccaccGattggtcaatgatgacaagc	8	14	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:171406587G>A	ENST00000351298.4	-	14	1544	c.1418C>T	c.(1417-1419)tCg>tTg	p.S473L	PLD1_ENST00000342215.6_Missense_Mutation_p.S473L|PLD1_ENST00000356327.5_Missense_Mutation_p.S473L|PLD1_ENST00000340989.4_Missense_Mutation_p.S473L	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	473	Catalytic.|PLD phosphodiesterase 1. {ECO:0000255|PROSITE-ProRule:PRU00153}.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	AAAGGCCACCGATTGGTCAAT	0.532																																					p.S473L	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.C1418T						.						121	99	107					3																	171406587		2203	4300	6503	SO:0001583	missense	5337	exon14			GCCACCGATTGGT	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"Pleckstrin homology (PH) domain containing"	9067	protein-coding gene	gene with protein product	"choline phosphatase 1"	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.1418C>T	chr3.hg19:g.171406587G>A	ENSP00000342793:p.Ser473Leu	83.0	0.0		98.0	4.0	NM_002662		Missense_Mutation	SNP	ENST00000351298.4	hg19	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.177091	0.57692	.	.	ENSG00000075651	ENST00000356327;ENST00000351298;ENST00000342215;ENST00000340989	T;T;T;T	0.32515	3.35;3.34;1.45;3.2	5.3	4.42	0.53409	Phospholipase D/Transphosphatidylase (3);	0.078156	0.64402	D	0.000007	T	0.23727	0.0574	L	0.31157	0.91	0.80722	D	1	B;B	0.29481	0.245;0.065	B;B	0.28232	0.087;0.036	T	0.03503	-1.1030	10	0.31617	T	0.26	-11.1924	14.3925	0.66989	0.0717:0.0:0.9283:0.0	.	496;473	Q59EA4;Q13393	.;PLD1_HUMAN	L	473	ENSP00000348681:S473L;ENSP00000342793:S473L;ENSP00000339936:S473L;ENSP00000340326:S473L	ENSP00000340326:S473L	S	-	2	0	PLD1	172889281	1.000000	0.71417	0.824000	0.32777	0.355000	0.29361	9.781000	0.99029	1.364000	0.46038	0.655000	0.94253	TCG	.	.		0.532	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		A	171406587	G	A	171406587	3	1	43	1	0	0	0	0	1	0	0	0	12054	1059	37	1	1862	1	PLD1	3	171406587	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	6641815	171406587	26615843	87	5169										
FNDC3B	64778	hgsc.bcm.edu	37	chr3	172013157	172013157	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgtttttcttcctcaggtttCtaatattcaggcaagagcag	8	8	4	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:172013157C>T	ENST00000336824.4	+	8	953	c.854C>T	c.(853-855)tCt>tTt	p.S285F	FNDC3B_ENST00000416957.1_Missense_Mutation_p.S285F|FNDC3B_ENST00000415807.2_Missense_Mutation_p.S285F	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	285	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.S285Y(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		CCTCAGGTTTCTAATATTCAG	0.433																																					p.S285F		Atlas-SNP	.											FNDC3B,rectum,carcinoma,0,1	FNDC3B	118	.	1	Substitution - Missense(1)	large_intestine(1)	c.C854T						.						173	171	171					3																	172013157		2203	4300	6503	SO:0001583	missense	64778	exon8			AGGTTTCTAATAT	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.854C>T	chr3.hg19:g.172013157C>T	ENSP00000338523:p.Ser285Phe	107.0	1.0		107.0	5.0	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	hg19	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.076572	0.76415	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.60424	0.19;0.19;0.19	5.98	5.98	0.97165	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.152355	0.64402	D	0.000012	T	0.77890	0.4198	M	0.79011	2.435	0.80722	D	1	P;D	0.57257	0.705;0.979	P;D	0.69824	0.595;0.966	T	0.78929	-0.2010	10	0.87932	D	0	-22.3578	19.2296	0.93833	0.0:1.0:0.0:0.0	.	285;285	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	F	285	ENSP00000411242:S285F;ENSP00000338523:S285F;ENSP00000389094:S285F	ENSP00000338523:S285F	S	+	2	0	FNDC3B	173495851	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.715000	0.61909	2.835000	0.97688	0.650000	0.86243	TCT	.	.		0.433	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		T	172013157	C	T	172013157	3	4	43	1	0	0	0	0	1	0	0	0	5978	913	32	3	880	3	FNDC3B	3	172013157	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	606570	172013157	26009273	88	5170										
MCF2L2	23101	hgsc.bcm.edu	37	chr3	183028819	183028819	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atccagttgaactaataaccTttcaagaaagaatgagaaag	7	6	1	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:183028819T>C	ENST00000328913.3	-	9	1176		c.e9-2		MCF2L2_ENST00000414362.2_Splice_Site|MCF2L2_ENST00000473233.1_Splice_Site|MCF2L2_ENST00000447025.2_Splice_Site	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2								Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			ACTAATAACCTTTCAAGAAAG	0.408																																					.		Atlas-SNP	.											.	MCF2L2	164	.	0			c.879-2A>G						.						76	76	76					3																	183028819		2203	4300	6503	SO:0001630	splice_region_variant	23101	exon10			ATAACCTTTCAAG	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.879-2A>G	chr3.hg19:g.183028819T>C		66.0	0.0		73.0	5.0	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Splice_Site	SNP	ENST00000328913.3	hg19	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.722125	0.48728	.	.	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000414362	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4612	0.67450	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MCF2L2	184511513	1.000000	0.71417	1.000000	0.80357	0.686000	0.39977	6.829000	0.75314	2.092000	0.63282	0.533000	0.62120	.	.	.		0.408	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	Intron	C	183028819	T	C	183028819	5	2	43	1	0	0	0	0	0	0	1	0	9389	1623	56	2	2555	2	MCF2L2	3	183028819	Splice_Site	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	11015662	183028819	14993611	89	5171										
VPS8	23355	hgsc.bcm.edu	37	chr3	184646287	184646287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcatagttcaatttgaagagAgtcgactcatccggatggca	11	8	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr3:184646287A>G	ENST00000437079.3	+	32	2851	c.2680A>G	c.(2680-2682)Agt>Ggt	p.S894G	VPS8_ENST00000446204.2_Missense_Mutation_p.S802G|VPS8_ENST00000287546.4_Missense_Mutation_p.S894G|VPS8_ENST00000436792.2_Missense_Mutation_p.S892G|VPS8_ENST00000463687.1_3'UTR	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	894							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			ATTTGAAGAGAGTCGACTCAT	0.333																																					p.S894G		Atlas-SNP	.											.	VPS8	109	.	0			c.A2680G						.						124	117	119					3																	184646287		1837	4101	5938	SO:0001583	missense	23355	exon31			GAAGAGAGTCGAC	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"KIAA0804"	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.2680A>G	chr3.hg19:g.184646287A>G	ENSP00000397879:p.Ser894Gly	61.0	0.0		92.0	4.0	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	hg19	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	A	12.07	1.828382	0.32329	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.79	5.79	0.91817	Quinonprotein alcohol dehydrogenase-like (1);	0.394966	0.33916	N	0.004421	T	0.11665	0.0284	N	0.12182	0.205	0.34986	D	0.754568	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.15870	0.001;0.014;0.002	T	0.15780	-1.0425	10	0.32370	T	0.25	-8.2684	15.8033	0.78473	1.0:0.0:0.0:0.0	.	894;802;892	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	G	894;894;892;802	ENSP00000287546:S894G;ENSP00000397879:S894G;ENSP00000404704:S892G;ENSP00000405483:S802G	ENSP00000287546:S894G	S	+	1	0	VPS8	186128981	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.496000	0.73670	2.213000	0.71641	0.455000	0.32223	AGT	.	.		0.333	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		G	184646287	A	G	184646287	3	3	43	1	0	0	0	0	1	0	0	0	17233	304	11	2	2798	2	VPS8	3	184646287	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1617468	184646287	13376143	90	5172										
SEPSECS	51091	hgsc.bcm.edu	37	chr4	25160704	25160704	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	agagttcaagtgtactttcaTcccagccattctctggacac	7	12	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:25160704T>C	ENST00000382103.2	-	2	212	c.140A>G	c.(139-141)gAt>gGt	p.D47G	PI4K2B_ENST00000512921.1_5'Flank|SEPSECS_ENST00000302922.3_Intron	NM_016955.3	NP_058651.3	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	47					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	pyridoxal phosphate binding (GO:0030170)|transferase activity, transferring selenium-containing groups (GO:0016785)|tRNA binding (GO:0000049)	p.D47G(2)		endometrium(1)|large_intestine(4)|lung(2)|stomach(1)	8		Breast(46;0.173)				TGTACTTTCATCCCAGCCATT	0.363																																					p.D47G		Atlas-SNP	.											SEPSECS_ENST00000382103,NS,carcinoma,0,2	SEPSECS	55	.	2	Substitution - Missense(2)	prostate(1)|kidney(1)	c.A140G						.						118	108	111					4																	25160704		1865	4098	5963	SO:0001583	missense	51091	exon2			CTTTCATCCCAGC	AJ238617	CCDS3432.1, CCDS3432.2	4p15.2	2008-10-27			ENSG00000109618	ENSG00000109618			30605	protein-coding gene	gene with protein product	"soluble liver antigen/liver pancreas antigen"	613009				16230358, 10931155, 17142313, 17194211	Standard	NM_016955		Approved	SLA/LP, SLA	uc003grg.3	Q9HD40	OTTHUMG00000128563	ENST00000382103.2:c.140A>G	chr4.hg19:g.25160704T>C	ENSP00000371535:p.Asp47Gly	57.0	1.0		84.0	6.0	NM_016955	A8K8W1|Q0D2P3|Q17RT1|Q9NXZ5|Q9UGM9|Q9Y353	Missense_Mutation	SNP	ENST00000382103.2	hg19	CCDS3432.2	.	.	.	.	.	.	.	.	.	.	T	13.10	2.137631	0.37728	.	.	ENSG00000109618	ENST00000382103;ENST00000513285	D;D	0.81908	-1.55;-1.55	5.71	5.71	0.89125	Pyridoxal phosphate-dependent transferase, major domain (1);	0.188853	0.56097	D	0.000029	D	0.84257	0.5432	M	0.72894	2.215	0.80722	D	1	B;B	0.25904	0.137;0.028	B;B	0.32533	0.147;0.008	T	0.82750	-0.0303	10	0.56958	D	0.05	-2.1426	15.9715	0.80025	0.0:0.0:0.0:1.0	.	46;47	Q9HD40-3;Q9HD40	.;SPCS_HUMAN	G	47;132	ENSP00000371535:D47G;ENSP00000423361:D132G	ENSP00000371535:D47G	D	-	2	0	SEPSECS	24769802	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.862000	0.48388	2.165000	0.68154	0.528000	0.53228	GAT	.	.		0.363	SEPSECS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250414.2	NM_016955		C	25160704	T	C	25160704	3	2	43	1	0	0	0	0	1	0	0	0	14073	1435	50	2	1405	2	SEPSECS	4	25160704	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10		25160704	165993572	91	5173										
RFC1	5981	hgsc.bcm.edu	37	chr4	39352986	39352986	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	accttgatttcctttattccTttctttgcttttaaagtttc	3	9	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:39352986T>C	ENST00000381897.1	-	2	247	c.114A>G	c.(112-114)aaA>aaG	p.K38K	RFC1_ENST00000349703.2_Silent_p.K38K|RFC1_ENST00000418436.1_5'UTR	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	38					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						CCTTTATTCCTTTCTTTGCTT	0.259																																					p.K38K	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.A114G						.						100	99	99					4																	39352986		2201	4298	6499	SO:0001819	synonymous_variant	5981	exon2			TATTCCTTTCTTT	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.114A>G	chr4.hg19:g.39352986T>C		73.0	0.0		70.0	4.0	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	ENST00000381897.1	hg19	CCDS56329.1																																																																																			.	.		0.259	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		C	39352986	T	C	39352986	2	2	43	1	0	0	0	0	0	0	0	1	13259	1606	56	2		2	RFC1	4	39352986	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	14192282	39352986	151801290	92	5174										
GNPDA2	132789	hgsc.bcm.edu	37	chr4	44709828	44709828	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tagcatcttcatcgcatacaAaaatagtccggggatgctgc	9	10	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:44709828A>G	ENST00000295448.3	-	6	866	c.710T>C	c.(709-711)tTt>tCt	p.F237S	GNPDA2_ENST00000511187.1_5'UTR|GNPDA2_ENST00000507917.1_Missense_Mutation_p.F203S|GNPDA2_ENST00000509756.1_Missense_Mutation_p.F237S|GNPDA2_ENST00000507534.1_Missense_Mutation_p.F167S|RP11-700J17.2_ENST00000610267.1_RNA	NM_138335.2	NP_612208.1	Q8TDQ7	GNPI2_HUMAN	glucosamine-6-phosphate deaminase 2	237					carbohydrate metabolic process (GO:0005975)|N-acetylglucosamine metabolic process (GO:0006044)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	glucosamine-6-phosphate deaminase activity (GO:0004342)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(1)|lung(7)|ovary(1)	11						ATCGCATACAAAAATAGTCCG	0.413																																					p.F237S	Colon(54;743 1010 7604 16453 19544)	Atlas-SNP	.											.	GNPDA2	28	.	0			c.T710C						.						92	84	87					4																	44709828		2203	4300	6503	SO:0001583	missense	132789	exon6			CATACAAAAATAG	AF247786	CCDS3469.1, CCDS59472.1, CCDS59473.1	4p13	2006-04-12			ENSG00000163281	ENSG00000163281	3.5.99.6		21526	protein-coding gene	gene with protein product	"glucosamine-6-phosphate isomerase"	613222				12965206	Standard	NM_001270880		Approved	SB52	uc003gwy.4	Q8TDQ7	OTTHUMG00000099415	ENST00000295448.3:c.710T>C	chr4.hg19:g.44709828A>G	ENSP00000295448:p.Phe237Ser	74.0	0.0		89.0	4.0	NM_138335	B4DJF3|Q2VYF1|Q59EA7|Q8NCZ8|Q96BJ4|Q96NC6	Missense_Mutation	SNP	ENST00000295448.3	hg19	CCDS3469.1	.	.	.	.	.	.	.	.	.	.	A	19.36	3.812079	0.70797	.	.	ENSG00000163281	ENST00000507917;ENST00000295448;ENST00000507534;ENST00000509756	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.62925	0.2468	M	0.72479	2.2	0.80722	D	1	P;D;D	0.89917	0.954;1.0;1.0	B;D;D	0.77004	0.439;0.989;0.966	T	0.67348	-0.5693	10	0.87932	D	0	-16.869	14.125	0.65215	1.0:0.0:0.0:0.0	.	203;237;237	Q2VYF1;Q8TDQ7-3;Q8TDQ7	.;.;GNPI2_HUMAN	S	203;237;167;237	ENSP00000425868:F203S;ENSP00000295448:F237S;ENSP00000427423:F167S;ENSP00000424061:F237S	ENSP00000295448:F237S	F	-	2	0	GNPDA2	44404585	1.000000	0.71417	1.000000	0.80357	0.551000	0.35334	8.761000	0.91691	2.180000	0.69256	0.533000	0.62120	TTT	.	.		0.413	GNPDA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216874.3	NM_138335		G	44709828	A	G	44709828	3	3	43	1	0	0	0	0	1	0	0	0	6551	14	1	2	128	2	GNPDA2	4	44709828	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	5356842	44709828	146444448	93	5175										
PROL1	58503	hgsc.bcm.edu	37	chr4	71275489	71275489	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccccaaataaacatcaccacCgcagatacaacaatcaccac	2	17	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:71275489C>T	ENST00000399575.2	+	3	618	c.444C>T	c.(442-444)acC>acT	p.T148T	PROL1_ENST00000514338.1_3'UTR	NM_021225.4	NP_067048.4	Q99935	PROL1_HUMAN	proline rich, lacrimal 1	148	Thr-rich.				negative regulation of endopeptidase activity (GO:0010951)|regulation of sensory perception of pain (GO:0051930)|retina homeostasis (GO:0001895)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)|peptidase inhibitor activity (GO:0030414)	p.T148T(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	15		all_hematologic(202;0.196)				ACATCACCACCGCAGATACAA	0.448																																					p.T148T		Atlas-SNP	.											PROL1,NS,carcinoma,0,1	PROL1	46	.	1	Substitution - coding silent(1)	kidney(1)	c.C444T						.						189	211	204					4																	71275489		1975	4164	6139	SO:0001819	synonymous_variant	58503	exon3			CACCACCGCAGAT	S83198	CCDS43235.1	4q13.3	2011-10-28	2005-02-07		ENSG00000171199	ENSG00000171199			17279	protein-coding gene	gene with protein product		608936	"proline rich 1"			8670737	Standard	NM_021225		Approved	BPLP, PRL1, opiorphin	uc003hfi.3	Q99935	OTTHUMG00000160845	ENST00000399575.2:c.444C>T	chr4.hg19:g.71275489C>T		174.0	0.0		134.0	91.0	NM_021225	A8MZ07|P85047	Silent	SNP	ENST00000399575.2	hg19	CCDS43235.1																																																																																			.	.		0.448	PROL1-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000362639.1	NM_021225		T	71275489	C	T	71275489	2	4	43	1	0	0	0	0	0	0	0	1	12566	639	23	1		1	PROL1	4	71275489	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	26565661	71275489	119878787	94	5176										
RUFY3	22902	hgsc.bcm.edu	37	chr4	71588361	71588361	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gatcacacaggctgccatggAgaccatctacctttgcaaat	8	12	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:71588361A>G	ENST00000226328.4	+	1	634	c.71A>G	c.(70-72)gAg>gGg	p.E24G	RUFY3_ENST00000381006.3_Missense_Mutation_p.E24G|RUFY3_ENST00000417478.2_Intron|RUFY3_ENST00000536664.1_5'Flank	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	24					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			GCTGCCATGGAGACCATCTAC	0.547																																					p.E24G		Atlas-SNP	.											.	RUFY3	61	.	0			c.A71G						.						216	177	191					4																	71588361		2203	4300	6503	SO:0001583	missense	22902	exon1			CCATGGAGACCAT	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.71A>G	chr4.hg19:g.71588361A>G	ENSP00000226328:p.Glu24Gly	86.0	0.0		98.0	4.0	NM_001037442	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	hg19	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.866401	0.91511	.	.	ENSG00000018189	ENST00000381006;ENST00000226328	T;T	0.14266	2.9;2.52	5.64	5.64	0.86602	.	0.054650	0.64402	D	0.000001	T	0.28101	0.0693	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.981	D;D	0.78314	0.991;0.932	T	0.01776	-1.1276	10	0.72032	D	0.01	-6.7551	15.8666	0.79069	1.0:0.0:0.0:0.0	.	24;24	Q7L099-3;Q7L099	.;RUFY3_HUMAN	G	24	ENSP00000370394:E24G;ENSP00000226328:E24G	ENSP00000226328:E24G	E	+	2	0	RUFY3	71807225	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.148000	0.66965	0.528000	0.53228	GAG	.	.		0.547	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		G	71588361	A	G	71588361	3	3	43	1	0	0	0	0	1	0	0	0	13755	304	11	2	435	2	RUFY3	4	71588361	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	312872	71588361	119565915	95	5177										
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72306489	72306489	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctgaagttcctgtgcccacaAggtaagctgctctcctacct	8	14	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:72306489A>G	ENST00000264485.5	+	8	1081	c.964A>G	c.(964-966)Agg>Ggg	p.R322G	SLC4A4_ENST00000425175.1_Splice_Site_p.R322G|SLC4A4_ENST00000512686.1_Splice_Site_p.R278G|SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000340595.3_Splice_Site_p.R278G|SLC4A4_ENST00000351898.6_Splice_Site_p.R322G	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	322					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	TGTGCCCACAAGGTAAGCTGC	0.473																																					p.R322G		Atlas-SNP	.											.	SLC4A4	269	.	0			c.A964G						.						198	167	177					4																	72306489		2203	4300	6503	SO:0001630	splice_region_variant	8671	exon8			CCCACAAGGTAAG	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.965+1A>G	chr4.hg19:g.72306489A>G		133.0	0.0		99.0	4.0	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.951071	0.73787	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000512686;ENST00000340595	T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12	5.15	2.48	0.30137	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	D	0.89283	0.6671	M	0.92367	3.3	0.80722	D	1	D;D;P;D;D;D	0.76494	0.985;0.999;0.949;0.992;0.998;0.976	D;D;P;D;D;D	0.73708	0.924;0.979;0.875;0.94;0.981;0.948	D	0.90894	0.4763	10	0.87932	D	0	.	12.3566	0.55178	0.6088:0.3912:0.0:0.0	.	322;322;278;278;302;322	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1-3;Q9Y6R3;Q9Y6R1	.;.;.;.;.;S4A4_HUMAN	G	322;322;322;278;278	ENSP00000264485:R322G;ENSP00000393557:R322G;ENSP00000307349:R322G;ENSP00000422400:R278G;ENSP00000344272:R278G	ENSP00000264485:R322G	R	+	1	2	SLC4A4	72525353	0.974000	0.33945	0.903000	0.35520	0.972000	0.66771	2.525000	0.45598	0.883000	0.36040	0.533000	0.62120	AGG	.	.		0.473	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	Missense_Mutation	G	72306489	A	G	72306489	5	3	43	1	0	0	0	0	0	0	1	0	14671	86	3	2	1111	2	SLC4A4	4	72306489	Splice_Site	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	718128	72306489	118847787	96	5178										
CCDC158	339965	hgsc.bcm.edu	37	chr4	77247091	77247091	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgaaccttcaactgaactagTtaggagtgagtgcactggag	12	7	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:77247091T>C	ENST00000388914.3	-	22	3228	c.3076A>G	c.(3076-3078)Act>Gct	p.T1026A		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	1026	Ser-rich.									breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						ACTGAACTAGTTAGGAGTGAG	0.373																																					p.T1026A		Atlas-SNP	.											.	CCDC158	114	.	0			c.A3076G						.						170	165	166					4																	77247091		1863	4109	5972	SO:0001583	missense	339965	exon22			AACTAGTTAGGAG	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.3076A>G	chr4.hg19:g.77247091T>C	ENSP00000373566:p.Thr1026Ala	60.0	0.0		80.0	4.0	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	hg19	CCDS43242.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.616427	0.46736	.	.	ENSG00000163749	ENST00000388914;ENST00000318586	T	0.35421	1.31	4.83	3.57	0.40892	.	0.135985	0.34245	N	0.004136	T	0.19248	0.0462	N	0.24115	0.695	0.41628	D	0.989001	P	0.36990	0.577	B	0.38264	0.269	T	0.08207	-1.0733	10	0.05833	T	0.94	.	7.3456	0.26662	0.1946:0.0:0.0:0.8054	.	1026	Q5M9N0	CD158_HUMAN	A	1026;446	ENSP00000373566:T1026A	ENSP00000316815:T446A	T	-	1	0	CCDC158	77466115	0.976000	0.34144	0.743000	0.31040	0.279000	0.26890	2.034000	0.41145	2.169000	0.68431	0.374000	0.22700	ACT	.	.		0.373	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		C	77247091	T	C	77247091	3	2	43	1	0	0	0	0	1	0	0	0	2792	1725	60	2	277	2	CCDC158	4	77247091	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	4940602	77247091	113907185	97	5179										
CCDC158	339965	hgsc.bcm.edu	37	chr4	77324342	77324342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aagatcttcattatttgattCccaagcttttgattccatat	4	8	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:77324342C>T	ENST00000388914.3	-	2	171	c.19G>A	c.(19-21)Gaa>Aaa	p.E7K	SNORD50_ENST00000362987.1_RNA|CCDC158_ENST00000434846.2_Missense_Mutation_p.E7K|CCDC158_ENST00000504868.1_5'UTR	NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	7										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						TTATTTGATTCCCAAGCTTTT	0.323																																					p.E7K		Atlas-SNP	.											CCDC158,NS,carcinoma,0,1	CCDC158	114	.	0			c.G19A						.						133	124	126					4																	77324342		1806	4063	5869	SO:0001583	missense	339965	exon2			TTGATTCCCAAGC	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.19G>A	chr4.hg19:g.77324342C>T	ENSP00000373566:p.Glu7Lys	55.0	0.0		44.0	2.0	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	hg19	CCDS43242.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.217333	0.58560	.	.	ENSG00000163749	ENST00000388914;ENST00000318586;ENST00000434846	T;T	0.46819	0.99;0.86	4.06	4.06	0.47325	.	0.000000	0.43260	D	0.000586	T	0.29783	0.0744	N	0.14661	0.345	0.29528	N	0.853008	P;B	0.37330	0.59;0.447	B;B	0.34652	0.187;0.051	T	0.36456	-0.9747	10	0.66056	D	0.02	.	12.0512	0.53507	0.0:1.0:0.0:0.0	.	7;7	Q5M9N0-3;Q5M9N0	.;CD158_HUMAN	K	7	ENSP00000373566:E7K;ENSP00000401742:E7K	ENSP00000316815:E7K	E	-	1	0	CCDC158	77543366	0.994000	0.37717	0.968000	0.41197	0.512000	0.34134	1.999000	0.40806	2.550000	0.86006	0.655000	0.94253	GAA	.	.		0.323	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		T	77324342	C	T	77324342	3	4	43	1	0	0	0	0	1	0	0	0	2792	864	30	3	3414	3	CCDC158	4	77324342	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	77251	77324342	113829934	98	5180										
SPARCL1	8404	hgsc.bcm.edu	37	chr4	88411956	88411956	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acaagtcactggatcctggcAgacacagtgaggttttccct	10	11	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:88411956A>G	ENST00000282470.6	-	6	1836	c.1366T>C	c.(1366-1368)Tgc>Cgc	p.C456R	SPARCL1_ENST00000418378.1_Missense_Mutation_p.C456R|SPARCL1_ENST00000503414.1_Missense_Mutation_p.C331R	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	456	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		GGATCCTGGCAGACACAGTGA	0.438																																					p.C456R		Atlas-SNP	.											.	SPARCL1	59	.	0			c.T1366C						.						133	132	133					4																	88411956		2203	4300	6503	SO:0001583	missense	8404	exon6			CCTGGCAGACACA	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"EF-hand domain containing"	11220	protein-coding gene	gene with protein product		606041	"SPARC-like 1 (mast9, hevin)"			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.1366T>C	chr4.hg19:g.88411956A>G	ENSP00000282470:p.Cys456Arg	155.0	0.0		98.0	4.0	NM_004684	B4E2Z0|E7ESU2|Q14800	Missense_Mutation	SNP	ENST00000282470.6	hg19	CCDS3622.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.981429	0.74474	.	.	ENSG00000152583	ENST00000282470;ENST00000418378;ENST00000438050;ENST00000503414	D;D;D	0.90900	-2.75;-2.75;-2.75	5.17	5.17	0.71159	Proteinase inhibitor I1, Kazal (2);Osteonectin-like, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.95487	0.8534	M	0.84773	2.715	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96078	0.9051	10	0.87932	D	0	-8.5084	14.5292	0.67912	1.0:0.0:0.0:0.0	.	456	Q14515	SPRL1_HUMAN	R	456;456;331;331	ENSP00000282470:C456R;ENSP00000414856:C456R;ENSP00000422903:C331R	ENSP00000282470:C456R	C	-	1	0	SPARCL1	88630980	1.000000	0.71417	0.991000	0.47740	0.827000	0.46813	7.866000	0.87056	2.260000	0.74910	0.528000	0.53228	TGC	.	.		0.438	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2			G	88411956	A	G	88411956	3	3	43	1	0	0	0	0	1	0	0	0	15011	188	7	2	652	2	SPARCL1	4	88411956	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	11087614	88411956	102742320	99	5181										
DSPP	1834	hgsc.bcm.edu	37	chr4	88535745	88535745	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cagtaagtcagacagcagtgAcagcaacagcagtgacagta	11	9	1	3	rs200924212		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:88535745A>G	ENST00000282478.7	+	4	1964	c.1931A>G	c.(1930-1932)gAc>gGc	p.D644G	DSPP_ENST00000399271.1_Missense_Mutation_p.D644G|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	644	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gacagcagtgacagcaacagc	0.483																																					p.D644G		Atlas-SNP	.											.	DSPP	174	.	0			c.A1931G						.						122	140	134					4																	88535745		1797	3285	5082	SO:0001583	missense	1834	exon5			GCAGTGACAGCAA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.1931A>G	chr4.hg19:g.88535745A>G	ENSP00000282478:p.Asp644Gly	159.0	0.0		110.0	6.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.716185	0.00706	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87729	-2.29;-2.29	0.737	0.737	0.18314	.	.	.	.	.	T	0.78084	0.4228	L	0.36672	1.1	0.09310	N	1	B	0.27625	0.183	B	0.15870	0.014	T	0.67229	-0.5723	8	0.56958	D	0.05	.	.	.	.	.	644	Q9NZW4	DSPP_HUMAN	G	644	ENSP00000382213:D644G;ENSP00000282478:D644G	ENSP00000282478:D644G	D	+	2	0	DSPP	88754769	0.001000	0.12720	0.155000	0.22561	0.002000	0.02628	0.867000	0.27968	0.539000	0.28788	0.147000	0.16070	GAC	.	.		0.483	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		G	88535745	A	G	88535745	3	3	43	1	0	0	0	0	1	0	0	0	4784	275	10	2	1945	2	DSPP	4	88535745	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	123789	88535745	102618531	100	5182										
EMCN	51705	hgsc.bcm.edu	37	chr4	101396223	101396223	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttacttgttaaaaaagtagcTgttgacatcagagacatttt	7	5	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:101396223T>C	ENST00000296420.4	-	3	409	c.231A>G	c.(229-231)acA>acG	p.T77T	EMCN_ENST00000502327.1_5'UTR|EMCN_ENST00000305864.3_Silent_p.T77T|EMCN_ENST00000511970.1_Silent_p.T77T	NM_001159694.1|NM_016242.3	NP_001153166.1|NP_057326.2	Q9ULC0	MUCEN_HUMAN	endomucin	77	Thr-rich.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)		AAAAAGTAGCTGTTGACATCA	0.239																																					p.T77T		Atlas-SNP	.											.	EMCN	37	.	0			c.A231G						.						49	54	53					4																	101396223		2184	4274	6458	SO:0001819	synonymous_variant	51705	exon3			AGTAGCTGTTGAC	AF205940	CCDS3655.1, CCDS54782.1	4q22.1	2008-02-05			ENSG00000164035	ENSG00000164035		"Mucins"	16041	protein-coding gene	gene with protein product		608350				11418125, 11594763	Standard	NM_016242		Approved	MUC14	uc003hvr.3	Q9ULC0	OTTHUMG00000131051	ENST00000296420.4:c.231A>G	chr4.hg19:g.101396223T>C		56.0	0.0		38.0	4.0	NM_001159694	A8K716|B4E347|Q8NEY5|Q8WWE7|Q9NRM8	Silent	SNP	ENST00000296420.4	hg19	CCDS3655.1																																																																																			.	.		0.239	EMCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253699.2	NM_016242		C	101396223	T	C	101396223	2	2	43	1	0	0	0	0	0	0	0	1	5088	1567	55	2		2	EMCN	4	101396223	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	12860478	101396223	89758053	101	5183										
NFKB1	4790	hgsc.bcm.edu	37	chr4	103531782	103531782	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctctctatgacctggatgacTcttgggaaaatgcaggagag	12	8	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:103531782T>C	ENST00000505458.1	+	20	2552	c.2275T>C	c.(2275-2277)Tct>Cct	p.S759P	NFKB1_ENST00000394820.4_Missense_Mutation_p.S759P|NFKB1_ENST00000226574.4_Missense_Mutation_p.S760P|NFKB1_ENST00000600343.1_Missense_Mutation_p.S579P			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	759	Interaction with CFLAR.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	CCTGGATGACTCTTGGGAAAA	0.512																																					p.S760P		Atlas-SNP	.											.	NFKB1	78	.	0			c.T2278C						.						134	130	132					4																	103531782		2203	4300	6503	SO:0001583	missense	4790	exon20			GATGACTCTTGGG	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.2275T>C	chr4.hg19:g.103531782T>C	ENSP00000424790:p.Ser759Pro	77.0	0.0		46.0	4.0	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	hg19	CCDS54783.1	.	.	.	.	.	.	.	.	.	.	T	15.75	2.926826	0.52759	.	.	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000505458	T;T;T	0.36878	1.23;1.23;1.23	4.62	3.44	0.39384	Ankyrin repeat-containing domain (2);	0.686712	0.13698	N	0.369051	T	0.24661	0.0598	L	0.34521	1.04	0.37283	D	0.907912	P;P;P	0.43633	0.536;0.722;0.813	B;B;B	0.41299	0.203;0.189;0.353	T	0.07731	-1.0757	10	0.24483	T	0.36	.	5.4659	0.16642	0.1337:0.0:0.2903:0.576	.	579;759;760	B3KVE8;P19838;P19838-2	.;NFKB1_HUMAN;.	P	760;759;759	ENSP00000226574:S760P;ENSP00000378297:S759P;ENSP00000424790:S759P	ENSP00000226574:S760P	S	+	1	0	NFKB1	103750820	0.879000	0.30193	0.999000	0.59377	0.964000	0.63967	1.046000	0.30354	1.935000	0.56089	0.533000	0.62120	TCT	.	.		0.512	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			C	103531782	T	C	103531782	3	2	43	1	0	0	0	0	1	0	0	0	10384	1551	54	2	2352	2	NFKB1	4	103531782	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2135559	103531782	87622494	102	5184										
BDH2	56898	hgsc.bcm.edu	37	chr4	104013835	104013835	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtttcttctttgtgacatcaAggacacgagtttgaatacct	8	8	3	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:104013835A>G	ENST00000296424.4	-	4	290	c.170T>C	c.(169-171)cTt>cCt	p.L57P		NM_020139.3	NP_064524.3	Q9BUT1	BDH2_HUMAN	3-hydroxybutyrate dehydrogenase, type 2	57					epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|heme metabolic process (GO:0042168)|iron ion homeostasis (GO:0055072)|siderophore biosynthetic process (GO:0019290)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.02e-08)		TGTGACATCAAGGACACGAGT	0.338																																					p.L57P		Atlas-SNP	.											.	BDH2	18	.	0			c.T170C						.						76	77	77					4																	104013835		2203	4300	6503	SO:0001583	missense	56898	exon4			ACATCAAGGACAC	AF164790	CCDS3663.1	4q24	2011-09-14			ENSG00000164039	ENSG00000164039	1.1.1.30	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	32389	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 15C, member 1"		"dehydrogenase/reductase (SDR family) member 6"	DHRS6		16380372, 19027726	Standard	XM_005263140		Approved	UCPA-OR, FLJ13261, UNQ6308, PRO20933, SDR15C1	uc003hwz.3	Q9BUT1	OTTHUMG00000074039	ENST00000296424.4:c.170T>C	chr4.hg19:g.104013835A>G	ENSP00000296424:p.Leu57Pro	199.0	0.0		135.0	6.0	NM_020139	A8K295|B4DUF6|Q503A0|Q6IA46|Q6UWD3|Q9H8S8|Q9NRX8	Missense_Mutation	SNP	ENST00000296424.4	hg19	CCDS3663.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.831689	0.50845	.	.	ENSG00000164039	ENST00000296424;ENST00000504285;ENST00000509245	T;D;D	0.88354	1.77;-2.37;-2.37	4.83	4.83	0.62350	NAD(P)-binding domain (1);	0.128387	0.48286	D	0.000183	D	0.93913	0.8052	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94619	0.7811	10	0.87932	D	0	.	13.7077	0.62651	1.0:0.0:0.0:0.0	.	57	Q9BUT1	BDH2_HUMAN	P	57	ENSP00000296424:L57P;ENSP00000427442:L57P;ENSP00000422891:L57P	ENSP00000296424:L57P	L	-	2	0	BDH2	104233284	1.000000	0.71417	0.199000	0.23439	0.395000	0.30598	7.419000	0.80179	1.942000	0.56320	0.459000	0.35465	CTT	.	.		0.338	BDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157159.2	NM_020139		G	104013835	A	G	104013835	3	3	43	1	0	0	0	0	1	0	0	0	1391	72	3	2	595	2	BDH2	4	104013835	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	482053	104013835	87140441	103	5185										
GAR1	54433	hgsc.bcm.edu	37	chr4	110739158	110739158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atgtaccacagatgaaaataAggtgccttatttcaatgctc	7	8	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:110739158A>G	ENST00000226796.6	+	3	545	c.281A>G	c.(280-282)aAg>aGg	p.K94R	RP11-602N24.3_ENST00000609440.1_lincRNA|GAR1_ENST00000394631.3_Missense_Mutation_p.K94R	NM_018983.3	NP_061856.1	Q9NY12	GAR1_HUMAN	GAR1 ribonucleoprotein	94					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|pseudouridine synthesis (GO:0001522)|rRNA processing (GO:0006364)	box H/ACA snoRNP complex (GO:0031429)|nucleolus (GO:0005730)|nucleus (GO:0005634)	cation channel activity (GO:0005261)|poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	9						GATGAAAATAAGGTGCCTTAT	0.333																																					p.K94R		Atlas-SNP	.											.	GAR1	16	.	0			c.A281G						.						126	123	124					4																	110739158		2203	4300	6503	SO:0001583	missense	54433	exon3			AAAATAAGGTGCC	AJ276003	CCDS34050.1	4q	2013-07-31	2013-07-31	2008-10-13	ENSG00000109534	ENSG00000109534			14264	protein-coding gene	gene with protein product		606468	"nucleolar protein family A, member 1 (H/ACA small nucleolar RNPs)", "GAR1 ribonucleoprotein homolog (yeast)"	NOLA1		10757788	Standard	XM_005263069		Approved		uc003hzu.3	Q9NY12	OTTHUMG00000161108	ENST00000226796.6:c.281A>G	chr4.hg19:g.110739158A>G	ENSP00000226796:p.Lys94Arg	71.0	0.0		49.0	4.0	NM_018983	Q5MJQ2	Missense_Mutation	SNP	ENST00000226796.6	hg19	CCDS34050.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.050995	0.55218	.	.	ENSG00000109534	ENST00000394631;ENST00000226796	.	.	.	4.94	4.94	0.65067	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.047654	0.85682	D	0.000000	T	0.35219	0.0924	N	0.16478	0.41	0.43617	D	0.995991	B;B	0.27416	0.148;0.178	B;B	0.27380	0.048;0.079	T	0.23762	-1.0179	9	0.45353	T	0.12	.	9.4458	0.38697	0.9202:0.0:0.0798:0.0	.	94;94	Q9NY12-2;Q9NY12	.;GAR1_HUMAN	R	94	.	ENSP00000226796:K94R	K	+	2	0	GAR1	110958607	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.087000	0.57671	1.975000	0.57531	0.533000	0.62120	AAG	.	.		0.333	GAR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363810.2			G	110739158	A	G	110739158	3	3	43	1	0	0	0	0	1	0	0	0	6248	72	3	2	287	2	GAR1	4	110739158	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	6725323	110739158	80415118	104	5186										
AP1AR	55435	hgsc.bcm.edu	37	chr4	113187842	113187842	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtggaaatgacgacagcacaTccttagatctagagtgggaa	12	7	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:113187842T>C	ENST00000274000.5	+	9	968	c.613T>C	c.(613-615)Tcc>Ccc	p.S205P	AP1AR_ENST00000309703.6_Missense_Mutation_p.S172P	NM_018569.4	NP_061039.3	Q63HQ0	AP1AR_HUMAN	adaptor-related protein complex 1 associated regulatory protein	205	Sufficient for association with the Arp2/3 complex.				cellular protein localization (GO:0034613)|negative regulation of cell motility (GO:2000146)|negative regulation of receptor recycling (GO:0001920)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|protein transport (GO:0015031)|regulation of Arp2/3 complex-mediated actin nucleation (GO:0034315)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|transport vesicle (GO:0030133)	AP-1 adaptor complex binding (GO:0035650)|kinesin binding (GO:0019894)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	9						CGACAGCACATCCTTAGATCT	0.333																																					p.S205P		Atlas-SNP	.											.	AP1AR	25	.	0			c.T613C						.						126	125	125					4																	113187842		2203	4300	6503	SO:0001583	missense	55435	exon9			AGCACATCCTTAG	AL136628	CCDS3696.1, CCDS47125.1	4q25	2009-09-28	2009-09-25	2009-09-25	ENSG00000138660	ENSG00000138660			28808	protein-coding gene	gene with protein product	"gamma1-adaptin brefeldin A resistance"	610851	"chromosome 4 open reading frame 16"	C4orf16		15775984	Standard	NM_018569		Approved	PRO0971, 2C18, gamma-BAR	uc003iaj.4	Q63HQ0	OTTHUMG00000132849	ENST00000274000.5:c.613T>C	chr4.hg19:g.113187842T>C	ENSP00000274000:p.Ser205Pro	125.0	0.0		92.0	4.0	NM_018569	B2RCV7|Q96GG6|Q9H0V0|Q9P1L4	Missense_Mutation	SNP	ENST00000274000.5	hg19	CCDS3696.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.592478	0.86953	.	.	ENSG00000138660	ENST00000274000;ENST00000309703	T;T	0.59224	0.28;0.37	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.73289	0.3568	M	0.62723	1.935	0.58432	D	0.99999	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.76342	-0.2994	10	0.72032	D	0.01	-16.0643	15.3104	0.74026	0.0:0.0:0.0:1.0	.	172;205	Q63HQ0-2;Q63HQ0	.;AP1AR_HUMAN	P	205;172	ENSP00000274000:S205P;ENSP00000309023:S172P	ENSP00000274000:S205P	S	+	1	0	AP1AR	113407291	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.170000	0.77587	2.025000	0.59659	0.533000	0.62120	TCC	.	.		0.333	AP1AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256323.2	NM_018569		C	113187842	T	C	113187842	3	2	43	1	0	0	0	0	1	0	0	0	730	1435	50	2	647	2	AP1AR	4	113187842	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2448684	113187842	77966434	105	5187										
MYOZ2	51778	hgsc.bcm.edu	37	chr4	120079180	120079180	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cttttgattaaatacagcacAgtattgctatgcagaatggg	9	6	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:120079180A>G	ENST00000307128.5	+	4	463	c.250A>G	c.(250-252)Agt>Ggt	p.S84G		NM_016599.4	NP_057683.1			myozenin 2											endometrium(1)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						AATACAGCACAGTATTGCTAT	0.398																																					p.S84G		Atlas-SNP	.											MYOZ2,NS,carcinoma,0,1	MYOZ2	34	.	0			c.A250G						.						109	109	109					4																	120079180		2203	4300	6503	SO:0001583	missense	51778	exon4			CAGCACAGTATTG	AF249873	CCDS3711.1	4q26-q27	2014-09-17	2002-01-07	2002-01-11	ENSG00000172399	ENSG00000172399			1330	protein-coding gene	gene with protein product		605602	"chromosome 4 open reading frame 5"	C4orf5		8619474, 9110174	Standard	NM_016599		Approved	CS-1	uc003icp.4	Q9NPC6	OTTHUMG00000132968	ENST00000307128.5:c.250A>G	chr4.hg19:g.120079180A>G	ENSP00000306997:p.Ser84Gly	59.0	1.0		38.0	2.0	NM_016599		Missense_Mutation	SNP	ENST00000307128.5	hg19	CCDS3711.1	.	.	.	.	.	.	.	.	.	.	A	8.500	0.863935	0.17250	.	.	ENSG00000172399	ENST00000307128	T	0.64438	-0.1	5.7	4.52	0.55395	.	1.230050	0.05045	N	0.477128	T	0.35451	0.0932	N	0.02158	-0.66	0.22787	N	0.998736	B	0.02656	0.0	B	0.08055	0.003	T	0.32241	-0.9914	10	0.11794	T	0.64	-0.1179	7.7009	0.28621	0.7692:0.1529:0.0779:0.0	.	84	Q9NPC6	MYOZ2_HUMAN	G	84	ENSP00000306997:S84G	ENSP00000306997:S84G	S	+	1	0	MYOZ2	120298628	0.983000	0.35010	0.761000	0.31378	0.873000	0.50193	2.962000	0.49176	0.974000	0.38366	-0.331000	0.08364	AGT	.	.		0.398	MYOZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256526.2			G	120079180	A	G	120079180	3	3	43	1	0	0	0	0	1	0	0	0	10105	188	7	2	260	2	MYOZ2	4	120079180	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	6891338	120079180	71075096	106	5188										
PHF17	79960	hgsc.bcm.edu	37	chr4	129792723	129792723	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aagtgaaggcaaaaccctgcTgaagcagccagacctgtgtg	12	10	0	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:129792723T>C	ENST00000226319.6	+	11	2115	c.1835T>C	c.(1834-1836)cTg>cCg	p.L612P	PHF17_ENST00000452328.2_Missense_Mutation_p.L600P|PHF17_ENST00000512960.1_Missense_Mutation_p.L612P	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						AAAACCCTGCTGAAGCAGCCA	0.483																																					p.L612P		Atlas-SNP	.											.	PHF17	63	.	0			c.T1835C						.						60	65	63					4																	129792723		2203	4300	6503	SO:0001583	missense	79960	exon11			CCCTGCTGAAGCA																												ENST00000226319.6:c.1835T>C	chr4.hg19:g.129792723T>C	ENSP00000226319:p.Leu612Pro	81.0	0.0		73.0	4.0	NM_199320		Missense_Mutation	SNP	ENST00000226319.6	hg19	CCDS34062.1	.	.	.	.	.	.	.	.	.	.	T	2.301	-0.360169	0.05103	.	.	ENSG00000077684	ENST00000226319;ENST00000452328;ENST00000512960;ENST00000535321	T;T;T	0.41065	1.01;1.01;1.01	4.45	-4.95	0.03048	.	2.083190	0.01822	N	0.034131	T	0.21227	0.0511	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.08680	-1.0710	9	.	.	.	.	4.7514	0.13063	0.2325:0.3486:0.0:0.4189	.	600;612	Q6IE81-2;Q6IE81	.;JADE1_HUMAN	P	612;600;612;612	ENSP00000226319:L612P;ENSP00000388015:L600P;ENSP00000425730:L612P	.	L	+	2	0	PHF17	130012173	0.000000	0.05858	0.000000	0.03702	0.081000	0.17604	0.133000	0.15912	-0.987000	0.03494	-0.250000	0.11733	CTG	.	.		0.483	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1			C	129792723	T	C	129792723	3	2	43	1	0	0	0	0	1	0	0	0	11837	1580	55	2	1900	2	PHF17	4	129792723	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	9713543	129792723	61361553	107	5189										
INPP4B	8821	hgsc.bcm.edu	37	chr4	143067030	143067030	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atggcatctgttaatgaaggTtccttttctccatcattgtt	7	8	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:143067030T>C	ENST00000513000.1	-	19	2116	c.1683A>G	c.(1681-1683)gaA>gaG	p.E561E	INPP4B_ENST00000509777.1_Silent_p.E561E|INPP4B_ENST00000308502.4_Silent_p.E561E|INPP4B_ENST00000262992.4_Silent_p.E561E|INPP4B_ENST00000508116.1_Silent_p.E561E	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	561					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					TTAATGAAGGTTCCTTTTCTC	0.408																																					p.E561E		Atlas-SNP	.											.	INPP4B	132	.	0			c.A1683G						.						190	164	173					4																	143067030		2203	4300	6503	SO:0001819	synonymous_variant	8821	exon19			TGAAGGTTCCTTT	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.1683A>G	chr4.hg19:g.143067030T>C		107.0	0.0		91.0	4.0	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	hg19	CCDS3757.1																																																																																			.	.		0.408	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		C	143067030	T	C	143067030	2	2	43	1	0	0	0	0	0	0	0	1	7762	1722	60	2		2	INPP4B	4	143067030	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	13274307	143067030	48087246	108	5190										
PRMT10	90826	hgsc.bcm.edu	37	chr4	148559746	148559746	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atgctgagtacaagttcctcTcccatttcaacctggatggg	9	11	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:148559746T>C	ENST00000322396.6	-	12	2717	c.2475A>G	c.(2473-2475)ggA>ggG	p.G825G	TMEM184C_ENST00000508208.1_Intron|PRMT10_ENST00000541232.1_Silent_p.G712G	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		825	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)	p.G825G(2)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						CAAGTTCCTCTCCCATTTCAA	0.408																																					p.G825G		Atlas-SNP	.											PRMT10,NS,carcinoma,0,1	PRMT10	68	.	2	Substitution - coding silent(2)	lung(2)	c.A2475G						.						205	183	190					4																	148559746		2203	4300	6503	SO:0001819	synonymous_variant	90826	exon12			TTCCTCTCCCATT																												ENST00000322396.6:c.2475A>G	chr4.hg19:g.148559746T>C		129.0	0.0		100.0	4.0	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Silent	SNP	ENST00000322396.6	hg19	CCDS3771.1																																																																																			.	.		0.408	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			C	148559746	T	C	148559746	2	2	43	1	0	0	0	0	0	0	0	1	12548	1538	54	2		2	PRMT10	4	148559746	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5492716	148559746	42594530	109	5191										
RXFP1	59350	hgsc.bcm.edu	37	chr4	159526291	159526291	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttatcatgatcttcagaagcTgtaagaaaatacttaattcc	5	7	3	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:159526291T>C	ENST00000307765.5	+	5	715	c.464T>C	c.(463-465)cTg>cCg	p.L155P	RXFP1_ENST00000343542.5_Splice_Site_p.L155P|RXFP1_ENST00000423548.1_Splice_Site_p.L155P|RXFP1_ENST00000460056.2_Splice_Site_p.L74P|RXFP1_ENST00000448688.2_Splice_Site_p.L74P|RXFP1_ENST00000470033.1_Splice_Site_p.L122P	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	155					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		CTTCAGAAGCTGTAAGAAAAT	0.338																																					p.L182P		Atlas-SNP	.											.	RXFP1	98	.	0			c.T545C						.						38	37	38					4																	159526291		1824	4065	5889	SO:0001630	splice_region_variant	59350	exon5			AGAAGCTGTAAGA	AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"GPCR / Class A : Relaxin family peptide receptors"	19718	protein-coding gene	gene with protein product		606654	"leucine-rich repeat-containing G protein-coupled receptor 7"	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.464+1T>C	chr4.hg19:g.159526291T>C		133.0	0.0		89.0	5.0	NM_001253727	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Missense_Mutation	SNP	ENST00000307765.5	hg19	CCDS43276.1	.	.	.	.	.	.	.	.	.	.	T	17.15	3.314905	0.60524	.	.	ENSG00000171509	ENST00000460056;ENST00000307765;ENST00000423548;ENST00000448688;ENST00000343542;ENST00000470033	D;D;D;D;D;D	0.81908	-1.55;-1.55;-1.55;-1.55;-1.55;-1.55	5.75	5.75	0.90469	.	0.071887	0.56097	D	0.000022	D	0.93609	0.7959	H	0.99555	4.625	0.80722	D	1	P;P;P;P;P;P	0.46912	0.886;0.738;0.886;0.862;0.862;0.886	P;P;P;P;P;P	0.51806	0.68;0.464;0.68;0.551;0.551;0.68	D	0.95862	0.8884	10	0.87932	D	0	.	15.0485	0.71846	0.0:0.0:0.0:1.0	.	166;182;74;155;122;155	B3KV27;B4DGP2;B4DHD1;Q9HBX9-4;Q9HBX9-2;Q9HBX9	.;.;.;.;.;RXFP1_HUMAN	P	74;155;155;74;155;122	ENSP00000423306:L74P;ENSP00000303248:L155P;ENSP00000405841:L155P;ENSP00000414885:L74P;ENSP00000345889:L155P;ENSP00000420712:L122P	ENSP00000303248:L155P	L	+	2	0	RXFP1	159745741	1.000000	0.71417	0.990000	0.47175	0.433000	0.31745	5.735000	0.68587	2.196000	0.70406	0.455000	0.32223	CTG	.	.		0.338	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634	Missense_Mutation	C	159526291	T	C	159526291	5	2	43	1	0	0	0	0	0	0	1	0	13774	1594	55	2	482	2	RXFP1	4	159526291	Splice_Site	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	10966545	159526291	31627985	110	5192										
CPE	1363	hgsc.bcm.edu	37	chr4	166418679	166418679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttaggttgattttgaactgGagtcattttctgaaaggaaa	10	3	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr4:166418679G>A	ENST00000402744.4	+	9	1628	c.1348G>A	c.(1348-1350)Gag>Aag	p.E450K		NM_001873.2	NP_001864.1	P16870	CBPE_HUMAN	carboxypeptidase E	450					cardiac left ventricle morphogenesis (GO:0003214)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|insulin processing (GO:0030070)|metabolic process (GO:0008152)|neuropeptide signaling pathway (GO:0007218)|protein localization to membrane (GO:0072657)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)	carboxypeptidase activity (GO:0004180)|cell adhesion molecule binding (GO:0050839)|metallocarboxypeptidase activity (GO:0004181)|neurexin family protein binding (GO:0042043)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	26	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TTTTGAACTGGAGTCATTTTC	0.289																																					p.E450K		Atlas-SNP	.											CPE,NS,carcinoma,0,1	CPE	65	.	0			c.G1348A						.						86	91	89					4																	166418679		2202	4291	6493	SO:0001583	missense	1363	exon9			GAACTGGAGTCAT	X51405	CCDS3810.1	4q32.3	2012-02-10			ENSG00000109472	ENSG00000109472	3.4.17.10		2303	protein-coding gene	gene with protein product	"carboxypeptidase H", "enkephalin convertase", "insulin granule-associated carboxypeptidase", "cobalt-stimulated chromaffin granule carboxypeptidase"	114855				2334405	Standard	NM_001873		Approved		uc003irg.4	P16870	OTTHUMG00000150252	ENST00000402744.4:c.1348G>A	chr4.hg19:g.166418679G>A	ENSP00000386104:p.Glu450Lys	47.0	0.0		28.0	2.0	NM_001873	A8K4N1|B3KR42|B4DFN4|D3DP33|Q9UIU9	Missense_Mutation	SNP	ENST00000402744.4	hg19	CCDS3810.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.758016	0.49468	.	.	ENSG00000109472	ENST00000402744	T	0.44083	0.93	6.08	6.08	0.98989	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.120251	0.56097	D	0.000027	T	0.41789	0.1174	N	0.04148	-0.265	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.28808	-1.0032	10	0.07030	T	0.85	-12.1631	20.6647	0.99678	0.0:0.0:1.0:0.0	.	450	P16870	CBPE_HUMAN	K	450	ENSP00000386104:E450K	ENSP00000386104:E450K	E	+	1	0	CPE	166638129	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.698000	0.91311	2.890000	0.99128	0.655000	0.94253	GAG	.	.		0.289	CPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317094.2	NM_001873		A	166418679	G	A	166418679	3	1	43	1	0	0	0	0	1	0	0	0	3801	1175	41	3	1382	3	CPE	4	166418679	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	6892388	166418679	24735597	111	5193										
FAM105A	54491	hgsc.bcm.edu	37	chr5	14609107	14609107	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcacctgaattctgtaggcgAcacatgtggactagagcagg	12	9	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:14609107A>G	ENST00000274217.3	+	7	998	c.878A>G	c.(877-879)gAc>gGc	p.D293G		NM_019018.2	NP_061891.1	Q9NUU6	F105A_HUMAN	family with sequence similarity 105, member A	293	OTU.									large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Lung NSC(4;0.00592)					TCTGTAGGCGACACATGTGGA	0.453																																					p.D293G		Atlas-SNP	.											FAM105A,caecum,carcinoma,0,1	FAM105A	32	.	0			c.A878G						.						157	161	160					5																	14609107		2203	4300	6503	SO:0001583	missense	54491	exon7			TAGGCGACACATG		CCDS3884.1	5p15.2	2014-02-24			ENSG00000145569	ENSG00000145569		"OTU domain containing"	25629	protein-coding gene	gene with protein product						12477932	Standard	NM_019018		Approved	FLJ11127, NET20	uc003jfj.3	Q9NUU6	OTTHUMG00000131056	ENST00000274217.3:c.878A>G	chr5.hg19:g.14609107A>G	ENSP00000274217:p.Asp293Gly	88.0	0.0		87.0	4.0	NM_019018	Q53H50|Q9H037	Missense_Mutation	SNP	ENST00000274217.3	hg19	CCDS3884.1	.	.	.	.	.	.	.	.	.	.	A	9.861	1.196316	0.22037	.	.	ENSG00000145569	ENST00000274217	T	0.16743	2.32	5.04	5.04	0.67666	.	0.000000	0.64402	D	0.000001	T	0.39462	0.1079	M	0.65975	2.015	0.39940	D	0.974401	D	0.89917	1.0	D	0.87578	0.998	T	0.21348	-1.0248	10	0.35671	T	0.21	-25.1344	14.7769	0.69736	1.0:0.0:0.0:0.0	.	293	Q9NUU6	F105A_HUMAN	G	293	ENSP00000274217:D293G	ENSP00000274217:D293G	D	+	2	0	FAM105A	14662107	1.000000	0.71417	0.958000	0.39756	0.026000	0.11368	5.410000	0.66381	1.885000	0.54596	0.528000	0.53228	GAC	.	.		0.453	FAM105A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253710.1	NM_019018		G	14609107	A	G	14609107	3	3	43	1	0	0	0	0	1	0	0	0	5392	275	10	2	904	2	FAM105A	5	14609107	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10		14609107	166306153	112	5194										
SPEF2	79925	hgsc.bcm.edu	37	chr5	35628606	35628606	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttccagtggctatctacttGgagaagttctacacaagttt	8	8	2	1	rs78964548		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:35628606G>T	ENST00000356031.3	+	2	257	c.103G>T	c.(103-105)Gga>Tga	p.G35*	SPEF2_ENST00000440995.2_Nonsense_Mutation_p.G35*|SPEF2_ENST00000509059.1_Nonsense_Mutation_p.G35*|SPEF2_ENST00000282469.6_Nonsense_Mutation_p.G35*	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	35	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTATCTACTTGGAGAAGTTCT	0.353																																					p.G35X		Atlas-SNP	.											.	SPEF2	324	.	0			c.G103T						.						138	137	137					5																	35628606		2203	4300	6503	SO:0001587	stop_gained	79925	exon2			CTACTTGGAGAAG	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.103G>T	chr5.hg19:g.35628606G>T	ENSP00000348314:p.Gly35*	94.0	0.0		92.0	4.0	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Nonsense_Mutation	SNP	ENST00000356031.3	hg19	CCDS43309.1	.	.	.	.	.	.	.	.	.	.	G	34	5.325836	0.95708	.	.	ENSG00000152582	ENST00000282469;ENST00000356031;ENST00000509059;ENST00000510777;ENST00000440995	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.4177	0.83748	0.0:0.0:1.0:0.0	.	.	.	.	X	35	.	ENSP00000282469:G35X	G	+	1	0	SPEF2	35664363	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.625000	0.67770	2.658000	0.90341	0.655000	0.94253	GGA	.	.		0.353	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		T	35628606	G	T	35628606	4	4	43	1	0	0	0	0	0	1	0	0	15050	1349	47	3	109	3	SPEF2	5	35628606	Nonsense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	21019499	35628606	145286654	113	5195										
SPEF2	79925	hgsc.bcm.edu	37	chr5	35792503	35792503	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttggtgaccctgaaccttggCacaaacaactttcctagtaa	7	11	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:35792503C>T	ENST00000356031.3	+	31	4663	c.4509C>T	c.(4507-4509)ggC>ggT	p.G1503G	SPEF2_ENST00000440995.2_Silent_p.G1498G|SPEF2_ENST00000303129.4_Silent_p.G300G|CTD-2113L7.1_ENST00000510433.1_RNA	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1503					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGAACCTTGGCACAAACAACT	0.343																																					p.G1503G		Atlas-SNP	.											.	SPEF2	324	.	0			c.C4509T						.						125	117	120					5																	35792503		1876	4113	5989	SO:0001819	synonymous_variant	79925	exon31			CCTTGGCACAAAC	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.4509C>T	chr5.hg19:g.35792503C>T		70.0	0.0		89.0	4.0	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Silent	SNP	ENST00000356031.3	hg19	CCDS43309.1																																																																																			.	.		0.343	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		T	35792503	C	T	35792503	2	4	43	1	0	0	0	0	0	0	0	1	15050	697	25	3		3	SPEF2	5	35792503	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	163897	35792503	145122757	114	5196										
C5orf33	133686	hgsc.bcm.edu	37	chr5	36219720	36219720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaactcaccacgatagaactTctgtaaggcttctggaaagg	10	9	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:36219720T>C	ENST00000381937.4	-	5	621	c.622A>G	c.(622-624)Aag>Gag	p.K208E	NADK2_ENST00000282512.3_Missense_Mutation_p.K45E|NADK2_ENST00000506945.1_Missense_Mutation_p.K45E|NADK2_ENST00000514504.1_Missense_Mutation_p.K208E|NADK2-AS1_ENST00000501794.2_RNA|NADK2_ENST00000397338.1_Missense_Mutation_p.K45E	NM_001085411.1	NP_001078880.1	Q4G0N4	NAKD2_HUMAN	NAD kinase 2, mitochondrial	208					NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|NAD+ kinase activity (GO:0003951)|protein homodimerization activity (GO:0042803)	p.K45*(1)|p.K45delK(1)									CGATAGAACTTCTGTAAGGCT	0.353																																					p.K208E		Atlas-SNP	.											NADKD1,NS,carcinoma,0,1	NADKD1	47	.	2	Substitution - Nonsense(1)|Deletion - In frame(1)	ovary(2)	c.A622G						.						114	110	112					5																	36219720		2203	4300	6503	SO:0001583	missense	133686	exon5			AGAACTTCTGTAA	BC062567	CCDS3917.1, CCDS47197.1, CCDS75235.1	5p13.2	2013-04-30	2013-04-30	2013-04-30	ENSG00000152620	ENSG00000152620			26404	protein-coding gene	gene with protein product	"mitochondrial NAD kinase"	615787	"chromosome 5 open reading frame 33", "NAD kinase domain containing 1"	C5orf33, NADKD1		23616928	Standard	NM_001085411		Approved	FLJ30596, MNADK	uc003jkf.4	Q4G0N4	OTTHUMG00000131105	ENST00000381937.4:c.622A>G	chr5.hg19:g.36219720T>C	ENSP00000371362:p.Lys208Glu	32.0	0.0		50.0	2.0	NM_001085411	B5MC93|Q6UTX5|Q96NM0	Missense_Mutation	SNP	ENST00000381937.4	hg19	CCDS47197.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.030185	0.93575	.	.	ENSG00000152620	ENST00000397338;ENST00000282512;ENST00000381937;ENST00000506945;ENST00000514504;ENST00000511088	T;T;T;T;T;T	0.42900	0.98;0.98;0.96;0.98;0.96;0.98	5.77	5.77	0.91146	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	0.133059	0.64402	D	0.000003	T	0.51193	0.1660	M	0.69358	2.11	0.58432	D	0.999996	P;P;P	0.45044	0.849;0.669;0.611	P;B;B	0.47251	0.542;0.304;0.324	T	0.55341	-0.8156	10	0.62326	D	0.03	-14.6788	15.0723	0.72046	0.0:0.0:0.0:1.0	.	45;208;208	B7Z8V7;Q4G0N4-2;Q4G0N4	.;.;NAKD1_HUMAN	E	45;45;208;45;208;45	ENSP00000380499:K45E;ENSP00000282512:K45E;ENSP00000371362:K208E;ENSP00000422250:K45E;ENSP00000421029:K208E;ENSP00000426084:K45E	ENSP00000282512:K45E	K	-	1	0	NADKD1	36255477	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.018000	0.64054	2.187000	0.69744	0.528000	0.53228	AAG	.	.		0.353	NADK2-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367541.1	NM_153013		C	36219720	T	C	36219720	3	2	43	1	0	0	0	0	1	0	0	0	2294	1792	62	2	738	2	C5orf33	5	36219720	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	427217	36219720	144695540	115	5197										
NIPBL	25836	hgsc.bcm.edu	37	chr5	36984922	36984922	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggttagcattgatcttcatcAggcaggaagagtggactctc	12	8	4	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:36984922A>G	ENST00000282516.8	+	10	2139	c.1640A>G	c.(1639-1641)cAg>cGg	p.Q547R	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Missense_Mutation_p.Q547R	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	547					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			GATCTTCATCAGGCAGGAAGA	0.458																																					p.Q547R		Atlas-SNP	.											.	NIPBL	513	.	0			c.A1640G						.						167	174	171					5																	36984922		2203	4300	6503	SO:0001583	missense	25836	exon10			TTCATCAGGCAGG	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.1640A>G	chr5.hg19:g.36984922A>G	ENSP00000282516:p.Gln547Arg	57.0	0.0		100.0	4.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	hg19	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	A	14.70	2.614287	0.46631	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.95272	-3.64;-3.66	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.91331	0.7266	L	0.29908	0.895	0.46954	D	0.999266	P;P	0.42584	0.678;0.784	B;B	0.42555	0.219;0.391	D	0.90855	0.4734	10	0.34782	T	0.22	.	15.9259	0.79615	1.0:0.0:0.0:0.0	.	547;547	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	R	547	ENSP00000282516:Q547R;ENSP00000406266:Q547R	ENSP00000282516:Q547R	Q	+	2	0	NIPBL	37020679	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.593000	0.74100	2.164000	0.68074	0.528000	0.53228	CAG	.	.		0.458	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		G	36984922	A	G	36984922	3	3	43	1	0	0	0	0	1	0	0	0	10437	188	7	2	1674	2	NIPBL	5	36984922	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	765202	36984922	143930338	116	5198										
HCN1	348980	hgsc.bcm.edu	37	chr5	45303811	45303811	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tacccacggctccttctcgtAtgatataatctccaggttga	7	12	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:45303811A>G	ENST00000303230.4	-	6	1565	c.1508T>C	c.(1507-1509)aTa>aCa	p.I503T		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	503					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						TCCTTCTCGTATGATATAATC	0.408																																					p.I503T		Atlas-SNP	.											.	HCN1	298	.	0			c.T1508C						.						113	113	113					5																	45303811		2203	4300	6503	SO:0001583	missense	348980	exon6			TCTCGTATGATAT	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1508T>C	chr5.hg19:g.45303811A>G	ENSP00000307342:p.Ile503Thr	114.0	0.0		131.0	55.0	NM_021072		Missense_Mutation	SNP	ENST00000303230.4	hg19	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.537042	0.85812	.	.	ENSG00000164588	ENST00000303230	D	0.94092	-3.35	5.62	5.62	0.85841	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.64402	D	0.000001	D	0.97636	0.9225	H	0.94698	3.57	0.80722	D	1	D	0.69078	0.997	D	0.77557	0.99	D	0.98779	1.0731	10	0.87932	D	0	.	16.1172	0.81314	1.0:0.0:0.0:0.0	.	503	O60741	HCN1_HUMAN	T	503	ENSP00000307342:I503T	ENSP00000307342:I503T	I	-	2	0	HCN1	45339568	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.287000	0.95975	2.266000	0.75297	0.533000	0.62120	ATA	.	.		0.408	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		G	45303811	A	G	45303811	3	3	43	1	0	0	0	0	1	0	0	0	7005	449	16	2	1176	2	HCN1	5	45303811	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	8318889	45303811	135611449	117	5199										
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56178549	56178549	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aaagatgatgtgaatcataaTcaaaagtgcaaagagaagat	9	3	2	5			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:56178549T>C	ENST00000399503.3	+	14	3522	c.3522T>C	c.(3520-3522)aaT>aaC	p.N1174N		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1174					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TGAATCATAATCAAAAGTGCA	0.418																																					p.N1174N		Atlas-SNP	.											.	MAP3K1	355	.	0			c.T3522C						.						77	76	76					5																	56178549		2037	4221	6258	SO:0001819	synonymous_variant	4214	exon14			TCATAATCAAAAG	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.3522T>C	chr5.hg19:g.56178549T>C		98.0	0.0		94.0	4.0	NM_005921		Silent	SNP	ENST00000399503.3	hg19	CCDS43318.1																																																																																			.	.		0.418	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		C	56178549	T	C	56178549	2	2	43	1	0	0	0	0	0	0	0	1	9252	1432	50	2		2	MAP3K1	5	56178549	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	10874738	56178549	124736711	118	5200										
KIF2A	3796	hgsc.bcm.edu	37	chr5	61669513	61669513	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atacctcttatgtatttataGggtcaaagaattgactgtag	8	5	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:61669513G>A	ENST00000401507.3	+	17	1957		c.e17-1		KIF2A_ENST00000509663.2_Intron|KIF2A_ENST00000407818.3_Splice_Site|KIF2A_ENST00000506857.1_Splice_Site|KIF2A_ENST00000381103.2_Splice_Site	NM_001243953.1|NM_004520.4	NP_001230882.1|NP_004511.2	O00139	KIF2A_HUMAN	kinesin heavy chain member 2A						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|nervous system development (GO:0007399)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	15		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		TGTATTTATAGGGTCAAAGAA	0.388																																					.		Atlas-SNP	.											.	KIF2A	69	.	0			c.1761-1G>A						.						94	87	89					5																	61669513		2203	4300	6503	SO:0001630	splice_region_variant	3796	exon18			TTTATAGGGTCAA	BC031828	CCDS3980.2, CCDS47216.1, CCDS58949.1	5q12-q13	2008-02-05	2006-09-26	2006-09-26	ENSG00000068796	ENSG00000068796		"Kinesins"	6318	protein-coding gene	gene with protein product		602591	"kinesin heavy chain member 2"	KIF2		9177777	Standard	NM_001098511		Approved	HK2	uc003jsz.4	O00139	OTTHUMG00000097755	ENST00000401507.3:c.1647-1G>A	chr5.hg19:g.61669513G>A		63.0	0.0		85.0	40.0	NM_001098511	A5YM42|A5YM54|B4DY54|D3DW97|E9PB70|Q7Z5I3|Q8N5Q7	Splice_Site	SNP	ENST00000401507.3	hg19	CCDS3980.2	.	.	.	.	.	.	.	.	.	.	G	11.47	1.648587	0.29336	.	.	ENSG00000068796	ENST00000401507;ENST00000381103;ENST00000407818;ENST00000506857;ENST00000512006	.	.	.	6.17	4.41	0.53225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3488	0.60589	0.1269:0.0:0.8731:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIF2A	61705270	1.000000	0.71417	0.980000	0.43619	0.071000	0.16799	9.439000	0.97543	0.941000	0.37499	0.655000	0.94253	.	.	.		0.388	KIF2A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317989.1	NM_004520	Intron	A	61669513	G	A	61669513	5	1	43	1	0	0	0	0	0	0	1	0	8306	1014	35	3	1830	3	KIF2A	5	61669513	Splice_Site	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	5490964	61669513	119245747	119	5201										
AP3B1	8546	hgsc.bcm.edu	37	chr5	77471657	77471657	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttgtaggacaatatactgcAcctccctagaaatcaaaaga	6	9	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:77471657A>G	ENST00000255194.6	-	10	1221	c.1046T>C	c.(1045-1047)gTg>gCg	p.V349A	AP3B1_ENST00000519295.1_Missense_Mutation_p.V300A	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	349					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		AATATACTGCACCTCCCTAGA	0.308									Hermansky-Pudlak syndrome																												p.V349A		Atlas-SNP	.											.	AP3B1	94	.	0			c.T1046C						.						134	142	139					5																	77471657		2202	4296	6498	SO:0001583	missense	8546	exon10	Familial Cancer Database	HPS, HPS1-8	TACTGCACCTCCC	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1046T>C	chr5.hg19:g.77471657A>G	ENSP00000255194:p.Val349Ala	60.0	0.0		85.0	4.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	A	17.85	3.489424	0.64074	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.18810	2.19;2.19	4.82	4.82	0.62117	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.120339	0.56097	D	0.000034	T	0.24736	0.0600	L	0.58925	1.835	0.58432	D	0.999999	P	0.37370	0.592	B	0.37091	0.241	T	0.05115	-1.0905	10	0.62326	D	0.03	-13.7065	14.3773	0.66886	1.0:0.0:0.0:0.0	.	349	O00203	AP3B1_HUMAN	A	349;300;349;253	ENSP00000255194:V349A;ENSP00000430597:V300A	ENSP00000255194:V349A	V	-	2	0	AP3B1	77507413	1.000000	0.71417	0.986000	0.45419	0.988000	0.76386	8.962000	0.93254	1.797000	0.52628	0.383000	0.25322	GTG	.	.		0.308	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			G	77471657	A	G	77471657	3	3	43	1	0	0	0	0	1	0	0	0	744	159	6	2	2310	2	AP3B1	5	77471657	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	15802144	77471657	103443603	120	5202										
RASA1	5921	hgsc.bcm.edu	37	chr5	86682657	86682657	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttcaggagccctacatggaAggtgtcaatccattcatcaa	8	10	4	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:86682657A>G	ENST00000274376.6	+	23	3426	c.2862A>G	c.(2860-2862)gaA>gaG	p.E954E	RASA1_ENST00000456692.2_Silent_p.E777E|RASA1_ENST00000512763.1_Silent_p.E787E|RASA1_ENST00000506290.1_Silent_p.E788E	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	954					blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.E777E(1)|p.E954E(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		CCTACATGGAAGGTGTCAATC	0.333																																					p.E954E		Atlas-SNP	.											RASA1_ENST00000456692,NS,carcinoma,0,2	RASA1	213	.	2	Substitution - coding silent(2)	kidney(2)	c.A2862G						.						153	151	152					5																	86682657		2203	4300	6503	SO:0001819	synonymous_variant	5921	exon23			CATGGAAGGTGTC		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.2862A>G	chr5.hg19:g.86682657A>G		66.0	0.0		62.0	4.0	NM_002890	B2R6W3|Q9UDI1	Silent	SNP	ENST00000274376.6	hg19	CCDS34200.1																																																																																			.	.		0.333	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		G	86682657	A	G	86682657	2	3	43	1	0	0	0	0	0	0	0	1	13075	69	3	2		2	RASA1	5	86682657	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	9211000	86682657	94232603	121	5203										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112874844	112874844	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acaactggatatacaaacaaAgaaatgttaaaatataaaaa	4	4	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:112874844A>G	ENST00000161863.4	+	8	1389	c.1176A>G	c.(1174-1176)aaA>aaG	p.K392K	YTHDC2_ENST00000515883.1_Silent_p.K392K	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	392					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		ATACAAACAAAGAAATGTTAA	0.229																																					p.K392K		Atlas-SNP	.											.	YTHDC2	118	.	0			c.A1176G						.						13	15	14					5																	112874844		2033	4170	6203	SO:0001819	synonymous_variant	64848	exon8			AAACAAAGAAATG	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.1176A>G	chr5.hg19:g.112874844A>G		55.0	0.0		63.0	4.0	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	hg19	CCDS4113.1																																																																																			.	.		0.229	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		G	112874844	A	G	112874844	2	3	43	1	0	0	0	0	0	0	0	1	17512	69	3	2		2	YTHDC2	5	112874844	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	26192187	112874844	68040416	122	5204										
PRRC1	133619	hgsc.bcm.edu	37	chr5	126859184	126859184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaagaaaaatgatggaagagAgtggaatagagacaacacca	12	4	0	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:126859184A>G	ENST00000296666.8	+	2	201	c.13A>G	c.(13-15)Agt>Ggt	p.S5G	PRRC1_ENST00000442138.2_Missense_Mutation_p.S5G|PRRC1_ENST00000512635.2_Missense_Mutation_p.S5G	NM_130809.3	NP_570721.1	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	5						Golgi apparatus (GO:0005794)				endometrium(1)|large_intestine(1)|lung(4)	6		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)		GATGGAAGAGAGTGGAATAGA	0.378																																					p.S5G		Atlas-SNP	.											.	PRRC1	22	.	0			c.A13G						.						114	98	103					5																	126859184		2203	4300	6503	SO:0001583	missense	133619	exon2			GAAGAGAGTGGAA	AJ515429	CCDS4143.1, CCDS68943.1	5q23.2	2008-02-05			ENSG00000164244	ENSG00000164244			28164	protein-coding gene	gene with protein product						15541471	Standard	NM_130809		Approved	FLJ32875	uc003kuk.3	Q96M27	OTTHUMG00000128982	ENST00000296666.8:c.13A>G	chr5.hg19:g.126859184A>G	ENSP00000296666:p.Ser5Gly	67.0	0.0		67.0	4.0	NM_130809	Q69YM8|Q7L2U7|Q86Y42|Q8IVJ4|Q8IVL4|Q8NEZ7|Q96AJ3	Missense_Mutation	SNP	ENST00000296666.8	hg19	CCDS4143.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.577166	0.86645	.	.	ENSG00000164244	ENST00000296666;ENST00000442138;ENST00000330542;ENST00000414018;ENST00000512635;ENST00000512535	.	.	.	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.65575	0.2704	L	0.34521	1.04	0.54753	D	0.999981	D;D	0.71674	0.997;0.998	D;D	0.80764	0.97;0.994	T	0.68953	-0.5273	9	0.87932	D	0	-21.3415	12.9591	0.58447	1.0:0.0:0.0:0.0	.	5;5	Q96M27;Q96M27-5	PRRC1_HUMAN;.	G	5	.	ENSP00000296666:S5G	S	+	1	0	PRRC1	126887083	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.511000	0.81718	2.180000	0.69256	0.528000	0.53228	AGT	.	.		0.378	PRRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250971.3	NM_130809		G	126859184	A	G	126859184	3	3	43	1	0	0	0	0	1	0	0	0	12616	304	11	2	15	2	PRRC1	5	126859184	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	13984340	126859184	54056076	123	5205										
FAM13B	51306	hgsc.bcm.edu	37	chr5	137354156	137354156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctgccgaagccactccactgTctcagcatttccattgactt	6	15	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:137354156T>C	ENST00000033079.3	-	4	656	c.205A>G	c.(205-207)Aca>Gca	p.T69A	FAM13B_ENST00000425075.2_5'UTR|FAM13B_ENST00000420893.2_Missense_Mutation_p.T69A	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	69	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						CACTCCACTGTCTCAGCATTT	0.448																																					p.T69A		Atlas-SNP	.											.	FAM13B	46	.	0			c.A205G						.						143	132	136					5																	137354156		2203	4300	6503	SO:0001583	missense	51306	exon4			CCACTGTCTCAGC	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.205A>G	chr5.hg19:g.137354156T>C	ENSP00000033079:p.Thr69Ala	95.0	0.0		97.0	4.0	NM_001101800	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	hg19	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.296644	0.60086	.	.	ENSG00000031003	ENST00000033079;ENST00000420893;ENST00000514310;ENST00000502471;ENST00000509596	T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22	5.91	4.74	0.60224	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.120607	0.64402	D	0.000020	T	0.22003	0.0530	N	0.16708	0.43	0.34644	D	0.720919	B;D	0.63046	0.264;0.992	B;D	0.67231	0.124;0.95	T	0.24190	-1.0167	10	0.18710	T	0.47	-10.5397	12.5456	0.56197	0.1248:0.0:0.0:0.8752	.	69;69	Q9NYF5-2;Q9NYF5	.;FA13B_HUMAN	A	69	ENSP00000033079:T69A;ENSP00000388521:T69A;ENSP00000425326:T69A;ENSP00000424785:T69A;ENSP00000422311:T69A	ENSP00000033079:T69A	T	-	1	0	FAM13B	137382055	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.238000	0.72350	1.045000	0.40225	0.533000	0.62120	ACA	.	.		0.448	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			C	137354156	T	C	137354156	3	2	43	1	0	0	0	0	1	0	0	0	5458	1667	58	2	2692	2	FAM13B	5	137354156	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	10494972	137354156	43561104	124	5206										
CDC23	8697	hgsc.bcm.edu	37	chr5	137537070	137537070	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcaagttctcgagcttggtgTtttttgctgagctccactct	9	10	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:137537070T>C	ENST00000394886.2	-	5	513	c.483A>G	c.(481-483)aaA>aaG	p.K161K		NM_004661.3	NP_004652.2	Q9UJX2	CDC23_HUMAN	cell division cycle 23	161					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of exit from mitosis (GO:0007096)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(6)|prostate(2)|skin(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GAGCTTGGTGTTTTTTGCTGA	0.403																																					p.K161K		Atlas-SNP	.											.	CDC23	46	.	0			c.A483G						.						118	118	118					5																	137537070		2203	4300	6503	SO:0001819	synonymous_variant	8697	exon5			TTGGTGTTTTTTG	AF053977	CCDS4200.2	5q31	2013-01-17	2013-01-17		ENSG00000094880	ENSG00000094880		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1724	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 8"	603462	"CDC23 (cell division cycle 23, yeast, homolog)", "cell division cycle 23 homolog (S. cerevisiae)"			9790767	Standard	NM_004661		Approved	APC8, ANAPC8, CUT23	uc003lcl.3	Q9UJX2	OTTHUMG00000129198	ENST00000394886.2:c.483A>G	chr5.hg19:g.137537070T>C		75.0	0.0		72.0	4.0	NM_004661	A8K6E5|B4E3A2|B7WP05|D3DQB7|O75433|Q53FN2|Q9BS73	Silent	SNP	ENST00000394886.2	hg19	CCDS4200.2																																																																																			.	.		0.403	CDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251275.2			C	137537070	T	C	137537070	2	2	43	1	0	0	0	0	0	0	0	1	3063	1722	60	2		2	CDC23	5	137537070	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	182914	137537070	43378190	125	5207										
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140724262	140724262	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctctgatggtggcgaccctgTccactctggcaacttgcaca	10	14	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:140724262T>C	ENST00000253812.6	+	1	662	c.662T>C	c.(661-663)gTc>gCc	p.V221A	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	221	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCGACCCTGTCCACTCTGGC	0.537																																					p.V221A		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.T662C						.						48	50	49					5																	140724262		2195	4296	6491	SO:0001583	missense	56112	exon1			ACCCTGTCCACTC	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.662T>C	chr5.hg19:g.140724262T>C	ENSP00000253812:p.Val221Ala	74.0	0.0		95.0	4.0	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	hg19	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	0.011	-1.697041	0.00725	.	.	ENSG00000254245	ENST00000253812	T	0.00958	5.5	5.65	3.2	0.36748	Cadherin (3);Cadherin-like (1);	0.663319	0.11337	N	0.574477	T	0.00724	0.0024	N	0.13198	0.31	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.15052	0.012;0.003	T	0.43845	-0.9366	10	0.06757	T	0.87	.	9.5601	0.39364	0.0:0.2082:0.0:0.7918	.	221;221	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	A	221	ENSP00000253812:V221A	ENSP00000253812:V221A	V	+	2	0	PCDHGA3	140704446	0.000000	0.05858	0.008000	0.14137	0.781000	0.44180	0.056000	0.14256	0.478000	0.27488	0.533000	0.62120	GTC	.	.		0.537	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		C	140724262	T	C	140724262	3	2	43	1	0	0	0	0	1	0	0	0	11564	1667	58	2	664	2	PCDHGA3	5	140724262	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3187192	140724262	40190998	126	5208										
PCDHGA11	56105	hgsc.bcm.edu	37	chr5	140803211	140803211	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tatcattttaggcaaatgtgAcccgacaagtaatcaggtga	9	7	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:140803211A>G	ENST00000398587.2	+	1	2450	c.2417A>G	c.(2416-2418)gAc>gGc	p.D806G	PCDHGB6_ENST00000520790.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB8P_ENST00000502926.1_RNA|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	806					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCAAATGTGACCCGACAAGT	0.443																																					p.D806G		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.A2417G						.						45	50	48					5																	140803211		2190	4299	6489	SO:0001583	missense	56105	exon1			AATGTGACCCGAC	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"Cadherins / Protocadherins : Clustered"	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.2417A>G	chr5.hg19:g.140803211A>G	ENSP00000381589:p.Asp806Gly	98.0	0.0		84.0	5.0	NM_032091	B7ZVY8|Q9Y5D8|Q9Y5D9	Missense_Mutation	SNP	ENST00000398587.2	hg19	CCDS47294.1	.	.	.	.	.	.	.	.	.	.	a	16.92	3.254503	0.59212	.	.	ENSG00000253873	ENST00000398587	T	0.46451	0.87	5.42	4.26	0.50523	.	.	.	.	.	T	0.27489	0.0675	N	0.17800	0.525	0.80722	D	1	B;B	0.14012	0.001;0.009	B;B	0.17979	0.001;0.02	T	0.04509	-1.0946	9	0.29301	T	0.29	.	10.4744	0.44657	0.9218:0.0:0.0782:0.0	.	806;806	Q9Y5H2;Q9Y5H2-2	PCDGB_HUMAN;.	G	806	ENSP00000381589:D806G	ENSP00000381589:D806G	D	+	2	0	PCDHGA11	140783395	0.954000	0.32549	0.005000	0.12908	0.962000	0.63368	2.095000	0.41729	0.999000	0.39023	0.533000	0.62120	GAC	.	.		0.443	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914		G	140803211	A	G	140803211	3	3	43	1	0	0	0	0	1	0	0	0	11561	275	10	2	2419	2	PCDHGA11	5	140803211	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	78949	140803211	40112049	127	5209										
FCHSD1	89848	hgsc.bcm.edu	37	chr5	141024179	141024179	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gggattgtcactgtcttggcTgctctctgggagggagaggt	17	7	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:141024179T>C	ENST00000435817.2	-	16	1653	c.1603A>G	c.(1603-1605)Agc>Ggc	p.S535G	FCHSD1_ENST00000523856.1_5'UTR|FCHSD1_ENST00000522783.1_Missense_Mutation_p.S461G|FCHSD1_ENST00000522126.1_3'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	535									FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGTCTTGGCTGCTCTCTGGG	0.552																																					p.S535G		Atlas-SNP	.											.	FCHSD1	51	.	0			c.A1603G						.						67	70	69					5																	141024179		1944	4147	6091	SO:0001583	missense	89848	exon16			CTTGGCTGCTCTC	AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.1603A>G	chr5.hg19:g.141024179T>C	ENSP00000399259:p.Ser535Gly	69.0	0.0		82.0	4.0	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	hg19	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	T	0.941	-0.709535	0.03230	.	.	ENSG00000197948	ENST00000435817;ENST00000522783	T;T	0.14391	2.51;2.51	5.57	-6.79	0.01715	.	0.582533	0.16375	N	0.217176	T	0.03305	0.0096	N	0.03608	-0.345	0.26524	N	0.974374	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.27673	-1.0067	10	0.21540	T	0.41	-5.7401	2.9155	0.05751	0.1955:0.2091:0.0961:0.4992	.	215;535	Q86WN1-2;Q86WN1	.;FCSD1_HUMAN	G	535;461	ENSP00000399259:S535G;ENSP00000428677:S461G	ENSP00000399259:S535G	S	-	1	0	FCHSD1	141004363	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.899000	0.01600	-1.504000	0.01810	-1.049000	0.02347	AGC	.	.		0.552	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449		C	141024179	T	C	141024179	3	2	43	1	0	0	0	0	1	0	0	0	5797	1580	55	2	489	2	FCHSD1	5	141024179	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	220968	141024179	39891081	128	5210										
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156721863	156721863	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cgcagctgttcccgggccatTcccaggtgagactgtccttg	12	14	0	1	rs397712438|rs397781034|rs5872508|rs200051515		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:156721863T>C	ENST00000347377.6	+	4	710	c.279T>C	c.(277-279)atT>atC	p.I93I	CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000541131.1_Intron|CYFIP2_ENST00000318218.6_Silent_p.I93I|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000377576.3_Silent_p.I93I|CYFIP2_ENST00000521420.1_Intron	NM_001037332.2	NP_001032409.2			cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCCGGGCCATTCCCAGGTGAG	0.522																																					p.I93I		Atlas-SNP	.											.	CYFIP2	354	.	0			c.T279C						.						114	122	120					5																	156721863		2140	4280	6420	SO:0001819	synonymous_variant	26999	exon4			GGCCATTCCCAGG	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000347377.6:c.279T>C	chr5.hg19:g.156721863T>C		185.0	0.0		199.0	9.0	NM_001037332		Silent	SNP	ENST00000347377.6	hg19																																																																																				.	.		0.522	CYFIP2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001037332		C	156721863	T	C	156721863	2	2	43	1	0	0	0	0	0	0	0	1	4140	1771	62	2		2	CYFIP2	5	156721863	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	15697684	156721863	24193397	129	5211										
WWC1	23286	hgsc.bcm.edu	37	chr5	167871522	167871522	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gctgtgtctgctctgttggaAcagacagcagtggagctgga	15	8	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:167871522A>G	ENST00000265293.4	+	17	2959	c.2457A>G	c.(2455-2457)gaA>gaG	p.E819E	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Silent_p.E819E	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	819	Glu-rich.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		ctctgttggaacagacagcag	0.577																																					p.E819E		Atlas-SNP	.											.	WWC1	98	.	0			c.A2457G						.						50	46	48					5																	167871522		2198	4298	6496	SO:0001819	synonymous_variant	23286	exon17			GTTGGAACAGACA	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2457A>G	chr5.hg19:g.167871522A>G		89.0	0.0		96.0	4.0	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Silent	SNP	ENST00000265293.4	hg19	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	A	7.505	0.653486	0.14580	.	.	ENSG00000113645	ENST00000393895;ENST00000524228	.	.	.	4.44	3.28	0.37604	.	.	.	.	.	T	0.55273	0.1910	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49428	-0.8941	4	.	.	.	.	6.727	0.23363	0.8936:0.0:0.1064:0.0	.	.	.	.	A	781;596	.	.	T	+	1	0	WWC1	167804100	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	1.638000	0.37165	0.852000	0.35287	0.379000	0.24179	ACA	.	.		0.577	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		G	167871522	A	G	167871522	2	3	43	1	0	0	0	0	0	0	0	1	17426	40	2	2		2	WWC1	5	167871522	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	11149659	167871522	13043738	130	5212										
RANBP17	64901	hgsc.bcm.edu	37	chr5	170610408	170610408	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aacaaccttctacacagcgcTcactcgccttctgatggtag	7	14	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr5:170610408T>C	ENST00000523189.1	+	18	2176	c.2012T>C	c.(2011-2013)cTc>cCc	p.L671P	RANBP17_ENST00000521759.1_3'UTR	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	671					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TACACAGCGCTCACTCGCCTT	0.408			T	TRD@	ALL																																p.L671P		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.T2012C						.						89	81	84					5																	170610408		2203	4300	6503	SO:0001583	missense	64901	exon18			CAGCGCTCACTCG	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.2012T>C	chr5.hg19:g.170610408T>C	ENSP00000427975:p.Leu671Pro	88.0	0.0		98.0	4.0	NM_022897	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	hg19	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.958405	0.74016	.	.	ENSG00000204764	ENST00000523189;ENST00000534916	T	0.76316	-1.01	5.35	5.35	0.76521	Armadillo-type fold (1);	0.000000	0.53938	D	0.000055	D	0.89273	0.6668	M	0.88310	2.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	D	0.91226	0.5010	10	0.87932	D	0	-10.0203	13.8571	0.63534	0.0:0.0:0.0:1.0	.	671;671	Q546R4;Q9H2T7	.;RBP17_HUMAN	P	671;101	ENSP00000427975:L671P	ENSP00000427975:L671P	L	+	2	0	RANBP17	170543013	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.761000	0.74945	2.140000	0.66376	0.459000	0.35465	CTC	.	.		0.408	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		C	170610408	T	C	170610408	3	2	43	1	0	0	0	0	1	0	0	0	13042	1551	54	2	2082	2	RANBP17	5	170610408	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2738886	170610408	10304852	131	5213										
TXNDC5	81567	hgsc.bcm.edu	37	chr6	7884705	7884705	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctcccaagtaggagccagagTcttacaatgaccacacctaa	7	13	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:7884705T>C	ENST00000379757.4	-	9	1100	c.1063A>G	c.(1063-1065)Act>Gct	p.T355A	TXNDC5_ENST00000539054.1_Missense_Mutation_p.T283A|TXNDC5_ENST00000473453.1_Missense_Mutation_p.T247A|BLOC1S5-TXNDC5_ENST00000439343.2_3'UTR	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	355	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	protein disulfide isomerase activity (GO:0003756)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(2)	22	Ovarian(93;0.0398)					GGAGCCAGAGTCTTACAATGA	0.493																																					p.T355A	Ovarian(119;1430 1625 3928 26125 34589)	Atlas-SNP	.											.	TXNDC5	33	.	0			c.A1063G						.						77	70	72					6																	7884705		2203	4300	6503	SO:0001583	missense	81567	exon9			CCAGAGTCTTACA	AK025006	CCDS4505.1, CCDS47369.1	6p24.3	2011-10-19	2009-02-23		ENSG00000239264	ENSG00000239264		"Protein disulfide isomerases"	21073	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 15"		"thioredoxin domain containing 5"				Standard	NM_001145549		Approved	MGC3178, FLJ21353, FLJ90810, EndoPDI, Hcc-2, ERp46, PDIA15	uc003mxv.3	Q8NBS9	OTTHUMG00000014216	ENST00000379757.4:c.1063A>G	chr6.hg19:g.7884705T>C	ENSP00000369081:p.Thr355Ala	49.0	0.0		82.0	4.0	NM_030810	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Missense_Mutation	SNP	ENST00000379757.4	hg19	CCDS4505.1	.	.	.	.	.	.	.	.	.	.	T	13.68	2.310369	0.40895	.	.	ENSG00000239264	ENST00000539054;ENST00000379757;ENST00000473453	T;T;T	0.19394	2.15;2.15;2.15	5.75	4.59	0.56863	Thioredoxin domain (1);Thioredoxin, conserved site (1);Thioredoxin-like fold (3);	0.123769	0.64402	D	0.000001	T	0.03220	0.0094	N	0.02708	-0.52	0.29571	N	0.849867	B;B	0.06786	0.0;0.001	B;B	0.16289	0.005;0.015	T	0.34477	-0.9827	10	0.40728	T	0.16	.	11.6927	0.51525	0.0:0.0688:0.0:0.9312	.	283;355	Q86UY0;Q8NBS9	.;TXND5_HUMAN	A	283;355;247	ENSP00000442453:T283A;ENSP00000369081:T355A;ENSP00000420784:T247A	ENSP00000442453:T283A	T	-	1	0	TXNDC5	7829704	1.000000	0.71417	0.997000	0.53966	0.912000	0.54170	6.098000	0.71458	1.007000	0.39238	0.528000	0.53228	ACT	.	.		0.493	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810		C	7884705	T	C	7884705	3	2	43	1	0	0	0	0	1	0	0	0	16814	1667	58	2	243	2	TXNDC5	6	7884705	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10		7884705	163230362	132	5214										
NFKBIL1	4795	hgsc.bcm.edu	37	chr6	31525591	31525591	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaagctccagggtgagctggAggacgagtggcaggaagtca	18	7	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:31525591A>G	ENST00000376148.4	+	3	635	c.521A>G	c.(520-522)gAg>gGg	p.E174G	NFKBIL1_ENST00000376145.4_Intron	NM_005007.3	NP_004998.3	Q9UBC1	IKBL1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1	174					cellular response to lipopolysaccharide (GO:0071222)|cytoplasmic sequestering of transcription factor (GO:0042994)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)	cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7						GGTGAGCTGGAGGACGAGTGG	0.567																																					p.E174G		Atlas-SNP	.											.	NFKBIL1	17	.	0			c.A521G						.						94	72	80					6																	31525591		2203	4300	6503	SO:0001583	missense	4795	exon3			AGCTGGAGGACGA	X77909	CCDS4700.1, CCDS47399.1, CCDS47400.1	6p21.3	2010-02-17			ENSG00000204498	ENSG00000204498			7800	protein-coding gene	gene with protein product		601022		NFKBIL		8081366	Standard	NM_005007		Approved	IKBL	uc003nub.3	Q9UBC1	OTTHUMG00000031038	ENST00000376148.4:c.521A>G	chr6.hg19:g.31525591A>G	ENSP00000365318:p.Glu174Gly	60.0	0.0		94.0	4.0	NM_005007	A6NL91|B4DUW1|Q14625|Q5HYU4|Q5RJ72|Q5ST96|Q5STV4|Q5STV5|Q9UBX4	Missense_Mutation	SNP	ENST00000376148.4	hg19	CCDS4700.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.857136	0.71834	.	.	ENSG00000204498	ENST00000376146;ENST00000542852;ENST00000376148	T;T	0.35789	1.7;1.29	5.54	5.54	0.83059	.	0.187622	0.44688	D	0.000438	T	0.31009	0.0783	N	0.14661	0.345	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.75484	0.986;0.986	T	0.34477	-0.9827	10	0.62326	D	0.03	-16.2798	11.9958	0.53201	1.0:0.0:0.0:0.0	.	151;174	Q5STV6;Q9UBC1	.;IKBL1_HUMAN	G	151;151;174	ENSP00000365316:E151G;ENSP00000365318:E174G	ENSP00000365316:E151G	E	+	2	0	NFKBIL1	31633570	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.935000	0.63498	2.326000	0.78906	0.533000	0.62120	GAG	.	.		0.567	NFKBIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076036.3	NM_005007		G	31525591	A	G	31525591	3	3	43	1	0	0	0	0	1	0	0	0	10390	304	11	2	531	2	NFKBIL1	6	31525591	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	23640886	31525591	139589476	133	5215										
HSPA1L	3305	hgsc.bcm.edu	37	chr6	31778417	31778417	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catggccctctcgccctcatAcacctggatcagcaccccgg	8	19	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:31778417A>G	ENST00000375654.4	-	2	1522	c.1333T>C	c.(1333-1335)Tat>Cat	p.Y445H	HSPA1L_ENST00000417199.3_Missense_Mutation_p.Y445H	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	445					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						TCGCCCTCATACACCTGGATC	0.567																																					p.Y445H		Atlas-SNP	.											.	HSPA1L	185	.	0			c.T1333C						.						140	136	137					6																	31778417		2203	4300	6503	SO:0001583	missense	3305	exon2			CCTCATACACCTG	D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"Heat shock proteins / HSP70"	5234	protein-coding gene	gene with protein product		140559	"heat shock 70kD protein-like 1"			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.1333T>C	chr6.hg19:g.31778417A>G	ENSP00000364805:p.Tyr445His	239.0	0.0		365.0	118.0	NM_005527	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Missense_Mutation	SNP	ENST00000375654.4	hg19	CCDS34413.1	.	.	.	.	.	.	.	.	.	.	A	11.72	1.724276	0.30593	.	.	ENSG00000204390	ENST00000375654;ENST00000417199;ENST00000375653	T;T	0.07216	3.21;3.21	5.14	5.14	0.70334	.	0.000000	0.31734	N	0.007146	T	0.31451	0.0797	H	0.95645	3.7	0.45580	D	0.998523	D	0.65815	0.995	D	0.78314	0.991	T	0.46610	-0.9179	10	0.87932	D	0	-11.4216	12.941	0.58345	1.0:0.0:0.0:0.0	.	445	P34931	HS71L_HUMAN	H	445;445;390	ENSP00000364805:Y445H;ENSP00000387691:Y445H	ENSP00000364804:Y390H	Y	-	1	0	HSPA1L	31886396	1.000000	0.71417	0.114000	0.21550	0.001000	0.01503	9.139000	0.94554	2.156000	0.67533	0.477000	0.44152	TAT	.	.		0.567	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			G	31778417	A	G	31778417	3	3	43	1	0	0	0	0	1	0	0	0	7419	391	14	2	596	2	HSPA1L	6	31778417	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	252826	31778417	139336650	134	5216										
SLC44A4	80736	hgsc.bcm.edu	37	chr6	31833556	31833556	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caaatgccaatgacccagtgTggtaactgcagagggtgtta	12	8	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:31833556T>C	ENST00000229729.6	-	15	1513	c.1493A>G	c.(1492-1494)cAc>cGc	p.H498R	NEU1_ENST00000375631.4_5'Flank|SLC44A4_ENST00000544672.1_Missense_Mutation_p.H422R|SLC44A4_ENST00000375562.4_Missense_Mutation_p.H456R	NM_025257.2	NP_079533.2	Q53GD3	CTL4_HUMAN	solute carrier family 44, member 4	498					acetylcholine biosynthetic process (GO:0008292)|acetylcholine secretion (GO:0061526)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of cell growth (GO:0030307)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.H498R(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(1)|urinary_tract(2)	35					Choline(DB00122)	TGACCCAGTGTGGTAACTGCA	0.577																																					p.H498R		Atlas-SNP	.											SLC44A4,NS,NS,0,1	SLC44A4	67	.	1	Substitution - Missense(1)	NS(1)	c.A1493G						.						107	119	115					6																	31833556		1511	2709	4220	SO:0001583	missense	80736	exon15			CCAGTGTGGTAAC	AF134726	CCDS4724.2, CCDS54989.1, CCDS54990.1	6p21.3	2014-02-17	2005-09-06	2005-09-06	ENSG00000204385	ENSG00000204385		"Solute carriers"	13941	protein-coding gene	gene with protein product		606107	"chromosome 6 open reading frame 29"	C6orf29		10677542, 15715662, 24379411	Standard	NM_025257		Approved	NG22, CTL4, FLJ14491, TPPT	uc010jti.3	Q53GD3	OTTHUMG00000031133	ENST00000229729.6:c.1493A>G	chr6.hg19:g.31833556T>C	ENSP00000229729:p.His498Arg	26.0	0.0		41.0	2.0	NM_025257	A2BED3|B0UXX8|B0UZY8|B4DU94|B4DWM2|E9PEK7|Q5JP84|Q5JQ93|Q658S8|Q6UX89|Q8TEW4|Q96C58|Q96K59|Q9Y332	Missense_Mutation	SNP	ENST00000229729.6	hg19	CCDS4724.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.73|17.73	3.461402|3.461402	0.63513|0.63513	.|.	.|.	ENSG00000204385|ENSG00000204385	ENST00000229729;ENST00000375562;ENST00000544672|ENST00000414427	T;T;T|.	0.26518|.	1.73;1.73;1.73|.	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84790|0.84790	0.5550|0.5550	H|H	0.95645|0.95645	3.7|3.7	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.87578|.	0.998|.	D|D	0.89303|0.89303	0.3627|0.3627	10|5	0.87932|.	D|.	0|.	-14.753|-14.753	14.5868|14.5868	0.68331|0.68331	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	498|.	Q53GD3|.	CTL4_HUMAN|.	R|A	498;456;422|382	ENSP00000229729:H498R;ENSP00000364712:H456R;ENSP00000444109:H422R|.	ENSP00000229729:H498R|.	H|T	-|-	2|1	0|0	SLC44A4|SLC44A4	31941535|31941535	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	7.701000|7.701000	0.84566|0.84566	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	CAC|ACA	.	.		0.577	SLC44A4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076234.3			C	31833556	T	C	31833556	3	2	43	1	0	0	0	0	1	0	0	0	14653	1696	59	2	667	2	SLC44A4	6	31833556	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	55139	31833556	139281511	135	5217										
BRD2	6046	hgsc.bcm.edu	37	chr6	32946061	32946061	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gacaaggggcctagggcaccCcgcccacctcaacctaagaa	10	16	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:32946061C>T	ENST00000374825.4	+	10	3438	c.1737C>T	c.(1735-1737)ccC>ccT	p.P579P	BRD2_ENST00000395289.2_Silent_p.P579P|BRD2_ENST00000443797.2_Silent_p.P459P|BRD2_ENST00000374831.4_Silent_p.P579P|BRD2_ENST00000395287.1_Silent_p.P579P|BRD2_ENST00000449085.2_Silent_p.P532P	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	579					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						CTAGGGCACCCCGCCCACCTC	0.547																																					p.P579P		Atlas-SNP	.											.	BRD2	70	.	0			c.C1737T						.						124	129	127					6																	32946061		1511	2709	4220	SO:0001819	synonymous_variant	6046	exon10			GGCACCCCGCCCA	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"bromodomain-containing 2"			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1737C>T	chr6.hg19:g.32946061C>T		60.0	0.0		98.0	4.0	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	hg19	CCDS4762.1	.	.	.	.	.	.	.	.	.	.	C	7.987	0.752349	0.15778	.	.	ENSG00000204256	ENST00000449025	T	0.24908	1.83	5.24	-4.01	0.04045	.	0.132292	0.35151	N	0.003403	T	0.11793	0.0287	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.10776	-1.0615	7	0.29301	T	0.29	-3.1127	8.1492	0.31130	0.0:0.3299:0.1137:0.5564	.	.	.	.	L	585	ENSP00000409613:P585L	ENSP00000409613:P585L	P	+	2	0	BRD2	33054039	0.000000	0.05858	0.555000	0.28281	0.666000	0.39218	-0.547000	0.06055	-0.713000	0.04981	-0.311000	0.09066	CCC	.	.		0.547	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			T	32946061	C	T	32946061	2	4	43	1	0	0	0	0	0	0	0	1	1504	610	22	3		3	BRD2	6	32946061	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	1112505	32946061	138169006	136	5218										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42227243	42227243	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	taagggggcagctcgtgggtGgggtccaggagcaggtggtc	21	7	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:42227243G>T	ENST00000372922.4	-	9	2665	c.2103C>A	c.(2101-2103)ccC>ccA	p.P701P	TRERF1_ENST00000541110.1_Silent_p.P721P|TRERF1_ENST00000354325.2_Silent_p.P618P|TRERF1_ENST00000372917.4_Silent_p.P618P|TRERF1_ENST00000340840.2_Silent_p.P618P	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	701	Interacts with CREBBP.|Pro-rich.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GCTCGTGGGTGGGGTCCAGGA	0.711																																					p.P701P		Atlas-SNP	.											.	TRERF1	124	.	0			c.C2103A						.						15	20	18					6																	42227243		2188	4282	6470	SO:0001819	synonymous_variant	55809	exon9			GTGGGTGGGGTCC	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.2103C>A	chr6.hg19:g.42227243G>T		61.0	0.0		158.0	60.0	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	hg19	CCDS4867.1																																																																																			.	.		0.711	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		T	42227243	G	T	42227243	2	4	43	1	0	0	0	0	0	0	0	1	16490	1335	47	3		3	TRERF1	6	42227243	Silent	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	9281182	42227243	128887824	137	5219										
KLC4	89953	hgsc.bcm.edu	37	chr6	43039095	43039095	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gacccgtgcccatgtacaggAgtttgggtctgtggatggtg	16	8	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:43039095A>G	ENST00000394056.2	+	10	1733	c.1238A>G	c.(1237-1239)gAg>gGg	p.E413G	KLC4_ENST00000479388.1_Missense_Mutation_p.E413G|KLC4_ENST00000347162.5_Missense_Mutation_p.E413G|KLC4_ENST00000259708.3_Missense_Mutation_p.E431G|RP11-387M24.5_ENST00000606123.1_RNA|KLC4_ENST00000394058.1_Missense_Mutation_p.E413G|KLC4_ENST00000453940.2_Missense_Mutation_p.E336G			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	413						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			CATGTACAGGAGTTTGGGTCT	0.542																																					p.E431G		Atlas-SNP	.											.	KLC4	89	.	0			c.A1292G						.						80	81	81					6																	43039095		2203	4300	6503	SO:0001583	missense	89953	exon9			TACAGGAGTTTGG	AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"Tetratricopeptide (TTC) repeat domain containing"	21624	protein-coding gene	gene with protein product			"kinesin-like 8"	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.1238A>G	chr6.hg19:g.43039095A>G	ENSP00000377620:p.Glu413Gly	79.0	0.0		106.0	5.0	NM_201523	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	hg19	CCDS4883.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.397173	0.62177	.	.	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	T;T;T;T;T;T	0.80653	-1.38;1.19;-1.4;-1.38;-1.38;-1.38	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000020	D	0.85898	0.5804	M	0.65975	2.015	0.80722	D	1	B;D;D	0.89917	0.116;1.0;1.0	B;D;D	0.79108	0.021;0.992;0.982	D	0.87094	0.2174	10	0.56958	D	0.05	-23.791	15.1124	0.72368	1.0:0.0:0.0:0.0	.	336;431;413	B4DME9;Q9NSK0-3;Q9NSK0	.;.;KLC4_HUMAN	G	413;336;431;413;413;413	ENSP00000340221:E413G;ENSP00000395806:E336G;ENSP00000259708:E431G;ENSP00000418031:E413G;ENSP00000377620:E413G;ENSP00000377622:E413G	ENSP00000259708:E431G	E	+	2	0	KLC4	43147073	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.035000	0.64158	2.221000	0.72209	0.528000	0.53228	GAG	.	.		0.542	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		G	43039095	A	G	43039095	3	3	43	1	0	0	0	0	1	0	0	0	8345	304	11	2	1395	2	KLC4	6	43039095	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	811852	43039095	128075972	138	5220										
BACH2	60468	hgsc.bcm.edu	37	chr6	90661469	90661469	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	agcaggagtcctccaggttgTgcatgcgcaggaactcagca	13	11	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:90661469T>C	ENST00000257749.4	-	7	1063	c.356A>G	c.(355-357)cAc>cGc	p.H119R	RP3-512E2.2_ENST00000445838.1_RNA|RP3-512E2.2_ENST00000413986.1_RNA|BACH2_ENST00000537989.1_Missense_Mutation_p.H119R|BACH2_ENST00000343122.3_Missense_Mutation_p.H119R	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	119						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		CTCCAGGTTGTGCATGCGCAG	0.582																																					p.H119R		Atlas-SNP	.											.	BACH2	224	.	0			c.A356G						.						55	48	50					6																	90661469		2203	4300	6503	SO:0001583	missense	60468	exon5			AGGTTGTGCATGC	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.356A>G	chr6.hg19:g.90661469T>C	ENSP00000257749:p.His119Arg	105.0	0.0		95.0	4.0	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Missense_Mutation	SNP	ENST00000257749.4	hg19	CCDS5026.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.372886	0.61624	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122	T;T;T	0.66280	-0.2;-0.2;-0.2	5.79	5.79	0.91817	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.60534	0.2276	L	0.28344	0.845	0.58432	D	0.999995	D	0.71674	0.998	D	0.80764	0.994	T	0.62709	-0.6797	10	0.36615	T	0.2	-23.3607	16.1293	0.81414	0.0:0.0:0.0:1.0	.	119	Q9BYV9	BACH2_HUMAN	R	119	ENSP00000257749:H119R;ENSP00000437473:H119R;ENSP00000345642:H119R	ENSP00000257749:H119R	H	-	2	0	BACH2	90718190	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.212000	0.71576	0.460000	0.39030	CAC	.	.		0.582	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		C	90661469	T	C	90661469	3	2	43	1	0	0	0	0	1	0	0	0	1284	1696	59	2	2181	2	BACH2	6	90661469	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	47622374	90661469	80453598	139	5221										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119324140	119324140	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctcgatctttcaactgcaaaAgttgagacattgctgacttc	7	10	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:119324140A>G	ENST00000338891.7	-	9	2455	c.2012T>C	c.(2011-2013)cTt>cCt	p.L671P	FAM184A_ENST00000352896.5_Missense_Mutation_p.L551P|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000368475.4_Missense_Mutation_p.L551P|FAM184A_ENST00000521531.1_Missense_Mutation_p.L671P	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	671						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						CAACTGCAAAAGTTGAGACAT	0.348																																					p.L671P		Atlas-SNP	.											FAM184A,NS,carcinoma,0,1	FAM184A	109	.	0			c.T2012C						.						144	139	140					6																	119324140		1859	4104	5963	SO:0001583	missense	79632	exon9			TGCAAAAGTTGAG	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2012T>C	chr6.hg19:g.119324140A>G	ENSP00000342604:p.Leu671Pro	54.0	0.0		40.0	2.0	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	hg19	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.452951	0.84209	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.55721	0.1938	M	0.64997	1.995	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.999	T	0.59611	-0.7422	10	0.66056	D	0.02	-8.6211	16.4461	0.83932	1.0:0.0:0.0:0.0	.	671;551;671	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	P	671;551;551;671	ENSP00000342604:L671P;ENSP00000326608:L551P;ENSP00000357460:L551P;ENSP00000430442:L671P	ENSP00000342604:L671P	L	-	2	0	FAM184A	119365839	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.721000	0.84768	2.285000	0.76669	0.528000	0.53228	CTT	.	.		0.348	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		G	119324140	A	G	119324140	3	3	43	1	0	0	0	0	1	0	0	0	5516	72	3	2	1450	2	FAM184A	6	119324140	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	28662671	119324140	51790927	140	5222										
TBPL1	9519	hgsc.bcm.edu	37	chr6	134305776	134305776	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aatctctaagagctacattaCagattttttcaacaggaagt	6	7	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:134305776C>T	ENST00000237264.4	+	6	723	c.448C>T	c.(448-450)Cag>Tag	p.Q150*	TBPL1_ENST00000367871.1_Nonsense_Mutation_p.Q150*|TBPL1_ENST00000477527.1_Intron	NM_001253676.1|NM_004865.3	NP_001240605.1|NP_004856.1	P62380	TBPL1_HUMAN	TBP-like 1	150					acrosome assembly (GO:0001675)|DNA-templated transcription, initiation (GO:0006352)|dTTP biosynthetic process (GO:0006235)|regulation of transcription, DNA-templated (GO:0006355)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	6	Colorectal(23;0.221)|Breast(56;0.247)			GBM - Glioblastoma multiforme(68;0.00591)|OV - Ovarian serous cystadenocarcinoma(155;0.00848)		AGCTACATTACAGATTTTTTC	0.323																																					p.Q150X		Atlas-SNP	.											.	TBPL1	20	.	0			c.C448T						.						47	47	47					6																	134305776		2203	4298	6501	SO:0001587	stop_gained	9519	exon6			ACATTACAGATTT	AB020881	CCDS5168.1	6q22.1-q22.3	2008-05-23			ENSG00000028839	ENSG00000028839			11589	protein-coding gene	gene with protein product		605521				10082669, 10220372, 15767669	Standard	NM_001253676		Approved	TLP, STUD, TRF2, TLF	uc010kgg.3	P62380	OTTHUMG00000015609	ENST00000237264.4:c.448C>T	chr6.hg19:g.134305776C>T	ENSP00000237264:p.Gln150*	159.0	0.0		84.0	4.0	NM_004865	A8K8F5|O95753|Q9BWD5|Q9Z2Z0	Nonsense_Mutation	SNP	ENST00000237264.4	hg19	CCDS5168.1	.	.	.	.	.	.	.	.	.	.	C	37	6.448344	0.97577	.	.	ENSG00000028839	ENST00000367871;ENST00000237264	.	.	.	5.83	5.83	0.93111	.	0.049220	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-7.5705	19.1704	0.93575	0.0:1.0:0.0:0.0	.	.	.	.	X	150	.	ENSP00000237264:Q150X	Q	+	1	0	TBPL1	134347469	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.712000	0.68407	2.771000	0.95319	0.650000	0.86243	CAG	.	.		0.323	TBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042294.2			T	134305776	C	T	134305776	4	4	43	1	0	0	0	0	0	1	0	0	15660	479	17	3	466	3	TBPL1	6	134305776	Nonsense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	14981636	134305776	36809291	141	5223										
IFNGR1	3459	hgsc.bcm.edu	37	chr6	137540422	137540422	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggtgcccatctcagccctgcTcacaccctgcatgacaaggg	10	16	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:137540422T>C	ENST00000367739.4	-	1	164	c.43A>G	c.(43-45)Agc>Ggc	p.S15G	IFNGR1_ENST00000478333.1_5'UTR|IFNGR1_ENST00000543628.1_5'Flank|IFNGR1_ENST00000367735.2_5'UTR	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	15					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)			central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	TCAGCCCTGCTCACACCCTGC	0.687																																					p.S15G		Atlas-SNP	.											.	IFNGR1	46	.	0			c.A43G						.						42	42	42					6																	137540422		2201	4300	6501	SO:0001583	missense	3459	exon1			CCCTGCTCACACC		CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"Interferons", "CD molecules"	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.43A>G	chr6.hg19:g.137540422T>C	ENSP00000356713:p.Ser15Gly	104.0	0.0		98.0	5.0	NM_000416	B4DFT7|E1P587|Q53Y96	Missense_Mutation	SNP	ENST00000367739.4	hg19	CCDS5185.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.254332	0.59212	.	.	ENSG00000027697	ENST00000367739;ENST00000418947;ENST00000458076	T;D	0.82344	-0.74;-1.6	4.13	2.95	0.34219	.	1.324970	0.04835	N	0.439442	T	0.81128	0.4758	L	0.57536	1.79	0.25550	N	0.987097	D	0.55605	0.972	P	0.59825	0.864	T	0.64398	-0.6417	10	0.41790	T	0.15	-1.7691	7.8264	0.29318	0.0:0.0:0.2113:0.7887	.	15	P15260	INGR1_HUMAN	G	15	ENSP00000356713:S15G;ENSP00000389249:S15G	ENSP00000356713:S15G	S	-	1	0	IFNGR1	137582115	0.010000	0.17322	0.029000	0.17559	0.184000	0.23303	1.603000	0.36794	0.901000	0.36495	0.533000	0.62120	AGC	.	.		0.687	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1			C	137540422	T	C	137540422	3	2	43	1	0	0	0	0	1	0	0	0	7558	1551	54	2	1454	2	IFNGR1	6	137540422	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3234646	137540422	33574645	142	5224										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157256613	157256613	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttttaggacatgtctcaggAaggctatggaactagatctc	10	7	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr6:157256613A>G	ENST00000350026.5	+	4	1902	c.1901A>G	c.(1900-1902)gAa>gGa	p.E634G	ARID1B_ENST00000346085.5_Missense_Mutation_p.E647G|ARID1B_ENST00000275248.4_Missense_Mutation_p.E576G|ARID1B_ENST00000367148.1_Missense_Mutation_p.E634G	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	634					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		ATGTCTCAGGAAGGCTATGGA	0.368																																					p.E647G		Atlas-SNP	.											.	ARID1B	320	.	0			c.A1940G						.						174	163	167					6																	157256613		2203	4300	6503	SO:0001583	missense	57492	exon5			CTCAGGAAGGCTA	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.1901A>G	chr6.hg19:g.157256613A>G	ENSP00000055163:p.Glu634Gly	99.0	0.0		73.0	4.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284890	0.80803	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000354354;ENST00000535255;ENST00000414678;ENST00000319584	T;T;T;T;T;T	0.22945	4.62;4.64;4.67;4.67;4.33;1.93	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000004	T	0.32645	0.0836	L	0.38175	1.15	0.41782	D	0.989823	D;D;D;D	0.89917	0.99;0.999;1.0;1.0	D;D;D;D	0.80764	0.972;0.986;0.994;0.994	T	0.14420	-1.0473	10	0.72032	D	0.01	.	15.9855	0.80147	1.0:0.0:0.0:0.0	.	4;634;647;576	F5H333;Q8NFD5;Q8NFD5-2;G3XAA0	.;ARI1B_HUMAN;.;.	G	647;634;634;576;55;4;133;56	ENSP00000344546:E647G;ENSP00000055163:E634G;ENSP00000356116:E634G;ENSP00000275248:E576G;ENSP00000412835:E133G;ENSP00000313006:E56G	ENSP00000275248:E576G	E	+	2	0	ARID1B	157298305	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.141000	0.77330	2.179000	0.69175	0.528000	0.53228	GAA	.	.		0.368	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		G	157256613	A	G	157256613	3	3	43	1	0	0	0	0	1	0	0	0	914	246	9	2	1958	2	ARID1B	6	157256613	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	19716191	157256613	13858454	143	5225										
FOXK1	221937	hgsc.bcm.edu	37	chr7	4794874	4794874	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtgtttctccgcaggatgagTcaaagccgccgttctcctac	10	13	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:4794874T>C	ENST00000328914.4	+	4	910	c.910T>C	c.(910-912)Tca>Cca	p.S304P	FOXK1_ENST00000446823.1_Missense_Mutation_p.S141P	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GCAGGATGAGTCAAAGCCGCC	0.632																																					p.S304P		Atlas-SNP	.											.	FOXK1	64	.	0			c.T910C						.						58	49	52					7																	4794874		2203	4300	6503	SO:0001583	missense	221937	exon4			GATGAGTCAAAGC	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.910T>C	chr7.hg19:g.4794874T>C	ENSP00000328720:p.Ser304Pro	42.0	0.0		59.0	4.0	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	hg19	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	T	17.26	3.343591	0.61073	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.95447	-3.71;-3.71	5.35	5.35	0.76521	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (1);	0.000000	0.85682	D	0.000000	D	0.96855	0.8973	M	0.62723	1.935	0.52501	D	0.999952	D;D	0.71674	0.998;0.997	D;D	0.81914	0.995;0.972	D	0.96357	0.9263	10	0.37606	T	0.19	.	14.5447	0.68020	0.0:0.0:0.0:1.0	.	304;141	P85037;P85037-2	FOXK1_HUMAN;.	P	141;68;304;187	ENSP00000394442:S141P;ENSP00000328720:S304P	ENSP00000328720:S304P	S	+	1	0	FOXK1	4761400	1.000000	0.71417	1.000000	0.80357	0.229000	0.25112	4.991000	0.63883	2.026000	0.59711	0.533000	0.62120	TCA	.	.		0.632	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			C	4794874	T	C	4794874	3	2	43	1	0	0	0	0	1	0	0	0	6022	1667	58	2	924	2	FOXK1	7	4794874	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10		4794874	154343789	144	5226										
PAPOLB	56903	hgsc.bcm.edu	37	chr7	4899811	4899811	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgctaatcaatgggcctgtcTtcatagtgctagtagatgaa	10	7	3	2	rs557252177		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:4899811T>C	ENST00000404991.1	-	1	1814	c.1628A>G	c.(1627-1629)aAg>aGg	p.K543R	RADIL_ENST00000536091.1_Intron|RADIL_ENST00000399583.3_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	543					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		TGGGCCTGTCTTCATAGTGCT	0.453																																					p.K544R		Atlas-SNP	.											.	PAPOLB	93	.	0			c.A1631G						.						113	105	107					7																	4899811		1980	4186	6166	SO:0001583	missense	56903	exon1			CCTGTCTTCATAG	AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.1628A>G	chr7.hg19:g.4899811T>C	ENSP00000384700:p.Lys543Arg	69.0	0.0		77.0	4.0	NM_020144	Q75LH1|Q8NE14	Missense_Mutation	SNP	ENST00000404991.1	hg19		.	.	.	.	.	.	.	.	.	.	T	9.985	1.229099	0.22542	.	.	ENSG00000218823	ENST00000404991	.	.	.	3.84	3.84	0.44239	.	.	.	.	.	T	0.26159	0.0638	N	0.12746	0.255	0.31992	N	0.604462	B	0.11235	0.004	B	0.10450	0.005	T	0.19679	-1.0298	8	0.26408	T	0.33	.	5.9879	0.19444	0.0:0.1136:0.0:0.8864	.	544	A4D1Z6	.	R	543	.	ENSP00000384700:K543R	K	-	2	0	PAPOLB	4866337	1.000000	0.71417	0.765000	0.31456	0.985000	0.73830	1.287000	0.33284	1.982000	0.57802	0.482000	0.46254	AAG	.	.		0.453	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144		C	4899811	T	C	4899811	3	2	43	1	0	0	0	0	1	0	0	0	11439	1609	56	2	286	2	PAPOLB	7	4899811	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	104937	4899811	154238852	145	5227										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5355649	5355649	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gggggatcctgcccgtgtctCcgtcgtcaaactccacggtg	13	14	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:5355649C>G	ENST00000430969.1	-	25	7148	c.6800G>C	c.(6799-6801)gGa>gCa	p.G2267A	TNRC18_ENST00000399537.4_Missense_Mutation_p.G2267A	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2267							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GCCCGTGTCTCCGTCGTCAAA	0.602																																					p.G2267A		Atlas-SNP	.											.	TNRC18	311	.	0			c.G6800C						.						56	51	52					7																	5355649		1568	3582	5150	SO:0001583	missense	84629	exon25			GTGTCTCCGTCGT	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.6800G>C	chr7.hg19:g.5355649C>G	ENSP00000395538:p.Gly2267Ala	65.0	0.0		66.0	27.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	c	17.92	3.506922	0.64410	.	.	ENSG00000182095	ENST00000399537;ENST00000430969	T;T	0.58652	0.32;0.32	4.46	4.46	0.54185	.	.	.	.	.	T	0.74665	0.3746	M	0.72353	2.195	0.47341	D	0.999393	D	0.89917	1.0	D	0.87578	0.998	T	0.76460	-0.2951	9	0.45353	T	0.12	.	16.6933	0.85327	0.0:1.0:0.0:0.0	.	2267	O15417	TNC18_HUMAN	A	2267	ENSP00000382452:G2267A;ENSP00000395538:G2267A	ENSP00000382452:G2267A	G	-	2	0	TNRC18	5322175	1.000000	0.71417	0.838000	0.33150	0.286000	0.27126	7.420000	0.80191	2.010000	0.58986	0.511000	0.50034	GGA	.	.		0.602	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	5355649	C	G	5355649	3	3	43	1	0	0	0	0	1	0	0	0	16354	855	30	4	2130	4	TNRC18	7	5355649	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	455838	5355649	153783014	146	5228										
SP8	221833	hgsc.bcm.edu	37	chr7	20824956	20824956	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaggagccgccgccgccgccCccgccgccgccgccgctgcc	14	24	0	0	rs201180283		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:20824956C>G	ENST00000361443.4	-	3	663	c.426G>C	c.(424-426)ggG>ggC	p.G142G	SP8_ENST00000418710.2_Silent_p.G160G	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	142					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						cgccgccgcccccgccgccgc	0.741																																					p.G160G		Atlas-SNP	.											.	SP8	43	.	0			c.G480C						.						2	2	2					7																	20824956		542	1367	1909	SO:0001819	synonymous_variant	221833	exon2			GCCGCCCCCGCCG		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.426G>C	chr7.hg19:g.20824956C>G		2.0	0.0		10.0	6.0	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	hg19	CCDS5372.1																																																																																			.	.		0.741	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			G	20824956	C	G	20824956	2	3	43	1	0	0	0	0	0	0	0	1	14985	610	22	4		4	SP8	7	20824956	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	15469307	20824956	138313707	147	5229										
KLHL7	55975	hgsc.bcm.edu	37	chr7	23145743	23145743	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gttggcgggtttcatgggcgTcatgaataacatgcggaaac	14	7	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:23145743T>C	ENST00000339077.5	+	1	341	c.98T>C	c.(97-99)gTc>gCc	p.V33A	KLHL7_ENST00000539124.1_5'UTR|KLHL7_ENST00000479288.1_3'UTR|KLHL7_ENST00000409689.1_5'Flank|KLHL7-AS1_ENST00000419813.1_lincRNA|KLHL7_ENST00000410047.1_5'Flank|KLHL7_ENST00000322275.5_Missense_Mutation_p.V33A|KLHL7_ENST00000542558.1_5'UTR|KLHL7_ENST00000322231.7_5'UTR|KLHL7_ENST00000545771.1_5'Flank	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	33					protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTCATGGGCGTCATGAATAAC	0.597																																					p.V33A		Atlas-SNP	.											.	KLHL7	102	.	0			c.T98C						.						59	49	52					7																	23145743		2202	4300	6502	SO:0001583	missense	55975	exon1			TGGGCGTCATGAA		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"Kelch-like", "BTB/POZ domain containing"	15646	protein-coding gene	gene with protein product	"retinitis pigmentosa 42"	611119	"kelch-like 7 (Drosophila)"			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.98T>C	chr7.hg19:g.23145743T>C	ENSP00000343273:p.Val33Ala	59.0	0.0		52.0	4.0	NM_001172428	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Missense_Mutation	SNP	ENST00000339077.5	hg19	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.852242	0.71719	.	.	ENSG00000122550	ENST00000538858;ENST00000536369;ENST00000339077;ENST00000322275	T;T	0.70631	-0.5;-0.5	4.87	4.87	0.63330	BTB/POZ fold (2);	0.139712	0.47455	D	0.000232	T	0.49490	0.1560	N	0.08118	0	0.80722	D	1	B;P	0.39847	0.001;0.691	B;B	0.40199	0.002;0.322	T	0.52961	-0.8505	10	0.07030	T	0.85	.	14.916	0.70798	0.0:0.0:0.0:1.0	.	33;33	Q8IXQ5;Q8IXQ5-3	KLHL7_HUMAN;.	A	33	ENSP00000343273:V33A;ENSP00000323270:V33A	ENSP00000323270:V33A	V	+	2	0	KLHL7	23112268	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	5.567000	0.67378	2.163000	0.67991	0.482000	0.46254	GTC	.	.		0.597	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846		C	23145743	T	C	23145743	3	2	43	1	0	0	0	0	1	0	0	0	8403	1667	58	2	100	2	KLHL7	7	23145743	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2320787	23145743	135992920	148	5230										
FAM188B	84182	hgsc.bcm.edu	37	chr7	30821784	30821784	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atatatgacctttcagatgaAgatgcaggatggagaacatc	10	6	1	5			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:30821784A>G	ENST00000265299.6	+	3	452	c.375A>G	c.(373-375)gaA>gaG	p.E125E	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	125										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TTTCAGATGAAGATGCAGGAT	0.373																																					p.E125E		Atlas-SNP	.											.	FAM188B	62	.	0			c.A375G						.						76	66	69					7																	30821784		1883	4119	6002	SO:0001819	synonymous_variant	84182	exon3			AGATGAAGATGCA	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 67"	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.375A>G	chr7.hg19:g.30821784A>G		49.0	0.0		77.0	4.0	NM_032222	Q71AZ7|Q9H6D2	Silent	SNP	ENST00000265299.6	hg19	CCDS43565.1																																																																																			.	.		0.373	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222		G	30821784	A	G	30821784	2	3	43	1	0	0	0	0	0	0	0	1	5520	69	3	2		2	FAM188B	7	30821784	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	7676041	30821784	128316879	149	5231										
AVL9	23080	hgsc.bcm.edu	37	chr7	32609744	32609744	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cctttttcgacaacagaaacAcctcagtgatgccattgtgg	8	11	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:32609744A>G	ENST00000318709.4	+	11	1549	c.1328A>G	c.(1327-1329)cAc>cGc	p.H443R	AVL9_ENST00000404479.1_Intron|AVL9_ENST00000409301.1_Missense_Mutation_p.H443R	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	443					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						CAACAGAAACACCTCAGTGAT	0.438																																					p.H443R		Atlas-SNP	.											.	AVL9	66	.	0			c.A1328G						.						266	256	259					7																	32609744		2203	4300	6503	SO:0001583	missense	23080	exon11			AGAAACACCTCAG	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"KIAA0241"	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1328A>G	chr7.hg19:g.32609744A>G	ENSP00000315568:p.His443Arg	91.0	0.0		123.0	5.0	NM_015060	Q92573	Missense_Mutation	SNP	ENST00000318709.4	hg19	CCDS34613.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.869688	0.91587	.	.	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000446718	T;T;T	0.41400	1.0;1.0;1.0	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.48857	0.1523	N	0.17838	0.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.983;0.998	T	0.41610	-0.9499	10	0.21014	T	0.42	-12.9117	16.1708	0.81812	1.0:0.0:0.0:0.0	.	443;443	Q8NBF6-2;Q8NBF6	.;AVL9_HUMAN	R	443;443;443;374	ENSP00000315568:H443R;ENSP00000387011:H443R;ENSP00000395134:H374R	ENSP00000315568:H443R	H	+	2	0	AVL9	32576269	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.284000	0.95882	2.225000	0.72522	0.533000	0.62120	CAC	.	.		0.438	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		G	32609744	A	G	32609744	3	3	43	1	0	0	0	0	1	0	0	0	1228	159	6	2	1370	2	AVL9	7	32609744	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1787960	32609744	126528919	150	5232										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47873952	47873952	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttaccttgcgtggctcctgTgcgtctggtatccttcccca	9	14	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:47873952T>C	ENST00000289672.2	-	40	6209	c.6159A>G	c.(6157-6159)gcA>gcG	p.A2053A		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2053					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GTGGCTCCTGTGCGTCTGGTA	0.408																																					p.A2053A		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A6159G						.						132	118	123					7																	47873952		2203	4300	6503	SO:0001819	synonymous_variant	168507	exon40			CTCCTGTGCGTCT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.6159A>G	chr7.hg19:g.47873952T>C		77.0	0.0		73.0	4.0	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	hg19	CCDS34633.1																																																																																			.	.		0.408	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		C	47873952	T	C	47873952	2	2	43	1	0	0	0	0	0	0	0	1	11973	1683	59	2		2	PKD1L1	7	47873952	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	15264208	47873952	111264711	151	5233										
LANCL2	55915	hgsc.bcm.edu	37	chr7	55466298	55466298	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atcacaaactcagaagtgacTgtgagtcccaggaatgtgtc	10	9	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:55466298T>C	ENST00000254770.2	+	3	1083	c.505T>C	c.(505-507)Tgt>Cgt	p.C169R	LANCL2_ENST00000486376.1_3'UTR	NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	169					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			CAGAAGTGACTGTGAGTCCCA	0.478																																					p.C169R		Atlas-SNP	.											.	LANCL2	54	.	0			c.T505C						.						57	52	54					7																	55466298		2203	4300	6503	SO:0001583	missense	55915	exon3			AGTGACTGTGAGT	AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434			6509	protein-coding gene	gene with protein product	"testis-specific adriamycin sensitivity protein", "G protein-coupled receptor 69B"	612919	"LanC (bacterial lantibiotic synthetase component C)-like 2"	GPR69B		11762191	Standard	NM_018697		Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.505T>C	chr7.hg19:g.55466298T>C	ENSP00000254770:p.Cys169Arg	88.0	0.0		82.0	4.0	NM_018697	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Missense_Mutation	SNP	ENST00000254770.2	hg19	CCDS5517.1	.	.	.	.	.	.	.	.	.	.	T	3.861	-0.029863	0.07543	.	.	ENSG00000132434	ENST00000254770	T	0.39229	1.09	5.54	-1.04	0.10068	Six-hairpin glycosidase-like (1);	0.534882	0.21667	N	0.070928	T	0.10465	0.0256	N	0.00729	-1.24	0.09310	N	0.999996	B	0.14012	0.009	B	0.15052	0.012	T	0.33777	-0.9855	10	0.19147	T	0.46	.	5.7589	0.18188	0.4958:0.0:0.2349:0.2693	.	169	Q9NS86	LANC2_HUMAN	R	169	ENSP00000254770:C169R	ENSP00000254770:C169R	C	+	1	0	LANCL2	55433792	0.000000	0.05858	0.000000	0.03702	0.329000	0.28539	0.483000	0.22292	0.068000	0.16574	0.459000	0.35465	TGT	.	.		0.478	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697		C	55466298	T	C	55466298	3	2	43	1	0	0	0	0	1	0	0	0	8630	1580	55	2	515	2	LANCL2	7	55466298	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	7592346	55466298	103672365	152	5234										
ZNF117	51351	hgsc.bcm.edu	37	chr7	64439846	64439846	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttttctatatcttcttagggTcactttctggaaagaatctc	6	8	6	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:64439846T>C	ENST00000282869.6	-	4	1387	c.103A>G	c.(103-105)Acc>Gcc	p.T35A		NM_015852.3	NP_056936.2	Q03924	ZN117_HUMAN	zinc finger protein 117	35					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(1)|skin(1)	22		Lung NSC(55;0.0295)|all_lung(88;0.0691)				CTTCTTAGGGTCACTTTCTGG	0.343																																					p.T35A		Atlas-SNP	.											.	ZNF117	56	.	0			c.A103G						.						47	48	48					7																	64439846		2086	4242	6328	SO:0001583	missense	51351	exon4			TTAGGGTCACTTT	M27879	CCDS43593.1	7q11.2	2013-01-08	2006-06-12		ENSG00000152926	ENSG00000152926		"Zinc fingers, C2H2-type"	12897	protein-coding gene	gene with protein product		194624	"zinc finger protein 117 (HPF9)"			1427907	Standard	NM_015852		Approved	HPF9, H-plk	uc003ttr.2	Q03924	OTTHUMG00000156631	ENST00000282869.6:c.103A>G	chr7.hg19:g.64439846T>C	ENSP00000282869:p.Thr35Ala	68.0	0.0		60.0	4.0	NM_015852	Q02313|Q7Z7Q7	Missense_Mutation	SNP	ENST00000282869.6	hg19	CCDS43593.1	.	.	.	.	.	.	.	.	.	.	.	7.157	0.584955	0.13749	.	.	ENSG00000152926	ENST00000398695;ENST00000282869	T	0.08193	3.12	1.59	0.306	0.15806	.	.	.	.	.	T	0.06781	0.0173	L	0.37507	1.11	0.09310	N	1	B	0.16802	0.019	B	0.19391	0.025	T	0.37361	-0.9709	9	0.66056	D	0.02	.	4.1993	0.10458	0.0:0.445:0.0:0.555	.	35	Q03924	ZN117_HUMAN	A	35	ENSP00000282869:T35A	ENSP00000282869:T35A	T	-	1	0	ZNF117	64077281	0.008000	0.16893	0.000000	0.03702	0.010000	0.07245	0.543000	0.23237	-0.263000	0.09378	0.254000	0.18369	ACC	.	.		0.343	ZNF117-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344863.3	NM_024498		C	64439846	T	C	64439846	3	2	43	1	0	0	0	0	1	0	0	0	17732	1667	58	2	1352	2	ZNF117	7	64439846	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	8973548	64439846	94698817	153	5235										
FKBP6	8468	hgsc.bcm.edu	37	chr7	72744311	72744311	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttgagattgagctgcttgacTtcctggactgtgctgagtca	12	8	1	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:72744311T>C	ENST00000252037.4	+	4	493	c.424T>C	c.(424-426)Ttc>Ctc	p.F142L	TRIM50_ENST00000333149.2_5'Flank|FKBP6_ENST00000431982.2_Missense_Mutation_p.F137L|FKBP6_ENST00000413573.2_Missense_Mutation_p.F112L|TRIM50_ENST00000493498.1_5'Flank	NM_003602.3	NP_003593.3	O75344	FKBP6_HUMAN	FK506 binding protein 6, 36kDa	142	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|piRNA metabolic process (GO:0034587)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|synaptonemal complex (GO:0000795)	FK506 binding (GO:0005528)|Hsp90 protein binding (GO:0051879)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	16		Lung NSC(55;0.0908)|all_lung(88;0.198)				GCTGCTTGACTTCCTGGACTG	0.502																																					p.F142L		Atlas-SNP	.											.	FKBP6	35	.	0			c.T424C						.						112	101	105					7																	72744311		2203	4300	6503	SO:0001583	missense	8468	exon4			CTTGACTTCCTGG	AF038847	CCDS43595.1, CCDS47604.1, CCDS64670.1	7q11.23	2009-01-05	2002-08-29		ENSG00000077800	ENSG00000077800			3722	protein-coding gene	gene with protein product	"FK506 binding protein 6 (36kD)", "peptidylprolyl cis-trans isomerase", "rotamase", "immunophilin FKBP36"	604839	"FK506-binding protein 6 (36kD)"			9782077, 19001379	Standard	NM_003602		Approved	PPIase, FKBP36	uc003tya.2	O75344	OTTHUMG00000150520	ENST00000252037.4:c.424T>C	chr7.hg19:g.72744311T>C	ENSP00000252037:p.Phe142Leu	69.0	0.0		117.0	6.0	NM_003602	B4DXT7|G3V0I2|Q7Z4T4|Q9UDS0	Missense_Mutation	SNP	ENST00000252037.4	hg19	CCDS43595.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.713311	0.89112	.	.	ENSG00000077800	ENST00000431982;ENST00000442793;ENST00000413573;ENST00000252037	T;T;T;T	0.54071	1.0;1.0;0.59;1.0	4.93	4.93	0.64822	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (1);	0.049620	0.85682	D	0.000000	T	0.64068	0.2565	L	0.46885	1.475	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.66979	0.948;0.938	T	0.66400	-0.5933	10	0.59425	D	0.04	-18.0584	13.4692	0.61273	0.0:0.0:0.0:1.0	.	137;142	O75344-2;O75344	.;FKBP6_HUMAN	L	137;137;112;142	ENSP00000416277:F137L;ENSP00000402360:F137L;ENSP00000394952:F112L;ENSP00000252037:F142L	ENSP00000252037:F142L	F	+	1	0	FKBP6	72382247	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	7.598000	0.82745	1.877000	0.54381	0.477000	0.44152	TTC	.	.		0.502	FKBP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318723.1	NM_003602		C	72744311	T	C	72744311	3	2	43	1	0	0	0	0	1	0	0	0	5920	1609	56	2	484	2	FKBP6	7	72744311	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	8304465	72744311	86394352	154	5236										
HGF	3082	hgsc.bcm.edu	37	chr7	81358964	81358964	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catgtcatgctcgtgaggatActgagaatcccaacgctgac	10	11	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:81358964A>G	ENST00000222390.5	-	8	1223	c.997T>C	c.(997-999)Tat>Cat	p.Y333H	HGF_ENST00000457544.2_Missense_Mutation_p.Y328H	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	333	Kringle 3. {ECO:0000255|PROSITE- ProRule:PRU00121}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						TCGTGAGGATACTGAGAATCC	0.438																																					p.Y333H		Atlas-SNP	.											.	HGF	171	.	0			c.T997C						.						154	141	145					7																	81358964		2203	4300	6503	SO:0001583	missense	3082	exon8			GAGGATACTGAGA		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.997T>C	chr7.hg19:g.81358964A>G	ENSP00000222390:p.Tyr333His	60.0	0.0		83.0	5.0	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Missense_Mutation	SNP	ENST00000222390.5	hg19	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	A	10.63	1.403435	0.25291	.	.	ENSG00000019991	ENST00000222390;ENST00000457544	T;T	0.62498	0.02;0.02	5.76	4.63	0.57726	Kringle (4);Kringle-like fold (1);	0.170349	0.52532	D	0.000073	T	0.38081	0.1027	N	0.12637	0.245	0.80722	D	1	B;B	0.15930	0.007;0.015	B;B	0.18561	0.013;0.022	T	0.24119	-1.0169	10	0.15952	T	0.53	.	7.0421	0.25025	0.7955:0.0:0.0714:0.1331	.	328;333	P14210-3;P14210	.;HGF_HUMAN	H	333;328	ENSP00000222390:Y333H;ENSP00000391238:Y328H	ENSP00000222390:Y333H	Y	-	1	0	HGF	81196900	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.894000	0.28350	2.182000	0.69389	0.533000	0.62120	TAT	.	.		0.438	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		G	81358964	A	G	81358964	3	3	43	1	0	0	0	0	1	0	0	0	7094	391	14	2	1233	2	HGF	7	81358964	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	8614653	81358964	77779699	155	5237										
TECPR1	25851	hgsc.bcm.edu	37	chr7	97873966	97873966	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	agaattccacttcttgtcttTcgtgtaggtggcgggaaagt	12	7	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:97873966T>C	ENST00000447648.2	-	5	747	c.448A>G	c.(448-450)Aaa>Gaa	p.K150E	TECPR1_ENST00000542604.1_Missense_Mutation_p.K71E|TECPR1_ENST00000379795.3_Missense_Mutation_p.K150E			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	150					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TTCTTGTCTTTCGTGTAGGTG	0.567																																					p.K150E		Atlas-SNP	.											.	TECPR1	77	.	0			c.A448G						.						99	102	101					7																	97873966		1948	4130	6078	SO:0001583	missense	25851	exon5			TGTCTTTCGTGTA		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.448A>G	chr7.hg19:g.97873966T>C	ENSP00000404923:p.Lys150Glu	56.0	0.0		75.0	4.0	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Missense_Mutation	SNP	ENST00000447648.2	hg19	CCDS47648.1	.	.	.	.	.	.	.	.	.	.	T	8.419	0.845965	0.16963	.	.	ENSG00000205356	ENST00000447648;ENST00000379795;ENST00000542604	D;D;T	0.94046	-3.34;-3.34;1.46	5.2	2.8	0.32819	Ferlin/Peroxisome membrane (1);	0.088931	0.85682	D	0.000000	D	0.89663	0.6780	L	0.61036	1.89	0.26140	N	0.980298	P;B	0.40834	0.73;0.444	B;B	0.42959	0.318;0.403	T	0.79017	-0.1975	10	0.06891	T	0.86	-13.4199	7.1024	0.25344	0.0:0.0787:0.1611:0.7602	.	71;150	F5GX57;Q7Z6L1	.;TCPR1_HUMAN	E	150;150;71	ENSP00000404923:K150E;ENSP00000369121:K150E;ENSP00000441121:K71E	ENSP00000369121:K150E	K	-	1	0	TECPR1	97711902	0.964000	0.33143	0.275000	0.24674	0.674000	0.39518	3.330000	0.52068	0.306000	0.22856	-0.406000	0.06334	AAA	.	.		0.567	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395		C	97873966	T	C	97873966	3	2	43	1	0	0	0	0	1	0	0	0	15758	1792	62	2	3137	2	TECPR1	7	97873966	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	16515002	97873966	61264697	156	5238										
TMEM130	222865	hgsc.bcm.edu	37	chr7	98460878	98460878	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttgccagtaagcaccagcggGgtgtggatccagtggaagcg	16	9	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:98460878G>T	ENST00000416379.2	-	2	235	c.231C>A	c.(229-231)acC>acA	p.T77T	TMEM130_ENST00000345589.4_Intron|TMEM130_ENST00000546258.1_Silent_p.T58T|TMEM130_ENST00000450876.1_5'UTR|TMEM130_ENST00000339375.4_Silent_p.T77T			Q8N3G9	TM130_HUMAN	transmembrane protein 130	77						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	25	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GCACCAGCGGGGTGTGGATCC	0.657																																					p.T77T		Atlas-SNP	.											.	TMEM130	54	.	0			c.C231A						.						60	58	59					7																	98460878		2203	4300	6503	SO:0001819	synonymous_variant	222865	exon2			CAGCGGGGTGTGG		CCDS5658.1, CCDS47649.1, CCDS47650.1	7q22.1	2006-03-09			ENSG00000166448	ENSG00000166448			25429	protein-coding gene	gene with protein product						12975309	Standard	NM_152913		Approved	DKFZp761L1417, FLJ42643	uc003upo.3	Q8N3G9	OTTHUMG00000154419	ENST00000416379.2:c.231C>A	chr7.hg19:g.98460878G>T		74.0	0.0		94.0	39.0	NM_152913	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Silent	SNP	ENST00000416379.2	hg19	CCDS47650.1																																																																																			.	.		0.657	TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913		T	98460878	G	T	98460878	2	4	43	1	0	0	0	0	0	0	0	1	16058	1219	43	3		3	TMEM130	7	98460878	Silent	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	586912	98460878	60677785	157	5239										
C7orf43	55262	hgsc.bcm.edu	37	chr7	99755336	99755336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcaatcgcaggtagccttgaTctctgacctctggtgcctca	10	13	3	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:99755336T>C	ENST00000316937.3	-	3	742	c.557A>G	c.(556-558)gAt>gGt	p.D186G	C7orf43_ENST00000498638.1_5'Flank|C7orf43_ENST00000457641.1_5'UTR|MIR4658_ENST00000584344.1_RNA|C7orf43_ENST00000419841.1_5'UTR|C7orf43_ENST00000394035.2_5'Flank	NM_018275.3	NP_060745.3	Q8WVR3	CG043_HUMAN	chromosome 7 open reading frame 43	186										breast(1)|endometrium(3)|large_intestine(3)|lung(2)|prostate(1)	10	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTAGCCTTGATCTCTGACCTC	0.572											OREG0018198	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D186G		Atlas-SNP	.											.	C7orf43	28	.	0			c.A557G						.						114	118	117					7																	99755336		2203	4300	6503	SO:0001583	missense	55262	exon3			CCTTGATCTCTGA		CCDS5687.1	7q22.1	2011-11-25			ENSG00000146826	ENSG00000146826			25604	protein-coding gene	gene with protein product						12477932	Standard	NM_018275		Approved	FLJ10925	uc003utr.3	Q8WVR3	OTTHUMG00000154862	ENST00000316937.3:c.557A>G	chr7.hg19:g.99755336T>C	ENSP00000324741:p.Asp186Gly	62.0	0.0	1346	95.0	4.0	NM_018275	A4D2A9|D6W5U4|Q9BQJ1|Q9BUB6|Q9NV47	Missense_Mutation	SNP	ENST00000316937.3	hg19	CCDS5687.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.036074	0.75617	.	.	ENSG00000146826	ENST00000316937	T	0.30714	1.52	5.91	5.91	0.95273	.	0.062472	0.64402	D	0.000007	T	0.18425	0.0442	N	0.08118	0	0.80722	D	1	P	0.46512	0.879	B	0.42827	0.399	T	0.04976	-1.0914	10	0.52906	T	0.07	-13.0401	10.3604	0.43989	0.0:0.0:0.1645:0.8355	.	186	Q8WVR3	CG043_HUMAN	G	186	ENSP00000324741:D186G	ENSP00000324741:D186G	D	-	2	0	C7orf43	99593272	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.089000	0.71384	2.263000	0.75096	0.379000	0.24179	GAT	.	.		0.572	C7orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337395.2	NM_018275		C	99755336	T	C	99755336	3	2	43	1	0	0	0	0	1	0	0	0	2395	1435	50	2	1221	2	C7orf43	7	99755336	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1294458	99755336	59383327	158	5240										
MLL5	55904	hgsc.bcm.edu	37	chr7	104717613	104717613	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aaatccgatttgaataccaaCaatttgctcttcaaacctcc	3	12	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:104717613C>T	ENST00000311117.3	+	10	1517	c.972C>T	c.(970-972)aaC>aaT	p.N324N	KMT2E_ENST00000257745.4_Silent_p.N324N|KMT2E_ENST00000334877.4_Silent_p.N324N|KMT2E_ENST00000476671.1_Silent_p.N324N|KMT2E_ENST00000334914.7_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	324					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										TGAATACCAACAATTTGCTCT	0.343																																					p.N324N		Atlas-SNP	.											.	MLL5	173	.	0			c.C972T						.						76	69	71					7																	104717613		2203	4299	6502	SO:0001819	synonymous_variant	55904	exon9			TACCAACAATTTG	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.972C>T	chr7.hg19:g.104717613C>T		65.0	0.0		97.0	4.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Silent	SNP	ENST00000311117.3	hg19	CCDS34723.1																																																																																			.	.		0.343	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104717613	C	T	104717613	2	4	43	1	0	0	0	0	0	0	0	1	9633	477	17	3		3	MLL5	7	104717613	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	4962277	104717613	54421050	159	5241										
TMEM168	64418	hgsc.bcm.edu	37	chr7	112423763	112423763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ataagcttacctgccaggaaActgctcccaaaatcgctgtt	7	12	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:112423763A>G	ENST00000312814.6	-	2	1678	c.1118T>C	c.(1117-1119)gTt>gCt	p.V373A	TMEM168_ENST00000454074.1_Missense_Mutation_p.V373A	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	373						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						CTGCCAGGAAACTGCTCCCAA	0.398																																					p.V373A		Atlas-SNP	.											.	TMEM168	84	.	0			c.T1118C						.						112	112	112					7																	112423763		2203	4300	6503	SO:0001583	missense	64418	exon2			CAGGAAACTGCTC		CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.1118T>C	chr7.hg19:g.112423763A>G	ENSP00000323068:p.Val373Ala	33.0	0.0		75.0	4.0	NM_022484	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Missense_Mutation	SNP	ENST00000312814.6	hg19	CCDS5757.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.105945	0.77096	.	.	ENSG00000146802	ENST00000312814;ENST00000454074;ENST00000418785;ENST00000441474	.	.	.	6.07	6.07	0.98685	.	0.112361	0.64402	D	0.000010	T	0.60143	0.2246	L	0.53249	1.67	0.80722	D	1	P	0.46784	0.884	P	0.44623	0.455	T	0.64563	-0.6378	9	0.72032	D	0.01	-17.6008	16.6406	0.85098	1.0:0.0:0.0:0.0	.	373	Q9H0V1	TM168_HUMAN	A	373;373;13;25	.	ENSP00000323068:V373A	V	-	2	0	TMEM168	112210999	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.306000	0.96204	2.326000	0.78906	0.533000	0.62120	GTT	.	.		0.398	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		G	112423763	A	G	112423763	3	3	43	1	0	0	0	0	1	0	0	0	16098	43	2	2	991	2	TMEM168	7	112423763	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	7706150	112423763	46714900	160	5242										
ING3	54556	hgsc.bcm.edu	37	chr7	120607623	120607623	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tctcaccatacgacaacagaTcatattcctgaaaagaaatt	4	10	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:120607623T>C	ENST00000315870.5	+	7	625	c.477T>C	c.(475-477)gaT>gaC	p.D159D	ING3_ENST00000431467.1_Silent_p.D144D	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3	159					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|positive regulation of apoptotic process (GO:0043065)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	12	all_neural(327;0.117)					CGACAACAGATCATATTCCTG	0.299																																					p.D159D		Atlas-SNP	.											.	ING3	36	.	0			c.T477C						.						73	75	75					7																	120607623		2203	4296	6499	SO:0001819	synonymous_variant	54556	exon7			AACAGATCATATT	AF074968	CCDS5778.1, CCDS35497.1	7q31	2013-01-28			ENSG00000071243	ENSG00000071243		"Zinc fingers, PHD-type"	14587	protein-coding gene	gene with protein product		607493				12080476	Standard	NM_019071		Approved	p47ING3, FLJ20089, Eaf4, MEAF4	uc003vjn.3	Q9NXR8	OTTHUMG00000141270	ENST00000315870.5:c.477T>C	chr7.hg19:g.120607623T>C		54.0	0.0		87.0	4.0	NM_019071	A8K790|O60394|Q567P3|Q6GMT3|Q7Z762|Q969G0|Q96DT4|Q9HC99|Q9P081	Silent	SNP	ENST00000315870.5	hg19	CCDS5778.1																																																																																			.	.		0.299	ING3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280453.2	NM_019071		C	120607623	T	C	120607623	2	2	43	1	0	0	0	0	0	0	0	1	7746	1432	50	2		2	ING3	7	120607623	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	8183860	120607623	38531040	161	5243										
CREB3L2	64764	hgsc.bcm.edu	37	chr7	137612918	137612918	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcattgaagctgtcactggtGgtaatgtgggtgaagggcga	16	5	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:137612918G>A	ENST00000330387.6	-	2	648	c.297C>T	c.(295-297)acC>acT	p.T99T	CREB3L2_ENST00000456390.1_Silent_p.T99T|CREB3L2_ENST00000452463.1_Silent_p.T99T|CREB3L2_ENST00000458726.1_Silent_p.T36T	NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	99					cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)		FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						TGTCACTGGTGGTAATGTGGG	0.582			T	FUS	fibromyxoid sarcoma																																p.T99T		Atlas-SNP	.		Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	.	CREB3L2	62	.	0			c.C297T						.						49	36	41					7																	137612918		2202	4299	6501	SO:0001819	synonymous_variant	64764	exon2			ACTGGTGGTAATG	AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158		"basic leucine zipper proteins"	23720	protein-coding gene	gene with protein product		608834					Standard	NM_194071		Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.297C>T	chr7.hg19:g.137612918G>A		186.0	0.0		360.0	23.0	NM_001253775	Q6P454|Q6ZMR6	Silent	SNP	ENST00000330387.6	hg19	CCDS34760.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.384817	0.42308	.	.	ENSG00000182158	ENST00000420629	T	0.55760	0.5	5.59	-0.0727	0.13738	.	.	.	.	.	T	0.51024	0.1650	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.51364	-0.8715	6	0.87932	D	0	1.1491	2.8513	0.05559	0.282:0.2118:0.4074:0.0987	.	.	.	.	L	33	ENSP00000402889:P33L	ENSP00000402889:P33L	P	-	2	0	CREB3L2	137263458	0.026000	0.19158	0.008000	0.14137	0.738000	0.42128	-0.137000	0.10389	0.037000	0.15575	0.655000	0.94253	CCA	.	.		0.582	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341462.1	NM_194071		A	137612918	G	A	137612918	2	1	43	1	0	0	0	0	0	0	0	1	3859	1335	47	3		3	CREB3L2	7	137612918	Silent	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	17005295	137612918	21525745	162	5244										
AKR1D1	6718	hgsc.bcm.edu	37	chr7	137782670	137782670	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atggttatatcacaagtcaaAtctgtgtgccacttgggagg	11	7	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:137782670A>G	ENST00000242375.3	+	4	479	c.437A>G	c.(436-438)aAt>aGt	p.N146S	AKR1D1_ENST00000468877.2_3'UTR|AKR1D1_ENST00000432161.1_Missense_Mutation_p.N146S|AKR1D1_ENST00000411726.2_Missense_Mutation_p.N146S	NM_005989.3	NP_005980.1	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1	146					androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|C21-steroid hormone metabolic process (GO:0008207)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|steroid binding (GO:0005496)			endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	23					Azelaic Acid(DB00548)|Finasteride(DB01216)	CACAAGTCAAATCTGTGTGCC	0.299																																					p.N146S		Atlas-SNP	.											.	AKR1D1	52	.	0			c.A437G						.						126	128	127					7																	137782670		2203	4299	6502	SO:0001583	missense	6718	exon4			AGTCAAATCTGTG	Z28339	CCDS5846.1, CCDS55169.1, CCDS55170.1	7q32-q33	2012-12-04	2012-12-04		ENSG00000122787	ENSG00000122787	1.3.99.6	"Aldo-keto reductases"	388	protein-coding gene	gene with protein product	"delta 4-3-ketosteroid-5-beta-reductase"	604741	"aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5-beta-reductase)"	SRD5B1		7508385, 10343119	Standard	NM_005989		Approved		uc003vtz.3	P51857	OTTHUMG00000155787	ENST00000242375.3:c.437A>G	chr7.hg19:g.137782670A>G	ENSP00000242375:p.Asn146Ser	29.0	0.0		52.0	4.0	NM_001190907	A1L4P6|A8K060|B4DPN3|B4DPN8	Missense_Mutation	SNP	ENST00000242375.3	hg19	CCDS5846.1	.	.	.	.	.	.	.	.	.	.	A	13.06	2.123910	0.37533	.	.	ENSG00000122787	ENST00000297463;ENST00000432161;ENST00000411726;ENST00000242375;ENST00000438242	T;T;T;T	0.48836	0.8;1.92;0.8;0.8	5.14	3.97	0.46021	NADP-dependent oxidoreductase domain (3);	0.182530	0.50627	D	0.000107	T	0.35008	0.0917	N	0.04636	-0.2	0.32396	N	0.552565	P;P;B	0.46512	0.879;0.581;0.019	P;B;B	0.51657	0.676;0.115;0.041	T	0.49606	-0.8922	10	0.59425	D	0.04	.	9.5377	0.39233	0.8424:0.0:0.0:0.1576	.	146;146;146	B4DPN8;B4DPN3;P51857	.;.;AK1D1_HUMAN	S	24;146;146;146;90	ENSP00000389197:N146S;ENSP00000402374:N146S;ENSP00000242375:N146S;ENSP00000397042:N90S	ENSP00000242375:N146S	N	+	2	0	AKR1D1	137433210	0.973000	0.33851	0.567000	0.28434	0.195000	0.23768	7.901000	0.87382	0.948000	0.37687	-0.333000	0.08304	AAT	.	.		0.299	AKR1D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341637.1	NM_005989		G	137782670	A	G	137782670	3	3	43	1	0	0	0	0	1	0	0	0	473	101	4	2	451	2	AKR1D1	7	137782670	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	169752	137782670	21355993	163	5245										
SSPO	23145	hgsc.bcm.edu	37	chr7	149489269	149489269	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tctggccaggtcacgtgcccAcctgattggccctgcggcag	13	15	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr7:149489269A>G	ENST00000378016.2	+	0	5514							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TCACGTGCCCACCTGATTGGC	0.657																																					p.P1838P		Atlas-SNP	.											.	.	.	.	0			c.A5514G						.						33	34	33					7																	149489269		1995	4154	6149			23145	exon36			GTGCCCACCTGAT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149489269A>G		42.0	0.0		99.0	4.0	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149489269	A	G	149489269	1	3	43	0	1	0	0	0	0	0	0	0	15204	146	6	2		2	SSPO	7	149489269	RNA	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	11706599	149489269	9649394	164	5246										
NEFL	4747	hgsc.bcm.edu	37	chr8	24811079	24811079	+	RNA	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttcagagggggggctcatccTtggcttcctcagccttggca	13	12	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:24811079T>A	ENST00000221169.5	-	0	1994							P07196	NFL_HUMAN	neurofilament, light polypeptide						anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|intermediate filament organization (GO:0045109)|locomotion (GO:0040011)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron apoptotic process (GO:0043524)|neurofilament bundle assembly (GO:0033693)|neuromuscular process controlling balance (GO:0050885)|neuron projection morphogenesis (GO:0048812)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of axonogenesis (GO:0050772)|protein polymerization (GO:0051258)|regulation of axon diameter (GO:0031133)|response to corticosterone (GO:0051412)|response to peptide hormone (GO:0043434)|response to toxic substance (GO:0009636)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|neurofilament (GO:0005883)	identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|protein C-terminus binding (GO:0008022)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		GGGCTCATCCTTGGCTTCCTC	0.567																																					p.K467M		Atlas-SNP	.											.	NEFL	47	.	0			c.A1400T						.						49	51	51					8																	24811079		1966	4155	6121			4747	exon3			TCATCCTTGGCTT		CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"Intermediate filaments type IV"	7739	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 110"	162280	"neurofilament, light polypeptide 68kDa"			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		chr8.hg19:g.24811079T>A		52.0	0.0		30.0	24.0	NM_006158	B9ZVN2|Q16154|Q8IU72	Missense_Mutation	SNP	ENST00000221169.5	hg19																																																																																				.	.		0.567	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158		A	24811079	T	A	24811079	1	1	43	0	1	0	0	0	0	0	0	0	10324	1609	56	4		4	NEFL	8	24811079	RNA	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10		24811079	121552943	165	5247										
IDO1	3620	hgsc.bcm.edu	37	chr8	39776332	39776332	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctaactactgtattttaatcAggtcttgccaagaaatattg	6	7	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:39776332A>G	ENST00000518237.1	+	4	942		c.e4-1		RP11-44K6.4_ENST00000522970.1_RNA|RP11-44K6.3_ENST00000517623.1_RNA|IDO1_ENST00000522495.1_Splice_Site	NM_002164.5	NP_002155.1	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1						cellular nitrogen compound metabolic process (GO:0034641)|cytokine production involved in inflammatory response (GO:0002534)|female pregnancy (GO:0007565)|kynurenic acid biosynthetic process (GO:0034276)|multicellular organismal response to stress (GO:0033555)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response (GO:0002678)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of type 2 immune response (GO:0002830)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|swimming behavior (GO:0036269)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytosol (GO:0005829)|smooth muscle contractile fiber (GO:0030485)|stereocilium bundle (GO:0032421)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(2)	12					L-Tryptophan(DB00150)|Melatonin(DB01065)	TATTTTAATCAGGTCTTGCCA	0.388																																					.		Atlas-SNP	.											.	IDO1	43	.	0			c.304-2A>G						.						101	95	97					8																	39776332		1857	4089	5946	SO:0001630	splice_region_variant	3620	exon4			TTAATCAGGTCTT	M34455	CCDS47847.1	8p12-p11	2009-01-07	2009-01-07	2009-01-07		ENSG00000131203	1.13.11.52		6059	protein-coding gene	gene with protein product		147435	"indoleamine-pyrrole 2,3 dioxygenase"	IDO, INDO		2109605, 8404046	Standard	NM_002164		Approved		uc003xnm.3	P14902		ENST00000518237.1:c.304-1A>G	chr8.hg19:g.39776332A>G		71.0	0.0		60.0	4.0	NM_002164	Q540B4	Splice_Site	SNP	ENST00000518237.1	hg19	CCDS47847.1	.	.	.	.	.	.	.	.	.	.	A	14.47	2.544293	0.45280	.	.	ENSG00000131203	ENST00000519154;ENST00000522495;ENST00000518237	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6362	0.56685	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IDO1	39895489	1.000000	0.71417	0.939000	0.37840	0.507000	0.33981	7.242000	0.78210	2.233000	0.73108	0.455000	0.32223	.	.	.		0.388	IDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376987.1	NM_002164	Intron	G	39776332	A	G	39776332	5	3	43	1	0	0	0	0	0	0	1	0	7510	202	7	2	316	2	IDO1	8	39776332	Splice_Site	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	14965253	39776332	106587690	166	5248										
LRRC67	286187	hgsc.bcm.edu	37	chr8	67900622	67900622	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tctcttaaaaattatattaaTataaatatgtacccagtgat	3	5	1	1	rs570555073		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:67900622T>C	ENST00000324682.5	-	6	827	c.683A>G	c.(682-684)tAt>tGt	p.Y228C	PPP1R42_ENST00000522909.1_Intron	NM_001013626.2	NP_001013648.1	Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	0	LRRCT.				regulation of phosphatase activity (GO:0010921)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|manchette (GO:0002177)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)	actin binding (GO:0003779)|dynein binding (GO:0045502)|tubulin binding (GO:0015631)										attatattaatataaatatGT	0.313																																					p.Y228C		Atlas-SNP	.											.	PPP1R42	2	.	0			c.A683G						.						19	20	20					8																	67900622		2079	4102	6181	SO:0001583	missense	286187	exon6			TATTAATATAAAT	BC055413	CCDS34902.1	8q13.1-q13.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000178125	ENSG00000178125		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	33732	protein-coding gene	gene with protein product	"testis leucine-rich repeat"		"leucine rich repeat containing 67"	LRRC67			Standard	NM_001013626		Approved	dtr, TLLR	uc003xxc.3	Q7Z4L9	OTTHUMG00000164745	ENST00000324682.5:c.683A>G	chr8.hg19:g.67900622T>C	ENSP00000315035:p.Tyr228Cys	3.0	0.0		19.0	10.0	NM_001013626		Missense_Mutation	SNP	ENST00000324682.5	hg19	CCDS34902.1	.	.	.	.	.	.	.	.	.	.	T	14.05	2.420933	0.42918	.	.	ENSG00000178125	ENST00000324682	T	0.38722	1.12	5.26	5.26	0.73747	.	1.715750	0.03082	N	0.158618	T	0.43809	0.1264	.	.	.	0.25321	N	0.989111	P	0.44816	0.844	B	0.42555	0.391	T	0.39396	-0.9616	9	0.59425	D	0.04	.	10.6756	0.45783	0.1428:0.0:0.0:0.8572	.	228	Q7Z4L9-2	.	C	228	ENSP00000315035:Y228C	ENSP00000315035:Y228C	Y	-	2	0	LRRC67	68063176	0.981000	0.34729	0.998000	0.56505	0.874000	0.50279	1.343000	0.33930	2.116000	0.64780	0.528000	0.53228	TAT	.	.		0.313	PPP1R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380034.2	NM_001013626		C	67900622	T	C	67900622	3	2	43	1	0	0	0	0	1	0	0	0	9028	1406	49	2	7	2	LRRC67	8	67900622	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	28124290	67900622	78463400	167	5249										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73849087	73849087	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aagtgggccaggaaggctctGtcggaaacaagctccaacaa	12	10	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:73849087G>A	ENST00000523207.1	+	3	2085	c.1497G>A	c.(1495-1497)ctG>ctA	p.L499L		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	499					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GGAAGGCTCTGTCGGAAACAA	0.552																																					p.L499L		Atlas-SNP	.											.	KCNB2	228	.	0			c.G1497A						.						106	114	112					8																	73849087		2203	4300	6503	SO:0001819	synonymous_variant	9312	exon3			GGCTCTGTCGGAA	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.1497G>A	chr8.hg19:g.73849087G>A		17.0	0.0		48.0	12.0	NM_004770	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	hg19	CCDS6209.1																																																																																			.	.		0.552	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		A	73849087	G	A	73849087	2	1	43	1	0	0	0	0	0	0	0	1	8022	1364	48	3		3	KCNB2	8	73849087	Silent	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	5948465	73849087	72514935	168	5250										
HNF4G	3174	hgsc.bcm.edu	37	chr8	76456117	76456118	+	Frame_Shift_Ins	INS	-	-	ACAGAGC													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tctgtgtgctatctgtggggINSacagagcaacaggaaaacac							TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:76456117_76456118insACAGAGC	ENST00000354370.1	+	3	319_320	c.49_50insACAGAGC	c.(49-51)gacfs	p.-19fs	HNF4G_ENST00000396423.2_Frame_Shift_Ins_p.-56fs			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma						endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			TATCTGTGGGGACAGAGCAACA	0.455																																					p.D54fs		Pindel	.											.	HNF4G	111	.	0			c.160_161insACAGAGC						.																																			SO:0001589	frameshift_variant	3174	exon2			.		CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749		"Nuclear hormone receptors"	5026	protein-coding gene	gene with protein product		605966				8622695, 12220494	Standard	NM_004133		Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.50_56dupACAGAGC	chr8.hg19:g.76456118_76456124dupACAGAGC	ENSP00000346339:p.Ala19fs	0.0	0.0		130.0	12.0	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Frame_Shift_Ins	INS	ENST00000354370.1	hg19																																																																																				.	.		0.455	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133		ACAGAGC	76456118	-	ACAGAGC	76456117	7	5	43	1	0	1	1	0	0	0	0	0	7263	1174	41	0	166	0	HNF4G	8	76456117	Frame_Shift_Ins	INS	-	TCGA-BC-A3KF-01A-11D-A20W-10	2607030	76456117	69907905	169	5251										
RNF19A	25897	hgsc.bcm.edu	37	chr8	101271049	101271049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	taacagtagcaaagcgggtgTgataatcactggaaccatga	11	7	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:101271049T>C	ENST00000519449.1	-	11	2568	c.2252A>G	c.(2251-2253)cAc>cGc	p.H751R	RNF19A_ENST00000341084.2_Missense_Mutation_p.H751R|RNF19A_ENST00000523255.1_5'Flank	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	751	Interaction with CASR.				microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			AAAGCGGGTGTGATAATCACT	0.408																																					p.H751R		Atlas-SNP	.											.	RNF19A	67	.	0			c.A2252G						.						101	99	100					8																	101271049		2203	4300	6503	SO:0001583	missense	25897	exon11			CGGGTGTGATAAT	AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.2252A>G	chr8.hg19:g.101271049T>C	ENSP00000428968:p.His751Arg	70.0	0.0		99.0	4.0	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	hg19	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.596398	0.46318	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.84070	-1.8;-1.8	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.79834	0.4514	L	0.50333	1.59	0.58432	D	0.999999	P	0.37466	0.596	B	0.34722	0.188	T	0.81376	-0.0961	10	0.62326	D	0.03	.	16.1016	0.81175	0.0:0.0:0.0:1.0	.	751	Q9NV58	RN19A_HUMAN	R	751	ENSP00000428968:H751R;ENSP00000342667:H751R	ENSP00000342667:H751R	H	-	2	0	RNF19A	101340225	1.000000	0.71417	0.972000	0.41901	0.954000	0.61252	7.495000	0.81514	2.274000	0.75844	0.477000	0.44152	CAC	.	.		0.408	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		C	101271049	T	C	101271049	3	2	43	1	0	0	0	0	1	0	0	0	13485	1696	59	2	268	2	RNF19A	8	101271049	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	24814932	101271049	45092973	170	5252										
UBR5	51366	hgsc.bcm.edu	37	chr8	103300480	103300480	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcctcttctccagccacaccCtccaccacctcaacctaaat	1	21	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:103300480C>T	ENST00000520539.1	-	36	5334	c.4728G>A	c.(4726-4728)gaG>gaA	p.E1576E	UBR5_ENST00000220959.4_Silent_p.E1576E|UBR5_ENST00000519528.1_5'UTR|UBR5_ENST00000521922.1_Silent_p.E1570E	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	1576					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			CAGCCACACCCTCCACCACCT	0.413																																					p.E1576E	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.G4728A						.						158	139	145					8																	103300480		2203	4300	6503	SO:0001819	synonymous_variant	51366	exon36			CACACCCTCCACC	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.4728G>A	chr8.hg19:g.103300480C>T		75.0	0.0		141.0	35.0	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	hg19	CCDS34933.1																																																																																			.	.		0.413	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		T	103300480	C	T	103300480	2	4	43	1	0	0	0	0	0	0	0	1	16920	680	24	3		3	UBR5	8	103300480	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	2029431	103300480	43063542	171	5253										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110457871	110457871	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcagaggaattatcccaagcAgaggtactccaatatctgcc	8	11	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:110457871A>G	ENST00000378402.5	+	38	5877	c.5773A>G	c.(5773-5775)Aga>Gga	p.R1925G		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1925	IPT/TIG 12.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TATCCCAAGCAGAGGTACTCC	0.318										HNSCC(38;0.096)																											p.R1925G		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A5773G						.						16	16	16					8																	110457871		1826	4089	5915	SO:0001583	missense	93035	exon38			CCAAGCAGAGGTA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5773A>G	chr8.hg19:g.110457871A>G	ENSP00000367655:p.Arg1925Gly	52.0	0.0		84.0	30.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	A	4.041	0.005151	0.07866	.	.	ENSG00000205038	ENST00000378402	T	0.77620	-1.11	6.03	4.85	0.62838	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.530979	0.19590	N	0.110642	T	0.69415	0.3108	L	0.40543	1.245	0.50171	D	0.999857	B	0.02656	0.0	B	0.12156	0.007	T	0.63161	-0.6699	10	0.41790	T	0.15	.	11.0488	0.47874	0.8612:0.0:0.0:0.1388	.	1925	Q86WI1	PKHL1_HUMAN	G	1925	ENSP00000367655:R1925G	ENSP00000367655:R1925G	R	+	1	2	PKHD1L1	110527047	0.141000	0.22595	0.175000	0.22980	0.011000	0.07611	1.002000	0.29796	1.065000	0.40693	0.533000	0.62120	AGA	.	.		0.318	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		G	110457871	A	G	110457871	3	3	43	1	0	0	0	0	1	0	0	0	11981	180	7	2	5923	2	PKHD1L1	8	110457871	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	7157391	110457871	35906151	172	5254										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113331087	113331087	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttgacaaactggaggtgctcCatccatctgcagtcgttctc	9	12	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:113331087C>T	ENST00000297405.5	-	47	7583	c.7339G>A	c.(7339-7341)Gga>Aga	p.G2447R	CSMD3_ENST00000343508.3_Missense_Mutation_p.G2407R|CSMD3_ENST00000352409.3_Missense_Mutation_p.G2377R|CSMD3_ENST00000455883.2_Missense_Mutation_p.G2343R	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2447	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GGAGGTGCTCCATCCATCTGC	0.328										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G2447R		Atlas-SNP	.											CSMD3_ENST00000343508,NS,malignant_melanoma,0,2	CSMD3	2325	.	0			c.G7339A						.						107	97	100					8																	113331087		2203	4300	6503	SO:0001583	missense	114788	exon47			GTGCTCCATCCAT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7339G>A	chr8.hg19:g.113331087C>T	ENSP00000297405:p.Gly2447Arg	26.0	0.0		39.0	2.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.626087	0.87560	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7	5.82	5.82	0.92795	Complement control module (2);Sushi/SCR/CCP (3);	0.076577	0.52532	D	0.000079	T	0.55337	0.1914	M	0.78049	2.395	0.51233	D	0.999916	P;D;D	0.76494	0.948;0.958;0.999	P;P;D	0.80764	0.848;0.906;0.994	T	0.52779	-0.8530	10	0.49607	T	0.09	.	20.1059	0.97895	0.0:1.0:0.0:0.0	.	2343;2447;2407	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	R	2407;2447;1717;2343;2377	ENSP00000345799:G2407R;ENSP00000297405:G2447R;ENSP00000341558:G1717R;ENSP00000412263:G2343R;ENSP00000343124:G2377R	ENSP00000297405:G2447R	G	-	1	0	CSMD3	113400263	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.606000	0.54095	2.770000	0.95276	0.579000	0.79373	GGA	.	.		0.328	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113331087	C	T	113331087	3	4	43	1	0	0	0	0	1	0	0	0	3948	603	21	3	3884	3	CSMD3	8	113331087	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	2873216	113331087	33032935	173	5255										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116430680	116430680	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aacaccggagcctctacgccTctgaaacaggggaaaaaaac	9	12	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:116430680T>C	ENST00000220888.5	-	5	2821	c.2662A>G	c.(2662-2664)Agg>Ggg	p.R888G	TRPS1_ENST00000395715.3_Splice_Site_p.R901G|TRPS1_ENST00000519076.1_Splice_Site_p.R642G|TRPS1_ENST00000520276.1_Splice_Site_p.R892G			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	888					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CCTCTACGCCTCTGAAACAGG	0.468									Langer-Giedion syndrome																												p.R901G		Atlas-SNP	.											.	TRPS1	516	.	0			c.A2701G						.						84	86	86					8																	116430680		1905	4119	6024	SO:0001630	splice_region_variant	7227	exon6	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	TACGCCTCTGAAA	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2662-1A>G	chr8.hg19:g.116430680T>C		104.0	0.0		114.0	5.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.53|16.53	3.149075|3.149075	0.57151|0.57151	.|.	.|.	ENSG00000104447|ENSG00000104447	ENST00000518018|ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276	.|D;D;D;D	.|0.99671	.|-6.35;-6.35;-6.35;-6.35	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99199|0.99199	0.9722|0.9722	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.999;1.0	.|D;D;D	.|0.83275	.|0.996;0.991;0.996	D|D	0.99890|0.99890	1.1132|1.1132	5|10	.|0.72032	.|D	.|0.01	.|.	16.1671|16.1671	0.81777|0.81777	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|892;888;901	.|Q9UHF7-3;Q9UHF7;Q9UHF7-2	.|.;TRPS1_HUMAN;.	G|G	12|901;888;642;892	.|ENSP00000379065:R901G;ENSP00000220888:R888G;ENSP00000428910:R642G;ENSP00000428680:R892G	.|ENSP00000220888:R888G	E|R	-|-	2|1	0|2	TRPS1|TRPS1	116499856|116499856	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.116000|6.116000	0.71571|0.71571	2.224000|2.224000	0.72417|0.72417	0.528000|0.528000	0.53228|0.53228	GAG|AGG	.	.		0.468	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112	Missense_Mutation	C	116430680	T	C	116430680	5	2	43	1	0	0	0	0	0	0	1	0	16608	1565	54	2	1191	2	TRPS1	8	116430680	Splice_Site	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3099593	116430680	29933342	174	5256										
DERL1	79139	hgsc.bcm.edu	37	chr8	124037286	124037286	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tctgctggcctcccatcaaaAgctcctggaaacaaaaacaa	6	13	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:124037286A>G	ENST00000259512.4	-	3	570	c.270T>C	c.(268-270)gcT>gcC	p.A90A	RP11-557C18.3_ENST00000521258.1_RNA|DERL1_ENST00000523036.1_5'UTR|DERL1_ENST00000405944.3_Silent_p.A90A|DERL1_ENST00000519018.1_5'UTR|DERL1_ENST00000419562.2_Intron	NM_001134671.2|NM_024295.5	NP_001128143.1|NP_077271.1	Q9BUN8	DERL1_HUMAN	derlin 1	90					endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|intracellular transport of viral protein in host cell (GO:0019060)|response to unfolded protein (GO:0006986)|retrograde protein transport, ER to cytosol (GO:0030970)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)	MHC class I protein binding (GO:0042288)|receptor activity (GO:0004872)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	8	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			TCCCATCAAAAGCTCCTGGAA	0.388																																					p.A90A		Atlas-SNP	.											.	DERL1	27	.	0			c.T270C						.						58	55	56					8																	124037286		2203	4300	6503	SO:0001819	synonymous_variant	79139	exon3			ATCAAAAGCTCCT	BC002457	CCDS6337.1, CCDS47915.1	8q24.13	2012-02-01	2012-02-01		ENSG00000136986	ENSG00000136986			28454	protein-coding gene	gene with protein product		608813	"Der1-like domain family, member 1"			12975309, 15215855	Standard	NM_024295		Approved	MGC3067, PRO2577, FLJ13784, DER1, DER-1, derlin-1	uc003ypl.3	Q9BUN8	OTTHUMG00000165080	ENST00000259512.4:c.270T>C	chr8.hg19:g.124037286A>G		37.0	0.0		61.0	4.0	NM_001134671	B3KW41|E9PH19	Silent	SNP	ENST00000259512.4	hg19	CCDS6337.1																																																																																			.	.		0.388	DERL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381714.2	NM_024295		G	124037286	A	G	124037286	2	3	43	1	0	0	0	0	0	0	0	1	4448	59	3	2		2	DERL1	8	124037286	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	7606606	124037286	22326736	175	5257										
KCNK9	51305	hgsc.bcm.edu	37	chr8	140631049	140631049	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggtagtcaacgtgatgaagcAgtagtagtaggcgtggaaga	16	4	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:140631049A>G	ENST00000520439.1	-	2	640	c.577T>C	c.(577-579)Tgc>Cgc	p.C193R	KCNK9_ENST00000523477.1_5'Flank|KCNK9_ENST00000303015.1_Missense_Mutation_p.C193R	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	193					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	GTGATGAAGCAGTAGTAGTAG	0.587																																					p.C193R		Atlas-SNP	.											.	KCNK9	100	.	0			c.T577C						.						87	85	86					8																	140631049		2203	4300	6503	SO:0001583	missense	51305	exon2			TGAAGCAGTAGTA	AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.577T>C	chr8.hg19:g.140631049A>G	ENSP00000430676:p.Cys193Arg	87.0	0.0		141.0	46.0	NM_016601	Q2M290|Q540F2	Missense_Mutation	SNP	ENST00000520439.1	hg19	CCDS6377.1	.	.	.	.	.	.	.	.	.	.	A	19.81	3.897449	0.72639	.	.	ENSG00000169427	ENST00000522317;ENST00000303015;ENST00000520439	T;T;T	0.31769	1.48;1.48;1.48	5.85	5.85	0.93711	Ion transport 2 (1);	0.000000	0.85682	D	0.000000	T	0.69441	0.3111	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.80819	-0.1212	10	0.87932	D	0	.	15.4187	0.74995	1.0:0.0:0.0:0.0	.	193	Q9NPC2	KCNK9_HUMAN	R	193	ENSP00000429847:C193R;ENSP00000302166:C193R;ENSP00000430676:C193R	ENSP00000302166:C193R	C	-	1	0	KCNK9	140700231	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.117000	0.94347	2.222000	0.72286	0.533000	0.62120	TGC	.	.		0.587	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601		G	140631049	A	G	140631049	3	3	43	1	0	0	0	0	1	0	0	0	8081	188	7	2	551	2	KCNK9	8	140631049	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	16593763	140631049	5732973	176	5258										
SLURP1	57152	hgsc.bcm.edu	37	chr8	143823269	143823269	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcaggctgtgtcctctggctTgcagcgggtaatggtcctgc	15	11	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:143823269T>C	ENST00000246515.1	-	2	155	c.130A>G	c.(130-132)Aag>Gag	p.K44E		NM_020427.2	NP_065160.1	P55000	SLUR1_HUMAN	secreted LY6/PLAUR domain containing 1	44	UPAR/Ly6.				cell activation (GO:0001775)|cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			breast(1)|lung(7)|ovary(1)	9	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TCCTCTGGCTTGCAGCGGGTA	0.647																																					p.K44E		Atlas-SNP	.											.	SLURP1	16	.	0			c.A130G						.						106	94	98					8																	143823269		2201	4299	6500	SO:0001583	missense	57152	exon2			CTGGCTTGCAGCG	AY579080	CCDS6387.1	8q24.3	2004-11-16			ENSG00000126233	ENSG00000126233			18746	protein-coding gene	gene with protein product	"lymphocyte antigen 6-like secreted", "ARS component B"	606119				11285253, 10211827	Standard	NM_020427		Approved	ARS, ANUP, MDM, ArsB, LY6LS	uc003ywy.3	P55000	OTTHUMG00000164685	ENST00000246515.1:c.130A>G	chr8.hg19:g.143823269T>C	ENSP00000246515:p.Lys44Glu	43.0	0.0		100.0	4.0	NM_020427	Q53YJ6|Q6PUA6|Q92483	Missense_Mutation	SNP	ENST00000246515.1	hg19	CCDS6387.1	.	.	.	.	.	.	.	.	.	.	T	7.483	0.649117	0.14516	.	.	ENSG00000126233	ENST00000246515	T	0.69175	-0.38	3.81	-0.688	0.11317	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	0.687158	0.13123	N	0.412023	T	0.55970	0.1954	M	0.65975	2.015	0.09310	N	1	P	0.43885	0.82	B	0.41088	0.347	T	0.46789	-0.9166	10	0.17832	T	0.49	-16.5723	4.1918	0.10424	0.0:0.1256:0.4235:0.4508	.	44	P55000	SLUR1_HUMAN	E	44	ENSP00000246515:K44E	ENSP00000246515:K44E	K	-	1	0	SLURP1	143820271	0.037000	0.19845	0.168000	0.22838	0.254000	0.26022	0.381000	0.20619	0.037000	0.15575	0.379000	0.24179	AAG	.	.		0.647	SLURP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379741.1	NM_020427		C	143823269	T	C	143823269	3	2	43	1	0	0	0	0	1	0	0	0	14771	1821	63	2	189	2	SLURP1	8	143823269	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3192220	143823269	2540753	177	5259										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144940614	144940614	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cacggggtcgatgacgaagcCggtggccgcctgcgcctcca	15	15	0	1	rs200821582		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:144940614C>T	ENST00000525985.1	-	2	6879	c.6808G>A	c.(6808-6810)Ggc>Agc	p.G2270S				P58107	EPIPL_HUMAN	epiplakin 1	2270						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)	p.G2270S(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ATGACGAAGCCGGTGGCCGCC	0.721																																					p.G2270S		Atlas-SNP	.											EPPK1,NS,carcinoma,0,1	EPPK1	199	.	1	Substitution - Missense(1)	lung(1)	c.G6808A						.	C	SER/GLY	1,4305		0,1,2152	38	37	37		6808	4.6	1	8		37	2,8468		0,2,4233	no	missense	EPPK1	NM_031308.1	56	0,3,6385	TT,TC,CC		0.0236,0.0232,0.0235	probably-damaging	2270/2420	144940614	3,12773	2153	4235	6388	SO:0001583	missense	83481	exon1			CGAAGCCGGTGGC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6808G>A	chr8.hg19:g.144940614C>T	ENSP00000436337:p.Gly2270Ser	3.0	1.0		20.0	8.0	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.600172	0.96614	2.32E-4	2.36E-4	ENSG00000227184	ENST00000525985	D	0.86497	-2.13	4.63	4.63	0.57726	.	.	.	.	.	D	0.94935	0.8362	M	0.93150	3.385	0.52501	D	0.999952	D	0.89917	1.0	D	0.97110	1.0	D	0.95948	0.8952	9	0.72032	D	0.01	.	15.1031	0.72299	0.0:1.0:0.0:0.0	.	2270	E9PPU0	.	S	2270	ENSP00000436337:G2270S	ENSP00000436337:G2270S	G	-	1	0	EPPK1	145012602	1.000000	0.71417	0.984000	0.44739	0.988000	0.76386	7.595000	0.82710	2.416000	0.81992	0.586000	0.80456	GGC	.	C|0.998;T|0.002		0.721	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144940614	C	T	144940614	3	4	43	1	0	0	0	0	1	0	0	0	5192	652	23	1	458	1	EPPK1	8	144940614	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	1117345	144940614	1423408	178	5260										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144944633	144944633	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gccgcacaccgcccacagctCccaggccgcacaggtacctg	10	20	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr8:144944633C>T	ENST00000525985.1	-	2	2860	c.2789G>A	c.(2788-2790)gGa>gAa	p.G930E				P58107	EPIPL_HUMAN	epiplakin 1	930						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCCCACAGCTCCCAGGCCGCA	0.682																																					p.G930E		Atlas-SNP	.											.	EPPK1	199	.	0			c.G2789A						.						14	18	17					8																	144944633		2051	4175	6226	SO:0001583	missense	83481	exon1			ACAGCTCCCAGGC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.2789G>A	chr8.hg19:g.144944633C>T	ENSP00000436337:p.Gly930Glu	14.0	0.0		35.0	12.0	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.54	3.152170	0.57259	.	.	ENSG00000227184	ENST00000525985	T	0.72615	-0.67	4.94	4.04	0.47022	.	.	.	.	.	T	0.64692	0.2621	N	0.19112	0.55	0.09310	N	1	D	0.58268	0.982	P	0.57620	0.824	T	0.51513	-0.8696	9	0.23891	T	0.37	.	6.6665	0.23042	0.0:0.7232:0.1825:0.0943	.	930	E9PPU0	.	E	930	ENSP00000436337:G930E	ENSP00000436337:G930E	G	-	2	0	EPPK1	145016621	0.011000	0.17503	0.031000	0.17742	0.002000	0.02628	1.450000	0.35134	1.271000	0.44313	0.655000	0.94253	GGA	.	.		0.682	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144944633	C	T	144944633	3	4	43	1	0	0	0	0	1	0	0	0	5192	855	30	3	4477	3	EPPK1	8	144944633	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	4019	144944633	1419389	179	5261										
PLAA	9373	hgsc.bcm.edu	37	chr9	26905635	26905635	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgtacagcatttgaatcatcActgataagtgttccaagagc	8	8	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:26905635A>G	ENST00000397292.3	-	14	2679	c.2262T>C	c.(2260-2262)agT>agC	p.S754S		NM_001031689.2	NP_001026859.1	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	754	PUL. {ECO:0000255|PROSITE- ProRule:PRU00729}.				inflammatory response (GO:0006954)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	phospholipase A2 activator activity (GO:0016005)			breast(1)|endometrium(7)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	17		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		TTGAATCATCACTGATAAGTG	0.373																																					p.S754S	Melanoma(175;2670 2735 14091 35526)	Atlas-SNP	.											.	PLAA	48	.	0			c.T2262C						.						107	105	106					9																	26905635		2203	4300	6503	SO:0001819	synonymous_variant	9373	exon14			ATCATCACTGATA	AF083395	CCDS35000.1	9p21	2013-01-10			ENSG00000137055	ENSG00000137055		"WD repeat domain containing"	9043	protein-coding gene	gene with protein product	"DOA1 homolog (S. cerevisiae)"	603873				9931468, 10644453	Standard	NM_001031689		Approved	PLAP, PLA2P, FLJ11281, FLJ12699, DOA1	uc003zqd.3	Q9Y263	OTTHUMG00000019708	ENST00000397292.3:c.2262T>C	chr9.hg19:g.26905635A>G		103.0	0.0		76.0	4.0	NM_001031689	Q53EU5|Q5VY33|Q9NUL8|Q9NVE9|Q9UF53|Q9Y5L1	Silent	SNP	ENST00000397292.3	hg19	CCDS35000.1																																																																																			.	.		0.373	PLAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051958.2	NM_001031689		G	26905635	A	G	26905635	2	3	43	1	0	0	0	0	0	0	0	1	12020	156	6	2		2	PLAA	9	26905635	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10		26905635	114307796	180	5262										
FANCG	2189	hgsc.bcm.edu	37	chr9	35077012	35077012	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgctgtgtacacctggaccaAcacaggccgtggacacaggc	12	13	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:35077012A>G	ENST00000378643.3	-	6	1224	c.733T>C	c.(733-735)Ttg>Ctg	p.L245L	FANCG_ENST00000476212.1_5'Flank	NM_004629.1	NP_004620.1	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	245					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|mitochondrion organization (GO:0007005)|ovarian follicle development (GO:0001541)|response to radiation (GO:0009314)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	damaged DNA binding (GO:0003684)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|stomach(1)	28			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			ACCTGGACCAACACAGGCCGT	0.537			"Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks																													p.L245L		Atlas-SNP	.	yes	Rec		Fanconi anaemia G	9	9p13	2189	"Fanconi anemia, complementation group G"		L	.	FANCG	56	.	0			c.T733C						.						88	92	91					9																	35077012		2203	4300	6503	SO:0001819	synonymous_variant	2189	exon6			GGACCAACACAGG	AJ007669	CCDS6574.1	9p13	2014-09-17			ENSG00000221829	ENSG00000221829		"Fanconi anemia, complementation groups"	3588	protein-coding gene	gene with protein product	"DNA repair protein XRCC9", "X-ray repair, complementing defective, in Chinese hamster, 9", "X-ray repair complementing defective repair in Chinese hamster cells 9"	602956		XRCC9		9256465, 9382107	Standard	NM_004629		Approved	FAG	uc003zwb.1	O15287	OTTHUMG00000019850	ENST00000378643.3:c.733T>C	chr9.hg19:g.35077012A>G		83.0	0.0		93.0	4.0	NM_004629		Silent	SNP	ENST00000378643.3	hg19	CCDS6574.1																																																																																			.	.		0.537	FANCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052269.1	NM_004629		G	35077012	A	G	35077012	2	3	43	1	0	0	0	0	0	0	0	1	5676	40	2	2		2	FANCG	9	35077012	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	8171377	35077012	106136419	181	5263										
CCIN	881	hgsc.bcm.edu	37	chr9	36169807	36169807	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctccgagcaaaatgtggaggAgctgcttcgtggggctcagt	15	9	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:36169807A>T	ENST00000335119.2	+	1	419	c.308A>T	c.(307-309)gAg>gTg	p.E103V		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	103	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			AATGTGGAGGAGCTGCTTCGT	0.522																																					p.E103V		Atlas-SNP	.											.	CCIN	56	.	0			c.A308T						.						84	72	76					9																	36169807		2203	4300	6503	SO:0001583	missense	881	exon1			TGGAGGAGCTGCT	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"BTB/POZ domain containing"	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.308A>T	chr9.hg19:g.36169807A>T	ENSP00000334996:p.Glu103Val	104.0	0.0		126.0	46.0	NM_005893	Q9BXG7	Missense_Mutation	SNP	ENST00000335119.2	hg19	CCDS6599.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.926934	0.52759	.	.	ENSG00000185972	ENST00000335119	T	0.72615	-0.67	5.26	5.26	0.73747	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.56097	D	0.000040	T	0.69287	0.3094	M	0.61703	1.905	0.38593	D	0.95047	D	0.54207	0.965	P	0.46419	0.516	T	0.69684	-0.5079	10	0.21540	T	0.41	.	11.8391	0.52344	1.0:0.0:0.0:0.0	.	103	Q13939	CALI_HUMAN	V	103	ENSP00000334996:E103V	ENSP00000334996:E103V	E	+	2	0	CCIN	36159807	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.309000	0.65774	2.118000	0.64928	0.379000	0.24179	GAG	.	.		0.522	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893		T	36169807	A	T	36169807	3	4	43	1	0	0	0	0	1	0	0	0	2880	304	11	4	310	4	CCIN	9	36169807	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1092795	36169807	105043624	182	5264										
C9orf85	138241	hgsc.bcm.edu	37	chr9	74561974	74561974	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcagcgctgtaaagaagttcTtgagtggcgtgtaaaataca	11	6	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:74561974T>C	ENST00000377031.3	+	2	345	c.155T>C	c.(154-156)cTt>cCt	p.L52P	C9orf85_ENST00000334731.2_Missense_Mutation_p.L52P|C9orf85_ENST00000486911.2_Missense_Mutation_p.L52P			Q96MD7	CI085_HUMAN	chromosome 9 open reading frame 85	52	Lys-rich.									kidney(2)|large_intestine(1)|lung(4)	7						AAAGAAGTTCTTGAGTGGCGT	0.343																																					p.L52P		Atlas-SNP	.											.	C9orf85	28	.	0			c.T155C						.						95	86	89					9																	74561974		2203	4300	6503	SO:0001583	missense	138241	exon2			AAGTTCTTGAGTG	BC010179	CCDS6639.1	9q21.2	2012-03-16			ENSG00000155621	ENSG00000155621			28784	protein-coding gene	gene with protein product						12477932	Standard	NM_182505		Approved	MGC61599	uc004ain.3	Q96MD7	OTTHUMG00000020002	ENST00000377031.3:c.155T>C	chr9.hg19:g.74561974T>C	ENSP00000366230:p.Leu52Pro	61.0	0.0		81.0	4.0	NM_182505	Q5W0N1|Q5W0N3|Q6PJW9|Q86U95	Missense_Mutation	SNP	ENST00000377031.3	hg19		.	.	.	.	.	.	.	.	.	.	T	19.93	3.918533	0.73098	.	.	ENSG00000155621	ENST00000334731;ENST00000377031	T	0.35789	1.29	5.69	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.57651	0.2068	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.60459	-0.7259	10	0.87932	D	0	-15.2433	10.6569	0.45680	0.0:0.0763:0.0:0.9237	.	52	Q96MD7-1	.	P	52	ENSP00000366230:L52P	ENSP00000334289:L52P	L	+	2	0	C9orf85	73751794	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.175000	0.77632	0.998000	0.38996	0.454000	0.30748	CTT	.	.		0.343	C9orf85-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052628.2	NM_182505		C	74561974	T	C	74561974	3	2	43	1	0	0	0	0	1	0	0	0	2503	1609	56	2	161	2	C9orf85	9	74561974	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	38392167	74561974	66651457	183	5265										
PHF2	5253	hgsc.bcm.edu	37	chr9	96438992	96438992	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acctccacctccaccacgccAgcctctaccaccccggcctc	4	25	1	0	rs10821200		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:96438992A>T	ENST00000359246.4	+	21	3316	c.2949A>T	c.(2947-2949)ccA>ccT	p.P983P	PHF2_ENST00000375376.4_Silent_p.P214P	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	983	Ser/Thr-rich.				liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		ccaccacgccagcctctacca	0.667																																					p.P983P		Atlas-SNP	.											PHF2,caecum,carcinoma,0,1	PHF2	113	.	0			c.A2949T						.						87	65	72					9																	96438992		2163	4255	6418	SO:0001819	synonymous_variant	5253	exon21			CACGCCAGCCTCT	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	8920	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1E", "centromere protein 35"	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.2949A>T	chr9.hg19:g.96438992A>T		23.0	1.0		43.0	6.0	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	hg19	CCDS35069.1																																																																																			.	.		0.667	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		T	96438992	A	T	96438992	2	4	43	1	0	0	0	0	0	0	0	1	11839	175	7	4		4	PHF2	9	96438992	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	21877018	96438992	44774439	184	5266										
TDRD7	23424	hgsc.bcm.edu	37	chr9	100222509	100222509	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttacttctttatccagctaAgagaaagcagcttttgagaa	7	7	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:100222509A>G	ENST00000355295.4	+	7	1200	c.905A>G	c.(904-906)aAg>aGg	p.K302R	TDRD7_ENST00000422139.2_Missense_Mutation_p.K228R	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	302	HTH OST-type 2. {ECO:0000255|PROSITE- ProRule:PRU00975}.				germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				TATCCAGCTAAGAGAAAGCAG	0.403																																					p.K302R		Atlas-SNP	.											.	TDRD7	78	.	0			c.A905G						.						79	80	80					9																	100222509		2203	4300	6503	SO:0001583	missense	23424	exon7			CAGCTAAGAGAAA	AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"Tudor domain containing"	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.905A>G	chr9.hg19:g.100222509A>G	ENSP00000347444:p.Lys302Arg	100.0	0.0		96.0	4.0	NM_014290	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Missense_Mutation	SNP	ENST00000355295.4	hg19	CCDS6725.1	.	.	.	.	.	.	.	.	.	.	A	13.69	2.312093	0.40895	.	.	ENSG00000196116	ENST00000355295;ENST00000422139	T;T	0.14766	2.48;2.51	5.54	4.36	0.52297	.	0.489199	0.25804	N	0.028193	T	0.12390	0.0301	L	0.50333	1.59	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.07849	-1.0751	10	0.33940	T	0.23	-16.8141	7.0874	0.25266	0.7758:0.1471:0.0771:0.0	.	302	Q8NHU6	TDRD7_HUMAN	R	302;228	ENSP00000347444:K302R;ENSP00000413608:K228R	ENSP00000347444:K302R	K	+	2	0	TDRD7	99262330	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.837000	0.39201	0.992000	0.38840	0.533000	0.62120	AAG	.	.		0.403	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290		G	100222509	A	G	100222509	3	3	43	1	0	0	0	0	1	0	0	0	15750	72	3	2	927	2	TDRD7	9	100222509	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	3783517	100222509	40990922	185	5267										
ANKS6	203286	hgsc.bcm.edu	37	chr9	101544811	101544811	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cattttttgcacgaagagtgAcatcggccccttggtttagc	10	10	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:101544811A>G	ENST00000353234.4	-	5	1204	c.1157T>C	c.(1156-1158)gTc>gCc	p.V386A	ANKS6_ENST00000540940.1_Missense_Mutation_p.V191A|ANKS6_ENST00000375018.1_Missense_Mutation_p.V386A|ANKS6_ENST00000375019.2_Missense_Mutation_p.V85A			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	386						cilium (GO:0005929)|cytoplasm (GO:0005737)				endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				ACGAAGAGTGACATCGGCCCC	0.433																																					p.V386A		Atlas-SNP	.											.	ANKS6	59	.	0			c.T1157C						.						134	126	129					9																	101544811		1888	4111	5999	SO:0001583	missense	203286	exon5			AGAGTGACATCGG	AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26724	protein-coding gene	gene with protein product		615370	"sterile alpha motif domain containing 6", "ankyrin repeat domain 14"	SAMD6, ANKRD14		23793029	Standard	XM_005251793		Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000353234.4:c.1157T>C	chr9.hg19:g.101544811A>G	ENSP00000297837:p.Val386Ala	81.0	0.0		90.0	4.0	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	hg19	CCDS43856.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.751332	0.89753	.	.	ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.5	5.5	0.81552	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.74756	0.3758	L	0.41236	1.265	0.58432	D	0.999992	D	0.76494	0.999	D	0.78314	0.991	T	0.77233	-0.2663	10	0.72032	D	0.01	-23.678	13.5651	0.61813	1.0:0.0:0.0:0.0	.	386	Q68DC2	ANKS6_HUMAN	A	85;386;386;191	ENSP00000364159:V85A;ENSP00000364158:V386A;ENSP00000297837:V386A;ENSP00000442189:V191A	ENSP00000297837:V386A	V	-	2	0	ANKS6	100584632	1.000000	0.71417	0.992000	0.48379	0.926000	0.56050	8.661000	0.91125	2.083000	0.62718	0.533000	0.62120	GTC	.	.		0.433	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		G	101544811	A	G	101544811	3	3	43	1	0	0	0	0	1	0	0	0	692	275	10	2	1502	2	ANKS6	9	101544811	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1322302	101544811	39668620	186	5268										
LCN2	3934	hgsc.bcm.edu	37	chr9	130911936	130911936	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctgcagcagaacttccaggaCaaccaagtaaggggccaaga	11	11	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:130911936C>A	ENST00000373017.1	+	2	369	c.132C>A	c.(130-132)gaC>gaA	p.D44E	LCN2_ENST00000470902.1_3'UTR|LCN2_ENST00000373013.2_Missense_Mutation_p.D44E|LCN2_ENST00000372998.1_Missense_Mutation_p.D44E|LCN2_ENST00000540948.1_Missense_Mutation_p.D44E|LCN2_ENST00000277480.2_Missense_Mutation_p.D44E			P80188	NGAL_HUMAN	lipocalin 2	44					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|small molecule binding (GO:0036094)|transporter activity (GO:0005215)			central_nervous_system(1)|lung(3)|prostate(2)|skin(1)|urinary_tract(1)	8						ACTTCCAGGACAACCAAGTAA	0.637																																					p.D44E		Atlas-SNP	.											.	LCN2	12	.	0			c.C132A						.						61	62	62					9																	130911936		2203	4300	6503	SO:0001583	missense	3934	exon1			CCAGGACAACCAA		CCDS6892.1	9q34	2011-10-24	2007-12-18		ENSG00000148346	ENSG00000148346		"Lipocalins"	6526	protein-coding gene	gene with protein product	"oncogene 24p3", "neutrophil gelatinase-associated lipocalin", "siderocalin"	600181	"lipocalin 2 (oncogene 24p3)"			7683678	Standard	NM_005564		Approved	NGAL, 24p3	uc004bto.1	P80188	OTTHUMG00000020734	ENST00000373017.1:c.132C>A	chr9.hg19:g.130911936C>A	ENSP00000362108:p.Asp44Glu	68.0	0.0		75.0	29.0	NM_005564	A6NII8|B4DWV4|B7ZAA2|P30150|Q5SYV9|Q5SYW0|Q6FGL5|Q92683	Missense_Mutation	SNP	ENST00000373017.1	hg19	CCDS6892.1	.	.	.	.	.	.	.	.	.	.	C	9.271	1.045625	0.19748	.	.	ENSG00000148346	ENST00000373017;ENST00000277480;ENST00000373013;ENST00000540948;ENST00000372998	T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.02	3.45	-4.42	0.03579	Lipocalin conserved site (1);Calycin-like (1);Calycin (1);	1.755640	0.02919	N	0.137663	T	0.09598	0.0236	N	0.24115	0.695	0.09310	N	1	B;B;B	0.20261	0.043;0.025;0.025	B;B;B	0.18561	0.022;0.01;0.01	T	0.20806	-1.0264	10	0.02654	T	1	-3.6543	1.6794	0.02829	0.1697:0.4154:0.1722:0.2427	.	44;45;44	P80188-2;B2ZDQ1;P80188	.;.;NGAL_HUMAN	E	44	ENSP00000362108:D44E;ENSP00000277480:D44E;ENSP00000362104:D44E;ENSP00000441666:D44E;ENSP00000362089:D44E	ENSP00000277480:D44E	D	+	3	2	LCN2	129951757	0.000000	0.05858	0.000000	0.03702	0.602000	0.36980	-3.139000	0.00587	-0.919000	0.03803	0.456000	0.33151	GAC	.	.		0.637	LCN2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054375.1	NM_005564		A	130911936	C	A	130911936	3	1	43	1	0	0	0	0	1	0	0	0	8693	477	17	3	134	3	LCN2	9	130911936	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	29367125	130911936	10301495	187	5269										
GTF3C4	9329	hgsc.bcm.edu	37	chr9	135562687	135562687	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaaggtgtttgctccatgacAgcattgcccggcatccagct	11	12	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:135562687A>G	ENST00000372146.4	+	4	2941	c.2377A>G	c.(2377-2379)Agc>Ggc	p.S793G		NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	793					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		GCTCCATGACAGCATTGCCCG	0.527																																					p.S793G	Pancreas(142;417 1875 11086 31973 47667)	Atlas-SNP	.											.	GTF3C4	53	.	0			c.A2377G						.						239	233	235					9																	135562687		2203	4300	6503	SO:0001583	missense	9329	exon4			CATGACAGCATTG	AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"Chromatin-modifying enzymes / K-acetyltransferases", "General transcription factors"	4667	protein-coding gene	gene with protein product		604892	"general transcription factor IIIC, polypeptide 4 (90kD)"			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.2377A>G	chr9.hg19:g.135562687A>G	ENSP00000361219:p.Ser793Gly	76.0	0.0		78.0	4.0	NM_012204	Q5VZJ7	Missense_Mutation	SNP	ENST00000372146.4	hg19	CCDS6953.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.093657	0.76870	.	.	ENSG00000125484	ENST00000372146	T	0.48836	0.8	5.58	5.58	0.84498	Transcription factor IIIC, putative zinc-finger (1);	0.125061	0.64402	D	0.000001	T	0.45316	0.1336	N	0.12182	0.205	0.47094	D	0.999315	D	0.56287	0.975	P	0.59012	0.85	T	0.39742	-0.9599	10	0.23302	T	0.38	-32.194	14.5866	0.68328	1.0:0.0:0.0:0.0	.	793	Q9UKN8	TF3C4_HUMAN	G	793	ENSP00000361219:S793G	ENSP00000361219:S793G	S	+	1	0	GTF3C4	134552508	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.047000	0.64232	2.132000	0.65825	0.528000	0.53228	AGC	.	.		0.527	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1			G	135562687	A	G	135562687	3	3	43	1	0	0	0	0	1	0	0	0	6884	188	7	2	2391	2	GTF3C4	9	135562687	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	4650751	135562687	5650744	188	5270										
SARDH	1757	hgsc.bcm.edu	37	chr9	136578161	136578161	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggctgctgcccggactcaccTgcgctgttgaagccacagcc	12	16	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:136578161T>C	ENST00000371872.4	-	9	1493	c.1236A>G	c.(1234-1236)gcA>gcG	p.A412A	SARDH_ENST00000422262.2_Splice_Site_p.A244A|SARDH_ENST00000439388.1_Splice_Site_p.A412A	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	412					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CGGACTCACCTGCGCTGTTGA	0.662																																					p.A412A		Atlas-SNP	.											.	SARDH	112	.	0			c.A1236G						.						32	34	33					9																	136578161		2202	4300	6502	SO:0001630	splice_region_variant	1757	exon9			CTCACCTGCGCTG		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1237+1A>G	chr9.hg19:g.136578161T>C		26.0	0.0		41.0	15.0	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	hg19	CCDS6978.1																																																																																			.	.		0.662	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		Silent	C	136578161	T	C	136578161	5	2	43	1	0	0	0	0	0	0	1	0	13856	1594	55	2	1572	2	SARDH	9	136578161	Splice_Site	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1015474	136578161	4635270	189	5271										
PMPCA	23203	hgsc.bcm.edu	37	chr9	139306975	139306975	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aggatcgagatatgaagcgaAataccttagtggaattgctc	11	6	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr9:139306975A>G	ENST00000371717.3	+	3	317	c.308A>G	c.(307-309)aAa>aGa	p.K103R	PMPCA_ENST00000371720.1_Missense_Mutation_p.K103R|PMPCA_ENST00000399219.3_Missense_Mutation_p.N4D|SDCCAG3_ENST00000298537.7_5'Flank|SDCCAG3_ENST00000357365.3_5'Flank|SDCCAG3_ENST00000371725.3_5'Flank	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	103					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	14		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		TATGAAGCGAAATACCTTAGT	0.308																																					p.K103R		Atlas-SNP	.											.	PMPCA	29	.	0			c.A308G						.						87	86	87					9																	139306975		2201	4297	6498	SO:0001583	missense	23203	exon3			AAGCGAAATACCT	D21064	CCDS35180.1, CCDS65192.1	9q34.3	2008-02-05	2003-06-13	2003-06-20	ENSG00000165688	ENSG00000165688			18667	protein-coding gene	gene with protein product		613036	"inositol polyphosphate-5-phosphatase, 72 kD"	INPP5E		8590280, 7788527	Standard	NM_015160		Approved	KIAA0123, Alpha-MPP	uc004chl.3	Q10713	OTTHUMG00000020926	ENST00000371717.3:c.308A>G	chr9.hg19:g.139306975A>G	ENSP00000360782:p.Lys103Arg	82.0	0.0		94.0	4.0	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371717.3	hg19	CCDS35180.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.94|16.94	3.261105|3.261105	0.59431|0.59431	.|.	.|.	ENSG00000165688|ENSG00000165688	ENST00000371720;ENST00000371717|ENST00000399219	T;T|T	0.18657|0.12672	2.2;2.2|2.66	4.96|4.96	4.96|4.96	0.65561|0.65561	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.08268|0.08268	0.0206|0.0206	L|L	0.29908|0.29908	0.895|0.895	0.28300|0.28300	N|N	0.923179|0.923179	P;P|P	0.38335|0.39665	0.584;0.627|0.682	B;B|B	0.42062|0.27380	0.348;0.374|0.079	T|T	0.09729|0.09729	-1.0661|-1.0661	10|9	0.17832|0.08179	T|T	0.49|0.78	.|.	14.1026|14.1026	0.65068|0.65068	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	103;103|4	B4DRK5;Q10713|B4DKL3	.;MPPA_HUMAN|.	R|D	103|4	ENSP00000360785:K103R;ENSP00000360782:K103R|ENSP00000416702:N4D	ENSP00000360782:K103R|ENSP00000416702:N4D	K|N	+|+	2|1	0|0	PMPCA|PMPCA	138426796|138426796	1.000000|1.000000	0.71417|0.71417	0.722000|0.722000	0.30670|0.30670	0.925000|0.925000	0.55904|0.55904	8.978000|8.978000	0.93450|0.93450	1.966000|1.966000	0.57179|0.57179	0.533000|0.533000	0.62120|0.62120	AAA|AAT	.	.		0.308	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160		G	139306975	A	G	139306975	3	3	43	1	0	0	0	0	1	0	0	0	12149	14	1	2	318	2	PMPCA	9	139306975	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	2728814	139306975	1906456	190	5272										
CCDC3	83643	hgsc.bcm.edu	37	chr10	13040436	13040436	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aaggctagaaaacatccttcTgttctcttgagtgtctggga	10	8	3	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:13040436T>C	ENST00000378825.3	-	2	577	c.451A>G	c.(451-453)Aga>Gga	p.R151G	CCDC3_ENST00000378839.1_Missense_Mutation_p.R26G	NM_031455.3	NP_113643.1	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3	151						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	11		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			AACATCCTTCTGTTCTCTTGA	0.458																																					p.R151G		Atlas-SNP	.											.	CCDC3	27	.	0			c.A451G						.						128	115	119					10																	13040436		2203	4300	6503	SO:0001583	missense	83643	exon2			TCCTTCTGTTCTC	BC051334	CCDS7093.1, CCDS60484.1	10p14	2004-02-13			ENSG00000151468	ENSG00000151468			23813	protein-coding gene	gene with protein product							Standard	NM_031455		Approved	DKFZp761F241	uc001ilq.1	Q9BQI4	OTTHUMG00000017689	ENST00000378825.3:c.451A>G	chr10.hg19:g.13040436T>C	ENSP00000368102:p.Arg151Gly	83.0	0.0		94.0	26.0	NM_031455	Q5VYV8|Q5VYV9	Missense_Mutation	SNP	ENST00000378825.3	hg19	CCDS7093.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.814588	0.70912	.	.	ENSG00000151468	ENST00000378839;ENST00000378825	.	.	.	4.92	3.76	0.43208	.	0.042937	0.85682	D	0.000000	T	0.67088	0.2856	M	0.72894	2.215	0.48696	D	0.999695	D	0.60575	0.988	P	0.56216	0.794	T	0.67325	-0.5699	9	0.46703	T	0.11	-3.219	11.3499	0.49581	0.0:0.0:0.1522:0.8478	.	151	Q9BQI4	CCDC3_HUMAN	G	26;151	.	ENSP00000368102:R151G	R	-	1	2	CCDC3	13080442	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.910000	0.39927	0.809000	0.34255	0.379000	0.24179	AGA	.	.		0.458	CCDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046829.1	NM_031455		C	13040436	T	C	13040436	3	2	43	1	0	0	0	0	1	0	0	0	2806	1588	55	2	369	2	CCDC3	10	13040436	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10		13040436	122494311	191	5273										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26442791	26442791	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tctcataggtaatctgccacAttctaaaactaaaaatgtta	4	8	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:26442791A>T	ENST00000265944.5	+	24	2814	c.2648A>T	c.(2647-2649)cAt>cTt	p.H883L	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	883	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AATCTGCCACATTCTAAAACT	0.294																																					p.H883L		Atlas-SNP	.											.	MYO3A	371	.	0			c.A2648T						.						33	36	35					10																	26442791		2196	4288	6484	SO:0001583	missense	53904	exon24			TGCCACATTCTAA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2648A>T	chr10.hg19:g.26442791A>T	ENSP00000265944:p.His883Leu	140.0	0.0		142.0	6.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.387816	0.25031	.	.	ENSG00000095777	ENST00000265944	T	0.70045	-0.45	5.46	3.11	0.35812	Myosin head, motor domain (2);	0.095322	0.64402	N	0.000001	T	0.49762	0.1576	L	0.41415	1.275	0.80722	D	1	B	0.06786	0.001	B	0.12837	0.008	T	0.24764	-1.0151	10	0.10902	T	0.67	.	6.5446	0.22398	0.7604:0.0:0.0776:0.162	.	883	Q8NEV4	MYO3A_HUMAN	L	883	ENSP00000265944:H883L	ENSP00000265944:H883L	H	+	2	0	MYO3A	26482797	1.000000	0.71417	0.986000	0.45419	0.812000	0.45895	2.348000	0.44045	0.370000	0.24538	0.377000	0.23210	CAT	.	.		0.294	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26442791	A	T	26442791	3	4	43	1	0	0	0	0	1	0	0	0	10085	217	8	4	2734	4	MYO3A	10	26442791	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	13402355	26442791	109091956	192	5274										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27349321	27349321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttcctcctgctttatttggaAcagaatctttcatttcaatg	5	9	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:27349321A>G	ENST00000376087.4	-	15	1682	c.1517T>C	c.(1516-1518)gTt>gCt	p.V506A	ANKRD26_ENST00000436985.2_Missense_Mutation_p.V522A	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	506					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TTTATTTGGAACAGAATCTTT	0.284																																					p.V506A		Atlas-SNP	.											.	ANKRD26	179	.	0			c.T1517C						.						106	103	104					10																	27349321		1803	4069	5872	SO:0001583	missense	22852	exon15			TTTGGAACAGAAT	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.1517T>C	chr10.hg19:g.27349321A>G	ENSP00000365255:p.Val506Ala	88.0	0.0		124.0	5.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	hg19	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.072952	0.36566	.	.	ENSG00000107890	ENST00000376087;ENST00000436985	T;T	0.36157	1.35;1.27	4.5	0.6	0.17524	.	1.170640	0.06861	U	0.799102	T	0.30978	0.0782	L	0.51422	1.61	0.09310	N	1	B;B;B	0.14012	0.002;0.001;0.009	B;B;B	0.12156	0.006;0.003;0.007	T	0.34750	-0.9816	10	0.62326	D	0.03	.	4.0926	0.09976	0.4988:0.1815:0.3197:0.0	.	506;506;522	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	A	506;522	ENSP00000365255:V506A;ENSP00000405112:V522A	ENSP00000365255:V506A	V	-	2	0	ANKRD26	27389327	0.106000	0.21978	0.052000	0.19188	0.846000	0.48090	1.273000	0.33121	-0.148000	0.11234	0.260000	0.18958	GTT	.	.		0.284	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			G	27349321	A	G	27349321	3	3	43	1	0	0	0	0	1	0	0	0	654	43	2	2	3695	2	ANKRD26	10	27349321	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	906530	27349321	108185426	193	5275										
KIAA1462	57608	hgsc.bcm.edu	37	chr10	30317392	30317392	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcttggtccgagtcccagttTggaactttttgagcttggtt	11	8	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:30317392T>C	ENST00000375377.1	-	3	1786	c.1685A>G	c.(1684-1686)cAa>cGa	p.Q562R		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	562					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						AGTCCCAGTTTGGAACTTTTT	0.463																																					p.Q562R		Atlas-SNP	.											.	KIAA1462	162	.	0			c.A1685G						.						99	100	100					10																	30317392		1873	4111	5984	SO:0001583	missense	57608	exon3			CCAGTTTGGAACT	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"junctional protein associated with coronary artery disease"	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.1685A>G	chr10.hg19:g.30317392T>C	ENSP00000364526:p.Gln562Arg	24.0	0.0		40.0	4.0	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	hg19	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	T	13.65	2.301727	0.40694	.	.	ENSG00000165757	ENST00000375377	T	0.11821	2.74	5.62	5.62	0.85841	.	0.161766	0.51477	D	0.000081	T	0.12008	0.0292	N	0.22421	0.69	0.30408	N	0.779399	B	0.19817	0.039	B	0.18871	0.023	T	0.05500	-1.0881	10	0.72032	D	0.01	-21.2059	15.806	0.78513	0.0:0.0:0.0:1.0	.	562	Q9P266	K1462_HUMAN	R	562	ENSP00000364526:Q562R	ENSP00000364526:Q562R	Q	-	2	0	KIAA1462	30357398	1.000000	0.71417	0.956000	0.39512	0.166000	0.22503	4.534000	0.60622	2.142000	0.66516	0.459000	0.35465	CAA	.	.		0.463	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		C	30317392	T	C	30317392	3	2	43	1	0	0	0	0	1	0	0	0	8243	1812	63	2	2402	2	KIAA1462	10	30317392	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2968071	30317392	105217355	194	5276										
EPC1	80314	hgsc.bcm.edu	37	chr10	32576101	32576101	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcattgaagactggcagtgcAgcaggactcgtctgttgggg	16	8	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:32576101A>G	ENST00000263062.8	-	7	1346	c.1077T>C	c.(1075-1077)gcT>gcC	p.A359A	EPC1_ENST00000319778.6_Silent_p.A359A|EPC1_ENST00000375110.2_Silent_p.A309A	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	359					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				CTGGCAGTGCAGCAGGACTCG	0.458																																					p.A359A		Atlas-SNP	.											.	EPC1	74	.	0			c.T1077C						.						153	135	141					10																	32576101		2203	4300	6503	SO:0001819	synonymous_variant	80314	exon7			CAGTGCAGCAGGA	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.1077T>C	chr10.hg19:g.32576101A>G		48.0	0.0		71.0	4.0	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Silent	SNP	ENST00000263062.8	hg19	CCDS7172.1																																																																																			.	.		0.458	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			G	32576101	A	G	32576101	2	3	43	1	0	0	0	0	0	0	0	1	5162	175	7	2		2	EPC1	10	32576101	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	2258709	32576101	102958646	195	5277										
ANK3	288	hgsc.bcm.edu	37	chr10	61874003	61874003	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccagaatgaatggggcttgaAacaagattgacattgtctaa	10	6	1	5			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:61874003A>G	ENST00000280772.2	-	26	3119	c.2928T>C	c.(2926-2928)gtT>gtC	p.V976V	ANK3_ENST00000355288.2_Silent_p.V110V|ANK3_ENST00000373827.2_Silent_p.V970V|ANK3_ENST00000503366.1_Silent_p.V977V	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	976					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TGGGGCTTGAAACAAGATTGA	0.343																																					p.V977V		Atlas-SNP	.											ANK3_ENST00000395293,NS,carcinoma,0,3	ANK3	703	.	0			c.T2931C						.						85	78	80					10																	61874003		2203	4300	6503	SO:0001819	synonymous_variant	288	exon27			GCTTGAAACAAGA	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.2928T>C	chr10.hg19:g.61874003A>G		45.0	0.0		44.0	2.0	NM_001204404	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.305170	0.23736	.	.	ENSG00000151150	ENST00000467420	.	.	.	5.48	1.44	0.22558	.	.	.	.	.	T	0.43700	0.1259	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19549	-1.0302	4	.	.	.	.	2.7304	0.05225	0.2278:0.1239:0.5211:0.1272	.	.	.	.	S	1	.	.	F	-	2	0	ANK3	61544009	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	0.690000	0.25451	-0.006000	0.14370	-0.242000	0.12053	TTT	.	.		0.343	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		G	61874003	A	G	61874003	2	3	43	1	0	0	0	0	0	0	0	1	622	1	1	2		2	ANK3	10	61874003	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	29297902	61874003	73660744	196	5278										
MYPN	84665	hgsc.bcm.edu	37	chr10	69918260	69918260	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tagatgctacaaaatttgtcAgcttctgagggtcagctggt	11	7	3	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:69918260A>G	ENST00000358913.5	+	7	1823	c.1335A>G	c.(1333-1335)tcA>tcG	p.S445S	MYPN_ENST00000354393.2_Silent_p.S170S|MYPN_ENST00000373675.3_Silent_p.S445S|RN7SKP202_ENST00000410439.1_RNA|MYPN_ENST00000540630.1_Silent_p.S445S	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	445	Ig-like 2.|Interaction with CARP.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						AAAATTTGTCAGCTTCTGAGG	0.348																																					p.S445S		Atlas-SNP	.											.	MYPN	189	.	0			c.A1335G						.						91	90	91					10																	69918260		2203	4300	6503	SO:0001819	synonymous_variant	84665	exon7			TTTGTCAGCTTCT	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1335A>G	chr10.hg19:g.69918260A>G		61.0	0.0		89.0	4.0	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	hg19	CCDS7275.1																																																																																			.	.		0.348	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		G	69918260	A	G	69918260	2	3	43	1	0	0	0	0	0	0	0	1	10107	175	7	2		2	MYPN	10	69918260	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	8044257	69918260	65616487	197	5279										
TTC18	118491	hgsc.bcm.edu	37	chr10	75058853	75058853	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gatctgtatgtggtagtcacTcactgcctaagaaaatacaa	8	8	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:75058853T>C	ENST00000310715.3	-	15	1654	c.1534A>G	c.(1534-1536)Agt>Ggt	p.S512G	TTC18_ENST00000355577.3_5'UTR|snoU13_ENST00000459292.1_RNA|TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000394865.1_Missense_Mutation_p.S512G|TTC18_ENST00000401621.2_Missense_Mutation_p.S512G|TTC18_ENST00000340329.3_Intron	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		512						extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					TGGTAGTCACTCACTGCCTAA	0.393																																					p.S512G		Atlas-SNP	.											.	TTC18	106	.	0			c.A1534G						.						82	77	79					10																	75058853		2203	4300	6503	SO:0001583	missense	118491	exon15			AGTCACTCACTGC																												ENST00000310715.3:c.1534A>G	chr10.hg19:g.75058853T>C	ENSP00000310829:p.Ser512Gly	55.0	0.0		85.0	4.0	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	hg19	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	T	12.05	1.821197	0.32237	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000372928;ENST00000394865	D;D;D	0.94457	-3.43;-3.43;-3.43	5.35	4.0	0.46444	.	0.628928	0.16871	N	0.196120	D	0.91202	0.7228	L	0.44542	1.39	0.23632	N	0.997248	B;B	0.24368	0.082;0.102	B;B	0.29942	0.109;0.047	D	0.84685	0.0719	10	0.49607	T	0.09	-14.3771	9.4665	0.38816	0.0:0.0983:0.0:0.9017	.	512;512	Q5T0N1-2;Q5T0N1	.;TTC18_HUMAN	G	512	ENSP00000310829:S512G;ENSP00000384479:S512G;ENSP00000378334:S512G	ENSP00000310829:S512G	S	-	1	0	TTC18	74728859	1.000000	0.71417	0.997000	0.53966	0.941000	0.58515	1.341000	0.33907	2.022000	0.59522	0.455000	0.32223	AGT	.	.		0.393	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	75058853	T	C	75058853	3	2	43	1	0	0	0	0	1	0	0	0	16700	1551	54	2	1887	2	TTC18	10	75058853	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5140593	75058853	60475894	198	5280										
RGR	5995	hgsc.bcm.edu	37	chr10	86018358	86018358	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caggggaatctggcagtgccTctcaccgcagaagagggaga	15	10	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:86018358T>C	ENST00000359452.4	+	7	889	c.851T>C	c.(850-852)cTc>cCc	p.L284P	RGR_ENST00000358110.5_Missense_Mutation_p.L242P|RGR_ENST00000479725.1_3'UTR	NM_001012720.1|NM_002921.3	NP_001012738.1|NP_002912.2	P47804	RGR_HUMAN	retinal G protein coupled receptor	280					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	17						TGGCAGTGCCTCTCACCGCAG	0.607																																					p.L284P	NSCLC(15;204 545 5889 6385 32445)	Atlas-SNP	.											.	RGR	42	.	0			c.T851C						.						87	74	78					10																	86018358		2203	4300	6503	SO:0001583	missense	5995	exon7			AGTGCCTCTCACC	BC011349	CCDS7374.1, CCDS41543.1	10q23	2013-02-14			ENSG00000148604	ENSG00000148604		"GPCR / Class A : Opsin receptors"	9990	protein-coding gene	gene with protein product	"RGR-opsin"	600342				8641686	Standard	NM_002921		Approved	RP44	uc001kdd.1	P47804	OTTHUMG00000018636	ENST00000359452.4:c.851T>C	chr10.hg19:g.86018358T>C	ENSP00000352427:p.Leu284Pro	65.0	0.0		117.0	5.0	NM_002921	A6NKK7|Q96FC5	Missense_Mutation	SNP	ENST00000359452.4	hg19	CCDS7374.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.703835	0.88924	.	.	ENSG00000148604	ENST00000359452;ENST00000358110	T;T	0.51325	0.71;0.71	4.95	3.78	0.43462	.	0.143549	0.48286	D	0.000190	T	0.64283	0.2584	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.972	D;D;P	0.73380	0.969;0.98;0.786	T	0.66344	-0.5947	10	0.87932	D	0	.	10.3927	0.44181	0.0:0.0:0.164:0.8359	.	242;284;280	P47804-3;P47804-2;P47804	.;.;RGR_HUMAN	P	284;242	ENSP00000352427:L284P;ENSP00000350823:L242P	ENSP00000350823:L242P	L	+	2	0	RGR	86008338	1.000000	0.71417	0.007000	0.13788	0.730000	0.41778	5.271000	0.65553	0.939000	0.37446	0.533000	0.62120	CTC	.	.		0.607	RGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049116.1	NM_002921		C	86018358	T	C	86018358	3	2	43	1	0	0	0	0	1	0	0	0	13306	1551	54	2	877	2	RGR	10	86018358	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	10959505	86018358	49516389	199	5281										
PTEN	5728	hgsc.bcm.edu	37	chr10	89653817	89653817	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttattgctatgggatttcctGcagaaagacttgaaggcgta	11	6	0	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:89653817G>A	ENST00000371953.3	+	2	1472	c.115G>A	c.(115-117)Gca>Aca	p.A39T		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	39	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(8)|p.Y27fs*1(2)|p.A39T(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GGGATTTCCTGCAGAAAGACT	0.289		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.A39T		Atlas-SNP	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,colon,carcinoma,-2,1	PTEN	3652	.	48	Whole gene deletion(37)|Unknown(8)|Deletion - Frameshift(2)|Substitution - Missense(1)	prostate(14)|central_nervous_system(9)|skin(8)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|ovary(3)|breast(2)|soft_tissue(1)|urinary_tract(1)|NS(1)|kidney(1)	c.G115A	GRCh37	CM083057	PTEN	M		.						111	111	111					10																	89653817		2203	4296	6499	SO:0001583	missense	5728	exon2	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	TTTCCTGCAGAAA	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.115G>A	chr10.hg19:g.89653817G>A	ENSP00000361021:p.Ala39Thr	66.0	1.0		88.0	4.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	35	5.510400	0.96386	.	.	ENSG00000171862	ENST00000371953	D	0.98567	-5.0	5.19	5.19	0.71726	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.98883	0.9622	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99624	1.0984	9	.	.	.	-9.7723	17.4682	0.87639	0.0:0.0:1.0:0.0	.	39	P60484	PTEN_HUMAN	T	39	ENSP00000361021:A39T	.	A	+	1	0	PTEN	89643797	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.022000	0.93678	2.421000	0.82119	0.655000	0.94253	GCA	.	.		0.289	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89653817	G	A	89653817	3	1	43	1	0	0	0	0	1	0	0	0	12750	1319	46	3	121	3	PTEN	10	89653817	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	3635459	89653817	45880930	200	5282										
MARCH5	54708	hgsc.bcm.edu	37	chr10	94109142	94109142	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aaggtctggatgttatggagAgagctgatcctttattcctt	11	6	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:94109142A>G	ENST00000358935.2	+	4	738	c.406A>G	c.(406-408)Aga>Gga	p.R136G	MARCH5_ENST00000467521.2_3'UTR	NM_017824.4	NP_060294.1	Q9NX47	MARH5_HUMAN	membrane-associated ring finger (C3HC4) 5	136					negative regulation of cell aging (GO:0090344)|positive regulation of mitochondrial fission (GO:0090141)|protein autoubiquitination (GO:0051865)|protein localization to mitochondrion (GO:0070585)|protein polyubiquitination (GO:0000209)|regulation of mitochondrial fission (GO:0090140)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	GTPase binding (GO:0051020)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						TGTTATGGAGAGAGCTGATCC	0.383																																					p.R136G		Atlas-SNP	.											.	MARCH5	28	.	0			c.A406G						.						167	159	162					10																	94109142		2203	4300	6503	SO:0001583	missense	54708	exon4			ATGGAGAGAGCTG	BC015480	CCDS7420.1	10q23.32-q23.33	2013-01-09	2005-01-26	2005-01-27	ENSG00000198060	ENSG00000198060		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	26025	protein-coding gene	gene with protein product		610637	"ring finger protein 153"	RNF153		14722266	Standard	XM_005269923		Approved	FLJ20445, MARCH-V	uc001khx.1	Q9NX47	OTTHUMG00000018757	ENST00000358935.2:c.406A>G	chr10.hg19:g.94109142A>G	ENSP00000351813:p.Arg136Gly	87.0	0.0		97.0	4.0	NM_017824		Missense_Mutation	SNP	ENST00000358935.2	hg19	CCDS7420.1	.	.	.	.	.	.	.	.	.	.	A	14.45	2.538717	0.45176	.	.	ENSG00000198060	ENST00000358935	T	0.46063	0.88	5.93	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.36441	0.0967	L	0.47716	1.5	0.58432	D	0.999995	B	0.09022	0.002	B	0.10450	0.005	T	0.09930	-1.0652	10	0.34782	T	0.22	-13.2259	11.9167	0.52769	0.7128:0.2872:0.0:0.0	.	136	Q9NX47	MARH5_HUMAN	G	136	ENSP00000351813:R136G	ENSP00000351813:R136G	R	+	1	2	MARCH5	94099122	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.841000	0.55850	1.053000	0.40415	0.482000	0.46254	AGA	.	.		0.383	MARCH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049388.1	NM_017824		G	94109142	A	G	94109142	3	3	43	1	0	0	0	0	1	0	0	0	9313	296	11	2	420	2	MARCH5	10	94109142	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	4455325	94109142	41425605	201	5283										
SMC3	9126	hgsc.bcm.edu	37	chr10	112338437	112338437	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gctggtttttctcgaagcaaTccttattatattgttaaaca	6	7	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:112338437T>C	ENST00000361804.4	+	7	528	c.402T>C	c.(400-402)aaT>aaC	p.N134N	SMC3_ENST00000462899.1_3'UTR|snoU13_ENST00000458966.1_RNA	NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	134					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		CTCGAAGCAATCCTTATTATA	0.303																																					p.N134N		Atlas-SNP	.											.	SMC3	103	.	0			c.T402C						.						95	91	92					10																	112338437		2203	4300	6503	SO:0001819	synonymous_variant	9126	exon7			AAGCAATCCTTAT	AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.402T>C	chr10.hg19:g.112338437T>C		51.0	0.0		55.0	4.0	NM_005445	A8K156|O60464|Q5T482	Silent	SNP	ENST00000361804.4	hg19	CCDS31285.1																																																																																			.	.		0.303	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		C	112338437	T	C	112338437	2	2	43	1	0	0	0	0	0	0	0	1	14799	1432	50	2		2	SMC3	10	112338437	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	18229295	112338437	23196310	202	5284										
FAM160B1	57700	hgsc.bcm.edu	37	chr10	116605202	116605202	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	taatttcatttctttcctggTttgattattgtgatcagctc	6	7	3	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:116605202T>C	ENST00000369248.4	+	8	1425	c.1090T>C	c.(1090-1092)Ttt>Ctt	p.F364L	FAM160B1_ENST00000369250.3_Missense_Mutation_p.F364L	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	364										NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						TCTTTCCTGGTTTGATTATTG	0.308																																					p.F364L		Atlas-SNP	.											.	FAM160B1	107	.	0			c.T1090C						.						114	106	109					10																	116605202		2203	4300	6503	SO:0001583	missense	57700	exon8			TCCTGGTTTGATT	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"KIAA1600"	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.1090T>C	chr10.hg19:g.116605202T>C	ENSP00000358251:p.Phe364Leu	78.0	0.0		80.0	4.0	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Missense_Mutation	SNP	ENST00000369248.4	hg19	CCDS31290.1	.	.	.	.	.	.	.	.	.	.	T	11.44	1.638410	0.29157	.	.	ENSG00000151553	ENST00000369248;ENST00000369250	T;T	0.19669	2.13;2.13	5.43	5.43	0.79202	.	0.049336	0.85682	D	0.000000	T	0.09247	0.0228	N	0.03253	-0.375	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.15052	0.012;0.003	T	0.11991	-1.0565	10	0.02654	T	1	-29.9027	15.7673	0.78138	0.0:0.0:0.0:1.0	.	364;364	Q5W0V3-2;Q5W0V3	.;F16B1_HUMAN	L	364	ENSP00000358251:F364L;ENSP00000358253:F364L	ENSP00000358251:F364L	F	+	1	0	FAM160B1	116595192	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.768000	0.62293	2.186000	0.69663	0.450000	0.29827	TTT	.	.		0.308	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351		C	116605202	T	C	116605202	3	2	43	1	0	0	0	0	1	0	0	0	5475	1725	60	2	1120	2	FAM160B1	10	116605202	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	4266765	116605202	18929545	203	5285										
HMX2	3167	hgsc.bcm.edu	37	chr10	124909334	124909334	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccaccttcgacatgaagcgcTacctgagcagctcggagcgc	11	15	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:124909334T>C	ENST00000339992.3	+	2	774	c.517T>C	c.(517-519)Tac>Cac	p.Y173H		NM_005519.1	NP_005510.1	A2RU54	HMX2_HUMAN	H6 family homeobox 2	173					brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|lung(4)|prostate(1)	7		all_neural(114;0.169)|Colorectal(57;0.207)|Glioma(114;0.222)		Colorectal(40;0.123)|COAD - Colon adenocarcinoma(40;0.141)		CATGAAGCGCTACCTGAGCAG	0.652																																					p.Y173H		Atlas-SNP	.											.	HMX2	21	.	0			c.T517C						.						19	20	20					10																	124909334		2188	4261	6449	SO:0001583	missense	3167	exon2			AAGCGCTACCTGA		CCDS31305.1	10q26.13	2011-06-20	2007-07-09		ENSG00000188816	ENSG00000188816		"Homeoboxes / ANTP class : NKL subclass"	5018	protein-coding gene	gene with protein product		600647	"homeo box (H6 family) 2"			7647458	Standard	XM_005269743		Approved	NKX5-2	uc001lhc.1	A2RU54	OTTHUMG00000019198	ENST00000339992.3:c.517T>C	chr10.hg19:g.124909334T>C	ENSP00000341108:p.Tyr173His	66.0	0.0		82.0	37.0	NM_005519	B2RNV5	Missense_Mutation	SNP	ENST00000339992.3	hg19	CCDS31305.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.722846	0.89298	.	.	ENSG00000188816	ENST00000339992	D	0.97328	-4.34	5.3	5.3	0.74995	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98645	0.9546	M	0.90252	3.1	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.99787	1.1030	10	0.87932	D	0	.	15.4082	0.74897	0.0:0.0:0.0:1.0	.	173	A2RU54	HMX2_HUMAN	H	173	ENSP00000341108:Y173H	ENSP00000341108:Y173H	Y	+	1	0	HMX2	124899324	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.780000	0.85658	2.212000	0.71576	0.533000	0.62120	TAC	.	.		0.652	HMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050841.1	XM_370580		C	124909334	T	C	124909334	3	2	43	1	0	0	0	0	1	0	0	0	7256	1522	53	2	523	2	HMX2	10	124909334	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	8304132	124909334	10625413	204	5286										
INPP5A	3632	hgsc.bcm.edu	37	chr10	134523851	134523851	+	Frame_Shift_Del	DEL	T	T	-													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttggttgcagtgcctttgacTtggtgaatatccatcttttc							TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr10:134523851delT	ENST00000368594.3	+	8	815	c.538delT	c.(538-540)ttgfs	p.L180fs	INPP5A_ENST00000368593.3_Frame_Shift_Del_p.L180fs|INPP5A_ENST00000487614.1_3'UTR	NM_005539.3	NP_005530.3	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase, 40kDa	180					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|PH domain binding (GO:0042731)			cervix(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		TGCCTTTGACTTGGTGAATAT	0.542																																					p.D179fs	Pancreas(63;823 1267 11107 20380 51626)	Atlas-Indel,Pindel	.											.	INPP5A	77	.	0			c.537delC						.						97	77	84					10																	134523851		2203	4300	6503	SO:0001589	frameshift_variant	3632	exon8			.	X77567	CCDS7669.2	10q26.3	2008-08-07	2002-08-29		ENSG00000068383	ENSG00000068383	3.1.3.56		6076	protein-coding gene	gene with protein product	"CTCL tumor antigen HD-CL-02", "43 kDa inositol polyphosphate 5-phophatase", "inositol polyphosphate 5-phophatase, 40kDa", "InsP3 5-phosphatase", "type I inositol-1,4,5-trisphosphate 5-phosphatase"	600106	"inositol polyphosphate-5-phosphatase, 40kD"			8013665	Standard	NM_005539		Approved	5PTASE	uc001llp.3	Q14642	OTTHUMG00000019293	ENST00000368594.3:c.538delT	chr10.hg19:g.134523851delT	ENSP00000357583:p.Leu180fs	99.0	0.0		137.0	55.0	NM_005539	D3DXI3|Q14640|Q5JSF1	Frame_Shift_Del	DEL	ENST00000368594.3	hg19	CCDS7669.2																																																																																			.	.		0.542	INPP5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051085.1	NM_005539		-	134523851	T	-	134523851	7	5	43	1	0	1	0	1	0	0	0	0	7763	1606	56	0	568	0	INPP5A	10	134523851	Frame_Shift_Del	DEL	T	TCGA-BC-A3KF-01A-11D-A20W-10	9614517	134523851	1010896	205	5287										
AP2A2	161	hgsc.bcm.edu	37	chr11	992671	992671	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acgtgcagggctacgcggccAagactgtgttcgaggtatgg	16	9	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:992671A>T	ENST00000448903.2	+	11	1579	c.1438A>T	c.(1438-1440)Aag>Tag	p.K480*	AP2A2_ENST00000534328.1_Intron|AP2A2_ENST00000332231.5_Nonsense_Mutation_p.K481*	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	480					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		CTACGCGGCCAAGACTGTGTT	0.577																																					p.K481X		Atlas-SNP	.											.	AP2A2	50	.	0			c.A1441T						.						94	92	93					11																	992671		2173	4253	6426	SO:0001587	stop_gained	161	exon11			GCGGCCAAGACTG	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.1438A>T	chr11.hg19:g.992671A>T	ENSP00000413234:p.Lys480*	118.0	0.0		155.0	65.0	NM_001242837	O75403|Q53ET1|Q96SI8	Nonsense_Mutation	SNP	ENST00000448903.2	hg19	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	A	38	7.273358	0.98179	.	.	ENSG00000183020	ENST00000448903;ENST00000332231;ENST00000448757;ENST00000529125;ENST00000452310	.	.	.	3.5	3.5	0.40072	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.4067	12.7311	0.57199	1.0:0.0:0.0:0.0	.	.	.	.	X	480;481;481;217;220	.	ENSP00000327694:K481X	K	+	1	0	AP2A2	982671	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	9.190000	0.94934	1.560000	0.49568	0.379000	0.24179	AAG	.	.		0.577	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		T	992671	A	T	992671	4	4	43	1	0	0	0	0	0	1	0	0	740	131	5	4	1480	4	AP2A2	11	992671	Nonsense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10		992671	134013845	206	5288										
OR51I2	390064	hgsc.bcm.edu	37	chr11	5475431	5475431	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgaggaacgcctcaaagctcTcaacacatgtgtgtcacata	8	11	3	1	rs199654892|rs35301588	byFrequency	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:5475431T>A	ENST00000341449.2	+	1	794	c.713T>A	c.(712-714)cTc>cAc	p.L238H	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	238					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTCAAAGCTCTCAACACATGT	0.498																																					p.L238H		Atlas-SNP	.											.	OR51I2	76	.	0			c.T713A						.						282	237	252					11																	5475431		2201	4297	6498	SO:0001583	missense	390064	exon1			AAGCTCTCAACAC	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"GPCR / Class A : Olfactory receptors"	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.713T>A	chr11.hg19:g.5475431T>A	ENSP00000341987:p.Leu238His	206.0	0.0		230.0	14.0	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	hg19	CCDS31383.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.594810	0.46318	.	.	ENSG00000187918	ENST00000341449	T	0.00207	8.55	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.110868	0.40908	D	0.000997	T	0.00875	0.0029	H	0.95574	3.69	0.31649	N	0.647016	D	0.76494	0.999	D	0.66847	0.947	T	0.03325	-1.1048	10	0.87932	D	0	.	14.7227	0.69320	0.0:0.0:0.0:1.0	.	238	Q9H344	O51I2_HUMAN	H	238	ENSP00000341987:L238H	ENSP00000341987:L238H	L	+	2	0	OR51I2	5432007	0.880000	0.30214	1.000000	0.80357	0.415000	0.31203	5.792000	0.69052	2.343000	0.79666	0.533000	0.62120	CTC	.	.		0.498	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754		A	5475431	T	A	5475431	3	1	43	1	0	0	0	0	1	0	0	0	11110	1551	54	4	715	4	OR51I2	11	5475431	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	4482760	5475431	129531085	207	5289										
LDHA	3939	hgsc.bcm.edu	37	chr11	18425285	18425285	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttgctggtgtctctctgaagActctgcacccagatttaggg	11	10	3	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:18425285A>G	ENST00000422447.3	+	6	910	c.637A>G	c.(637-639)Act>Gct	p.T213A	LDHA_ENST00000227157.4_Missense_Mutation_p.T213A|LDHA_ENST00000540430.1_Missense_Mutation_p.T242A|LDHA_ENST00000430553.2_Missense_Mutation_p.T155A|AC084117.3_ENST00000496975.2_RNA|LDHA_ENST00000542179.1_Missense_Mutation_p.T213A|LDHA_ENST00000379412.5_Missense_Mutation_p.T213A|LDHA_ENST00000396222.2_Missense_Mutation_p.T213A	NM_001135239.1|NM_005566.3	NP_001128711.1|NP_005557.1	P00338	LDHA_HUMAN	lactate dehydrogenase A	213					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|cellular response to extracellular stimulus (GO:0031668)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	L-lactate dehydrogenase activity (GO:0004459)			central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(4)	12						CTCTCTGAAGACTCTGCACCC	0.388																																					p.T242A		Atlas-SNP	.											.	LDHA	118	.	0			c.A724G						.						147	141	143					11																	18425285		2199	4293	6492	SO:0001583	missense	3939	exon6			CTGAAGACTCTGC	X02152	CCDS7839.1, CCDS44549.1, CCDS53609.1, CCDS53610.1, CCDS53611.1	11p15.1	2012-10-02			ENSG00000134333	ENSG00000134333	1.1.1.27		6535	protein-coding gene	gene with protein product		150000				3000353	Standard	NM_005566		Approved		uc010rdd.2	P00338	OTTHUMG00000167721	ENST00000422447.3:c.637A>G	chr11.hg19:g.18425285A>G	ENSP00000395337:p.Thr213Ala	64.0	0.0		68.0	5.0	NM_001165414	B4DKQ2|B7Z5E3|D3DQY3|F8W819|Q53G53|Q6IBM7|Q6ZNV1|Q9UDE8|Q9UDE9	Missense_Mutation	SNP	ENST00000422447.3	hg19	CCDS7839.1	.	.	.	.	.	.	.	.	.	.	A	10.22	1.289613	0.23478	.	.	ENSG00000134333	ENST00000422447;ENST00000430553;ENST00000396222;ENST00000541620;ENST00000445376;ENST00000227157;ENST00000540430;ENST00000379412;ENST00000542179	T;T;T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01;0.01;0.01	5.34	2.93	0.34026	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.646731	0.16302	N	0.220393	T	0.39489	0.1080	N	0.25144	0.715	0.20926	N	0.999825	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.001;0.002;0.002;0.0;0.0	T	0.18053	-1.0349	10	0.29301	T	0.29	-0.0884	0.9978	0.01470	0.4256:0.1542:0.1021:0.318	.	242;155;186;213;213	B7Z5E3;B4DKQ2;B4DJI1;F8W819;P00338	.;.;.;.;LDHA_HUMAN	A	213;155;213;185;186;213;242;213;213	ENSP00000395337:T213A;ENSP00000406172:T155A;ENSP00000379524:T213A;ENSP00000227157:T213A;ENSP00000445175:T242A;ENSP00000368722:T213A;ENSP00000445331:T213A	ENSP00000227157:T213A	T	+	1	0	LDHA	18381861	0.508000	0.26154	0.998000	0.56505	0.986000	0.74619	1.005000	0.29834	0.371000	0.24564	0.477000	0.44152	ACT	.	.		0.388	LDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258172.2	NM_005566		G	18425285	A	G	18425285	3	3	43	1	0	0	0	0	1	0	0	0	8707	275	10	2	746	2	LDHA	11	18425285	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	12949854	18425285	116581231	208	5290										
SYT13	57586	hgsc.bcm.edu	37	chr11	45307751	45307751	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcgcgatcacaggcaccgacAgcaccatggtgcccgctccc	11	18	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:45307751A>G	ENST00000020926.3	-	1	119	c.8T>C	c.(7-9)cTg>cCg	p.L3P		NM_001247987.1|NM_020826.2	NP_001234916.1|NP_065877.1	Q7L8C5	SYT13_HUMAN	synaptotagmin XIII	3					vesicle-mediated transport (GO:0016192)	integral component of plasma membrane (GO:0005887)|transport vesicle (GO:0030133)				breast(1)|large_intestine(3)|lung(16)|ovary(1)|skin(2)	23						AGGCACCGACAGCACCATGGT	0.741																																					p.L3P		Atlas-SNP	.											.	SYT13	45	.	0			c.T8C						.						9	8	8					11																	45307751		2156	4212	6368	SO:0001583	missense	57586	exon1			ACCGACAGCACCA	AB037848	CCDS31470.1	11p12-p11	2013-01-21			ENSG00000019505	ENSG00000019505		"Synaptotagmins"	14962	protein-coding gene	gene with protein product		607716				11171101	Standard	NM_020826		Approved	KIAA1427	uc001myq.2	Q7L8C5	OTTHUMG00000166504	ENST00000020926.3:c.8T>C	chr11.hg19:g.45307751A>G	ENSP00000020926:p.Leu3Pro	24.0	0.0		61.0	4.0	NM_020826	A8K4P4|D3DQP1|Q9BQS3|Q9H041|Q9P2C0	Missense_Mutation	SNP	ENST00000020926.3	hg19	CCDS31470.1	.	.	.	.	.	.	.	.	.	.	A	19.26	3.792786	0.70452	.	.	ENSG00000019505	ENST00000020926	T	0.11169	2.8	3.75	3.75	0.43078	.	0.000000	0.41605	U	0.000855	T	0.15652	0.0377	N	0.14661	0.345	0.58432	D	0.999997	D	0.71674	0.998	D	0.79784	0.993	T	0.05649	-1.0872	10	0.87932	D	0	.	9.9836	0.41828	1.0:0.0:0.0:0.0	.	3	Q7L8C5	SYT13_HUMAN	P	3	ENSP00000020926:L3P	ENSP00000020926:L3P	L	-	2	0	SYT13	45264327	0.968000	0.33430	0.999000	0.59377	0.853000	0.48598	2.281000	0.43452	1.333000	0.45449	0.254000	0.18369	CTG	.	.		0.741	SYT13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390110.1	NM_020826		G	45307751	A	G	45307751	3	3	43	1	0	0	0	0	1	0	0	0	15484	188	7	2	1296	2	SYT13	11	45307751	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	26882466	45307751	89698765	209	5291										
CKAP5	9793	hgsc.bcm.edu	37	chr11	46819406	46819406	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aagctctttggcagggtagaAgcagtgcagtggcggaaact	15	7	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:46819406A>G	ENST00000529230.1	-	11	1333	c.1287T>C	c.(1285-1287)gcT>gcC	p.A429A	CKAP5_ENST00000415402.1_Silent_p.A429A|CKAP5_ENST00000312055.5_Silent_p.A429A|CKAP5_ENST00000354558.3_Silent_p.A429A|CKAP5_ENST00000532321.1_5'UTR			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	429					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						GCAGGGTAGAAGCAGTGCAGT	0.413																																					p.A429A	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.T1287C						.						155	154	155					11																	46819406		2201	4299	6500	SO:0001819	synonymous_variant	9793	exon11			GGTAGAAGCAGTG		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.1287T>C	chr11.hg19:g.46819406A>G		69.0	0.0		100.0	4.0	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Silent	SNP	ENST00000529230.1	hg19	CCDS31477.1																																																																																			.	.		0.413	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		G	46819406	A	G	46819406	2	3	43	1	0	0	0	0	0	0	0	1	3447	59	3	2		2	CKAP5	11	46819406	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1511655	46819406	88187110	210	5292										
FNBP4	23360	hgsc.bcm.edu	37	chr11	47788670	47788670	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcggcagtcaccgcggtggtGgtggtcgtcgccgccgacgg	19	13	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:47788670G>C	ENST00000263773.5	-	1	183	c.171C>G	c.(169-171)acC>acG	p.T57T	FNBP4_ENST00000534003.1_5'UTR	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	57						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						CCGCGGTGGTGGTGGTCGTCG	0.751																																					p.T57T		Atlas-SNP	.											.	FNBP4	99	.	0			c.C171G						.																																			SO:0001819	synonymous_variant	23360	exon1			GGTGGTGGTGGTC	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.171C>G	chr11.hg19:g.47788670G>C		0.0	0.0		7.0	5.0	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Silent	SNP	ENST00000263773.5	hg19	CCDS41644.1																																																																																			.	.		0.751	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			C	47788670	G	C	47788670	2	2	43	1	0	0	0	0	0	0	0	1	5975	1335	47	4		4	FNBP4	11	47788670	Silent	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	969264	47788670	87217846	211	5293										
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579735	55579736	+	Missense_Mutation	DNP	GG	GG	TT													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttattgcaggcccagttcaGgcaatagtggagatgctgac							TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:55579735_55579736GG>TT	ENST00000333973.2	+	1	882_883	c.793_794GG>TT	c.(793-795)GGc>TTc	p.G265F		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				GCCCAGTTCAGGCAATAGTGGA	0.485																																					p.G265C|p.G265V		Atlas-SNP	.											.	OR5L1	145	.	0			c.G793T|c.G794T						.																																			SO:0001583	missense	219437	exon1			AGTTCAGGCAATA|GTTCAGGCAATAG	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	Exception_encountered	chr11.hg19:g.55579735_55579736delinsTT	ENSP00000335529:p.Gly265Phe	58.0|60.0	0.0		82.0	34.0	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	hg19	CCDS31509.1																																																																																			.	.		0.485	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		TT	55579736	GG	TT	55579735	3	4	43	1	0	0	0	0	1	0	0	0	11179	1000	35	3	795	3	OR5L1	11	55579735	Missense_Mutation	DNP	GG	TCGA-BC-A3KF-01A-11D-A20W-10	7791065	55579735	79426781	212	5294										
MS4A6A	64231	hgsc.bcm.edu	37	chr11	59947440	59947440	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cacacaagatctggatagtcTgtgggaagagaaagtgagat	13	5	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:59947440T>C	ENST00000530839.1	-	4	640		c.e4-2		MS4A6A_ENST00000532169.1_Splice_Site|MS4A6A_ENST00000529054.1_Splice_Site|MS4A6A_ENST00000529906.1_5'Flank|MS4A6A_ENST00000426738.2_Intron|MS4A6A_ENST00000528851.1_Splice_Site|MS4A6A_ENST00000420732.2_Splice_Site|MS4A6A_ENST00000323961.3_Splice_Site|MS4A6A_ENST00000533023.1_Intron|MS4A6A_ENST00000412309.2_Splice_Site	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A							integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTGGATAGTCTGTGGGAAGAG	0.453																																					.		Atlas-SNP	.											.	MS4A6A	85	.	0			c.148-2A>G						.						86	80	82					11																	59947440		2201	4295	6496	SO:0001630	splice_region_variant	64231	exon4			ATAGTCTGTGGGA	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.148-2A>G	chr11.hg19:g.59947440T>C		88.0	0.0		89.0	4.0	NM_152851	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Splice_Site	SNP	ENST00000530839.1	hg19	CCDS7981.1	.	.	.	.	.	.	.	.	.	.	T	6.404	0.442636	0.12164	.	.	ENSG00000110077	ENST00000323961;ENST00000528851;ENST00000420732;ENST00000530839;ENST00000529054;ENST00000412309;ENST00000532169;ENST00000534596	.	.	.	4.28	4.28	0.50868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0387	0.42144	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MS4A6A	59704016	0.999000	0.42202	0.488000	0.27440	0.261000	0.26267	3.223000	0.51231	1.926000	0.55796	0.529000	0.55759	.	.	.		0.453	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		Intron	C	59947440	T	C	59947440	5	2	43	1	0	0	0	0	0	0	1	0	9873	1594	55	2	647	2	MS4A6A	11	59947440	Splice_Site	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	4367705	59947440	75059076	213	5295										
INCENP	3619	hgsc.bcm.edu	37	chr11	61906200	61906200	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttcagttctgagcagaaggaAccccccgaggaggctgagcc	13	12	2	3	rs150865728|rs34042792		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:61906200A>G	ENST00000394818.3	+	6	1333	c.1131A>G	c.(1129-1131)gaA>gaG	p.E377E	INCENP_ENST00000278849.4_Silent_p.E377E	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	377					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						AGCAGAAGGAACCCCCCGAGG	0.627																																					p.E377E		Atlas-SNP	.											.	INCENP	122	.	0			c.A1131G						.	A	,	1,4403	2.1+/-5.4	0,1,2201	50	54	52		1131,1131	-1.8	0	11	dbSNP_134	52	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	INCENP	NM_001040694.1,NM_020238.2	,	0,1,6500	GG,GA,AA		0.0,0.0227,0.0077	,	377/919,377/915	61906200	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	3619	exon6			GAAGGAACCCCCC	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"inner centromere protein antigens (135kD, 155kD)"			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1131A>G	chr11.hg19:g.61906200A>G		34.0	0.0		40.0	4.0	NM_001040694	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	hg19	CCDS44624.1																																																																																			.	A|1.000;G|0.000		0.627	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		G	61906200	A	G	61906200	2	3	43	1	0	0	0	0	0	0	0	1	7742	40	2	2		2	INCENP	11	61906200	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1958760	61906200	73100316	214	5296										
NUDT22	84304	hgsc.bcm.edu	37	chr11	63994260	63994260	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aggccatcactgccatctggGagacccggctaaaggcccaa	11	14	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:63994260G>A	ENST00000279206.3	+	2	292	c.136G>A	c.(136-138)Gag>Aag	p.E46K	TRPT1_ENST00000540472.1_5'Flank|TRPT1_ENST00000394547.3_5'Flank|RP11-783K16.14_ENST00000534988.1_RNA|TRPT1_ENST00000317459.6_5'Flank|TRPT1_ENST00000546133.1_5'Flank|TRPT1_ENST00000541278.1_5'Flank|TRPT1_ENST00000394546.2_5'Flank|TRPT1_ENST00000546089.1_5'Flank|NUDT22_ENST00000441250.2_Missense_Mutation_p.E46K	NM_001128612.2|NM_032344.2	NP_001122084.1|NP_115720	Q9BRQ3	NUD22_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 22	46							hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8						TGCCATCTGGGAGACCCGGCT	0.692																																					p.E46K		Atlas-SNP	.											.	NUDT22	24	.	0			c.G136A						.						52	52	52					11																	63994260		2201	4297	6498	SO:0001583	missense	84304	exon2			ATCTGGGAGACCC	BC006129	CCDS8061.1, CCDS44640.1	11q13.1	2008-02-05			ENSG00000149761	ENSG00000149761		"Nudix motif containing"	28189	protein-coding gene	gene with protein product						12477932	Standard	NM_032344		Approved	MGC13045	uc009ype.4	Q9BRQ3	OTTHUMG00000167791	ENST00000279206.3:c.136G>A	chr11.hg19:g.63994260G>A	ENSP00000279206:p.Glu46Lys	78.0	0.0		93.0	4.0	NM_001128613	C9JY06|Q71RD5	Missense_Mutation	SNP	ENST00000279206.3	hg19	CCDS8061.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.211742	0.58452	.	.	ENSG00000149761	ENST00000539325;ENST00000279206;ENST00000441250;ENST00000428347;ENST00000536237	T;T;T;T	0.44482	0.92;2.26;2.25;1.5	4.55	4.55	0.56014	.	0.292060	0.38005	N	0.001853	T	0.32852	0.0843	L	0.36672	1.1	0.41193	D	0.986318	B;B;B	0.25955	0.138;0.012;0.034	B;B;B	0.24701	0.055;0.009;0.019	T	0.10132	-1.0643	10	0.29301	T	0.29	-12.6074	13.0094	0.58724	0.0:0.1638:0.8362:0.0	.	46;46;46	Q9BRQ3-2;C9JY06;Q9BRQ3	.;.;NUD22_HUMAN	K	46	ENSP00000444022:E46K;ENSP00000279206:E46K;ENSP00000407970:E46K;ENSP00000401085:E46K	ENSP00000279206:E46K	E	+	1	0	NUDT22	63750836	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.152000	0.42272	2.528000	0.85240	0.491000	0.48974	GAG	.	.		0.692	NUDT22-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396304.2	NM_032344		A	63994260	G	A	63994260	3	1	43	1	0	0	0	0	1	0	0	0	10748	1175	41	3	138	3	NUDT22	11	63994260	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	2088060	63994260	71012256	215	5297										
SART1	9092	hgsc.bcm.edu	37	chr11	65745300	65745300	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cacacaggacttcaaggagaAggacggctacaaacccgacg	11	12	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:65745300A>G	ENST00000312397.5	+	17	2194	c.2102A>G	c.(2101-2103)aAg>aGg	p.K701R		NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells	701					cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TTCAAGGAGAAGGACGGCTAC	0.587																																					p.K701R		Atlas-SNP	.											.	SART1	41	.	0			c.A2102G						.						93	79	83					11																	65745300		2201	4296	6497	SO:0001583	missense	9092	exon17			AGGAGAAGGACGG	AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"	605941	"squamous cell carcinoma antigen recognised by T cells"			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771	ENST00000312397.5:c.2102A>G	chr11.hg19:g.65745300A>G	ENSP00000310448:p.Lys701Arg	72.0	0.0		82.0	4.0	NM_005146	A6NDN1|Q53GB5	Missense_Mutation	SNP	ENST00000312397.5	hg19	CCDS31611.1	.	.	.	.	.	.	.	.	.	.	A	18.71	3.682236	0.68042	.	.	ENSG00000175467	ENST00000312397;ENST00000542816	T	0.27104	1.69	4.96	4.96	0.65561	.	0.123932	0.52532	D	0.000077	T	0.45316	0.1336	L	0.55481	1.735	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.43081	-0.9413	10	0.87932	D	0	-41.6454	12.5837	0.56406	1.0:0.0:0.0:0.0	.	701	O43290	SNUT1_HUMAN	R	701;543	ENSP00000310448:K701R	ENSP00000310448:K701R	K	+	2	0	SART1	65501876	1.000000	0.71417	0.998000	0.56505	0.128000	0.20619	8.686000	0.91250	1.869000	0.54173	0.402000	0.26972	AAG	.	.		0.587	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1			G	65745300	A	G	65745300	3	3	43	1	0	0	0	0	1	0	0	0	13861	72	3	2	2168	2	SART1	11	65745300	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1751040	65745300	69261216	216	5298										
GSTP1	2950	hgsc.bcm.edu	37	chr11	67352159	67352159	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catgcctcccccaacagctaTacgggcagctccccaagttc	7	18	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:67352159T>C	ENST00000398606.3	+	4	397	c.148T>C	c.(148-150)Tac>Cac	p.Y50H	GSTP1_ENST00000398603.1_Missense_Mutation_p.Y50H|GSTP1_ENST00000498765.1_3'UTR	NM_000852.3	NP_000843.1	P09211	GSTP1_HUMAN	glutathione S-transferase pi 1	50	GST N-terminal.				cellular response to lipopolysaccharide (GO:0071222)|central nervous system development (GO:0007417)|common myeloid progenitor cell proliferation (GO:0035726)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biosynthetic process (GO:0009890)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of leukocyte proliferation (GO:0070664)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|nitric oxide storage (GO:0035732)|positive regulation of superoxide anion generation (GO:0032930)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of stress-activated MAPK cascade (GO:0032872)|response to reactive oxygen species (GO:0000302)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|TRAF2-GSTP1 complex (GO:0097057)|vesicle (GO:0031982)	dinitrosyl-iron complex binding (GO:0035731)|glutathione transferase activity (GO:0004364)|JUN kinase binding (GO:0008432)|kinase regulator activity (GO:0019207)|nitric oxide binding (GO:0070026)|S-nitrosoglutathione binding (GO:0035730)			central_nervous_system(1)|cervix(1)|endometrium(4)|lung(2)|ovary(1)	9					Busulfan(DB01008)|Carboplatin(DB00958)|Chlorambucil(DB00291)|Cisplatin(DB00515)|Clomipramine(DB01242)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	CCAACAGCTATACGGGCAGCT	0.642																																					p.Y50H		Atlas-SNP	.											.	GSTP1	21	.	0			c.T148C						.						89	101	97					11																	67352159		2020	4163	6183	SO:0001583	missense	2950	exon4			CAGCTATACGGGC	U12472	CCDS41679.1	11q13.2	2014-09-17	2008-07-18		ENSG00000084207	ENSG00000084207	2.5.1.18	"Glutathione S-transferases / Soluble"	4638	protein-coding gene	gene with protein product		134660		FAEES3, GST3		1885604, 7587384, 19915149	Standard	NM_000852		Approved	GSTP	uc001omf.3	P09211	OTTHUMG00000137430	ENST00000398606.3:c.148T>C	chr11.hg19:g.67352159T>C	ENSP00000381607:p.Tyr50His	92.0	0.0		116.0	48.0	NM_000852	O00460|Q15690|Q5TZY3	Missense_Mutation	SNP	ENST00000398606.3	hg19	CCDS41679.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.659769	0.47572	.	.	ENSG00000084207	ENST00000398606;ENST00000398603	T;T	0.06528	3.29;3.29	5.65	3.22	0.36961	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.440715	0.20425	N	0.092595	T	0.19167	0.0460	M	0.78916	2.43	0.25396	N	0.988486	D	0.55172	0.97	D	0.64237	0.923	T	0.16100	-1.0414	9	0.87932	D	0	-11.2425	6.068	0.19873	0.0:0.0853:0.1624:0.7523	.	50	P09211	GSTP1_HUMAN	H	50	ENSP00000381607:Y50H;ENSP00000381604:Y50H	ENSP00000381604:Y50H	Y	+	1	0	GSTP1	67108735	0.999000	0.42202	0.309000	0.25155	0.033000	0.12548	3.847000	0.55895	0.971000	0.38288	0.529000	0.55759	TAC	.	.		0.642	GSTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268504.1	NM_000852		C	67352159	T	C	67352159	3	2	43	1	0	0	0	0	1	0	0	0	6853	1406	49	2	162	2	GSTP1	11	67352159	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1606859	67352159	67654357	217	5299										
CHKA	1119	hgsc.bcm.edu	37	chr11	67821492	67821492	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcttctggtggaaataggcaTcaaaccttgcttgggcgtag	12	8	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:67821492T>C	ENST00000265689.4	-	12	1363	c.1337A>G	c.(1336-1338)gAt>gGt	p.D446G	CHKA_ENST00000533728.1_5'UTR|RP11-802E16.3_ENST00000534517.1_RNA|RP11-802E16.3_ENST00000526897.1_RNA|RP11-802E16.3_ENST00000529934.1_RNA|CHKA_ENST00000356135.5_Missense_Mutation_p.D428G	NM_001277.2	NP_001268.2	P35790	CHKA_HUMAN	choline kinase alpha	446					CDP-choline pathway (GO:0006657)|choline metabolic process (GO:0019695)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|choline binding (GO:0033265)|choline kinase activity (GO:0004103)|cholinesterase activity (GO:0004104)|drug binding (GO:0008144)|ethanolamine kinase activity (GO:0004305)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	13					Choline(DB00122)	GAAATAGGCATCAAACCTTGC	0.587																																					p.D446G		Atlas-SNP	.											.	CHKA	41	.	0			c.A1337G						.						130	98	109					11																	67821492		2200	4294	6494	SO:0001583	missense	1119	exon12			TAGGCATCAAACC	D10704	CCDS8178.1, CCDS8179.1	11q13.1	2008-02-05	2004-04-19	2004-04-21	ENSG00000110721	ENSG00000110721	2.7.1.32		1937	protein-coding gene	gene with protein product		118491	"choline kinase"	CHK		1618328, 15003397	Standard	NM_001277		Approved	CKI	uc001onj.3	P35790	OTTHUMG00000167424	ENST00000265689.4:c.1337A>G	chr11.hg19:g.67821492T>C	ENSP00000265689:p.Asp446Gly	69.0	0.0		82.0	4.0	NM_001277	Q8NE29	Missense_Mutation	SNP	ENST00000265689.4	hg19	CCDS8178.1	.	.	.	.	.	.	.	.	.	.	T	15.51	2.855347	0.51376	.	.	ENSG00000110721	ENST00000265689;ENST00000356135	T;T	0.58652	0.32;0.32	4.76	4.76	0.60689	Protein kinase-like domain (1);	0.272209	0.34676	N	0.003772	T	0.63498	0.2516	L	0.49126	1.545	0.58432	D	0.999999	P;B	0.34955	0.477;0.419	P;P	0.49752	0.621;0.455	T	0.58358	-0.7650	10	0.19590	T	0.45	-15.1956	14.4096	0.67106	0.0:0.0:0.0:1.0	.	428;446	P35790-2;P35790	.;CHKA_HUMAN	G	446;428	ENSP00000265689:D446G;ENSP00000348454:D428G	ENSP00000265689:D446G	D	-	2	0	CHKA	67578068	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.335000	0.72949	1.993000	0.58246	0.379000	0.24179	GAT	.	.		0.587	CHKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394570.1	NM_001277		C	67821492	T	C	67821492	3	2	43	1	0	0	0	0	1	0	0	0	3349	1435	50	2	40	2	CHKA	11	67821492	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	469333	67821492	67185024	218	5300										
KRTAP5-10	387273	hgsc.bcm.edu	37	chr11	71277087	71277087	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtaagccctgctgctgctccTcaggctgtggatcctgctgc	12	14	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:71277087T>G	ENST00000398531.1	+	1	479	c.454T>G	c.(454-456)Tca>Gca	p.S152A	KRTAP5-10_ENST00000376536.4_Missense_Mutation_p.S104A	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	152	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						ctgctgctcctcaggctgtgg	0.632																																					p.S152A		Atlas-SNP	.											.	KRTAP5-10	37	.	0			c.T454G						.						87	106	99					11																	71277087		2200	4293	6493	SO:0001583	missense	387273	exon1			TGCTCCTCAGGCT	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"Keratin associated proteins"	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.454T>G	chr11.hg19:g.71277087T>G	ENSP00000381542:p.Ser152Ala	157.0	0.0		145.0	51.0	NM_001012710	B9EHA4	Missense_Mutation	SNP	ENST00000398531.1	hg19	CCDS41684.1	.	.	.	.	.	.	.	.	.	.	.	5.031	0.191477	0.09547	.	.	ENSG00000204572	ENST00000398531;ENST00000376536	T;T	0.01133	5.29;5.59	1.13	-0.0925	0.13656	.	.	.	.	.	T	0.01695	0.0054	M	0.69823	2.125	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.40270	-0.9572	9	0.48119	T	0.1	.	4.4099	0.11427	0.0:0.2215:0.0:0.7785	.	152	Q6L8G5	KR510_HUMAN	A	152;104	ENSP00000381542:S152A;ENSP00000365719:S104A	ENSP00000365719:S104A	S	+	1	0	KRTAP5-10	70954735	0.040000	0.19996	0.001000	0.08648	0.067000	0.16453	0.110000	0.15437	-0.020000	0.14032	0.260000	0.18958	TCA	.	.		0.632	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2			G	71277087	T	G	71277087	3	3	43	1	0	0	0	0	1	0	0	0	8568	1551	54	5	456	5	KRTAP5-10	11	71277087	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3455595	71277087	63729429	219	5301										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73020389	73020389	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cctcctgctcctcctcctccAtcgccgcctcctatcctgtc	4	23	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:73020389A>T	ENST00000263674.3	+	1	1056	c.706A>T	c.(706-708)Atc>Ttc	p.I236F	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	236					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CTCCTCCTCCATCGCCGCCTC	0.677																																					p.I236F		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.A706T						.						12	15	14					11																	73020389		2048	3983	6031	SO:0001583	missense	9828	exon1			TCCTCCATCGCCG	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.706A>T	chr11.hg19:g.73020389A>T	ENSP00000263674:p.Ile236Phe	160.0	0.0		226.0	14.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	A	12.21	1.870463	0.33069	.	.	ENSG00000110237	ENST00000263674	T	0.59638	0.25	4.61	0.695	0.18070	.	0.993735	0.08148	N	0.990484	T	0.35480	0.0933	N	0.24115	0.695	0.19775	N	0.999951	P	0.35982	0.531	B	0.24394	0.053	T	0.25117	-1.0141	10	0.54805	T	0.06	-1.1385	5.2264	0.15397	0.6445:0.1573:0.1981:0.0	.	236	Q96PE2	ARHGH_HUMAN	F	236	ENSP00000263674:I236F	ENSP00000263674:I236F	I	+	1	0	ARHGEF17	72698037	0.000000	0.05858	0.765000	0.31456	0.926000	0.56050	-0.104000	0.10923	0.647000	0.30713	0.379000	0.24179	ATC	.	.		0.677	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		T	73020389	A	T	73020389	3	4	43	1	0	0	0	0	1	0	0	0	900	217	8	4	708	4	ARHGEF17	11	73020389	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1743302	73020389	61986127	220	5302										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73785299	73785299	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtaggtgaggagagcataccTttcaagctcaagtgcattgc	12	8	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:73785299T>C	ENST00000334126.7	-	24	5176	c.4950A>G	c.(4948-4950)aaA>aaG	p.K1650K	C2CD3_ENST00000313663.7_Splice_Site_p.K1650K			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1650	C2 2.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					AGAGCATACCTTTCAAGCTCA	0.483																																					p.K1650K		Atlas-SNP	.											.	C2CD3	288	.	0			c.A4950G						.						85	70	75					11																	73785299		2200	4293	6493	SO:0001630	splice_region_variant	26005	exon24			CATACCTTTCAAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.4951+1A>G	chr11.hg19:g.73785299T>C		89.0	0.0		100.0	4.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Silent	SNP	ENST00000334126.7	hg19																																																																																				.	.		0.483	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	Silent	C	73785299	T	C	73785299	5	2	43	1	0	0	0	0	0	0	1	0	2156	1623	56	2	973	2	C2CD3	11	73785299	Splice_Site	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	764910	73785299	61221217	221	5303										
C11orf30	56946	hgsc.bcm.edu	37	chr11	76227256	76227256	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atggctgcaacccctggagcTgcaacctatgtgaaaactac	9	12	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:76227256T>C	ENST00000529032.1	+	10	1584	c.1584T>C	c.(1582-1584)gcT>gcC	p.A528A	C11orf30_ENST00000525919.1_Silent_p.A529A|C11orf30_ENST00000533248.1_Silent_p.A542A|C11orf30_ENST00000334736.3_Silent_p.A528A|C11orf30_ENST00000524767.1_Silent_p.A543A|C11orf30_ENST00000524490.1_Silent_p.A444A|C11orf30_ENST00000525038.1_Silent_p.A543A|C11orf30_ENST00000343878.3_Silent_p.A528A			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	528	Thr-rich.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						CCCCTGGAGCTGCAACCTATG	0.463																																					p.A528A		Atlas-SNP	.											.	C11orf30	123	.	0			c.T1584C						.						119	114	116					11																	76227256		2200	4292	6492	SO:0001819	synonymous_variant	56946	exon11			TGGAGCTGCAACC	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.1584T>C	chr11.hg19:g.76227256T>C		68.0	0.0		95.0	4.0	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Silent	SNP	ENST00000529032.1	hg19	CCDS8244.1																																																																																			.	.		0.463	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193		C	76227256	T	C	76227256	2	2	43	1	0	0	0	0	0	0	0	1	1638	1567	55	2		2	C11orf30	11	76227256	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2441957	76227256	58779260	222	5304										
PAK1	5058	hgsc.bcm.edu	37	chr11	77090324	77090324	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tctggctgttggatgtcttcTtcgagttgtaaaactccaac	9	9	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:77090324T>C	ENST00000356341.3	-	4	932	c.401A>G	c.(400-402)aAg>aGg	p.K134R	PAK1_ENST00000528203.1_Missense_Mutation_p.K36R|PAK1_ENST00000278568.4_Missense_Mutation_p.K134R|PAK1_ENST00000530617.1_Missense_Mutation_p.K134R	NM_002576.4	NP_002567.3	Q13153	PAK1_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 1	134	Autoregulatory region.|Interaction with CRIPAK.				actin cytoskeleton reorganization (GO:0031532)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to insulin stimulus (GO:0032869)|dendrite development (GO:0016358)|exocytosis (GO:0006887)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor clustering (GO:0043113)|response to hypoxia (GO:0001666)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|wound healing (GO:0042060)	axon (GO:0030424)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|Z disc (GO:0030018)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1)	29	all_cancers(14;1.75e-18)					GGATGTCTTCTTCGAGTTGTA	0.478																																					p.K134R		Atlas-SNP	.											.	PAK1	89	.	0			c.A401G						.						184	183	183					11																	77090324		2200	4292	6492	SO:0001583	missense	5058	exon4			GTCTTCTTCGAGT	U51120	CCDS8250.1, CCDS44687.1	11q13-q14	2008-06-17	2008-06-17						8590	protein-coding gene	gene with protein product	"STE20 homolog, yeast"	602590	"p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)", "p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)"			8805275, 9533029	Standard	NM_002576		Approved		uc001oyg.4	Q13153		ENST00000356341.3:c.401A>G	chr11.hg19:g.77090324T>C	ENSP00000348696:p.Lys134Arg	59.0	0.0		112.0	5.0	NM_001128620	O75561|Q13567|Q32M53|Q32M54|Q86W79	Missense_Mutation	SNP	ENST00000356341.3	hg19	CCDS8250.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.626498	0.66901	.	.	ENSG00000149269	ENST00000356341;ENST00000530617;ENST00000278568;ENST00000528203	T;T;T;T	0.71817	-0.54;-0.57;-0.57;-0.6	5.32	5.32	0.75619	.	0.041769	0.85682	D	0.000000	T	0.64371	0.2592	M	0.64997	1.995	0.58432	D	0.999996	P;B;B;B	0.37781	0.608;0.004;0.017;0.03	B;B;B;B	0.27380	0.079;0.003;0.015;0.021	T	0.66180	-0.5988	10	0.33940	T	0.23	.	15.5743	0.76362	0.0:0.0:0.0:1.0	.	36;134;134;134	E9PM17;B3KNX7;Q13153;Q13153-2	.;.;PAK1_HUMAN;.	R	134;134;134;36	ENSP00000348696:K134R;ENSP00000433423:K134R;ENSP00000278568:K134R;ENSP00000433211:K36R	ENSP00000278568:K134R	K	-	2	0	PAK1	76767972	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.698000	0.84413	2.139000	0.66308	0.460000	0.39030	AAG	.	.		0.478	PAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382083.2	NM_002576		C	77090324	T	C	77090324	3	2	43	1	0	0	0	0	1	0	0	0	11408	1609	56	2	1337	2	PAK1	11	77090324	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	863068	77090324	57916192	223	5305										
PCF11	51585	hgsc.bcm.edu	37	chr11	82872485	82872485	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gttgcaacatttatttgtgtGtttgaaaaggtacatatgca	9	4	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:82872485G>A	ENST00000298281.4	+	2	761	c.309G>A	c.(307-309)gtG>gtA	p.V103V		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	103	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TTATTTGTGTGTTTGAAAAGG	0.308																																					p.V103V		Atlas-SNP	.											.	PCF11	220	.	0			c.G309A						.						81	74	76					11																	82872485		1805	4067	5872	SO:0001819	synonymous_variant	51585	exon2			TTGTGTGTTTGAA	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.309G>A	chr11.hg19:g.82872485G>A		66.0	0.0		87.0	5.0	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	hg19	CCDS44689.1																																																																																			.	.		0.308	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		A	82872485	G	A	82872485	2	1	43	1	0	0	0	0	0	0	0	1	11582	1364	48	3		3	PCF11	11	82872485	Silent	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	5782161	82872485	52134031	224	5306										
TMEM126A	84233	hgsc.bcm.edu	37	chr11	85365266	85365266	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttcttacaacagacttaacTtacagatgttttgtaagttt	5	6	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:85365266T>C	ENST00000304511.2	+	3	355	c.246T>C	c.(244-246)acT>acC	p.T82T	TMEM126A_ENST00000528105.1_Silent_p.T12T|TMEM126A_ENST00000532180.1_Silent_p.T12T	NM_032273.3	NP_115649.1	Q9H061	T126A_HUMAN	transmembrane protein 126A	82					optic nerve development (GO:0021554)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(2)|stomach(1)	7		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				CAGACTTAACTTACAGATGTT	0.378																																					p.T82T		Atlas-SNP	.											.	TMEM126A	20	.	0			c.T246C						.						128	121	123					11																	85365266		2203	4299	6502	SO:0001819	synonymous_variant	84233	exon3			CTTAACTTACAGA		CCDS8268.1, CCDS58165.1	11q14.1	2011-03-25			ENSG00000171202	ENSG00000171202			25382	protein-coding gene	gene with protein product		612988				11230166	Standard	NM_032273		Approved	DKFZp586C1924, OPA7	uc001par.3	Q9H061	OTTHUMG00000166975	ENST00000304511.2:c.246T>C	chr11.hg19:g.85365266T>C		64.0	0.0		61.0	4.0	NM_032273	B2R570|E9PI16	Silent	SNP	ENST00000304511.2	hg19	CCDS8268.1																																																																																			.	.		0.378	TMEM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392177.1	NM_032273		C	85365266	T	C	85365266	2	2	43	1	0	0	0	0	0	0	0	1	16053	1596	56	2		2	TMEM126A	11	85365266	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2492781	85365266	49641250	225	5307										
CCDC83	220047	hgsc.bcm.edu	37	chr11	85627242	85627242	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtttggggacactgatatgaAgtacttactatatgaggatg	12	4	0	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:85627242A>G	ENST00000342404.3	+	10	1262	c.1046A>G	c.(1045-1047)aAg>aGg	p.K349R	RP11-90K17.2_ENST00000531414.1_RNA|CCDC83_ENST00000280245.4_Missense_Mutation_p.K380R|CCDC83_ENST00000376067.1_Missense_Mutation_p.K249R			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	349										breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				ACTGATATGAAGTACTTACTA	0.343																																					p.K380R		Atlas-SNP	.											.	CCDC83	48	.	0			c.A1139G						.						119	128	125					11																	85627242		2202	4299	6501	SO:0001583	missense	220047	exon11			ATATGAAGTACTT	AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.1046A>G	chr11.hg19:g.85627242A>G	ENSP00000344512:p.Lys349Arg	91.0	0.0		62.0	4.0	NM_173556	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Missense_Mutation	SNP	ENST00000342404.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.978|8.978	0.974696|0.974696	0.18736|0.18736	.|.	.|.	ENSG00000150676|ENSG00000150676	ENST00000280245;ENST00000376067;ENST00000342404|ENST00000526729	T;T;T|.	0.44482|.	0.92;0.92;0.92|.	5.02|5.02	3.85|3.85	0.44370|0.44370	.|.	0.587434|.	0.17323|.	N|.	0.178424|.	T|T	0.49098|0.49098	0.1537|0.1537	M|M	0.70595|0.70595	2.14|2.14	0.09310|0.09310	N|N	1|1	P;P;P|.	0.47910|.	0.782;0.822;0.902|.	B;B;B|.	0.38458|.	0.274;0.268;0.268|.	T|T	0.40757|0.40757	-0.9546|-0.9546	9|5	.|.	.|.	.|.	-24.4625|-24.4625	7.6134|7.6134	0.28144|0.28144	0.9017:0.0:0.0983:0.0|0.9017:0.0:0.0983:0.0	.|.	249;349;380|.	Q8IWF9-3;Q8IWF9;Q8IWF9-2|.	.;CCD83_HUMAN;.|.	R|G	380;249;349|254	ENSP00000280245:K380R;ENSP00000365235:K249R;ENSP00000344512:K349R|.	.|.	K|S	+|+	2|1	0|0	CCDC83|CCDC83	85304890|85304890	0.003000|0.003000	0.15002|0.15002	0.028000|0.028000	0.17463|0.17463	0.169000|0.169000	0.22640|0.22640	1.471000|1.471000	0.35365|0.35365	2.096000|2.096000	0.63516|0.63516	0.482000|0.482000	0.46254|0.46254	AAG|AGT	.	.		0.343	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556		G	85627242	A	G	85627242	3	3	43	1	0	0	0	0	1	0	0	0	2859	72	3	2	1177	2	CCDC83	11	85627242	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	261976	85627242	49379274	226	5308										
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94335097	94335097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cgagagctttctgaactgctTgagaagagttgcaggttcca	12	8	1	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:94335097T>C	ENST00000299001.6	+	12	1728	c.1517T>C	c.(1516-1518)tTg>tCg	p.L506S	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	506					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CTGAACTGCTTGAGAAGAGTT	0.363																																					p.L506S		Atlas-SNP	.											.	PIWIL4	70	.	0			c.T1517C						.						130	127	128					11																	94335097		2201	4298	6499	SO:0001583	missense	143689	exon12			ACTGCTTGAGAAG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1517T>C	chr11.hg19:g.94335097T>C	ENSP00000299001:p.Leu506Ser	131.0	0.0		74.0	4.0	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	hg19	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	T	18.18	3.566781	0.65651	.	.	ENSG00000134627	ENST00000299001	T	0.08193	3.12	5.24	5.24	0.73138	Ribonuclease H-like (1);	0.000000	0.50627	D	0.000108	T	0.31949	0.0813	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.08597	-1.0714	10	0.87932	D	0	-18.4283	14.2686	0.66138	0.0:0.0:0.0:1.0	.	506	Q7Z3Z4	PIWL4_HUMAN	S	506	ENSP00000299001:L506S	ENSP00000299001:L506S	L	+	2	0	PIWIL4	93974745	1.000000	0.71417	1.000000	0.80357	0.628000	0.37860	6.194000	0.72082	2.216000	0.71823	0.528000	0.53228	TTG	.	.		0.363	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		C	94335097	T	C	94335097	3	2	43	1	0	0	0	0	1	0	0	0	11969	1821	63	2	1563	2	PIWIL4	11	94335097	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	8707855	94335097	40671419	227	5309										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105774565	105774565	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctctgctctgacttatgatgGagtccttgtgatggctgaaa	11	8	2	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:105774565G>A	ENST00000530497.1	+	7	911	c.911G>A	c.(910-912)gGa>gAa	p.G304E	GRIA4_ENST00000393127.2_Missense_Mutation_p.G304E|GRIA4_ENST00000393125.2_Missense_Mutation_p.G304E|GRIA4_ENST00000525187.1_Missense_Mutation_p.G304E|GRIA4_ENST00000428631.2_Missense_Mutation_p.G304E|GRIA4_ENST00000282499.5_Missense_Mutation_p.G304E			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	304					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		ACTTATGATGGAGTCCTTGTG	0.418																																					p.G304E		Atlas-SNP	.											.	GRIA4	380	.	0			c.G911A						.						147	141	143					11																	105774565		2202	4299	6501	SO:0001583	missense	2893	exon8			ATGATGGAGTCCT	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.911G>A	chr11.hg19:g.105774565G>A	ENSP00000435775:p.Gly304Glu	104.0	0.0		99.0	4.0	NM_001077244	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.457096	0.84317	.	.	ENSG00000152578	ENST00000393125;ENST00000282499;ENST00000393127;ENST00000428631;ENST00000530497;ENST00000525187	T;T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8;1.8	5.65	5.65	0.86999	Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000001	T	0.42449	0.1203	L	0.34521	1.04	0.80722	D	1	B;D;D	0.63880	0.037;0.986;0.993	B;D;D	0.66497	0.098;0.913;0.944	T	0.22871	-1.0204	10	0.87932	D	0	.	20.0855	0.97800	0.0:0.0:1.0:0.0	.	304;304;304	P48058;G3V164;Q86XE8	GRIA4_HUMAN;.;.	E	304	ENSP00000376833:G304E;ENSP00000282499:G304E;ENSP00000376835:G304E;ENSP00000415551:G304E;ENSP00000435775:G304E;ENSP00000432180:G304E	ENSP00000282499:G304E	G	+	2	0	GRIA4	105279775	0.994000	0.37717	1.000000	0.80357	0.996000	0.88848	2.174000	0.42482	2.813000	0.96785	0.655000	0.94253	GGA	.	.		0.418	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			A	105774565	G	A	105774565	3	1	43	1	0	0	0	0	1	0	0	0	6779	1174	41	3	937	3	GRIA4	11	105774565	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	11439468	105774565	29231951	228	5310										
ZBTB16	7704	hgsc.bcm.edu	37	chr11	114112895	114112895	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cctgtctcccacaggcactgAcatggccgtcttctgtctgc	9	16	4	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:114112895A>G	ENST00000335953.4	+	5	1840	c.1460A>G	c.(1459-1461)gAc>gGc	p.D487G	ZBTB16_ENST00000535379.1_3'UTR|ZBTB16_ENST00000392996.2_Missense_Mutation_p.D487G|RP11-64D24.2_ENST00000544925.1_RNA	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	487					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		ACAGGCACTGACATGGCCGTC	0.602																																					p.D487G		Atlas-SNP	.											.	ZBTB16	101	.	0			c.A1460G						.						84	55	65					11																	114112895		2201	4296	6497	SO:0001583	missense	7704	exon5			GCACTGACATGGC	Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12930	protein-coding gene	gene with protein product	"promyelocytic leukaemia zinc finger"	176797	"zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.1460A>G	chr11.hg19:g.114112895A>G	ENSP00000338157:p.Asp487Gly	61.0	0.0		54.0	4.0	NM_006006	Q8TAL4	Missense_Mutation	SNP	ENST00000335953.4	hg19	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.417968	0.83449	.	.	ENSG00000109906	ENST00000335953;ENST00000392996;ENST00000310883	T;T	0.10960	2.82;2.82	5.33	5.33	0.75918	Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.12305	0.0299	L	0.41632	1.29	0.53005	D	0.999969	B	0.17268	0.021	B	0.18871	0.023	T	0.03068	-1.1076	10	0.87932	D	0	-17.7069	15.6241	0.76840	1.0:0.0:0.0:0.0	.	487	Q05516	ZBT16_HUMAN	G	487;487;364	ENSP00000338157:D487G;ENSP00000376721:D487G	ENSP00000309507:D364G	D	+	2	0	ZBTB16	113618105	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.426000	0.80270	2.145000	0.66743	0.533000	0.62120	GAC	.	.		0.602	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		G	114112895	A	G	114112895	3	3	43	1	0	0	0	0	1	0	0	0	17541	275	10	2	1474	2	ZBTB16	11	114112895	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	8338330	114112895	20893621	229	5311										
STT3A	3703	hgsc.bcm.edu	37	chr11	125474114	125474114	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gttcctggatatatctcccgAtctgtggctggctcctatga	10	11	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:125474114A>T	ENST00000529196.1	+	7	686	c.480A>T	c.(478-480)cgA>cgT	p.R160R	STT3A_ENST00000392708.4_Silent_p.R160R|STT3A_ENST00000531491.1_Silent_p.R68R			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	160					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.R160R(1)		NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		ATATCTCCCGATCTGTGGCTG	0.423																																					p.R160R		Atlas-SNP	.											STT3A,NS,carcinoma,0,1	STT3A	52	.	1	Substitution - coding silent(1)	endometrium(1)	c.A480T						.						125	117	119					11																	125474114		2201	4299	6500	SO:0001819	synonymous_variant	3703	exon6			CTCCCGATCTGTG	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"dolichyl-diphosphooligosaccharide protein glycotransferase"	601134	"integral membrane protein 1", "STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)", "STT3A, cataylic subunit of the oligosaccharyltransferase complex"	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.480A>T	chr11.hg19:g.125474114A>T		144.0	1.0		92.0	68.0	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	hg19	CCDS8458.1																																																																																			.	.		0.423	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713		T	125474114	A	T	125474114	2	4	43	1	0	0	0	0	0	0	0	1	15348	320	12	4		4	STT3A	11	125474114	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	11361219	125474114	9532402	230	5312										
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128932193	128932193	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acctggaatccgtgcttgccTctccaccatgtgcttaacac	7	15	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr11:128932193T>C	ENST00000310343.9	-	9	902	c.903A>G	c.(901-903)agA>agG	p.R301R	ARHGAP32_ENST00000524655.1_Silent_p.R227R	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	301	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						CGTGCTTGCCTCTCCACCATG	0.383																																					p.R301R		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.A903G						.						129	119	122					11																	128932193		1566	3579	5145	SO:0001819	synonymous_variant	9743	exon9			CTTGCCTCTCCAC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.903A>G	chr11.hg19:g.128932193T>C		42.0	0.0		33.0	4.0	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	hg19	CCDS44769.1																																																																																			.	.		0.383	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		C	128932193	T	C	128932193	2	2	43	1	0	0	0	0	0	0	0	1	881	1548	54	2		2	ARHGAP32	11	128932193	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3458079	128932193	6074323	231	5313										
DCP1B	196513	hgsc.bcm.edu	37	chr12	2062353	2062353	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgctgctgctgctgctgctgGtggagagtctgcggaggctc	17	10	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:2062353G>C	ENST00000280665.6	-	7	832	c.753C>G	c.(751-753)caC>caG	p.H251Q	DCP1B_ENST00000540622.1_Missense_Mutation_p.H125Q|DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000397173.4_Missense_Mutation_p.H149Q	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	251				H -> HQ (in Ref. 1; AAN62764, 2; BAB71118 and 4; AAH15368/AAH43437). {ECO:0000305}.	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			gctgctgctgGTGGAGAGTCT	0.552																																					p.H251Q		Atlas-SNP	.											DCP1B,rectum,carcinoma,0,1	DCP1B	63	.	0			c.C753G						.						36	42	40					12																	2062353		2203	4300	6503	SO:0001583	missense	196513	exon7			CTGCTGGTGGAGA	AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"DCP1 decapping enzyme homolog B (S. cerevisiae)"			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.753C>G	chr12.hg19:g.2062353G>C	ENSP00000280665:p.His251Gln	13.0	0.0		20.0	3.0	NM_152640	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Missense_Mutation	SNP	ENST00000280665.6	hg19	CCDS31727.1	.	.	.	.	.	.	.	.	.	.	G	0.029	-1.346987	0.01266	.	.	ENSG00000151065	ENST00000280665;ENST00000397173;ENST00000540622	T;T;T	0.17054	2.32;2.31;2.3	4.5	0.369	0.16151	.	1.548950	0.03620	N	0.236163	T	0.16769	0.0403	L	0.36672	1.1	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.41822	-0.9487	10	0.12766	T	0.61	0.002	15.1763	0.72913	0.0:0.5449:0.4551:0.0	.	149;251	B4DRD1;Q8IZD4	.;DCP1B_HUMAN	Q	251;149;125	ENSP00000280665:H251Q;ENSP00000380358:H149Q;ENSP00000444374:H125Q	ENSP00000280665:H251Q	H	-	3	2	DCP1B	1932614	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	-0.086000	0.11233	-0.095000	0.12351	-0.835000	0.03068	CAC	.	.		0.552	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640		C	2062353	G	C	2062353	3	2	43	1	0	0	0	0	1	0	0	0	4301	1252	44	4	1112	4	DCP1B	12	2062353	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10		2062353	131789542	232	5314										
PLEKHG6	55200	hgsc.bcm.edu	37	chr12	6436467	6436467	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccacctggtggtgacagaagAcacagatgaagatgctcccc	11	12	0	6			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:6436467A>G	ENST00000396988.3	+	15	1948	c.1718A>G	c.(1717-1719)gAc>gGc	p.D573G	PLEKHG6_ENST00000304581.8_Missense_Mutation_p.D103G|PLEKHG6_ENST00000449001.2_Missense_Mutation_p.D541G|PLEKHG6_ENST00000011684.7_Missense_Mutation_p.D573G	NM_001144856.1	NP_001138328.1	Q3KR16	PKHG6_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	573						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(4)	23						GTGACAGAAGACACAGATGAA	0.562											OREG0021622	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D573G		Atlas-SNP	.											.	PLEKHG6	62	.	0			c.A1718G						.						144	136	138					12																	6436467		2203	4300	6503	SO:0001583	missense	55200	exon15			CAGAAGACACAGA	AK001527	CCDS8541.1, CCDS44808.1	12p13.31	2013-01-11			ENSG00000008323	ENSG00000008323		"Pleckstrin homology (PH) domain containing"	25562	protein-coding gene	gene with protein product		611743					Standard	NM_018173		Approved	FLJ10665	uc001qnr.3	Q3KR16	OTTHUMG00000168266	ENST00000396988.3:c.1718A>G	chr12.hg19:g.6436467A>G	ENSP00000380185:p.Asp573Gly	98.0	0.0	634	85.0	4.0	NM_001144856	Q3SWR1|Q8N1P1|Q8WYY1|Q9H8F4|Q9NVK9	Missense_Mutation	SNP	ENST00000396988.3	hg19	CCDS8541.1	.	.	.	.	.	.	.	.	.	.	A	10.88	1.476935	0.26511	.	.	ENSG00000008323	ENST00000011684;ENST00000396988;ENST00000449001;ENST00000304581	T;T;T	0.65732	-0.06;-0.06;-0.17	5.45	4.23	0.50019	.	0.000000	0.64402	D	0.000016	T	0.66446	0.2790	L	0.36672	1.1	0.09310	N	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.994	T	0.55347	-0.8155	10	0.42905	T	0.14	-30.1755	7.9911	0.30242	0.8185:0.0:0.0:0.1815	.	541;573	Q3KR16-2;Q3KR16	.;PKHG6_HUMAN	G	573;573;541;103	ENSP00000011684:D573G;ENSP00000380185:D573G;ENSP00000393194:D541G	ENSP00000011684:D573G	D	+	2	0	PLEKHG6	6306728	0.993000	0.37304	0.186000	0.23195	0.073000	0.16967	1.826000	0.39092	2.059000	0.61396	0.533000	0.62120	GAC	.	.		0.562	PLEKHG6-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399031.1	NM_018173		G	6436467	A	G	6436467	3	3	43	1	0	0	0	0	1	0	0	0	12083	275	10	2	1818	2	PLEKHG6	12	6436467	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	4374114	6436467	127415428	233	5315										
CLECL1	160365	hgsc.bcm.edu	37	chr12	9885713	9885713	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caaagaaacttctgataagtAaattgagatggcaaatttcc	7	6	1	3	rs200639830		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:9885713A>T	ENST00000327839.3	-	1	182	c.148T>A	c.(148-150)Tac>Aac	p.Y50N		NM_172004.3	NP_742001.1	Q8IZS7	CLCL1_HUMAN	C-type lectin-like 1	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|kidney(1)|large_intestine(4)|lung(3)	9						TCTGATAAGTAAATTGAGATG	0.403																																					p.Y50N		Atlas-SNP	.											.	CLECL1	18	.	0			c.T148A						.						77	80	79					12																	9885713		2203	4300	6503	SO:0001583	missense	160365	exon1			ATAAGTAAATTGA	AF518873	CCDS8603.1, CCDS73441.1	12p13.31	2007-06-21				ENSG00000184293			24462	protein-coding gene	gene with protein product	"dendritic cell associated lectin 1"	607467				12421943	Standard	NM_172004		Approved	DCAL1	uc001qwi.3	Q8IZS7		ENST00000327839.3:c.148T>A	chr12.hg19:g.9885713A>T	ENSP00000331766:p.Tyr50Asn	56.0	0.0		102.0	6.0	NM_001267701		Missense_Mutation	SNP	ENST00000327839.3	hg19	CCDS8603.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.915|6.915	0.538458|0.538458	0.13250|0.13250	.|.	.|.	ENSG00000184293|ENSG00000184293	ENST00000542530|ENST00000327839	.|T	.|0.56275	.|0.47	1.86|1.86	0.666|0.666	0.17901|0.17901	.|.	.|.	.|.	.|.	.|.	T|T	0.21590|0.21590	0.0520|0.0520	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	.|P	.|0.51147	.|0.942	.|B	.|0.39217	.|0.294	T|T	0.08027|0.08027	-1.0742|-1.0742	5|8	.|.	.|.	.|.	.|.	3.7406|3.7406	0.08528|0.08528	0.7983:0.0:0.2017:0.0|0.7983:0.0:0.2017:0.0	.|.	.|50	.|Q8IZS7	.|CLCL1_HUMAN	L|N	1|50	.|ENSP00000331766:Y50N	.|.	F|Y	-|-	3|1	2|0	CLECL1|CLECL1	9776980|9776980	0.002000|0.002000	0.14202|0.14202	0.001000|0.001000	0.08648|0.08648	0.004000|0.004000	0.04260|0.04260	1.812000|1.812000	0.38952|0.38952	0.170000|0.170000	0.19704|0.19704	-0.463000|-0.463000	0.05309|0.05309	TTT|TAC	.	.		0.403	CLECL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399815.1	NM_172004		T	9885713	A	T	9885713	3	4	43	1	0	0	0	0	1	0	0	0	3525	362	13	4	363	4	CLECL1	12	9885713	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	3449246	9885713	123966182	234	5316										
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14829836	14829836	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttagaagggaattcccaggAgacagcgtcagaacaaggac	12	8	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:14829836A>G	ENST00000261170.3	-	7	1036	c.900T>C	c.(898-900)tcT>tcC	p.S300S	RP11-174G6.1_ENST00000501178.2_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	300					intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	AATTCCCAGGAGACAGCGTCA	0.343																																					p.S300S		Atlas-SNP	.											.	GUCY2C	126	.	0			c.T900C						.						72	71	71					12																	14829836		2203	4300	6503	SO:0001819	synonymous_variant	2984	exon7			CCCAGGAGACAGC		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.900T>C	chr12.hg19:g.14829836A>G		138.0	0.0		94.0	4.0	NM_004963	B2RMY6	Silent	SNP	ENST00000261170.3	hg19	CCDS8664.1																																																																																			.	.		0.343	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			G	14829836	A	G	14829836	2	3	43	1	0	0	0	0	0	0	0	1	6905	291	11	2		2	GUCY2C	12	14829836	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	4944123	14829836	119022059	235	5317										
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14836124	14836124	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catcagcctggttaaggtttCtttatagtcacatgacaatc	7	9	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:14836124C>T	ENST00000261170.3	-	4	599	c.463G>A	c.(463-465)Gaa>Aaa	p.E155K	RP11-174G6.1_ENST00000501178.2_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	155					intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	GTTAAGGTTTCTTTATAGTCA	0.408																																					p.E155K		Atlas-SNP	.											GUCY2C,NS,carcinoma,0,1	GUCY2C	126	.	0			c.G463A						.						90	84	86					12																	14836124		2203	4300	6503	SO:0001583	missense	2984	exon4			AGGTTTCTTTATA		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.463G>A	chr12.hg19:g.14836124C>T	ENSP00000261170:p.Glu155Lys	63.0	0.0		36.0	2.0	NM_004963	B2RMY6	Missense_Mutation	SNP	ENST00000261170.3	hg19	CCDS8664.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.271348	0.40194	.	.	ENSG00000070019	ENST00000261170	T	0.73575	-0.76	5.46	5.46	0.80206	Extracellular ligand-binding receptor (1);	0.430696	0.26788	N	0.022491	T	0.71871	0.3391	L	0.60455	1.87	0.34441	D	0.699563	P	0.38223	0.623	B	0.41988	0.372	T	0.73675	-0.3908	10	0.11182	T	0.66	.	14.8157	0.70034	0.0:1.0:0.0:0.0	.	155	P25092	GUC2C_HUMAN	K	155	ENSP00000261170:E155K	ENSP00000261170:E155K	E	-	1	0	GUCY2C	14727391	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.188000	0.42612	2.567000	0.86603	0.655000	0.94253	GAA	.	.		0.408	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			T	14836124	C	T	14836124	3	4	43	1	0	0	0	0	1	0	0	0	6905	922	32	3	2854	3	GUCY2C	12	14836124	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	6288	14836124	119015771	236	5318										
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14840921	14840921	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aggtcgaggccttcacaggtGctactccggcagtcgcctga	13	13	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:14840921G>T	ENST00000261170.3	-	2	430	c.294C>A	c.(292-294)agC>agA	p.S98R	RP11-174G6.1_ENST00000501178.2_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	98					intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	CTTCACAGGTGCTACTCCGGC	0.483																																					p.S98R		Atlas-SNP	.											.	GUCY2C	126	.	0			c.C294A						.						100	95	97					12																	14840921		2203	4300	6503	SO:0001583	missense	2984	exon2			ACAGGTGCTACTC		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.294C>A	chr12.hg19:g.14840921G>T	ENSP00000261170:p.Ser98Arg	53.0	0.0		34.0	25.0	NM_004963	B2RMY6	Missense_Mutation	SNP	ENST00000261170.3	hg19	CCDS8664.1	.	.	.	.	.	.	.	.	.	.	G	19.19	3.778838	0.70107	.	.	ENSG00000070019	ENST00000261170	T	0.75938	-0.98	5.48	1.53	0.23141	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.82107	0.4965	M	0.74881	2.28	0.43187	D	0.995011	D	0.89917	1.0	D	0.79784	0.993	T	0.80155	-0.1500	10	0.87932	D	0	.	7.3263	0.26557	0.3561:0.0:0.6439:0.0	.	98	P25092	GUC2C_HUMAN	R	98	ENSP00000261170:S98R	ENSP00000261170:S98R	S	-	3	2	GUCY2C	14732188	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.803000	0.27083	0.354000	0.24105	0.591000	0.81541	AGC	.	.		0.483	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			T	14840921	G	T	14840921	3	4	43	1	0	0	0	0	1	0	0	0	6905	1310	46	3	3031	3	GUCY2C	12	14840921	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	4797	14840921	119010974	237	5319										
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18837138	18837138	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctattaaaccttgaccttcaAcaacaaaacgtatcaatgcc	3	12	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:18837138A>C	ENST00000538330.1	-	10	1394	c.1013T>G	c.(1012-1014)gTt>gGt	p.V338G	PLCZ1_ENST00000539875.1_Missense_Mutation_p.V363G|PLCZ1_ENST00000541695.1_3'UTR|PLCZ1_ENST00000435379.1_Missense_Mutation_p.V361G|PLCZ1_ENST00000447925.2_Missense_Mutation_p.V554G|PLCZ1_ENST00000266505.7_Missense_Mutation_p.V556G|PLCZ1_ENST00000534932.1_Missense_Mutation_p.V37G					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					TTGACCTTCAACAACAAAACG	0.323																																					p.V556G		Atlas-SNP	.											PLCZ1,NS,carcinoma,0,1	PLCZ1	107	.	0			c.T1667G						.						105	103	104					12																	18837138		2202	4298	6500	SO:0001583	missense	89869	exon14			CCTTCAACAACAA	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000538330.1:c.1013T>G	chr12.hg19:g.18837138A>C	ENSP00000445880:p.Val338Gly	32.0	0.0		23.0	2.0	NM_033123		Missense_Mutation	SNP	ENST00000538330.1	hg19		.	.	.	.	.	.	.	.	.	.	A	18.01	3.527203	0.64860	.	.	ENSG00000139151	ENST00000534932;ENST00000538330;ENST00000266505;ENST00000447925;ENST00000435379;ENST00000539875	T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48	5.15	1.53	0.23141	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.209202	0.40469	N	0.001085	T	0.56906	0.2017	M	0.94021	3.485	0.80722	D	1	D;D	0.61697	0.99;0.99	P;D	0.63703	0.89;0.917	T	0.59752	-0.7395	10	0.66056	D	0.02	.	7.3986	0.26950	0.7088:0.0:0.2912:0.0	.	556;338	Q86YW0;Q8N7S5	PLCZ1_HUMAN;.	G	37;338;556;554;361;363	ENSP00000438826:V37G;ENSP00000445880:V338G;ENSP00000266505:V556G;ENSP00000402358:V554G;ENSP00000400504:V361G;ENSP00000445026:V363G	ENSP00000266505:V556G	V	-	2	0	PLCZ1	18728405	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.544000	0.53640	0.440000	0.26502	0.533000	0.62120	GTT	.	.		0.323	PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000401666.3	NM_033123		C	18837138	A	C	18837138	3	2	43	1	0	0	0	0	1	0	0	0	12053	43	2	5	167	5	PLCZ1	12	18837138	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	3996217	18837138	115014757	238	5320										
TM7SF3	51768	hgsc.bcm.edu	37	chr12	27128524	27128524	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgatgtaggaaaggcttgtgGaccagtaactgtcaatggct	13	6	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:27128524G>A	ENST00000343028.4	-	11	1580	c.1355C>T	c.(1354-1356)tCc>tTc	p.S452F	RP11-421F16.3_ENST00000500632.1_RNA	NM_016551.2	NP_057635.1	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3	452						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	18	Colorectal(261;0.0847)					AAGGCTTGTGGACCAGTAACT	0.443																																					p.S452F		Atlas-SNP	.											.	TM7SF3	41	.	0			c.C1355T						.						126	111	116					12																	27128524		2203	4300	6503	SO:0001583	missense	51768	exon11			CTTGTGGACCAGT	AB032470	CCDS8710.1	12q11-q12	2012-08-10			ENSG00000064115	ENSG00000064115			23049	protein-coding gene	gene with protein product		605181				10828615	Standard	NM_016551		Approved		uc010sjl.2	Q9NS93	OTTHUMG00000169243	ENST00000343028.4:c.1355C>T	chr12.hg19:g.27128524G>A	ENSP00000342322:p.Ser452Phe	127.0	0.0		101.0	73.0	NM_016551	B3KMZ3|Q9NUS4	Missense_Mutation	SNP	ENST00000343028.4	hg19	CCDS8710.1	.	.	.	.	.	.	.	.	.	.	G	10.43	1.347733	0.24426	.	.	ENSG00000064115	ENST00000343028;ENST00000545344;ENST00000537406	T	0.30448	1.53	5.52	-0.586	0.11694	.	0.248069	0.42548	N	0.000699	T	0.08537	0.0212	N	0.02011	-0.69	0.27910	N	0.93865	B	0.02656	0.0	B	0.04013	0.001	T	0.34254	-0.9836	10	0.11182	T	0.66	-3.8215	6.6569	0.22992	0.3947:0.0:0.2307:0.3746	.	452	Q9NS93	TM7S3_HUMAN	F	452;166;70	ENSP00000342322:S452F	ENSP00000342322:S452F	S	-	2	0	TM7SF3	27019791	1.000000	0.71417	0.740000	0.30986	0.902000	0.53008	2.500000	0.45381	-0.256000	0.09473	-0.271000	0.10264	TCC	.	.		0.443	TM7SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403033.1	NM_016551		A	27128524	G	A	27128524	3	1	43	1	0	0	0	0	1	0	0	0	15990	1174	41	3	365	3	TM7SF3	12	27128524	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	8291386	27128524	106723371	239	5321										
ARID2	196528	hgsc.bcm.edu	37	chr12	46231166	46231166	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttcatactgttacaaaatgTctaatgtcaagggatagatt	7	5	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:46231166T>C	ENST00000334344.6	+	9	1258	c.1086T>C	c.(1084-1086)tgT>tgC	p.C362C	ARID2_ENST00000444670.1_5'Flank|ARID2_ENST00000422737.1_Silent_p.C213C|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	362					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TTACAAAATGTCTAATGTCAA	0.303			"N, S, F"		hepatocellular carcinoma																																p.C362C		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.T1086C						.						83	91	88					12																	46231166		2203	4295	6498	SO:0001819	synonymous_variant	196528	exon9			AAAATGTCTAATG		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1086T>C	chr12.hg19:g.46231166T>C		73.0	0.0		84.0	4.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Silent	SNP	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.303	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		C	46231166	T	C	46231166	2	2	43	1	0	0	0	0	0	0	0	1	915	1673	58	2		2	ARID2	12	46231166	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	19102642	46231166	87620729	240	5322										
DDX23	9416	hgsc.bcm.edu	37	chr12	49226344	49226344	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cgctgggggcatggtggccgTgaacatgactgtctacgaaa	15	9	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:49226344T>C	ENST00000308025.3	-	14	1895	c.1816A>G	c.(1816-1818)Acg>Gcg	p.T606A		NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	606	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						ATGGTGGCCGTGAACATGACT	0.587																																					p.T606A		Atlas-SNP	.											.	DDX23	82	.	0			c.A1816G						.						45	39	41					12																	49226344		2203	4300	6503	SO:0001583	missense	9416	exon14			TGGCCGTGAACAT	AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"DEAD-boxes"	17347	protein-coding gene	gene with protein product		612172	"PRP28 homolog, yeast"			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.1816A>G	chr12.hg19:g.49226344T>C	ENSP00000310723:p.Thr606Ala	53.0	0.0		73.0	4.0	NM_004818	B2R600|B4DH15|O43188	Missense_Mutation	SNP	ENST00000308025.3	hg19	CCDS8770.1	.	.	.	.	.	.	.	.	.	.	T	33	5.257996	0.95368	.	.	ENSG00000174243	ENST00000308025	T	0.11277	2.79	5.65	5.65	0.86999	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.049681	0.85682	D	0.000000	T	0.24928	0.0605	L	0.48362	1.52	0.80722	D	1	D	0.55385	0.971	P	0.62298	0.9	T	0.00233	-1.1894	10	0.87932	D	0	-16.2225	14.9931	0.71406	0.0:0.0:0.0:1.0	.	606	Q9BUQ8	DDX23_HUMAN	A	606	ENSP00000310723:T606A	ENSP00000310723:T606A	T	-	1	0	DDX23	47512611	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.542000	0.82095	2.371000	0.80710	0.533000	0.62120	ACG	.	.		0.587	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818		C	49226344	T	C	49226344	3	2	43	1	0	0	0	0	1	0	0	0	4352	1696	59	2	662	2	DDX23	12	49226344	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2995178	49226344	84625551	241	5323										
FKBP11	51303	hgsc.bcm.edu	37	chr12	49318403	49318403	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggtctctggtcagggaggtgTcaataatacgtccatctacc	11	10	4	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:49318403T>C	ENST00000550765.1	-	3	622	c.224A>G	c.(223-225)gAc>gGc	p.D75G	FKBP11_ENST00000453172.2_Missense_Mutation_p.D75G|CCDC65_ENST00000266984.5_Intron|AC073610.5_ENST00000537495.1_Intron|FKBP11_ENST00000444214.2_5'UTR|FKBP11_ENST00000552878.1_Missense_Mutation_p.D75G|RP11-302B13.5_ENST00000398092.4_Intron	NM_016594.2	NP_057678.1	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11, 19 kDa	75	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			kidney(1)|large_intestine(3)|lung(1)	5						CAGGGAGGTGTCAATAATACG	0.542											OREG0021773	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D75G		Atlas-SNP	.											.	FKBP11	12	.	0			c.A224G						.						145	131	136					12																	49318403		2203	4300	6503	SO:0001583	missense	51303	exon3			GAGGTGTCAATAA	AF238079	CCDS8773.1, CCDS44870.1, CCDS44871.1	12q13.12	2008-08-04	2002-08-29			ENSG00000134285			18624	protein-coding gene	gene with protein product		610571	"FK506 binding protein 11 (19 kDa)"			12036304, 16596453	Standard	NM_016594		Approved	FKBP19	uc001rsp.3	Q9NYL4		ENST00000550765.1:c.224A>G	chr12.hg19:g.49318403T>C	ENSP00000449751:p.Asp75Gly	54.0	0.0	961	91.0	4.0	NM_016594	B4DWB7	Missense_Mutation	SNP	ENST00000550765.1	hg19	CCDS8773.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.690300	0.48097	.	.	ENSG00000134285	ENST00000550765;ENST00000552878;ENST00000453172	T;T;T	0.63417	-0.04;-0.04;-0.04	4.5	4.5	0.54988	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.054834	0.64402	D	0.000001	D	0.83202	0.5203	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.87576	0.2481	10	0.87932	D	0	-11.4586	13.1354	0.59405	0.0:0.0:0.0:1.0	.	75;75	B4DWB7;Q9NYL4	.;FKB11_HUMAN	G	75	ENSP00000449751:D75G;ENSP00000447911:D75G;ENSP00000396874:D75G	ENSP00000396874:D75G	D	-	2	0	FKBP11	47604670	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.772000	0.75001	1.810000	0.52873	0.533000	0.62120	GAC	.	.		0.542	FKBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408927.1	NM_016594		C	49318403	T	C	49318403	3	2	43	1	0	0	0	0	1	0	0	0	5911	1667	58	2	454	2	FKBP11	12	49318403	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	92059	49318403	84533492	242	5324										
LMBR1L	55716	hgsc.bcm.edu	37	chr12	49498580	49498580	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtagtagttccgaggcagggAgagcagcacctcattgctga	14	9	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:49498580A>G	ENST00000267102.8	-	4	622	c.280T>C	c.(280-282)Tcc>Ccc	p.S94P	LMBR1L_ENST00000553204.1_5'UTR|LMBR1L_ENST00000395141.4_Missense_Mutation_p.S89P|LMBR1L_ENST00000547382.1_Missense_Mutation_p.S94P	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	94					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CGAGGCAGGGAGAGCAGCACC	0.592																																					p.S94P		Atlas-SNP	.											.	LMBR1L	61	.	0			c.T280C						.						125	89	101					12																	49498580		2203	4300	6503	SO:0001583	missense	55716	exon4			GCAGGGAGAGCAG	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"limb region 1 homolog (mouse)-like"			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.280T>C	chr12.hg19:g.49498580A>G	ENSP00000267102:p.Ser94Pro	82.0	0.0		100.0	4.0	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Missense_Mutation	SNP	ENST00000267102.8	hg19	CCDS8780.2	.	.	.	.	.	.	.	.	.	.	A	17.05	3.290183	0.59976	.	.	ENSG00000139636	ENST00000267102;ENST00000547382;ENST00000395141;ENST00000547675;ENST00000551854;ENST00000551782	T;T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26;1.26	6.07	6.07	0.98685	LMBR1-like membrane protein (1);	0.107607	0.64402	D	0.000005	T	0.54224	0.1845	M	0.61703	1.905	0.47183	D	0.999341	P;D;D	0.67145	0.95;0.984;0.996	P;P;P	0.62298	0.698;0.855;0.9	T	0.49652	-0.8917	10	0.33940	T	0.23	.	15.6114	0.76721	1.0:0.0:0.0:0.0	.	94;94;89	Q6UX01-3;Q6UX01;Q6UX01-4	.;LMBRL_HUMAN;.	P	94;94;89;94;99;94	ENSP00000267102:S94P;ENSP00000447329:S94P;ENSP00000378573:S89P;ENSP00000447240:S94P;ENSP00000446641:S99P;ENSP00000449633:S94P	ENSP00000267102:S94P	S	-	1	0	LMBR1L	47784847	1.000000	0.71417	0.994000	0.49952	0.421000	0.31385	5.802000	0.69122	2.326000	0.78906	0.533000	0.62120	TCC	.	.		0.592	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113		G	49498580	A	G	49498580	3	3	43	1	0	0	0	0	1	0	0	0	8850	304	11	2	1245	2	LMBR1L	12	49498580	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	180177	49498580	84353315	243	5325										
BIN2	51411	hgsc.bcm.edu	37	chr12	51693495	51693495	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccgaccccgcttggcaattcTctcctgacccagggtaatga	9	15	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:51693495T>C	ENST00000267012.4	-	6	473	c.412A>G	c.(412-414)Aga>Gga	p.R138G	BIN2_ENST00000452142.2_Missense_Mutation_p.R106G|BIN2_ENST00000544402.1_Missense_Mutation_p.R112G|BIN2_ENST00000604560.1_Missense_Mutation_p.R111G	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	138	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell chemotaxis (GO:0060326)|membrane tubulation (GO:0097320)|phagocytosis, engulfment (GO:0006911)|podosome assembly (GO:0071800)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|podosome (GO:0002102)	phospholipid binding (GO:0005543)			NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						TTGGCAATTCTCTCCTGACCC	0.507																																					p.R138G		Atlas-SNP	.											.	BIN2	58	.	0			c.A412G						.						94	91	92					12																	51693495		2203	4300	6503	SO:0001583	missense	51411	exon6			CAATTCTCTCCTG	AF146531	CCDS8811.1	12q13.13	2012-01-23			ENSG00000110934	ENSG00000110934			1053	protein-coding gene	gene with protein product		605936				10903846	Standard	XM_005268957		Approved	BRAP-1	uc001ryg.3	Q9UBW5		ENST00000267012.4:c.412A>G	chr12.hg19:g.51693495T>C	ENSP00000267012:p.Arg138Gly	39.0	0.0		71.0	4.0	NM_016293	Q86VV0|Q9NWK4|Q9UKN4	Missense_Mutation	SNP	ENST00000267012.4	hg19	CCDS8811.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.710147	0.68730	.	.	ENSG00000110934	ENST00000452142;ENST00000267012;ENST00000544402	T;T;T	0.64260	-0.09;-0.09;-0.09	5.05	3.83	0.44106	BAR (3);	0.000000	0.85682	D	0.000000	T	0.77294	0.4109	M	0.83774	2.66	0.36007	D	0.837806	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.69824	0.958;0.962;0.966	D	0.83569	0.0111	10	0.66056	D	0.02	-9.568	10.3602	0.43989	0.0:0.0:0.1637:0.8363	.	112;106;138	F5H0W4;Q9UBW5-2;Q9UBW5	.;.;BIN2_HUMAN	G	106;138;112	ENSP00000410217:R106G;ENSP00000267012:R138G;ENSP00000445874:R112G	ENSP00000267012:R138G	R	-	1	2	BIN2	49979762	0.996000	0.38824	1.000000	0.80357	0.855000	0.48748	1.901000	0.39838	2.260000	0.74910	0.533000	0.62120	AGA	.	.		0.507	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1			C	51693495	T	C	51693495	3	2	43	1	0	0	0	0	1	0	0	0	1433	1559	54	2	1317	2	BIN2	12	51693495	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2194915	51693495	82158400	244	5326										
GRASP	160622	hgsc.bcm.edu	37	chr12	52407934	52407934	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgcagcaaaccctgtatgagAagtggggagagtacaggtcc	14	8	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:52407934A>G	ENST00000293662.4	+	7	711	c.631A>G	c.(631-633)Aag>Gag	p.K211E	GRASP_ENST00000552049.1_Missense_Mutation_p.K68E|GRASP_ENST00000380039.2_Missense_Mutation_p.K68E|GRASP_ENST00000552963.1_3'UTR	NM_181711.2	NP_859062.1	Q7Z6J2	GRASP_HUMAN	GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein	211	Interaction with PSCD3. {ECO:0000250}.				protein localization (GO:0008104)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				central_nervous_system(1)|large_intestine(1)|lung(1)|skin(2)	5				BRCA - Breast invasive adenocarcinoma(357;0.0967)		CCTGTATGAGAAGTGGGGAGA	0.572																																					p.K211E		Atlas-SNP	.											.	GRASP	23	.	0			c.A631G						.						80	68	72					12																	52407934		2202	4300	6502	SO:0001583	missense	160622	exon7			TATGAGAAGTGGG	AC019244	CCDS8817.1, CCDS61124.1	12q13.13	2011-09-02			ENSG00000161835	ENSG00000161835			18707	protein-coding gene	gene with protein product		612027				10828067	Standard	NM_001271856		Approved		uc001rzo.2	Q7Z6J2	OTTHUMG00000169595	ENST00000293662.4:c.631A>G	chr12.hg19:g.52407934A>G	ENSP00000293662:p.Lys211Glu	74.0	0.0		99.0	4.0	NM_181711	Q6PIF8|Q7Z741	Missense_Mutation	SNP	ENST00000293662.4	hg19	CCDS8817.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.590597	0.86851	.	.	ENSG00000161835	ENST00000293662;ENST00000552049;ENST00000546756;ENST00000380039	T;T	0.66099	-0.19;0.1	4.07	4.07	0.47477	.	0.000000	0.85682	D	0.000000	T	0.74137	0.3677	M	0.61703	1.905	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.991	T	0.76501	-0.2936	10	0.72032	D	0.01	-0.0184	10.9268	0.47195	1.0:0.0:0.0:0.0	.	68;211	Q7Z6J2-2;Q7Z6J2	.;GRASP_HUMAN	E	211;68;81;68	ENSP00000293662:K211E;ENSP00000448476:K81E	ENSP00000293662:K211E	K	+	1	0	GRASP	50694201	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.920000	0.87521	1.849000	0.53698	0.377000	0.23210	AAG	.	.		0.572	GRASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404972.1			G	52407934	A	G	52407934	3	3	43	1	0	0	0	0	1	0	0	0	6764	247	9	2	657	2	GRASP	12	52407934	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	714439	52407934	81443961	245	5327										
STAT6	6778	hgsc.bcm.edu	37	chr12	57499264	57499264	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggaatacctggtgacgagggTtctcaggacttcatccagcc	12	11	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:57499264T>C	ENST00000300134.3	-	8	1124	c.799A>G	c.(799-801)Acc>Gcc	p.T267A	STAT6_ENST00000556155.1_Missense_Mutation_p.T267A|STAT6_ENST00000454075.3_Missense_Mutation_p.T267A|STAT6_ENST00000538913.2_Missense_Mutation_p.T157A|STAT6_ENST00000543873.2_Missense_Mutation_p.T267A|STAT6_ENST00000537215.2_Missense_Mutation_p.T157A	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	267					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						GTGACGAGGGTTCTCAGGACT	0.622																																					p.T267A		Atlas-SNP	.											.	STAT6	69	.	0			c.A799G						.						53	58	56					12																	57499264		2203	4300	6503	SO:0001583	missense	6778	exon8			CGAGGGTTCTCAG	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"SH2 domain containing"	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.799A>G	chr12.hg19:g.57499264T>C	ENSP00000300134:p.Thr267Ala	42.0	0.0		77.0	4.0	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	hg19	CCDS8931.1	.	.	.	.	.	.	.	.	.	.	T	4.072	0.011193	0.07912	.	.	ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516	T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	5.19	2.85	0.33270	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);p53-like transcription factor, DNA-binding (1);	0.412136	0.26481	N	0.024130	T	0.59555	0.2202	L	0.29908	0.895	0.18873	N	0.999987	B;B	0.06786	0.0;0.001	B;B	0.10450	0.005;0.004	T	0.37454	-0.9705	10	0.09590	T	0.72	-6.5242	6.4315	0.21798	0.0:0.1902:0.0:0.8098	.	267;267	A8K4S9;P42226	.;STAT6_HUMAN	A	267;157;157;267;267;157;267;157;267	ENSP00000300134:T267A;ENSP00000445409:T157A;ENSP00000438451:T267A;ENSP00000451742:T267A;ENSP00000444530:T157A;ENSP00000401486:T267A	ENSP00000300134:T267A	T	-	1	0	STAT6	55785531	0.000000	0.05858	0.066000	0.19879	0.841000	0.47740	-0.136000	0.10405	0.455000	0.26910	0.533000	0.62120	ACC	.	.		0.622	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		C	57499264	T	C	57499264	3	2	43	1	0	0	0	0	1	0	0	0	15285	1725	60	2	1804	2	STAT6	12	57499264	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5091330	57499264	76352631	246	5328										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80714407	80714407	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggctttttcatcatattcacAgattctagtgtcaaagcatc	6	9	5	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:80714407A>T	ENST00000547103.1	+	33	3987	c.3981A>T	c.(3979-3981)acA>acT	p.T1327T	OTOGL_ENST00000458043.2_Silent_p.T1327T			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1327					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TCATATTCACAGATTCTAGTG	0.373																																					p.T1327T		Atlas-SNP	.											.	OTOGL	235	.	0			c.A3981T						.						56	53	54					12																	80714407		1844	4098	5942	SO:0001819	synonymous_variant	283310	exon33			ATTCACAGATTCT	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.3981A>T	chr12.hg19:g.80714407A>T		68.0	0.0		86.0	52.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Silent	SNP	ENST00000547103.1	hg19																																																																																				.	.		0.373	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		T	80714407	A	T	80714407	2	4	43	1	0	0	0	0	0	0	0	1	1709	175	7	4		4	C12orf64	12	80714407	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	23215143	80714407	53137488	247	5329										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80747200	80747200	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggttctatggacacacttccTgtttgaatctaagagaagac	9	8	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:80747200T>C	ENST00000547103.1	+	45	5446	c.5440T>C	c.(5440-5442)Tgt>Cgt	p.C1814R	OTOGL_ENST00000458043.2_Missense_Mutation_p.C1826R|OTOGL_ENST00000546620.1_5'Flank			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1814					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						ACACACTTCCTGTTTGAATCT	0.473																																					p.C1826R		Atlas-SNP	.											.	OTOGL	235	.	0			c.T5476C						.						72	70	70					12																	80747200		1943	4144	6087	SO:0001583	missense	283310	exon45			ACTTCCTGTTTGA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5440T>C	chr12.hg19:g.80747200T>C	ENSP00000447211:p.Cys1814Arg	89.0	0.0		131.0	6.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.18	2.458902	0.43634	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.81415	-1.49;-1.49	5.74	4.57	0.56435	.	.	.	.	.	D	0.89125	0.6626	M	0.92691	3.335	0.58432	D	0.999997	.	.	.	.	.	.	D	0.87798	0.2623	7	0.24483	T	0.36	.	12.1334	0.53957	0.1286:0.0:0.0:0.8714	.	.	.	.	R	1814;1826	ENSP00000447211:C1814R;ENSP00000400895:C1826R	ENSP00000400895:C1826R	C	+	1	0	OTOGL	79271331	1.000000	0.71417	0.399000	0.26333	0.218000	0.24690	5.600000	0.67599	0.982000	0.38575	0.533000	0.62120	TGT	.	.		0.473	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		C	80747200	T	C	80747200	3	2	43	1	0	0	0	0	1	0	0	0	1709	1580	55	2	5654	2	C12orf64	12	80747200	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	32793	80747200	53104695	248	5330										
PLEKHG7	440107	hgsc.bcm.edu	37	chr12	93155594	93155594	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cctcttagttacgaaaactaAgtgcaacaaaaaggtaaaat	6	7	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:93155594A>G	ENST00000344636.3	+	9	951	c.767A>G	c.(766-768)aAg>aGg	p.K256R		NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	256	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						ACGAAAACTAAGTGCAACAAA	0.318																																					p.K256R		Atlas-SNP	.											.	PLEKHG7	38	.	0			c.A767G						.						71	67	68					12																	93155594		2198	4295	6493	SO:0001583	missense	440107	exon9			AAACTAAGTGCAA	AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"Pleckstrin homology (PH) domain containing"	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.767A>G	chr12.hg19:g.93155594A>G	ENSP00000344961:p.Lys256Arg	34.0	0.0		77.0	4.0	NM_001004330	B2RNR7	Missense_Mutation	SNP	ENST00000344636.3	hg19	CCDS31873.1	.	.	.	.	.	.	.	.	.	.	A	15.10	2.734292	0.48939	.	.	ENSG00000187510	ENST00000344636	T	0.66815	-0.23	5.38	4.19	0.49359	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.200532	0.53938	D	0.000060	T	0.51041	0.1651	L	0.47716	1.5	0.51767	D	0.999936	P	0.44281	0.831	B	0.32980	0.156	T	0.46803	-0.9165	10	0.14656	T	0.56	-14.1153	11.4409	0.50096	0.9269:0.0:0.0731:0.0	.	256	Q6ZR37	PKHG7_HUMAN	R	256	ENSP00000344961:K256R	ENSP00000344961:K256R	K	+	2	0	PLEKHG7	91679725	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	6.038000	0.70964	0.934000	0.37316	0.391000	0.25812	AAG	.	.		0.318	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330		G	93155594	A	G	93155594	3	3	43	1	0	0	0	0	1	0	0	0	12084	72	3	2	797	2	PLEKHG7	12	93155594	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	12408394	93155594	40696301	249	5331										
SRRM4	84530	hgsc.bcm.edu	37	chr12	119568550	119568550	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	actcccgccgctgctccaagAccctctgcaaggacagccct	8	19	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:119568550A>G	ENST00000267260.4	+	8	1070	c.682A>G	c.(682-684)Acc>Gcc	p.T228A	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	228	Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						CTGCTCCAAGACCCTCTGCAA	0.647																																					p.T228A		Atlas-SNP	.											.	SRRM4	131	.	0			c.A682G						.						24	30	28					12																	119568550		1927	4122	6049	SO:0001583	missense	84530	exon8			TCCAAGACCCTCT	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"neural-specific SR-related protein of 100 kDa"	613103	"KIAA1853"	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.682A>G	chr12.hg19:g.119568550A>G	ENSP00000267260:p.Thr228Ala	16.0	0.0		43.0	4.0	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	hg19	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	A	19.41	3.822999	0.71028	.	.	ENSG00000139767	ENST00000267260	T	0.21932	1.98	5.07	3.93	0.45458	.	0.756494	0.12339	N	0.477628	T	0.15435	0.0372	L	0.36672	1.1	0.21604	N	0.999627	B	0.02656	0.0	B	0.04013	0.001	T	0.10800	-1.0614	10	0.34782	T	0.22	-9.589	5.7856	0.18331	0.794:0.0:0.206:0.0	.	228	A7MD48	SRRM4_HUMAN	A	228	ENSP00000267260:T228A	ENSP00000267260:T228A	T	+	1	0	SRRM4	118052933	0.894000	0.30519	1.000000	0.80357	0.985000	0.73830	1.557000	0.36299	1.909000	0.55274	0.368000	0.22195	ACC	.	.		0.647	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		G	119568550	A	G	119568550	3	3	43	1	0	0	0	0	1	0	0	0	15186	275	10	2	712	2	SRRM4	12	119568550	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	26412956	119568550	14283345	250	5332										
LRRC43	254050	hgsc.bcm.edu	37	chr12	122676094	122676094	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aagaaggcgaaatgaatgagTccgcgggcgtcctggccgag	16	9	0	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:122676094T>C	ENST00000339777.4	+	6	1097	c.1069T>C	c.(1069-1071)Tcc>Ccc	p.S357P	LRRC43_ENST00000425921.1_Missense_Mutation_p.S172P	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	357	Glu-rich.									NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		AATGAATGAGTCCGCGGGCGT	0.532											OREG0022219	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S357P		Atlas-SNP	.											.	LRRC43	105	.	0			c.T1069C						.						81	81	81					12																	122676094		1905	4118	6023	SO:0001583	missense	254050	exon6			AATGAGTCCGCGG	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.1069T>C	chr12.hg19:g.122676094T>C	ENSP00000344233:p.Ser357Pro	27.0	0.0	1520	79.0	4.0	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	hg19	CCDS45001.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.288273	0.23478	.	.	ENSG00000158113	ENST00000339777;ENST00000289014;ENST00000425921	T;T	0.56275	0.47;0.91	5.39	-2.78	0.05859	.	1.733180	0.02914	N	0.137085	T	0.25232	0.0613	N	0.08118	0	0.09310	N	1	B	0.32653	0.379	B	0.28139	0.086	T	0.05257	-1.0896	9	.	.	.	-0.2897	1.3738	0.02216	0.1846:0.2531:0.105:0.4573	.	357	Q8N309	LRC43_HUMAN	P	357;228;172	ENSP00000344233:S357P;ENSP00000416628:S172P	.	S	+	1	0	LRRC43	121242047	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.676000	0.05221	-0.304000	0.08843	-1.795000	0.00624	TCC	.	.		0.532	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		C	122676094	T	C	122676094	3	2	43	1	0	0	0	0	1	0	0	0	9010	1667	58	2	1091	2	LRRC43	12	122676094	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3107544	122676094	11175801	251	5333										
TCTN2	79867	hgsc.bcm.edu	37	chr12	124158356	124158356	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tctctgacccataatgcctcAggcaagtgaagtctttgact	8	11	3	3	rs111689585		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:124158356A>T	ENST00000303372.5	+	4	590	c.462A>T	c.(460-462)tcA>tcT	p.S154S	TCTN2_ENST00000426174.2_Splice_Site_p.S153S	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	154					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		ATAATGCCTCAGGCAAGTGAA	0.443																																					p.S154S		Atlas-SNP	.											.	TCTN2	50	.	0			c.A462T						.						173	169	170					12																	124158356		2203	4300	6503	SO:0001630	splice_region_variant	79867	exon4			TGCCTCAGGCAAG	AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"Tectonic proteins"	25774	protein-coding gene	gene with protein product	"Meckel syndrome, type 8"	613846	"chromosome 12 open reading frame 38"	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.463+1A>T	chr12.hg19:g.124158356A>T		143.0	0.0		216.0	118.0	NM_024809	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	hg19	CCDS9253.1																																																																																			.	A|0.500;G|0.500		0.443	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809	Silent	T	124158356	A	T	124158356	5	4	43	1	0	0	0	0	0	0	1	0	15738	202	7	4	476	4	TCTN2	12	124158356	Splice_Site	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1482262	124158356	9693539	252	5334										
DHX37	57647	hgsc.bcm.edu	37	chr12	125435267	125435267	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atcttagtggtctccacgatTtcctggtagaccacaaactc	7	12	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:125435267T>C	ENST00000308736.2	-	22	3050	c.2952A>G	c.(2950-2952)gaA>gaG	p.E984E	DHX37_ENST00000544745.1_Silent_p.E771E	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	984							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		TCTCCACGATTTCCTGGTAGA	0.587																																					p.E984E		Atlas-SNP	.											.	DHX37	114	.	0			c.A2952G						.						78	83	82					12																	125435267		2203	4300	6503	SO:0001819	synonymous_variant	57647	exon22			CACGATTTCCTGG	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.2952A>G	chr12.hg19:g.125435267T>C		62.0	0.0		95.0	4.0	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	hg19	CCDS9261.1																																																																																			.	.		0.587	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		C	125435267	T	C	125435267	2	2	43	1	0	0	0	0	0	0	0	1	4512	1838	64	2		2	DHX37	12	125435267	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1276911	125435267	8416628	253	5335										
DHX37	57647	hgsc.bcm.edu	37	chr12	125451369	125451369	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gccttcttggccctggccctTgacttcttaaacttccgcat	7	15	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:125451369T>A	ENST00000308736.2	-	12	1658	c.1560A>T	c.(1558-1560)tcA>tcT	p.S520S	DHX37_ENST00000544745.1_Silent_p.S307S	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	520	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		CCCTGGCCCTTGACTTCTTAA	0.617																																					p.S520S		Atlas-SNP	.											.	DHX37	114	.	0			c.A1560T						.						119	115	116					12																	125451369		2203	4300	6503	SO:0001819	synonymous_variant	57647	exon12			GGCCCTTGACTTC	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.1560A>T	chr12.hg19:g.125451369T>A		155.0	0.0		168.0	69.0	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	hg19	CCDS9261.1																																																																																			.	.		0.617	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		A	125451369	T	A	125451369	2	1	43	1	0	0	0	0	0	0	0	1	4512	1799	63	4		4	DHX37	12	125451369	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	16102	125451369	8400526	254	5336										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126138907	126138907	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaaccctgttgacattacacTcccatcagaggagtgcacaa	8	12	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr12:126138907T>C	ENST00000299308.3	+	9	2896	c.2888T>C	c.(2887-2889)cTc>cCc	p.L963P	TMEM132B_ENST00000535886.1_Missense_Mutation_p.L475P	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	963						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		GACATTACACTCCCATCAGAG	0.507																																					p.L963P		Atlas-SNP	.											.	TMEM132B	207	.	0			c.T2888C						.						75	72	73					12																	126138907		1921	4130	6051	SO:0001583	missense	114795	exon9			TTACACTCCCATC	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.2888T>C	chr12.hg19:g.126138907T>C	ENSP00000299308:p.Leu963Pro	83.0	0.0		86.0	4.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	hg19	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	T	5.140	0.211523	0.09757	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.09350	3.8;2.99	5.3	4.15	0.48705	.	0.000000	0.53938	D	0.000050	T	0.04952	0.0133	N	0.10837	0.055	0.80722	D	1	B	0.19583	0.037	B	0.19148	0.024	T	0.22068	-1.0227	10	0.02654	T	1	.	10.9829	0.47506	0.0:0.0732:0.0:0.9268	.	963	Q14DG7	T132B_HUMAN	P	963;475	ENSP00000299308:L963P;ENSP00000440436:L475P	ENSP00000299308:L963P	L	+	2	0	TMEM132B	124704860	1.000000	0.71417	0.023000	0.16930	0.570000	0.35934	4.348000	0.59379	0.860000	0.35481	0.533000	0.62120	CTC	.	.		0.507	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		C	126138907	T	C	126138907	3	2	43	1	0	0	0	0	1	0	0	0	16061	1551	54	2	2922	2	TMEM132B	12	126138907	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	687538	126138907	7712988	255	5337										
BRCA2	675	hgsc.bcm.edu	37	chr13	32912226	32912226	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaaactgtttagtgatattgAgaatattagtgaggaaactt	10	2	0	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr13:32912226A>G	ENST00000380152.3	+	11	3967	c.3734A>G	c.(3733-3735)gAg>gGg	p.E1245G	BRCA2_ENST00000544455.1_Missense_Mutation_p.E1245G			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1245					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AGTGATATTGAGAATATTAGT	0.343			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.E1245G	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2	812	.	0			c.A3734G						.						46	47	46					13																	32912226		2203	4299	6502	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	ATATTGAGAATAT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.3734A>G	chr13.hg19:g.32912226A>G	ENSP00000369497:p.Glu1245Gly	39.0	0.0		39.0	4.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	19.88	3.909787	0.72983	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.81078	-1.45;-1.45	5.72	5.72	0.89469	.	0.176318	0.39834	N	0.001251	D	0.88403	0.6427	M	0.66939	2.045	0.46774	D	0.999195	D	0.76494	0.999	D	0.70935	0.971	D	0.89571	0.3813	10	0.87932	D	0	.	15.9966	0.80256	1.0:0.0:0.0:0.0	.	1245	P51587	BRCA2_HUMAN	G	1245	ENSP00000369497:E1245G;ENSP00000439902:E1245G	ENSP00000369497:E1245G	E	+	2	0	BRCA2	31810226	1.000000	0.71417	0.926000	0.36857	0.834000	0.47266	6.820000	0.75267	2.177000	0.69029	0.528000	0.53228	GAG	.	.		0.343	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32912226	A	G	32912226	3	3	43	1	0	0	0	0	1	0	0	0	1501	304	11	2	3772	2	BRCA2	13	32912226	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10		32912226	82257652	256	5338										
CCDC122	160857	hgsc.bcm.edu	37	chr13	44433973	44433973	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttttatgtgcttttattttTgcataatatgcattatattt	4	3	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr13:44433973T>C	ENST00000444614.3	-	5	648	c.390A>G	c.(388-390)gcA>gcG	p.A130A	CCDC122_ENST00000476570.2_5'UTR|CCDC122_ENST00000281508.3_Silent_p.A130A	NM_144974.3	NP_659411.2	Q5T0U0	CC122_HUMAN	coiled-coil domain containing 122	130										endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9		Lung NSC(96;7.5e-06)|Breast(139;0.00765)|Hepatocellular(98;0.00826)|Prostate(109;0.0143)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000767)|BRCA - Breast invasive adenocarcinoma(63;0.128)		CTTTTATTTTTGCATAATATG	0.294																																					p.A130A		Atlas-SNP	.											.	CCDC122	21	.	0			c.A390G						.						112	110	110					13																	44433973		2203	4298	6501	SO:0001819	synonymous_variant	160857	exon5			TATTTTTGCATAA	AK056408	CCDS9390.2	13q14.11	2008-10-30			ENSG00000151773	ENSG00000151773			26478	protein-coding gene	gene with protein product		613408					Standard	NM_144974		Approved	FLJ31846	uc010acf.3	Q5T0U0	OTTHUMG00000017413	ENST00000444614.3:c.390A>G	chr13.hg19:g.44433973T>C		63.0	0.0		49.0	35.0	NM_144974	B2RP70|B7ZMI9|Q96MV0	Silent	SNP	ENST00000444614.3	hg19	CCDS9390.2																																																																																			.	.		0.294	CCDC122-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276172.4	NM_144974		C	44433973	T	C	44433973	2	2	43	1	0	0	0	0	0	0	0	1	2760	1799	63	2		2	CCDC122	13	44433973	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	11521747	44433973	70735905	257	5339										
RCBTB2	1102	hgsc.bcm.edu	37	chr13	49073817	49073817	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	taggtattccaggaaggcccGgtaaacaggatatgaaaatt	11	6	0	1	rs529818415		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr13:49073817G>A	ENST00000344532.3	-	13	1747	c.1324C>T	c.(1324-1326)Cgg>Tgg	p.R442W	RCBTB2_ENST00000430805.2_Missense_Mutation_p.R447W|RCBTB2_ENST00000544492.1_Missense_Mutation_p.R168W	NM_001268.2	NP_001259.1	O95199	RCBT2_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	442	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				positive regulation of Ran GTPase activity (GO:0032853)	acrosomal vesicle (GO:0001669)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			breast(5)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(3)	31		all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116)		AGGAAGGCCCGGTAAACAGGA	0.408													G|||	0	0	0	0	5008	,	,		21051	0		0	False		,,,				2504	0				p.R442W		Atlas-SNP	.											.	RCBTB2	62	.	0			c.C1324T						.						133	130	131					13																	49073817		2203	4300	6503	SO:0001583	missense	1102	exon13			AGGCCCGGTAAAC	AF060219	CCDS9411.1, CCDS73570.1, CCDS73571.1, CCDS73572.1	13q14.3	2013-01-08	2005-05-09	2005-05-09	ENSG00000136161	ENSG00000136161		"BTB/POZ domain containing"	1914	protein-coding gene	gene with protein product		603524	"chromosome condensation 1-like"	CHC1L		9806834	Standard	XM_005266242		Approved		uc001vch.3	O95199	OTTHUMG00000016902	ENST00000344532.3:c.1324C>T	chr13.hg19:g.49073817G>A	ENSP00000345144:p.Arg442Trp	81.0	0.0		67.0	5.0	NM_001268	B2RDW8	Missense_Mutation	SNP	ENST00000344532.3	hg19	CCDS9411.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.455952	0.43634	.	.	ENSG00000136161	ENST00000344532;ENST00000450343;ENST00000452987;ENST00000430805;ENST00000544492	T;T;T	0.69175	-0.38;-0.38;-0.38	5.09	4.22	0.49857	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.79986	0.4541	M	0.66297	2.02	0.80722	D	1	B;D;D;B	0.89917	0.244;0.999;1.0;0.125	B;D;D;B	0.87578	0.117;0.953;0.998;0.117	T	0.82571	-0.0391	10	0.87932	D	0	.	15.1174	0.72413	0.0:0.0:0.8573:0.1427	.	168;447;394;442	B4E372;B4DWG0;B3KVB1;O95199	.;.;.;RCBT2_HUMAN	W	442;394;447;447;168	ENSP00000345144:R442W;ENSP00000389910:R447W;ENSP00000443862:R168W	ENSP00000345144:R442W	R	-	1	2	RCBTB2	47971818	1.000000	0.71417	0.988000	0.46212	0.987000	0.75469	4.023000	0.57211	1.237000	0.43756	0.478000	0.44815	CGG	.	.		0.408	RCBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044888.2	NM_001268		A	49073817	G	A	49073817	3	1	43	1	0	0	0	0	1	0	0	0	13187	1115	39	1	343	1	RCBTB2	13	49073817	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	4639844	49073817	66096061	258	5340										
CYSLTR2	57105	hgsc.bcm.edu	37	chr13	49281801	49281801	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gggtttatgcaaagacagacTgcataaagctttggttatca	10	6	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr13:49281801T>C	ENST00000282018.3	+	1	851	c.848T>C	c.(847-849)cTg>cCg	p.L283P		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	283					immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell death (GO:0010942)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteinyl leukotriene receptor activity (GO:0001631)|leukotriene receptor activity (GO:0004974)			endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)	AAAGACAGACTGCATAAAGCT	0.458																																					p.L283P		Atlas-SNP	.											.	CYSLTR2	55	.	0			c.T848C						.						167	145	152					13																	49281801		2203	4300	6503	SO:0001583	missense	57105	exon1			ACAGACTGCATAA	AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207		"GPCR / Class A : Leukotriene receptors"	18274	protein-coding gene	gene with protein product		605666				10913337, 1085123	Standard	NM_020377		Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.848T>C	chr13.hg19:g.49281801T>C	ENSP00000282018:p.Leu283Pro	88.0	0.0		71.0	4.0	NM_020377	Q9HCQ2	Missense_Mutation	SNP	ENST00000282018.3	hg19	CCDS9412.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.147339	0.37923	.	.	ENSG00000152207	ENST00000282018	T	0.32753	1.44	5.51	4.3	0.51218	GPCR, rhodopsin-like superfamily (1);	0.265818	0.24796	N	0.035531	T	0.57330	0.2046	M	0.87381	2.88	0.46798	D	0.999209	D	0.62365	0.991	D	0.66847	0.947	T	0.62520	-0.6837	10	0.87932	D	0	.	11.0643	0.47966	0.139:0.0:0.0:0.861	.	283	Q9NS75	CLTR2_HUMAN	P	283	ENSP00000282018:L283P	ENSP00000282018:L283P	L	+	2	0	CYSLTR2	48179802	1.000000	0.71417	0.411000	0.26484	0.327000	0.28475	5.009000	0.63998	0.903000	0.36546	0.533000	0.62120	CTG	.	.		0.458	CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1			C	49281801	T	C	49281801	3	2	43	1	0	0	0	0	1	0	0	0	4204	1580	55	2	850	2	CYSLTR2	13	49281801	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	207984	49281801	65888077	259	5341										
CAB39L	81617	hgsc.bcm.edu	37	chr13	49913821	49913821	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atttgatattacctttaaagActgtctcttagtaacataat	4	6	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr13:49913821A>G	ENST00000355854.4	-	7	1179	c.682T>C	c.(682-684)Tct>Cct	p.S228P	CAB39L_ENST00000347776.5_Missense_Mutation_p.S228P|CAB39L_ENST00000409308.1_Missense_Mutation_p.S228P|CAB39L_ENST00000410043.1_Missense_Mutation_p.S228P|CAB39L_ENST00000409130.1_Missense_Mutation_p.S84P	NM_030925.2	NP_112187.2	Q9H9S4	CB39L_HUMAN	calcium binding protein 39-like	228					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|stomach(1)	12		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)		ACCTTTAAAGACTGTCTCTTA	0.313																																					p.S228P		Atlas-SNP	.											.	CAB39L	35	.	0			c.T682C						.						48	48	48					13																	49913821		2196	4295	6491	SO:0001583	missense	81617	exon7			TTAAAGACTGTCT	AK022639	CCDS9416.2	13q14.11	2008-02-05			ENSG00000102547	ENSG00000102547			20290	protein-coding gene	gene with protein product		612175					Standard	NM_030925		Approved	bA103J18.3, FLJ12577, MO2L	uc001vcw.3	Q9H9S4	OTTHUMG00000016914	ENST00000355854.4:c.682T>C	chr13.hg19:g.49913821A>G	ENSP00000348113:p.Ser228Pro	126.0	0.0		92.0	4.0	NM_030925	Q5TAW6|Q6WG71|Q96FG1|Q9BZ33	Missense_Mutation	SNP	ENST00000355854.4	hg19	CCDS9416.2	.	.	.	.	.	.	.	.	.	.	A	24.0	4.482094	0.84747	.	.	ENSG00000102547	ENST00000355854;ENST00000347776;ENST00000378341;ENST00000409308;ENST00000409130;ENST00000425242;ENST00000410043	T;T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22;1.22	5.43	5.43	0.79202	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.71151	0.3306	H	0.95850	3.73	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	T	0.81502	-0.0904	9	.	.	.	-19.2664	14.6657	0.68907	1.0:0.0:0.0:0.0	.	228	Q9H9S4	CB39L_HUMAN	P	228;228;205;228;84;171;228	ENSP00000348113:S228P;ENSP00000261669:S228P;ENSP00000386375:S228P;ENSP00000387245:S84P;ENSP00000416719:S171P;ENSP00000386328:S228P	.	S	-	1	0	CAB39L	48811822	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.827000	0.92041	2.071000	0.62044	0.418000	0.28097	TCT	.	.		0.313	CAB39L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044908.3	NM_030925		G	49913821	A	G	49913821	3	3	43	1	0	0	0	0	1	0	0	0	2528	275	10	2	343	2	CAB39L	13	49913821	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	632020	49913821	65256057	260	5342										
ATP7B	540	hgsc.bcm.edu	37	chr13	52532539	52532539	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cacagggctcctctccgcctTctcagccacagcaaccacca	6	20	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr13:52532539T>C	ENST00000242839.4	-	8	2419	c.2263A>G	c.(2263-2265)Aag>Gag	p.K755E	ATP7B_ENST00000400370.3_Intron|ATP7B_ENST00000542656.1_3'UTR|ATP7B_ENST00000418097.2_Missense_Mutation_p.K755E|ATP7B_ENST00000400366.3_Missense_Mutation_p.K644E|ATP7B_ENST00000417240.2_Missense_Mutation_p.K27E|ATP7B_ENST00000344297.5_Intron|ATP7B_ENST00000482841.1_Intron|ATP7B_ENST00000448424.2_Intron	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	755					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CTCTCCGCCTTCTCAGCCACA	0.552									Wilson disease																												p.K755E		Atlas-SNP	.											ATP7B,rectum,carcinoma,0,1	ATP7B	123	.	0			c.A2263G						.						112	118	116					13																	52532539		2081	4217	6298	SO:0001583	missense	540	exon8	Familial Cancer Database		CCGCCTTCTCAGC	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.2263A>G	chr13.hg19:g.52532539T>C	ENSP00000242839:p.Lys755Glu	99.0	0.0		88.0	5.0	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	hg19	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.380353	0.61845	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000417240;ENST00000418097	D;D;D;D	0.95137	-3.62;-3.62;-3.62;-3.62	5.54	3.12	0.35913	ATPase,  P-type, cytoplasmic transduction domain A (1);	0.340362	0.34986	N	0.003532	D	0.90693	0.7080	L	0.38692	1.165	0.80722	D	1	P;B;B;P	0.38129	0.619;0.0;0.103;0.491	B;B;B;B	0.44108	0.441;0.001;0.024;0.184	D	0.84076	0.0382	10	0.19590	T	0.45	-7.6007	8.1175	0.30953	0.0:0.071:0.1469:0.782	.	755;27;644;755	F5H748;E7EQQ2;P35670-3;P35670	.;.;.;ATP7B_HUMAN	E	755;644;27;755	ENSP00000242839:K755E;ENSP00000383217:K644E;ENSP00000390360:K27E;ENSP00000393343:K755E	ENSP00000242839:K755E	K	-	1	0	ATP7B	51430540	1.000000	0.71417	0.984000	0.44739	0.884000	0.51177	2.560000	0.45896	0.386000	0.24997	0.460000	0.39030	AAG	.	.		0.552	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		C	52532539	T	C	52532539	3	2	43	1	0	0	0	0	1	0	0	0	1191	1792	62	2	2190	2	ATP7B	13	52532539	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2618718	52532539	62637339	261	5343										
VPS36	51028	hgsc.bcm.edu	37	chr13	52992177	52992177	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttgcacgcattcactaaatcTtctggtgagagcaactaata	7	9	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr13:52992177T>C	ENST00000378060.4	-	11	882	c.855A>G	c.(853-855)gaA>gaG	p.E285E		NM_001282168.1|NM_001282169.1|NM_016075.2	NP_001269097.1|NP_001269098.1|NP_057159.2	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36 homolog (S. cerevisiae)	285					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	17		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		TCACTAAATCTTCTGGTGAGA	0.373																																					p.E285E		Atlas-SNP	.											.	VPS36	38	.	0			c.A855G						.						82	75	77					13																	52992177		2203	4300	6503	SO:0001819	synonymous_variant	51028	exon11			TAAATCTTCTGGT	AF151903	CCDS9434.1, CCDS73577.1	13q14.13	2008-02-05	2007-01-12	2005-08-02	ENSG00000136100	ENSG00000136100			20312	protein-coding gene	gene with protein product		610903	"chromosome 13 open reading frame 9", "vacuolar protein sorting 36 homolog (yeast)"	C13orf9		11278625, 15755741	Standard	NM_016075		Approved	CGI-145, Eap45	uc001vgs.3	Q86VN1	OTTHUMG00000016964	ENST00000378060.4:c.855A>G	chr13.hg19:g.52992177T>C		55.0	0.0		41.0	4.0	NM_016075	A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3	Silent	SNP	ENST00000378060.4	hg19	CCDS9434.1																																																																																			.	.		0.373	VPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045059.3			C	52992177	T	C	52992177	2	2	43	1	0	0	0	0	0	0	0	1	17219	1606	56	2		2	VPS36	13	52992177	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	459638	52992177	62177701	262	5344										
SLITRK6	84189	hgsc.bcm.edu	37	chr13	86369191	86369191	+	Frame_Shift_Del	DEL	T	T	-													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgttttaagatttaccttagTtagaggaacccctgaaaaaa							TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr13:86369191delT	ENST00000400286.2	-	2	2051	c.1453delA	c.(1453-1455)actfs	p.T485fs		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	485					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		TTTACCTTAGTTAGAGGAACC	0.368																																					p.T485fs		Atlas-Indel,Pindel	.											.	SLITRK6	150	.	0			c.1454delC						.						80	80	80					13																	86369191		1807	4066	5873	SO:0001589	frameshift_variant	84189	exon2			.	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.1453delA	chr13.hg19:g.86369191delT	ENSP00000383143:p.Thr485fs	60.0	0.0		62.0	53.0	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Frame_Shift_Del	DEL	ENST00000400286.2	hg19	CCDS41903.1																																																																																			.	.		0.368	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		-	86369191	T	-	86369191	7	5	43	1	0	1	0	1	0	0	0	0	14762	1725	60	0	1076	0	SLITRK6	13	86369191	Frame_Shift_Del	DEL	T	TCGA-BC-A3KF-01A-11D-A20W-10	33377014	86369191	28800687	263	5345										
TEP1	7011	hgsc.bcm.edu	37	chr14	20840992	20840992	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggtgtgtgccgaggaccagaTcagagcaccaatgtggcctg	15	10	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:20840992T>C	ENST00000262715.5	-	49	7016	c.6976A>G	c.(6976-6978)Atc>Gtc	p.I2326V	TEP1_ENST00000545983.1_Intron|TEP1_ENST00000556935.1_Missense_Mutation_p.I2218V	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2326					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GAGGACCAGATCAGAGCACCA	0.512																																					p.I2326V		Atlas-SNP	.											.	TEP1	224	.	0			c.A6976G						.						117	103	108					14																	20840992		2203	4300	6503	SO:0001583	missense	7011	exon49			ACCAGATCAGAGC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.6976A>G	chr14.hg19:g.20840992T>C	ENSP00000262715:p.Ile2326Val	69.0	0.0		98.0	5.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	T	0.161	-1.081192	0.01888	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.17370	2.28;2.28	5.91	-2.06	0.07298	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	1.308390	0.04774	N	0.428499	T	0.08358	0.0208	N	0.20685	0.6	0.26731	N	0.970588	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.31696	-0.9934	10	0.12103	T	0.63	-1.0348	1.5854	0.02643	0.129:0.1545:0.238:0.4786	.	2218;1669;2326	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	V	2326;2326;2218	ENSP00000262715:I2326V;ENSP00000452574:I2218V	ENSP00000262715:I2326V	I	-	1	0	TEP1	19910832	0.170000	0.23016	0.519000	0.27824	0.071000	0.16799	-0.683000	0.05179	-0.112000	0.11979	0.533000	0.62120	ATC	.	.		0.512	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		C	20840992	T	C	20840992	3	2	43	1	0	0	0	0	1	0	0	0	15774	1435	50	2	935	2	TEP1	14	20840992	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10		20840992	86508548	264	5346										
NDRG2	57447	hgsc.bcm.edu	37	chr14	21488710	21488710	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgggatcaatgttgatgaggAcaagaccttcaacagtgtcc	11	8	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:21488710A>G	ENST00000556147.1	-	8	1440	c.500T>C	c.(499-501)gTc>gCc	p.V167A	NDRG2_ENST00000397844.2_Missense_Mutation_p.V153A|NDRG2_ENST00000397851.2_Missense_Mutation_p.V167A|NDRG2_ENST00000298687.5_Missense_Mutation_p.V167A|NDRG2_ENST00000298684.5_Intron|NDRG2_ENST00000397853.3_Missense_Mutation_p.V167A|NDRG2_ENST00000554277.1_5'UTR|NDRG2_ENST00000554143.1_Missense_Mutation_p.V153A|NDRG2_ENST00000350792.3_Missense_Mutation_p.V153A|NDRG2_ENST00000554104.1_Missense_Mutation_p.V80A|NDRG2_ENST00000403829.3_Missense_Mutation_p.V163A|NDRG2_ENST00000553503.1_Missense_Mutation_p.V153A|NDRG2_ENST00000397858.1_Missense_Mutation_p.V167A|NDRG2_ENST00000555158.1_Missense_Mutation_p.V153A|NDRG2_ENST00000397856.3_Missense_Mutation_p.V153A|NDRG2_ENST00000397855.3_Intron|NDRG2_ENST00000397847.2_Missense_Mutation_p.V167A|NDRG2_ENST00000360463.3_Missense_Mutation_p.V153A			Q9UN36	NDRG2_HUMAN	NDRG family member 2	167					cell differentiation (GO:0030154)|negative regulation of cytokine production (GO:0001818)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of platelet-derived growth factor production (GO:0090361)|regulation of vascular endothelial growth factor production (GO:0010574)|substantia nigra development (GO:0021762)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)				breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	23	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		GTTGATGAGGACAAGACCTTC	0.557																																					p.V167A		Atlas-SNP	.											.	NDRG2	37	.	0			c.T500C						.						110	87	95					14																	21488710		2203	4300	6503	SO:0001583	missense	57447	exon8			ATGAGGACAAGAC	AB033074	CCDS9564.1, CCDS9565.1, CCDS61384.1, CCDS61386.1, CCDS73613.1	14q11.2	2008-07-09			ENSG00000165795	ENSG00000165795			14460	protein-coding gene	gene with protein product		605272				10831399	Standard	NM_201535		Approved	KIAA1248, SYLD	uc001vyx.3	Q9UN36	OTTHUMG00000029619	ENST00000556147.1:c.500T>C	chr14.hg19:g.21488710A>G	ENSP00000451712:p.Val167Ala	66.0	0.0		84.0	4.0	NM_201537	B3KUE3|B4DE86|B7WP11|B7WPD5|D3DS07|D3DS10|Q567T1|Q68DW2|Q86U08|Q86U46|Q96FD3|Q96FT0|Q96JU0|Q96PN0|Q9BQH5|Q9ULH2	Missense_Mutation	SNP	ENST00000556147.1	hg19	CCDS9565.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.9|24.9	4.581141|4.581141	0.86748|0.86748	.|.	.|.	ENSG00000165795|ENSG00000165795	ENST00000553593|ENST00000298687;ENST00000350792;ENST00000554770;ENST00000397858;ENST00000557633;ENST00000554104;ENST00000555158;ENST00000553503;ENST00000397853;ENST00000360463;ENST00000556147;ENST00000554143;ENST00000397851;ENST00000397847;ENST00000397856;ENST00000397844;ENST00000403829;ENST00000556008;ENST00000556366;ENST00000556974;ENST00000555026;ENST00000553867;ENST00000557169;ENST00000555869;ENST00000557182;ENST00000555733;ENST00000555384;ENST00000554094;ENST00000553442;ENST00000556420;ENST00000553784;ENST00000557149;ENST00000555142	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.27104	.|1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69	5.55|5.55	4.39|4.39	0.52855|0.52855	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.52709|0.52709	0.1751|0.1751	M|M	0.86268|0.86268	2.805|2.805	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.91635	.|0.999;0.999;0.998;0.998;0.999	T|T	0.57522|0.57522	-0.7797|-0.7797	5|10	.|0.87932	.|D	.|0	-20.1741|-20.1741	10.4698|10.4698	0.44629|0.44629	0.8544:0.0:0.0:0.1456|0.8544:0.0:0.0:0.1456	.|.	.|163;167;153;148;167	.|B4DE86;Q9UN36-3;Q9UN36-5;G3V3N4;Q9UN36	.|.;.;.;.;NDRG2_HUMAN	P|A	83|167;153;148;167;110;80;153;153;167;153;167;153;167;167;153;153;163;153;80;153;153;167;153;153;112;167;167;153;153;153;167;153;153	.|ENSP00000298687:V167A;ENSP00000344620:V153A;ENSP00000380956:V167A;ENSP00000450835:V110A;ENSP00000452216:V80A;ENSP00000452038:V153A;ENSP00000452306:V153A;ENSP00000380951:V167A;ENSP00000353649:V153A;ENSP00000451712:V167A;ENSP00000452006:V153A;ENSP00000380949:V167A;ENSP00000380945:V167A;ENSP00000380954:V153A;ENSP00000380943:V153A;ENSP00000385889:V163A;ENSP00000451966:V153A;ENSP00000452413:V80A;ENSP00000452362:V153A;ENSP00000451274:V153A;ENSP00000450691:V167A;ENSP00000452334:V153A;ENSP00000451105:V153A;ENSP00000450545:V112A;ENSP00000452482:V167A;ENSP00000451094:V167A;ENSP00000452278:V153A;ENSP00000450493:V153A;ENSP00000451951:V153A;ENSP00000451059:V167A;ENSP00000452592:V153A;ENSP00000450513:V153A	.|ENSP00000298687:V167A	S|V	-|-	1|2	0|0	NDRG2|NDRG2	20558550|20558550	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.989000|0.989000	0.77384|0.77384	8.565000|8.565000	0.90730|0.90730	1.019000|1.019000	0.39547|0.39547	0.533000|0.533000	0.62120|0.62120	TCC|GTC	.	.		0.557	NDRG2-013	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411717.1			G	21488710	A	G	21488710	3	3	43	1	0	0	0	0	1	0	0	0	10261	275	10	2	651	2	NDRG2	14	21488710	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	647718	21488710	85860830	265	5347										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23532238	23532238	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tggtaatggaaactccggacTtctgctggctaatggaacgt	12	8	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:23532238T>C	ENST00000262710.1	-	14	3284	c.2957A>G	c.(2956-2958)aAg>aGg	p.K986R	ACIN1_ENST00000555053.1_Missense_Mutation_p.K973R|ACIN1_ENST00000357481.2_Missense_Mutation_p.K228R|ACIN1_ENST00000397341.3_Missense_Mutation_p.K228R|ACIN1_ENST00000605057.1_Missense_Mutation_p.K928R|ACIN1_ENST00000557515.1_Missense_Mutation_p.K227R|ACIN1_ENST00000457657.1_Missense_Mutation_p.K946R|ACIN1_ENST00000338631.6_Missense_Mutation_p.K259R	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	986					apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		AACTCCGGACTTCTGCTGGCT	0.483																																					p.K986R		Atlas-SNP	.											.	ACIN1	147	.	0			c.A2957G						.						175	162	166					14																	23532238		2203	4300	6503	SO:0001583	missense	22985	exon14			CCGGACTTCTGCT	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.2957A>G	chr14.hg19:g.23532238T>C	ENSP00000262710:p.Lys986Arg	71.0	0.0		82.0	4.0	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	T	18.03	3.531915	0.64972	.	.	ENSG00000100813	ENST00000557515;ENST00000338631;ENST00000357481;ENST00000262710;ENST00000457657;ENST00000397341;ENST00000555053	T;T;T;T;T;T	0.19394	3.42;3.42;2.2;2.21;3.42;2.15	5.5	4.35	0.52113	.	0.000000	0.42964	D	0.000622	T	0.26304	0.0642	L	0.40543	1.245	0.48341	D	0.999634	P;P;P;P;P	0.41498	0.708;0.584;0.752;0.607;0.607	P;B;P;B;B	0.53062	0.595;0.39;0.717;0.254;0.254	T	0.03641	-1.1017	10	0.22109	T	0.4	-21.1323	8.4596	0.32921	0.0:0.1566:0.0:0.8434	.	973;986;946;259;228	G3V3M7;Q9UKV3;E7EQT4;Q9UKV3-2;Q9UKV3-3	.;ACINU_HUMAN;.;.;.	R	227;259;228;986;946;228;973	ENSP00000345541:K259R;ENSP00000350073:K228R;ENSP00000262710:K986R;ENSP00000405677:K946R;ENSP00000380502:K228R;ENSP00000451328:K973R	ENSP00000262710:K986R	K	-	2	0	ACIN1	22602078	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.855000	0.48333	1.092000	0.41356	0.533000	0.62120	AAG	.	.		0.483	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23532238	T	C	23532238	3	2	43	1	0	0	0	0	1	0	0	0	142	1609	56	2	1092	2	ACIN1	14	23532238	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2043528	23532238	83817302	266	5348										
CTSG	1511	hgsc.bcm.edu	37	chr14	25044539	25044539	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aaccctccacatctgctctgAcctgctggactctggatctg	8	15	4	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:25044539A>G	ENST00000216336.2	-	2	171	c.135T>C	c.(133-135)ggT>ggC	p.G45G		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	45	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|defense response to fungus (GO:0050832)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|negative regulation of growth of symbiont in host (GO:0044130)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|positive regulation of immune response (GO:0050778)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	heparin binding (GO:0008201)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(265;0.0269)		ATCTGCTCTGACCTGCTGGAC	0.592																																					p.G45G		Atlas-SNP	.											.	CTSG	63	.	0			c.T135C						.						121	116	118					14																	25044539		2203	4300	6503	SO:0001819	synonymous_variant	1511	exon2			GCTCTGACCTGCT	M16117	CCDS9631.1	14q12	2013-02-25			ENSG00000100448	ENSG00000100448		"Cathepsins", "Endogenous ligands"	2532	protein-coding gene	gene with protein product		116830				2569462	Standard	NM_001911		Approved	CG	uc001wpq.3	P08311	OTTHUMG00000140182	ENST00000216336.2:c.135T>C	chr14.hg19:g.25044539A>G		68.0	0.0		82.0	4.0	NM_001911	Q6IBJ6|Q9UCA5|Q9UCU6	Silent	SNP	ENST00000216336.2	hg19	CCDS9631.1																																																																																			.	.		0.592	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2	NM_001911		G	25044539	A	G	25044539	2	3	43	1	0	0	0	0	0	0	0	1	4037	262	10	2		2	CTSG	14	25044539	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1512301	25044539	82305001	267	5349										
BAZ1A	11177	hgsc.bcm.edu	37	chr14	35272095	35272095	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcgtttgggaggtctccctcTtcgtctgttagcaggactga	12	10	3	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:35272095T>C	ENST00000382422.2	-	6	1153	c.826A>G	c.(826-828)Aga>Gga	p.R276G	BAZ1A_ENST00000358716.4_Missense_Mutation_p.R276G|AL355885.1_ENST00000581314.1_RNA|BAZ1A_ENST00000360310.1_Missense_Mutation_p.R276G			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	276					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		GGTCTCCCTCTTCGTCTGTTA	0.353																																					p.R276G		Atlas-SNP	.											.	BAZ1A	128	.	0			c.A826G						.						118	120	119					14																	35272095		2203	4300	6503	SO:0001583	missense	11177	exon7			TCCCTCTTCGTCT	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.826A>G	chr14.hg19:g.35272095T>C	ENSP00000371859:p.Arg276Gly	39.0	0.0		68.0	4.0	NM_182648	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Missense_Mutation	SNP	ENST00000382422.2	hg19	CCDS9651.1	.	.	.	.	.	.	.	.	.	.	T	13.38	2.218559	0.39201	.	.	ENSG00000198604	ENST00000358716;ENST00000382422;ENST00000360310	T;T;T	0.59638	0.25;0.25;0.25	5.42	4.25	0.50352	.	0.050989	0.85682	D	0.000000	T	0.49423	0.1556	L	0.43152	1.355	0.44562	D	0.997526	P;P	0.46859	0.885;0.817	B;B	0.42495	0.389;0.217	T	0.45512	-0.9256	10	0.41790	T	0.15	.	10.5901	0.45304	0.0:0.0:0.3318:0.6681	.	276;276	Q9NRL2-2;Q9NRL2	.;BAZ1A_HUMAN	G	276	ENSP00000351555:R276G;ENSP00000371859:R276G;ENSP00000353458:R276G	ENSP00000351555:R276G	R	-	1	2	BAZ1A	34341846	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.745000	0.38278	0.953000	0.37825	0.533000	0.62120	AGA	.	.		0.353	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			C	35272095	T	C	35272095	3	2	43	1	0	0	0	0	1	0	0	0	1329	1617	56	2	3928	2	BAZ1A	14	35272095	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	10227556	35272095	72077445	268	5350										
PPP2R3C	55012	hgsc.bcm.edu	37	chr14	35585916	35585916	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	taaataaatccatttcttcaTcttttaattcttgttcactt	1	8	5	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:35585916T>C	ENST00000261475.5	-	2	439	c.86A>G	c.(85-87)gAt>gGt	p.D29G	PPP2R3C_ENST00000555644.1_Missense_Mutation_p.D29G	NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	29					activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		CATTTCTTCATCTTTTAATTC	0.303																																					p.D29G		Atlas-SNP	.											PPP2R3C,right_upper_lobe,carcinoma,0,1	PPP2R3C	44	.	0			c.A86G						.						64	66	66					14																	35585916		2202	4298	6500	SO:0001583	missense	55012	exon2			TCTTCATCTTTTA	AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	17485	protein-coding gene	gene with protein product		615902	"chromosome 14 open reading frame 10", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.86A>G	chr14.hg19:g.35585916T>C	ENSP00000261475:p.Asp29Gly	39.0	0.0		55.0	4.0	NM_017917	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Missense_Mutation	SNP	ENST00000261475.5	hg19	CCDS9654.1	.	.	.	.	.	.	.	.	.	.	T	15.39	2.817984	0.50633	.	.	ENSG00000092020	ENST00000261475;ENST00000554361;ENST00000555644;ENST00000557278	T	0.49720	0.77	5.02	5.02	0.67125	.	0.154878	0.56097	D	0.000023	T	0.36138	0.0956	L	0.29908	0.895	0.40099	D	0.976348	B;P;B	0.34977	0.073;0.478;0.102	B;B;B	0.33960	0.059;0.173;0.049	T	0.20009	-1.0288	10	0.24483	T	0.36	-9.371	15.0444	0.71816	0.0:0.0:0.0:1.0	.	29;29;29	G3V2K1;Q86US5;Q969Q6	.;.;P2R3C_HUMAN	G	29	ENSP00000450716:D29G	ENSP00000261475:D29G	D	-	2	0	PPP2R3C	34655667	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.085000	0.64468	1.999000	0.58509	0.459000	0.35465	GAT	.	.		0.303	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917		C	35585916	T	C	35585916	3	2	43	1	0	0	0	0	1	0	0	0	12402	1435	50	2	1323	2	PPP2R3C	14	35585916	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	313821	35585916	71763624	269	5351										
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36128344	36128344	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tctaagaatatccgacctacCgtgcaggaccagagggctca	10	12	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:36128344C>T	ENST00000389698.3	-	27	4259	c.3869G>A	c.(3868-3870)cGa>cAa	p.R1290Q	RALGAPA1_ENST00000258840.6_Splice_Site_p.R1337Q|RALGAPA1_ENST00000307138.6_Splice_Site_p.R1290Q|RALGAPA1_ENST00000382366.3_Splice_Site_p.R1303Q	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1290					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TCCGACCTACCGTGCAGGACC	0.368																																					p.R1290Q		Atlas-SNP	.											RALGAPA1_ENST00000307138,bladder,carcinoma,0,2	RALGAPA1	289	.	0			c.G3869A						.						63	60	61					14																	36128344		2202	4300	6502	SO:0001630	splice_region_variant	253959	exon27			ACCTACCGTGCAG	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.3869+1G>A	chr14.hg19:g.36128344C>T		27.0	1.0		28.0	2.0	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	C	36	5.774933	0.96922	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.88463	0.6443	M	0.75615	2.305	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.98;0.999;0.994	D	0.87228	0.2258	9	.	.	.	-7.1273	20.0763	0.97746	0.0:1.0:0.0:0.0	.	1337;1303;1290;1290	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	Q	1290;1290;1290;1337;1303;1337	ENSP00000374348:R1290Q;ENSP00000302647:R1290Q;ENSP00000258840:R1337Q;ENSP00000371803:R1303Q;ENSP00000451877:R1337Q	.	R	-	2	0	RALGAPA1	35198095	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.636000	0.74299	2.756000	0.94617	0.655000	0.94253	CGA	.	.		0.368	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	Missense_Mutation	T	36128344	C	T	36128344	5	4	43	1	0	0	0	0	0	0	1	0	13028	666	23	1	2450	1	RALGAPA1	14	36128344	Splice_Site	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	542428	36128344	71221196	270	5352										
CLEC14A	161198	hgsc.bcm.edu	37	chr14	38725216	38725216	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cagaggaggcacagggcgaaCgccggcctcattctctgagg	15	12	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:38725216C>A	ENST00000342213.2	-	1	358	c.12G>T	c.(10-12)gcG>gcT	p.A4A		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	4						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		ACAGGGCGAACGCCGGCCTCA	0.726																																					p.A4A		Atlas-SNP	.											.	CLEC14A	83	.	0			c.G12T						.						2	2	2					14																	38725216		1382	2852	4234	SO:0001819	synonymous_variant	161198	exon1			GGCGAACGCCGGC		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"C-type lectin domain containing"	19832	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 27"	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.12G>T	chr14.hg19:g.38725216C>A		38.0	0.0		85.0	46.0	NM_175060	Q695G9|Q6PWT6|Q8N5V5	Silent	SNP	ENST00000342213.2	hg19	CCDS9667.1																																																																																			.	.		0.726	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		A	38725216	C	A	38725216	2	1	43	1	0	0	0	0	0	0	0	1	3501	523	19	1		1	CLEC14A	14	38725216	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	2596872	38725216	68624324	271	5353										
FANCM	57697	hgsc.bcm.edu	37	chr14	45623916	45623916	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaagggatgacacggtcaaaAaatgaacttggccgaaatga	12	6	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:45623916A>G	ENST00000267430.5	+	7	1285	c.1200A>G	c.(1198-1200)aaA>aaG	p.K400K	FANCM_ENST00000542564.2_Silent_p.K374K|FANCM_ENST00000556036.1_Silent_p.K400K	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	400					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						CACGGTCAAAAAATGAACTTG	0.284								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.K400K		Atlas-SNP	.											.	FANCM	225	.	0			c.A1200G						.						74	72	73					14																	45623916		2203	4300	6503	SO:0001819	synonymous_variant	57697	exon7	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GTCAAAAAATGAA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.1200A>G	chr14.hg19:g.45623916A>G		68.0	0.0		75.0	23.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Silent	SNP	ENST00000267430.5	hg19	CCDS32070.1																																																																																			.	.		0.284	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45623916	A	G	45623916	2	3	43	1	0	0	0	0	0	0	0	1	5679	11	1	2		2	FANCM	14	45623916	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	6898700	45623916	61725624	272	5354										
WDHD1	11169	hgsc.bcm.edu	37	chr14	55408356	55408356	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caaccacacgttttcgcttcTttgcttcagttccttcactt	4	14	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:55408356T>C	ENST00000360586.3	-	26	3307	c.3242A>G	c.(3241-3243)aAg>aGg	p.K1081R	WDHD1_ENST00000420358.2_Missense_Mutation_p.K958R|WDHD1_ENST00000359167.4_Missense_Mutation_p.K599R|WDHD1_ENST00000421192.1_Missense_Mutation_p.K958R	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	1081					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						TTTTCGCTTCTTTGCTTCAGT	0.373																																					p.K1081R		Atlas-SNP	.											.	WDHD1	82	.	0			c.A3242G						.						147	151	150					14																	55408356		2202	4300	6502	SO:0001583	missense	11169	exon26			CGCTTCTTTGCTT	AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"WD repeat domain containing"	23170	protein-coding gene	gene with protein product	"CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.3242A>G	chr14.hg19:g.55408356T>C	ENSP00000353793:p.Lys1081Arg	138.0	0.0		82.0	4.0	NM_007086	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	hg19	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	T	18.79	3.698135	0.68386	.	.	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.65364	0.21;0.66;-0.15	5.68	5.68	0.88126	High mobility group, HMG1/HMG2 (2);	0.000000	0.85682	D	0.000000	T	0.78162	0.4240	M	0.76002	2.32	0.53688	D	0.999971	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.79135	-0.1928	10	0.48119	T	0.1	.	14.1504	0.65381	0.0:0.0:0.0:1.0	.	599;1081	F8W7P7;O75717	.;WDHD1_HUMAN	R	1081;599;958	ENSP00000353793:K1081R;ENSP00000352085:K599R;ENSP00000391049:K958R	ENSP00000352085:K599R	K	-	2	0	WDHD1	54478106	1.000000	0.71417	1.000000	0.80357	0.376000	0.30014	4.985000	0.63845	2.166000	0.68216	0.533000	0.62120	AAG	.	.		0.373	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086		C	55408356	T	C	55408356	3	2	43	1	0	0	0	0	1	0	0	0	17286	1609	56	2	151	2	WDHD1	14	55408356	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	9784440	55408356	51941184	273	5355										
SPTB	6710	hgsc.bcm.edu	37	chr14	65249105	65249105	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cgctgatccacttgttgaggTcagcatgggtctgcaagcgc	13	11	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:65249105T>C	ENST00000389721.5	-	19	4201	c.4169A>G	c.(4168-4170)gAc>gGc	p.D1390G	SPTB_ENST00000389722.3_Missense_Mutation_p.D1390G|SPTB_ENST00000556626.1_Missense_Mutation_p.D1390G|SPTB_ENST00000542895.1_Missense_Mutation_p.D1390G|SPTB_ENST00000389720.3_Missense_Mutation_p.D1390G	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1390					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CTTGTTGAGGTCAGCATGGGT	0.622																																					p.D1390G		Atlas-SNP	.											.	SPTB	378	.	0			c.A4169G						.						104	94	97					14																	65249105		2203	4300	6503	SO:0001583	missense	6710	exon19			TTGAGGTCAGCAT		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4169A>G	chr14.hg19:g.65249105T>C	ENSP00000374371:p.Asp1390Gly	100.0	0.0		94.0	4.0	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.701811	0.88924	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000553938;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48;0.48	5.36	5.36	0.76844	.	0.048891	0.85682	D	0.000000	T	0.73567	0.3603	M	0.81682	2.555	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.991;0.964	T	0.77702	-0.2489	10	0.72032	D	0.01	.	14.6216	0.68588	0.0:0.0:0.0:1.0	.	174;1390;1394	E7EV95;P11277;Q59FP5	.;SPTB1_HUMAN;.	G	1394;1390;174;55;1390;1390;1390;1390	ENSP00000374372:D1390G;ENSP00000451324:D55G;ENSP00000451752:D1390G;ENSP00000374371:D1390G;ENSP00000443882:D1390G;ENSP00000374370:D1390G	ENSP00000334218:D174G	D	-	2	0	SPTB	64318858	1.000000	0.71417	0.997000	0.53966	0.886000	0.51366	6.290000	0.72712	2.165000	0.68154	0.379000	0.24179	GAC	.	.		0.622	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			C	65249105	T	C	65249105	3	2	43	1	0	0	0	0	1	0	0	0	15133	1667	58	2	2954	2	SPTB	14	65249105	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	9840749	65249105	42100435	274	5356										
LTBP2	4053	hgsc.bcm.edu	37	chr14	75070369	75070369	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tggttggtgctgtttgctgtTgtccatcctgggcagcactg	14	9	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:75070369T>C	ENST00000261978.4	-	2	920	c.534A>G	c.(532-534)acA>acG	p.T178T	LTBP2_ENST00000557425.1_Intron|LTBP2_ENST00000556690.1_Silent_p.T178T	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	178					protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		TGTTTGCTGTTGTCCATCCTG	0.552																																					p.T178T		Atlas-SNP	.											.	LTBP2	158	.	0			c.A534G						.						389	267	309					14																	75070369		2203	4300	6503	SO:0001819	synonymous_variant	4053	exon2			TGCTGTTGTCCAT		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.534A>G	chr14.hg19:g.75070369T>C		165.0	0.0		94.0	4.0	NM_000428	Q99907|Q9NS51	Silent	SNP	ENST00000261978.4	hg19	CCDS9831.1																																																																																			.	.		0.552	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		C	75070369	T	C	75070369	2	2	43	1	0	0	0	0	0	0	0	1	9083	1799	63	2		2	LTBP2	14	75070369	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	9821264	75070369	32279171	275	5357										
YLPM1	56252	hgsc.bcm.edu	37	chr14	75230847	75230847	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cttcctcgcaatcctatttgAgccattcccagtcctacttg	5	15	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:75230847A>G	ENST00000552421.1	+	1	779	c.655A>G	c.(655-657)Agc>Ggc	p.S219G	YLPM1_ENST00000325680.7_Missense_Mutation_p.S219G|YLPM1_ENST00000238571.3_Missense_Mutation_p.S219G			P49750	YLPM1_HUMAN	YLP motif containing 1	219					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		ATCCTATTTGAGCCATTCCCA	0.592																																					p.S219G		Atlas-SNP	.											.	YLPM1	298	.	0			c.A655G						.						104	109	108					14																	75230847		2002	4167	6169	SO:0001583	missense	56252	exon1			TATTTGAGCCATT	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.655A>G	chr14.hg19:g.75230847A>G	ENSP00000447921:p.Ser219Gly	129.0	0.0		91.0	4.0	NM_019589	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.838	1.190255	0.21954	.	.	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571	T;T;T	0.24723	1.84;1.84;1.84	4.55	3.39	0.38822	.	0.232528	0.31092	N	0.008276	T	0.11153	0.0272	N	0.08118	0	0.19945	N	0.999942	B	0.28636	0.218	B	0.30029	0.11	T	0.26503	-1.0101	10	0.16896	T	0.51	-5.33	7.5504	0.27793	0.7604:0.2396:0.0:0.0	.	219	P49750-4	.	G	219	ENSP00000447921:S219G;ENSP00000324463:S219G;ENSP00000238571:S219G	ENSP00000238571:S219G	S	+	1	0	YLPM1	74300600	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.507000	0.35758	1.901000	0.55032	0.528000	0.53228	AGC	.	.		0.592	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		G	75230847	A	G	75230847	3	3	43	1	0	0	0	0	1	0	0	0	17501	304	11	2	657	2	YLPM1	14	75230847	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	160478	75230847	32118693	276	5358										
C14orf166B	145497	hgsc.bcm.edu	37	chr14	77292857	77292857	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcatgcacatccaattcccaTcaaagcctactcttcccagg	4	16	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:77292857T>C	ENST00000393774.3	+	1	143	c.19T>C	c.(19-21)Tca>Cca	p.S7P	C14orf166B_ENST00000460005.1_3'UTR|C14orf166B_ENST00000450042.2_5'UTR|C14orf166B_ENST00000216453.5_5'Flank	NM_194287.2	NP_919263.2														breast(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(1)	18			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		CCAATTCCCATCAAAGCCTAC	0.547																																					p.S7P	Ovarian(165;1056 1958 32571 36789 48728)	Atlas-SNP	.											.	C14orf166B	52	.	0			c.T19C						.						68	71	70					14																	77292857		692	1591	2283	SO:0001583	missense	145497	exon1			TTCCCATCAAAGC																												ENST00000393774.3:c.19T>C	chr14.hg19:g.77292857T>C	ENSP00000377369:p.Ser7Pro	83.0	0.0		73.0	5.0	NM_194287		Missense_Mutation	SNP	ENST00000393774.3	hg19	CCDS9853.2	.	.	.	.	.	.	.	.	.	.	T	0.794	-0.757828	0.03019	.	.	ENSG00000100565	ENST00000393774;ENST00000555189	T	0.37058	1.22	5.23	-1.77	0.07982	.	.	.	.	.	T	0.13756	0.0333	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.19811	-1.0294	9	0.34782	T	0.22	.	0.2718	0.00232	0.2958:0.2877:0.1449:0.2717	.	7	Q0VAA2	CN16B_HUMAN	P	7	ENSP00000377369:S7P	ENSP00000216450:S7P	S	+	1	0	C14orf166B	76362610	0.016000	0.18221	0.002000	0.10522	0.016000	0.09150	-0.442000	0.06871	-0.333000	0.08476	-0.621000	0.04028	TCA	.	.		0.547	C14orf166B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316592.1			C	77292857	T	C	77292857	3	2	43	1	0	0	0	0	1	0	0	0	1759	1435	50	2	21	2	C14orf166B	14	77292857	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2062010	77292857	30056683	277	5359										
WDR20	91833	hgsc.bcm.edu	37	chr14	102676047	102676047	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aaactctgggaacgcccctgTgtcctcgaatggaagatgtt	11	10	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr14:102676047T>C	ENST00000342702.3	+	3	1571	c.1540T>C	c.(1540-1542)Tgt>Cgt	p.C514R	WDR20_ENST00000335263.5_Missense_Mutation_p.C514R|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000499851.2_Missense_Mutation_p.C257R|WDR20_ENST00000556807.1_Missense_Mutation_p.C453R|WDR20_ENST00000556511.2_Missense_Mutation_p.C453R|WDR20_ENST00000545563.1_Missense_Mutation_p.C341R|WDR20_ENST00000424963.2_Missense_Mutation_p.C390R|WDR20_ENST00000454394.2_Missense_Mutation_p.C545R	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	514										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						AACGCCCCTGTGTCCTCGAAT	0.418											OREG0022939	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C545R		Atlas-SNP	.											.	WDR20	35	.	0			c.T1633C						.						96	93	94					14																	102676047		2203	4300	6503	SO:0001583	missense	91833	exon4			CCCCTGTGTCCTC	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.1540T>C	chr14.hg19:g.102676047T>C	ENSP00000341037:p.Cys514Arg	103.0	0.0	1368	61.0	4.0	NM_001242417	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Missense_Mutation	SNP	ENST00000342702.3	hg19	CCDS9969.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.12|17.12	3.308261|3.308261	0.60305|0.60305	.|.	.|.	ENSG00000140153|ENSG00000140153	ENST00000335263;ENST00000299135;ENST00000424963;ENST00000342702;ENST00000556807;ENST00000499851;ENST00000454394;ENST00000401892;ENST00000545563|ENST00000556511	D;D;D;D;D;D;D|.	0.92199|.	-2.99;-2.99;-2.99;-2.99;-2.99;-2.99;-2.99|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78622|0.78622	0.4312|0.4312	M|M	0.82716|0.82716	2.605|2.605	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;0.992;1.0|.	D;D;D;D;D;D;D|.	0.97110|.	0.999;0.999;0.998;1.0;1.0;0.982;0.999|.	T|T	0.80358|0.80358	-0.1416|-0.1416	10|5	0.72032|.	D|.	0.01|.	.|.	16.2159|16.2159	0.82217|0.82217	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	545;526;453;514;453;390;514|.	E7EUY8;Q5JPH5;G3V2F8;Q8TBZ3-2;F8W9S4;B3KR43;Q8TBZ3|.	.;.;.;.;.;.;WDR20_HUMAN|.	R|A	514;453;390;514;453;257;545;444;341|444	ENSP00000335434:C514R;ENSP00000395793:C390R;ENSP00000341037:C514R;ENSP00000450636:C453R;ENSP00000443641:C257R;ENSP00000406084:C545R;ENSP00000437927:C341R|.	ENSP00000299135:C453R|.	C|V	+|+	1|2	0|0	WDR20|WDR20	101745800|101745800	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.691000|7.691000	0.84191|0.84191	2.243000|2.243000	0.73865|0.73865	0.533000|0.533000	0.62120|0.62120	TGT|GTG	.	.		0.418	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		C	102676047	T	C	102676047	3	2	43	1	0	0	0	0	1	0	0	0	17295	1696	59	2	1567	2	WDR20	14	102676047	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	25383190	102676047	4673493	278	5360										
TRPM1	4308	hgsc.bcm.edu	37	chr15	31355371	31355371	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gacaggatgtccgaggcacgTccgctgccatcacaaatcac	10	14	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:31355371T>C	ENST00000256552.6	-	8	1062	c.915A>G	c.(913-915)ggA>ggG	p.G305G	MIR211_ENST00000384969.1_RNA|TRPM1_ENST00000397795.2_Silent_p.G283G|TRPM1_ENST00000542188.1_Silent_p.G322G	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CCGAGGCACGTCCGCTGCCAT	0.577																																					p.G322G		Atlas-SNP	.											.	TRPM1	183	.	0			c.A966G						.						61	66	64					15																	31355371		2052	4210	6262	SO:0001819	synonymous_variant	4308	exon7			GGCACGTCCGCTG	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.915A>G	chr15.hg19:g.31355371T>C		61.0	0.0		94.0	36.0	NM_001252020		Silent	SNP	ENST00000256552.6	hg19	CCDS58346.1																																																																																			.	.		0.577	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		C	31355371	T	C	31355371	2	2	43	1	0	0	0	0	0	0	0	1	16600	1654	58	2		2	TRPM1	15	31355371	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10		31355371	71176021	279	5361										
RYR3	6263	hgsc.bcm.edu	37	chr15	33993260	33993260	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aatgagttagcgctgagcttAgaggaaccagacctcgagaa	12	8	0	5			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:33993260A>G	ENST00000389232.4	+	42	6532	c.6462A>G	c.(6460-6462)ttA>ttG	p.L2154L	RYR3_ENST00000415757.3_Silent_p.L2154L	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2154	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CGCTGAGCTTAGAGGAACCAG	0.582											OREG0023030	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L2154L		Atlas-SNP	.											.	RYR3	760	.	0			c.A6462G						.						60	64	63					15																	33993260		2003	4183	6186	SO:0001819	synonymous_variant	6263	exon42			GAGCTTAGAGGAA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.6462A>G	chr15.hg19:g.33993260A>G		60.0	0.0	844	72.0	4.0	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.582	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			G	33993260	A	G	33993260	2	3	43	1	0	0	0	0	0	0	0	1	13785	417	15	2		2	RYR3	15	33993260	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	2637889	33993260	68538132	280	5362										
AQR	9716	hgsc.bcm.edu	37	chr15	35222481	35222481	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtagagaagtaattctatcaTagtgaattgtggtcatctca	9	5	4	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:35222481T>A	ENST00000156471.5	-	12	1217	c.992A>T	c.(991-993)tAt>tTt	p.Y331F		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	331					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		AATTCTATCATAGTGAATTGT	0.323																																					p.Y331F		Atlas-SNP	.											.	AQR	139	.	0			c.A992T						.						147	141	143					15																	35222481		1816	4072	5888	SO:0001583	missense	9716	exon12			CTATCATAGTGAA	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.992A>T	chr15.hg19:g.35222481T>A	ENSP00000156471:p.Tyr331Phe	27.0	0.0		35.0	11.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	hg19	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.973549	0.92919	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.94650	-3.48	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.97832	0.9288	M	0.93854	3.465	0.58432	D	0.999999	D	0.89917	1.0	D	0.74348	0.983	D	0.98019	1.0370	10	0.37606	T	0.19	-17.9983	16.1448	0.81559	0.0:0.0:0.0:1.0	.	331	O60306	AQR_HUMAN	F	331	ENSP00000156471:Y331F	ENSP00000156471:Y331F	Y	-	2	0	AQR	33009773	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.920000	0.87521	2.216000	0.71823	0.482000	0.46254	TAT	.	.		0.323	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		A	35222481	T	A	35222481	3	1	43	1	0	0	0	0	1	0	0	0	835	1406	49	4	3561	4	AQR	15	35222481	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1229221	35222481	67308911	281	5363										
PLCB2	5330	hgsc.bcm.edu	37	chr15	40584596	40584596	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggaagatgaagagcgcaggcAtggtgaggggcatgttgctc	18	6	0	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:40584596A>G	ENST00000260402.3	-	22	2624	c.2375T>C	c.(2374-2376)aTg>aCg	p.M792T	PLCB2_ENST00000456256.2_Missense_Mutation_p.M792T|PLCB2_ENST00000557821.1_Missense_Mutation_p.M788T	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	792					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		GAGCGCAGGCATGGTGAGGGG	0.607																																					p.M792T		Atlas-SNP	.											.	PLCB2	177	.	0			c.T2375C						.						78	87	84					15																	40584596		2110	4232	6342	SO:0001583	missense	5330	exon22			GCAGGCATGGTGA		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.2375T>C	chr15.hg19:g.40584596A>G	ENSP00000260402:p.Met792Thr	64.0	0.0		80.0	4.0	NM_004573	A8K6J2|B9EGH5	Missense_Mutation	SNP	ENST00000260402.3	hg19	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	A	17.79	3.476398	0.63737	.	.	ENSG00000137841	ENST00000260402;ENST00000456256	T;T	0.13307	2.6;2.6	5.1	5.1	0.69264	C2 calcium/lipid-binding domain, CaLB (1);	0.049953	0.85682	D	0.000000	T	0.21468	0.0517	L	0.39898	1.24	0.80722	D	1	D;P;P	0.60575	0.988;0.602;0.508	P;B;B	0.52957	0.714;0.055;0.129	T	0.00645	-1.1629	10	0.66056	D	0.02	.	15.0426	0.71803	1.0:0.0:0.0:0.0	.	792;788;792	B9EGH5;Q00722-2;Q00722	.;.;PLCB2_HUMAN	T	792	ENSP00000260402:M792T;ENSP00000411991:M792T	ENSP00000260402:M792T	M	-	2	0	PLCB2	38371888	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.074000	0.93998	2.142000	0.66516	0.533000	0.62120	ATG	.	.		0.607	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			G	40584596	A	G	40584596	3	3	43	1	0	0	0	0	1	0	0	0	12037	217	8	2	1226	2	PLCB2	15	40584596	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	5362115	40584596	61946796	282	5364										
MGA	23269	hgsc.bcm.edu	37	chr15	42003112	42003112	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	actatttccccttctacctcTtattctttgaaacctcattc	1	14	4	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:42003112T>C	ENST00000570161.1	+	7	2649	c.2649T>C	c.(2647-2649)tcT>tcC	p.S883S	MGA_ENST00000566586.1_Silent_p.S883S|MGA_ENST00000219905.7_Silent_p.S883S|MGA_ENST00000545763.1_Silent_p.S883S|MGA_ENST00000389936.4_Silent_p.S883S			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CTTCTACCTCTTATTCTTTGA	0.413																																					p.S883S		Atlas-SNP	.											.	MGA	264	.	0			c.T2649C						.						137	132	134					15																	42003112		1852	4089	5941	SO:0001819	synonymous_variant	23269	exon8			TACCTCTTATTCT	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.2649T>C	chr15.hg19:g.42003112T>C		61.0	0.0		65.0	4.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.413	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		C	42003112	T	C	42003112	2	2	43	1	0	0	0	0	0	0	0	1	9549	1596	56	2		2	MGA	15	42003112	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1418516	42003112	60528280	283	5365										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42173320	42173320	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gatcaaagtcagggtcaggcTcagctgggagggccatcttc	14	10	5	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:42173320T>C	ENST00000320955.6	-	13	2797	c.2570A>G	c.(2569-2571)gAg>gGg	p.E857G		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	857					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		AGGGTCAGGCTCAGCTGGGAG	0.597																																					p.E822G		Atlas-SNP	.											.	SPTBN5	171	.	0			c.A2465G						.						59	64	62					15																	42173320		2032	4190	6222	SO:0001583	missense	51332	exon13			TCAGGCTCAGCTG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.2570A>G	chr15.hg19:g.42173320T>C	ENSP00000317790:p.Glu857Gly	98.0	0.0		100.0	4.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	9.740	1.164692	0.21538	.	.	ENSG00000137877	ENST00000320955	T	0.68181	-0.31	4.17	3.02	0.34903	.	0.857644	0.10341	N	0.686334	T	0.53012	0.1770	L	0.32530	0.975	0.09310	N	1	B	0.14805	0.011	B	0.08055	0.003	T	0.39251	-0.9623	10	0.33141	T	0.24	.	7.6684	0.28445	0.0:0.0:0.2154:0.7846	.	857	Q9NRC6	SPTN5_HUMAN	G	857	ENSP00000317790:E857G	ENSP00000317790:E857G	E	-	2	0	SPTBN5	39960612	0.149000	0.22717	0.001000	0.08648	0.015000	0.08874	1.983000	0.40648	0.463000	0.27118	0.379000	0.24179	GAG	.	.		0.597	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		C	42173320	T	C	42173320	3	2	43	1	0	0	0	0	1	0	0	0	15137	1551	54	2	8678	2	SPTBN5	15	42173320	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	170208	42173320	60358072	284	5366										
MAPK6	5597	hgsc.bcm.edu	37	chr15	52350974	52350974	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caaacctttaactcagctgcTtccaggaattagtcgagaag	8	10	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:52350974T>C	ENST00000261845.5	+	4	1652	c.845T>C	c.(844-846)cTt>cCt	p.L282P	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	282	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		ACTCAGCTGCTTCCAGGAATT	0.448																																					p.L282P		Atlas-SNP	.											.	MAPK6	70	.	0			c.T845C						.						78	68	71					15																	52350974		2195	4293	6488	SO:0001583	missense	5597	exon4			AGCTGCTTCCAGG	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"Mitogen-activated protein kinase cascade / Kinases"	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.845T>C	chr15.hg19:g.52350974T>C	ENSP00000261845:p.Leu282Pro	76.0	0.0		94.0	4.0	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	hg19	CCDS10147.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.646411	0.87958	.	.	ENSG00000069956	ENST00000261845	T	0.41758	0.99	5.08	5.08	0.68730	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.49098	0.1537	N	0.16368	0.405	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.56872	-0.7907	10	0.87932	D	0	-8.0325	14.8562	0.70338	0.0:0.0:0.0:1.0	.	282	Q16659	MK06_HUMAN	P	282	ENSP00000261845:L282P	ENSP00000261845:L282P	L	+	2	0	MAPK6	50138266	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.031000	0.88826	1.931000	0.55961	0.377000	0.23210	CTT	.	.		0.448	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748		C	52350974	T	C	52350974	3	2	43	1	0	0	0	0	1	0	0	0	9290	1609	56	2	855	2	MAPK6	15	52350974	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	10177654	52350974	50180418	285	5367										
DAPK2	23604	hgsc.bcm.edu	37	chr15	64275877	64275877	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccggctcgcccggctctgccGcttcttgatgaacttggctg	12	15	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:64275877G>A	ENST00000457488.1	-	3	199	c.169C>T	c.(169-171)Cgg>Tgg	p.R57W	DAPK2_ENST00000558069.1_Missense_Mutation_p.R57W|DAPK2_ENST00000261891.3_Missense_Mutation_p.R57W|DAPK2_ENST00000558482.1_5'UTR	NM_014326.3	NP_055141.2	Q9UIK4	DAPK2_HUMAN	death-associated protein kinase 2	57	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	11				LUAD - Lung adenocarcinoma(2;0.215)		CGGCTCTGCCGCTTCTTGATG	0.622																																					p.R57W		Atlas-SNP	.											.	DAPK2	31	.	0			c.C169T						.						35	35	35					15																	64275877		2203	4300	6503	SO:0001583	missense	23604	exon3			TCTGCCGCTTCTT	AB018001	CCDS10188.1	15q22.1	2008-07-18			ENSG00000035664	ENSG00000035664			2675	protein-coding gene	gene with protein product						10376525	Standard	XM_005254265		Approved	DRP-1, MGC119312	uc002amr.3	Q9UIK4	OTTHUMG00000132947	ENST00000457488.1:c.169C>T	chr15.hg19:g.64275877G>A	ENSP00000408277:p.Arg57Trp	39.0	0.0		108.0	20.0	NM_014326	E9JGM7|O75892|Q24JS1	Missense_Mutation	SNP	ENST00000457488.1	hg19	CCDS10188.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.438708	0.83885	.	.	ENSG00000035664	ENST00000261891;ENST00000457488	T;T	0.67698	-0.28;-0.28	5.35	3.38	0.38709	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.78342	0.4268	M	0.62154	1.92	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79157	-0.1919	10	0.87932	D	0	.	13.1348	0.59403	0.0:0.0:0.6989:0.3011	.	57;57	E9JGM7;Q9UIK4	.;DAPK2_HUMAN	W	57	ENSP00000261891:R57W;ENSP00000408277:R57W	ENSP00000261891:R57W	R	-	1	2	DAPK2	62062930	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.616000	0.61197	0.557000	0.29117	0.555000	0.69702	CGG	.	.		0.622	DAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256479.1	NM_014326		A	64275877	G	A	64275877	3	1	43	1	0	0	0	0	1	0	0	0	4238	1086	38	1	983	1	DAPK2	15	64275877	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	11924903	64275877	38255515	286	5368										
DPP8	54878	hgsc.bcm.edu	37	chr15	65739300	65739300	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	agatgcagttcataatgttcTcccgattcaggaactcttat	7	9	4	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:65739300T>C	ENST00000341861.5	-	20	4199	c.2619A>G	c.(2617-2619)ggA>ggG	p.G873G	DPP8_ENST00000339244.5_Silent_p.G700G|DPP8_ENST00000300141.6_Silent_p.G857G|DPP8_ENST00000321118.7_Silent_p.G824G|DPP8_ENST00000559233.1_Silent_p.G873G|DPP8_ENST00000321147.6_Silent_p.G822G|DPP8_ENST00000358939.4_Silent_p.G757G	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	873					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CATAATGTTCTCCCGATTCAG	0.343																																					p.G873G		Atlas-SNP	.											.	DPP8	78	.	0			c.A2619G						.						148	145	146					15																	65739300		2201	4299	6500	SO:0001819	synonymous_variant	54878	exon21			ATGTTCTCCCGAT	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"dipeptidyl peptidase VIII", "dipeptidyl peptidase IV-related protein-1", "prolyl dipeptidase DPP8"	606819	"dipeptidylpeptidase 8"			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.2619A>G	chr15.hg19:g.65739300T>C		50.0	0.0		112.0	5.0	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Silent	SNP	ENST00000341861.5	hg19	CCDS10207.1																																																																																			.	.		0.343	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743		C	65739300	T	C	65739300	2	2	43	1	0	0	0	0	0	0	0	1	4734	1538	54	2		2	DPP8	15	65739300	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1463423	65739300	36792092	287	5369										
CPEB1	64506	hgsc.bcm.edu	37	chr15	83296065	83296065	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcattactacacgtggagagAgcaggtgcttcctggttgtc	13	9	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:83296065A>G	ENST00000562019.1	-	2	385	c.69T>C	c.(67-69)gcT>gcC	p.A23A	CPEB1_ENST00000568757.1_5'UTR|CPEB1_ENST00000450751.2_5'UTR|CPEB1_ENST00000568128.1_Silent_p.A23A|CPEB1_ENST00000563800.1_Silent_p.A50A			Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding protein 1	23					cellular response to amino acid stimulus (GO:0071230)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|mRNA processing (GO:0006397)|negative regulation of cytoplasmic translation (GO:2000766)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(1)|skin(1)	28			BRCA - Breast invasive adenocarcinoma(143;0.229)			ACGTGGAGAGAGCAGGTGCTT	0.393																																					p.A23A		Atlas-SNP	.											.	CPEB1	114	.	0			c.T69C						.						98	96	97					15																	83296065		1886	4118	6004	SO:0001819	synonymous_variant	64506	exon2			GGAGAGAGCAGGT	AF329402	CCDS42072.1, CCDS45329.1, CCDS45330.1, CCDS42072.2, CCDS45329.2, CCDS45330.2	15q25.1	2008-02-05				ENSG00000214575			21744	protein-coding gene	gene with protein product		607342				11223249	Standard	NM_001079533		Approved	FLJ13203, CPEB	uc002biv.3	Q9BZB8		ENST00000562019.1:c.69T>C	chr15.hg19:g.83296065A>G		57.0	0.0		87.0	4.0	NM_030594	B7Z6C6|Q86W46|Q8IV41|Q9BZB7|Q9H8V5	Silent	SNP	ENST00000562019.1	hg19																																																																																				.	.		0.393	CPEB1-006	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000421102.1	NM_030594		G	83296065	A	G	83296065	2	3	43	1	0	0	0	0	0	0	0	1	3802	291	11	2		2	CPEB1	15	83296065	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	17556765	83296065	19235327	288	5370										
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85438313	85438313	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccaaagctgaggaggtttctCaagcctcagggccatccccg	11	14	2	1	rs371921369|rs2277576		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr15:85438313C>T	ENST00000286749.3	+	5	510	c.420C>T	c.(418-420)ctC>ctT	p.L140L	SLC28A1_ENST00000537703.1_Silent_p.L62L|SLC28A1_ENST00000338602.2_Silent_p.L140L|SLC28A1_ENST00000537216.1_Silent_p.L140L|SLC28A1_ENST00000394573.1_Silent_p.L140L|SLC28A1_ENST00000537624.1_Silent_p.L140L|SLC28A1_ENST00000538177.1_Silent_p.L140L			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	140			L -> LV (in A). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.L140L(2)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GGAGGTTTCTCAAGCCTCAGG	0.637																																					p.L140L		Atlas-SNP	.											SLC28A1_ENST00000338602,NS,carcinoma,0,1	SLC28A1	118	.	2	Substitution - coding silent(2)	lung(2)	c.C420T						.						45	47	47					15																	85438313		2203	4298	6501	SO:0001819	synonymous_variant	9154	exon6			GTTTCTCAAGCCT	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"Solute carriers"	11001	protein-coding gene	gene with protein product		606207	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.420C>T	chr15.hg19:g.85438313C>T		67.0	1.0		124.0	5.0	NM_201651	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	hg19	CCDS10334.1																																																																																			.	.		0.637	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			T	85438313	C	T	85438313	2	4	43	1	0	0	0	0	0	0	0	1	14546	813	29	3		3	SLC28A1	15	85438313	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	2142248	85438313	17093079	289	5371										
WDR90	197335	hgsc.bcm.edu	37	chr16	699822	699822	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gggtggacgagtggaagcgcTccgccaagcagggggacgtg	20	9	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:699822T>C	ENST00000293879.4	+	2	70	c.70T>C	c.(70-72)Tcc>Ccc	p.S24P	WDR90_ENST00000549091.1_Missense_Mutation_p.S24P|AL022341.3_ENST00000455294.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	24										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GTGGAAGCGCTCCGCCAAGCA	0.751																																					p.S24P		Atlas-SNP	.											.	WDR90	107	.	0			c.T70C						.						5	7	6					16																	699822		1828	3983	5811	SO:0001583	missense	197335	exon2			AAGCGCTCCGCCA	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.70T>C	chr16.hg19:g.699822T>C	ENSP00000293879:p.Ser24Pro	33.0	0.0		37.0	4.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.685818	0.47991	.	.	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.44083	0.93;0.93	4.33	4.33	0.51752	.	0.000000	0.28052	U	0.016793	T	0.60235	0.2253	M	0.65975	2.015	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.995	D;D;P	0.71184	0.952;0.972;0.885	T	0.64093	-0.6488	10	0.66056	D	0.02	.	12.6356	0.56681	0.0:0.0:0.0:1.0	.	24;24;24	Q96KV7;C9JMK1;Q96KV7-3	WDR90_HUMAN;.;.	P	24	ENSP00000448122:S24P;ENSP00000293879:S24P	ENSP00000293879:S24P	S	+	1	0	WDR90	639823	0.999000	0.42202	0.864000	0.33941	0.151000	0.21798	3.170000	0.50816	1.734000	0.51633	0.496000	0.49642	TCC	.	.		0.751	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		C	699822	T	C	699822	3	2	43	1	0	0	0	0	1	0	0	0	17352	1551	54	2	76	2	WDR90	16	699822	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10		699822	89654931	290	5372										
CCNF	899	hgsc.bcm.edu	37	chr16	2487180	2487180	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgaatggcctgaaggcctctCgcttcttcagtctcgctgag	11	12	4	3	rs138913390		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:2487180C>T	ENST00000397066.4	+	5	485	c.397C>T	c.(397-399)Cgc>Tgc	p.R133C		NM_001761.2	NP_001752.2	P41002	CCNF_HUMAN	cyclin F	133					mitotic nuclear division (GO:0007067)|negative regulation of centrosome duplication (GO:0010826)|placenta development (GO:0001890)|protein ubiquitination (GO:0016567)|re-entry into mitotic cell cycle (GO:0000320)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	centriole (GO:0005814)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(2)|lung(5)|prostate(4)|skin(1)	20		Ovarian(90;0.17)				GAAGGCCTCTCGCTTCTTCAG	0.607																																					p.R133C		Atlas-SNP	.											.	CCNF	110	.	0			c.C397T						.	C	CYS/ARG	1,4395	2.1+/-5.4	0,1,2197	93	92	92		397	5	0.9	16	dbSNP_134	92	0,8600		0,0,4300	no	missense	CCNF	NM_001761.2	180	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	133/787	2487180	1,12995	2198	4300	6498	SO:0001583	missense	899	exon5			GCCTCTCGCTTCT	Z36714	CCDS10467.1	16p13.3	2008-02-05			ENSG00000162063	ENSG00000162063		"F-boxes /  "other""	1591	protein-coding gene	gene with protein product		600227				7896286	Standard	NM_001761		Approved	FBX1, FBXO1	uc002cqd.1	P41002	OTTHUMG00000128858	ENST00000397066.4:c.397C>T	chr16.hg19:g.2487180C>T	ENSP00000380256:p.Arg133Cys	47.0	0.0		58.0	4.0	NM_001761	B2R8H3|Q96EG9	Missense_Mutation	SNP	ENST00000397066.4	hg19	CCDS10467.1	.	.	.	.	.	.	.	.	.	.	C	17.77	3.470467	0.63625	2.27E-4	0.0	ENSG00000162063	ENST00000397066;ENST00000293968	T	0.26067	1.76	5.92	4.98	0.66077	.	0.263540	0.45126	D	0.000392	T	0.29061	0.0722	L	0.60455	1.87	0.58432	D	0.999999	D	0.55605	0.972	B	0.42386	0.386	T	0.12553	-1.0543	10	0.87932	D	0	-23.4429	13.8262	0.63352	0.0:0.9263:0.0:0.0737	.	133	P41002	CCNF_HUMAN	C	133;48	ENSP00000380256:R133C	ENSP00000293968:R48C	R	+	1	0	CCNF	2427181	1.000000	0.71417	0.931000	0.37212	0.384000	0.30261	5.888000	0.69758	1.518000	0.48934	-0.136000	0.14681	CGC	.	C|1.000;T|0.000		0.607	CCNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250801.1	NM_001761		T	2487180	C	T	2487180	3	4	43	1	0	0	0	0	1	0	0	0	2924	884	31	1	415	1	CCNF	16	2487180	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	1787358	2487180	87867573	291	5373										
OR1F1	4992	hgsc.bcm.edu	37	chr16	3254975	3254975	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gccttctccacctgtggttcTcacctggctgtggttctcct	9	15	3	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:3254975T>C	ENST00000304646.2	+	1	729	c.729T>C	c.(727-729)tcT>tcC	p.S243S	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	243					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(2)|lung(7)	11						CCTGTGGTTCTCACCTGGCTG	0.493																																					p.S243S		Atlas-SNP	.											.	OR1F1	36	.	0			c.T729C						.						205	187	193					16																	3254975		2197	4300	6497	SO:0001819	synonymous_variant	4992	exon1			TGGTTCTCACCTG	Y14442	CCDS10496.1	16p13.3	2012-08-09			ENSG00000168124	ENSG00000168124		"GPCR / Class A : Olfactory receptors"	8194	protein-coding gene	gene with protein product		603232		OR1F4, OR1F6, OR1F7, OR1F8, OR1F9, OR1F5, OR1F10, OR1F13P		9288094, 9500546	Standard	NM_012360		Approved	Olfmf, OR16-36, OR16-37, OR16-88, OR16-89, OR16-90, OLFMF, OR3-145	uc010uwu.2	O43749	OTTHUMG00000133153	ENST00000304646.2:c.729T>C	chr16.hg19:g.3254975T>C		158.0	0.0		83.0	4.0	NM_012360	O15246|Q6IFL5	Silent	SNP	ENST00000304646.2	hg19	CCDS10496.1																																																																																			.	.		0.493	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1			C	3254975	T	C	3254975	2	2	43	1	0	0	0	0	0	0	0	1	10965	1538	54	2		2	OR1F1	16	3254975	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	767795	3254975	87099778	292	5374										
ADCY9	115	hgsc.bcm.edu	37	chr16	4039054	4039054	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctgatccaggaagttcaggcTgaactgattaatgggcggct	13	8	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:4039054T>C	ENST00000294016.3	-	6	2789	c.2251A>G	c.(2251-2253)Agc>Ggc	p.S751G	ADCY9_ENST00000571889.1_5'Flank	NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	751					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AAGTTCAGGCTGAACTGATTA	0.448																																					p.S751G		Atlas-SNP	.											.	ADCY9	151	.	0			c.A2251G						.						132	121	125					16																	4039054		2197	4300	6497	SO:0001583	missense	115	exon6			TCAGGCTGAACTG	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2251A>G	chr16.hg19:g.4039054T>C	ENSP00000294016:p.Ser751Gly	54.0	0.0		37.0	4.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	hg19	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	t	33	5.290889	0.95546	.	.	ENSG00000162104	ENST00000294016	D	0.84660	-1.88	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.90580	0.7047	L	0.55481	1.735	0.53688	D	0.99997	D	0.69078	0.997	D	0.75020	0.985	D	0.91244	0.5024	10	0.72032	D	0.01	.	16.564	0.84574	0.0:0.0:0.0:1.0	.	751	O60503	ADCY9_HUMAN	G	751	ENSP00000294016:S751G	ENSP00000294016:S751G	S	-	1	0	ADCY9	3979055	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.037000	0.88933	2.314000	0.78098	0.454000	0.30748	AGC	.	.		0.448	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			C	4039054	T	C	4039054	3	2	43	1	0	0	0	0	1	0	0	0	301	1580	55	2	1834	2	ADCY9	16	4039054	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	784079	4039054	86315699	293	5375										
ERCC4	2072	hgsc.bcm.edu	37	chr16	14024746	14024746	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aaagcttttggtcagaattcAggtgggagattaaaatacta	10	4	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:14024746A>G	ENST00000311895.7	+	5	981	c.972A>G	c.(970-972)tcA>tcG	p.S324S	CTD-2135D7.2_ENST00000575137.1_RNA|ERCC4_ENST00000575156.1_Splice_Site_p.S324S|CTD-2135D7.2_ENST00000570663.1_RNA	NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	324	Helicase-like.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						GTCAGAATTCAGGTGGGAGAT	0.353			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.S324S		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"excision repair cross-complementing rodent repair deficiency, complementation group 4"		E	.	ERCC4	100	.	0			c.A972G						.						39	39	39					16																	14024746		2197	4300	6497	SO:0001630	splice_region_variant	2072	exon5	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GAATTCAGGTGGG	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"xeroderma pigmentosum, complementation group F"	133520	"excision repair cross-complementing rodent repair deficiency, complementation group 4"	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.973+1A>G	chr16.hg19:g.14024746A>G		66.0	0.0		54.0	4.0	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Silent	SNP	ENST00000311895.7	hg19	CCDS32390.1																																																																																			.	.		0.353	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236	Silent	G	14024746	A	G	14024746	5	3	43	1	0	0	0	0	0	0	1	0	5217	202	7	2	990	2	ERCC4	16	14024746	Splice_Site	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	9985692	14024746	76330007	294	5376										
USP31	57478	hgsc.bcm.edu	37	chr16	23117594	23117594	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aaggatcaaaagtgttgctcTgtttctgacaatgaggacac	10	7	3	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:23117594T>C	ENST00000219689.7	-	4	892	c.893A>G	c.(892-894)cAg>cGg	p.Q298R		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	229	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		AGTGTTGCTCTGTTTCTGACA	0.363																																					p.Q298R		Atlas-SNP	.											.	USP31	122	.	0			c.A893G						.						106	106	106					16																	23117594		2197	4300	6497	SO:0001583	missense	57478	exon4			TTGCTCTGTTTCT	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.893A>G	chr16.hg19:g.23117594T>C	ENSP00000219689:p.Gln298Arg	92.0	0.0		113.0	5.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	hg19	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.653026	0.88056	.	.	ENSG00000103404	ENST00000219689	T	0.29655	1.56	5.82	5.82	0.92795	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.172968	0.43579	D	0.000558	T	0.44603	0.1301	L	0.38838	1.175	0.80722	D	1	D	0.64830	0.994	D	0.76575	0.988	T	0.17048	-1.0382	10	0.23302	T	0.38	-14.6144	15.3651	0.74516	0.0:0.0:0.0:1.0	.	298	Q70CQ4	UBP31_HUMAN	R	298	ENSP00000219689:Q298R	ENSP00000219689:Q298R	Q	-	2	0	USP31	23025095	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.649000	0.83500	2.222000	0.72286	0.533000	0.62120	CAG	.	.		0.363	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		C	23117594	T	C	23117594	3	2	43	1	0	0	0	0	1	0	0	0	17077	1580	55	2	3217	2	USP31	16	23117594	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	9092848	23117594	67237159	295	5377										
ITGAL	3683	hgsc.bcm.edu	37	chr16	30507878	30507878	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gggggctgagagccagatgaTcgtgctgaggtgagatgggt	20	5	0	5			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:30507878T>C	ENST00000356798.6	+	15	2003	c.1823T>C	c.(1822-1824)aTc>aCc	p.I608T	RP11-297C4.1_ENST00000563751.1_RNA|ITGAL_ENST00000358164.5_Missense_Mutation_p.I525T|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	608					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	AGCCAGATGATCGTGCTGAGG	0.468																																					p.I608T	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.T1823C						.						92	78	82					16																	30507878		2197	4300	6497	SO:0001583	missense	3683	exon15			AGATGATCGTGCT		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1823T>C	chr16.hg19:g.30507878T>C	ENSP00000349252:p.Ile608Thr	81.0	0.0		119.0	6.0	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	hg19	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.048303	0.36181	.	.	ENSG00000005844	ENST00000356798;ENST00000358164	T;T	0.55052	0.54;0.54	5.94	5.94	0.96194	.	0.562934	0.17117	N	0.186415	T	0.50137	0.1598	L	0.56199	1.76	0.80722	D	1	B;B	0.26876	0.162;0.096	B;B	0.21546	0.035;0.024	T	0.50197	-0.8856	10	0.72032	D	0.01	.	13.9183	0.63914	0.0:0.0:0.0:1.0	.	525;608	Q96HB1;P20701	.;ITAL_HUMAN	T	608;525	ENSP00000349252:I608T;ENSP00000350886:I525T	ENSP00000349252:I608T	I	+	2	0	ITGAL	30415379	0.633000	0.27181	0.977000	0.42913	0.246000	0.25737	4.432000	0.59922	2.272000	0.75746	0.460000	0.39030	ATC	.	.		0.468	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			C	30507878	T	C	30507878	3	2	43	1	0	0	0	0	1	0	0	0	7895	1435	50	2	1881	2	ITGAL	16	30507878	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	7390284	30507878	59846875	296	5378										
ZNF646	9726	hgsc.bcm.edu	37	chr16	31088548	31088548	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cactgtccccactgcccccgTgtcttccggctcccccggga	9	21	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:31088548T>C	ENST00000394979.2	+	1	1326	c.903T>C	c.(901-903)cgT>cgC	p.R301R	ZNF668_ENST00000300849.4_5'Flank|ZNF646_ENST00000300850.5_Silent_p.R301R			O15015	ZN646_HUMAN	zinc finger protein 646	301					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						ACTGCCCCCGTGTCTTCCGGC	0.597																																					p.R301R		Atlas-SNP	.											.	ZNF646	133	.	0			c.T903C						.						62	60	61					16																	31088548		2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			CCCCCGTGTCTTC	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.903T>C	chr16.hg19:g.31088548T>C		58.0	0.0		87.0	4.0	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	hg19																																																																																				.	.		0.597	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		C	31088548	T	C	31088548	2	2	43	1	0	0	0	0	0	0	0	1	18077	1683	59	2		2	ZNF646	16	31088548	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	580670	31088548	59266205	297	5379										
CDH5	1003	hgsc.bcm.edu	37	chr16	66423413	66423413	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acatcaatgacaacttccccTtcttcacccagagtgagccc	5	16	3	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:66423413T>C	ENST00000341529.3	+	5	917	c.769T>C	c.(769-771)Ttc>Ctc	p.F257L	CDH5_ENST00000563425.2_Missense_Mutation_p.F257L	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	257	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	CAACTTCCCCTTCTTCACCCA	0.607																																					p.F257L		Atlas-SNP	.											.	CDH5	111	.	0			c.T769C						.						55	53	54					16																	66423413		2202	4300	6502	SO:0001583	missense	1003	exon5			TTCCCCTTCTTCA	X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"CD molecules", "Cadherins / Major cadherins"	1764	protein-coding gene	gene with protein product	"VE-cadherin"	601120	"cadherin 5, type 2, VE-cadherin (vascular epithelium)"			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.769T>C	chr16.hg19:g.66423413T>C	ENSP00000344115:p.Phe257Leu	84.0	0.0		75.0	4.0	NM_001795	Q4VAI5|Q4VAI6	Missense_Mutation	SNP	ENST00000341529.3	hg19	CCDS10804.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.466979	0.43839	.	.	ENSG00000179776	ENST00000341529;ENST00000379531	T	0.36520	1.25	5.69	3.39	0.38822	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.15219	0.0367	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05225	-1.0898	9	0.52906	T	0.07	.	4.9485	0.14002	0.6954:0.0:0.1612:0.1434	.	257	P33151	CADH5_HUMAN	L	257	ENSP00000344115:F257L	ENSP00000344115:F257L	F	+	1	0	CDH5	64980914	0.001000	0.12720	1.000000	0.80357	0.983000	0.72400	0.774000	0.26675	0.392000	0.25172	-0.339000	0.08088	TTC	.	.		0.607	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795		C	66423413	T	C	66423413	3	2	43	1	0	0	0	0	1	0	0	0	3115	1609	56	2	783	2	CDH5	16	66423413	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	35334865	66423413	23931340	298	5380										
E2F4	1874	hgsc.bcm.edu	37	chr16	67229817	67229817	+	Missense_Mutation	SNP	G	G	A													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cagcagcagcagcagcagcaGcagcagcagcagcagcaaca					rs140980388		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:67229817G>A	ENST00000379378.3	+	7	1000	c.941G>A	c.(940-942)aGc>aAc	p.S314N		NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	314	Poly-Ser.				blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		agcagcagcagcagcagcagc	0.602																																					p.S314N		Atlas-SNP	.											.	E2F4	25	.	0			c.G941A						.						40	44	42					16																	67229817		2197	4291	6488	SO:0001583	missense	1874	exon7			GCAGCAGCAGCAG	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975	ENST00000379378.3:c.941G>A	chr16.hg19:g.67229817G>A	ENSP00000368686:p.Ser314Asn	53.0	0.0		84.0	15.0	NM_001950	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	hg19	CCDS32464.1	.	.	.	.	.	.	.	.	.	.	g	7.432	0.638851	0.14386	.	.	ENSG00000205250	ENST00000379378	D	0.83591	-1.74	2.15	2.15	0.27550	.	1.244700	0.06489	U	0.734309	T	0.73799	0.3633	N	0.22421	0.69	0.27325	N	0.956935	P	0.48350	0.909	P	0.45506	0.483	T	0.63537	-0.6615	10	0.16896	T	0.51	.	7.8521	0.29462	0.0:0.0:1.0:0.0	.	314	Q16254	E2F4_HUMAN	N	314	ENSP00000368686:S314N	ENSP00000368686:S314N	S	+	2	0	E2F4	65787318	1.000000	0.71417	0.997000	0.53966	0.074000	0.17049	0.847000	0.27696	1.540000	0.49301	0.467000	0.42956	AGC	.	.		0.602	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		A	67229817	G	A	67229817	3	1	43	1	0	0	0	0	1	0	0	0	4871	971	34	3	967	3	E2F4	16	67229817	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	806404	67229817	23124936	299	5381	24	2								
E2F4	1874	hgsc.bcm.edu	37	chr16	67229823	67229823	+	Missense_Mutation	SNP	G	G	A													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cagcagcagcagcagcagcaGcagcagcagcaacagtaaca							TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:67229823G>A	ENST00000379378.3	+	7	1006	c.947G>A	c.(946-948)aGc>aAc	p.S316N		NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	316	Poly-Ser.				blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		agcagcagcagcagcagcagc	0.612																																					p.S316N		Atlas-SNP	.											.	E2F4	25	.	0			c.G947A						.						43	47	46					16																	67229823		2198	4299	6497	SO:0001583	missense	1874	exon7			GCAGCAGCAGCAG	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975	ENST00000379378.3:c.947G>A	chr16.hg19:g.67229823G>A	ENSP00000368686:p.Ser316Asn	53.0	0.0		89.0	11.0	NM_001950	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	hg19	CCDS32464.1	.	.	.	.	.	.	.	.	.	.	g	6.844	0.525009	0.13066	.	.	ENSG00000205250	ENST00000379378	D	0.85556	-2.0	2.3	2.3	0.28687	.	1.331100	0.05353	U	0.532219	T	0.73528	0.3598	N	0.08118	0	0.23653	N	0.997193	P	0.48350	0.909	P	0.45506	0.483	T	0.65952	-0.6043	10	0.17832	T	0.49	.	8.179	0.31300	0.0:0.0:1.0:0.0	.	316	Q16254	E2F4_HUMAN	N	316	ENSP00000368686:S316N	ENSP00000368686:S316N	S	+	2	0	E2F4	65787324	0.992000	0.36948	0.999000	0.59377	0.063000	0.16089	-0.571000	0.05889	1.624000	0.50355	0.655000	0.94253	AGC	.	.		0.612	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		A	67229823	G	A	67229823	3	1	43	1	0	0	0	0	1	0	0	0	4871	971	34	3	973	3	E2F4	16	67229823	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	6	67229823	23124930	300	5382	24	2								
KCTD19	146212	hgsc.bcm.edu	37	chr16	67337084	67337084	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cgctgcactcgcactcgatgAgggccaccgtctcagccagc	11	17	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:67337084A>G	ENST00000304372.5	-	4	663	c.608T>C	c.(607-609)cTc>cCc	p.L203P	KCTD19_ENST00000562860.1_5'UTR	NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	203					protein homooligomerization (GO:0051260)					endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		GCACTCGATGAGGGCCACCGT	0.617																																					p.L203P		Atlas-SNP	.											.	KCTD19	82	.	0			c.T608C						.						76	78	77					16																	67337084		2079	4198	6277	SO:0001583	missense	146212	exon4			TCGATGAGGGCCA	AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 19"				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.608T>C	chr16.hg19:g.67337084A>G	ENSP00000305702:p.Leu203Pro	99.0	0.0		111.0	5.0	NM_001100915	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	hg19	CCDS42179.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449620	0.84101	.	.	ENSG00000168676	ENST00000304372	T	0.72051	-0.62	5.82	5.82	0.92795	BTB/POZ fold (1);	0.000000	0.53938	D	0.000047	T	0.74764	0.3759	N	0.24115	0.695	0.58432	D	0.999997	D	0.89917	1.0	D	0.83275	0.996	T	0.78306	-0.2255	10	0.87932	D	0	-9.1363	13.5596	0.61782	1.0:0.0:0.0:0.0	.	203	Q17RG1	KCD19_HUMAN	P	203	ENSP00000305702:L203P	ENSP00000305702:L203P	L	-	2	0	KCTD19	65894585	1.000000	0.71417	0.994000	0.49952	0.965000	0.64279	6.054000	0.71096	2.225000	0.72522	0.533000	0.62120	CTC	.	.		0.617	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367		G	67337084	A	G	67337084	3	3	43	1	0	0	0	0	1	0	0	0	8115	304	11	2	2224	2	KCTD19	16	67337084	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	107261	67337084	23017669	301	5383										
TSNAXIP1	80152	hgsc.bcm.edu	37	chr16	67861436	67861436	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gggaacaatacatggatgagAaggacgagtacttacagcag	13	6	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:67861436A>G	ENST00000562787.1	-	0	2345				TSNAXIP1_ENST00000388833.3_Missense_Mutation_p.K564E|TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.K549E|TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.K618E|CENPT_ENST00000562947.1_5'Flank	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T						chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		CATGGATGAGAAGGACGAGTA	0.562																																					p.K564E		Atlas-SNP	.											.	TSNAXIP1	66	.	0			c.A1690G						.						113	110	111					16																	67861436		2198	4300	6498	SO:0001628	intergenic_variant	55815	exon15			GATGAGAAGGACG	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3			chr16.hg19:g.67861436A>G		67.0	0.0		85.0	4.0	NM_018430	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	hg19	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.392167	0.42410	.	.	ENSG00000102904	ENST00000415766;ENST00000388833	.	.	.	5.65	5.65	0.86999	.	0.058377	0.64402	D	0.000002	T	0.72112	0.3420	M	0.64997	1.995	0.37134	D	0.901403	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.998;0.999	D;D;D;D;D	0.85130	0.994;0.997;0.996;0.994;0.994	T	0.78137	-0.2321	9	0.72032	D	0.01	-44.9555	12.1892	0.54261	1.0:0.0:0.0:0.0	.	549;618;272;564;549	E7ENJ7;B4DXD0;Q2TAA8-2;Q2TAA8;B4E1H3	.;.;.;TXIP1_HUMAN;.	E	549;564	.	ENSP00000373485:K564E	K	+	1	0	TSNAXIP1	66418937	1.000000	0.71417	0.997000	0.53966	0.003000	0.03518	3.356000	0.52269	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.562	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		G	67861436	A	G	67861436	1	3	43	0	1	0	0	0	0	0	0	0	16647	247	9	2		2	TSNAXIP1	16	67861436	IGR	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	524352	67861436	22493317	302	5384										
EDC4	23644	hgsc.bcm.edu	37	chr16	67916365	67916365	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccatcgcccgagcagctgcaGacacattacaagggccgatg	11	14	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:67916365G>A	ENST00000358933.5	+	25	3549	c.3310G>A	c.(3310-3312)Gac>Aac	p.D1104N	CTC-479C5.10_ENST00000572067.1_lincRNA|NRN1L_ENST00000339176.3_5'Flank	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	1104					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		AGCAGCTGCAGACACATTACA	0.602																																					p.D1104N		Atlas-SNP	.											.	EDC4	101	.	0			c.G3310A						.						58	59	58					16																	67916365		2198	4300	6498	SO:0001583	missense	23644	exon25			GCTGCAGACACAT	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.3310G>A	chr16.hg19:g.67916365G>A	ENSP00000351811:p.Asp1104Asn	70.0	0.0		89.0	33.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	hg19	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	G	17.29	3.352703	0.61293	.	.	ENSG00000038358	ENST00000358933	.	.	.	6.04	6.04	0.98038	.	0.045285	0.85682	D	0.000000	T	0.42404	0.1201	N	0.13098	0.295	0.51767	D	0.999936	B	0.26672	0.156	B	0.17098	0.017	T	0.25882	-1.0119	9	0.18710	T	0.47	-25.5092	20.1899	0.98228	0.0:0.0:1.0:0.0	.	1104	Q6P2E9	EDC4_HUMAN	N	1104	.	ENSP00000351811:D1104N	D	+	1	0	EDC4	66473866	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.711000	0.98735	2.873000	0.98535	0.563000	0.77884	GAC	.	.		0.602	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		A	67916365	G	A	67916365	3	1	43	1	0	0	0	0	1	0	0	0	4910	942	33	3	3408	3	EDC4	16	67916365	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	54929	67916365	22438388	303	5385										
NOB1	28987	hgsc.bcm.edu	37	chr16	69783156	69783156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gatcgatgttgggcaaagggTttctccagaacatgaaggaa	13	6	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:69783156T>C	ENST00000268802.5	-	5	514	c.485A>G	c.(484-486)aAc>aGc	p.N162S		NM_014062.1	NP_054781.1	Q9ULX3	NOB1_HUMAN	NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)	162					visual perception (GO:0007601)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GGGCAAAGGGTTTCTCCAGAA	0.473																																					p.N162S		Atlas-SNP	.											.	NOB1	24	.	0			c.A485G						.						65	62	63					16																	69783156		2198	4300	6498	SO:0001583	missense	28987	exon5			AAAGGGTTTCTCC	AB026125	CCDS10884.1	16q22.1	2008-02-05	2006-04-20	2006-04-20	ENSG00000141101	ENSG00000141101			29540	protein-coding gene	gene with protein product	"nin one binding protein"	613586	"PSMD8 binding protein 1"	PSMD8BP1		16172919	Standard	NM_014062		Approved	NOB1P, ART-4, MST158	uc002exs.4	Q9ULX3	OTTHUMG00000137576	ENST00000268802.5:c.485A>G	chr16.hg19:g.69783156T>C	ENSP00000268802:p.Asn162Ser	51.0	0.0		71.0	4.0	NM_014062	Q7L6B7|Q7M4M4|Q7Z4B5|Q9NWB0	Missense_Mutation	SNP	ENST00000268802.5	hg19	CCDS10884.1	.	.	.	.	.	.	.	.	.	.	T	8.943	0.966211	0.18659	.	.	ENSG00000141101	ENST00000268802	T	0.29655	1.56	5.42	-1.75	0.08031	.	0.345423	0.34200	N	0.004170	T	0.12518	0.0304	N	0.22421	0.69	0.28403	N	0.918533	B	0.09022	0.002	B	0.04013	0.001	T	0.08743	-1.0707	9	.	.	.	.	0.4658	0.00523	0.3171:0.1343:0.2216:0.327	.	162	Q9ULX3	NOB1_HUMAN	S	162	ENSP00000268802:N162S	.	N	-	2	0	NOB1	68340657	0.964000	0.33143	0.947000	0.38551	0.824000	0.46624	0.626000	0.24492	-0.174000	0.10743	0.528000	0.53228	AAC	.	.		0.473	NOB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268958.2	NM_014062		C	69783156	T	C	69783156	3	2	43	1	0	0	0	0	1	0	0	0	10520	1725	60	2	773	2	NOB1	16	69783156	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1866791	69783156	20571597	304	5386										
SF3B3	23450	hgsc.bcm.edu	37	chr16	70588379	70588379	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgcctacatcattgtgtcttTcgtgaatgccaccctagtgt	8	11	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:70588379T>C	ENST00000302516.5	+	12	1644	c.1433T>C	c.(1432-1434)tTc>tCc	p.F478S		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	478					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				ATTGTGTCTTTCGTGAATGCC	0.423																																					p.F478S		Atlas-SNP	.											.	SF3B3	99	.	0			c.T1433C						.						169	149	156					16																	70588379		2198	4300	6498	SO:0001583	missense	23450	exon12			TGTCTTTCGTGAA	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.1433T>C	chr16.hg19:g.70588379T>C	ENSP00000305790:p.Phe478Ser	73.0	0.0		85.0	4.0	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	hg19	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	T	33	5.227121	0.95173	.	.	ENSG00000189091	ENST00000302516	T	0.47528	0.84	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.75517	0.3860	M	0.92738	3.34	0.80722	D	1	D	0.61080	0.989	D	0.68039	0.955	T	0.81773	-0.0779	10	0.66056	D	0.02	.	16.4069	0.83677	0.0:0.0:0.0:1.0	.	478	Q15393	SF3B3_HUMAN	S	478	ENSP00000305790:F478S	ENSP00000305790:F478S	F	+	2	0	SF3B3	69145880	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.806000	0.86020	2.272000	0.75746	0.460000	0.39030	TTC	.	.		0.423	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		C	70588379	T	C	70588379	3	2	43	1	0	0	0	0	1	0	0	0	14167	1783	62	2	1475	2	SF3B3	16	70588379	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	805223	70588379	19766374	305	5387										
IL34	146433	hgsc.bcm.edu	37	chr16	70688456	70688456	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cacagatcttgggatcttccTtggcgtggccttggggaatg	14	9	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:70688456T>A	ENST00000288098.2	+	2	427	c.44T>A	c.(43-45)cTt>cAt	p.L15H	IL34_ENST00000566361.1_5'UTR|IL34_ENST00000569641.1_Intron|IL34_ENST00000429149.2_Missense_Mutation_p.L15H	NM_001172772.1	NP_001166243.1	Q6ZMJ4	IL34_HUMAN	interleukin 34	15					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	extracellular space (GO:0005615)	macrophage colony-stimulating factor receptor binding (GO:0005157)			breast(1)|central_nervous_system(1)|kidney(9)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(2)	17						GGGATCTTCCTTGGCGTGGCC	0.572											OREG0023916	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L15H		Atlas-SNP	.											.	IL34	26	.	0			c.T44A						.						383	253	297					16																	70688456		2198	4300	6498	SO:0001583	missense	146433	exon3			TCTTCCTTGGCGT	BC029804	CCDS10895.1	16q22.1	2008-08-01	2008-06-04	2008-06-04	ENSG00000157368	ENSG00000157368		"Interleukins and interleukin receptors"	28529	protein-coding gene	gene with protein product		612081	"chromosome 16 open reading frame 77"	C16orf77		18467591	Standard	NM_152456		Approved	MGC34647, IL-34	uc002ezh.2	Q6ZMJ4	OTTHUMG00000137581	ENST00000288098.2:c.44T>A	chr16.hg19:g.70688456T>A	ENSP00000288098:p.Leu15His	165.0	0.0	1124	190.0	68.0	NM_152456	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	Missense_Mutation	SNP	ENST00000288098.2	hg19	CCDS10895.1	.	.	.	.	.	.	.	.	.	.	T	11.84	1.759491	0.31137	.	.	ENSG00000157368	ENST00000429149;ENST00000288098	T;T	0.51071	0.72;0.72	4.89	4.89	0.63831	.	0.102151	0.39274	N	0.001412	T	0.62756	0.2454	M	0.75447	2.3	0.09310	N	0.999999	D;D	0.69078	0.997;0.997	D;D	0.63192	0.912;0.912	T	0.58578	-0.7612	10	0.87932	D	0	-6.13	8.871	0.35316	0.0:0.0:0.1888:0.8112	.	15;15	Q6ZMJ4-2;Q6ZMJ4	.;IL34_HUMAN	H	15	ENSP00000397863:L15H;ENSP00000288098:L15H	ENSP00000288098:L15H	L	+	2	0	IL34	69245957	1.000000	0.71417	0.889000	0.34880	0.017000	0.09413	2.881000	0.48538	1.835000	0.53391	0.379000	0.24179	CTT	.	.		0.572	IL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268971.3	NM_152456		A	70688456	T	A	70688456	3	1	43	1	0	0	0	0	1	0	0	0	7703	1609	56	4	50	4	IL34	16	70688456	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	100077	70688456	19666297	306	5388										
FA2H	79152	hgsc.bcm.edu	37	chr16	74761274	74761274	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acaggagaggctttcgccagTccaccaggtcctgcaagaga	12	12	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr16:74761274T>C	ENST00000219368.3	-	3	443	c.374A>G	c.(373-375)gAc>gGc	p.D125G	FA2H_ENST00000544337.1_Intron	NM_024306.4	NP_077282.3	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	125					cell death (GO:0008219)|central nervous system myelin maintenance (GO:0032286)|fatty acid biosynthetic process (GO:0006633)|lipid modification (GO:0030258)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of cell proliferation (GO:0042127)|regulation of hair cycle (GO:0042634)|sebaceous gland cell differentiation (GO:0001949)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	fatty acid alpha-hydroxylase activity (GO:0080132)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						CTTTCGCCAGTCCACCAGGTC	0.557																																					p.D125G		Atlas-SNP	.											.	FA2H	21	.	0			c.A374G						.						60	57	58					16																	74761274		2198	4300	6498	SO:0001583	missense	79152	exon3			CGCCAGTCCACCA	BC002679	CCDS10911.1	16q23	2013-03-04	2003-10-29	2003-10-31	ENSG00000103089	ENSG00000103089		"Fatty acid hydroxylase domain containing"	21197	protein-coding gene	gene with protein product	"fatty acid hydroxylase"	611026	"fatty acid hydroxylase domain containing 1", "spastic paraplegia 35 (autosomal recessive)"	FAXDC1, SPG35		20104589	Standard	NM_024306		Approved	FAAH, FLJ25287	uc002fde.2	Q7L5A8	OTTHUMG00000137603	ENST00000219368.3:c.374A>G	chr16.hg19:g.74761274T>C	ENSP00000219368:p.Asp125Gly	41.0	0.0		53.0	4.0	NM_024306	B7Z8T6|O75213|Q96DK1|Q9H1A5	Missense_Mutation	SNP	ENST00000219368.3	hg19	CCDS10911.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.816930	0.90790	.	.	ENSG00000103089	ENST00000219368	D	0.91577	-2.87	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.96266	0.8782	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97154	0.9833	10	0.87932	D	0	-13.4363	15.7053	0.77573	0.0:0.0:0.0:1.0	.	125	Q7L5A8	FA2H_HUMAN	G	125	ENSP00000219368:D125G	ENSP00000219368:D125G	D	-	2	0	FA2H	73318775	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.811000	0.86092	2.119000	0.64992	0.533000	0.62120	GAC	.	.		0.557	FA2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269015.2	NM_024306		C	74761274	T	C	74761274	3	2	43	1	0	0	0	0	1	0	0	0	5357	1667	58	2	764	2	FA2H	16	74761274	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	4072818	74761274	15593479	307	5389										
VPS53	55275	hgsc.bcm.edu	37	chr17	465918	465918	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cacggcacccccttcatcagTgttgggcttaggtggcccct	11	15	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:465918T>C	ENST00000571805.1	-	14	1517	c.1381A>G	c.(1381-1383)Act>Gct	p.T461A	VPS53_ENST00000574029.1_Intron|VPS53_ENST00000291074.5_Missense_Mutation_p.T432A|VPS53_ENST00000401468.3_Missense_Mutation_p.T184A|VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000437048.2_Missense_Mutation_p.T461A|VPS53_ENST00000446250.2_Missense_Mutation_p.T263A			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	461					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		CCTTCATCAGTGTTGGGCTTA	0.512																																					p.T461A		Atlas-SNP	.											.	VPS53	109	.	0			c.A1381G						.						66	62	63					17																	465918		2203	4300	6503	SO:0001583	missense	55275	exon14			CATCAGTGTTGGG		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"vacuolar protein sorting 53 (yeast)"			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.1381A>G	chr17.hg19:g.465918T>C	ENSP00000459312:p.Thr461Ala	81.0	0.0		80.0	4.0	NM_001128159	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	hg19		.	.	.	.	.	.	.	.	.	.	T	8.857	0.946010	0.18356	.	.	ENSG00000141252	ENST00000437048;ENST00000446250;ENST00000291074;ENST00000401468;ENST00000389040	T;T;T;T;T	0.44881	1.49;1.5;1.5;0.91;1.48	5.97	4.88	0.63580	.	0.299613	0.41500	D	0.000865	T	0.22003	0.0530	L	0.27053	0.805	0.35481	D	0.798209	B;B;B;B;B	0.15719	0.014;0.001;0.0;0.0;0.0	B;B;B;B;B	0.17098	0.017;0.007;0.003;0.001;0.009	T	0.24621	-1.0155	10	0.02654	T	1	-1.4858	4.7658	0.13132	0.1493:0.1356:0.0:0.7151	.	184;461;263;461;432	E7EVT8;Q5VIR6-4;G3V0H8;Q5VIR6;Q5VIR6-2	.;.;.;VPS53_HUMAN;.	A	461;263;432;184;413	ENSP00000401435:T461A;ENSP00000394386:T263A;ENSP00000291074:T432A;ENSP00000384294:T184A;ENSP00000373692:T413A	ENSP00000291074:T432A	T	-	1	0	VPS53	412668	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	1.742000	0.38248	2.281000	0.76405	0.533000	0.62120	ACT	.	.		0.512	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289		C	465918	T	C	465918	3	2	43	1	0	0	0	0	1	0	0	0	17230	1696	59	2	1168	2	VPS53	17	465918	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10		465918	80729292	308	5390										
FLII	2314	hgsc.bcm.edu	37	chr17	18148691	18148691	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcaggccttcaggctcagctTgatctccacctggctagtct	10	14	4	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:18148691T>C	ENST00000327031.4	-	29	3877	c.3652A>G	c.(3652-3654)Aag>Gag	p.K1218E	FLII_ENST00000379450.4_Missense_Mutation_p.K1132E|FLII_ENST00000545457.2_Missense_Mutation_p.K1163E|FLII_ENST00000579294.1_Missense_Mutation_p.K1207E|FLII_ENST00000578558.1_Intron	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1218					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					AGGCTCAGCTTGATCTCCACC	0.647																																					p.K1218E		Atlas-SNP	.											.	FLII	79	.	0			c.A3652G						.						83	84	83					17																	18148691		2203	4300	6503	SO:0001583	missense	2314	exon29			TCAGCTTGATCTC	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"flightless I (Drosophila) homolog"			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.3652A>G	chr17.hg19:g.18148691T>C	ENSP00000324573:p.Lys1218Glu	51.0	0.0		120.0	5.0	NM_002018	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	hg19	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	T	35	5.451160	0.96205	.	.	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T;T	0.55234	0.53;0.94;0.53	5.42	5.42	0.78866	Gelsolin domain (1);	0.048627	0.85682	D	0.000000	T	0.66674	0.2813	L	0.45470	1.425	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.998;0.999	D;D;D;D	0.81914	0.965;0.965;0.99;0.995	T	0.69829	-0.5039	10	0.87932	D	0	-22.6087	15.4544	0.75302	0.0:0.0:0.0:1.0	.	1132;1132;1218;1187	E7EPM0;B4DIL0;Q13045;B4DIX0	.;.;FLII_HUMAN;.	E	1218;1097;1132	ENSP00000324573:K1218E;ENSP00000438536:K1097E;ENSP00000368763:K1132E	ENSP00000324573:K1218E	K	-	1	0	FLII	18089416	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.738000	0.68613	2.054000	0.61138	0.533000	0.62120	AAG	.	.		0.647	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		C	18148691	T	C	18148691	3	2	43	1	0	0	0	0	1	0	0	0	5933	1821	63	2	165	2	FLII	17	18148691	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	17682773	18148691	63046519	309	5391										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26961916	26961916	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ctccttactttcatccttcaTcagctcgtagttatcatgaa	4	12	4	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:26961916T>C	ENST00000528896.2	-	16	2763	c.2689A>G	c.(2689-2691)Atg>Gtg	p.M897V	KIAA0100_ENST00000389003.3_Missense_Mutation_p.M754V|RP11-192H23.7_ENST00000577814.1_RNA|KIAA0100_ENST00000544884.1_Missense_Mutation_p.M754V|RP11-192H23.7_ENST00000583787.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	897						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					TCATCCTTCATCAGCTCGTAG	0.478																																					p.M897V		Atlas-SNP	.											.	KIAA0100	175	.	0			c.A2689G						.						219	239	232					17																	26961916		2203	4300	6503	SO:0001583	missense	9703	exon16			CCTTCATCAGCTC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.2689A>G	chr17.hg19:g.26961916T>C	ENSP00000436773:p.Met897Val	50.0	0.0		74.0	5.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.493281	0.64186	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.24350	1.86;1.86	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.45856	0.1363	M	0.61703	1.905	0.80722	D	1	P	0.49447	0.924	P	0.60682	0.878	T	0.18178	-1.0345	10	0.30854	T	0.27	.	16.2996	0.82804	0.0:0.0:0.0:1.0	.	897	Q14667	K0100_HUMAN	V	897;867;897;754	ENSP00000436773:M897V;ENSP00000446443:M754V	ENSP00000005905:M897V	M	-	1	0	KIAA0100	23986043	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.828000	0.69307	2.252000	0.74401	0.455000	0.32223	ATG	.	.		0.478	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		C	26961916	T	C	26961916	3	2	43	1	0	0	0	0	1	0	0	0	8163	1435	50	2	4114	2	KIAA0100	17	26961916	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	8813225	26961916	54233294	310	5392										
SLFN12L	100506736	hgsc.bcm.edu	37	chr17	33807038	33807038	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcagcagagcacacacagctCgtgagacattttcattctgc	8	12	3	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:33807038C>A	ENST00000260908.7	-	2	308	c.191G>T	c.(190-192)cGa>cTa	p.R64L	RP11-686D22.9_ENST00000587076.1_RNA|SLFN12L_ENST00000361112.4_Missense_Mutation_p.R93L|SLFN12L_ENST00000449046.1_Missense_Mutation_p.R95L	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	64						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						ACACACAGCTCGTGAGACATT	0.403																																					p.R64L		Atlas-SNP	.											.	SLFN12L	140	.	0			c.G191T						.						90	75	79					17																	33807038		692	1591	2283	SO:0001583	missense	100506736	exon2			ACAGCTCGTGAGA	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.191G>T	chr17.hg19:g.33807038C>A	ENSP00000437635:p.Arg64Leu	144.0	0.0		163.0	71.0	NM_001195790	F5H6G3	Missense_Mutation	SNP	ENST00000260908.7	hg19	CCDS56026.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.995899	0.54147	.	.	ENSG00000205045	ENST00000260908;ENST00000361112;ENST00000449046	T;T;T	0.03920	3.77;3.87;3.76	2.72	-5.44	0.02624	.	.	.	.	.	T	0.03564	0.0102	N	0.11560	0.145	0.09310	N	1	P	0.49696	0.927	P	0.49999	0.628	T	0.27157	-1.0082	9	0.46703	T	0.11	.	5.9558	0.19273	0.0:0.5432:0.1875:0.2692	.	93	Q6IEE8-2	.	L	64;93;95	ENSP00000437635:R64L;ENSP00000354412:R93L;ENSP00000389348:R95L	ENSP00000437635:R64L	R	-	2	0	SLFN12L	30831151	0.000000	0.05858	0.000000	0.03702	0.398000	0.30690	-2.933000	0.00687	-1.156000	0.02818	0.205000	0.17691	CGA	.	.		0.403	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206		A	33807038	C	A	33807038	3	1	43	1	0	0	0	0	1	0	0	0	14750	884	31	1	1587	1	SLFN12L	17	33807038	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	6845122	33807038	47388172	311	5393										
ACACA	6871	hgsc.bcm.edu	37	chr17	35766386	35766386	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgacatcagagtagaccaccAcatcctctcatcattgcgcc	6	15	3	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:35766386A>G	ENST00000394395.2	+	0	0				RP11-378E13.4_ENST00000590364.1_RNA|ACACA_ENST00000416895.1_5'UTR|ACACA_ENST00000353139.5_Missense_Mutation_p.W2R|TADA2A_ENST00000225396.6_5'Flank|TADA2A_ENST00000417170.1_5'Flank|TADA2A_ENST00000586023.1_5'Flank|ACACA_ENST00000589665.1_5'UTR	NM_001166105.1	NP_001159577.1	O75478	TAD2A_HUMAN	transcriptional adaptor 2A						chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)|skin(1)	13						gtagacCACCACATCCTCTCA	0.438																																					p.W2R		Atlas-SNP	.											.	ACACA	395	.	0			c.T4C						.						229	238	235					17																	35766386		2094	4227	6321	SO:0001631	upstream_gene_variant	31	exon1			ACCACCACATCCT	AK022767	CCDS11319.1, CCDS45656.1	17q12-q21	2014-04-10	2009-10-02	2009-10-02	ENSG00000108264	ENSG00000276234			11531	protein-coding gene	gene with protein product		602276	"transcriptional adaptor 2 (ADA2 homolog, yeast)-like"	TADA2L		8552087	Standard	XM_006722043		Approved	ADA2, hADA2, ADA2A	uc002hnt.3	O75478	OTTHUMG00000188469		chr17.hg19:g.35766386A>G	Exception_encountered	85.0	0.0		85.0	4.0	NM_198834	A8MVD0|B3KMU9|Q9BVJ0|Q9UCW2|Q9UP49	Missense_Mutation	SNP	ENST00000394395.2	hg19	CCDS11319.1	.	.	.	.	.	.	.	.	.	.	A	14.84	2.656778	0.47467	.	.	ENSG00000132142	ENST00000353139	D	0.94828	-3.53	4.42	3.31	0.37934	.	0.493351	0.17435	N	0.174325	D	0.90380	0.6989	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	D	0.86518	0.1814	9	0.87932	D	0	-0.0511	6.2662	0.20928	0.8822:0.0:0.1178:0.0	.	2	Q13085-4	.	R	2	ENSP00000344789:W2R	ENSP00000344789:W2R	W	-	1	0	ACACA	32840499	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.195000	0.42677	1.005000	0.39183	0.528000	0.53228	TGG	.	.		0.438	TADA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256677.3	NM_001488		G	35766386	A	G	35766386	1	3	43	0	1	0	0	0	0	0	0	0	106	159	6	2		2	ACACA	17	35766386	5'Flank	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1959348	35766386	45428824	312	5394										
GHDC	84514	hgsc.bcm.edu	37	chr17	40342899	40342899	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	attgtaggcaccaaccactcGcaccacatcacccaggcggc	8	17	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:40342899G>A	ENST00000301671.8	-	6	1546	c.1105C>T	c.(1105-1107)Cga>Tga	p.R369*	GHDC_ENST00000428494.2_Nonsense_Mutation_p.R330*|GHDC_ENST00000590520.1_5'Flank|GHDC_ENST00000587427.1_Nonsense_Mutation_p.R369*|GHDC_ENST00000436923.2_Nonsense_Mutation_p.R369*|GHDC_ENST00000593209.1_Nonsense_Mutation_p.R369*|GHDC_ENST00000414034.3_Nonsense_Mutation_p.R369*			Q8N2G8	GHDC_HUMAN	GH3 domain containing	369						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		CCAACCACTCGCACCACATCA	0.627																																					p.R369X		Atlas-SNP	.											.	GHDC	63	.	0			c.C1105T						.						92	91	91					17																	40342899		2203	4300	6503	SO:0001587	stop_gained	84514	exon7			CCACTCGCACCAC	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.1105C>T	chr17.hg19:g.40342899G>A	ENSP00000301671:p.Arg369*	59.0	0.0		55.0	25.0	NM_001142623	B4DQS4|E9PDB5|Q9BXM6	Nonsense_Mutation	SNP	ENST00000301671.8	hg19	CCDS11422.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.070655	0.76301	.	.	ENSG00000167925	ENST00000393854;ENST00000428494;ENST00000414034;ENST00000301671;ENST00000436923	.	.	.	4.18	4.18	0.49190	.	0.643001	0.15310	N	0.269145	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.0714	13.8103	0.63260	0.0:0.0:1.0:0.0	.	.	.	.	X	313;330;369;369;369	.	ENSP00000301671:R369X	R	-	1	2	GHDC	37596425	0.238000	0.23825	0.049000	0.19019	0.218000	0.24690	3.442000	0.52900	2.146000	0.66826	0.561000	0.74099	CGA	.	.		0.627	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		A	40342899	G	A	40342899	4	1	43	1	0	0	0	0	0	1	0	0	6377	1095	38	1	592	1	GHDC	17	40342899	Nonsense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	4576513	40342899	40852311	313	5395										
STAT3	6774	hgsc.bcm.edu	37	chr17	40500452	40500452	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccagaaactgccgcagctccAttgggaagctgtcactgtag	11	12	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:40500452A>T	ENST00000264657.5	-	2	395	c.83T>A	c.(82-84)aTg>aAg	p.M28K	STAT3_ENST00000404395.3_Missense_Mutation_p.M28K|STAT3_ENST00000588969.1_Missense_Mutation_p.M28K|STAT3_ENST00000389272.3_Intron|STAT3_ENST00000585517.1_Missense_Mutation_p.M28K	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	28					acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		CCGCAGCTCCATTGGGAAGCT	0.493									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.M28K		Atlas-SNP	.											.	STAT3	268	.	0			c.T83A						.						94	89	91					17																	40500452		2203	4300	6503	SO:0001583	missense	6774	exon2	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	AGCTCCATTGGGA	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610		"SH2 domain containing"	11364	protein-coding gene	gene with protein product		102582				7512451	Standard	NM_139276		Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.83T>A	chr17.hg19:g.40500452A>T	ENSP00000264657:p.Met28Lys	106.0	0.0		110.0	50.0	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	hg19	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.027571	0.93518	.	.	ENSG00000168610	ENST00000264657;ENST00000404395	T;T	0.54071	0.59;0.59	5.28	5.28	0.74379	STAT transcription factor, protein interaction (4);	0.000000	0.85682	D	0.000000	T	0.72969	0.3527	M	0.81497	2.545	0.80722	D	1	D;P;P	0.53462	0.96;0.845;0.845	D;P;P	0.66979	0.948;0.899;0.899	T	0.76694	-0.2865	10	0.62326	D	0.03	-30.1868	15.3678	0.74538	1.0:0.0:0.0:0.0	.	28;28;28	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	K	28	ENSP00000264657:M28K;ENSP00000384943:M28K	ENSP00000264657:M28K	M	-	2	0	STAT3	37753978	1.000000	0.71417	0.996000	0.52242	0.949000	0.60115	8.972000	0.93424	2.219000	0.72066	0.533000	0.62120	ATG	.	.		0.493	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		T	40500452	A	T	40500452	3	4	43	1	0	0	0	0	1	0	0	0	15281	217	8	4	2321	4	STAT3	17	40500452	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	157553	40500452	40694758	314	5396										
VEZF1	7716	hgsc.bcm.edu	37	chr17	56056598	56056598	+	Silent	SNP	T	T	C													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cttgtcacatgttgttgttgTtgttgttgctgctgctgctg							TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:56056598T>C	ENST00000581208.1	-	5	1093	c.1053A>G	c.(1051-1053)caA>caG	p.Q351Q	VEZF1_ENST00000584396.1_Silent_p.Q342Q	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	351	Poly-Gln.			Missing (in Ref. 1; BAA05663). {ECO:0000305}.	angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						gttgttgttgttgttgttgct	0.473																																					p.Q351Q		Atlas-SNP	.											.	VEZF1	50	.	0			c.A1053G						.						185	168	174					17																	56056598		2203	4300	6503	SO:0001819	synonymous_variant	7716	exon5			TTGTTGTTGTTGT	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"Zinc fingers, C2H2-type"	12949	protein-coding gene	gene with protein product		606747	"zinc finger protein 161"	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.1053A>G	chr17.hg19:g.56056598T>C		123.0	0.0		142.0	10.0	NM_007146		Silent	SNP	ENST00000581208.1	hg19	CCDS32687.1																																																																																			.	.		0.473	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1			C	56056598	T	C	56056598	2	2	43	1	0	0	0	0	0	0	0	1	17170	1722	60	2		2	VEZF1	17	56056598	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	15556146	56056598	25138612	315	5397	25	2								
VEZF1	7716	hgsc.bcm.edu	37	chr17	56056601	56056601	+	Silent	SNP	T	T	C													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtcacatgttgttgttgttgTtgttgctgctgctgctgctg							TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:56056601T>C	ENST00000581208.1	-	5	1090	c.1050A>G	c.(1048-1050)caA>caG	p.Q350Q	VEZF1_ENST00000584396.1_Silent_p.Q341Q	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	350	Poly-Gln.			Missing (in Ref. 1; BAA05663). {ECO:0000305}.	angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						gttgttgttgttgttgctgct	0.473																																					p.Q350Q		Atlas-SNP	.											.	VEZF1	50	.	0			c.A1050G						.						173	159	164					17																	56056601		2203	4300	6503	SO:0001819	synonymous_variant	7716	exon5			TTGTTGTTGTTGC	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"Zinc fingers, C2H2-type"	12949	protein-coding gene	gene with protein product		606747	"zinc finger protein 161"	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.1050A>G	chr17.hg19:g.56056601T>C		118.0	0.0		142.0	13.0	NM_007146		Silent	SNP	ENST00000581208.1	hg19	CCDS32687.1																																																																																			.	.		0.473	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1			C	56056601	T	C	56056601	2	2	43	1	0	0	0	0	0	0	0	1	17170	1722	60	2		2	VEZF1	17	56056601	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3	56056601	25138609	316	5398	25	2								
MPO	4353	hgsc.bcm.edu	37	chr17	56350840	56350841	+	Missense_Mutation	DNP	AT	AT	GG													0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggacacgggggttgggttccAtgggctggtaccgattgtcc					rs536522394	byFrequency	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A|T	A|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:56350840_56350841AT>GG	ENST00000225275.3	-	9	1731_1732	c.1555_1556AT>CC	c.(1555-1557)ATg>CCg	p.M519P	MPO_ENST00000340482.3_Missense_Mutation_p.M551P|MPO_ENST00000578493.1_5'Flank	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	519					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	GTTGGGTTCCATGGGCTGGTAC	0.609																																					p.M519T|p.M519L		Atlas-SNP	.											.	MPO	114	.	0			c.T1556C|c.A1555C						.																																			SO:0001583	missense	4353	exon9			GGTTCCATGGGCT|GTTCCATGGGCTG		CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.1555_1556delinsGG	chr17.hg19:g.56350840_56350841delinsGG	ENSP00000225275:p.Met519Pro	42.0|43.0	0.0		61.0|62.0	5.0|6.0	NM_000250	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	hg19	CCDS11604.1																																																																																			.	.		0.609	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			GG	56350841	AT	GG	56350840	3	3	43	1	0	0	0	0	1	0	0	0	9741	217	8	2	697	2	MPO	17	56350840	Missense_Mutation	DNP	AT	TCGA-BC-A3KF-01A-11D-A20W-10	294239	56350840	24844370	317	5399										
PRR11	55771	hgsc.bcm.edu	37	chr17	57247212	57247212	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttcagtccaagctaattacAcctcctcctccaccaccctc	2	19	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:57247212A>G	ENST00000262293.4	+	2	411	c.99A>G	c.(97-99)acA>acG	p.T33T		NM_018304.3	NP_060774.2	Q96HE9	PRR11_HUMAN	proline rich 11	33						cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|pancreas(1)	16	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					AGCTAATTACACCTCCTCCTC	0.388																																					p.T33T		Atlas-SNP	.											.	PRR11	36	.	0			c.A99G						.						94	93	94					17																	57247212		2203	4300	6503	SO:0001819	synonymous_variant	55771	exon2			AATTACACCTCCT		CCDS11614.1	17q23.2	2005-12-13				ENSG00000068489			25619	protein-coding gene	gene with protein product		615920				11799066	Standard	NM_018304		Approved	FLJ11029	uc002ixf.2	Q96HE9		ENST00000262293.4:c.99A>G	chr17.hg19:g.57247212A>G		122.0	0.0		129.0	6.0	NM_018304	Q9NUZ7|Q9NXE9	Silent	SNP	ENST00000262293.4	hg19	CCDS11614.1																																																																																			.	.		0.388	PRR11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445949.1	NM_018304		G	57247212	A	G	57247212	2	3	43	1	0	0	0	0	0	0	0	1	12595	146	6	2		2	PRR11	17	57247212	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	896372	57247212	23947998	318	5400										
INTS2	57508	hgsc.bcm.edu	37	chr17	59984985	59984985	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aaaggacagaactgctggtcTctctttttctctgaaagaaa	8	8	3	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:59984985T>C	ENST00000444766.3	-	8	1064	c.989A>G	c.(988-990)gAg>gGg	p.E330G	INTS2_ENST00000251334.6_Missense_Mutation_p.E322G	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	330					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						ACTGCTGGTCTCTCTTTTTCT	0.423																																					p.E330G		Atlas-SNP	.											.	INTS2	89	.	0			c.A989G						.						36	35	35					17																	59984985		1870	4094	5964	SO:0001583	missense	57508	exon8			CTGGTCTCTCTTT	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.989A>G	chr17.hg19:g.59984985T>C	ENSP00000414237:p.Glu330Gly	96.0	0.0		121.0	5.0	NM_020748	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	hg19	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.010608	0.54361	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.48836	0.8	5.52	5.52	0.82312	.	0.045770	0.85682	D	0.000000	T	0.42063	0.1186	L	0.44542	1.39	0.80722	D	1	B	0.29301	0.241	B	0.29942	0.109	T	0.24297	-1.0164	9	.	.	.	-13.0156	15.6487	0.77073	0.0:0.0:0.0:1.0	.	330	Q9H0H0	INT2_HUMAN	G	330;329	ENSP00000414237:E330G	.	E	-	2	0	INTS2	57339767	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.499000	0.81566	2.106000	0.64143	0.533000	0.62120	GAG	.	.		0.423	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		C	59984985	T	C	59984985	3	2	43	1	0	0	0	0	1	0	0	0	7787	1551	54	2	2697	2	INTS2	17	59984985	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2737773	59984985	21210225	319	5401										
ABCA8	10351	hgsc.bcm.edu	37	chr17	66879991	66879991	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttccattccagacatcgaagAgtaaaaagaaaaatgataaa	6	6	0	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:66879991A>G	ENST00000269080.2	-	27	3665	c.3528T>C	c.(3526-3528)acT>acC	p.T1176T	ABCA8_ENST00000430352.2_Silent_p.T1216T|ABCA8_ENST00000586539.1_Silent_p.T1216T	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1176					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GACATCGAAGAGTAAAAAGAA	0.284																																					p.T1176T		Atlas-SNP	.											.	ABCA8	213	.	0			c.T3528C						.						47	47	47					17																	66879991		2203	4297	6500	SO:0001819	synonymous_variant	10351	exon27			TCGAAGAGTAAAA	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3528T>C	chr17.hg19:g.66879991A>G		104.0	0.0		111.0	5.0	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	hg19	CCDS11680.1																																																																																			.	.		0.284	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		G	66879991	A	G	66879991	2	3	43	1	0	0	0	0	0	0	0	1	38	291	11	2		2	ABCA8	17	66879991	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	6895006	66879991	14315219	320	5402										
SOX9	6662	hgsc.bcm.edu	37	chr17	70120374	70120374	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cagccacgcggcaggccaggGcaccggcctctactccacct	11	19	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr17:70120374G>T	ENST00000245479.2	+	3	1748	c.1376G>T	c.(1375-1377)gGc>gTc	p.G459V		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	459					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			GCAGGCCAGGGCACCGGCCTC	0.647																																					p.G459V	Pancreas(42;83 1041 2320 35205 39456)	Atlas-SNP	.											.	SOX9	91	.	0			c.G1376T						.						148	141	144					17																	70120374		2203	4300	6503	SO:0001583	missense	6662	exon3			GCCAGGGCACCGG	S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.1376G>T	chr17.hg19:g.70120374G>T	ENSP00000245479:p.Gly459Val	67.0	0.0		77.0	33.0	NM_000346	Q53Y80	Missense_Mutation	SNP	ENST00000245479.2	hg19	CCDS11689.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.658077	0.47467	.	.	ENSG00000125398	ENST00000245479;ENST00000455872	T	0.75938	-0.98	4.27	3.27	0.37495	.	0.288040	0.38005	N	0.001847	T	0.58694	0.2140	L	0.34521	1.04	0.80722	D	1	B	0.32245	0.361	B	0.29440	0.102	T	0.54899	-0.8224	10	0.41790	T	0.15	.	7.0933	0.25295	0.0889:0.0:0.7391:0.1721	.	459	P48436	SOX9_HUMAN	V	459;395	ENSP00000245479:G459V	ENSP00000245479:G459V	G	+	2	0	SOX9	67631969	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	5.228000	0.65310	0.882000	0.36016	0.462000	0.41574	GGC	.	.		0.647	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		T	70120374	G	T	70120374	3	4	43	1	0	0	0	0	1	0	0	0	14973	1203	42	3	1386	3	SOX9	17	70120374	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	3240383	70120374	11074836	321	5403										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2738452	2738452	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tacagggtctgcttcctgatGtgcaagtaccaacatctgta	9	10	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr18:2738452G>A	ENST00000320876.6	+	26	3672	c.3334G>A	c.(3334-3336)Gtg>Atg	p.V1112M	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.V1112M	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1112					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GCTTCCTGATGTGCAAGTACC	0.383																																					p.V1112M		Atlas-SNP	.											.	SMCHD1	88	.	0			c.G3334A						.						123	111	115					18																	2738452		1885	4108	5993	SO:0001583	missense	23347	exon26			CCTGATGTGCAAG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.3334G>A	chr18.hg19:g.2738452G>A	ENSP00000326603:p.Val1112Met	88.0	0.0		82.0	4.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.536586	0.85812	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.30182	1.54;1.55	5.22	5.22	0.72569	.	0.139747	0.47455	D	0.000233	T	0.55353	0.1915	M	0.62723	1.935	0.40555	D	0.981152	D	0.71674	0.998	D	0.78314	0.991	T	0.58973	-0.7541	10	0.87932	D	0	-15.3187	19.1396	0.93443	0.0:0.0:1.0:0.0	.	1112	A6NHR9	SMHD1_HUMAN	M	1112	ENSP00000326603:V1112M;ENSP00000261598:V1112M	ENSP00000261598:V1112M	V	+	1	0	SMCHD1	2728452	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.026000	0.76455	2.573000	0.86826	0.585000	0.79938	GTG	.	.		0.383	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			A	2738452	G	A	2738452	3	1	43	1	0	0	0	0	1	0	0	0	14803	1377	48	3	3436	3	SMCHD1	18	2738452	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10		2738452	75338796	322	5404										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9255794	9255794	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaaagaaaaacctttgaaaaAgaaaagaagataaaacatga	7	3	0	6			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr18:9255794A>G	ENST00000262126.4	+	9	2769	c.2529A>G	c.(2527-2529)aaA>aaG	p.K843K	ANKRD12_ENST00000400020.3_Silent_p.K820K|ANKRD12_ENST00000383440.2_Silent_p.K820K	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	843						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CCTTTGAAAAAGAAAAGAAGA	0.294																																					p.K843K		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A2529G						.						25	27	26					18																	9255794		2194	4280	6474	SO:0001819	synonymous_variant	23253	exon9			TGAAAAAGAAAAG	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.2529A>G	chr18.hg19:g.9255794A>G		66.0	0.0		86.0	4.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Silent	SNP	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.294	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		G	9255794	A	G	9255794	2	3	43	1	0	0	0	0	0	0	0	1	640	69	3	2		2	ANKRD12	18	9255794	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	6517342	9255794	68821454	323	5405										
PSMG2	56984	hgsc.bcm.edu	37	chr18	12718587	12718587	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggctgtgccagagtcattgtTctttcaagcagtcattcata	9	9	5	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr18:12718587T>C	ENST00000317615.6	+	4	1042	c.360T>C	c.(358-360)gtT>gtC	p.V120V	PSMG2_ENST00000590217.1_Silent_p.V120V|PSMG2_ENST00000585331.2_Silent_p.V89V	NM_020232.4	NP_064617.2			proteasome (prosome, macropain) assembly chaperone 2											lung(1)|prostate(2)|skin(1)	4						GAGTCATTGTTCTTTCAAGCA	0.378																																					p.V120V		Atlas-SNP	.											.	PSMG2	17	.	0			c.T360C						.						143	133	136					18																	12718587		2203	4300	6503	SO:0001819	synonymous_variant	56984	exon4			CATTGTTCTTTCA	AF276707	CCDS11862.1, CCDS67440.1	18p11.21	2012-01-25	2007-10-23	2007-10-23	ENSG00000128789	ENSG00000128789			24929	protein-coding gene	gene with protein product	"hepatocellular carcinoma susceptibility protein", "CD40 ligand-activated specific transcript 3"	609702	"tumor necrosis factor superfamily, member 5-induced protein 1"	TNFSF5IP1		11854909, 12147697, 17189198	Standard	NM_147163		Approved	HCCA3, MDS003, MGC15092, CLAST3, HsT1707, PAC2	uc002krk.3	Q969U7	OTTHUMG00000131703	ENST00000317615.6:c.360T>C	chr18.hg19:g.12718587T>C		75.0	0.0		84.0	4.0	NM_020232		Silent	SNP	ENST00000317615.6	hg19	CCDS11862.1																																																																																			.	.		0.378	PSMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254615.1	NM_020232		C	12718587	T	C	12718587	2	2	43	1	0	0	0	0	0	0	0	1	12724	1770	62	2		2	PSMG2	18	12718587	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	3462793	12718587	65358661	324	5406										
RIOK3	8780	hgsc.bcm.edu	37	chr18	21061218	21061218	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	atttttgaaagatgatggagAcccaccactactatatgatg	8	7	0	5			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr18:21061218A>G	ENST00000339486.3	+	13	2152	c.1535A>G	c.(1534-1536)gAc>gGc	p.D512G	RIOK3_ENST00000577501.1_Missense_Mutation_p.D509G|RIOK3_ENST00000581585.1_Missense_Mutation_p.D496G	NM_003831.3	NP_003822.2	O14730	RIOK3_HUMAN	RIO kinase 3	512	Protein kinase.				chromosome segregation (GO:0007059)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(2)	10	all_cancers(21;0.000106)|all_epithelial(16;6.74e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GATGATGGAGACCCACCACTA	0.378																																					p.D512G		Atlas-SNP	.											.	RIOK3	42	.	0			c.A1535G						.						98	92	94					18																	21061218		2203	4300	6503	SO:0001583	missense	8780	exon13			ATGGAGACCCACC	AF013591	CCDS11877.1	18q11.2	2012-12-10	2012-12-10	2003-06-25	ENSG00000101782	ENSG00000101782			11451	protein-coding gene	gene with protein product		603579	"sudD (suppressor of bimD6, Aspergillus nidulans) homolog", "RIO kinase 3 (yeast)"	SUDD		9602165	Standard	NM_003831		Approved		uc002kui.4	O14730	OTTHUMG00000131813	ENST00000339486.3:c.1535A>G	chr18.hg19:g.21061218A>G	ENSP00000341874:p.Asp512Gly	49.0	0.0		65.0	4.0	NM_003831	Q8IXN9	Missense_Mutation	SNP	ENST00000339486.3	hg19	CCDS11877.1	.	.	.	.	.	.	.	.	.	.	A	0.194	-1.050687	0.01981	.	.	ENSG00000101782	ENST00000339486	T	0.07021	3.23	6.04	3.31	0.37934	.	0.217594	0.47093	N	0.000245	T	0.02455	0.0075	N	0.00926	-1.1	0.22127	N	0.999342	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.0;0.0;0.0	T	0.46345	-0.9198	10	0.11485	T	0.65	-10.8054	9.7321	0.40368	0.3:0.0:0.7:0.0	.	256;496;509;512	E7ESK5;B4E1Q4;O14730-2;O14730	.;.;.;RIOK3_HUMAN	G	512	ENSP00000341874:D512G	ENSP00000341874:D512G	D	+	2	0	RIOK3	19315216	0.999000	0.42202	0.635000	0.29338	0.341000	0.28922	2.928000	0.48908	0.448000	0.26722	-0.248000	0.11899	GAC	.	.		0.378	RIOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254756.1	NM_003831		G	21061218	A	G	21061218	3	3	43	1	0	0	0	0	1	0	0	0	13394	275	10	2	1585	2	RIOK3	18	21061218	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	8342631	21061218	57016030	325	5407										
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56008984	56008984	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gagcctcagatccgccggccTcgtagcctcagctcgccaac	10	18	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr18:56008984T>C	ENST00000400345.3	+	15	1615	c.1332T>C	c.(1330-1332)ccT>ccC	p.P444P	NEDD4L_ENST00000357895.5_Silent_p.P436P|NEDD4L_ENST00000431212.2_Silent_p.P323P|NEDD4L_ENST00000256832.7_Silent_p.P303P|NEDD4L_ENST00000382850.4_Silent_p.P424P|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000586263.1_Silent_p.P416P|NEDD4L_ENST00000256830.9_Intron|NEDD4L_ENST00000435432.2_Silent_p.P303P|NEDD4L_ENST00000456986.1_Silent_p.P323P|NEDD4L_ENST00000356462.6_Silent_p.P380P|NEDD4L_ENST00000456173.2_Silent_p.P303P	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	444					cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						TCCGCCGGCCTCGTAGCCTCA	0.517																																					p.P444P		Atlas-SNP	.											.	NEDD4L	126	.	0			c.T1332C						.						59	66	63					18																	56008984		2043	4184	6227	SO:0001819	synonymous_variant	23327	exon15			CCGGCCTCGTAGC	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1332T>C	chr18.hg19:g.56008984T>C		84.0	0.0		90.0	4.0	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	hg19	CCDS45872.1																																																																																			.	.		0.517	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			C	56008984	T	C	56008984	2	2	43	1	0	0	0	0	0	0	0	1	10320	1538	54	2		2	NEDD4L	18	56008984	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	34947766	56008984	22068264	326	5408										
PHLPP1	23239	hgsc.bcm.edu	37	chr18	60563017	60563017	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tatgttttctctaatagcttAcagacatttttgttggatgg	8	5	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr18:60563017A>G	ENST00000262719.5	+	6	2451	c.2217A>G	c.(2215-2217)ttA>ttG	p.L739L	PHLPP1_ENST00000400316.4_Silent_p.L227L			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	739					apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						CTAATAGCTTACAGACATTTT	0.328																																					p.L739L		Atlas-SNP	.											.	PHLPP1	164	.	0			c.A2217G						.						117	110	112					18																	60563017		1821	4072	5893	SO:0001819	synonymous_variant	23239	exon6			TAGCTTACAGACA	AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.2217A>G	chr18.hg19:g.60563017A>G		63.0	0.0		56.0	4.0	NM_194449	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Silent	SNP	ENST00000262719.5	hg19	CCDS45881.2																																																																																			.	.		0.328	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		G	60563017	A	G	60563017	2	3	43	1	0	0	0	0	0	0	0	1	11863	388	14	2		2	PHLPP1	18	60563017	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	4554033	60563017	17514231	327	5409										
SERPINB12	89777	hgsc.bcm.edu	37	chr18	61232745	61232745	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	aattggcttcatagaggaggTgaaggcacagatcctggaaa	13	6	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr18:61232745T>C	ENST00000269491.1	+	6	713	c.713T>C	c.(712-714)gTg>gCg	p.V238A	SERPINB12_ENST00000382768.1_Missense_Mutation_p.V258A	NM_080474.1	NP_536722.1	Q96P63	SPB12_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 12	238					hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of protein catabolic process (GO:0042177)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(5)|lung(19)|skin(1)	26						ATAGAGGAGGTGAAGGCACAG	0.483																																					p.V238A		Atlas-SNP	.											.	SERPINB12	55	.	0			c.T713C						.						158	139	146					18																	61232745		2203	4300	6503	SO:0001583	missense	89777	exon6			AGGAGGTGAAGGC	AF411191	CCDS11984.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166634	ENSG00000166634		"Serine (or cysteine) peptidase inhibitors"	14220	protein-coding gene	gene with protein product		615662	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 12"			24172014	Standard	NM_080474		Approved	YUKOPIN	uc010xen.2	Q96P63	OTTHUMG00000132789	ENST00000269491.1:c.713T>C	chr18.hg19:g.61232745T>C	ENSP00000269491:p.Val238Ala	53.0	0.0		62.0	6.0	NM_080474	Q3SYB4	Missense_Mutation	SNP	ENST00000269491.1	hg19	CCDS11984.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.488975	0.26686	.	.	ENSG00000166634	ENST00000269491;ENST00000382768	D;D	0.82526	-1.62;-1.62	5.59	5.59	0.84812	Serpin domain (3);	0.704404	0.12673	N	0.448613	T	0.76807	0.4039	L	0.33245	0.995	0.24245	N	0.995344	B;B	0.30824	0.201;0.296	B;B	0.33846	0.171;0.109	T	0.66264	-0.5967	10	0.30854	T	0.27	.	12.3322	0.55046	0.1263:0.0:0.0:0.8737	.	258;238	Q3SYB4;Q96P63	.;SPB12_HUMAN	A	238;258	ENSP00000269491:V238A;ENSP00000372218:V258A	ENSP00000269491:V238A	V	+	2	0	SERPINB12	59383725	0.008000	0.16893	0.309000	0.25155	0.076000	0.17211	1.785000	0.38684	2.254000	0.74563	0.528000	0.53228	GTG	.	.		0.483	SERPINB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256197.1	NM_080474		C	61232745	T	C	61232745	3	2	43	1	0	0	0	0	1	0	0	0	14114	1696	59	2	735	2	SERPINB12	18	61232745	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	669728	61232745	16844503	328	5410										
DOT1L	84444	hgsc.bcm.edu	37	chr19	2216382	2216382	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgtccctgcacctgcgtgggAagggcgccctgggccgcgag	17	14	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:2216382A>G	ENST00000398665.3	+	20	2062	c.2026A>G	c.(2026-2028)Aag>Gag	p.K676E	DOT1L_ENST00000608122.1_3'UTR|AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	676					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGCGTGGGAAGGGCGCCCT	0.667																																					p.K676E		Atlas-SNP	.											.	DOT1L	205	.	0			c.A2026G						.						28	32	31					19																	2216382		2033	4167	6200	SO:0001583	missense	84444	exon20			CGTGGGAAGGGCG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.2026A>G	chr19.hg19:g.2216382A>G	ENSP00000381657:p.Lys676Glu	70.0	0.0		106.0	5.0	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.851861	0.51270	.	.	ENSG00000104885	ENST00000398665;ENST00000221482	T	0.27402	1.67	5.13	5.13	0.70059	.	0.179593	0.50627	D	0.000104	T	0.50786	0.1636	M	0.61703	1.905	0.09310	N	0.999998	D	0.71674	0.998	D	0.66084	0.941	T	0.47724	-0.9095	10	0.87932	D	0	-19.9061	14.1294	0.65242	1.0:0.0:0.0:0.0	.	676	Q8TEK3-2	.	E	676	ENSP00000381657:K676E	ENSP00000221482:K676E	K	+	1	0	DOT1L	2167382	1.000000	0.71417	0.088000	0.20740	0.020000	0.10135	8.375000	0.90135	1.928000	0.55862	0.533000	0.62120	AAG	.	.		0.667	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		G	2216382	A	G	2216382	3	3	43	1	0	0	0	0	1	0	0	0	4711	247	9	2	2104	2	DOT1L	19	2216382	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10		2216382	56912601	329	5411										
MPND	84954	hgsc.bcm.edu	37	chr19	4345914	4345914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtacaaaggccagaaactggAcaagtacaaggccacctggc	11	11	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:4345914A>G	ENST00000262966.8	+	3	534	c.467A>G	c.(466-468)gAc>gGc	p.D156G	MPND_ENST00000359935.4_Missense_Mutation_p.D156G|AC007292.4_ENST00000594776.1_RNA|AC007292.7_ENST00000598582.1_RNA|MPND_ENST00000599840.1_Missense_Mutation_p.D156G	NM_032868.4	NP_116257.2	Q8N594	MPND_HUMAN	MPN domain containing	156							peptidase activity (GO:0008233)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGAAACTGGACAAGTACAAG	0.637																																					p.D156G		Atlas-SNP	.											.	MPND	28	.	0			c.A467G						.						30	35	33					19																	4345914		2117	4254	6371	SO:0001583	missense	84954	exon3			AACTGGACAAGTA		CCDS42470.1, CCDS54200.1, CCDS74261.1	19p13.3	2014-08-12			ENSG00000008382				25934	protein-coding gene	gene with protein product							Standard	XM_005259663		Approved	FLJ14981	uc002mae.3	Q8N594	OTTHUMG00000181914	ENST00000262966.8:c.467A>G	chr19.hg19:g.4345914A>G	ENSP00000262966:p.Asp156Gly	89.0	0.0		116.0	5.0	NM_032868	Q96SJ0|Q9Y2P1|Q9Y2P2	Missense_Mutation	SNP	ENST00000262966.8	hg19	CCDS42470.1	.	.	.	.	.	.	.	.	.	.	a	12.69	2.014520	0.35511	.	.	ENSG00000008382	ENST00000262966;ENST00000359935	T;T	0.50277	0.75;0.75	4.24	4.24	0.50183	.	0.124737	0.51477	D	0.000085	T	0.45756	0.1358	M	0.66939	2.045	0.46336	D	0.998993	B;B;B	0.30542	0.096;0.182;0.284	B;B;B	0.28011	0.081;0.085;0.085	T	0.52472	-0.8571	10	0.87932	D	0	-39.2889	11.5543	0.50739	1.0:0.0:0.0:0.0	.	156;156;156	Q8N594-2;A6NI36;Q8N594	.;.;MPND_HUMAN	G	156	ENSP00000262966:D156G;ENSP00000353015:D156G	ENSP00000262966:D156G	D	+	2	0	MPND	4296914	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.157000	0.58144	1.665000	0.50811	0.402000	0.26972	GAC	.	.		0.637	MPND-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458292.1	NM_032868		G	4345914	A	G	4345914	3	3	43	1	0	0	0	0	1	0	0	0	9740	275	10	2	477	2	MPND	19	4345914	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	2129532	4345914	54783069	330	5412										
TICAM1	148022	hgsc.bcm.edu	37	chr19	4817286	4817286	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgagctgaacaaggagtagaTgaaggaggaggaggaggagg	20	2	0	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:4817286T>A	ENST00000248244.5	-	2	1333	c.1104A>T	c.(1102-1104)tcA>tcT	p.S368S		NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	368	Pro-rich.				apoptotic signaling pathway (GO:0097190)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of protein homodimerization activity (GO:0043496)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|ripoptosome (GO:0097342)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		AAGGAGTAGATGAaggaggag	0.522																																					p.S368S		Atlas-SNP	.											.	TICAM1	69	.	0			c.A1104T						.						45	48	47					19																	4817286		2203	4300	6503	SO:0001819	synonymous_variant	148022	exon2			AGTAGATGAAGGA	AB086380	CCDS12136.1	19p13.3	2014-09-17				ENSG00000127666			18348	protein-coding gene	gene with protein product		607601				12539043, 12471095	Standard	NM_182919		Approved	TRIF, TICAM-1, MGC35334, PRVTIRB	uc002mbi.4	Q8IUC6		ENST00000248244.5:c.1104A>T	chr19.hg19:g.4817286T>A		166.0	0.0		193.0	10.0	NM_182919	B3Y691|O75532|Q86XP8|Q96GA0	Silent	SNP	ENST00000248244.5	hg19	CCDS12136.1																																																																																			.	.		0.522	TICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450435.1	NM_014261		A	4817286	T	A	4817286	2	1	43	1	0	0	0	0	0	0	0	1	15907	1451	51	4		4	TICAM1	19	4817286	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	471372	4817286	54311697	331	5413										
TMEM146	257062	hgsc.bcm.edu	37	chr19	5737210	5737210	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgttatactggaagtttgttTtgtgtggtaagtataagtgt	12	1	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:5737210T>C	ENST00000381624.3	+	6	514	c.453T>C	c.(451-453)ttT>ttC	p.F151F	CATSPERD_ENST00000381614.2_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	151					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											GAAGTTTGTTTTGTGTGGTAA	0.338																																					p.F151F		Atlas-SNP	.											.	.	.	.	0			c.T453C						.						201	173	182					19																	5737210		1824	4091	5915	SO:0001819	synonymous_variant	257062	exon6			TTTGTTTTGTGTG	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.453T>C	chr19.hg19:g.5737210T>C		77.0	0.0		60.0	4.0	NM_152784	Q6ZRP1	Silent	SNP	ENST00000381624.3	hg19	CCDS12149.2																																																																																			.	.		0.338	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		C	5737210	T	C	5737210	2	2	43	1	0	0	0	0	0	0	0	1	16075	1838	64	2		2	TMEM146	19	5737210	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	919924	5737210	53391773	332	5414										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10112330	10112330	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tccccagctcggttccactgTcagggtccaagctcctctga	9	16	2	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:10112330T>C	ENST00000264828.3	-	8	1065	c.980A>G	c.(979-981)gAc>gGc	p.D327G		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	327	Nonhelical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			GGTTCCACTGTCAGGGTCCAA	0.562											OREG0025228	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D327G		Atlas-SNP	.											.	COL5A3	243	.	0			c.A980G						.						87	86	86					19																	10112330		2203	4300	6503	SO:0001583	missense	50509	exon8			CCACTGTCAGGGT	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.980A>G	chr19.hg19:g.10112330T>C	ENSP00000264828:p.Asp327Gly	71.0	0.0	662	99.0	39.0	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	T	9.307	1.054540	0.19907	.	.	ENSG00000080573	ENST00000264828	D	0.89617	-2.54	4.88	0.97	0.19692	.	0.752143	0.11294	N	0.578891	T	0.72614	0.3482	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.57087	-0.7871	10	0.22109	T	0.4	.	3.6501	0.08199	0.0:0.2717:0.1921:0.5362	.	327	P25940	CO5A3_HUMAN	G	327	ENSP00000264828:D327G	ENSP00000264828:D327G	D	-	2	0	COL5A3	9973330	0.002000	0.14202	0.001000	0.08648	0.227000	0.25037	0.039000	0.13884	-0.055000	0.13244	0.379000	0.24179	GAC	.	.		0.562	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		C	10112330	T	C	10112330	3	2	43	1	0	0	0	0	1	0	0	0	3700	1667	58	2	4497	2	COL5A3	19	10112330	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	4375120	10112330	49016653	333	5415										
ZNF709	163051	hgsc.bcm.edu	37	chr19	12575010	12575010	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtgagtcctttcatgcattcGaacagaactagaacaactga	8	9	1	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:12575010G>A	ENST00000397732.3	-	4	1897	c.1726C>T	c.(1726-1728)Cga>Tga	p.R576*	ZNF709_ENST00000428311.1_Nonsense_Mutation_p.R576*|CTD-3105H18.18_ENST00000598753.1_Intron	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	576					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|upper_aerodigestive_tract(3)	6						TCATGCATTCGAACAGAACTA	0.418																																					p.R576X	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											.	ZNF709	80	.	0			c.C1726T						.						142	150	147					19																	12575010		2202	4300	6502	SO:0001587	stop_gained	163051	exon4			GCATTCGAACAGA	AK095600	CCDS42504.1	19p13.2	2013-01-08			ENSG00000242852	ENSG00000242852		"Zinc fingers, C2H2-type", "-"	20629	protein-coding gene	gene with protein product							Standard	NM_152601		Approved	FLJ38281	uc002mtv.4	Q8N972	OTTHUMG00000156406	ENST00000397732.3:c.1726C>T	chr19.hg19:g.12575010G>A	ENSP00000380840:p.Arg576*	57.0	0.0		72.0	4.0	NM_152601	A8K4E6	Nonsense_Mutation	SNP	ENST00000397732.3	hg19	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	G	37	6.530123	0.97641	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	.	.	.	2.89	-0.709	0.11237	.	.	.	.	.	.	.	.	.	.	.	0.48288	D	0.999626	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	1.5721	0.02617	0.2167:0.1626:0.4556:0.1652	.	.	.	.	X	576	.	ENSP00000404127:R576X	R	-	1	2	ZNF709;CTD-2192J16.17	12436010	0.000000	0.05858	0.000000	0.03702	0.778000	0.44026	-0.393000	0.07305	-0.040000	0.13580	-0.150000	0.13652	CGA	.	.		0.418	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		A	12575010	G	A	12575010	4	1	43	1	0	0	0	0	0	1	0	0	18128	1066	37	1	203	1	ZNF709	19	12575010	Nonsense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	2462680	12575010	46553973	334	5416										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15302655	15302655	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tggacagtcgtccacgttcaCttcacaattctgaccctcaa	6	14	4	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:15302655C>T	ENST00000263388.2	-	5	778	c.703G>A	c.(703-705)Gtg>Atg	p.V235M		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	235					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TCCACGTTCACTTCACAATTC	0.607																																					p.V235M		Atlas-SNP	.											.	NOTCH3	340	.	0			c.G703A						.						116	92	100					19																	15302655		2203	4300	6503	SO:0001583	missense	4854	exon5			CGTTCACTTCACA	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.703G>A	chr19.hg19:g.15302655C>T	ENSP00000263388:p.Val235Met	95.0	0.0		99.0	4.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	c	10.73	1.433183	0.25813	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.90444	-2.67	5.44	3.25	0.37280	EGF-like calcium-binding, conserved site (1);	0.000000	0.29602	N	0.011693	D	0.86879	0.6039	L	0.48174	1.505	0.20403	N	0.99991	P;P	0.43352	0.804;0.626	P;B	0.45856	0.495;0.227	T	0.78370	-0.2230	10	0.46703	T	0.11	.	4.762	0.13113	0.0:0.5923:0.1625:0.2452	.	238;235	Q59FL3;Q9UM47	.;NOTC3_HUMAN	M	235;237	ENSP00000263388:V235M	ENSP00000263388:V235M	V	-	1	0	NOTCH3	15163655	0.970000	0.33590	0.755000	0.31263	0.472000	0.32918	1.454000	0.35178	0.630000	0.30394	0.558000	0.71614	GTG	.	.		0.607	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		T	15302655	C	T	15302655	3	4	43	1	0	0	0	0	1	0	0	0	10559	565	20	3	6378	3	NOTCH3	19	15302655	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	2727645	15302655	43826328	335	5417										
MED26	9441	hgsc.bcm.edu	37	chr19	16687921	16687921	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcctttggctgcaagcagggTccagggggcttgcccaggcc	16	13	0	0	rs372755647		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:16687921T>C	ENST00000263390.3	-	3	982	c.720A>G	c.(718-720)ggA>ggG	p.G240G	CTC-429P9.4_ENST00000593962.1_5'Flank|CTD-3222D19.2_ENST00000409035.1_Silent_p.G248G	NM_004831.3	NP_004822.2	O95402	MED26_HUMAN	mediator complex subunit 26	240	Pro-rich.				gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	8						GCAAGCAGGGTCCAGGGGGCT	0.672																																					p.G240G		Atlas-SNP	.											.	MED26	25	.	0			c.A720G						.	T		0,4406		0,0,2203	27	31	29		720	-8.5	0.3	19		29	1,8591		0,1,4295	no	coding-synonymous	MED26	NM_004831.3		0,1,6498	CC,CT,TT		0.0116,0.0,0.0077		240/601	16687921	1,12997	2203	4296	6499	SO:0001819	synonymous_variant	9441	exon3			GCAGGGTCCAGGG	AF104253	CCDS12347.1	19p13.11	2008-02-05	2007-07-30	2007-07-30		ENSG00000105085			2376	protein-coding gene	gene with protein product		605043	"cofactor required for Sp1 transcriptional activation, subunit 7, 70kDa"	CRSP7		9989412	Standard	NM_004831		Approved	CRSP70	uc002nen.1	O95402		ENST00000263390.3:c.720A>G	chr19.hg19:g.16687921T>C		66.0	0.0		99.0	4.0	NM_004831	A1A4S3|Q0VGB6	Silent	SNP	ENST00000263390.3	hg19	CCDS12347.1																																																																																			.	.		0.672	MED26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461178.1	NM_004831		C	16687921	T	C	16687921	2	2	43	1	0	0	0	0	0	0	0	1	9453	1654	58	2		2	MED26	19	16687921	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1385266	16687921	42441062	336	5418										
PDE4C	5143	hgsc.bcm.edu	37	chr19	18333125	18333125	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cacacgagagcccattttccAggtcaaagctgaaaggagag	11	10	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:18333125A>G	ENST00000355502.3	-	6	1122	c.251T>C	c.(250-252)cTg>cCg	p.L84P	PDE4C_ENST00000594617.3_Missense_Mutation_p.L84P|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000447275.3_5'UTR|PDE4C_ENST00000539010.1_5'Flank|PDE4C_ENST00000598111.2_5'Flank|PDE4C_ENST00000594465.3_Missense_Mutation_p.L84P|PDE4C_ENST00000597297.1_5'Flank|PDE4C_ENST00000262805.12_Missense_Mutation_p.L52P			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	84					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	CCCATTTTCCAGGTCAAAGCT	0.652																																					p.L84P		Atlas-SNP	.											.	PDE4C	80	.	0			c.T251C						.						37	39	38					19																	18333125		2203	4300	6503	SO:0001583	missense	5143	exon3			TTTTCCAGGTCAA		CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"Phosphodiesterases"	8782	protein-coding gene	gene with protein product	"phosphodiesterase E1 dunce homolog (Drosophila)"	600128	"phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.251T>C	chr19.hg19:g.18333125A>G	ENSP00000347689:p.Leu84Pro	38.0	0.0		66.0	4.0	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	hg19	CCDS12373.1	.	.	.	.	.	.	.	.	.	.	A	19.38	3.816918	0.70912	.	.	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000543547	T;T	0.71817	0.95;-0.6	4.35	4.35	0.52113	.	1.648800	0.04170	N	0.324672	T	0.79131	0.4394	L	0.54323	1.7	0.80722	D	1	P;P;P	0.47962	0.903;0.712;0.886	P;P;P	0.52758	0.514;0.534;0.708	T	0.65948	-0.6044	10	0.87932	D	0	.	12.4205	0.55518	1.0:0.0:0.0:0.0	.	193;84;52	B7Z2S3;Q08493;Q08493-3	.;PDE4C_HUMAN;.	P	163;84;72;52;193	ENSP00000347689:L84P;ENSP00000262805:L52P	ENSP00000262805:L52P	L	-	2	0	PDE4C	18194125	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	6.979000	0.76154	1.615000	0.50252	0.254000	0.18369	CTG	.	.		0.652	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1			G	18333125	A	G	18333125	3	3	43	1	0	0	0	0	1	0	0	0	11650	188	7	2	1943	2	PDE4C	19	18333125	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1645204	18333125	40795858	337	5419										
KIAA0892	23383	hgsc.bcm.edu	37	chr19	19466193	19466193	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cagcctccccgaacacaaccTcatcacggtacgggtgtggg	11	15	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:19466193T>C	ENST00000392313.6	+	18	1939	c.1760T>C	c.(1759-1761)cTc>cCc	p.L587P	MAU2_ENST00000262815.8_Missense_Mutation_p.L587P	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	587					maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						GAACACAACCTCATCACGGTA	0.597																																					p.L587P		Atlas-SNP	.											.	MAU2	38	.	0			c.T1760C						.						88	81	84					19																	19466193		2203	4300	6503	SO:0001583	missense	23383	exon18			ACAACCTCATCAC	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"sister chromatid cohesion 4"	614560	"KIAA0892", "MAU2 chromatid cohesion factor homolog (C. elegans)"	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.1760T>C	chr19.hg19:g.19466193T>C	ENSP00000376127:p.Leu587Pro	33.0	0.0		57.0	4.0	NM_015329	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Missense_Mutation	SNP	ENST00000392313.6	hg19	CCDS32969.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.7|24.7	4.562407|4.562407	0.86335|0.86335	.|.	.|.	ENSG00000129933|ENSG00000129933	ENST00000392313;ENST00000262815|ENST00000262816;ENST00000499453	.|.	.|.	.|.	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|T	0.71702|0.71702	0.3371|0.3371	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	D;D;D|.	0.76494|.	0.983;0.983;0.999|.	P;P;P|.	0.60541|.	0.731;0.827;0.876|.	T|T	0.71510|0.71510	-0.4571|-0.4571	9|5	0.87932|.	D|.	0|.	.|.	14.3201|14.3201	0.66479|0.66479	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	163;192;587|.	Q9Y6X3-3;Q9Y6X3-2;Q9Y6X3|.	.;.;SCC4_HUMAN|.	P|P	587|31	.|.	ENSP00000262815:L587P|.	L|S	+|+	2|1	0|0	MAU2|MAU2	19327193|19327193	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	7.537000|7.537000	0.82033|0.82033	2.072000|2.072000	0.62099|0.62099	0.459000|0.459000	0.35465|0.35465	CTC|TCA	.	.		0.597	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329		C	19466193	T	C	19466193	3	2	43	1	0	0	0	0	1	0	0	0	8205	1551	54	2	1830	2	KIAA0892	19	19466193	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1133068	19466193	39662790	338	5420										
ZNF566	84924	hgsc.bcm.edu	37	chr19	36940828	36940828	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttgtgagtttttccattattTcccactgggttgattctatt	7	7	1	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:36940828T>C	ENST00000434377.2	-	5	389	c.308A>G	c.(307-309)gAa>gGa	p.E103G	ZNF566_ENST00000454319.1_Missense_Mutation_p.E104G|ZNF566_ENST00000424129.2_Missense_Mutation_p.E103G|ZNF566_ENST00000493391.1_5'UTR|ZNF566_ENST00000392170.2_Missense_Mutation_p.E104G	NM_032838.4	NP_116227.1	Q969W8	ZN566_HUMAN	zinc finger protein 566	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24	Esophageal squamous(110;0.162)					TTCCATTATTTCCCACTGGGT	0.368																																					p.E104G		Atlas-SNP	.											.	ZNF566	40	.	0			c.A311G						.						108	113	111					19																	36940828		2203	4300	6503	SO:0001583	missense	84924	exon5			ATTATTTCCCACT	AK074497	CCDS12494.1, CCDS46061.1, CCDS74346.1	19q13.12	2013-01-08						"Zinc fingers, C2H2-type", "-"	25919	protein-coding gene	gene with protein product						12477932	Standard	NM_001145343		Approved	FLJ14779, MGC12515	uc010xtf.2	Q969W8		ENST00000434377.2:c.308A>G	chr19.hg19:g.36940828T>C	ENSP00000415520:p.Glu103Gly	120.0	0.0		95.0	4.0	NM_001145343	B7ZL95|Q2M3J1	Missense_Mutation	SNP	ENST00000434377.2	hg19	CCDS12494.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.886484	0.33348	.	.	ENSG00000186017	ENST00000454319;ENST00000434377;ENST00000392170;ENST00000424129;ENST00000452939;ENST00000427002	T;T;T;T;T;T	0.05925	3.47;3.47;3.47;3.47;3.37;5.93	4.4	2.06	0.26882	.	0.501050	0.16834	N	0.197623	T	0.11623	0.0283	L	0.49126	1.545	0.26839	N	0.968426	P;D	0.71674	0.94;0.998	B;P	0.61477	0.416;0.889	T	0.15235	-1.0444	10	0.25106	T	0.35	.	4.3257	0.11039	0.3053:0.0:0.1752:0.5195	.	104;103	B7ZL95;Q969W8	.;ZN566_HUMAN	G	104;103;104;103;103;104	ENSP00000394207:E104G;ENSP00000415520:E103G;ENSP00000376010:E104G;ENSP00000401259:E103G;ENSP00000411526:E103G;ENSP00000400651:E104G	ENSP00000376010:E104G	E	-	2	0	ZNF566	41632668	0.000000	0.05858	0.962000	0.40283	0.516000	0.34256	-0.023000	0.12456	0.794000	0.33899	0.454000	0.30748	GAA	.	.		0.368	ZNF566-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000341054.1	NM_032838		C	36940828	T	C	36940828	3	2	43	1	0	0	0	0	1	0	0	0	18012	1783	62	2	952	2	ZNF566	19	36940828	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	17474635	36940828	22188155	339	5421										
ZNF573	126231	hgsc.bcm.edu	37	chr19	38229627	38229627	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccatacattttaaaggccttTccacattctttacattcata	2	11	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:38229627T>C	ENST00000590414.2	-	4	1785	c.1764A>G	c.(1762-1764)ggA>ggG	p.G588G	ZNF573_ENST00000392138.1_Silent_p.G501G|ZNF573_ENST00000339503.4_Silent_p.G530G|ZNF573_ENST00000357309.3_Silent_p.G500G|ZNF573_ENST00000536220.1_Silent_p.G500G			Q86YE8	ZN573_HUMAN	zinc finger protein 573	588					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			TAAAGGCCTTTCCACATTCTT	0.393																																					p.G588G		Atlas-SNP	.											ZNF573,NS,carcinoma,0,1	ZNF573	63	.	0			c.A1764G						.						77	78	78					19																	38229627		2203	4300	6503	SO:0001819	synonymous_variant	126231	exon5			GGCCTTTCCACAT	AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"Zinc fingers, C2H2-type", "-"	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.1764A>G	chr19.hg19:g.38229627T>C		61.0	0.0		49.0	2.0	NM_001172690	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Silent	SNP	ENST00000590414.2	hg19	CCDS59381.1																																																																																			.	.		0.393	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360		C	38229627	T	C	38229627	2	2	43	1	0	0	0	0	0	0	0	1	18020	1770	62	2		2	ZNF573	19	38229627	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1288799	38229627	20899356	340	5422										
PAPL	390928	hgsc.bcm.edu	37	chr19	39591791	39591791	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gctcattcaccctgcccaggTccgcaaaggcctccaaggca	9	17	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:39591791T>C	ENST00000331256.5	+	9	1191	c.917T>C	c.(916-918)gTc>gCc	p.V306A	PAPL_ENST00000594229.1_Splice_Site_p.S265P	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		306						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										CCTGCCCAGGTCCGCAAAGGC	0.612																																					p.V306A		Atlas-SNP	.											.	.	.	.	0			c.T917C						.						57	50	53					19																	39591791		2203	4300	6503	SO:0001630	splice_region_variant	0	exon9			CCCAGGTCCGCAA																												ENST00000331256.5:c.916-1T>C	chr19.hg19:g.39591791T>C		20.0	0.0		26.0	4.0	NM_001004318	B2RN68	Missense_Mutation	SNP	ENST00000331256.5	hg19	CCDS33018.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.674224	0.88445	.	.	ENSG00000183760	ENST00000331256	.	.	.	5.43	5.43	0.79202	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	T	0.74733	0.3755	M	0.79475	2.455	0.53688	D	0.999974	D	0.63880	0.993	P	0.61132	0.884	T	0.73350	-0.4010	9	0.23302	T	0.38	-35.1554	13.4493	0.61161	0.0:0.0:0.0:1.0	.	306	Q6ZNF0	PAPL_HUMAN	A	306	.	ENSP00000327557:V306A	V	+	2	0	AC011443.1	44283631	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.376000	0.66178	2.057000	0.61298	0.533000	0.62120	GTC	.	.		0.612	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		Missense_Mutation	C	39591791	T	C	39591791	5	2	43	1	0	0	0	0	0	0	1	0	11436	1681	58	2	947	2	PAPL	19	39591791	Splice_Site	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1362164	39591791	19537192	341	5423										
PSMC4	5704	hgsc.bcm.edu	37	chr19	40486011	40486011	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cagaggatcctgctggagctGctgaatcagatggatggatt	14	7	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:40486011G>A	ENST00000157812.2	+	8	1074	c.876G>A	c.(874-876)ctG>ctA	p.L292L	PSMC4_ENST00000455878.2_Silent_p.L261L	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	292					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TGCTGGAGCTGCTGAATCAGA	0.562																																					p.L292L	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.G876A						.						146	143	144					19																	40486011		2203	4300	6503	SO:0001819	synonymous_variant	5704	exon8			GGAGCTGCTGAAT	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9551	protein-coding gene	gene with protein product	"protease 26S subunit 6", "Tat-binding protein 7", "MB67 interacting protein"	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.876G>A	chr19.hg19:g.40486011G>A		224.0	0.0		259.0	108.0	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	hg19	CCDS12547.1																																																																																			.	.		0.562	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503		A	40486011	G	A	40486011	2	1	43	1	0	0	0	0	0	0	0	1	12701	1306	46	3		3	PSMC4	19	40486011	Silent	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	894220	40486011	18642972	342	5424										
LYPD5	284348	hgsc.bcm.edu	37	chr19	44306520	44306520	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gagcagaatgactctggggaCccccattgccattgctgagc	12	12	1	3	rs575058964		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:44306520C>T	ENST00000377950.3	-	1	93	c.13G>A	c.(13-15)Gtc>Atc	p.V5I	LYPD5_ENST00000414615.2_Intron|LYPD5_ENST00000594013.1_5'Flank	NM_001031749.2	NP_001026919.2	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5	5						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	8		Prostate(69;0.0352)				ACTCTGGGGACCCCCATTGCC	0.602																																					p.V5I		Atlas-SNP	.											LYPD5_ENST00000377950,colon,carcinoma,0,1	LYPD5	22	.	0			c.G13A						.						64	73	70					19																	44306520		692	1591	2283	SO:0001583	missense	284348	exon1			TGGGGACCCCCAT	AK055031	CCDS12631.1, CCDS46096.1	19q13.31	2008-02-05				ENSG00000159871			26397	protein-coding gene	gene with protein product						12477932	Standard	NM_182573		Approved	FLJ30469	uc002oxm.4	Q6UWN5		ENST00000377950.3:c.13G>A	chr19.hg19:g.44306520C>T	ENSP00000367185:p.Val5Ile	59.0	0.0		92.0	4.0	NM_001031749	Q6PEX9|Q96DR2	Missense_Mutation	SNP	ENST00000377950.3	hg19	CCDS46096.1	.	.	.	.	.	.	.	.	.	.	C	5.781	0.328509	0.10956	.	.	ENSG00000159871	ENST00000377950	T	0.06608	3.28	3.73	-5.05	0.02955	.	1.632970	0.04862	N	0.444244	T	0.03390	0.0098	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.42378	-0.9455	10	0.37606	T	0.19	-0.2188	0.3171	0.00297	0.3761:0.2004:0.1378:0.2857	.	5	Q6UWN5	LYPD5_HUMAN	I	5	ENSP00000367185:V5I	ENSP00000367185:V5I	V	-	1	0	LYPD5	48998360	0.000000	0.05858	0.000000	0.03702	0.514000	0.34195	-0.539000	0.06113	-0.894000	0.03925	0.585000	0.79938	GTC	.	.		0.602	LYPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463611.1	NM_182573		T	44306520	C	T	44306520	3	4	43	1	0	0	0	0	1	0	0	0	9122	507	18	3	762	3	LYPD5	19	44306520	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	3820509	44306520	14822463	343	5425										
HRC	3270	hgsc.bcm.edu	37	chr19	49657916	49657916	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcctcctcctcctcctcctcTtctccttcatcatcttcccc	0	23	5	0	rs7409255		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:49657916T>C	ENST00000252825.4	-	1	765	c.579A>G	c.(577-579)gaA>gaG	p.E193E	HRC_ENST00000595625.1_Silent_p.E193E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	193	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cctcctcctcttcTCCTTCAT	0.557																																					p.E193E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A579G						.						119	95	103					19																	49657916		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCTCCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.579A>G	chr19.hg19:g.49657916T>C		88.0	0.0		157.0	12.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.557	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657916	T	C	49657916	2	2	43	1	0	0	0	0	0	0	0	1	7361	1606	56	2		2	HRC	19	49657916	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	5351396	49657916	9471067	344	5426										
PRR12	57479	hgsc.bcm.edu	37	chr19	50100971	50100971	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcttgcctgacctggtctccAgctgccgctcccgtccggcc	11	19	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:50100971A>T	ENST00000418929.2	+	4	3391	c.3379A>T	c.(3379-3381)Agc>Tgc	p.S1127C		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CCTGGTCTCCAGCTGCCGCTC	0.706																																					p.S1127C		Atlas-SNP	.											.	PRR12	157	.	0			c.A3379T						.						8	12	11					19																	50100971		1960	4078	6038	SO:0001583	missense	57479	exon4			GTCTCCAGCTGCC	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.3379A>T	chr19.hg19:g.50100971A>T	ENSP00000394510:p.Ser1127Cys	58.0	0.0		109.0	43.0	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.216213	0.39201	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	4.58	4.58	0.56647	.	0.000000	0.53938	D	0.000052	T	0.74696	0.3750	L	0.60455	1.87	0.52501	D	0.999954	D	0.89917	1.0	D	0.85130	0.997	T	0.77645	-0.2510	9	0.87932	D	0	-23.8701	13.0387	0.58887	1.0:0.0:0.0:0.0	.	1127	Q9ULL5-3	.	C	1127;307;307	.	ENSP00000246798:S307C	S	+	1	0	PRR12	54792783	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	7.411000	0.80078	1.917000	0.55516	0.402000	0.26972	AGC	.	.		0.706	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		T	50100971	A	T	50100971	3	4	43	1	0	0	0	0	1	0	0	0	12596	188	7	4	3393	4	PRR12	19	50100971	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	443055	50100971	9028012	345	5427										
SIGLEC5	8778	hgsc.bcm.edu	37	chr19	52130941	52130941	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggccgggctcgaaaggagcaTctgcagtgcagaccctcagc	14	13	2	1	rs533765364		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:52130941T>C	ENST00000534261.2	-	7	1455	c.1056A>G	c.(1054-1056)agA>agG	p.R352R	SIGLEC5_ENST00000222107.4_Silent_p.R352R|SIGLEC5_ENST00000570106.2_Silent_p.R352R|SIGLEC5_ENST00000429354.3_Silent_p.R352R|SIGLEC5_ENST00000599649.1_Silent_p.R352R			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	352					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		GAAAGGAGCATCTGCAGTGCA	0.662													G|||	1	0.000199681	0	0.0014	5008	,	,		15181	0		0	False		,,,				2504	0				p.R352R		Atlas-SNP	.											.	SIGLEC5	67	.	0			c.A1056G						.						11	14	13					19																	52130941		2189	4285	6474	SO:0001819	synonymous_variant	8778	exon6			GGAGCATCTGCAG	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1056A>G	chr19.hg19:g.52130941T>C		29.0	0.0		34.0	13.0	NM_003830		Silent	SNP	ENST00000534261.2	hg19	CCDS33088.1																																																																																			.	.		0.662	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830		C	52130941	T	C	52130941	2	2	43	1	0	0	0	0	0	0	0	1	14326	1432	50	2		2	SIGLEC5	19	52130941	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2029970	52130941	6998042	346	5428										
ZNF665	79788	hgsc.bcm.edu	37	chr19	53668046	53668046	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tacacttataaggtttctcaCcagtgtgaattctctgatga	7	8	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:53668046C>T	ENST00000600412.1	-	2	1617	c.1502G>A	c.(1501-1503)gGt>gAt	p.G501D	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Missense_Mutation_p.G566D			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	501					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G501V(1)|p.G566V(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		AGGTTTCTCACCAGTGTGAAT	0.393																																					p.G566D		Atlas-SNP	.											ZNF665,NS,carcinoma,0,1	ZNF665	136	.	2	Substitution - Missense(2)	lung(2)	c.G1697A						.						118	124	122					19																	53668046		2202	4300	6502	SO:0001583	missense	79788	exon4			TTCTCACCAGTGT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1502G>A	chr19.hg19:g.53668046C>T	ENSP00000469154:p.Gly501Asp	77.0	0.0		71.0	3.0	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.17	2.753190	0.49362	.	.	ENSG00000197497	ENST00000396424	T	0.26660	1.72	2.44	1.32	0.21799	.	.	.	.	.	T	0.36386	0.0965	L	0.36672	1.1	0.26375	N	0.976824	D	0.89917	1.0	D	0.97110	1.0	T	0.13176	-1.0519	9	0.87932	D	0	.	7.5654	0.27876	0.0:0.849:0.0:0.151	.	566	Q9H7R5-2	.	D	566	ENSP00000379702:G566D	ENSP00000379702:G566D	G	-	2	0	ZNF665	58359858	0.029000	0.19370	0.014000	0.15608	0.020000	0.10135	2.365000	0.44196	0.290000	0.22444	0.543000	0.68304	GGT	.	.		0.393	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		T	53668046	C	T	53668046	3	4	43	1	0	0	0	0	1	0	0	0	18088	507	18	3	343	3	ZNF665	19	53668046	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	1537105	53668046	5460937	347	5429										
VN1R2	317701	hgsc.bcm.edu	37	chr19	53762214	53762214	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tcaccatcaaccctaggaacTccaggtgggcagagatgaaa	10	11	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:53762214T>C	ENST00000341702.3	+	1	670	c.586T>C	c.(586-588)Tcc>Ccc	p.S196P		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	196					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		CCCTAGGAACTCCAGGTGGGC	0.488																																					p.S196P		Atlas-SNP	.											.	VN1R2	71	.	0			c.T586C						.						44	45	45					19																	53762214		2203	4300	6503	SO:0001583	missense	317701	exon1			AGGAACTCCAGGT	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.586T>C	chr19.hg19:g.53762214T>C	ENSP00000351244:p.Ser196Pro	66.0	0.0		112.0	6.0	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	hg19	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	T	10.04	1.241976	0.22796	.	.	ENSG00000196131	ENST00000341702	T	0.15017	2.46	2.94	2.94	0.34122	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.24851	0.0603	M	0.71296	2.17	0.26533	N	0.974211	B	0.24483	0.104	B	0.35688	0.208	T	0.17379	-1.0371	9	0.46703	T	0.11	.	9.7653	0.40557	0.0:0.0:0.0:1.0	.	196	Q8NFZ6	VN1R2_HUMAN	P	196	ENSP00000351244:S196P	ENSP00000351244:S196P	S	+	1	0	VN1R2	58454026	0.023000	0.18921	0.506000	0.27664	0.191000	0.23601	0.030000	0.13688	1.619000	0.50296	0.486000	0.48141	TCC	.	.		0.488	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		C	53762214	T	C	53762214	3	2	43	1	0	0	0	0	1	0	0	0	17194	1551	54	2	588	2	VN1R2	19	53762214	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	94168	53762214	5366769	348	5430										
TMEM150B	284417	hgsc.bcm.edu	37	chr19	55832397	55832397	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caggcatcagcgacaggtagCcccacatgccgggctctgca	12	15	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:55832397C>A	ENST00000326652.4	-	3	190	c.8G>T	c.(7-9)gGc>gTc	p.G3V	TMEM150B_ENST00000438693.1_Missense_Mutation_p.G3V	NM_001282011.1	NP_001268940.1	A6NC51	T150B_HUMAN	transmembrane protein 150B	3						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)	3						CGACAGGTAGCCCCACATGCC	0.602																																					p.G3V		Atlas-SNP	.											.	TMEM150B	19	.	0			c.G8T						.						50	52	51					19																	55832397		2084	4215	6299	SO:0001583	missense	284417	exon3			AGGTAGCCCCACA	BC020862	CCDS42629.1	19q13.42	2009-06-12	2009-06-12	2009-06-12		ENSG00000180061			34415	protein-coding gene	gene with protein product			"transmembrane protein 224"	TMEM224			Standard	XM_005258812		Approved		uc010esw.1	A6NC51		ENST00000326652.4:c.8G>T	chr19.hg19:g.55832397C>A	ENSP00000320757:p.Gly3Val	126.0	0.0		163.0	78.0	NM_001085488	B7ZW71	Missense_Mutation	SNP	ENST00000326652.4	hg19	CCDS42629.1	.	.	.	.	.	.	.	.	.	.	C	6.308	0.424854	0.11987	.	.	ENSG00000180061	ENST00000326652;ENST00000438693	T;T	0.45276	0.9;0.9	4.26	3.22	0.36961	.	0.819449	0.10486	N	0.668948	T	0.33498	0.0865	L	0.50333	1.59	0.37809	D	0.927986	B	0.33694	0.421	B	0.32393	0.145	T	0.10382	-1.0632	10	0.16896	T	0.51	-9.8093	7.6425	0.28303	0.0:0.8748:0.0:0.1252	.	3	A6NC51	T150B_HUMAN	V	3	ENSP00000320757:G3V;ENSP00000412658:G3V	ENSP00000320757:G3V	G	-	2	0	TMEM150B	60524209	0.977000	0.34250	0.998000	0.56505	0.055000	0.15305	0.634000	0.24614	0.906000	0.36621	0.456000	0.33151	GGC	.	.		0.602	TMEM150B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452685.1	NM_001085488		A	55832397	C	A	55832397	3	1	43	1	0	0	0	0	1	0	0	0	16083	739	26	3	717	3	TMEM150B	19	55832397	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	2070183	55832397	3296586	349	5431										
ZNF446	55663	hgsc.bcm.edu	37	chr19	58991708	58991708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acctgcagagacgagactggAgccggctgccacccccagga	13	15	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:58991708A>G	ENST00000594369.1	+	7	1349	c.968A>G	c.(967-969)gAg>gGg	p.E323G	ZNF446_ENST00000335841.4_Missense_Mutation_p.S295G|ZNF446_ENST00000596341.1_Missense_Mutation_p.E272G	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	323	Pro-rich.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		ACGAGACTGGAGCCGGCTGCC	0.672																																					p.E323G		Atlas-SNP	.											.	ZNF446	22	.	0			c.A968G						.						17	15	15					19																	58991708		2191	4291	6482	SO:0001583	missense	55663	exon7			GACTGGAGCCGGC		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"Zinc fingers, C2H2-type", "-", "-", "-"	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.968A>G	chr19.hg19:g.58991708A>G	ENSP00000472802:p.Glu323Gly	80.0	0.0		58.0	4.0	NM_017908		Missense_Mutation	SNP	ENST00000594369.1	hg19	CCDS12982.1	.	.	.	.	.	.	.	.	.	.	A	13.92	2.381940	0.42207	.	.	ENSG00000083838	ENST00000335841;ENST00000540481;ENST00000391694	.	.	.	2.22	1.19	0.21007	.	0.500759	0.14845	N	0.295056	T	0.14874	0.0359	N	0.08118	0	0.09310	N	1	B	0.15719	0.014	B	0.09377	0.004	T	0.15093	-1.0449	9	0.34782	T	0.22	-0.016	2.6516	0.05001	0.5531:0.2805:0.1663:0.0	.	323	Q9NWS9	ZN446_HUMAN	G	323;323;220	.	ENSP00000336565:E323G	E	+	2	0	ZNF446	63683520	0.000000	0.05858	0.003000	0.11579	0.021000	0.10359	0.171000	0.16685	0.296000	0.22592	0.454000	0.30748	GAG	.	.		0.672	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908		G	58991708	A	G	58991708	3	3	43	1	0	0	0	0	1	0	0	0	17934	304	11	2	990	2	ZNF446	19	58991708	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	3159311	58991708	137275	350	5432										
TRIM28	10155	hgsc.bcm.edu	37	chr19	59061183	59061183	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcctcagcctggatggtgcaGacagcactggcgtggtggcc	16	12	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr19:59061183G>T	ENST00000253024.5	+	14	2351	c.2062G>T	c.(2062-2064)Gac>Tac	p.D688Y	TRIM28_ENST00000341753.6_Missense_Mutation_p.D606Y	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28	688					convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GGATGGTGCAGACAGCACTGG	0.602																																					p.D688Y		Atlas-SNP	.											.	TRIM28	46	.	0			c.G2062T						.						86	79	81					19																	59061183		2203	4300	6503	SO:0001583	missense	10155	exon14			GGTGCAGACAGCA		CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	16384	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 157"	601742	"tripartite motif-containing 28"			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.2062G>T	chr19.hg19:g.59061183G>T	ENSP00000253024:p.Asp688Tyr	75.0	0.0		39.0	33.0	NM_005762	O00677|Q7Z632|Q93040|Q96IM1	Missense_Mutation	SNP	ENST00000253024.5	hg19	CCDS12985.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.658806	0.47467	.	.	ENSG00000130726	ENST00000253024;ENST00000341753	T;T	0.68624	-0.14;-0.34	4.75	1.25	0.21368	.	0.657402	0.14773	N	0.299295	T	0.48660	0.1512	N	0.08118	0	0.09310	N	1	P;P;P	0.47545	0.897;0.478;0.834	P;B;B	0.50192	0.634;0.092;0.334	T	0.34750	-0.9816	10	0.54805	T	0.06	-27.267	3.7431	0.08537	0.2032:0.0:0.6035:0.1934	.	606;688;688	Q13263-2;B2R8R5;Q13263	.;.;TIF1B_HUMAN	Y	688;606	ENSP00000253024:D688Y;ENSP00000342232:D606Y	ENSP00000253024:D688Y	D	+	1	0	TRIM28	63752995	0.765000	0.28485	0.034000	0.17996	0.916000	0.54674	2.107000	0.41844	0.730000	0.32425	0.443000	0.29094	GAC	.	.		0.602	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467074.1	NM_005762		T	59061183	G	T	59061183	3	4	43	1	0	0	0	0	1	0	0	0	16517	942	33	3	2116	3	TRIM28	19	59061183	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	69475	59061183	67800	351	5433										
NSFL1C	55968	hgsc.bcm.edu	37	chr20	1434946	1434946	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggcggtagccacctcctgcaAatggctataagggacaagtt	12	10	0	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr20:1434946A>G	ENST00000216879.4	-	5	1316	c.449T>C	c.(448-450)tTt>tCt	p.F150S	NSFL1C_ENST00000476071.1_Missense_Mutation_p.F152S|NSFL1C_ENST00000461211.1_5'UTR|NSFL1C_ENST00000350991.4_Missense_Mutation_p.F152S|NSFL1C_ENST00000381658.4_Missense_Mutation_p.F39S|NSFL1C_ENST00000353088.2_Intron	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)	150						chromosome (GO:0005694)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	16						ACCTCCTGCAAATGGCTATAA	0.473																																					p.F150S		Atlas-SNP	.											.	NSFL1C	38	.	0			c.T449C						.						77	68	71					20																	1434946		2203	4300	6503	SO:0001583	missense	55968	exon5			CCTGCAAATGGCT	AF112211	CCDS13015.1, CCDS13016.1, CCDS56175.1	20p13	2011-06-28			ENSG00000088833	ENSG00000088833		"UBX domain containing"	15912	protein-coding gene	gene with protein product	"SHP1 homolog (S. cerevisiae)", "UBX domain protein 2C"	606610				11042152	Standard	NM_016143		Approved	dJ776F14.1, p47, UBXD10, UBX1, UBXN2C	uc002wfc.3	Q9UNZ2	OTTHUMG00000031665	ENST00000216879.4:c.449T>C	chr20.hg19:g.1434946A>G	ENSP00000216879:p.Phe150Ser	56.0	0.0		79.0	5.0	NM_016143	A2A2L1|B2RD74|Q5JXA4|Q5JXA5|Q7Z533|Q9H102|Q9NVL9|Q9UI06	Missense_Mutation	SNP	ENST00000216879.4	hg19	CCDS13015.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.712239	0.89112	.	.	ENSG00000088833	ENST00000476071;ENST00000216879;ENST00000381658;ENST00000350991	T;T;T;T	0.68479	-0.33;-0.33;0.13;-0.3	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.83751	0.5322	M	0.88775	2.98	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.75484	0.986;0.979	D	0.86937	0.2077	10	0.87932	D	0	-8.4678	14.1151	0.65149	1.0:0.0:0.0:0.0	.	39;150	Q9UNZ2-6;Q9UNZ2	.;NSF1C_HUMAN	S	152;150;39;152	ENSP00000418529:F152S;ENSP00000216879:F150S;ENSP00000371074:F39S;ENSP00000202584:F152S	ENSP00000216879:F150S	F	-	2	0	NSFL1C	1382946	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.180000	0.89694	2.317000	0.78254	0.460000	0.39030	TTT	.	.		0.473	NSFL1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077525.2	NM_016143		G	1434946	A	G	1434946	3	3	43	1	0	0	0	0	1	0	0	0	10681	14	1	2	683	2	NSFL1C	20	1434946	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10		1434946	61590574	352	5434										
PTPRA	5786	hgsc.bcm.edu	37	chr20	3007357	3007357	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	taacatcaatcaaaatccagAatgacaagatgcggactgga	8	8	2	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr20:3007357A>T	ENST00000216877.6	+	17	2012	c.1612A>T	c.(1612-1614)Aat>Tat	p.N538Y	PTPRA_ENST00000380393.3_Missense_Mutation_p.N547Y|PTPRA_ENST00000399903.2_Missense_Mutation_p.N547Y|PTPRA_ENST00000318266.5_Missense_Mutation_p.N538Y|PTPRA_ENST00000425918.2_Missense_Mutation_p.N558Y|PTPRA_ENST00000358719.4_Missense_Mutation_p.N403Y|PTPRA_ENST00000356147.3_Missense_Mutation_p.N538Y	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	547	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CAAAATCCAGAATGACAAGAT	0.458																																					p.N547Y		Atlas-SNP	.											.	PTPRA	75	.	0			c.A1639T						.						92	72	79					20																	3007357		2203	4300	6503	SO:0001583	missense	5786	exon22			ATCCAGAATGACA		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.1612A>T	chr20.hg19:g.3007357A>T	ENSP00000216877:p.Asn538Tyr	68.0	0.0		107.0	49.0	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Missense_Mutation	SNP	ENST00000216877.6	hg19	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	A	15.58	2.874915	0.51695	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000542217;ENST00000425918;ENST00000318266;ENST00000356147	T;T;T;T;T;T;T	0.03772	3.85;3.85;3.85;3.81;3.84;3.85;3.85	5.28	4.15	0.48705	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.000000	0.85682	U	0.000000	T	0.09335	0.0230	L	0.28504	0.86	0.80722	D	1	D;D;D	0.76494	0.977;0.999;0.993	P;D;D	0.85130	0.755;0.997;0.935	T	0.13282	-1.0515	10	0.05351	T	0.99	.	12.3806	0.55305	0.859:0.141:0.0:0.0	.	558;547;538	B7Z2A4;P18433;P18433-4	.;PTPRA_HUMAN;.	Y	547;538;547;403;157;558;538;538	ENSP00000369756:N547Y;ENSP00000216877:N538Y;ENSP00000382787:N547Y;ENSP00000351559:N403Y;ENSP00000393553:N558Y;ENSP00000314568:N538Y;ENSP00000348468:N538Y	ENSP00000216877:N538Y	N	+	1	0	PTPRA	2955357	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	9.287000	0.95975	0.909000	0.36697	0.459000	0.35465	AAT	.	.		0.458	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			T	3007357	A	T	3007357	3	4	43	1	0	0	0	0	1	0	0	0	12810	246	9	4	1697	4	PTPRA	20	3007357	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	1572411	3007357	60018163	353	5435										
ABHD12	26090	hgsc.bcm.edu	37	chr20	25300910	25300910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catcctcataccacatctggTctttgccttgggcgttcttc	7	14	4	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr20:25300910T>C	ENST00000339157.5	-	4	739	c.467A>G	c.(466-468)gAc>gGc	p.D156G	ABHD12_ENST00000376542.3_Missense_Mutation_p.D156G	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	156					adult walking behavior (GO:0007628)|phosphatidylserine catabolic process (GO:0006660)|response to auditory stimulus (GO:0010996)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)	acylglycerol lipase activity (GO:0047372)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	12						CCACATCTGGTCTTTGCCTTG	0.567																																					p.D156G		Atlas-SNP	.											.	ABHD12	46	.	0			c.A467G						.						151	105	120					20																	25300910		2203	4300	6503	SO:0001583	missense	26090	exon4			ATCTGGTCTTTGC	AL117442	CCDS13172.1, CCDS42857.1	20p11.21	2007-04-24	2006-03-10	2006-03-10	ENSG00000100997	ENSG00000100997		"Abhydrolase domain containing"	15868	protein-coding gene	gene with protein product		613599	"chromosome 20 open reading frame 22"	C20orf22			Standard	NM_015600		Approved	DKFZP434P106, dJ965G21.2, BEM46L2, ABHD12A	uc002wuq.3	Q8N2K0	OTTHUMG00000032121	ENST00000339157.5:c.467A>G	chr20.hg19:g.25300910T>C	ENSP00000341408:p.Asp156Gly	64.0	0.0		81.0	4.0	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Missense_Mutation	SNP	ENST00000339157.5	hg19	CCDS42857.1	.	.	.	.	.	.	.	.	.	.	T	16.94	3.261354	0.59431	.	.	ENSG00000100997	ENST00000376542;ENST00000339157;ENST00000526543;ENST00000450393	T;T;T	0.56444	0.46;0.46;0.46	5.75	4.66	0.58398	.	0.393509	0.32785	N	0.005660	T	0.47097	0.1427	L	0.55743	1.74	0.58432	D	0.999996	B;P;P	0.43287	0.024;0.688;0.802	B;B;B	0.40477	0.03;0.095;0.33	T	0.36939	-0.9727	10	0.30854	T	0.27	-0.0022	11.0318	0.47779	0.0:0.0728:0.0:0.9272	.	111;156;156	Q5T712;Q8N2K0;Q8N2K0-2	.;ABD12_HUMAN;.	G	156;156;118;111	ENSP00000365725:D156G;ENSP00000341408:D156G;ENSP00000413311:D111G	ENSP00000341408:D156G	D	-	2	0	ABHD12	25248910	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.899000	0.56288	1.030000	0.39839	0.533000	0.62120	GAC	.	.		0.567	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600		C	25300910	T	C	25300910	3	2	43	1	0	0	0	0	1	0	0	0	76	1667	58	2	831	2	ABHD12	20	25300910	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	22293553	25300910	37724610	354	5436										
MYH7B	57644	hgsc.bcm.edu	37	chr20	33575459	33575459	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	agggaacgagtacgtgaccaAgggccagagtgtggagcagg	18	7	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr20:33575459A>T	ENST00000262873.7	+	15	1465	c.1373A>T	c.(1372-1374)aAg>aTg	p.K458M	MIR499A_ENST00000384903.1_RNA	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	416	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			TACGTGACCAAGGGCCAGAGT	0.662																																					p.K458M		Atlas-SNP	.											.	MYH7B	145	.	0			c.A1373T						.						97	106	103					20																	33575459		2071	4202	6273	SO:0001583	missense	57644	exon17			TGACCAAGGGCCA	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.1373A>T	chr20.hg19:g.33575459A>T	ENSP00000262873:p.Lys458Met	70.0	0.0		141.0	32.0	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	hg19	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.221462	0.79464	.	.	ENSG00000078814	ENST00000262873	D	0.88741	-2.42	3.53	3.53	0.40419	Myosin head, motor domain (2);	0.000000	0.37623	N	0.002007	D	0.95755	0.8619	H	0.96633	3.855	0.58432	D	0.999994	D	0.58268	0.982	D	0.65233	0.933	D	0.96837	0.9615	10	0.87932	D	0	.	13.1334	0.59395	1.0:0.0:0.0:0.0	.	416	A7E2Y1	MYH7B_HUMAN	M	458	ENSP00000262873:K458M	ENSP00000262873:K458M	K	+	2	0	MYH7B	33039120	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.109000	0.94291	1.849000	0.53698	0.459000	0.35465	AAG	.	.		0.662	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33575459	A	T	33575459	3	4	43	1	0	0	0	0	1	0	0	0	10049	72	3	4	1431	4	MYH7B	20	33575459	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	8274549	33575459	29450061	355	5437										
C20orf152	140894	hgsc.bcm.edu	37	chr20	34611572	34611572	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtgaatgcgacacacgacccTtgatcctgatgagcctggga	12	11	0	4			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr20:34611572T>C	ENST00000373973.3	+	11	1491	c.1318T>C	c.(1318-1320)Ttg>Ctg	p.L440L	CNBD2_ENST00000349339.1_Silent_p.L436L|CNBD2_ENST00000538900.1_Intron			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	440																	CACACGACCCTTGATCCTGAT	0.463																																					p.L436L		Atlas-SNP	.											.	.	.	.	0			c.T1306C						.						108	104	105					20																	34611572		2203	4300	6503	SO:0001819	synonymous_variant	140894	exon11			CGACCCTTGATCC	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 152", "cyclic nucleotide (cNMP) binding domain containing 1"	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.1318T>C	chr20.hg19:g.34611572T>C		71.0	0.0		95.0	4.0	NM_080834	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Silent	SNP	ENST00000373973.3	hg19																																																																																				.	.		0.463	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834		C	34611572	T	C	34611572	2	2	43	1	0	0	0	0	0	0	0	1	2094	1606	56	2		2	C20orf152	20	34611572	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	1036113	34611572	28413948	356	5438										
WFDC13	164237	hgsc.bcm.edu	37	chr20	44334544	44334544	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gtcatcatgcctgccaactgAggcatatttcctagatcatt	7	11	3	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr20:44334544A>G	ENST00000305479.2	+	3	390	c.282A>G	c.(280-282)tgA>tgG	p.*94W	WFDC10B_ENST00000330523.5_5'Flank|MIR3617_ENST00000577518.1_RNA|WFDC10B_ENST00000335769.2_5'Flank	NM_172005.1	NP_742002.1	Q8IUB5	WFD13_HUMAN	WAP four-disulfide core domain 13	0						extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			skin(1)|upper_aerodigestive_tract(1)	2		Myeloproliferative disorder(115;0.0122)				CTGCCAACTGAGGCATATTTC	0.393																																					p.X94W		Atlas-SNP	.											.	WFDC13	6	.	0			c.A282G						.						110	101	104					20																	44334544		2203	4300	6503	SO:0001578	stop_lost	164237	exon3			CAACTGAGGCATA	AF454505	CCDS13367.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000168634	ENSG00000168634		"WAP four-disulfide core domain containing"	16131	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 138"	C20orf138		12206714	Standard	NM_172005		Approved	dJ601O1.3, WAP13	uc002xpd.3	Q8IUB5	OTTHUMG00000046333	ENST00000305479.2:c.282A>G	chr20.hg19:g.44334544A>G	ENSP00000302938:p.*94Trpext*48	58.0	0.0		96.0	4.0	NM_172005	Q5TEU7|Q8WWK7	Missense_Mutation	SNP	ENST00000305479.2	hg19	CCDS13367.1	.	.	.	.	.	.	.	.	.	.	A	1.236	-0.622688	0.03636	.	.	ENSG00000168634	ENST00000305479	.	.	.	2.97	1.82	0.25136	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.3021	0.15783	0.7455:0.0:0.0:0.2545	.	.	.	.	W	94	.	.	X	+	3	0	WFDC13	43767958	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	0.501000	0.22578	0.519000	0.28406	0.402000	0.26972	TGA	.	.		0.393	WFDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106946.1			G	44334544	A	G	44334544	4	3	43	1	0	0	0	0	0	0	0	0	17366	317	11	2	292	2	WFDC13	20	44334544	Nonstop_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	9722972	44334544	18690976	357	5439										
USP25	29761	hgsc.bcm.edu	37	chr21	17163836	17163836	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttaagagttcttgaagccagCatagcagagaataaagcatg	10	6	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr21:17163836C>T	ENST00000285679.6	+	5	777	c.408C>T	c.(406-408)agC>agT	p.S136S	USP25_ENST00000547201.1_3'UTR|USP25_ENST00000285681.2_Silent_p.S136S|USP25_ENST00000400183.2_Silent_p.S136S|USP25_ENST00000351097.5_Silent_p.S136S	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	136					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		TTGAAGCCAGCATAGCAGAGA	0.378																																					p.S136S		Atlas-SNP	.											USP25,colon,carcinoma,0,1	USP25	156	.	0			c.C408T						.						113	115	114					21																	17163836		2202	4300	6502	SO:0001819	synonymous_variant	29761	exon5			AGCCAGCATAGCA	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.408C>T	chr21.hg19:g.17163836C>T		62.0	0.0		60.0	4.0	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Silent	SNP	ENST00000285679.6	hg19	CCDS33515.1																																																																																			.	.		0.378	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			T	17163836	C	T	17163836	2	4	43	1	0	0	0	0	0	0	0	1	17071	709	25	3		3	USP25	21	17163836	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10		17163836	30966059	358	5440										
RNF160	26046	hgsc.bcm.edu	37	chr21	30329699	30329699	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttttcccattcactgtcgttCggcattacacttccaatata	4	12	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr21:30329699C>T	ENST00000361371.5	-	15	2926	c.2847G>A	c.(2845-2847)ccG>ccA	p.P949P	LTN1_ENST00000389194.2_Silent_p.P995P			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	949					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						CACTGTCGTTCGGCATTACAC	0.383																																					p.P995P		Atlas-SNP	.											.	LTN1	141	.	0			c.G2985A						.						97	86	90					21																	30329699		2203	4300	6503	SO:0001819	synonymous_variant	26046	exon15			GTCGTTCGGCATT	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"RING-type (C3HC4) zinc fingers"	13082	protein-coding gene	gene with protein product	"listerin"	613083	"chromosome 21 open reading frame 98", "zinc finger protein 294", "ring finger protein 160"	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.2847G>A	chr21.hg19:g.30329699C>T		64.0	0.0		68.0	4.0	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Silent	SNP	ENST00000361371.5	hg19																																																																																				.	.		0.383	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		T	30329699	C	T	30329699	2	4	43	1	0	0	0	0	0	0	0	1	13470	871	31	1		1	RNF160	21	30329699	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	13165863	30329699	17800196	359	5441										
CLIC6	54102	hgsc.bcm.edu	37	chr21	36081737	36081737	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cctgatgaaatagatgcctaCagcaccgaggatgtcactgt	10	10	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr21:36081737C>T	ENST00000360731.3	+	6	1854	c.1854C>T	c.(1852-1854)taC>taT	p.Y618Y	CLIC6_ENST00000349499.2_Silent_p.Y600Y			Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6	618	GST C-terminal.					chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19						TAGATGCCTACAGCACCGAGG	0.473																																					p.Y600Y		Atlas-SNP	.											.	CLIC6	49	.	0			c.C1800T						.						118	109	112					21																	36081737		2203	4300	6503	SO:0001819	synonymous_variant	54102	exon5			TGCCTACAGCACC	AF426169	CCDS13638.1	21q22.12	2012-09-26			ENSG00000159212	ENSG00000159212		"Ion channels / Chloride channels : Intracellular"	2065	protein-coding gene	gene with protein product		615321		CLIC1L		10830953	Standard	NM_053277		Approved	CLIC5	uc002yuf.1	Q96NY7	OTTHUMG00000086237	ENST00000360731.3:c.1854C>T	chr21.hg19:g.36081737C>T		52.0	0.0		61.0	4.0	NM_053277	A8K0U8|Q8IX31	Silent	SNP	ENST00000360731.3	hg19																																																																																				.	.		0.473	CLIC6-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000194156.1			T	36081737	C	T	36081737	2	4	43	1	0	0	0	0	0	0	0	1	3532	489	17	3		3	CLIC6	21	36081737	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	5752038	36081737	12048158	360	5442										
PRDM15	63977	hgsc.bcm.edu	37	chr21	43223051	43223051	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tttcccgtgcttcccttcggCcaaatcctcctgctccagag	7	17	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr21:43223051C>T	ENST00000269844.3	-	30	3972	c.3862G>A	c.(3862-3864)Gcc>Acc	p.A1288T	PRDM15_ENST00000538201.1_Missense_Mutation_p.A942T|PRDM15_ENST00000422911.1_Missense_Mutation_p.A979T|PRDM15_ENST00000398548.1_Missense_Mutation_p.A959T|PRDM15_ENST00000447207.2_Missense_Mutation_p.A922T|PRDM15_ENST00000470586.1_5'UTR	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1288					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						TTCCCTTCGGCCAAATCCTCC	0.612																																					p.A1288T		Atlas-SNP	.											.	PRDM15	110	.	0			c.G3862A						.						125	137	133					21																	43223051		2203	4300	6503	SO:0001583	missense	63977	exon30			CTTCGGCCAAATC	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.3862G>A	chr21.hg19:g.43223051C>T	ENSP00000269844:p.Ala1288Thr	29.0	0.0		58.0	4.0	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	hg19	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	c	13.76	2.334408	0.41297	.	.	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844	T;T;T;T;T	0.08102	3.18;3.19;3.19;3.18;3.13	4.9	2.94	0.34122	.	.	.	.	.	T	0.04634	0.0126	N	0.08118	0	0.09310	N	1	B;B;B	0.27229	0.031;0.001;0.172	B;B;B	0.22386	0.009;0.003;0.039	T	0.41662	-0.9496	9	0.19147	T	0.46	-19.0707	12.8528	0.57867	0.0:0.3899:0.6101:0.0	.	1288;979;959	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	T	979;959;942;922;1288	ENSP00000408592:A979T;ENSP00000381556:A959T;ENSP00000444044:A942T;ENSP00000390245:A922T;ENSP00000269844:A1288T	ENSP00000269844:A1288T	A	-	1	0	PRDM15	42096120	0.998000	0.40836	0.187000	0.23214	0.863000	0.49368	1.353000	0.34045	1.000000	0.39049	0.479000	0.44913	GCC	.	.		0.612	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		T	43223051	C	T	43223051	3	4	43	1	0	0	0	0	1	0	0	0	12468	739	26	3	669	3	PRDM15	21	43223051	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	7141314	43223051	4906844	361	5443										
PCNT	5116	hgsc.bcm.edu	37	chr21	47783761	47783761	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgcattgcagccagtgtgggCgggagccgcccacagcccag	15	14	0	0	rs578233518		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr21:47783761C>T	ENST00000359568.5	+	14	2628	c.2521C>T	c.(2521-2523)Cgg>Tgg	p.R841W	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	841					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CCAGTGTGGGCGGGAGCCGCC	0.667													C|||	1	0.000199681	0	0	5008	,	,		17809	0		0	False		,,,				2504	0.001				p.R841W		Atlas-SNP	.											.	PCNT	283	.	0			c.C2521T						.						70	82	78					21																	47783761		2200	4285	6485	SO:0001583	missense	5116	exon14			TGTGGGCGGGAGC	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.2521C>T	chr21.hg19:g.47783761C>T	ENSP00000352572:p.Arg841Trp	74.0	0.0		82.0	41.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.851286	0.51270	.	.	ENSG00000160299	ENST00000359568	T	0.26223	1.75	4.43	1.47	0.22746	.	1.622470	0.04257	N	0.339623	T	0.37210	0.0995	L	0.44542	1.39	0.25862	N	0.983816	D;D	0.76494	0.999;0.999	P;P	0.59546	0.859;0.824	T	0.12967	-1.0527	10	0.56958	D	0.05	.	5.1827	0.15169	0.1601:0.6588:0.0:0.1811	.	723;841	O95613-2;O95613	.;PCNT_HUMAN	W	841	ENSP00000352572:R841W	ENSP00000352572:R841W	R	+	1	2	PCNT	46608189	0.271000	0.24162	0.896000	0.35187	0.274000	0.26718	0.285000	0.18883	0.301000	0.22738	0.491000	0.48974	CGG	.	.		0.667	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47783761	C	T	47783761	3	4	43	1	0	0	0	0	1	0	0	0	11599	759	27	1	2575	1	PCNT	21	47783761	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	4560710	47783761	346134	362	5444										
SERPIND1	3053	hgsc.bcm.edu	37	chr22	21138492	21138492	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	accctcgaagcgcaactgacAccccgggtggtggagagatg	14	12	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr22:21138492A>G	ENST00000215727.5	+	3	1405	c.1122A>G	c.(1120-1122)acA>acG	p.T374T	SERPIND1_ENST00000406799.1_Silent_p.T374T|PI4KA_ENST00000466162.1_Intron|PI4KA_ENST00000255882.6_Intron|PI4KA_ENST00000572273.1_Intron	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	374					blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)|Sulodexide(DB06271)	CGCAACTGACACCCCGGGTGG	0.522											OREG0026325	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T374T		Atlas-SNP	.											.	SERPIND1	92	.	0			c.A1122G						.						77	69	72					22																	21138492		2203	4300	6503	SO:0001819	synonymous_variant	3053	exon3			ACTGACACCCCGG	M12849	CCDS13783.1	22q11.21	2014-02-18	2005-08-18		ENSG00000099937	ENSG00000099937		"Serine (or cysteine) peptidase inhibitors"	4838	protein-coding gene	gene with protein product	"heparin cofactor II"	142360	"serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1"	HCF2		1671335, 24172014	Standard	XM_005261597		Approved	HC-II, HLS2, HC2, D22S673	uc002ztb.1	P05546	OTTHUMG00000150755	ENST00000215727.5:c.1122A>G	chr22.hg19:g.21138492A>G		57.0	0.0	746	78.0	4.0	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Silent	SNP	ENST00000215727.5	hg19	CCDS13783.1																																																																																			.	.		0.522	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185		G	21138492	A	G	21138492	2	3	43	1	0	0	0	0	0	0	0	1	14125	146	6	2		2	SERPIND1	22	21138492	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10		21138492	30166074	363	5445										
THAP7	80764	hgsc.bcm.edu	37	chr22	21354195	21354195	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	catgctgctgctcagctgcaTggcaaagtcctgcacatgct	10	13	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr22:21354195T>C	ENST00000215742.4	-	4	1078	c.904A>G	c.(904-906)Atg>Gtg	p.M302V	THAP7-AS1_ENST00000452284.1_RNA|THAP7-AS1_ENST00000429962.1_RNA|THAP7_ENST00000399133.2_Missense_Mutation_p.M302V|THAP7-AS1_ENST00000436079.1_RNA	NM_030573.2	NP_085050.2	Q9BT49	THAP7_HUMAN	THAP domain containing 7	302					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nuclear speck (GO:0016607)	C2H2 zinc finger domain binding (GO:0070742)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)			cervix(1)|lung(2)|prostate(3)|skin(1)|stomach(1)	8	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			CTCAGCTGCATGGCAAAGTCC	0.642																																					p.M302V		Atlas-SNP	.											.	THAP7	15	.	0			c.A904G						.						30	31	31					22																	21354195		2202	4298	6500	SO:0001583	missense	80764	exon4			GCTGCATGGCAAA	BC004346	CCDS13787.1	22q11.2	2013-01-25			ENSG00000184436	ENSG00000184436		"THAP (C2CH-type zinc finger) domain containing"	23190	protein-coding gene	gene with protein product		609518				12575992	Standard	NM_030573		Approved	MGC10963	uc002ztr.1	Q9BT49	OTTHUMG00000150879	ENST00000215742.4:c.904A>G	chr22.hg19:g.21354195T>C	ENSP00000215742:p.Met302Val	67.0	0.0		88.0	4.0	NM_030573	B2RD97|D3DX40	Missense_Mutation	SNP	ENST00000215742.4	hg19	CCDS13787.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.226125	0.39300	.	.	ENSG00000184436	ENST00000215742;ENST00000399133	D;D	0.95756	-3.8;-3.8	4.83	2.57	0.30868	.	0.071376	0.53938	D	0.000049	D	0.86426	0.5930	N	0.08118	0	0.28818	N	0.897874	B	0.06786	0.001	B	0.01281	0.0	T	0.79040	-0.1966	10	0.51188	T	0.08	-9.8685	5.1657	0.15084	0.0:0.0975:0.2829:0.6196	.	302	Q9BT49	THAP7_HUMAN	V	302	ENSP00000215742:M302V;ENSP00000382084:M302V	ENSP00000215742:M302V	M	-	1	0	THAP7	19684195	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.322000	0.33689	0.979000	0.38497	0.533000	0.62120	ATG	.	.		0.642	THAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320405.1	NM_030573		C	21354195	T	C	21354195	3	2	43	1	0	0	0	0	1	0	0	0	15864	1464	51	2	29	2	THAP7	22	21354195	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	215703	21354195	29950371	364	5446										
UBE2L3	7332	hgsc.bcm.edu	37	chr22	21922044	21922044	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	caaatccaagatggcggccaGcaggaggctgatgaaggtaa	14	8	0	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr22:21922044G>T	ENST00000342192.4	+	1	209	c.11G>T	c.(10-12)aGc>aTc	p.S4I	UBE2L3_ENST00000545681.1_Missense_Mutation_p.S4I|UBE2L3_ENST00000458578.2_Intron	NM_003347.3	NP_003338.1	P68036	UB2L3_HUMAN	ubiquitin-conjugating enzyme E2L 3	4					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein K11-linked ubiquitination (GO:0070979)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)|ubiquitin-protein transferase activity (GO:0004842)		UBE2L3/KRAS(2)	large_intestine(4)	4	Colorectal(54;0.105)					ATGGCGGCCAGCAGGAGGCTG	0.706																																					p.S4I		Atlas-SNP	.											.	UBE2L3	11	.	0			c.G11T						.						16	18	17					22																	21922044		2173	4259	6432	SO:0001583	missense	7332	exon1			CGGCCAGCAGGAG	AJ000519	CCDS13790.1, CCDS58795.1, CCDS58796.1	22q11.2	2007-02-05			ENSG00000185651	ENSG00000185651		"Ubiquitin-conjugating enzymes E2"	12488	protein-coding gene	gene with protein product		603721				8672131, 9693040	Standard	NM_001256356		Approved	UBCH7	uc031rxe.1	P68036	OTTHUMG00000150823	ENST00000342192.4:c.11G>T	chr22.hg19:g.21922044G>T	ENSP00000344259:p.Ser4Ile	141.0	0.0		153.0	57.0	NM_003347	B2R4A7|B4DDG1|B4DSZ4|E7EWS7|P51966|P70653|Q9HAV1	Missense_Mutation	SNP	ENST00000342192.4	hg19	CCDS13790.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.879892	0.51801	.	.	ENSG00000185651	ENST00000342192;ENST00000545681	T;T	0.71579	-0.58;1.52	4.53	3.48	0.39840	Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	L	0.60904	1.88	0.22199	N	0.999299	B;B;B	0.19817	0.013;0.039;0.039	B;B;B	0.29598	0.015;0.104;0.104	T	0.55153	-0.8185	10	0.37606	T	0.19	.	8.7098	0.34376	0.1084:0.0:0.8916:0.0	.	4;4;4	B4DDG1;P68036;A8K4W8	.;UB2L3_HUMAN;.	I	4	ENSP00000344259:S4I;ENSP00000445931:S4I	ENSP00000344259:S4I	S	+	2	0	UBE2L3	20252044	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.180000	0.58296	2.344000	0.79699	0.558000	0.71614	AGC	.	.		0.706	UBE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320219.1	NM_198157		T	21922044	G	T	21922044	3	4	43	1	0	0	0	0	1	0	0	0	16878	971	34	3	13	3	UBE2L3	22	21922044	Missense_Mutation	SNP	G	TCGA-BC-A3KF-01A-11D-A20W-10	567849	21922044	29382522	365	5447										
PLA2G3	50487	hgsc.bcm.edu	37	chr22	31531911	31531911	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acaccctgatggccctagggTctctggaacagctgtaagga	12	11	1	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr22:31531911T>C	ENST00000215885.3	-	7	1580	c.1328A>G	c.(1327-1329)gAc>gGc	p.D443G		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	443					acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						GGCCCTAGGGTCTCTGGAACA	0.592																																					p.D443G		Atlas-SNP	.											.	PLA2G3	85	.	0			c.A1328G						.						38	40	40					22																	31531911		2203	4300	6503	SO:0001583	missense	50487	exon7			CTAGGGTCTCTGG	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.1328A>G	chr22.hg19:g.31531911T>C	ENSP00000215885:p.Asp443Gly	38.0	0.0		72.0	4.0	NM_015715	O95768	Missense_Mutation	SNP	ENST00000215885.3	hg19	CCDS13889.1	.	.	.	.	.	.	.	.	.	.	T	4.324	0.059549	0.08339	.	.	ENSG00000100078	ENST00000215885	T	0.31769	1.48	5.27	0.165	0.14995	Phospholipase A2 (2);	0.512740	0.20560	N	0.089936	T	0.22589	0.0545	L	0.55103	1.725	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.18618	-1.0331	10	0.54805	T	0.06	-10.0515	3.1596	0.06516	0.1883:0.3471:0.0:0.4645	.	443	Q9NZ20	PA2G3_HUMAN	G	443	ENSP00000215885:D443G	ENSP00000215885:D443G	D	-	2	0	PLA2G3	29861911	0.002000	0.14202	0.039000	0.18376	0.298000	0.27526	0.408000	0.21065	0.075000	0.16796	0.533000	0.62120	GAC	.	.		0.592	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715		C	31531911	T	C	31531911	3	2	43	1	0	0	0	0	1	0	0	0	12009	1667	58	2	205	2	PLA2G3	22	31531911	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	9609867	31531911	19772655	366	5448										
SEPT3	55964	hgsc.bcm.edu	37	chr22	42392914	42392914	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acccccctgcagggagaaggCctcctgggcactgtccttcc	11	17	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr22:42392914C>T	ENST00000396426.3	+	11	1275	c.1020C>T	c.(1018-1020)ggC>ggT	p.G340G	SEPT3_ENST00000396425.3_3'UTR|WBP2NL_ENST00000328823.9_5'Flank|SEPT3_ENST00000406029.1_Silent_p.G276G|SEPT3_ENST00000328414.8_3'UTR	NM_145733.2	NP_663786.2	Q9UH03	SEPT3_HUMAN	septin 3	340					cell cycle (GO:0007049)|cell division (GO:0051301)	cell junction (GO:0030054)|septin complex (GO:0031105)|synapse (GO:0045202)	GTP binding (GO:0005525)			breast(1)|kidney(3)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17						AGGGAGAAGGCCTCCTGGGCA	0.582																																					p.G340G		Atlas-SNP	.											.	SEPT3	53	.	0			c.C1020T						.						170	152	158					22																	42392914		2203	4300	6503	SO:0001819	synonymous_variant	55964	exon11			AGAAGGCCTCCTG	AF285107	CCDS14026.2, CCDS14027.2	22q13.2	2013-01-21			ENSG00000100167	ENSG00000100167		"Septins"	10750	protein-coding gene	gene with protein product		608314		SEP3			Standard	NM_019106		Approved		uc003bbr.4	Q9UH03	OTTHUMG00000030494	ENST00000396426.3:c.1020C>T	chr22.hg19:g.42392914C>T		90.0	0.0		88.0	4.0	NM_145733	B1AHR0|Q2NKJ7|Q59GF7|Q6IBZ6|Q8N3P3|Q9HD35	Silent	SNP	ENST00000396426.3	hg19	CCDS14026.2																																																																																			.	.		0.582	SEPT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322051.1	NM_145734		T	42392914	C	T	42392914	2	4	43	1	0	0	0	0	0	0	0	1	14080	726	26	3		3	SEPT3	22	42392914	Silent	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	10861003	42392914	8911652	367	5449										
TCF20	6942	hgsc.bcm.edu	37	chr22	42610352	42610352	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	tgctgagaagggtgttgttgTtgctgcggttgctgctgctg	17	6	0	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr22:42610352T>C	ENST00000359486.3	-	1	1096	c.960A>G	c.(958-960)caA>caG	p.Q320Q	TCF20_ENST00000335626.4_Silent_p.Q320Q	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	320	Poly-Gln.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						GGtgttgttgttgctgcggtt	0.512																																					p.Q320Q		Atlas-SNP	.											.	TCF20	164	.	0			c.A960G						.						83	82	82					22																	42610352		2203	4300	6503	SO:0001819	synonymous_variant	6942	exon1			TTGTTGTTGCTGC	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.960A>G	chr22.hg19:g.42610352T>C		128.0	0.0		193.0	9.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Silent	SNP	ENST00000359486.3	hg19	CCDS14033.1																																																																																			.	.		0.512	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		C	42610352	T	C	42610352	2	2	43	1	0	0	0	0	0	0	0	1	15705	1722	60	2		2	TCF20	22	42610352	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	217438	42610352	8694214	368	5450										
LDOC1L	84247	hgsc.bcm.edu	37	chr22	44892949	44892949	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ggaacccctgatagttgttgCgcaaggggctgtcaggttgc	15	9	1	1	rs374819770		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr22:44892949C>T	ENST00000341255.3	-	2	997	c.488G>A	c.(487-489)cGc>cAc	p.R163H		NM_032287.2	NP_115663.2	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	163										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(3)|prostate(2)	11		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)		ATAGTTGTTGCGCAAGGGGCT	0.607																																					p.R163H		Atlas-SNP	.											.	LDOC1L	24	.	0			c.G488A						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	42	44	43		488	3.1	1	22		43	0,8600		0,0,4300	no	missense	LDOC1L	NM_032287.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	163/240	44892949	1,13005	2203	4300	6503	SO:0001583	missense	84247	exon2			TTGTTGCGCAAGG	CR456439	CCDS33662.1	22q13.3	2006-09-06			ENSG00000188636	ENSG00000188636			13343	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_032287		Approved	dJ1033E15.2, DKFZp761O17121, Mart6, Mar6	uc003beu.1	Q6ICC9	OTTHUMG00000150465	ENST00000341255.3:c.488G>A	chr22.hg19:g.44892949C>T	ENSP00000340434:p.Arg163His	78.0	0.0		98.0	36.0	NM_032287	Q6ZTR1	Missense_Mutation	SNP	ENST00000341255.3	hg19	CCDS33662.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.587931	0.46110	2.27E-4	0.0	ENSG00000188636	ENST00000341255	T	0.18338	2.22	3.1	3.1	0.35709	.	0.187151	0.24070	N	0.041823	T	0.06142	0.0159	N	0.08118	0	0.30172	N	0.801228	P	0.37997	0.614	B	0.25987	0.065	T	0.17561	-1.0365	10	0.19147	T	0.46	-5.6274	9.9334	0.41537	0.0:1.0:0.0:0.0	.	163	Q6ICC9	LDOCL_HUMAN	H	163	ENSP00000340434:R163H	ENSP00000340434:R163H	R	-	2	0	LDOC1L	43271613	0.923000	0.31300	1.000000	0.80357	0.994000	0.84299	3.073000	0.50057	2.054000	0.61138	0.591000	0.81541	CGC	.	.		0.607	LDOC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318222.1	NM_032287		T	44892949	C	T	44892949	3	4	43	1	0	0	0	0	1	0	0	0	8719	768	27	1	235	1	LDOC1L	22	44892949	Missense_Mutation	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	2282597	44892949	6411617	369	5451										
TYMP	1890	hgsc.bcm.edu	37	chr22	50967939	50967939	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acgcaccgatctgtgcgcccTgcgcgctcccattcaccaca	8	19	2	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chr22:50967939T>C	ENST00000252029.3	-	2	362	c.200A>G	c.(199-201)cAg>cGg	p.Q67R	TYMP_ENST00000395681.1_Missense_Mutation_p.Q67R|TYMP_ENST00000395680.1_Missense_Mutation_p.Q67R|TYMP_ENST00000395678.3_Missense_Mutation_p.Q67R	NM_001113755.2|NM_001113756.2|NM_001257988.1|NM_001257989.1|NM_001953.4	NP_001107227.1|NP_001107228.1|NP_001244917.1|NP_001244918.1|NP_001944.1	P19971	TYPH_HUMAN	thymidine phosphorylase	67					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)|DNA replication (GO:0006260)|mitochondrial genome maintenance (GO:0000002)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphorylase activity (GO:0004645)|platelet-derived growth factor receptor binding (GO:0005161)|pyrimidine-nucleoside phosphorylase activity (GO:0016154)|thymidine phosphorylase activity (GO:0009032)|transferase activity, transferring pentosyl groups (GO:0016763)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Cidofovir(DB00369)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Trifluridine(DB00432)	CTGTGCGCCCTGCGCGCTCCC	0.687																																					p.Q67R		Atlas-SNP	.											.	TYMP	25	.	0			c.A200G						.						41	45	44					22																	50967939		2202	4298	6500	SO:0001583	missense	1890	exon2			GCGCCCTGCGCGC	M63193	CCDS14096.1, CCDS58811.1	22q13	2014-09-17	2008-01-21	2008-01-21	ENSG00000025708	ENSG00000025708	2.4.2.4		3148	protein-coding gene	gene with protein product	"gliostatin"	131222	"endothelial cell growth factor 1 (platelet-derived)"	MNGIE, ECGF1		1590793, 11733540	Standard	NM_001113755		Approved		uc003bme.5	P19971	OTTHUMG00000150249	ENST00000252029.3:c.200A>G	chr22.hg19:g.50967939T>C	ENSP00000252029:p.Gln67Arg	103.0	0.0		96.0	4.0	NM_001257989	A8MW15|H9KVA0|Q13390|Q8WVB7	Missense_Mutation	SNP	ENST00000252029.3	hg19	CCDS14096.1	.	.	.	.	.	.	.	.	.	.	T	15.64	2.894293	0.52121	.	.	ENSG00000025708	ENST00000395680;ENST00000395681;ENST00000252029;ENST00000395678;ENST00000425169	D;D;D;D;D	0.92249	-3.0;-3.0;-3.0;-3.0;-3.0	4.77	4.77	0.60923	Glycosyl transferase, family 3, N-terminal (2);Glycosyl transferase, family 3, subgroup, N-terminal (1);	0.134858	0.51477	D	0.000095	D	0.84902	0.5575	N	0.17723	0.515	0.38071	D	0.936369	B;B;B;B	0.23891	0.043;0.093;0.093;0.093	B;B;B;B	0.17098	0.017;0.016;0.016;0.016	D	0.83923	0.0302	10	0.87932	D	0	-1.9173	10.6743	0.45776	0.0:0.0:0.0:1.0	.	67;67;67;67	B4DVR2;B2RBL3;E5KRG5;P19971	.;.;.;TYPH_HUMAN	R	67	ENSP00000379037:Q67R;ENSP00000379038:Q67R;ENSP00000252029:Q67R;ENSP00000379036:Q67R;ENSP00000395875:Q67R	ENSP00000252029:Q67R	Q	-	2	0	TYMP	49314805	1.000000	0.71417	0.292000	0.24919	0.494000	0.33585	2.886000	0.48578	1.784000	0.52394	0.368000	0.22195	CAG	.	.		0.687	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317081.1	NM_001953		C	50967939	T	C	50967939	3	2	43	1	0	0	0	0	1	0	0	0	16826	1580	55	2	1284	2	TYMP	22	50967939	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	6074990	50967939	336627	370	5452										
ASMTL	8623	hgsc.bcm.edu	37	chrX	1522164	1522164	+	Nonstop_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gaacatgctgcctgggcttcAgggggccactttggtggcca	15	11	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chrX:1522164A>C	ENST00000381317.3	-	13	1896	c.1864T>G	c.(1864-1866)Tga>Gga	p.*622G	ASMTL_ENST00000534940.1_Nonstop_Mutation_p.*564G|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000602357.1_RNA|ASMTL-AS1_ENST00000443929.1_RNA|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000425740.2_RNA|ASMTL_ENST00000416733.2_Nonstop_Mutation_p.*546G|ASMTL_ENST00000381333.4_Nonstop_Mutation_p.*606G	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	0						cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CCTGGGCTTCAGGGGGCCACT	0.607																																					p.X622G		Atlas-SNP	.											.	ASMTL	56	.	0			c.T1864G						.						47	49	49					X																	1522164		1952	4068	6020	SO:0001578	stop_lost	8623	exon13			GGCTTCAGGGGGC	Y15521	CCDS43917.1, CCDS55362.1, CCDS55363.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000169093	ENSG00000169093		"Pseudoautosomal regions / PAR1"	751	protein-coding gene	gene with protein product		300162, 400011				9736779	Standard	NM_004192		Approved		uc004cpx.2	O95671	OTTHUMG00000021057	ENST00000381317.3:c.1864T>G	chrX.hg19:g.1522164A>C	ENSP00000370718:p.*622Argext*30	66.0	0.0		81.0	8.0	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	hg19	CCDS43917.1	.	.	.	.	.	.	.	.	.	.	a	0.022	-1.412479	0.01145	.	.	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	.	.	.	0.752	0.752	0.18398	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	546;564;606;622	.	.	X	-	1	0	ASMTL	1482164	0.914000	0.31030	0.007000	0.13788	0.157000	0.22087	0.652000	0.24888	0.572000	0.29383	0.097000	0.15509	TGA	.	.		0.607	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192		C	1522164	A	C	1522164	4	2	43	1	0	0	0	0	0	0	0	0	1046	201	7	5	5	5	ASMTL	23	1522164	Nonstop_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10		1522164	153748396	371	5453										
PRKX	5613	hgsc.bcm.edu	37	chrX	3631158	3631158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ccagcgtgtcaaagtcctgcAggctgtacacaggcggctcc	12	14	1	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chrX:3631158A>G	ENST00000262848.5	-	1	491	c.137T>C	c.(136-138)cTg>cCg	p.L46P		NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	46					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				AAAGTCCTGCAGGCTGTACAC	0.721																																					p.L46P		Atlas-SNP	.											.	PRKX	29	.	0			c.T137C						.						7	6	6					X																	3631158		2100	4114	6214	SO:0001583	missense	5613	exon1			TCCTGCAGGCTGT		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.137T>C	chrX.hg19:g.3631158A>G	ENSP00000262848:p.Leu46Pro	38.0	0.0		74.0	4.0	NM_005044		Missense_Mutation	SNP	ENST00000262848.5	hg19	CCDS14125.1	.	.	.	.	.	.	.	.	.	.	A	15.68	2.906548	0.52333	.	.	ENSG00000183943	ENST00000262848	T	0.08896	3.04	1.08	1.08	0.20341	Protein kinase-like domain (1);	0.152029	0.27193	U	0.020484	T	0.10594	0.0259	N	0.19112	0.55	0.80722	D	1	D	0.69078	0.997	D	0.66196	0.942	T	0.21008	-1.0258	10	0.87932	D	0	.	4.161	0.10284	1.0:0.0:0.0:0.0	.	46	P51817	PRKX_HUMAN	P	46	ENSP00000262848:L46P	ENSP00000262848:L46P	L	-	2	0	PRKX	3641158	0.876000	0.30132	0.010000	0.14722	0.167000	0.22549	0.403000	0.20982	0.400000	0.25396	0.242000	0.17961	CTG	.	.		0.721	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044		G	3631158	A	G	3631158	3	3	43	1	0	0	0	0	1	0	0	0	12539	188	7	2	971	2	PRKX	23	3631158	Missense_Mutation	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	2108994	3631158	151639402	372	5454										
RBBP7	5931	hgsc.bcm.edu	37	chrX	16876930	16876930	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	cttcgtgattgattttaattTcacattcaatttttcctgtt	4	7	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chrX:16876930T>C	ENST00000380087.2	-	4	710	c.350A>G	c.(349-351)gAa>gGa	p.E117G	RBBP7_ENST00000404022.1_Missense_Mutation_p.E108G|RBBP7_ENST00000380084.4_Missense_Mutation_p.E161G			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7	117					cell proliferation (GO:0008283)|cellular heat acclimation (GO:0070370)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	RNA binding (GO:0003723)			biliary_tract(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	25	Hepatocellular(33;0.0997)					GATTTTAATTTCACATTCAAT	0.378																																					p.E161G		Atlas-SNP	.											.	RBBP7	58	.	0			c.A482G						.						178	142	154					X																	16876930		2203	4300	6503	SO:0001583	missense	5931	exon4			TTAATTTCACATT	U35143	CCDS14179.1, CCDS56598.1	Xp22.22	2013-01-10	2001-11-28		ENSG00000102054	ENSG00000102054		"WD repeat domain containing"	9890	protein-coding gene	gene with protein product	"G1/S transition control protein-binding protein RbAp46", "retinoblastoma-binding protein 7", "retinoblastoma-binding protein RbAp46", "histone acetyltransferase type B subunit 2", "retinoblastoma-binding protein p46"	300825	"retinoblastoma-binding protein 7"			7503932	Standard	NM_002893		Approved	RbAp46	uc004cxs.2	Q16576	OTTHUMG00000021198	ENST00000380087.2:c.350A>G	chrX.hg19:g.16876930T>C	ENSP00000369427:p.Glu117Gly	87.0	0.0		91.0	4.0	NM_001198719	Q5JP00	Missense_Mutation	SNP	ENST00000380087.2	hg19	CCDS14179.1	.	.	.	.	.	.	.	.	.	.	T	17.65	3.442351	0.63067	.	.	ENSG00000102054	ENST00000380087;ENST00000380084;ENST00000404022;ENST00000416035	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.11	5.17	5.17	0.71159	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.64193	0.2576	M	0.67953	2.075	0.58432	D	0.999993	P;P;P	0.48834	0.462;0.916;0.581	B;B;B	0.40199	0.078;0.322;0.111	T	0.69117	-0.5230	10	0.51188	T	0.08	-18.6204	13.4083	0.60926	0.0:0.0:0.0:1.0	.	108;117;161	E9PC52;Q16576;Q5JP00	.;RBBP7_HUMAN;.	G	117;161;108;37	ENSP00000369427:E117G;ENSP00000369424:E161G;ENSP00000386068:E108G;ENSP00000392714:E37G	ENSP00000369424:E161G	E	-	2	0	RBBP7	16786851	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.993000	0.88291	1.829000	0.53265	0.481000	0.45027	GAA	.	.		0.378	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893		C	16876930	T	C	16876930	3	2	43	1	0	0	0	0	1	0	0	0	13119	1783	62	2	963	2	RBBP7	23	16876930	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	13245772	16876930	138393630	373	5455										
YY2	404281	hgsc.bcm.edu	37	chrX	21875262	21875262	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttgaaagggaagaaacttccTcctggggggttaccaggcat	13	8	0	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chrX:21875262T>A	ENST00000429584.2	+	1	1158	c.660T>A	c.(658-660)ccT>ccA	p.P220P	MBTPS2_ENST00000379484.5_Intron|MBTPS2_ENST00000365779.2_Intron|MBTPS2_ENST00000465888.1_3'UTR	NM_206923.3	NP_996806.2	O15391	TYY2_HUMAN	YY2 transcription factor	220					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	19						AGAAACTTCCTCCTGGGGGGT	0.488																																					p.P220P		Atlas-SNP	.											.	YY2	43	.	0			c.T660A						.						130	144	139					X																	21875262		2203	4300	6503	SO:0001819	synonymous_variant	404281	exon1			ACTTCCTCCTGGG	AK091850	CCDS14202.1	Xp22.2-p22.1	2011-02-11			ENSG00000230797	ENSG00000230797		"Zinc fingers, C2H2-type"	31684	protein-coding gene	gene with protein product	"transcription factor yin yang 2"	300570				14702039	Standard	NM_206923		Approved	ZNF631	uc011mjp.2	O15391	OTTHUMG00000021236	ENST00000429584.2:c.660T>A	chrX.hg19:g.21875262T>A		87.0	0.0		110.0	46.0	NM_206923	B2RP10|Q6Q1S4	Silent	SNP	ENST00000429584.2	hg19	CCDS14202.1																																																																																			.	.		0.488	YY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056025.1	NM_206923		A	21875262	T	A	21875262	2	1	43	1	0	0	0	0	0	0	0	1	17524	1538	54	4		4	YY2	23	21875262	Silent	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	4998332	21875262	133395298	374	5456										
RLIM	51132	hgsc.bcm.edu	37	chrX	73814206	73814206	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gctgtagtcgtctcagcaacTcttcctcagtactttcacct	6	14	4	0			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chrX:73814206T>A	ENST00000332687.6	-	3	406	c.188A>T	c.(187-189)gAg>gTg	p.E63V	RLIM_ENST00000349225.2_Missense_Mutation_p.E63V	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	63					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TCTCAGCAACTCTTCCTCAGT	0.423																																					p.E63V	Esophageal Squamous(169;1899 1923 14997 18818 32118)	Atlas-SNP	.											.	RLIM	90	.	0			c.A188T						.						137	112	120					X																	73814206		2203	4300	6503	SO:0001583	missense	51132	exon4			AGCAACTCTTCCT	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.188A>T	chrX.hg19:g.73814206T>A	ENSP00000328059:p.Glu63Val	94.0	0.0		108.0	34.0	NM_183353	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	hg19	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	T	19.02	3.746403	0.69418	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.09073	3.02;3.02	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.31263	0.0791	M	0.79123	2.44	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.03597	-1.1021	10	0.87932	D	0	-5.8686	15.3627	0.74492	0.0:0.0:0.0:1.0	.	63	Q9NVW2	RNF12_HUMAN	V	63	ENSP00000328059:E63V;ENSP00000253571:E63V	ENSP00000328059:E63V	E	-	2	0	RLIM	73730931	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.499000	0.81566	2.011000	0.59026	0.481000	0.45027	GAG	.	.		0.423	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		A	73814206	T	A	73814206	3	1	43	1	0	0	0	0	1	0	0	0	13405	1551	54	4	1694	4	RLIM	23	73814206	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	51938944	73814206	81456354	375	5457										
ATRX	546	hgsc.bcm.edu	37	chrX	76812950	76812950	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	gcatgggagtatccctcttcTtcttcttttctgaattaggg	9	9	5	1			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chrX:76812950T>C	ENST00000373344.5	-	30	6885	c.6671A>G	c.(6670-6672)aAg>aGg	p.K2224R	ATRX_ENST00000395603.3_Missense_Mutation_p.K2186R|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2224	Interaction with MECP2.|Poly-Lys.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						ATCCCTCTTCTTCTTCTTTTC	0.363			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.K2224R		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.A6671G						.						111	111	111					X																	76812950		2203	4294	6497	SO:0001583	missense	546	exon30			CTCTTCTTCTTCT	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.6671A>G	chrX.hg19:g.76812950T>C	ENSP00000362441:p.Lys2224Arg	80.0	0.0		98.0	4.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	hg19	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	T	12.57	1.977387	0.34848	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	D;D	0.92647	-3.07;-3.08	5.67	4.51	0.55191	.	0.145185	0.49916	D	0.000127	D	0.87091	0.6091	L	0.41415	1.275	0.80722	D	1	B;B	0.31968	0.058;0.349	B;B	0.29942	0.022;0.109	T	0.82764	-0.0296	10	0.41790	T	0.15	-11.6655	10.6901	0.45867	0.0:0.0754:0.0:0.9246	.	2186;2224	P46100-4;P46100	.;ATRX_HUMAN	R	2224;2186	ENSP00000362441:K2224R;ENSP00000378967:K2186R	ENSP00000362441:K2224R	K	-	2	0	ATRX	76699606	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.449000	0.66619	0.782000	0.33613	0.481000	0.45027	AAG	.	.		0.363	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		C	76812950	T	C	76812950	3	2	43	1	0	0	0	0	1	0	0	0	1208	1609	56	2	831	2	ATRX	23	76812950	Missense_Mutation	SNP	T	TCGA-BC-A3KF-01A-11D-A20W-10	2998744	76812950	78457610	376	5458										
ATRX	546	hgsc.bcm.edu	37	chrX	76856034	76856034	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	ttcactattattgcccacacCtgatcaaaagaaatatggtt	5	9	2	2			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chrX:76856034C>T	ENST00000373344.5	-	23	5781		c.e23-1		ATRX_ENST00000395603.3_Splice_Site|ATRX_ENST00000480283.1_Splice_Site	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked						ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TTGCCCACACCTGATCAAAAG	0.353			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														.		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.5567-1G>A						.						162	143	149					X																	76856034		2203	4296	6499	SO:0001630	splice_region_variant	546	exon24			CCACACCTGATCA	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.5567-1G>A	chrX.hg19:g.76856034C>T		92.0	0.0		104.0	47.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Splice_Site	SNP	ENST00000373344.5	hg19	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.413158	0.25465	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	.	.	.	5.05	4.17	0.49024	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1957	0.59736	0.0:0.7029:0.2971:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATRX	76742690	1.000000	0.71417	0.975000	0.42487	0.424000	0.31475	5.696000	0.68287	0.878000	0.35920	-0.347000	0.07816	.	.	.		0.353	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	Intron	T	76856034	C	T	76856034	5	4	43	1	0	0	0	0	0	0	1	0	1208	695	24	3	1964	3	ATRX	23	76856034	Splice_Site	SNP	C	TCGA-BC-A3KF-01A-11D-A20W-10	43084	76856034	78414526	377	5459										
GPR119	139760	hgsc.bcm.edu	37	chrX	129518585	129518585	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.016	6	1	0.664294045518438	0.802688638334779	0.642150910667823	0.118881118881119	0.692854020979022	0	acctccttctgccaataggcAtagatgagtgggttgagcag	12	9	1	3			TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	g.chrX:129518585A>G	ENST00000276218.2	-	1	926	c.837T>C	c.(835-837)taT>taC	p.Y279Y		NM_178471.2	NP_848566.1	Q8TDV5	GP119_HUMAN	G protein-coupled receptor 119	279					insulin secretion (GO:0030073)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(1)	11						GCCAATAGGCATAGATGAGTG	0.572																																					p.Y279Y		Atlas-SNP	.											.	GPR119	34	.	0			c.T837C						.						77	70	73					X																	129518585		2203	4300	6503	SO:0001819	synonymous_variant	139760	exon1			ATAGGCATAGATG	AY288416	CCDS14625.1	Xq26.1	2014-01-30			ENSG00000147262	ENSG00000147262		"GPCR / Class A : Orphans"	19060	protein-coding gene	gene with protein product		300513				12044878, 14623098	Standard	NM_178471		Approved	hGPCR2, GPCR2	uc011muv.2	Q8TDV5	OTTHUMG00000022397	ENST00000276218.2:c.837T>C	chrX.hg19:g.129518585A>G		133.0	0.0		95.0	6.0	NM_178471	Q495H7|Q4VBN3	Silent	SNP	ENST00000276218.2	hg19	CCDS14625.1																																																																																			.	.		0.572	GPR119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058270.1	NM_178471		G	129518585	A	G	129518585	2	3	43	1	0	0	0	0	0	0	0	1	6642	224	8	2		2	GPR119	23	129518585	Silent	SNP	A	TCGA-BC-A3KF-01A-11D-A20W-10	52662551	129518585	25751975	378	5460										
AURKAIP1	54998	hgsc.bcm.edu	37	chr1	1309702	1309702	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggaccagcatctcctccagcTccagctgggcccccttgcga	10	18	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:1309702T>C	ENST00000338370.3	-	2	576	c.176A>G	c.(175-177)gAg>gGg	p.E59G	AURKAIP1_ENST00000378853.3_Missense_Mutation_p.E59G|AURKAIP1_ENST00000489799.1_5'UTR|AURKAIP1_ENST00000338338.5_Missense_Mutation_p.E59G|AURKAIP1_ENST00000321751.5_Missense_Mutation_p.E59G			Q9NWT8	AKIP_HUMAN	aurora kinase A interacting protein 1	59					negative regulation of mitosis (GO:0045839)|positive regulation of proteolysis (GO:0045862)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				kidney(1)|lung(2)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.82e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CTCCTCCAGCTCCAGCTGGGC	0.697																																					p.E59G		Atlas-SNP	.											.	AURKAIP1	12	.	0			c.A176G						.						19	23	22					1																	1309702		2198	4291	6489	SO:0001583	missense	54998	exon3			TCCAGCTCCAGCT		CCDS25.1	1p36.33	2014-02-12			ENSG00000175756	ENSG00000175756			24114	protein-coding gene	gene with protein product		609183				12244051	Standard	NM_017900		Approved	AKIP, AIP, FLJ20608	uc009vkb.1	Q9NWT8	OTTHUMG00000001413	ENST00000338370.3:c.176A>G	chr1.hg19:g.1309702T>C	ENSP00000342676:p.Glu59Gly	33.0	0.0		47.0	4.0	NM_001127230	Q5TA36|Q8TBD3	Missense_Mutation	SNP	ENST00000338370.3	hg19	CCDS25.1	.	.	.	.	.	.	.	.	.	.	t	17.56	3.420883	0.62622	.	.	ENSG00000175756	ENST00000338338;ENST00000338370;ENST00000321751;ENST00000378853	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	4.82	2.36	0.29203	.	0.228388	0.36167	N	0.002754	T	0.46658	0.1404	M	0.66297	2.02	0.36460	D	0.866637	P	0.49635	0.926	P	0.44597	0.454	T	0.55114	-0.8191	10	0.51188	T	0.08	-15.2419	9.8135	0.40838	0.0:0.0:0.3345:0.6655	.	59	Q9NWT8	AKIP_HUMAN	G	59	ENSP00000340656:E59G;ENSP00000342676:E59G;ENSP00000319778:E59G;ENSP00000368130:E59G	ENSP00000319778:E59G	E	-	2	0	AURKAIP1	1299565	1.000000	0.71417	0.073000	0.20177	0.981000	0.71138	3.361000	0.52306	0.289000	0.22422	0.533000	0.62120	GAG	.	.		0.697	AURKAIP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008273.1	NM_017900		C	1309702	T	C	1309702	3	2	44	1	0	0	0	0	1	0	0	0	1222	1551	54	2	431	2	AURKAIP1	1	1309702	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10		1309702	247940919	1	5461										
PRKCZ	5590	hgsc.bcm.edu	37	chr1	2116024	2116024	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcctattgtttttccaagctGgagaagaagcaggcgctccc	10	11	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:2116024G>A	ENST00000400921.2	+	14	1712	c.1029G>A	c.(1027-1029)ctG>ctA	p.L343L	RP11-181G12.2_ENST00000444529.1_RNA|RP11-181G12.2_ENST00000333854.2_RNA|PRKCZ_ENST00000400920.1_Silent_p.L343L|RP11-181G12.2_ENST00000536678.1_RNA|PRKCZ_ENST00000479263.1_3'UTR|C1orf86_ENST00000400919.3_3'UTR	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta	526	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	TTTCCAAGCTGGAGAAGAAGC	0.522																																					p.L526L		Atlas-SNP	.											.	PRKCZ	84	.	0			c.G1578A						.						40	36	37					1																	2116024		2203	4300	6503	SO:0001819	synonymous_variant	5590	exon17			CAAGCTGGAGAAG	BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.1029G>A	chr1.hg19:g.2116024G>A		104.0	0.0		90.0	4.0	NM_002744	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Silent	SNP	ENST00000400921.2	hg19	CCDS41229.1																																																																																			.	.		0.522	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		A	2116024	G	A	2116024	2	1	44	1	0	0	0	0	0	0	0	1	12529	1335	47	3		3	PRKCZ	1	2116024	Silent	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	806322	2116024	247134597	2	5462										
NOL9	79707	hgsc.bcm.edu	37	chr1	6592674	6592674	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acgtcgatttctcatcttggTcttgctttttgtgtacaagc	8	9	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:6592674T>C	ENST00000377705.5	-	8	1416	c.1384A>G	c.(1384-1386)Acc>Gcc	p.T462A		NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	462					maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		CTCATCTTGGTCTTGCTTTTT	0.448																																					p.T462A		Atlas-SNP	.											.	NOL9	49	.	0			c.A1384G						.						209	206	207					1																	6592674		2203	4300	6503	SO:0001583	missense	79707	exon8			TCTTGGTCTTGCT	AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408			26265	protein-coding gene	gene with protein product	"polynucleotide 5'-kinase"					21063389	Standard	NM_024654		Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.1384A>G	chr1.hg19:g.6592674T>C	ENSP00000366934:p.Thr462Ala	190.0	0.0		196.0	8.0	NM_024654	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	Missense_Mutation	SNP	ENST00000377705.5	hg19	CCDS80.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.251157	0.39797	.	.	ENSG00000162408	ENST00000377705	T	0.16597	2.33	6.04	-9.52	0.00578	Pre-mRNA cleavage complex II Clp1 (1);	1.229220	0.05457	N	0.550536	T	0.06416	0.0165	N	0.19112	0.55	0.22127	N	0.999345	B	0.09022	0.002	B	0.06405	0.002	T	0.31641	-0.9936	10	0.11182	T	0.66	-3.7002	2.233	0.04001	0.1945:0.2208:0.0938:0.491	.	462	Q5SY16	NOL9_HUMAN	A	462	ENSP00000366934:T462A	ENSP00000366934:T462A	T	-	1	0	NOL9	6515261	0.058000	0.20735	0.251000	0.24312	0.894000	0.52154	-1.209000	0.03002	-1.367000	0.02152	-0.527000	0.04329	ACC	.	.		0.448	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002625.1	NM_024654		C	6592674	T	C	6592674	3	2	44	1	0	0	0	0	1	0	0	0	10537	1667	58	2	744	2	NOL9	1	6592674	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4476650	6592674	242657947	3	5463										
PRDM2	7799	hgsc.bcm.edu	37	chr1	14057576	14057576	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaggacttccggaggaagtgAggcttttcccttctgctgtt	13	9	1	1	rs542897882		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:14057576A>G	ENST00000235372.7	+	3	947	c.91A>G	c.(91-93)Agg>Ggg	p.R31G	PRDM2_ENST00000376048.5_Missense_Mutation_p.R31G|PRDM2_ENST00000311066.5_Missense_Mutation_p.R31G	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	31	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		GGAGGAAGTGAGGCTTTTCCC	0.567																																					p.R31G		Atlas-SNP	.											.	PRDM2	147	.	0			c.A91G						.						131	115	120					1																	14057576		2203	4300	6503	SO:0001583	missense	7799	exon3			GAAGTGAGGCTTT	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"Chromatin-modifying enzymes / K-methyltransferases"	9347	protein-coding gene	gene with protein product	"retinoblastoma protein-binding zinc finger protein", "retinoblastoma protein-interacting zinc finger protein", "MTE-binding protein", "zinc-finger DNA-binding protein", "GATA-3 binding protein G3B"	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.91A>G	chr1.hg19:g.14057576A>G	ENSP00000235372:p.Arg31Gly	103.0	0.0		104.0	5.0	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	hg19	CCDS150.1	.	.	.	.	.	.	.	.	.	.	A	31	5.088303	0.94100	.	.	ENSG00000116731	ENST00000484063;ENST00000376048;ENST00000235372;ENST00000311066;ENST00000400800	T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89	5.91	5.91	0.95273	SET domain (2);	0.214556	0.51477	D	0.000092	T	0.81004	0.4733	M	0.62723	1.935	0.45676	D	0.998596	D;D;P	0.60160	0.978;0.987;0.564	P;P;B	0.57679	0.673;0.825;0.177	T	0.82581	-0.0386	10	0.62326	D	0.03	.	12.7354	0.57220	1.0:0.0:0.0:0.0	.	31;31;31	Q13029;Q13029-2;B1AJZ4	PRDM2_HUMAN;.;.	G	31	ENSP00000423010:R31G;ENSP00000365216:R31G;ENSP00000235372:R31G;ENSP00000312352:R31G	ENSP00000235372:R31G	R	+	1	2	PRDM2	13930163	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.760000	0.62235	2.269000	0.75478	0.533000	0.62120	AGG	.	.		0.567	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		G	14057576	A	G	14057576	3	3	44	1	0	0	0	0	1	0	0	0	12470	295	11	2	97	2	PRDM2	1	14057576	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	7464902	14057576	235193045	4	5464										
CELA2B	51032	hgsc.bcm.edu	37	chr1	15802955	15802955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctttctcttttcacagcccTcagttgtggggtctccactt	7	14	4	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:15802955T>C	ENST00000375910.3	+	2	69	c.44T>C	c.(43-45)cTc>cCc	p.L15P	CELA2B_ENST00000494280.1_3'UTR	NM_015849.2	NP_056933	P08218	CEL2B_HUMAN	chymotrypsin-like elastase family, member 2B	15						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8						TTCACAGCCCTCAGTTGTGGG	0.522																																					p.L15P		Atlas-SNP	.											.	CELA2B	37	.	0			c.T44C						.						115	110	112					1																	15802955		2203	4300	6503	SO:0001583	missense	51032	exon2			CAGCCCTCAGTTG		CCDS30605.1	1p36.21	2009-07-09			ENSG00000215704	ENSG00000215704			29995	protein-coding gene	gene with protein product	"pancreatic elastase IIB"	609444				3646943, 16327289	Standard	NM_015849		Approved	RP11-265F14.2, ELA2B	uc001awl.3	P08218	OTTHUMG00000002259	ENST00000375910.3:c.44T>C	chr1.hg19:g.15802955T>C	ENSP00000365075:p.Leu15Pro	161.0	0.0		149.0	10.0	NM_015849	Q14D16|Q6ISM5|Q96QV5	Missense_Mutation	SNP	ENST00000375910.3	hg19	CCDS30605.1	.	.	.	.	.	.	.	.	.	.	T	10.36	1.328974	0.24167	.	.	ENSG00000215704	ENST00000375910	D	0.92805	-3.11	4.39	4.39	0.52855	.	0.831288	0.09945	U	0.735425	D	0.90689	0.7079	L	0.35723	1.085	0.39019	D	0.9597	D	0.54047	0.964	P	0.50791	0.65	D	0.86931	0.2073	10	0.44086	T	0.13	.	10.0215	0.42046	0.0:0.0:0.0:1.0	.	15	P08218	CEL2B_HUMAN	P	15	ENSP00000365075:L15P	ENSP00000365075:L15P	L	+	2	0	CELA2B	15675542	0.985000	0.35326	0.221000	0.23827	0.089000	0.18198	1.786000	0.38694	1.631000	0.50456	0.172000	0.16884	CTC	.	.		0.522	CELA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006448.1	NM_015849		C	15802955	T	C	15802955	3	2	44	1	0	0	0	0	1	0	0	0	3214	1551	54	2	50	2	CELA2B	1	15802955	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1745379	15802955	233447666	5	5465										
SPEN	23013	hgsc.bcm.edu	37	chr1	16255127	16255127	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cagataaagaacgaacttttGatccggagagagtggagaga	13	5	0	5			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:16255127G>C	ENST00000375759.3	+	11	2596	c.2392G>C	c.(2392-2394)Gat>Cat	p.D798H		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	798	Arg-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		ACGAACTTTTGATCCGGAGAG	0.438																																					p.D798H		Atlas-SNP	.											.	SPEN	374	.	0			c.G2392C						.						77	83	81					1																	16255127		2203	4300	6503	SO:0001583	missense	23013	exon11			ACTTTTGATCCGG		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.2392G>C	chr1.hg19:g.16255127G>C	ENSP00000364912:p.Asp798His	45.0	0.0		43.0	16.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.695394	0.48202	.	.	ENSG00000065526	ENST00000375759	T	0.10763	2.84	4.89	4.89	0.63831	.	.	.	.	.	T	0.22399	0.0540	L	0.51422	1.61	0.46061	D	0.998847	D	0.60160	0.987	P	0.54460	0.753	T	0.00380	-1.1776	9	0.51188	T	0.08	-0.8309	18.2394	0.89961	0.0:0.0:1.0:0.0	.	798	Q96T58	MINT_HUMAN	H	798	ENSP00000364912:D798H	ENSP00000364912:D798H	D	+	1	0	SPEN	16127714	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	8.647000	0.91057	2.525000	0.85131	0.563000	0.77884	GAT	.	.		0.438	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		C	16255127	G	C	16255127	3	2	44	1	0	0	0	0	1	0	0	0	15053	1290	45	4	2434	4	SPEN	1	16255127	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	452172	16255127	232995494	6	5466										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22183660	22183660	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcagtttcccgttgtgcaggCgggtccacaccagggtatag	14	11	0	0	rs561392976	byFrequency	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:22183660C>T	ENST00000374695.3	-	44	5502	c.5423G>A	c.(5422-5424)cGc>cAc	p.R1808H	HSPG2_ENST00000430507.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1808	Ig-like C2-type 3.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GTTGTGCAGGCGGGTCCACAC	0.607													C|||	3	0.000599042	0	0	5008	,	,		17559	0.002		0	False		,,,				2504	0.001				p.R1808H		Atlas-SNP	.											.	HSPG2	311	.	0			c.G5423A						.						108	116	113					1																	22183660		2203	4300	6503	SO:0001583	missense	3339	exon44			TGCAGGCGGGTCC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.5423G>A	chr1.hg19:g.22183660C>T	ENSP00000363827:p.Arg1808His	235.0	0.0		202.0	90.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.974153	0.92919	.	.	ENSG00000142798	ENST00000374695	T	0.13420	2.59	4.85	4.85	0.62838	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37348	N	0.002122	T	0.32071	0.0817	L	0.49640	1.575	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.01476	-1.1345	10	0.54805	T	0.06	.	15.8147	0.78592	0.0:1.0:0.0:0.0	.	1808	P98160	PGBM_HUMAN	H	1808	ENSP00000363827:R1808H	ENSP00000363827:R1808H	R	-	2	0	HSPG2	22056247	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	7.047000	0.76599	2.424000	0.82194	0.655000	0.94253	CGC	.	.		0.607	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		T	22183660	C	T	22183660	3	4	44	1	0	0	0	0	1	0	0	0	7439	768	27	1	7968	1	HSPG2	1	22183660	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	5928533	22183660	227066961	7	5467										
FGR	2268	hgsc.bcm.edu	37	chr1	27950421	27950421	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	caatttcttgcagaacacacAgcccattccaggttccctgc	6	15	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:27950421A>G	ENST00000374005.3	-	3	295	c.7T>C	c.(7-9)Tgt>Cgt	p.C3R	FGR_ENST00000468038.1_5'UTR|FGR_ENST00000545953.1_Missense_Mutation_p.C3R|FGR_ENST00000374004.1_Missense_Mutation_p.C3R|FGR_ENST00000399173.1_Missense_Mutation_p.C3R	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	3					blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CAGAACACACAGCCCATTCCA	0.602																																					p.C3R		Atlas-SNP	.											.	FGR	39	.	0			c.T7C						.						58	55	56					1																	27950421		2203	4300	6503	SO:0001583	missense	2268	exon3			ACACACAGCCCAT	BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"SH2 domain containing"	3697	protein-coding gene	gene with protein product		164940	"Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog", "v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog", "feline Gardner-Rasheed sarcoma viral oncogene homolog"	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.7T>C	chr1.hg19:g.27950421A>G	ENSP00000363117:p.Cys3Arg	84.0	0.0		86.0	4.0	NM_001042729	D3DPL7|Q9UIQ3	Missense_Mutation	SNP	ENST00000374005.3	hg19	CCDS305.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202503	0.79127	.	.	ENSG00000000938	ENST00000374005;ENST00000545953;ENST00000399173;ENST00000374004;ENST00000374003;ENST00000457296	T;D;T;T;T;D	0.86694	-1.02;-2.16;-1.02;-1.02;-1.02;-1.67	4.92	4.92	0.64577	.	0.000000	0.64402	D	0.000007	D	0.87724	0.6249	L	0.46157	1.445	0.58432	D	0.999998	P	0.51449	0.945	P	0.52627	0.704	D	0.88920	0.3365	10	0.87932	D	0	.	12.6197	0.56595	1.0:0.0:0.0:0.0	.	3	P09769	FGR_HUMAN	R	3	ENSP00000363117:C3R;ENSP00000445302:C3R;ENSP00000382126:C3R;ENSP00000363116:C3R;ENSP00000363115:C3R;ENSP00000407670:C3R	ENSP00000363115:C3R	C	-	1	0	FGR	27823008	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.301000	0.72782	2.139000	0.66308	0.533000	0.62120	TGT	.	.		0.602	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248		G	27950421	A	G	27950421	3	3	44	1	0	0	0	0	1	0	0	0	5882	188	7	2	1626	2	FGR	1	27950421	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	5766761	27950421	221300200	8	5468										
ZSCAN20	7579	hgsc.bcm.edu	37	chr1	33960764	33960764	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtggactgtgggaagtgcttCagtgagcgctccaagctcat	14	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:33960764C>T	ENST00000361328.3	+	8	2973	c.2820C>T	c.(2818-2820)ttC>ttT	p.F940F		NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	940					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GGAAGTGCTTCAGTGAGCGCT	0.522																																					p.F940F		Atlas-SNP	.											.	ZSCAN20	107	.	0			c.C2820T						.						80	91	87					1																	33960764		2170	4285	6455	SO:0001819	synonymous_variant	7579	exon8			GTGCTTCAGTGAG	X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"-", "Zinc fingers, C2H2-type"	13093	protein-coding gene	gene with protein product		611315	"zinc finger protein 31 (KOX 29)", "zinc finger protein 31"	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.2820C>T	chr1.hg19:g.33960764C>T		53.0	0.0		78.0	4.0	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Silent	SNP	ENST00000361328.3	hg19	CCDS41300.1																																																																																			.	.		0.522	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		T	33960764	C	T	33960764	2	4	44	1	0	0	0	0	0	0	0	1	18247	825	29	3		3	ZSCAN20	1	33960764	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	6010343	33960764	215289857	9	5469										
GJB4	127534	hgsc.bcm.edu	37	chr1	35227120	35227120	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcctggtcacgtgcccctcaCtgctcgtggtcatgcacgtg	11	15	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:35227120C>A	ENST00000339480.1	+	2	635	c.265C>A	c.(265-267)Ctg>Atg	p.L89M	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	89					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				GTGCCCCTCACTGCTCGTGGT	0.642																																					p.L89M		Atlas-SNP	.											.	GJB4	51	.	0			c.C265A						.						109	83	92					1																	35227120		2203	4300	6503	SO:0001583	missense	127534	exon2			CCCTCACTGCTCG		CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"Ion channels / Gap junction proteins (connexins)"	4286	protein-coding gene	gene with protein product	"connexin 30.3"	605425	"gap junction protein, beta 4 (connexin 30.3)", "gap junction protein, beta 4"				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.265C>A	chr1.hg19:g.35227120C>A	ENSP00000345868:p.Leu89Met	122.0	0.0		105.0	50.0	NM_153212	B3KQ82	Missense_Mutation	SNP	ENST00000339480.1	hg19	CCDS383.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.005993	0.74932	.	.	ENSG00000189433	ENST00000339480	D	0.99277	-5.67	5.73	4.82	0.62117	Connexin, N-terminal (1);	0.081359	0.51477	D	0.000084	D	0.99378	0.9781	M	0.89414	3.03	0.32657	N	0.518609	D	0.60575	0.988	P	0.62740	0.906	D	0.99804	1.1037	10	0.72032	D	0.01	.	14.4153	0.67145	0.0:0.9285:0.0:0.0715	.	89	Q9NTQ9	CXB4_HUMAN	M	89	ENSP00000345868:L89M	ENSP00000345868:L89M	L	+	1	2	GJB4	34999707	0.990000	0.36364	0.954000	0.39281	0.978000	0.69477	2.982000	0.49337	1.440000	0.47531	0.655000	0.94253	CTG	.	.		0.642	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212		A	35227120	C	A	35227120	3	1	44	1	0	0	0	0	1	0	0	0	6418	564	20	3	267	3	GJB4	1	35227120	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1266356	35227120	214023501	10	5470										
ZMYM1	79830	hgsc.bcm.edu	37	chr1	35570358	35570358	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aatagttcaaagagtattacAgcatataagcaggtatgaat	8	4	1	2	rs573224051	byFrequency	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:35570358A>G	ENST00000373330.1	+	7	969	c.795A>G	c.(793-795)acA>acG	p.T265T	ZMYM1_ENST00000359858.4_Silent_p.T265T|ZMYM1_ENST00000373329.1_3'UTR			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	265						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AGAGTATTACAGCATATAAGC	0.388													A|||	2	0.000399361	0	0	5008	,	,		18353	0.002		0	False		,,,				2504	0				p.T265T		Atlas-SNP	.											.	ZMYM1	86	.	0			c.A795G						.						69	62	64					1																	35570358		1866	4117	5983	SO:0001819	synonymous_variant	79830	exon6			TATTACAGCATAT	AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"Zinc fingers, MYM type"	26253	protein-coding gene	gene with protein product			"zinc finger, MYM domain containing 1"			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.795A>G	chr1.hg19:g.35570358A>G		103.0	0.0		96.0	5.0	NM_024772	D3DPR7|Q7Z3Q4	Silent	SNP	ENST00000373330.1	hg19	CCDS41302.1																																																																																			.	.		0.388	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772		G	35570358	A	G	35570358	2	3	44	1	0	0	0	0	0	0	0	1	17714	175	7	2		2	ZMYM1	1	35570358	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	343238	35570358	213680263	11	5471										
ZNF691	51058	hgsc.bcm.edu	37	chr1	43316759	43316759	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agaaggagcatgggcaagagAgcctgtcggatgaactgcaa	15	7	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:43316759A>G	ENST00000372506.1	+	4	470	c.130A>G	c.(130-132)Agc>Ggc	p.S44G	ZNF691_ENST00000397044.3_Missense_Mutation_p.S75G|ZNF691_ENST00000372502.1_Missense_Mutation_p.S66G|ZNF691_ENST00000372508.3_Missense_Mutation_p.S44G|ZNF691_ENST00000372504.1_Missense_Mutation_p.S66G|ZNF691_ENST00000372507.1_Missense_Mutation_p.S44G	NM_001242739.1	NP_001229668.1	Q5VV52	ZN691_HUMAN	zinc finger protein 691	75						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(2)|ovary(2)|prostate(1)	7	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGGGCAAGAGAGCCTGTCGGA	0.562																																					p.S75G		Atlas-SNP	.											.	ZNF691	30	.	0			c.A223G						.						96	98	97					1																	43316759		2203	4300	6503	SO:0001583	missense	51058	exon4			CAAGAGAGCCTGT		CCDS476.1, CCDS55595.1	1p34.2	2013-01-08			ENSG00000164011	ENSG00000164011		"Zinc fingers, C2H2-type"	28028	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001242739		Approved	Zfp691	uc021omh.1	Q5VV52	OTTHUMG00000007623	ENST00000372506.1:c.130A>G	chr1.hg19:g.43316759A>G	ENSP00000361584:p.Ser44Gly	98.0	0.0		94.0	5.0	NM_001242739	A8MXP6|B4DJR7|O95878|Q9NWE8	Missense_Mutation	SNP	ENST00000372506.1	hg19	CCDS476.1	.	.	.	.	.	.	.	.	.	.	A	10.18	1.279112	0.23307	.	.	ENSG00000164011	ENST00000372508;ENST00000372507;ENST00000372506;ENST00000397044;ENST00000372504;ENST00000397034;ENST00000372503;ENST00000372502	T;T;T;T;T;T;T	0.09445	3.01;3.01;3.01;2.98;2.98;4.31;2.98	5.21	5.21	0.72293	.	0.185558	0.39407	N	0.001371	T	0.08133	0.0203	N	0.14661	0.345	0.29673	N	0.842309	B;B	0.20887	0.049;0.049	B;B	0.22386	0.039;0.039	T	0.08806	-1.0704	10	0.62326	D	0.03	-11.1885	13.6769	0.62460	1.0:0.0:0.0:0.0	.	75;75	B4DJR7;Q5VV52	.;ZN691_HUMAN	G	44;44;44;75;66;75;75;66	ENSP00000361586:S44G;ENSP00000361585:S44G;ENSP00000361584:S44G;ENSP00000380237:S75G;ENSP00000361582:S66G;ENSP00000380228:S75G;ENSP00000361580:S66G	ENSP00000361580:S66G	S	+	1	0	ZNF691	43089346	0.007000	0.16637	0.994000	0.49952	0.656000	0.38851	0.484000	0.22308	2.281000	0.76405	0.533000	0.62120	AGC	.	.		0.562	ZNF691-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020192.1	NM_015911		G	43316759	A	G	43316759	3	3	44	1	0	0	0	0	1	0	0	0	18111	304	11	2	132	2	ZNF691	1	43316759	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	7746401	43316759	205933862	12	5472										
TTC22	55001	hgsc.bcm.edu	37	chr1	55248004	55248004	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agagactgccttacctggccGatgtccaggtacgccttgaa	11	12	0	2	rs576430473		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:55248004G>A	ENST00000371276.4	-	6	1270	c.1167C>T	c.(1165-1167)atC>atT	p.I389I		NM_001114108.1	NP_001107580.1	Q5TAA0	TTC22_HUMAN	tetratricopeptide repeat domain 22	389										kidney(1)|large_intestine(1)|lung(7)|skin(1)	10						TTACCTGGCCGATGTCCAGGT	0.572													G|||	1	0.000199681	8e-04	0	5008	,	,		21591	0		0	False		,,,				2504	0				p.I389I		Atlas-SNP	.											.	TTC22	40	.	0			c.C1167T						.						54	52	53					1																	55248004		692	1591	2283	SO:0001819	synonymous_variant	55001	exon6			CTGGCCGATGTCC	AK000626	CCDS598.1, CCDS44152.1	1p32.3	2013-01-11			ENSG00000006555	ENSG00000006555		"Tetratricopeptide (TTC) repeat domain containing"	26067	protein-coding gene	gene with protein product							Standard	NM_017904		Approved	FLJ20619	uc009vzt.1	Q5TAA0	OTTHUMG00000009916	ENST00000371276.4:c.1167C>T	chr1.hg19:g.55248004G>A		42.0	0.0		68.0	24.0	NM_001114108	Q9NWT4	Silent	SNP	ENST00000371276.4	hg19	CCDS44152.1																																																																																			.	.		0.572	TTC22-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027438.1	NM_017904		A	55248004	G	A	55248004	2	1	44	1	0	0	0	0	0	0	0	1	16704	1048	37	1		1	TTC22	1	55248004	Silent	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	11931245	55248004	194002617	13	5473										
NEGR1	257194	hgsc.bcm.edu	37	chr1	72058553	72058553	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcttgttggcagccacacagGtataattgccgaagtgctcc	11	11	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:72058553G>A	ENST00000357731.5	-	6	1126	c.887C>T	c.(886-888)aCc>aTc	p.T296I	NEGR1_ENST00000306821.3_Missense_Mutation_p.T168I|NEGR1_ENST00000434200.1_Missense_Mutation_p.T250I	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1	296	Ig-like C2-type 3.				feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|positive regulation of neuron projection development (GO:0010976)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(4)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		AGCCACACAGGTATAATTGCC	0.473																																					p.T296I		Atlas-SNP	.											NEGR1,ampulla_of_Vater,carcinoma,0,1	NEGR1	60	.	0			c.C887T						.						134	128	130					1																	72058553		2203	4300	6503	SO:0001583	missense	257194	exon6			ACACAGGTATAAT	AK092307	CCDS661.1	1p31.1	2013-01-11			ENSG00000172260	ENSG00000172260		"Immunoglobulin superfamily / I-set domain containing"	17302	protein-coding gene	gene with protein product	"a kindred of IgLON", "neurotractin", "IgLON family member 4"	613173				10075727	Standard	NM_173808		Approved	KILON, MGC46680, Ntra, IGLON4	uc001dfw.3	Q7Z3B1	OTTHUMG00000009698	ENST00000357731.5:c.887C>T	chr1.hg19:g.72058553G>A	ENSP00000350364:p.Thr296Ile	216.0	0.0		209.0	0.0	NM_173808	Q5VT21|Q6UY06|Q8N440|Q8NAQ3	Missense_Mutation	SNP	ENST00000357731.5	hg19	CCDS661.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939870	0.92526	.	.	ENSG00000172260	ENST00000357731;ENST00000306821;ENST00000434200	T;T;T	0.74947	-0.89;-0.89;-0.89	5.83	5.83	0.93111	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.83667	0.5304	M	0.67569	2.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82078	-0.0635	10	0.48119	T	0.1	-15.3455	20.1162	0.97934	0.0:0.0:1.0:0.0	.	250;296	B4DI94;Q7Z3B1	.;NEGR1_HUMAN	I	296;168;250	ENSP00000350364:T296I;ENSP00000305938:T168I;ENSP00000413294:T250I	ENSP00000305938:T168I	T	-	2	0	NEGR1	71831141	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	9.414000	0.97362	2.756000	0.94617	0.655000	0.94253	ACC	.	.		0.473	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4	NM_173808		A	72058553	G	A	72058553	3	1	44	1	0	0	0	0	1	0	0	0	10326	1261	44	3	185	3	NEGR1	1	72058553	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	16810549	72058553	177192068	14	5474										
USP33	23032	hgsc.bcm.edu	37	chr1	78183652	78183652	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggctgaagatccaagccttcTagcggaaatgaaacatgggt	12	8	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:78183652T>C	ENST00000370793.1	-	18	2257	c.1911A>G	c.(1909-1911)ctA>ctG	p.L637L	USP33_ENST00000370794.3_Silent_p.L606L|USP33_ENST00000370792.3_Silent_p.L629L|USP33_ENST00000357428.1_Silent_p.L637L	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	637	USP.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						CCAAGCCTTCTAGCGGAAATG	0.368																																					p.L637L	Melanoma(152;72 1870 11110 26780 42647)	Atlas-SNP	.											.	USP33	87	.	0			c.A1911G						.						124	130	128					1																	78183652		2203	4300	6503	SO:0001819	synonymous_variant	23032	exon18			GCCTTCTAGCGGA	AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"Ubiquitin-specific peptidases"	20059	protein-coding gene	gene with protein product		615146	"ubiquitin specific protease 33"			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.1911A>G	chr1.hg19:g.78183652T>C		193.0	0.0		175.0	84.0	NM_015017	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Silent	SNP	ENST00000370793.1	hg19	CCDS678.1	.	.	.	.	.	.	.	.	.	.	T	2.483	-0.319298	0.05386	.	.	ENSG00000077254	ENST00000481579	.	.	.	4.7	-3.18	0.05186	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.9442	0.35749	0.103:0.7222:0.0:0.1748	.	.	.	.	W	242	.	.	X	-	2	0	USP33	77956240	0.994000	0.37717	0.361000	0.25849	0.375000	0.29983	0.369000	0.20416	-0.751000	0.04734	-1.553000	0.00894	TAG	.	.		0.368	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017		C	78183652	T	C	78183652	2	2	44	1	0	0	0	0	0	0	0	1	17079	1509	53	2		2	USP33	1	78183652	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	6125099	78183652	171066969	15	5475										
CYR61	3491	hgsc.bcm.edu	37	chr1	86048133	86048133	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctcgcatcctatacaacccTttacaaggccagaaatgtat	5	13	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:86048133T>C	ENST00000451137.2	+	4	893	c.669T>C	c.(667-669)ccT>ccC	p.P223P		NM_001554.4	NP_001545.2	O00622	CYR61_HUMAN	cysteine-rich, angiogenic inducer, 61	223					anatomical structure morphogenesis (GO:0009653)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|chondroblast differentiation (GO:0060591)|chorio-allantoic fusion (GO:0060710)|extracellular matrix organization (GO:0030198)|intussusceptive angiogenesis (GO:0002041)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of apoptotic process (GO:0043066)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|reactive oxygen species metabolic process (GO:0072593)|regulation of cell growth (GO:0001558)|regulation of ERK1 and ERK2 cascade (GO:0070372)|ventricular septum development (GO:0003281)|wound healing, spreading of cells (GO:0044319)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|prostate(1)	5				all cancers(265;0.0216)|Epithelial(280;0.0441)		TATACAACCCTTTACAAGGCC	0.453											OREG0013583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P223P		Atlas-SNP	.											.	CYR61	18	.	0			c.T669C						.						89	84	86					1																	86048133		2203	4300	6503	SO:0001819	synonymous_variant	3491	exon4			CAACCCTTTACAA	AF031385	CCDS706.1	1p22.3	2008-02-05			ENSG00000142871	ENSG00000142871			2654	protein-coding gene	gene with protein product		602369		IGFBP10		9135077	Standard	NM_001554		Approved	GIG1, CCN1	uc001dle.3	O00622	OTTHUMG00000010577	ENST00000451137.2:c.669T>C	chr1.hg19:g.86048133T>C		100.0	0.0	1241	100.0	4.0	NM_001554	O14934|O43775|Q9BZL7	Silent	SNP	ENST00000451137.2	hg19	CCDS706.1																																																																																			.	.		0.453	CYR61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029187.1	NM_001554		C	86048133	T	C	86048133	2	2	44	1	0	0	0	0	0	0	0	1	4201	1596	56	2		2	CYR61	1	86048133	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	7864481	86048133	163202488	16	5476										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86913417	86913417	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cactgccacagttgagccagAgactggagatcctgttacgc	11	12	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:86913417A>G	ENST00000370565.4	+	11	2102	c.1940A>G	c.(1939-1941)gAg>gGg	p.E647G		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	647					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		GTTGAGCCAGAGACTGGAGAT	0.433																																					p.E647G	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.A1940G						.						83	80	81					1																	86913417		2203	4300	6503	SO:0001583	missense	9635	exon11			AGCCAGAGACTGG		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1940A>G	chr1.hg19:g.86913417A>G	ENSP00000359596:p.Glu647Gly	75.0	0.0		74.0	6.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	A	6.383	0.438750	0.12104	.	.	ENSG00000137975	ENST00000370565	T	0.33216	1.42	5.72	4.6	0.57074	Domain of unknown function DUF1973 (1);	0.252260	0.37623	N	0.002012	T	0.15392	0.0371	M	0.80422	2.495	0.09310	N	1	B	0.11235	0.004	B	0.17433	0.018	T	0.33214	-0.9877	10	0.52906	T	0.07	-9.1903	3.3521	0.07156	0.6491:0.1413:0.0739:0.1358	.	647	Q9UQC9	CLCA2_HUMAN	G	647	ENSP00000359596:E647G	ENSP00000359596:E647G	E	+	2	0	CLCA2	86686005	0.993000	0.37304	0.657000	0.29651	0.017000	0.09413	2.602000	0.46257	1.018000	0.39521	0.533000	0.62120	GAG	.	.		0.433	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		G	86913417	A	G	86913417	3	3	44	1	0	0	0	0	1	0	0	0	3460	304	11	2	1982	2	CLCA2	1	86913417	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	865284	86913417	162337204	17	5477										
HFM1	164045	hgsc.bcm.edu	37	chr1	91788716	91788716	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcttttcatttatccttaacTgtatatctagaaattccttg	3	8	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:91788716T>C	ENST00000370425.3	-	22	2566	c.2468A>G	c.(2467-2469)cAg>cGg	p.Q823R	HFM1_ENST00000370424.3_Missense_Mutation_p.Q502R|HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_Missense_Mutation_p.Q55R	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	823	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TATCCTTAACTGTATATCTAG	0.284																																					p.Q823R		Atlas-SNP	.											.	HFM1	188	.	0			c.A2468G						.						64	69	67					1																	91788716		2203	4278	6481	SO:0001583	missense	164045	exon22			CTTAACTGTATAT	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2468A>G	chr1.hg19:g.91788716T>C	ENSP00000359454:p.Gln823Arg	107.0	0.0		118.0	5.0	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	hg19	CCDS30769.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	5.258|5.258	0.233136|0.233136	0.09969|0.09969	.|.	.|.	ENSG00000162669|ENSG00000162669	ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421|ENST00000430465	T;T;T|.	0.59906|.	0.23;0.23;0.23|.	5.18|5.18	4.05|4.05	0.47172|0.47172	Sec63 domain (2);|.	0.064498|.	0.64402|.	D|.	0.000006|.	T|T	0.30479|0.30479	0.0766|0.0766	L|L	0.33293|0.33293	1|1	0.34702|0.34702	D|D	0.726858|0.726858	B;B;B|.	0.33448|.	0.021;0.412;0.116|.	B;B;B|.	0.37387|.	0.012;0.248;0.037|.	T|T	0.11227|0.11227	-1.0596|-1.0596	10|5	0.28530|.	T|.	0.3|.	.|.	10.8879|10.8879	0.46978|0.46978	0.0:0.074:0.0:0.926|0.0:0.074:0.0:0.926	.|.	502;78;823|.	A6NGI5;B1B0B5;A2PYH4|.	.;.;HFM1_HUMAN|.	R|G	823;55;502;507|79	ENSP00000359454:Q823R;ENSP00000294696:Q55R;ENSP00000359453:Q502R|.	ENSP00000294696:Q55R|.	Q|S	-|-	2|1	0|0	HFM1|HFM1	91561304|91561304	1.000000|1.000000	0.71417|0.71417	0.900000|0.900000	0.35374|0.35374	0.812000|0.812000	0.45895|0.45895	4.874000|4.874000	0.63064|0.63064	0.811000|0.811000	0.34303|0.34303	0.533000|0.533000	0.62120|0.62120	CAG|AGT	.	.		0.284	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		C	91788716	T	C	91788716	3	2	44	1	0	0	0	0	1	0	0	0	7092	1580	55	2	1911	2	HFM1	1	91788716	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4875299	91788716	157461905	18	5478										
MTF2	22823	hgsc.bcm.edu	37	chr1	93545089	93545089	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cactgaagtgaccgaatgagGtgagagaccttggcctggga	15	8	0	5			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:93545089G>T	ENST00000370298.4	+	1	294		c.e1+1		MTF2_ENST00000545708.1_Splice_Site|MTF2_ENST00000370303.4_Splice_Site|MTF2_ENST00000471953.1_Splice_Site|MTF2_ENST00000540243.1_Splice_Site	NM_001164392.1|NM_007358.3	NP_001157864.1|NP_031384	Q9Y483	MTF2_HUMAN	metal response element binding transcription factor 2						chromatin modification (GO:0016568)|negative regulation of histone H3-K27 methylation (GO:0061086)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|segment specification (GO:0007379)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)		ACCGAATGAGGTGAGAGACCT	0.557																																					.		Atlas-SNP	.											.	MTF2	51	.	0			c.5+1G>T						.						98	96	97					1																	93545089		2203	4300	6503	SO:0001630	splice_region_variant	22823	exon1			AATGAGGTGAGAG	AJ010014	CCDS742.1, CCDS53340.1, CCDS53341.1	1p22.1	2013-01-28			ENSG00000143033	ENSG00000143033		"Tudor domain containing", "Zinc fingers, PHD-type"	29535	protein-coding gene	gene with protein product	"polycomb-like 2", "tudor domain containing 19A"	609882				15563832	Standard	NM_007358		Approved	M96, PCL2, TDRD19A	uc009wdj.3	Q9Y483	OTTHUMG00000010161	ENST00000370298.4:c.5+1G>T	chr1.hg19:g.93545089G>T		124.0	0.0		104.0	53.0	NM_001164392	A6NGQ9|A8K2Q3|B1AKT5|B1AKT6|Q9UES9|Q9UP40	Splice_Site	SNP	ENST00000370298.4	hg19	CCDS742.1	.	.	.	.	.	.	.	.	.	.	g	14.22	2.470170	0.43839	.	.	ENSG00000143033	ENST00000370298;ENST00000370303	.	.	.	3.9	2.02	0.26589	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.2582	0.26189	0.0959:0.1707:0.7334:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MTF2	93317677	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.299000	0.65716	0.625000	0.30304	-0.372000	0.07161	.	.	.		0.557	MTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028075.3	NM_007358	Intron	T	93545089	G	T	93545089	5	4	44	1	0	0	0	0	0	0	1	0	9932	1275	44	3	8	3	MTF2	1	93545089	Splice_Site	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	1756373	93545089	155705532	19	5479										
STXBP3	6814	hgsc.bcm.edu	37	chr1	109342913	109342913	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgtccagcagtatggaatggTtcaggagctgtaaggtaaat	13	5	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:109342913T>C	ENST00000370008.3	+	17	1571	c.1521T>C	c.(1519-1521)ggT>ggC	p.G507G		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	507					blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		TATGGAATGGTTCAGGAGCTG	0.338																																					p.G507G		Atlas-SNP	.											.	STXBP3	44	.	0			c.T1521C						.						82	83	82					1																	109342913		2203	4300	6503	SO:0001819	synonymous_variant	6814	exon17			GAATGGTTCAGGA	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1521T>C	chr1.hg19:g.109342913T>C		60.0	0.0		84.0	4.0	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Silent	SNP	ENST00000370008.3	hg19	CCDS790.1																																																																																			.	.		0.338	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		C	109342913	T	C	109342913	2	2	44	1	0	0	0	0	0	0	0	1	15369	1712	60	2		2	STXBP3	1	109342913	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	15797824	109342913	139907708	20	5480										
KCNC4	3749	hgsc.bcm.edu	37	chr1	110775556	110775556	+	3'UTR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctgccaagacgccctctcgTccaactatgcccaggctgaa	8	17	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:110775556T>C	ENST00000369787.3	+	0	2560				KCNC4_ENST00000413138.3_3'UTR|KCNC4_ENST00000412512.2_Intron|KCNC4_ENST00000438661.2_Missense_Mutation_p.S615P	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4						potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(2)	32		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		CGCCCTCTCGTCCAACTATGC	0.557																																					p.S615P		Atlas-SNP	.											.	KCNC4	113	.	0			c.T1843C						.						60	63	62					1																	110775556		1991	4158	6149	SO:0001624	3_prime_UTR_variant	3749	exon4			CTCTCGTCCAACT	BC101769	CCDS821.1, CCDS44193.1	1p21	2012-07-05			ENSG00000116396	ENSG00000116396		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6236	protein-coding gene	gene with protein product		176265	"chromosome 1 open reading frame 30"	C1orf30		1920536, 1740329, 16382104	Standard	NM_004978		Approved	Kv3.4, HKSHIIIC	uc001dzh.3	Q03721	OTTHUMG00000011037	ENST00000369787.3:c.*625T>C	chr1.hg19:g.110775556T>C		117.0	0.0		120.0	5.0	NM_001039574	Q3MIM4|Q5TBI6	Missense_Mutation	SNP	ENST00000369787.3	hg19	CCDS821.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.652584	0.29336	.	.	ENSG00000116396	ENST00000438661	D	0.97378	-4.36	5.32	4.18	0.49190	.	.	.	.	.	D	0.86619	0.5976	.	.	.	0.24935	N	0.991897	B	0.02656	0.0	B	0.01281	0.0	T	0.78059	-0.2352	8	0.29301	T	0.29	.	4.2265	0.10582	0.1744:0.0972:0.0:0.7284	.	615	Q03721-3	.	P	615	ENSP00000393655:S615P	ENSP00000393655:S615P	S	+	1	0	KCNC4	110577079	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.502000	0.22594	1.026000	0.39733	0.533000	0.62120	TCC	.	.		0.557	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		C	110775556	T	C	110775556	1	2	44	0	1	0	0	0	0	0	0	0	8026	1667	58	2		2	KCNC4	1	110775556	3'UTR	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1432643	110775556	138475065	21	5481										
DENND2C	163259	hgsc.bcm.edu	37	chr1	115168554	115168554	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tttttgtttgatgtttttgcAgtggcttcttgacagtgtct	10	5	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:115168554A>G	ENST00000393274.1	-	4	677	c.52T>C	c.(52-54)Tgc>Cgc	p.C18R	DENND2C_ENST00000393276.3_Missense_Mutation_p.C18R|DENND2C_ENST00000393277.1_Missense_Mutation_p.C18R|DENND2C_ENST00000481894.1_5'Flank	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	18					positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATGTTTTTGCAGTGGCTTCTT	0.388																																					p.C18R		Atlas-SNP	.											.	DENND2C	105	.	0			c.T52C						.						108	110	110					1																	115168554		2203	4300	6503	SO:0001583	missense	163259	exon4			TTTTGCAGTGGCT		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"DENN/MADD domain containing"	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.52T>C	chr1.hg19:g.115168554A>G	ENSP00000376955:p.Cys18Arg	93.0	0.0		60.0	5.0	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Missense_Mutation	SNP	ENST00000393274.1	hg19	CCDS58018.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.194974	0.78902	.	.	ENSG00000175984	ENST00000393276;ENST00000393274;ENST00000369540;ENST00000393277	T;T;T	0.14766	2.48;3.09;2.87	5.71	5.71	0.89125	.	0.061327	0.64402	D	0.000002	T	0.24005	0.0581	L	0.56769	1.78	0.80722	D	1	D;P	0.76494	0.999;0.866	D;P	0.68621	0.959;0.576	T	0.00768	-1.1574	10	0.49607	T	0.09	.	16.0314	0.80579	1.0:0.0:0.0:0.0	.	18;18	Q68D51;Q68D51-3	DEN2C_HUMAN;.	R	18	ENSP00000376957:C18R;ENSP00000376955:C18R;ENSP00000376958:C18R	ENSP00000358553:C18R	C	-	1	0	DENND2C	114970077	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.311000	0.72835	2.187000	0.69744	0.524000	0.50904	TGC	.	.		0.388	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459		G	115168554	A	G	115168554	3	3	44	1	0	0	0	0	1	0	0	0	4432	188	7	2	2631	2	DENND2C	1	115168554	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	4392998	115168554	134082067	22	5482										
SYCP1	6847	hgsc.bcm.edu	37	chr1	115537378	115537378	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aggaacaataatccaccagcTtctcatctttgtgtcaaaac	5	11	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:115537378T>C	ENST00000369522.3	+	31	3003	c.2763T>C	c.(2761-2763)gcT>gcC	p.A921A	SYCP1_ENST00000477590.1_3'UTR|SYCP1_ENST00000369518.1_Silent_p.A921A	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	921					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATCCACCAGCTTCTCATCTTT	0.294																																					p.A921A		Atlas-SNP	.											.	SYCP1	149	.	0			c.T2763C						.						34	37	36					1																	115537378		2199	4289	6488	SO:0001819	synonymous_variant	6847	exon31			ACCAGCTTCTCAT	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2763T>C	chr1.hg19:g.115537378T>C		162.0	0.0		98.0	4.0	NM_003176	O14963|Q5VXJ6	Silent	SNP	ENST00000369522.3	hg19	CCDS879.1																																																																																			.	.		0.294	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		C	115537378	T	C	115537378	2	2	44	1	0	0	0	0	0	0	0	1	15446	1596	56	2		2	SYCP1	1	115537378	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	368824	115537378	133713243	23	5483										
CD101	9398	hgsc.bcm.edu	37	chr1	117556295	117556295	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gatcttctctctgggcccagAggatgaaggcgcctacagat	12	11	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:117556295A>G	ENST00000256652.4	+	4	1167	c.1109A>G	c.(1108-1110)gAg>gGg	p.E370G	CD101_ENST00000369470.1_Missense_Mutation_p.E370G	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	370	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CTGGGCCCAGAGGATGAAGGC	0.517																																					p.E370G		Atlas-SNP	.											.	CD101	95	.	0			c.A1109G						.						70	71	70					1																	117556295		2203	4300	6503	SO:0001583	missense	9398	exon4			GCCCAGAGGATGA	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.1109A>G	chr1.hg19:g.117556295A>G	ENSP00000256652:p.Glu370Gly	208.0	0.0		89.0	4.0	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	hg19	CCDS891.1	.	.	.	.	.	.	.	.	.	.	A	15.44	2.834369	0.50951	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.03181	4.02;4.02	5.85	4.72	0.59763	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.099909	0.43579	D	0.000548	T	0.06050	0.0157	L	0.60845	1.875	0.35926	D	0.832159	D	0.76494	0.999	D	0.68943	0.961	T	0.21552	-1.0242	10	0.44086	T	0.13	-14.7109	8.8907	0.35432	0.9156:0.0:0.0844:0.0	.	370	Q93033	IGSF2_HUMAN	G	370	ENSP00000256652:E370G;ENSP00000358482:E370G	ENSP00000256652:E370G	E	+	2	0	CD101	117357818	0.984000	0.35163	0.913000	0.36048	0.222000	0.24845	2.690000	0.47001	1.036000	0.39998	0.533000	0.62120	GAG	.	.		0.517	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		G	117556295	A	G	117556295	3	3	44	1	0	0	0	0	1	0	0	0	2964	304	11	2	1123	2	CD101	1	117556295	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2018917	117556295	131694326	24	5484										
ZNF697	90874	hgsc.bcm.edu	37	chr1	120168499	120168499	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atcccagctttctcctcaccTgtgcagatgtcgggcactgc	9	15	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:120168499T>C	ENST00000421812.2	-	2	344	c.225A>G	c.(223-225)acA>acG	p.T75T		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	75					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		TCTCCTCACCTGTGCAGATGT	0.507																																					p.T75T		Atlas-SNP	.											.	ZNF697	26	.	0			c.A225G						.						80	82	81					1																	120168499		1972	4140	6112	SO:0001630	splice_region_variant	90874	exon2			CTCACCTGTGCAG	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"Zinc fingers, C2H2-type"	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.226+1A>G	chr1.hg19:g.120168499T>C		125.0	0.0		80.0	4.0	NM_001080470	Q96IT2	Silent	SNP	ENST00000421812.2	hg19	CCDS44202.1																																																																																			.	.		0.507	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286	Silent	C	120168499	T	C	120168499	5	2	44	1	0	0	0	0	0	0	1	0	18115	1594	55	2	1420	2	ZNF697	1	120168499	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2612204	120168499	129082122	25	5485										
RFX5	5993	hgsc.bcm.edu	37	chr1	151318753	151318753	+	Frame_Shift_Del	DEL	C	C	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	caccacctgggggggcccttCccccagtcttggggctctta					rs569159154		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:151318753delC	ENST00000290524.4	-	3	222	c.44delG	c.(43-45)ggafs	p.G15fs	RFX5_ENST00000452513.2_Frame_Shift_Del_p.G15fs|RFX5_ENST00000452671.2_Frame_Shift_Del_p.G15fs|RFX5_ENST00000368870.2_Frame_Shift_Del_p.G15fs|RP11-126K1.6_ENST00000455503.1_RNA|RFX5_ENST00000478564.1_5'UTR	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	15					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GGGGGCCCTTCCCCCAGTCTT	0.557																																					p.G15fs		Atlas-INDEL	.											.	RFX5	69	.	0			c.45delA						.						85	89	88					1																	151318753		2203	4300	6503	SO:0001589	frameshift_variant	5993	exon3			.		CCDS994.1	1q21	2014-09-17			ENSG00000143390	ENSG00000143390			9986	protein-coding gene	gene with protein product		601863				9401005	Standard	XM_005245405		Approved		uc001exw.1	P48382	OTTHUMG00000012495	ENST00000290524.4:c.44delG	chr1.hg19:g.151318753delC	ENSP00000290524:p.Gly15fs	118.0	0.0		247.0	16.0	NM_000449	B7Z848|D3DV19|E9PFU4|Q5VWC3	Frame_Shift_Del	DEL	ENST00000290524.4	hg19	CCDS994.1																																																																																			.	.		0.557	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449		-	151318753	C	-	151318753	7	5	44	1	0	1	0	1	0	0	0	0	13281	855	30	0	1842	0	RFX5	1	151318753	Frame_Shift_Del	DEL	C	TCGA-BC-A3KG-01A-11D-A20W-10	31150254	151318753	97931868	26	5486										
KLHDC9	126823	hgsc.bcm.edu	37	chr1	161068355	161068355	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gccgtgcccccgggtcgggcCgcaggctcaggctgggcctg	18	16	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:161068355C>T	ENST00000368011.4	+	1	172	c.30C>T	c.(28-30)gcC>gcT	p.A10A	PFDN2_ENST00000468311.1_5'Flank|KLHDC9_ENST00000392192.2_Silent_p.A10A|KLHDC9_ENST00000490724.2_Intron	NM_152366.4	NP_689579.3	Q8NEP7	KLDC9_HUMAN	kelch domain containing 9	10										lung(5)|upper_aerodigestive_tract(1)	6	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			CGGGTCGGGCCGCAGGCTCAG	0.701																																					p.A10A		Atlas-SNP	.											.	KLHDC9	16	.	0			c.C30T						.						9	10	9					1																	161068355		2181	4250	6431	SO:0001819	synonymous_variant	126823	exon1			TCGGGCCGCAGGC	BC022077	CCDS30919.1, CCDS41425.1	1q23.3	2008-02-05			ENSG00000162755	ENSG00000162755			28489	protein-coding gene	gene with protein product	"kelch/ankyrin repeat containing cyclin A1 interacting protein"					15159402	Standard	NM_152366		Approved	KARCA1	uc001fxr.3	Q8NEP7	OTTHUMG00000031479	ENST00000368011.4:c.30C>T	chr1.hg19:g.161068355C>T		36.0	0.0		87.0	4.0	NM_001007255	Q5SY56|Q6NXT9|Q6PKN4|Q8N5E1|Q8NA16	Silent	SNP	ENST00000368011.4	hg19	CCDS30919.1																																																																																			.	.		0.701	KLHDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077092.1	NM_152366		T	161068355	C	T	161068355	2	4	44	1	0	0	0	0	0	0	0	1	8373	639	23	1		1	KLHDC9	1	161068355	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	9749602	161068355	88182266	27	5487										
NIT1	4817	hgsc.bcm.edu	37	chr1	161088600	161088600	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggcttcatcaccaggcctccTcacagattcctgtcccttct	6	17	4	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:161088600T>C	ENST00000368009.2	+	2	103	c.27T>C	c.(25-27)ccT>ccC	p.P9P	NIT1_ENST00000368007.4_Intron|DEDD_ENST00000489249.1_5'Flank|PFDN2_ENST00000368010.3_5'Flank|PFDN2_ENST00000468311.1_5'Flank|NIT1_ENST00000368008.1_Silent_p.P9P|NIT1_ENST00000496861.1_3'UTR|NIT1_ENST00000392190.5_5'UTR	NM_005600.2	NP_005591.1	Q86X76	NIT1_HUMAN	nitrilase 1	9					nitrogen compound metabolic process (GO:0006807)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	nitrilase activity (GO:0000257)			NS(1)|breast(2)|endometrium(2)|large_intestine(3)|lung(3)|prostate(1)	12	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			CCAGGCCTCCTCACAGATTCC	0.498																																					p.P9P		Atlas-SNP	.											.	NIT1	41	.	0			c.T27C						.						161	136	144					1																	161088600		2203	4300	6503	SO:0001819	synonymous_variant	4817	exon2			GCCTCCTCACAGA	AF069984	CCDS1218.1, CCDS53401.1, CCDS53402.1, CCDS53403.1	1q21-q22	2008-05-14			ENSG00000158793	ENSG00000158793			7828	protein-coding gene	gene with protein product		604618				9671749	Standard	NM_005600		Approved		uc001fxv.2	Q86X76	OTTHUMG00000031473	ENST00000368009.2:c.27T>C	chr1.hg19:g.161088600T>C		94.0	0.0		147.0	6.0	NM_001185092	B1AQP3|D3DVF4|O76091	Silent	SNP	ENST00000368009.2	hg19	CCDS1218.1																																																																																			.	.		0.498	NIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077060.1			C	161088600	T	C	161088600	2	2	44	1	0	0	0	0	0	0	0	1	10442	1538	54	2		2	NIT1	1	161088600	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	20245	161088600	88162021	28	5488										
NCF2	4688	hgsc.bcm.edu	37	chr1	183532683	183532683	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccgtgtacttgtagtgcaccTtgagtgtgtagggcatggga	15	7	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:183532683T>G	ENST00000367535.3	-	12	1315	c.1064A>C	c.(1063-1065)aAg>aCg	p.K355T	NCF2_ENST00000413720.1_Missense_Mutation_p.K310T|NCF2_ENST00000418089.1_Missense_Mutation_p.K274T|NCF2_ENST00000367536.1_Missense_Mutation_p.K355T|NCF2_ENST00000469280.1_5'UTR	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	355	OPR.				aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	GTAGTGCACCTTGAGTGTGTA	0.542																																					p.K355T		Atlas-SNP	.											.	NCF2	69	.	0			c.A1064C						.						124	106	112					1																	183532683		2203	4300	6503	SO:0001583	missense	4688	exon13			TGCACCTTGAGTG	BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"Tetratricopeptide (TTC) repeat domain containing"	7661	protein-coding gene	gene with protein product	"NADPH oxidase activator 2", "chronic granulomatous disease, autosomal 2"	608515	"neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.1064A>C	chr1.hg19:g.183532683T>G	ENSP00000356505:p.Lys355Thr	135.0	0.0		301.0	57.0	NM_001127651	B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Missense_Mutation	SNP	ENST00000367535.3	hg19	CCDS1356.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.218117	0.79464	.	.	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000413720;ENST00000418089;ENST00000367535;ENST00000420553;ENST00000419402	T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78	5.74	4.61	0.57282	Phox/Bem1p (2);	0.000000	0.85682	D	0.000000	T	0.68137	0.2968	M	0.83483	2.645	0.52501	D	0.999954	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.993;0.999;1.0	T	0.69412	-0.5152	10	0.49607	T	0.09	-55.1311	10.1685	0.42895	0.0:0.0752:0.0:0.9248	.	274;310;355	E9PHJ2;E9PHX3;P19878	.;.;NCF2_HUMAN	T	355;427;310;274;355;6;94	ENSP00000356506:K355T;ENSP00000399294:K310T;ENSP00000407217:K274T;ENSP00000356505:K355T;ENSP00000397228:K6T;ENSP00000406198:K94T	ENSP00000356505:K355T	K	-	2	0	NCF2	181799306	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.266000	0.65525	1.020000	0.39573	0.529000	0.55759	AAG	.	.		0.542	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1	NM_000433		G	183532683	T	G	183532683	3	3	44	1	0	0	0	0	1	0	0	0	10226	1609	56	5	532	5	NCF2	1	183532683	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	22444083	183532683	65717938	29	5489										
LRRN2	10446	hgsc.bcm.edu	37	chr1	204589102	204589102	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cacccaagctagcaagagtgGggccacgagaagcctcatgg	13	12	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:204589102G>A	ENST00000367175.1	-	1	2231	c.19C>T	c.(19-21)Cca>Tca	p.P7S	LRRN2_ENST00000367177.3_Missense_Mutation_p.P7S|LRRN2_ENST00000367176.3_Missense_Mutation_p.P7S|LRRN2_ENST00000496057.1_5'UTR			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	7			P -> L (in dbSNP:rs3789044).		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			AGCAAGAGTGGGGCCACGAGA	0.617																																					p.P7S		Atlas-SNP	.											LRRN2,brain,primitive_neuroectodermal_tumour-medulloblastoma,+2,1	LRRN2	81	.	0			c.C19T						.						14	16	15					1																	204589102		2186	4293	6479	SO:0001583	missense	10446	exon3			AGAGTGGGGCCAC	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"Immunoglobulin superfamily / I-set domain containing"	16914	protein-coding gene	gene with protein product	"leucine rich and ankyrin repeats 1", "fibronectin type III, immunoglobulin and leucine rich repeat domain 7"	605492	"leucine rich repeat neuronal 5"	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.19C>T	chr1.hg19:g.204589102G>A	ENSP00000356143:p.Pro7Ser	126.0	0.0		274.0	0.0	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	hg19	CCDS1448.1	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.513003	0.00975	.	.	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.16597	2.33;2.33;2.33	5.79	1.74	0.24563	.	0.360808	0.20218	N	0.096750	T	0.03915	0.0110	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42344	-0.9457	10	0.07644	T	0.81	.	4.6551	0.12613	0.2809:0.1776:0.5416:0.0	.	7	O75325	LRRN2_HUMAN	S	7	ENSP00000356144:P7S;ENSP00000356145:P7S;ENSP00000356143:P7S	ENSP00000356143:P7S	P	-	1	0	LRRN2	202855725	0.496000	0.26059	0.963000	0.40424	0.292000	0.27327	1.078000	0.30754	0.765000	0.33221	0.650000	0.86243	CCA	.	.		0.617	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338		A	204589102	G	A	204589102	3	1	44	1	0	0	0	0	1	0	0	0	9044	1232	43	3	2126	3	LRRN2	1	204589102	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	21056419	204589102	44661519	30	5490										
NFASC	23114	hgsc.bcm.edu	37	chr1	204971735	204971735	+	Frame_Shift_Del	DEL	A	A	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gttccccaggcaaccatacgAaaaaaactgtcccagttaag							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:204971735delA	ENST00000401399.1	+	26	3347	c.3148delA	c.(3148-3150)aaafs	p.K1051fs	NFASC_ENST00000367172.4_Frame_Shift_Del_p.K1158fs|NFASC_ENST00000404076.1_Intron|NFASC_ENST00000339876.6_Frame_Shift_Del_p.K1051fs|NFASC_ENST00000338586.6_Frame_Shift_Del_p.K1035fs|NFASC_ENST00000367169.4_Intron|NFASC_ENST00000495396.1_3'UTR|NFASC_ENST00000367171.4_Frame_Shift_Del_p.K1143fs|NFASC_ENST00000360049.4_Intron|NFASC_ENST00000367170.4_Frame_Shift_Del_p.K1079fs|NFASC_ENST00000539706.1_Intron|NFASC_ENST00000404907.1_Intron|NFASC_ENST00000513543.1_Intron|NFASC_ENST00000338515.6_Intron			O94856	NFASC_HUMAN	neurofascin	1158	Thr-rich.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CAACCATACGAAAAAAACTGT	0.537																																					p.T1049fs		Atlas-INDEL	.											.	NFASC	396	.	0			c.3147delG						.						59	55	56					1																	204971735		1567	3582	5149	SO:0001589	frameshift_variant	23114	exon27			.	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.3148delA	chr1.hg19:g.204971735delA	ENSP00000385637:p.Lys1051fs	112.0	0.0		212.0	16.0	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Frame_Shift_Del	DEL	ENST00000401399.1	hg19	CCDS53460.1																																																																																			.	.		0.537	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		-	204971735	A	-	204971735	7	5	44	1	0	1	0	1	0	0	0	0	10368	247	9	0	3659	0	NFASC	1	204971735	Frame_Shift_Del	DEL	A	TCGA-BC-A3KG-01A-11D-A20W-10	382633	204971735	44278886	31	5491										
C1orf116	79098	hgsc.bcm.edu	37	chr1	207196403	207196403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agtctgctctctttcctgggAgctggatggtgtgtggagct	15	8	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:207196403A>G	ENST00000359470.5	-	4	955	c.706T>C	c.(706-708)Tcc>Ccc	p.S236P	C1orf116_ENST00000461135.2_5'UTR	NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	236						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.S236P(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					CTTTCCTGGGAGCTGGATGGT	0.602																																					p.S236P		Atlas-SNP	.											C1orf116,caecum,carcinoma,+2,2	C1orf116	64	.	1	Substitution - Missense(1)	ovary(1)	c.T706C						.						182	183	183					1																	207196403		2203	4300	6503	SO:0001583	missense	79098	exon4			CCTGGGAGCTGGA		CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795			28667	protein-coding gene	gene with protein product	"specifically androgen-regulated gene"	611680				15525603, 9389513	Standard	NM_023938		Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.706T>C	chr1.hg19:g.207196403A>G	ENSP00000352447:p.Ser236Pro	95.0	1.0		170.0	7.0	NM_023938	C9JV41|Q658X3	Missense_Mutation	SNP	ENST00000359470.5	hg19	CCDS1475.1	.	.	.	.	.	.	.	.	.	.	A	8.930	0.963133	0.18583	.	.	ENSG00000182795	ENST00000359470	T	0.08984	3.03	5.03	-6.82	0.01698	.	1.195680	0.06276	N	0.696552	T	0.04048	0.0113	N	0.19112	0.55	0.09310	N	0.999994	B	0.02656	0.0	B	0.04013	0.001	T	0.43097	-0.9412	10	0.30854	T	0.27	2.6199	3.0472	0.06158	0.4839:0.1058:0.2938:0.1166	.	236	Q9BW04	SARG_HUMAN	P	236	ENSP00000352447:S236P	ENSP00000352447:S236P	S	-	1	0	C1orf116	205263026	0.001000	0.12720	0.001000	0.08648	0.013000	0.08279	-0.444000	0.06854	-0.988000	0.03489	-0.912000	0.02778	TCC	.	.		0.602	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088973.1	NM_024115		G	207196403	A	G	207196403	3	3	44	1	0	0	0	0	1	0	0	0	1991	304	11	2	1103	2	C1orf116	1	207196403	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2224668	207196403	42054218	32	5492										
PARP1	142	hgsc.bcm.edu	37	chr1	226570841	226570841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gggggaatatacggtcctgtTttttaaccttcaatttcttg	9	7	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:226570841T>C	ENST00000366794.5	-	8	1198	c.1055A>G	c.(1054-1056)aAa>aGa	p.K352R		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	352					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		ACGGTCCTGTTTTTTAACCTT	0.502								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.K352R		Atlas-SNP	.											PARP1,NS,carcinoma,0,1	PARP1	100	.	0			c.A1055G						.						115	143	134					1																	226570841		2203	4300	6503	SO:0001583	missense	142	exon8			TCCTGTTTTTTAA	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"Poly (ADP-ribose) polymerases"	270	protein-coding gene	gene with protein product		173870	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)", "poly (ADP-ribose) polymerase family, member 1"	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.1055A>G	chr1.hg19:g.226570841T>C	ENSP00000355759:p.Lys352Arg	86.0	0.0		251.0	0.0	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	hg19	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	T	8.952	0.968513	0.18659	.	.	ENSG00000143799	ENST00000366794	T	0.10192	2.9	5.27	2.95	0.34219	.	0.147960	0.64402	N	0.000015	T	0.04724	0.0128	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42258	-0.9462	10	0.15952	T	0.53	-10.5467	7.8417	0.29402	0.0:0.2327:0.0:0.7673	.	352	P09874	PARP1_HUMAN	R	352	ENSP00000355759:K352R	ENSP00000355759:K352R	K	-	2	0	PARP1	224637464	0.897000	0.30589	0.987000	0.45799	0.573000	0.36030	0.922000	0.28734	0.323000	0.23307	0.459000	0.35465	AAA	.	.		0.502	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		C	226570841	T	C	226570841	3	2	44	1	0	0	0	0	1	0	0	0	11463	1841	64	2	2053	2	PARP1	1	226570841	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	19374438	226570841	22679780	33	5493										
OR2C3	81472	hgsc.bcm.edu	37	chr1	247695757	247695757	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtttctagtgagggtcgtgtGgagaagcccaggaggacaaa	16	6	1	2	rs61746303|rs386641879	byFrequency	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr1:247695757G>C	ENST00000366487.3	-	2	418	c.57C>G	c.(55-57)tcC>tcG	p.S19S	GCSAML_ENST00000531662.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000366489.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S19S(1)|p.S18S(1)		breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			AGGGTCGTGTGGAGAAGCCCA	0.488																																					p.S19S		Atlas-SNP	.											OR2C3,NS,carcinoma,0,2	OR2C3	92	.	2	Substitution - coding silent(2)	prostate(2)	c.C57G						.						78	73	74					1																	247695757		2203	4300	6503	SO:0001819	synonymous_variant	81472	exon2			TCGTGTGGAGAAG	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"GPCR / Class A : Olfactory receptors"	15005	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily C, member 4"	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.57C>G	chr1.hg19:g.247695757G>C		149.0	0.0		446.0	0.0	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Silent	SNP	ENST00000366487.3	hg19	CCDS1634.2																																																																																			.	G|0.996;A|0.004		0.488	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074		C	247695757	G	C	247695757	2	2	44	1	0	0	0	0	0	0	0	1	11002	1335	47	4		4	OR2C3	1	247695757	Silent	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	21124916	247695757	1554864	34	5494										
NOL10	79954	hgsc.bcm.edu	37	chr2	10729763	10729763	+	Frame_Shift_Del	DEL	T	T	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttcttccttttttcactaaTttttgaaacaagtggattca							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:10729763delT	ENST00000381685.5	-	18	1642	c.1537delA	c.(1537-1539)attfs	p.I513fs	NOL10_ENST00000542668.1_Frame_Shift_Del_p.I463fs|NOL10_ENST00000538384.1_Frame_Shift_Del_p.I487fs|NOL10_ENST00000345985.3_Frame_Shift_Del_p.I463fs|AC092687.5_ENST00000414538.1_RNA	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	513						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		TTTTCACTAATTTTTGAAACA	0.343																																					p.I513fs		Atlas-INDEL	.											.	NOL10	22	.	0			c.1538delT						.						77	73	74					2																	10729763		2200	4296	6496	SO:0001589	frameshift_variant	79954	exon18			.	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"polyglutamine binding protein 5"	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1537delA	chr2.hg19:g.10729763delT	ENSP00000371101:p.Ile513fs	120.0	0.0		140.0	10.0	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Frame_Shift_Del	DEL	ENST00000381685.5	hg19	CCDS1673.2																																																																																			.	.		0.343	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894		-	10729763	T	-	10729763	7	5	44	1	0	1	0	1	0	0	0	0	10529	1493	52	0	545	0	NOL10	2	10729763	Frame_Shift_Del	DEL	T	TCGA-BC-A3KG-01A-11D-A20W-10		10729763	232469610	35	5495										
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37455073	37455073	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agtagcctttctacttcaccAgacacaactcctttcatatt	3	13	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:37455073A>G	ENST00000234170.5	-	2	1408	c.1263T>C	c.(1261-1263)tcT>tcC	p.S421S		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	421					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				CTACTTCACCAGACACAACTC	0.378																																					p.S421S		Atlas-SNP	.											.	CEBPZ	68	.	0			c.T1263C						.						118	120	119					2																	37455073		2202	4300	6502	SO:0001819	synonymous_variant	10153	exon2			TTCACCAGACACA	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1263T>C	chr2.hg19:g.37455073A>G		128.0	0.0		135.0	6.0	NM_005760	Q8NE75	Silent	SNP	ENST00000234170.5	hg19	CCDS1787.1																																																																																			.	.		0.378	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		G	37455073	A	G	37455073	2	3	44	1	0	0	0	0	0	0	0	1	3206	175	7	2		2	CEBPZ	2	37455073	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	26725310	37455073	205744300	36	5496										
UGP2	7360	hgsc.bcm.edu	37	chr2	64112780	64112780	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcaaaggacgtgtcttactcAggggaaaatacagaagcttg	12	7	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:64112780A>G	ENST00000337130.5	+	6	1109	c.633A>G	c.(631-633)tcA>tcG	p.S211S	UGP2_ENST00000394417.2_Silent_p.S200S|UGP2_ENST00000487469.1_3'UTR|UGP2_ENST00000445915.2_Silent_p.S220S|UGP2_ENST00000467648.2_Silent_p.S200S|ACA59_ENST00000515966.1_RNA	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	211					carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)			endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						TGTCTTACTCAGGGGAAAATA	0.383																																					p.S211S		Atlas-SNP	.											.	UGP2	38	.	0			c.A633G						.						146	159	154					2																	64112780		2203	4300	6503	SO:0001819	synonymous_variant	7360	exon6			TTACTCAGGGGAA		CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"UDP-glucose pyrophosphorylase 1"	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.633A>G	chr2.hg19:g.64112780A>G		69.0	0.0		70.0	5.0	NM_006759	Q07131|Q0P6K2|Q86Y81|Q9BU15	Silent	SNP	ENST00000337130.5	hg19	CCDS1875.1																																																																																			.	.		0.383	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759		G	64112780	A	G	64112780	2	3	44	1	0	0	0	0	0	0	0	1	16958	175	7	2		2	UGP2	2	64112780	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	26657707	64112780	179086593	37	5497										
C2orf68	388969	hgsc.bcm.edu	37	chr2	85836675	85836675	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgctgctttcaccggactcTtcatagtctgggttgcgtgg	12	11	4	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:85836675T>C	ENST00000306336.5	-	3	305	c.261A>G	c.(259-261)gaA>gaG	p.E87E	USP39_ENST00000450066.2_5'Flank|C2orf68_ENST00000478626.1_5'Flank|USP39_ENST00000459775.1_Intron	NM_001013649.3	NP_001013671.2	Q2NKX9	CB068_HUMAN	chromosome 2 open reading frame 68	87										breast(1)|central_nervous_system(1)|endometrium(1)	3						CACCGGACTCTTCATAGTCTG	0.542																																					p.E87E		Atlas-SNP	.											.	C2orf68	5	.	0			c.A261G						.						123	125	124					2																	85836675		1964	4158	6122	SO:0001819	synonymous_variant	388969	exon3			GGACTCTTCATAG		CCDS42704.1	2p11.2	2008-07-18			ENSG00000168887	ENSG00000168887			34353	protein-coding gene	gene with protein product							Standard	NM_001013649		Approved		uc002sqc.2	Q2NKX9	OTTHUMG00000153088	ENST00000306336.5:c.261A>G	chr2.hg19:g.85836675T>C		95.0	0.0		75.0	4.0	NM_001013649	B4DT10|Q4G0J7|Q6ZVA6	Silent	SNP	ENST00000306336.5	hg19	CCDS42704.1																																																																																			.	.		0.542	C2orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329451.1	NM_001013649		C	85836675	T	C	85836675	2	2	44	1	0	0	0	0	0	0	0	1	2189	1606	56	2		2	C2orf68	2	85836675	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	21723895	85836675	157362698	38	5498										
KDM3A	55818	hgsc.bcm.edu	37	chr2	86693761	86693761	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acctacaaaggcttcttctaAggcagaattggaaattgcca	8	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:86693761A>G	ENST00000409556.1	+	11	1639	c.1274A>G	c.(1273-1275)aAg>aGg	p.K425R	KDM3A_ENST00000542128.1_Missense_Mutation_p.K373R|KDM3A_ENST00000312912.5_Missense_Mutation_p.K425R|KDM3A_ENST00000409064.1_Missense_Mutation_p.K425R|KDM3A_ENST00000485171.1_3'UTR			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	425					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						GCTTCTTCTAAGGCAGAATTG	0.463																																					p.K425R	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.A1274G						.						141	135	137					2																	86693761		2203	4300	6503	SO:0001583	missense	55818	exon10			CTTCTAAGGCAGA	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"Chromatin-modifying enzymes / K-demethylases"	20815	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 2A"	611512	"jumonji domain containing 1", "jumonji domain containing 1A"	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.1274A>G	chr2.hg19:g.86693761A>G	ENSP00000386660:p.Lys425Arg	137.0	0.0		146.0	6.0	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	hg19	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	A	0.613	-0.824114	0.02755	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	5.81	-2.25	0.06888	.	1.344860	0.04482	N	0.377894	T	0.31734	0.0806	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.05852	-1.0860	10	0.13470	T	0.59	.	0.628	0.00789	0.3337:0.1076:0.2202:0.3384	.	373;425	F5H070;Q9Y4C1	.;KDM3A_HUMAN	R	425;425;425;425;373	ENSP00000386660:K425R;ENSP00000323659:K425R;ENSP00000386516:K425R;ENSP00000438324:K373R	ENSP00000323659:K425R	K	+	2	0	KDM3A	86547272	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-0.578000	0.05841	-0.735000	0.04837	-1.450000	0.01041	AAG	.	.		0.463	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		G	86693761	A	G	86693761	3	3	44	1	0	0	0	0	1	0	0	0	8135	72	3	2	1308	2	KDM3A	2	86693761	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	857086	86693761	156505612	39	5499										
CCDC93	54520	hgsc.bcm.edu	37	chr2	118677924	118677924	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cacggctggggatgttcaggAggccttcgctttcaccttgg	14	11	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:118677924A>G	ENST00000376300.2	-	24	2028	c.1891T>C	c.(1891-1893)Tcc>Ccc	p.S631P	CCDC93_ENST00000319432.5_Missense_Mutation_p.S630P|HTR5BP_ENST00000434708.1_RNA	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	631										breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						GATGTTCAGGAGGCCTTCGCT	0.483																																					p.S631P		Atlas-SNP	.											.	CCDC93	70	.	0			c.T1891C						.						98	92	94					2																	118677924		2203	4300	6503	SO:0001583	missense	54520	exon24			TTCAGGAGGCCTT	BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.1891T>C	chr2.hg19:g.118677924A>G	ENSP00000365477:p.Ser631Pro	51.0	0.0		56.0	5.0	NM_019044	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Missense_Mutation	SNP	ENST00000376300.2	hg19	CCDS2121.2	.	.	.	.	.	.	.	.	.	.	A	20.6	4.015326	0.75161	.	.	ENSG00000125633	ENST00000376300;ENST00000319432	T;T	0.20332	2.08;2.08	4.83	4.83	0.62350	.	0.061141	0.64402	D	0.000002	T	0.16981	0.0408	N	0.16478	0.41	0.34455	D	0.701096	D	0.54397	0.966	P	0.47299	0.543	T	0.21109	-1.0255	10	0.66056	D	0.02	.	10.6937	0.45886	1.0:0.0:0.0:0.0	.	631	Q567U6	CCD93_HUMAN	P	631;630	ENSP00000365477:S631P;ENSP00000324135:S630P	ENSP00000324135:S630P	S	-	1	0	CCDC93	118394394	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.756000	0.62205	2.021000	0.59480	0.482000	0.46254	TCC	.	.		0.483	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044		G	118677924	A	G	118677924	3	3	44	1	0	0	0	0	1	0	0	0	2874	304	11	2	8	2	CCDC93	2	118677924	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	31984163	118677924	124521449	40	5500										
UPP2	151531	hgsc.bcm.edu	37	chr2	158958553	158958553	+	5'UTR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttcttgacatcaatttaaggTgacttttcacatagtagaga	7	6	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:158958553T>C	ENST00000005756.4	+	0	172				UPP2_ENST00000460456.1_3'UTR|UPP2_ENST00000409859.4_Splice_Site_p.V50A|UPP2_ENST00000605860.1_Splice_Site_p.V50A	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2						nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	CAATTTAAGGTGACTTTTCAC	0.353																																					p.V50A		Atlas-SNP	.											.	UPP2	60	.	0			c.T149C						.						122	130	128					2																	158958553		2203	4300	6503	SO:0001623	5_prime_UTR_variant	151531	exon3			TTAAGGTGACTTT	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.-23T>C	chr2.hg19:g.158958553T>C		140.0	0.0		146.0	6.0	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	hg19	CCDS2207.1	.	.	.	.	.	.	.	.	.	.	T	5.147	0.212677	0.09757	.	.	ENSG00000007001	ENST00000409859	T	0.35605	1.3	4.42	-3.51	0.04696	.	.	.	.	.	T	0.16128	0.0388	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.25398	-1.0133	6	0.24483	T	0.36	.	0.0738	0.00025	0.3194:0.1998:0.1637:0.3171	.	.	.	.	A	50	ENSP00000387230:V50A	ENSP00000387230:V50A	V	+	2	0	UPP2	158666799	0.624000	0.27102	0.000000	0.03702	0.001000	0.01503	-0.108000	0.10857	-0.533000	0.06323	-0.256000	0.11100	GTG	.	.		0.353	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355		C	158958553	T	C	158958553	1	2	44	0	1	0	0	0	0	0	0	0	17028	1710	59	2		2	UPP2	2	158958553	5'UTR	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	40280629	158958553	84240820	41	5501										
TANC1	85461	hgsc.bcm.edu	37	chr2	159954261	159954261	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tatagggtgagcttggccaaAggtgtctcgatgtctctgcc	13	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:159954261A>G	ENST00000263635.6	+	4	411	c.174A>G	c.(172-174)aaA>aaG	p.K58K	TANC1_ENST00000454300.1_Silent_p.K58K	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	58					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GCTTGGCCAAAGGTGTCTCGA	0.522																																					p.K58K		Atlas-SNP	.											.	TANC1	157	.	0			c.A174G						.						171	162	165					2																	159954261		2029	4174	6203	SO:0001819	synonymous_variant	85461	exon4			GGCCAAAGGTGTC	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.174A>G	chr2.hg19:g.159954261A>G		104.0	0.0		95.0	4.0	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	hg19	CCDS42766.1																																																																																			.	.		0.522	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			G	159954261	A	G	159954261	2	3	44	1	0	0	0	0	0	0	0	1	15559	69	3	2		2	TANC1	2	159954261	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	995708	159954261	83245112	42	5502										
GRB14	2888	hgsc.bcm.edu	37	chr2	165350955	165350955	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acttactggtataatttgaaAgtgctttattttttgtccat	6	5	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:165350955A>G	ENST00000263915.3	-	13	2000	c.1462T>C	c.(1462-1464)Ttt>Ctt	p.F488L	GRB14_ENST00000543549.1_Missense_Mutation_p.F401L|GRB14_ENST00000497306.1_Intron	NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	488	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						ATAATTTGAAAGTGCTTTATT	0.333																																					p.F488L		Atlas-SNP	.											.	GRB14	73	.	0			c.T1462C						.						140	145	143					2																	165350955		2203	4300	6503	SO:0001583	missense	2888	exon13			TTTGAAAGTGCTT		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.1462T>C	chr2.hg19:g.165350955A>G	ENSP00000263915:p.Phe488Leu	152.0	0.0		164.0	7.0	NM_004490	B7Z7F9|Q7Z6I1	Missense_Mutation	SNP	ENST00000263915.3	hg19	CCDS2222.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.253284	0.80135	.	.	ENSG00000115290	ENST00000263915;ENST00000543549	D;D	0.89050	-2.46;-2.46	5.38	5.38	0.77491	SH2 motif (5);	0.045758	0.85682	D	0.000000	D	0.88804	0.6536	L	0.60845	1.875	0.58432	D	0.999998	B;P	0.36909	0.133;0.573	B;B	0.40982	0.117;0.345	D	0.89569	0.3812	10	0.66056	D	0.02	-11.0512	15.6864	0.77415	1.0:0.0:0.0:0.0	.	401;488	B7Z7F9;Q14449	.;GRB14_HUMAN	L	488;401	ENSP00000263915:F488L;ENSP00000443699:F401L	ENSP00000263915:F488L	F	-	1	0	GRB14	165059201	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.295000	0.78780	2.175000	0.68902	0.533000	0.62120	TTT	.	.		0.333	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			G	165350955	A	G	165350955	3	3	44	1	0	0	0	0	1	0	0	0	6766	72	3	2	168	2	GRB14	2	165350955	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	5396694	165350955	77848418	43	5503										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166854614	166854614	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aggttcaaggtgaagaaggaCccaaagatgatgaaaataac	11	5	1	5			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:166854614C>T	ENST00000303395.4	-	23	4409	c.4410G>A	c.(4408-4410)ggG>ggA	p.G1470G	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Silent_p.G1459G|SCN1A_ENST00000409050.1_Silent_p.G1442G|SCN1A_ENST00000423058.2_Silent_p.G1470G			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1470			G -> W (in EIEE6; dbSNP:rs121917924). {ECO:0000269|PubMed:17561957}.		adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGAAGAAGGACCCAAAGATGA	0.338																																					p.G1470G		Atlas-SNP	.											.	SCN1A	641	.	0			c.G4410A						.						90	81	84					2																	166854614		2203	4292	6495	SO:0001819	synonymous_variant	6323	exon23			GAAGGACCCAAAG	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.4410G>A	chr2.hg19:g.166854614C>T		254.0	0.0		227.0	105.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166854614	C	T	166854614	2	4	44	1	0	0	0	0	0	0	0	1	13929	494	18	3		3	SCN1A	2	166854614	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1503659	166854614	76344759	44	5504										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167318900	167318900	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aatttctctctgttcttaccTggtgataaagtacttcaggg	8	8	4	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:167318900T>C	ENST00000409855.1	-	9	1208	c.1082A>G	c.(1081-1083)cAg>cGg	p.Q361R		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	361				Q -> L (in Ref. 1; AAA59899). {ECO:0000305}.	membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TGTTCTTACCTGGTGATAAAG	0.368																																					p.Q361R		Atlas-SNP	.											.	SCN7A	410	.	0			c.A1082G						.						52	47	49					2																	167318900		1839	4099	5938	SO:0001630	splice_region_variant	6332	exon9			CTTACCTGGTGAT	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.1083+1A>G	chr2.hg19:g.167318900T>C		116.0	0.0		120.0	5.0	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	hg19	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	16.68	3.191161	0.58017	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992;ENST00000441411	D;D;D	0.97328	-4.34;-4.34;-4.34	4.14	4.14	0.48551	Ion transport (1);	0.000000	0.45361	D	0.000368	D	0.97670	0.9236	M	0.76170	2.325	0.31735	N	0.636589	D	0.64830	0.994	D	0.76575	0.988	D	0.96468	0.9346	10	0.66056	D	0.02	.	7.2748	0.26277	0.313:0.0:0.0:0.687	.	361	Q01118	SCN7A_HUMAN	R	361	ENSP00000386796:Q361R;ENSP00000413699:Q361R;ENSP00000403846:Q361R	ENSP00000259060:Q361R	Q	-	2	0	SCN7A	167027146	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	1.352000	0.34033	1.626000	0.50381	0.397000	0.26171	CAG	.	.		0.368	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		Missense_Mutation	C	167318900	T	C	167318900	5	2	44	1	0	0	0	0	0	0	1	0	13938	1594	55	2	4034	2	SCN7A	2	167318900	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	464286	167318900	75880473	45	5505										
KLHL23	151230	hgsc.bcm.edu	37	chr2	170592618	170592618	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	caggtattaccactgtgcagTcaccttgggtggctgtgtct	12	10	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:170592618T>C	ENST00000392647.2	+	2	1338	c.1094T>C	c.(1093-1095)gTc>gCc	p.V365A	KLHL23_ENST00000602521.1_Intron|KLHL23_ENST00000272797.4_Missense_Mutation_p.V365A	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	365										breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						CACTGTGCAGTCACCTTGGGT	0.443																																					p.V365A		Atlas-SNP	.											.	KLHL23	52	.	0			c.T1094C						.						191	185	187					2																	170592618		2203	4300	6503	SO:0001583	missense	151230	exon2			GTGCAGTCACCTT	BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160		"Kelch-like", "BTB/POZ domain containing"	27506	protein-coding gene	gene with protein product			"kelch-like 23 (Drosophila)"				Standard	NM_144711		Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000392647.2:c.1094T>C	chr2.hg19:g.170592618T>C	ENSP00000376419:p.Val365Ala	111.0	0.0		108.0	5.0	NM_144711	Q8N9B9|Q96FT8	Missense_Mutation	SNP	ENST00000392647.2	hg19	CCDS2236.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.572641	0.45798	.	.	ENSG00000213160	ENST00000272797;ENST00000392647;ENST00000437875	T;T;T	0.78126	-1.15;-1.15;-1.15	5.8	5.8	0.92144	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.62295	0.2416	N	0.11724	0.165	0.30790	N	0.7410129999999999	B	0.20052	0.041	B	0.31101	0.124	T	0.59894	-0.7368	9	0.02654	T	1	.	16.1508	0.81622	0.0:0.0:0.0:1.0	.	365	Q8NBE8	KLH23_HUMAN	A	365;365;186	ENSP00000272797:V365A;ENSP00000376419:V365A;ENSP00000394732:V186A	ENSP00000272797:V365A	V	+	2	0	KLHL23	170300864	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.264000	0.72527	2.207000	0.71202	0.528000	0.53228	GTC	.	.		0.443	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711		C	170592618	T	C	170592618	3	2	44	1	0	0	0	0	1	0	0	0	8387	1667	58	2	1096	2	KLHL23	2	170592618	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	3273718	170592618	72606755	46	5506										
TTN	7273	hgsc.bcm.edu	37	chr2	179454987	179454987	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcggatagtttggcctactcTcacggtaataacatcacgac	9	11	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:179454987T>C	ENST00000591111.1	-	254	56766	c.56542A>G	c.(56542-56544)Aga>Gga	p.R18848G	TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R11549G|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R11616G|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R20489G|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R17921G|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R11424G|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589907.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18848	Ig-like 107.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGGCCTACTCTCACGGTAATA	0.443																																					p.R20489G		Atlas-SNP	.											.	TTN	18412	.	0			c.A61465G						.						199	181	187					2																	179454987		1958	4145	6103	SO:0001583	missense	7273	exon304			CTACTCTCACGGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.56542A>G	chr2.hg19:g.179454987T>C	ENSP00000465570:p.Arg18848Gly	174.0	0.0		158.0	7.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	7.630	0.678731	0.14841	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.96	1.93	0.25924	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.80747	0.4682	M	0.78916	2.43	0.50171	D	0.999851	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.82957	-0.0199	9	0.87932	D	0	.	14.5767	0.68252	0.0:0.0:0.483:0.517	.	11424;11549;11616;18848	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	17921;11424;11616;11549;11422	ENSP00000343764:R17921G;ENSP00000434586:R11424G;ENSP00000340554:R11616G;ENSP00000352154:R11549G	ENSP00000340554:R11616G	R	-	1	2	TTN	179163233	0.987000	0.35691	0.651000	0.29564	0.872000	0.50106	1.935000	0.40173	0.454000	0.26884	0.533000	0.62120	AGA	.	.		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179454987	T	C	179454987	3	2	44	1	0	0	0	0	1	0	0	0	16750	1559	54	2	46750	2	TTN	2	179454987	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	8862369	179454987	63744386	47	5507										
TTN	7273	hgsc.bcm.edu	37	chr2	179596303	179596303	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcgatcttctttatgaaggaTgggggttctaacagaagaat	11	5	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:179596303T>C	ENST00000591111.1	-	57	16463	c.16239A>G	c.(16237-16239)ccA>ccG	p.P5413P	TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.P5730P|TTN_ENST00000342992.6_Silent_p.P4486P|TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	12231	Ig-like 35.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTATGAAGGATGGGGGTTCTA	0.468																																					p.P5730P		Atlas-SNP	.											.	TTN	18412	.	0			c.A17190G						.						36	36	36					2																	179596303		1854	4092	5946	SO:0001819	synonymous_variant	7273	exon59			GAAGGATGGGGGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.16239A>G	chr2.hg19:g.179596303T>C		66.0	0.0		62.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179596303	T	C	179596303	2	2	44	1	0	0	0	0	0	0	0	1	16750	1451	51	2		2	TTN	2	179596303	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	141316	179596303	63603070	48	5508										
TTN	7273	hgsc.bcm.edu	37	chr2	179632568	179632568	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttgacacgttgcctcctgccAccactgtgtacttcccagca	7	16	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:179632568A>G	ENST00000591111.1	-	40	9613	c.9389T>C	c.(9388-9390)gTg>gCg	p.V3130A	TTN_ENST00000359218.5_Missense_Mutation_p.V3084A|TTN_ENST00000360870.5_Missense_Mutation_p.V3130A|TTN_ENST00000342175.6_Missense_Mutation_p.V3084A|TTN_ENST00000589042.1_Missense_Mutation_p.V3130A|TTN_ENST00000342992.6_Missense_Mutation_p.V3130A|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V3084A|TTN-AS1_ENST00000610005.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13462	Ig-like 18.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCTCCTGCCACCACTGTGTA	0.443																																					p.V3130A		Atlas-SNP	.											.	TTN	18412	.	0			c.T9389C						.						105	107	106					2																	179632568		2203	4300	6503	SO:0001583	missense	7273	exon40			CCTGCCACCACTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.9389T>C	chr2.hg19:g.179632568A>G	ENSP00000465570:p.Val3130Ala	107.0	0.0		117.0	5.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.20	3.329921	0.60743	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	6.03	6.03	0.97812	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.82522	0.5055	M	0.79614	2.46	0.40108	D	0.976456	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.83275	0.994;0.994;0.994;0.994;0.996	D	0.85171	0.0998	9	0.87932	D	0	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	3084;3084;3084;3130;3130	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	A	3130;3084;3084;3084;3084;3130	ENSP00000343764:V3130A;ENSP00000434586:V3084A;ENSP00000340554:V3084A;ENSP00000352154:V3084A;ENSP00000354117:V3130A	ENSP00000340554:V3084A	V	-	2	0	TTN	179340813	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	8.962000	0.93254	2.302000	0.77476	0.533000	0.62120	GTG	.	.		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179632568	A	G	179632568	3	3	44	1	0	0	0	0	1	0	0	0	16750	159	6	2	101891	2	TTN	2	179632568	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	36265	179632568	63566805	49	5509										
TTN	7273	hgsc.bcm.edu	37	chr2	179642440	179642440	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atcacgcttaccatcatgaaAccagaacgtctctggcatag	7	12	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:179642440A>G	ENST00000591111.1	-	25	4695	c.4471T>C	c.(4471-4473)Ttt>Ctt	p.F1491L	TTN_ENST00000359218.5_Missense_Mutation_p.F1445L|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.F1491L|TTN_ENST00000342175.6_Missense_Mutation_p.F1445L|TTN_ENST00000589042.1_Missense_Mutation_p.F1491L|TTN_ENST00000342992.6_Missense_Mutation_p.F1491L|TTN_ENST00000460472.2_Missense_Mutation_p.F1445L			Q8WZ42	TITIN_HUMAN	titin	12357	Ig-like 6.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCATCATGAAACCAGAACGTC	0.323																																					p.F1491L		Atlas-SNP	.											.	TTN	18412	.	0			c.T4471C						.						80	77	78					2																	179642440		2203	4300	6503	SO:0001583	missense	7273	exon25			CATGAAACCAGAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.4471T>C	chr2.hg19:g.179642440A>G	ENSP00000465570:p.Phe1491Leu	59.0	0.0		77.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.40	3.380327	0.61845	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;-0.69	5.8	5.8	0.92144	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.75946	0.3919	N	0.21373	0.66	0.40716	D	0.982619	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.85130	0.992;0.992;0.992;0.992;0.997	T	0.80221	-0.1472	9	0.87932	D	0	.	16.1547	0.81649	1.0:0.0:0.0:0.0	.	1445;1445;1445;1491;1491	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	L	1491;1445;1445;1445;1445;1491	ENSP00000343764:F1491L;ENSP00000434586:F1445L;ENSP00000340554:F1445L;ENSP00000352154:F1445L;ENSP00000354117:F1491L	ENSP00000340554:F1445L	F	-	1	0	TTN	179350685	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.307000	0.96226	2.221000	0.72209	0.528000	0.53228	TTT	.	.		0.323	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179642440	A	G	179642440	3	3	44	1	0	0	0	0	1	0	0	0	16750	43	2	2	106869	2	TTN	2	179642440	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	9872	179642440	63556933	50	5510										
TTN	7273	hgsc.bcm.edu	37	chr2	179645980	179645980	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	accggtttgtttgttgtaacTcactttgtatctttatgtaa	7	6	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:179645980T>C	ENST00000591111.1	-	21	3615	c.3391A>G	c.(3391-3393)Agt>Ggt	p.S1131G	TTN_ENST00000359218.5_Missense_Mutation_p.S1085G|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.S1131G|TTN_ENST00000342175.6_Missense_Mutation_p.S1085G|TTN_ENST00000589042.1_Missense_Mutation_p.S1131G|TTN_ENST00000342992.6_Missense_Mutation_p.S1131G|TTN_ENST00000460472.2_Missense_Mutation_p.S1085G			Q8WZ42	TITIN_HUMAN	titin	33348	Ig-like 4.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGTTGTAACTCACTTTGTAT	0.353																																					p.S1131G		Atlas-SNP	.											.	TTN	18412	.	0			c.A3391G						.						200	176	184					2																	179645980		2203	4300	6503	SO:0001583	missense	7273	exon21			TGTAACTCACTTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.3391A>G	chr2.hg19:g.179645980T>C	ENSP00000465570:p.Ser1131Gly	135.0	0.0		143.0	8.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.58	1.389902	0.25118	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33	5.91	5.91	0.95273	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.64305	0.2586	L	0.56769	1.78	0.20489	N	0.999893	B;B;B;B;P	0.38504	0.101;0.101;0.101;0.183;0.634	B;B;B;B;B	0.36845	0.138;0.138;0.138;0.096;0.234	T	0.64063	-0.6495	9	0.87932	D	0	.	12.8053	0.57610	0.0:0.0:0.1363:0.8637	.	1085;1085;1085;1131;1131	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	G	1131;1085;1085;1085;1085;1131	ENSP00000343764:S1131G;ENSP00000434586:S1085G;ENSP00000340554:S1085G;ENSP00000352154:S1085G;ENSP00000354117:S1131G	ENSP00000340554:S1085G	S	-	1	0	TTN	179354225	0.998000	0.40836	1.000000	0.80357	0.743000	0.42351	2.551000	0.45820	2.252000	0.74401	0.528000	0.53228	AGT	.	.		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179645980	T	C	179645980	3	2	44	1	0	0	0	0	1	0	0	0	16750	1551	54	2	107965	2	TTN	2	179645980	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	3540	179645980	63553393	51	5511										
ASNSD1	54529	hgsc.bcm.edu	37	chr2	190531152	190531152	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	actcaaattttgtttaattaTctttcctcctgtaagaatga	4	7	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:190531152T>C	ENST00000260952.4	+	4	707	c.294T>C	c.(292-294)taT>taC	p.Y98Y	ASNSD1_ENST00000607062.1_Intron|ASNSD1_ENST00000607535.1_3'UTR	NM_019048.2	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1	98	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				asparagine biosynthetic process (GO:0006529)|glutamine metabolic process (GO:0006541)		asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(3)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)			TGTTTAATTATCTTTCCTCCT	0.328																																					p.Y98Y		Atlas-SNP	.											.	ASNSD1	63	.	0			c.T294C						.						122	129	126					2																	190531152		2203	4300	6503	SO:0001819	synonymous_variant	54529	exon4			TAATTATCTTTCC	AY116969	CCDS2300.1	2q32.2	2012-09-20			ENSG00000138381	ENSG00000138381			24910	protein-coding gene	gene with protein product							Standard	NM_019048		Approved	NS3TP1, FLJ20752, NBLA00058	uc002uqt.3	Q9NWL6	OTTHUMG00000132665	ENST00000260952.4:c.294T>C	chr2.hg19:g.190531152T>C		49.0	0.0		52.0	4.0	NM_019048	D3DPH6|Q3LIC3|Q4ZG45	Silent	SNP	ENST00000260952.4	hg19	CCDS2300.1																																																																																			.	.		0.328	ASNSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255919.3	NM_019048		C	190531152	T	C	190531152	2	2	44	1	0	0	0	0	0	0	0	1	1049	1442	50	2		2	ASNSD1	2	190531152	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	10885172	190531152	52668221	52	5512										
ORMDL1	94101	hgsc.bcm.edu	37	chr2	190636521	190636521	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tattaattccaaagatccgaAcaccatgtagttgtggcatt	7	8	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:190636521A>G	ENST00000325795.3	-	3	1220	c.434T>C	c.(433-435)gTt>gCt	p.V145A	ORMDL1_ENST00000496543.1_5'UTR|ORMDL1_ENST00000392350.3_Missense_Mutation_p.V145A|ORMDL1_ENST00000392349.4_Missense_Mutation_p.V145A			Q9P0S3	ORML1_HUMAN	ORMDL sphingolipid biosynthesis regulator 1	145					ceramide metabolic process (GO:0006672)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(1)|urinary_tract(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00177)|Epithelial(96;0.0317)|all cancers(119;0.0889)			AAAGATCCGAACACCATGTAG	0.353																																					p.V145A		Atlas-SNP	.											.	ORMDL1	8	.	0			c.T434C						.						80	82	81					2																	190636521		2203	4300	6503	SO:0001583	missense	94101	exon5			ATCCGAACACCAT		CCDS2301.1	2q32	2014-06-16	2014-06-16		ENSG00000128699	ENSG00000128699			16036	protein-coding gene	gene with protein product		610073	"ORM1 (S. cerevisiae)-like 1", "ORM1-like 1 (S. cerevisiae)"			12093374, 23066021	Standard	NM_016467		Approved		uc002ure.4	Q9P0S3	OTTHUMG00000132661	ENST00000325795.3:c.434T>C	chr2.hg19:g.190636521A>G	ENSP00000326869:p.Val145Ala	90.0	0.0		89.0	4.0	NM_016467	B2R8W3|D3DPH9	Missense_Mutation	SNP	ENST00000325795.3	hg19	CCDS2301.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.279823	0.80692	.	.	ENSG00000128699	ENST00000392350;ENST00000325795;ENST00000392349	.	.	.	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.80899	0.4712	M	0.85710	2.77	0.80722	D	1	D	0.59357	0.985	D	0.73708	0.981	D	0.84384	0.0551	9	0.87932	D	0	-13.5471	15.2365	0.73436	1.0:0.0:0.0:0.0	.	145	Q9P0S3	ORML1_HUMAN	A	145	.	ENSP00000326869:V145A	V	-	2	0	ORMDL1	190344766	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.224000	0.78042	2.184000	0.69523	0.533000	0.62120	GTT	.	.		0.353	ORMDL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335275.1	NM_016467		G	190636521	A	G	190636521	3	3	44	1	0	0	0	0	1	0	0	0	11278	43	2	2	31	2	ORMDL1	2	190636521	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	105369	190636521	52562852	53	5513										
GLS	2744	hgsc.bcm.edu	37	chr2	191796332	191796332	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gagacactttgcaaaaaaacTtgatcctcgaagagaaggtg	10	7	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:191796332T>C	ENST00000320717.3	+	14	1877	c.1619T>C	c.(1618-1620)cTt>cCt	p.L540P	GLS_ENST00000409428.1_Missense_Mutation_p.L45P|GLS_ENST00000338435.4_Missense_Mutation_p.L540P|GLS_ENST00000409215.1_Missense_Mutation_p.L45P|GLS_ENST00000409626.1_Missense_Mutation_p.L111P|GLS_ENST00000471443.1_3'UTR	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	540					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate secretion (GO:0014047)|glutamine catabolic process (GO:0006543)|neurotransmitter secretion (GO:0007269)|protein homotetramerization (GO:0051289)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|small molecule metabolic process (GO:0044281)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamine(DB00130)	GCAAAAAAACTTGATCCTCGA	0.313																																					p.L540P		Atlas-SNP	.											.	GLS	47	.	0			c.T1619C						.						74	75	74					2																	191796332		2203	4296	6499	SO:0001583	missense	2744	exon14			AAAAACTTGATCC	AB020645	CCDS2308.1, CCDS58744.1	2q32-q34	2013-01-10			ENSG00000115419	ENSG00000115419	3.5.1.2	"Ankyrin repeat domain containing"	4331	protein-coding gene	gene with protein product		138280				10048485	Standard	NM_014905		Approved	KIAA0838, GLS1	uc002usf.3	O94925	OTTHUMG00000132701	ENST00000320717.3:c.1619T>C	chr2.hg19:g.191796332T>C	ENSP00000317379:p.Leu540Pro	96.0	0.0		78.0	4.0	NM_014905	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	hg19	CCDS2308.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.822874	0.50739	.	.	ENSG00000115419	ENST00000320717;ENST00000338435;ENST00000409626;ENST00000457316;ENST00000409428;ENST00000409215;ENST00000412247	T;T;T	0.55413	0.8;0.73;0.52	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.62282	0.2415	L	0.61218	1.895	0.80722	D	1	P;P;P;P;D	0.63046	0.825;0.921;0.81;0.921;0.992	B;B;B;B;P	0.52109	0.273;0.357;0.203;0.357;0.69	T	0.64723	-0.6340	10	0.51188	T	0.08	-18.7187	16.0417	0.80687	0.0:0.0:0.0:1.0	.	111;540;194;540;540	B7Z2P1;A8K132;Q68D38;O94925;O94925-3	.;.;.;GLSK_HUMAN;.	P	540;540;111;111;45;45;61	ENSP00000317379:L540P;ENSP00000340689:L540P;ENSP00000387177:L45P	ENSP00000317379:L540P	L	+	2	0	GLS	191504577	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.963000	0.56773	2.198000	0.70561	0.482000	0.46254	CTT	.	.		0.313	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			C	191796332	T	C	191796332	3	2	44	1	0	0	0	0	1	0	0	0	6471	1609	56	2	1673	2	GLS	2	191796332	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1159811	191796332	51403041	54	5514										
SGOL2	151246	hgsc.bcm.edu	37	chr2	201400866	201400866	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaatgagcagtctttctgagGtaagtagaatttatatgtaa	9	3	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:201400866G>A	ENST00000357799.4	+	4	485		c.e4+1		SGOL2_ENST00000409203.3_Splice_Site|SGOL2_ENST00000469840.1_Splice_Site	NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)						meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						TCTTTCTGAGGTAAGTAGAAT	0.308																																					.		Atlas-SNP	.											.	SGOL2	126	.	0			c.387+1G>A						.						119	119	119					2																	201400866		1815	4064	5879	SO:0001630	splice_region_variant	151246	exon4			TCTGAGGTAAGTA	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.387+1G>A	chr2.hg19:g.201400866G>A		84.0	0.0		84.0	4.0	NM_001160033	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Splice_Site	SNP	ENST00000357799.4	hg19	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.544565	0.65198	.	.	ENSG00000163535	ENST00000357799;ENST00000409203	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7126	0.85389	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SGOL2	201109111	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	5.379000	0.66196	2.716000	0.92895	0.563000	0.77884	.	.	.		0.308	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	Intron	A	201400866	G	A	201400866	5	1	44	1	0	0	0	0	0	0	1	0	14232	1275	44	3	398	3	SGOL2	2	201400866	Splice_Site	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	9604534	201400866	41798507	55	5515										
CASP10	843	hgsc.bcm.edu	37	chr2	202074279	202074279	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	taatcatctgaagaaattggTcccaaggtgagagctctttt	9	7	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:202074279T>C	ENST00000272879.5	+	9	1593	c.1409T>C	c.(1408-1410)gTc>gCc	p.V470A	CASP10_ENST00000313728.7_Missense_Mutation_p.V403A|CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000346817.5_Missense_Mutation_p.V427A|CASP10_ENST00000492363.1_3'UTR|CASP10_ENST00000448480.1_Missense_Mutation_p.V427A|CASP10_ENST00000286186.6_Missense_Mutation_p.V470A	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	470					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						AAGAAATTGGTCCCAAGGTGA	0.388																																					p.V470A		Atlas-SNP	.											.	CASP10	95	.	0			c.T1409C						.						63	65	65					2																	202074279		2203	4298	6501	SO:0001583	missense	843	exon9			AATTGGTCCCAAG	U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	3.4.22.63	"Caspases"	1500	protein-coding gene	gene with protein product		601762	"caspase 10, apoptosis-related cysteine protease"			8755496	Standard	NM_032974		Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000272879.5:c.1409T>C	chr2.hg19:g.202074279T>C	ENSP00000272879:p.Val470Ala	103.0	0.0		92.0	6.0	NM_032977	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Missense_Mutation	SNP	ENST00000272879.5	hg19	CCDS2338.1	.	.	.	.	.	.	.	.	.	.	T	13.19	2.161981	0.38217	.	.	ENSG00000003400	ENST00000286186;ENST00000272879;ENST00000346817;ENST00000313728;ENST00000448480	T;T;T;T;T	0.19938	2.11;4.26;2.11;2.11;4.26	4.82	3.62	0.41486	Peptidase C14, caspase precursor p45, core (1);	0.212741	0.39407	N	0.001366	T	0.22322	0.0538	N	0.11131	0.1	0.52099	D	0.999949	P;D;D;D;D	0.89917	0.725;1.0;1.0;0.996;0.997	P;D;D;P;D	0.91635	0.493;0.998;0.999;0.881;0.992	T	0.04242	-1.0966	10	0.11794	T	0.64	.	11.3339	0.49492	0.0:0.0:0.1526:0.8474	.	403;427;470;427;470	Q92851-6;Q92851-5;Q92851;Q92851-2;Q92851-4	.;.;CASPA_HUMAN;.;.	A	470;470;427;403;427	ENSP00000286186:V470A;ENSP00000272879:V470A;ENSP00000237865:V427A;ENSP00000314599:V403A;ENSP00000396835:V427A	ENSP00000272879:V470A	V	+	2	0	CASP10	201782524	1.000000	0.71417	0.845000	0.33349	0.504000	0.33889	7.267000	0.78462	0.659000	0.30945	0.528000	0.53228	GTC	.	.		0.388	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977		C	202074279	T	C	202074279	3	2	44	1	0	0	0	0	1	0	0	0	2671	1667	58	2	1439	2	CASP10	2	202074279	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	673413	202074279	41125094	56	5516										
ALS2CR8	79800	hgsc.bcm.edu	37	chr2	203848290	203848290	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaacaagaacccaaagaaccAgcattgtctatggaagcaaa	7	9	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:203848290A>G	ENST00000402905.3	+	16	2442	c.2121A>G	c.(2119-2121)ccA>ccG	p.P707P	WDR12_ENST00000477723.1_Intron|CARF_ENST00000428585.1_Silent_p.P631P|CARF_ENST00000438828.2_Silent_p.P707P|CARF_ENST00000414439.1_Silent_p.P605P|CARF_ENST00000545253.1_Silent_p.P619P|CARF_ENST00000320443.8_Silent_p.P707P|CARF_ENST00000545262.1_Silent_p.P631P	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	707					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CCAAAGAACCAGCATTGTCTA	0.313																																					p.P707P		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.A2121G						.						87	85	86					2																	203848290		1802	4072	5874	SO:0001819	synonymous_variant	79800	exon17			AGAACCAGCATTG	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.2121A>G	chr2.hg19:g.203848290A>G		53.0	0.0		79.0	5.0	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Silent	SNP	ENST00000402905.3	hg19	CCDS42801.1																																																																																			.	.		0.313	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		G	203848290	A	G	203848290	2	3	44	1	0	0	0	0	0	0	0	1	555	175	7	2		2	ALS2CR8	2	203848290	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1774011	203848290	39351083	57	5517										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	203881127	203881127	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aatggcatccagagagaggcTctttgaactttggatgcttt	11	7	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:203881127T>C	ENST00000449802.1	+	2	353	c.20T>C	c.(19-21)cTc>cCc	p.L7P	WDR12_ENST00000477723.1_5'Flank|NBEAL1_ENST00000478884.1_3'UTR	NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	7										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AGAGAGAGGCTCTTTGAACTT	0.313																																					p.L7P		Atlas-SNP	.											.	NBEAL1	266	.	0			c.T20C						.						97	98	97					2																	203881127		692	1591	2283	SO:0001583	missense	65065	exon2			AGAGGCTCTTTGA	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.20T>C	chr2.hg19:g.203881127T>C	ENSP00000399903:p.Leu7Pro	76.0	0.0		74.0	4.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.495795	0.64186	.	.	ENSG00000144426	ENST00000449802;ENST00000340268	T	0.61510	0.1	4.83	4.83	0.62350	.	.	.	.	.	T	0.66137	0.2759	L	0.41824	1.3	0.80722	D	1	D;D	0.69078	0.989;0.997	P;D	0.80764	0.726;0.994	T	0.69000	-0.5261	9	0.87932	D	0	.	11.1321	0.48354	0.0:0.0:0.0:1.0	.	7;7	Q6ZS30;A2RUL1	NBEL1_HUMAN;.	P	7	ENSP00000399903:L7P	ENSP00000344985:L7P	L	+	2	0	NBEAL1	203589372	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.894000	0.56250	1.937000	0.56155	0.533000	0.62120	CTC	.	.		0.313	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			C	203881127	T	C	203881127	3	2	44	1	0	0	0	0	1	0	0	0	10197	1551	54	2	22	2	NBEAL1	2	203881127	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	32837	203881127	39318246	58	5518										
VWC2L	402117	hgsc.bcm.edu	37	chr2	215301371	215301371	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agccctctccatgtgaatggTgtcgctgtgagcccagcaat	11	12	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:215301371T>C	ENST00000312504.5	+	3	1211	c.409T>C	c.(409-411)Tgt>Cgt	p.C137R	VWC2L_ENST00000427124.1_Intron|AC107218.3_ENST00000412896.1_RNA|AC107218.3_ENST00000437883.1_RNA	NM_001080500.2	NP_001073969.1	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain containing protein 2-like	137	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				breast(1)|endometrium(1)|large_intestine(3)|lung(10)|prostate(1)	16						ATGTGAATGGTGTCGCTGTGA	0.443																																					p.C137R		Atlas-SNP	.											.	VWC2L	40	.	0			c.T409C						.						108	106	106					2																	215301371		2006	4157	6163	SO:0001583	missense	402117	exon3			GAATGGTGTCGCT	AB374231	CCDS46509.1	2q34-q35	2011-01-25	2011-01-25		ENSG00000174453	ENSG00000174453			37203	protein-coding gene	gene with protein product			"von Willebrand factor C domain-containing protein 2-like"				Standard	NM_001080500		Approved		uc002vet.2	B2RUY7	OTTHUMG00000154811	ENST00000312504.5:c.409T>C	chr2.hg19:g.215301371T>C	ENSP00000308976:p.Cys137Arg	119.0	0.0		154.0	7.0	NM_001080500	A6NC69|B2RUW7|B7X8X1	Missense_Mutation	SNP	ENST00000312504.5	hg19	CCDS46509.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.214110	0.79352	.	.	ENSG00000174453	ENST00000312504	D	0.82984	-1.67	5.87	5.87	0.94306	von Willebrand factor, type C (3);	.	.	.	.	D	0.93671	0.7978	H	0.94698	3.57	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95246	0.8355	9	0.87932	D	0	-1.9073	16.2713	0.82622	0.0:0.0:0.0:1.0	.	137	B2RUY7	VWC2L_HUMAN	R	137	ENSP00000308976:C137R	ENSP00000308976:C137R	C	+	1	0	VWC2L	215009616	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.036000	0.88901	2.232000	0.73038	0.528000	0.53228	TGT	.	.		0.443	VWC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337175.1	NM_001080500		C	215301371	T	C	215301371	3	2	44	1	0	0	0	0	1	0	0	0	17259	1696	59	2	415	2	VWC2L	2	215301371	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	11420244	215301371	27898002	59	5519										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215884303	215884303	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttttgcttggatctccagtcAgcaaatctctcactttttta	5	10	4	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:215884303A>G	ENST00000272895.7	-	12	1724	c.1505T>C	c.(1504-1506)cTg>cCg	p.L502P	AC072062.3_ENST00000602182.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.L184P|AC072062.3_ENST00000437897.3_RNA|AC072062.3_ENST00000419251.1_RNA|AC072062.3_ENST00000595058.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	502					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ATCTCCAGTCAGCAAATCTCT	0.378																																					p.L502P	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.T1505C						.						67	69	68					2																	215884303		2203	4300	6503	SO:0001583	missense	26154	exon12			CCAGTCAGCAAAT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.1505T>C	chr2.hg19:g.215884303A>G	ENSP00000272895:p.Leu502Pro	140.0	0.0		115.0	5.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.770406	0.49680	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	T;T	0.67698	-0.28;-0.28	5.9	4.72	0.59763	.	0.125547	0.36167	N	0.002759	T	0.69913	0.3164	L	0.27053	0.805	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.69654	0.957;0.965	T	0.72507	-0.4272	10	0.87932	D	0	.	11.6442	0.51250	0.8516:0.1484:0.0:0.0	.	502;184	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	P	502;184	ENSP00000272895:L502P;ENSP00000374312:L184P	ENSP00000272895:L502P	L	-	2	0	ABCA12	215592548	1.000000	0.71417	0.998000	0.56505	0.839000	0.47603	5.683000	0.68189	1.017000	0.39495	0.519000	0.50382	CTG	.	.		0.378	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215884303	A	G	215884303	3	3	44	1	0	0	0	0	1	0	0	0	30	188	7	2	6450	2	ABCA12	2	215884303	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	582932	215884303	27315070	60	5520										
MRPL44	65080	hgsc.bcm.edu	37	chr2	224824697	224824697	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gttacagagcagtggacctgAgaggactgcacttttcatca	11	9	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:224824697A>G	ENST00000258383.3	+	2	695	c.626A>G	c.(625-627)gAg>gGg	p.E209G		NM_022915.3	NP_075066.1	Q9H9J2	RM44_HUMAN	mitochondrial ribosomal protein L44	209	RNase III.				mitochondrial translational elongation (GO:0070125)|RNA processing (GO:0006396)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		all_lung(227;0.00679)|Lung NSC(271;0.00855)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;2.51e-10)|all cancers(144;7.89e-08)|Lung(261;0.00705)|LUSC - Lung squamous cell carcinoma(224;0.008)		AGTGGACCTGAGAGGACTGCA	0.418																																					p.E209G		Atlas-SNP	.											.	MRPL44	31	.	0			c.A626G						.						70	69	69					2																	224824697		2203	4300	6503	SO:0001583	missense	65080	exon2			GACCTGAGAGGAC	AK022763	CCDS2459.1	2p24.3-p24.1	2012-09-13			ENSG00000135900	ENSG00000135900		"Mitochondrial ribosomal proteins / large subunits"	16650	protein-coding gene	gene with protein product	"39S ribosomal protein L44, mitochondrial"	611849					Standard	NM_022915		Approved	FLJ12701, FLJ13990	uc002vnr.4	Q9H9J2	OTTHUMG00000133164	ENST00000258383.3:c.626A>G	chr2.hg19:g.224824697A>G	ENSP00000258383:p.Glu209Gly	82.0	0.0		94.0	4.0	NM_022915	Q53S16|Q6IA62|Q9H821	Missense_Mutation	SNP	ENST00000258383.3	hg19	CCDS2459.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.391985	0.42410	.	.	ENSG00000135900	ENST00000258383	T	0.51574	0.7	5.7	0.475	0.16774	Ribonuclease III (3);	0.523903	0.22034	N	0.065555	T	0.35278	0.0926	L	0.51422	1.61	0.42515	D	0.992989	B	0.06786	0.001	B	0.09377	0.004	T	0.13575	-1.0504	10	0.54805	T	0.06	-11.752	4.6655	0.12664	0.6434:0.0:0.226:0.1306	.	209	Q9H9J2	RM44_HUMAN	G	209	ENSP00000258383:E209G	ENSP00000258383:E209G	E	+	2	0	MRPL44	224532941	1.000000	0.71417	0.973000	0.42090	0.936000	0.57629	3.197000	0.51028	0.120000	0.18254	0.528000	0.53228	GAG	.	.		0.418	MRPL44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256866.2	NM_022915		G	224824697	A	G	224824697	3	3	44	1	0	0	0	0	1	0	0	0	9817	304	11	2	632	2	MRPL44	2	224824697	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	8940394	224824697	18374676	61	5521										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227942736	227942736	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cacaggtcctgctttgcctgGggggcccagaggtccaggaa	15	12	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:227942736G>A	ENST00000396625.3	-	25	2068	c.1861C>T	c.(1861-1863)Cca>Tca	p.P621S	COL4A4_ENST00000329662.7_Missense_Mutation_p.P621S	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	621	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GCTTTGCCTGGGGGGCCCAGA	0.592																																					p.P621S		Atlas-SNP	.											.	COL4A4	215	.	0			c.C1861T						.						29	32	31					2																	227942736		1813	4077	5890	SO:0001583	missense	1286	exon25			TGCCTGGGGGGCC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.1861C>T	chr2.hg19:g.227942736G>A	ENSP00000379866:p.Pro621Ser	76.0	0.0		84.0	4.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	hg19	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.535342	0.45176	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.96587	-4.06;-4.06	5.82	5.82	0.92795	.	.	.	.	.	D	0.97654	0.9231	M	0.66560	2.04	0.23260	N	0.998021	D	0.71674	0.998	D	0.66847	0.947	D	0.93741	0.7050	9	0.44086	T	0.13	.	17.8873	0.88861	0.0:0.0:1.0:0.0	.	621	P53420	CO4A4_HUMAN	S	621	ENSP00000379866:P621S;ENSP00000328553:P621S	ENSP00000328553:P621S	P	-	1	0	COL4A4	227650980	1.000000	0.71417	0.059000	0.19551	0.016000	0.09150	6.389000	0.73199	2.765000	0.95021	0.650000	0.86243	CCA	.	.		0.592	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		A	227942736	G	A	227942736	3	1	44	1	0	0	0	0	1	0	0	0	3695	1232	43	3	3307	3	COL4A4	2	227942736	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	3118039	227942736	15256637	62	5522										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228881536	228881536	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctaatctatttgcacacttcTctgcttgcgagggagagcca	9	11	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:228881536T>C	ENST00000392056.3	-	7	4080	c.4034A>G	c.(4033-4035)gAg>gGg	p.E1345G	SPHKAP_ENST00000344657.5_Missense_Mutation_p.E1345G	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1345						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TGCACACTTCTCTGCTTGCGA	0.512																																					p.E1345G		Atlas-SNP	.											.	SPHKAP	750	.	0			c.A4034G						.						92	81	85					2																	228881536		2203	4300	6503	SO:0001583	missense	80309	exon7			CACTTCTCTGCTT		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4034A>G	chr2.hg19:g.228881536T>C	ENSP00000375909:p.Glu1345Gly	163.0	0.0		173.0	7.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	hg19	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	T	12.11	1.839466	0.32513	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.12774	2.65;2.65	5.92	3.52	0.40303	.	0.582699	0.20019	N	0.100942	T	0.11580	0.0282	L	0.50919	1.6	0.09310	N	1	B;B;B	0.29862	0.004;0.006;0.259	B;B;B	0.22753	0.004;0.007;0.041	T	0.17623	-1.0363	10	0.38643	T	0.18	-6.5395	7.6833	0.28526	0.0:0.0722:0.1418:0.786	.	376;1345;1345	B3KR30;Q2M3C7;Q2M3C7-2	.;SPKAP_HUMAN;.	G	1345	ENSP00000375909:E1345G;ENSP00000339886:E1345G	ENSP00000339886:E1345G	E	-	2	0	SPHKAP	228589780	0.873000	0.30073	0.010000	0.14722	0.004000	0.04260	3.522000	0.53480	1.015000	0.39444	0.533000	0.62120	GAG	.	.		0.512	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		C	228881536	T	C	228881536	3	2	44	1	0	0	0	0	1	0	0	0	15063	1551	54	2	1092	2	SPHKAP	2	228881536	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	938800	228881536	14317837	63	5523										
SAG	6295	hgsc.bcm.edu	37	chr2	234237222	234237222	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctggcagttcttcatgtctgAcaagcccctgcaccttgcgg	10	14	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:234237222A>G	ENST00000409110.1	+	8	841	c.611A>G	c.(610-612)gAc>gGc	p.D204G	SAG_ENST00000449594.2_Missense_Mutation_p.D70G	NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	204					cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		TTCATGTCTGACAAGCCCCTG	0.612																																					p.D204G		Atlas-SNP	.											.	SAG	77	.	0			c.A611G						.						94	93	93					2																	234237222		1995	4169	6164	SO:0001583	missense	6295	exon8			TGTCTGACAAGCC		CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"arrestin 1"	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.611A>G	chr2.hg19:g.234237222A>G	ENSP00000386444:p.Asp204Gly	109.0	0.0		97.0	5.0	NM_000541	A0FDN6|Q53SV3|Q99858	Missense_Mutation	SNP	ENST00000409110.1	hg19	CCDS46545.1	.	.	.	.	.	.	.	.	.	.	A	18.43	3.622767	0.66787	.	.	ENSG00000130561	ENST00000252857;ENST00000409110;ENST00000449594	T;T	0.06449	3.3;3.3	4.19	4.19	0.49359	Immunoglobulin E-set (1);Arrestin, C-terminal (1);Arrestin-like, C-terminal (1);	0.095533	0.64402	D	0.000001	T	0.13756	0.0333	M	0.86097	2.795	0.54753	D	0.999983	B;B	0.28178	0.113;0.202	B;B	0.30782	0.071;0.12	T	0.02037	-1.1225	10	0.52906	T	0.07	-23.8596	13.7339	0.62807	1.0:0.0:0.0:0.0	.	70;204	B7Z7L5;P10523	.;ARRS_HUMAN	G	204;204;70	ENSP00000386444:D204G;ENSP00000392889:D70G	ENSP00000252857:D204G	D	+	2	0	SAG	233901961	1.000000	0.71417	0.992000	0.48379	0.965000	0.64279	6.010000	0.70753	1.898000	0.54952	0.533000	0.62120	GAC	.	.		0.612	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1	NM_000541		G	234237222	A	G	234237222	3	3	44	1	0	0	0	0	1	0	0	0	13823	275	10	2	637	2	SAG	2	234237222	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	5355686	234237222	8962151	64	5524										
CXCR7	57007	hgsc.bcm.edu	37	chr2	237489341	237489341	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggccaagaccacaggctatgAcacgcactgctacatcttga	9	13	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr2:237489341A>T	ENST00000272928.3	+	2	543	c.233A>T	c.(232-234)gAc>gTc	p.D78V		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	78					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)										ACAGGCTATGACACGCACTGC	0.542																																					p.D78V		Atlas-SNP	.											.	CXCR7	72	.	0			c.A233T						.						179	143	155					2																	237489341		2203	4300	6503	SO:0001583	missense	57007	exon2			GCTATGACACGCA	BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"CD molecules", "GPCR / Class A : Chemokine receptors : Atypical"	23692	protein-coding gene	gene with protein product		610376	"chemokine orphan receptor 1", "chemokine (C-X-C motif) receptor 7"	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.233A>T	chr2.hg19:g.237489341A>T	ENSP00000272928:p.Asp78Val	171.0	0.0		159.0	79.0	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	hg19	CCDS2516.1	.	.	.	.	.	.	.	.	.	.	A	18.77	3.695508	0.68386	.	.	ENSG00000144476	ENST00000447924;ENST00000272928	T;T	0.34072	1.38;1.38	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.051051	0.85682	D	0.000000	T	0.12347	0.0300	N	0.00060	-2.335	0.80722	D	1	P	0.47484	0.896	P	0.46049	0.502	T	0.58549	-0.7617	10	0.54805	T	0.06	.	15.7428	0.77914	1.0:0.0:0.0:0.0	.	78	P25106	CXCR7_HUMAN	V	78	ENSP00000405945:D78V;ENSP00000272928:D78V	ENSP00000272928:D78V	D	+	2	0	CXCR7	237154080	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	7.283000	0.78640	2.117000	0.64856	0.460000	0.39030	GAC	.	.		0.542	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		T	237489341	A	T	237489341	3	4	44	1	0	0	0	0	1	0	0	0	4098	275	10	4	235	4	CXCR7	2	237489341	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	3252119	237489341	5710032	65	5525										
IRAK2	3656	hgsc.bcm.edu	37	chr3	10251316	10251316	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cagccggcctttctccagccTcctgaagaagatgcccctca	8	17	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:10251316T>C	ENST00000256458.4	+	4	558	c.468T>C	c.(466-468)ccT>ccC	p.P156P		NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	156					activation of MAPK activity (GO:0000187)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						TTCTCCAGCCTCCTGAAGAAG	0.597																																					p.P156P		Atlas-SNP	.											.	IRAK2	113	.	0			c.T468C						.						155	164	161					3																	10251316		2203	4300	6503	SO:0001819	synonymous_variant	3656	exon4			CCAGCCTCCTGAA	AF026273	CCDS33697.1	3p25.2	2008-08-18			ENSG00000134070	ENSG00000134070			6113	protein-coding gene	gene with protein product		603304				9374458	Standard	XR_245126		Approved		uc003bve.1	O43187	OTTHUMG00000155358	ENST00000256458.4:c.468T>C	chr3.hg19:g.10251316T>C		85.0	0.0		87.0	7.0	NM_001570	B4DQZ6|Q08AG6|Q5K546	Silent	SNP	ENST00000256458.4	hg19	CCDS33697.1																																																																																			.	.		0.597	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339623.1			C	10251316	T	C	10251316	2	2	44	1	0	0	0	0	0	0	0	1	7832	1538	54	2		2	IRAK2	3	10251316	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10		10251316	187771114	66	5526										
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37170627	37170627	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gggcagcccgttttgctgccAgccttgcctctgcctgaaaa	11	14	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:37170627A>G	ENST00000336686.4	-	3	184	c.104T>C	c.(103-105)cTg>cCg	p.L35P	LRRFIP2_ENST00000396428.2_Missense_Mutation_p.L35P|LRRFIP2_ENST00000421276.2_Missense_Mutation_p.L35P|LRRFIP2_ENST00000440230.1_Missense_Mutation_p.L35P|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.L35P|LRRFIP2_ENST00000354379.4_Missense_Mutation_p.L35P			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	35	DVL3-binding.				Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						TTTTGCTGCCAGCCTTGCCTC	0.403																																					p.L35P		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.T104C						.						120	122	121					3																	37170627		2203	4300	6503	SO:0001583	missense	9209	exon4			GCTGCCAGCCTTG	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.104T>C	chr3.hg19:g.37170627A>G	ENSP00000338727:p.Leu35Pro	90.0	0.0		90.0	4.0	NM_001134369	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	hg19	CCDS2664.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.785562	0.90282	.	.	ENSG00000093167	ENST00000421307;ENST00000354379;ENST00000336686;ENST00000421276;ENST00000396428;ENST00000440230;ENST00000416425;ENST00000438374;ENST00000434749;ENST00000436858;ENST00000452742	T;T;T;T;T;T;T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44;0.44;0.44;0.44;0.44;0.44;0.44	5.37	5.37	0.77165	.	0.101878	0.53938	D	0.000042	T	0.70850	0.3271	M	0.67700	2.07	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;1.0	T	0.74432	-0.3667	10	0.87932	D	0	-0.0963	15.321	0.74120	1.0:0.0:0.0:0.0	.	35;35;35;35	A8MXR0;Q9Y608-2;Q9Y608-4;Q9Y608	.;.;.;LRRF2_HUMAN	P	35	ENSP00000392217:L35P;ENSP00000346349:L35P;ENSP00000338727:L35P;ENSP00000416364:L35P;ENSP00000379705:L35P;ENSP00000405480:L35P;ENSP00000409574:L35P;ENSP00000412206:L35P;ENSP00000416907:L35P;ENSP00000416013:L35P;ENSP00000391360:L35P	ENSP00000338727:L35P	L	-	2	0	LRRFIP2	37145631	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.878000	0.92393	2.157000	0.67596	0.533000	0.62120	CTG	.	.		0.403	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		G	37170627	A	G	37170627	3	3	44	1	0	0	0	0	1	0	0	0	9037	188	7	2	2165	2	LRRFIP2	3	37170627	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	26919311	37170627	160851803	67	5527										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37365457	37365457	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aatcattatcttctgaactgTcagaagtattaaaagcccgt	6	8	4	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:37365457T>C	ENST00000361924.2	+	14	2454	c.2080T>C	c.(2080-2082)Tca>Cca	p.S694P	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.S716P	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	694	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TTCTGAACTGTCAGAAGTATT	0.363																																					p.S716P		Atlas-SNP	.											.	GOLGA4	173	.	0			c.T2146C						.						32	36	34					3																	37365457		2196	4270	6466	SO:0001583	missense	2803	exon15			GAACTGTCAGAAG	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.2080T>C	chr3.hg19:g.37365457T>C	ENSP00000354486:p.Ser694Pro	115.0	0.0		115.0	5.0	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	hg19	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	T	17.01	3.280162	0.59758	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000429018;ENST00000437131	T;T;T	0.28666	1.65;1.65;1.6	5.22	0.9	0.19278	.	0.295030	0.18662	N	0.134692	T	0.47002	0.1422	M	0.72894	2.215	0.32918	D	0.515446	D;D;D;D	0.67145	0.996;0.989;0.989;0.985	D;P;P;P	0.64410	0.925;0.885;0.885;0.756	T	0.58031	-0.7708	10	0.59425	D	0.04	.	8.8404	0.35137	0.1101:0.0:0.3072:0.5827	.	694;694;716;694	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	P	694;716;255;565	ENSP00000354486:S694P;ENSP00000349305:S716P;ENSP00000405842:S565P	ENSP00000349305:S716P	S	+	1	0	GOLGA4	37340461	0.995000	0.38212	0.880000	0.34516	0.901000	0.52897	1.818000	0.39012	0.355000	0.24131	0.533000	0.62120	TCA	.	.		0.363	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		C	37365457	T	C	37365457	3	2	44	1	0	0	0	0	1	0	0	0	6563	1667	58	2	2204	2	GOLGA4	3	37365457	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	194830	37365457	160656973	68	5528										
ZNF197	10168	hgsc.bcm.edu	37	chr3	44684620	44684620	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	attctgaagaagagcctcatTttacatcaaaggttccacac	6	10	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:44684620T>C	ENST00000396058.1	+	5	2165	c.1998T>C	c.(1996-1998)atT>atC	p.I666I	ZNF197_ENST00000344387.4_Silent_p.I666I|ZNF197_ENST00000383745.2_Intron|ZNF197_ENST00000383744.4_Intron|RP11-944L7.4_ENST00000457331.1_RNA			O14709	ZN197_HUMAN	zinc finger protein 197	666					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I666M(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		AGAGCCTCATTTTACATCAAA	0.408																																					p.I666I		Atlas-SNP	.											ZNF197,NS,carcinoma,0,1	ZNF197	81	.	1	Substitution - Missense(1)	ovary(1)	c.T1998C						.						60	62	61					3																	44684620		2203	4300	6503	SO:0001819	synonymous_variant	10168	exon6			CCTCATTTTACAT	AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"Zinc fingers, C2H2-type", "-", "-", "-"	12988	protein-coding gene	gene with protein product			"zinc finger protein 166"	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.1998T>C	chr3.hg19:g.44684620T>C		85.0	0.0		88.0	4.0	NM_006991	B2RAH8|Q86VG0	Silent	SNP	ENST00000396058.1	hg19	CCDS2717.1																																																																																			.	.		0.408	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991		C	44684620	T	C	44684620	2	2	44	1	0	0	0	0	0	0	0	1	17774	1829	64	2		2	ZNF197	3	44684620	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	7319163	44684620	153337810	69	5529										
QARS	5859	hgsc.bcm.edu	37	chr3	49140816	49140816	+	Frame_Shift_Del	DEL	C	C	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttgatcattttgccatctgCccacttcagcacagcccgag							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:49140816delC	ENST00000306125.6	-	5	815	c.478delG	c.(478-480)gcafs	p.A160fs	QARS_ENST00000420147.2_Frame_Shift_Del_p.A178fs|QARS_ENST00000470225.1_5'Flank|QARS_ENST00000414533.1_Frame_Shift_Del_p.A149fs			P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	160					brain development (GO:0007420)|gene expression (GO:0010467)|glutaminyl-tRNA aminoacylation (GO:0006425)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|glutamine-tRNA ligase activity (GO:0004819)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	L-Glutamine(DB00130)	TTGCCATCTGCCCACTTCAGC	0.517																																					p.A160fs		Atlas-INDEL	.											.	QARS	55	.	0			c.479delC						.						140	125	130					3																	49140816		2203	4300	6503	SO:0001589	frameshift_variant	5859	exon5			.	X76013	CCDS2788.1, CCDS63633.1	3p21.31	2011-07-01			ENSG00000172053	ENSG00000172053	6.1.1.18	"Aminoacyl tRNA synthetases / Class I"	9751	protein-coding gene	gene with protein product	"glutamine tRNA ligase"	603727				8078941, 10393422	Standard	NM_005051		Approved		uc003cvx.4	P47897	OTTHUMG00000156774	ENST00000306125.6:c.478delG	chr3.hg19:g.49140816delC	ENSP00000307567:p.Ala160fs	122.0	0.0		140.0	12.0	NM_005051	B4DWJ2	Frame_Shift_Del	DEL	ENST00000306125.6	hg19	CCDS2788.1																																																																																			.	.		0.517	QARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345689.2	NM_005051		-	49140816	C	-	49140816	7	5	44	1	0	1	0	1	0	0	0	0	12886	739	26	0	1929	0	QARS	3	49140816	Frame_Shift_Del	DEL	C	TCGA-BC-A3KG-01A-11D-A20W-10	4456196	49140816	148881614	70	5530										
RBM6	10180	hgsc.bcm.edu	37	chr3	50005375	50005375	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaggtagggatgctcctccaTctgacttcaggggccggggc	16	11	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:50005375T>C	ENST00000266022.4	+	3	776	c.517T>C	c.(517-519)Tct>Cct	p.S173P	RBM6_ENST00000422955.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.S41P|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000442092.1_Intron|RBM6_ENST00000539992.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	173					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TGCTCCTCCATCTGACTTCAG	0.473																																					p.S173P		Atlas-SNP	.											.	RBM6	85	.	0			c.T517C						.						59	62	61					3																	50005375		2203	4300	6503	SO:0001583	missense	10180	exon3			CCTCCATCTGACT	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"RNA binding motif (RRM) containing", "G patch domain containing"	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.517T>C	chr3.hg19:g.50005375T>C	ENSP00000266022:p.Ser173Pro	117.0	0.0		94.0	5.0	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	hg19	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	T	8.024	0.760258	0.15914	.	.	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.32272	1.48;1.46	5.88	-3.95	0.04118	.	0.437866	0.21957	N	0.066654	T	0.10852	0.0265	N	0.17082	0.46	0.58432	D	0.99999	B	0.02656	0.0	B	0.01281	0.0	T	0.17961	-1.0352	9	.	.	.	-0.6504	0.8832	0.01239	0.2603:0.2736:0.1116:0.3545	.	173	P78332	RBM6_HUMAN	P	173;41	ENSP00000266022:S173P;ENSP00000396466:S41P	.	S	+	1	0	RBM6	49980379	0.001000	0.12720	0.890000	0.34922	0.996000	0.88848	-0.515000	0.06290	-0.508000	0.06540	0.459000	0.35465	TCT	.	.		0.473	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		C	50005375	T	C	50005375	3	2	44	1	0	0	0	0	1	0	0	0	13159	1435	50	2	523	2	RBM6	3	50005375	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	864559	50005375	148017055	71	5531										
NEK4	6787	hgsc.bcm.edu	37	chr3	52797562	52797562	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gatgctcctcacagacggccTttcttcaggccttttgctca	8	14	4	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:52797562T>C	ENST00000233027.5	-	5	947	c.745A>G	c.(745-747)Agg>Ggg	p.R249G	NEK4_ENST00000383721.4_Missense_Mutation_p.R249G|NEK4_ENST00000535191.1_Missense_Mutation_p.R160G	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		ACAGACGGCCTTTCTTCAGGC	0.438																																					p.R249G		Atlas-SNP	.											.	NEK4	51	.	0			c.A745G						.						181	185	184					3																	52797562		2203	4300	6503	SO:0001583	missense	6787	exon5			ACGGCCTTTCTTC	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"serine/threonine protein kinase-2"	601959	"serine/threonine kinase 2", "NIMA (never in mitosis gene a)-related kinase 4"	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.745A>G	chr3.hg19:g.52797562T>C	ENSP00000233027:p.Arg249Gly	92.0	0.0		91.0	4.0	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	hg19	CCDS2863.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.082841	0.76642	.	.	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;T;T	0.72051	-0.62;-0.58;-0.62;-0.58	5.56	5.56	0.83823	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.057791	0.64402	D	0.000003	D	0.90882	0.7135	H	0.99689	4.705	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93735	0.7045	10	0.87932	D	0	.	11.6712	0.51401	0.0:0.0:0.148:0.852	.	160;249;249	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	G	249;160;249;160	ENSP00000233027:R249G;ENSP00000437703:R160G;ENSP00000373227:R249G;ENSP00000419666:R160G	ENSP00000233027:R249G	R	-	1	2	NEK4	52772602	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.564000	0.45931	2.114000	0.64651	0.533000	0.62120	AGG	.	.		0.438	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157		C	52797562	T	C	52797562	3	2	44	1	0	0	0	0	1	0	0	0	10335	1608	56	2	1828	2	NEK4	3	52797562	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2792187	52797562	145224868	72	5532										
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69225784	69225784	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggttaactgggtcctccagtTcccagaagcatttgtagaag	11	9	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:69225784T>C	ENST00000398540.3	-	22	2958	c.2875A>G	c.(2875-2877)Aac>Gac	p.N959D	FRMD4B_ENST00000478263.1_Missense_Mutation_p.N611D|FRMD4B_ENST00000542259.1_Missense_Mutation_p.N905D	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	959					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		GTCCTCCAGTTCCCAGAAGCA	0.383																																					p.N959D		Atlas-SNP	.											.	FRMD4B	90	.	0			c.A2875G						.						95	91	92					3																	69225784		1885	4117	6002	SO:0001583	missense	23150	exon22			TCCAGTTCCCAGA	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.2875A>G	chr3.hg19:g.69225784T>C	ENSP00000381549:p.Asn959Asp	78.0	0.0		69.0	4.0	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	hg19	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	T	19.41	3.823104	0.71143	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000478263	D;D	0.84298	-1.83;-1.81	5.69	5.69	0.88448	.	0.257041	0.41396	D	0.000882	T	0.81489	0.4833	M	0.66939	2.045	0.34642	D	0.72072	B;P	0.39665	0.115;0.682	B;B	0.30401	0.056;0.115	D	0.86266	0.1658	10	0.33940	T	0.23	-19.7622	14.5303	0.67920	0.0:0.0:0.0:1.0	.	803;959	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	D	959;905;611	ENSP00000381549:N959D;ENSP00000437658:N905D	ENSP00000381549:N959D	N	-	1	0	FRMD4B	69308474	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.829000	0.62737	2.180000	0.69256	0.482000	0.46254	AAC	.	.		0.383	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			C	69225784	T	C	69225784	3	2	44	1	0	0	0	0	1	0	0	0	6060	1783	62	2	237	2	FRMD4B	3	69225784	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	16428222	69225784	128796646	73	5533										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89156972	89156972	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttcggggaactgattccgcAgccttccaatgaaggtaagc	11	11	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:89156972A>G	ENST00000336596.2	+	1	299	c.74A>G	c.(73-75)cAg>cGg	p.Q25R	EPHA3_ENST00000452448.2_Missense_Mutation_p.Q25R|EPHA3_ENST00000494014.1_Missense_Mutation_p.Q25R	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	25					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CTGATTCCGCAGCCTTCCAAT	0.597										TSP Lung(6;0.00050)																											p.Q25R		Atlas-SNP	.											.	EPHA3	501	.	0			c.A74G						.						125	99	108					3																	89156972		2203	4300	6503	SO:0001583	missense	2042	exon1			TTCCGCAGCCTTC	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.74A>G	chr3.hg19:g.89156972A>G	ENSP00000337451:p.Gln25Arg	139.0	0.0		136.0	6.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	1.632	-0.518856	0.04171	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.71934	-0.59;2.85;-0.61	5.46	3.0	0.34707	.	0.608349	0.16348	N	0.218354	T	0.51568	0.1682	N	0.14661	0.345	0.30642	N	0.756385	B;B	0.14012	0.009;0.009	B;B	0.17098	0.003;0.017	T	0.43877	-0.9364	9	.	.	.	.	11.6203	0.51113	0.7183:0.2817:0.0:0.0	.	25;25	P29320;P29320-2	EPHA3_HUMAN;.	R	25	ENSP00000337451:Q25R;ENSP00000399926:Q25R;ENSP00000419190:Q25R	.	Q	+	2	0	EPHA3	89239662	0.999000	0.42202	0.433000	0.26760	0.306000	0.27790	3.012000	0.49575	0.337000	0.23665	0.379000	0.24179	CAG	.	.		0.597	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		G	89156972	A	G	89156972	3	3	44	1	0	0	0	0	1	0	0	0	5170	188	7	2	76	2	EPHA3	3	89156972	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	19931188	89156972	108865458	74	5534										
CBLB	868	hgsc.bcm.edu	37	chr3	105464838	105464838	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aatgccatgtaacctggatgTgtcacagctaagaaattcca	8	9	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:105464838T>C	ENST00000264122.4	-	6	1089	c.768A>G	c.(766-768)acA>acG	p.T256T	CBLB_ENST00000405772.1_Silent_p.T256T|CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000394027.3_Silent_p.T278T|CBLB_ENST00000403724.1_Silent_p.T256T	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	256	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|SH2-like.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						AACCTGGATGTGTCACAGCTA	0.333			Mis S		AML																																p.T256T	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.A768G						.						119	125	123					3																	105464838		2203	4300	6503	SO:0001819	synonymous_variant	868	exon6			TGGATGTGTCACA	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"RING-type (C3HC4) zinc fingers"	1542	protein-coding gene	gene with protein product		604491	"Cas-Br-M (murine) ectropic retroviral transforming sequence b", "Cas-Br-M (murine) ecotropic retroviral transforming sequence b"			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.768A>G	chr3.hg19:g.105464838T>C		84.0	0.0		91.0	4.0	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Silent	SNP	ENST00000264122.4	hg19	CCDS2948.1																																																																																			.	.		0.333	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662		C	105464838	T	C	105464838	2	2	44	1	0	0	0	0	0	0	0	1	2703	1683	59	2		2	CBLB	3	105464838	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	16307866	105464838	92557592	75	5535										
MORC1	27136	hgsc.bcm.edu	37	chr3	108705728	108705728	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgagctgatttttttttaccTtggtttaaaagaggaatttc	8	4	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:108705728T>C	ENST00000483760.1	-	21	2236	c.2193A>G	c.(2191-2193)caA>caG	p.Q731Q	MORC1_ENST00000232603.5_Splice_Site_p.Q752Q					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						TTTTTTTACCTTGGTTTAAAA	0.284																																					p.Q752Q		Atlas-SNP	.											.	MORC1	211	.	0			c.A2256G						.						23	22	22					3																	108705728		2174	4263	6437	SO:0001630	splice_region_variant	27136	exon22			TTTACCTTGGTTT	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2194+1A>G	chr3.hg19:g.108705728T>C		69.0	0.0		79.0	6.0	NM_014429		Silent	SNP	ENST00000483760.1	hg19																																																																																				.	.		0.284	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		Silent	C	108705728	T	C	108705728	5	2	44	1	0	0	0	0	0	0	1	0	9710	1623	56	2	726	2	MORC1	3	108705728	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	3240890	108705728	89316702	76	5536										
CASR	846	hgsc.bcm.edu	37	chr3	121980428	121980428	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aacaagaatcaattcaagtcTttcctccgaaccatccccaa	3	14	3	1	rs200545177		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:121980428T>C	ENST00000490131.1	+	4	918	c.546T>C	c.(544-546)tcT>tcC	p.S182S	CASR_ENST00000296154.5_Silent_p.S182S|CASR_ENST00000498619.1_Silent_p.S182S	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	182					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	AATTCAAGTCTTTCCTCCGAA	0.507																																					p.S182S		Atlas-SNP	.											.	CASR	190	.	0			c.T546C						.						129	136	133					3																	121980428		2203	4300	6503	SO:0001819	synonymous_variant	846	exon4			CAAGTCTTTCCTC	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.546T>C	chr3.hg19:g.121980428T>C		106.0	0.0		98.0	5.0	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Silent	SNP	ENST00000490131.1	hg19	CCDS3010.1																																																																																			.	.		0.507	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		C	121980428	T	C	121980428	2	2	44	1	0	0	0	0	0	0	0	1	2684	1596	56	2		2	CASR	3	121980428	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	13274700	121980428	76042002	77	5537										
PARP14	54625	hgsc.bcm.edu	37	chr3	122418450	122418450	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gataaacgatgaaatgaggcGttgtcactgtgagctcacgt	12	7	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:122418450G>A	ENST00000474629.2	+	6	1315	c.1049G>A	c.(1048-1050)cGt>cAt	p.R350H		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	350					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		GAAATGAGGCGTTGTCACTGT	0.453																																					p.R350H		Atlas-SNP	.											.	PARP14	242	.	0			c.G1049A						.						125	119	121					3																	122418450		2007	4183	6190	SO:0001583	missense	54625	exon6			TGAGGCGTTGTCA	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1049G>A	chr3.hg19:g.122418450G>A	ENSP00000418194:p.Arg350His	140.0	0.0		141.0	59.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	G	3.512	-0.099552	0.07010	.	.	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.72615	-0.67	5.32	-7.96	0.01144	.	1.152660	0.06396	N	0.717941	T	0.49440	0.1557	L	0.27053	0.805	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.04013	0.0;0.001	T	0.34750	-0.9816	10	0.14656	T	0.56	.	9.3574	0.38175	0.3934:0.0:0.5036:0.103	.	350;350	Q460N5-4;Q460N5	.;PAR14_HUMAN	H	350;269	ENSP00000418194:R350H	ENSP00000381228:R269H	R	+	2	0	PARP14	123901140	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-2.098000	0.01347	-1.718000	0.01383	-0.302000	0.09304	CGT	.	.		0.453	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		A	122418450	G	A	122418450	3	1	44	1	0	0	0	0	1	0	0	0	11467	1145	40	1	1071	1	PARP14	3	122418450	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	438022	122418450	75603980	78	5538										
PIK3R4	30849	hgsc.bcm.edu	37	chr3	130463932	130463932	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cgaccaggccttctcggtgcTtggctcgagcaactttaaaa	10	12	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:130463932T>C	ENST00000356763.3	-	2	688	c.131A>G	c.(130-132)aAg>aGg	p.K44R		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	44	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						TTCTCGGTGCTTGGCTCGAGC	0.423																																					p.K44R		Atlas-SNP	.											.	PIK3R4	145	.	0			c.A131G						.						60	62	61					3																	130463932		2203	4299	6502	SO:0001583	missense	30849	exon2			CGGTGCTTGGCTC	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.131A>G	chr3.hg19:g.130463932T>C	ENSP00000349205:p.Lys44Arg	82.0	0.0		105.0	5.0	NM_014602	Q2TBF4	Missense_Mutation	SNP	ENST00000356763.3	hg19	CCDS3067.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.069380	0.36470	.	.	ENSG00000196455	ENST00000356763	T	0.10763	2.84	5.0	5.0	0.66597	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.07863	0.0197	N	0.16790	0.44	0.80722	D	1	B	0.28439	0.212	B	0.32677	0.15	T	0.26258	-1.0108	10	0.09843	T	0.71	-23.2301	15.0074	0.71524	0.0:0.0:0.0:1.0	.	44	Q99570	PI3R4_HUMAN	R	44	ENSP00000349205:K44R	ENSP00000349205:K44R	K	-	2	0	PIK3R4	131946622	1.000000	0.71417	0.994000	0.49952	0.983000	0.72400	6.222000	0.72249	2.014000	0.59158	0.459000	0.35465	AAG	.	.		0.423	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		C	130463932	T	C	130463932	3	2	44	1	0	0	0	0	1	0	0	0	11930	1609	56	2	4021	2	PIK3R4	3	130463932	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	8045482	130463932	67558498	79	5539										
ATP2C1	27032	hgsc.bcm.edu	37	chr3	130716555	130716555	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttaaaatacttgtttcatcAataatcattgtttgtgggac	6	6	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:130716555A>G	ENST00000510168.1	+	25	2899	c.2349A>G	c.(2347-2349)tcA>tcG	p.S783S	ATP2C1_ENST00000504381.1_Silent_p.S728S|ATP2C1_ENST00000507488.2_Silent_p.S767S|ATP2C1_ENST00000428331.2_Silent_p.S783S|ATP2C1_ENST00000504948.1_Silent_p.S767S|ATP2C1_ENST00000508532.1_Silent_p.S783S|ATP2C1_ENST00000328560.8_Silent_p.S783S|ATP2C1_ENST00000359644.3_Silent_p.S783S|ATP2C1_ENST00000422190.2_Silent_p.S783S|ATP2C1_ENST00000513801.1_Silent_p.S767S|ATP2C1_ENST00000393221.4_Silent_p.S817S|ATP2C1_ENST00000505330.1_Silent_p.S767S|ATP2C1_ENST00000533801.2_Silent_p.S778S			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	783					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TTGTTTCATCAATAATCATTG	0.363									Hailey-Hailey disease																												p.S817S	Esophageal Squamous(99;456 1443 27647 34099 42636)	Atlas-SNP	.											.	ATP2C1	94	.	0			c.A2451G						.						169	176	174					3																	130716555		2203	4300	6503	SO:0001819	synonymous_variant	27032	exon24	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	TTCATCAATAATC	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"ATPases / P-type"	13211	protein-coding gene	gene with protein product	"secretory pathway Ca2+/Mn2+ ATPase 1", "calcium-transporting ATPase type 2C member 1"	604384	"benign chronic pemphigus (Hailey-Hailey disease)"	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.2349A>G	chr3.hg19:g.130716555A>G		118.0	0.0		97.0	4.0	NM_001199181	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Silent	SNP	ENST00000510168.1	hg19	CCDS46914.1	.	.	.	.	.	.	.	.	.	.	A	9.760	1.169801	0.21621	.	.	ENSG00000017260	ENST00000504612;ENST00000508660	.	.	.	5.73	-3.52	0.04682	.	.	.	.	.	T	0.38585	0.1046	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35076	-0.9803	4	.	.	.	.	1.8669	0.03200	0.2513:0.384:0.178:0.1867	.	.	.	.	R	737;301	.	.	Q	+	2	0	ATP2C1	132199245	0.736000	0.28164	0.982000	0.44146	0.969000	0.65631	-0.002000	0.12924	-0.428000	0.07339	-1.271000	0.01417	CAA	.	.		0.363	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486		G	130716555	A	G	130716555	2	3	44	1	0	0	0	0	0	0	0	1	1143	117	5	2		2	ATP2C1	3	130716555	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	252623	130716555	67305875	80	5540										
SLC25A36	55186	hgsc.bcm.edu	37	chr3	140692752	140692752	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgcttctacaatggaaaatgAtgaagagtctgtgaaagaag	11	4	2	5			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:140692752A>G	ENST00000324194.6	+	6	815	c.647A>G	c.(646-648)gAt>gGt	p.D216G	SLC25A36_ENST00000446041.2_Missense_Mutation_p.D216G|SLC25A36_ENST00000453248.2_Missense_Mutation_p.D190G|RP11-231L11.3_ENST00000513802.1_RNA			Q96CQ1	S2536_HUMAN	solute carrier family 25 (pyrimidine nucleotide carrier ), member 36	216				D -> G (in Ref. 1; BAA91715). {ECO:0000305}.	response to estradiol (GO:0032355)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						ATGGAAAATGATGAAGAGTCT	0.358																																					p.D216G		Atlas-SNP	.											.	SLC25A36	24	.	0			c.A647G						.						68	69	68					3																	140692752		2203	4300	6503	SO:0001583	missense	55186	exon6			AAAATGATGAAGA	AK001480	CCDS3114.1, CCDS46927.1	3q23	2013-05-22	2012-03-29		ENSG00000114120	ENSG00000114120		"Solute carriers"	25554	protein-coding gene	gene with protein product			"solute carrier family 25, member 36"				Standard	NM_001104647		Approved	FLJ10618, PNC2	uc003etr.2	Q96CQ1	OTTHUMG00000160260	ENST00000324194.6:c.647A>G	chr3.hg19:g.140692752A>G	ENSP00000320688:p.Asp216Gly	65.0	0.0		84.0	4.0	NM_018155	A8MYF7|Q05CY1|Q9H0G8|Q9NVN5	Missense_Mutation	SNP	ENST00000324194.6	hg19	CCDS46927.1	.	.	.	.	.	.	.	.	.	.	A	10.50	1.366807	0.24771	.	.	ENSG00000114120	ENST00000446041;ENST00000324194;ENST00000453248	T;T;T	0.80393	-1.34;-1.35;-1.37	6.01	3.65	0.41850	Mitochondrial carrier domain (2);	0.327981	0.39407	N	0.001374	T	0.59059	0.2166	N	0.11284	0.12	0.47214	D	0.999355	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.002;0.002	T	0.43065	-0.9414	10	0.13853	T	0.58	-11.1626	7.8468	0.29431	0.8516:0.0:0.1484:0.0	.	190;216;216	B4DL01;Q96CQ1-3;Q96CQ1	.;.;S2536_HUMAN	G	216;216;190	ENSP00000401938:D216G;ENSP00000320688:D216G;ENSP00000391521:D190G	ENSP00000320688:D216G	D	+	2	0	SLC25A36	142175442	1.000000	0.71417	0.730000	0.30809	0.917000	0.54804	3.237000	0.51344	0.533000	0.28675	0.528000	0.53228	GAT	.	.		0.358	SLC25A36-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359929.1	NM_018155		G	140692752	A	G	140692752	3	3	44	1	0	0	0	0	1	0	0	0	14515	333	12	2	669	2	SLC25A36	3	140692752	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	9976197	140692752	57329678	81	5541										
MME	4311	hgsc.bcm.edu	37	chr3	154802054	154802054	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	actggagatcagcctctcggTccttgtcctgctcctcacca	8	16	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:154802054T>C	ENST00000460393.1	+	2	218	c.98T>C	c.(97-99)gTc>gCc	p.V33A	MME_ENST00000492661.1_Missense_Mutation_p.V33A|MME_ENST00000493237.1_Missense_Mutation_p.V33A|MME_ENST00000382989.3_Missense_Mutation_p.V33A|MME_ENST00000360490.2_Missense_Mutation_p.V33A|MME_ENST00000462745.1_Missense_Mutation_p.V33A	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	33					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	AGCCTCTCGGTCCTTGTCCTG	0.478																																					p.V33A		Atlas-SNP	.											.	MME	133	.	0			c.T98C						.						186	174	178					3																	154802054		2203	4300	6503	SO:0001583	missense	4311	exon2			TCTCGGTCCTTGT		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.98T>C	chr3.hg19:g.154802054T>C	ENSP00000418525:p.Val33Ala	225.0	0.0		198.0	8.0	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	hg19	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.025968	0.75390	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000481828;ENST00000382989;ENST00000462745;ENST00000493237;ENST00000360490;ENST00000491026;ENST00000473730;ENST00000462837	D;D;D;D;D;D;D;D;D	0.93366	-1.71;-1.71;-2.11;-1.71;-1.71;-1.71;-3.21;-3.16;-2.78	5.27	5.27	0.74061	.	0.147680	0.48767	D	0.000162	D	0.91600	0.7346	M	0.62723	1.935	0.40833	D	0.9836	P	0.41450	0.75	B	0.38683	0.279	D	0.92499	0.6007	10	0.59425	D	0.04	-20.1127	13.7325	0.62797	0.0:0.0:0.0:1.0	.	33	P08473	NEP_HUMAN	A	33	ENSP00000420389:V33A;ENSP00000418525:V33A;ENSP00000420101:V33A;ENSP00000419653:V33A;ENSP00000417079:V33A;ENSP00000353679:V33A;ENSP00000418791:V33A;ENSP00000420542:V33A;ENSP00000417595:V33A	ENSP00000353679:V33A	V	+	2	0	MME	156284748	1.000000	0.71417	0.939000	0.37840	0.899000	0.52679	3.796000	0.55507	2.126000	0.65437	0.482000	0.46254	GTC	.	.		0.478	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		C	154802054	T	C	154802054	3	2	44	1	0	0	0	0	1	0	0	0	9654	1667	58	2	100	2	MME	3	154802054	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	14109302	154802054	43220376	82	5542										
MCCC1	56922	hgsc.bcm.edu	37	chr3	182751790	182751790	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	attacttactgtttttaccaTctttaagagtcatgtttctg	5	7	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:182751790T>C	ENST00000265594.4	-	14	1816	c.1670A>G	c.(1669-1671)gAt>gGt	p.D557G	MCCC1_ENST00000492597.1_Missense_Mutation_p.D448G|MCCC1_ENST00000489909.1_5'UTR|MCCC1_ENST00000539926.1_Missense_Mutation_p.D422G	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	557					biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	GTTTTTACCATCTTTAAGAGT	0.323																																					p.D557G		Atlas-SNP	.											.	MCCC1	87	.	0			c.A1670G						.						82	85	84					3																	182751790		2203	4300	6503	SO:0001583	missense	56922	exon14			TTACCATCTTTAA	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1670A>G	chr3.hg19:g.182751790T>C	ENSP00000265594:p.Asp557Gly	98.0	0.0		89.0	6.0	NM_020166	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	hg19	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.561956	0.27915	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176	D;D;D;D	0.95656	-3.77;-3.71;-3.57;-3.48	5.39	4.24	0.50183	.	0.285828	0.39083	N	0.001476	D	0.92227	0.7535	L	0.56769	1.78	0.38053	D	0.93582	P;B;B	0.37122	0.583;0.164;0.001	B;B;B	0.33750	0.169;0.118;0.002	D	0.89555	0.3802	10	0.25751	T	0.34	.	10.4088	0.44280	0.0:0.078:0.0:0.922	.	510;448;557	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	G	557;448;407;422;510	ENSP00000265594:D557G;ENSP00000419898:D448G;ENSP00000441253:D422G;ENSP00000420433:D510G	ENSP00000265594:D557G	D	-	2	0	MCCC1	184234484	1.000000	0.71417	0.942000	0.38095	0.630000	0.37929	3.451000	0.52964	0.892000	0.36259	0.482000	0.46254	GAT	.	.		0.323	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		C	182751790	T	C	182751790	3	2	44	1	0	0	0	0	1	0	0	0	9383	1435	50	2	531	2	MCCC1	3	182751790	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	27949736	182751790	15270640	83	5543										
PIGZ	80235	hgsc.bcm.edu	37	chr3	196674726	196674726	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	caggaggcccatttgtgcagAggcctggaggccgacttgca	15	11	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr3:196674726A>G	ENST00000412723.1	-	3	1188	c.1042T>C	c.(1042-1044)Tct>Cct	p.S348P		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	348					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		ATTTGTGCAGAGGCCTGGAGG	0.652																																					p.S348P		Atlas-SNP	.											.	PIGZ	34	.	0			c.T1042C						.						48	57	54					3																	196674726		2203	4299	6502	SO:0001583	missense	80235	exon3			GTGCAGAGGCCTG	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	30596	protein-coding gene	gene with protein product	"GPI mannosyltransferase 4", "dol-P-Man dependent GPI mannosyltransferase"	611671	"phosphatidylinositol glycan, class Z"			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.1042T>C	chr3.hg19:g.196674726A>G	ENSP00000413405:p.Ser348Pro	104.0	0.0		86.0	4.0	NM_025163	Q9H9G6	Missense_Mutation	SNP	ENST00000412723.1	hg19	CCDS3324.1	.	.	.	.	.	.	.	.	.	.	A	4.739	0.137419	0.09032	.	.	ENSG00000119227	ENST00000412723	T	0.12255	2.7	4.65	2.18	0.27775	.	1.037100	0.07610	N	0.925248	T	0.10252	0.0251	N	0.21194	0.64	0.09310	N	0.999999	P	0.38677	0.642	B	0.42163	0.378	T	0.30119	-0.9989	10	0.37606	T	0.19	-0.0476	1.6041	0.02680	0.5587:0.1646:0.0942:0.1825	.	348	Q86VD9	PIGZ_HUMAN	P	348	ENSP00000413405:S348P	ENSP00000413405:S348P	S	-	1	0	PIGZ	198159123	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.185000	0.09684	0.359000	0.24239	0.459000	0.35465	TCT	.	.		0.652	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163		G	196674726	A	G	196674726	3	3	44	1	0	0	0	0	1	0	0	0	11914	304	11	2	701	2	PIGZ	3	196674726	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	13922936	196674726	1347704	84	5544										
WHSC2	7469	hgsc.bcm.edu	37	chr4	1993397	1993397	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	catgagcacccaggggtccgAgtcgaggctggcgagctgga	17	11	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:1993397A>C	ENST00000411638.2	-	2	271	c.256T>G	c.(256-258)Tcg>Gcg	p.S86A	NELFA_ENST00000382882.3_Missense_Mutation_p.S97A|NELFA_ENST00000542778.1_Intron	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A	86					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)										CAGGGGTCCGAGTCGAGGCTG	0.602																																					p.S97A		Atlas-SNP	.											.	.	.	.	0			c.T289G						.						111	120	117					4																	1993397		2203	4300	6503	SO:0001583	missense	7469	exon2			GGTCCGAGTCGAG	AF101434	CCDS3358.2	4p16.3	2013-01-31	2013-01-31	2013-01-31	ENSG00000185049	ENSG00000185049			12768	protein-coding gene	gene with protein product		606026	"Wolf-Hirschhorn syndrome candidate 2"	WHSC2		10409432	Standard	NM_005663		Approved	NELF-A	uc003gem.3	Q9H3P2	OTTHUMG00000089967	ENST00000411638.2:c.256T>G	chr4.hg19:g.1993397A>C	ENSP00000399165:p.Ser86Ala	121.0	0.0		133.0	45.0	NM_005663	A2A2T1|O95392	Missense_Mutation	SNP	ENST00000411638.2	hg19		.	.	.	.	.	.	.	.	.	.	A	17.29	3.351947	0.61183	.	.	ENSG00000185049	ENST00000382882;ENST00000416258;ENST00000411638;ENST00000431323;ENST00000455762	T;T;T;T	0.49432	1.52;0.78;1.52;1.52	5.18	5.18	0.71444	.	0.061993	0.64402	D	0.000002	T	0.40694	0.1127	L	0.52126	1.63	0.80722	D	1	B	0.31817	0.341	B	0.28305	0.088	T	0.41502	-0.9505	10	0.62326	D	0.03	-23.6281	10.2797	0.43532	0.9223:0.0:0.0777:0.0	.	86	Q9H3P2	NELFA_HUMAN	A	97;90;86;102;16	ENSP00000372335:S97A;ENSP00000387647:S90A;ENSP00000399165:S86A;ENSP00000395761:S102A	ENSP00000372335:S97A	S	-	1	0	WHSC2	1963195	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.180000	0.65048	1.955000	0.56771	0.379000	0.24179	TCG	.	.		0.602	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663		C	1993397	A	C	1993397	3	2	44	1	0	0	0	0	1	0	0	0	17379	304	11	5	1370	5	WHSC2	4	1993397	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10		1993397	189160879	85	5545										
ZFYVE28	57732	hgsc.bcm.edu	37	chr4	2306482	2306482	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctcctgggtggcgaccgcagAgtccagggaagtgggcgatt	17	10	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:2306482A>G	ENST00000290974.2	-	8	1924	c.1585T>C	c.(1585-1587)Tct>Cct	p.S529P	ZFYVE28_ENST00000515312.1_Missense_Mutation_p.S459P|ZFYVE28_ENST00000511071.1_Missense_Mutation_p.S499P|RP11-478C1.7_ENST00000510632.1_RNA	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	529					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						GCGACCGCAGAGTCCAGGGAA	0.657																																					p.S529P		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.T1585C						.						36	40	39					4																	2306482		2200	4284	6484	SO:0001583	missense	57732	exon8			CCGCAGAGTCCAG	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"Zinc fingers, FYVE domain containing"	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.1585T>C	chr4.hg19:g.2306482A>G	ENSP00000290974:p.Ser529Pro	93.0	0.0		87.0	4.0	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Missense_Mutation	SNP	ENST00000290974.2	hg19	CCDS33942.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.791366	0.50102	.	.	ENSG00000159733	ENST00000290974;ENST00000511071;ENST00000515312	T;T;T	0.60040	0.24;0.22;0.24	3.81	-4.14	0.03892	.	1.410490	0.04189	N	0.327910	T	0.54631	0.1870	M	0.64997	1.995	0.09310	N	1	B;P	0.51351	0.002;0.944	B;P	0.47346	0.002;0.544	T	0.53129	-0.8482	10	0.44086	T	0.13	.	3.346	0.07136	0.3769:0.4099:0.0808:0.1324	.	499;529	Q9HCC9-2;Q9HCC9	.;LST2_HUMAN	P	529;499;459	ENSP00000290974:S529P;ENSP00000425706:S499P;ENSP00000426299:S459P	ENSP00000290974:S529P	S	-	1	0	ZFYVE28	2276280	0.484000	0.25964	0.000000	0.03702	0.018000	0.09664	0.394000	0.20834	-1.030000	0.03312	0.254000	0.18369	TCT	.	.		0.657	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371		G	2306482	A	G	2306482	3	3	44	1	0	0	0	0	1	0	0	0	17685	304	11	2	1102	2	ZFYVE28	4	2306482	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	313085	2306482	188847794	86	5546										
MSX1	4487	hgsc.bcm.edu	37	chr4	4864457	4864457	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gccccccagcctgcaccctcCgcaaacacaagacgaaccgt	7	20	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:4864457C>T	ENST00000382723.4	+	2	733	c.499C>T	c.(499-501)Cgc>Tgc	p.R167C	MSX1_ENST00000468421.1_3'UTR	NM_002448.3	NP_002439.2	P28360	MSX1_HUMAN	msh homeobox 1	167					activation of meiosis (GO:0090427)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway involved in heart development (GO:0061312)|bone morphogenesis (GO:0060349)|cartilage morphogenesis (GO:0060536)|cell morphogenesis (GO:0000902)|cellular response to nicotine (GO:0071316)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic nail plate morphogenesis (GO:0035880)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|mammary gland epithelium development (GO:0061180)|mesenchymal cell proliferation (GO:0010463)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902255)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of odontogenesis (GO:0042481)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			endometrium(3)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	11				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CTGCACCCTCCGCAAACACAA	0.597																																					p.R167C		Atlas-SNP	.											.	MSX1	19	.	0			c.C499T						.						61	78	72					4																	4864457		2191	4269	6460	SO:0001583	missense	4487	exon2			ACCCTCCGCAAAC	M97676	CCDS3378.2	4p16.2	2011-06-20	2006-11-21		ENSG00000163132	ENSG00000163132		"Homeoboxes / ANTP class : NKL subclass"	7391	protein-coding gene	gene with protein product		142983	"msh (Drosophila) homeo box homolog 1 (formerly homeo box 7)", "msh homeobox homolog 1 (Drosophila)"	HOX7		1685479, 1973146	Standard	NM_002448		Approved	HYD1, OFC5	uc003gif.3	P28360	OTTHUMG00000090335	ENST00000382723.4:c.499C>T	chr4.hg19:g.4864457C>T	ENSP00000372170:p.Arg167Cys	83.0	0.0		88.0	36.0	NM_002448	A0SZU5|A8K3M1|Q96NY4	Missense_Mutation	SNP	ENST00000382723.4	hg19	CCDS3378.2	.	.	.	.	.	.	.	.	.	.	C	21.3	4.129346	0.77549	.	.	ENSG00000163132	ENST00000382723	D	0.95171	-3.63	4.96	4.96	0.65561	Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.97129	0.9062	M	0.85777	2.775	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.97515	1.0069	10	0.87932	D	0	-10.6849	13.2139	0.59844	0.1593:0.8407:0.0:0.0	.	161	P28360	MSX1_HUMAN	C	167	ENSP00000372170:R167C	ENSP00000372170:R167C	R	+	1	0	MSX1	4915358	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	1.396000	0.34531	2.456000	0.83038	0.462000	0.41574	CGC	.	.		0.597	MSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206700.3			T	4864457	C	T	4864457	3	4	44	1	0	0	0	0	1	0	0	0	9904	652	23	1	505	1	MSX1	4	4864457	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	2557975	4864457	186289819	87	5547										
CPEB2	132864	hgsc.bcm.edu	37	chr4	15060074	15060074	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttcttctctttcaagaagagAgctcagttcaggcactcatt	7	10	6	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:15060074A>G	ENST00000507071.1	+	8	1243	c.1156A>G	c.(1156-1158)Agc>Ggc	p.S386G	CPEB2_ENST00000541112.1_Missense_Mutation_p.S823G|CPEB2_ENST00000538197.1_Missense_Mutation_p.S831G|RP11-665G4.1_ENST00000502344.1_RNA|CPEB2_ENST00000259997.5_Missense_Mutation_p.S394G|CPEB2_ENST00000345451.3_Missense_Mutation_p.S356G|CPEB2_ENST00000382401.3_Missense_Mutation_p.S359G|CPEB2_ENST00000382395.3_Missense_Mutation_p.S364G|RP11-665G4.1_ENST00000513384.1_RNA|CPEB2_ENST00000442003.2_Missense_Mutation_p.S804G			Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding protein 2	386	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to arsenic-containing substance (GO:0071243)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to oxidative stress (GO:0034599)|negative regulation of cytoplasmic translation (GO:2000766)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of GTPase activity (GO:0034260)	cytoplasm (GO:0005737)|messenger ribonucleoprotein complex (GO:1990124)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|ribosome binding (GO:0043022)|translation repressor activity, nucleic acid binding (GO:0000900)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(3)	14						TCAAGAAGAGAGCTCAGTTCA	0.363																																					p.S831G		Atlas-SNP	.											.	CPEB2	77	.	0			c.A2491G						.						143	145	144					4																	15060074		2203	4300	6503	SO:0001583	missense	132864	exon9			GAAGAGAGCTCAG	AY247744	CCDS56325.1, CCDS56326.1	4p15.33	2013-02-12			ENSG00000137449	ENSG00000137449		"RNA binding motif (RRM) containing"	21745	protein-coding gene	gene with protein product		610605				12672660	Standard	NM_182485		Approved		uc003gnk.2	Q7Z5Q1	OTTHUMG00000090669	ENST00000507071.1:c.1156A>G	chr4.hg19:g.15060074A>G	ENSP00000424084:p.Ser386Gly	126.0	0.0		129.0	6.0	NM_001177382	E7EPM3|F5H160|Q3B8N6|Q3MI89|Q3MI90|Q3MI92|Q7Z5Q0	Missense_Mutation	SNP	ENST00000507071.1	hg19		.	.	.	.	.	.	.	.	.	.	A	18.61	3.660210	0.67586	.	.	ENSG00000137449	ENST00000538197;ENST00000541112;ENST00000442003;ENST00000507071;ENST00000345451;ENST00000382395;ENST00000382401;ENST00000259997;ENST00000382391;ENST00000509684	T;T;T;T;T;T;T;T;T	0.06294	3.32;3.32;3.32;3.32;3.32;3.32;3.32;3.32;3.32	5.76	5.76	0.90799	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.227041	0.56097	D	0.000039	T	0.09291	0.0229	N	0.25789	0.76	0.54753	D	0.999982	B;B;B;B;B;B	0.32245	0.164;0.001;0.01;0.028;0.001;0.361	B;B;B;B;B;B	0.41374	0.134;0.001;0.018;0.04;0.001;0.355	T	0.23691	-1.0181	10	0.62326	D	0.03	-10.5656	16.0607	0.80836	1.0:0.0:0.0:0.0	.	359;364;804;831;356;386	Q7Z5Q1-4;Q7Z5Q1-6;E7EPM3;F5H160;Q7Z5Q1-5;Q7Z5Q1	.;.;.;.;.;CPEB2_HUMAN	G	831;823;804;386;356;364;359;394;373;39	ENSP00000443985:S831G;ENSP00000437884:S823G;ENSP00000414270:S804G;ENSP00000424084:S386G;ENSP00000334058:S356G;ENSP00000371832:S364G;ENSP00000371838:S359G;ENSP00000259997:S394G;ENSP00000423890:S39G	ENSP00000259997:S394G	S	+	1	0	CPEB2	14669172	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.200000	0.70718	0.477000	0.44152	AGC	.	.		0.363	CPEB2-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000207349.2	XM_059607		G	15060074	A	G	15060074	3	3	44	1	0	0	0	0	1	0	0	0	3803	304	11	2	2534	2	CPEB2	4	15060074	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	10195617	15060074	176094202	88	5548										
STIM2	57620	hgsc.bcm.edu	37	chr4	27000885	27000885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acgaaccttcatttatgatcTcccagttgaaaatcagtgac	6	10	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:27000885T>C	ENST00000467011.1	+	5	966	c.541T>C	c.(541-543)Tcc>Ccc	p.S181P	STIM2_ENST00000382009.3_Missense_Mutation_p.S268P|STIM2_ENST00000467087.1_Missense_Mutation_p.S181P|STIM2_ENST00000465503.1_Missense_Mutation_p.S181P|STIM2_ENST00000412829.2_Missense_Mutation_p.S268P|STIM2_ENST00000237364.5_Missense_Mutation_p.S268P	NM_001169117.1	NP_001162588	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	181	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				ATTTATGATCTCCCAGTTGAA	0.343																																					p.S181P		Atlas-SNP	.											.	STIM2	77	.	0			c.T541C						.						114	104	108					4																	27000885		2203	4300	6503	SO:0001583	missense	57620	exon5			ATGATCTCCCAGT	AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"Sterile alpha motif (SAM) domain containing"	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467011.1:c.541T>C	chr4.hg19:g.27000885T>C	ENSP00000419383:p.Ser181Pro	83.0	0.0		96.0	4.0	NM_001169118	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Missense_Mutation	SNP	ENST00000467011.1	hg19	CCDS54752.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.480216	0.63849	.	.	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000467011;ENST00000412829;ENST00000465503	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	5.77	4.56	0.56223	.	0.386184	0.31370	N	0.007774	T	0.48114	0.1482	M	0.62723	1.935	0.25619	N	0.986428	P;P;P	0.45176	0.852;0.809;0.773	P;P;B	0.47134	0.539;0.539;0.404	T	0.46735	-0.9170	10	0.72032	D	0.01	.	12.3285	0.55024	0.1268:0.0:0.0:0.8732	.	268;268;268	A6H8L7;E9PGD0;F5GXJ4	.;.;.	P	181;268;268;181;268;181	ENSP00000419073:S181P;ENSP00000371439:S268P;ENSP00000237364:S268P;ENSP00000419383:S181P;ENSP00000404812:S268P;ENSP00000417569:S181P	ENSP00000237364:S268P	S	+	1	0	STIM2	26609983	0.000000	0.05858	0.888000	0.34837	0.981000	0.71138	0.295000	0.19065	1.076000	0.40961	0.533000	0.62120	TCC	.	.		0.343	STIM2-003	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000356861.1	NM_020860		C	27000885	T	C	27000885	3	2	44	1	0	0	0	0	1	0	0	0	15299	1551	54	2	559	2	STIM2	4	27000885	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	11940811	27000885	164153391	89	5549										
GABRA2	2555	hgsc.bcm.edu	37	chr4	46312234	46312234	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aatgagcatccattgggaaaTcctccaagtgcattgggcat	10	9	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:46312234T>C	ENST00000510861.1	-	6	688	c.515A>G	c.(514-516)gAt>gGt	p.D172G	GABRA2_ENST00000514090.1_Missense_Mutation_p.D172G|GABRA2_ENST00000381620.4_Missense_Mutation_p.D172G|GABRA2_ENST00000540012.1_Missense_Mutation_p.D117G|GABRA2_ENST00000507069.1_Missense_Mutation_p.D172G|GABRA2_ENST00000515082.1_Missense_Mutation_p.D172G|GABRA2_ENST00000356504.1_Missense_Mutation_p.D172G			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	172					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	CATTGGGAAATCCTCCAAGTG	0.383																																					p.D172G		Atlas-SNP	.											.	GABRA2	134	.	0			c.A515G						.						136	133	134					4																	46312234		2203	4300	6503	SO:0001583	missense	2555	exon6			GGGAAATCCTCCA		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.515A>G	chr4.hg19:g.46312234T>C	ENSP00000421828:p.Asp172Gly	124.0	0.0		109.0	5.0	NM_000807	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	hg19	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.909925	0.92107	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000540012;ENST00000507069;ENST00000515082	T;T;T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12	5.9	5.9	0.94986	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.89487	0.6729	M	0.87547	2.89	0.80722	D	1	D;D;D	0.89917	0.997;0.982;1.0	D;P;D	0.97110	0.976;0.879;1.0	D	0.91083	0.4901	10	0.72032	D	0.01	.	15.5133	0.75802	0.0:0.0:0.0:1.0	.	117;172;172	B7Z1H8;G5E9Z6;P47869	.;.;GBRA2_HUMAN	G	172;172;172;172;117;172;172	ENSP00000421828:D172G;ENSP00000421300:D172G;ENSP00000371033:D172G;ENSP00000348897:D172G;ENSP00000444409:D117G;ENSP00000427603:D172G;ENSP00000423840:D172G	ENSP00000348897:D172G	D	-	2	0	GABRA2	46006991	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.021000	0.88750	2.251000	0.74343	0.528000	0.53228	GAT	.	.		0.383	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			C	46312234	T	C	46312234	3	2	44	1	0	0	0	0	1	0	0	0	6169	1435	50	2	860	2	GABRA2	4	46312234	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	19311349	46312234	144842042	90	5550										
ATP10D	57205	hgsc.bcm.edu	37	chr4	47559792	47559792	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctccatcgcttaacagtgggAaagagccatcttctggagtt	10	10	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:47559792A>G	ENST00000273859.3	+	12	2205	c.1936A>G	c.(1936-1938)Aaa>Gaa	p.K646E	AC092597.3_ENST00000508081.1_RNA	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	646					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						TAACAGTGGGAAAGAGCCATC	0.483																																					p.K646E		Atlas-SNP	.											.	ATP10D	168	.	0			c.A1936G						.						72	77	76					4																	47559792		2203	4300	6503	SO:0001583	missense	57205	exon12			AGTGGGAAAGAGC	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.1936A>G	chr4.hg19:g.47559792A>G	ENSP00000273859:p.Lys646Glu	83.0	0.0		72.0	4.0	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	hg19	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	A	11.15	1.555392	0.27739	.	.	ENSG00000145246	ENST00000273859	T	0.38722	1.12	5.48	5.48	0.80851	HAD-like domain (1);	0.361702	0.31041	N	0.008375	T	0.40297	0.1111	L	0.59436	1.845	0.80722	D	1	B	0.25904	0.137	B	0.30401	0.115	T	0.23904	-1.0175	10	0.09843	T	0.71	-17.6818	14.7444	0.69480	1.0:0.0:0.0:0.0	.	646	Q9P241	AT10D_HUMAN	E	646	ENSP00000273859:K646E	ENSP00000273859:K646E	K	+	1	0	ATP10D	47254549	1.000000	0.71417	0.915000	0.36163	0.014000	0.08584	6.471000	0.73562	2.085000	0.62840	0.459000	0.35465	AAA	.	.		0.483	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		G	47559792	A	G	47559792	3	3	44	1	0	0	0	0	1	0	0	0	1118	247	9	2	1978	2	ATP10D	4	47559792	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1247558	47559792	143594484	91	5551										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79186220	79186220	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctggaaaatgttgcccgcaGtgctctgcaagatcctgctc	10	13	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:79186220G>T	ENST00000325942.6	+	7	1085	c.645G>T	c.(643-645)caG>caT	p.Q215H	FRAS1_ENST00000264899.6_Missense_Mutation_p.Q215H|FRAS1_ENST00000264895.6_Missense_Mutation_p.Q215H	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	215	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GTTGCCCGCAGTGCTCTGCAA	0.478																																					p.Q215H		Atlas-SNP	.											.	FRAS1	779	.	0			c.G645T						.						92	96	95					4																	79186220		2040	4173	6213	SO:0001583	missense	80144	exon7			CCCGCAGTGCTCT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.645G>T	chr4.hg19:g.79186220G>T	ENSP00000326330:p.Gln215His	97.0	0.0		98.0	6.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	15.77|15.77|15.77	2.932689|2.932689|2.932689	0.52866|0.52866|0.52866	.|.|.	.|.|.	ENSG00000138759|ENSG00000138759|ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000264899;ENST00000380674|ENST00000502446|ENST00000508900	T;T;T|.|.	0.72835|.|.	-0.69;-0.69;-0.69|.|.	5.14|5.14|5.14	4.3|4.3|4.3	0.51218|0.51218|0.51218	.|.|.	0.292426|.|.	0.34555|.|.	N|.|.	0.003874|.|.	T|T|T	0.47525|0.47525|0.47525	0.1450|0.1450|0.1450	L|L|L	0.38838|0.38838|0.38838	1.175|1.175|1.175	0.37974|0.37974|0.37974	D|D|D	0.933399|0.933399|0.933399	P;P|.|.	0.49961|.|.	0.93;0.93|.|.	P;P|.|.	0.59948|.|.	0.866;0.866|.|.	T|T|T	0.48822|0.48822|0.48822	-0.9001|-0.9001|-0.9001	10|5|5	0.72032|.|.	D|.|.	0.01|.|.	.|.|.	8.6603|8.6603|8.6603	0.34088|0.34088|0.34088	0.2143:0.0:0.7857:0.0|0.2143:0.0:0.7857:0.0|0.2143:0.0:0.7857:0.0	.|.|.	215;215|.|.	E9PHH6;A2RRR8|.|.	.;.|.|.	H|I|L	215|144|58	ENSP00000326330:Q215H;ENSP00000264895:Q215H;ENSP00000264899:Q215H|.|.	ENSP00000264895:Q215H|.|.	Q|S|V	+|+|+	3|2|1	2|0|0	FRAS1|FRAS1|FRAS1	79405244|79405244|79405244	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.365000|0.365000|0.365000	0.29674|0.29674|0.29674	2.956000|2.956000|2.956000	0.49129|0.49129|0.49129	1.540000|1.540000|1.540000	0.49301|0.49301|0.49301	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	CAG|AGT|GTG	.	.		0.478	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			T	79186220	G	T	79186220	3	4	44	1	0	0	0	0	1	0	0	0	6050	1020	36	3	671	3	FRAS1	4	79186220	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	31626428	79186220	111968056	92	5552										
ANXA3	306	hgsc.bcm.edu	37	chr4	79512700	79512700	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	attctgatttggtttcagtaTacaagaagagtcttggagat	10	4	3	4	rs376948856		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:79512700T>C	ENST00000264908.6	+	7	785	c.406T>C	c.(406-408)Tac>Cac	p.Y136H	ANXA3_ENST00000512884.1_Missense_Mutation_p.Y97H|ANXA3_ENST00000503570.2_Missense_Mutation_p.Y97H	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	136					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						GGTTTCAGTATACAAGAAGAG	0.333																																					p.Y136H	GBM(2;126 157 27790 28920 42492)	Atlas-SNP	.											.	ANXA3	35	.	0			c.T406C						.	T	HIS/TYR	0,4406		0,0,2203	110	114	112		406	3.8	0.2	4		112	1,8599	1.2+/-3.3	0,1,4299	no	missense	ANXA3	NM_005139.2	83	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	136/324	79512700	1,13005	2203	4300	6503	SO:0001583	missense	306	exon7			TCAGTATACAAGA	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"Annexins"	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.406T>C	chr4.hg19:g.79512700T>C	ENSP00000264908:p.Tyr136His	101.0	0.0		84.0	4.0	NM_005139	B2R9W6|Q6LET2	Missense_Mutation	SNP	ENST00000264908.6	hg19	CCDS3584.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392335	0.62066	0.0	1.16E-4	ENSG00000138772	ENST00000264908;ENST00000512884;ENST00000503570;ENST00000514171	T;T;T;T	0.04862	3.54;3.54;3.54;3.54	4.95	3.76	0.43208	Annexin repeat, conserved site (1);	0.282328	0.33916	N	0.004437	T	0.20170	0.0485	M	0.70595	2.14	0.40556	D	0.981166	D	0.55605	0.972	D	0.68192	0.956	T	0.00425	-1.1747	10	0.59425	D	0.04	.	9.6492	0.39886	0.0:0.0836:0.0:0.9164	.	136	P12429	ANXA3_HUMAN	H	136;97;97;136	ENSP00000264908:Y136H;ENSP00000423068:Y97H;ENSP00000421015:Y97H;ENSP00000421512:Y136H	ENSP00000264908:Y136H	Y	+	1	0	ANXA3	79731724	0.998000	0.40836	0.174000	0.22961	0.982000	0.71751	3.487000	0.53222	0.905000	0.36596	0.477000	0.44152	TAC	.	.		0.333	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139		C	79512700	T	C	79512700	3	2	44	1	0	0	0	0	1	0	0	0	719	1406	49	2	428	2	ANXA3	4	79512700	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	326480	79512700	111641576	93	5553										
SEC31A	22872	hgsc.bcm.edu	37	chr4	83791555	83791555	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	caattcaggatctgccatgcTccaagcaattgccaaaatcc	6	13	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:83791555T>C	ENST00000395310.2	-	8	987	c.805A>G	c.(805-807)Agc>Ggc	p.S269G	SEC31A_ENST00000513858.1_Missense_Mutation_p.S269G|SEC31A_ENST00000326950.5_Missense_Mutation_p.S269G|SEC31A_ENST00000505472.1_Missense_Mutation_p.S269G|SEC31A_ENST00000508479.1_Missense_Mutation_p.S269G|SEC31A_ENST00000436790.2_5'UTR|SEC31A_ENST00000505984.1_Missense_Mutation_p.S269G|SEC31A_ENST00000264405.5_Missense_Mutation_p.S41G|SEC31A_ENST00000311785.7_Missense_Mutation_p.S269G|SEC31A_ENST00000348405.4_Missense_Mutation_p.S269G|SEC31A_ENST00000500777.2_Missense_Mutation_p.S269G|SEC31A_ENST00000443462.2_Missense_Mutation_p.S264G|SEC31A_ENST00000448323.1_Missense_Mutation_p.S269G|SEC31A_ENST00000508502.1_Missense_Mutation_p.S269G|SEC31A_ENST00000509142.1_Missense_Mutation_p.S269G|SEC31A_ENST00000432794.1_Missense_Mutation_p.S269G|SEC31A_ENST00000355196.2_Missense_Mutation_p.S269G	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	269	Interaction with SEC13.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				TCTGCCATGCTCCAAGCAATT	0.393																																					p.S269G		Atlas-SNP	.											.	SEC31A	227	.	0			c.A805G						.						146	132	136					4																	83791555		2203	4300	6503	SO:0001583	missense	22872	exon8			CCATGCTCCAAGC	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.805A>G	chr4.hg19:g.83791555T>C	ENSP00000378721:p.Ser269Gly	70.0	0.0		77.0	4.0	NM_001077206	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Missense_Mutation	SNP	ENST00000395310.2	hg19	CCDS3596.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.073830	0.76415	.	.	ENSG00000138674	ENST00000348405;ENST00000513858;ENST00000395310;ENST00000443462;ENST00000509142;ENST00000432794;ENST00000448323;ENST00000326950;ENST00000311785;ENST00000505472;ENST00000500777;ENST00000508502;ENST00000355196;ENST00000264405;ENST00000505984;ENST00000508479	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.72942	1.6;1.6;1.6;1.08;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;-0.7;1.6;1.6	5.08	5.08	0.68730	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84973	0.5591	M	0.84948	2.725	0.80722	D	1	D;D;D;D;D;D;D;D;D;B	0.71674	0.992;0.987;0.99;0.998;0.99;0.967;0.996;0.996;0.99;0.438	P;P;D;D;D;P;D;D;P;B	0.83275	0.897;0.869;0.979;0.996;0.921;0.839;0.937;0.99;0.897;0.358	D	0.86029	0.1512	10	0.42905	T	0.14	-14.2828	15.1495	0.72687	0.0:0.0:0.0:1.0	.	264;269;269;269;269;269;269;269;269;41	B4DIW6;B7ZL00;O94979-5;D6RHZ5;O94979-6;O94979-4;O94979-3;O94979-2;O94979;O94979-7	.;.;.;.;.;.;.;.;SC31A_HUMAN;.	G	269;269;269;264;269;269;269;269;269;269;269;269;269;41;269;269	ENSP00000337602:S269G;ENSP00000426886:S269G;ENSP00000378721:S269G;ENSP00000408027:S264G;ENSP00000426569:S269G;ENSP00000407944:S269G;ENSP00000400926:S269G;ENSP00000325087:S269G;ENSP00000309070:S269G;ENSP00000421633:S269G;ENSP00000421464:S269G;ENSP00000424635:S269G;ENSP00000347329:S269G;ENSP00000264405:S41G;ENSP00000424451:S269G;ENSP00000425999:S269G	ENSP00000264405:S41G	S	-	1	0	SEC31A	84010579	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.943000	0.70211	2.027000	0.59764	0.454000	0.30748	AGC	.	.		0.393	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		C	83791555	T	C	83791555	3	2	44	1	0	0	0	0	1	0	0	0	14013	1551	54	2	2937	2	SEC31A	4	83791555	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4278855	83791555	107362721	94	5554										
HELQ	113510	hgsc.bcm.edu	37	chr4	84368176	84368176	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gagttctataccaaaacttgAcaaacctgaaatctagaata	5	8	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:84368176A>G	ENST00000295488.3	-	4	1366	c.1204T>C	c.(1204-1206)Tca>Cca	p.S402P	HELQ_ENST00000510985.1_Intron	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	402	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						CCAAAACTTGACAAACCTGAA	0.388								Other identified genes with known or suspected DNA repair function																													p.S402P		Atlas-SNP	.											.	HELQ	95	.	0			c.T1204C						.						33	32	33					4																	84368176		2203	4300	6503	SO:0001583	missense	113510	exon4			AACTTGACAAACC	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1204T>C	chr4.hg19:g.84368176A>G	ENSP00000295488:p.Ser402Pro	95.0	0.0		95.0	4.0	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	hg19	CCDS3603.1	.	.	.	.	.	.	.	.	.	.	A	16.78	3.216941	0.58452	.	.	ENSG00000163312	ENST00000295488	T	0.15718	2.4	5.44	5.44	0.79542	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.266906	0.37577	N	0.002038	T	0.48537	0.1505	M	0.92268	3.29	0.80722	D	1	D	0.76494	0.999	D	0.70487	0.969	T	0.57236	-0.7846	10	0.48119	T	0.1	-32.4597	11.7528	0.51857	0.853:0.147:0.0:0.0	.	402	Q8TDG4	HELQ_HUMAN	P	402	ENSP00000295488:S402P	ENSP00000295488:S402P	S	-	1	0	HELQ	84587200	1.000000	0.71417	1.000000	0.80357	0.677000	0.39632	3.985000	0.56930	2.187000	0.69744	0.477000	0.44152	TCA	.	.		0.388	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		G	84368176	A	G	84368176	3	3	44	1	0	0	0	0	1	0	0	0	7056	275	10	2	2161	2	HELQ	4	84368176	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	576621	84368176	106786100	95	5555										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85722810	85722810	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaagagaacttacctcaacaCcatgggttccagagcctgag	9	11	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:85722810C>A	ENST00000295888.4	-	17	3222	c.2815G>T	c.(2815-2817)Gtg>Ttg	p.V939L	WDFY3_ENST00000322366.6_Missense_Mutation_p.V939L|WDFY3-AS1_ENST00000510449.1_RNA|WDFY3_ENST00000512267.1_5'Flank	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	939					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TACCTCAACACCATGGGTTCC	0.473																																					p.V939L		Atlas-SNP	.											WDFY3,NS,carcinoma,0,1	WDFY3	314	.	0			c.G2815T						.						116	119	118					4																	85722810		2203	4300	6503	SO:0001583	missense	23001	exon17			TCAACACCATGGG	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.2815G>T	chr4.hg19:g.85722810C>A	ENSP00000295888:p.Val939Leu	45.0	0.0		47.0	2.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.421944	0.62622	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.44482	0.92;0.92	5.95	5.95	0.96441	.	0.109140	0.64402	D	0.000007	T	0.46249	0.1383	L	0.58101	1.795	0.58432	D	0.999996	B	0.19583	0.037	B	0.19391	0.025	T	0.31971	-0.9924	10	0.54805	T	0.06	.	20.4024	0.99000	0.0:1.0:0.0:0.0	.	939	Q8IZQ1	WDFY3_HUMAN	L	939	ENSP00000318466:V939L;ENSP00000295888:V939L	ENSP00000295888:V939L	V	-	1	0	WDFY3	85941834	1.000000	0.71417	1.000000	0.80357	0.664000	0.39144	7.487000	0.81328	2.827000	0.97445	0.650000	0.86243	GTG	.	.		0.473	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85722810	C	A	85722810	3	1	44	1	0	0	0	0	1	0	0	0	17285	507	18	3	7973	3	WDFY3	4	85722810	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1354634	85722810	105431466	96	5556										
MTTP	4547	hgsc.bcm.edu	37	chr4	100532580	100532580	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aacctgaacatctttcagtaCattgggaaggctggtcttca	9	9	4	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:100532580C>T	ENST00000265517.5	+	14	2162	c.1959C>T	c.(1957-1959)taC>taT	p.Y653Y	MTTP_ENST00000457717.1_Silent_p.Y653Y|MTTP_ENST00000511045.1_Silent_p.Y680Y|RP11-766F14.1_ENST00000508578.1_RNA			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	653	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	TCTTTCAGTACATTGGGAAGG	0.428																																					p.Y653Y		Atlas-SNP	.											.	MTTP	127	.	0			c.C1959T						.						170	155	160					4																	100532580		2203	4300	6503	SO:0001819	synonymous_variant	4547	exon15			TCAGTACATTGGG		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"microsomal triglyceride transfer protein (large polypeptide, 88kD)", "microsomal triglyceride transfer protein (large polypeptide, 88kDa)"	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.1959C>T	chr4.hg19:g.100532580C>T		144.0	0.0		142.0	68.0	NM_000253	A8K428|Q08AM4|Q6P5T3	Silent	SNP	ENST00000265517.5	hg19	CCDS3651.1																																																																																			.	.		0.428	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			T	100532580	C	T	100532580	2	4	44	1	0	0	0	0	0	0	0	1	9973	489	17	3		3	MTTP	4	100532580	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	14809770	100532580	90621696	97	5557										
SGMS2	166929	hgsc.bcm.edu	37	chr4	108817100	108817100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgaaatgggcattttctgtaTcagaaataaatgggattata	9	3	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:108817100T>C	ENST00000394684.4	+	3	948	c.391T>C	c.(391-393)Tca>Cca	p.S131P	RP11-286E11.1_ENST00000513071.1_RNA|RP11-286E11.1_ENST00000499098.1_RNA|SGMS2_ENST00000394686.3_Missense_Mutation_p.S131P|SGMS2_ENST00000359079.4_Missense_Mutation_p.S131P	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	131					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		ATTTTCTGTATCAGAAATAAA	0.403																																					p.S131P		Atlas-SNP	.											.	SGMS2	39	.	0			c.T391C						.						83	90	88					4																	108817100		2203	4300	6503	SO:0001583	missense	166929	exon2			TCTGTATCAGAAA	BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.391T>C	chr4.hg19:g.108817100T>C	ENSP00000378176:p.Ser131Pro	109.0	0.0		121.0	5.0	NM_001136257	A8K2S9|B2RA61	Missense_Mutation	SNP	ENST00000394684.4	hg19	CCDS3677.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145026	0.77888	.	.	ENSG00000164023	ENST00000394684;ENST00000359079;ENST00000394686	T;T;T	0.49432	0.78;0.78;0.78	5.49	5.49	0.81192	.	0.056268	0.64402	D	0.000001	T	0.44871	0.1314	L	0.52905	1.665	0.58432	D	0.999997	P	0.43477	0.808	B	0.39027	0.288	T	0.41484	-0.9506	9	.	.	.	-26.5589	15.887	0.79258	0.0:0.0:0.0:1.0	.	131	Q8NHU3	SMS2_HUMAN	P	131	ENSP00000378176:S131P;ENSP00000351981:S131P;ENSP00000378178:S131P	.	S	+	1	0	SGMS2	109036549	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.093000	0.71422	2.208000	0.71279	0.533000	0.62120	TCA	.	.		0.403	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621		C	108817100	T	C	108817100	3	2	44	1	0	0	0	0	1	0	0	0	14230	1435	50	2	393	2	SGMS2	4	108817100	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	8284520	108817100	82337176	98	5558										
HADH	3033	hgsc.bcm.edu	37	chr4	108940796	108940796	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctggcctccatttcttcaacCcagtgcctgtcatgaaactt	6	14	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:108940796C>T	ENST00000309522.3	+	4	669	c.520C>T	c.(520-522)Cca>Tca	p.P174S	HADH_ENST00000403312.1_Missense_Mutation_p.P233S|HADH_ENST00000454409.2_Missense_Mutation_p.P178S|HADH_ENST00000505878.1_Missense_Mutation_p.P178S|HADH_ENST00000603302.1_Missense_Mutation_p.P174S	NM_005327.4	NP_005318	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase	502					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	15		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000168)		TTTCTTCAACCCAGTGCCTGT	0.507																																					p.P174S		Atlas-SNP	.											.	HADH	40	.	0			c.C520T						.						155	145	148					4																	108940796		2203	4300	6503	SO:0001583	missense	3033	exon4			TTCAACCCAGTGC	X96752	CCDS3678.1, CCDS54790.1	4q22-q26	2012-10-02	2010-04-30		ENSG00000138796	ENSG00000138796	1.1.1.35		4799	protein-coding gene	gene with protein product		601609	"L-3-hydroxyacyl-Coenzyme A dehydrogenase, short chain", "hydroxyacyl-Coenzyme A dehydrogenase"	HADHSC		975867, 16176262	Standard	NM_001184705		Approved	HADH1, SCHAD	uc010ilx.3	Q16836	OTTHUMG00000131810	ENST00000309522.3:c.520C>T	chr4.hg19:g.108940796C>T	ENSP00000312288:p.Pro174Ser	121.0	0.0		111.0	55.0	NM_005327	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000309522.3	hg19	CCDS3678.1	.	.	.	.	.	.	.	.	.	.	C	31	5.090892	0.94149	.	.	ENSG00000138796	ENST00000403312;ENST00000309522;ENST00000505878;ENST00000454409	D;D;D	0.93604	-3.25;-3.25;-3.25	5.37	5.37	0.77165	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.98488	0.9496	H	0.99475	4.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.99785	1.1029	10	0.87932	D	0	-12.7194	19.1228	0.93371	0.0:1.0:0.0:0.0	.	233;178;174	Q16836-2;E9PF18;Q16836	.;.;HCDH_HUMAN	S	174;174;178;178	ENSP00000312288:P174S;ENSP00000425952:P178S;ENSP00000395167:P178S	ENSP00000312288:P174S	P	+	1	0	HADH	109160245	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.818000	0.86416	2.505000	0.84491	0.655000	0.94253	CCA	.	.		0.507	HADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254750.2	NM_005327		T	108940796	C	T	108940796	3	4	44	1	0	0	0	0	1	0	0	0	6951	623	22	3	534	3	HADH	4	108940796	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	123696	108940796	82213480	99	5559										
PDE5A	8654	hgsc.bcm.edu	37	chr4	120528278	120528278	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttgacaacaatgggtctaagAggccggtcaaattcagaggc	12	8	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:120528278A>G	ENST00000354960.3	-	2	646	c.327T>C	c.(325-327)ccT>ccC	p.P109P	PDE5A_ENST00000264805.5_Silent_p.P67P|PDE5A_ENST00000394439.1_Silent_p.P57P	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	109					blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	TGGGTCTAAGAGGCCGGTCAA	0.502																																					p.P109P		Atlas-SNP	.											.	PDE5A	83	.	0			c.T327C						.						86	85	85					4																	120528278		2203	4300	6503	SO:0001819	synonymous_variant	8654	exon2			TCTAAGAGGCCGG	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.327T>C	chr4.hg19:g.120528278A>G		75.0	0.0		76.0	4.0	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Silent	SNP	ENST00000354960.3	hg19	CCDS3713.1																																																																																			.	.		0.502	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		G	120528278	A	G	120528278	2	3	44	1	0	0	0	0	0	0	0	1	11653	291	11	2		2	PDE5A	4	120528278	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	11587482	120528278	70625998	100	5560										
FAT4	79633	hgsc.bcm.edu	37	chr4	126240400	126240400	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctgtttgctatcaatgaaaAgaatggcactattagtctgc	8	8	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:126240400A>G	ENST00000394329.3	+	1	2847	c.2834A>G	c.(2833-2835)aAg>aGg	p.K945R		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	945	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATCAATGAAAAGAATGGCACT	0.478																																					p.K945R		Atlas-SNP	.											.	FAT4	1752	.	0			c.A2834G						.						62	65	64					4																	126240400		1940	4148	6088	SO:0001583	missense	79633	exon1			ATGAAAAGAATGG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.2834A>G	chr4.hg19:g.126240400A>G	ENSP00000377862:p.Lys945Arg	114.0	0.0		83.0	5.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	0.103	-1.149829	0.01714	.	.	ENSG00000196159	ENST00000394329	T	0.01767	4.65	5.1	2.57	0.30868	Cadherin (4);Cadherin-like (1);	0.830857	0.09651	N	0.773731	T	0.01523	0.0049	L	0.27975	0.815	0.80722	D	1	B	0.13594	0.008	B	0.16722	0.016	T	0.45498	-0.9257	10	0.15952	T	0.53	.	4.5503	0.12108	0.6999:0.0:0.1602:0.1399	.	945	Q6V0I7	FAT4_HUMAN	R	945	ENSP00000377862:K945R	ENSP00000377862:K945R	K	+	2	0	FAT4	126459850	1.000000	0.71417	0.993000	0.49108	0.040000	0.13550	3.401000	0.52601	0.372000	0.24591	0.533000	0.62120	AAG	.	.		0.478	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		G	126240400	A	G	126240400	3	3	44	1	0	0	0	0	1	0	0	0	5700	72	3	2	2836	2	FAT4	4	126240400	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	5712122	126240400	64913876	101	5561										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186567931	186567931	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttctgtctggaggatcccagTcatgcctagaaataaacaat	8	9	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:186567931T>C	ENST00000284776.7	-	10	1084	c.575A>G	c.(574-576)gAc>gGc	p.D192G	SORBS2_ENST00000418609.1_Missense_Mutation_p.D96G|SORBS2_ENST00000448662.2_Missense_Mutation_p.D261G|SORBS2_ENST00000431808.1_Missense_Mutation_p.D192G|SORBS2_ENST00000319471.9_Missense_Mutation_p.D278G|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000437304.2_Missense_Mutation_p.D371G|SORBS2_ENST00000355634.5_Missense_Mutation_p.D292G|SORBS2_ENST00000393528.3_Missense_Mutation_p.D238G|SORBS2_ENST00000449407.2_Missense_Mutation_p.D263G	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	192					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		AGGATCCCAGTCATGCCTAGA	0.343																																					p.D371G	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.A1112G						.						83	84	83					4																	186567931		2203	4300	6503	SO:0001583	missense	8470	exon11			TCCCAGTCATGCC		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.575A>G	chr4.hg19:g.186567931T>C	ENSP00000284776:p.Asp192Gly	75.0	0.0		69.0	4.0	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	hg19	CCDS3845.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	21.2|21.2|21.2	4.118889|4.118889|4.118889	0.77323|0.77323|0.77323	.|.|.	.|.|.	ENSG00000154556|ENSG00000154556|ENSG00000154556	ENST00000284776;ENST00000448662;ENST00000431808;ENST00000418609;ENST00000437304;ENST00000319471;ENST00000449407;ENST00000355634;ENST00000393528;ENST00000319454;ENST00000451974|ENST00000445625|ENST00000438278	T;T;T;T;T;T;T;T;T;T;T|.|.	0.34667|.|.	1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35|.|.	5.25|5.25|5.25	5.25|5.25|5.25	0.73442|0.73442|0.73442	.|.|.	0.048195|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|.	0.70193|0.70193|.	0.3196|0.3196|.	L|L|L	0.59436|0.59436|0.59436	1.845|1.845|1.845	0.46149|0.46149|0.46149	D|D|D	0.99889|0.99889|0.99889	P;D;D;P;D;D;D;D;D;P;D;D;P;P;D;D|.|.	0.76494|.|.	0.925;0.997;0.993;0.859;0.998;0.957;0.998;0.999;0.969;0.859;0.986;0.998;0.614;0.933;0.997;0.997|.|.	P;D;P;P;D;P;D;D;P;P;P;D;B;P;D;D|.|.	0.83275|.|.	0.665;0.942;0.9;0.665;0.991;0.709;0.978;0.996;0.818;0.665;0.872;0.987;0.347;0.461;0.96;0.942|.|.	T|T|.	0.69087|0.69087|.	-0.5238|-0.5238|.	10|5|.	0.59425|.|.	D|.|.	0.04|.|.	-34.503|-34.503|-34.503	15.324|15.324|15.324	0.74144|0.74144|0.74144	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	255;238;261;96;111;111;96;238;292;192;263;371;261;238;192;238|.|.	B7Z3D7;G3XAI0;C9JKV9;B7Z3X6;B7Z997;O94875-6;B3KPU4;O94875-4;B3KPQ7;O94875;E9PAS5;E9PAW4;B7Z1G5;O94875-5;O94875-3;O94875-2|.|.	.;.;.;.;.;.;.;.;.;SRBS2_HUMAN;.;.;.;.;.;.|.|.	G|A|W	192;261;192;96;371;278;263;292;238;238;49|90|135	ENSP00000284776:D192G;ENSP00000409158:D261G;ENSP00000411764:D192G;ENSP00000397482:D96G;ENSP00000396008:D371G;ENSP00000322182:D278G;ENSP00000397262:D263G;ENSP00000347852:D292G;ENSP00000377162:D238G;ENSP00000321983:D238G;ENSP00000401818:D49G|.|.	ENSP00000284776:D192G|.|.	D|T|X	-|-|-	2|1|3	0|0|0	SORBS2|SORBS2|SORBS2	186804925|186804925|186804925	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	7.428000|7.428000|7.428000	0.80296|0.80296|0.80296	2.197000|2.197000|2.197000	0.70478|0.70478|0.70478	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	GAC|ACT|TGA	.	.		0.343	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		C	186567931	T	C	186567931	3	2	44	1	0	0	0	0	1	0	0	0	14943	1667	58	2	3087	2	SORBS2	4	186567931	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	60327531	186567931	4586345	102	5562										
FAT1	2195	hgsc.bcm.edu	37	chr4	187538165	187538165	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaagagctgcttaccttttcAcaaactggactgttgtcatt	8	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr4:187538165A>G	ENST00000441802.2	-	11	9278	c.9069T>C	c.(9067-9069)tgT>tgC	p.C3023C		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3023	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TTACCTTTTCACAAACTGGAC	0.388										HNSCC(5;0.00058)																											p.C3023C	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T9069C						.						200	176	184					4																	187538165		1928	4122	6050	SO:0001819	synonymous_variant	2195	exon11			CTTTTCACAAACT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.9069T>C	chr4.hg19:g.187538165A>G		190.0	0.0		131.0	6.0	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.388	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187538165	A	G	187538165	2	3	44	1	0	0	0	0	0	0	0	1	5697	157	6	2		2	FAT1	4	187538165	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	970234	187538165	3616111	103	5563										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32089623	32089623	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctaaatctcctaagtgtagAgcagagggcagggcgccccg	13	12	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:32089623A>G	ENST00000438447.1	+	20	6457	c.6069A>G	c.(6067-6069)agA>agG	p.R2023R	PDZD2_ENST00000282493.3_Silent_p.R2023R			O15018	PDZD2_HUMAN	PDZ domain containing 2	2023					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CTAAGTGTAGAGCAGAGGGCA	0.627																																					p.R2023R		Atlas-SNP	.											.	PDZD2	306	.	0			c.A6069G						.						135	147	143					5																	32089623		2203	4300	6503	SO:0001819	synonymous_variant	23037	exon19			GTGTAGAGCAGAG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.6069A>G	chr5.hg19:g.32089623A>G		36.0	0.0		57.0	4.0	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	hg19	CCDS34137.1																																																																																			.	.		0.627	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			G	32089623	A	G	32089623	2	3	44	1	0	0	0	0	0	0	0	1	11710	301	11	2		2	PDZD2	5	32089623	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10		32089623	148825637	104	5564										
WDR70	55100	hgsc.bcm.edu	37	chr5	37752658	37752658	+	Frame_Shift_Del	DEL	A	A	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	caaagaatgagccagaatggAaaaaacgtaaaatttgaaga							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:37752658delA	ENST00000265107.4	+	18	2104	c.1948delA	c.(1948-1950)aaafs	p.K651fs		NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	651							enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GCCAGAATGGAAAAAACGTAA	0.373																																					p.W649X		Atlas-INDEL	.											.	WDR70	76	.	0			c.1947delG						.						79	77	78					5																	37752658		2203	4300	6503	SO:0001589	frameshift_variant	55100	exon18			.	BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068		"WD repeat domain containing"	25495	protein-coding gene	gene with protein product						12477932	Standard	NM_018034		Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000265107.4:c.1948delA	chr5.hg19:g.37752658delA	ENSP00000265107:p.Lys651fs	83.0	0.0		180.0	11.0	NM_018034	Q9H053	Frame_Shift_Del	DEL	ENST00000265107.4	hg19	CCDS34147.1																																																																																			.	.		0.373	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034		-	37752658	A	-	37752658	7	5	44	1	0	1	0	1	0	0	0	0	17336	247	9	0	2018	0	WDR70	5	37752658	Frame_Shift_Del	DEL	A	TCGA-BC-A3KG-01A-11D-A20W-10	5663035	37752658	143162602	105	5565										
DHX29	54505	hgsc.bcm.edu	37	chr5	54563641	54563641	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttctctgtcataactgcagCtagtgttgcctatccataaa	6	11	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:54563641C>T	ENST00000251636.5	-	22	3452	c.3304G>A	c.(3304-3306)Gct>Act	p.A1102T	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	1102						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				ATAACTGCAGCTAGTGTTGCC	0.353																																					p.A1102T		Atlas-SNP	.											.	DHX29	116	.	0			c.G3304A						.						103	88	93					5																	54563641		2203	4300	6503	SO:0001583	missense	54505	exon22			CTGCAGCTAGTGT	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"DEAH-boxes"	15815	protein-coding gene	gene with protein product		612720	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.3304G>A	chr5.hg19:g.54563641C>T	ENSP00000251636:p.Ala1102Thr	66.0	0.0		68.0	32.0	NM_019030	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Missense_Mutation	SNP	ENST00000251636.5	hg19	CCDS34158.1	.	.	.	.	.	.	.	.	.	.	C	32	5.125601	0.94429	.	.	ENSG00000067248	ENST00000251636	T	0.02709	4.19	5.55	5.55	0.83447	Helicase-associated domain (2);	0.000000	0.85682	D	0.000000	T	0.17534	0.0421	M	0.81614	2.55	0.58432	D	0.999999	D	0.60575	0.988	D	0.68192	0.956	T	0.00074	-1.2123	10	0.87932	D	0	.	19.5112	0.95142	0.0:1.0:0.0:0.0	.	1102	Q7Z478	DHX29_HUMAN	T	1102	ENSP00000251636:A1102T	ENSP00000251636:A1102T	A	-	1	0	DHX29	54599398	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	7.456000	0.80751	2.626000	0.88956	0.557000	0.71058	GCT	.	.		0.353	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030		T	54563641	C	T	54563641	3	4	44	1	0	0	0	0	1	0	0	0	4505	797	28	3	829	3	DHX29	5	54563641	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	16810983	54563641	126351619	106	5566										
IL31RA	133396	hgsc.bcm.edu	37	chr5	55212851	55212851	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agtaccagatcatctgtgtgAggaaggagccccaaatccat	10	10	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:55212851A>G	ENST00000447346.2	+	15	2263	c.2198A>G	c.(2197-2199)gAg>gGg	p.E733G	IL31RA_ENST00000490985.1_Missense_Mutation_p.E591G|IL31RA_ENST00000396834.1_Intron|IL31RA_ENST00000354961.4_Intron|IL31RA_ENST00000359040.5_Intron	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	701					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				CATCTGTGTGAGGAAGGAGCC	0.468																																					p.E733G		Atlas-SNP	.											.	IL31RA	84	.	0			c.A2198G						.						54	60	58					5																	55212851		2203	4300	6503	SO:0001583	missense	133396	exon15			TGTGTGAGGAAGG	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.2198A>G	chr5.hg19:g.55212851A>G	ENSP00000415900:p.Glu733Gly	108.0	0.0		100.0	4.0	NM_139017	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	hg19	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	A	10.68	1.419540	0.25552	.	.	ENSG00000164509	ENST00000447346;ENST00000490985	T;T	0.52754	0.86;0.65	5.65	1.95	0.26073	.	0.581254	0.17930	N	0.157211	T	0.33000	0.0848	L	0.38531	1.155	0.09310	N	0.999999	B	0.11235	0.004	B	0.12156	0.007	T	0.19516	-1.0303	9	.	.	.	0.6464	7.5383	0.27723	0.7519:0.0:0.248:0.0	.	733	Q8NI17-2	.	G	733;591	ENSP00000415900:E733G;ENSP00000427533:E591G	.	E	+	2	0	IL31RA	55248608	0.978000	0.34361	0.002000	0.10522	0.001000	0.01503	1.024000	0.30077	0.159000	0.19401	-0.400000	0.06385	GAG	.	.		0.468	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		G	55212851	A	G	55212851	3	3	44	1	0	0	0	0	1	0	0	0	7700	304	11	2	2256	2	IL31RA	5	55212851	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	649210	55212851	125702409	107	5567										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71493243	71493243	+	Frame_Shift_Del	DEL	A	A	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tctccctacagaagtcattgAaaaaccaccagcagttccag							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:71493243delA	ENST00000296755.7	+	5	4359	c.4061delA	c.(4060-4062)gaafs	p.E1354fs		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1354					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		GAAGTCATTGAAAAACCACCA	0.483																																					p.E1354fs	Melanoma(17;367 822 11631 31730 47712)	Atlas-INDEL	.											.	MAP1B	243	.	0			c.4060delG						.						77	79	78					5																	71493243		2203	4300	6503	SO:0001589	frameshift_variant	4131	exon5			.	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4061delA	chr5.hg19:g.71493243delA	ENSP00000296755:p.Glu1354fs	133.0	0.0		139.0	10.0	NM_005909	A2BDK5	Frame_Shift_Del	DEL	ENST00000296755.7	hg19	CCDS4012.1																																																																																			.	.		0.483	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		-	71493243	A	-	71493243	7	5	44	1	0	1	0	1	0	0	0	0	9237	246	9	0	4079	0	MAP1B	5	71493243	Frame_Shift_Del	DEL	A	TCGA-BC-A3KG-01A-11D-A20W-10	16280392	71493243	109422017	108	5568										
RGNEF	64283	hgsc.bcm.edu	37	chr5	73076546	73076546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aggaaagaacagctatgcccTccagcggtgcagaaactgaa	11	10	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:73076546T>C	ENST00000426542.2	+	6	906	c.886T>C	c.(886-888)Tcc>Ccc	p.S296P	ARHGEF28_ENST00000287898.5_Missense_Mutation_p.S296P|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.S296P|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.S296P|CTC-575I10.1_ENST00000506717.1_RNA|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.S296P|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.S296P			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	296					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										AGCTATGCCCTCCAGCGGTGC	0.478																																					p.S296P		Atlas-SNP	.											NP_001073948_1,NS,carcinoma,0,2	.	.	.	0			c.T886C						.						37	42	41					5																	73076546		1994	4150	6144	SO:0001583	missense	64283	exon7			ATGCCCTCCAGCG		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.886T>C	chr5.hg19:g.73076546T>C	ENSP00000412175:p.Ser296Pro	56.0	0.0		60.0	3.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	T	9.119	1.008623	0.19199	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542	T;T;T;T;T;T	0.11063	3.06;3.05;3.05;2.81;3.05;3.05	5.47	2.85	0.33270	.	.	.	.	.	T	0.18341	0.0440	M	0.65975	2.015	0.09310	N	1	P;P;D;P	0.59767	0.627;0.855;0.986;0.911	B;B;P;P	0.51016	0.184;0.36;0.656;0.466	T	0.08452	-1.0721	9	0.59425	D	0.04	.	6.9073	0.24315	0.1493:0.0:0.156:0.6947	.	296;296;296;296	Q8N1W1;E9PC75;Q8N1W1-2;Q8N1W1-4	RGNEF_HUMAN;.;.;.	P	296	ENSP00000296794:S296P;ENSP00000441913:S296P;ENSP00000441436:S296P;ENSP00000287898:S296P;ENSP00000411459:S296P;ENSP00000412175:S296P	ENSP00000287898:S296P	S	+	1	0	RP11-428C6.1	73112302	0.010000	0.17322	0.120000	0.21714	0.038000	0.13279	1.303000	0.33470	0.976000	0.38417	0.533000	0.62120	TCC	.	.		0.478	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			C	73076546	T	C	73076546	3	2	44	1	0	0	0	0	1	0	0	0	13298	1551	54	2	908	2	RGNEF	5	73076546	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1583303	73076546	107838714	109	5569										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101794140	101794140	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccaagtttcagatctttaagTctgctgtcaaaaaaatgaag	7	7	4	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:101794140T>C	ENST00000506729.1	-	6	1248	c.1077A>G	c.(1075-1077)agA>agG	p.R359R	SLCO6A1_ENST00000514551.1_5'UTR|SLCO6A1_ENST00000379810.1_Intron|SLCO6A1_ENST00000379807.3_Silent_p.R359R|SLCO6A1_ENST00000389019.3_Silent_p.R297R|SLCO6A1_ENST00000513675.1_Intron			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	359						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		GATCTTTAAGTCTGCTGTCAA	0.303																																					p.R359R		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.A1077G						.						141	141	141					5																	101794140		2202	4298	6500	SO:0001819	synonymous_variant	133482	exon6			TTTAAGTCTGCTG	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1077A>G	chr5.hg19:g.101794140T>C		108.0	0.0		109.0	5.0	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Silent	SNP	ENST00000506729.1	hg19	CCDS34206.1																																																																																			.	.		0.303	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		C	101794140	T	C	101794140	2	2	44	1	0	0	0	0	0	0	0	1	14747	1664	58	2		2	SLCO6A1	5	101794140	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	28717594	101794140	79121120	110	5570										
ACSL6	23305	hgsc.bcm.edu	37	chr5	131296298	131296298	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttcagggtcaggcacaacaAtgcctaccaaaaaggcctgc	9	13	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:131296298A>G	ENST00000379240.1	-	19	1952	c.1799T>C	c.(1798-1800)aTt>aCt	p.I600T	AC034228.4_ENST00000446275.1_RNA|ACSL6_ENST00000431707.1_Missense_Mutation_p.I580T|ACSL6_ENST00000379264.2_Missense_Mutation_p.I625T|ACSL6_ENST00000543479.1_Missense_Mutation_p.I600T|ACSL6_ENST00000379272.2_Missense_Mutation_p.I615T|ACSL6_ENST00000379249.3_Missense_Mutation_p.I600T|ACSL6_ENST00000379255.1_Missense_Mutation_p.I525T|ACSL6_ENST00000379244.1_Missense_Mutation_p.I600T|ACSL6_ENST00000296869.4_Missense_Mutation_p.I625T|ACSL6_ENST00000544770.1_Missense_Mutation_p.I509T|ACSL6_ENST00000357096.1_Missense_Mutation_p.I525T|ACSL6_ENST00000379246.1_Missense_Mutation_p.I611T			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	600					acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGGCACAACAATGCCTACCAA	0.453																																					p.I625T		Atlas-SNP	.											.	ACSL6	169	.	0			c.T1874C						.						119	108	112					5																	131296298		2203	4300	6503	SO:0001583	missense	23305	exon19			ACAACAATGCCTA	AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"Acyl-CoA synthetase family"	16496	protein-coding gene	gene with protein product		604443	"fatty-acid-Coenzyme A ligase, long-chain 6"	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.1799T>C	chr5.hg19:g.131296298A>G	ENSP00000368542:p.Ile600Thr	107.0	0.0		92.0	4.0	NM_001009185	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Missense_Mutation	SNP	ENST00000379240.1	hg19		.	.	.	.	.	.	.	.	.	.	A	19.74	3.883552	0.72410	.	.	ENSG00000164398	ENST00000379249;ENST00000379264;ENST00000379272;ENST00000357096;ENST00000379255;ENST00000296869;ENST00000379246;ENST00000379244;ENST00000544770;ENST00000379240;ENST00000431707;ENST00000543479	T;T;T;T;T;T;T;T;T;T;T;T	0.20881	2.04;2.85;2.85;2.85;2.85;2.85;2.85;2.85;2.85;2.85;2.85;2.85	5.81	4.64	0.57946	.	0.132929	0.64402	D	0.000002	T	0.55752	0.1940	H	0.97023	3.925	0.80722	D	1	P;P;P;B;P;P;P	0.48911	0.661;0.917;0.865;0.238;0.754;0.754;0.917	P;P;P;B;P;P;P	0.58721	0.571;0.844;0.659;0.367;0.799;0.764;0.764	T	0.68819	-0.5308	10	0.87932	D	0	.	12.3476	0.55130	0.8733:0.0:0.0:0.1266	.	600;615;590;600;525;625;625	Q9UKU0-3;Q9UKU0-6;B4DFW3;Q9UKU0;Q9UKU0-7;Q9UKU0-1;Q9UKU0-8	.;.;.;ACSL6_HUMAN;.;.;.	T	600;625;615;525;525;625;611;600;509;600;580;600	ENSP00000368551:I600T;ENSP00000368566:I625T;ENSP00000368574:I615T;ENSP00000349608:I525T;ENSP00000368557:I525T;ENSP00000296869:I625T;ENSP00000368548:I611T;ENSP00000368546:I600T;ENSP00000445154:I509T;ENSP00000368542:I600T;ENSP00000413329:I580T;ENSP00000442124:I600T	ENSP00000296869:I625T	I	-	2	0	ACSL6	131324197	1.000000	0.71417	0.964000	0.40570	0.777000	0.43975	9.339000	0.96797	1.004000	0.39156	0.533000	0.62120	ATT	.	.		0.453	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256		G	131296298	A	G	131296298	3	3	44	1	0	0	0	0	1	0	0	0	181	101	4	2	306	2	ACSL6	5	131296298	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	29502158	131296298	49618962	111	5571										
PSD2	84249	hgsc.bcm.edu	37	chr5	139216497	139216497	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctggatggtggcaacccctTcctggatgtcccacaggcgc	12	15	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:139216497T>C	ENST00000274710.3	+	10	1710	c.1505T>C	c.(1504-1506)tTc>tCc	p.F502S		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	502					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCAACCCCTTCCTGGATGTC	0.587																																					p.F502S		Atlas-SNP	.											.	PSD2	88	.	0			c.T1505C						.						172	152	159					5																	139216497		2203	4300	6503	SO:0001583	missense	84249	exon10			ACCCCTTCCTGGA	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1505T>C	chr5.hg19:g.139216497T>C	ENSP00000274710:p.Phe502Ser	108.0	0.0		106.0	6.0	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.661535	0.67700	.	.	ENSG00000146005	ENST00000274710	T	0.15487	2.42	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.24812	0.0602	M	0.73962	2.25	0.80722	D	1	B	0.19706	0.038	B	0.18561	0.022	T	0.03000	-1.1084	10	0.59425	D	0.04	.	15.3435	0.74317	0.0:0.0:0.0:1.0	.	502	Q9BQI7	PSD2_HUMAN	S	502	ENSP00000274710:F502S	ENSP00000274710:F502S	F	+	2	0	PSD2	139196681	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.629000	0.83207	2.041000	0.60428	0.454000	0.30748	TTC	.	.		0.587	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		C	139216497	T	C	139216497	3	2	44	1	0	0	0	0	1	0	0	0	12659	1783	62	2	1539	2	PSD2	5	139216497	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	7920199	139216497	41698763	112	5572										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140574361	140574361	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tggacgtgaggggcgctgagAccctgtcccagagctaccag	15	12	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:140574361A>G	ENST00000239446.4	+	1	2420	c.2236A>G	c.(2236-2238)Acc>Gcc	p.T746A		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	746					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGGCGCTGAGACCCTGTCCCA	0.617																																					p.T746A		Atlas-SNP	.											.	PCDHB10	177	.	0			c.A2236G						.						78	87	84					5																	140574361		2203	4300	6503	SO:0001583	missense	56126	exon1			GCTGAGACCCTGT	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.2236A>G	chr5.hg19:g.140574361A>G	ENSP00000239446:p.Thr746Ala	107.0	0.0		111.0	5.0	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	hg19	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	a	14.42	2.531183	0.45073	.	.	ENSG00000120324	ENST00000239446	T	0.48201	0.82	3.28	3.28	0.37604	.	.	.	.	.	T	0.62295	0.2416	M	0.78916	2.43	0.34060	D	0.657162	D	0.89917	1.0	D	0.87578	0.998	T	0.66964	-0.5790	9	0.19147	T	0.46	.	7.3849	0.26876	0.8048:0.0:0.0:0.1952	.	746	Q9UN67	PCDBA_HUMAN	A	746	ENSP00000239446:T746A	ENSP00000239446:T746A	T	+	1	0	PCDHB10	140554545	0.003000	0.15002	0.850000	0.33497	0.105000	0.19272	1.201000	0.32259	1.508000	0.48769	0.248000	0.18094	ACC	.	.		0.617	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		G	140574361	A	G	140574361	3	3	44	1	0	0	0	0	1	0	0	0	11544	275	10	2	2238	2	PCDHB10	5	140574361	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1357864	140574361	40340899	113	5573										
PCDHGA2	56113	hgsc.bcm.edu	37	chr5	140718779	140718779	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tctttgctctgaacccgcgaAgcggcagcttggtcactgcg	12	13	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:140718779A>G	ENST00000394576.2	+	1	241	c.241A>G	c.(241-243)Agc>Ggc	p.S81G	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	81	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAACCCGCGAAGCGGCAGCTT	0.572																																					p.S81G		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.A241G						.						59	64	62					5																	140718779		2203	4300	6503	SO:0001583	missense	56113	exon1			CCGCGAAGCGGCA	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"Cadherins / Protocadherins : Clustered"	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.241A>G	chr5.hg19:g.140718779A>G	ENSP00000378077:p.Ser81Gly	160.0	0.0		158.0	7.0	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	hg19	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	9.349	1.065053	0.20067	.	.	ENSG00000081853	ENST00000394576	T	0.17370	2.28	5.08	2.67	0.31697	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	0.000000	0.49305	U	0.000145	T	0.24928	0.0605	M	0.85859	2.78	0.09310	N	1	B;B	0.17465	0.016;0.022	B;B	0.26770	0.073;0.068	T	0.21655	-1.0239	10	0.49607	T	0.09	.	9.2827	0.37737	0.8498:0.0:0.1502:0.0	.	81;81	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	G	81	ENSP00000378077:S81G	ENSP00000378077:S81G	S	+	1	0	PCDHGA2	140698963	0.024000	0.19004	0.411000	0.26484	0.390000	0.30446	3.093000	0.50217	0.358000	0.24211	-0.353000	0.07706	AGC	.	.		0.572	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		G	140718779	A	G	140718779	3	3	44	1	0	0	0	0	1	0	0	0	11563	72	3	2	243	2	PCDHGA2	5	140718779	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	144418	140718779	40196481	114	5574										
DIAPH1	1729	hgsc.bcm.edu	37	chr5	140896440	140896440	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agcttgcacggccaaccaacTccttggcttcctcaaggatt	8	14	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:140896440T>C	ENST00000398557.4	-	28	3937	c.3797A>G	c.(3796-3798)gAg>gGg	p.E1266G	DIAPH1_ENST00000389057.5_Missense_Mutation_p.E1257G|DIAPH1_ENST00000520569.1_Missense_Mutation_p.E1209G|DIAPH1_ENST00000253811.6_Missense_Mutation_p.E1267G|DIAPH1_ENST00000389054.3_Missense_Mutation_p.E1263G|DIAPH1_ENST00000398566.3_Missense_Mutation_p.E1258G|DIAPH1_ENST00000398562.2_Missense_Mutation_p.E1242G|DIAPH1_ENST00000518047.1_Missense_Mutation_p.E1254G	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	1266					actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCAACCAACTCCTTGGCTTC	0.577																																					p.E1266G		Atlas-SNP	.											.	DIAPH1	64	.	0			c.A3797G						.						97	99	98					5																	140896440		2101	4213	6314	SO:0001583	missense	1729	exon28			ACCAACTCCTTGG	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.3797A>G	chr5.hg19:g.140896440T>C	ENSP00000381565:p.Glu1266Gly	94.0	0.0		107.0	5.0	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.900139	0.52227	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047	D;D;T;D;D;D;D;D	0.82526	-1.6;-1.6;-1.49;-1.62;-1.62;-1.6;-1.61;-1.62	5.19	5.19	0.71726	.	0.161191	0.42420	D	0.000720	T	0.71375	0.3332	L	0.29908	0.895	0.30512	N	0.769288	P;P	0.37781	0.608;0.608	B;B	0.32980	0.156;0.156	T	0.75291	-0.3369	10	0.72032	D	0.01	.	9.2136	0.37333	0.0:0.0847:0.0:0.9153	.	1257;1266	E9PEZ2;O60610	.;DIAP1_HUMAN	G	1263;1209;1242;1257;1258;1266;1267;1254	ENSP00000373706:E1263G;ENSP00000429282:E1209G;ENSP00000381570:E1242G;ENSP00000373709:E1257G;ENSP00000381572:E1258G;ENSP00000381565:E1266G;ENSP00000253811:E1267G;ENSP00000428268:E1254G	ENSP00000253811:E1267G	E	-	2	0	DIAPH1	140876624	0.998000	0.40836	0.999000	0.59377	0.940000	0.58332	4.248000	0.58760	2.180000	0.69256	0.460000	0.39030	GAG	.	.		0.577	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		C	140896440	T	C	140896440	3	2	44	1	0	0	0	0	1	0	0	0	4520	1551	54	2	25	2	DIAPH1	5	140896440	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	177661	140896440	40018820	115	5575										
FBXO38	81545	hgsc.bcm.edu	37	chr5	147807148	147807148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agaggactctgaggccatggAggagggagatgcagagagtt	18	5	1	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:147807148A>G	ENST00000340253.5	+	15	2459	c.2291A>G	c.(2290-2292)gAg>gGg	p.E764G	CTD-2283N19.1_ENST00000520980.2_RNA|FBXO38_ENST00000513826.1_Intron|FBXO38_ENST00000394370.3_Missense_Mutation_p.E764G|FBXO38_ENST00000296701.6_Intron			Q6PIJ6	FBX38_HUMAN	F-box protein 38	764					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)			ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGGCCATGGAGGAGGGAGAT	0.597																																					p.E764G		Atlas-SNP	.											.	FBXO38	115	.	0			c.A2291G						.						52	49	50					5																	147807148		2203	4300	6503	SO:0001583	missense	81545	exon15			CCATGGAGGAGGG	BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.2291A>G	chr5.hg19:g.147807148A>G	ENSP00000342023:p.Glu764Gly	87.0	0.0		99.0	6.0	NM_030793	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	ENST00000340253.5	hg19		.	.	.	.	.	.	.	.	.	.	A	12.37	1.919021	0.33908	.	.	ENSG00000145868	ENST00000340253;ENST00000394370	T;T	0.33654	1.4;1.4	5.45	4.31	0.51392	.	0.543655	0.20710	N	0.087119	T	0.21022	0.0506	N	0.19112	0.55	0.80722	D	1	B;B	0.27732	0.187;0.0	B;B	0.30495	0.116;0.002	T	0.13791	-1.0496	10	0.49607	T	0.09	-11.7282	3.1944	0.06628	0.6712:0.0:0.1363:0.1925	.	764;764	Q6PIJ6-2;Q6PIJ6	.;FBX38_HUMAN	G	764	ENSP00000342023:E764G;ENSP00000377895:E764G	ENSP00000342023:E764G	E	+	2	0	FBXO38	147787341	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.570000	0.36439	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.597	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		G	147807148	A	G	147807148	3	3	44	1	0	0	0	0	1	0	0	0	5754	304	11	2	2345	2	FBXO38	5	147807148	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	6910708	147807148	33108112	116	5576										
PDGFRB	5159	hgsc.bcm.edu	37	chr5	149500490	149500490	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttcgagtcccgcatgatgtcTcgagccaggccaaagtcaca	10	13	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:149500490T>C	ENST00000261799.4	-	18	3016	c.2547A>G	c.(2545-2547)cgA>cgG	p.R849R		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	849	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GCATGATGTCTCGAGCCAGGC	0.577			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"																																p.R849R		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	PDGFRB,colon,carcinoma,0,1	PDGFRB	142	.	0			c.A2547G						.						137	118	124					5																	149500490		2203	4300	6503	SO:0001819	synonymous_variant	5159	exon18			GATGTCTCGAGCC	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.2547A>G	chr5.hg19:g.149500490T>C		226.0	2.0		212.0	9.0	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	hg19	CCDS4303.1																																																																																			.	.		0.577	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		C	149500490	T	C	149500490	2	2	44	1	0	0	0	0	0	0	0	1	11671	1538	54	2		2	PDGFRB	5	149500490	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1693342	149500490	31414770	117	5577										
CAMK2A	815	hgsc.bcm.edu	37	chr5	149652691	149652691	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctcctggccagccagcacctTcacacaccttcgcaccaccg	6	21	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:149652691T>C	ENST00000348628.6	-	2	759	c.94A>G	c.(94-96)Aag>Gag	p.K32E	CAMK2A_ENST00000398376.3_Missense_Mutation_p.K32E	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	32	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCCAGCACCTTCACACACCTT	0.582																																					p.K32E		Atlas-SNP	.											.	CAMK2A	42	.	0			c.A94G						.						109	115	113					5																	149652691		2203	4300	6503	SO:0001583	missense	815	exon2			GCACCTTCACACA	AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"CaM-kinase II alpha chain", "calcium/calmodulin-dependent protein kinase II alpha-B subunit", "CaM kinase II alpha subunit", "CaMK-II alpha subunit", "calcium/calmodulin-dependent protein kinase type II alpha chain"	114078	"calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.94A>G	chr5.hg19:g.149652691T>C	ENSP00000261793:p.Lys32Glu	157.0	0.0		149.0	6.0	NM_171825	Q9UL21|Q9Y2H4|Q9Y352	Missense_Mutation	SNP	ENST00000348628.6	hg19	CCDS43386.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.243867	0.79912	.	.	ENSG00000070808	ENST00000348628;ENST00000398376;ENST00000510347	T;T;T	0.64803	-0.12;-0.12;-0.12	5.94	5.94	0.96194	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65176	0.2666	N	0.20807	0.61	0.80722	D	1	B;D;B	0.61080	0.366;0.989;0.419	B;D;P	0.74674	0.361;0.984;0.494	T	0.61700	-0.7009	10	0.19147	T	0.46	.	15.3777	0.74625	0.0:0.0:0.0:1.0	.	32;32;32	Q9UQM7-2;Q9UQM7;A8K161	.;KCC2A_HUMAN;.	E	32	ENSP00000261793:K32E;ENSP00000381412:K32E;ENSP00000426607:K32E	ENSP00000261793:K32E	K	-	1	0	CAMK2A	149632884	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.654000	0.83653	2.272000	0.75746	0.460000	0.39030	AAG	.	.		0.582	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981		C	149652691	T	C	149652691	3	2	44	1	0	0	0	0	1	0	0	0	2601	1792	62	2	1447	2	CAMK2A	5	149652691	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	152201	149652691	31262569	118	5578										
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179331759	179331760	+	Missense_Mutation	DNP	GG	GG	AA													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctggtgcaggatgcggtaagGggccacgcgggcactggagt							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr5:179331759_179331760GG>AA	ENST00000356834.3	-	2	208_209	c.171_172CC>TT	c.(169-174)gcCCct>gcTTct	p.P58S	TBC1D9B_ENST00000355235.3_Missense_Mutation_p.P58S	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	58						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATGCGGTAAGGGGCCACGCGGG	0.668																																					p.P58S|p.A57A		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.C172T|c.C171T						.																																			SO:0001583	missense	23061	exon2			GGTAAGGGGCCAC|GTAAGGGGCCACG	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"EF-hand domain containing"	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.171_172delinsAA	chr5.hg19:g.179331759_179331760delinsAA	ENSP00000349291:p.Pro58Ser	182.0|187.0	0.0		133.0	64.0	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Missense_Mutation|Silent	SNP	ENST00000356834.3	hg19	CCDS43408.1																																																																																			.	.		0.668	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		AA	179331760	GG	AA	179331759	3	1	44	1	0	0	0	0	1	0	0	0	15643	1232	43	3	3664	3	TBC1D9B	5	179331759	Missense_Mutation	DNP	GG	TCGA-BC-A3KG-01A-11D-A20W-10	29679068	179331759	1583501	119	5579										
FAM50B	26240	hgsc.bcm.edu	37	chr6	3850605	3850605	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaaggacgaggagatggaggTcaccttcagctactgggacg	16	8	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:3850605T>C	ENST00000380274.1	+	1	986	c.560T>C	c.(559-561)gTc>gCc	p.V187A	FAM50B_ENST00000380272.3_Missense_Mutation_p.V187A			Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	187						nucleus (GO:0005634)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(3)|urinary_tract(3)	17	Ovarian(93;0.0925)	all_hematologic(90;0.108)				GAGATGGAGGTCACCTTCAGC	0.677																																					p.V187A		Atlas-SNP	.											.	FAM50B	44	.	0			c.T560C						.						46	46	46					6																	3850605		2203	4300	6503	SO:0001583	missense	26240	exon2			TGGAGGTCACCTT	Y18504	CCDS4487.1	6p25.2	2008-05-15			ENSG00000145945	ENSG00000145945			18789	protein-coding gene	gene with protein product		614686				10534398	Standard	NM_012135		Approved	D6S2654E, X5L	uc003mvu.3	Q9Y247	OTTHUMG00000014147	ENST00000380274.1:c.560T>C	chr6.hg19:g.3850605T>C	ENSP00000369627:p.Val187Ala	58.0	0.0		121.0	5.0	NM_012135	Q5T2L6	Missense_Mutation	SNP	ENST00000380274.1	hg19	CCDS4487.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.259721	0.80246	.	.	ENSG00000145945	ENST00000380274;ENST00000380272	.	.	.	4.25	4.25	0.50352	.	0.126918	0.50627	D	0.000120	T	0.44850	0.1313	L	0.55213	1.73	0.34403	D	0.695472	P	0.43412	0.806	P	0.48921	0.595	T	0.55042	-0.8202	9	0.87932	D	0	-31.4034	11.6884	0.51501	0.0:0.0:0.0:1.0	.	187	Q9Y247	FA50B_HUMAN	A	187	.	ENSP00000369625:V187A	V	+	2	0	FAM50B	3795604	0.942000	0.31987	0.515000	0.27774	0.957000	0.61999	2.624000	0.46444	1.930000	0.55929	0.397000	0.26171	GTC	.	.		0.677	FAM50B-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039693.1	NM_012135		C	3850605	T	C	3850605	3	2	44	1	0	0	0	0	1	0	0	0	5586	1667	58	2	562	2	FAM50B	6	3850605	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10		3850605	167264462	120	5580										
SYCP2L	221711	hgsc.bcm.edu	37	chr6	10928640	10928640	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cgttcttctgccatagcttcAgccggtccctccgttcgggg	11	15	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:10928640A>G	ENST00000283141.6	+	18	1741	c.1445A>G	c.(1444-1446)cAg>cGg	p.Q482R	RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	482						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			ccatagcttcagccggtccct	0.453																																					p.Q482R		Atlas-SNP	.											SYCP2L,right_lower_lobe,carcinoma,0,1	SYCP2L	101	.	0			c.A1445G						.						59	61	61					6																	10928640		1858	4090	5948	SO:0001583	missense	221711	exon18			AGCTTCAGCCGGT	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 177"	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.1445A>G	chr6.hg19:g.10928640A>G	ENSP00000283141:p.Gln482Arg	38.0	0.0		68.0	3.0	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Missense_Mutation	SNP	ENST00000283141.6	hg19	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	A	0.633	-0.816257	0.02776	.	.	ENSG00000153157	ENST00000283141	T	0.18174	2.23	0.0465	0.0465	0.14256	.	5.812810	0.01010	U	0.003811	T	0.02267	0.0070	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34304	-0.9834	9	0.20519	T	0.43	.	.	.	.	.	482	Q5T4T6	SYC2L_HUMAN	R	482	ENSP00000283141:Q482R	ENSP00000283141:Q482R	Q	+	2	0	SYCP2L	11036626	0.172000	0.23043	0.120000	0.21714	0.123000	0.20343	0.164000	0.16542	0.115000	0.18071	0.113000	0.15668	CAG	.	.		0.453	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		G	10928640	A	G	10928640	3	3	44	1	0	0	0	0	1	0	0	0	15448	188	7	2	1515	2	SYCP2L	6	10928640	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	7078035	10928640	160186427	121	5581										
OR2W1	26692	hgsc.bcm.edu	37	chr6	29012812	29012812	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgggaatccaggagagatgcAagaatgatggctgtgttacc	14	6	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:29012812A>C	ENST00000377175.1	-	1	205	c.141T>G	c.(139-141)ctT>ctG	p.L47L		NM_030903.3	NP_112165.1	Q9Y3N9	OR2W1_HUMAN	olfactory receptor, family 2, subfamily W, member 1	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|skin(1)	23						GGAGAGATGCAAGAATGATGG	0.418																																					p.L47L		Atlas-SNP	.											.	OR2W1	36	.	0			c.T141G						.						114	121	119					6																	29012812		1508	2708	4216	SO:0001819	synonymous_variant	26692	exon1			AGATGCAAGAATG	AL035402	CCDS4656.1	6p22.1	2012-08-09			ENSG00000204704	ENSG00000204704		"GPCR / Class A : Olfactory receptors"	8281	protein-coding gene	gene with protein product							Standard	NM_030903		Approved	hs6M1-15	uc003nlw.2	Q9Y3N9	OTTHUMG00000031048	ENST00000377175.1:c.141T>G	chr6.hg19:g.29012812A>C		244.0	0.0		408.0	37.0	NM_030903	B0S7Y5|Q5JNZ1|Q6IEU0|Q96R17|Q9GZL0|Q9GZL1	Silent	SNP	ENST00000377175.1	hg19	CCDS4656.1																																																																																			.	.		0.418	OR2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076053.2			C	29012812	A	C	29012812	2	2	44	1	0	0	0	0	0	0	0	1	11041	117	5	5		5	OR2W1	6	29012812	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	18084172	29012812	142102255	122	5582										
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31933561	31933561	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgttctcctctgtcccaggTcttgtttgccacagagacct	8	14	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:31933561T>C	ENST00000375394.2	+	18	2086	c.1973T>C	c.(1972-1974)gTc>gCc	p.V658A	SKIV2L_ENST00000544581.1_Splice_Site_p.V465A	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	658	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						CTGTCCCAGGTCTTGTTTGCC	0.532																																					p.V658A		Atlas-SNP	.											.	SKIV2L	97	.	0			c.T1973C						.						140	107	119					6																	31933561		1511	2709	4220	SO:0001630	splice_region_variant	6499	exon18			CCCAGGTCTTGTT		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.1972-1T>C	chr6.hg19:g.31933561T>C		119.0	0.0		144.0	7.0	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.352600	0.82132	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.79352	-1.26;-1.26	5.48	5.48	0.80851	Helicase, C-terminal (3);	0.060213	0.64402	D	0.000003	T	0.81828	0.4905	M	0.83118	2.625	0.50467	D	0.999874	D	0.54964	0.969	P	0.56434	0.798	T	0.81558	-0.0878	10	0.30078	T	0.28	-30.6061	14.5527	0.68078	0.0:0.0:0.0:1.0	.	658	Q15477	SKIV2_HUMAN	A	658;500;465	ENSP00000364543:V658A;ENSP00000442645:V465A	ENSP00000364543:V658A	V	+	2	0	SKIV2L	32041540	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.086000	0.57664	2.086000	0.62901	0.533000	0.62120	GTC	.	.		0.532	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3		Missense_Mutation	C	31933561	T	C	31933561	5	2	44	1	0	0	0	0	0	0	1	0	14374	1681	58	2	2043	2	SKIV2L	6	31933561	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2920749	31933561	139181506	123	5583										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38825330	38825330	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttcagatgttgtggacacacGattcagaagaggctttacgt	11	7	2	3	rs267601015		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:38825330G>T	ENST00000359357.3	+	40	5373	c.5119G>T	c.(5119-5121)Gat>Tat	p.D1707Y	DNAH8_ENST00000441566.1_Missense_Mutation_p.D1707Y|DNAH8_ENST00000449981.2_Missense_Mutation_p.D1924Y			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1707					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GTGGACACACGATTCAGAAGA	0.343																																					p.D1924Y		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,0,2	DNAH8	1239	.	0			c.G5770T						.						100	99	99					6																	38825330		2203	4300	6503	SO:0001583	missense	1769	exon42			ACACACGATTCAG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.5119G>T	chr6.hg19:g.38825330G>T	ENSP00000352312:p.Asp1707Tyr	220.0	0.0		363.0	0.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	G	20.7	4.042219	0.75732	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.27720	1.69;1.69;1.65	5.91	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.63426	0.2510	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78879	-0.2030	10	0.87932	D	0	.	17.0758	0.86586	0.0:0.1268:0.8731:0.0	.	1707	Q96JB1	DYH8_HUMAN	Y	1912;1912;1707;1707	ENSP00000333363:D1912Y;ENSP00000352312:D1707Y;ENSP00000402294:D1707Y	ENSP00000333363:D1912Y	D	+	1	0	DNAH8	38933308	1.000000	0.71417	0.993000	0.49108	0.964000	0.63967	9.551000	0.98112	1.478000	0.48253	0.655000	0.94253	GAT	.	.		0.343	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38825330	G	T	38825330	3	4	44	1	0	0	0	0	1	0	0	0	4609	1058	37	1	5269	1	DNAH8	6	38825330	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	6891769	38825330	132289737	124	5584										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38851761	38851761	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	taatatgcctgtgattaatgAgtggggagatcaggtatggc	14	4	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:38851761A>G	ENST00000359357.3	+	54	7849	c.7595A>G	c.(7594-7596)gAg>gGg	p.E2532G	DNAH8_ENST00000441566.1_Missense_Mutation_p.E2496G|DNAH8_ENST00000449981.2_Missense_Mutation_p.E2749G			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2532	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GTGATTAATGAGTGGGGAGAT	0.323																																					p.E2749G		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A8246G						.						98	102	100					6																	38851761		2203	4300	6503	SO:0001583	missense	1769	exon56			TTAATGAGTGGGG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.7595A>G	chr6.hg19:g.38851761A>G	ENSP00000352312:p.Glu2532Gly	54.0	0.0		92.0	4.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	A	24.2	4.507607	0.85282	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.17370	2.28;2.28;2.28	5.07	5.07	0.68467	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.50292	0.1607	H	0.97940	4.11	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.67898	-0.5551	10	0.41790	T	0.15	.	15.1103	0.72351	1.0:0.0:0.0:0.0	.	2532	Q96JB1	DYH8_HUMAN	G	2737;2737;2532;2496	ENSP00000333363:E2737G;ENSP00000352312:E2532G;ENSP00000402294:E2496G	ENSP00000333363:E2737G	E	+	2	0	DNAH8	38959739	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.277000	0.95755	2.030000	0.59900	0.454000	0.30748	GAG	.	.		0.323	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38851761	A	G	38851761	3	3	44	1	0	0	0	0	1	0	0	0	4609	304	11	2	7801	2	DNAH8	6	38851761	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	26431	38851761	132263306	125	5585										
EFHC1	114327	hgsc.bcm.edu	37	chr6	52303151	52303151	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agatgttcctatgtcaactgAggaacagtataggatccgtc	10	8	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:52303151A>G	ENST00000371068.5	+	3	438	c.335A>G	c.(334-336)gAg>gGg	p.E112G	EFHC1_ENST00000433625.2_Missense_Mutation_p.E21G|EFHC1_ENST00000491749.1_3'UTR|EFHC1_ENST00000538167.1_Missense_Mutation_p.E93G	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	112	DM10 1. {ECO:0000255|PROSITE- ProRule:PRU00665}.					axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					ATGTCAACTGAGGAACAGTAT	0.373																																					p.E112G		Atlas-SNP	.											.	EFHC1	68	.	0			c.A335G						.						51	46	47					6																	52303151		2203	4300	6503	SO:0001583	missense	114327	exon3			CAACTGAGGAACA	AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"EF-hand domain containing"	16406	protein-coding gene	gene with protein product	"myoclonin-1"	608815	"epilepsy, juvenile myoclonic 1"	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.335A>G	chr6.hg19:g.52303151A>G	ENSP00000360107:p.Glu112Gly	71.0	0.0		87.0	4.0	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Missense_Mutation	SNP	ENST00000371068.5	hg19	CCDS4942.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.449792	0.63290	.	.	ENSG00000096093	ENST00000371068;ENST00000433625;ENST00000538167	T;T;T	0.69175	-0.13;-0.38;-0.33	5.78	4.57	0.56435	Uncharacterised domain DM10 (2);	0.254365	0.45361	D	0.000379	T	0.51873	0.1700	M	0.64404	1.975	0.54753	D	0.999988	P;B;B	0.37663	0.604;0.061;0.007	B;B;B	0.40066	0.318;0.018;0.027	T	0.53711	-0.8400	10	0.25751	T	0.34	-6.4266	12.2989	0.54864	0.8735:0.0:0.0:0.1265	.	93;21;112	F5GZD8;B7Z2S4;Q5JVL4	.;.;EFHC1_HUMAN	G	112;21;93	ENSP00000360107:E112G;ENSP00000416492:E21G;ENSP00000444521:E93G	ENSP00000360107:E112G	E	+	2	0	EFHC1	52411110	1.000000	0.71417	0.996000	0.52242	0.943000	0.58893	5.069000	0.64370	2.205000	0.71048	0.533000	0.62120	GAG	.	.		0.373	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		G	52303151	A	G	52303151	3	3	44	1	0	0	0	0	1	0	0	0	4948	304	11	2	355	2	EFHC1	6	52303151	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	13451390	52303151	118811916	126	5586										
TRAM2	9697	hgsc.bcm.edu	37	chr6	52370844	52370844	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acttacagtttctcgttgttTtcatctgcaaagtagaagag	8	7	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:52370844T>C	ENST00000182527.3	-	8	716	c.717A>G	c.(715-717)gaA>gaG	p.E239E	EFHC1_ENST00000433625.2_Intron	NM_012288.3	NP_036420.1	Q15035	TRAM2_HUMAN	translocation associated membrane protein 2	239	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				collagen biosynthetic process (GO:0032964)|protein transport (GO:0015031)	integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(1)|lung(7)|prostate(1)|skin(1)	13	Lung NSC(77;0.109)					TCTCGTTGTTTTCATCTGCAA	0.607																																					p.E239E		Atlas-SNP	.											.	TRAM2	27	.	0			c.A717G						.						85	88	87					6																	52370844		2203	4300	6503	SO:0001819	synonymous_variant	9697	exon8			GTTGTTTTCATCT	D31762	CCDS34477.1	6p21.1-p12	2008-02-05			ENSG00000065308	ENSG00000065308			16855	protein-coding gene	gene with protein product		608485				7584044, 10594243	Standard	NM_012288		Approved	KIAA0057	uc003paq.3	Q15035	OTTHUMG00000014850	ENST00000182527.3:c.717A>G	chr6.hg19:g.52370844T>C		95.0	0.0		96.0	4.0	NM_012288	A8K6T6	Silent	SNP	ENST00000182527.3	hg19	CCDS34477.1																																																																																			.	.		0.607	TRAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040910.1	NM_012288		C	52370844	T	C	52370844	2	2	44	1	0	0	0	0	0	0	0	1	16468	1838	64	2		2	TRAM2	6	52370844	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	67693	52370844	118744223	127	5587										
DST	667	hgsc.bcm.edu	37	chr6	56497659	56497659	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccccatgctttacctctttcTgcagatttaagaagttcttg	6	11	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:56497659T>C	ENST00000361203.3	-	24	3172	c.3165A>G	c.(3163-3165)gcA>gcG	p.A1055A	DST_ENST00000421834.2_Silent_p.A1055A|DST_ENST00000370765.6_Silent_p.A729A|DST_ENST00000312431.6_Silent_p.A1055A|DST_ENST00000370769.4_Silent_p.A1055A|DST_ENST00000446842.2_Silent_p.A729A|DST_ENST00000518935.1_Silent_p.A729A|DST_ENST00000370788.2_Silent_p.A1055A|DST_ENST00000370754.5_Silent_p.A1233A|DST_ENST00000244364.6_Silent_p.A729A			Q03001	DYST_HUMAN	dystonin	1055					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TACCTCTTTCTGCAGATTTAA	0.378																																					p.A729A		Atlas-SNP	.											.	DST	1427	.	0			c.A2187G						.						93	95	94					6																	56497659		2203	4300	6503	SO:0001819	synonymous_variant	667	exon14			TCTTTCTGCAGAT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.3165A>G	chr6.hg19:g.56497659T>C		92.0	0.0		128.0	47.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.378	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56497659	T	C	56497659	2	2	44	1	0	0	0	0	0	0	0	1	4785	1567	55	2		2	DST	6	56497659	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4126815	56497659	114617408	128	5588										
COL9A1	1297	hgsc.bcm.edu	37	chr6	70991132	70991132	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggaactccaggggggcccggAggcccgggaggaccctgctc	18	14	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:70991132A>G	ENST00000357250.6	-	8	995	c.837T>C	c.(835-837)ccT>ccC	p.P279P	COL9A1_ENST00000320755.7_Silent_p.P36P|COL9A1_ENST00000370499.4_Silent_p.P36P|COL9A1_ENST00000489611.1_5'Flank|COL9A1_ENST00000370496.3_Silent_p.P279P	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	279	Collagen-like 1.|Triple-helical region (COL3).			PP -> AS (in Ref. 1; CAA38276/CAA38277). {ECO:0000305}.	axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						GGGGGCCCGGAGGCCCGGGAG	0.597																																					p.P279P		Atlas-SNP	.											.	COL9A1	228	.	0			c.T837C						.						22	26	24					6																	70991132		2203	4300	6503	SO:0001819	synonymous_variant	1297	exon8			GCCCGGAGGCCCG		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.837T>C	chr6.hg19:g.70991132A>G		90.0	0.0		104.0	5.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Silent	SNP	ENST00000357250.6	hg19	CCDS4971.1																																																																																			.	.		0.597	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			G	70991132	A	G	70991132	2	3	44	1	0	0	0	0	0	0	0	1	3709	291	11	2		2	COL9A1	6	70991132	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	14493473	70991132	100123935	129	5589										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75801079	75801079	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acttgtcttgcaactgctcgCatcatgttctgggaagcaat	9	10	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:75801079C>T	ENST00000322507.8	-	62	9021	c.8712G>A	c.(8710-8712)atG>atA	p.M2904I	COL12A1_ENST00000483888.2_Missense_Mutation_p.M2900I|COL12A1_ENST00000511023.1_5'UTR|COL12A1_ENST00000345356.6_Missense_Mutation_p.M1740I|COL12A1_ENST00000416123.2_Missense_Mutation_p.M2828I	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2904	Nonhelical region (NC2).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CAACTGCTCGCATCATGTTCT	0.308																																					p.M2904I		Atlas-SNP	.											.	COL12A1	385	.	0			c.G8712A						.						177	167	170					6																	75801079		1852	4113	5965	SO:0001583	missense	1303	exon62			TGCTCGCATCATG	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.8712G>A	chr6.hg19:g.75801079C>T	ENSP00000325146:p.Met2904Ile	72.0	0.0		79.0	4.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	32	5.152458	0.94645	.	.	ENSG00000111799	ENST00000322507;ENST00000425443;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	D;D;D;D;D	0.91945	-2.94;-2.94;-2.94;-2.94;-2.94	5.96	5.96	0.96718	.	0.039016	0.85682	D	0.000000	D	0.93654	0.7973	L	0.43152	1.355	0.53005	D	0.999961	D;D	0.71674	0.998;0.989	D;D	0.79784	0.993;0.958	D	0.91514	0.5229	10	0.33940	T	0.23	.	20.4082	0.99013	0.0:1.0:0.0:0.0	.	1740;2904	Q99715-2;Q99715	.;COCA1_HUMAN	I	2904;542;2828;1740;2828;2900	ENSP00000325146:M2904I;ENSP00000399812:M542I;ENSP00000305147:M1740I;ENSP00000412864:M2828I;ENSP00000421216:M2900I	ENSP00000325146:M2904I	M	-	3	0	COL12A1	75857799	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.484000	0.81180	2.814000	0.96858	0.655000	0.94253	ATG	.	.		0.308	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75801079	C	T	75801079	3	4	44	1	0	0	0	0	1	0	0	0	3671	710	25	3	499	3	COL12A1	6	75801079	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	4809947	75801079	95313988	130	5590										
PRDM1	639	hgsc.bcm.edu	37	chr6	106553568	106553568	+	Frame_Shift_Del	DEL	C	C	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atgaaggacaaggcctgtagCcccacaagcgggtctcccac							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:106553568delC	ENST00000369096.4	+	5	1767	c.1533delC	c.(1531-1533)agcfs	p.S511fs	PRDM1_ENST00000369089.3_Frame_Shift_Del_p.S377fs|PRDM1_ENST00000369091.2_Frame_Shift_Del_p.S475fs	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	511					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		AGGCCTGTAGCCCCACAAGCG	0.677			"D, N, Mis, F, S"		DLBCL																																p.S511fs		Atlas-INDEL	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.	PRDM1	195	.	0			c.1532delG						.						24	29	27					6																	106553568		2192	4279	6471	SO:0001589	frameshift_variant	639	exon5			.		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"Zinc fingers, C2H2-type"	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.1533delC	chr6.hg19:g.106553568delC	ENSP00000358092:p.Ser511fs	118.0	0.0		145.0	10.0	NM_001198	B2REA6|E1P5E0|Q86WM7	Frame_Shift_Del	DEL	ENST00000369096.4	hg19	CCDS5054.2																																																																																			.	.		0.677	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			-	106553568	C	-	106553568	7	5	44	1	0	1	0	1	0	0	0	0	12462	738	26	0	1564	0	PRDM1	6	106553568	Frame_Shift_Del	DEL	C	TCGA-BC-A3KG-01A-11D-A20W-10	30752489	106553568	64561499	131	5591										
NUS1	116150	hgsc.bcm.edu	37	chr6	118024821	118024821	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgaagttcggtcctgtggacAgcacattaggctttcttccc	10	11	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:118024821A>G	ENST00000368494.3	+	4	914	c.745A>G	c.(745-747)Agc>Ggc	p.S249G		NM_138459.3	NP_612468.1	Q96E22	NGBR_HUMAN	nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae)	249					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|intracellular cholesterol transport (GO:0032367)|protein glycosylation (GO:0006486)|sterol homeostasis (GO:0055092)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|prostate(2)	8		all_cancers(87;0.0395)|all_epithelial(87;0.0301)		GBM - Glioblastoma multiforme(226;0.02)|OV - Ovarian serous cystadenocarcinoma(136;0.115)|all cancers(137;0.146)		TCCTGTGGACAGCACATTAGG	0.388																																					p.S249G		Atlas-SNP	.											.	NUS1	15	.	0			c.A745G						.						187	170	176					6																	118024821		2203	4298	6501	SO:0001583	missense	116150	exon4			GTGGACAGCACAT	BC013026	CCDS5118.1	6q22.1	2012-12-13	2006-11-24	2006-11-24	ENSG00000153989	ENSG00000153989			21042	protein-coding gene	gene with protein product	"Nogo-B receptor", "transport and golgi organization 14 homolog (Drosophila)"	610463	"chromosome 6 open reading frame 68"	C6orf68			Standard	NM_138459		Approved	MGC7199, NgBR, TANGO14	uc003pxw.3	Q96E22	OTTHUMG00000015458	ENST00000368494.3:c.745A>G	chr6.hg19:g.118024821A>G	ENSP00000357480:p.Ser249Gly	105.0	0.0		135.0	6.0	NM_138459	B2RWQ4|O00251	Missense_Mutation	SNP	ENST00000368494.3	hg19	CCDS5118.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.761177	0.89932	.	.	ENSG00000153989	ENST00000368494	T	0.54479	0.57	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.69735	0.3144	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.74441	-0.3664	10	0.51188	T	0.08	-12.8437	15.6873	0.77421	1.0:0.0:0.0:0.0	.	249	Q96E22	NGBR_HUMAN	G	249	ENSP00000357480:S249G	ENSP00000357480:S249G	S	+	1	0	NUS1	118131514	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.601000	0.90864	2.107000	0.64212	0.482000	0.46254	AGC	.	.		0.388	NUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041989.1	NM_138459		G	118024821	A	G	118024821	3	3	44	1	0	0	0	0	1	0	0	0	10786	188	7	2	759	2	NUS1	6	118024821	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	11471253	118024821	53090246	132	5592										
TRDN	10345	hgsc.bcm.edu	37	chr6	123653052	123653052	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tttagggaagctggaactttCtcttctttccctttaatagg	8	8	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:123653052C>T	ENST00000398178.3	-	23	1464	c.1443G>A	c.(1441-1443)gaG>gaA	p.E481E	TRDN_ENST00000334268.4_Silent_p.E481E	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	481					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		CTGGAACTTTCTCTTCTTTCC	0.333																																					p.E481E		Atlas-SNP	.											TRDN,colon,carcinoma,0,1	TRDN	88	.	0			c.G1443A						.						74	70	71					6																	123653052		1792	4045	5837	SO:0001819	synonymous_variant	10345	exon23			AACTTTCTCTTCT	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1443G>A	chr6.hg19:g.123653052C>T		58.0	0.0		68.0	3.0	NM_006073	A5D6W5|F5H2W7|Q6NSB8	Silent	SNP	ENST00000398178.3	hg19	CCDS55053.1																																																																																			.	.		0.333	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	123653052	C	T	123653052	2	4	44	1	0	0	0	0	0	0	0	1	16483	912	32	3		3	TRDN	6	123653052	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	5628231	123653052	47462015	133	5593										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129465145	129465145	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atattcgcctgagatttcagAggatccgcacactgaatgct	9	10	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:129465145A>G	ENST00000421865.2	+	5	788	c.739A>G	c.(739-741)Agg>Ggg	p.R247G		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	247	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.R247G(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GAGATTTCAGAGGATCCGCAC	0.433																																					p.R247G		Atlas-SNP	.											LAMA2,NS,carcinoma,-1,1	LAMA2	481	.	1	Substitution - Missense(1)	lung(1)	c.A739G						.						119	111	114					6																	129465145		2203	4300	6503	SO:0001583	missense	3908	exon5			TTTCAGAGGATCC	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.739A>G	chr6.hg19:g.129465145A>G	ENSP00000400365:p.Arg247Gly	110.0	2.0		143.0	6.0	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.675569	0.67928	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.80393	-1.37	5.43	4.25	0.50352	Laminin, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.81470	0.4829	M	0.71871	2.18	0.47308	D	0.999387	P;P	0.44281	0.698;0.831	P;P	0.54759	0.696;0.76	D	0.83652	0.0156	10	0.87932	D	0	.	11.7661	0.51930	0.7214:0.2786:0.0:0.0	.	247;247	A6NF00;P24043	.;LAMA2_HUMAN	G	247	ENSP00000400365:R247G	ENSP00000346769:R247G	R	+	1	2	LAMA2	129506838	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	1.475000	0.35409	0.967000	0.38186	0.383000	0.25322	AGG	.	.		0.433	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			G	129465145	A	G	129465145	3	3	44	1	0	0	0	0	1	0	0	0	8615	295	11	2	757	2	LAMA2	6	129465145	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	5812093	129465145	41649922	134	5594										
MYB	4602	hgsc.bcm.edu	37	chr6	135517124	135517124	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttagaatttgcagaaacacTccaatttatagattctgtaa	5	7	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:135517124T>C	ENST00000367814.4	+	9	1373	c.1187T>C	c.(1186-1188)cTc>cCc	p.L396P	MYB_ENST00000316528.8_Missense_Mutation_p.L396P|MYB_ENST00000534044.1_Missense_Mutation_p.L396P|MYB_ENST00000525369.1_Intron|MYB_ENST00000534121.1_Intron|MYB_ENST00000442647.2_Missense_Mutation_p.L393P|MYB_ENST00000528774.1_Missense_Mutation_p.L393P|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000533624.1_Missense_Mutation_p.L361P|MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000341911.5_Missense_Mutation_p.L396P|MYB_ENST00000527615.1_Missense_Mutation_p.L396P	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	396	Leucine-zipper.|Negative regulatory domain. {ECO:0000250}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		GCAGAAACACTCCAATTTATA	0.393			T	NFIB	adenoid cystic carcinoma																																p.L396P		Atlas-SNP	.		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	MYB	137	.	0			c.T1187C						.						61	62	62					6																	135517124		2203	4300	6503	SO:0001583	missense	4602	exon9			AAACACTCCAATT		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.1187T>C	chr6.hg19:g.135517124T>C	ENSP00000356788:p.Leu396Pro	69.0	0.0		83.0	5.0	NM_001161659	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	hg19	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	T	17.99	3.522969	0.64747	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000528774;ENST00000534044;ENST00000533624	T;T;T;T;T;T;T;T	0.52754	1.62;1.14;1.53;1.13;0.65;1.65;1.08;1.21	5.95	5.95	0.96441	.	0.123637	0.56097	D	0.000032	T	0.54935	0.1889	L	0.46157	1.445	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.996;0.991;0.995;0.999;1.0;0.999;0.996	P;P;P;D;D;D;P	0.91635	0.823;0.77;0.885;0.998;0.999;0.971;0.853	T	0.60291	-0.7292	10	0.87932	D	0	-10.9835	14.9948	0.71421	0.0:0.0:0.0:1.0	.	361;396;393;393;396;396;396	E9PI07;E9PLZ5;P10242-2;E9PNL6;P10242-4;P10242;Q708E1	.;.;.;.;.;MYB_HUMAN;.	P	396;393;396;396;396;396;393;396;361	ENSP00000339992:L396P;ENSP00000410825:L393P;ENSP00000326328:L396P;ENSP00000356788:L396P;ENSP00000433227:L396P;ENSP00000434723:L393P;ENSP00000435055:L396P;ENSP00000436605:L361P	ENSP00000237302:L396P	L	+	2	0	MYB	135558817	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.687000	0.74552	2.279000	0.76181	0.533000	0.62120	CTC	.	.		0.393	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4			C	135517124	T	C	135517124	3	2	44	1	0	0	0	0	1	0	0	0	10016	1551	54	2	1221	2	MYB	6	135517124	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	6051979	135517124	35597943	135	5595										
IFNGR1	3459	hgsc.bcm.edu	37	chr6	137528138	137528138	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acggtaaaaacagggacctgTggcatgatctggtactccca	11	10	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:137528138T>C	ENST00000367739.4	-	2	283	c.162A>G	c.(160-162)ccA>ccG	p.P54P	IFNGR1_ENST00000543628.1_Silent_p.P26P|IFNGR1_ENST00000367735.2_Silent_p.P44P|IFNGR1_ENST00000478333.1_5'UTR	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	54					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)			central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	CAGGGACCTGTGGCATGATCT	0.353																																					p.P54P		Atlas-SNP	.											.	IFNGR1	46	.	0			c.A162G						.						127	125	126					6																	137528138		2203	4300	6503	SO:0001819	synonymous_variant	3459	exon2			GACCTGTGGCATG		CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"Interferons", "CD molecules"	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.162A>G	chr6.hg19:g.137528138T>C		86.0	0.0		93.0	4.0	NM_000416	B4DFT7|E1P587|Q53Y96	Silent	SNP	ENST00000367739.4	hg19	CCDS5185.1																																																																																			.	.		0.353	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1			C	137528138	T	C	137528138	2	2	44	1	0	0	0	0	0	0	0	1	7558	1683	59	2		2	IFNGR1	6	137528138	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2011014	137528138	33586929	136	5596										
TXLNB	167838	hgsc.bcm.edu	37	chr6	139576758	139576758	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttcgcctgaagtttccactcTgctgcctggttcagcaacta	8	13	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:139576758T>C	ENST00000358430.3	-	7	1252	c.1020A>G	c.(1018-1020)gcA>gcG	p.A340A		NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	340						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		GTTTCCACTCTGCTGCCTGGT	0.488																																					p.A340A		Atlas-SNP	.											.	TXLNB	96	.	0			c.A1020G						.						100	82	88					6																	139576758		2203	4300	6503	SO:0001819	synonymous_variant	167838	exon7			CCACTCTGCTGCC		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"chromosome 6 open reading frame 198"	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.1020A>G	chr6.hg19:g.139576758T>C		103.0	0.0		98.0	4.0	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Silent	SNP	ENST00000358430.3	hg19	CCDS34545.1	.	.	.	.	.	.	.	.	.	.	T	10.88	1.476436	0.26511	.	.	ENSG00000164440	ENST00000367652	.	.	.	5.87	3.19	0.36642	.	.	.	.	.	T	0.41834	0.1176	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35992	-0.9766	4	.	.	.	-19.9312	6.8414	0.23965	0.2154:0.072:0.0:0.7125	.	.	.	.	G	53	.	.	R	-	1	2	TXLNB	139618451	0.999000	0.42202	1.000000	0.80357	0.963000	0.63663	0.374000	0.20501	1.166000	0.42689	0.533000	0.62120	AGA	.	.		0.488	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235		C	139576758	T	C	139576758	2	2	44	1	0	0	0	0	0	0	0	1	16803	1567	55	2		2	TXLNB	6	139576758	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2048620	139576758	31538309	137	5597										
NMBR	4829	hgsc.bcm.edu	37	chr6	142400004	142400004	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtccgcagcaatgcccctgaCgtctgcatgtccatggggtt	12	13	1	1	rs149123905		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:142400004C>T	ENST00000258042.1	-	2	599	c.459G>A	c.(457-459)acG>acA	p.T153T	NMBR_ENST00000480652.1_5'Flank	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	153					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)			breast(2)|central_nervous_system(3)|endometrium(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;9.93e-06)|GBM - Glioblastoma multiforme(68;0.0013)		ATGCCCCTGACGTCTGCATGT	0.493													C|||	1	0.000199681	0	0	5008	,	,		17023	0		0	False		,,,				2504	0.001				p.T153T		Atlas-SNP	.											.	NMBR	62	.	0			c.G459A						.	C		1,4405	2.1+/-5.4	0,1,2202	71	59	63		459	-10.8	0	6	dbSNP_134	63	0,8600		0,0,4300	no	coding-synonymous	NMBR	NM_002511.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		153/391	142400004	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4829	exon2			CCCTGACGTCTGC		CCDS5196.1	6q24.1	2014-02-21			ENSG00000135577	ENSG00000135577		"GPCR / Class A : Bombesin receptors"	7843	protein-coding gene	gene with protein product	"bombesin receptor 1"	162341					Standard	NM_002511		Approved	BB1	uc003qiu.3	P28336	OTTHUMG00000015704	ENST00000258042.1:c.459G>A	chr6.hg19:g.142400004C>T		134.0	0.0		160.0	20.0	NM_002511	E9KL38|Q5VUK8	Silent	SNP	ENST00000258042.1	hg19	CCDS5196.1																																																																																			.	C|1.000;T|0.000		0.493	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1			T	142400004	C	T	142400004	2	4	44	1	0	0	0	0	0	0	0	1	10496	523	19	1		1	NMBR	6	142400004	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	2823246	142400004	28715063	138	5598										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152665262	152665262	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaggtggttgaggacttggcTctaaatccggctggactgca	15	8	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:152665262T>A	ENST00000367255.5	-	74	12780	c.12179A>T	c.(12178-12180)gAg>gTg	p.E4060V	SYNE1_ENST00000341594.5_Missense_Mutation_p.E3925V|SYNE1_ENST00000448038.1_Missense_Mutation_p.E3989V|SYNE1_ENST00000265368.4_Missense_Mutation_p.E4060V|SYNE1_ENST00000423061.1_Missense_Mutation_p.E3989V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4060			E -> D (in dbSNP:rs4645434).		cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGGACTTGGCTCTAAATCCGG	0.493										HNSCC(10;0.0054)																											p.E4060V		Atlas-SNP	.											SYNE1_ENST00000423061,colon,carcinoma,-1,3	SYNE1	3227	.	0			c.A12179T						.						106	103	104					6																	152665262		2203	4300	6503	SO:0001583	missense	23345	exon74			CTTGGCTCTAAAT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.12179A>T	chr6.hg19:g.152665262T>A	ENSP00000356224:p.Glu4060Val	130.0	0.0		149.0	0.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	8.654	0.898855	0.17686	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	5.76	5.76	0.90799	.	0.176957	0.39341	N	0.001392	T	0.12860	0.0312	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.32717	0.381;0.381;0.381;0.178	B;B;B;B	0.32342	0.085;0.085;0.085;0.144	T	0.08310	-1.0728	10	0.27785	T	0.31	.	16.3668	0.83335	0.0:0.0:0.0:1.0	.	4060;4060;4060;3989	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	V	4060;3989;4060;3989;3925	ENSP00000356224:E4060V;ENSP00000396024:E3989V;ENSP00000265368:E4060V;ENSP00000390975:E3989V;ENSP00000341887:E3925V	ENSP00000265368:E4060V	E	-	2	0	SYNE1	152706955	1.000000	0.71417	0.020000	0.16555	0.201000	0.24016	3.865000	0.56033	2.322000	0.78497	0.528000	0.53228	GAG	.	.		0.493	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152665262	T	A	152665262	3	1	44	1	0	0	0	0	1	0	0	0	15460	1551	54	4	14579	4	SYNE1	6	152665262	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	10265258	152665262	18449805	139	5599										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152740820	152740820	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aagcagcagctcatcaaattGctggtgttcagcaaccacag	9	11	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:152740820G>T	ENST00000367255.5	-	40	5906	c.5305C>A	c.(5305-5307)Caa>Aaa	p.Q1769K	SYNE1_ENST00000341594.5_Missense_Mutation_p.Q1806K|SYNE1_ENST00000448038.1_Missense_Mutation_p.Q1776K|SYNE1_ENST00000265368.4_Missense_Mutation_p.Q1769K|SYNE1_ENST00000423061.1_Missense_Mutation_p.Q1776K	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1769					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCATCAAATTGCTGGTGTTCA	0.353										HNSCC(10;0.0054)																											p.Q1776K		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C5326A						.						79	78	79					6																	152740820		2203	4300	6503	SO:0001583	missense	23345	exon40			CAAATTGCTGGTG	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.5305C>A	chr6.hg19:g.152740820G>T	ENSP00000356224:p.Gln1769Lys	189.0	0.0		247.0	80.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	13.23	2.175436	0.38413	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000018	T	0.17916	0.0430	L	0.52364	1.645	0.80722	D	1	B;B;B;B	0.27013	0.067;0.166;0.166;0.029	B;B;B;B	0.19391	0.017;0.025;0.025;0.019	T	0.02942	-1.1091	10	0.21014	T	0.42	.	14.0245	0.64577	0.0:0.0:0.8488:0.1512	.	1752;1769;1769;1776	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	K	1769;1776;1769;1776;1806	ENSP00000356224:Q1769K;ENSP00000396024:Q1776K;ENSP00000265368:Q1769K;ENSP00000390975:Q1776K;ENSP00000341887:Q1806K	ENSP00000265368:Q1769K	Q	-	1	0	SYNE1	152782513	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.505000	0.53356	2.594000	0.87642	0.650000	0.86243	CAA	.	.		0.353	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152740820	G	T	152740820	3	4	44	1	0	0	0	0	1	0	0	0	15460	1328	46	3	21589	3	SYNE1	6	152740820	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	75558	152740820	18374247	140	5600										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157099208	157099208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cggcggcagcggcggcatccTcttcctcctcgtcgggcccg	14	18	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:157099208T>C	ENST00000350026.5	+	1	146	c.145T>C	c.(145-147)Tct>Cct	p.S49P	ARID1B_ENST00000367148.1_Missense_Mutation_p.S49P|ARID1B_ENST00000346085.5_Missense_Mutation_p.S49P|RP11-230C9.2_ENST00000603191.1_lincRNA|MIR4466_ENST00000606121.1_RNA|RP11-230C9.3_ENST00000604792.1_RNA|ARID1B_ENST00000275248.4_5'UTR	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	49	Ser-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GGCGGCATCCTCTTCCTCCTC	0.731																																					p.S49P		Atlas-SNP	.											.	ARID1B	320	.	0			c.T145C						.						5	11	9					6																	157099208		1493	2707	4200	SO:0001583	missense	57492	exon1			GCATCCTCTTCCT	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.145T>C	chr6.hg19:g.157099208T>C	ENSP00000055163:p.Ser49Pro	70.0	0.0		84.0	6.0	NM_017519	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	t	6.920	0.539429	0.13250	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148	T;T;T	0.49720	0.77;0.77;0.77	2.26	2.26	0.28386	.	.	.	.	.	T	0.28896	0.0717	L	0.35542	1.07	0.80722	D	1	.	.	.	.	.	.	T	0.15867	-1.0422	7	0.87932	D	0	.	7.5154	0.27598	0.0:0.0:0.0:1.0	.	.	.	.	P	49	ENSP00000344546:S49P;ENSP00000055163:S49P;ENSP00000356116:S49P	ENSP00000344546:S49P	S	+	1	0	ARID1B	157140900	1.000000	0.71417	0.997000	0.53966	0.637000	0.38172	2.997000	0.49457	0.791000	0.33826	0.307000	0.20424	TCT	.	.		0.731	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		C	157099208	T	C	157099208	3	2	44	1	0	0	0	0	1	0	0	0	914	1551	54	2	147	2	ARID1B	6	157099208	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4358388	157099208	14015859	141	5601										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157528676	157528676	+	Frame_Shift_Del	DEL	T	T	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcgagaaatgtccatggcgcTtttatcgaaccttgcccaag							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:157528676delT	ENST00000350026.5	+	19	6363	c.6362delT	c.(6361-6363)cttfs	p.L2122fs	ARID1B_ENST00000367148.1_Frame_Shift_Del_p.L2175fs|ARID1B_ENST00000275248.4_Frame_Shift_Del_p.L2117fs|ARID1B_ENST00000346085.5_Frame_Shift_Del_p.L2135fs	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	2122					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		TCCATGGCGCTTTTATCGAAC	0.493																																					p.L2134fs		Atlas-INDEL	.											.	ARID1B	320	.	0			c.6400delC						.						174	178	177					6																	157528676		2203	4296	6499	SO:0001589	frameshift_variant	57492	exon20			.	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.6362delT	chr6.hg19:g.157528676delT	ENSP00000055163:p.Leu2122fs	123.0	0.0		153.0	10.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Frame_Shift_Del	DEL	ENST00000350026.5	hg19	CCDS5251.2																																																																																			.	.		0.493	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		-	157528676	T	-	157528676	7	5	44	1	0	1	0	1	0	0	0	0	914	1609	56	0	6479	0	ARID1B	6	157528676	Frame_Shift_Del	DEL	T	TCGA-BC-A3KG-01A-11D-A20W-10	429468	157528676	13586391	142	5602										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160511067	160511067	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tggagccaacatatgccaggTgaagcccaacgatcagcact	10	12	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:160511067T>C	ENST00000356956.1	+	44	6735	c.6587T>C	c.(6586-6588)gTg>gCg	p.V2196A		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2196					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	ATATGCCAGGTGAAGCCCAAC	0.502																																					p.V2196A		Atlas-SNP	.											.	IGF2R	251	.	0			c.T6587C						.						103	91	95					6																	160511067		2203	4300	6503	SO:0001583	missense	3482	exon44			GCCAGGTGAAGCC	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.6587T>C	chr6.hg19:g.160511067T>C	ENSP00000349437:p.Val2196Ala	129.0	0.0		150.0	6.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.237888	0.58886	.	.	ENSG00000197081	ENST00000356956	T	0.03152	4.03	5.52	3.03	0.35002	Mannose-6-phosphate receptor, binding (1);	0.344338	0.29940	N	0.010817	T	0.03053	0.0090	M	0.80982	2.52	0.27535	N	0.950979	P	0.43938	0.822	B	0.40285	0.325	T	0.17471	-1.0368	10	0.62326	D	0.03	-9.6607	12.5508	0.56225	0.0:0.0:0.2632:0.7368	.	2196	P11717	MPRI_HUMAN	A	2196	ENSP00000349437:V2196A	ENSP00000349437:V2196A	V	+	2	0	IGF2R	160431057	0.998000	0.40836	0.010000	0.14722	0.369000	0.29798	2.935000	0.48963	0.427000	0.26145	0.454000	0.30748	GTG	.	.		0.502	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160511067	T	C	160511067	3	2	44	1	0	0	0	0	1	0	0	0	7585	1696	59	2	6761	2	IGF2R	6	160511067	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2982391	160511067	10604000	143	5603										
LPA	4018	hgsc.bcm.edu	37	chr6	161027527	161027527	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	accttgttcagaaggagcctCtaggcttggaatcggggtaa	13	8	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:161027527C>T	ENST00000316300.5	-	17	2811	c.2767G>A	c.(2767-2769)Gag>Aag	p.E923K	LPA_ENST00000447678.1_Missense_Mutation_p.E923K			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3431	Kringle 8. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GAAGGAGCCTCTAGGCTTGGA	0.547																																					p.E923K		Atlas-SNP	.											.	LPA	237	.	0			c.G2767A						.						87	89	88					6																	161027527		1948	4196	6144	SO:0001583	missense	4018	exon18			GAGCCTCTAGGCT	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.2767G>A	chr6.hg19:g.161027527C>T	ENSP00000321334:p.Glu923Lys	111.0	0.0		112.0	5.0	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	hg19	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	c	12.38	1.921269	0.33908	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	D;D	0.86627	-2.15;-2.15	2.1	-0.879	0.10613	Kringle (1);	.	.	.	.	T	0.78201	0.4246	L	0.60455	1.87	0.09310	N	1	P	0.45715	0.865	P	0.57620	0.824	T	0.70230	-0.4929	9	0.06625	T	0.88	.	8.3239	0.32145	0.0:0.4153:0.5846:0.0	.	3431	P08519	APOA_HUMAN	K	923	ENSP00000321334:E923K;ENSP00000395608:E923K	ENSP00000321334:E923K	E	-	1	0	LPA	160947517	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-1.884000	0.01622	-0.515000	0.06479	0.184000	0.17185	GAG	.	.		0.547	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	161027527	C	T	161027527	3	4	44	1	0	0	0	0	1	0	0	0	8912	922	32	3	3447	3	LPA	6	161027527	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	516460	161027527	10087540	144	5604										
UNC93A	54346	hgsc.bcm.edu	37	chr6	167711454	167711454	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gacccttccagaagagcagcTcacgtcctgtggggccagtg	13	13	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:167711454T>C	ENST00000230256.3	+	4	696	c.521T>C	c.(520-522)cTc>cCc	p.L174P	UNC93A_ENST00000366829.2_Intron	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GAAGAGCAGCTCACGTCCTGT	0.547																																					p.L174P		Atlas-SNP	.											.	UNC93A	66	.	0			c.T521C						.						136	116	123					6																	167711454		2203	4300	6503	SO:0001583	missense	54346	exon4			AGCAGCTCACGTC	AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"unc93 (C.elegans) homolog A"			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.521T>C	chr6.hg19:g.167711454T>C	ENSP00000230256:p.Leu174Pro	82.0	0.0		98.0	5.0	NM_018974	B3KRP5|Q4QQJ4|Q5JZD6	Missense_Mutation	SNP	ENST00000230256.3	hg19	CCDS5300.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490305	0.26686	.	.	ENSG00000112494	ENST00000230256	T	0.06142	3.34	5.21	5.21	0.72293	Major facilitator superfamily domain, general substrate transporter (1);	0.244021	0.34777	N	0.003697	T	0.06280	0.0162	M	0.85373	2.75	0.80722	D	1	B	0.23442	0.085	B	0.23716	0.048	T	0.03112	-1.1071	10	0.39692	T	0.17	-26.6477	12.8095	0.57631	0.0:0.0:0.0:1.0	.	174	Q86WB7	UN93A_HUMAN	P	174	ENSP00000230256:L174P	ENSP00000230256:L174P	L	+	2	0	UNC93A	167631444	0.996000	0.38824	0.143000	0.22291	0.018000	0.09664	5.536000	0.67180	1.948000	0.56530	0.533000	0.62120	CTC	.	.		0.547	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974		C	167711454	T	C	167711454	3	2	44	1	0	0	0	0	1	0	0	0	17011	1551	54	2	535	2	UNC93A	6	167711454	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	6683927	167711454	3403613	145	5605										
C6orf70	55780	hgsc.bcm.edu	37	chr6	170176070	170176070	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgaaacaaatgcctgccacTctttgattacaaaaatgacg	6	10	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr6:170176070T>C	ENST00000366773.3	+	15	1462	c.1429T>C	c.(1429-1431)Tct>Cct	p.S477P	ERMARD_ENST00000366772.2_Missense_Mutation_p.S477P|ERMARD_ENST00000588451.1_Missense_Mutation_p.S341P|ERMARD_ENST00000418781.3_Missense_Mutation_p.S477P|ERMARD_ENST00000392095.4_Missense_Mutation_p.S351P	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	477					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TGCCTGCCACTCTTTGATTAC	0.383																																					p.S477P		Atlas-SNP	.											.	C6orf70	63	.	0			c.T1429C						.						110	99	102					6																	170176070		2203	4300	6503	SO:0001583	missense	55780	exon15			TGCCACTCTTTGA	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"chromosome 6 open reading frame 70"	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.1429T>C	chr6.hg19:g.170176070T>C	ENSP00000355735:p.Ser477Pro	105.0	0.0		125.0	5.0	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	hg19	CCDS34576.1	.	.	.	.	.	.	.	.	.	.	.	10.35	1.326875	0.24080	.	.	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095;ENST00000366771	T;T	0.46451	0.88;0.87	5.27	-0.153	0.13403	.	0.675743	0.14454	N	0.318575	T	0.15869	0.0382	M	0.70595	2.14	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.12156	0.007;0.004;0.002	T	0.17715	-1.0360	10	0.35671	T	0.21	.	1.8222	0.03113	0.2696:0.0838:0.1383:0.5083	.	477;477;477	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	P	477;477;477;351;125	ENSP00000355735:S477P;ENSP00000375945:S351P	ENSP00000355733:S125P	S	+	1	0	C6orf70	169917995	0.001000	0.12720	0.016000	0.15963	0.016000	0.09150	-0.007000	0.12810	0.383000	0.24910	0.456000	0.33151	TCT	.	.		0.383	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341		C	170176070	T	C	170176070	3	2	44	1	0	0	0	0	1	0	0	0	2372	1551	54	2	1487	2	C6orf70	6	170176070	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2464616	170176070	938997	146	5606										
IQCE	23288	hgsc.bcm.edu	37	chr7	2629557	2629557	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccagaaactaagtgtgatggAgagctcaaaatcacacgccg	10	10	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:2629557A>G	ENST00000402050.2	+	14	1245	c.1061A>G	c.(1060-1062)gAg>gGg	p.E354G	IQCE_ENST00000325979.7_Missense_Mutation_p.E289G|IQCE_ENST00000404984.1_Missense_Mutation_p.E303G|IQCE_ENST00000438376.2_Missense_Mutation_p.E338G	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	354						mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		AGTGTGATGGAGAGCTCAAAA	0.507																																					p.E354G		Atlas-SNP	.											.	IQCE	66	.	0			c.A1061G						.						52	61	58					7																	2629557		2063	4216	6279	SO:0001583	missense	23288	exon14			TGATGGAGAGCTC	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.1061A>G	chr7.hg19:g.2629557A>G	ENSP00000385597:p.Glu354Gly	110.0	0.0		100.0	5.0	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	hg19	CCDS43542.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.451979	0.63290	.	.	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979;ENST00000427817	T;T;T;T	0.17854	2.27;2.25;2.26;2.26	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.36580	0.0972	L	0.58669	1.825	0.20403	N	0.999903	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;0.999	D;D;D;D;D;D	0.76575	0.948;0.962;0.988;0.942;0.931;0.943	T	0.17228	-1.0376	10	0.66056	D	0.02	-31.5709	11.9375	0.52882	1.0:0.0:0.0:0.0	.	289;338;289;354;354;338	B4DXN1;B4DDX4;Q6IPM2-2;Q6IPM2;B3KRY4;Q6IPM2-4	.;.;.;IQCE_HUMAN;.;.	G	354;303;338;289;161	ENSP00000385597:E354G;ENSP00000385945:E303G;ENSP00000396178:E338G;ENSP00000313772:E289G	ENSP00000313772:E289G	E	+	2	0	IQCE	2596083	0.997000	0.39634	0.144000	0.22314	0.015000	0.08874	3.231000	0.51294	2.074000	0.62210	0.533000	0.62120	GAG	.	.		0.507	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558		G	2629557	A	G	2629557	3	3	44	1	0	0	0	0	1	0	0	0	7815	304	11	2	1115	2	IQCE	7	2629557	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10		2629557	156509106	147	5607										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5410486	5410486	+	Frame_Shift_Del	DEL	C	C	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgtctcgggtgtcagctgcaCccccaggtccagggcggcgg							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:5410486delC	ENST00000430969.1	-	11	4087	c.3739delG	c.(3739-3741)gtgfs	p.V1247fs	TNRC18_ENST00000399537.4_Frame_Shift_Del_p.V1247fs	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1247							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GTCAGCTGCACCCCCAGGTCC	0.697																																					p.V1247fs		Atlas-INDEL	.											.	TNRC18	311	.	0			c.3740delT						.						14	17	16					7																	5410486		1989	4160	6149	SO:0001589	frameshift_variant	84629	exon11			.	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.3739delG	chr7.hg19:g.5410486delC	ENSP00000395538:p.Val1247fs	168.0	0.0		144.0	10.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Frame_Shift_Del	DEL	ENST00000430969.1	hg19	CCDS47534.1																																																																																			.	.		0.697	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				-	5410486	C	-	5410486	7	5	44	1	0	1	0	1	0	0	0	0	16354	507	18	0	5247	0	TNRC18	7	5410486	Frame_Shift_Del	DEL	C	TCGA-BC-A3KG-01A-11D-A20W-10	2780929	5410486	153728177	148	5608										
GLI3	2737	hgsc.bcm.edu	37	chr7	42005877	42005877	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcctgtggcagccgcgtactTggccttgaggcggtactgct	14	12	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:42005877T>A	ENST00000395925.3	-	15	2878	c.2794A>T	c.(2794-2796)Aag>Tag	p.K932*	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	932					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GCCGCGTACTTGGCCTTGAGG	0.721									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.K932X		Atlas-SNP	.											.	GLI3	312	.	0			c.A2794T						.						15	20	18					7																	42005877		2189	4277	6466	SO:0001587	stop_gained	2737	exon15	Familial Cancer Database	;	CGTACTTGGCCTT		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.2794A>T	chr7.hg19:g.42005877T>A	ENSP00000379258:p.Lys932*	68.0	0.0		111.0	9.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Nonsense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	T	41	8.717418	0.98927	.	.	ENSG00000106571	ENST00000395925	.	.	.	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.4522	0.67392	0.0:0.0:0.0:1.0	.	.	.	.	X	932	.	ENSP00000379258:K932X	K	-	1	0	GLI3	41972402	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.971000	0.88012	1.798000	0.52647	0.379000	0.24179	AAG	.	.		0.721	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		A	42005877	T	A	42005877	4	1	44	1	0	0	0	0	0	1	0	0	6447	1821	63	4	1952	4	GLI3	7	42005877	Nonsense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	36595391	42005877	117132786	149	5609										
ZMIZ2	83637	hgsc.bcm.edu	37	chr7	44796547	44796547	+	Splice_Site	DEL	T	T	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gattcctgcttcctcataggTtttggggaaccccatgggcc							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:44796547delT	ENST00000309315.4	+	4	290	c.167delT	c.(166-168)gtt>gt	p.V56fs	ZMIZ2_ENST00000441627.1_Splice_Site_p.V56fs|ZMIZ2_ENST00000413916.1_Intron|ZMIZ2_ENST00000433667.1_Intron|ZMIZ2_ENST00000265346.7_Splice_Site_p.V56fs	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	56	Gly-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						TCCTCATAGGTTTTGGGGAAC	0.592																																					p.V56fs	NSCLC(20;604 852 1948 16908 50522)	Atlas-INDEL	.											.	ZMIZ2	82	.	0			c.166delG						.						113	115	114					7																	44796547		1973	4147	6120	SO:0001630	splice_region_variant	83637	exon3			.	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"Zinc fingers, MIZ-type"	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.166-1T>-	chr7.hg19:g.44796547delT		165.0	0.0		151.0	10.0	NM_174929	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Frame_Shift_Del	DEL	ENST00000309315.4	hg19	CCDS43576.1																																																																																			.	.		0.592	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449	Frame_Shift_Del	-	44796547	T	-	44796547	8	5	44	1	0	1	0	1	0	0	1	0	17712	1739	60	0	177	0	ZMIZ2	7	44796547	Splice_Site	DEL	T	TCGA-BC-A3KG-01A-11D-A20W-10	2790670	44796547	114342116	150	5610										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48315670	48315670	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcttcaggaatatgcaaatgAggattactccagaatgatag	10	6	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:48315670A>G	ENST00000435803.1	+	17	6431	c.6407A>G	c.(6406-6408)gAg>gGg	p.E2136G		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2136					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.E2081V(1)|p.E2136V(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TATGCAAATGAGGATTACTCC	0.353																																					p.E2136G		Atlas-SNP	.											ABCA13_ENST00000435803,NS,lymphoid_neoplasm,0,2	ABCA13	1192	.	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.A6407G						.						37	32	34					7																	48315670		1818	4077	5895	SO:0001583	missense	154664	exon17			CAAATGAGGATTA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.6407A>G	chr7.hg19:g.48315670A>G	ENSP00000411096:p.Glu2136Gly	66.0	1.0		71.0	4.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	10.26	1.302426	0.23736	.	.	ENSG00000179869	ENST00000435803	T	0.16457	2.34	4.99	-2.42	0.06542	.	0.943144	0.08766	N	0.897032	T	0.09774	0.0240	L	0.27053	0.805	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.39800	-0.9596	9	.	.	.	.	6.2881	0.21045	0.4624:0.1511:0.3865:0.0	.	2136	Q86UQ4	ABCAD_HUMAN	G	2136	ENSP00000411096:E2136G	.	E	+	2	0	ABCA13	48286216	0.138000	0.22547	0.000000	0.03702	0.420000	0.31355	0.681000	0.25320	-0.232000	0.09811	0.397000	0.26171	GAG	.	.		0.353	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48315670	A	G	48315670	3	3	44	1	0	0	0	0	1	0	0	0	31	304	11	2	6302	2	ABCA13	7	48315670	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	3519123	48315670	110822993	151	5611										
SUMF2	25870	hgsc.bcm.edu	37	chr7	56136261	56136261	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cagacagcagagatggtgacGggcctgtgcgggaggcgaca	18	9	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:56136261G>A	ENST00000413756.1	+	2	177	c.154G>A	c.(154-156)Ggg>Agg	p.G52R	SUMF2_ENST00000395436.2_Missense_Mutation_p.G71R|SUMF2_ENST00000434526.2_Missense_Mutation_p.G71R|SUMF2_ENST00000275607.9_Intron|SUMF2_ENST00000342190.6_Missense_Mutation_p.G71R|SUMF2_ENST00000437307.2_Missense_Mutation_p.G52R|SUMF2_ENST00000395435.2_Missense_Mutation_p.G71R			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	52					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			AGATGGTGACGGGCCTGTGCG	0.493																																					p.G71R		Atlas-SNP	.											SUMF2_ENST00000342190,NS,carcinoma,0,4	SUMF2	56	.	0			c.G211A						.						69	62	64					7																	56136261		2203	4300	6503	SO:0001583	missense	25870	exon2			GGTGACGGGCCTG	AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103			20415	protein-coding gene	gene with protein product		607940				12757706	Standard	NM_015411		Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.154G>A	chr7.hg19:g.56136261G>A	ENSP00000406445:p.Gly52Arg	98.0	0.0		112.0	0.0	NM_015411	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Missense_Mutation	SNP	ENST00000413756.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.99	2.102779	0.37145	.	.	ENSG00000129103	ENST00000395436;ENST00000434526;ENST00000395435;ENST00000413952;ENST00000342190;ENST00000437307;ENST00000413756;ENST00000451338	D;D;D;D;D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38;-3.38;-3.38;-3.38;-3.38	5.01	4.13	0.48395	C-type lectin fold (1);Formylglycine-generating sulphatase enzyme domain (2);	0.276505	0.41712	D	0.000834	D	0.93331	0.7874	L	0.31845	0.965	0.80722	D	1	P;D;D;D;D;D	0.89917	0.868;0.999;0.966;0.999;1.0;1.0	P;P;B;P;D;D	0.72075	0.483;0.887;0.308;0.87;0.96;0.976	D	0.92822	0.6273	10	0.66056	D	0.02	-15.0969	8.9043	0.35515	0.1732:0.0:0.8268:0.0	.	52;71;71;52;71;71	Q8NBJ7-5;A8MXB9;E7EMF9;Q8NBJ7;F8WA42;C9JL30	.;.;.;SUMF2_HUMAN;.;.	R	71;71;71;71;71;52;52;49	ENSP00000378824:G71R;ENSP00000400922:G71R;ENSP00000378823:G71R;ENSP00000414434:G71R;ENSP00000341938:G71R;ENSP00000415989:G52R;ENSP00000406445:G52R;ENSP00000410796:G49R	ENSP00000341938:G71R	G	+	1	0	SUMF2	56103755	1.000000	0.71417	1.000000	0.80357	0.238000	0.25445	2.971000	0.49248	1.248000	0.43934	0.484000	0.47621	GGG	.	.		0.493	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411		A	56136261	G	A	56136261	3	1	44	1	0	0	0	0	1	0	0	0	15401	1116	39	1	217	1	SUMF2	7	56136261	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	7820591	56136261	103002402	152	5612										
PION	54103	hgsc.bcm.edu	37	chr7	76990177	76990177	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aatgccctttgtcatgtgtgAcccaacattctcaagagaag	8	10	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:76990177A>G	ENST00000257626.7	-	14	1069	c.991T>C	c.(991-993)Tca>Cca	p.S331P		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	331					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										GTCATGTGTGACCCAACATTC	0.458																																					p.S331P		Atlas-SNP	.											.	PION	74	.	0			c.T991C						.						228	188	201					7																	76990177		2203	4300	6503	SO:0001583	missense	54103	exon14			TGTGTGACCCAAC		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"pigeon homolog (Drosophila)"	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.991T>C	chr7.hg19:g.76990177A>G	ENSP00000257626:p.Ser331Pro	219.0	0.0		93.0	4.0	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Missense_Mutation	SNP	ENST00000257626.7	hg19	CCDS34672.2	.	.	.	.	.	.	.	.	.	.	A	11.76	1.734723	0.30774	.	.	ENSG00000186088	ENST00000257626	T	0.19669	2.13	5.98	2.25	0.28309	.	0.532611	0.17215	U	0.182580	T	0.14227	0.0344	L	0.41236	1.265	0.09310	N	1	B;B	0.14438	0.01;0.004	B;B	0.11329	0.006;0.006	T	0.15292	-1.0442	10	0.33141	T	0.24	.	4.4751	0.11731	0.6973:0.0:0.1576:0.1451	.	331;331	A4D1B5-3;A4D1B5	.;GSAP_HUMAN	P	331	ENSP00000257626:S331P	ENSP00000257626:S331P	S	-	1	0	PION	76828113	0.838000	0.29461	0.099000	0.21106	0.031000	0.12232	1.769000	0.38522	1.097000	0.41459	0.482000	0.46254	TCA	.	.		0.458	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439		G	76990177	A	G	76990177	3	3	44	1	0	0	0	0	1	0	0	0	11943	275	10	2	1645	2	PION	7	76990177	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	20853916	76990177	82148486	153	5613										
PCLO	27445	hgsc.bcm.edu	37	chr7	82476475	82476475	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agtcttacacatatttctgcTtccccactttgctgactaat	4	12	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:82476475T>G	ENST00000333891.9	-	11	14080	c.13743A>C	c.(13741-13743)gaA>gaC	p.E4581D	PCLO_ENST00000423517.2_Missense_Mutation_p.E4581D|PCLO_ENST00000426442.2_5'UTR	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.E4581E(2)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ATATTTCTGCTTCCCCACTTT	0.358																																					p.E4581D		Atlas-SNP	.											PCLO_ENST00000333891,NS,carcinoma,0,2	PCLO	1506	.	2	Substitution - coding silent(2)	endometrium(2)	c.A13743C						.						119	116	117					7																	82476475		1865	4095	5960	SO:0001583	missense	27445	exon11			TTCTGCTTCCCCA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.13743A>C	chr7.hg19:g.82476475T>G	ENSP00000334319:p.Glu4581Asp	35.0	0.0		26.0	2.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	12.54	1.969477	0.34754	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.19806	2.14;2.12	5.6	5.6	0.85130	.	.	.	.	.	T	0.45458	0.1343	M	0.79258	2.445	0.80722	D	1	D;D;D	0.69078	0.988;0.988;0.997	D;D;D	0.79108	0.98;0.98;0.992	T	0.47799	-0.9089	9	0.87932	D	0	.	10.1804	0.42963	0.0:0.0745:0.0:0.9255	.	4581;4581;78	Q9Y6V0-5;Q9Y6V0-6;Q32P40	.;.;.	D	4581;4581;77	ENSP00000334319:E4581D;ENSP00000388393:E4581D	ENSP00000334319:E4581D	E	-	3	2	PCLO	82314411	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.937000	0.40193	2.134000	0.65973	0.383000	0.25322	GAA	.	.		0.358	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82476475	T	G	82476475	3	3	44	1	0	0	0	0	1	0	0	0	11592	1606	56	5	1762	5	PCLO	7	82476475	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	5486298	82476475	76662188	154	5614										
PCLO	27445	hgsc.bcm.edu	37	chr7	82578936	82578936	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttagccatatctggatgcagTactttctgtggacttatatc	8	8	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:82578936T>C	ENST00000333891.9	-	6	11305	c.10968A>G	c.(10966-10968)gtA>gtG	p.V3656V	PCLO_ENST00000423517.2_Silent_p.V3656V|PCLO_ENST00000437081.1_Silent_p.V376V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTGGATGCAGTACTTTCTGTG	0.473																																					p.V3656V		Atlas-SNP	.											.	PCLO	1506	.	0			c.A10968G						.						192	187	189					7																	82578936		1925	4125	6050	SO:0001819	synonymous_variant	27445	exon6			ATGCAGTACTTTC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.10968A>G	chr7.hg19:g.82578936T>C		175.0	0.0		90.0	4.0	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.473	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82578936	T	C	82578936	2	2	44	1	0	0	0	0	0	0	0	1	11592	1625	57	2		2	PCLO	7	82578936	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	102461	82578936	76559727	155	5615										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83029465	83029465	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggttttttatgggcaggtttTatggcctggtacattagtgg	14	4	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:83029465T>G	ENST00000307792.3	-	11	1712	c.1245A>C	c.(1243-1245)atA>atC	p.I415I	SEMA3E_ENST00000427262.1_Silent_p.I355I	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	415	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				GGGCAGGTTTTATGGCCTGGT	0.423																																					p.I415I		Atlas-SNP	.											.	SEMA3E	125	.	0			c.A1245C						.						204	185	191					7																	83029465		2203	4300	6503	SO:0001819	synonymous_variant	9723	exon11			AGGTTTTATGGCC	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1245A>C	chr7.hg19:g.83029465T>G		403.0	0.0		178.0	157.0	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	hg19	CCDS34674.1																																																																																			.	.		0.423	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		G	83029465	T	G	83029465	2	3	44	1	0	0	0	0	0	0	0	1	14043	1744	61	5		5	SEMA3E	7	83029465	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	450529	83029465	76109198	156	5616										
C7orf64	84060	hgsc.bcm.edu	37	chr7	92163807	92163807	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcagagatgtctggattttgTaaagctgctttgaacacttc	9	7	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:92163807T>C	ENST00000265732.5	+	4	581	c.540T>C	c.(538-540)tgT>tgC	p.C180C	RBM48_ENST00000481551.1_Silent_p.C180C	NM_032120.2	NP_115496.2	Q5RL73	RBM48_HUMAN	RNA binding motif protein 48	180						nucleus (GO:0005634)	RNA binding (GO:0003723)										CTGGATTTTGTAAAGCTGCTT	0.363																																					p.C180C		Atlas-SNP	.											.	.	.	.	0			c.T540C						.						127	112	116					7																	92163807		1847	4096	5943	SO:0001819	synonymous_variant	84060	exon4			ATTTTGTAAAGCT	AL136619	CCDS43615.1	7q21.2	2013-02-12	2011-12-09	2011-12-09	ENSG00000127993	ENSG00000127993		"RNA binding motif (RRM) containing"	21785	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 64"	C7orf64			Standard	NM_032120		Approved	DKFZp564O0523, HSPC304	uc003ulz.3	Q5RL73	OTTHUMG00000159535	ENST00000265732.5:c.540T>C	chr7.hg19:g.92163807T>C		114.0	0.0		65.0	4.0	NM_032120	B7Z2K5|B7ZL51|Q5H9T2|Q8IYW7|Q96NS0|Q9H0V7	Silent	SNP	ENST00000265732.5	hg19	CCDS43615.1																																																																																			.	.		0.363	RBM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356076.1	NM_032120		C	92163807	T	C	92163807	2	2	44	1	0	0	0	0	0	0	0	1	2412	1644	57	2		2	C7orf64	7	92163807	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	9134342	92163807	66974856	157	5617										
TAF6	6878	hgsc.bcm.edu	37	chr7	99707891	99707891	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccagggcgtcttctcgtccaCccagctctgtaaggggaagg	13	13	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:99707891C>T	ENST00000344095.4	-	11	1615	c.1090G>A	c.(1090-1092)Gtg>Atg	p.V364M	TAF6_ENST00000437822.2_Missense_Mutation_p.V401M|TAF6_ENST00000472509.1_Missense_Mutation_p.V421M|TAF6_ENST00000452041.1_Missense_Mutation_p.V364M|TAF6_ENST00000418432.2_Missense_Mutation_p.V288M|TAF6_ENST00000453269.2_Missense_Mutation_p.V364M|AP4M1_ENST00000421755.1_3'UTR	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	364					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TTCTCGTCCACCCAGCTCTGT	0.507																																					p.V401M		Atlas-SNP	.											.	TAF6	55	.	0			c.G1201A						.						153	154	153					7																	99707891		2203	4300	6503	SO:0001583	missense	6878	exon11			CGTCCACCCAGCT		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD", "transcription initiation factor TFIID 70 kD subunit"	602955	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.1090G>A	chr7.hg19:g.99707891C>T	ENSP00000344537:p.Val364Met	119.0	0.0		51.0	4.0	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	hg19	CCDS5686.1	.	.	.	.	.	.	.	.	.	.	c	16.82	3.228220	0.58777	.	.	ENSG00000106290	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822	T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	5.24	4.36	0.52297	Domain of unknown function DUF1546 (1);	0.207592	0.41396	D	0.000893	T	0.56108	0.1963	N	0.11064	0.09	0.35234	D	0.777172	D;P;P;P;D	0.54601	0.967;0.891;0.911;0.852;0.967	P;B;P;P;P	0.52909	0.646;0.376;0.51;0.51;0.713	T	0.64888	-0.6301	10	0.31617	T	0.26	-18.2586	11.8099	0.52177	0.0:0.9155:0.0:0.0845	.	401;364;354;364;288	B4DT11;P49848-2;A4D299;P49848;B3KUR4	.;.;.;TAF6_HUMAN;.	M	364;421;364;364;288;401	ENSP00000389575:V364M;ENSP00000419760:V421M;ENSP00000416396:V364M;ENSP00000344537:V364M;ENSP00000407980:V288M;ENSP00000399982:V401M	ENSP00000344537:V364M	V	-	1	0	TAF6	99545827	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.395000	0.44459	1.438000	0.47492	0.556000	0.70494	GTG	.	.		0.507	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		T	99707891	C	T	99707891	3	4	44	1	0	0	0	0	1	0	0	0	15545	507	18	3	963	3	TAF6	7	99707891	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	7544084	99707891	59430772	158	5618										
EPHB4	2050	hgsc.bcm.edu	37	chr7	100417891	100417891	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggcaggacccttctcctgacAggggcttgaaggtgccctgg	15	12	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:100417891A>G	ENST00000358173.3	-	5	1304	c.836T>C	c.(835-837)cTg>cCg	p.L279P	RN7SL750P_ENST00000582814.1_RNA|EPHB4_ENST00000477446.1_5'UTR|EPHB4_ENST00000360620.3_Missense_Mutation_p.L279P	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	279	Cys-rich.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					TTCTCCTGACAGGGGCTTGAA	0.587																																					p.L279P	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.T836C						.						106	121	116					7																	100417891		2203	4300	6503	SO:0001583	missense	2050	exon5			CCTGACAGGGGCT	AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3395	protein-coding gene	gene with protein product		600011	"EphB4"	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.836T>C	chr7.hg19:g.100417891A>G	ENSP00000350896:p.Leu279Pro	74.0	0.0		42.0	4.0	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	hg19	CCDS5706.1	.	.	.	.	.	.	.	.	.	.	A	10.15	1.270609	0.23221	.	.	ENSG00000196411	ENST00000360620;ENST00000358173	T;T	0.15487	2.42;2.42	5.35	2.86	0.33363	Tyrosine-protein kinase ephrin type A/B receptor-like (1);	0.592988	0.13804	N	0.361588	T	0.14313	0.0346	L	0.41573	1.285	0.09310	N	0.999999	P;P;B;B	0.35821	0.523;0.523;0.202;0.355	B;B;B;B	0.35859	0.212;0.14;0.089;0.129	T	0.14727	-1.0462	10	0.37606	T	0.19	.	8.6553	0.34060	0.4441:0.0:0.0:0.5559	.	279;279;279;279	B5A972;B5A970;Q96L35;P54760	.;.;.;EPHB4_HUMAN	P	279	ENSP00000353833:L279P;ENSP00000350896:L279P	ENSP00000350896:L279P	L	-	2	0	EPHB4	100255827	0.003000	0.15002	0.220000	0.23810	0.983000	0.72400	1.087000	0.30865	0.290000	0.22444	0.533000	0.62120	CTG	.	.		0.587	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		G	100417891	A	G	100417891	3	3	44	1	0	0	0	0	1	0	0	0	5179	188	7	2	2179	2	EPHB4	7	100417891	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	710000	100417891	58720772	159	5619										
CUX1	1523	hgsc.bcm.edu	37	chr7	101833103	101833103	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgttttcagcaactggaagAaaaactcaaaggccaggctg	10	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:101833103A>G	ENST00000292535.7	+	12	1066	c.1028A>G	c.(1027-1029)gAa>gGa	p.E343G	CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000550008.2_Missense_Mutation_p.E343G|CUX1_ENST00000556210.1_Missense_Mutation_p.E343G|CUX1_ENST00000546411.2_Missense_Mutation_p.E343G|CUX1_ENST00000425244.2_Missense_Mutation_p.E308G|CUX1_ENST00000547394.2_Missense_Mutation_p.E338G|CUX1_ENST00000292538.4_Missense_Mutation_p.E354G|CUX1_ENST00000437600.4_Missense_Mutation_p.E352G|CUX1_ENST00000549414.2_Missense_Mutation_p.E343G|CUX1_ENST00000360264.3_Missense_Mutation_p.E354G|CUX1_ENST00000393824.3_Missense_Mutation_p.E315G	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	343					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						CAACTGGAAGAAAAACTCAAA	0.537																																					p.E354G		Atlas-SNP	.											.	CUX1	253	.	0			c.A1061G						.						101	99	100					7																	101833103		2203	4300	6503	SO:0001583	missense	1523	exon12			TGGAAGAAAAACT	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1028A>G	chr7.hg19:g.101833103A>G	ENSP00000292535:p.Glu343Gly	162.0	0.0		100.0	4.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	A	18.94	3.728807	0.69074	.	.	ENSG00000257923	ENST00000292538;ENST00000547394;ENST00000360264;ENST00000425244;ENST00000437600;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T;T;T;T;T	0.62232	1.39;1.39;0.04;1.42;1.39;0.06;0.06;0.08;0.13;0.13	4.94	4.94	0.65067	.	0.117279	0.56097	D	0.000023	T	0.67702	0.2921	L	0.43923	1.385	0.58432	D	0.999997	P;D;P;P;P;P;D	0.58268	0.932;0.97;0.953;0.864;0.949;0.932;0.982	B;P;P;P;B;P;P	0.58077	0.345;0.683;0.631;0.514;0.31;0.468;0.832	T	0.69347	-0.5169	10	0.51188	T	0.08	-26.8634	13.4706	0.61279	1.0:0.0:0.0:0.0	.	315;343;308;338;352;354;354	B4DZZ2;P39880;B3KV79;G3V1Z6;Q13948-2;Q13948;P39880-3	.;CUX1_HUMAN;.;.;.;CASP_HUMAN;.	G	354;338;354;308;352;343;343;343;343;343	ENSP00000292538:E354G;ENSP00000449371:E338G;ENSP00000353401:E354G;ENSP00000409745:E308G;ENSP00000414091:E352G;ENSP00000292535:E343G;ENSP00000446630:E343G;ENSP00000447373:E343G;ENSP00000450125:E343G;ENSP00000451558:E343G	ENSP00000292535:E343G	E	+	2	0	CUX1	101619823	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.967000	0.76079	1.967000	0.57214	0.459000	0.35465	GAA	.	.		0.537	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		G	101833103	A	G	101833103	3	3	44	1	0	0	0	0	1	0	0	0	4066	246	9	2	1141	2	CUX1	7	101833103	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1415212	101833103	57305560	160	5620										
CUX1	1523	hgsc.bcm.edu	37	chr7	101837150	101837150	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agtccatggagtttgcaccgTccgagggcgctgggacacag	15	11	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:101837150T>A	ENST00000292535.7	+	13	1143	c.1105T>A	c.(1105-1107)Tcc>Acc	p.S369T	CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000550008.2_Missense_Mutation_p.S369T|CUX1_ENST00000556210.1_Missense_Mutation_p.S369T|CUX1_ENST00000546411.2_Missense_Mutation_p.S369T|CUX1_ENST00000425244.2_Missense_Mutation_p.S334T|CUX1_ENST00000547394.2_Missense_Mutation_p.S364T|CUX1_ENST00000292538.4_Missense_Mutation_p.S380T|CUX1_ENST00000437600.4_Missense_Mutation_p.S378T|CUX1_ENST00000549414.2_Missense_Mutation_p.S369T|CUX1_ENST00000360264.3_Missense_Mutation_p.S380T|CUX1_ENST00000393824.3_Missense_Mutation_p.S341T|SNORA48_ENST00000517015.1_RNA	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	369					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						GTTTGCACCGTCCGAGGGCGC	0.527																																					p.S380T		Atlas-SNP	.											CUX1_ENST00000292538,NS,carcinoma,0,2	CUX1	253	.	0			c.T1138A						.						82	68	73					7																	101837150		2203	4300	6503	SO:0001583	missense	1523	exon13			GCACCGTCCGAGG	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1105T>A	chr7.hg19:g.101837150T>A	ENSP00000292535:p.Ser369Thr	94.0	0.0		58.0	0.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	T	1.936	-0.444817	0.04604	.	.	ENSG00000257923	ENST00000292538;ENST00000547394;ENST00000360264;ENST00000425244;ENST00000437600;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T;T;T;T;T	0.61510	1.47;1.46;0.1;1.49;1.48;0.11;0.11;0.13;0.2;0.19	5.71	1.86	0.25419	.	0.191530	0.46758	D	0.000274	T	0.46014	0.1371	L	0.42245	1.32	0.22446	N	0.999094	B;B;B;B;B;B;B	0.30361	0.112;0.044;0.094;0.006;0.277;0.006;0.073	B;B;B;B;B;B;B	0.30495	0.033;0.014;0.024;0.012;0.116;0.005;0.053	T	0.34453	-0.9828	10	0.46703	T	0.11	-6.7303	8.9888	0.36010	0.0:0.0646:0.3714:0.564	.	341;369;334;364;378;380;380	B4DZZ2;P39880;B3KV79;G3V1Z6;Q13948-2;Q13948;P39880-3	.;CUX1_HUMAN;.;.;.;CASP_HUMAN;.	T	380;364;380;334;378;369;369;369;369;369	ENSP00000292538:S380T;ENSP00000449371:S364T;ENSP00000353401:S380T;ENSP00000409745:S334T;ENSP00000414091:S378T;ENSP00000292535:S369T;ENSP00000446630:S369T;ENSP00000447373:S369T;ENSP00000450125:S369T;ENSP00000451558:S369T	ENSP00000292535:S369T	S	+	1	0	CUX1	101623870	0.139000	0.22563	0.005000	0.12908	0.890000	0.51754	0.438000	0.21559	0.072000	0.16694	0.459000	0.35465	TCC	.	.		0.527	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		A	101837150	T	A	101837150	3	1	44	1	0	0	0	0	1	0	0	0	4066	1667	58	4	1222	4	CUX1	7	101837150	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4047	101837150	57301513	161	5621										
MLL5	55904	hgsc.bcm.edu	37	chr7	104742347	104742347	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aattaggaacaagcaaaagaAgaaaatgctagcaagccaac	8	7	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:104742347A>G	ENST00000311117.3	+	17	2447	c.1902A>G	c.(1900-1902)gaA>gaG	p.E634E	KMT2E_ENST00000334877.4_Silent_p.E634E|KMT2E_ENST00000257745.4_Silent_p.E634E|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334914.7_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	634					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.E634E(1)									AAGCAAAAGAAGAAAATGCTA	0.353																																					p.E634E		Atlas-SNP	.											MLL5,NS,carcinoma,0,1	MLL5	173	.	1	Substitution - coding silent(1)	lung(1)	c.A1902G						.						35	38	37					7																	104742347		2201	4298	6499	SO:0001819	synonymous_variant	55904	exon16			AAAAGAAGAAAAT	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.1902A>G	chr7.hg19:g.104742347A>G		69.0	0.0		40.0	3.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Silent	SNP	ENST00000311117.3	hg19	CCDS34723.1																																																																																			.	.		0.353	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			G	104742347	A	G	104742347	2	3	44	1	0	0	0	0	0	0	0	1	9633	69	3	2		2	MLL5	7	104742347	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2905197	104742347	54396316	162	5622										
FOXP2	93986	hgsc.bcm.edu	37	chr7	114174697	114174697	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccaggcagcaagacaacttcTtttacagcagcaaacaagtg	8	11	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:114174697T>C	ENST00000393494.2	+	3	473	c.194T>C	c.(193-195)cTt>cCt	p.L65P	FOXP2_ENST00000390668.3_Missense_Mutation_p.L64P|FOXP2_ENST00000403559.4_Missense_Mutation_p.L65P|FOXP2_ENST00000350908.4_Missense_Mutation_p.L65P|FOXP2_ENST00000393489.3_5'UTR|FOXP2_ENST00000459666.1_3'UTR|FOXP2_ENST00000408937.3_Missense_Mutation_p.L65P|FOXP2_ENST00000378237.3_Missense_Mutation_p.L65P|FOXP2_ENST00000360232.4_Missense_Mutation_p.L65P|FOXP2_ENST00000393500.3_5'UTR|FOXP2_ENST00000393498.2_Missense_Mutation_p.L65P			O15409	FOXP2_HUMAN	forkhead box P2	65	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						AGACAACTTCTTTTACAGCAG	0.363																																					p.L65P		Atlas-SNP	.											.	FOXP2	133	.	0			c.T194C						.						125	130	128					7																	114174697		2203	4300	6503	SO:0001583	missense	93986	exon2			AACTTCTTTTACA	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"Forkhead boxes"	13875	protein-coding gene	gene with protein product	"trinucleotide repeat containing 10", "forkhead/winged-helix transcription factor", "speech and language disorder 1", "CAG repeat protein 44"	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.194T>C	chr7.hg19:g.114174697T>C	ENSP00000377132:p.Leu65Pro	174.0	0.0		99.0	4.0	NM_001172767	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	hg19	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.992796	0.54041	.	.	ENSG00000128573	ENST00000324462;ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000378237;ENST00000360232;ENST00000452963;ENST00000390668	T;D;T;T;T;T;T	0.94497	1.32;-3.44;1.56;1.32;1.32;1.32;-0.63	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000004	D	0.96617	0.8896	M	0.65498	2.005	0.80722	D	1	D;P;P;P;D;D;D	0.89917	1.0;0.662;0.535;0.925;1.0;1.0;0.99	D;B;P;P;D;D;P	0.91635	0.997;0.353;0.556;0.677;0.997;0.999;0.836	D	0.97237	0.9888	10	0.87932	D	0	.	15.0588	0.71936	0.0:0.0:0.0:1.0	.	65;65;65;64;65;65;65	B7ZLK5;B4DLD9;O15409-6;Q8N6B5;O15409;O15409-4;O15409-5	.;.;.;.;FOXP2_HUMAN;.;.	P	65;65;65;65;65;65;65;65;65;64	ENSP00000377132:L65P;ENSP00000386200:L65P;ENSP00000385069:L65P;ENSP00000265436:L65P;ENSP00000367482:L65P;ENSP00000353367:L65P;ENSP00000375084:L64P	ENSP00000319424:L65P	L	+	2	0	FOXP2	113961933	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.236000	0.78154	1.984000	0.57885	0.528000	0.53228	CTT	.	.		0.363	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		C	114174697	T	C	114174697	3	2	44	1	0	0	0	0	1	0	0	0	6035	1609	56	2	200	2	FOXP2	7	114174697	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	9432350	114174697	44963966	163	5623										
CAPZA2	830	hgsc.bcm.edu	37	chr7	116557794	116557794	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttcatagactgccatcagtgAgaattatcagacaatgtcgg	9	8	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:116557794A>G	ENST00000361183.3	+	10	873	c.734A>G	c.(733-735)gAg>gGg	p.E245G	CAPZA2_ENST00000458284.2_3'UTR	NM_006136.2	NP_006127.1	P47755	CAZA2_HUMAN	capping protein (actin filament) muscle Z-line, alpha 2	245					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|WASH complex (GO:0071203)				endometrium(2)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	13	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)			GCCATCAGTGAGAATTATCAG	0.348																																					p.E245G		Atlas-SNP	.											.	CAPZA2	29	.	0			c.A734G						.						140	134	136					7																	116557794		2203	4300	6503	SO:0001583	missense	830	exon10			TCAGTGAGAATTA		CCDS5768.1	7q31.2-q31.3	2008-07-18			ENSG00000198898	ENSG00000198898			1490	protein-coding gene	gene with protein product	"F-actin capping protein alpha-2 subunit"	601571					Standard	NM_006136		Approved	CAPZ, CAPPA2	uc003vil.3	P47755	OTTHUMG00000023185	ENST00000361183.3:c.734A>G	chr7.hg19:g.116557794A>G	ENSP00000354947:p.Glu245Gly	161.0	0.0		94.0	5.0	NM_006136	B4DG50	Missense_Mutation	SNP	ENST00000361183.3	hg19	CCDS5768.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.000519	0.74818	.	.	ENSG00000198898	ENST00000361183	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.85017	0.5601	M	0.90977	3.165	0.80722	D	1	D	0.61080	0.989	D	0.68943	0.961	D	0.88577	0.3134	9	0.87932	D	0	-14.6346	15.8386	0.78824	1.0:0.0:0.0:0.0	.	245	P47755	CAZA2_HUMAN	G	245	.	ENSP00000354947:E245G	E	+	2	0	CAPZA2	116345030	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.245000	0.95431	2.135000	0.66039	0.383000	0.25322	GAG	.	.		0.348	CAPZA2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059506.4	NM_006136		G	116557794	A	G	116557794	3	3	44	1	0	0	0	0	1	0	0	0	2643	304	11	2	772	2	CAPZA2	7	116557794	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2383097	116557794	42580869	164	5624										
KCND2	3751	hgsc.bcm.edu	37	chr7	119915322	119915322	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acagtgccgtgcggatcaagCccaggtcacattaaagaact	10	11	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:119915322C>T	ENST00000331113.4	+	1	1601	c.636C>T	c.(634-636)agC>agT	p.S212S		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	212					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	GCGGATCAAGCCCAGGTCACA	0.532																																					p.S212S		Atlas-SNP	.											.	KCND2	194	.	0			c.C636T						.						118	108	112					7																	119915322		2203	4300	6503	SO:0001819	synonymous_variant	3751	exon1			ATCAAGCCCAGGT	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.636C>T	chr7.hg19:g.119915322C>T		225.0	0.0		98.0	4.0	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Silent	SNP	ENST00000331113.4	hg19	CCDS5776.1																																																																																			.	.		0.532	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		T	119915322	C	T	119915322	2	4	44	1	0	0	0	0	0	0	0	1	8028	738	26	3		3	KCND2	7	119915322	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	3357528	119915322	39223341	165	5625										
CADPS2	93664	hgsc.bcm.edu	37	chr7	122255249	122255249	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcttactgtggccttgaggcTtcggcctggtctgtctgaag	14	10	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:122255249T>C	ENST00000449022.2	-	6	1228	c.1209A>G	c.(1207-1209)gaA>gaG	p.E403E	CADPS2_ENST00000412584.2_Silent_p.E403E|CADPS2_ENST00000334010.7_Silent_p.E403E|CADPS2_ENST00000313070.7_Silent_p.E403E	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	403	C2.				cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						GCCTTGAGGCTTCGGCCTGGT	0.398																																					p.E403E		Atlas-SNP	.											.	CADPS2	116	.	0			c.A1209G						.						81	73	75					7																	122255249		1874	4092	5966	SO:0001819	synonymous_variant	93664	exon6			TGAGGCTTCGGCC		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.1209A>G	chr7.hg19:g.122255249T>C		156.0	0.0		62.0	4.0	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Silent	SNP	ENST00000449022.2	hg19	CCDS55158.1	.	.	.	.	.	.	.	.	.	.	T	9.230	1.035672	0.19590	.	.	ENSG00000081803	ENST00000397721	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	T	0.61553	0.2356	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60855	-0.7180	4	.	.	.	-21.3133	10.1681	0.42893	0.0:0.0746:0.0:0.9254	.	.	.	.	G	52	.	.	S	-	1	0	CADPS2	122042485	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.996000	0.40776	2.136000	0.66102	0.533000	0.62120	AGC	.	.		0.398	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		C	122255249	T	C	122255249	2	2	44	1	0	0	0	0	0	0	0	1	2573	1606	56	2		2	CADPS2	7	122255249	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2339927	122255249	36883414	166	5626										
GRM8	2918	hgsc.bcm.edu	37	chr7	126409939	126409939	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cattaaaatttacagcccgaAtataaccaagtagctctttc	4	10	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:126409939A>G	ENST00000339582.2	-	7	2145	c.1337T>C	c.(1336-1338)aTt>aCt	p.I446T	GRM8_ENST00000358373.3_Missense_Mutation_p.I446T|GRM8_ENST00000405249.1_Missense_Mutation_p.I446T|GRM8_ENST00000444921.2_Missense_Mutation_p.I446T|GRM8_ENST00000480995.1_5'UTR			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	446					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				TACAGCCCGAATATAACCAAG	0.413										HNSCC(24;0.065)																											p.I446T		Atlas-SNP	.											.	GRM8	377	.	0			c.T1337C						.						119	110	113					7																	126409939		2203	4300	6503	SO:0001583	missense	2918	exon6			GCCCGAATATAAC		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1337T>C	chr7.hg19:g.126409939A>G	ENSP00000344173:p.Ile446Thr	128.0	0.0		61.0	4.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	hg19	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.320245	0.81469	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249	D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27	5.78	5.78	0.91487	Extracellular ligand-binding receptor (1);	0.054564	0.64402	D	0.000001	D	0.94079	0.8102	M	0.89095	3.005	0.80722	D	1	D;P;D	0.61080	0.989;0.763;0.98	D;B;P	0.67103	0.949;0.085;0.772	D	0.95024	0.8163	10	0.87932	D	0	.	15.287	0.73835	1.0:0.0:0.0:0.0	.	446;446;446	O00222-3;O00222-2;O00222	.;.;GRM8_HUMAN	T	446	ENSP00000344173:I446T;ENSP00000409790:I446T;ENSP00000351142:I446T;ENSP00000385731:I446T	ENSP00000344173:I446T	I	-	2	0	GRM8	126197175	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.335000	0.96500	2.190000	0.69967	0.533000	0.62120	ATT	.	.		0.413	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			G	126409939	A	G	126409939	3	3	44	1	0	0	0	0	1	0	0	0	6812	101	4	2	1459	2	GRM8	7	126409939	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	4154690	126409939	32728724	167	5627										
CHRM2	1129	hgsc.bcm.edu	37	chr7	136699964	136699964	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttatgaatctgctcatcatcAgctttgacaggtacttctgt	7	9	5	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:136699964A>G	ENST00000445907.2	+	3	880	c.352A>G	c.(352-354)Agc>Ggc	p.S118G	hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000586239.1_RNA|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000397608.3_Missense_Mutation_p.S118G|hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000597642.1_RNA|CHRM2_ENST00000320658.5_Missense_Mutation_p.S118G|hsa-mir-490_ENST00000593789.1_RNA|CHRM2_ENST00000453373.1_Missense_Mutation_p.S118G|CHRM2_ENST00000401861.1_Missense_Mutation_p.S118G|CHRM2_ENST00000402486.3_Missense_Mutation_p.S118G|hsa-mir-490_ENST00000439694.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	118					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	GCTCATCATCAGCTTTGACAG	0.502																																					p.S118G		Atlas-SNP	.											.	CHRM2	167	.	0			c.A352G						.						139	131	133					7																	136699964		2203	4300	6503	SO:0001583	missense	1129	exon3			ATCATCAGCTTTG		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.352A>G	chr7.hg19:g.136699964A>G	ENSP00000399745:p.Ser118Gly	195.0	0.0		97.0	4.0	NM_001006632	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	hg19	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	A	19.09	3.759649	0.69763	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	T;T;T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44;-1.44;-1.44	5.61	5.61	0.85477	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.90800	0.7111	M	0.90425	3.115	0.80722	D	1	D	0.65815	0.995	D	0.63877	0.919	D	0.92708	0.6180	10	0.87932	D	0	-12.7738	15.8611	0.79021	1.0:0.0:0.0:0.0	.	118	P08172	ACM2_HUMAN	G	118	ENSP00000399745:S118G;ENSP00000415386:S118G;ENSP00000319984:S118G;ENSP00000380733:S118G;ENSP00000384937:S118G;ENSP00000384401:S118G	ENSP00000319984:S118G	S	+	1	0	CHRM2	136350504	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.281000	0.95811	2.145000	0.66743	0.529000	0.55759	AGC	.	.		0.502	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			G	136699964	A	G	136699964	3	3	44	1	0	0	0	0	1	0	0	0	3379	188	7	2	354	2	CHRM2	7	136699964	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	10290025	136699964	22438699	168	5628										
OR9A4	130075	hgsc.bcm.edu	37	chr7	141618691	141618691	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	actaaatgttgatgaattacTctagtgccactgaattttat	6	6	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:141618691T>C	ENST00000548136.1	+	1	75	c.16T>C	c.(16-18)Tct>Cct	p.S6P	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22	Melanoma(164;0.0171)					GATGAATTACTCTAGTGCCAC	0.358																																					p.S6P		Atlas-SNP	.											.	OR9A4	58	.	0			c.T16C						.						196	196	196					7																	141618691		2031	4193	6224	SO:0001583	missense	130075	exon1			AATTACTCTAGTG		CCDS43661.1	7q34	2012-10-03			ENSG00000258083	ENSG00000258083		"GPCR / Class A : Olfactory receptors"	15095	protein-coding gene	gene with protein product							Standard	NM_001001656		Approved		uc003vwu.1	Q8NGU2	OTTHUMG00000158370	ENST00000548136.1:c.16T>C	chr7.hg19:g.141618691T>C	ENSP00000448789:p.Ser6Pro	138.0	0.0		85.0	4.0	NM_001001656	B9EGV6|Q6IFI4	Missense_Mutation	SNP	ENST00000548136.1	hg19	CCDS43661.1	.	.	.	.	.	.	.	.	.	.	.	14.49	2.552376	0.45487	.	.	ENSG00000258083	ENST00000548136	T	0.54479	0.57	3.88	1.28	0.21552	.	.	.	.	.	T	0.64283	0.2584	M	0.87038	2.855	0.09310	N	1	P	0.45634	0.863	P	0.52909	0.713	T	0.56220	-0.8015	9	0.87932	D	0	-7.2456	4.1593	0.10275	0.3796:0.0:0.1811:0.4393	.	6	Q8NGU2	OR9A4_HUMAN	P	6	ENSP00000448789:S6P	ENSP00000386148:S6P	S	+	1	0	OR9A4	141265160	0.000000	0.05858	0.072000	0.20136	0.853000	0.48598	0.127000	0.15790	0.136000	0.18733	0.523000	0.50628	TCT	.	.		0.358	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656		C	141618691	T	C	141618691	3	2	44	1	0	0	0	0	1	0	0	0	11258	1551	54	2	18	2	OR9A4	7	141618691	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4918727	141618691	17519972	169	5629										
PRKAG2	51422	hgsc.bcm.edu	37	chr7	151372542	151372542	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tagtgtgtcggtgatgccagTggaggcctggtcgggctctg	18	8	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr7:151372542T>C	ENST00000287878.4	-	4	1152	c.648A>G	c.(646-648)ccA>ccG	p.P216P	PRKAG2_ENST00000492843.1_Silent_p.P92P|PRKAG2_ENST00000433631.2_Silent_p.P92P|PRKAG2_ENST00000392801.2_Silent_p.P172P|PRKAG2_ENST00000461529.1_5'Flank	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	216					ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	GTGATGCCAGTGGAGGCCTGG	0.617																																					p.P216P		Atlas-SNP	.											.	PRKAG2	86	.	0			c.A648G						.						53	51	52					7																	151372542		2203	4300	6503	SO:0001819	synonymous_variant	51422	exon4			TGCCAGTGGAGGC	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"AMPK gamma2"	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.648A>G	chr7.hg19:g.151372542T>C		162.0	0.0		71.0	59.0	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Silent	SNP	ENST00000287878.4	hg19	CCDS5928.1																																																																																			.	.		0.617	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		C	151372542	T	C	151372542	2	2	44	1	0	0	0	0	0	0	0	1	12513	1683	59	2		2	PRKAG2	7	151372542	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	9753851	151372542	7766121	170	5630										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3216824	3216824	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	accaattcttcggctgaaggCagggactccaggatcatcac	10	12	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:3216824C>A	ENST00000520002.1	-	22	3712	c.3157G>T	c.(3157-3159)Gcc>Tcc	p.A1053S	CSMD1_ENST00000602557.1_Missense_Mutation_p.A1053S|CSMD1_ENST00000539096.1_Missense_Mutation_p.A1052S|CSMD1_ENST00000400186.3_Missense_Mutation_p.A1053S|CSMD1_ENST00000537824.1_Missense_Mutation_p.A1052S|CSMD1_ENST00000542608.1_Missense_Mutation_p.A1052S|CSMD1_ENST00000602723.1_Missense_Mutation_p.A1053S			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1053	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CGGCTGAAGGCAGGGACTCCA	0.458																																					p.A1052S		Atlas-SNP	.											.	CSMD1	1469	.	0			c.G3154T						.						54	60	58					8																	3216824		2195	4299	6494	SO:0001583	missense	64478	exon21			TGAAGGCAGGGAC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3157G>T	chr8.hg19:g.3216824C>A	ENSP00000430733:p.Ala1053Ser	151.0	0.0		86.0	72.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	15.00|15.00	2.704479|2.704479	0.48412|0.48412	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096|ENST00000335551	T;T;T;T;T|.	0.62788|.	0.0;0.0;0.0;0.0;0.0|.	5.24|5.24	5.24|5.24	0.73138|0.73138	Complement control module (2);Sushi/SCR/CCP (3);|.	0.000000|.	0.64402|.	U|.	0.000001|.	T|T	0.55465|0.55465	0.1922|0.1922	N|N	0.25245|0.25245	0.725|0.725	0.47407|0.47407	D|D	0.999414|0.999414	P;B;P|.	0.40681|.	0.727;0.132;0.564|.	B;B;P|.	0.45753|.	0.214;0.223;0.492|.	T|T	0.51100|0.51100	-0.8748|-0.8748	10|5	0.15952|.	T|.	0.53|.	.|.	18.8469|18.8469	0.92210|0.92210	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1053;1053;1053|.	E5RIG2;Q96PZ7;Q96PZ7-4|.	.;CSMD1_HUMAN;.|.	S|F	1053;1053;915;1052;1052;1052|532	ENSP00000383047:A1053S;ENSP00000430733:A1053S;ENSP00000441462:A1052S;ENSP00000446243:A1052S;ENSP00000441675:A1052S|.	ENSP00000320445:A915S|.	A|C	-|-	1|2	0|0	CSMD1|CSMD1	3204231|3204231	0.995000|0.995000	0.38212|0.38212	1.000000|1.000000	0.80357|0.80357	0.947000|0.947000	0.59692|0.59692	3.085000|3.085000	0.50151|0.50151	2.432000|2.432000	0.82394|0.82394	0.550000|0.550000	0.68814|0.68814	GCC|TGC	.	.		0.458	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3216824	C	A	3216824	3	1	44	1	0	0	0	0	1	0	0	0	3946	710	25	3	7740	3	CSMD1	8	3216824	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10		3216824	143147198	171	5631										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10480616	10480616	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aggaaggtgatcttcttggcTggcgtgaccttggtgaccga	15	8	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:10480616T>C	ENST00000382483.3	-	2	319	c.96A>G	c.(94-96)ccA>ccG	p.P32P	RP1L1_ENST00000329335.3_5'UTR	NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	32					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TCTTCTTGGCTGGCGTGACCT	0.642																																					p.P32P		Atlas-SNP	.											.	RP1L1	453	.	0			c.A96G						.						40	45	43					8																	10480616		2061	4180	6241	SO:0001819	synonymous_variant	94137	exon2			CTTGGCTGGCGTG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.96A>G	chr8.hg19:g.10480616T>C		134.0	0.0		71.0	4.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	hg19	CCDS43708.1																																																																																			.	.		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			C	10480616	T	C	10480616	2	2	44	1	0	0	0	0	0	0	0	1	13548	1567	55	2		2	RP1L1	8	10480616	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	7263792	10480616	135883406	172	5632										
MTUS1	57509	hgsc.bcm.edu	37	chr8	17611715	17611715	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gatgaggcactggtctgctgAggtctgggcgtgacctttga	16	8	2	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:17611715A>G	ENST00000262102.6	-	2	1826	c.1602T>C	c.(1600-1602)ccT>ccC	p.P534P	MTUS1_ENST00000381869.3_Silent_p.P534P|MTUS1_ENST00000381862.3_Silent_p.P534P|MTUS1_ENST00000519263.1_Silent_p.P534P	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	534					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TGGTCTGCTGAGGTCTGGGCG	0.453																																					p.P534P		Atlas-SNP	.											.	MTUS1	144	.	0			c.T1602C						.						207	200	202					8																	17611715		2069	4201	6270	SO:0001819	synonymous_variant	57509	exon2			CTGCTGAGGTCTG	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.1602T>C	chr8.hg19:g.17611715A>G		176.0	0.0		94.0	4.0	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	hg19	CCDS43717.1																																																																																			.	.		0.453	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		G	17611715	A	G	17611715	2	3	44	1	0	0	0	0	0	0	0	1	9974	291	11	2		2	MTUS1	8	17611715	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	7131099	17611715	128752307	173	5633										
DPYSL2	1808	hgsc.bcm.edu	37	chr8	26435798	26435798	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atcaggggaagaaaaatattCcacgcatcacggtgagtttg	11	7	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:26435798C>T	ENST00000311151.5	+	1	440	c.28C>T	c.(28-30)Cca>Tca	p.P10S	DPYSL2_ENST00000523027.1_5'Flank|DPYSL2_ENST00000521913.1_Intron	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	10					axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)			breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		GAAAAATATTCCACGCATCAC	0.458																																					p.P10S		Atlas-SNP	.											.	DPYSL2	49	.	0			c.C28T						.						77	81	80					8																	26435798		2203	4300	6503	SO:0001583	missense	1808	exon1			AATATTCCACGCA	D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964			3014	protein-coding gene	gene with protein product		602463				8973361	Standard	NM_001197293		Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000311151.5:c.28C>T	chr8.hg19:g.26435798C>T	ENSP00000309539:p.Pro10Ser	60.0	0.0		25.0	4.0	NM_001386	A8K5H2|B4DR31|D3DSS7|O00424	Missense_Mutation	SNP	ENST00000311151.5	hg19	CCDS6051.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.664595	0.67700	.	.	ENSG00000092964	ENST00000311151;ENST00000522745	D;D	0.85411	-1.98;-1.98	5.42	5.42	0.78866	.	0.059187	0.64402	D	0.000002	D	0.91520	0.7322	M	0.68593	2.085	0.80722	D	1	B;D	0.63880	0.177;0.993	B;D	0.70227	0.097;0.968	D	0.92189	0.5758	10	0.87932	D	0	-5.0952	18.0367	0.89305	0.0:1.0:0.0:0.0	.	10;10	Q53ET2;Q16555	.;DPYL2_HUMAN	S	10	ENSP00000309539:P10S;ENSP00000428909:P10S	ENSP00000309539:P10S	P	+	1	0	DPYSL2	26491715	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.183000	0.72002	2.562000	0.86427	0.549000	0.68633	CCA	.	.		0.458	DPYSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216904.3	NM_001386		T	26435798	C	T	26435798	3	4	44	1	0	0	0	0	1	0	0	0	4749	855	30	3	30	3	DPYSL2	8	26435798	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	8824083	26435798	119928224	174	5634										
SCARA5	286133	hgsc.bcm.edu	37	chr8	27823939	27823939	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcctgctcttacctgctaagAtgaagatgcccacaagaatc	8	12	1	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:27823939A>G	ENST00000354914.3	-	3	718	c.233T>C	c.(232-234)aTc>aCc	p.I78T	SCARA5_ENST00000301906.4_Intron|SCARA5_ENST00000524352.1_Missense_Mutation_p.I78T|SCARA5_ENST00000380385.2_Missense_Mutation_p.I78T|SCARA5_ENST00000518030.1_Intron	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	78					cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)			central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		ACCTGCTAAGATGAAGATGCC	0.542																																					p.I78T		Atlas-SNP	.											.	SCARA5	53	.	0			c.T233C						.						71	72	72					8																	27823939		2203	4300	6503	SO:0001583	missense	286133	exon3			GCTAAGATGAAGA	AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"scavenger receptor class A, member 5 (putative)"			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.233T>C	chr8.hg19:g.27823939A>G	ENSP00000346990:p.Ile78Thr	172.0	0.0		113.0	5.0	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	hg19	CCDS6064.1	.	.	.	.	.	.	.	.	.	.	A	19.39	3.819373	0.71028	.	.	ENSG00000168079	ENST00000354914;ENST00000380385;ENST00000524352	D;D;D	0.94000	-2.61;-3.33;-3.03	5.82	5.82	0.92795	.	0.129012	0.49916	D	0.000125	D	0.95484	0.8533	M	0.68317	2.08	0.80722	D	1	D;D;D	0.61080	0.989;0.989;0.981	D;D;D	0.75020	0.985;0.985;0.966	D	0.94200	0.7449	10	0.29301	T	0.29	.	12.574	0.56354	1.0:0.0:0.0:0.0	.	78;78;78	Q6ZMJ2-4;Q6ZMJ2-2;Q6ZMJ2	.;.;SCAR5_HUMAN	T	78	ENSP00000346990:I78T;ENSP00000369746:I78T;ENSP00000428663:I78T	ENSP00000346990:I78T	I	-	2	0	SCARA5	27879858	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.110000	0.64622	2.225000	0.72522	0.460000	0.39030	ATC	.	.		0.542	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833		G	27823939	A	G	27823939	3	3	44	1	0	0	0	0	1	0	0	0	13895	333	12	2	1282	2	SCARA5	8	27823939	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1388141	27823939	118540083	175	5635										
ELP3	55140	hgsc.bcm.edu	37	chr8	27987036	27987036	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	caggtattctgagagaagccTcacaaagtgtattggaatta	10	6	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:27987036T>C	ENST00000256398.8	+	8	1012	c.635T>C	c.(634-636)cTc>cCc	p.L212P	ELP3_ENST00000524103.1_Missense_Mutation_p.L140P|ELP3_ENST00000542181.1_Missense_Mutation_p.L83P|ELP3_ENST00000537665.1_Missense_Mutation_p.L93P|ELP3_ENST00000380353.4_Missense_Mutation_p.L120P|ELP3_ENST00000521015.1_Missense_Mutation_p.L198P	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3	212					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		GAGAGAAGCCTCACAAAGTGT	0.393																																					p.L212P		Atlas-SNP	.											ELP3,NS,carcinoma,0,1	ELP3	36	.	0			c.T635C						.						134	132	133					8																	27987036		2203	4300	6503	SO:0001583	missense	55140	exon8			GAAGCCTCACAAA		CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"Chromatin-modifying enzymes / K-acetyltransferases", "Elongator acetyltransferase complex subunits"	20696	protein-coding gene	gene with protein product		612722	"elongation protein 3 homolog (S. cerevisiae)"			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.635T>C	chr8.hg19:g.27987036T>C	ENSP00000256398:p.Leu212Pro	130.0	1.0		72.0	3.0	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Missense_Mutation	SNP	ENST00000256398.8	hg19	CCDS6065.1	.	.	.	.	.	.	.	.	.	.	T	11.85	1.761245	0.31137	.	.	ENSG00000134014	ENST00000521015;ENST00000256398;ENST00000542181;ENST00000524103;ENST00000524024;ENST00000537665;ENST00000380353	T;T;T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36;-1.36;-1.36	4.53	3.34	0.38264	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);Radical SAM (1);	0.374738	0.26062	N	0.026562	T	0.73877	0.3643	L	0.38838	1.175	0.51233	D	0.999917	B;B	0.30542	0.284;0.162	B;B	0.40101	0.319;0.251	T	0.68047	-0.5512	10	0.39692	T	0.17	-3.4446	7.2576	0.26185	0.4027:0.0:0.0:0.5973	.	93;212	B4DE19;Q9H9T3	.;ELP3_HUMAN	P	198;212;83;140;155;93;120	ENSP00000428449:L198P;ENSP00000256398:L212P;ENSP00000439242:L83P;ENSP00000429180:L140P;ENSP00000445558:L93P;ENSP00000369711:L120P	ENSP00000256398:L212P	L	+	2	0	ELP3	28042955	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.299000	0.51826	0.850000	0.35239	0.533000	0.62120	CTC	.	.		0.393	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091		C	27987036	T	C	27987036	3	2	44	1	0	0	0	0	1	0	0	0	5083	1551	54	2	665	2	ELP3	8	27987036	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	163097	27987036	118376986	176	5636										
LEPROTL1	23484	hgsc.bcm.edu	37	chr8	29959445	29959445	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttgtcctttggaggagcaatCggactgatgtttttgatgct	12	6	0	2	rs372366525		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:29959445C>T	ENST00000321250.8	+	2	163	c.48C>T	c.(46-48)atC>atT	p.I16I	LEPROTL1_ENST00000518001.1_Intron|LEPROTL1_ENST00000442880.2_Silent_p.I16I|LEPROTL1_ENST00000523116.1_Silent_p.I16I|LEPROTL1_ENST00000518192.1_Silent_p.I39I	NM_015344.2	NP_056159.2	O95214	LERL1_HUMAN	leptin receptor overlapping transcript-like 1	16						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)	5				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		GAGGAGCAATCGGACTGATGT	0.299																																					p.I16I		Atlas-SNP	.											.	LEPROTL1	16	.	0			c.C48T						.	C	,	0,4406		0,0,2203	100	95	97		48,48	-2.4	0.4	8		97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	LEPROTL1	NM_001128208.1,NM_015344.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	16/170,16/132	29959445	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23484	exon2			AGCAATCGGACTG	AF063605	CCDS6075.1, CCDS47834.1	8p12	2014-09-11			ENSG00000104660	ENSG00000104660			6555	protein-coding gene	gene with protein product		607338				11342119	Standard	NM_015344		Approved	my047, Vps55	uc003xhx.2	O95214	OTTHUMG00000163820	ENST00000321250.8:c.48C>T	chr8.hg19:g.29959445C>T		91.0	0.0		35.0	4.0	NM_001128208	E9PHP8|Q9BW48	Silent	SNP	ENST00000321250.8	hg19	CCDS6075.1																																																																																			.	.		0.299	LEPROTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375771.2			T	29959445	C	T	29959445	2	4	44	1	0	0	0	0	0	0	0	1	8742	874	31	1		1	LEPROTL1	8	29959445	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1972409	29959445	116404577	177	5637										
UNC5D	137970	hgsc.bcm.edu	37	chr8	35606082	35606082	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgaggtgctcctgagtcctGaagtcacctgtggtcctcca	11	13	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:35606082G>T	ENST00000404895.2	+	12	2132	c.1804G>T	c.(1804-1806)Gaa>Taa	p.E602*	UNC5D_ENST00000420357.1_Nonsense_Mutation_p.E535*|UNC5D_ENST00000449677.1_Nonsense_Mutation_p.E178*|UNC5D_ENST00000453357.2_Nonsense_Mutation_p.E597*|UNC5D_ENST00000416672.1_Nonsense_Mutation_p.E607*|UNC5D_ENST00000287272.2_Nonsense_Mutation_p.E533*	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	602	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		CCTGAGTCCTGAAGTCACCTG	0.483																																					p.E602X		Atlas-SNP	.											UNC5D_ENST00000404895,NS,carcinoma,0,2	UNC5D	393	.	0			c.G1804T						.						165	138	147					8																	35606082		2203	4300	6503	SO:0001587	stop_gained	137970	exon12			AGTCCTGAAGTCA	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.1804G>T	chr8.hg19:g.35606082G>T	ENSP00000385143:p.Glu602*	141.0	0.0		72.0	3.0	NM_080872	Q8WYP7	Nonsense_Mutation	SNP	ENST00000404895.2	hg19	CCDS6093.2	.	.	.	.	.	.	.	.	.	.	G	38	7.047981	0.98025	.	.	ENSG00000156687	ENST00000404895;ENST00000420357;ENST00000287272;ENST00000416672;ENST00000453357;ENST00000449677	.	.	.	6.07	6.07	0.98685	.	0.085303	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-22.8037	20.6593	0.99626	0.0:0.0:1.0:0.0	.	.	.	.	X	602;535;533;607;597;178	.	ENSP00000287272:E533X	E	+	1	0	UNC5D	35725624	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.286000	0.95898	2.885000	0.99019	0.655000	0.94253	GAA	.	.		0.483	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			T	35606082	G	T	35606082	4	4	44	1	0	0	0	0	0	1	0	0	17010	1291	45	3	1850	3	UNC5D	8	35606082	Nonsense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	5646637	35606082	110757940	178	5638										
IDO1	3620	hgsc.bcm.edu	37	chr8	39785359	39785359	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tttcctataggacatgctgcTcagttcctccaggacatgag	9	11	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:39785359T>C	ENST00000518237.1	+	10	1506	c.867T>C	c.(865-867)gcT>gcC	p.A289A	RP11-44K6.3_ENST00000517623.1_RNA|IDO1_ENST00000522495.1_Silent_p.A289A	NM_002164.5	NP_002155.1	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1	289					cellular nitrogen compound metabolic process (GO:0034641)|cytokine production involved in inflammatory response (GO:0002534)|female pregnancy (GO:0007565)|kynurenic acid biosynthetic process (GO:0034276)|multicellular organismal response to stress (GO:0033555)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response (GO:0002678)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of type 2 immune response (GO:0002830)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|swimming behavior (GO:0036269)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytosol (GO:0005829)|smooth muscle contractile fiber (GO:0030485)|stereocilium bundle (GO:0032421)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(2)	12					L-Tryptophan(DB00150)|Melatonin(DB01065)	GACATGCTGCTCAGTTCCTCC	0.488																																					p.A289A		Atlas-SNP	.											.	IDO1	43	.	0			c.T867C						.						30	28	29					8																	39785359		1975	4168	6143	SO:0001819	synonymous_variant	3620	exon10			TGCTGCTCAGTTC	M34455	CCDS47847.1	8p12-p11	2009-01-07	2009-01-07	2009-01-07		ENSG00000131203	1.13.11.52		6059	protein-coding gene	gene with protein product		147435	"indoleamine-pyrrole 2,3 dioxygenase"	IDO, INDO		2109605, 8404046	Standard	NM_002164		Approved		uc003xnm.3	P14902		ENST00000518237.1:c.867T>C	chr8.hg19:g.39785359T>C		106.0	0.0		41.0	4.0	NM_002164	Q540B4	Silent	SNP	ENST00000518237.1	hg19	CCDS47847.1																																																																																			.	.		0.488	IDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376987.1	NM_002164		C	39785359	T	C	39785359	2	2	44	1	0	0	0	0	0	0	0	1	7510	1538	54	2		2	IDO1	8	39785359	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4179277	39785359	106578663	179	5639										
AP3M2	10947	hgsc.bcm.edu	37	chr8	42026560	42026560	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atacatgaccaaagctgggaAgttccaagttcgaacctgaa	9	9	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:42026560A>G	ENST00000518421.1	+	10	1529	c.1238A>G	c.(1237-1239)aAg>aGg	p.K413R	AP3M2_ENST00000520685.1_3'UTR|AP3M2_ENST00000174653.3_Missense_Mutation_p.K413R|AP3M2_ENST00000396926.3_Missense_Mutation_p.K413R	NM_001134296.1	NP_001127768.1	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	413	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|stomach(1)	17	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)			AAAGCTGGGAAGTTCCAAGTT	0.393																																					p.K413R		Atlas-SNP	.											AP3M2,NS,carcinoma,0,1	AP3M2	41	.	0			c.A1238G						.						88	85	86					8																	42026560		2203	4300	6503	SO:0001583	missense	10947	exon10			CTGGGAAGTTCCA	D38293	CCDS6125.1	8p11.2	2008-07-07			ENSG00000070718	ENSG00000070718			570	protein-coding gene	gene with protein product		610469				7601449	Standard	NM_006803		Approved	CLA20, AP47B	uc003xoo.3	P53677	OTTHUMG00000164060	ENST00000518421.1:c.1238A>G	chr8.hg19:g.42026560A>G	ENSP00000428787:p.Lys413Arg	68.0	0.0		36.0	2.0	NM_001134296	B2RCR0|D3DSY2|Q7Z472	Missense_Mutation	SNP	ENST00000518421.1	hg19	CCDS6125.1	.	.	.	.	.	.	.	.	.	.	A	13.17	2.157304	0.38119	.	.	ENSG00000070718	ENST00000518421;ENST00000174653;ENST00000396926	T;T;T	0.19806	2.12;2.12;2.12	5.72	4.57	0.56435	Clathrin adaptor, mu subunit, C-terminal (3);	0.044909	0.85682	N	0.000000	T	0.13372	0.0324	N	0.16708	0.43	0.80722	D	1	B	0.17038	0.02	B	0.23150	0.044	T	0.09207	-1.0685	10	0.22706	T	0.39	-18.4385	11.5293	0.50599	0.9303:0.0:0.0697:0.0	.	413	P53677	AP3M2_HUMAN	R	413	ENSP00000428787:K413R;ENSP00000174653:K413R;ENSP00000380132:K413R	ENSP00000174653:K413R	K	+	2	0	AP3M2	42145717	1.000000	0.71417	0.994000	0.49952	0.783000	0.44284	7.174000	0.77620	1.000000	0.39049	-0.326000	0.08463	AAG	.	.		0.393	AP3M2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376996.1			G	42026560	A	G	42026560	3	3	44	1	0	0	0	0	1	0	0	0	748	72	3	2	1268	2	AP3M2	8	42026560	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2241201	42026560	104337462	180	5640										
HGSNAT	138050	hgsc.bcm.edu	37	chr8	43016586	43016586	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttctctttttctagctgtgAgcattgcattccttattggt	7	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:43016586A>G	ENST00000458501.2	+	5	583	c.583A>G	c.(583-585)Agc>Ggc	p.S195G	HGSNAT_ENST00000379644.4_Missense_Mutation_p.S167G			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	195					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)	p.S195G(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			TCTAGCTGTGAGCATTGCATT	0.393																																					p.S167G		Atlas-SNP	.											HGSNAT_ENST00000458501,NS,carcinoma,0,1	HGSNAT	85	.	1	Substitution - Missense(1)	kidney(1)	c.A499G						.						261	221	234					8																	43016586		1909	4129	6038	SO:0001583	missense	138050	exon5			GCTGTGAGCATTG		CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"transmembrane protein 76"	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.583A>G	chr8.hg19:g.43016586A>G	ENSP00000389524:p.Ser195Gly	185.0	0.0		107.0	5.0	NM_152419	B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	hg19		.	.	.	.	.	.	.	.	.	.	A	10.01	1.233725	0.22626	.	.	ENSG00000165102	ENST00000458501;ENST00000332689;ENST00000379644	D;D	0.92149	-2.98;-2.98	5.59	-5.0	0.03001	.	1.394720	0.04099	N	0.312656	T	0.81875	0.4915	N	0.25647	0.755	0.26532	N	0.974231	B	0.02656	0.0	B	0.04013	0.001	T	0.66264	-0.5967	10	0.25751	T	0.34	1.5796	0.4844	0.00553	0.2652:0.1275:0.2348:0.3725	.	195	Q68CP4	HGNAT_HUMAN	G	195;167;167	ENSP00000389524:S195G;ENSP00000368965:S167G	ENSP00000327833:S167G	S	+	1	0	HGSNAT	43135743	0.010000	0.17322	0.026000	0.17262	0.125000	0.20455	-0.106000	0.10890	-0.363000	0.08101	-0.256000	0.11100	AGC	.	.		0.393	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038		G	43016586	A	G	43016586	3	3	44	1	0	0	0	0	1	0	0	0	7097	304	11	2	517	2	HGSNAT	8	43016586	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	990026	43016586	103347436	181	5641										
EFCAB1	79645	hgsc.bcm.edu	37	chr8	49643943	49643943	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtcatctgtcattccaaatgTcacatgcaggatgtttcgaa	8	9	4	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:49643943T>C	ENST00000262103.3	-	2	258	c.178A>G	c.(178-180)Aca>Gca	p.T60A	EFCAB1_ENST00000521002.1_Intron|EFCAB1_ENST00000523092.1_Intron|EFCAB1_ENST00000433756.1_Intron	NM_024593.3	NP_078869.1	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1	60							calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(2)	14		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				ATTCCAAATGTCACATGCAGG	0.403																																					p.T60A		Atlas-SNP	.											.	EFCAB1	27	.	0			c.A178G						.						125	112	116					8																	49643943		2203	4300	6503	SO:0001583	missense	79645	exon2			CAAATGTCACATG		CCDS6145.1, CCDS47853.1	8q11.21	2013-01-10			ENSG00000034239	ENSG00000034239		"EF-hand domain containing"	25678	protein-coding gene	gene with protein product						12477932	Standard	NM_024593		Approved	FLJ11767	uc003xqo.2	Q9HAE3	OTTHUMG00000164203	ENST00000262103.3:c.178A>G	chr8.hg19:g.49643943T>C	ENSP00000262103:p.Thr60Ala	186.0	0.0		109.0	6.0	NM_024593	B4DSB4|E7EVN7	Missense_Mutation	SNP	ENST00000262103.3	hg19	CCDS6145.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.284472	0.40394	.	.	ENSG00000034239	ENST00000262103;ENST00000450553	T	0.67345	-0.26	4.67	4.67	0.58626	EF-hand-like domain (1);	0.338534	0.32578	N	0.005904	T	0.57902	0.2085	L	0.46885	1.475	0.53688	D	0.999977	B	0.17268	0.021	B	0.12156	0.007	T	0.54410	-0.8298	10	0.27785	T	0.31	.	12.3807	0.55305	0.0:0.0:0.0:1.0	.	60	Q9HAE3	EFCB1_HUMAN	A	60	ENSP00000262103:T60A	ENSP00000262103:T60A	T	-	1	0	EFCAB1	49806496	1.000000	0.71417	0.830000	0.32933	0.912000	0.54170	3.481000	0.53179	2.082000	0.62665	0.528000	0.53228	ACA	.	.		0.403	EFCAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377778.1	NM_024593		C	49643943	T	C	49643943	3	2	44	1	0	0	0	0	1	0	0	0	4935	1667	58	2	477	2	EFCAB1	8	49643943	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	6627357	49643943	96720079	182	5642										
NSMAF	8439	hgsc.bcm.edu	37	chr8	59514660	59514660	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tatttagggcccctactggcTtactgagatcccggaaggtt	11	10	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:59514660T>C	ENST00000038176.3	-	14	1294	c.1082A>G	c.(1081-1083)aAg>aGg	p.K361R	NSMAF_ENST00000427130.2_Missense_Mutation_p.K392R|NSMAF_ENST00000519858.1_5'UTR	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	361	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				CCCTACTGGCTTACTGAGATC	0.408																																					p.K392R		Atlas-SNP	.											.	NSMAF	156	.	0			c.A1175G						.						112	113	113					8																	59514660		2203	4300	6503	SO:0001583	missense	8439	exon14			ACTGGCTTACTGA	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.1082A>G	chr8.hg19:g.59514660T>C	ENSP00000038176:p.Lys361Arg	131.0	0.0		87.0	4.0	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	hg19	CCDS6173.1	.	.	.	.	.	.	.	.	.	.	T	17.06	3.292177	0.59976	.	.	ENSG00000035681	ENST00000038176;ENST00000427130	D;D	0.82433	-1.61;-1.61	5.96	3.62	0.41486	BEACH domain (4);	0.040345	0.85682	N	0.000000	T	0.79793	0.4507	L	0.61218	1.895	0.39776	D	0.97223	B;B;B	0.25772	0.036;0.134;0.016	B;B;B	0.31101	0.04;0.124;0.077	T	0.72456	-0.4288	9	.	.	.	.	10.3215	0.43769	0.0:0.127:0.0:0.873	.	392;361;361	Q92636-2;A8K9G4;Q92636	.;.;FAN_HUMAN	R	361;392	ENSP00000038176:K361R;ENSP00000411012:K392R	.	K	-	2	0	NSMAF	59677214	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	4.889000	0.63171	0.518000	0.28383	0.533000	0.62120	AAG	.	.		0.408	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		C	59514660	T	C	59514660	3	2	44	1	0	0	0	0	1	0	0	0	10683	1609	56	2	1743	2	NSMAF	8	59514660	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	9870717	59514660	86849362	183	5643										
CSPP1	79848	hgsc.bcm.edu	37	chr8	68007674	68007674	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaagaacttctgaaccaaagAcgactagaggaggacagata	11	7	1	5			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:68007674A>G	ENST00000262210.5	+	6	688	c.657A>G	c.(655-657)agA>agG	p.R219R	CSPP1_ENST00000412460.1_5'UTR	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	254					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			TGAACCAAAGACGACTAGAGG	0.368																																					p.R219R		Atlas-SNP	.											.	CSPP1	129	.	0			c.A657G						.						107	99	101					8																	68007674		1830	4093	5923	SO:0001819	synonymous_variant	79848	exon6			CCAAAGACGACTA	AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.657A>G	chr8.hg19:g.68007674A>G		98.0	0.0		60.0	4.0	NM_024790	A6ND63|Q70F00|Q8TBC1	Silent	SNP	ENST00000262210.5	hg19	CCDS43744.1																																																																																			.	.		0.368	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		G	68007674	A	G	68007674	2	3	44	1	0	0	0	0	0	0	0	1	3964	272	10	2		2	CSPP1	8	68007674	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	8493014	68007674	78356348	184	5644										
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68178248	68178248	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctatgacacttacaaatctaTcccttgttctattatttctt	2	10	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:68178248T>C	ENST00000262215.3	-	14	2505	c.2116A>G	c.(2116-2118)Ata>Gta	p.I706V	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.I160V	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	706					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TACAAATCTATCCCTTGTTCT	0.388																																					p.I706V		Atlas-SNP	.											ARFGEF1,NS,carcinoma,0,1	ARFGEF1	196	.	0			c.A2116G						.						118	109	112					8																	68178248		2201	4300	6501	SO:0001583	missense	10565	exon14			AATCTATCCCTTG	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.2116A>G	chr8.hg19:g.68178248T>C	ENSP00000262215:p.Ile706Val	176.0	0.0		80.0	4.0	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	hg19	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433254	0.83776	.	.	ENSG00000066777	ENST00000520381;ENST00000262215	T;T	0.53423	0.62;0.62	5.49	5.49	0.81192	Armadillo-type fold (1);SEC7-like (4);	0.000000	0.85682	D	0.000000	T	0.67116	0.2859	M	0.66560	2.04	0.80722	D	1	D;D	0.64830	0.994;0.98	D;P	0.85130	0.997;0.881	T	0.68303	-0.5444	10	0.49607	T	0.09	.	15.583	0.76459	0.0:0.0:0.0:1.0	.	706;160	Q9Y6D6;E5RIF2	BIG1_HUMAN;.	V	160;706	ENSP00000428429:I160V;ENSP00000262215:I706V	ENSP00000262215:I706V	I	-	1	0	ARFGEF1	68340802	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.963000	0.87922	2.094000	0.63399	0.477000	0.44152	ATA	.	.		0.388	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		C	68178248	T	C	68178248	3	2	44	1	0	0	0	0	1	0	0	0	852	1435	50	2	3537	2	ARFGEF1	8	68178248	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	170574	68178248	78185774	185	5645										
GDAP1	54332	hgsc.bcm.edu	37	chr8	75276266	75276266	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggtgaatccttcaccctggcAgacgtctcactcgctgtcac	9	15	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:75276266A>G	ENST00000220822.7	+	6	821	c.741A>G	c.(739-741)gcA>gcG	p.A247A	GDAP1_ENST00000521096.1_3'UTR|GDAP1_ENST00000434412.2_Silent_p.A179A	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	247	GST C-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			TCACCCTGGCAGACGTCTCAC	0.498																																					p.A247A		Atlas-SNP	.											.	GDAP1	36	.	0			c.A741G						.						64	63	63					8																	75276266		2203	4300	6503	SO:0001819	synonymous_variant	54332	exon6			CCTGGCAGACGTC		CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"Charcot-Marie-Tooth neuropathy 4A"	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.741A>G	chr8.hg19:g.75276266A>G		85.0	0.0		53.0	4.0	NM_018972	A8K957|E7FJF3|E7FJF4	Silent	SNP	ENST00000220822.7	hg19	CCDS34911.1																																																																																			.	.		0.498	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379061.1	NM_018972		G	75276266	A	G	75276266	2	3	44	1	0	0	0	0	0	0	0	1	6315	175	7	2		2	GDAP1	8	75276266	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	7098018	75276266	71087756	186	5646										
CRISPLD1	83690	hgsc.bcm.edu	37	chr8	75929308	75929308	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atgtcctgctggctgtttggAtagtaaagctaaagttattg	11	5	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:75929308A>G	ENST00000262207.4	+	9	1424	c.956A>G	c.(955-957)gAt>gGt	p.D319G	CRISPLD1_ENST00000523524.1_Missense_Mutation_p.D131G|CRISPLD1_ENST00000517786.1_Missense_Mutation_p.D133G	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	319	LCCL 1. {ECO:0000255|PROSITE- ProRule:PRU00123}.				face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			GGCTGTTTGGATAGTAAAGCT	0.279																																					p.D319G		Atlas-SNP	.											.	CRISPLD1	94	.	0			c.A956G						.						90	94	93					8																	75929308		2203	4295	6498	SO:0001583	missense	83690	exon9			GTTTGGATAGTAA	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.956A>G	chr8.hg19:g.75929308A>G	ENSP00000262207:p.Asp319Gly	102.0	0.0		45.0	4.0	NM_031461	B2RA60|B7Z929	Missense_Mutation	SNP	ENST00000262207.4	hg19	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.789317	0.49997	.	.	ENSG00000121005	ENST00000262207;ENST00000523524;ENST00000517786	D;D;D	0.89746	-2.56;-2.56;-2.56	5.12	3.97	0.46021	LCCL (5);	0.103797	0.64402	N	0.000004	D	0.86723	0.6001	L	0.45470	1.425	0.52501	D	0.999954	B;B	0.33171	0.09;0.4	B;B	0.40410	0.171;0.328	D	0.84316	0.0513	10	0.44086	T	0.13	.	11.2695	0.49131	0.9281:0.0:0.0719:0.0	.	133;319	B7Z929;Q9H336	.;CRLD1_HUMAN	G	319;131;133	ENSP00000262207:D319G;ENSP00000430105:D131G;ENSP00000429746:D133G	ENSP00000262207:D319G	D	+	2	0	CRISPLD1	76091863	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	6.862000	0.75484	1.070000	0.40811	-0.280000	0.10049	GAT	.	.		0.279	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		G	75929308	A	G	75929308	3	3	44	1	0	0	0	0	1	0	0	0	3884	333	12	2	986	2	CRISPLD1	8	75929308	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	653042	75929308	70434714	187	5647										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77616580	77616580	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gataccctgcaacgaatgtgCcacttcttttcccagtttac	6	13	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:77616580C>T	ENST00000521891.2	+	2	705	c.257C>T	c.(256-258)gCc>gTc	p.A86V	ZFHX4_ENST00000050961.6_Missense_Mutation_p.A86V|ZFHX4_ENST00000518282.1_Missense_Mutation_p.A86V|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Missense_Mutation_p.A86V	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	86					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.A86V(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AACGAATGTGCCACTTCTTTT	0.507										HNSCC(33;0.089)																											p.A86V		Atlas-SNP	.											ZFHX4,NS,carcinoma,0,1	ZFHX4	878	.	1	Substitution - Missense(1)	lung(1)	c.C257T						.						179	178	178					8																	77616580		2083	4210	6293	SO:0001583	missense	79776	exon2			AATGTGCCACTTC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.257C>T	chr8.hg19:g.77616580C>T	ENSP00000430497:p.Ala86Val	153.0	0.0		72.0	3.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	17.42	3.384779	0.61956	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000520307;ENST00000523885;ENST00000517585;ENST00000523809;ENST00000518282	T;T;T;T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31;1.31;1.31;1.31	5.53	5.53	0.82687	Zinc finger, C2H2-like (1);	0.000000	0.44097	U	0.000482	T	0.42449	0.1203	N	0.14661	0.345	0.58432	D	0.999995	D;D;D;P	0.61697	0.982;0.972;0.99;0.822	P;P;P;B	0.59825	0.734;0.691;0.864;0.269	T	0.44345	-0.9334	10	0.66056	D	0.02	.	19.6556	0.95837	0.0:1.0:0.0:0.0	.	86;86;86;86	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	V	86	ENSP00000430497:A86V;ENSP00000399605:A86V;ENSP00000050961:A86V;ENSP00000428525:A86V;ENSP00000429495:A86V;ENSP00000427775:A86V;ENSP00000427739:A86V;ENSP00000430848:A86V	ENSP00000050961:A86V	A	+	2	0	ZFHX4	77779135	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.816000	0.69222	2.882000	0.98803	0.655000	0.94253	GCC	.	.		0.507	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77616580	C	T	77616580	3	4	44	1	0	0	0	0	1	0	0	0	17650	739	26	3	259	3	ZFHX4	8	77616580	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1687272	77616580	68747442	188	5648										
IL7	3574	hgsc.bcm.edu	37	chr8	79652274	79652274	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tatgtcttttaaaaaagttaAattcattattcaggcaattg	5	4	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:79652274A>G	ENST00000263851.4	-	3	791	c.191T>C	c.(190-192)tTt>tCt	p.F64S	IL7_ENST00000520269.1_Missense_Mutation_p.F64S|IL7_ENST00000541183.1_Missense_Mutation_p.F13S|IL7_ENST00000519833.1_5'UTR	NM_000880.3|NM_001199886.1|NM_001199887.1	NP_000871.1|NP_001186815.1|NP_001186816.1	P13232	IL7_HUMAN	interleukin 7	64					bone resorption (GO:0045453)|cell-cell signaling (GO:0007267)|homeostasis of number of cells within a tissue (GO:0048873)|humoral immune response (GO:0006959)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|organ morphogenesis (GO:0009887)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T cell differentiation (GO:0045582)|regulation of gene expression (GO:0010468)|T cell lineage commitment (GO:0002360)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|interleukin-7 receptor binding (GO:0005139)	p.F64C(1)		endometrium(2)|large_intestine(2)|lung(1)	5						AAAAAAGTTAAATTCATTATT	0.259																																					p.F64S		Atlas-SNP	.											IL7,colon,carcinoma,0,1	IL7	12	.	1	Substitution - Missense(1)	large_intestine(1)	c.T191C						.						45	47	46					8																	79652274		2196	4274	6470	SO:0001583	missense	3574	exon3			AAGTTAAATTCAT	J04156	CCDS6224.1, CCDS56541.1, CCDS75755.1, CCDS75756.1	8q12-q13	2008-07-03				ENSG00000104432		"Interleukins and interleukin receptors"	6023	protein-coding gene	gene with protein product		146660					Standard	NM_000880		Approved	IL-7	uc003ybg.3	P13232		ENST00000263851.4:c.191T>C	chr8.hg19:g.79652274A>G	ENSP00000263851:p.Phe64Ser	161.0	0.0		55.0	3.0	NM_000880	A0N0L3|Q5FBY5|Q5FBY9	Missense_Mutation	SNP	ENST00000263851.4	hg19	CCDS6224.1	.	.	.	.	.	.	.	.	.	.	A	5.531	0.282805	0.10458	.	.	ENSG00000104432	ENST00000263851;ENST00000520269;ENST00000379114;ENST00000541183	T;T;T	0.41400	1.0;1.0;1.0	5.02	2.04	0.26737	.	1.147940	0.06450	N	0.727483	T	0.20700	0.0498	N	0.08118	0	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.31888	-0.9927	9	.	.	.	.	3.7743	0.08654	0.2054:0.0:0.6037:0.1909	.	64;64	P13232;Q5FBY9	IL7_HUMAN;.	S	64;64;61;13	ENSP00000263851:F64S;ENSP00000427750:F64S;ENSP00000438922:F13S	.	F	-	2	0	IL7	79814829	1.000000	0.71417	0.987000	0.45799	0.866000	0.49608	0.679000	0.25291	0.800000	0.34041	-0.468000	0.05107	TTT	.	.		0.259	IL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379429.1			G	79652274	A	G	79652274	3	3	44	1	0	0	0	0	1	0	0	0	7713	14	1	2	358	2	IL7	8	79652274	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2035694	79652274	66711748	189	5649										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100790967	100790967	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaatatgccatctgaactagAatacatgattgtttccttca	5	8	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:100790967A>G	ENST00000358544.2	+	42	7673	c.7562A>G	c.(7561-7563)gAa>gGa	p.E2521G	VPS13B_ENST00000357162.2_Missense_Mutation_p.E2496G|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2521					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TCTGAACTAGAATACATGATT	0.418																																					p.E2521G	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A7562G						.						112	109	110					8																	100790967		2203	4300	6503	SO:0001583	missense	157680	exon42			AACTAGAATACAT	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.7562A>G	chr8.hg19:g.100790967A>G	ENSP00000351346:p.Glu2521Gly	222.0	0.0		109.0	5.0	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	17.41	3.383631	0.61845	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.72167	-0.63;-0.63	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.82398	0.5028	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	D	0.84164	0.0430	10	0.72032	D	0.01	.	15.876	0.79162	1.0:0.0:0.0:0.0	.	2496;2521	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	G	2496;2521	ENSP00000349685:E2496G;ENSP00000351346:E2521G	ENSP00000349685:E2496G	E	+	2	0	VPS13B	100860143	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.664000	0.91139	2.143000	0.66587	0.528000	0.53228	GAA	.	.		0.418	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100790967	A	G	100790967	3	3	44	1	0	0	0	0	1	0	0	0	17205	246	9	2	7918	2	VPS13B	8	100790967	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	21138693	100790967	45573055	190	5650										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110539227	110539227	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaaatatttatggctgcagtTtcaactttgaatataacttt	6	5	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:110539227T>C	ENST00000378402.5	+	77	12803	c.12699T>C	c.(12697-12699)gtT>gtC	p.V4233V		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4233					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TGGCTGCAGTTTCAACTTTGA	0.378										HNSCC(38;0.096)																											p.V4233V		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T12699C						.						71	73	73					8																	110539227		1907	4141	6048	SO:0001819	synonymous_variant	93035	exon77			TGCAGTTTCAACT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.12699T>C	chr8.hg19:g.110539227T>C		164.0	0.0		98.0	4.0	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.		0.378	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110539227	T	C	110539227	2	2	44	1	0	0	0	0	0	0	0	1	11981	1828	64	2		2	PKHD1L1	8	110539227	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	9748260	110539227	35824795	191	5651										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113317079	113317079	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggttttgtattcataatgggAgccattcacaattcgccatc	8	9	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:113317079A>G	ENST00000297405.5	-	52	8381	c.8137T>C	c.(8137-8139)Tcc>Ccc	p.S2713P	CSMD3_ENST00000455883.2_Intron|CSMD3_ENST00000343508.3_Missense_Mutation_p.S2673P|CSMD3_ENST00000352409.3_Missense_Mutation_p.S2643P	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2713	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TCATAATGGGAGCCATTCACA	0.403										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S2713P		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T8137C						.						98	84	89					8																	113317079		2203	4300	6503	SO:0001583	missense	114788	exon52			AATGGGAGCCATT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8137T>C	chr8.hg19:g.113317079A>G	ENSP00000297405:p.Ser2713Pro	187.0	0.0		91.0	5.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648658	0.87958	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000352409	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.18	5.18	0.71444	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000005	T	0.74831	0.3768	L	0.55213	1.73	0.58432	D	0.999995	D;D	0.76494	0.999;0.998	D;D	0.87578	0.998;0.947	T	0.75396	-0.3332	10	0.46703	T	0.11	.	15.3362	0.74255	1.0:0.0:0.0:0.0	.	2713;2673	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	P	2673;2713;1983;2643	ENSP00000345799:S2673P;ENSP00000297405:S2713P;ENSP00000341558:S1983P;ENSP00000343124:S2643P	ENSP00000297405:S2713P	S	-	1	0	CSMD3	113386255	1.000000	0.71417	0.939000	0.37840	0.998000	0.95712	9.255000	0.95524	2.060000	0.61445	0.533000	0.62120	TCC	.	.		0.403	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113317079	A	G	113317079	3	3	44	1	0	0	0	0	1	0	0	0	3948	304	11	2	3066	2	CSMD3	8	113317079	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2777852	113317079	33046943	192	5652										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113364738	113364738	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccactgctaggagtttgtggTtcaggacaggaatccaaacc	11	10	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:113364738T>C	ENST00000297405.5	-	39	6406	c.6162A>G	c.(6160-6162)gaA>gaG	p.E2054E	CSMD3_ENST00000455883.2_Silent_p.E1950E|CSMD3_ENST00000343508.3_Silent_p.E2014E|CSMD3_ENST00000352409.3_Silent_p.E1984E	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2054	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GAGTTTGTGGTTCAGGACAGG	0.333										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.E2054E		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A6162G						.						109	104	106					8																	113364738		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon39			TTGTGGTTCAGGA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6162A>G	chr8.hg19:g.113364738T>C		168.0	0.0		86.0	4.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.333	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113364738	T	C	113364738	2	2	44	1	0	0	0	0	0	0	0	1	3948	1722	60	2		2	CSMD3	8	113364738	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	47659	113364738	32999284	193	5653										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124371920	124371920	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctttccgaaaatttagtgggAggcacctatttaaaaagatt	8	6	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:124371920A>G	ENST00000287394.5	-	10	1270	c.1163T>C	c.(1162-1164)cTc>cCc	p.L388P	ATAD2_ENST00000534257.1_5'UTR|ATAD2_ENST00000521903.1_5'UTR	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	388					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			ATTTAGTGGGAGGCACCTATT	0.328																																					p.L388P		Atlas-SNP	.											.	ATAD2	160	.	0			c.T1163C						.						61	56	58					8																	124371920		2203	4300	6503	SO:0001583	missense	29028	exon10			AGTGGGAGGCACC	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.1163T>C	chr8.hg19:g.124371920A>G	ENSP00000287394:p.Leu388Pro	89.0	0.0		62.0	4.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	A	19.58	3.853696	0.71719	.	.	ENSG00000156802	ENST00000287394	D	0.94092	-3.35	5.18	5.18	0.71444	.	2.798200	0.02625	U	0.103685	D	0.97090	0.9049	M	0.71296	2.17	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88006	0.2759	10	0.72032	D	0.01	-7.6791	15.0201	0.71624	1.0:0.0:0.0:0.0	.	218;388	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	P	388	ENSP00000287394:L388P	ENSP00000287394:L388P	L	-	2	0	ATAD2	124441101	1.000000	0.71417	0.999000	0.59377	0.651000	0.38670	9.253000	0.95501	1.950000	0.56595	0.402000	0.26972	CTC	.	.		0.328	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		G	124371920	A	G	124371920	3	3	44	1	0	0	0	0	1	0	0	0	1071	304	11	2	3085	2	ATAD2	8	124371920	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	11007182	124371920	21992102	194	5654										
ZNF572	137209	hgsc.bcm.edu	37	chr8	125988660	125988660	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcagataaacttaaagagaaAccttcagaatggtctaaaag	8	6	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:125988660A>G	ENST00000319286.5	+	3	304	c.150A>G	c.(148-150)aaA>aaG	p.K50K		NM_152412.2	NP_689625.2	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	50					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	31	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TTAAAGAGAAACCTTCAGAAT	0.343										HNSCC(60;0.17)																											p.K50K		Atlas-SNP	.											ZNF572,NS,carcinoma,0,1	ZNF572	82	.	0			c.A150G						.						64	66	65					8																	125988660		2203	4300	6503	SO:0001819	synonymous_variant	137209	exon3			AGAGAAACCTTCA	BX537876	CCDS6354.1	8q24.13	2013-09-20			ENSG00000180938	ENSG00000180938		"Zinc fingers, C2H2-type"	26758	protein-coding gene	gene with protein product							Standard	NM_152412		Approved	FLJ38002	uc003yrr.3	Q7Z3I7	OTTHUMG00000164988	ENST00000319286.5:c.150A>G	chr8.hg19:g.125988660A>G		100.0	0.0		60.0	3.0	NM_152412	A1L4F1|Q8N1Q0	Silent	SNP	ENST00000319286.5	hg19	CCDS6354.1																																																																																			.	.		0.343	ZNF572-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381359.1	NM_152412		G	125988660	A	G	125988660	2	3	44	1	0	0	0	0	0	0	0	1	18019	40	2	2		2	ZNF572	8	125988660	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1616740	125988660	20375362	195	5655										
GSDMC	56169	hgsc.bcm.edu	37	chr8	130788517	130788517	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtcactgaagtggaacggtcCtgtcacaacagtttctgggg	13	9	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:130788517C>T	ENST00000276708.4	-	3	1116	c.235G>A	c.(235-237)Gga>Aga	p.G79R		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	79						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						TGGAACGGTCCTGTCACAACA	0.448																																					p.G79R		Atlas-SNP	.											.	GSDMC	71	.	0			c.G235A						.						164	130	142					8																	130788517		2203	4300	6503	SO:0001583	missense	56169	exon3			ACGGTCCTGTCAC	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"melanoma-derived leucine zipper, extra-nuclear factor"	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.235G>A	chr8.hg19:g.130788517C>T	ENSP00000276708:p.Gly79Arg	127.0	0.0		78.0	4.0	NM_031415	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	hg19	CCDS6360.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.065297	0.36470	.	.	ENSG00000147697	ENST00000276708	T	0.21734	1.99	3.97	-1.04	0.10068	.	2.568960	0.01164	N	0.006719	T	0.30510	0.0767	L	0.33339	1.005	0.09310	N	1	D	0.61080	0.989	P	0.59115	0.852	T	0.27054	-1.0085	10	0.62326	D	0.03	.	7.1891	0.25816	0.0:0.442:0.0:0.558	.	79	Q9BYG8	GSDMC_HUMAN	R	79	ENSP00000276708:G79R	ENSP00000276708:G79R	G	-	1	0	GSDMC	130857699	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.513000	0.06305	-0.104000	0.12154	0.585000	0.79938	GGA	.	.		0.448	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1			T	130788517	C	T	130788517	3	4	44	1	0	0	0	0	1	0	0	0	6827	690	24	3	1339	3	GSDMC	8	130788517	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	4799857	130788517	15575505	196	5656										
EFR3A	23167	hgsc.bcm.edu	37	chr8	132991670	132991670	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cacaagtttcatgaaaaaggTaagacatcttctaaaaaaat	5	6	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:132991670T>C	ENST00000254624.5	+	14	1800		c.e14+2		EFR3A_ENST00000334503.4_Splice_Site|EFR3A_ENST00000519656.1_Splice_Site	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)							extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			ATGAAAAAGGTAAGACATCTT	0.313																																					.		Atlas-SNP	.											.	EFR3A	96	.	0			c.1575+2T>C						.						30	27	28					8																	132991670		2192	4268	6460	SO:0001630	splice_region_variant	23167	exon14			AAAAGGTAAGACA	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.1575+2T>C	chr8.hg19:g.132991670T>C		143.0	0.0		52.0	4.0	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Splice_Site	SNP	ENST00000254624.5	hg19	CCDS34942.2	.	.	.	.	.	.	.	.	.	.	T	22.2	4.253666	0.80135	.	.	ENSG00000132294	ENST00000254624;ENST00000377917;ENST00000334503;ENST00000519656	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1795	0.65564	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	EFR3A	133060852	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.017000	0.76399	1.999000	0.58509	0.456000	0.33151	.	.	.		0.313	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137	Intron	C	132991670	T	C	132991670	5	2	44	1	0	0	0	0	0	0	1	0	4960	1652	57	2	1631	2	EFR3A	8	132991670	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2203153	132991670	13372352	197	5657										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133198356	133198356	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	accagtaacagaagccagtcTcccgagacagtctcatactc	7	14	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:133198356T>C	ENST00000388996.4	-	2	879	c.459A>G	c.(457-459)ggA>ggG	p.G153G	KCNQ3_ENST00000521134.1_Silent_p.G33G|KCNQ3_ENST00000519445.1_Silent_p.G153G	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	153					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GAAGCCAGTCTCCCGAGACAG	0.502																																					p.G153G		Atlas-SNP	.											.	KCNQ3	164	.	0			c.A459G						.						112	97	102					8																	133198356		2203	4300	6503	SO:0001819	synonymous_variant	3786	exon2			CCAGTCTCCCGAG	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.459A>G	chr8.hg19:g.133198356T>C		155.0	0.0		69.0	5.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	hg19	CCDS34943.1																																																																																			.	.		0.502	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		C	133198356	T	C	133198356	2	2	44	1	0	0	0	0	0	0	0	1	8093	1538	54	2		2	KCNQ3	8	133198356	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	206686	133198356	13165666	198	5658										
TG	7038	hgsc.bcm.edu	37	chr8	133941385	133941385	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gacgccaatgctcctgtggcTgtcagatccaaagttcctga	10	12	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:133941385T>C	ENST00000220616.4	+	23	4804	c.4764T>C	c.(4762-4764)gcT>gcC	p.A1588A	TG_ENST00000377869.1_Silent_p.A1531A|TG_ENST00000542445.1_Silent_p.A22A	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1588					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CTCCTGTGGCTGTCAGATCCA	0.448																																					p.A1588A		Atlas-SNP	.											.	TG	416	.	0			c.T4764C						.						142	121	128					8																	133941385		2203	4300	6503	SO:0001819	synonymous_variant	7038	exon23			TGTGGCTGTCAGA	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4764T>C	chr8.hg19:g.133941385T>C		149.0	0.0		93.0	4.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	T	4.882	0.163842	0.09287	.	.	ENSG00000042832	ENST00000519178	.	.	.	5.5	-4.06	0.03986	.	.	.	.	.	T	0.20455	0.0492	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30297	-0.9983	4	.	.	.	.	4.0516	0.09798	0.4078:0.0:0.204:0.3882	.	.	.	.	R	108	.	.	C	+	1	0	TG	134010567	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.237000	0.02922	-0.659000	0.05359	-1.236000	0.01555	TGT	.	.		0.448	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	133941385	T	C	133941385	2	2	44	1	0	0	0	0	0	0	0	1	15828	1567	55	2		2	TG	8	133941385	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	743029	133941385	12422637	199	5659										
HSF1	3297	hgsc.bcm.edu	37	chr8	145535035	145535035	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gttcctgatctcactggtgcAgtcaaaccggatcctggggg	13	11	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:145535035A>G	ENST00000528838.1	+	6	753	c.593A>G	c.(592-594)cAg>cGg	p.Q198R	HSF1_ENST00000400780.4_Missense_Mutation_p.Q133R	NM_005526.2	NP_005517.1	Q00613	HSF1_HUMAN	heat shock transcription factor 1	198	Hydrophobic repeat HR-A/B.				cellular response to heat (GO:0034605)|defense response (GO:0006952)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|female meiotic division (GO:0007143)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)|response to lipopolysaccharide (GO:0032496)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pronucleus (GO:0045120)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)|urinary_tract(2)	11	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)			TCACTGGTGCAGTCAAACCGG	0.637																																					p.Q198R		Atlas-SNP	.											.	HSF1	29	.	0			c.A593G						.						71	77	75					8																	145535035		2203	4296	6499	SO:0001583	missense	3297	exon6			TGGTGCAGTCAAA	M64673	CCDS6419.1	8q24.3	2014-04-10			ENSG00000185122	ENSG00000185122			5224	protein-coding gene	gene with protein product		140580				1871105	Standard	NM_005526		Approved	HSTF1	uc003zbt.4	Q00613	OTTHUMG00000174604	ENST00000528838.1:c.593A>G	chr8.hg19:g.145535035A>G	ENSP00000431512:p.Gln198Arg	128.0	0.0		90.0	5.0	NM_005526	A8K4L0|A8MW26|Q53XT4	Missense_Mutation	SNP	ENST00000528838.1	hg19	CCDS6419.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.261756	0.59431	.	.	ENSG00000185122	ENST00000528838;ENST00000533240;ENST00000400780	.	.	.	5.5	5.5	0.81552	.	0.061939	0.64402	D	0.000003	T	0.56485	0.1988	L	0.47016	1.485	0.48975	D	0.999739	B	0.27732	0.187	B	0.28638	0.092	T	0.56426	-0.7981	9	0.46703	T	0.11	-21.8322	13.5661	0.61819	1.0:0.0:0.0:0.0	.	198	Q00613	HSF1_HUMAN	R	198;133;133	.	ENSP00000383590:Q133R	Q	+	2	0	HSF1	145505843	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.831000	0.55776	2.082000	0.62665	0.533000	0.62120	CAG	.	.		0.637	HSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382053.1	NM_005526		G	145535035	A	G	145535035	3	3	44	1	0	0	0	0	1	0	0	0	7404	188	7	2	615	2	HSF1	8	145535035	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	11593650	145535035	828987	200	5660										
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145666353	145666353	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agccggggccacacacctgcTtctggtaagcctcagctgcc	11	16	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr8:145666353T>C	ENST00000409379.3	-	8	1036	c.1007A>G	c.(1006-1008)aAg>aGg	p.K336R	AC084125.4_ENST00000544423.1_RNA|AC084125.4_ENST00000442850.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	336					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						ACACACCTGCTTCTGGTAAGC	0.662																																					p.K336R		Atlas-SNP	.											TONSL_ENST00000409379,NS,carcinoma,0,2	TONSL	128	.	0			c.A1007G						.						82	82	82					8																	145666353		2203	4300	6503	SO:0001583	missense	4796	exon8			ACCTGCTTCTGGT		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.1007A>G	chr8.hg19:g.145666353T>C	ENSP00000386239:p.Lys336Arg	187.0	0.0		81.0	4.0	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	hg19	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	T	12.71	2.018147	0.35606	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.78595	-1.19	5.45	5.45	0.79879	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.415751	0.28382	N	0.015558	T	0.72486	0.3466	M	0.64997	1.995	0.28018	N	0.934636	B	0.20887	0.049	B	0.17433	0.018	T	0.64964	-0.6283	10	0.39692	T	0.17	-30.534	8.8792	0.35365	0.1667:0.0:0.0:0.8333	.	336	Q96HA7	TONSL_HUMAN	R	336	ENSP00000386239:K336R	ENSP00000386239:K336R	K	-	2	0	TONSL	145637161	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	1.875000	0.39578	2.077000	0.62373	0.459000	0.35465	AAG	.	.		0.662	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		C	145666353	T	C	145666353	3	2	44	1	0	0	0	0	1	0	0	0	10391	1609	56	2	3205	2	NFKBIL2	8	145666353	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	131318	145666353	697669	201	5661										
DOCK8	81704	hgsc.bcm.edu	37	chr9	434865	434865	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agaaacacaccaagaagaagTgctacacggaggctgccatg	11	10	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:434865T>C	ENST00000453981.1	+	39	5081	c.4969T>C	c.(4969-4971)Tgc>Cgc	p.C1657R	DOCK8_ENST00000432829.2_Missense_Mutation_p.C1589R|DOCK8_ENST00000382329.1_Missense_Mutation_p.C1124R|DOCK8_ENST00000469391.1_Missense_Mutation_p.C1557R			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1657	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CAAGAAGAAGTGCTACACGGA	0.562																																					p.C1657R		Atlas-SNP	.											.	DOCK8	401	.	0			c.T4969C						.						105	91	96					9																	434865		2203	4300	6503	SO:0001583	missense	81704	exon39			AAGAAGTGCTACA	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.4969T>C	chr9.hg19:g.434865T>C	ENSP00000408464:p.Cys1657Arg	109.0	0.0		80.0	4.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	T	16.07	3.019077	0.54576	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.68479	2.7;-0.33;-0.33;-0.33	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.64125	0.2570	L	0.57536	1.79	0.80722	D	1	P;P;P	0.43633	0.786;0.471;0.813	B;B;B	0.39660	0.191;0.191;0.306	T	0.70745	-0.4788	10	0.72032	D	0.01	.	14.7381	0.69430	0.0:0.0:0.0:1.0	.	1557;1124;1657	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	R	1657;1625;1589;1557;1124	ENSP00000408464:C1657R;ENSP00000394888:C1589R;ENSP00000419438:C1557R;ENSP00000371766:C1124R	ENSP00000287364:C1625R	C	+	1	0	DOCK8	424865	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	2.592000	0.46171	2.067000	0.61834	0.496000	0.49642	TGC	.	.		0.562	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		C	434865	T	C	434865	3	2	44	1	0	0	0	0	1	0	0	0	4695	1696	59	2	5123	2	DOCK8	9	434865	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10		434865	140778566	202	5662										
ERMP1	79956	hgsc.bcm.edu	37	chr9	5832863	5832863	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgctcgcgccgccgctaccCccggggctcctcttccgcgt	11	21	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:5832863C>T	ENST00000339450.5	-	1	254	c.165G>A	c.(163-165)ggG>ggA	p.G55G	ERMP1_ENST00000381506.3_5'Flank|ERMP1_ENST00000214893.5_5'Flank	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	55						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		CGCCGCTACCCCCGGGGCTCC	0.786																																					p.G55G		Atlas-SNP	.											.	ERMP1	63	.	0			c.G165A						.						2	3	3					9																	5832863		1220	2949	4169	SO:0001819	synonymous_variant	79956	exon1			GCTACCCCCGGGG	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"Felix-ina"	611156	"KIAA1815"	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.165G>A	chr9.hg19:g.5832863C>T		0.0	0.0		5.0	5.0	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Silent	SNP	ENST00000339450.5	hg19	CCDS34983.1																																																																																			.	.		0.786	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896		T	5832863	C	T	5832863	2	4	44	1	0	0	0	0	0	0	0	1	5238	610	22	3		3	ERMP1	9	5832863	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	5397998	5832863	135380568	203	5663										
C9orf93	203238	hgsc.bcm.edu	37	chr9	15777602	15777602	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttctttttctttgaagatccAaattccagaatttgtggaca	6	7	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:15777602A>G	ENST00000380701.3	+	19	3004	c.2676A>G	c.(2674-2676)ccA>ccG	p.P892P	RNU6-14P_ENST00000384630.1_RNA|CCDC171_ENST00000297641.3_Silent_p.P892P	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	892																	TTGAAGATCCAAATTCCAGAA	0.313																																					p.P892P		Atlas-SNP	.											.	.	.	.	0			c.A2676G						.						42	45	44					9																	15777602		2203	4300	6503	SO:0001819	synonymous_variant	203238	exon19			AGATCCAAATTCC	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.2676A>G	chr9.hg19:g.15777602A>G		57.0	0.0		38.0	4.0	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Silent	SNP	ENST00000380701.3	hg19	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	A	6.876	0.530993	0.13127	.	.	ENSG00000164989	ENST00000449575	.	.	.	5.72	-0.819	0.10829	.	.	.	.	.	T	0.51415	0.1673	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38394	-0.9663	4	.	.	.	-11.4078	6.7156	0.23302	0.5507:0.12:0.3292:0.0	.	.	.	.	R	132	.	.	Q	+	2	0	C9orf93	15767602	0.989000	0.36119	0.991000	0.47740	0.928000	0.56348	0.238000	0.18004	-0.387000	0.07809	-0.263000	0.10527	CAA	.	.		0.313	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		G	15777602	A	G	15777602	2	3	44	1	0	0	0	0	0	0	0	1	2508	117	5	2		2	C9orf93	9	15777602	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	9944739	15777602	125435829	204	5664										
IFNB1	3456	hgsc.bcm.edu	37	chr9	21077802	21077802	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaatccaagcaagttgtagcTcatggaaagagctgtagtgg	13	6	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:21077802T>C	ENST00000380232.2	-	1	141	c.67A>G	c.(67-69)Agc>Ggc	p.S23G		NM_002176.2	NP_002167.1	P01574	IFNB_HUMAN	interferon, beta 1, fibroblast	23					adaptive immune response (GO:0002250)|B cell activation involved in immune response (GO:0002312)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of viral genome replication (GO:0045071)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	12				GBM - Glioblastoma multiforme(5;7.45e-142)|Lung(24;2.42e-17)|LUSC - Lung squamous cell carcinoma(38;7.17e-11)		AAGTTGTAGCTCATGGAAAGA	0.468																																					p.S23G		Atlas-SNP	.											.	IFNB1	33	.	0			c.A67G						.						47	47	47					9																	21077802		2203	4300	6503	SO:0001583	missense	3456	exon1			TGTAGCTCATGGA		CCDS6495.1	9p22	2008-07-21			ENSG00000171855	ENSG00000171855		"Interferons"	5434	protein-coding gene	gene with protein product		147640		IFNB			Standard	NM_002176		Approved	IFB, IFF	uc003zok.3	P01574	OTTHUMG00000019652	ENST00000380232.2:c.67A>G	chr9.hg19:g.21077802T>C	ENSP00000369581:p.Ser23Gly	122.0	0.0		101.0	5.0	NM_002176	Q5VWC9	Missense_Mutation	SNP	ENST00000380232.2	hg19	CCDS6495.1	.	.	.	.	.	.	.	.	.	.	T	10.37	1.332228	0.24167	.	.	ENSG00000171855	ENST00000380232	T	0.17691	2.26	5.42	2.98	0.34508	Four-helical cytokine-like, core (1);	0.521400	0.20464	N	0.091829	T	0.10680	0.0261	L	0.41356	1.27	0.09310	N	1	B	0.21071	0.051	B	0.11329	0.006	T	0.37384	-0.9708	10	0.02654	T	1	-7.3599	8.4019	0.32592	0.0:0.1627:0.0:0.8373	.	23	P01574	IFNB_HUMAN	G	23	ENSP00000369581:S23G	ENSP00000369581:S23G	S	-	1	0	IFNB1	21067802	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.142000	0.16096	1.032000	0.39892	0.528000	0.53228	AGC	.	.		0.468	IFNB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051881.1	NM_002176		C	21077802	T	C	21077802	3	2	44	1	0	0	0	0	1	0	0	0	7555	1551	54	2	500	2	IFNB1	9	21077802	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	5300200	21077802	120135629	205	5665										
ELAVL2	1993	hgsc.bcm.edu	37	chr9	23731087	23731087	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctttctctgcatccttggggTcaatgtagttcacaaagcca	8	11	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:23731087T>C	ENST00000397312.2	-	3	540	c.266A>G	c.(265-267)gAc>gGc	p.D89G	ELAVL2_ENST00000223951.6_Missense_Mutation_p.D89G|ELAVL2_ENST00000544538.1_Missense_Mutation_p.D89G|ELAVL2_ENST00000380110.4_Missense_Mutation_p.D118G|ELAVL2_ENST00000380117.1_Missense_Mutation_p.D89G	NM_004432.3	NP_004423.2	Q12926	ELAV2_HUMAN	ELAV like neuron-specific RNA binding protein 2	89	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of transcription, DNA-templated (GO:0006355)		mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		ATCCTTGGGGTCAATGTAGTT	0.373																																					p.D89G		Atlas-SNP	.											.	ELAVL2	80	.	0			c.A266G						.						138	117	124					9																	23731087		2203	4299	6502	SO:0001583	missense	1993	exon3			TTGGGGTCAATGT	BC030692	CCDS6515.1, CCDS55298.1	9p21	2013-10-03	2013-10-03		ENSG00000107105	ENSG00000107105		"RNA binding motif (RRM) containing"	3313	protein-coding gene	gene with protein product	"Hu antigen B"	601673	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2", "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"			8812435	Standard	NM_004432		Approved	HuB, HEL-N1	uc003zpu.3	Q12926	OTTHUMG00000019700	ENST00000397312.2:c.266A>G	chr9.hg19:g.23731087T>C	ENSP00000380479:p.Asp89Gly	108.0	0.0		89.0	4.0	NM_001171195	D3DRK3|Q13235|Q59G15|Q8NEM4|Q9H1Q8	Missense_Mutation	SNP	ENST00000397312.2	hg19	CCDS6515.1	.	.	.	.	.	.	.	.	.	.	T	17.33	3.363107	0.61513	.	.	ENSG00000107105	ENST00000223951;ENST00000397312;ENST00000544538;ENST00000380110;ENST00000380117;ENST00000359598;ENST00000440102	T;T;T;T;T	0.77098	3.14;-1.07;-1.07;-1.07;3.14	5.87	5.87	0.94306	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.130344	0.64402	D	0.000001	D	0.85513	0.5714	M	0.79805	2.47	0.80722	D	1	B;B	0.23937	0.094;0.006	P;B	0.46275	0.51;0.069	T	0.80422	-0.1389	10	0.14656	T	0.56	.	16.2377	0.82389	0.0:0.0:0.0:1.0	.	89;89	Q12926;Q12926-2	ELAV2_HUMAN;.	G	89;89;89;89;89;117;89	ENSP00000223951:D89G;ENSP00000380479:D89G;ENSP00000440998:D89G;ENSP00000369460:D89G;ENSP00000412602:D89G	ENSP00000223951:D89G	D	-	2	0	ELAVL2	23721087	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.782000	0.68973	2.371000	0.80710	0.533000	0.62120	GAC	.	.		0.373	ELAVL2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051943.2	NM_004432		C	23731087	T	C	23731087	3	2	44	1	0	0	0	0	1	0	0	0	5052	1667	58	2	833	2	ELAVL2	9	23731087	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2653285	23731087	117482344	206	5666										
C9orf72	203228	hgsc.bcm.edu	37	chr9	27566850	27566850	+	Frame_Shift_Del	DEL	T	T	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atgaaacaataatcactcccTtttcagacaagacaaaaaac							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:27566850delT	ENST00000380003.3	-	2	332	c.269delA	c.(268-270)aagfs	p.K90fs	C9orf72_ENST00000379997.3_Frame_Shift_Del_p.K90fs|C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	90					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		AATCACTCCCTTTTCAGACAA	0.373																																					p.K90fs		Atlas-INDEL	.											.	C9orf72	48	.	0			c.270delG						.						97	93	94					9																	27566850		2203	4300	6503	SO:0001589	frameshift_variant	203228	exon2			.	AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.269delA	chr9.hg19:g.27566850delT	ENSP00000369339:p.Lys90fs	182.0	0.0		179.0	13.0	NM_018325	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Frame_Shift_Del	DEL	ENST00000380003.3	hg19	CCDS6522.1																																																																																			.	.		0.373	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325		-	27566850	T	-	27566850	7	5	44	1	0	1	0	1	0	0	0	0	2497	1609	56	0	1220	0	C9orf72	9	27566850	Frame_Shift_Del	DEL	T	TCGA-BC-A3KG-01A-11D-A20W-10	3835763	27566850	113646581	207	5667										
LINGO2	158038	hgsc.bcm.edu	37	chr9	27950199	27950199	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcattgtcccccacttctagAgacttcaggttatgtagatc	7	11	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:27950199A>G	ENST00000379992.2	-	6	920	c.471T>C	c.(469-471)tcT>tcC	p.S157S	LINGO2_ENST00000308675.3_Silent_p.S157S	NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	157						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		CCACTTCTAGAGACTTCAGGT	0.418																																					p.S157S		Atlas-SNP	.											.	LINGO2	244	.	0			c.T471C						.						69	64	66					9																	27950199		2203	4300	6503	SO:0001819	synonymous_variant	158038	exon7			TTCTAGAGACTTC	AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482		"Immunoglobulin superfamily / I-set domain containing"	21207	protein-coding gene	gene with protein product		609793	"leucine rich repeat neuronal 6C"	LRRN6C		14686891	Standard	NM_152570		Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.471T>C	chr9.hg19:g.27950199A>G		106.0	0.0		94.0	5.0	NM_001258282	A8K4K7|B2RPM5|Q6ZMD0	Silent	SNP	ENST00000379992.2	hg19	CCDS6524.1																																																																																			.	.		0.418	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051978.2	NM_152570		G	27950199	A	G	27950199	2	3	44	1	0	0	0	0	0	0	0	1	8824	291	11	2		2	LINGO2	9	27950199	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	383349	27950199	113263232	208	5668										
NDUFB6	4712	hgsc.bcm.edu	37	chr9	32572964	32572964	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tctgtgggggcagcaccggcTcccgagggctcagctcctgg	16	14	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:32572964T>C	ENST00000379847.3	-	1	196	c.95A>G	c.(94-96)gAg>gGg	p.E32G	NDUFB6_ENST00000350021.2_Missense_Mutation_p.E32G	NM_002493.4	NP_002484.1	O95139	NDUB6_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa	32					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.E32V(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|urinary_tract(1)	8			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00199)		CAGCACCGGCTCCCGAGGGCT	0.557											OREG0019131	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E32G		Atlas-SNP	.											NDUFB6,caecum,carcinoma,0,1	NDUFB6	12	.	1	Substitution - Missense(1)	large_intestine(1)	c.A95G						.						36	40	39					9																	32572964		2203	4300	6503	SO:0001583	missense	4712	exon1			ACCGGCTCCCGAG	AF035840	CCDS6528.1, CCDS6529.1, CCDS75826.1	9p13.2	2011-07-04	2002-08-29		ENSG00000165264	ENSG00000165264		"Mitochondrial respiratory chain complex / Complex I"	7701	protein-coding gene	gene with protein product	"NADH-ubiquinone oxidoreductase beta subunit, 6", "NADH-ubiquinone oxidoreductase B17 subunit", "complex I, mitochondrial respiratory chain, B17 subunit"	603322	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6 (17kD, B17)"			9763677, 9760212	Standard	NM_002493		Approved	B17, CI	uc003zre.2	O95139	OTTHUMG00000019741	ENST00000379847.3:c.95A>G	chr9.hg19:g.32572964T>C	ENSP00000369176:p.Glu32Gly	39.0	1.0	833	35.0	2.0	NM_001199987	A8K0Y7|Q5VYT2|Q6IB84	Missense_Mutation	SNP	ENST00000379847.3	hg19	CCDS6528.1	.	.	.	.	.	.	.	.	.	.	T	31	5.095150	0.94197	.	.	ENSG00000165264	ENST00000379847;ENST00000350021	.	.	.	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.78291	0.4260	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.81161	-0.1059	9	0.87932	D	0	-18.6602	14.2949	0.66304	0.0:0.0:0.0:1.0	.	32;32	Q5VYT2;O95139	.;NDUB6_HUMAN	G	32	.	ENSP00000297983:E32G	E	-	2	0	NDUFB6	32562964	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.571000	0.74000	2.271000	0.75665	0.533000	0.62120	GAG	.	.		0.557	NDUFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052001.1	NM_002493		C	32572964	T	C	32572964	3	2	44	1	0	0	0	0	1	0	0	0	10294	1551	54	2	307	2	NDUFB6	9	32572964	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4622765	32572964	108640467	209	5669										
TMEM215	401498	hgsc.bcm.edu	37	chr9	32784212	32784212	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atgacattaacccgaggactGggctggtggtggccctggtc	15	10	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:32784212G>T	ENST00000342743.5	+	2	396	c.31G>T	c.(31-33)Ggg>Tgg	p.G11W		NM_212558.2	NP_997723.2	Q68D42	TM215_HUMAN	transmembrane protein 215	11						integral component of membrane (GO:0016021)				endometrium(4)|kidney(1)|large_intestine(3)|lung(2)|prostate(2)	12						CCCGAGGACTGGGCTGGTGGT	0.562																																					p.G11W		Atlas-SNP	.											.	TMEM215	38	.	0			c.G31T						.						119	114	115					9																	32784212		2203	4300	6503	SO:0001583	missense	401498	exon2			AGGACTGGGCTGG		CCDS6530.1	9p21.1	2008-08-08			ENSG00000188133	ENSG00000188133			33816	protein-coding gene	gene with protein product							Standard	NM_212558		Approved		uc003zri.4	Q68D42	OTTHUMG00000129521	ENST00000342743.5:c.31G>T	chr9.hg19:g.32784212G>T	ENSP00000345468:p.Gly11Trp	388.0	1.0		433.0	180.0	NM_212558	Q6ZUU2	Missense_Mutation	SNP	ENST00000342743.5	hg19	CCDS6530.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.544356	0.45280	.	.	ENSG00000188133	ENST00000342743	.	.	.	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000002	T	0.65954	0.2741	L	0.27053	0.805	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.69997	-0.4993	9	0.87932	D	0	-20.2017	16.4706	0.84111	0.0:0.0:1.0:0.0	.	11	Q68D42	TM215_HUMAN	W	11	.	ENSP00000345468:G11W	G	+	1	0	TMEM215	32774212	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.536000	0.82023	2.494000	0.84150	0.462000	0.41574	GGG	.	.		0.562	TMEM215-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251701.1	NM_212558		T	32784212	G	T	32784212	3	4	44	1	0	0	0	0	1	0	0	0	16153	1348	47	3	33	3	TMEM215	9	32784212	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	211248	32784212	108429219	210	5670										
PIGO	84720	hgsc.bcm.edu	37	chr9	35092757	35092757	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgagtaggtatgaagaaatCgggacacctggcagagaaaa	13	6	0	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:35092757C>T	ENST00000378617.3	-	7	1521	c.1127G>A	c.(1126-1128)cGa>cAa	p.R376Q	PIGO_ENST00000341666.3_Missense_Mutation_p.R376Q|PIGO_ENST00000492770.1_5'Flank|PIGO_ENST00000298004.5_Missense_Mutation_p.R376Q|PIGO_ENST00000361778.2_Missense_Mutation_p.R376Q	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	376					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			ATGAAGAAATCGGGACACCTG	0.512																																					p.R376Q		Atlas-SNP	.											PIGO,NS,carcinoma,0,1	PIGO	86	.	0			c.G1127A						.						38	43	42					9																	35092757		2160	4183	6343	SO:0001583	missense	84720	exon8			AGAAATCGGGACA	AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"Phosphatidylinositol glycan anchor biosynthesis"	23215	protein-coding gene	gene with protein product		614730	"phosphatidylinositol glycan, class O"			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.1127G>A	chr9.hg19:g.35092757C>T	ENSP00000367880:p.Arg376Gln	55.0	0.0		49.0	2.0	NM_001201484	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Missense_Mutation	SNP	ENST00000378617.3	hg19	CCDS6575.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.100237	0.76983	.	.	ENSG00000165282	ENST00000298004;ENST00000378617;ENST00000341666;ENST00000361778	T;T;T;T	0.59638	0.36;0.25;0.25;0.36	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.76456	0.3990	M	0.73372	2.23	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.943	T	0.74699	-0.3577	10	0.46703	T	0.11	-14.9231	19.6982	0.96039	0.0:1.0:0.0:0.0	.	376;376	Q8TEQ8-2;Q8TEQ8	.;PIGO_HUMAN	Q	376	ENSP00000298004:R376Q;ENSP00000367880:R376Q;ENSP00000339382:R376Q;ENSP00000354678:R376Q	ENSP00000298004:R376Q	R	-	2	0	PIGO	35082757	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	5.473000	0.66774	2.894000	0.99253	0.655000	0.94253	CGA	.	.		0.512	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	NM_032634		T	35092757	C	T	35092757	3	4	44	1	0	0	0	0	1	0	0	0	11903	884	31	1	2162	1	PIGO	9	35092757	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	2308545	35092757	106120674	211	5671										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37745568	37745568	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cccaccacatccccctagagAccctcaaggacagagcagag	8	17	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:37745568A>G	ENST00000539465.1	+	16	4132	c.3539A>G	c.(3538-3540)gAc>gGc	p.D1180G	FRMPD1_ENST00000377765.3_Missense_Mutation_p.D1180G|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1180						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CCCCCTAGAGACCCTCAAGGA	0.488																																					p.D1180G		Atlas-SNP	.											.	FRMPD1	237	.	0			c.A3539G						.						55	58	57					9																	37745568		2203	4300	6503	SO:0001583	missense	22844	exon16			CTAGAGACCCTCA	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.3539A>G	chr9.hg19:g.37745568A>G	ENSP00000444411:p.Asp1180Gly	68.0	0.0		89.0	4.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	hg19	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.340980	0.24339	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.07567	3.18;3.18	5.01	-5.66	0.02451	.	2.508960	0.01261	N	0.009189	T	0.04679	0.0127	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34750	-0.9816	10	0.30078	T	0.28	7.9247	6.5175	0.22256	0.3243:0.2688:0.4069:0.0	.	1180	Q5SYB0	FRPD1_HUMAN	G	1180	ENSP00000366995:D1180G;ENSP00000444411:D1180G	ENSP00000366995:D1180G	D	+	2	0	FRMPD1	37735568	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-1.437000	0.02419	-1.347000	0.02208	0.459000	0.35465	GAC	.	.		0.488	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		G	37745568	A	G	37745568	3	3	44	1	0	0	0	0	1	0	0	0	6065	275	10	2	3597	2	FRMPD1	9	37745568	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2652811	37745568	103467863	212	5672										
PRKACG	5568	hgsc.bcm.edu	37	chr9	71628966	71628966	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggctaggaactcgttcacgcTctcctcctgctcggtgtcct	10	15	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:71628966T>C	ENST00000377276.2	-	1	73	c.43A>G	c.(43-45)Agc>Ggc	p.S15G		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	15					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						TCGTTCACGCTCTCCTCCTGC	0.682																																					p.S15G	Esophageal Squamous(110;2236 2623 32146)	Atlas-SNP	.											.	PRKACG	65	.	0			c.A43G						.						48	49	48					9																	71628966		2203	4300	6503	SO:0001583	missense	5568	exon1			TCACGCTCTCCTC	M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.43A>G	chr9.hg19:g.71628966T>C	ENSP00000366488:p.Ser15Gly	127.0	0.0		90.0	4.0	NM_002732	O60850|Q5VZ02|Q86YI1	Missense_Mutation	SNP	ENST00000377276.2	hg19	CCDS6625.1	.	.	.	.	.	.	.	.	.	.	T	10.17	1.275434	0.23307	.	.	ENSG00000165059	ENST00000377276	T	0.68025	-0.3	0.969	0.969	0.19686	Protein kinase-like domain (1);	.	.	.	.	T	0.58850	0.2151	L	0.60455	1.87	0.19575	N	0.999964	B	0.11235	0.004	B	0.16722	0.016	T	0.54708	-0.8253	9	0.66056	D	0.02	.	5.7336	0.18053	0.0:0.0:0.0:1.0	.	15	P22612	KAPCG_HUMAN	G	15	ENSP00000366488:S15G	ENSP00000366488:S15G	S	-	1	0	PRKACG	70818786	.	.	0.003000	0.11579	0.003000	0.03518	.	.	0.344000	0.23847	0.338000	0.21704	AGC	.	.		0.682	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1			C	71628966	T	C	71628966	3	2	44	1	0	0	0	0	1	0	0	0	12511	1551	54	2	1016	2	PRKACG	9	71628966	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	33883398	71628966	69584465	213	5673										
ANXA1	301	hgsc.bcm.edu	37	chr9	75775231	75775231	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aggtcaccttgaggaggttgTtttagctctgctaaaaactc	10	8	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:75775231T>C	ENST00000376911.1	+	4	1205	c.323T>C	c.(322-324)gTt>gCt	p.V108A	ANXA1_ENST00000257497.6_Missense_Mutation_p.V108A			P04083	ANXA1_HUMAN	annexin A1	108					alpha-beta T cell differentiation (GO:0046632)|arachidonic acid secretion (GO:0050482)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hydrogen peroxide (GO:0070301)|endocrine pancreas development (GO:0031018)|estrous cycle phase (GO:0060206)|gliogenesis (GO:0042063)|hepatocyte differentiation (GO:0070365)|inflammatory response (GO:0006954)|insulin secretion (GO:0030073)|keratinocyte differentiation (GO:0030216)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|neutrophil clearance (GO:0097350)|neutrophil homeostasis (GO:0001780)|peptide cross-linking (GO:0018149)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of neutrophil apoptotic process (GO:0033031)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of vesicle fusion (GO:0031340)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to interleukin-1 (GO:0070555)|response to peptide hormone (GO:0043434)|response to X-ray (GO:0010165)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cilium (GO:0005929)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)|phospholipid binding (GO:0005543)|protein binding, bridging (GO:0030674)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(5)	8		all_epithelial(88;2.54e-11)		OV - Ovarian serous cystadenocarcinoma(323;2.82e-06)|GBM - Glioblastoma multiforme(74;0.0325)	Amcinonide(DB00288)|Dexamethasone(DB01234)|Hydrocortisone(DB00741)	GAGGAGGTTGTTTTAGCTCTG	0.423																																					p.V108A		Atlas-SNP	.											.	ANXA1	27	.	0			c.T323C						.						119	120	120					9																	75775231		2203	4300	6503	SO:0001583	missense	301	exon5			AGGTTGTTTTAGC	X05908	CCDS6645.1	9q21.13	2013-02-25			ENSG00000135046	ENSG00000135046		"Annexins", "Endogenous ligands"	533	protein-coding gene	gene with protein product		151690		ANX1, LPC1		2936963	Standard	NM_000700		Approved		uc004ajf.1	P04083	OTTHUMG00000020016	ENST00000376911.1:c.323T>C	chr9.hg19:g.75775231T>C	ENSP00000366109:p.Val108Ala	98.0	0.0		93.0	4.0	NM_000700		Missense_Mutation	SNP	ENST00000376911.1	hg19	CCDS6645.1	.	.	.	.	.	.	.	.	.	.	T	14.74	2.626184	0.46840	.	.	ENSG00000135046	ENST00000257497;ENST00000456643;ENST00000415424;ENST00000376911	T;T;T;T	0.03635	3.86;3.86;3.86;3.86	5.92	-6.94	0.01633	Annexin repeat, conserved site (1);	0.357177	0.31760	N	0.007104	T	0.05318	0.0141	L	0.60012	1.86	0.33102	D	0.539362	B	0.12630	0.006	B	0.19148	0.024	T	0.02661	-1.1127	10	0.59425	D	0.04	.	20.448	0.99123	0.0:0.0998:0.0:0.9002	.	108	P04083	ANXA1_HUMAN	A	108;119;108;108	ENSP00000257497:V108A;ENSP00000412489:V119A;ENSP00000414013:V108A;ENSP00000366109:V108A	ENSP00000257497:V108A	V	+	2	0	ANXA1	74965051	0.001000	0.12720	0.011000	0.14972	0.925000	0.55904	-0.212000	0.09319	-1.470000	0.01888	-0.248000	0.11899	GTT	.	.		0.423	ANXA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052665.1	NM_000700		C	75775231	T	C	75775231	3	2	44	1	0	0	0	0	1	0	0	0	714	1725	60	2	337	2	ANXA1	9	75775231	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4146265	75775231	65438200	214	5674										
HNRNPK	3190	hgsc.bcm.edu	37	chr9	86591918	86591918	+	Frame_Shift_Del	DEL	G	G	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttaatacttacgtctgtacGgagagccttaatattcttgc							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:86591918delG	ENST00000376264.2	-	5	463	c.205delC	c.(205-207)cgtfs	p.R69fs	RP11-575L7.8_ENST00000448389.1_RNA|HNRNPK_ENST00000376281.4_Frame_Shift_Del_p.R69fs|HNRNPK_ENST00000351839.3_Frame_Shift_Del_p.R69fs|HNRNPK_ENST00000376263.3_Frame_Shift_Del_p.R69fs|HNRNPK_ENST00000360384.5_Frame_Shift_Del_p.R69fs	NM_002140.3|NM_031262.2	NP_002131.2|NP_112552.1	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K	69	2 X 22 AA approximate repeats.|5 X 4 AA repeats of G-X-G-G.|Interaction with ASFV p30.|KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.|Necessary for interaction with DDX1.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|regulation of low-density lipoprotein particle clearance (GO:0010988)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|single-stranded DNA binding (GO:0003697)	p.R69S(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|stomach(1)	19						ACGTCTGTACGGAGAGCCTTA	0.328																																					p.R69fs		Atlas-INDEL	.											.	HNRNPK	49	.	1	Substitution - Missense(1)	lung(1)	c.206delG						.						86	85	85					9																	86591918		2203	4300	6503	SO:0001589	frameshift_variant	3190	exon5			.		CCDS6667.1, CCDS6668.1	9q21.32-q21.33	2011-10-24		2008-04-18	ENSG00000165119	ENSG00000165119			5044	protein-coding gene	gene with protein product	"transformation upregulated nuclear protein"	600712		HNRPK		8107114	Standard	NM_031263		Approved	CSBP, TUNP	uc004anf.4	P61978	OTTHUMG00000020107	ENST00000376264.2:c.205delC	chr9.hg19:g.86591918delG	ENSP00000365440:p.Arg69fs	100.0	0.0		136.0	10.0	NM_031263	Q07244|Q15671|Q59F98|Q5T6W4|Q60577|Q922Y7|Q96J62	Frame_Shift_Del	DEL	ENST00000376264.2	hg19	CCDS6667.1																																																																																			.	.		0.328	HNRNPK-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052846.2			-	86591918	G	-	86591918	7	5	44	1	0	1	0	1	0	0	0	0	7278	1116	39	0	1276	0	HNRNPK	9	86591918	Frame_Shift_Del	DEL	G	TCGA-BC-A3KG-01A-11D-A20W-10	10816687	86591918	54621513	215	5675										
C9orf102	375748	hgsc.bcm.edu	37	chr9	98691001	98691001	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcttcatacctctcgtctagTtgcttgacgtgctacagcag	8	12	4	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:98691001T>C	ENST00000288985.7	+	11	1944	c.1639T>C	c.(1639-1641)Ttg>Ctg	p.L547L	ERCC6L2_ENST00000437817.1_Splice_Site_p.L358L|ERCC6L2_ENST00000466840.1_3'UTR	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	547	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)										TCTCGTCTAGTTGCTTGACGT	0.393																																					p.L547L		Atlas-SNP	.											.	.	.	.	0			c.T1639C						.						130	115	120					9																	98691001		2203	4300	6503	SO:0001630	splice_region_variant	375748	exon11			GTCTAGTTGCTTG	BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"chromosome 9 open reading frame 102", "excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.1639-1T>C	chr9.hg19:g.98691001T>C		87.0	0.0		103.0	5.0	NM_001010895	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Silent	SNP	ENST00000288985.7	hg19	CCDS35072.1																																																																																			.	.		0.393	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895	Silent	C	98691001	T	C	98691001	5	2	44	1	0	0	0	0	0	0	1	0	2447	1739	60	2	1681	2	C9orf102	9	98691001	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	12099083	98691001	42522430	216	5676										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113171160	113171160	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcttggcagacaaatacaggActtccgactgacttatagcc	9	11	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:113171160A>G	ENST00000401783.2	-	38	7056	c.6720T>C	c.(6718-6720)agT>agC	p.S2240S	SVEP1_ENST00000374469.1_Silent_p.S2217S|SVEP1_ENST00000297826.5_Silent_p.S166S	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2240	Sushi 14. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CAAATACAGGACTTCCGACTG	0.507																																					p.S2240S		Atlas-SNP	.											.	SVEP1	326	.	0			c.T6720C						.						131	135	134					9																	113171160		2035	4203	6238	SO:0001819	synonymous_variant	79987	exon38			TACAGGACTTCCG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.6720T>C	chr9.hg19:g.113171160A>G		42.0	0.0		74.0	4.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.		0.507	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	113171160	A	G	113171160	2	3	44	1	0	0	0	0	0	0	0	1	15435	272	10	2		2	SVEP1	9	113171160	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	14480159	113171160	28042271	217	5677										
KIAA1958	158405	hgsc.bcm.edu	37	chr9	115422320	115422320	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cgttcactcaggtctcccggAggcttggctcccacagctgc	11	16	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:115422320A>G	ENST00000337530.6	+	4	2418	c.2122A>G	c.(2122-2124)Agg>Ggg	p.R708G	KIAA1958_ENST00000536272.1_Missense_Mutation_p.R736G	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	708										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						GGTCTCCCGGAGGCTTGGCTC	0.617																																					p.R708G		Atlas-SNP	.											.	KIAA1958	52	.	0			c.A2122G						.						49	50	50					9																	115422320		2203	4300	6503	SO:0001583	missense	158405	exon4			TCCCGGAGGCTTG	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.2122A>G	chr9.hg19:g.115422320A>G	ENSP00000336940:p.Arg708Gly	74.0	0.0		78.0	4.0	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Missense_Mutation	SNP	ENST00000337530.6	hg19	CCDS35108.1	.	.	.	.	.	.	.	.	.	.	A	14.07	2.425989	0.43020	.	.	ENSG00000165185	ENST00000337530;ENST00000536272	.	.	.	5.95	4.79	0.61399	.	.	.	.	.	T	0.26448	0.0646	N	0.08118	0	0.24694	N	0.99329	B;B	0.19817	0.039;0.016	B;B	0.12156	0.007;0.004	T	0.23261	-1.0193	8	0.72032	D	0.01	.	12.7962	0.57560	0.8584:0.1416:0.0:0.0	.	736;708	B7ZKW6;Q8N8K9	.;K1958_HUMAN	G	708;736	.	ENSP00000336940:R708G	R	+	1	2	KIAA1958	114462141	1.000000	0.71417	0.991000	0.47740	0.998000	0.95712	4.442000	0.59988	1.048000	0.40298	0.533000	0.62120	AGG	.	.		0.617	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465		G	115422320	A	G	115422320	3	3	44	1	0	0	0	0	1	0	0	0	8273	295	11	2	2132	2	KIAA1958	9	115422320	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2251160	115422320	25791111	218	5678										
DFNB31	25861	hgsc.bcm.edu	37	chr9	117186678	117186678	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctccacagagacgctgccaCcacggtactcatccaggtag	9	16	1	1	rs117352600	byFrequency	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:117186678C>G	ENST00000362057.3	-	6	1520	c.1352G>C	c.(1351-1353)gGt>gCt	p.G451A	DFNB31_ENST00000374059.3_Missense_Mutation_p.G100A|DFNB31_ENST00000265134.6_Missense_Mutation_p.G68A	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	451					inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GACGCTGCCACCACGGTACTC	0.627																																					p.G451A		Atlas-SNP	.											DFNB31,NS,carcinoma,0,1	DFNB31	100	.	0			c.G1352C						.						98	79	86					9																	117186678		2203	4300	6503	SO:0001583	missense	25861	exon6			CTGCCACCACGGT	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"whirlin"	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.1352G>C	chr9.hg19:g.117186678C>G	ENSP00000354623:p.Gly451Ala	229.0	0.0		178.0	0.0	NM_001173425	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Missense_Mutation	SNP	ENST00000362057.3	hg19	CCDS6806.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.736298	0.30774	.	.	ENSG00000095397	ENST00000265134;ENST00000374059;ENST00000362057	T;T;T	0.06294	4.21;4.2;3.32	5.49	2.08	0.27032	.	0.580016	0.18819	N	0.130285	T	0.05273	0.0140	L	0.43152	1.355	0.80722	D	1	B;B;B	0.28512	0.139;0.139;0.214	B;B;B	0.30572	0.05;0.034;0.117	T	0.39165	-0.9627	10	0.33141	T	0.24	-2.7096	2.0825	0.03638	0.2411:0.3747:0.0:0.3842	.	451;451;100	B9EGE6;Q9P202;Q9P202-4	.;WHRN_HUMAN;.	A	68;100;451	ENSP00000265134:G68A;ENSP00000363172:G100A;ENSP00000354623:G451A	ENSP00000265134:G68A	G	-	2	0	DFNB31	116226499	0.453000	0.25721	0.081000	0.20488	0.944000	0.59088	2.923000	0.48868	0.771000	0.33359	0.561000	0.74099	GGT	.	C|0.997;T|0.003		0.627	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404		G	117186678	C	G	117186678	3	3	44	1	0	0	0	0	1	0	0	0	4457	507	18	4	1399	4	DFNB31	9	117186678	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1764358	117186678	24026753	219	5679										
CEP110	11064	hgsc.bcm.edu	37	chr9	123858738	123858738	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaatatgtgtaatctgcaaaAgcttaaccttgcaggaaatg	8	6	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:123858738A>G	ENST00000373855.1	+	6	778	c.518A>G	c.(517-519)aAg>aGg	p.K173R	CNTRL_ENST00000238341.5_Missense_Mutation_p.K173R|CNTRL_ENST00000373865.2_Missense_Mutation_p.K173R			Q7Z7A1	CNTRL_HUMAN	centriolin	173					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						AATCTGCAAAAGCTTAACCTT	0.328																																					p.K173R		Atlas-SNP	.											.	CNTRL	161	.	0			c.A518G						.						85	88	87					9																	123858738		2203	4299	6502	SO:0001583	missense	11064	exon4			TGCAAAAGCTTAA	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.518A>G	chr9.hg19:g.123858738A>G	ENSP00000362962:p.Lys173Arg	76.0	0.0		85.0	4.0	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	18.66	3.672550	0.67928	.	.	ENSG00000119397	ENST00000373865;ENST00000373855;ENST00000238341;ENST00000454238	T;T	0.54479	0.57;0.57	6.08	6.08	0.98989	.	.	.	.	.	T	0.50292	0.1607	L	0.41632	1.29	0.32248	N	0.571781	P	0.40931	0.733	P	0.46758	0.526	T	0.56475	-0.7973	9	0.20519	T	0.43	.	11.6641	0.51364	0.9296:0.0:0.0704:0.0	.	173	Q7Z7A1	CNTRL_HUMAN	R	173	ENSP00000362962:K173R;ENSP00000238341:K173R	ENSP00000238341:K173R	K	+	2	0	CNTRL	122898559	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.228000	0.58619	2.333000	0.79357	0.482000	0.46254	AAG	.	.		0.328	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123858738	A	G	123858738	3	3	44	1	0	0	0	0	1	0	0	0	3247	72	3	2	532	2	CEP110	9	123858738	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	6672060	123858738	17354693	220	5680										
CEP110	11064	hgsc.bcm.edu	37	chr9	123924501	123924501	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gagcaaagaaaaggaagatcTccaagagaaatgtgacattt	10	5	1	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:123924501T>C	ENST00000373855.1	+	34	5635	c.5375T>C	c.(5374-5376)cTc>cCc	p.L1792P	CNTRL_ENST00000373850.1_Missense_Mutation_p.L1240P|CNTRL_ENST00000238341.5_Missense_Mutation_p.L1792P|CNTRL_ENST00000373845.2_3'UTR			Q7Z7A1	CNTRL_HUMAN	centriolin	1792					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						AAGGAAGATCTCCAAGAGAAA	0.423																																					p.L1792P		Atlas-SNP	.											.	CNTRL	161	.	0			c.T5375C						.						74	75	75					9																	123924501		2203	4300	6503	SO:0001583	missense	11064	exon32			AAGATCTCCAAGA	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.5375T>C	chr9.hg19:g.123924501T>C	ENSP00000362962:p.Leu1792Pro	116.0	0.0		87.0	5.0	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.256716	0.80246	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000373850;ENST00000373845	T;T;T	0.54279	0.84;0.84;0.58	5.89	5.89	0.94794	.	.	.	.	.	T	0.70159	0.3192	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	T	0.71593	-0.4546	9	0.52906	T	0.07	.	15.4921	0.75615	0.0:0.0:0.0:1.0	.	1792	Q7Z7A1	CNTRL_HUMAN	P	1792;1792;1792;548;1240;474	ENSP00000362962:L1792P;ENSP00000238341:L1792P;ENSP00000362956:L1240P	ENSP00000238341:L1792P	L	+	2	0	CNTRL	122964322	1.000000	0.71417	0.985000	0.45067	0.988000	0.76386	5.284000	0.65627	2.257000	0.74773	0.460000	0.39030	CTC	.	.		0.423	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		C	123924501	T	C	123924501	3	2	44	1	0	0	0	0	1	0	0	0	3247	1551	54	2	5501	2	CEP110	9	123924501	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	65763	123924501	17288930	221	5681										
NEK6	10783	hgsc.bcm.edu	37	chr9	127101926	127101926	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aagtccgacatctggtccctGggctgtctgctgtacgaggt	13	11	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:127101926G>T	ENST00000320246.5	+	8	844	c.699G>T	c.(697-699)ctG>ctT	p.L233L	NEK6_ENST00000539416.1_Silent_p.L258L|NEK6_ENST00000546191.1_Silent_p.L233L|NEK6_ENST00000540326.1_Silent_p.L251L|NEK6_ENST00000373600.3_Silent_p.L267L|NEK6_ENST00000545174.1_Silent_p.L233L|NEK6_ENST00000373603.1_Silent_p.L233L|NEK6_ENST00000394199.2_Silent_p.L267L	NM_014397.5	NP_055212.2	Q9HC98	NEK6_HUMAN	NIMA-related kinase 6	233	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cellular senescence (GO:2000772)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinesin binding (GO:0019894)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15						TCTGGTCCCTGGGCTGTCTGC	0.602																																					p.L267L	NSCLC(122;934 1785 18647 44295 45571)	Atlas-SNP	.											.	NEK6	47	.	0			c.G801T						.						275	203	227					9																	127101926		2203	4300	6503	SO:0001819	synonymous_variant	10783	exon9			GTCCCTGGGCTGT	AF087909	CCDS6854.1, CCDS48015.1, CCDS55338.1, CCDS55339.1	9q33.3-q34.11	2012-11-15	2012-11-15		ENSG00000119408	ENSG00000119408			7749	protein-coding gene	gene with protein product	"putative serine-threonine protein kinase"	604884	"NIMA (never in mitosis gene a)-related kinase 6"			10702691	Standard	NM_001145001		Approved	SID6-1512	uc004boh.3	Q9HC98	OTTHUMG00000020650	ENST00000320246.5:c.699G>T	chr9.hg19:g.127101926G>T		257.0	0.0		238.0	10.0	NM_001166171	B7Z2D9|Q5TBG3|Q5TBG9|Q6FG86|Q6IAR3|Q96E83|Q9ULX2	Silent	SNP	ENST00000320246.5	hg19	CCDS6854.1																																																																																			.	.		0.602	NEK6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054016.1	NM_014397		T	127101926	G	T	127101926	2	4	44	1	0	0	0	0	0	0	0	1	10337	1335	47	3		3	NEK6	9	127101926	Silent	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	3177425	127101926	14111505	222	5682										
CEL	1056	hgsc.bcm.edu	37	chr9	135944115	135944115	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttgatggagacttcatccccGctgacccgatcaacctgtac	8	14	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:135944115G>T	ENST00000372080.4	+	8	977	c.961G>T	c.(961-963)Gct>Tct	p.A321S	CEL_ENST00000351304.7_Missense_Mutation_p.A318S	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	318					cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CTTCATCCCCGCTGACCCGAT	0.577																																					p.A321S		Atlas-SNP	.											.	CEL	71	.	0			c.G961T						.						28	33	31					9																	135944115		1894	4088	5982	SO:0001583	missense	1056	exon8			ATCCCCGCTGACC	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"bile salt-stimulated lipase"	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.961G>T	chr9.hg19:g.135944115G>T	ENSP00000361151:p.Ala321Ser	833.0	1.0		651.0	122.0	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	hg19	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.000645	0.35320	.	.	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.67171	-0.25;-0.25	5.46	2.58	0.30949	Carboxylesterase, type B (1);	0.095855	0.64402	D	0.000001	T	0.46600	0.1401	N	0.13272	0.32	0.09310	N	1	B	0.14438	0.01	B	0.20577	0.03	T	0.42413	-0.9453	10	0.87932	D	0	.	7.6018	0.28079	0.1456:0.0:0.7211:0.1332	.	318	P19835	CEL_HUMAN	S	321;318;321	ENSP00000361151:A321S;ENSP00000342217:A318S	ENSP00000304021:A321S	A	+	1	0	CEL	134933936	1.000000	0.71417	0.000000	0.03702	0.503000	0.33858	7.548000	0.82154	0.262000	0.21774	0.561000	0.74099	GCT	.	.		0.577	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1			T	135944115	G	T	135944115	3	4	44	1	0	0	0	0	1	0	0	0	3211	1087	38	1	991	1	CEL	9	135944115	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	8842189	135944115	5269316	223	5683										
AGPAT2	10555	hgsc.bcm.edu	37	chr9	139569213	139569213	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgaagaacttcttcttggtgTtgtagaaggaggagaaggaa	14	3	2	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:139569213T>C	ENST00000371696.2	-	5	700	c.635A>G	c.(634-636)aAc>aGc	p.N212S	AGPAT2_ENST00000538402.1_Missense_Mutation_p.N212S|AGPAT2_ENST00000371694.3_Missense_Mutation_p.N180S	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	212					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|epidermis development (GO:0008544)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)	6	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		CTTCTTGGTGTTGTAGAAGGA	0.632																																					p.N212S		Atlas-SNP	.											.	AGPAT2	17	.	0			c.A635G						.						95	85	88					9																	139569213		2203	4294	6497	SO:0001583	missense	10555	exon5			TTGGTGTTGTAGA	AF000237	CCDS7003.1, CCDS35181.1	9q34.3	2013-02-05	2013-02-05		ENSG00000169692	ENSG00000169692	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	325	protein-coding gene	gene with protein product	"LPAAT-beta", "lysophosphatidic acid acyltransferase, beta"	603100	"Berardinelli-Seip congenital lipodystrophy", "1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)"	BSCL		9242711, 9212163	Standard	NM_006412		Approved		uc004cii.1	O15120	OTTHUMG00000020936	ENST00000371696.2:c.635A>G	chr9.hg19:g.139569213T>C	ENSP00000360761:p.Asn212Ser	64.0	0.0		53.0	4.0	NM_006412	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Missense_Mutation	SNP	ENST00000371696.2	hg19	CCDS7003.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.189907	0.00302	.	.	ENSG00000169692	ENST00000371694;ENST00000371696;ENST00000538402	D;D;D	0.92911	-3.13;-3.13;-3.13	4.36	0.699	0.18093	.	0.956133	0.08683	N	0.909205	T	0.79924	0.4530	N	0.05280	-0.08	0.09310	N	1	B;B	0.11235	0.004;0.002	B;B	0.13407	0.009;0.004	T	0.65274	-0.6208	10	0.17369	T	0.5	-10.5002	6.5893	0.22638	0.0:0.3073:0.0:0.6927	.	180;212	O15120-2;O15120	.;PLCB_HUMAN	S	180;212;212	ENSP00000360759:N180S;ENSP00000360761:N212S;ENSP00000438919:N212S	ENSP00000360759:N180S	N	-	2	0	AGPAT2	138689034	0.038000	0.19896	0.003000	0.11579	0.044000	0.14063	0.397000	0.20883	0.187000	0.20147	0.338000	0.21704	AAC	.	.		0.632	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412		C	139569213	T	C	139569213	3	2	44	1	0	0	0	0	1	0	0	0	387	1725	60	2	209	2	AGPAT2	9	139569213	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	3625098	139569213	1644218	224	5684										
EHMT1	79813	hgsc.bcm.edu	37	chr9	140729307	140729307	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cccccaagtgccggcactcgAgcgcggccctggcccagcgt	13	19	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:140729307A>G	ENST00000460843.1	+	27	3826	c.3799A>G	c.(3799-3801)Agc>Ggc	p.S1267G		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1267					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		CCGGCACTCGAGCGCGGCCCT	0.687																																					p.S1267G		Atlas-SNP	.											.	EHMT1	196	.	0			c.A3799G						.						24	24	24					9																	140729307		2201	4298	6499	SO:0001583	missense	79813	exon27			CACTCGAGCGCGG	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	24650	protein-coding gene	gene with protein product		607001	"euchromatic histone methyltransferase 1"			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.3799A>G	chr9.hg19:g.140729307A>G	ENSP00000417980:p.Ser1267Gly	40.0	0.0		49.0	4.0	NM_024757	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	hg19	CCDS7050.2	.	.	.	.	.	.	.	.	.	.	A	13.56	2.275085	0.40194	.	.	ENSG00000181090	ENST00000460843	T	0.70399	-0.48	5.22	4.07	0.47477	.	0.346503	0.35179	N	0.003385	T	0.55401	0.1918	N	0.21448	0.665	0.33246	D	0.55791	B	0.06786	0.001	B	0.08055	0.003	T	0.59590	-0.7426	10	0.41790	T	0.15	.	11.1585	0.48501	0.9269:0.0:0.0731:0.0	.	1267	Q9H9B1	EHMT1_HUMAN	G	1267	ENSP00000417980:S1267G	ENSP00000417980:S1267G	S	+	1	0	EHMT1	139849128	0.950000	0.32346	0.554000	0.28268	0.953000	0.61014	2.658000	0.46733	0.930000	0.37217	0.459000	0.35465	AGC	.	.		0.687	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757		G	140729307	A	G	140729307	3	3	44	1	0	0	0	0	1	0	0	0	4985	304	11	2	3954	2	EHMT1	9	140729307	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1160094	140729307	484124	225	5685										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140878654	140878654	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gccgggaagctcctttgggaTcagtgtgctgcgggccctcc	15	13	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr9:140878654T>A	ENST00000371372.1	+	13	1866	c.1721T>A	c.(1720-1722)aTc>aAc	p.I574N	CACNA1B_ENST00000371355.4_Missense_Mutation_p.I575N|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371357.1_Missense_Mutation_p.I575N|CACNA1B_ENST00000371363.1_Missense_Mutation_p.I574N|CACNA1B_ENST00000277551.2_Missense_Mutation_p.I574N	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	574					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TCCTTTGGGATCAGTGTGCTG	0.627																																					p.I574N		Atlas-SNP	.											.	CACNA1B	266	.	0			c.T1721A						.						68	83	78					9																	140878654		2093	4218	6311	SO:0001583	missense	774	exon13			TTGGGATCAGTGT	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1721T>A	chr9.hg19:g.140878654T>A	ENSP00000360423:p.Ile574Asn	282.0	1.0		229.0	102.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.518029	0.64634	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.98792	-5.14;-5.14;-5.14;-5.14;-5.14	4.5	4.5	0.54988	.	0.101398	0.64402	D	0.000002	D	0.99269	0.9745	M	0.92077	3.27	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98994	1.0809	10	0.87932	D	0	.	14.1601	0.65441	0.0:0.0:0.0:1.0	.	574;574	B1AQK4;B1AQK6	.;.	N	574;574;574;575;575	ENSP00000360423:I574N;ENSP00000277551:I574N;ENSP00000360414:I574N;ENSP00000360408:I575N;ENSP00000360406:I575N	ENSP00000277551:I574N	I	+	2	0	CACNA1B	139998475	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.793000	0.85851	1.788000	0.52465	0.454000	0.30748	ATC	.	.		0.627	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		A	140878654	T	A	140878654	3	1	44	1	0	0	0	0	1	0	0	0	2541	1435	50	4	1771	4	CACNA1B	9	140878654	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	149347	140878654	334777	226	5686										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7608182	7608182	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cagcccccagctccccaccaCcacactctggttgcagggga	9	19	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:7608182C>A	ENST00000256861.6	-	13	2416	c.2338G>T	c.(2338-2340)Gtg>Ttg	p.V780L	ITIH5_ENST00000397146.2_Intron|ITIH5_ENST00000446830.2_Missense_Mutation_p.V562L|ITIH5_ENST00000298441.6_Missense_Mutation_p.V566L	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	780					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CTCCCCACCACCACACTCTGG	0.572																																					p.V780L		Atlas-SNP	.											.	ITIH5	343	.	0			c.G2338T						.						90	68	76					10																	7608182		2203	4300	6503	SO:0001583	missense	80760	exon13			CCACCACCACACT			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.2338G>T	chr10.hg19:g.7608182C>A	ENSP00000256861:p.Val780Leu	198.0	0.0		158.0	64.0	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	C	11.06	1.527890	0.27299	.	.	ENSG00000123243	ENST00000256861;ENST00000298441;ENST00000446830	T;T;T	0.11712	2.75;2.75;2.75	5.84	4.94	0.65067	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.422460	0.28312	N	0.015802	T	0.09247	0.0228	.	.	.	0.18873	N	0.999983	P;P	0.43938	0.822;0.787	B;B	0.40702	0.338;0.228	T	0.22591	-1.0212	9	0.25751	T	0.34	-13.8082	10.7982	0.46472	0.0:0.8562:0.0:0.1438	.	780;566	Q86UX2;Q86UX2-3	ITIH5_HUMAN;.	L	780;566;562	ENSP00000256861:V780L;ENSP00000298441:V566L;ENSP00000387969:V562L	ENSP00000256861:V780L	V	-	1	0	ITIH5	7648188	0.000000	0.05858	0.136000	0.22124	0.912000	0.54170	0.579000	0.23788	1.462000	0.47948	0.655000	0.94253	GTG	.	.		0.572	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		A	7608182	C	A	7608182	3	1	44	1	0	0	0	0	1	0	0	0	7916	507	18	3	540	3	ITIH5	10	7608182	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10		7608182	127926565	227	5687										
CDC123	8872	hgsc.bcm.edu	37	chr10	12259467	12259470	+	Splice_Site	DEL	GTAA	GTAA	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	actcgtgacttcactcagccGtaagtatctcttattctctc							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:12259467_12259470delGTAA	ENST00000281141.4	+	6	720		c.e6+1		CDC123_ENST00000378900.2_Splice_Site|CDC123_ENST00000455773.3_Splice_Site	NM_006023.2	NP_006014.2	O75794	CD123_HUMAN	cell division cycle 123						cell cycle arrest (GO:0007050)|cell division (GO:0051301)|positive regulation of cell proliferation (GO:0008284)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)		p.?(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12						TCACTCAGCCGTAAGTATCTCTTA	0.343																																					p.147_147del		Atlas-Indel,Pindel	.											.	CDC123	34	.	1	Unknown(1)	endometrium(1)	c.440_440del						.			1,4263		0,1,2131						5	1			82	1,8253		0,1,4126	no	splice-5	CDC123	NM_006023.2		0,2,6257	A1A1,A1R,RR		0.0121,0.0235,0.016				2,12516				SO:0001630	splice_region_variant	8872	exon6			.	BC001600	CCDS7090.1	10p13	2013-01-17	2013-01-17	2006-11-06	ENSG00000151465	ENSG00000151465			16827	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 7", "cell division cycle 123 homolog (S. cerevisiae)"	C10orf7		15319434	Standard	NM_006023		Approved	D123	uc001ill.3	O75794	OTTHUMG00000017680	ENST00000281141.4:c.440+1GTAA>-	chr10.hg19:g.12259467_12259470delGTAA		107.0	0.0		73.0	24.0	NM_006023	A8JZZ7|Q14107|Q5T0L4|Q5T0L5|Q5T0L7|Q5T0L8|Q5T0L9	Frame_Shift_Del	DEL	ENST00000281141.4	hg19	CCDS7090.1																																																																																			.	.		0.343	CDC123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046801.1	NM_006023	Intron	-	12259470	GTAA	-	12259467	8	5	44	1	0	1	0	1	0	0	1	0	3057	1159	40	0	463	0	CDC123	10	12259467	Splice_Site	DEL	GTAA	TCGA-BC-A3KG-01A-11D-A20W-10	4651285	12259467	123275280	228	5688										
CDC123	8872	hgsc.bcm.edu	37	chr10	12280454	12280454	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgactttttttctcctttacAgttgtgttcgatatatacag	6	7	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:12280454A>G	ENST00000281141.4	+	10	968		c.e10-1		CDC123_ENST00000378900.2_Splice_Site|CDC123_ENST00000455773.3_Splice_Site	NM_006023.2	NP_006014.2	O75794	CD123_HUMAN	cell division cycle 123						cell cycle arrest (GO:0007050)|cell division (GO:0051301)|positive regulation of cell proliferation (GO:0008284)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12						TCTCCTTTACAGTTGTGTTCG	0.299																																					.		Atlas-SNP	.											.	CDC123	34	.	0			c.689-2A>G						.						77	80	79					10																	12280454		2202	4299	6501	SO:0001630	splice_region_variant	8872	exon10			CTTTACAGTTGTG	BC001600	CCDS7090.1	10p13	2013-01-17	2013-01-17	2006-11-06	ENSG00000151465	ENSG00000151465			16827	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 7", "cell division cycle 123 homolog (S. cerevisiae)"	C10orf7		15319434	Standard	NM_006023		Approved	D123	uc001ill.3	O75794	OTTHUMG00000017680	ENST00000281141.4:c.689-1A>G	chr10.hg19:g.12280454A>G		82.0	0.0		77.0	4.0	NM_006023	A8JZZ7|Q14107|Q5T0L4|Q5T0L5|Q5T0L7|Q5T0L8|Q5T0L9	Splice_Site	SNP	ENST00000281141.4	hg19	CCDS7090.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.976359	0.74360	.	.	ENSG00000151465	ENST00000281141;ENST00000378900;ENST00000455773;ENST00000440613	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.519	0.67838	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDC123	12320460	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.080000	0.76837	2.079000	0.62486	0.482000	0.46254	.	.	.		0.299	CDC123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046801.1	NM_006023	Intron	G	12280454	A	G	12280454	5	3	44	1	0	0	0	0	0	0	1	0	3057	202	7	2	725	2	CDC123	10	12280454	Splice_Site	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	20987	12280454	123254293	229	5689										
KIF5B	3799	hgsc.bcm.edu	37	chr10	32308888	32308888	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acatcattttctggttttggCtgacgaaagaaaaaaataat	7	5	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:32308888C>T	ENST00000302418.4	-	20	2662		c.e20-1		KIF5B_ENST00000493889.1_Splice_Site	NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B						ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)		KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				CTGGTTTTGGCTGACGAAAGA	0.323			T	"RET, ALK"	NSCLC																																.		Atlas-SNP	.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	KIF5B	81	.	0			c.2205-1G>A						.						183	172	176					10																	32308888		2203	4298	6501	SO:0001630	splice_region_variant	3799	exon21			TTTTGGCTGACGA	X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.2205-1G>A	chr10.hg19:g.32308888C>T		102.0	0.0		125.0	5.0	NM_004521	A0AVB2|Q5VZ85	Splice_Site	SNP	ENST00000302418.4	hg19	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.083391	0.36758	.	.	ENSG00000170759	ENST00000302418	.	.	.	5.33	4.41	0.53225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2919	0.73872	0.1414:0.8586:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIF5B	32348894	1.000000	0.71417	0.999000	0.59377	0.359000	0.29487	7.818000	0.86416	1.216000	0.43427	-0.518000	0.04402	.	.	.		0.323	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521	Intron	T	32308888	C	T	32308888	5	4	44	1	0	0	0	0	0	0	1	0	8315	811	28	3	711	3	KIF5B	10	32308888	Splice_Site	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	20028434	32308888	103225859	230	5690										
CCNY	219771	hgsc.bcm.edu	37	chr10	35857995	35857995	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccctcaggccatctctcgccTctgcgaggacaagtacaagg	10	15	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:35857995T>C	ENST00000374704.4	+	10	1103	c.923T>C	c.(922-924)cTc>cCc	p.L308P	CCNY_ENST00000374706.1_Missense_Mutation_p.L254P|CCNY_ENST00000339497.5_Missense_Mutation_p.L283P|CCNY_ENST00000265375.9_Missense_Mutation_p.L254P	NM_145012.4	NP_659449.3	Q8ND76	CCNY_HUMAN	cyclin Y	308					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	8						ATCTCTCGCCTCTGCGAGGAC	0.617																																					p.L308P		Atlas-SNP	.											.	CCNY	22	.	0			c.T923C						.						59	51	54					10																	35857995		2203	4300	6503	SO:0001583	missense	219771	exon10			CTCGCCTCTGCGA	AF413522, AY504868	CCDS7189.1, CCDS7190.1, CCDS60513.1	10p11.22	2011-01-25	2007-02-09	2007-02-09	ENSG00000108100	ENSG00000108100			23354	protein-coding gene	gene with protein product		612786	"chromosome 10 open reading frame 9"	C10orf9		20441050	Standard	XM_005252388		Approved	CFP1, CBCP1	uc001iyw.4	Q8ND76	OTTHUMG00000017955	ENST00000374704.4:c.923T>C	chr10.hg19:g.35857995T>C	ENSP00000363836:p.Leu308Pro	55.0	0.0		74.0	4.0	NM_145012	B7ZKX9|D3DRY9|Q2M3V4|Q2TU96|Q6NT86|Q7Z4U7|Q8TEX2|Q8TEX3|Q96M99|Q96P45	Missense_Mutation	SNP	ENST00000374704.4	hg19	CCDS7189.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.697299	0.88830	.	.	ENSG00000108100	ENST00000374706;ENST00000537547;ENST00000374704;ENST00000339497;ENST00000265375;ENST00000456784	T;T;T;T	0.35048	1.33;1.33;1.38;1.33	5.41	5.41	0.78517	.	0.061257	0.64402	D	0.000005	T	0.56978	0.2022	M	0.64404	1.975	0.80722	D	1	P;D;D	0.89917	0.955;0.999;1.0	P;D;D	0.79108	0.707;0.985;0.992	T	0.56123	-0.8031	10	0.41790	T	0.15	-18.3654	15.4376	0.75157	0.0:0.0:0.0:1.0	.	175;283;308	B7Z8E4;Q8ND76-2;Q8ND76	.;.;CCNY_HUMAN	P	254;308;308;283;254;175	ENSP00000363838:L254P;ENSP00000363836:L308P;ENSP00000344275:L283P;ENSP00000265375:L254P	ENSP00000265375:L254P	L	+	2	0	CCNY	35898001	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.004000	0.88535	2.053000	0.61076	0.533000	0.62120	CTC	.	.		0.617	CCNY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047568.2	NM_181698		C	35857995	T	C	35857995	3	2	44	1	0	0	0	0	1	0	0	0	2938	1551	54	2	961	2	CCNY	10	35857995	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	3549107	35857995	99676752	231	5691										
PPYR1	5540	hgsc.bcm.edu	37	chr10	47087681	47087681	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aggccatccccatctgccacGggaacctcatcttcttagtg	8	15	4	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:47087681G>T	ENST00000395716.1	+	2	983	c.898G>T	c.(898-900)Ggg>Tgg	p.G300W	NPY4R_ENST00000374312.1_Missense_Mutation_p.G300W			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	300					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)	p.G300W(1)									CATCTGCCACGGGAACCTCAT	0.547																																					p.G300W		Atlas-SNP	.											PPYR1,NS,carcinoma,0,1	PPYR1	54	.	1	Substitution - Missense(1)	lung(1)	c.G898T						.						182	155	164					10																	47087681		2203	4300	6503	SO:0001583	missense	5540	exon3			TGCCACGGGAACC		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"GPCR / Class A : Neuropeptide receptors : Y"	9329	protein-coding gene	gene with protein product		601790	"pancreatic polypeptide receptor 1"	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.898G>T	chr10.hg19:g.47087681G>T	ENSP00000379066:p.Gly300Trp	218.0	0.0		235.0	0.0	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Missense_Mutation	SNP	ENST00000395716.1	hg19	CCDS31193.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.218785	0.58560	.	.	ENSG00000204174	ENST00000374312;ENST00000395716	T;T	0.54071	0.59;0.59	5.18	3.31	0.37934	GPCR, rhodopsin-like superfamily (1);	0.181622	0.47455	D	0.000240	T	0.62221	0.2410	M	0.65498	2.005	0.35149	D	0.769569	D	0.64830	0.994	D	0.66084	0.941	T	0.68845	-0.5301	10	0.45353	T	0.12	.	5.0708	0.14606	0.1836:0.1737:0.6426:0.0	.	300	P50391	NPY4R_HUMAN	W	300	ENSP00000363431:G300W;ENSP00000379066:G300W	ENSP00000363431:G300W	G	+	1	0	PPYR1	46507687	0.959000	0.32827	0.982000	0.44146	0.963000	0.63663	1.986000	0.40677	1.344000	0.45657	0.655000	0.94253	GGG	.	.		0.547	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1			T	47087681	G	T	47087681	3	4	44	1	0	0	0	0	1	0	0	0	12428	1116	39	1	900	1	PPYR1	10	47087681	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	11229686	47087681	88447066	232	5692										
ANK3	288	hgsc.bcm.edu	37	chr10	61822911	61822911	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	attgttctcatctgcaaaacTtctggtgcctgaaatatttc	6	9	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:61822911T>C	ENST00000280772.2	-	40	12744	c.12553A>G	c.(12553-12555)Agt>Ggt	p.S4185G	ANK3_ENST00000373827.2_Missense_Mutation_p.S1566G|ANK3_ENST00000355288.2_Missense_Mutation_p.S706G|RP11-388P9.2_ENST00000414383.1_RNA|ANK3_ENST00000503366.1_Missense_Mutation_p.S1573G	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	4185					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TCTGCAAAACTTCTGGTGCCT	0.323																																					p.S4185G		Atlas-SNP	.											.	ANK3	703	.	0			c.A12553G						.						90	83	85					10																	61822911		2203	4300	6503	SO:0001583	missense	288	exon40			CAAAACTTCTGGT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.12553A>G	chr10.hg19:g.61822911T>C	ENSP00000280772:p.Ser4185Gly	86.0	0.0		90.0	5.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.396551	0.62177	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000373820;ENST00000355288;ENST00000423532;ENST00000503366;ENST00000395299;ENST00000373817	D;T;T;T;T	0.93488	-3.23;0.34;0.34;0.34;0.34	5.38	5.38	0.77491	DEATH-like (2);	0.000000	0.49305	D	0.000149	D	0.92967	0.7762	L	0.27053	0.805	0.80722	D	1	P;P;B;P;P;D;D	0.56968	0.749;0.875;0.354;0.551;0.941;0.965;0.978	B;B;B;P;P;P;P	0.58172	0.206;0.377;0.101;0.673;0.737;0.834;0.688	D	0.94082	0.7345	10	0.72032	D	0.01	.	15.3904	0.74739	0.0:0.0:0.0:1.0	.	1573;706;1566;4185;807;706;105	E9PE32;A8KA62;Q5CZH9;Q12955;F5GXK0;B1AQT2;B1AQT0	.;.;.;ANK3_HUMAN;.;.;.	G	4185;1566;164;706;706;1573;1552;807	ENSP00000280772:S4185G;ENSP00000362933:S1566G;ENSP00000362926:S164G;ENSP00000347436:S706G;ENSP00000425236:S1573G	ENSP00000280772:S4185G	S	-	1	0	ANK3	61492917	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.023000	0.70848	2.048000	0.60808	0.383000	0.25322	AGT	.	.		0.323	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61822911	T	C	61822911	3	2	44	1	0	0	0	0	1	0	0	0	622	1609	56	2	909	2	ANK3	10	61822911	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	14735230	61822911	73711836	233	5693										
RHOBTB1	9886	hgsc.bcm.edu	37	chr10	62671170	62671170	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcacgtgggtggccagcagcTgatactgcgtgagtgtggtg	18	8	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:62671170T>C	ENST00000337910.5	-	3	468	c.131A>G	c.(130-132)cAg>cGg	p.Q44R	RNU2-72P_ENST00000411175.1_RNA|RHOBTB1_ENST00000357917.4_Missense_Mutation_p.Q44R	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	44	Rho-like.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					GGCCAGCAGCTGATACTGCGT	0.567																																					p.Q44R		Atlas-SNP	.											.	RHOBTB1	61	.	0			c.A131G						.						153	121	132					10																	62671170		2203	4300	6503	SO:0001583	missense	9886	exon3			AGCAGCTGATACT	AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"BTB/POZ domain containing"	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.131A>G	chr10.hg19:g.62671170T>C	ENSP00000338671:p.Gln44Arg	109.0	0.0		111.0	5.0	NM_014836		Missense_Mutation	SNP	ENST00000337910.5	hg19	CCDS7261.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.302673	0.81136	.	.	ENSG00000072422	ENST00000357917;ENST00000337910;ENST00000536302	T;T	0.21543	2.0;2.0	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000001	T	0.21550	0.0519	N	0.21583	0.68	0.80722	D	1	B	0.28470	0.213	B	0.37943	0.261	T	0.08289	-1.0729	10	0.62326	D	0.03	.	15.9648	0.79961	0.0:0.0:0.0:1.0	.	44	O94844	RHBT1_HUMAN	R	44	ENSP00000350595:Q44R;ENSP00000338671:Q44R	ENSP00000338671:Q44R	Q	-	2	0	RHOBTB1	62341176	1.000000	0.71417	1.000000	0.80357	0.423000	0.31445	7.904000	0.87408	2.238000	0.73509	0.397000	0.26171	CAG	.	.		0.567	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			C	62671170	T	C	62671170	3	2	44	1	0	0	0	0	1	0	0	0	13348	1580	55	2	1995	2	RHOBTB1	10	62671170	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	848259	62671170	72863577	234	5694										
C10orf107	219621	hgsc.bcm.edu	37	chr10	63441027	63441027	+	Frame_Shift_Del	DEL	A	A	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttctctattattcagtattcAaaatttatgactttactagc					rs12359246		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:63441027delA	ENST00000330194.2	+	2	332	c.27delA	c.(25-27)tcafs	p.S9fs		NM_173554.2	NP_775825.1	Q8IVU9	CJ107_HUMAN	chromosome 10 open reading frame 107	9										breast(1)|kidney(1)|lung(4)|prostate(1)|skin(1)	8	Prostate(12;0.016)					TTCAGTATTCAAAATTTATGA	0.274																																					p.S9X		Atlas-INDEL	.											.	C10orf107	24	.	0			c.26delC						.						80	84	83					10																	63441027		2199	4273	6472	SO:0001589	frameshift_variant	219621	exon2			.	BC041932	CCDS7262.1	10q21.3	2012-06-01			ENSG00000183346	ENSG00000183346			28678	protein-coding gene	gene with protein product						12477932	Standard	NM_173554		Approved	bA63A2.1, Em:AC022398.2, MGC44593	uc010qik.2	Q8IVU9	OTTHUMG00000018295	ENST00000330194.2:c.27delA	chr10.hg19:g.63441027delA	ENSP00000328698:p.Ser9fs	75.0	0.0		102.0	10.0	NM_173554	Q5T1B8	Frame_Shift_Del	DEL	ENST00000330194.2	hg19	CCDS7262.1																																																																																			.	.		0.274	C10orf107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048228.2	NM_173554		-	63441027	A	-	63441027	7	5	44	1	0	1	0	1	0	0	0	0	1583	117	5	0	29	0	C10orf107	10	63441027	Frame_Shift_Del	DEL	A	TCGA-BC-A3KG-01A-11D-A20W-10	769857	63441027	72093720	235	5695										
HNRNPH3	3189	hgsc.bcm.edu	37	chr10	70101436	70101436	+	Splice_Site	DEL	G	G	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggctacggaagagatggaatGggtatgtaaagtttttaaaa					rs146848138		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:70101436delG	ENST00000265866.7	+	8	1035	c.870delG	c.(868-870)atg>at	p.M290fs	HNRNPH3_ENST00000469172.1_3'UTR|HNRNPH3_ENST00000354695.5_Splice_Site_p.M275fs|HNRNPH3_ENST00000441000.2_Splice_Site_p.M182fs	NM_012207.2|NM_021644.3	NP_036339.1|NP_067676.2	P31942	HNRH3_HUMAN	heterogeneous nuclear ribonucleoprotein H3 (2H9)	290	Gly-rich.				epithelial cell differentiation (GO:0030855)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)	11						GAGATGGAATGGGTATGTAAA	0.388																																					p.M290fs		Atlas-INDEL	.											.	HNRNPH3	33	.	0			c.869delT						.						107	113	111					10																	70101436		2203	4300	6503	SO:0001630	splice_region_variant	3189	exon8			.		CCDS7278.1, CCDS7279.1	10q22	2013-02-12		2008-04-18	ENSG00000096746	ENSG00000096746		"RNA binding motif (RRM) containing"	5043	protein-coding gene	gene with protein product		602324		HNRPH3		8999868	Standard	NM_021644		Approved	2H9	uc001jnw.4	P31942	OTTHUMG00000018349	ENST00000265866.7:c.871+1G>-	chr10.hg19:g.70101436delG		132.0	0.0		115.0	10.0	NM_012207	A8K682|B3KRE1|Q9BSX1|Q9NP53|Q9NP96|Q9NPA7|Q9NPI4|Q9UFU4|Q9Y4J5	Frame_Shift_Del	DEL	ENST00000265866.7	hg19	CCDS7278.1																																																																																			.	.		0.388	HNRNPH3-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090165.1		Frame_Shift_Del	-	70101436	G	-	70101436	8	5	44	1	0	1	0	1	0	0	1	0	7277	1362	47	0	896	0	HNRNPH3	10	70101436	Splice_Site	DEL	G	TCGA-BC-A3KG-01A-11D-A20W-10	6660409	70101436	65433311	236	5696										
VPS26A	9559	hgsc.bcm.edu	37	chr10	70917887	70917887	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gttcaccagcttgccacctaTcctgatgttaacaactctat	5	13	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:70917887T>C	ENST00000373382.1	+	6	1124	c.471T>C	c.(469-471)taT>taC	p.Y157Y	VPS26A_ENST00000541711.1_Silent_p.Y46Y|VPS26A_ENST00000546041.1_Silent_p.Y140Y|VPS26A_ENST00000489794.1_Silent_p.Y132Y|VPS26A_ENST00000395098.1_Silent_p.Y157Y|VPS26A_ENST00000490696.1_Intron|VPS26A_ENST00000263559.6_Silent_p.Y157Y			O75436	VP26A_HUMAN	vacuolar protein sorting 26 homolog A (S. pombe)	157					retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|vesicle (GO:0031982)	protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)	8						TTGCCACCTATCCTGATGTTA	0.313																																					p.Y157Y	Colon(90;545 1358 4729 6702 16773)	Atlas-SNP	.											.	VPS26A	24	.	0			c.T471C						.						91	88	89					10																	70917887		2203	4300	6503	SO:0001819	synonymous_variant	9559	exon5			CACCTATCCTGAT	AF054179	CCDS7286.1, CCDS41536.1	10q21.1	2007-01-12	2007-01-12	2005-10-11	ENSG00000122958	ENSG00000122958			12711	protein-coding gene	gene with protein product		605506	"vacuolar protein sorting 26 (yeast homolog)", "vacuolar protein sorting 26 (yeast)", "vacuolar protein sorting 26 homolog A (yeast)"	VPS26		1638986, 9653160	Standard	NM_004896		Approved	Hbeta58, PEP8A	uc001jpb.3	O75436	OTTHUMG00000018376	ENST00000373382.1:c.471T>C	chr10.hg19:g.70917887T>C		107.0	0.0		87.0	4.0	NM_004896	A8MZ56|B2RDD3|Q8TBH4|Q9H982	Silent	SNP	ENST00000373382.1	hg19	CCDS7286.1																																																																																			.	.		0.313	VPS26A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048403.1	NM_004896		C	70917887	T	C	70917887	2	2	44	1	0	0	0	0	0	0	0	1	17212	1442	50	2		2	VPS26A	10	70917887	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	816451	70917887	64616860	237	5697										
C10orf54	64115	hgsc.bcm.edu	37	chr10	73515148	73515148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgcctgcctttgcttgtagAccaggagcaggatgaggggg	16	9	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:73515148A>G	ENST00000394957.3	-	4	702	c.644T>C	c.(643-645)gTc>gCc	p.V215A	CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	215					BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						TTGCTTGTAGACCAGGAGCAG	0.632																																					p.V215A		Atlas-SNP	.											.	C10orf54	29	.	0			c.T644C						.						53	42	46					10																	73515148		2203	4299	6502	SO:0001583	missense	64115	exon4			TTGTAGACCAGGA	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"Immunoglobulin superfamily / V-set domain containing"	30085	protein-coding gene	gene with protein product	"stress induced secreted protein 1"	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.644T>C	chr10.hg19:g.73515148A>G	ENSP00000378409:p.Val215Ala	98.0	0.0		100.0	4.0	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Missense_Mutation	SNP	ENST00000394957.3	hg19	CCDS31218.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.489134	0.84962	.	.	ENSG00000107738	ENST00000394957;ENST00000263569	T	0.55052	0.54	5.22	5.22	0.72569	.	0.109143	0.64402	D	0.000008	T	0.62454	0.2429	M	0.64997	1.995	0.58432	D	0.999994	P;D	0.61080	0.953;0.989	P;P	0.52957	0.551;0.714	T	0.67848	-0.5564	10	0.87932	D	0	-19.6454	15.1123	0.72368	1.0:0.0:0.0:0.0	.	215;215	A4ZYV1;Q9H7M9	.;GI24_HUMAN	A	215;211	ENSP00000378409:V215A	ENSP00000263569:V211A	V	-	2	0	C10orf54	73185154	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.318000	0.79029	1.982000	0.57802	0.379000	0.24179	GTC	.	.		0.632	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153		G	73515148	A	G	73515148	3	3	44	1	0	0	0	0	1	0	0	0	1609	275	10	2	307	2	C10orf54	10	73515148	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2597261	73515148	62019599	238	5698										
PPP3CB	5532	hgsc.bcm.edu	37	chr10	75206313	75206313	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttttgtttcttatgatttctTtccgggctgcagctgaacct	8	9	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:75206313T>C	ENST00000360663.5	-	11	1316	c.1205A>G	c.(1204-1206)aAa>aGa	p.K402R	PPP3CB_ENST00000544628.1_Missense_Mutation_p.K30R|PPP3CB_ENST00000394828.2_Missense_Mutation_p.K403R|PPP3CB_ENST00000545874.1_Missense_Mutation_p.K317R|PPP3CB_ENST00000394829.2_Missense_Mutation_p.K403R|PPP3CB_ENST00000342558.3_Missense_Mutation_p.K402R|PPP3CB_ENST00000394822.2_Missense_Mutation_p.K420R			P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta isozyme	402	Calmodulin-binding. {ECO:0000255}.				axon extension (GO:0048675)|calcium ion-dependent exocytosis (GO:0017156)|cellular response to drug (GO:0035690)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|learning (GO:0007612)|locomotion involved in locomotory behavior (GO:0031987)|memory (GO:0007613)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of transcription, DNA-templated (GO:0045893)|protein dephosphorylation (GO:0006470)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)|social behavior (GO:0035176)|T cell activation (GO:0042110)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein phosphatase 2B binding (GO:0030346)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(7)|skin(1)|urinary_tract(1)	22	Prostate(51;0.0119)					TATGATTTCTTTCCGGGCTGC	0.373																																					p.K403R		Atlas-SNP	.											.	PPP3CB	68	.	0			c.A1208G						.						157	144	148					10																	75206313		2203	4300	6503	SO:0001583	missense	5532	exon11			ATTTCTTTCCGGG	M29551	CCDS7328.1, CCDS44436.1, CCDS44437.1	10q22.2	2010-03-17	2010-03-05		ENSG00000107758	ENSG00000107758	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9315	protein-coding gene	gene with protein product	"calcineurin A beta", "protein phosphatase 2B, catalytic subunit, beta isoform"	114106	"protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform (calcineurin A beta)", "protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform"	CALNB		1659808, 2558868	Standard	XM_005269944		Approved	CALNA2, CNA2, PP2Bbeta	uc001juf.3	P16298	OTTHUMG00000018472	ENST00000360663.5:c.1205A>G	chr10.hg19:g.75206313T>C	ENSP00000353881:p.Lys402Arg	79.0	0.0		98.0	4.0	NM_001142354	P16299|Q5F2F9|Q8N1F0|Q8N3W4	Missense_Mutation	SNP	ENST00000360663.5	hg19	CCDS7328.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.557922	0.27827	.	.	ENSG00000107758	ENST00000360663;ENST00000394829;ENST00000394828;ENST00000394823;ENST00000544628;ENST00000430762;ENST00000342558;ENST00000545874;ENST00000394822	T;T;T;T;T;T;T	0.05319	3.46;3.46;3.46;3.46;3.46;3.46;3.46	5.12	5.12	0.69794	.	0.075858	0.53938	N	0.000042	T	0.12944	0.0314	L	0.31578	0.945	0.80722	D	1	D;B;B;D;B	0.76494	0.999;0.016;0.014;0.998;0.004	D;B;B;D;B	0.87578	0.998;0.036;0.036;0.991;0.019	T	0.19160	-1.0314	10	0.07813	T	0.8	.	14.9301	0.70908	0.0:0.0:0.0:1.0	.	420;317;402;403;402	P16298-2;F5H0F8;P16298-3;Q8N1F0;P16298	.;.;.;.;PP2BB_HUMAN	R	402;403;403;74;30;64;402;317;420	ENSP00000353881:K402R;ENSP00000378306:K403R;ENSP00000378305:K403R;ENSP00000437596:K30R;ENSP00000343147:K402R;ENSP00000439876:K317R;ENSP00000378299:K420R	ENSP00000343147:K402R	K	-	2	0	PPP3CB	74876319	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.841000	0.86834	1.924000	0.55735	0.477000	0.44152	AAA	.	.		0.373	PPP3CB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048669.1	NM_021132		C	75206313	T	C	75206313	3	2	44	1	0	0	0	0	1	0	0	0	12410	1841	64	2	385	2	PPP3CB	10	75206313	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1691165	75206313	60328434	239	5699										
GLUD1	2746	hgsc.bcm.edu	37	chr10	88817488	88817488	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgccgtgggtacaatgggaAtagttccaccatgctttcca	10	11	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:88817488A>G	ENST00000277865.4	-	11	1550	c.1454T>C	c.(1453-1455)aTt>aCt	p.I485T	GLUD1_ENST00000537649.1_Missense_Mutation_p.I318T|GLUD1_ENST00000465164.1_5'Flank|GLUD1_ENST00000544149.1_Missense_Mutation_p.I352T	NM_005271.3	NP_005262.1	P00367	DHE3_HUMAN	glutamate dehydrogenase 1	485					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamine metabolic process (GO:0006541)|positive regulation of insulin secretion (GO:0032024)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|tricarboxylic acid metabolic process (GO:0072350)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|leucine binding (GO:0070728)|NAD+ binding (GO:0070403)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(11)|prostate(1)	22					Hexachlorophene(DB00756)	TACAATGGGAATAGTTCCACC	0.403																																					p.I485T		Atlas-SNP	.											.	GLUD1	30	.	0			c.T1454C						.						185	168	174					10																	88817488		2203	4300	6503	SO:0001583	missense	2746	exon11			ATGGGAATAGTTC	M20867	CCDS7382.1	10q23.2	2010-03-17			ENSG00000148672	ENSG00000148672	1.4.1.3		4335	protein-coding gene	gene with protein product		138130		GLUD		2757358	Standard	NM_005271		Approved	GDH	uc001keh.3	P00367	OTTHUMG00000018666	ENST00000277865.4:c.1454T>C	chr10.hg19:g.88817488A>G	ENSP00000277865:p.Ile485Thr	126.0	0.0		66.0	4.0	NM_005271	B3KV55|B4DGN5|Q5TBU3	Missense_Mutation	SNP	ENST00000277865.4	hg19	CCDS7382.1	.	.	.	.	.	.	.	.	.	.	A	18.14	3.557841	0.65425	.	.	ENSG00000148672	ENST00000277865;ENST00000394415;ENST00000537649;ENST00000535802;ENST00000513510;ENST00000544149	D;D;D	0.96587	-4.06;-4.06;-4.06	4.98	4.98	0.66077	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.96793	0.8953	M	0.84433	2.695	0.80722	D	1	B;P	0.43885	0.294;0.82	B;P	0.46026	0.149;0.501	D	0.97057	0.9768	10	0.54805	T	0.06	.	14.996	0.71431	1.0:0.0:0.0:0.0	.	352;485	B4DGN5;P00367	.;DHE3_HUMAN	T	485;442;318;184;417;352	ENSP00000277865:I485T;ENSP00000439291:I318T;ENSP00000444732:I352T	ENSP00000277865:I485T	I	-	2	0	GLUD1	88807468	1.000000	0.71417	0.942000	0.38095	0.979000	0.70002	8.928000	0.92853	2.011000	0.59026	0.248000	0.18094	ATT	.	.		0.403	GLUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049188.1	NM_005271		G	88817488	A	G	88817488	3	3	44	1	0	0	0	0	1	0	0	0	6484	101	4	2	234	2	GLUD1	10	88817488	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	13611175	88817488	46717259	240	5700										
FAS	355	hgsc.bcm.edu	37	chr10	90768720	90768720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaccaaactttttttgtaacTctactgtatgtgaacactgt	5	8	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:90768720T>C	ENST00000355279.2	+	4	409	c.409T>C	c.(409-411)Tct>Cct	p.S137P	FAS_ENST00000357339.2_Missense_Mutation_p.S137P|FAS_ENST00000352159.4_Missense_Mutation_p.S137P|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000355740.2_Missense_Mutation_p.S137P			P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	TTTTTGTAACTCTACTGTATG	0.363																																					p.S137P		Atlas-SNP	.											.	FAS	47	.	0			c.T409C						.						352	379	370					10																	90768720		2203	4300	6503	SO:0001583	missense	355	exon4			TGTAACTCTACTG	M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"Tumor necrosis factor receptor superfamily", "CD molecules"	11920	protein-coding gene	gene with protein product	"TNF receptor superfamily member 6"	134637	"tumor necrosis factor receptor superfamily, member 6", "Fas (TNF receptor superfamily, member 6)"	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.409T>C	chr10.hg19:g.90768720T>C	ENSP00000347426:p.Ser137Pro	142.0	0.0		97.0	4.0	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355279.2	hg19	CCDS7395.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.775538	0.31411	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000357339;ENST00000355279;ENST00000371875	D;D;D;D	0.91996	-2.95;-2.95;-2.95;-2.95	4.21	-8.42	0.00957	TNFR/CD27/30/40/95 cysteine-rich region (3);	.	.	.	.	D	0.89784	0.6815	L	0.34521	1.04	0.09310	N	1	D;P;D	0.58620	0.979;0.642;0.983	P;B;P	0.61800	0.83;0.348;0.894	D	0.87133	0.2198	9	0.45353	T	0.12	-0.0355	7.8547	0.29474	0.5971:0.0:0.143:0.2599	.	137;137;137	P25445-6;Q5T9P3;P25445	.;.;TNR6_HUMAN	P	164;137;137;137;137;137	ENSP00000347979:S137P;ENSP00000345601:S137P;ENSP00000349896:S137P;ENSP00000347426:S137P	ENSP00000345601:S137P	S	+	1	0	FAS	90758700	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.087000	0.01360	-3.492000	0.00153	-1.236000	0.01555	TCT	.	.		0.363	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2			C	90768720	T	C	90768720	3	2	44	1	0	0	0	0	1	0	0	0	5689	1551	54	2	423	2	FAS	10	90768720	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1951232	90768720	44766027	241	5701										
HPSE2	60495	hgsc.bcm.edu	37	chr10	100904127	100904127	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aatcttgcagcctttctgttTatctaaggcaacatcacttc	5	11	4	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:100904127T>C	ENST00000370552.3	-	3	537	c.478A>G	c.(478-480)Aaa>Gaa	p.K160E	HPSE2_ENST00000370546.1_Missense_Mutation_p.K160E|HPSE2_ENST00000404542.1_Intron|HPSE2_ENST00000370549.1_Missense_Mutation_p.K160E	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	160					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		CCTTTCTGTTTATCTAAGGCA	0.403																																					p.K160E		Atlas-SNP	.											HPSE2_ENST00000370546,caecum,carcinoma,0,2	HPSE2	203	.	0			c.A478G						.						101	101	101					10																	100904127		2203	4300	6503	SO:0001583	missense	60495	exon3			TCTGTTTATCTAA	AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"urofacial syndrome", "heparanase 2"	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.478A>G	chr10.hg19:g.100904127T>C	ENSP00000359583:p.Lys160Glu	74.0	0.0		29.0	2.0	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	hg19	CCDS7477.1	.	.	.	.	.	.	.	.	.	.	T	9.426	1.084193	0.20309	.	.	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546	T;T;T	0.28255	7.22;1.62;7.22	5.81	5.81	0.92471	Glycoside hydrolase, superfamily (1);	0.060394	0.64402	D	0.000006	T	0.29389	0.0732	L	0.51422	1.61	0.80722	D	1	B;B;B	0.20052	0.015;0.041;0.009	B;B;B	0.20184	0.016;0.028;0.007	T	0.09684	-1.0663	10	0.12430	T	0.62	-5.7058	16.1498	0.81605	0.0:0.0:0.0:1.0	.	160;160;160	Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;HPSE2_HUMAN	E	160	ENSP00000359583:K160E;ENSP00000359580:K160E;ENSP00000359577:K160E	ENSP00000359577:K160E	K	-	1	0	HPSE2	100894117	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.658000	0.61497	2.216000	0.71823	0.528000	0.53228	AAA	.	.		0.403	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		C	100904127	T	C	100904127	3	2	44	1	0	0	0	0	1	0	0	0	7354	1763	61	2	1378	2	HPSE2	10	100904127	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	10135407	100904127	34630620	242	5702										
FBXW4	6468	hgsc.bcm.edu	37	chr10	103427709	103427709	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggatggtgtgtaagcactgcCccagccggcctgaggccaaa	14	12	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:103427709C>T	ENST00000331272.7	-	5	1322	c.704G>A	c.(703-705)gGg>gAg	p.G235E		NM_022039.3	NP_071322.1	P57775	FBXW4_HUMAN	F-box and WD repeat domain containing 4	235					cartilage development (GO:0051216)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|positive regulation of mesenchymal cell proliferation (GO:0002053)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	ubiquitin ligase complex (GO:0000151)				breast(3)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	15		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)		TAAGCACTGCCCCAGCCGGCC	0.552																																					p.G235E		Atlas-SNP	.											.	FBXW4	39	.	0			c.G704A						.						107	106	106					10																	103427709		2203	4300	6503	SO:0001583	missense	6468	exon5			CACTGCCCCAGCC	AF281859	CCDS31271.1	10q24	2013-01-09	2007-02-08	2005-03-12	ENSG00000107829	ENSG00000107829		"F-boxes / WD-40 domains", "WD repeat domain containing"	10847	protein-coding gene	gene with protein product		608071	"split hand/foot malformation (ectrodactyly) type 3", "F-box and WD-40 domain protein 4"	SHFM3		8723077, 7912888	Standard	XM_005270053		Approved	Fbw4, dactylin	uc001kto.3	P57775	OTTHUMG00000018938	ENST00000331272.7:c.704G>A	chr10.hg19:g.103427709C>T	ENSP00000359149:p.Gly235Glu	98.0	0.0		47.0	4.0	NM_022039	Q5SVS1|Q96IM6	Missense_Mutation	SNP	ENST00000331272.7	hg19	CCDS31271.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.984101	0.93044	.	.	ENSG00000107829	ENST00000331272;ENST00000389046;ENST00000457105;ENST00000431477	T	0.75938	-0.98	5.75	5.75	0.90469	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.115021	0.64402	D	0.000011	T	0.78528	0.4297	L	0.45352	1.415	0.58432	D	0.999997	D	0.69078	0.997	P	0.61874	0.895	T	0.69844	-0.5035	10	0.02654	T	1	-16.5182	20.3046	0.98621	0.0:1.0:0.0:0.0	.	235	P57775	FBXW4_HUMAN	E	235;235;148;191	ENSP00000359149:G235E	ENSP00000359149:G235E	G	-	2	0	FBXW4	103417699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.315000	0.59172	2.878000	0.98634	0.650000	0.86243	GGG	.	.		0.552	FBXW4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049979.2	NM_022039		T	103427709	C	T	103427709	3	4	44	1	0	0	0	0	1	0	0	0	5775	623	22	3	554	3	FBXW4	10	103427709	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	2523582	103427709	32107038	243	5703										
PCGF6	84108	hgsc.bcm.edu	37	chr10	105110543	105110543	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgtcctcctcctcctcctctTcttcctcctccagctcctct	2	22	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:105110543T>C	ENST00000369847.3	-	1	348	c.281A>G	c.(280-282)gAa>gGa	p.E94G	PCGF6_ENST00000490296.1_5'UTR|PCGF6_ENST00000337211.4_Missense_Mutation_p.E94G	NM_001011663.1	NP_001011663.1	Q9BYE7	PCGF6_HUMAN	polycomb group ring finger 6	94	Glu-rich.				negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E94A(2)		autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(3)	8		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)		ctcctcctcttcttcctcctc	0.642																																					p.E94G		Atlas-SNP	.											RNF134,colon,carcinoma,0,2	PCGF6	23	.	2	Substitution - Missense(2)	large_intestine(2)	c.A281G						.						15	14	14					10																	105110543		2195	4298	6493	SO:0001583	missense	84108	exon1			TCCTCTTCTTCCT	AB047006	CCDS7546.1, CCDS31275.1	10q24.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000156374	ENSG00000156374		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	21156	protein-coding gene	gene with protein product		607816	"ring finger protein 134"	RNF134		12167161	Standard	NM_032154		Approved	MBLR	uc001kwt.3	Q9BYE7	OTTHUMG00000018982	ENST00000369847.3:c.281A>G	chr10.hg19:g.105110543T>C	ENSP00000358862:p.Glu94Gly	52.0	0.0		65.0	3.0	NM_001011663	A8K3R4|Q5SYD1|Q5SYD6|Q96ID9|Q96SJ1	Missense_Mutation	SNP	ENST00000369847.3	hg19	CCDS31275.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.797435	0.31777	.	.	ENSG00000156374	ENST00000369847;ENST00000337211	T;T	0.36340	1.31;1.26	4.54	4.54	0.55810	.	0.415183	0.22337	N	0.061399	T	0.20740	0.0499	N	0.19112	0.55	0.32275	N	0.568315	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.13469	-1.0508	10	0.27785	T	0.31	.	6.7061	0.23252	0.0:0.1044:0.0:0.8956	.	94;94	Q9BYE7-3;Q9BYE7	.;PCGF6_HUMAN	G	94	ENSP00000358862:E94G;ENSP00000338845:E94G	ENSP00000338845:E94G	E	-	2	0	PCGF6	105100533	0.993000	0.37304	0.976000	0.42696	0.117000	0.20001	3.380000	0.52448	1.900000	0.55004	0.402000	0.26972	GAA	.	.		0.642	PCGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050132.1	NM_032154		C	105110543	T	C	105110543	3	2	44	1	0	0	0	0	1	0	0	0	11587	1783	62	2	811	2	PCGF6	10	105110543	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1682834	105110543	30424204	244	5704										
NRAP	4892	hgsc.bcm.edu	37	chr10	115401184	115401184	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cgtctgtccataccaactccTtcatagcggcctctcatgtg	7	15	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:115401184T>C	ENST00000359988.3	-	13	1507	c.1263A>G	c.(1261-1263)gaA>gaG	p.E421E	NRAP_ENST00000369360.3_Silent_p.E386E|NRAP_ENST00000369358.4_Silent_p.E421E|NRAP_ENST00000360478.3_Silent_p.E386E	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TACCAACTCCTTCATAGCGGC	0.458																																					p.E421E		Atlas-SNP	.											.	NRAP	208	.	0			c.A1263G						.						180	160	167					10																	115401184		2203	4300	6503	SO:0001819	synonymous_variant	4892	exon13			AACTCCTTCATAG		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.1263A>G	chr10.hg19:g.115401184T>C		170.0	0.0		94.0	4.0	NM_001261463		Silent	SNP	ENST00000359988.3	hg19	CCDS7579.1																																																																																			.	.		0.458	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		C	115401184	T	C	115401184	2	2	44	1	0	0	0	0	0	0	0	1	10647	1606	56	2		2	NRAP	10	115401184	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	10290641	115401184	20133563	245	5705										
C10orf81	79949	hgsc.bcm.edu	37	chr10	115526208	115526208	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttatgaaaatgaagtctgcAaacaagattactttattaaa	5	5	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:115526208A>G	ENST00000369310.3	+	2	611	c.49A>G	c.(49-51)Aaa>Gaa	p.K17E	PLEKHS1_ENST00000361048.1_Missense_Mutation_p.K23E|PLEKHS1_ENST00000369312.4_5'UTR	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	17	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.																TGAAGTCTGCAAACAAGATTA	0.358																																					p.K23E		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.A67G						.						100	100	100					10																	115526208		2203	4300	6503	SO:0001583	missense	79949	exon3			GTCTGCAAACAAG	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"Pleckstrin homology (PH) domain containing"	26285	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 81"	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000369310.3:c.49A>G	chr10.hg19:g.115526208A>G	ENSP00000358316:p.Lys17Glu	178.0	0.0		79.0	4.0	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	hg19	CCDS53580.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.125332	0.77436	.	.	ENSG00000148735	ENST00000361048;ENST00000369310	T;T	0.32023	1.47;1.47	5.45	5.45	0.79879	.	0.264668	0.36482	N	0.002577	T	0.57315	0.2045	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;0.993	D;P	0.74674	0.984;0.84	T	0.60727	-0.7206	10	0.44086	T	0.13	-17.4847	13.7666	0.62999	1.0:0.0:0.0:0.0	.	17;23	Q5SXH7-5;Q5SXH7-4	.;.	E	23;17	ENSP00000354332:K23E;ENSP00000358316:K17E	ENSP00000354332:K23E	K	+	1	0	C10orf81	115516198	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.398000	0.66308	2.068000	0.61886	0.533000	0.62120	AAA	.	.		0.358	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889		G	115526208	A	G	115526208	3	3	44	1	0	0	0	0	1	0	0	0	1621	131	5	2	73	2	C10orf81	10	115526208	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	125024	115526208	20008539	246	5706										
ABLIM1	3983	hgsc.bcm.edu	37	chr10	116201493	116201493	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aatcttacccggtgaagcccAtttcttccatagccagggag	9	12	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:116201493A>G	ENST00000277895.5	-	18	2083	c.1986T>C	c.(1984-1986)aaT>aaC	p.N662N	ABLIM1_ENST00000533213.2_Silent_p.N602N|ABLIM1_ENST00000369266.3_Silent_p.N339N|ABLIM1_ENST00000369252.4_Silent_p.N602N|ABLIM1_ENST00000369253.2_Silent_p.N285N|ABLIM1_ENST00000392952.3_Silent_p.N339N	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	662					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		GGTGAAGCCCATTTCTTCCAT	0.428																																					p.N662N		Atlas-SNP	.											.	ABLIM1	131	.	0			c.T1986C						.						148	140	143					10																	116201493		2203	4300	6503	SO:0001819	synonymous_variant	3983	exon18			AAGCCCATTTCTT	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1986T>C	chr10.hg19:g.116201493A>G		123.0	0.0		75.0	4.0	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Silent	SNP	ENST00000277895.5	hg19	CCDS7590.1	.	.	.	.	.	.	.	.	.	.	A	10.47	1.358606	0.24598	.	.	ENSG00000099204	ENST00000392955	.	.	.	5.93	-0.75	0.11080	.	.	.	.	.	T	0.55529	0.1926	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48399	-0.9039	4	.	.	.	.	9.6473	0.39875	0.5941:0.0:0.4059:0.0	.	.	.	.	T	536	.	.	M	-	2	0	ABLIM1	116191483	0.786000	0.28738	0.847000	0.33407	0.997000	0.91878	0.060000	0.14342	-0.353000	0.08224	0.533000	0.62120	ATG	.	.		0.428	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			G	116201493	A	G	116201493	2	3	44	1	0	0	0	0	0	0	0	1	94	214	8	2		2	ABLIM1	10	116201493	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	675285	116201493	19333254	247	5707										
GFRA1	2674	hgsc.bcm.edu	37	chr10	118029096	118029096	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggaatcctccagcagatcatTtcctaaaaacaacagaaaga	6	10	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:118029096T>C	ENST00000355422.6	-	4	887	c.337A>G	c.(337-339)Aat>Gat	p.N113D	GFRA1_ENST00000490345.1_5'Flank|GFRA1_ENST00000369236.1_Missense_Mutation_p.N113D|GFRA1_ENST00000439649.3_Missense_Mutation_p.N113D	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	113					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		AGCAGATCATTTCCTAAAAAC	0.368																																					p.N113D	Ovarian(128;329 1725 45498 46808 50759)	Atlas-SNP	.											.	GFRA1	107	.	0			c.A337G						.						101	94	96					10																	118029096		2203	4300	6503	SO:0001583	missense	2674	exon4			GATCATTTCCTAA	AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.337A>G	chr10.hg19:g.118029096T>C	ENSP00000347591:p.Asn113Asp	94.0	0.0		60.0	5.0	NM_005264	A8KA21|O15507|O43912	Missense_Mutation	SNP	ENST00000355422.6	hg19	CCDS44481.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.581710	0.65992	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000369234	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.45296	0.1335	L	0.43152	1.355	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.986	T	0.20773	-1.0265	10	0.12430	T	0.62	-18.4179	15.9451	0.79787	0.0:0.0:0.0:1.0	.	113;113	P56159;P56159-2	GFRA1_HUMAN;.	D	113	ENSP00000393725:N113D;ENSP00000358239:N113D;ENSP00000347591:N113D;ENSP00000358237:N113D	ENSP00000347591:N113D	N	-	1	0	GFRA1	118019086	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.301000	0.78850	2.177000	0.69029	0.533000	0.62120	AAT	.	.		0.368	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793		C	118029096	T	C	118029096	3	2	44	1	0	0	0	0	1	0	0	0	6355	1841	64	2	1092	2	GFRA1	10	118029096	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1827603	118029096	17505651	248	5708										
SLC18A2	6571	hgsc.bcm.edu	37	chr10	119015120	119015120	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttgacagagtcagaaggggAcacccctaaccacgctgctg	11	13	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:119015120A>G	ENST00000298472.5	+	9	990	c.847A>G	c.(847-849)Aca>Gca	p.T283A	SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	283					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	TCAGAAGGGGACACCCCTAAC	0.607																																					p.T283A		Atlas-SNP	.											.	SLC18A2	58	.	0			c.A847G						.						58	59	59					10																	119015120		2203	4300	6503	SO:0001583	missense	6571	exon9			AAGGGGACACCCC	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"Solute carriers"	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.847A>G	chr10.hg19:g.119015120A>G	ENSP00000298472:p.Thr283Ala	48.0	0.0		33.0	4.0	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Missense_Mutation	SNP	ENST00000298472.5	hg19	CCDS7599.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.317942	0.40996	.	.	ENSG00000165646	ENST00000298472	T	0.56611	0.45	5.07	5.07	0.68467	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.51483	0.1677	L	0.56396	1.775	0.53005	D	0.999969	B	0.27498	0.18	B	0.37451	0.25	T	0.47045	-0.9147	10	0.22706	T	0.39	-18.7903	10.39	0.44162	0.9229:0.0:0.0771:0.0	.	283	Q05940	VMAT2_HUMAN	A	283	ENSP00000298472:T283A	ENSP00000298472:T283A	T	+	1	0	SLC18A2	119005110	1.000000	0.71417	0.996000	0.52242	0.815000	0.46073	7.365000	0.79537	2.027000	0.59764	0.460000	0.39030	ACA	.	.		0.607	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054		G	119015120	A	G	119015120	3	3	44	1	0	0	0	0	1	0	0	0	14441	275	10	2	877	2	SLC18A2	10	119015120	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	986024	119015120	16519627	249	5709										
PLEKHA1	59338	hgsc.bcm.edu	37	chr10	124172507	124172507	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggtgaatgtgggaaaaagcaAgtgtcttacagaactgatat	12	4	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:124172507A>G	ENST00000368990.3	+	6	545	c.414A>G	c.(412-414)caA>caG	p.Q138Q	PLEKHA1_ENST00000433307.1_Silent_p.Q138Q|PLEKHA1_ENST00000494222.1_3'UTR|PLEKHA1_ENST00000368988.1_Silent_p.Q138Q|PLEKHA1_ENST00000538022.1_Silent_p.Q138Q|PLEKHA1_ENST00000368989.2_Silent_p.Q138Q	NM_001001974.2	NP_001001974.1	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	138					androgen metabolic process (GO:0008209)|B cell receptor signaling pathway (GO:0050853)|cellular response to hydrogen peroxide (GO:0070301)|establishment of protein localization (GO:0045184)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|multicellular organism growth (GO:0035264)|negative regulation of protein kinase B signaling (GO:0051898)|palate development (GO:0060021)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|ruffle organization (GO:0031529)|skeletal system morphogenesis (GO:0048705)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GGAAAAAGCAAGTGTCTTACA	0.373																																					p.Q138Q		Atlas-SNP	.											.	PLEKHA1	33	.	0			c.A414G						.						133	121	125					10																	124172507		2203	4300	6503	SO:0001819	synonymous_variant	59338	exon6			AAAGCAAGTGTCT	AF286160	CCDS7629.1, CCDS55730.1	10q26.3	2013-01-10	2002-01-14		ENSG00000107679	ENSG00000107679		"Pleckstrin homology (PH) domain containing"	14335	protein-coding gene	gene with protein product	"tandem PH domain containing protein-1"	607772	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 1"			11001876, 15485858	Standard	NM_001001974		Approved	TAPP1	uc001lge.2	Q9HB21	OTTHUMG00000019184	ENST00000368990.3:c.414A>G	chr10.hg19:g.124172507A>G		179.0	0.0		79.0	4.0	NM_021622	B3KQ55|D3DRE2|Q9BVK0	Silent	SNP	ENST00000368990.3	hg19	CCDS7629.1																																																																																			.	.		0.373	PLEKHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050783.1	NM_001001974		G	124172507	A	G	124172507	2	3	44	1	0	0	0	0	0	0	0	1	12064	69	3	2		2	PLEKHA1	10	124172507	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	5157387	124172507	11362240	250	5710										
MKI67	4288	hgsc.bcm.edu	37	chr10	129899614	129899614	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgctgcaggctggctttttgTctttcttgatctcaggcaca	10	10	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr10:129899614T>C	ENST00000368654.3	-	14	9988	c.9613A>G	c.(9613-9615)Aca>Gca	p.T3205A	MKI67_ENST00000368653.3_Missense_Mutation_p.T2845A	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3205					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGGCTTTTTGTCTTTCTTGAT	0.493																																					p.T3205A		Atlas-SNP	.											.	MKI67	363	.	0			c.A9613G						.						152	134	140					10																	129899614		2203	4300	6503	SO:0001583	missense	4288	exon14			TTTTTGTCTTTCT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.9613A>G	chr10.hg19:g.129899614T>C	ENSP00000357643:p.Thr3205Ala	192.0	0.0		99.0	5.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.524706	0.27299	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01821	4.67;4.62	2.99	-5.98	0.02220	.	3.283010	0.01334	N	0.011353	T	0.01489	0.0048	N	0.24115	0.695	0.09310	N	1	B;B	0.22080	0.0;0.064	B;B	0.20955	0.001;0.032	T	0.44757	-0.9307	10	0.08381	T	0.77	.	9.5944	0.39565	0.0:0.5699:0.2547:0.1754	.	2845;3205	P46013-2;P46013	.;KI67_HUMAN	A	3205;2845;3204	ENSP00000357643:T3205A;ENSP00000357642:T2845A	ENSP00000357642:T2845A	T	-	1	0	MKI67	129789604	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.000000	0.03693	-2.878000	0.00320	-0.468000	0.05107	ACA	.	.		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		C	129899614	T	C	129899614	3	2	44	1	0	0	0	0	1	0	0	0	9607	1667	58	2	165	2	MKI67	10	129899614	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	5727107	129899614	5635133	251	5711										
LSP1	4046	hgsc.bcm.edu	37	chr11	1904750	1904750	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cccagaggacactgtccaggAcaacctgggggccgcagggg	16	13	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:1904750A>G	ENST00000311604.3	+	4	633	c.458A>G	c.(457-459)gAc>gGc	p.D153G	LSP1_ENST00000405957.2_Missense_Mutation_p.D91G|LSP1_ENST00000381775.1_Missense_Mutation_p.D281G|LSP1_ENST00000406638.2_Missense_Mutation_p.D91G|LSP1_ENST00000485341.1_3'UTR	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	153					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		ACTGTCCAGGACAACCTGGGG	0.632																																					p.D281G		Atlas-SNP	.											.	LSP1	59	.	0			c.A842G						.						49	54	52					11																	1904750		2202	4299	6501	SO:0001583	missense	4046	exon5			TCCAGGACAACCT	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.458A>G	chr11.hg19:g.1904750A>G	ENSP00000308383:p.Asp153Gly	179.0	0.0		146.0	6.0	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Missense_Mutation	SNP	ENST00000311604.3	hg19	CCDS31334.1	.	.	.	.	.	.	.	.	.	.	.	7.130	0.579794	0.13686	.	.	ENSG00000130592	ENST00000311604;ENST00000446808;ENST00000381775;ENST00000405957;ENST00000457279;ENST00000429923;ENST00000406638;ENST00000417766;ENST00000432093	T;T;T;T;T;T;T;T;T	0.48836	1.76;0.8;1.69;1.76;1.76;0.92;1.76;1.81;1.81	2.13	-0.301	0.12800	.	0.637869	0.11587	N	0.549162	T	0.12390	0.0301	N	0.00583	-1.355	0.19575	N	0.999967	B;B	0.12630	0.006;0.0	B;B	0.08055	0.003;0.0	T	0.24693	-1.0153	10	0.22109	T	0.4	.	2.5753	0.04805	0.5083:0.2788:0.213:0.0	.	281;153	E9PFP3;P33241	.;LSP1_HUMAN	G	153;91;281;91;144;136;91;91;91	ENSP00000308383:D153G;ENSP00000402543:D91G;ENSP00000371194:D281G;ENSP00000383932:D91G;ENSP00000400346:D144G;ENSP00000400999:D136G;ENSP00000384022:D91G;ENSP00000416363:D91G;ENSP00000412405:D91G	ENSP00000308383:D153G	D	+	2	0	LSP1	1861326	0.124000	0.22315	0.077000	0.20336	0.077000	0.17291	-0.045000	0.12003	-0.057000	0.13199	0.375000	0.23000	GAC	.	.		0.632	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339		G	1904750	A	G	1904750	3	3	44	1	0	0	0	0	1	0	0	0	9072	275	10	2	472	2	LSP1	11	1904750	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10		1904750	133101766	252	5712										
FAM160A2	84067	hgsc.bcm.edu	37	chr11	6244470	6244470	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgagccctgtggccagcaccTatgagaagttaccaaaagct	10	11	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:6244470T>C	ENST00000449352.2	-	4	1041		c.e4-2		FAM160A2_ENST00000265978.4_Splice_Site|FAM160A2_ENST00000524416.1_Splice_Site			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2						early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GGCCAGCACCTATGAGAAGTT	0.453																																					.		Atlas-SNP	.											.	FAM160A2	100	.	0			c.778-2A>G						.						72	74	73					11																	6244470		2201	4296	6497	SO:0001630	splice_region_variant	84067	exon5			AGCACCTATGAGA		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 56"	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.778-2A>G	chr11.hg19:g.6244470T>C		94.0	0.0		96.0	4.0	NM_001098794	Q9C0A4|Q9H0N3|Q9H624	Splice_Site	SNP	ENST00000449352.2	hg19	CCDS44530.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.521942	0.64747	.	.	ENSG00000051009	ENST00000449352;ENST00000442917;ENST00000265978;ENST00000524416	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4376	0.67293	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAM160A2	6201046	1.000000	0.71417	0.989000	0.46669	0.846000	0.48090	5.745000	0.68672	2.205000	0.71048	0.528000	0.53228	.	.	.		0.453	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127	Intron	C	6244470	T	C	6244470	5	2	44	1	0	0	0	0	0	0	1	0	5474	1536	53	2	2220	2	FAM160A2	11	6244470	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4339720	6244470	128762046	253	5713										
LDHC	3948	hgsc.bcm.edu	37	chr11	18467858	18467858	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaaaaatcttaggagagtgcAcccagtttccaccatggtta	9	9	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:18467858A>G	ENST00000541669.1	+	7	923	c.812A>G	c.(811-813)cAc>cGc	p.H271R	LDHC_ENST00000546146.1_Intron|LDHC_ENST00000536880.1_Missense_Mutation_p.H257R|LDHC_ENST00000535809.1_Intron|LDHC_ENST00000544105.1_Intron|LDHC_ENST00000537486.1_Intron|LDHC_ENST00000280704.4_Missense_Mutation_p.H271R			P07864	LDHC_HUMAN	lactate dehydrogenase C	271					ATP biosynthetic process (GO:0006754)|cellular carbohydrate metabolic process (GO:0044262)|lactate biosynthetic process from pyruvate (GO:0019244)|lactate oxidation (GO:0019516)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|motile cilium (GO:0031514)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGGAGAGTGCACCCAGTTTCC	0.383																																					p.H271R		Atlas-SNP	.											.	LDHC	37	.	0			c.A812G						.						147	145	146					11																	18467858		2199	4293	6492	SO:0001583	missense	3948	exon7			GAGTGCACCCAGT	AY286300	CCDS7840.1	11p15.1	2012-10-02			ENSG00000166796	ENSG00000166796	1.1.1.27		6544	protein-coding gene	gene with protein product	"cancer/testis antigen 32"	150150					Standard	NM_002301		Approved	CT32	uc001mom.4	P07864	OTTHUMG00000167722	ENST00000541669.1:c.812A>G	chr11.hg19:g.18467858A>G	ENSP00000437783:p.His271Arg	84.0	0.0		108.0	5.0	NM_002301	D3DQY4|Q6GSG8|Q7Z7J4	Missense_Mutation	SNP	ENST00000541669.1	hg19	CCDS7840.1	.	.	.	.	.	.	.	.	.	.	A	17.23	3.337946	0.60963	.	.	ENSG00000166796	ENST00000541669;ENST00000280704;ENST00000536880	T;T;T	0.66638	-0.22;-0.22;-0.22	4.88	3.72	0.42706	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.78742	0.4331	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79531	-0.1765	10	0.56958	D	0.05	-16.9389	8.6746	0.34172	0.9086:0.0:0.0914:0.0	.	271	P07864	LDHC_HUMAN	R	271;271;257	ENSP00000437783:H271R;ENSP00000280704:H271R;ENSP00000439555:H257R	ENSP00000280704:H271R	H	+	2	0	LDHC	18424434	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	8.285000	0.89914	2.045000	0.60652	0.459000	0.35465	CAC	.	.		0.383	LDHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395892.1	NM_017448		G	18467858	A	G	18467858	3	3	44	1	0	0	0	0	1	0	0	0	8711	159	6	2	834	2	LDHC	11	18467858	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	12223388	18467858	116538658	254	5714										
PRDM11	56981	hgsc.bcm.edu	37	chr11	45204634	45204634	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cggcccctatgaggggcagaTctccacccaggacaaatcag	11	14	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:45204634T>C	ENST00000530656.1	+	4	548	c.548T>C	c.(547-549)aTc>aCc	p.I183T	PRDM11_ENST00000528980.1_3'UTR|PRDM11_ENST00000263765.4_Missense_Mutation_p.I183T|PRDM11_ENST00000424263.2_Missense_Mutation_p.I149T			Q9NQV5	PRD11_HUMAN	PR domain containing 11	183	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						GAGGGGCAGATCTCCACCCAG	0.562											OREG0020926	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I149T	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											.	PRDM11	53	.	0			c.T446C						.						59	59	59					11																	45204634		2203	4299	6502	SO:0001583	missense	56981	exon4			GGCAGATCTCCAC	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"PR-domain containing protein 11"						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.548T>C	chr11.hg19:g.45204634T>C	ENSP00000435976:p.Ile183Thr	112.0	0.0	929	100.0	4.0	NM_001256695	Q8N9F1	Missense_Mutation	SNP	ENST00000530656.1	hg19		.	.	.	.	.	.	.	.	.	.	T	21.0	4.077491	0.76528	.	.	ENSG00000019485	ENST00000263765;ENST00000530656;ENST00000526442;ENST00000424263	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.02	5.02	0.67125	SET domain (2);	0.000000	0.64402	D	0.000006	T	0.53818	0.1820	M	0.64567	1.98	0.42188	D	0.991719	P	0.48694	0.914	B	0.44044	0.439	T	0.61227	-0.7105	10	0.62326	D	0.03	-24.9399	13.302	0.60330	0.0:0.0:0.0:1.0	.	183	Q9NQV5	PRD11_HUMAN	T	183;183;149;149	ENSP00000263765:I183T;ENSP00000435976:I183T;ENSP00000431898:I149T;ENSP00000394314:I149T	ENSP00000263765:I183T	I	+	2	0	PRDM11	45161210	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.081000	0.76844	1.877000	0.54381	0.397000	0.26171	ATC	.	.		0.562	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229		C	45204634	T	C	45204634	3	2	44	1	0	0	0	0	1	0	0	0	12464	1435	50	2	562	2	PRDM11	11	45204634	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	26736776	45204634	89801882	255	5715										
OR4C12	283093	hgsc.bcm.edu	37	chr11	50003747	50003747	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atgtgttctgcataggcttgAgccatacacccattaaagga	9	9	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:50003747A>T	ENST00000335238.4	-	1	324	c.291T>A	c.(289-291)gcT>gcA	p.A97A		NM_001005270.2	NP_001005270.2	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C, member 12	97						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(4)|large_intestine(3)|liver(1)|lung(19)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	36						CATAGGCTTGAGCCATACACC	0.418																																					p.A97A		Atlas-SNP	.											.	OR4C12	82	.	0			c.T291A						.						123	123	123					11																	50003747		2201	4296	6497	SO:0001819	synonymous_variant	283093	exon1			GGCTTGAGCCATA	BK004413	CCDS31496.1	11p11.12	2012-08-09			ENSG00000221954	ENSG00000221954		"GPCR / Class A : Olfactory receptors"	15168	protein-coding gene	gene with protein product							Standard	NM_001005270		Approved		uc010ria.2	Q96R67	OTTHUMG00000166687	ENST00000335238.4:c.291T>A	chr11.hg19:g.50003747A>T		224.0	0.0		209.0	99.0	NM_001005270	B2RNF0|Q6IF49	Silent	SNP	ENST00000335238.4	hg19	CCDS31496.1																																																																																			.	.		0.418	OR4C12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391104.1	NM_001005270		T	50003747	A	T	50003747	2	4	44	1	0	0	0	0	0	0	0	1	11055	291	11	4		4	OR4C12	11	50003747	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	4799113	50003747	85002769	256	5716										
OR5W2	390148	hgsc.bcm.edu	37	chr11	55681562	55681562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cattagacccacagaagcatAggcggaaggccagtgtcata	11	10	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:55681562A>G	ENST00000344514.1	-	1	496	c.497T>C	c.(496-498)cTa>cCa	p.L166P		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						ACAGAAGCATAGGCGGAAGGC	0.428																																					p.L166P	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.,1	OR5W2	112	.	0			c.T497C						.						88	78	81					11																	55681562		2201	4296	6497	SO:0001583	missense	390148	exon1			AAGCATAGGCGGA	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"GPCR / Class A : Olfactory receptors"	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.497T>C	chr11.hg19:g.55681562A>G	ENSP00000342448:p.Leu166Pro	101.0	0.0		99.0	4.0	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	hg19	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	A	11.36	1.615401	0.28801	.	.	ENSG00000187612	ENST00000344514	T	0.00301	8.21	4.77	4.77	0.60923	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31472	N	0.007581	T	0.01387	0.0045	H	0.99261	4.49	0.23023	N	0.998411	D	0.89917	1.0	D	0.91635	0.999	T	0.25641	-1.0126	10	0.87932	D	0	.	12.2509	0.54597	1.0:0.0:0.0:0.0	.	166	Q8NH69	OR5W2_HUMAN	P	166	ENSP00000342448:L166P	ENSP00000342448:L166P	L	-	2	0	OR5W2	55438138	0.213000	0.23551	0.031000	0.17742	0.065000	0.16274	4.611000	0.61162	1.781000	0.52344	0.448000	0.29417	CTA	.	.		0.428	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		G	55681562	A	G	55681562	3	3	44	1	0	0	0	0	1	0	0	0	11194	420	15	2	437	2	OR5W2	11	55681562	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	5677815	55681562	79324954	257	5717										
P2RX3	5024	hgsc.bcm.edu	37	chr11	57114119	57114119	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cggactctacgccaacagagTcatggatgtgtctgattacg	11	10	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:57114119T>C	ENST00000263314.2	+	2	255	c.221T>C	c.(220-222)gTc>gCc	p.V74A		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	74					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						GCCAACAGAGTCATGGATGTG	0.552																																					p.V74A		Atlas-SNP	.											.	P2RX3	55	.	0			c.T221C						.						136	95	109					11																	57114119		2201	4296	6497	SO:0001583	missense	5024	exon2			ACAGAGTCATGGA	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.221T>C	chr11.hg19:g.57114119T>C	ENSP00000263314:p.Val74Ala	138.0	0.0		144.0	6.0	NM_002559	Q6DK37|Q9UQB6	Missense_Mutation	SNP	ENST00000263314.2	hg19	CCDS7953.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.823015	0.90873	.	.	ENSG00000109991	ENST00000439993;ENST00000263314	T	0.05996	3.36	4.66	4.66	0.58398	.	0.141200	0.48767	D	0.000169	T	0.24509	0.0594	M	0.85373	2.75	0.41368	D	0.987477	D	0.63046	0.992	P	0.62740	0.906	T	0.02411	-1.1163	10	0.87932	D	0	-34.7111	11.7302	0.51732	0.0:0.0:0.0:1.0	.	74	P56373	P2RX3_HUMAN	A	74	ENSP00000263314:V74A	ENSP00000263314:V74A	V	+	2	0	P2RX3	56870695	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.838000	0.75359	1.950000	0.56595	0.459000	0.35465	GTC	.	.		0.552	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559		C	57114119	T	C	57114119	3	2	44	1	0	0	0	0	1	0	0	0	11350	1667	58	2	227	2	P2RX3	11	57114119	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1432557	57114119	77892397	258	5718										
SLC22A9	114571	hgsc.bcm.edu	37	chr11	63149671	63149671	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaaagaactggaggcagcacAaaaaaaaaaaccttctctgt	7	8	1	1	rs564236291|rs76547355|rs78765214	byFrequency	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:63149671A>C	ENST00000279178.3	+	6	1244	c.995A>C	c.(994-996)cAa>cCa	p.Q332P	SLC22A9_ENST00000310969.4_3'UTR	NM_080866.2	NP_543142.2	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion transporter), member 9	332					hormone transport (GO:0009914)|short-chain fatty acid import (GO:0015913)|sodium-independent organic anion transport (GO:0043252)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	anion:anion antiporter activity (GO:0015301)|short-chain fatty acid uptake transporter activity (GO:0015636)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	18						GAGGCAGCACAAAAAAAAAAA	0.398																																					p.Q332P		Atlas-SNP	.											.,5	SLC22A9	77	.	0			c.A995C						.						133	130	131					11																	63149671		2201	4298	6499	SO:0001583	missense	114571	exon6			CAGCACAAAAAAA	AP001880	CCDS8043.1	11q12.3	2014-05-20	2008-01-11		ENSG00000149742	ENSG00000149742		"Solute carriers"	16261	protein-coding gene	gene with protein product		607579				11327718, 17393504	Standard	NM_080866		Approved	OAT4, FLJ23666, UST3, OAT7	uc001nww.3	Q8IVM8	OTTHUMG00000167805	ENST00000279178.3:c.995A>C	chr11.hg19:g.63149671A>C	ENSP00000279178:p.Gln332Pro	117.0	1.0		123.0	7.0	NM_080866	A0AVB7|A4PB24|Q8TCC8|Q8TEC0|Q8WYN7	Missense_Mutation	SNP	ENST00000279178.3	hg19	CCDS8043.1	.	.	.	.	.	.	.	.	.	.	A	10.94	1.493804	0.26774	.	.	ENSG00000149742	ENST00000279178	T	0.58940	0.3	0.0465	0.0465	0.14256	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	3.812700	0.01193	N	0.007392	T	0.54854	0.1884	N	0.08118	0	0.09310	N	1	D	0.67145	0.996	D	0.67725	0.953	T	0.50591	-0.8810	9	0.38643	T	0.18	.	.	.	.	.	332	Q8IVM8	S22A9_HUMAN	P	332	ENSP00000279178:Q332P	ENSP00000279178:Q332P	Q	+	2	0	SLC22A9	62906247	0.001000	0.12720	0.005000	0.12908	0.600000	0.36913	0.132000	0.15891	0.115000	0.18071	0.113000	0.15668	CAA	.	A|0.500;C|0.500		0.398	SLC22A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396371.1	NM_080866		C	63149671	A	C	63149671	3	2	44	1	0	0	0	0	1	0	0	0	14476	130	5	5	1017	5	SLC22A9	11	63149671	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	6035552	63149671	71856845	259	5719										
MUS81	80198	hgsc.bcm.edu	37	chr11	65632582	65632582	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tctctgctcactcctcacctTcagtgacttcaacgcaggag	7	15	5	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:65632582T>C	ENST00000308110.4	+	13	1716	c.1367T>C	c.(1366-1368)tTc>tCc	p.F456S	EFEMP2_ENST00000532648.1_5'Flank|MUS81_ENST00000533035.1_Missense_Mutation_p.F381S	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	456					DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		CTCCTCACCTTCAGTGACTTC	0.602								Homologous recombination																													p.F456S		Atlas-SNP	.											.	MUS81	68	.	0			c.T1367C						.						158	167	164					11																	65632582		2201	4296	6497	SO:0001583	missense	80198	exon13			TCACCTTCAGTGA		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"	606591	"MUS81 endonuclease homolog (yeast)", "MUS81 endonuclease homolog (S. cerevisiae)"			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.1367T>C	chr11.hg19:g.65632582T>C	ENSP00000307853:p.Phe456Ser	124.0	0.0		108.0	5.0	NM_025128	Q9H7D9	Missense_Mutation	SNP	ENST00000308110.4	hg19	CCDS8115.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.741650	0.89573	.	.	ENSG00000172732	ENST00000533035;ENST00000308110;ENST00000437855	T;T	0.19394	2.15;2.36	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.52370	0.1730	M	0.89287	3.02	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.60786	-0.7194	10	0.87932	D	0	-22.5993	12.7462	0.57283	0.0:0.0:0.0:1.0	.	456	Q96NY9	MUS81_HUMAN	S	381;456;456	ENSP00000432287:F381S;ENSP00000307853:F456S	ENSP00000307853:F456S	F	+	2	0	MUS81	65389158	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.334000	0.72944	2.265000	0.75225	0.459000	0.35465	TTC	.	.		0.602	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128		C	65632582	T	C	65632582	3	2	44	1	0	0	0	0	1	0	0	0	9997	1783	62	2	1417	2	MUS81	11	65632582	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2482911	65632582	69373934	260	5720										
C11orf80	79703	hgsc.bcm.edu	37	chr11	66581347	66581347	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	caactacacatatttctataTggacctttgggtctgcctct	6	11	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:66581347T>C	ENST00000360962.4	+	10	1057	c.1050T>C	c.(1048-1050)taT>taC	p.Y350Y	C11orf80_ENST00000540737.1_Silent_p.Y185Y|C11orf80_ENST00000532565.2_Silent_p.Y132Y|C11orf80_ENST00000346672.4_Silent_p.Y196Y|C11orf80_ENST00000525449.2_Silent_p.Y195Y|C11orf80_ENST00000527634.1_Silent_p.Y133Y	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	350										autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						TATTTCTATATGGACCTTTGG	0.353																																					p.Y350Y		Atlas-SNP	.											.	C11orf80	31	.	0			c.T1050C						.						80	74	75					11																	66581347		1830	4078	5908	SO:0001819	synonymous_variant	79703	exon10			TCTATATGGACCT			11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.1050T>C	chr11.hg19:g.66581347T>C		90.0	0.0		98.0	4.0	NM_024650	Q9H677	Silent	SNP	ENST00000360962.4	hg19	CCDS53664.1																																																																																			.	.		0.353	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024650		C	66581347	T	C	66581347	2	2	44	1	0	0	0	0	0	0	0	1	1666	1471	51	2		2	C11orf80	11	66581347	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	948765	66581347	68425169	261	5721										
CPT1A	1374	hgsc.bcm.edu	37	chr11	68530124	68530124	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cgggtccaccatggcccgcaCgaagtcgcatgactcagtgg	13	14	1	1	rs573452454		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:68530124C>T	ENST00000265641.5	-	15	2000	c.1846G>A	c.(1846-1848)Gtg>Atg	p.V616M	CPT1A_ENST00000539743.1_Missense_Mutation_p.V616M|CPT1A_ENST00000376618.2_Missense_Mutation_p.V616M|CPT1A_ENST00000540367.1_Missense_Mutation_p.V616M|CPT1A_ENST00000537756.2_5'UTR	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	616					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	ATGGCCCGCACGAAGTCGCAT	0.607													C|||	1	0.000199681	8e-04	0	5008	,	,		18473	0		0	False		,,,				2504	0				p.V616M		Atlas-SNP	.											.	CPT1A	89	.	0			c.G1846A						.						73	65	68					11																	68530124		2200	4294	6494	SO:0001583	missense	1374	exon15			CCCGCACGAAGTC	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.1846G>A	chr11.hg19:g.68530124C>T	ENSP00000265641:p.Val616Met	80.0	0.0		84.0	34.0	NM_001876	Q8TCU0|Q9BWK0	Missense_Mutation	SNP	ENST00000265641.5	hg19	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.572108	0.86542	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	D;D;D;D	0.83914	-1.78;-1.78;-1.78;-1.78	5.57	5.57	0.84162	.	0.133714	0.50627	D	0.000102	D	0.94023	0.8085	H	0.95260	3.645	0.80722	D	1	D;D	0.89917	0.994;1.0	D;D	0.68943	0.915;0.961	D	0.95158	0.8279	10	0.87932	D	0	.	19.912	0.97027	0.0:1.0:0.0:0.0	.	616;616	P50416;P50416-2	CPT1A_HUMAN;.	M	616	ENSP00000439084:V616M;ENSP00000365803:V616M;ENSP00000265641:V616M;ENSP00000446108:V616M	ENSP00000265641:V616M	V	-	1	0	CPT1A	68286700	1.000000	0.71417	0.967000	0.41034	0.444000	0.32077	7.354000	0.79424	2.783000	0.95769	0.655000	0.94253	GTG	.	.		0.607	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876		T	68530124	C	T	68530124	3	4	44	1	0	0	0	0	1	0	0	0	3833	536	19	1	535	1	CPT1A	11	68530124	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1948777	68530124	66476392	262	5722										
CTTN	2017	hgsc.bcm.edu	37	chr11	70279767	70279767	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttttagaggacagcacctacGatgagtacgagaacgatctg	11	8	1	3	rs144726386		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:70279767G>T	ENST00000301843.8	+	17	1665	c.1459G>T	c.(1459-1461)Gat>Tat	p.D487Y	CTTN_ENST00000346329.3_Missense_Mutation_p.D450Y|CTTN_ENST00000376561.3_Missense_Mutation_p.D450Y|CTTN_ENST00000538675.1_Missense_Mutation_p.D171Y	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	487					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)		p.D487N(1)|p.D450N(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		CAGCACCTACGATGAGTACGA	0.537																																					p.D487Y		Atlas-SNP	.											CTTN_ENST00000376561,NS,carcinoma,0,2	CTTN	162	.	2	Substitution - Missense(2)	cervix(2)	c.G1459T						.						153	147	149					11																	70279767		2200	4294	6494	SO:0001583	missense	2017	exon17			ACCTACGATGAGT	AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.1459G>T	chr11.hg19:g.70279767G>T	ENSP00000301843:p.Asp487Tyr	163.0	1.0		167.0	0.0	NM_005231	Q8N707|Q96H99	Missense_Mutation	SNP	ENST00000301843.8	hg19	CCDS41680.1	.	.	.	.	.	.	.	.	.	.	G	8.931	0.963545	0.18583	.	.	ENSG00000085733	ENST00000346329;ENST00000301843;ENST00000376561;ENST00000538675;ENST00000529736	T;T;T;T;T	0.35048	1.4;1.4;1.33;1.7;1.69	4.96	4.04	0.47022	Src homology-3 domain (1);	0.231118	0.36409	N	0.002619	T	0.53222	0.1783	L	0.52759	1.655	0.48185	D	0.999608	D;D;D;B	0.89917	1.0;0.999;0.996;0.426	D;D;D;B	0.97110	1.0;0.997;0.956;0.044	T	0.50659	-0.8802	10	0.38643	T	0.18	-26.7345	15.244	0.73493	0.0:0.1412:0.8588:0.0	.	171;450;487;450	B4E358;Q96H99;Q14247;Q8N707	.;.;SRC8_HUMAN;.	Y	450;487;450;171;144	ENSP00000317189:D450Y;ENSP00000301843:D487Y;ENSP00000365745:D450Y;ENSP00000439762:D171Y;ENSP00000431421:D144Y	ENSP00000301843:D487Y	D	+	1	0	CTTN	69957415	0.692000	0.27719	0.014000	0.15608	0.017000	0.09413	2.595000	0.46197	1.058000	0.40530	-0.180000	0.13094	GAT	.	G|1.000;A|0.000		0.537	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		T	70279767	G	T	70279767	3	4	44	1	0	0	0	0	1	0	0	0	4046	1058	37	1	1517	1	CTTN	11	70279767	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	1749643	70279767	64726749	263	5723										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73020687	73020687	+	Frame_Shift_Del	DEL	C	C	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcccccaacatctccaagagCccctagagaagaaggactcc							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:73020687delC	ENST00000263674.3	+	1	1354	c.1004delC	c.(1003-1005)gccfs	p.A335fs	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	335					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						TCTCCAAGAGCCCCTAGAGAA	0.592																																					p.A335fs		Atlas-INDEL	.											.	ARHGEF17	117	.	0			c.1003delG						.						47	57	54					11																	73020687		2176	4249	6425	SO:0001589	frameshift_variant	9828	exon1			.	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.1004delC	chr11.hg19:g.73020687delC	ENSP00000263674:p.Ala335fs	97.0	0.0		133.0	10.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Frame_Shift_Del	DEL	ENST00000263674.3	hg19	CCDS8221.1																																																																																			.	.		0.592	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		-	73020687	C	-	73020687	7	5	44	1	0	1	0	1	0	0	0	0	900	739	26	0	1006	0	ARHGEF17	11	73020687	Frame_Shift_Del	DEL	C	TCGA-BC-A3KG-01A-11D-A20W-10	2740920	73020687	61985829	264	5724										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73817537	73817537	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acacagatccaatgacttctGgctgagaaagaaggaaagag	11	7	1	5	rs555646012	byFrequency	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:73817537G>A	ENST00000334126.7	-	13	2190	c.1964C>T	c.(1963-1965)cCa>cTa	p.P655L	C2CD3_ENST00000313663.7_Splice_Site_p.P655L			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	655					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					AATGACTTCTGGCTGAGAAAG	0.383																																					p.P655L		Atlas-SNP	.											.	C2CD3	288	.	0			c.C1964T						.						64	62	63					11																	73817537		2200	4293	6493	SO:0001630	splice_region_variant	26005	exon13			ACTTCTGGCTGAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1963-1C>T	chr11.hg19:g.73817537G>A		111.0	0.0		99.0	4.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	G	22.9	4.355025	0.82243	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.21543	2.0;2.07	5.47	5.47	0.80525	.	0.058059	0.64402	D	0.000001	T	0.43322	0.1242	M	0.68952	2.095	0.52099	D	0.99994	D	0.69078	0.997	P	0.61132	0.884	T	0.29458	-1.0011	10	0.87932	D	0	-11.5497	17.4704	0.87645	0.0:0.0:1.0:0.0	.	655	Q4AC94-1	.	L	655	ENSP00000334379:P655L;ENSP00000323339:P655L	ENSP00000323339:P655L	P	-	2	0	C2CD3	73495185	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	6.069000	0.71209	2.728000	0.93425	0.591000	0.81541	CCA	.	.		0.383	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	Missense_Mutation	A	73817537	G	A	73817537	5	1	44	1	0	0	0	0	0	0	1	0	2156	1362	47	3	4003	3	C2CD3	11	73817537	Splice_Site	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	796850	73817537	61188979	265	5725										
SERPINH1	871	hgsc.bcm.edu	37	chr11	75277809	75277809	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gccgactgtacggacccagcTcagtgagcttcgctgatgac	12	13	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:75277809T>C	ENST00000524558.1	+	2	1850	c.415T>C	c.(415-417)Tca>Cca	p.S139P	SERPINH1_ENST00000533603.1_Missense_Mutation_p.S139P|SERPINH1_ENST00000358171.3_Missense_Mutation_p.S139P|SERPINH1_ENST00000525876.1_5'Flank|SERPINH1_ENST00000530284.1_Missense_Mutation_p.S139P			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	139					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					CGGACCCAGCTCAGTGAGCTT	0.642																																					p.S139P		Atlas-SNP	.											.	SERPINH1	33	.	0			c.T415C						.						38	35	36					11																	75277809		2200	4292	6492	SO:0001583	missense	871	exon2			CCCAGCTCAGTGA	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"Serine (or cysteine) peptidase inhibitors"	1546	protein-coding gene	gene with protein product		600943	"serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2", "serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.415T>C	chr11.hg19:g.75277809T>C	ENSP00000434412:p.Ser139Pro	167.0	0.0		154.0	7.0	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Missense_Mutation	SNP	ENST00000524558.1	hg19	CCDS8239.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.453767	0.63290	.	.	ENSG00000149257	ENST00000533603;ENST00000358171;ENST00000526397;ENST00000421448;ENST00000529643;ENST00000525492;ENST00000530284;ENST00000532356;ENST00000524558;ENST00000528990;ENST00000533449;ENST00000525611;ENST00000528760	D;D;D;T;T;D;D;D;T;D;D	0.88586	-2.4;-2.4;-2.4;-0.97;-0.97;-2.4;-2.4;-2.4;-0.97;-2.4;-2.4	4.98	4.98	0.66077	Serpin domain (3);	0.056941	0.64402	D	0.000001	D	0.93628	0.7965	M	0.79258	2.445	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.70487	0.969;0.941	D	0.94288	0.7526	10	0.87932	D	0	.	12.9296	0.58280	0.0:0.0:0.0:1.0	.	139;139	E9PPV6;P50454	.;SERPH_HUMAN	P	139;139;139;118;139;92;139;139;139;139;139;139;139	ENSP00000434657:S139P;ENSP00000350894:S139P;ENSP00000434964:S139P;ENSP00000435936:S139P;ENSP00000434482:S92P;ENSP00000436305:S139P;ENSP00000436040:S139P;ENSP00000434412:S139P;ENSP00000431827:S139P;ENSP00000435452:S139P;ENSP00000437108:S139P	ENSP00000350894:S139P	S	+	1	0	SERPINH1	74955457	1.000000	0.71417	0.995000	0.50966	0.800000	0.45204	4.004000	0.57068	2.000000	0.58554	0.460000	0.39030	TCA	.	.		0.642	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353		C	75277809	T	C	75277809	3	2	44	1	0	0	0	0	1	0	0	0	14132	1551	54	2	417	2	SERPINH1	11	75277809	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1460272	75277809	59728707	266	5726										
NAALAD2	10003	hgsc.bcm.edu	37	chr11	89892488	89892488	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agtatcggacctggctttacAgggagtgattctttcaggta	12	7	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:89892488A>G	ENST00000534061.1	+	8	1202	c.972A>G	c.(970-972)acA>acG	p.T324T	NAALAD2_ENST00000375944.3_Intron|NAALAD2_ENST00000321955.4_Intron|NAALAD2_ENST00000525171.1_Intron	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	324	NAALADase.				neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CTGGCTTTACAGGGAGTGATT	0.368																																					p.T324T		Atlas-SNP	.											.	NAALAD2	113	.	0			c.A972G						.						127	122	123					11																	89892488		2201	4299	6500	SO:0001819	synonymous_variant	10003	exon8			CTTTACAGGGAGT	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.972A>G	chr11.hg19:g.89892488A>G		122.0	0.0		126.0	6.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Silent	SNP	ENST00000534061.1	hg19	CCDS8288.1																																																																																			.	.		0.368	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		G	89892488	A	G	89892488	2	3	44	1	0	0	0	0	0	0	0	1	10137	175	7	2		2	NAALAD2	11	89892488	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	14614679	89892488	45114028	267	5727										
GPR83	10888	hgsc.bcm.edu	37	chr11	94113691	94113691	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	accagcagagggcaaagaggActaccaccagcatcaacatc	9	13	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:94113691A>G	ENST00000243673.2	-	4	1067	c.896T>C	c.(895-897)gTc>gCc	p.V299A	GPR83_ENST00000539203.2_Missense_Mutation_p.V257A	NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83	299					response to glucocorticoid (GO:0051384)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GGCAAAGAGGACTACCACCAG	0.532																																					p.V299A		Atlas-SNP	.											.	GPR83	47	.	0			c.T896C						.						147	103	118					11																	94113691		2201	4298	6499	SO:0001583	missense	10888	exon4			AAGAGGACTACCA	AF236081	CCDS8297.1	11q21	2012-08-21	2003-07-30	2003-08-01	ENSG00000123901	ENSG00000123901		"GPCR / Class A : Orphans"	4523	protein-coding gene	gene with protein product		605569	"G protein-coupled receptor 72"	GPR72		10760605, 11060465	Standard	NM_016540		Approved		uc001pet.2	Q9NYM4	OTTHUMG00000167779	ENST00000243673.2:c.896T>C	chr11.hg19:g.94113691A>G	ENSP00000243673:p.Val299Ala	150.0	0.0		123.0	7.0	NM_016540	B0M0K5|Q6NWR4|Q9P1Y8	Missense_Mutation	SNP	ENST00000243673.2	hg19	CCDS8297.1	.	.	.	.	.	.	.	.	.	.	A	9.765	1.171005	0.21621	.	.	ENSG00000123901	ENST00000243673;ENST00000539203	T;T	0.59906	0.23;0.23	5.21	5.21	0.72293	GPCR, rhodopsin-like superfamily (1);	0.184952	0.46758	D	0.000280	T	0.43478	0.1249	N	0.26162	0.8	0.38212	D	0.94049	B	0.14012	0.009	B	0.23419	0.046	T	0.38585	-0.9654	10	0.10111	T	0.7	.	13.9262	0.63964	1.0:0.0:0.0:0.0	.	299	Q9NYM4	GPR83_HUMAN	A	299;257	ENSP00000243673:V299A;ENSP00000441550:V257A	ENSP00000243673:V299A	V	-	2	0	GPR83	93753339	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.767000	0.55288	1.967000	0.57214	0.533000	0.62120	GTC	.	.		0.532	GPR83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396232.1	NM_016540		G	94113691	A	G	94113691	3	3	44	1	0	0	0	0	1	0	0	0	6721	275	10	2	379	2	GPR83	11	94113691	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	4221203	94113691	40892825	268	5728										
ALKBH8	91801	hgsc.bcm.edu	37	chr11	107396182	107396182	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttactacagttacaaggtgTttgcctcactttcctaaatg	6	10	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:107396182T>C	ENST00000428149.2	-	9	1166	c.1015A>G	c.(1015-1017)Aca>Gca	p.T339A	ALKBH8_ENST00000429370.1_Intron|ALKBH8_ENST00000417449.2_Missense_Mutation_p.T342A|ALKBH8_ENST00000389568.3_Missense_Mutation_p.T339A	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	339					cellular response to DNA damage stimulus (GO:0006974)|tRNA methylation (GO:0030488)	cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|RNA binding (GO:0003723)|tRNA (uracil) methyltransferase activity (GO:0016300)			breast(2)|large_intestine(2)|lung(5)	9		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)		TTACAAGGTGTTTGCCTCACT	0.373																																					p.T339A		Atlas-SNP	.											.	ALKBH8	88	.	0			c.A1015G						.						141	115	123					11																	107396182		692	1591	2283	SO:0001583	missense	91801	exon9			AAGGTGTTTGCCT	AF086489	CCDS8337.2, CCDS73376.1	11q22.3	2013-10-04			ENSG00000137760	ENSG00000137760	2.1.1.229	"Alkylation repair homologs", "RNA binding motif (RRM) containing"	25189	protein-coding gene	gene with protein product		613306				20123966	Standard	NM_138775		Approved	MGC10235	uc009yxp.3	Q96BT7	OTTHUMG00000157008	ENST00000428149.2:c.1015A>G	chr11.hg19:g.107396182T>C	ENSP00000415885:p.Thr339Ala	106.0	0.0		99.0	4.0	NM_138775	B1Q2M0|B4DEF6|Q8N989	Missense_Mutation	SNP	ENST00000428149.2	hg19	CCDS8337.2	.	.	.	.	.	.	.	.	.	.	T	6.172	0.399869	0.11696	.	.	ENSG00000137760	ENST00000428149;ENST00000389568;ENST00000417449	T;T;T	0.43294	0.96;0.96;0.95	5.83	4.71	0.59529	.	0.459276	0.23342	N	0.049221	T	0.38665	0.1049	M	0.70595	2.14	0.21325	N	0.999724	B;B	0.27140	0.011;0.169	B;B	0.27380	0.008;0.079	T	0.34750	-0.9816	10	0.08179	T	0.78	-19.9623	10.8681	0.46866	0.0:0.0732:0.0:0.9268	.	339;342	Q96BT7;Q96BT7-4	ALKB8_HUMAN;.	A	339;339;342	ENSP00000415885:T339A;ENSP00000374219:T339A;ENSP00000397673:T342A	ENSP00000374219:T339A	T	-	1	0	ALKBH8	106901392	0.464000	0.25807	0.273000	0.24645	0.441000	0.31987	1.852000	0.39348	1.052000	0.40392	0.477000	0.44152	ACA	.	.		0.373	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775		C	107396182	T	C	107396182	3	2	44	1	0	0	0	0	1	0	0	0	533	1725	60	2	995	2	ALKBH8	11	107396182	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	13282491	107396182	27610334	269	5729										
FAM55A	120400	hgsc.bcm.edu	37	chr11	114393611	114393611	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aactacctactttttacaacTttggggaagtagtagatcca	7	8	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:114393611T>C	ENST00000424269.1	-	4	1097	c.1098A>G	c.(1096-1098)aaA>aaG	p.K366K	NXPE1_ENST00000536271.1_Silent_p.K82K|NXPE1_ENST00000251921.2_Silent_p.K224K			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	366						extracellular region (GO:0005576)											TTTTTACAACTTTGGGGAAGT	0.358																																					p.K224K		Atlas-SNP	.											.	NXPE1	8	.	0			c.A672G						.						67	63	64					11																	114393611		2201	4296	6497	SO:0001819	synonymous_variant	120400	exon5			TACAACTTTGGGG	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"family with sequence similarity 55, member A"	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.1098A>G	chr11.hg19:g.114393611T>C		118.0	0.0		96.0	4.0	NM_152315	B0YJ13	Silent	SNP	ENST00000424269.1	hg19																																																																																				.	.		0.358	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315		C	114393611	T	C	114393611	2	2	44	1	0	0	0	0	0	0	0	1	5592	1606	56	2		2	FAM55A	11	114393611	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	6997429	114393611	20612905	270	5730										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117314661	117314661	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgccccggccggcagaggtgAcggcggccacccacagcaga	15	16	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:117314661A>G	ENST00000321322.6	-	21	3984	c.3983T>C	c.(3982-3984)gTc>gCc	p.V1328A	DSCAML1_ENST00000527706.1_Missense_Mutation_p.V1058A	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1268	Ig-like C2-type 10.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GGCAGAGGTGACGGCGGCCAC	0.642																																					p.V1328A		Atlas-SNP	.											.	DSCAML1	286	.	0			c.T3983C						.						31	30	30					11																	117314661		2200	4296	6496	SO:0001583	missense	57453	exon21			GAGGTGACGGCGG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.3983T>C	chr11.hg19:g.117314661A>G	ENSP00000315465:p.Val1328Ala	68.0	0.0		64.0	4.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.476160	0.84640	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.61859	0.07;0.07	4.59	4.59	0.56863	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.69187	0.3083	L	0.58669	1.825	0.80722	D	1	D	0.59357	0.985	D	0.64595	0.927	T	0.67929	-0.5543	9	0.33940	T	0.23	.	14.1423	0.65327	1.0:0.0:0.0:0.0	.	1268	Q8TD84	DSCL1_HUMAN	A	1058;1328;1035	ENSP00000434335:V1058A;ENSP00000315465:V1328A	ENSP00000315465:V1328A	V	-	2	0	DSCAML1	116819871	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	7.259000	0.78381	1.916000	0.55485	0.260000	0.18958	GTC	.	.		0.642	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		G	117314661	A	G	117314661	3	3	44	1	0	0	0	0	1	0	0	0	4771	275	10	2	2410	2	DSCAML1	11	117314661	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2921050	117314661	17691855	271	5731										
MLL	4297	hgsc.bcm.edu	37	chr11	118377090	118377090	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agacggtagacgctcctaatAgcatgggactggagcagaac	13	9	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:118377090A>G	ENST00000389506.5	+	27	10474	c.10474A>G	c.(10474-10476)Agc>Ggc	p.S3492G	KMT2A_ENST00000534358.1_Missense_Mutation_p.S3495G|KMT2A_ENST00000354520.4_Missense_Mutation_p.S3454G			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3492					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CGCTCCTAATAGCATGGGACT	0.547																																					p.S3495G		Atlas-SNP	.											.	MLL	548	.	0			c.A10483G						.						114	116	115					11																	118377090		2200	4295	6495	SO:0001583	missense	4297	exon27			CCTAATAGCATGG	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.10474A>G	chr11.hg19:g.118377090A>G	ENSP00000374157:p.Ser3492Gly	145.0	0.0		164.0	7.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	2.183	-0.387148	0.04932	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;T	0.81659	-1.52;-1.52;-1.49	5.53	0.697	0.18081	.	0.779687	0.13079	N	0.415426	T	0.62097	0.2400	N	0.24115	0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42361	-0.9456	10	0.20046	T	0.44	.	4.512	0.11915	0.5893:0.1596:0.2511:0.0	.	3495;3492	E9PQG7;Q03164	.;MLL1_HUMAN	G	3495;3492;3454;2402	ENSP00000436786:S3495G;ENSP00000374157:S3492G;ENSP00000346516:S3454G	ENSP00000346516:S3454G	S	+	1	0	MLL	117882300	0.004000	0.15560	0.000000	0.03702	0.199000	0.23934	1.909000	0.39917	0.153000	0.19213	0.482000	0.46254	AGC	.	.		0.547	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		G	118377090	A	G	118377090	3	3	44	1	0	0	0	0	1	0	0	0	9629	420	15	2	10580	2	MLL	11	118377090	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1062429	118377090	16629426	272	5732										
HMBS	3145	hgsc.bcm.edu	37	chr11	118963697	118963697	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cggctcagatagcatacaagAgaccatgcaggctaccatcc	9	13	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:118963697A>G	ENST00000278715.3	+	13	1029	c.878A>G	c.(877-879)gAg>gGg	p.E293G	HMBS_ENST00000392841.1_Missense_Mutation_p.E276G|HMBS_ENST00000544387.1_Missense_Mutation_p.E253G|HMBS_ENST00000542729.1_Missense_Mutation_p.E236G|HMBS_ENST00000543090.1_Missense_Mutation_p.E262G|HMBS_ENST00000537841.1_Missense_Mutation_p.E276G|HMBS_ENST00000442944.2_Missense_Mutation_p.E276G	NM_000190.3	NP_000181.2	P08397	HEM3_HUMAN	hydroxymethylbilane synthase	293					heme biosynthetic process (GO:0006783)|peptidyl-pyrromethane cofactor linkage (GO:0018160)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	hydroxymethylbilane synthase activity (GO:0004418)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		AGCATACAAGAGACCATGCAG	0.512																																					p.E293G		Atlas-SNP	.											.	HMBS	27	.	0			c.A878G						.						97	97	97					11																	118963697		2200	4295	6495	SO:0001583	missense	3145	exon13			TACAAGAGACCAT	X04808	CCDS8409.1, CCDS41726.1, CCDS58186.1, CCDS58187.1	11q23.3	2013-07-10			ENSG00000256269	ENSG00000256269	2.5.1.61		4982	protein-coding gene	gene with protein product		609806	"uroporphyrinogen I synthase", "porphobilinogen deaminase", "porphyria, acute; Chester type"	PBGD, UPS, PORC		8432552, 17298217	Standard	NM_001258208		Approved		uc001puz.1	P08397	OTTHUMG00000168295	ENST00000278715.3:c.878A>G	chr11.hg19:g.118963697A>G	ENSP00000278715:p.Glu293Gly	178.0	0.0		156.0	7.0	NM_000190	A8K2L0|G3V1P4|G5EA58|P08396|Q16012	Missense_Mutation	SNP	ENST00000278715.3	hg19	CCDS8409.1	.	.	.	.	.	.	.	.	.	.	a	21.7	4.192535	0.78902	.	.	ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000149397	ENST00000278715;ENST00000537841;ENST00000542729;ENST00000544387;ENST00000543090;ENST00000392841;ENST00000442944	D;D;D;D;D;D;D	0.98178	-4.77;-4.77;-4.77;-4.77;-4.77;-4.77;-4.77	5.24	5.24	0.73138	Porphobilinogen deaminase, C-terminal (3);	0.152799	0.56097	D	0.000023	D	0.96327	0.8802	L	0.33753	1.03	0.80722	D	1	B;P;B;P	0.41131	0.223;0.694;0.0;0.739	B;B;B;P	0.47251	0.142;0.29;0.001;0.542	D	0.94985	0.8129	10	0.16420	T	0.52	-15.2548	12.6299	0.56651	1.0:0.0:0.0:0.0	.	236;262;253;293	G3V1P4;F5H345;G5EA58;P08397	.;.;.;HEM3_HUMAN	G	293;276;236;253;262;276;276	ENSP00000278715:E293G;ENSP00000444730:E276G;ENSP00000443058:E236G;ENSP00000438424:E253G;ENSP00000445429:E262G;ENSP00000376584:E276G;ENSP00000392041:E276G	ENSP00000392041:E276G	E	+	2	0	CTD-2589C9.4;HMBS	118468907	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	8.266000	0.89871	2.187000	0.69744	0.529000	0.55759	GAG	.	.		0.512	HMBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399188.1	NM_000190		G	118963697	A	G	118963697	3	3	44	1	0	0	0	0	1	0	0	0	7228	304	11	2	928	2	HMBS	11	118963697	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	586607	118963697	16042819	273	5733										
MCAM	4162	hgsc.bcm.edu	37	chr11	119185942	119185942	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acttccacctccaccagctcAggcgcaggctgctcagcctc	8	19	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:119185942A>G	ENST00000264036.4	-	2	113	c.99T>C	c.(97-99)ccT>ccC	p.P33P	MCAM_ENST00000530144.2_5'UTR|MCAM_ENST00000392814.1_5'Flank	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	33	Ig-like V-type 1.				anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		CCACCAGCTCAGGCGCAGGCT	0.682																																					p.P33P		Atlas-SNP	.											.	MCAM	57	.	0			c.T99C						.						43	38	40					11																	119185942		2199	4295	6494	SO:0001819	synonymous_variant	4162	exon2			CAGCTCAGGCGCA	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6934	protein-coding gene	gene with protein product	"Gicerin"	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.99T>C	chr11.hg19:g.119185942A>G		83.0	0.0		66.0	5.0	NM_006500	O95812|Q59E86|Q6PHR3|Q6ZTR2	Silent	SNP	ENST00000264036.4	hg19	CCDS31690.1																																																																																			.	.		0.682	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2			G	119185942	A	G	119185942	2	3	44	1	0	0	0	0	0	0	0	1	9377	175	7	2		2	MCAM	11	119185942	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	222245	119185942	15820574	274	5734										
ZNF202	7753	hgsc.bcm.edu	37	chr11	123598256	123598256	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gatatctgggacccaaggctCttcctctctaacctgggaga	10	12	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:123598256C>T	ENST00000529691.1	-	6	1099	c.880G>A	c.(880-882)Gag>Aag	p.E294K	ZNF202_ENST00000336139.4_Missense_Mutation_p.E294K|ZNF202_ENST00000530393.1_Missense_Mutation_p.E294K			O95125	ZN202_HUMAN	zinc finger protein 202	294	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		ACCCAAGGCTCTTCCTCTCTA	0.483																																					p.E294K		Atlas-SNP	.											ZNF202,bladder,carcinoma,0,1	ZNF202	72	.	0			c.G880A						.						104	100	101					11																	123598256		2202	4299	6501	SO:0001583	missense	7753	exon8			AAGGCTCTTCCTC	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"Zinc fingers, C2H2-type", "-", "-", "-"	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.880G>A	chr11.hg19:g.123598256C>T	ENSP00000433881:p.Glu294Lys	196.0	0.0		186.0	8.0	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	hg19	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.608230	0.46527	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691	T;T;T	0.09073	3.02;3.02;3.02	4.86	4.86	0.63082	Krueppel-associated box (3);	0.000000	0.48767	D	0.000175	T	0.17704	0.0425	L	0.45352	1.415	0.44956	D	0.997978	D	0.67145	0.996	P	0.61070	0.883	T	0.01956	-1.1240	10	0.25106	T	0.35	-20.9101	15.528	0.75928	0.0:1.0:0.0:0.0	.	294	O95125	ZN202_HUMAN	K	294	ENSP00000337724:E294K;ENSP00000432504:E294K;ENSP00000433881:E294K	ENSP00000337724:E294K	E	-	1	0	ZNF202	123103466	0.852000	0.29690	1.000000	0.80357	0.998000	0.95712	3.302000	0.51849	2.524000	0.85096	0.650000	0.86243	GAG	.	.		0.483	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		T	123598256	C	T	123598256	3	4	44	1	0	0	0	0	1	0	0	0	17778	922	32	3	1074	3	ZNF202	11	123598256	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	4412314	123598256	11408260	275	5735										
VWA5A	4013	hgsc.bcm.edu	37	chr11	124013240	124013240	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gatctagccaagatcctaggTatgagtttggaagaaataat	10	5	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:124013240T>C	ENST00000456829.2	+	17	2366	c.2115T>C	c.(2113-2115)ggT>ggC	p.G705G	VWA5A_ENST00000392748.1_Silent_p.G705G|VWA5A_ENST00000360334.4_3'UTR	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	705										autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						AGATCCTAGGTATGAGTTTGG	0.418																																					p.G705G		Atlas-SNP	.											.	VWA5A	102	.	0			c.T2115C						.						115	107	110					11																	124013240		2201	4299	6500	SO:0001819	synonymous_variant	4013	exon16			CCTAGGTATGAGT	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"loss of heterozygosity, 11, chromosomal region 2, gene A"	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.2115T>C	chr11.hg19:g.124013240T>C		103.0	0.0		90.0	40.0	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Silent	SNP	ENST00000456829.2	hg19	CCDS8444.1																																																																																			.	.		0.418	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622		C	124013240	T	C	124013240	2	2	44	1	0	0	0	0	0	0	0	1	17257	1625	57	2		2	VWA5A	11	124013240	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	414984	124013240	10993276	276	5736										
SPA17	53340	hgsc.bcm.edu	37	chr11	124551288	124551288	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atatttttattatttagaaaCcaactttgatccagcagaat	4	6	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:124551288C>T	ENST00000532692.1	+	2	1579	c.158C>T	c.(157-159)aCc>aTc	p.T53I	SIAE_ENST00000525730.1_Intron|SPA17_ENST00000227135.2_Missense_Mutation_p.T53I|SPA17_ENST00000524614.1_3'UTR			Q15506	SP17_HUMAN	sperm autoantigenic protein 17	53					binding of sperm to zona pellucida (GO:0007339)|epithelial cilium movement (GO:0003351)|single fertilization (GO:0007338)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|primary cilium (GO:0072372)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	5	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0223)		TATTTAGAAACCAACTTTGAT	0.328																																					p.T53I		Atlas-SNP	.											.	SPA17	16	.	0			c.C158T						.						71	75	73					11																	124551288		2201	4299	6500	SO:0001583	missense	53340	exon3			TAGAAACCAACTT	AF334735	CCDS8450.1	11q24.2	2009-03-12			ENSG00000064199	ENSG00000064199			11210	protein-coding gene	gene with protein product	"cancer/testis antigen 22"	608621				8688458	Standard	NM_017425		Approved	SP17, CT22	uc001qap.3	Q15506	OTTHUMG00000165927	ENST00000532692.1:c.158C>T	chr11.hg19:g.124551288C>T	ENSP00000432305:p.Thr53Ile	70.0	0.0		63.0	4.0	NM_017425	B2R4F2|Q9BXF7	Missense_Mutation	SNP	ENST00000532692.1	hg19	CCDS8450.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.241748	0.79912	.	.	ENSG00000064199	ENST00000227135;ENST00000532692	.	.	.	5.49	5.49	0.81192	.	0.155983	0.41396	D	0.000882	T	0.64427	0.2597	M	0.66939	2.045	0.40998	D	0.984903	D	0.59767	0.986	P	0.47206	0.541	T	0.71052	-0.4704	9	0.72032	D	0.01	-7.8147	18.1401	0.89637	0.0:1.0:0.0:0.0	.	53	Q15506	SP17_HUMAN	I	53	.	ENSP00000227135:T53I	T	+	2	0	SPA17	124056498	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.842000	0.48230	2.582000	0.87167	0.460000	0.39030	ACC	.	.		0.328	SPA17-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387075.1	NM_017425		T	124551288	C	T	124551288	3	4	44	1	0	0	0	0	1	0	0	0	14986	507	18	3	164	3	SPA17	11	124551288	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	538048	124551288	10455228	277	5737										
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134072792	134072792	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gttagatgtctgcctttggtAggaaaaagctttaaaaaaaa	9	4	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr11:134072792A>G	ENST00000534548.2	-	13	1598	c.1534T>C	c.(1534-1536)Tac>Cac	p.Y512H		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	512					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		TGCCTTTGGTAGGAAAAAGCT	0.358																																					p.Y512H		Atlas-SNP	.											.	NCAPD3	141	.	0			c.T1534C						.						111	106	108					11																	134072792		2201	4297	6498	SO:0001583	missense	23310	exon13			TTTGGTAGGAAAA	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.1534T>C	chr11.hg19:g.134072792A>G	ENSP00000433681:p.Tyr512His	95.0	0.0		103.0	5.0	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	hg19	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	A	0.041	-1.283995	0.01398	.	.	ENSG00000151503	ENST00000534548	T	0.64991	-0.13	4.86	3.73	0.42828	Armadillo-type fold (1);	1.698150	0.02702	N	0.111819	T	0.46092	0.1375	N	0.14661	0.345	0.25224	N	0.989883	B	0.02656	0.0	B	0.01281	0.0	T	0.32745	-0.9895	10	0.15499	T	0.54	4.6814	7.6688	0.28447	0.9016:0.0:0.0984:0.0	.	512	P42695	CNDD3_HUMAN	H	512	ENSP00000433681:Y512H	ENSP00000431612:Y512H	Y	-	1	0	NCAPD3	133578002	0.529000	0.26322	0.022000	0.16811	0.003000	0.03518	0.786000	0.26844	0.802000	0.34089	-0.280000	0.10049	TAC	.	.		0.358	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		G	134072792	A	G	134072792	3	3	44	1	0	0	0	0	1	0	0	0	10215	420	15	2	3054	2	NCAPD3	11	134072792	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	9521504	134072792	933724	278	5738										
C12orf4	57102	hgsc.bcm.edu	37	chr12	4599703	4599703	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	catacctgtggtactagaaaTtgcactgtcctagaaattcc	7	10	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:4599703T>C	ENST00000261250.3	-	13	1638	c.1551A>G	c.(1549-1551)caA>caG	p.Q517Q	C12orf4_ENST00000545746.1_Silent_p.Q517Q	NM_020374.2	NP_065107.1	Q9NQ89	CL004_HUMAN	chromosome 12 open reading frame 4	517										NS(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)		GTACTAGAAATTGCACTGTCC	0.383																																					p.Q517Q		Atlas-SNP	.											.	C12orf4	58	.	0			c.A1551G						.						110	107	108					12																	4599703		2203	4300	6503	SO:0001819	synonymous_variant	57102	exon13			TAGAAATTGCACT	AJ272205	CCDS8528.1	12p13.3	2012-08-10			ENSG00000047621	ENSG00000047621			1184	protein-coding gene	gene with protein product							Standard	NM_020374		Approved		uc001qms.3	Q9NQ89	OTTHUMG00000168258	ENST00000261250.3:c.1551A>G	chr12.hg19:g.4599703T>C		56.0	0.0		95.0	4.0	NM_020374	D3DUQ8|Q6MZH5	Silent	SNP	ENST00000261250.3	hg19	CCDS8528.1																																																																																			.	.		0.383	C12orf4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398992.1	NM_020374		C	4599703	T	C	4599703	2	2	44	1	0	0	0	0	0	0	0	1	1687	1490	52	2		2	C12orf4	12	4599703	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10		4599703	129252192	279	5739										
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18841042	18841042	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccattttttttaattacacgAgtctgctgcttcatttgatc	5	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:18841042A>G	ENST00000538330.1	-	9	1299	c.918T>C	c.(916-918)acT>acC	p.T306T	PLCZ1_ENST00000541695.1_Silent_p.T387T|PLCZ1_ENST00000539875.1_Silent_p.T331T|PLCZ1_ENST00000534932.1_Silent_p.T5T|PLCZ1_ENST00000447925.2_Silent_p.T522T|PLCZ1_ENST00000266505.7_Silent_p.T524T|PLCZ1_ENST00000435379.1_Silent_p.T329T					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					TAATTACACGAGTCTGCTGCT	0.318																																					p.T524T		Atlas-SNP	.											.	PLCZ1	107	.	0			c.T1572C						.						91	95	93					12																	18841042		2203	4297	6500	SO:0001819	synonymous_variant	89869	exon13			TACACGAGTCTGC	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000538330.1:c.918T>C	chr12.hg19:g.18841042A>G		78.0	0.0		82.0	4.0	NM_033123		Silent	SNP	ENST00000538330.1	hg19																																																																																				.	.		0.318	PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000401666.3	NM_033123		G	18841042	A	G	18841042	2	3	44	1	0	0	0	0	0	0	0	1	12053	291	11	2		2	PLCZ1	12	18841042	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	14241339	18841042	115010853	280	5740										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19518932	19518932	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cacagaccgcaaatcataaaCcagaagagcatcctgaagaa	7	11	1	5			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:19518932C>T	ENST00000299275.6	+	24	3151	c.3145C>T	c.(3145-3147)Cca>Tca	p.P1049S	PLEKHA5_ENST00000539256.1_Missense_Mutation_p.P807S|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.P1112S|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.P1038S|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.P1107S|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.P993S|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.P1215S|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.P1031S|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.P1107S	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	1049					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					AAATCATAAACCAGAAGAGCA	0.323																																					p.P1215S	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.C3643T						.						80	73	75					12																	19518932		2203	4300	6503	SO:0001583	missense	54477	exon30			CATAAACCAGAAG	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.3145C>T	chr12.hg19:g.19518932C>T	ENSP00000299275:p.Pro1049Ser	34.0	0.0		48.0	4.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	C	4.245	0.044378	0.08196	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000538972	T;T;T;T;T;T;T;T;T;T	0.08896	3.04;3.04;3.04;3.04;3.04;3.04;3.04;3.04;3.04;3.04	4.45	-7.17	0.01511	.	1.993890	0.02465	N	0.086916	T	0.03608	0.0103	N	0.12182	0.205	0.09310	N	1	B;B;B;B;B	0.15719	0.004;0.002;0.002;0.002;0.014	B;B;B;B;B	0.13407	0.006;0.002;0.003;0.002;0.009	T	0.37244	-0.9714	10	0.13853	T	0.58	1.1337	3.6818	0.08313	0.1868:0.239:0.4378:0.1364	.	1031;1038;993;1049;1107	F5H0I0;E7EME8;Q9HAU0-5;Q9HAU0;Q9HAU0-2	.;.;.;PKHA5_HUMAN;.	S	1112;1107;993;1215;1049;807;1107;1038;1031;330	ENSP00000325155:P1112S;ENSP00000347560:P1107S;ENSP00000352104:P993S;ENSP00000404296:P1215S;ENSP00000299275:P1049S;ENSP00000440611:P807S;ENSP00000439673:P1107S;ENSP00000400411:P1038S;ENSP00000439837:P1031S;ENSP00000443553:P330S	ENSP00000299275:P1049S	P	+	1	0	PLEKHA5	19410199	0.028000	0.19301	0.000000	0.03702	0.018000	0.09664	-0.597000	0.05713	-1.126000	0.02929	0.460000	0.39030	CCA	.	.		0.323	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		T	19518932	C	T	19518932	3	4	44	1	0	0	0	0	1	0	0	0	12068	507	18	3	3557	3	PLEKHA5	12	19518932	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	677890	19518932	114332963	281	5741										
LST-3TM12	338821	hgsc.bcm.edu	37	chr12	21207384	21207385	+	Splice_Site	DNP	AG	AG	CT													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atatttcaaaaattatttttAggtgttttataactgtagct							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:21207384_21207385AG>CT	ENST00000421593.2	+	10	1356		c.e10-1		RP11-125O5.2_ENST00000590779.1_5'Flank|LST3_ENST00000540229.1_Intron|SLCO1B7_ENST00000554957.1_Splice_Site|LST3_ENST00000381541.3_Splice_Site|SLCO1B3_ENST00000553473.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						AATTATTTTTAGGTGTTTTATA	0.332																																					.		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.1357-2A>C|c.1357-1G>T						.																																			SO:0001630	splice_region_variant	338821	exon10			ATTTTTAGGTGTT|TTTTTAGGTGTTT	AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"Solute carriers"	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	Exception_encountered	chr12.hg19:g.21207384_21207385delinsCT		122.0|124.0	0.0		179.0|182.0	28.0|30.0	NM_001009562	Q71QF0	Splice_Site	SNP	ENST00000421593.2	hg19	CCDS44843.1																																																																																			.	.		0.332	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	Intron	CT	21207385	AG	CT	21207384	5	2	44	1	0	0	0	0	0	0	1	0	9075	434	15	5	1393	5	LST-3TM12	12	21207384	Splice_Site	DNP	AG	TCGA-BC-A3KG-01A-11D-A20W-10	1688452	21207384	112644511	282	5742										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32138119	32138119	+	Frame_Shift_Del	DEL	T	T	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acattcaaattaggtgactcTttgtcaaacccaaacgaaag							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:32138119delT	ENST00000312561.4	+	4	4644	c.4230delT	c.(4228-4230)tctfs	p.S1410fs	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1410																	TAGGTGACTCTTTGTCAAACC	0.348																																					p.S1410fs		Atlas-INDEL	.											.	.	.	.	0			c.4229delC						.						80	84	82					12																	32138119		2203	4299	6502	SO:0001589	frameshift_variant	55196	exon4			.	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.4230delT	chr12.hg19:g.32138119delT	ENSP00000310338:p.Ser1410fs	153.0	0.0		161.0	10.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Frame_Shift_Del	DEL	ENST00000312561.4	hg19	CCDS8725.2																																																																																			.	.		0.348	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		-	32138119	T	-	32138119	7	5	44	1	0	1	0	1	0	0	0	0	1684	1596	56	0	4232	0	C12orf35	12	32138119	Frame_Shift_Del	DEL	T	TCGA-BC-A3KG-01A-11D-A20W-10	10930735	32138119	101713776	283	5743										
PUS7L	83448	hgsc.bcm.edu	37	chr12	44132189	44132189	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtaagaaacaattttatggcTttcatcttaaaaaatcaagc	5	6	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:44132189T>C	ENST00000416848.2	-	6	1856	c.1368A>G	c.(1366-1368)aaA>aaG	p.K456K	PUS7L_ENST00000431332.3_Silent_p.K143K|RP11-210N13.1_ENST00000548437.1_RNA|PUS7L_ENST00000344862.5_Silent_p.K456K|PUS7L_ENST00000551923.1_Silent_p.K456K	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	456	TRUD. {ECO:0000255|PROSITE- ProRule:PRU00342}.				pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		ATTTTATGGCTTTCATCTTAA	0.294																																					p.K456K		Atlas-SNP	.											.	PUS7L	73	.	0			c.A1368G						.						96	96	96					12																	44132189		2203	4294	6497	SO:0001819	synonymous_variant	83448	exon6			TATGGCTTTCATC	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.1368A>G	chr12.hg19:g.44132189T>C		77.0	0.0		95.0	5.0	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Silent	SNP	ENST00000416848.2	hg19	CCDS8743.1																																																																																			.	.		0.294	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		C	44132189	T	C	44132189	2	2	44	1	0	0	0	0	0	0	0	1	12849	1606	56	2		2	PUS7L	12	44132189	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	11994070	44132189	89719706	284	5744										
KRT84	3890	hgsc.bcm.edu	37	chr12	52771877	52771877	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcggacgctggagctgcggcCgccgctgcagctgctgaagc	17	14	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:52771877C>A	ENST00000257951.3	-	9	1810	c.1744G>T	c.(1744-1746)Ggc>Tgc	p.G582C	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	582	Tail.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GAGCTGCGGCCGCCGCTGCAG	0.677																																					p.G582C		Atlas-SNP	.											.	KRT84	61	.	0			c.G1744T						.						12	14	13					12																	52771877		2182	4273	6455	SO:0001583	missense	3890	exon9			TGCGGCCGCCGCT	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"-", "Intermediate filaments type II, keratins (basic)"	6461	protein-coding gene	gene with protein product	"hard keratin type II 4"	602766	"keratin, hair, basic, 4"	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.1744G>T	chr12.hg19:g.52771877C>A	ENSP00000257951:p.Gly582Cys	209.0	0.0		162.0	72.0	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	hg19	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.524879	0.27299	.	.	ENSG00000161849	ENST00000257951	D	0.82984	-1.67	3.57	2.66	0.31614	.	0.230288	0.22348	N	0.061253	D	0.82710	0.5096	L	0.36672	1.1	0.09310	N	1	D	0.76494	0.999	D	0.64410	0.925	T	0.70923	-0.4740	10	0.87932	D	0	.	6.1951	0.20546	0.0:0.8602:0.0:0.1398	.	582	Q9NSB2	KRT84_HUMAN	C	582	ENSP00000257951:G582C	ENSP00000257951:G582C	G	-	1	0	KRT84	51058144	0.697000	0.27767	0.207000	0.23584	0.189000	0.23516	1.818000	0.39012	1.991000	0.58162	0.462000	0.41574	GGC	.	.		0.677	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		A	52771877	C	A	52771877	3	1	44	1	0	0	0	0	1	0	0	0	8507	652	23	1	62	1	KRT84	12	52771877	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	8639688	52771877	81080018	285	5745										
MFSD5	84975	hgsc.bcm.edu	37	chr12	53646714	53646714	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggctaaaccccctggaagggCctgcagcaatccctccttcc	9	17	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:53646714C>T	ENST00000329548.4	+	2	286	c.95C>T	c.(94-96)gCc>gTc	p.A32V	MFSD5_ENST00000534842.1_Missense_Mutation_p.A139V	NM_032889.4	NP_116278.3	Q6N075	MFSD5_HUMAN	major facilitator superfamily domain containing 5	32					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(3)|urinary_tract(1)	16						CCTGGAAGGGCCTGCAGCAAT	0.577																																					p.A139V		Atlas-SNP	.											.	MFSD5	40	.	0			c.C416T						.						104	111	108					12																	53646714		2203	4300	6503	SO:0001583	missense	84975	exon2			GAAGGGCCTGCAG	AK097576	CCDS8851.1, CCDS53796.1	12q13.13	2012-03-09			ENSG00000182544	ENSG00000182544			28156	protein-coding gene	gene with protein product							Standard	NM_032889		Approved	MGC11308	uc001sch.2	Q6N075	OTTHUMG00000170028	ENST00000329548.4:c.95C>T	chr12.hg19:g.53646714C>T	ENSP00000332624:p.Ala32Val	149.0	0.0		174.0	84.0	NM_001170790	G3V1N7|Q6NW04|Q8N7W8|Q8NCK0|Q96IA5	Missense_Mutation	SNP	ENST00000329548.4	hg19	CCDS8851.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.708820	0.30322	.	.	ENSG00000182544	ENST00000551660;ENST00000534842;ENST00000328704;ENST00000329548	.	.	.	4.3	3.41	0.39046	.	0.000000	0.85682	D	0.000000	T	0.43590	0.1254	L	0.33339	1.005	0.49130	D	0.999753	B;B	0.29988	0.065;0.264	B;B	0.27715	0.033;0.082	T	0.33752	-0.9856	9	0.37606	T	0.19	-8.2227	10.7748	0.46343	0.0:0.9055:0.0:0.0945	.	32;139	Q6N075;G3V1N7	MFSD5_HUMAN;.	V	139;139;139;32	.	ENSP00000331231:A139V	A	+	2	0	MFSD5	51932981	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.012000	0.29924	1.037000	0.40024	0.561000	0.74099	GCC	.	.		0.577	MFSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406896.1	NM_032889		T	53646714	C	T	53646714	3	4	44	1	0	0	0	0	1	0	0	0	9543	739	26	3	422	3	MFSD5	12	53646714	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	874837	53646714	80205181	286	5746										
GPR84	53831	hgsc.bcm.edu	37	chr12	54756956	54756956	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tggcctcatcagtcctggccAcatggttggagtggatgctt	13	10	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:54756956A>G	ENST00000551809.1	-	1	1315	c.680T>C	c.(679-681)gTg>gCg	p.V227A	RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA|GPR84_ENST00000267015.3_Missense_Mutation_p.V227A			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	227						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						AGTCCTGGCCACATGGTTGGA	0.557																																					p.V227A		Atlas-SNP	.											.	GPR84	38	.	0			c.T680C						.						177	162	167					12																	54756956		2203	4300	6503	SO:0001583	missense	53831	exon2			CTGGCCACATGGT	AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.680T>C	chr12.hg19:g.54756956A>G	ENSP00000450310:p.Val227Ala	95.0	0.0		97.0	41.0	NM_020370	B6V9G7	Missense_Mutation	SNP	ENST00000551809.1	hg19	CCDS8878.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.672176	0.29693	.	.	ENSG00000139572	ENST00000267015;ENST00000551809	T;T	0.60672	0.17;0.17	4.5	4.5	0.54988	GPCR, rhodopsin-like superfamily (1);	0.325101	0.22054	N	0.065272	T	0.44095	0.1277	L	0.40543	1.245	0.35004	D	0.756234	B	0.29909	0.261	B	0.29524	0.103	T	0.47971	-0.9075	10	0.07990	T	0.79	-11.5828	12.0877	0.53706	1.0:0.0:0.0:0.0	.	227	Q9NQS5	GPR84_HUMAN	A	227	ENSP00000267015:V227A;ENSP00000450310:V227A	ENSP00000267015:V227A	V	-	2	0	GPR84	53043223	0.923000	0.31300	0.971000	0.41717	0.664000	0.39144	1.456000	0.35201	2.023000	0.59567	0.459000	0.35465	GTG	.	.		0.557	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			G	54756956	A	G	54756956	3	3	44	1	0	0	0	0	1	0	0	0	6722	159	6	2	514	2	GPR84	12	54756956	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1110242	54756956	79094939	287	5747										
AGAP2	6302	hgsc.bcm.edu	37	chr12	58135818	58135818	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atgtcgtctgacttctgctcTcactgcagctacaacgaact	7	13	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:58135818T>C	ENST00000257910.3	+	0	0				TSPAN31_ENST00000553221.1_Intron|AGAP2_ENST00000257897.3_Missense_Mutation_p.R13G|TSPAN31_ENST00000547992.1_5'Flank	NM_005981.3	NP_005972.1	Q12999	TSN31_HUMAN	tetraspanin 31						positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(1)|kidney(1)|lung(5)	7	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			ACTTCTGCTCTCACTGCAGCT	0.597																																					p.R13G		Atlas-SNP	.											.	AGAP2	167	.	0			c.A37G						.						201	160	174					12																	58135818		2203	4300	6503	SO:0001631	upstream_gene_variant	116986	exon1			CTGCTCTCACTGC		CCDS8952.1	12q13-q14	2013-02-14	2005-08-16	2005-08-16		ENSG00000135452		"Tetraspanins"	10539	protein-coding gene	gene with protein product		181035	"sarcoma amplified sequence"	SAS			Standard	NM_005981		Approved		uc001spt.3	Q12999			chr12.hg19:g.58135818T>C	Exception_encountered	125.0	0.0		123.0	5.0	NM_014770	O00577|Q53X76	Missense_Mutation	SNP	ENST00000257910.3	hg19	CCDS8952.1	.	.	.	.	.	.	.	.	.	.	t	13.26	2.184917	0.38609	.	.	ENSG00000135439	ENST00000257897	T	0.39229	1.09	4.76	3.52	0.40303	.	.	.	.	.	T	0.31796	0.0808	.	.	.	0.80722	D	1	B	0.25609	0.13	B	0.19391	0.025	T	0.28808	-1.0032	8	0.87932	D	0	.	8.0692	0.30678	0.0:0.0:0.2056:0.7944	.	13	Q99490-2	.	G	13	ENSP00000257897:R13G	ENSP00000257897:R13G	R	-	1	2	AGAP2	56422085	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	2.613000	0.46351	1.924000	0.55735	0.235000	0.17854	AGA	.	.		0.597	TSPAN31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408778.1			C	58135818	T	C	58135818	1	2	44	0	1	0	0	0	0	0	0	0	368	1559	54	2		2	AGAP2	12	58135818	5'Flank	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	3378862	58135818	75716077	288	5748										
USP15	9958	hgsc.bcm.edu	37	chr12	62696641	62696641	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atactgttgccaactgaaggTtggaataaacttgtcagctg	10	7	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:62696641T>C	ENST00000280377.5	+	3	346	c.288T>C	c.(286-288)ggT>ggC	p.G96G	USP15_ENST00000353364.3_Silent_p.G96G|USP15_ENST00000312635.6_Silent_p.G96G|USP15_ENST00000393654.3_Silent_p.G96G|USP15_ENST00000550632.1_3'UTR	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	96	DUSP. {ECO:0000255|PROSITE- ProRule:PRU00613}.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		CAACTGAAGGTTGGAATAAAC	0.343																																					p.G96G	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.T288C						.						122	121	121					12																	62696641		2203	4300	6503	SO:0001819	synonymous_variant	9958	exon3			TGAAGGTTGGAAT	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.288T>C	chr12.hg19:g.62696641T>C		96.0	0.0		112.0	5.0	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	hg19	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.253303	0.22965	.	.	ENSG00000135655	ENST00000549237	.	.	.	5.72	4.79	0.61399	.	.	.	.	.	T	0.60301	0.2258	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58509	-0.7624	4	.	.	.	-7.1095	9.6221	0.39727	0.0:0.6711:0.2567:0.0722	.	.	.	.	A	92	.	.	V	+	2	0	USP15	60982908	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.005000	0.40864	1.403000	0.46800	-0.321000	0.08615	GTT	.	.		0.343	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		C	62696641	T	C	62696641	2	2	44	1	0	0	0	0	0	0	0	1	17061	1712	60	2		2	USP15	12	62696641	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4560823	62696641	71155254	289	5749										
MSRB3	253827	hgsc.bcm.edu	37	chr12	65762781	65762781	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tttctttctctttgcaggtcAgaaaccaaatttgactccgg	7	10	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:65762781A>G	ENST00000355192.3	+	4	414	c.288A>G	c.(286-288)tcA>tcG	p.S96S	MSRB3_ENST00000535664.1_Silent_p.S89S|MSRB3_ENST00000308259.5_Silent_p.S89S|MSRB3_ENST00000540804.1_Silent_p.S96S	NM_198080.3	NP_932346.1	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3	96					protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		TTTGCAGGTCAGAAACCAAAT	0.348																																					p.S96S		Atlas-SNP	.											.	MSRB3	80	.	0			c.A288G						.						37	41	40					12																	65762781		2202	4298	6500	SO:0001819	synonymous_variant	253827	exon4			CAGGTCAGAAACC	BX640871	CCDS8973.1, CCDS31853.1	12q14.3	2011-11-29			ENSG00000174099	ENSG00000174099			27375	protein-coding gene	gene with protein product		613719	"deafness, autosomal recessive 74"	DFNB74		21185009	Standard	NM_198080		Approved	FLJ36866, DKFZp686C1178	uc021qzy.1	Q8IXL7	OTTHUMG00000168866	ENST00000355192.3:c.288A>G	chr12.hg19:g.65762781A>G		172.0	0.0		97.0	5.0	NM_198080	B4DR19|B7ZAQ0|Q6UXS2	Silent	SNP	ENST00000355192.3	hg19	CCDS8973.1	.	.	.	.	.	.	.	.	.	.	A	6.773	0.511578	0.12944	.	.	ENSG00000174099	ENST00000541189;ENST00000446731	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	T	0.63331	0.2502	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62364	-0.6870	4	.	.	.	-23.5263	11.1184	0.48275	0.8621:0.0:0.0:0.1379	.	.	.	.	G	105;48	.	.	R	+	1	2	MSRB3	64049048	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.267000	0.43329	2.242000	0.73789	0.460000	0.39030	AGA	.	.		0.348	MSRB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401421.1	NM_198080		G	65762781	A	G	65762781	2	3	44	1	0	0	0	0	0	0	0	1	9898	175	7	2		2	MSRB3	12	65762781	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	3066140	65762781	68089114	290	5750										
IFNG	3458	hgsc.bcm.edu	37	chr12	68553390	68553390	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gccaagatataacttgtataTttcatcgtttccgagagaat	7	7	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:68553390T>C	ENST00000229135.3	-	1	137	c.6A>G	c.(4-6)aaA>aaG	p.K2K	IFNG-AS1_ENST00000536914.1_RNA	NM_000619.2	NP_000610.2	P01579	IFNG_HUMAN	interferon, gamma	2					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell cycle arrest (GO:0007050)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to interleukin-18 (GO:0071351)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|extrinsic apoptotic signaling pathway (GO:0097191)|humoral immune response (GO:0006959)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of myelination (GO:0031642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil apoptotic process (GO:0001781)|neutrophil chemotaxis (GO:0030593)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity (GO:0060550)|positive regulation of fructose 1,6-bisphosphate metabolic process (GO:0060552)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|regulation of insulin secretion (GO:0050796)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of the force of heart contraction (GO:0002026)|response to drug (GO:0042493)|response to virus (GO:0009615)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|interferon-gamma receptor binding (GO:0005133)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Glucosamine(DB01296)|Olsalazine(DB01250)	AACTTGTATATTTCATCGTTT	0.383																																					p.K2K		Atlas-SNP	.											.	IFNG	38	.	0			c.A6G						.						33	30	31					12																	68553390		2203	4297	6500	SO:0001819	synonymous_variant	3458	exon1			TGTATATTTCATC		CCDS8980.1	12q14	2007-10-17			ENSG00000111537	ENSG00000111537		"Interferons"	5438	protein-coding gene	gene with protein product		147570					Standard	NM_000619		Approved		uc001stw.1	P01579	OTTHUMG00000169113	ENST00000229135.3:c.6A>G	chr12.hg19:g.68553390T>C		59.0	0.0		100.0	4.0	NM_000619	B5BU88|Q53ZV4	Silent	SNP	ENST00000229135.3	hg19	CCDS8980.1																																																																																			.	.		0.383	IFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402301.1			C	68553390	T	C	68553390	2	2	44	1	0	0	0	0	0	0	0	1	7557	1490	52	2		2	IFNG	12	68553390	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2790609	68553390	65298505	291	5751										
IL26	55801	hgsc.bcm.edu	37	chr12	68619375	68619375	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctaatacttactggaatcgtTgctttgagccatgctgcttt	8	9	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:68619375T>C	ENST00000229134.4	-	1	226	c.162A>G	c.(160-162)gcA>gcG	p.A54A	IFNG-AS1_ENST00000536914.1_RNA	NM_018402.1	NP_060872.1	Q9NPH9	IL26_HUMAN	interleukin 26	54					cell-cell signaling (GO:0007267)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000515)		CTGGAATCGTTGCTTTGAGCC	0.403																																					p.A54A		Atlas-SNP	.											.	IL26	32	.	0			c.A162G						.						235	213	220					12																	68619375		2203	4300	6503	SO:0001819	synonymous_variant	55801	exon1			AATCGTTGCTTTG	AJ251549	CCDS8981.1	12q15	2008-08-04			ENSG00000111536	ENSG00000111536		"Interleukins and interleukin receptors"	17119	protein-coding gene	gene with protein product		605679				10729163, 11528524	Standard	NM_018402		Approved	AK155, IL-26	uc001stx.1	Q9NPH9	OTTHUMG00000169114	ENST00000229134.4:c.162A>G	chr12.hg19:g.68619375T>C		73.0	0.0		94.0	4.0	NM_018402		Silent	SNP	ENST00000229134.4	hg19	CCDS8981.1																																																																																			.	.		0.403	IL26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402302.1	NM_018402		C	68619375	T	C	68619375	2	2	44	1	0	0	0	0	0	0	0	1	7688	1799	63	2		2	IL26	12	68619375	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	65985	68619375	65232520	292	5752										
E2F7	144455	hgsc.bcm.edu	37	chr12	77421889	77421889	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgttacccatagtcttgggAgaggcaaggtctgtggaatc	13	8	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:77421889A>G	ENST00000322886.7	-	11	2149	c.1914T>C	c.(1912-1914)tcT>tcC	p.S638S	E2F7_ENST00000416496.2_Silent_p.S638S	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	638					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						TAGTCTTGGGAGAGGCAAGGT	0.418																																					p.S638S		Atlas-SNP	.											.	E2F7	201	.	0			c.T1914C						.						90	87	88					12																	77421889		2203	4300	6503	SO:0001819	synonymous_variant	144455	exon11			CTTGGGAGAGGCA	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.1914T>C	chr12.hg19:g.77421889A>G		135.0	0.0		125.0	6.0	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	hg19	CCDS9016.1																																																																																			.	.		0.418	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		G	77421889	A	G	77421889	2	3	44	1	0	0	0	0	0	0	0	1	4874	291	11	2		2	E2F7	12	77421889	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	8802514	77421889	56430006	293	5753										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80722448	80722448	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttttttccatgtaaagggtTgaaggatgcttgccctactg	10	8	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:80722448T>C	ENST00000547103.1	+	35	4182	c.4176T>C	c.(4174-4176)gtT>gtC	p.V1392V	OTOGL_ENST00000458043.2_Silent_p.V1392V			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1392					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TGTAAAGGGTTGAAGGATGCT	0.348																																					p.V1392V		Atlas-SNP	.											.	OTOGL	235	.	0			c.T4176C						.						99	87	91					12																	80722448		1847	4090	5937	SO:0001819	synonymous_variant	283310	exon35			AAGGGTTGAAGGA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.4176T>C	chr12.hg19:g.80722448T>C		148.0	0.0		124.0	6.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Silent	SNP	ENST00000547103.1	hg19																																																																																				.	.		0.348	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		C	80722448	T	C	80722448	2	2	44	1	0	0	0	0	0	0	0	1	1709	1799	63	2		2	C12orf64	12	80722448	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	3300559	80722448	53129447	294	5754										
HCFC2	29915	hgsc.bcm.edu	37	chr12	104461781	104461781	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccccctccttctggtttaccTccttgtcctcggcttggaca	7	17	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:104461781T>C	ENST00000229330.4	+	3	473	c.369T>C	c.(367-369)ccT>ccC	p.P123P		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	123					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						CTGGTTTACCTCCTTGTCCTC	0.403																																					p.P123P	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-SNP	.											.	HCFC2	94	.	0			c.T369C						.						248	240	243					12																	104461781		2203	4300	6503	SO:0001819	synonymous_variant	29915	exon3			TTTACCTCCTTGT	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.369T>C	chr12.hg19:g.104461781T>C		54.0	0.0		76.0	4.0	NM_013320	B2R8Q5|C0H5X3	Silent	SNP	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.403	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		C	104461781	T	C	104461781	2	2	44	1	0	0	0	0	0	0	0	1	7002	1538	54	2		2	HCFC2	12	104461781	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	23739333	104461781	29390114	295	5755										
ANKRD13A	88455	hgsc.bcm.edu	37	chr12	110468463	110468463	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttgttagaaattcccttgttTcatgtcttaaatgcacggat	7	7	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:110468463T>C	ENST00000261739.4	+	12	1414	c.1248T>C	c.(1246-1248)ttT>ttC	p.F416F	C12orf76_ENST00000546651.2_Intron	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	416						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						TTCCCTTGTTTCATGTCTTAA	0.333																																					p.F416F		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.T1248C						.						55	53	54					12																	110468463		2203	4300	6503	SO:0001819	synonymous_variant	88455	exon12			CTTGTTTCATGTC	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"Ankyrin repeat domain containing"	21268	protein-coding gene	gene with protein product		615123	"ankyrin repeat domain 13"	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.1248T>C	chr12.hg19:g.110468463T>C		53.0	0.0		29.0	4.0	NM_033121	O60736	Silent	SNP	ENST00000261739.4	hg19	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	T	9.167	1.020254	0.19433	.	.	ENSG00000076513	ENST00000547639	T	0.48522	0.81	5.94	1.93	0.25924	.	0.000000	0.85682	D	0.000000	T	0.53142	0.1778	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52653	-0.8547	7	0.59425	D	0.04	-19.254	8.8073	0.34945	0.0:0.3575:0.0:0.6425	.	.	.	.	S	269	ENSP00000449781:F269S	ENSP00000449781:F269S	F	+	2	0	ANKRD13A	108952846	0.994000	0.37717	1.000000	0.80357	0.999000	0.98932	0.253000	0.18296	0.505000	0.28104	0.528000	0.53228	TTC	.	.		0.333	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		C	110468463	T	C	110468463	2	2	44	1	0	0	0	0	0	0	0	1	641	1780	62	2		2	ANKRD13A	12	110468463	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	6006682	110468463	23383432	296	5756										
RNFT2	84900	hgsc.bcm.edu	37	chr12	117290508	117290508	+	3'UTR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gagaagattgatgaaagtgcAggtgtgtaaggaaatagaac	14	2	0	5			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:117290508A>G	ENST00000392549.2	+	0	1970				RNFT2_ENST00000319176.7_3'UTR|RNFT2_ENST00000407967.3_Silent_p.A418A|RNFT2_ENST00000551251.1_3'UTR	NM_001109903.1	NP_001103373.1	Q96EX2	RNFT2_HUMAN	ring finger protein, transmembrane 2							integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	6	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		ATGAaagtgcaggtgtgtaag	0.458																																					p.A418A		Atlas-SNP	.											.	RNFT2	28	.	0			c.A1254G						.						135	141	139					12																	117290508		2203	4300	6503	SO:0001624	3_prime_UTR_variant	84900	exon11			AAGTGCAGGTGTG	AK027533	CCDS9180.2, CCDS44987.1	12q24.22	2013-01-09	2008-02-26	2008-02-26	ENSG00000135119	ENSG00000135119		"RING-type (C3HC4) zinc fingers"	25905	protein-coding gene	gene with protein product			"transmembrane protein 118"	TMEM118		12477932	Standard	NM_032814		Approved	FLJ14627	uc009zwn.3	Q96EX2	OTTHUMG00000150882	ENST00000392549.2:c.*402A>G	chr12.hg19:g.117290508A>G		105.0	0.0		104.0	5.0	NM_032814	E9PAM7|Q96SU5	Silent	SNP	ENST00000392549.2	hg19	CCDS44987.1																																																																																			.	.		0.458	RNFT2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032814		G	117290508	A	G	117290508	1	3	44	0	1	0	0	0	0	0	0	0	13517	175	7	2		2	RNFT2	12	117290508	3'UTR	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	6822045	117290508	16561387	297	5757										
SBNO1	55206	hgsc.bcm.edu	37	chr12	123813423	123813423	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cactcccattatgtttggaaGaaatttttccgtatttaaac	5	8	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr12:123813423G>T	ENST00000602398.1	-	10	1281	c.1154C>A	c.(1153-1155)tCt>tAt	p.S385Y	SBNO1_ENST00000420886.2_Missense_Mutation_p.S385Y|SBNO1_ENST00000267176.4_Missense_Mutation_p.S384Y|SBNO1_ENST00000602750.1_Missense_Mutation_p.S384Y			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	385					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		ATGTTTGGAAGAAATTTTTCC	0.328																																					p.S385Y		Atlas-SNP	.											SBNO1,NS,carcinoma,0,1	SBNO1	138	.	0			c.C1154A						.						66	66	66					12																	123813423		2203	4300	6503	SO:0001583	missense	55206	exon9			TTGGAAGAAATTT	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.1154C>A	chr12.hg19:g.123813423G>T	ENSP00000473665:p.Ser385Tyr	37.0	0.0		33.0	2.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	hg19	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.691780	0.88735	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	D;D	0.93366	-3.21;-3.21	5.53	5.53	0.82687	Helicase/UvrB domain (1);	0.000000	0.85682	D	0.000000	D	0.96852	0.8972	M	0.86178	2.8	0.80722	D	1	P;P;D	0.64830	0.933;0.942;0.994	P;P;D	0.65010	0.796;0.674;0.931	D	0.96535	0.9396	10	0.49607	T	0.09	-17.9778	19.4671	0.94946	0.0:0.0:1.0:0.0	.	385;384;383	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	Y	385;384;384	ENSP00000387361:S385Y;ENSP00000267176:S384Y	ENSP00000267176:S384Y	S	-	2	0	SBNO1	122379376	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	9.869000	0.99810	2.603000	0.88011	0.313000	0.20887	TCT	.	.		0.328	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		T	123813423	G	T	123813423	3	4	44	1	0	0	0	0	1	0	0	0	13877	942	33	3	3119	3	SBNO1	12	123813423	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	6522915	123813423	10038472	298	5758										
GJB6	10804	hgsc.bcm.edu	37	chr13	20797265	20797265	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttctgctttttaatgtcctCtatgtctttgaaatcattcc	4	10	4	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:20797265C>T	ENST00000356192.6	-	5	975	c.355G>A	c.(355-357)Gag>Aag	p.E119K	GJB6_ENST00000400065.3_Missense_Mutation_p.E119K|GJB6_ENST00000400066.3_Missense_Mutation_p.E119K|GJB6_ENST00000241124.6_Missense_Mutation_p.E119K	NM_001110219.2	NP_001103689.1	O95452	CXB6_HUMAN	gap junction protein, beta 6, 30kDa	119					apoptotic process (GO:0006915)|cell communication (GO:0007154)|ear morphogenesis (GO:0042471)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|sensory perception of sound (GO:0007605)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)				biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	9		all_cancers(29;2.04e-22)|all_epithelial(30;1.19e-19)|all_lung(29;2.27e-18)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;2.17e-05)|Epithelial(112;0.00075)|OV - Ovarian serous cystadenocarcinoma(117;0.00978)|Lung(94;0.0238)|GBM - Glioblastoma multiforme(144;0.0323)|LUSC - Lung squamous cell carcinoma(192;0.0744)		TTAATGTCCTCTATGTCTTTG	0.502																																					p.E119K		Atlas-SNP	.											.	GJB6	33	.	0			c.G355A						.						80	69	72					13																	20797265		2203	4300	6503	SO:0001583	missense	10804	exon4			TGTCCTCTATGTC	AJ005585	CCDS9291.1	13q12	2010-01-06	2007-11-06		ENSG00000121742	ENSG00000121742		"Ion channels / Gap junction proteins (connexins)"	4288	protein-coding gene	gene with protein product	"connexin 30"	604418	"ectodermal dysplasia 2, hidrotic (Clouston syndrome)", "gap junction protein, beta 6 (connexin 30)", "gap junction protein, beta 6"	DFNA3, ED2		10471490, 8845850	Standard	NM_006783		Approved	EDH, HED, CX30	uc001und.4	O95452	OTTHUMG00000016515	ENST00000356192.6:c.355G>A	chr13.hg19:g.20797265C>T	ENSP00000348521:p.Glu119Lys	84.0	0.0		51.0	4.0	NM_001110220	B3KQN2|Q5Q1H9|Q5Q1I0|Q5Q1I1|Q5T5U0|Q8IUP0	Missense_Mutation	SNP	ENST00000356192.6	hg19	CCDS9291.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.388609	0.25118	.	.	ENSG00000121742	ENST00000241124;ENST00000400065;ENST00000400066;ENST00000356192	D;D;D;D	0.97642	-4.47;-4.47;-4.47;-4.47	5.28	5.28	0.74379	.	0.268407	0.31010	N	0.008429	D	0.95950	0.8681	L	0.55103	1.725	0.53005	D	0.999965	P	0.35456	0.502	B	0.39419	0.299	D	0.94993	0.8136	10	0.24483	T	0.36	.	18.9412	0.92605	0.0:1.0:0.0:0.0	.	119	O95452	CXB6_HUMAN	K	119	ENSP00000241124:E119K;ENSP00000382938:E119K;ENSP00000382939:E119K;ENSP00000348521:E119K	ENSP00000241124:E119K	E	-	1	0	GJB6	19695265	0.991000	0.36638	0.716000	0.30569	0.104000	0.19210	3.052000	0.49893	2.450000	0.82876	0.655000	0.94253	GAG	.	.		0.502	GJB6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272906.1			T	20797265	C	T	20797265	3	4	44	1	0	0	0	0	1	0	0	0	6420	922	32	3	434	3	GJB6	13	20797265	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10		20797265	94372613	299	5759										
XPO4	64328	hgsc.bcm.edu	37	chr13	21442811	21442811	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atgtgctctgcatgctggcgTtgttcattattgaccatgga	11	8	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:21442811T>C	ENST00000255305.6	-	2	170	c.99A>G	c.(97-99)caA>caG	p.Q33Q	XPO4_ENST00000490513.1_5'UTR|XPO4_ENST00000400602.2_Silent_p.Q33Q			Q9C0E2	XPO4_HUMAN	exportin 4	33					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		CATGCTGGCGTTGTTCATTAT	0.323																																					p.Q33Q		Atlas-SNP	.											.	XPO4	153	.	0			c.A99G						.						158	151	153					13																	21442811		1914	4127	6041	SO:0001819	synonymous_variant	64328	exon2			CTGGCGTTGTTCA	AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"Exportins"	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.99A>G	chr13.hg19:g.21442811T>C		71.0	0.0		102.0	5.0	NM_022459	Q5VUZ5|Q8N3V6|Q9H934	Silent	SNP	ENST00000255305.6	hg19	CCDS41872.1																																																																																			.	.		0.323	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459		C	21442811	T	C	21442811	2	2	44	1	0	0	0	0	0	0	0	1	17461	1722	60	2		2	XPO4	13	21442811	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	645546	21442811	93727067	300	5760										
NBEA	26960	hgsc.bcm.edu	37	chr13	35756614	35756614	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gagagactacaagaactggaAgccaaccaggtagaaacatc	10	9	0	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:35756614A>G	ENST00000400445.3	+	29	5314	c.4780A>G	c.(4780-4782)Agc>Ggc	p.S1594G	NBEA_ENST00000540320.1_Missense_Mutation_p.S1594G|NBEA_ENST00000379939.2_Missense_Mutation_p.S1591G|NBEA_ENST00000310336.4_Missense_Mutation_p.S1594G	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1594					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AAGAACTGGAAGCCAACCAGG	0.378																																					p.S1594G		Atlas-SNP	.											.	NBEA	340	.	0			c.A4780G						.						124	115	118					13																	35756614		1838	4086	5924	SO:0001583	missense	26960	exon29			ACTGGAAGCCAAC	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.4780A>G	chr13.hg19:g.35756614A>G	ENSP00000383295:p.Ser1594Gly	126.0	0.0		87.0	4.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	15.40	2.823753	0.50739	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	5.11	3.93	0.45458	.	0.161285	0.56097	N	0.000033	T	0.38401	0.1039	L	0.29908	0.895	0.80722	D	1	B;B	0.25441	0.035;0.126	B;B	0.21546	0.018;0.035	T	0.15009	-1.0452	10	0.33141	T	0.24	.	10.796	0.46461	0.9258:0.0:0.0742:0.0	.	1594;1591	Q8NFP9;Q5T321	NBEA_HUMAN;.	G	1594;1594;1591;1594;253	ENSP00000440951:S1594G;ENSP00000383295:S1594G;ENSP00000369271:S1591G;ENSP00000308534:S1594G	ENSP00000308534:S1594G	S	+	1	0	NBEA	34654614	1.000000	0.71417	0.996000	0.52242	0.979000	0.70002	5.947000	0.70242	0.969000	0.38237	0.383000	0.25322	AGC	.	.		0.378	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35756614	A	G	35756614	3	3	44	1	0	0	0	0	1	0	0	0	10196	72	3	2	4894	2	NBEA	13	35756614	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	14313803	35756614	79413264	301	5761										
STOML3	161003	hgsc.bcm.edu	37	chr13	39542653	39542653	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccggatcccccacagttcggTggcatcatcaagtaaagtct	9	13	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:39542653T>C	ENST00000379631.4	-	6	879	c.535A>G	c.(535-537)Acc>Gcc	p.T179A	STOML3_ENST00000423210.1_Missense_Mutation_p.T170A	NM_145286.2	NP_660329.1	Q8TAV4	STML3_HUMAN	stomatin (EPB72)-like 3	179					signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	11		Lung NSC(96;1.42e-05)|Prostate(109;0.00851)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;2.93e-08)|Epithelial(112;3.64e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00107)|BRCA - Breast invasive adenocarcinoma(63;0.00349)|GBM - Glioblastoma multiforme(144;0.0137)		CACAGTTCGGTGGCATCATCA	0.463																																					p.T179A		Atlas-SNP	.											.	STOML3	47	.	0			c.A535G						.						79	82	81					13																	39542653		2203	4300	6503	SO:0001583	missense	161003	exon6			GTTCGGTGGCATC	BC025760	CCDS9367.1, CCDS45040.1	13q13.2	2004-03-05			ENSG00000133115	ENSG00000133115			19420	protein-coding gene	gene with protein product		608327				12122055	Standard	NM_145286		Approved	SRO, Epb7.2l	uc001uwx.3	Q8TAV4	OTTHUMG00000016763	ENST00000379631.4:c.535A>G	chr13.hg19:g.39542653T>C	ENSP00000368952:p.Thr179Ala	96.0	0.0		50.0	4.0	NM_145286	B4E285|Q5JS35	Missense_Mutation	SNP	ENST00000379631.4	hg19	CCDS9367.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.039303	0.75617	.	.	ENSG00000133115	ENST00000379631;ENST00000423210	D;D	0.93811	-3.29;-3.29	5.68	5.68	0.88126	Band 7/stomatin-like, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.96175	0.8753	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.96539	0.9399	10	0.72032	D	0.01	-21.4531	14.7487	0.69508	0.0:0.0:0.0:1.0	.	170;179	B4E285;Q8TAV4	.;STML3_HUMAN	A	179;170	ENSP00000368952:T179A;ENSP00000401989:T170A	ENSP00000368952:T179A	T	-	1	0	STOML3	38440653	1.000000	0.71417	0.997000	0.53966	0.520000	0.34377	5.980000	0.70516	2.165000	0.68154	0.533000	0.62120	ACC	.	.		0.463	STOML3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044604.2			C	39542653	T	C	39542653	3	2	44	1	0	0	0	0	1	0	0	0	15330	1696	59	2	348	2	STOML3	13	39542653	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	3786039	39542653	75627225	302	5762										
SLC25A30	253512	hgsc.bcm.edu	37	chr13	45973083	45973083	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atctgctcttacctgtaacaAgcaatccagggttcctgtgt	8	11	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:45973083A>G	ENST00000539591.1	-	7	755	c.592T>C	c.(592-594)Ttg>Ctg	p.L198L				Q5SVS4	KMCP1_HUMAN	solute carrier family 25, member 30	249					mitochondrial transport (GO:0006839)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.95e-05)		ACCTGTAACAAGCAATCCAGG	0.408																																					p.L249L		Atlas-SNP	.											.	SLC25A30	24	.	0			c.T745C						.						123	102	109					13																	45973083		2203	4300	6503	SO:0001819	synonymous_variant	253512	exon8			GTAACAAGCAATC	AK074457	CCDS31967.1, CCDS66539.1	13q14	2013-05-22			ENSG00000174032	ENSG00000174032		"Solute carriers"	27371	protein-coding gene	gene with protein product		610793					Standard	XM_005266321		Approved		uc001vag.3	Q5SVS4	OTTHUMG00000016853	ENST00000539591.1:c.592T>C	chr13.hg19:g.45973083A>G		116.0	0.0		61.0	4.0	NM_001010875	B2RN96|B4DZK3|F5H8H8	Silent	SNP	ENST00000539591.1	hg19																																																																																				.	.		0.408	SLC25A30-201	KNOWN	basic	protein_coding	protein_coding		XM_170736		G	45973083	A	G	45973083	2	3	44	1	0	0	0	0	0	0	0	1	14509	69	3	2		2	SLC25A30	13	45973083	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	6430430	45973083	69196795	303	5763										
WDFY2	115825	hgsc.bcm.edu	37	chr13	52301856	52301856	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtgtttatcggtgaccactcAggccaagtaacaatcctcaa	8	11	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:52301856A>G	ENST00000298125.5	+	6	708	c.528A>G	c.(526-528)tcA>tcG	p.S176S		NM_052950.3	NP_443182.1	Q96P53	WDFY2_HUMAN	WD repeat and FYVE domain containing 2	176							metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	16		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)		GTGACCACTCAGGCCAAGTAA	0.403																																					p.S176S		Atlas-SNP	.											.	WDFY2	36	.	0			c.A528G						.						143	127	133					13																	52301856		2203	4300	6503	SO:0001819	synonymous_variant	115825	exon6			CCACTCAGGCCAA	AF411978	CCDS9429.1	13q14.12	2013-01-09	2003-03-13		ENSG00000139668	ENSG00000139668		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20482	protein-coding gene	gene with protein product		610418	"WD40 and FYVE domain containing 2"				Standard	NM_052950		Approved	ZFYVE22	uc001vfp.3	Q96P53	OTTHUMG00000017407	ENST00000298125.5:c.528A>G	chr13.hg19:g.52301856A>G		101.0	0.0		99.0	4.0	NM_052950	B1AL86|Q96CS1	Silent	SNP	ENST00000298125.5	hg19	CCDS9429.1																																																																																			.	.		0.403	WDFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045985.3	NM_052950		G	52301856	A	G	52301856	2	3	44	1	0	0	0	0	0	0	0	1	17284	175	7	2		2	WDFY2	13	52301856	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	6328773	52301856	62868022	304	5764										
C13orf34	79866	hgsc.bcm.edu	37	chr13	73320191	73320191	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tttctcaccaattgaatttcAgataggagagactccactct	6	10	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:73320191A>G	ENST00000390667.5	+	9	945	c.848A>G	c.(847-849)cAg>cGg	p.Q283R	BORA_ENST00000377815.3_Missense_Mutation_p.Q213R	NM_024808.2	NP_079084.2	Q6PGQ7	BORA_HUMAN	bora, aurora kinase A activator	283					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of mitosis (GO:0007088)|regulation of mitotic spindle organization (GO:0060236)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)	protein kinase binding (GO:0019901)	p.Q283R(1)									ATTGAATTTCAGATAGGAGAG	0.348																																					p.Q283R		Atlas-SNP	.											C13orf34,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.A848G						.						116	109	111					13																	73320191		1810	4073	5883	SO:0001583	missense	79866	exon9			AATTTCAGATAGG	BC025367	CCDS9446.1, CCDS66560.1, CCDS9446.2, CCDS73583.1	13q22.1	2013-08-13	2011-08-09	2011-08-09	ENSG00000136122	ENSG00000136122			24724	protein-coding gene	gene with protein product		610510	"chromosome 13 open reading frame 34"	C13orf34		16890155, 18378770, 18566290, 19487276	Standard	NM_001286746		Approved	FLJ22624	uc001viv.1	Q6PGQ7	OTTHUMG00000017068	ENST00000390667.5:c.848A>G	chr13.hg19:g.73320191A>G	ENSP00000375082:p.Gln283Arg	137.0	0.0		91.0	5.0	NM_024808	B4DQ30|Q5W0P3|Q5W0P4|Q86YC6|Q96IW9|Q9H640	Missense_Mutation	SNP	ENST00000390667.5	hg19	CCDS9446.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.893912	0.33442	.	.	ENSG00000136122	ENST00000377815;ENST00000390667	T;T	0.33216	1.42;1.43	5.69	5.69	0.88448	.	0.424023	0.28317	N	0.015781	T	0.49029	0.1533	M	0.62723	1.935	0.39911	D	0.97403	D;P;D;P	0.60575	0.988;0.902;0.988;0.902	P;P;P;P	0.57960	0.778;0.52;0.83;0.52	T	0.52487	-0.8569	10	0.59425	D	0.04	-6.1825	15.9518	0.79846	1.0:0.0:0.0:0.0	.	213;283;343;283	B4DQ30;A8K631;B5LMG6;Q6PGQ7	.;.;.;BORA_HUMAN	R	213;283	ENSP00000367046:Q213R;ENSP00000375082:Q283R	ENSP00000367046:Q213R	Q	+	2	0	BORA	72218192	1.000000	0.71417	0.911000	0.35937	0.150000	0.21749	6.748000	0.74877	2.180000	0.69256	0.533000	0.62120	CAG	.	.		0.348	BORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045245.3	NM_024808		G	73320191	A	G	73320191	3	3	44	1	0	0	0	0	1	0	0	0	1730	188	7	2	878	2	C13orf34	13	73320191	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	21018335	73320191	41849687	305	5765										
PIBF1	10464	hgsc.bcm.edu	37	chr13	73366611	73366611	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaattggaggagaaacttaaTgatgcacttcaccagaagca	10	7	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:73366611T>C	ENST00000326291.6	+	3	617	c.279T>C	c.(277-279)aaT>aaC	p.N93N		NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	93						centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		AGAAACTTAATGATGCACTTC	0.284																																					p.N93N		Atlas-SNP	.											.	PIBF1	65	.	0			c.T279C						.						57	63	61					13																	73366611		2203	4297	6500	SO:0001819	synonymous_variant	10464	exon3			ACTTAATGATGCA	AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"progesterone-induced blocking factor 1"	607532	"chromosome 13 open reading frame 24"	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.279T>C	chr13.hg19:g.73366611T>C		138.0	0.0		95.0	4.0	NM_006346	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Silent	SNP	ENST00000326291.6	hg19	CCDS31991.1																																																																																			.	.		0.284	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346		C	73366611	T	C	73366611	2	2	44	1	0	0	0	0	0	0	0	1	11888	1461	51	2		2	PIBF1	13	73366611	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	46420	73366611	41803267	306	5766										
SCEL	8796	hgsc.bcm.edu	37	chr13	78176797	78176797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttttttccaaagaagacaaaAtctcgaatctgttgctaaag	6	7	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:78176797A>G	ENST00000349847.3	+	17	1070	c.986A>G	c.(985-987)aAt>aGt	p.N329S	SCEL_ENST00000377246.3_Missense_Mutation_p.N309S|SCEL_ENST00000535157.1_Missense_Mutation_p.N307S|SCEL-AS1_ENST00000457528.2_RNA|SCEL_ENST00000469982.1_Intron|SCEL-AS1_ENST00000456280.2_RNA	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	329	16 X approximate tandem repeats.				embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		AGAAGACAAAATCTCGAATCT	0.348																																					p.N329S		Atlas-SNP	.											.	SCEL	85	.	0			c.A986G						.						132	140	137					13																	78176797		2203	4300	6503	SO:0001583	missense	8796	exon17			GACAAAATCTCGA	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.986A>G	chr13.hg19:g.78176797A>G	ENSP00000302579:p.Asn329Ser	118.0	0.0		94.0	4.0	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	hg19	CCDS9459.1	.	.	.	.	.	.	.	.	.	.	A	14.06	2.423341	0.43020	.	.	ENSG00000136155	ENST00000535157;ENST00000377246;ENST00000349847	T;T;T	0.21734	1.99;1.99;1.99	3.93	2.74	0.32292	.	0.298408	0.23716	N	0.045279	T	0.09818	0.0241	N	0.08118	0	0.21020	N	0.999803	B;B;B	0.12013	0.004;0.004;0.005	B;B;B	0.15484	0.013;0.007;0.01	T	0.21177	-1.0253	10	0.66056	D	0.02	-6.007	6.0949	0.20015	0.8805:0.0:0.1195:0.0	.	307;309;329	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	S	307;309;329	ENSP00000437895:N307S;ENSP00000366454:N309S;ENSP00000302579:N329S	ENSP00000302579:N329S	N	+	2	0	SCEL	77074798	0.228000	0.23718	0.924000	0.36721	0.474000	0.32979	1.191000	0.32138	0.679000	0.31345	0.533000	0.62120	AAT	.	.		0.348	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777		G	78176797	A	G	78176797	3	3	44	1	0	0	0	0	1	0	0	0	13903	101	4	2	1048	2	SCEL	13	78176797	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	4810186	78176797	36993081	307	5767										
DOCK9	23348	hgsc.bcm.edu	37	chr13	99537983	99537983	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttgggtttcaacgacatcccTcttcttcgtgcttcctttac	6	13	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:99537983T>C	ENST00000376460.1	-	20	2319	c.2239A>G	c.(2239-2241)Agg>Ggg	p.R747G	DOCK9_ENST00000339416.2_Missense_Mutation_p.R748G|DOCK9_ENST00000448493.2_Missense_Mutation_p.R759G|DOCK9_ENST00000442173.1_Missense_Mutation_p.R747G	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	748	DHR-1.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ACGACATCCCTCTTCTTCGTG	0.398																																					p.R748G		Atlas-SNP	.											.	DOCK9	311	.	0			c.A2242G						.						120	123	122					13																	99537983		1881	4112	5993	SO:0001583	missense	23348	exon20			CATCCCTCTTCTT	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.2239A>G	chr13.hg19:g.99537983T>C	ENSP00000365643:p.Arg747Gly	122.0	0.0		100.0	4.0	NM_001130049	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	hg19	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	T	17.00	3.275942	0.59649	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	T;T;T;T	0.19938	2.43;2.52;2.11;2.13	6.03	6.03	0.97812	.	0.091405	0.64402	D	0.000001	T	0.17238	0.0414	N	0.17082	0.46	0.42605	D	0.993296	B;B;B;B;B	0.33940	0.14;0.433;0.004;0.0;0.037	B;B;B;B;B	0.35353	0.099;0.201;0.016;0.001;0.099	T	0.05666	-1.0871	10	0.62326	D	0.03	.	16.5582	0.84512	0.0:0.0:0.0:1.0	.	748;747;747;747;748	A6H8Z6;E9PFM9;B3KX25;Q9BZ29-5;Q9BZ29	.;.;.;.;DOCK9_HUMAN	G	747;748;748;748;747;748;759;747	ENSP00000365643:R747G;ENSP00000341086:R748G;ENSP00000401958:R759G;ENSP00000406883:R747G	ENSP00000341086:R748G	R	-	1	2	DOCK9	98335984	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.675000	0.61619	2.308000	0.77769	0.533000	0.62120	AGG	.	.		0.398	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		C	99537983	T	C	99537983	3	2	44	1	0	0	0	0	1	0	0	0	4696	1550	54	2	4176	2	DOCK9	13	99537983	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	21361186	99537983	15631895	308	5768										
GPR183	1880	hgsc.bcm.edu	37	chr13	99947814	99947814	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaaacatgccccaagcagaaTccagggaagagatttagttt	10	8	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:99947814T>C	ENST00000376414.4	-	2	669	c.586A>G	c.(586-588)Att>Gtt	p.I196V	UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	196					G-protein coupled receptor signaling pathway (GO:0007186)|humoral immune response (GO:0006959)|immune response (GO:0006955)|mature B cell differentiation involved in immune response (GO:0002313)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|oxysterol binding (GO:0008142)			cervix(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	23						CCAAGCAGAATCCAGGGAAGA	0.423																																					p.I196V		Atlas-SNP	.											.	GPR183	38	.	0			c.A586G						.						81	79	80					13																	99947814		2203	4300	6503	SO:0001583	missense	1880	exon2			GCAGAATCCAGGG	L08177	CCDS9492.1	13q32.3	2012-08-21	2008-07-21	2008-07-21	ENSG00000169508	ENSG00000169508		"GPCR / Class A : Orphans"	3128	protein-coding gene	gene with protein product	"EBV-induced G-protein coupled receptor 2"	605741	"Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor)"	EBI2		8383238	Standard	NM_004951		Approved		uc001vog.3	P32249	OTTHUMG00000017263	ENST00000376414.4:c.586A>G	chr13.hg19:g.99947814T>C	ENSP00000365596:p.Ile196Val	180.0	0.0		144.0	6.0	NM_004951	B2R8N5|Q53F99|Q5JUH7	Missense_Mutation	SNP	ENST00000376414.4	hg19	CCDS9492.1	.	.	.	.	.	.	.	.	.	.	T	8.742	0.919164	0.17982	.	.	ENSG00000169508	ENST00000376414	T	0.36520	1.25	5.76	5.76	0.90799	GPCR, rhodopsin-like superfamily (1);	0.150199	0.64402	D	0.000016	T	0.21347	0.0514	N	0.05351	-0.065	0.39609	D	0.969853	B	0.23854	0.092	B	0.24541	0.054	T	0.12863	-1.0531	9	.	.	.	.	16.0843	0.81031	0.0:0.0:0.0:1.0	.	196	P32249	GP183_HUMAN	V	196	ENSP00000365596:I196V	.	I	-	1	0	GPR183	98745815	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.896000	0.56266	2.191000	0.70037	0.533000	0.62120	ATT	.	.		0.423	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045582.2	NM_004951		C	99947814	T	C	99947814	3	2	44	1	0	0	0	0	1	0	0	0	6686	1435	50	2	503	2	GPR183	13	99947814	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	409831	99947814	15222064	309	5769										
ANKRD10	55608	hgsc.bcm.edu	37	chr13	111532117	111532117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cagtgtccccaaacccgtggTagtgtccatagtacaggtta	10	11	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:111532117T>C	ENST00000267339.2	-	6	1264	c.1130A>G	c.(1129-1131)tAc>tGc	p.Y377C	ANKRD10_ENST00000375758.5_3'UTR	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	377										central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)	9	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			AAACCCGTGGTAGTGTCCATA	0.552																																					p.Y377C		Atlas-SNP	.											.	ANKRD10	24	.	0			c.A1130G						.						152	110	124					13																	111532117		2203	4300	6503	SO:0001583	missense	55608	exon6			CCGTGGTAGTGTC	AK000100	CCDS9520.1, CCDS66580.1	13q33.3	2013-01-10			ENSG00000088448	ENSG00000088448		"Ankyrin repeat domain containing"	20265	protein-coding gene	gene with protein product							Standard	NM_017664		Approved	FLJ20093	uc001vrn.3	Q9NXR5	OTTHUMG00000017349	ENST00000267339.2:c.1130A>G	chr13.hg19:g.111532117T>C	ENSP00000267339:p.Tyr377Cys	80.0	0.0		77.0	4.0	NM_017664	Q5VW12|Q9BV12	Missense_Mutation	SNP	ENST00000267339.2	hg19	CCDS9520.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.050857	0.75960	.	.	ENSG00000088448	ENST00000267339	T	0.79749	-1.3	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.89019	0.6596	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.90405	0.4405	10	0.87932	D	0	-22.7768	15.4534	0.75294	0.0:0.0:0.0:1.0	.	377	Q9NXR5	ANR10_HUMAN	C	377	ENSP00000267339:Y377C	ENSP00000267339:Y377C	Y	-	2	0	ANKRD10	110330118	1.000000	0.71417	0.990000	0.47175	0.913000	0.54294	5.954000	0.70298	2.051000	0.60960	0.528000	0.53228	TAC	.	.		0.552	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1			C	111532117	T	C	111532117	3	2	44	1	0	0	0	0	1	0	0	0	638	1638	57	2	136	2	ANKRD10	13	111532117	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	11584303	111532117	3637761	310	5770										
MCF2L	23263	hgsc.bcm.edu	37	chr13	113739231	113739231	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agatttccagatctatgagaAgtactgtcagaacaagcccc	8	10	2	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr13:113739231A>G	ENST00000375608.3	+	20	2235	c.2177A>G	c.(2176-2178)aAg>aGg	p.K726R	MCF2L_ENST00000375604.2_Missense_Mutation_p.K753R|MCF2L_ENST00000423482.2_Missense_Mutation_p.K694R|MCF2L_ENST00000442652.2_Missense_Mutation_p.K726R|MCF2L_ENST00000535094.2_Missense_Mutation_p.K696R|MCF2L_ENST00000375601.3_Missense_Mutation_p.K700R|MCF2L_ENST00000397030.1_Missense_Mutation_p.K729R|MCF2L_ENST00000421756.1_Missense_Mutation_p.K700R|MCF2L_ENST00000375597.4_Missense_Mutation_p.K694R|MCF2L_ENST00000434480.2_Missense_Mutation_p.K702R			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	726	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				ATCTATGAGAAGTACTGTCAG	0.582																																					p.K696R		Atlas-SNP	.											.	MCF2L	182	.	0			c.A2087G						.						128	122	124					13																	113739231		2203	4300	6503	SO:0001583	missense	23263	exon19			ATGAGAAGTACTG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.2177A>G	chr13.hg19:g.113739231A>G	ENSP00000364758:p.Lys726Arg	123.0	0.0		81.0	4.0	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	hg19		.	.	.	.	.	.	.	.	.	.	A	21.3	4.128925	0.77549	.	.	ENSG00000126217	ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000440749	T;T;T;T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	4.64	4.64	0.57946	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.69975	0.3171	L	0.41356	1.27	0.51012	D	0.9999	P;P;D;D;P;P	0.69078	0.869;0.722;0.997;0.997;0.515;0.892	P;P;D;D;P;P	0.71656	0.605;0.605;0.951;0.974;0.505;0.813	T	0.69840	-0.5036	10	0.40728	T	0.16	.	14.1203	0.65182	1.0:0.0:0.0:0.0	.	694;696;753;658;694;726	E9PDN8;O15068-9;G5E9A1;E2QRA2;O15068-4;O15068	.;.;.;.;.;MCF2L_HUMAN	R	726;726;753;729;696;700;700;702;694;694;537	ENSP00000364758:K726R;ENSP00000401422:K726R;ENSP00000364754:K753R;ENSP00000380225:K729R;ENSP00000440374:K696R;ENSP00000397285:K700R;ENSP00000364751:K700R;ENSP00000407722:K702R;ENSP00000405639:K694R;ENSP00000364747:K694R	ENSP00000364747:K694R	K	+	2	0	MCF2L	112787232	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	4.960000	0.63673	1.732000	0.51606	0.248000	0.18094	AAG	.	.		0.582	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			G	113739231	A	G	113739231	3	3	44	1	0	0	0	0	1	0	0	0	9388	72	3	2	2427	2	MCF2L	13	113739231	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2207114	113739231	1430647	311	5771										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64600817	64600817	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aatttgatgaaaactatgcaTctcttgaaaaggacctggaa	8	6	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr14:64600817T>C	ENST00000344113.4	+	78	14757	c.14545T>C	c.(14545-14547)Tct>Cct	p.S4849P	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000357395.3_Missense_Mutation_p.S1234P|SYNE2_ENST00000394768.2_Missense_Mutation_p.S1234P|SYNE2_ENST00000554584.1_Missense_Mutation_p.S4766P|SYNE2_ENST00000555002.1_Missense_Mutation_p.S1483P|SYNE2_ENST00000358025.3_Missense_Mutation_p.S4849P	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4849					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAACTATGCATCTCTTGAAAA	0.353																																					p.S4849P		Atlas-SNP	.											.	SYNE2	577	.	0			c.T14545C						.						131	135	133					14																	64600817		2203	4300	6503	SO:0001583	missense	23224	exon78			TATGCATCTCTTG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.14545T>C	chr14.hg19:g.64600817T>C	ENSP00000341781:p.Ser4849Pro	142.0	0.0		75.0	4.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.485329	0.26598	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.58506	0.68;3.99;0.68;0.33;4.04;3.99	5.95	3.47	0.39725	.	0.406135	0.21002	N	0.081843	T	0.59636	0.2208	M	0.64997	1.995	0.19775	N	0.999958	P;P;D	0.56287	0.942;0.891;0.975	P;B;P	0.53450	0.708;0.37;0.726	T	0.53330	-0.8454	10	0.49607	T	0.09	.	3.582	0.07957	0.1214:0.0694:0.2811:0.5281	.	1234;4849;4849	Q8WXH0-7;Q8WXH0;Q8WXH0-2	.;SYNE2_HUMAN;.	P	4849;1234;4849;4766;4766;1483;1234	ENSP00000350719:S4849P;ENSP00000349969:S1234P;ENSP00000341781:S4849P;ENSP00000452570:S4766P;ENSP00000450831:S1483P;ENSP00000378249:S1234P	ENSP00000261678:S4766P	S	+	1	0	SYNE2	63670570	0.011000	0.17503	0.983000	0.44433	0.997000	0.91878	0.600000	0.24104	0.431000	0.26258	0.459000	0.35465	TCT	.	.		0.353	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		C	64600817	T	C	64600817	3	2	44	1	0	0	0	0	1	0	0	0	15461	1435	50	2	14851	2	SYNE2	14	64600817	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10		64600817	42748723	312	5772										
ESR2	2100	hgsc.bcm.edu	37	chr14	64727316	64727316	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctccaggagggtgagcactAgctgctcggggctcagggcg	17	12	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr14:64727316A>G	ENST00000341099.4	-	5	1220	c.803T>C	c.(802-804)cTa>cCa	p.L268P	ESR2_ENST00000542956.1_Missense_Mutation_p.L268P|ESR2_ENST00000353772.3_Missense_Mutation_p.L268P|ESR2_ENST00000358599.5_Missense_Mutation_p.L268P|ESR2_ENST00000555483.1_5'UTR|ESR2_ENST00000554572.1_Missense_Mutation_p.L268P|ESR2_ENST00000555278.1_Missense_Mutation_p.L268P|ESR2_ENST00000553796.1_Missense_Mutation_p.L268P|ESR2_ENST00000557772.1_Missense_Mutation_p.L268P|ESR2_ENST00000267525.6_Missense_Mutation_p.L268P|ESR2_ENST00000357782.2_Missense_Mutation_p.L268P	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	268	Steroid-binding.				brain development (GO:0007420)|cell-cell signaling (GO:0007267)|epithelial cell maturation involved in prostate gland development (GO:0060743)|extracellular negative regulation of signal transduction (GO:1900116)|gene expression (GO:0010467)|hormone-mediated apoptotic signaling pathway (GO:0008628)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|ovarian follicle development (GO:0001541)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|uterus development (GO:0060065)|vagina development (GO:0060068)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor antagonist activity (GO:0048019)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	GGTGAGCACTAGCTGCTCGGG	0.682																																					p.L268P		Atlas-SNP	.											.	ESR2	82	.	0			c.T803C						.						35	37	36					14																	64727316		2203	4299	6502	SO:0001583	missense	2100	exon4			AGCACTAGCTGCT	X99101	CCDS9762.1, CCDS32096.1, CCDS55920.1, CCDS61469.1, CCDS61470.1	14q21-q22	2013-01-16			ENSG00000140009	ENSG00000140009		"Nuclear hormone receptors"	3468	protein-coding gene	gene with protein product		601663				8769313	Standard	NM_001214902		Approved	NR3A2, Erb	uc001xha.1	Q92731	OTTHUMG00000141306	ENST00000341099.4:c.803T>C	chr14.hg19:g.64727316A>G	ENSP00000343925:p.Leu268Pro	170.0	0.0		94.0	4.0	NM_001214902	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Missense_Mutation	SNP	ENST00000341099.4	hg19	CCDS9762.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.074584	0.76415	.	.	ENSG00000140009	ENST00000556275;ENST00000542956;ENST00000554572;ENST00000353772;ENST00000358599;ENST00000555278;ENST00000553796;ENST00000357782;ENST00000557772;ENST00000341099;ENST00000267525	D;D;D;D;D;D;D;D;D;D;T	0.91996	-2.93;-2.86;-2.86;-2.86;-2.86;-2.95;-2.93;-2.95;-2.93;-2.76;0.4	5.74	5.74	0.90152	Nuclear hormone receptor, ligand-binding (2);	0.177454	0.50627	D	0.000118	D	0.96374	0.8817	M	0.84433	2.695	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.993;0.996;0.999;0.999;0.996	D	0.96973	0.9710	10	0.87932	D	0	.	16.0363	0.80631	1.0:0.0:0.0:0.0	.	268;268;268;268;268	Q92731-7;Q92731;Q92731-6;Q92731-5;F1D8N3	.;ESR2_HUMAN;.;.;.	P	268	ENSP00000452485:L268P;ENSP00000441792:L268P;ENSP00000450699:L268P;ENSP00000335551:L268P;ENSP00000351412:L268P;ENSP00000450488:L268P;ENSP00000452426:L268P;ENSP00000350427:L268P;ENSP00000451582:L268P;ENSP00000343925:L268P;ENSP00000267525:L268P	ENSP00000267525:L268P	L	-	2	0	ESR2	63797069	1.000000	0.71417	1.000000	0.80357	0.494000	0.33585	5.987000	0.70571	2.193000	0.70182	0.460000	0.39030	CTA	.	.		0.682	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1			G	64727316	A	G	64727316	3	3	44	1	0	0	0	0	1	0	0	0	5259	420	15	2	895	2	ESR2	14	64727316	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	126499	64727316	42622224	313	5773										
NEK9	91754	hgsc.bcm.edu	37	chr14	75563856	75563856	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acaggtccgggacatgatgcAgagatccaaaaataggccga	12	9	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr14:75563856A>G	ENST00000238616.5	-	17	2278	c.2120T>C	c.(2119-2121)cTg>cCg	p.L707P		NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	707					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		GACATGATGCAGAGATCCAAA	0.527																																					p.L707P		Atlas-SNP	.											.	NEK9	64	.	0			c.T2120C						.						90	78	82					14																	75563856		2203	4300	6503	SO:0001583	missense	91754	exon17			TGATGCAGAGATC	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"NIMA (never in mitosis gene a)- related kinase 9"			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.2120T>C	chr14.hg19:g.75563856A>G	ENSP00000238616:p.Leu707Pro	89.0	0.0		68.0	4.0	NM_033116	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Missense_Mutation	SNP	ENST00000238616.5	hg19	CCDS9839.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.592777	0.86953	.	.	ENSG00000119638	ENST00000238616	T	0.80824	-1.42	5.72	5.72	0.89469	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.84092	0.5396	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.995;0.999	D	0.83543	0.0097	10	0.36615	T	0.2	.	16.3035	0.82836	1.0:0.0:0.0:0.0	.	707;50	Q8TD19;Q6PKF2	NEK9_HUMAN;.	P	707	ENSP00000238616:L707P	ENSP00000238616:L707P	L	-	2	0	NEK9	74633609	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.287000	0.95975	2.299000	0.77371	0.528000	0.53228	CTG	.	.		0.527	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116		G	75563856	A	G	75563856	3	3	44	1	0	0	0	0	1	0	0	0	10340	188	7	2	843	2	NEK9	14	75563856	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	10836540	75563856	31785684	314	5774										
SPATA7	55812	hgsc.bcm.edu	37	chr14	88899513	88899513	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgtatctgagtttcattgaaGatgtaacagatgaaattttg	9	3	2	5			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr14:88899513G>A	ENST00000393545.4	+	10	1406	c.1117G>A	c.(1117-1119)Gat>Aat	p.D373N	SPATA7_ENST00000356583.5_Missense_Mutation_p.D341N|SPATA7_ENST00000045347.7_Missense_Mutation_p.D373N|SPATA7_ENST00000556553.1_Missense_Mutation_p.D341N	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	373					response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						TTTCATTGAAGATGTAACAGA	0.269																																					p.D373N		Atlas-SNP	.											SPATA7,NS,carcinoma,0,1	SPATA7	58	.	0			c.G1117A						.						82	84	83					14																	88899513		2199	4272	6471	SO:0001583	missense	55812	exon10			ATTGAAGATGTAA	AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"Leber congenital amaurosis 3"	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.1117G>A	chr14.hg19:g.88899513G>A	ENSP00000377176:p.Asp373Asn	60.0	0.0		40.0	2.0	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Missense_Mutation	SNP	ENST00000393545.4	hg19	CCDS9883.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.553794	0.45487	.	.	ENSG00000042317	ENST00000556553;ENST00000393545;ENST00000356583;ENST00000045347;ENST00000554802	T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75	5.08	4.18	0.49190	.	0.208574	0.40144	N	0.001162	T	0.20981	0.0505	L	0.33245	0.995	0.34791	D	0.735754	B;B;B;B	0.33448	0.412;0.412;0.385;0.197	B;B;B;B	0.35688	0.119;0.192;0.208;0.119	T	0.28459	-1.0043	10	0.35671	T	0.21	-9.0797	11.8403	0.52350	0.0885:0.0:0.9115:0.0	.	373;341;341;373	Q9P0W8-3;A8K3L6;Q9P0W8-2;Q9P0W8	.;.;.;SPAT7_HUMAN	N	341;373;341;373;5	ENSP00000451128:D341N;ENSP00000377176:D373N;ENSP00000348991:D341N;ENSP00000045347:D373N;ENSP00000451019:D5N	ENSP00000045347:D373N	D	+	1	0	SPATA7	87969266	1.000000	0.71417	0.996000	0.52242	0.950000	0.60333	3.475000	0.53136	1.241000	0.43820	0.591000	0.81541	GAT	.	.		0.269	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1			A	88899513	G	A	88899513	3	1	44	1	0	0	0	0	1	0	0	0	15029	942	33	3	1155	3	SPATA7	14	88899513	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	13335657	88899513	18450027	315	5775										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94155183	94155183	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcccccctctgcaatgcagcAagggtaagacccttactatt	7	14	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr14:94155183A>G	ENST00000393151.2	+	45	7199	c.7199A>G	c.(7198-7200)cAa>cGa	p.Q2400R	UNC79_ENST00000256339.4_Missense_Mutation_p.Q2223R|UNC79_ENST00000555664.1_Missense_Mutation_p.Q2361R|UNC79_ENST00000553484.1_Missense_Mutation_p.Q2422R			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2400					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						GCAATGCAGCAAGGGTAAGAC	0.517																																					p.Q2223R		Atlas-SNP	.											.	UNC79	366	.	0			c.A6668G						.						88	78	81					14																	94155183		2203	4300	6503	SO:0001583	missense	57578	exon45			TGCAGCAAGGGTA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7199A>G	chr14.hg19:g.94155183A>G	ENSP00000376858:p.Gln2400Arg	122.0	0.0		77.0	5.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	A	25.8	4.670953	0.88348	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.19806	2.12;2.14;2.12;2.12	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.43656	0.1257	L	0.61218	1.895	0.58432	D	0.999999	D	0.60575	0.988	D	0.65874	0.939	T	0.33777	-0.9855	10	0.72032	D	0.01	-10.5258	16.1082	0.81241	1.0:0.0:0.0:0.0	.	2422	C9JQL1	.	R	2223;2361;2422;2400;2422	ENSP00000256339:Q2223R;ENSP00000450868:Q2361R;ENSP00000451360:Q2422R;ENSP00000376858:Q2400R	ENSP00000256339:Q2223R	Q	+	2	0	KIAA1409	93224936	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.263000	0.95617	2.268000	0.75426	0.459000	0.35465	CAA	.	.		0.517	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		G	94155183	A	G	94155183	3	3	44	1	0	0	0	0	1	0	0	0	8239	130	5	2	6834	2	KIAA1409	14	94155183	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	5255670	94155183	13194357	316	5776										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94158267	94158267	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tagggtgacacccagcatccTtcagctaatggcccataaca	8	13	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr14:94158267T>C	ENST00000393151.2	+	47	7562	c.7562T>C	c.(7561-7563)cTt>cCt	p.L2521P	UNC79_ENST00000256339.4_Missense_Mutation_p.L2344P|UNC79_ENST00000555664.1_Missense_Mutation_p.L2482P|UNC79_ENST00000553484.1_Missense_Mutation_p.L2543P			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2521					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CCCAGCATCCTTCAGCTAATG	0.473																																					p.L2344P		Atlas-SNP	.											.	UNC79	366	.	0			c.T7031C						.						132	121	124					14																	94158267		2203	4300	6503	SO:0001583	missense	57578	exon47			GCATCCTTCAGCT	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7562T>C	chr14.hg19:g.94158267T>C	ENSP00000376858:p.Leu2521Pro	159.0	0.0		72.0	4.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	T	23.7	4.446465	0.84101	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.56776	0.46;0.52;0.44;0.46	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.73079	0.3541	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76526	-0.2927	10	0.87932	D	0	-18.2659	16.1668	0.81768	0.0:0.0:0.0:1.0	.	2543	C9JQL1	.	P	2344;2482;2543;2521;2543	ENSP00000256339:L2344P;ENSP00000450868:L2482P;ENSP00000451360:L2543P;ENSP00000376858:L2521P	ENSP00000256339:L2344P	L	+	2	0	KIAA1409	93228020	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.040000	0.89188	2.210000	0.71456	0.533000	0.62120	CTT	.	.		0.473	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		C	94158267	T	C	94158267	3	2	44	1	0	0	0	0	1	0	0	0	8239	1609	56	2	7205	2	KIAA1409	14	94158267	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	3084	94158267	13191273	317	5777										
SERPINA6	866	hgsc.bcm.edu	37	chr14	94776279	94776279	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atgggcaccttcaccacagtTgtctcgtccacatagaagtt	8	12	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr14:94776279T>C	ENST00000341584.3	-	3	824	c.678A>G	c.(676-678)acA>acG	p.T226T		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	226					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	TCACCACAGTTGTCTCGTCCA	0.557																																					p.T226T		Atlas-SNP	.											.	SERPINA6	102	.	0			c.A678G						.						131	102	112					14																	94776279		2203	4300	6503	SO:0001819	synonymous_variant	866	exon3			CACAGTTGTCTCG	J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"Serine (or cysteine) peptidase inhibitors"	1540	protein-coding gene	gene with protein product	"corticosteroid binding globulin", "transcortin"	122500	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.678A>G	chr14.hg19:g.94776279T>C		126.0	0.0		76.0	4.0	NM_001756	A8K456|Q7Z2Q9	Silent	SNP	ENST00000341584.3	hg19	CCDS9924.1																																																																																			.	.		0.557	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756		C	94776279	T	C	94776279	2	2	44	1	0	0	0	0	0	0	0	1	14108	1799	63	2		2	SERPINA6	14	94776279	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	618012	94776279	12573261	318	5778										
PPP2R5C	5527	hgsc.bcm.edu	37	chr14	102252487	102252487	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	caaggtttagcgcaagcaatAatagagaacttcaaaaacta	7	7	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr14:102252487A>G	ENST00000328724.5	+	3	235	c.226A>G	c.(226-228)Aat>Gat	p.N76D	PPP2R5C_ENST00000556068.1_3'UTR|PPP2R5C_ENST00000422945.2_Intron|PPP2R5C_ENST00000554442.1_Missense_Mutation_p.N76D	NM_001161726.1	NP_001155198.1	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	19					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CGCAAGCAATAATAGAGAACT	0.353																																					p.N76D		Atlas-SNP	.											.	PPP2R5C	74	.	0			c.A226G						.						37	32	33					14																	102252487		1563	3574	5137	SO:0001583	missense	5527	exon3			AGCAATAATAGAG	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000328724.5:c.226A>G	chr14.hg19:g.102252487A>G	ENSP00000329009:p.Asn76Asp	178.0	0.0		100.0	4.0	NM_001161726	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Missense_Mutation	SNP	ENST00000328724.5	hg19	CCDS53911.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.167986	0.78339	.	.	ENSG00000078304	ENST00000554442;ENST00000328724	T	0.45276	0.9	5.25	4.11	0.48088	.	0.000000	0.85682	D	0.000000	T	0.23330	0.0564	.	.	.	0.80722	D	1	B;P	0.40619	0.021;0.724	B;B	0.35470	0.029;0.203	T	0.03403	-1.1040	9	0.11182	T	0.66	-16.9017	9.9581	0.41680	0.9185:0.0:0.0815:0.0	.	76;76	Q6ZN33;G3V292	.;.	D	76	ENSP00000329009:N76D	ENSP00000329009:N76D	N	+	1	0	PPP2R5C	101322240	1.000000	0.71417	0.981000	0.43875	0.979000	0.70002	5.067000	0.64357	0.841000	0.35020	0.459000	0.35465	AAT	.	.		0.353	PPP2R5C-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414362.1	NM_002719		G	102252487	A	G	102252487	3	3	44	1	0	0	0	0	1	0	0	0	12406	362	13	2	236	2	PPP2R5C	14	102252487	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	7476208	102252487	5097053	319	5779										
TRMT61A	115708	hgsc.bcm.edu	37	chr14	103999139	103999139	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtcttcctggacatcccatcAccctgggaggccgtgggcca	12	15	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr14:103999139A>G	ENST00000389749.4	+	3	659	c.552A>G	c.(550-552)tcA>tcG	p.S184S		NM_152307.2	NP_689520.2	Q96FX7	TRM61_HUMAN	tRNA methyltransferase 61 homolog A (S. cerevisiae)	184						nucleus (GO:0005634)|tRNA (m1A) methyltransferase complex (GO:0031515)	tRNA (adenine-N1-)-methyltransferase activity (GO:0016429)			skin(1)	1						ACATCCCATCACCCTGGGAGG	0.697																																					p.S184S		Atlas-SNP	.											.	TRMT61A	15	.	0			c.A552G						.						17	22	20					14																	103999139		2030	4165	6195	SO:0001819	synonymous_variant	115708	exon3			CCCATCACCCTGG	AK097771	CCDS41994.1	14q32	2009-01-09	2009-01-09	2009-01-09		ENSG00000166166			23790	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 172"	C14orf172		16043508	Standard	NM_152307		Approved	FLJ40452, GCD14, Gcd14p, hTRM61	uc010aws.3	Q96FX7		ENST00000389749.4:c.552A>G	chr14.hg19:g.103999139A>G		180.0	0.0		98.0	4.0	NM_152307	A6NN78|Q8N7Q9	Silent	SNP	ENST00000389749.4	hg19	CCDS41994.1	.	.	.	.	.	.	.	.	.	.	A	1.890	-0.455669	0.04540	.	.	ENSG00000166166	ENST00000299202	.	.	.	5.1	-6.64	0.01801	.	.	.	.	.	T	0.34366	0.0895	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41805	-0.9488	4	.	.	.	-4.2072	0.6469	0.00819	0.3398:0.2493:0.2204:0.1906	.	.	.	.	R	86	.	.	H	+	2	0	TRMT61A	103068892	0.001000	0.12720	0.833000	0.33012	0.005000	0.04900	-1.636000	0.02016	-1.031000	0.03308	-0.648000	0.03929	CAC	.	.		0.697	TRMT61A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414988.1	NM_152307		G	103999139	A	G	103999139	2	3	44	1	0	0	0	0	0	0	0	1	16584	146	6	2		2	TRMT61A	14	103999139	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1746652	103999139	3350401	320	5780										
NDN	4692	hgsc.bcm.edu	37	chr15	23931946	23931946	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggatgaggctggtgcgccggAggatgctcctgcaccacttc	15	12	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:23931946A>G	ENST00000331837.4	-	1	504	c.419T>C	c.(418-420)cTc>cCc	p.L140P		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	140	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		GGTGCGCCGGAGGATGCTCCT	0.582									Prader-Willi syndrome																												p.L140P		Atlas-SNP	.											.	NDN	79	.	0			c.T419C						.						61	59	60					15																	23931946		2203	4300	6503	SO:0001583	missense	4692	exon1	Familial Cancer Database	Prader-Labhart-Willi syndrome	CGCCGGAGGATGC	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"Prader-Willi syndrome chromosome region"	602117	"necdin (mouse) homolog", "necdin homolog (mouse)"			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.419T>C	chr15.hg19:g.23931946A>G	ENSP00000332643:p.Leu140Pro	91.0	0.0		94.0	4.0	NM_002487	B2R6Z5	Missense_Mutation	SNP	ENST00000331837.4	hg19	CCDS10014.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.707947	0.48412	.	.	ENSG00000182636	ENST00000331837	T	0.06768	3.26	3.87	2.76	0.32466	.	0.346719	0.29314	N	0.012519	T	0.21307	0.0513	M	0.72118	2.19	0.45747	D	0.99864	D	0.76494	0.999	D	0.75484	0.986	T	0.00812	-1.1556	10	0.72032	D	0.01	.	5.1451	0.14981	0.87:0.0:0.13:0.0	.	140	Q99608	NECD_HUMAN	P	140	ENSP00000332643:L140P	ENSP00000332643:L140P	L	-	2	0	NDN	21483039	0.995000	0.38212	0.519000	0.27824	0.887000	0.51463	2.471000	0.45127	1.717000	0.51406	0.459000	0.35465	CTC	.	.		0.582	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487		G	23931946	A	G	23931946	3	3	44	1	0	0	0	0	1	0	0	0	10256	304	11	2	550	2	NDN	15	23931946	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10		23931946	78599446	321	5781										
FMN1	342184	hgsc.bcm.edu	37	chr15	33194132	33194132	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttagaagctcgcgtgatgaTctctacctttctgtgcaagg	10	10	2	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:33194132T>C	ENST00000559047.1	-	10	3486	c.3487A>G	c.(3487-3489)Atc>Gtc	p.I1163V	FMN1_ENST00000561249.1_Missense_Mutation_p.I1065V|FMN1_ENST00000334528.9_Missense_Mutation_p.I940V			Q68DA7	FMN1_HUMAN	formin 1	1163	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		CGCGTGATGATCTCTACCTTT	0.418																																					p.I940V		Atlas-SNP	.											.	FMN1	174	.	0			c.A2818G						.						100	95	96					15																	33194132		1852	4106	5958	SO:0001583	missense	342184	exon9			TGATGATCTCTAC	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.3487A>G	chr15.hg19:g.33194132T>C	ENSP00000454047:p.Ile1163Val	68.0	0.0		116.0	5.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.40	3.616114	0.66672	.	.	ENSG00000248905	ENST00000334528	T	0.16324	2.35	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	L	0.38175	1.15	.	.	.	P	0.36110	0.537	P	0.47251	0.542	T	0.12708	-1.0537	9	0.41790	T	0.15	.	16.2035	0.82105	0.0:0.0:0.0:1.0	.	940	Q68DA7-5	.	V	940	ENSP00000333950:I940V	ENSP00000333950:I940V	I	-	1	0	FMN1	30981424	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.756000	0.62205	2.304000	0.77564	0.528000	0.53228	ATC	.	.		0.418	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		C	33194132	T	C	33194132	3	2	44	1	0	0	0	0	1	0	0	0	5957	1435	50	2	808	2	FMN1	15	33194132	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	9262186	33194132	69337260	322	5782										
SPRED1	161742	hgsc.bcm.edu	37	chr15	38643506	38643506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaattaagaagtcaaaacgaAgaaaagaggatggtgaacgt	11	3	1	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:38643506A>G	ENST00000299084.4	+	7	1836	c.976A>G	c.(976-978)Aga>Gga	p.R326G		NM_152594.2	NP_689807.1	Q7Z699	SPRE1_HUMAN	sprouty-related, EVH1 domain containing 1	326					inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)			kidney(6)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		GTCAAAACGAAGAAAAGAGGA	0.413									Legius syndrome																												p.R326G	Melanoma(196;2146 2959 7698 16532)	Atlas-SNP	.											.	SPRED1	51	.	0			c.A976G						.						76	74	75					15																	38643506		2200	4297	6497	SO:0001583	missense	161742	exon7	Familial Cancer Database	Neurofibromatosis type 1 - like syndrome, SPRED1 disorder	AAACGAAGAAAAG	AK091222	CCDS32193.1	15q14	2014-06-13			ENSG00000166068	ENSG00000166068			20249	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 147"	609291					Standard	NM_152594		Approved	FLJ33903, PPP1R147	uc001zka.4	Q7Z699		ENST00000299084.4:c.976A>G	chr15.hg19:g.38643506A>G	ENSP00000299084:p.Arg326Gly	56.0	0.0		98.0	4.0	NM_152594	B2RPJ8|Q05D53|Q8N256	Missense_Mutation	SNP	ENST00000299084.4	hg19	CCDS32193.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.786401	0.49997	.	.	ENSG00000166068	ENST00000299084	D	0.86297	-2.1	6.01	4.83	0.62350	.	0.000000	0.85682	D	0.000000	D	0.85991	0.5826	M	0.72894	2.215	0.49299	D	0.999774	B	0.15719	0.014	B	0.15484	0.013	D	0.84290	0.0499	10	0.66056	D	0.02	-15.946	13.047	0.58933	0.866:0.134:0.0:0.0	.	326	Q7Z699	SPRE1_HUMAN	G	326	ENSP00000299084:R326G	ENSP00000299084:R326G	R	+	1	2	SPRED1	36430798	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.963000	0.56773	2.312000	0.78011	0.514000	0.50259	AGA	.	.		0.413	SPRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418217.1			G	38643506	A	G	38643506	3	3	44	1	0	0	0	0	1	0	0	0	15107	64	3	2	1002	2	SPRED1	15	38643506	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	5449374	38643506	63887886	323	5783										
C15orf23	90417	hgsc.bcm.edu	37	chr15	40678607	40678607	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agagtctcttacctgttaggTccaaagaagtcgatgtttcc	9	9	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:40678607T>C	ENST00000249776.8	+	3	464	c.349T>C	c.(349-351)Tcc>Ccc	p.S117P	KNSTRN_ENST00000448395.2_Missense_Mutation_p.S117P|KNSTRN_ENST00000608100.1_Missense_Mutation_p.S39P|KNSTRN_ENST00000416151.2_Missense_Mutation_p.S117P	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein																		ACCTGTTAGGTCCAAAGAAGT	0.453																																					p.S117P		Atlas-SNP	.											.	.	.	.	0			c.T349C						.						86	82	83					15																	40678607		1893	4122	6015	SO:0001583	missense	90417	exon3			GTTAGGTCCAAAG	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"small kinetochore-associated protein", "kinetochore-localized astrin-binding protein", "TRAF4 associated factor 1"	614718	"chromosome 15 open reading frame 23"	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.349T>C	chr15.hg19:g.40678607T>C	ENSP00000249776:p.Ser117Pro	108.0	0.0		183.0	9.0	NM_033286		Missense_Mutation	SNP	ENST00000249776.8	hg19	CCDS42021.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.741170	0.69304	.	.	ENSG00000128944	ENST00000249776;ENST00000416151;ENST00000448395	T;T;T	0.34072	1.39;1.38;1.41	5.15	4.01	0.46588	.	0.716608	0.13766	N	0.364232	T	0.42449	0.1203	L	0.34521	1.04	0.26709	N	0.971015	D;D;D	0.63880	0.993;0.993;0.993	P;P;P	0.61132	0.884;0.884;0.884	T	0.18085	-1.0348	10	0.54805	T	0.06	-3.1168	8.0448	0.30542	0.1804:0.0:0.0:0.8196	.	117;117;117	Q9Y448-2;Q9Y448-3;Q9Y448	.;.;T4AF1_HUMAN	P	117	ENSP00000249776:S117P;ENSP00000391233:S117P;ENSP00000393001:S117P	ENSP00000249776:S117P	S	+	1	0	C15orf23	38465899	0.300000	0.24435	0.994000	0.49952	0.933000	0.57130	1.213000	0.32407	0.957000	0.37930	0.533000	0.62120	TCC	.	.		0.453	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761		C	40678607	T	C	40678607	3	2	44	1	0	0	0	0	1	0	0	0	1787	1667	58	2	359	2	C15orf23	15	40678607	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2035101	40678607	61852785	324	5784										
UBR1	197131	hgsc.bcm.edu	37	chr15	43363075	43363075	+	Frame_Shift_Del	DEL	T	T	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttttatcactgaaggaaataTtttcctggcttggacaatta							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:43363075delT	ENST00000290650.4	-	5	655	c.577delA	c.(577-579)atafs	p.I193fs	UBR1_ENST00000382177.2_Frame_Shift_Del_p.I193fs	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	193					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GAAGGAAATATTTTCCTGGCT	0.363																																					p.I193fs		Atlas-INDEL	.											.	UBR1	124	.	0			c.578delT						.						119	115	117					15																	43363075		2203	4299	6502	SO:0001589	frameshift_variant	197131	exon5			.		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.577delA	chr15.hg19:g.43363075delT	ENSP00000290650:p.Ile193fs	74.0	0.0		130.0	12.0	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Frame_Shift_Del	DEL	ENST00000290650.4	hg19	CCDS10091.1																																																																																			.	.		0.363	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		-	43363075	T	-	43363075	7	5	44	1	0	1	0	1	0	0	0	0	16916	1493	52	0	4844	0	UBR1	15	43363075	Frame_Shift_Del	DEL	T	TCGA-BC-A3KG-01A-11D-A20W-10	2684468	43363075	59168317	325	5785										
C15orf43	145645	hgsc.bcm.edu	37	chr15	45250636	45250636	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcatgcctactatctctctgCggtagctaatgccaaaataa	6	11	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:45250636C>T	ENST00000340827.3	+	3	229	c.212C>T	c.(211-213)gCg>gTg	p.A71V		NM_152448.2	NP_689661.1	Q8NHR7	CO043_HUMAN	chromosome 15 open reading frame 43	71										NS(1)|breast(2)|large_intestine(1)|lung(2)|skin(2)	8		all_cancers(109;3.68e-08)|all_epithelial(112;1.05e-06)|Lung NSC(122;1.42e-05)|all_lung(180;0.000112)|Melanoma(134;0.0192)		all cancers(107;7.64e-17)|GBM - Glioblastoma multiforme(94;2.03e-06)		TATCTCTCTGCGGTAGCTAAT	0.383																																					p.A71V		Atlas-SNP	.											.	C15orf43	19	.	0			c.C212T						.						95	95	95					15																	45250636		2196	4298	6494	SO:0001583	missense	145645	exon3			TCTCTGCGGTAGC	BC029537	CCDS10115.1	15q21.1	2006-02-03			ENSG00000167014	ENSG00000167014			28520	protein-coding gene	gene with protein product							Standard	NM_152448		Approved	MGC33951	uc001zuk.4	Q8NHR7	OTTHUMG00000131264	ENST00000340827.3:c.212C>T	chr15.hg19:g.45250636C>T	ENSP00000340644:p.Ala71Val	117.0	0.0		141.0	73.0	NM_152448		Missense_Mutation	SNP	ENST00000340827.3	hg19	CCDS10115.1	.	.	.	.	.	.	.	.	.	.	c	19.28	3.797020	0.70567	.	.	ENSG00000167014	ENST00000340827	T	0.48522	0.81	4.45	3.53	0.40419	.	0.000000	0.64402	D	0.000014	T	0.30039	0.0752	L	0.29908	0.895	0.34047	D	0.655732	D	0.56287	0.975	B	0.37422	0.249	T	0.50355	-0.8838	10	0.72032	D	0.01	.	8.2804	0.31898	0.0:0.8909:0.0:0.1091	.	71	Q8NHR7	CO043_HUMAN	V	71	ENSP00000340644:A71V	ENSP00000340644:A71V	A	+	2	0	C15orf43	43037928	0.998000	0.40836	1.000000	0.80357	0.976000	0.68499	2.048000	0.41278	1.231000	0.43661	0.643000	0.83706	GCG	.	.		0.383	C15orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254032.1	NM_152448		T	45250636	C	T	45250636	3	4	44	1	0	0	0	0	1	0	0	0	1799	768	27	1	222	1	C15orf43	15	45250636	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1887561	45250636	57280756	326	5786										
DTWD1	56986	hgsc.bcm.edu	37	chr15	49917370	49917370	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tggtttgaatgaagaatgtcTctcaatccacctatatttct	6	8	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:49917370T>C	ENST00000251250.6	+	3	213	c.6T>C	c.(4-6)tcT>tcC	p.S2S	DTWD1_ENST00000558653.1_Silent_p.S2S|DTWD1_ENST00000559223.1_3'UTR|DTWD1_ENST00000403028.3_Silent_p.S2S|DTWD1_ENST00000329873.5_Silent_p.S2S	NM_020234.5	NP_064619.2	Q8N5C7	DTWD1_HUMAN	DTW domain containing 1	2										endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;0.0384)		all cancers(107;3.27e-08)|GBM - Glioblastoma multiforme(94;7.6e-05)		GAAGAATGTCTCTCAATCCAC	0.323																																					p.S2S		Atlas-SNP	.											.	DTWD1	22	.	0			c.T6C						.						32	33	33					15																	49917370		2193	4291	6484	SO:0001819	synonymous_variant	56986	exon2			AATGTCTCTCAAT	BC032535	CCDS10132.1	15q21.2	2005-08-09			ENSG00000104047	ENSG00000104047			30926	protein-coding gene	gene with protein product							Standard	NM_020234		Approved	MDS009, MGC111207	uc001zxs.3	Q8N5C7	OTTHUMG00000131567	ENST00000251250.6:c.6T>C	chr15.hg19:g.49917370T>C		112.0	0.0		94.0	4.0	NM_001144955	Q567Q3|Q8WVG9|Q9NRU6	Silent	SNP	ENST00000251250.6	hg19	CCDS10132.1																																																																																			.	.		0.323	DTWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254431.2	NM_020234		C	49917370	T	C	49917370	2	2	44	1	0	0	0	0	0	0	0	1	4793	1538	54	2		2	DTWD1	15	49917370	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4666734	49917370	52614022	327	5787										
ADAM10	102	hgsc.bcm.edu	37	chr15	58902675	58902675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcgaccactgaagtgcctacTccactgcacagaccctgtac	7	16	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:58902675T>C	ENST00000260408.3	-	14	2289	c.1846A>G	c.(1846-1848)Agt>Ggt	p.S616G	ADAM10_ENST00000396140.2_Missense_Mutation_p.S315G|ADAM10_ENST00000402627.1_Intron|ADAM10_ENST00000561288.1_Intron	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	616	Cys-rich.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		AAGTGCCTACTCCACTGCACA	0.448																																					p.S616G		Atlas-SNP	.											.	ADAM10	59	.	0			c.A1846G						.						85	78	81					15																	58902675		2192	4292	6484	SO:0001583	missense	102	exon14			GCCTACTCCACTG	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"ADAM metallopeptidase domain containing", "CD molecules"	188	protein-coding gene	gene with protein product		602192	"a disintegrin and metalloproteinase domain 10"			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.1846A>G	chr15.hg19:g.58902675T>C	ENSP00000260408:p.Ser616Gly	118.0	0.0		149.0	8.0	NM_001110	B4DU28|Q10742|Q92650	Missense_Mutation	SNP	ENST00000260408.3	hg19	CCDS10167.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.484275	0.26598	.	.	ENSG00000137845	ENST00000260408;ENST00000396136;ENST00000396140	T;T	0.25749	1.78;3.08	5.37	4.23	0.50019	.	0.622514	0.19699	N	0.108083	T	0.14657	0.0354	N	0.24115	0.695	0.33716	D	0.616368	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.17098	0.017;0.017;0.007	T	0.16808	-1.0390	10	0.15066	T	0.55	-0.0574	7.4057	0.26989	0.0:0.1209:0.1327:0.7464	.	315;435;616	B4DU28;A8MY20;O14672	.;.;ADA10_HUMAN	G	616;435;315	ENSP00000260408:S616G;ENSP00000379444:S315G	ENSP00000260408:S616G	S	-	1	0	ADAM10	56689967	0.115000	0.22152	0.922000	0.36590	0.888000	0.51559	0.423000	0.21313	2.154000	0.67381	0.533000	0.62120	AGT	.	.		0.448	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110		C	58902675	T	C	58902675	3	2	44	1	0	0	0	0	1	0	0	0	234	1551	54	2	412	2	ADAM10	15	58902675	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	8985305	58902675	43628717	328	5788										
ZNF609	23060	hgsc.bcm.edu	37	chr15	64792108	64792108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaaaggagaaggagaacagcTcatctaagagcaagaaggag	13	5	2	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:64792108T>C	ENST00000326648.3	+	1	618	c.490T>C	c.(490-492)Tca>Cca	p.S164P	ZNF609_ENST00000416172.1_Missense_Mutation_p.S164P	NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	164						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGAGAACAGCTCATCTAAGAG	0.567																																					p.S164P		Atlas-SNP	.											.	ZNF609	106	.	0			c.T490C						.						57	54	55					15																	64792108		2203	4299	6502	SO:0001583	missense	23060	exon1			AACAGCTCATCTA	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"Zinc fingers, C2H2-type"	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.490T>C	chr15.hg19:g.64792108T>C	ENSP00000316527:p.Ser164Pro	138.0	0.0		152.0	7.0	NM_015042	Q0D2I2	Missense_Mutation	SNP	ENST00000326648.3	hg19	CCDS32270.1	.	.	.	.	.	.	.	.	.	.	.	16.20	3.057189	0.55325	.	.	ENSG00000180357	ENST00000416172;ENST00000326648	T	0.52057	0.68	5.5	4.37	0.52481	.	0.231325	0.36972	N	0.002314	T	0.47358	0.1441	M	0.69823	2.125	0.50313	D	0.999864	B;B	0.24768	0.111;0.046	B;B	0.26202	0.067;0.019	T	0.47381	-0.9122	10	0.62326	D	0.03	-3.2333	10.1414	0.42738	0.0:0.0762:0.0:0.9238	.	164;164	E7ERY8;O15014	.;ZN609_HUMAN	P	164	ENSP00000316527:S164P	ENSP00000316527:S164P	S	+	1	0	ZNF609	62579161	0.997000	0.39634	0.993000	0.49108	0.987000	0.75469	1.566000	0.36396	1.021000	0.39600	0.529000	0.55759	TCA	.	.		0.567	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833		C	64792108	T	C	64792108	3	2	44	1	0	0	0	0	1	0	0	0	18050	1551	54	2	492	2	ZNF609	15	64792108	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	5889433	64792108	37739284	329	5789										
NEO1	4756	hgsc.bcm.edu	37	chr15	73418808	73418808	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgaaacagccttctcccttaGtcagagtcattggtcaggat	9	10	4	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:73418808G>T	ENST00000339362.5	+	5	1222	c.775G>T	c.(775-777)Gtc>Ttc	p.V259F	NEO1_ENST00000558964.1_Missense_Mutation_p.V259F|NEO1_ENST00000560262.1_Missense_Mutation_p.V259F|NEO1_ENST00000261908.6_Missense_Mutation_p.V259F			Q92859	NEO1_HUMAN	neogenin 1	259	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						TTCTCCCTTAGTCAGAGTCAT	0.378																																					p.V259F		Atlas-SNP	.											.	NEO1	102	.	0			c.G775T						.						157	145	149					15																	73418808		2198	4297	6495	SO:0001583	missense	4756	exon4			CCCTTAGTCAGAG	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.775G>T	chr15.hg19:g.73418808G>T	ENSP00000341198:p.Val259Phe	64.0	0.0		89.0	5.0	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	hg19	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	G	12.88	2.069529	0.36470	.	.	ENSG00000067141	ENST00000339362;ENST00000261908	T;T	0.69306	-0.39;-0.39	5.65	2.37	0.29283	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.410317	0.27696	N	0.018237	T	0.65238	0.2672	M	0.71581	2.175	0.21553	N	0.999643	B;B;B	0.29552	0.051;0.136;0.248	B;B;B	0.38655	0.073;0.278;0.278	T	0.61768	-0.6995	10	0.72032	D	0.01	-2.0476	5.3899	0.16237	0.5772:0.0:0.4228:0.0	.	259;259;259	B7ZKM9;B7ZKN0;Q92859	.;.;NEO1_HUMAN	F	259	ENSP00000341198:V259F;ENSP00000261908:V259F	ENSP00000261908:V259F	V	+	1	0	NEO1	71205861	0.863000	0.29885	0.991000	0.47740	0.504000	0.33889	2.117000	0.41939	0.729000	0.32403	0.467000	0.42956	GTC	.	.		0.378	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		T	73418808	G	T	73418808	3	4	44	1	0	0	0	0	1	0	0	0	10345	1029	36	3	789	3	NEO1	15	73418808	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	8626700	73418808	29112584	330	5790										
CYP1A1	1543	hgsc.bcm.edu	37	chr15	75015113	75015113	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgatgagggtgaaggtgtagAggtcgggccggcccttgaaa	18	6	0	5			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:75015113A>G	ENST00000379727.3	-	2	524	c.326T>C	c.(325-327)cTc>cCc	p.L109P	CYP1A1_ENST00000395049.4_Missense_Mutation_p.L109P|CYP1A1_ENST00000567032.1_Missense_Mutation_p.L109P|CYP1A1_ENST00000395048.2_Missense_Mutation_p.L109P|CYP1A1_ENST00000564596.1_Intron			P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 1	109					9-cis-retinoic acid biosynthetic process (GO:0042904)|aging (GO:0007568)|amine metabolic process (GO:0009308)|arachidonic acid metabolic process (GO:0019369)|camera-type eye development (GO:0043010)|cell proliferation (GO:0008283)|cellular lipid metabolic process (GO:0044255)|cellular response to organic cyclic compound (GO:0071407)|coumarin metabolic process (GO:0009804)|dibenzo-p-dioxin catabolic process (GO:0019341)|digestive tract development (GO:0048565)|drug metabolic process (GO:0017144)|embryo development ending in birth or egg hatching (GO:0009792)|epoxygenase P450 pathway (GO:0019373)|flavonoid metabolic process (GO:0009812)|hepatocyte differentiation (GO:0070365)|hydrogen peroxide biosynthetic process (GO:0050665)|insecticide metabolic process (GO:0017143)|maternal process involved in parturition (GO:0060137)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|response to antibiotic (GO:0046677)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to food (GO:0032094)|response to herbicide (GO:0009635)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to iron(III) ion (GO:0010041)|response to lipopolysaccharide (GO:0032496)|response to nematode (GO:0009624)|response to virus (GO:0009615)|response to vitamin A (GO:0033189)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|demethylase activity (GO:0032451)|flavonoid 3'-monooxygenase activity (GO:0016711)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on diphenols and related substances as donors (GO:0016679)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)|vitamin D 24-hydroxylase activity (GO:0070576)			autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(7)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Acetaminophen(DB00316)|Albendazole(DB00518)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Caffeine(DB00201)|Carvedilol(DB01136)|Chloroquine(DB00608)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Clenbuterol(DB01407)|Clobetasol propionate(DB01013)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonidine(DB00575)|Clozapine(DB00363)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Dexamethasone(DB01234)|Dexmedetomidine(DB00633)|Diclofenac(DB00586)|Dicyclomine(DB00804)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Ethanol(DB00898)|Flunarizine(DB04841)|Fluorescein(DB00693)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Granisetron(DB00889)|Haloperidol(DB00502)|Isoprenaline(DB01064)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lorcaserin(DB04871)|Mebendazole(DB00643)|Melatonin(DB01065)|Menadione(DB00170)|Methoxsalen(DB00553)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitroprusside(DB00325)|Norfloxacin(DB01059)|Omeprazole(DB00338)|Ouabain(DB01092)|Oxaliplatin(DB00526)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Prazosin(DB00457)|Primaquine(DB01087)|Progesterone(DB00396)|Propofol(DB00818)|Propranolol(DB00571)|Pyridoxine(DB00165)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Riluzole(DB00740)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiabendazole(DB00730)|Ticlopidine(DB00208)|Toremifene(DB00539)|Tretinoin(DB00755)|Vitamin A(DB00162)|Warfarin(DB00682)	GAAGGTGTAGAGGTCGGGCCG	0.647									Endometrial Cancer, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.L109P		Atlas-SNP	.											.	CYP1A1	60	.	0			c.T326C						.						48	47	48					15																	75015113		2197	4295	6492	SO:0001583	missense	1543	exon2	Familial Cancer Database	;AIMAH, Cushing disease, Adrenal, Familial	GTGTAGAGGTCGG	BC023019	CCDS10268.1	15q24.1	2007-12-14	2003-01-14		ENSG00000140465	ENSG00000140465	1.14.14.1	"Cytochrome P450s"	2595	protein-coding gene	gene with protein product		108330	"cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1"	CYP1		15128046	Standard	NM_000499		Approved	P450DX, P1-450, P450-C, CP11	uc002ayp.4	P04798	OTTHUMG00000142812	ENST00000379727.3:c.326T>C	chr15.hg19:g.75015113A>G	ENSP00000369050:p.Leu109Pro	78.0	0.0		86.0	4.0	NM_000499	A4F3V9|A4F3W0|Q53G18	Missense_Mutation	SNP	ENST00000379727.3	hg19	CCDS10268.1	.	.	.	.	.	.	.	.	.	.	A	16.61	3.171699	0.57584	.	.	ENSG00000140465	ENST00000379727;ENST00000395048;ENST00000395049;ENST00000268062	T;T;T	0.68025	-0.3;-0.3;-0.3	5.23	5.23	0.72850	.	0.059927	0.64402	D	0.000002	D	0.84737	0.5538	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	D	0.88246	0.2913	10	0.87932	D	0	.	15.1201	0.72434	1.0:0.0:0.0:0.0	.	109;109	E7EMT5;P04798	.;CP1A1_HUMAN	P	109	ENSP00000369050:L109P;ENSP00000378488:L109P;ENSP00000378489:L109P	ENSP00000268062:L109P	L	-	2	0	CYP1A1	72802166	1.000000	0.71417	1.000000	0.80357	0.311000	0.27955	9.158000	0.94723	1.968000	0.57251	0.379000	0.24179	CTC	.	.		0.647	CYP1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286396.1	NM_000499		G	75015113	A	G	75015113	3	3	44	1	0	0	0	0	1	0	0	0	4151	304	11	2	1236	2	CYP1A1	15	75015113	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1596305	75015113	27516279	331	5791										
SCAMP5	192683	hgsc.bcm.edu	37	chr15	75308993	75308993	+	Frame_Shift_Del	DEL	G	G	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcgcgtggctgatcggaggcGggggagccaccaactttggc							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:75308993delG	ENST00000361900.6	+	5	403	c.196delG	c.(196-198)gggfs	p.G67fs	SCAMP5_ENST00000562212.1_Frame_Shift_Del_p.G67fs|SCAMP5_ENST00000545456.1_Intron|SCAMP5_ENST00000565923.1_3'UTR|SCAMP5_ENST00000568081.1_5'Flank|SCAMP5_ENST00000425597.3_Frame_Shift_Del_p.G67fs	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	67					exocytosis (GO:0006887)|negative regulation of endocytosis (GO:0045806)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of cytokine secretion (GO:0050715)|protein transport (GO:0015031)|response to endoplasmic reticulum stress (GO:0034976)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)|trans-Golgi network membrane (GO:0032588)				large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	5						GATCGGAGGCGGGGGAGCCAC	0.597																																					p.G65fs		Atlas-INDEL	.											.	SCAMP5	34	.	0			c.195delC						.						114	120	118					15																	75308993		2157	4252	6409	SO:0001589	frameshift_variant	192683	exon5			.	AL833230	CCDS45306.1	15q24.2	2014-05-20			ENSG00000198794	ENSG00000198794		"Secretory carrier membrane proteins"	30386	protein-coding gene	gene with protein product		613766				12477932	Standard	NM_001178111		Approved	MGC24969	uc002azk.2	Q8TAC9	OTTHUMG00000172704	ENST00000361900.6:c.196delG	chr15.hg19:g.75308993delG	ENSP00000355387:p.Gly67fs	123.0	0.0		155.0	10.0	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Frame_Shift_Del	DEL	ENST00000361900.6	hg19	CCDS45306.1																																																																																			.	.		0.597	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967		-	75308993	G	-	75308993	7	5	44	1	0	1	0	1	0	0	0	0	13889	1116	39	0	206	0	SCAMP5	15	75308993	Frame_Shift_Del	DEL	G	TCGA-BC-A3KG-01A-11D-A20W-10	293880	75308993	27222399	332	5792										
MAN2C1	4123	hgsc.bcm.edu	37	chr15	75653703	75653703	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cacgggagccatccaggcccTcccagaaaaatgtatggtgc	11	13	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:75653703T>C	ENST00000267978.5	-	11	1284	c.1238A>G	c.(1237-1239)gAg>gGg	p.E413G	MAN2C1_ENST00000569482.1_Missense_Mutation_p.E413G|MAN2C1_ENST00000563622.1_Missense_Mutation_p.E314G|MAN2C1_ENST00000565683.1_Missense_Mutation_p.E413G|MAN2C1_ENST00000563539.1_5'Flank	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	413					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						ATCCAGGCCCTCCCAGAAAAA	0.617																																					p.E413G		Atlas-SNP	.											.	MAN2C1	76	.	0			c.A1238G						.						30	30	30					15																	75653703		2180	4278	6458	SO:0001583	missense	4123	exon11			AGGCCCTCCCAGA	AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.1238A>G	chr15.hg19:g.75653703T>C	ENSP00000267978:p.Glu413Gly	90.0	0.0		72.0	5.0	NM_001256494	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Missense_Mutation	SNP	ENST00000267978.5	hg19	CCDS32298.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.032717	0.75504	.	.	ENSG00000140400	ENST00000267978	T	0.81163	-1.46	5.33	5.33	0.75918	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.050242	0.85682	D	0.000000	D	0.90283	0.6961	M	0.91768	3.24	0.53688	D	0.999978	D;D;D	0.60575	0.971;0.988;0.988	P;D;D	0.66979	0.811;0.948;0.932	D	0.91618	0.5308	10	0.66056	D	0.02	-31.8377	10.5227	0.44929	0.0:0.0786:0.0:0.9214	.	195;413;413	B4DVP6;Q68EM8;Q9NTJ4	.;.;MA2C1_HUMAN	G	413	ENSP00000267978:E413G	ENSP00000267978:E413G	E	-	2	0	MAN2C1	73440756	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	5.709000	0.68384	2.015000	0.59207	0.459000	0.35465	GAG	.	.		0.617	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1			C	75653703	T	C	75653703	3	2	44	1	0	0	0	0	1	0	0	0	9227	1551	54	2	1948	2	MAN2C1	15	75653703	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	344710	75653703	26877689	333	5793										
SGK269	79834	hgsc.bcm.edu	37	chr15	77471450	77471450	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gctctttctctttgtcatccTcctcatctgttttccgacgg	6	14	5	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:77471450T>C	ENST00000560626.2	-	4	3294	c.2819A>G	c.(2818-2820)gAg>gGg	p.E940G	PEAK1_ENST00000312493.4_Missense_Mutation_p.E940G|PEAK1_ENST00000558305.1_Missense_Mutation_p.E940G			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	940					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TTTGTCATCCTCCTCATCTGT	0.522																																					p.E940G		Atlas-SNP	.											.	.	.	.	0			c.A2819G						.						114	131	125					15																	77471450		2000	4173	6173	SO:0001583	missense	0	exon5			TCATCCTCCTCAT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.2819A>G	chr15.hg19:g.77471450T>C	ENSP00000452796:p.Glu940Gly	97.0	0.0		106.0	5.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	T	19.85	3.903481	0.72754	.	.	ENSG00000173517	ENST00000312493	T	0.73575	-0.76	5.91	5.91	0.95273	.	0.080647	0.44902	D	0.000417	T	0.56587	0.1995	N	0.19112	0.55	0.41705	D	0.989425	P	0.36282	0.546	B	0.30401	0.115	T	0.60037	-0.7341	10	0.37606	T	0.19	-6.8164	10.6452	0.45615	0.0:0.0708:0.0:0.9292	.	940	Q9H792	PEAK1_HUMAN	G	940	ENSP00000309230:E940G	ENSP00000309230:E940G	E	-	2	0	AC087465.1	75258505	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.685000	0.84117	2.254000	0.74563	0.533000	0.62120	GAG	.	.		0.522	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			C	77471450	T	C	77471450	3	2	44	1	0	0	0	0	1	0	0	0	14226	1551	54	2	2437	2	SGK269	15	77471450	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1817747	77471450	25059942	334	5794										
AP3B2	8120	hgsc.bcm.edu	37	chr15	83331627	83331627	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gccagcccctcgccagctacCcggtgcagcagctcctgccg	11	20	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:83331627C>A	ENST00000261722.3	-	22	2802	c.2595G>T	c.(2593-2595)cgG>cgT	p.R865R	AP3B2_ENST00000535359.1_Silent_p.R884R|RP11-752G15.3_ENST00000560650.1_RNA|AP3B2_ENST00000535348.1_Silent_p.R833R	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	865					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			CGCCAGCTACCCGGTGCAGCA	0.602																																					p.R865R		Atlas-SNP	.											.	AP3B2	103	.	0			c.G2595T						.						26	32	30					15																	83331627		2038	4200	6238	SO:0001819	synonymous_variant	8120	exon22			AGCTACCCGGTGC	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.2595G>T	chr15.hg19:g.83331627C>A		61.0	0.0		70.0	42.0	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	hg19	CCDS45331.1																																																																																			.	.		0.602	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			A	83331627	C	A	83331627	2	1	44	1	0	0	0	0	0	0	0	1	745	610	22	3		3	AP3B2	15	83331627	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	5860177	83331627	19199765	335	5795										
NMB	4828	hgsc.bcm.edu	37	chr15	85200578	85200578	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctcttcttgcccatgaagtgAcctggaaaggaggtgtccag	12	10	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:85200578A>G	ENST00000360476.3	-	2	554	c.159T>C	c.(157-159)ggT>ggC	p.G53G	NMB_ENST00000394588.3_Splice_Site_p.G53G			P08949	NMB_HUMAN	neuromedin B	53					arachidonic acid secretion (GO:0050482)|cell-cell signaling (GO:0007267)|glucose homeostasis (GO:0042593)|negative regulation of hormone secretion (GO:0046888)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hormone secretion (GO:0046887)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|neuron projection (GO:0043005)	hormone activity (GO:0005179)			endometrium(1)	1				all cancers(203;3.5e-06)		CCATGAAGTGACCTGGAAAGG	0.572																																					p.G53G		Atlas-SNP	.											.	NMB	14	.	0			c.T159C						.						24	18	20					15																	85200578		2197	4292	6489	SO:0001630	splice_region_variant	4828	exon2			GAAGTGACCTGGA		CCDS10332.1, CCDS42076.1	15q25.2-q25.3	2013-09-19			ENSG00000197696	ENSG00000197696			7842	protein-coding gene	gene with protein product		162340				2458345	Standard	NM_021077		Approved	MGC2277, MGC3936, MGC17211	uc002bla.3	P08949	OTTHUMG00000148666	ENST00000360476.3:c.158-1T>C	chr15.hg19:g.85200578A>G		87.0	0.0		78.0	5.0	NM_205858	Q96A06|Q96HH5	Silent	SNP	ENST00000360476.3	hg19	CCDS10332.1																																																																																			.	.		0.572	NMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308995.1	NM_021077	Silent	G	85200578	A	G	85200578	5	3	44	1	0	0	0	0	0	0	1	0	10495	289	10	2	318	2	NMB	15	85200578	Splice_Site	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1868951	85200578	17330814	336	5796										
C15orf42	90381	hgsc.bcm.edu	37	chr15	90167599	90167599	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acccagcgtagctgcatctcTctcctgccctgttccctcaa	6	18	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:90167599T>C	ENST00000268138.7	+	20	4163	c.4058T>C	c.(4057-4059)cTc>cCc	p.L1353P	TICRR_ENST00000560985.1_Missense_Mutation_p.L1352P|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1353	Pro-rich.				cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										GCTGCATCTCTCTCCTGCCCT	0.517																																					p.L1353P		Atlas-SNP	.											.	.	.	.	0			c.T4058C						.						120	121	121					15																	90167599		2200	4299	6499	SO:0001583	missense	90381	exon20			CATCTCTCTCCTG	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.4058T>C	chr15.hg19:g.90167599T>C	ENSP00000268138:p.Leu1353Pro	53.0	0.0		56.0	4.0	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	hg19	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	T	8.993	0.978132	0.18812	.	.	ENSG00000140534	ENST00000268138	T	0.08807	3.05	3.81	-0.15	0.13416	.	0.954574	0.08561	N	0.927581	T	0.06781	0.0173	L	0.43152	1.355	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44034	-0.9354	10	0.27785	T	0.31	0.0232	3.2449	0.06793	0.1845:0.2259:0.0:0.5895	.	1353	Q7Z2Z1	TICRR_HUMAN	P	1353	ENSP00000268138:L1353P	ENSP00000268138:L1353P	L	+	2	0	C15orf42	87968603	0.000000	0.05858	0.001000	0.08648	0.406000	0.30931	-1.021000	0.03615	-0.258000	0.09446	0.533000	0.62120	CTC	.	.		0.517	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		C	90167599	T	C	90167599	3	2	44	1	0	0	0	0	1	0	0	0	1798	1551	54	2	4136	2	C15orf42	15	90167599	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4967021	90167599	12363793	337	5797										
ALDH1A3	220	hgsc.bcm.edu	37	chr15	101425535	101425535	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agtttgctacatgtaaccctTcaactcgggagcaaatatgt	8	9	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr15:101425535T>C	ENST00000329841.5	+	2	695	c.163T>C	c.(163-165)Tca>Cca	p.S55P	ALDH1A3_ENST00000560555.1_3'UTR|RP11-66B24.8_ENST00000558568.1_lincRNA|ALDH1A3_ENST00000346623.6_Missense_Mutation_p.S55P	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3	55					embryonic eye morphogenesis (GO:0048048)|face development (GO:0060324)|inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|nucleus accumbens development (GO:0021768)|olfactory pit development (GO:0060166)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|positive regulation of apoptotic process (GO:0043065)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoic acid metabolic process (GO:0042573)|retinol metabolic process (GO:0042572)|righting reflex (GO:0060013)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|thyroid hormone binding (GO:0070324)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(7)|lung(9)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	27	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		Vitamin A(DB00162)	ATGTAACCCTTCAACTCGGGA	0.348																																					p.S55P		Atlas-SNP	.											.	ALDH1A3	61	.	0			c.T163C						.						94	95	95					15																	101425535		2203	4300	6503	SO:0001583	missense	220	exon2			AACCCTTCAACTC	U07919	CCDS10389.1	15q26	2010-05-07			ENSG00000184254	ENSG00000184254	1.2.1.5	"Aldehyde dehydrogenases"	409	protein-coding gene	gene with protein product	"retinaldehyde dehydrogenase 3"	600463		ALDH6		7698756	Standard	XR_111558		Approved	RALDH3	uc002bwn.4	P47895	OTTHUMG00000149870	ENST00000329841.5:c.163T>C	chr15.hg19:g.101425535T>C	ENSP00000332256:p.Ser55Pro	87.0	0.0		83.0	4.0	NM_000693	Q6NT64	Missense_Mutation	SNP	ENST00000329841.5	hg19	CCDS10389.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.679746	0.88542	.	.	ENSG00000184254	ENST00000329841;ENST00000415812;ENST00000346623	T	0.16897	2.31	5.71	5.71	0.89125	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.060855	0.64402	D	0.000004	T	0.41259	0.1151	M	0.92507	3.315	0.31158	N	0.70464	D;D;P	0.57257	0.97;0.979;0.913	P;P;P	0.52386	0.697;0.643;0.618	T	0.63024	-0.6729	10	0.72032	D	0.01	.	11.6347	0.51196	0.0:0.0:0.1484:0.8516	.	66;55;55	Q7Z3A2;B2R5T2;P47895	.;.;AL1A3_HUMAN	P	55;55;66	ENSP00000332256:S55P	ENSP00000332256:S55P	S	+	1	0	ALDH1A3	99243058	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	4.776000	0.62354	2.179000	0.69175	0.459000	0.35465	TCA	.	.		0.348	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313620.2			C	101425535	T	C	101425535	3	2	44	1	0	0	0	0	1	0	0	0	492	1783	62	2	169	2	ALDH1A3	15	101425535	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	11257936	101425535	1105857	338	5798										
IGFALS	3483	hgsc.bcm.edu	37	chr16	1841743	1841743	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggcccgcagcgcgttcctgcTcaggtccagctcccggagct	13	17	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:1841743T>C	ENST00000215539.3	-	2	786	c.676A>G	c.(676-678)Agc>Ggc	p.S226G	IGFALS_ENST00000415638.3_Missense_Mutation_p.S264G			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit	226					cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						GCGTTCCTGCTCAGGTCCAGC	0.697																																					p.S264G		Atlas-SNP	.											.	IGFALS	29	.	0			c.A790G						.						24	22	23					16																	1841743		2148	4254	6402	SO:0001583	missense	3483	exon2			TCCTGCTCAGGTC	M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638	ENST00000215539.3:c.676A>G	chr16.hg19:g.1841743T>C	ENSP00000215539:p.Ser226Gly	93.0	0.0		97.0	5.0	NM_001146006	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	hg19	CCDS10446.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.742377	0.49151	.	.	ENSG00000099769	ENST00000215539;ENST00000415638	D;D	0.82344	-1.6;-1.6	5.09	3.99	0.46301	.	0.098049	0.64402	D	0.000002	D	0.85084	0.5616	L	0.38531	1.155	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.76575	0.988;0.95	D	0.84221	0.0461	10	0.59425	D	0.04	.	9.4588	0.38772	0.0:0.0855:0.0:0.9145	.	264;226	E9PGU3;P35858	.;ALS_HUMAN	G	226;264	ENSP00000215539:S226G;ENSP00000416683:S264G	ENSP00000215539:S226G	S	-	1	0	IGFALS	1781744	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.929000	0.63455	0.798000	0.33994	0.448000	0.29417	AGC	.	.		0.697	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2			C	1841743	T	C	1841743	3	2	44	1	0	0	0	0	1	0	0	0	7586	1551	54	2	1145	2	IGFALS	16	1841743	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10		1841743	88513010	339	5799										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2814503	2814503	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	taactccccactcagggagaAcagctttggatcacctttag	8	12	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:2814503A>G	ENST00000301740.8	+	11	4523	c.3974A>G	c.(3973-3975)aAc>aGc	p.N1325S		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1325	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						CTCAGGGAGAACAGCTTTGGA	0.433																																					p.N1325S		Atlas-SNP	.											.	SRRM2	263	.	0			c.A3974G						.						101	108	106					16																	2814503		2197	4300	6497	SO:0001583	missense	23524	exon11			GGGAGAACAGCTT	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.3974A>G	chr16.hg19:g.2814503A>G	ENSP00000301740:p.Asn1325Ser	73.0	0.0		74.0	4.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	A	12.30	1.895845	0.33442	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.23348	1.91	6.11	5.03	0.67393	.	0.347767	0.28360	N	0.015634	T	0.09468	0.0233	N	0.02916	-0.46	0.24954	N	0.991774	B	0.14438	0.01	B	0.06405	0.002	T	0.28650	-1.0037	10	0.13470	T	0.59	-15.9798	8.2168	0.31516	0.9138:0.0:0.0862:0.0	.	1325	Q9UQ35	SRRM2_HUMAN	S	1325;1325;577	ENSP00000301740:N1325S	ENSP00000301740:N1325S	N	+	2	0	SRRM2	2754504	0.979000	0.34478	1.000000	0.80357	0.897000	0.52465	2.392000	0.44433	2.343000	0.79666	0.533000	0.62120	AAC	.	.		0.433	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			G	2814503	A	G	2814503	3	3	44	1	0	0	0	0	1	0	0	0	15184	43	2	2	4012	2	SRRM2	16	2814503	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	972760	2814503	87540250	340	5800										
CIITA	4261	hgsc.bcm.edu	37	chr16	11001915	11001915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcaaggccttggaggcggcgGgccaagacttctccctggac	15	13	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:11001915G>A	ENST00000324288.8	+	11	2699	c.2566G>A	c.(2566-2568)Ggc>Agc	p.G856S	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	856					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						GGAGGCGGCGGGCCAAGACTT	0.647			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.G856S		Atlas-SNP	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	CIITA_ENST00000324288,NS,carcinoma,0,1	CIITA	92	.	0			c.G2566A						.						15	17	16					16																	11001915		2196	4290	6486	SO:0001583	missense	4261	exon11			GCGGCGGGCCAAG	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2566G>A	chr16.hg19:g.11001915G>A	ENSP00000316328:p.Gly856Ser	154.0	0.0		148.0	0.0	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	hg19	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	G	1.253	-0.617942	0.03663	.	.	ENSG00000179583	ENST00000324288;ENST00000388910	T	0.50548	0.74	4.86	3.89	0.44902	.	0.111166	0.40385	N	0.001118	T	0.29524	0.0736	L	0.39397	1.21	0.34964	D	0.752507	B;B;B;B	0.28667	0.077;0.017;0.126;0.219	B;B;B;B	0.27715	0.021;0.009;0.082;0.074	T	0.23583	-1.0184	10	0.06494	T	0.89	.	4.861	0.13583	0.1966:0.1787:0.6247:0.0	.	856;856;808;856	A0N0N9;P33076;F2Z2G8;Q96KL4	.;C2TA_HUMAN;.;.	S	856;808	ENSP00000316328:G856S	ENSP00000316328:G856S	G	+	1	0	CIITA	10909416	0.344000	0.24827	0.431000	0.26735	0.061000	0.15899	1.411000	0.34702	0.989000	0.38761	0.655000	0.94253	GGC	.	.		0.647	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		A	11001915	G	A	11001915	3	1	44	1	0	0	0	0	1	0	0	0	3430	1232	43	3	2608	3	CIITA	16	11001915	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	8187412	11001915	79352838	341	5801										
XYLT1	64131	hgsc.bcm.edu	37	chr16	17211555	17211555	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agaggcgcaacgaggaatttGgtctctgcaactggcaccca	12	11	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:17211555G>T	ENST00000261381.6	-	11	2589	c.2505C>A	c.(2503-2505)acC>acA	p.T835T		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	835					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CGAGGAATTTGGTCTCTGCAA	0.542																																					p.T835T		Atlas-SNP	.											.	XYLT1	147	.	0			c.C2505A						.						84	81	82					16																	17211555		2197	4300	6497	SO:0001819	synonymous_variant	64131	exon11			GAATTTGGTCTCT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.2505C>A	chr16.hg19:g.17211555G>T		218.0	0.0		216.0	107.0	NM_022166	Q9H1B6	Silent	SNP	ENST00000261381.6	hg19	CCDS10569.1																																																																																			.	.		0.542	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		T	17211555	G	T	17211555	2	4	44	1	0	0	0	0	0	0	0	1	17478	1335	47	3		3	XYLT1	16	17211555	Silent	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	6209640	17211555	73143198	342	5802										
KIF22	3835	hgsc.bcm.edu	37	chr16	29810070	29810070	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agagatctaccaggagaaggTgaggccccgtgctggttggg	17	8	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:29810070T>G	ENST00000160827.4	+	4	589		c.e4+2		KIF22_ENST00000569382.2_Splice_Site|KIF22_ENST00000400751.5_Splice_Site|KIF22_ENST00000561482.1_Splice_Site|KIF22_ENST00000400750.2_Splice_Site	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA repair (GO:0006281)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)			endometrium(1)|large_intestine(1)|lung(11)|skin(1)	14						CAGGAGAAGGTGAGGCCCCGT	0.567																																					.		Atlas-SNP	.											.	KIF22	29	.	0			c.549+2T>G						.						30	33	32					16																	29810070		2197	4296	6493	SO:0001630	splice_region_variant	3835	exon4			AGAAGGTGAGGCC	D38751	CCDS10653.1, CCDS58444.1	16p11.2	2008-03-03	2003-01-09	2003-01-10	ENSG00000079616	ENSG00000079616		"Kinesins"	6391	protein-coding gene	gene with protein product		603213	"kinesin-like 4"	KNSL4		8599929, 11416179	Standard	NM_007317		Approved	Kid, OBP-1, OBP-2	uc002dts.4	Q14807	OTTHUMG00000097771	ENST00000160827.4:c.549+2T>G	chr16.hg19:g.29810070T>G		109.0	0.0		84.0	5.0	NM_007317	B2R5M0|B7Z265|O60845|O94814|Q53F58|Q9BT46	Splice_Site	SNP	ENST00000160827.4	hg19	CCDS10653.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336063	0.60963	.	.	ENSG00000079616	ENST00000160827;ENST00000400751	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3589	0.66757	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIF22	29717571	1.000000	0.71417	0.993000	0.49108	0.790000	0.44656	4.200000	0.58433	2.274000	0.75844	0.533000	0.62120	.	.	.		0.567	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2		Intron	G	29810070	T	G	29810070	5	3	44	1	0	0	0	0	0	0	1	0	8299	1710	59	5	565	5	KIF22	16	29810070	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	12598515	29810070	60544683	343	5803										
BCL7C	9274	hgsc.bcm.edu	37	chr16	30904020	30904020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccccaggactgggctctgtgCccttttgcagggaaccttcc	11	15	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:30904020C>T	ENST00000215115.4	-	4	1344	c.329G>A	c.(328-330)gGc>gAc	p.G110D	BCL7C_ENST00000380317.4_Missense_Mutation_p.G110D|AC106782.20_ENST00000572471.1_RNA|MIR4519_ENST00000565573.1_RNA|MIR4519_ENST00000564901.1_RNA|MIR762_ENST00000390236.1_RNA|MIR4519_ENST00000570025.1_RNA	NM_004765.2	NP_004756.2	Q8WUZ0	BCL7C_HUMAN	B-cell CLL/lymphoma 7C	110	Pro-rich.				apoptotic process (GO:0006915)					large_intestine(1)|lung(3)|prostate(1)|skin(1)	6			Colorectal(24;0.198)			GGGCTCTGTGCCCTTTTGCAG	0.637																																					p.G110D		Atlas-SNP	.											.	BCL7C	30	.	0			c.G329A						.						57	63	61					16																	30904020		2197	4300	6497	SO:0001583	missense	9274	exon4			TCTGTGCCCTTTT	AJ223980	CCDS10693.1, CCDS67012.1	16p11	2012-11-19			ENSG00000099385	ENSG00000099385			1006	protein-coding gene	gene with protein product		605847				9931421	Standard	NM_004765		Approved		uc002dzv.3	Q8WUZ0	OTTHUMG00000177719	ENST00000215115.4:c.329G>A	chr16.hg19:g.30904020C>T	ENSP00000215115:p.Gly110Asp	113.0	0.0		100.0	5.0	NM_004765	O43770|Q6PD89	Missense_Mutation	SNP	ENST00000215115.4	hg19	CCDS10693.1	.	.	.	.	.	.	.	.	.	.	C	13.78	2.340199	0.41398	.	.	ENSG00000099385	ENST00000380317;ENST00000215115	T;T	0.42513	0.97;0.98	5.08	5.08	0.68730	.	0.110120	0.39909	N	0.001230	T	0.49474	0.1559	N	0.25380	0.74	0.46521	D	0.999089	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.29150	-1.0021	10	0.10636	T	0.68	-2.623	17.6012	0.88025	0.0:1.0:0.0:0.0	.	110;110	Q8WUZ0;Q8WUZ0-2	BCL7C_HUMAN;.	D	110	ENSP00000369674:G110D;ENSP00000215115:G110D	ENSP00000215115:G110D	G	-	2	0	BCL7C	30811521	0.941000	0.31946	1.000000	0.80357	0.992000	0.81027	1.144000	0.31565	2.519000	0.84933	0.561000	0.74099	GGC	.	.		0.637	BCL7C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255547.3	NM_004765		T	30904020	C	T	30904020	3	4	44	1	0	0	0	0	1	0	0	0	1380	739	26	3	336	3	BCL7C	16	30904020	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1093950	30904020	59450733	344	5804										
PHKB	5257	hgsc.bcm.edu	37	chr16	47531308	47531308	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gggtttttattttttcttttAggctcagtttatgaacctct	7	6	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:47531308A>G	ENST00000323584.5	+	2	100		c.e2-1		PHKB_ENST00000567402.1_Splice_Site|PHKB_ENST00000455779.1_Splice_Site|PHKB_ENST00000566044.1_Splice_Site|PHKB_ENST00000299167.8_Splice_Site	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta						carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				TTTTTCTTTTAGGCTCAGTTT	0.313																																					.		Atlas-SNP	.											PHKB_ENST00000323584,NS,carcinoma,0,3	PHKB	298	.	0			c.77-2A>G						.						43	45	44					16																	47531308		2201	4297	6498	SO:0001630	splice_region_variant	5257	exon2			TCTTTTAGGCTCA		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.77-1A>G	chr16.hg19:g.47531308A>G		17.0	0.0		10.0	2.0	NM_000293	Q8N4T5	Splice_Site	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.164763	0.78339	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7168	0.77674	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PHKB	46088809	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	7.564000	0.82326	2.126000	0.65437	0.482000	0.46254	.	.	.		0.313	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1		Intron	G	47531308	A	G	47531308	5	3	44	1	0	0	0	0	0	0	1	0	11854	434	15	2	140	2	PHKB	16	47531308	Splice_Site	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	16627288	47531308	42823445	345	5805										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48595062	48595062	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gacttctttgggacttggagAggcaacagaaggtgaaaggc	15	6	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:48595062A>G	ENST00000262384.3	-	2	1728	c.1492T>C	c.(1492-1494)Tct>Cct	p.S498P	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	498					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				GGACTTGGAGAGGCAACAGAA	0.448																																					p.S498P		Atlas-SNP	.											.	N4BP1	121	.	0			c.T1492C						.						143	146	145					16																	48595062		1913	4121	6034	SO:0001583	missense	9683	exon2			TTGGAGAGGCAAC	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.1492T>C	chr16.hg19:g.48595062A>G	ENSP00000262384:p.Ser498Pro	169.0	0.0		103.0	5.0	NM_153029	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	hg19	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	A	4.145	0.025216	0.08054	.	.	ENSG00000102921	ENST00000262384	T	0.43294	0.95	6.08	1.96	0.26148	.	0.692420	0.15023	N	0.284865	T	0.14270	0.0345	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30650	-0.9971	10	0.07030	T	0.85	-2.386	5.3727	0.16148	0.3122:0.1363:0.5515:0.0	.	498	O75113	N4BP1_HUMAN	P	498	ENSP00000262384:S498P	ENSP00000262384:S498P	S	-	1	0	N4BP1	47152563	0.000000	0.05858	0.005000	0.12908	0.720000	0.41350	-0.630000	0.05502	0.137000	0.18759	-0.462000	0.05337	TCT	.	.		0.448	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		G	48595062	A	G	48595062	3	3	44	1	0	0	0	0	1	0	0	0	10118	304	11	2	1222	2	N4BP1	16	48595062	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1063754	48595062	41759691	346	5806										
TPPP3	51673	hgsc.bcm.edu	37	chr16	67425009	67425009	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccagccatgtctgtgctcgcTgccatgccaccctatagaga	9	15	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:67425009T>C	ENST00000564104.1	-	1	847	c.6A>G	c.(4-6)gcA>gcG	p.A2A	TPPP3_ENST00000562206.1_Silent_p.A2A|RNU1-123P_ENST00000458950.1_RNA|TPPP3_ENST00000290942.5_Silent_p.A2A|TPPP3_ENST00000393957.2_Silent_p.A2A			Q9BW30	TPPP3_HUMAN	tubulin polymerization-promoting protein family member 3	2					microtubule bundle formation (GO:0001578)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	tubulin binding (GO:0015631)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0336)|Epithelial(162;0.0781)		CTGTGCTCGCTGCCATGCCAC	0.597																																					p.A2A		Atlas-SNP	.											.	TPPP3	13	.	0			c.A6G						.						62	56	58					16																	67425009		2198	4300	6498	SO:0001819	synonymous_variant	51673	exon3			GCTCGCTGCCATG	BC000691	CCDS10835.1	16q22.1	2008-02-05			ENSG00000159713	ENSG00000159713			24162	protein-coding gene	gene with protein product						15590652, 17105200	Standard	XM_005255979		Approved	CGI-38, p25gamma, p20	uc002etb.3	Q9BW30	OTTHUMG00000137516	ENST00000564104.1:c.6A>G	chr16.hg19:g.67425009T>C		115.0	0.0		58.0	4.0	NM_016140	Q49AH9|Q9Y326|Q9Y6H0	Silent	SNP	ENST00000564104.1	hg19	CCDS10835.1																																																																																			.	.		0.597	TPPP3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421787.2	NM_015964		C	67425009	T	C	67425009	2	2	44	1	0	0	0	0	0	0	0	1	16430	1567	55	2		2	TPPP3	16	67425009	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	18829947	67425009	22929744	347	5807										
CENPT	80152	hgsc.bcm.edu	37	chr16	67863958	67863958	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aggcattgacctcctctgccTctcctgccagaaactgggct	9	15	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:67863958T>C	ENST00000562787.1	-	12	1444	c.896A>G	c.(895-897)gAg>gGg	p.E299G	CENPT_ENST00000564817.1_Missense_Mutation_p.E299G|CENPT_ENST00000562947.1_5'Flank|CENPT_ENST00000219172.3_Missense_Mutation_p.E299G|CENPT_ENST00000440851.2_Missense_Mutation_p.E299G	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T	299	Flexible stalk domain. {ECO:0000250}.				chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		CTCCTCTGCCTCTCCTGCCAG	0.572																																					p.E299G		Atlas-SNP	.											.	CENPT	26	.	0			c.A896G						.						64	65	65					16																	67863958		2018	4193	6211	SO:0001583	missense	80152	exon12			TCTGCCTCTCCTG	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3		ENST00000562787.1:c.896A>G	chr16.hg19:g.67863958T>C	ENSP00000457810:p.Glu299Gly	109.0	0.0		59.0	4.0	NM_025082	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	hg19	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.550697	0.45383	.	.	ENSG00000102901	ENST00000440851;ENST00000436104;ENST00000219172	T;T	0.46063	0.88;0.88	3.83	-1.6	0.08426	.	1.368410	0.05054	N	0.478714	T	0.26484	0.0647	L	0.36672	1.1	0.20638	N	0.999879	B;B;B	0.27732	0.027;0.187;0.187	B;B;B	0.24701	0.018;0.055;0.038	T	0.11227	-1.0596	10	0.24483	T	0.36	-2.4585	0.2782	0.00241	0.3999:0.1786:0.2016:0.2199	.	57;299;299	F5H5A6;Q96BT3;B3KPB2	.;CENPT_HUMAN;.	G	299;57;299	ENSP00000400140:E299G;ENSP00000219172:E299G	ENSP00000219172:E299G	E	-	2	0	CENPT	66421459	0.003000	0.15002	0.000000	0.03702	0.269000	0.26545	0.297000	0.19101	-0.411000	0.07530	-1.548000	0.00902	GAG	.	.		0.572	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		C	67863958	T	C	67863958	3	2	44	1	0	0	0	0	1	0	0	0	3244	1551	54	2	809	2	CENPT	16	67863958	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	438949	67863958	22490795	348	5808										
ZFP90	146198	hgsc.bcm.edu	37	chr16	68598370	68598370	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaatgtattgactgtgggaaAgcctttagtcaaagttcatc	10	6	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr16:68598370A>G	ENST00000570495.1	+	5	1972	c.1680A>G	c.(1678-1680)aaA>aaG	p.K560K	ZFP90_ENST00000563169.2_Silent_p.K560K|ZFP90_ENST00000398253.2_Silent_p.K560K			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	560					negative regulation of DNA binding (GO:0043392)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		ACTGTGGGAAAGCCTTTAGTC	0.433																																					p.K560K		Atlas-SNP	.											.	ZFP90	67	.	0			c.A1680G						.						82	94	90					16																	68598370		2193	4299	6492	SO:0001819	synonymous_variant	146198	exon4			TGGGAAAGCCTTT	AK074332	CCDS42183.1	16q22.1	2013-01-08	2012-11-27			ENSG00000184939		"Zinc fingers, C2H2-type", "-"	23329	protein-coding gene	gene with protein product		609451	"zinc finger protein 90 homolog (mouse)"			7576184	Standard	NM_133458		Approved	KIAA1954, NK10, ZNF756	uc002ewc.3	Q8TF47		ENST00000570495.1:c.1680A>G	chr16.hg19:g.68598370A>G		51.0	0.0		44.0	4.0	NM_133458	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Silent	SNP	ENST00000570495.1	hg19	CCDS42183.1																																																																																			.	.		0.433	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375		G	68598370	A	G	68598370	2	3	44	1	0	0	0	0	0	0	0	1	17669	69	3	2		2	ZFP90	16	68598370	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	734412	68598370	21756383	349	5809										
TP53	7157	hgsc.bcm.edu	37	chr17	7577565	7577565	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgccgcccatgcaggaactgTtacacatgtagttgtagtgg	12	9	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:7577565T>C	ENST00000269305.4	-	7	905	c.716A>G	c.(715-717)aAc>aGc	p.N239S	TP53_ENST00000359597.4_Missense_Mutation_p.N239S|TP53_ENST00000445888.2_Missense_Mutation_p.N239S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.N239S|TP53_ENST00000455263.2_Missense_Mutation_p.N239S|TP53_ENST00000420246.2_Missense_Mutation_p.N239S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	239	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		N -> D (in sporadic cancers; somatic mutation).|N -> H (in a sporadic cancer; somatic mutation).|N -> I (in a sporadic cancer; somatic mutation).|N -> K (in sporadic cancers; somatic mutation).|N -> S (in sporadic cancers; somatic mutation).|N -> T (in sporadic cancers; somatic mutation).|N -> Y (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.N239S(28)|p.0?(8)|p.?(5)|p.N239T(4)|p.M237_N239delMCN(4)|p.N146S(3)|p.N239_C242delNSSC(3)|p.N239fs*25(2)|p.N239_S240delNS(2)|p.Y236_M243delYMCNSSCM(1)|p.N239fs*1(1)|p.N239_S240insN(1)|p.V225fs*23(1)|p.N239fs*6(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.M144_N146delMCN(1)|p.C238fs*21(1)|p.N239I(1)|p.H233fs*6(1)|p.N239*(1)|p.H233_C242del10(1)|p.N239_C242>S(1)|p.N239fs*>48(1)|p.N146fs*>10(1)|p.N239_C242del(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAGGAACTGTTACACATGTA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.N239S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,-1,40	TP53	33396	.	76	Substitution - Missense(36)|Deletion - In frame(14)|Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(5)|Insertion - Frameshift(4)|Substitution - Nonsense(1)|Insertion - In frame(1)|Complex - frameshift(1)|Complex - deletion inframe(1)	biliary_tract(10)|urinary_tract(6)|lung(6)|ovary(6)|upper_aerodigestive_tract(5)|haematopoietic_and_lymphoid_tissue(5)|oesophagus(5)|breast(5)|bone(5)|central_nervous_system(4)|large_intestine(4)|endometrium(4)|kidney(4)|stomach(3)|thyroid(1)|soft_tissue(1)|liver(1)|pancreas(1)	c.A716G						.						135	105	115					17																	7577565		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GAACTGTTACACA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.716A>G	chr17.hg19:g.7577565T>C	ENSP00000269305:p.Asn239Ser	265.0	0.0		110.0	98.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.565663	0.86439	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99760	-6.66;-6.66;-6.66;-6.66;-6.66;-6.66;-6.66;-6.66	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99736	0.9896	M	0.87381	2.88	0.58432	D	0.999991	D;B;D;D;D;D	0.89917	0.988;0.31;0.999;0.98;0.99;1.0	P;B;D;P;P;D	0.87578	0.826;0.104;0.981;0.815;0.891;0.998	D	0.97237	0.9888	10	0.87932	D	0	-35.9081	12.3101	0.54924	0.0:0.0:0.0:1.0	.	239;239;146;239;239;239	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	S	239;239;239;239;239;239;228;146;107;146	ENSP00000410739:N239S;ENSP00000352610:N239S;ENSP00000269305:N239S;ENSP00000398846:N239S;ENSP00000391127:N239S;ENSP00000391478:N239S;ENSP00000425104:N107S;ENSP00000423862:N146S	ENSP00000269305:N239S	N	-	2	0	TP53	7518290	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.770000	0.85390	2.074000	0.62210	0.379000	0.24179	AAC	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577565	T	C	7577565	3	2	44	1	0	0	0	0	1	0	0	0	16396	1725	60	2	574	2	TP53	17	7577565	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10		7577565	73617645	350	5810										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7636446	7636446	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ttcattcgccaagcaccagtTcccatcacctgggagaactt	7	14	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:7636446T>C	ENST00000572933.1	+	5	1901	c.441T>C	c.(439-441)gtT>gtC	p.V147V	DNAH2_ENST00000570791.1_Silent_p.V147V|DNAH2_ENST00000389173.2_Silent_p.V147V|DNAH2_ENST00000082259.3_Silent_p.V147V			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	147	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				AAGCACCAGTTCCCATCACCT	0.587																																					p.V147V		Atlas-SNP	.											.	DNAH2	498	.	0			c.T441C						.						97	90	93					17																	7636446		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon4			ACCAGTTCCCATC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.441T>C	chr17.hg19:g.7636446T>C		146.0	0.0		95.0	5.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.		0.587	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		C	7636446	T	C	7636446	2	2	44	1	0	0	0	0	0	0	0	1	4604	1770	62	2		2	DNAH2	17	7636446	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	58881	7636446	73558764	351	5811										
CHD3	1107	hgsc.bcm.edu	37	chr17	7810554	7810554	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acagcagaattggggagaagAtggagacagaggtgtgtggc	18	4	0	5			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:7810554A>G	ENST00000330494.7	+	31	4927	c.4777A>G	c.(4777-4779)Atg>Gtg	p.M1593V	CHD3_ENST00000358181.4_Missense_Mutation_p.M1593V|SCARNA21_ENST00000517026.1_RNA|CHD3_ENST00000380358.4_Missense_Mutation_p.M1652V	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1593	Required for interaction with PCNT.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				TGGGGAGAAGATGGAGACAGA	0.572																																					p.M1652V		Atlas-SNP	.											.	CHD3	169	.	0			c.A4954G						.						115	119	117					17																	7810554		2203	4300	6503	SO:0001583	missense	1107	exon31			GAGAAGATGGAGA	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.4777A>G	chr17.hg19:g.7810554A>G	ENSP00000332628:p.Met1593Val	128.0	0.0		83.0	5.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	A	4.407	0.075230	0.08485	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	D;D;D	0.89485	-2.52;-2.48;-2.46	4.54	3.46	0.39613	.	0.108333	0.41194	D	0.000921	T	0.75413	0.3846	N	0.08118	0	0.33675	D	0.611388	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.72030	-0.4413	10	0.29301	T	0.29	-14.3174	9.5615	0.39371	0.9145:0.0:0.0855:0.0	.	169;1593;1593;1652	B3KWV4;Q12873-2;Q12873;E9PG89	.;.;CHD3_HUMAN;.	V	1652;1593;1593	ENSP00000369716:M1652V;ENSP00000350907:M1593V;ENSP00000332628:M1593V	ENSP00000332628:M1593V	M	+	1	0	CHD3	7751279	0.843000	0.29541	1.000000	0.80357	0.612000	0.37316	0.612000	0.24283	0.877000	0.35895	-0.521000	0.04368	ATG	.	.		0.572	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		G	7810554	A	G	7810554	3	3	44	1	0	0	0	0	1	0	0	0	3328	333	12	2	5180	2	CHD3	17	7810554	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	174108	7810554	73384656	352	5812										
MYH4	4622	hgsc.bcm.edu	37	chr17	10354170	10354170	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtttgcctcgggatagctgaGaaaccatagcatctttttca	9	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:10354170G>T	ENST00000255381.2	-	29	4018	c.3908C>A	c.(3907-3909)tCt>tAt	p.S1303Y	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1303					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						GGATAGCTGAGAAACCATAGC	0.378																																					p.S1303Y		Atlas-SNP	.											.	MYH4	349	.	0			c.C3908A						.						161	147	152					17																	10354170		2203	4300	6503	SO:0001583	missense	4622	exon29			AGCTGAGAAACCA		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.3908C>A	chr17.hg19:g.10354170G>T	ENSP00000255381:p.Ser1303Tyr	249.0	0.0		145.0	124.0	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.258015	0.80246	.	.	ENSG00000141048	ENST00000255381	T	0.79940	-1.32	5.71	5.71	0.89125	Myosin tail (1);	0.000000	0.37304	U	0.002144	D	0.92482	0.7613	M	0.93241	3.395	0.50632	D	0.999886	D	0.69078	0.997	D	0.71184	0.972	D	0.93703	0.7017	10	0.87932	D	0	.	18.9878	0.92779	0.0:0.0:1.0:0.0	.	1303	Q9Y623	MYH4_HUMAN	Y	1303	ENSP00000255381:S1303Y	ENSP00000255381:S1303Y	S	-	2	0	MYH4	10294895	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.763000	0.68818	2.850000	0.98022	0.655000	0.94253	TCT	.	.		0.378	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10354170	G	T	10354170	3	4	44	1	0	0	0	0	1	0	0	0	10046	942	33	3	1959	3	MYH4	17	10354170	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	2543616	10354170	70841040	353	5813										
MYH3	4621	hgsc.bcm.edu	37	chr17	10543929	10543929	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggtcaatatcaatggatgccAgaagcttttcacaggctttc	9	9	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:10543929A>G	ENST00000583535.1	-	20	2327	c.2240T>C	c.(2239-2241)cTg>cCg	p.L747P	MYH3_ENST00000226209.7_Missense_Mutation_p.L747P	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	747	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						AATGGATGCCAGAAGCTTTTC	0.448																																					p.L747P		Atlas-SNP	.											.	MYH3	227	.	0			c.T2240C						.						146	131	136					17																	10543929		2203	4300	6503	SO:0001583	missense	4621	exon20			GATGCCAGAAGCT		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.2240T>C	chr17.hg19:g.10543929A>G	ENSP00000464317:p.Leu747Pro	169.0	0.0		94.0	4.0	NM_002470	Q15492	Missense_Mutation	SNP	ENST00000583535.1	hg19	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	A	19.14	3.770302	0.69992	.	.	ENSG00000109063	ENST00000226209	D	0.91792	-2.91	5.52	5.52	0.82312	Myosin head, motor domain (2);	.	.	.	.	D	0.98040	0.9354	H	0.99368	4.535	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99771	1.1024	9	0.87932	D	0	.	15.9319	0.79668	1.0:0.0:0.0:0.0	.	747	P11055	MYH3_HUMAN	P	747	ENSP00000226209:L747P	ENSP00000226209:L747P	L	-	2	0	MYH3	10484654	1.000000	0.71417	0.957000	0.39632	0.928000	0.56348	9.287000	0.95975	2.225000	0.72522	0.459000	0.35465	CTG	.	.		0.448	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		G	10543929	A	G	10543929	3	3	44	1	0	0	0	0	1	0	0	0	10045	188	7	2	3670	2	MYH3	17	10543929	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	189759	10543929	70651281	354	5814										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11648192	11648192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgaagagaggagaccctgacCggcctgaggaccaggtcctg	15	11	0	5	rs375918058		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:11648192C>T	ENST00000262442.4	+	31	6258	c.6190C>T	c.(6190-6192)Cgg>Tgg	p.R2064W	DNAH9_ENST00000454412.2_Missense_Mutation_p.R2064W	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2064					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGACCCTGACCGGCCTGAGGA	0.577																																					p.R2064W		Atlas-SNP	.											DNAH9,NS,carcinoma,0,1	DNAH9	695	.	0			c.C6190T						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	63	56	59		6190	4.5	1	17		59	0,8600		0,0,4300	no	missense	DNAH9	NM_001372.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	2064/4487	11648192	1,13005	2203	4300	6503	SO:0001583	missense	1770	exon31			CCTGACCGGCCTG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6190C>T	chr17.hg19:g.11648192C>T	ENSP00000262442:p.Arg2064Trp	160.0	0.0		67.0	3.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480558	0.84747	2.27E-4	0.0	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.27557	1.7;1.66	5.46	4.47	0.54385	.	0.679543	0.13145	N	0.410309	T	0.66268	0.2772	M	0.93106	3.38	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.72276	-0.4341	10	0.66056	D	0.02	.	15.4422	0.75195	0.1401:0.8599:0.0:0.0	.	2064	Q9NYC9	DYH9_HUMAN	W	2064;2064;646	ENSP00000262442:R2064W;ENSP00000414874:R2064W	ENSP00000262442:R2064W	R	+	1	2	DNAH9	11588917	0.797000	0.28877	1.000000	0.80357	0.970000	0.65996	1.561000	0.36342	1.264000	0.44198	0.650000	0.86243	CGG	.	.		0.577	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11648192	C	T	11648192	3	4	44	1	0	0	0	0	1	0	0	0	4610	643	23	1	6312	1	DNAH9	17	11648192	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1104263	11648192	69547018	355	5815										
SHMT1	6470	hgsc.bcm.edu	37	chr17	18232099	18232099	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gccaggcagagggaagagagAggcgaagctctcaacctcct	14	11	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:18232099A>G	ENST00000316694.3	-	12	1551	c.1417T>C	c.(1417-1419)Tct>Cct	p.S473P	RP1-178F10.3_ENST00000577764.1_lincRNA|SHMT1_ENST00000352886.6_Missense_Mutation_p.S393P|SHMT1_ENST00000354098.3_Missense_Mutation_p.S434P|SHMT1_ENST00000539052.1_Missense_Mutation_p.S335P	NM_004169.3	NP_004160.3	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	473					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|folic acid metabolic process (GO:0046655)|glycine biosynthetic process from serine (GO:0019264)|L-serine catabolic process (GO:0006565)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase biosynthetic process (GO:0009113)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	amino acid binding (GO:0016597)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)	13					Glycine(DB00145)|Mimosine(DB01055)|Tetrahydrofolic acid(DB00116)	GGGAAGAGAGAGGCGAAGCTC	0.637																																					p.S473P		Atlas-SNP	.											.	SHMT1	36	.	0			c.T1417C						.						26	25	25					17																	18232099		2203	4299	6502	SO:0001583	missense	6470	exon12			AGAGAGAGGCGAA		CCDS11196.1, CCDS11197.1, CCDS62112.1	17p11.2	2010-04-23			ENSG00000176974	ENSG00000176974	2.1.2.1		10850	protein-coding gene	gene with protein product	"cytoplasmic serine hydroxymethyltransferase", "14 kDa protein"	182144				8505317	Standard	NM_004169		Approved	CSHMT, SHMT, MGC15229, MGC24556	uc002gta.3	P34896	OTTHUMG00000059094	ENST00000316694.3:c.1417T>C	chr17.hg19:g.18232099A>G	ENSP00000318868:p.Ser473Pro	84.0	0.0		85.0	4.0	NM_004169	B4DPM9|D3DXD0|Q96HY0|Q9UMD1|Q9UMD2	Missense_Mutation	SNP	ENST00000316694.3	hg19	CCDS11196.1	.	.	.	.	.	.	.	.	.	.	A	9.270	1.045465	0.19748	.	.	ENSG00000176974	ENST00000316694;ENST00000395684;ENST00000352886;ENST00000539052;ENST00000354098;ENST00000395685	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	5.37	-3.73	0.04398	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.415553	0.27043	N	0.021204	T	0.38719	0.1051	M	0.81682	2.555	0.09310	N	1	B;P;B	0.37663	0.042;0.604;0.007	B;B;B	0.41088	0.066;0.347;0.018	T	0.44019	-0.9355	10	0.41790	T	0.15	-6.1079	11.6982	0.51556	0.2492:0.585:0.0:0.1658	.	436;434;473	A8MYA6;P34896-2;P34896	.;.;GLYC_HUMAN	P	473;248;393;335;434;436	ENSP00000318868:S473P;ENSP00000345881:S393P;ENSP00000440089:S335P;ENSP00000318805:S434P	ENSP00000318868:S473P	S	-	1	0	SHMT1	18172824	0.002000	0.14202	0.000000	0.03702	0.202000	0.24057	0.688000	0.25422	-0.491000	0.06697	0.533000	0.62120	TCT	.	.		0.637	SHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130831.2	NM_004169		G	18232099	A	G	18232099	3	3	44	1	0	0	0	0	1	0	0	0	14300	304	11	2	38	2	SHMT1	17	18232099	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	6583907	18232099	62963111	356	5816										
SEBOX	147007	hgsc.bcm.edu	37	chr17	26692221	26692221	+	IGR	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gggccgtgccagagggccatGccaggctgtgcccacaccag	15	15	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:26692221G>C	ENST00000292114.3	+	0	3148				VTN_ENST00000536498.1_Intron|TMEM199_ENST00000509083.1_Intron|SARM1_ENST00000379061.4_Intron|VTN_ENST00000438614.1_Intron|VTN_ENST00000431468.1_Missense_Mutation_p.H11D|CTB-96E2.7_ENST00000577850.1_RNA|CTB-96E2.3_ENST00000591482.1_RNA|CTB-96E2.2_ENST00000555059.2_Intron	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		AGAGGGCCATGCCAGGCTGTG	0.612																																					p.H11D		Atlas-SNP	.											.	SEBOX	20	.	0			c.C31G						.						38	44	42					17																	26692221		1984	4161	6145	SO:0001628	intergenic_variant	645832	exon1			GGCCATGCCAGGC	AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 32"	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498		chr17.hg19:g.26692221G>C		97.0	0.0		91.0	4.0	NM_001080837		Missense_Mutation	SNP	ENST00000292114.3	hg19	CCDS11228.1	.	.	.	.	.	.	.	.	.	.	g	7.242	0.601512	0.13939	.	.	ENSG00000109072	ENST00000431468;ENST00000247029	D	0.91521	-2.86	.	.	.	.	.	.	.	.	T	0.76962	0.4061	N	0.08118	0	0.33615	D	0.604127	P	0.34662	0.462	B	0.36534	0.227	T	0.71391	-0.4607	7	0.11794	T	0.64	.	.	.	.	.	11	Q9HB31	SEBOX_HUMAN	D	11;15	ENSP00000416240:H11D	ENSP00000247029:H15D	H	-	1	0	VTN	23716348	0.498000	0.26075	0.650000	0.29550	0.207000	0.24258	0.075000	0.14686	0.073000	0.16731	0.074000	0.15403	CAT	.	.		0.612	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464		C	26692221	G	C	26692221	1	2	44	0	1	0	0	0	0	0	0	0	13992	1319	46	4		4	SEBOX	17	26692221	IGR	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	8460122	26692221	54502989	357	5817										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26948170	26948170	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttgctgggcttgctgtgccTcagctggctggttccaatct	12	12	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:26948170T>C	ENST00000528896.2	-	28	5152	c.5078A>G	c.(5077-5079)gAg>gGg	p.E1693G	KIAA0100_ENST00000579924.2_5'Flank|KIAA0100_ENST00000389003.3_Missense_Mutation_p.E1550G|KIAA0100_ENST00000544884.1_Missense_Mutation_p.E1550G	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	1693						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					TTGCTGTGCCTCAGCTGGCTG	0.458																																					p.E1693G		Atlas-SNP	.											.	KIAA0100	175	.	0			c.A5078G						.						61	56	58					17																	26948170		2203	4300	6503	SO:0001583	missense	9703	exon28			TGTGCCTCAGCTG	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.5078A>G	chr17.hg19:g.26948170T>C	ENSP00000436773:p.Glu1693Gly	99.0	0.0		123.0	5.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.207486	0.39003	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.25250	1.81;1.81	5.53	5.53	0.82687	.	0.101164	0.64402	D	0.000001	T	0.10208	0.0250	N	0.01168	-0.975	0.51233	D	0.999914	P	0.47762	0.9	B	0.39706	0.307	T	0.32268	-0.9913	10	0.34782	T	0.22	.	14.5272	0.67897	0.0:0.0:0.0:1.0	.	1693	Q14667	K0100_HUMAN	G	1693;1663;1693;1550	ENSP00000436773:E1693G;ENSP00000446443:E1550G	ENSP00000005905:E1693G	E	-	2	0	KIAA0100	23972297	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	5.648000	0.67930	2.231000	0.72958	0.459000	0.35465	GAG	.	.		0.458	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		C	26948170	T	C	26948170	3	2	44	1	0	0	0	0	1	0	0	0	8163	1551	54	2	1677	2	KIAA0100	17	26948170	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	255949	26948170	54247040	358	5818										
CCT6B	10693	hgsc.bcm.edu	37	chr17	33278993	33278993	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tatctgttcctaatttatgcTtcatctccattatttctacc	2	11	4	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:33278993T>C	ENST00000314144.5	-	5	705	c.590A>G	c.(589-591)aAg>aGg	p.K197R	CCT6B_ENST00000421975.3_Missense_Mutation_p.K197R|CCT6B_ENST00000436961.3_Missense_Mutation_p.K152R	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	197					chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				TAATTTATGCTTCATCTCCAT	0.308																																					p.K197R		Atlas-SNP	.											.	CCT6B	63	.	0			c.A590G						.						103	96	98					17																	33278993		2203	4300	6503	SO:0001583	missense	10693	exon5			TTATGCTTCATCT	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"Heat Shock Proteins / Chaperonins"	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.590A>G	chr17.hg19:g.33278993T>C	ENSP00000327191:p.Lys197Arg	100.0	0.0		96.0	4.0	NM_006584	B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	hg19	CCDS32617.1	.	.	.	.	.	.	.	.	.	.	T	10.72	1.428399	0.25726	.	.	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.79454	-0.23;-1.27;-1.27	4.75	3.68	0.42216	.	0.044381	0.85682	N	0.000000	T	0.65375	0.2685	L	0.37507	1.11	0.45161	D	0.998172	B;B;B	0.10296	0.001;0.003;0.002	B;B;B	0.17979	0.013;0.02;0.013	T	0.56715	-0.7933	10	0.25106	T	0.35	-6.6445	8.3908	0.32526	0.0:0.094:0.0:0.906	.	152;197;197	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	R	197;197;152	ENSP00000398044:K197R;ENSP00000327191:K197R;ENSP00000400917:K152R	ENSP00000327191:K197R	K	-	2	0	CCT6B	30303106	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	4.029000	0.57253	0.964000	0.38108	0.533000	0.62120	AAG	.	.		0.308	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584		C	33278993	T	C	33278993	3	2	44	1	0	0	0	0	1	0	0	0	2960	1609	56	2	1042	2	CCT6B	17	33278993	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	6330823	33278993	47916217	359	5819										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37863315	37863315	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctggacatgctccgccaccTctaccagggctgccaggtgg	12	16	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:37863315T>C	ENST00000269571.5	+	2	305	c.146T>C	c.(145-147)cTc>cCc	p.L49P	ERBB2_ENST00000584601.1_Missense_Mutation_p.L19P|ERBB2_ENST00000406381.2_Missense_Mutation_p.L19P|ERBB2_ENST00000578199.1_Missense_Mutation_p.L19P|ERBB2_ENST00000540147.1_Missense_Mutation_p.L19P|ERBB2_ENST00000584450.1_Missense_Mutation_p.L49P|ERBB2_ENST00000540042.1_Missense_Mutation_p.L19P|ERBB2_ENST00000541774.1_Missense_Mutation_p.L34P|ERBB2_ENST00000445658.2_Intron			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	49					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.L49H(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CTCCGCCACCTCTACCAGGGC	0.642		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.L49P		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	ERBB2,colon,carcinoma,0,2	ERBB2	429	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.T146C						.						43	38	39					17																	37863315		2203	4300	6503	SO:0001583	missense	2064	exon2			GCCACCTCTACCA	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.146T>C	chr17.hg19:g.37863315T>C	ENSP00000269571:p.Leu49Pro	158.0	2.0		168.0	7.0	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	hg19	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.560683	0.45590	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000269571;ENST00000540147;ENST00000540042	D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75	5.23	5.23	0.72850	.	.	.	.	.	D	0.88698	0.6507	L	0.55481	1.735	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.994;0.971;0.991	D	0.89628	0.3853	9	0.72032	D	0.01	.	14.2408	0.65956	0.0:0.0:0.0:1.0	.	19;34;49;49	F5H1T4;P04626-4;P04626;Q9UK79	.;.;ERBB2_HUMAN;.	P	19;34;49;19;19	ENSP00000385185:L19P;ENSP00000446466:L34P;ENSP00000269571:L49P;ENSP00000443562:L19P;ENSP00000446382:L19P	ENSP00000269571:L49P	L	+	2	0	ERBB2	35116841	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.882000	0.69714	2.200000	0.70718	0.459000	0.35465	CTC	.	.		0.642	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			C	37863315	T	C	37863315	3	2	44	1	0	0	0	0	1	0	0	0	5208	1551	54	2	152	2	ERBB2	17	37863315	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4584322	37863315	43331895	360	5820										
BRCA1	672	hgsc.bcm.edu	37	chr17	41276097	41276097	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tttgtacttcttcaacgcgaAgagcagataaatccatttct	6	9	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:41276097A>G	ENST00000357654.3	-	2	135	c.17T>C	c.(16-18)cTt>cCt	p.L6P	BRCA1_ENST00000346315.3_Missense_Mutation_p.L6P|BRCA1_ENST00000309486.4_5'UTR|BRCA1_ENST00000354071.3_Missense_Mutation_p.L6P|BRCA1_ENST00000351666.3_Missense_Mutation_p.L6P|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000491747.2_Missense_Mutation_p.L6P|NBR2_ENST00000460115.1_RNA|BRCA1_ENST00000471181.2_Missense_Mutation_p.L6P|BRCA1_ENST00000352993.3_Missense_Mutation_p.L6P|BRCA1_ENST00000468300.1_Missense_Mutation_p.L6P|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000493795.1_5'UTR	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	6					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TTCAACGCGAAGAGCAGATAA	0.308			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.L6P		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.T17C						.						106	92	97					17																	41276097		2202	4299	6501	SO:0001583	missense	672	exon1	Familial Cancer Database		ACGCGAAGAGCAG	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.17T>C	chr17.hg19:g.41276097A>G	ENSP00000350283:p.Leu6Pro	165.0	0.0		98.0	4.0	NM_007298	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	hg19	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	A	7.954	0.745464	0.15710	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000352993;ENST00000346315;ENST00000351666;ENST00000468300;ENST00000471181;ENST00000491747;ENST00000478531;ENST00000470026;ENST00000477152;ENST00000494123;ENST00000476777;ENST00000489037	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87	3.83	0.603	0.17541	.	0.751799	0.11314	N	0.576860	T	0.72732	0.3497	L	0.29908	0.895	0.09310	N	0.999995	B;B;B;B;B;B;B	0.27882	0.021;0.012;0.008;0.036;0.061;0.192;0.031	B;B;B;B;B;B;B	0.25140	0.026;0.011;0.013;0.058;0.018;0.024;0.016	T	0.62478	-0.6846	10	0.72032	D	0.01	-0.6375	2.7625	0.05311	0.5326:0.0:0.1973:0.27	.	6;6;6;6;6;6;6	E7ETR2;E7EMP0;Q5YLB2;P38398-3;Q6IN79;E9PFC7;P38398	.;.;.;.;.;.;BRCA1_HUMAN	P	6	ENSP00000350283:L6P;ENSP00000326002:L6P;ENSP00000312236:L6P;ENSP00000246907:L6P;ENSP00000338007:L6P;ENSP00000417148:L6P;ENSP00000418960:L6P;ENSP00000420705:L6P;ENSP00000420412:L6P;ENSP00000419274:L6P;ENSP00000419988:L6P;ENSP00000419103:L6P;ENSP00000417554:L6P;ENSP00000420781:L6P	ENSP00000246907:L6P	L	-	2	0	BRCA1	38529623	0.801000	0.28930	0.012000	0.15200	0.757000	0.42996	1.242000	0.32755	0.070000	0.16634	0.334000	0.21626	CTT	.	.		0.308	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		G	41276097	A	G	41276097	3	3	44	1	0	0	0	0	1	0	0	0	1500	72	3	2	5732	2	BRCA1	17	41276097	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	3412782	41276097	39919113	361	5821										
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42960512	42960512	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgagtctgttcaattaaacaAtccacaaaacatgtctaaaa	4	8	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:42960512A>G	ENST00000426333.2	-	6	738	c.441T>C	c.(439-441)gaT>gaC	p.D147D	RN7SL405P_ENST00000582502.1_RNA|EFTUD2_ENST00000402521.3_Silent_p.D112D|EFTUD2_ENST00000592576.1_Intron|EFTUD2_ENST00000591382.1_Silent_p.D147D	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	147	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				CAATTAAACAATCCACAAAAC	0.418																																					p.D147D	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.T441C						.						110	93	99					17																	42960512		2203	4300	6503	SO:0001819	synonymous_variant	9343	exon6			TAAACAATCCACA	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.441T>C	chr17.hg19:g.42960512A>G		156.0	0.0		86.0	4.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Silent	SNP	ENST00000426333.2	hg19	CCDS11489.1																																																																																			.	.		0.418	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		G	42960512	A	G	42960512	2	3	44	1	0	0	0	0	0	0	0	1	4963	98	4	2		2	EFTUD2	17	42960512	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1684415	42960512	38234698	362	5822										
ERN1	2081	hgsc.bcm.edu	37	chr17	62125246	62125246	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	actggagctgcttctctaggCtccagaagaacgggtgtttg	13	9	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:62125246C>T	ENST00000433197.3	-	19	2596	c.2501G>A	c.(2500-2502)aGc>aAc	p.S834N		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						CTTCTCTAGGCTCCAGAAGAA	0.438																																					p.S834N		Atlas-SNP	.											.	ERN1	102	.	0			c.G2501A						.						88	87	87					17																	62125246		1899	4116	6015	SO:0001583	missense	2081	exon19			TCTAGGCTCCAGA	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"inositol-requiring enzyme 1"	604033	"ER to nucleus signalling 1"			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.2501G>A	chr17.hg19:g.62125246C>T	ENSP00000401445:p.Ser834Asn	81.0	0.0		57.0	4.0	NM_001433		Missense_Mutation	SNP	ENST00000433197.3	hg19	CCDS45762.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.214490	0.58452	.	.	ENSG00000178607	ENST00000433197	T	0.50001	0.76	5.32	4.32	0.51571	Protein kinase-like domain (1);	0.268637	0.47852	D	0.000215	T	0.29126	0.0724	N	0.17838	0.53	0.45528	D	0.998483	B	0.09022	0.002	B	0.04013	0.001	T	0.07501	-1.0769	10	0.18710	T	0.47	-8.8444	9.1781	0.37125	0.0:0.7764:0.1435:0.0801	.	834	O75460	ERN1_HUMAN	N	834	ENSP00000401445:S834N	ENSP00000401445:S834N	S	-	2	0	ERN1	59478978	1.000000	0.71417	0.996000	0.52242	0.980000	0.70556	2.360000	0.44151	1.310000	0.45006	0.561000	0.74099	AGC	.	.		0.438	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		T	62125246	C	T	62125246	3	4	44	1	0	0	0	0	1	0	0	0	5239	797	28	3	448	3	ERN1	17	62125246	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	19164734	62125246	19069964	363	5823										
PITPNC1	26207	hgsc.bcm.edu	37	chr17	65665662	65665662	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcagagaagacaggacggggAcagttgagggaaggctggag	19	5	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:65665662A>G	ENST00000581322.1	+	7	501	c.501A>G	c.(499-501)ggA>ggG	p.G167G	PITPNC1_ENST00000299954.9_Silent_p.G167G|PITPNC1_ENST00000335257.6_Silent_p.G167G|PITPNC1_ENST00000580974.1_Silent_p.G167G			Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein, cytoplasmic 1	167					phospholipid transport (GO:0015914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)			breast(1)|kidney(2)|large_intestine(3)|liver(2)|lung(4)|prostate(2)|skin(3)	17	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			CAGGACGGGGACAGTTGAGGG	0.423																																					p.G167G		Atlas-SNP	.											.	PITPNC1	47	.	0			c.A501G						.						78	77	77					17																	65665662		1890	4123	6013	SO:0001819	synonymous_variant	26207	exon7			ACGGGGACAGTTG	AF171102	CCDS58587.1, CCDS58588.1	17q24.3	2008-02-05							21045	protein-coding gene	gene with protein product		605134				10531358	Standard	NM_012417		Approved	RDGBB1, RDGBB, RDGB-BETA	uc002jgc.4	Q9UKF7		ENST00000581322.1:c.501A>G	chr17.hg19:g.65665662A>G		111.0	0.0		98.0	4.0	NM_012417	A8K473|J3QR20|Q96I07	Silent	SNP	ENST00000581322.1	hg19	CCDS58588.1																																																																																			.	.		0.423	PITPNC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447194.1	NM_012417		G	65665662	A	G	65665662	2	3	44	1	0	0	0	0	0	0	0	1	11958	262	10	2		2	PITPNC1	17	65665662	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	3540416	65665662	15529548	364	5824										
NUP85	79902	hgsc.bcm.edu	37	chr17	73205985	73205985	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaggatgtagatgtttactcTcaaatcttgagaaaactctt	7	6	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:73205985T>C	ENST00000245544.4	+	3	266	c.195T>C	c.(193-195)tcT>tcC	p.S65S	NUP85_ENST00000541827.1_Silent_p.S19S|NUP85_ENST00000579324.1_5'UTR|NUP85_ENST00000579298.1_Silent_p.S65S|NUP85_ENST00000447371.2_5'UTR|NUP85_ENST00000449421.2_3'UTR	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	65					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			ATGTTTACTCTCAAATCTTGA	0.368																																					p.S65S		Atlas-SNP	.											.	NUP85	44	.	0			c.T195C						.						72	76	75					17																	73205985		2203	4300	6503	SO:0001819	synonymous_variant	79902	exon3			TTACTCTCAAATC	AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450			8734	protein-coding gene	gene with protein product		170285				8124707	Standard	XM_005257690		Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000245544.4:c.195T>C	chr17.hg19:g.73205985T>C		79.0	0.0		99.0	4.0	NM_024844	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Silent	SNP	ENST00000245544.4	hg19	CCDS32730.1																																																																																			.	.		0.368	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844		C	73205985	T	C	73205985	2	2	44	1	0	0	0	0	0	0	0	1	10779	1538	54	2		2	NUP85	17	73205985	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	7540323	73205985	7989225	365	5825										
RHBDF2	79651	hgsc.bcm.edu	37	chr17	74473785	74473787	+	In_Frame_Del	DEL	TCC	TCC	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgtctgccccatcgaccacaTcctcctccaggaagctcggg							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:74473785_74473787delTCC	ENST00000313080.4	-	7	1113_1115	c.840_842delGGA	c.(838-843)gaggat>gat	p.E280del	RHBDF2_ENST00000592378.1_5'Flank|RHBDF2_ENST00000389760.4_In_Frame_Del_p.E251del|RHBDF2_ENST00000591885.1_In_Frame_Del_p.E251del	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	280					negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(4)|skin(1)	27						ATCGACCACATCCTCCTCCAGGA	0.64																																					p.281_281del		Atlas-Indel,Pindel	.											.	RHBDF2	57	.	0			c.841_843del						.																																			SO:0001651	inframe_deletion	79651	exon7			.	BC016034	CCDS32743.1, CCDS32744.1	17q25.3	2014-09-17	2006-02-22	2006-02-22		ENSG00000129667			20788	protein-coding gene	gene with protein product		614404	"rhomboid, veinlet-like 6 (Drosophila)", "tylosis with oesophageal cancer"	RHBDL6, TOC		12838346, 22265016	Standard	NM_024599		Approved	FLJ22341, RHBDL5, TOCG	uc002jrq.2	Q6PJF5		ENST00000313080.4:c.840_842delGGA	chr17.hg19:g.74473791_74473793delTCC	ENSP00000322775:p.Glu280del	88.0	0.0		38.0	28.0	NM_024599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	In_Frame_Del	DEL	ENST00000313080.4	hg19	CCDS32743.1																																																																																			.	.		0.64	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599		-	74473787	TCC	-	74473785	7	5	44	1	0	1	0	1	0	0	0	0	13335	1435	50	0	1780	0	RHBDF2	17	74473785	In_Frame_Del	DEL	TCC	TCGA-BC-A3KG-01A-11D-A20W-10	1267800	74473785	6721425	366	5826										
MXRA7	439921	hgsc.bcm.edu	37	chr17	74681182	74681182	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctcctccagctcctctttggTcatcatcttcttgtactggt	6	14	5	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:74681182T>C	ENST00000355797.3	-	3	480	c.472A>G	c.(472-474)Acc>Gcc	p.T158A	MXRA7_ENST00000592148.1_Missense_Mutation_p.T201A|MXRA7_ENST00000589082.1_Missense_Mutation_p.T3A|MXRA7_ENST00000585519.1_Missense_Mutation_p.T3A|MXRA7_ENST00000588114.1_Missense_Mutation_p.T3A|MXRA7_ENST00000375036.2_Missense_Mutation_p.T158A|MXRA7_ENST00000449428.2_Missense_Mutation_p.T158A	NM_001008528.1	NP_001008528.1	P84157	MXRA7_HUMAN	matrix-remodelling associated 7	158						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						TCCTCTTTGGTCATCATCTTC	0.622																																					p.T158A		Atlas-SNP	.											.	MXRA7	11	.	0			c.A472G						.						168	156	160					17																	74681182		2203	4300	6503	SO:0001583	missense	439921	exon3			CTTTGGTCATCAT	BC053983	CCDS32745.1, CCDS32746.1, CCDS45786.1	17q25.1	2007-08-01				ENSG00000182534			7541	protein-coding gene	gene with protein product							Standard	XM_005257382		Approved	FLJ46603, TMAP1, PS1TP1	uc002jsk.1	P84157		ENST00000355797.3:c.472A>G	chr17.hg19:g.74681182T>C	ENSP00000348050:p.Thr158Ala	194.0	0.0		127.0	6.0	NM_001008529	Q0P5W3	Missense_Mutation	SNP	ENST00000355797.3	hg19	CCDS32745.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.114136	0.37339	.	.	ENSG00000182534	ENST00000355797;ENST00000449428;ENST00000375036;ENST00000392488	T;T;T	0.38887	1.11;1.11;1.11	5.27	5.27	0.74061	.	0.065190	0.64402	D	0.000014	T	0.63674	0.2531	M	0.70595	2.14	0.22819	N	0.998693	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.83275	0.996;0.996;0.96	T	0.59537	-0.7436	10	0.59425	D	0.04	-34.9645	14.8581	0.70355	0.0:0.0:0.0:1.0	.	158;158;158	P84157-2;P84157-3;P84157	.;.;MXRA7_HUMAN	A	158	ENSP00000348050:T158A;ENSP00000391466:T158A;ENSP00000364176:T158A	ENSP00000348050:T158A	T	-	1	0	MXRA7	72192777	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.144000	0.42197	1.997000	0.58415	0.379000	0.24179	ACC	.	.		0.622	MXRA7-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450983.1	NM_001008529		C	74681182	T	C	74681182	3	2	44	1	0	0	0	0	1	0	0	0	10013	1667	58	2	205	2	MXRA7	17	74681182	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	207397	74681182	6514028	367	5827										
DNAH17	9489	hgsc.bcm.edu	37	chr17	76421461	76421461	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccgtacacgtaggagccctcTcgcggaggagcggtcatgtc	14	13	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:76421461T>C	ENST00000262764.6	+	0	2201				DNAH17_ENST00000389840.5_Silent_p.R4392R|AC061992.1_ENST00000600087.1_5'Flank|DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000585328.1_Silent_p.R4364R	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			AGGAGCCCTCTCGCGGAGGAG	0.547																																					p.R4369R	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	DNAH17	347	.	0			c.A13107G						.						114	113	113					17																	76421461		2203	4300	6503	SO:0001628	intergenic_variant	8632	exon80			GCCCTCTCGCGGA		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			chr17.hg19:g.76421461T>C		148.0	0.0		63.0	5.0	NM_173628	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Silent	SNP	ENST00000262764.6	hg19	CCDS42391.1																																																																																			.	.		0.547	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419		C	76421461	T	C	76421461	1	2	44	0	1	0	0	0	0	0	0	0	4603	1538	54	2		2	DNAH17	17	76421461	IGR	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1740279	76421461	4773749	368	5828										
CARD14	79092	hgsc.bcm.edu	37	chr17	78163550	78163550	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggctgacctctctctgccccAggcggagaaggacattctgg	13	13	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:78163550A>G	ENST00000573882.1	+	8	1379		c.e8-1		CARD14_ENST00000344227.2_Splice_Site|CARD14_ENST00000573754.1_Splice_Site|CARD14_ENST00000392434.2_Splice_Site|CARD14_ENST00000570421.1_Splice_Site			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14						activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TCTCTGCCCCAGGCGGAGAAG	0.677																																					.		Atlas-SNP	.											CARD14_ENST00000309710,right_upper_lobe,carcinoma,0,2	CARD14	98	.	0			c.844-2A>G						.						10	13	12					17																	78163550		2180	4246	6426	SO:0001630	splice_region_variant	79092	exon6			TGCCCCAGGCGGA	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"psoriasis susceptibility 2"	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.844-1A>G	chr17.hg19:g.78163550A>G		125.0	0.0		92.0	5.0	NM_001257970	B8QQJ3|Q9BVB5	Splice_Site	SNP	ENST00000573882.1	hg19	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	A	11.94	1.789921	0.31685	.	.	ENSG00000141527	ENST00000344227;ENST00000392434;ENST00000309710	.	.	.	3.9	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.359	0.43982	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CARD14	75778145	1.000000	0.71417	0.777000	0.31699	0.384000	0.30261	4.838000	0.62803	1.640000	0.50565	0.383000	0.25322	.	.	.		0.677	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		Intron	G	78163550	A	G	78163550	5	3	44	1	0	0	0	0	0	0	1	0	2648	202	7	2	860	2	CARD14	17	78163550	Splice_Site	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1742089	78163550	3031660	369	5829										
C17orf101	79701	hgsc.bcm.edu	37	chr17	80373502	80373502	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cggggctcggtccttcttggTgctgagaacagaaaacaggc	14	10	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr17:80373502T>C	ENST00000313056.5	-	2	227	c.76A>G	c.(76-78)Acc>Gcc	p.T26A	Y_RNA_ENST00000364369.1_RNA|OGFOD3_ENST00000329197.5_Splice_Site_p.T26A|HEXDC_ENST00000337014.6_5'Flank	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	26						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)										TCCTTCTTGGTGCTGAGAACA	0.627																																					p.T26A		Atlas-SNP	.											.	.	.	.	0			c.A76G						.						22	22	22					17																	80373502		2202	4300	6502	SO:0001630	splice_region_variant	79701	exon2			TCTTGGTGCTGAG	BC023602	CCDS11811.1, CCDS11812.1	17q25.3	2012-10-23	2012-10-23	2012-10-23	ENSG00000181396	ENSG00000181396			26174	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 101"	C17orf101		12477932	Standard	NM_175902		Approved	FLJ22222	uc002keu.2	Q6PK18		ENST00000313056.5:c.75-1A>G	chr17.hg19:g.80373502T>C		40.0	0.0		39.0	4.0	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Missense_Mutation	SNP	ENST00000313056.5	hg19	CCDS11811.1	.	.	.	.	.	.	.	.	.	.	T	5.200	0.222353	0.09863	.	.	ENSG00000181396	ENST00000313056;ENST00000329197	T;T	0.30981	1.97;1.51	4.8	1.3	0.21679	.	1.190410	0.06440	N	0.725797	T	0.14141	0.0342	N	0.19112	0.55	0.09310	N	1	B;B	0.18013	0.002;0.025	B;B	0.13407	0.001;0.009	T	0.25813	-1.0121	10	0.05721	T	0.95	-19.1623	0.563	0.00682	0.1721:0.1931:0.1785:0.4563	.	26;26	Q6PK18;Q6PK18-2	CQ101_HUMAN;.	A	26	ENSP00000320116:T26A;ENSP00000330075:T26A	ENSP00000320116:T26A	T	-	1	0	C17orf101	77966791	0.311000	0.24536	0.019000	0.16419	0.197000	0.23852	0.497000	0.22514	0.179000	0.19938	0.533000	0.62120	ACC	.	.		0.627	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	Missense_Mutation	C	80373502	T	C	80373502	5	2	44	1	0	0	0	0	0	0	1	0	1850	1710	59	2	1092	2	C17orf101	17	80373502	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2209952	80373502	821708	370	5830										
NDC80	10403	hgsc.bcm.edu	37	chr18	2578924	2578924	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atgtttttctgatttctcatAggtatccttttgcactatcc	5	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr18:2578924A>G	ENST00000261597.4	+	6	658		c.e6-1			NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component						attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GATTTCTCATAGGTATCCTTT	0.348																																					.		Atlas-SNP	.											.	NDC80	62	.	0			c.477-2A>G						.						79	75	76					18																	2578924		2203	4300	6503	SO:0001630	splice_region_variant	10403	exon6			TCTCATAGGTATC	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.477-1A>G	chr18.hg19:g.2578924A>G		90.0	0.0		79.0	4.0	NM_006101	Q6PJX2	Splice_Site	SNP	ENST00000261597.4	hg19	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	A	6.054	0.378338	0.11466	.	.	ENSG00000080986	ENST00000261597;ENST00000543946	.	.	.	4.65	4.65	0.58169	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.884	0.46955	0.8424:0.1576:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NDC80	2568924	1.000000	0.71417	0.638000	0.29380	0.981000	0.71138	7.783000	0.85696	2.048000	0.60808	0.454000	0.30748	.	.	.		0.348	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	Intron	G	2578924	A	G	2578924	5	3	44	1	0	0	0	0	0	0	1	0	10251	434	15	2	493	2	NDC80	18	2578924	Splice_Site	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10		2578924	75498324	371	5831										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3086103	3086103	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	catccactgatatctccctcTcatctttgtaccacacaata	2	15	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr18:3086103T>C	ENST00000356443.4	-	30	4517	c.4184A>G	c.(4183-4185)gAg>gGg	p.E1395G	MYOM1_ENST00000400569.3_Missense_Mutation_p.E1395G|MYOM1_ENST00000261606.7_Missense_Mutation_p.E1299G	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1395	Ig-like C2-type 4.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TATCTCCCTCTCATCTTTGTA	0.328																																					p.E1395G		Atlas-SNP	.											.	MYOM1	192	.	0			c.A4184G						.						157	142	146					18																	3086103		1869	4096	5965	SO:0001583	missense	8736	exon30			TCCCTCTCATCTT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4184A>G	chr18.hg19:g.3086103T>C	ENSP00000348821:p.Glu1395Gly	74.0	0.0		74.0	5.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	4.856	0.159101	0.09236	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.63255	-0.03;-0.03;-0.03	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.270699	0.42172	D	0.000741	T	0.36771	0.0979	N	0.01705	-0.755	0.41370	D	0.987482	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30031	-0.9992	10	0.21540	T	0.41	.	16.0953	0.81117	0.0:0.0:0.0:1.0	.	1299;1395	P52179-2;P52179	.;MYOM1_HUMAN	G	1395;1395;1299	ENSP00000348821:E1395G;ENSP00000383413:E1395G;ENSP00000261606:E1299G	ENSP00000261606:E1299G	E	-	2	0	MYOM1	3076103	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	3.997000	0.57016	2.204000	0.70986	0.383000	0.25322	GAG	.	.		0.328	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		C	3086103	T	C	3086103	3	2	44	1	0	0	0	0	1	0	0	0	10100	1551	54	2	909	2	MYOM1	18	3086103	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	507179	3086103	74991145	372	5832										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9256481	9256481	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aaagaaaagaggttagtgaaTgatgatttaatgcagacaag	11	2	0	6			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr18:9256481T>C	ENST00000262126.4	+	9	3456	c.3216T>C	c.(3214-3216)aaT>aaC	p.N1072N	ANKRD12_ENST00000383440.2_Silent_p.N1049N|RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Silent_p.N1049N	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1072						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						GGTTAGTGAATGATGATTTAA	0.338																																					p.N1072N		Atlas-SNP	.											.	ANKRD12	167	.	0			c.T3216C						.						106	113	111					18																	9256481		2200	4294	6494	SO:0001819	synonymous_variant	23253	exon9			AGTGAATGATGAT	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.3216T>C	chr18.hg19:g.9256481T>C		86.0	0.0		83.0	4.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Silent	SNP	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.338	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		C	9256481	T	C	9256481	2	2	44	1	0	0	0	0	0	0	0	1	640	1461	51	2		2	ANKRD12	18	9256481	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	6170378	9256481	68820767	373	5833										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9258341	9258341	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaatctcaacaaagcattttAtcaagtctggaaaaccattc	5	9	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr18:9258341A>T	ENST00000262126.4	+	9	5316	c.5076A>T	c.(5074-5076)ttA>ttT	p.L1692F	ANKRD12_ENST00000383440.2_Missense_Mutation_p.L1669F|RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Missense_Mutation_p.L1669F	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1692						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						AAAGCATTTTATCAAGTCTGG	0.348																																					p.L1692F		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A5076T						.						43	39	40					18																	9258341		2203	4300	6503	SO:0001583	missense	23253	exon9			CATTTTATCAAGT	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5076A>T	chr18.hg19:g.9258341A>T	ENSP00000262126:p.Leu1692Phe	59.0	0.0		65.0	4.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	17.08	3.296553	0.60086	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.61040	0.14;0.14	5.33	2.94	0.34122	.	0.505173	0.19543	N	0.111741	T	0.57888	0.2084	L	0.32530	0.975	0.40439	D	0.980025	D;P	0.56746	0.977;0.933	P;P	0.58873	0.847;0.518	T	0.55218	-0.8175	10	0.38643	T	0.18	-4.8767	9.4447	0.38690	0.8548:0.0:0.1452:0.0	.	1669;1692	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	F	1669;1692	ENSP00000372932:L1669F;ENSP00000262126:L1692F	ENSP00000262126:L1692F	L	+	3	2	ANKRD12	9248341	1.000000	0.71417	0.999000	0.59377	0.711000	0.40976	1.963000	0.40452	0.962000	0.38057	0.533000	0.62120	TTA	.	.		0.348	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		T	9258341	A	T	9258341	3	4	44	1	0	0	0	0	1	0	0	0	640	446	16	4	5106	4	ANKRD12	18	9258341	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1860	9258341	68818907	374	5834										
CEP192	55125	hgsc.bcm.edu	37	chr18	13071058	13071058	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gatcttgaaaatatttgtgcAgccatttggacctcagtatg	9	7	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr18:13071058A>G	ENST00000325971.8	+	26	5000	c.3407A>G	c.(3406-3408)cAg>cGg	p.Q1136R	CEP192_ENST00000430049.2_Missense_Mutation_p.Q1257R|CEP192_ENST00000506447.1_Missense_Mutation_p.Q1732R			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1136					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ATATTTGTGCAGCCATTTGGA	0.373																																					p.Q1732R		Atlas-SNP	.											.	CEP192	340	.	0			c.A5195G						.						88	86	87					18																	13071058		2203	4300	6503	SO:0001583	missense	55125	exon28			TTGTGCAGCCATT	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.3407A>G	chr18.hg19:g.13071058A>G	ENSP00000317156:p.Gln1136Arg	118.0	0.0		112.0	5.0	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	A	6.117	0.389777	0.11581	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.41400	1.0;1.0;1.0	5.35	4.18	0.49190	.	0.279464	0.29293	N	0.012580	T	0.47395	0.1443	L	0.54323	1.7	0.26227	N	0.979068	P;P;P	0.47910	0.902;0.681;0.634	P;B;B	0.51701	0.677;0.204;0.167	T	0.35226	-0.9797	10	0.42905	T	0.14	-1.8017	9.8998	0.41340	0.647:0.0:0.0:0.353	.	1257;1732;334	C9JT09;E9PF99;Q9HCK3	.;.;.	R	1732;1136;1136;1257	ENSP00000427550:Q1732R;ENSP00000317156:Q1136R;ENSP00000389190:Q1257R	ENSP00000317156:Q1136R	Q	+	2	0	CEP192	13061058	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	3.824000	0.55723	0.841000	0.35020	0.528000	0.53228	CAG	.	.		0.373	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		G	13071058	A	G	13071058	3	3	44	1	0	0	0	0	1	0	0	0	3253	188	7	2	5301	2	CEP192	18	13071058	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	3812717	13071058	65006190	375	5835										
C18orf1	753	hgsc.bcm.edu	37	chr18	13643356	13643356	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcctccccttcccctccgccAggaagggtgcctgtggcctt	10	18	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr18:13643356A>G	ENST00000359446.5	+	5	804		c.e5-1		LDLRAD4_ENST00000586765.1_Intron|LDLRAD4_ENST00000361205.4_Splice_Site|LDLRAD4_ENST00000585931.1_Splice_Site|RP11-701H16.4_ENST00000588397.1_RNA|LDLRAD4_ENST00000399848.3_Intron|LDLRAD4_ENST00000587757.1_Splice_Site|LDLRAD4_ENST00000592991.1_Splice_Site	NM_001276251.1	NP_001263180.1	O15165	LRAD4_HUMAN	low density lipoprotein receptor class A domain containing 4						negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	early endosome membrane (GO:0031901)|endosome (GO:0005768)|integral component of membrane (GO:0016021)	R-SMAD binding (GO:0070412)										CCCCTCCGCCAGGAAGGGTGC	0.652																																					.		Atlas-SNP	.											.	.	.	.	0			c.226-2A>G						.						10	8	9					18																	13643356		2197	4281	6478	SO:0001630	splice_region_variant	753	exon3			TCCGCCAGGAAGG	AF009424, AF009428	CCDS32793.1, CCDS32794.1, CCDS32795.1, CCDS42415.1, CCDS62392.1, CCDS62393.1	18p11.21	2014-04-29	2012-10-24	2012-10-24	ENSG00000168675	ENSG00000168675			1224	protein-coding gene	gene with protein product	"clone 22"	606571	"chromosome 18 open reading frame 1"	C18orf1		9479497, 9129712, 24627487	Standard	NM_181482		Approved		uc002ksb.3	O15165	OTTHUMG00000181925	ENST00000359446.5:c.337-1A>G	chr18.hg19:g.13643356A>G		251.0	0.0		199.0	8.0	NM_001003674	B3KNT9|E9PAY9|K7EN38|O15166|O15167|O15168|Q5U646|Q6NXP3	Splice_Site	SNP	ENST00000359446.5	hg19	CCDS32793.1	.	.	.	.	.	.	.	.	.	.	A	18.06	3.540032	0.65085	.	.	ENSG00000168675	ENST00000361205;ENST00000359446;ENST00000361303	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9913	0.71390	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C18orf1	13633356	1.000000	0.71417	0.993000	0.49108	0.660000	0.38997	7.988000	0.88194	2.013000	0.59113	0.528000	0.53228	.	.	.		0.652	LDLRAD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458326.1	NM_181481	Intron	G	13643356	A	G	13643356	5	3	44	1	0	0	0	0	0	0	1	0	1896	202	7	2	430	2	C18orf1	18	13643356	Splice_Site	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	572298	13643356	64433892	376	5836										
DSG3	1830	hgsc.bcm.edu	37	chr18	29056124	29056124	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtgacagaaagggtgatctgTcccatttccagtgttcctgg	12	9	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr18:29056124T>C	ENST00000257189.4	+	16	2984	c.2901T>C	c.(2899-2901)tgT>tgC	p.C967C		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	967					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GGGTGATCTGTCCCATTTCCA	0.512																																					p.C967C		Atlas-SNP	.											.	DSG3	172	.	0			c.T2901C						.						140	127	131					18																	29056124		2203	4300	6503	SO:0001819	synonymous_variant	1830	exon16			GATCTGTCCCATT	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2901T>C	chr18.hg19:g.29056124T>C		109.0	0.0		111.0	5.0	NM_001944	A8K2V2	Silent	SNP	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.512	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		C	29056124	T	C	29056124	2	2	44	1	0	0	0	0	0	0	0	1	4780	1673	58	2		2	DSG3	18	29056124	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	15412768	29056124	49021124	377	5837										
TTR	7276	hgsc.bcm.edu	37	chr18	29172906	29172906	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atggtcaaagttctagatgcTgtccgaggcagtcctgccat	11	10	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr18:29172906T>A	ENST00000237014.3	+	2	294	c.117T>A	c.(115-117)gcT>gcA	p.A39A		NM_000371.3	NP_000362.1	P02766	TTHY_HUMAN	transthyretin	39					extracellular matrix organization (GO:0030198)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	hormone binding (GO:0042562)|identical protein binding (GO:0042802)			cervix(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	13			OV - Ovarian serous cystadenocarcinoma(10;0.00523)		Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diflunisal(DB00861)|Dimethyl sulfoxide(DB01093)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TTCTAGATGCTGTCCGAGGCA	0.502																																					p.A39A		Atlas-SNP	.											.	TTR	21	.	0			c.T117A						.						140	115	123					18																	29172906		2203	4300	6503	SO:0001819	synonymous_variant	7276	exon2			AGATGCTGTCCGA	M10605	CCDS11899.1	18q12.1	2014-09-17	2008-07-31		ENSG00000118271	ENSG00000118271			12405	protein-coding gene	gene with protein product		176300	"prealbumin, amyloidosis type I", "carpal tunnel syndrome 1"	PALB, CTS1		8309582	Standard	NM_000371		Approved	HsT2651, CTS	uc002kwx.4	P02766	OTTHUMG00000131984	ENST00000237014.3:c.117T>A	chr18.hg19:g.29172906T>A		145.0	0.0		144.0	64.0	NM_000371	Q549C7|Q6IB96|Q9UBZ6|Q9UCM9	Silent	SNP	ENST00000237014.3	hg19	CCDS11899.1																																																																																			.	.		0.502	TTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254948.1	NM_000371		A	29172906	T	A	29172906	2	1	44	1	0	0	0	0	0	0	0	1	16753	1567	55	4		4	TTR	18	29172906	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	116782	29172906	48904342	378	5838										
PIGN	23556	hgsc.bcm.edu	37	chr18	59806257	59806257	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tactgcatttgtaaacatgcTctctgctttgaagagatcag	8	8	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr18:59806257T>C	ENST00000357637.5	-	13	1490	c.1075A>G	c.(1075-1077)Agc>Ggc	p.S359G	PIGN_ENST00000400334.3_Missense_Mutation_p.S359G	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	359					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				GTAAACATGCTCTCTGCTTTG	0.343																																					p.S359G		Atlas-SNP	.											.	PIGN	62	.	0			c.A1075G						.						62	57	58					18																	59806257		1830	4089	5919	SO:0001583	missense	23556	exon13			ACATGCTCTCTGC	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.1075A>G	chr18.hg19:g.59806257T>C	ENSP00000350263:p.Ser359Gly	154.0	0.0		174.0	8.0	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Missense_Mutation	SNP	ENST00000357637.5	hg19	CCDS45879.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.504461	0.85176	.	.	ENSG00000197563	ENST00000357637;ENST00000400334	T;T	0.26660	1.72;1.72	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.37156	0.0993	M	0.80028	2.48	0.58432	D	0.999996	P;P	0.43885	0.82;0.82	B;B	0.42593	0.392;0.392	T	0.28839	-1.0031	9	.	.	.	-10.5543	15.3535	0.74409	0.0:0.0:0.0:1.0	.	359;359	B2RCI8;O95427	.;PIGN_HUMAN	G	359	ENSP00000350263:S359G;ENSP00000383188:S359G	.	S	-	1	0	PIGN	57957237	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.945000	0.63568	2.267000	0.75376	0.477000	0.44152	AGC	.	.		0.343	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		C	59806257	T	C	59806257	3	2	44	1	0	0	0	0	1	0	0	0	11902	1551	54	2	1796	2	PIGN	18	59806257	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	30633351	59806257	18270991	379	5839										
MIER2	54531	hgsc.bcm.edu	37	chr19	327183	327183	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctcgtgggaggtcacggacGgggtgaggtcgtcagcagat	18	9	2	2	rs201881025	byFrequency	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:327183G>T	ENST00000264819.4	-	5	453	c.443C>A	c.(442-444)cCg>cAg	p.P148Q	MIER2_ENST00000592722.1_5'Flank	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	148					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(4)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTCACGGACGGGGTGAGGTC	0.527																																					p.P148Q		Atlas-SNP	.											MIER2,lower_third,carcinoma,0,1	MIER2	51	.	0			c.C443A						.						230	206	214					19																	327183		2203	4300	6503	SO:0001583	missense	54531	exon5			ACGGACGGGGTGA	AB033019	CCDS32855.1	19p13.3	2008-02-05	2006-04-20	2006-04-20		ENSG00000105556			29210	protein-coding gene	gene with protein product			"KIAA1193"	KIAA1193		10574462	Standard	NM_017550		Approved		uc002lok.1	Q8N344		ENST00000264819.4:c.443C>A	chr19.hg19:g.327183G>T	ENSP00000264819:p.Pro148Gln	139.0	0.0		101.0	0.0	NM_017550	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	hg19	CCDS32855.1	.	.	.	.	.	.	.	.	.	.	.	19.76	3.888213	0.72524	.	.	ENSG00000105556	ENST00000264819	T	0.35236	1.32	5.27	5.27	0.74061	.	0.000000	0.47852	D	0.000209	T	0.56396	0.1982	M	0.64567	1.98	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.50866	-0.8777	10	0.30854	T	0.27	-18.6425	16.085	0.81038	0.0:0.0:1.0:0.0	.	148	Q8N344	MIER2_HUMAN	Q	148	ENSP00000264819:P148Q	ENSP00000264819:P148Q	P	-	2	0	MIER2	278183	1.000000	0.71417	0.819000	0.32651	0.736000	0.42039	8.384000	0.90160	2.474000	0.83562	0.650000	0.86243	CCG	.	G|0.998;A|0.002		0.527	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843		T	327183	G	T	327183	3	4	44	1	0	0	0	0	1	0	0	0	9590	1116	39	1	1234	1	MIER2	19	327183	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10		327183	58801800	380	5840										
REXO1	57455	hgsc.bcm.edu	37	chr19	1828117	1828117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgtgggtggcctggagttgTccaccacgtacttgccactg	13	12	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:1828117T>C	ENST00000170168.4	-	2	765	c.671A>G	c.(670-672)gAc>gGc	p.D224G	REXO1_ENST00000587524.1_5'UTR	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	224						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGGAGTTGTCCACCACGTA	0.682																																					p.D224G		Atlas-SNP	.											.	REXO1	55	.	0			c.A671G						.						40	45	44					19																	1828117		2196	4281	6477	SO:0001583	missense	57455	exon2			GAGTTGTCCACCA	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"elongin A binding protein 1"	609614	"transcription elongation factor B polypeptide 3 binding protein 1"	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.671A>G	chr19.hg19:g.1828117T>C	ENSP00000170168:p.Asp224Gly	50.0	0.0		72.0	4.0	NM_020695	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	hg19	CCDS32866.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.968891	0.53614	.	.	ENSG00000079313	ENST00000170168;ENST00000413153	T	0.53640	0.61	4.13	4.13	0.48395	.	0.000000	0.85682	D	0.000000	T	0.66674	0.2813	M	0.75264	2.295	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.70824	-0.4767	10	0.66056	D	0.02	-27.6895	12.4807	0.55839	0.0:0.0:0.0:1.0	.	178;224	F5H016;Q8N1G1	.;REXO1_HUMAN	G	224;178	ENSP00000170168:D224G	ENSP00000170168:D224G	D	-	2	0	REXO1	1779117	1.000000	0.71417	0.924000	0.36721	0.064000	0.16182	7.113000	0.77095	1.734000	0.51633	0.459000	0.35465	GAC	.	.		0.682	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		C	1828117	T	C	1828117	3	2	44	1	0	0	0	0	1	0	0	0	13256	1667	58	2	3054	2	REXO1	19	1828117	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1500934	1828117	57300866	381	5841										
C19orf36	113177	hgsc.bcm.edu	37	chr19	2098975	2098975	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgtggtggtttcatgaacagAccacgctcctctgccttctc	9	13	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:2098975A>G	ENST00000395301.3	+	9	619	c.555A>G	c.(553-555)agA>agG	p.R185R	MOB3A_ENST00000357066.3_5'Flank|IZUMO4_ENST00000588003.1_3'UTR|IZUMO4_ENST00000395307.2_Intron	NM_001039846.1	NP_001034935.1	Q1ZYL8	IZUM4_HUMAN	IZUMO family member 4	185						extracellular region (GO:0005576)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	6						TCATGAACAGACCACGCTCCT	0.607																																					p.R185R		Atlas-SNP	.											.	IZUMO4	25	.	0			c.A555G						.						93	103	100					19																	2098975		2143	4232	6375	SO:0001630	splice_region_variant	113177	exon9			GAACAGACCACGC	BC014609	CCDS35499.1, CCDS42458.1	19p13.3	2014-02-17	2010-07-29	2010-07-29	ENSG00000099840	ENSG00000099840		"-"	26950	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 36"	C19orf36		12975309, 19658160, 22957301	Standard	XM_005259480		Approved		uc002luw.1	Q1ZYL8	OTTHUMG00000141290	ENST00000395301.3:c.555-1A>G	chr19.hg19:g.2098975A>G		107.0	0.0		98.0	4.0	NM_001039846	A7RA93|A7RA94|Q6UXA2|Q96FT6|Q96L02	Silent	SNP	ENST00000395301.3	hg19	CCDS42458.1																																																																																			.	.		0.607	IZUMO4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280536.3	NM_052878	Silent	G	2098975	A	G	2098975	5	3	44	1	0	0	0	0	0	0	1	0	1923	289	10	2	589	2	C19orf36	19	2098975	Splice_Site	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	270858	2098975	57030008	382	5842										
ACSBG2	81616	hgsc.bcm.edu	37	chr19	6161259	6161259	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcctagagcccctaaaagcgAtcatccagtacagactgcca	8	14	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:6161259A>G	ENST00000586696.1	+	6	817	c.541A>G	c.(541-543)Atc>Gtc	p.I181V	ACSBG2_ENST00000588304.1_Missense_Mutation_p.I131V|ACSBG2_ENST00000252669.5_Missense_Mutation_p.I181V|ACSBG2_ENST00000591403.1_Missense_Mutation_p.I181V|ACSBG2_ENST00000588485.1_5'UTR			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	181					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCTAAAAGCGATCATCCAGTA	0.522																																					p.I181V		Atlas-SNP	.											.	ACSBG2	83	.	0			c.A541G						.						97	88	91					19																	6161259		2203	4300	6503	SO:0001583	missense	81616	exon6			AAAGCGATCATCC		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.541A>G	chr19.hg19:g.6161259A>G	ENSP00000465589:p.Ile181Val	93.0	0.0		88.0	4.0	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	hg19	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	A	8.218	0.801916	0.16397	.	.	ENSG00000130377	ENST00000252669	T	0.09163	3.01	4.65	4.65	0.58169	AMP-dependent synthetase/ligase (1);	0.000000	0.37348	N	0.002122	T	0.15435	0.0372	L	0.33710	1.025	0.48236	D	0.999612	B;D	0.53885	0.276;0.963	P;P	0.57720	0.557;0.826	T	0.09292	-1.0681	10	0.17369	T	0.5	-45.9474	11.0323	0.47781	1.0:0.0:0.0:0.0	.	181;181	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	V	181	ENSP00000252669:I181V	ENSP00000252669:I181V	I	+	1	0	ACSBG2	6112259	0.926000	0.31397	0.068000	0.19968	0.033000	0.12548	3.388000	0.52509	2.026000	0.59711	0.467000	0.42956	ATC	.	.		0.522	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		G	6161259	A	G	6161259	3	3	44	1	0	0	0	0	1	0	0	0	174	333	12	2	559	2	ACSBG2	19	6161259	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	4062284	6161259	52967724	383	5843										
EPOR	2057	hgsc.bcm.edu	37	chr19	11491862	11491862	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aggttgctcagcacacactcGgtgcggccctccaggatctc	11	15	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:11491862G>T	ENST00000222139.6	-	5	713	c.609C>A	c.(607-609)acC>acA	p.T203T	EPOR_ENST00000592375.2_Silent_p.T203T	NM_000121.3	NP_000112.1	P19235	EPOR_HUMAN	erythropoietin receptor	203	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brain development (GO:0007420)|decidualization (GO:0046697)|erythropoietin-mediated signaling pathway (GO:0038162)|heart development (GO:0007507)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	erythropoietin receptor activity (GO:0004900)|identical protein binding (GO:0042802)			endometrium(1)|lung(2)|ovary(1)|urinary_tract(1)	5					Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)|Epoetin Zeta(DB08923)|Peginesatide(DB08894)	GCACACACTCGGTGCGGCCCT	0.677											OREG0025255	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T203T		Atlas-SNP	.											.	EPOR	26	.	0			c.C609A						.						3	4	4					19																	11491862		1948	3854	5802	SO:0001819	synonymous_variant	2057	exon5			ACACTCGGTGCGG	M34986	CCDS12260.1	19p13.3-p13.2	2013-02-11				ENSG00000187266		"Fibronectin type III domain containing"	3416	protein-coding gene	gene with protein product		133171					Standard	NM_000121		Approved		uc002mrj.2	P19235		ENST00000222139.6:c.609C>A	chr19.hg19:g.11491862G>T		63.0	0.0	672	25.0	22.0	NM_000121	B2RCG4|Q15443|Q2M205	Silent	SNP	ENST00000222139.6	hg19	CCDS12260.1																																																																																			.	.		0.677	EPOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458791.1			T	11491862	G	T	11491862	2	4	44	1	0	0	0	0	0	0	0	1	5191	1103	39	1		1	EPOR	19	11491862	Silent	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	5330603	11491862	47637121	384	5844										
RGL3	57139	hgsc.bcm.edu	37	chr19	11527335	11527335	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgtaccgctgtcttcttgatCtctaccctgggaagaggccc	10	13	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:11527335C>T	ENST00000380456.3	-	4	441	c.378G>A	c.(376-378)gaG>gaA	p.E126E	RGL3_ENST00000393423.3_Silent_p.E126E	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	126	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						TCTTCTTGATCTCTACCCTGG	0.562																																					p.E126E	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.G378A						.						96	89	92					19																	11527335		2203	4300	6503	SO:0001819	synonymous_variant	57139	exon4			CTTGATCTCTACC	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.378G>A	chr19.hg19:g.11527335C>T		132.0	0.0		66.0	4.0	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Silent	SNP	ENST00000380456.3	hg19	CCDS32910.1																																																																																			.	.		0.562	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867		T	11527335	C	T	11527335	2	4	44	1	0	0	0	0	0	0	0	1	13293	912	32	3		3	RGL3	19	11527335	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	35473	11527335	47601648	385	5845										
ACP5	54	hgsc.bcm.edu	37	chr19	11687318	11687318	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atctgagttgccacatagtgTcactgtgtccagcataaaaa	8	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:11687318T>C	ENST00000592828.1	-	6	877	c.475A>G	c.(475-477)Aca>Gca	p.T159A	ACP5_ENST00000218758.5_Missense_Mutation_p.T159A|ACP5_ENST00000433365.2_Missense_Mutation_p.T159A|ACP5_ENST00000412435.2_Missense_Mutation_p.T159A|ACP5_ENST00000590420.1_Intron	NM_001111034.1	NP_001104504.1	P13686	PPA5_HUMAN	acid phosphatase 5, tartrate resistant	159					bone morphogenesis (GO:0060349)|bone resorption (GO:0045453)|defense response to Gram-positive bacterium (GO:0050830)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of superoxide anion generation (GO:0032929)|negative regulation of tumor necrosis factor production (GO:0032720)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	acid phosphatase activity (GO:0003993)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	9						CCACATAGTGTCACTGTGTCC	0.557																																					p.T159A		Atlas-SNP	.											.	ACP5	30	.	0			c.A475G						.						79	80	80					19																	11687318		2203	4300	6503	SO:0001583	missense	54	exon5			ATAGTGTCACTGT	X14618	CCDS12265.1	19p13.2	2012-10-02			ENSG00000102575	ENSG00000102575	3.1.3.2		124	protein-coding gene	gene with protein product	"tartrate-resistant acid phosphatase"	171640				8449511, 2338077	Standard	NM_001611		Approved	TRAP	uc002msj.4	P13686	OTTHUMG00000182036	ENST00000592828.1:c.475A>G	chr19.hg19:g.11687318T>C	ENSP00000468767:p.Thr159Ala	132.0	0.0		60.0	4.0	NM_001111034	A8K3V2|Q2TAB1|Q6IAS6|Q9UCJ5|Q9UCJ6|Q9UCJ7	Missense_Mutation	SNP	ENST00000592828.1	hg19	CCDS12265.1	.	.	.	.	.	.	.	.	.	.	t	1.834	-0.469146	0.04445	.	.	ENSG00000102575	ENST00000218758;ENST00000412435;ENST00000433365	D;D;D	0.84442	-1.85;-1.85;-1.85	5.32	4.3	0.51218	Metallophosphoesterase domain (1);	0.432598	0.27991	N	0.017034	T	0.70762	0.3261	N	0.17594	0.5	0.58432	D	0.999998	B	0.12013	0.005	B	0.20767	0.031	T	0.59193	-0.7500	10	0.15952	T	0.53	-14.1409	7.5348	0.27704	0.0:0.1705:0.0:0.8295	.	159	P13686	PPA5_HUMAN	A	159	ENSP00000218758:T159A;ENSP00000392374:T159A;ENSP00000413456:T159A	ENSP00000218758:T159A	T	-	1	0	ACP5	11548318	0.035000	0.19736	0.642000	0.29436	0.018000	0.09664	0.534000	0.23098	0.864000	0.35578	0.533000	0.62120	ACA	.	.		0.557	ACP5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458881.1			C	11687318	T	C	11687318	3	2	44	1	0	0	0	0	1	0	0	0	164	1667	58	2	510	2	ACP5	19	11687318	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	159983	11687318	47441665	386	5846										
ZNF564	163050	hgsc.bcm.edu	37	chr19	12638001	12638001	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	catactttacatttataaggTccatccccagtgtgcctaat	5	11	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:12638001T>C	ENST00000339282.7	-	4	1117	c.921A>G	c.(919-921)ggA>ggG	p.G307G	ZNF709_ENST00000428311.1_Intron|CTD-2192J16.21_ENST00000601420.1_RNA|CTD-2192J16.20_ENST00000593682.1_3'UTR	NM_144976.3	NP_659413.1	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						ATTTATAAGGTCCATCCCCAG	0.388																																					p.G307G		Atlas-SNP	.											.	ZNF564	55	.	0			c.A921G						.						51	57	55					19																	12638001		2117	4254	6371	SO:0001819	synonymous_variant	163050	exon4			ATAAGGTCCATCC	BC028367	CCDS42505.1	19p13.2	2013-09-19			ENSG00000249709	ENSG00000249709		"Zinc fingers, C2H2-type", "-"	31106	protein-coding gene	gene with protein product							Standard	NM_144976		Approved	MGC26914		Q8TBZ8	OTTHUMG00000156418	ENST00000339282.7:c.921A>G	chr19.hg19:g.12638001T>C		80.0	0.0		53.0	4.0	NM_144976	B9EGT4|Q6P1K6	Silent	SNP	ENST00000339282.7	hg19	CCDS42505.1																																																																																			.	.		0.388	ZNF564-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344120.2	NM_144976		C	12638001	T	C	12638001	2	2	44	1	0	0	0	0	0	0	0	1	18010	1654	58	2		2	ZNF564	19	12638001	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	950683	12638001	46490982	387	5847										
PRDX2	7001	hgsc.bcm.edu	37	chr19	12911584	12911584	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gctaattactgtcatcatccTtaaagacttgggcggcaatg	9	9	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:12911584T>C	ENST00000301522.2	-	3	386				PRDX2_ENST00000435703.1_Missense_Mutation_p.R135G|CTD-2659N19.10_ENST00000585496.1_RNA|PRDX2_ENST00000334482.5_Intron	NM_005809.4	NP_005800.3	P32119	PRDX2_HUMAN	peroxiredoxin 2						cellular response to oxidative stress (GO:0034599)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of apoptotic process (GO:0042981)|removal of superoxide radicals (GO:0019430)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)|thioredoxin peroxidase activity (GO:0008379)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4						gtcatcatccttaaagacttg	0.448																																					p.R135G		Atlas-SNP	.											.	PRDX2	20	.	0			c.A403G						.						93	95	94					19																	12911584		1271	2268	3539	SO:0001627	intron_variant	7001	exon3			TCATCCTTAAAGA		CCDS12281.1	19p13.2	2008-07-17			ENSG00000167815	ENSG00000167815			9353	protein-coding gene	gene with protein product	"thioredoxin-dependent peroxide reductase 1", "thiol-specific antioxidant 1", "natural killer-enhancing factor B", "thioredoxin peroxidase 1", "torin"	600538		TDPX1		7607688	Standard	NM_005809		Approved	PRP, NKEFB, TSA, PRXII, PRX2, MGC4104	uc002mvd.4	P32119	OTTHUMG00000134285	ENST00000301522.2:c.257+145A>G	chr19.hg19:g.12911584T>C		166.0	0.0		93.0	4.0	NM_181738	A8K0C0|P31945|P32118|P35701|Q6FHG4|Q92763|Q9UC23	Missense_Mutation	SNP	ENST00000301522.2	hg19	CCDS12281.1	.	.	.	.	.	.	.	.	.	.	T	11.00	1.510123	0.27036	.	.	ENSG00000167815	ENST00000435703	T	0.53206	0.63	3.75	-1.07	0.09968	.	.	.	.	.	T	0.35248	0.0925	.	.	.	0.09310	N	1	B	0.25105	0.118	B	0.16289	0.015	T	0.25676	-1.0125	8	0.87932	D	0	.	10.4652	0.44602	0.0:0.0:0.607:0.393	.	135	A8K0C0	.	G	135	ENSP00000408905:R135G	ENSP00000408905:R135G	R	-	1	2	PRDX2	12772584	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.055000	0.11807	-0.367000	0.08052	0.379000	0.24179	AGG	.	.		0.448	PRDX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258950.2	NM_005809		C	12911584	T	C	12911584	1	2	44	0	1	0	0	0	0	0	0	0	12477	1608	56	2		2	PRDX2	19	12911584	Intron	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	273583	12911584	46217399	388	5848										
DNASE2	1777	hgsc.bcm.edu	37	chr19	12987072	12987072	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tctggttcacattcagaaccTgccagatatccgagcagtta	8	11	3	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:12987072T>C	ENST00000222219.3	-	6	907	c.815A>G	c.(814-816)cAg>cGg	p.Q272R	DNASE2_ENST00000538460.1_Missense_Mutation_p.Q217R	NM_001375.2	NP_001366.1	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal	272					apoptotic DNA fragmentation (GO:0006309)|DNA metabolic process (GO:0006259)|erythrocyte differentiation (GO:0030218)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)|DNA binding (GO:0003677)			breast(1)|large_intestine(1)|lung(4)|ovary(1)	7						ATTCAGAACCTGCCAGATATC	0.567																																					p.Q272R		Atlas-SNP	.											.	DNASE2	23	.	0			c.A815G						.						73	66	68					19																	12987072		2203	4300	6503	SO:0001583	missense	1777	exon6			AGAACCTGCCAGA	AF045937	CCDS12284.1	19p13.2	2012-10-02			ENSG00000105612	ENSG00000105612	3.1.22.1		2960	protein-coding gene	gene with protein product		126350		DNL, DNL2		1586130	Standard	NM_001375		Approved		uc002mvn.1	O00115		ENST00000222219.3:c.815A>G	chr19.hg19:g.12987072T>C	ENSP00000222219:p.Gln272Arg	157.0	0.0		95.0	4.0	NM_001375	B2RD06|B7Z4K6|O43910	Missense_Mutation	SNP	ENST00000222219.3	hg19	CCDS12284.1	.	.	.	.	.	.	.	.	.	.	T	3.412	-0.119902	0.06838	.	.	ENSG00000105612	ENST00000222219;ENST00000538460	T;T	0.14144	2.53;2.53	4.75	2.64	0.31445	.	0.648987	0.16136	N	0.227968	T	0.09862	0.0242	L	0.43152	1.355	0.09310	N	1	B;B	0.12630	0.006;0.005	B;B	0.15052	0.004;0.012	T	0.33727	-0.9857	10	0.10111	T	0.7	.	7.5244	0.27647	0.0:0.1631:0.0:0.8369	.	217;272	B7Z4K6;O00115	.;DNS2A_HUMAN	R	272;217	ENSP00000222219:Q272R;ENSP00000445988:Q217R	ENSP00000222219:Q272R	Q	-	2	0	DNASE2	12848072	0.115000	0.22152	0.002000	0.10522	0.051000	0.14879	3.007000	0.49536	1.792000	0.52537	0.379000	0.24179	CAG	.	.		0.567	DNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451790.1			C	12987072	T	C	12987072	3	2	44	1	0	0	0	0	1	0	0	0	4666	1580	55	2	271	2	DNASE2	19	12987072	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	75488	12987072	46141911	389	5849										
SLC35E1	79939	hgsc.bcm.edu	37	chr19	16677349	16677349	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gctgtacaactcaccaagtcGctgctgaccaggaaagccga	10	13	1	1	rs371476983		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:16677349G>A	ENST00000595753.1	-	4	767	c.750C>T	c.(748-750)agC>agT	p.S250S	CTD-3222D19.10_ENST00000597851.1_RNA|CTD-3222D19.2_ENST00000409035.1_3'UTR|SLC35E1_ENST00000431408.1_Silent_p.S94S	NM_024881.4	NP_079157.3	Q96K37	S35E1_HUMAN	solute carrier family 35, member E1	250					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.S106R(1)		central_nervous_system(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(2)|ovary(1)	15						TCACCAAGTCGCTGCTGACCA	0.532																																					p.S250S		Atlas-SNP	.											SLC35E1,medulla,primitive_neuroectodermal_tumour-medulloblastoma,0,1	SLC35E1	48	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.C750T						.	G		0,4406		0,0,2203	67	66	67		750	-6.7	0.6	19		67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC35E1	NM_024881.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		250/411	16677349	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79939	exon4			CAAGTCGCTGCTG	AK024313	CCDS12346.2	19p13.11	2013-05-22			ENSG00000127526	ENSG00000127526		"Solute carriers"	20803	protein-coding gene	gene with protein product							Standard	NM_024881		Approved	FLJ14251	uc010xph.2	Q96K37	OTTHUMG00000152575	ENST00000595753.1:c.750C>T	chr19.hg19:g.16677349G>A		67.0	0.0		50.0	2.0	NM_024881	Q8NBQ2|Q96JV7	Silent	SNP	ENST00000595753.1	hg19	CCDS12346.2																																																																																			.	.		0.532	SLC35E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326809.2	NM_024881		A	16677349	G	A	16677349	2	1	44	1	0	0	0	0	0	0	0	1	14599	1078	38	1		1	SLC35E1	19	16677349	Silent	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	3690277	16677349	42451634	390	5850										
MYO9B	4650	hgsc.bcm.edu	37	chr19	17296790	17296790	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agcccttctttatccgctgcAtccgttccaatgctgaaaag	7	13	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:17296790A>G	ENST00000594824.1	+	18	2704	c.2557A>G	c.(2557-2559)Atc>Gtc	p.I853V	MYO9B_ENST00000397274.2_Missense_Mutation_p.I853V|MYO9B_ENST00000595618.1_Missense_Mutation_p.I853V			Q13459	MYO9B_HUMAN	myosin IXB	853	Actin-binding.|Myosin motor.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						TATCCGCTGCATCCGTTCCAA	0.532																																					p.I853V		Atlas-SNP	.											.	MYO9B	264	.	0			c.A2557G						.						94	94	94					19																	17296790		1956	4137	6093	SO:0001583	missense	4650	exon18			CGCTGCATCCGTT		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"Myosins / Myosin superfamily : Class IX"	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.2557A>G	chr19.hg19:g.17296790A>G	ENSP00000471367:p.Ile853Val	127.0	0.0		76.0	4.0	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.7	4.192570	0.78902	.	.	ENSG00000099331	ENST00000397274	D	0.91407	-2.84	5.21	3.14	0.36123	Myosin head, motor domain (2);	0.107097	0.41097	N	0.000948	D	0.93494	0.7924	M	0.71920	2.185	0.39077	D	0.960827	P;P;D	0.64830	0.938;0.938;0.994	P;P;D	0.70227	0.895;0.895;0.968	D	0.92702	0.6175	10	0.72032	D	0.01	.	9.2272	0.37414	0.8691:0.0:0.1309:0.0	.	853;853;859	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	V	853	ENSP00000380444:I853V	ENSP00000380444:I853V	I	+	1	0	MYO9B	17157790	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.902000	0.56310	0.409000	0.25649	0.533000	0.62120	ATC	.	.		0.532	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			G	17296790	A	G	17296790	3	3	44	1	0	0	0	0	1	0	0	0	10094	217	8	2	2623	2	MYO9B	19	17296790	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	619441	17296790	41832193	391	5851										
PGLS	25796	hgsc.bcm.edu	37	chr19	17622717	17622717	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctggacgctgggcttctgcgAcgagcgcctcgtgcccttcg	14	15	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:17622717A>G	ENST00000252603.2	+	1	280	c.236A>G	c.(235-237)gAc>gGc	p.D79G	CTD-3131K8.2_ENST00000596643.1_lincRNA	NM_012088.2	NP_036220.1	O95336	6PGL_HUMAN	6-phosphogluconolactonase	79					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	6-phosphogluconolactonase activity (GO:0017057)|monosaccharide binding (GO:0048029)			endometrium(1)|lung(1)	2						GGCTTCTGCGACGAGCGCCTC	0.726																																					p.D79G		Atlas-SNP	.											.	PGLS	12	.	0			c.A236G						.						4	4	4					19																	17622717		1887	3720	5607	SO:0001583	missense	25796	exon1			TCTGCGACGAGCG	AJ243972	CCDS12361.1	19p13.2	2008-02-05				ENSG00000130313	3.1.1.31		8903	protein-coding gene	gene with protein product		604951				10518023	Standard	NM_012088		Approved	6PGL	uc002ngw.3	O95336		ENST00000252603.2:c.236A>G	chr19.hg19:g.17622717A>G	ENSP00000252603:p.Asp79Gly	107.0	0.0		94.0	4.0	NM_012088		Missense_Mutation	SNP	ENST00000252603.2	hg19	CCDS12361.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.724584	0.89298	.	.	ENSG00000130313	ENST00000252603	T	0.73575	-0.76	4.91	4.91	0.64330	Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1);	0.000000	0.85682	D	0.000000	D	0.91264	0.7246	H	0.99211	4.47	0.58432	D	0.999998	D	0.69078	0.997	D	0.79108	0.992	D	0.93425	0.6780	10	0.87932	D	0	-32.9105	10.9196	0.47156	1.0:0.0:0.0:0.0	.	79	O95336	6PGL_HUMAN	G	79	ENSP00000252603:D79G	ENSP00000252603:D79G	D	+	2	0	PGLS	17483717	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	6.477000	0.73591	1.834000	0.53371	0.402000	0.26972	GAC	.	.		0.726	PGLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464154.1			G	17622717	A	G	17622717	3	3	44	1	0	0	0	0	1	0	0	0	11801	275	10	2	238	2	PGLS	19	17622717	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	325927	17622717	41506266	392	5852										
ZNF507	22847	hgsc.bcm.edu	37	chr19	32843842	32843842	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttcattggaaattgatgaaCaaagaaaaactaaaccagat	6	6	1	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:32843842C>A	ENST00000311921.4	+	2	298	c.106C>A	c.(106-108)Caa>Aaa	p.Q36K	ZNF507_ENST00000544431.1_Missense_Mutation_p.Q36K|ZNF507_ENST00000355898.5_Missense_Mutation_p.Q36K	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	36					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					AATTGATGAACAAAGAAAAAC	0.363																																					p.Q36K		Atlas-SNP	.											.	ZNF507	92	.	0			c.C106A						.						79	77	78					19																	32843842		2203	4300	6503	SO:0001583	missense	22847	exon3			GATGAACAAAGAA	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"Zinc fingers, C2H2-type"	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.106C>A	chr19.hg19:g.32843842C>A	ENSP00000312277:p.Gln36Lys	106.0	0.0		125.0	5.0	NM_001136156	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Missense_Mutation	SNP	ENST00000311921.4	hg19	CCDS32985.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.505816	0.44558	.	.	ENSG00000168813	ENST00000355898;ENST00000311921;ENST00000544431	T;T;T	0.10382	3.21;3.21;2.88	5.5	4.47	0.54385	.	0.052456	0.85682	D	0.000000	T	0.28764	0.0713	M	0.65498	2.005	0.37694	D	0.923943	D;D	0.69078	0.982;0.997	P;D	0.64144	0.734;0.922	T	0.18304	-1.0341	10	0.59425	D	0.04	.	14.513	0.67800	0.1467:0.8533:0.0:0.0	.	36;36	Q8TCN5;Q8TCN5-2	ZN507_HUMAN;.	K	36	ENSP00000348162:Q36K;ENSP00000312277:Q36K;ENSP00000441549:Q36K	ENSP00000312277:Q36K	Q	+	1	0	ZNF507	37535682	1.000000	0.71417	0.992000	0.48379	0.854000	0.48673	2.630000	0.46494	1.449000	0.47699	0.491000	0.48974	CAA	.	.		0.363	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910		A	32843842	C	A	32843842	3	1	44	1	0	0	0	0	1	0	0	0	17968	479	17	3	108	3	ZNF507	19	32843842	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	15221125	32843842	26285141	393	5853										
ZNF781	163115	hgsc.bcm.edu	37	chr19	38160811	38160811	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tctcactagtgtgagttctcTtatgttgaatcaatgttgaa	8	6	3	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:38160811T>C	ENST00000590008.1	-	5	1091	c.239A>G	c.(238-240)aAg>aGg	p.K80R	ZNF781_ENST00000593040.1_5'Flank|ZFP30_ENST00000586732.1_Intron|ZNF781_ENST00000358582.4_Missense_Mutation_p.K80R			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	80					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						GTGAGTTCTCTTATGTTGAAT	0.388																																					p.K80R		Atlas-SNP	.											.	ZNF781	66	.	0			c.A239G						.						116	116	116					19																	38160811		2203	4300	6503	SO:0001583	missense	163115	exon4			GTTCTCTTATGTT	AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"Zinc fingers, C2H2-type"	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.239A>G	chr19.hg19:g.38160811T>C	ENSP00000466370:p.Lys80Arg	65.0	0.0		73.0	4.0	NM_152605	Q2VPJ8	Missense_Mutation	SNP	ENST00000590008.1	hg19	CCDS12507.1	.	.	.	.	.	.	.	.	.	.	T	11.53	1.666019	0.29604	.	.	ENSG00000196381	ENST00000358582;ENST00000545586	T	0.17854	2.25	2.23	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13841	0.0335	L	0.28458	0.855	0.18873	N	0.999989	B	0.22003	0.063	B	0.32465	0.146	T	0.36504	-0.9745	9	0.66056	D	0.02	.	6.0011	0.19521	0.0:0.1456:0.0:0.8544	.	80	Q8N8C0	ZN781_HUMAN	R	80	ENSP00000351391:K80R	ENSP00000351391:K80R	K	-	2	0	ZNF781	42852651	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.407000	0.07178	0.118000	0.18165	0.443000	0.29094	AAG	.	.		0.388	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605		C	38160811	T	C	38160811	3	2	44	1	0	0	0	0	1	0	0	0	18169	1609	56	2	748	2	ZNF781	19	38160811	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	5316969	38160811	20968172	394	5854										
CAPN12	147968	hgsc.bcm.edu	37	chr19	39226821	39226821	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcgccggcgtgggcggtgctCggcaccaccaggtagtggcc	17	14	0	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:39226821C>G	ENST00000328867.4	-	12	1820	c.1512G>C	c.(1510-1512)ccG>ccC	p.P504P	CAPN12_ENST00000601953.1_Silent_p.P355P|CTD-2540F13.2_ENST00000602255.1_RNA	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	504	Domain III.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GGGCGGTGCTCGGCACCACCA	0.746																																					p.P504P		Atlas-SNP	.											.	CAPN12	43	.	0			c.G1512C						.						5	6	6					19																	39226821		1557	2830	4387	SO:0001819	synonymous_variant	147968	exon12			GGTGCTCGGCACC	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"EF-hand domain containing"	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1512G>C	chr19.hg19:g.39226821C>G		55.0	0.0		31.0	15.0	NM_144691		Silent	SNP	ENST00000328867.4	hg19	CCDS12519.1																																																																																			.	.		0.746	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			G	39226821	C	G	39226821	2	3	44	1	0	0	0	0	0	0	0	1	2627	871	31	4		4	CAPN12	19	39226821	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	1066010	39226821	19902162	395	5855										
PSMC4	5704	hgsc.bcm.edu	37	chr19	40478358	40478358	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gaacctgaaaaaggaatttcTccatgcccaggaggaggtga	12	8	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:40478358T>C	ENST00000157812.2	+	3	416	c.218T>C	c.(217-219)cTc>cCc	p.L73P	PSMC4_ENST00000455878.2_Intron	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	73				L -> F (in Ref. 4; AAC32612). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					AAGGAATTTCTCCATGCCCAG	0.522																																					p.L73P	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.T218C						.						78	78	78					19																	40478358		2203	4300	6503	SO:0001583	missense	5704	exon3			AATTTCTCCATGC	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9551	protein-coding gene	gene with protein product	"protease 26S subunit 6", "Tat-binding protein 7", "MB67 interacting protein"	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.218T>C	chr19.hg19:g.40478358T>C	ENSP00000157812:p.Leu73Pro	63.0	0.0		92.0	5.0	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Missense_Mutation	SNP	ENST00000157812.2	hg19	CCDS12547.1	.	.	.	.	.	.	.	.	.	.	t	21.1	4.097558	0.76870	.	.	ENSG00000013275	ENST00000157812	D	0.94376	-3.41	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	D	0.94631	0.8269	M	0.63843	1.955	0.80722	D	1	D	0.56968	0.978	P	0.59825	0.864	D	0.93612	0.6940	10	0.35671	T	0.21	-4.659	12.4603	0.55729	0.0:0.0:0.0:1.0	.	73	P43686	PRS6B_HUMAN	P	73	ENSP00000157812:L73P	ENSP00000157812:L73P	L	+	2	0	PSMC4	45170198	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.381000	0.79718	1.843000	0.53566	0.459000	0.35465	CTC	.	.		0.522	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503		C	40478358	T	C	40478358	3	2	44	1	0	0	0	0	1	0	0	0	12701	1551	54	2	228	2	PSMC4	19	40478358	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1251537	40478358	18650625	396	5856										
PSMC4	5704	hgsc.bcm.edu	37	chr19	40478370	40478370	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggaatttctccatgcccaggAggaggtgaagcgaatccaaa	12	9	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:40478370A>G	ENST00000157812.2	+	3	428	c.230A>G	c.(229-231)gAg>gGg	p.E77G	PSMC4_ENST00000455878.2_Splice_Site_p.E46G	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	77					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CATGCCCAGGAGGAGGTGAAG	0.512																																					p.E77G	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.A230G						.						74	74	74					19																	40478370		2203	4300	6503	SO:0001583	missense	5704	exon3			CCCAGGAGGAGGT	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9551	protein-coding gene	gene with protein product	"protease 26S subunit 6", "Tat-binding protein 7", "MB67 interacting protein"	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.230A>G	chr19.hg19:g.40478370A>G	ENSP00000157812:p.Glu77Gly	65.0	0.0		95.0	4.0	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Missense_Mutation	SNP	ENST00000157812.2	hg19	CCDS12547.1	.	.	.	.	.	.	.	.	.	.	a	24.3	4.511413	0.85389	.	.	ENSG00000013275	ENST00000157812;ENST00000455878	D;D	0.95103	-3.61;-3.52	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	D	0.95771	0.8624	L	0.52266	1.64	0.80722	D	1	B;D	0.89917	0.178;1.0	B;D	0.91635	0.088;0.999	D	0.95711	0.8758	10	0.56958	D	0.05	-3.8069	12.4603	0.55729	1.0:0.0:0.0:0.0	.	46;77	P43686-2;P43686	.;PRS6B_HUMAN	G	77;46	ENSP00000157812:E77G;ENSP00000413869:E46G	ENSP00000157812:E77G	E	+	2	0	PSMC4	45170210	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.132000	0.77251	1.843000	0.53566	0.459000	0.35465	GAG	.	.		0.512	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503		G	40478370	A	G	40478370	3	3	44	1	0	0	0	0	1	0	0	0	12701	318	11	2	240	2	PSMC4	19	40478370	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	12	40478370	18650613	397	5857										
LIG1	3978	hgsc.bcm.edu	37	chr19	48636271	48636271	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cccgtcatatttgtattcgcAggtgaaagctgcctcctcaa	8	12	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:48636271A>G	ENST00000263274.7	-	18	2112	c.1693T>C	c.(1693-1695)Tgc>Cgc	p.C565R	LIG1_ENST00000427526.2_Missense_Mutation_p.C534R|LIG1_ENST00000536218.1_Missense_Mutation_p.C497R	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	565					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	TTGTATTCGCAGGTGAAAGCT	0.567								Nucleotide excision repair (NER)																													p.C565R		Atlas-SNP	.											.	LIG1	151	.	0			c.T1693C						.						181	167	172					19																	48636271		2203	4300	6503	SO:0001583	missense	3978	exon18			ATTCGCAGGTGAA		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.1693T>C	chr19.hg19:g.48636271A>G	ENSP00000263274:p.Cys565Arg	102.0	0.0		124.0	5.0	NM_000234	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	hg19	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.313989	0.81358	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526;ENST00000536218	T;T;T	0.81330	-1.48;-1.48;-1.48	5.48	5.48	0.80851	DNA ligase, ATP-dependent, central (1);	0.000000	0.85682	D	0.000000	D	0.93609	0.7959	H	0.98594	4.275	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.95656	0.8711	10	0.87932	D	0	-26.6684	13.8169	0.63297	1.0:0.0:0.0:0.0	.	534;497;565	B4DTU4;F5GZ28;P18858	.;.;DNLI1_HUMAN	R	565;596;534;497	ENSP00000263274:C565R;ENSP00000442841:C534R;ENSP00000441531:C497R	ENSP00000263274:C565R	C	-	1	0	LIG1	53328083	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.964000	0.87933	2.215000	0.71742	0.533000	0.62120	TGC	.	.		0.567	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		G	48636271	A	G	48636271	3	3	44	1	0	0	0	0	1	0	0	0	8790	188	7	2	1110	2	LIG1	19	48636271	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	8157901	48636271	10492712	398	5858										
TULP2	7288	hgsc.bcm.edu	37	chr19	49385453	49385453	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggtaacgactcagtagcgacTcctgttcctagaaggtaaag	11	9	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:49385453T>C	ENST00000221399.3	-	12	1427	c.1283A>G	c.(1282-1284)gAg>gGg	p.E428G		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	428					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		CAGTAGCGACTCCTGTTCCTA	0.522																																					p.E428G		Atlas-SNP	.											.	TULP2	60	.	0			c.A1283G						.						72	64	67					19																	49385453		2203	4300	6503	SO:0001583	missense	7288	exon12			AGCGACTCCTGTT	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"cancer/testis antigen 65"	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.1283A>G	chr19.hg19:g.49385453T>C	ENSP00000221399:p.Glu428Gly	70.0	0.0		89.0	5.0	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	hg19	CCDS12739.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.113029	0.37242	.	.	ENSG00000104804	ENST00000221399	D	0.86694	-2.16	4.49	3.47	0.39725	Tubby, C-terminal (3);	0.236440	0.41294	N	0.000913	D	0.88190	0.6370	L	0.61218	1.895	0.42735	D	0.993723	P	0.49559	0.925	P	0.52957	0.714	D	0.87546	0.2462	10	0.87932	D	0	-16.2848	8.5097	0.33208	0.0:0.0938:0.0:0.9062	.	428	O00295	TULP2_HUMAN	G	428	ENSP00000221399:E428G	ENSP00000221399:E428G	E	-	2	0	TULP2	54077265	1.000000	0.71417	0.810000	0.32431	0.041000	0.13682	5.596000	0.67570	0.858000	0.35431	-0.451000	0.05528	GAG	.	.		0.522	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323		C	49385453	T	C	49385453	3	2	44	1	0	0	0	0	1	0	0	0	16789	1551	54	2	287	2	TULP2	19	49385453	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	749182	49385453	9743530	399	5859										
MED25	81857	hgsc.bcm.edu	37	chr19	50333046	50333046	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cggcccctctcctacagcggGggatccacttctccattgtg	10	16	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:50333046G>A	ENST00000312865.6	+	6	582	c.529G>A	c.(529-531)Ggg>Agg	p.G177R	MED25_ENST00000538643.1_Intron	NM_030973.3	NP_112235.2	Q71SY5	MED25_HUMAN	mediator complex subunit 25	177	Interaction with the Mediator complex.				cell death (GO:0008219)|gene expression (GO:0010467)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of chromatin binding (GO:0035563)|positive regulation of mediator complex assembly (GO:2001178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|transcription factor binding (GO:0008134)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	17		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		CCTACAGCGGGGGATCCACTT	0.662																																					p.G177R	GBM(51;894 1657 37868)	Atlas-SNP	.											.	MED25	98	.	0			c.G529A						.						12	11	11					19																	50333046		2200	4293	6493	SO:0001583	missense	81857	exon6			CAGCGGGGGATCC	AL136746	CCDS33075.1	19q13.3	2014-09-17	2007-07-30			ENSG00000104973			28845	protein-coding gene	gene with protein product		610197	"mediator of RNA polymerase II transcription, subunit 25 homolog (S. cerevisiae)"			9110174, 11230166	Standard	NM_030973		Approved	ARC92, ACID1, TCBAP0758, DKFZp434K0512	uc002ppw.2	Q71SY5		ENST00000312865.6:c.529G>A	chr19.hg19:g.50333046G>A	ENSP00000326767:p.Gly177Arg	147.0	0.0		167.0	83.0	NM_030973	A8K095|B9TX30|O95783|Q6P143|Q6QMH5|Q707U4|Q8TB55|Q9H0L5|Q9HB34	Missense_Mutation	SNP	ENST00000312865.6	hg19	CCDS33075.1	.	.	.	.	.	.	.	.	.	.	G	36	5.913557	0.97099	.	.	ENSG00000104973	ENST00000355584;ENST00000377077;ENST00000312881;ENST00000312865;ENST00000456294;ENST00000542221;ENST00000544580	T	0.77750	-1.12	5.38	4.35	0.52113	.	0.054424	0.64402	D	0.000001	T	0.82217	0.4989	L	0.40543	1.245	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.83705	0.0184	10	0.66056	D	0.02	.	12.8803	0.58014	0.0786:0.0:0.9214:0.0	.	177	Q71SY5	MED25_HUMAN	R	177	ENSP00000326767:G177R	ENSP00000326767:G177R	G	+	1	0	MED25	55024858	1.000000	0.71417	0.638000	0.29380	0.929000	0.56500	7.993000	0.88291	1.503000	0.48686	0.655000	0.94253	GGG	.	.		0.662	MED25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465316.1	NM_030973		A	50333046	G	A	50333046	3	1	44	1	0	0	0	0	1	0	0	0	9452	1232	43	3	551	3	MED25	19	50333046	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	947593	50333046	8795937	400	5860										
C19orf41	126123	hgsc.bcm.edu	37	chr19	50666320	50666320	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcctgcagctgctccaactgGaagcgactggggatgagggc	16	11	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:50666320G>A	ENST00000293405.3	-	1	132	c.132C>T	c.(130-132)ttC>ttT	p.F44F		NM_152358.2	NP_689571.2	Q6UXV1	IZUM2_HUMAN	IZUMO family member 2	44						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						GCTCCAACTGGAAGCGACTGG	0.701																																					p.F44F		Atlas-SNP	.											.	IZUMO2	26	.	0			c.C132T						.						23	28	26					19																	50666320		1948	4132	6080	SO:0001819	synonymous_variant	126123	exon1			CAACTGGAAGCGA	AY358196	CCDS12792.2	19q13.33	2014-02-17	2010-07-29	2010-07-29	ENSG00000161652	ENSG00000161652		"-"	28518	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 41"	C19orf41		19658160, 22957301	Standard	XM_006723007		Approved	MGC33947, SCRL	uc002prp.1	Q6UXV1	OTTHUMG00000074063	ENST00000293405.3:c.132C>T	chr19.hg19:g.50666320G>A		196.0	0.0		178.0	76.0	NM_152358	Q5GRG3|Q5GRG4|Q6ZNM5|Q8NHR8	Silent	SNP	ENST00000293405.3	hg19	CCDS12792.2																																																																																			.	.		0.701	IZUMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157232.1	NM_152358		A	50666320	G	A	50666320	2	1	44	1	0	0	0	0	0	0	0	1	1926	1165	41	3		3	C19orf41	19	50666320	Silent	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	333274	50666320	8462663	401	5861										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52002711	52002711	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	caggatatgttgagtcggacAgccctggtcatggtcacgcc	13	11	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:52002711A>G	ENST00000291707.3	-	3	1123	c.1068T>C	c.(1066-1068)gcT>gcC	p.A356A	SIGLEC12_ENST00000598614.1_Silent_p.A238A	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	356	Ig-like C2-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		TGAGTCGGACAGCCCTGGTCA	0.607																																					p.A356A		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.T1068C						.						55	51	52					19																	52002711		2203	4300	6503	SO:0001819	synonymous_variant	89858	exon3			TCGGACAGCCCTG	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1068T>C	chr19.hg19:g.52002711A>G		194.0	0.0		154.0	7.0	NM_053003	Q8IYH7	Silent	SNP	ENST00000291707.3	hg19	CCDS12833.1																																																																																			.	.		0.607	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		G	52002711	A	G	52002711	2	3	44	1	0	0	0	0	0	0	0	1	14323	175	7	2		2	SIGLEC12	19	52002711	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1336391	52002711	7126272	402	5862										
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55594861	55594861	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aggacccagttgagaaacagCtacagcacgagcggaggcgc	14	11	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:55594861C>T	ENST00000201647.6	+	13	1386	c.1330C>T	c.(1330-1332)Cta>Tta	p.L444L	EPS8L1_ENST00000540810.1_Silent_p.L380L|EPS8L1_ENST00000586329.1_Silent_p.L426L|EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000588359.1_Silent_p.L98L|EPS8L1_ENST00000245618.5_Silent_p.L317L	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	444					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		TGAGAAACAGCTACAGCACGA	0.716																																					p.L444L	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.C1330T						.						9	12	11					19																	55594861		2163	4228	6391	SO:0001819	synonymous_variant	54869	exon13			AAACAGCTACAGC	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.1330C>T	chr19.hg19:g.55594861C>T		80.0	0.0		89.0	4.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Silent	SNP	ENST00000201647.6	hg19	CCDS12914.1																																																																																			.	.		0.716	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		T	55594861	C	T	55594861	2	4	44	1	0	0	0	0	0	0	0	1	5197	796	28	3		3	EPS8L1	19	55594861	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	3592150	55594861	3534122	403	5863										
SYT5	6861	hgsc.bcm.edu	37	chr19	55687412	55687412	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	taatccagggagtactgcagTcgtcctagctcatgcttgtc	10	11	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr19:55687412T>C	ENST00000354308.3	-	4	702	c.333A>G	c.(331-333)cgA>cgG	p.R111R	SYT5_ENST00000590851.1_Silent_p.R108R|SYT5_ENST00000592935.1_5'Flank|CTD-2587H24.5_ENST00000591665.1_RNA|SYT5_ENST00000537500.1_Silent_p.R111R	NM_003180.2	NP_003171.2	O00445	SYT5_HUMAN	synaptotagmin V	111			R -> Q (in dbSNP:rs11542503). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		calcium ion-dependent exocytosis (GO:0017156)|energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|dense core granule (GO:0031045)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		AGTACTGCAGTCGTCCTAGCT	0.602																																					p.R111R		Atlas-SNP	.											.	SYT5	45	.	0			c.A333G						.						149	146	147					19																	55687412		2203	4300	6503	SO:0001819	synonymous_variant	6861	exon4			CTGCAGTCGTCCT	X96783	CCDS12919.1, CCDS74455.1	19q13.42	2014-07-02			ENSG00000129990	ENSG00000129990		"Synaptotagmins"	11513	protein-coding gene	gene with protein product	"synaptotagmin 5"	600782				9177789	Standard	XM_006723338		Approved		uc002qjn.1	O00445	OTTHUMG00000180669	ENST00000354308.3:c.333A>G	chr19.hg19:g.55687412T>C		108.0	0.0		98.0	4.0	NM_003180	B3KWJ8|B7Z300|Q86X72	Silent	SNP	ENST00000354308.3	hg19	CCDS12919.1																																																																																			.	.		0.602	SYT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452501.1	NM_003180		C	55687412	T	C	55687412	2	2	44	1	0	0	0	0	0	0	0	1	15492	1654	58	2		2	SYT5	19	55687412	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	92551	55687412	3441571	404	5864										
SIRPD	128646	hgsc.bcm.edu	37	chr20	1532596	1532596	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggtccatttggtaaggtattGggtacgctgcaactcaagat	12	7	1	1	rs144302855		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:1532596G>C	ENST00000381623.3	-	2	1351	c.162C>G	c.(160-162)ccC>ccG	p.P54P	SIRPD_ENST00000381621.1_Silent_p.P54P			Q9H106	SIRPD_HUMAN	signal-regulatory protein delta	54	Ig-like V-type.					extracellular region (GO:0005576)		p.P54P(1)		breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)	15						GTAAGGTATTGGGTACGCTGC	0.438																																					p.P54P		Atlas-SNP	.											.	SIRPD	34	.	1	Substitution - coding silent(1)	lung(1)	c.C162G						.						127	120	122					20																	1532596		2203	4300	6503	SO:0001819	synonymous_variant	128646	exon2			GGTATTGGGTACG	AL049634	CCDS13018.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000125900	ENSG00000125900		"Signal-regulatory proteins", "Immunoglobulin superfamily / V-set domain containing"	16248	protein-coding gene	gene with protein product			"protein tyrosine phosphatase, non-receptor type substrate 1-like 2"	PTPNS1L2		16339511	Standard	NM_178460		Approved	dJ576H24.4	uc002wfi.3	Q9H106	OTTHUMG00000031674	ENST00000381623.3:c.162C>G	chr20.hg19:g.1532596G>C		164.0	0.0		165.0	7.0	NM_178460	B3KS88|Q5TFQ6	Silent	SNP	ENST00000381623.3	hg19	CCDS13018.1																																																																																			.	G|1.000;A|0.000		0.438	SIRPD-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077552.1	NM_178460		C	1532596	G	C	1532596	2	2	44	1	0	0	0	0	0	0	0	1	14350	1335	47	4		4	SIRPD	20	1532596	Silent	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10		1532596	61492924	405	5865										
C20orf194	25943	hgsc.bcm.edu	37	chr20	3356928	3356928	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agtacagatggacgctatccGatttaatcaatataattaca	6	7	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:3356928G>A	ENST00000252032.9	-	4	372	c.305C>T	c.(304-306)tCg>tTg	p.S102L		NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	102										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						GACGCTATCCGATTTAATCAA	0.333																																					p.S102L		Atlas-SNP	.											C20orf194,colon,carcinoma,0,1	C20orf194	83	.	0			c.C305T						.						83	75	78					20																	3356928		1837	4097	5934	SO:0001583	missense	25943	exon4			CTATCCGATTTAA	AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.305C>T	chr20.hg19:g.3356928G>A	ENSP00000252032:p.Ser102Leu	109.0	2.0		94.0	6.0	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	hg19	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.521577	0.44866	.	.	ENSG00000088854	ENST00000252032	T	0.17691	2.26	5.4	5.4	0.78164	.	0.231822	0.36374	N	0.002626	T	0.07279	0.0184	N	0.02539	-0.55	0.80722	D	1	B	0.14805	0.011	B	0.10450	0.005	T	0.35500	-0.9786	10	0.27082	T	0.32	.	11.7576	0.51884	0.0826:0.0:0.9174:0.0	.	102	Q5TEA3	CT194_HUMAN	L	102	ENSP00000252032:S102L	ENSP00000252032:S102L	S	-	2	0	C20orf194	3304928	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.082000	0.64450	2.693000	0.91896	0.491000	0.48974	TCG	.	.		0.333	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984		A	3356928	G	A	3356928	3	1	44	1	0	0	0	0	1	0	0	0	2101	1059	37	1	3364	1	C20orf194	20	3356928	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	1824332	3356928	59668592	406	5866										
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3672111	3672111	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agagtgggcacaggctccgcGtgcagccgccggtcattcca	14	14	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:3672111G>A	ENST00000344754.4	-	17	4466	c.4467C>T	c.(4465-4467)caC>caT	p.H1489H	SIGLEC1_ENST00000202578.4_Silent_p.H1489H	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1489	Ig-like C2-type 15.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CAGGCTCCGCGTGCAGCCGCC	0.672																																					p.H1489H		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C4467T						.						66	67	66					20																	3672111		2203	4300	6503	SO:0001819	synonymous_variant	6614	exon17			CTCCGCGTGCAGC	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.4467C>T	chr20.hg19:g.3672111G>A		363.0	0.0		358.0	174.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	hg19	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	G	0.074	-1.195928	0.01594	.	.	ENSG00000088827	ENST00000419548	.	.	.	5.34	-9.34	0.00636	.	.	.	.	.	T	0.14874	0.0359	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.18871	-1.0323	4	.	.	.	.	1.8855	0.03237	0.4812:0.1018:0.1642:0.2527	.	.	.	.	C	303	.	.	R	-	1	0	SIGLEC1	3620111	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.686000	0.01929	-1.228000	0.02568	-0.140000	0.14226	CGC	.	.		0.672	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		A	3672111	G	A	3672111	2	1	44	1	0	0	0	0	0	0	0	1	14320	1136	40	1		1	SIGLEC1	20	3672111	Silent	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	315183	3672111	59353409	407	5867										
HAO1	54363	hgsc.bcm.edu	37	chr20	7915282	7915282	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atccttggatacagcttccaTctagaattaaaaaataaaat	4	7	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:7915282T>C	ENST00000378789.3	-	2	189	c.138A>G	c.(136-138)agA>agG	p.R46R		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	46	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				cellular nitrogen compound metabolic process (GO:0034641)|fatty acid alpha-oxidation (GO:0001561)|glycolate catabolic process (GO:0046296)|glyoxylate metabolic process (GO:0046487)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|glycolate oxidase activity (GO:0008891)|glyoxylate oxidase activity (GO:0047969)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)	p.R46S(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						ACAGCTTCCATCTAGaattaa	0.343																																					p.R46R		Atlas-SNP	.											HAO1,NS,carcinoma,0,1	HAO1	71	.	1	Substitution - Missense(1)	ovary(1)	c.A138G						.						29	26	27					20																	7915282		2203	4300	6503	SO:0001630	splice_region_variant	54363	exon2			CTTCCATCTAGAA	AL021879	CCDS13100.1	20p12	2005-01-10			ENSG00000101323	ENSG00000101323	1.1.3.15		4809	protein-coding gene	gene with protein product		605023		GOX1		9891009	Standard	NM_017545		Approved	GOX	uc002wmw.1	Q9UJM8	OTTHUMG00000031841	ENST00000378789.3:c.138-1A>G	chr20.hg19:g.7915282T>C		51.0	0.0		54.0	3.0	NM_017545	Q14CQ0|Q9UPZ0|Q9Y3I7	Silent	SNP	ENST00000378789.3	hg19	CCDS13100.1																																																																																			.	.		0.343	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2		Silent	C	7915282	T	C	7915282	5	2	44	1	0	0	0	0	0	0	1	0	6960	1449	50	2	1002	2	HAO1	20	7915282	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4243171	7915282	55110238	408	5868										
SNAP25	6616	hgsc.bcm.edu	37	chr20	10277665	10277665	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcgtgtagtggacgaacgggAgcagatggccatcagtggcg	17	8	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:10277665A>G	ENST00000254976.2	+	6	585	c.374A>G	c.(373-375)gAg>gGg	p.E125G	SNAP25_ENST00000495883.1_3'UTR|SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000453544.1_RNA|SNAP25_ENST00000304886.2_Missense_Mutation_p.E125G	NM_130811.2	NP_570824.1	P60880	SNP25_HUMAN	synaptosomal-associated protein, 25kDa	125					energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long-term synaptic potentiation (GO:0060291)|neurotransmitter secretion (GO:0007269)|neurotransmitter uptake (GO:0001504)|regulation of establishment of protein localization (GO:0070201)|regulation of insulin secretion (GO:0050796)|regulation of neuron projection development (GO:0010975)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|SNARE complex (GO:0031201)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|trans-Golgi network (GO:0005802)	calcium-dependent protein binding (GO:0048306)			endometrium(1)|large_intestine(2)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	18					Botulinum Toxin Type A(DB00083)	GACGAACGGGAGCAGATGGCC	0.507																																					p.E125G		Atlas-SNP	.											.	SNAP25	79	.	0			c.A374G						.						71	67	68					20																	10277665		2203	4300	6503	SO:0001583	missense	6616	exon6			AACGGGAGCAGAT		CCDS13109.1, CCDS13110.1	20p12-p11.2	2008-08-01	2002-08-29		ENSG00000132639	ENSG00000132639			11132	protein-coding gene	gene with protein product	"resistance to inhibitors of cholinesterase 4 homolog"	600322	"synaptosomal-associated protein, 25kD"	SNAP		8661740, 10692432	Standard	NM_003081		Approved	SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2	uc002wnr.2	P60880	OTTHUMG00000031863	ENST00000254976.2:c.374A>G	chr20.hg19:g.10277665A>G	ENSP00000254976:p.Glu125Gly	116.0	0.0		122.0	5.0	NM_003081	B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45	Missense_Mutation	SNP	ENST00000254976.2	hg19	CCDS13110.1	.	.	.	.	.	.	.	.	.	.	A	12.38	1.921159	0.33908	.	.	ENSG00000132639	ENST00000254976;ENST00000304886	.	.	.	5.86	5.86	0.93980	SNAP-25 (1);	0.000000	0.85682	D	0.000000	T	0.77377	0.4121	M	0.75447	2.3	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.69824	0.962;0.966	T	0.74671	-0.3587	9	0.23302	T	0.38	-0.6447	16.2652	0.82574	1.0:0.0:0.0:0.0	.	125;125	P60880-2;P60880	.;SNP25_HUMAN	G	125	.	ENSP00000254976:E125G	E	+	2	0	SNAP25	10225665	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.241000	0.73720	0.528000	0.53228	GAG	.	.		0.507	SNAP25-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077976.3	NM_130811		G	10277665	A	G	10277665	3	3	44	1	0	0	0	0	1	0	0	0	14845	304	11	2	514	2	SNAP25	20	10277665	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2362383	10277665	52747855	409	5869										
RRBP1	6238	hgsc.bcm.edu	37	chr20	17640671	17640671	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cagccttcgaagtgagaaccTggatggaattcactacagag	11	9	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:17640671T>C	ENST00000377813.1	-	3	785	c.482A>G	c.(481-483)cAg>cGg	p.Q161R	RRBP1_ENST00000377807.2_Missense_Mutation_p.Q161R|RRBP1_ENST00000455029.2_Intron|RRBP1_ENST00000246043.4_Missense_Mutation_p.Q161R|RRBP1_ENST00000360807.4_Missense_Mutation_p.Q161R			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	161					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						AGTGAGAACCTGGATGGAATT	0.557																																					p.Q161R		Atlas-SNP	.											.	RRBP1	157	.	0			c.A482G						.						77	64	68					20																	17640671		2203	4300	6503	SO:0001583	missense	6238	exon2			AGAACCTGGATGG	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"ribosome binding protein 1 (dog 180kD homolog)", "ribosome binding protein 1 homolog 180kDa (dog)"			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.482A>G	chr20.hg19:g.17640671T>C	ENSP00000367044:p.Gln161Arg	91.0	0.0		77.0	5.0	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Missense_Mutation	SNP	ENST00000377813.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.63	3.177373	0.57692	.	.	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000398782	T;T;T;T	0.42131	0.98;1.86;0.98;1.86	4.06	4.06	0.47325	.	0.000000	0.33075	N	0.005313	T	0.32675	0.0837	L	0.43152	1.355	0.80722	D	1	P	0.46512	0.879	B	0.40256	0.324	T	0.09271	-1.0682	10	0.39692	T	0.17	-21.8668	9.5679	0.39409	0.0:0.0:0.1912:0.8088	.	161	Q9P2E9-3	.	R	161	ENSP00000354045:Q161R;ENSP00000367044:Q161R;ENSP00000367038:Q161R;ENSP00000246043:Q161R	ENSP00000246043:Q161R	Q	-	2	0	RRBP1	17588671	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	4.419000	0.59835	1.852000	0.53769	0.460000	0.39030	CAG	.	.		0.557	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576		C	17640671	T	C	17640671	3	2	44	1	0	0	0	0	1	0	0	0	13693	1580	55	2	2547	2	RRBP1	20	17640671	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	7363006	17640671	45384849	410	5870										
RIN2	54453	hgsc.bcm.edu	37	chr20	19981288	19981288	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agttgcatttcaggaggtcaAcagtggttgcacaggaaaga	13	6	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:19981288A>G	ENST00000255006.6	+	12	2692	c.2543A>G	c.(2542-2544)aAc>aGc	p.N848S	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Missense_Mutation_p.N366S	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	799	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						CAGGAGGTCAACAGTGGTTGC	0.502																																					p.N848S		Atlas-SNP	.											.	RIN2	126	.	0			c.A2543G						.						144	140	142					20																	19981288		2011	4194	6205	SO:0001583	missense	54453	exon12			AGGTCAACAGTGG	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.2543A>G	chr20.hg19:g.19981288A>G	ENSP00000255006:p.Asn848Ser	102.0	0.0		88.0	4.0	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	hg19	CCDS56182.1	.	.	.	.	.	.	.	.	.	.	A	8.181	0.793849	0.16327	.	.	ENSG00000132669	ENST00000255006;ENST00000440354	T;T	0.15718	2.4;2.4	5.69	1.01	0.19927	Ras-association (3);	0.313274	0.40554	N	0.001064	T	0.06234	0.0161	N	0.03608	-0.345	0.45307	D	0.998306	B;B	0.21520	0.0;0.057	B;B	0.20955	0.002;0.032	T	0.38993	-0.9635	9	.	.	.	-20.4559	9.0633	0.36447	0.7184:0.0:0.2816:0.0	.	366;799	E7EPJ1;Q8WYP3	.;RIN2_HUMAN	S	848;366	ENSP00000255006:N848S;ENSP00000391239:N366S	.	N	+	2	0	RIN2	19929288	0.972000	0.33761	0.993000	0.49108	0.852000	0.48524	0.638000	0.24674	-0.086000	0.12550	-0.464000	0.05259	AAC	.	.		0.502	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			G	19981288	A	G	19981288	3	3	44	1	0	0	0	0	1	0	0	0	13387	43	2	2	2438	2	RIN2	20	19981288	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	2340617	19981288	43044232	411	5871										
NAPB	63908	hgsc.bcm.edu	37	chr20	23383705	23383705	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	agcctcttctattcttgtgtTtcctctgagaaaaagttaaa	6	8	4	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:23383705T>C	ENST00000377026.4	-	2	188	c.103A>G	c.(103-105)Aac>Gac	p.N35D	NAPB_ENST00000472855.1_5'UTR|NAPB_ENST00000432543.2_Missense_Mutation_p.N35D|NAPB_ENST00000398425.3_5'UTR	NM_001283018.1|NM_001283020.1|NM_022080.2	NP_001269947.1|NP_001269949.1|NP_071363.1	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, beta	35					intracellular protein transport (GO:0006886)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	extracellular vesicular exosome (GO:0070062)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					ATTCTTGTGTTTCCTCTGAGA	0.328																																					p.N35D		Atlas-SNP	.											.	NAPB	22	.	0			c.A103G						.						79	75	76					20																	23383705		2201	4300	6501	SO:0001583	missense	63908	exon2			TTGTGTTTCCTCT	AK022817	CCDS13152.1, CCDS63241.1, CCDS63242.1, CCDS74710.1	20p12.3-p11.21	2008-08-01			ENSG00000125814	ENSG00000125814			15751	protein-coding gene	gene with protein product		611270				8455721	Standard	NM_022080		Approved	SNAP-BETA, SNAPB	uc002wta.3	Q9H115	OTTHUMG00000032062	ENST00000377026.4:c.103A>G	chr20.hg19:g.23383705T>C	ENSP00000366225:p.Asn35Asp	92.0	0.0		82.0	4.0	NM_022080	B4DK44|Q4G0M0|Q4G187|Q5JXF9|Q8N3C4	Missense_Mutation	SNP	ENST00000377026.4	hg19	CCDS13152.1	.	.	.	.	.	.	.	.	.	.	T	15.32	2.799639	0.50208	.	.	ENSG00000125814	ENST00000377026;ENST00000432543	T;T	0.75367	1.63;-0.93	5.95	5.95	0.96441	Tetratricopeptide-like helical (1);	0.343450	0.33591	N	0.004749	T	0.64638	0.2616	N	0.20881	0.62	0.80722	D	1	B;B;B	0.26147	0.143;0.143;0.072	B;B;B	0.29077	0.062;0.098;0.098	T	0.61787	-0.6991	10	0.39692	T	0.17	0.4372	15.5971	0.76595	0.0:0.0:0.0:1.0	.	35;35;35	B4DK44;B4DIV0;Q9H115	.;.;SNAB_HUMAN	D	35	ENSP00000366225:N35D;ENSP00000413600:N35D	ENSP00000366225:N35D	N	-	1	0	NAPB	23331705	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.382000	0.52463	2.279000	0.76181	0.533000	0.62120	AAC	.	.		0.328	NAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078317.2	NM_022080		C	23383705	T	C	23383705	3	2	44	1	0	0	0	0	1	0	0	0	10171	1841	64	2	833	2	NAPB	20	23383705	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	3402417	23383705	39641815	412	5872										
ACSS1	84532	hgsc.bcm.edu	37	chr20	25002140	25002140	+	Frame_Shift_Del	DEL	A	A	-													0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccgatgtcggccacacagccAaagatgtcacctggctggtg							TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:25002140delA	ENST00000323482.4	-	6	1072	c.993delT	c.(991-993)tttfs	p.F331fs	ACSS1_ENST00000542618.1_Frame_Shift_Del_p.F210fs|ACSS1_ENST00000432802.2_Frame_Shift_Del_p.F331fs|ACSS1_ENST00000537502.1_Frame_Shift_Del_p.F248fs	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	331					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CCACACAGCCAAAGATGTCAC	0.557																																					p.G332fs		Atlas-INDEL	.											.	ACSS1	46	.	0			c.994delG						.						92	77	82					20																	25002140		2203	4300	6503	SO:0001589	frameshift_variant	84532	exon6			.		CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"Acyl-CoA synthetase family"	16091	protein-coding gene	gene with protein product		614355	"acetyl-Coenzyme A synthetase 2 (AMP forming)-like"	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.993delT	chr20.hg19:g.25002140delA	ENSP00000316924:p.Phe331fs	176.0	0.0		166.0	10.0	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Frame_Shift_Del	DEL	ENST00000323482.4	hg19	CCDS13167.1																																																																																			.	.		0.557	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501		-	25002140	A	-	25002140	7	5	44	1	0	1	0	1	0	0	0	0	188	127	5	0	1112	0	ACSS1	20	25002140	Frame_Shift_Del	DEL	A	TCGA-BC-A3KG-01A-11D-A20W-10	1618435	25002140	38023380	413	5873										
VSX1	30813	hgsc.bcm.edu	37	chr20	25057157	25057157	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atcttcacttcctggcttccTtatcatccccatggattttt	4	13	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:25057157T>C	ENST00000376709.4	-	5	1101	c.838A>G	c.(838-840)Agg>Ggg	p.R280G	VSX1_ENST00000444511.2_Intron|VSX1_ENST00000424574.1_Intron|VSX1_ENST00000451258.1_Intron|VSX1_ENST00000429762.3_Intron	NM_014588.5	NP_055403.2	Q9NZR4	VSX1_HUMAN	visual system homeobox 1	280					neuron maturation (GO:0042551)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(3)|lung(2)	6						CCTGGCTTCCTTATCATCCCC	0.368																																					p.R280G		Atlas-SNP	.											.	VSX1	20	.	0			c.A838G						.						90	99	96					20																	25057157		2203	4300	6503	SO:0001583	missense	30813	exon5			GCTTCCTTATCAT	AF176797	CCDS13168.1, CCDS13169.1, CCDS58766.1, CCDS58767.1	20p11.21	2014-02-14	2007-07-12		ENSG00000100987	ENSG00000100987		"Homeoboxes / PRD class"	12723	protein-coding gene	gene with protein product		605020	"posterior polymorphous corneal dystrophy", "visual system homeobox 1 homolog, CHX10-like (zebrafish)"	PPCD		10673340	Standard	NM_001256272		Approved	PPD, PPCD1	uc002wuf.4	Q9NZR4	OTTHUMG00000032111	ENST00000376709.4:c.838A>G	chr20.hg19:g.25057157T>C	ENSP00000365899:p.Arg280Gly	88.0	0.0		97.0	4.0	NM_014588	B9EGJ4|D1MF28|Q0GM60|Q0GM61|Q0GM62|Q0GM63|Q0GM64|Q0GM65|Q5TF40|Q5TF41|Q9HCU3|Q9NU27	Missense_Mutation	SNP	ENST00000376709.4	hg19	CCDS13168.1	.	.	.	.	.	.	.	.	.	.	T	12.45	1.940829	0.34283	.	.	ENSG00000100987	ENST00000376709	D	0.92397	-3.03	3.77	3.77	0.43336	.	0.156351	0.56097	D	0.000026	D	0.88183	0.6368	L	0.55834	1.745	0.33126	D	0.542457	B	0.14438	0.01	B	0.06405	0.002	D	0.87015	0.2125	10	0.34782	T	0.22	.	9.9927	0.41881	0.0:0.0:0.0:1.0	.	280	Q9NZR4	VSX1_HUMAN	G	280	ENSP00000365899:R280G	ENSP00000365899:R280G	R	-	1	2	VSX1	25005157	0.847000	0.29606	0.942000	0.38095	0.937000	0.57800	1.913000	0.39956	1.576000	0.49790	0.533000	0.62120	AGG	.	.		0.368	VSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078384.3			C	25057157	T	C	25057157	3	2	44	1	0	0	0	0	1	0	0	0	17246	1608	56	2	263	2	VSX1	20	25057157	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	55017	25057157	37968363	414	5874										
CBFA2T2	9139	hgsc.bcm.edu	37	chr20	32217714	32217714	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctgggagtgcagattctctcAgcaatggtaaggggagagtc	15	7	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:32217714A>G	ENST00000346541.3	+	9	1786	c.1249A>G	c.(1249-1251)Agc>Ggc	p.S417G	CBFA2T2_ENST00000397800.1_Missense_Mutation_p.S388G|CBFA2T2_ENST00000359606.3_Missense_Mutation_p.S427G|CBFA2T2_ENST00000375279.2_Missense_Mutation_p.S417G|CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000342704.6_Missense_Mutation_p.S408G|CBFA2T2_ENST00000492345.1_Missense_Mutation_p.S388G	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	417					epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						AGATTCTCTCAGCAATGGTAA	0.483																																					p.S417G	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-SNP	.											.	CBFA2T2	93	.	0			c.A1249G						.						46	45	45					20																	32217714		2203	4300	6503	SO:0001583	missense	9139	exon9			TCTCTCAGCAATG	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"Zinc fingers, MYND-type"	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.1249A>G	chr20.hg19:g.32217714A>G	ENSP00000262653:p.Ser417Gly	95.0	0.0		104.0	5.0	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Missense_Mutation	SNP	ENST00000346541.3	hg19	CCDS13221.1	.	.	.	.	.	.	.	.	.	.	A	13.65	2.301204	0.40694	.	.	ENSG00000078699	ENST00000397803;ENST00000375279;ENST00000342704;ENST00000346541;ENST00000397800;ENST00000359606	T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;1.42	5.73	4.64	0.57946	.	0.617048	0.18818	N	0.130327	T	0.30792	0.0776	N	0.19112	0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.06991	-1.0796	10	0.33141	T	0.24	-14.9003	8.4422	0.32822	0.8174:0.0:0.1826:0.0	.	417;408	O43439;F8W6D7	MTG8R_HUMAN;.	G	191;417;408;417;388;427	ENSP00000364428:S417G;ENSP00000345810:S408G;ENSP00000262653:S417G;ENSP00000380902:S388G;ENSP00000352622:S427G	ENSP00000345810:S408G	S	+	1	0	CBFA2T2	31681375	0.862000	0.29867	0.998000	0.56505	0.986000	0.74619	1.867000	0.39499	1.106000	0.41623	0.533000	0.62120	AGC	.	.		0.483	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		G	32217714	A	G	32217714	3	3	44	1	0	0	0	0	1	0	0	0	2699	188	7	2	1317	2	CBFA2T2	20	32217714	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	7160557	32217714	30807806	415	5875										
MYH7B	57644	hgsc.bcm.edu	37	chr20	33586333	33586333	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggggagctgagtcgcctgctAgaggagaaggagtgtctgat	18	6	1	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:33586333A>G	ENST00000262873.7	+	32	4112	c.4020A>G	c.(4018-4020)ctA>ctG	p.L1340L		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1298						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GTCGCCTGCTAGAGGAGAAGG	0.642																																					p.L1340L		Atlas-SNP	.											.	MYH7B	145	.	0			c.A4020G						.						42	48	46					20																	33586333		2095	4218	6313	SO:0001819	synonymous_variant	57644	exon34			CCTGCTAGAGGAG	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.4020A>G	chr20.hg19:g.33586333A>G		80.0	0.0		88.0	4.0	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	hg19	CCDS42869.1																																																																																			.	.		0.642	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		G	33586333	A	G	33586333	2	3	44	1	0	0	0	0	0	0	0	1	10049	407	15	2		2	MYH7B	20	33586333	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1368619	33586333	29439187	416	5876										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35437068	35437068	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ctcctggctccagaatttctGctccagcctccgctggaggc	10	16	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:35437068G>T	ENST00000357779.3	-	8	2274	c.1948C>A	c.(1948-1950)Cag>Aag	p.Q650K	SOGA1_ENST00000237536.4_Missense_Mutation_p.Q888K|SOGA1_ENST00000456801.2_Missense_Mutation_p.Q491K|SOGA1_ENST00000279034.6_Missense_Mutation_p.Q650K			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	650					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						CAGAATTTCTGCTCCAGCCTC	0.577											OREG0025909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q888K		Atlas-SNP	.											.	SOGA1	136	.	0			c.C2662A						.						36	39	38					20																	35437068		1923	4140	6063	SO:0001583	missense	140710	exon8			ATTTCTGCTCCAG	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.1948C>A	chr20.hg19:g.35437068G>T	ENSP00000350424:p.Gln650Lys	86.0	0.0	855	61.0	25.0	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.96	2.988168	0.53934	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.32346	0.0826	L	0.36672	1.1	0.53688	D	0.999977	P	0.43412	0.806	B	0.35073	0.195	T	0.07177	-1.0786	10	0.23302	T	0.38	-43.3312	17.8379	0.88706	0.0:0.0:1.0:0.0	.	650	O94964-4	.	K	888;650;491;650	ENSP00000237536:Q888K;ENSP00000279034:Q650K;ENSP00000413886:Q491K;ENSP00000350424:Q650K	ENSP00000237536:Q888K	Q	-	1	0	KIAA0889	34870482	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.493000	0.60341	2.745000	0.94114	0.655000	0.94253	CAG	.	.		0.577	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		T	35437068	G	T	35437068	3	4	44	1	0	0	0	0	1	0	0	0	2085	1328	46	3	2417	3	C20orf117	20	35437068	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	1850735	35437068	27588452	417	5877										
SRC	6714	hgsc.bcm.edu	37	chr20	36028552	36028552	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	accaccagggtggccatcaaAaccctgaagcctggcacgat	10	14	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:36028552A>G	ENST00000373578.2	+	10	1243	c.894A>G	c.(892-894)aaA>aaG	p.K298K	SRC_ENST00000445403.1_Silent_p.K298K|SRC_ENST00000477066.1_3'UTR|SRC_ENST00000373558.2_Silent_p.K304K|SRC_ENST00000373567.2_Silent_p.K298K|SRC_ENST00000358208.4_Silent_p.K298K|SRC_ENST00000360723.4_Silent_p.K304K	NM_198291.1	NP_938033.1	P12931	SRC_HUMAN	SRC proto-oncogene, non-receptor tyrosine kinase	298	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cellular response to progesterone stimulus (GO:0071393)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|membrane organization (GO:0061024)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of protein homooligomerization (GO:0032463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oogenesis (GO:0048477)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of integrin activation (GO:0033625)|positive regulation of podosome assembly (GO:0071803)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone receptor signaling pathway (GO:0050847)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of bone resorption (GO:0045124)|regulation of caveolin-mediated endocytosis (GO:2001286)|regulation of cell-cell adhesion (GO:0022407)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of epithelial cell migration (GO:0010632)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of protein binding (GO:0043393)|regulation of vascular permeability (GO:0043114)|response to interleukin-1 (GO:0070555)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|T cell costimulation (GO:0031295)|transforming growth factor beta receptor signaling pathway (GO:0007179)|uterus development (GO:0060065)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|growth factor receptor binding (GO:0070851)|heme binding (GO:0020037)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(16)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)			Bosutinib(DB06616)|Dasatinib(DB01254)|Ponatinib(DB08901)	TGGCCATCAAAACCCTGAAGC	0.592																																					p.K298K		Atlas-SNP	.											.	SRC	52	.	0			c.A894G						.						80	67	71					20																	36028552		2203	4300	6503	SO:0001819	synonymous_variant	6714	exon10			CATCAAAACCCTG	AF077754	CCDS13294.1	20q12-q13	2014-06-25	2014-06-25		ENSG00000197122	ENSG00000197122		"SH2 domain containing"	11283	protein-coding gene	gene with protein product		190090	"v-src avian sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog"	SRC1		2582238	Standard	NM_005417		Approved	ASV, c-src	uc002xgy.3	P12931	OTTHUMG00000032417	ENST00000373578.2:c.894A>G	chr20.hg19:g.36028552A>G		127.0	0.0		95.0	5.0	NM_005417	E1P5V4|Q76P87|Q86VB9|Q9H5A8	Silent	SNP	ENST00000373578.2	hg19	CCDS13294.1																																																																																			.	.		0.592	SRC-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268142.1	NM_005417		G	36028552	A	G	36028552	2	3	44	1	0	0	0	0	0	0	0	1	15149	11	1	2		2	SRC	20	36028552	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	591484	36028552	26996968	418	5878										
CTSA	5476	hgsc.bcm.edu	37	chr20	44520238	44520238	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccgcgccgccgccgctgttcCtgctgctgctgctgctgctg	13	18	0	0	rs3080212|rs11468075|rs10582052|rs397784956|rs397839006	byFrequency	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:44520238C>T	ENST00000372459.2	+	1	224	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L	NEURL2_ENST00000372518.4_5'Flank|RP3-337O18.9_ENST00000607703.1_RNA|CTSA_ENST00000372484.3_Silent_p.L29L|CTSA_ENST00000191018.5_Silent_p.L11L|CTSA_ENST00000354880.5_Silent_p.L29L			P10619	PPGB_HUMAN	cathepsin A	11					glycosphingolipid metabolic process (GO:0006687)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|enzyme activator activity (GO:0008047)|serine-type carboxypeptidase activity (GO:0004185)	p.L29delL(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				gccgctgttcctgctgctgct	0.706																																					p.L29L		Atlas-SNP	.											.,5	CTSA	52	.	1	Deletion - In frame(1)	breast(1)	c.C85T						.						8	10	10					20																	44520238		2013	3921	5934	SO:0001819	synonymous_variant	5476	exon2			CTGTTCCTGCTGC	M22960	CCDS13385.2, CCDS46609.1, CCDS54467.1	20q13.12	2012-02-10	2006-12-05	2006-12-05	ENSG00000064601	ENSG00000064601	3.4.16.5	"Cathepsins"	9251	protein-coding gene	gene with protein product	"carboxypeptidase C", "lysosomal protective protein", "carboxypeptidase-L", "carboxypeptidase Y-like kininase", "deamidase", "lysosomal carboxypeptidase A", "urinary kininase"	613111	"protective protein for beta-galactosidase (galactosialidosis)"	GSL, PPGB		2071143	Standard	NM_000308		Approved		uc002xqh.3	P10619	OTTHUMG00000033078	ENST00000372459.2:c.31C>T	chr20.hg19:g.44520238C>T		35.0	0.0		48.0	2.0	NM_000308	B2R798|Q561W6|Q5JZH1|Q96KJ2|Q9BR08|Q9BW68	Silent	SNP	ENST00000372459.2	hg19	CCDS46609.1																																																																																			.	.		0.706	CTSA-012	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471297.2	NM_000308		T	44520238	C	T	44520238	2	4	44	1	0	0	0	0	0	0	0	1	4031	680	24	3		3	CTSA	20	44520238	Silent	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	8491686	44520238	18505282	419	5879										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58487429	58487429	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tgttaaattaaaattttaccTcatatttatcaagaaatgct	3	5	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:58487429T>C	ENST00000357552.3	-	13	1100	c.875A>G	c.(874-876)gAg>gGg	p.E292G	SYCP2_ENST00000371001.2_Splice_Site_p.E292G			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	292					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			AAATTTTACCTCATATTTATC	0.234																																					p.E292G		Atlas-SNP	.											.	SYCP2	204	.	0			c.A875G						.						9	9	9					20																	58487429		2072	4160	6232	SO:0001630	splice_region_variant	10388	exon12			TTTACCTCATATT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.876+1A>G	chr20.hg19:g.58487429T>C		77.0	0.0		85.0	4.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.328628	0.81690	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.25085	2.06;2.06;1.82	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000001	T	0.52948	0.1766	M	0.78637	2.42	0.43408	D	0.99554	D;D	0.89917	1.0;1.0	D;D	0.91635	0.988;0.999	T	0.57441	-0.7811	10	0.87932	D	0	-20.0419	14.8452	0.70254	0.0:0.0:0.0:1.0	.	292;292	A2A341;Q9BX26	.;SYCP2_HUMAN	G	292	ENSP00000360040:E292G;ENSP00000350162:E292G;ENSP00000402456:E292G	ENSP00000350162:E292G	E	-	2	0	SYCP2	57920824	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.595000	0.74109	2.299000	0.77371	0.533000	0.62120	GAG	.	.		0.234	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	Missense_Mutation	C	58487429	T	C	58487429	5	2	44	1	0	0	0	0	0	0	1	0	15447	1565	54	2	3849	2	SYCP2	20	58487429	Splice_Site	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	13967191	58487429	4538091	420	5880										
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62594753	62594753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccttgcgcagcctctcgcgcTcctcctgctcgcccccttcg	8	22	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr20:62594753T>C	ENST00000450537.1	-	11	1799	c.1739A>G	c.(1738-1740)gAg>gGg	p.E580G	ZNF512B_ENST00000217130.3_Missense_Mutation_p.E580G|ZNF512B_ENST00000369888.1_Missense_Mutation_p.E580G			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	580					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CCTCTCGCGCTCCTCCTGCTC	0.741																																					p.E580G		Atlas-SNP	.											.	ZNF512B	72	.	0			c.A1739G						.						7	8	8					20																	62594753		2143	4230	6373	SO:0001583	missense	57473	exon11			TCGCGCTCCTCCT	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.1739A>G	chr20.hg19:g.62594753T>C	ENSP00000393795:p.Glu580Gly	39.0	0.0		50.0	4.0	NM_020713	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	hg19	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.349538	0.82132	.	.	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.28069	1.63;1.63;1.63	4.51	4.51	0.55191	.	0.000000	0.85682	D	0.000000	T	0.51329	0.1668	M	0.61703	1.905	0.58432	D	0.999998	D	0.89917	1.0	D	0.79784	0.993	T	0.55315	-0.8160	10	0.87932	D	0	-31.4643	13.1253	0.59351	0.0:0.0:0.0:1.0	.	580	Q96KM6	Z512B_HUMAN	G	580	ENSP00000358904:E580G;ENSP00000393795:E580G;ENSP00000217130:E580G	ENSP00000217130:E580G	E	-	2	0	ZNF512B	62065197	0.648000	0.27313	0.998000	0.56505	0.895000	0.52256	1.990000	0.40717	1.804000	0.52760	0.379000	0.24179	GAG	.	.		0.741	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		C	62594753	T	C	62594753	3	2	44	1	0	0	0	0	1	0	0	0	17972	1551	54	2	967	2	ZNF512B	20	62594753	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	4107324	62594753	430767	421	5881										
GRIK1	2897	hgsc.bcm.edu	37	chr21	30949468	30949468	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	accatatccctccaactattCtggtcgatagagctttgggc	8	12	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr21:30949468C>T	ENST00000399907.1	-	14	2357	c.1946G>A	c.(1945-1947)aGa>aAa	p.R649K	GRIK1_ENST00000399914.1_Missense_Mutation_p.R634K|GRIK1_ENST00000327783.4_Missense_Mutation_p.R649K|GRIK1_ENST00000309434.7_Missense_Mutation_p.R651K|GRIK1_ENST00000389125.3_Missense_Mutation_p.R634K|GRIK1_ENST00000389124.2_Missense_Mutation_p.R649K|GRIK1_ENST00000399909.1_Missense_Mutation_p.R634K|GRIK1_ENST00000399913.1_Missense_Mutation_p.R649K|GRIK1_ENST00000535441.1_Missense_Mutation_p.R651K	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	649					adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	TCCAACTATTCTGGTCGATAG	0.463																																					p.R649K		Atlas-SNP	.											.	GRIK1	293	.	0			c.G1946A						.						107	99	102					21																	30949468		2203	4300	6503	SO:0001583	missense	2897	exon14			ACTATTCTGGTCG		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.1946G>A	chr21.hg19:g.30949468C>T	ENSP00000382791:p.Arg649Lys	169.0	0.0		138.0	6.0	NM_000830	Q13001|Q86SU9	Missense_Mutation	SNP	ENST00000399907.1	hg19	CCDS42913.1	.	.	.	.	.	.	.	.	.	.	C	34	5.368720	0.95900	.	.	ENSG00000171189	ENST00000327783;ENST00000389125;ENST00000399913;ENST00000399914;ENST00000535441;ENST00000541508;ENST00000389124;ENST00000399907;ENST00000399909;ENST00000309434	T;T;T;T;T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68	5.3	5.3	0.74995	Ionotropic glutamate receptor (2);	0.088817	0.85682	D	0.000000	D	0.88819	0.6540	M	0.94142	3.5	0.80722	D	1	D;D;D;D	0.65815	0.995;0.995;0.995;0.993	D;D;D;D	0.72338	0.977;0.968;0.968;0.946	D	0.91433	0.5167	10	0.87932	D	0	.	18.7417	0.91775	0.0:1.0:0.0:0.0	.	634;649;649;634	E7EPY9;E9PD61;P39086;P39086-2	.;.;GRIK1_HUMAN;.	K	649;634;649;634;651;510;649;649;634;651	ENSP00000327687:R649K;ENSP00000373777:R634K;ENSP00000382797:R649K;ENSP00000382798:R634K;ENSP00000446326:R651K;ENSP00000373776:R649K;ENSP00000382791:R649K;ENSP00000382793:R634K;ENSP00000311646:R651K	ENSP00000311646:R651K	R	-	2	0	GRIK1	29871339	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.540000	0.82074	2.765000	0.95021	0.650000	0.86243	AGA	.	.		0.463	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1			T	30949468	C	T	30949468	3	4	44	1	0	0	0	0	1	0	0	0	6782	913	32	3	986	3	GRIK1	21	30949468	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10		30949468	17180427	422	5882										
BRWD1	54014	hgsc.bcm.edu	37	chr21	40571299	40571299	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	atttctgactttaagctctgTtcatcttcagaattatgtaa	5	7	5	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr21:40571299T>C	ENST00000333229.2	-	40	5370	c.5043A>G	c.(5041-5043)gaA>gaG	p.E1681E	BRWD1_ENST00000342449.3_Silent_p.E1681E|BRWD1_ENST00000380800.3_Silent_p.E1681E	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1681					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TTAAGCTCTGTTCATCTTCAG	0.398																																					p.E1681E	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A5043G						.						59	57	58					21																	40571299		2203	4300	6503	SO:0001819	synonymous_variant	54014	exon40			GCTCTGTTCATCT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.5043A>G	chr21.hg19:g.40571299T>C		72.0	0.0		84.0	4.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	hg19	CCDS13662.1																																																																																			.	.		0.398	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		C	40571299	T	C	40571299	2	2	44	1	0	0	0	0	0	0	0	1	1527	1722	60	2		2	BRWD1	21	40571299	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	9621831	40571299	7558596	423	5883										
KRTAP10-12	386685	hgsc.bcm.edu	37	chr21	46117817	46117817	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cctggcctcctgcgggtcccTcctctgccgccccacatgtt	9	20	1	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr21:46117817T>C	ENST00000400365.3	+	1	731	c.701T>C	c.(700-702)cTc>cCc	p.L234P	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	234						keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						TGCGGGTCCCTCCTCTGCCGC	0.721																																					p.L234P		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.T701C						.						32	43	39					21																	46117817		2118	4232	6350	SO:0001583	missense	386685	exon1			GGTCCCTCCTCTG	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"Keratin associated proteins"	20533	protein-coding gene	gene with protein product			"keratin associated protein 18-12"	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.701T>C	chr21.hg19:g.46117817T>C	ENSP00000383216:p.Leu234Pro	81.0	0.0		79.0	5.0	NM_198699	B2RPA3	Missense_Mutation	SNP	ENST00000400365.3	hg19	CCDS42967.1	.	.	.	.	.	.	.	.	.	.	t	6.901	0.535861	0.13188	.	.	ENSG00000189169	ENST00000400365	T	0.00808	5.67	3.58	3.58	0.41010	.	.	.	.	.	T	0.04227	0.0117	M	0.84433	2.695	0.40862	D	0.98384	D	0.71674	0.998	D	0.65874	0.939	T	0.20472	-1.0274	9	0.49607	T	0.09	.	5.8006	0.18412	0.0:0.1284:0.0:0.8716	.	234	P60413	KR10C_HUMAN	P	234	ENSP00000383216:L234P	ENSP00000383216:L234P	L	+	2	0	KRTAP10-12	44942245	0.276000	0.24211	0.994000	0.49952	0.017000	0.09413	1.089000	0.30890	1.381000	0.46364	0.369000	0.22263	CTC	.	.		0.721	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		C	46117817	T	C	46117817	3	2	44	1	0	0	0	0	1	0	0	0	8517	1551	54	2	703	2	KRTAP10-12	21	46117817	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	5546518	46117817	2012078	424	5884										
PCBP3	54039	hgsc.bcm.edu	37	chr21	47330925	47330925	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	catccagtgcgtcaagcagaTctgtgtggtcatgctggagg	14	9	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr21:47330925T>C	ENST00000400314.1	+	9	919	c.581T>C	c.(580-582)aTc>aCc	p.I194T	PCBP3_ENST00000400304.1_Missense_Mutation_p.I162T|PCBP3_ENST00000400310.1_Missense_Mutation_p.I194T|PCBP3_ENST00000400309.1_Missense_Mutation_p.I194T|PCBP3_ENST00000449640.1_Missense_Mutation_p.I194T|PCBP3_ENST00000400308.1_Missense_Mutation_p.I194T			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	194					mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		GTCAAGCAGATCTGTGTGGTC	0.647																																					p.I194T		Atlas-SNP	.											.	PCBP3	82	.	0			c.T581C						.						86	93	91					21																	47330925		2178	4273	6451	SO:0001583	missense	54039	exon7			AGCAGATCTGTGT	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"poly(rC)-binding protein 3"			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.581T>C	chr21.hg19:g.47330925T>C	ENSP00000383168:p.Ile194Thr	98.0	0.0		82.0	4.0	NM_001130141	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Missense_Mutation	SNP	ENST00000400314.1	hg19	CCDS42974.2	.	.	.	.	.	.	.	.	.	.	T	23.4	4.410186	0.83340	.	.	ENSG00000183570	ENST00000400314;ENST00000400310;ENST00000400309;ENST00000400308;ENST00000449640;ENST00000346743;ENST00000400305;ENST00000400304	T;T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13;0.13	5.74	5.74	0.90152	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.81997	0.4941	H	0.96175	3.78	0.80722	D	1	B;B;P;P;B;B;B	0.37330	0.21;0.304;0.59;0.497;0.176;0.403;0.304	P;B;P;B;B;P;B	0.53549	0.553;0.364;0.729;0.428;0.364;0.663;0.326	D	0.85695	0.1309	10	0.62326	D	0.03	-14.3865	16.0357	0.80628	0.0:0.0:0.0:1.0	.	162;194;162;194;194;194;194	Q5MJP6;P57721-3;E9PFP8;P57721-2;P57721-4;P57721;P57721-5	.;.;.;.;.;PCBP3_HUMAN;.	T	194;194;194;194;194;194;170;162	ENSP00000383168:I194T;ENSP00000383165:I194T;ENSP00000383164:I194T;ENSP00000383163:I194T;ENSP00000401198:I194T;ENSP00000383160:I170T;ENSP00000383159:I162T	ENSP00000330225:I194T	I	+	2	0	PCBP3	46155353	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.588000	0.82629	2.192000	0.70111	0.528000	0.53228	ATC	.	.		0.647	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2			C	47330925	T	C	47330925	3	2	44	1	0	0	0	0	1	0	0	0	11511	1435	50	2	607	2	PCBP3	21	47330925	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	1213108	47330925	798970	425	5885										
COL6A1	1291	hgsc.bcm.edu	37	chr21	47421253	47421253	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	acttcgagattgccaaggacTtcgtcgtcaaggtcatcgac	10	11	2	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr21:47421253T>C	ENST00000361866.3	+	30	2023	c.1909T>C	c.(1909-1911)Ttc>Ctc	p.F637L	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	637	C-terminal globular domain.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		TGCCAAGGACTTCGTCGTCAA	0.647																																					p.F637L		Atlas-SNP	.											.	COL6A1	101	.	0			c.T1909C						.						127	126	126					21																	47421253		2203	4300	6503	SO:0001583	missense	1291	exon30			AAGGACTTCGTCG	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"Collagens"	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.1909T>C	chr21.hg19:g.47421253T>C	ENSP00000355180:p.Phe637Leu	55.0	0.0		44.0	4.0	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	hg19	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	T	34	5.325800	0.95708	.	.	ENSG00000142156	ENST00000361866	D	0.86627	-2.15	5.2	5.2	0.72013	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.94178	0.8132	M	0.88775	2.98	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.94726	0.7905	10	0.52906	T	0.07	-14.4548	15.0511	0.71872	0.0:0.0:0.0:1.0	.	637	P12109	CO6A1_HUMAN	L	637	ENSP00000355180:F637L	ENSP00000355180:F637L	F	+	1	0	COL6A1	46245681	1.000000	0.71417	0.998000	0.56505	0.745000	0.42441	7.084000	0.76866	1.968000	0.57251	0.445000	0.29226	TTC	.	.		0.647	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		C	47421253	T	C	47421253	3	2	44	1	0	0	0	0	1	0	0	0	3701	1609	56	2	2027	2	COL6A1	21	47421253	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	90328	47421253	708642	426	5886										
LSS	4047	hgsc.bcm.edu	37	chr21	47636415	47636415	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	accagagtgtggaggggtgtGccggtgcccagtcaggaaac	17	9	1	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr21:47636415G>A	ENST00000397728.3	-	7	749	c.671C>T	c.(670-672)gCa>gTa	p.A224V	LSS_ENST00000464357.1_5'UTR|LSS_ENST00000522411.1_Missense_Mutation_p.A213V|LSS_ENST00000457828.2_Missense_Mutation_p.A144V|LSS_ENST00000356396.4_Missense_Mutation_p.A224V	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	224					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					GGAGGGGTGTGCCGGTGCCCA	0.657																																					p.A224V	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.C671T						.						29	31	30					21																	47636415		2203	4300	6503	SO:0001583	missense	4047	exon7			GGGTGTGCCGGTG	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.671C>T	chr21.hg19:g.47636415G>A	ENSP00000380837:p.Ala224Val	107.0	0.0		93.0	4.0	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	hg19	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002397	0.74932	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411;ENST00000450351	T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19	5.58	5.58	0.84498	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.055632	0.64402	D	0.000001	T	0.24661	0.0598	L	0.31157	0.91	0.80722	D	1	P;P	0.40681	0.727;0.607	B;B	0.23574	0.047;0.021	T	0.04752	-1.0929	10	0.32370	T	0.25	.	19.156	0.93510	0.0:0.0:1.0:0.0	.	213;224	E9PEI9;P48449	.;ERG7_HUMAN	V	224;144;224;213;225	ENSP00000348762:A224V;ENSP00000409191:A144V;ENSP00000380837:A224V;ENSP00000429133:A213V;ENSP00000391368:A225V	ENSP00000348762:A224V	A	-	2	0	LSS	46460843	1.000000	0.71417	0.275000	0.24674	0.185000	0.23345	6.511000	0.73733	2.645000	0.89757	0.655000	0.94253	GCA	.	.		0.657	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			A	47636415	G	A	47636415	3	1	44	1	0	0	0	0	1	0	0	0	9074	1319	46	3	1591	3	LSS	21	47636415	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	215162	47636415	493480	427	5887										
THAP7	80764	hgsc.bcm.edu	37	chr22	21354223	21354223	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcctgcacatgctccttcagAgtctggcgggcatctgcctg	11	14	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr22:21354223A>G	ENST00000215742.4	-	4	1050	c.876T>C	c.(874-876)acT>acC	p.T292T	THAP7-AS1_ENST00000452284.1_RNA|THAP7-AS1_ENST00000429962.1_RNA|THAP7-AS1_ENST00000436079.1_RNA|THAP7_ENST00000399133.2_Silent_p.T292T	NM_030573.2	NP_085050.2	Q9BT49	THAP7_HUMAN	THAP domain containing 7	292					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nuclear speck (GO:0016607)	C2H2 zinc finger domain binding (GO:0070742)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)			cervix(1)|lung(2)|prostate(3)|skin(1)|stomach(1)	8	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			GCTCCTTCAGAGTCTGGCGGG	0.662																																					p.T292T		Atlas-SNP	.											.	THAP7	15	.	0			c.T876C						.						31	32	31					22																	21354223		2201	4298	6499	SO:0001819	synonymous_variant	80764	exon4			CTTCAGAGTCTGG	BC004346	CCDS13787.1	22q11.2	2013-01-25			ENSG00000184436	ENSG00000184436		"THAP (C2CH-type zinc finger) domain containing"	23190	protein-coding gene	gene with protein product		609518				12575992	Standard	NM_030573		Approved	MGC10963	uc002ztr.1	Q9BT49	OTTHUMG00000150879	ENST00000215742.4:c.876T>C	chr22.hg19:g.21354223A>G		143.0	0.0		140.0	6.0	NM_030573	B2RD97|D3DX40	Silent	SNP	ENST00000215742.4	hg19	CCDS13787.1																																																																																			.	.		0.662	THAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320405.1	NM_030573		G	21354223	A	G	21354223	2	3	44	1	0	0	0	0	0	0	0	1	15864	291	11	2		2	THAP7	22	21354223	Silent	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10		21354223	29950343	428	5888										
HPS4	89781	hgsc.bcm.edu	37	chr22	26860271	26860271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggccaggatggtcttcgagcTgctcttgggctccatgctgg	15	11	2	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr22:26860271T>C	ENST00000398145.2	-	11	1941	c.1325A>G	c.(1324-1326)cAg>cGg	p.Q442R	HPS4_ENST00000336873.5_Missense_Mutation_p.Q442R|HPS4_ENST00000493455.2_5'Flank|HPS4_ENST00000398141.1_Missense_Mutation_p.Q455R|HPS4_ENST00000402105.3_Missense_Mutation_p.Q437R	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	442					blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						GTCTTCGAGCTGCTCTTGGGC	0.617									Hermansky-Pudlak syndrome																												p.Q442R		Atlas-SNP	.											.	HPS4	123	.	0			c.A1325G						.						94	90	91					22																	26860271		2203	4300	6503	SO:0001583	missense	89781	exon11	Familial Cancer Database	HPS, HPS1-8	TCGAGCTGCTCTT		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099			15844	protein-coding gene	gene with protein product		606682				11836498, 12663659	Standard	NM_022081		Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.1325A>G	chr22.hg19:g.26860271T>C	ENSP00000381213:p.Gln442Arg	89.0	0.0		98.0	4.0	NM_022081	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Missense_Mutation	SNP	ENST00000398145.2	hg19	CCDS13835.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.261430	0.23051	.	.	ENSG00000100099	ENST00000398145;ENST00000398141;ENST00000402105;ENST00000336873;ENST00000312736;ENST00000422379	T;T;T;T;T	0.57273	1.48;1.46;1.48;1.48;0.41	4.83	-5.99	0.02213	.	1.684920	0.02902	N	0.135548	T	0.44244	0.1284	M	0.67953	2.075	0.09310	N	1	B;B;B;B;B;B	0.14012	0.002;0.002;0.009;0.004;0.004;0.009	B;B;B;B;B;B	0.12156	0.004;0.004;0.007;0.007;0.006;0.007	T	0.34477	-0.9827	10	0.66056	D	0.02	0.005	0.6657	0.00850	0.3913:0.2059:0.1129:0.2899	.	442;442;442;442;455;437	Q6ICH6;Q6P1K3;Q9NQG7;A8K2E6;Q9NQG7-4;Q9NQG7-3	.;.;HPS4_HUMAN;.;.;.	R	442;455;437;442;460;460	ENSP00000381213:Q442R;ENSP00000381210:Q455R;ENSP00000384185:Q437R;ENSP00000338457:Q442R;ENSP00000415081:Q460R	ENSP00000325840:Q460R	Q	-	2	0	HPS4	25190271	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.360000	0.02600	-1.040000	0.03271	-0.438000	0.05819	CAG	.	.		0.617	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081		C	26860271	T	C	26860271	3	2	44	1	0	0	0	0	1	0	0	0	7350	1580	55	2	817	2	HPS4	22	26860271	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	5506048	26860271	24444295	429	5889										
EMID1	129080	hgsc.bcm.edu	37	chr22	29611591	29611591	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cgtgagtggaggtgctgcccTgggcactcaggagtgagctg	18	9	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr22:29611591T>C	ENST00000404820.3	+	3	418	c.291T>C	c.(289-291)ccT>ccC	p.P97P	EMID1_ENST00000404755.3_Silent_p.P97P|EMID1_ENST00000484039.1_3'UTR|EMID1_ENST00000334018.6_Silent_p.P97P			Q96A84	EMID1_HUMAN	EMI domain containing 1	97	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)|skin(3)	12						GGTGCTGCCCTGGGCACTCAG	0.637																																					p.P97P		Atlas-SNP	.											.	EMID1	33	.	0			c.T291C						.						96	88	90					22																	29611591		2203	4300	6503	SO:0001819	synonymous_variant	129080	exon3			CTGCCCTGGGCAC	AJ416090	CCDS33630.1	22q12.2	2009-08-04			ENSG00000186998	ENSG00000186998		"EMI domain containing"	18036	protein-coding gene	gene with protein product	"emilin and multimerin-domain containing protein 1", "putative emu1"	608926				12221002	Standard	NM_001267895		Approved	EMU1, hEmu1, EMI5	uc003aem.4	Q96A84	OTTHUMG00000151013	ENST00000404820.3:c.291T>C	chr22.hg19:g.29611591T>C		91.0	0.0		100.0	4.0	NM_001267895	B0QYK6|Q6ICG1|Q86SS7	Silent	SNP	ENST00000404820.3	hg19																																																																																				.	.		0.637	EMID1-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321075.1	NM_133455		C	29611591	T	C	29611591	2	2	44	1	0	0	0	0	0	0	0	1	5093	1567	55	2		2	EMID1	22	29611591	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	2751320	29611591	21692975	430	5890										
GCAT	23464	hgsc.bcm.edu	37	chr22	38204108	38204108	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccgcggagctggcacttggaAgagtgagcgggtcatcacgt	16	10	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr22:38204108A>G	ENST00000248924.6	+	1	190	c.134A>G	c.(133-135)aAg>aGg	p.K45R	GCAT_ENST00000323205.6_Missense_Mutation_p.K45R|GCAT_ENST00000415371.1_3'UTR	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	45					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	GGCACTTGGAAGAGTGAGCGG	0.682																																					p.K45R		Atlas-SNP	.											.	GCAT	27	.	0			c.A134G						.						30	20	24					22																	38204108		2192	4289	6481	SO:0001583	missense	23464	exon1			CTTGGAAGAGTGA	AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"2-amino-3-ketobutyrate coenzyme A ligase"	607422	"glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.134A>G	chr22.hg19:g.38204108A>G	ENSP00000248924:p.Lys45Arg	118.0	0.0		77.0	4.0	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Missense_Mutation	SNP	ENST00000248924.6	hg19	CCDS13957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	36|36	5.752845|5.752845	0.96890|0.96890	.|.	.|.	ENSG00000100116|ENSG00000100116	ENST00000323205;ENST00000248924;ENST00000445195;ENST00000394944|ENST00000451984	D;D;D|.	0.98666|.	-5.06;-3.3;-3.32|.	4.6|4.6	4.6|4.6	0.57074|0.57074	Pyridoxal phosphate-dependent transferase, major domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74658|0.74658	0.3745|0.3745	M|M	0.77616|0.77616	2.38|2.38	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.999|.	D;D|.	0.91635|.	0.999;0.996|.	T|T	0.76615|0.76615	-0.2894|-0.2894	10|5	0.87932|.	D|.	0|.	-25.2705|-25.2705	14.4519|14.4519	0.67392|0.67392	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	45;45|.	E2QC23;O75600|.	.;KBL_HUMAN|.	R|G	45|30	ENSP00000371110:K45R;ENSP00000248924:K45R;ENSP00000406719:K45R|.	ENSP00000248924:K45R|.	K|R	+|+	2|1	0|2	GCAT|GCAT	36534054|36534054	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	6.367000|6.367000	0.73099|0.73099	2.058000|2.058000	0.61347|0.61347	0.533000|0.533000	0.62120|0.62120	AAG|AGA	.	.		0.682	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2		G	38204108	A	G	38204108	3	3	44	1	0	0	0	0	1	0	0	0	6292	72	3	2	136	2	GCAT	22	38204108	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	8592517	38204108	13100458	431	5891										
SCUBE1	80274	hgsc.bcm.edu	37	chr22	43627876	43627876	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gttgttgaccaggcactcgtTgatgtctgtgggagccaagg	15	8	1	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr22:43627876T>C	ENST00000360835.4	-	8	976	c.850A>G	c.(850-852)Aac>Gac	p.N284D	Z82214.2_ENST00000419643.1_RNA	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	284	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				AGGCACTCGTTGATGTCTGTG	0.632																																					p.N284D		Atlas-SNP	.											.	SCUBE1	105	.	0			c.A850G						.						67	54	58					22																	43627876		2203	4300	6503	SO:0001583	missense	80274	exon8			ACTCGTTGATGTC		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.850A>G	chr22.hg19:g.43627876T>C	ENSP00000354080:p.Asn284Asp	207.0	0.0		77.0	4.0	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	hg19	CCDS14048.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.945|8.945	0.966837|0.966837	0.18659|0.18659	.|.	.|.	ENSG00000159307|ENSG00000159307	ENST00000360835;ENST00000434132|ENST00000449304	T|.	0.26810|.	1.71|.	4.47|4.47	3.44|3.44	0.39384|0.39384	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);|.	0.095657|.	0.64402|.	D|.	0.000001|.	T|T	0.20210|0.20210	0.0486|0.0486	N|N	0.02960|0.02960	-0.455|-0.455	0.80722|0.80722	D|D	1|1	B|.	0.02656|.	0.0|.	B|.	0.06405|.	0.002|.	T|T	0.06991|0.06991	-1.0796|-1.0796	10|5	0.02654|.	T|.	1|.	.|.	4.396|4.396	0.11363|0.11363	0.0:0.2678:0.0:0.7322|0.0:0.2678:0.0:0.7322	.|.	284|.	Q8IWY4|.	SCUB1_HUMAN|.	D|R	284|137	ENSP00000354080:N284D|.	ENSP00000354080:N284D|.	N|Q	-|-	1|2	0|0	SCUBE1|SCUBE1	41957820|41957820	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	5.732000|5.732000	0.68563|0.68563	2.002000|2.002000	0.58637|0.58637	0.459000|0.459000	0.35465|0.35465	AAC|CAA	.	.		0.632	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050		C	43627876	T	C	43627876	3	2	44	1	0	0	0	0	1	0	0	0	13959	1812	63	2	2176	2	SCUBE1	22	43627876	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	5423768	43627876	7676690	432	5892										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51143468	51143468	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ccagggtggcaaccgcctcgTcatgaaggttgtgtctgtga	14	10	2	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chr22:51143468T>C	ENST00000414786.2	+	16	2158	c.1931T>C	c.(1930-1932)gTc>gCc	p.V644A	SHANK3_ENST00000262795.3_Missense_Mutation_p.V674A|SHANK3_ENST00000445220.2_Missense_Mutation_p.V659A			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	658	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		AACCGCCTCGTCATGAAGGTT	0.612																																					p.V644A		Atlas-SNP	.											.	SHANK3	96	.	0			c.T1931C						.						96	112	106					22																	51143468		2174	4272	6446	SO:0001583	missense	85358	exon16			GCCTCGTCATGAA	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.1931T>C	chr22.hg19:g.51143468T>C	ENSP00000464552:p.Val644Ala	149.0	0.0		61.0	5.0	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	T	18.34	3.602988	0.66445	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.25250	1.81;1.81	4.43	4.43	0.53597	PDZ/DHR/GLGF (4);	.	.	.	.	T	0.21227	0.0511	N	0.25647	0.755	0.22096	N	0.999363	P;P	0.46142	0.873;0.775	B;P	0.46510	0.422;0.519	T	0.06625	-1.0816	9	0.38643	T	0.18	.	6.5334	0.22339	0.0:0.1074:0.0:0.8926	.	659;674	Q9BYB0;F2Z3L0	SHAN3_HUMAN;.	A	674;659	ENSP00000442518:V674A;ENSP00000446078:V659A	ENSP00000442518:V674A	V	+	2	0	SHANK3	49490334	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.081000	0.50120	1.869000	0.54173	0.482000	0.46254	GTC	.	.		0.612	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		C	51143468	T	C	51143468	3	2	44	1	0	0	0	0	1	0	0	0	14281	1667	58	2	2087	2	SHANK3	22	51143468	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	7515592	51143468	161098	433	5893										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	6069292	6069292	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gcataggggacccctaagtaCtgctccactggacccaagat	10	13	0	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chrX:6069292C>A	ENST00000381095.3	-	2	843	c.216G>T	c.(214-216)caG>caT	p.Q72H	NLGN4X_ENST00000381092.1_Missense_Mutation_p.Q72H|NLGN4X_ENST00000538097.1_Missense_Mutation_p.Q72H|NLGN4X_ENST00000275857.6_Missense_Mutation_p.Q72H|NLGN4X_ENST00000469740.1_5'UTR|NLGN4X_ENST00000381093.2_Missense_Mutation_p.Q72H	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	72					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						CCCCTAAGTACTGCTCCACTG	0.542																																					p.Q72H		Atlas-SNP	.											.	NLGN4X	191	.	0			c.G216T						.						96	83	88					X																	6069292		2203	4300	6503	SO:0001583	missense	57502	exon2			TAAGTACTGCTCC	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.216G>T	chrX.hg19:g.6069292C>A	ENSP00000370485:p.Gln72His	378.0	0.0		304.0	139.0	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.456250	0.63401	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34	4.2	-8.4	0.00965	Carboxylesterase, type B (1);	.	.	.	.	T	0.80757	0.4684	M	0.86268	2.805	0.48696	D	0.99969	D;D;D	0.89917	1.0;1.0;0.99	D;D;P	0.79784	0.984;0.993;0.795	D	0.87332	0.2325	9	0.62326	D	0.03	.	18.999	0.92826	0.0:0.7632:0.0:0.2368	.	72;72;72	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	H	72	ENSP00000370485:Q72H;ENSP00000370483:Q72H;ENSP00000275857:Q72H;ENSP00000370482:Q72H;ENSP00000439203:Q72H	ENSP00000275857:Q72H	Q	-	3	2	NLGN4X	6079292	0.044000	0.20184	0.773000	0.31616	0.903000	0.53119	-0.995000	0.03712	-2.273000	0.00681	-0.380000	0.06706	CAG	.	.		0.542	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		A	6069292	C	A	6069292	3	1	44	1	0	0	0	0	1	0	0	0	10473	564	20	3	2254	3	NLGN4X	23	6069292	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10		6069292	149201268	434	5894										
TCEANC	170082	hgsc.bcm.edu	37	chrX	13681572	13681572	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gtaattgacagaggaacactTttccttcccagctgggtgcg	11	10	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chrX:13681572T>A	ENST00000380600.1	+	2	1032	c.945T>A	c.(943-945)ctT>ctA	p.L315L	TCEANC_ENST00000314720.4_Silent_p.L345L|TCEANC_ENST00000490617.1_3'UTR|TCEANC_ENST00000545566.1_Silent_p.L315L|TCEANC_ENST00000544987.1_Silent_p.L315L			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	315					regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						GAGGAACACTTTTCCTTCCCA	0.423																																					p.L345L		Atlas-SNP	.											.	TCEANC	29	.	0			c.T1035A						.						50	41	44					X																	13681572		1913	4100	6013	SO:0001819	synonymous_variant	170082	exon4			AACACTTTTCCTT		CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.945T>A	chrX.hg19:g.13681572T>A		156.0	0.0		144.0	72.0	NM_152634	A6NI06|B2RDM3	Silent	SNP	ENST00000380600.1	hg19																																																																																				.	.		0.423	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055796.1	NM_152634		A	13681572	T	A	13681572	2	1	44	1	0	0	0	0	0	0	0	1	15693	1828	64	4		4	TCEANC	23	13681572	Silent	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	7612280	13681572	141588988	435	5895										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20194413	20194413	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	aggatcaaaatagaatgtatCttcaggcctgcccgttgcag	10	9	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chrX:20194413C>A	ENST00000379565.3	-	13	1264	c.1057G>T	c.(1057-1059)Gat>Tat	p.D353Y	RPS6KA3_ENST00000544447.1_Missense_Mutation_p.D325Y|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.D324Y|RPS6KA3_ENST00000540702.1_Missense_Mutation_p.D325Y	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	353	AGC-kinase C-terminal.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TAGAATGTATCTTCAGGCCTG	0.333																																					p.D353Y		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.G1057T						.						80	77	78					X																	20194413		2203	4300	6503	SO:0001583	missense	6197	exon13			ATGTATCTTCAGG	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1057G>T	chrX.hg19:g.20194413C>A	ENSP00000368884:p.Asp353Tyr	314.0	0.0		353.0	146.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.501688	0.85176	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.3	5.3	0.74995	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.91486	0.7312	H	0.95611	3.695	0.80722	D	1	P;D;B;D	0.76494	0.503;0.999;0.022;0.994	P;D;B;D	0.66847	0.803;0.947;0.097;0.927	D	0.94048	0.7315	10	0.72032	D	0.01	.	18.0569	0.89366	0.0:1.0:0.0:0.0	.	325;324;325;353	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	Y	353;325;324;325	ENSP00000368884:D353Y;ENSP00000440220:D325Y;ENSP00000368865:D324Y;ENSP00000444837:D325Y	ENSP00000368865:D324Y	D	-	1	0	RPS6KA3	20104334	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.346000	0.79347	2.198000	0.70561	0.513000	0.50165	GAT	.	.		0.333	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		A	20194413	C	A	20194413	3	1	44	1	0	0	0	0	1	0	0	0	13667	913	32	3	1205	3	RPS6KA3	23	20194413	Missense_Mutation	SNP	C	TCGA-BC-A3KG-01A-11D-A20W-10	6512841	20194413	135076147	436	5896										
ZNF157	7712	hgsc.bcm.edu	37	chrX	47272506	47272506	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cttccgaatgaagatgactcTcaataatcatcaaagaactc	5	10	3	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chrX:47272506T>C	ENST00000377073.3	+	4	1120	c.1034T>C	c.(1033-1035)cTc>cCc	p.L345P		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	345					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						AAGATGACTCTCAATAATCAT	0.418																																					p.L345P		Atlas-SNP	.											.	ZNF157	46	.	0			c.T1034C						.						42	38	39					X																	47272506		2203	4299	6502	SO:0001583	missense	7712	exon4			TGACTCTCAATAA	U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"Zinc fingers, C2H2-type", "-"	12942	protein-coding gene	gene with protein product		300024	"zinc finger protein 157 (HZF22)"			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.1034T>C	chrX.hg19:g.47272506T>C	ENSP00000366273:p.Leu345Pro	97.0	0.0		107.0	5.0	NM_003446	Q96LE9	Missense_Mutation	SNP	ENST00000377073.3	hg19	CCDS14278.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.104671	0.56291	.	.	ENSG00000147117	ENST00000377073	T	0.53857	0.6	3.18	3.18	0.36537	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.71500	0.3347	M	0.85197	2.74	0.51233	D	0.999912	D	0.89917	1.0	D	0.97110	1.0	T	0.74719	-0.3570	9	0.87932	D	0	.	9.0532	0.36389	0.0:0.0:0.0:1.0	.	345	P51786	ZN157_HUMAN	P	345	ENSP00000366273:L345P	ENSP00000366273:L345P	L	+	2	0	ZNF157	47157450	0.998000	0.40836	0.294000	0.24946	0.996000	0.88848	7.089000	0.76909	1.486000	0.48398	0.486000	0.48141	CTC	.	.		0.418	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446		C	47272506	T	C	47272506	3	2	44	1	0	0	0	0	1	0	0	0	17752	1551	54	2	1048	2	ZNF157	23	47272506	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	27078093	47272506	107998054	437	5897										
WNK3	65267	hgsc.bcm.edu	37	chrX	54265313	54265313	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	cacactaccttgacggacttTtgatctcttgaaaaagctgg	8	10	1	3			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chrX:54265313T>C	ENST00000375159.2	-	17	3870	c.3871A>G	c.(3871-3873)Aaa>Gaa	p.K1291E	WNK3_ENST00000375169.3_Intron|WNK3_ENST00000354646.2_Missense_Mutation_p.K1291E			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1291					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						TGACGGACTTTTGATCTCTTG	0.383																																					p.K1291E		Atlas-SNP	.											.	WNK3	218	.	0			c.A3871G						.						85	72	76					X																	54265313		2203	4300	6503	SO:0001583	missense	65267	exon18			GGACTTTTGATCT	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.3871A>G	chrX.hg19:g.54265313T>C	ENSP00000364301:p.Lys1291Glu	84.0	0.0		95.0	4.0	NM_020922	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	hg19	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	T	15.38	2.817316	0.50633	.	.	ENSG00000196632	ENST00000354646;ENST00000375159	T;T	0.73575	-0.76;-0.76	5.03	5.03	0.67393	.	0.000000	0.56097	D	0.000027	T	0.66557	0.2801	L	0.27053	0.805	0.31471	N	0.668321	D	0.60575	0.988	P	0.52343	0.696	T	0.64097	-0.6487	10	0.05351	T	0.99	-16.7075	12.8618	0.57918	0.0:0.0:0.0:1.0	.	1291	Q9BYP7	WNK3_HUMAN	E	1291	ENSP00000346667:K1291E;ENSP00000364301:K1291E	ENSP00000346667:K1291E	K	-	1	0	WNK3	54282038	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.037000	0.57311	1.676000	0.50930	0.441000	0.28932	AAA	.	.		0.383	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		C	54265313	T	C	54265313	3	2	44	1	0	0	0	0	1	0	0	0	17394	1850	64	2	1559	2	WNK3	23	54265313	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	6992807	54265313	101005247	438	5898										
DCAF12L2	340578	hgsc.bcm.edu	37	chrX	125299293	125299293	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	gagccgctcacagctacggtGtcactcagccaggcgactgc	12	15	3	0			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chrX:125299293G>T	ENST00000360028.2	-	1	641	c.615C>A	c.(613-615)gaC>gaA	p.D205E	DCAF12L2_ENST00000538699.1_Missense_Mutation_p.D205E			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	205										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						CAGCTACGGTGTCACTCAGCC	0.652																																					p.D205E		Atlas-SNP	.											.	DCAF12L2	157	.	0			c.C615A						.						47	49	48					X																	125299293		2203	4299	6502	SO:0001583	missense	340578	exon1			TACGGTGTCACTC	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"WD repeat domain containing"	32950	protein-coding gene	gene with protein product			"WD repeat domain 40C"	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.615C>A	chrX.hg19:g.125299293G>T	ENSP00000353128:p.Asp205Glu	266.0	0.0		246.0	49.0	NM_001013628	B2RN42	Missense_Mutation	SNP	ENST00000360028.2	hg19	CCDS43991.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.102377	0.37145	.	.	ENSG00000198354	ENST00000538699;ENST00000360028	T;T	0.62788	0.0;0.0	3.87	2.05	0.26809	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.34959	N	0.003555	T	0.73737	0.3625	M	0.76170	2.325	0.35008	D	0.756662	D	0.89917	1.0	D	0.87578	0.998	T	0.77233	-0.2663	10	0.62326	D	0.03	.	7.1017	0.25340	0.244:0.0:0.756:0.0	.	205	Q5VW00	DC122_HUMAN	E	205	ENSP00000441489:D205E;ENSP00000353128:D205E	ENSP00000353128:D205E	D	-	3	2	DCAF12L2	125126974	1.000000	0.71417	0.908000	0.35775	0.044000	0.14063	1.602000	0.36783	0.409000	0.25649	0.544000	0.68410	GAC	.	.		0.652	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		T	125299293	G	T	125299293	3	4	44	1	0	0	0	0	1	0	0	0	4267	1368	48	3	780	3	DCAF12L2	23	125299293	Missense_Mutation	SNP	G	TCGA-BC-A3KG-01A-11D-A20W-10	71033980	125299293	29971267	439	5899										
MAGEC2	51438	hgsc.bcm.edu	37	chrX	141291446	141291446	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	ggactcctcactgaatgagcTccatgaaaaagaggagcagc	11	10	1	4			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chrX:141291446T>C	ENST00000247452.3	-	3	675	c.328A>G	c.(328-330)Agc>Ggc	p.S110G		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	110	Ser-rich.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					CTGAATGAGCTCCATGAAAAA	0.537										HNSCC(46;0.14)																											p.S110G		Atlas-SNP	.											.	MAGEC2	102	.	0			c.A328G						.						75	72	73					X																	141291446		2203	4300	6503	SO:0001583	missense	51438	exon3			ATGAGCTCCATGA	AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"cancer/testis antigen 10"	300468	"melanoma antigen, family E, 1, cancer/testis specific"	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.328A>G	chrX.hg19:g.141291446T>C	ENSP00000354660:p.Ser110Gly	68.0	0.0		91.0	4.0	NM_016249	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Missense_Mutation	SNP	ENST00000247452.3	hg19	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	7.177	0.588735	0.13812	.	.	ENSG00000046774	ENST00000247452	T	0.05139	3.49	1.16	-2.32	0.06745	Melanoma associated antigen, MAGE, N-terminal (1);	0.798826	0.10596	U	0.656147	T	0.03220	0.0094	N	0.19112	0.55	0.09310	N	1	P	0.36048	0.534	B	0.32864	0.154	T	0.35475	-0.9787	10	0.52906	T	0.07	.	2.1628	0.03829	0.0:0.2538:0.3243:0.4219	.	110	Q9UBF1	MAGC2_HUMAN	G	110	ENSP00000354660:S110G	ENSP00000354660:S110G	S	-	1	0	MAGEC2	141119112	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.797000	0.04570	-0.746000	0.04766	-0.451000	0.05528	AGC	.	.		0.537	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		C	141291446	T	C	141291446	3	2	44	1	0	0	0	0	1	0	0	0	9190	1551	54	2	797	2	MAGEC2	23	141291446	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	15992153	141291446	13979114	440	5900										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142717432	142717432	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcctcaggttcagtctagctAagggtgctccggaaaagatg	12	9	3	1			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chrX:142717432A>G	ENST00000381779.4	-	2	1718	c.1493T>C	c.(1492-1494)tTa>tCa	p.L498S	SLITRK4_ENST00000356928.1_Missense_Mutation_p.L498S|SLITRK4_ENST00000338017.4_Missense_Mutation_p.L498S	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	498						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					CAGTCTAGCTAAGGGTGCTCC	0.453																																					p.L498S		Atlas-SNP	.											.	SLITRK4	162	.	0			c.T1493C						.						103	108	106					X																	142717432		2203	4300	6503	SO:0001583	missense	139065	exon2			CTAGCTAAGGGTG	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.1493T>C	chrX.hg19:g.142717432A>G	ENSP00000371198:p.Leu498Ser	273.0	0.0		244.0	113.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.914539	0.52546	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.80653	-1.4;-1.4;-1.4	5.38	5.38	0.77491	.	0.000000	0.64402	U	0.000004	D	0.91270	0.7248	M	0.91561	3.22	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92915	0.6350	10	0.72032	D	0.01	-5.2205	13.372	0.60719	1.0:0.0:0.0:0.0	.	498	Q8IW52	SLIK4_HUMAN	S	498	ENSP00000371198:L498S;ENSP00000349400:L498S;ENSP00000336627:L498S	ENSP00000336627:L498S	L	-	2	0	SLITRK4	142545098	1.000000	0.71417	0.863000	0.33907	0.968000	0.65278	9.287000	0.95975	1.910000	0.55303	0.486000	0.48141	TTA	.	.		0.453	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		G	142717432	A	G	142717432	3	3	44	1	0	0	0	0	1	0	0	0	14760	372	13	2	1024	2	SLITRK4	23	142717432	Missense_Mutation	SNP	A	TCGA-BC-A3KG-01A-11D-A20W-10	1425986	142717432	12553128	441	5901										
PNMA3	29944	hgsc.bcm.edu	37	chrX	152226392	152226392	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0203619909502262	9	1	1.00189924815969	1.09466769706337	0.991397159604561	0.0111670480549199	0.241259836031806	0	tcctggtttcctggccctggTgaagctcctgcgtgaggagg	15	11	0	2			TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	g.chrX:152226392T>C	ENST00000370264.4	+	1	1006	c.980T>C	c.(979-981)gTg>gCg	p.V327A	PNMA3_ENST00000370265.4_Missense_Mutation_p.V327A|PNMA3_ENST00000447306.1_Missense_Mutation_p.V327A			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	327					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16	Acute lymphoblastic leukemia(192;6.56e-05)					ctggccctggtgaagctcctg	0.567																																					p.V327A		Atlas-SNP	.											.	PNMA3	81	.	0			c.T980C						.						40	41	40					X																	152226392		2203	4300	6503	SO:0001583	missense	29944	exon2			CCCTGGTGAAGCT	AF083116	CCDS35435.2, CCDS65344.1	Xq28	2012-02-09	2012-02-09		ENSG00000183837	ENSG00000183837		"Paraneoplastic Ma antigens"	18742	protein-coding gene	gene with protein product	"paraneoplastic cancer-testis-brain antigen"	300675	"paraneoplastic antigen MA3"			11558790	Standard	NM_013364		Approved	MA5, MA3, MGC132756, MGC132758	uc004fhc.2	Q9UL41	OTTHUMG00000024195	ENST00000370264.4:c.980T>C	chrX.hg19:g.152226392T>C	ENSP00000359286:p.Val327Ala	126.0	0.0		91.0	4.0	NM_013364	D3DWT7|Q9H0A4	Missense_Mutation	SNP	ENST00000370264.4	hg19	CCDS35435.2	.	.	.	.	.	.	.	.	.	.	t	13.13	2.144452	0.37825	.	.	ENSG00000183837	ENST00000370265;ENST00000447306;ENST00000370264	T;T;T	0.09817	2.94;2.94;2.94	1.67	1.67	0.24075	.	.	.	.	.	T	0.13457	0.0326	L	0.43152	1.355	0.09310	N	1	P	0.50943	0.94	P	0.50659	0.647	T	0.14420	-1.0473	9	0.66056	D	0.02	.	4.9316	0.13919	0.0:0.0:0.0:1.0	.	327	Q9UL41	PNMA3_HUMAN	A	327	ENSP00000359288:V327A;ENSP00000407642:V327A;ENSP00000359286:V327A	ENSP00000359286:V327A	V	+	2	0	PNMA3	151977048	0.007000	0.16637	0.004000	0.12327	0.098000	0.18820	1.989000	0.40707	0.923000	0.37045	0.237000	0.17872	GTG	.	.		0.567	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364		C	152226392	T	C	152226392	3	2	44	1	0	0	0	0	1	0	0	0	12164	1696	59	2	982	2	PNMA3	23	152226392	Missense_Mutation	SNP	T	TCGA-BC-A3KG-01A-11D-A20W-10	9508960	152226392	3044168	442	5902										
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77528719	77528719	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	accttttggacctgatgaatGtacaatgtacctctcccatg	7	11	1	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr1:77528719G>A	ENST00000477717.1	+	5	1074	c.839G>A	c.(838-840)tGt>tAt	p.C280Y		NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	280					glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						CCTGATGAATGTACAATGTAC	0.413																																					p.C280Y		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.G839A						.						137	132	134					1																	77528719		2203	4300	6503	SO:0001583	missense	81849	exon5			ATGAATGTACAAT		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.839G>A	chr1.hg19:g.77528719G>A	ENSP00000417583:p.Cys280Tyr	176.0	0.0		142.0	70.0	NM_030965	B1AK82	Missense_Mutation	SNP	ENST00000477717.1	hg19	CCDS673.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.687610	0.88639	.	.	ENSG00000117069	ENST00000477717;ENST00000438953	T	0.30448	1.53	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.55800	0.1943	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.58747	-0.7582	10	0.87932	D	0	-37.385	20.3422	0.98769	0.0:0.0:1.0:0.0	.	280	Q9BVH7	SIA7E_HUMAN	Y	280;190	ENSP00000417583:C280Y	ENSP00000406658:C190Y	C	+	2	0	ST6GALNAC5	77301307	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.414000	0.97362	2.810000	0.96702	0.655000	0.94253	TGT	.	.		0.413	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		A	77528719	G	A	77528719	3	1	45	1	0	0	0	0	1	0	0	0	15242	1377	48	3	857	3	ST6GALNAC5	1	77528719	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		77528719	171721902	1	5903										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109814047	109814047	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ttcgccgtcctcctgctgctGagcgccacgtggctgctggc	13	16	0	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr1:109814047G>A	ENST00000271332.3	+	27	7777	c.7716G>A	c.(7714-7716)ctG>ctA	p.L2572L	CELSR2_ENST00000498157.1_3'UTR	NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2572					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TCCTGCTGCTGAGCGCCACGT	0.632																																					p.L2572L	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.G7716A						.						97	82	87					1																	109814047		2203	4300	6503	SO:0001819	synonymous_variant	1952	exon27			GCTGCTGAGCGCC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.7716G>A	chr1.hg19:g.109814047G>A		179.0	0.0		154.0	76.0	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	hg19	CCDS796.1																																																																																			.	.		0.632	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		A	109814047	G	A	109814047	2	1	45	1	0	0	0	0	0	0	0	1	3224	1277	45	3		3	CELSR2	1	109814047	Silent	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	32285328	109814047	139436574	2	5904										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118535171	118535171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ggcgcatctgtagcacactgGggctcttgagtatggcaccc	13	12	2	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr1:118535171G>A	ENST00000336338.5	-	36	5344	c.5279C>T	c.(5278-5280)cCc>cTc	p.P1760L		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1760						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TAGCACACTGGGGCTCTTGAG	0.478																																					p.P1760L		Atlas-SNP	.											.	SPAG17	263	.	0			c.C5279T						.						110	105	107					1																	118535171		2203	4300	6503	SO:0001583	missense	200162	exon36			ACACTGGGGCTCT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5279C>T	chr1.hg19:g.118535171G>A	ENSP00000337804:p.Pro1760Leu	151.0	0.0		119.0	58.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252587	0.59212	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.74421	-0.84	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.84502	0.5486	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.85812	0.1380	10	0.87932	D	0	.	18.3968	0.90502	0.0:0.0:1.0:0.0	.	1760	Q6Q759	SPG17_HUMAN	L	1760;240	ENSP00000337804:P1760L	ENSP00000337804:P1760L	P	-	2	0	SPAG17	118336694	1.000000	0.71417	0.318000	0.25279	0.215000	0.24574	4.648000	0.61425	2.634000	0.89283	0.655000	0.94253	CCC	.	.		0.478	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118535171	G	A	118535171	3	1	45	1	0	0	0	0	1	0	0	0	14994	1232	43	3	1444	3	SPAG17	1	118535171	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	8721124	118535171	130715450	3	5905										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1371215	1371215	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	cggcttcatggacagtcagaGtcttgccagaaaatacatgt	10	9	3	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr2:1371215G>T	ENST00000308624.5	+	17	1718	c.1589G>T	c.(1588-1590)aGt>aTt	p.S530I	SNTG2_ENST00000407292.1_Missense_Mutation_p.S403I	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	530					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		GACAGTCAGAGTCTTGCCAGA	0.463																																					p.S530I		Atlas-SNP	.											.	SNTG2	125	.	0			c.G1589T						.						55	52	53					2																	1371215		692	1591	2283	SO:0001583	missense	54221	exon17			GTCAGAGTCTTGC	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.1589G>T	chr2.hg19:g.1371215G>T	ENSP00000311837:p.Ser530Ile	157.0	0.0		235.0	53.0	NM_018968	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	hg19	CCDS46220.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.912658	0.52439	.	.	ENSG00000172554	ENST00000308624;ENST00000407292	T;T	0.71341	0.98;-0.56	4.91	4.91	0.64330	.	0.048636	0.85682	D	0.000000	T	0.81307	0.4795	M	0.69823	2.125	0.58432	D	0.999998	D;P	0.59767	0.986;0.933	P;P	0.58454	0.839;0.486	D	0.84132	0.0412	10	0.72032	D	0.01	.	17.7172	0.88341	0.0:0.0:1.0:0.0	.	403;530	Q9NY99-2;Q9NY99	.;SNTG2_HUMAN	I	530;403	ENSP00000311837:S530I;ENSP00000385020:S403I	ENSP00000311837:S530I	S	+	2	0	SNTG2	1350222	1.000000	0.71417	0.921000	0.36526	0.079000	0.17450	5.389000	0.66255	2.247000	0.74100	0.655000	0.94253	AGT	.	.		0.463	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		T	1371215	G	T	1371215	3	4	45	1	0	0	0	0	1	0	0	0	14890	1029	36	3	1655	3	SNTG2	2	1371215	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		1371215	241828158	4	5906										
THADA	63892	hgsc.bcm.edu	37	chr2	43779386	43779386	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tcctgttatacagtggactcGcccatacattggaaatgctg	9	10	0	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr2:43779386G>A	ENST00000405006.4	-	18	3118	c.2767C>T	c.(2767-2769)Cga>Tga	p.R923*	THADA_ENST00000415080.2_Nonsense_Mutation_p.R633*|THADA_ENST00000330266.7_Nonsense_Mutation_p.R633*|THADA_ENST00000405975.2_Nonsense_Mutation_p.R923*|THADA_ENST00000402360.2_Nonsense_Mutation_p.R923*	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	923								p.R923*(1)		breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				CAGTGGACTCGCCCATACATT	0.408																																					p.R923X		Atlas-SNP	.											THADA,NS,carcinoma,0,1	THADA	131	.	1	Substitution - Nonsense(1)	lung(1)	c.C2767T						.						55	56	56					2																	43779386		1940	4132	6072	SO:0001587	stop_gained	63892	exon18			GGACTCGCCCATA	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.2767C>T	chr2.hg19:g.43779386G>A	ENSP00000385995:p.Arg923*	179.0	0.0		319.0	229.0	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Nonsense_Mutation	SNP	ENST00000405006.4	hg19	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	G	36	5.951656	0.97139	.	.	ENSG00000115970	ENST00000330266;ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006;ENST00000402360	.	.	.	5.56	3.72	0.42706	.	0.071578	0.56097	D	0.000032	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	8.8461	0.35170	0.0736:0.0:0.5989:0.3275	.	.	.	.	X	633;923;924;633;923;923	.	ENSP00000331105:R633X	R	-	1	2	THADA	43632890	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	2.171000	0.42453	0.780000	0.33566	0.591000	0.81541	CGA	.	.		0.408	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		A	43779386	G	A	43779386	4	1	45	1	0	0	0	0	0	1	0	0	15855	1095	38	1	3178	1	THADA	2	43779386	Nonsense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	42408171	43779386	199419987	5	5907										
KDM3A	55818	hgsc.bcm.edu	37	chr2	86669229	86669229	+	Frame_Shift_Del	DEL	T	T	-													0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ggggaggaggtttctcagtcTgtccgcagccgacggcagcg							TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr2:86669229delT	ENST00000409556.1	+	3	424	c.59delT	c.(58-60)ctgfs	p.L20fs	KDM3A_ENST00000542128.1_Frame_Shift_Del_p.L20fs|KDM3A_ENST00000409064.1_Frame_Shift_Del_p.L20fs|KDM3A_ENST00000312912.5_Frame_Shift_Del_p.L20fs			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	20					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						TTTCTCAGTCTGTCCGCAGCC	0.632																																					p.L20fs	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-Indel,Pindel	.											.	KDM3A	179	.	0			c.58delC						.						79	80	79					2																	86669229		2203	4300	6503	SO:0001589	frameshift_variant	55818	exon2			.	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"Chromatin-modifying enzymes / K-demethylases"	20815	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 2A"	611512	"jumonji domain containing 1", "jumonji domain containing 1A"	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.59delT	chr2.hg19:g.86669229delT	ENSP00000386660:p.Leu20fs	159.0	0.0		92.0	58.0	NM_018433	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Frame_Shift_Del	DEL	ENST00000409556.1	hg19	CCDS1990.1																																																																																			.	.		0.632	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		-	86669229	T	-	86669229	7	5	45	1	0	1	0	1	0	0	0	0	8135	1580	55	0	61	0	KDM3A	2	86669229	Frame_Shift_Del	DEL	T	TCGA-BC-A5W4-01A-11D-A28X-10	42889843	86669229	156530144	6	5908										
CCDC74B	91409	hgsc.bcm.edu	37	chr2	130898811	130898811	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tcttccaggtccgccttctgGgggacgtcagcttttgaatc	11	12	3	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr2:130898811G>T	ENST00000310463.6	-	4	740	c.603C>A	c.(601-603)ccC>ccA	p.P201P	MED15P9_ENST00000427638.1_RNA|CCDC74B_ENST00000409943.3_Silent_p.P135P|CCDC74B_ENST00000392984.3_Silent_p.P303P|CCDC74B_ENST00000409128.1_Silent_p.P177P	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	201								p.P201P(1)		endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					CCGCCTTCTGGGGGACGTCAG	0.592																																					p.P201P		Atlas-SNP	.											CCDC74B,NS,carcinoma,0,1	CCDC74B	27	.	1	Substitution - coding silent(1)	endometrium(1)	c.C603A						.						163	115	131					2																	130898811		2203	4276	6479	SO:0001819	synonymous_variant	91409	exon4			CTTCTGGGGGACG		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.603C>A	chr2.hg19:g.130898811G>T		230.0	1.0		158.0	75.0	NM_207310	Q6NW18	Silent	SNP	ENST00000310463.6	hg19	CCDS2155.1																																																																																			.	.		0.592	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310		T	130898811	G	T	130898811	2	4	45	1	0	0	0	0	0	0	0	1	2850	1219	43	3		3	CCDC74B	2	130898811	Silent	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	44229582	130898811	112300562	7	5909										
ITGB6	3694	hgsc.bcm.edu	37	chr2	161055767	161055767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tgcacctcccagggcacagcCacctaggtttagacccagca	9	16	0	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr2:161055767C>T	ENST00000283249.2	-	2	301	c.64G>A	c.(64-66)Ggc>Agc	p.G22S	ITGB6_ENST00000409872.1_Missense_Mutation_p.G22S|ITGB6_ENST00000409967.2_Missense_Mutation_p.G22S|ITGB6_ENST00000428609.2_Intron|ITGB6_ENST00000485635.1_Intron	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	22					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						AGGGCACAGCCACCTAGGTTT	0.458																																					p.G22S		Atlas-SNP	.											.	ITGB6	68	.	0			c.G64A						.						73	71	72					2																	161055767		2203	4300	6503	SO:0001583	missense	3694	exon2			CACAGCCACCTAG		CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"Integrins"	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.64G>A	chr2.hg19:g.161055767C>T	ENSP00000283249:p.Gly22Ser	587.0	1.0		474.0	92.0	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Missense_Mutation	SNP	ENST00000283249.2	hg19	CCDS2212.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.819480	0.50633	.	.	ENSG00000115221	ENST00000283249;ENST00000409967;ENST00000409872	D;D;D	0.84370	-1.84;-1.84;-1.84	5.68	4.7	0.59300	.	0.291814	0.35903	N	0.002902	T	0.49541	0.1563	N	0.00382	-1.575	0.32350	N	0.558545	B	0.02656	0.0	B	0.04013	0.001	T	0.57189	-0.7854	10	0.09843	T	0.71	.	3.7443	0.08542	0.0:0.6614:0.0:0.3386	.	22	P18564	ITB6_HUMAN	S	22	ENSP00000283249:G22S;ENSP00000386828:G22S;ENSP00000386367:G22S	ENSP00000283249:G22S	G	-	1	0	ITGB6	160764013	0.994000	0.37717	1.000000	0.80357	0.976000	0.68499	1.849000	0.39318	2.688000	0.91661	0.563000	0.77884	GGC	.	.		0.458	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888		T	161055767	C	T	161055767	3	4	45	1	0	0	0	0	1	0	0	0	7908	594	21	3	2358	3	ITGB6	2	161055767	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	30156956	161055767	82143606	8	5910										
AGPS	8540	hgsc.bcm.edu	37	chr2	178301722	178301722	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	aaacaggtcattgtcttcatGagatatttttgctcagggaa	9	6	4	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr2:178301722G>C	ENST00000264167.4	+	5	723	c.577G>C	c.(577-579)Gag>Cag	p.E193Q	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	193					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			TTGTCTTCATGAGATATTTTT	0.294																																					p.E193Q		Atlas-SNP	.											AGPS,NS,carcinoma,0,1	AGPS	56	.	0			c.G577C						.						113	118	116					2																	178301722		2203	4299	6502	SO:0001583	missense	8540	exon5			CTTCATGAGATAT	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.577G>C	chr2.hg19:g.178301722G>C	ENSP00000264167:p.Glu193Gln	48.0	0.0		44.0	2.0	NM_003659	A5D8U9|Q2TU35	Missense_Mutation	SNP	ENST00000264167.4	hg19	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.446194	0.84101	.	.	ENSG00000018510	ENST00000264167;ENST00000536686	D	0.81996	-1.56	5.06	5.06	0.68205	FAD-binding, type 2 (1);	0.000000	0.85682	D	0.000000	D	0.91395	0.7285	M	0.81802	2.56	0.80722	D	1	D	0.76494	0.999	D	0.70227	0.968	D	0.92388	0.5919	10	0.72032	D	0.01	.	18.7748	0.91907	0.0:0.0:1.0:0.0	.	193	O00116	ADAS_HUMAN	Q	193;63	ENSP00000264167:E193Q	ENSP00000264167:E193Q	E	+	1	0	AGPS	178009968	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.412000	0.90232	2.495000	0.84180	0.655000	0.94253	GAG	.	.		0.294	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			C	178301722	G	C	178301722	3	2	45	1	0	0	0	0	1	0	0	0	394	1291	45	4	595	4	AGPS	2	178301722	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	17245955	178301722	64897651	9	5911										
TTN	7273	hgsc.bcm.edu	37	chr2	179494983	179494983	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	cttacgcttaactcggaggtGggcactagatttaacattgg	11	8	0	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr2:179494983G>T	ENST00000591111.1	-	189	39567	c.39343C>A	c.(39343-39345)Cac>Aac	p.H13115N	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.H5883N|TTN_ENST00000589042.1_Missense_Mutation_p.H14756N|TTN_ENST00000342992.6_Missense_Mutation_p.H12188N|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.H5816N|TTN_ENST00000460472.2_Missense_Mutation_p.H5691N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13115					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.H12188N(2)|p.H5883N(1)|p.H5691N(1)|p.H5816N(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTCGGAGGTGGGCACTAGAT	0.388																																					p.H14756N		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,0,5	TTN	18412	.	5	Substitution - Missense(5)	lung(5)	c.C44266A						.						92	94	93					2																	179494983		1850	4087	5937	SO:0001583	missense	7273	exon239			GGAGGTGGGCACT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.39343C>A	chr2.hg19:g.179494983G>T	ENSP00000465570:p.His13115Asn	137.0	1.0		106.0	52.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.73	2.622476	0.46840	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	6.04	6.04	0.98038	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.17408	0.0418	N	0.02181	-0.65	0.46927	D	0.99925	P;P;P;P	0.44734	0.842;0.842;0.842;0.828	B;B;B;B	0.33750	0.169;0.169;0.169;0.169	T	0.30765	-0.9967	9	0.87932	D	0	.	20.5948	0.99439	0.0:0.0:1.0:0.0	.	5691;5816;5883;13115	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	12188;5691;5883;5816;5691	ENSP00000343764:H12188N;ENSP00000434586:H5691N;ENSP00000340554:H5883N;ENSP00000352154:H5816N	ENSP00000340554:H5883N	H	-	1	0	TTN	179203228	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	5.339000	0.65953	2.873000	0.98535	0.563000	0.77884	CAC	.	.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179494983	G	T	179494983	3	4	45	1	0	0	0	0	1	0	0	0	16750	1348	47	3	63923	3	TTN	2	179494983	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	1193261	179494983	63704390	10	5912										
ARMC9	80210	hgsc.bcm.edu	37	chr2	232087516	232087516	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ctaaagccagcaacacgccaAagcttttaacaatatatgta	5	10	0	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr2:232087516A>G	ENST00000349938.4	+	6	774	c.580A>G	c.(580-582)Aag>Gag	p.K194E	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	194						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		CAACACGCCAAAGCTTTTAAC	0.343																																					p.K194E		Atlas-SNP	.											.	ARMC9	129	.	0			c.A580G						.						66	67	66					2																	232087516		2201	4298	6499	SO:0001583	missense	80210	exon6			ACGCCAAAGCTTT	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"Armadillo repeat containing"	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.580A>G	chr2.hg19:g.232087516A>G	ENSP00000258417:p.Lys194Glu	131.0	0.0		125.0	56.0	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	hg19	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.196343	0.58126	.	.	ENSG00000135931	ENST00000349938;ENST00000359743	T	0.17213	2.29	5.59	5.59	0.84812	.	0.143260	0.64402	D	0.000007	T	0.12305	0.0299	N	0.22421	0.69	0.32951	D	0.519779	B	0.25351	0.124	B	0.21151	0.033	T	0.11867	-1.0570	10	0.32370	T	0.25	-20.9629	12.835	0.57767	0.8642:0.1358:0.0:0.0	.	194	Q7Z3E5	ARMC9_HUMAN	E	194	ENSP00000258417:K194E	ENSP00000258417:K194E	K	+	1	0	ARMC9	231795760	1.000000	0.71417	0.980000	0.43619	0.987000	0.75469	5.890000	0.69774	2.118000	0.64928	0.533000	0.62120	AAG	.	.		0.343	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139		G	232087516	A	G	232087516	3	3	45	1	0	0	0	0	1	0	0	0	958	15	1	2	598	2	ARMC9	2	232087516	Missense_Mutation	SNP	A	TCGA-BC-A5W4-01A-11D-A28X-10	52592533	232087516	11111857	11	5913										
ANO10	55129	hgsc.bcm.edu	37	chr3	43618347	43618347	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tccatgtcgaagtaaatcatCatgacatacagtgagaaata	7	7	2	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr3:43618347C>T	ENST00000292246.3	-	6	1169	c.999G>A	c.(997-999)atG>atA	p.M333I	ANO10_ENST00000451430.2_Missense_Mutation_p.M222I|ANO10_ENST00000414522.2_Missense_Mutation_p.M333I|ANO10_ENST00000396091.3_Missense_Mutation_p.M267I|ANO10_ENST00000350459.4_Intron	NM_018075.3	NP_060545.3	Q9NW15	ANO10_HUMAN	anoctamin 10	333					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)	p.M333I(1)		NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						AGTAAATCATCATGACATACA	0.512																																					p.M333I		Atlas-SNP	.											ANO10,NS,carcinoma,0,1	ANO10	70	.	1	Substitution - Missense(1)	lung(1)	c.G999A						.						108	83	91					3																	43618347		2203	4300	6503	SO:0001583	missense	55129	exon6			AATCATCATGACA	AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25519	protein-coding gene	gene with protein product		613726	"transmembrane protein 16K"	TMEM16K		12477932, 24692353	Standard	NM_001204831		Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000292246.3:c.999G>A	chr3.hg19:g.43618347C>T	ENSP00000292246:p.Met333Ile	288.0	0.0		202.0	92.0	NM_018075	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	Missense_Mutation	SNP	ENST00000292246.3	hg19	CCDS2710.2	.	.	.	.	.	.	.	.	.	.	C	32	5.131456	0.94473	.	.	ENSG00000160746	ENST00000292246;ENST00000396091;ENST00000414522;ENST00000451430	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.75722	0.3888	M	0.69523	2.12	0.80722	D	1	D;D;D;D	0.76494	0.986;0.999;0.992;0.998	D;D;D;D	0.79108	0.939;0.992;0.966;0.983	T	0.69774	-0.5054	10	0.02654	T	1	.	19.7321	0.96186	0.0:1.0:0.0:0.0	.	222;333;267;333	Q9NW15-4;C9JHS1;Q9NW15-3;Q9NW15	.;.;.;ANO10_HUMAN	I	333;267;333;222	ENSP00000292246:M333I;ENSP00000379398:M267I;ENSP00000396990:M333I;ENSP00000394119:M222I	ENSP00000292246:M333I	M	-	3	0	ANO10	43593351	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.668000	0.90789	0.655000	0.94253	ATG	.	.		0.512	ANO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256649.2	NM_018075		T	43618347	C	T	43618347	3	4	45	1	0	0	0	0	1	0	0	0	696	826	29	3	1015	3	ANO10	3	43618347	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10		43618347	154404083	12	5914										
CCDC71	64925	hgsc.bcm.edu	37	chr3	49200783	49200783	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	agcagctttggccagtgttcGagctaccttggcctgggctg	14	11	0	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr3:49200783G>C	ENST00000321895.6	-	2	965	c.859C>G	c.(859-861)Cga>Gga	p.R287G		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	287										endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCCAGTGTTCGAGCTACCTTG	0.632																																					p.R287G		Atlas-SNP	.											.	CCDC71	33	.	0			c.C859G						.						54	51	52					3																	49200783		2203	4300	6503	SO:0001583	missense	64925	exon2			GTGTTCGAGCTAC	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.859C>G	chr3.hg19:g.49200783G>C	ENSP00000319006:p.Arg287Gly	34.0	0.0		23.0	12.0	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Missense_Mutation	SNP	ENST00000321895.6	hg19	CCDS2790.1	.	.	.	.	.	.	.	.	.	.	G	2.713	-0.268423	0.05716	.	.	ENSG00000177352	ENST00000321895	T	0.32515	1.45	4.06	2.16	0.27623	.	1.271780	0.05558	N	0.568761	T	0.20455	0.0492	N	0.17474	0.49	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.27054	-1.0085	10	0.72032	D	0.01	-17.4736	5.7061	0.17909	0.1107:0.4019:0.4874:0.0	.	287	Q8IV32	CCD71_HUMAN	G	287	ENSP00000319006:R287G	ENSP00000319006:R287G	R	-	1	2	CCDC71	49175787	0.663000	0.27448	0.002000	0.10522	0.168000	0.22595	0.722000	0.25925	0.617000	0.30160	0.491000	0.48974	CGA	.	.		0.632	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903		C	49200783	G	C	49200783	3	2	45	1	0	0	0	0	1	0	0	0	2846	1066	37	4	548	4	CCDC71	3	49200783	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	5582436	49200783	148821647	13	5915										
MUSTN1	389125	hgsc.bcm.edu	37	chr3	52867655	52867655	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	cactctcgcatgacctggtaGgtcttggacttgatttcctg	10	11	2	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr3:52867655G>T	ENST00000446157.2	-	2	390	c.120C>A	c.(118-120)acC>acA	p.T40T	RP5-966M1.6_ENST00000513520.1_5'UTR|ITIH4_ENST00000266041.4_5'Flank|ITIH4_ENST00000346281.5_5'Flank|TMEM110-MUSTN1_ENST00000504329.1_Silent_p.T330T|MUSTN1_ENST00000486659.1_Silent_p.T45T|ITIH4_ENST00000406595.1_5'Flank|ITIH4_ENST00000485816.1_5'Flank|ITIH4_ENST00000434759.3_5'Flank|RP5-966M1.6_ENST00000468472.1_Silent_p.T40T	NM_205853.3	NP_995325	Q8IVN3	MSTN1_HUMAN	musculoskeletal, embryonic nuclear protein 1	40						nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	7				BRCA - Breast invasive adenocarcinoma(193;6.56e-05)|Kidney(197;0.000586)|KIRC - Kidney renal clear cell carcinoma(197;0.000755)|OV - Ovarian serous cystadenocarcinoma(275;0.0471)		TGACCTGGTAGGTCTTGGACT	0.592																																					p.T330T		Atlas-SNP	.											.	.	.	.	0			c.C990A						.						143	152	149					3																	52867655		1988	4167	6155	SO:0001819	synonymous_variant	100526772	exon9			CTGGTAGGTCTTG		CCDS46846.1	3p21.31	2004-03-10				ENSG00000272573			22144	protein-coding gene	gene with protein product							Standard	NM_205853		Approved	Mustang		Q8IVN3		ENST00000446157.2:c.120C>A	chr3.hg19:g.52867655G>T		96.0	0.0		99.0	43.0	NM_001198974		Silent	SNP	ENST00000446157.2	hg19	CCDS46846.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.738391	0.30774	.	.	ENSG00000243696	ENST00000513520	.	.	.	5.21	1.1	0.20463	.	.	.	.	.	T	0.51024	0.1650	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36456	-0.9747	4	.	.	.	-6.2345	4.9396	0.13958	0.0716:0.1143:0.3616:0.4526	.	.	.	.	I	3	.	.	L	-	1	2	MUSTN1	52842695	0.416000	0.25424	1.000000	0.80357	0.976000	0.68499	-0.425000	0.07017	0.206000	0.20587	0.455000	0.32223	CTA	.	.		0.592	MUSTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352933.2	XM_371644		T	52867655	G	T	52867655	2	4	45	1	0	0	0	0	0	0	0	1	9999	987	35	3		3	MUSTN1	3	52867655	Silent	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	3666872	52867655	145154775	14	5916										
FLNB	2317	hgsc.bcm.edu	37	chr3	58107094	58107094	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	atgcctagtgacacctgtgaCaggccgggagaacagcacgg	14	11	0	3			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr3:58107094C>G	ENST00000295956.4	+	20	3155	c.2990C>G	c.(2989-2991)aCa>aGa	p.T997R	FLNB_ENST00000493452.1_Missense_Mutation_p.T828R|FLNB_ENST00000419752.2_Missense_Mutation_p.T828R|FLNB_ENST00000358537.3_Missense_Mutation_p.T997R|FLNB_ENST00000357272.4_Missense_Mutation_p.T997R|FLNB_ENST00000348383.5_Missense_Mutation_p.T997R|FLNB_ENST00000490882.1_Missense_Mutation_p.T997R|FLNB_ENST00000429972.2_Missense_Mutation_p.T997R	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	997					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		ACACCTGTGACAGGCCGGGAG	0.627																																					p.T997R		Atlas-SNP	.											.	FLNB	430	.	0			c.C2990G						.						121	103	109					3																	58107094		2203	4300	6503	SO:0001583	missense	2317	exon20			CTGTGACAGGCCG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.2990C>G	chr3.hg19:g.58107094C>G	ENSP00000295956:p.Thr997Arg	153.0	0.0		103.0	52.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	C	8.977	0.974338	0.18736	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	T;T;T;T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05;1.05;1.05;1.05	5.99	3.26	0.37387	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.728589	0.13697	N	0.369101	T	0.20577	0.0495	N	0.04203	-0.255	0.09310	N	1	B;B;B;B;B;B	0.21147	0.042;0.03;0.052;0.002;0.052;0.052	B;B;B;B;B;B	0.28784	0.056;0.034;0.094;0.02;0.094;0.094	T	0.29971	-0.9994	10	0.16420	T	0.52	.	8.1735	0.31268	0.0:0.666:0.0:0.334	.	997;997;828;828;997;997	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	R	997;997;997;997;997;997;828;828	ENSP00000295956:T997R;ENSP00000420213:T997R;ENSP00000351339:T997R;ENSP00000415599:T997R;ENSP00000232447:T997R;ENSP00000349819:T997R;ENSP00000418510:T828R;ENSP00000414532:T828R	ENSP00000295956:T997R	T	+	2	0	FLNB	58082134	0.000000	0.05858	0.001000	0.08648	0.879000	0.50718	0.205000	0.17356	0.877000	0.35895	0.655000	0.94253	ACA	.	.		0.627	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		G	58107094	C	G	58107094	3	3	45	1	0	0	0	0	1	0	0	0	5942	478	17	4	3068	4	FLNB	3	58107094	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	5239439	58107094	139915336	15	5917										
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73433851	73433851	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tcggccgaaatgaaagactcGttgctgaagggcaggtcgcc	14	10	0	3	rs553747931		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr3:73433851G>A	ENST00000263666.4	-	10	1980	c.1866C>T	c.(1864-1866)aaC>aaT	p.N622N	PDZRN3_ENST00000462146.2_Silent_p.N279N|PDZRN3_ENST00000535920.1_Silent_p.N344N|PDZRN3_ENST00000466780.1_Silent_p.N279N|PDZRN3_ENST00000479530.1_Silent_p.N339N|PDZRN3_ENST00000466348.1_5'Flank	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	622					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TGAAAGACTCGTTGCTGAAGG	0.667													G|||	1	0.000199681	8e-04	0	5008	,	,		18231	0		0	False		,,,				2504	0				p.N622N		Atlas-SNP	.											PDZRN3,colon,carcinoma,0,1	PDZRN3	196	.	0			c.C1866T						.						77	78	78					3																	73433851		2203	4300	6503	SO:0001819	synonymous_variant	23024	exon10			AGACTCGTTGCTG	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.1866C>T	chr3.hg19:g.73433851G>A		111.0	1.0		55.0	26.0	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	hg19	CCDS33789.1	.	.	.	.	.	.	.	.	.	.	G	6.175	0.400531	0.11696	.	.	ENSG00000121440	ENST00000494559	.	.	.	4.77	-3.32	0.04973	.	.	.	.	.	T	0.50854	0.1640	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47129	-0.9141	4	.	.	.	.	7.7794	0.29056	0.4812:0.0:0.4142:0.1047	.	.	.	.	M	219	.	.	T	-	2	0	PDZRN3	73516541	0.001000	0.12720	0.969000	0.41365	0.954000	0.61252	-2.013000	0.01450	-0.581000	0.05937	-0.140000	0.14226	ACG	.	.		0.667	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		A	73433851	G	A	73433851	2	1	45	1	0	0	0	0	0	0	0	1	11718	1136	40	1		1	PDZRN3	3	73433851	Silent	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	15326757	73433851	124588579	16	5918										
EPHA6	285220	hgsc.bcm.edu	37	chr3	97194245	97194245	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	attctcgtgatagccaccgcCgctgttggcggattcactct	10	13	3	1	rs372907476		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr3:97194245C>T	ENST00000514100.1	+	5	362	c.120C>T	c.(118-120)gcC>gcT	p.A40A	EPHA6_ENST00000502694.1_Silent_p.A40A|EPHA6_ENST00000389672.5_Silent_p.A648A|EPHA6_ENST00000442602.2_Silent_p.A14A	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	554	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						TAGCCACCGCCGCTGTTGGCG	0.418																																					p.A648A		Atlas-SNP	.											.	EPHA6	439	.	0			c.C1944T						.	C	,	1,3819		0,1,1909	78	81	80		1944,120	-12.1	0	3		80	0,8252		0,0,4126	no	coding-synonymous,coding-synonymous	EPHA6	NM_001080448.2,NM_173655.2	,	0,1,6035	TT,TC,CC		0.0,0.0262,0.0083	,	648/1131,40/335	97194245	1,12071	1910	4126	6036	SO:0001819	synonymous_variant	285220	exon8			CACCGCCGCTGTT	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000514100.1:c.120C>T	chr3.hg19:g.97194245C>T		89.0	0.0		83.0	14.0	NM_001080448	D6RAL5	Silent	SNP	ENST00000514100.1	hg19																																																																																				.	.		0.418	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448		T	97194245	C	T	97194245	2	4	45	1	0	0	0	0	0	0	0	1	5173	639	23	1		1	EPHA6	3	97194245	Silent	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	23760394	97194245	100828185	17	5919										
LRRC33	375387	hgsc.bcm.edu	37	chr3	196386948	196386948	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	cttgtcaggaaacgccctgaCggaggacatggcagccctca	12	13	2	1	rs368543951		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr3:196386948C>T	ENST00000328557.4	+	3	637	c.434C>T	c.(433-435)aCg>aTg	p.T145M		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	145					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											AACGCCCTGACGGAGGACATG	0.657																																					p.T145M		Atlas-SNP	.											LRRC33,caecum,carcinoma,0,1	LRRC33	91	.	0			c.C434T						.	C	MET/THR	0,4406		0,0,2203	28	30	29		434	6.2	1	3		29	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRRC33	NM_198565.1	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	145/693	196386948	1,13005	2203	4300	6503	SO:0001583	missense	375387	exon3			CCCTGACGGAGGA	AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"leucine rich repeat containing 33"	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.434C>T	chr3.hg19:g.196386948C>T	ENSP00000328625:p.Thr145Met	97.0	1.0		43.0	7.0	NM_198565		Missense_Mutation	SNP	ENST00000328557.4	hg19	CCDS3319.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405404	0.62288	0.0	1.16E-4	ENSG00000174004	ENST00000328557	T	0.01113	5.32	6.17	6.17	0.99709	.	0.292555	0.38381	N	0.001718	T	0.06690	0.0171	M	0.83118	2.625	0.80722	D	1	D	0.76494	0.999	D	0.63033	0.91	T	0.00115	-1.2038	10	0.87932	D	0	.	13.4429	0.61123	0.1239:0.7567:0.1194:0.0	.	145	Q86YC3	LRC33_HUMAN	M	145	ENSP00000328625:T145M	ENSP00000328625:T145M	T	+	2	0	LRRC33	197871345	0.768000	0.28519	0.990000	0.47175	0.909000	0.53808	1.506000	0.35747	2.941000	0.99782	0.655000	0.94253	ACG	.	.		0.657	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565		T	196386948	C	T	196386948	3	4	45	1	0	0	0	0	1	0	0	0	8997	536	19	1	440	1	LRRC33	3	196386948	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	99192703	196386948	1635482	18	5920										
WDR1	9948	hgsc.bcm.edu	37	chr4	10077080	10077080	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tgctcgtccagccaggccagGctgctgacatggtgcagccg	14	14	0	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr4:10077080G>A	ENST00000499869.2	-	15	1936	c.1743C>T	c.(1741-1743)agC>agT	p.S581S	WDR1_ENST00000382452.2_Silent_p.S581S|WDR1_ENST00000515743.1_5'UTR|WDR1_ENST00000502702.1_Silent_p.S441S|RP11-448G15.3_ENST00000561486.1_RNA|WDR1_ENST00000382451.2_Silent_p.S441S			O75083	WDR1_HUMAN	WD repeat domain 1	581					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		GCCAGGCCAGGCTGCTGACAT	0.557																																					p.S581S		Atlas-SNP	.											.	WDR1	93	.	0			c.C1743T						.						47	53	51					4																	10077080		2123	4233	6356	SO:0001819	synonymous_variant	9948	exon15			GGCCAGGCTGCTG	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"WD repeat domain containing"	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.1743C>T	chr4.hg19:g.10077080G>A		387.0	1.0		200.0	68.0	NM_017491	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Silent	SNP	ENST00000499869.2	hg19	CCDS54740.1																																																																																			.	.		0.557	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1			A	10077080	G	A	10077080	2	1	45	1	0	0	0	0	0	0	0	1	17287	1194	42	3		3	WDR1	4	10077080	Silent	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		10077080	181077196	19	5921										
ARL9	132946	hgsc.bcm.edu	37	chr4	57389953	57389953	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ggaagatgttcttgtttggaAcctacctgactaagaatggc	11	7	1	3			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr4:57389953A>G	ENST00000360096.2	+	4	597	c.283A>G	c.(283-285)Acc>Gcc	p.T95A		NM_206919.1	NP_996802.1	Q6T311	ARL9_HUMAN	ADP-ribosylation factor-like 9	159					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			lung(2)	2	Glioma(25;0.08)|all_neural(26;0.101)					CTTGTTTGGAACCTACCTGAC	0.468																																					p.T95A		Atlas-SNP	.											.	ARL9	10	.	0			c.A283G						.						134	128	130					4																	57389953		2010	4180	6190	SO:0001583	missense	132946	exon4			TTTGGAACCTACC	AY439003	CCDS59474.1	4q12	2014-05-09				ENSG00000196503		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	23592	protein-coding gene	gene with protein product		612405					Standard	NM_206919		Approved		uc003hby.1	Q6T311		ENST00000360096.2:c.283A>G	chr4.hg19:g.57389953A>G	ENSP00000353210:p.Thr95Ala	201.0	0.0		91.0	80.0	NM_206919		Missense_Mutation	SNP	ENST00000360096.2	hg19	CCDS59474.1	.	.	.	.	.	.	.	.	.	.	A	17.54	3.414259	0.62511	.	.	ENSG00000196503	ENST00000360096	.	.	.	5.32	5.32	0.75619	.	0.092344	0.85682	D	0.000000	T	0.68430	0.3000	L	0.42008	1.315	0.48511	D	0.999666	D	0.89917	1.0	D	0.91635	0.999	T	0.75096	-0.3438	8	0.56958	D	0.05	-19.5799	13.5348	0.61641	1.0:0.0:0.0:0.0	.	159	Q6T311	ARL9_HUMAN	A	159	.	ENSP00000353210:T159A	T	+	1	0	ARL9	57084710	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.257000	0.78362	2.133000	0.65898	0.455000	0.32223	ACC	.	.		0.468	ARL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467724.1	NM_206919		G	57389953	A	G	57389953	3	3	45	1	0	0	0	0	1	0	0	0	948	43	2	2	293	2	ARL9	4	57389953	Missense_Mutation	SNP	A	TCGA-BC-A5W4-01A-11D-A28X-10	47312873	57389953	133764323	20	5922										
VCAN	1462	hgsc.bcm.edu	37	chr5	82835447	82835447	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	agtcacattttttcttagctActgcattagtaactgaatct	5	8	3	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr5:82835447A>C	ENST00000265077.3	+	8	7190	c.6625A>C	c.(6625-6627)Act>Cct	p.T2209P	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Missense_Mutation_p.T1222P|VCAN_ENST00000342785.4_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2209	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	TTTCTTAGCTACTGCATTAGT	0.378																																					p.T2209P		Atlas-SNP	.											.	VCAN	498	.	0			c.A6625C						.						92	89	90					5																	82835447		2203	4300	6503	SO:0001583	missense	1462	exon8			TTAGCTACTGCAT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.6625A>C	chr5.hg19:g.82835447A>C	ENSP00000265077:p.Thr2209Pro	123.0	0.0		109.0	58.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	8.926	0.962297	0.18583	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	T;T;T	0.34472	1.36;1.36;3.02	5.93	-5.58	0.02512	.	0.761271	0.12327	N	0.478717	T	0.22475	0.0542	L	0.60455	1.87	0.09310	N	0.999999	B;B	0.29188	0.236;0.016	B;B	0.22386	0.039;0.003	T	0.29427	-1.0012	10	0.66056	D	0.02	.	0.5685	0.00691	0.3764:0.2353:0.1566:0.2317	.	1222;2209	P13611-2;P13611	.;CSPG2_HUMAN	P	2209;1222;1222	ENSP00000265077:T2209P;ENSP00000340062:T1222P;ENSP00000426251:T1222P	ENSP00000265077:T2209P	T	+	1	0	VCAN	82871203	0.000000	0.05858	0.015000	0.15790	0.026000	0.11368	-0.428000	0.06991	-0.514000	0.06488	-0.256000	0.11100	ACT	.	.		0.378	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		C	82835447	A	C	82835447	3	2	45	1	0	0	0	0	1	0	0	0	17153	391	14	5	6651	5	VCAN	5	82835447	Missense_Mutation	SNP	A	TCGA-BC-A5W4-01A-11D-A28X-10		82835447	98079813	21	5923										
GFRA3	2676	hgsc.bcm.edu	37	chr5	137593407	137593407	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	cggcagcgcgcagttgggggCgatggtgttgcgccggcgct	20	11	0	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr5:137593407C>T	ENST00000274721.3	-	4	952	c.706G>A	c.(706-708)Gcc>Acc	p.A236T	GFRA3_ENST00000378362.3_Missense_Mutation_p.A205T	NM_001496.3	NP_001487.2	O60609	GFRA3_HUMAN	GDNF family receptor alpha 3	236					nervous system development (GO:0007399)|neuron migration (GO:0001764)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extrinsic component of membrane (GO:0019898)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|receptor binding (GO:0005102)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CAGTTGGGGGCGATGGTGTTG	0.697																																					p.A236T		Atlas-SNP	.											GFRA3,colon,carcinoma,0,1	GFRA3	36	.	0			c.G706A						.						13	16	15					5																	137593407		2183	4260	6443	SO:0001583	missense	2676	exon4			TGGGGGCGATGGT	AY358997	CCDS4201.1	5q31.1-q31.3	2008-02-05			ENSG00000146013	ENSG00000146013			4245	protein-coding gene	gene with protein product		605710				9407096	Standard	NM_001496		Approved	GFRa-3	uc003lcn.3	O60609	OTTHUMG00000129200	ENST00000274721.3:c.706G>A	chr5.hg19:g.137593407C>T	ENSP00000274721:p.Ala236Thr	15.0	0.0		8.0	5.0	NM_001496	B2RA36|B4DMY9|Q6UW20|Q8IUZ2	Missense_Mutation	SNP	ENST00000274721.3	hg19	CCDS4201.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.747712	0.89663	.	.	ENSG00000146013	ENST00000274721;ENST00000378362	T;T	0.63255	-0.03;-0.03	4.81	4.81	0.61882	GDNF/GAS1 (2);	0.127634	0.52532	D	0.000078	T	0.73125	0.3547	L	0.60455	1.87	0.42105	D	0.991352	D;D	0.89917	1.0;1.0	D;D	0.91635	0.964;0.999	T	0.69811	-0.5044	10	0.22706	T	0.39	-12.7809	13.371	0.60713	0.0:1.0:0.0:0.0	.	205;236	O60609-2;O60609	.;GFRA3_HUMAN	T	236;205	ENSP00000274721:A236T;ENSP00000367613:A205T	ENSP00000274721:A236T	A	-	1	0	GFRA3	137621306	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.251000	0.65438	2.212000	0.71576	0.655000	0.94253	GCC	.	.		0.697	GFRA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251277.1	NM_001496		T	137593407	C	T	137593407	3	4	45	1	0	0	0	0	1	0	0	0	6357	768	27	1	516	1	GFRA3	5	137593407	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	54757960	137593407	43321853	22	5924										
FLT4	2324	hgsc.bcm.edu	37	chr5	180048543	180048543	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tccccgcggccagcctcaccCtgcaccgacaggtacttctt	8	19	2	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr5:180048543C>T	ENST00000261937.6	-	13	2097	c.2019G>A	c.(2017-2019)caG>caA	p.Q673Q	FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000393347.3_Splice_Site_p.Q673Q|FLT4_ENST00000502649.1_Splice_Site_p.Q673Q	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	673					blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGCCTCACCCTGCACCGACA	0.672																																					p.Q673Q	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.G2019A						.						32	33	33					5																	180048543		2196	4292	6488	SO:0001630	splice_region_variant	2324	exon13			CTCACCCTGCACC	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.2020+1G>A	chr5.hg19:g.180048543C>T		164.0	0.0		59.0	18.0	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	hg19	CCDS4457.1																																																																																			.	.		0.672	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		Silent	T	180048543	C	T	180048543	5	4	45	1	0	0	0	0	0	0	1	0	5952	695	24	3	2152	3	FLT4	5	180048543	Splice_Site	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	42455136	180048543	866717	23	5925										
ZNF76	7629	hgsc.bcm.edu	37	chr6	35262247	35262247	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tttcaggtcacaatcattacCtctggggctgtggtggctga	12	9	4	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr6:35262247C>T	ENST00000373953.3	+	13	1775	c.1509C>T	c.(1507-1509)acC>acT	p.T503T	ZNF76_ENST00000440666.2_Silent_p.T477T|ZNF76_ENST00000339411.5_Silent_p.T448T	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	503					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						CAATCATTACCTCTGGGGCTG	0.507											OREG0017373	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T503T	Esophageal Squamous(52;92 1039 20612 23956 34676)	Atlas-SNP	.											.	ZNF76	37	.	0			c.C1509T						.						207	159	175					6																	35262247		2203	4300	6503	SO:0001819	synonymous_variant	7629	exon13			CATTACCTCTGGG	M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"Zinc fingers, C2H2-type"	13149	protein-coding gene	gene with protein product		194549	"zinc finger protein 76 (expressed in testis)"	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.1509C>T	chr6.hg19:g.35262247C>T		332.0	0.0	854	104.0	5.0	NM_003427	Q9BQB2	Silent	SNP	ENST00000373953.3	hg19	CCDS4801.1	.	.	.	.	.	.	.	.	.	.	C	8.492	0.862300	0.17178	.	.	ENSG00000065029	ENST00000498555	.	.	.	5.62	1.85	0.25348	.	.	.	.	.	T	0.29783	0.0744	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.12837	-1.0532	4	.	.	.	.	4.0448	0.09768	0.155:0.5064:0.0:0.3386	.	.	.	.	L	36	.	.	P	+	2	0	ZNF76	35370225	0.704000	0.27836	0.998000	0.56505	0.980000	0.70556	-0.274000	0.08537	0.051000	0.15978	0.650000	0.86243	CCT	.	.		0.507	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427		T	35262247	C	T	35262247	2	4	45	1	0	0	0	0	0	0	0	1	18150	668	24	3		3	ZNF76	6	35262247	Silent	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10		35262247	135852820	24	5926										
HSP90AB1	3326	hgsc.bcm.edu	37	chr6	44219604	44219604	+	Frame_Shift_Del	DEL	C	C	-													0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	catgaaggagacacagaagtCcatctattacatcactggtg							TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr6:44219604delC	ENST00000371554.1	+	9	1659	c.1445delC	c.(1444-1446)tccfs	p.S482fs	HSP90AB1_ENST00000353801.3_Frame_Shift_Del_p.S482fs|SLC35B2_ENST00000495706.1_5'Flank|HSP90AB1_ENST00000371646.5_Frame_Shift_Del_p.S482fs|MIR4647_ENST00000583964.1_RNA			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	482					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			ACACAGAAGTCCATCTATTAC	0.502																																					p.S482fs		Atlas-Indel,Pindel	.											.	HSP90AB1	83	.	0			c.1444delT						.						126	124	125					6																	44219604		2203	4300	6503	SO:0001589	frameshift_variant	3326	exon9			.	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"Heat shock proteins / HSPC"	5258	protein-coding gene	gene with protein product		140572	"heat shock 90kD protein 1, beta", "heat shock 90kDa protein 1, beta"	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.1445delC	chr6.hg19:g.44219604delC	ENSP00000360609:p.Ser482fs	160.0	0.0		46.0	30.0	NM_001271969	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Frame_Shift_Del	DEL	ENST00000371554.1	hg19	CCDS4909.1																																																																																			.	.		0.502	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355		-	44219604	C	-	44219604	7	5	45	1	0	1	0	1	0	0	0	0	7411	855	30	0	1475	0	HSP90AB1	6	44219604	Frame_Shift_Del	DEL	C	TCGA-BC-A5W4-01A-11D-A28X-10	8957357	44219604	126895463	25	5927										
THEMIS	387357	hgsc.bcm.edu	37	chr6	128134854	128134854	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ttcttgatgcctggtactttTtgtggatcacaatggttttc	9	7	2	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr6:128134854T>C	ENST00000368248.2	-	4	1080	c.932A>G	c.(931-933)aAa>aGa	p.K311R	THEMIS_ENST00000368250.1_Missense_Mutation_p.K232R|THEMIS_ENST00000543064.1_Missense_Mutation_p.K311R|THEMIS_ENST00000537166.1_Missense_Mutation_p.K276R	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	311	CABIT 2.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						CTGGTACTTTTTGTGGATCAC	0.423																																					p.K311R		Atlas-SNP	.											.	THEMIS	168	.	0			c.A932G						.						102	107	106					6																	128134854		2203	4300	6503	SO:0001583	missense	387357	exon4			TACTTTTTGTGGA	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.932A>G	chr6.hg19:g.128134854T>C	ENSP00000357231:p.Lys311Arg	118.0	0.0		59.0	46.0	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	hg19	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	T	7.622	0.677051	0.14841	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166;ENST00000434358	T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;2.41	5.59	5.59	0.84812	.	0.404730	0.29473	N	0.012044	T	0.14356	0.0347	M	0.70595	2.14	0.36782	D	0.884385	P;P	0.45531	0.86;0.698	B;P	0.45276	0.439;0.475	T	0.08848	-1.0702	10	0.18276	T	0.48	-6.8041	15.7742	0.78198	0.0:0.0:0.0:1.0	.	311;311	F5H1J9;Q8N1K5	.;THMS1_HUMAN	R	232;311;311;276;79	ENSP00000357233:K232R;ENSP00000439594:K311R;ENSP00000357231:K311R;ENSP00000439863:K276R;ENSP00000387740:K79R	ENSP00000357231:K311R	K	-	2	0	THEMIS	128176547	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	4.755000	0.62198	2.135000	0.66039	0.374000	0.22700	AAA	.	.		0.423	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		C	128134854	T	C	128134854	3	2	45	1	0	0	0	0	1	0	0	0	15875	1841	64	2	1126	2	THEMIS	6	128134854	Missense_Mutation	SNP	T	TCGA-BC-A5W4-01A-11D-A28X-10	83915250	128134854	42980213	26	5928										
SNX13	23161	hgsc.bcm.edu	37	chr7	17890006	17890006	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	cgctgtattcttgagtcacaTaccttctttacgaatagtaa	6	9	3	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr7:17890006T>C	ENST00000409389.1	-	11	1201	c.1029A>G	c.(1027-1029)gtA>gtG	p.V343V	SNX13_ENST00000428135.3_Silent_p.V343V			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	343					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					TTGAGTCACATACCTTCTTTA	0.289																																					p.V343V		Atlas-SNP	.											.	SNX13	113	.	0			c.A1029G						.						80	70	73					7																	17890006		1838	4085	5923	SO:0001819	synonymous_variant	23161	exon11			GTCACATACCTTC	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"Sorting nexins"	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.1029A>G	chr7.hg19:g.17890006T>C		78.0	0.0		62.0	27.0	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Silent	SNP	ENST00000409389.1	hg19																																																																																				.	.		0.289	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132		C	17890006	T	C	17890006	2	2	45	1	0	0	0	0	0	0	0	1	14899	1393	49	2		2	SNX13	7	17890006	Silent	SNP	T	TCGA-BC-A5W4-01A-11D-A28X-10		17890006	141248657	27	5929										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18869095	18869095	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	attccgcagggggttctgctTttttaattcagttgcaatta	9	7	2	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr7:18869095T>A	ENST00000432645.2	+	18	2381	c.2381T>A	c.(2380-2382)tTt>tAt	p.F794Y	HDAC9_ENST00000401921.1_Missense_Mutation_p.F753Y|HDAC9_ENST00000406451.4_Missense_Mutation_p.F794Y|HDAC9_ENST00000441542.2_Missense_Mutation_p.F797Y	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	794	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	GGGTTCTGCTTTTTTAATTCA	0.358																																					p.F797Y		Atlas-SNP	.											.	HDAC9	560	.	0			c.T2390A						.						91	85	87					7																	18869095		1816	4085	5901	SO:0001583	missense	9734	exon18			TCTGCTTTTTTAA	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.2381T>A	chr7.hg19:g.18869095T>A	ENSP00000410337:p.Phe794Tyr	70.0	0.0		67.0	15.0	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	hg19	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	T	8.375	0.836301	0.16891	.	.	ENSG00000048052	ENST00000406451;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000341009	T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43	5.31	5.31	0.75309	Histone deacetylase domain (2);	0.000000	0.64402	D	0.000004	T	0.56124	0.1964	L	0.38649	1.16	0.80722	D	1	B;B;B;B;B;B	0.18166	0.002;0.025;0.021;0.021;0.026;0.021	B;B;B;B;B;B	0.25759	0.014;0.063;0.018;0.018;0.03;0.018	T	0.52139	-0.8615	10	0.27785	T	0.31	-48.3102	11.3354	0.49500	0.136:0.0:0.0:0.864	.	794;42;753;797;794;794	Q9UKV0-4;Q8N926;Q9UKV0-6;Q9UKV0-7;Q9UKV0;Q9UKV0-5	.;.;.;.;HDAC9_HUMAN;.	Y	794;753;794;797;706	ENSP00000384657:F794Y;ENSP00000383912:F753Y;ENSP00000410337:F794Y;ENSP00000408617:F797Y	ENSP00000339165:F706Y	F	+	2	0	HDAC9	18835620	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.525000	0.45598	2.129000	0.65627	0.528000	0.53228	TTT	.	.		0.358	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			A	18869095	T	A	18869095	3	1	45	1	0	0	0	0	1	0	0	0	7023	1841	64	4	2511	4	HDAC9	7	18869095	Missense_Mutation	SNP	T	TCGA-BC-A5W4-01A-11D-A28X-10	979089	18869095	140269568	28	5930										
SKAP2	8935	hgsc.bcm.edu	37	chr7	26765154	26765154	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ataattctcctctctcatcaTaatcctcaggaataatatca	2	11	6	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr7:26765154T>C	ENST00000345317.2	-	9	1002	c.689A>G	c.(688-690)tAt>tGt	p.Y230C	SKAP2_ENST00000539623.1_Missense_Mutation_p.Y58C|SKAP2_ENST00000489977.1_5'UTR	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	230					B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						TCTCTCATCATAATCCTCAGG	0.279																																					p.Y230C		Atlas-SNP	.											.	SKAP2	40	.	0			c.A689G						.						112	110	110					7																	26765154		2203	4300	6503	SO:0001583	missense	8935	exon9			TCATCATAATCCT		CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"Pleckstrin homology (PH) domain containing"	15687	protein-coding gene	gene with protein product		605215	"src family associated phosphoprotein 2"	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.689A>G	chr7.hg19:g.26765154T>C	ENSP00000005587:p.Tyr230Cys	64.0	0.0		44.0	24.0	NM_003930	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Missense_Mutation	SNP	ENST00000345317.2	hg19	CCDS5400.1	.	.	.	.	.	.	.	.	.	.	T	9.568	1.120292	0.20877	.	.	ENSG00000005020	ENST00000345317;ENST00000539623;ENST00000535331	T;T	0.29917	2.07;1.55	5.86	3.4	0.38934	.	0.509488	0.22178	N	0.063543	T	0.14399	0.0348	N	0.08118	0	0.19775	N	0.99996	P;B	0.36495	0.556;0.31	B;B	0.35899	0.112;0.213	T	0.09796	-1.0658	10	0.49607	T	0.09	-15.7547	6.148	0.20296	0.1426:0.0772:0.0:0.7801	.	215;230	B7Z5N4;O75563	.;SKAP2_HUMAN	C	230;58;215	ENSP00000005587:Y230C;ENSP00000443593:Y58C	ENSP00000005587:Y230C	Y	-	2	0	SKAP2	26731679	0.997000	0.39634	0.079000	0.20413	0.990000	0.78478	5.239000	0.65371	0.434000	0.26340	0.533000	0.62120	TAT	.	.		0.279	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214128.1			C	26765154	T	C	26765154	3	2	45	1	0	0	0	0	1	0	0	0	14371	1406	49	2	406	2	SKAP2	7	26765154	Missense_Mutation	SNP	T	TCGA-BC-A5W4-01A-11D-A28X-10	7896059	26765154	132373509	29	5931										
GLI3	2737	hgsc.bcm.edu	37	chr7	42004352	42004352	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tttggtcatagaactgaccaGagtaattctgcagattagag	10	6	2	5			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr7:42004352G>T	ENST00000395925.3	-	15	4403	c.4319C>A	c.(4318-4320)tCt>tAt	p.S1440Y	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1440					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GAACTGACCAGAGTAATTCTG	0.522									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.S1440Y		Atlas-SNP	.											.	GLI3	312	.	0			c.C4319A						.						64	66	65					7																	42004352		2203	4300	6503	SO:0001583	missense	2737	exon15	Familial Cancer Database	;	TGACCAGAGTAAT		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.4319C>A	chr7.hg19:g.42004352G>T	ENSP00000379258:p.Ser1440Tyr	222.0	0.0		196.0	88.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.801593	0.70682	.	.	ENSG00000106571	ENST00000395925	T	0.14766	2.48	5.62	5.62	0.85841	.	0.112923	0.64402	D	0.000007	T	0.34395	0.0896	L	0.52011	1.625	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.00619	-1.1641	10	0.41790	T	0.15	.	19.6632	0.95882	0.0:0.0:1.0:0.0	.	1440	P10071	GLI3_HUMAN	Y	1440	ENSP00000379258:S1440Y	ENSP00000379258:S1440Y	S	-	2	0	GLI3	41970877	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.442000	0.66575	2.625000	0.88918	0.655000	0.94253	TCT	.	.		0.522	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42004352	G	T	42004352	3	4	45	1	0	0	0	0	1	0	0	0	6447	942	33	3	427	3	GLI3	7	42004352	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	15239198	42004352	117134311	30	5932										
BPGM	669	hgsc.bcm.edu	37	chr7	134346580	134346580	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	gagcagatggctttgaatcaTggtgaagaacaagtgaggct	14	5	1	5			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr7:134346580T>C	ENST00000393132.2	+	3	810	c.321T>C	c.(319-321)caT>caC	p.H107H	BPGM_ENST00000344924.3_Silent_p.H107H|BPGM_ENST00000418040.1_Silent_p.H107H	NM_199186.2	NP_954655.1	P07738	PMGE_HUMAN	2,3-bisphosphoglycerate mutase	107					carbohydrate metabolic process (GO:0005975)|erythrocyte development (GO:0048821)|glycolytic process (GO:0006096)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)			breast(1)|endometrium(1)|lung(2)|stomach(1)	5						CTTTGAATCATGGTGAAGAAC	0.512																																					p.H107H		Atlas-SNP	.											.	BPGM	12	.	0			c.T321C						.						83	74	77					7																	134346580		2203	4300	6503	SO:0001819	synonymous_variant	669	exon3			GAATCATGGTGAA	BC017050	CCDS5833.1	7q33	2012-10-02			ENSG00000172331	ENSG00000172331	5.4.2.4		1093	protein-coding gene	gene with protein product		613896					Standard	NM_199186		Approved		uc003vrw.3	P07738	OTTHUMG00000155380	ENST00000393132.2:c.321T>C	chr7.hg19:g.134346580T>C		301.0	1.0		294.0	120.0	NM_199186	A4D1N9	Silent	SNP	ENST00000393132.2	hg19	CCDS5833.1																																																																																			.	.		0.512	BPGM-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339763.1	NM_001724		C	134346580	T	C	134346580	2	2	45	1	0	0	0	0	0	0	0	1	1490	1461	51	2		2	BPGM	7	134346580	Silent	SNP	T	TCGA-BC-A5W4-01A-11D-A28X-10	92342228	134346580	24792083	31	5933										
PTK2B	2185	hgsc.bcm.edu	37	chr8	27255270	27255270	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tcaatcctgggaaaaacttcAaactggtcaaatgcactgtc	7	10	3	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr8:27255270A>T	ENST00000397501.1	+	7	977	c.169A>T	c.(169-171)Aaa>Taa	p.K57*	PTK2B_ENST00000346049.5_Nonsense_Mutation_p.K57*|PTK2B_ENST00000420218.2_Nonsense_Mutation_p.K57*|PTK2B_ENST00000517339.1_Nonsense_Mutation_p.K57*|PTK2B_ENST00000338238.4_Nonsense_Mutation_p.K57*|PTK2B_ENST00000544172.1_Nonsense_Mutation_p.K57*	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	57	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	GAAAAACTTCAAACTGGTCAA	0.517																																					p.K57X		Atlas-SNP	.											.	PTK2B	304	.	0			c.A169T						.						149	137	141					8																	27255270		2203	4300	6503	SO:0001587	stop_gained	2185	exon7			AACTTCAAACTGG	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"protein tyrosine kinase 2 beta", "PTK2B protein tyrosine kinase 2 beta"	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.169A>T	chr8.hg19:g.27255270A>T	ENSP00000380638:p.Lys57*	286.0	0.0		236.0	97.0	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Nonsense_Mutation	SNP	ENST00000397501.1	hg19	CCDS6057.1	.	.	.	.	.	.	.	.	.	.	A	44	10.540794	0.99424	.	.	ENSG00000120899	ENST00000397501;ENST00000539100;ENST00000338238;ENST00000544172;ENST00000522338;ENST00000521164;ENST00000346049;ENST00000420218;ENST00000522517;ENST00000412793;ENST00000517339	.	.	.	4.79	4.79	0.61399	.	0.060402	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.3454	0.55118	1.0:0.0:0.0:0.0	.	.	.	.	X	57;62;57;57;57;57;57;57;57;57;57	.	ENSP00000342242:K57X	K	+	1	0	PTK2B	27311187	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.890000	0.69774	2.018000	0.59344	0.533000	0.62120	AAA	.	.		0.517	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103		T	27255270	A	T	27255270	4	4	45	1	0	0	0	0	0	1	0	0	12776	131	5	4	171	4	PTK2B	8	27255270	Nonsense_Mutation	SNP	A	TCGA-BC-A5W4-01A-11D-A28X-10		27255270	119108752	32	5934										
TLE1	7088	hgsc.bcm.edu	37	chr9	84208095	84208095	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	gttgagggtgttgatctggcGagcatgccgggggattccgg	19	7	1	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr9:84208095G>T	ENST00000376499.3	-	15	2490	c.1426C>A	c.(1426-1428)Cgc>Agc	p.R476S		NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	476					multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						TTGATCTGGCGAGCATGCCGG	0.612																																					p.R476S	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	Atlas-SNP	.											.	TLE1	81	.	0			c.C1426A						.						117	111	113					9																	84208095		2203	4300	6503	SO:0001583	missense	7088	exon15			TCTGGCGAGCATG		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"WD repeat domain containing"	11837	protein-coding gene	gene with protein product	"enhancer of split groucho 1"	600189	"transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.1426C>A	chr9.hg19:g.84208095G>T	ENSP00000365682:p.Arg476Ser	237.0	0.0		136.0	50.0	NM_005077	A8K495|Q5T3G4|Q969V9	Missense_Mutation	SNP	ENST00000376499.3	hg19	CCDS6661.1	.	.	.	.	.	.	.	.	.	.	g	35	5.563760	0.96527	.	.	ENSG00000196781	ENST00000376499	T	0.11495	2.77	5.96	5.96	0.96718	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.43433	0.1247	M	0.88570	2.965	0.80722	D	1	D;D;P	0.67145	0.968;0.996;0.782	P;D;B	0.76575	0.581;0.988;0.233	T	0.44590	-0.9318	10	0.87932	D	0	-23.6887	20.422	0.99049	0.0:0.0:1.0:0.0	.	461;502;476	B4DEF9;Q59EF7;Q04724	.;.;TLE1_HUMAN	S	476	ENSP00000365682:R476S	ENSP00000365682:R476S	R	-	1	0	TLE1	83397915	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.872000	0.87187	2.832000	0.97577	0.655000	0.94253	CGC	.	.		0.612	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077		T	84208095	G	T	84208095	3	4	45	1	0	0	0	0	1	0	0	0	15953	1058	37	1	910	1	TLE1	9	84208095	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		84208095	57005336	33	5935										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113173839	113173839	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	gggaattgtctgctaggctgTaaccatcagagcagtagtag	13	7	2	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr9:113173839T>C	ENST00000401783.2	-	37	6488	c.6152A>G	c.(6151-6153)tAc>tGc	p.Y2051C	SVEP1_ENST00000297826.5_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.Y2028C	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2051	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TGCTAGGCTGTAACCATCAGA	0.532																																					p.Y2051C		Atlas-SNP	.											.	SVEP1	326	.	0			c.A6152G						.						48	49	49					9																	113173839		1966	4147	6113	SO:0001583	missense	79987	exon37			AGGCTGTAACCAT	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.6152A>G	chr9.hg19:g.113173839T>C	ENSP00000384917:p.Tyr2051Cys	80.0	0.0		64.0	43.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.320446	0.81469	.	.	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.72394	-0.65;-0.65	5.98	5.98	0.97165	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.85982	0.5824	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88089	0.2812	10	0.87932	D	0	.	16.4728	0.84119	0.0:0.0:0.0:1.0	.	2051	Q4LDE5	SVEP1_HUMAN	C	2051;2028	ENSP00000384917:Y2051C;ENSP00000363593:Y2028C	ENSP00000363593:Y2028C	Y	-	2	0	SVEP1	112213660	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.840000	0.86819	2.296000	0.77279	0.482000	0.46254	TAC	.	.		0.532	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113173839	T	C	113173839	3	2	45	1	0	0	0	0	1	0	0	0	15435	1638	57	2	4611	2	SVEP1	9	113173839	Missense_Mutation	SNP	T	TCGA-BC-A5W4-01A-11D-A28X-10	28965744	113173839	28039592	34	5936										
TTC16	158248	hgsc.bcm.edu	37	chr9	130493535	130493535	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ctgagtatgcccaaggccagGgccagaggtccagcaaggct	14	12	0	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr9:130493535G>C	ENST00000373289.3	+	14	2553	c.2473G>C	c.(2473-2475)Ggc>Cgc	p.G825R	TTC16_ENST00000489226.1_3'UTR|TOR2A_ENST00000472723.1_5'Flank	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	825										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						CCAAGGCCAGGGCCAGAGGTC	0.607																																					p.G825R		Atlas-SNP	.											.	TTC16	55	.	0			c.G2473C						.						44	49	47					9																	130493535		2202	4300	6502	SO:0001583	missense	158248	exon14			GGCCAGGGCCAGA	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"Tetratricopeptide (TTC) repeat domain containing"	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.2473G>C	chr9.hg19:g.130493535G>C	ENSP00000362386:p.Gly825Arg	297.0	0.0		186.0	51.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	G	10.84	1.465281	0.26335	.	.	ENSG00000167094	ENST00000373289	T	0.19105	2.17	4.52	-4.92	0.03075	.	1.353330	0.04720	N	0.419182	T	0.15132	0.0365	L	0.40543	1.245	0.09310	N	1	B;B	0.29432	0.244;0.244	B;B	0.29176	0.099;0.099	T	0.32877	-0.9890	10	0.51188	T	0.08	-1.1371	4.1494	0.10230	0.3232:0.0:0.3783:0.2984	.	812;825	B4DZ42;Q8NEE8	.;TTC16_HUMAN	R	825	ENSP00000362386:G825R	ENSP00000362386:G825R	G	+	1	0	TTC16	129533356	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.678000	0.01942	-0.796000	0.04456	-0.672000	0.03802	GGC	.	.		0.607	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965		C	130493535	G	C	130493535	3	2	45	1	0	0	0	0	1	0	0	0	16698	1232	43	4	2527	4	TTC16	9	130493535	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	17319696	130493535	10719896	35	5937										
ZDHHC12	84885	hgsc.bcm.edu	37	chr9	131483968	131483968	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	cacagaagcaccaccagctgCagcgccaggtagaccacaaa	9	15	0	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr9:131483968C>T	ENST00000372663.4	-	4	456	c.444G>A	c.(442-444)ctG>ctA	p.L148L	ZDHHC12_ENST00000372667.5_Silent_p.L162L|ZDHHC12_ENST00000372672.2_Silent_p.L148L|ZDHHC12_ENST00000467312.1_5'UTR|RP11-545E17.3_ENST00000443631.1_RNA	NM_032799.4	NP_116188	Q96GR4	ZDH12_HUMAN	zinc finger, DHHC-type containing 12	148					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|ovary(2)|upper_aerodigestive_tract(1)	4						CCACCAGCTGCAGCGCCAGGT	0.647																																					p.L148L		Atlas-SNP	.											.	ZDHHC12	14	.	0			c.G444A						.						157	143	148					9																	131483968		2203	4300	6503	SO:0001819	synonymous_variant	84885	exon4			CAGCTGCAGCGCC	AK027430	CCDS6909.1	9q34.11	2008-02-05			ENSG00000160446	ENSG00000160446		"Zinc fingers, DHHC-type"	19159	protein-coding gene	gene with protein product							Standard	NM_032799		Approved	ZNF400, FLJ14524	uc004bvy.3	Q96GR4	OTTHUMG00000020756	ENST00000372663.4:c.444G>A	chr9.hg19:g.131483968C>T		618.0	0.0		267.0	31.0	NM_032799	A6NH95|B2RE03|Q5T265|Q5T267|Q5T268|Q86VT5|Q96T09	Silent	SNP	ENST00000372663.4	hg19	CCDS6909.1																																																																																			.	.		0.647	ZDHHC12-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054484.1	NM_032799		T	131483968	C	T	131483968	2	4	45	1	0	0	0	0	0	0	0	1	17617	697	25	3		3	ZDHHC12	9	131483968	Silent	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	990433	131483968	9729463	36	5938										
POLR3A	11128	hgsc.bcm.edu	37	chr10	79769701	79769701	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ttgaagcaatgatttggcaaGccttggctcgatcaaagaaa	10	7	1	3			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr10:79769701G>T	ENST00000372371.3	-	13	1828	c.1691C>A	c.(1690-1692)gCt>gAt	p.A564D		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	564					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			GATTTGGCAAGCCTTGGCTCG	0.433																																					p.A564D		Atlas-SNP	.											.	POLR3A	104	.	0			c.C1691A						.						98	89	92					10																	79769701		2203	4300	6503	SO:0001583	missense	11128	exon13			TGGCAAGCCTTGG	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"RNA polymerase subunits"	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.1691C>A	chr10.hg19:g.79769701G>T	ENSP00000361446:p.Ala564Asp	211.0	0.0		78.0	4.0	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	hg19	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	G	32	5.168745	0.94768	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.80123	-1.34	5.42	5.42	0.78866	RNA polymerase Rpb1, domain 3 (1);	0.103842	0.64402	D	0.000003	D	0.85318	0.5669	M	0.85373	2.75	0.80722	D	1	P	0.44006	0.824	B	0.43575	0.424	D	0.86416	0.1751	9	.	.	.	-16.7773	19.5838	0.95484	0.0:0.0:1.0:0.0	.	564	O14802	RPC1_HUMAN	D	564	ENSP00000361446:A564D	.	A	-	2	0	POLR3A	79439707	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.307000	0.96226	2.704000	0.92352	0.655000	0.94253	GCT	.	.		0.433	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		T	79769701	G	T	79769701	3	4	45	1	0	0	0	0	1	0	0	0	12237	971	34	3	2557	3	POLR3A	10	79769701	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		79769701	55765046	37	5939										
MYOF	26509	hgsc.bcm.edu	37	chr10	95111015	95111015	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ggaccatgtatagatttggcGccctttgagggggaagaatg	15	6	0	3	rs553662967		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr10:95111015G>A	ENST00000359263.4	-	35	3859	c.3860C>T	c.(3859-3861)gCg>gTg	p.A1287V	MYOF_ENST00000358334.5_Missense_Mutation_p.A1274V|MYOF_ENST00000371501.4_Missense_Mutation_p.A1287V|MYOF_ENST00000371502.4_Missense_Mutation_p.A1287V	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1287					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TAGATTTGGCGCCCTTTGAGG	0.498													G|||	1	0.000199681	0	0	5008	,	,		19560	0		0	False		,,,				2504	0.001				p.A1287V		Atlas-SNP	.											.	MYOF	177	.	0			c.C3860T						.						59	59	59					10																	95111015		1939	4128	6067	SO:0001583	missense	26509	exon35			TTTGGCGCCCTTT	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.3860C>T	chr10.hg19:g.95111015G>A	ENSP00000352208:p.Ala1287Val	208.0	0.0		71.0	15.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.217516	0.39201	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	D;D;D;D	0.83419	-1.72;-1.71;-1.72;-1.7	6.17	3.07	0.35406	C2 calcium/lipid-binding domain, CaLB (1);	0.054833	0.64402	D	0.000001	T	0.73001	0.3531	L	0.42245	1.32	0.41689	D	0.98933	B;P	0.37500	0.358;0.597	B;B	0.28553	0.091;0.066	T	0.71686	-0.4518	10	0.40728	T	0.16	-18.6632	12.5276	0.56096	0.0:0.2381:0.6383:0.1235	.	1274;1287	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	V	1274;1287;1287;1287	ENSP00000351094:A1274V;ENSP00000352208:A1287V;ENSP00000360556:A1287V;ENSP00000360557:A1287V	ENSP00000351094:A1274V	A	-	2	0	MYOF	95101005	0.996000	0.38824	0.875000	0.34327	0.920000	0.55202	2.811000	0.47986	0.866000	0.35629	0.655000	0.94253	GCG	.	.		0.498	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		A	95111015	G	A	95111015	3	1	45	1	0	0	0	0	1	0	0	0	10098	1087	38	1	2405	1	MYOF	10	95111015	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	15341314	95111015	40423732	38	5940										
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468748	56468748	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tacagcctaaggaataaggaTgtgaaagaggctctgaaaaa	11	5	1	3			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr11:56468748T>C	ENST00000312153.1	+	1	885	c.885T>C	c.(883-885)gaT>gaC	p.D295D		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						GGAATAAGGATGTGAAAGAGG	0.368																																					p.D295D		Atlas-SNP	.											.	.	.	.	0			c.T885C						.						99	105	103					11																	56468748		2201	4296	6497	SO:0001819	synonymous_variant	504191	exon1			TAAGGATGTGAAA	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"GPCR / Class A : Olfactory receptors"	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.885T>C	chr11.hg19:g.56468748T>C		49.0	0.0		36.0	5.0	NM_001013358	Q6IEU9|Q8NGQ0	Silent	SNP	ENST00000312153.1	hg19	CCDS31536.1																																																																																			.	.		0.368	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		C	56468748	T	C	56468748	2	2	45	1	0	0	0	0	0	0	0	1	11259	1461	51	2		2	OR9G1	11	56468748	Silent	SNP	T	TCGA-BC-A5W4-01A-11D-A28X-10		56468748	78537768	39	5941										
ZDHHC5	25921	hgsc.bcm.edu	37	chr11	57466587	57466587	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	gtcacccccactcccgggccGtgaggaagaaccaggcttgg	13	15	1	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr11:57466587G>T	ENST00000287169.3	+	11	3041	c.1679G>T	c.(1678-1680)cGt>cTt	p.R560L	ZDHHC5_ENST00000527985.1_Missense_Mutation_p.R507L	NM_015457.2	NP_056272.2	Q9C0B5	ZDHC5_HUMAN	zinc finger, DHHC-type containing 5	560					protein palmitoylation (GO:0018345)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(3)|lung(5)|skin(1)	18						CTCCCGGGCCGTGAGGAAGAA	0.587																																					p.R560L		Atlas-SNP	.											.	ZDHHC5	49	.	0			c.G1679T						.						67	73	71					11																	57466587		2201	4296	6497	SO:0001583	missense	25921	exon11			CGGGCCGTGAGGA	AB051535	CCDS7965.1	11q13.1	2008-05-02			ENSG00000156599	ENSG00000156599		"Zinc fingers, DHHC-type"	18472	protein-coding gene	gene with protein product		614586				11214970	Standard	NM_015457		Approved	KIAA1748, ZNF375	uc001nkx.1	Q9C0B5	OTTHUMG00000167198	ENST00000287169.3:c.1679G>T	chr11.hg19:g.57466587G>T	ENSP00000287169:p.Arg560Leu	92.0	0.0		63.0	15.0	NM_015457	Q2TGF0|Q6ZMF0|Q8TAK8|Q9H923|Q9UFI7	Missense_Mutation	SNP	ENST00000287169.3	hg19	CCDS7965.1	.	.	.	.	.	.	.	.	.	.	G	12.10	1.835843	0.32421	.	.	ENSG00000156599	ENST00000527985;ENST00000287169	T;T	0.59638	0.25;1.25	5.3	3.38	0.38709	.	0.340347	0.27951	N	0.017181	T	0.43144	0.1234	L	0.29908	0.895	0.40417	D	0.979806	B	0.18968	0.032	B	0.17722	0.019	T	0.37056	-0.9722	10	0.66056	D	0.02	-1.4425	8.4462	0.32843	0.2373:0.0:0.7627:0.0	.	560	Q9C0B5	ZDHC5_HUMAN	L	507;560	ENSP00000432202:R507L;ENSP00000287169:R560L	ENSP00000287169:R560L	R	+	2	0	ZDHHC5	57223163	0.000000	0.05858	0.938000	0.37757	0.933000	0.57130	0.386000	0.20702	0.773000	0.33404	0.655000	0.94253	CGT	.	.		0.587	ZDHHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393694.1	NM_015457		T	57466587	G	T	57466587	3	4	45	1	0	0	0	0	1	0	0	0	17633	1145	40	1	1717	1	ZDHHC5	11	57466587	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	997839	57466587	77539929	40	5942										
PRCP	5547	hgsc.bcm.edu	37	chr11	82571056	82571056	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	agataatgtccccttcattaCcagtgtagaaaagtattgat	7	7	1	3			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr11:82571056C>A	ENST00000313010.3	-	2	466	c.272G>T	c.(271-273)gGt>gTt	p.G91V	PRCP_ENST00000393399.2_Missense_Mutation_p.G112V|PRCP_ENST00000535099.1_Intron	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	91					angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						CCCTTCATTACCAGTGTAGAA	0.333																																					p.G112V		Atlas-SNP	.											.	PRCP	69	.	0			c.G335T						.						102	95	97					11																	82571056		2203	4297	6500	SO:0001583	missense	5547	exon3			TCATTACCAGTGT	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.272G>T	chr11.hg19:g.82571056C>A	ENSP00000317362:p.Gly91Val	155.0	0.0		125.0	31.0	NM_199418	A8MU24|B2R7B7|B3KRK5|B5BU34	Missense_Mutation	SNP	ENST00000313010.3	hg19	CCDS8262.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.344058	0.82022	.	.	ENSG00000137509	ENST00000313010;ENST00000393399;ENST00000529671;ENST00000532809	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.71	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.68860	0.3047	H	0.96777	3.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80756	-0.1240	9	.	.	.	-17.7051	14.6012	0.68443	0.0:0.93:0.0:0.07	.	91;112	P42785;A8MU24	PCP_HUMAN;.	V	91;112;50;37	ENSP00000317362:G91V;ENSP00000377055:G112V;ENSP00000434771:G50V;ENSP00000437169:G37V	.	G	-	2	0	PRCP	82248704	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.486000	0.81215	1.423000	0.47198	0.491000	0.48974	GGT	.	.		0.333	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040		A	82571056	C	A	82571056	3	1	45	1	0	0	0	0	1	0	0	0	12461	507	18	3	1250	3	PRCP	11	82571056	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	25104469	82571056	52435460	41	5943										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2229596	2229596	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	aacgccaccaattccaacctGgtaagtccaccatcctcaag	5	16	1	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr12:2229596G>T	ENST00000347598.4	+	3	477	c.477G>T	c.(475-477)ctG>ctT	p.L159L	CACNA1C_ENST00000399603.1_Splice_Site_p.L159L|CACNA1C_ENST00000406454.3_Splice_Site_p.L159L|CACNA1C_ENST00000399634.1_Splice_Site_p.L159L|CACNA1C_ENST00000399629.1_Splice_Site_p.L159L|CACNA1C_ENST00000399621.1_Splice_Site_p.L159L|CACNA1C_ENST00000327702.7_Splice_Site_p.L159L|CACNA1C_ENST00000399591.1_Splice_Site_p.L159L|CACNA1C_ENST00000399597.1_Splice_Site_p.L159L|CACNA1C_ENST00000399655.1_Splice_Site_p.L159L|CACNA1C_ENST00000335762.5_Splice_Site_p.L159L|CACNA1C_ENST00000399641.1_Splice_Site_p.L159L|CACNA1C_ENST00000399617.1_Splice_Site_p.L159L|CACNA1C_ENST00000399644.1_Splice_Site_p.L159L|CACNA1C_ENST00000399649.1_Splice_Site_p.L159L|CACNA1C_ENST00000399637.1_Splice_Site_p.L159L|CACNA1C_ENST00000399606.1_Splice_Site_p.L159L|CACNA1C_ENST00000399595.1_Splice_Site_p.L159L|CACNA1C_ENST00000399601.1_Splice_Site_p.L159L|CACNA1C_ENST00000402845.3_Splice_Site_p.L159L|CACNA1C_ENST00000480911.1_Splice_Site_p.L159L|CACNA1C_ENST00000399638.1_Splice_Site_p.L159L|CACNA1C_ENST00000344100.3_Splice_Site_p.L159L	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	159					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ATTCCAACCTGGTAAGTCCAC	0.423																																					p.L159L		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.G477T						.						139	140	139					12																	2229596		2055	4222	6277	SO:0001630	splice_region_variant	775	exon3			CAACCTGGTAAGT	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.477+1G>T	chr12.hg19:g.2229596G>T		224.0	1.0		101.0	86.0	NM_001129831	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	hg19	CCDS44788.1																																																																																			.	.		0.423	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	Silent	T	2229596	G	T	2229596	5	4	45	1	0	0	0	0	0	0	1	0	2542	1362	47	3	487	3	CACNA1C	12	2229596	Splice_Site	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		2229596	131622299	42	5944										
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42853904	42853904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ataatcggaagtggcatgggCgtactgtccgtagagatcag	14	7	1	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr12:42853904C>T	ENST00000455697.1	-	8	2488	c.2203G>A	c.(2203-2205)Gcc>Acc	p.A735T	PRICKLE1_ENST00000345127.3_Missense_Mutation_p.A735T|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.A735T|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.A735T|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.A735T|RP11-328C8.4_ENST00000547824.1_RNA	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	735					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		GTGGCATGGGCGTACTGTCCG	0.502																																					p.A735T		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.G2203A						.						124	123	123					12																	42853904		2203	4300	6503	SO:0001583	missense	144165	exon8			CATGGGCGTACTG	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.2203G>A	chr12.hg19:g.42853904C>T	ENSP00000401060:p.Ala735Thr	92.0	0.0		78.0	27.0	NM_001144882	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	hg19	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	C	9.836	1.189713	0.21954	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	D;D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9;-1.9	5.34	1.44	0.22558	.	0.454273	0.22030	N	0.065602	T	0.70815	0.3267	N	0.22421	0.69	0.09310	N	1	B	0.13594	0.008	B	0.04013	0.001	T	0.56697	-0.7936	10	0.37606	T	0.19	-1.1705	5.5579	0.17127	0.0:0.4873:0.2418:0.2709	.	735	Q96MT3	PRIC1_HUMAN	T	735	ENSP00000401060:A735T;ENSP00000398947:A735T;ENSP00000448359:A735T;ENSP00000345064:A735T;ENSP00000449819:A735T	ENSP00000345064:A735T	A	-	1	0	PRICKLE1	41140171	0.014000	0.17966	0.085000	0.20634	0.913000	0.54294	-0.037000	0.12164	0.062000	0.16340	-0.119000	0.15052	GCC	.	.		0.502	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			T	42853904	C	T	42853904	3	4	45	1	0	0	0	0	1	0	0	0	12498	768	27	1	296	1	PRICKLE1	12	42853904	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	40624308	42853904	90997991	43	5945										
TAOK3	51347	hgsc.bcm.edu	37	chr12	118588808	118588808	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	caaaaaatttaatctcatctGtagtcctccttaggaaaatc	4	9	2	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr12:118588808G>T	ENST00000392533.3	-	21	3181	c.2691C>A	c.(2689-2691)taC>taA	p.Y897*	TAOK3_ENST00000537952.1_Nonsense_Mutation_p.Y437*|TAOK3_ENST00000543709.1_Intron|TAOK3_ENST00000419821.2_Nonsense_Mutation_p.Y897*|TAOK3_ENST00000536979.1_Nonsense_Mutation_p.Y92*	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	897					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AATCTCATCTGTAGTCCTCCT	0.348																																					p.Y897X		Atlas-SNP	.											.	TAOK3	151	.	0			c.C2691A						.						97	99	98					12																	118588808		2203	4300	6503	SO:0001587	stop_gained	51347	exon21			TCATCTGTAGTCC	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.2691C>A	chr12.hg19:g.118588808G>T	ENSP00000376317:p.Tyr897*	37.0	0.0		36.0	6.0	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Nonsense_Mutation	SNP	ENST00000392533.3	hg19	CCDS9188.1	.	.	.	.	.	.	.	.	.	.	A	41	8.823435	0.98968	.	.	ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000536979;ENST00000537952	.	.	.	5.35	4.21	0.49690	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.40524	D	0.980869	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.8786	0.35360	0.7878:0.0:0.2122:0.0	.	.	.	.	X	897;897;92;437	.	ENSP00000376317:Y897X	Y	-	3	2	TAOK3	117073191	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.303000	0.51858	0.488000	0.27723	-0.254000	0.11334	TAC	.	.		0.348	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281		T	118588808	G	T	118588808	4	4	45	1	0	0	0	0	0	1	0	0	15564	1372	48	3	9	3	TAOK3	12	118588808	Nonsense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	75734904	118588808	15263087	44	5946										
DCLK1	9201	hgsc.bcm.edu	37	chr13	36700222	36700222	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	accctcggctgtatctctgcGccttatcccgctcgtcgaag	9	16	1	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr13:36700222G>A	ENST00000360631.3	-	2	264	c.53C>T	c.(52-54)gCg>gTg	p.A18V	DCLK1_ENST00000255448.4_Missense_Mutation_p.A18V|DCLK1_ENST00000379892.4_Missense_Mutation_p.A18V			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	18					axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		GTATCTCTGCGCCTTATCCCG	0.622																																					p.A18V		Atlas-SNP	.											DCLK1_ENST00000255448,colon,carcinoma,0,2	DCLK1	350	.	0			c.C53T						.						61	62	62					13																	36700222		2203	4300	6503	SO:0001583	missense	9201	exon2			CTCTGCGCCTTAT	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.53C>T	chr13.hg19:g.36700222G>A	ENSP00000353846:p.Ala18Val	69.0	0.0		22.0	21.0	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.01	2.706275	0.48412	.	.	ENSG00000133083	ENST00000255448;ENST00000360631;ENST00000539451;ENST00000379892	T;T;T	0.67523	-0.27;-0.27;1.88	5.67	5.67	0.87782	.	0.110579	0.64402	D	0.000012	T	0.56848	0.2013	N	0.22421	0.69	0.50632	D	0.999889	B	0.22346	0.068	B	0.18263	0.021	T	0.51379	-0.8713	10	0.44086	T	0.13	.	19.7802	0.96413	0.0:0.0:1.0:0.0	.	18	O15075-2	.	V	18	ENSP00000255448:A18V;ENSP00000353846:A18V;ENSP00000369222:A18V	ENSP00000255448:A18V	A	-	2	0	DCLK1	35598222	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.096000	0.64535	2.675000	0.91044	0.655000	0.94253	GCG	.	.		0.622	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		A	36700222	G	A	36700222	3	1	45	1	0	0	0	0	1	0	0	0	4293	1087	38	1	2204	1	DCLK1	13	36700222	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		36700222	78469656	45	5947										
PRKD1	5587	hgsc.bcm.edu	37	chr14	30066720	30066720	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	catgagatatttccttccagGgatttggtggatacatgaaa	10	6	0	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr14:30066720G>T	ENST00000331968.5	-	16	2640	c.2411C>A	c.(2410-2412)cCc>cAc	p.P804H	PRKD1_ENST00000415220.2_Missense_Mutation_p.P812H	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	804	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		TTCCTTCCAGGGATTTGGTGG	0.308																																					p.P804H		Atlas-SNP	.											.	PRKD1	316	.	0			c.C2411A						.						123	120	121					14																	30066720		2203	4300	6503	SO:0001583	missense	5587	exon16			TTCCAGGGATTTG		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2411C>A	chr14.hg19:g.30066720G>T	ENSP00000333568:p.Pro804His	87.0	0.0		78.0	41.0	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	hg19	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.484553	0.84854	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	T;T	0.64991	-0.13;-0.13	5.44	5.44	0.79542	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.75766	0.3894	L	0.49126	1.545	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.75388	-0.3335	10	0.52906	T	0.07	-13.8582	19.6286	0.95691	0.0:0.0:1.0:0.0	.	804	Q15139	KPCD1_HUMAN	H	804;812	ENSP00000333568:P804H;ENSP00000390535:P812H	ENSP00000333568:P804H	P	-	2	0	PRKD1	29136471	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.692000	0.91855	0.650000	0.86243	CCC	.	.		0.308	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		T	30066720	G	T	30066720	3	4	45	1	0	0	0	0	1	0	0	0	12530	1232	43	3	339	3	PRKD1	14	30066720	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		30066720	77282820	46	5948										
TRPM1	4308	hgsc.bcm.edu	37	chr15	31294718	31294718	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	cttggggaaatagtttcttcTtttttagagtctgtctgtct	9	6	5	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr15:31294718T>A	ENST00000256552.6	-	28	4332	c.4185A>T	c.(4183-4185)aaA>aaT	p.K1395N	TRPM1_ENST00000542188.1_Missense_Mutation_p.K1412N|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Missense_Mutation_p.K1373N	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		TAGTTTCTTCTTTTTTAGAGT	0.358																																					p.K1412N		Atlas-SNP	.											.	TRPM1	183	.	0			c.A4236T						.						167	155	159					15																	31294718		1847	4091	5938	SO:0001583	missense	4308	exon27			TTCTTCTTTTTTA	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.4185A>T	chr15.hg19:g.31294718T>A	ENSP00000256552:p.Lys1395Asn	50.0	0.0		43.0	18.0	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	hg19	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	T	3.670	-0.067798	0.07228	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.51817	0.71;0.69;0.71	5.05	-2.17	0.07059	.	1.825870	0.02729	N	0.114868	T	0.21631	0.0521	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.14727	-1.0462	10	0.48119	T	0.1	-4.0268	0.8112	0.01093	0.3583:0.1736:0.2959:0.1721	.	1367;1373	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	N	1373;1412;1395;1373	ENSP00000380897:K1373N;ENSP00000437849:K1412N;ENSP00000256552:K1395N	ENSP00000256552:K1395N	K	-	3	2	TRPM1	29082010	0.000000	0.05858	0.000000	0.03702	0.353000	0.29299	-0.760000	0.04756	-0.051000	0.13334	0.528000	0.53228	AAA	.	.		0.358	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		A	31294718	T	A	31294718	3	1	45	1	0	0	0	0	1	0	0	0	16600	1606	56	4	696	4	TRPM1	15	31294718	Missense_Mutation	SNP	T	TCGA-BC-A5W4-01A-11D-A28X-10		31294718	71236674	47	5949										
LCMT2	9836	hgsc.bcm.edu	37	chr15	43622043	43622043	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ctcatctgctcatagaccacGaaaagggcattaggaaaacg	9	10	3	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr15:43622043G>C	ENST00000305641.5	-	1	760	c.645C>G	c.(643-645)ttC>ttG	p.F215L	LCMT2_ENST00000544735.1_Intron|LCMT2_ENST00000567039.1_Intron|ADAL_ENST00000389651.4_5'Flank|ADAL_ENST00000428046.3_5'Flank|ADAL_ENST00000422466.2_5'Flank	NM_014793.4	NP_055608.2	O60294	TYW4_HUMAN	leucine carboxyl methyltransferase 2	215					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(1)|urinary_tract(1)	20		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)	CATAGACCACGAAAAGGGCAT	0.607																																					p.F215L		Atlas-SNP	.											.	LCMT2	48	.	0			c.C645G						.						42	36	38					15																	43622043		2201	4299	6500	SO:0001583	missense	9836	exon1			GACCACGAAAAGG	AF265443	CCDS10094.1	15q15.3	2007-01-26			ENSG00000168806	ENSG00000168806			17558	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 4"	611246				9628581, 17150819	Standard	NM_014793		Approved	KIAA0547, MGC9534, TYW4, PPM2	uc001zrg.3	O60294	OTTHUMG00000130705	ENST00000305641.5:c.645C>G	chr15.hg19:g.43622043G>C	ENSP00000307214:p.Phe215Leu	256.0	0.0		101.0	53.0	NM_014793	Q4JFT6|Q96B55|Q9NR10	Missense_Mutation	SNP	ENST00000305641.5	hg19	CCDS10094.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.283413	0.59867	.	.	ENSG00000168806	ENST00000305641	T	0.21734	1.99	5.39	3.5	0.40072	.	0.000000	0.85682	D	0.000000	T	0.15522	0.0374	L	0.46947	1.48	0.80722	D	1	P	0.48998	0.918	B	0.37480	0.251	T	0.03184	-1.1063	10	0.38643	T	0.18	-20.1703	8.3786	0.32457	0.1783:0.0:0.8217:0.0	.	215	O60294	LCMT2_HUMAN	L	215	ENSP00000307214:F215L	ENSP00000307214:F215L	F	-	3	2	LCMT2	41409335	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	0.579000	0.23788	0.817000	0.34445	0.655000	0.94253	TTC	.	.		0.607	LCMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253205.1	NM_014793		C	43622043	G	C	43622043	3	2	45	1	0	0	0	0	1	0	0	0	8688	1049	37	4	1419	4	LCMT2	15	43622043	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	12327325	43622043	58909349	48	5950										
ZNF710	374655	hgsc.bcm.edu	37	chr15	90611162	90611162	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	cggcgggttcgaccgtggaaCgccacaagaaggcccagctg	15	13	0	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr15:90611162C>T	ENST00000268154.4	+	2	1044	c.793C>T	c.(793-795)Cgc>Tgc	p.R265C		NM_198526.2	NP_940928.2	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(1)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	19	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			GACCGTGGAACGCCACAAGAA	0.652																																					p.R265C		Atlas-SNP	.											.	ZNF710	50	.	0			c.C793T						.						43	51	48					15																	90611162		2199	4295	6494	SO:0001583	missense	374655	exon2			GTGGAACGCCACA	AK094712	CCDS10358.1	15q26.1	2013-01-08			ENSG00000140548	ENSG00000140548		"Zinc fingers, C2H2-type"	25352	protein-coding gene	gene with protein product							Standard	XM_005254905		Approved	DKFZp547K1113, FLJ37393, FLJ00306	uc002bov.2	Q8N1W2	OTTHUMG00000149812	ENST00000268154.4:c.793C>T	chr15.hg19:g.90611162C>T	ENSP00000268154:p.Arg265Cys	196.0	0.0		94.0	51.0	NM_198526	A0AVS3|Q6ZMK9|Q8NDU0	Missense_Mutation	SNP	ENST00000268154.4	hg19	CCDS10358.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.398143	0.62177	.	.	ENSG00000140548	ENST00000268154	T	0.10005	2.92	4.96	4.96	0.65561	.	0.465853	0.18202	N	0.148465	T	0.07818	0.0196	N	0.22421	0.69	0.53005	D	0.999967	D	0.56968	0.978	B	0.34452	0.183	T	0.24154	-1.0168	10	0.87932	D	0	-65.6362	16.951	0.86245	0.0:1.0:0.0:0.0	.	265	Q8N1W2	ZN710_HUMAN	C	265	ENSP00000268154:R265C	ENSP00000268154:R265C	R	+	1	0	ZNF710	88412166	0.994000	0.37717	1.000000	0.80357	0.867000	0.49689	1.469000	0.35343	2.574000	0.86865	0.561000	0.74099	CGC	.	.		0.652	ZNF710-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313423.1	NM_198526		T	90611162	C	T	90611162	3	4	45	1	0	0	0	0	1	0	0	0	18130	536	19	1	795	1	ZNF710	15	90611162	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	46989119	90611162	11920230	49	5951										
UBN1	29855	hgsc.bcm.edu	37	chr16	4924702	4924702	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ttctggctacaaagagctgtCctgccaggctcccctcaata	8	14	2	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr16:4924702C>A	ENST00000396658.4	+	14	2994	c.2291C>A	c.(2290-2292)tCc>tAc	p.S764Y	UBN1_ENST00000590769.1_Missense_Mutation_p.S764Y|UBN1_ENST00000545171.1_Missense_Mutation_p.S764Y|UBN1_ENST00000262376.6_Missense_Mutation_p.S764Y	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	764					chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						AAAGAGCTGTCCTGCCAGGCT	0.557																																					p.S764Y		Atlas-SNP	.											.	UBN1	88	.	0			c.C2291A						.						59	65	63					16																	4924702		2197	4300	6497	SO:0001583	missense	29855	exon15			AGCTGTCCTGCCA	AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.2291C>A	chr16.hg19:g.4924702C>A	ENSP00000379894:p.Ser764Tyr	49.0	0.0		24.0	4.0	NM_001079514	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Missense_Mutation	SNP	ENST00000396658.4	hg19	CCDS10525.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.252105	0.59212	.	.	ENSG00000118900	ENST00000262376;ENST00000545171;ENST00000396658	T;T;T	0.29655	1.56;1.56;1.56	5.14	4.18	0.49190	.	0.523236	0.19361	N	0.116159	T	0.38480	0.1042	L	0.32530	0.975	0.32514	N	0.537184	P;P	0.47545	0.763;0.897	P;P	0.54590	0.549;0.756	T	0.52472	-0.8571	10	0.72032	D	0.01	-1.4924	14.246	0.65988	0.0:0.8515:0.1485:0.0	.	764;764	Q9NPG3-2;Q9NPG3	.;UBN1_HUMAN	Y	764	ENSP00000262376:S764Y;ENSP00000442379:S764Y;ENSP00000379894:S764Y	ENSP00000262376:S764Y	S	+	2	0	UBN1	4864703	0.984000	0.35163	0.968000	0.41197	0.938000	0.57974	3.617000	0.54181	1.400000	0.46741	0.462000	0.41574	TCC	.	.		0.557	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936		A	4924702	C	A	4924702	3	1	45	1	0	0	0	0	1	0	0	0	16907	855	30	3	2345	3	UBN1	16	4924702	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10		4924702	85430051	50	5952										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70894680	70894680	+	Frame_Shift_Del	DEL	C	C	-													0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	cccactggaccctcggagctCtgggttgcgctgatggccac							TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr16:70894680delC	ENST00000393567.2	-	70	12052	c.11902delG	c.(11902-11904)gagfs	p.E3968fs		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3968					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CCTCGGAGCTCTGGGTTGCGC	0.562																																					p.E3968fs		Atlas-INDEL	.											.	HYDIN	788	.	0			c.11903delA						.						1	1	1					16																	70894680		905	2004	2909	SO:0001589	frameshift_variant	54768	exon70			.	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.11902delG	chr16.hg19:g.70894680delC	ENSP00000377197:p.Glu3968fs	65.0	0.0		74.0	12.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Frame_Shift_Del	DEL	ENST00000393567.2	hg19	CCDS59269.1																																																																																			.	.		0.562	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			-	70894680	C	-	70894680	7	5	45	1	0	1	0	1	0	0	0	0	7476	922	32	0	3531	0	HYDIN	16	70894680	Frame_Shift_Del	DEL	C	TCGA-BC-A5W4-01A-11D-A28X-10	65969978	70894680	19460073	51	5953										
TP53	7157	hgsc.bcm.edu	37	chr17	7577111	7577111	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	gccggtctctcccaggacagGcacaaacacgcacctcaaag	9	16	2	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr17:7577111G>C	ENST00000269305.4	-	8	1016	c.827C>G	c.(826-828)gCc>gGc	p.A276G	TP53_ENST00000420246.2_Missense_Mutation_p.A276G|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.A276G|TP53_ENST00000455263.2_Missense_Mutation_p.A276G|TP53_ENST00000445888.2_Missense_Mutation_p.A276G	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	276	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		A -> D (in sporadic cancers; somatic mutation).|A -> G (in sporadic cancers; somatic mutation).|A -> P (in sporadic cancers; somatic mutation).|A -> S (in sporadic cancers; somatic mutation).|A -> T (in sporadic cancers; somatic mutation).|A -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.A276V(7)|p.A276D(6)|p.A276G(4)|p.?(2)|p.A276fs*69(2)|p.A276_R283delACPGRDRR(1)|p.C275fs*20(1)|p.A276fs*64(1)|p.A276fs*68(1)|p.L265_K305del41(1)|p.A276_C277delAC(1)|p.F270_D281del12(1)|p.V274_P278del(1)|p.A276fs*70(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCCAGGACAGGCACAAACACG	0.547		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.A276G	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,NS,0,1	TP53	33396	.	42	Substitution - Missense(17)|Whole gene deletion(8)|Deletion - In frame(7)|Deletion - Frameshift(5)|Unknown(2)|Complex - frameshift(2)|Insertion - Frameshift(1)	upper_aerodigestive_tract(6)|central_nervous_system(6)|breast(5)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|bone(4)|stomach(3)|urinary_tract(2)|oesophagus(2)|skin(2)|prostate(2)|ovary(1)|pancreas(1)	c.C827G						.						72	62	65					17																	7577111		2203	4300	6503	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGACAGGCACAAA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.827C>G	chr17.hg19:g.7577111G>C	ENSP00000269305:p.Ala276Gly	127.0	0.0		46.0	41.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.046851	0.93740	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99859	-7.24;-7.24;-7.24;-7.24;-7.24;-7.24	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99866	0.9937	M	0.89715	3.055	0.80722	D	1	D;D;D;P	0.63880	0.993;0.988;0.988;0.909	D;D;D;P	0.68483	0.93;0.936;0.958;0.89	D	0.96378	0.9279	10	0.87932	D	0	-17.5913	15.662	0.77193	0.0:0.0:1.0:0.0	.	276;276;276;276	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	G	276;276;276;276;276;265;144	ENSP00000352610:A276G;ENSP00000269305:A276G;ENSP00000398846:A276G;ENSP00000391127:A276G;ENSP00000391478:A276G;ENSP00000425104:A144G	ENSP00000269305:A276G	A	-	2	0	TP53	7517836	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.573000	0.98181	2.556000	0.86216	0.462000	0.41574	GCC	.	.		0.547	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577111	G	C	7577111	3	2	45	1	0	0	0	0	1	0	0	0	16396	1203	42	4	459	4	TP53	17	7577111	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		7577111	73618099	52	5954										
OMG	4974	hgsc.bcm.edu	37	chr17	29622317	29622317	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tgcagctgctgcttcatgtgAattgatagtctctgtggatg	12	7	2	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr17:29622317A>T	ENST00000247271.4	-	2	1294	c.1033T>A	c.(1033-1035)Tca>Aca	p.S345T	NF1_ENST00000356175.3_Intron|NF1_ENST00000358273.4_Intron	NM_002544.4	NP_002535.3	P23515	OMGP_HUMAN	oligodendrocyte myelin glycoprotein	345					cell adhesion (GO:0007155)|negative regulation of axonogenesis (GO:0050771)|neuron projection regeneration (GO:0031102)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|regulation of collateral sprouting of intact axon in response to injury (GO:0048683)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.0?(8)|p.?(3)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|stomach(1)	13		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;1.81e-13)|Epithelial(4;4.04e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.49e-12)|GBM - Glioblastoma multiforme(4;0.121)		GCTTCATGTGAATTGATAGTC	0.438																																					p.S345T		Atlas-SNP	.											.	OMG	30	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.T1033A						.						367	329	342					17																	29622317		2203	4300	6503	SO:0001583	missense	4974	exon2			CATGTGAATTGAT		CCDS11265.1	17q11-q12	2008-07-18			ENSG00000126861	ENSG00000126861			8135	protein-coding gene	gene with protein product		164345				1899288, 2277079	Standard	NM_002544		Approved	OMGP	uc002hgj.3	P23515	OTTHUMG00000132870	ENST00000247271.4:c.1033T>A	chr17.hg19:g.29622317A>T	ENSP00000247271:p.Ser345Thr	170.0	0.0		136.0	42.0	NM_002544	E1P659	Missense_Mutation	SNP	ENST00000247271.4	hg19	CCDS11265.1	.	.	.	.	.	.	.	.	.	.	A	11.51	1.661015	0.29515	.	.	ENSG00000126861	ENST00000247271	T	0.71934	-0.61	5.41	3.16	0.36331	.	0.458819	0.18257	N	0.146767	T	0.48370	0.1496	N	0.19112	0.55	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.24440	-1.0160	10	0.22109	T	0.4	-0.0223	3.8006	0.08757	0.6622:0.1284:0.072:0.1374	.	345	P23515	OMGP_HUMAN	T	345	ENSP00000247271:S345T	ENSP00000247271:S345T	S	-	1	0	OMG	26646443	0.467000	0.25831	0.453000	0.27007	0.929000	0.56500	0.946000	0.29069	0.415000	0.25817	-0.438000	0.05819	TCA	.	.		0.438	OMG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256350.2	NM_002544		T	29622317	A	T	29622317	3	4	45	1	0	0	0	0	1	0	0	0	10875	246	9	4	293	4	OMG	17	29622317	Missense_Mutation	SNP	A	TCGA-BC-A5W4-01A-11D-A28X-10	22045206	29622317	51572893	53	5955										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5428441	5428441	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ccacttgcacaaactcctaaCataatttctaccccttctga	2	15	2	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr18:5428441C>G	ENST00000341928.2	-	9	1276	c.936G>C	c.(934-936)atG>atC	p.M312I	EPB41L3_ENST00000540638.2_Missense_Mutation_p.M312I|EPB41L3_ENST00000400111.3_Missense_Mutation_p.M312I|EPB41L3_ENST00000342933.3_Missense_Mutation_p.M312I|EPB41L3_ENST00000544123.1_Missense_Mutation_p.M312I|EPB41L3_ENST00000542652.2_5'UTR	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	312	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						AAACTCCTAACATAATTTCTA	0.388																																					p.M312I		Atlas-SNP	.											.	EPB41L3	222	.	0			c.G936C						.						118	127	124					18																	5428441		2203	4300	6503	SO:0001583	missense	23136	exon9			TCCTAACATAATT	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.936G>C	chr18.hg19:g.5428441C>G	ENSP00000343158:p.Met312Ile	94.0	0.0		79.0	35.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	C	17.23	3.337402	0.60963	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1	5.31	5.31	0.75309	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.90967	0.7160	L	0.48362	1.52	0.80722	D	1	P;P;P;B;P	0.48911	0.692;0.681;0.917;0.022;0.726	P;B;D;B;P	0.63488	0.633;0.389;0.915;0.027;0.694	D	0.89652	0.3870	10	0.36615	T	0.2	.	18.973	0.92722	0.0:1.0:0.0:0.0	.	312;312;203;312;312	F5GX05;Q9Y2J2-3;A8K968;Q9Y2J2-2;Q9Y2J2	.;.;.;.;E41L3_HUMAN	I	312;203;312;203;312;312	ENSP00000343158:M312I;ENSP00000441174:M312I;ENSP00000341138:M312I;ENSP00000382981:M312I	ENSP00000343158:M312I	M	-	3	0	EPB41L3	5418441	1.000000	0.71417	0.997000	0.53966	0.827000	0.46813	6.029000	0.70895	2.455000	0.83008	0.655000	0.94253	ATG	.	.		0.388	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		G	5428441	C	G	5428441	3	3	45	1	0	0	0	0	1	0	0	0	5156	478	17	4	2383	4	EPB41L3	18	5428441	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10		5428441	72648807	54	5956										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9255937	9255939	+	In_Frame_Del	DEL	CTG	CTG	-													0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	aggtgagaagagcaaaaataCtgctgctattaaaaaaactg					rs568282731		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr18:9255937_9255939delCTG	ENST00000262126.4	+	9	2912_2914	c.2672_2674delCTG	c.(2671-2676)actgct>act	p.A893del	ANKRD12_ENST00000383440.2_In_Frame_Del_p.A870del|ANKRD12_ENST00000400020.3_In_Frame_Del_p.A870del	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	893						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						AGCAAAAATACTGCTGCTATTAA	0.345																																					p.891_891del		Atlas-INDEL	.											.	ANKRD12	167	.	0			c.2671_2673del						.																																			SO:0001651	inframe_deletion	23253	exon9			.	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.2672_2674delCTG	chr18.hg19:g.9255940_9255942delCTG	ENSP00000262126:p.Ala893del	45.0	0.0		49.0	12.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	In_Frame_Del	DEL	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.345	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		-	9255939	CTG	-	9255937	7	5	45	1	0	1	0	1	0	0	0	0	640	565	20	0	2702	0	ANKRD12	18	9255937	In_Frame_Del	DEL	CTG	TCGA-BC-A5W4-01A-11D-A28X-10	3827496	9255937	68821311	55	5957										
TYK2	7297	hgsc.bcm.edu	37	chr19	10475628	10475628	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	gtaggcccacagtggctcccGcggcctgtctgccggctggc	15	16	1	0	rs550060811		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr19:10475628G>A	ENST00000525621.1	-	8	1589	c.1108C>T	c.(1108-1110)Cgg>Tgg	p.R370W	TYK2_ENST00000524462.1_Missense_Mutation_p.R185W|TYK2_ENST00000529370.1_Missense_Mutation_p.R370W|TYK2_ENST00000264818.6_Missense_Mutation_p.R370W	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	370	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			AGTGGCTCCCGCGGCCTGTCT	0.617													G|||	1	0.000199681	0	0	5008	,	,		18461	0		0	False		,,,				2504	0.001				p.R370W		Atlas-SNP	.											.	TYK2	126	.	0			c.C1108T						.						48	50	49					19																	10475628		2203	4300	6503	SO:0001583	missense	7297	exon8			GCTCCCGCGGCCT		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.1108C>T	chr19.hg19:g.10475628G>A	ENSP00000431885:p.Arg370Trp	95.0	0.0		68.0	14.0	NM_003331	Q6QB10|Q96CH0	Missense_Mutation	SNP	ENST00000525621.1	hg19	CCDS12236.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.572705	0.45798	.	.	ENSG00000105397	ENST00000524462;ENST00000525621;ENST00000264818;ENST00000543792;ENST00000529370	T;T;T;T	0.10668	2.85;2.85;2.85;2.85	4.22	-1.01	0.10169	FERM domain (1);	1.740170	0.03671	N	0.243955	T	0.09113	0.0225	N	0.08118	0	0.09310	N	1	D;D	0.65815	0.995;0.989	P;P	0.48677	0.517;0.586	T	0.32877	-0.9890	10	0.66056	D	0.02	-2.09	8.252	0.31732	0.0:0.1173:0.3931:0.4895	.	370;370	E9PPF2;P29597	.;TYK2_HUMAN	W	185;370;370;117;370	ENSP00000433203:R185W;ENSP00000431885:R370W;ENSP00000264818:R370W;ENSP00000432728:R370W	ENSP00000264818:R370W	R	-	1	2	TYK2	10336628	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.215000	0.17562	-0.156000	0.11079	-0.514000	0.04452	CGG	.	.		0.617	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1			A	10475628	G	A	10475628	3	1	45	1	0	0	0	0	1	0	0	0	16825	1086	38	1	2527	1	TYK2	19	10475628	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		10475628	48653355	56	5958										
BAX	581	hgsc.bcm.edu	37	chr19	49464295	49464295	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ggagcaggtcacagtggtgcCctctccccatcttcagatca	10	14	5	1			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr19:49464295C>T	ENST00000345358.7	+	5	526				BAX_ENST00000539787.1_Intron|BAX_ENST00000354470.3_Intron|BAX_ENST00000415969.2_Intron|BAX_ENST00000293288.8_Missense_Mutation_p.P200S|BAX_ENST00000391871.3_Intron|CTD-2639E6.9_ENST00000599784.1_lincRNA	NM_138761.3|NM_138764.4	NP_620116.1|NP_620119.2	Q07812	BAX_HUMAN	BCL2-associated X protein						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell homeostatic proliferation (GO:0002358)|B cell negative selection (GO:0002352)|B cell receptor apoptotic signaling pathway (GO:1990117)|blood vessel remodeling (GO:0001974)|cellular response to organic substance (GO:0071310)|cellular response to UV (GO:0034644)|cerebral cortex development (GO:0021987)|development of secondary sexual characteristics (GO:0045136)|ectopic germ cell programmed cell death (GO:0035234)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells within a tissue (GO:0048873)|hypothalamus development (GO:0021854)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein binding (GO:0032091)|neuron apoptotic process (GO:0051402)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic DNA fragmentation (GO:1902512)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of developmental pigmentation (GO:0048087)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-embryonic camera-type eye morphogenesis (GO:0048597)|protein homooligomerization (GO:0051260)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)|protein oligomerization (GO:0051259)|regulation of cell cycle (GO:0051726)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|release of matrix enzymes from mitochondria (GO:0032976)|response to axon injury (GO:0048678)|response to gamma radiation (GO:0010332)|response to salt stress (GO:0009651)|response to toxic substance (GO:0009636)|retina development in camera-type eye (GO:0060041)|retinal cell apoptotic process (GO:1990009)|retinal cell programmed cell death (GO:0046666)|Sertoli cell proliferation (GO:0060011)|spermatid differentiation (GO:0048515)|T cell homeostatic proliferation (GO:0001777)|thymocyte apoptotic process (GO:0070242)|transformed cell apoptotic process (GO:0006927)|vagina development (GO:0060068)|viral process (GO:0016032)	BAX complex (GO:0097144)|Bcl-2 family protein complex (GO:0097136)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrial permeability transition pore complex (GO:0005757)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(4)	17		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)		ACAGTGGTGCCCTCTCCCCAT	0.622																																					p.P200S		Atlas-SNP	.											.	BAX	69	.	0			c.C598T						.						80	59	66					19																	49464295		2197	4290	6487	SO:0001627	intron_variant	581	exon5			TGGTGCCCTCTCC		CCDS12742.1, CCDS12743.1, CCDS12744.1, CCDS12745.1, CCDS12745.2	19q13.3-q13.4	2014-03-07			ENSG00000087088	ENSG00000087088			959	protein-coding gene	gene with protein product		600040				8358790	Standard	NM_138761		Approved	BCL2L4	uc002plf.1	Q07812	OTTHUMG00000160476	ENST00000345358.7:c.474+124C>T	chr19.hg19:g.49464295C>T		22.0	0.0		28.0	14.0	NM_004324	A8K4W1|P55269|Q07814|Q07815|Q8WZ49|Q9NR76|Q9NYG7|Q9UCZ6|Q9UCZ7|Q9UQD6	Missense_Mutation	SNP	ENST00000345358.7	hg19	CCDS12742.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.652901	0.29336	.	.	ENSG00000087088	ENST00000293288	T	0.13089	2.62	2.67	-1.75	0.08031	.	0.148125	0.42548	U	0.000681	T	0.05456	0.0144	.	.	.	0.09310	N	0.999993	B	0.19706	0.038	B	0.19391	0.025	T	0.28522	-1.0041	8	.	.	.	.	0.9509	0.01376	0.2932:0.364:0.1967:0.1461	.	200	Q07812-2	.	S	200	ENSP00000293288:P200S	.	P	+	1	0	BAX	54156107	0.000000	0.05858	0.000000	0.03702	0.197000	0.23852	-0.728000	0.04925	-0.263000	0.09378	0.462000	0.41574	CCT	.	.		0.622	BAX-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360767.1	NM_138763		T	49464295	C	T	49464295	1	4	45	0	1	0	0	0	0	0	0	0	1328	623	22	3		3	BAX	19	49464295	Intron	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	38988667	49464295	9664688	57	5959										
SIGLEC14	100049587	hgsc.bcm.edu	37	chr19	52149062	52149062	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	attgagctggacagttctctCcgtggtcacctgagctcctt	10	12	2	2			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr19:52149062C>T	ENST00000360844.6	-	3	714	c.673G>A	c.(673-675)Gag>Aag	p.E225K	SIGLEC5_ENST00000534261.2_5'Flank|SIGLEC5_ENST00000222107.4_Intron|SIGLEC5_ENST00000599649.1_Intron|SIGLEC5_ENST00000429354.3_Intron	NM_001098612.1	NP_001092082.1	Q08ET2	SIG14_HUMAN	sialic acid binding Ig-like lectin 14	225	Ig-like C2-type 1.				cell adhesion (GO:0007155)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.E225K(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	29		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000965)|OV - Ovarian serous cystadenocarcinoma(262;0.0195)		ACAGTTCTCTCCGTGGTCACC	0.627																																					p.E225K		Atlas-SNP	.											SIGLEC14,NS,carcinoma,0,2	SIGLEC14	46	.	2	Substitution - Missense(2)	endometrium(2)	c.G673A						.						69	68	69					19																	52149062		2070	4205	6275	SO:0001583	missense	100049587	exon3			TTCTCTCCGTGGT	AY854038	CCDS42604.1	19q13.41	2013-01-29			ENSG00000254415	ENSG00000254415		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	32926	protein-coding gene	gene with protein product						17012248	Standard	NM_001098612		Approved		uc002pxf.4	Q08ET2	OTTHUMG00000165511	ENST00000360844.6:c.673G>A	chr19.hg19:g.52149062C>T	ENSP00000354090:p.Glu225Lys	695.0	1.0		441.0	196.0	NM_001098612	Q6UXG0	Missense_Mutation	SNP	ENST00000360844.6	hg19	CCDS42604.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.371648	0.61624	.	.	ENSG00000254415	ENST00000360844	D	0.86865	-2.18	3.1	2.02	0.26589	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.145914	0.31335	N	0.007839	T	0.80602	0.4654	M	0.62723	1.935	0.20821	N	0.999847	P	0.42993	0.797	B	0.33846	0.171	T	0.72620	-0.4238	10	0.54805	T	0.06	.	8.0781	0.30729	0.0:0.7485:0.2515:0.0	.	225	Q08ET2	SIG14_HUMAN	K	225	ENSP00000354090:E225K	ENSP00000354090:E225K	E	-	1	0	SIGLEC14	56840874	0.002000	0.14202	0.334000	0.25495	0.939000	0.58152	0.012000	0.13287	0.617000	0.30160	0.514000	0.50259	GAG	.	.		0.627	SIGLEC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466899.2	NM_001098612		T	52149062	C	T	52149062	3	4	45	1	0	0	0	0	1	0	0	0	14324	864	30	3	537	3	SIGLEC14	19	52149062	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	2684767	52149062	6979921	58	5960										
NLRP11	204801	hgsc.bcm.edu	37	chr19	56321586	56321586	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	tcataggctaattgaagtatGtagaacacatctgacgaaac	8	7	2	3			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr19:56321586G>A	ENST00000589093.1	-	3	483	c.390C>T	c.(388-390)taC>taT	p.Y130Y	NLRP11_ENST00000360133.3_Silent_p.Y130Y|NLRP11_ENST00000592953.1_Silent_p.Y31Y|NLRP11_ENST00000443188.1_Silent_p.Y130Y|NLRP11_ENST00000589824.2_Silent_p.Y130Y			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	130							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		ATTGAAGTATGTAGAACACAT	0.353																																					p.Y130Y		Atlas-SNP	.											.	NLRP11	139	.	0			c.C390T						.						56	53	54					19																	56321586		2203	4300	6503	SO:0001819	synonymous_variant	204801	exon5			AAGTATGTAGAAC	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.390C>T	chr19.hg19:g.56321586G>A		131.0	0.0		107.0	55.0	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Silent	SNP	ENST00000589093.1	hg19	CCDS12935.1																																																																																			.	.		0.353	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		A	56321586	G	A	56321586	2	1	45	1	0	0	0	0	0	0	0	1	10482	1372	48	3		3	NLRP11	19	56321586	Silent	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10	4172524	56321586	2807397	59	5961										
BMP2	650	hgsc.bcm.edu	37	chr20	6759153	6759153	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ggtgaatcagaatgcaagcaGgtgggaaagttttgatgtca	14	4	2	3			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr20:6759153G>T	ENST00000378827.4	+	3	1827	c.608G>T	c.(607-609)aGg>aTg	p.R203M		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	203					activation of MAPK activity (GO:0000187)|atrioventricular valve morphogenesis (GO:0003181)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|bone mineralization (GO:0030282)|bone mineralization involved in bone maturation (GO:0035630)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiocyte differentiation (GO:0035051)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation (GO:0002062)|corticotropin hormone secreting cell differentiation (GO:0060128)|embryo development (GO:0009790)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchyme development (GO:0060485)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of calcium-independent cell-cell adhesion (GO:0051042)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|pericardium development (GO:0060039)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of odontogenesis (GO:0042482)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of Wnt signaling pathway by BMP signaling pathway (GO:0060804)|protein destabilization (GO:0031648)|protein phosphorylation (GO:0006468)|proteoglycan metabolic process (GO:0006029)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP receptor binding (GO:0070700)|phosphatase activator activity (GO:0019211)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)|retinol dehydrogenase activity (GO:0004745)|SMAD binding (GO:0046332)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	13						AATGCAAGCAGGTGGGAAAGT	0.493																																					p.R203M		Atlas-SNP	.											.	BMP2	45	.	0			c.G608T						.						55	57	56					20																	6759153		2203	4300	6503	SO:0001583	missense	650	exon3			CAAGCAGGTGGGA		CCDS13099.1	20p12	2014-01-30			ENSG00000125845	ENSG00000125845		"Bone morphogenetic proteins", "Endogenous ligands"	1069	protein-coding gene	gene with protein product		112261		BMP2A		2376592	Standard	NM_001200		Approved		uc002wmu.1	P12643	OTTHUMG00000031833	ENST00000378827.4:c.608G>T	chr20.hg19:g.6759153G>T	ENSP00000368104:p.Arg203Met	100.0	0.0		96.0	44.0	NM_001200		Missense_Mutation	SNP	ENST00000378827.4	hg19	CCDS13099.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.745024	0.49151	.	.	ENSG00000125845	ENST00000378827	T	0.65732	-0.17	5.7	-3.76	0.04359	Transforming growth factor-beta, N-terminal (1);	0.330970	0.35838	N	0.002949	T	0.69717	0.3142	M	0.82716	2.605	0.21878	N	0.999492	B	0.30793	0.295	P	0.44518	0.452	T	0.72033	-0.4412	10	0.72032	D	0.01	.	14.3182	0.66465	0.8386:0.0:0.1614:0.0	.	203	P12643	BMP2_HUMAN	M	203	ENSP00000368104:R203M	ENSP00000368104:R203M	R	+	2	0	BMP2	6707153	1.000000	0.71417	0.086000	0.20670	0.995000	0.86356	2.139000	0.42149	-0.453000	0.07076	0.650000	0.86243	AGG	.	.		0.493	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3			T	6759153	G	T	6759153	3	4	45	1	0	0	0	0	1	0	0	0	1459	1000	35	3	614	3	BMP2	20	6759153	Missense_Mutation	SNP	G	TCGA-BC-A5W4-01A-11D-A28X-10		6759153	56266367	60	5962										
CHD6	84181	hgsc.bcm.edu	37	chr20	40045242	40045242	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	gctcaccttgtggatctgggCcgccaatgctgcgccgttgc	13	14	2	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chr20:40045242C>T	ENST00000373233.3	-	33	6649	c.6472G>A	c.(6472-6474)Gcc>Acc	p.A2158T	CHD6_ENST00000480022.1_5'Flank	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2158					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				TGGATCTGGGCCGCCAATGCT	0.547																																					p.A2158T		Atlas-SNP	.											CHD6,NS,carcinoma,0,1	CHD6	312	.	0			c.G6472A						.						97	86	90					20																	40045242		2203	4300	6503	SO:0001583	missense	84181	exon33			TCTGGGCCGCCAA	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.6472G>A	chr20.hg19:g.40045242C>T	ENSP00000362330:p.Ala2158Thr	89.0	0.0		64.0	20.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	C	4.346	0.063610	0.08388	.	.	ENSG00000124177	ENST00000373233	D	0.85861	-2.04	5.46	2.27	0.28462	.	0.209320	0.34002	N	0.004356	T	0.63803	0.2542	N	0.12569	0.235	0.30644	N	0.75615	B	0.09022	0.002	B	0.04013	0.001	T	0.49560	-0.8927	10	0.10636	T	0.68	-8.2947	2.7837	0.05368	0.3849:0.3722:0.1255:0.1174	.	2158	Q8TD26	CHD6_HUMAN	T	2158	ENSP00000362330:A2158T	ENSP00000362330:A2158T	A	-	1	0	CHD6	39478656	0.031000	0.19500	0.931000	0.37212	0.070000	0.16714	0.244000	0.18124	0.694000	0.31654	0.655000	0.94253	GCC	.	.		0.547	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			T	40045242	C	T	40045242	3	4	45	1	0	0	0	0	1	0	0	0	3331	739	26	3	1695	3	CHD6	20	40045242	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	33286089	40045242	22980278	61	5963										
PIN4	5303	hgsc.bcm.edu	37	chrX	71401594	71401594	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	ggcttctaaaggggcttgtaCggcaactggagcggttcagc	15	9	2	0	rs375360841		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chrX:71401594C>A	ENST00000373669.2	+	1	66	c.34C>A	c.(34-36)Cgg>Agg	p.R12R	PIN4_ENST00000423432.2_Silent_p.R12R|PIN4_ENST00000218432.5_Silent_p.R12R	NM_006223.3	NP_006214.2	Q9Y237	PIN4_HUMAN	protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)	0	Necessary for association with the pre- rRNP complexes.|Necessary for nuclear localization and DNA-binding.				protein folding (GO:0006457)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome (GO:0030684)|spindle (GO:0005819)	bent DNA binding (GO:0003681)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(2)	3	Renal(35;0.156)					GGGGCTTGTACGGCAACTGGA	0.542																																					p.R12R		Atlas-SNP	.											.	PIN4	8	.	0			c.C34A						.						64	59	61					X																	71401594		2203	4300	6503	SO:0001819	synonymous_variant	5303	exon1			CTTGTACGGCAAC	AB009690	CCDS14417.1, CCDS55447.1	Xq13.1	2008-02-05	2006-01-12		ENSG00000102309	ENSG00000102309			8992	protein-coding gene	gene with protein product		300252	"protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)"			16522211, 17875217	Standard	NM_006223		Approved	PAR14, PAR17, EPVH	uc004eam.3	Q9Y237	OTTHUMG00000021811	ENST00000373669.2:c.34C>A	chrX.hg19:g.71401594C>A		243.0	2.0		171.0	163.0	NM_001170747	A8E0G6|B3KXM0|F5H1P5|Q0D2H3|Q3MHV0|Q52M21|Q5HYW6|Q6IRW4	Silent	SNP	ENST00000373669.2	hg19	CCDS14417.1																																																																																			.	.		0.542	PIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057175.2	NM_006223		A	71401594	C	A	71401594	2	1	45	1	0	0	0	0	0	0	0	1	11940	527	19	1		1	PIN4	23	71401594	Silent	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10		71401594	83868966	62	5964										
TAF9B	51616	hgsc.bcm.edu	37	chrX	77392438	77392438	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.699428571428571	0.999183673469388	0.608198757763975	1	1	0	taggagtagtaggtttgctaCtaacagcaccaacacttaat	8	8	0	0			TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	g.chrX:77392438C>A	ENST00000341864.5	-	5	549	c.455G>T	c.(454-456)aGt>aTt	p.S152I		NM_015975.4	NP_057059.2	Q9HBM6	TAF9B_HUMAN	TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa	152					DNA-templated transcription, initiation (GO:0006352)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell growth (GO:0030307)|programmed cell death (GO:0012501)|protein stabilization (GO:0050821)|response to organic cyclic compound (GO:0014070)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	14						AGGTTTGCTACTAACAGCACC	0.403																																					p.S152I		Atlas-SNP	.											.	TAF9B	30	.	0			c.G455T						.						159	127	138					X																	77392438		2203	4296	6499	SO:0001583	missense	51616	exon5			TTGCTACTAACAG	AF220509	CCDS35340.1	Xq13.1-q21.1	2010-08-16	2006-01-04	2006-01-04	ENSG00000187325	ENSG00000187325			17306	protein-coding gene	gene with protein product		300754	"TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa"	TAF9L		15899866	Standard	XM_005262142		Approved	TAFII31L, DN-7, DN7, TFIID-31	uc004eda.3	Q9HBM6	OTTHUMG00000021887	ENST00000341864.5:c.455G>T	chrX.hg19:g.77392438C>A	ENSP00000339917:p.Ser152Ile	107.0	0.0		83.0	5.0	NM_015975	B2RUZ9|Q9Y2S3	Missense_Mutation	SNP	ENST00000341864.5	hg19	CCDS35340.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.275270	0.40194	.	.	ENSG00000187325	ENST00000341864	T	0.32753	1.44	4.84	2.01	0.26516	.	0.222198	0.46442	D	0.000282	T	0.20495	0.0493	L	0.43923	1.385	0.41892	D	0.990373	B	0.22909	0.077	B	0.18871	0.023	T	0.07046	-1.0793	10	0.38643	T	0.18	-0.9529	3.7105	0.08418	0.0:0.4785:0.1828:0.3388	.	152	Q9HBM6	TAF9B_HUMAN	I	152	ENSP00000339917:S152I	ENSP00000339917:S152I	S	-	2	0	TAF9B	77279094	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	0.844000	0.27654	0.101000	0.17610	0.600000	0.82982	AGT	.	.		0.403	TAF9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057308.1	NM_015975		A	77392438	C	A	77392438	3	1	45	1	0	0	0	0	1	0	0	0	15551	565	20	3	312	3	TAF9B	23	77392438	Missense_Mutation	SNP	C	TCGA-BC-A5W4-01A-11D-A28X-10	5990844	77392438	77878122	63	5965										
GPBP1L1	60313	hgsc.bcm.edu	37	chr1	46124754	46124754	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	gcaggaacaaaatcatgctgCgccatttaggtccagtgtct	10	10	2	0	rs144406702		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr1:46124754C>A	ENST00000290795.3	-	3	1227	c.6G>T	c.(4-6)gcG>gcT	p.A2A	GPBP1L1_ENST00000355105.3_Silent_p.A2A			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	2					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					AATCATGCTGCGCCATTTAGG	0.413																																					p.A2A		Atlas-SNP	.											GPBP1L1,colon,carcinoma,0,1	GPBP1L1	43	.	0			c.G6T						.						142	132	136					1																	46124754		2203	4300	6503	SO:0001819	synonymous_variant	60313	exon4			ATGCTGCGCCATT		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.6G>T	chr1.hg19:g.46124754C>A		112.0	0.0		51.0	3.0	NM_021639	D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	hg19	CCDS528.1																																																																																			.	C|1.000;T|0.000		0.413	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639		A	46124754	C	A	46124754	2	1	46	1	0	0	0	0	0	0	0	1	6604	755	27	1		1	GPBP1L1	1	46124754	Silent	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10		46124754	203125867	1	5966										
INSRR	3645	hgsc.bcm.edu	37	chr1	156815550	156815550	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ggactccatctcggcctcagGatccccgtcttcgccgtcga	10	17	3	0			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr1:156815550G>T	ENST00000368195.3	-	10	2431	c.2035C>A	c.(2035-2037)Cct>Act	p.P679T	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	679	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TCGGCCTCAGGATCCCCGTCT	0.652																																					p.P679T		Atlas-SNP	.											.	INSRR	309	.	0			c.C2035A						.						40	36	37					1																	156815550		2203	4300	6503	SO:0001583	missense	3645	exon10			CCTCAGGATCCCC	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2035C>A	chr1.hg19:g.156815550G>T	ENSP00000357178:p.Pro679Thr	76.0	0.0		81.0	4.0	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	G	2.916	-0.224202	0.06061	.	.	ENSG00000027644	ENST00000368195	T	0.43688	0.94	4.58	2.66	0.31614	Fibronectin, type III (3);	0.520885	0.16212	N	0.224460	T	0.10423	0.0255	.	.	.	0.31210	N	0.698806	B	0.02656	0.0	B	0.01281	0.0	T	0.22208	-1.0223	9	0.22706	T	0.39	.	8.0	0.30291	0.0914:0.1623:0.7462:0.0	.	679	P14616	INSRR_HUMAN	T	679	ENSP00000357178:P679T	ENSP00000357178:P679T	P	-	1	0	INSRR	155082174	0.107000	0.21998	0.009000	0.14445	0.021000	0.10359	2.842000	0.48230	0.635000	0.30488	-0.305000	0.09177	CCT	.	.		0.652	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		T	156815550	G	T	156815550	3	4	46	1	0	0	0	0	1	0	0	0	7783	1174	41	3	1909	3	INSRR	1	156815550	Missense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10	110690796	156815550	92435071	2	5967										
POU2F1	5451	hgsc.bcm.edu	37	chr1	167384897	167384897	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	aaccctgttagcttggtctcTgccgccgcagcatctgcagg	11	14	2	0			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr1:167384897T>C	ENST00000541643.3	+	17	2244	c.2082T>C	c.(2080-2082)tcT>tcC	p.S694S	POU2F1_ENST00000367862.5_Silent_p.S706S|POU2F1_ENST00000420254.3_Intron|POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000429375.2_Silent_p.S654S|POU2F1_ENST00000367866.2_Silent_p.S717S			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	694					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						GCTTGGTCTCTGCCGCCGCAG	0.592																																					p.S717S		Atlas-SNP	.											.	POU2F1	120	.	0			c.T2151C						.						146	134	138					1																	167384897		2203	4300	6503	SO:0001819	synonymous_variant	5451	exon16			GGTCTCTGCCGCC	BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190		"Homeoboxes / POU class"	9212	protein-coding gene	gene with protein product		164175	"POU domain class 2, transcription factor 1"	OTF1		1887216	Standard	NM_002697		Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000541643.3:c.2082T>C	chr1.hg19:g.167384897T>C		133.0	0.0		80.0	21.0	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Silent	SNP	ENST00000541643.3	hg19																																																																																				.	.		0.592	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697		C	167384897	T	C	167384897	2	2	46	1	0	0	0	0	0	0	0	1	12280	1567	55	2		2	POU2F1	1	167384897	Silent	SNP	T	TCGA-BC-A69H-01A-11D-A30V-10	10569347	167384897	81865724	3	5968										
PKP1	5317	hgsc.bcm.edu	37	chr1	201294914	201294914	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ggccgcagaagctgcccggcTtctcctgtctgacatgtggt	13	13	2	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr1:201294914T>C	ENST00000352845.3	+	13	2117	c.2117T>C	c.(2116-2118)cTt>cCt	p.L706P	PKP1_ENST00000367324.3_Missense_Mutation_p.L685P|PKP1_ENST00000263946.3_Missense_Mutation_p.L706P			Q13835	PKP1_HUMAN	plakophilin 1	706					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						GCTGCCCGGCTTCTCCTGTCT	0.562																																					p.L706P		Atlas-SNP	.											.	PKP1	127	.	0			c.T2117C						.						67	62	64					1																	201294914		2203	4300	6503	SO:0001583	missense	5317	exon13			CCCGGCTTCTCCT	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"Armadillo repeat containing"	9023	protein-coding gene	gene with protein product	"ectodermal dysplasia/skin fragility syndrome"	601975	"plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.2117T>C	chr1.hg19:g.201294914T>C	ENSP00000295597:p.Leu706Pro	139.0	0.0		116.0	25.0	NM_000299	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	hg19	CCDS30966.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.110130	0.77210	.	.	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.50277	0.75;0.75;0.75	5.29	5.29	0.74685	Armadillo-like helical (1);Armadillo-type fold (1);	0.149594	0.44483	D	0.000451	T	0.63295	0.2499	L	0.53249	1.67	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.76575	0.968;0.988;0.982	T	0.61840	-0.6980	10	0.37606	T	0.19	-2.7201	15.2179	0.73285	0.0:0.0:0.0:1.0	.	293;685;706	Q14BN3;Q13835-2;Q13835	.;.;PKP1_HUMAN	P	685;706;706	ENSP00000356293:L685P;ENSP00000263946:L706P;ENSP00000295597:L706P	ENSP00000263946:L706P	L	+	2	0	PKP1	199561537	0.999000	0.42202	0.985000	0.45067	0.926000	0.56050	5.471000	0.66762	1.992000	0.58205	0.533000	0.62120	CTT	.	.		0.562	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		C	201294914	T	C	201294914	3	2	46	1	0	0	0	0	1	0	0	0	11993	1609	56	2	2167	2	PKP1	1	201294914	Missense_Mutation	SNP	T	TCGA-BC-A69H-01A-11D-A30V-10	33910017	201294914	47955707	4	5969										
USH2A	7399	hgsc.bcm.edu	37	chr1	215802343	215802343	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	tgctgcggatactcacaggtGtcccagaccggggaattttg	13	10	1	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr1:215802343G>A	ENST00000307340.3	-	71	15718	c.15332C>T	c.(15331-15333)aCa>aTa	p.T5111I	SNORD116_ENST00000365628.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.T5135I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	5111					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACTCACAGGTGTCCCAGACCG	0.498										HNSCC(13;0.011)																											p.T5111I		Atlas-SNP	.											.	USH2A	1168	.	0			c.C15332T						.						111	114	113					1																	215802343		2203	4300	6503	SO:0001583	missense	7399	exon71			ACAGGTGTCCCAG	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.15332C>T	chr1.hg19:g.215802343G>A	ENSP00000305941:p.Thr5111Ile	164.0	0.0		109.0	13.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.081370	0.76528	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.13778	2.59;2.56	5.67	5.67	0.87782	.	0.202390	0.24187	U	0.040742	T	0.22666	0.0547	L	0.60455	1.87	0.40500	D	0.980631	P	0.50272	0.933	P	0.44860	0.462	T	0.01071	-1.1461	10	0.62326	D	0.03	.	19.7686	0.96352	0.0:0.0:1.0:0.0	.	5111	O75445	USH2A_HUMAN	I	5111;5135	ENSP00000305941:T5111I;ENSP00000355910:T5135I	ENSP00000305941:T5111I	T	-	2	0	USH2A	213868966	0.992000	0.36948	0.971000	0.41717	0.811000	0.45836	4.681000	0.61663	2.665000	0.90641	0.591000	0.81541	ACA	.	.		0.498	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	215802343	G	A	215802343	3	1	46	1	0	0	0	0	1	0	0	0	17051	1377	48	3	284	3	USH2A	1	215802343	Missense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10	14507429	215802343	33448278	5	5970										
AMMECR1L	83607	hgsc.bcm.edu	37	chr2	128628831	128628831	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	tggtgtcattacctggttaaCgtgtattccctgagtcctga	10	9	1	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr2:128628831C>T	ENST00000272647.5	-	4	770	c.510G>A	c.(508-510)acG>acA	p.T170T	AMMECR1L_ENST00000393001.1_Silent_p.T170T	NM_001199140.1	NP_001186069.1	Q6DCA0	AMERL_HUMAN	AMMECR1-like	170	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.									central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	9	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.07)		ACCTGGTTAACGTGTATTCCC	0.458																																					p.T170T		Atlas-SNP	.											.	AMMECR1L	22	.	0			c.G510A						.						74	72	73					2																	128628831		2203	4300	6503	SO:0001819	synonymous_variant	83607	exon4			GGTTAACGTGTAT		CCDS2152.1	2q21	2012-11-15	2012-11-15		ENSG00000144233	ENSG00000144233			28658	protein-coding gene	gene with protein product			"AMME chromosomal region gene 1-like"				Standard	NM_001199140		Approved	MGC4268	uc002tpl.3	Q6DCA0	OTTHUMG00000131535	ENST00000272647.5:c.510G>A	chr2.hg19:g.128628831C>T		74.0	0.0		44.0	10.0	NM_031445	B4E276	Silent	SNP	ENST00000272647.5	hg19	CCDS2152.1																																																																																			.	.		0.458	AMMECR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254392.1	NM_031445		T	128628831	C	T	128628831	2	4	46	1	0	0	0	0	0	0	0	1	579	523	19	1		1	AMMECR1L	2	128628831	Silent	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10		128628831	114570542	6	5971										
IL5RA	3568	hgsc.bcm.edu	37	chr3	3137002	3137002	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	cctgcaaatatccattccttGtattgtgtatttttacttca	4	9	1	0			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr3:3137002G>T	ENST00000446632.2	-	8	1410	c.836C>A	c.(835-837)aCa>aAa	p.T279K	IL5RA_ENST00000256452.3_Missense_Mutation_p.T279K|IL5RA_ENST00000418488.2_Intron|IL5RA_ENST00000430514.2_Missense_Mutation_p.T279K|IL5RA_ENST00000445864.2_Intron|IL5RA_ENST00000438560.1_Missense_Mutation_p.T279K|IL5RA_ENST00000383846.1_Missense_Mutation_p.T279K|IL5RA_ENST00000456302.1_Missense_Mutation_p.T279K|IL5RA_ENST00000311981.8_Missense_Mutation_p.T279K	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	279	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)			cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		TCCATTCCTTGTATTGTGTAT	0.328																																					p.T279K	GBM(169;430 2801 24955 28528)	Atlas-SNP	.											.	IL5RA	55	.	0			c.C836A						.						72	72	72					3																	3137002		2203	4300	6503	SO:0001583	missense	3568	exon8			TTCCTTGTATTGT	M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"Interleukins and interleukin receptors", "CD molecules"	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.836C>A	chr3.hg19:g.3137002G>T	ENSP00000412209:p.Thr279Lys	161.0	0.0		116.0	51.0	NM_001243099	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Missense_Mutation	SNP	ENST00000446632.2	hg19	CCDS2559.1	.	.	.	.	.	.	.	.	.	.	G	4.694	0.129079	0.08981	.	.	ENSG00000091181	ENST00000446632;ENST00000438560;ENST00000256452;ENST00000383846;ENST00000311981;ENST00000430514;ENST00000456302	D;D;D;D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99;-1.99;-1.99;-1.99	5.0	0.227	0.15359	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.788201	0.11359	N	0.572071	T	0.77870	0.4195	L	0.56396	1.775	0.09310	N	1	B;P;P;B	0.49090	0.418;0.919;0.763;0.177	B;B;B;B	0.43052	0.068;0.406;0.293;0.049	T	0.66118	-0.6003	10	0.06236	T	0.91	-1.3347	6.7952	0.23721	0.5903:0.0:0.4097:0.0	.	279;279;279;279	B4E2G0;Q01344-3;Q01344-2;Q01344	.;.;.;IL5RA_HUMAN	K	279	ENSP00000412209:T279K;ENSP00000390753:T279K;ENSP00000256452:T279K;ENSP00000373358:T279K;ENSP00000309196:T279K;ENSP00000400400:T279K;ENSP00000392059:T279K	ENSP00000256452:T279K	T	-	2	0	IL5RA	3112002	0.004000	0.15560	0.001000	0.08648	0.027000	0.11550	0.569000	0.23638	0.098000	0.17522	-0.345000	0.07892	ACA	.	.		0.328	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2			T	3137002	G	T	3137002	3	4	46	1	0	0	0	0	1	0	0	0	7709	1377	48	3	472	3	IL5RA	3	3137002	Missense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10		3137002	194885428	7	5972										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10417206	10417206	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	cacgccaatgatgaagaactTgacaaagtactgcacgtaga	9	9	0	5			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr3:10417206T>C	ENST00000352432.4	-	10	1393	c.1324A>G	c.(1324-1326)Aag>Gag	p.K442E	ATP2B2_ENST00000397077.1_Missense_Mutation_p.K397E|ATP2B2_ENST00000360273.2_Missense_Mutation_p.K442E|ATP2B2_ENST00000343816.4_Missense_Mutation_p.K428E|ATP2B2_ENST00000383800.4_Missense_Mutation_p.K397E			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	442					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						ATGAAGAACTTGACAAAGTAC	0.587																																					p.K442E	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A1324G						.						96	89	91					3																	10417206		2203	4300	6503	SO:0001583	missense	491	exon11			AGAACTTGACAAA	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.1324A>G	chr3.hg19:g.10417206T>C	ENSP00000324172:p.Lys442Glu	135.0	0.0		126.0	13.0	NM_001001331	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.760115	0.89932	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42;-2.42	4.48	4.48	0.54585	ATPase, P-type, ATPase-associated domain (1);	0.096864	0.64402	D	0.000001	D	0.82416	0.5032	N	0.20483	0.58	0.80722	D	1	P;B;B	0.48089	0.905;0.099;0.233	B;B;B	0.43508	0.422;0.042;0.245	D	0.83890	0.0284	10	0.45353	T	0.12	-28.7124	13.9721	0.64247	0.0:0.0:0.0:1.0	.	377;409;442	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	E	442;397;397;442;428;377;298;442	ENSP00000324172:K442E;ENSP00000373311:K397E;ENSP00000380267:K397E;ENSP00000353414:K442E;ENSP00000344677:K428E;ENSP00000414854:K298E	ENSP00000342954:K442E	K	-	1	0	ATP2B2	10392206	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.868000	0.87116	1.884000	0.54569	0.459000	0.35465	AAG	.	.		0.587	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		C	10417206	T	C	10417206	3	2	46	1	0	0	0	0	1	0	0	0	1140	1821	63	2	2459	2	ATP2B2	3	10417206	Missense_Mutation	SNP	T	TCGA-BC-A69H-01A-11D-A30V-10	7280204	10417206	187605224	8	5973										
PXK	54899	hgsc.bcm.edu	37	chr3	58395296	58395296	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	actgacaagagctcagtcccAccatggatctgaggaggaaa	11	10	2	3			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr3:58395296A>G	ENST00000356151.2	+	15	1455	c.1346A>G	c.(1345-1347)cAc>cGc	p.H449R	PXK_ENST00000479241.1_Missense_Mutation_p.H432R|PXK_ENST00000302779.5_Missense_Mutation_p.H432R|PXK_ENST00000536660.1_Missense_Mutation_p.H312R|PXK_ENST00000484288.1_Missense_Mutation_p.H449R|PXK_ENST00000383715.4_Missense_Mutation_p.H432R|PXK_ENST00000463280.1_Missense_Mutation_p.H416R|PXK_ENST00000383716.3_Missense_Mutation_p.H416R	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase											cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		GCTCAGTCCCACCATGGATCT	0.418																																					p.H449R		Atlas-SNP	.											.	PXK	89	.	0			c.A1346G						.						62	62	62					3																	58395296		2203	4300	6503	SO:0001583	missense	54899	exon15			AGTCCCACCATGG	AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.1346A>G	chr3.hg19:g.58395296A>G	ENSP00000348472:p.His449Arg	253.0	1.0		196.0	93.0	NM_017771		Missense_Mutation	SNP	ENST00000356151.2	hg19	CCDS2889.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.52|19.52	3.843105|3.843105	0.71488|0.71488	.|.	.|.	ENSG00000168297|ENSG00000168297	ENST00000356151;ENST00000302779;ENST00000383716;ENST00000463280;ENST00000383715;ENST00000484288;ENST00000479241;ENST00000536660;ENST00000536750|ENST00000479134;ENST00000495557	T;T;T;T;T;T;T;T|.	0.32023|.	3.11;3.11;3.11;1.5;1.48;1.5;1.47;3.11|.	5.75|5.75	5.75|5.75	0.90469|0.90469	Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71476|0.71476	0.3344|0.3344	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.71674|.	0.997;0.996;0.994;0.998;0.996;0.996|.	D;D;D;D;D;P|.	0.70016|.	0.933;0.918;0.917;0.967;0.918;0.89|.	T|T	0.70498|0.70498	-0.4855|-0.4855	10|5	0.23302|.	T|.	0.38|.	-14.7244|-14.7244	14.9154|14.9154	0.70792|0.70792	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	416;416;416;449;432;449|.	E9PD56;Q7Z7A4-6;B4DID9;Q7Z7A4;Q7Z7A4-4;Q7Z7A4-2|.	.;.;.;PXK_HUMAN;.;.|.	R|A	449;432;416;416;432;449;432;312;312|204;21	ENSP00000348472:H449R;ENSP00000305045:H432R;ENSP00000373222:H416R;ENSP00000417903:H416R;ENSP00000373221:H432R;ENSP00000417915:H449R;ENSP00000419049:H432R;ENSP00000438356:H312R|.	ENSP00000305045:H432R|.	H|T	+|+	2|1	0|0	PXK|PXK	58370336|58370336	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.787000|0.787000	0.44495|0.44495	6.908000|6.908000	0.75730|0.75730	2.315000|2.315000	0.78130|0.78130	0.519000|0.519000	0.50382|0.50382	CAC|ACC	.	.		0.418	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771		G	58395296	A	G	58395296	3	3	46	1	0	0	0	0	1	0	0	0	12864	159	6	2	1404	2	PXK	3	58395296	Missense_Mutation	SNP	A	TCGA-BC-A69H-01A-11D-A30V-10	47978090	58395296	139627134	9	5974										
FGFR3	2261	hgsc.bcm.edu	37	chr4	1807577	1807577	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	gactactccttcgacacctgCaagccgcccgaggagcagct	10	16	0	0			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr4:1807577C>T	ENST00000260795.2	+	12	1848	c.1746C>T	c.(1744-1746)tgC>tgT	p.C582C	FGFR3_ENST00000440486.2_Silent_p.C582C|FGFR3_ENST00000481110.2_Silent_p.C583C|FGFR3_ENST00000352904.1_Silent_p.C470C|FGFR3_ENST00000412135.2_Silent_p.C470C|FGFR3_ENST00000340107.4_Silent_p.C584C			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	582	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TCGACACCTGCAAGCCGCCCG	0.682		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.C584C		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3	3320	.	0			c.C1752T						.						43	53	50					4																	1807577		2203	4298	6501	SO:0001819	synonymous_variant	2261	exon13	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	CACCTGCAAGCCG	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.1746C>T	chr4.hg19:g.1807577C>T		76.0	0.0		54.0	16.0	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	hg19	CCDS3353.1																																																																																			.	.		0.682	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		T	1807577	C	T	1807577	2	4	46	1	0	0	0	0	0	0	0	1	5875	718	25	3		3	FGFR3	4	1807577	Silent	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10		1807577	189346699	10	5975										
SH3BP2	6452	hgsc.bcm.edu	37	chr4	2829348	2829348	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	tgcagactatgagcacgacgAtgaggatgactcctacctgg	12	10	0	4			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr4:2829348A>G	ENST00000356331.5	+	7	794	c.533A>G	c.(532-534)gAt>gGt	p.D178G	SH3BP2_ENST00000435136.2_Missense_Mutation_p.D178G|SH3BP2_ENST00000511747.1_Missense_Mutation_p.D178G|SH3BP2_ENST00000442312.2_Missense_Mutation_p.D206G|SH3BP2_ENST00000503393.2_Missense_Mutation_p.D235G|SH3BP2_ENST00000452765.2_Missense_Mutation_p.D178G|SH3BP2_ENST00000515183.1_3'UTR	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	178					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		GAGCACGACGATGAGGATGAC	0.652									Cherubism																												p.D235G		Atlas-SNP	.											.	SH3BP2	43	.	0			c.A704G						.						52	37	42					4																	2829348		2201	4298	6499	SO:0001583	missense	6452	exon7	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	ACGACGATGAGGA	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	10825	protein-coding gene	gene with protein product		602104	"Cherubism"			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.533A>G	chr4.hg19:g.2829348A>G	ENSP00000348685:p.Asp178Gly	127.0	0.0		67.0	30.0	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Missense_Mutation	SNP	ENST00000356331.5	hg19	CCDS33944.1	.	.	.	.	.	.	.	.	.	.	a	14.47	2.544300	0.45280	.	.	ENSG00000087266	ENST00000452765;ENST00000508385;ENST00000512014;ENST00000442312;ENST00000435136;ENST00000511747;ENST00000503393;ENST00000356331	D;T;T;D;D;D;D;D	0.95171	-3.63;1.87;1.82;-3.63;-3.63;-3.63;-3.63;-3.63	4.8	4.8	0.61643	.	0.106622	0.64402	D	0.000010	D	0.95956	0.8683	M	0.64997	1.995	0.80722	D	1	D;D;D;D;D	0.71674	0.993;0.997;0.998;0.997;0.997	P;D;D;D;D	0.81914	0.853;0.989;0.995;0.989;0.989	D	0.95349	0.8445	10	0.46703	T	0.11	-21.8009	10.749	0.46198	1.0:0.0:0.0:0.0	.	206;153;153;235;178	B4DT04;Q6ZVU3;Q6ZTK4;D6R919;P78314	.;.;.;.;3BP2_HUMAN	G	178;178;178;206;178;178;235;178	ENSP00000409746:D178G;ENSP00000424917:D178G;ENSP00000424105:D178G;ENSP00000388152:D206G;ENSP00000403231:D178G;ENSP00000424846:D178G;ENSP00000422168:D235G;ENSP00000348685:D178G	ENSP00000348685:D178G	D	+	2	0	SH3BP2	2799146	0.994000	0.37717	0.046000	0.18839	0.083000	0.17756	4.982000	0.63825	1.806000	0.52798	0.392000	0.25879	GAT	.	.		0.652	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023		G	2829348	A	G	2829348	3	3	46	1	0	0	0	0	1	0	0	0	14260	333	12	2	814	2	SH3BP2	4	2829348	Missense_Mutation	SNP	A	TCGA-BC-A69H-01A-11D-A30V-10	1021771	2829348	188324928	11	5976										
FHDC1	85462	hgsc.bcm.edu	37	chr4	153896514	153896514	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	tccagggttcccagggcatgGaggagacctcccagctgact	13	13	0	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr4:153896514G>T	ENST00000511601.1	+	12	2259	c.2071G>T	c.(2071-2073)Gag>Tag	p.E691*	FHDC1_ENST00000260008.3_Nonsense_Mutation_p.E691*			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	691									ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					CCAGGGCATGGAGGAGACCTC	0.617																																					p.E691X		Atlas-SNP	.											.	FHDC1	102	.	0			c.G2071T						.						44	46	46					4																	153896514		2203	4300	6503	SO:0001587	stop_gained	85462	exon11			GGCATGGAGGAGA	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.2071G>T	chr4.hg19:g.153896514G>T	ENSP00000427567:p.Glu691*	71.0	0.0		29.0	12.0	NM_033393		Nonsense_Mutation	SNP	ENST00000511601.1	hg19	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	G	37	6.463344	0.97585	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	.	.	.	5.19	1.17	0.20885	.	0.740846	0.13614	N	0.374944	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.3028	0.87187	0.0:0.4784:0.5216:0.0	.	.	.	.	X	691	.	ENSP00000260008:E691X	E	+	1	0	FHDC1	154115964	0.162000	0.22906	0.003000	0.11579	0.007000	0.05969	1.423000	0.34837	-0.035000	0.13691	0.563000	0.77884	GAG	.	.		0.617	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		T	153896514	G	T	153896514	4	4	46	1	0	0	0	0	0	1	0	0	5884	1175	41	3	2113	3	FHDC1	4	153896514	Nonsense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10	151067166	153896514	37257762	12	5977										
CCNJL	79616	hgsc.bcm.edu	37	chr5	159686508	159686508	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	cctctaggaagtaatgggcaTactccttgaggcactctttg	10	10	2	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr5:159686508T>G	ENST00000393977.3	-	5	980	c.695A>C	c.(694-696)tAt>tCt	p.Y232S	CCNJL_ENST00000519673.1_Missense_Mutation_p.Y184S|CCNJL_ENST00000257536.7_Missense_Mutation_p.Y184S|CCNJL_ENST00000377503.2_5'UTR|CCNJL_ENST00000541762.1_Missense_Mutation_p.Y183S	NM_024565.5	NP_078841.3	Q8IV13	CCNJL_HUMAN	cyclin J-like	232						nucleus (GO:0005634)				endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTAATGGGCATACTCCTTGAG	0.637																																					p.Y232S		Atlas-SNP	.											.	CCNJL	36	.	0			c.A695C						.						68	73	71					5																	159686508		2068	4189	6257	SO:0001583	missense	79616	exon5			TGGGCATACTCCT	BC013353	CCDS4350.2	5q33.3	2008-10-31			ENSG00000135083	ENSG00000135083			25876	protein-coding gene	gene with protein product						12477932	Standard	XM_005265982		Approved	FLJ14166	uc003lyb.1	Q8IV13	OTTHUMG00000130325	ENST00000393977.3:c.695A>C	chr5.hg19:g.159686508T>G	ENSP00000377547:p.Tyr232Ser	48.0	0.0		31.0	7.0	NM_024565	Q6ZN43|Q9H7W8	Missense_Mutation	SNP	ENST00000393977.3	hg19	CCDS4350.2	.	.	.	.	.	.	.	.	.	.	T	20.5	4.001583	0.74818	.	.	ENSG00000135083	ENST00000393977;ENST00000257536;ENST00000519673;ENST00000541762	T;T;T;T	0.21734	1.99;1.99;1.99;1.99	5.41	4.22	0.49857	Cyclin, C-terminal (1);Cyclin-like (3);	0.064020	0.64402	D	0.000004	T	0.41880	0.1178	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.995;0.999;1.0	T	0.25012	-1.0144	10	0.87932	D	0	-11.5958	11.3202	0.49417	0.1365:0.0:0.0:0.8635	.	184;184;232	E7EN43;B4DZA8;Q8IV13	.;.;CCNJL_HUMAN	S	232;184;184;183	ENSP00000377547:Y232S;ENSP00000257536:Y184S;ENSP00000427960:Y184S;ENSP00000446367:Y183S	ENSP00000257536:Y184S	Y	-	2	0	CCNJL	159619086	1.000000	0.71417	0.473000	0.27253	0.946000	0.59487	5.018000	0.64054	0.842000	0.35045	0.533000	0.62120	TAT	.	.		0.637	CCNJL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252674.1	NM_024565		G	159686508	T	G	159686508	3	3	46	1	0	0	0	0	1	0	0	0	2931	1406	49	5	624	5	CCNJL	5	159686508	Missense_Mutation	SNP	T	TCGA-BC-A69H-01A-11D-A30V-10		159686508	21228752	13	5978										
EYS	346007	hgsc.bcm.edu	37	chr6	65612320	65612320	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	aaattgttgaccatatcttcAcagtcaccataatcctggca	5	11	3	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr6:65612320A>G	ENST00000370621.3	-	17	3241	c.2715T>C	c.(2713-2715)tgT>tgC	p.C905C	EYS_ENST00000503581.1_Silent_p.C905C|EYS_ENST00000370616.2_Silent_p.C905C			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	905	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CCATATCTTCACAGTCACCAT	0.343																																					p.C905C		Atlas-SNP	.											.	EYS	527	.	0			c.T2715C						.						153	127	135					6																	65612320		692	1591	2283	SO:0001819	synonymous_variant	346007	exon17			ATCTTCACAGTCA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2715T>C	chr6.hg19:g.65612320A>G		203.0	0.0		121.0	26.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	hg19																																																																																				.	.		0.343	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	65612320	A	G	65612320	2	3	46	1	0	0	0	0	0	0	0	1	5334	157	6	2		2	EYS	6	65612320	Silent	SNP	A	TCGA-BC-A69H-01A-11D-A30V-10		65612320	105502747	14	5979										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3165845	3165845	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	cacactcacctatgcacgaaGgtagtggtttgtcccacact	8	13	1	0			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr8:3165845G>T	ENST00000520002.1	-	25	4370	c.3815C>A	c.(3814-3816)cCt>cAt	p.P1272H	CSMD1_ENST00000542608.1_Missense_Mutation_p.P1271H|CSMD1_ENST00000539096.1_Missense_Mutation_p.P1271H|CSMD1_ENST00000537824.1_Missense_Mutation_p.P1271H|CSMD1_ENST00000602723.1_Missense_Mutation_p.P1272H|CSMD1_ENST00000602557.1_Missense_Mutation_p.P1272H|CSMD1_ENST00000400186.3_Missense_Mutation_p.P1272H			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1272	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TATGCACGAAGGTAGTGGTTT	0.502																																					p.P1271H		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C3812A						.						118	112	114					8																	3165845		2095	4225	6320	SO:0001583	missense	64478	exon24			CACGAAGGTAGTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3815C>A	chr8.hg19:g.3165845G>T	ENSP00000430733:p.Pro1272His	71.0	0.0		22.0	4.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.01	3.000811	0.54254	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11	5.22	4.31	0.51392	Complement control module (2);Sushi/SCR/CCP (3);	0.068318	0.64402	N	0.000014	D	0.93171	0.7825	H	0.99555	4.625	0.80722	D	1	D;D;D	0.89917	0.992;1.0;1.0	P;D;D	0.81914	0.873;0.995;0.985	D	0.95834	0.8860	10	0.87932	D	0	.	15.1701	0.72865	0.0:0.0:0.8586:0.1414	.	1272;1272;1272	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	H	1272;1272;1134;1271;1271;1271	ENSP00000383047:P1272H;ENSP00000430733:P1272H;ENSP00000441462:P1271H;ENSP00000446243:P1271H;ENSP00000441675:P1271H	ENSP00000320445:P1134H	P	-	2	0	CSMD1	3153252	1.000000	0.71417	0.851000	0.33527	0.204000	0.24138	7.663000	0.83820	2.414000	0.81942	0.561000	0.74099	CCT	.	.		0.502	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3165845	G	T	3165845	3	4	46	1	0	0	0	0	1	0	0	0	3946	1000	35	3	7070	3	CSMD1	8	3165845	Missense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10		3165845	143198177	15	5980										
MTMR7	9108	hgsc.bcm.edu	37	chr8	17163407	17163407	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ccattaactgccaaacacacTcaatgaactggtcaataact	4	12	2	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr8:17163407T>G	ENST00000180173.5	-	11	1245	c.1211A>C	c.(1210-1212)gAg>gCg	p.E404A	MTMR7_ENST00000398099.3_5'UTR|MTMR7_ENST00000521857.1_Missense_Mutation_p.E404A	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	404	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		CCAAACACACTCAATGAACTG	0.363																																					p.E404A		Atlas-SNP	.											.	MTMR7	75	.	0			c.A1211C						.						102	101	101					8																	17163407		2203	4300	6503	SO:0001583	missense	9108	exon11			ACACACTCAATGA	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1211A>C	chr8.hg19:g.17163407T>G	ENSP00000180173:p.Glu404Ala	142.0	0.0		33.0	14.0	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	hg19	CCDS34851.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.506771	0.85282	.	.	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.93426	-3.22;-3.22	4.87	4.87	0.63330	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.97340	0.9130	M	0.92122	3.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98342	1.0539	10	0.87932	D	0	.	14.9478	0.71047	0.0:0.0:0.0:1.0	.	404;404	Q9Y216-2;Q9Y216	.;MTMR7_HUMAN	A	404	ENSP00000180173:E404A;ENSP00000429733:E404A	ENSP00000180173:E404A	E	-	2	0	MTMR7	17207778	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.868000	0.87116	2.180000	0.69256	0.460000	0.39030	GAG	.	.		0.363	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686		G	17163407	T	G	17163407	3	3	46	1	0	0	0	0	1	0	0	0	9957	1551	54	5	787	5	MTMR7	8	17163407	Missense_Mutation	SNP	T	TCGA-BC-A69H-01A-11D-A30V-10	13997562	17163407	129200615	16	5981										
RFX3	5991	hgsc.bcm.edu	37	chr9	3247979	3247979	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	tatttagactgaagtgtaatTctggcttatttttaataacc	6	5	1	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:3247979T>A	ENST00000382004.3	-	16	2280				RFX3_ENST00000358730.2_Missense_Mutation_p.E674V|RFX3_ENST00000302303.1_Missense_Mutation_p.E674V	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)						cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		GAAGTGTAATTCTGGCTTATT	0.453																																					p.E674V		Atlas-SNP	.											.	RFX3	156	.	0			c.A2021T						.						95	100	98					9																	3247979		2203	4300	6503	SO:0001627	intron_variant	5991	exon16			TGTAATTCTGGCT	AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.1968+52A>T	chr9.hg19:g.3247979T>A		66.0	0.0		32.0	12.0	NM_002919	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	hg19	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	T	10.92	1.486314	0.26686	.	.	ENSG00000080298	ENST00000358730;ENST00000302303	T;T	0.59906	0.23;0.23	4.08	2.92	0.33932	.	.	.	.	.	T	0.43344	0.1243	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27297	-1.0078	8	0.32370	T	0.25	.	9.4539	0.38743	0.0:0.0:0.1935:0.8065	.	674	P48380-2	.	V	674	ENSP00000351574:E674V;ENSP00000303847:E674V	ENSP00000303847:E674V	E	-	2	0	RFX3	3237979	0.960000	0.32886	0.003000	0.11579	0.040000	0.13550	2.298000	0.43602	0.688000	0.31529	0.402000	0.26972	GAA	.	.		0.453	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		A	3247979	T	A	3247979	1	1	46	0	1	0	0	0	0	0	0	0	13279	1783	62	4		4	RFX3	9	3247979	Intron	SNP	T	TCGA-BC-A69H-01A-11D-A30V-10		3247979	137965452	17	5982										
PLAA	9373	hgsc.bcm.edu	37	chr9	26905887	26905887	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	atcatgagtttttgtcctgcCtggccaacaaaacaattgca	7	10	1	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:26905887C>G	ENST00000397292.3	-	14	2427	c.2010G>C	c.(2008-2010)caG>caC	p.Q670H		NM_001031689.2	NP_001026859.1	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	670	PUL. {ECO:0000255|PROSITE- ProRule:PRU00729}.				inflammatory response (GO:0006954)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	phospholipase A2 activator activity (GO:0016005)			breast(1)|endometrium(7)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	17		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		TTTGTCCTGCCTGGCCAACAA	0.443																																					p.Q670H	Melanoma(175;2670 2735 14091 35526)	Atlas-SNP	.											.	PLAA	48	.	0			c.G2010C						.						83	79	80					9																	26905887		2203	4300	6503	SO:0001583	missense	9373	exon14			TCCTGCCTGGCCA	AF083395	CCDS35000.1	9p21	2013-01-10			ENSG00000137055	ENSG00000137055		"WD repeat domain containing"	9043	protein-coding gene	gene with protein product	"DOA1 homolog (S. cerevisiae)"	603873				9931468, 10644453	Standard	NM_001031689		Approved	PLAP, PLA2P, FLJ11281, FLJ12699, DOA1	uc003zqd.3	Q9Y263	OTTHUMG00000019708	ENST00000397292.3:c.2010G>C	chr9.hg19:g.26905887C>G	ENSP00000380460:p.Gln670His	198.0	0.0		93.0	22.0	NM_001031689	Q53EU5|Q5VY33|Q9NUL8|Q9NVE9|Q9UF53|Q9Y5L1	Missense_Mutation	SNP	ENST00000397292.3	hg19	CCDS35000.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.48|10.48	1.362073|1.362073	0.24684|0.24684	.|.	.|.	ENSG00000137055|ENSG00000137055	ENST00000517642|ENST00000397292	.|T	.|0.49432	.|0.78	6.07|6.07	6.07|6.07	0.98685|0.98685	.|PUL (2);	.|0.402261	.|0.31495	.|N	.|0.007554	T|T	0.34745|0.34745	0.0908|0.0908	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	T|T	0.36407|0.36407	-0.9749|-0.9749	5|10	.|0.48119	.|T	.|0.1	-3.1398|-3.1398	4.1806|4.1806	0.10374|0.10374	0.1536:0.5945:0.1479:0.104|0.1536:0.5945:0.1479:0.104	.|.	.|670	.|Q9Y263	.|PLAP_HUMAN	R|H	288|670	.|ENSP00000380460:Q670H	.|ENSP00000380460:Q670H	G|Q	-|-	1|3	0|2	PLAA|PLAA	26895887|26895887	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	0.868000|0.868000	0.27982|0.27982	2.885000|2.885000	0.99019|0.99019	0.655000|0.655000	0.94253|0.94253	GGC|CAG	.	.		0.443	PLAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051958.2	NM_001031689		G	26905887	C	G	26905887	3	3	46	1	0	0	0	0	1	0	0	0	12020	680	24	4	381	4	PLAA	9	26905887	Missense_Mutation	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	23657908	26905887	114307544	18	5983										
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104499796	104499796	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	tggcagatcgcccaggcctgCctcgatggccatcactactt	10	15	1	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:104499796C>G	ENST00000361820.3	-	1	1066	c.466G>C	c.(466-468)Gca>Cca	p.A156P		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	156					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	CCCAGGCCTGCCTCGATGGCC	0.587																																					p.A156P		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G466C						.						102	96	98					9																	104499796		2203	4300	6503	SO:0001583	missense	116443	exon1			GGCCTGCCTCGAT		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.466G>C	chr9.hg19:g.104499796C>G	ENSP00000355155:p.Ala156Pro	108.0	0.0		54.0	19.0	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.765044	0.69878	.	.	ENSG00000198785	ENST00000361820	D	0.86562	-2.14	4.98	4.98	0.66077	.	0.206037	0.42548	N	0.000699	D	0.88190	0.6370	L	0.48642	1.525	0.52099	D	0.999943	D	0.60575	0.988	P	0.51657	0.676	D	0.87667	0.2538	10	0.38643	T	0.18	.	18.2597	0.90031	0.0:1.0:0.0:0.0	.	156	Q8TCU5	NMD3A_HUMAN	P	156	ENSP00000355155:A156P	ENSP00000355155:A156P	A	-	1	0	GRIN3A	103539617	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.853000	0.48317	2.304000	0.77564	0.655000	0.94253	GCA	.	.		0.587	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			G	104499796	C	G	104499796	3	3	46	1	0	0	0	0	1	0	0	0	6792	739	26	4	2917	4	GRIN3A	9	104499796	Missense_Mutation	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	77593909	104499796	36713635	19	5984										
TMEM38B	55151	hgsc.bcm.edu	37	chr9	108536210	108536210	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ttttgaggatacattgagttGgatgctatttggctggcagc	13	5	0	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:108536210G>A	ENST00000374692.3	+	6	842	c.725G>A	c.(724-726)tGg>tAg	p.W242*	TMEM38B_ENST00000374688.1_Nonsense_Mutation_p.W188*	NM_018112.1	NP_060582.1	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B	242						integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13						ACATTGAGTTGGATGCTATTT	0.408																																					p.W242X		Atlas-SNP	.											.	TMEM38B	31	.	0			c.G725A						.						117	113	114					9																	108536210		2203	4300	6503	SO:0001587	stop_gained	55151	exon6			TGAGTTGGATGCT	BC031938	CCDS6768.1	9q31.3	2013-05-23	2004-12-21	2004-12-22	ENSG00000095209	ENSG00000095209			25535	protein-coding gene	gene with protein product		611236	"chromosome 9 open reading frame 87"	C9orf87		17611541, 23316006	Standard	NM_018112		Approved	FLJ10493, bA219P18.1, D4Ertd89e, TRIC-B	uc004bcu.2	Q9NVV0	OTTHUMG00000020429	ENST00000374692.3:c.725G>A	chr9.hg19:g.108536210G>A	ENSP00000363824:p.Trp242*	158.0	0.0		95.0	34.0	NM_018112	Q5JR63|Q5SVN5|Q5SVN6|Q5VTE2|Q6IA97	Nonsense_Mutation	SNP	ENST00000374692.3	hg19	CCDS6768.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.481203	0.44147	.	.	ENSG00000095209	ENST00000374692;ENST00000374688	.	.	.	4.81	4.81	0.61882	.	0.609679	0.17087	N	0.187523	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-3.5522	13.5504	0.61728	0.0:0.0:1.0:0.0	.	.	.	.	X	242;188	.	ENSP00000363820:W188X	W	+	2	0	TMEM38B	107576031	1.000000	0.71417	0.843000	0.33291	0.129000	0.20672	2.106000	0.41835	2.641000	0.89580	0.585000	0.79938	TGG	.	.		0.408	TMEM38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053517.1	NM_018112		A	108536210	G	A	108536210	4	1	46	1	0	0	0	0	0	1	0	0	16175	1357	47	3	747	3	TMEM38B	9	108536210	Nonsense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10	4036414	108536210	32677221	20	5985										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113312149	113312149	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	cttcatgcaatgcccggcgaGctaaagcctcaaattcttca	7	13	4	0			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:113312149G>C	ENST00000401783.2	-	2	1103	c.767C>G	c.(766-768)gCt>gGt	p.A256G	SVEP1_ENST00000374469.1_Missense_Mutation_p.A233G|SVEP1_ENST00000374461.1_Missense_Mutation_p.A233G|SVEP1_ENST00000302728.8_Missense_Mutation_p.A256G|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	256	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TGCCCGGCGAGCTAAAGCCTC	0.473																																					p.A256G		Atlas-SNP	.											.	SVEP1	326	.	0			c.C767G						.						66	62	63					9																	113312149		1920	4123	6043	SO:0001583	missense	79987	exon2			CGGCGAGCTAAAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.767C>G	chr9.hg19:g.113312149G>C	ENSP00000384917:p.Ala256Gly	171.0	0.0		83.0	16.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	33	5.224356	0.95139	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17	5.38	5.38	0.77491	von Willebrand factor, type A (2);	0.000000	0.85682	D	0.000000	D	0.88440	0.6437	M	0.75447	2.3	0.50467	D	0.999879	P;P;D	0.89917	0.892;0.928;1.0	P;P;D	0.83275	0.579;0.809;0.996	D	0.89042	0.3449	10	0.72032	D	0.01	.	19.497	0.95077	0.0:0.0:1.0:0.0	.	256;256;256	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	G	256;233;256;233	ENSP00000384917:A256G;ENSP00000363593:A233G;ENSP00000304118:A256G;ENSP00000363585:A233G	ENSP00000304118:A256G	A	-	2	0	SVEP1	112351970	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.420000	0.97426	2.677000	0.91161	0.563000	0.77884	GCT	.	.		0.473	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113312149	G	C	113312149	3	2	46	1	0	0	0	0	1	0	0	0	15435	971	34	4	10136	4	SVEP1	9	113312149	Missense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10	4775939	113312149	27901282	21	5986										
FAM78A	286336	hgsc.bcm.edu	37	chr9	134136583	134136583	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	gacgctggggtaaaagttgtCattcatgctgatgatgaact	12	6	2	3			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:134136583C>T	ENST00000372271.3	-	2	845	c.478G>A	c.(478-480)Gac>Aac	p.D160N	FAM78A_ENST00000247295.4_5'UTR|FAM78A_ENST00000372269.3_Missense_Mutation_p.D157N	NM_033387.3	NP_203745.2	Q5JUQ0	FA78A_HUMAN	family with sequence similarity 78, member A	160										NS(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.15e-05)|Epithelial(140;0.000267)		TAAAAGTTGTCATTCATGCTG	0.582																																					p.D160N		Atlas-SNP	.											.	FAM78A	28	.	0			c.G478A						.						127	117	120					9																	134136583		2203	4300	6503	SO:0001583	missense	286336	exon2			AGTTGTCATTCAT	AK095423	CCDS6941.2	9q34	2008-02-05	2005-07-18	2005-07-18	ENSG00000126882	ENSG00000126882			25465	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 59"	C9orf59		11214971	Standard	NM_033387		Approved	FLJ00024	uc004cak.3	Q5JUQ0	OTTHUMG00000020821	ENST00000372271.3:c.478G>A	chr9.hg19:g.134136583C>T	ENSP00000361345:p.Asp160Asn	57.0	0.0		30.0	7.0	NM_033387	Q86VQ9|Q9H7P4	Missense_Mutation	SNP	ENST00000372271.3	hg19	CCDS6941.2	.	.	.	.	.	.	.	.	.	.	C	27.4	4.828590	0.90955	.	.	ENSG00000126882	ENST00000372269;ENST00000372271;ENST00000464831	.	.	.	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.79233	0.4411	M	0.75777	2.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.82364	-0.0494	9	0.87932	D	0	-41.4748	17.1064	0.86664	0.0:1.0:0.0:0.0	.	160;157	Q5JUQ0;Q5JUQ2	FA78A_HUMAN;.	N	157;160;129	.	ENSP00000361343:D157N	D	-	1	0	FAM78A	133126404	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	7.776000	0.85560	2.337000	0.79520	0.462000	0.41574	GAC	.	.		0.582	FAM78A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054720.1	NM_033387		T	134136583	C	T	134136583	3	4	46	1	0	0	0	0	1	0	0	0	5634	826	29	3	377	3	FAM78A	9	134136583	Missense_Mutation	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	20824434	134136583	7076848	22	5987										
RET	5979	hgsc.bcm.edu	37	chr10	43600449	43600449	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	gacagcctggaggtgagcacGcgctgggccctggaccgcga	17	13	0	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr10:43600449G>A	ENST00000355710.3	+	4	907	c.675G>A	c.(673-675)acG>acA	p.T225T	RET_ENST00000340058.5_Silent_p.T225T	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	225	Cadherin. {ECO:0000255|PROSITE- ProRule:PRU00043}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	AGGTGAGCACGCGCTGGGCCC	0.731		1	"T, Mis, N, F"	"H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"	"medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"	"medullary thyroid,  papillary thyroid, pheochromocytoma"	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												p.T225T	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	.	RET	916	.	0			c.G675A						.						22	21	22					10																	43600449		2192	4283	6475	SO:0001819	synonymous_variant	5979	exon4	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	GAGCACGCGCTGG	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"Cadherins / Cadherin-related"	9967	protein-coding gene	gene with protein product	"cadherin-related family member 16"	164761	"multiple endocrine neoplasia and medullary thyroid carcinoma 1", "Hirschsprung disease 1"	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.675G>A	chr10.hg19:g.43600449G>A		59.0	0.0		40.0	13.0	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	hg19	CCDS7200.1																																																																																			.	.		0.731	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		A	43600449	G	A	43600449	2	1	46	1	0	0	0	0	0	0	0	1	13250	1074	38	1		1	RET	10	43600449	Silent	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10		43600449	91934298	23	5988										
RBP3	5949	hgsc.bcm.edu	37	chr10	48389747	48389747	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ctgggatcctcagacgcagcCtgcaggccggcattgagctt	13	13	1	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr10:48389747C>T	ENST00000224600.4	-	1	1244	c.1131G>A	c.(1129-1131)caG>caA	p.Q377Q	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	377	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	CAGACGCAGCCTGCAGGCCGG	0.652																																					p.Q377Q		Atlas-SNP	.											.	RBP3	152	.	0			c.G1131A						.						33	36	35					10																	48389747		2202	4300	6502	SO:0001819	synonymous_variant	5949	exon1			CGCAGCCTGCAGG	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.1131G>A	chr10.hg19:g.48389747C>T		57.0	0.0		41.0	15.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	hg19	CCDS7218.1																																																																																			.	.		0.652	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		T	48389747	C	T	48389747	2	4	46	1	0	0	0	0	0	0	0	1	13172	680	24	3		3	RBP3	10	48389747	Silent	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	4789298	48389747	87145000	24	5989										
CTSD	1509	hgsc.bcm.edu	37	chr11	1778644	1778644	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	gcacgttgttgacggagatgCgggggtaggccatgcccagg	18	9	0	2	rs371522391		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr11:1778644C>T	ENST00000236671.2	-	5	746	c.614G>A	c.(613-615)cGc>cAc	p.R205H	RP11-295K3.1_ENST00000427721.1_Missense_Mutation_p.A76T|AC068580.6_ENST00000449248.1_RNA	NM_001909.4	NP_001900.1	P07339	CATD_HUMAN	cathepsin D	205					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic vacuole assembly (GO:0000045)|cell death (GO:0008219)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(1)|large_intestine(4)|lung(8)	13		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	GACGGAGATGCGGGGGTAGGC	0.587																																					p.R205H		Atlas-SNP	.											.	CTSD	26	.	0			c.G614A						.	C	HIS/ARG	1,4403	2.1+/-5.4	0,1,2201	194	126	149		614	-2.9	1	11		149	0,8598		0,0,4299	no	missense	CTSD	NM_001909.4	29	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	benign	205/413	1778644	1,13001	2202	4299	6501	SO:0001583	missense	1509	exon5			GAGATGCGGGGGT	M11233	CCDS7725.1	11p15.5	2009-06-26	2006-12-05		ENSG00000117984	ENSG00000117984	3.4.23.5	"Cathepsins"	2529	protein-coding gene	gene with protein product	"ceroid-lipofuscinosis, neuronal 10"	116840	"cathepsin D (lysosomal aspartyl protease)"	CPSD		3927292	Standard	NM_001909		Approved	CLN10	uc001luc.2	P07339	OTTHUMG00000044760	ENST00000236671.2:c.614G>A	chr11.hg19:g.1778644C>T	ENSP00000236671:p.Arg205His	61.0	0.0		68.0	34.0	NM_001909	Q6IB57	Missense_Mutation	SNP	ENST00000236671.2	hg19	CCDS7725.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	14.78|14.78	2.637977|2.637977	0.47153|0.47153	2.27E-4|2.27E-4	0.0|0.0	ENSG00000250644|ENSG00000117984	ENST00000427721|ENST00000236671;ENST00000438213;ENST00000367196	.|T;T;T	.|0.58358	.|0.34;0.34;0.38	4.11|4.11	-2.92|-2.92	0.05615|0.05615	.|Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	.|0.778438	.|0.12176	.|N	.|0.492528	T|T	0.38026|0.38026	0.1025|0.1025	L|L	0.56280|0.56280	1.765|1.765	0.26796|0.26796	N|N	0.969301|0.969301	.|B	.|0.23249	.|0.082	.|B	.|0.13407	.|0.009	T|T	0.28073|0.28073	-1.0055|-1.0055	5|10	.|0.39692	.|T	.|0.17	.|.	3.7053|3.7053	0.08398|0.08398	0.3688:0.2628:0.0:0.3683|0.3688:0.2628:0.0:0.3683	.|.	.|205	.|P07339	.|CATD_HUMAN	T|H	76|205;190;170	.|ENSP00000236671:R205H;ENSP00000415036:R190H;ENSP00000356164:R170H	.|ENSP00000236671:R205H	A|R	-|-	1|2	0|0	RP11-295K3.1|CTSD	1735220|1735220	0.010000|0.010000	0.17322|0.17322	0.960000|0.960000	0.40013|0.40013	0.752000|0.752000	0.42762|0.42762	-0.155000|-0.155000	0.10115|0.10115	-0.137000|-0.137000	0.11455|0.11455	0.472000|0.472000	0.43445|0.43445	GCA|CGC	.	.		0.587	CTSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104272.5	NM_001909		T	1778644	C	T	1778644	3	4	46	1	0	0	0	0	1	0	0	0	4034	768	27	1	644	1	CTSD	11	1778644	Missense_Mutation	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10		1778644	133227872	25	5990										
OR52N4	390072	hgsc.bcm.edu	37	chr11	5776243	5776243	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	tgcatcttctggtttcatctCaaggacattggatttgatga	9	7	4	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr11:5776243C>G	ENST00000317254.3	+	1	321	c.273C>G	c.(271-273)ctC>ctG	p.L91L	TRIM5_ENST00000380027.1_Intron	NM_001005175.2	NP_001005175.3	Q8NGI2	O52N4_HUMAN	olfactory receptor, family 52, subfamily N, member 4 (gene/pseudogene)	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;1.87e-10)|LUSC - Lung squamous cell carcinoma(625;0.114)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.197)		GGTTTCATCTCAAGGACATTG	0.468																																					p.L91L		Atlas-SNP	.											OR52N4,right_upper_lobe,carcinoma,0,1	OR52N4	55	.	0			c.C273G						.						145	148	147					11																	5776243		2201	4297	6498	SO:0001819	synonymous_variant	390072	exon1			TCATCTCAAGGAC	AB065813	CCDS44528.1	11p15.4	2013-10-10	2013-10-10		ENSG00000181074	ENSG00000181074		"GPCR / Class A : Olfactory receptors"	15230	protein-coding gene	gene with protein product			"olfactory receptor, family 52, subfamily N, member 4"				Standard	NM_001005175		Approved		uc001mbu.3	Q8NGI2	OTTHUMG00000066887	ENST00000317254.3:c.273C>G	chr11.hg19:g.5776243C>G		123.0	0.0		74.0	12.0	NM_001005175	B2RNP8|Q6IF77	Silent	SNP	ENST00000317254.3	hg19	CCDS44528.1																																																																																			.	.		0.468	OR52N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143350.1	NM_001005175		G	5776243	C	G	5776243	2	3	46	1	0	0	0	0	0	0	0	1	11138	813	29	4		4	OR52N4	11	5776243	Silent	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	3997599	5776243	129230273	26	5991										
NRXN2	9379	hgsc.bcm.edu	37	chr11	64434901	64434901	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	agctgtggctgccagctccaCccccagcccgccggccctgg	12	20	0	0	rs143130600		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr11:64434901C>A	ENST00000377551.1	-	8	1830	c.1619G>T	c.(1618-1620)gGt>gTt	p.G540V	NRXN2_ENST00000377559.3_Missense_Mutation_p.G509V|NRXN2_ENST00000409571.1_Missense_Mutation_p.G533V|NRXN2_ENST00000265459.6_Missense_Mutation_p.G540V			Q9P2S2	NRX2A_HUMAN	neurexin 2	540	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						GCCAGCTCCACCCCCAGCCCG	0.657																																					p.G540V		Atlas-SNP	.											.	NRXN2	247	.	0			c.G1619T						.						49	52	51					11																	64434901		2201	4297	6498	SO:0001583	missense	9379	exon9			GCTCCACCCCCAG		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"neurexin II"	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.1619G>T	chr11.hg19:g.64434901C>A	ENSP00000366774:p.Gly540Val	81.0	0.0		49.0	11.0	NM_015080	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	hg19	CCDS8077.1	.	.	.	.	.	.	.	.	.	.	C	4.594	0.110325	0.08780	.	.	ENSG00000110076	ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571	T;T;T;T	0.62788	0.0;0.12;0.0;0.12	4.3	-1.63	0.08345	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	1.182110	0.06903	N	0.806307	T	0.38081	0.1027	N	0.03608	-0.345	0.09310	N	0.999998	B;B;B	0.28605	0.217;0.008;0.0	B;B;B	0.31946	0.138;0.065;0.002	T	0.37267	-0.9713	10	0.52906	T	0.07	.	7.6893	0.28559	0.1966:0.5605:0.2429:0.0	.	509;540;286	Q9P2S2-2;Q9P2S2;E7EV67	.;NRX2A_HUMAN;.	V	540;509;540;509;533	ENSP00000366774:G540V;ENSP00000366782:G509V;ENSP00000265459:G540V;ENSP00000386416:G533V	ENSP00000265459:G540V	G	-	2	0	NRXN2	64191477	0.000000	0.05858	0.042000	0.18584	0.282000	0.26991	0.093000	0.15086	-0.128000	0.11641	-0.502000	0.04539	GGT	.	C|1.000;T|0.000		0.657	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		A	64434901	C	A	64434901	3	1	46	1	0	0	0	0	1	0	0	0	10675	507	18	3	3848	3	NRXN2	11	64434901	Missense_Mutation	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	58658658	64434901	70571615	27	5992										
NLRX1	79671	hgsc.bcm.edu	37	chr11	119052990	119052990	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	acgtggcgtacaacggtgctGgtgacacagcggccctggcc	15	13	0	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr11:119052990G>A	ENST00000409109.1	+	9	3129	c.2542G>A	c.(2542-2544)Ggt>Agt	p.G848S	NLRX1_ENST00000525863.1_Missense_Mutation_p.G848S|NLRX1_ENST00000409265.4_Missense_Mutation_p.G848S|NLRX1_ENST00000292199.2_Missense_Mutation_p.G848S|NLRX1_ENST00000409991.1_Missense_Mutation_p.G848S	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	848	Required for the repression of MAVS- induced interferon signaling.				innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CAACGGTGCTGGTGACACAGC	0.682																																					p.G848S		Atlas-SNP	.											.	NLRX1	128	.	0			c.G2542A						.						60	63	62					11																	119052990		2200	4295	6495	SO:0001583	missense	79671	exon9			GGTGCTGGTGACA	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"Nucleotide-binding domain and leucine rich repeat containing"	29890	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat containing X1", "NOD-like receptor X1", "NLR family, X1"	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.2542G>A	chr11.hg19:g.119052990G>A	ENSP00000387334:p.Gly848Ser	56.0	0.0		25.0	7.0	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	hg19	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.617421	0.46736	.	.	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63	4.52	2.58	0.30949	.	0.216054	0.37012	N	0.002285	T	0.46908	0.1417	L	0.55743	1.74	0.21416	N	0.999691	D;B	0.55800	0.973;0.386	P;B	0.53593	0.73;0.079	T	0.26780	-1.0093	10	0.33940	T	0.23	.	3.9576	0.09396	0.312:0.188:0.5:0.0	.	848;848	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	S	848	ENSP00000386851:G848S;ENSP00000292199:G848S;ENSP00000386858:G848S;ENSP00000387334:G848S;ENSP00000433442:G848S	ENSP00000292199:G848S	G	+	1	0	NLRX1	118558200	1.000000	0.71417	0.631000	0.29282	0.912000	0.54170	2.704000	0.47118	1.131000	0.42111	0.407000	0.27541	GGT	.	.		0.682	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722		A	119052990	G	A	119052990	3	1	46	1	0	0	0	0	1	0	0	0	10494	1348	47	3	2572	3	NLRX1	11	119052990	Missense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10	54618089	119052990	15953526	28	5993										
EEA1	8411	hgsc.bcm.edu	37	chr12	93205205	93205205	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	aactgagtagtaatcttattTaactcctttagaaaagtaca	5	6	1	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr12:93205205T>C	ENST00000322349.8	-	17	2313	c.2049A>G	c.(2047-2049)ttA>ttG	p.L683L		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	683	Gln/Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TAATCTTATTTAACTCCTTTA	0.313																																					p.L683L		Atlas-SNP	.											.	EEA1	104	.	0			c.A2049G						.						51	51	51					12																	93205205		2201	4298	6499	SO:0001819	synonymous_variant	8411	exon17			CTTATTTAACTCC	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.2049A>G	chr12.hg19:g.93205205T>C		48.0	0.0		43.0	11.0	NM_003566	Q14221	Silent	SNP	ENST00000322349.8	hg19	CCDS31874.1																																																																																			.	.		0.313	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		C	93205205	T	C	93205205	2	2	46	1	0	0	0	0	0	0	0	1	4923	1751	61	2		2	EEA1	12	93205205	Silent	SNP	T	TCGA-BC-A69H-01A-11D-A30V-10		93205205	40646690	29	5994										
MAP4K5	11183	hgsc.bcm.edu	37	chr14	50911780	50911780	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	aatagaagaagtctctgccaCaggcccacaacttgggctac	9	12	1	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr14:50911780C>A	ENST00000013125.4	-	18	1636	c.1318G>T	c.(1318-1320)Gtg>Ttg	p.V440L		NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	440					activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					GTCTCTGCCACAGGCCCACAA	0.423																																					p.V440L		Atlas-SNP	.											.	MAP4K5	48	.	0			c.G1318T						.						100	94	96					14																	50911780		1856	4092	5948	SO:0001583	missense	11183	exon18			CTGCCACAGGCCC	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6867	protein-coding gene	gene with protein product	"germinal center kinase-related"	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.1318G>T	chr14.hg19:g.50911780C>A	ENSP00000013125:p.Val440Leu	122.0	0.0		73.0	16.0	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	hg19		.	.	.	.	.	.	.	.	.	.	C	7.563	0.665175	0.14710	.	.	ENSG00000012983	ENST00000013125	T	0.13538	2.58	5.39	0.0837	0.14434	Protein kinase-like domain (1);	1.242570	0.05155	N	0.496721	T	0.05502	0.0145	N	0.08118	0	0.09310	N	1	B;B;B	0.14438	0.01;0.008;0.01	B;B;B	0.10450	0.004;0.005;0.002	T	0.35724	-0.9777	10	0.08381	T	0.77	.	1.8258	0.03120	0.1142:0.3798:0.2568:0.2492	.	114;440;440	B3KWC4;B2R928;Q9Y4K4	.;.;M4K5_HUMAN	L	440	ENSP00000013125:V440L	ENSP00000013125:V440L	V	-	1	0	MAP4K5	49981530	0.506000	0.26139	0.469000	0.27204	0.924000	0.55760	0.366000	0.20365	-0.003000	0.14444	-0.152000	0.13540	GTG	.	.		0.423	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575		A	50911780	C	A	50911780	3	1	46	1	0	0	0	0	1	0	0	0	9272	478	17	3	1282	3	MAP4K5	14	50911780	Missense_Mutation	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10		50911780	56437760	30	5995										
CYLD	1540	hgsc.bcm.edu	37	chr16	50815217	50815217	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	gcactcggtatttcacctgtGccctgaagaaggcgctgttt	11	11	1	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr16:50815217G>A	ENST00000427738.3	+	9	1784	c.1579G>A	c.(1579-1581)Gcc>Acc	p.A527T	CYLD_ENST00000566206.1_Missense_Mutation_p.A524T|CYLD_ENST00000569418.1_Missense_Mutation_p.A524T|RP11-327F22.4_ENST00000564510.1_RNA|CYLD_ENST00000564326.1_Missense_Mutation_p.A524T|CYLD_ENST00000311559.9_Missense_Mutation_p.A527T|CYLD_ENST00000568704.2_Intron|CYLD_ENST00000398568.2_Missense_Mutation_p.A524T|CYLD_ENST00000540145.1_Missense_Mutation_p.A527T|RP11-327F22.4_ENST00000575917.1_RNA			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	527	CAP-Gly 3. {ECO:0000255|PROSITE- ProRule:PRU00045}.|Interaction with IKBKG/NEMO.|Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				TTTCACCTGTGCCCTGAAGAA	0.483			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.A527T		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.G1579A						.						102	98	100					16																	50815217		1932	4141	6073	SO:0001583	missense	1540	exon11	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	ACCTGTGCCCTGA	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1579G>A	chr16.hg19:g.50815217G>A	ENSP00000392025:p.Ala527Thr	105.0	0.0		55.0	17.0	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	hg19	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.174382	0.57692	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T	0.74526	-0.85;-0.85;-0.85	6.02	6.02	0.97574	Cytoskeleton-associated protein, Gly-rich domain (4);	0.046658	0.85682	D	0.000000	T	0.76169	0.3950	L	0.28014	0.82	0.58432	D	0.999997	D;D;P;P	0.59767	0.98;0.986;0.867;0.891	P;P;B;B	0.58721	0.818;0.844;0.288;0.412	T	0.69323	-0.5175	10	0.16896	T	0.51	-5.9624	20.5407	0.99260	0.0:0.0:1.0:0.0	.	524;527;524;527	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	T	527;527;524;524	ENSP00000445447:A527T;ENSP00000308928:A527T;ENSP00000381574:A524T	ENSP00000308928:A527T	A	+	1	0	CYLD	49372718	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.934000	0.75880	2.865000	0.98341	0.655000	0.94253	GCC	.	.		0.483	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			A	50815217	G	A	50815217	3	1	46	1	0	0	0	0	1	0	0	0	4145	1319	46	3	1609	3	CYLD	16	50815217	Missense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10		50815217	39539536	31	5996										
TAF1C	9013	hgsc.bcm.edu	37	chr16	84214736	84214736	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	agcaggacacgttcccctttCtggcacgaagcctctgcccc	9	17	2	0			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr16:84214736C>A	ENST00000567759.1	-	11	1481	c.1299G>T	c.(1297-1299)caG>caT	p.Q433H	TAF1C_ENST00000341690.6_Missense_Mutation_p.Q340H|TAF1C_ENST00000541676.1_Missense_Mutation_p.Q340H|TAF1C_ENST00000378541.4_Missense_Mutation_p.Q433H|TAF1C_ENST00000570117.1_Missense_Mutation_p.Q101H|TAF1C_ENST00000566732.1_Missense_Mutation_p.Q407H	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	433					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						GTTCCCCTTTCTGGCACGAAG	0.612																																					p.Q433H		Atlas-SNP	.											.	TAF1C	60	.	0			c.G1299T						.						84	87	86					16																	84214736		2200	4300	6500	SO:0001583	missense	9013	exon11			CCCTTTCTGGCAC	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.1299G>T	chr16.hg19:g.84214736C>A	ENSP00000455265:p.Gln433His	114.0	0.0		54.0	28.0	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	hg19	CCDS32496.1	.	.	.	.	.	.	.	.	.	.	C	9.568	1.120224	0.20877	.	.	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690	T;T;T	0.62498	0.02;0.02;0.02	4.56	3.61	0.41365	.	0.115077	0.38436	N	0.001681	T	0.74313	0.3700	M	0.70595	2.14	0.31335	N	0.684381	D;D;D	0.76494	0.997;0.999;0.997	D;D;D	0.85130	0.995;0.997;0.995	T	0.75476	-0.3304	10	0.59425	D	0.04	-29.1612	8.6093	0.33793	0.0:0.8957:0.0:0.1043	.	407;433;340	Q15572-6;Q15572;Q15572-2	.;TAF1C_HUMAN;.	H	433;340;340	ENSP00000367802:Q433H;ENSP00000437900:Q340H;ENSP00000345305:Q340H	ENSP00000345305:Q340H	Q	-	3	2	TAF1C	82772237	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	1.118000	0.31246	1.141000	0.42275	-0.137000	0.14449	CAG	.	.		0.612	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353		A	84214736	C	A	84214736	3	1	46	1	0	0	0	0	1	0	0	0	15536	912	32	3	1326	3	TAF1C	16	84214736	Missense_Mutation	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	33399519	84214736	6140017	32	5997										
TP53	7157	hgsc.bcm.edu	37	chr17	7579389	7579399	+	Frame_Shift_Del	DEL	GGGAAGGGACA	GGGAAGGGACA	-													0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	gctgccctggtaggttttctGggaagggacagaagatgaca							TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	GGGAAGGGACA	GGGAAGGGACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr17:7579389_7579399delGGGAAGGGACA	ENST00000269305.4	-	4	477_487	c.288_298delTGTCCCTTCCC	c.(286-300)tctgtcccttcccagfs	p.VPSQ97fs	TP53_ENST00000420246.2_Frame_Shift_Del_p.VPSQ97fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.VPSQ97fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Frame_Shift_Del_p.VPSQ97fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.VPSQ97fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.VPSQ97fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	97	Interaction with WWOX.		V -> A (in a sporadic cancer; somatic mutation).|V -> F (in a sporadic cancer; somatic mutation).|V -> I (in familial cancer not matching LFS; germline mutation and in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q100*(12)|p.0?(8)|p.P98S(4)|p.S99fs*48(3)|p.S99fs*23(3)|p.P98L(3)|p.V97V(3)|p.Q100fs*37(3)|p.G59fs*23(3)|p.S99F(2)|p.V97I(1)|p.V73fs*9(1)|p.V97A(1)|p.P98fs*26(1)|p.S99P(1)|p.W91fs*13(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.S99fs*24(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TAGGTTTTCTGGGAAGGGACAGAAGATGACA	0.645		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.97_100del	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	.	TP53	33396	.	53	Deletion - Frameshift(17)|Substitution - Nonsense(12)|Substitution - Missense(12)|Whole gene deletion(8)|Substitution - coding silent(3)|Insertion - Frameshift(1)	upper_aerodigestive_tract(7)|haematopoietic_and_lymphoid_tissue(7)|ovary(5)|large_intestine(4)|lung(4)|skin(4)|bone(4)|central_nervous_system(3)|kidney(3)|adrenal_gland(2)|urinary_tract(2)|breast(2)|pancreas(2)|stomach(1)|eye(1)|oesophagus(1)|liver(1)	c.289_299del	GRCh37	CM045203	TP53	M		.																																			SO:0001589	frameshift_variant	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.288_298delTGTCCCTTCCC	chr17.hg19:g.7579389_7579399delGGGAAGGGACA	ENSP00000269305:p.Val97fs	190.0	0.0		64.0	23.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.645	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7579399	GGGAAGGGACA	-	7579389	7	5	46	1	0	1	0	1	0	0	0	0	16396	1357	47	0	1004	0	TP53	17	7579389	Frame_Shift_Del	DEL	GGGAAGGGACA	TCGA-BC-A69H-01A-11D-A30V-10		7579389	73615821	33	5998										
HGS	9146	hgsc.bcm.edu	37	chr17	79660939	79660939	+	Frame_Shift_Del	DEL	C	C	-													0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	cttcgtaccccaaggcggagCccatgccctcggcctcctca							TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr17:79660939delC	ENST00000329138.4	+	11	1015	c.880delC	c.(880-882)cccfs	p.P294fs		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	294	Interaction with SNX1. {ECO:0000250}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CAAGGCGGAGCCCATGCCCTC	0.662																																					p.E293fs		Atlas-Indel,Pindel	.											.	HGS	54	.	0			c.879delG						.						38	42	41					17																	79660939		2202	4300	6502	SO:0001589	frameshift_variant	9146	exon11			.	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"Zinc fingers, FYVE domain containing"	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.880delC	chr17.hg19:g.79660939delC	ENSP00000331201:p.Pro294fs	28.0	0.0		54.0	15.0	NM_004712	Q9NR36	Frame_Shift_Del	DEL	ENST00000329138.4	hg19	CCDS11784.1																																																																																			.	.		0.662	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712		-	79660939	C	-	79660939	7	5	46	1	0	1	0	1	0	0	0	0	7096	739	26	0	922	0	HGS	17	79660939	Frame_Shift_Del	DEL	C	TCGA-BC-A69H-01A-11D-A30V-10	72081550	79660939	1534271	34	5999										
FASN	2194	hgsc.bcm.edu	37	chr17	80051623	80051623	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	cccagacgccagtgtgtgttCctcggagtgaatctgggttg	14	10	1	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr17:80051623C>T	ENST00000306749.2	-	4	523	c.305G>A	c.(304-306)gGa>gAa	p.G102E		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	102	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	AGTGTGTGTTCCTCGGAGTGA	0.677																																					p.G102E	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G305A						.						55	51	53					17																	80051623		2200	4295	6495	SO:0001583	missense	2194	exon4			TGTGTTCCTCGGA	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.305G>A	chr17.hg19:g.80051623C>T	ENSP00000304592:p.Gly102Glu	45.0	0.0		68.0	40.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.518479	0.85495	.	.	ENSG00000169710	ENST00000306749	T	0.38077	1.16	4.38	4.38	0.52667	Beta-ketoacyl synthase, N-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.066543	0.64402	D	0.000014	T	0.63885	0.2549	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71873	-0.4461	10	0.87932	D	0	-42.0902	16.5418	0.84386	0.0:1.0:0.0:0.0	.	102	P49327	FAS_HUMAN	E	102	ENSP00000304592:G102E	ENSP00000304592:G102E	G	-	2	0	FASN	77644912	1.000000	0.71417	0.381000	0.26106	0.805000	0.45488	5.836000	0.69375	2.006000	0.58801	0.561000	0.74099	GGA	.	.		0.677	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80051623	C	T	80051623	3	4	46	1	0	0	0	0	1	0	0	0	5691	855	30	3	7390	3	FASN	17	80051623	Missense_Mutation	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	390684	80051623	1143587	35	6000										
FOXK2	3607	hgsc.bcm.edu	37	chr17	80477826	80477826	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	acccgcgggcggcggggccgGgggcggcggggccgggggcg	27	13	0	0			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr17:80477826G>C	ENST00000335255.5	+	1	236	c.62G>C	c.(61-63)gGg>gCg	p.G21A		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	21	Gly-rich.			AAAAALSGAGTPPAGGGAGGGGAGGGGSPPGGWAVARLEGR EFEYLMKKRSVTIGRNSSQGSVDVSMGHSSFISRRHLEIFT PPGGGGHGGAAPELPPAQPRPDAGGDFYLRCLGKNG -> Q (in Ref. 1; CAA43200). {ECO:0000305}.	positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ggcggggccgggggcggcggg	0.846																																					p.G21A		Atlas-SNP	.											FOXK2,NS,carcinoma,0,1	FOXK2	46	.	0			c.G62C						.						1	1	1					17																	80477826		122	223	345	SO:0001583	missense	3607	exon1			GGGCCGGGGGCGG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.62G>C	chr17.hg19:g.80477826G>C	ENSP00000335677:p.Gly21Ala	1.0	0.0		4.0	2.0	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	hg19	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	.	2.177	-0.388435	0.04932	.	.	ENSG00000141568	ENST00000335255;ENST00000335241	D	0.93076	-3.16	1.8	1.8	0.24995	.	.	.	.	.	D	0.89375	0.6697	N	0.08118	0	0.25222	N	0.98989	D;D;D	0.71674	0.998;0.996;0.998	D;D;D	0.68621	0.959;0.91;0.959	T	0.80350	-0.1419	9	0.14252	T	0.57	.	6.724	0.23346	0.0:0.0:1.0:0.0	.	21;21;21	Q01167-3;Q01167;Q01167-2	.;FOXK2_HUMAN;.	A	21	ENSP00000335677:G21A	ENSP00000334321:G21A	G	+	2	0	FOXK2	78071115	0.917000	0.31117	0.403000	0.26384	0.773000	0.43773	0.923000	0.28757	0.820000	0.34516	0.486000	0.48141	GGG	.	.		0.846	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		C	80477826	G	C	80477826	3	2	46	1	0	0	0	0	1	0	0	0	6023	1232	43	4	64	4	FOXK2	17	80477826	Missense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10	426203	80477826	717384	36	6001										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7002349	7002349	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	tagtagccagaagtacacacAtcacaatggtcacctgctgt	8	11	2	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr18:7002349A>G	ENST00000389658.3	-	30	4389	c.4296T>C	c.(4294-4296)gaT>gaC	p.D1432D		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1432	Laminin EGF-like 15. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AAGTACACACATCACAATGGT	0.507																																					p.D1432D		Atlas-SNP	.											.	LAMA1	458	.	0			c.T4296C						.						227	183	198					18																	7002349		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon30			ACACACATCACAA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.4296T>C	chr18.hg19:g.7002349A>G		52.0	0.0		37.0	9.0	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.507	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	7002349	A	G	7002349	2	3	46	1	0	0	0	0	0	0	0	1	8614	214	8	2		2	LAMA1	18	7002349	Silent	SNP	A	TCGA-BC-A69H-01A-11D-A30V-10		7002349	71074899	37	6002										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17040002	17040002	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	gggtgaggcgcagtggccgcTgcacatactggaactcatac	14	11	1	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr19:17040002T>A	ENST00000443236.1	-	24	3066	c.3035A>T	c.(3034-3036)cAg>cTg	p.Q1012L		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	965						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CAGTGGCCGCTGCACATACTG	0.587																																					p.Q1012L		Atlas-SNP	.											.	CPAMD8	192	.	0			c.A3035T						.						48	55	53					19																	17040002		2096	4227	6323	SO:0001583	missense	27151	exon24			GGCCGCTGCACAT	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.3035A>T	chr19.hg19:g.17040002T>A	ENSP00000402505:p.Gln1012Leu	37.0	0.0		30.0	5.0	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	hg19	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.98|15.98	2.992975|2.992975	0.54041|0.54041	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	3.4|3.4	2.32|2.32	0.28847|0.28847	.|.	0.196250|.	0.33364|.	U|.	0.004989|.	T|T	0.59487|0.59487	0.2197|0.2197	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	P|.	0.44195|.	0.828|.	B|.	0.33750|.	0.169|.	T|T	0.52343|0.52343	-0.8588|-0.8588	9|5	0.28530|.	T|.	0.3|.	.|.	9.3067|9.3067	0.37878|0.37878	0.0:0.0:0.1819:0.8181|0.0:0.0:0.1819:0.8181	.|.	965|.	Q8IZJ3|.	CPMD8_HUMAN|.	L|C	1012|1023	.|.	ENSP00000291440:Q1012L|.	Q|S	-|-	2|1	0|0	CPAMD8|CPAMD8	16901002|16901002	1.000000|1.000000	0.71417|0.71417	0.509000|0.509000	0.27700|0.27700	0.897000|0.897000	0.52465|0.52465	3.063000|3.063000	0.49978|0.49978	0.213000|0.213000	0.20722|0.20722	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.587	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		A	17040002	T	A	17040002	3	1	46	1	0	0	0	0	1	0	0	0	3797	1580	55	4	2839	4	CPAMD8	19	17040002	Missense_Mutation	SNP	T	TCGA-BC-A69H-01A-11D-A30V-10		17040002	42088981	38	6003										
CILP2	148113	hgsc.bcm.edu	37	chr19	19655201	19655201	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	cgtggacccccgagacctcaCctcggcggcgtctgccccca	11	20	2	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr19:19655201C>A	ENST00000291495.5	+	8	1932	c.1847C>A	c.(1846-1848)aCc>aAc	p.T616N	CILP2_ENST00000586018.1_Missense_Mutation_p.T622N	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	616						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CGAGACCTCACCTCGGCGGCG	0.692																																					p.T616N		Atlas-SNP	.											.	CILP2	84	.	0			c.C1847A						.						46	55	52					19																	19655201		2200	4298	6498	SO:0001583	missense	148113	exon8			ACCTCACCTCGGC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1847C>A	chr19.hg19:g.19655201C>A	ENSP00000291495:p.Thr616Asn	71.0	0.0		41.0	17.0	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	hg19	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.902375	0.33628	.	.	ENSG00000160161	ENST00000291495	T	0.44881	0.91	4.37	3.32	0.38043	.	0.539436	0.19585	N	0.110752	T	0.29256	0.0728	N	0.19112	0.55	0.26737	N	0.970478	B;B	0.24092	0.097;0.097	B;B	0.26094	0.051;0.066	T	0.26883	-1.0090	10	0.66056	D	0.02	-13.3451	11.028	0.47757	0.0:0.6349:0.3651:0.0	.	616;616	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	N	616	ENSP00000291495:T616N	ENSP00000291495:T616N	T	+	2	0	CILP2	19516201	0.355000	0.24921	0.014000	0.15608	0.785000	0.44390	3.087000	0.50167	0.819000	0.34492	0.485000	0.47835	ACC	.	.		0.692	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		A	19655201	C	A	19655201	3	1	46	1	0	0	0	0	1	0	0	0	3432	507	18	3	1877	3	CILP2	19	19655201	Missense_Mutation	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	2615199	19655201	39473782	39	6004										
RBM42	79171	hgsc.bcm.edu	37	chr19	36120133	36120133	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ggtcctggcgctggcatcccGggcaaaagcggcgaggaacg	17	12	0	0	rs371589146		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr19:36120133G>T	ENST00000262633.4	+	1	183	c.78G>T	c.(76-78)ccG>ccT	p.P26P	RBM42_ENST00000589559.1_Silent_p.P26P|RBM42_ENST00000589871.1_Silent_p.P26P|RBM42_ENST00000592202.1_Silent_p.P26P|RBM42_ENST00000586618.1_Silent_p.P26P|RBM42_ENST00000588161.1_Silent_p.P26P|RBM42_ENST00000360475.4_Silent_p.P26P	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	26						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(7)|lung(9)|prostate(1)	21	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CTGGCATCCCGGGCAAAAGCG	0.687																																					p.P26P		Atlas-SNP	.											.	RBM42	40	.	0			c.G78T						.						11	12	11					19																	36120133		1960	3804	5764	SO:0001819	synonymous_variant	79171	exon1			CATCCCGGGCAAA	BC004204	CCDS12468.1	19q13.12	2013-02-12				ENSG00000126254		"RNA binding motif (RRM) containing"	28117	protein-coding gene	gene with protein product		613232				12477932	Standard	NM_024321		Approved	MGC10433	uc002oan.3	Q9BTD8		ENST00000262633.4:c.78G>T	chr19.hg19:g.36120133G>T		35.0	0.0		27.0	11.0	NM_024321	O00320|Q8N5R7|Q9BU66	Silent	SNP	ENST00000262633.4	hg19	CCDS12468.1																																																																																			.	.		0.687	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321		T	36120133	G	T	36120133	2	4	46	1	0	0	0	0	0	0	0	1	13151	1103	39	1		1	RBM42	19	36120133	Silent	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10	16464932	36120133	23008850	40	6005										
ZBTB32	27033	hgsc.bcm.edu	37	chr19	36207170	36207170	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	gaggttttcactcaagcatcAgatggagacgcactaccgag	11	10	3	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr19:36207170A>T	ENST00000392197.2	+	6	1478	c.1160A>T	c.(1159-1161)cAg>cTg	p.Q387L	KMT2B_ENST00000420124.1_5'Flank|KMT2B_ENST00000222270.7_5'Flank|ZBTB32_ENST00000262630.3_Missense_Mutation_p.Q387L|KMT2B_ENST00000341701.1_5'Flank|KMT2B_ENST00000607650.1_RNA			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	387					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTCAAGCATCAGATGGAGACG	0.627																																					p.Q387L		Atlas-SNP	.											.	ZBTB32	33	.	0			c.A1160T						.						36	33	34					19																	36207170		2203	4300	6503	SO:0001583	missense	27033	exon5			AGCATCAGATGGA	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16763	protein-coding gene	gene with protein product	"repressor of GATA"	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.1160A>T	chr19.hg19:g.36207170A>T	ENSP00000376035:p.Gln387Leu	82.0	0.0		81.0	27.0	NM_014383	Q8WVP2	Missense_Mutation	SNP	ENST00000392197.2	hg19	CCDS12471.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.442828	0.83993	.	.	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.07327	3.2;3.2	4.72	4.72	0.59763	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45867	D	0.000321	T	0.15435	0.0372	N	0.21142	0.635	0.49130	D	0.999756	D	0.76494	0.999	D	0.87578	0.998	T	0.05582	-1.0876	10	0.39692	T	0.17	-14.3215	12.206	0.54353	1.0:0.0:0.0:0.0	.	387	Q9Y2Y4	ZBT32_HUMAN	L	387	ENSP00000262630:Q387L;ENSP00000376035:Q387L	ENSP00000262630:Q387L	Q	+	2	0	ZBTB32	40899010	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.085000	0.76875	1.983000	0.57843	0.459000	0.35465	CAG	.	.		0.627	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383		T	36207170	A	T	36207170	3	4	46	1	0	0	0	0	1	0	0	0	17550	188	7	4	1174	4	ZBTB32	19	36207170	Missense_Mutation	SNP	A	TCGA-BC-A69H-01A-11D-A30V-10	87037	36207170	22921813	41	6006										
PTOV1	53635	hgsc.bcm.edu	37	chr19	50361895	50361895	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ctgaagagcctgtgccggatCatggacaatggcttcgtgag	14	9	1	3	rs376020024		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr19:50361895C>A	ENST00000601675.1	+	10	1130	c.1026C>A	c.(1024-1026)atC>atA	p.I342I	PTOV1_ENST00000601638.1_Silent_p.I310I|AC018766.5_ENST00000599259.1_RNA|AC018766.5_ENST00000593654.1_RNA|PTOV1_ENST00000600603.1_Silent_p.I310I|PTOV1_ENST00000599732.1_Silent_p.I342I|PTOV1_ENST00000598325.1_3'UTR|AC018766.4_ENST00000596624.1_RNA|PTOV1_ENST00000221557.9_Silent_p.I310I|AC018766.5_ENST00000601893.1_RNA|PTOV1_ENST00000391842.1_Silent_p.I342I			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	342	Interaction with FLOT1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(5)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)	16		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		TGTGCCGGATCATGGACAATG	0.662																																					p.I342I		Atlas-SNP	.											.	PTOV1	41	.	0			c.C1026A						.	C		2,4404		0,2,2201	42	28	33		1026	2.4	0.9	19		33	0,8600		0,0,4300	no	coding-synonymous	PTOV1	NM_017432.3		0,2,6501	AA,AC,CC		0.0,0.0454,0.0154		342/417	50361895	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	53635	exon10			CCGGATCATGGAC	AF238381	CCDS12782.1	19q13.33	2014-08-28	2008-09-12		ENSG00000104960	ENSG00000104960			9632	protein-coding gene	gene with protein product		610195				12598323, 15713644	Standard	XM_005258998		Approved		uc002pqf.1	Q86YD1	OTTHUMG00000183162	ENST00000601675.1:c.1026C>A	chr19.hg19:g.50361895C>A		81.0	0.0		52.0	25.0	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Silent	SNP	ENST00000601675.1	hg19	CCDS12782.1																																																																																			.	.		0.662	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432		A	50361895	C	A	50361895	2	1	46	1	0	0	0	0	0	0	0	1	12782	816	29	3		3	PTOV1	19	50361895	Silent	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	14154725	50361895	8767088	42	6007										
TMEM90B	79953	hgsc.bcm.edu	37	chr20	24565510	24565510	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	agagcgactactcaagcgacAcagagagtgaggacaatttc	11	9	1	3			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr20:24565510A>G	ENST00000376862.3	+	3	1132	c.499A>G	c.(499-501)Aca>Gca	p.T167A		NM_024893.1	NP_079169.1	Q9H7V2	SYNG1_HUMAN	synapse differentiation inducing 1	167					intracellular protein transport (GO:0006886)|positive regulation of synapse assembly (GO:0051965)|response to biotic stimulus (GO:0009607)|synaptic vesicle clustering (GO:0097091)	cell body (GO:0044297)|cell junction (GO:0030054)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	glutamate receptor binding (GO:0035254)|protein homodimerization activity (GO:0042803)	p.T167A(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	24						CTCAAGCGACACAGAGAGTGA	0.562																																					p.T167A		Atlas-SNP	.											SYNDIG1,NS,carcinoma,0,1	SYNDIG1	58	.	1	Substitution - Missense(1)	lung(1)	c.A499G						.						140	132	135					20																	24565510		2203	4300	6503	SO:0001583	missense	79953	exon3			AGCGACACAGAGA	AK024282	CCDS13164.1	20p11.21	2011-06-30	2011-06-30	2011-06-30	ENSG00000101463	ENSG00000101463			15885	protein-coding gene	gene with protein product	"interferon induced transmembrane protein domain containing 5", "synapse differentiation induced gene 1"	614311	"chromosome 20 open reading frame 39", "transmembrane protein 90B"	C20orf39, TMEM90B		20152115	Standard	NM_024893		Approved	FLJ14220, IFITMD5, SynDIG1	uc002wtw.1	Q9H7V2	OTTHUMG00000032104	ENST00000376862.3:c.499A>G	chr20.hg19:g.24565510A>G	ENSP00000366058:p.Thr167Ala	60.0	1.0		64.0	29.0	NM_024893	Q6IA30|Q9H514	Missense_Mutation	SNP	ENST00000376862.3	hg19	CCDS13164.1	.	.	.	.	.	.	.	.	.	.	A	13.58	2.278997	0.40294	.	.	ENSG00000101463	ENST00000376862	D	0.90620	-2.7	5.1	5.1	0.69264	.	0.078921	0.52532	D	0.000063	D	0.88746	0.6520	L	0.47716	1.5	0.41539	D	0.988501	P	0.47762	0.9	P	0.45538	0.484	D	0.89491	0.3757	10	0.56958	D	0.05	-16.4836	12.8475	0.57837	1.0:0.0:0.0:0.0	.	167	Q9H7V2	SYNG1_HUMAN	A	167	ENSP00000366058:T167A	ENSP00000366058:T167A	T	+	1	0	SYNDIG1	24513510	0.992000	0.36948	0.997000	0.53966	0.670000	0.39368	3.706000	0.54830	1.930000	0.55929	0.459000	0.35465	ACA	.	.		0.562	SYNDIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078376.1	NM_024893		G	24565510	A	G	24565510	3	3	46	1	0	0	0	0	1	0	0	0	16234	159	6	2	505	2	TMEM90B	20	24565510	Missense_Mutation	SNP	A	TCGA-BC-A69H-01A-11D-A30V-10		24565510	38460010	43	6008										
SUN5	140732	hgsc.bcm.edu	37	chr20	31577506	31577506	+	Splice_Site	DEL	T	T	-													0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ttttctgggccattttttgcTgaaaaggcagaaaacacaag							TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr20:31577506delT	ENST00000356173.3	-	9	627		c.e9-2		SUN5_ENST00000375523.3_Splice_Site	NM_080675.3	NP_542406.2	Q8TC36	SUN5_HUMAN	Sad1 and UNC84 domain containing 5						spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	25						CATTTTTTGCTGAAAAGGCAG	0.512																																					.		Pindel	.											.	SUN5	63	.	0			c.535-1A>-						.						166	128	141					20																	31577506		2203	4300	6503	SO:0001630	splice_region_variant	140732	exon10			.	AL121756	CCDS13209.1	20q11.21	2010-01-27	2010-01-27	2010-01-27	ENSG00000167098	ENSG00000167098			16252	protein-coding gene	gene with protein product	"testis and spermatogenesis related gene 4"	613942	"sperm associated antigen 4-like"	SPAG4L		9691178, 10373309	Standard	NM_080675		Approved	dJ726C3.1, TSARG4	uc002wyi.3	Q8TC36	OTTHUMG00000032239	ENST00000356173.3:c.535-2A>-	chr20.hg19:g.31577506delT		79.0	0.0		66.0	18.0	NM_080675	A6NJ82|Q5T9R0	Splice_Site	DEL	ENST00000356173.3	hg19	CCDS13209.1																																																																																			.	.		0.512	SUN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078659.1	NM_080675	Intron	-	31577506	T	-	31577506	8	5	46	1	0	1	0	1	0	0	1	0	15409	1594	55	0	626	0	SUN5	20	31577506	Splice_Site	DEL	T	TCGA-BC-A69H-01A-11D-A30V-10	7011996	31577506	31448014	44	6009										
DSCAM	1826	hgsc.bcm.edu	37	chr21	42080424	42080424	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ttctaattttccctgaaggaTtttcagctgtgcaataataa	6	7	2	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr21:42080424T>A	ENST00000400454.1	-	2	794	c.317A>T	c.(316-318)aAt>aTt	p.N106I		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	106	Ig-like C2-type 1.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CCCTGAAGGATTTTCAGCTGT	0.463																																					p.N106I	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.A317T						.						114	109	111					21																	42080424		1885	4110	5995	SO:0001583	missense	1826	exon2			GAAGGATTTTCAG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.317A>T	chr21.hg19:g.42080424T>A	ENSP00000383303:p.Asn106Ile	69.0	0.0		46.0	15.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.272051	0.80469	.	.	ENSG00000171587	ENST00000400454	T	0.56941	0.43	5.22	5.22	0.72569	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.78149	0.4238	M	0.91818	3.245	0.53688	D	0.999977	D	0.76494	0.999	D	0.87578	0.998	D	0.83855	0.0265	10	0.87932	D	0	.	15.1068	0.72326	0.0:0.0:0.0:1.0	.	106	O60469	DSCAM_HUMAN	I	106	ENSP00000383303:N106I	ENSP00000383303:N106I	N	-	2	0	DSCAM	41002294	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.603000	0.82811	1.980000	0.57719	0.477000	0.44152	AAT	.	.		0.463	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	42080424	T	A	42080424	3	1	46	1	0	0	0	0	1	0	0	0	4770	1493	52	4	5849	4	DSCAM	21	42080424	Missense_Mutation	SNP	T	TCGA-BC-A69H-01A-11D-A30V-10		42080424	6049471	45	6010										
SIK1	150094	hgsc.bcm.edu	37	chr21	44841639	44841639	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	atttgccagaacttcttccgCgcctcgttctcactcaggtg	8	14	3	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr21:44841639C>T	ENST00000270162.6	-	5	510	c.378G>A	c.(376-378)gcG>gcA	p.A126A		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	126	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	ACTTCTTCCGCGCCTCGTTCT	0.572																																					p.A126A		Atlas-SNP	.											SIK1,caecum,carcinoma,0,1	SIK1	65	.	0			c.G378A						.						67	61	63					21																	44841639		2203	4300	6503	SO:0001819	synonymous_variant	150094	exon5			CTTCCGCGCCTCG	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"myocardial SNF1-like kinase"	605705	"SNF1-like kinase"	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.378G>A	chr21.hg19:g.44841639C>T		111.0	0.0		78.0	24.0	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Silent	SNP	ENST00000270162.6	hg19	CCDS33575.1																																																																																			.	.		0.572	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		T	44841639	C	T	44841639	2	4	46	1	0	0	0	0	0	0	0	1	14332	755	27	1		1	SIK1	21	44841639	Silent	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	2761215	44841639	3288256	46	6011										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350826	50350826	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	gtacttctcccagttgggagGaggagggcgaggaggaggaa	19	6	1	0			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chrX:50350826G>T	ENST00000289292.7	-	6	3599	c.3316C>A	c.(3316-3318)Cct>Act	p.P1106T	SHROOM4_ENST00000460112.3_Missense_Mutation_p.P990T|SHROOM4_ENST00000376020.2_Missense_Mutation_p.P1106T			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1106	Poly-Pro.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					CAGTTGGGAGGAGGAGGGCGA	0.587																																					p.P1106T		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C3316A						.						39	34	35					X																	50350826		2203	4300	6503	SO:0001583	missense	57477	exon6			TGGGAGGAGGAGG	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3316C>A	chrX.hg19:g.50350826G>T	ENSP00000289292:p.Pro1106Thr	92.0	0.0		30.0	17.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.958479	0.53400	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.25250	2.24;2.24;1.81	5.74	5.74	0.90152	.	0.193727	0.44483	D	0.000447	T	0.34919	0.0914	L	0.34521	1.04	0.49213	D	0.999763	D	0.58268	0.982	P	0.55112	0.769	T	0.07009	-1.0795	10	0.87932	D	0	.	16.1551	0.81657	0.0:0.0:1.0:0.0	.	1106	Q9ULL8	SHRM4_HUMAN	T	1106;1106;990	ENSP00000289292:P1106T;ENSP00000365188:P1106T;ENSP00000421450:P990T	ENSP00000289292:P1106T	P	-	1	0	SHROOM4	50367566	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.125000	0.77193	2.418000	0.82041	0.513000	0.50165	CCT	.	.		0.587	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		T	50350826	G	T	50350826	3	4	46	1	0	0	0	0	1	0	0	0	14311	1174	41	3	1181	3	SHROOM4	23	50350826	Missense_Mutation	SNP	G	TCGA-BC-A69H-01A-11D-A30V-10		50350826	104919734	47	6012										
MSN	4478	hgsc.bcm.edu	37	chrX	64951035	64951044	+	Frame_Shift_Del	DEL	ACACCGTGGC	ACACCGTGGC	-													0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	atccaggtgtggcatgaggaAcaccgtggcatgctcaggta					rs373340100		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	ACACCGTGGC	ACACCGTGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chrX:64951035_64951044delACACCGTGGC	ENST00000360270.5	+	5	706_715	c.534_543delACACCGTGGC	c.(532-543)gaacaccgtggcfs	p.EHRG178fs		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	178	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|establishment of endothelial barrier (GO:0061028)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|regulation of lymphocyte migration (GO:2000401)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|uropod (GO:0001931)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|structural constituent of cytoskeleton (GO:0005200)	p.R180R(1)	MSN/ALK(6)	breast(4)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	43						GGCATGAGGAACACCGTGGCATGCTCAGGT	0.524			T	ALK	ALCL																																p.178_181del		Pindel	.		Dom	yes		X	Xq11.2-q12	4478	moesin		L	.	MSN	89	.	1	Substitution - coding silent(1)	ovary(1)	c.533_542del						.																																			SO:0001589	frameshift_variant	4478	exon5			.	M69066	CCDS14382.1	Xq11.1	2010-10-20			ENSG00000147065	ENSG00000147065			7373	protein-coding gene	gene with protein product		309845				1924289, 7628534	Standard	XM_005262269		Approved		uc004dwf.3	P26038	OTTHUMG00000021723	ENST00000360270.5:c.534_543delACACCGTGGC	chrX.hg19:g.64951035_64951044delACACCGTGGC	ENSP00000353408:p.Glu178fs	154.0	0.0		56.0	17.0	NM_002444		Frame_Shift_Del	DEL	ENST00000360270.5	hg19	CCDS14382.1																																																																																			.	.		0.524	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444		-	64951044	ACACCGTGGC	-	64951035	7	5	46	1	0	1	0	1	0	0	0	0	9894	40	2	0	552	0	MSN	23	64951035	Frame_Shift_Del	DEL	ACACCGTGGC	TCGA-BC-A69H-01A-11D-A30V-10	14600209	64951035	90319525	48	6013										
PABPC5	140886	hgsc.bcm.edu	37	chrX	90690699	90690699	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	tataagaagttcaggcctgcTggccctctgcgattcacccg	10	13	3	1			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chrX:90690699T>A	ENST00000312600.3	+	2	337	c.123T>A	c.(121-123)gcT>gcA	p.A41A	PABPC5-AS1_ENST00000456187.1_RNA|PABPC5_ENST00000373105.1_Intron	NM_080832.2	NP_543022.1	Q96DU9	PABP5_HUMAN	poly(A) binding protein, cytoplasmic 5	41	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.					mitochondrion (GO:0005739)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(1)|pancreas(1)	42						TCAGGCCTGCTGGCCCTCTGC	0.572																																					p.A41A		Atlas-SNP	.											.	PABPC5	92	.	0			c.T123A						.						53	41	45					X																	90690699		2203	4300	6503	SO:0001819	synonymous_variant	140886	exon2			GCCTGCTGGCCCT	AJ278963	CCDS14460.1	Xq21.3	2013-02-12	2001-11-28		ENSG00000174740	ENSG00000174740		"RNA binding motif (RRM) containing"	13629	protein-coding gene	gene with protein product		300407	"poly(A)-binding protein, cytoplasmic 5"			11374897	Standard	NM_080832		Approved	PABP5	uc004efg.3	Q96DU9	OTTHUMG00000021959	ENST00000312600.3:c.123T>A	chrX.hg19:g.90690699T>A		53.0	0.0		16.0	10.0	NM_080832	A8K240|Q5JQF4|Q6P529|Q9UFE5	Silent	SNP	ENST00000312600.3	hg19	CCDS14460.1																																																																																			.	.		0.572	PABPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057429.1	NM_080832		A	90690699	T	A	90690699	2	1	46	1	0	0	0	0	0	0	0	1	11376	1567	55	4		4	PABPC5	23	90690699	Silent	SNP	T	TCGA-BC-A69H-01A-11D-A30V-10	25739664	90690699	64579861	49	6014										
GLRA4	441509	hgsc.bcm.edu	37	chrX	102978843	102978843	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ggaagttcttgaggtccatcAggcaggacaaaatgagggtc	14	7	2	2			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chrX:102978843A>C	ENST00000372617.4	-	5	938	c.518T>G	c.(517-519)cTg>cGg	p.L173R	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	173						cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			cervix(1)|endometrium(2)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GAGGTCCATCAGGCAGGACAA	0.527																																					p.L173R		Atlas-SNP	.											.	GLRA4	86	.	0			c.T518G						.						117	110	112					X																	102978843		2034	4174	6208	SO:0001583	missense	441509	exon5			TCCATCAGGCAGG	Z93848	CCDS43980.2	Xq22.2	2012-01-16			ENSG00000188828	ENSG00000188828		"Ligand-gated ion channels / Glycine receptors"	31715	protein-coding gene	gene with protein product							Standard	NM_001024452		Approved		uc011mse.2	Q5JXX5	OTTHUMG00000022110	ENST00000372617.4:c.518T>G	chrX.hg19:g.102978843A>C	ENSP00000361700:p.Leu173Arg	280.0	1.0		102.0	69.0	NM_001024452		Missense_Mutation	SNP	ENST00000372617.4	hg19	CCDS43980.2	.	.	.	.	.	.	.	.	.	.	G	14.46	2.541146	0.45280	.	.	ENSG00000188828	ENST00000372617	T	0.78364	-1.17	5.46	5.46	0.80206	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.61060	0.2317	N	0.10874	0.06	0.32898	D	0.512749	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.64162	-0.6472	10	0.59425	D	0.04	.	11.2816	0.49197	0.0905:0.0:0.9095:0.0	.	173;132	Q5JXX5;B9WSA6	GLRA4_HUMAN;.	R	173	ENSP00000361700:L173R	ENSP00000361700:L173R	L	-	2	0	GLRA4	102865499	1.000000	0.71417	0.888000	0.34837	0.570000	0.35934	6.795000	0.75140	1.085000	0.41206	-0.170000	0.13304	CTG	.	.		0.527	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452		C	102978843	A	C	102978843	3	2	46	1	0	0	0	0	1	0	0	0	6465	188	7	5	850	5	GLRA4	23	102978843	Missense_Mutation	SNP	A	TCGA-BC-A69H-01A-11D-A30V-10	12288144	102978843	52291717	50	6015										
RAB9B	51209	hgsc.bcm.edu	37	chrX	103080318	103080318	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.890598290598291	1.60307692307692	0.616568047337278	1	1	0	ttgtgcctcctcagtagtcaCttgcctatcctctttgtcta	6	13	4	0			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chrX:103080318C>T	ENST00000243298.2	-	3	681	c.397G>A	c.(397-399)Gtg>Atg	p.V133M		NM_016370.2	NP_057454.1	Q9NP90	RAB9B_HUMAN	RAB9B, member RAS oncogene family	133					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|lung(11)	14						TCAGTAGTCACTTGCCTATCC	0.433																																					p.V133M		Atlas-SNP	.											.	RAB9B	24	.	0			c.G397A						.						230	220	223					X																	103080318		2203	4300	6503	SO:0001583	missense	51209	exon3			TAGTCACTTGCCT	AB036693	CCDS14515.1	Xq22.1-q22.3	2010-04-19			ENSG00000123570	ENSG00000123570		"RAB, member RAS oncogene"	14090	protein-coding gene	gene with protein product		300285				11043518	Standard	NM_016370		Approved	RAB9L	uc004ell.2	Q9NP90	OTTHUMG00000022112	ENST00000243298.2:c.397G>A	chrX.hg19:g.103080318C>T	ENSP00000243298:p.Val133Met	91.0	0.0		24.0	17.0	NM_016370	B2R8M0|Q52LX2	Missense_Mutation	SNP	ENST00000243298.2	hg19	CCDS14515.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.148687	0.57151	.	.	ENSG00000123570	ENST00000243298	D	0.83914	-1.78	5.51	5.51	0.81932	Small GTP-binding protein domain (1);	0.056566	0.64402	D	0.000001	D	0.91744	0.7389	M	0.91818	3.245	0.58432	D	0.999999	D	0.89917	1.0	D	0.77004	0.989	D	0.92703	0.6176	10	0.87932	D	0	0.0455	9.3971	0.38408	0.0:0.9014:0.0:0.0986	.	133	Q9NP90	RAB9B_HUMAN	M	133	ENSP00000243298:V133M	ENSP00000243298:V133M	V	-	1	0	RAB9B	102966974	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.088000	0.71371	2.311000	0.77944	0.600000	0.82982	GTG	.	.		0.433	RAB9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057746.1			T	103080318	C	T	103080318	3	4	46	1	0	0	0	0	1	0	0	0	12974	565	20	3	212	3	RAB9B	23	103080318	Missense_Mutation	SNP	C	TCGA-BC-A69H-01A-11D-A30V-10	101475	103080318	52190242	51	6016										
GNB1	2782	hgsc.bcm.edu	37	chr1	1721974	1721974	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	agcaagagaaaggctcatgaCatctccagtgtgtccggtaa	11	9	2	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:1721974C>A	ENST00000378609.4	-	9	890	c.559G>T	c.(559-561)Gtc>Ttc	p.V187F		NM_001282539.1|NM_002074.3	NP_001269468.1|NP_002065.1	P62873	GBB1_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1	187					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|blood coagulation (GO:0007596)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	12	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		AGGCTCATGACATCTCCAGTG	0.562																																					p.V187F		Atlas-SNP	.											.	GNB1	39	.	0			c.G559T						.						152	108	123					1																	1721974		2203	4300	6503	SO:0001583	missense	2782	exon9			TCATGACATCTCC	BC004186	CCDS34.1, CCDS72685.1	1p36.33	2013-01-10			ENSG00000078369	ENSG00000078369		"WD repeat domain containing"	4396	protein-coding gene	gene with protein product		139380					Standard	NM_002074		Approved		uc001aif.3	P62873	OTTHUMG00000000940	ENST00000378609.4:c.559G>T	chr1.hg19:g.1721974C>A	ENSP00000367872:p.Val187Phe	87.0	0.0		124.0	44.0	NM_002074	B1AJZ7|P04697|P04901|Q1RMY8	Missense_Mutation	SNP	ENST00000378609.4	hg19	CCDS34.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.452542|5.452542	0.96223|0.96223	.|.	.|.	ENSG00000078369|ENSG00000078369	ENST00000424622|ENST00000378609;ENST00000455156;ENST00000378606	.|T	.|0.73897	.|-0.79	5.43|5.43	5.43|5.43	0.79202|0.79202	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.055920	.|0.64402	.|D	.|0.000001	D|D	0.91998|0.91998	0.7465|0.7465	H|H	0.98333|0.98333	4.205|4.205	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.77004	.|0.989	D|D	0.94971|0.94971	0.8117|0.8117	5|10	.|0.87932	.|D	.|0	-13.3509|-13.3509	18.2284|18.2284	0.89926|0.89926	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|187	.|P62873	.|GBB1_HUMAN	I|F	44|187;87;187	.|ENSP00000367872:V187F	.|ENSP00000367869:V187F	M|V	-|-	3|1	0|0	GNB1|GNB1	1711834|1711834	1.000000|1.000000	0.71417|0.71417	0.954000|0.954000	0.39281|0.39281	0.983000|0.983000	0.72400|0.72400	7.586000|7.586000	0.82596|0.82596	2.538000|2.538000	0.85594|0.85594	0.655000|0.655000	0.94253|0.94253	ATG|GTC	.	.		0.562	GNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002762.3	NM_002074		A	1721974	C	A	1721974	3	1	47	1	0	0	0	0	1	0	0	0	6523	478	17	3	475	3	GNB1	1	1721974	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10		1721974	247528647	1	6017										
XKR8	55113	hgsc.bcm.edu	37	chr1	28293332	28293332	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gacggtggccaccatcctctAtttctcctggttcaacgtgg	10	13	3	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:28293332A>G	ENST00000373884.5	+	3	1417	c.809A>G	c.(808-810)tAt>tGt	p.Y270C		NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	270					engulfment of apoptotic cell (GO:0043652)|phosphatidylserine exposure on apoptotic cell surface (GO:0070782)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(1)	4		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;4.72e-24)|Colorectal(126;1.52e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00572)|READ - Rectum adenocarcinoma(331;0.0526)		ACCATCCTCTATTTCTCCTGG	0.632																																					p.Y270C		Atlas-SNP	.											.	XKR8	15	.	0			c.A809G						.						23	24	23					1																	28293332		2203	4299	6502	SO:0001583	missense	55113	exon3			TCCTCTATTTCTC	AK091615	CCDS315.1	1p35.3	2008-02-05	2006-01-12		ENSG00000158156	ENSG00000158156			25508	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 8"			12477932	Standard	NM_018053		Approved	FLJ10307	uc001bph.1	Q9H6D3	OTTHUMG00000003912	ENST00000373884.5:c.809A>G	chr1.hg19:g.28293332A>G	ENSP00000362991:p.Tyr270Cys	78.0	0.0		110.0	50.0	NM_018053		Missense_Mutation	SNP	ENST00000373884.5	hg19	CCDS315.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.746479	0.89663	.	.	ENSG00000158156	ENST00000373884	T	0.64803	-0.12	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.74612	0.3739	M	0.76838	2.35	0.80722	D	1	D	0.54964	0.969	P	0.55965	0.788	T	0.75915	-0.3149	10	0.39692	T	0.17	.	15.2805	0.73781	1.0:0.0:0.0:0.0	.	270	Q9H6D3	XKR8_HUMAN	C	270	ENSP00000362991:Y270C	ENSP00000362991:Y270C	Y	+	2	0	XKR8	28165919	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.855000	0.92236	2.019000	0.59389	0.533000	0.62120	TAT	.	.		0.632	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053		G	28293332	A	G	28293332	3	3	47	1	0	0	0	0	1	0	0	0	17452	449	16	2	819	2	XKR8	1	28293332	Missense_Mutation	SNP	A	TCGA-BC-A8YO-01A-11D-A36X-10	26571358	28293332	220957289	2	6018										
HECTD3	79654	hgsc.bcm.edu	37	chr1	45474271	45474271	+	Frame_Shift_Del	DEL	C	C	-													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tgccttctaggcgtggatatCgcaccagactagttggctgg							TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:45474271delC	ENST00000372172.4	-	8	1246	c.1175delG	c.(1174-1176)cgafs	p.R392fs	HECTD3_ENST00000372168.3_5'Flank	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	392	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					GCGTGGATATCGCACCAGACT	0.562																																					p.R392fs		Atlas-Indel,Pindel	.											.	HECTD3	158	.	0			c.1176delA						.						179	174	175					1																	45474271		2069	4204	6273	SO:0001589	frameshift_variant	79654	exon8			.	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.1175delG	chr1.hg19:g.45474271delC	ENSP00000361245:p.Arg392fs	80.0	0.0		118.0	39.0	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Frame_Shift_Del	DEL	ENST00000372172.4	hg19	CCDS41318.1																																																																																			.	.		0.562	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		-	45474271	C	-	45474271	7	5	47	1	0	1	0	1	0	0	0	0	7050	884	31	0	1466	0	HECTD3	1	45474271	Frame_Shift_Del	DEL	C	TCGA-BC-A8YO-01A-11D-A36X-10	17180939	45474271	203776350	3	6019										
CACHD1	57685	hgsc.bcm.edu	37	chr1	65147714	65147714	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	acactcggtttatagctgcgGtcatcgaacgacatgcacac	9	12	1	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:65147714G>C	ENST00000371073.2	+	26	3511	c.3511G>C	c.(3511-3513)Gtc>Ctc	p.V1171L	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Missense_Mutation_p.V1120L			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1171					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						TATAGCTGCGGTCATCGAACG	0.473																																					p.V1120L		Atlas-SNP	.											CACHD1,colon,carcinoma,0,1	CACHD1	125	.	0			c.G3358C						.						119	106	111					1																	65147714		2203	4300	6503	SO:0001583	missense	57685	exon26			GCTGCGGTCATCG	AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.3511G>C	chr1.hg19:g.65147714G>C	ENSP00000360113:p.Val1171Leu	244.0	0.0		310.0	132.0	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	hg19		.	.	.	.	.	.	.	.	.	.	G	16.83	3.232356	0.58777	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.23950	1.88;1.89	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.28101	0.0693	N	0.22421	0.69	0.80722	D	1	P	0.44690	0.841	P	0.58820	0.846	T	0.02214	-1.1194	10	0.44086	T	0.13	-28.5069	20.2985	0.98592	0.0:0.0:1.0:0.0	.	1171	Q5VU97	CAHD1_HUMAN	L	1171;1120	ENSP00000360113:V1171L;ENSP00000290039:V1120L	ENSP00000290039:V1120L	V	+	1	0	CACHD1	64920302	1.000000	0.71417	0.964000	0.40570	0.754000	0.42855	9.374000	0.97172	2.793000	0.96121	0.655000	0.94253	GTC	.	.		0.473	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		C	65147714	G	C	65147714	3	2	47	1	0	0	0	0	1	0	0	0	2539	1261	44	4	3460	4	CACHD1	1	65147714	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	19673443	65147714	184102907	4	6020										
APOA1BP	128240	hgsc.bcm.edu	37	chr1	156562201	156562201	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	aggagcccccctactgtcctGgtcatctgtggcccggggaa	13	14	2	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:156562201G>T	ENST00000368235.3	+	3	379	c.336G>T	c.(334-336)ctG>ctT	p.L112L	APOA1BP_ENST00000368234.3_Silent_p.L112L|APOA1BP_ENST00000368233.3_Silent_p.L112L|APOA1BP_ENST00000467374.1_3'UTR	NM_144772.2	NP_658985.2			apolipoprotein A-I binding protein											central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTACTGTCCTGGTCATCTGTG	0.582																																					p.L112L		Atlas-SNP	.											.	APOA1BP	16	.	0			c.G336T						.						100	101	101					1																	156562201		2203	4300	6503	SO:0001819	synonymous_variant	128240	exon3			TGTCCTGGTCATC	AJ315849	CCDS1145.1	1q21	2008-08-14			ENSG00000163382	ENSG00000163382			18453	protein-coding gene	gene with protein product	"apoA-I binding protein"	608862				11991719, 17533573	Standard	NM_144772		Approved	AIBP, MGC119143, MGC119144, MGC119145, YJEFN1	uc001fph.3	Q8NCW5	OTTHUMG00000033206	ENST00000368235.3:c.336G>T	chr1.hg19:g.156562201G>T		46.0	0.0		105.0	64.0	NM_144772		Silent	SNP	ENST00000368235.3	hg19	CCDS1145.1																																																																																			.	.		0.582	APOA1BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081044.1	NM_144772		T	156562201	G	T	156562201	2	4	47	1	0	0	0	0	0	0	0	1	781	1335	47	3		3	APOA1BP	1	156562201	Silent	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	91414487	156562201	92688420	5	6021										
OLFML2B	25903	hgsc.bcm.edu	37	chr1	161989951	161989951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gccctcagacatagccttgaCcttgtcatagtcccccagca	7	16	2	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr1:161989951C>T	ENST00000294794.3	-	2	619	c.196G>A	c.(196-198)Gtc>Atc	p.V66I	OLFML2B_ENST00000367940.2_Missense_Mutation_p.V66I	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	66					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			ATAGCCTTGACCTTGTCATAG	0.567																																					p.V66I		Atlas-SNP	.											.	OLFML2B	114	.	0			c.G196A						.						69	67	68					1																	161989951		2203	4300	6503	SO:0001583	missense	25903	exon2			CCTTGACCTTGTC	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.196G>A	chr1.hg19:g.161989951C>T	ENSP00000294794:p.Val66Ile	58.0	0.0		92.0	38.0	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	hg19	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.738110	0.89573	.	.	ENSG00000162745	ENST00000294794;ENST00000367940	T;T	0.50277	0.75;0.75	4.33	4.33	0.51752	.	.	.	.	.	T	0.47967	0.1474	L	0.56199	1.76	0.35513	D	0.800825	D;D	0.62365	0.976;0.991	P;P	0.55222	0.609;0.771	T	0.55477	-0.8135	8	0.87932	D	0	.	14.7277	0.69357	0.0:1.0:0.0:0.0	.	66;66	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	I	66	ENSP00000294794:V66I;ENSP00000356917:V66I	ENSP00000294794:V66I	V	-	1	0	OLFML2B	160256575	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.078000	0.76821	2.404000	0.81709	0.561000	0.74099	GTC	.	.		0.567	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		T	161989951	C	T	161989951	3	4	47	1	0	0	0	0	1	0	0	0	10867	507	18	3	2084	3	OLFML2B	1	161989951	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10	5427750	161989951	87260670	6	6022										
CPSF3	51692	hgsc.bcm.edu	37	chr2	9613123	9613123	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tggctgcacagagactgtacGaggccctgacgccagttcac	12	13	1	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:9613123G>A	ENST00000238112.3	+	18	2238	c.2032G>A	c.(2032-2034)Gag>Aag	p.E678K	IAH1_ENST00000545602.1_5'Flank|CPSF3_ENST00000460593.1_Missense_Mutation_p.E641K|IAH1_ENST00000470914.1_5'Flank|IAH1_ENST00000482918.1_5'Flank|IAH1_ENST00000497473.1_5'Flank|CPSF3_ENST00000489403.1_3'UTR	NM_016207.3	NP_057291.1	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3, 73kDa	678					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	5'-3' exonuclease activity (GO:0008409)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		GAGACTGTACGAGGCCCTGAC	0.438																																					p.E678K	Colon(194;1259 2048 3845 5218 19985)	Atlas-SNP	.											.	CPSF3	63	.	0			c.G2032A						.						86	78	81					2																	9613123		2203	4300	6503	SO:0001583	missense	51692	exon18			CTGTACGAGGCCC	AF171877	CCDS1664.1	2p25.1	2009-01-06	2002-08-29		ENSG00000119203	ENSG00000119203			2326	protein-coding gene	gene with protein product		606029	"cleavage and polyadenylation specific factor 3, 73kD subunit"			8929409	Standard	NM_016207		Approved	CPSF-73, CPSF73, YSH1	uc002qzo.2	Q9UKF6	OTTHUMG00000090415	ENST00000238112.3:c.2032G>A	chr2.hg19:g.9613123G>A	ENSP00000238112:p.Glu678Lys	62.0	0.0		98.0	40.0	NM_016207	O14769|Q53RS2|Q96F36	Missense_Mutation	SNP	ENST00000238112.3	hg19	CCDS1664.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.808479	0.31961	.	.	ENSG00000119203	ENST00000238112;ENST00000540142;ENST00000460593	T;T	0.42513	0.97;0.97	5.24	5.24	0.73138	-end-processing endonuclease polyadenylation factor C-term (1);Pre-mRNA 3&apos (1);	0.171767	0.47852	D	0.000209	T	0.34716	0.0907	L	0.38175	1.15	0.58432	D	0.999991	B	0.20459	0.045	B	0.26416	0.069	T	0.19063	-1.0317	10	0.06236	T	0.91	-5.1796	18.8183	0.92086	0.0:0.0:1.0:0.0	.	678	Q9UKF6	CPSF3_HUMAN	K	678;400;641	ENSP00000238112:E678K;ENSP00000418957:E641K	ENSP00000238112:E678K	E	+	1	0	CPSF3	9530574	1.000000	0.71417	0.976000	0.42696	0.837000	0.47467	8.615000	0.90920	2.453000	0.82957	0.561000	0.74099	GAG	.	.		0.438	CPSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206843.1	NM_016207		A	9613123	G	A	9613123	3	1	47	1	0	0	0	0	1	0	0	0	3828	1059	37	1	2102	1	CPSF3	2	9613123	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10		9613123	233586250	7	6023										
KCNF1	3754	hgsc.bcm.edu	37	chr2	11052594	11052594	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	agcctcccggagccgggcagCcagagctccgctgccagcga	14	17	0	1			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:11052594C>T	ENST00000295082.1	+	1	532	c.42C>T	c.(40-42)agC>agT	p.S14S		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	14					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)	p.S14R(1)		NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		AGCCGGGCAGCCAGAGCTCCG	0.746																																					p.S14S		Atlas-SNP	.											KCNF1,NS,carcinoma,0,1	KCNF1	70	.	1	Substitution - Missense(1)	lung(1)	c.C42T						.						7	8	8					2																	11052594		2165	4249	6414	SO:0001819	synonymous_variant	3754	exon1			GGGCAGCCAGAGC	AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.42C>T	chr2.hg19:g.11052594C>T		25.0	0.0		38.0	18.0	NM_002236	O43527|Q585L3	Silent	SNP	ENST00000295082.1	hg19	CCDS1676.1																																																																																			.	.		0.746	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236		T	11052594	C	T	11052594	2	4	47	1	0	0	0	0	0	0	0	1	8035	738	26	3		3	KCNF1	2	11052594	Silent	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10	1439471	11052594	232146779	8	6024										
PFN4	375189	hgsc.bcm.edu	37	chr2	24342547	24342547	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ttcacgacaaccacaccagtGttctcctgtataaagaatat	5	11	2	1			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:24342547G>A	ENST00000313213.4	-	4	632	c.261C>T	c.(259-261)aaC>aaT	p.N87N	PFN4_ENST00000465360.1_5'UTR	NM_199346.1	NP_955378.1	Q8NHR9	PROF4_HUMAN	profilin family, member 4	87					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	lipid binding (GO:0008289)			breast(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCACACCAGTGTTCTCCTGTA	0.453																																					p.N87N		Atlas-SNP	.											.	PFN4	16	.	0			c.C261T						.						85	80	82					2																	24342547		2203	4300	6503	SO:0001819	synonymous_variant	375189	exon4			ACCAGTGTTCTCC	BC029523	CCDS1709.1	2p24.1	2008-02-05			ENSG00000176732	ENSG00000176732			31103	protein-coding gene	gene with protein product							Standard	NM_199346		Approved		uc002rfa.1	Q8NHR9	OTTHUMG00000090816	ENST00000313213.4:c.261C>T	chr2.hg19:g.24342547G>A		41.0	0.0		39.0	16.0	NM_199346	Q53TL9	Silent	SNP	ENST00000313213.4	hg19	CCDS1709.1																																																																																			.	.		0.453	PFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207617.2	NM_199346		A	24342547	G	A	24342547	2	1	47	1	0	0	0	0	0	0	0	1	11779	1368	48	3		3	PFN4	2	24342547	Silent	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	13289953	24342547	218856826	9	6025										
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43956801	43956801	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ttggctttatcatctgactgTtgcagctggaagcaacaatg	10	8	2	1			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:43956801T>C	ENST00000282406.4	+	18	2857	c.2747T>C	c.(2746-2748)gTt>gCt	p.V916A		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	916	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CATCTGACTGTTGCAGCTGGA	0.328																																					p.V916A		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.T2747C						.						96	92	94					2																	43956801		2203	4300	6503	SO:0001583	missense	130271	exon18			TGACTGTTGCAGC	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.2747T>C	chr2.hg19:g.43956801T>C	ENSP00000282406:p.Val916Ala	75.0	0.0		113.0	44.0	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	T	18.80	3.701077	0.68501	.	.	ENSG00000152527	ENST00000282406	T	0.21734	1.99	5.38	5.38	0.77491	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.065813	0.64402	D	0.000011	T	0.45736	0.1357	M	0.78801	2.425	0.58432	D	0.999998	P;P	0.51351	0.944;0.835	P;B	0.61201	0.885;0.352	T	0.44065	-0.9352	10	0.51188	T	0.08	-18.5117	15.3875	0.74714	0.0:0.0:0.0:1.0	.	916;353	Q8IVE3;Q8IVE3-2	PKHH2_HUMAN;.	A	916	ENSP00000282406:V916A	ENSP00000282406:V916A	V	+	2	0	PLEKHH2	43810305	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.572000	0.82409	2.019000	0.59389	0.528000	0.53228	GTT	.	.		0.328	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		C	43956801	T	C	43956801	3	2	47	1	0	0	0	0	1	0	0	0	12086	1725	60	2	2813	2	PLEKHH2	2	43956801	Missense_Mutation	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10	19614254	43956801	199242572	10	6026										
DYTN	391475	hgsc.bcm.edu	37	chr2	207572184	207572184	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	cgagcttcccagaaacttggAcgcagtaggacctgctgaat	11	11	0	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:207572184A>G	ENST00000452335.2	-	3	254	c.138T>C	c.(136-138)cgT>cgC	p.R46R	DYTN_ENST00000477734.1_5'Flank	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	46						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		AGAAACTTGGACGCAGTAGGA	0.493																																					p.R46R		Atlas-SNP	.											.	DYTN	168	.	0			c.T138C						.						46	46	46					2																	207572184		1885	4119	6004	SO:0001819	synonymous_variant	391475	exon3			ACTTGGACGCAGT	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.138T>C	chr2.hg19:g.207572184A>G		127.0	0.0		186.0	79.0	NM_001093730		Silent	SNP	ENST00000452335.2	hg19	CCDS46502.1																																																																																			.	.		0.493	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			G	207572184	A	G	207572184	2	3	47	1	0	0	0	0	0	0	0	1	4863	262	10	2		2	DYTN	2	207572184	Silent	SNP	A	TCGA-BC-A8YO-01A-11D-A36X-10	163615383	207572184	35627189	11	6027										
FN1	2335	hgsc.bcm.edu	37	chr2	216299523	216299523	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	actgttgatttatctgatagTgttttccattgtcataacaa	6	6	2	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr2:216299523T>C	ENST00000359671.1	-	2	438	c.173A>G	c.(172-174)cAc>cGc	p.H58R	FN1_ENST00000421182.1_Missense_Mutation_p.H58R|AC012462.1_ENST00000412951.1_RNA|FN1_ENST00000446046.1_Missense_Mutation_p.H58R|FN1_ENST00000443816.1_Missense_Mutation_p.H58R|FN1_ENST00000356005.4_Missense_Mutation_p.H58R|FN1_ENST00000426059.1_Missense_Mutation_p.H58R|FN1_ENST00000354785.4_Missense_Mutation_p.H58R|FN1_ENST00000357009.2_Missense_Mutation_p.H58R|FN1_ENST00000323926.6_Missense_Mutation_p.H58R|FN1_ENST00000432072.2_Missense_Mutation_p.H58R|FN1_ENST00000345488.5_Missense_Mutation_p.H58R|FN1_ENST00000346544.3_Missense_Mutation_p.H58R|FN1_ENST00000336916.4_Missense_Mutation_p.H58R|FN1_ENST00000357867.4_Missense_Mutation_p.H58R			P02751	FINC_HUMAN	fibronectin 1	58	Fibrin- and heparin-binding 1.|Fibronectin type-I 1. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TATCTGATAGTGTTTTCCATT	0.393																																					p.H58R		Atlas-SNP	.											.	FN1	521	.	0			c.A173G						.						189	170	176					2																	216299523		2203	4300	6503	SO:0001583	missense	2335	exon2			TGATAGTGTTTTC		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.173A>G	chr2.hg19:g.216299523T>C	ENSP00000352696:p.His58Arg	69.0	0.0		85.0	37.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.79	3.698852	0.68501	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000426059	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	6.06	6.06	0.98353	.	0.083281	0.52532	D	0.000071	T	0.43634	0.1256	N	0.08118	0	0.38596	D	0.950543	P;D;B;P;P;P;P;P;P;P;P	0.61697	0.495;0.99;0.001;0.801;0.61;0.662;0.731;0.93;0.61;0.61;0.913	B;D;B;P;B;B;B;P;B;B;P	0.74348	0.356;0.983;0.004;0.569;0.154;0.239;0.395;0.596;0.154;0.154;0.519	T	0.48281	-0.9049	10	0.19147	T	0.46	.	16.6093	0.84858	0.0:0.0:0.0:1.0	.	58;58;58;58;58;58;58;58;58;58;58	E9PG29;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.;.	R	58	ENSP00000394423:H58R;ENSP00000323534:H58R;ENSP00000338200:H58R;ENSP00000350534:H58R;ENSP00000346839:H58R;ENSP00000352696:H58R;ENSP00000265312:H58R;ENSP00000273049:H58R;ENSP00000349509:H58R;ENSP00000410422:H58R;ENSP00000415018:H58R;ENSP00000399538:H58R;ENSP00000348285:H58R;ENSP00000398907:H58R	ENSP00000265313:H58R	H	-	2	0	FN1	216007768	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.843000	0.55865	2.324000	0.78689	0.533000	0.62120	CAC	.	.		0.393	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		C	216299523	T	C	216299523	3	2	47	1	0	0	0	0	1	0	0	0	5970	1696	59	2	7473	2	FN1	2	216299523	Missense_Mutation	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10	8727339	216299523	26899850	12	6028										
RRP9	9136	hgsc.bcm.edu	37	chr3	51970364	51970364	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gcttgctgcggtcaccagagGcctgcagggatgaagacaat	14	10	1	3			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr3:51970364G>C	ENST00000232888.6	-	8	717	c.644C>G	c.(643-645)gCc>gGc	p.A215G		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	215					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		GTCACCAGAGGCCTGCAGGGA	0.607																																					p.A215G		Atlas-SNP	.											.	RRP9	40	.	0			c.C644G						.						112	112	112					3																	51970364		2203	4300	6503	SO:0001630	splice_region_variant	9136	exon8			CCAGAGGCCTGCA	AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"WD repeat domain containing"	16829	protein-coding gene	gene with protein product			"RNA, U3 small nucleolar interacting protein 2"	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.643-1C>G	chr3.hg19:g.51970364G>C		106.0	0.0		154.0	65.0	NM_004704	B2R996|Q8IZ30	Missense_Mutation	SNP	ENST00000232888.6	hg19	CCDS2837.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.936879	0.73557	.	.	ENSG00000114767	ENST00000232888	T	0.70045	-0.45	5.3	5.3	0.74995	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.86083	0.5848	M	0.90922	3.16	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.89186	0.3547	10	0.87932	D	0	-19.0591	18.5692	0.91129	0.0:0.0:1.0:0.0	.	215	O43818	U3IP2_HUMAN	G	215	ENSP00000232888:A215G	ENSP00000232888:A215G	A	-	2	0	RRP9	51945404	1.000000	0.71417	1.000000	0.80357	0.290000	0.27261	7.342000	0.79310	2.494000	0.84150	0.655000	0.94253	GCC	.	.		0.607	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704	Missense_Mutation	C	51970364	G	C	51970364	5	2	47	1	0	0	0	0	0	0	1	0	13706	1217	42	4	815	4	RRP9	3	51970364	Splice_Site	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10		51970364	146052066	13	6029										
ADCY5	111	hgsc.bcm.edu	37	chr3	123003495	123003495	+	Frame_Shift_Del	DEL	A	A	-													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	cattgaggaagtaggtcatcAtctcgcctttgcccttgacc							TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr3:123003495delA	ENST00000462833.1	-	21	4958	c.3746delT	c.(3745-3747)atgfs	p.M1250fs	ADCY5_ENST00000491190.1_Frame_Shift_Del_p.M908fs|RP11-797D24.4_ENST00000608436.1_RNA|ADCY5_ENST00000309879.5_Frame_Shift_Del_p.M900fs	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	1250					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		GTAGGTCATCATCTCGCCTTT	0.607																																					p.M1249fs		Pindel	.											.	ADCY5	169	.	0			c.3747delG						.						184	163	170					3																	123003495		2203	4300	6503	SO:0001589	frameshift_variant	111	exon21			.	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.3746delT	chr3.hg19:g.123003495delA	ENSP00000419361:p.Met1250fs	51.0	0.0		81.0	27.0	NM_183357	B7Z8A6|Q7RTV7|Q8NFM3	Frame_Shift_Del	DEL	ENST00000462833.1	hg19	CCDS3022.1																																																																																			.	.		0.607	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		-	123003495	A	-	123003495	7	5	47	1	0	1	0	1	0	0	0	0	297	217	8	0	43	0	ADCY5	3	123003495	Frame_Shift_Del	DEL	A	TCGA-BC-A8YO-01A-11D-A36X-10	71033131	123003495	75018935	14	6030										
MGLL	11343	hgsc.bcm.edu	37	chr3	127540605	127540605	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tctgcattgaccaggtgaggGaggtcctggtagggaatgct	16	7	1	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr3:127540605G>T	ENST00000434178.2	-	2	953	c.57C>A	c.(55-57)ctC>ctA	p.L19L	MGLL_ENST00000453507.2_Silent_p.L29L|MGLL_ENST00000265052.5_Silent_p.L29L|MGLL_ENST00000398104.1_Silent_p.L19L			Q99685	MGLL_HUMAN	monoglyceride lipase	19					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						CCAGGTGAGGGAGGTCCTGGT	0.557																																					p.L29L		Atlas-SNP	.											MGLL,NS,carcinoma,0,1	MGLL	19	.	0			c.C87A						.						120	125	124					3																	127540605		1904	4111	6015	SO:0001819	synonymous_variant	11343	exon2			GTGAGGGAGGTCC	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.57C>A	chr3.hg19:g.127540605G>T		78.0	0.0		126.0	51.0	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	ENST00000434178.2	hg19	CCDS43148.1																																																																																			.	.		0.557	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283		T	127540605	G	T	127540605	2	4	47	1	0	0	0	0	0	0	0	1	9565	1161	41	3		3	MGLL	3	127540605	Silent	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	4537110	127540605	70481825	15	6031										
SLC25A36	55186	hgsc.bcm.edu	37	chr3	140660913	140660913	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gagaatgagccagagggacaCgctggtgcatctgtttgccg	15	9	1	3			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr3:140660913C>T	ENST00000324194.6	+	1	185	c.17C>T	c.(16-18)aCg>aTg	p.T6M	SLC25A36_ENST00000507429.1_Missense_Mutation_p.T6M|SLC25A36_ENST00000446041.2_Missense_Mutation_p.T6M|SLC25A36_ENST00000393015.4_3'UTR|SLC25A36_ENST00000453248.2_Missense_Mutation_p.T6M			Q96CQ1	S2536_HUMAN	solute carrier family 25 (pyrimidine nucleotide carrier ), member 36	6					response to estradiol (GO:0032355)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						CAGAGGGACACGCTGGTGCAT	0.721																																					p.T6M		Atlas-SNP	.											.	SLC25A36	24	.	0			c.C17T						.						65	47	54					3																	140660913		1787	3423	5210	SO:0001583	missense	55186	exon1			GGGACACGCTGGT	AK001480	CCDS3114.1, CCDS46927.1	3q23	2013-05-22	2012-03-29		ENSG00000114120	ENSG00000114120		"Solute carriers"	25554	protein-coding gene	gene with protein product			"solute carrier family 25, member 36"				Standard	NM_001104647		Approved	FLJ10618, PNC2	uc003etr.2	Q96CQ1	OTTHUMG00000160260	ENST00000324194.6:c.17C>T	chr3.hg19:g.140660913C>T	ENSP00000320688:p.Thr6Met	128.0	0.0		178.0	89.0	NM_018155	A8MYF7|Q05CY1|Q9H0G8|Q9NVN5	Missense_Mutation	SNP	ENST00000324194.6	hg19	CCDS46927.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.870636	0.51588	.	.	ENSG00000114120	ENST00000446041;ENST00000507429;ENST00000324194;ENST00000453248	T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22	4.88	4.0	0.46444	Mitochondrial carrier domain (2);	0.259837	0.43919	D	0.000513	T	0.72716	0.3495	L	0.47190	1.495	0.52099	D	0.999942	P;B;P;P	0.46952	0.535;0.291;0.887;0.48	B;B;B;B	0.44085	0.228;0.146;0.44;0.146	T	0.74185	-0.3747	10	0.56958	D	0.05	-7.9419	10.9965	0.47580	0.0:0.8116:0.1884:0.0	.	6;6;6;6	B4DL01;Q96CQ1-3;Q96CQ1;F6SDC8	.;.;S2536_HUMAN;.	M	6	ENSP00000401938:T6M;ENSP00000421470:T6M;ENSP00000320688:T6M;ENSP00000391521:T6M	ENSP00000320688:T6M	T	+	2	0	SLC25A36	142143603	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	2.019000	0.41001	1.248000	0.43934	0.561000	0.74099	ACG	.	.		0.721	SLC25A36-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359929.1	NM_018155		T	140660913	C	T	140660913	3	4	47	1	0	0	0	0	1	0	0	0	14515	536	19	1	19	1	SLC25A36	3	140660913	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10	13120308	140660913	57361517	16	6032										
EVC2	132884	hgsc.bcm.edu	37	chr4	5624510	5624510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tggctgagttctgcaggcgcCgcagctcgtcggtggccttt	15	12	1	1	rs139717271		TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:5624510C>T	ENST00000344408.5	-	14	2308	c.2255G>A	c.(2254-2256)cGg>cAg	p.R752Q	EVC2_ENST00000310917.2_Missense_Mutation_p.R672Q|EVC2_ENST00000344938.1_Missense_Mutation_p.R752Q	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	752					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CTGCAGGCGCCGCAGCTCGTC	0.647																																					p.R752Q		Atlas-SNP	.											EVC2,colon,carcinoma,-1,1	EVC2	202	.	0			c.G2255A						.	C	GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	50	47	48		2015,2255	4.5	1	4	dbSNP_134	48	0,8600		0,0,4300	no	missense,missense	EVC2	NM_001166136.1,NM_147127.4	43,43	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	672/1229,752/1309	5624510	2,13004	2203	4300	6503	SO:0001583	missense	132884	exon14			AGGCGCCGCAGCT	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2255G>A	chr4.hg19:g.5624510C>T	ENSP00000342144:p.Arg752Gln	116.0	0.0		143.0	61.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	22.4	4.278417	0.80692	4.54E-4	0.0	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74315	-0.83;-0.82;-0.82	5.32	4.48	0.54585	.	0.235349	0.34291	N	0.004084	T	0.72938	0.3523	L	0.54323	1.7	0.27599	N	0.949033	D	0.71674	0.998	P	0.51895	0.683	T	0.64019	-0.6505	10	0.18710	T	0.47	-27.5673	9.3644	0.38215	0.0:0.819:0.0:0.181	.	752	Q86UK5	LBN_HUMAN	Q	752;672;752	ENSP00000339954:R752Q;ENSP00000311683:R672Q;ENSP00000342144:R752Q	ENSP00000311683:R672Q	R	-	2	0	EVC2	5675411	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.807000	0.47955	1.245000	0.43885	0.462000	0.41574	CGG	.	C|1.000;T|0.000		0.647	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		T	5624510	C	T	5624510	3	4	47	1	0	0	0	0	1	0	0	0	5288	652	23	1	1707	1	EVC2	4	5624510	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10		5624510	185529766	17	6033										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20535222	20535222	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	agcaacaataagatcacagaTattgaggagggagcatttga	11	5	1	4			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:20535222T>C	ENST00000504154.1	+	18	1968	c.1716T>C	c.(1714-1716)gaT>gaC	p.D572D	SLIT2_ENST00000503823.1_Silent_p.D564D|SLIT2_ENST00000503837.1_Silent_p.D568D|SLIT2_ENST00000273739.5_Silent_p.D576D	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	572					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						AGATCACAGATATTGAGGAGG	0.328																																					p.D572D		Atlas-SNP	.											.	SLIT2	290	.	0			c.T1716C						.						93	94	94					4																	20535222		2203	4300	6503	SO:0001819	synonymous_variant	9353	exon18			CACAGATATTGAG	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1716T>C	chr4.hg19:g.20535222T>C		587.0	0.0		634.0	274.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	hg19	CCDS3426.1																																																																																			.	.		0.328	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			C	20535222	T	C	20535222	2	2	47	1	0	0	0	0	0	0	0	1	14755	1403	49	2		2	SLIT2	4	20535222	Silent	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10	14910712	20535222	170619054	18	6034										
ALB	213	hgsc.bcm.edu	37	chr4	74284021	74284024	+	Frame_Shift_Del	DEL	AAAC	AAAC	-													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	agaaggagagacaaatcaagAaacaaacgtgaggagtattt					rs142299078	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	AAAC	AAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:74284021_74284024delAAAC	ENST00000503124.1	+	10	1402_1405	c.1195_1198delAAAC	c.(1195-1200)aaacaafs	p.KQ399fs	ALB_ENST00000509063.1_Frame_Shift_Del_p.KQ549fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Frame_Shift_Del_p.KQ434fs|ALB_ENST00000415165.2_Frame_Shift_Del_p.KQ357fs|ALB_ENST00000295897.4_Frame_Shift_Del_p.KQ549fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACAAATCAAGAAACAAACGTGAGG	0.368																																					p.548_549del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.1644_1647del						.																																			SO:0001589	frameshift_variant	213	exon12			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1195_1198delAAAC	chr4.hg19:g.74284025_74284028delAAAC	ENSP00000421027:p.Lys399fs	36.0	0.0		41.0	17.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.368	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74284024	AAAC	-	74284021	7	5	47	1	0	1	0	1	0	0	0	0	486	247	9	0	1691	0	ALB	4	74284021	Frame_Shift_Del	DEL	AAAC	TCGA-BC-A8YO-01A-11D-A36X-10	53748799	74284021	116870255	19	6035										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85758098	85758098	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	atacctgtacaaaaactttcTggagtagtcctcgacgttct	7	10	2	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:85758098T>A	ENST00000295888.4	-	7	967	c.560A>T	c.(559-561)cAg>cTg	p.Q187L	WDFY3_ENST00000322366.6_Missense_Mutation_p.Q187L	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	187					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AAAAACTTTCTGGAGTAGTCC	0.408																																					p.Q187L		Atlas-SNP	.											.	WDFY3	314	.	0			c.A560T						.						92	79	84					4																	85758098		2203	4300	6503	SO:0001583	missense	23001	exon7			ACTTTCTGGAGTA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.560A>T	chr4.hg19:g.85758098T>A	ENSP00000295888:p.Gln187Leu	343.0	1.0		464.0	173.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.837935	0.91117	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.68025	-0.29;-0.3	5.76	5.76	0.90799	.	0.054736	0.85682	D	0.000000	T	0.81211	0.4775	M	0.71581	2.175	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.996	T	0.82835	-0.0261	10	0.62326	D	0.03	.	16.0697	0.80914	0.0:0.0:0.0:1.0	.	187;187	E2QRK8;Q8IZQ1	.;WDFY3_HUMAN	L	187	ENSP00000318466:Q187L;ENSP00000295888:Q187L	ENSP00000295888:Q187L	Q	-	2	0	WDFY3	85977122	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.542000	0.82095	2.190000	0.69967	0.374000	0.22700	CAG	.	.		0.408	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85758098	T	A	85758098	3	1	47	1	0	0	0	0	1	0	0	0	17285	1580	55	4	10311	4	WDFY3	4	85758098	Missense_Mutation	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10	11474077	85758098	105396178	20	6036										
UBE2D3	7323	hgsc.bcm.edu	37	chr4	103730836	103730837	+	Frame_Shift_Ins	INS	-	-	T													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	cttaatacttacaggtcccaINStaattgtggcttgccaatga							TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:103730836_103730837insT	ENST00000453744.2	-	4	625_626	c.112_113insA	c.(112-114)atgfs	p.M38fs	UBE2D3_ENST00000350435.7_Frame_Shift_Ins_p.M32fs|UBE2D3_ENST00000394801.4_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000394804.2_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000513098.1_5'UTR|UBE2D3_ENST00000507845.1_Frame_Shift_Ins_p.M9fs|UBE2D3_ENST00000394803.5_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000502404.1_Frame_Shift_Ins_p.M9fs|UBE2D3_ENST00000343106.5_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000338145.3_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000321805.7_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000504211.1_Frame_Shift_Ins_p.M9fs|UBE2D3_ENST00000357194.6_Frame_Shift_Ins_p.M40fs|UBE2D3_ENST00000349311.8_Frame_Shift_Ins_p.M38fs|UBE2D3_ENST00000505207.1_Frame_Shift_Ins_p.M9fs	NM_181891.1	NP_871620.1	P61077	UB2D3_HUMAN	ubiquitin-conjugating enzyme E2D 3	38					apoptotic process (GO:0006915)|BMP signaling pathway (GO:0030509)|cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|lung(3)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)		TACAGGTCCCATAATTGTGGCT	0.277																																					p.M40fs		Pindel	.											.	UBE2D3	25	.	0			c.119_120insA						.																																			SO:0001589	frameshift_variant	7323	exon3			.	U39318	CCDS3659.1, CCDS3660.1, CCDS3661.1, CCDS75172.1	4q24	2011-05-19	2011-05-19		ENSG00000109332	ENSG00000109332		"Ubiquitin-conjugating enzymes E2"	12476	protein-coding gene	gene with protein product		602963	"ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)"			8530467	Standard	NM_181886		Approved	UbcH5C	uc003hwl.3	P61077	OTTHUMG00000131119	ENST00000453744.2:c.113dupA	chr4.hg19:g.103730837_103730837dupT	ENSP00000396901:p.Met38fs	489.0	0.0		615.0	120.0	NM_181893	A6NJ93|A6NJB1|A6NM99|P47986|Q6IB88|Q6NXS4|Q8N924	Frame_Shift_Ins	INS	ENST00000453744.2	hg19	CCDS3660.1																																																																																			.	.		0.277	UBE2D3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253791.2	NM_181893		T	103730837	-	T	103730836	7	5	47	1	0	1	1	0	0	0	0	0	16865	217	8	0	403	0	UBE2D3	4	103730836	Frame_Shift_Ins	INS	-	TCGA-BC-A8YO-01A-11D-A36X-10	17972738	103730836	87423440	21	6037										
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119951193	119951193	+	Frame_Shift_Del	DEL	G	G	-													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ggcgagcttgagcgagaggcGgacgaggaggaagaaggtga							TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:119951193delG	ENST00000429713.2	+	4	1445	c.1263delG	c.(1261-1263)gcgfs	p.A421fs	SYNPO2_ENST00000434046.2_Frame_Shift_Del_p.A421fs|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Frame_Shift_Del_p.A421fs	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	421						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AGCGAGAGGCGGACGAGGAGG	0.517																																					p.A421fs		Atlas-Indel,Pindel	.											SYNPO2_ENST00000434046,NS,carcinoma,0,3	SYNPO2	353	.	0			c.1262delC						.						162	155	158					4																	119951193		2203	4300	6503	SO:0001589	frameshift_variant	171024	exon4			.	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.1263delG	chr4.hg19:g.119951193delG	ENSP00000395143:p.Ala421fs	194.0	0.0		246.0	123.0	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Frame_Shift_Del	DEL	ENST00000429713.2	hg19	CCDS47129.1																																																																																			.	.		0.517	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			-	119951193	G	-	119951193	7	5	47	1	0	1	0	1	0	0	0	0	15472	1103	39	0	1277	0	SYNPO2	4	119951193	Frame_Shift_Del	DEL	G	TCGA-BC-A8YO-01A-11D-A36X-10	16220357	119951193	71203083	22	6038										
PDE5A	8654	hgsc.bcm.edu	37	chr4	120481478	120481478	+	Frame_Shift_Del	DEL	A	A	-													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	atgtatcagatgatttttctAattcctcacactccatgtga							TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:120481478delA	ENST00000354960.3	-	7	1491	c.1172delT	c.(1171-1173)ttafs	p.L391fs	PDE5A_ENST00000394439.1_Frame_Shift_Del_p.L339fs|PDE5A_ENST00000264805.5_Frame_Shift_Del_p.L349fs	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	391	GAF 2.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	TGATTTTTCTAATTCCTCACA	0.318																																					p.L391fs		Pindel	.											.	PDE5A	83	.	0			c.1173delA						.						94	88	90					4																	120481478		2203	4298	6501	SO:0001589	frameshift_variant	8654	exon7			.	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1172delT	chr4.hg19:g.120481478delA	ENSP00000347046:p.Leu391fs	150.0	0.0		214.0	62.0	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Frame_Shift_Del	DEL	ENST00000354960.3	hg19	CCDS3713.1																																																																																			.	.		0.318	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		-	120481478	A	-	120481478	7	5	47	1	0	1	0	1	0	0	0	0	11653	372	13	0	1515	0	PDE5A	4	120481478	Frame_Shift_Del	DEL	A	TCGA-BC-A8YO-01A-11D-A36X-10	530285	120481478	70672798	23	6039										
GLRA3	8001	hgsc.bcm.edu	37	chr4	175636670	175636670	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tgcattatacatgtttgtacAtccatgggaaaattcttgag	8	6	1	1			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr4:175636670A>G	ENST00000274093.3	-	5	1045	c.543T>C	c.(541-543)gaT>gaC	p.D181D	GLRA3_ENST00000340217.5_Silent_p.D181D	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	181					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)|Ivermectin(DB00602)|Lindane(DB00431)	ATGTTTGTACATCCATGGGAA	0.274																																					p.D181D		Atlas-SNP	.											.	GLRA3	76	.	0			c.T543C						.						79	82	81					4																	175636670		2203	4295	6498	SO:0001819	synonymous_variant	8001	exon5			TTGTACATCCATG	AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"Ligand-gated ion channels / Glycine receptors"	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.543T>C	chr4.hg19:g.175636670A>G		389.0	1.0		555.0	230.0	NM_001042543	D3DP44|O75816|Q5D0E3	Silent	SNP	ENST00000274093.3	hg19	CCDS3822.1																																																																																			.	.		0.274	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1			G	175636670	A	G	175636670	2	3	47	1	0	0	0	0	0	0	0	1	6464	214	8	2		2	GLRA3	4	175636670	Silent	SNP	A	TCGA-BC-A8YO-01A-11D-A36X-10	55155192	175636670	15517606	24	6040										
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1219158	1219158	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	atgtttgggaacatggagggCgtcgttgtgcccctgcagga	16	8	0	0	rs141604151		TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr5:1219158C>T	ENST00000304460.10	+	9	1370	c.1314C>T	c.(1312-1314)ggC>ggT	p.G438G		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	438					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			ACATGGAGGGCGTCGTTGTGC	0.587																																					p.G438G		Atlas-SNP	.											.	SLC6A19	99	.	0			c.C1314T						.	C		0,4406		0,0,2203	318	250	273		1314	-8.6	0.4	5	dbSNP_134	273	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC6A19	NM_001003841.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		438/635	1219158	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	340024	exon9			GGAGGGCGTCGTT	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1314C>T	chr5.hg19:g.1219158C>T		62.0	0.0		139.0	39.0	NM_001003841	A8K446	Silent	SNP	ENST00000304460.10	hg19	CCDS34130.1																																																																																			.	C|1.000;T|0.000		0.587	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		T	1219158	C	T	1219158	2	4	47	1	0	0	0	0	0	0	0	1	14697	755	27	1		1	SLC6A19	5	1219158	Silent	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10		1219158	179696102	25	6041										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37170312	37170312	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	caccacatcctcttaggtttGattcttggctttcccctaaa	5	13	2	1			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr5:37170312G>C	ENST00000508244.1	-	32	6386	c.6293C>G	c.(6292-6294)tCa>tGa	p.S2098*	C5orf42_ENST00000274258.7_Nonsense_Mutation_p.S978*|C5orf42_ENST00000425232.2_Nonsense_Mutation_p.S2098*			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2098						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TCTTAGGTTTGATTCTTGGCT	0.413																																					p.S2098X		Atlas-SNP	.											.	C5orf42	422	.	0			c.C6293G						.						186	181	183					5																	37170312		2203	4300	6503	SO:0001587	stop_gained	65250	exon33			AGGTTTGATTCTT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.6293C>G	chr5.hg19:g.37170312G>C	ENSP00000421690:p.Ser2098*	102.0	0.0		152.0	67.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Nonsense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	58	32.101669	0.99979	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	.	.	.	5.79	3.57	0.40892	.	1.506760	0.04150	N	0.321100	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	9.2163	0.37348	0.3276:0.0:0.6724:0.0	.	.	.	.	X	2098;2098;978;1146;978	.	ENSP00000274258:S978X	S	-	2	0	C5orf42	37206069	0.000000	0.05858	0.001000	0.08648	0.744000	0.42396	0.174000	0.16743	0.509000	0.28195	0.555000	0.69702	TCA	.	.		0.413	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37170312	G	C	37170312	4	2	47	1	0	0	0	0	0	1	0	0	2303	1294	45	4	3380	4	C5orf42	5	37170312	Nonsense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	35951154	37170312	143744948	26	6042										
WDR36	134430	hgsc.bcm.edu	37	chr5	110445911	110445911	+	Frame_Shift_Del	DEL	A	A	-													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gtggatataacttcttgtggAaactttgctgtaattggcct							TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr5:110445911delA	ENST00000513710.2	+	13	1522	c.1518delA	c.(1516-1518)ggafs	p.G506fs	WDR36_ENST00000506538.2_Frame_Shift_Del_p.G506fs|WDR36_ENST00000505303.1_Frame_Shift_Del_p.G450fs			Q8NI36	WDR36_HUMAN	WD repeat domain 36	506					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		CTTCTTGTGGAAACTTTGCTG	0.348																																					p.G506fs		Atlas-Indel,Pindel	.											.	WDR36	111	.	0			c.1517delG						.						160	160	160					5																	110445911		2202	4300	6502	SO:0001589	frameshift_variant	134430	exon13			.	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.1518delA	chr5.hg19:g.110445911delA	ENSP00000424628:p.Gly506fs	94.0	0.0		97.0	40.0	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Frame_Shift_Del	DEL	ENST00000513710.2	hg19	CCDS4102.1																																																																																			.	.		0.348	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		-	110445911	A	-	110445911	7	5	47	1	0	1	0	1	0	0	0	0	17305	233	9	0	1568	0	WDR36	5	110445911	Frame_Shift_Del	DEL	A	TCGA-BC-A8YO-01A-11D-A36X-10	73275599	110445911	70469349	27	6043										
RBM22	55696	hgsc.bcm.edu	37	chr5	150071321	150071321	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ggtgacaaggtgctaggggcTgctgtgttttccagcatgag	16	7	0	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr5:150071321T>G	ENST00000199814.4	-	11	1376	c.1255A>C	c.(1255-1257)Agc>Cgc	p.S419R	RBM22_ENST00000447771.2_Missense_Mutation_p.S370R|RBM22_ENST00000540000.1_Missense_Mutation_p.S370R	NM_018047.2	NP_060517.1	Q9NW64	RBM22_HUMAN	RNA binding motif protein 22	419					cellular response to drug (GO:0035690)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of RNA splicing (GO:0033120)|protein import into nucleus, translocation (GO:0000060)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium-dependent protein binding (GO:0048306)|metal ion binding (GO:0046872)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|snRNA binding (GO:0017069)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(1)	17		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCTAGGGGCTGCTGTGTTTT	0.512																																					p.S419R		Atlas-SNP	.											.	RBM22	33	.	0			c.A1255C						.						105	107	107					5																	150071321		2203	4300	6503	SO:0001583	missense	55696	exon11			AGGGGCTGCTGTG	AL136933	CCDS34278.1	5q33.1	2013-02-12			ENSG00000086589	ENSG00000086589		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	25503	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 47"	612430				20013661, 19133299	Standard	NM_018047		Approved	FLJ10290, ZC3H16, fSAP47, Cwc2	uc031slu.1	Q9NW64	OTTHUMG00000163589	ENST00000199814.4:c.1255A>C	chr5.hg19:g.150071321T>G	ENSP00000199814:p.Ser419Arg	57.0	0.0		79.0	27.0	NM_018047	A6NDM5|B4DLI9|O95607	Missense_Mutation	SNP	ENST00000199814.4	hg19	CCDS34278.1	.	.	.	.	.	.	.	.	.	.	T	13.99	2.401385	0.42613	.	.	ENSG00000086589	ENST00000199814;ENST00000540000;ENST00000447771	.	.	.	6.02	6.02	0.97574	.	0.122178	0.85682	D	0.000000	T	0.43523	0.1251	N	0.08118	0	0.46701	D	0.999168	B	0.31910	0.346	B	0.35655	0.207	T	0.49744	-0.8907	9	0.59425	D	0.04	-28.0363	16.5446	0.84426	0.0:0.0:0.0:1.0	.	419	Q9NW64	RBM22_HUMAN	R	419;370;370	.	ENSP00000199814:S419R	S	-	1	0	RBM22	150051514	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	4.573000	0.60893	2.311000	0.77944	0.533000	0.62120	AGC	.	.		0.512	RBM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374431.2	NM_018047		G	150071321	T	G	150071321	3	3	47	1	0	0	0	0	1	0	0	0	13137	1580	55	5	11	5	RBM22	5	150071321	Missense_Mutation	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10	39625410	150071321	30843939	28	6044										
BOD1	91272	hgsc.bcm.edu	37	chr5	173036375	173036375	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tttgtggcctgaagatgtggTtaagttttggatccaccacc	11	8	0	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr5:173036375T>C	ENST00000311086.4	-	3	648	c.425A>G	c.(424-426)aAc>aGc	p.N142S	BOD1_ENST00000285908.5_Intron|BOD1_ENST00000480951.1_Intron|BOD1_ENST00000471339.1_5'Flank	NM_138369.2	NP_612378.1	Q96IK1	BOD1_HUMAN	biorientation of chromosomes in cell division 1	142					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|kinetochore (GO:0000776)				endometrium(1)|large_intestine(2)|lung(2)|ovary(2)	7						GAAGATGTGGTTAAGTTTTGG	0.493																																					p.N142S		Atlas-SNP	.											.	BOD1	15	.	0			c.A425G						.						157	141	146					5																	173036375		2203	4300	6503	SO:0001583	missense	91272	exon3			ATGTGGTTAAGTT	AY303777	CCDS4389.1, CCDS54951.1	5q35.2	2013-10-11	2009-03-04	2009-03-04	ENSG00000145919	ENSG00000145919			25114	protein-coding gene	gene with protein product	"biorientation defective 1"		"family with sequence similarity 44, member B"	FAM44B		17938248	Standard	NM_138369		Approved		uc003mcq.2	Q96IK1	OTTHUMG00000130540	ENST00000311086.4:c.425A>G	chr5.hg19:g.173036375T>C	ENSP00000309644:p.Asn142Ser	65.0	0.0		109.0	44.0	NM_138369	B4DXH8|Q9BTW1	Missense_Mutation	SNP	ENST00000311086.4	hg19	CCDS4389.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.099105	0.76983	.	.	ENSG00000145919	ENST00000311086;ENST00000462674	.	.	.	5.65	5.65	0.86999	.	0.085313	0.85682	D	0.000000	T	0.54935	0.1889	L	0.34521	1.04	0.80722	D	1	P	0.41498	0.752	P	0.46479	0.518	T	0.51450	-0.8704	9	0.28530	T	0.3	-38.5526	15.8715	0.79122	0.0:0.0:0.0:1.0	.	142	Q96IK1	BOD1_HUMAN	S	142;37	.	ENSP00000309644:N142S	N	-	2	0	BOD1	172968981	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.684000	0.84104	2.155000	0.67459	0.533000	0.62120	AAC	.	.		0.493	BOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252963.1	NM_138369		C	173036375	T	C	173036375	3	2	47	1	0	0	0	0	1	0	0	0	1482	1725	60	2	168	2	BOD1	5	173036375	Missense_Mutation	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10	22965054	173036375	7878885	29	6045										
HIST1H4C	8364	hgsc.bcm.edu	37	chr6	26104293	26104293	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	cggctattcgccgtttggctCggcgcggtggcgtcaagcgc	16	13	1	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr6:26104293C>G	ENST00000377803.2	+	1	190	c.118C>G	c.(118-120)Cgg>Ggg	p.R40G		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	40					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7						CCGTTTGGCTCGGCGCGGTGG	0.542																																					p.R40G		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.C118G						.						62	62	62					6																	26104293		2203	4300	6503	SO:0001583	missense	8364	exon1			TTGGCTCGGCGCG	X60486	CCDS4583.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000197061	ENSG00000197061		"Histones / Replication-dependent"	4787	protein-coding gene	gene with protein product		602827	"H4 histone family, member G", "histone 1, H4c"	H4FG		9119399, 12408966	Standard	NM_003542		Approved	H4/g, dJ221C16.1	uc003ngi.3	P62805	OTTHUMG00000014429	ENST00000377803.2:c.118C>G	chr6.hg19:g.26104293C>G	ENSP00000367034:p.Arg40Gly	96.0	0.0		146.0	7.0	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377803.2	hg19	CCDS4583.1	.	.	.	.	.	.	.	.	.	.	.	17.58	3.424850	0.62733	.	.	ENSG00000197061	ENST00000377803	T	0.77620	-1.11	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	D	0.83695	0.5310	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.85878	0.1420	7	0.87932	D	0	.	16.8752	0.86050	0.0:1.0:0.0:0.0	.	.	.	.	G	40	ENSP00000367034:R40G	ENSP00000367034:R40G	R	+	1	2	HIST1H4C	26212272	1.000000	0.71417	0.734000	0.30879	0.009000	0.06853	7.642000	0.83385	2.538000	0.85594	0.561000	0.74099	CGG	.	.		0.542	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542		G	26104293	C	G	26104293	3	3	47	1	0	0	0	0	1	0	0	0	7176	875	31	4	120	4	HIST1H4C	6	26104293	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10		26104293	145010774	30	6046										
FAM83B	222584	hgsc.bcm.edu	37	chr6	54805688	54805688	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	atcaaataactatatatataAaaccttgggtgtaaataagc	5	5	1	0	rs239798	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr6:54805688A>G	ENST00000306858.7	+	5	2035	c.1919A>G	c.(1918-1920)aAa>aGa	p.K640R	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	640			K -> T (in dbSNP:rs239798). {ECO:0000269|PubMed:15489334}.					p.K640T(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					TATATATATAAAACCTTGGGT	0.373																																					p.K640R		Atlas-SNP	.											FAM83B,NS,carcinoma,0,1	FAM83B	186	.	1	Substitution - Missense(1)	prostate(1)	c.A1919G						.						41	43	42					6																	54805688		2198	4297	6495	SO:0001583	missense	222584	exon5			TATATAAAACCTT	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 143"	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.1919A>G	chr6.hg19:g.54805688A>G	ENSP00000304078:p.Lys640Arg	218.0	1.0		266.0	113.0	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	hg19	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.022864	0.75275	.	.	ENSG00000168143	ENST00000306858	T	0.30182	1.54	5.55	4.66	0.58398	.	0.865524	0.10264	N	0.695617	T	0.08492	0.0211	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.16012	-1.0417	9	0.45353	T	0.12	-7.5696	15.0301	0.71698	0.2604:0.7396:0.0:0.0	.	640	Q5T0W9	FA83B_HUMAN	R	640	ENSP00000304078:K640R	ENSP00000304078:K640R	K	+	2	0	FAM83B	54913647	0.528000	0.26314	0.067000	0.19924	0.901000	0.52897	4.107000	0.57811	0.801000	0.34066	-0.121000	0.15023	AAA	.	A|0.690;C|0.310		0.373	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		G	54805688	A	G	54805688	3	3	47	1	0	0	0	0	1	0	0	0	5642	14	1	2	1933	2	FAM83B	6	54805688	Missense_Mutation	SNP	A	TCGA-BC-A8YO-01A-11D-A36X-10	28701395	54805688	116309379	31	6047										
PRDM13	59336	hgsc.bcm.edu	37	chr6	100061789	100061789	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tatgcgcagctgccccctgcGccggggttgcccctcgagcg	14	17	0	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr6:100061789G>T	ENST00000369215.4	+	4	1583	c.1278G>T	c.(1276-1278)gcG>gcT	p.A426A		NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	426					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1)	17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		TGCCCCCTGCGCCGGGGTTGC	0.756																																					p.A426A		Atlas-SNP	.											.	PRDM13	65	.	0			c.G1278T						.						8	9	9					6																	100061789		1499	3370	4869	SO:0001819	synonymous_variant	59336	exon4			CCCTGCGCCGGGG	AY004253	CCDS43487.1	6q16.2	2012-03-28			ENSG00000112238	ENSG00000112238			13998	protein-coding gene	gene with protein product							Standard	NM_021620		Approved		uc003pqg.1	Q9H4Q3	OTTHUMG00000015269	ENST00000369215.4:c.1278G>T	chr6.hg19:g.100061789G>T		36.0	0.0		55.0	18.0	NM_021620	Q5TGC1|Q5TGC2	Silent	SNP	ENST00000369215.4	hg19	CCDS43487.1																																																																																			.	.		0.756	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2			T	100061789	G	T	100061789	2	4	47	1	0	0	0	0	0	0	0	1	12466	1074	38	1		1	PRDM13	6	100061789	Silent	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	45256101	100061789	71053278	32	6048										
NR2E1	7101	hgsc.bcm.edu	37	chr6	108502144	108502144	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tttgcctgtctaaaatgcatCgtcactttcaaagccggtaa	7	10	3	0	rs368041869		TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr6:108502144C>A	ENST00000368986.4	+	7	1581	c.873C>A	c.(871-873)atC>atA	p.I291I	NR2E1_ENST00000368983.3_Silent_p.I328I	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	291	Ligand-binding. {ECO:0000250}.				aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.I291I(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		TAAAATGCATCGTCACTTTCA	0.458																																					p.I291I		Atlas-SNP	.											NR2E1,NS,carcinoma,0,1	NR2E1	57	.	1	Substitution - coding silent(1)	endometrium(1)	c.C873A						.						160	157	158					6																	108502144		2203	4300	6503	SO:0001819	synonymous_variant	7101	exon7			ATGCATCGTCACT	Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"Nuclear hormone receptors"	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.873C>A	chr6.hg19:g.108502144C>A		112.0	0.0		154.0	70.0	NM_003269	Q6ZMP8	Silent	SNP	ENST00000368986.4	hg19	CCDS5063.1																																																																																			.	.		0.458	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2			A	108502144	C	A	108502144	2	1	47	1	0	0	0	0	0	0	0	1	10634	874	31	1		1	NR2E1	6	108502144	Silent	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10	8440355	108502144	62612923	33	6049										
COL10A1	1300	hgsc.bcm.edu	37	chr6	116442516	116442516	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ttctggccctcgttccccagGagggccttggggacctggtg	15	13	1	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr6:116442516G>T	ENST00000327673.4	-	2	1170	c.763C>A	c.(763-765)Cct>Act	p.P255T	AL121963.1_ENST00000430695.1_Missense_Mutation_p.G57V|COL10A1_ENST00000243222.4_Missense_Mutation_p.P255T|NT5DC1_ENST00000319550.4_Intron			Q03692	COAA1_HUMAN	collagen, type X, alpha 1	255	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	cell cortex (GO:0005938)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	13		all_cancers(87;0.0176)|all_epithelial(87;0.0263)|Colorectal(196;0.234)		all cancers(137;0.0157)|OV - Ovarian serous cystadenocarcinoma(136;0.0325)|GBM - Glioblastoma multiforme(226;0.0446)|Epithelial(106;0.0711)		CGTTCCCCAGGAGGGCCTTGG	0.597																																					p.P255T		Atlas-SNP	.											.	COL10A1	51	.	0			c.C763A						.						43	48	47					6																	116442516		2203	4299	6502	SO:0001583	missense	1300	exon3			CCCCAGGAGGGCC		CCDS5105.1	6q21-q22	2013-01-16	2008-07-29		ENSG00000123500	ENSG00000123500		"Collagens"	2185	protein-coding gene	gene with protein product	"Schmid metaphyseal chondrodysplasia"	120110				2037056	Standard	XM_006715332		Approved		uc003pwm.3	Q03692	OTTHUMG00000015426	ENST00000327673.4:c.763C>A	chr6.hg19:g.116442516G>T	ENSP00000327368:p.Pro255Thr	57.0	0.0		88.0	41.0	NM_000493	A1L4P2	Missense_Mutation	SNP	ENST00000327673.4	hg19	CCDS5105.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.06|10.06	1.246837|1.246837	0.22796|0.22796	.|.	.|.	ENSG00000234188|ENSG00000123500	ENST00000430695|ENST00000243222;ENST00000327673	.|D;D	.|0.96651	.|-4.08;-4.08	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.224117	.|0.46442	.|D	.|0.000285	D|D	0.90830|0.90830	0.7120|0.7120	L|L	0.39898|0.39898	1.24|1.24	0.40748|0.40748	D|D	0.982893|0.982893	.|B	.|0.17465	.|0.022	.|B	.|0.15052	.|0.012	D|D	0.87037|0.87037	0.2138|0.2138	6|10	0.34782|0.42905	T|T	0.22|0.14	.|.	13.3219|13.3219	0.60438|0.60438	0.0724:0.0:0.9276:0.0|0.0724:0.0:0.9276:0.0	.|.	.|255	.|Q03692	.|COAA1_HUMAN	V|T	57|255	.|ENSP00000243222:P255T;ENSP00000327368:P255T	ENSP00000415795:G57V|ENSP00000243222:P255T	G|P	+|-	2|1	0|0	AL121963.1|COL10A1	116549209|116549209	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.458000|0.458000	0.32498|0.32498	3.491000|3.491000	0.53252|0.53252	2.825000|2.825000	0.97269|0.97269	0.655000|0.655000	0.94253|0.94253	GGA|CCT	.	.		0.597	COL10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041926.1			T	116442516	G	T	116442516	3	4	47	1	0	0	0	0	1	0	0	0	3668	1174	41	3	1283	3	COL10A1	6	116442516	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	7940372	116442516	54672551	34	6050										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7421217	7421217	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	cccattgtgccctttgggccTgggaagccttgtggtccttg	13	12	0	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr7:7421217T>A	ENST00000399429.3	-	28	2303	c.2163A>T	c.(2161-2163)ccA>ccT	p.P721P		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	721					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCTTTGGGCCTGGGAAGCCTT	0.473																																					p.P721P		Atlas-SNP	.											.	COL28A1	113	.	0			c.A2163T						.						196	194	195					7																	7421217		1871	4104	5975	SO:0001819	synonymous_variant	340267	exon28			TGGGCCTGGGAAG	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2163A>T	chr7.hg19:g.7421217T>A		126.0	0.0		136.0	50.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.473	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		A	7421217	T	A	7421217	2	1	47	1	0	0	0	0	0	0	0	1	3688	1567	55	4		4	COL28A1	7	7421217	Silent	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10		7421217	151717446	35	6051										
GTF2I	2969	hgsc.bcm.edu	37	chr7	74114719	74114719	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gatcttgcaaccctgaaatgGattttggagaacaaagcagg	11	7	1	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr7:74114719G>T	ENST00000324896.4	+	5	905	c.516G>T	c.(514-516)tgG>tgT	p.W172C	AC083884.8_ENST00000450426.2_RNA|GTF2I_ENST00000346152.4_Missense_Mutation_p.W172C|GTF2I_ENST00000353920.4_Missense_Mutation_p.W172C|GTF2I_ENST00000416070.1_Missense_Mutation_p.W172C|AC083884.8_ENST00000594967.1_RNA|AC083884.8_ENST00000434256.1_RNA|GTF2I_ENST00000443166.1_Missense_Mutation_p.W172C	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	172					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						CCCTGAAATGGATTTTGGAGA	0.438																																					p.W172C		Atlas-SNP	.											.	GTF2I	40	.	0			c.G516T						.						107	109	108					7																	74114719		2203	4300	6503	SO:0001583	missense	2969	exon5			GAAATGGATTTTG	U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"General transcription factors"	4659	protein-coding gene	gene with protein product		601679	"general transcription factor II, i"	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.516G>T	chr7.hg19:g.74114719G>T	ENSP00000322542:p.Trp172Cys	168.0	0.0		252.0	116.0	NM_032999	O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Missense_Mutation	SNP	ENST00000324896.4	hg19	CCDS5573.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.888334	0.52014	.	.	ENSG00000077809	ENST00000324896;ENST00000539339;ENST00000353920;ENST00000346152;ENST00000416070;ENST00000443166	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	5.51	5.51	0.81932	.	0.287858	0.30869	N	0.008717	T	0.64972	0.2647	M	0.68317	2.08	0.80722	D	1	D;B;D;D;D;B	0.89917	0.992;0.168;1.0;0.99;1.0;0.127	D;B;D;D;D;B	0.91635	0.95;0.085;0.998;0.917;0.999;0.189	T	0.66854	-0.5818	10	0.72032	D	0.01	-6.6822	18.3968	0.90502	0.0:0.0:1.0:0.0	.	172;172;172;172;172;172	Q499G6;P78347-2;P78347-3;P78347-4;P78347;Q86U51	.;.;.;.;GTF2I_HUMAN;.	C	172;167;172;172;172;172	ENSP00000322542:W172C;ENSP00000322671:W172C;ENSP00000322599:W172C;ENSP00000387651:W172C;ENSP00000404240:W172C	ENSP00000322542:W172C	W	+	3	0	GTF2I	73752655	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.517000	0.60503	2.594000	0.87642	0.484000	0.47621	TGG	.	.		0.438	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252708.1	NM_032999		T	74114719	G	T	74114719	3	4	47	1	0	0	0	0	1	0	0	0	6876	1183	41	3	530	3	GTF2I	7	74114719	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	66693502	74114719	85023944	36	6052										
TUSC3	7991	hgsc.bcm.edu	37	chr8	15480625	15480625	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	aagtagagcagctgatggaaTggagttccagacgctcaatc	12	8	1	3			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr8:15480625T>C	ENST00000503731.1	+	2	323	c.175T>C	c.(175-177)Tgg>Cgg	p.W59R	TUSC3_ENST00000506802.1_Missense_Mutation_p.W59R|TUSC3_ENST00000382020.4_Missense_Mutation_p.W59R|TUSC3_ENST00000509380.1_Missense_Mutation_p.W59R|TUSC3_ENST00000503191.1_3'UTR	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	59	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		GCTGATGGAATGGAGTTCCAG	0.348																																					p.W59R		Atlas-SNP	.											.	TUSC3	98	.	0			c.T175C						.						66	66	66					8																	15480625		2203	4300	6503	SO:0001583	missense	7991	exon2			ATGGAATGGAGTT	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.175T>C	chr8.hg19:g.15480625T>C	ENSP00000424544:p.Trp59Arg	79.0	0.0		64.0	47.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433993	0.83776	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.44482	0.94;0.92;0.94;0.94	5.59	5.59	0.84812	Thioredoxin-like fold (1);	0.104887	0.64402	D	0.000001	T	0.54175	0.1842	L	0.39245	1.2	0.58432	D	0.999997	D;D;D;D;D;D	0.76494	0.992;0.992;0.994;0.984;0.999;0.999	D;D;D;P;D;D	0.83275	0.946;0.938;0.991;0.823;0.984;0.996	T	0.45745	-0.9240	10	0.22706	T	0.39	-11.8531	15.2531	0.73564	0.0:0.0:0.0:1.0	.	59;59;59;59;59;59	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	R	59	ENSP00000371450:W59R;ENSP00000425777:W59R;ENSP00000423426:W59R;ENSP00000424544:W59R	ENSP00000221167:W59R	W	+	1	0	TUSC3	15524996	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.263000	0.75096	0.528000	0.53228	TGG	.	.		0.348	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		C	15480625	T	C	15480625	3	2	47	1	0	0	0	0	1	0	0	0	16793	1464	51	2	181	2	TUSC3	8	15480625	Missense_Mutation	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10		15480625	130883397	37	6053										
FAM135B	51059	hgsc.bcm.edu	37	chr8	139263216	139263216	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ggtggaagtgcaggccaagcGttcggctgctgaccatcggt	16	10	0	1			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr8:139263216G>T	ENST00000395297.1	-	6	580	c.410C>A	c.(409-411)aCg>aAg	p.T137K		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	137										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CAGGCCAAGCGTTCGGCTGCT	0.592										HNSCC(54;0.14)																											p.T137K		Atlas-SNP	.											LOC51059,colon,carcinoma,0,2	FAM135B	423	.	0			c.C410A						.						108	122	117					8																	139263216		2159	4243	6402	SO:0001583	missense	51059	exon6			CCAAGCGTTCGGC	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.410C>A	chr8.hg19:g.139263216G>T	ENSP00000378710:p.Thr137Lys	104.0	0.0		130.0	56.0	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	hg19	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	G	18.96	3.734272	0.69189	.	.	ENSG00000147724	ENST00000395297;ENST00000160713	T	0.15834	2.39	5.61	4.74	0.60224	.	0.060370	0.64402	D	0.000004	T	0.32852	0.0843	M	0.77820	2.39	0.51767	D	0.999931	P	0.49559	0.925	P	0.50896	0.653	T	0.16958	-1.0385	10	0.62326	D	0.03	-1.1655	13.6346	0.62215	0.0744:0.0:0.9256:0.0	.	137	Q49AJ0	F135B_HUMAN	K	137	ENSP00000378710:T137K	ENSP00000160713:T137K	T	-	2	0	FAM135B	139332398	1.000000	0.71417	0.246000	0.24233	0.118000	0.20060	5.802000	0.69122	1.390000	0.46547	0.655000	0.94253	ACG	.	.		0.592	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139263216	G	T	139263216	3	4	47	1	0	0	0	0	1	0	0	0	5454	1145	40	1	3870	1	FAM135B	8	139263216	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	123782591	139263216	7100806	38	6054										
RMI1	80010	hgsc.bcm.edu	37	chr9	86616608	86616608	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tcccagagttacagatgttcTagatcctgcattaggtcctt	8	10	1	3			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr9:86616608T>G	ENST00000325875.3	+	3	1039	c.707T>G	c.(706-708)cTa>cGa	p.L236R		NM_024945.2	NP_079221.2	Q9H9A7	RMI1_HUMAN	RecQ mediated genome instability 1	236					DNA replication (GO:0006260)|glucose homeostasis (GO:0042593)|multicellular organism growth (GO:0035264)|reduction of food intake in response to dietary excess (GO:0002023)|response to glucose (GO:0009749)	nucleus (GO:0005634)				biliary_tract(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						ACAGATGTTCTAGATCCTGCA	0.378																																					p.L236R		Atlas-SNP	.											.	RMI1	50	.	0			c.T707G						.						107	106	106					9																	86616608		2203	4299	6502	SO:0001583	missense	80010	exon3			ATGTTCTAGATCC	AK022950	CCDS6669.1	9q22.1	2013-06-10	2013-06-10	2006-06-12	ENSG00000178966	ENSG00000178966			25764	protein-coding gene	gene with protein product	"BLM-Associated Polypeptide, 75 kDa"	610404	"chromosome 9 open reading frame 76", "RMI1, RecQ mediated genome instability 1, homolog (S. cerevisiae)"	C9orf76		15775963, 20826341	Standard	NM_024945		Approved	FLJ12888, BLAP75	uc004anq.4	Q9H9A7	OTTHUMG00000020113	ENST00000325875.3:c.707T>G	chr9.hg19:g.86616608T>G	ENSP00000317039:p.Leu236Arg	96.0	0.0		135.0	64.0	NM_024945	Q05BX1|Q05CW3|Q5SQG8|Q5SQG9|Q6P1Q4|Q6PI89|Q7Z6L6	Missense_Mutation	SNP	ENST00000325875.3	hg19	CCDS6669.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.178430	0.38511	.	.	ENSG00000178966	ENST00000445877;ENST00000325875	T;T	0.51071	0.72;1.31	5.62	2.04	0.26737	.	0.227208	0.28088	N	0.016646	T	0.57169	0.2035	M	0.66939	2.045	0.22127	N	0.99934	D	0.71674	0.998	P	0.60789	0.879	T	0.47156	-0.9139	10	0.34782	T	0.22	-10.1409	9.0664	0.36467	0.0:0.2095:0.0:0.7905	.	236	Q9H9A7	RMI1_HUMAN	R	236	ENSP00000402433:L236R;ENSP00000317039:L236R	ENSP00000317039:L236R	L	+	2	0	RMI1	85806428	0.179000	0.23135	0.094000	0.20943	0.940000	0.58332	1.847000	0.39299	0.499000	0.27970	0.533000	0.62120	CTA	.	.		0.378	RMI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052870.1	NM_024945		G	86616608	T	G	86616608	3	3	47	1	0	0	0	0	1	0	0	0	13410	1522	53	5	709	5	RMI1	9	86616608	Missense_Mutation	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10		86616608	54596823	39	6055										
RAD23B	5887	hgsc.bcm.edu	37	chr9	110091936	110091936	+	Nonstop_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gcagaactttgatgaagattGaaagggacttttttatatct	9	4	1	5			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr9:110091936G>T	ENST00000358015.3	+	10	1580	c.1229G>T	c.(1228-1230)tGa>tTa	p.*410L	RAD23B_ENST00000416373.2_Nonstop_Mutation_p.*338L	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	0					DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						GATGAAGATTGAAAGGGACTT	0.398								Direct reversal of damage;Nucleotide excision repair (NER)																													p.X410L		Atlas-SNP	.											.	RAD23B	31	.	0			c.G1229T						.						65	65	65					9																	110091936		2203	4299	6502	SO:0001578	stop_lost	5887	exon10			AAGATTGAAAGGG		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"XP-C repair complementing protein", "XP-C repair complementing complex 58 kDa"	600062	"RAD23 (S. cerevisiae) homolog B"			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.1229G>T	chr9.hg19:g.110091936G>T	ENSP00000350708:p.*410Leuext*62	45.0	0.0		51.0	22.0	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	hg19	CCDS6769.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.060214	0.36373	.	.	ENSG00000119318	ENST00000358015;ENST00000416373	.	.	.	4.34	3.43	0.39272	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2193	0.54425	0.0849:0.0:0.9151:0.0	.	.	.	.	L	410;338	.	.	X	+	2	2	RAD23B	109131757	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.737000	0.47393	0.930000	0.37217	0.563000	0.77884	TGA	.	.		0.398	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874		T	110091936	G	T	110091936	4	4	47	1	0	0	0	0	0	0	0	0	12998	1285	45	3	1267	3	RAD23B	9	110091936	Nonstop_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	23475328	110091936	31121495	40	6056										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55849778	55849778	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	aaaaactctctgaggatctcCattctcaatggcatatgtta	6	9	3	1			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr10:55849778C>A	ENST00000320301.6	-	16	2357	c.1963G>T	c.(1963-1965)Gga>Tga	p.G655*	PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000437009.1_Intron|PCDH15_ENST00000395432.2_Nonsense_Mutation_p.G618*|PCDH15_ENST00000373957.3_Nonsense_Mutation_p.G633*|PCDH15_ENST00000395446.1_Nonsense_Mutation_p.G655*|PCDH15_ENST00000395430.1_Nonsense_Mutation_p.G655*|PCDH15_ENST00000409834.1_Nonsense_Mutation_p.G266*|PCDH15_ENST00000373955.1_Nonsense_Mutation_p.G655*|PCDH15_ENST00000373965.2_Nonsense_Mutation_p.G662*|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Nonsense_Mutation_p.G660*|PCDH15_ENST00000361849.3_Nonsense_Mutation_p.G655*|PCDH15_ENST00000395438.1_Nonsense_Mutation_p.G655*|PCDH15_ENST00000395433.1_Nonsense_Mutation_p.G633*|PCDH15_ENST00000395445.1_Nonsense_Mutation_p.G662*	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	655	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TGAGGATCTCCATTCTCAATG	0.348										HNSCC(58;0.16)																											p.G660X		Atlas-SNP	.											.	PCDH15	1715	.	0			c.G1978T						.						67	68	67					10																	55849778		2203	4300	6503	SO:0001587	stop_gained	65217	exon17			GATCTCCATTCTC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1963G>T	chr10.hg19:g.55849778C>A	ENSP00000322604:p.Gly655*	86.0	0.0		106.0	43.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Nonsense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	44	10.563949	0.99428	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000373955	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.6329	0.91366	0.0:1.0:0.0:0.0	.	.	.	.	X	662;660;655;655;266;662;655;618;655;633;633;655;655;660;655	.	ENSP00000322604:G655X	G	-	1	0	PCDH15	55519784	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.099000	0.64554	2.937000	0.99478	0.650000	0.86243	GGA	.	.		0.348	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55849778	C	A	55849778	4	1	47	1	0	0	0	0	0	1	0	0	11520	603	21	3	5595	3	PCDH15	10	55849778	Nonsense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10		55849778	79684969	41	6057										
SLC6A5	9152	hgsc.bcm.edu	37	chr11	20660007	20660007	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gtttctctctcctgttagggTggaatttacatgtttcagct	9	8	3	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:20660007T>C	ENST00000525748.1	+	13	2145	c.1872T>C	c.(1870-1872)ggT>ggC	p.G624G	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	624					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	CCTGTTAGGGTGGAATTTACA	0.453																																					p.G624G		Atlas-SNP	.											.	SLC6A5	151	.	0			c.T1872C						.						368	274	306					11																	20660007		2203	4300	6503	SO:0001819	synonymous_variant	9152	exon13			TTAGGGTGGAATT	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"Solute carriers"	11051	protein-coding gene	gene with protein product	"glycine transporter 2"	604159	"solute carrier family 6 (neurotransmitter transporter, glycine), member 5"	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.1872T>C	chr11.hg19:g.20660007T>C		32.0	0.0		71.0	27.0	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	hg19	CCDS7854.1																																																																																			.	.		0.453	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211		C	20660007	T	C	20660007	2	2	47	1	0	0	0	0	0	0	0	1	14702	1683	59	2		2	SLC6A5	11	20660007	Silent	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10		20660007	114346509	42	6058										
PPFIA1	8500	hgsc.bcm.edu	37	chr11	70194365	70194365	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	aaagtcgagttggcagtggaAgtctagacaatcttggtcgt	13	6	2	1			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:70194365A>C	ENST00000253925.7	+	16	2217	c.2002A>C	c.(2002-2004)Agt>Cgt	p.S668R	PPFIA1_ENST00000389547.3_Missense_Mutation_p.S668R|AP000487.6_ENST00000528607.1_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	668					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TGGCAGTGGAAGTCTAGACAA	0.502																																					p.S668R		Atlas-SNP	.											.	PPFIA1	114	.	0			c.A2002C						.						211	171	185					11																	70194365		2200	4294	6494	SO:0001583	missense	8500	exon16			AGTGGAAGTCTAG	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"Sterile alpha motif (SAM) domain containing"	9245	protein-coding gene	gene with protein product	"Liprin-alpha1"	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.2002A>C	chr11.hg19:g.70194365A>C	ENSP00000253925:p.Ser668Arg	98.0	0.0		105.0	44.0	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	hg19	CCDS31627.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.33|10.33	1.319566|1.319566	0.23994|0.23994	.|.	.|.	ENSG00000131626|ENSG00000131626	ENST00000528750|ENST00000253925;ENST00000389547;ENST00000544950	.|T;T	.|0.49139	.|0.79;0.79	5.65|5.65	4.51|4.51	0.55191|0.55191	.|.	.|0.089199	.|0.46442	.|D	.|0.000286	T|T	0.45357|0.45357	0.1338|0.1338	L|L	0.60455|0.60455	1.87|1.87	0.37560|0.37560	D|D	0.919014|0.919014	.|P;B	.|0.40834	.|0.73;0.264	.|B;B	.|0.39027	.|0.288;0.078	T|T	0.54248|0.54248	-0.8322|-0.8322	5|10	.|0.66056	.|D	.|0.02	.|.	12.1312|12.1312	0.53944|0.53944	0.8715:0.0:0.0:0.1285|0.8715:0.0:0.0:0.1285	.|.	.|668;668	.|Q13136;Q13136-2	.|LIPA1_HUMAN;.	D|R	71|668;668;155	.|ENSP00000253925:S668R;ENSP00000374198:S668R	.|ENSP00000253925:S668R	E|S	+|+	3|1	2|0	PPFIA1|PPFIA1	69872013|69872013	1.000000|1.000000	0.71417|0.71417	0.003000|0.003000	0.11579|0.11579	0.114000|0.114000	0.19823|0.19823	7.277000|7.277000	0.78572|0.78572	0.947000|0.947000	0.37659|0.37659	0.533000|0.533000	0.62120|0.62120	GAA|AGT	.	.		0.502	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		C	70194365	A	C	70194365	3	2	47	1	0	0	0	0	1	0	0	0	12318	72	3	5	2060	5	PPFIA1	11	70194365	Missense_Mutation	SNP	A	TCGA-BC-A8YO-01A-11D-A36X-10	49534358	70194365	64812151	43	6059										
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101833550	101833550	+	Frame_Shift_Del	DEL	T	T	-													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ttatcttaaggcattaattaTaaatcagagctttaagtttg							TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:101833550delT	ENST00000263468.8	+	6	2054	c.1784delT	c.(1783-1785)atafs	p.I595fs	KIAA1377_ENST00000537689.1_Frame_Shift_Del_p.I396fs	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	595										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		GCATTAATTATAAATCAGAGC	0.289																																					p.I595X		Atlas-Indel,Pindel	.											.	KIAA1377	111	.	0			c.1783delA						.						33	39	37					11																	101833550		2195	4275	6470	SO:0001589	frameshift_variant	57562	exon6			.	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.1784delT	chr11.hg19:g.101833550delT	ENSP00000263468:p.Ile595fs	115.0	0.0		160.0	62.0	NM_020802	Q4G0U6	Frame_Shift_Del	DEL	ENST00000263468.8	hg19	CCDS31658.1																																																																																			.	.		0.289	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		-	101833550	T	-	101833550	7	5	47	1	0	1	0	1	0	0	0	0	8236	1406	49	0	1806	0	KIAA1377	11	101833550	Frame_Shift_Del	DEL	T	TCGA-BC-A8YO-01A-11D-A36X-10	31639185	101833550	33172966	44	6060										
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101849150	101849150	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tttagagcagaaaagacaaaAccctggatctgtaggacaga	10	7	1	4			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:101849150A>G	ENST00000263468.8	+	7	3188	c.2918A>G	c.(2917-2919)aAc>aGc	p.N973S	KIAA1377_ENST00000537689.1_Missense_Mutation_p.N774S	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	973										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AAAAGACAAAACCCTGGATCT	0.328																																					p.N973S		Atlas-SNP	.											.	KIAA1377	111	.	0			c.A2918G						.						136	147	144					11																	101849150		2203	4299	6502	SO:0001583	missense	57562	exon7			GACAAAACCCTGG	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.2918A>G	chr11.hg19:g.101849150A>G	ENSP00000263468:p.Asn973Ser	184.0	0.0		163.0	8.0	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	hg19	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.790827	0.31685	.	.	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.07021	3.23;3.23	5.09	-0.895	0.10560	.	0.555420	0.17103	N	0.186932	T	0.07999	0.0200	L	0.57536	1.79	0.09310	N	1	B	0.24426	0.103	B	0.28011	0.085	T	0.29427	-1.0012	10	0.32370	T	0.25	-2.271	5.225	0.15389	0.2348:0.3499:0.0:0.4153	.	973	Q9P2H0	K1377_HUMAN	S	973;774	ENSP00000263468:N973S;ENSP00000443184:N774S	ENSP00000263468:N973S	N	+	2	0	KIAA1377	101354360	0.025000	0.19082	0.523000	0.27875	0.908000	0.53690	0.058000	0.14301	0.193000	0.20303	0.455000	0.32223	AAC	.	.		0.328	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		G	101849150	A	G	101849150	3	3	47	1	0	0	0	0	1	0	0	0	8236	43	2	2	2944	2	KIAA1377	11	101849150	Missense_Mutation	SNP	A	TCGA-BC-A8YO-01A-11D-A36X-10	15600	101849150	33157366	45	6061										
TECTA	7007	hgsc.bcm.edu	37	chr11	121037416	121037416	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gatcaatgacagacagtgcaCcggcatcgagggggaagatt	14	8	1	3			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:121037416C>A	ENST00000392793.1	+	18	5784	c.5513C>A	c.(5512-5514)aCc>aAc	p.T1838N	TECTA_ENST00000264037.2_Missense_Mutation_p.T1838N			O75443	TECTA_HUMAN	tectorin alpha	1838	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AGACAGTGCACCGGCATCGAG	0.493																																					p.T1838N		Atlas-SNP	.											.	TECTA	329	.	0			c.C5513A						.						140	123	129					11																	121037416		2203	4299	6502	SO:0001583	missense	7007	exon17			AGTGCACCGGCAT	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.5513C>A	chr11.hg19:g.121037416C>A	ENSP00000376543:p.Thr1838Asn	62.0	0.0		104.0	12.0	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	C	7.831	0.719814	0.15372	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	D;D	0.81908	-1.55;-1.55	6.05	4.1	0.47936	Zona pellucida sperm-binding protein (3);	0.813870	0.11699	N	0.538141	T	0.65801	0.2726	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.16722	0.016	T	0.48352	-0.9043	10	0.10377	T	0.69	.	10.8388	0.46702	0.1311:0.8018:0.0:0.0671	.	1838	O75443	TECTA_HUMAN	N	1838	ENSP00000376543:T1838N;ENSP00000264037:T1838N	ENSP00000264037:T1838N	T	+	2	0	TECTA	120542626	0.000000	0.05858	0.128000	0.21923	0.945000	0.59286	1.072000	0.30678	1.568000	0.49683	0.650000	0.86243	ACC	.	.		0.493	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	121037416	C	A	121037416	3	1	47	1	0	0	0	0	1	0	0	0	15762	507	18	3	5579	3	TECTA	11	121037416	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10	19188266	121037416	13969100	46	6062										
VSIG2	23584	hgsc.bcm.edu	37	chr11	124618542	124618542	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tccacccagcatccctaccgGtcacagagagggtcagctca	9	16	3	1	rs560008973	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr11:124618542G>C	ENST00000326621.5	-	5	804	c.704C>G	c.(703-705)aCc>aGc	p.T235S	RP11-677M14.2_ENST00000531241.1_RNA|VSIG2_ENST00000403470.1_Missense_Mutation_p.T235S	NM_014312.3	NP_055127.2	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2	235						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(5)	19	all_hematologic(175;0.215)	Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0215)		ATCCCTACCGGTCACAGAGAG	0.622																																					p.T235S		Atlas-SNP	.											.	VSIG2	38	.	0			c.C704G						.						92	81	85					11																	124618542		2201	4299	6500	SO:0001583	missense	23584	exon5			CTACCGGTCACAG	AF061022	CCDS8452.1	11q24	2013-01-11			ENSG00000019102	ENSG00000019102		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing"	17149	protein-coding gene	gene with protein product		606011				9862345	Standard	NM_014312		Approved	CTXL, CTH	uc001qas.3	Q96IQ7	OTTHUMG00000150357	ENST00000326621.5:c.704C>G	chr11.hg19:g.124618542G>C	ENSP00000318684:p.Thr235Ser	71.0	0.0		94.0	43.0	NM_014312	O95791|Q9NX42	Missense_Mutation	SNP	ENST00000326621.5	hg19	CCDS8452.1	.	.	.	.	.	.	.	.	.	.	G	10.63	1.402838	0.25291	.	.	ENSG00000019102	ENST00000326621;ENST00000403470	T;T	0.12984	2.63;2.63	5.65	5.65	0.86999	Immunoglobulin-like fold (1);	0.088528	0.47852	D	0.000220	T	0.15349	0.0370	L	0.60455	1.87	0.35212	D	0.775236	B	0.23540	0.087	B	0.20577	0.03	T	0.10613	-1.0622	10	0.15066	T	0.55	.	15.093	0.72211	0.0:0.0:1.0:0.0	.	235	Q96IQ7	VSIG2_HUMAN	S	235	ENSP00000318684:T235S;ENSP00000385013:T235S	ENSP00000318684:T235S	T	-	2	0	VSIG2	124123752	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.361000	0.44160	2.941000	0.99782	0.655000	0.94253	ACC	.	.		0.622	VSIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317785.1	NM_014312		C	124618542	G	C	124618542	3	2	47	1	0	0	0	0	1	0	0	0	17239	1261	44	4	291	4	VSIG2	11	124618542	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	3581126	124618542	10387974	47	6063										
NID2	22795	hgsc.bcm.edu	37	chr14	52481919	52481919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gggcacgtactggtcatcccGgggggtgccaccgtagtgct	16	12	1	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr14:52481919G>A	ENST00000216286.5	-	15	3102	c.3103C>T	c.(3103-3105)Cgg>Tgg	p.R1035W	NID2_ENST00000541773.1_Missense_Mutation_p.R934W	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1035	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					TGGTCATCCCGGGGGGTGCCA	0.622																																					p.R1035W		Atlas-SNP	.											.	NID2	201	.	0			c.C3103T						.						50	47	48					14																	52481919		2203	4300	6503	SO:0001583	missense	22795	exon15			CATCCCGGGGGGT	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.3103C>T	chr14.hg19:g.52481919G>A	ENSP00000216286:p.Arg1035Trp	106.0	0.0		145.0	64.0	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.48|15.48	2.847145|2.847145	0.51164|0.51164	.|.	.|.	ENSG00000087303|ENSG00000087303	ENST00000556572|ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T|T;T	0.62364|0.63913	0.03|-0.07;-0.07	5.67|5.67	-0.0259|-0.0259	0.13933|0.13933	.|Thyroglobulin type-1 (4);	.|0.527175	.|0.23090	.|N	.|0.052051	T|T	0.68513|0.68513	0.3009|0.3009	L|L	0.49640|0.49640	1.575|1.575	0.09310|0.09310	N|N	0.999995|0.999995	.|D;D;D;D	.|0.89917	.|0.999;0.999;1.0;0.999	.|D;P;D;D	.|0.68765	.|0.932;0.9;0.96;0.957	T|T	0.61792|0.61792	-0.6990|-0.6990	6|10	.|0.72032	.|D	.|0.01	.|.	9.7544|9.7544	0.40494|0.40494	0.0:0.1675:0.3884:0.444|0.0:0.1675:0.3884:0.444	.|.	.|629;934;1037;1035	.|E7EPP3;Q14112-2;Q5CZI2;Q14112	.|.;.;.;NID2_HUMAN	L|W	303|1035;629;934;1037	ENSP00000452190:P303L|ENSP00000216286:R1035W;ENSP00000443730:R934W	.|ENSP00000216286:R1035W	P|R	-|-	2|1	0|2	NID2|NID2	51551669|51551669	0.000000|0.000000	0.05858|0.05858	0.066000|0.066000	0.19879|0.19879	0.477000|0.477000	0.33069|0.33069	0.144000|0.144000	0.16135|0.16135	-0.324000|-0.324000	0.08589|0.08589	-0.169000|-0.169000	0.13324|0.13324	CCG|CGG	.	.		0.622	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			A	52481919	G	A	52481919	3	1	47	1	0	0	0	0	1	0	0	0	10424	1115	39	1	1056	1	NID2	14	52481919	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10		52481919	54867621	48	6064										
RYR3	6263	hgsc.bcm.edu	37	chr15	33990117	33990117	+	Frame_Shift_Del	DEL	C	C	-													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	acaaggtgttttaccagcatCccaacctcatgagagtcctg							TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr15:33990117delC	ENST00000389232.4	+	40	6239	c.6169delC	c.(6169-6171)cccfs	p.P2057fs	RYR3_ENST00000415757.3_Frame_Shift_Del_p.P2057fs	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2057	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTACCAGCATCCCAACCTCAT	0.448																																					p.H2056fs		Atlas-Indel,Pindel	.											.	RYR3	760	.	0			c.6168delT						.						172	164	167					15																	33990117		2040	4221	6261	SO:0001589	frameshift_variant	6263	exon40			.		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.6169delC	chr15.hg19:g.33990117delC	ENSP00000373884:p.Pro2057fs	147.0	0.0		221.0	90.0	NM_001243996	O15175|Q15412	Frame_Shift_Del	DEL	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.448	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			-	33990117	C	-	33990117	7	5	47	1	0	1	0	1	0	0	0	0	13785	855	30	0	6327	0	RYR3	15	33990117	Frame_Shift_Del	DEL	C	TCGA-BC-A8YO-01A-11D-A36X-10		33990117	68541275	49	6065										
TYRO3	7301	hgsc.bcm.edu	37	chr15	41865504	41865699	+	Splice_Site	DEL	GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	-													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	tctccctcaatgccccttgtAggctggcagaggacatgaca					rs77680822|rs62001448|rs370070955|rs367718441|rs370573528|rs529826589|rs140748026|rs150084536|rs377334532|rs142510731|rs202087157|rs116540200	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr15:41865504_41865699delGTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	ENST00000263798.3	+	17	2209_2369	c.1985_2145delGTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	c.(1984-2145)agtacgaattctggaggactcgagggtgggagacagcagcaggtgccaagaggagctagctgatggtcggctcctgcctgggacagtatctgctatgcatgggggtagcttgggagcaaagatgcaaagatgtcctggctcttgtgggcctgtgagcatggc>a	p.STNSGGLEGGRQQQVPRGAS*WSAPAWDSICYAWG*LGSKDAKMSWLLWACEHG662fs	TYRO3_ENST00000559066.1_Splice_Site_p.STNSGGLEGGRQQQVPRGAS*WSAPAWDSICYAWG*LGSKDAKMSWLLWACEHG617fs	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	662	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.?(2)|p.R670R(1)|p.L686L(1)|p.G675R(1)|p.R678R(1)|p.L694L(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TGCCCCTTGTAGGCTGGCAGAGGACATGACAGTGTGTGTGGCTGACTTCGGACTCTCCCGGAAGATCTACAGTGGGGACTACTATCGTCAAGGCTGTGCCTCCAAACTGCCTGTCAAGTGGCTGGCCCTGGAGAGCCTGGCCGACAACCTGTATACTGTGCAGAGTGACGTGGTGAGCAGGGTGGCCCGTGAAGCTTGGTGGGGACGAGTGTGAGA	0.581																																					p.662_662del		Pindel	.											.	TYRO3	169	.	7	Substitution - coding silent(4)|Unknown(2)|Substitution - Missense(1)	lung(6)|stomach(1)	c.1985_1985del						.																																			SO:0001630	splice_region_variant	7301	exon16			.	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.2145+1GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG>-	chr15.hg19:g.41865504_41865699delGTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG		78.0	0.0		86.0	12.0	NM_006293	O14953|Q86VR3	Frame_Shift_Del	DEL	ENST00000263798.3	hg19	CCDS10080.1																																																																																			.	.		0.581	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Frame_Shift_Del	-	41865699	GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	-	41865504	8	5	47	1	0	1	0	1	0	0	1	0	16829	434	15	0	2050	0	TYRO3	15	41865504	Splice_Site	DEL	GTACGAATTCTGGAGGACTCGAGGGTGGGAGACAGCAGCAGGTGCCAAGAGGAGCTAGCTGATGGTCGGCTCCTGCCTGGGACAGTATCTGCTATGCATGGGGGTAGCTTGGGAGCAAAGATGCAAAGATGTCCTGGCTCTTGTGGGCCTGTGAGCATGGCAGAAGGCTGACTCTCTCCCTCAATGCCCCTTGTAG	TCGA-BC-A8YO-01A-11D-A36X-10	7875387	41865504	60665888	50	6066										
HCN4	10021	hgsc.bcm.edu	37	chr15	73635902	73635902	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ggggatggaggaaatgaaatCtaccatgaaccagcttttca	11	7	2	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr15:73635902C>A	ENST00000261917.3	-	2	2026	c.1033G>T	c.(1033-1035)Gat>Tat	p.D345Y	RP11-272D12.1_ENST00000558742.1_RNA|RP11-272D12.1_ENST00000557981.1_RNA	NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	345					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GAAATGAAATCTACCATGAAC	0.537																																					p.D345Y		Atlas-SNP	.											.	HCN4	150	.	0			c.G1033T						.						112	97	102					15																	73635902		2198	4297	6495	SO:0001583	missense	10021	exon2			TGAAATCTACCAT	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1033G>T	chr15.hg19:g.73635902C>A	ENSP00000261917:p.Asp345Tyr	99.0	0.0		162.0	58.0	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	hg19	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.587899	0.86851	.	.	ENSG00000138622	ENST00000261917	D	0.99399	-5.83	5.34	5.34	0.76211	Ion transport (1);	.	.	.	.	D	0.99708	0.9888	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97514	1.0068	9	0.87932	D	0	.	19.4036	0.94640	0.0:1.0:0.0:0.0	.	345	Q9Y3Q4	HCN4_HUMAN	Y	345	ENSP00000261917:D345Y	ENSP00000261917:D345Y	D	-	1	0	HCN4	71422955	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.671000	0.83941	2.657000	0.90304	0.655000	0.94253	GAT	.	.		0.537	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		A	73635902	C	A	73635902	3	1	47	1	0	0	0	0	1	0	0	0	7008	913	32	3	2606	3	HCN4	15	73635902	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10	31770398	73635902	28895490	51	6067										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99482513	99482513	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	gacggcatggcatacctcaaCgccaataagttcgtccacag	9	13	1	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr15:99482513C>A	ENST00000268035.6	+	18	3992	c.3381C>A	c.(3379-3381)aaC>aaA	p.N1127K	IGF1R_ENST00000558762.1_Missense_Mutation_p.N1126K	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1127	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	CATACCTCAACGCCAATAAGT	0.488																																					p.N1127K		Atlas-SNP	.											.	IGF1R	147	.	0			c.C3381A						.						163	151	155					15																	99482513		2197	4297	6494	SO:0001583	missense	3480	exon18			CCTCAACGCCAAT	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.3381C>A	chr15.hg19:g.99482513C>A	ENSP00000268035:p.Asn1127Lys	99.0	0.0		167.0	75.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201698	0.79015	.	.	ENSG00000140443	ENST00000268035	D	0.88975	-2.45	5.9	-4.89	0.03103	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000008	D	0.88081	0.6341	N	0.22421	0.69	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77557	0.99;0.972	D	0.85675	0.1297	10	0.66056	D	0.02	.	15.7659	0.78126	0.0:0.2581:0.0:0.7419	.	1126;1127	C9J5X1;P08069	.;IGF1R_HUMAN	K	1127	ENSP00000268035:N1127K	ENSP00000268035:N1127K	N	+	3	2	IGF1R	97300036	0.036000	0.19791	0.936000	0.37596	0.976000	0.68499	-0.646000	0.05403	-0.764000	0.04651	-0.768000	0.03414	AAC	.	.		0.488	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99482513	C	A	99482513	3	1	47	1	0	0	0	0	1	0	0	0	7580	535	19	1	3451	1	IGF1R	15	99482513	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10	25846611	99482513	3048879	52	6068										
TP53	7157	hgsc.bcm.edu	37	chr17	7577589	7577594	+	In_Frame_Del	DEL	GTGGTA	GTGGTA	-													0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	acatgtagttgtagtggatgGtggtacagtcagagccaacc							TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	GTGGTA	GTGGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr17:7577589_7577594delGTGGTA	ENST00000269305.4	-	7	876_881	c.687_692delTACCAC	c.(685-693)tgtaccacc>tgc	p.TT230del	TP53_ENST00000413465.2_In_Frame_Del_p.TT230del|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_In_Frame_Del_p.TT230del|TP53_ENST00000445888.2_In_Frame_Del_p.TT230del|TP53_ENST00000359597.4_In_Frame_Del_p.TT230del|TP53_ENST00000420246.2_In_Frame_Del_p.TT230del	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	230	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		T -> A (in sporadic cancers; somatic mutation).|T -> I (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9450901}.|T -> N (in sporadic cancers; somatic mutation).|T -> P (in sporadic cancers; somatic mutation).|T -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C229fs*10(9)|p.T230I(9)|p.0?(8)|p.?(5)|p.C229*(3)|p.T231S(3)|p.T231A(2)|p.T231I(2)|p.C229_H233delCTTIH(2)|p.T231fs*16(2)|p.T230fs*6(2)|p.T230N(2)|p.T230P(2)|p.T230S(2)|p.T230fs*17(2)|p.V225fs*23(1)|p.C136fs*10(1)|p.T231del(1)|p.T231N(1)|p.T230fs*9(1)|p.C229_T230insX(1)|p.D228fs*12(1)|p.C229_I232del(1)|p.S227_I232delSDCTTI(1)|p.T230_Y234delTTIHY(1)|p.C229fs*1(1)|p.T230A(1)|p.T230T(1)|p.C229C(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTAGTGGATGGTGGTACAGTCAGAGC	0.534		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.230_231del	Pancreas(47;798 1329 9957 10801)	Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,colon,carcinoma,-1,16	TP53	33396	.	69	Substitution - Missense(24)|Deletion - Frameshift(19)|Whole gene deletion(8)|Deletion - In frame(6)|Unknown(5)|Substitution - Nonsense(3)|Substitution - coding silent(2)|Insertion - In frame(1)|Complex - frameshift(1)	breast(9)|biliary_tract(8)|ovary(7)|upper_aerodigestive_tract(6)|oesophagus(6)|central_nervous_system(5)|large_intestine(5)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|skin(3)|lung(3)|stomach(2)|urinary_tract(2)|thyroid(1)|soft_tissue(1)|thymus(1)|pancreas(1)|prostate(1)|liver(1)	c.688_693del	GRCh37	CD076915	TP53	D		.																																			SO:0001651	inframe_deletion	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.687_692delTACCAC	chr17.hg19:g.7577589_7577594delGTGGTA	ENSP00000269305:p.Thr230_Thr231del	68.0	0.0		47.0	20.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	In_Frame_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.534	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7577594	GTGGTA	-	7577589	7	5	47	1	0	1	0	1	0	0	0	0	16396	1261	44	0	598	0	TP53	17	7577589	In_Frame_Del	DEL	GTGGTA	TCGA-BC-A8YO-01A-11D-A36X-10		7577589	73617621	53	6069										
LASS4	79603	hgsc.bcm.edu	37	chr19	8326959	8326959	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ccctcggagccgggtggccgGgcgtctgaccaacaggcaca	15	15	1	1			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:8326959G>A	ENST00000251363.5	+	12	1451	c.1151G>A	c.(1150-1152)gGg>gAg	p.G384E	CERS4_ENST00000559450.1_Missense_Mutation_p.G384E|CERS4_ENST00000558331.1_Missense_Mutation_p.G333E|CERS4_ENST00000559336.1_Missense_Mutation_p.G296E|CERS4_ENST00000595722.1_3'UTR	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	384					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										CGGGTGGCCGGGCGTCTGACC	0.692																																					p.G384E		Atlas-SNP	.											.	.	.	.	0			c.G1151A						.						6	8	8					19																	8326959		2146	4215	6361	SO:0001583	missense	79603	exon12			TGGCCGGGCGTCT		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"Homeoboxes / CERS class"	23747	protein-coding gene	gene with protein product		615334	"LAG1 longevity assurance homolog 4 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 4"	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.1151G>A	chr19.hg19:g.8326959G>A	ENSP00000251363:p.Gly384Glu	63.0	0.0		66.0	32.0	NM_024552	D6W665	Missense_Mutation	SNP	ENST00000251363.5	hg19	CCDS12197.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.838467	0.32513	.	.	ENSG00000090661	ENST00000251363	T	0.05513	3.43	4.94	2.71	0.32032	.	7.123110	0.00166	N	0.000005	T	0.09335	0.0230	M	0.65498	2.005	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.52223	-0.8604	10	0.08179	T	0.78	-10.1263	6.599	0.22691	0.1002:0.182:0.7178:0.0	.	384;384	Q53HF9;Q9HA82	.;CERS4_HUMAN	E	384	ENSP00000251363:G384E	ENSP00000251363:G384E	G	+	2	0	CERS4	8232959	0.006000	0.16342	0.002000	0.10522	0.006000	0.05464	1.672000	0.37523	0.443000	0.26582	0.491000	0.48974	GGG	.	.		0.692	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552		A	8326959	G	A	8326959	3	1	47	1	0	0	0	0	1	0	0	0	8650	1232	43	3	1189	3	LASS4	19	8326959	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10		8326959	50802024	54	6070										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610154	10610154	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ctcagcgaagttggcgatgcCgatggcattgctggggtcca	15	10	1	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:10610154C>T	ENST00000171111.5	-	2	1103	c.556G>A	c.(556-558)Ggc>Agc	p.G186S	KEAP1_ENST00000588024.1_5'UTR|KEAP1_ENST00000393623.2_Missense_Mutation_p.G186S	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	186	BACK.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	TTGGCGATGCCGATGGCATTG	0.592																																					p.G186S		Atlas-SNP	.											.	KEAP1	182	.	0			c.G556A						.						105	85	92					19																	10610154		2203	4300	6503	SO:0001583	missense	9817	exon2			CGATGCCGATGGC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.556G>A	chr19.hg19:g.10610154C>T	ENSP00000171111:p.Gly186Ser	55.0	0.0		42.0	31.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.990571	0.93106	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.70282	-0.47;-0.47	4.81	4.81	0.61882	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	D	0.82912	0.5140	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85287	0.1065	10	0.87932	D	0	.	15.3825	0.74669	0.0:1.0:0.0:0.0	.	186	Q14145	KEAP1_HUMAN	S	186	ENSP00000171111:G186S;ENSP00000377245:G186S	ENSP00000171111:G186S	G	-	1	0	KEAP1	10471154	1.000000	0.71417	0.996000	0.52242	0.916000	0.54674	5.912000	0.69948	2.232000	0.73038	0.561000	0.74099	GGC	.	.		0.592	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		T	10610154	C	T	10610154	3	4	47	1	0	0	0	0	1	0	0	0	8150	652	23	1	1338	1	KEAP1	19	10610154	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10	2283195	10610154	48518829	55	6071										
DOCK6	57572	hgsc.bcm.edu	37	chr19	11339628	11339628	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ggtctcaccatgagctggaaGaagaaccaggcgtgctggag	15	9	1	3			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:11339628G>C	ENST00000294618.7	-	23	2813	c.2802C>G	c.(2800-2802)ttC>ttG	p.F934L	DOCK6_ENST00000319867.7_Missense_Mutation_p.F273L	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	934					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						TGAGCTGGAAGAAGAACCAGG	0.627																																					p.F934L		Atlas-SNP	.											.	DOCK6	104	.	0			c.C2802G						.						39	44	42					19																	11339628		2119	4237	6356	SO:0001583	missense	57572	exon23			CTGGAAGAAGAAC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.2802C>G	chr19.hg19:g.11339628G>C	ENSP00000294618:p.Phe934Leu	93.0	0.0		57.0	44.0	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	hg19	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.041759	0.35989	.	.	ENSG00000130158	ENST00000294618;ENST00000319867	T;T	0.28666	1.6;1.6	4.4	2.24	0.28232	.	0.060416	0.64402	N	0.000002	T	0.34221	0.0890	L	0.43152	1.355	0.52099	D	0.99994	P;D	0.65815	0.538;0.995	B;P	0.60886	0.217;0.88	T	0.13415	-1.0510	10	0.30078	T	0.28	-22.689	3.6724	0.08279	0.2711:0.0:0.5517:0.1773	.	273;934	C9IZV6;Q96HP0	.;DOCK6_HUMAN	L	934;273	ENSP00000294618:F934L;ENSP00000321556:F273L	ENSP00000294618:F934L	F	-	3	2	DOCK6	11200628	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	4.387000	0.59626	0.402000	0.25451	-0.372000	0.07161	TTC	.	.		0.627	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		C	11339628	G	C	11339628	3	2	47	1	0	0	0	0	1	0	0	0	4693	933	33	4	3445	4	DOCK6	19	11339628	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	729474	11339628	47789355	56	6072										
MAST1	22983	hgsc.bcm.edu	37	chr19	12977547	12977547	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	agcccgtggaaatccgccagTtctcttcctgctctccgcgc	9	17	2	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:12977547T>C	ENST00000251472.4	+	18	2149	c.2110T>C	c.(2110-2112)Ttc>Ctc	p.F704L		NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1											NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						AATCCGCCAGTTCTCTTCCTG	0.617																																					p.F704L		Atlas-SNP	.											.	MAST1	214	.	0			c.T2110C						.						84	55	65					19																	12977547		2203	4300	6503	SO:0001583	missense	22983	exon18			CGCCAGTTCTCTT	AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.2110T>C	chr19.hg19:g.12977547T>C	ENSP00000251472:p.Phe704Leu	54.0	0.0		63.0	48.0	NM_014975		Missense_Mutation	SNP	ENST00000251472.4	hg19	CCDS32921.1	.	.	.	.	.	.	.	.	.	.	T	35	5.526622	0.96431	.	.	ENSG00000105613	ENST00000251472;ENST00000542153	T	0.22945	1.93	4.84	4.84	0.62591	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.53433	0.1796	M	0.89287	3.02	0.58432	D	0.999999	D	0.61697	0.99	D	0.63283	0.913	T	0.63229	-0.6684	10	0.87932	D	0	-29.8221	12.6644	0.56833	0.0:0.0:0.0:1.0	.	704	Q9Y2H9	MAST1_HUMAN	L	704	ENSP00000251472:F704L	ENSP00000251472:F704L	F	+	1	0	MAST1	12838547	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.967000	0.87967	1.947000	0.56498	0.455000	0.32223	TTC	.	.		0.617	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975		C	12977547	T	C	12977547	3	2	47	1	0	0	0	0	1	0	0	0	9333	1725	60	2	2180	2	MAST1	19	12977547	Missense_Mutation	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10	1637919	12977547	46151436	57	6073										
CYP2A6	1548	hgsc.bcm.edu	37	chr19	41352896	41352896	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ctccagcccttgcagcaactGaaaggcctgttgctgtggtc	11	13	0	1	rs138978736	byFrequency	TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:41352896G>C	ENST00000301141.5	-	5	735	c.715C>G	c.(715-717)Cag>Gag	p.Q239E	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	239					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)	p.Q239K(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TGCAGCAACTGAAAGGCCTGT	0.547																																					p.Q239E		Atlas-SNP	.											CYP2A6,NS,carcinoma,0,1	CYP2A6	69	.	1	Substitution - Missense(1)	prostate(1)	c.C715G						.						131	100	110					19																	41352896		2203	4300	6503	SO:0001583	missense	1548	exon5			GCAACTGAAAGGC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.715C>G	chr19.hg19:g.41352896G>C	ENSP00000301141:p.Gln239Glu	116.0	0.0		130.0	49.0	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	hg19	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	7.281	0.609113	0.14066	.	.	ENSG00000255974	ENST00000301141	T	0.67345	-0.26	2.37	2.37	0.29283	.	0.270324	0.36066	N	0.002815	T	0.43366	0.1244	N	0.10809	0.05	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.32693	-0.9897	10	0.52906	T	0.07	.	7.7566	0.28927	0.0:0.0:0.4111:0.5889	.	239;239	Q13120;P11509	.;CP2A6_HUMAN	E	239	ENSP00000301141:Q239E	ENSP00000301141:Q239E	Q	-	1	0	CYP2A6	46044736	0.000000	0.05858	0.022000	0.16811	0.818000	0.46254	0.131000	0.15870	0.174000	0.19809	-0.874000	0.02982	CAG	.	.		0.547	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		C	41352896	G	C	41352896	3	2	47	1	0	0	0	0	1	0	0	0	4164	1299	45	4	789	4	CYP2A6	19	41352896	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	28375349	41352896	17776087	58	6074										
ZNF816A	125893	hgsc.bcm.edu	37	chr19	53454513	53454513	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ggttactaattttccctttaGtctgaaacatgtggagttca	8	7	2	1			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:53454513G>T	ENST00000357666.4	-	5	815	c.515C>A	c.(514-516)aCt>aAt	p.T172N	ZNF816_ENST00000434371.2_Intron|ZNF816_ENST00000444460.2_Missense_Mutation_p.T172N|ZNF321P_ENST00000391777.3_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	172					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						TTTCCCTTTAGTCTGAAACAT	0.403																																					p.T172N		Atlas-SNP	.											.	ZNF816	73	.	0			c.C515A						.						133	146	142					19																	53454513		2203	4300	6503	SO:0001583	missense	125893	exon4			CCTTTAGTCTGAA	BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"Zinc fingers, C2H2-type", "-"	26995	protein-coding gene	gene with protein product			"zinc finger protein 816A"	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.515C>A	chr19.hg19:g.53454513G>T	ENSP00000350295:p.Thr172Asn	110.0	0.0		107.0	47.0	NM_001202457	A8K7H5|Q3KR39|Q659B3	Missense_Mutation	SNP	ENST00000357666.4	hg19	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	N	8.663	0.901000	0.17760	.	.	ENSG00000180257	ENST00000357666;ENST00000444460	T;T	0.05717	3.4;3.4	1.77	1.77	0.24775	.	.	.	.	.	T	0.08935	0.0221	M	0.80028	2.48	0.80722	D	1	B	0.29432	0.244	B	0.21917	0.037	T	0.05801	-1.0863	9	0.52906	T	0.07	.	6.8841	0.24189	0.0:0.0:1.0:0.0	.	172	Q0VGE8	ZN816_HUMAN	N	172	ENSP00000350295:T172N;ENSP00000403266:T172N	ENSP00000350295:T172N	T	-	2	0	ZNF816	58146325	.	.	0.006000	0.13384	0.014000	0.08584	.	.	0.955000	0.37878	0.185000	0.17295	ACT	.	.		0.403	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		T	53454513	G	T	53454513	3	4	47	1	0	0	0	0	1	0	0	0	18192	1029	36	3	1444	3	ZNF816A	19	53454513	Missense_Mutation	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	12101617	53454513	5674470	59	6075										
LILRA3	11026	hgsc.bcm.edu	37	chr19	54802753	54802753	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	cacgacaggacccggctgcaCtgagagtgatggcttcttag	13	11	1	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:54802753C>A	ENST00000251390.3	-	5	779	c.688G>T	c.(688-690)Gtg>Ttg	p.V230L	LILRA3_ENST00000391745.1_Missense_Mutation_p.V247L|LILRA3_ENST00000391744.3_Missense_Mutation_p.V166L	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	230	Ig-like C2-type 3.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCCGGCTGCACTGAGAGTGAT	0.592																																					p.V230L		Atlas-SNP	.											.	LILRA3	65	.	0			c.G688T						.						57	54	55					19																	54802753		2193	4168	6361	SO:0001583	missense	11026	exon5			GCTGCACTGAGAG	U91926		19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.688G>T	chr19.hg19:g.54802753C>A	ENSP00000251390:p.Val230Leu	88.0	0.0		102.0	86.0	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	hg19	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	C	9.074	0.997727	0.19043	.	.	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.00724	5.78;5.78;5.78	2.11	-0.771	0.11002	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.991840	0.02621	N	0.103220	T	0.03053	0.0090	M	0.86740	2.835	0.09310	N	1	P;B	0.40834	0.73;0.221	P;B	0.49226	0.603;0.285	T	0.35525	-0.9785	10	0.87932	D	0	.	4.9791	0.14155	0.0:0.4595:0.0:0.5405	.	230;230	E7EU74;Q8N6C8	.;LIRA3_HUMAN	L	230;166;247	ENSP00000251390:V230L;ENSP00000375624:V166L;ENSP00000375625:V247L	ENSP00000251390:V230L	V	-	1	0	LILRA3	59494565	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.760000	0.00786	-0.204000	0.10235	-0.232000	0.12228	GTG	.	.		0.592	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1			A	54802753	C	A	54802753	3	1	47	1	0	0	0	0	1	0	0	0	8795	565	20	3	643	3	LILRA3	19	54802753	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10	1348240	54802753	4326230	60	6076										
LILRA5	353514	hgsc.bcm.edu	37	chr19	54822850	54822850	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	agctgtgagtccaaggtccaGgagagcttgtggtctccttc	13	10	1	2			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:54822850G>A	ENST00000301219.3	-	5	665	c.546C>T	c.(544-546)tcC>tcT	p.S182S	LILRA5_ENST00000446712.3_Silent_p.S170S|LILRA5_ENST00000432233.3_Silent_p.S182S|AC008984.2_ENST00000507363.1_RNA|LILRA5_ENST00000346508.3_Silent_p.S170S	NM_021250.2	NP_067073.1	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5	182	Ig-like C2-type 2.				innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCAAGGTCCAGGAGAGCTTGT	0.597																																					p.S182S		Atlas-SNP	.											.	LILRA5	49	.	0			c.C546T						.						58	58	58					19																	54822850		2203	4300	6503	SO:0001819	synonymous_variant	353514	exon5			GGTCCAGGAGAGC	AF212842	CCDS12888.1, CCDS12889.1	19q13.4	2013-01-11	2005-05-13	2005-05-13	ENSG00000187116	ENSG00000187116		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16309	protein-coding gene	gene with protein product		606047		LILRB7		10941842	Standard	NM_181986		Approved	ILT11, LIR9, CD85, CD85f	uc002qfe.3	A6NI73	OTTHUMG00000065357	ENST00000301219.3:c.546C>T	chr19.hg19:g.54822850G>A		98.0	0.0		157.0	82.0	NM_181879	A6NHI3	Silent	SNP	ENST00000301219.3	hg19	CCDS12888.1																																																																																			.	.		0.597	LILRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140231.1	NM_181985		A	54822850	G	A	54822850	2	1	47	1	0	0	0	0	0	0	0	1	8797	987	35	3		3	LILRA5	19	54822850	Silent	SNP	G	TCGA-BC-A8YO-01A-11D-A36X-10	20097	54822850	4306133	61	6077										
EPN1	29924	hgsc.bcm.edu	37	chr19	56196948	56196948	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	ccctgctgcgcgacgaggacCggctgcgggaagagcgggcg	19	13	0	1	rs369409343		TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr19:56196948C>T	ENST00000270460.6	+	3	726	c.415C>T	c.(415-417)Cgg>Tgg	p.R139W	AC010525.2_ENST00000390145.1_RNA|EPN1_ENST00000411543.2_Missense_Mutation_p.R250W|EPN1_ENST00000591743.1_3'UTR|EPN1_ENST00000085079.7_Missense_Mutation_p.R139W	NM_001130072.1	NP_001123544.1	Q9Y6I3	EPN1_HUMAN	epsin 1	139	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|female pregnancy (GO:0007565)|in utero embryonic development (GO:0001701)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|Notch signaling pathway (GO:0007219)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	17		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)		CGACGAGGACCGGCTGCGGGA	0.667																																					p.R250W		Atlas-SNP	.											.	EPN1	98	.	0			c.C748T						.	C	TRP/ARG,TRP/ARG,TRP/ARG	0,4390		0,0,2195	34	38	37		748,415,415	2.6	1	19		37	1,8597		0,1,4298	no	missense,missense,missense	EPN1	NM_001130071.1,NM_001130072.1,NM_013333.3	101,101,101	0,1,6493	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	250/663,139/577,139/551	56196948	1,12987	2195	4299	6494	SO:0001583	missense	29924	exon4			GAGGACCGGCTGC	AF073727	CCDS46198.1, CCDS46199.1, CCDS46200.1	19q13.42	2014-08-12			ENSG00000063245	ENSG00000063245			21604	protein-coding gene	gene with protein product		607262				9723620, 10557078	Standard	NM_001130072		Approved		uc002qlx.3	Q9Y6I3	OTTHUMG00000180911	ENST00000270460.6:c.415C>T	chr19.hg19:g.56196948C>T	ENSP00000270460:p.Arg139Trp	66.0	0.0		118.0	47.0	NM_001130071	Q86ST3|Q9HA18	Missense_Mutation	SNP	ENST00000270460.6	hg19	CCDS46199.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.165868	0.57476	0.0	1.16E-4	ENSG00000063245	ENST00000270460;ENST00000085079;ENST00000544375;ENST00000411543	T;T;T	0.48836	0.8;0.8;0.8	4.74	2.63	0.31362	Epsin domain, N-terminal (1);ENTH/VHS (2);Epsin-like, N-terminal (2);	0.054891	0.64402	D	0.000002	T	0.73032	0.3535	H	0.96430	3.82	0.80722	D	1	D;P;D;B	0.89917	1.0;0.709;1.0;0.249	D;B;D;B	0.87578	0.998;0.055;0.998;0.022	T	0.75147	-0.3420	10	0.87932	D	0	-26.7111	5.7931	0.18371	0.1592:0.6664:0.0:0.1744	.	100;250;139;139	B4DU91;Q9Y6I3-1;Q9Y6I3;Q9Y6I3-3	.;.;EPN1_HUMAN;.	W	139;139;100;250	ENSP00000270460:R139W;ENSP00000085079:R139W;ENSP00000406209:R250W	ENSP00000085079:R139W	R	+	1	2	EPN1	60888760	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.744000	0.38268	1.377000	0.46286	0.555000	0.69702	CGG	.	.		0.667	EPN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453610.1	NM_013333		T	56196948	C	T	56196948	3	4	47	1	0	0	0	0	1	0	0	0	5187	643	23	1	762	1	EPN1	19	56196948	Missense_Mutation	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10	1374098	56196948	2932035	62	6078										
MCM5	4174	hgsc.bcm.edu	37	chr22	35802596	35802596	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	cctggcatcatcatcgcggcCtctgcggtccgtgccaaggc	12	16	3	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chr22:35802596C>T	ENST00000216122.4	+	5	628	c.474C>T	c.(472-474)gcC>gcT	p.A158A	MCM5_ENST00000382011.5_Silent_p.A115A	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	158					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						TCATCGCGGCCTCTGCGGTCC	0.602																																					p.A158A		Atlas-SNP	.											.	MCM5	54	.	0			c.C474T						.						86	65	72					22																	35802596		2203	4300	6503	SO:0001819	synonymous_variant	4174	exon5			CGCGGCCTCTGCG		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)", "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.474C>T	chr22.hg19:g.35802596C>T		33.0	0.0		55.0	25.0	NM_006739	O60785|Q14578|Q9BTJ4|Q9BWL8	Silent	SNP	ENST00000216122.4	hg19	CCDS13915.1																																																																																			.	.		0.602	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3			T	35802596	C	T	35802596	2	4	47	1	0	0	0	0	0	0	0	1	9399	668	24	3		3	MCM5	22	35802596	Silent	SNP	C	TCGA-BC-A8YO-01A-11D-A36X-10		35802596	15501970	63	6079										
MAOB	4129	hgsc.bcm.edu	37	chrX	43698229	43698229	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	3	1	1.28111111111111	3.66031746031746	0	0.166666666666667	0.751940625889747	0	caacataggatcctccaaggTccacatatttaaccttttgg	6	11	0	0			TCGA-BC-A8YO-01A-11D-A36X-10	TCGA-BC-A8YO-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	907824f7-f279-4739-823a-b02fe8e76822	fc2c7c4d-4ea8-465f-9c5f-cc21ac19a8ad	g.chrX:43698229T>A	ENST00000378069.4	-	3	311	c.164A>T	c.(163-165)gAc>gTc	p.D55V	MAOB_ENST00000487544.1_5'UTR|MAOB_ENST00000538942.1_Missense_Mutation_p.D39V|MAOB_ENST00000536181.1_Missense_Mutation_p.D39V	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	55					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	TCCTCCAAGGTCCACATATTT	0.363																																					p.D55V		Atlas-SNP	.											.	MAOB	52	.	0			c.A164T						.						113	97	103					X																	43698229		2203	4300	6503	SO:0001583	missense	4129	exon3			CCAAGGTCCACAT		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.164A>T	chrX.hg19:g.43698229T>A	ENSP00000367309:p.Asp55Val	102.0	0.0		70.0	51.0	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.027345	0.75390	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	T;T;T	0.20881	2.04;2.04;2.04	5.3	5.3	0.74995	Amine oxidase (1);	0.000000	0.85682	D	0.000000	T	0.59197	0.2176	H	0.95539	3.685	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.72956	-0.4134	10	0.87932	D	0	-26.0184	14.4948	0.67680	0.0:0.0:0.0:1.0	.	39;55;55	B7Z5H3;Q8TBI1;P27338	.;.;AOFB_HUMAN	V	55;39;39	ENSP00000367309:D55V;ENSP00000441613:D39V;ENSP00000442240:D39V	ENSP00000367309:D55V	D	-	2	0	MAOB	43583173	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	5.767000	0.68850	1.871000	0.54225	0.417000	0.27973	GAC	.	.		0.363	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		A	43698229	T	A	43698229	3	1	47	1	0	0	0	0	1	0	0	0	9235	1667	58	4	1450	4	MAOB	23	43698229	Missense_Mutation	SNP	T	TCGA-BC-A8YO-01A-11D-A36X-10		43698229	111572331	64	6080										
DNAJB4	11080	hgsc.bcm.edu	37	chr1	78479088	78479088	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ctcgaaaaaggctaaacgctGatggaaggagttacagatct	11	7	1	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr1:78479088G>A	ENST00000370763.5	+	2	822	c.565G>A	c.(565-567)Gat>Aat	p.D189N	DNAJB4_ENST00000487931.1_3'UTR|GIPC2_ENST00000476882.1_Intron	NM_007034.3	NP_008965.2	Q9UDY4	DNJB4_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 4	189					protein folding (GO:0006457)|response to heat (GO:0009408)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|unfolded protein binding (GO:0051082)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10						GCTAAACGCTGATGGAAGGAG	0.373																																					p.D189N		Atlas-SNP	.											.	DNAJB4	30	.	0			c.G565A						.						89	95	93					1																	78479088		2203	4300	6503	SO:0001583	missense	11080	exon2			AACGCTGATGGAA	U40992	CCDS684.1	1p31.1	2011-09-02			ENSG00000162616	ENSG00000162616		"Heat shock proteins / DNAJ (HSP40)"	14886	protein-coding gene	gene with protein product		611327				9546042, 11147971	Standard	NM_007034		Approved	HLJ1	uc001dij.3	Q9UDY4	OTTHUMG00000040905	ENST00000370763.5:c.565G>A	chr1.hg19:g.78479088G>A	ENSP00000359799:p.Asp189Asn	59.0	0.0		108.0	46.0	NM_007034	B2R824|Q13431	Missense_Mutation	SNP	ENST00000370763.5	hg19	CCDS684.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.829812	0.71258	.	.	ENSG00000162616	ENST00000370763	D	0.83673	-1.75	5.33	5.33	0.75918	HSP40/DnaJ peptide-binding (1);	0.000000	0.85682	D	0.000000	T	0.69314	0.3097	L	0.35341	1.055	0.80722	D	1	B	0.29378	0.243	B	0.29785	0.107	T	0.68716	-0.5335	10	0.35671	T	0.21	.	19.088	0.93213	0.0:0.0:1.0:0.0	.	189	Q9UDY4	DNJB4_HUMAN	N	189	ENSP00000359799:D189N	ENSP00000359799:D189N	D	+	1	0	DNAJB4	78251676	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	9.864000	0.99589	2.476000	0.83614	0.650000	0.86243	GAT	.	.		0.373	DNAJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098248.3			A	78479088	G	A	78479088	3	1	48	1	0	0	0	0	1	0	0	0	4624	1290	45	3	571	3	DNAJB4	1	78479088	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10		78479088	170771533	1	6081										
BCAN	63827	hgsc.bcm.edu	37	chr1	156618360	156618360	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gccttctcttctccacccagGagaactgttcctgggtgacc	9	15	2	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr1:156618360G>C	ENST00000329117.5	+	6	1106	c.770G>C	c.(769-771)gGa>gCa	p.G257A	RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Splice_Site_p.G257A	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	257	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ctccacCCAGGAGAACTGTTC	0.597																																					p.G257A		Atlas-SNP	.											.	BCAN	174	.	0			c.G770C						.						64	66	65					1																	156618360		2203	4300	6503	SO:0001630	splice_region_variant	63827	exon6			ACCCAGGAGAACT	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.770-1G>C	chr1.hg19:g.156618360G>C		75.0	0.0		85.0	32.0	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	G	14.41	2.527213	0.44969	.	.	ENSG00000132692	ENST00000255029;ENST00000329117;ENST00000424639;ENST00000361588	T;T;T	0.10099	2.91;2.91;2.91	4.65	4.65	0.58169	C-type lectin fold (1);Link (3);	0.000000	0.64402	D	0.000018	T	0.36690	0.0976	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.52290	-0.8595	9	.	.	.	.	16.2642	0.82565	0.0:0.0:1.0:0.0	.	257;257	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	A	198;257;155;257	ENSP00000331210:G257A;ENSP00000401709:G155A;ENSP00000354925:G257A	.	G	+	2	0	BCAN	154884984	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	9.648000	0.98483	2.415000	0.81967	0.555000	0.69702	GGA	.	.		0.597	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	Missense_Mutation	C	156618360	G	C	156618360	5	2	48	1	0	0	0	0	0	0	1	0	1345	1188	41	4	788	4	BCAN	1	156618360	Splice_Site	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	78139272	156618360	92632261	2	6082										
CD244	51744	hgsc.bcm.edu	37	chr1	160801203	160801203	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gcagggttctgggctttaggTtgactctttccaatctgcaa	11	9	3	1	rs146201991		TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr1:160801203T>G	ENST00000368033.3	-	9	1129	c.1047A>C	c.(1045-1047)caA>caC	p.Q349H	CD244_ENST00000481677.1_5'Flank|CD244_ENST00000368034.4_Missense_Mutation_p.Q344H|CD244_ENST00000322302.7_Missense_Mutation_p.Q252H			Q9BZW8	CD244_HUMAN	CD244 molecule, natural killer cell receptor 2B4	349					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(1)|large_intestine(3)|lung(12)|ovary(1)|urinary_tract(1)	18	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			GGGCTTTAGGTTGACTCTTTC	0.458																																					p.Q349H		Atlas-SNP	.											.	CD244	77	.	0			c.A1047C						.						124	121	122					1																	160801203		2203	4300	6503	SO:0001583	missense	51744	exon9			TTTAGGTTGACTC	AF105261	CCDS1210.1, CCDS53398.1, CCDS53399.1	1q23.1	2013-01-11	2006-03-29		ENSG00000122223	ENSG00000122223		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18171	protein-coding gene	gene with protein product		605554	"natural killer cell receptor 2B4", "CD244 natural killer cell receptor 2B4"			3772297, 10458320	Standard	NM_016382		Approved	2B4, NAIL, NKR2B4, Nmrk, SLAMF4	uc009wtq.3	Q9BZW8	OTTHUMG00000028606	ENST00000368033.3:c.1047A>C	chr1.hg19:g.160801203T>G	ENSP00000357012:p.Gln349His	74.0	0.0		115.0	17.0	NM_001166663	Q5VYI2|Q5VYI6|Q5VYI7|Q96T47|Q9NQD2|Q9NQD3|Q9Y288	Missense_Mutation	SNP	ENST00000368033.3	hg19	CCDS53399.1	.	.	.	.	.	.	.	.	.	.	t	11.37	1.619532	0.28801	.	.	ENSG00000122223	ENST00000368034;ENST00000368033;ENST00000322302	T;T;T	0.31247	3.52;2.93;1.5	3.83	-7.67	0.01272	.	3.115750	0.00960	N	0.003086	T	0.06050	0.0157	N	0.24115	0.695	0.09310	N	1	B;B;D	0.54601	0.248;0.0;0.967	B;B;P	0.46049	0.097;0.0;0.502	T	0.40365	-0.9567	10	0.25106	T	0.35	-19.522	2.4305	0.04470	0.2163:0.4013:0.2192:0.1632	.	252;349;344	Q9BZW8-4;Q9BZW8;Q9BZW8-2	.;CD244_HUMAN;.	H	344;349;252	ENSP00000357013:Q344H;ENSP00000357012:Q349H;ENSP00000313619:Q252H	ENSP00000313619:Q252H	Q	-	3	2	CD244	159067827	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.105000	0.01339	-2.682000	0.00408	-1.224000	0.01588	CAA	.	T|1.000;C|0.000		0.458	CD244-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071469.1	NM_016382		G	160801203	T	G	160801203	3	3	48	1	0	0	0	0	1	0	0	0	2989	1722	60	5	69	5	CD244	1	160801203	Missense_Mutation	SNP	T	TCGA-BD-A2L6-01A-11D-A20W-10	4182843	160801203	88449418	3	6083										
LRRN2	10446	hgsc.bcm.edu	37	chr1	204588961	204588961	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	caggaataggtcattgcagtCcacagtggtagcctcgcggt	13	10	1	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr1:204588961C>A	ENST00000367175.1	-	1	2372	c.160G>T	c.(160-162)Gac>Tac	p.D54Y	LRRN2_ENST00000367176.3_Missense_Mutation_p.D54Y|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367177.3_Missense_Mutation_p.D54Y			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	54	LRRNT.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			TCATTGCAGTCCACAGTGGTA	0.652																																					p.D54Y		Atlas-SNP	.											.	LRRN2	81	.	0			c.G160T						.						50	47	48					1																	204588961		2203	4300	6503	SO:0001583	missense	10446	exon3			TGCAGTCCACAGT	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"Immunoglobulin superfamily / I-set domain containing"	16914	protein-coding gene	gene with protein product	"leucine rich and ankyrin repeats 1", "fibronectin type III, immunoglobulin and leucine rich repeat domain 7"	605492	"leucine rich repeat neuronal 5"	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.160G>T	chr1.hg19:g.204588961C>A	ENSP00000356143:p.Asp54Tyr	80.0	0.0		83.0	36.0	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	hg19	CCDS1448.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.989520	0.74589	.	.	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.25414	1.8;1.8;1.8	5.53	5.53	0.82687	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.45126	D	0.000381	T	0.56426	0.1984	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60757	-0.7200	10	0.87932	D	0	.	19.1097	0.93312	0.0:1.0:0.0:0.0	.	54	O75325	LRRN2_HUMAN	Y	54	ENSP00000356144:D54Y;ENSP00000356145:D54Y;ENSP00000356143:D54Y	ENSP00000356143:D54Y	D	-	1	0	LRRN2	202855584	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.816000	0.86201	2.597000	0.87782	0.650000	0.86243	GAC	.	.		0.652	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338		A	204588961	C	A	204588961	3	1	48	1	0	0	0	0	1	0	0	0	9044	855	30	3	1985	3	LRRN2	1	204588961	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	43787758	204588961	44661660	4	6084										
CR1	1378	hgsc.bcm.edu	37	chr1	207739189	207739189	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	attttcttctttagatttcaAttaaaaggcagctctgctag	6	7	4	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr1:207739189A>G	ENST00000367049.4	+	24	3873	c.3873A>G	c.(3871-3873)caA>caG	p.Q1291Q	CR1_ENST00000400960.2_Silent_p.Q841Q|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367052.1_Intron|CR1_ENST00000367053.1_Silent_p.Q841Q|CR1_ENST00000367051.1_Silent_p.Q841Q	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	841	Sushi 20. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TTAGATTTCAATTAAAAGGCA	0.413																																					p.Q1291Q		Atlas-SNP	.											.	CR1	354	.	0			c.A3873G						.						255	225	234					1																	207739189		1821	4092	5913	SO:0001819	synonymous_variant	1378	exon24			ATTTCAATTAAAA	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.3873A>G	chr1.hg19:g.207739189A>G		379.0	0.0		525.0	218.0	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	hg19	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	a	9.830	1.188053	0.21954	.	.	ENSG00000203710	ENST00000529814	.	.	.	2.72	-5.44	0.02624	.	.	.	.	.	T	0.16811	0.0404	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.22730	-1.0208	4	.	.	.	.	1.3663	0.02202	0.2803:0.1695:0.3832:0.167	.	.	.	.	S	367	.	.	N	+	2	0	CR1	205805812	0.000000	0.05858	0.000000	0.03702	0.807000	0.45602	-1.367000	0.02583	-1.411000	0.02032	0.254000	0.18369	AAT	.	.		0.413	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		G	207739189	A	G	207739189	2	3	48	1	0	0	0	0	0	0	0	1	3842	98	4	2		2	CR1	1	207739189	Silent	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	3150228	207739189	41511432	5	6085										
SLC30A1	7779	hgsc.bcm.edu	37	chr1	211749145	211749145	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gttgccaaacatgtaattcaTgaacttcctcaactccttca	4	12	3	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr1:211749145T>A	ENST00000367001.4	-	2	1238	c.1109A>T	c.(1108-1110)cAt>cTt	p.H370L		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	370					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		ATGTAATTCATGAACTTCCTC	0.358																																					p.H370L		Atlas-SNP	.											.	SLC30A1	27	.	0			c.A1109T						.						81	79	80					1																	211749145		2203	4300	6503	SO:0001583	missense	7779	exon2			AATTCATGAACTT	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.1109A>T	chr1.hg19:g.211749145T>A	ENSP00000355968:p.His370Leu	39.0	0.0		60.0	25.0	NM_021194	Q0VAK9|Q9BZF6	Missense_Mutation	SNP	ENST00000367001.4	hg19	CCDS1499.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327221	0.81690	.	.	ENSG00000170385	ENST00000367001	T	0.61274	0.12	5.69	5.69	0.88448	.	0.090564	0.85682	D	0.000000	D	0.82939	0.5146	H	0.95328	3.655	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	D	0.88299	0.2948	10	0.87932	D	0	-9.5283	15.9538	0.79865	0.0:0.0:0.0:1.0	.	370	Q9Y6M5	ZNT1_HUMAN	L	370	ENSP00000355968:H370L	ENSP00000355968:H370L	H	-	2	0	SLC30A1	209815768	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.748000	0.85085	2.170000	0.68504	0.460000	0.39030	CAT	.	.		0.358	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			A	211749145	T	A	211749145	3	1	48	1	0	0	0	0	1	0	0	0	14568	1464	51	4	418	4	SLC30A1	1	211749145	Missense_Mutation	SNP	T	TCGA-BD-A2L6-01A-11D-A20W-10	4009956	211749145	37501476	6	6086										
USH2A	7399	hgsc.bcm.edu	37	chr1	216420124	216420124	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gaagacctgttacccctaatTtgcaaggacattgtcctgtt	8	10	0	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr1:216420124T>A	ENST00000307340.3	-	13	2998	c.2612A>T	c.(2611-2613)aAa>aTa	p.K871I	USH2A_ENST00000366942.3_Missense_Mutation_p.K871I|USH2A_ENST00000366943.2_Missense_Mutation_p.K871I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	871	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TACCCCTAATTTGCAAGGACA	0.423										HNSCC(13;0.011)																											p.K871I		Atlas-SNP	.											.	USH2A	1168	.	0			c.A2612T						.						235	212	220					1																	216420124		2203	4300	6503	SO:0001583	missense	7399	exon13			CCTAATTTGCAAG	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.2612A>T	chr1.hg19:g.216420124T>A	ENSP00000305941:p.Lys871Ile	157.0	0.0		236.0	86.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.983905	0.74474	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.64618	-0.11;-0.11;-0.11	6.03	4.91	0.64330	EGF-like, laminin (4);	0.000000	0.45867	D	0.000332	D	0.85075	0.5614	H	0.97390	3.995	0.44890	D	0.9979	D;D	0.69078	0.975;0.997	P;D	0.71870	0.805;0.975	D	0.88746	0.3247	10	0.87932	D	0	.	11.9264	0.52823	0.0:0.0673:0.0:0.9327	.	871;871	O75445-2;O75445	.;USH2A_HUMAN	I	871	ENSP00000305941:K871I;ENSP00000355910:K871I;ENSP00000355909:K871I	ENSP00000305941:K871I	K	-	2	0	USH2A	214486747	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	4.270000	0.58896	1.112000	0.41740	0.533000	0.62120	AAA	.	.		0.423	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216420124	T	A	216420124	3	1	48	1	0	0	0	0	1	0	0	0	17051	1841	64	4	13250	4	USH2A	1	216420124	Missense_Mutation	SNP	T	TCGA-BD-A2L6-01A-11D-A20W-10	4670979	216420124	32830497	7	6087										
SOS1	6654	hgsc.bcm.edu	37	chr2	39213099	39213099	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ttgtcgtggaggaacaggcgGcccagcaatggaatgaaggt	16	7	0	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr2:39213099G>A	ENST00000426016.1	-	24	3954	c.3868C>T	c.(3868-3870)Ccg>Tcg	p.P1290S	SOS1_ENST00000395038.2_Missense_Mutation_p.P1275S|SOS1_ENST00000402219.2_Missense_Mutation_p.P1290S			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	1290					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				GGAACAGGCGGCCCAGCAATG	0.507									Noonan syndrome																												p.P1290S		Atlas-SNP	.											.	SOS1	134	.	0			c.C3868T						.						266	239	248					2																	39213099		2203	4300	6503	SO:0001583	missense	6654	exon23	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CAGGCGGCCCAGC	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.3868C>T	chr2.hg19:g.39213099G>A	ENSP00000387784:p.Pro1290Ser	426.0	0.0		536.0	206.0	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	hg19	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099887	0.56183	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038	D;D;D	0.84944	-1.92;-1.92;-1.81	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.82176	0.4980	L	0.55990	1.75	0.80722	D	1	P	0.39809	0.689	B	0.33254	0.16	D	0.84644	0.0697	10	0.62326	D	0.03	.	18.8284	0.92127	0.0:0.0:1.0:0.0	.	1290	Q07889	SOS1_HUMAN	S	1290;1290;1007;1275	ENSP00000387784:P1290S;ENSP00000384675:P1290S;ENSP00000378479:P1275S	ENSP00000378479:P1275S	P	-	1	0	SOS1	39066603	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	6.554000	0.73923	2.677000	0.91161	0.563000	0.77884	CCG	.	.		0.507	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		A	39213099	G	A	39213099	3	1	48	1	0	0	0	0	1	0	0	0	14951	1203	42	3	137	3	SOS1	2	39213099	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10		39213099	203986274	8	6088										
GPR75	10936	hgsc.bcm.edu	37	chr2	54081699	54081699	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	aaggctggatcgaagaaggaCaagaagacaatgaagttgcc	13	6	0	4			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr2:54081699C>T	ENST00000394705.2	-	2	465	c.195G>A	c.(193-195)ttG>ttA	p.L65L	ASB3_ENST00000498475.2_Intron|GPR75-ASB3_ENST00000352846.3_Intron|ASB3_ENST00000406625.2_Intron	NM_006794.3	NP_006785.1	O95800	GPR75_HUMAN	G protein-coupled receptor 75	65	Phe-rich.				chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of neuron death (GO:1901214)	integral component of plasma membrane (GO:0005887)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CGAAGAAGGACAAGAAGACAA	0.478																																					p.L65L		Atlas-SNP	.											.	GPR75	55	.	0			c.G195A						.						60	56	57					2																	54081699		2203	4300	6503	SO:0001819	synonymous_variant	10936	exon2			GAAGGACAAGAAG	AF101472	CCDS1849.1	2p16	2012-08-21			ENSG00000119737	ENSG00000119737		"GPCR / Class A : Orphans"	4526	protein-coding gene	gene with protein product		606704				10381362	Standard	NM_006794		Approved	WI-31133	uc002rxo.3	O95800	OTTHUMG00000129280	ENST00000394705.2:c.195G>A	chr2.hg19:g.54081699C>T		174.0	0.0		230.0	96.0	NM_006794	B2RC02|Q6NWR2	Silent	SNP	ENST00000394705.2	hg19	CCDS1849.1																																																																																			.	.		0.478	GPR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251403.2			T	54081699	C	T	54081699	2	4	48	1	0	0	0	0	0	0	0	1	6716	477	17	3		3	GPR75	2	54081699	Silent	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	14868600	54081699	189117674	9	6089										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71592562	71592563	+	Frame_Shift_Ins	INS	-	-	A													0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tatatctttttactagatagINSaaaaaaagcattagaagatg							TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr2:71592562_71592563insA	ENST00000409544.1	+	6	2351_2352	c.1721_1722insA	c.(1720-1725)agaaaafs	p.RK574fs	ZNF638_ENST00000355812.3_Frame_Shift_Ins_p.RK574fs|ZNF638_ENST00000264447.4_Frame_Shift_Ins_p.RK574fs|ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000377802.2_Frame_Shift_Ins_p.RK574fs	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	574	Arg-rich.				regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TTACTAGATAGAAAAAAAGCAT	0.342																																					p.R574fs		Atlas-INDEL	.											.	ZNF638	179	.	0			c.1721_1722insA						.																																			SO:0001589	frameshift_variant	27332	exon6			.	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.1728dupA	chr2.hg19:g.71592569_71592569dupA	ENSP00000386433:p.Arg574fs	31.0	0.0		65.0	23.0	NM_001252612	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Frame_Shift_Ins	INS	ENST00000409544.1	hg19	CCDS1917.1																																																																																			.	.		0.342	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		A	71592563	-	A	71592562	7	5	48	1	0	1	1	0	0	0	0	0	18070	942	33	0	1739	0	ZNF638	2	71592562	Frame_Shift_Ins	INS	-	TCGA-BD-A2L6-01A-11D-A20W-10	17510863	71592562	171606811	10	6090										
NCKAP1	10787	hgsc.bcm.edu	37	chr2	183847561	183847561	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	taacttacttatctataaagTcgtctgcactcttctttggc	5	10	4	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr2:183847561T>C	ENST00000361354.4	-	12	1568	c.1196A>G	c.(1195-1197)gAc>gGc	p.D399G	NCKAP1_ENST00000360982.2_Missense_Mutation_p.D405G	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	399					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			ATCTATAAAGTCGTCTGCACT	0.343																																					p.D405G		Atlas-SNP	.											.	NCKAP1	105	.	0			c.A1214G						.						39	38	38					2																	183847561		2202	4300	6502	SO:0001583	missense	10787	exon13			ATAAAGTCGTCTG	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.1196A>G	chr2.hg19:g.183847561T>C	ENSP00000355348:p.Asp399Gly	109.0	0.0		208.0	93.0	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Missense_Mutation	SNP	ENST00000361354.4	hg19	CCDS2287.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.647551	0.87958	.	.	ENSG00000061676	ENST00000361354;ENST00000360982	T;T	0.44482	0.92;0.92	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.65729	0.2719	M	0.84683	2.71	0.80722	D	1	D;D	0.63880	0.993;0.991	P;P	0.61275	0.886;0.818	T	0.72666	-0.4224	10	0.72032	D	0.01	-11.9836	15.2429	0.73485	0.0:0.0:0.0:1.0	.	399;405	Q9Y2A7;Q9Y2A7-2	NCKP1_HUMAN;.	G	399;405	ENSP00000355348:D399G;ENSP00000354251:D405G	ENSP00000354251:D405G	D	-	2	0	NCKAP1	183555806	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.019000	0.88732	2.011000	0.59026	0.533000	0.62120	GAC	.	.		0.343	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		C	183847561	T	C	183847561	3	2	48	1	0	0	0	0	1	0	0	0	10230	1667	58	2	2270	2	NCKAP1	2	183847561	Missense_Mutation	SNP	T	TCGA-BD-A2L6-01A-11D-A20W-10	112254999	183847561	59351812	11	6091										
SPEG	10290	hgsc.bcm.edu	37	chr2	220354314	220354314	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ctgcaggctgcccggccagcGgagcccaccctacccagtac	11	19	0	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr2:220354314G>A	ENST00000312358.7	+	36	8706	c.8574G>A	c.(8572-8574)gcG>gcA	p.A2858A	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2858	Pro-rich.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CCCGGCCAGCGGAGCCCACCC	0.652																																					p.A2858A		Atlas-SNP	.											.	SPEG	272	.	0			c.G8574A						.						81	90	87					2																	220354314		1991	4134	6125	SO:0001819	synonymous_variant	10290	exon36			GCCAGCGGAGCCC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.8574G>A	chr2.hg19:g.220354314G>A		88.0	0.0		109.0	34.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.652	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220354314	G	A	220354314	2	1	48	1	0	0	0	0	0	0	0	1	15051	1103	39	1		1	SPEG	2	220354314	Silent	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	36506753	220354314	22845059	12	6092										
PTPN23	25930	hgsc.bcm.edu	37	chr3	47453376	47453376	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	cagcaccgaaacccatgtggAgcgcgtgctgagcctgcagt	13	13	0	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr3:47453376A>T	ENST00000265562.4	+	21	4069	c.3992A>T	c.(3991-3993)gAg>gTg	p.E1331V	PTPN23_ENST00000431726.1_Missense_Mutation_p.E1205V	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1331	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACCCATGTGGAGCGCGTGCTG	0.627																																					p.E1331V		Atlas-SNP	.											.	PTPN23	85	.	0			c.A3992T						.						67	60	63					3																	47453376		2203	4300	6503	SO:0001583	missense	25930	exon21			ATGTGGAGCGCGT	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.3992A>T	chr3.hg19:g.47453376A>T	ENSP00000265562:p.Glu1331Val	169.0	0.0		226.0	93.0	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	hg19	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	A	17.18	3.323313	0.60634	.	.	ENSG00000076201	ENST00000265562	T	0.81163	-1.46	4.34	4.34	0.51931	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.064498	0.64402	D	0.000014	T	0.80665	0.4666	N	0.12920	0.275	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.83812	0.0242	10	0.87932	D	0	-23.649	12.6697	0.56860	1.0:0.0:0.0:0.0	.	1331	Q9H3S7	PTN23_HUMAN	V	1331	ENSP00000265562:E1331V	ENSP00000265562:E1331V	E	+	2	0	PTPN23	47428380	1.000000	0.71417	0.951000	0.38953	0.205000	0.24178	8.580000	0.90784	1.824000	0.53156	0.460000	0.39030	GAG	.	.		0.627	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		T	47453376	A	T	47453376	3	4	48	1	0	0	0	0	1	0	0	0	12803	304	11	4	4074	4	PTPN23	3	47453376	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10		47453376	150569054	13	6093										
USP19	10869	hgsc.bcm.edu	37	chr3	49153563	49153563	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	cgatgcgagaagccgtgaaaCagaaggtgcactgctctggc	14	10	1	3			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr3:49153563C>T	ENST00000398888.2	-	9	1403	c.1085G>A	c.(1084-1086)tGt>tAt	p.C362Y	USP19_ENST00000434032.2_Missense_Mutation_p.C463Y|USP19_ENST00000398898.2_Missense_Mutation_p.C400Y|USP19_ENST00000488993.1_5'Flank|USP19_ENST00000453664.1_Missense_Mutation_p.C453Y|USP19_ENST00000398892.3_Missense_Mutation_p.C400Y|USP19_ENST00000417901.1_Missense_Mutation_p.C463Y|USP19_ENST00000398896.1_Missense_Mutation_p.C168Y	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	362	CS 2. {ECO:0000255|PROSITE- ProRule:PRU00547}.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGCCGTGAAACAGAAGGTGCA	0.582																																					p.C463Y		Atlas-SNP	.											.	USP19	158	.	0			c.G1388A						.						38	40	39					3																	49153563		2052	4201	6253	SO:0001583	missense	10869	exon10			GTGAAACAGAAGG	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"Zinc fingers, MYND-type", "Ubiquitin-specific peptidases"	12617	protein-coding gene	gene with protein product		614471	"ubiquitin specific protease 19"			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.1085G>A	chr3.hg19:g.49153563C>T	ENSP00000381863:p.Cys362Tyr	100.0	0.0		177.0	80.0	NM_001199160	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	hg19	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	C	15.30	2.791609	0.50102	.	.	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032;ENST00000306026;ENST00000425298	T;T;T;T;T;T;T;T	0.13901	2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55	5.92	4.95	0.65309	Domain of unknown function DUF1872 (1);CS-like domain (1);HSP20-like chaperone (1);	0.274056	0.47852	D	0.000211	T	0.10766	0.0263	L	0.29908	0.895	0.34642	D	0.720707	P;P;P;P;P;P;P	0.44241	0.615;0.829;0.615;0.565;0.635;0.785;0.565	B;B;B;B;B;B;B	0.41917	0.37;0.296;0.296;0.229;0.323;0.254;0.213	T	0.05500	-1.0881	10	0.59425	D	0.04	-15.4006	7.5374	0.27719	0.0:0.8206:0.0:0.1794	.	526;463;453;362;400;448;168	A5PKX8;E9PEG8;E7EN22;O94966;B5MEG5;O94966-2;E7ESU0	.;.;.;UBP19_HUMAN;.;.;.	Y	168;400;463;453;400;362;463;448;448	ENSP00000381870:C168Y;ENSP00000381872:C400Y;ENSP00000395260:C463Y;ENSP00000400090:C453Y;ENSP00000381867:C400Y;ENSP00000381863:C362Y;ENSP00000401197:C463Y;ENSP00000303503:C448Y	ENSP00000303503:C448Y	C	-	2	0	USP19	49128567	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.453000	0.52978	2.818000	0.97014	0.655000	0.94253	TGT	.	.		0.582	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		T	49153563	C	T	49153563	3	4	48	1	0	0	0	0	1	0	0	0	17065	478	17	3	2943	3	USP19	3	49153563	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	1700187	49153563	148868867	14	6094										
TF	7018	hgsc.bcm.edu	37	chr3	133476711	133476712	+	Frame_Shift_Ins	INS	-	-	G													0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ctgcccacgggtttttaaaaINSgtcccccccaggatggatgc							TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr3:133476711_133476712insG	ENST00000402696.3	+	8	1454_1455	c.969_970insG	c.(970-972)gtcfs	p.V324fs	TF_ENST00000264998.3_Frame_Shift_Ins_p.V197fs	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	324	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	GGTTTTTAAAAGTCCCCCCCAG	0.485																																					p.K323fs		Atlas-INDEL	.											.	TF	116	.	0			c.969_970insG						.																																			SO:0001589	frameshift_variant	7018	exon8			.		CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.970dupG	chr3.hg19:g.133476712_133476712dupG	ENSP00000385834:p.Val324fs	99.0	0.0		153.0	54.0	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Frame_Shift_Ins	INS	ENST00000402696.3	hg19	CCDS3080.1																																																																																			.	.		0.485	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063		G	133476712	-	G	133476711	7	5	48	1	0	1	1	0	0	0	0	0	15800	69	3	0	999	0	TF	3	133476711	Frame_Shift_Ins	INS	-	TCGA-BD-A2L6-01A-11D-A20W-10	84323148	133476711	64545719	15	6095										
G3BP2	9908	hgsc.bcm.edu	37	chr4	76579227	76579227	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gaagaaacagtaccactaggAggcaggtttttactggtcac	11	8	1	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr4:76579227A>C	ENST00000359707.4	-	8	1550	c.765T>G	c.(763-765)ccT>ccG	p.P255P	G3BP2_ENST00000502654.1_5'Flank|G3BP2_ENST00000395719.3_Silent_p.P255P|G3BP2_ENST00000357854.3_Intron	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	GTPase activating protein (SH3 domain) binding protein 2	255					cytoplasmic sequestering of NF-kappaB (GO:0007253)|mRNA transport (GO:0051028)|Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|receptor signaling complex scaffold activity (GO:0030159)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TACCACTAGGAGGCAGGTTTT	0.448																																					p.P255P		Atlas-SNP	.											.	G3BP2	52	.	0			c.T765G						.						86	84	85					4																	76579227		2203	4300	6503	SO:0001819	synonymous_variant	9908	exon8			ACTAGGAGGCAGG	AB014560	CCDS3571.1, CCDS3572.1	4q21.1	2013-02-12	2006-11-01		ENSG00000138757	ENSG00000138757		"RNA binding motif (RRM) containing"	30291	protein-coding gene	gene with protein product	"Ras-GTPase activating protein SH3 domain-binding protein 2"					9734811, 9575347	Standard	NM_203504		Approved	KIAA0660	uc003his.3	Q9UN86	OTTHUMG00000130097	ENST00000359707.4:c.765T>G	chr4.hg19:g.76579227A>C		57.0	0.0		43.0	29.0	NM_012297	A8K6X1|O60606|O75149|Q9UPA1	Silent	SNP	ENST00000359707.4	hg19	CCDS3571.1																																																																																			.	.		0.448	G3BP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252399.2	NM_012297		C	76579227	A	C	76579227	2	2	48	1	0	0	0	0	0	0	0	1	6150	291	11	5		5	G3BP2	4	76579227	Silent	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10		76579227	114575049	16	6096										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85711036	85711036	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	atgggagaatttcataaaatGaggactcttcactaaaatca	7	6	4	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr4:85711036G>A	ENST00000295888.4	-	22	3919	c.3512C>T	c.(3511-3513)tCa>tTa	p.S1171L	WDFY3_ENST00000322366.6_Missense_Mutation_p.S1171L	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1171					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TTCATAAAATGAGGACTCTTC	0.398																																					p.S1171L		Atlas-SNP	.											.	WDFY3	314	.	0			c.C3512T						.						84	83	84					4																	85711036		2203	4300	6503	SO:0001583	missense	23001	exon22			TAAAATGAGGACT	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.3512C>T	chr4.hg19:g.85711036G>A	ENSP00000295888:p.Ser1171Leu	139.0	1.0		113.0	82.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.365241	0.61513	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.67345	-0.26;-0.26	4.85	4.85	0.62838	Concanavalin A-like lectin/glucanase (1);	0.056192	0.64402	D	0.000001	T	0.60431	0.2268	L	0.41824	1.3	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	T	0.56667	-0.7941	10	0.40728	T	0.16	.	18.3293	0.90263	0.0:0.0:1.0:0.0	.	1171	Q8IZQ1	WDFY3_HUMAN	L	1171	ENSP00000318466:S1171L;ENSP00000295888:S1171L	ENSP00000295888:S1171L	S	-	2	0	WDFY3	85930060	1.000000	0.71417	0.981000	0.43875	0.978000	0.69477	7.580000	0.82523	2.365000	0.80145	0.561000	0.74099	TCA	.	.		0.398	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85711036	G	A	85711036	3	1	48	1	0	0	0	0	1	0	0	0	17285	1294	45	3	7256	3	WDFY3	4	85711036	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	9131809	85711036	105443240	17	6097										
MAD2L1	4085	hgsc.bcm.edu	37	chr4	120982128	120982128	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tttctgagacttttctctggGtgcactgtcaaaaaaaaatc	7	8	3	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr4:120982128G>T	ENST00000296509.6	-	4	685	c.346C>A	c.(346-348)Ccc>Acc	p.P116T		NM_002358.3	NP_002349.1	Q13257	MD2L1_HUMAN	MAD2 mitotic arrest deficient-like 1 (yeast)	116	HORMA. {ECO:0000255|PROSITE- ProRule:PRU00109}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(2)|kidney(2)|large_intestine(2)|lung(3)	9						TTTTCTCTGGGTGCACTGTCA	0.353																																					p.P116T		Atlas-SNP	.											.	MAD2L1	17	.	0			c.C346A						.						50	50	50					4																	120982128		2203	4298	6501	SO:0001583	missense	4085	exon4			CTCTGGGTGCACT	U65410	CCDS3715.1	4q27	2013-01-17	2001-11-28		ENSG00000164109	ENSG00000164109			6763	protein-coding gene	gene with protein product		601467	"MAD2 (mitotic arrest deficient, yeast, homolog)-like 1"			8824189, 9345911	Standard	NM_002358		Approved	MAD2, HSMAD2	uc003idl.2	Q13257	OTTHUMG00000132967	ENST00000296509.6:c.346C>A	chr4.hg19:g.120982128G>T	ENSP00000296509:p.Pro116Thr	113.0	0.0		156.0	62.0	NM_002358	Q53F56|Q548X9|Q6IRW7|Q8IZX3	Missense_Mutation	SNP	ENST00000296509.6	hg19	CCDS3715.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.470958	0.43942	.	.	ENSG00000164109	ENST00000296509	.	.	.	5.16	4.31	0.51392	DNA-binding HORMA (4);	0.173317	0.52532	D	0.000073	T	0.45994	0.1370	L	0.38953	1.18	0.53688	D	0.99997	B	0.32939	0.391	B	0.33295	0.161	T	0.31280	-0.9949	9	0.13108	T	0.6	-3.5224	14.5615	0.68140	0.0:0.2774:0.7226:0.0	.	116	Q13257	MD2L1_HUMAN	T	116	.	ENSP00000296509:P116T	P	-	1	0	MAD2L1	121201576	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.892000	0.63193	1.283000	0.44513	0.561000	0.74099	CCC	.	.		0.353	MAD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256525.2			T	120982128	G	T	120982128	3	4	48	1	0	0	0	0	1	0	0	0	9157	1261	44	3	279	3	MAD2L1	4	120982128	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	35271092	120982128	70172148	18	6098										
SPEF2	79925	hgsc.bcm.edu	37	chr5	35793440	35793440	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	atcacttttgagcagtatatGcaggttgttaccagcacctg	9	9	1	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr5:35793440G>T	ENST00000356031.3	+	32	4888	c.4734G>T	c.(4732-4734)atG>atT	p.M1578I	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000440995.2_Missense_Mutation_p.M1573I|SPEF2_ENST00000303129.4_Missense_Mutation_p.M375I	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1578					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AGCAGTATATGCAGGTTGTTA	0.478																																					p.M1578I		Atlas-SNP	.											.	SPEF2	324	.	0			c.G4734T						.						86	89	88					5																	35793440		2050	4184	6234	SO:0001583	missense	79925	exon32			GTATATGCAGGTT	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.4734G>T	chr5.hg19:g.35793440G>T	ENSP00000348314:p.Met1578Ile	161.0	0.0		202.0	71.0	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	hg19	CCDS43309.1	.	.	.	.	.	.	.	.	.	.	G	12.70	2.017307	0.35606	.	.	ENSG00000152582	ENST00000356031;ENST00000440995;ENST00000303129	T;T;T	0.62232	0.04;0.04;0.04	5.88	1.86	0.25419	.	0.918493	0.09581	N	0.782820	T	0.49779	0.1577	L	0.40543	1.245	0.24303	N	0.995118	B;B;B	0.32968	0.392;0.019;0.003	B;B;B	0.34093	0.175;0.004;0.002	T	0.40850	-0.9541	10	0.38643	T	0.18	.	5.5934	0.17313	0.2149:0.0:0.5432:0.2419	.	375;1573;1578	Q9C093-4;Q9C093-2;Q9C093	.;.;SPEF2_HUMAN	I	1578;1573;375	ENSP00000348314:M1578I;ENSP00000412125:M1573I;ENSP00000303843:M375I	ENSP00000303843:M375I	M	+	3	0	SPEF2	35829197	0.962000	0.33011	0.999000	0.59377	0.989000	0.77384	0.304000	0.19228	0.830000	0.34757	-0.150000	0.13652	ATG	.	.		0.478	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		T	35793440	G	T	35793440	3	4	48	1	0	0	0	0	1	0	0	0	15050	1319	46	3	4881	3	SPEF2	5	35793440	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10		35793440	145121820	19	6099										
SLC38A9	153129	hgsc.bcm.edu	37	chr5	54952566	54952566	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ggttgctattattggtactcAgtatagtgtctgtgtcatta	10	5	3	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr5:54952566A>C	ENST00000396865.2	-	9	1325	c.734T>G	c.(733-735)cTg>cGg	p.L245R	SLC38A9_ENST00000318672.3_Missense_Mutation_p.L245R|SLC38A9_ENST00000515629.1_Missense_Mutation_p.L182R|SLC38A9_ENST00000539768.1_Missense_Mutation_p.L245R|SLC38A9_ENST00000512595.1_Missense_Mutation_p.L218R|SLC38A9_ENST00000416547.2_Missense_Mutation_p.L121R	NM_173514.3	NP_775785.2	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	245					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				ATTGGTACTCAGTATAGTGTC	0.323																																					p.L245R		Atlas-SNP	.											.	SLC38A9	50	.	0			c.T734G						.						112	109	110					5																	54952566		2201	4299	6500	SO:0001583	missense	153129	exon9			GTACTCAGTATAG		CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058		"Solute carriers"	26907	protein-coding gene	gene with protein product							Standard	NM_173514		Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000396865.2:c.734T>G	chr5.hg19:g.54952566A>C	ENSP00000380074:p.Leu245Arg	86.0	0.0		107.0	38.0	NM_173514	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	Missense_Mutation	SNP	ENST00000396865.2	hg19	CCDS3968.1	.	.	.	.	.	.	.	.	.	.	A	14.32	2.501485	0.44455	.	.	ENSG00000177058	ENST00000396865;ENST00000318672;ENST00000539768;ENST00000515629;ENST00000416547;ENST00000512595;ENST00000512208	T;T;T;T;T;T;T	0.50813	1.82;1.82;0.81;1.85;1.85;1.37;0.73	6.01	1.13	0.20643	.	0.368947	0.31648	N	0.007297	T	0.44953	0.1318	L	0.43152	1.355	0.39951	D	0.974538	P;P	0.43633	0.813;0.602	P;B	0.51055	0.657;0.354	T	0.26018	-1.0115	10	0.27082	T	0.32	-3.5205	7.9605	0.30068	0.5489:0.0:0.4511:0.0	.	218;245	B3KXV1;Q8NBW4	.;S38A9_HUMAN	R	245;245;245;182;121;218;182	ENSP00000380074:L245R;ENSP00000316596:L245R;ENSP00000437771:L245R;ENSP00000420934:L182R;ENSP00000397429:L121R;ENSP00000427335:L218R;ENSP00000426413:L182R	ENSP00000316596:L245R	L	-	2	0	SLC38A9	54988323	0.992000	0.36948	0.508000	0.27688	0.832000	0.47134	1.265000	0.33027	0.181000	0.19994	0.523000	0.50628	CTG	.	.		0.323	SLC38A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253912.2	NM_173514		C	54952566	A	C	54952566	3	2	48	1	0	0	0	0	1	0	0	0	14626	188	7	5	983	5	SLC38A9	5	54952566	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	19159126	54952566	125962694	20	6100										
CDKN1A	1026	hgsc.bcm.edu	37	chr6	36652024	36652024	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ccaggaggcccgtgagcgatGgaacttcgactttgtcaccg	13	12	1	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr6:36652024G>T	ENST00000405375.1	+	2	381	c.146G>T	c.(145-147)tGg>tTg	p.W49L	CDKN1A_ENST00000244741.5_Missense_Mutation_p.W49L|CDKN1A_ENST00000448526.2_Missense_Mutation_p.W83L|CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000373711.2_Missense_Mutation_p.W49L	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	49					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)	p.W49*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						CGTGAGCGATGGAACTTCGAC	0.667																																					p.W49L		Atlas-SNP	.											CDKN1A,bladder,carcinoma,0,2	CDKN1A	27	.	1	Substitution - Nonsense(1)	urinary_tract(1)	c.G146T						.						57	51	53					6																	36652024		2203	4300	6503	SO:0001583	missense	1026	exon2			AGCGATGGAACTT	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.146G>T	chr6.hg19:g.36652024G>T	ENSP00000384849:p.Trp49Leu	32.0	0.0		78.0	44.0	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	hg19	CCDS4824.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.733646	0.89482	.	.	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68	5.06	5.06	0.68205	.	0.000000	0.49916	D	0.000129	D	0.95484	0.8533	M	0.90252	3.1	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.986;0.993	D	0.95850	0.8874	10	0.87932	D	0	-33.4034	13.8081	0.63246	0.0:0.0:1.0:0.0	.	83;49;49	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	L	83;49;49;49	ENSP00000409259:W83L;ENSP00000244741:W49L;ENSP00000384849:W49L;ENSP00000362815:W49L	ENSP00000244741:W49L	W	+	2	0	CDKN1A	36760002	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	6.535000	0.73838	2.642000	0.89623	0.561000	0.74099	TGG	.	.		0.667	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467		T	36652024	G	T	36652024	3	4	48	1	0	0	0	0	1	0	0	0	3160	1357	47	3	148	3	CDKN1A	6	36652024	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10		36652024	134463043	21	6101										
KLHL32	114792	hgsc.bcm.edu	37	chr6	97562045	97562045	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	atgcctgtgggaaggagccaCcattgtgtggcagtcatggg	16	8	1	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr6:97562045C>A	ENST00000369261.4	+	7	1377	c.1014C>A	c.(1012-1014)caC>caA	p.H338Q	KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000539200.1_Missense_Mutation_p.H269Q|KLHL32_ENST00000536676.1_Missense_Mutation_p.H302Q	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	338										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		GAAGGAGCCACCATTGTGTGG	0.562																																					p.H338Q		Atlas-SNP	.											.	KLHL32	85	.	0			c.C1014A						.						93	89	90					6																	97562045		2203	4300	6503	SO:0001583	missense	114792	exon7			GAGCCACCATTGT	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"Kelch-like", "BTB/POZ domain containing"	21221	protein-coding gene	gene with protein product			"BTB and kelch domain containing 5", "KIAA1900", "kelch-like 32 (Drosophila)"	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.1014C>A	chr6.hg19:g.97562045C>A	ENSP00000358265:p.His338Gln	43.0	0.0		81.0	25.0	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	hg19	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.735171	0.30774	.	.	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200	T;T;T	0.66815	-0.23;-0.23;-0.23	5.36	3.19	0.36642	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.49864	0.1582	L	0.31664	0.95	0.80722	D	1	D;D;P;D	0.89917	0.988;0.999;0.647;1.0	P;D;P;D	0.87578	0.875;0.996;0.621;0.998	T	0.55095	-0.8194	10	0.06757	T	0.87	.	8.1486	0.31126	0.0:0.7176:0.0:0.2824	.	269;302;338;338	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	Q	338;302;269	ENSP00000358265:H338Q;ENSP00000440382:H302Q;ENSP00000441527:H269Q	ENSP00000358265:H338Q	H	+	3	2	KLHL32	97668766	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	0.538000	0.23160	0.561000	0.29186	0.655000	0.94253	CAC	.	.		0.562	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		A	97562045	C	A	97562045	3	1	48	1	0	0	0	0	1	0	0	0	8395	506	18	3	1036	3	KLHL32	6	97562045	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	60910021	97562045	73553022	22	6102										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129571345	129571345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	agaacgtgttctccagcttaTgattatcttagaggtagagt	10	6	2	4			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr6:129571345T>C	ENST00000421865.2	+	13	1920	c.1871T>C	c.(1870-1872)aTg>aCg	p.M624T		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	624	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CTCCAGCTTATGATTATCTTA	0.413																																					p.M624T		Atlas-SNP	.											.	LAMA2	481	.	0			c.T1871C						.						150	130	136					6																	129571345		2203	4300	6503	SO:0001583	missense	3908	exon13			AGCTTATGATTAT	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.1871T>C	chr6.hg19:g.129571345T>C	ENSP00000400365:p.Met624Thr	53.0	0.0		97.0	60.0	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	T	0.070	-1.204561	0.01568	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.35236	1.32	5.69	1.63	0.23807	Laminin B type IV (2);Laminin B, subgroup (1);	0.382752	0.29676	N	0.011482	T	0.05914	0.0154	N	0.17474	0.49	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.31194	-0.9952	10	0.30078	T	0.28	.	2.5455	0.04736	0.2488:0.0735:0.1283:0.5494	.	624;624	A6NF00;P24043	.;LAMA2_HUMAN	T	624	ENSP00000400365:M624T	ENSP00000346769:M624T	M	+	2	0	LAMA2	129613038	0.999000	0.42202	0.021000	0.16686	0.085000	0.17905	1.265000	0.33027	0.479000	0.27511	0.533000	0.62120	ATG	.	.		0.413	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			C	129571345	T	C	129571345	3	2	48	1	0	0	0	0	1	0	0	0	8615	1464	51	2	1921	2	LAMA2	6	129571345	Missense_Mutation	SNP	T	TCGA-BD-A2L6-01A-11D-A20W-10	32009300	129571345	41543722	23	6103										
PCLO	27445	hgsc.bcm.edu	37	chr7	82784756	82784756	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tggccctggctgttgagctgGagtctttccaactccaggag	13	11	1	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr7:82784756G>T	ENST00000333891.9	-	2	1538	c.1201C>A	c.(1201-1203)Cca>Aca	p.P401T	PCLO_ENST00000423517.2_Missense_Mutation_p.P401T	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGTTGAGCTGGAGTCTTTCCA	0.587																																					p.P401T		Atlas-SNP	.											.	PCLO	1506	.	0			c.C1201A						.						89	91	90					7																	82784756		2004	4181	6185	SO:0001583	missense	27445	exon2			GAGCTGGAGTCTT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.1201C>A	chr7.hg19:g.82784756G>T	ENSP00000334319:p.Pro401Thr	145.0	0.0		209.0	73.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	2.847	-0.239193	0.05944	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.14766	2.5;2.48	4.47	2.65	0.31530	.	.	.	.	.	T	0.10465	0.0256	L	0.47016	1.485	0.09310	N	0.999991	B;B	0.32829	0.386;0.386	B;B	0.22601	0.04;0.04	T	0.27191	-1.0081	9	0.87932	D	0	.	4.7342	0.12979	0.2752:0.1608:0.564:0.0	.	401;401	Q9Y6V0-5;Q9Y6V0-6	.;.	T	401	ENSP00000334319:P401T;ENSP00000388393:P401T	ENSP00000334319:P401T	P	-	1	0	PCLO	82622692	0.000000	0.05858	0.004000	0.12327	0.312000	0.27988	0.260000	0.18424	0.604000	0.29930	0.655000	0.94253	CCA	.	.		0.587	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82784756	G	T	82784756	3	4	48	1	0	0	0	0	1	0	0	0	11592	1174	41	3	14340	3	PCLO	7	82784756	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10		82784756	76353907	24	6104										
TAS2R41	259287	hgsc.bcm.edu	37	chr7	143175217	143175217	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gggggtctcggccgacagttCttccatctacactggcactt	11	13	3	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr7:143175217C>T	ENST00000408916.1	+	1	252	c.252C>T	c.(250-252)ttC>ttT	p.F84F	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	84					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					GCCGACAGTTCTTCCATCTAC	0.547																																					p.F84F		Atlas-SNP	.											.	TAS2R41	43	.	0			c.C252T						.						108	108	108					7																	143175217		2004	4175	6179	SO:0001819	synonymous_variant	259287	exon1			ACAGTTCTTCCAT	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.252C>T	chr7.hg19:g.143175217C>T		81.0	0.0		91.0	11.0	NM_176883	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Silent	SNP	ENST00000408916.1	hg19	CCDS43663.1																																																																																			.	.		0.547	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1			T	143175217	C	T	143175217	2	4	48	1	0	0	0	0	0	0	0	1	15594	912	32	3		3	TAS2R41	7	143175217	Silent	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	60390461	143175217	15963446	25	6105										
KIF13B	23303	hgsc.bcm.edu	37	chr8	28971063	28971063	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	catcttttttaggagactctGtgcaaaaccctagagaaaaa	7	8	2	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr8:28971063G>C	ENST00000524189.1	-	32	3885	c.3847C>G	c.(3847-3849)Cag>Gag	p.Q1283E	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1283					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		AGGAGACTCTGTGCAAAACCC	0.363																																					p.Q1283E		Atlas-SNP	.											.	KIF13B	192	.	0			c.C3847G						.						41	37	38					8																	28971063		1812	4070	5882	SO:0001583	missense	23303	exon32			GACTCTGTGCAAA	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3847C>G	chr8.hg19:g.28971063G>C	ENSP00000427900:p.Gln1283Glu	30.0	0.0		60.0	19.0	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	hg19	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.772837	0.49680	.	.	ENSG00000197892	ENST00000524189	T	0.75367	-0.93	5.5	5.5	0.81552	.	0.058286	0.64402	D	0.000001	T	0.66036	0.2749	L	0.33245	0.995	0.80722	D	1	B	0.21309	0.054	B	0.17433	0.018	T	0.59289	-0.7482	10	0.17832	T	0.49	.	19.6014	0.95563	0.0:0.0:1.0:0.0	.	1283	F8VPJ2	.	E	1283	ENSP00000427900:Q1283E	ENSP00000427900:Q1283E	Q	-	1	0	KIF13B	29026982	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.298000	0.78815	2.854000	0.98071	0.655000	0.94253	CAG	.	.		0.363	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			C	28971063	G	C	28971063	3	2	48	1	0	0	0	0	1	0	0	0	8284	1386	48	4	1669	4	KIF13B	8	28971063	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10		28971063	117392959	26	6106										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113668402	113668402	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ctttcataatgaatcttgaaAccattattggaacgactgtt	6	7	2	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr8:113668402A>G	ENST00000297405.5	-	18	3229	c.2985T>C	c.(2983-2985)ggT>ggC	p.G995G	CSMD3_ENST00000343508.3_Silent_p.G955G|CSMD3_ENST00000352409.3_Silent_p.G995G|CSMD3_ENST00000455883.2_Silent_p.G891G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	995	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GAATCTTGAAACCATTATTGG	0.308										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G995G		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T2985C						.						58	65	62					8																	113668402		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon18			CTTGAAACCATTA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2985T>C	chr8.hg19:g.113668402A>G		72.0	0.0		115.0	37.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.308	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113668402	A	G	113668402	2	3	48	1	0	0	0	0	0	0	0	1	3948	30	2	2		2	CSMD3	8	113668402	Silent	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	84697339	113668402	32695620	27	6107										
PTK2	5747	hgsc.bcm.edu	37	chr8	141684416	141684416	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ccttgacaccctcgttgtagCtgtcagcagggctgctgagg	13	12	1	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr8:141684416C>T	ENST00000522684.1	-	29	2919	c.2690G>A	c.(2689-2691)aGc>aAc	p.S897N	PTK2_ENST00000521059.1_Missense_Mutation_p.S897N|PTK2_ENST00000519465.1_Missense_Mutation_p.S525N|PTK2_ENST00000395218.2_Missense_Mutation_p.S907N|PTK2_ENST00000535192.1_Missense_Mutation_p.S851N|PTK2_ENST00000538769.1_Missense_Mutation_p.S565N|PTK2_ENST00000519419.1_Missense_Mutation_p.S941N|PTK2_ENST00000517887.1_Missense_Mutation_p.S941N|PTK2_ENST00000340930.3_Missense_Mutation_p.S907N|PTK2_ENST00000430260.2_Missense_Mutation_p.S207N	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	897	Interaction with TGFB1I1.|Pro-rich.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			CTCGTTGTAGCTGTCAGCAGG	0.572																																					p.S919N		Atlas-SNP	.											.	PTK2	311	.	0			c.G2756A						.						48	40	43					8																	141684416		2203	4300	6503	SO:0001583	missense	5747	exon29			TTGTAGCTGTCAG	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9611	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 71"	600758	"PTK2 protein tyrosine kinase 2"			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.2690G>A	chr8.hg19:g.141684416C>T	ENSP00000429911:p.Ser897Asn	75.0	0.0		76.0	29.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.199674	0.79015	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986	T;T;T;T;T;T;T;T;T;T;T;T	0.77877	-0.98;-1.0;-0.98;-0.99;-0.98;-1.13;-0.97;-1.06;-0.97;-0.99;1.42;-0.99	5.96	5.09	0.68999	.	0.075131	0.85682	D	0.000000	T	0.72882	0.3516	L	0.27053	0.805	0.47584	D	0.99946	B;P;B;B;B;B;P;P;B;P	0.38788	0.425;0.647;0.258;0.376;0.258;0.376;0.647;0.609;0.159;0.469	B;P;B;B;B;B;P;B;B;B	0.44623	0.233;0.455;0.138;0.177;0.103;0.104;0.455;0.258;0.103;0.149	T	0.73113	-0.4085	10	0.40728	T	0.16	.	15.465	0.75394	0.0:0.9336:0.0:0.0664	.	907;592;817;897;919;851;849;724;565;525	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	N	897;851;525;941;897;849;907;818;592;569;907;565;941;207;595	ENSP00000429911:S897N;ENSP00000438009:S851N;ENSP00000429170:S525N;ENSP00000429082:S941N;ENSP00000429474:S897N;ENSP00000378644:S907N;ENSP00000428492:S569N;ENSP00000341189:S907N;ENSP00000445742:S565N;ENSP00000429129:S941N;ENSP00000403416:S207N;ENSP00000430603:S595N	ENSP00000341189:S907N	S	-	2	0	PTK2	141753598	1.000000	0.71417	0.988000	0.46212	0.986000	0.74619	5.852000	0.69488	1.536000	0.49237	0.650000	0.86243	AGC	.	.		0.572	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		T	141684416	C	T	141684416	3	4	48	1	0	0	0	0	1	0	0	0	12775	797	28	3	484	3	PTK2	8	141684416	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	28016014	141684416	4679606	28	6108										
FAM83H	286077	hgsc.bcm.edu	37	chr8	144808725	144808725	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tggggctcagcagctgcctaAgacgcaaggagcctttgcgc	14	12	1	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr8:144808725A>C	ENST00000388913.3	-	5	3031	c.2906T>G	c.(2905-2907)cTt>cGt	p.L969R		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	969					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CAGCTGCCTAAGACGCAAGGA	0.701																																					p.L969R		Atlas-SNP	.											.	FAM83H	68	.	0			c.T2906G						.						13	15	14					8																	144808725		1856	4019	5875	SO:0001583	missense	286077	exon5			TGCCTAAGACGCA	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.2906T>G	chr8.hg19:g.144808725A>C	ENSP00000373565:p.Leu969Arg	34.0	0.0		59.0	24.0	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	hg19	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	a	16.36	3.101373	0.56183	.	.	ENSG00000180921	ENST00000388913	T	0.37411	1.2	4.87	4.87	0.63330	.	3.735730	0.01511	U	0.017920	T	0.55305	0.1912	L	0.34521	1.04	0.35170	D	0.771512	D	0.89917	1.0	D	0.76575	0.988	T	0.25779	-1.0122	10	0.44086	T	0.13	.	13.7052	0.62633	1.0:0.0:0.0:0.0	.	969	Q6ZRV2	FA83H_HUMAN	R	969	ENSP00000373565:L969R	ENSP00000373565:L969R	L	-	2	0	FAM83H	144880713	1.000000	0.71417	0.923000	0.36655	0.450000	0.32258	5.107000	0.64603	1.844000	0.53588	0.450000	0.29827	CTT	.	.		0.701	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		C	144808725	A	C	144808725	3	2	48	1	0	0	0	0	1	0	0	0	5648	72	3	5	637	5	FAM83H	8	144808725	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	3124309	144808725	1555297	29	6109										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2039826	2039826	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gcagcagcagcaacagcagcCgcagcagcagccgccgcaac	12	17	0	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr9:2039826C>A	ENST00000382203.1	+	4	925	c.716C>A	c.(715-717)cCg>cAg	p.P239Q	SMARCA2_ENST00000382194.1_Missense_Mutation_p.P239Q|RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000349721.2_Missense_Mutation_p.P239Q|SMARCA2_ENST00000357248.2_Missense_Mutation_p.P239Q|SMARCA2_ENST00000491574.1_3'UTR			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	239				Missing (in Ref. 1; CAA51407). {ECO:0000305}.	aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		caacagcagccgcagcagcag	0.572																																					p.P239Q		Atlas-SNP	.											.	SMARCA2	313	.	0			c.C716A						.						13	15	14					9																	2039826		2188	4274	6462	SO:0001583	missense	6595	exon4			AGCAGCCGCAGCA	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.716C>A	chr9.hg19:g.2039826C>A	ENSP00000371638:p.Pro239Gln	57.0	0.0		49.0	5.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	C	16.28	3.078929	0.55753	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000450198;ENST00000382203;ENST00000382194	T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21	4.2	1.75	0.24633	.	0.568985	0.17295	N	0.179486	T	0.17874	0.0429	N	0.12182	0.205	0.58432	D	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04930	-1.0917	10	0.36615	T	0.2	-0.1223	6.1406	0.20257	0.6736:0.1696:0.0:0.1568	.	239;239	P51531-2;P51531	.;SMCA2_HUMAN	Q	239	ENSP00000265773:P239Q;ENSP00000349788:P239Q;ENSP00000392081:P239Q;ENSP00000371638:P239Q;ENSP00000371629:P239Q	ENSP00000265773:P239Q	P	+	2	0	SMARCA2	2029826	0.000000	0.05858	0.372000	0.25991	0.518000	0.34316	-0.298000	0.08265	0.381000	0.24851	-0.275000	0.10095	CCG	.	.		0.572	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2039826	C	A	2039826	3	1	48	1	0	0	0	0	1	0	0	0	14784	652	23	1	726	1	SMARCA2	9	2039826	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10		2039826	139173605	30	6110										
LRRC19	64922	hgsc.bcm.edu	37	chr9	26995539	26995539	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ttaattttcttcacataattCatggatatctatatatttgt	3	5	4	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr9:26995539C>A	ENST00000380055.5	-	5	1203	c.1093G>T	c.(1093-1095)Gaa>Taa	p.E365*	IFT74_ENST00000429045.2_Intron|LRRC19_ENST00000482770.1_5'UTR|IFT74_ENST00000443698.1_Intron|IFT74_ENST00000380062.5_Intron|IFT74_ENST00000433700.1_Intron	NM_022901.2	NP_075052.1	Q9H756	LRC19_HUMAN	leucine rich repeat containing 19	365						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)	6		all_neural(11;1.81e-09)		Lung(218;1.06e-05)|LUSC - Lung squamous cell carcinoma(38;0.0001)		TCACATAATTCATGGATATCT	0.279																																					p.E365X		Atlas-SNP	.											.	LRRC19	24	.	0			c.G1093T						.						45	45	45					9																	26995539		2197	4293	6490	SO:0001587	stop_gained	64922	exon5			ATAATTCATGGAT	AK024955	CCDS6518.1	9p21.1	2008-02-05			ENSG00000184434	ENSG00000184434			23379	protein-coding gene	gene with protein product							Standard	NM_022901		Approved	FLJ21302	uc003zqh.3	Q9H756	OTTHUMG00000019710	ENST00000380055.5:c.1093G>T	chr9.hg19:g.26995539C>A	ENSP00000369395:p.Glu365*	56.0	0.0		92.0	39.0	NM_022901	A0AV00|B9EG91	Nonsense_Mutation	SNP	ENST00000380055.5	hg19	CCDS6518.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.052030	0.36181	.	.	ENSG00000184434	ENST00000380055	.	.	.	5.55	5.55	0.83447	.	0.137436	0.45606	D	0.000360	.	.	.	.	.	.	0.38383	D	0.945174	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-15.0338	13.7555	0.62935	0.0:0.9266:0.0:0.0734	.	.	.	.	X	365	.	ENSP00000369395:E365X	E	-	1	0	LRRC19	26985539	0.989000	0.36119	0.318000	0.25279	0.202000	0.24057	2.361000	0.44160	2.616000	0.88540	0.585000	0.79938	GAA	.	.		0.279	LRRC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051961.2	NM_022901		A	26995539	C	A	26995539	4	1	48	1	0	0	0	0	0	1	0	0	8984	835	29	3	23	3	LRRC19	9	26995539	Nonsense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	24955713	26995539	114217892	31	6111										
C9orf85	138241	hgsc.bcm.edu	37	chr9	74586499	74586499	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gcctgtgaacttgaagtttgCgcaaaatgtggaaagaaaga	12	5	0	4			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr9:74586499C>T	ENST00000377031.3	+	3	478	c.288C>T	c.(286-288)tgC>tgT	p.C96C	C9orf85_ENST00000334731.2_Silent_p.C96C|C9orf85_ENST00000486911.2_Intron			Q96MD7	CI085_HUMAN	chromosome 9 open reading frame 85	96										kidney(2)|large_intestine(1)|lung(4)	7						TTGAAGTTTGCGCAAAATGTG	0.308																																					p.C96C		Atlas-SNP	.											.	C9orf85	28	.	0			c.C288T						.						148	135	139					9																	74586499		2203	4300	6503	SO:0001819	synonymous_variant	138241	exon3			AGTTTGCGCAAAA	BC010179	CCDS6639.1	9q21.2	2012-03-16			ENSG00000155621	ENSG00000155621			28784	protein-coding gene	gene with protein product						12477932	Standard	NM_182505		Approved	MGC61599	uc004ain.3	Q96MD7	OTTHUMG00000020002	ENST00000377031.3:c.288C>T	chr9.hg19:g.74586499C>T		48.0	0.0		65.0	33.0	NM_182505	Q5W0N1|Q5W0N3|Q6PJW9|Q86U95	Silent	SNP	ENST00000377031.3	hg19																																																																																				.	.		0.308	C9orf85-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052628.2	NM_182505		T	74586499	C	T	74586499	2	4	48	1	0	0	0	0	0	0	0	1	2503	776	27	1		1	C9orf85	9	74586499	Silent	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	47590960	74586499	66626932	32	6112										
MUSK	4593	hgsc.bcm.edu	37	chr9	113550088	113550088	+	Frame_Shift_Del	DEL	T	T	-													0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	aggcagccctcatggcagaaTttgacaaccctaacattgtg							TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr9:113550088delT	ENST00000374448.4	+	14	2031	c.1897delT	c.(1897-1899)tttfs	p.F633fs	MUSK_ENST00000374438.1_Frame_Shift_Del_p.F149fs|MUSK_ENST00000416899.2_Frame_Shift_Del_p.F625fs|MUSK_ENST00000189978.5_Frame_Shift_Del_p.F633fs	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	633	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						CATGGCAGAATTTGACAACCC	0.428																																					p.E632fs		Atlas-Indel,Pindel	.											.	MUSK	112	.	0			c.1896delA						.						48	46	46					9																	113550088		1877	4105	5982	SO:0001589	frameshift_variant	4593	exon13			.	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.1897delT	chr9.hg19:g.113550088delT	ENSP00000363571:p.Phe633fs	89.0	0.0		124.0	52.0	NM_005592	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Frame_Shift_Del	DEL	ENST00000374448.4	hg19	CCDS48005.1																																																																																			.	.		0.428	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				-	113550088	T	-	113550088	7	5	48	1	0	1	0	1	0	0	0	0	9998	1493	52	0	1983	0	MUSK	9	113550088	Frame_Shift_Del	DEL	T	TCGA-BD-A2L6-01A-11D-A20W-10	38963589	113550088	27663343	33	6113										
ORM1	5004	hgsc.bcm.edu	37	chr9	117086007	117086007	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ggagtacaataagtcggttcAggagatccaagcaaccttct	10	9	2	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr9:117086007A>T	ENST00000259396.8	+	2	257	c.179A>T	c.(178-180)cAg>cTg	p.Q60L	ORM1_ENST00000538816.1_3'UTR	NM_000607.2	NP_000598.2	P02763	A1AG1_HUMAN	orosomucoid 1	60					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(2)|large_intestine(4)|lung(2)	8		Myeloproliferative disorder(63;0.163)			Abiraterone(DB05812)|Acenocoumarol(DB01418)|Ajmaline(DB01426)|Alfentanil(DB00802)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aprindine(DB01429)|Bupropion(DB01156)|Canagliflozin(DB08907)|Celecoxib(DB00482)|Chlorpromazine(DB00477)|Desipramine(DB01151)|Disopyramide(DB00280)|Doxazosin(DB00590)|Doxepin(DB01142)|Erlotinib(DB00530)|Fluoxetine(DB00472)|Gefitinib(DB00317)|Imatinib(DB00619)|Imipramine(DB00458)|Ivacaftor(DB08820)|Maprotiline(DB00934)|Mirabegron(DB08893)|Nateglinide(DB00731)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxycodone(DB00497)|Penbutolol(DB01359)|Pethidine(DB00454)|Phenprocoumon(DB00946)|Pitavastatin(DB08860)|Prazosin(DB00457)|Propranolol(DB00571)|Quinidine(DB00908)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Tamsulosin(DB00706)|Telaprevir(DB05521)|Thalidomide(DB01041)|Trazodone(DB00656)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Vismodegib(DB08828)|Warfarin(DB00682)	AAGTCGGTTCAGGAGATCCAA	0.517																																					p.Q60L		Atlas-SNP	.											.	ORM1	20	.	0			c.A179T						.						129	124	126					9																	117086007		2203	4300	6503	SO:0001583	missense	5004	exon2			CGGTTCAGGAGAT		CCDS6803.1	9q32	2013-09-19			ENSG00000229314	ENSG00000229314		"Lipocalins"	8498	protein-coding gene	gene with protein product		138600					Standard	NM_000607		Approved		uc004bik.4	P02763	OTTHUMG00000021012	ENST00000259396.8:c.179A>T	chr9.hg19:g.117086007A>T	ENSP00000259396:p.Gln60Leu	222.0	0.0		353.0	156.0	NM_000607	B7ZKQ5|Q5T539|Q5U067|Q8TC16	Missense_Mutation	SNP	ENST00000259396.8	hg19	CCDS6803.1	.	.	.	.	.	.	.	.	.	.	A	11.60	1.686756	0.29962	.	.	ENSG00000229314	ENST00000259396	T	0.08193	3.12	4.77	-2.6	0.06190	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.458180	0.03745	N	0.255645	T	0.11495	0.0280	L	0.58101	1.795	0.09310	N	1	B	0.16166	0.016	B	0.13407	0.009	T	0.46176	-0.9210	10	0.66056	D	0.02	-0.5495	10.5234	0.44934	0.7599:0.0:0.2401:0.0	.	60	P02763	A1AG1_HUMAN	L	60	ENSP00000259396:Q60L	ENSP00000259396:Q60L	Q	+	2	0	ORM1	116125828	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.143000	0.10296	-0.439000	0.07222	0.383000	0.25322	CAG	.	.		0.517	ORM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055426.1			T	117086007	A	T	117086007	3	4	48	1	0	0	0	0	1	0	0	0	11276	188	7	4	185	4	ORM1	9	117086007	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	3535919	117086007	24127424	34	6114										
ENG	2022	hgsc.bcm.edu	37	chr9	130587248	130587248	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	atcttgaaggagtattctccAgtggtctaatggtggggaga	14	5	3	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr9:130587248A>T	ENST00000373203.4	-	7	1222	c.822T>A	c.(820-822)acT>acA	p.T274T	RP11-228B15.4_ENST00000439298.1_RNA|ENG_ENST00000344849.3_Silent_p.T274T|ENG_ENST00000480266.1_5'UTR	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	274	Required for interaction with EGL.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						AGTATTCTCCAGTGGTCTAAT	0.577									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia																												p.T274T		Atlas-SNP	.											.	ENG	44	.	0			c.T822A						.						69	76	74					9																	130587248		2203	4300	6503	SO:0001819	synonymous_variant	2022	exon7	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	TTCTCCAGTGGTC	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"CD molecules"	3349	protein-coding gene	gene with protein product		131195	"Osler-Rendu-Weber syndrome 1"	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.822T>A	chr9.hg19:g.130587248A>T		34.0	0.0		40.0	17.0	NM_001114753	Q14248|Q14926|Q5T9C0	Silent	SNP	ENST00000373203.4	hg19	CCDS48029.1																																																																																			.	.		0.577	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1			T	130587248	A	T	130587248	2	4	48	1	0	0	0	0	0	0	0	1	5119	175	7	4		4	ENG	9	130587248	Silent	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	13501241	130587248	10626183	35	6115										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88259978	88259978	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	aactggtcccacaacttacaCcccctttctttgcctgattc	4	16	1	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr10:88259978C>T	ENST00000298767.5	-	3	1494	c.1022G>A	c.(1021-1023)gGt>gAt	p.G341D		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	341	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						ACAACTTACACCCCCTTTCTT	0.443																																					p.G341D		Atlas-SNP	.											.	WAPAL	81	.	0			c.G1022A						.						191	161	171					10																	88259978		2203	4300	6503	SO:0001583	missense	23063	exon3			CTTACACCCCCTT	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.1022G>A	chr10.hg19:g.88259978C>T	ENSP00000298767:p.Gly341Asp	67.0	0.0		69.0	46.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	C	8.496	0.863198	0.17250	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.29655	1.56	5.77	3.92	0.45320	.	0.476548	0.21051	N	0.080998	T	0.19366	0.0465	N	0.22421	0.69	0.80722	D	1	B;B;B	0.17038	0.012;0.012;0.02	B;B;B	0.21360	0.018;0.008;0.034	T	0.05146	-1.0903	10	0.20519	T	0.43	.	9.3555	0.38164	0.0:0.577:0.3452:0.0778	.	341;341;384	B2RTX8;Q7Z5K2;Q7Z5K2-2	.;WAPL_HUMAN;.	D	426;341;426	ENSP00000298767:G341D	ENSP00000298767:G341D	G	-	2	0	WAPAL	88249958	0.918000	0.31147	0.930000	0.37139	0.911000	0.54048	1.399000	0.34566	0.782000	0.33613	0.650000	0.86243	GGT	.	.		0.443	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		T	88259978	C	T	88259978	3	4	48	1	0	0	0	0	1	0	0	0	17263	507	18	3	2618	3	WAPAL	10	88259978	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10		88259978	47274769	36	6116										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720811	89720812	+	Frame_Shift_Ins	INS	-	-	A													0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tatctagtacttactttaacINSaaaaaatgatcttgacaaag					rs587783058|rs121913291		TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr10:89720811_89720812insA	ENST00000371953.3	+	8	2319_2320	c.962_963insA	c.(961-966)acaaaafs	p.TK321fs	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	321	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.T321fs*23(9)|p.T321fs*3(7)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.N323fs*2(2)|p.T319_K332del(1)|p.T321fs*22(1)|p.G165_*404del(1)|p.L316fs*1(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.T321fs*6(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		CTTACTTTAACAAAAAATGATC	0.327	N323fs*2(MFE319_ENDOMETRIUM)|N323fs*2(RL952_ENDOMETRIUM)|N323fs*2(SKUT1_SOFT_TISSUE)	31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.T321fs		Atlas-INDEL	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.,1	PTEN	3652	.	73	Whole gene deletion(37)|Deletion - Frameshift(20)|Insertion - Frameshift(10)|Deletion - In frame(4)|Unknown(2)	endometrium(18)|prostate(16)|central_nervous_system(12)|skin(7)|lung(4)|ovary(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|urinary_tract(2)|large_intestine(1)|stomach(1)|soft_tissue(1)|pancreas(1)	c.962_963insA						.																																			SO:0001589	frameshift_variant	5728	exon8	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.968dupA	chr10.hg19:g.89720817_89720817dupA	ENSP00000361021:p.Thr321fs	171.0	0.0		170.0	110.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Ins	INS	ENST00000371953.3	hg19	CCDS31238.1																																																																																			.	.		0.327	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89720812	-	A	89720811	7	5	48	1	0	1	1	0	0	0	0	0	12750	478	17	0	992	0	PTEN	10	89720811	Frame_Shift_Ins	INS	-	TCGA-BD-A2L6-01A-11D-A20W-10	1460833	89720811	45813936	37	6117										
C11orf35	256329	hgsc.bcm.edu	37	chr11	556881	556881	+	Frame_Shift_Del	DEL	G	G	-													0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gcctgcaccagcgcttgctcGgaggaagcgcggtggtcccg							TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr11:556881delG	ENST00000329451.3	-	8	992	c.930delC	c.(928-930)tccfs	p.S310fs	RP11-496I9.1_ENST00000527113.1_RNA|RP11-496I9.1_ENST00000527620.1_RNA	NM_173573.2	NP_775844.2	Q8IXW0	LMTD2_HUMAN		310										NS(1)|breast(1)|central_nervous_system(1)|lung(4)|pancreas(1)	8		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCGCTTGCTCGGAGGAAGCGC	0.701																																					p.E311fs		Atlas-INDEL	.											.	C11orf35	22	.	0			c.931delG						.						12	15	14					11																	556881		2181	4288	6469	SO:0001589	frameshift_variant	256329	exon8			.																												ENST00000329451.3:c.930delC	chr11.hg19:g.556881delG	ENSP00000331167:p.Ser310fs	25.0	0.0		37.0	13.0	NM_173573		Frame_Shift_Del	DEL	ENST00000329451.3	hg19	CCDS7701.1																																																																																			.	.		0.701	C11orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254973.2			-	556881	G	-	556881	7	5	48	1	0	1	0	1	0	0	0	0	1640	1103	39	0	1002	0	C11orf35	11	556881	Frame_Shift_Del	DEL	G	TCGA-BD-A2L6-01A-11D-A20W-10		556881	134449635	38	6118										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17418492	17418492	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	aggggcgatgagggcattgaCgtgcttcagcaccggcttca	15	10	2	2	rs138642224	byFrequency	TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr11:17418492C>A	ENST00000389817.3	-	33	4158	c.4090G>T	c.(4090-4092)Gtc>Ttc	p.V1364F	ABCC8_ENST00000302539.4_Missense_Mutation_p.V1365F			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1364	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	AGGGCATTGACGTGCTTCAGC	0.612																																					p.V1364F		Atlas-SNP	.											.	ABCC8	170	.	0			c.G4090T						.						121	93	102					11																	17418492		2200	4293	6493	SO:0001583	missense	6833	exon33			CATTGACGTGCTT	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.4090G>T	chr11.hg19:g.17418492C>A	ENSP00000374467:p.Val1364Phe	135.0	0.0		195.0	78.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Missense_Mutation	SNP	ENST00000389817.3	hg19	CCDS31437.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.32|18.32	3.597040|3.597040	0.66332|0.66332	.|.	.|.	ENSG00000006071|ENSG00000006071	ENST00000528374|ENST00000389817;ENST00000302539	.|D;D	.|0.95171	.|-3.63;-3.63	4.83|4.83	4.83|4.83	0.62350|0.62350	.|ABC transporter-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.95667|0.95667	0.8591|0.8591	L|L	0.43646|0.43646	1.37|1.37	0.80722|0.80722	D|D	1|1	.|D	.|0.61080	.|0.989	.|D	.|0.64144	.|0.922	D|D	0.96374|0.96374	0.9276|0.9276	5|10	.|0.87932	.|D	.|0	.|.	18.2867|18.2867	0.90117|0.90117	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1364	.|Q09428	.|ABCC8_HUMAN	L|F	191|1364;1365	.|ENSP00000374467:V1364F;ENSP00000303960:V1365F	.|ENSP00000303960:V1365F	R|V	-|-	2|1	0|0	ABCC8|ABCC8	17375068|17375068	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.022000|0.022000	0.10575|0.10575	4.794000|4.794000	0.62482|0.62482	2.386000|2.386000	0.81285|0.81285	0.555000|0.555000	0.69702|0.69702	CGT|GTC	.	C|0.999;T|0.001		0.612	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		A	17418492	C	A	17418492	3	1	48	1	0	0	0	0	1	0	0	0	58	536	19	1	683	1	ABCC8	11	17418492	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	16861611	17418492	117588024	39	6119										
AGBL2	79841	hgsc.bcm.edu	37	chr11	47712149	47712149	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	agacagtagaagggctgctgCccatcatccgtgttgttctt	11	10	2	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr11:47712149C>T	ENST00000525123.1	-	10	1395	c.1110G>A	c.(1108-1110)ggG>ggA	p.G370G	AGBL2_ENST00000357610.3_Silent_p.G370G|AGBL2_ENST00000528244.1_Silent_p.G332G|AGBL2_ENST00000529712.1_5'UTR|AGBL2_ENST00000298861.4_Silent_p.G370G	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	370						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						AGGGCTGCTGCCCATCATCCG	0.463																																					p.G370G		Atlas-SNP	.											.	AGBL2	73	.	0			c.G1110A						.						178	152	161					11																	47712149		2201	4298	6499	SO:0001819	synonymous_variant	79841	exon10			CTGCTGCCCATCA		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"cytoplasmic carboxypeptidase 2"					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.1110G>A	chr11.hg19:g.47712149C>T		157.0	0.0		216.0	97.0	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Silent	SNP	ENST00000525123.1	hg19	CCDS7944.1																																																																																			.	.		0.463	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783		T	47712149	C	T	47712149	2	4	48	1	0	0	0	0	0	0	0	1	376	726	26	3		3	AGBL2	11	47712149	Silent	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	30293657	47712149	87294367	40	6120										
ADAMTS15	170689	hgsc.bcm.edu	37	chr11	130343256	130343256	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gccccgggtccgctactcctTctatctgcccaaagagcctc	8	18	2	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr11:130343256T>G	ENST00000299164.2	+	8	2393	c.2393T>G	c.(2392-2394)tTc>tGc	p.F798C		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15	798	Spacer.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(8)|urinary_tract(1)	36	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		CGCTACTCCTTCTATCTGCCC	0.652																																					p.F798C		Atlas-SNP	.											.	ADAMTS15	103	.	0			c.T2393G						.						95	110	105					11																	130343256		2201	4296	6497	SO:0001583	missense	170689	exon8			ACTCCTTCTATCT	AJ315733	CCDS8488.1	11q25	2008-02-01	2005-08-19		ENSG00000166106	ENSG00000166106		"ADAM metallopeptidases with thrombospondin type 1 motif"	16305	protein-coding gene	gene with protein product		607509	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 15"			11867212	Standard	NM_139055		Approved		uc010scd.2	Q8TE58	OTTHUMG00000165657	ENST00000299164.2:c.2393T>G	chr11.hg19:g.130343256T>G	ENSP00000299164:p.Phe798Cys	122.0	0.0		150.0	74.0	NM_139055	Q32MI6	Missense_Mutation	SNP	ENST00000299164.2	hg19	CCDS8488.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.057315	0.76074	.	.	ENSG00000166106	ENST00000299164	T	0.61510	0.1	5.91	5.91	0.95273	ADAM-TS Spacer 1 (1);	.	.	.	.	T	0.80628	0.4659	M	0.90309	3.105	0.80722	D	1	D	0.76494	0.999	D	0.72075	0.976	D	0.84819	0.0795	9	0.87932	D	0	.	16.3436	0.83110	0.0:0.0:0.0:1.0	.	798	Q8TE58	ATS15_HUMAN	C	798	ENSP00000299164:F798C	ENSP00000299164:F798C	F	+	2	0	ADAMTS15	129848466	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.816000	0.55658	2.269000	0.75478	0.533000	0.62120	TTC	.	.		0.652	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	NM_139055		G	130343256	T	G	130343256	3	3	48	1	0	0	0	0	1	0	0	0	260	1783	62	5	2423	5	ADAMTS15	11	130343256	Missense_Mutation	SNP	T	TCGA-BD-A2L6-01A-11D-A20W-10	82631107	130343256	4663260	41	6121										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2558277	2558277	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tagattttataattgtggttGtggggtaagtatcactgtct	11	3	2	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr12:2558277G>T	ENST00000347598.4	+	4	613	c.613G>T	c.(613-615)Gtg>Ttg	p.V205L	CACNA1C_ENST00000399644.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399629.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399606.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000335762.5_Missense_Mutation_p.V205L|CACNA1C_ENST00000399638.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399634.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000327702.7_Missense_Mutation_p.V205L|CACNA1C_ENST00000399621.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000406454.3_Missense_Mutation_p.V205L|CACNA1C_ENST00000399649.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399591.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000480911.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399655.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399601.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399637.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000344100.3_Missense_Mutation_p.V205L|CACNA1C_ENST00000402845.3_Missense_Mutation_p.V205L|CACNA1C_ENST00000399595.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399603.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399597.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399617.1_Missense_Mutation_p.V205L|CACNA1C_ENST00000399641.1_Missense_Mutation_p.V205L	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	205					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AATTGTGGTTGTGGGGTAAGT	0.468																																					p.V205L		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.G613T						.						65	67	67					12																	2558277		1852	4059	5911	SO:0001583	missense	775	exon4			GTGGTTGTGGGGT	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.613G>T	chr12.hg19:g.2558277G>T	ENSP00000266376:p.Val205Leu	118.0	0.0		97.0	60.0	NM_001129831	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.064643	0.76187	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97279	-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32;-4.32	4.71	4.71	0.59529	Ion transport (1);	0.206543	0.41500	N	0.000878	D	0.97111	0.9056	L	0.35593	1.075	0.58432	D	0.999999	D;D;B;D;D;D;D;B;D;D;D;B;B;D;B;D;D;D;D;D	0.76494	0.968;0.996;0.002;0.985;0.999;0.959;0.998;0.019;0.97;0.999;0.99;0.066;0.112;0.998;0.05;0.99;0.998;0.998;0.959;0.959	D;D;B;D;D;D;D;B;P;D;D;B;B;D;B;D;D;D;D;D	0.80764	0.963;0.987;0.026;0.976;0.994;0.949;0.994;0.061;0.721;0.994;0.98;0.053;0.199;0.994;0.075;0.98;0.994;0.994;0.949;0.949	D	0.96683	0.9505	10	0.34782	T	0.22	.	17.9253	0.88982	0.0:0.0:1.0:0.0	.	205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-11;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	L	205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;205;46	ENSP00000336982:V205L;ENSP00000382563:V205L;ENSP00000437936:V205L;ENSP00000382552:V205L;ENSP00000382547:V205L;ENSP00000382506:V205L;ENSP00000382530:V205L;ENSP00000382546:V205L;ENSP00000382500:V205L;ENSP00000382549:V205L;ENSP00000266376:V205L;ENSP00000382515:V205L;ENSP00000382510:V205L;ENSP00000341092:V205L;ENSP00000382537:V205L;ENSP00000329877:V205L;ENSP00000382557:V205L;ENSP00000385724:V205L;ENSP00000382512:V205L;ENSP00000382542:V205L;ENSP00000382526:V205L;ENSP00000385896:V205L;ENSP00000382504:V205L	ENSP00000323129:V46L	V	+	1	0	CACNA1C	2428538	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	7.589000	0.82641	2.470000	0.83445	0.638000	0.83543	GTG	.	.		0.468	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2558277	G	T	2558277	3	4	48	1	0	0	0	0	1	0	0	0	2542	1377	48	3	627	3	CACNA1C	12	2558277	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10		2558277	131293618	42	6122										
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14650961	14650961	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tggacgttttgggcctttctGtgatcctcagtcaacagatg	11	9	3	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr12:14650961G>T	ENST00000540793.1	+	14	3922	c.3767G>T	c.(3766-3768)tGt>tTt	p.C1256F	ATF7IP_ENST00000536444.1_Missense_Mutation_p.C1255F|ATF7IP_ENST00000261168.4_Missense_Mutation_p.C1256F|ATF7IP_ENST00000544627.1_Missense_Mutation_p.C1264F			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	1256	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Interaction with MBD1.				DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						GGGCCTTTCTGTGATCCTCAG	0.423																																					p.C1256F		Atlas-SNP	.											.	ATF7IP	136	.	0			c.G3767T						.						169	173	171					12																	14650961		2203	4300	6503	SO:0001583	missense	55729	exon15			CTTTCTGTGATCC	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.3767G>T	chr12.hg19:g.14650961G>T	ENSP00000444589:p.Cys1256Phe	85.0	0.0		56.0	38.0	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	hg19	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444804	0.83993	.	.	ENSG00000171681	ENST00000261168;ENST00000536444;ENST00000544627;ENST00000540793	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	6.17	6.17	0.99709	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.53286	0.1787	L	0.48642	1.525	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.47302	-0.9128	10	0.87932	D	0	-12.7129	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1255;1256	G3V1U0;Q6VMQ6	.;MCAF1_HUMAN	F	1256;1255;1264;1256	ENSP00000261168:C1256F;ENSP00000445955:C1255F;ENSP00000440440:C1264F;ENSP00000444589:C1256F	ENSP00000261168:C1256F	C	+	2	0	ATF7IP	14542228	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.863000	0.99569	2.941000	0.99782	0.655000	0.94253	TGT	.	.		0.423	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		T	14650961	G	T	14650961	3	4	48	1	0	0	0	0	1	0	0	0	1087	1377	48	3	3821	3	ATF7IP	12	14650961	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	12092684	14650961	119200934	43	6123										
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50190101	50190101	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gtgggcaggccttgcgccccCtctggggacagctctcctcc	13	17	2	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr12:50190101C>G	ENST00000335999.6	-	8	1743	c.1542G>C	c.(1540-1542)gaG>gaC	p.E514D		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	510	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CTTGCGCCCCCTCTGGGGACA	0.672																																					p.E514D		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.G1542C						.						13	15	14					12																	50190101		2078	4193	6271	SO:0001583	missense	57701	exon8			CGCCCCCTCTGGG	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.1542G>C	chr12.hg19:g.50190101C>G	ENSP00000337998:p.Glu514Asp	85.0	0.0		126.0	52.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Missense_Mutation	SNP	ENST00000335999.6	hg19	CCDS41781.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.590|3.590	-0.083794|-0.083794	0.07141|0.07141	.|.	.|.	ENSG00000167566|ENSG00000167566	ENST00000335999;ENST00000354423|ENST00000433948	T|.	0.47869|.	0.83|.	4.73|4.73	0.729|0.729	0.18266|0.18266	.|.	0.298342|.	0.24321|.	N|.	0.039550|.	T|T	0.22975|0.22975	0.0555|0.0555	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	0.999999|0.999999	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.27640|0.27640	-1.0068|-1.0068	10|5	0.13470|.	T|.	0.59|.	-15.7334|-15.7334	8.1321|8.1321	0.31033|0.31033	0.0:0.3345:0.5062:0.1593|0.0:0.3345:0.5062:0.1593	.|.	510;510|.	E2QRB5;Q9HCH0-2|.	.;.|.	D|R	514;510|229	ENSP00000337998:E514D|.	ENSP00000337998:E514D|.	E|G	-|-	3|1	2|0	NCKAP5L|NCKAP5L	48476368|48476368	0.993000|0.993000	0.37304|0.37304	0.725000|0.725000	0.30721|0.30721	0.680000|0.680000	0.39746|0.39746	-0.022000|-0.022000	0.12480|0.12480	-0.058000|-0.058000	0.13177|0.13177	0.561000|0.561000	0.74099|0.74099	GAG|GGG	.	.		0.672	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		G	50190101	C	G	50190101	3	3	48	1	0	0	0	0	1	0	0	0	10233	680	24	4	2486	4	NCKAP5L	12	50190101	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	35539140	50190101	83661794	44	6124										
FAIM2	23017	hgsc.bcm.edu	37	chr12	50291319	50291319	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	caccagaaagtaaagagagcCacgacagccaaggtcaccag	10	12	1	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr12:50291319C>T	ENST00000320634.3	-	4	457	c.363G>A	c.(361-363)gtG>gtA	p.V121V	FAIM2_ENST00000550890.1_Silent_p.V75V	NM_012306.3	NP_036438.2	Q9BWQ8	LFG2_HUMAN	Fas apoptotic inhibitory molecule 2	121					apoptotic process (GO:0006915)|cerebellar granular layer development (GO:0021681)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum development (GO:0021549)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of neuron apoptotic process (GO:0043523)|response to ischemia (GO:0002931)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|postsynaptic membrane (GO:0045211)				endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|skin(2)	14						TAAAGAGAGCCACGACAGCCA	0.597																																					p.V121V		Atlas-SNP	.											.	FAIM2	32	.	0			c.G363A						.						67	63	65					12																	50291319		2203	4300	6503	SO:0001819	synonymous_variant	23017	exon4			GAGAGCCACGACA	AB023167	CCDS8791.1	12q13	2010-03-18				ENSG00000135472			17067	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 2"	604306				10231032, 10535980	Standard	NM_012306		Approved	KIAA0950, LFG, NMP35, LIFEGUARD, TMBIM2, LFG2	uc001rvj.2	Q9BWQ8	OTTHUMG00000169808	ENST00000320634.3:c.363G>A	chr12.hg19:g.50291319C>T		136.0	0.0		178.0	69.0	NM_012306	A8K1W6|B3KR08|Q9UJY9|Q9Y2F7	Silent	SNP	ENST00000320634.3	hg19	CCDS8791.1																																																																																			.	.		0.597	FAIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405984.1	NM_012306		T	50291319	C	T	50291319	2	4	48	1	0	0	0	0	0	0	0	1	5381	581	21	3		3	FAIM2	12	50291319	Silent	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	101218	50291319	83560576	45	6125										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124915190	124915190	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	cgctcctgcagctcgcgctgCttgcggatctcagggaactg	13	14	1	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr12:124915190C>A	ENST00000405201.1	-	9	1026	c.1026G>T	c.(1024-1026)aaG>aaT	p.K342N	NCOR2_ENST00000404621.1_Missense_Mutation_p.K342N|NCOR2_ENST00000429285.2_Missense_Mutation_p.K342N|NCOR2_ENST00000356219.3_Missense_Mutation_p.K342N|NCOR2_ENST00000404121.2_5'UTR|NCOR2_ENST00000397355.1_Missense_Mutation_p.K342N			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	342					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GCTCGCGCTGCTTGCGGATCT	0.662																																					p.K342N		Atlas-SNP	.											.	NCOR2	475	.	0			c.G1026T						.						76	83	81					12																	124915190		2054	4198	6252	SO:0001583	missense	9612	exon11			GCGCTGCTTGCGG	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1026G>T	chr12.hg19:g.124915190C>A	ENSP00000384018:p.Lys342Asn	63.0	0.0		85.0	43.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.75|11.75	1.730714|1.730714	0.30684|0.30684	.|.	.|.	ENSG00000196498|ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000429285;ENST00000458234;ENST00000420698;ENST00000448008|ENST00000542927	T;T;T;T;T;T;T;T|.	0.49432|.	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78|.	3.75|3.75	3.75|3.75	0.43078|0.43078	.|.	0.203636|.	0.40908|.	N|.	0.001000|.	T|T	0.70868|0.70868	0.3273|0.3273	M|M	0.73598|0.73598	2.24|2.24	0.80722|0.80722	D|D	1|1	D;D;D|.	0.76494|.	0.998;0.998;0.999|.	D;D;D|.	0.83275|.	0.991;0.991;0.996|.	T|T	0.71497|0.71497	-0.4575|-0.4575	10|5	0.87932|.	D|.	0|.	-39.1233|-39.1233	10.8781|10.8781	0.46923|0.46923	0.0:0.9068:0.0:0.0932|0.0:0.9068:0.0:0.0932	.|.	342;342;342|.	C9J0Q5;C9J239;C9JFD3|.	.;.;.|.	N|I	342;342;342;342;342;342;342;342;244|265	ENSP00000384018:K342N;ENSP00000384202:K342N;ENSP00000348551:K342N;ENSP00000380513:K342N;ENSP00000400281:K342N;ENSP00000402808:K342N;ENSP00000405367:K342N;ENSP00000403034:K244N|.	ENSP00000348551:K342N|.	K|S	-|-	3|2	2|0	NCOR2|NCOR2	123481143|123481143	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.935000|0.935000	0.57460|0.57460	1.168000|1.168000	0.31859|0.31859	2.104000|2.104000	0.64026|0.64026	0.462000|0.462000	0.41574|0.41574	AAG|AGC	.	.		0.662	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124915190	C	A	124915190	3	1	48	1	0	0	0	0	1	0	0	0	10245	796	28	3	6698	3	NCOR2	12	124915190	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	74623871	124915190	8936705	46	6126										
CYSLTR2	57105	hgsc.bcm.edu	37	chr13	49281716	49281716	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ccatcatcatcaccttgatcAtcttcttcttgtgtttcctg	4	13	7	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr13:49281716A>G	ENST00000282018.3	+	1	766	c.763A>G	c.(763-765)Atc>Gtc	p.I255V		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	255					immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell death (GO:0010942)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteinyl leukotriene receptor activity (GO:0001631)|leukotriene receptor activity (GO:0004974)			endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)	CACCTTGATCATCTTCTTCTT	0.488																																					p.I255V		Atlas-SNP	.											.	CYSLTR2	55	.	0			c.A763G						.						140	125	130					13																	49281716		2203	4300	6503	SO:0001583	missense	57105	exon1			TTGATCATCTTCT	AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207		"GPCR / Class A : Leukotriene receptors"	18274	protein-coding gene	gene with protein product		605666				10913337, 1085123	Standard	NM_020377		Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.763A>G	chr13.hg19:g.49281716A>G	ENSP00000282018:p.Ile255Val	25.0	0.0		49.0	15.0	NM_020377	Q9HCQ2	Missense_Mutation	SNP	ENST00000282018.3	hg19	CCDS9412.1	.	.	.	.	.	.	.	.	.	.	A	11.41	1.631129	0.28978	.	.	ENSG00000152207	ENST00000282018	T	0.67698	-0.28	5.65	0.362	0.16113	GPCR, rhodopsin-like superfamily (1);	0.423702	0.21166	N	0.079066	T	0.41259	0.1151	L	0.28556	0.865	0.23862	N	0.996637	B	0.25850	0.136	B	0.23852	0.049	T	0.28522	-1.0041	10	0.02654	T	1	.	4.4136	0.11445	0.3053:0.4989:0.0814:0.1145	.	255	Q9NS75	CLTR2_HUMAN	V	255	ENSP00000282018:I255V	ENSP00000282018:I255V	I	+	1	0	CYSLTR2	48179717	0.682000	0.27624	1.000000	0.80357	0.887000	0.51463	0.838000	0.27572	0.384000	0.24942	0.533000	0.62120	ATC	.	.		0.488	CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1			G	49281716	A	G	49281716	3	3	48	1	0	0	0	0	1	0	0	0	4204	217	8	2	765	2	CYSLTR2	13	49281716	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10		49281716	65888162	47	6127										
CLYBL	171425	hgsc.bcm.edu	37	chr13	100515304	100515304	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	cttgaacaaccaatgaatttAatcccttttgtggaaactgc	6	9	0	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr13:100515304A>C	ENST00000376360.1	+	4	525	c.498A>C	c.(496-498)ttA>ttC	p.L166F	CLYBL_ENST00000376354.1_Intron|CLYBL_ENST00000376355.3_Intron|CLYBL_ENST00000444838.2_Intron|CLYBL_ENST00000339105.4_Missense_Mutation_p.L166F			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	166						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)			NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CAATGAATTTAATCCCTTTTG	0.333																																					p.L166F		Atlas-SNP	.											.	CLYBL	48	.	0			c.A498C						.						88	88	88					13																	100515304		2203	4300	6503	SO:0001583	missense	171425	exon4			GAATTTAATCCCT	AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246			18355	protein-coding gene	gene with protein product		609686					Standard	XM_005254030		Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.498A>C	chr13.hg19:g.100515304A>C	ENSP00000365538:p.Leu166Phe	38.0	0.0		65.0	20.0	NM_206808	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	hg19	CCDS32002.1	.	.	.	.	.	.	.	.	.	.	A	18.65	3.668739	0.67814	.	.	ENSG00000125246	ENST00000376360;ENST00000339105;ENST00000416504	T;T;T	0.38887	1.11;1.11;1.11	5.42	5.42	0.78866	Aldehyde-lyase domain (1);Pyruvate/Phosphoenolpyruvate kinase (2);	0.066402	0.64402	D	0.000007	T	0.48021	0.1477	M	0.69248	2.105	0.80722	D	1	P	0.49961	0.93	P	0.51866	0.682	T	0.52586	-0.8556	10	0.51188	T	0.08	0.3097	5.3713	0.16140	0.7214:0.0:0.0822:0.1964	.	166	Q8N0X4	CLYBL_HUMAN	F	166;166;83	ENSP00000365538:L166F;ENSP00000342991:L166F;ENSP00000403408:L83F	ENSP00000342991:L166F	L	+	3	2	CLYBL	99313305	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.934000	0.40163	2.180000	0.69256	0.460000	0.39030	TTA	.	.		0.333	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1			C	100515304	A	C	100515304	3	2	48	1	0	0	0	0	1	0	0	0	3575	359	13	5	512	5	CLYBL	13	100515304	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	51233588	100515304	14654574	48	6128										
ING1	3621	hgsc.bcm.edu	37	chr13	111371870	111371870	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ggcggcagcgcaggctgacaAgcccaacagcaagcgctcac	13	15	1	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr13:111371870A>G	ENST00000375774.3	+	2	1322	c.860A>G	c.(859-861)aAg>aGg	p.K287R	ING1_ENST00000375775.3_Missense_Mutation_p.K75R|ING1_ENST00000338450.7_Missense_Mutation_p.K100R|ING1_ENST00000333219.7_Missense_Mutation_p.K144R	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	287					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CAGGCTGACAAGCCCAACAGC	0.687																																					p.K287R		Atlas-SNP	.											.	ING1	106	.	0			c.A860G						.						28	27	27					13																	111371870		2200	4293	6493	SO:0001583	missense	3621	exon2			CTGACAAGCCCAA		CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"Zinc fingers, PHD-type"	6062	protein-coding gene	gene with protein product	"inhibitor of growth 1", "tumor suppressor ING1", "growth inhibitor ING1", "growth inhibitory protein ING1"	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.860A>G	chr13.hg19:g.111371870A>G	ENSP00000364929:p.Lys287Arg	43.0	0.0		55.0	4.0	NM_005537	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Missense_Mutation	SNP	ENST00000375774.3	hg19	CCDS9517.1	.	.	.	.	.	.	.	.	.	.	A	13.80	2.346561	0.41599	.	.	ENSG00000153487	ENST00000338450;ENST00000333219;ENST00000375775;ENST00000375774	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.46	5.46	0.80206	.	0.101744	0.64402	D	0.000002	T	0.58864	0.2152	L	0.57536	1.79	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.99	D;D;D	0.77004	0.989;0.98;0.979	T	0.53989	-0.8360	10	0.20519	T	0.43	-49.3307	15.5207	0.75862	1.0:0.0:0.0:0.0	.	287;144;100	Q9UK53;Q5T9H0;Q9UK53-4	ING1_HUMAN;.;.	R	100;144;75;287	ENSP00000345202:K100R;ENSP00000328436:K144R;ENSP00000364930:K75R;ENSP00000364929:K287R	ENSP00000328436:K144R	K	+	2	0	ING1	110169871	1.000000	0.71417	0.986000	0.45419	0.067000	0.16453	6.467000	0.73547	2.071000	0.62044	0.402000	0.26972	AAG	.	.		0.687	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537		G	111371870	A	G	111371870	3	3	48	1	0	0	0	0	1	0	0	0	7744	72	3	2	1014	2	ING1	13	111371870	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	10856566	111371870	3798008	49	6129										
PRKCH	5583	hgsc.bcm.edu	37	chr14	61909960	61909960	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ggcagcccacctactgctctCactgcagggagtttatctgg	11	13	2	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr14:61909960C>G	ENST00000332981.5	+	3	944	c.559C>G	c.(559-561)Cac>Gac	p.H187D	PRKCH_ENST00000555082.1_Missense_Mutation_p.H26D	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	187					blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		CTACTGCTCTCACTGCAGGGA	0.502																																					p.H187D	Melanoma(135;863 1779 8064 14443 26348)	Atlas-SNP	.											.	PRKCH	89	.	0			c.C559G						.						124	100	108					14																	61909960		2203	4300	6503	SO:0001583	missense	5583	exon3			TGCTCTCACTGCA	M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.559C>G	chr14.hg19:g.61909960C>G	ENSP00000329127:p.His187Asp	85.0	0.0		133.0	71.0	NM_006255	B4DJN5|Q16246|Q8NE03	Missense_Mutation	SNP	ENST00000332981.5	hg19	CCDS9752.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.705663	0.89018	.	.	ENSG00000027075	ENST00000556778;ENST00000555906;ENST00000332981;ENST00000555082;ENST00000553830;ENST00000553831;ENST00000553265;ENST00000556164;ENST00000557585;ENST00000557473	D;D;D;D;D;D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23;-3.23;-3.23;-3.23;-3.23;-3.23	5.66	5.66	0.87406	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);Diacylglycerol/phorbol-ester binding (1);	0.000000	0.64402	D	0.000002	D	0.98083	0.9368	H	0.97465	4.01	0.80722	D	1	D	0.54397	0.966	D	0.68943	0.961	D	0.98455	1.0593	10	0.54805	T	0.06	.	19.7525	0.96273	0.0:1.0:0.0:0.0	.	187	P24723	KPCL_HUMAN	D	26;26;187;26;129;26;26;26;26;26	ENSP00000452055:H26D;ENSP00000451205:H26D;ENSP00000329127:H187D;ENSP00000450981:H26D;ENSP00000452588:H129D;ENSP00000450959:H26D;ENSP00000451933:H26D;ENSP00000452330:H26D;ENSP00000451930:H26D;ENSP00000452528:H26D	ENSP00000329127:H187D	H	+	1	0	PRKCH	60979713	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.770000	0.85390	2.666000	0.90696	0.563000	0.77884	CAC	.	.		0.502	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255		G	61909960	C	G	61909960	3	3	48	1	0	0	0	0	1	0	0	0	12525	826	29	4	569	4	PRKCH	14	61909960	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10		61909960	45439580	50	6130										
RYR3	6263	hgsc.bcm.edu	37	chr15	34109151	34109151	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ttgaagagaaactagtacagGatttggctgtaagtactgac	11	5	0	3			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr15:34109151G>T	ENST00000389232.4	+	75	10661	c.10591G>T	c.(10591-10593)Gat>Tat	p.D3531Y	RYR3_ENST00000415757.3_Missense_Mutation_p.D3526Y	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3531					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ACTAGTACAGGATTTGGCTGT	0.423																																					p.D3531Y		Atlas-SNP	.											.	RYR3	760	.	0			c.G10591T						.						57	54	55					15																	34109151		1865	4108	5973	SO:0001583	missense	6263	exon75			GTACAGGATTTGG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10591G>T	chr15.hg19:g.34109151G>T	ENSP00000373884:p.Asp3531Tyr	95.0	0.0		128.0	42.0	NM_001036	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.874939	0.72180	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D	0.97089	-4.24	5.11	4.19	0.49359	.	0.057072	0.64402	D	0.000002	D	0.96734	0.8934	M	0.78049	2.395	0.80722	D	1	P;P	0.48503	0.911;0.74	P;P	0.45946	0.461;0.498	D	0.96602	0.9445	10	0.87932	D	0	.	13.5624	0.61797	0.0746:0.0:0.9254:0.0	.	3526;3531	Q15413-2;Q15413	.;RYR3_HUMAN	Y	3531;3530;3526	ENSP00000373884:D3531Y	ENSP00000354735:D3526Y	D	+	1	0	RYR3	31896443	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.657000	0.98554	1.368000	0.46115	0.655000	0.94253	GAT	.	.		0.423	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34109151	G	T	34109151	3	4	48	1	0	0	0	0	1	0	0	0	13785	1174	41	3	10889	3	RYR3	15	34109151	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10		34109151	68422241	51	6131										
C15orf55	256646	hgsc.bcm.edu	37	chr15	34640560	34640560	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tgcacctccatttgtgacagCatctaatgtgaagaccattc	7	11	1	3			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr15:34640560C>T	ENST00000333756.4	+	2	562	c.407C>T	c.(406-408)gCa>gTa	p.A136V	NUTM1_ENST00000438749.3_Missense_Mutation_p.A154V|NUTM1_ENST00000537011.1_Missense_Mutation_p.A164V	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	136	Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)											TTTGTGACAGCATCTAATGTG	0.562																																					p.A136V		Atlas-SNP	.											.	C15orf55	110	.	0			c.C407T						.						67	58	61					15																	34640560		2201	4298	6499	SO:0001583	missense	256646	exon2			TGACAGCATCTAA	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"nuclear protein in testis"	608963	"chromosome 15 open reading frame 55"	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.407C>T	chr15.hg19:g.34640560C>T	ENSP00000329448:p.Ala136Val	117.0	0.0		112.0	39.0	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	hg19	CCDS32190.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.341155	0.41498	.	.	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000354999;ENST00000333756	T;T;T	0.28895	1.59;1.59;1.59	5.69	4.78	0.61160	Nuclear Testis  protein, N-terminal (1);	0.456783	0.20699	N	0.087312	T	0.49081	0.1536	M	0.80183	2.485	0.09310	N	1	D;D;P	0.63046	0.992;0.99;0.751	P;P;B	0.55545	0.778;0.67;0.357	T	0.49254	-0.8959	10	0.87932	D	0	.	10.4922	0.44756	0.0:0.9111:0.0:0.0889	.	154;164;136	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	V	164;154;136;136	ENSP00000444896:A164V;ENSP00000407031:A154V;ENSP00000329448:A136V	ENSP00000329448:A136V	A	+	2	0	C15orf55	32427852	0.010000	0.17322	0.003000	0.11579	0.090000	0.18270	2.098000	0.41757	1.414000	0.47017	0.655000	0.94253	GCA	.	.		0.562	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		T	34640560	C	T	34640560	3	4	48	1	0	0	0	0	1	0	0	0	1805	710	25	3	413	3	C15orf55	15	34640560	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	531409	34640560	67890832	52	6132										
DUOX1	53905	hgsc.bcm.edu	37	chr15	45440496	45440496	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	catcgagatctccaacaactGcctgtccaaggcccagctgg	9	15	1	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr15:45440496G>C	ENST00000321429.4	+	22	3076	c.2669G>C	c.(2668-2670)tGc>tCc	p.C890S	DUOX1_ENST00000389037.3_Missense_Mutation_p.C890S|DUOX1_ENST00000561166.1_Missense_Mutation_p.C536S	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	890					cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		TCCAACAACTGCCTGTCCAAG	0.577																																					p.C890S		Atlas-SNP	.											.	DUOX1	125	.	0			c.G2669C						.						96	82	87					15																	45440496		2198	4298	6496	SO:0001583	missense	53905	exon22			ACAACTGCCTGTC	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.2669G>C	chr15.hg19:g.45440496G>C	ENSP00000317997:p.Cys890Ser	126.0	0.0		147.0	68.0	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	hg19	CCDS32221.1	.	.	.	.	.	.	.	.	.	.	G	6.243	0.413011	0.11812	.	.	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	T;T	0.61742	0.08;0.08	5.04	5.04	0.67666	EF-hand-like domain (1);	0.203512	0.52532	D	0.000066	T	0.49201	0.1543	L	0.41573	1.285	0.43787	D	0.996327	P;B	0.40794	0.729;0.038	B;B	0.43251	0.413;0.013	T	0.44375	-0.9332	10	0.02654	T	1	-35.5421	16.2575	0.82525	0.0:0.0:1.0:0.0	.	23;890	Q9NT13;Q9NRD9	.;DUOX1_HUMAN	S	890	ENSP00000317997:C890S;ENSP00000373689:C890S	ENSP00000317997:C890S	C	+	2	0	DUOX1	43227788	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.890000	0.63178	2.780000	0.95670	0.655000	0.94253	TGC	.	.		0.577	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		C	45440496	G	C	45440496	3	2	48	1	0	0	0	0	1	0	0	0	4802	1319	46	4	2747	4	DUOX1	15	45440496	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	10799936	45440496	57090896	53	6133										
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81234212	81234212	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tgttgttcctgaagctgaaaGctcagaacgagagagagaag	13	6	1	5			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr15:81234212G>T	ENST00000394685.3	+	26	3849	c.3430G>T	c.(3430-3432)Gct>Tct	p.A1144S	RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_Missense_Mutation_p.A1144S|KIAA1199_ENST00000220244.3_Missense_Mutation_p.A1144S			Q8WUJ3	CEMIP_HUMAN		1144					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GAAGCTGAAAGCTCAGAACGA	0.493																																					p.A1144S		Atlas-SNP	.											.	KIAA1199	118	.	0			c.G3430T						.						64	67	66					15																	81234212		2203	4300	6503	SO:0001583	missense	57214	exon25			CTGAAAGCTCAGA																												ENST00000394685.3:c.3430G>T	chr15.hg19:g.81234212G>T	ENSP00000378177:p.Ala1144Ser	54.0	0.0		78.0	30.0	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	hg19	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.300051	0.81136	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249	T;T;T	0.50548	0.74;0.74;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.65312	0.2679	M	0.71036	2.16	0.39517	D	0.968442	D	0.67145	0.996	P	0.57620	0.824	T	0.65298	-0.6202	10	0.44086	T	0.13	-23.631	19.9504	0.97197	0.0:0.0:1.0:0.0	.	1144	Q8WUJ3	K1199_HUMAN	S	1144	ENSP00000220244:A1144S;ENSP00000378177:A1144S;ENSP00000348583:A1144S	ENSP00000220244:A1144S	A	+	1	0	KIAA1199	79021267	1.000000	0.71417	0.508000	0.27688	0.959000	0.62525	9.063000	0.93927	2.720000	0.93068	0.591000	0.81541	GCT	.	.		0.493	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			T	81234212	G	T	81234212	3	4	48	1	0	0	0	0	1	0	0	0	8222	971	34	3	3524	3	KIAA1199	15	81234212	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	35793716	81234212	21297180	54	6134										
SLCO3A1	28232	hgsc.bcm.edu	37	chr15	92459662	92459662	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ctacatcgacgaccacgtgcGgaggaaggactcctcgctct	11	14	1	0	rs534712973		TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr15:92459662G>A	ENST00000318445.6	+	2	834	c.620G>A	c.(619-621)cGg>cAg	p.R207Q	SLCO3A1_ENST00000424469.2_Missense_Mutation_p.R207Q	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	207					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	GACCACGTGCGGAGGAAGGAC	0.582																																					p.R207Q		Atlas-SNP	.											.	SLCO3A1	84	.	0			c.G620A						.						20	21	21					15																	92459662		2198	4298	6496	SO:0001583	missense	28232	exon2			ACGTGCGGAGGAA	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"Solute carriers"	10952	protein-coding gene	gene with protein product		612435	"solute carrier family 21 (organic anion transporter), member 11"	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.620G>A	chr15.hg19:g.92459662G>A	ENSP00000320634:p.Arg207Gln	109.0	0.0		122.0	50.0	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Missense_Mutation	SNP	ENST00000318445.6	hg19	CCDS10371.1	.	.	.	.	.	.	.	.	.	.	G	19.43	3.825441	0.71143	.	.	ENSG00000176463	ENST00000318445;ENST00000424469	T;T	0.80909	-1.43;-1.43	5.44	4.53	0.55603	Major facilitator superfamily domain, general substrate transporter (1);	0.340480	0.27447	N	0.019329	T	0.74512	0.3726	L	0.56769	1.78	0.80722	D	1	P;P;P	0.51791	0.89;0.948;0.646	B;B;B	0.37601	0.131;0.254;0.227	T	0.75941	-0.3140	10	0.46703	T	0.11	.	13.0234	0.58802	0.0772:0.0:0.9228:0.0	.	149;207;207	Q9UIG8-3;Q9UIG8-2;Q9UIG8	.;.;SO3A1_HUMAN	Q	207	ENSP00000320634:R207Q;ENSP00000387846:R207Q	ENSP00000320634:R207Q	R	+	2	0	SLCO3A1	90260666	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	5.289000	0.65656	1.302000	0.44855	0.655000	0.94253	CGG	.	.		0.582	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272		A	92459662	G	A	92459662	3	1	48	1	0	0	0	0	1	0	0	0	14743	1116	39	1	626	1	SLCO3A1	15	92459662	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	11225450	92459662	10071730	55	6135										
VWA3A	146177	hgsc.bcm.edu	37	chr16	22120822	22120822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ggcatttggcctcatcaaagGggccagagtcagcatcctca	11	12	4	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr16:22120822G>A	ENST00000389398.5	+	7	599	c.503G>A	c.(502-504)gGg>gAg	p.G168E	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	168						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		CTCATCAAAGGGGCCAGAGTC	0.517																																					p.G168E		Atlas-SNP	.											.	VWA3A	115	.	0			c.G503A						.						102	87	91					16																	22120822		692	1591	2283	SO:0001583	missense	146177	exon7			TCAAAGGGGCCAG	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.503G>A	chr16.hg19:g.22120822G>A	ENSP00000374049:p.Gly168Glu	33.0	0.0		55.0	18.0	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	hg19	CCDS45441.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.430752	0.62844	.	.	ENSG00000175267	ENST00000310694;ENST00000389398	T	0.14022	2.54	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000020	T	0.35595	0.0937	M	0.64404	1.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.01528	-1.1332	10	0.36615	T	0.2	.	17.5529	0.87881	0.0:0.0:1.0:0.0	.	168	A6NCI4	VWA3A_HUMAN	E	68;168	ENSP00000374049:G168E	ENSP00000308827:G68E	G	+	2	0	VWA3A	22028323	1.000000	0.71417	0.995000	0.50966	0.828000	0.46876	5.398000	0.66308	2.481000	0.83766	0.650000	0.86243	GGG	.	.		0.517	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			A	22120822	G	A	22120822	3	1	48	1	0	0	0	0	1	0	0	0	17255	1232	43	3	529	3	VWA3A	16	22120822	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10		22120822	68233931	56	6136										
PLK1	5347	hgsc.bcm.edu	37	chr16	23700573	23700573	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ccctagggtatcagctctgtGataacagcgtgggggtgctc	14	10	2	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr16:23700573G>C	ENST00000300093.4	+	8	1396	c.1285G>C	c.(1285-1287)Gat>Cat	p.D429H	CTD-2196E14.5_ENST00000566143.1_RNA	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	429	POLO box 1. {ECO:0000255|PROSITE- ProRule:PRU00154}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		TCAGCTCTGTGATAACAGCGT	0.552																																					p.D429H	Colon(12;240 564 27038 33155)	Atlas-SNP	.											.	PLK1	67	.	0			c.G1285C						.						102	93	96					16																	23700573		2197	4300	6497	SO:0001583	missense	5347	exon8			CTCTGTGATAACA		CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"polo-like kinase (Drosophila)"	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.1285G>C	chr16.hg19:g.23700573G>C	ENSP00000300093:p.Asp429His	135.0	0.0		226.0	29.0	NM_005030	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	hg19	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.542350	0.65198	.	.	ENSG00000166851	ENST00000300093;ENST00000425844	T	0.15718	2.4	5.3	5.3	0.74995	POLO box duplicated domain (2);	0.000000	0.85682	D	0.000000	T	0.55689	0.1936	H	0.95402	3.665	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70051	-0.4978	10	0.87932	D	0	-32.0468	16.4424	0.83906	0.0:0.0:1.0:0.0	.	429	P53350	PLK1_HUMAN	H	429;332	ENSP00000300093:D429H	ENSP00000300093:D429H	D	+	1	0	PLK1	23608074	1.000000	0.71417	1.000000	0.80357	0.366000	0.29705	9.415000	0.97375	2.489000	0.83994	0.650000	0.86243	GAT	.	.		0.552	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		C	23700573	G	C	23700573	3	2	48	1	0	0	0	0	1	0	0	0	12103	1290	45	4	1315	4	PLK1	16	23700573	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	1579751	23700573	66654180	57	6137										
WDR59	79726	hgsc.bcm.edu	37	chr16	74943789	74943789	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	cagctctggccacgcttcacTttctgcagggctgtgtcctt	10	14	3	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr16:74943789T>C	ENST00000262144.6	-	15	1546	c.1416A>G	c.(1414-1416)aaA>aaG	p.K472K		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	472	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.									breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						CACGCTTCACTTTCTGCAGGG	0.483																																					p.K472K		Atlas-SNP	.											.	WDR59	66	.	0			c.A1416G						.						37	37	37					16																	74943789		2198	4300	6498	SO:0001819	synonymous_variant	79726	exon15			CTTCACTTTCTGC	AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"WD repeat domain containing"	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.1416A>G	chr16.hg19:g.74943789T>C		123.0	0.0		203.0	95.0	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Silent	SNP	ENST00000262144.6	hg19	CCDS32488.1																																																																																			.	.		0.483	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581		C	74943789	T	C	74943789	2	2	48	1	0	0	0	0	0	0	0	1	17323	1606	56	2		2	WDR59	16	74943789	Silent	SNP	T	TCGA-BD-A2L6-01A-11D-A20W-10	51243216	74943789	15410964	58	6138										
MON1B	22879	hgsc.bcm.edu	37	chr16	77228317	77228317	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	cagtcagcagcccagctgcgGggggagctgctagctgtgca	16	12	1	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr16:77228317G>T	ENST00000248248.3	+	4	911	c.561G>T	c.(559-561)cgG>cgT	p.R187R	MON1B_ENST00000320859.6_Intron|MON1B_ENST00000545553.1_Silent_p.R41R|MON1B_ENST00000439557.2_Silent_p.R78R	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	187										breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						CCCAGCTGCGGGGGGAGCTGC	0.602																																					p.R187R		Atlas-SNP	.											.	MON1B	55	.	0			c.G561T						.						95	93	93					16																	77228317		2198	4300	6498	SO:0001819	synonymous_variant	22879	exon4			GCTGCGGGGGGAG	BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"MON1 homolog B (yeast)"			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.561G>T	chr16.hg19:g.77228317G>T		46.0	0.0		90.0	37.0	NM_014940	B4DDZ0|O94949	Silent	SNP	ENST00000248248.3	hg19	CCDS10925.1																																																																																			.	.		0.602	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940		T	77228317	G	T	77228317	2	4	48	1	0	0	0	0	0	0	0	1	9708	1219	43	3		3	MON1B	16	77228317	Silent	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	2284528	77228317	13126436	59	6139										
SDR42E1	93517	hgsc.bcm.edu	37	chr16	82033315	82033315	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gactatcctgggaaggtgtcTttgttctccaggcccataga	11	10	2	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr16:82033315T>C	ENST00000328945.5	-	3	710	c.583A>G	c.(583-585)Aga>Gga	p.R195G	SDR42E1_ENST00000534209.1_5'Flank	NM_145168.2	NP_660151.2	Q8WUS8	D42E1_HUMAN	short chain dehydrogenase/reductase family 42E, member 1	195					steroid biosynthetic process (GO:0006694)	integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)			NS(2)|endometrium(1)|lung(4)|skin(3)	10						GGAAGGTGTCTTTGTTCTCCA	0.552																																					p.R195G		Atlas-SNP	.											.	SDR42E1	26	.	0			c.A583G						.						111	111	111					16																	82033315		1976	4164	6140	SO:0001583	missense	93517	exon3			GGTGTCTTTGTTC	AF161368	CCDS42205.1	16q23.3	2011-09-14				ENSG00000184860	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	29834	protein-coding gene	gene with protein product						19027726	Standard	NM_145168		Approved	HSPC105	uc002fgu.3	Q8WUS8		ENST00000328945.5:c.583A>G	chr16.hg19:g.82033315T>C	ENSP00000332407:p.Arg195Gly	105.0	0.0		128.0	6.0	NM_145168	B2RDS1|Q9P0D1	Missense_Mutation	SNP	ENST00000328945.5	hg19	CCDS42205.1	.	.	.	.	.	.	.	.	.	.	T	18.81	3.702878	0.68501	.	.	ENSG00000184860	ENST00000328945;ENST00000532128	D;D	0.87571	-2.27;-1.87	5.76	5.76	0.90799	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.88919	0.6568	M	0.64170	1.965	0.58432	D	0.999999	P	0.46859	0.885	P	0.51297	0.665	D	0.89438	0.3721	10	0.62326	D	0.03	-24.1762	11.2905	0.49247	0.0:0.0:0.1522:0.8478	.	195	Q8WUS8	D42E1_HUMAN	G	195;192	ENSP00000332407:R195G;ENSP00000434529:R192G	ENSP00000332407:R195G	R	-	1	2	SDR42E1	80590816	0.997000	0.39634	0.988000	0.46212	0.989000	0.77384	2.668000	0.46816	2.191000	0.70037	0.533000	0.62120	AGA	.	.		0.552	SDR42E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388081.2	NM_145168		C	82033315	T	C	82033315	3	2	48	1	0	0	0	0	1	0	0	0	13988	1617	56	2	602	2	SDR42E1	16	82033315	Missense_Mutation	SNP	T	TCGA-BD-A2L6-01A-11D-A20W-10	4804998	82033315	8321438	60	6140										
C17orf48	56985	hgsc.bcm.edu	37	chr17	10614393	10614393	+	Frame_Shift_Del	DEL	T	T	-													0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tctatcctgacaaaatgatgTtgaaagggagaggcagagtt							TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr17:10614393delT	ENST00000379774.4	+	4	1052	c.961delT	c.(961-963)ttgfs	p.L321fs	ADPRM_ENST00000609540.1_3'UTR	NM_020233.4	NP_064618.3	Q3LIE5	ADPRM_HUMAN	ADP-ribose/CDP-alcohol diphosphatase, manganese-dependent	321							ADP-ribose diphosphatase activity (GO:0047631)|CDP-glycerol diphosphatase activity (GO:0047734)|metal ion binding (GO:0046872)										CAAAATGATGTTGAAAGGGAG	0.383																																					p.M320fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.960delG						.						99	99	99					17																	10614393		2203	4300	6503	SO:0001589	frameshift_variant	56985	exon4			.	BC070155	CCDS11159.2	17p13.1	2012-07-20	2012-07-20	2012-07-20	ENSG00000170222	ENSG00000170222	3.6.1.13, 3.6.1.16, 3.6.1.53		30925	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 48"	C17orf48		18352857	Standard	XM_005256738		Approved	MDS006	uc002gmt.3	Q3LIE5	OTTHUMG00000130366	ENST00000379774.4:c.961delT	chr17.hg19:g.10614393delT	ENSP00000369099:p.Leu321fs	66.0	0.0		63.0	39.0	NM_020233	A8K9B4|D3DTS4|Q9BVD4|Q9NRU8	Frame_Shift_Del	DEL	ENST00000379774.4	hg19	CCDS11159.2																																																																																			.	.		0.383	ADPRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252732.2	NM_020233		-	10614393	T	-	10614393	7	5	48	1	0	1	0	1	0	0	0	0	1861	1722	60	0	971	0	C17orf48	17	10614393	Frame_Shift_Del	DEL	T	TCGA-BD-A2L6-01A-11D-A20W-10		10614393	70580817	61	6141										
NOS2	4843	hgsc.bcm.edu	37	chr17	26110007	26110007	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ggatcctcccaatgcagcgtGgggcattgcgccaggcctgc	14	14	0	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr17:26110007G>A	ENST00000313735.6	-	6	826	c.593C>T	c.(592-594)cCa>cTa	p.P198L		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	198					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	AATGCAGCGTGGGGCATTGCG	0.577																																					p.P198L		Atlas-SNP	.											.	NOS2	113	.	0			c.C593T						.						204	147	166					17																	26110007		2203	4300	6503	SO:0001583	missense	4843	exon6			CAGCGTGGGGCAT	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"nitric oxide synthase 2A (inducible, hepatocytes)"	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.593C>T	chr17.hg19:g.26110007G>A	ENSP00000327251:p.Pro198Leu	233.0	0.0		318.0	116.0	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	hg19	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.307413	0.81247	.	.	ENSG00000007171	ENST00000313735;ENST00000379105;ENST00000302153	T	0.24908	1.83	5.62	5.62	0.85841	Nitric oxide synthase, oxygenase domain (3);	0.000000	0.85682	D	0.000000	T	0.61135	0.2323	M	0.90814	3.15	0.80722	D	1	D;D	0.89917	0.993;1.0	D;D	0.97110	0.933;1.0	T	0.68830	-0.5305	10	0.87932	D	0	.	18.6591	0.91465	0.0:0.0:1.0:0.0	.	198;198	F8WEM3;P35228	.;NOS2_HUMAN	L	198	ENSP00000327251:P198L	ENSP00000305638:P198L	P	-	2	0	NOS2	23134134	1.000000	0.71417	0.998000	0.56505	0.373000	0.29922	9.781000	0.99029	2.664000	0.90586	0.603000	0.83216	CCA	.	.		0.577	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		A	26110007	G	A	26110007	3	1	48	1	0	0	0	0	1	0	0	0	10552	1348	47	3	2956	3	NOS2	17	26110007	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	15495614	26110007	55085203	62	6142										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62020305	62020305	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tgaagatgatgatgaagatcAtgttgatgttgtacaggatg	13	2	1	7			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr17:62020305A>G	ENST00000435607.1	-	23	4245	c.4169T>C	c.(4168-4170)aTg>aCg	p.M1390T	SCN4A_ENST00000578147.1_Missense_Mutation_p.M1390T	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1390					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GATGAAGATCATGTTGATGTT	0.507																																					p.M1390T		Atlas-SNP	.											.	SCN4A	205	.	0			c.T4169C						.						239	223	228					17																	62020305		2203	4300	6503	SO:0001583	missense	6329	exon23			AAGATCATGTTGA	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.4169T>C	chr17.hg19:g.62020305A>G	ENSP00000396320:p.Met1390Thr	359.0	0.0		394.0	152.0	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	A	14.79	2.639486	0.47153	.	.	ENSG00000007314	ENST00000435607	D	0.98400	-4.91	3.87	3.87	0.44632	Ion transport (1);	0.193855	0.47093	D	0.000247	D	0.95698	0.8601	L	0.37466	1.105	0.44006	D	0.996714	B	0.31893	0.345	B	0.32864	0.154	D	0.95435	0.8520	10	0.72032	D	0.01	.	12.3276	0.55020	1.0:0.0:0.0:0.0	.	1390	P35499	SCN4A_HUMAN	T	1390	ENSP00000396320:M1390T	ENSP00000396320:M1390T	M	-	2	0	SCN4A	59374037	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.087000	0.94110	1.760000	0.52011	0.379000	0.24179	ATG	.	.		0.507	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		G	62020305	A	G	62020305	3	3	48	1	0	0	0	0	1	0	0	0	13935	217	8	2	1349	2	SCN4A	17	62020305	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	35910298	62020305	19174905	63	6143										
GPR142	350383	hgsc.bcm.edu	37	chr17	72363763	72363763	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ggaagacaaatcaatggtgtCccatgcacagaaaagccagc	10	10	1	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr17:72363763C>T	ENST00000335666.4	+	1	167	c.119C>T	c.(118-120)tCc>tTc	p.S40F		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	40						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						TCAATGGTGTCCCATGCACAG	0.542																																					p.S40F		Atlas-SNP	.											.	GPR142	74	.	0			c.C119T						.						118	96	103					17																	72363763		2203	4300	6503	SO:0001583	missense	350383	exon1			TGGTGTCCCATGC	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"GPCR / Class A : Orphans"	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.119C>T	chr17.hg19:g.72363763C>T	ENSP00000335158:p.Ser40Phe	90.0	0.0		108.0	34.0	NM_181790	A4CYJ8|Q86SL3	Missense_Mutation	SNP	ENST00000335666.4	hg19	CCDS11698.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.900822	0.52227	.	.	ENSG00000257008	ENST00000335666	T	0.71698	-0.59	2.09	2.09	0.27110	.	.	.	.	.	T	0.61664	0.2365	N	0.08118	0	0.35323	D	0.784908	D	0.59357	0.985	P	0.56278	0.795	T	0.71255	-0.4647	9	0.87932	D	0	.	9.8751	0.41197	0.0:1.0:0.0:0.0	.	40	Q7Z601	GP142_HUMAN	F	40	ENSP00000335158:S40F	ENSP00000335158:S40F	S	+	2	0	GPR142	69875358	0.998000	0.40836	0.029000	0.17559	0.010000	0.07245	3.861000	0.56002	1.174000	0.42811	0.650000	0.86243	TCC	.	.		0.542	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790		T	72363763	C	T	72363763	3	4	48	1	0	0	0	0	1	0	0	0	6658	855	30	3	121	3	GPR142	17	72363763	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	10343458	72363763	8831447	64	6144										
RHBDF2	79651	hgsc.bcm.edu	37	chr17	74473344	74473344	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gctggcagagagtgggggggActcaaagacatcatcaggca	16	8	3	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr17:74473344A>T	ENST00000313080.4	-	8	1198	c.925T>A	c.(925-927)Tcc>Acc	p.S309T	RHBDF2_ENST00000592378.1_5'Flank|RHBDF2_ENST00000591885.1_Missense_Mutation_p.S280T|RHBDF2_ENST00000389760.4_Missense_Mutation_p.S280T	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	309					negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(4)|skin(1)	27						AGTGGGGGGGACTCAAAGACA	0.582																																					p.S309T		Atlas-SNP	.											.	RHBDF2	57	.	0			c.T925A						.						31	37	35					17																	74473344		2202	4299	6501	SO:0001583	missense	79651	exon8			GGGGGGACTCAAA	BC016034	CCDS32743.1, CCDS32744.1	17q25.3	2014-09-17	2006-02-22	2006-02-22		ENSG00000129667			20788	protein-coding gene	gene with protein product		614404	"rhomboid, veinlet-like 6 (Drosophila)", "tylosis with oesophageal cancer"	RHBDL6, TOC		12838346, 22265016	Standard	NM_024599		Approved	FLJ22341, RHBDL5, TOCG	uc002jrq.2	Q6PJF5		ENST00000313080.4:c.925T>A	chr17.hg19:g.74473344A>T	ENSP00000322775:p.Ser309Thr	49.0	0.0		70.0	22.0	NM_024599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Missense_Mutation	SNP	ENST00000313080.4	hg19	CCDS32743.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.561507	0.65538	.	.	ENSG00000129667	ENST00000313080;ENST00000389760;ENST00000389762	T;T	0.70045	-0.45;-0.45	5.54	5.54	0.83059	.	0.058379	0.64402	D	0.000001	T	0.74951	0.3784	L	0.41710	1.295	0.50313	D	0.999868	D;P;P;P	0.76494	0.999;0.938;0.84;0.675	D;P;P;B	0.85130	0.997;0.557;0.773;0.28	T	0.73142	-0.4076	10	0.33141	T	0.24	-20.856	15.678	0.77344	1.0:0.0:0.0:0.0	.	280;255;309;280	B7Z8H4;Q6ZWP8;Q6PJF5;Q6PJF5-2	.;.;RHDF2_HUMAN;.	T	309;280;255	ENSP00000322775:S309T;ENSP00000374410:S280T	ENSP00000322775:S309T	S	-	1	0	RHBDF2	71984939	1.000000	0.71417	0.997000	0.53966	0.746000	0.42486	8.701000	0.91331	2.098000	0.63641	0.533000	0.62120	TCC	.	.		0.582	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599		T	74473344	A	T	74473344	3	4	48	1	0	0	0	0	1	0	0	0	13335	275	10	4	1693	4	RHBDF2	17	74473344	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	2109581	74473344	6721866	65	6145										
ROCK1	6093	hgsc.bcm.edu	37	chr18	18629104	18629105	+	Frame_Shift_Ins	INS	-	-	A													0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tgatgtccctttcttcccagINSaaaaaagcagaatcagatct					rs35810558		TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr18:18629104_18629105insA	ENST00000399799.2	-	4	1302_1303	c.362_363insT	c.(361-363)ttcfs	p.F121fs		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	121	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TTTCTTCCCAGAAAAAAGCAGA	0.361																																					p.F121fs		Atlas-INDEL	.											.,1	ROCK1	162	.	0			c.363_364insT						.																																			SO:0001589	frameshift_variant	6093	exon4			.		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.363dupT	chr18.hg19:g.18629110_18629110dupA	ENSP00000382697:p.Phe121fs	83.0	0.0		127.0	13.0	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Frame_Shift_Ins	INS	ENST00000399799.2	hg19	CCDS11870.2																																																																																			.	.		0.361	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		A	18629105	-	A	18629104	7	5	48	1	0	1	1	0	0	0	0	0	13532	933	33	0	3821	0	ROCK1	18	18629104	Frame_Shift_Ins	INS	-	TCGA-BD-A2L6-01A-11D-A20W-10		18629104	59448144	66	6146										
MEX3C	51320	hgsc.bcm.edu	37	chr18	48723394	48723394	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	agctcggccgcctccggggcCccgggccggccgggcggagc	19	18	0	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr18:48723394C>A	ENST00000591040.1	-	2	43				MEX3C_ENST00000592416.1_5'Flank			Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		cctccggggccccgggccggc	0.786																																					p.G99G		Atlas-SNP	.											.	MEX3C	77	.	0			c.G297T						.						9	9	9					18																	48723394		1281	2866	4147	SO:0001627	intron_variant	51320	exon1			CGGGGCCCCGGGC	BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	28040	protein-coding gene	gene with protein product		611005	"ring finger and KH domain containing 2", "mex-3 homolog C (C. elegans)"	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693	ENST00000591040.1:c.757-19448G>T	chr18.hg19:g.48723394C>A		12.0	0.0		14.0	7.0	NM_016626	A1L022|Q9NZE3	Silent	SNP	ENST00000591040.1	hg19																																																																																				.	.		0.786	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000449559.1	NM_016626		A	48723394	C	A	48723394	1	1	48	0	1	0	0	0	0	0	0	0	9520	610	22	3		3	MEX3C	18	48723394	Intron	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	30094290	48723394	29353854	67	6147										
MAST1	22983	hgsc.bcm.edu	37	chr19	12978549	12978549	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gccccctccatgcagcaagcGattctccgcgtccgaggcca	10	18	1	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr19:12978549G>C	ENST00000251472.4	+	20	2363	c.2324G>C	c.(2323-2325)cGa>cCa	p.R775P		NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1											NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						TGCAGCAAGCGATTCTCCGCG	0.682																																					p.R775P		Atlas-SNP	.											.	MAST1	214	.	0			c.G2324C						.						7	7	7					19																	12978549		2139	4185	6324	SO:0001583	missense	22983	exon20			GCAAGCGATTCTC	AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.2324G>C	chr19.hg19:g.12978549G>C	ENSP00000251472:p.Arg775Pro	41.0	0.0		55.0	13.0	NM_014975		Missense_Mutation	SNP	ENST00000251472.4	hg19	CCDS32921.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.423921	0.83667	.	.	ENSG00000105613	ENST00000251472	T	0.68765	-0.35	4.44	4.44	0.53790	.	0.071807	0.56097	D	0.000031	T	0.74627	0.3741	L	0.46819	1.47	0.58432	D	0.999997	D	0.67145	0.996	D	0.64144	0.922	T	0.77536	-0.2551	10	0.66056	D	0.02	-22.8863	15.0031	0.71489	0.0:0.0:1.0:0.0	.	775	Q9Y2H9	MAST1_HUMAN	P	775	ENSP00000251472:R775P	ENSP00000251472:R775P	R	+	2	0	MAST1	12839549	1.000000	0.71417	0.996000	0.52242	0.519000	0.34347	6.595000	0.74109	2.229000	0.72834	0.543000	0.68304	CGA	.	.		0.682	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975		C	12978549	G	C	12978549	3	2	48	1	0	0	0	0	1	0	0	0	9333	1058	37	4	2402	4	MAST1	19	12978549	Missense_Mutation	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10		12978549	46150434	68	6148										
GPI	2821	hgsc.bcm.edu	37	chr19	34887542	34887542	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tccagacccagcaccccataCggaagggtctgcatcacaag	9	15	2	1	rs373085760		TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr19:34887542C>A	ENST00000356487.5	+	14	1490	c.1249C>A	c.(1249-1251)Cgg>Agg	p.R417R	GPI_ENST00000586425.1_Silent_p.R417R|GPI_ENST00000415930.3_Silent_p.R428R	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase	417					aldehyde catabolic process (GO:0046185)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|hemostasis (GO:0007599)|humoral immune response (GO:0006959)|learning or memory (GO:0007611)|methylglyoxal biosynthetic process (GO:0019242)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucose-6-phosphate isomerase activity (GO:0004347)|intramolecular transferase activity (GO:0016866)|monosaccharide binding (GO:0048029)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	25	Esophageal squamous(110;0.162)					GCACCCCATACGGAAGGGTCT	0.592																																					p.R428R		Atlas-SNP	.											.	GPI	63	.	0			c.C1282A						.						53	47	49					19																	34887542		2203	4300	6503	SO:0001819	synonymous_variant	2821	exon14			CCCATACGGAAGG	M61214	CCDS12437.1, CCDS54246.1	19q13.1	2012-10-02	2010-05-11			ENSG00000105220	5.3.1.9		4458	protein-coding gene	gene with protein product		172400	"glucose phosphate isomerase"			2387591, 8575767	Standard	NM_001184722		Approved	AMF, NLK	uc002nvg.2	P06744		ENST00000356487.5:c.1249C>A	chr19.hg19:g.34887542C>A		74.0	0.0		109.0	32.0	NM_001184722	B4DG39|Q9BRD3|Q9BSK5|Q9UHE6	Silent	SNP	ENST00000356487.5	hg19	CCDS12437.1																																																																																			.	.		0.592	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451693.3			A	34887542	C	A	34887542	2	1	48	1	0	0	0	0	0	0	0	1	6619	527	19	1		1	GPI	19	34887542	Silent	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	21908993	34887542	24241441	69	6149										
HIF3A	64344	hgsc.bcm.edu	37	chr19	46812017	46812017	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	gggcgcaccctcaacctcaaGgcggccacctggaaggtgcg	14	15	2	0			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr19:46812017G>A	ENST00000377670.4	+	5	577	c.546G>A	c.(544-546)aaG>aaA	p.K182K	HIF3A_ENST00000244303.6_Silent_p.K113K|HIF3A_ENST00000420102.2_Silent_p.K131K|HIF3A_ENST00000600383.1_Silent_p.K113K|HIF3A_ENST00000300862.3_Silent_p.K180K|RNU6-924P_ENST00000362926.1_RNA|HIF3A_ENST00000472815.1_Silent_p.K113K|HIF3A_ENST00000339613.2_Silent_p.K126K|HIF3A_ENST00000525854.1_3'UTR	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	182					cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		TCAACCTCAAGGCGGCCACCT	0.677																																					p.K182K		Atlas-SNP	.											.	HIF3A	154	.	0			c.G546A						.						15	13	14					19																	46812017		2198	4286	6484	SO:0001819	synonymous_variant	64344	exon5			CCTCAAGGCGGCC	AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"Basic helix-loop-helix proteins"	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.546G>A	chr19.hg19:g.46812017G>A		43.0	0.0		67.0	22.0	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Silent	SNP	ENST00000377670.4	hg19	CCDS12681.2	.	.	.	.	.	.	.	.	.	.	G	10.04	1.242571	0.22796	.	.	ENSG00000124440	ENST00000472815	.	.	.	4.8	-1.7	0.08159	.	.	.	.	.	T	0.55016	0.1894	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51671	-0.8676	4	.	.	.	.	9.5928	0.39557	0.4783:0.0:0.5217:0.0	.	.	.	.	S	155	.	.	G	+	1	0	HIF3A	51503857	1.000000	0.71417	0.977000	0.42913	0.939000	0.58152	0.884000	0.28214	-0.123000	0.11745	-0.254000	0.11334	GGC	.	.		0.677	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3			A	46812017	G	A	46812017	2	1	48	1	0	0	0	0	0	0	0	1	7114	991	35	3		3	HIF3A	19	46812017	Silent	SNP	G	TCGA-BD-A2L6-01A-11D-A20W-10	11924475	46812017	12316966	70	6150										
CSNK2A1	1457	hgsc.bcm.edu	37	chr20	489179	489184	+	In_Frame_Del	DEL	GGCACG	GGCACG	-													0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tgtaaactctggccctgcttGgcacgggtcccgacatgtca					rs138114936	byFrequency	TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	GGCACG	GGCACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr20:489179_489184delGGCACG	ENST00000217244.3	-	3	387_392	c.12_17delCGTGCC	c.(10-18)cccgtgcca>cca	p.4_6PVP>P	CSNK2A1_ENST00000400227.3_In_Frame_Del_p.4_6PVP>P|CSNK2A1_ENST00000349736.5_In_Frame_Del_p.4_6PVP>P|CSNK2A1_ENST00000400217.2_Intron	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	4					axon guidance (GO:0007411)|chaperone-mediated protein folding (GO:0061077)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	ATP binding (GO:0005524)|Hsp90 protein binding (GO:0051879)|protein N-terminus binding (GO:0047485)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			GGCCCTGCTTGGCACGGGTCCCGACA	0.495																																					p.5_6del		Atlas-Indel,Pindel	.											.	CSNK2A1	36	.	0			c.13_18del						.																																			SO:0001651	inframe_deletion	1457	exon2			.	M55265	CCDS13003.1, CCDS13004.1	20p13	2013-01-17			ENSG00000101266	ENSG00000101266			2457	protein-coding gene	gene with protein product		115440				2174700, 1766873	Standard	NM_177559		Approved		uc002wdx.1	P68400	OTTHUMG00000031636	ENST00000217244.3:c.12_17delCGTGCC	chr20.hg19:g.489179_489184delGGCACG	ENSP00000217244:p.Pro4_Val5del	141.0	0.0		199.0	37.0	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	In_Frame_Del	DEL	ENST00000217244.3	hg19	CCDS13003.1																																																																																			.	.		0.495	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895		-	489184	GGCACG	-	489179	7	5	48	1	0	1	0	1	0	0	0	0	3959	1348	47	0	1206	0	CSNK2A1	20	489179	In_Frame_Del	DEL	GGCACG	TCGA-BD-A2L6-01A-11D-A20W-10		489179	62536341	71	6151										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20177325	20177325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ttgccctcaaccccattttcCggcactacaccaagttcttt	4	16	2	0	rs142308308		TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr20:20177325C>T	ENST00000245957.5	+	16	1778	c.1702C>T	c.(1702-1704)Cgg>Tgg	p.R568W	C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000389656.3_5'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		568										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		CCCCATTTTCCGGCACTACAC	0.468																																					p.R568W		Atlas-SNP	.											.	C20orf26	188	.	0			c.C1702T						.	C	TRP/ARG	0,4406		0,0,2203	146	128	134		1702	4.8	1	20	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	no	missense	C20orf26	NM_015585.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	568/1238	20177325	1,13005	2203	4300	6503	SO:0001583	missense	26074	exon16			ATTTTCCGGCACT																												ENST00000245957.5:c.1702C>T	chr20.hg19:g.20177325C>T	ENSP00000245957:p.Arg568Trp	108.0	0.0		199.0	113.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	hg19	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.297695	0.81025	0.0	1.16E-4	ENSG00000089101	ENST00000343997;ENST00000339482;ENST00000389655;ENST00000245957	T	0.58210	0.35	5.83	4.83	0.62350	.	0.239742	0.36854	N	0.002374	T	0.60090	0.2242	L	0.42245	1.32	0.80722	D	1	D;D	0.76494	0.999;0.998	P;P	0.59221	0.854;0.731	T	0.62101	-0.6925	10	0.72032	D	0.01	.	13.5742	0.61864	0.2721:0.7279:0.0:0.0	.	548;568	F8W6K4;Q8NHU2	.;CT026_HUMAN	W	508;136;548;568	ENSP00000245957:R568W	ENSP00000245957:R568W	R	+	1	2	C20orf26	20125325	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.387000	0.44389	2.741000	0.93983	0.655000	0.94253	CGG	.	C|1.000;T|0.000		0.468	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			T	20177325	C	T	20177325	3	4	48	1	0	0	0	0	1	0	0	0	2108	643	23	1	1792	1	C20orf26	20	20177325	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	19688146	20177325	42848195	72	6152										
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28211905	28211905	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	aataaggtaaaaacgaactaCcttgggctgcaaaacgaaga	9	7	0	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr21:28211905C>A	ENST00000284984.3	-	7	2483		c.e7+1			NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1						heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		AAACGAACTACCTTGGGCTGC	0.418																																					.		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.2028+1G>T						.						124	121	122					21																	28211905		2203	4300	6503	SO:0001630	splice_region_variant	9510	exon8			GAACTACCTTGGG	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.2028+1G>T	chr21.hg19:g.28211905C>A		27.0	0.0		27.0	12.0	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Splice_Site	SNP	ENST00000284984.3	hg19	CCDS33524.1	.	.	.	.	.	.	.	.	.	.	C	19.47	3.833592	0.71258	.	.	ENSG00000154734	ENST00000284984	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6142	0.95626	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADAMTS1	27133776	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	7.320000	0.79064	2.941000	0.99782	0.655000	0.94253	.	.	.		0.418	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2		Intron	A	28211905	C	A	28211905	5	1	48	1	0	0	0	0	0	0	1	0	255	521	18	3	886	3	ADAMTS1	21	28211905	Splice_Site	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10		28211905	19917990	73	6153										
KRTAP13-4	284827	hgsc.bcm.edu	37	chr21	31802993	31802993	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	acggatccagattctgctacCcaaactacttggcttctgga	8	12	2	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr21:31802993C>A	ENST00000334068.2	+	1	422	c.400C>A	c.(400-402)Cca>Aca	p.P134T		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	134						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						ATTCTGCTACCCAAACTACTT	0.468																																					p.P134T	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.C400A						.						99	92	94					21																	31802993		2203	4300	6503	SO:0001583	missense	284827	exon1			TGCTACCCAAACT	AP001708	CCDS13592.1	21q22.1	2006-03-13			ENSG00000186971	ENSG00000186971		"Keratin associated proteins"	18926	protein-coding gene	gene with protein product						12359730	Standard	NM_181600		Approved	KAP13.4	uc011acw.2	Q3LI77	OTTHUMG00000057770	ENST00000334068.2:c.400C>A	chr21.hg19:g.31802993C>A	ENSP00000334834:p.Pro134Thr	127.0	0.0		193.0	92.0	NM_181600	A2RRL3	Missense_Mutation	SNP	ENST00000334068.2	hg19	CCDS13592.1	.	.	.	.	.	.	.	.	.	.	-	16.27	3.076530	0.55753	.	.	ENSG00000186971	ENST00000334068	T	0.10763	2.84	4.5	4.5	0.54988	.	0.148962	0.30695	N	0.009076	T	0.37237	0.0996	M	0.89095	3.005	0.09310	N	1	D	0.71674	0.998	D	0.69824	0.966	T	0.26677	-1.0096	10	0.87932	D	0	.	13.4325	0.61064	0.0:1.0:0.0:0.0	.	134	Q3LI77	KR134_HUMAN	T	134	ENSP00000334834:P134T	ENSP00000334834:P134T	P	+	1	0	KRTAP13-4	30724864	0.008000	0.16893	0.028000	0.17463	0.004000	0.04260	1.081000	0.30791	2.412000	0.81896	0.650000	0.86243	CCA	.	.		0.468	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1			A	31802993	C	A	31802993	3	1	48	1	0	0	0	0	1	0	0	0	8534	623	22	3	402	3	KRTAP13-4	21	31802993	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	3591088	31802993	16326902	74	6154										
C21orf59	56683	hgsc.bcm.edu	37	chr21	33976524	33976524	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	ggggtaaacaatcatcaccgCgcctcgaagctggtccaagg	12	12	2	0	rs367724246		TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chr21:33976524C>A	ENST00000290155.3	-	4	1067	c.445G>T	c.(445-447)Gcg>Tcg	p.A149S	C21orf59_ENST00000540881.1_Missense_Mutation_p.A93S|AP000275.65_ENST00000553001.1_Missense_Mutation_p.A149S|C21orf59_ENST00000382549.4_Missense_Mutation_p.A149S	NM_021254.2	NP_067077.1	P57076	CU059_HUMAN	chromosome 21 open reading frame 59	149						cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|prostate(1)|skin(1)	5						ATCATCACCGCGCCTCGAAGC	0.493																																					p.A149S		Atlas-SNP	.											.	C21orf59	11	.	0			c.G445T						.						129	108	115					21																	33976524		2203	4300	6503	SO:0001583	missense	56683	exon4			TCACCGCGCCTCG	AF282851	CCDS13617.1	21q22.11	2014-02-03	2003-07-22		ENSG00000159079	ENSG00000159079			1301	protein-coding gene	gene with protein product		615494	"chromosome 21 open reading frame 48"	C21orf48		24094744	Standard	NM_021254		Approved	FLJ20467, FBB18, CILD26	uc002yqc.3	P57076	OTTHUMG00000179510	ENST00000290155.3:c.445G>T	chr21.hg19:g.33976524C>A	ENSP00000290155:p.Ala149Ser	108.0	0.0		172.0	78.0	NM_021254	Q53FH0	Missense_Mutation	SNP	ENST00000290155.3	hg19	CCDS13617.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.881309	0.91740	.	.	ENSG00000159079	ENST00000553001;ENST00000440966;ENST00000382549;ENST00000290155;ENST00000543202;ENST00000540881;ENST00000458138	.	.	.	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.83358	0.5237	M	0.84326	2.69	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.977;0.992;1.0;0.999;1.0;1.0	D;D;P;P;D;P;D;D	0.91635	0.999;0.998;0.788;0.831;0.997;0.874;0.998;0.999	D	0.85121	0.0969	9	0.54805	T	0.06	-16.3074	18.2748	0.90078	0.0:1.0:0.0:0.0	.	93;149;149;149;149;30;149;149	F5GXV2;Q53FH0;C9J818;P57076;D3DSE6;Q8N9H5;Q96NJ2;F8VZ95	.;.;.;CU059_HUMAN;.;.;.;.	S	149;149;149;149;149;93;132	.	ENSP00000290155:A149S	A	-	1	0	C21orf59	32898395	1.000000	0.71417	0.243000	0.24186	0.699000	0.40488	7.647000	0.83462	2.539000	0.85634	0.563000	0.77884	GCG	.	.		0.493	C21orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139431.1	NM_021254		A	33976524	C	A	33976524	3	1	48	1	0	0	0	0	1	0	0	0	2132	768	27	1	443	1	C21orf59	21	33976524	Missense_Mutation	SNP	C	TCGA-BD-A2L6-01A-11D-A20W-10	2173531	33976524	14153371	75	6155										
TAF1	6872	hgsc.bcm.edu	37	chrX	70604840	70604840	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	cagattgtaaatatggggaaActgtttactgccatacatct	8	7	1	1			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chrX:70604840A>G	ENST00000373790.4	+	14	2215	c.2164A>G	c.(2164-2166)Act>Gct	p.T722A	TAF1_ENST00000276072.3_Missense_Mutation_p.T743A|TAF1_ENST00000449580.1_Missense_Mutation_p.T722A|TAF1_ENST00000423759.1_Missense_Mutation_p.T743A	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	722	Histone acetyltransferase (HAT).				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				ATATGGGGAAACTGTTTACTG	0.388																																					p.T743A		Atlas-SNP	.											.	TAF1	439	.	0			c.A2227G						.						142	122	129					X																	70604840		2203	4300	6503	SO:0001583	missense	6872	exon14			GGGGAAACTGTTT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.2164A>G	chrX.hg19:g.70604840A>G	ENSP00000362895:p.Thr722Ala	74.0	0.0		104.0	82.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	20.4	3.990674	0.74589	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.16457	2.34;2.34;2.34;2.34	5.32	4.11	0.48088	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.000000	0.85682	D	0.000000	T	0.38321	0.1036	M	0.81112	2.525	0.49798	D	0.999828	P;P	0.51057	0.891;0.941	P;P	0.60012	0.867;0.79	T	0.26018	-1.0115	10	0.52906	T	0.07	.	11.5744	0.50854	0.8533:0.1467:0.0:0.0	.	722;743	P21675;P21675-2	TAF1_HUMAN;.	A	722;722;743;743	ENSP00000362895:T722A;ENSP00000389000:T722A;ENSP00000406549:T743A;ENSP00000276072:T743A	ENSP00000276072:T743A	T	+	1	0	TAF1	70521565	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.910000	0.92685	1.773000	0.52216	0.481000	0.45027	ACT	.	.		0.388	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		G	70604840	A	G	70604840	3	3	48	1	0	0	0	0	1	0	0	0	15528	43	2	2	2281	2	TAF1	23	70604840	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10		70604840	84665720	76	6156										
AFF2	2334	hgsc.bcm.edu	37	chrX	148037577	148037577	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0649350649350649	5	1	1.38973095869648	2.06474313863476	1.14104226082448	1	1	0	tggagcttcatgacccaccaAgaggccgcaacaaagccact	9	14	1	2			TCGA-BD-A2L6-01A-11D-A20W-10	TCGA-BD-A2L6-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45885dc7-e1ae-4db7-a384-59865f009277	c37989ed-705e-458e-a38d-819266a434f5	g.chrX:148037577A>G	ENST00000370460.2	+	11	2481	c.2002A>G	c.(2002-2004)Aga>Gga	p.R668G	AFF2_ENST00000370457.5_Missense_Mutation_p.R635G|AFF2_ENST00000342251.3_Missense_Mutation_p.R635G|AFF2_ENST00000286437.5_Missense_Mutation_p.R309G	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	668					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					TGACCCACCAAGAGGCCGCAA	0.512																																					p.R668G		Atlas-SNP	.											.	AFF2	679	.	0			c.A2002G						.						83	88	87					X																	148037577		2203	4300	6503	SO:0001583	missense	2334	exon11			CCACCAAGAGGCC	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.2002A>G	chrX.hg19:g.148037577A>G	ENSP00000359489:p.Arg668Gly	30.0	0.0		50.0	42.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	hg19	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.650378	0.67472	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.67	4.49	0.54785	.	0.113755	0.64402	D	0.000010	T	0.56337	0.1978	N	0.24115	0.695	0.33313	D	0.566365	D;P;P;P;P;P	0.53312	0.959;0.902;0.902;0.902;0.902;0.92	P;P;P;P;P;P	0.50860	0.652;0.52;0.52;0.52;0.52;0.652	T	0.67051	-0.5768	10	0.49607	T	0.09	.	11.8392	0.52344	0.8517:0.1483:0.0:0.0	.	309;633;635;629;658;668	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	G	668;635;635;309	ENSP00000359489:R668G;ENSP00000359486:R635G;ENSP00000345459:R635G;ENSP00000286437:R309G	ENSP00000286437:R309G	R	+	1	2	AFF2	147845277	1.000000	0.71417	0.936000	0.37596	0.955000	0.61496	4.237000	0.58681	0.753000	0.32945	0.486000	0.48141	AGA	.	.		0.512	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		G	148037577	A	G	148037577	3	3	48	1	0	0	0	0	1	0	0	0	357	64	3	2	2099	2	AFF2	23	148037577	Missense_Mutation	SNP	A	TCGA-BD-A2L6-01A-11D-A20W-10	77432737	148037577	7232983	77	6157										
KIAA0562	9731	hgsc.bcm.edu	37	chr1	3754080	3754080	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gggcaaatcaaaaggtcttcGcatctagagaacaaaaagga	10	7	3	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:3754080G>A	ENST00000378230.3	-	9	1219	c.895C>T	c.(895-897)Cga>Tga	p.R299*	CEP104_ENST00000460038.1_5'Flank	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	299						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)	p.R299*(1)		breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						AAAGGTCTTCGCATCTAGAGA	0.453																																					p.R299X		Atlas-SNP	.											CEP104,colon,carcinoma,0,1	CEP104	79	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C895T						.						53	58	56					1																	3754080		2203	4300	6503	SO:0001587	stop_gained	9731	exon9			GTCTTCGCATCTA	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"glycine, glutamate, thienylcyclohexylpiperidine binding protein"		"KIAA0562"	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.895C>T	chr1.hg19:g.3754080G>A	ENSP00000367476:p.Arg299*	53.0	0.0		61.0	3.0	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Nonsense_Mutation	SNP	ENST00000378230.3	hg19	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	G	37	6.176452	0.97348	.	.	ENSG00000116198	ENST00000378230	.	.	.	5.44	1.19	0.21007	.	0.639794	0.15563	N	0.255851	.	.	.	.	.	.	0.46167	D	0.998909	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	13.3671	0.60692	0.0:0.0:0.4562:0.5438	.	.	.	.	X	299	.	ENSP00000367476:R299X	R	-	1	2	CEP104	3743940	0.993000	0.37304	0.079000	0.20413	0.216000	0.24613	1.558000	0.36309	-0.035000	0.13691	0.555000	0.69702	CGA	.	.		0.453	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		A	3754080	G	A	3754080	4	1	49	1	0	0	0	0	0	1	0	0	8193	1095	38	1	1938	1	KIAA0562	1	3754080	Nonsense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10		3754080	245496541	1	6158										
KLHL21	9903	hgsc.bcm.edu	37	chr1	6653499	6653499	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	atcgctgccactgtccaactCgaagccacgcccacccgaga	8	18	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:6653499C>T	ENST00000377658.4	-	4	1771	c.1720G>A	c.(1720-1722)Gag>Aag	p.E574K	KLHL21_ENST00000467612.1_Missense_Mutation_p.E207K|KLHL21_ENST00000377663.3_3'UTR	NM_014851.2	NP_055666.2	Q9UJP4	KLH21_HUMAN	kelch-like family member 21	574					chromosome passenger complex localization to spindle midzone (GO:0035853)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|regulation of cytokinesis (GO:0032465)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|polar microtubule (GO:0005827)				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|prostate(2)	8	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)		CTGTCCAACTCGAAGCCACGC	0.687																																					p.E574K		Atlas-SNP	.											KLHL21,right_upper_lobe,carcinoma,0,1	KLHL21	27	.	0			c.G1720A						.						60	56	58					1																	6653499		2203	4300	6503	SO:0001583	missense	9903	exon4			CCAACTCGAAGCC	AK090472	CCDS30575.1	1p36	2013-01-30	2013-01-30		ENSG00000162413	ENSG00000162413		"Kelch-like", "BTB/POZ domain containing"	29041	protein-coding gene	gene with protein product			"kelch-like 21 (Drosophila)"				Standard	XM_005263542		Approved	KIAA0469	uc001aoa.3	Q9UJP4	OTTHUMG00000001437	ENST00000377658.4:c.1720G>A	chr1.hg19:g.6653499C>T	ENSP00000366886:p.Glu574Lys	50.0	1.0		51.0	3.0	NM_014851	B3KQP2|O75057|Q5SY26|Q5SY28|Q8N4I6|Q8NF10	Missense_Mutation	SNP	ENST00000377658.4	hg19	CCDS30575.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.967263	0.53507	.	.	ENSG00000162413	ENST00000377658;ENST00000505933	T	0.72505	-0.66	5.33	4.4	0.53042	.	1.549940	0.03705	N	0.249336	T	0.58764	0.2145	N	0.19112	0.55	0.80722	D	1	B	0.12013	0.005	B	0.06405	0.002	T	0.55477	-0.8135	10	0.54805	T	0.06	.	7.1029	0.25348	0.0:0.8336:0.0:0.1664	.	574	Q9UJP4	KLH21_HUMAN	K	574;12	ENSP00000366886:E574K	ENSP00000366886:E574K	E	-	1	0	KLHL21	6576086	0.229000	0.23729	0.997000	0.53966	0.621000	0.37620	1.751000	0.38339	2.655000	0.90218	0.655000	0.94253	GAG	.	.		0.687	KLHL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004188.1	NM_014851		T	6653499	C	T	6653499	3	4	49	1	0	0	0	0	1	0	0	0	8385	893	31	1	77	1	KLHL21	1	6653499	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	2899419	6653499	242597122	2	6159										
KAZ	23254	hgsc.bcm.edu	37	chr1	15287300	15287300	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	caagtcctctgaggtcctctCggccaccgagctcagggtcc	11	16	3	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:15287300C>T	ENST00000376030.2	+	2	641	c.347C>T	c.(346-348)tCg>tTg	p.S116L	KAZN_ENST00000503743.1_Missense_Mutation_p.S116L|KAZN_ENST00000422387.2_Missense_Mutation_p.S116L|KAZN_ENST00000361144.5_Missense_Mutation_p.S110L|KAZN_ENST00000400797.3_Missense_Mutation_p.S22L|KAZN_ENST00000400798.2_Missense_Mutation_p.S22L	NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	116					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						GAGGTCCTCTCGGCCACCGAG	0.617																																					p.S116L		Atlas-SNP	.											.	KAZN	57	.	0			c.C347T						.						30	29	29					1																	15287300		2203	4300	6503	SO:0001583	missense	23254	exon2			TCCTCTCGGCCAC	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.347C>T	chr1.hg19:g.15287300C>T	ENSP00000365198:p.Ser116Leu	51.0	0.0		85.0	5.0	NM_015209	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	hg19	CCDS152.2	.	.	.	.	.	.	.	.	.	.	C	25.6	4.651026	0.88056	.	.	ENSG00000189337	ENST00000376030;ENST00000503743;ENST00000422387;ENST00000361144;ENST00000376028;ENST00000400798;ENST00000400797	T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.67757	0.2927	M	0.68952	2.095	0.80722	D	1	D;D;P;P	0.89917	1.0;1.0;0.519;0.772	D;D;B;B	0.83275	0.991;0.996;0.113;0.078	T	0.62348	-0.6873	10	0.30854	T	0.27	-2.9242	18.8652	0.92289	0.0:1.0:0.0:0.0	.	116;22;110;116	Q674X7-2;Q674X7-4;Q674X7-3;Q674X7	.;.;.;KAZRN_HUMAN	L	116;116;116;110;22;22;22	ENSP00000365198:S116L;ENSP00000426015:S116L;ENSP00000391728:S116L;ENSP00000354727:S110L;ENSP00000365196:S22L;ENSP00000383602:S22L;ENSP00000383601:S22L	ENSP00000354727:S110L	S	+	2	0	KAZN	15159887	1.000000	0.71417	0.952000	0.39060	0.984000	0.73092	7.298000	0.78815	2.709000	0.92574	0.561000	0.74099	TCG	.	.		0.617	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		T	15287300	C	T	15287300	3	4	49	1	0	0	0	0	1	0	0	0	7997	893	31	1	565	1	KAZ	1	15287300	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	8633801	15287300	233963321	3	6160										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22159859	22159872	+	Frame_Shift_Del	DEL	AAGTAGGGCACCAC	AAGTAGGGCACCAC	-													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aggagtagggggtctgcgtgAagtagggcaccacccgctct							TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	AAGTAGGGCACCAC	AAGTAGGGCACCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:22159859_22159872delAAGTAGGGCACCAC	ENST00000374695.3	-	80	11063_11076	c.10984_10997delGTGGTGCCCTACTT	c.(10984-10998)gtggtgccctacttcfs	p.VVPYF3662fs	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3662	Ig-like C2-type 22.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GGTCTGCGTGAAGTAGGGCACCACCCGCTCTGCC	0.603																																					p.3662_3666del		Atlas-Indel,Pindel	.											.	HSPG2	311	.	0			c.10985_10998del						.																																			SO:0001589	frameshift_variant	3339	exon80			.	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.10984_10997delGTGGTGCCCTACTT	chr1.hg19:g.22159859_22159872delAAGTAGGGCACCAC	ENSP00000363827:p.Val3662fs	83.0	0.0		106.0	10.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Frame_Shift_Del	DEL	ENST00000374695.3	hg19	CCDS30625.1																																																																																			.	.		0.603	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		-	22159872	AAGTAGGGCACCAC	-	22159859	7	5	49	1	0	1	0	1	0	0	0	0	7439	246	9	0	2250	0	HSPG2	1	22159859	Frame_Shift_Del	DEL	AAGTAGGGCACCAC	TCGA-BD-A3EP-01A-11D-A22F-10	6872559	22159859	227090762	4	6161										
ZNF683	257101	hgsc.bcm.edu	37	chr1	26691310	26691310	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccgagcgctggggtgccccaGctcattgaccatcatcagca	11	15	3	1	rs144078461|rs145815386|rs372936882	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:26691310G>C	ENST00000436292.1	-	4	847	c.727C>G	c.(727-729)Ctg>Gtg	p.L243V	ZNF683_ENST00000374204.1_Missense_Mutation_p.L243V|ZNF683_ENST00000349618.3_Missense_Mutation_p.L243V|ZNF683_ENST00000403843.1_Missense_Mutation_p.L243V			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	243					natural killer cell differentiation (GO:0001779)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L228_W235delLGHPSARW(1)|p.L243_W250delLGHPSARW(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	15		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		GGGTGCCCCAGCTCATTGACC	0.637																																					p.L243V		Atlas-SNP	.											.	ZNF683	51	.	2	Deletion - In frame(2)	large_intestine(2)	c.C727G						.						38	51	46					1																	26691310		2111	4285	6396	SO:0001583	missense	257101	exon4			GCCCCAGCTCATT	BC029505	CCDS279.2	1p36.11	2013-01-08			ENSG00000176083	ENSG00000176083		"Zinc fingers, C2H2-type"	28495	protein-coding gene	gene with protein product	"hypothetical protein MGC33414"					12477932	Standard	NM_173574		Approved	MGC33414	uc009vsj.1	Q8IZ20	OTTHUMG00000003521	ENST00000436292.1:c.727C>G	chr1.hg19:g.26691310G>C	ENSP00000388792:p.Leu243Val	0.0	0.0		7.0	6.0	NM_173574	Q5T141|Q5T146|Q5T147|Q5T149|Q8NEN4	Missense_Mutation	SNP	ENST00000436292.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.901	1.206758	0.22205	.	.	ENSG00000176083	ENST00000403843;ENST00000436292;ENST00000374204;ENST00000349618;ENST00000455900;ENST00000451801	T;T;T;T;T;T	0.18016	2.9;2.9;2.92;2.92;2.24;2.25	4.74	-1.94	0.07571	.	0.482467	0.17752	N	0.163192	T	0.06050	0.0157	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12837	0.008;0.004	T	0.34700	-0.9818	10	0.21014	T	0.42	-0.0116	4.8538	0.13549	0.3374:0.2722:0.3904:0.0	.	243;243	Q8IZ20-2;Q8IZ20	.;ZN683_HUMAN	V	243;243;243;243;251;243	ENSP00000384782:L243V;ENSP00000388792:L243V;ENSP00000363320:L243V;ENSP00000344095:L243V;ENSP00000411289:L251V;ENSP00000411290:L243V	ENSP00000344095:L243V	L	-	1	2	ZNF683	26563897	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.807000	0.04520	-0.257000	0.09459	-0.264000	0.10439	CTG	.	.		0.637	ZNF683-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009794.2	NM_173574		C	26691310	G	C	26691310	3	2	49	1	0	0	0	0	1	0	0	0	18105	962	34	4	799	4	ZNF683	1	26691310	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	4531451	26691310	222559311	5	6162										
TINAGL1	64129	hgsc.bcm.edu	37	chr1	32052549	32052549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cgtgctgggcgtctggggccGcgtgggcatggaggacatgg	21	9	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:32052549G>A	ENST00000271064.7	+	12	1449	c.1373G>A	c.(1372-1374)cGc>cAc	p.R458H	TINAGL1_ENST00000481165.1_3'UTR|TINAGL1_ENST00000457433.2_Missense_Mutation_p.R427H	NM_001204415.1|NM_022164.2	NP_001191344.1|NP_071447.1	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1	458					endosomal transport (GO:0016197)|immune response (GO:0006955)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type peptidase activity (GO:0008234)|extracellular matrix structural constituent (GO:0005201)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			breast(2)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(4)|prostate(1)|skin(3)|urinary_tract(1)	18		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		GTCTGGGGCCGCGTGGGCATG	0.697																																					p.R458H		Atlas-SNP	.											TINAGL1,right_upper_lobe,carcinoma,0,1	TINAGL1	35	.	0			c.G1373A						.						27	32	30					1																	32052549		2199	4295	6494	SO:0001583	missense	64129	exon12			GGGGCCGCGTGGG	AB050716	CCDS343.1, CCDS55586.1, CCDS72745.1	1p34.3	2014-04-22	2005-08-18	2005-08-18	ENSG00000142910	ENSG00000142910			19168	protein-coding gene	gene with protein product			"lipocalin 7", "TINAG-like 1"	LCN7		11170462	Standard	NM_022164		Approved	P3ECSL, LIECG3, ARG1, TINAGRP	uc001bta.3	Q9GZM7	OTTHUMG00000003884	ENST00000271064.7:c.1373G>A	chr1.hg19:g.32052549G>A	ENSP00000271064:p.Arg458His	49.0	0.0		10.0	2.0	NM_022164	A8K9Q5|B4DPK6|D3DPN8|Q8TEJ9|Q8WZ23|Q96GZ4|Q96JW3	Missense_Mutation	SNP	ENST00000271064.7	hg19	CCDS343.1	.	.	.	.	.	.	.	.	.	.	g	18.44	3.625174	0.66901	.	.	ENSG00000142910	ENST00000457433;ENST00000271064	T;T	0.69306	-0.39;0.07	3.95	3.95	0.45737	.	0.000000	0.85682	D	0.000000	T	0.75895	0.3912	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.76969	-0.2762	10	0.46703	T	0.11	.	15.151	0.72700	0.0:0.0:1.0:0.0	.	427;458	B4DPK6;Q9GZM7	.;TINAL_HUMAN	H	427;458	ENSP00000395137:R427H;ENSP00000271064:R458H	ENSP00000271064:R458H	R	+	2	0	TINAGL1	31825136	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.943000	0.92975	1.932000	0.55993	0.462000	0.41574	CGC	.	.		0.697	TINAGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011072.1	NM_022164		A	32052549	G	A	32052549	3	1	49	1	0	0	0	0	1	0	0	0	15937	1087	38	1	1415	1	TINAGL1	1	32052549	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	5361239	32052549	217198072	6	6163										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34006774	34006774	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tccatgtccggtccttggtgCagctcagcacagatactcta	9	13	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:34006774C>T	ENST00000373381.4	-	59	9589	c.9413G>A	c.(9412-9414)tGc>tAc	p.C3138Y		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3110	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTCCTTGGTGCAGCTCAGCAC	0.498																																					p.C2994Y		Atlas-SNP	.											.	CSMD2	946	.	0			c.G8981A						.						176	159	165					1																	34006774		2203	4300	6503	SO:0001583	missense	114784	exon58			TTGGTGCAGCTCA	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.9413G>A	chr1.hg19:g.34006774C>T	ENSP00000362479:p.Cys3138Tyr	117.0	0.0		123.0	5.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	C	25.9	4.683884	0.88639	.	.	ENSG00000121904	ENST00000373381	D	0.92595	-3.07	5.58	5.58	0.84498	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.98157	0.9391	H	0.99435	4.565	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	1.0;1.0	D	0.99572	1.0971	10	0.72032	D	0.01	.	18.5585	0.91093	0.0:1.0:0.0:0.0	.	2994;3138	Q7Z408;E7EUA6	CSMD2_HUMAN;.	Y	3138	ENSP00000362479:C3138Y	ENSP00000241312:C2994Y	C	-	2	0	CSMD2	33779361	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.736000	0.84948	2.622000	0.88805	0.462000	0.41574	TGC	.	.		0.498	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34006774	C	T	34006774	3	4	49	1	0	0	0	0	1	0	0	0	3947	710	25	3	1530	3	CSMD2	1	34006774	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1954225	34006774	215243847	7	6164										
FOXD3	27022	hgsc.bcm.edu	37	chr1	63789224	63789224	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cagaagaagctgaccctgagCggcatctgcgagttcatcag	12	11	3	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:63789224C>T	ENST00000371116.2	+	1	495	c.495C>T	c.(493-495)agC>agT	p.S165S	RP4-792G4.2_ENST00000431294.1_RNA|RP4-792G4.2_ENST00000427268.1_RNA|RP4-792G4.2_ENST00000426393.1_RNA|RP4-792G4.2_ENST00000449386.1_RNA|RP4-792G4.2_ENST00000418244.1_RNA	NM_012183.2	NP_036315.1	Q9UJU5	FOXD3_HUMAN	forkhead box D3	165					embryonic placenta development (GO:0001892)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|trophectodermal cell differentiation (GO:0001829)	nuclear chromatin (GO:0000790)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|lung(2)|upper_aerodigestive_tract(1)	5						TGACCCTGAGCGGCATCTGCG	0.587																																					p.S165S	Pancreas(68;276 1750 11966 31252)	Atlas-SNP	.											FOXD3,right_upper_lobe,carcinoma,0,1	FOXD3	15	.	0			c.C495T						.						68	76	73					1																	63789224		2203	4300	6503	SO:0001819	synonymous_variant	27022	exon1			CCTGAGCGGCATC	AF197560	CCDS624.1	1p31.3	2008-04-10			ENSG00000187140	ENSG00000187140		"Forkhead boxes"	3804	protein-coding gene	gene with protein product		611539				8499623	Standard	NM_012183		Approved	Genesis, HFH2	uc001dax.2	Q9UJU5	OTTHUMG00000009141	ENST00000371116.2:c.495C>T	chr1.hg19:g.63789224C>T		70.0	0.0		69.0	3.0	NM_012183	Q9BYM2|Q9UDD1	Silent	SNP	ENST00000371116.2	hg19	CCDS624.1																																																																																			.	.		0.587	FOXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025331.1			T	63789224	C	T	63789224	2	4	49	1	0	0	0	0	0	0	0	1	6006	767	27	1		1	FOXD3	1	63789224	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	29782450	63789224	185461397	8	6165										
JAK1	3716	hgsc.bcm.edu	37	chr1	65335078	65335078	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggacagccatccctagacacTcgttctcaatatcatgtcca	6	14	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:65335078T>A	ENST00000342505.4	-	6	811	c.563A>T	c.(562-564)gAg>gTg	p.E188V		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	188	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CCCTAGACACTCGTTCTCAAT	0.512			Mis		ALL																																p.E188V		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A563T						.						145	139	141					1																	65335078		2023	4191	6214	SO:0001583	missense	3716	exon6			AGACACTCGTTCT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.563A>T	chr1.hg19:g.65335078T>A	ENSP00000343204:p.Glu188Val	100.0	0.0		123.0	35.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.665413	0.88251	.	.	ENSG00000162434	ENST00000342505	T	0.72725	-0.68	5.33	5.33	0.75918	FERM central domain (1);Band 4.1 domain (1);FERM domain (1);	.	.	.	.	D	0.83004	0.5160	M	0.85859	2.78	0.58432	D	0.999999	D	0.76494	0.999	D	0.83275	0.996	D	0.86395	0.1738	9	0.87932	D	0	.	15.6084	0.76692	0.0:0.0:0.0:1.0	.	188	P23458	JAK1_HUMAN	V	188	ENSP00000343204:E188V	ENSP00000343204:E188V	E	-	2	0	JAK1	65107666	1.000000	0.71417	0.999000	0.59377	0.767000	0.43475	7.676000	0.84012	2.152000	0.67230	0.533000	0.62120	GAG	.	.		0.512	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		A	65335078	T	A	65335078	3	1	49	1	0	0	0	0	1	0	0	0	7946	1551	54	4	2981	4	JAK1	1	65335078	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	1545854	65335078	183915543	9	6166										
PTPN22	26191	hgsc.bcm.edu	37	chr1	114380935	114380935	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	caaaactagctcttcttttgCacttatttcagaagtcctaa	4	10	3	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:114380935C>T	ENST00000359785.5	-	13	1222	c.1087G>A	c.(1087-1089)Gca>Aca	p.A363T	PTPN22_ENST00000528414.1_Missense_Mutation_p.A308T|PTPN22_ENST00000525799.1_Missense_Mutation_p.A236T|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000420377.2_Missense_Mutation_p.A363T|PTPN22_ENST00000538253.1_Missense_Mutation_p.A119T	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	363					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCTTCTTTTGCACTTATTTCA	0.348																																					p.A363T		Atlas-SNP	.											.	PTPN22	90	.	0			c.G1087A						.						125	104	111					1																	114380935		2203	4300	6503	SO:0001583	missense	26191	exon13			CTTTTGCACTTAT	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.1087G>A	chr1.hg19:g.114380935C>T	ENSP00000352833:p.Ala363Thr	99.0	0.0		100.0	4.0	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	hg19	CCDS863.1	.	.	.	.	.	.	.	.	.	.	C	8.282	0.815667	0.16607	.	.	ENSG00000134242	ENST00000359785;ENST00000528414;ENST00000538253;ENST00000420377;ENST00000525799;ENST00000354605	T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48	5.82	2.71	0.32032	.	0.662724	0.14465	N	0.317950	T	0.09024	0.0223	L	0.43152	1.355	0.09310	N	1	P;P;P;B;P;P	0.48764	0.763;0.915;0.736;0.003;0.828;0.736	B;B;B;B;B;B	0.41946	0.295;0.321;0.205;0.003;0.371;0.205	T	0.11179	-1.0598	10	0.14656	T	0.56	.	6.5743	0.22555	0.0:0.6854:0.1438:0.1707	.	119;236;363;308;363;363	F5H2S8;E9PPI1;E9PMT0;E9PLD8;G5E984;Q9Y2R2	.;.;.;.;.;PTN22_HUMAN	T	363;308;119;363;236;363	ENSP00000352833:A363T;ENSP00000435176:A308T;ENSP00000439372:A119T;ENSP00000388229:A363T;ENSP00000432674:A236T	ENSP00000346621:A363T	A	-	1	0	PTPN22	114182458	0.000000	0.05858	0.028000	0.17463	0.006000	0.05464	0.394000	0.20834	0.730000	0.32425	-0.345000	0.07892	GCA	.	.		0.348	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		T	114380935	C	T	114380935	3	4	49	1	0	0	0	0	1	0	0	0	12802	710	25	3	1395	3	PTPN22	1	114380935	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	49045857	114380935	134869686	10	6167										
WDR3	10885	hgsc.bcm.edu	37	chr1	118495158	118495158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttttctcctccagggtcatcAccaggaaatatggtgtttgg	10	9	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:118495158A>G	ENST00000349139.5	+	19	2071	c.2024A>G	c.(2023-2025)cAc>cGc	p.H675R		NM_006784.2	NP_006775.1	Q9UNX4	WDR3_HUMAN	WD repeat domain 3	675						nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(9)|liver(2)|lung(22)|prostate(2)|upper_aerodigestive_tract(1)	49	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		CAGGGTCATCACCAGGAAATA	0.393																																					p.H675R		Atlas-SNP	.											.	WDR3	81	.	0			c.A2024G						.						77	78	78					1																	118495158		2203	4300	6503	SO:0001583	missense	10885	exon19			GTCATCACCAGGA	AF083217	CCDS898.1	1p12	2013-01-09			ENSG00000065183	ENSG00000065183		"WD repeat domain containing"	12755	protein-coding gene	gene with protein product		604737				10395803	Standard	NM_006784		Approved	FLJ12796, UTP12, DIP2	uc010oxe.1	Q9UNX4	OTTHUMG00000012197	ENST00000349139.5:c.2024A>G	chr1.hg19:g.118495158A>G	ENSP00000308179:p.His675Arg	93.0	0.0		93.0	4.0	NM_006784		Missense_Mutation	SNP	ENST00000349139.5	hg19	CCDS898.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.784104	0.70222	.	.	ENSG00000065183	ENST00000349139	T	0.59083	0.29	5.96	5.96	0.96718	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.043669	0.85682	D	0.000000	T	0.28995	0.0720	N	0.16201	0.385	0.80722	D	1	P	0.36789	0.57	B	0.38106	0.265	T	0.20638	-1.0269	10	0.23891	T	0.37	-15.8671	16.4311	0.83844	1.0:0.0:0.0:0.0	.	675	Q9UNX4	WDR3_HUMAN	R	675	ENSP00000308179:H675R	ENSP00000308179:H675R	H	+	2	0	WDR3	118296681	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.125000	0.94402	2.277000	0.76020	0.528000	0.53228	CAC	.	.		0.393	WDR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033720.2	NM_006784		G	118495158	A	G	118495158	3	3	49	1	0	0	0	0	1	0	0	0	17300	159	6	2	2094	2	WDR3	1	118495158	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	4114223	118495158	130755463	11	6168										
LCE1E	353135	hgsc.bcm.edu	37	chr1	152759984	152759984	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctctgggggctgctgcagctCtgggggaggtggctgctgcc	19	11	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:152759984C>A	ENST00000368770.3	+	2	262	c.209C>A	c.(208-210)tCt>tAt	p.S70Y	LCE1E_ENST00000368771.1_Missense_Mutation_p.S70Y	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	70	Cys-rich.				keratinization (GO:0031424)					lung(5)|stomach(1)	6	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCTGCAGCTCTGGGGGAGGT	0.682																																					p.S70Y		Atlas-SNP	.											.	LCE1E	26	.	0			c.C209A						.						35	44	41					1																	152759984		2203	4298	6501	SO:0001583	missense	353135	exon2			GCAGCTCTGGGGG	BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"Late cornified envelopes"	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.209C>A	chr1.hg19:g.152759984C>A	ENSP00000357759:p.Ser70Tyr	134.0	0.0		95.0	46.0	NM_178353	D3DV30	Missense_Mutation	SNP	ENST00000368770.3	hg19	CCDS1024.1	.	.	.	.	.	.	.	.	.	.	C	9.777	1.174286	0.21704	.	.	ENSG00000186226	ENST00000368771;ENST00000368770	T;T	0.06294	3.32;3.32	4.06	4.06	0.47325	.	0.000000	0.34959	N	0.003545	T	0.17195	0.0413	M	0.87900	2.915	0.27825	N	0.941652	D	0.69078	0.997	D	0.78314	0.991	T	0.01360	-1.1375	10	0.87932	D	0	.	11.9094	0.52731	0.0:1.0:0.0:0.0	.	70	Q5T753	LCE1E_HUMAN	Y	70	ENSP00000357760:S70Y;ENSP00000357759:S70Y	ENSP00000357759:S70Y	S	+	2	0	LCE1E	151026608	0.996000	0.38824	1.000000	0.80357	0.773000	0.43773	1.958000	0.40402	2.237000	0.73441	0.514000	0.50259	TCT	.	.		0.682	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353		A	152759984	C	A	152759984	3	1	49	1	0	0	0	0	1	0	0	0	8672	913	32	3	211	3	LCE1E	1	152759984	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	34264826	152759984	96490637	12	6169										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153907287	153907287	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgacacctgctcctgctgctGctgctgctgctgctgctgtt	11	14	0	1	rs3835302|rs199597671		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:153907287G>C	ENST00000361217.4	-	18	3140	c.2722C>G	c.(2722-2724)Cag>Gag	p.Q908E	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	908	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tcctgctgctgctgctgctgc	0.632																																					p.Q908E		Atlas-SNP	.											.	DENND4B	210	.	0			c.C2722G						.						23	27	26					1																	153907287		2184	4281	6465	SO:0001583	missense	9909	exon18			GCTGCTGCTGCTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2722C>G	chr1.hg19:g.153907287G>C	ENSP00000354597:p.Gln908Glu	25.0	0.0		51.0	6.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	1.785	-0.481073	0.04383	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06294	3.33;3.32	2.67	0.673	0.17941	.	5.053470	0.00166	N	0.000001	T	0.00815	0.0027	N	0.14661	0.345	0.19300	N	0.999977	B	0.02656	0.0	B	0.04013	0.001	T	0.26573	-1.0099	10	0.02654	T	1	-2.4288	3.3651	0.07201	0.1454:0.0:0.5849:0.2697	.	908	O75064	DEN4B_HUMAN	E	908;919	ENSP00000354597:Q908E;ENSP00000357635:Q919E	ENSP00000354597:Q908E	Q	-	1	0	DENND4B	152173911	0.943000	0.32029	0.986000	0.45419	0.760000	0.43138	0.537000	0.23144	0.194000	0.20326	0.271000	0.19318	CAG	.	.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153907287	G	C	153907287	3	2	49	1	0	0	0	0	1	0	0	0	4436	1328	46	4	1812	4	DENND4B	1	153907287	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	1147303	153907287	95343334	13	6170										
RAG1AP1	55974	hgsc.bcm.edu	37	chr1	155110121	155110121	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggctcctggtacccaaccctGaggcccggcttcagcagttg	12	15	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:155110121G>A	ENST00000368404.4	+	4	429	c.367G>A	c.(367-369)Gag>Aag	p.E123K	SLC50A1_ENST00000484157.1_Missense_Mutation_p.E58K|SLC50A1_ENST00000368401.5_Missense_Mutation_p.E68K|SLC50A1_ENST00000368405.3_Intron|SLC50A1_ENST00000303343.8_Intron	NM_018845.3	NP_061333.2	Q9BRV3	SWET1_HUMAN	solute carrier family 50 (sugar efflux transporter), member 1	123					carbohydrate transport (GO:0008643)|DNA recombination (GO:0006310)|glucoside transport (GO:0042946)|positive regulation of gene expression, epigenetic (GO:0045815)	endomembrane system (GO:0012505)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucoside transmembrane transporter activity (GO:0042947)			endometrium(1)|lung(1)|ovary(1)|skin(1)	4						ACCCAACCCTGAGGCCCGGCT	0.582																																					p.E123K		Atlas-SNP	.											.	SLC50A1	16	.	0			c.G367A						.						74	76	75					1																	155110121		2203	4300	6503	SO:0001583	missense	55974	exon4			AACCCTGAGGCCC	AF126023, AF126024	CCDS1093.1, CCDS44238.1, CCDS44239.1, CCDS72929.1, CCDS72930.1	1q22	2013-07-17	2013-07-17	2010-11-30	ENSG00000169241	ENSG00000169241		"Solute carriers"	30657	protein-coding gene	gene with protein product	"stromal cell protein"	613683	"recombination activating gene 1 activating protein 1"	RAG1AP1		21107422	Standard	NM_018845		Approved	SCP, RP11-540D14.5, slv, RZPDo834D038D, HsSWEET1, SWEET1	uc001fhj.4	Q9BRV3	OTTHUMG00000035333	ENST00000368404.4:c.367G>A	chr1.hg19:g.155110121G>A	ENSP00000357389:p.Glu123Lys	68.0	0.0		97.0	28.0	NM_018845	Q5SR64|Q6IAK6|Q96DC5|Q9UHQ2|Q9UHQ3	Missense_Mutation	SNP	ENST00000368404.4	hg19	CCDS1093.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.440450	0.63067	.	.	ENSG00000169241	ENST00000484157;ENST00000368404;ENST00000368401	.	.	.	5.08	3.15	0.36227	.	0.792831	0.12180	N	0.492158	T	0.10551	0.0258	N	0.08118	0	0.09310	N	0.999997	D;P	0.62365	0.991;0.615	P;B	0.56434	0.798;0.28	T	0.05920	-1.0856	9	0.20519	T	0.43	-1.0217	5.9692	0.19342	0.2946:0.0:0.7054:0.0	.	68;123	Q9BRV3-2;Q9BRV3	.;SWET1_HUMAN	K	58;123;68	.	ENSP00000357386:E68K	E	+	1	0	SLC50A1	153376745	0.016000	0.18221	0.003000	0.11579	0.944000	0.59088	1.819000	0.39022	1.434000	0.47414	0.655000	0.94253	GAG	.	.		0.582	SLC50A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085505.1	NM_018845		A	155110121	G	A	155110121	3	1	49	1	0	0	0	0	1	0	0	0	13019	1291	45	3	381	3	RAG1AP1	1	155110121	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	1202834	155110121	94140500	14	6171										
FAM189B	10712	hgsc.bcm.edu	37	chr1	155223732	155223732	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	actctggacagggccggaggAggggaacagagggacagcac	18	9	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:155223732A>G	ENST00000361361.2	-	4	940	c.431T>C	c.(430-432)cTc>cCc	p.L144P	SCAMP3_ENST00000472397.1_5'Flank|FAM189B_ENST00000472550.1_Intron|FAM189B_ENST00000350210.2_Intron|FAM189B_ENST00000368368.3_Missense_Mutation_p.L125P	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	144						integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						GGGCCGGAGGAGGGGAACAGA	0.607																																					p.L144P		Atlas-SNP	.											.	FAM189B	51	.	0			c.T431C						.						69	82	77					1																	155223732		2203	4300	6503	SO:0001583	missense	10712	exon4			CGGAGGAGGGGAA	AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 2"	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.431T>C	chr1.hg19:g.155223732A>G	ENSP00000354958:p.Leu144Pro	57.0	0.0		95.0	6.0	NM_006589	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	hg19	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	A	10.46	1.355854	0.24598	.	.	ENSG00000160767	ENST00000368368;ENST00000361361	T;T	0.03004	4.08;4.08	4.05	4.05	0.47172	.	0.000000	0.37669	N	0.001983	T	0.01905	0.0060	L	0.34521	1.04	0.52501	D	0.999955	B;B	0.29909	0.261;0.261	B;B	0.38562	0.276;0.161	T	0.52689	-0.8542	10	0.34782	T	0.22	.	9.5821	0.39495	1.0:0.0:0.0:0.0	.	125;144	B1AVS5;P81408	.;F189B_HUMAN	P	125;144	ENSP00000357352:L125P;ENSP00000354958:L144P	ENSP00000354958:L144P	L	-	2	0	FAM189B	153490356	0.992000	0.36948	0.582000	0.28627	0.974000	0.67602	4.108000	0.57817	1.832000	0.53329	0.459000	0.35465	CTC	.	.		0.607	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589		G	155223732	A	G	155223732	3	3	49	1	0	0	0	0	1	0	0	0	5522	304	11	2	1611	2	FAM189B	1	155223732	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	113611	155223732	94026889	15	6172										
KIRREL	55243	hgsc.bcm.edu	37	chr1	158061246	158061246	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggggtgctatccacgctcacCatcaacaatgtcatggaggc	11	12	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:158061246C>T	ENST00000359209.6	+	11	1438	c.1371C>T	c.(1369-1371)acC>acT	p.T457T	KIRREL_ENST00000368173.3_Silent_p.T473T|KIRREL_ENST00000392272.2_Silent_p.T354T|KIRREL_ENST00000360089.4_Silent_p.T293T|KIRREL_ENST00000416935.2_Silent_p.T357T|KIRREL_ENST00000368172.1_Silent_p.T271T			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	457	Ig-like C2-type 5.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)	p.T293T(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					CCACGCTCACCATCAACAATG	0.577																																					p.T457T		Atlas-SNP	.											KIRREL,NS,carcinoma,0,1	KIRREL	346	.	1	Substitution - coding silent(1)	ovary(1)	c.C1371T						.						158	138	145					1																	158061246		2203	4300	6503	SO:0001819	synonymous_variant	55243	exon11			GCTCACCATCAAC	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15734	protein-coding gene	gene with protein product	"nephrin-like protein 1"	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.1371C>T	chr1.hg19:g.158061246C>T		57.0	0.0		64.0	12.0	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Silent	SNP	ENST00000359209.6	hg19	CCDS1172.2																																																																																			.	.		0.577	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240		T	158061246	C	T	158061246	2	4	49	1	0	0	0	0	0	0	0	1	8333	581	21	3		3	KIRREL	1	158061246	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	2837514	158061246	91189375	16	6173										
DCAF6	55827	hgsc.bcm.edu	37	chr1	168034975	168034975	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	actgcctgcagccacatccgTttgacccaagtaagatatct	7	13	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:168034975T>C	ENST00000312263.6	+	16	2518	c.2314T>C	c.(2314-2316)Ttt>Ctt	p.F772L	DCAF6_ENST00000367840.3_Missense_Mutation_p.F863L|DCAF6_ENST00000432587.2_Missense_Mutation_p.F832L|DCAF6_ENST00000367843.3_Missense_Mutation_p.F792L	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	772					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						GCCACATCCGTTTGACCCAAG	0.383																																					p.F863L		Atlas-SNP	.											.	DCAF6	99	.	0			c.T2587C						.						66	64	65					1																	168034975		2203	4300	6503	SO:0001583	missense	55827	exon19			CATCCGTTTGACC	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.2314T>C	chr1.hg19:g.168034975T>C	ENSP00000311949:p.Phe772Leu	63.0	0.0		87.0	4.0	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	hg19	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.211692	0.79240	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.60171	0.21;0.21;0.21;0.21	5.41	5.41	0.78517	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.161154	0.64402	D	0.000020	T	0.56978	0.2022	L	0.55743	1.74	0.37751	D	0.925968	B;P;B;B;B	0.42620	0.126;0.785;0.191;0.316;0.387	B;P;B;B;B	0.53988	0.28;0.739;0.075;0.229;0.146	T	0.56768	-0.7924	9	0.32370	T	0.25	.	15.7437	0.77922	0.0:0.0:0.0:1.0	.	832;445;863;772;792	B4DNB8;Q9P0U0;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;.;DCAF6_HUMAN;.	L	792;832;772;863	ENSP00000356817:F792L;ENSP00000396238:F832L;ENSP00000311949:F772L;ENSP00000356814:F863L	ENSP00000311949:F772L	F	+	1	0	DCAF6	166301599	1.000000	0.71417	0.919000	0.36401	0.478000	0.33099	7.512000	0.81728	2.184000	0.69523	0.459000	0.35465	TTT	.	.		0.383	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		C	168034975	T	C	168034975	3	2	49	1	0	0	0	0	1	0	0	0	4276	1725	60	2	2440	2	DCAF6	1	168034975	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	9973729	168034975	81215646	17	6174										
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173476077	173476077	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttacactgccatacacaatgAtaacaaatttcatggtcata	4	9	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:173476077A>C	ENST00000367714.3	-	25	3565	c.3143T>G	c.(3142-3144)aTc>aGc	p.I1048S	SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	1048					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										ATACACAATGATAACAAATTT	0.333																																					p.I1048S		Atlas-SNP	.											.	.	.	.	0			c.T3143G						.						136	125	129					1																	173476077		2203	4300	6503	SO:0001583	missense	284525	exon25			ACAATGATAACAA	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.3143T>G	chr1.hg19:g.173476077A>C	ENSP00000356687:p.Ile1048Ser	169.0	0.0		184.0	38.0	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	hg19	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.356160	0.61293	.	.	ENSG00000162753	ENST00000367714	T	0.06849	3.25	5.58	5.58	0.84498	.	0.215417	0.32671	N	0.005785	T	0.09686	0.0238	M	0.68952	2.095	0.58432	D	0.999997	D	0.54397	0.966	P	0.49012	0.598	T	0.01287	-1.1395	10	0.87932	D	0	-30.2794	12.1245	0.53909	1.0:0.0:0.0:0.0	.	1048	Q5TAH2	S9A11_HUMAN	S	1048	ENSP00000356687:I1048S	ENSP00000356687:I1048S	I	-	2	0	SLC9A11	171742700	0.558000	0.26554	0.206000	0.23566	0.889000	0.51656	4.799000	0.62517	2.123000	0.65237	0.421000	0.28195	ATC	.	.		0.333	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		C	173476077	A	C	173476077	3	2	49	1	0	0	0	0	1	0	0	0	14726	333	12	5	247	5	SLC9A11	1	173476077	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	5441102	173476077	75774544	18	6175										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200957983	200957983	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggagcagatggttctgggagGagcctgccatatccgtctgc	15	10	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:200957983G>A	ENST00000422435.2	-	22	3525	c.3209C>T	c.(3208-3210)tCc>tTc	p.S1070F	KIF21B_ENST00000332129.2_Missense_Mutation_p.S1070F|KIF21B_ENST00000461742.2_Missense_Mutation_p.S1070F|KIF21B_ENST00000360529.5_Missense_Mutation_p.S1070F	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1070					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						GTTCTGGGAGGAGCCTGCCAT	0.627																																					p.S1070F		Atlas-SNP	.											.	KIF21B	208	.	0			c.C3209T						.						30	30	30					1																	200957983		2203	4300	6503	SO:0001583	missense	23046	exon22			TGGGAGGAGCCTG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.3209C>T	chr1.hg19:g.200957983G>A	ENSP00000411831:p.Ser1070Phe	90.0	0.0		103.0	6.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	hg19	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.592732	0.66219	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17	4.67	4.67	0.58626	Prefoldin (1);	0.063366	0.64402	D	0.000003	D	0.82797	0.5115	L	0.56769	1.78	0.53688	D	0.999976	D;P;P;D	0.63880	0.989;0.93;0.93;0.993	P;P;P;P	0.61132	0.768;0.564;0.564;0.884	D	0.84268	0.0487	10	0.72032	D	0.01	.	11.4646	0.50230	0.0838:0.0:0.9162:0.0	.	1070;1070;1070;1070	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	F	1070	ENSP00000328494:S1070F;ENSP00000353724:S1070F;ENSP00000433808:S1070F;ENSP00000411831:S1070F	ENSP00000328494:S1070F	S	-	2	0	KIF21B	199224606	1.000000	0.71417	0.982000	0.44146	0.682000	0.39822	6.789000	0.75110	2.305000	0.77605	0.491000	0.48974	TCC	.	.		0.627	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200957983	G	A	200957983	3	1	49	1	0	0	0	0	1	0	0	0	8298	1174	41	3	1717	3	KIF21B	1	200957983	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	27481906	200957983	48292638	19	6176										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200978071	200978071	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cccatggtgtacgtcttcccGgcccccgtctgcattggcaa	10	16	2	0	rs199591058		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:200978071G>A	ENST00000422435.2	-	3	589	c.273C>T	c.(271-273)gcC>gcT	p.A91A	KIF21B_ENST00000332129.2_Silent_p.A91A|KIF21B_ENST00000461742.2_Silent_p.A91A|KIF21B_ENST00000360529.5_Silent_p.A91A	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	91	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A91A(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						ACGTCTTCCCGGCCCCCGTCT	0.602																																					p.A91A		Atlas-SNP	.											KIF21B,NS,carcinoma,0,1	KIF21B	208	.	1	Substitution - coding silent(1)	endometrium(1)	c.C273T						.	G		0,4406		0,0,2203	99	84	89		273	-7.2	0.7	1		89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIF21B	NM_017596.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		91/1625	200978071	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23046	exon3			CTTCCCGGCCCCC	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.273C>T	chr1.hg19:g.200978071G>A		29.0	0.0		41.0	2.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	G|0.999;A|0.001		0.602	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200978071	G	A	200978071	2	1	49	1	0	0	0	0	0	0	0	1	8298	1103	39	1		1	KIF21B	1	200978071	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	20088	200978071	48272550	20	6177										
IGFN1	91156	hgsc.bcm.edu	37	chr1	201182025	201182025	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggtgggacccatgaagggccAgggggctttaagggtgggga	21	6	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:201182025A>G	ENST00000335211.4	+	12	8134	c.8004A>G	c.(8002-8004)ccA>ccG	p.P2668P	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Intron	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	0						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ATGAAGGGCCAGGGGGCTTTA	0.617																																					p.P2668P		Atlas-SNP	.											.	IGFN1	220	.	0			c.A8004G						.						12	14	14					1																	201182025		692	1590	2282	SO:0001819	synonymous_variant	91156	exon12			AGGGCCAGGGGGC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.8004A>G	chr1.hg19:g.201182025A>G		70.0	0.0		95.0	4.0	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	hg19	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.363010	0.24684	.	.	ENSG00000163395	ENST00000412892	.	.	.	3.01	0.454	0.16644	.	.	.	.	.	T	0.21718	0.0523	.	.	.	0.18873	N	0.999987	.	.	.	.	.	.	T	0.23726	-1.0180	4	.	.	.	.	2.5428	0.04730	0.4482:0.0:0.1308:0.4209	.	.	.	.	G	86	.	.	R	+	1	2	IGFN1	199448648	0.043000	0.20138	0.001000	0.08648	0.616000	0.37450	0.407000	0.21049	-0.120000	0.11809	0.402000	0.26972	AGG	.	.		0.617	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		G	201182025	A	G	201182025	2	3	49	1	0	0	0	0	0	0	0	1	7599	175	7	2		2	IGFN1	1	201182025	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	203954	201182025	48068596	21	6178										
KLHDC8A	55220	hgsc.bcm.edu	37	chr1	205306696	205306696	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctgggtggaatgcttccgccGtctccaggacagtgggttga	15	10	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:205306696G>A	ENST00000367156.3	-	9	1700	c.884C>T	c.(883-885)aCg>aTg	p.T295M	KLHDC8A_ENST00000460687.1_Missense_Mutation_p.T161M|KLHDC8A_ENST00000367155.3_Missense_Mutation_p.T295M|KLHDC8A_ENST00000539253.1_Missense_Mutation_p.T295M|KLHDC8A_ENST00000537168.1_Missense_Mutation_p.T182M	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	295										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			TGCTTCCGCCGTCTCCAGGAC	0.577																																					p.T295M		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.C884T						.						133	148	143					1																	205306696		2203	4300	6503	SO:0001583	missense	55220	exon6			TCCGCCGTCTCCA		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.884C>T	chr1.hg19:g.205306696G>A	ENSP00000356124:p.Thr295Met	46.0	0.0		87.0	5.0	NM_018203	B3KU70|Q9NVG5	Missense_Mutation	SNP	ENST00000367156.3	hg19	CCDS30985.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.574133	0.86542	.	.	ENSG00000162873	ENST00000367155;ENST00000367156;ENST00000539253;ENST00000537168	T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91	5.34	5.34	0.76211	Kelch-type beta propeller (1);	0.047999	0.85682	D	0.000000	D	0.87289	0.6140	M	0.85299	2.745	0.52099	D	0.999941	D;D	0.89917	1.0;0.999	D;D	0.64687	0.923;0.928	D	0.89270	0.3604	10	0.87932	D	0	-17.4262	18.6459	0.91410	0.0:0.0:1.0:0.0	.	182;295	F5H5F1;Q8IYD2	.;KLD8A_HUMAN	M	295;295;295;182	ENSP00000356123:T295M;ENSP00000356124:T295M;ENSP00000442229:T295M;ENSP00000443447:T182M	ENSP00000356123:T295M	T	-	2	0	KLHDC8A	203573319	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	9.094000	0.94168	2.500000	0.84329	0.591000	0.81541	ACG	.	.		0.577	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203		A	205306696	G	A	205306696	3	1	49	1	0	0	0	0	1	0	0	0	8371	1145	40	1	172	1	KLHDC8A	1	205306696	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	4124671	205306696	43943925	22	6179										
FCAMR	83953	hgsc.bcm.edu	37	chr1	207133090	207133090	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aagcataaacagggccagcaTggtagagacaggagccaggg	15	8	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:207133090T>C	ENST00000324852.4	-	7	1981	c.1507A>G	c.(1507-1509)Atg>Gtg	p.M503V	FCAMR_ENST00000486178.1_5'UTR|FCAMR_ENST00000450945.2_Silent_p.P235P|FCAMR_ENST00000400962.3_Silent_p.P235P	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	458					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(1)	11						AGGGCCAGCATGGTAGAGACA	0.532																																					p.M503V	Ovarian(199;1883 2142 16966 44409 45154)	Atlas-SNP	.											.	FCAMR	125	.	0			c.A1507G						.						147	143	144					1																	207133090		1568	3582	5150	SO:0001583	missense	83953	exon7			CCAGCATGGTAGA	AF354295	CCDS41460.1, CCDS53468.1	1q32.1	2013-01-14			ENSG00000162897	ENSG00000162897		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	24692	protein-coding gene	gene with protein product		605484				11779189	Standard	NM_001122979		Approved	FKSG87, FCA/MR, CD351	uc001hfa.4	Q8WWV6	OTTHUMG00000036579	ENST00000324852.4:c.1507A>G	chr1.hg19:g.207133090T>C	ENSP00000316491:p.Met503Val	93.0	0.0		88.0	23.0	NM_001170631	Q32M82|Q8WWV5|Q96SA2	Missense_Mutation	SNP	ENST00000324852.4	hg19	CCDS53468.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.528754	0.00959	.	.	ENSG00000162897	ENST00000324852	T	0.03663	3.85	4.63	-8.22	0.01037	.	.	.	.	.	T	0.01029	0.0034	.	.	.	0.24552	N	0.994019	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42832	-0.9428	8	0.02654	T	1	-1.0385	2.1438	0.03782	0.2183:0.4507:0.1091:0.2219	.	478;458	D2KTA8;Q8WWV6	.;FCAMR_HUMAN	V	503	ENSP00000316491:M503V	ENSP00000316491:M503V	M	-	1	0	FCAMR	205199713	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.284000	0.02793	-1.872000	0.01136	-1.229000	0.01577	ATG	.	.		0.532	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029		C	207133090	T	C	207133090	3	2	49	1	0	0	0	0	1	0	0	0	5780	1464	51	2	234	2	FCAMR	1	207133090	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	1826394	207133090	42117531	23	6180										
PRSS38	339501	hgsc.bcm.edu	37	chr1	228033905	228033905	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gctggctggctggtcagtgcTgtgaggtcaggatacccact	15	10	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:228033905T>C	ENST00000366757.3	+	5	1001	c.977T>C	c.(976-978)cTg>cCg	p.L326P		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	326						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						TGGTCAGTGCTGTGAGGTCAG	0.622																																					p.L326P		Atlas-SNP	.											.	PRSS38	55	.	0			c.T977C						.						72	68	69					1																	228033905		2203	4300	6503	SO:0001583	missense	339501	exon5			CAGTGCTGTGAGG		CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"Serine peptidases / Serine peptidases"	29625	protein-coding gene	gene with protein product	"marapsin 2"					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.977T>C	chr1.hg19:g.228033905T>C	ENSP00000355719:p.Leu326Pro	30.0	0.0		52.0	4.0	NM_183062	Q7RTY6	Missense_Mutation	SNP	ENST00000366757.3	hg19	CCDS1563.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.619038	0.46736	.	.	ENSG00000185888	ENST00000366757	D	0.89552	-2.53	4.31	3.14	0.36123	.	0.303615	0.18164	N	0.149661	D	0.85660	0.5748	N	0.08118	0	0.23260	N	0.998025	D	0.89917	1.0	D	0.68192	0.956	T	0.76011	-0.3115	10	0.87932	D	0	.	7.422	0.27077	0.1938:0.0:0.0:0.8062	.	326	A1L453	PRS38_HUMAN	P	326	ENSP00000355719:L326P	ENSP00000355719:L326P	L	+	2	0	PRSS38	226100528	0.058000	0.20735	0.019000	0.16419	0.148000	0.21650	1.533000	0.36040	0.734000	0.32515	0.460000	0.39030	CTG	.	.		0.622	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062		C	228033905	T	C	228033905	3	2	49	1	0	0	0	0	1	0	0	0	12639	1580	55	2	995	2	PRSS38	1	228033905	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	20900815	228033905	21216716	24	6181										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228511085	228511085	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgcaggatgggtatcctgtgAgctttgactgcgtggtgaca	15	7	0	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:228511085A>G	ENST00000422127.1	+	56	15474	c.15430A>G	c.(15430-15432)Agc>Ggc	p.S5144G	OBSCN_ENST00000570156.2_Missense_Mutation_p.S6101G|OBSCN_ENST00000366709.4_Missense_Mutation_p.S2263G|OBSCN_ENST00000284548.11_Missense_Mutation_p.S5144G|OBSCN_ENST00000366707.4_Missense_Mutation_p.S2778G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5144	Ig-like 49.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTATCCTGTGAGCTTTGACTG	0.517																																					p.S6101G		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A18301G						.						75	77	77					1																	228511085		2130	4228	6358	SO:0001583	missense	84033	exon67			CCTGTGAGCTTTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15430A>G	chr1.hg19:g.228511085A>G	ENSP00000409493:p.Ser5144Gly	90.0	0.0		122.0	5.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.928582	0.92389	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.07	5.07	0.68467	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.81612	0.4859	M	0.79926	2.475	0.39861	D	0.973371	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.82673	-0.0341	10	0.36615	T	0.2	.	14.9992	0.71459	1.0:0.0:0.0:0.0	.	5144;5144	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	5144;5144;2778;2263	ENSP00000284548:S5144G;ENSP00000409493:S5144G;ENSP00000355668:S2778G;ENSP00000355670:S2263G	ENSP00000284548:S5144G	S	+	1	0	OBSCN	226577708	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	7.073000	0.76784	2.125000	0.65367	0.533000	0.62120	AGC	.	.		0.517	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228511085	A	G	228511085	3	3	49	1	0	0	0	0	1	0	0	0	10821	304	11	2	15648	2	OBSCN	1	228511085	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	477180	228511085	20739536	25	6182										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228547659	228547659	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aggtgcccaggagctcatcgGggcatctcttcacactgccc	11	15	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:228547659G>T	ENST00000422127.1	+	80	18705				OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366709.4_Missense_Mutation_p.G3475W|OBSCN_ENST00000284548.11_Missense_Mutation_p.G6356W|OBSCN_ENST00000366707.4_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GAGCTCATCGGGGCATCTCTT	0.647																																					p.G6356W		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G19066T						.						20	23	22					1																	228547659		1917	4119	6036	SO:0001627	intron_variant	84033	exon81			TCATCGGGGCATC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18662-2618G>T	chr1.hg19:g.228547659G>T		77.0	0.0		113.0	6.0	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.932384	0.52866	.	.	ENSG00000154358	ENST00000284548;ENST00000366709	T;T	0.57273	0.41;0.55	4.3	-1.09	0.09904	.	.	.	.	.	T	0.50103	0.1596	M	0.62723	1.935	0.09310	N	1	D	0.57257	0.979	P	0.47162	0.54	T	0.44982	-0.9292	9	0.59425	D	0.04	.	6.5145	0.22240	0.223:0.363:0.414:0.0	.	6356	Q5VST9-3	.	W	6356;3475	ENSP00000284548:G6356W;ENSP00000355670:G3475W	ENSP00000284548:G6356W	G	+	1	0	OBSCN	226614282	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.552000	0.23376	-0.413000	0.07507	-0.300000	0.09419	GGG	.	.		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228547659	G	T	228547659	1	4	49	0	1	0	0	0	0	0	0	0	10821	1232	43	3		3	OBSCN	1	228547659	Intron	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	36574	228547659	20702962	26	6183										
ACTN2	88	hgsc.bcm.edu	37	chr1	236906307	236906307	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aacacctggctgagaagttcAggcagaaggcctcaacgcac	11	12	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:236906307A>G	ENST00000366578.4	+	11	1385	c.1219A>G	c.(1219-1221)Agg>Ggg	p.R407G	ACTN2_ENST00000492634.1_3'UTR|ACTN2_ENST00000542672.1_Missense_Mutation_p.R407G|ACTN2_ENST00000546208.1_5'UTR	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	407					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			TGAGAAGTTCAGGCAGAAGGC	0.532																																					p.R407G		Atlas-SNP	.											ACTN2,caecum,carcinoma,0,1	ACTN2	191	.	0			c.A1219G						.						106	97	100					1																	236906307		2203	4300	6503	SO:0001583	missense	88	exon11			AAGTTCAGGCAGA	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.1219A>G	chr1.hg19:g.236906307A>G	ENSP00000355537:p.Arg407Gly	48.0	0.0		62.0	3.0	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	hg19	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	A	11.06	1.527879	0.27299	.	.	ENSG00000077522	ENST00000542672;ENST00000366578;ENST00000545611	T;T	0.51071	0.72;0.72	5.47	1.69	0.24217	.	0.618137	0.16636	N	0.205861	T	0.56441	0.1985	M	0.85710	2.77	0.42436	D	0.992697	B;B;B;B	0.31640	0.069;0.002;0.333;0.108	B;B;B;B	0.36567	0.133;0.012;0.228;0.044	T	0.62201	-0.6904	10	0.72032	D	0.01	.	14.3868	0.66949	0.4847:0.5153:0.0:0.0	.	192;407;177;407	B7Z4K1;B2RCS5;Q59FD9;P35609	.;.;.;ACTN2_HUMAN	G	407;407;176	ENSP00000443495:R407G;ENSP00000355537:R407G	ENSP00000355537:R407G	R	+	1	2	ACTN2	234972930	0.042000	0.20092	0.479000	0.27329	0.436000	0.31835	0.578000	0.23773	0.084000	0.17077	0.533000	0.62120	AGG	.	.		0.532	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		G	236906307	A	G	236906307	3	3	49	1	0	0	0	0	1	0	0	0	205	179	7	2	1261	2	ACTN2	1	236906307	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	8358648	236906307	12344314	27	6184										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370636	240370636	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccgagtttcaaaccagccacGaacactctgtttcctctgcc	6	16	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:240370636G>T	ENST00000319653.9	+	5	2754	c.2524G>T	c.(2524-2526)Gaa>Taa	p.E842*		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	842	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.E985K(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AACCAGCCACGAACACTCTGT	0.557																																					p.E842X		Atlas-SNP	.											FMN2,NS,malignant_melanoma,0,3	FMN2	451	.	1	Substitution - Missense(1)	skin(1)	c.G2524T						.						105	100	102					1																	240370636		2203	4300	6503	SO:0001587	stop_gained	56776	exon5			AGCCACGAACACT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2524G>T	chr1.hg19:g.240370636G>T	ENSP00000318884:p.Glu842*	88.0	0.0		120.0	5.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Nonsense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	38	6.812801	0.97857	.	.	ENSG00000155816	ENST00000319653	.	.	.	4.09	4.09	0.47781	.	0.190914	0.35436	N	0.003211	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8328	0.52305	0.0:0.1769:0.8231:0.0	.	.	.	.	X	842	.	.	E	+	1	0	FMN2	238437259	0.041000	0.20044	0.720000	0.30636	0.550000	0.35303	1.026000	0.30103	2.270000	0.75569	0.555000	0.69702	GAA	.	.		0.557	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240370636	G	T	240370636	4	4	49	1	0	0	0	0	0	1	0	0	5958	1059	37	1	2542	1	FMN2	1	240370636	Nonsense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	3464329	240370636	8879985	28	6185										
COLEC11	78989	hgsc.bcm.edu	37	chr2	3652045	3652045	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cctgctctgtgcagatcctcGtccctggcctcaaaggtaac	9	15	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:3652045G>A	ENST00000349077.4	+	2	218	c.115G>A	c.(115-117)Gtc>Atc	p.V39I	COLEC11_ENST00000402922.1_5'Flank|AC010907.2_ENST00000456450.1_RNA|COLEC11_ENST00000382062.2_Missense_Mutation_p.V39I|COLEC11_ENST00000418971.2_Missense_Mutation_p.V53I|COLEC11_ENST00000236693.7_Silent_p.S9S|COLEC11_ENST00000404205.1_5'Flank|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000403096.3_5'Flank|COLEC11_ENST00000402794.1_5'Flank	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	39					developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)	p.S9S(1)|p.V53L(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		GCAGATCCTCGTCCCTGGCCT	0.642																																					p.V53I		Atlas-SNP	.											COLEC11_ENST00000418971,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,2	COLEC11	93	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	central_nervous_system(2)	c.G157A						.						119	107	111					2																	3652045		2203	4300	6503	SO:0001583	missense	78989	exon3			ATCCTCGTCCCTG	BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"Collectins"	17213	protein-coding gene	gene with protein product	"Collectin K1"	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.115G>A	chr2.hg19:g.3652045G>A	ENSP00000339168:p.Val39Ile	89.0	0.0		83.0	4.0	NM_001255985	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Missense_Mutation	SNP	ENST00000349077.4	hg19	CCDS1649.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.140485	0.37825	.	.	ENSG00000118004	ENST00000382062;ENST00000349077;ENST00000438814;ENST00000418971	D;D;D;D	0.91631	-1.76;-2.03;-2.88;-2.16	4.83	3.95	0.45737	.	0.122413	0.53938	D	0.000042	D	0.88104	0.6347	.	.	.	0.51012	D	0.999905	P;B;P;P	0.38129	0.564;0.109;0.59;0.619	B;B;B;B	0.36989	0.077;0.031;0.113;0.238	D	0.85377	0.1117	9	0.26408	T	0.33	-30.3903	14.5751	0.68240	0.0:0.147:0.853:0.0	.	39;39;39;39	Q9BWP8-5;Q9BWP8-3;Q9BWP8-2;Q9BWP8	.;.;.;COL11_HUMAN	I	39;39;53;53	ENSP00000371494:V39I;ENSP00000339168:V39I;ENSP00000393167:V53I;ENSP00000411770:V53I	ENSP00000339168:V39I	V	+	1	0	COLEC11	3629920	1.000000	0.71417	0.705000	0.30386	0.885000	0.51271	4.185000	0.58330	1.167000	0.42706	-0.150000	0.13652	GTC	.	.		0.642	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027		A	3652045	G	A	3652045	3	1	49	1	0	0	0	0	1	0	0	0	3713	1145	40	1	117	1	COLEC11	2	3652045	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10		3652045	239547328	29	6186										
RHOB	388	hgsc.bcm.edu	37	chr2	20647265	20647265	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aagctggtggtggtgggcgaCggcgcgtgtggcaagacgtg	21	7	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:20647265C>T	ENST00000272233.4	+	1	431	c.39C>T	c.(37-39)gaC>gaT	p.D13D		NM_004040.2	NP_004031.1	P62745	RHOB_HUMAN	ras homolog family member B	13					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|GTP catabolic process (GO:0006184)|negative regulation of cell cycle (GO:0045786)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|transformed cell apoptotic process (GO:0006927)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|kidney(1)|lung(2)|ovary(1)|urinary_tract(2)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)	all_epithelial(98;4.19e-09)|Lung NSC(108;0.00452)|Ovarian(717;0.0164)		OV - Ovarian serous cystadenocarcinoma(76;1.14e-22)|Epithelial(75;7.84e-19)	Botulinum Toxin Type A(DB00083)	TGGTGGGCGACGGCGCGTGTG	0.682																																					p.D13D		Atlas-SNP	.											RHOB,colon,carcinoma,0,1	RHOB	18	.	0			c.C39T						.						75	76	76					2																	20647265		2203	4300	6503	SO:0001819	synonymous_variant	388	exon1			GGGCGACGGCGCG		CCDS1699.1	2p24	2012-02-27	2012-02-27	2004-03-24	ENSG00000143878	ENSG00000143878			668	protein-coding gene	gene with protein product	"oncogene RHO H6"	165370	"ras homolog gene family, member B"	ARH6, ARHB		3283705, 16278215	Standard	NM_004040		Approved	RhoB, RHOH6, MST081	uc002rdv.3	P62745	OTTHUMG00000090755	ENST00000272233.4:c.39C>T	chr2.hg19:g.20647265C>T		33.0	0.0		27.0	2.0	NM_004040	B2R692|P01121|Q5U0H6|Q7RTN5|Q7RTR9|Q9CUV7	Silent	SNP	ENST00000272233.4	hg19	CCDS1699.1																																																																																			.	.		0.682	RHOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207500.1	NM_004040		T	20647265	C	T	20647265	2	4	49	1	0	0	0	0	0	0	0	1	13347	535	19	1		1	RHOB	2	20647265	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	16995220	20647265	222552108	30	6187										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	23980414	23980414	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	attttcagtcgaagtttctgGtttttcttttgactggtcct	8	7	3	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:23980414G>T	ENST00000238789.5	-	25	4295	c.3952C>A	c.(3952-3954)Cca>Aca	p.P1318T	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	1318						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAGTTTCTGGTTTTTCTTTT	0.393																																					p.P1318T		Atlas-SNP	.											.	ATAD2B	110	.	0			c.C3952A						.						181	175	177					2																	23980414		1823	4085	5908	SO:0001583	missense	54454	exon25			TTTCTGGTTTTTC	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.3952C>A	chr2.hg19:g.23980414G>T	ENSP00000238789:p.Pro1318Thr	186.0	0.0		219.0	53.0	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	hg19	CCDS46227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.12|11.12	1.545640|1.545640	0.27652|0.27652	.|.	.|.	ENSG00000119778|ENSG00000119778	ENST00000381024|ENST00000238789;ENST00000546030	.|D	.|0.91351	.|-2.83	5.27|5.27	3.36|3.36	0.38483|0.38483	.|.	.|2.650130	.|0.01891	.|N	.|0.038537	D|D	0.82426|0.82426	0.5034|0.5034	N|N	0.12182|0.12182	0.205|0.205	0.31462|0.31462	N|N	0.669472|0.669472	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.06405	.|0.001;0.002	T|T	0.72261|0.72261	-0.4345|-0.4345	5|10	.|0.24483	.|T	.|0.36	.|.	6.5557|6.5557	0.22460|0.22460	0.077:0.1065:0.6428:0.1738|0.077:0.1065:0.6428:0.1738	.|.	.|1318;1313	.|Q9ULI0;Q9ULI0-2	.|ATD2B_HUMAN;.	K|T	593|1318;486	.|ENSP00000238789:P1318T	.|ENSP00000238789:P1318T	N|P	-|-	3|1	2|0	ATAD2B|ATAD2B	23833918|23833918	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.989000|0.989000	0.77384|0.77384	1.311000|1.311000	0.33562|0.33562	1.355000|1.355000	0.45865|0.45865	0.563000|0.563000	0.77884|0.77884	AAC|CCA	.	.		0.393	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		T	23980414	G	T	23980414	3	4	49	1	0	0	0	0	1	0	0	0	1072	1261	44	3	440	3	ATAD2B	2	23980414	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	3333149	23980414	219218959	31	6188										
C2orf44	80304	hgsc.bcm.edu	37	chr2	24261849	24261849	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aggctgctgcctactgccacCaccagcctcaggccatcctg	9	18	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:24261849C>T	ENST00000295148.4	-	2	573	c.516G>A	c.(514-516)gtG>gtA	p.V172V	C2orf44_ENST00000406895.3_Silent_p.V172V	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	172									C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTACTGCCACCACCAGCCTCA	0.547			T	ALK	NSCLC																																p.V172V		Atlas-SNP	.		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	C2orf44	56	.	0			c.G516A						.						53	47	49					2																	24261849		2203	4300	6503	SO:0001819	synonymous_variant	80304	exon2			TGCCACCACCAGC	AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.516G>A	chr2.hg19:g.24261849C>T		77.0	0.0		83.0	21.0	NM_025203	D6W532|Q8IYK0|Q9HBP5	Silent	SNP	ENST00000295148.4	hg19	CCDS1705.1																																																																																			.	.		0.547	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203		T	24261849	C	T	24261849	2	4	49	1	0	0	0	0	0	0	0	1	2170	581	21	3		3	C2orf44	2	24261849	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	281435	24261849	218937524	32	6189										
AGBL5	60509	hgsc.bcm.edu	37	chr2	27278977	27278977	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaaggggctgcttcatgtacGgaaacagctttagtgatgag	13	6	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:27278977G>A	ENST00000360131.4	+	7	1495	c.1336G>A	c.(1336-1338)Gga>Aga	p.G446R	AGBL5_ENST00000323064.8_Missense_Mutation_p.G446R|RP11-503P10.1_ENST00000607407.1_RNA	NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	446					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCATGTACGGAAACAGCTT	0.502																																					p.G446R		Atlas-SNP	.											AGBL5_ENST00000323064,lower_third,carcinoma,0,2	AGBL5	126	.	0			c.G1336A						.						124	124	124					2																	27278977		2203	4300	6503	SO:0001583	missense	60509	exon7			ATGTACGGAAACA	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 5"	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.1336G>A	chr2.hg19:g.27278977G>A	ENSP00000353249:p.Gly446Arg	40.0	0.0		48.0	2.0	NM_021831	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Missense_Mutation	SNP	ENST00000360131.4	hg19	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	G	33	5.231204	0.95207	.	.	ENSG00000084693	ENST00000323064;ENST00000360131	T;T	0.33865	1.39;1.39	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.73001	0.3531	M	0.94142	3.5	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.79799	-0.1651	10	0.87932	D	0	-21.4622	20.0291	0.97531	0.0:0.0:1.0:0.0	.	446;446;446	Q8NDL9;Q8NDL9-3;Q8NDL9-2	CBPC5_HUMAN;.;.	R	446	ENSP00000323681:G446R;ENSP00000353249:G446R	ENSP00000323681:G446R	G	+	1	0	AGBL5	27132481	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.359000	0.97115	2.838000	0.97847	0.561000	0.74099	GGA	.	.		0.502	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831		A	27278977	G	A	27278977	3	1	49	1	0	0	0	0	1	0	0	0	378	1117	39	1	1358	1	AGBL5	2	27278977	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	3017128	27278977	215920396	33	6190										
IFT172	26160	hgsc.bcm.edu	37	chr2	27679434	27679434	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agtcccagcttattaagcagTctaactgcagcctctcctcc	6	15	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:27679434T>C	ENST00000260570.3	-	30	3418	c.3315A>G	c.(3313-3315)agA>agG	p.R1105R		NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	1105					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					TATTAAGCAGTCTAACTGCAG	0.562																																					p.R1105R		Atlas-SNP	.											.	IFT172	119	.	0			c.A3315G						.						127	119	121					2																	27679434		2203	4300	6503	SO:0001819	synonymous_variant	26160	exon30			AAGCAGTCTAACT	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.3315A>G	chr2.hg19:g.27679434T>C		74.0	0.0		81.0	4.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Silent	SNP	ENST00000260570.3	hg19	CCDS1755.1																																																																																			.	.		0.562	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		C	27679434	T	C	27679434	2	2	49	1	0	0	0	0	0	0	0	1	7566	1664	58	2		2	IFT172	2	27679434	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	400457	27679434	215519939	34	6191										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32613893	32613893	+	Frame_Shift_Del	DEL	A	A	-													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccattgtaaatgaactcaagAaaataaatcaaaatgttgct							TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:32613893delA	ENST00000421745.2	+	4	855	c.721delA	c.(721-723)aaafs	p.K241fs		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	241					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TGAACTCAAGAAAATAAATCA	0.448																																					p.K240fs	Pancreas(94;175 1509 16028 18060 45422)	Atlas-Indel,Pindel	.											.	BIRC6	838	.	0			c.720delG						.						154	131	138					2																	32613893		2203	4300	6503	SO:0001589	frameshift_variant	57448	exon4			.	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.721delA	chr2.hg19:g.32613893delA	ENSP00000393596:p.Lys241fs	168.0	0.0		171.0	30.0	NM_016252	Q9ULD1	Frame_Shift_Del	DEL	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.		0.448	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		-	32613893	A	-	32613893	7	5	49	1	0	1	0	1	0	0	0	0	1438	247	9	0	735	0	BIRC6	2	32613893	Frame_Shift_Del	DEL	A	TCGA-BD-A3EP-01A-11D-A22F-10	4934459	32613893	210585480	35	6192										
CYP26B1	56603	hgsc.bcm.edu	37	chr2	72359542	72359542	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agctccaccgccagcaccttCaggaacagcttggccaggtg	11	15	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:72359542C>T	ENST00000001146.2	-	6	1556	c.1353G>A	c.(1351-1353)ctG>ctA	p.L451L	CYP26B1_ENST00000412253.1_Silent_p.L260L|CYP26B1_ENST00000546307.1_Silent_p.L376L	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily B, polypeptide 1	451					bone morphogenesis (GO:0060349)|cell fate determination (GO:0001709)|cellular response to retinoic acid (GO:0071300)|cornification (GO:0070268)|embryonic limb morphogenesis (GO:0030326)|establishment of skin barrier (GO:0061436)|male meiosis (GO:0007140)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of tongue muscle cell differentiation (GO:2001037)|proximal/distal pattern formation (GO:0009954)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|tongue morphogenesis (GO:0043587)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						CCAGCACCTTCAGGAACAGCT	0.672																																					p.L451L		Atlas-SNP	.											.	CYP26B1	73	.	0			c.G1353A						.						48	43	45					2																	72359542		2203	4300	6503	SO:0001819	synonymous_variant	56603	exon6			CACCTTCAGGAAC		CCDS1919.1, CCDS62934.1	2p12	2006-11-24			ENSG00000003137	ENSG00000003137		"Cytochrome P450s"	20581	protein-coding gene	gene with protein product		605207				10545224	Standard	NM_019885		Approved	P450RAI-2	uc002sih.2	Q9NR63	OTTHUMG00000129756	ENST00000001146.2:c.1353G>A	chr2.hg19:g.72359542C>T		94.0	0.0		93.0	4.0	NM_019885	B2R8M7|B7Z2K6|B7Z2P4|B7Z3B8|E4W5W7|Q32MC0|Q53TW1|Q9NP41	Silent	SNP	ENST00000001146.2	hg19	CCDS1919.1																																																																																			.	.		0.672	CYP26B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251969.1	NM_019885		T	72359542	C	T	72359542	2	4	49	1	0	0	0	0	0	0	0	1	4158	813	29	3		3	CYP26B1	2	72359542	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	39745649	72359542	170839831	36	6193										
INO80B	83444	hgsc.bcm.edu	37	chr2	74682605	74682605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gaaaaaacacaagaagcacaAgaagaaacacaagaagaaac	7	7	0	5			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:74682605A>G	ENST00000233331.7	+	2	225	c.131A>G	c.(130-132)aAg>aGg	p.K44R	WBP1_ENST00000233615.2_5'Flank|WBP1_ENST00000409737.1_5'Flank|INO80B_ENST00000409917.1_Missense_Mutation_p.K44R|WBP1_ENST00000393972.3_5'Flank|INO80B_ENST00000469849.1_Intron	NM_031288.3	NP_112578.2	Q9C086	IN80B_HUMAN	INO80 complex subunit B	44	Lys-rich.				chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	13						aagaagcacaagaagaaacac	0.547																																					p.K44R		Atlas-SNP	.											INO80B,NS,carcinoma,0,1	INO80B	37	.	0			c.A131G						.						75	89	84					2																	74682605		2203	4300	6503	SO:0001583	missense	83444	exon2			AGCACAAGAAGAA	AB054538	CCDS1942.2	2p13.1	2011-07-06	2008-08-07	2008-08-07	ENSG00000115274	ENSG00000115274		"Zinc fingers, HIT-type", "INO80 complex subunits"	13324	protein-coding gene	gene with protein product	"PAP-1 binding protein", "IES2 homolog (S. cerevisiae)"		"high mobility group AT-hook 1-like 4", "zinc finger, HIT type 4"	HMGA1L4, ZNHIT4		16230350	Standard	NM_031288		Approved	HMGIYL4, PAPA-1, hIes2, PAP-1BP, IES2	uc002slg.3	Q9C086	OTTHUMG00000129959	ENST00000233331.7:c.131A>G	chr2.hg19:g.74682605A>G	ENSP00000233331:p.Lys44Arg	39.0	0.0		49.0	2.0	NM_031288		Missense_Mutation	SNP	ENST00000233331.7	hg19	CCDS1942.2	.	.	.	.	.	.	.	.	.	.	A	26.1	4.709684	0.89018	.	.	ENSG00000115274	ENST00000233331;ENST00000431187;ENST00000409917;ENST00000409493	T;T;T;T	0.55930	0.58;0.54;0.57;0.49	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.50514	0.1620	N	0.08118	0	0.52501	D	0.999956	D;D;D;D	0.69078	0.997;0.993;0.993;0.988	D;D;D;D	0.75020	0.985;0.968;0.956;0.981	T	0.52366	-0.8585	10	0.23891	T	0.37	-23.5868	13.4809	0.61334	1.0:0.0:0.0:0.0	.	62;44;44;44	B4DJ31;B4DJ22;Q9C086;B8ZZ93	.;.;IN80B_HUMAN;.	R	44;44;44;49	ENSP00000233331:K44R;ENSP00000389887:K44R;ENSP00000387267:K44R;ENSP00000386937:K49R	ENSP00000233331:K44R	K	+	2	0	INO80B	74536113	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.616000	0.83018	2.067000	0.61834	0.460000	0.39030	AAG	.	.		0.547	INO80B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252223.2	NM_031288		G	74682605	A	G	74682605	3	3	49	1	0	0	0	0	1	0	0	0	7756	72	3	2	137	2	INO80B	2	74682605	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	2323063	74682605	168516768	37	6194										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84932627	84932627	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	caggcctgattggccatcagCaaagcaacttcttggtgact	10	11	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:84932627C>A	ENST00000237449.6	+	51	8491	c.8483C>A	c.(8482-8484)gCa>gAa	p.A2828E	DNAH6_ENST00000389394.3_Missense_Mutation_p.A2828E			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2828	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TGGCCATCAGCAAAGCAACTT	0.328																																					p.A2828E		Atlas-SNP	.											.	DNAH6	194	.	0			c.C8483A						.						61	50	53					2																	84932627		692	1591	2283	SO:0001583	missense	1768	exon52			CATCAGCAAAGCA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.8483C>A	chr2.hg19:g.84932627C>A	ENSP00000237449:p.Ala2828Glu	65.0	0.0		105.0	19.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.580866	0.86748	.	.	ENSG00000115423	ENST00000389394;ENST00000237449	T;T	0.80480	-1.38;-1.38	5.49	5.49	0.81192	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.47455	D	0.000226	D	0.93986	0.8074	H	0.98048	4.135	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95827	0.8855	10	0.87932	D	0	.	18.5012	0.90882	0.0:1.0:0.0:0.0	.	2828	Q9C0G6	DYH6_HUMAN	E	2828	ENSP00000374045:A2828E;ENSP00000237449:A2828E	ENSP00000237449:A2828E	A	+	2	0	DNAH6	84786138	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.845000	0.55880	2.727000	0.93392	0.650000	0.86243	GCA	.	.		0.328	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84932627	C	A	84932627	3	1	49	1	0	0	0	0	1	0	0	0	4607	710	25	3	8685	3	DNAH6	2	84932627	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	10250022	84932627	158266746	38	6195										
REV1	51455	hgsc.bcm.edu	37	chr2	100019562	100019562	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tttagatgaagtaaaggattCtttggcactaagagcagatg	11	4	1	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:100019562C>A	ENST00000258428.3	-	20	3402	c.3174G>T	c.(3172-3174)aaG>aaT	p.K1058N	RP11-527J8.1_ENST00000608144.1_RNA|REV1_ENST00000393445.3_Missense_Mutation_p.K1057N|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	1058					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)	p.K1058K(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTAAAGGATTCTTTGGCACTA	0.358								Direct reversal of damage																													p.K1058N		Atlas-SNP	.											REV1,colon,carcinoma,0,1	REV1	100	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3174T						.						31	28	29					2																	100019562		2201	4297	6498	SO:0001583	missense	51455	exon20			AGGATTCTTTGGC	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.3174G>T	chr2.hg19:g.100019562C>A	ENSP00000258428:p.Lys1058Asn	50.0	0.0		51.0	3.0	NM_016316	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	hg19	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.748285	0.69533	.	.	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.33865	1.39;1.39	5.95	3.16	0.36331	.	0.043184	0.85682	D	0.000000	T	0.51770	0.1694	M	0.73598	2.24	0.52099	D	0.999949	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.987	T	0.51260	-0.8728	10	0.56958	D	0.05	.	3.4149	0.07372	0.0:0.4766:0.1973:0.3261	.	1058;1057	Q9UBZ9;Q9UBZ9-2	REV1_HUMAN;.	N	1057;1058	ENSP00000377091:K1057N;ENSP00000258428:K1058N	ENSP00000258428:K1058N	K	-	3	2	REV1	99385994	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.918000	0.28678	0.839000	0.34971	0.655000	0.94253	AAG	.	.		0.358	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		A	100019562	C	A	100019562	3	1	49	1	0	0	0	0	1	0	0	0	13254	912	32	3	597	3	REV1	2	100019562	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	15086935	100019562	143179811	39	6196										
TBC1D8	11138	hgsc.bcm.edu	37	chr2	101656711	101656711	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcagatgtagctgtcagaggCgaacatccgccccgtggtgt	14	11	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:101656711C>T	ENST00000376840.4	-	6	963	c.964G>A	c.(964-966)Gcc>Acc	p.A322T	TBC1D8_ENST00000409318.1_Missense_Mutation_p.A337T			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	322	GRAM 2.				blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.A337T(1)		breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						CTGTCAGAGGCGAACATCCGC	0.577																																					p.A322T		Atlas-SNP	.											TBC1D8,NS,carcinoma,0,1	TBC1D8	169	.	1	Substitution - Missense(1)	ovary(1)	c.G964A						.						69	73	72					2																	101656711		2042	4188	6230	SO:0001583	missense	11138	exon6			CAGAGGCGAACAT	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"BUB2-like protein 1", "vascular Rab-GAP/TBC-containing protein"					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.964G>A	chr2.hg19:g.101656711C>T	ENSP00000366036:p.Ala322Thr	60.0	0.0		61.0	3.0	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Missense_Mutation	SNP	ENST00000376840.4	hg19	CCDS46375.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.583712	0.28268	.	.	ENSG00000204634	ENST00000376840;ENST00000409318	D;D	0.86769	-2.17;-2.17	5.86	-7.1	0.01547	GRAM (2);	0.503517	0.20539	N	0.090356	T	0.66247	0.2770	N	0.08118	0	0.09310	N	0.999995	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.002	T	0.52586	-0.8556	10	0.41790	T	0.15	-9.2577	8.092	0.30805	0.1779:0.4128:0.0:0.4093	.	337;322	B7Z6L4;O95759	.;TBCD8_HUMAN	T	322;337	ENSP00000366036:A322T;ENSP00000386856:A337T	ENSP00000366036:A322T	A	-	1	0	TBC1D8	101023143	0.000000	0.05858	0.054000	0.19295	0.601000	0.36947	-0.415000	0.07106	-1.140000	0.02877	-1.147000	0.01851	GCC	.	.		0.577	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063		T	101656711	C	T	101656711	3	4	49	1	0	0	0	0	1	0	0	0	15640	768	27	1	2518	1	TBC1D8	2	101656711	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1637149	101656711	141542662	40	6197										
LCT	3938	hgsc.bcm.edu	37	chr2	136566972	136566972	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttctcccagttgggaaaatcCgagaccaggagatagagaag	12	8	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:136566972C>T	ENST00000264162.2	-	8	2955	c.2945G>A	c.(2944-2946)cGg>cAg	p.R982Q	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	982	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	TGGGAAAATCCGAGACCAGGA	0.498																																					p.R982Q		Atlas-SNP	.											.	LCT	309	.	0			c.G2945A						.						74	79	77					2																	136566972		2203	4300	6503	SO:0001583	missense	3938	exon8			AAAATCCGAGACC	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.2945G>A	chr2.hg19:g.136566972C>T	ENSP00000264162:p.Arg982Gln	68.0	0.0		85.0	5.0	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	hg19	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	32	5.188696	0.94923	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.61158	0.13	5.78	5.78	0.91487	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.047713	0.85682	D	0.000000	D	0.84853	0.5564	H	0.96365	3.81	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89003	0.3423	10	0.87932	D	0	-30.6945	20.0139	0.97470	0.0:1.0:0.0:0.0	.	982	P09848	LPH_HUMAN	Q	982;414	ENSP00000264162:R982Q	ENSP00000264162:R982Q	R	-	2	0	LCT	136283442	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.818000	0.86416	2.724000	0.93272	0.563000	0.77884	CGG	.	.		0.498	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		T	136566972	C	T	136566972	3	4	49	1	0	0	0	0	1	0	0	0	8702	652	23	1	2878	1	LCT	2	136566972	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	34910261	136566972	106632401	41	6198										
PKP4	8502	hgsc.bcm.edu	37	chr2	159481873	159481873	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggactgttcatgacatggagCaattcggacagcagcagtat	12	8	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:159481873C>T	ENST00000389759.3	+	7	1199	c.1087C>T	c.(1087-1089)Caa>Taa	p.Q363*	PKP4_ENST00000389757.3_Nonsense_Mutation_p.Q363*	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	363					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						TGACATGGAGCAATTCGGACA	0.552										HNSCC(62;0.18)																											p.Q363X		Atlas-SNP	.											.	PKP4	133	.	0			c.C1087T						.						86	73	78					2																	159481873		2203	4300	6503	SO:0001587	stop_gained	8502	exon7			ATGGAGCAATTCG	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.1087C>T	chr2.hg19:g.159481873C>T	ENSP00000374409:p.Gln363*	223.0	0.0		268.0	48.0	NM_001005476	Q86W91	Nonsense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	C	37	6.094775	0.97276	.	.	ENSG00000144283	ENST00000428353;ENST00000389757;ENST00000389759	.	.	.	5.67	4.78	0.61160	.	0.353767	0.29646	N	0.011565	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-1.4514	16.2064	0.82133	0.1343:0.8657:0.0:0.0	.	.	.	.	X	215;363;363	.	ENSP00000374407:Q363X	Q	+	1	0	PKP4	159190119	0.995000	0.38212	0.289000	0.24876	0.998000	0.95712	5.278000	0.65592	1.499000	0.48617	0.655000	0.94253	CAA	.	.		0.552	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			T	159481873	C	T	159481873	4	4	49	1	0	0	0	0	0	1	0	0	11996	711	25	3	1109	3	PKP4	2	159481873	Nonsense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	22914901	159481873	83717500	42	6199										
FAP	2191	hgsc.bcm.edu	37	chr2	163031427	163031427	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctgctataccacatttgaaaAgaccagttccagatgcaagg	8	10	0	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:163031427A>G	ENST00000188790.4	-	22	2126	c.1919T>C	c.(1918-1920)cTt>cCt	p.L640P	FAP_ENST00000443424.1_Missense_Mutation_p.L615P|AC007750.5_ENST00000418968.3_RNA	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						ACATTTGAAAAGACCAGTTCC	0.398																																					p.L640P		Atlas-SNP	.											.	FAP	122	.	0			c.T1919C						.						122	108	113					2																	163031427		2203	4300	6503	SO:0001583	missense	2191	exon22			TTGAAAAGACCAG	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.1919T>C	chr2.hg19:g.163031427A>G	ENSP00000188790:p.Leu640Pro	86.0	0.0		93.0	4.0	NM_004460		Missense_Mutation	SNP	ENST00000188790.4	hg19	CCDS33311.1	.	.	.	.	.	.	.	.	.	.	A	18.17	3.565427	0.65651	.	.	ENSG00000078098	ENST00000188790;ENST00000443424	T;T	0.49432	0.78;0.78	5.42	5.42	0.78866	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.238619	0.37715	N	0.001973	T	0.47210	0.1433	L	0.39085	1.19	0.80722	D	1	B;B;B	0.28605	0.007;0.005;0.217	B;B;B	0.38616	0.078;0.021;0.277	T	0.48885	-0.8995	10	0.56958	D	0.05	-20.5135	15.7747	0.78204	1.0:0.0:0.0:0.0	.	615;119;640	B4DLR2;Q12884-2;Q12884	.;.;SEPR_HUMAN	P	640;615	ENSP00000188790:L640P;ENSP00000411391:L615P	ENSP00000188790:L640P	L	-	2	0	FAP	162739673	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.777000	0.91781	2.194000	0.70268	0.533000	0.62120	CTT	.	.		0.398	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			G	163031427	A	G	163031427	3	3	49	1	0	0	0	0	1	0	0	0	5681	72	3	2	383	2	FAP	2	163031427	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	3549554	163031427	80167946	43	6200										
TNS1	7145	hgsc.bcm.edu	37	chr2	218713231	218713231	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gctccatggggtaggacttgTccagaccgttggtcagtggg	16	9	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:218713231T>C	ENST00000171887.4	-	17	2086	c.1634A>G	c.(1633-1635)gAc>gGc	p.D545G	TNS1_ENST00000419504.1_Missense_Mutation_p.D545G|TNS1_ENST00000480665.1_5'UTR|TNS1_ENST00000430930.1_Missense_Mutation_p.D545G	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	545					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GTAGGACTTGTCCAGACCGTT	0.657																																					p.D545G		Atlas-SNP	.											.	TNS1	251	.	0			c.A1634G						.						53	60	57					2																	218713231		2203	4299	6502	SO:0001583	missense	7145	exon17			GACTTGTCCAGAC	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1634A>G	chr2.hg19:g.218713231T>C	ENSP00000171887:p.Asp545Gly	95.0	0.0		67.0	4.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	T	12.89	2.072243	0.36566	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903	D;D;D;D	0.95069	-2.98;-2.98;-2.99;-3.6	4.79	4.79	0.61399	.	0.587686	0.17541	N	0.170538	D	0.94974	0.8374	L	0.55990	1.75	0.80722	D	1	D;D;P;P;P	0.59357	0.958;0.985;0.89;0.89;0.791	P;P;B;B;B	0.55923	0.604;0.787;0.318;0.318;0.272	D	0.93468	0.6816	10	0.30854	T	0.27	.	14.4915	0.67654	0.0:0.0:0.0:1.0	.	545;599;545;545;545	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	G	545;545;545;670	ENSP00000171887:D545G;ENSP00000408724:D545G;ENSP00000406016:D545G;ENSP00000405460:D670G	ENSP00000171887:D545G	D	-	2	0	TNS1	218421476	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	4.390000	0.59646	2.013000	0.59113	0.459000	0.35465	GAC	.	.		0.657	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		C	218713231	T	C	218713231	3	2	49	1	0	0	0	0	1	0	0	0	16358	1667	58	2	3641	2	TNS1	2	218713231	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	55681804	218713231	24486142	44	6201										
TNS1	7145	hgsc.bcm.edu	37	chr2	218762666	218762666	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggtccagctcacagctgtccTccatggtccggctcacactc	9	17	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:218762666T>A	ENST00000171887.4	-	6	475	c.23A>T	c.(22-24)gAg>gTg	p.E8V	TNS1_ENST00000419504.1_Missense_Mutation_p.E8V|TNS1_ENST00000310858.6_Missense_Mutation_p.E39V|TNS1_ENST00000430930.1_Missense_Mutation_p.E8V	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	8	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		ACAGCTGTCCTCCATGGTCCG	0.587																																					p.E8V		Atlas-SNP	.											.,2	TNS1	251	.	0			c.A23T						.						126	93	104					2																	218762666		2203	4300	6503	SO:0001583	missense	7145	exon6			CTGTCCTCCATGG	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.23A>T	chr2.hg19:g.218762666T>A	ENSP00000171887:p.Glu8Val	44.0	0.0		48.0	4.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	T	33	5.205287	0.95033	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554;ENST00000310858;ENST00000413280;ENST00000439083;ENST00000423413;ENST00000449814	D;D;D;D;D;D;D;D;D	0.99252	-3.18;-3.17;-3.18;-3.63;-3.97;-3.93;-5.63;-4.93;-4.72	5.42	5.42	0.78866	Phosphatase tensin type (1);	0.050950	0.85682	D	0.000000	D	0.99248	0.9738	M	0.67517	2.055	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.981;0.997;1.0;1.0;1.0	D;P;D;D;D;D	0.85130	0.997;0.874;0.946;0.982;0.997;0.997	D	0.99509	1.0955	10	0.87932	D	0	.	15.6246	0.76845	0.0:0.0:0.0:1.0	.	8;62;39;8;8;8	B2RU35;A1L0S7;Q6IPI5;Q9HBL0;E9PGF5;E9PF55	.;.;.;TENS1_HUMAN;.;.	V	8;8;8;133;76;39;8;8;73;8	ENSP00000171887:E8V;ENSP00000408724:E8V;ENSP00000406016:E8V;ENSP00000405460:E133V;ENSP00000400383:E76V;ENSP00000308321:E39V;ENSP00000395615:E8V;ENSP00000404477:E8V;ENSP00000411349:E73V	ENSP00000171887:E8V	E	-	2	0	TNS1	218470911	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.066000	0.71185	2.274000	0.75844	0.533000	0.62120	GAG	.	.		0.587	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218762666	T	A	218762666	3	1	49	1	0	0	0	0	1	0	0	0	16358	1551	54	4	5296	4	TNS1	2	218762666	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	49435	218762666	24436707	45	6202										
FEV	54738	hgsc.bcm.edu	37	chr2	219849754	219849754	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggtccctggtacctggcaggTacatgttgatcagcaggggc	15	10	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:219849754T>C	ENST00000295727.1	-	1	625	c.44A>G	c.(43-45)tAc>tGc	p.Y15C		NM_017521.2	NP_059991.1	Q99581	FEV_HUMAN	FEV (ETS oncogene family)	15					cell differentiation (GO:0030154)|neuron fate specification (GO:0048665)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)		EWSR1/FEV(11)|FUS/FEV(2)	large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	4		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACCTGGCAGGTACATGTTGAT	0.697			T	"EWSR1,  FUS"	Ewing sarcoma																																p.Y15C	NSCLC(198;941 2228 4658 24163 34665)	Atlas-SNP	.		Dom	yes		2	2q36	54738	FEV protein - (HSRNAFEV)		M	.	FEV	10	.	0			c.A44G						.						9	9	9					2																	219849754		2130	4192	6322	SO:0001583	missense	54738	exon1			GGCAGGTACATGT		CCDS2428.1	2q36	2008-02-05			ENSG00000163497	ENSG00000163497			18562	protein-coding gene	gene with protein product		607150	"FEV (fifth Ewing variant)"			9121764	Standard	NM_017521		Approved	Pet-1	uc002vji.1	Q99581	OTTHUMG00000133080	ENST00000295727.1:c.44A>G	chr2.hg19:g.219849754T>C	ENSP00000295727:p.Tyr15Cys	48.0	0.0		73.0	4.0	NM_017521		Missense_Mutation	SNP	ENST00000295727.1	hg19	CCDS2428.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.019993	0.54576	.	.	ENSG00000163497	ENST00000295727	T	0.40476	1.03	3.6	3.6	0.41247	.	1.997360	0.02604	U	0.101365	T	0.50871	0.1641	N	0.14661	0.345	0.47276	D	0.999378	D	0.67145	0.996	D	0.74674	0.984	T	0.41556	-0.9502	10	0.45353	T	0.12	.	11.3339	0.49492	0.0:0.0:0.0:1.0	.	15	Q99581	FEV_HUMAN	C	15	ENSP00000295727:Y15C	ENSP00000295727:Y15C	Y	-	2	0	FEV	219557998	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.737000	0.62066	1.496000	0.48567	0.460000	0.39030	TAC	.	.		0.697	FEV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256725.1			C	219849754	T	C	219849754	3	2	49	1	0	0	0	0	1	0	0	0	5830	1638	57	2	684	2	FEV	2	219849754	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	1087088	219849754	23349619	46	6203										
SPEG	10290	hgsc.bcm.edu	37	chr2	220333895	220333895	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cagctcgaagctggagaagaTgccatccattcccgaggagc	12	12	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:220333895T>C	ENST00000312358.7	+	13	3641	c.3509T>C	c.(3508-3510)aTg>aCg	p.M1170T	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1170					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.M1170R(1)		breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CTGGAGAAGATGCCATCCATT	0.672																																					p.M1170T		Atlas-SNP	.											SPEG,NS,carcinoma,0,1	SPEG	272	.	1	Substitution - Missense(1)	kidney(1)	c.T3509C						.						37	44	42					2																	220333895		2173	4275	6448	SO:0001583	missense	10290	exon13			AGAAGATGCCATC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.3509T>C	chr2.hg19:g.220333895T>C	ENSP00000311684:p.Met1170Thr	69.0	0.0		63.0	4.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	T	15.16	2.752470	0.49362	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.64260	-0.09	4.77	4.77	0.60923	.	0.000000	0.51477	D	0.000098	T	0.67878	0.2940	L	0.27053	0.805	0.80722	D	1	D	0.71674	0.998	D	0.72338	0.977	T	0.72330	-0.4326	10	0.72032	D	0.01	.	14.4658	0.67482	0.0:0.0:0.0:1.0	.	1170	Q15772	SPEG_HUMAN	T	1170	ENSP00000311684:M1170T	ENSP00000265327:M1170T	M	+	2	0	SPEG	220042139	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.829000	0.86735	2.015000	0.59207	0.533000	0.62120	ATG	.	.		0.672	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		C	220333895	T	C	220333895	3	2	49	1	0	0	0	0	1	0	0	0	15051	1464	51	2	3571	2	SPEG	2	220333895	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	484141	220333895	22865478	47	6204										
COL4A4	1286	hgsc.bcm.edu	37	chr2	228012135	228012135	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctgaggatactcaccagggaCctgtggccaaggacttggtc	13	11	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:228012135C>T	ENST00000396625.3	-	2	272	c.65G>A	c.(64-66)gGt>gAt	p.G22D	COL4A4_ENST00000329662.7_Missense_Mutation_p.G22D	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	22					axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TCACCAGGGACCTGTGGCCAA	0.413																																					p.G22D		Atlas-SNP	.											.	COL4A4	215	.	0			c.G65A						.						246	258	254					2																	228012135		1919	4135	6054	SO:0001583	missense	1286	exon2			CAGGGACCTGTGG		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.65G>A	chr2.hg19:g.228012135C>T	ENSP00000379866:p.Gly22Asp	62.0	0.0		56.0	8.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	hg19	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	c	0.261	-0.999385	0.02128	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.90004	-2.6;-2.55	4.59	-6.5	0.01884	.	.	.	.	.	T	0.69931	0.3166	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60219	-0.7306	9	0.11182	T	0.66	.	2.3552	0.04293	0.1402:0.3799:0.1208:0.3591	.	22	P53420	CO4A4_HUMAN	D	22	ENSP00000379866:G22D;ENSP00000328553:G22D	ENSP00000328553:G22D	G	-	2	0	COL4A4	227720379	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.870000	0.04228	-1.041000	0.03266	-1.945000	0.00491	GGT	.	.		0.413	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		T	228012135	C	T	228012135	3	4	49	1	0	0	0	0	1	0	0	0	3695	507	18	3	5195	3	COL4A4	2	228012135	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	7678240	228012135	15187238	48	6205										
SH3BP4	23677	hgsc.bcm.edu	37	chr2	235950464	235950464	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gccacgtcgcccctggggagAcccagcagatctccatgaaa	11	15	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:235950464A>G	ENST00000409212.1	+	4	1558	c.1051A>G	c.(1051-1053)Acc>Gcc	p.T351A	SH3BP4_ENST00000392011.2_Missense_Mutation_p.T351A|SH3BP4_ENST00000344528.4_Missense_Mutation_p.T351A			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	351					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		CCCTGGGGAGACCCAGCAGAT	0.622																																					p.T351A		Atlas-SNP	.											.	SH3BP4	109	.	0			c.A1051G						.						28	30	29					2																	235950464		2203	4300	6503	SO:0001583	missense	23677	exon4			GGGGAGACCCAGC	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.1051A>G	chr2.hg19:g.235950464A>G	ENSP00000386862:p.Thr351Ala	54.0	0.0		68.0	4.0	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	hg19	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	A	8.864	0.947616	0.18356	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000409212;ENST00000344528	T;T;T	0.41065	1.01;1.01;1.01	5.62	5.62	0.85841	ZU5 (1);	0.190156	0.56097	D	0.000036	T	0.42040	0.1185	L	0.53249	1.67	0.42239	D	0.991924	B;B	0.24823	0.112;0.112	B;B	0.30029	0.11;0.11	T	0.27297	-1.0078	10	0.30854	T	0.27	-0.5749	14.651	0.68797	1.0:0.0:0.0:0.0	.	351;351	A8K594;Q9P0V3	.;SH3B4_HUMAN	A	351	ENSP00000375867:T351A;ENSP00000386862:T351A;ENSP00000340237:T351A	ENSP00000340237:T351A	T	+	1	0	SH3BP4	235615203	0.846000	0.29590	0.912000	0.35992	0.946000	0.59487	5.972000	0.70448	2.129000	0.65627	0.533000	0.62120	ACC	.	.		0.622	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			G	235950464	A	G	235950464	3	3	49	1	0	0	0	0	1	0	0	0	14261	275	10	2	1057	2	SH3BP4	2	235950464	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	7938329	235950464	7248909	49	6206										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238289663	238289663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gatgaacaccagggaggagtCgaaagcgatctcttccagct	12	10	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:238289663C>T	ENST00000295550.4	-	5	2244	c.1792G>A	c.(1792-1794)Gac>Aac	p.D598N	COL6A3_ENST00000409809.1_Missense_Mutation_p.D392N|COL6A3_ENST00000392004.3_Missense_Mutation_p.D392N|COL6A3_ENST00000346358.4_Missense_Mutation_p.D598N|COL6A3_ENST00000353578.4_Missense_Mutation_p.D392N|COL6A3_ENST00000392003.2_Missense_Mutation_p.D191N|COL6A3_ENST00000472056.1_Missense_Mutation_p.D191N|COL6A3_ENST00000347401.3_Missense_Mutation_p.D397N	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	598	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D598N(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AGGGAGGAGTCGAAAGCGATC	0.592																																					p.D598N		Atlas-SNP	.											COL6A3_ENST00000392004,colon,carcinoma,0,3	COL6A3	608	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1792A						.						81	74	77					2																	238289663		2203	4300	6503	SO:0001583	missense	1293	exon5			AGGAGTCGAAAGC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.1792G>A	chr2.hg19:g.238289663C>T	ENSP00000295550:p.Asp598Asn	49.0	0.0		56.0	3.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.893663	0.52121	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	D;D;D;D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	5.81	5.81	0.92471	von Willebrand factor, type A (3);	0.109102	0.40064	N	0.001193	D	0.89026	0.6598	L	0.55017	1.72	0.20563	N	0.999885	P;D;D;D;D;P	0.89917	0.854;0.999;0.992;1.0;1.0;0.854	B;D;D;D;D;B	0.76575	0.141;0.97;0.912;0.982;0.988;0.141	T	0.80547	-0.1334	10	0.20519	T	0.43	.	20.0804	0.97772	0.0:1.0:0.0:0.0	.	598;191;191;392;392;598	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	N	598;397;392;191;392;598;392;191;598	ENSP00000295550:D598N;ENSP00000315609:D397N;ENSP00000315873:D392N;ENSP00000418285:D191N;ENSP00000386844:D392N;ENSP00000295546:D598N;ENSP00000375861:D392N;ENSP00000375860:D191N;ENSP00000389539:D598N	ENSP00000295550:D598N	D	-	1	0	COL6A3	237954402	0.923000	0.31300	0.610000	0.28997	0.125000	0.20455	2.267000	0.43329	2.738000	0.93877	0.655000	0.94253	GAC	.	.		0.592	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238289663	C	T	238289663	3	4	49	1	0	0	0	0	1	0	0	0	3703	884	31	1	7948	1	COL6A3	2	238289663	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	2339199	238289663	4909710	50	6207										
ILKAP	80895	hgsc.bcm.edu	37	chr2	239079271	239079271	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgttgcaggctgcttcgtagCgggcgtcggctgcggacttc	16	11	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:239079271C>T	ENST00000254654.3	-	12	1260	c.1085G>A	c.(1084-1086)cGc>cAc	p.R362H		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	362	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)		TGCTTCGTAGCGGGCGTCGGC	0.612																																					p.R362H		Atlas-SNP	.											ILKAP,NS,carcinoma,0,1	ILKAP	42	.	0			c.G1085A						.						43	43	43					2																	239079271		2203	4300	6503	SO:0001583	missense	80895	exon12			TCGTAGCGGGCGT	AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	15566	protein-coding gene	gene with protein product			"integrin-linked kinase-associated serine/threonine phosphatase 2C"				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.1085G>A	chr2.hg19:g.239079271C>T	ENSP00000254654:p.Arg362His	111.0	0.0		69.0	3.0	NM_030768	B3KM39	Missense_Mutation	SNP	ENST00000254654.3	hg19	CCDS2526.1	.	.	.	.	.	.	.	.	.	.	C	15.05	2.719602	0.48728	.	.	ENSG00000132323	ENST00000254654	T	0.17213	2.29	5.69	5.69	0.88448	Protein phosphatase 2C-like (5);	0.112628	0.64402	D	0.000012	T	0.15825	0.0381	L	0.42632	1.34	0.44852	D	0.997862	B	0.31125	0.309	B	0.33042	0.157	T	0.05582	-1.0876	10	0.12766	T	0.61	-0.4038	13.5499	0.61726	0.156:0.844:0.0:0.0	.	362	Q9H0C8	ILKAP_HUMAN	H	362	ENSP00000254654:R362H	ENSP00000254654:R362H	R	-	2	0	ILKAP	238744010	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	2.581000	0.46077	2.688000	0.91661	0.563000	0.77884	CGC	.	.		0.612	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768		T	239079271	C	T	239079271	3	4	49	1	0	0	0	0	1	0	0	0	7723	768	27	1	97	1	ILKAP	2	239079271	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	789608	239079271	4120102	51	6208										
OR6B3	150681	hgsc.bcm.edu	37	chr2	240984862	240984862	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cagcatggtggccaggagtgGaaacaccaggatgatgaagg	16	7	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:240984862G>C	ENST00000319423.4	-	1	627	c.628C>G	c.(628-630)Cca>Gca	p.P210A	PRR21_ENST00000408934.1_5'Flank	NM_173351.1	NP_775486.1	Q8NGW1	OR6B3_HUMAN	olfactory receptor, family 6, subfamily B, member 3	210						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(10)|lung(4)|ovary(2)|prostate(1)	18		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;1.05e-29)|all cancers(36;3.52e-28)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)		GCCAGGAGTGGAAACACCAGG	0.587																																					p.P210A		Atlas-SNP	.											.	OR6B3	37	.	0			c.C628G						.						63	70	68					2																	240984862		2141	4244	6385	SO:0001583	missense	150681	exon1			GGAGTGGAAACAC		CCDS42837.1	2q37.3	2013-09-23	2002-11-13	2002-11-15	ENSG00000178586	ENSG00000178586		"GPCR / Class A : Olfactory receptors"	15042	protein-coding gene	gene with protein product			"olfactory receptor, family 6, subfamily B, member 3 pseudogene"	OR6B3P			Standard	NM_173351		Approved	OR6B3Q	uc010zoe.2	Q8NGW1	OTTHUMG00000152399	ENST00000319423.4:c.628C>G	chr2.hg19:g.240984862G>C	ENSP00000322435:p.Pro210Ala	256.0	0.0		279.0	55.0	NM_173351	Q6IFH3	Missense_Mutation	SNP	ENST00000319423.4	hg19	CCDS42837.1	.	.	.	.	.	.	.	.	.	.	g	10.32	1.317894	0.23994	.	.	ENSG00000178586	ENST00000319423	T	0.56275	0.47	4.09	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.145705	0.31519	N	0.007506	T	0.66056	0.2751	M	0.64676	1.99	0.33789	D	0.625263	D	0.76494	0.999	D	0.75484	0.986	T	0.73786	-0.3873	10	0.36615	T	0.2	.	12.1077	0.53821	0.0:0.1752:0.8248:0.0	.	210	Q8NGW1	OR6B3_HUMAN	A	210	ENSP00000322435:P210A	ENSP00000322435:P210A	P	-	1	0	OR6B3	240633535	0.263000	0.24083	0.177000	0.23020	0.045000	0.14185	0.989000	0.29629	1.267000	0.44247	-0.243000	0.11985	CCA	.	.		0.587	OR6B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326078.1			C	240984862	G	C	240984862	3	2	49	1	0	0	0	0	1	0	0	0	11198	1174	41	4	370	4	OR6B3	2	240984862	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	1905591	240984862	2214511	52	6209										
SCN11A	11280	hgsc.bcm.edu	37	chr3	38921489	38921489	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	caggcactggtgaaatacttTccaaatccgaaggctaccca	8	12	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:38921489T>C	ENST00000302328.3	-	19	3543	c.3345A>G	c.(3343-3345)ggA>ggG	p.G1115G	SCN11A_ENST00000450244.1_Silent_p.G1115G|SCN11A_ENST00000456224.3_Silent_p.G1077G|SCN11A_ENST00000444237.2_Silent_p.G1115G	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1115					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGAAATACTTTCCAAATCCGA	0.403																																					p.G1115G		Atlas-SNP	.											.	SCN11A	296	.	0			c.A3345G						.						76	72	73					3																	38921489		2203	4300	6503	SO:0001819	synonymous_variant	11280	exon19			ATACTTTCCAAAT	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.3345A>G	chr3.hg19:g.38921489T>C		80.0	0.0		88.0	4.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.		0.403	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		C	38921489	T	C	38921489	2	2	49	1	0	0	0	0	0	0	0	1	13928	1770	62	2		2	SCN11A	3	38921489	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10		38921489	159100941	53	6210										
WDR6	11180	hgsc.bcm.edu	37	chr3	49052272	49052272	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cttcagggcttggcacccccTccctgactctccaggcccac	8	20	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:49052272T>C	ENST00000608424.1	+	6	2956	c.2917T>C	c.(2917-2919)Tcc>Ccc	p.S973P	WDR6_ENST00000448293.1_Missense_Mutation_p.S922P|WDR6_ENST00000395474.3_Missense_Mutation_p.S1003P|WDR6_ENST00000415265.2_Missense_Mutation_p.S421P|DALRD3_ENST00000496568.1_5'Flank			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	973					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		TGGCACCCCCTCCCTGACTCT	0.617																																					p.S1003P		Atlas-SNP	.											.	WDR6	79	.	0			c.T3007C						.						76	82	80					3																	49052272		2203	4300	6503	SO:0001583	missense	11180	exon6			ACCCCCTCCCTGA	AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"WD repeat domain containing"	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.2917T>C	chr3.hg19:g.49052272T>C	ENSP00000477389:p.Ser973Pro	62.0	0.0		104.0	5.0	NM_018031	B4DHK2|Q3MIT1|Q9UF63	Missense_Mutation	SNP	ENST00000608424.1	hg19		.	.	.	.	.	.	.	.	.	.	T	9.177	1.022694	0.19433	.	.	ENSG00000178252	ENST00000395474;ENST00000415265;ENST00000448293	T;T;T	0.65549	-0.16;0.21;0.21	5.21	4.03	0.46877	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.380708	0.31484	N	0.007567	T	0.39860	0.1094	N	0.08118	0	0.20074	N	0.999939	P;B;B	0.35328	0.495;0.175;0.002	B;B;B	0.38264	0.269;0.126;0.01	T	0.21759	-1.0236	10	0.35671	T	0.21	-11.6107	6.665	0.23035	0.0:0.0809:0.2938:0.6253	.	421;973;922	E9PBK6;Q9NNW5;E9PDU5	.;WDR6_HUMAN;.	P	1003;421;922	ENSP00000378857:S1003P;ENSP00000412195:S421P;ENSP00000413432:S922P	ENSP00000378857:S1003P	S	+	1	0	WDR6	49027276	0.697000	0.27767	0.749000	0.31150	0.233000	0.25261	1.839000	0.39220	0.921000	0.36994	0.459000	0.35465	TCC	.	.		0.617	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1			C	49052272	T	C	49052272	3	2	49	1	0	0	0	0	1	0	0	0	17325	1551	54	2	3029	2	WDR6	3	49052272	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	10130783	49052272	148970158	54	6211										
USP4	7375	hgsc.bcm.edu	37	chr3	49362451	49362451	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cagggatgttgaatagcttcCgcatctctttctcgatggtt	10	9	2	1	rs117411669	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:49362451C>A	ENST00000265560.4	-	5	555	c.509G>T	c.(508-510)cGg>cTg	p.R170L	USP4_ENST00000416417.1_Missense_Mutation_p.R170L|USP4_ENST00000415188.1_Missense_Mutation_p.R170L|USP4_ENST00000351842.4_Missense_Mutation_p.R170L	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	170	Necessary for interaction with SART3. {ECO:0000269|PubMed:20595234}.|Ubiquitin-like 1.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		GAATAGCTTCCGCATCTCTTT	0.488																																					p.R170L		Atlas-SNP	.											.	USP4	72	.	0			c.G509T						.						162	162	162					3																	49362451		2203	4300	6503	SO:0001583	missense	7375	exon5			AGCTTCCGCATCT	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"Ubiquitin-specific peptidases"	12627	protein-coding gene	gene with protein product		603486	"ubiquitin specific protease 4 (proto-oncogene)"	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.509G>T	chr3.hg19:g.49362451C>A	ENSP00000265560:p.Arg170Leu	131.0	0.0		150.0	42.0	NM_001251877	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Missense_Mutation	SNP	ENST00000265560.4	hg19	CCDS2793.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.966271	0.92855	.	.	ENSG00000114316	ENST00000351842;ENST00000265560;ENST00000416417;ENST00000415188	T;T;T	0.30981	2.01;2.16;1.51	5.51	5.51	0.81932	.	0.061185	0.64402	D	0.000002	T	0.57198	0.2037	M	0.74467	2.265	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.76575	0.988;0.94	T	0.56282	-0.8005	10	0.46703	T	0.11	-17.6222	17.9838	0.89150	0.0:1.0:0.0:0.0	.	170;170	Q13107-2;Q13107	.;UBP4_HUMAN	L	170	ENSP00000341028:R170L;ENSP00000265560:R170L;ENSP00000400623:R170L	ENSP00000265560:R170L	R	-	2	0	USP4	49337455	1.000000	0.71417	0.951000	0.38953	0.626000	0.37791	5.974000	0.70465	2.604000	0.88044	0.491000	0.48974	CGG	.	C|0.999;T|0.001		0.488	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		A	49362451	C	A	49362451	3	1	49	1	0	0	0	0	1	0	0	0	17086	652	23	1	2454	1	USP4	3	49362451	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	310179	49362451	148659979	55	6212										
CACNA2D2	9254	hgsc.bcm.edu	37	chr3	50413239	50413239	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cccccagccctgcctccttaCctcatccagggacttgacca	6	20	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:50413239C>T	ENST00000479441.1	-	20	1845		c.e20+1		CACNA2D2_ENST00000424201.2_Splice_Site|CACNA2D2_ENST00000429770.1_Splice_Site|CACNA2D2_ENST00000395083.1_Splice_Site|CACNA2D2_ENST00000266039.3_Splice_Site|CACNA2D2_ENST00000360963.3_Splice_Site|CACNA2D2_ENST00000435965.1_Splice_Site|CACNA2D2_ENST00000423994.2_Splice_Site			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2						energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TGCCTCCTTACCTCATCCAGG	0.627																																					.		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.1845+1G>A						.						86	77	80					3																	50413239		2203	4300	6503	SO:0001630	splice_region_variant	9254	exon21			TCCTTACCTCATC	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"Calcium channel subunits"	1400	protein-coding gene	gene with protein product	"gene 26"	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.1845+1G>A	chr3.hg19:g.50413239C>T		58.0	0.0		76.0	4.0	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Splice_Site	SNP	ENST00000479441.1	hg19	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	C	18.43	3.622034	0.66787	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0303	0.58839	0.0:0.9186:0.0:0.0814	.	.	.	.	.	-1	.	.	.	-	.	.	CACNA2D2	50388243	1.000000	0.71417	0.996000	0.52242	0.677000	0.39632	7.647000	0.83462	2.126000	0.65437	0.462000	0.41574	.	.	.		0.627	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030	Intron	T	50413239	C	T	50413239	5	4	49	1	0	0	0	0	0	0	1	0	2551	521	18	3	1692	3	CACNA2D2	3	50413239	Splice_Site	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1050788	50413239	147609191	56	6213										
HEMK1	51409	hgsc.bcm.edu	37	chr3	50614592	50614592	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cggatcaggagccatctcccTcagcctgctgagccagctcc	10	17	3	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:50614592T>C	ENST00000232854.4	+	5	1076	c.524T>C	c.(523-525)cTc>cCc	p.L175P	HEMK1_ENST00000455834.1_Missense_Mutation_p.L175P|HEMK1_ENST00000434410.1_Missense_Mutation_p.L175P	NM_016173.3	NP_057257.1	Q9Y5R4	HEMK1_HUMAN	HemK methyltransferase family member 1	175					DNA methylation (GO:0006306)	mitochondrion (GO:0005739)	DNA binding (GO:0003677)|N-methyltransferase activity (GO:0008170)|protein methyltransferase activity (GO:0008276)			lung(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000283)|KIRC - Kidney renal clear cell carcinoma(197;0.0179)|Kidney(197;0.0212)		GCCATCTCCCTCAGCCTGCTG	0.632																																					p.L175P		Atlas-SNP	.											.	HEMK1	17	.	0			c.T524C						.						51	53	52					3																	50614592		2203	4300	6503	SO:0001583	missense	51409	exon5			TCTCCCTCAGCCT	AF172244	CCDS2830.1	3p21	2008-02-05			ENSG00000114735	ENSG00000114735			24923	protein-coding gene	gene with protein product						10690633	Standard	XM_005265218		Approved	MTQ1	uc003dav.3	Q9Y5R4	OTTHUMG00000156849	ENST00000232854.4:c.524T>C	chr3.hg19:g.50614592T>C	ENSP00000232854:p.Leu175Pro	73.0	0.0		69.0	4.0	NM_016173		Missense_Mutation	SNP	ENST00000232854.4	hg19	CCDS2830.1	.	.	.	.	.	.	.	.	.	.	T	17.82	3.483225	0.63962	.	.	ENSG00000114735	ENST00000434410;ENST00000232854;ENST00000455834;ENST00000443894	T;T;T;T	0.68765	2.28;2.28;2.28;-0.35	5.2	5.2	0.72013	Methyltransferase small (1);	0.066463	0.64402	D	0.000011	D	0.86727	0.6002	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90005	0.4117	10	0.72032	D	0.01	-19.166	11.3894	0.49804	0.0:0.0:0.0:1.0	.	175	Q9Y5R4	HEMK1_HUMAN	P	175;175;175;13	ENSP00000404843:L175P;ENSP00000232854:L175P;ENSP00000404334:L175P;ENSP00000404168:L13P	ENSP00000232854:L175P	L	+	2	0	HEMK1	50589596	1.000000	0.71417	0.993000	0.49108	0.633000	0.38033	5.195000	0.65131	2.198000	0.70561	0.533000	0.62120	CTC	.	.		0.632	HEMK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346231.1	NM_016173		C	50614592	T	C	50614592	3	2	49	1	0	0	0	0	1	0	0	0	7060	1551	54	2	538	2	HEMK1	3	50614592	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	201353	50614592	147407838	57	6214										
GNL3	26354	hgsc.bcm.edu	37	chr3	52727767	52727767	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aacggaaagaaaggaagcagGaggagagggaggatgacaaa	17	3	0	3	rs111396798|rs374163260	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:52727767G>C	ENST00000418458.1	+	13	1617	c.1444G>C	c.(1444-1446)Gag>Cag	p.E482Q	SNORD69_ENST00000391150.1_RNA|SNORD19B_ENST00000459623.1_RNA|GNL3_ENST00000394799.2_Missense_Mutation_p.E470Q|SNORD19_ENST00000410413.1_RNA|GLT8D1_ENST00000463827.1_5'Flank	NM_014366.4|NM_206826.1	NP_055181.3|NP_996562.1	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)	482	Acidic. {ECO:0000250}.				cell proliferation (GO:0008283)|GTP catabolic process (GO:0006184)|regulation of cell proliferation (GO:0042127)|ribosome biogenesis (GO:0042254)	extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|large_intestine(3)|lung(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		AAGGAAGCAGGAGGAGAGGGA	0.418																																					p.E482Q		Atlas-SNP	.											GNL3,NS,carcinoma,0,1	GNL3	37	.	0			c.G1444C						.						93	112	105					3																	52727767		2202	4300	6502	SO:0001583	missense	26354	exon13			AAGCAGGAGGAGA	AK027514	CCDS2861.1, CCDS43100.1	3p21.1	2005-01-10			ENSG00000163938	ENSG00000163938			29931	protein-coding gene	gene with protein product		608011				11085516, 12464630	Standard	NM_014366		Approved	C77032, E2IG3, MGC800, NS, nucleostemin	uc003dfd.3	Q9BVP2	OTTHUMG00000158752	ENST00000418458.1:c.1444G>C	chr3.hg19:g.52727767G>C	ENSP00000395772:p.Glu482Gln	123.0	0.0		134.0	10.0	NM_014366	B2RDC1|Q5PU80|Q96SV6|Q96SV7|Q9UJY0	Missense_Mutation	SNP	ENST00000418458.1	hg19	CCDS2861.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.122420	0.37436	.	.	ENSG00000163938	ENST00000418458;ENST00000394799	T;T	0.30981	1.51;1.51	5.23	4.36	0.52297	.	0.635861	0.18255	N	0.146817	T	0.17280	0.0415	N	0.08118	0	0.25314	N	0.989178	P	0.49961	0.93	B	0.42319	0.383	T	0.04281	-1.0963	10	0.41790	T	0.15	.	11.162	0.48520	0.0843:0.0:0.9157:0.0	.	482	Q9BVP2	GNL3_HUMAN	Q	482;470	ENSP00000395772:E482Q;ENSP00000378278:E470Q	ENSP00000378278:E470Q	E	+	1	0	GNL3	52702807	0.272000	0.24172	0.650000	0.29550	0.067000	0.16453	1.481000	0.35476	1.443000	0.47586	0.511000	0.50034	GAG	.	.		0.418	GNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352032.1	NM_014366		C	52727767	G	C	52727767	3	2	49	1	0	0	0	0	1	0	0	0	6545	1175	41	4	1494	4	GNL3	3	52727767	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	2113175	52727767	145294663	58	6215										
C3orf63	23272	hgsc.bcm.edu	37	chr3	56680996	56680996	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gggatttatttctgggagctGagtataagaattttttatca	10	3	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:56680996G>A	ENST00000493960.2	-	14	1779	c.1769C>T	c.(1768-1770)tCa>tTa	p.S590L	FAM208A_ENST00000431842.2_Missense_Mutation_p.S194L|FAM208A_ENST00000355628.5_Missense_Mutation_p.S590L	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	590							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						TCTGGGAGCTGAGTATAAGAA	0.303																																					p.S590L		Atlas-SNP	.											.	FAM208A	113	.	0			c.C1769T						.						30	33	32					3																	56680996		2198	4294	6492	SO:0001583	missense	23272	exon14			GGAGCTGAGTATA	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 63"	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1769C>T	chr3.hg19:g.56680996G>A	ENSP00000417509:p.Ser590Leu	201.0	0.0		241.0	31.0	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	9.606	1.129899	0.21041	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.11821	2.74;2.91;2.91	5.38	5.38	0.77491	.	0.246251	0.29178	N	0.012916	T	0.11879	0.0289	N	0.25647	0.755	0.34260	D	0.679742	B;P;P	0.35272	0.045;0.493;0.493	B;B;B	0.39258	0.031;0.215;0.295	T	0.21177	-1.0253	10	0.26408	T	0.33	-1.2621	12.6157	0.56576	0.0747:0.0:0.9253:0.0	.	590;590;194	Q9UK61-3;Q9UK61-4;Q9UK61-2	.;.;.	L	194;590;590	ENSP00000399410:S194L;ENSP00000417509:S590L;ENSP00000347845:S590L	ENSP00000347845:S590L	S	-	2	0	C3orf63	56656036	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.899000	0.63245	2.793000	0.96121	0.655000	0.94253	TCA	.	.		0.303	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		A	56680996	G	A	56680996	3	1	49	1	0	0	0	0	1	0	0	0	2241	1294	45	3	3347	3	C3orf63	3	56680996	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	3953229	56680996	141341434	59	6216										
MORC1	27136	hgsc.bcm.edu	37	chr3	108723940	108723940	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggatctctcagctagtttgaCattttctggcagagctactg	10	9	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:108723940C>A	ENST00000483760.1	-	18	1970	c.1927G>T	c.(1927-1929)Gtc>Ttc	p.V643F	MORC1_ENST00000232603.5_Missense_Mutation_p.V664F					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						GCTAGTTTGACATTTTCTGGC	0.338																																					p.V664F		Atlas-SNP	.											.	MORC1	211	.	0			c.G1990T						.						96	100	99					3																	108723940		2203	4300	6503	SO:0001583	missense	27136	exon19			GTTTGACATTTTC	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.1927G>T	chr3.hg19:g.108723940C>A	ENSP00000417282:p.Val643Phe	108.0	0.0		119.0	25.0	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.09	2.729876	0.48833	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.08193	3.14;3.12	4.44	-0.535	0.11879	.	0.929268	0.08916	N	0.875125	T	0.04679	0.0127	L	0.27053	0.805	0.09310	N	1	P;P	0.40476	0.718;0.718	B;B	0.33690	0.168;0.168	T	0.38542	-0.9656	10	0.33940	T	0.23	0.1732	4.2726	0.10794	0.0:0.4279:0.1757:0.3964	.	643;664	E7ERX1;Q86VD1	.;MORC1_HUMAN	F	664;643	ENSP00000232603:V664F;ENSP00000417282:V643F	ENSP00000232603:V664F	V	-	1	0	MORC1	110206630	0.000000	0.05858	0.000000	0.03702	0.740000	0.42216	-0.877000	0.04197	-0.114000	0.11936	0.557000	0.71058	GTC	.	.		0.338	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			A	108723940	C	A	108723940	3	1	49	1	0	0	0	0	1	0	0	0	9710	478	17	3	1004	3	MORC1	3	108723940	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	52042944	108723940	89298490	60	6217										
CASR	846	hgsc.bcm.edu	37	chr3	121980604	121980604	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tatctgcatcgacttcagtgAactcatctcccagtactctg	6	13	5	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:121980604A>T	ENST00000490131.1	+	4	1094	c.722A>T	c.(721-723)gAa>gTa	p.E241V	CASR_ENST00000296154.5_Missense_Mutation_p.E241V|CASR_ENST00000498619.1_Missense_Mutation_p.E241V	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	241					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	GACTTCAGTGAACTCATCTCC	0.512																																					p.E241V		Atlas-SNP	.											.	CASR	190	.	0			c.A722T						.						165	177	173					3																	121980604		2203	4300	6503	SO:0001583	missense	846	exon4			TCAGTGAACTCAT	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.722A>T	chr3.hg19:g.121980604A>T	ENSP00000418685:p.Glu241Val	182.0	0.0		221.0	20.0	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	hg19	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	A	11.11	1.542488	0.27563	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.87729	-2.29;-2.29;-2.29	6.17	6.17	0.99709	Extracellular ligand-binding receptor (1);	0.045100	0.85682	D	0.000000	D	0.83580	0.5285	L	0.42008	1.315	0.53005	D	0.99996	B;B	0.32409	0.37;0.248	B;B	0.30316	0.114;0.047	D	0.83400	0.0022	10	0.72032	D	0.01	.	16.0034	0.80327	1.0:0.0:0.0:0.0	.	241;241	E7ENE0;P41180	.;CASR_HUMAN	V	241	ENSP00000418685:E241V;ENSP00000420194:E241V;ENSP00000296154:E241V	ENSP00000296154:E241V	E	+	2	0	CASR	123463294	1.000000	0.71417	0.921000	0.36526	0.354000	0.29330	7.211000	0.77933	2.371000	0.80710	0.533000	0.62120	GAA	.	.		0.512	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		T	121980604	A	T	121980604	3	4	49	1	0	0	0	0	1	0	0	0	2684	246	9	4	732	4	CASR	3	121980604	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	13256664	121980604	76041826	61	6218										
PDIA5	10954	hgsc.bcm.edu	37	chr3	122849447	122849447	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gaacactcctctgtcctcgtCatgttccacgccccatgtga	7	16	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:122849447C>A	ENST00000316218.7	+	11	989	c.894C>A	c.(892-894)gtC>gtA	p.V298V		NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	298	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		CTGTCCTCGTCATGTTCCACG	0.562																																					p.V298V		Atlas-SNP	.											.	PDIA5	66	.	0			c.C894A						.						144	119	127					3																	122849447		2203	4300	6503	SO:0001819	synonymous_variant	10954	exon11			CCTCGTCATGTTC	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"Protein disulfide isomerases"	24811	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 5"			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.894C>A	chr3.hg19:g.122849447C>A		113.0	0.0		121.0	26.0	NM_006810	D3DN95|Q9BV43	Silent	SNP	ENST00000316218.7	hg19	CCDS3020.1																																																																																			.	.		0.562	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810		A	122849447	C	A	122849447	2	1	49	1	0	0	0	0	0	0	0	1	11680	813	29	3		3	PDIA5	3	122849447	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	868843	122849447	75172983	62	6219										
CPNE4	131034	hgsc.bcm.edu	37	chr3	131624109	131624109	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tttcattggacatgcctaccTcaaaccactgcccatgagac	6	14	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:131624109T>A	ENST00000512055.1	-	6	2305	c.179A>T	c.(178-180)gAg>gTg	p.E60V	CPNE4_ENST00000429747.1_Splice_Site_p.E60V|CPNE4_ENST00000502818.1_Splice_Site_p.E78V|CPNE4_ENST00000511604.1_Splice_Site_p.E60V|CPNE4_ENST00000512332.1_Splice_Site_p.E78V			Q96A23	CPNE4_HUMAN	copine IV	60	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						CATGCCTACCTCAAACCACTG	0.443																																					p.E60V		Atlas-SNP	.											.	CPNE4	112	.	0			c.A179T						.						135	125	129					3																	131624109		2203	4300	6503	SO:0001630	splice_region_variant	131034	exon2			CCTACCTCAAACC	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.180+1A>T	chr3.hg19:g.131624109T>A		126.0	0.0		133.0	27.0	NM_130808	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	hg19	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.195935	0.78902	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818;ENST00000505881;ENST00000514999;ENST00000505957	T;T;T;T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;1.06	5.56	5.56	0.83823	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.048095	0.85682	D	0.000000	D	0.83912	0.5357	M	0.89785	3.06	0.80722	D	1	D;D	0.61697	0.99;0.99	P;D	0.64321	0.854;0.924	D	0.87615	0.2506	10	0.87932	D	0	-14.8361	15.7219	0.77718	0.0:0.0:0.0:1.0	.	78;60	Q96A23-2;Q96A23	.;CPNE4_HUMAN	V	60;60;78;60;78;60;60;60	ENSP00000421705:E60V;ENSP00000411904:E60V;ENSP00000424853:E78V;ENSP00000423811:E60V;ENSP00000421646:E78V;ENSP00000425506:E60V;ENSP00000427561:E60V;ENSP00000421394:E60V	ENSP00000411904:E60V	E	-	2	0	CPNE4	133106799	1.000000	0.71417	1.000000	0.80357	0.553000	0.35397	7.698000	0.84413	2.112000	0.64535	0.533000	0.62120	GAG	.	.		0.443	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808	Missense_Mutation	A	131624109	T	A	131624109	5	1	49	1	0	0	0	0	0	0	1	0	3816	1565	54	4	1554	4	CPNE4	3	131624109	Splice_Site	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	8774662	131624109	66398321	63	6220										
ACAD11	84129	hgsc.bcm.edu	37	chr3	132337601	132337601	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaacaagttccagagaccctCgactttggccatttcctgtc	7	13	0	1	rs542883164		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:132337601C>T	ENST00000264990.6	-	11	2262	c.1291G>A	c.(1291-1293)Gag>Aag	p.E431K	ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000481970.2_Missense_Mutation_p.E431K|ACAD11_ENST00000355458.3_Missense_Mutation_p.E431K	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	431					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)			breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						CAGAGACCCTCGACTTTGGCC	0.418													C|||	1	0.000199681	8e-04	0	5008	,	,		15389	0		0	False		,,,				2504	0				p.E431K		Atlas-SNP	.											.	ACAD11	78	.	0			c.G1291A						.						68	65	66					3																	132337601		2203	4300	6503	SO:0001583	missense	84129	exon11			GACCCTCGACTTT	BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"acyl-Coenzyme A dehydrogenase family, member 11"				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.1291G>A	chr3.hg19:g.132337601C>T	ENSP00000264990:p.Glu431Lys	202.0	0.0		238.0	63.0	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Missense_Mutation	SNP	ENST00000264990.6	hg19	CCDS3074.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.361158	0.82353	.	.	ENSG00000240303	ENST00000355458;ENST00000264990;ENST00000481970	D;D;T	0.99701	-6.45;-6.45;1.85	5.52	5.52	0.82312	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	.	.	.	.	D	0.99507	0.9824	M	0.66560	2.04	0.80722	D	1	P;D	0.64830	0.908;0.994	B;P	0.57101	0.158;0.813	D	0.98826	1.0749	9	0.56958	D	0.05	.	19.3995	0.94621	0.0:1.0:0.0:0.0	.	431;431	D6RDI8;Q709F0	.;ACD11_HUMAN	K	431	ENSP00000347636:E431K;ENSP00000264990:E431K;ENSP00000420907:E431K	ENSP00000264990:E431K	E	-	1	0	ACAD11	133820291	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	4.549000	0.60726	2.754000	0.94517	0.650000	0.86243	GAG	.	.		0.418	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169		T	132337601	C	T	132337601	3	4	49	1	0	0	0	0	1	0	0	0	109	893	31	1	1091	1	ACAD11	3	132337601	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	713492	132337601	65684829	64	6221										
ATP11B	23200	hgsc.bcm.edu	37	chr3	182566270	182566270	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gttttattttacaggtgttgCggtatacactggaatggaaa	11	4	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:182566270C>T	ENST00000323116.5	+	10	1036	c.776C>T	c.(775-777)gCg>gTg	p.A259V	ATP11B_ENST00000482794.1_3'UTR	NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	259					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			ACAGGTGTTGCGGTATACACT	0.303																																					p.A259V		Atlas-SNP	.											ATP11B,NS,carcinoma,0,1	ATP11B	115	.	0			c.C776T						.						54	56	55					3																	182566270		2203	4294	6497	SO:0001583	missense	23200	exon10			GTGTTGCGGTATA	AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"ATPases / P-type"	13553	protein-coding gene	gene with protein product		605869	"ATPase, Class VI, type 11B"			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.776C>T	chr3.hg19:g.182566270C>T	ENSP00000321195:p.Ala259Val	190.0	0.0		232.0	59.0	NM_014616	Q96FN1|Q9UKK7	Missense_Mutation	SNP	ENST00000323116.5	hg19	CCDS33896.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.3|22.3	4.272222|4.272222	0.80580|0.80580	.|.	.|.	ENSG00000058063|ENSG00000058063	ENST00000323116|ENST00000498086	D|.	0.82803|.	-1.65|.	5.4|5.4	5.4|5.4	0.78164|0.78164	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.54224|0.54224	0.1845|0.1845	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.76071|.	0.987|.	T|T	0.49021|0.49021	-0.8982|-0.8982	10|5	0.02654|.	T|.	1|.	.|.	19.2267|19.2267	0.93820|0.93820	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	259|.	Q9Y2G3|.	AT11B_HUMAN|.	V|W	259|60	ENSP00000321195:A259V|.	ENSP00000321195:A259V|.	A|R	+|+	2|1	0|2	ATP11B|ATP11B	184048964|184048964	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.542000|0.542000	0.35054|0.35054	7.360000|7.360000	0.79487|0.79487	2.563000|2.563000	0.86464|0.86464	0.551000|0.551000	0.68910|0.68910	GCG|CGG	.	.		0.303	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616		T	182566270	C	T	182566270	3	4	49	1	0	0	0	0	1	0	0	0	1120	768	27	1	814	1	ATP11B	3	182566270	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	50228669	182566270	15456160	65	6222										
HRG	3273	hgsc.bcm.edu	37	chr3	186383833	186383833	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttaacaaaatgaaggcactcAttgcagcactgcttttgatc	7	9	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:186383833A>G	ENST00000232003.4	+	1	93	c.13A>G	c.(13-15)Att>Gtt	p.I5V	HRG_ENST00000468154.1_Intron|RP11-134F2.2_ENST00000455926.1_RNA|RP11-134F2.2_ENST00000428501.1_RNA	NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	5					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		GAAGGCACTCATTGCAGCACT	0.448																																					p.I5V		Atlas-SNP	.											.	HRG	81	.	0			c.A13G						.						104	90	94					3																	186383833		2203	4300	6503	SO:0001583	missense	3273	exon1			GCACTCATTGCAG		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.13A>G	chr3.hg19:g.186383833A>G	ENSP00000232003:p.Ile5Val	106.0	0.0		111.0	26.0	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	hg19	CCDS3280.1	.	.	.	.	.	.	.	.	.	.	A	0.015	-1.547153	0.00926	.	.	ENSG00000113905	ENST00000232003	T	0.16897	2.31	5.6	-8.96	0.00761	.	1.332170	0.04902	N	0.451571	T	0.09905	0.0243	L	0.39898	1.24	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.43572	-0.9383	10	0.02654	T	1	5.4587	9.548	0.39293	0.2499:0.541:0.2092:0.0	.	5	P04196	HRG_HUMAN	V	5	ENSP00000232003:I5V	ENSP00000232003:I5V	I	+	1	0	HRG	187866527	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-2.547000	0.00931	-1.503000	0.01812	-0.316000	0.08728	ATT	.	.		0.448	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		G	186383833	A	G	186383833	3	3	49	1	0	0	0	0	1	0	0	0	7363	217	8	2	15	2	HRG	3	186383833	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	3817563	186383833	11638597	66	6223										
HES1	3280	hgsc.bcm.edu	37	chr3	193854818	193854818	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtgaagcacctccggaacctGcagcgggcgcagatgacggg	16	12	0	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:193854818G>A	ENST00000232424.3	+	3	509	c.273G>A	c.(271-273)ctG>ctA	p.L91L		NM_005524.3	NP_005515.1	P30042	ES1_HUMAN	hes family bHLH transcription factor 1	0						mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6	all_cancers(143;7.3e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;3.65e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.48e-05)		TCCGGAACCTGCAGCGGGCGC	0.627																																					p.L91L		Atlas-SNP	.											HES1,NS,carcinoma,0,1	HES1	23	.	0			c.G273A						.						48	51	50					3																	193854818		2203	4300	6503	SO:0001819	synonymous_variant	3280	exon3			GAACCTGCAGCGG	L19314	CCDS3305.1	3q28-q29	2013-10-17	2013-10-17	2003-01-10	ENSG00000114315	ENSG00000114315		"Basic helix-loop-helix proteins"	5192	protein-coding gene	gene with protein product		139605	"hairy homolog (Drosophila)", "hairy and enhancer of split 1, (Drosophila)"	HRY		8020957	Standard	NM_005524		Approved	FLJ20408, HES-1, Hes1, bHLHb39	uc003ftq.2	Q14469	OTTHUMG00000155984	ENST00000232424.3:c.273G>A	chr3.hg19:g.193854818G>A		59.0	0.0		64.0	3.0	NM_005524	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Silent	SNP	ENST00000232424.3	hg19	CCDS3305.1																																																																																			.	.		0.627	HES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342632.1			A	193854818	G	A	193854818	2	1	49	1	0	0	0	0	0	0	0	1	7074	1306	46	3		3	HES1	3	193854818	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	7470985	193854818	4167612	67	6224										
SLBP	7884	hgsc.bcm.edu	37	chr4	1701341	1701341	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcaattgtgttcttcccataGttgatctgcttctgtctcct	7	11	4	1	rs200085408		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:1701341G>C	ENST00000489418.1	-	5	795	c.429C>G	c.(427-429)aaC>aaG	p.N143K	SLBP_ENST00000488267.1_Missense_Mutation_p.N108K|SLBP_ENST00000429429.2_Missense_Mutation_p.N104K|SLBP_ENST00000318386.4_Missense_Mutation_p.N150K	NM_006527.2	NP_006518.1	Q14493	SLBP_HUMAN	stem-loop binding protein	143	RNA-binding.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA transport (GO:0051028)|nuclear cell cycle DNA replication (GO:0033260)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	histone pre-mRNA DCP binding (GO:0071208)|histone pre-mRNA stem-loop binding (GO:0071207)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|lung(2)	5		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.0055)			TCTTCCCATAGTTGATCTGCT	0.423																																					p.N143K		Atlas-SNP	.											.	SLBP	12	.	0			c.C429G						.						169	155	160					4																	1701341		2203	4300	6503	SO:0001583	missense	7884	exon5			CCCATAGTTGATC	Z71188	CCDS3350.1	4p16.3	2008-02-11	2008-02-11		ENSG00000163950	ENSG00000163950			10904	protein-coding gene	gene with protein product	"histone binding protein"	602422	"stem-loop (histone) binding protein"			9049306, 1338771	Standard	NM_006527		Approved	HBP	uc003gdi.1	Q14493	OTTHUMG00000089349	ENST00000489418.1:c.429C>G	chr4.hg19:g.1701341G>C	ENSP00000417686:p.Asn143Lys	195.0	0.0		264.0	49.0	NM_006527	B3KRJ5	Missense_Mutation	SNP	ENST00000489418.1	hg19	CCDS3350.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	19.50|19.50|19.50	3.838587|3.838587|3.838587	0.71373|0.71373|0.71373	.|.|.	.|.|.	ENSG00000163950|ENSG00000163950|ENSG00000163950	ENST00000480936|ENST00000429429;ENST00000489418;ENST00000460392;ENST00000318386;ENST00000488267|ENST00000483348	.|.|.	.|.|.	.|.|.	5.19|5.19|5.19	3.16|3.16|3.16	0.36331|0.36331|0.36331	.|.|.	.|0.144333|.	.|0.64402|.	.|D|.	.|0.000012|.	T|T|T	0.63070|0.63070|0.63070	0.2480|0.2480|0.2480	M|M|M	0.66939|0.66939|0.66939	2.045|2.045|2.045	0.58432|0.58432|0.58432	D|D|D	0.999994|0.999994|0.999994	.|D;P;P;P;P|.	.|0.62365|.	.|0.991;0.915;0.835;0.734;0.915|.	.|P;P;P;P;P|.	.|0.54026|.	.|0.74;0.72;0.466;0.549;0.72|.	T|T|T	0.61451|0.61451|0.61451	-0.7060|-0.7060|-0.7060	5|9|5	.|0.39692|.	.|T|.	.|0.17|.	-5.3723|-5.3723|-5.3723	9.3219|9.3219|9.3219	0.37968|0.37968|0.37968	0.2754:0.0:0.7246:0.0|0.2754:0.0:0.7246:0.0|0.2754:0.0:0.7246:0.0	.|.|.	.|108;150;104;123;143|.	.|E7EUV9;F8W8D3;B3KRJ5;C9IY53;Q14493|.	.|.;.;.;.;SLBP_HUMAN|.	V|K|S	151|104;143;123;150;108|98	.|.|.	.|ENSP00000316490:N150K|.	L|N|T	-|-|-	1|3|2	2|2|0	SLBP|SLBP|SLBP	1671139|1671139|1671139	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	2.337000|2.337000|2.337000	0.43947|0.43947|0.43947	1.201000|1.201000|1.201000	0.43203|0.43203|0.43203	0.644000|0.644000|0.644000	0.83932|0.83932|0.83932	CTA|AAC|ACT	.	G|0.999;C|0.001		0.423	SLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203176.1	NM_006527		C	1701341	G	C	1701341	3	2	49	1	0	0	0	0	1	0	0	0	14387	1020	36	4	399	4	SLBP	4	1701341	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10		1701341	189452935	68	6225										
EVC2	132884	hgsc.bcm.edu	37	chr4	5642500	5642500	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcagaagggcaatgatatccTtgctgatttgtgttcgacaa	11	7	0	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:5642500T>C	ENST00000344408.5	-	10	1264	c.1211A>G	c.(1210-1212)aAg>aGg	p.K404R	EVC2_ENST00000344938.1_Missense_Mutation_p.K404R|EVC2_ENST00000310917.2_Missense_Mutation_p.K324R	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	404					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						aatgatatccttgctgatttg	0.433																																					p.K404R		Atlas-SNP	.											.	EVC2	202	.	0			c.A1211G						.						89	88	88					4																	5642500		2203	4300	6503	SO:0001583	missense	132884	exon10			ATATCCTTGCTGA	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1211A>G	chr4.hg19:g.5642500T>C	ENSP00000342144:p.Lys404Arg	115.0	0.0		141.0	6.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	T	10.17	1.275725	0.23307	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.80214	-1.35;-1.35;-1.35	4.25	0.463	0.16700	.	0.288637	0.28859	N	0.013920	T	0.69967	0.3170	L	0.46157	1.445	0.31990	N	0.604743	B	0.21688	0.059	B	0.24541	0.054	T	0.63341	-0.6659	10	0.32370	T	0.25	-11.5439	7.5097	0.27566	0.0:0.2685:0.0:0.7315	.	404	Q86UK5	LBN_HUMAN	R	404;324;404	ENSP00000339954:K404R;ENSP00000311683:K324R;ENSP00000342144:K404R	ENSP00000311683:K324R	K	-	2	0	EVC2	5693401	1.000000	0.71417	0.974000	0.42286	0.550000	0.35303	1.198000	0.32223	0.161000	0.19458	0.482000	0.46254	AAG	.	.		0.433	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		C	5642500	T	C	5642500	3	2	49	1	0	0	0	0	1	0	0	0	5288	1609	56	2	2767	2	EVC2	4	5642500	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	3941159	5642500	185511776	69	6226										
EVC	2121	hgsc.bcm.edu	37	chr4	5798818	5798818	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctccggaggctggcactccgCggcaacgccctggccaccct	12	19	0	0	rs535012160		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:5798818C>T	ENST00000264956.6	+	14	2140	c.1956C>T	c.(1954-1956)cgC>cgT	p.R652R	EVC_ENST00000382674.2_Silent_p.R652R|EVC_ENST00000515113.1_3'UTR	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	652					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				TGGCACTCCGCGGCAACGCCC	0.672													C|||	1	0.000199681	0	0	5008	,	,		18521	0		0.001	False		,,,				2504	0				p.R652R		Atlas-SNP	.											EVC,NS,carcinoma,0,1	EVC	90	.	0			c.C1956T						.						42	42	42					4																	5798818		2203	4298	6501	SO:0001819	synonymous_variant	2121	exon14			ACTCCGCGGCAAC	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.1956C>T	chr4.hg19:g.5798818C>T		143.0	0.0		122.0	5.0	NM_153717		Silent	SNP	ENST00000264956.6	hg19	CCDS3383.1																																																																																			.	.		0.672	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			T	5798818	C	T	5798818	2	4	49	1	0	0	0	0	0	0	0	1	5287	755	27	1		1	EVC	4	5798818	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	156318	5798818	185355458	70	6227										
WDR1	9948	hgsc.bcm.edu	37	chr4	10099482	10099482	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cctgtaatctcgcccacagaAgagccactatcccagaggaa	8	14	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:10099482A>G	ENST00000499869.2	-	5	604	c.411T>C	c.(409-411)tcT>tcC	p.S137S	WDR1_ENST00000382452.2_Silent_p.S137S|WDR1_ENST00000502702.1_Intron|WDR1_ENST00000382451.2_Intron			O75083	WDR1_HUMAN	WD repeat domain 1	137					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		CGCCCACAGAAGAGCCACTAT	0.493																																					p.S137S		Atlas-SNP	.											.	WDR1	93	.	0			c.T411C						.						52	52	52					4																	10099482		1989	4172	6161	SO:0001819	synonymous_variant	9948	exon5			CACAGAAGAGCCA	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"WD repeat domain containing"	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.411T>C	chr4.hg19:g.10099482A>G		57.0	0.0		92.0	4.0	NM_017491	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Silent	SNP	ENST00000499869.2	hg19	CCDS54740.1																																																																																			.	.		0.493	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1			G	10099482	A	G	10099482	2	3	49	1	0	0	0	0	0	0	0	1	17287	59	3	2		2	WDR1	4	10099482	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	4300664	10099482	181054794	71	6228										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537513	88537513	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gacagcagtgacagcaatgaAagcagcgacagcagtgacag	13	9	0	3	rs112275895		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:88537513A>C	ENST00000282478.7	+	4	3732	c.3699A>C	c.(3697-3699)gaA>gaC	p.E1233D	DSPP_ENST00000399271.1_Missense_Mutation_p.E1233D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1233	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcaatgaaagcagcgaca	0.547																																					p.E1233D		Atlas-SNP	.											.	DSPP	174	.	0			c.A3699C						.																																			SO:0001583	missense	1834	exon5			CAATGAAAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3699A>C	chr4.hg19:g.88537513A>C	ENSP00000282478:p.Glu1233Asp	158.0	0.0		221.0	21.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.785366	0.00628	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	2.61	-5.21	0.02815	.	.	.	.	.	T	0.57213	0.2038	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.57347	-0.7827	9	0.02654	T	1	.	0.7125	0.00926	0.2623:0.1881:0.1298:0.4197	.	1233	Q9NZW4	DSPP_HUMAN	D	1233	ENSP00000382213:E1233D;ENSP00000282478:E1233D	ENSP00000282478:E1233D	E	+	3	2	DSPP	88756537	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-2.769000	0.00780	-2.252000	0.00699	-3.496000	0.00033	GAA	.	A|0.500;C|0.500		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537513	A	C	88537513	3	2	49	1	0	0	0	0	1	0	0	0	4784	11	1	5	3713	5	DSPP	4	88537513	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	78438031	88537513	102616763	72	6229										
UCP1	7350	hgsc.bcm.edu	37	chr4	141484320	141484320	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttagatcatatgttactagcTctgtacaattgatgatgaca	7	6	2	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:141484320T>C	ENST00000262999.3	-	4	647	c.572A>G	c.(571-573)gAg>gGg	p.E191G		NM_021833.4	NP_068605.1	P25874	UCP1_HUMAN	uncoupling protein 1 (mitochondrial, proton carrier)	191					brown fat cell differentiation (GO:0050873)|cellular metabolic process (GO:0044237)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|stomach(1)	16	all_hematologic(180;0.162)					TGTTACTAGCTCTGTACAATT	0.343																																					p.E191G		Atlas-SNP	.											.	UCP1	33	.	0			c.A572G						.						132	131	132					4																	141484320		2203	4300	6503	SO:0001583	missense	7350	exon4			ACTAGCTCTGTAC	X51955	CCDS3753.1	4q28-q31	2013-05-22			ENSG00000109424	ENSG00000109424		"Solute carriers"	12517	protein-coding gene	gene with protein product		113730		UCP		2380264	Standard	NM_021833		Approved	SLC25A7	uc011chj.2	P25874	OTTHUMG00000133415	ENST00000262999.3:c.572A>G	chr4.hg19:g.141484320T>C	ENSP00000262999:p.Glu191Gly	139.0	0.0		122.0	6.0	NM_021833	Q13218|Q4KMZ3|Q68G66	Missense_Mutation	SNP	ENST00000262999.3	hg19	CCDS3753.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.341173	0.81911	.	.	ENSG00000109424	ENST00000262999	T	0.78246	-1.16	5.22	5.22	0.72569	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.88194	0.6371	M	0.83012	2.62	0.54753	D	0.999982	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	D	0.89852	0.4010	10	0.87932	D	0	.	13.3259	0.60459	0.0:0.0:0.0:1.0	.	190;191	Q4KMT7;P25874	.;UCP1_HUMAN	G	191	ENSP00000262999:E191G	ENSP00000262999:E191G	E	-	2	0	UCP1	141703770	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	7.388000	0.79795	2.105000	0.64084	0.491000	0.48974	GAG	.	.		0.343	UCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257273.1			C	141484320	T	C	141484320	3	2	49	1	0	0	0	0	1	0	0	0	16945	1551	54	2	361	2	UCP1	4	141484320	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	52946807	141484320	49669956	73	6230										
WWC2	80014	hgsc.bcm.edu	37	chr4	184233492	184233492	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	acatttttattcccttttccAggctgaacagtccaaagaag	6	10	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:184233492A>G	ENST00000403733.3	+	22	3583		c.e22-1		WWC2_ENST00000448232.2_Splice_Site|WWC2_ENST00000513834.1_Splice_Site|WWC2_ENST00000508747.1_Splice_Site|WWC2_ENST00000504005.1_Splice_Site	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2						negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.?(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TCCCTTTTCCAGGCTGAACAG	0.463																																					.		Atlas-SNP	.											WWC2,NS,carcinoma,0,1	WWC2	78	.	1	Unknown(1)	lung(1)	c.3385-2A>G						.						103	109	107					4																	184233492		2203	4300	6503	SO:0001630	splice_region_variant	80014	exon22			TTTTCCAGGCTGA	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.3385-1A>G	chr4.hg19:g.184233492A>G		28.0	0.0		27.0	2.0	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Splice_Site	SNP	ENST00000403733.3	hg19	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	A	10.66	1.413279	0.25465	.	.	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005;ENST00000508747	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1939	0.59728	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WWC2	184470486	1.000000	0.71417	0.998000	0.56505	0.099000	0.18886	5.182000	0.65059	2.037000	0.60232	0.529000	0.55759	.	.	.		0.463	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	Intron	G	184233492	A	G	184233492	5	3	49	1	0	0	0	0	0	0	1	0	17427	202	7	2	3469	2	WWC2	4	184233492	Splice_Site	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	42749172	184233492	6920784	74	6231										
CCDC111	201973	hgsc.bcm.edu	37	chr4	185615700	185615700	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aagagtttacaacagatgaaGcagatgaaactaggagcaat	10	5	0	5	rs372438124|rs145762735|rs200746705	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:185615700G>A	ENST00000314970.6	+	14	1883	c.1450G>A	c.(1450-1452)Gca>Aca	p.A484T	PRIMPOL_ENST00000510864.1_3'UTR|PRIMPOL_ENST00000515774.1_Missense_Mutation_p.A355T|PRIMPOL_ENST00000503752.1_Missense_Mutation_p.A484T|PRIMPOL_ENST00000512834.1_Missense_Mutation_p.A483T	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	484	Interaction with RPA1.				mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)										AACAGATGAAGCAGATGAAAC	0.408																																					p.A484T		Atlas-SNP	.											.,1	CCDC111	43	.	0			c.G1450A						.																																			SO:0001583	missense	201973	exon14			GATGAAGCAGATG	AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"coiled-coil domain containing 111"	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.1450G>A	chr4.hg19:g.185615700G>A	ENSP00000313816:p.Ala484Thr	71.0	0.0		53.0	8.0	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Missense_Mutation	SNP	ENST00000314970.6	hg19	CCDS3837.1	.	.	.	.	.	.	.	.	.	.	G	9.738	1.164122	0.21538	.	.	ENSG00000164306	ENST00000314970;ENST00000515774;ENST00000503752;ENST00000512834;ENST00000508001	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	4.03	-1.96	0.07525	.	0.576826	0.13630	N	0.373802	T	0.09247	0.0228	N	0.01576	-0.805	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.38520	-0.9657	10	0.13108	T	0.6	-9.4298	9.7225	0.40311	0.6661:0.0:0.3339:0.0	.	355;484;483	D3DP56;Q96LW4;D6RDM1	.;CC111_HUMAN;.	T	484;355;484;483;158	ENSP00000313816:A484T;ENSP00000421913:A355T;ENSP00000420860:A484T;ENSP00000425316:A483T	ENSP00000313816:A484T	A	+	1	0	CCDC111	185852694	0.000000	0.05858	0.003000	0.11579	0.213000	0.24496	-0.261000	0.08694	-0.358000	0.08162	0.543000	0.68304	GCA	.	.		0.408	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683		A	185615700	G	A	185615700	3	1	49	1	0	0	0	0	1	0	0	0	2750	971	34	3	1496	3	CCDC111	4	185615700	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	1382208	185615700	5538576	75	6232										
ISL1	3670	hgsc.bcm.edu	37	chr5	50683549	50683549	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggcgctggcgacccgctcagTcccctgcatccagcgcggcc	13	19	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:50683549T>C	ENST00000230658.7	+	3	1029	c.444T>C	c.(442-444)agT>agC	p.S148S	ISL1_ENST00000505475.2_3'UTR|ISL1_ENST00000511384.1_Silent_p.S148S	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1	148					atrial septum morphogenesis (GO:0060413)|axon regeneration (GO:0031103)|cardiac cell fate determination (GO:0060913)|cardiac muscle cell myoblast differentiation (GO:0060379)|cardiac right ventricle morphogenesis (GO:0003215)|cellular response to glucocorticoid stimulus (GO:0071385)|endocardial cushion morphogenesis (GO:0003203)|innervation (GO:0060384)|mesenchymal cell differentiation (GO:0048762)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of protein homodimerization activity (GO:0090074)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate specification (GO:0048665)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|pancreas development (GO:0031016)|peripheral nervous system neuron axonogenesis (GO:0048936)|pharyngeal system development (GO:0060037)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage colony-stimulating factor production (GO:1901258)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|retinal ganglion cell axon guidance (GO:0031290)|secondary heart field specification (GO:0003139)|sensory system development (GO:0048880)|spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron differentiation (GO:0021522)|trigeminal nerve development (GO:0021559)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(11)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		Lung NSC(810;0.000845)|Breast(144;0.0411)				ACCCGCTCAGTCCCCTGCATC	0.662																																					p.S148S		Atlas-SNP	.											.	ISL1	65	.	0			c.T444C						.						34	37	36					5																	50683549		2042	4189	6231	SO:0001819	synonymous_variant	3670	exon3			GCTCAGTCCCCTG	BC031213	CCDS43314.1	5q11.2	2012-03-09	2007-07-13		ENSG00000016082	ENSG00000016082		"Homeoboxes / LIM class"	6132	protein-coding gene	gene with protein product		600366	"ISL1 transcription factor, LIM/homeodomain, (islet-1)"			7912209	Standard	NM_002202		Approved	Isl-1, ISLET1	uc003jor.3	P61371	OTTHUMG00000162281	ENST00000230658.7:c.444T>C	chr5.hg19:g.50683549T>C		107.0	0.0		99.0	4.0	NM_002202	P20663|P47894	Silent	SNP	ENST00000230658.7	hg19	CCDS43314.1	.	.	.	.	.	.	.	.	.	.	T	4.727	0.135128	0.09032	.	.	ENSG00000016082	ENST00000505475	.	.	.	5.41	1.03	0.20045	.	0.088274	0.85682	D	0.000000	T	0.63331	0.2502	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63193	-0.6692	6	0.87932	D	0	.	9.0877	0.36592	0.0:0.6683:0.0:0.3317	.	.	.	.	P	95	.	ENSP00000421737:S95P	S	+	1	0	ISL1	50719306	0.993000	0.37304	0.999000	0.59377	0.271000	0.26615	0.370000	0.20433	0.129000	0.18514	0.374000	0.22700	TCC	.	.		0.662	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3	NM_002202		C	50683549	T	C	50683549	2	2	49	1	0	0	0	0	0	0	0	1	7865	1664	58	2		2	ISL1	5	50683549	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10		50683549	130231711	76	6233										
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64748641	64748641	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cacaaaccgttcaatgctcaCtgatctcttctgtctgtggt	7	12	5	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:64748641C>T	ENST00000536360.1	-	5	1549	c.736G>A	c.(736-738)Gtg>Atg	p.V246M				Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6	246						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		TCAATGCTCACTGATCTCTTC	0.433																																					p.V246M		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.G736A						.						211	182	192					5																	64748641		2203	4300	6503	SO:0001583	missense	11174	exon5			TGCTCACTGATCT	AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192		"ADAM metallopeptidases with thrombospondin type 1 motif"	222	protein-coding gene	gene with protein product	"a disintegrin and metalloproteinase with thrombospondin motifs 6"	605008	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6"			10464288	Standard	NM_197941		Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000536360.1:c.736G>A	chr5.hg19:g.64748641C>T	ENSP00000440995:p.Val246Met	251.0	0.0		324.0	58.0	NM_197941	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Missense_Mutation	SNP	ENST00000536360.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.04	2.417701	0.42918	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680;ENST00000536360	T;T;T	0.62105	0.11;0.23;0.05	5.49	3.72	0.42706	Metallopeptidase, catalytic domain (1);	0.188644	0.45606	D	0.000349	T	0.51924	0.1703	L	0.36672	1.1	0.51012	D	0.999902	B	0.23806	0.091	B	0.28784	0.094	T	0.49283	-0.8956	10	0.59425	D	0.04	.	9.9769	0.41789	0.0:0.7833:0.0:0.2167	.	246	Q9UKP5	ATS6_HUMAN	M	246	ENSP00000370443:V246M;ENSP00000423551:V246M;ENSP00000440995:V246M	ENSP00000261306:V246M	V	-	1	0	ADAMTS6	64784397	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.373000	0.34272	0.689000	0.31550	0.563000	0.77884	GTG	.	.		0.433	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941		T	64748641	C	T	64748641	3	4	49	1	0	0	0	0	1	0	0	0	270	565	20	3	2701	3	ADAMTS6	5	64748641	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	14065092	64748641	116166619	77	6234										
GFM2	84340	hgsc.bcm.edu	37	chr5	74021855	74021855	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tactttcagcatactcaaacTcaatcacaggcataacagat	4	11	4	1	rs145997856		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:74021855T>A	ENST00000296805.3	-	18	2280	c.1823A>T	c.(1822-1824)gAg>gTg	p.E608V	GFM2_ENST00000509430.1_Missense_Mutation_p.E608V|RNU6-658P_ENST00000384606.1_RNA|GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000345239.2_Missense_Mutation_p.E561V	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		ATACTCAAACTCAATCACAGG	0.418																																					p.E608V		Atlas-SNP	.											.	GFM2	38	.	0			c.A1823T						.						124	127	126					5																	74021855		2203	4300	6503	SO:0001583	missense	84340	exon18			TCAAACTCAATCA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1823A>T	chr5.hg19:g.74021855T>A	ENSP00000296805:p.Glu608Val	102.0	0.0		122.0	10.0	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	-	0.827	-0.746541	0.03065	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000509430	T;T;T	0.45276	0.9;0.9;0.9	.	.	.	Ribosomal protein S5 domain 2-type fold (1);Translation elongation factor EFG/EF2, domain IV (2);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.349225	0.33309	N	0.005048	T	0.23688	0.0573	N	0.14661	0.345	0.09310	N	1	B;.;B	0.31752	0.0;.;0.338	B;.;B	0.36030	0.009;.;0.216	T	0.16512	-1.0400	8	0.87932	D	0	.	.	.	.	.	608;561;608	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	V	608;561;608	ENSP00000296805:E608V;ENSP00000296804:E561V;ENSP00000427004:E608V	ENSP00000296805:E608V	E	-	2	0	GFM2	74057611	0.640000	0.27243	0.005000	0.12908	0.054000	0.15201	0.784000	0.26816	0.000000	0.14550	0.000000	0.15137	GAG	.	.		0.418	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		A	74021855	T	A	74021855	3	1	49	1	0	0	0	0	1	0	0	0	6350	1551	54	4	532	4	GFM2	5	74021855	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	9273214	74021855	106893405	78	6235										
ERAP2	64167	hgsc.bcm.edu	37	chr5	96237302	96237302	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctgctggtggttaaacaagaCgggtgttcactccgactgca	12	10	1	1	rs560261135		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:96237302C>T	ENST00000437043.3	+	11	2376	c.1665C>T	c.(1663-1665)gaC>gaT	p.D555D	ERAP2_ENST00000515095.1_3'UTR|ERAP2_ENST00000379904.4_Silent_p.D510D|CTD-2260A17.2_ENST00000501338.1_Intron	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	555					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D555D(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		TTAAACAAGACGGGTGTTCAC	0.537																																					p.D555D		Atlas-SNP	.											ERAP2,NS,carcinoma,0,2	ERAP2	77	.	1	Substitution - coding silent(1)	prostate(1)	c.C1665T						.						74	73	73					5																	96237302		2203	4300	6503	SO:0001819	synonymous_variant	64167	exon11			ACAAGACGGGTGT	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"leukocyte-derived arginine aminopeptidase"	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1665C>T	chr5.hg19:g.96237302C>T		60.0	0.0		44.0	2.0	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Silent	SNP	ENST00000437043.3	hg19	CCDS4086.1																																																																																			.	.		0.537	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350		T	96237302	C	T	96237302	2	4	49	1	0	0	0	0	0	0	0	1	5206	535	19	1		1	ERAP2	5	96237302	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	22215447	96237302	84677958	79	6236										
PCDHB4	56131	hgsc.bcm.edu	37	chr5	140503780	140503780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccgagggcccctttccagggCatctggtggacgtaagcggc	15	13	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:140503780C>T	ENST00000194152.1	+	1	2200	c.2200C>T	c.(2200-2202)Cat>Tat	p.H734Y		NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	734					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTTCCAGGGCATCTGGTGGA	0.647																																					p.H734Y		Atlas-SNP	.											PCDHB4,right_upper_lobe,carcinoma,0,1	PCDHB4	177	.	0			c.C2200T						.						81	93	89					5																	140503780		2203	4300	6503	SO:0001583	missense	56131	exon1			CCAGGGCATCTGG	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"Cadherins / Protocadherins : Clustered"	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.2200C>T	chr5.hg19:g.140503780C>T	ENSP00000194152:p.His734Tyr	47.0	0.0		33.0	2.0	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	hg19	CCDS4246.1	.	.	.	.	.	.	.	.	.	.	C	10.01	1.234736	0.22626	.	.	ENSG00000081818	ENST00000194152	T	0.49432	0.78	4.57	4.57	0.56435	.	.	.	.	.	T	0.60495	0.2273	H	0.94582	3.555	0.31702	N	0.640558	B	0.20368	0.044	B	0.19666	0.026	T	0.68731	-0.5331	9	0.72032	D	0.01	.	11.7507	0.51847	0.1759:0.8241:0.0:0.0	.	734	Q9Y5E5	PCDB4_HUMAN	Y	734	ENSP00000194152:H734Y	ENSP00000194152:H734Y	H	+	1	0	PCDHB4	140483964	0.000000	0.05858	0.994000	0.49952	0.084000	0.17831	-0.274000	0.08537	2.533000	0.85409	0.561000	0.74099	CAT	.	.		0.647	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		T	140503780	C	T	140503780	3	4	49	1	0	0	0	0	1	0	0	0	11553	710	25	3	2202	3	PCDHB4	5	140503780	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	44266478	140503780	40411480	80	6237										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141335035	141335035	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tccttgtccacatctttgtgGgactgcccgacttcacaagg	9	13	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:141335035G>A	ENST00000231484.3	-	1	3592	c.2382C>T	c.(2380-2382)tcC>tcT	p.S794S	AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	794					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATCTTTGTGGGACTGCCCGA	0.617																																					p.S794S		Atlas-SNP	.											.	PCDH12	133	.	0			c.C2382T						.						38	33	35					5																	141335035		2203	4300	6503	SO:0001819	synonymous_variant	51294	exon1			TTTGTGGGACTGC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2382C>T	chr5.hg19:g.141335035G>A		70.0	0.0		77.0	4.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	hg19	CCDS4269.1																																																																																			.	.		0.617	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141335035	G	A	141335035	2	1	49	1	0	0	0	0	0	0	0	1	11519	1219	43	3		3	PCDH12	5	141335035	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	831255	141335035	39580225	81	6238										
SLC6A7	6534	hgsc.bcm.edu	37	chr5	149578931	149578931	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgtgaagtcttcgggcaaggTgaagcctgggaggccccgga	17	9	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:149578931T>C	ENST00000230671.2	+	5	1094		c.e5+2		SLC6A7_ENST00000524041.1_Splice_Site	NM_014228.3	NP_055043.2	Q99884	SC6A7_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 7						proline transport (GO:0015824)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	TCGggcaaggtgaagcctggg	0.607																																					.		Atlas-SNP	.											.	SLC6A7	52	.	0			c.723+2T>C						.						70	67	68					5																	149578931		2203	4300	6503	SO:0001630	splice_region_variant	6534	exon5			GCAAGGTGAAGCC	S80071	CCDS4305.1	5q32	2013-07-19	2013-07-19		ENSG00000011083	ENSG00000011083		"Solute carriers"	11054	protein-coding gene	gene with protein product	"brain-specific L-proline transporter", "sodium-dependent proline transporter"	606205	"solute carrier family 6 (neurotransmitter transporter, L-proline), member 7"			7651355	Standard	NM_014228		Approved	PROT	uc003lrr.3	Q99884	OTTHUMG00000130046	ENST00000230671.2:c.723+2T>C	chr5.hg19:g.149578931T>C		78.0	0.0		95.0	4.0	NM_014228	Q0VG81|Q52LU6	Splice_Site	SNP	ENST00000230671.2	hg19	CCDS4305.1																																																																																			.	.		0.607	SLC6A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252325.1	NM_014228	Intron	C	149578931	T	C	149578931	5	2	49	1	0	0	0	0	0	0	1	0	14704	1710	59	2	743	2	SLC6A7	5	149578931	Splice_Site	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	8243896	149578931	31336329	82	6239										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168093513	168093513	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctctccacctcttctacaaaCgaggagccgtccgtgcactg	8	16	3	0	rs558199905		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:168093513C>T	ENST00000519560.1	-	36	4937	c.4518G>A	c.(4516-4518)tcG>tcA	p.S1506S	SLIT3_ENST00000332966.8_Silent_p.S1513S|CTC-558O2.2_ENST00000520041.1_RNA	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1506	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTTCTACAAACGAGGAGCCGT	0.632													c|||	1	0.000199681	8e-04	0	5008	,	,		14541	0		0	False		,,,				2504	0				p.S1513S	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											SLIT3,NS,lymphoid_neoplasm,0,1	SLIT3	224	.	0			c.G4539A						.						44	35	38					5																	168093513		2203	4300	6503	SO:0001819	synonymous_variant	6586	exon36			TACAAACGAGGAG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.4518G>A	chr5.hg19:g.168093513C>T		31.0	0.0		49.0	2.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.632	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		T	168093513	C	T	168093513	2	4	49	1	0	0	0	0	0	0	0	1	14756	523	19	1		1	SLIT3	5	168093513	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	18514582	168093513	12821747	83	6240										
BTNL9	153579	hgsc.bcm.edu	37	chr5	180486679	180486679	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcccacatcttcaccttccaCgacaccttctcgggcgcgct	6	19	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:180486679C>T	ENST00000327705.9	+	11	1656	c.1425C>T	c.(1423-1425)caC>caT	p.H475H	BTNL9_ENST00000376842.3_Silent_p.H476H	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	475	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)		p.H475H(1)		breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCACCTTCCACGACACCTTCT	0.672																																					p.H475H		Atlas-SNP	.											BTNL9,NS,carcinoma,0,1	BTNL9	58	.	1	Substitution - coding silent(1)	lung(1)	c.C1425T						.						38	37	38					5																	180486679		2203	4299	6502	SO:0001819	synonymous_variant	153579	exon11			CTTCCACGACACC	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.1425C>T	chr5.hg19:g.180486679C>T		45.0	0.0		42.0	2.0	NM_152547	A6NL42|Q6P660|Q96DM5	Silent	SNP	ENST00000327705.9	hg19	CCDS4460.2																																																																																			.	.		0.672	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547		T	180486679	C	T	180486679	2	4	49	1	0	0	0	0	0	0	0	1	1570	535	19	1		1	BTNL9	5	180486679	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	12393166	180486679	428581	84	6241										
GCM2	9247	hgsc.bcm.edu	37	chr6	10877430	10877430	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cctcagctgcaggcgggaacCgtcgggcagggtgcaggcct	17	13	1	0	rs550449754		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:10877430C>T	ENST00000379491.4	-	2	433	c.286G>A	c.(286-288)Ggt>Agt	p.G96S	SYCP2L_ENST00000543878.1_Intron|RP11-637O19.3_ENST00000480294.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	96					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.G96C(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				AGGCGGGAACCGTCGGGCAGG	0.627													C|||	1	0.000199681	8e-04	0	5008	,	,		17261	0		0	False		,,,				2504	0				p.G96S		Atlas-SNP	.											GCM2,NS,carcinoma,0,1	GCM2	81	.	1	Substitution - Missense(1)	lung(1)	c.G286A						.						76	69	72					6																	10877430		2203	4300	6503	SO:0001583	missense	9247	exon2			GGGAACCGTCGGG	AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"glial cells missing (Drosophila) homolog b"	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.286G>A	chr6.hg19:g.10877430C>T	ENSP00000368805:p.Gly96Ser	42.0	1.0		52.0	3.0	NM_004752	D3GDV6|Q5THN5	Missense_Mutation	SNP	ENST00000379491.4	hg19	CCDS4517.1	.	.	.	.	.	.	.	.	.	.	C	32	5.112433	0.94339	.	.	ENSG00000124827	ENST00000379491	D	0.84800	-1.9	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.91734	0.7386	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91804	0.5454	10	0.72032	D	0.01	-26.3182	19.8215	0.96599	0.0:1.0:0.0:0.0	.	96	O75603	GCM2_HUMAN	S	96	ENSP00000368805:G96S	ENSP00000368805:G96S	G	-	1	0	GCM2	10985416	1.000000	0.71417	0.986000	0.45419	0.580000	0.36256	7.434000	0.80377	2.679000	0.91253	0.650000	0.86243	GGT	.	.		0.627	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1			T	10877430	C	T	10877430	3	4	49	1	0	0	0	0	1	0	0	0	6306	652	23	1	1250	1	GCM2	6	10877430	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10		10877430	160237637	85	6242										
MUC21	394263	hgsc.bcm.edu	37	chr6	30955247	30955247	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cagcacaacctccagtggggCcaacacagccaccaactctg	8	17	1	0	rs144122059		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:30955247C>T	ENST00000376296.3	+	2	1536	c.1295C>T	c.(1294-1296)gCc>gTc	p.A432V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	432	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGTGGGGCCAACACAGCC	0.582																																					p.A432V		Atlas-SNP	.											.	MUC21	98	.	0			c.C1295T						.						129	124	126					6																	30955247		2203	4300	6503	SO:0001583	missense	394263	exon2			GTGGGGCCAACAC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1295C>T	chr6.hg19:g.30955247C>T	ENSP00000365473:p.Ala432Val	87.0	0.0		163.0	10.0	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	hg19	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	c	10.36	1.328172	0.24080	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02737	4.18	3.94	-0.192	0.13248	.	.	.	.	.	T	0.00412	0.0013	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43766	-0.9371	9	0.30854	T	0.27	-0.829	4.0611	0.09839	0.0:0.4049:0.1757:0.4193	.	432	Q5SSG8	MUC21_HUMAN	V	282;432	ENSP00000365473:A432V	ENSP00000365473:A432V	A	+	2	0	MUC21	31063226	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.873000	0.04214	0.118000	0.18165	-0.464000	0.05259	GCC	.	.		0.582	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		T	30955247	C	T	30955247	3	4	49	1	0	0	0	0	1	0	0	0	9986	739	26	3	1301	3	MUC21	6	30955247	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	20077817	30955247	140159820	86	6243										
BAT2	7916	hgsc.bcm.edu	37	chr6	31599160	31599160	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aagcaggccgaaagcctgccCgcggagtcgggagtggaggc	18	11	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:31599160C>A	ENST00000376033.2	+	16	2944	c.2710C>A	c.(2710-2712)Cgc>Agc	p.R904S	PRRC2A_ENST00000376007.4_Missense_Mutation_p.R904S	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	904	4 X 57 AA type A repeats.			PARGVGSGGQ -> LPASRSGA (in Ref. 1; AAA35585/AAA35586 and 8; CAA78744). {ECO:0000305}.		cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						AAAGCCTGCCCGCGGAGTCGG	0.647																																					p.R904S		Atlas-SNP	.											PRRC2A,NS,carcinoma,0,1	PRRC2A	152	.	0			c.C2710A						.						24	20	22					6																	31599160		1508	2707	4215	SO:0001583	missense	7916	exon16			CCTGCCCGCGGAG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.2710C>A	chr6.hg19:g.31599160C>A	ENSP00000365201:p.Arg904Ser	71.0	0.0		44.0	2.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	hg19	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	C	7.015	0.557633	0.13436	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01665	4.7;4.7	4.93	4.93	0.64822	.	0.271232	0.27072	N	0.021080	T	0.00608	0.0020	N	0.19112	0.55	0.35546	D	0.803462	P	0.44090	0.826	B	0.35510	0.204	T	0.60919	-0.7167	10	0.87932	D	0	-9.0305	7.311	0.26475	0.0:0.8212:0.0:0.1788	.	904	P48634	PRC2A_HUMAN	S	904;893;904;904;129	ENSP00000365175:R904S;ENSP00000365201:R904S	ENSP00000365175:R904S	R	+	1	0	PRRC2A	31707139	0.005000	0.15991	0.925000	0.36789	0.496000	0.33645	0.874000	0.28065	2.566000	0.86566	0.561000	0.74099	CGC	.	.		0.647	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		A	31599160	C	A	31599160	3	1	49	1	0	0	0	0	1	0	0	0	1319	652	23	1	2768	1	BAT2	6	31599160	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	643913	31599160	139515907	87	6244										
MEA1	4201	hgsc.bcm.edu	37	chr6	42980713	42980713	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttcaacgctgtagctccctcCtcatcttcatcttcactctc	3	17	7	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:42980713C>A	ENST00000244711.3	-	3	511	c.357G>T	c.(355-357)gaG>gaT	p.E119D	KLHDC3_ENST00000244670.8_5'Flank|KLHDC3_ENST00000326974.4_5'Flank	NM_014623.2	NP_055438.1	Q16626	MEA1_HUMAN	male-enhanced antigen 1	119					cell differentiation (GO:0030154)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)				central_nervous_system(1)|large_intestine(3)|lung(1)|skin(1)	6			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			TAGCTCCCTCCTCATCTTCAT	0.493																																					p.E119D		Atlas-SNP	.											.	MEA1	11	.	0			c.G357T						.						201	186	191					6																	42980713		2203	4300	6503	SO:0001583	missense	4201	exon3			TCCCTCCTCATCT		CCDS4879.1	6p21.3-p21.1	2008-08-15	2005-06-02	2005-06-02	ENSG00000124733	ENSG00000124733			6986	protein-coding gene	gene with protein product		143170	"male-enhanced antigen"	MEA		2813404, 12444059	Standard	NM_014623		Approved		uc003otk.3	Q16626	OTTHUMG00000014717	ENST00000244711.3:c.357G>T	chr6.hg19:g.42980713C>A	ENSP00000244711:p.Glu119Asp	74.0	0.0		120.0	9.0	NM_014623	Q5TC36|Q9BV01	Missense_Mutation	SNP	ENST00000244711.3	hg19	CCDS4879.1	.	.	.	.	.	.	.	.	.	.	c	11.38	1.620830	0.28889	.	.	ENSG00000124733	ENST00000244711	T	0.54479	0.57	5.8	3.1	0.35709	.	0.195088	0.45606	D	0.000344	T	0.16938	0.0407	N	0.24115	0.695	0.32265	N	0.56969	P	0.41978	0.767	B	0.38683	0.279	T	0.08953	-1.0697	10	0.17369	T	0.5	-9.8121	10.9106	0.47106	0.0:0.7931:0.0:0.2069	.	119	Q16626	MEA1_HUMAN	D	119	ENSP00000244711:E119D	ENSP00000244711:E119D	E	-	3	2	MEA1	43088691	0.514000	0.26202	0.993000	0.49108	0.338000	0.28826	-0.081000	0.11321	0.403000	0.25479	-0.964000	0.02622	GAG	.	.		0.493	MEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040574.2			A	42980713	C	A	42980713	3	1	49	1	0	0	0	0	1	0	0	0	9429	680	24	3	208	3	MEA1	6	42980713	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	11381553	42980713	128134354	88	6245										
CAPN11	11131	hgsc.bcm.edu	37	chr6	44148727	44148727	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttgccgctgcatgatcaaccTcatggatgtatcctcctgtc	8	13	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:44148727T>C	ENST00000398776.1	+	18	1900	c.1862T>C	c.(1861-1863)cTc>cCc	p.L621P	CAPN11_ENST00000542245.1_Missense_Mutation_p.L621P	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	621	Domain IV.|EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			ATGATCAACCTCATGGATGTA	0.582																																					p.L621P		Atlas-SNP	.											.	CAPN11	66	.	0			c.T1862C						.						243	247	246					6																	44148727		2045	4194	6239	SO:0001583	missense	11131	exon18			TCAACCTCATGGA	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1862T>C	chr6.hg19:g.44148727T>C	ENSP00000381758:p.Leu621Pro	56.0	0.0		98.0	4.0	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	hg19	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	t	18.80	3.701779	0.68501	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	T;T	0.79940	-1.32;-1.32	5.01	3.85	0.44370	EF-hand-like domain (1);	0.556403	0.15143	N	0.278189	D	0.90181	0.6931	H	0.96691	3.865	0.58432	D	0.999996	D;D	0.76494	0.999;0.993	D;P	0.67382	0.951;0.879	D	0.90751	0.4657	10	0.87932	D	0	.	9.9795	0.41804	0.0:0.0798:0.0:0.9202	.	275;621	B4DT90;Q9UMQ6	.;CAN11_HUMAN	P	621	ENSP00000381758:L621P;ENSP00000441078:L621P	ENSP00000381758:L621P	L	+	2	0	CAPN11	44256705	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	6.108000	0.71522	0.941000	0.37499	-0.507000	0.04495	CTC	.	.		0.582	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			C	44148727	T	C	44148727	3	2	49	1	0	0	0	0	1	0	0	0	2626	1551	54	2	1932	2	CAPN11	6	44148727	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	1168014	44148727	126966340	89	6246										
DEFB113	245927	hgsc.bcm.edu	37	chr6	49936572	49936572	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgcaacttctcttgttttttTctgtggaactaggaaaaagt	8	6	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:49936572T>A	ENST00000398718.1	-	2	66	c.67A>T	c.(67-69)Aaa>Taa	p.K23*		NM_001037729.1	NP_001032818.1	Q30KQ7	DB113_HUMAN	defensin, beta 113	23					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Lung NSC(77;0.042)					CTTGTTTTTTTCTGTGGAACT	0.353																																					p.K23X		Atlas-SNP	.											.	DEFB113	18	.	0			c.A67T						.						83	80	81					6																	49936572		1845	4089	5934	SO:0001587	stop_gained	245927	exon2			TTTTTTTCTGTGG	DQ012017	CCDS43472.1	6p12.3	2010-03-30			ENSG00000214642	ENSG00000214642		"Defensins, beta"	18094	protein-coding gene	gene with protein product						11854508, 16033865	Standard	NM_001037729		Approved	DEFB-13	uc011dwq.2	Q30KQ7	OTTHUMG00000160210	ENST00000398718.1:c.67A>T	chr6.hg19:g.49936572T>A	ENSP00000381703:p.Lys23*	99.0	0.0		97.0	21.0	NM_001037729		Nonsense_Mutation	SNP	ENST00000398718.1	hg19	CCDS43472.1	.	.	.	.	.	.	.	.	.	.	T	7.878	0.729576	0.15507	.	.	ENSG00000214642	ENST00000398718	.	.	.	4.15	-1.11	0.09840	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.3815	3.9562	0.09391	0.0:0.2118:0.3772:0.411	.	.	.	.	X	23	.	.	K	-	1	0	DEFB113	50044531	0.942000	0.31987	0.098000	0.21074	0.081000	0.17604	0.491000	0.22419	-0.040000	0.13580	-0.472000	0.04984	AAA	.	.		0.353	DEFB113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359666.1			A	49936572	T	A	49936572	4	1	49	1	0	0	0	0	0	1	0	0	4404	1792	62	4	177	4	DEFB113	6	49936572	Nonsense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	5787845	49936572	121178495	90	6247										
BMP5	653	hgsc.bcm.edu	37	chr6	55639030	55639030	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aagaccagcagattttacgtTgatactgcgtcctagaacgt	9	9	0	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:55639030T>C	ENST00000370830.3	-	4	1542	c.844A>G	c.(844-846)Aac>Gac	p.N282D	BMP5_ENST00000446683.2_Missense_Mutation_p.N282D	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	282					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			GATTTTACGTTGATACTGCGT	0.428																																					p.N282D		Atlas-SNP	.											.	BMP5	94	.	0			c.A844G						.						162	143	150					6																	55639030		2203	4300	6503	SO:0001583	missense	653	exon4			TTACGTTGATACT		CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"Bone morphogenetic proteins", "Endogenous ligands"	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.844A>G	chr6.hg19:g.55639030T>C	ENSP00000359866:p.Asn282Asp	175.0	0.0		230.0	32.0	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Missense_Mutation	SNP	ENST00000370830.3	hg19	CCDS4958.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.489979	0.26686	.	.	ENSG00000112175	ENST00000370830;ENST00000446683	T;T	0.63744	-0.06;-0.06	5.74	5.74	0.90152	Transforming growth factor-beta, N-terminal (1);	0.167852	0.64402	D	0.000006	T	0.45357	0.1338	N	0.26130	0.795	0.50171	D	0.999852	P;P	0.46621	0.866;0.881	P;P	0.48921	0.515;0.595	T	0.41305	-0.9516	10	0.22109	T	0.4	.	16.0486	0.80740	0.0:0.0:0.0:1.0	.	282;282	B4E0Y4;P22003	.;BMP5_HUMAN	D	282	ENSP00000359866:N282D;ENSP00000391818:N282D	ENSP00000359866:N282D	N	-	1	0	BMP5	55746989	1.000000	0.71417	0.998000	0.56505	0.145000	0.21501	7.694000	0.84235	2.183000	0.69458	0.533000	0.62120	AAC	.	.		0.428	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1			C	55639030	T	C	55639030	3	2	49	1	0	0	0	0	1	0	0	0	1463	1812	63	2	536	2	BMP5	6	55639030	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	5702458	55639030	115476037	91	6248										
MCHR2	84539	hgsc.bcm.edu	37	chr6	100382375	100382375	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gggaaaaaaaaagttgttatCgtcaaataaagtgtatacct	8	4	1	0	rs267600746		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:100382375C>A	ENST00000281806.2	-	5	920	c.606G>T	c.(604-606)acG>acT	p.T202T	MCHR2_ENST00000369212.2_Silent_p.T202T	NM_001040179.1	NP_001035269.1	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.T202T(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	39		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		AAGTTGTTATCGTCAAATAAA	0.333													C|||	1	0.000199681	0	0.0014	5008	,	,		18433	0		0	False		,,,				2504	0				p.T202T		Atlas-SNP	.											MCHR2,NS,carcinoma,-1,1	MCHR2	97	.	1	Substitution - coding silent(1)	skin(1)	c.G606T						.						73	72	72					6																	100382375		2203	4298	6501	SO:0001819	synonymous_variant	84539	exon5			TGTTATCGTCAAA	AF347063	CCDS5044.1	6q16	2012-08-08	2006-02-15	2006-02-15	ENSG00000152034	ENSG00000152034		"GPCR / Class A : MCH receptors"	20867	protein-coding gene	gene with protein product		606111	"G protein-coupled receptor 145"	GPR145		11355873, 11274220	Standard	NM_032503		Approved	SLT, MCH2, MCH2R	uc003pqi.1	Q969V1	OTTHUMG00000015270	ENST00000281806.2:c.606G>T	chr6.hg19:g.100382375C>A		42.0	0.0		58.0	3.0	NM_001040179	B3KVW4|E1P5D7|Q5VTV7|Q6Q377|Q9BXA8	Silent	SNP	ENST00000281806.2	hg19	CCDS5044.1																																																																																			.	.		0.333	MCHR2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041620.2	NM_032503		A	100382375	C	A	100382375	2	1	49	1	0	0	0	0	0	0	0	1	9392	871	31	1		1	MCHR2	6	100382375	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	44743345	100382375	70732692	92	6249										
DSE	29940	hgsc.bcm.edu	37	chr6	116757465	116757465	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctttcatcaggcagagagatGgtctctataaaatgtactgg	10	7	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:116757465G>C	ENST00000331677.3	+	7	2278	c.1834G>C	c.(1834-1836)Ggt>Cgt	p.G612R	DSE_ENST00000452085.3_Missense_Mutation_p.G612R|DSE_ENST00000537543.1_Missense_Mutation_p.G631R|DSE_ENST00000359564.2_Missense_Mutation_p.G612R			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	612					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		GCAGAGAGATGGTCTCTATAA	0.488																																					p.G612R		Atlas-SNP	.											.	DSE	98	.	0			c.G1834C						.						123	110	115					6																	116757465		2203	4300	6503	SO:0001583	missense	29940	exon6			AGAGATGGTCTCT	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"squamous cell carcinoma antigen recognized by T cells 2"	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.1834G>C	chr6.hg19:g.116757465G>C	ENSP00000332151:p.Gly612Arg	52.0	0.0		135.0	6.0	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	hg19	CCDS5107.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.370207	0.61624	.	.	ENSG00000111817	ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	6.01	6.01	0.97437	.	0.250132	0.47455	D	0.000228	T	0.61825	0.2378	L	0.56769	1.78	0.54753	D	0.999989	P;P	0.49635	0.926;0.926	P;B	0.47626	0.552;0.413	T	0.64833	-0.6314	10	0.62326	D	0.03	-16.2979	20.5211	0.99222	0.0:0.0:1.0:0.0	.	631;612	B7Z765;Q9UL01	.;DSE_HUMAN	R	612;631;612;612	ENSP00000404049:G612R;ENSP00000441152:G631R;ENSP00000332151:G612R;ENSP00000352567:G612R	ENSP00000332151:G612R	G	+	1	0	DSE	116864158	1.000000	0.71417	0.997000	0.53966	0.959000	0.62525	7.935000	0.87658	2.861000	0.98227	0.650000	0.86243	GGT	.	.		0.488	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352		C	116757465	G	C	116757465	3	2	49	1	0	0	0	0	1	0	0	0	4776	1348	47	4	1852	4	DSE	6	116757465	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	16375090	116757465	54357602	93	6250										
LTV1	84946	hgsc.bcm.edu	37	chr6	144184607	144184607	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcatttaaactggagaaaagAaggcaagaaaaagagctgct	11	5	0	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:144184607A>G	ENST00000367576.5	+	11	1505	c.1371A>G	c.(1369-1371)agA>agG	p.R457R	ZC2HC1B_ENST00000237275.6_5'Flank|ZC2HC1B_ENST00000539295.1_5'Flank	NM_032860.3	NP_116249.2	Q96GA3	LTV1_HUMAN	LTV1 ribosome biogenesis factor	457						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)		TGGAGAAAAGAAGGCAAGAAA	0.378																																					p.R457R		Atlas-SNP	.											.	LTV1	48	.	0			c.A1371G						.						99	98	99					6																	144184607		2203	4300	6503	SO:0001819	synonymous_variant	84946	exon11			GAAAAGAAGGCAA	BC009855	CCDS5201.1	6q24.2	2014-02-03	2014-02-03	2006-02-06	ENSG00000135521	ENSG00000135521			21173	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 93", "LTV1 homolog (S. cerevisiae)"	C6orf93			Standard	NM_032860		Approved	FLJ14909, dJ468K18.4	uc003qjs.3	Q96GA3	OTTHUMG00000015733	ENST00000367576.5:c.1371A>G	chr6.hg19:g.144184607A>G		201.0	0.0		260.0	77.0	NM_032860	Q96JX8	Silent	SNP	ENST00000367576.5	hg19	CCDS5201.1																																																																																			.	.		0.378	LTV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042532.1	NM_032860		G	144184607	A	G	144184607	2	3	49	1	0	0	0	0	0	0	0	1	9090	243	9	2		2	LTV1	6	144184607	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	27427142	144184607	26930460	94	6251										
UTRN	7402	hgsc.bcm.edu	37	chr6	145021342	145021342	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	acaaatgcctattggaggagAtgttccagccttacagctcc	9	11	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:145021342A>G	ENST00000367545.3	+	52	7772	c.7772A>G	c.(7771-7773)gAt>gGt	p.D2591G	UTRN_ENST00000367526.4_Missense_Mutation_p.D146G	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2591					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ATTGGAGGAGATGTTCCAGCC	0.388																																					p.D2591G		Atlas-SNP	.											.	UTRN	327	.	0			c.A7772G						.						119	112	114					6																	145021342		2203	4300	6503	SO:0001583	missense	7402	exon52			GAGGAGATGTTCC	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.7772A>G	chr6.hg19:g.145021342A>G	ENSP00000356515:p.Asp2591Gly	62.0	0.0		94.0	4.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.577040	0.86645	.	.	ENSG00000152818	ENST00000367545;ENST00000367526	T;T	0.48522	0.81;0.81	5.64	5.64	0.86602	.	0.000000	0.48767	D	0.000177	T	0.54663	0.1872	M	0.72894	2.215	0.58432	D	0.999996	P	0.43094	0.799	P	0.53518	0.728	T	0.60796	-0.7192	10	0.87932	D	0	.	15.8735	0.79141	1.0:0.0:0.0:0.0	.	2591	P46939	UTRO_HUMAN	G	2591;146	ENSP00000356515:D2591G;ENSP00000356496:D146G	ENSP00000356496:D146G	D	+	2	0	UTRN	145063035	1.000000	0.71417	0.824000	0.32777	0.978000	0.69477	8.671000	0.91174	2.149000	0.67028	0.533000	0.62120	GAT	.	.		0.388	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			G	145021342	A	G	145021342	3	3	49	1	0	0	0	0	1	0	0	0	17118	333	12	2	7978	2	UTRN	6	145021342	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	836735	145021342	26093725	95	6252										
SASH1	23328	hgsc.bcm.edu	37	chr6	148846461	148846461	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tggaggatttgacttgacgaAtcgctctctgcacgttggca	12	9	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:148846461A>G	ENST00000367467.3	+	11	1719	c.1244A>G	c.(1243-1245)aAt>aGt	p.N415S	AL033378.1_ENST00000411390.2_RNA	NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	415					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GACTTGACGAATCGCTCTCTG	0.453																																					p.N415S		Atlas-SNP	.											.	SASH1	123	.	0			c.A1244G						.						216	198	204					6																	148846461		2203	4300	6503	SO:0001583	missense	23328	exon11			TGACGAATCGCTC	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1244A>G	chr6.hg19:g.148846461A>G	ENSP00000356437:p.Asn415Ser	61.0	0.0		67.0	17.0	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	hg19	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	A	18.97	3.735475	0.69189	.	.	ENSG00000111961	ENST00000367467;ENST00000535767	T	0.43688	0.94	5.63	5.63	0.86233	.	0.196718	0.53938	D	0.000057	T	0.48150	0.1484	L	0.43152	1.355	0.51767	D	0.999932	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.42849	-0.9427	10	0.40728	T	0.16	-33.4466	16.1339	0.81465	1.0:0.0:0.0:0.0	.	396;415	Q6P4R9;O94885	.;SASH1_HUMAN	S	415;176	ENSP00000356437:N415S	ENSP00000356437:N415S	N	+	2	0	SASH1	148888154	1.000000	0.71417	0.384000	0.26145	0.821000	0.46438	7.102000	0.77005	2.271000	0.75665	0.533000	0.62120	AAT	.	.		0.453	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		G	148846461	A	G	148846461	3	3	49	1	0	0	0	0	1	0	0	0	13863	101	4	2	1286	2	SASH1	6	148846461	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	3825119	148846461	22268606	96	6253										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157522125	157522125	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcctcagcagaatatgtgggCagcacgcaatgatatgcctt	11	10	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:157522125C>A	ENST00000350026.5	+	17	4359	c.4358C>A	c.(4357-4359)gCa>gAa	p.A1453E	ARID1B_ENST00000346085.5_Missense_Mutation_p.A1466E|ARID1B_ENST00000367148.1_Missense_Mutation_p.A1506E|ARID1B_ENST00000275248.4_Missense_Mutation_p.A1448E	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1453					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		AATATGTGGGCAGCACGCAAT	0.632																																					p.A1466E		Atlas-SNP	.											.	ARID1B	320	.	0			c.C4397A						.						43	47	45					6																	157522125		2203	4296	6499	SO:0001583	missense	57492	exon18			TGTGGGCAGCACG	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.4358C>A	chr6.hg19:g.157522125C>A	ENSP00000055163:p.Ala1453Glu	69.0	0.0		126.0	16.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	C	11.91	1.778375	0.31502	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.02032	4.82;4.83;4.82;4.82;4.49	5.08	5.08	0.68730	.	0.175751	0.50627	D	0.000120	T	0.00845	0.0028	N	0.08118	0	0.36525	D	0.870411	B;B;B	0.19200	0.02;0.034;0.034	B;B;B	0.21708	0.016;0.036;0.036	T	0.61564	-0.7037	10	0.27785	T	0.31	.	18.8669	0.92296	0.0:1.0:0.0:0.0	.	1453;1466;1448	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	E	1466;1453;1506;1448;975	ENSP00000344546:A1466E;ENSP00000055163:A1453E;ENSP00000356116:A1506E;ENSP00000275248:A1448E;ENSP00000412835:A975E	ENSP00000275248:A1448E	A	+	2	0	ARID1B	157563817	0.931000	0.31567	0.957000	0.39632	0.958000	0.62258	2.049000	0.41288	2.528000	0.85240	0.591000	0.81541	GCA	.	.		0.632	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		A	157522125	C	A	157522125	3	1	49	1	0	0	0	0	1	0	0	0	914	710	25	3	4467	3	ARID1B	6	157522125	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	8675664	157522125	13592942	97	6254										
MRPL18	29074	hgsc.bcm.edu	37	chr6	160212008	160212008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cctgtcaaccagctccgagcCggcagcgaaacctgaagtgg	12	14	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:160212008C>T	ENST00000367034.4	+	2	211	c.89C>T	c.(88-90)cCg>cTg	p.P30L	TCP1_ENST00000420894.2_5'Flank|TCP1_ENST00000321394.7_5'Flank|TCP1_ENST00000544255.1_5'Flank|MRPL18_ENST00000480842.1_3'UTR|TCP1_ENST00000546023.1_5'Flank|TCP1_ENST00000392168.2_5'Flank	NM_014161.3	NP_054880.2	Q9H0U6	RM18_HUMAN	mitochondrial ribosomal protein L18	30					rRNA import into mitochondrion (GO:0035928)|translation (GO:0006412)	extracellular space (GO:0005615)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	11		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.79e-06)		AGCTCCGAGCCGGCAGCGAAA	0.582																																					p.P30L		Atlas-SNP	.											MRPL18,NS,malignant_melanoma,0,1	MRPL18	25	.	0			c.C89T						.						28	31	30					6																	160212008		2203	4300	6503	SO:0001583	missense	29074	exon2			CCGAGCCGGCAGC	AF161556	CCDS5270.1	6q25.3	2012-09-13			ENSG00000112110	ENSG00000112110		"Mitochondrial ribosomal proteins / large subunits"	14477	protein-coding gene	gene with protein product		611831				11042152, 11551941	Standard	NM_014161		Approved	HSPC071	uc003qsw.4	Q9H0U6	OTTHUMG00000015942	ENST00000367034.4:c.89C>T	chr6.hg19:g.160212008C>T	ENSP00000356001:p.Pro30Leu	52.0	0.0		68.0	3.0	NM_014161	Q5TAP9|Q9NZW8	Missense_Mutation	SNP	ENST00000367034.4	hg19	CCDS5270.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.802409	0.31869	.	.	ENSG00000112110	ENST00000367034	T	0.42513	0.97	5.32	4.45	0.53987	.	0.391638	0.26635	N	0.023282	T	0.20981	0.0505	M	0.65975	2.015	0.19575	N	0.999968	P	0.36768	0.569	B	0.30495	0.116	T	0.12915	-1.0529	10	0.20046	T	0.44	-8.8481	15.0244	0.71656	0.0:0.8567:0.1433:0.0	.	30	Q9H0U6	RM18_HUMAN	L	30	ENSP00000356001:P30L	ENSP00000356001:P30L	P	+	2	0	MRPL18	160131998	0.009000	0.17119	0.000000	0.03702	0.002000	0.02628	2.472000	0.45136	1.458000	0.47871	-0.176000	0.13171	CCG	.	.		0.582	MRPL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042925.1			T	160212008	C	T	160212008	3	4	49	1	0	0	0	0	1	0	0	0	9792	652	23	1	95	1	MRPL18	6	160212008	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	2689883	160212008	10903059	98	6255										
SUN1	23353	hgsc.bcm.edu	37	chr7	882841	882841	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtgtgtgtgtttttttttttAggtcttgatgatgatggtga	13	1	1	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:882841A>G	ENST00000405266.1	+	4	475		c.e4-1		SUN1_ENST00000425407.2_Splice_Site|SUN1_ENST00000401592.1_Splice_Site|SUN1_ENST00000457378.2_Splice_Site|SUN1_ENST00000452783.2_Intron|SUN1_ENST00000456758.2_Splice_Site|SUN1_ENST00000389574.3_Splice_Site|SUN1_ENST00000403868.1_Splice_Site			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1						cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTTTTTTTTTAGGTCTTGATG	0.284																																					.		Atlas-SNP	.											.	SUN1	157	.	0			c.452-2A>G						.						90	89	89					7																	882841		1826	4091	5917	SO:0001630	splice_region_variant	23353	exon5			TTTTTTAGGTCTT	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"Sad1 unc-84 domain protein 1"	607723	"unc-84 homolog A (C. elegans)"	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.452-1A>G	chr7.hg19:g.882841A>G		78.0	0.0		90.0	5.0	NM_001171946	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Splice_Site	SNP	ENST00000405266.1	hg19		.	.	.	.	.	.	.	.	.	.	a	7.211	0.595337	0.13875	.	.	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000435699;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407	.	.	.	4.59	4.59	0.56863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9403	0.64050	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SUN1	849367	1.000000	0.71417	0.975000	0.42487	0.731000	0.41821	6.498000	0.73679	1.839000	0.53478	0.482000	0.46254	.	.	.		0.284	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	Intron	G	882841	A	G	882841	5	3	49	1	0	0	0	0	0	0	1	0	15406	434	15	2	531	2	SUN1	7	882841	Splice_Site	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10		882841	158255822	99	6256										
LFNG	3955	hgsc.bcm.edu	37	chr7	2552880	2552880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aggatggacggacagatggaCagatggatggatggatggat	18	3	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:2552880C>T	ENST00000402506.1	+	2	263	c.137C>T	c.(136-138)aCa>aTa	p.T46I		NM_001166355.1	NP_001159827.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		gacagatggacagatggatgg	0.562																																					p.T46I		Atlas-SNP	.											.	LFNG	57	.	0			c.C137T						.						133	125	127					7																	2552880		1568	3582	5150	SO:0001583	missense	3955	exon2			GATGGACAGATGG	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"Beta 3-glycosyltransferases"	6560	protein-coding gene	gene with protein product		602576	"lunatic fringe (Drosophila) homolog", "lunatic fringe homolog (Drosophila)"			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000402506.1:c.137C>T	chr7.hg19:g.2552880C>T	ENSP00000385764:p.Thr46Ile	53.0	0.0		75.0	7.0	NM_001166355	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Missense_Mutation	SNP	ENST00000402506.1	hg19	CCDS55081.1	.	.	.	.	.	.	.	.	.	.	C	7.077	0.569507	0.13560	.	.	ENSG00000106003	ENST00000402506	T	0.73258	-0.73	2.36	1.47	0.22746	.	.	.	.	.	T	0.49047	0.1534	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.46133	-0.9213	7	0.87932	D	0	.	4.9157	0.13844	0.0:0.8209:0.0:0.1791	.	.	.	.	I	46	ENSP00000385764:T46I	ENSP00000385764:T46I	T	+	2	0	LFNG	2519406	0.000000	0.05858	0.003000	0.11579	0.032000	0.12392	-0.432000	0.06956	0.564000	0.29238	0.491000	0.48974	ACA	.	.		0.562	LFNG-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000325023.1	NM_002304		T	2552880	C	T	2552880	3	4	49	1	0	0	0	0	1	0	0	0	8746	478	17	3	143	3	LFNG	7	2552880	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1670039	2552880	156585783	100	6257										
SP4	6671	hgsc.bcm.edu	37	chr7	21469601	21469601	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agctttgccagtgataaacaAcgtggctgccggaggaggga	15	8	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:21469601A>G	ENST00000222584.3	+	3	1036	c.818A>G	c.(817-819)aAc>aGc	p.N273S		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	273					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						GTGATAAACAACGTGGCTGCC	0.512																																					p.N273S		Atlas-SNP	.											.	SP4	91	.	0			c.A818G						.						71	65	67					7																	21469601		2203	4300	6503	SO:0001583	missense	6671	exon3			TAAACAACGTGGC		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.818A>G	chr7.hg19:g.21469601A>G	ENSP00000222584:p.Asn273Ser	130.0	0.0		174.0	44.0	NM_003112	O60402|Q32M52	Missense_Mutation	SNP	ENST00000222584.3	hg19	CCDS5373.1	.	.	.	.	.	.	.	.	.	.	A	0.398	-0.919762	0.02396	.	.	ENSG00000105866	ENST00000222584	T	0.07021	3.23	4.94	1.24	0.21308	.	0.132837	0.64402	N	0.000002	T	0.02767	0.0083	N	0.04090	-0.28	0.44234	D	0.997076	B	0.06786	0.001	B	0.04013	0.001	T	0.46456	-0.9190	10	0.02654	T	1	.	8.1388	0.31071	0.6845:0.0:0.3155:0.0	.	273	Q02446	SP4_HUMAN	S	273	ENSP00000222584:N273S	ENSP00000222584:N273S	N	+	2	0	SP4	21436126	0.950000	0.32346	0.930000	0.37139	0.996000	0.88848	2.331000	0.43894	0.057000	0.16193	0.533000	0.62120	AAC	.	.		0.512	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		G	21469601	A	G	21469601	3	3	49	1	0	0	0	0	1	0	0	0	14981	43	2	2	828	2	SP4	7	21469601	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	18916721	21469601	137669062	101	6258										
HOXA5	3202	hgsc.bcm.edu	37	chr7	27181672	27181672	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtagcgcgtgtaggccgtccGggcccttttgccttccgggc	15	14	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:27181672G>A	ENST00000222726.3	-	2	655	c.595C>T	c.(595-597)Cgg>Tgg	p.R199W	HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000521197.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA3_ENST00000521401.1_5'Flank|HOXA5_ENST00000520854.1_5'UTR	NM_019102.3	NP_061975.2	P20719	HXA5_HUMAN	homeobox A5	199					anterior/posterior pattern specification (GO:0009952)|bronchiole development (GO:0060435)|cell migration (GO:0016477)|cell-cell signaling involved in mammary gland development (GO:0060764)|embryonic skeletal system morphogenesis (GO:0048704)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|intestinal epithelial cell maturation (GO:0060574)|lung alveolus development (GO:0048286)|lung goblet cell differentiation (GO:0060480)|lung-associated mesenchyme development (GO:0060484)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal-epithelial cell signaling (GO:0060638)|multicellular organism growth (GO:0035264)|negative regulation of angiogenesis (GO:0016525)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of apoptotic process (GO:0043065)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|respiratory system process (GO:0003016)|thyroid gland development (GO:0030878)|trachea cartilage morphogenesis (GO:0060535)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(12)|skin(1)	16						TAGGCCGTCCGGGCCCTTTTG	0.562											OREG0017911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R199W	Colon(119;75 2200 7557 42868)	Atlas-SNP	.											HOXA5,NS,carcinoma,0,1	HOXA5	43	.	0			c.C595T						.						69	67	68					7																	27181672		2203	4300	6503	SO:0001583	missense	3202	exon2			CCGTCCGGGCCCT		CCDS5406.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106004	ENSG00000106004		"Homeoboxes / ANTP class : HOXL subclass"	5106	protein-coding gene	gene with protein product		142952	"homeo box A5"	HOX1C, HOX1		1973146, 1358459	Standard	NM_019102		Approved		uc003syn.2	P20719	OTTHUMG00000023214	ENST00000222726.3:c.595C>T	chr7.hg19:g.27181672G>A	ENSP00000222726:p.Arg199Trp	56.0	0.0	792	79.0	4.0	NM_019102	A4D179|O43367|Q96CY6	Missense_Mutation	SNP	ENST00000222726.3	hg19	CCDS5406.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.906675	0.52333	.	.	ENSG00000106004	ENST00000222726	D	0.99186	-5.53	4.76	2.83	0.33086	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99625	0.9863	H	0.99682	4.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97771	1.0226	10	0.87932	D	0	.	13.2228	0.59899	0.0:0.0:0.7094:0.2906	.	199	P20719	HXA5_HUMAN	W	199	ENSP00000222726:R199W	ENSP00000222726:R199W	R	-	1	2	HOXA5	27148197	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.944000	0.49034	0.470000	0.27294	0.543000	0.68304	CGG	.	.		0.562	HOXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358705.1			A	27181672	G	A	27181672	3	1	49	1	0	0	0	0	1	0	0	0	7304	1115	39	1	221	1	HOXA5	7	27181672	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	5712071	27181672	131956991	102	6259										
DDX56	54606	hgsc.bcm.edu	37	chr7	44612257	44612257	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccaaaagctccagggagtcaCgaagtttcaggctgtcttgc	11	11	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:44612257C>A	ENST00000258772.5	-	4	576	c.470G>T	c.(469-471)cGt>cTt	p.R157L	DDX56_ENST00000485367.1_5'UTR|DDX56_ENST00000431640.1_Missense_Mutation_p.R157L	NM_001257189.1|NM_019082.3	NP_001244118.1|NP_061955.1	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 56	157	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)	16						CAGGGAGTCACGAAGTTTCAG	0.517																																					p.R157L		Atlas-SNP	.											.	DDX56	36	.	0			c.G470T						.						143	139	140					7																	44612257		2203	4300	6503	SO:0001583	missense	54606	exon4			GAGTCACGAAGTT	AJ131712	CCDS5492.1, CCDS59053.1	7p13	2012-02-23	2012-02-23		ENSG00000136271	ENSG00000136271		"DEAD-boxes"	18193	protein-coding gene	gene with protein product	"nucleolar helicase of 61 kDa"	608023	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 56"			10749921	Standard	NM_019082		Approved	NOH61	uc003tlg.4	Q9NY93	OTTHUMG00000129211	ENST00000258772.5:c.470G>T	chr7.hg19:g.44612257C>A	ENSP00000258772:p.Arg157Leu	133.0	0.0		209.0	51.0	NM_001257189	A4D2K9|C9JV95|Q6IAE2|Q9H9I8	Missense_Mutation	SNP	ENST00000258772.5	hg19	CCDS5492.1	.	.	.	.	.	.	.	.	.	.	.	11.51	1.660906	0.29515	.	.	ENSG00000136271	ENST00000258772;ENST00000431640	T;T	0.32753	1.44;1.44	5.48	1.7	0.24286	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.245391	0.41097	D	0.000958	T	0.19604	0.0471	L	0.28400	0.85	0.35968	D	0.835132	B;B	0.13145	0.006;0.007	B;B	0.17979	0.02;0.01	T	0.15838	-1.0423	10	0.22109	T	0.4	-2.929	9.567	0.39405	0.0:0.7103:0.0:0.2897	.	157;157	C9JV95;Q9NY93	.;DDX56_HUMAN	L	157	ENSP00000258772:R157L;ENSP00000393488:R157L	ENSP00000258772:R157L	R	-	2	0	DDX56	44578782	0.196000	0.23350	0.038000	0.18304	0.964000	0.63967	0.585000	0.23879	0.105000	0.17753	-0.140000	0.14226	CGT	.	.		0.517	DDX56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251291.1	NM_019082		A	44612257	C	A	44612257	3	1	49	1	0	0	0	0	1	0	0	0	4376	536	19	1	1217	1	DDX56	7	44612257	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	17430585	44612257	114526406	103	6260										
POMZP3	22932	hgsc.bcm.edu	37	chr7	76240786	76240786	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cataccatgcctgcggttacAgggaagcagacgtggaccac	12	12	0	1	rs71819724	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:76240786A>C	ENST00000310842.4	-	6	1244	c.560T>G	c.(559-561)cTg>cGg	p.L187R	UPK3B_ENST00000443097.2_Intron|POMZP3_ENST00000275569.4_Intron|AC004980.7_ENST00000418663.1_RNA|UPK3B_ENST00000419923.2_Intron	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	187										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				CTGCGGTTACAGGGAAGCAGA	0.517																																					p.L187R		Atlas-SNP	.											.	POMZP3	19	.	0			c.T560G						.						51	55	54					7																	76240786		1684	3181	4865	SO:0001583	missense	22932	exon6			GGTTACAGGGAAG	U10099	CCDS5590.1, CCDS43606.1	7q11.2	2010-06-24	2010-06-24		ENSG00000146707	ENSG00000146707			9203	protein-coding gene	gene with protein product	"POM-ZP3 fusion protein", "POM121/ZP3 fusion protein"	600587	"POM (POM121 rat homolog) and ZP3 fusion", "POM (POM121 homolog, rat) and ZP3 fusion"			7789967	Standard	NM_012230		Approved	POM-ZP3, POM121	uc003uft.3	Q6PJE2	OTTHUMG00000023514	ENST00000310842.4:c.560T>G	chr7.hg19:g.76240786A>C	ENSP00000309233:p.Leu187Arg	92.0	0.0		137.0	8.0	NM_012230	F6STJ3|Q12903|Q9BWB4	Missense_Mutation	SNP	ENST00000310842.4	hg19	CCDS43606.1	.	.	.	.	.	.	.	.	.	.	N	12.82	2.052691	0.36181	.	.	ENSG00000146707	ENST00000310842	T	0.27256	1.68	.	.	.	.	48.261100	0.00760	U	0.001131	T	0.23926	0.0579	N	0.08118	0	0.09310	N	1	P	0.51240	0.943	P	0.55011	0.766	T	0.19745	-1.0296	8	0.87932	D	0	.	.	.	.	.	187	Q6PJE2	POZP3_HUMAN	R	187	ENSP00000309233:L187R	ENSP00000309233:L187R	L	-	2	0	POMZP3	76078722	0.049000	0.20398	0.276000	0.24689	0.537000	0.34900	-0.663000	0.05299	0.000000	0.14550	0.000000	0.15137	CTG	.	.		0.517	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341775.1	NM_012230		C	76240786	A	C	76240786	3	2	49	1	0	0	0	0	1	0	0	0	12256	188	7	5	14	5	POMZP3	7	76240786	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	31628529	76240786	82897877	104	6261										
PCLO	27445	hgsc.bcm.edu	37	chr7	82389961	82389961	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	taatacagagctacctgaagAgaatgtcctgcaggacttag	10	8	0	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:82389961A>G	ENST00000333891.9	-	24	15619	c.15282T>C	c.(15280-15282)tcT>tcC	p.S5094S		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTACCTGAAGAGAATGTCCTG	0.308																																					p.S5094S		Atlas-SNP	.											.	PCLO	1506	.	0			c.T15282C						.						118	117	118					7																	82389961		1823	4072	5895	SO:0001819	synonymous_variant	27445	exon24			CTGAAGAGAATGT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.15282T>C	chr7.hg19:g.82389961A>G		390.0	0.0		508.0	113.0	NM_033026		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.308	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82389961	A	G	82389961	2	3	49	1	0	0	0	0	0	0	0	1	11592	291	11	2		2	PCLO	7	82389961	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	6149175	82389961	76748702	105	6262										
FZD1	8321	hgsc.bcm.edu	37	chr7	90894459	90894459	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gggcccgggccggggcagcaAccgccgccgccgcctcagca	16	19	1	0	rs71292991|rs139480179	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:90894459A>G	ENST00000287934.2	+	1	677	c.264A>G	c.(262-264)caA>caG	p.Q88Q		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	88					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.Q88_P89insP(2)|p.Q88_P89insA(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			cggggcAGCAACCGCCGCCGC	0.741																																					p.Q88Q		Atlas-SNP	.											.,4	FZD1	64	.	3	Insertion - In frame(3)	breast(2)|liver(1)	c.A264G						.						10	11	11					7																	90894459		2176	4257	6433	SO:0001819	synonymous_variant	8321	exon1			GCAGCAACCGCCG	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"GPCR / Class F : Frizzled receptors"	4038	protein-coding gene	gene with protein product	"Wnt receptor", "frizzled, Drosophila, homolog of, 1"	603408	"frizzled (Drosophila) homolog 1", "frizzled homolog 1 (Drosophila)", "frizzled 1, seven transmembrane spanning receptor", "frizzled family receptor 1"			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.264A>G	chr7.hg19:g.90894459A>G		2.0	0.0		4.0	2.0	NM_003505	A4D1E8|O94815|Q549T8	Silent	SNP	ENST00000287934.2	hg19	CCDS5620.1																																																																																			.	.		0.741	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		G	90894459	A	G	90894459	2	3	49	1	0	0	0	0	0	0	0	1	6136	40	2	2		2	FZD1	7	90894459	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	8504498	90894459	68244204	106	6263										
BUD31	8896	hgsc.bcm.edu	37	chr7	99017026	99017026	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cgttgcagggccgcatcatcGagtgcacacactgtggctgt	13	12	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:99017026G>A	ENST00000403633.2	+	6	926	c.397G>A	c.(397-399)Gag>Aag	p.E133K	PTCD1_ENST00000292478.4_3'UTR|BUD31_ENST00000222969.5_Missense_Mutation_p.E133K|BUD31_ENST00000431419.1_Missense_Mutation_p.E104K|BUD31_ENST00000456893.1_Missense_Mutation_p.E92K			P41223	BUD31_HUMAN	BUD31 homolog (S. cerevisiae)	133					regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	4	all_cancers(62;1.76e-08)|all_epithelial(64;1.63e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CCGCATCATCGAGTGCACACA	0.647																																					p.E133K		Atlas-SNP	.											BUD31,NS,carcinoma,0,1	BUD31	12	.	0			c.G397A						.						138	105	116					7																	99017026		2203	4300	6503	SO:0001583	missense	8896	exon6			ATCATCGAGTGCA	BC022821	CCDS5663.1	7q22.1	2012-06-07	2007-01-12	2006-03-16	ENSG00000106245	ENSG00000106245			29629	protein-coding gene	gene with protein product	"G10 maternal transcript homolog (Xenopus laevis)", "functional spliceosome-associated protein 17"	603477	"BUD31 homolog (yeast)"			7841202	Standard	NM_003910		Approved	YCR063W, EDG-2, EDG2, G10, fSAP17, Cwc14	uc003uqg.4	P41223	OTTHUMG00000154602	ENST00000403633.2:c.397G>A	chr7.hg19:g.99017026G>A	ENSP00000386023:p.Glu133Lys	57.0	0.0		71.0	3.0	NM_003910	A4D274|B7Z4S9|D6W5S6|Q6IB53|Q9UDV1	Missense_Mutation	SNP	ENST00000403633.2	hg19	CCDS5663.1	.	.	.	.	.	.	.	.	.	.	G	36	5.685340	0.96784	.	.	ENSG00000106245	ENST00000403633;ENST00000222969;ENST00000456893;ENST00000431419	.	.	.	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.82962	0.5151	M	0.83852	2.665	0.80722	D	1	D	0.69078	0.997	D	0.68353	0.957	D	0.85445	0.1157	9	0.72032	D	0.01	-24.6234	18.2539	0.90012	0.0:0.0:1.0:0.0	.	133	P41223	BUD31_HUMAN	K	133;133;92;104	.	ENSP00000222969:E133K	E	+	1	0	BUD31	98854962	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.986000	0.93492	2.625000	0.88918	0.655000	0.94253	GAG	.	.		0.647	BUD31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336275.1	NM_003910		A	99017026	G	A	99017026	3	1	49	1	0	0	0	0	1	0	0	0	1576	1059	37	1	411	1	BUD31	7	99017026	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	8122567	99017026	60121637	107	6264										
CNPY4	245812	hgsc.bcm.edu	37	chr7	99722425	99722425	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaggggaggaagagcaggagGaggaggaggaagaggaggaa	23	1	0	2	rs373606882|rs141457365	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:99722425G>C	ENST00000262932.3	+	6	793	c.661G>C	c.(661-663)Gag>Cag	p.E221Q	CNPY4_ENST00000480692.1_3'UTR|MBLAC1_ENST00000398075.2_5'Flank|RP11-506M12.1_ENST00000494221.1_RNA	NM_152755.1	NP_689968.1	Q8N129	CNPY4_HUMAN	canopy FGF signaling regulator 4	221	Glu-rich.					extracellular region (GO:0005576)				breast(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					agagcaggaggaggaggagga	0.502																																					p.E221Q		Atlas-SNP	.											.	CNPY4	18	.	0			c.G661C						.						115	123	120					7																	99722425		2203	4300	6503	SO:0001583	missense	245812	exon6			CAGGAGGAGGAGG	AK075537	CCDS34701.1	7q22.1	2013-07-23	2013-07-23		ENSG00000166997	ENSG00000166997			28631	protein-coding gene	gene with protein product	"protein associated with TLR4"	610047	"canopy 4 homolog (zebrafish)"			12975309	Standard	NM_152755		Approved	MGC40499, PRAT4B	uc003uto.3	Q8N129	OTTHUMG00000154817	ENST00000262932.3:c.661G>C	chr7.hg19:g.99722425G>C	ENSP00000262932:p.Glu221Gln	24.0	0.0		38.0	5.0	NM_152755	Q8WUN9	Missense_Mutation	SNP	ENST00000262932.3	hg19	CCDS34701.1	.	.	.	.	.	.	.	.	.	.	G	5.539	0.284285	0.10513	.	.	ENSG00000166997	ENST00000262932	T	0.32988	1.43	4.51	-0.822	0.10819	.	0.852017	0.10394	N	0.680049	T	0.13457	0.0326	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33701	-0.9858	10	0.19147	T	0.46	.	8.1283	0.31012	0.1925:0.1573:0.6502:0.0	.	221	Q8N129	CNPY4_HUMAN	Q	221	ENSP00000262932:E221Q	ENSP00000262932:E221Q	E	+	1	0	CNPY4	99560361	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-0.091000	0.11146	-0.071000	0.12886	0.561000	0.74099	GAG	.	.		0.502	CNPY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337224.4	NM_152755		C	99722425	G	C	99722425	3	2	49	1	0	0	0	0	1	0	0	0	3632	1175	41	4	683	4	CNPY4	7	99722425	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	705399	99722425	59416238	108	6265										
STAG3	10734	hgsc.bcm.edu	37	chr7	99787154	99787154	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agcgtcagtatgaggctgaaAgaaacaaggggccagggcag	16	7	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:99787154A>G	ENST00000426455.1	+	8	1209	c.802A>G	c.(802-804)Aga>Gga	p.R268G	STAG3_ENST00000317296.5_Missense_Mutation_p.R268G|STAG3_ENST00000394018.2_Missense_Mutation_p.R210G	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	268					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGAGGCTGAAAGAAACAAGGG	0.507																																					p.R268G		Atlas-SNP	.											.	STAG3	121	.	0			c.A802G						.						123	132	129					7																	99787154		2203	4300	6503	SO:0001583	missense	10734	exon8			GCTGAAAGAAACA	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.802A>G	chr7.hg19:g.99787154A>G	ENSP00000400359:p.Arg268Gly	63.0	0.0		96.0	4.0	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	hg19	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	20.2	3.951549	0.73787	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000339784;ENST00000317296	T;T;T	0.47528	0.84;0.84;0.84	5.23	1.09	0.20402	STAG (1);	0.201076	0.24592	N	0.037210	T	0.64450	0.2599	M	0.73598	2.24	0.35792	D	0.822449	D;B	0.67145	0.996;0.153	D;B	0.67900	0.954;0.18	T	0.73232	-0.4048	10	0.87932	D	0	-8.616	13.1012	0.59219	0.5532:0.4468:0.0:0.0	.	210;268	B4DZ10;Q9UJ98	.;STAG3_HUMAN	G	268;210;226;268	ENSP00000400359:R268G;ENSP00000377586:R210G;ENSP00000319318:R268G	ENSP00000319318:R268G	R	+	1	2	STAG3	99625090	0.920000	0.31207	0.996000	0.52242	0.996000	0.88848	0.533000	0.23082	0.017000	0.15025	-0.173000	0.13275	AGA	.	.		0.507	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		G	99787154	A	G	99787154	3	3	49	1	0	0	0	0	1	0	0	0	15259	64	3	2	828	2	STAG3	7	99787154	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	64729	99787154	59351509	109	6266										
LRRC17	10234	hgsc.bcm.edu	37	chr7	102575002	102575002	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tctgaacagttgtgtaatgaAgaagaaaaggaacaattgga	11	3	1	4	rs3832497|rs77576273|rs531650613	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:102575002A>T	ENST00000339431.4	+	2	937	c.642A>T	c.(640-642)gaA>gaT	p.E214D	FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379306.3_Intron|LRRC17_ENST00000249377.4_Missense_Mutation_p.E214D|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000393772.2_Intron	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	214	LRRCT 1.			Missing (in Ref. 2; AAQ89248). {ECO:0000305}.	bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						TGTGTAATGAAGAAGAAAAGG	0.438																																					p.E214D		Atlas-SNP	.											.	LRRC17	45	.	0			c.A642T						.						19	11	14					7																	102575002		1944	3733	5677	SO:0001583	missense	10234	exon2			TAATGAAGAAGAA	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.642A>T	chr7.hg19:g.102575002A>T	ENSP00000344242:p.Glu214Asp	8.0	0.0		25.0	5.0	NM_005824	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	hg19	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.419589	0.25552	.	.	ENSG00000128606	ENST00000339431;ENST00000249377	T;T	0.62639	0.22;0.01	5.28	2.92	0.33932	.	0.000000	0.56097	D	0.000026	T	0.46190	0.1380	L	0.37850	1.14	0.37180	D	0.903456	B;B	0.18013	0.015;0.025	B;B	0.20184	0.012;0.028	T	0.36648	-0.9739	10	0.34782	T	0.22	-31.8822	4.9104	0.13820	0.7178:0.0:0.1465:0.1357	.	214;214	Q8N6Y2;Q8N6Y2-2	LRC17_HUMAN;.	D	214	ENSP00000344242:E214D;ENSP00000249377:E214D	ENSP00000249377:E214D	E	+	3	2	LRRC17	102362238	1.000000	0.71417	0.874000	0.34290	0.990000	0.78478	2.097000	0.41748	0.416000	0.25844	0.460000	0.39030	GAA	.	.		0.438	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824		T	102575002	A	T	102575002	3	4	49	1	0	0	0	0	1	0	0	0	8982	69	3	4	644	4	LRRC17	7	102575002	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	2787848	102575002	56563661	110	6267										
DOCK4	9732	hgsc.bcm.edu	37	chr7	111381259	111381259	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aatatcggttgacagctgggTaacttaacgggctgtttcag	12	7	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:111381259T>C	ENST00000437633.1	-	46	5160	c.4904A>G	c.(4903-4905)tAc>tGc	p.Y1635C	DOCK4_ENST00000428084.1_Missense_Mutation_p.Y1644C|DOCK4_ENST00000494651.2_Missense_Mutation_p.Y518C	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1635					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				GACAGCTGGGTAACTTAACGG	0.423																																					p.Y1635C		Atlas-SNP	.											.	DOCK4	365	.	0			c.A4904G						.						204	201	202					7																	111381259		1862	4108	5970	SO:0001583	missense	9732	exon46			GCTGGGTAACTTA		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.4904A>G	chr7.hg19:g.111381259T>C	ENSP00000404179:p.Tyr1635Cys	71.0	0.0		95.0	4.0	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.73|17.73	3.462103|3.462103	0.63513|0.63513	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000423057;ENST00000445943|ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288	.|T;T;T	.|0.05996	.|4.1;3.36;4.1	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.19046|0.19046	0.0457|0.0457	L|L	0.51422|0.51422	1.61|1.61	0.58432|0.58432	D|D	0.999991|0.999991	.|D;D;D;D;D	.|0.67145	.|0.994;0.994;0.989;0.989;0.996	.|P;P;P;P;D	.|0.66847	.|0.783;0.892;0.887;0.887;0.947	T|T	0.00196|0.00196	-1.1931|-1.1931	5|10	.|0.51188	.|T	.|0.08	.|.	15.5536|15.5536	0.76173|0.76173	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|542;518;1680;1635;1644	.|B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2	.|.;.;.;DOCK4_HUMAN;.	A|C	1096;1668|1623;1644;518;1635;1632	.|ENSP00000410746:Y1644C;ENSP00000440944:Y518C;ENSP00000404179:Y1635C	.|ENSP00000345432:Y1632C	T|Y	-|-	1|2	0|0	DOCK4|DOCK4	111168495|111168495	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.694000|4.694000	0.61760|0.61760	2.260000|2.260000	0.74910|0.74910	0.533000|0.533000	0.62120|0.62120	ACC|TAC	.	.		0.423	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		C	111381259	T	C	111381259	3	2	49	1	0	0	0	0	1	0	0	0	4691	1638	57	2	1024	2	DOCK4	7	111381259	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	8806257	111381259	47757404	111	6268										
METTL2B	55798	hgsc.bcm.edu	37	chr7	128117152	128117152	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcagggacaatgtggagtggTcggaagagcaagccgcggcg	18	8	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:128117152T>C	ENST00000262432.8	+	2	164	c.127T>C	c.(127-129)Tcg>Ccg	p.S43P	RP11-212P7.3_ENST00000462662.1_RNA|METTL2B_ENST00000480046.1_Intron	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	43					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TGTGGAGTGGTCGGAAGAGCA	0.587											OREG0018295	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S43P		Atlas-SNP	.											.	METTL2B	34	.	0			c.T127C						.						37	50	46					7																	128117152		2203	4297	6500	SO:0001583	missense	55798	exon2			GAGTGGTCGGAAG	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"methyltransferase like 2"	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.127T>C	chr7.hg19:g.128117152T>C	ENSP00000262432:p.Ser43Pro	92.0	0.0	1562	116.0	5.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	hg19	CCDS5803.2	.	.	.	.	.	.	.	.	.	.	T	13.27	2.186819	0.38609	.	.	ENSG00000165055	ENST00000262432	D	0.83075	-1.68	2.52	-0.338	0.12651	.	0.171024	0.53938	D	0.000057	T	0.70360	0.3215	L	0.41710	1.295	0.80722	D	1	B	0.15719	0.014	B	0.19946	0.027	T	0.56786	-0.7921	10	0.62326	D	0.03	0.0689	3.0759	0.06246	0.2097:0.1354:0.0:0.6549	.	43	Q6P1Q9	MTL2B_HUMAN	P	43	ENSP00000262432:S43P	ENSP00000262432:S43P	S	+	1	0	METTL2B	127904388	1.000000	0.71417	0.844000	0.33320	0.161000	0.22273	3.519000	0.53458	-0.186000	0.10533	0.163000	0.16589	TCG	.	.		0.587	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396		C	128117152	T	C	128117152	3	2	49	1	0	0	0	0	1	0	0	0	9509	1667	58	2	133	2	METTL2B	7	128117152	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	16735893	128117152	31021511	112	6269										
CUL1	8454	hgsc.bcm.edu	37	chr7	148456419	148456422	+	Frame_Shift_Del	DEL	CTGT	CTGT	-													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcattggtgacttggagagaCtgtctgttcaggccactgaa							TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	CTGT	CTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:148456419_148456422delCTGT	ENST00000325222.4	+	5	786_789	c.507_510delCTGT	c.(505-510)gactgtfs	p.DC169fs	CUL1_ENST00000602748.1_Frame_Shift_Del_p.DC169fs|CUL1_ENST00000409469.1_Frame_Shift_Del_p.DC169fs	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	169					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			CTTGGAGAGACTGTCTGTTCAGGC	0.397																																					p.169_170del		Atlas-Indel,Pindel	.											.	CUL1	80	.	0			c.506_509del						.																																			SO:0001589	frameshift_variant	8454	exon5			.	U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.507_510delCTGT	chr7.hg19:g.148456423_148456426delCTGT	ENSP00000326804:p.Asp169fs	123.0	0.0		180.0	29.0	NM_003592	D3DWG3|O60719|Q08AL6|Q8IYW1	Frame_Shift_Del	DEL	ENST00000325222.4	hg19	CCDS34772.1																																																																																			.	.		0.397	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		-	148456422	CTGT	-	148456419	7	5	49	1	0	1	0	1	0	0	0	0	4056	564	20	0	521	0	CUL1	7	148456419	Frame_Shift_Del	DEL	CTGT	TCGA-BD-A3EP-01A-11D-A22F-10	20339267	148456419	10682244	113	6270										
SCARA5	286133	hgsc.bcm.edu	37	chr8	27779159	27779159	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggcgcaggtcctcggtgaccGcgttgagcatggccagctcc	15	14	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:27779159G>A	ENST00000354914.3	-	4	1330	c.845C>T	c.(844-846)gCg>gTg	p.A282V	SCARA5_ENST00000301906.4_Missense_Mutation_p.A239V|SCARA5_ENST00000518030.1_Missense_Mutation_p.A239V|SCARA5_ENST00000524352.1_Missense_Mutation_p.A282V|SCARA5_ENST00000380385.2_Intron	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	282					cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)			central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		CTCGGTGACCGCGTTGAGCAT	0.677																																					p.A282V		Atlas-SNP	.											SCARA5,NS,lymphoid_neoplasm,0,1	SCARA5	53	.	0			c.C845T						.						73	53	60					8																	27779159		2203	4300	6503	SO:0001583	missense	286133	exon4			GTGACCGCGTTGA	AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"scavenger receptor class A, member 5 (putative)"			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.845C>T	chr8.hg19:g.27779159G>A	ENSP00000346990:p.Ala282Val	45.0	0.0		30.0	3.0	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	hg19	CCDS6064.1	.	.	.	.	.	.	.	.	.	.	G	8.161	0.789615	0.16258	.	.	ENSG00000168079	ENST00000354914;ENST00000517320;ENST00000524352;ENST00000518030;ENST00000301906	D;D;D;D	0.90385	-2.29;-2.66;-2.58;-2.58	4.52	-0.912	0.10504	.	1.061850	0.07302	N	0.874184	T	0.67249	0.2873	N	0.01352	-0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.59974	-0.7353	10	0.10902	T	0.67	.	0.1936	0.00137	0.2933:0.144:0.2588:0.3039	.	282;239;282	Q6ZMJ2-2;Q6ZMJ2-3;Q6ZMJ2	.;.;SCAR5_HUMAN	V	282;82;282;239;239	ENSP00000346990:A282V;ENSP00000428663:A282V;ENSP00000430713:A239V;ENSP00000301906:A239V	ENSP00000301906:A239V	A	-	2	0	SCARA5	27835078	0.003000	0.15002	0.001000	0.08648	0.923000	0.55619	0.950000	0.29122	-0.048000	0.13401	0.456000	0.33151	GCG	.	.		0.677	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833		A	27779159	G	A	27779159	3	1	49	1	0	0	0	0	1	0	0	0	13895	1087	38	1	666	1	SCARA5	8	27779159	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10		27779159	118584863	114	6271										
TEX15	56154	hgsc.bcm.edu	37	chr8	30701385	30701385	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	atcataccaaagcaagcttcGcaatgttggttcaccttcta	6	11	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:30701385G>A	ENST00000256246.2	-	1	5223	c.5149C>T	c.(5149-5151)Cga>Tga	p.R1717*		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1717					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.R1717*(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AGCAAGCTTCGCAATGTTGGT	0.388																																					p.R1717X		Atlas-SNP	.											TEX15,rectum,carcinoma,0,1	TEX15	350	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C5149T						.						142	133	136					8																	30701385		2203	4300	6503	SO:0001587	stop_gained	56154	exon1			AGCTTCGCAATGT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.5149C>T	chr8.hg19:g.30701385G>A	ENSP00000256246:p.Arg1717*	99.0	1.0		91.0	30.0	NM_031271		Nonsense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	G	44	11.233117	0.99534	.	.	ENSG00000133863	ENST00000256246	.	.	.	5.69	4.79	0.61399	.	0.000000	0.48767	D	0.000161	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.4557	0.55702	0.0:0.0:0.6716:0.3283	.	.	.	.	X	1717	.	ENSP00000256246:R1717X	R	-	1	2	TEX15	30820927	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.381000	0.52455	1.323000	0.45263	0.563000	0.77884	CGA	.	.		0.388	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30701385	G	A	30701385	4	1	49	1	0	0	0	0	0	1	0	0	15794	1095	38	1	3236	1	TEX15	8	30701385	Nonsense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	2922226	30701385	115662637	115	6272										
IKBKB	3551	hgsc.bcm.edu	37	chr8	42176090	42176090	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttcaagagcccaagaggaatCtcgccttcttccagctgagg	10	12	3	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:42176090C>G	ENST00000520810.1	+	13	1447	c.1261C>G	c.(1261-1263)Ctc>Gtc	p.L421V	IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000416505.2_Missense_Mutation_p.L362V|IKBKB_ENST00000520835.1_Missense_Mutation_p.L419V|IKBKB_ENST00000379708.3_Missense_Mutation_p.L198V	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	421					B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CAAGAGGAATCTCGCCTTCTT	0.527																																					p.L421V		Atlas-SNP	.											.	IKBKB	88	.	0			c.C1261G						.						87	84	85					8																	42176090		2203	4300	6503	SO:0001583	missense	3551	exon13			AGGAATCTCGCCT	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.1261C>G	chr8.hg19:g.42176090C>G	ENSP00000430684:p.Leu421Val	100.0	0.0		77.0	12.0	NM_001556	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	hg19	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.736000	0.69189	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	D;D;D;T	0.83755	-1.62;-1.76;-1.58;1.89	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.90383	0.6990	M	0.79258	2.445	0.58432	D	0.999999	D;D;D;D;D	0.76494	0.999;0.997;0.997;0.995;0.995	D;D;D;P;D	0.78314	0.991;0.966;0.991;0.831;0.953	D	0.89706	0.3908	10	0.44086	T	0.13	-24.9799	14.2701	0.66147	0.0:0.927:0.0:0.073	.	362;419;198;372;421	B4E0U4;O14920-2;B3KRB7;Q59GL9;O14920	.;.;.;.;IKKB_HUMAN	V	421;362;419;198	ENSP00000430684:L421V;ENSP00000404920:L362V;ENSP00000430868:L419V;ENSP00000369030:L198V	ENSP00000369030:L198V	L	+	1	0	IKBKB	42295247	0.992000	0.36948	0.180000	0.23079	0.606000	0.37113	3.446000	0.52928	2.740000	0.93945	0.555000	0.69702	CTC	.	.		0.527	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			G	42176090	C	G	42176090	3	3	49	1	0	0	0	0	1	0	0	0	7620	913	32	4	1307	4	IKBKB	8	42176090	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	11474705	42176090	104187932	116	6273										
COPS5	10987	hgsc.bcm.edu	37	chr8	67974167	67974167	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agatttcatcgatactctgaGcttcctgcatgttgttggcc	9	10	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:67974167G>A	ENST00000357849.4	-	1	385	c.65C>T	c.(64-66)gCt>gTt	p.A22V	COPS5_ENST00000519963.1_5'UTR|AC109335.1_ENST00000578628.1_RNA|CSPP1_ENST00000412460.1_5'Flank|COPS5_ENST00000517736.1_Intron|CSPP1_ENST00000262210.5_5'Flank	NM_006837.2	NP_006828.2	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5	22					cullin deneddylation (GO:0010388)|exosomal secretion (GO:1990182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein deneddylation (GO:0000338)|protein deubiquitination (GO:0016579)|regulation of cell cycle (GO:0051726)|regulation of JNK cascade (GO:0046328)|transcription from RNA polymerase II promoter (GO:0006366)|translation (GO:0006412)|translational initiation (GO:0006413)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 3 complex (GO:0005852)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|transcription coactivator activity (GO:0003713)|translation initiation factor activity (GO:0003743)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(3)	14	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)			GATACTCTGAGCTTCCTGCAT	0.557																																					p.A22V		Atlas-SNP	.											.	COPS5	29	.	0			c.C65T						.						149	135	139					8																	67974167		2203	4300	6503	SO:0001583	missense	10987	exon1			CTCTGAGCTTCCT	U65928	CCDS6198.1	8q13.1	2013-03-14	2013-03-14		ENSG00000121022	ENSG00000121022			2240	protein-coding gene	gene with protein product		604850	"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 5", "COP9 constitutive photomorphogenic homolog subunit 5 (Arabidopsis)"			8837781, 9341143	Standard	NM_006837		Approved	JAB1, SGN5, MOV-34, CSN5	uc003xxe.3	Q92905	OTTHUMG00000164563	ENST00000357849.4:c.65C>T	chr8.hg19:g.67974167G>A	ENSP00000350512:p.Ala22Val	71.0	0.0		92.0	7.0	NM_006837	O15386|Q6AW95|Q86WQ4|Q9BQ17	Missense_Mutation	SNP	ENST00000357849.4	hg19	CCDS6198.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559240	0.27827	.	.	ENSG00000121022	ENST00000357849	.	.	.	5.68	5.68	0.88126	.	0.102356	0.64402	D	0.000001	T	0.13586	0.0329	N	0.00358	-1.6	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38520	-0.9657	9	0.02654	T	1	-11.8083	12.4651	0.55753	0.0764:0.0:0.9236:0.0	.	22	Q92905	CSN5_HUMAN	V	22	.	ENSP00000350512:A22V	A	-	2	0	COPS5	68136721	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.806000	0.75195	2.838000	0.97847	0.655000	0.94253	GCT	.	.		0.557	COPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379245.2			A	67974167	G	A	67974167	3	1	49	1	0	0	0	0	1	0	0	0	3738	971	34	3	971	3	COPS5	8	67974167	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	25798077	67974167	78389855	117	6274										
PREX2	80243	hgsc.bcm.edu	37	chr8	68972975	68972975	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggcctgaggaaggcgtgcacTtgggacaagcattattagaa	14	7	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:68972975T>C	ENST00000288368.4	+	11	1577	c.1300T>C	c.(1300-1302)Ttg>Ctg	p.L434L	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	434	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AGGCGTGCACTTGGGACAAGC	0.358																																					p.L434L		Atlas-SNP	.											.	PREX2	614	.	0			c.T1300C						.						113	115	114					8																	68972975		2203	4300	6503	SO:0001819	synonymous_variant	80243	exon11			GTGCACTTGGGAC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1300T>C	chr8.hg19:g.68972975T>C		109.0	0.0		97.0	4.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	hg19	CCDS6201.1																																																																																			.	.		0.358	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		C	68972975	T	C	68972975	2	2	49	1	0	0	0	0	0	0	0	1	12489	1606	56	2		2	PREX2	8	68972975	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	998808	68972975	77391047	118	6275										
CRISPLD1	83690	hgsc.bcm.edu	37	chr8	75927121	75927121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cccacctagttttggaggggGctgtagagaaaatctgtgct	13	8	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:75927121G>A	ENST00000262207.4	+	6	1169	c.701G>A	c.(700-702)gGc>gAc	p.G234D	CRISPLD1_ENST00000523524.1_Missense_Mutation_p.G46D|CRISPLD1_ENST00000517786.1_Missense_Mutation_p.G48D	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	234					face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			TTTGGAGGGGGCTGTAGAGAA	0.428																																					p.G234D		Atlas-SNP	.											.	CRISPLD1	94	.	0			c.G701A						.						57	52	53					8																	75927121		2203	4300	6503	SO:0001583	missense	83690	exon6			GAGGGGGCTGTAG	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.701G>A	chr8.hg19:g.75927121G>A	ENSP00000262207:p.Gly234Asp	141.0	0.0		143.0	31.0	NM_031461	B2RA60|B7Z929	Missense_Mutation	SNP	ENST00000262207.4	hg19	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.381005	0.82792	.	.	ENSG00000121005	ENST00000262207;ENST00000523524;ENST00000517786	T;T;D	0.82711	0.27;-1.23;-1.64	4.69	4.69	0.59074	.	0.112857	0.64402	D	0.000010	D	0.82346	0.5017	M	0.67397	2.05	0.53005	D	0.999963	P;P	0.52577	0.954;0.514	B;B	0.41412	0.356;0.159	D	0.84987	0.0892	10	0.49607	T	0.09	.	17.8197	0.88647	0.0:0.0:1.0:0.0	.	48;234	B7Z929;Q9H336	.;CRLD1_HUMAN	D	234;46;48	ENSP00000262207:G234D;ENSP00000430105:G46D;ENSP00000429746:G48D	ENSP00000262207:G234D	G	+	2	0	CRISPLD1	76089676	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.604000	0.82830	2.429000	0.82318	0.460000	0.39030	GGC	.	.		0.428	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		A	75927121	G	A	75927121	3	1	49	1	0	0	0	0	1	0	0	0	3884	1203	42	3	719	3	CRISPLD1	8	75927121	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	6954146	75927121	70436901	119	6276										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77762578	77762578	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	acctgcagccgtgacagctgAggggtctgggaaatattcag	14	9	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:77762578A>G	ENST00000521891.2	+	9	4392	c.3944A>G	c.(3943-3945)gAg>gGg	p.E1315G	ZFHX4_ENST00000518282.1_Missense_Mutation_p.E1289G|ZFHX4_ENST00000455469.2_Missense_Mutation_p.E1270G|ZFHX4_ENST00000050961.6_Missense_Mutation_p.E1270G	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GTGACAGCTGAGGGGTCTGGG	0.493										HNSCC(33;0.089)																											p.E1315G		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A3944G						.						48	52	50					8																	77762578		1921	4133	6054	SO:0001583	missense	79776	exon9			CAGCTGAGGGGTC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.3944A>G	chr8.hg19:g.77762578A>G	ENSP00000430497:p.Glu1315Gly	78.0	0.0		92.0	5.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	9.876	1.200222	0.22121	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.54675	0.56;0.62;0.59;0.57	5.17	3.99	0.46301	.	0.196425	0.24750	U	0.035906	T	0.45438	0.1342	L	0.47716	1.5	0.48830	D	0.99971	B;B;B	0.13594	0.005;0.008;0.008	B;B;B	0.18561	0.01;0.022;0.022	T	0.30563	-0.9974	10	0.31617	T	0.26	.	12.4307	0.55573	0.8601:0.1399:0.0:0.0	.	1270;1270;1315	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	G	1315;1315;1270;1270;1289	ENSP00000430497:E1315G;ENSP00000399605:E1270G;ENSP00000050961:E1270G;ENSP00000430848:E1289G	ENSP00000050961:E1270G	E	+	2	0	ZFHX4	77925133	1.000000	0.71417	0.340000	0.25575	0.517000	0.34286	5.421000	0.66447	0.953000	0.37825	0.459000	0.35465	GAG	.	.		0.493	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		G	77762578	A	G	77762578	3	3	49	1	0	0	0	0	1	0	0	0	17650	304	11	2	3974	2	ZFHX4	8	77762578	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	1835457	77762578	68601444	120	6277										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100829851	100829851	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gttcagcattacattggtcaAgatggacaagctgtagttcg	11	7	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:100829851A>C	ENST00000358544.2	+	45	8367	c.8256A>C	c.(8254-8256)caA>caC	p.Q2752H	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.Q2727H	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2752					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ACATTGGTCAAGATGGACAAG	0.398																																					p.Q2752H	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A8256C						.						110	104	106					8																	100829851		2203	4300	6503	SO:0001583	missense	157680	exon45			TGGTCAAGATGGA	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.8256A>C	chr8.hg19:g.100829851A>C	ENSP00000351346:p.Gln2752His	147.0	0.0		232.0	49.0	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.237867	0.39598	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.70045	-0.45;-0.45	5.61	-1.03	0.10102	.	0.398694	0.25759	N	0.028484	T	0.36386	0.0965	N	0.08118	0	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.003	T	0.03818	-1.1001	10	0.48119	T	0.1	.	2.745	0.05264	0.5313:0.1103:0.2513:0.1071	.	2727;2752	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	H	2727;2752	ENSP00000349685:Q2727H;ENSP00000351346:Q2752H	ENSP00000349685:Q2727H	Q	+	3	2	VPS13B	100899027	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	0.661000	0.25023	0.143000	0.18926	0.533000	0.62120	CAA	.	.		0.398	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		C	100829851	A	C	100829851	3	2	49	1	0	0	0	0	1	0	0	0	17205	69	3	5	8624	5	VPS13B	8	100829851	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	23067273	100829851	45534171	121	6278										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124382155	124382155	+	Missense_Mutation	SNP	A	A	T													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccatcttcttcatcttcatcAtcttcatcatcatcatcatc					rs373904648		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:124382155A>T	ENST00000287394.5	-	7	944	c.837T>A	c.(835-837)gaT>gaA	p.D279E	ATAD2_ENST00000534257.1_5'Flank|ATAD2_ENST00000521903.1_5'UTR	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	279	Asp-rich.				ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			catcttcatcatcttcatcat	0.373																																					p.D279E		Atlas-SNP	.											.	ATAD2	160	.	0			c.T837A						.						270	209	230					8																	124382155		2203	4300	6503	SO:0001583	missense	29028	exon7			TTCATCATCTTCA	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.837T>A	chr8.hg19:g.124382155A>T	ENSP00000287394:p.Asp279Glu	135.0	0.0		210.0	20.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	A	0.804	-0.754275	0.03041	.	.	ENSG00000156802	ENST00000287394	T	0.15718	2.4	3.43	-6.86	0.01676	.	1.759450	0.01899	N	0.039043	T	0.08358	0.0208	L	0.27053	0.805	0.58432	D	0.999999	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.0	T	0.45702	-0.9243	10	0.02654	T	1	-1.7868	4.1656	0.10305	0.2875:0.0:0.1907:0.5219	.	109;279	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	E	279	ENSP00000287394:D279E	ENSP00000287394:D279E	D	-	3	2	ATAD2	124451336	0.679000	0.27596	0.008000	0.14137	0.002000	0.02628	-0.320000	0.08028	-2.138000	0.00808	-1.800000	0.00619	GAT	.	.		0.373	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		T	124382155	A	T	124382155	3	4	49	1	0	0	0	0	1	0	0	0	1071	214	8	4	3423	4	ATAD2	8	124382155	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	23552304	124382155	21981867	122	6279	26	2								
ATAD2	29028	hgsc.bcm.edu	37	chr8	124382158	124382158	+	Missense_Mutation	SNP	T	T	A													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcttcttcatcttcatcatcTtcatcatcatcatcatcatc					rs373904648|rs374184884|rs145137934|rs112640031|rs371096883|rs373069275|rs113064839	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:124382158T>A	ENST00000287394.5	-	7	941	c.834A>T	c.(832-834)gaA>gaT	p.E278D	ATAD2_ENST00000534257.1_5'Flank|ATAD2_ENST00000521903.1_De_novo_Start_OutOfFrame	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	278	Asp-rich.				ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			cttcatcatcttcatcatcat	0.378																																					p.E278D		Atlas-SNP	.											.	ATAD2	160	.	0			c.A834T						.						260	205	224					8																	124382158		2203	4300	6503	SO:0001583	missense	29028	exon7			ATCATCTTCATCA	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.834A>T	chr8.hg19:g.124382158T>A	ENSP00000287394:p.Glu278Asp	133.0	0.0		204.0	19.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	t	0.007	-1.995361	0.00435	.	.	ENSG00000156802	ENST00000287394	T	0.05786	3.39	3.43	-2.99	0.05497	.	1.396170	0.03921	N	0.283542	T	0.02929	0.0087	N	0.03608	-0.345	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.0	T	0.49133	-0.8971	10	0.10902	T	0.67	-2.6732	9.3965	0.38406	0.5472:0.0:0.0:0.4528	.	108;278	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	D	278	ENSP00000287394:E278D	ENSP00000287394:E278D	E	-	3	2	ATAD2	124451339	0.007000	0.16637	0.018000	0.16275	0.001000	0.01503	-1.836000	0.01690	-0.689000	0.05149	-4.187000	0.00009	GAA	.	.		0.378	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		A	124382158	T	A	124382158	3	1	49	1	0	0	0	0	1	0	0	0	1071	1606	56	4	3426	4	ATAD2	8	124382158	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	3	124382158	21981864	123	6280	26	2								
ANXA13	312	hgsc.bcm.edu	37	chr8	124705521	124705521	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aacgcaagctcatcagtgccCcagcggccttcccctgcctc	8	19	2	0	rs146521013		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:124705521C>T	ENST00000419625.1	-	8	630	c.558G>A	c.(556-558)tgG>tgA	p.W186*	ANXA13_ENST00000262219.6_Nonsense_Mutation_p.W227*	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	186					cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			CATCAGTGCCCCAGCGGCCTT	0.463																																					p.W227X		Atlas-SNP	.											.	ANXA13	38	.	0			c.G681A						.						142	143	142					8																	124705521		2203	4300	6503	SO:0001587	stop_gained	312	exon9			AGTGCCCCAGCGG	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"Annexins"	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.558G>A	chr8.hg19:g.124705521C>T	ENSP00000390809:p.Trp186*	90.0	0.0		166.0	9.0	NM_001003954	Q9BQR5	Nonsense_Mutation	SNP	ENST00000419625.1	hg19	CCDS47917.1	.	.	.	.	.	.	.	.	.	.	C	36	5.644737	0.96704	.	.	ENSG00000104537	ENST00000262219;ENST00000419625	.	.	.	5.41	5.41	0.78517	.	0.314542	0.39909	N	0.001227	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.3145	0.90215	0.0:1.0:0.0:0.0	.	.	.	.	X	227;186	.	ENSP00000262219:W227X	W	-	3	0	ANXA13	124774702	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.234000	0.43035	2.701000	0.92244	0.650000	0.86243	TGG	.	C|1.000;A|0.000		0.463	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306		T	124705521	C	T	124705521	4	4	49	1	0	0	0	0	0	1	0	0	717	624	22	3	408	3	ANXA13	8	124705521	Nonsense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	323363	124705521	21658501	124	6281										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144940354	144940354	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	taggccacgtccacgggcacGcggtggctgtgcacggggtc	17	13	0	0	rs375604799		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:144940354G>A	ENST00000525985.1	-	2	7139	c.7068C>T	c.(7066-7068)cgC>cgT	p.R2356R				P58107	EPIPL_HUMAN	epiplakin 1	2356						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCACGGGCACGCGGTGGCTGT	0.692																																					p.R2356R		Atlas-SNP	.											.	EPPK1	199	.	0			c.C7068T						.	G		2,4332		0,2,2165	195	189	191		7068	1.3	1	8		191	0,8472		0,0,4236	no	coding-synonymous	EPPK1	NM_031308.1		0,2,6401	AA,AG,GG		0.0,0.0461,0.0156		2356/2420	144940354	2,12804	2167	4236	6403	SO:0001819	synonymous_variant	83481	exon1			GGGCACGCGGTGG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.7068C>T	chr8.hg19:g.144940354G>A		23.0	0.0		22.0	10.0	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	hg19																																																																																				.	.		0.692	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144940354	G	A	144940354	2	1	49	1	0	0	0	0	0	0	0	1	5192	1074	38	1		1	EPPK1	8	144940354	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	20234833	144940354	1423668	125	6282										
OPLAH	26873	hgsc.bcm.edu	37	chr8	145112137	145112137	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	atgtgcaccgtgtccatgccCagggcccgggcgatggcaca	14	14	0	0	rs546232581		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:145112137C>T	ENST00000426825.1	-	11	1590	c.1509G>A	c.(1507-1509)ctG>ctA	p.L503L	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	503					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGTCCATGCCCAGGGCCCGGG	0.657																																					p.L503L		Atlas-SNP	.											.	OPLAH	78	.	0			c.G1509A						.						20	25	23					8																	145112137		2128	4227	6355	SO:0001819	synonymous_variant	26873	exon11			CATGCCCAGGGCC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.1509G>A	chr8.hg19:g.145112137C>T		77.0	0.0		43.0	9.0	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Silent	SNP	ENST00000426825.1	hg19																																																																																				.	.		0.657	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		T	145112137	C	T	145112137	2	4	49	1	0	0	0	0	0	0	0	1	10885	581	21	3		3	OPLAH	8	145112137	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	171783	145112137	1251885	126	6283										
OPLAH	26873	hgsc.bcm.edu	37	chr8	145112386	145112386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gatgggccggcacatggcctCgttggccacgcgcacgaacc	14	15	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:145112386C>T	ENST00000426825.1	-	10	1468	c.1387G>A	c.(1387-1389)Gag>Aag	p.E463K	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	463					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CACATGGCCTCGTTGGCCACG	0.701																																					p.E463K		Atlas-SNP	.											OPLAH,NS,carcinoma,0,1	OPLAH	78	.	0			c.G1387A						.						13	17	16					8																	145112386		2080	4210	6290	SO:0001583	missense	26873	exon10			TGGCCTCGTTGGC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.1387G>A	chr8.hg19:g.145112386C>T	ENSP00000475943:p.Glu463Lys	62.0	0.0		14.0	2.0	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.51	2.556270	0.45487	.	.	ENSG00000178814	ENST00000426825	.	.	.	4.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.78528	0.4297	.	.	.	0.50813	D	0.999898	D	0.89917	1.0	D	0.97110	1.0	D	0.84723	0.0741	7	0.87932	D	0	.	14.2922	0.66286	0.0:1.0:0.0:0.0	.	463	O14841	OPLA_HUMAN	K	463	.	ENSP00000412071:E463K	E	-	1	0	OPLAH	145184374	1.000000	0.71417	0.998000	0.56505	0.913000	0.54294	7.100000	0.76989	2.025000	0.59659	0.467000	0.42956	GAG	.	.		0.701	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		T	145112386	C	T	145112386	3	4	49	1	0	0	0	0	1	0	0	0	10885	893	31	1	2553	1	OPLAH	8	145112386	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	249	145112386	1251636	127	6284										
CPSF1	29894	hgsc.bcm.edu	37	chr8	145634528	145634528	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtgggcggatgcgcctgtttGtacacggcgtacatggcgcc	16	11	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:145634528G>T	ENST00000349769.3	-	2	109	c.15C>A	c.(13-15)taC>taA	p.Y5*	GS1-393G12.14_ENST00000607491.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	5					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			GCGCCTGTTTGTACACGGCGT	0.677																																					p.Y5X	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.C15A						.						91	84	86					8																	145634528		2203	4300	6503	SO:0001587	stop_gained	29894	exon2			CTGTTTGTACACG	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.15C>A	chr8.hg19:g.145634528G>T	ENSP00000339353:p.Tyr5*	42.0	0.0		30.0	8.0	NM_013291	Q96AF0	Nonsense_Mutation	SNP	ENST00000349769.3	hg19	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	G	38	6.704147	0.97776	.	.	ENSG00000071894	ENST00000349769;ENST00000531042	.	.	.	5.14	3.3	0.37823	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.0503	8.4787	0.33030	0.0846:0.0:0.7636:0.1518	.	.	.	.	X	5	.	ENSP00000339353:Y5X	Y	-	3	2	CPSF1	145605336	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.793000	0.69060	1.162000	0.42619	0.556000	0.70494	TAC	.	.		0.677	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		T	145634528	G	T	145634528	4	4	49	1	0	0	0	0	0	1	0	0	3826	1372	48	3	4464	3	CPSF1	8	145634528	Nonsense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	522142	145634528	729494	128	6285										
TEK	7010	hgsc.bcm.edu	37	chr9	27190548	27190548	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcttccaaagcccctgaatgCcccaaacgtgattgacactg	7	14	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:27190548C>G	ENST00000380036.4	+	10	1791	c.1349C>G	c.(1348-1350)gCc>gGc	p.A450G	TEK_ENST00000406359.4_Missense_Mutation_p.A407G|TEK_ENST00000519097.1_Missense_Mutation_p.A303G	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	450	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CCCCTGAATGCCCCAAACGTG	0.418																																					p.A450G		Atlas-SNP	.											.	TEK	250	.	0			c.C1349G						.						186	179	182					9																	27190548		2203	4300	6503	SO:0001583	missense	7010	exon10			TGAATGCCCCAAA	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.1349C>G	chr9.hg19:g.27190548C>G	ENSP00000369375:p.Ala450Gly	184.0	0.0		183.0	17.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490725	0.64074	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000346448;ENST00000406359;ENST00000519080	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	5.55	5.55	0.83447	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.43919	U	0.000513	T	0.69043	0.3067	L	0.53249	1.67	0.46149	D	0.998891	P;P;D;P	0.69078	0.611;0.866;0.997;0.801	B;P;D;B	0.80764	0.253;0.61;0.994;0.334	T	0.69109	-0.5232	10	0.54805	T	0.06	.	17.6716	0.88220	0.0:1.0:0.0:0.0	.	303;483;407;450	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	G	303;450;407;407;260	ENSP00000430686:A303G;ENSP00000369375:A450G;ENSP00000383977:A407G;ENSP00000428337:A260G	ENSP00000343716:A407G	A	+	2	0	TEK	27180548	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.702000	0.61817	2.610000	0.88304	0.591000	0.81541	GCC	.	.		0.418	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			G	27190548	C	G	27190548	3	3	49	1	0	0	0	0	1	0	0	0	15766	739	26	4	1387	4	TEK	9	27190548	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10		27190548	114022883	129	6286										
NAA35	60560	hgsc.bcm.edu	37	chr9	88631506	88631506	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgtcaacattgagtcgtgccGatggctctcaaatggcagag	12	9	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:88631506G>A	ENST00000361671.5	+	18	1754	c.1621G>A	c.(1621-1623)Gat>Aat	p.D541N		NM_024635.3	NP_078911.3	Q5VZE5	NAA35_HUMAN	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	541					negative regulation of apoptotic process (GO:0043066)|smooth muscle cell proliferation (GO:0048659)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	25						GAGTCGTGCCGATGGCTCTCA	0.378																																					p.D541N		Atlas-SNP	.											.	NAA35	50	.	0			c.G1621A						.						102	96	98					9																	88631506		2203	4300	6503	SO:0001583	missense	60560	exon18			CGTGCCGATGGCT	AK025266	CCDS6673.1	9q22.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000135040	ENSG00000135040		"N(alpha)-acetyltransferase subunits"	24340	protein-coding gene	gene with protein product			"MAK10 homolog, amino-acid N-acetyltransferase subunit (S. cerevisiae)"	MAK10		14702039, 19660095	Standard	NM_024635		Approved	FLJ21613, FLJ22643, bA379P1.1	uc004aoi.4	Q5VZE5	OTTHUMG00000020131	ENST00000361671.5:c.1621G>A	chr9.hg19:g.88631506G>A	ENSP00000354972:p.Asp541Asn	81.0	0.0		69.0	4.0	NM_024635	Q5VZE6|Q9H631|Q9H703	Missense_Mutation	SNP	ENST00000361671.5	hg19	CCDS6673.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055047	0.75960	.	.	ENSG00000135040	ENST00000361671	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.44117	0.1278	L	0.34521	1.04	0.80722	D	1	P	0.37398	0.593	B	0.26202	0.067	T	0.37478	-0.9704	9	0.19590	T	0.45	-14.8571	19.169	0.93569	0.0:0.0:1.0:0.0	.	541	Q5VZE5	NAA35_HUMAN	N	541	.	ENSP00000354972:D541N	D	+	1	0	NAA35	87821326	1.000000	0.71417	0.990000	0.47175	0.880000	0.50808	9.544000	0.98092	2.527000	0.85204	0.491000	0.48974	GAT	.	.		0.378	NAA35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052906.1	NM_024635		A	88631506	G	A	88631506	3	1	49	1	0	0	0	0	1	0	0	0	10132	1058	37	1	1687	1	NAA35	9	88631506	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	61440958	88631506	52581925	130	6287										
FGD3	89846	hgsc.bcm.edu	37	chr9	95768397	95768397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcaagaactttgaccgagccGtagggctggtgagcacgtgg	15	9	1	3	rs371917520		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:95768397G>A	ENST00000375482.3	+	6	1268	c.772G>A	c.(772-774)Gta>Ata	p.V258I	FGD3_ENST00000337352.6_Missense_Mutation_p.V258I|FGD3_ENST00000416701.2_Missense_Mutation_p.V258I	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	258	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.V258I(2)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						TGACCGAGCCGTAGGGCTGGT	0.582																																					p.V258I		Atlas-SNP	.											FGD3_ENST00000375482,colon,carcinoma,0,4	FGD3	116	.	2	Substitution - Missense(2)	endometrium(2)	c.G772A						.	G	ILE/VAL,ILE/VAL	0,4332		0,0,2166	64	70	68		772,772	-6.4	0	9		68	1,8571		0,1,4285	no	missense,missense	FGD3	NM_033086.2,NM_001083536.1	29,29	0,1,6451	AA,AG,GG		0.0117,0.0,0.0077	benign,benign	258/726,258/726	95768397	1,12903	2166	4286	6452	SO:0001583	missense	89846	exon6			CGAGCCGTAGGGC	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16027	protein-coding gene	gene with protein product			"FGD1 family, member 3"			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.772G>A	chr9.hg19:g.95768397G>A	ENSP00000364631:p.Val258Ile	45.0	0.0		50.0	2.0	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Missense_Mutation	SNP	ENST00000375482.3	hg19	CCDS43849.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.758422	0.49468	0.0	1.17E-4	ENSG00000127084	ENST00000375482;ENST00000416701;ENST00000337352	T;T;T	0.62941	-0.01;-0.01;-0.01	4.54	-6.4	0.01944	Dbl homology (DH) domain (5);	0.689202	0.12020	N	0.507040	T	0.38799	0.1054	N	0.11651	0.15	0.80722	D	1	B;P;B	0.45240	0.194;0.854;0.381	B;B;B	0.40256	0.146;0.324;0.163	T	0.44097	-0.9350	10	0.30854	T	0.27	.	16.6006	0.84815	0.8497:0.0:0.1503:0.0	.	258;258;258	Q5JSP0-2;F8W7P2;Q5JSP0	.;.;FGD3_HUMAN	I	258	ENSP00000364631:V258I;ENSP00000413833:V258I;ENSP00000336914:V258I	ENSP00000336914:V258I	V	+	1	0	FGD3	94808218	0.316000	0.24580	0.005000	0.12908	0.975000	0.68041	1.023000	0.30065	-1.330000	0.02255	0.655000	0.94253	GTA	.	.		0.582	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086		A	95768397	G	A	95768397	3	1	49	1	0	0	0	0	1	0	0	0	5842	1145	40	1	786	1	FGD3	9	95768397	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	7136891	95768397	45445034	131	6288										
WNK2	65268	hgsc.bcm.edu	37	chr9	96021717	96021717	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgcccccgcaacccacgctgCcccctcaacctgtgttgccc	7	22	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:96021717C>A	ENST00000297954.4	+	11	2887	c.2887C>A	c.(2887-2889)Ccc>Acc	p.P963T	WNK2_ENST00000395477.2_Missense_Mutation_p.P963T|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.P575T|WNK2_ENST00000349097.3_Missense_Mutation_p.P575T	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	963					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						ACCCACGCTGCCCCCTCAACC	0.692																																					p.P963T		Atlas-SNP	.											.	WNK2	277	.	0			c.C2887A						.						45	42	43					9																	96021717		2177	4250	6427	SO:0001583	missense	65268	exon11			ACGCTGCCCCCTC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.2887C>A	chr9.hg19:g.96021717C>A	ENSP00000297954:p.Pro963Thr	31.0	0.0		21.0	4.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	c|c|c	1.974|1.974|1.974	-0.435765|-0.435765|-0.435765	0.04636|0.04636|0.04636	.|.|.	.|.|.	ENSG00000165238|ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730|ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277	.|.|T;T;T;T	.|.|0.70045	.|.|-0.45;-0.4;0.12;0.12	1.82|1.82|1.82	-1.72|-1.72|-1.72	0.08107|0.08107|0.08107	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|.|T	0.34745|.|0.34745	0.0908|.|0.0908	N|N|N	0.08118|0.08118|0.08118	0|0|0	0.09310|0.09310|0.09310	N|N|N	0.999991|0.999991|0.999991	.|.|B;B;B;B;B	.|.|0.24317	.|.|0.101;0.038;0.061;0.101;0.061	.|.|B;B;B;B;B	.|.|0.12837	.|.|0.008;0.008;0.006;0.008;0.006	T|.|T	0.17623|.|0.17623	-1.0363|.|-1.0363	5|.|8	.|.|.	.|.|.	.|.|.	.|.|.	1.4464|1.4464|1.4464	0.02365|0.02365|0.02365	0.3453:0.3433:0.0:0.3115|0.3453:0.3433:0.0:0.3115|0.3453:0.3433:0.0:0.3115	.|.|.	.|.|963;963;566;963;963	.|.|Q9Y3S1-2;Q9Y3S1-4;A6PVR4;F8W9F9;Q9Y3S1	.|.|.;.;.;.;WNK2_HUMAN	D|X|T	566|958|963;963;575;575	.|.|ENSP00000297954:P963T;ENSP00000378860:P963T;ENSP00000297876:P575T;ENSP00000411181:P575T	.|.|.	A|C|P	+|+|+	2|3|1	0|2|0	WNK2|WNK2|WNK2	95061538|95061538|95061538	0.023000|0.023000|0.023000	0.18921|0.18921|0.18921	0.038000|0.038000|0.038000	0.18304|0.18304|0.18304	0.040000|0.040000|0.040000	0.13550|0.13550|0.13550	1.441000|1.441000|1.441000	0.35035|0.35035|0.35035	0.478000|0.478000|0.478000	0.27488|0.27488|0.27488	0.482000|0.482000|0.482000	0.46254|0.46254|0.46254	GCC|TGC|CCC	.	.		0.692	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		A	96021717	C	A	96021717	3	1	49	1	0	0	0	0	1	0	0	0	17393	739	26	3	2929	3	WNK2	9	96021717	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	253320	96021717	45191714	132	6289										
ZNF618	114991	hgsc.bcm.edu	37	chr9	116812389	116812389	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcttctaatcaaacggaggcGgctgctcagtccagaagata	11	10	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:116812389G>A	ENST00000374126.5	+	15	2906	c.2807G>A	c.(2806-2808)cGg>cAg	p.R936Q	ZNF618_ENST00000288466.7_Missense_Mutation_p.R843Q|ZNF618_ENST00000470105.1_3'UTR			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	936					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R843Q(1)|p.R936Q(1)		breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						AAACGGAGGCGGCTGCTCAGT	0.483																																					p.R843Q		Atlas-SNP	.											ZNF618_ENST00000374126,NS,NS,0,2	ZNF618	184	.	2	Substitution - Missense(2)	NS(2)	c.G2528A						.						71	78	76					9																	116812389		1865	4103	5968	SO:0001583	missense	114991	exon14			GGAGGCGGCTGCT	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"Zinc fingers, C2H2-type"	29416	protein-coding gene	gene with protein product	"neural precursor cell expressed, developmentally down-regulated 10"					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.2807G>A	chr9.hg19:g.116812389G>A	ENSP00000363241:p.Arg936Gln	39.0	0.0		36.0	2.0	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Missense_Mutation	SNP	ENST00000374126.5	hg19		.	.	.	.	.	.	.	.	.	.	G	12.95	2.090912	0.36855	.	.	ENSG00000157657	ENST00000374126;ENST00000288466	T;T	0.21543	2.0;2.0	5.93	5.93	0.95920	Ribonuclease H-like (1);	0.063525	0.64402	D	0.000005	T	0.40670	0.1126	.	.	.	0.53005	D	0.999963	D;P;B	0.71674	0.998;0.499;0.144	D;B;B	0.66602	0.945;0.013;0.013	T	0.01819	-1.1267	9	0.17832	T	0.49	-3.1706	19.3319	0.94293	0.0:0.0:1.0:0.0	.	903;936;843	B9EG82;Q5T7W0;Q5T7W0-2	.;ZN618_HUMAN;.	Q	936;843	ENSP00000363241:R936Q;ENSP00000288466:R843Q	ENSP00000288466:R843Q	R	+	2	0	ZNF618	115852210	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	5.957000	0.70323	2.815000	0.96918	0.561000	0.74099	CGG	.	.		0.483	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983		A	116812389	G	A	116812389	3	1	49	1	0	0	0	0	1	0	0	0	18057	1116	39	1	2582	1	ZNF618	9	116812389	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	20790672	116812389	24401042	133	6290										
COL27A1	85301	hgsc.bcm.edu	37	chr9	117068878	117068878	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tacactacctcagcaacctcAtccagagcattaagacgccc	5	16	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:117068878A>G	ENST00000356083.3	+	58	5408	c.5017A>G	c.(5017-5019)Atc>Gtc	p.I1673V		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1673	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						CAGCAACCTCATCCAGAGCAT	0.567											OREG0019417	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I1673V		Atlas-SNP	.											COL27A1,colon,carcinoma,0,1	COL27A1	200	.	0			c.A5017G						.						76	77	77					9																	117068878		2203	4300	6503	SO:0001583	missense	85301	exon58			AACCTCATCCAGA	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.5017A>G	chr9.hg19:g.117068878A>G	ENSP00000348385:p.Ile1673Val	56.0	0.0	1478	50.0	2.0	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.749458	0.49257	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.90900	-2.75	5.2	4.06	0.47325	Fibrillar collagen, C-terminal (2);	.	.	.	.	D	0.85881	0.5800	L	0.56340	1.77	0.52501	D	0.999953	B	0.32781	0.384	B	0.33196	0.159	T	0.78602	-0.2140	9	0.16896	T	0.51	.	8.8977	0.35474	0.91:0.0:0.09:0.0	.	1673	Q8IZC6	CORA1_HUMAN	V	1673;1680	ENSP00000348385:I1673V	ENSP00000348385:I1673V	I	+	1	0	COL27A1	116108699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.131000	0.77243	0.807000	0.34208	0.460000	0.39030	ATC	.	.		0.567	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		G	117068878	A	G	117068878	3	3	49	1	0	0	0	0	1	0	0	0	3687	217	8	2	5247	2	COL27A1	9	117068878	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	256489	117068878	24144553	134	6291										
TNC	3371	hgsc.bcm.edu	37	chr9	117848274	117848274	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctgtgaagccctcgtggcagAtgcactggccgtccacgcag	13	14	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:117848274A>G	ENST00000350763.4	-	3	2147	c.1736T>C	c.(1735-1737)aTc>aCc	p.I579T	TNC_ENST00000423613.2_Missense_Mutation_p.I579T|TNC_ENST00000346706.3_Missense_Mutation_p.I579T|TNC_ENST00000542877.1_Missense_Mutation_p.I579T|TNC_ENST00000535648.1_Missense_Mutation_p.I579T|TNC_ENST00000537320.1_Missense_Mutation_p.I579T|TNC_ENST00000345230.3_Missense_Mutation_p.I579T|TNC_ENST00000341037.4_Missense_Mutation_p.I579T|TNC_ENST00000340094.3_Missense_Mutation_p.I579T	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	579	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CTCGTGGCAGATGCACTGGCC	0.597																																					p.I579T		Atlas-SNP	.											.	TNC	282	.	0			c.T1736C						.						85	61	69					9																	117848274		2203	4300	6503	SO:0001583	missense	3371	exon3			TGGCAGATGCACT		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.1736T>C	chr9.hg19:g.117848274A>G	ENSP00000265131:p.Ile579Thr	77.0	0.0		110.0	6.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	A	10.82	1.457564	0.26161	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.03607	3.87;3.87;3.87;3.87;3.87;3.87;3.87;3.87;3.87	5.95	3.61	0.41365	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.879489	0.10084	N	0.717986	T	0.04634	0.0126	L	0.39020	1.185	0.29269	N	0.870809	B;B	0.13594	0.008;0.0	B;B	0.10450	0.005;0.001	T	0.27640	-1.0068	10	0.48119	T	0.1	.	10.3075	0.43689	0.8667:0.0:0.1333:0.0	.	579;579	E9PC84;P24821	.;TENA_HUMAN	T	579	ENSP00000344400:I579T;ENSP00000438152:I579T;ENSP00000344555:I579T;ENSP00000345861:I579T;ENSP00000265131:I579T;ENSP00000339553:I579T;ENSP00000411406:I579T;ENSP00000443478:I579T;ENSP00000442242:I579T	ENSP00000344400:I579T	I	-	2	0	TNC	116888095	0.987000	0.35691	0.582000	0.28627	0.715000	0.41141	4.481000	0.60250	0.501000	0.28013	0.460000	0.39030	ATC	.	.		0.597	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		G	117848274	A	G	117848274	3	3	49	1	0	0	0	0	1	0	0	0	16285	333	12	2	4973	2	TNC	9	117848274	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	779396	117848274	23365157	135	6292										
ODF2	4957	hgsc.bcm.edu	37	chr9	131256869	131256872	+	Frame_Shift_Del	DEL	TGAG	TGAG	-													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	atcacggaggcgaagctggcTgagtgccaagaccaactgca							TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	TGAG	TGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:131256869_131256872delTGAG	ENST00000434106.3	+	17	2196_2199	c.1833_1836delTGAG	c.(1831-1836)gctgagfs	p.AE611fs	ODF2_ENST00000546203.1_Frame_Shift_Del_p.AE592fs|ODF2_ENST00000372791.3_Frame_Shift_Del_p.AE592fs|ODF2_ENST00000444119.2_Frame_Shift_Del_p.AE587fs|ODF2_ENST00000604420.1_Frame_Shift_Del_p.AE611fs|ODF2_ENST00000393533.2_Frame_Shift_Del_p.AE611fs|ODF2_ENST00000351030.3_Frame_Shift_Del_p.AE606fs|ODF2_ENST00000448249.3_Frame_Shift_Del_p.AE530fs|ODF2_ENST00000393527.3_Frame_Shift_Del_p.AE587fs|ODF2_ENST00000372814.3_Frame_Shift_Del_p.AE655fs|ODF2_ENST00000372807.5_Frame_Shift_Del_p.AE606fs	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	611					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)	p.E588G(1)|p.E656G(1)|p.E612G(1)		autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						CGAAGCTGGCTGAGTGCCAAGACC	0.578																																					p.675_676del		Atlas-Indel,Pindel	.											ODF2_ENST00000372814,NS,carcinoma,0,3	ODF2	227	.	3	Substitution - Missense(3)	kidney(3)	c.2024_2027del						.																																			SO:0001589	frameshift_variant	4957	exon17			.	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"cancer/testis antigen 134"	602015	"outer dense fibre of sperm tails 2"			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1833_1836delTGAG	chr9.hg19:g.131256869_131256872delTGAG	ENSP00000403453:p.Ala611fs	63.0	0.0		102.0	22.0	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Frame_Shift_Del	DEL	ENST00000434106.3	hg19	CCDS56588.1																																																																																			.	.		0.578	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			-	131256872	TGAG	-	131256869	7	5	49	1	0	1	0	1	0	0	0	0	10836	1567	55	0	1950	0	ODF2	9	131256869	Frame_Shift_Del	DEL	TGAG	TCGA-BD-A3EP-01A-11D-A22F-10	13408595	131256869	9956562	136	6293										
SETX	23064	hgsc.bcm.edu	37	chr9	135204112	135204112	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	atttgtgaaggtctctgtctAtctgagaatccgttaaggtg	11	6	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:135204112A>G	ENST00000224140.5	-	10	3055	c.2873T>C	c.(2872-2874)aTa>aCa	p.I958T	SETX_ENST00000372169.2_Missense_Mutation_p.I958T|SETX_ENST00000393220.1_Missense_Mutation_p.I958T	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	958					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GTCTCTGTCTATCTGAGAATC	0.423																																					p.I958T		Atlas-SNP	.											.	SETX	234	.	0			c.T2873C						.						99	95	96					9																	135204112		2203	4300	6503	SO:0001583	missense	23064	exon10			CTGTCTATCTGAG	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.2873T>C	chr9.hg19:g.135204112A>G	ENSP00000224140:p.Ile958Thr	173.0	0.0		206.0	29.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.997014	0.54147	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.87887	-2.21;-2.31;-1.92	5.63	5.63	0.86233	.	7739.210000	0.00166	N	0.000000	D	0.84683	0.5526	N	0.24115	0.695	0.33344	D	0.570162	B;B;B	0.30361	0.277;0.181;0.277	B;B;B	0.30495	0.116;0.054;0.116	T	0.68659	-0.5350	10	0.87932	D	0	.	15.329	0.74190	1.0:0.0:0.0:0.0	.	958;958;958	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	T	958	ENSP00000224140:I958T;ENSP00000361242:I958T;ENSP00000376913:I958T	ENSP00000224140:I958T	I	-	2	0	SETX	134193933	0.844000	0.29557	0.974000	0.42286	0.954000	0.61252	3.164000	0.50770	2.281000	0.76405	0.533000	0.62120	ATA	.	.		0.423	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		G	135204112	A	G	135204112	3	3	49	1	0	0	0	0	1	0	0	0	14156	449	16	2	5228	2	SETX	9	135204112	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	3947243	135204112	6009319	137	6294										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137593180	137593180	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tggatgaggaggtgtttgagGtgagcaggagggcagaccaa	19	4	0	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:137593180G>A	ENST00000371817.3	+	4	1068		c.e4+1		COL5A1_ENST00000464187.1_Splice_Site	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1						axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GGTGTTTGAGGTGAGCAGGAG	0.617																																					.		Atlas-SNP	.											.	COL5A1	323	.	0			c.654+1G>A						.						112	89	96					9																	137593180		2202	4298	6500	SO:0001630	splice_region_variant	1289	exon4			TTTGAGGTGAGCA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.654+1G>A	chr9.hg19:g.137593180G>A		68.0	0.0		91.0	4.0	NM_000093	Q15094|Q5SUX4	Splice_Site	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149789	0.78001	.	.	ENSG00000130635	ENST00000371817	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5036	0.90890	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL5A1	136733001	1.000000	0.71417	0.994000	0.49952	0.754000	0.42855	9.489000	0.97949	2.428000	0.82296	0.491000	0.48974	.	.	.		0.617	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Intron	A	137593180	G	A	137593180	5	1	49	1	0	0	0	0	0	0	1	0	3698	1275	44	3	669	3	COL5A1	9	137593180	Splice_Site	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	2389068	137593180	3620251	138	6295										
GPSM1	26086	hgsc.bcm.edu	37	chr9	139250948	139250948	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcagggcacctccgaggccaCggcgagccccaggagccggg	17	16	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:139250948C>T	ENST00000440944.1	+	13	1987	c.1767C>T	c.(1765-1767)caC>caT	p.H589H	GPSM1_ENST00000392944.1_Silent_p.H80H|GPSM1_ENST00000429455.1_Silent_p.H80H	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	589					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)	p.H566H(1)		biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		TCCGAGGCCACGGCGAGCCCC	0.711																																					p.H589H		Atlas-SNP	.											GPSM1,NS,carcinoma,0,1	GPSM1	50	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1767T						.						24	32	29					9																	139250948		2199	4298	6497	SO:0001819	synonymous_variant	26086	exon13			AGGCCACGGCGAG	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"Tetratricopeptide (TTC) repeat domain containing"	17858	protein-coding gene	gene with protein product	"AGS3 homolog (C. elegans)"	609491	"G-protein signalling modulator 1 (AGS3-like, C. elegans)"			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1767C>T	chr9.hg19:g.139250948C>T		44.0	1.0		16.0	3.0	NM_001145638	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Silent	SNP	ENST00000440944.1	hg19	CCDS48055.1																																																																																			.	.		0.711	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		T	139250948	C	T	139250948	2	4	49	1	0	0	0	0	0	0	0	1	6743	535	19	1		1	GPSM1	9	139250948	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1657768	139250948	1962483	139	6296										
CARD9	64170	hgsc.bcm.edu	37	chr9	139265325	139265325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtcacggttccgcatgagcgCggcgcccttctcctcactct	10	17	4	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:139265325C>T	ENST00000371732.5	-	4	760	c.595G>A	c.(595-597)Gcg>Acg	p.A199T	CARD9_ENST00000315908.7_Missense_Mutation_p.A199T|CARD9_ENST00000371734.3_Missense_Mutation_p.A199T	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	199					defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		CGCATGAGCGCGGCGCCCTTC	0.726																																					p.A199T		Atlas-SNP	.											CARD9,colon,carcinoma,0,1	CARD9	47	.	0			c.G595A						.						23	25	24					9																	139265325		2196	4296	6492	SO:0001583	missense	64170	exon4			TGAGCGCGGCGCC	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.595G>A	chr9.hg19:g.139265325C>T	ENSP00000360797:p.Ala199Thr	56.0	0.0		28.0	3.0	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Missense_Mutation	SNP	ENST00000371732.5	hg19	CCDS6997.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.992165	0.93167	.	.	ENSG00000187796	ENST00000371734;ENST00000371732;ENST00000315908	T;T;T	0.37584	1.19;1.19;1.19	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.61073	0.2318	M	0.76574	2.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.996;0.996	T	0.63804	-0.6554	10	0.49607	T	0.09	-34.6344	16.9898	0.86350	0.0:1.0:0.0:0.0	.	95;199;199;199	B4DIK5;Q9H257-2;Q5SXM5;Q9H257	.;.;.;CARD9_HUMAN	T	199	ENSP00000360799:A199T;ENSP00000360797:A199T;ENSP00000323719:A199T	ENSP00000323719:A199T	A	-	1	0	CARD9	138385146	1.000000	0.71417	0.494000	0.27515	0.743000	0.42351	4.453000	0.60061	2.251000	0.74343	0.563000	0.77884	GCG	.	.		0.726	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813		T	139265325	C	T	139265325	3	4	49	1	0	0	0	0	1	0	0	0	2654	768	27	1	1108	1	CARD9	9	139265325	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	14377	139265325	1948106	140	6297										
PITRM1	10531	hgsc.bcm.edu	37	chr10	3208566	3208567	+	Missense_Mutation	DNP	CT	CT	TG													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tccatgggagtagtacggaaCtgcacgctagggaaggagaa					rs28416720|rs33996077|rs4266975|rs148472807|rs114690446	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:3208566_3208567CT>TG	ENST00000224949.4	-	4	306_307	c.272_273AG>CA	c.(271-273)cAG>cCA	p.Q91P	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000451104.2_Missense_Mutation_p.Q59P|PITRM1_ENST00000380989.2_Missense_Mutation_p.Q91P|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	91					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TAGTACGGAACTGCACGCTAGG	0.49																																					p.Q91Q|p.Q91P		Atlas-SNP	.											PITRM1,colon,carcinoma,-1,3|PITRM1,colon,carcinoma,0,3	PITRM1	109	.	0			c.G273A|c.A272C						.																																			SO:0001583	missense	10531	exon4			ACGGAACTGCACG|CGGAACTGCACGC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.272_273delinsTG	chr10.hg19:g.3208566_3208567delinsTG	ENSP00000224949:p.Gln91Pro	14.0|13.0	0.0		31.0|30.0	9.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent|Missense_Mutation	SNP	ENST00000224949.4	hg19	CCDS59208.1																																																																																			.	.		0.49	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			TG	3208567	CT	TG	3208566	3	4	49	1	0	0	0	0	1	0	0	0	11962	564	20	3	2936	3	PITRM1	10	3208566	Missense_Mutation	DNP	CT	TCGA-BD-A3EP-01A-11D-A22F-10		3208566	132326181	141	6298										
MSRB2	22921	hgsc.bcm.edu	37	chr10	23393130	23393130	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgagtggcaaaagaaactaaCcccggagcagttctacgtca	10	10	2	2	rs201493683		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:23393130C>G	ENST00000376510.3	+	2	279	c.176C>G	c.(175-177)aCc>aGc	p.T59S		NM_012228.3	NP_036360.3	Q9Y3D2	MSRB2_HUMAN	methionine sulfoxide reductase B2	59					actin filament polymerization (GO:0030041)|protein repair (GO:0030091)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)	actin binding (GO:0003779)|peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	9					L-Methionine(DB00134)	AAGAAACTAACCCCGGAGCAG	0.443																																					p.T59S	Esophageal Squamous(89;1240 1363 4973 30188 42299)	Atlas-SNP	.											.	MSRB2	21	.	0			c.C176G						.						83	81	82					10																	23393130		1908	4129	6037	SO:0001583	missense	22921	exon2			AACTAACCCCGGA	AF122004	CCDS41495.1	10p12	2004-12-07	2004-12-06	2004-12-07	ENSG00000148450	ENSG00000148450			17061	protein-coding gene	gene with protein product		613782	"methionine sulfoxide reductase B"	MSRB		8749308, 10375640	Standard	NM_012228		Approved	PILB, CGI-131, CBS1, CBS-1	uc001iro.3	Q9Y3D2	OTTHUMG00000017812	ENST00000376510.3:c.176C>G	chr10.hg19:g.23393130C>G	ENSP00000365693:p.Thr59Ser	101.0	0.0		117.0	25.0	NM_012228	Q17R44|Q4G1C7|Q9Y5W6	Missense_Mutation	SNP	ENST00000376510.3	hg19	CCDS41495.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.097652	0.56075	.	.	ENSG00000148450	ENST00000376510	T	0.78003	-1.14	4.79	3.88	0.44766	Mss4-like (1);Methionine sulphoxide reductase B (3);	0.053873	0.64402	D	0.000001	T	0.69450	0.3112	L	0.33710	1.025	0.36486	D	0.868135	B	0.25235	0.121	B	0.34590	0.186	T	0.71567	-0.4554	10	0.51188	T	0.08	-1.569	9.252	0.37560	0.0:0.897:0.0:0.103	.	59	Q9Y3D2	MSRB2_HUMAN	S	59	ENSP00000365693:T59S	ENSP00000365693:T59S	T	+	2	0	MSRB2	23433136	0.993000	0.37304	0.997000	0.53966	0.869000	0.49853	2.713000	0.47194	1.325000	0.45301	0.557000	0.71058	ACC	.	C|0.999;T|0.001		0.443	MSRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047205.1	NM_012228		G	23393130	C	G	23393130	3	3	49	1	0	0	0	0	1	0	0	0	9897	507	18	4	182	4	MSRB2	10	23393130	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	20184564	23393130	112141617	142	6299										
CBARA1	10367	hgsc.bcm.edu	37	chr10	74293540	74293540	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tttattatatattgatccagAcccaagtctgtaaaagaaaa	5	6	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:74293540A>G	ENST00000361114.5	-	5	597	c.501T>C	c.(499-501)ggT>ggC	p.G167G	MICU1_ENST00000398761.4_Silent_p.G167G|MICU1_ENST00000401998.3_Silent_p.G167G	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	167					calcium ion import (GO:0070509)|calcium ion transmembrane import into mitochondrion (GO:0036444)|defense response (GO:0006952)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein homooligomerization (GO:0051260)	calcium channel complex (GO:0034704)|integral component of mitochondrial membrane (GO:0032592)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										ATTGATCCAGACCCAAGTCTG	0.303																																					p.G167G		Atlas-SNP	.											.	.	.	.	0			c.T501C						.						62	61	61					10																	74293540		1800	4063	5863	SO:0001819	synonymous_variant	10367	exon5			ATCCAGACCCAAG	Y17711	CCDS55714.1, CCDS55715.1	10q22.1	2013-01-10	2011-06-23	2011-06-23	ENSG00000107745	ENSG00000107745		"EF-hand domain containing"	1530	protein-coding gene	gene with protein product		605084	"calcium binding atopy-related autoantigen 1"	CBARA1		9806765, 20693986	Standard	NM_006077		Approved	CALC, EFHA3, FLJ12684	uc001jtb.2	Q9BPX6	OTTHUMG00000018437	ENST00000361114.5:c.501T>C	chr10.hg19:g.74293540A>G		45.0	0.0		54.0	4.0	NM_001195518	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Silent	SNP	ENST00000361114.5	hg19	CCDS55715.1																																																																																			.	.		0.303	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077		G	74293540	A	G	74293540	2	3	49	1	0	0	0	0	0	0	0	1	2698	262	10	2		2	CBARA1	10	74293540	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	50900410	74293540	61241207	143	6300										
MYST4	23522	hgsc.bcm.edu	37	chr10	76781899	76781899	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gaagaggatgaagaggaggaAgaagaggaagaagaagaaga	18	0	0	9			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:76781899A>G	ENST00000287239.4	+	16	3771	c.3282A>G	c.(3280-3282)gaA>gaG	p.E1094E	KAT6B_ENST00000490365.1_3'UTR|RP11-77G23.5_ENST00000436608.1_RNA|KAT6B_ENST00000372714.1_Silent_p.E802E|KAT6B_ENST00000372711.1_Silent_p.E911E|KAT6B_ENST00000372724.1_Silent_p.E802E|KAT6B_ENST00000372725.1_Silent_p.E802E|RP11-77G23.2_ENST00000413431.1_RNA	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1094	Poly-Glu.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										aagaggaggaagaagaggaag	0.463											OREG0020273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E1094E		Atlas-SNP	.											.	.	.	.	0			c.A3282G						.						42	38	39					10																	76781899		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon16			GGAGGAAGAAGAG	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.3282A>G	chr10.hg19:g.76781899A>G		90.0	0.0	1170	108.0	14.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.463	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		G	76781899	A	G	76781899	2	3	49	1	0	0	0	0	0	0	0	1	10114	69	3	2		2	MYST4	10	76781899	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	2488359	76781899	58752848	144	6301										
PLAC9	219348	hgsc.bcm.edu	37	chr10	81901931	81901931	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	acgccgtctagatgtcatggAggaggtaacagggtggtttg	16	6	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:81901931A>G	ENST00000372263.3	+	2	200	c.158A>G	c.(157-159)gAg>gGg	p.E53G	PLAC9_ENST00000372267.2_Missense_Mutation_p.E53G|PLAC9_ENST00000372270.2_Missense_Mutation_p.E11G	NM_001012973.1	NP_001012991.1	Q5JTB6	PLAC9_HUMAN	placenta-specific 9	53						extracellular region (GO:0005576)				kidney(1)|ovary(1)	2	Prostate(51;0.0095)|all_epithelial(25;0.175)		Colorectal(32;0.109)			GATGTCATGGAGGAGGTAACA	0.552																																					p.E53G		Atlas-SNP	.											.	PLAC9	9	.	0			c.A158G						.						135	93	107					10																	81901931		2203	4300	6503	SO:0001583	missense	219348	exon2			TCATGGAGGAGGT		CCDS31232.1	10q23.2	2008-02-04			ENSG00000189129	ENSG00000189129			19255	protein-coding gene	gene with protein product		612857					Standard	NM_001012973		Approved		uc001kbp.1	Q5JTB6	OTTHUMG00000018596	ENST00000372263.3:c.158A>G	chr10.hg19:g.81901931A>G	ENSP00000361337:p.Glu53Gly	40.0	0.0		52.0	4.0	NM_001012973		Missense_Mutation	SNP	ENST00000372263.3	hg19	CCDS31232.1	.	.	.	.	.	.	.	.	.	.	A	10.39	1.336328	0.24253	.	.	ENSG00000189129	ENST00000372270;ENST00000372267;ENST00000372263	.	.	.	3.74	2.62	0.31277	.	0.179151	0.26935	N	0.021756	T	0.40423	0.1116	.	.	.	0.35800	D	0.823069	B	0.23058	0.079	B	0.21546	0.035	T	0.47100	-0.9143	8	0.87932	D	0	.	5.6218	0.17461	0.877:0.0:0.123:0.0	.	53	Q5JTB6	PLAC9_HUMAN	G	11;53;53	.	ENSP00000361337:E53G	E	+	2	0	PLAC9	81891911	1.000000	0.71417	0.759000	0.31340	0.440000	0.31957	1.994000	0.40757	0.817000	0.34445	0.439000	0.28862	GAG	.	.		0.552	PLAC9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049019.1	NM_001012973		G	81901931	A	G	81901931	3	3	49	1	0	0	0	0	1	0	0	0	12026	304	11	2	164	2	PLAC9	10	81901931	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	5120032	81901931	53632816	145	6302										
LDB3	11155	hgsc.bcm.edu	37	chr10	88466389	88466389	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgcctctcccagtgcggcttCgccacccctggccacagctg	10	19	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:88466389C>T	ENST00000361373.4	+	7	1019	c.998C>T	c.(997-999)tCg>tTg	p.S333L	LDB3_ENST00000429277.2_Intron|LDB3_ENST00000352360.5_Intron|LDB3_ENST00000458213.2_Intron|LDB3_ENST00000263066.6_Intron	NM_007078.2	NP_009009.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						AGTGCGGCTTCGCCACCCCTG	0.687																																					p.S333L		Atlas-SNP	.											LDB3,right_upper_lobe,carcinoma,-1,1	LDB3	164	.	0			c.C998T						.						51	50	50					10																	88466389		2203	4299	6502	SO:0001583	missense	11155	exon7			CGGCTTCGCCACC	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"cypher", "oracle", "Z-band alternatively spliced PDZ motif protein"	605906	"cardiomyopathy, dilated 1C (autosomal dominant)"	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.998C>T	chr10.hg19:g.88466389C>T	ENSP00000355296:p.Ser333Leu	82.0	0.0		27.0	3.0	NM_007078		Missense_Mutation	SNP	ENST00000361373.4	hg19	CCDS7377.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.256973	0.39896	.	.	ENSG00000122367	ENST00000361373	T	0.53423	0.62	5.52	3.03	0.35002	.	0.331826	0.17113	N	0.186533	T	0.30759	0.0775	N	0.25647	0.755	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.08764	-1.0706	10	0.28530	T	0.3	.	7.6515	0.28350	0.0:0.7206:0.17:0.1094	.	333	O75112	LDB3_HUMAN	L	333	ENSP00000355296:S333L	ENSP00000355296:S333L	S	+	2	0	LDB3	88456369	0.997000	0.39634	1.000000	0.80357	0.844000	0.47949	1.197000	0.32211	1.368000	0.46115	0.655000	0.94253	TCG	.	.		0.687	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2			T	88466389	C	T	88466389	3	4	49	1	0	0	0	0	1	0	0	0	8706	893	31	1	1360	1	LDB3	10	88466389	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	6564458	88466389	47068358	146	6303										
C10orf12	26148	hgsc.bcm.edu	37	chr10	98742889	98742889	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaagccaagtgtcaatgaacGcccctctgagaaagatgctg	10	10	2	3	rs141178994		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:98742889G>A	ENST00000286067.2	+	1	1849	c.1742G>A	c.(1741-1743)cGc>cAc	p.R581H		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	581								p.R581H(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		GTCAATGAACGCCCCTCTGAG	0.522																																					p.R581H		Atlas-SNP	.											C10orf12,colon,carcinoma,0,1	C10orf12	94	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1742A						.	G	HIS/ARG	0,4406		0,0,2203	48	55	53		1742	-3.3	0	10	dbSNP_134	53	1,8599	1.2+/-3.3	0,1,4299	no	missense	C10orf12	NM_015652.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	581/1248	98742889	1,13005	2203	4300	6503	SO:0001583	missense	26148	exon1			ATGAACGCCCCTC	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.1742G>A	chr10.hg19:g.98742889G>A	ENSP00000286067:p.Arg581His	83.0	1.0		71.0	4.0	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	hg19	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	G	0.082	-1.182323	0.01633	0.0	1.16E-4	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.06528	3.29	4.94	-3.26	0.05064	.	1.241240	0.05944	N	0.637619	T	0.02888	0.0086	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46679	-0.9174	10	0.35671	T	0.21	0.7721	10.8904	0.46992	0.4179:0.0:0.5821:0.0	.	581	Q8N655	CJ012_HUMAN	H	581;415	ENSP00000286067:R581H	ENSP00000286067:R581H	R	+	2	0	C10orf12	98732879	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.007000	0.13174	-0.439000	0.07222	-1.267000	0.01435	CGC	.	G|1.000;A|0.000		0.522	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		A	98742889	G	A	98742889	3	1	49	1	0	0	0	0	1	0	0	0	1591	1087	38	1	1744	1	C10orf12	10	98742889	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	10276500	98742889	36791858	147	6304										
LOXL4	84171	hgsc.bcm.edu	37	chr10	100013493	100013493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aatacagctggctgagcgggCggtcctccaagtaggccgtc	14	12	0	1	rs375427147		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:100013493C>T	ENST00000260702.3	-	11	1802	c.1652G>A	c.(1651-1653)cGc>cAc	p.R551H	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	551	Lysyl-oxidase like.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		GCTGAGCGGGCGGTCCTCCAA	0.627																																					p.R551H		Atlas-SNP	.											.	LOXL4	60	.	0			c.G1652A						.	C	HIS/ARG	0,4406		0,0,2203	76	73	74		1652	4.9	1	10		74	1,8599	1.2+/-3.3	0,1,4299	no	missense	LOXL4	NM_032211.6	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	551/757	100013493	1,13005	2203	4300	6503	SO:0001583	missense	84171	exon11			AGCGGGCGGTCCT	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.1652G>A	chr10.hg19:g.100013493C>T	ENSP00000260702:p.Arg551His	39.0	0.0		37.0	5.0	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Missense_Mutation	SNP	ENST00000260702.3	hg19	CCDS7473.1	.	.	.	.	.	.	.	.	.	.	C	34	5.348214	0.95807	0.0	1.16E-4	ENSG00000138131	ENST00000260702	T	0.32753	1.44	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.64670	0.2619	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73401	-0.3994	10	0.66056	D	0.02	.	16.9772	0.86316	0.0:1.0:0.0:0.0	.	551	Q96JB6	LOXL4_HUMAN	H	551	ENSP00000260702:R551H	ENSP00000260702:R551H	R	-	2	0	LOXL4	100003483	1.000000	0.71417	0.999000	0.59377	0.935000	0.57460	7.651000	0.83577	2.536000	0.85505	0.491000	0.48974	CGC	.	.		0.627	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211		T	100013493	C	T	100013493	3	4	49	1	0	0	0	0	1	0	0	0	8911	768	27	1	638	1	LOXL4	10	100013493	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1270604	100013493	35521254	148	6305										
HPS1	3257	hgsc.bcm.edu	37	chr10	100179909	100179909	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcgcgccagctggatcagagAccagacctggggaaaagaca	14	11	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:100179909A>G	ENST00000325103.6	-	18	1983	c.1750T>C	c.(1750-1752)Tct>Cct	p.S584P	HPS1_ENST00000361490.4_Missense_Mutation_p.S584P|HPS1_ENST00000467246.1_5'UTR	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	584					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		TGGATCAGAGACCAGACCTGG	0.582									Hermansky-Pudlak syndrome																												p.S584P		Atlas-SNP	.											.	HPS1	65	.	0			c.T1750C						.						134	116	122					10																	100179909		2203	4300	6503	SO:0001583	missense	3257	exon18	Familial Cancer Database	HPS, HPS1-8	TCAGAGACCAGAC	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"Hermansky-Pudlak syndrome"	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.1750T>C	chr10.hg19:g.100179909A>G	ENSP00000326649:p.Ser584Pro	69.0	0.0		75.0	4.0	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Missense_Mutation	SNP	ENST00000325103.6	hg19	CCDS7475.1	.	.	.	.	.	.	.	.	.	.	A	19.52	3.843616	0.71488	.	.	ENSG00000107521	ENST00000325103;ENST00000361490;ENST00000407891	T;T	0.47528	0.84;0.84	5.45	0.523	0.17060	.	0.576373	0.19226	N	0.119539	T	0.61274	0.2334	M	0.79475	2.455	0.80722	D	1	D;D;D	0.53312	0.959;0.959;0.959	P;P;P	0.54100	0.742;0.742;0.742	T	0.69752	-0.5060	10	0.62326	D	0.03	.	16.0411	0.80683	0.4704:0.5296:0.0:0.0	.	551;584;585	Q92902-2;Q8WXE5;D3DR62	.;.;.	P	584;584;551	ENSP00000326649:S584P;ENSP00000355310:S584P	ENSP00000326649:S584P	S	-	1	0	HPS1	100169899	0.995000	0.38212	1.000000	0.80357	0.929000	0.56500	0.362000	0.20284	0.082000	0.17018	0.459000	0.35465	TCT	.	.		0.582	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639		G	100179909	A	G	100179909	3	3	49	1	0	0	0	0	1	0	0	0	7348	275	10	2	364	2	HPS1	10	100179909	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	166416	100179909	35354838	149	6306										
GBF1	8729	hgsc.bcm.edu	37	chr10	104118303	104118303	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtgcccactcccatctcctcTgcaagttcagaagctgcctc	7	17	3	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:104118303T>C	ENST00000369983.3	+	10	1088	c.828T>C	c.(826-828)tcT>tcC	p.S276S		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	276					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCATCTCCTCTGCAAGTTCAG	0.512																																					p.S276S		Atlas-SNP	.											.	GBF1	142	.	0			c.T828C						.						118	110	113					10																	104118303		2203	4300	6503	SO:0001819	synonymous_variant	8729	exon10			CTCCTCTGCAAGT	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.828T>C	chr10.hg19:g.104118303T>C		74.0	0.0		74.0	4.0	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Silent	SNP	ENST00000369983.3	hg19	CCDS7533.1																																																																																			.	.		0.512	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			C	104118303	T	C	104118303	2	2	49	1	0	0	0	0	0	0	0	1	6279	1567	55	2		2	GBF1	10	104118303	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	3938394	104118303	31416444	150	6307										
GBF1	8729	hgsc.bcm.edu	37	chr10	104125298	104125298	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	accctcggctggacaagaagAtgattggagagtttgtgagt	14	6	0	5			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:104125298A>G	ENST00000369983.3	+	18	2508	c.2248A>G	c.(2248-2250)Atg>Gtg	p.M750V		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	750	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GGACAAGAAGATGATTGGAGA	0.498																																					p.M751V		Atlas-SNP	.											.	GBF1	142	.	0			c.A2251G						.						115	111	112					10																	104125298		2203	4300	6503	SO:0001583	missense	8729	exon18			AAGAAGATGATTG	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.2248A>G	chr10.hg19:g.104125298A>G	ENSP00000359000:p.Met750Val	131.0	0.0		117.0	6.0	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.892879	0.91889	.	.	ENSG00000107862	ENST00000369983	T	0.53206	0.63	5.79	5.79	0.91817	SEC7-like (4);	0.000000	0.85682	D	0.000000	T	0.59783	0.2219	L	0.45581	1.43	0.80722	D	1	D;D;P	0.67145	0.996;0.991;0.906	P;D;P	0.63033	0.904;0.91;0.626	T	0.56643	-0.7945	10	0.35671	T	0.21	-19.3013	16.1303	0.81428	1.0:0.0:0.0:0.0	.	750;750;750	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	V	750	ENSP00000359000:M750V	ENSP00000359000:M750V	M	+	1	0	GBF1	104115288	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.094000	0.94168	2.218000	0.71995	0.533000	0.62120	ATG	.	.		0.498	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			G	104125298	A	G	104125298	3	3	49	1	0	0	0	0	1	0	0	0	6279	333	12	2	2314	2	GBF1	10	104125298	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	6995	104125298	31409449	151	6308										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105202983	105202983	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	acctggagaacatgtacggcTctcaggagtccctgaccaag	11	12	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:105202983T>C	ENST00000369797.3	+	33	5111	c.5017T>C	c.(5017-5019)Tct>Cct	p.S1673P		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1673					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CATGTACGGCTCTCAGGAGTC	0.552																																					p.S1673P		Atlas-SNP	.											.	PDCD11	160	.	0			c.T5017C						.						94	80	85					10																	105202983		2203	4300	6503	SO:0001583	missense	22984	exon33			TACGGCTCTCAGG	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5017T>C	chr10.hg19:g.105202983T>C	ENSP00000358812:p.Ser1673Pro	63.0	0.0		92.0	4.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	hg19	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	T	19.40	3.819707	0.71028	.	.	ENSG00000148843	ENST00000369797	T	0.36520	1.25	5.51	4.33	0.51752	Tetratricopeptide-like helical (1);	0.101091	0.64402	D	0.000003	T	0.34745	0.0908	L	0.33245	0.995	0.39191	D	0.962966	D	0.56968	0.978	P	0.50192	0.634	T	0.28267	-1.0049	10	0.72032	D	0.01	-11.5805	10.0005	0.41927	0.3219:0.0:0.0:0.6781	.	1673	Q14690	RRP5_HUMAN	P	1673	ENSP00000358812:S1673P	ENSP00000358812:S1673P	S	+	1	0	PDCD11	105192973	1.000000	0.71417	0.993000	0.49108	0.837000	0.47467	3.161000	0.50747	2.088000	0.63022	0.454000	0.30748	TCT	.	.		0.552	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			C	105202983	T	C	105202983	3	2	49	1	0	0	0	0	1	0	0	0	11626	1551	54	2	5143	2	PDCD11	10	105202983	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	1077685	105202983	30331764	152	6309										
CALHM2	51063	hgsc.bcm.edu	37	chr10	105209279	105209279	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgctcttccctggccgtgagTgaggaagggtccacgaactc	13	12	1	2	rs201668640		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:105209279T>C	ENST00000260743.5	-	3	943	c.420A>G	c.(418-420)tcA>tcG	p.S140S	CALHM2_ENST00000369788.3_Silent_p.S140S|CALHM2_ENST00000494180.1_5'Flank|CALHM2_ENST00000393235.1_Silent_p.S140S|RP11-225H22.7_ENST00000608063.1_RNA	NM_015916.4	NP_057000.2	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	140					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|skin(1)	11						TGGCCGTGAGTGAGGAAGGGT	0.607																																					p.S140S		Atlas-SNP	.											.	CALHM2	30	.	0			c.A420G						.						78	68	71					10																	105209279		2203	4300	6503	SO:0001819	synonymous_variant	51063	exon3			CGTGAGTGAGGAA	BC000039	CCDS7549.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000138172	ENSG00000138172			23493	protein-coding gene	gene with protein product		612235	"family with sequence similarity 26, member B"	FAM26B		18585350	Standard	NM_015916		Approved		uc001kxa.3	Q9HA72	OTTHUMG00000018990	ENST00000260743.5:c.420A>G	chr10.hg19:g.105209279T>C		60.0	0.0		55.0	4.0	NM_015916	D3DR94|O95893|Q6ZUV9	Silent	SNP	ENST00000260743.5	hg19	CCDS7549.1																																																																																			.	T|0.999;C|0.001		0.607	CALHM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050159.1	NM_015916		C	105209279	T	C	105209279	2	2	49	1	0	0	0	0	0	0	0	1	2585	1683	59	2		2	CALHM2	10	105209279	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	6296	105209279	30325468	153	6310										
PDCD4	27250	hgsc.bcm.edu	37	chr10	112641040	112641040	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tccggtgatgaagaaaatgcTgggactgaggaaataaagaa	13	4	0	5			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:112641040T>C	ENST00000280154.7	+	3	367	c.93T>C	c.(91-93)gcT>gcC	p.A31A	PDCD4_ENST00000393104.2_Silent_p.A20A	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	31					apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		AAGAAAATGCTGGGACTGAGG	0.338																																					p.A31A	Ovarian(115;1498 1603 9363 40056 40885)	Atlas-SNP	.											.	PDCD4	39	.	0			c.T93C						.						82	92	88					10																	112641040		2203	4300	6503	SO:0001819	synonymous_variant	27250	exon3			AAATGCTGGGACT	U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"nuclear antigen H731"	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.93T>C	chr10.hg19:g.112641040T>C		92.0	0.0		91.0	4.0	NM_014456	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Silent	SNP	ENST00000280154.7	hg19	CCDS7567.1																																																																																			.	.		0.338	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456		C	112641040	T	C	112641040	2	2	49	1	0	0	0	0	0	0	0	1	11630	1567	55	2		2	PDCD4	10	112641040	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	7431761	112641040	22893707	154	6311										
NHLRC2	374354	hgsc.bcm.edu	37	chr10	115644138	115644138	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gatgtagtttttggaacatcAggtatgtgaacttttgatat	10	3	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:115644138A>G	ENST00000369301.3	+	5	1250	c.1038A>G	c.(1036-1038)tcA>tcG	p.S346S		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	346										breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		TTGGAACATCAGGTATGTGAA	0.338																																					p.S346S		Atlas-SNP	.											.	NHLRC2	56	.	0			c.A1038G						.						108	100	103					10																	115644138		2203	4300	6503	SO:0001630	splice_region_variant	374354	exon5			AACATCAGGTATG	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.1039+1A>G	chr10.hg19:g.115644138A>G		90.0	0.0		87.0	4.0	NM_198514	Q8N1H1|Q8N5A6	Silent	SNP	ENST00000369301.3	hg19	CCDS7585.1																																																																																			.	.		0.338	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514	Silent	G	115644138	A	G	115644138	5	3	49	1	0	0	0	0	0	0	1	0	10415	202	7	2	1056	2	NHLRC2	10	115644138	Splice_Site	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	3003098	115644138	19890609	155	6312										
DOCK1	1793	hgsc.bcm.edu	37	chr10	129172467	129172467	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaaaccgcatgagctgcaccGtcaatgtgctggtgagtgaa	12	9	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:129172467G>A	ENST00000280333.6	+	35	3710	c.3601G>A	c.(3601-3603)Gtc>Atc	p.V1201I		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1201					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.V1201I(2)		NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GAGCTGCACCGTCAATGTGCT	0.443																																					p.V1201I		Atlas-SNP	.											DOCK1,colon,carcinoma,-1,2	DOCK1	188	.	2	Substitution - Missense(2)	ovary(1)|central_nervous_system(1)	c.G3601A						.						56	56	56					10																	129172467		1964	4167	6131	SO:0001583	missense	1793	exon35			TGCACCGTCAATG	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.3601G>A	chr10.hg19:g.129172467G>A	ENSP00000280333:p.Val1201Ile	70.0	0.0		66.0	3.0	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	hg19		.	.	.	.	.	.	.	.	.	.	G	28.1	4.894732	0.91962	.	.	ENSG00000150760	ENST00000280333	T	0.38240	1.15	5.52	5.52	0.82312	.	0.071608	0.56097	D	0.000037	T	0.60932	0.2307	M	0.87097	2.86	0.80722	D	1	D;D;D	0.69078	0.994;0.995;0.997	P;P;P	0.54544	0.755;0.559;0.693	T	0.67654	-0.5615	10	0.72032	D	0.01	.	19.2287	0.93829	0.0:0.0:1.0:0.0	.	1201;1267;1201	B2RUU3;A8MU08;Q14185	.;.;DOCK1_HUMAN	I	1201	ENSP00000280333:V1201I	ENSP00000280333:V1201I	V	+	1	0	DOCK1	129062457	1.000000	0.71417	0.961000	0.40146	0.795000	0.44927	9.575000	0.98187	2.878000	0.98634	0.650000	0.86243	GTC	.	.		0.443	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		A	129172467	G	A	129172467	3	1	49	1	0	0	0	0	1	0	0	0	4686	1145	40	1	3739	1	DOCK1	10	129172467	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	13528329	129172467	6362280	156	6313										
CALY	50632	hgsc.bcm.edu	37	chr10	135140482	135140482	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccatggcgaaggcgatcatcCgtgcggtgggcagctggcag	17	11	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:135140482C>A	ENST00000252939.4	-	4	353	c.260G>T	c.(259-261)cGg>cTg	p.R87L	CALY_ENST00000368556.2_Missense_Mutation_p.R87L|CALY_ENST00000368558.1_Missense_Mutation_p.R87L|RP11-122K13.14_ENST00000605518.1_lincRNA|CALY_ENST00000467611.1_5'Flank|ZNF511_ENST00000368554.4_Intron	NM_015722.3	NP_056537.1	Q9NYX4	CALY_HUMAN	calcyon neuron-specific vesicular protein	87					clathrin coat assembly (GO:0048268)|dopamine receptor signaling pathway (GO:0007212)|endocytosis (GO:0006897)|positive regulation of endocytosis (GO:0045807)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)	clathrin light chain binding (GO:0032051)			kidney(1)|lung(2)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;6.94e-06)|OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)	Apomorphine(DB00714)|Clozapine(DB00363)|Trifluoperazine(DB00831)	GGCGATCATCCGTGCGGTGGG	0.672																																					p.R87L		Atlas-SNP	.											CALY,colon,carcinoma,0,1	CALY	19	.	0			c.G260T						.						49	39	42					10																	135140482		2200	4292	6492	SO:0001583	missense	50632	exon4			ATCATCCGTGCGG	AF225903	CCDS7678.1	10q26.3	2008-07-02	2008-01-16	2008-01-16	ENSG00000130643	ENSG00000130643			17938	protein-coding gene	gene with protein product		604647	"dopamine receptor D1 interacting protein"	DRD1IP		10698743, 17623072	Standard	NM_015722		Approved	CALCYON, NSG3	uc001lmo.2	Q9NYX4	OTTHUMG00000019310	ENST00000252939.4:c.260G>T	chr10.hg19:g.135140482C>A	ENSP00000252939:p.Arg87Leu	82.0	1.0		39.0	2.0	NM_015722	Q5VWX3|Q5VWY5|Q5VWY6	Missense_Mutation	SNP	ENST00000252939.4	hg19	CCDS7678.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.257847	0.39896	.	.	ENSG00000130643	ENST00000252939;ENST00000368558;ENST00000368556	.	.	.	4.27	4.27	0.50696	.	0.072991	0.53938	D	0.000050	T	0.61400	0.2344	L	0.48877	1.53	0.34212	D	0.674436	D	0.89917	1.0	D	0.85130	0.997	T	0.63102	-0.6712	9	0.15952	T	0.53	-7.0591	12.414	0.55483	0.0:1.0:0.0:0.0	.	87	Q9NYX4	CALY_HUMAN	L	87	.	ENSP00000252939:R87L	R	-	2	0	CALY	134990472	0.902000	0.30710	0.918000	0.36340	0.421000	0.31385	3.111000	0.50360	2.371000	0.80710	0.643000	0.83706	CGG	.	.		0.672	CALY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051122.1	NM_015722		A	135140482	C	A	135140482	3	1	49	1	0	0	0	0	1	0	0	0	2597	652	23	1	401	1	CALY	10	135140482	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	5968015	135140482	394265	157	6314										
RRM1	6240	hgsc.bcm.edu	37	chr11	4153626	4153626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	caccagcaacatctatactcGcagagtcttgtcaggagaat	8	11	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:4153626G>A	ENST00000300738.5	+	16	2084	c.1880G>A	c.(1879-1881)cGc>cAc	p.R627H	RRM1_ENST00000537197.1_Missense_Mutation_p.R289H|RRM1_ENST00000423050.2_Missense_Mutation_p.R530H|RRM1_ENST00000534285.1_Missense_Mutation_p.R405H	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	627					cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	ATCTATACTCGCAGAGTCTTG	0.453																																					p.R627H	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.G1880A						.						140	132	134					11																	4153626		2201	4298	6499	SO:0001583	missense	6240	exon16			ATACTCGCAGAGT	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"ribonucleotide reductase M1 polypeptide"			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.1880G>A	chr11.hg19:g.4153626G>A	ENSP00000300738:p.Arg627His	75.0	0.0		93.0	4.0	NM_001033	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	hg19	CCDS7750.1	.	.	.	.	.	.	.	.	.	.	G	30	5.055544	0.93793	.	.	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	5.07	5.07	0.68467	Ribonucleoside-diphosphate reductase, alpha subunit (1);Ribonucleotide reductase large subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75583	0.3869	M	0.89163	3.01	0.80722	D	1	D	0.89917	1.0	D	0.63033	0.91	T	0.81346	-0.0974	10	0.87932	D	0	-6.0041	17.39	0.87427	0.0:0.0:1.0:0.0	.	627	P23921	RIR1_HUMAN	H	627;530;540;405;405;289	ENSP00000300738:R627H;ENSP00000390539:R530H;ENSP00000431464:R405H;ENSP00000442148:R289H	ENSP00000300738:R627H	R	+	2	0	RRM1	4110202	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.379000	0.97198	2.515000	0.84797	0.650000	0.86243	CGC	.	.		0.453	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		A	4153626	G	A	4153626	3	1	49	1	0	0	0	0	1	0	0	0	13696	1087	38	1	1942	1	RRM1	11	4153626	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10		4153626	130852890	158	6315										
OR51G2	81282	hgsc.bcm.edu	37	chr11	4936238	4936238	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcagagcataagagaagaggAtgagcagtgagtctataccc	12	7	2	5			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:4936238A>C	ENST00000322013.3	-	1	684	c.656T>G	c.(655-657)aTc>aGc	p.I219S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGAGAAGAGGATGAGCAGTGA	0.517																																					p.I219S		Atlas-SNP	.											.	OR51G2	70	.	0			c.T656G						.						144	113	123					11																	4936238		2201	4298	6499	SO:0001583	missense	81282	exon1			AAGAGGATGAGCA	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"GPCR / Class A : Olfactory receptors"	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.656T>G	chr11.hg19:g.4936238A>C	ENSP00000322593:p.Ile219Ser	101.0	0.0		116.0	32.0	NM_001005238	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	hg19	CCDS31365.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.160945	0.78226	.	.	ENSG00000176893	ENST00000322013	T	0.00333	8.07	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000092	T	0.01661	0.0053	H	0.98199	4.17	0.53688	D	0.999978	D	0.89917	1.0	D	0.91635	0.999	T	0.08066	-1.0740	10	0.87932	D	0	.	14.7226	0.69317	1.0:0.0:0.0:0.0	.	219	Q8NGK0	O51G2_HUMAN	S	219	ENSP00000322593:I219S	ENSP00000322593:I219S	I	-	2	0	OR51G2	4892814	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	5.806000	0.69150	2.343000	0.79666	0.533000	0.62120	ATC	.	.		0.517	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		C	4936238	A	C	4936238	3	2	49	1	0	0	0	0	1	0	0	0	11108	333	12	5	292	5	OR51G2	11	4936238	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	782612	4936238	130070278	159	6316										
OR51I1	390063	hgsc.bcm.edu	37	chr11	5462447	5462447	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gatgaagaacatctggaccaGgcaagcattaaacgcaacat	9	9	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:5462447G>T	ENST00000380211.1	-	1	297	c.298C>A	c.(298-300)Ctg>Atg	p.L100M	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	100					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L100L(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATCTGGACCAGGCAAGCATTA	0.453																																					p.L100M		Atlas-SNP	.											OR51I1,NS,carcinoma,0,1	OR51I1	66	.	1	Substitution - coding silent(1)	lung(1)	c.C298A						.						140	123	129					11																	5462447		2201	4297	6498	SO:0001583	missense	390063	exon1			GGACCAGGCAAGC	BK004429	CCDS31382.1	11p15.4	2012-08-09			ENSG00000167359	ENSG00000167359		"GPCR / Class A : Olfactory receptors"	15200	protein-coding gene	gene with protein product							Standard	NM_001005288		Approved		uc010qze.2	Q9H343	OTTHUMG00000066908	ENST00000380211.1:c.298C>A	chr11.hg19:g.5462447G>T	ENSP00000369559:p.Leu100Met	89.0	0.0		139.0	37.0	NM_001005288	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	hg19	CCDS31382.1	.	.	.	.	.	.	.	.	.	.	G	10.54	1.378082	0.24944	.	.	ENSG00000167359	ENST00000317283;ENST00000321307;ENST00000380211	T	0.21543	2.0	5.78	1.53	0.23141	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43416	D	0.000565	T	0.32466	0.0830	L	0.54323	1.7	0.09310	N	1	D	0.76494	0.999	D	0.83275	0.996	T	0.06734	-1.0810	10	0.49607	T	0.09	.	3.7444	0.08542	0.3241:0.0:0.5063:0.1696	.	100	Q9H343	O51I1_HUMAN	M	85;97;100	ENSP00000369559:L100M	ENSP00000348350:L85M	L	-	1	2	OR51I1	5419023	0.000000	0.05858	0.976000	0.42696	0.329000	0.28539	-2.635000	0.00868	0.266000	0.21894	-0.290000	0.09829	CTG	.	.		0.453	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288		T	5462447	G	T	5462447	3	4	49	1	0	0	0	0	1	0	0	0	11109	991	35	3	650	3	OR51I1	11	5462447	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	526209	5462447	129544069	160	6317										
SMPD1	322	hgsc.bcm.edu	37	chr11	6413367	6413367	+	IGR	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gggagccctggctgcctgccGaagccctgcgcaccctcagg	14	17	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:6413367G>A	ENST00000609360.1	-	0	2642				SMPD1_ENST00000342245.4_Missense_Mutation_p.E358K|SMPD1_ENST00000299397.3_Missense_Mutation_p.E358K|SMPD1_ENST00000356761.2_Missense_Mutation_p.E358K|SMPD1_ENST00000527275.1_Missense_Mutation_p.E357K|APBB1_ENST00000526240.1_5'Flank	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)						apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GCTGCCTGCCGAAGCCCTGCG	0.577																																					p.E358K	GBM(147;1810 2556 5672 39622)	Atlas-SNP	.											SMPD1_ENST00000342245,NS,carcinoma,0,2	SMPD1	108	.	0			c.G1072A						.						52	50	51					11																	6413367		2201	4296	6497	SO:0001628	intergenic_variant	6609	exon2			CCTGCCGAAGCCC	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213			chr11.hg19:g.6413367G>A		76.0	0.0		95.0	4.0	NM_000543	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.18	2.159477	0.38119	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	D;D;D;D	0.94650	-3.48;-1.97;-3.03;-3.03	5.01	3.01	0.34805	Metallophosphoesterase domain (1);	0.556195	0.18471	N	0.140212	D	0.87842	0.6279	L	0.46885	1.475	0.09310	N	1	P;B;P	0.41624	0.757;0.451;0.507	B;B;B	0.31495	0.131;0.08;0.131	T	0.80585	-0.1317	10	0.37606	T	0.19	-22.1764	5.2868	0.15706	0.084:0.1428:0.6264:0.1468	.	357;358;356	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	K	358;358;358;357	ENSP00000299397:E358K;ENSP00000349203:E358K;ENSP00000340409:E358K;ENSP00000435350:E357K	ENSP00000299397:E358K	E	+	1	0	SMPD1	6369943	0.697000	0.27767	0.996000	0.52242	0.992000	0.81027	3.175000	0.50855	2.336000	0.79503	0.561000	0.74099	GAA	.	.		0.577	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164		A	6413367	G	A	6413367	1	1	49	0	1	0	0	0	0	0	0	0	14819	1059	37	1		1	SMPD1	11	6413367	IGR	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	950920	6413367	128593149	161	6318										
ZNF143	7702	hgsc.bcm.edu	37	chr11	9537864	9537864	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtcatctcctcagcaggaacGcactctgttgctatggttac	9	12	4	0	rs572827042		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:9537864G>A	ENST00000396602.2	+	14	1760	c.1641G>A	c.(1639-1641)acG>acA	p.T547T	ZNF143_ENST00000530463.1_Silent_p.T546T|ZNF143_ENST00000299606.2_Silent_p.T519T|ZNF143_ENST00000396597.3_Silent_p.T516T|ZNF143_ENST00000396604.1_Silent_p.T546T	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	547					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T547T(1)		endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		CAGCAGGAACGCACTCTGTTG	0.473																																					p.T547T		Atlas-SNP	.											ZNF143,NS,carcinoma,0,1	ZNF143	38	.	1	Substitution - coding silent(1)	lung(1)	c.G1641A						.						101	75	84					11																	9537864		2201	4294	6495	SO:0001819	synonymous_variant	7702	exon14			AGGAACGCACTCT	U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"Zinc fingers, C2H2-type"	12928	protein-coding gene	gene with protein product		603433	"zinc finger protein 143 (clone pHZ-1)"				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.1641G>A	chr11.hg19:g.9537864G>A		42.0	0.0		34.0	2.0	NM_003442	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Silent	SNP	ENST00000396602.2	hg19	CCDS7799.2	.	.	.	.	.	.	.	.	.	.	A	9.521	1.108420	0.20714	.	.	ENSG00000166478	ENST00000447186	.	.	.	5.82	3.48	0.39840	.	.	.	.	.	T	0.59376	0.2189	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53143	-0.8480	4	.	.	.	.	9.5411	0.39252	0.7316:0.0:0.2684:0.0	.	.	.	.	T	73	.	.	A	+	1	0	ZNF143	9494440	0.991000	0.36638	1.000000	0.80357	0.981000	0.71138	0.407000	0.21049	0.467000	0.27218	-0.254000	0.11334	GCA	.	.		0.473	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442		A	9537864	G	A	9537864	2	1	49	1	0	0	0	0	0	0	0	1	17747	1074	38	1		1	ZNF143	11	9537864	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	3124497	9537864	125468652	162	6319										
AMPD3	272	hgsc.bcm.edu	37	chr11	10503698	10503698	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgcgcggctcgcctaccaccGcttcccgcggatcacatccc	9	20	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:10503698G>T	ENST00000396554.3	+	4	883	c.542G>T	c.(541-543)cGc>cTc	p.R181L	AMPD3_ENST00000444303.2_Missense_Mutation_p.R13L	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	172					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		GCCTACCACCGCTTCCCGCGG	0.612																																					p.R181L		Atlas-SNP	.											.	AMPD3	68	.	0			c.G542T						.						85	91	89					11																	10503698		2201	4294	6495	SO:0001583	missense	272	exon4			ACCACCGCTTCCC	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"erythrocyte-specific AMP deaminase"	102772	"adenosine monophosphate deaminase (isoform E)"			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.542G>T	chr11.hg19:g.10503698G>T	ENSP00000379802:p.Arg181Leu	51.0	0.0		69.0	10.0	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Missense_Mutation	SNP	ENST00000396554.3	hg19	CCDS7802.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004679	0.93287	.	.	ENSG00000133805	ENST00000444303;ENST00000396554;ENST00000524866;ENST00000396553;ENST00000528723;ENST00000529507	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	5.88	4.97	0.65823	.	0.097493	0.64402	D	0.000001	T	0.60157	0.2247	M	0.84683	2.71	0.54753	D	0.999986	D;B;D	0.54397	0.966;0.447;0.966	P;B;P	0.52514	0.701;0.242;0.701	T	0.67530	-0.5647	10	0.52906	T	0.07	-14.7447	15.134	0.72549	0.0676:0.0:0.9324:0.0	.	179;172;181	B7Z763;Q01432;A0AUX0	.;AMPD3_HUMAN;.	L	13;181;172;172;179;172	ENSP00000396000:R13L;ENSP00000379802:R181L;ENSP00000433284:R172L;ENSP00000379801:R172L;ENSP00000436987:R179L;ENSP00000431648:R172L	ENSP00000379801:R172L	R	+	2	0	AMPD3	10460274	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	6.666000	0.74446	1.489000	0.48450	0.655000	0.94253	CGC	.	.		0.612	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480		T	10503698	G	T	10503698	3	4	49	1	0	0	0	0	1	0	0	0	587	1087	38	1	576	1	AMPD3	11	10503698	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	965834	10503698	124502818	163	6320										
CCDC34	91057	hgsc.bcm.edu	37	chr11	27384473	27384473	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccacgtcttcctcatcatccAcgtcttcctcatcctccccg	3	21	5	0	rs77142757		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:27384473A>C	ENST00000328697.6	-	1	942	c.269T>G	c.(268-270)gTg>gGg	p.V90G	CCDC34_ENST00000317945.6_Missense_Mutation_p.V90G	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	90	Asp-rich.									endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						CTCATCATCCACGTCTTCCTC	0.572																																					p.V90G		Atlas-SNP	.											.	CCDC34	48	.	0			c.T269G						.						198	172	181					11																	27384473		2202	4299	6501	SO:0001583	missense	91057	exon1			TCATCCACGTCTT	AF382034	CCDS7863.1, CCDS31448.1	11p14.1	2010-03-30			ENSG00000109881	ENSG00000109881			25079	protein-coding gene	gene with protein product		612324				11173847	Standard	NM_080654		Approved	NY-REN-41, L15, RAMA3	uc001mrh.1	Q96HJ3	OTTHUMG00000166211	ENST00000328697.6:c.269T>G	chr11.hg19:g.27384473A>C	ENSP00000330240:p.Val90Gly	116.0	0.0		98.0	13.0	NM_030771	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	Missense_Mutation	SNP	ENST00000328697.6	hg19	CCDS31448.1	.	.	.	.	.	.	.	.	.	.	-	0.162	-1.080247	0.01888	.	.	ENSG00000109881	ENST00000328697;ENST00000317945	T;T	0.25579	1.79;1.79	.	.	.	.	0.390690	0.08080	U	1.000000	T	0.11196	0.0273	N	0.08118	0	0.24817	N	0.99261	.	.	.	.	.	.	T	0.35822	-0.9773	6	0.22109	T	0.4	.	.	.	.	.	90;90	Q96HJ3-2;Q96HJ3	.;CCD34_HUMAN	G	90	ENSP00000330240:V90G;ENSP00000321563:V90G	ENSP00000321563:V90G	V	-	2	0	CCDC34	27341049	0.021000	0.18746	0.328000	0.25416	0.257000	0.26127	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GTG	.	A|1.000;C|0.000		0.572	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771		C	27384473	A	C	27384473	3	2	49	1	0	0	0	0	1	0	0	0	2809	159	6	5	960	5	CCDC34	11	27384473	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	16880775	27384473	107622043	164	6321										
C11orf74	119710	hgsc.bcm.edu	37	chr11	36631742	36631742	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	attccttaattgtcatgagcAaacatatgatgaagaatttc	6	6	1	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:36631742A>G	ENST00000334307.5	+	2	204	c.89A>G	c.(88-90)cAa>cGa	p.Q30R	C11orf74_ENST00000446510.2_Missense_Mutation_p.Q30R|C11orf74_ENST00000534635.1_Missense_Mutation_p.Q30R|C11orf74_ENST00000347206.4_Missense_Mutation_p.Q30R	NM_138787.2	NP_620142.2	Q86VG3	CK074_HUMAN	chromosome 11 open reading frame 74	30										breast(1)|kidney(1)|large_intestine(1)|lung(5)	8	all_lung(20;0.226)	all_hematologic(20;0.0118)				TGTCATGAGCAAACATATGAT	0.313																																					p.G30G		Atlas-SNP	.											.	C11orf74	22	.	0			c.G89G						.						83	83	83					11																	36631742		2202	4298	6500	SO:0001583	missense	119710	exon2			ATGAGCAAACATA	AK095997, BC009561	CCDS7904.1, CCDS60762.1	11p12	2012-08-10			ENSG00000166352	ENSG00000166352			25142	protein-coding gene	gene with protein product						12477932	Standard	NM_001276722		Approved	FLJ38678, HEPIS	uc031pzr.1	Q86VG3	OTTHUMG00000166397	ENST00000334307.5:c.89A>G	chr11.hg19:g.36631742A>G	ENSP00000334848:p.Gln30Arg	57.0	0.0		81.0	4.0	NM_138787	D3DR18|Q96DD6	Silent	SNP	ENST00000334307.5	hg19	CCDS7904.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.268274	0.80469	.	.	ENSG00000166352	ENST00000334307;ENST00000531554;ENST00000347206;ENST00000534635;ENST00000446510;ENST00000530697;ENST00000527108;ENST00000532470	.	.	.	6.17	6.17	0.99709	.	0.208574	0.34932	N	0.003563	T	0.79540	0.4463	M	0.78801	2.425	0.45580	D	0.998528	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.81922	-0.0711	9	0.87932	D	0	-21.2486	14.5632	0.68156	1.0:0.0:0.0:0.0	.	30;30	Q86VG3;Q86VG3-2	CK074_HUMAN;.	R	30	.	ENSP00000334848:Q30R	Q	+	2	0	C11orf74	36588318	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	2.766000	0.47629	2.371000	0.80710	0.533000	0.62120	CAA	.	.		0.313	C11orf74-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389567.1	NM_138787		G	36631742	A	G	36631742	3	3	49	1	0	0	0	0	1	0	0	0	1664	130	5	2	91	2	C11orf74	11	36631742	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	9247269	36631742	98374774	165	6322										
OR4C46	119749	hgsc.bcm.edu	37	chr11	51515417	51515417	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gatatgtgctcattgtggtcAccatcactgccagcccatca	8	13	4	0	rs372979385|rs148928414|rs545486160	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:51515417A>C	ENST00000328188.1	+	1	136	c.136A>C	c.(136-138)Acc>Ccc	p.T46P		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	46						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						CATTGTGGTCACCATCACTGC	0.463																																					p.T46P		Atlas-SNP	.											.	OR4C46	96	.	0			c.A136C						.						233	233	233					11																	51515417		2198	4296	6494	SO:0001583	missense	119749	exon1			GTGGTCACCATCA		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"GPCR / Class A : Olfactory receptors"	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.136A>C	chr11.hg19:g.51515417A>C	ENSP00000329056:p.Thr46Pro	78.0	0.0		117.0	26.0	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	hg19	CCDS31498.1	.	.	.	.	.	.	.	.	.	.	.	14.40	2.523554	0.44866	.	.	ENSG00000185926	ENST00000328188	T	0.03094	4.05	2.63	2.63	0.31362	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41500	D	0.000862	T	0.19644	0.0472	H	0.95437	3.67	0.09310	N	0.999999	D	0.58620	0.983	D	0.65233	0.933	T	0.07654	-1.0761	10	0.87932	D	0	.	5.0922	0.14713	0.7359:0.0:0.0:0.264	.	46	A6NHA9	O4C46_HUMAN	P	46	ENSP00000329056:T46P	ENSP00000329056:T46P	T	+	1	0	OR4C46	51371993	0.000000	0.05858	0.022000	0.16811	0.119000	0.20118	-0.272000	0.08560	1.239000	0.43787	0.113000	0.15668	ACC	.	.		0.463	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703		C	51515417	A	C	51515417	3	2	49	1	0	0	0	0	1	0	0	0	11060	159	6	5	138	5	OR4C46	11	51515417	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	14883675	51515417	83491099	166	6323										
OR5AS1	219447	hgsc.bcm.edu	37	chr11	55798847	55798847	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaatgaatggtatttaaatcGtttaagaatagtcaatatct	6	3	2	2	rs201114315		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:55798847G>A	ENST00000313555.1	+	1	953	c.953G>A	c.(952-954)cGt>cAt	p.R318H		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	318						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					TATTTAAATCGTTTAAGAATA	0.259																																					p.R318H		Atlas-SNP	.											OR5AS1,NS,carcinoma,0,1	OR5AS1	121	.	0			c.G953A						.	G	HIS/ARG	0,4370		0,0,2185	43	53	50		953	-3.4	0	11		50	2,8570		0,2,4284	yes	missense	OR5AS1	NM_001001921.1	29	0,2,6469	AA,AG,GG		0.0233,0.0,0.0155	benign	318/325	55798847	2,12940	2185	4286	6471	SO:0001583	missense	219447	exon1			TAAATCGTTTAAG	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"GPCR / Class A : Olfactory receptors"	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.953G>A	chr11.hg19:g.55798847G>A	ENSP00000324111:p.Arg318His	26.0	0.0		35.0	2.0	NM_001001921	Q6IFB8	Missense_Mutation	SNP	ENST00000313555.1	hg19	CCDS31516.1	.	.	.	.	.	.	.	.	.	.	G	8.970	0.972697	0.18736	0.0	2.33E-4	ENSG00000181785	ENST00000313555	T	0.00364	7.81	4.07	-3.43	0.04810	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09596	-1.0667	9	0.32370	T	0.25	.	5.4905	0.16773	0.3208:0.2938:0.3854:0.0	.	318	Q8N127	O5AS1_HUMAN	H	318	ENSP00000324111:R318H	ENSP00000324111:R318H	R	+	2	0	OR5AS1	55555423	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.250000	0.08830	-0.563000	0.06078	-0.333000	0.08304	CGT	.	.		0.259	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921		A	55798847	G	A	55798847	3	1	49	1	0	0	0	0	1	0	0	0	11155	1145	40	1	955	1	OR5AS1	11	55798847	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	4283430	55798847	79207669	167	6324										
MS4A6A	64231	hgsc.bcm.edu	37	chr11	59947379	59947379	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtaaaatttggagagaaggaAgcagatgccaaaatgatccc	11	6	0	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:59947379A>G	ENST00000530839.1	-	4	699	c.207T>C	c.(205-207)gcT>gcC	p.A69A	MS4A6A_ENST00000532169.1_Silent_p.A69A|MS4A6A_ENST00000529054.1_Silent_p.A97A|MS4A6A_ENST00000529906.1_5'UTR|MS4A6A_ENST00000420732.2_Silent_p.A69A|MS4A6A_ENST00000412309.2_Silent_p.A97A|MS4A6A_ENST00000533023.1_Intron|MS4A6A_ENST00000528851.1_Silent_p.A69A|MS4A6A_ENST00000426738.2_Intron|MS4A6A_ENST00000323961.3_Silent_p.A69A	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	69						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GAGAGAAGGAAGCAGATGCCA	0.438																																					p.A97A		Atlas-SNP	.											.	MS4A6A	85	.	0			c.T291C						.						100	92	95					11																	59947379		2201	4295	6496	SO:0001819	synonymous_variant	64231	exon4			GAAGGAAGCAGAT	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.207T>C	chr11.hg19:g.59947379A>G		95.0	0.0		121.0	5.0	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Silent	SNP	ENST00000530839.1	hg19	CCDS7981.1																																																																																			.	.		0.438	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1			G	59947379	A	G	59947379	2	3	49	1	0	0	0	0	0	0	0	1	9873	59	3	2		2	MS4A6A	11	59947379	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	4148532	59947379	75059137	168	6325										
TMEM138	51524	hgsc.bcm.edu	37	chr11	61131933	61131933	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gctgtcctatgacctctttgTcaattccttctcagaactgc	6	13	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:61131933T>C	ENST00000278826.6	+	2	630	c.71T>C	c.(70-72)gTc>gCc	p.V24A	TMEM138_ENST00000540194.1_3'UTR|CYB561A3_ENST00000544118.1_5'Flank|CYB561A3_ENST00000447532.2_5'Flank|CYB561A3_ENST00000426130.2_5'Flank|TMEM138_ENST00000381787.2_5'Flank|CYB561A3_ENST00000294072.4_5'Flank|CYB561A3_ENST00000540317.1_5'Flank|CYB561A3_ENST00000546151.1_5'Flank|TMEM138_ENST00000542946.1_Missense_Mutation_p.V24A	NM_016464.4	NP_057548.1	Q9NPI0	TM138_HUMAN	transmembrane protein 138	24					cilium assembly (GO:0042384)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|vacuole (GO:0005773)				central_nervous_system(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5						GACCTCTTTGTCAATTCCTTC	0.517																																					p.V24A		Atlas-SNP	.											.	TMEM138	16	.	0			c.T71C						.						185	156	166					11																	61131933		2203	4299	6502	SO:0001583	missense	51524	exon2			TCTTTGTCAATTC	AF151030	CCDS8005.1	11q12.2	2014-01-28			ENSG00000149483	ENSG00000149483			26944	protein-coding gene	gene with protein product		614459					Standard	NM_016464		Approved	HSPC196, JBTS16	uc001nrl.2	Q9NPI0	OTTHUMG00000168145	ENST00000278826.6:c.71T>C	chr11.hg19:g.61131933T>C	ENSP00000278826:p.Val24Ala	68.0	0.0		99.0	4.0	NM_016464	A6NGA7|B4E044|Q5JPE1	Missense_Mutation	SNP	ENST00000278826.6	hg19	CCDS8005.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.395067	0.62066	.	.	ENSG00000149483	ENST00000278826;ENST00000542946	D;T	0.89681	-2.55;-1.25	5.32	4.2	0.49525	.	0.000000	0.64402	D	0.000002	D	0.86456	0.5937	M	0.61703	1.905	0.80722	D	1	P;B;B	0.41450	0.75;0.054;0.031	B;B;B	0.39152	0.292;0.043;0.043	D	0.85489	0.1184	10	0.87932	D	0	-18.1327	10.5792	0.45246	0.0:0.0759:0.0:0.9241	.	24;24;24	B4E044;Q9NPI0-2;Q9NPI0	.;.;TM138_HUMAN	A	24	ENSP00000278826:V24A;ENSP00000445792:V24A	ENSP00000278826:V24A	V	+	2	0	TMEM138	60888509	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.986000	0.70563	0.872000	0.35775	0.460000	0.39030	GTC	.	.		0.517	TMEM138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398399.2	NM_016464		C	61131933	T	C	61131933	3	2	49	1	0	0	0	0	1	0	0	0	16068	1667	58	2	73	2	TMEM138	11	61131933	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	1184554	61131933	73874583	169	6326										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65357652	65357652	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgggcgggcggctgaggtggAgatgcagctgaggagcctca	20	8	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:65357652A>G	ENST00000309295.4	+	15	4419	c.4154A>G	c.(4153-4155)gAg>gGg	p.E1385G	EHBP1L1_ENST00000533364.1_5'Flank	NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	1385						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GCTGAGGTGGAGATGCAGCTG	0.602																																					p.E1385G		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.A4154G						.						64	76	72					11																	65357652		2149	4257	6406	SO:0001583	missense	254102	exon15			AGGTGGAGATGCA	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.4154A>G	chr11.hg19:g.65357652A>G	ENSP00000312671:p.Glu1385Gly	53.0	0.0		90.0	5.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	A	16.73	3.203325	0.58234	.	.	ENSG00000173442	ENST00000309295	T	0.58652	0.32	4.36	4.36	0.52297	Domain of unknown function DUF3585 (1);	0.000000	0.64402	D	0.000006	T	0.78394	0.4276	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81604	-0.0857	10	0.59425	D	0.04	.	9.903	0.41359	1.0:0.0:0.0:0.0	.	1385	Q8N3D4	EH1L1_HUMAN	G	1385	ENSP00000312671:E1385G	ENSP00000312671:E1385G	E	+	2	0	EHBP1L1	65114228	1.000000	0.71417	0.997000	0.53966	0.204000	0.24138	5.838000	0.69388	1.849000	0.53698	0.460000	0.39030	GAG	.	.		0.602	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		G	65357652	A	G	65357652	3	3	49	1	0	0	0	0	1	0	0	0	4978	304	11	2	4212	2	EHBP1L1	11	65357652	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	4225719	65357652	69648864	170	6327										
OVOL1	5017	hgsc.bcm.edu	37	chr11	65561586	65561586	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttcctgcccgctggctttgaAcatgagccttcgagactcta	9	13	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:65561586A>G	ENST00000335987.3	+	2	537	c.185A>G	c.(184-186)aAc>aGc	p.N62S	OVOL1_ENST00000532448.1_5'UTR|RP11-770G2.5_ENST00000531155.1_RNA	NM_004561.3	NP_004552.2	O14753	OVOL1_HUMAN	ovo-like zinc finger 1	62					cytoskeleton organization (GO:0007010)|epidermal cell differentiation (GO:0009913)|germline cell cycle switching, mitotic to meiotic cell cycle (GO:0051729)|kidney development (GO:0001822)|mesoderm development (GO:0007498)|negative regulation of meiotic cell cycle phase transition (GO:1901994)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6				READ - Rectum adenocarcinoma(159;0.17)		CTGGCTTTGAACATGAGCCTT	0.647																																					p.N62S		Atlas-SNP	.											.	OVOL1	15	.	0			c.A185G						.						82	85	84					11																	65561586		2201	4297	6498	SO:0001583	missense	5017	exon2			CTTTGAACATGAG	BC059408	CCDS8112.1	11q13	2013-10-17	2013-10-17		ENSG00000172818	ENSG00000172818		"Zinc fingers, C2H2-type"	8525	protein-coding gene	gene with protein product		602313	"ovo (Drosophila) homolog-like 1", "ovo-like 1(Drosophila)"			9383297	Standard	NM_004561		Approved	HOVO1	uc001ofp.3	O14753	OTTHUMG00000166600	ENST00000335987.3:c.185A>G	chr11.hg19:g.65561586A>G	ENSP00000337862:p.Asn62Ser	81.0	0.0		92.0	4.0	NM_004561	Q6PCB1	Missense_Mutation	SNP	ENST00000335987.3	hg19	CCDS8112.1	.	.	.	.	.	.	.	.	.	.	A	10.22	1.289065	0.23478	.	.	ENSG00000172818	ENST00000335987	T	0.07567	3.18	4.65	4.65	0.58169	.	0.693200	0.13231	N	0.403679	T	0.05318	0.0141	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35126	-0.9801	10	0.52906	T	0.07	-23.0656	10.7778	0.46361	1.0:0.0:0.0:0.0	.	62	O14753	OVOL1_HUMAN	S	62	ENSP00000337862:N62S	ENSP00000337862:N62S	N	+	2	0	OVOL1	65318162	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.701000	0.37825	1.863000	0.54032	0.533000	0.62120	AAC	.	.		0.647	OVOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390690.1	NM_004561		G	65561586	A	G	65561586	3	3	49	1	0	0	0	0	1	0	0	0	11335	43	2	2	191	2	OVOL1	11	65561586	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	203934	65561586	69444930	171	6328										
KDM2A	22992	hgsc.bcm.edu	37	chr11	66982895	66982895	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	caacaaatgccatcttggagAtgcagtaccctaaagtgcag	9	10	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:66982895A>T	ENST00000529006.2	+	7	1017	c.571A>T	c.(571-573)Atg>Ttg	p.M191L	KDM2A_ENST00000398645.2_Missense_Mutation_p.M191L|KDM2A_ENST00000526258.1_3'UTR	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	191	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						CATCTTGGAGATGCAGTACCC	0.478																																					p.M191L		Atlas-SNP	.											.	KDM2A	80	.	0			c.A571T						.						101	98	99					11																	66982895		2001	4168	6169	SO:0001583	missense	22992	exon7			TTGGAGATGCAGT	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13606	protein-coding gene	gene with protein product	"F-box protein FBL11", "jumonji C domain-containing histone demethylase 1A"	605657	"F-box and leucine-rich repeat protein 11"	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.571A>T	chr11.hg19:g.66982895A>T	ENSP00000432786:p.Met191Leu	66.0	0.0		81.0	18.0	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Missense_Mutation	SNP	ENST00000529006.2	hg19	CCDS44657.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.390848	0.82902	.	.	ENSG00000173120	ENST00000398645;ENST00000529006	T;T	0.69435	-0.4;-0.4	5.76	5.76	0.90799	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	T	0.60958	0.2309	L	0.55103	1.725	0.80722	D	1	B	0.30455	0.28	B	0.25987	0.065	T	0.58160	-0.7685	10	0.24483	T	0.36	-3.2157	15.2488	0.73526	1.0:0.0:0.0:0.0	.	191	Q9Y2K7	KDM2A_HUMAN	L	191	ENSP00000381640:M191L;ENSP00000432786:M191L	ENSP00000381640:M191L	M	+	1	0	KDM2A	66739471	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.942000	0.92970	2.201000	0.70794	0.533000	0.62120	ATG	.	.		0.478	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308		T	66982895	A	T	66982895	3	4	49	1	0	0	0	0	1	0	0	0	8133	333	12	4	593	4	KDM2A	11	66982895	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	1421309	66982895	68023621	172	6329										
MTL5	9633	hgsc.bcm.edu	37	chr11	68475846	68475846	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ataagcaccttccaaattccTccaggatcatctgctctgcc	5	15	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:68475846T>C	ENST00000255087.5	-	10	1640	c.1457A>G	c.(1456-1458)gAg>gGg	p.E486G		NM_004923.3	NP_004914.2	Q9Y4I5	MTL5_HUMAN	metallothionein-like 5, testis-specific (tesmin)	486					cell differentiation (GO:0030154)|cellular metal ion homeostasis (GO:0006875)|multicellular organismal development (GO:0007275)|response to metal ion (GO:0010038)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	15	Esophageal squamous(3;4.37e-12)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.185)			TCCAAATTCCTCCAGGATCAT	0.483																																					p.E486G		Atlas-SNP	.											.	MTL5	37	.	0			c.A1457G						.						124	120	122					11																	68475846		2200	4294	6494	SO:0001583	missense	9633	exon10			AATTCCTCCAGGA	U86074	CCDS8184.1, CCDS44661.1	11q13.2-q13.3	2007-01-03			ENSG00000132749	ENSG00000132749			7446	protein-coding gene	gene with protein product	"CXC domain containing 2"	604374				1091092	Standard	XR_428932		Approved	CXCDC2	uc001ooc.3	Q9Y4I5	OTTHUMG00000167891	ENST00000255087.5:c.1457A>G	chr11.hg19:g.68475846T>C	ENSP00000255087:p.Glu486Gly	132.0	0.0		149.0	6.0	NM_004923	A8K8J3|Q4G182|Q6P2E2|Q8NCC8	Missense_Mutation	SNP	ENST00000255087.5	hg19	CCDS8184.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582750	0.86748	.	.	ENSG00000132749	ENST00000255087	T	0.37235	1.21	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000001	T	0.61426	0.2346	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	T	0.67417	-0.5676	10	0.87932	D	0	-24.7053	14.256	0.66053	0.0:0.0:0.0:1.0	.	486	Q9Y4I5	MTL5_HUMAN	G	486	ENSP00000255087:E486G	ENSP00000255087:E486G	E	-	2	0	MTL5	68232422	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.074000	0.76791	2.016000	0.59253	0.329000	0.21502	GAG	.	.		0.483	MTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396844.1	NM_004923		C	68475846	T	C	68475846	3	2	49	1	0	0	0	0	1	0	0	0	9945	1551	54	2	73	2	MTL5	11	68475846	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	1492951	68475846	66530670	173	6330										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78775891	78775891	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gctccggccccacagacgcaCggggtgctcaggggacagca	15	15	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:78775891C>T	ENST00000278550.7	-	6	847	c.385G>A	c.(385-387)Gtg>Atg	p.V129M		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	129	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CACAGACGCACGGGGTGCTCA	0.647																																					p.V129M		Atlas-SNP	.											.	.	.	.	0			c.G385A						.						31	31	31					11																	78775891		692	1591	2283	SO:0001583	missense	26011	exon6			GACGCACGGGGTG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.385G>A	chr11.hg19:g.78775891C>T	ENSP00000278550:p.Val129Met	45.0	0.0		48.0	12.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.009528	0.54361	.	.	ENSG00000149256	ENST00000278550	T	0.39229	1.09	4.69	3.78	0.43462	Teneurin intracellular, N-terminal (2);	0.078666	0.49916	N	0.000135	T	0.19644	0.0472	N	0.04203	-0.255	0.46927	D	0.99925	B;B	0.29085	0.232;0.028	B;B	0.24269	0.052;0.018	T	0.06463	-1.0825	9	.	.	.	.	13.1	0.59214	0.0:0.9217:0.0:0.0783	.	129;129	G3CAT1;Q6N022	.;TEN4_HUMAN	M	129	ENSP00000278550:V129M	.	V	-	1	0	ODZ4	78453539	0.998000	0.40836	0.867000	0.34043	0.986000	0.74619	3.884000	0.56175	1.325000	0.45301	0.563000	0.77884	GTG	.	.		0.647	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78775891	C	T	78775891	3	4	49	1	0	0	0	0	1	0	0	0	10846	536	19	1	8040	1	ODZ4	11	78775891	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	10300045	78775891	56230625	174	6331										
CTSC	1075	hgsc.bcm.edu	37	chr11	88070831	88070831	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggcgagcagcaaggagggccCagcacccatgctgcagggag	17	12	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:88070831C>A	ENST00000227266.5	-	1	124	c.10G>T	c.(10-12)Ggg>Tgg	p.G4W	CTSC_ENST00000524463.1_Missense_Mutation_p.G4W|CTSC_ENST00000393301.4_5'UTR|CTSC_ENST00000529974.1_Missense_Mutation_p.G4W	NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	4					aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)	p.G4W(1)		large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AAGGAGGGCCCAGCACCCATG	0.657																																					p.G4W		Atlas-SNP	.											CTSC,NS,carcinoma,0,1	CTSC	46	.	1	Substitution - Missense(1)	ovary(1)	c.G10T						.						10	11	11					11																	88070831		2189	4282	6471	SO:0001583	missense	1075	exon1			AGGGCCCAGCACC	AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"Cathepsins"	2528	protein-coding gene	gene with protein product	"dipeptidyl peptidase 1"	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.10G>T	chr11.hg19:g.88070831C>A	ENSP00000227266:p.Gly4Trp	85.0	0.0		43.0	3.0	NM_148170	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	ENST00000227266.5	hg19	CCDS8282.1	.	.	.	.	.	.	.	.	.	.	C	5.816	0.334889	0.11013	.	.	ENSG00000109861	ENST00000393302;ENST00000227266;ENST00000524463;ENST00000529974	T	0.70986	-0.53	4.71	-9.42	0.00610	.	10.698900	0.00166	N	0.000002	T	0.36580	0.0972	N	0.01800	-0.715	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42137	-0.9469	9	.	.	.	.	5.3711	0.16140	0.115:0.4781:0.2502:0.1567	.	4;4;4	Q2HIY8;P53634-2;P53634	.;.;CATC_HUMAN	W	4	ENSP00000227266:G4W	.	G	-	1	0	CTSC	87710479	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.846000	0.01676	-3.971000	0.00086	-1.157000	0.01802	GGG	.	.		0.657	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814		A	88070831	C	A	88070831	3	1	49	1	0	0	0	0	1	0	0	0	4033	594	21	3	1540	3	CTSC	11	88070831	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	9294940	88070831	46935685	175	6332										
FAT3	120114	hgsc.bcm.edu	37	chr11	92616495	92616495	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtggcccccaacctccccgcCgtgtcaccctgccgctccga	9	22	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:92616495C>A	ENST00000298047.6	+	23	12890	c.12873C>A	c.(12871-12873)gcC>gcA	p.A4291A	FAT3_ENST00000533797.1_Silent_p.A626A|FAT3_ENST00000525166.1_Silent_p.A4141A|FAT3_ENST00000489716.1_3'UTR|FAT3_ENST00000409404.2_Silent_p.A4291A			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4291					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ACCTCCCCGCCGTGTCACCCT	0.652										TCGA Ovarian(4;0.039)																											p.A4291A		Atlas-SNP	.											.	FAT3	1822	.	0			c.C12873A						.						22	28	26					11																	92616495		2021	4085	6106	SO:0001819	synonymous_variant	120114	exon23			CCCCGCCGTGTCA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12873C>A	chr11.hg19:g.92616495C>A		36.0	0.0		25.0	10.0	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	hg19																																																																																				.	.		0.652	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92616495	C	A	92616495	2	1	49	1	0	0	0	0	0	0	0	1	5699	639	23	1		1	FAT3	11	92616495	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	4545664	92616495	42390021	176	6333										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103027464	103027464	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cgtggagcattgccaaaagaAcagacacgcttcaacagagt	10	10	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:103027464A>G	ENST00000375735.2	+	26	4236	c.4092A>G	c.(4090-4092)gaA>gaG	p.E1364E	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Silent_p.E1364E	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1364	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGCCAAAAGAACAGACACGCT	0.348																																					p.E1364E		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A4092G						.						56	56	56					11																	103027464		1847	4090	5937	SO:0001819	synonymous_variant	79659	exon26			AAAAGAACAGACA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.4092A>G	chr11.hg19:g.103027464A>G		67.0	0.0		81.0	4.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.348	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103027464	A	G	103027464	2	3	49	1	0	0	0	0	0	0	0	1	4848	40	2	2		2	DYNC2H1	11	103027464	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	10410969	103027464	31979052	177	6334										
NCAM1	4684	hgsc.bcm.edu	37	chr11	113085206	113085206	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tccatcacctggaggacttcTacccggaacatcagcagcga	9	14	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:113085206T>A	ENST00000533760.1	+	8	1277	c.678T>A	c.(676-678)tcT>tcA	p.S226S	NCAM1_ENST00000401611.2_Silent_p.S343S|NCAM1_ENST00000316851.7_Silent_p.S334S|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	344	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		GGAGGACTTCTACCCGGAACA	0.522																																					p.S344S		Atlas-SNP	.											.	NCAM1	372	.	0			c.T1032A						.						60	62	61					11																	113085206		1914	4123	6037	SO:0001819	synonymous_variant	4684	exon9			GACTTCTACCCGG		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.678T>A	chr11.hg19:g.113085206T>A		81.0	0.0		112.0	11.0	NM_001242608	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Silent	SNP	ENST00000533760.1	hg19																																																																																				.	.		0.522	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		A	113085206	T	A	113085206	2	1	49	1	0	0	0	0	0	0	0	1	10211	1509	53	4		4	NCAM1	11	113085206	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	10057742	113085206	21921310	178	6335										
TECTA	7007	hgsc.bcm.edu	37	chr11	121058616	121058616	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	acctgtcgctttcacgtcacCgtctttaaattcatagggga	8	11	4	0	rs559874132		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:121058616C>T	ENST00000392793.1	+	21	6346	c.6075C>T	c.(6073-6075)acC>acT	p.T2025T	TECTA_ENST00000264037.2_Silent_p.T2025T			O75443	TECTA_HUMAN	tectorin alpha	2025	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TTCACGTCACCGTCTTTAAAT	0.438													C|||	1	0.000199681	0	0	5008	,	,		22638	0		0	False		,,,				2504	0.001				p.T2025T		Atlas-SNP	.											.	TECTA	329	.	0			c.C6075T						.						183	159	167					11																	121058616		2203	4299	6502	SO:0001819	synonymous_variant	7007	exon20			CGTCACCGTCTTT	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.6075C>T	chr11.hg19:g.121058616C>T		93.0	0.0		89.0	24.0	NM_005422		Silent	SNP	ENST00000392793.1	hg19	CCDS8434.1																																																																																			.	.		0.438	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		T	121058616	C	T	121058616	2	4	49	1	0	0	0	0	0	0	0	1	15762	639	23	1		1	TECTA	11	121058616	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	7973410	121058616	13947900	179	6336										
GRAMD1B	57476	hgsc.bcm.edu	37	chr11	123489856	123489856	+	Frame_Shift_Del	DEL	C	C	-													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	atgggcccagctcttagagtCccaacaaaagtaccacgata					rs148264959	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:123489856delC	ENST00000529750.1	+	19	2378	c.2051delC	c.(2050-2052)tccfs	p.S684fs	GRAMD1B_ENST00000450171.2_Frame_Shift_Del_p.S371fs|GRAMD1B_ENST00000456860.2_Frame_Shift_Del_p.S691fs|GRAMD1B_ENST00000322282.7_Frame_Shift_Del_p.S684fs	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	684						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		CTCTTAGAGTCCCAACAAAAG	0.522																																					p.S684fs		Atlas-Indel,Pindel	.											.	GRAMD1B	122	.	0			c.2050delT						.						55	52	53					11																	123489856		1923	4119	6042	SO:0001589	frameshift_variant	57476	exon19			.	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.2051delC	chr11.hg19:g.123489856delC	ENSP00000436500:p.Ser684fs	49.0	0.0		50.0	14.0	NM_020716	Q6UW85|Q9ULL9	Frame_Shift_Del	DEL	ENST00000529750.1	hg19	CCDS53720.1																																																																																			.	.		0.522	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		-	123489856	C	-	123489856	7	5	49	1	0	1	0	1	0	0	0	0	6757	855	30	0	2125	0	GRAMD1B	11	123489856	Frame_Shift_Del	DEL	C	TCGA-BD-A3EP-01A-11D-A22F-10	2431240	123489856	11516660	180	6337										
ACRV1	56	hgsc.bcm.edu	37	chr11	125542541	125542541	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcatataatttgcatcctcgTtccatgggagaagaggttca	10	8	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:125542541T>C	ENST00000533904.1	-	4	1087	c.745A>G	c.(745-747)Acg>Gcg	p.T249A	ACRV1_ENST00000345274.1_Missense_Mutation_p.T139A|ACRV1_ENST00000527795.1_Missense_Mutation_p.T179A|CHEK1_ENST00000428830.2_Intron|ACRV1_ENST00000425431.1_Missense_Mutation_p.T105A|ACRV1_ENST00000353070.1_Missense_Mutation_p.T65A|ACRV1_ENST00000530048.1_Missense_Mutation_p.T194A|ACRV1_ENST00000348856.3_Missense_Mutation_p.T149A|ACRV1_ENST00000315608.3_Missense_Mutation_p.T230A|ACRV1_ENST00000445562.1_Missense_Mutation_p.T154A|ACRV1_ENST00000453509.1_Missense_Mutation_p.T160A			P26436	ASPX_HUMAN	acrosomal vesicle protein 1	249					multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				kidney(1)|large_intestine(3)|lung(2)	6	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0179)|Lung NSC(97;0.0185)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0713)		TGCATCCTCGTTCCATGGGAG	0.453																																					p.T249A		Atlas-SNP	.											.	ACRV1	21	.	0			c.A745G						.						189	163	172					11																	125542541		2201	4299	6500	SO:0001583	missense	56	exon4			TCCTCGTTCCATG	AK223335	CCDS8460.1, CCDS8461.1, CCDS44759.1, CCDS44761.1	11q24.2	2012-05-16			ENSG00000134940	ENSG00000134940			127	protein-coding gene	gene with protein product	"sperm protein 10"	102525				1693291, 8288254	Standard	NM_001612		Approved	SPACA2, SP-10, D11S4365	uc001qcs.3	P26436	OTTHUMG00000165854	ENST00000533904.1:c.745A>G	chr11.hg19:g.125542541T>C	ENSP00000432816:p.Thr249Ala	76.0	0.0		88.0	4.0	NM_001612	Q53FF4	Missense_Mutation	SNP	ENST00000533904.1	hg19	CCDS8460.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.646568	0.67358	.	.	ENSG00000134940	ENST00000533904;ENST00000433875;ENST00000257382;ENST00000426183;ENST00000453509;ENST00000445562;ENST00000348856;ENST00000345274;ENST00000425431;ENST00000353070;ENST00000315608;ENST00000530048;ENST00000527795	T;T;T;T;T;T;T;T;T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75	4.28	4.28	0.50868	.	0.374057	0.23483	N	0.047686	T	0.46946	0.1419	M	0.72118	2.19	0.34724	D	0.729022	D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;1.0;0.996;0.999;1.0;0.999;0.999;0.992	D;D;D;D;D;D;D;D;P	0.87578	0.996;0.979;0.998;0.99;0.997;0.998;0.963;0.995;0.85	T	0.60326	-0.7285	10	0.56958	D	0.05	-5.3828	10.1032	0.42517	0.0:0.0:0.0:1.0	.	249;230;139;65;154;194;105;179;160	P26436;P26436-2;P26436-8;P26436-11;P26436-6;P26436-3;P26436-10;P26436-4;P26436-5	ASPX_HUMAN;.;.;.;.;.;.;.;.	A	249;230;194;179;160;154;149;139;105;65;230;194;179	ENSP00000432816:T249A;ENSP00000407846:T230A;ENSP00000257382:T194A;ENSP00000411583:T179A;ENSP00000397448:T160A;ENSP00000412653:T154A;ENSP00000257385:T149A;ENSP00000257383:T139A;ENSP00000395453:T105A;ENSP00000257386:T65A;ENSP00000317684:T230A;ENSP00000433720:T194A;ENSP00000436819:T179A	ENSP00000257382:T194A	T	-	1	0	ACRV1	125047751	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.139000	0.50577	2.158000	0.67659	0.533000	0.62120	ACG	.	.		0.453	ACRV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386722.1	NM_001612		C	125542541	T	C	125542541	3	2	49	1	0	0	0	0	1	0	0	0	172	1725	60	2	56	2	ACRV1	11	125542541	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	2052685	125542541	9463975	181	6338										
APLP2	334	hgsc.bcm.edu	37	chr11	129991652	129991652	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaagaagaggaagaggaagaTgaagaggaagaggaagagga	18	0	0	8	rs3837393|rs71750553|rs1063201	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:129991652T>G	ENST00000263574.5	+	5	732	c.660T>G	c.(658-660)gaT>gaG	p.D220E	APLP2_ENST00000539648.1_Missense_Mutation_p.D64E|APLP2_ENST00000278756.7_Missense_Mutation_p.D230E|APLP2_ENST00000345598.5_Intron|APLP2_ENST00000543137.1_Missense_Mutation_p.D127E|APLP2_ENST00000528499.1_Missense_Mutation_p.D220E|APLP2_ENST00000338167.5_Missense_Mutation_p.D220E	NM_001642.2	NP_001633.1	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2	220	Asp/Glu-rich (highly acidic).|Poly-Glu.				cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0197)|Lung(977;0.24)		aagaggaagatgaagaggaag	0.418																																					p.D230E		Atlas-SNP	.											.	APLP2	71	.	0			c.T690G						.						91	89	90					11																	129991652		2201	4297	6498	SO:0001583	missense	334	exon5			GGAAGATGAAGAG	L19597	CCDS8486.1, CCDS44773.1, CCDS44774.1, CCDS44775.1, CCDS58196.1	11q24	2008-02-05			ENSG00000084234	ENSG00000084234			598	protein-coding gene	gene with protein product		104776		APPL2		10702673	Standard	NM_001642		Approved	APPH	uc021qsg.1	Q06481	OTTHUMG00000165767	ENST00000263574.5:c.660T>G	chr11.hg19:g.129991652T>G	ENSP00000263574:p.Asp220Glu	111.0	0.0		150.0	9.0	NM_001243299	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Missense_Mutation	SNP	ENST00000263574.5	hg19	CCDS8486.1	.	.	.	.	.	.	.	.	.	.	G	1.814	-0.473995	0.04414	.	.	ENSG00000084234	ENST00000528499;ENST00000539648;ENST00000263574;ENST00000338167;ENST00000278756;ENST00000543137	D;D;D;D;D;D	0.94457	-3.43;-3.36;-1.79;-1.9;-1.91;-1.9	4.5	-9.01	0.00744	.	0.365080	0.29806	N	0.011148	T	0.80839	0.4700	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B	0.04013	0.001;0.0;0.001;0.001;0.001;0.001	T	0.67106	-0.5754	10	0.12766	T	0.61	-1.3135	1.0637	0.01606	0.399:0.184:0.1083:0.3086	.	64;220;220;214;220;220	F5H845;Q06481;Q06481-2;B4E3I5;Q06481-4;Q06481-3	.;APLP2_HUMAN;.;.;.;.	E	220;64;220;220;230;127	ENSP00000435914:D220E;ENSP00000443728:D64E;ENSP00000263574:D220E;ENSP00000345444:D220E;ENSP00000278756:D230E;ENSP00000444122:D127E	ENSP00000263574:D220E	D	+	3	2	APLP2	129496862	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	-2.113000	0.01331	-5.053000	0.00023	-1.251000	0.01509	GAT	.	.		0.418	APLP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386109.1	NM_001642		G	129991652	T	G	129991652	3	3	49	1	0	0	0	0	1	0	0	0	779	1461	51	5	678	5	APLP2	11	129991652	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	4449111	129991652	5014864	182	6339										
OPCML	4978	hgsc.bcm.edu	37	chr11	132527021	132527021	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccgggacgttttgggatgatTgtctgtctgcacagagcagg	15	8	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:132527021T>A	ENST00000331898.7	-	2	939	c.361A>T	c.(361-363)Aat>Tat	p.N121Y	OPCML_ENST00000524381.1_Missense_Mutation_p.N114Y|OPCML_ENST00000374778.4_Missense_Mutation_p.N80Y|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000541867.1_Missense_Mutation_p.N121Y	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	121	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		TTGGGATGATTGTCTGTCTGC	0.502																																					p.N121Y		Atlas-SNP	.											.	OPCML	166	.	0			c.A361T						.						220	181	194					11																	132527021		2201	4297	6498	SO:0001583	missense	4978	exon2			GATGATTGTCTGT	BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.361A>T	chr11.hg19:g.132527021T>A	ENSP00000330862:p.Asn121Tyr	175.0	0.0		243.0	54.0	NM_002545	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	hg19	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.795007	0.90453	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	5.83	5.83	0.93111	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.052133	0.85682	D	0.000000	T	0.77280	0.4107	M	0.70275	2.135	0.52099	D	0.999949	D;D;D;D	0.58620	0.966;0.983;0.966;0.966	D;P;P;P	0.64321	0.924;0.908;0.889;0.842	T	0.79713	-0.1688	10	0.72032	D	0.01	-20.5804	16.1846	0.81942	0.0:0.0:0.0:1.0	.	121;114;121;121	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	Y	121;114;80;88;121	ENSP00000330862:N121Y;ENSP00000434750:N114Y;ENSP00000363910:N80Y;ENSP00000445496:N121Y	ENSP00000330862:N121Y	N	-	1	0	OPCML	132032231	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.190000	0.72057	2.229000	0.72834	0.533000	0.62120	AAT	.	.		0.502	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		A	132527021	T	A	132527021	3	1	49	1	0	0	0	0	1	0	0	0	10883	1812	63	4	700	4	OPCML	11	132527021	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	2535369	132527021	2479495	183	6340										
CCDC77	84318	hgsc.bcm.edu	37	chr12	520926	520926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cacgtaggcgaacagttgtcTccaaacgtggtgttgccgtc	12	11	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:520926T>C	ENST00000239830.4	+	4	231	c.52T>C	c.(52-54)Tcc>Ccc	p.S18P	CCDC77_ENST00000540344.1_3'UTR|CCDC77_ENST00000422000.1_5'UTR|CCDC77_ENST00000540180.1_5'UTR|CCDC77_ENST00000412006.2_5'UTR	NM_032358.3	NP_115734.1	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77	18						centrosome (GO:0005813)|membrane (GO:0016020)				cervix(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			AACAGTTGTCTCCAAACGTGG	0.468																																					p.S18P		Atlas-SNP	.											.	CCDC77	35	.	0			c.T52C						.						83	73	76					12																	520926		2203	4300	6503	SO:0001583	missense	84318	exon4			GTTGTCTCCAAAC	AK027638	CCDS8503.1, CCDS44781.1	12p13.33	2006-02-16			ENSG00000120647	ENSG00000120647			28203	protein-coding gene	gene with protein product						12477932	Standard	NM_001130148		Approved	MGC13183	uc001qig.3	Q9BR77	OTTHUMG00000129214	ENST00000239830.4:c.52T>C	chr12.hg19:g.520926T>C	ENSP00000239830:p.Ser18Pro	56.0	0.0		77.0	4.0	NM_032358	B4DDE8	Missense_Mutation	SNP	ENST00000239830.4	hg19	CCDS8503.1	.	.	.	.	.	.	.	.	.	.	T	8.999	0.979608	0.18812	.	.	ENSG00000120647	ENST00000535052;ENST00000239830	T;T	0.56941	0.43;0.43	4.5	-8.91	0.00778	.	1.710740	0.02799	N	0.122922	T	0.32194	0.0821	N	0.17082	0.46	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.25433	-1.0132	10	0.51188	T	0.08	13.3553	8.0285	0.30451	0.0:0.4114:0.3232:0.2654	.	18	Q9BR77	CCD77_HUMAN	P	18	ENSP00000443209:S18P;ENSP00000239830:S18P	ENSP00000239830:S18P	S	+	1	0	CCDC77	391187	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.974000	0.03794	-1.814000	0.01224	-0.388000	0.06559	TCC	.	.		0.468	CCDC77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251296.1	NM_032358		C	520926	T	C	520926	3	2	49	1	0	0	0	0	1	0	0	0	2853	1551	54	2	58	2	CCDC77	12	520926	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10		520926	133330969	184	6341										
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	653566	653566	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tggcagctctatccagcagcTcaggaggaacctgcatttcc	10	13	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:653566T>C	ENST00000266383.5	+	4	426	c.413T>C	c.(412-414)cTc>cCc	p.L138P	B4GALNT3_ENST00000544638.1_3'UTR	NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	138					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			ATCCAGCAGCTCAGGAGGAAC	0.617																																					p.L138P		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.T413C						.						131	114	120					12																	653566		2203	4300	6503	SO:0001583	missense	283358	exon4			AGCAGCTCAGGAG	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.413T>C	chr12.hg19:g.653566T>C	ENSP00000266383:p.Leu138Pro	32.0	0.0		46.0	5.0	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.273531	0.80580	.	.	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.23950	1.88;1.88	4.73	4.73	0.59995	PA14 (2);	0.000000	0.64402	D	0.000001	T	0.51058	0.1652	M	0.79011	2.435	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.71870	0.975;0.951	T	0.57406	-0.7817	10	0.72032	D	0.01	-20.2878	14.2118	0.65769	0.0:0.0:0.0:1.0	.	40;138	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	P	138;40	ENSP00000266383:L138P;ENSP00000322953:L40P	ENSP00000266383:L138P	L	+	2	0	B4GALNT3	523827	1.000000	0.71417	0.984000	0.44739	0.944000	0.59088	7.609000	0.82925	1.757000	0.51966	0.402000	0.26972	CTC	.	.		0.617	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		C	653566	T	C	653566	3	2	49	1	0	0	0	0	1	0	0	0	1268	1551	54	2	427	2	B4GALNT3	12	653566	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	132640	653566	133198329	185	6342										
SLC38A1	81539	hgsc.bcm.edu	37	chr12	46599923	46599923	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggtaactatcaccaccagaaCgcggccatccacgtaccagg	9	15	1	1	rs369346779		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:46599923C>T	ENST00000398637.5	-	9	1280	c.586G>A	c.(586-588)Gtt>Att	p.V196I	SLC38A1_ENST00000439706.1_Missense_Mutation_p.V196I|SLC38A1_ENST00000546893.1_Missense_Mutation_p.V196I|SLC38A1_ENST00000549049.1_Missense_Mutation_p.V196I|SLC38A1_ENST00000549633.1_5'UTR|SLC38A1_ENST00000552197.1_Missense_Mutation_p.V196I	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	196					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)			NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			ACCACCAGAACGCGGCCATCC	0.393																																					p.V196I		Atlas-SNP	.											SLC38A1,colon,carcinoma,0,1	SLC38A1	58	.	0			c.G586A						.	C	ILE/VAL,ILE/VAL	0,3836		0,0,1918	87	90	89		586,586	-5.6	0	12		89	1,8287		0,1,4143	no	missense,missense	SLC38A1	NM_001077484.1,NM_030674.3	29,29	0,1,6061	TT,TC,CC		0.0121,0.0,0.0082	benign,benign	196/488,196/488	46599923	1,12123	1918	4144	6062	SO:0001583	missense	81539	exon9			CCAGAACGCGGCC	AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"Solute carriers"	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.586G>A	chr12.hg19:g.46599923C>T	ENSP00000381634:p.Val196Ile	34.0	0.0		39.0	2.0	NM_030674	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Missense_Mutation	SNP	ENST00000398637.5	hg19	CCDS41774.1	.	.	.	.	.	.	.	.	.	.	C	9.492	1.100901	0.20552	0.0	1.21E-4	ENSG00000111371	ENST00000549049;ENST00000439706;ENST00000398637;ENST00000546893;ENST00000552197	T;T;T;T;T	0.02525	4.26;4.26;4.26;4.26;4.26	5.7	-5.61	0.02489	.	0.669277	0.13946	N	0.351847	T	0.00815	0.0027	N	0.01352	-0.895	0.09310	N	1	B;B;B	0.12630	0.006;0.003;0.0	B;B;B	0.13407	0.009;0.005;0.003	T	0.44050	-0.9353	10	0.29301	T	0.29	-0.7853	2.2946	0.04147	0.2037:0.2101:0.3999:0.1863	.	196;196;196	B5MEC5;F8VX04;Q9H2H9	.;.;S38A1_HUMAN	I	196	ENSP00000449607:V196I;ENSP00000398142:V196I;ENSP00000381634:V196I;ENSP00000447853:V196I;ENSP00000449756:V196I	ENSP00000381634:V196I	V	-	1	0	SLC38A1	44886190	0.000000	0.05858	0.001000	0.08648	0.650000	0.38633	-0.721000	0.04963	-0.512000	0.06505	-0.463000	0.05309	GTT	.	.		0.393	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2			T	46599923	C	T	46599923	3	4	49	1	0	0	0	0	1	0	0	0	14616	536	19	1	913	1	SLC38A1	12	46599923	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	45946357	46599923	87251972	186	6343										
SLC38A2	54407	hgsc.bcm.edu	37	chr12	46756927	46756927	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agcaattctgactcaacatgTtctacagggaaagaccaaaa	7	9	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:46756927T>C	ENST00000256689.5	-	13	1500	c.1056A>G	c.(1054-1056)gaA>gaG	p.E352E	SLC38A2_ENST00000551374.1_Splice_Site_p.E190E|SLC38A2_ENST00000547252.1_5'Flank	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	352					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		ACTCAACATGTTCTACAGGGA	0.393																																					p.E352E	Ovarian(9;448 492 8335 28722 40361)	Atlas-SNP	.											.	SLC38A2	36	.	0			c.A1056G						.						137	128	131					12																	46756927		2203	4300	6503	SO:0001630	splice_region_variant	54407	exon13			AACATGTTCTACA	AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"Solute carriers"	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.1055-1A>G	chr12.hg19:g.46756927T>C		64.0	0.0		75.0	4.0	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Silent	SNP	ENST00000256689.5	hg19	CCDS8749.1																																																																																			.	.		0.393	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1		Silent	C	46756927	T	C	46756927	5	2	49	1	0	0	0	0	0	0	1	0	14619	1739	60	2	480	2	SLC38A2	12	46756927	Splice_Site	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	157004	46756927	87094968	187	6344										
LMBR1L	55716	hgsc.bcm.edu	37	chr12	49500745	49500745	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gggagggaaatcaaagtaccTgtggtgaactcagcaggctt	14	7	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:49500745T>C	ENST00000267102.8	-	2	498	c.156A>G	c.(154-156)acA>acG	p.T52T	LMBR1L_ENST00000547382.1_Splice_Site_p.T52T|LMBR1L_ENST00000395141.4_5'Flank|LMBR1L_ENST00000553204.1_5'UTR	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	52	LCN1-binding.				endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TCAAAGTACCTGTGGTGAACT	0.522																																					p.T52T		Atlas-SNP	.											.	LMBR1L	61	.	0			c.A156G						.						122	138	133					12																	49500745		2113	4236	6349	SO:0001630	splice_region_variant	55716	exon2			AGTACCTGTGGTG	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"limb region 1 homolog (mouse)-like"			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.157+1A>G	chr12.hg19:g.49500745T>C		97.0	0.0		119.0	5.0	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Silent	SNP	ENST00000267102.8	hg19	CCDS8780.2																																																																																			.	.		0.522	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113	Silent	C	49500745	T	C	49500745	5	2	49	1	0	0	0	0	0	0	1	0	8850	1594	55	2	1377	2	LMBR1L	12	49500745	Splice_Site	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	2743818	49500745	84351150	188	6345										
FAIM2	23017	hgsc.bcm.edu	37	chr12	50281167	50281167	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	caaggagctagaccacactcAccaatgtaaatacacccgct	6	14	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:50281167A>T	ENST00000320634.3	-	11	896		c.e11+1		FAIM2_ENST00000550890.1_Splice_Site	NM_012306.3	NP_036438.2	Q9BWQ8	LFG2_HUMAN	Fas apoptotic inhibitory molecule 2						apoptotic process (GO:0006915)|cerebellar granular layer development (GO:0021681)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum development (GO:0021549)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of neuron apoptotic process (GO:0043523)|response to ischemia (GO:0002931)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|postsynaptic membrane (GO:0045211)				endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|skin(2)	14						GACCACACTCACCAATGTAAA	0.577																																					.		Atlas-SNP	.											.	FAIM2	32	.	0			c.801+2T>A						.						129	95	106					12																	50281167		2203	4300	6503	SO:0001630	splice_region_variant	23017	exon12			ACACTCACCAATG	AB023167	CCDS8791.1	12q13	2010-03-18				ENSG00000135472			17067	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 2"	604306				10231032, 10535980	Standard	NM_012306		Approved	KIAA0950, LFG, NMP35, LIFEGUARD, TMBIM2, LFG2	uc001rvj.2	Q9BWQ8	OTTHUMG00000169808	ENST00000320634.3:c.801+1T>A	chr12.hg19:g.50281167A>T		32.0	0.0		47.0	10.0	NM_012306	A8K1W6|B3KR08|Q9UJY9|Q9Y2F7	Splice_Site	SNP	ENST00000320634.3	hg19	CCDS8791.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.449226	0.63178	.	.	ENSG00000135472	ENST00000320634;ENST00000550890;ENST00000550635;ENST00000552669	.	.	.	4.36	4.36	0.52297	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8714	0.41177	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAIM2	48567434	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	5.056000	0.64287	1.841000	0.53522	0.379000	0.24179	.	.	.		0.577	FAIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405984.1	NM_012306	Intron	T	50281167	A	T	50281167	5	4	49	1	0	0	0	0	0	0	1	0	5381	173	6	4	155	4	FAIM2	12	50281167	Splice_Site	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	780422	50281167	83570728	189	6346										
AQP5	362	hgsc.bcm.edu	37	chr12	50357929	50357929	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gctcttttggccctgcggtgGtcatgaatcggttcagcccc	12	13	3	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:50357929G>C	ENST00000293599.6	+	3	731	c.583G>C	c.(583-585)Gtc>Ctc	p.V195L	RP11-469H8.6_ENST00000550214.1_RNA|RP11-469H8.6_ENST00000552379.1_RNA|RP11-469H8.6_ENST00000550530.1_RNA	NM_001651.2	NP_001642.1	P55064	AQP5_HUMAN	aquaporin 5	195					camera-type eye morphogenesis (GO:0048593)|carbon dioxide transport (GO:0015670)|excretion (GO:0007588)|odontogenesis (GO:0042476)|pancreatic juice secretion (GO:0030157)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)			large_intestine(1)|lung(3)	4						CCCTGCGGTGGTCATGAATCG	0.607																																					p.V195L		Atlas-SNP	.											.	AQP5	19	.	0			c.G583C						.						126	105	112					12																	50357929		2203	4300	6503	SO:0001583	missense	362	exon3			GCGGTGGTCATGA	U46569	CCDS8793.1	12q13	2013-09-10				ENSG00000161798		"Ion channels / Aquaporins"	638	protein-coding gene	gene with protein product		600442				8621489, 23830519	Standard	NM_001651		Approved		uc001rvo.3	P55064	OTTHUMG00000169710	ENST00000293599.6:c.583G>C	chr12.hg19:g.50357929G>C	ENSP00000293599:p.Val195Leu	82.0	0.0		107.0	15.0	NM_001651	Q6FGW8	Missense_Mutation	SNP	ENST00000293599.6	hg19	CCDS8793.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.784050	0.31593	.	.	ENSG00000161798	ENST00000293599	D	0.86497	-2.13	5.07	0.489	0.16854	Aquaporin-like (2);	0.424918	0.19449	N	0.113991	T	0.74809	0.3765	N	0.25286	0.73	0.32061	N	0.595644	B	0.02656	0.0	B	0.08055	0.003	T	0.66448	-0.5921	10	0.31617	T	0.26	-36.1104	8.0666	0.30665	0.4327:0.0:0.5673:0.0	.	195	P55064	AQP5_HUMAN	L	195	ENSP00000293599:V195L	ENSP00000293599:V195L	V	+	1	0	AQP5	48644196	0.018000	0.18449	0.860000	0.33809	0.724000	0.41520	0.077000	0.14738	0.244000	0.21351	0.655000	0.94253	GTC	.	.		0.607	AQP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405542.2	NM_001651		C	50357929	G	C	50357929	3	2	49	1	0	0	0	0	1	0	0	0	829	1261	44	4	593	4	AQP5	12	50357929	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	76762	50357929	83493966	190	6347										
C12orf44	60673	hgsc.bcm.edu	37	chr12	52470885	52470885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gggacgtgcagccctacctgTacaagatctccttccagatc	9	14	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:52470885T>C	ENST00000336854.4	+	4	1046	c.568T>C	c.(568-570)Tac>Cac	p.Y190H	OR7E47P_ENST00000546390.1_RNA|RP11-1100L3.7_ENST00000550301.1_RNA	NM_001098673.1|NM_021934.4	NP_001092143.1|NP_068753.2	Q9BSB4	ATGA1_HUMAN		190					autophagic vacuole assembly (GO:0000045)	pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein complex binding (GO:0032403)			endometrium(1)|lung(2)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(357;0.0978)		GCCCTACCTGTACAAGATCTC	0.572																																					p.Y190H		Atlas-SNP	.											.	C12orf44	14	.	0			c.T568C						.						105	92	96					12																	52470885		2203	4300	6503	SO:0001583	missense	60673	exon4			TACCTGTACAAGA																												ENST00000336854.4:c.568T>C	chr12.hg19:g.52470885T>C	ENSP00000338990:p.Tyr190His	72.0	0.0		97.0	4.0	NM_001098673	Q9HAE2|Q9HBN1	Missense_Mutation	SNP	ENST00000336854.4	hg19	CCDS8820.1	.	.	.	.	.	.	.	.	.	.	T	16.28	3.079662	0.55753	.	.	ENSG00000123395	ENST00000336854;ENST00000553049;ENST00000550984	.	.	.	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.38746	0.1052	N	0.11560	0.145	0.58432	D	0.999998	B	0.11235	0.004	B	0.09377	0.004	T	0.23261	-1.0193	9	0.41790	T	0.15	-26.5336	13.7571	0.62943	0.0:0.0:0.0:1.0	.	190	Q9BSB4	ATGA1_HUMAN	H	190	.	ENSP00000338990:Y190H	Y	+	1	0	C12orf44	50757152	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.455000	0.80726	2.145000	0.66743	0.533000	0.62120	TAC	.	.		0.572	C12orf44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405063.1			C	52470885	T	C	52470885	3	2	49	1	0	0	0	0	1	0	0	0	1692	1638	57	2	574	2	C12orf44	12	52470885	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	2112956	52470885	81381010	191	6348										
ITGA7	3679	hgsc.bcm.edu	37	chr12	56088716	56088716	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccaggccaatgactggctgcCcactcagtgcaaacagggct	11	14	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:56088716C>T	ENST00000555728.1	-	16	2202	c.2174G>A	c.(2173-2175)gGg>gAg	p.G725E	ITGA7_ENST00000257880.7_Missense_Mutation_p.G725E|ITGA7_ENST00000452168.2_Missense_Mutation_p.G588E|ITGA7_ENST00000553804.1_Missense_Mutation_p.G685E|ITGA7_ENST00000394230.2_Missense_Mutation_p.G685E|ITGA7_ENST00000347027.6_Missense_Mutation_p.G675E|ITGA7_ENST00000394229.2_Missense_Mutation_p.G681E|ITGA7_ENST00000257879.6_Missense_Mutation_p.G681E			Q13683	ITA7_HUMAN	integrin, alpha 7	725					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GACTGGCTGCCCACTCAGTGC	0.612																																					p.G685E		Atlas-SNP	.											.	ITGA7	194	.	0			c.G2054A						.						52	52	52					12																	56088716		2203	4300	6503	SO:0001583	missense	3679	exon15			GGCTGCCCACTCA		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.2174G>A	chr12.hg19:g.56088716C>T	ENSP00000452387:p.Gly725Glu	49.0	0.0		61.0	6.0	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Missense_Mutation	SNP	ENST00000555728.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.89	2.371490	0.42003	.	.	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000555728	T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	4.95	4.95	0.65309	Integrin alpha-2 (1);	0.201844	0.42294	N	0.000730	T	0.44912	0.1316	L	0.43152	1.355	0.48901	D	0.999723	B;B;B;P	0.39601	0.007;0.368;0.017;0.68	B;B;B;P	0.44860	0.018;0.329;0.051;0.462	T	0.40997	-0.9533	10	0.49607	T	0.09	.	9.6719	0.40017	0.0:0.9039:0.0:0.0961	.	588;725;685;744	Q13683-13;Q13683;Q13683-3;Q4LE35	.;ITA7_HUMAN;.;.	E	685;681;675;588;725;685;681;725	ENSP00000452120:G685E;ENSP00000257879:G681E;ENSP00000343009:G675E;ENSP00000393844:G588E;ENSP00000257880:G725E;ENSP00000377777:G685E;ENSP00000377776:G681E;ENSP00000452387:G725E	ENSP00000257879:G681E	G	-	2	0	ITGA7	54374983	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.267000	0.58877	2.471000	0.83476	0.561000	0.74099	GGG	.	.		0.612	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		T	56088716	C	T	56088716	3	4	49	1	0	0	0	0	1	0	0	0	7890	623	22	3	1415	3	ITGA7	12	56088716	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	3617831	56088716	77763179	192	6349										
ORMDL2	29095	hgsc.bcm.edu	37	chr12	56212815	56212815	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggtggcacacagcgaagtaaAccccaacacccgagtgatga	11	12	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:56212815A>G	ENST00000243045.5	+	2	227	c.32A>G	c.(31-33)aAc>aGc	p.N11S	SARNP_ENST00000336133.3_5'Flank|SARNP_ENST00000552080.1_5'Flank|ORMDL2_ENST00000550836.1_Intron|RP11-762I7.5_ENST00000546837.1_Intron|ORMDL2_ENST00000552672.1_Intron|SARNP_ENST00000444631.2_5'Flank|RP11-762I7.5_ENST00000552719.1_Intron|ORMDL2_ENST00000548974.1_Missense_Mutation_p.N11S	NM_014182.4	NP_054901.1	Q53FV1	ORML2_HUMAN	ORMDL sphingolipid biosynthesis regulator 2	11					ceramide metabolic process (GO:0006672)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|lung(3)	4						AGCGAAGTAAACCCCAACACC	0.527																																					p.N11S		Atlas-SNP	.											.	ORMDL2	8	.	0			c.A32G						.						154	128	137					12																	56212815		2203	4300	6503	SO:0001583	missense	29095	exon2			AAGTAAACCCCAA	AF395707	CCDS8893.1	12q13.2	2014-06-16	2014-06-16			ENSG00000123353			16037	protein-coding gene	gene with protein product		610074	"ORM1 (S. cerevisiae)-like 2", "ORM1-like 2 (S. cerevisiae)"			12093374, 23066021	Standard	NM_014182		Approved	HSPC160, adoplin-2, MST095, MSTP095	uc001shw.1	Q53FV1		ENST00000243045.5:c.32A>G	chr12.hg19:g.56212815A>G	ENSP00000243045:p.Asn11Ser	81.0	0.0		81.0	4.0	NM_014182	B2RA58|Q7Z4E5|Q8NFX0|Q9P004	Missense_Mutation	SNP	ENST00000243045.5	hg19	CCDS8893.1	.	.	.	.	.	.	.	.	.	.	A	14.96	2.692480	0.48202	.	.	ENSG00000123353	ENST00000243045;ENST00000548974	.	.	.	5.05	3.91	0.45181	.	0.000000	0.85682	D	0.000000	T	0.81777	0.4894	M	0.94063	3.49	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83198	-0.0080	9	0.56958	D	0.05	-16.2825	9.1752	0.37107	0.914:0.0:0.086:0.0	.	11	Q53FV1	ORML2_HUMAN	S	11	.	ENSP00000243045:N11S	N	+	2	0	ORMDL2	54499082	1.000000	0.71417	0.987000	0.45799	0.038000	0.13279	9.139000	0.94554	1.061000	0.40601	-0.256000	0.11100	AAC	.	.		0.527	ORMDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407934.1	NM_014182		G	56212815	A	G	56212815	3	3	49	1	0	0	0	0	1	0	0	0	11279	43	2	2	34	2	ORMDL2	12	56212815	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	124099	56212815	77639080	193	6350										
LRP1	4035	hgsc.bcm.edu	37	chr12	57577928	57577928	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggtcgcccggctcaatggctCcttccgctacgtggtgatct	12	14	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:57577928C>T	ENST00000243077.3	+	37	6456	c.5990C>T	c.(5989-5991)tCc>tTc	p.S1997F		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1997					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CTCAATGGCTCCTTCCGCTAC	0.592																																					p.S1997F		Atlas-SNP	.											.	LRP1	428	.	0			c.C5990T						.						74	58	64					12																	57577928		2203	4300	6503	SO:0001583	missense	4035	exon37			ATGGCTCCTTCCG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.5990C>T	chr12.hg19:g.57577928C>T	ENSP00000243077:p.Ser1997Phe	74.0	0.0		104.0	12.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	33	5.244038	0.95272	.	.	ENSG00000123384	ENST00000243077	D	0.96265	-3.96	4.84	4.84	0.62591	Six-bladed beta-propeller, TolB-like (1);	0.152639	0.43919	D	0.000507	D	0.98185	0.9400	M	0.86343	2.81	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.98316	1.0526	10	0.46703	T	0.11	.	16.9352	0.86201	0.0:1.0:0.0:0.0	.	1997	Q07954	LRP1_HUMAN	F	1997	ENSP00000243077:S1997F	ENSP00000243077:S1997F	S	+	2	0	LRP1	55864195	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.879000	0.69690	2.532000	0.85374	0.555000	0.69702	TCC	.	.		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57577928	C	T	57577928	3	4	49	1	0	0	0	0	1	0	0	0	8960	855	30	3	6136	3	LRP1	12	57577928	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1365113	57577928	76273967	194	6351										
GLIPR1L2	144321	hgsc.bcm.edu	37	chr12	75816822	75816822	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cataatggattggacaagaaAaataagcgattgaacactag	9	5	0	2	rs75261424		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:75816822A>G	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000378692.3_Intron|GLIPR1L2_ENST00000435775.1_Intron|GLIPR1L2_ENST00000320460.4_Silent_p.K241K|GLIPR1L2_ENST00000441218.1_Intron	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2							integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						TGGACAAGAAAAATAAGCGAT	0.313																																					p.K241K		Atlas-SNP	.											.	GLIPR1L2	54	.	0			c.A723G						.						109	111	110					12																	75816822		2203	4300	6503	SO:0001627	intron_variant	144321	exon4			CAAGAAAAATAAG	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.670+53A>G	chr12.hg19:g.75816822A>G		109.0	0.0		90.0	5.0	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Silent	SNP	ENST00000550916.1	hg19	CCDS58258.1																																																																																			.	.		0.313	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436		G	75816822	A	G	75816822	1	3	49	0	1	0	0	0	0	0	0	0	6451	11	1	2		2	GLIPR1L2	12	75816822	Intron	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	18238894	75816822	58035073	195	6352										
USP30	84749	hgsc.bcm.edu	37	chr12	109519740	109519740	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cttcttctcatgctgtagggTcacccattgaccctggacca	8	14	3	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:109519740T>C	ENST00000257548.5	+	9	876	c.783T>C	c.(781-783)ggT>ggC	p.G261G	USP30_ENST00000392784.2_Silent_p.G230G	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	261	USP.				mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(7)|kidney(1)|large_intestine(1)|liver(2)|lung(11)|prostate(1)|skin(3)|stomach(2)	28						TGCTGTAGGGTCACCCATTGA	0.443																																					p.G261G		Atlas-SNP	.											.	USP30	48	.	0			c.T783C						.						215	189	198					12																	109519740		2203	4300	6503	SO:0001819	synonymous_variant	84749	exon9			GTAGGGTCACCCA	BC022094	CCDS9123.2	12q23.3	2006-01-20	2005-08-08		ENSG00000135093	ENSG00000135093		"Ubiquitin-specific peptidases"	20065	protein-coding gene	gene with protein product		612492	"ubiquitin specific protease 30"			12838346	Standard	XM_005253962		Approved	MGC10702, FLJ40511	uc010sxi.2	Q70CQ3	OTTHUMG00000133613	ENST00000257548.5:c.783T>C	chr12.hg19:g.109519740T>C		94.0	0.0		155.0	7.0	NM_032663	Q8WTU7|Q96JX4|Q9BSS3	Silent	SNP	ENST00000257548.5	hg19	CCDS9123.2																																																																																			.	.		0.443	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663		C	109519740	T	C	109519740	2	2	49	1	0	0	0	0	0	0	0	1	17076	1654	58	2		2	USP30	12	109519740	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	33702918	109519740	24332155	196	6353										
NOS1	4842	hgsc.bcm.edu	37	chr12	117726019	117726019	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cagatgtactcagtgcatccCgtttcctggaagatcaagag	10	10	2	3	rs368611180	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:117726019C>A	ENST00000344089.3	-	6	1728	c.1043G>T	c.(1042-1044)cGg>cTg	p.R348L	NOS1_ENST00000338101.4_Silent_p.T329T|NOS1_ENST00000317775.6_Silent_p.T329T	NM_001204213.1|NM_001204214.1	NP_001191142.1|NP_001191143.1	Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.T329T(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CAGTGCATCCCGTTTCCTGGA	0.512																																					p.T329T	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											NOS1,NS,carcinoma,0,1	NOS1	240	.	1	Substitution - coding silent(1)	lung(1)	c.G987T						.						111	108	109					12																	117726019		1955	4160	6115	SO:0001583	missense	4842	exon5			GCATCCCGTTTCC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000344089.3:c.1043G>T	chr12.hg19:g.117726019C>A	ENSP00000339862:p.Arg348Leu	35.0	0.0		44.0	2.0	NM_000620		Silent	SNP	ENST00000344089.3	hg19		.	.	.	.	.	.	.	.	.	.	C	12.39	1.924686	0.34002	.	.	ENSG00000089250	ENST00000344089	T	0.08282	3.11	5.93	-3.56	0.04626	.	.	.	.	.	T	0.08537	0.0212	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.36696	-0.9737	6	0.87932	D	0	-11.6477	4.4175	0.11463	0.0795:0.288:0.1693:0.4632	.	.	.	.	L	348	ENSP00000339862:R348L	ENSP00000339862:R348L	R	-	2	0	NOS1	116210402	0.000000	0.05858	0.890000	0.34922	0.487000	0.33371	-3.658000	0.00401	-0.588000	0.05882	-1.008000	0.02478	CGG	.	.		0.512	NOS1-201	KNOWN	basic	protein_coding	protein_coding				A	117726019	C	A	117726019	3	1	49	1	0	0	0	0	1	0	0	0	10550	639	23	1	3417	1	NOS1	12	117726019	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	8206279	117726019	16125876	197	6354										
XPO4	64328	hgsc.bcm.edu	37	chr13	21375110	21375110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agattcaacttctgaaactcTgagaatggcagacaacagcc	8	10	3	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:21375110T>C	ENST00000255305.6	-	14	1908	c.1837A>G	c.(1837-1839)Aga>Gga	p.R613G	XPO4_ENST00000400602.2_Missense_Mutation_p.R613G			Q9C0E2	XPO4_HUMAN	exportin 4	613					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		TCTGAAACTCTGAGAATGGCA	0.358																																					p.R613G		Atlas-SNP	.											.	XPO4	153	.	0			c.A1837G						.						90	81	84					13																	21375110		1810	4073	5883	SO:0001583	missense	64328	exon14			AAACTCTGAGAAT	AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"Exportins"	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.1837A>G	chr13.hg19:g.21375110T>C	ENSP00000255305:p.Arg613Gly	90.0	0.0		89.0	4.0	NM_022459	Q5VUZ5|Q8N3V6|Q9H934	Missense_Mutation	SNP	ENST00000255305.6	hg19	CCDS41872.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.054300	0.55218	.	.	ENSG00000132953	ENST00000400602;ENST00000456108;ENST00000255305	T;T	0.65178	-0.14;-0.14	5.65	3.12	0.35913	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55081	0.1898	L	0.55481	1.735	0.52099	D	0.999945	B	0.30146	0.27	B	0.27076	0.076	T	0.50268	-0.8848	10	0.40728	T	0.16	-9.1414	12.507	0.55987	0.0:0.0:0.2639:0.7361	.	613	Q9C0E2	XPO4_HUMAN	G	613;483;613	ENSP00000383444:R613G;ENSP00000255305:R613G	ENSP00000255305:R613G	R	-	1	2	XPO4	20273110	0.999000	0.42202	0.483000	0.27378	0.935000	0.57460	3.155000	0.50700	0.378000	0.24764	0.533000	0.62120	AGA	.	.		0.358	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459		C	21375110	T	C	21375110	3	2	49	1	0	0	0	0	1	0	0	0	17461	1588	55	2	1658	2	XPO4	13	21375110	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10		21375110	93794768	198	6355										
SKA3	221150	hgsc.bcm.edu	37	chr13	21750551	21750551	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agcgctcgctgcagccgggcCgtctcgcagtccagcgtgct	14	16	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:21750551C>T	ENST00000314759.5	-	1	190	c.66G>A	c.(64-66)acG>acA	p.T22T	SKA3_ENST00000400018.3_Silent_p.T22T|MRP63_ENST00000309594.4_5'Flank	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	22					chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)		p.T22T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GCAGCCGGGCCGTCTCGCAGT	0.731																																					p.T22T		Atlas-SNP	.											SKA3,NS,carcinoma,0,1	SKA3	76	.	1	Substitution - coding silent(1)	ovary(1)	c.G66A						.						7	8	8					13																	21750551		2140	4233	6373	SO:0001819	synonymous_variant	221150	exon1			CCGGGCCGTCTCG	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 3"	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.66G>A	chr13.hg19:g.21750551C>T		22.0	0.0		16.0	2.0	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Silent	SNP	ENST00000314759.5	hg19	CCDS31946.1																																																																																			.	.		0.731	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061		T	21750551	C	T	21750551	2	4	49	1	0	0	0	0	0	0	0	1	14369	639	23	1		1	SKA3	13	21750551	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	375441	21750551	93419327	199	6356										
EFHA1	221154	hgsc.bcm.edu	37	chr13	22140947	22140947	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccaactcacgttccatttgcTcaaacatcactgagaagagg	7	12	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:22140947T>C	ENST00000382374.4	-	2	412	c.347A>G	c.(346-348)gAg>gGg	p.E116G		NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2	116					mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										TTCCATTTGCTCAAACATCAC	0.383																																					p.E116G		Atlas-SNP	.											.	EFHA1	33	.	0			c.A347G						.						63	61	62					13																	22140947		2202	4300	6502	SO:0001583	missense	221154	exon2			ATTTGCTCAAACA	AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"EF-hand domain containing"	31830	protein-coding gene	gene with protein product		610632	"EF hand domain family A1", "EF-hand domain family, member A1"	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.347A>G	chr13.hg19:g.22140947T>C	ENSP00000371811:p.Glu116Gly	57.0	0.0		80.0	4.0	NM_152726	Q8N0T6|Q8NAX8	Missense_Mutation	SNP	ENST00000382374.4	hg19	CCDS9297.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.169989	0.57584	.	.	ENSG00000165487	ENST00000382374	T	0.80566	-1.39	5.22	5.22	0.72569	.	0.151435	0.64402	D	0.000012	T	0.64271	0.2583	N	0.12182	0.205	0.58432	D	0.999996	P	0.42871	0.792	B	0.37650	0.255	T	0.65257	-0.6212	10	0.22706	T	0.39	-18.8093	14.091	0.64990	0.0:0.0:0.0:1.0	.	116	Q8IYU8	EFHA1_HUMAN	G	116	ENSP00000371811:E116G	ENSP00000371811:E116G	E	-	2	0	EFHA1	21038947	1.000000	0.71417	0.993000	0.49108	0.581000	0.36288	5.140000	0.64807	1.957000	0.56846	0.528000	0.53228	GAG	.	.		0.383	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726		C	22140947	T	C	22140947	3	2	49	1	0	0	0	0	1	0	0	0	4945	1551	54	2	1001	2	EFHA1	13	22140947	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	390396	22140947	93028931	200	6357										
BRCA2	675	hgsc.bcm.edu	37	chr13	32937423	32937423	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctgtgtttctgacataatttCattgagcgcaaatatatctg	7	7	3	2	rs80359048		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:32937423C>T	ENST00000380152.3	+	18	8317	c.8084C>T	c.(8083-8085)tCa>tTa	p.S2695L	BRCA2_ENST00000544455.1_Missense_Mutation_p.S2695L			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2695					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.S2695*(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		GACATAATTTCATTGAGCGCA	0.368			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.S2695L	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	BRCA2_ENST00000544455,NS,carcinoma,0,2	BRCA2	812	.	2	Substitution - Nonsense(2)	lung(2)	c.C8084T						.	C	LEU/SER	0,4406		0,0,2203	100	97	98	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	8084	4.1	0.2	13	dbSNP_132	98	1,8599	1.2+/-3.3	0,1,4299	no	missense	BRCA2	NM_000059.3	145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	2695/3419	32937423	1,13005	2203	4300	6503	SO:0001583	missense	675	exon18	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TAATTTCATTGAG	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8084C>T	chr13.hg19:g.32937423C>T	ENSP00000369497:p.Ser2695Leu	98.0	0.0		124.0	5.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.180052	0.57800	0.0	1.16E-4	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.80909	-1.43;-1.43	4.94	4.1	0.47936	Nucleic acid-binding, OB-fold-like (1);BRCA2, oligonucleotide/oligosaccharide-binding 1 (1);	0.068240	0.64402	D	0.000013	T	0.79924	0.4530	M	0.79123	2.44	0.38522	D	0.948745	P	0.37636	0.603	B	0.35039	0.194	D	0.83490	0.0069	10	0.87932	D	0	.	13.655	0.62333	0.0:0.9243:0.0:0.0757	.	2695	P51587	BRCA2_HUMAN	L	2695	ENSP00000369497:S2695L;ENSP00000439902:S2695L	ENSP00000369497:S2695L	S	+	2	0	BRCA2	31835423	0.667000	0.27484	0.153000	0.22517	0.524000	0.34500	3.023000	0.49666	1.217000	0.43442	0.313000	0.20887	TCA	.	.		0.368	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		T	32937423	C	T	32937423	3	4	49	1	0	0	0	0	1	0	0	0	1501	838	29	3	8150	3	BRCA2	13	32937423	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	10796476	32937423	82232455	201	6358										
LHFP	10186	hgsc.bcm.edu	37	chr13	40175086	40175086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gaggaggccacaacccaggcCggtcactatggtgcagatcc	13	13	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:40175086C>T	ENST00000379589.3	-	2	730	c.268G>A	c.(268-270)Ggc>Agc	p.G90S	LHFP_ENST00000495922.1_5'Flank	NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	90						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)		HMGA2/LHFP(2)	breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		CAACCCAGGCCGGTCACTATG	0.607			T	HMGA2	lipoma																																p.G90S		Atlas-SNP	.		Dom	yes		13	13q12	10186	lipoma HMGIC fusion partner		M	LHFP,NS,carcinoma,0,1	LHFP	31	.	0			c.G268A						.						145	134	138					13																	40175086		2203	4300	6503	SO:0001583	missense	10186	exon2			CCAGGCCGGTCAC	AF098807	CCDS9369.1	13q12	2008-07-18			ENSG00000183722	ENSG00000183722			6586	protein-coding gene	gene with protein product		606710				10329012	Standard	NM_005780		Approved	MGC22429	uc001uxf.3	Q9Y693	OTTHUMG00000016767	ENST00000379589.3:c.268G>A	chr13.hg19:g.40175086C>T	ENSP00000368908:p.Gly90Ser	56.0	0.0		71.0	3.0	NM_005780	B2R7M2|Q53FC0|Q96SH5	Missense_Mutation	SNP	ENST00000379589.3	hg19	CCDS9369.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.012607	0.93346	.	.	ENSG00000183722	ENST00000379589	T	0.72282	-0.64	5.38	5.38	0.77491	.	0.000000	0.64402	D	0.000001	T	0.80571	0.4648	M	0.67397	2.05	0.80722	D	1	D	0.76494	0.999	P	0.58391	0.838	T	0.80202	-0.1480	9	.	.	.	.	18.101	0.89505	0.0:1.0:0.0:0.0	.	90	Q9Y693	LHFP_HUMAN	S	90	ENSP00000368908:G90S	.	G	-	1	0	LHFP	39073086	1.000000	0.71417	0.956000	0.39512	0.541000	0.35023	7.409000	0.80053	2.522000	0.85027	0.655000	0.94253	GGC	.	.		0.607	LHFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044619.1	NM_005780		T	40175086	C	T	40175086	3	4	49	1	0	0	0	0	1	0	0	0	8772	652	23	1	346	1	LHFP	13	40175086	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	7237663	40175086	74994792	202	6359										
PHF11	51131	hgsc.bcm.edu	37	chr13	50080776	50080776	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggatattacttataggtgtcTttcaggttgcagaaaagatg	11	4	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:50080776T>C	ENST00000378319.3	+	2	141	c.100T>C	c.(100-102)Ttt>Ctt	p.F34L	PHF11_ENST00000488958.1_5'UTR|PHF11_ENST00000357596.3_5'UTR	NM_001040443.1	NP_001035533.1	Q9UIL8	PHF11_HUMAN	PHD finger protein 11	34					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(3)|lung(1)	4		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		TATAGGTGTCTTTCAGGTTGC	0.418																																					p.F34L		Atlas-SNP	.											.	PHF11	20	.	0			c.T100C						.						95	89	91					13																	50080776		2203	4300	6503	SO:0001583	missense	51131	exon2			GGTGTCTTTCAGG	AB011031	CCDS31975.1, CCDS41887.1	13q14.11	2014-05-20			ENSG00000136147	ENSG00000136147		"Zinc fingers, PHD-type"	17024	protein-coding gene	gene with protein product	"IgE responsiveness (atopic)"	607796				10508479, 15057823	Standard	XM_005266417		Approved	NY-REN-34, BCAP, IGER	uc001vdb.3	Q9UIL8	OTTHUMG00000016916	ENST00000378319.3:c.100T>C	chr13.hg19:g.50080776T>C	ENSP00000367570:p.Phe34Leu	45.0	0.0		54.0	4.0	NM_001040443	Q5W0A4|Q5W0A6|Q9Y5A2	Missense_Mutation	SNP	ENST00000378319.3	hg19	CCDS31975.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077362	0.36662	.	.	ENSG00000136147	ENST00000378319	T	0.72725	-0.68	4.78	4.78	0.61160	.	0.780292	0.11255	N	0.583203	T	0.61553	0.2356	L	0.48642	1.525	0.80722	D	1	B;B	0.16166	0.002;0.016	B;B	0.10450	0.003;0.005	T	0.51228	-0.8732	10	0.11182	T	0.66	-3.2169	10.8893	0.46986	0.0:0.0:0.0:1.0	.	34;34	B4DTX8;Q9UIL8	.;PHF11_HUMAN	L	34	ENSP00000367570:F34L	ENSP00000367570:F34L	F	+	1	0	PHF11	48978777	0.991000	0.36638	1.000000	0.80357	0.708000	0.40852	2.456000	0.44997	2.156000	0.67533	0.528000	0.53228	TTT	.	.		0.418	PHF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044915.1	NM_016119		C	50080776	T	C	50080776	3	2	49	1	0	0	0	0	1	0	0	0	11831	1609	56	2	106	2	PHF11	13	50080776	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	9905690	50080776	65089102	203	6360										
NEK3	4752	hgsc.bcm.edu	37	chr13	52718058	52718058	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcaaaattcttactttttttCttggtgtgttatgcttcgaa	6	6	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:52718058C>T	ENST00000400357.2	-	9	2162	c.869G>A	c.(868-870)aGa>aAa	p.R290K	NEK3_ENST00000452082.2_Missense_Mutation_p.R311K|NEK3_ENST00000339406.3_Missense_Mutation_p.R290K|NEK3_ENST00000378101.2_Missense_Mutation_p.R290K			P51956	NEK3_HUMAN	NIMA-related kinase 3	290					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		TACTTTTTTTCTTGGTGTGTT	0.244																																					p.R290K		Atlas-SNP	.											.	NEK3	41	.	0			c.G869A						.						65	52	56					13																	52718058		1612	3644	5256	SO:0001583	missense	4752	exon10			TTTTTTCTTGGTG	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"serine/threonine-protein kinase NEK3", "phosphorylase B kinase kinase", "glycogen synthase A kinase", "hydroxyalkyl-protein kinase"	604044	"NIMA (never in mitosis gene a)-related kinase 3"			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.869G>A	chr13.hg19:g.52718058C>T	ENSP00000383210:p.Arg290Lys	80.0	0.0		112.0	6.0	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	hg19	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	C	2.676	-0.276501	0.05679	.	.	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.70986	-0.36;-0.36;-0.53;-0.4;-0.37	5.78	2.6	0.31112	.	1.743130	0.02684	N	0.109966	T	0.47135	0.1429	.	.	.	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.45483	-0.9258	9	0.05833	T	0.94	.	6.2114	0.20631	0.0:0.5806:0.0:0.4194	rs3837575	311;284	Q6ZN64;F8VS47	.;.	K	290;290;290;311;284	ENSP00000339429:R290K;ENSP00000367341:R290K;ENSP00000383210:R290K;ENSP00000404197:R311K;ENSP00000448716:R284K	ENSP00000448782:R290K	R	-	2	0	NEK3	51616059	0.656000	0.27385	0.004000	0.12327	0.110000	0.19582	0.640000	0.24705	0.163000	0.19507	0.591000	0.81541	AGA	.	.		0.244	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3			T	52718058	C	T	52718058	3	4	49	1	0	0	0	0	1	0	0	0	10334	913	32	3	679	3	NEK3	13	52718058	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	2637282	52718058	62451820	204	6361										
GPC5	2262	hgsc.bcm.edu	37	chr13	92380785	92380785	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttaatgttttctatttaaaaGgtaaataggatttgtggccg	9	3	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:92380785G>T	ENST00000377067.3	+	4	1392		c.e4-1		GPC5_ENST00000483422.1_Splice_Site	NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5						carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				CTATTTAAAAGGTAAATAGGA	0.403																																					.		Atlas-SNP	.											GPC5,NS,carcinoma,0,1	GPC5	140	.	0			c.1021-1G>T						.						91	96	94					13																	92380785		2203	4300	6503	SO:0001630	splice_region_variant	2262	exon4			TTAAAAGGTAAAT	AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"Proteoglycans / Cell Surface : Glypicans"	4453	protein-coding gene	gene with protein product	"glypican proteoglycan 5"	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.1021-1G>T	chr13.hg19:g.92380785G>T		48.0	0.0		71.0	3.0	NM_004466	B2R726|O60436|Q9BX27	Splice_Site	SNP	ENST00000377067.3	hg19	CCDS9468.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.922269	0.73213	.	.	ENSG00000179399	ENST00000377067	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3925	0.87436	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPC5	91178786	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.826000	0.69293	2.792000	0.96026	0.557000	0.71058	.	.	.		0.403	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466	Intron	T	92380785	G	T	92380785	5	4	49	1	0	0	0	0	0	0	1	0	6609	1014	35	3	1034	3	GPC5	13	92380785	Splice_Site	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	39662727	92380785	22789093	205	6362										
OR11G2	390439	hgsc.bcm.edu	37	chr14	20666182	20666182	+	Missense_Mutation	SNP	G	G	A													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	taactctcacttgcaaaaaaGgccctgtgatagagcttgtc					rs77471263		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:20666182G>A	ENST00000357366.3	+	1	688	c.688G>A	c.(688-690)Ggc>Agc	p.G230S		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		TTGCAAAAAAGGCCCTGTGAT	0.458																																					p.G230S		Atlas-SNP	.											.	OR11G2	73	.	0			c.G688A						.						137	136	136					14																	20666182		2203	4300	6503	SO:0001583	missense	390439	exon1			AAAAAAGGCCCTG		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"GPCR / Class A : Olfactory receptors"	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.688G>A	chr14.hg19:g.20666182G>A	ENSP00000349930:p.Gly230Ser	229.0	0.0		322.0	26.0	NM_001005503	Q6IF09|Q96R33	Missense_Mutation	SNP	ENST00000357366.3	hg19	CCDS32032.1	.	.	.	.	.	.	.	.	.	.	g	3.284	-0.146469	0.06627	.	.	ENSG00000196832	ENST00000357366	T	0.00029	8.91	4.93	-0.555	0.11807	GPCR, rhodopsin-like superfamily (1);	0.809795	0.10548	N	0.661787	T	0.00039	0.0001	N	0.00746	-1.225	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04115	-1.0976	10	0.48119	T	0.1	.	4.3832	0.11304	0.0809:0.1204:0.2455:0.5532	rs55781225;rs59982948	230	Q8NGC1	O11G2_HUMAN	S	230	ENSP00000349930:G230S	ENSP00000349930:G230S	G	+	1	0	OR11G2	19736022	0.000000	0.05858	0.002000	0.10522	0.062000	0.15995	-0.406000	0.07187	-0.288000	0.09051	-0.271000	0.10264	GGC	.	.		0.458	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1			A	20666182	G	A	20666182	3	1	49	1	0	0	0	0	1	0	0	0	10934	1000	35	3	690	3	OR11G2	14	20666182	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10		20666182	86683358	206	6363	27	2								
OR11G2	390439	hgsc.bcm.edu	37	chr14	20666184	20666184	+	Silent	SNP	C	C	G													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	actctcacttgcaaaaaaggCcctgtgatagagcttgtctt					rs74538160		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:20666184C>G	ENST00000357366.3	+	1	690	c.690C>G	c.(688-690)ggC>ggG	p.G230G		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		GCAAAAAAGGCCCTGTGATAG	0.458																																					p.G230G		Atlas-SNP	.											.	OR11G2	73	.	0			c.C690G						.						140	139	139					14																	20666184		2203	4300	6503	SO:0001819	synonymous_variant	390439	exon1			AAAAGGCCCTGTG		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"GPCR / Class A : Olfactory receptors"	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.690C>G	chr14.hg19:g.20666184C>G		223.0	0.0		316.0	15.0	NM_001005503	Q6IF09|Q96R33	Silent	SNP	ENST00000357366.3	hg19	CCDS32032.1																																																																																			.	.		0.458	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1			G	20666184	C	G	20666184	2	3	49	1	0	0	0	0	0	0	0	1	10934	726	26	4		4	OR11G2	14	20666184	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	2	20666184	86683356	207	6364	27	2								
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21555549	21555549	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccctcccttcccggcctttcGccgggagcctgctccctgcc	9	22	0	0	rs373398882		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:21555549G>A	ENST00000298694.4	+	21	4441	c.4314G>A	c.(4312-4314)tcG>tcA	p.S1438S	ARHGEF40_ENST00000298693.3_Intron|RP11-998D10.7_ENST00000554733.2_lincRNA			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	1438						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						CCGGCCTTTCGCCGGGAGCCT	0.697																																					p.S1438S		Atlas-SNP	.											ARHGEF40_ENST00000298694,NS,carcinoma,0,1	ARHGEF40	84	.	0			c.G4314A						.	G		0,4400		0,0,2200	39	45	43		4314	-10.6	0.6	14		43	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	ARHGEF40	NM_018071.3		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		1438/1520	21555549	1,12995	2200	4298	6498	SO:0001819	synonymous_variant	55701	exon21			CCTTTCGCCGGGA		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"Rho guanine nucleotide exchange factors"	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.4314G>A	chr14.hg19:g.21555549G>A		18.0	1.0		14.0	2.0	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	hg19	CCDS32041.1																																																																																			.	.		0.697	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			A	21555549	G	A	21555549	2	1	49	1	0	0	0	0	0	0	0	1	5934	1074	38	1		1	FLJ10357	14	21555549	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	889365	21555549	85793991	208	6365										
ABHD4	63874	hgsc.bcm.edu	37	chr14	23072501	23072501	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcgatctgcttggcttcgggCgaagctcaaggccagcattc	12	12	2	0	rs148116289		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:23072501C>T	ENST00000428304.2	+	3	389	c.319C>T	c.(319-321)Cga>Tga	p.R107*	ABHD4_ENST00000544562.1_3'UTR	NM_022060.2	NP_071343.2	Q8TB40	ABHD4_HUMAN	abhydrolase domain containing 4	107					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(3)|prostate(1)	14	all_cancers(95;5.49e-05)			GBM - Glioblastoma multiforme(265;0.0153)		TGGCTTCGGGCGAAGCTCAAG	0.607																																					p.R107X		Atlas-SNP	.											ABHD4,colon,carcinoma,0,1	ABHD4	30	.	0			c.C319T						.	C	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	46	45	45		319	-0.8	1	14	dbSNP_134	45	0,8600		0,0,4300	no	stop-gained	ABHD4	NM_022060.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		107/343	23072501	1,13005	2203	4300	6503	SO:0001587	stop_gained	63874	exon3			TTCGGGCGAAGCT	AK022878	CCDS9572.1	14q11.1	2006-10-06			ENSG00000100439	ENSG00000100439		"Abhydrolase domain containing"	20154	protein-coding gene	gene with protein product							Standard	NM_022060		Approved	FLJ12816	uc001wgm.3	Q8TB40	OTTHUMG00000028686	ENST00000428304.2:c.319C>T	chr14.hg19:g.23072501C>T	ENSP00000414558:p.Arg107*	53.0	0.0		87.0	4.0	NM_022060	B4DDH7|Q9H9E0	Nonsense_Mutation	SNP	ENST00000428304.2	hg19	CCDS9572.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.489471	0.64074	2.27E-4	0.0	ENSG00000100439	ENST00000428304;ENST00000216327;ENST00000542041	.	.	.	5.6	-0.807	0.10872	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	-6.2819	15.5016	0.75703	0.5876:0.4124:0.0:0.0	.	.	.	.	X	107;41;83	.	ENSP00000216327:R41X	R	+	1	2	ABHD4	22142341	0.993000	0.37304	0.992000	0.48379	0.796000	0.44982	0.426000	0.21363	-0.029000	0.13827	0.655000	0.94253	CGA	.	C|1.000;T|0.000		0.607	ABHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071623.3			T	23072501	C	T	23072501	4	4	49	1	0	0	0	0	0	1	0	0	84	760	27	1	329	1	ABHD4	14	23072501	Nonsense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1516952	23072501	84277039	209	6366										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23548777	23548777	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tttctgctgttgcttgatgcTgaacgagaacgtgaacgtga	12	7	1	5			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:23548777T>A	ENST00000262710.1	-	6	2268	c.1941A>T	c.(1939-1941)tcA>tcT	p.S647S	ACIN1_ENST00000457657.1_Silent_p.S607S|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000605057.1_Silent_p.S589S|ACIN1_ENST00000555053.1_Silent_p.S647S	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	647	Ser-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		TGCTTGATGCTGAACGAGAAC	0.493																																					p.S647S		Atlas-SNP	.											.	ACIN1	147	.	0			c.A1941T						.						222	211	215					14																	23548777		2203	4300	6503	SO:0001819	synonymous_variant	22985	exon6			TGATGCTGAACGA	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1941A>T	chr14.hg19:g.23548777T>A		148.0	0.0		240.0	15.0	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	hg19	CCDS9587.1																																																																																			.	.		0.493	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		A	23548777	T	A	23548777	2	1	49	1	0	0	0	0	0	0	0	1	142	1567	55	4		4	ACIN1	14	23548777	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	476276	23548777	83800763	210	6367			1	7		3	3	1126	T		6.333347e-05
ACIN1	22985	hgsc.bcm.edu	37	chr14	23549875	23549875	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccttcctcttcttcatcatcTtcttcctcctcctcctcctc	0	21	6	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:23549875T>A	ENST00000262710.1	-	6	1170	c.843A>T	c.(841-843)gaA>gaT	p.E281D	ACIN1_ENST00000457657.1_Missense_Mutation_p.E241D|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000605057.1_Missense_Mutation_p.E223D|ACIN1_ENST00000555053.1_Missense_Mutation_p.E281D	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	281	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		cttcatcatcttcttcctcct	0.448																																					p.E281D		Atlas-SNP	.											.	ACIN1	147	.	0			c.A843T						.						152	140	144					14																	23549875		2203	4300	6503	SO:0001583	missense	22985	exon6			ATCATCTTCTTCC	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.843A>T	chr14.hg19:g.23549875T>A	ENSP00000262710:p.Glu281Asp	141.0	0.0		210.0	10.0	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	T	1.446	-0.566196	0.03910	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.19532	2.14;2.14;2.14	5.57	-4.9	0.03094	.	.	.	.	.	T	0.05547	0.0146	N	0.03608	-0.345	0.09310	N	0.999991	B;B	0.14012	0.009;0.003	B;B	0.13407	0.009;0.004	T	0.39313	-0.9620	9	0.11485	T	0.65	-2.0759	1.0346	0.01545	0.1683:0.2523:0.3136:0.2658	.	281;281	G3V3M7;Q9UKV3	.;ACINU_HUMAN	D	281;241;281	ENSP00000262710:E281D;ENSP00000405677:E241D;ENSP00000451328:E281D	ENSP00000262710:E281D	E	-	3	2	ACIN1	22619715	0.061000	0.20836	0.065000	0.19835	0.152000	0.21847	-0.672000	0.05244	-0.454000	0.07066	0.528000	0.53228	GAA	.	.		0.448	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		A	23549875	T	A	23549875	3	1	49	1	0	0	0	0	1	0	0	0	142	1606	56	4	3385	4	ACIN1	14	23549875	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	1098	23549875	83799665	211	6368			1	7		3	3	1126	T		6.333347e-05
ACIN1	22985	hgsc.bcm.edu	37	chr14	23549902	23549902	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcctcctcctcctcctcttcTtcctcctctgttttcaaatt	1	18	4	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:23549902T>C	ENST00000262710.1	-	6	1143	c.816A>G	c.(814-816)gaA>gaG	p.E272E	ACIN1_ENST00000457657.1_Silent_p.E232E|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000605057.1_Silent_p.E214E|ACIN1_ENST00000555053.1_Silent_p.E272E	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	272	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		cctcctcttcttcctcctctG	0.478																																					p.E272E		Atlas-SNP	.											.	ACIN1	147	.	0			c.A816G						.						123	121	122					14																	23549902		2203	4300	6503	SO:0001819	synonymous_variant	22985	exon6			CTCTTCTTCCTCC	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.816A>G	chr14.hg19:g.23549902T>C		118.0	0.0		182.0	11.0	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	hg19	CCDS9587.1																																																																																			.	.		0.478	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23549902	T	C	23549902	2	2	49	1	0	0	0	0	0	0	0	1	142	1606	56	2		2	ACIN1	14	23549902	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	27	23549902	83799638	212	6369			1	7		3	3	1126	T		6.333347e-05
SCFD1	23256	hgsc.bcm.edu	37	chr14	31107344	31107345	+	Frame_Shift_Ins	INS	-	-	ACTAT													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgataggatcttcgaaatcaINSactatatgaatcatattatt							TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:31107344_31107345insACTAT	ENST00000458591.2	+	5	553_554	c.326_327insACTAT	c.(325-330)caactafs	p.-111fs	SCFD1_ENST00000421551.3_Frame_Shift_Ins_p.-52fs|SCFD1_ENST00000541123.1_5'UTR|SCFD1_ENST00000544052.2_Frame_Shift_Ins_p.-44fs|SCFD1_ENST00000396629.2_Frame_Shift_Ins_p.-19fs	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1						post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		CTTCGAAATCAACTATATGAAT	0.287																																					p.Q109fs		Pindel	.											.	SCFD1	43	.	0			c.326_327insACTAT						.																																			SO:0001589	frameshift_variant	23256	exon5			.	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 163"	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.327_331dupACTAT	chr14.hg19:g.31107345_31107349dupACTAT	ENSP00000390783:p.Tyr111fs	0.0	0.0		210.0	40.0	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Frame_Shift_Ins	INS	ENST00000458591.2	hg19	CCDS9639.1																																																																																			.	.		0.287	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835		ACTAT	31107345	-	ACTAT	31107344	7	5	49	1	0	1	1	0	0	0	0	0	13904	130	5	0	344	0	SCFD1	14	31107344	Frame_Shift_Ins	INS	-	TCGA-BD-A3EP-01A-11D-A22F-10	7557442	31107344	76242196	213	6370										
PPP2R3C	55012	hgsc.bcm.edu	37	chr14	35577440	35577440	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agacttttgctgtgaaaaatTgcctaagaaaagaaaataaa	7	4	0	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:35577440T>A	ENST00000261475.5	-	5	760	c.407A>T	c.(406-408)cAa>cTa	p.Q136L	PPP2R3C_ENST00000555644.1_Missense_Mutation_p.Q136L	NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	136					activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		TGTGAAAAATTGCCTAAGAAA	0.284																																					p.Q136L		Atlas-SNP	.											.	PPP2R3C	44	.	0			c.A407T						.						47	51	50					14																	35577440		2202	4295	6497	SO:0001583	missense	55012	exon5			AAAAATTGCCTAA	AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	17485	protein-coding gene	gene with protein product		615902	"chromosome 14 open reading frame 10", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.407A>T	chr14.hg19:g.35577440T>A	ENSP00000261475:p.Gln136Leu	53.0	0.0		102.0	17.0	NM_017917	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Missense_Mutation	SNP	ENST00000261475.5	hg19	CCDS9654.1	.	.	.	.	.	.	.	.	.	.	T	12.60	1.987577	0.35036	.	.	ENSG00000092020	ENST00000261475;ENST00000554361;ENST00000555644;ENST00000557278	T;T	0.28069	1.63;1.63	5.53	5.53	0.82687	.	0.277847	0.41097	D	0.000953	T	0.11922	0.0290	N	0.02539	-0.55	0.37520	D	0.917518	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.19877	-1.0292	10	0.09338	T	0.73	-7.8834	11.6506	0.51286	0.0:0.0:0.1481:0.8519	.	136;136	Q86US5;Q969Q6	.;P2R3C_HUMAN	L	136;108;136;136	ENSP00000261475:Q136L;ENSP00000450716:Q108L	ENSP00000261475:Q136L	Q	-	2	0	PPP2R3C	34647191	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	4.810000	0.62598	2.104000	0.64026	0.528000	0.53228	CAA	.	.		0.284	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917		A	35577440	T	A	35577440	3	1	49	1	0	0	0	0	1	0	0	0	12402	1812	63	4	990	4	PPP2R3C	14	35577440	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	4470096	35577440	71772100	214	6371										
MAP4K5	11183	hgsc.bcm.edu	37	chr14	50923302	50923302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	atctaatggtatgacgaatgAttgcatggggctgtgaatat	12	4	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:50923302A>G	ENST00000013125.4	-	14	1265	c.947T>C	c.(946-948)aTc>aCc	p.I316T	RP11-406H23.2_ENST00000555257.1_lincRNA	NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	316					activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					ATGACGAATGATTGCATGGGG	0.318																																					p.I316T		Atlas-SNP	.											.	MAP4K5	48	.	0			c.T947C						.						64	59	61					14																	50923302		1844	4086	5930	SO:0001583	missense	11183	exon14			CGAATGATTGCAT	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6867	protein-coding gene	gene with protein product	"germinal center kinase-related"	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.947T>C	chr14.hg19:g.50923302A>G	ENSP00000013125:p.Ile316Thr	64.0	0.0		127.0	7.0	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	hg19		.	.	.	.	.	.	.	.	.	.	A	16.33	3.092439	0.55968	.	.	ENSG00000012983	ENST00000013125	T	0.12984	2.63	5.8	5.8	0.92144	Protein kinase-like domain (1);	0.427648	0.27773	N	0.017917	T	0.08802	0.0218	N	0.14661	0.345	0.30483	N	0.772132	B;B	0.12013	0.0;0.005	B;B	0.09377	0.0;0.004	T	0.13495	-1.0507	10	0.12430	T	0.62	.	15.1301	0.72517	1.0:0.0:0.0:0.0	.	316;316	B2R928;Q9Y4K4	.;M4K5_HUMAN	T	316	ENSP00000013125:I316T	ENSP00000013125:I316T	I	-	2	0	MAP4K5	49993052	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.751000	0.62169	2.213000	0.71641	0.528000	0.53228	ATC	.	.		0.318	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575		G	50923302	A	G	50923302	3	3	49	1	0	0	0	0	1	0	0	0	9272	333	12	2	1669	2	MAP4K5	14	50923302	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	15345862	50923302	56426238	215	6372										
WDHD1	11169	hgsc.bcm.edu	37	chr14	55467661	55467661	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgattagaccattaatactaCctgcagctaaatattgccca	5	10	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:55467661C>T	ENST00000360586.3	-	9	808	c.743G>A	c.(742-744)gGt>gAt	p.G248D	WDHD1_ENST00000420358.2_Missense_Mutation_p.G125D|WDHD1_ENST00000421192.1_Missense_Mutation_p.G125D	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	248					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						ATTAATACTACCTGCAGCTAA	0.333																																					p.G248D		Atlas-SNP	.											.	WDHD1	82	.	0			c.G743A						.						159	163	162					14																	55467661		2203	4300	6503	SO:0001583	missense	11169	exon9			ATACTACCTGCAG	AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"WD repeat domain containing"	23170	protein-coding gene	gene with protein product	"CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.743G>A	chr14.hg19:g.55467661C>T	ENSP00000353793:p.Gly248Asp	207.0	0.0		306.0	128.0	NM_007086	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	hg19	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.040405	0.93630	.	.	ENSG00000198554	ENST00000360586;ENST00000421192;ENST00000420358	T;T;T	0.70164	4.5;-0.46;-0.46	5.56	5.56	0.83823	WD40/YVTN repeat-like-containing domain (1);Translation initiation factor 2A, beta propellor-like domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.87014	0.6072	M	0.93898	3.47	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.89426	0.3713	10	0.59425	D	0.04	.	19.5251	0.95201	0.0:1.0:0.0:0.0	.	248	O75717	WDHD1_HUMAN	D	248;125;125	ENSP00000353793:G248D;ENSP00000391049:G125D;ENSP00000399349:G125D	ENSP00000353793:G248D	G	-	2	0	WDHD1	54537411	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.562000	0.67346	2.615000	0.88500	0.591000	0.81541	GGT	.	.		0.333	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086		T	55467661	C	T	55467661	3	4	49	1	0	0	0	0	1	0	0	0	17286	507	18	3	2718	3	WDHD1	14	55467661	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	4544359	55467661	51881879	216	6373										
SNAPC1	6617	hgsc.bcm.edu	37	chr14	62233751	62233751	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aactgtgtcaaccaaaacaaAaggtaatacttagtgagtta	7	6	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:62233751A>G	ENST00000216294.4	+	2	390	c.286A>G	c.(286-288)Aag>Gag	p.K96E	RP11-618G20.1_ENST00000555937.1_RNA	NM_003082.3	NP_003073.1	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex, polypeptide 1, 43kDa	96	SNAPC3-binding.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		ACCAAAACAAAAGGTAATACT	0.274																																					p.K96E	NSCLC(27;223 907 37180 39193 46568)	Atlas-SNP	.											.	SNAPC1	32	.	0			c.A286G						.						84	82	82					14																	62233751		2203	4298	6501	SO:0001583	missense	6617	exon2			AAACAAAAGGTAA	Z47542	CCDS9755.1	14q22	2008-08-11	2002-08-29		ENSG00000023608	ENSG00000023608			11134	protein-coding gene	gene with protein product		600591	"small nuclear RNA activating complex, polypeptide 1, 43kD"			9644240	Standard	NM_003082		Approved	SNAP43, PTFgamma	uc001xft.3	Q16533	OTTHUMG00000140343	ENST00000216294.4:c.286A>G	chr14.hg19:g.62233751A>G	ENSP00000216294:p.Lys96Glu	97.0	0.0		86.0	4.0	NM_003082		Missense_Mutation	SNP	ENST00000216294.4	hg19	CCDS9755.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.292265	0.80914	.	.	ENSG00000023608	ENST00000216294	.	.	.	6.06	4.86	0.63082	.	0.142009	0.64402	D	0.000004	T	0.74711	0.3752	M	0.80422	2.495	0.42701	D	0.993611	D	0.58970	0.984	P	0.56612	0.802	T	0.78996	-0.1983	9	0.62326	D	0.03	-21.1355	12.9864	0.58594	0.7604:0.2396:0.0:0.0	.	96	Q16533	SNPC1_HUMAN	E	96	.	ENSP00000216294:K96E	K	+	1	0	SNAPC1	61303504	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.686000	0.54685	2.324000	0.78689	0.533000	0.62120	AAG	.	.		0.274	SNAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276976.2	NM_003082		G	62233751	A	G	62233751	3	3	49	1	0	0	0	0	1	0	0	0	14849	15	1	2	292	2	SNAPC1	14	62233751	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	6766090	62233751	45115789	217	6374										
NEK9	91754	hgsc.bcm.edu	37	chr14	75590877	75590877	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aggcatcacgacgttccttcTcagacagccgggtcaaatcg	10	13	3	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:75590877T>C	ENST00000238616.5	-	2	427	c.269A>G	c.(268-270)gAg>gGg	p.E90G	RP11-950C14.7_ENST00000556236.1_RNA	NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	90	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		ACGTTCCTTCTCAGACAGCCG	0.468																																					p.E90G		Atlas-SNP	.											.	NEK9	64	.	0			c.A269G						.						175	131	146					14																	75590877		2203	4300	6503	SO:0001583	missense	91754	exon2			TCCTTCTCAGACA	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"NIMA (never in mitosis gene a)- related kinase 9"			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.269A>G	chr14.hg19:g.75590877T>C	ENSP00000238616:p.Glu90Gly	125.0	0.0		133.0	6.0	NM_033116	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Missense_Mutation	SNP	ENST00000238616.5	hg19	CCDS9839.1	.	.	.	.	.	.	.	.	.	.	T	35	5.441862	0.96187	.	.	ENSG00000119638	ENST00000238616;ENST00000540227	T	0.67345	-0.26	6.17	6.17	0.99709	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.67524	0.2902	L	0.39467	1.215	0.80722	D	1	P	0.52692	0.955	P	0.49085	0.6	T	0.69154	-0.5220	10	0.52906	T	0.07	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	90	Q8TD19	NEK9_HUMAN	G	90;72	ENSP00000238616:E90G	ENSP00000238616:E90G	E	-	2	0	NEK9	74660630	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.213000	0.72194	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.468	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116		C	75590877	T	C	75590877	3	2	49	1	0	0	0	0	1	0	0	0	10340	1551	54	2	2754	2	NEK9	14	75590877	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	13357126	75590877	31758663	218	6375										
DICER1	23405	hgsc.bcm.edu	37	chr14	95556981	95556981	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agtgactctgaccttcccgtCgtaagttctctcagccgggc	10	14	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:95556981C>T	ENST00000526495.1	-	29	5914	c.5623G>A	c.(5623-5625)Gac>Aac	p.D1875N	DICER1_ENST00000541352.1_Silent_p.T1820T|DICER1_ENST00000527414.1_Missense_Mutation_p.D1875N|DICER1_ENST00000527416.2_5'UTR|DICER1_ENST00000556045.1_Missense_Mutation_p.D773N|DICER1_ENST00000343455.3_Missense_Mutation_p.D1875N|DICER1_ENST00000393063.1_Missense_Mutation_p.D1875N			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1875	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		ACCTTCCCGTCGTAAGTTCTC	0.423			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.D1875N		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.G5623A						.						165	168	167					14																	95556981		2203	4300	6503	SO:0001583	missense	23405	exon28	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	TCCCGTCGTAAGT	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.5623G>A	chr14.hg19:g.95556981C>T	ENSP00000437256:p.Asp1875Asn	211.0	0.0		326.0	118.0	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	hg19	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	C	33	5.227452	0.95173	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000556045	T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07	6.07	6.07	0.98685	Double-stranded RNA-binding (2);	0.095905	0.64402	D	0.000001	T	0.52725	0.1752	.	.	.	0.80722	D	1	B;P	0.48589	0.431;0.912	B;B	0.34138	0.104;0.176	T	0.54403	-0.8299	9	0.34782	T	0.22	-26.5162	20.6593	0.99626	0.0:1.0:0.0:0.0	.	773;1875	B3KRG4;Q9UPY3	.;DICER_HUMAN	N	1875;1875;1875;1875;773	ENSP00000343745:D1875N;ENSP00000437256:D1875N;ENSP00000376783:D1875N;ENSP00000435681:D1875N;ENSP00000451041:D773N	ENSP00000343745:D1875N	D	-	1	0	DICER1	94626734	1.000000	0.71417	0.571000	0.28486	0.931000	0.56810	7.324000	0.79115	2.885000	0.99019	0.655000	0.94253	GAC	.	.		0.423	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			T	95556981	C	T	95556981	3	4	49	1	0	0	0	0	1	0	0	0	4523	884	31	1	149	1	DICER1	14	95556981	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	19966104	95556981	11792559	219	6376										
ZNF839	55778	hgsc.bcm.edu	37	chr14	102798159	102798159	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcaggggagcagagggcgtcGccaagcaaagccaggctcaa	16	11	1	1	rs368513189		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:102798159G>A	ENST00000558850.1	+	3	1394	c.1044G>A	c.(1042-1044)tcG>tcA	p.S348S	ZNF839_ENST00000559185.1_Silent_p.S348S|ZNF839_ENST00000442396.2_Silent_p.S464S|ZNF839_ENST00000262236.5_Silent_p.S348S	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	348							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AGAGGGCGTCGCCAAGCAAAG	0.567																																					p.S464S		Atlas-SNP	.											ZNF839,NS,carcinoma,0,1	ZNF839	41	.	0			c.G1392A						.	G		1,4027		0,1,2013	26	30	29		1392	-7.6	0	14		29	0,8354		0,0,4177	no	coding-synonymous	ZNF839	NM_018335.3		0,1,6190	AA,AG,GG		0.0,0.0248,0.0081		464/928	102798159	1,12381	2014	4177	6191	SO:0001819	synonymous_variant	55778	exon3			GGCGTCGCCAAGC	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 131"	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.1044G>A	chr14.hg19:g.102798159G>A		24.0	0.0		38.0	3.0	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	hg19	CCDS58336.1																																																																																			.	.		0.567	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335		A	102798159	G	A	102798159	2	1	49	1	0	0	0	0	0	0	0	1	18203	1074	38	1		1	ZNF839	14	102798159	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	7241178	102798159	4551381	220	6377										
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105360106	105360106	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gggctcttgcaggtgatcttCgataacctgatgctgaaccc	11	11	2	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:105360106C>T	ENST00000414716.3	+	16	4419	c.4191C>T	c.(4189-4191)ttC>ttT	p.F1397F	CEP170B_ENST00000556508.1_Silent_p.F1362F|CEP170B_ENST00000418279.1_Silent_p.F1327F|CEP170B_ENST00000453495.1_Silent_p.F1433F	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	1432						cytoplasm (GO:0005737)|microtubule (GO:0005874)											AGGTGATCTTCGATAACCTGA	0.652																																					p.F1397F		Atlas-SNP	.											KIAA0284_ENST00000414716,NS,carcinoma,0,2	.	.	.	0			c.C4191T						.						40	43	42					14																	105360106		2021	4165	6186	SO:0001819	synonymous_variant	283638	exon16			GATCTTCGATAAC	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.4191C>T	chr14.hg19:g.105360106C>T		24.0	0.0		45.0	3.0	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	hg19	CCDS45175.1																																																																																			.	.		0.652	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		T	105360106	C	T	105360106	2	4	49	1	0	0	0	0	0	0	0	1	8175	883	31	1		1	KIAA0284	14	105360106	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	2561947	105360106	1989434	221	6378										
GPR132	29933	hgsc.bcm.edu	37	chr14	105517685	105517686	+	Frame_Shift_Ins	INS	-	-	T													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaaaggcagcggctttgacgINSaggagaaccaggtggtacgg							TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:105517685_105517686insT	ENST00000329797.3	-	4	1699_1700	c.788_789insA	c.(787-789)ctcfs	p.L263fs	GPR132_ENST00000539291.2_Frame_Shift_Ins_p.L263fs|GPR132_ENST00000546679.1_5'Flank|GPR132_ENST00000392585.2_Frame_Shift_Ins_p.L254fs	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	263					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		CGGCTTTGACGAGGAGAACCAG	0.574																																					p.L263fs		Atlas-INDEL	.											.	GPR132	40	.	0			c.789_790insA						.																																			SO:0001589	frameshift_variant	29933	exon4			.	AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"GPCR / Class A : Orphans"	17482	protein-coding gene	gene with protein product	"G2 accumulation"	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.788_789insA	chr14.hg19:g.105517685_105517686insT	ENSP00000328818:p.Leu263fs	59.0	0.0		193.0	39.0	NM_013345	A8K7X7|B4E144|Q9BSU2	Frame_Shift_Ins	INS	ENST00000329797.3	hg19	CCDS9997.1																																																																																			.	.		0.574	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345		T	105517686	-	T	105517685	7	5	49	1	0	1	1	0	0	0	0	0	6650	1045	37	0	357	0	GPR132	14	105517685	Frame_Shift_Ins	INS	-	TCGA-BD-A3EP-01A-11D-A22F-10	157579	105517685	1831855	222	6379	28	2								
GPR132	29933	hgsc.bcm.edu	37	chr14	105517686	105517686	+	Missense_Mutation	SNP	A	A	T													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaaaggcagcggctttgacgAggagaaccaggtggtacggg							TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:105517686A>T	ENST00000329797.3	-	4	1699	c.788T>A	c.(787-789)cTc>cAc	p.L263H	GPR132_ENST00000539291.2_Missense_Mutation_p.L263H|GPR132_ENST00000546679.1_5'Flank|GPR132_ENST00000392585.2_Missense_Mutation_p.L254H	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	263					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		GGCTTTGACGAGGAGAACCAG	0.577																																					p.L263H		Atlas-SNP	.											.	GPR132	40	.	0			c.T788A						.						102	103	103					14																	105517686		2203	4300	6503	SO:0001583	missense	29933	exon4			TTGACGAGGAGAA	AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"GPCR / Class A : Orphans"	17482	protein-coding gene	gene with protein product	"G2 accumulation"	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.788T>A	chr14.hg19:g.105517686A>T	ENSP00000328818:p.Leu263His	59.0	0.0		193.0	41.0	NM_013345	A8K7X7|B4E144|Q9BSU2	Missense_Mutation	SNP	ENST00000329797.3	hg19	CCDS9997.1	.	.	.	.	.	.	.	.	.	.	A	18.50	3.638117	0.67130	.	.	ENSG00000183484	ENST00000329797;ENST00000392585;ENST00000539291	T;T;T	0.47869	0.83;0.83;0.83	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.70404	0.3220	M	0.84219	2.685	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.75955	-0.3135	10	0.87932	D	0	.	13.857	0.63534	1.0:0.0:0.0:0.0	.	254;263	B4E144;Q9UNW8	.;GP132_HUMAN	H	263;254;263	ENSP00000328818:L263H;ENSP00000376364:L254H;ENSP00000438094:L263H	ENSP00000328818:L263H	L	-	2	0	GPR132	104588731	1.000000	0.71417	0.412000	0.26496	0.288000	0.27193	9.071000	0.93980	1.865000	0.54081	0.460000	0.39030	CTC	.	.		0.577	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345		T	105517686	A	T	105517686	3	4	49	1	0	0	0	0	1	0	0	0	6650	304	11	4	358	4	GPR132	14	105517686	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	1	105517686	1831854	223	6380	28	2								
BTBD6	90135	hgsc.bcm.edu	37	chr14	105716119	105716119	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tggaagccaagaacgcctgcGtcctgctgtcccagagccgg	13	14	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:105716119G>A	ENST00000392554.3	+	4	865	c.568G>A	c.(568-570)Gtc>Atc	p.V190I	BRF1_ENST00000546474.1_Intron|BRF1_ENST00000440513.3_Intron|BTBD6_ENST00000536364.1_Missense_Mutation_p.V190I|BRF1_ENST00000327359.3_Intron|BRF1_ENST00000392557.4_5'Flank|BTBD6_ENST00000463376.2_Missense_Mutation_p.V115I|BRF1_ENST00000551787.1_5'Flank|BTBD6_ENST00000327471.3_Missense_Mutation_p.V115I|BRF1_ENST00000446501.2_5'Flank|BRF1_ENST00000379932.4_5'Flank|BRF1_ENST00000379937.2_Intron			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	190						cytoplasm (GO:0005737)				endometrium(1)|lung(3)	4		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391)	Epithelial(152;0.18)		GAACGCCTGCGTCCTGCTGTC	0.592																																					p.V190I		Atlas-SNP	.											.	BTBD6	24	.	0			c.G568A						.						49	53	51					14																	105716119		2202	4300	6502	SO:0001583	missense	90135	exon5			GCCTGCGTCCTGC	AF353674	CCDS10002.1, CCDS10002.2	14q32.33	2013-01-08			ENSG00000184887	ENSG00000184887		"BTB/POZ domain containing"	19897	protein-coding gene	gene with protein product							Standard	NM_033271		Approved	BDPL	uc010tyq.2	Q96KE9	OTTHUMG00000029887	ENST00000392554.3:c.568G>A	chr14.hg19:g.105716119G>A	ENSP00000376337:p.Val190Ile	50.0	0.0		99.0	31.0	NM_033271	Q8IVQ7|Q9BR94	Missense_Mutation	SNP	ENST00000392554.3	hg19	CCDS10002.2	.	.	.	.	.	.	.	.	.	.	G	16.82	3.228519	0.58777	.	.	ENSG00000184887	ENST00000536364;ENST00000537513;ENST00000392554;ENST00000463376;ENST00000327471	T;T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.69;-0.69	4.63	4.63	0.57726	BTB/Kelch-associated (1);	0.000000	0.85682	D	0.000000	T	0.70133	0.3189	L	0.52905	1.665	0.80722	D	1	B	0.31519	0.327	B	0.31245	0.126	T	0.71189	-0.4666	10	0.44086	T	0.13	-44.1425	14.9721	0.71243	0.0:0.0:1.0:0.0	.	190	Q96KE9	BTBD6_HUMAN	I	190;190;190;115;115	ENSP00000443091:V190I;ENSP00000446223:V190I;ENSP00000376337:V190I;ENSP00000418150:V115I;ENSP00000329361:V115I	ENSP00000329361:V115I	V	+	1	0	BTBD6	104787164	1.000000	0.71417	0.985000	0.45067	0.710000	0.40934	6.556000	0.73932	2.102000	0.63906	0.462000	0.41574	GTC	.	.		0.592	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4			A	105716119	G	A	105716119	3	1	49	1	0	0	0	0	1	0	0	0	1547	1145	40	1	582	1	BTBD6	14	105716119	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	198433	105716119	1633421	224	6381										
OCA2	4948	hgsc.bcm.edu	37	chr15	28230328	28230328	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cacccgtccccgggagagccGgtatgcctggccacacacac	11	18	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr15:28230328G>A	ENST00000354638.3	-	13	1401	c.1246C>T	c.(1246-1248)Cgg>Tgg	p.R416W	OCA2_ENST00000353809.5_Missense_Mutation_p.R392W|OCA2_ENST00000382996.2_Missense_Mutation_p.R416W	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	416					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)	p.R416G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		CGGGAGAGCCGGTATGCCTGG	0.567									Oculocutaneous Albinism																												p.R416W		Atlas-SNP	.											OCA2,NS,carcinoma,0,1	OCA2	173	.	1	Substitution - Missense(1)	lung(1)	c.C1246T						.						81	64	70					15																	28230328		2203	4300	6503	SO:0001583	missense	4948	exon13	Familial Cancer Database		AGAGCCGGTATGC		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"melanocyte-specific transporter protein"	611409	"oculocutaneous albinism II (pink-eye dilution (murine) homolog)", "eye color 3 (brown)", "eye color 2 (central brown)", "oculocutaneous albinism II (pink-eye dilution homolog, mouse)"	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1246C>T	chr15.hg19:g.28230328G>A	ENSP00000346659:p.Arg416Trp	50.0	0.0		40.0	3.0	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	hg19	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	G	32	5.184732	0.94885	.	.	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.85556	-2.0;-2.0;-2.0	5.03	3.12	0.35913	Divalent ion symporter (1);	0.347413	0.30850	N	0.008744	D	0.89588	0.6758	M	0.69823	2.125	0.25752	N	0.985042	D;D	0.69078	0.997;0.994	P;P	0.59825	0.864;0.846	D	0.83610	0.0133	10	0.87932	D	0	0.0027	13.4265	0.61028	0.0:0.0:0.7138:0.2862	.	392;416	Q04671-2;Q04671	.;P_HUMAN	W	416;392;416	ENSP00000346659:R416W;ENSP00000261276:R392W;ENSP00000372457:R416W	ENSP00000261276:R392W	R	-	1	2	OCA2	25903923	0.995000	0.38212	0.218000	0.23776	0.738000	0.42128	2.287000	0.43505	0.592000	0.29728	0.561000	0.74099	CGG	.	.		0.567	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275		A	28230328	G	A	28230328	3	1	49	1	0	0	0	0	1	0	0	0	10824	1115	39	1	1318	1	OCA2	15	28230328	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10		28230328	74301064	225	6382										
TMEM87A	25963	hgsc.bcm.edu	37	chr15	42556385	42556385	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccttaagtttttccaaatacAactctacttcttctgcctgg	4	12	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr15:42556385A>C	ENST00000389834.4	-	4	572	c.308T>G	c.(307-309)tTg>tGg	p.L103W	TMEM87A_ENST00000568432.1_5'UTR|TMEM87A_ENST00000307216.6_Missense_Mutation_p.L103W|TMEM87A_ENST00000448392.1_Missense_Mutation_p.L42W	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	103						integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		TTCCAAATACAACTCTACTTC	0.353																																					p.L103W		Atlas-SNP	.											.	TMEM87A	56	.	0			c.T308G						.						123	123	123					15																	42556385		2203	4299	6502	SO:0001583	missense	25963	exon4			AAATACAACTCTA	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.308T>G	chr15.hg19:g.42556385A>C	ENSP00000374484:p.Leu103Trp	211.0	0.0		220.0	69.0	NM_001110503	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Missense_Mutation	SNP	ENST00000389834.4	hg19	CCDS32205.1	.	.	.	.	.	.	.	.	.	.	A	5.471	0.271964	0.10349	.	.	ENSG00000103978	ENST00000389834;ENST00000448392;ENST00000535305;ENST00000307216	.	.	.	5.12	0.727	0.18254	.	1.021790	0.07834	N	0.961879	T	0.14787	0.0357	N	0.08118	0	0.09310	N	1	B;P;P	0.39862	0.139;0.612;0.692	B;B;B	0.38712	0.013;0.062;0.28	T	0.13845	-1.0494	9	0.52906	T	0.07	-0.0032	2.9635	0.05900	0.0888:0.1558:0.4345:0.3208	.	103;42;103	Q8NBN3;Q8NBN3-3;Q8NBN3-2	TM87A_HUMAN;.;.	W	103;42;79;103	.	ENSP00000305894:L103W	L	-	2	0	TMEM87A	40343677	0.004000	0.15560	0.465000	0.27155	0.041000	0.13682	0.013000	0.13310	0.011000	0.14865	-1.075000	0.02238	TTG	.	.		0.353	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497		C	42556385	A	C	42556385	3	2	49	1	0	0	0	0	1	0	0	0	16225	131	5	5	1473	5	TMEM87A	15	42556385	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	14326057	42556385	59975007	226	6383										
ZNF609	23060	hgsc.bcm.edu	37	chr15	64967011	64967011	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaagattccttccaagagccTaaagtcagcccgtcccattg	7	13	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr15:64967011T>A	ENST00000326648.3	+	4	2086	c.1958T>A	c.(1957-1959)cTa>cAa	p.L653Q		NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	653						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCCAAGAGCCTAAAGTCAGCC	0.473																																					p.L653Q		Atlas-SNP	.											.	ZNF609	106	.	0			c.T1958A						.						59	63	61					15																	64967011		2203	4299	6502	SO:0001583	missense	23060	exon4			AGAGCCTAAAGTC	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"Zinc fingers, C2H2-type"	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.1958T>A	chr15.hg19:g.64967011T>A	ENSP00000316527:p.Leu653Gln	90.0	0.0		107.0	5.0	NM_015042	Q0D2I2	Missense_Mutation	SNP	ENST00000326648.3	hg19	CCDS32270.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.017690	0.54576	.	.	ENSG00000180357	ENST00000326648	T	0.51071	0.72	5.79	5.79	0.91817	.	0.279106	0.36519	N	0.002555	T	0.52869	0.1761	L	0.50333	1.59	0.54753	D	0.999988	P	0.45176	0.852	P	0.50896	0.653	T	0.43556	-0.9384	10	0.17832	T	0.49	-9.2984	16.1298	0.81418	0.0:0.0:0.0:1.0	.	653	O15014	ZN609_HUMAN	Q	653	ENSP00000316527:L653Q	ENSP00000316527:L653Q	L	+	2	0	ZNF609	62754064	1.000000	0.71417	0.989000	0.46669	0.978000	0.69477	6.289000	0.72696	2.208000	0.71279	0.482000	0.46254	CTA	.	.		0.473	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833		A	64967011	T	A	64967011	3	1	49	1	0	0	0	0	1	0	0	0	18050	1522	53	4	1972	4	ZNF609	15	64967011	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	22410626	64967011	37564381	227	6384										
TMC3	342125	hgsc.bcm.edu	37	chr15	81625157	81625157	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccccaatataaaaatgaggaGcccgacggaggtctatcagg	11	10	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr15:81625157G>T	ENST00000359440.5	-	22	3041	c.2906C>A	c.(2905-2907)gCt>gAt	p.A969D	RP11-761I4.3_ENST00000560973.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.A970D|RP11-761I4.3_ENST00000559781.1_RNA|RP11-761I4.3_ENST00000560851.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						AAAATGAGGAGCCCGACGGAG	0.562																																					p.A969D		Atlas-SNP	.											.	TMC3	112	.	0			c.C2906A						.						14	15	14					15																	81625157		1832	4072	5904	SO:0001583	missense	342125	exon22			TGAGGAGCCCGAC	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.2906C>A	chr15.hg19:g.81625157G>T	ENSP00000352413:p.Ala969Asp	47.0	0.0		72.0	18.0	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	hg19	CCDS45324.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.124492	0.37533	.	.	ENSG00000188869	ENST00000359440	T	0.64991	-0.13	5.42	0.139	0.14798	.	1.300320	0.06203	U	0.683653	T	0.53514	0.1801	L	0.54323	1.7	0.09310	N	1	B	0.31125	0.309	B	0.25140	0.058	T	0.47169	-0.9138	10	0.72032	D	0.01	0.0156	5.7645	0.18219	0.1932:0.0:0.5731:0.2337	.	969	Q7Z5M5	TMC3_HUMAN	D	969	ENSP00000352413:A969D	ENSP00000352413:A969D	A	-	2	0	TMC3	79412212	0.044000	0.20184	0.000000	0.03702	0.013000	0.08279	2.217000	0.42880	0.009000	0.14813	0.655000	0.94253	GCT	.	.		0.562	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		T	81625157	G	T	81625157	3	4	49	1	0	0	0	0	1	0	0	0	16001	971	34	3	400	3	TMC3	15	81625157	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	16658146	81625157	20906235	228	6385										
RAB40C	57799	hgsc.bcm.edu	37	chr16	675504	675504	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	accgctggatcaaggagatcGatgaggtaggcctgggtccg	16	9	1	2	rs141847125		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:675504G>A	ENST00000248139.3	+	4	540	c.337G>A	c.(337-339)Gat>Aat	p.D113N	RAB40C_ENST00000538492.1_Missense_Mutation_p.D113N|RAB40C_ENST00000539661.1_Missense_Mutation_p.D113N|RAB40C_ENST00000535977.1_Missense_Mutation_p.D113N	NM_021168.4	NP_066991.3	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	113					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	6		Hepatocellular(780;0.0218)				CAAGGAGATCGATGAGGTAGG	0.642																																					p.D113N	Melanoma(123;1631 1690 28262 44104 44957)	Atlas-SNP	.											RAB40C,NS,carcinoma,0,1	RAB40C	32	.	0			c.G337A						.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	0,4402		0,0,2201	76	62	67		337,337,337,337,337	5.1	0.9	16	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	RAB40C	NM_001172663.1,NM_001172664.1,NM_001172665.1,NM_001172666.1,NM_021168.4	23,23,23,23,23	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign,benign	113/282,113/282,113/282,113/263,113/282	675504	1,13001	2201	4300	6501	SO:0001583	missense	57799	exon4			GAGATCGATGAGG	Z84779	CCDS10413.1	16p13.3	2008-07-28	2003-10-14		ENSG00000197562	ENSG00000197562		"RAB, member RAS oncogene"	18285	protein-coding gene	gene with protein product			"RAS-like, family 8, member C"	RASL8C		11697911, 18485483	Standard	NM_021168		Approved	RARL	uc021szv.1	Q96S21	OTTHUMG00000047854	ENST00000248139.3:c.337G>A	chr16.hg19:g.675504G>A	ENSP00000248139:p.Asp113Asn	40.0	0.0		40.0	2.0	NM_021168	A2IDE2|D3DU54|O60795|Q4TT41|Q5PXE8|Q6PIU5	Missense_Mutation	SNP	ENST00000248139.3	hg19	CCDS10413.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.626602	0.66901	0.0	1.16E-4	ENSG00000197562	ENST00000535977;ENST00000539661;ENST00000538492;ENST00000248139	T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31	5.06	5.06	0.68205	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	N	0.17631	0.505	0.80722	D	1	P;P	0.35411	0.5;0.5	B;B	0.37198	0.243;0.243	T	0.75622	-0.3254	10	0.59425	D	0.04	.	17.7613	0.88465	0.0:0.0:1.0:0.0	.	113;113	Q96S21;Q5PXE8	RB40C_HUMAN;.	N	113	ENSP00000438492:D113N;ENSP00000445050:D113N;ENSP00000438382:D113N;ENSP00000248139:D113N	ENSP00000248139:D113N	D	+	1	0	RAB40C	615505	1.000000	0.71417	0.936000	0.37596	0.477000	0.33069	9.691000	0.98679	2.507000	0.84556	0.655000	0.94253	GAT	.	G|1.000;A|0.000		0.642	RAB40C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109079.4	NM_021168		A	675504	G	A	675504	3	1	49	1	0	0	0	0	1	0	0	0	12957	1058	37	1	351	1	RAB40C	16	675504	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10		675504	89679249	229	6386										
XYLT1	64131	hgsc.bcm.edu	37	chr16	17211760	17211760	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcccccacttctgcatacccAccggctcatccatgggcccc	6	21	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:17211760A>G	ENST00000261381.6	-	11	2384	c.2300T>C	c.(2299-2301)gTg>gCg	p.V767A		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	767					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CTGCATACCCACCGGCTCATC	0.562																																					p.V767A		Atlas-SNP	.											.	XYLT1	147	.	0			c.T2300C						.						132	109	117					16																	17211760		2197	4300	6497	SO:0001583	missense	64131	exon11			ATACCCACCGGCT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.2300T>C	chr16.hg19:g.17211760A>G	ENSP00000261381:p.Val767Ala	154.0	0.0		144.0	7.0	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	hg19	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.385672	0.82792	.	.	ENSG00000103489	ENST00000261381	T	0.48522	0.81	5.08	5.08	0.68730	.	0.055804	0.64402	D	0.000001	T	0.62073	0.2398	M	0.62016	1.91	0.58432	D	0.999999	D	0.63046	0.992	P	0.60541	0.876	T	0.64188	-0.6466	10	0.51188	T	0.08	-20.0042	14.3324	0.66566	1.0:0.0:0.0:0.0	.	767	Q86Y38	XYLT1_HUMAN	A	767	ENSP00000261381:V767A	ENSP00000261381:V767A	V	-	2	0	XYLT1	17119261	1.000000	0.71417	0.680000	0.29994	0.911000	0.54048	7.514000	0.81750	2.026000	0.59711	0.379000	0.24179	GTG	.	.		0.562	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		G	17211760	A	G	17211760	3	3	49	1	0	0	0	0	1	0	0	0	17478	159	6	2	587	2	XYLT1	16	17211760	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	16536256	17211760	73142993	230	6387										
ARHGAP17	55114	hgsc.bcm.edu	37	chr16	24955110	24955110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	accttcagggaagaaccagtCggcatgctgaatgatgggtt	13	8	1	3	rs149340407		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:24955110C>T	ENST00000289968.6	-	15	1384	c.1315G>A	c.(1315-1317)Gac>Aac	p.D439N	ARHGAP17_ENST00000303665.5_Missense_Mutation_p.D439N|ARHGAP17_ENST00000441763.2_3'UTR	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	439	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		AAGAACCAGTCGGCATGCTGA	0.413																																					p.D439N		Atlas-SNP	.											ARHGAP17_ENST00000289968,NS,carcinoma,0,2	ARHGAP17	138	.	0			c.G1315A						.						121	99	107					16																	24955110		2197	4300	6497	SO:0001583	missense	55114	exon15			ACCAGTCGGCATG	AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"Rho GTPase activating proteins"	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.1315G>A	chr16.hg19:g.24955110C>T	ENSP00000289968:p.Asp439Asn	89.0	1.0		74.0	5.0	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Missense_Mutation	SNP	ENST00000289968.6	hg19	CCDS32409.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.549485	0.65311	.	.	ENSG00000140750	ENST00000289968;ENST00000303665;ENST00000455311	T;T	0.12879	2.64;2.64	5.91	4.95	0.65309	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.160830	0.29126	N	0.013078	T	0.17959	0.0431	M	0.76727	2.345	0.80722	D	1	B;B	0.28324	0.056;0.207	B;B	0.17433	0.018;0.009	T	0.01805	-1.1270	10	0.66056	D	0.02	.	12.1212	0.53893	0.0:0.9149:0.0:0.0851	.	439;439	Q68EM7-2;Q68EM7	.;RHG17_HUMAN	N	439	ENSP00000289968:D439N;ENSP00000303130:D439N	ENSP00000289968:D439N	D	-	1	0	ARHGAP17	24862611	1.000000	0.71417	0.890000	0.34922	0.871000	0.50021	4.533000	0.60615	1.473000	0.48159	0.655000	0.94253	GAC	.	C|1.000;A|0.000		0.413	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054		T	24955110	C	T	24955110	3	4	49	1	0	0	0	0	1	0	0	0	867	884	31	1	1354	1	ARHGAP17	16	24955110	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	7743350	24955110	65399643	231	6388										
SULT1A2	6799	hgsc.bcm.edu	37	chr16	28606943	28606943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gggagctcggtgacacttttCcaggtcaccgccctggtaga	13	12	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:28606943C>T	ENST00000395630.1	-	3	552	c.202G>A	c.(202-204)Gaa>Aaa	p.E68K	SULT1A2_ENST00000533150.1_Missense_Mutation_p.E68K|SULT1A2_ENST00000335715.4_Missense_Mutation_p.E68K	NM_177528.2	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2	68					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine biosynthetic process (GO:0009309)|catecholamine metabolic process (GO:0006584)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|sulfotransferase activity (GO:0008146)			NS(2)|breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|skin(2)	14						TGACACTTTTCCAGGTCACCG	0.587																																					p.E68K		Atlas-SNP	.											.	SULT1A2	27	.	0			c.G202A						.						94	86	89					16																	28606943		2197	4300	6497	SO:0001583	missense	6799	exon3			ACTTTTCCAGGTC	U34804	CCDS10636.1	16p12.1	2008-02-05			ENSG00000197165	ENSG00000197165	2.8.2.1	"Sulfotransferases, cytosolic"	11454	protein-coding gene	gene with protein product		601292		STP2		8661000, 8912648	Standard	NM_001054		Approved	HAST4	uc002dqh.2	P50226	OTTHUMG00000048082	ENST00000395630.1:c.202G>A	chr16.hg19:g.28606943C>T	ENSP00000378992:p.Glu68Lys	99.0	0.0		121.0	47.0	NM_001054	A9QY25|P78393|Q14CJ7	Missense_Mutation	SNP	ENST00000395630.1	hg19	CCDS10636.1	.	.	.	.	.	.	.	.	.	.	c	9.160	1.018388	0.19355	.	.	ENSG00000197165	ENST00000533150;ENST00000335715;ENST00000395630;ENST00000526384	D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66	4.7	1.52	0.23074	Sulfotransferase domain (1);	0.411184	0.24403	N	0.038833	T	0.72779	0.3503	L	0.47078	1.49	0.19945	N	0.999944	B	0.06786	0.001	B	0.08055	0.003	T	0.61505	-0.7049	10	0.48119	T	0.1	.	4.6656	0.12664	0.0:0.539:0.1788:0.2822	.	68	P50226	ST1A2_HUMAN	K	68	ENSP00000435271:E68K;ENSP00000338742:E68K;ENSP00000378992:E68K;ENSP00000435358:E68K	ENSP00000338742:E68K	E	-	1	0	SULT1A2	28514444	0.006000	0.16342	0.036000	0.18154	0.031000	0.12232	0.366000	0.20365	0.383000	0.24910	0.556000	0.70494	GAA	.	.		0.587	SULT1A2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109415.2	NM_001054		T	28606943	C	T	28606943	3	4	49	1	0	0	0	0	1	0	0	0	15388	864	30	3	709	3	SULT1A2	16	28606943	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	3651833	28606943	61747810	232	6389										
SPNS1	83985	hgsc.bcm.edu	37	chr16	28986619	28986619	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gaccaggaggggctgcagcgCatcaccggcctgtctcccgg	15	15	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:28986619C>T	ENST00000311008.11	+	1	524	c.147C>T	c.(145-147)cgC>cgT	p.R49R	SPNS1_ENST00000565975.1_Silent_p.R94R|SPNS1_ENST00000334536.8_Silent_p.R49R|SPNS1_ENST00000352260.7_Silent_p.R49R|RP11-264B17.4_ENST00000567209.1_RNA|SPNS1_ENST00000323081.8_5'UTR|RP11-264B17.3_ENST00000569969.1_RNA	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	49					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)		p.R49R(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						GGCTGCAGCGCATCACCGGCC	0.677																																					p.R49R		Atlas-SNP	.											SPNS1,NS,carcinoma,0,1	SPNS1	47	.	1	Substitution - coding silent(1)	lung(1)	c.C147T						.						21	25	24					16																	28986619		2196	4299	6495	SO:0001819	synonymous_variant	83985	exon1			GCAGCGCATCACC	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.147C>T	chr16.hg19:g.28986619C>T		42.0	0.0		46.0	2.0	NM_001142451	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	hg19	CCDS10646.1																																																																																			.	.		0.677	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038		T	28986619	C	T	28986619	2	4	49	1	0	0	0	0	0	0	0	1	15089	697	25	3		3	SPNS1	16	28986619	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	379676	28986619	61368134	233	6390										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30750366	30750366	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgtcaccatttcaacgtcccCacccaaacggaagaggggcc	9	15	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:30750366C>G	ENST00000262518.4	+	34	9390	c.9005C>G	c.(9004-9006)cCa>cGa	p.P3002R	SRCAP_ENST00000395059.2_Missense_Mutation_p.P2940R|SRCAP_ENST00000344771.4_Missense_Mutation_p.P2844R|RP11-2C24.4_ENST00000483578.1_lincRNA	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	3002	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TCAACGTCCCCACCCAAACGG	0.597																																					p.P3002R		Atlas-SNP	.											.	SRCAP	298	.	0			c.C9005G						.						149	117	127					16																	30750366		2197	4300	6497	SO:0001583	missense	10847	exon34			CGTCCCCACCCAA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.9005C>G	chr16.hg19:g.30750366C>G	ENSP00000262518:p.Pro3002Arg	54.0	0.0		84.0	6.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	8.005	0.756188	0.15846	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.93488	-3.2;-3.23;-3.22	5.13	5.13	0.70059	.	0.000000	0.49916	D	0.000133	D	0.91546	0.7330	N	0.08118	0	0.28469	N	0.915492	D;D	0.69078	0.997;0.995	D;P	0.65010	0.931;0.854	D	0.87078	0.2164	10	0.87932	D	0	-8.6141	13.9377	0.64034	0.0:1.0:0.0:0.0	.	2940;3002	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	R	3002;2940;2844	ENSP00000262518:P3002R;ENSP00000378499:P2940R;ENSP00000343042:P2844R	ENSP00000262518:P3002R	P	+	2	0	SRCAP	30657867	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.813000	0.69201	2.663000	0.90544	0.563000	0.77884	CCA	.	.		0.597	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		G	30750366	C	G	30750366	3	3	49	1	0	0	0	0	1	0	0	0	15150	594	21	4	9131	4	SRCAP	16	30750366	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1763747	30750366	59604387	234	6391										
RLTPR	146206	hgsc.bcm.edu	37	chr16	67686234	67686234	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccgaggagaaggaagaggagAaggagaaggtaagtggtttt	18	2	0	4	rs144268948|rs374451388	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:67686234A>G	ENST00000334583.6	+	27	3137	c.2809A>G	c.(2809-2811)Aag>Gag	p.K937E	RLTPR_ENST00000545661.1_Missense_Mutation_p.K901E	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	937	Pro-rich.				cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		ggaagaggagaaggagaaggT	0.557																																					p.K937E		Atlas-SNP	.											.	RLTPR	124	.	0			c.A2809G						.						52	55	54					16																	67686234		1955	4157	6112	SO:0001583	missense	146206	exon27			GAGGAGAAGGAGA	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.2809A>G	chr16.hg19:g.67686234A>G	ENSP00000334958:p.Lys937Glu	15.0	0.0		10.0	4.0	NM_001013838	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	hg19	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	A	0.044	-1.274756	0.01410	.	.	ENSG00000159753	ENST00000334583;ENST00000398282;ENST00000545661	T;T	0.12569	2.67;2.67	3.05	-3.05	0.05396	.	1.639460	0.03537	N	0.223270	T	0.03053	0.0090	N	0.00210	-1.845	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39623	-0.9605	10	0.17832	T	0.49	-8.7017	8.1769	0.31287	0.6821:0.0:0.3179:0.0	.	901;937	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	E	937;34;901	ENSP00000334958:K937E;ENSP00000441481:K901E	ENSP00000334958:K937E	K	+	1	0	RLTPR	66243735	0.001000	0.12720	0.006000	0.13384	0.033000	0.12548	-0.018000	0.12568	-0.705000	0.05035	-1.280000	0.01385	AAG	.	.		0.557	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		G	67686234	A	G	67686234	3	3	49	1	0	0	0	0	1	0	0	0	13409	247	9	2	2915	2	RLTPR	16	67686234	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	36935868	67686234	22668519	235	6392										
EDC4	23644	hgsc.bcm.edu	37	chr16	67912905	67912905	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaaaccaggaggagggccacGcctgcttcagctccatctcg	11	14	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:67912905G>A	ENST00000358933.5	+	12	1572	c.1333G>A	c.(1333-1335)Gcc>Acc	p.A445T	EDC4_ENST00000574770.1_3'UTR|AC040162.1_ENST00000408599.1_RNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	445					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		GGAGGGCCACGCCTGCTTCAG	0.597																																					p.A445T		Atlas-SNP	.											EDC4,colon,carcinoma,0,1	EDC4	101	.	0			c.G1333A						.						69	58	62					16																	67912905		2198	4300	6498	SO:0001583	missense	23644	exon12			GGCCACGCCTGCT	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.1333G>A	chr16.hg19:g.67912905G>A	ENSP00000351811:p.Ala445Thr	31.0	0.0		60.0	3.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	hg19	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.601849	0.87055	.	.	ENSG00000038358	ENST00000358933;ENST00000536072	.	.	.	5.53	5.53	0.82687	.	0.050730	0.85682	D	0.000000	T	0.55800	0.1943	L	0.31294	0.92	0.80722	D	1	D;D;D	0.67145	0.996;0.964;0.985	P;B;P	0.50617	0.646;0.359;0.466	T	0.50250	-0.8850	9	0.30854	T	0.27	-18.2934	17.412	0.87488	0.0:0.0:1.0:0.0	.	377;64;445	B7Z7V8;Q6P2E9-2;Q6P2E9	.;.;EDC4_HUMAN	T	445;377	.	ENSP00000351811:A445T	A	+	1	0	EDC4	66470406	1.000000	0.71417	0.979000	0.43373	0.848000	0.48234	9.657000	0.98554	2.882000	0.98803	0.655000	0.94253	GCC	.	.		0.597	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		A	67912905	G	A	67912905	3	1	49	1	0	0	0	0	1	0	0	0	4910	1087	38	1	1379	1	EDC4	16	67912905	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	226671	67912905	22441848	236	6393										
CTRL	1506	hgsc.bcm.edu	37	chr16	67964673	67964673	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gggctctgcgtttgatgatcGgtcatactcgcccaggacaa	12	11	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:67964673G>A	ENST00000574481.1	-	4	835	c.274C>T	c.(274-276)Cga>Tga	p.R92*	CTRL_ENST00000576408.1_5'UTR	NM_001907.2	NP_001898.1	P40313	CTRL_HUMAN	chymotrypsin-like	92	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|urinary_tract(1)	4		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		TTTGATGATCGGTCATACTCG	0.637																																					p.R92X		Atlas-SNP	.											.	CTRL	11	.	0			c.C274T						.						64	66	65					16																	67964673		2198	4300	6498	SO:0001587	stop_gained	1506	exon4			ATGATCGGTCATA		CCDS10852.1	16q22.1	2008-02-05			ENSG00000141086	ENSG00000141086			2524	protein-coding gene	gene with protein product		118888				8268911	Standard	NM_001907		Approved		uc002euw.3	P40313	OTTHUMG00000137552	ENST00000574481.1:c.274C>T	chr16.hg19:g.67964673G>A	ENSP00000458537:p.Arg92*	86.0	0.0		80.0	4.0	NM_001907		Nonsense_Mutation	SNP	ENST00000574481.1	hg19	CCDS10852.1	.	.	.	.	.	.	.	.	.	.	G	37	6.444316	0.97572	.	.	ENSG00000141086	ENST00000319955	.	.	.	5.42	3.38	0.38709	.	0.328530	0.28476	N	0.015212	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	0.175	8.5848	0.33651	0.0721:0.0:0.6548:0.2731	.	.	.	.	X	92	.	ENSP00000322629:R92X	R	-	1	2	CTRL	66522174	0.992000	0.36948	0.009000	0.14445	0.152000	0.21847	2.609000	0.46317	1.350000	0.45770	0.655000	0.94253	CGA	.	.		0.637	CTRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268886.3			A	67964673	G	A	67964673	4	1	49	1	0	0	0	0	0	1	0	0	4030	1124	39	1	536	1	CTRL	16	67964673	Nonsense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	51768	67964673	22390080	237	6394										
COG4	25839	hgsc.bcm.edu	37	chr16	70543864	70543864	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgcaaagatgactgcagctcTccgatcactcatgtctgtcc	8	13	4	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:70543864T>C	ENST00000323786.5	-	6	820	c.799A>G	c.(799-801)Aga>Gga	p.R267G	COG4_ENST00000393612.4_Missense_Mutation_p.R263G	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	263					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				ACTGCAGCTCTCCGATCACTC	0.478																																					p.R267G		Atlas-SNP	.											COG4,colon,carcinoma,0,1	COG4	64	.	0			c.A799G						.						134	116	122					16																	70543864		2198	4300	6498	SO:0001583	missense	25839	exon6			CAGCTCTCCGATC	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"Components of oligomeric golgi complex"	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.799A>G	chr16.hg19:g.70543864T>C	ENSP00000315775:p.Arg267Gly	83.0	0.0		66.0	3.0	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	ENST00000323786.5	hg19	CCDS10892.2	.	.	.	.	.	.	.	.	.	.	T	21.3	4.126204	0.77549	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000393612	T;T	0.48201	0.84;0.82	5.61	3.25	0.37280	Conserved oligomeric Golgi complex, subunit 4 (2);	0.000000	0.85682	D	0.000000	T	0.67664	0.2917	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	0.994;1.0	D;D	0.79784	0.914;0.993	T	0.70163	-0.4947	10	0.87932	D	0	-12.1058	13.3485	0.60589	0.0:0.0:0.4654:0.5346	.	262;263	Q6PIW8;Q9H9E3	.;COG4_HUMAN	G	267;263;263	ENSP00000315775:R267G;ENSP00000377236:R263G	ENSP00000315775:R267G	R	-	1	2	COG4	69101365	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	2.155000	0.42301	0.361000	0.24292	0.421000	0.28195	AGA	.	.		0.478	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3			C	70543864	T	C	70543864	3	2	49	1	0	0	0	0	1	0	0	0	3662	1559	54	2	1626	2	COG4	16	70543864	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	2579191	70543864	19810889	238	6395										
MON1B	22879	hgsc.bcm.edu	37	chr16	77227419	77227419	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aggccctgtcaagcacctctCggctctggagtcctgcagcc	11	16	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:77227419C>T	ENST00000248248.3	+	3	570	c.220C>T	c.(220-222)Cgg>Tgg	p.R74W	MON1B_ENST00000545553.1_Intron|MON1B_ENST00000439557.2_Intron|MON1B_ENST00000320859.6_Missense_Mutation_p.R74W	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	74										breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						AAGCACCTCTCGGCTCTGGAG	0.637																																					p.R74W		Atlas-SNP	.											MON1B,colon,carcinoma,0,1	MON1B	55	.	0			c.C220T						.						55	57	56					16																	77227419		2198	4300	6498	SO:0001583	missense	22879	exon3			ACCTCTCGGCTCT	BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"MON1 homolog B (yeast)"			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.220C>T	chr16.hg19:g.77227419C>T	ENSP00000248248:p.Arg74Trp	54.0	0.0		44.0	3.0	NM_014940	B4DDZ0|O94949	Missense_Mutation	SNP	ENST00000248248.3	hg19	CCDS10925.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.688529	0.29962	.	.	ENSG00000103111	ENST00000248248;ENST00000320859	.	.	.	3.61	1.59	0.23543	.	1.974950	0.02637	N	0.104904	T	0.11452	0.0279	N	0.08118	0	0.20563	N	0.999886	P	0.51537	0.946	B	0.30495	0.116	T	0.25187	-1.0139	9	0.72032	D	0.01	.	6.3215	0.21221	0.1184:0.4881:0.3935:0.0	.	74	Q7L1V2	MON1B_HUMAN	W	74	.	ENSP00000248248:R74W	R	+	1	2	MON1B	75784920	0.035000	0.19736	0.231000	0.23993	0.194000	0.23727	0.899000	0.28417	0.476000	0.27440	0.563000	0.77884	CGG	.	.		0.637	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940		T	77227419	C	T	77227419	3	4	49	1	0	0	0	0	1	0	0	0	9708	875	31	1	226	1	MON1B	16	77227419	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	6683555	77227419	13127334	239	6396										
SENP3	26168	hgsc.bcm.edu	37	chr17	7470288	7470288	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tatgataaactccgtaccaaAgggttatgatggggtgaaaa	11	5	0	3	rs76586164		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:7470288A>G	ENST00000429205.2	+	8	1356	c.1307A>G	c.(1306-1308)aAg>aGg	p.K436R	SENP3_ENST00000321337.7_Splice_Site|SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000578868.1_3'UTR			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	436	Protease.					cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				TCCGTACCAAAGGGTTATGAT	0.398																																					p.K436R		Atlas-SNP	.											.	SENP3	18	.	0			c.A1307G						.						193	199	197					17																	7470288		989	2111	3100	SO:0001630	splice_region_variant	26168	exon8			TACCAAAGGGTTA	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"SUMO1/sentrin/SMT3 specific protease 3"			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.1306-1A>G	chr17.hg19:g.7470288A>G		178.0	0.0		155.0	14.0	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Missense_Mutation	SNP	ENST00000429205.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.4|20.4	3.977344|3.977344	0.74360|0.74360	.|.	.|.	ENSG00000161956|ENSG00000161956	ENST00000321337|ENST00000429205	.|T	.|0.28895	.|1.59	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	.|.	.|.	.|.	.|.	.|T	.|0.54902	.|0.1887	.|.	.|.	.|.	0.58432|0.58432	D|D	0.999999|0.999999	.|D	.|0.69078	.|0.997	.|D	.|0.77004	.|0.989	.|T	.|0.55755	.|-0.8091	.|8	.|0.45353	.|T	.|0.12	.|-15.252	13.941|13.941	0.64054|0.64054	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|436	.|Q9H4L4	.|SENP3_HUMAN	.|R	-1|436	.|ENSP00000403712:K436R	.|ENSP00000403712:K436R	.|K	+|+	.|2	.|0	SENP3|SENP3	7411012|7411012	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	0.000000|0.000000	0.12993|0.12993	2.179000|2.179000	0.69175|0.69175	0.421000|0.421000	0.28195|0.28195	.|AAG	.	A|0.500;G|0.500		0.398	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	Missense_Mutation	G	7470288	A	G	7470288	5	3	49	1	0	0	0	0	0	0	1	0	14063	69	3	2	1330	2	SENP3	17	7470288	Splice_Site	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10		7470288	73724922	240	6397										
TP53	7157	hgsc.bcm.edu	37	chr17	7578478	7578478	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggacgcgggtgccgggcgggGgtgtggaatcaacccacagc	19	11	1	0	rs137852790|rs137852791		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:7578478G>T	ENST00000269305.4	-	5	641	c.452C>A	c.(451-453)cCc>cAc	p.P151H	TP53_ENST00000455263.2_Missense_Mutation_p.P151H|TP53_ENST00000420246.2_Missense_Mutation_p.P151H|TP53_ENST00000413465.2_Missense_Mutation_p.P151H|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.P151H|TP53_ENST00000445888.2_Missense_Mutation_p.P151H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	151	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> R (in sporadic cancers; somatic mutation).|P -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934874). {ECO:0000269|PubMed:7682763}.|P -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P151H(31)|p.P151R(9)|p.0?(8)|p.P151L(7)|p.T150fs*16(6)|p.?(5)|p.P58H(2)|p.P19H(2)|p.P151_V173del23(1)|p.P152_P153del(1)|p.P152fs*28(1)|p.T57fs*16(1)|p.P151del(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.P153fs*28(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.P58R(1)|p.Q144_G154del11(1)|p.P19R(1)|p.Q144fs*16(1)|p.P152fs*14(1)|p.P151fs*30(1)|p.T18fs*16(1)|p.T150_P151delTP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCCGGGCGGGGGTGTGGAATC	0.607		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.P151H	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,-1,2	TP53	33396	.	90	Substitution - Missense(53)|Deletion - Frameshift(14)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Insertion - Frameshift(2)	lung(17)|large_intestine(13)|ovary(10)|skin(8)|oesophagus(8)|breast(6)|stomach(5)|haematopoietic_and_lymphoid_tissue(5)|central_nervous_system(4)|bone(4)|upper_aerodigestive_tract(3)|soft_tissue(2)|urinary_tract(2)|liver(2)|vulva(1)	c.C452A						.						54	55	55					17																	7578478		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGCGGGGGTGTGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.452C>A	chr17.hg19:g.7578478G>T	ENSP00000269305:p.Pro151His	61.0	0.0		68.0	17.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.040562	0.55003	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99887	-7.53;-7.53;-7.53;-7.53;-7.53;-7.53;-7.53;-7.53;-7.53	5.59	4.63	0.57726	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.110207	0.64402	D	0.000007	D	0.99891	0.9948	M	0.91406	3.205	0.53688	D	0.999972	D;P;D;P;P;P;D	0.89917	0.99;0.807;1.0;0.793;0.948;0.84;1.0	P;P;D;P;P;P;D	0.97110	0.84;0.754;0.995;0.625;0.841;0.868;1.0	D	0.96236	0.9172	10	0.87932	D	0	-14.1156	12.4691	0.55777	0.0812:0.0:0.9188:0.0	.	112;151;151;58;151;151;151	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	151;151;151;151;151;151;140;58;19;58;19;151	ENSP00000410739:P151H;ENSP00000352610:P151H;ENSP00000269305:P151H;ENSP00000398846:P151H;ENSP00000391127:P151H;ENSP00000391478:P151H;ENSP00000425104:P19H;ENSP00000423862:P58H;ENSP00000424104:P151H	ENSP00000269305:P151H	P	-	2	0	TP53	7519203	1.000000	0.71417	0.974000	0.42286	0.058000	0.15608	6.711000	0.74675	1.515000	0.48885	0.655000	0.94253	CCC	.	.		0.607	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578478	G	T	7578478	3	4	49	1	0	0	0	0	1	0	0	0	16396	1232	43	3	846	3	TP53	17	7578478	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	108190	7578478	73616732	241	6398										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7674169	7674169	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggcctttgagaaggatgtggAccactgggaacgctgcctct	14	10	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:7674169A>G	ENST00000572933.1	+	27	5740	c.4280A>G	c.(4279-4281)gAc>gGc	p.D1427G	DNAH2_ENST00000389173.2_Missense_Mutation_p.D1427G			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1427	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				AAGGATGTGGACCACTGGGAA	0.502																																					p.D1427G		Atlas-SNP	.											.	DNAH2	498	.	0			c.A4280G						.						176	152	160					17																	7674169		2203	4300	6503	SO:0001583	missense	146754	exon26			ATGTGGACCACTG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.4280A>G	chr17.hg19:g.7674169A>G	ENSP00000458355:p.Asp1427Gly	113.0	0.0		122.0	6.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.193466	0.78902	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.61859	0.07	4.84	4.84	0.62591	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	T	0.74435	0.3716	M	0.81802	2.56	0.80722	D	1	D	0.63880	0.993	D	0.68621	0.959	T	0.74694	-0.3579	10	0.33940	T	0.23	.	13.8202	0.63315	1.0:0.0:0.0:0.0	.	1427	Q9P225	DYH2_HUMAN	G	1427	ENSP00000373825:D1427G	ENSP00000353818:D1427G	D	+	2	0	DNAH2	7614894	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	6.099000	0.71466	2.151000	0.67156	0.455000	0.32223	GAC	.	.		0.502	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		G	7674169	A	G	7674169	3	3	49	1	0	0	0	0	1	0	0	0	4604	275	10	2	4382	2	DNAH2	17	7674169	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	95691	7674169	73521041	242	6399										
MYH10	4628	hgsc.bcm.edu	37	chr17	8480586	8480586	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtcctttcttcctttatgtgAagaagcaacatgggcaaggt	10	8	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:8480586A>G	ENST00000269243.4	-	5	739	c.601T>C	c.(601-603)Tca>Cca	p.S201P	MYH10_ENST00000379980.4_Missense_Mutation_p.S201P|MYH10_ENST00000396239.1_Missense_Mutation_p.S201P|MYH10_ENST00000360416.3_Missense_Mutation_p.S201P	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	201	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CCTTTATGTGAAGAAGCAACA	0.343																																					p.S201P		Atlas-SNP	.											.	MYH10	148	.	0			c.T601C						.						114	116	116					17																	8480586		2203	4300	6503	SO:0001583	missense	4628	exon5			TATGTGAAGAAGC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.601T>C	chr17.hg19:g.8480586A>G	ENSP00000269243:p.Ser201Pro	89.0	0.0		87.0	4.0	NM_005964	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	hg19	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.842738	0.91197	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47	5.01	5.01	0.66863	Myosin head, motor domain (2);	0.060192	0.64402	D	0.000002	D	0.93164	0.7823	M	0.75085	2.285	0.80722	D	1	P;D;B	0.53312	0.595;0.959;0.452	P;P;P	0.61397	0.868;0.888;0.778	D	0.93742	0.7051	10	0.62326	D	0.03	.	14.8427	0.70237	1.0:0.0:0.0:0.0	.	201;201;201	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	P	201	ENSP00000269243:S201P;ENSP00000353590:S201P;ENSP00000379539:S201P;ENSP00000369315:S201P	ENSP00000269243:S201P	S	-	1	0	MYH10	8421311	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.776000	0.91776	2.223000	0.72356	0.533000	0.62120	TCA	.	.		0.343	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			G	8480586	A	G	8480586	3	3	49	1	0	0	0	0	1	0	0	0	10039	246	9	2	5477	2	MYH10	17	8480586	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	806417	8480586	72714624	243	6400										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26961982	26961982	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gaaaacccatgagaagtgctCaacctttaagagtagatcag	9	8	2	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:26961982C>A	ENST00000528896.2	-	16	2697	c.2623G>T	c.(2623-2625)Gag>Tag	p.E875*	RP11-192H23.7_ENST00000577814.1_RNA|KIAA0100_ENST00000544884.1_Nonsense_Mutation_p.E732*|RP11-192H23.7_ENST00000583787.1_RNA|KIAA0100_ENST00000389003.3_Nonsense_Mutation_p.E732*	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	875						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					GAGAAGTGCTCAACCTTTAAG	0.473																																					p.E875X		Atlas-SNP	.											KIAA0100,right_upper_lobe,carcinoma,0,1	KIAA0100	175	.	0			c.G2623T						.						162	180	174					17																	26961982		2203	4300	6503	SO:0001587	stop_gained	9703	exon16			AGTGCTCAACCTT	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.2623G>T	chr17.hg19:g.26961982C>A	ENSP00000436773:p.Glu875*	71.0	1.0		89.0	4.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Nonsense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	c	40	8.404047	0.98796	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	.	.	.	5.89	4.92	0.64577	.	0.474372	0.25427	N	0.030748	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.0105	0.47659	0.0:0.1154:0.6419:0.2427	.	.	.	.	X	875;845;875;732	.	ENSP00000005905:E875X	E	-	1	0	KIAA0100	23986109	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.798000	0.38814	1.509000	0.48786	-0.234000	0.12200	GAG	.	.		0.473	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		A	26961982	C	A	26961982	4	1	49	1	0	0	0	0	0	1	0	0	8163	835	29	3	4180	3	KIAA0100	17	26961982	Nonsense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	18481396	26961982	54233228	244	6401										
CCDC55	84081	hgsc.bcm.edu	37	chr17	28499575	28499575	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tacagacctctgtgagtgaaAgccttcagagggaagctgct	12	9	2	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:28499575A>G	ENST00000247026.5	+	3	193	c.130A>G	c.(130-132)Agc>Ggc	p.S44G	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	44					developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						TGTGAGTGAAAGCCTTCAGAG	0.393																																					p.S44G		Atlas-SNP	.											.	NSRP1	49	.	0			c.A130G						.						60	58	59					17																	28499575		2203	4300	6503	SO:0001583	missense	84081	exon3			AGTGAAAGCCTTC	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"coiled-coil domain containing 55"	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.130A>G	chr17.hg19:g.28499575A>G	ENSP00000247026:p.Ser44Gly	65.0	0.0		96.0	4.0	NM_032141	Q6FI71	Missense_Mutation	SNP	ENST00000247026.5	hg19	CCDS11255.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.039002	0.93630	.	.	ENSG00000126653	ENST00000247026	T	0.51325	0.71	5.73	5.73	0.89815	.	0.038368	0.85682	D	0.000000	T	0.65312	0.2679	M	0.77616	2.38	0.80722	D	1	D	0.69078	0.997	P	0.60012	0.867	T	0.65010	-0.6272	10	0.33141	T	0.24	-10.367	15.1352	0.72558	1.0:0.0:0.0:0.0	.	44	Q9H0G5	NSRP1_HUMAN	G	44	ENSP00000247026:S44G	ENSP00000247026:S44G	S	+	1	0	NSRP1	25523701	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.683000	0.68189	2.308000	0.77769	0.533000	0.62120	AGC	.	.		0.393	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141		G	28499575	A	G	28499575	3	3	49	1	0	0	0	0	1	0	0	0	2827	72	3	2	140	2	CCDC55	17	28499575	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	1537593	28499575	52695635	245	6402										
MYO19	80179	hgsc.bcm.edu	37	chr17	34856750	34856750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tccagccaccctggatgcagCgggcacactgctccagcacc	10	18	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:34856750C>T	ENST00000431794.3	-	23	2819	c.2297G>A	c.(2296-2298)cGc>cAc	p.R766H	MYO19_ENST00000268852.9_Missense_Mutation_p.R566H	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	766	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CTGGATGCAGCGGGCACACTG	0.672																																					p.R766H		Atlas-SNP	.											MYO19_ENST00000431794,NS,carcinoma,0,2	MYO19	130	.	0			c.G2297A						.						18	21	20					17																	34856750		2138	4243	6381	SO:0001583	missense	80179	exon24			ATGCAGCGGGCAC	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"Myosins / Myosin superfamily : Class XIX"	26234	protein-coding gene	gene with protein product			"myosin head domain containing 1"	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.2297G>A	chr17.hg19:g.34856750C>T	ENSP00000409936:p.Arg766His	67.0	1.0		44.0	2.0	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	hg19	CCDS54112.1	.	.	.	.	.	.	.	.	.	.	C	11.59	1.684872	0.29872	.	.	ENSG00000141140	ENST00000431794;ENST00000268852	T;T	0.71579	-0.58;-0.58	5.12	3.09	0.35607	.	0.000000	0.38897	N	0.001535	T	0.52597	0.1744	L	0.38838	1.175	0.80722	D	1	B;B	0.27700	0.186;0.03	B;B	0.12837	0.008;0.004	T	0.51980	-0.8636	10	0.46703	T	0.11	.	4.3091	0.10962	0.1823:0.6288:0.0:0.1889	.	766;566	Q96H55;Q96H55-4	MYO19_HUMAN;.	H	766;566	ENSP00000409936:R766H;ENSP00000268852:R566H	ENSP00000268852:R566H	R	-	2	0	MYO19	31930863	0.999000	0.42202	1.000000	0.80357	0.949000	0.60115	0.752000	0.26362	1.267000	0.44247	0.462000	0.41574	CGC	.	.		0.672	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109		T	34856750	C	T	34856750	3	4	49	1	0	0	0	0	1	0	0	0	10076	768	27	1	631	1	MYO19	17	34856750	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	6357175	34856750	46338460	246	6403										
CACNB1	782	hgsc.bcm.edu	37	chr17	37341067	37341067	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttgagcgacggtcccaccagGatgatgggcctcatggaagg	15	10	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:37341067G>T	ENST00000394303.3	-	8	906	c.699C>A	c.(697-699)atC>atA	p.I233I	CACNB1_ENST00000582877.1_5'Flank|CACNB1_ENST00000394310.3_Silent_p.I233I|CACNB1_ENST00000344140.5_Silent_p.I278I	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit	233					axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GTCCCACCAGGATGATGGGCC	0.592																																					p.I278I	Esophageal Squamous(5;100 366 38393 41452 45827)	Atlas-SNP	.											.	CACNB1	89	.	0			c.C834A						.						57	50	52					17																	37341067		2203	4300	6503	SO:0001819	synonymous_variant	782	exon8			CACCAGGATGATG		CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"Calcium channel subunits"	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.699C>A	chr17.hg19:g.37341067G>T		89.0	0.0		131.0	23.0	NM_199247	A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Silent	SNP	ENST00000394303.3	hg19	CCDS42311.1																																																																																			.	.		0.592	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3			T	37341067	G	T	37341067	2	4	49	1	0	0	0	0	0	0	0	1	2554	1164	41	3		3	CACNB1	17	37341067	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	2484317	37341067	43854143	247	6404										
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44249469	44249469	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgaaccggatatggtgtgctTcagctgctgcgtcagtgaga	14	8	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:44249469T>C	ENST00000262419.6	-	2	511	c.41A>G	c.(40-42)gAa>gGa	p.E14G	KANSL1_ENST00000574590.1_Missense_Mutation_p.E14G|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000575318.1_Missense_Mutation_p.E14G|KANSL1_ENST00000572904.1_Missense_Mutation_p.E14G|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000432791.1_Missense_Mutation_p.E14G	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	14					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											ATGGTGTGCTTCAGCTGCTGC	0.597																																					p.E14G		Atlas-SNP	.											KIAA1267,NS,neuroblastoma,0,1	.	.	.	0			c.A41G						.						59	70	66					17																	44249469		2203	4300	6503	SO:0001583	missense	284058	exon2			TGTGCTTCAGCTG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"centromere protein 36"	612452	"KIAA1267"	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.41A>G	chr17.hg19:g.44249469T>C	ENSP00000262419:p.Glu14Gly	32.0	1.0		65.0	3.0	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	hg19	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.219184	0.58560	.	.	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.19938	2.11;2.11	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.35278	0.0926	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72075	0.976;0.976	T	0.09707	-1.0662	10	0.72032	D	0.01	-12.3283	15.3292	0.74193	0.0:0.0:0.0:1.0	.	14;14	C9JHY2;Q7Z3B3	.;K1267_HUMAN	G	14	ENSP00000262419:E14G;ENSP00000387393:E14G	ENSP00000262419:E14G	E	-	2	0	KIAA1267	41605246	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.484000	0.81180	2.291000	0.77112	0.533000	0.62120	GAA	.	.		0.597	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		C	44249469	T	C	44249469	3	2	49	1	0	0	0	0	1	0	0	0	8228	1783	62	2	3332	2	KIAA1267	17	44249469	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	6908402	44249469	36945741	248	6405										
CDC27	996	hgsc.bcm.edu	37	chr17	45232068	45232068	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggggctccggtggatggcacAtcaattacaggaggtgtatt	15	7	1	0	rs74710570		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:45232068A>G	ENST00000066544.3	-	8	1020	c.927T>C	c.(925-927)gaT>gaC	p.D309D	CDC27_ENST00000531206.1_Silent_p.D309D|CDC27_ENST00000446365.2_Silent_p.D248D|CDC27_ENST00000527547.1_Silent_p.D309D|CDC27_ENST00000528748.1_5'Flank	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	309					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TGGATGGCACATCAATTACAG	0.373																																					p.D309D		Atlas-SNP	.											.	CDC27	337	.	0			c.T927C						.						49	49	49					17																	45232068		2203	4300	6503	SO:0001819	synonymous_variant	996	exon8			TGGCACATCAATT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.927T>C	chr17.hg19:g.45232068A>G		50.0	0.0		101.0	5.0	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.373	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			G	45232068	A	G	45232068	2	3	49	1	0	0	0	0	0	0	0	1	3068	214	8	2		2	CDC27	17	45232068	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	982599	45232068	35963142	249	6406										
LRRC46	90506	hgsc.bcm.edu	37	chr17	45914305	45914305	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcaaggggaggagacagtccCtgaggccgtctcctcacccc	13	15	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:45914305C>T	ENST00000269025.4	+	8	1148	c.785C>T	c.(784-786)cCt>cTt	p.P262L		NM_033413.3	NP_219481.1	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	262										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	9						GAGACAGTCCCTGAGGCCGTC	0.647																																					p.P262L		Atlas-SNP	.											.	LRRC46	25	.	0			c.C785T						.						80	85	83					17																	45914305		2203	4300	6503	SO:0001583	missense	90506	exon8			CAGTCCCTGAGGC		CCDS11518.1	17q21.32	2005-08-09				ENSG00000141294			25047	protein-coding gene	gene with protein product						12477932	Standard	NM_033413		Approved	MGC16309	uc002ima.3	Q96FV0		ENST00000269025.4:c.785C>T	chr17.hg19:g.45914305C>T	ENSP00000269025:p.Pro262Leu	86.0	0.0		114.0	6.0	NM_033413	A8K9Q0	Missense_Mutation	SNP	ENST00000269025.4	hg19	CCDS11518.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.299764	0.40694	.	.	ENSG00000141294	ENST00000269025	T	0.74526	-0.85	4.98	2.97	0.34412	.	0.462400	0.18525	N	0.138655	T	0.68201	0.2975	M	0.68317	2.08	0.09310	N	1	B;B	0.30068	0.267;0.267	B;B	0.28139	0.086;0.086	T	0.63107	-0.6711	10	0.87932	D	0	-2.1674	6.3328	0.21279	0.1825:0.7229:0.0:0.0946	.	262;262	A8K9Q0;Q96FV0	.;LRC46_HUMAN	L	262	ENSP00000269025:P262L	ENSP00000269025:P262L	P	+	2	0	LRRC46	43269304	0.001000	0.12720	0.001000	0.08648	0.151000	0.21798	0.347000	0.20014	0.617000	0.30160	0.551000	0.68910	CCT	.	.		0.647	LRRC46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441377.1	NM_033413		T	45914305	C	T	45914305	3	4	49	1	0	0	0	0	1	0	0	0	9012	681	24	3	815	3	LRRC46	17	45914305	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	682237	45914305	35280905	250	6407										
EME1	146956	hgsc.bcm.edu	37	chr17	48452982	48452982	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	atcatgtgactggaaaaagcCctttccaaagatccctgaag	8	10	1	3	rs75511911		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:48452982C>A	ENST00000338165.4	+	2	495	c.413C>A	c.(412-414)cCc>cAc	p.P138H	EME1_ENST00000393271.2_Missense_Mutation_p.P138H|MRPL27_ENST00000442592.3_5'Flank|MRPL27_ENST00000225969.4_5'Flank|MRPL27_ENST00000507088.1_5'Flank|EME1_ENST00000511648.2_Missense_Mutation_p.P138H|MRPL27_ENST00000503633.1_5'Flank	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	138					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			TGGAAAAAGCCCTTTCCAAAG	0.483								Direct reversal of damage;Homologous recombination																													p.P138H		Atlas-SNP	.											.	EME1	39	.	0			c.C413A						.						77	81	80					17																	48452982		2203	4300	6503	SO:0001583	missense	146956	exon2			AAAAGCCCTTTCC	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"	610885	"essential meiotic endonuclease 1 homolog 1 (S. pombe)"			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.413C>A	chr17.hg19:g.48452982C>A	ENSP00000339897:p.Pro138His	129.0	0.0		172.0	8.0	NM_152463	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	hg19	CCDS11565.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754870	0.49362	.	.	ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511648	T;T;T	0.13778	2.56;2.56;2.56	4.57	4.57	0.56435	.	0.717920	0.12531	N	0.460753	T	0.20861	0.0502	L	0.32530	0.975	0.58432	D	0.999999	D;D	0.71674	0.998;0.997	P;P	0.61592	0.891;0.781	T	0.01232	-1.1411	10	0.51188	T	0.08	-33.761	7.0041	0.24826	0.0:0.845:0.0:0.155	.	138;138	Q96AY2-2;Q96AY2	.;EME1_HUMAN	H	138	ENSP00000339897:P138H;ENSP00000376952:P138H;ENSP00000421700:P138H	ENSP00000339897:P138H	P	+	2	0	EME1	45807981	0.000000	0.05858	0.621000	0.29145	0.790000	0.44656	0.319000	0.19522	2.357000	0.79964	0.650000	0.86243	CCC	.	.		0.483	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463		A	48452982	C	A	48452982	3	1	49	1	0	0	0	0	1	0	0	0	5090	623	22	3	415	3	EME1	17	48452982	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	2538677	48452982	32742228	251	6408										
MYCBPAP	84073	hgsc.bcm.edu	37	chr17	48603556	48603556	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gaaagcccagatgtggacagCaccaagagcccctgggagcc	13	13	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:48603556C>T	ENST00000323776.5	+	14	2388	c.2226C>T	c.(2224-2226)agC>agT	p.S742S	MYCBPAP_ENST00000436259.2_Silent_p.S705S	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			ATGTGGACAGCACCAAGAGCC	0.602																																					p.S742S		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.C2226T						.						90	94	92					17																	48603556		2203	4300	6503	SO:0001819	synonymous_variant	84073	exon14			GGACAGCACCAAG	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.2226C>T	chr17.hg19:g.48603556C>T		55.0	0.0		65.0	22.0	NM_032133		Silent	SNP	ENST00000323776.5	hg19	CCDS32680.2																																																																																			.	.		0.602	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133		T	48603556	C	T	48603556	2	4	49	1	0	0	0	0	0	0	0	1	10028	709	25	3		3	MYCBPAP	17	48603556	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	150574	48603556	32591654	252	6409										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62045610	62045610	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcaggtttcccatgaagagcTgcagtcctaccagcgcaaag	10	12	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:62045610T>C	ENST00000435607.1	-	6	885	c.809A>G	c.(808-810)cAg>cGg	p.Q270R	SCN4A_ENST00000578147.1_Missense_Mutation_p.Q270R	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	270			Q -> K (in PMC). {ECO:0000269|PubMed:16786525, ECO:0000269|PubMed:18166706}.		membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CATGAAGAGCTGCAGTCCTAC	0.567																																					p.Q270R		Atlas-SNP	.											.	SCN4A	205	.	0			c.A809G						.						120	125	123					17																	62045610		2173	4286	6459	SO:0001583	missense	6329	exon6			AAGAGCTGCAGTC	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.809A>G	chr17.hg19:g.62045610T>C	ENSP00000396320:p.Gln270Arg	143.0	0.0		186.0	8.0	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.887691	0.91814	.	.	ENSG00000007314	ENST00000435607	D	0.98978	-5.29	5.21	5.21	0.72293	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99527	0.9831	H	0.96805	3.885	0.53688	D	0.999979	D	0.89917	1.0	D	0.97110	1.0	D	0.98032	1.0377	10	0.87932	D	0	.	14.4261	0.67218	0.0:0.0:0.0:1.0	.	270	P35499	SCN4A_HUMAN	R	270	ENSP00000396320:Q270R	ENSP00000396320:Q270R	Q	-	2	0	SCN4A	59399342	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.868000	0.87116	2.194000	0.70268	0.533000	0.62120	CAG	.	.		0.567	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		C	62045610	T	C	62045610	3	2	49	1	0	0	0	0	1	0	0	0	13935	1580	55	2	4777	2	SCN4A	17	62045610	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	13442054	62045610	19149600	253	6410										
ARSG	22901	hgsc.bcm.edu	37	chr17	66352820	66352820	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccacacaggaaccttcaaagAgactgttacactgacgtggc	9	12	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:66352820A>G	ENST00000448504.2	+	6	1375	c.579A>G	c.(577-579)agA>agG	p.R193R	ARSG_ENST00000452479.2_Silent_p.R29R|ARSG_ENST00000582154.1_3'UTR	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	193					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			ACCTTCAAAGAGACTGTTACA	0.458																																					p.R193R		Atlas-SNP	.											.	ARSG	55	.	0			c.A579G						.						94	76	82					17																	66352820		2203	4300	6503	SO:0001819	synonymous_variant	22901	exon6			TCAAAGAGACTGT	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"Arylsulfatase family"	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.579A>G	chr17.hg19:g.66352820A>G		81.0	0.0		111.0	5.0	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	hg19	CCDS11676.1																																																																																			.	.		0.458	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960		G	66352820	A	G	66352820	2	3	49	1	0	0	0	0	0	0	0	1	992	301	11	2		2	ARSG	17	66352820	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	4307210	66352820	14842390	254	6411										
FAM20A	54757	hgsc.bcm.edu	37	chr17	66538299	66538299	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cacttggcgaagaagcacacGttgctcgctggaggatgggg	16	9	0	1	rs367996001		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:66538299G>A	ENST00000592554.1	-	7	1658	c.936C>T	c.(934-936)aaC>aaT	p.N312N	FAM20A_ENST00000226094.5_5'UTR|AC079210.1_ENST00000600820.1_5'Flank|PRKAR1A_ENST00000588188.2_Intron	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	312					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					AGAAGCACACGTTGCTCGCTG	0.577																																					p.N312N		Atlas-SNP	.											FAM20A,NS,carcinoma,0,1	FAM20A	35	.	0			c.C936T						.	G		1,4405	2.1+/-5.4	0,1,2202	89	72	77		936	5.1	1	17		77	0,8600		0,0,4300	no	coding-synonymous	FAM20A	NM_017565.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		312/542	66538299	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	54757	exon7			GCACACGTTGCTC	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.936C>T	chr17.hg19:g.66538299G>A		37.0	0.0		48.0	2.0	NM_017565	B2RN47|B2RN49|Q9UF95	Silent	SNP	ENST00000592554.1	hg19	CCDS11679.1																																																																																			.	.		0.577	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565		A	66538299	G	A	66538299	2	1	49	1	0	0	0	0	0	0	0	1	5542	1136	40	1		1	FAM20A	17	66538299	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	185479	66538299	14656911	255	6412										
ABCA10	10349	hgsc.bcm.edu	37	chr17	67190119	67190119	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agagagttgagtattataaaTagtggctgatcctataaata	9	3	0	3	rs140723420|rs111599831|rs79987301	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:67190119T>A	ENST00000269081.4	-	14	2266	c.1357A>T	c.(1357-1359)Att>Ttt	p.I453F	ABCA10_ENST00000416101.2_Intron	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	453	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					GTATTATAAATAGTGGCTGAT	0.289																																					p.I453F		Atlas-SNP	.											.,1	ABCA10	209	.	0			c.A1357T						.						37	58	52					17																	67190119		1986	4296	6282	SO:0001583	missense	10349	exon14			TATAAATAGTGGC	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.1357A>T	chr17.hg19:g.67190119T>A	ENSP00000269081:p.Ile453Phe	0.0	0.0		18.0	9.0	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	hg19	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.484425	0.84854	.	.	ENSG00000154263	ENST00000269081	D	0.94417	-3.42	3.71	3.71	0.42584	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.32655	U	0.005806	D	0.92619	0.7655	L	0.52011	1.625	0.80722	D	1	P;P	0.46859	0.885;0.884	P;P	0.48141	0.464;0.568	D	0.91756	0.5416	10	0.66056	D	0.02	.	7.5133	0.27585	0.0:0.099:0.0:0.901	.	453;453	E5RFN6;Q8WWZ4	.;ABCAA_HUMAN	F	453	ENSP00000269081:I453F	ENSP00000269081:I453F	I	-	1	0	ABCA10	64701714	0.987000	0.35691	0.043000	0.18650	0.903000	0.53119	2.098000	0.41757	1.531000	0.49152	0.455000	0.32223	ATT	.	.		0.289	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		A	67190119	T	A	67190119	3	1	49	1	0	0	0	0	1	0	0	0	29	1406	49	4	3382	4	ABCA10	17	67190119	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	651820	67190119	14005091	256	6413										
KIF19	124602	hgsc.bcm.edu	37	chr17	72348385	72348385	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cctggccgtcccgcagcgccTggaagagctctacgaagtgt	13	14	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:72348385T>C	ENST00000389916.4	+	14	2024	c.1886T>C	c.(1885-1887)cTg>cCg	p.L629P	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	629					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						CCGCAGCGCCTGGAAGAGCTC	0.697																																					p.L629P		Atlas-SNP	.											.	KIF19	102	.	0			c.T1886C						.						28	34	32					17																	72348385		1940	4131	6071	SO:0001583	missense	124602	exon14			AGCGCCTGGAAGA	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.1886T>C	chr17.hg19:g.72348385T>C	ENSP00000374566:p.Leu629Pro	76.0	0.0		51.0	4.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	T	20.4	3.990669	0.74589	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.78364	-1.17;-1.13	5.23	5.23	0.72850	.	.	.	.	.	D	0.86381	0.5919	M	0.70595	2.14	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.74023	0.911;0.982	D	0.87031	0.2135	9	0.51188	T	0.08	.	14.1488	0.65367	0.0:0.0:0.0:1.0	.	629;587	Q2TAC6;F8VW50	KIF19_HUMAN;.	P	587;629	ENSP00000449134:L587P;ENSP00000374566:L629P	ENSP00000374566:L629P	L	+	2	0	KIF19	69859980	1.000000	0.71417	0.621000	0.29145	0.509000	0.34042	4.289000	0.59013	1.988000	0.58038	0.374000	0.22700	CTG	.	.		0.697	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		C	72348385	T	C	72348385	3	2	49	1	0	0	0	0	1	0	0	0	8291	1580	55	2	1940	2	KIF19	17	72348385	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	5158266	72348385	8846825	257	6414										
FBF1	85302	hgsc.bcm.edu	37	chr17	73915902	73915902	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	acagctcttcgttctctctcCggagccgctcctcccgttgc	8	18	3	0	rs374900201		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:73915902C>T	ENST00000586717.1	-	19	2216	c.1943G>A	c.(1942-1944)cGg>cAg	p.R648Q	FBF1_ENST00000319129.5_Missense_Mutation_p.R647Q|FBF1_ENST00000389570.4_Missense_Mutation_p.R648Q			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	648					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						GTTCTCTCTCCGGAGCCGCTC	0.632																																					p.R647Q		Atlas-SNP	.											.	FBF1	48	.	0			c.G1940A						.	C	GLN/ARG	0,4058		0,0,2029	89	90	90		1940	1.6	1	17		90	1,8359		0,1,4179	no	missense	FBF1	NM_001080542.1	43	0,1,6208	TT,TC,CC		0.012,0.0,0.0081	benign	647/1134	73915902	1,12417	2029	4180	6209	SO:0001583	missense	85302	exon19			TCTCTCCGGAGCC	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.1943G>A	chr17.hg19:g.73915902C>T	ENSP00000465132:p.Arg648Gln	74.0	0.0		86.0	4.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.74	2.624379	0.46840	0.0	1.2E-4	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.18810	2.2;2.19	5.15	1.61	0.23674	.	.	.	.	.	T	0.11024	0.0269	N	0.25789	0.76	0.41875	D	0.990293	P;P;B	0.45283	0.855;0.541;0.341	B;B;B	0.34489	0.184;0.064;0.048	T	0.20405	-1.0276	9	0.21014	T	0.42	-19.3766	10.6484	0.45634	0.0:0.6896:0.0:0.3104	.	662;648;647	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	Q	648;648;647;661	ENSP00000374221:R648Q;ENSP00000324292:R647Q	ENSP00000324292:R647Q	R	-	2	0	FBF1	71427497	0.113000	0.22115	0.994000	0.49952	0.750000	0.42670	0.833000	0.27504	0.589000	0.29677	-0.126000	0.14955	CGG	.	.		0.632	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		T	73915902	C	T	73915902	3	4	49	1	0	0	0	0	1	0	0	0	5703	652	23	1	1505	1	FBF1	17	73915902	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1567517	73915902	7279308	258	6415										
ENPP7	339221	hgsc.bcm.edu	37	chr17	77704969	77704969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggctcccggggccggagcacCggtacaaagtcagggctccc	15	15	1	0	rs193920826		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:77704969C>T	ENST00000328313.5	+	1	289	c.68C>T	c.(67-69)cCg>cTg	p.P23L		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GCCGGAGCACCGGTACAAAGT	0.652																																					p.P23L		Atlas-SNP	.											ENPP7,NS,adenoma,0,1	ENPP7	63	.	0			c.C68T						.						28	27	27					17																	77704969		2202	4299	6501	SO:0001583	missense	339221	exon1			GAGCACCGGTACA	AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"alkaline sphingomyelinase"					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.68C>T	chr17.hg19:g.77704969C>T	ENSP00000332656:p.Pro23Leu	45.0	0.0		42.0	3.0	NM_178543		Missense_Mutation	SNP	ENST00000328313.5	hg19	CCDS11763.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.742901	0.49151	.	.	ENSG00000182156	ENST00000328313	T	0.74737	-0.87	4.59	4.59	0.56863	Alkaline-phosphatase-like, core domain (1);	1.015840	0.07879	N	0.969273	T	0.55386	0.1917	N	0.08118	0	0.58432	D	0.999996	B	0.29955	0.263	B	0.17979	0.02	T	0.50725	-0.8794	10	0.54805	T	0.06	-28.7668	10.2818	0.43543	0.0:0.9057:0.0:0.0943	.	23	Q6UWV6	ENPP7_HUMAN	L	23	ENSP00000332656:P23L	ENSP00000332656:P23L	P	+	2	0	ENPP7	75319564	1.000000	0.71417	0.020000	0.16555	0.003000	0.03518	6.679000	0.74513	2.372000	0.80975	0.561000	0.74099	CCG	.	.		0.652	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543		T	77704969	C	T	77704969	3	4	49	1	0	0	0	0	1	0	0	0	5137	652	23	1	70	1	ENPP7	17	77704969	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	3789067	77704969	3490241	259	6416										
B3GNTL1	146712	hgsc.bcm.edu	37	chr17	80972391	80972391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cccgctggggcatcatgacgTcatcctgcagtaaagaacac	10	13	2	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:80972391T>C	ENST00000320865.3	-	5	360	c.347A>G	c.(346-348)gAc>gGc	p.D116G	B3GNTL1_ENST00000576599.1_5'UTR|B3GNTL1_ENST00000571954.1_5'UTR	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	116							transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			CATCATGACGTCATCCTGCAG	0.512																																					p.D116G		Atlas-SNP	.											.	B3GNTL1	40	.	0			c.A347G						.						128	99	109					17																	80972391		2203	4300	6503	SO:0001583	missense	146712	exon5			ATGACGTCATCCT	AY634364	CCDS32778.1	17q25.3	2013-02-22	2004-01-13	2004-01-14	ENSG00000175711	ENSG00000175711		"Glycosyltransferase family 2 domain containing"	21727	protein-coding gene	gene with protein product		615337					Standard	NM_001009905		Approved	B3GNT8	uc002kgg.1	Q67FW5	OTTHUMG00000177788	ENST00000320865.3:c.347A>G	chr17.hg19:g.80972391T>C	ENSP00000319979:p.Asp116Gly	73.0	0.0		118.0	5.0	NM_001009905	Q6GV30|Q8WUT3	Missense_Mutation	SNP	ENST00000320865.3	hg19	CCDS32778.1	.	.	.	.	.	.	.	.	.	.	t	13.66	2.304449	0.40795	.	.	ENSG00000175711	ENST00000320865	T	0.65549	-0.16	4.15	4.15	0.48705	Glycosyl transferase, family 2 (1);	0.000000	0.85682	U	0.000000	D	0.83986	0.5373	H	0.96691	3.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87366	0.2347	9	.	.	.	-27.4857	9.8082	0.40805	0.0:0.0:0.0:1.0	.	116	Q67FW5	B3GNL_HUMAN	G	116	ENSP00000319979:D116G	.	D	-	2	0	B3GNTL1	78565680	1.000000	0.71417	0.995000	0.50966	0.039000	0.13416	3.229000	0.51278	1.899000	0.54978	0.362000	0.22060	GAC	.	.		0.512	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905		C	80972391	T	C	80972391	3	2	49	1	0	0	0	0	1	0	0	0	1265	1667	58	2	770	2	B3GNTL1	17	80972391	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	3267422	80972391	222819	260	6417										
PTPRM	5797	hgsc.bcm.edu	37	chr18	8384641	8384641	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgtctctgctgacctggaagAggacatcatcagcaggatat	11	9	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr18:8384641A>G	ENST00000332175.8	+	28	4999	c.3962A>G	c.(3961-3963)gAg>gGg	p.E1321G	PTPRM_ENST00000580170.1_Missense_Mutation_p.E1334G|PTPRM_ENST00000400053.4_Missense_Mutation_p.E1259G|PTPRM_ENST00000444013.1_Missense_Mutation_p.E1108G|PTPRM_ENST00000400060.4_Missense_Mutation_p.E1335G	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1321	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GACCTGGAAGAGGACATCATC	0.463																																					p.E1334G		Atlas-SNP	.											.	PTPRM	185	.	0			c.A4001G						.						146	127	133					18																	8384641		2203	4300	6503	SO:0001583	missense	5797	exon30			TGGAAGAGGACAT	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3962A>G	chr18.hg19:g.8384641A>G	ENSP00000331418:p.Glu1321Gly	94.0	0.0		128.0	6.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	A	16.59	3.164727	0.57476	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82	5.41	5.41	0.78517	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.87943	0.6305	L	0.33293	1	0.58432	D	0.999999	P;B;D	0.69078	0.947;0.006;0.997	P;B;D	0.79108	0.88;0.004;0.992	D	0.87183	0.2229	10	0.35671	T	0.21	.	15.4745	0.75468	1.0:0.0:0.0:0.0	.	1108;1334;1321	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	G	1321;1335;1259;1108	ENSP00000331418:E1321G;ENSP00000382933:E1335G;ENSP00000382927:E1259G;ENSP00000387608:E1108G	ENSP00000331418:E1321G	E	+	2	0	PTPRM	8374641	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	6.281000	0.72632	2.049000	0.60858	0.372000	0.22366	GAG	.	.		0.463	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			G	8384641	A	G	8384641	3	3	49	1	0	0	0	0	1	0	0	0	12821	304	11	2	4119	2	PTPRM	18	8384641	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10		8384641	69692607	261	6418										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8813094	8813094	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tggcagacagtcacagcctgGtcatggacctgcgctggcag	14	12	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr18:8813094G>C	ENST00000306329.11	+	10	3679	c.3679G>C	c.(3679-3681)Gtc>Ctc	p.V1227L	SOGA2_ENST00000359865.3_Missense_Mutation_p.V908L|SOGA2_ENST00000518815.1_Missense_Mutation_p.V261L|SOGA2_ENST00000306285.7_Missense_Mutation_p.V261L|SOGA2_ENST00000400050.3_Missense_Mutation_p.V867L|SOGA2_ENST00000517570.1_Missense_Mutation_p.V867L																							TCACAGCCTGGTCATGGACCT	0.587																																					p.V908L		Atlas-SNP	.											.	.	.	.	0			c.G2722C						.						53	50	51					18																	8813094		2203	4300	6503	SO:0001583	missense	23255	exon12			AGCCTGGTCATGG																												ENST00000306329.11:c.3679G>C	chr18.hg19:g.8813094G>C	ENSP00000305027:p.Val1227Leu	135.0	0.0		156.0	14.0	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.56|18.56	3.650848|3.650848	0.67472|0.67472	.|.	.|.	ENSG00000168502|ENSG00000168502	ENST00000519823|ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050;ENST00000306285	.|T;T;T;T	.|0.36340	.|2.36;2.35;2.36;1.26	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	.|0.000000	.|0.43579	.|D	.|0.000549	T|T	0.38374|0.38374	0.1038|0.1038	M|M	0.77103|0.77103	2.36|2.36	0.31616|0.31616	N|N	0.6509|0.6509	.|B;B	.|0.31077	.|0.307;0.259	.|B;B	.|0.22753	.|0.031;0.041	T|T	0.53613|0.53613	-0.8414|-0.8414	5|10	.|0.54805	.|T	.|0.06	-25.4183|-25.4183	12.7885|12.7885	0.57520|0.57520	0.0787:0.0:0.9213:0.0|0.0787:0.0:0.9213:0.0	.|.	.|1218;908	.|Q9Y4B5;Q9Y4B5-3	.|CC165_HUMAN;.	A|L	41|929;867;908;867;261	.|ENSP00000429556:V867L;ENSP00000352927:V908L;ENSP00000382924:V867L;ENSP00000303670:V261L	.|ENSP00000303670:V261L	G|V	+|+	2|1	0|0	CCDC165|CCDC165	8803094|8803094	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	4.757000|4.757000	0.62213|0.62213	2.586000|2.586000	0.87340|0.87340	0.462000|0.462000	0.41574|0.41574	GGT|GTC	.	.		0.587	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			C	8813094	G	C	8813094	3	2	49	1	0	0	0	0	1	0	0	0	8203	1261	44	4	2760	4	KIAA0802	18	8813094	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	428453	8813094	69264154	262	6419										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34298575	34298575	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gccatgtaaaaacaaccgacGctgcagagaattcctgtggt	10	10	0	1	rs369061380		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr18:34298575G>A	ENST00000359247.4	+	15	2738	c.2738G>A	c.(2737-2739)cGc>cAc	p.R913H	FHOD3_ENST00000592128.1_De_novo_Start_OutOfFrame|FHOD3_ENST00000590592.1_Missense_Mutation_p.R1105H|FHOD3_ENST00000257209.4_Missense_Mutation_p.R930H|FHOD3_ENST00000591635.1_Missense_Mutation_p.R126H|FHOD3_ENST00000445677.1_Missense_Mutation_p.R892H	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	913	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				AACAACCGACGCTGCAGAGAA	0.473																																					p.R930H		Atlas-SNP	.											FHOD3,colon,carcinoma,0,1	FHOD3	210	.	0			c.G2789A						.	G	HIS/ARG	0,4406		0,0,2203	130	133	132		2789	4.5	1	18		132	1,8599	1.2+/-3.3	0,1,4299	no	missense	FHOD3	NM_025135.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	930/1440	34298575	1,13005	2203	4300	6503	SO:0001583	missense	80206	exon16			ACCGACGCTGCAG	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.2738G>A	chr18.hg19:g.34298575G>A	ENSP00000352186:p.Arg913His	68.0	0.0		67.0	3.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	hg19		.	.	.	.	.	.	.	.	.	.	G	9.057	0.993585	0.19043	0.0	1.16E-4	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.32988	1.44;1.43;1.44	4.46	4.46	0.54185	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.188903	0.48286	D	0.000198	T	0.44393	0.1291	L	0.56769	1.78	0.46241	D	0.99894	D;D;B	0.60575	0.985;0.988;0.063	P;P;B	0.54499	0.71;0.754;0.013	T	0.44467	-0.9326	10	0.52906	T	0.07	.	15.6858	0.77409	0.0:0.0:1.0:0.0	.	892;913;930	Q2V2M9-2;Q2V2M9;Q2V2M9-3	.;FHOD3_HUMAN;.	H	930;913;892	ENSP00000257209:R930H;ENSP00000352186:R913H;ENSP00000411430:R892H	ENSP00000257209:R930H	R	+	2	0	FHOD3	32552573	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	2.427000	0.44740	2.034000	0.60081	0.555000	0.69702	CGC	.	.		0.473	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		A	34298575	G	A	34298575	3	1	49	1	0	0	0	0	1	0	0	0	5891	1087	38	1	2851	1	FHOD3	18	34298575	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	25485481	34298575	43778673	263	6420										
SMAD2	4087	hgsc.bcm.edu	37	chr18	45375012	45375012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgatttaattcataatatgcTatcgaacaccaaaatgcagg	6	7	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr18:45375012T>C	ENST00000402690.2	-	8	1225	c.831A>G	c.(829-831)atA>atG	p.I277M	SMAD2_ENST00000586040.1_Missense_Mutation_p.I247M|SMAD2_ENST00000262160.6_Missense_Mutation_p.I277M|SMAD2_ENST00000356825.4_Missense_Mutation_p.I247M|SMAD2_ENST00000591214.1_Missense_Mutation_p.I247M	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	277	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						CATAATATGCTATCGAACACC	0.363																																					p.I277M		Atlas-SNP	.											.	SMAD2	85	.	0			c.A831G						.						86	80	82					18																	45375012		2203	4300	6503	SO:0001583	missense	4087	exon8			ATATGCTATCGAA	U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"SMADs"	6768	protein-coding gene	gene with protein product		601366	"MAD, mothers against decapentaplegic homolog 2 (Drosophila)", "SMAD, mothers against DPP homolog 2 (Drosophila)"	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.831A>G	chr18.hg19:g.45375012T>C	ENSP00000384449:p.Ile277Met	88.0	0.0		73.0	4.0	NM_005901		Missense_Mutation	SNP	ENST00000402690.2	hg19	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	T	19.78	3.891762	0.72524	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	D;D;D	0.98075	-4.7;-4.7;-4.7	5.81	4.64	0.57946	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98943	0.9641	M	0.93507	3.425	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.87578	0.998;0.975;0.994	D	0.99139	1.0855	10	0.87932	D	0	.	12.8817	0.58020	0.0:0.0:0.1407:0.8593	.	247;247;277	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	M	277;247;277	ENSP00000262160:I277M;ENSP00000349282:I247M;ENSP00000384449:I277M	ENSP00000262160:I277M	I	-	3	3	SMAD2	43629010	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.068000	0.64364	1.007000	0.39238	0.482000	0.46254	ATA	.	.		0.363	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901		C	45375012	T	C	45375012	3	2	49	1	0	0	0	0	1	0	0	0	14773	1512	53	2	588	2	SMAD2	18	45375012	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	11076437	45375012	32702236	264	6421										
LPPR3	79948	hgsc.bcm.edu	37	chr19	814544	814544	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tacgcccgcggcgatggcaaAggcgaagaccaggatgggct	16	11	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:814544A>G	ENST00000520876.3	-	7	799	c.721T>C	c.(721-723)Ttt>Ctt	p.F241L	LPPR3_ENST00000359894.2_Missense_Mutation_p.F269L|MIR3187_ENST00000583431.1_RNA	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		241						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										GCGATGGCAAAGGCGAAGACC	0.647																																					p.F269L		Atlas-SNP	.											.	.	.	.	0			c.T805C						.						60	61	61					19																	814544		2195	4300	6495	SO:0001583	missense	0	exon6			TGGCAAAGGCGAA																												ENST00000520876.3:c.721T>C	chr19.hg19:g.814544A>G	ENSP00000430297:p.Phe241Leu	32.0	0.0		32.0	4.0	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	hg19	CCDS58636.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.1|24.1	4.491003|4.491003	0.84962|0.84962	.|.	.|.	ENSG00000129951|ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876|ENST00000517665;ENST00000521445	T;T|.	0.72942|.	-0.7;-0.7|.	4.66|4.66	4.66|4.66	0.58398|0.58398	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.41604|0.41604	0.1166|0.1166	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	D|D	0.999991|0.999991	P;P;D|.	0.71674|.	0.92;0.884;0.998|.	P;P;D|.	0.80764|.	0.662;0.772;0.994|.	T|T	0.29882|0.29882	-0.9997|-0.9997	10|5	0.21540|.	T|.	0.41|.	-16.1034|-16.1034	13.2541|13.2541	0.60068|0.60068	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	242;241;269|.	Q6T4P5-2;Q6T4P5;Q6T4P5-3|.	.;LPPR3_HUMAN;.|.	L|P	242;269;241|29;190	ENSP00000352962:F269L;ENSP00000430297:F241L|.	ENSP00000300947:F242L|.	F|L	-|-	1|2	0|0	AC006273.1|AC006273.1	765544|765544	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.732000|0.732000	0.41865|0.41865	8.658000|8.658000	0.91110|0.91110	1.734000|1.734000	0.51633|0.51633	0.454000|0.454000	0.30748|0.30748	TTT|CTT	.	.		0.647	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3			G	814544	A	G	814544	3	3	49	1	0	0	0	0	1	0	0	0	8935	72	3	2	1443	2	LPPR3	19	814544	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10		814544	58314439	265	6422										
STXBP2	6813	hgsc.bcm.edu	37	chr19	7707395	7707395	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgacttgtgggtggagcttcGccacatgcatatcgcagatg	13	9	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:7707395G>A	ENST00000221283.5	+	10	906	c.875G>A	c.(874-876)cGc>cAc	p.R292H	STXBP2_ENST00000414284.2_Missense_Mutation_p.R289H|STXBP2_ENST00000441779.2_Missense_Mutation_p.R303H	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	292			R -> H (in FHL5; leads to a complete loss of the ability to interact with STX11). {ECO:0000269|PubMed:19804848}.		leukocyte mediated cytotoxicity (GO:0001909)|neutrophil degranulation (GO:0043312)|protein transport (GO:0015031)|regulation of mast cell degranulation (GO:0043304)|vesicle docking involved in exocytosis (GO:0006904)	azurophil granule (GO:0042582)|cytolytic granule (GO:0044194)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin-3 binding (GO:0030348)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	23						GTGGAGCTTCGCCACATGCAT	0.662																																					p.R303H		Atlas-SNP	.											STXBP2,colon,carcinoma,0,1	STXBP2	63	.	0			c.G908A						.						125	122	123					19																	7707395		2203	4300	6503	SO:0001583	missense	6813	exon10			AGCTTCGCCACAT	U63533	CCDS12181.1, CCDS45948.1, CCDS62522.1	19p13.3-p13.2	2014-09-17				ENSG00000076944			11445	protein-coding gene	gene with protein product		601717				8921365	Standard	NM_001127396		Approved	UNC18B, Hunc18b	uc010xjr.3	Q15833		ENST00000221283.5:c.875G>A	chr19.hg19:g.7707395G>A	ENSP00000221283:p.Arg292His	70.0	0.0		91.0	4.0	NM_001272034	B4E175|E7EQD5|Q9BU65	Missense_Mutation	SNP	ENST00000221283.5	hg19	CCDS12181.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.609163	0.66558	.	.	ENSG00000076944	ENST00000221283;ENST00000414284;ENST00000441779;ENST00000543902	T;T;T	0.81078	-1.45;-1.45;-1.45	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	D	0.91690	0.7373	M	0.92833	3.35	0.53688	D	0.999976	D;D;D;D	0.89917	1.0;0.997;1.0;1.0	D;D;D;D	0.91635	0.999;0.946;0.998;0.999	D	0.93738	0.7047	10	0.87932	D	0	-5.1595	15.1021	0.72288	0.0:0.0:1.0:0.0	.	303;258;289;292	E7EQD5;B4DY46;Q15833-2;Q15833	.;.;.;STXB2_HUMAN	H	292;289;303;292	ENSP00000221283:R292H;ENSP00000409471:R289H;ENSP00000413606:R303H	ENSP00000221283:R292H	R	+	2	0	STXBP2	7613395	1.000000	0.71417	0.641000	0.29422	0.022000	0.10575	9.860000	0.99555	2.147000	0.66899	0.591000	0.81541	CGC	.	.		0.662	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949		A	7707395	G	A	7707395	3	1	49	1	0	0	0	0	1	0	0	0	15368	1087	38	1	913	1	STXBP2	19	7707395	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	6892851	7707395	51421588	266	6423										
ZNF317	57693	hgsc.bcm.edu	37	chr19	9271064	9271064	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gagaatccacaccggggagaAgccttacgagtgcagcgact	13	11	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:9271064A>G	ENST00000247956.6	+	7	1048	c.743A>G	c.(742-744)aAg>aGg	p.K248R	ZNF317_ENST00000360385.3_Missense_Mutation_p.K216R	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						ACCGGGGAGAAGCCTTACGAG	0.547																																					p.K248R		Atlas-SNP	.											.	ZNF317	61	.	0			c.A743G						.						105	98	101					19																	9271064		2203	4300	6503	SO:0001583	missense	57693	exon7			GGGAGAAGCCTTA	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"Zinc fingers, C2H2-type", "-"	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.743A>G	chr19.hg19:g.9271064A>G	ENSP00000247956:p.Lys248Arg	56.0	0.0		93.0	4.0	NM_020933	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Missense_Mutation	SNP	ENST00000247956.6	hg19	CCDS12210.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.327789	0.60743	.	.	ENSG00000130803	ENST00000247956;ENST00000360385	T;T	0.24908	1.83;1.83	3.61	3.61	0.41365	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44483	D	0.000445	T	0.33294	0.0858	N	0.21142	0.635	0.41650	D	0.98912	D;D	0.76494	0.999;0.999	D;D	0.81914	0.991;0.995	T	0.12142	-1.0559	10	0.56958	D	0.05	-26.8205	10.7948	0.46453	1.0:0.0:0.0:0.0	.	216;248	Q96PQ6-2;Q96PQ6	.;ZN317_HUMAN	R	248;216	ENSP00000247956:K248R;ENSP00000353554:K216R	ENSP00000247956:K248R	K	+	2	0	ZNF317	9132064	0.828000	0.29307	0.380000	0.26093	0.330000	0.28571	1.604000	0.36804	1.882000	0.54519	0.482000	0.46254	AAG	.	.		0.547	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933		G	9271064	A	G	9271064	3	3	49	1	0	0	0	0	1	0	0	0	17850	72	3	2	765	2	ZNF317	19	9271064	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	1563669	9271064	49857919	267	6424										
CALR	811	hgsc.bcm.edu	37	chr19	13054664	13054664	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaagatgaggatgaggaggaTgaggaggacaaggaggaaga	19	1	0	5			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:13054664T>C	ENST00000316448.5	+	9	1264	c.1191T>C	c.(1189-1191)gaT>gaC	p.D397D	CTC-425F1.4_ENST00000589120.1_RNA|RAD23A_ENST00000541222.1_5'Flank|RAD23A_ENST00000316856.3_5'Flank|RAD23A_ENST00000586534.1_5'Flank|RAD23A_ENST00000592268.1_5'Flank	NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	397	Asp/Glu/Lys-rich.|C-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	atgaggaggatgaggaggaca	0.572																																					p.D397D		Atlas-SNP	.											.	CALR	31	.	0			c.T1191C						.						275	214	235					19																	13054664		2203	4296	6499	SO:0001819	synonymous_variant	811	exon9			GGAGGATGAGGAG	M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"Sicca syndrome antigen A (autoantigen Ro; calreticulin)", "autoantigen Ro"	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.1191T>C	chr19.hg19:g.13054664T>C		127.0	0.0		136.0	9.0	NM_004343	Q6IAT4|Q9UDG2	Silent	SNP	ENST00000316448.5	hg19	CCDS12288.1																																																																																			.	.		0.572	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343		C	13054664	T	C	13054664	2	2	49	1	0	0	0	0	0	0	0	1	2594	1461	51	2		2	CALR	19	13054664	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	3783600	13054664	46074319	268	6425										
PIK3R2	5296	hgsc.bcm.edu	37	chr19	18266738	18266738	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcgctctgtacccgttccgcCgggagcggccggaggacctg	16	15	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:18266738C>T	ENST00000593731.1	+	2	609	c.49C>T	c.(49-51)Cgg>Tgg	p.R17W	PIK3R2_ENST00000222254.8_Missense_Mutation_p.R17W			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	17	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	CCCGTTCCGCCGGGAGCGGCC	0.731																																					p.R17W		Atlas-SNP	.											.	PIK3R2	48	.	0			c.C49T						.						6	5	6					19																	18266738		1931	3824	5755	SO:0001583	missense	5296	exon2			TTCCGCCGGGAGC		CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"SH2 domain containing"	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.49C>T	chr19.hg19:g.18266738C>T	ENSP00000471914:p.Arg17Trp	17.0	0.0		16.0	7.0	NM_005027	Q5EAT5|Q9UPH9	Missense_Mutation	SNP	ENST00000593731.1	hg19	CCDS12371.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.489309	0.84962	.	.	ENSG00000105647	ENST00000222254	T	0.08008	3.14	4.34	3.18	0.36537	Src homology-3 domain (3);	0.064269	0.64402	D	0.000009	T	0.11665	0.0284	L	0.38175	1.15	0.30854	N	0.734226	D	0.69078	0.997	P	0.53490	0.727	T	0.01413	-1.1361	10	0.87932	D	0	-27.3178	8.7743	0.34751	0.3481:0.6519:0.0:0.0	.	17	O00459	P85B_HUMAN	W	17	ENSP00000222254:R17W	ENSP00000222254:R17W	R	+	1	2	PIK3R2	18127738	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.487000	0.66863	2.140000	0.66376	0.462000	0.41574	CGG	.	.		0.731	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027		T	18266738	C	T	18266738	3	4	49	1	0	0	0	0	1	0	0	0	11928	643	23	1	51	1	PIK3R2	19	18266738	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	5212074	18266738	40862245	269	6426										
ZNF714	148206	hgsc.bcm.edu	37	chr19	21299777	21299777	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aggtgtacaaaaaaggttatGaactaaaccagtgtttgaca	9	5	0	2	rs111443257		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:21299777G>A	ENST00000596143.1	+	5	632	c.307G>A	c.(307-309)Gaa>Aaa	p.E103K	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AAAAGGTTATGAACTAAACCA	0.328																																					p.E103K		Atlas-SNP	.											.	ZNF714	121	.	0			c.G307A						.						39	38	38					19																	21299777		2190	4291	6481	SO:0001583	missense	148206	exon5			GGTTATGAACTAA	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.307G>A	chr19.hg19:g.21299777G>A	ENSP00000472368:p.Glu103Lys	205.0	0.0		304.0	18.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	0.388	-0.924824	0.02377	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.394	0.394	0.16299	.	.	.	.	.	T	0.22322	0.0538	L	0.27975	0.815	0.09310	N	1	B;P	0.37781	0.004;0.608	B;B	0.35413	0.004;0.202	T	0.14062	-1.0486	7	0.56958	D	0.05	.	.	.	.	.	104;103	Q96N38-2;A6NEM4	.;.	K	103	.	ENSP00000291770:E103K	E	+	1	0	ZNF714	21091617	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	-0.857000	0.04286	0.452000	0.26830	0.456000	0.33151	GAA	.	.		0.328	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		A	21299777	G	A	21299777	3	1	49	1	0	0	0	0	1	0	0	0	18133	1291	45	3	317	3	ZNF714	19	21299777	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	3033039	21299777	37829206	270	6427										
ZNF429	353088	hgsc.bcm.edu	37	chr19	21720474	21720474	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agagaaaccttacaaatgtgAagaatgtggcaaagctttta	9	5	0	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:21720474A>T	ENST00000358491.4	+	4	1827	c.1619A>T	c.(1618-1620)gAa>gTa	p.E540V	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	540					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						TACAAATGTGAAGAATGTGGC	0.363																																					p.E540V		Atlas-SNP	.											.	ZNF429	338	.	0			c.A1619T						.						41	46	44					19																	21720474		2134	4269	6403	SO:0001583	missense	353088	exon4			AATGTGAAGAATG	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1619A>T	chr19.hg19:g.21720474A>T	ENSP00000351280:p.Glu540Val	32.0	0.0		42.0	10.0	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	1.769	-0.484820	0.04352	.	.	ENSG00000197013	ENST00000358491	T	0.07800	3.16	0.876	0.876	0.19138	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17619	0.0423	M	0.63169	1.94	0.09310	N	1	D	0.67145	0.996	D	0.63957	0.92	T	0.11251	-1.0595	9	0.48119	T	0.1	.	3.6737	0.08284	0.7461:0.0:0.2539:0.0	.	540	Q86V71	ZN429_HUMAN	V	540	ENSP00000351280:E540V	ENSP00000351280:E540V	E	+	2	0	ZNF429	21512314	0.000000	0.05858	0.285000	0.24819	0.285000	0.27093	-0.758000	0.04766	0.251000	0.21505	0.248000	0.18094	GAA	.	.		0.363	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		T	21720474	A	T	21720474	3	4	49	1	0	0	0	0	1	0	0	0	17917	246	9	4	1633	4	ZNF429	19	21720474	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	420697	21720474	37408509	271	6428										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30934614	30934614	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agctcagccatgccttccccGagctccatccccggcccaac	7	21	1	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:30934614G>A	ENST00000355537.3	+	2	292	c.145G>A	c.(145-147)Gag>Aag	p.E49K		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	49					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.E49K(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					TGCCTTCCCCGAGCTCCATCC	0.667																																					p.E49K		Atlas-SNP	.											ZNF536,rectum,carcinoma,0,2	ZNF536	424	.	1	Substitution - Missense(1)	large_intestine(1)	c.G145A						.						67	68	68					19																	30934614		2203	4300	6503	SO:0001583	missense	9745	exon2			TTCCCCGAGCTCC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.145G>A	chr19.hg19:g.30934614G>A	ENSP00000347730:p.Glu49Lys	58.0	0.0		47.0	2.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629857	0.46944	.	.	ENSG00000198597	ENST00000355537	T	0.09445	2.98	5.37	4.32	0.51571	.	0.160306	0.56097	D	0.000036	T	0.15652	0.0377	L	0.32530	0.975	0.50313	D	0.999861	P;D	0.69078	0.952;0.997	B;P	0.53954	0.278;0.738	T	0.08146	-1.0736	10	0.18710	T	0.47	-33.2908	16.3674	0.83338	0.0:0.1321:0.8679:0.0	.	49;49	A7E228;O15090	.;ZN536_HUMAN	K	49	ENSP00000347730:E49K	ENSP00000347730:E49K	E	+	1	0	ZNF536	35626454	1.000000	0.71417	0.966000	0.40874	0.941000	0.58515	7.788000	0.85771	1.382000	0.46385	0.462000	0.41574	GAG	.	.		0.667	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		A	30934614	G	A	30934614	3	1	49	1	0	0	0	0	1	0	0	0	17989	1059	37	1	147	1	ZNF536	19	30934614	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	9214140	30934614	28194369	272	6429										
ZNF507	22847	hgsc.bcm.edu	37	chr19	32873386	32873386	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cttccagatgctctctgtgtGggtatgtgtgtagccatcct	11	10	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:32873386G>C	ENST00000311921.4	+	5	2566	c.2374G>C	c.(2374-2376)Ggg>Cgg	p.G792R	ZNF507_ENST00000544431.1_Missense_Mutation_p.G796R|ZNF507_ENST00000355898.5_Missense_Mutation_p.G792R	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	792					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					CTCTCTGTGTGGGTATGTGTG	0.398																																					p.G792R		Atlas-SNP	.											.	ZNF507	92	.	0			c.G2374C						.						294	292	292					19																	32873386		2203	4300	6503	SO:0001583	missense	22847	exon6			CTGTGTGGGTATG	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"Zinc fingers, C2H2-type"	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.2374G>C	chr19.hg19:g.32873386G>C	ENSP00000312277:p.Gly792Arg	178.0	0.0		196.0	37.0	NM_001136156	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Missense_Mutation	SNP	ENST00000311921.4	hg19	CCDS32985.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.839148	0.91117	.	.	ENSG00000168813	ENST00000355898;ENST00000311921;ENST00000544431	T;T;T	0.36340	4.32;4.32;1.26	5.36	5.36	0.76844	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.043473	0.85682	D	0.000000	T	0.64170	0.2574	M	0.79343	2.45	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.67565	-0.5638	10	0.87932	D	0	.	19.4637	0.94929	0.0:0.0:1.0:0.0	.	792	Q8TCN5	ZN507_HUMAN	R	792;792;796	ENSP00000348162:G792R;ENSP00000312277:G792R;ENSP00000441549:G796R	ENSP00000312277:G792R	G	+	1	0	ZNF507	37565226	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.374000	0.97172	2.675000	0.91044	0.655000	0.94253	GGG	.	.		0.398	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910		C	32873386	G	C	32873386	3	2	49	1	0	0	0	0	1	0	0	0	17968	1348	47	4	2388	4	ZNF507	19	32873386	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	1938772	32873386	26255597	273	6430										
ZNF793	390927	hgsc.bcm.edu	37	chr19	38023312	38023312	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcacccaagaggagtggcacCggctgagtcctgctcagagg	14	12	2	3	rs201422659		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:38023312C>T	ENST00000587143.1	+	4	305	c.70C>T	c.(70-72)Cgg>Tgg	p.R24W	ZNF793_ENST00000587986.1_Missense_Mutation_p.R24W|ZNF793_ENST00000589319.1_Missense_Mutation_p.R24W|ZNF793_ENST00000588578.1_Missense_Mutation_p.R24W|ZNF793_ENST00000542455.1_Missense_Mutation_p.R24W|ZNF793_ENST00000445217.1_Missense_Mutation_p.R24W			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGAGTGGCACCGGCTGAGTCC	0.473													C|||	1	0.000199681	0	0.0014	5008	,	,		19875	0		0	False		,,,				2504	0				p.R24W	Melanoma(44;400 1431 1499 19093)	Atlas-SNP	.											ZNF793_ENST00000445217,colon,carcinoma,0,1	ZNF793	50	.	0			c.C70T						.						62	66	65					19																	38023312		2184	4299	6483	SO:0001583	missense	390927	exon6			TGGCACCGGCTGA	AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.70C>T	chr19.hg19:g.38023312C>T	ENSP00000468605:p.Arg24Trp	83.0	1.0		93.0	5.0	NM_001013659	E9PGN4|Q7Z3Q9	Missense_Mutation	SNP	ENST00000587143.1	hg19	CCDS46062.1	.	.	.	.	.	.	.	.	.	.	C	10.70	1.422892	0.25639	.	.	ENSG00000188227	ENST00000542455;ENST00000418827;ENST00000445217;ENST00000322299	T;T	0.01787	4.64;4.64	3.53	-1.31	0.09230	Krueppel-associated box (4);	.	.	.	.	T	0.01124	0.0037	N	0.20304	0.555	0.09310	N	1	B;B	0.13145	0.007;0.004	B;B	0.09377	0.004;0.001	T	0.48514	-0.9029	9	0.37606	T	0.19	.	0.6134	0.00765	0.4069:0.2371:0.1313:0.2247	.	24;24	Q6ZN11;E9PGN4	ZN793_HUMAN;.	W	24;24;24;23	ENSP00000444355:R24W;ENSP00000396402:R24W	ENSP00000318811:R23W	R	+	1	2	ZNF793	42715152	0.000000	0.05858	0.837000	0.33122	0.675000	0.39556	-0.261000	0.08694	-0.360000	0.08138	-0.217000	0.12591	CGG	.	.		0.473	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		T	38023312	C	T	38023312	3	4	49	1	0	0	0	0	1	0	0	0	18180	643	23	1	76	1	ZNF793	19	38023312	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	5149926	38023312	21105671	274	6431										
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47575245	47575245	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	catgtctgcgtgcatgtctgCgtgcatgtcagggtgcatgt	14	9	3	0	rs381976		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:47575245C>G	ENST00000253048.5	-	13	1973	c.1936G>C	c.(1936-1938)Gca>Cca	p.A646P	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	646	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		tgcatgtctgcgtgcatgtca	0.662																																					p.A646P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G1936C						.						31	35	34					19																	47575245		2118	4259	6377	SO:0001583	missense	23211	exon13			TGTCTGCGTGCAT	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"Zinc fingers, CCCH-type domain containing"	17808	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 7"	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1936G>C	chr19.hg19:g.47575245C>G	ENSP00000253048:p.Ala646Pro	52.0	0.0		67.0	15.0	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	hg19	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	G	1.939	-0.444005	0.04604	.	.	ENSG00000130749	ENST00000253048	T	0.17528	2.27	5.21	5.21	0.72293	.	0.405917	0.24076	N	0.041773	T	0.08044	0.0201	N	0.08118	0	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.32877	-0.9890	10	0.02654	T	1	.	13.2185	0.59873	0.0:0.1603:0.8397:0.0	rs381976;rs381976	646	Q9UPT8	ZC3H4_HUMAN	P	646	ENSP00000253048:A646P	ENSP00000253048:A646P	A	-	1	0	ZC3H4	52267085	1.000000	0.71417	0.916000	0.36221	0.011000	0.07611	4.019000	0.57181	1.200000	0.43188	-0.132000	0.14878	GCA	.	C|1.000;|0.000		0.662	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			G	47575245	C	G	47575245	3	3	49	1	0	0	0	0	1	0	0	0	17585	768	27	4	1987	4	ZC3H4	19	47575245	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	9551933	47575245	11553738	275	6432										
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47575267	47575267	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgcatgtcagggtgcatgtcCgggtgcatgtcggggtgcat	17	8	1	0	rs200656728		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:47575267C>G	ENST00000253048.5	-	13	1951	c.1914G>C	c.(1912-1914)ccG>ccC	p.P638P	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	638	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		ggtgcatgtccgggtgcatgt	0.667																																					p.P638P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G1914C						.						34	38	36					19																	47575267		2110	4239	6349	SO:0001819	synonymous_variant	23211	exon13			CATGTCCGGGTGC	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"Zinc fingers, CCCH-type domain containing"	17808	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 7"	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1914G>C	chr19.hg19:g.47575267C>G		56.0	0.0		65.0	6.0	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	hg19	CCDS42582.1																																																																																			.	C|1.000;A|0.000		0.667	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			G	47575267	C	G	47575267	2	3	49	1	0	0	0	0	0	0	0	1	17585	639	23	4		4	ZC3H4	19	47575267	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	22	47575267	11553716	276	6433										
EHD2	30846	hgsc.bcm.edu	37	chr19	48244338	48244338	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ccgtttgtggagcggggaccTgacgaggccatggaggacgg	19	9	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:48244338T>C	ENST00000263277.3	+	6	1532	c.1281T>C	c.(1279-1281)ccT>ccC	p.P427P	EHD2_ENST00000540884.1_3'UTR|EHD2_ENST00000538399.1_Silent_p.P291P	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	427					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		AGCGGGGACCTGACGAGGCCA	0.657																																					p.P427P		Atlas-SNP	.											EHD2,NS,carcinoma,0,1	EHD2	59	.	0			c.T1281C						.						60	55	57					19																	48244338		2203	4300	6503	SO:0001819	synonymous_variant	30846	exon6			GGGACCTGACGAG	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"EF-hand domain containing"	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.1281T>C	chr19.hg19:g.48244338T>C		28.0	0.0		16.0	2.0	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	hg19	CCDS12704.1																																																																																			.	.		0.657	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1			C	48244338	T	C	48244338	2	2	49	1	0	0	0	0	0	0	0	1	4980	1567	55	2		2	EHD2	19	48244338	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	669071	48244338	10884645	277	6434										
SPACA4	171169	hgsc.bcm.edu	37	chr19	49110448	49110448	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgcctgcgagccaccagctgCggccttgaggaacccgtcag	13	15	1	1	rs371143349		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:49110448C>T	ENST00000321762.1	+	1	449	c.213C>T	c.(211-213)tgC>tgT	p.C71C	FAM83E_ENST00000263266.3_Intron	NM_133498.2	NP_598005.1	Q8TDM5	SACA4_HUMAN	sperm acrosome associated 4	71	UPAR/Ly6 1.				cell adhesion (GO:0007155)	anchored component of membrane (GO:0031225)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)		p.C71C(1)|p.C71*(1)		central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	5		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000112)|GBM - Glioblastoma multiforme(486;0.00615)|Epithelial(262;0.0155)		CCACCAGCTGCGGCCTTGAGG	0.652													C|||	1	0.000199681	8e-04	0	5008	,	,		17724	0		0	False		,,,				2504	0				p.C71C		Atlas-SNP	.											SPACA4,NS,carcinoma,0,2	SPACA4	9	.	2	Substitution - Nonsense(1)|Substitution - coding silent(1)	lung(1)|central_nervous_system(1)	c.C213T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	35	32	33		,213	-3.8	0.7	19		33	1,8599		0,1,4299	no	intron,coding-synonymous	FAM83E,SPACA4	NM_017708.3,NM_133498.2	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	,71/125	49110448	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	171169	exon1			CAGCTGCGGCCTT		CCDS12725.1	19q13.33	2013-10-24			ENSG00000177202	ENSG00000177202			16441	protein-coding gene	gene with protein product		609932					Standard	NM_133498		Approved	SAMP14	uc002pjo.3	Q8TDM5	OTTHUMG00000183316	ENST00000321762.1:c.213C>T	chr19.hg19:g.49110448C>T		49.0	1.0		40.0	2.0	NM_133498		Silent	SNP	ENST00000321762.1	hg19	CCDS12725.1																																																																																			.	.		0.652	SPACA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466149.1	NM_133498		T	49110448	C	T	49110448	2	4	49	1	0	0	0	0	0	0	0	1	14989	776	27	1		1	SPACA4	19	49110448	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	866110	49110448	10018535	278	6435										
ALDH16A1	126133	hgsc.bcm.edu	37	chr19	49965915	49965915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggggcggcttcggagtggccGagggctggatggggccgtgg	24	8	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:49965915G>A	ENST00000293350.4	+	8	1164	c.1001G>A	c.(1000-1002)cGa>cAa	p.R334Q	CTD-3148I10.9_ENST00000599536.1_5'Flank|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.R283Q|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.R171Q|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.R169Q	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	334						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CGGAGTGGCCGAGGGCTGGAT	0.672																																					p.R334Q		Atlas-SNP	.											ALDH16A1,bladder,carcinoma,0,2	ALDH16A1	54	.	0			c.G1001A						.						36	39	38					19																	49965915		2203	4297	6500	SO:0001583	missense	126133	exon8			GTGGCCGAGGGCT	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"Aldehyde dehydrogenases"	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1001G>A	chr19.hg19:g.49965915G>A	ENSP00000293350:p.Arg334Gln	67.0	0.0		39.0	2.0	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	hg19	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.426447	0.62733	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.93	-4.21	0.03812	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	1.500260	0.03928	N	0.284783	T	0.23451	0.0567	L	0.45581	1.43	0.22412	N	0.999126	P;P;P	0.46142	0.709;0.873;0.873	B;B;B	0.38194	0.131;0.267;0.267	T	0.43097	-0.9412	10	0.49607	T	0.09	-13.5058	6.2294	0.20726	0.2432:0.3699:0.3869:0.0	.	171;283;334	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	Q	334;283;171;169	ENSP00000293350:R334Q;ENSP00000410142:R283Q;ENSP00000445088:R171Q;ENSP00000398675:R169Q	ENSP00000293350:R334Q	R	+	2	0	ALDH16A1	54657727	0.001000	0.12720	0.275000	0.24674	0.988000	0.76386	-0.352000	0.07701	-0.315000	0.08703	0.485000	0.47835	CGA	.	.		0.672	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		A	49965915	G	A	49965915	3	1	49	1	0	0	0	0	1	0	0	0	488	1058	37	1	1031	1	ALDH16A1	19	49965915	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	855467	49965915	9163068	279	6436										
C19orf75	284369	hgsc.bcm.edu	37	chr19	51770669	51770669	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	caggcgaagaaagctgcagcGatcagagcaaaaaagagctc	12	9	1	3	rs369648100		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:51770669G>T	ENST00000316401.7	+	5	834	c.453G>T	c.(451-453)gcG>gcT	p.A151A	SIGLECL1_ENST00000593968.1_3'UTR|SIGLECL1_ENST00000597824.1_Silent_p.A57A|CTD-3187F8.2_ENST00000597569.1_RNA	NM_173635.1	NP_775906.1	Q96PQ1	SIG12_HUMAN	SIGLEC family like 1	515	Ig-like V-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										AAGCTGCAGCGATCAGAGCAA	0.468																																					p.A151A		Atlas-SNP	.											C19orf75,rectum,carcinoma,0,1	.	.	.	0			c.G453T						.						117	118	117					19																	51770669		2203	4300	6503	SO:0001819	synonymous_variant	284369	exon5			TGCAGCGATCAGA	AK097554	CCDS12827.1	19q13.33	2013-03-20	2012-07-20	2012-07-20	ENSG00000179213	ENSG00000179213			26856	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 75", "sialic acid binding Ig-like lectin 23, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 7"	C19orf75, SIGLEC23P, SIGLECP7			Standard	NM_173635		Approved	FLJ40235	uc002pwb.1	Q8N7X8	OTTHUMG00000182881	ENST00000316401.7:c.453G>T	chr19.hg19:g.51770669G>T		44.0	0.0		64.0	3.0	NM_173635	Q8IYH7	Silent	SNP	ENST00000316401.7	hg19	CCDS12827.1																																																																																			.	.		0.468	SIGLECL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464161.2	NM_173635		T	51770669	G	T	51770669	2	4	49	1	0	0	0	0	0	0	0	1	1951	1045	37	1		1	C19orf75	19	51770669	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	1804754	51770669	7358314	280	6437										
ZNF816A	125893	hgsc.bcm.edu	37	chr19	53453990	53453990	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tttcgaccaaaagtcttgccAcactcattacacttgtaagg	6	11	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:53453990A>G	ENST00000357666.4	-	5	1338	c.1038T>C	c.(1036-1038)tgT>tgC	p.C346C	ZNF816_ENST00000434371.2_Intron|ZNF816_ENST00000444460.2_Silent_p.C346C|ZNF321P_ENST00000391777.3_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	346					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						AAGTCTTGCCACACTCATTAC	0.423																																					p.C346C		Atlas-SNP	.											.	ZNF816	73	.	0			c.T1038C						.						153	157	156					19																	53453990		2203	4300	6503	SO:0001819	synonymous_variant	125893	exon4			CTTGCCACACTCA	BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"Zinc fingers, C2H2-type", "-"	26995	protein-coding gene	gene with protein product			"zinc finger protein 816A"	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.1038T>C	chr19.hg19:g.53453990A>G		82.0	0.0		109.0	5.0	NM_001202457	A8K7H5|Q3KR39|Q659B3	Silent	SNP	ENST00000357666.4	hg19	CCDS33096.1																																																																																			.	.		0.423	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		G	53453990	A	G	53453990	2	3	49	1	0	0	0	0	0	0	0	1	18192	157	6	2		2	ZNF816A	19	53453990	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	1683321	53453990	5674993	281	6438										
PEG3	5178	hgsc.bcm.edu	37	chr19	57334962	57334962	+	Splice_Site	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggggatgggtactcaccactGaaagaatggactgagtgagg	16	6	1	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:57334962G>A	ENST00000326441.9	-	5	843	c.480C>T	c.(478-480)ttC>ttT	p.F160F	ZIM2_ENST00000599935.1_Silent_p.F34F|ZIM2_ENST00000221722.5_Silent_p.F34F|ZIM2_ENST00000593931.1_Silent_p.F34F|ZIM2_ENST00000593711.1_Silent_p.F34F|PEG3_ENST00000423103.2_Splice_Site_p.F160F|ZIM2_ENST00000391708.3_Silent_p.F34F|PEG3_ENST00000593695.1_Splice_Site_p.F34F|PEG3_ENST00000594706.1_5'Flank|ZIM2_ENST00000601070.1_Silent_p.F34F|PEG3_ENST00000598410.1_Silent_p.F34F	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	160					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		ACTCACCACTGAAAGAATGGA	0.577																																					p.F160F		Atlas-SNP	.											.	PEG3	414	.	0			c.C480T						.						243	172	196					19																	57334962		2203	4300	6503	SO:0001630	splice_region_variant	5178	exon4			ACCACTGAAAGAA	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.481+1C>T	chr19.hg19:g.57334962G>A		47.0	0.0		70.0	15.0	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	ENST00000326441.9	hg19	CCDS12948.1																																																																																			.	.		0.577	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		Silent	A	57334962	G	A	57334962	5	1	49	1	0	0	0	0	0	0	1	0	11729	1304	45	3	4316	3	PEG3	19	57334962	Splice_Site	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	3880972	57334962	1794021	282	6439										
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385536	58385536	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cccacattctccacattcatAatgttttttgtcagtgtgaa	5	10	3	1	rs200607098|rs377684394	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:58385536A>G	ENST00000435989.2	-	3	1456	c.1222T>C	c.(1222-1224)Tat>Cat	p.Y408H	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	408					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						CCACATTCATAATGTTTTTTG	0.393																																					p.Y408H		Atlas-SNP	.											.	ZNF814	93	.	0			c.T1222C						.						110	89	96					19																	58385536		692	1591	2283	SO:0001583	missense	730051	exon3			ATTCATAATGTTT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1222T>C	chr19.hg19:g.58385536A>G	ENSP00000410545:p.Tyr408His	118.0	0.0		201.0	12.0	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	11.27	1.588723	0.28357	.	.	ENSG00000204514	ENST00000435989;ENST00000376205	T	0.60040	0.22	2.33	1.27	0.21489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40171	0.1106	L	0.33753	1.03	0.09310	N	1	B	0.30741	0.293	B	0.28305	0.088	T	0.32052	-0.9921	9	0.54805	T	0.06	.	3.051	0.06169	0.6575:0.0:0.1336:0.2089	.	408	B7Z6K7	ZN814_HUMAN	H	408;270	ENSP00000410545:Y408H	ENSP00000365378:Y270H	Y	-	1	0	ZNF814	63077348	0.002000	0.14202	0.001000	0.08648	0.011000	0.07611	1.779000	0.38624	0.155000	0.19261	-0.804000	0.03201	TAT	.	.		0.393	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		G	58385536	A	G	58385536	3	3	49	1	0	0	0	0	1	0	0	0	18191	362	13	2	1349	2	ZNF814	19	58385536	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	1050574	58385536	743447	283	6440										
DOK5	55816	hgsc.bcm.edu	37	chr20	53226977	53226977	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctttcagacccgagacggggAggccatctatcagaaagtcc	11	12	3	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr20:53226977A>C	ENST00000262593.5	+	6	1000	c.650A>C	c.(649-651)gAg>gCg	p.E217A	DOK5_ENST00000395939.1_Missense_Mutation_p.E109A	NM_018431.3	NP_060901.2	Q9P104	DOK5_HUMAN	docking protein 5	217	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				MAPK cascade (GO:0000165)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)		receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|skin(1)	19			Colorectal(105;0.202)			CGAGACGGGGAGGCCATCTAT	0.483																																					p.E217A		Atlas-SNP	.											.	DOK5	54	.	0			c.A650C						.						86	77	80					20																	53226977		2203	4300	6503	SO:0001583	missense	55816	exon6			ACGGGGAGGCCAT	AF132732	CCDS13446.1, CCDS13447.1	20q13.2	2013-01-10	2002-11-28	2002-11-29	ENSG00000101134	ENSG00000101134		"Pleckstrin homology (PH) domain containing"	16173	protein-coding gene	gene with protein product		608334	"chromosome 20 open reading frame 180"	C20orf180		11470823	Standard	XM_005260451		Approved	dJ805C22.1	uc002xwy.3	Q9P104	OTTHUMG00000032778	ENST00000262593.5:c.650A>C	chr20.hg19:g.53226977A>C	ENSP00000262593:p.Glu217Ala	143.0	0.0		171.0	20.0	NM_018431	Q5T7Y0|Q5TE53|Q8TEW7|Q96H13|Q9BZ24|Q9NQF4|Q9Y411	Missense_Mutation	SNP	ENST00000262593.5	hg19	CCDS13446.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.430303	0.83776	.	.	ENSG00000101134	ENST00000262593;ENST00000395939	T;T	0.76448	-1.02;-1.02	5.54	5.54	0.83059	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (3);	0.000000	0.85682	D	0.000000	D	0.87192	0.6116	M	0.78223	2.4	0.58432	D	0.999999	P;P	0.52577	0.868;0.954	P;D	0.67725	0.563;0.953	D	0.87147	0.2206	10	0.42905	T	0.14	-14.1726	14.8793	0.70519	1.0:0.0:0.0:0.0	.	109;217	Q9P104-2;Q9P104	.;DOK5_HUMAN	A	217;109	ENSP00000262593:E217A;ENSP00000379270:E109A	ENSP00000262593:E217A	E	+	2	0	DOK5	52660384	1.000000	0.71417	0.995000	0.50966	0.969000	0.65631	9.181000	0.94874	2.115000	0.64714	0.533000	0.62120	GAG	.	.		0.483	DOK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079777.2			C	53226977	A	C	53226977	3	2	49	1	0	0	0	0	1	0	0	0	4702	304	11	5	672	5	DOK5	20	53226977	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10		53226977	9798543	284	6441										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57767832	57767832	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtgcccgcagaggacacagaCgcaaagagaactgctgcgcg	14	12	0	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr20:57767832C>T	ENST00000371030.2	+	1	1758	c.1758C>T	c.(1756-1758)gaC>gaT	p.D586D		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	586							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					AGGACACAGACGCAAAGAGAA	0.672																																					p.D586D		Atlas-SNP	.											ZNF831,NS,carcinoma,0,2	ZNF831	287	.	0			c.C1758T						.						19	23	22					20																	57767832		2033	4167	6200	SO:0001819	synonymous_variant	128611	exon1			CACAGACGCAAAG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.1758C>T	chr20.hg19:g.57767832C>T		36.0	0.0		34.0	2.0	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	hg19	CCDS42894.1																																																																																			.	.		0.672	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57767832	C	T	57767832	2	4	49	1	0	0	0	0	0	0	0	1	18200	535	19	1		1	ZNF831	20	57767832	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	4540855	57767832	5257688	285	6442										
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62597492	62597583	+	Splice_Site	DEL	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	-													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gacctgggacgagcccccatAccttttcttaccactgttcc					rs200518817|rs376642783|rs540039560|rs200940725|rs371234637|rs139142804|rs146666443	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr20:62597492_62597583delGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	ENST00000450537.1	-	5	1005_1095	c.945_1035delAGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTCGGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTC	c.(943-1035)agagggaggaacagtggtaagaaaaggtatgggggctcgtcccaggtcggggaggaacagtggtaagaaaaggtatgggggctcgtcccaggt>ag	p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs	ZNF512B_ENST00000217130.3_Splice_Site_p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs|ZNF512B_ENST00000369888.1_Splice_Site_p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGTCTGCTGATAGCAA	0.575																																					p.338_345del		Pindel	.											.	ZNF512B	72	.	0			c.1012_1034del						.																																			SO:0001630	splice_region_variant	57473	exon5			.	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.1034+1AGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTCGGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTC>-	chr20.hg19:g.62597492_62597583delGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT		0.0	0.0		121.0	11.0	NM_020713	Q08AK9|Q9ULM4	Frame_Shift_Del	DEL	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	.		0.575	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	Frame_Shift_Del	-	62597583	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	-	62597492	8	5	49	1	0	1	0	1	0	0	1	0	17972	405	14	0	1694	0	ZNF512B	20	62597492	Splice_Site	DEL	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	TCGA-BD-A3EP-01A-11D-A22F-10	4829660	62597492	428028	286	6443										
PCMTD2	55251	hgsc.bcm.edu	37	chr20	62904798	62904798	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	acccctcagatgacaacagcTgtgaagacttggaagaggaa	11	9	1	5			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr20:62904798T>C	ENST00000308824.6	+	6	1058	c.931T>C	c.(931-933)Tgt>Cgt	p.C311R	PCMTD2_ENST00000299468.7_Intron|PCMTD2_ENST00000369758.4_Missense_Mutation_p.C284R|PCMTD2_ENST00000266078.7_3'UTR|PCMTD2_ENST00000609372.1_Missense_Mutation_p.C161R	NM_018257.2	NP_060727.2	Q9NV79	PCMD2_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	311						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(9)|upper_aerodigestive_tract(1)	17	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					TGACAACAGCTGTGAAGACTT	0.517																																					p.C311R		Atlas-SNP	.											.	PCMTD2	35	.	0			c.T931C						.						84	103	96					20																	62904798		2203	4300	6503	SO:0001583	missense	55251	exon6			AACAGCTGTGAAG	AK001745	CCDS13559.1, CCDS46631.1	20q13.33	2012-10-02	2005-10-06	2005-10-06	ENSG00000203880	ENSG00000203880			15882	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 36"	C20orf36			Standard	NM_018257		Approved	FLJ10883	uc002yil.4	Q9NV79	OTTHUMG00000033029	ENST00000308824.6:c.931T>C	chr20.hg19:g.62904798T>C	ENSP00000307854:p.Cys311Arg	43.0	0.0		59.0	4.0	NM_018257	E1P5H3|Q8IW60|Q9H4K2	Missense_Mutation	SNP	ENST00000308824.6	hg19	CCDS13559.1	.	.	.	.	.	.	.	.	.	.	.	11.22	1.574402	0.28092	.	.	ENSG00000203880	ENST00000369758;ENST00000308824;ENST00000266078	T;T;T	0.41400	1.02;1.61;1.0	5.41	3.12	0.35913	.	0.368603	0.31358	N	0.007786	T	0.28167	0.0695	N	0.22421	0.69	0.58432	D	0.999992	B;B	0.29716	0.09;0.255	B;B	0.33042	0.033;0.157	T	0.04454	-1.0950	10	0.33940	T	0.23	-8.3258	8.6567	0.34068	0.1193:0.0:0.2496:0.6311	.	284;311	Q9NV79-2;Q9NV79	.;PCMD2_HUMAN	R	284;311;87	ENSP00000358773:C284R;ENSP00000307854:C311R;ENSP00000266078:C87R	ENSP00000266078:C87R	C	+	1	0	PCMTD2	62375242	0.985000	0.35326	0.253000	0.24343	0.963000	0.63663	0.585000	0.23879	0.344000	0.23847	-0.257000	0.10917	TGT	.	.		0.517	PCMTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080301.1	NM_018257		C	62904798	T	C	62904798	3	2	49	1	0	0	0	0	1	0	0	0	11596	1580	55	2	949	2	PCMTD2	20	62904798	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	307306	62904798	120722	287	6444										
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28212774	28212774	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgcatcggggcagtgtttggAgtcctccccaaatgtaaact	11	10	0	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:28212774A>G	ENST00000284984.3	-	5	1940	c.1486T>C	c.(1486-1488)Tcc>Ccc	p.S496P		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	496	Disintegrin.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		CAGTGTTTGGAGTCCTCCCCA	0.577																																					p.S496P		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.T1486C						.						73	63	66					21																	28212774		2203	4300	6503	SO:0001583	missense	9510	exon5			GTTTGGAGTCCTC	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.1486T>C	chr21.hg19:g.28212774A>G	ENSP00000284984:p.Ser496Pro	64.0	0.0		70.0	4.0	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	hg19	CCDS33524.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.694959	0.88830	.	.	ENSG00000154734	ENST00000284984	T	0.63255	-0.03	5.14	5.14	0.70334	ADAM, cysteine-rich (1);	.	.	.	.	D	0.82999	0.5159	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.86269	0.1660	9	0.49607	T	0.09	.	15.4124	0.74937	1.0:0.0:0.0:0.0	.	496	Q9UHI8	ATS1_HUMAN	P	496	ENSP00000284984:S496P	ENSP00000284984:S496P	S	-	1	0	ADAMTS1	27134645	1.000000	0.71417	0.933000	0.37362	0.894000	0.52154	8.761000	0.91691	2.284000	0.76573	0.528000	0.53228	TCC	.	.		0.577	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			G	28212774	A	G	28212774	3	3	49	1	0	0	0	0	1	0	0	0	255	304	11	2	1437	2	ADAMTS1	21	28212774	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10		28212774	19917121	288	6445										
RNF160	26046	hgsc.bcm.edu	37	chr21	30339226	30339226	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tttttttttttacttgacttCaatgagctcttcggcttctg	6	8	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:30339226C>T	ENST00000361371.5	-	10	1666	c.1587G>A	c.(1585-1587)ttG>ttA	p.L529L	LTN1_ENST00000389194.2_Silent_p.L575L|LTN1_ENST00000389195.2_Silent_p.L575L			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	529					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						TACTTGACTTCAATGAGCTCT	0.378																																					p.L575L		Atlas-SNP	.											LTN1,colon,carcinoma,0,1	LTN1	141	.	0			c.G1725A						.						67	63	64					21																	30339226		2203	4300	6503	SO:0001819	synonymous_variant	26046	exon10			TGACTTCAATGAG	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"RING-type (C3HC4) zinc fingers"	13082	protein-coding gene	gene with protein product	"listerin"	613083	"chromosome 21 open reading frame 98", "zinc finger protein 294", "ring finger protein 160"	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1587G>A	chr21.hg19:g.30339226C>T		104.0	0.0		110.0	5.0	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Silent	SNP	ENST00000361371.5	hg19																																																																																				.	.		0.378	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		T	30339226	C	T	30339226	2	4	49	1	0	0	0	0	0	0	0	1	13470	825	29	3		3	RNF160	21	30339226	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	2126452	30339226	17790669	289	6446										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34003927	34003927	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcatgcaacttacagaactcAaaacattactttgcgttgca	6	10	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:34003927A>T	ENST00000322229.7	-	31	4099	c.4100T>A	c.(4099-4101)tTg>tAg	p.L1367*	SYNJ1_ENST00000357345.3_3'UTR|SYNJ1_ENST00000433931.2_Nonsense_Mutation_p.L1406*|SYNJ1_ENST00000382491.3_Nonsense_Mutation_p.L1320*|SYNJ1_ENST00000382499.2_3'UTR			O43426	SYNJ1_HUMAN	synaptojanin 1	1367	Pro-rich.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						TACAGAACTCAAAACATTACT	0.458																																					p.L1406X		Atlas-SNP	.											.	SYNJ1	253	.	0			c.T4217A						.						70	75	74					21																	34003927		2203	4300	6503	SO:0001587	stop_gained	8867	exon32			GAACTCAAAACAT	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.4100T>A	chr21.hg19:g.34003927A>T	ENSP00000322234:p.Leu1367*	124.0	0.0		135.0	8.0	NM_003895	O43425|O94984|Q4KMR1	Nonsense_Mutation	SNP	ENST00000322229.7	hg19	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	A	41	8.763780	0.98945	.	.	ENSG00000159082	ENST00000382491;ENST00000433931;ENST00000322229	.	.	.	5.04	-0.125	0.13519	.	0.597733	0.14761	N	0.299971	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.9321	0.19144	0.4574:0.1409:0.4017:0.0	.	.	.	.	X	1320;1406;1367	.	ENSP00000322234:L1367X	L	-	2	0	SYNJ1	32925798	0.726000	0.28059	0.412000	0.26496	0.995000	0.86356	0.813000	0.27225	0.025000	0.15241	0.523000	0.50628	TTG	.	.		0.458	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	34003927	A	T	34003927	4	4	49	1	0	0	0	0	0	1	0	0	15467	131	5	4	625	4	SYNJ1	21	34003927	Nonsense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	3664701	34003927	14125968	290	6447										
KCNJ15	3772	hgsc.bcm.edu	37	chr21	39671581	39671581	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	aaccattggctatggagtccGttccatcacagaggaatgtc	10	10	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:39671581G>A	ENST00000328656.4	+	4	701	c.398G>A	c.(397-399)cGt>cAt	p.R133H	KCNJ15_ENST00000398934.1_Missense_Mutation_p.R133H|KCNJ15_ENST00000398930.1_Missense_Mutation_p.R133H|KCNJ15_ENST00000398932.1_Missense_Mutation_p.R133H|KCNJ15_ENST00000398938.2_Missense_Mutation_p.R133H	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	133					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	TATGGAGTCCGTTCCATCACA	0.502																																					p.C133Y		Atlas-SNP	.											KCNJ15,NS,carcinoma,0,1	KCNJ15	43	.	0			c.G398A						.						107	105	106					21																	39671581		2203	4300	6503	SO:0001583	missense	3772	exon4			GAGTCCGTTCCAT	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.398G>A	chr21.hg19:g.39671581G>A	ENSP00000331698:p.Arg133His	92.0	0.0		100.0	4.0	NM_002243	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	hg19	CCDS13656.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.918617	0.92249	.	.	ENSG00000157551	ENST00000328656;ENST00000398928;ENST00000398938;ENST00000398932;ENST00000438657;ENST00000398930;ENST00000398934;ENST00000398927;ENST00000419868	D;D;D;D;D;D;D;D;D	0.97016	-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21	5.83	5.83	0.93111	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.98789	0.9592	H	0.94734	3.575	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99236	1.0883	9	.	.	.	.	20.1338	0.98010	0.0:0.0:1.0:0.0	.	133	Q99712	IRK15_HUMAN	H	133	ENSP00000331698:R133H;ENSP00000381902:R133H;ENSP00000381911:R133H;ENSP00000381905:R133H;ENSP00000414487:R133H;ENSP00000381904:R133H;ENSP00000381907:R133H;ENSP00000381901:R133H;ENSP00000400849:R133H	.	R	+	2	0	KCNJ15	38593451	1.000000	0.71417	0.996000	0.52242	0.903000	0.53119	9.869000	0.99810	2.770000	0.95276	0.655000	0.94253	CGT	.	.		0.502	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		A	39671581	G	A	39671581	3	1	49	1	0	0	0	0	1	0	0	0	8058	1145	40	1	400	1	KCNJ15	21	39671581	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	5667654	39671581	8458314	291	6448										
DSCAM	1826	hgsc.bcm.edu	37	chr21	42064802	42064802	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gtacgcctccaccgaggaggGgataatgcacttgaagaccg	13	11	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:42064802G>T	ENST00000400454.1	-	3	919	c.442C>A	c.(442-444)Ccc>Acc	p.P148T		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	148	Ig-like C2-type 2.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				ACCGAGGAGGGGATAATGCAC	0.532																																					p.P148T	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.,1	DSCAM	347	.	0			c.C442A						.						143	140	141					21																	42064802		2027	4181	6208	SO:0001583	missense	1826	exon3			AGGAGGGGATAAT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.442C>A	chr21.hg19:g.42064802G>T	ENSP00000383303:p.Pro148Thr	52.0	0.0		52.0	3.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.235957	0.79800	.	.	ENSG00000171587	ENST00000400454	T	0.13196	2.61	5.93	4.87	0.63330	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.064020	0.64402	D	0.000005	T	0.39809	0.1092	M	0.91561	3.22	0.51233	D	0.999917	P	0.52842	0.956	P	0.55545	0.778	T	0.44757	-0.9307	10	0.49607	T	0.09	.	16.0065	0.80367	0.0745:0.0:0.9255:0.0	.	148	O60469	DSCAM_HUMAN	T	148	ENSP00000383303:P148T	ENSP00000383303:P148T	P	-	1	0	DSCAM	40986672	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.856000	0.86956	2.814000	0.96858	0.655000	0.94253	CCC	.	.		0.532	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		T	42064802	G	T	42064802	3	4	49	1	0	0	0	0	1	0	0	0	4770	1232	43	3	5720	3	DSCAM	21	42064802	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	2393221	42064802	6065093	292	6449										
TRAPPC10	7109	hgsc.bcm.edu	37	chr21	45523364	45523364	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agctcgggcacacaagtcctGgtcatccccagccaagatga	10	14	1	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:45523364G>A	ENST00000291574.4	+	23	3907	c.3732G>A	c.(3730-3732)ctG>ctA	p.L1244L		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	1244					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						CACAAGTCCTGGTCATCCCCA	0.607																																					p.L1244L		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.G3732A						.						39	36	37					21																	45523364		2203	4300	6503	SO:0001819	synonymous_variant	7109	exon23			AGTCCTGGTCATC	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"Trafficking protein particle complex"	11868	protein-coding gene	gene with protein product	"trafficking protein particle complex subunit 130", "TRAPP 130 kDa subunit"	602103	"transmembrane protein 1"	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.3732G>A	chr21.hg19:g.45523364G>A		106.0	0.0		58.0	4.0	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	hg19	CCDS13704.1																																																																																			.	.		0.607	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		A	45523364	G	A	45523364	2	1	49	1	0	0	0	0	0	0	0	1	16472	1335	47	3		3	TRAPPC10	21	45523364	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	3458562	45523364	2606531	293	6450										
C21orf70	85395	hgsc.bcm.edu	37	chr21	46380029	46380029	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cctcaggtgcagaggccaagAccgttttgcccaagaaggag	13	11	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:46380029A>G	ENST00000291634.6	+	3	346	c.298A>G	c.(298-300)Acc>Gcc	p.T100A	FAM207A_ENST00000397826.3_Missense_Mutation_p.T85A|FAM207A_ENST00000479127.1_3'UTR	NM_058190.2	NP_478070.1	Q9NSI2	F207A_HUMAN	family with sequence similarity 207, member A	100																	AGAGGCCAAGACCGTTTTGCC	0.577																																					p.T100A		Atlas-SNP	.											.	.	.	.	0			c.A298G						.						122	96	105					21																	46380029		2203	4300	6503	SO:0001583	missense	85395	exon3			GCCAAGACCGTTT		CCDS13718.1	21q22.3	2011-08-15	2011-08-15	2011-08-15	ENSG00000160256	ENSG00000160256			15811	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 70"	C21orf70			Standard	NM_058190		Approved	PRED56	uc002zgl.3	Q9NSI2	OTTHUMG00000090293	ENST00000291634.6:c.298A>G	chr21.hg19:g.46380029A>G	ENSP00000291634:p.Thr100Ala	69.0	0.0		62.0	4.0	NM_058190		Missense_Mutation	SNP	ENST00000291634.6	hg19	CCDS13718.1	.	.	.	.	.	.	.	.	.	.	A	0.019	-1.461415	0.01062	.	.	ENSG00000160256	ENST00000291634;ENST00000397826;ENST00000458015	T;T;T	0.39406	1.08;1.08;1.08	3.24	-4.79	0.03200	.	0.600804	0.17242	N	0.181492	T	0.18635	0.0447	N	0.13098	0.295	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.09377	0.002;0.004	T	0.31280	-0.9949	10	0.09843	T	0.71	-0.1904	11.2394	0.48960	0.2498:0.0:0.7502:0.0	.	85;100	Q9NSI2-2;Q9NSI2	.;F207A_HUMAN	A	100;85;85	ENSP00000291634:T100A;ENSP00000380926:T85A;ENSP00000404964:T85A	ENSP00000291634:T100A	T	+	1	0	C21orf70	45204457	0.000000	0.05858	0.002000	0.10522	0.230000	0.25150	-0.654000	0.05354	-1.117000	0.02965	-0.417000	0.06048	ACC	.	.		0.577	FAM207A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206639.1	NM_058190		G	46380029	A	G	46380029	3	3	49	1	0	0	0	0	1	0	0	0	2135	275	10	2	308	2	C21orf70	21	46380029	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	856665	46380029	1749866	294	6451										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47676785	47676785	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctcttcagcaatggggcactCtgcgctgggcgccagcgccc	13	16	3	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:47676785C>A	ENST00000397708.1	-	18	4104	c.3850G>T	c.(3850-3852)Gag>Tag	p.E1284*	AP001469.9_ENST00000430259.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP_ENST00000291688.1_Nonsense_Mutation_p.E1284*			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1284					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)	p.E1284K(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					ATGGGGCACTCTGCGCTGGGC	0.667																																					p.E1284X		Atlas-SNP	.											MCM3AP,NS,carcinoma,0,1	MCM3AP	146	.	1	Substitution - Missense(1)	ovary(1)	c.G3850T						.						15	19	17					21																	47676785		2199	4295	6494	SO:0001587	stop_gained	8888	exon17			GGCACTCTGCGCT	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.3850G>T	chr21.hg19:g.47676785C>A	ENSP00000380820:p.Glu1284*	79.0	0.0		31.0	2.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Nonsense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	C	41	9.035785	0.99044	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	.	.	.	5.59	4.69	0.59074	.	0.152400	0.56097	D	0.000025	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-25.131	16.3994	0.83633	0.0:0.8682:0.1318:0.0	.	.	.	.	X	1284	.	ENSP00000291688:E1284X	E	-	1	0	MCM3AP	46501213	1.000000	0.71417	0.997000	0.53966	0.498000	0.33706	5.315000	0.65810	1.333000	0.45449	0.655000	0.94253	GAG	.	.		0.667	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		A	47676785	C	A	47676785	4	1	49	1	0	0	0	0	0	1	0	0	9397	922	32	3	2140	3	MCM3AP	21	47676785	Nonsense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1296756	47676785	453110	295	6452										
SNAP29	9342	hgsc.bcm.edu	37	chr22	21235343	21235343	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	acttttatccaaagattgaaAgaagctataagtacaagtaa	6	5	0	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:21235343A>G	ENST00000215730.7	+	3	569	c.441A>G	c.(439-441)aaA>aaG	p.K147K		NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	147					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			AAAGATTGAAAGAAGCTATAA	0.378																																					p.K147K		Atlas-SNP	.											.	SNAP29	22	.	0			c.A441G						.						69	63	65					22																	21235343		2203	4300	6503	SO:0001819	synonymous_variant	9342	exon3			ATTGAAAGAAGCT	AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"soluble 29 kDa NSF attachment protein"	604202	"synaptosomal-associated protein, 29kD"			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.441A>G	chr22.hg19:g.21235343A>G		101.0	0.0		84.0	4.0	NM_004782		Silent	SNP	ENST00000215730.7	hg19	CCDS13784.1																																																																																			.	.		0.378	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782		G	21235343	A	G	21235343	2	3	49	1	0	0	0	0	0	0	0	1	14846	69	3	2		2	SNAP29	22	21235343	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10		21235343	30069223	296	6453										
MMP11	4320	hgsc.bcm.edu	37	chr22	24124435	24124435	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gctcagtactgggtgtacgaCggtgaaaagccagtcctggg	15	9	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:24124435C>T	ENST00000215743.3	+	7	1150	c.1098C>T	c.(1096-1098)gaC>gaT	p.D366D		NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	366					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D366D(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	gggtgtacgacggtgaaaagc	0.652																																					p.D366D		Atlas-SNP	.											MMP11,NS,carcinoma,0,1	MMP11	53	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1098T						.						63	65	64					22																	24124435		2203	4300	6503	SO:0001819	synonymous_variant	4320	exon7			GTACGACGGTGAA		CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"matrix metalloproteinase 11 (stromelysin 3)"	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.1098C>T	chr22.hg19:g.24124435C>T		39.0	0.0		39.0	2.0	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Silent	SNP	ENST00000215743.3	hg19	CCDS13816.1																																																																																			.	.		0.652	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940		T	24124435	C	T	24124435	2	4	49	1	0	0	0	0	0	0	0	1	9659	535	19	1		1	MMP11	22	24124435	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	2889092	24124435	27180131	297	6454										
SMARCB1	6598	hgsc.bcm.edu	37	chr22	24175869	24175869	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tgagatggagaagaagatccGcgaccaggacaggaacacga	14	8	0	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:24175869G>A	ENST00000263121.7	+	8	1293	c.1097G>A	c.(1096-1098)cGc>cAc	p.R366H	SMARCB1_ENST00000407082.3_Missense_Mutation_p.R320H|SMARCB1_ENST00000407422.3_Missense_Mutation_p.R357H|SMARCB1_ENST00000344921.6_Missense_Mutation_p.R375H|DERL3_ENST00000464023.1_5'Flank	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	366					ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)|p.R366P(1)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				AAGAAGATCCGCGACCAGGAC	0.632			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.R366H		Atlas-SNP	.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	SMARCB1,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	SMARCB1	586	.	4	Unknown(2)|Substitution - Missense(1)|Deletion - In frame(1)	central_nervous_system(4)	c.G1097A						.						126	108	114					22																	24175869		2203	4300	6503	SO:0001583	missense	6598	exon8			AGATCCGCGACCA	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.1097G>A	chr22.hg19:g.24175869G>A	ENSP00000263121:p.Arg366His	38.0	0.0		33.0	2.0	NM_003073	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Missense_Mutation	SNP	ENST00000263121.7	hg19	CCDS13817.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.041973	0.93685	.	.	ENSG00000099956	ENST00000344921;ENST00000263121;ENST00000407422;ENST00000407082	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	4.76	4.76	0.60689	.	0.100539	0.64402	D	0.000006	D	0.89577	0.6755	M	0.88979	2.995	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.991;0.987;0.991	D	0.90634	0.4569	10	0.48119	T	0.1	-16.5216	17.2148	0.86940	0.0:0.0:1.0:0.0	.	375;357;366	G5E975;Q17S11;Q12824	.;.;SNF5_HUMAN	H	375;366;357;320	ENSP00000340883:R375H;ENSP00000263121:R366H;ENSP00000383984:R357H;ENSP00000385226:R320H	ENSP00000263121:R366H	R	+	2	0	SMARCB1	22505869	1.000000	0.71417	0.909000	0.35828	0.991000	0.79684	9.552000	0.98115	2.387000	0.81309	0.543000	0.68304	CGC	.	.		0.632	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		A	24175869	G	A	24175869	3	1	49	1	0	0	0	0	1	0	0	0	14789	1087	38	1	1127	1	SMARCB1	22	24175869	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	51434	24175869	27128697	298	6455										
GGT1	2678	hgsc.bcm.edu	37	chr22	25023537	25023537	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gcactgctcacctgtctgtcGtcgcagaggacggcagtgct	13	13	2	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:25023537G>A	ENST00000400382.1	+	12	1914	c.1159G>A	c.(1159-1161)Gtc>Atc	p.V387I	GGT1_ENST00000400380.1_Missense_Mutation_p.V387I|GGT1_ENST00000404223.1_Missense_Mutation_p.V43I|GGT1_ENST00000403838.1_Missense_Mutation_p.V43I|GGT1_ENST00000404532.1_Missense_Mutation_p.V43I|GGT1_ENST00000401885.1_Missense_Mutation_p.V43I|GGT1_ENST00000406383.2_Missense_Mutation_p.V387I|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400383.1_Missense_Mutation_p.V387I|GGT1_ENST00000404920.1_Missense_Mutation_p.V43I|GGT1_ENST00000248923.4_Missense_Mutation_p.V387I			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	387					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	CCTGTCTGTCGTCGCAGAGGA	0.662																																					p.V387I		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	.	0			c.G1159A						.						13	14	14					22																	25023537		2192	4250	6442	SO:0001583	missense	2678	exon12			TCTGTCGTCGCAG	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"CD molecules", "Gamma-glutamyltransferases"	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1159G>A	chr22.hg19:g.25023537G>A	ENSP00000383232:p.Val387Ile	52.0	0.0		43.0	2.0	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	hg19	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	2.274	-0.366356	0.05069	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.07444	3.19;3.19;3.19;3.19;3.19;3.19;3.19;3.19;3.19;3.19;3.19	3.36	1.17	0.20885	.	0.198041	0.42172	N	0.000751	T	0.06280	0.0162	L	0.35249	1.045	0.34240	D	0.677567	B	0.15930	0.015	B	0.11329	0.006	T	0.22661	-1.0210	10	0.31617	T	0.26	-45.1165	8.9047	0.35517	0.1879:0.0:0.8121:0.0	.	387	P19440	GGT1_HUMAN	I	387;387;387;387;387;387;43;43;43;43;43	ENSP00000248923:V387I;ENSP00000393537:V387I;ENSP00000383232:V387I;ENSP00000383233:V387I;ENSP00000383231:V387I;ENSP00000385975:V387I;ENSP00000384381:V43I;ENSP00000385445:V43I;ENSP00000384820:V43I;ENSP00000385016:V43I;ENSP00000385001:V43I	ENSP00000248923:V387I	V	+	1	0	GGT1	23353537	1.000000	0.71417	0.127000	0.21898	0.210000	0.24377	2.905000	0.48727	0.255000	0.21593	-1.954000	0.00483	GTC	.	.		0.662	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430		A	25023537	G	A	25023537	3	1	49	1	0	0	0	0	1	0	0	0	6369	1145	40	1	1189	1	GGT1	22	25023537	Missense_Mutation	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	847668	25023537	26281029	299	6456										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26164267	26164267	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agcatcaatggtgagaaggcCcaggagctgggctccagtgc	15	10	1	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:26164267C>A	ENST00000407587.2	+	4	553	c.384C>A	c.(382-384)gcC>gcA	p.A128A	MYO18B_ENST00000536101.1_Silent_p.A128A|MYO18B_ENST00000335473.7_Silent_p.A128A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	128						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GTGAGAAGGCCCAGGAGCTGG	0.597																																					p.A128A		Atlas-SNP	.											.	MYO18B	322	.	0			c.C384A						.						39	45	43					22																	26164267		1995	4156	6151	SO:0001819	synonymous_variant	84700	exon4			GAAGGCCCAGGAG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.384C>A	chr22.hg19:g.26164267C>A		89.0	0.0		89.0	5.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26164267	C	A	26164267	2	1	49	1	0	0	0	0	0	0	0	1	10075	610	22	3		3	MYO18B	22	26164267	Silent	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	1140730	26164267	25140299	300	6457										
CRYBA4	1413	hgsc.bcm.edu	37	chr22	27026346	27026346	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ggctaccgaggatttcagtaTgtgctggaatgcgatcacca	12	9	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:27026346T>C	ENST00000354760.3	+	6	521	c.486T>C	c.(484-486)taT>taC	p.Y162Y	CRYBA4_ENST00000466315.1_3'UTR	NM_001886.2	NP_001877.1	P53673	CRBA4_HUMAN	crystallin, beta A4	162	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(6)|liver(1)|lung(6)|skin(3)|urinary_tract(2)	18						GATTTCAGTATGTGCTGGAAT	0.537																																					p.Y162Y		Atlas-SNP	.											.	CRYBA4	33	.	0			c.T486C						.						126	100	109					22																	27026346		2203	4300	6503	SO:0001819	synonymous_variant	1413	exon6			TCAGTATGTGCTG		CCDS13841.1	22q12.1	2008-06-10			ENSG00000196431	ENSG00000196431			2396	protein-coding gene	gene with protein product		123631				8999933, 960806	Standard	NM_001886		Approved		uc003acz.4	P53673	OTTHUMG00000150983	ENST00000354760.3:c.486T>C	chr22.hg19:g.27026346T>C		98.0	0.0		89.0	4.0	NM_001886	Q4VB22|Q6ICE4	Silent	SNP	ENST00000354760.3	hg19	CCDS13841.1																																																																																			.	.		0.537	CRYBA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320793.1	NM_001886		C	27026346	T	C	27026346	2	2	49	1	0	0	0	0	0	0	0	1	3911	1471	51	2		2	CRYBA4	22	27026346	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	862079	27026346	24278220	301	6458										
HMGXB4	10042	hgsc.bcm.edu	37	chr22	35660647	35660647	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ttgattatttctagatatttCgtctttggaatcgtcacaga	7	6	3	3	rs560951498		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:35660647C>T	ENST00000216106.5	+	5	394	c.266C>T	c.(265-267)tCg>tTg	p.S89L	HMGXB4_ENST00000444518.2_5'UTR	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	89					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CTAGATATTTCGTCTTTGGAA	0.403													C|||	1	0.000199681	8e-04	0	5008	,	,		21536	0		0	False		,,,				2504	0				p.S89L		Atlas-SNP	.											HMGXB4,NS,carcinoma,0,1	HMGXB4	52	.	0			c.C266T						.						100	109	106					22																	35660647		2201	4299	6500	SO:0001583	missense	10042	exon5			ATATTTCGTCTTT	AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"High mobility group / Non-canonical"	5003	protein-coding gene	gene with protein product		604702	"high-mobility group protein 2-like 1"	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.266C>T	chr22.hg19:g.35660647C>T	ENSP00000216106:p.Ser89Leu	50.0	0.0		42.0	2.0	NM_001003681	O75672|O75673|Q9UMT5	Missense_Mutation	SNP	ENST00000216106.5	hg19	CCDS33641.1	.	.	.	.	.	.	.	.	.	.	C	10.81	1.454587	0.26161	.	.	ENSG00000100281	ENST00000216106	T	0.19532	2.14	5.71	5.71	0.89125	.	0.513334	0.21865	N	0.067976	T	0.20292	0.0488	L	0.27053	0.805	0.80722	D	1	B	0.15141	0.012	B	0.12156	0.007	T	0.03344	-1.1046	10	0.72032	D	0.01	-1.1235	19.8545	0.96752	0.0:1.0:0.0:0.0	.	89	Q9UGU5	HMGX4_HUMAN	L	89	ENSP00000216106:S89L	ENSP00000216106:S89L	S	+	2	0	HMGXB4	33990647	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	5.311000	0.65786	2.695000	0.91970	0.563000	0.77884	TCG	.	.		0.403	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487		T	35660647	C	T	35660647	3	4	49	1	0	0	0	0	1	0	0	0	7248	893	31	1	280	1	HMGXB4	22	35660647	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	8634301	35660647	15643919	302	6459										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46794440	46794440	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cctgcatgcagcctcggaatCcacggcgcacggagaccttg	12	15	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:46794440C>A	ENST00000262738.3	-	11	5506	c.5507G>T	c.(5506-5508)gGa>gTa	p.G1836V		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1836	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GCCTCGGAATCCACGGCGCAC	0.672																																					p.G1836V		Atlas-SNP	.											.	CELSR1	242	.	0			c.G5507T						.						52	45	47					22																	46794440		2203	4300	6503	SO:0001583	missense	9620	exon11			CGGAATCCACGGC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5507G>T	chr22.hg19:g.46794440C>A	ENSP00000262738:p.Gly1836Val	97.0	0.0		71.0	22.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.062264	0.55432	.	.	ENSG00000075275	ENST00000262738	T	0.72505	-0.66	4.93	4.93	0.64822	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.64402	U	0.000002	D	0.85847	0.5792	M	0.85945	2.785	0.80722	D	1	D;P	0.89917	1.0;0.771	D;P	0.97110	1.0;0.475	D	0.87832	0.2645	10	0.56958	D	0.05	.	17.7518	0.88436	0.0:1.0:0.0:0.0	.	157;1836	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	V	1836	ENSP00000262738:G1836V	ENSP00000262738:G1836V	G	-	2	0	CELSR1	45173104	1.000000	0.71417	0.077000	0.20336	0.185000	0.23345	6.762000	0.74950	2.284000	0.76573	0.591000	0.81541	GGA	.	.		0.672	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46794440	C	A	46794440	3	1	49	1	0	0	0	0	1	0	0	0	3223	855	30	3	3637	3	CELSR1	22	46794440	Missense_Mutation	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	11133793	46794440	4510126	303	6460										
PLCXD1	55344	hgsc.bcm.edu	37	chrX	215776	215776	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	cgttgcaggagggttgttcgTggccggcatcaacctcacgg	15	11	2	0			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:215776T>C	ENST00000381657.2	+	7	1260	c.746T>C	c.(745-747)gTg>gCg	p.V249A	PLCXD1_ENST00000399012.1_Missense_Mutation_p.V249A|PLCXD1_ENST00000381663.3_Missense_Mutation_p.V249A	NM_018390.3	NP_060860.1	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 1	249					lipid metabolic process (GO:0006629)		phosphoric diester hydrolase activity (GO:0008081)			endometrium(3)|large_intestine(1)|lung(7)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGGTTGTTCGTGGCCGGCATC	0.617																																					p.V249A		Atlas-SNP	.											.	PLCXD1	18	.	0			c.T746C						.						111	96	101					X																	215776		2203	4296	6499	SO:0001583	missense	55344	exon7			TGTTCGTGGCCGG	AK002185	CCDS14103.1	Xp22.33 and Yp11.32	2010-07-28			ENSG00000182378	ENSG00000182378		"Pseudoautosomal regions / PAR1"	23148	protein-coding gene	gene with protein product							Standard	NM_018390		Approved	FLJ11323	uc004cpc.3	Q9NUJ7	OTTHUMG00000022693	ENST00000381657.2:c.746T>C	chrX.hg19:g.215776T>C	ENSP00000371073:p.Val249Ala	123.0	0.0		76.0	4.0	NM_018390	A2BH51|A2BH52	Missense_Mutation	SNP	ENST00000381657.2	hg19	CCDS14103.1	.	.	.	.	.	.	.	.	.	.	.	7.501	0.652707	0.14580	.	.	ENSG00000182378	ENST00000399012;ENST00000381657;ENST00000381663	T;T;T	0.29655	1.56;1.56;1.56	1.94	1.94	0.25998	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.000000	0.85682	D	0.000000	T	0.18676	0.0448	.	.	.	0.09310	N	1	B	0.26577	0.153	B	0.27796	0.083	T	0.16928	-1.0386	9	0.27082	T	0.32	-37.672	8.3073	0.32049	0.0:0.0:0.0:1.0	.	249	Q9NUJ7	PLCX1_HUMAN	A	249	ENSP00000381976:V249A;ENSP00000371073:V249A;ENSP00000371079:V249A	ENSP00000371073:V249A	V	+	2	0	PLCXD1	155776	1.000000	0.71417	0.644000	0.29465	0.029000	0.11900	4.999000	0.63934	0.835000	0.34877	0.337000	0.21675	GTG	.	.		0.617	PLCXD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058879.2	NM_018390		C	215776	T	C	215776	3	2	49	1	0	0	0	0	1	0	0	0	12050	1696	59	2	768	2	PLCXD1	23	215776	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10		215776	155054784	304	6461										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3241431	3241431	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tttatccttcgtctagattcAaacactctgcgaccttctgc	5	13	4	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:3241431A>T	ENST00000217939.6	-	5	2449	c.2295T>A	c.(2293-2295)ttT>ttA	p.F765L		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	765						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GTCTAGATTCAAACACTCTGC	0.448																																					p.F765L		Atlas-SNP	.											.	MXRA5	815	.	0			c.T2295A						.						123	107	113					X																	3241431		2203	4300	6503	SO:0001583	missense	25878	exon5			AGATTCAAACACT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2295T>A	chrX.hg19:g.3241431A>T	ENSP00000217939:p.Phe765Leu	280.0	0.0		210.0	81.0	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	a	10.84	1.462709	0.26248	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.64618	-0.11	3.63	-3.24	0.05094	.	0.000000	0.41605	U	0.000852	T	0.46268	0.1384	L	0.32530	0.975	0.25647	N	0.986139	B	0.15719	0.014	B	0.12156	0.007	T	0.28808	-1.0032	10	0.52906	T	0.07	.	12.7505	0.57306	0.8856:0.0:0.1144:0.0	.	765	Q9NR99	MXRA5_HUMAN	L	765	ENSP00000217939:F765L	ENSP00000217939:F765L	F	-	3	2	MXRA5	3251431	1.000000	0.71417	0.021000	0.16686	0.029000	0.11900	0.786000	0.26844	-0.933000	0.03737	-0.395000	0.06472	TTT	.	.		0.448	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3241431	A	T	3241431	3	4	49	1	0	0	0	0	1	0	0	0	10012	127	5	4	6203	4	MXRA5	23	3241431	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	3025655	3241431	152029129	305	6462										
FAM48B2	170067	hgsc.bcm.edu	37	chrX	24329882	24329884	+	IGR	DEL	TAA	TAA	-													0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gccgccacagcagcagcagcTaaagcaggagcagcagcagg					rs386824350		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	TAA	TAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:24329882_24329884delTAA								AC096509.1 (25088 upstream) : AC004552.1 (37041 downstream)																							cagcagcagctaaagcaggagca	0.631																																					p.517_518del		Atlas-INDEL	.											.	.	.	.	0			c.1550_1552del						.			32,3237		3,13,13,1401,422						-0.8	0			8	18,5770		4,3,7,2100,1567	no	coding	FAM48B2	NM_001136233.1		7,16,20,3501,1989	A1A1,A1R,A1,RR,R		0.311,0.9789,0.5521				50,9007				SO:0001628	intergenic_variant	170067	exon1			.																													chrX.hg19:g.24329882_24329884delTAA		170.0	0.0		162.0	10.0	NM_001136233		In_Frame_Del	DEL		hg19																																																																																				.	.	0	0.631									-	24329884	TAA	-	24329882	6	5	49	0	1	1	0	1	0	0	0	0	5582	1519	53	0		0	FAM48B2	23	24329882	IGR	DEL	TAA	TCGA-BD-A3EP-01A-11D-A22F-10	21088451	24329882	130940678	306	6463										
FAM48B2	170067	hgsc.bcm.edu	37	chrX	24329896	24329896	+	IGR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	agcagctaaagcaggagcagCagcaggagcaggagcaggag	17	8	0	0	rs386824350		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:24329896C>G								AC096509.1 (25102 upstream) : AC004552.1 (37029 downstream)																							gcaggagcagcagcaggagca	0.612																																					p.A513P		Atlas-SNP	.											.	.	.	.	0			c.G1537C						.						10	9	10					X																	24329896		689	1584	2273	SO:0001628	intergenic_variant	170067	exon1			GAGCAGCAGCAGG																													chrX.hg19:g.24329896C>G		177.0	0.0		177.0	25.0	NM_001136233		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.612									G	24329896	C	G	24329896	1	3	49	0	1	0	0	0	0	0	0	0	5582	710	25	4		4	FAM48B2	23	24329896	IGR	SNP	C	TCGA-BD-A3EP-01A-11D-A22F-10	14	24329896	130940664	307	6464										
KCND1	3750	hgsc.bcm.edu	37	chrX	48823420	48823420	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctaaagttggacacaatgacTggcacaggcagggcaatgac	12	9	0	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:48823420T>C	ENST00000218176.3	-	2	2512	c.1215A>G	c.(1213-1215)ccA>ccG	p.P405P	KCND1_ENST00000376477.1_Silent_p.P28P	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	405					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	ACACAATGACTGGCACAGGCA	0.577																																					p.P405P		Atlas-SNP	.											.	KCND1	63	.	0			c.A1215G						.						136	91	106					X																	48823420		2203	4300	6503	SO:0001819	synonymous_variant	3750	exon2			AATGACTGGCACA	AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.1215A>G	chrX.hg19:g.48823420T>C		82.0	0.0		88.0	6.0	NM_004979	A6NEF1|B2RCG0|O75671	Silent	SNP	ENST00000218176.3	hg19	CCDS14314.1																																																																																			.	.		0.577	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979		C	48823420	T	C	48823420	2	2	49	1	0	0	0	0	0	0	0	1	8027	1567	55	2		2	KCND1	23	48823420	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	24493524	48823420	106447140	308	6465										
TAF1	6872	hgsc.bcm.edu	37	chrX	70607151	70607151	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tcgtgctccaatttatcttcAtaagatgccagaaactgatt	6	9	2	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:70607151A>G	ENST00000373790.4	+	15	2315	c.2264A>G	c.(2263-2265)cAt>cGt	p.H755R	TAF1_ENST00000276072.3_Missense_Mutation_p.H776R|TAF1_ENST00000449580.1_Missense_Mutation_p.H755R|TAF1_ENST00000423759.1_Missense_Mutation_p.H776R	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	755	Histone acetyltransferase (HAT).				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				ATTTATCTTCATAAGATGCCA	0.373																																					p.H776R		Atlas-SNP	.											.	TAF1	439	.	0			c.A2327G						.						137	127	131					X																	70607151		2203	4300	6503	SO:0001583	missense	6872	exon15			ATCTTCATAAGAT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.2264A>G	chrX.hg19:g.70607151A>G	ENSP00000362895:p.His755Arg	256.0	0.0		235.0	86.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	20.9	4.068723	0.76301	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	5.03	5.03	0.67393	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.090151	0.85682	D	0.000000	T	0.52709	0.1751	M	0.89478	3.035	0.80722	D	1	D;P	0.76494	0.999;0.709	D;P	0.85130	0.997;0.781	T	0.62905	-0.6755	10	0.87932	D	0	.	14.1119	0.65126	1.0:0.0:0.0:0.0	.	755;776	P21675;P21675-2	TAF1_HUMAN;.	R	755;755;776;776	ENSP00000362895:H755R;ENSP00000389000:H755R;ENSP00000406549:H776R;ENSP00000276072:H776R	ENSP00000276072:H776R	H	+	2	0	TAF1	70523876	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.954000	0.93051	1.779000	0.52309	0.373000	0.22412	CAT	.	.		0.373	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		G	70607151	A	G	70607151	3	3	49	1	0	0	0	0	1	0	0	0	15528	217	8	2	2385	2	TAF1	23	70607151	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	21783731	70607151	84663409	309	6466										
GLA	2717	hgsc.bcm.edu	37	chrX	100658874	100658874	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctgccttctgaatctctttgGggagccatccaacagtcatc	8	13	3	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:100658874G>T	ENST00000218516.3	-	2	315	c.294C>A	c.(292-294)ccC>ccA	p.P98P	GLA_ENST00000479445.1_5'UTR|RPL36A-HNRNPH2_ENST00000409170.3_Intron	NM_000169.2	NP_000160.1	P06280	AGAL_HUMAN	galactosidase, alpha	98					glycoside catabolic process (GO:0016139)|glycosphingolipid catabolic process (GO:0046479)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide catabolic process (GO:0046477)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|oligosaccharide metabolic process (GO:0009311)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|catalytic activity (GO:0003824)|galactoside binding (GO:0016936)|hydrolase activity (GO:0016787)|protein homodimerization activity (GO:0042803)|raffinose alpha-galactosidase activity (GO:0052692)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						AATCTCTTTGGGGAGCCATCC	0.478																																					p.P98P	Colon(193;776 2816 31189 44474)	Atlas-SNP	.											.	GLA	43	.	0			c.C294A						.						190	171	177					X																	100658874		2203	4300	6503	SO:0001819	synonymous_variant	2717	exon2			TCTTTGGGGAGCC	X16889	CCDS14484.1	Xq21.3-q22	2014-09-17			ENSG00000102393	ENSG00000102393	3.2.1.22		4296	protein-coding gene	gene with protein product		300644					Standard	NM_000169		Approved	GALA	uc004ehl.1	P06280	OTTHUMG00000022026	ENST00000218516.3:c.294C>A	chrX.hg19:g.100658874G>T		135.0	0.0		99.0	36.0	NM_000169	Q6LER7	Silent	SNP	ENST00000218516.3	hg19	CCDS14484.1																																																																																			.	.		0.478	GLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057540.1			T	100658874	G	T	100658874	2	4	49	1	0	0	0	0	0	0	0	1	6434	1219	43	3		3	GLA	23	100658874	Silent	SNP	G	TCGA-BD-A3EP-01A-11D-A22F-10	30051723	100658874	54611686	310	6467										
COL4A6	1288	hgsc.bcm.edu	37	chrX	107418370	107418370	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	ctgagccttgagagcctttgTctcctttgagccaaaggttt	10	10	1	3			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:107418370T>C	ENST00000372216.4	-	30	3009	c.2909A>G	c.(2908-2910)gAc>gGc	p.D970G	COL4A6_ENST00000545689.1_Missense_Mutation_p.D969G|COL4A6_ENST00000394872.2_Missense_Mutation_p.D970G|COL4A6_ENST00000334504.7_Missense_Mutation_p.D969G|COL4A6_ENST00000538570.1_Missense_Mutation_p.D969G	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	970	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						AGAGCCTTTGTCTCCTTTGAG	0.537									Alport syndrome with Diffuse Leiomyomatosis																												p.D970G	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.A2909G						.						182	163	170					X																	107418370		2203	4300	6503	SO:0001583	missense	1288	exon30	Familial Cancer Database		CCTTTGTCTCCTT	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.2909A>G	chrX.hg19:g.107418370T>C	ENSP00000361290:p.Asp970Gly	122.0	0.0		106.0	5.0	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	hg19	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	T	14.92	2.679782	0.47886	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D;D	0.94138	-3.36;-3.36;-3.36;-3.36;-3.36	5.08	5.08	0.68730	.	0.154911	0.30437	N	0.009625	D	0.94059	0.8096	L	0.41632	1.29	0.29469	N	0.857154	D;D;D;P	0.71674	0.992;0.992;0.998;0.93	P;P;D;P	0.74674	0.893;0.893;0.984;0.839	D	0.90259	0.4299	10	0.66056	D	0.02	.	10.3079	0.43691	0.0:0.0:0.1629:0.8371	.	969;969;970;969	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	G	970;969;970;969;969;969	ENSP00000361290:D970G;ENSP00000334733:D969G;ENSP00000378340:D970G;ENSP00000443707:D969G;ENSP00000445236:D969G	ENSP00000334733:D969G	D	-	2	0	COL4A6	107305026	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.069000	0.50026	1.952000	0.56665	0.481000	0.45027	GAC	.	.		0.537	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			C	107418370	T	C	107418370	3	2	49	1	0	0	0	0	1	0	0	0	3697	1667	58	2	2230	2	COL4A6	23	107418370	Missense_Mutation	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	6759496	107418370	47852190	311	6468										
FATE1	89885	hgsc.bcm.edu	37	chrX	150884642	150884642	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gagatggaaatgtccctggcAgaagaactgaatcatggacg	13	7	1	4			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:150884642A>G	ENST00000370350.3	+	1	136	c.51A>G	c.(49-51)gcA>gcG	p.A17A		NM_033085.2	NP_149076.1	Q969F0	FATE1_HUMAN	fetal and adult testis expressed 1	17						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					TGTCCCTGGCAGAAGAACTGA	0.537																																					p.A17A		Atlas-SNP	.											.	FATE1	30	.	0			c.A51G						.						87	66	74					X																	150884642		2040	3766	5806	SO:0001819	synonymous_variant	89885	exon1			CCTGGCAGAAGAA	AF249872	CCDS14700.1	Xq28	2009-03-25			ENSG00000147378	ENSG00000147378			24683	protein-coding gene	gene with protein product	"cancer/testis antigen 43"	300450				11694338	Standard	NM_033085		Approved	FATE, CT43	uc004fex.3	Q969F0	OTTHUMG00000024172	ENST00000370350.3:c.51A>G	chrX.hg19:g.150884642A>G		175.0	0.0		146.0	40.0	NM_033085		Silent	SNP	ENST00000370350.3	hg19	CCDS14700.1																																																																																			.	.		0.537	FATE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060885.1	NM_033085		G	150884642	A	G	150884642	2	3	49	1	0	0	0	0	0	0	0	1	5701	175	7	2		2	FATE1	23	150884642	Silent	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	43466272	150884642	4385918	312	6469										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151815446	151815446	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	gttttttcatcagacttggaAagattcacgcttagcatact	7	8	3	2			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:151815446A>C	ENST00000370306.2	+	4	364	c.344A>C	c.(343-345)aAa>aCa	p.K115T		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	115					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CAGACTTGGAAAGATTCACGC	0.463																																					p.K115T		Atlas-SNP	.											.	GABRQ	131	.	0			c.A344C						.						247	191	210					X																	151815446		2203	4300	6503	SO:0001583	missense	55879	exon4			CTTGGAAAGATTC	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.344A>C	chrX.hg19:g.151815446A>C	ENSP00000359329:p.Lys115Thr	179.0	0.0		149.0	61.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	hg19	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	A	15.74	2.921464	0.52653	.	.	ENSG00000147402	ENST00000370306	T	0.76448	-1.02	5.51	4.38	0.52667	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.46758	D	0.000265	T	0.72811	0.3507	L	0.27975	0.815	0.32420	N	0.549513	P	0.51791	0.948	P	0.57425	0.82	T	0.76170	-0.3057	10	0.51188	T	0.08	.	3.7045	0.08395	0.7044:0.0:0.2956:0.0	.	115	Q9UN88	GBRT_HUMAN	T	115	ENSP00000359329:K115T	ENSP00000359329:K115T	K	+	2	0	GABRQ	151566102	1.000000	0.71417	0.999000	0.59377	0.478000	0.33099	4.577000	0.60922	1.844000	0.53588	0.441000	0.28932	AAA	.	.		0.463	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		C	151815446	A	C	151815446	3	2	49	1	0	0	0	0	1	0	0	0	6183	14	1	5	358	5	GABRQ	23	151815446	Missense_Mutation	SNP	A	TCGA-BD-A3EP-01A-11D-A22F-10	930804	151815446	3455114	313	6470										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153129904	153129904	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289389067524116	9	1	0.52503711821267	0.43924673941975	0.538176185235009	0.0127536231884058	0.250373760488177	0	tggttgtagctgacatactgTggcgaaagggaagccccacc	13	10	0	1			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:153129904T>C	ENST00000370060.1	-	25	3384	c.3195A>G	c.(3193-3195)ccA>ccG	p.P1065P	L1CAM_ENST00000538883.1_Silent_p.P1067P|L1CAM_ENST00000370057.3_Silent_p.P1065P|L1CAM_ENST00000361981.3_Silent_p.P1060P|L1CAM_ENST00000361699.4_Silent_p.P1065P|L1CAM_ENST00000543994.1_Silent_p.P1067P|L1CAM_ENST00000370055.1_Silent_p.P1060P	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	1065	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGACATACTGTGGCGAAAGGG	0.602																																					p.P1065P		Atlas-SNP	.											.	L1CAM	189	.	0			c.A3195G						.						125	109	115					X																	153129904		2203	4300	6503	SO:0001819	synonymous_variant	3897	exon24			ATACTGTGGCGAA	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.3195A>G	chrX.hg19:g.153129904T>C		80.0	0.0		97.0	4.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Silent	SNP	ENST00000370060.1	hg19	CCDS14733.1																																																																																			.	.		0.602	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		C	153129904	T	C	153129904	2	2	49	1	0	0	0	0	0	0	0	1	8597	1683	59	2		2	L1CAM	23	153129904	Silent	SNP	T	TCGA-BD-A3EP-01A-11D-A22F-10	1314458	153129904	2140656	314	6471										
UBE4B	10277	hgsc.bcm.edu	37	chr1	10197205	10197205	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tgcatgctcaccacctctctAttctgcctagttgccgtcgc	7	16	3	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr1:10197205A>G	ENST00000253251.8	+	16	2757	c.1918A>G	c.(1918-1920)Att>Gtt	p.I640V	UBE4B_ENST00000377157.3_Missense_Mutation_p.I524V|UBE4B_ENST00000343090.6_Missense_Mutation_p.I769V					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CCACCTCTCTATTCTGCCTAG	0.507																																					p.I769V		Atlas-SNP	.											.	UBE4B	233	.	0			c.A2305G						.						169	147	154					1																	10197205		2203	4300	6503	SO:0001583	missense	10277	exon17			CTCTCTATTCTGC	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.1918A>G	chr1.hg19:g.10197205A>G	ENSP00000253251:p.Ile640Val	205.0	0.0		85.0	38.0	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	A	17.78	3.473422	0.63737	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.42131	0.98;0.98;0.98	5.71	4.59	0.56863	Ubiquitin conjugation factor E4, core (1);	0.044914	0.85682	N	0.000000	T	0.31199	0.0789	L	0.37850	1.14	0.58432	D	0.999996	B;P;B	0.38922	0.276;0.651;0.234	B;B;B	0.37091	0.223;0.241;0.143	T	0.03597	-1.1021	10	0.20046	T	0.44	-15.8731	11.3889	0.49802	0.9295:0.0:0.0705:0.0	.	640;769;640	A8K8S9;O95155;O95155-2	.;UBE4B_HUMAN;.	V	640;524;769	ENSP00000253251:I640V;ENSP00000366362:I524V;ENSP00000343001:I769V	ENSP00000253251:I640V	I	+	1	0	UBE4B	10119792	1.000000	0.71417	0.985000	0.45067	0.996000	0.88848	7.473000	0.81007	1.009000	0.39289	0.533000	0.62120	ATT	.	.		0.507	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		G	10197205	A	G	10197205	3	3	50	1	0	0	0	0	1	0	0	0	16898	449	16	2	2371	2	UBE4B	1	10197205	Missense_Mutation	SNP	A	TCGA-BD-A3ER-01A-11D-A20W-10		10197205	239053416	1	6472										
KIAA1522	57648	hgsc.bcm.edu	37	chr1	33235826	33235826	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gtccatctccccccaggccaCctacctgtcgaagttgattc	7	17	1	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr1:33235826C>A	ENST00000373480.1	+	6	972	c.869C>A	c.(868-870)aCc>aAc	p.T290N	KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000373481.3_Missense_Mutation_p.T301N|KIAA1522_ENST00000401073.2_Missense_Mutation_p.T349N	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	290										breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				CCCCAGGCCACCTACCTGTCG	0.657																																					p.T349N		Atlas-SNP	.											.	KIAA1522	68	.	0			c.C1046A						.						43	46	45					1																	33235826		2041	4164	6205	SO:0001583	missense	57648	exon6			AGGCCACCTACCT	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.869C>A	chr1.hg19:g.33235826C>A	ENSP00000362579:p.Thr290Asn	113.0	0.0		76.0	33.0	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	hg19	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.325896	0.60743	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.29397	1.57;1.57;1.57	4.39	4.39	0.52855	.	0.000000	0.64402	D	0.000007	T	0.51702	0.1690	L	0.55481	1.735	0.51233	D	0.999911	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.81914	0.993;0.993;0.995	T	0.56962	-0.7892	10	0.87932	D	0	-17.2801	17.328	0.87255	0.0:1.0:0.0:0.0	.	301;290;349	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	N	349;301;290	ENSP00000383851:T349N;ENSP00000362580:T301N;ENSP00000362579:T290N	ENSP00000362579:T290N	T	+	2	0	KIAA1522	33008413	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.359000	0.79477	2.145000	0.66743	0.491000	0.48974	ACC	.	.		0.657	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			A	33235826	C	A	33235826	3	1	50	1	0	0	0	0	1	0	0	0	8247	507	18	3	1068	3	KIAA1522	1	33235826	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	23038621	33235826	216014795	2	6473										
CCDC18	343099	hgsc.bcm.edu	37	chr1	93687490	93687490	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	caagtatctgaagaaacaatCaaggctagtatgctaatact	7	7	2	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr1:93687490C>T	ENST00000343253.7	+	16	2671	c.2169C>T	c.(2167-2169)atC>atT	p.I723I	CCDC18_ENST00000334652.5_Silent_p.I19I|CCDC18_ENST00000421014.2_3'UTR|CCDC18_ENST00000401026.3_Silent_p.I724I|CCDC18_ENST00000557479.1_Silent_p.I842I|CCDC18_ENST00000338949.4_Silent_p.I479I			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	723										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		AAGAAACAATCAAGGCTAGTA	0.313																																					p.I724I		Atlas-SNP	.											.	CCDC18	93	.	0			c.C2172T						.						43	42	42					1																	93687490		1810	4072	5882	SO:0001819	synonymous_variant	343099	exon16			AACAATCAAGGCT			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.2169C>T	chr1.hg19:g.93687490C>T		268.0	0.0		137.0	28.0	NM_206886	Q6ZU17	Silent	SNP	ENST00000343253.7	hg19		.	.	.	.	.	.	.	.	.	.	C	10.55	1.380919	0.24944	.	.	ENSG00000122483	ENST00000370276	.	.	.	5.11	1.92	0.25849	.	.	.	.	.	T	0.37892	0.1020	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30679	-0.9970	4	.	.	.	.	5.0887	0.14696	0.1512:0.6191:0.1467:0.0831	.	.	.	.	L	777	.	.	S	+	2	0	CCDC18	93460078	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.712000	0.25779	1.213000	0.43380	0.555000	0.69702	TCA	.	.		0.313	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		T	93687490	C	T	93687490	2	4	50	1	0	0	0	0	0	0	0	1	2796	816	29	3		3	CCDC18	1	93687490	Silent	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	60451664	93687490	155563131	3	6474										
NTRK1	4914	hgsc.bcm.edu	37	chr1	156851414	156851414	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tggcccaggcacctcctgtcTacctggatgtcctgggctag	12	14	1	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr1:156851414T>A	ENST00000524377.1	+	17	2412	c.2371T>A	c.(2371-2373)Tac>Aac	p.Y791N	NTRK1_ENST00000392302.2_Missense_Mutation_p.Y755N|NTRK1_ENST00000358660.3_Missense_Mutation_p.Y788N|NTRK1_ENST00000368196.3_Missense_Mutation_p.Y785N|NTRK1_ENST00000531606.1_3'UTR	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	791		Interaction with PLCG1.			activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	ACCTCCTGTCTACCTGGATGT	0.692			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.Y791N		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1	287	.	0			c.T2371A						.						16	18	17					1																	156851414		2202	4298	6500	SO:0001583	missense	4914	exon17			CCTGTCTACCTGG	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.2371T>A	chr1.hg19:g.156851414T>A	ENSP00000431418:p.Tyr791Asn	131.0	0.0		161.0	23.0	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	hg19	CCDS1161.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.654632	0.88056	.	.	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	T;T;T;T	0.79247	-1.21;-1.22;-1.25;-1.24	5.01	5.01	0.66863	.	0.000000	0.56097	D	0.000035	D	0.88351	0.6413	M	0.91663	3.23	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	1.0;0.984;0.998;0.999	D	0.90951	0.4805	10	0.87932	D	0	.	13.6968	0.62585	0.0:0.0:0.0:1.0	.	788;785;791;755	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	N	755;785;791;788	ENSP00000376120:Y755N;ENSP00000357179:Y785N;ENSP00000431418:Y791N;ENSP00000351486:Y788N	ENSP00000351486:Y788N	Y	+	1	0	NTRK1	155118038	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.816000	0.86201	2.107000	0.64212	0.533000	0.62120	TAC	.	.		0.692	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		A	156851414	T	A	156851414	3	1	50	1	0	0	0	0	1	0	0	0	10715	1522	53	4	2567	4	NTRK1	1	156851414	Missense_Mutation	SNP	T	TCGA-BD-A3ER-01A-11D-A20W-10	63163924	156851414	92399207	4	6475										
CAMK1G	57172	hgsc.bcm.edu	37	chr1	209785182	209785182	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tgcaccacatgaggaagctaCacatgaacctgcacagcccg	9	14	0	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr1:209785182C>T	ENST00000009105.1	+	11	1206	c.961C>T	c.(961-963)Cac>Tac	p.H321Y	CAMK1G_ENST00000361322.2_Missense_Mutation_p.H321Y|CAMK1G_ENST00000494990.1_3'UTR			Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	321						calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|central_nervous_system(1)|large_intestine(8)|lung(8)|stomach(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		GAGGAAGCTACACATGAACCT	0.592																																					p.H321Y	Ovarian(163;530 1939 9680 28669 48710)	Atlas-SNP	.											.	CAMK1G	49	.	0			c.C961T						.						97	102	100					1																	209785182		2203	4300	6503	SO:0001583	missense	57172	exon11			AAGCTACACATGA		CCDS1486.1	1q32.2	2012-09-20			ENSG00000008118	ENSG00000008118			14585	protein-coding gene	gene with protein product		614994				12637513	Standard	NM_020439		Approved	VWS1, CLICKIII, dJ272L16.1	uc001hhd.3	Q96NX5	OTTHUMG00000036361	ENST00000009105.1:c.961C>T	chr1.hg19:g.209785182C>T	ENSP00000009105:p.His321Tyr	77.0	0.0		93.0	31.0	NM_020439	Q86UH5|Q9Y3J7	Missense_Mutation	SNP	ENST00000009105.1	hg19	CCDS1486.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.481968	0.63849	.	.	ENSG00000008118	ENST00000009105;ENST00000361322	T;T	0.68624	-0.34;-0.34	5.46	5.46	0.80206	Protein kinase-like domain (1);	0.284775	0.27181	N	0.020558	T	0.60818	0.2298	L	0.29908	0.895	0.51233	D	0.999915	B;B	0.29378	0.243;0.091	B;B	0.32211	0.142;0.091	T	0.61327	-0.7085	10	0.62326	D	0.03	.	19.4053	0.94646	0.0:1.0:0.0:0.0	.	321;321	Q96NX5-2;Q96NX5	.;KCC1G_HUMAN	Y	321	ENSP00000009105:H321Y;ENSP00000354861:H321Y	ENSP00000009105:H321Y	H	+	1	0	CAMK1G	207851805	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	5.081000	0.64444	2.579000	0.87056	0.558000	0.71614	CAC	.	.		0.592	CAMK1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088526.1	NM_020439		T	209785182	C	T	209785182	3	4	50	1	0	0	0	0	1	0	0	0	2600	478	17	3	999	3	CAMK1G	1	209785182	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	52933768	209785182	39465439	5	6476										
SLC30A10	55532	hgsc.bcm.edu	37	chr1	220101274	220101274	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gcgggtcctccgcgccctgaGgccccccgaaagcgccgggg	16	18	0	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr1:220101274G>T	ENST00000366926.3	-	1	670	c.509C>A	c.(508-510)cCt>cAt	p.P170H	SLC30A10_ENST00000536446.1_Intron|SLC30A10_ENST00000536992.1_Missense_Mutation_p.P170H	NM_018713.2	NP_061183.2	Q6XR72	ZNT10_HUMAN	solute carrier family 30, member 10	170					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	13				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)		CGCGCCCTGAGGCCCCCCGAA	0.766																																					p.P170H	Colon(76;360 1614 43677 51136)	Atlas-SNP	.											.	SLC30A10	58	.	0			c.C509A						.						4	5	5					1																	220101274		1963	3737	5700	SO:0001583	missense	55532	exon1			CCCTGAGGCCCCC	AY212919	CCDS31026.1	1q41	2013-05-22			ENSG00000196660	ENSG00000196660		"Solute carriers"	25355	protein-coding gene	gene with protein product	"zinc transporter 8"	611146				15154973	Standard	NR_046437		Approved	DKFZp547M236, ZnT-10, ZRC1, ZNT8	uc001hlw.3	Q6XR72	OTTHUMG00000037434	ENST00000366926.3:c.509C>A	chr1.hg19:g.220101274G>T	ENSP00000355893:p.Pro170His	0.0	0.0		11.0	9.0	NM_018713	Q49AL9|Q9NPW0	Missense_Mutation	SNP	ENST00000366926.3	hg19	CCDS31026.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.180964	0.57800	.	.	ENSG00000196660	ENST00000366926;ENST00000536992	T;T	0.79454	-0.07;-1.27	3.86	0.652	0.17823	.	0.942960	0.08699	N	0.906735	T	0.51126	0.1656	N	0.00566	-1.37	0.09310	N	1	P	0.47191	0.891	P	0.51415	0.669	T	0.47459	-0.9116	9	.	.	.	-11.3218	3.676	0.08292	0.4156:0.189:0.3954:0.0	.	170	Q6XR72	ZNT10_HUMAN	H	170	ENSP00000355893:P170H;ENSP00000440627:P170H	.	P	-	2	0	SLC30A10	218167897	0.001000	0.12720	0.003000	0.11579	0.005000	0.04900	0.292000	0.19011	0.407000	0.25591	-0.218000	0.12543	CCT	.	.		0.766	SLC30A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357709.1	NM_018713		T	220101274	G	T	220101274	3	4	50	1	0	0	0	0	1	0	0	0	14569	1000	35	3	964	3	SLC30A10	1	220101274	Missense_Mutation	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10	10316092	220101274	29149347	6	6477										
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233122171	233122171	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	agctcgtgcactgaggtggaCgtctggaggaatgtttggcg	17	7	1	1	rs371436171		TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr1:233122171C>A	ENST00000258229.9	-	33	6141	c.5907G>T	c.(5905-5907)acG>acT	p.T1969T	PCNXL2_ENST00000344698.2_Silent_p.T621T	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1969	Ser-rich.					integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CTGAGGTGGACGTCTGGAGGA	0.662																																					p.T1969T		Atlas-SNP	.											.	PCNXL2	204	.	0			c.G5907T						.						20	27	25					1																	233122171		2056	4186	6242	SO:0001819	synonymous_variant	80003	exon33			GGTGGACGTCTGG	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.5907G>T	chr1.hg19:g.233122171C>A		153.0	0.0		172.0	60.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Silent	SNP	ENST00000258229.9	hg19	CCDS44335.1																																																																																			.	.		0.662	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		A	233122171	C	A	233122171	2	1	50	1	0	0	0	0	0	0	0	1	11601	523	19	1		1	PCNXL2	1	233122171	Silent	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	13020897	233122171	16128450	7	6478										
HNRPLL	92906	hgsc.bcm.edu	37	chr2	38812823	38812825	+	In_Frame_Del	DEL	AGA	AGA	-													0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gcggattctgaattgagagcAgaagaactttgttgcctcct							TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr2:38812823_38812825delAGA	ENST00000449105.3	-	3	846_848	c.507_509delTCT	c.(505-510)cttctg>ctg	p.169_170LL>L	HNRNPLL_ENST00000378915.3_In_Frame_Del_p.169_170LL>L|HNRNPLL_ENST00000608859.1_In_Frame_Del_p.169_170LL>L|HNRNPLL_ENST00000409636.1_In_Frame_Del_p.164_165LL>L|HNRNPLL_ENST00000409328.1_In_Frame_Del_p.169_170LL>L|HNRNPLL_ENST00000358367.4_In_Frame_Del_p.169_170LL>L|HNRNPLL_ENST00000410076.1_In_Frame_Del_p.164_165LL>L			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	169	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										AATTGAGAGCAGAAGAACTTTGT	0.384																																					p.170_170del		Atlas-Indel,Pindel	.											.	HNRPLL	19	.	0			c.508_510del						.																																			SO:0001651	inframe_deletion	92906	exon3			.	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"RNA binding motif (RRM) containing"	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.507_509delTCT	chr2.hg19:g.38812826_38812828delAGA	ENSP00000390625:p.Leu171del	182.0	0.0		116.0	32.0	NM_138394	Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	In_Frame_Del	DEL	ENST00000449105.3	hg19																																																																																				.	.		0.384	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394		-	38812825	AGA	-	38812823	7	5	50	1	0	1	0	1	0	0	0	0	7286	188	7	0	1163	0	HNRPLL	2	38812823	In_Frame_Del	DEL	AGA	TCGA-BD-A3ER-01A-11D-A20W-10		38812823	204386550	8	6479										
DYSF	8291	hgsc.bcm.edu	37	chr2	71871124	71871124	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ttcatcgattggtggagcaaAttctttgcctccatagggga	11	8	2	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr2:71871124A>G	ENST00000258104.3	+	41	4717	c.4440A>G	c.(4438-4440)aaA>aaG	p.K1480K	DYSF_ENST00000429174.2_Silent_p.K1501K|DYSF_ENST00000409651.1_Silent_p.K1512K|DYSF_ENST00000410041.1_Silent_p.K1498K|DYSF_ENST00000409762.1_Silent_p.K1497K|DYSF_ENST00000413539.2_Silent_p.K1511K|DYSF_ENST00000409366.1_Silent_p.K1502K|DYSF_ENST00000409744.1_Silent_p.K1488K|DYSF_ENST00000394120.2_Silent_p.K1481K|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000410020.3_Silent_p.K1519K|DYSF_ENST00000409582.3_Silent_p.K1518K	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1480					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GGTGGAGCAAATTCTTTGCCT	0.493																																					p.K1519K		Atlas-SNP	.											.	DYSF	536	.	0			c.A4557G						.						98	81	87					2																	71871124		2203	4300	6503	SO:0001819	synonymous_variant	8291	exon42			GAGCAAATTCTTT	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4440A>G	chr2.hg19:g.71871124A>G		227.0	0.0		165.0	37.0	NM_001130987	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	hg19	CCDS1918.1																																																																																			.	.		0.493	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		G	71871124	A	G	71871124	2	3	50	1	0	0	0	0	0	0	0	1	4861	98	4	2		2	DYSF	2	71871124	Silent	SNP	A	TCGA-BD-A3ER-01A-11D-A20W-10	33058301	71871124	171328249	9	6480										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168101985	168101985	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gaaacaaagccattagactcTattaataaatcagaaactgt	5	7	2	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr2:168101985T>C	ENST00000409195.1	+	9	4172	c.4083T>C	c.(4081-4083)tcT>tcC	p.S1361S	XIRP2_ENST00000295237.9_Silent_p.S1361S|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Silent_p.S1139S|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1186					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CATTAGACTCTATTAATAAAT	0.368																																					p.S1361S		Atlas-SNP	.											.	XIRP2	914	.	0			c.T4083C						.						67	63	65					2																	168101985		1845	4088	5933	SO:0001819	synonymous_variant	129446	exon9			AGACTCTATTAAT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.4083T>C	chr2.hg19:g.168101985T>C		157.0	0.0		90.0	4.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.368	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		C	168101985	T	C	168101985	2	2	50	1	0	0	0	0	0	0	0	1	17445	1509	53	2		2	XIRP2	2	168101985	Silent	SNP	T	TCGA-BD-A3ER-01A-11D-A20W-10	96230861	168101985	75097388	10	6481										
LRP2	4036	hgsc.bcm.edu	37	chr2	170076975	170076975	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	aatactcacccacgagcaggAtcaacagttatgccaattgg	8	11	2	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr2:170076975A>G	ENST00000263816.3	-	34	5922	c.5637T>C	c.(5635-5637)gaT>gaC	p.D1879D		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1879					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CACGAGCAGGATCAACAGTTA	0.418																																					p.D1879D		Atlas-SNP	.											.	LRP2	751	.	0			c.T5637C						.						131	115	120					2																	170076975		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon34			AGCAGGATCAACA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.5637T>C	chr2.hg19:g.170076975A>G		148.0	0.0		79.0	7.0	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.		0.418	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170076975	A	G	170076975	2	3	50	1	0	0	0	0	0	0	0	1	8965	330	12	2		2	LRP2	2	170076975	Silent	SNP	A	TCGA-BD-A3ER-01A-11D-A20W-10	1974990	170076975	73122398	11	6482										
TTN	7273	hgsc.bcm.edu	37	chr2	179453288	179453288	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tggggtcttttgccaccaccGgtcttgaaggcaagcttggt	13	10	2	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr2:179453288G>T	ENST00000591111.1	-	254	58465	c.58241C>A	c.(58240-58242)cCg>cAg	p.P19414Q	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P12182Q|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P12115Q|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P11990Q|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P18487Q|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P21055Q|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19414	Fibronectin type-III 40. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCCACCACCGGTCTTGAAGG	0.403																																					p.P21055Q		Atlas-SNP	.											.	TTN	18412	.	0			c.C63164A						.						209	195	199					2																	179453288		1882	4110	5992	SO:0001583	missense	7273	exon304			ACCACCGGTCTTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.58241C>A	chr2.hg19:g.179453288G>T	ENSP00000465570:p.Pro19414Gln	236.0	0.0		138.0	41.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.77	2.633463	0.47049	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	6.16	6.16	0.99307	Fibronectin, type III (3);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.75236	0.3822	M	0.87456	2.885	0.58432	D	0.999999	D;D;D;D	0.61080	0.989;0.989;0.989;0.989	P;P;P;P	0.58013	0.831;0.831;0.831;0.831	T	0.77950	-0.2395	9	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	11990;12115;12182;19414	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	18487;11990;12182;12115;11988	ENSP00000343764:P18487Q;ENSP00000434586:P11990Q;ENSP00000340554:P12182Q;ENSP00000352154:P12115Q	ENSP00000340554:P12182Q	P	-	2	0	TTN	179161534	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.807000	0.99171	2.937000	0.99478	0.650000	0.86243	CCG	.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179453288	G	T	179453288	3	4	50	1	0	0	0	0	1	0	0	0	16750	1116	39	1	45051	1	TTN	2	179453288	Missense_Mutation	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10	9376313	179453288	63746085	12	6483										
FN1	2335	hgsc.bcm.edu	37	chr2	216271096	216271096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gctgatgggcagcctctgccCgtgctcgccaggcaggttga	15	13	1	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr2:216271096C>T	ENST00000359671.1	-	19	3116	c.2851G>A	c.(2851-2853)Ggg>Agg	p.G951R	FN1_ENST00000354785.4_Missense_Mutation_p.G951R|FN1_ENST00000357867.4_Missense_Mutation_p.G951R|FN1_ENST00000336916.4_Missense_Mutation_p.G951R|FN1_ENST00000346544.3_Missense_Mutation_p.G951R|FN1_ENST00000357009.2_Missense_Mutation_p.G951R|FN1_ENST00000421182.1_Missense_Mutation_p.G951R|FN1_ENST00000345488.5_Missense_Mutation_p.G951R|FN1_ENST00000446046.1_Missense_Mutation_p.G951R|FN1_ENST00000443816.1_Missense_Mutation_p.G951R|FN1_ENST00000356005.4_Missense_Mutation_p.G951R|FN1_ENST00000323926.6_Missense_Mutation_p.G951R|FN1_ENST00000432072.2_Missense_Mutation_p.G951R			P02751	FINC_HUMAN	fibronectin 1	951	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	AGCCTCTGCCCGTGCTCGCCA	0.587																																					p.G951R		Atlas-SNP	.											.	FN1	521	.	0			c.G2851A						.						65	61	63					2																	216271096		2203	4300	6503	SO:0001583	missense	2335	exon19			TCTGCCCGTGCTC		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.2851G>A	chr2.hg19:g.216271096C>T	ENSP00000352696:p.Gly951Arg	84.0	0.0		93.0	32.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.287730	0.95517	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42	6.03	6.03	0.97812	.	0.091260	0.47093	D	0.000247	T	0.63010	0.2475	L	0.31065	0.9	0.80722	D	1	D;D;D;D;D;P;D;D;D;D	0.89917	1.0;0.98;0.998;1.0;1.0;0.946;1.0;1.0;1.0;1.0	D;P;D;D;D;P;D;D;D;D	0.97110	0.995;0.593;0.927;1.0;0.997;0.507;1.0;1.0;1.0;1.0	T	0.53330	-0.8454	10	0.19147	T	0.46	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	951;951;951;951;951;951;951;951;951;951	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	R	951	ENSP00000394423:G951R;ENSP00000323534:G951R;ENSP00000338200:G951R;ENSP00000350534:G951R;ENSP00000346839:G951R;ENSP00000352696:G951R;ENSP00000265312:G951R;ENSP00000273049:G951R;ENSP00000349509:G951R;ENSP00000410422:G951R;ENSP00000415018:G951R;ENSP00000399538:G951R;ENSP00000348285:G951R	ENSP00000265313:G951R	G	-	1	0	FN1	215979341	0.991000	0.36638	0.322000	0.25334	0.994000	0.84299	4.181000	0.58303	2.861000	0.98227	0.655000	0.94253	GGG	.	.		0.587	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216271096	C	T	216271096	3	4	50	1	0	0	0	0	1	0	0	0	5970	652	23	1	4694	1	FN1	2	216271096	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	36817808	216271096	26928277	13	6484										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222290820	222290821	+	Frame_Shift_Ins	INS	-	-	T													0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ggacactgctcaaaatcttaINSttctggtgcgtgatggctgt							TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr2:222290820_222290821insT	ENST00000281821.2	-	17	2929_2930	c.2888_2889insA	c.(2887-2889)aatfs	p.N963fs	EPHA4_ENST00000469354.1_5'Flank|EPHA4_ENST00000409938.1_Frame_Shift_Ins_p.N963fs|EPHA4_ENST00000392071.4_Frame_Shift_Ins_p.N912fs|EPHA4_ENST00000409854.1_3'UTR	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	963	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		TCAAAATCTTATTCTGGTGCGT	0.47																																					p.N963fs		Atlas-Indel,Pindel	.											.	EPHA4	263	.	0			c.2889_2890insA						.																																			SO:0001589	frameshift_variant	2043	exon17			.	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.2889dupA	chr2.hg19:g.222290822_222290822dupT	ENSP00000281821:p.Asn963fs	193.0	0.0		155.0	37.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Frame_Shift_Ins	INS	ENST00000281821.2	hg19	CCDS2447.1																																																																																			.	.		0.47	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222290821	-	T	222290820	7	5	50	1	0	1	1	0	0	0	0	0	5171	446	16	0	75	0	EPHA4	2	222290820	Frame_Shift_Ins	INS	-	TCGA-BD-A3ER-01A-11D-A20W-10	6019724	222290820	20908553	14	6485										
C3orf33	285315	hgsc.bcm.edu	37	chr3	155493583	155493583	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	taatcgtccacgtagtttaaCatttcttcttataaattcta	3	8	3	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr3:155493583C>T	ENST00000340171.2	-	3	327	c.229G>A	c.(229-231)Gtt>Att	p.V77I	C3orf33_ENST00000534941.1_Missense_Mutation_p.V34I			Q6P1S2	CC033_HUMAN	chromosome 3 open reading frame 33	77					negative regulation of ERK1 and ERK2 cascade (GO:0070373)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)			breast(1)|kidney(1)|large_intestine(3)|lung(3)	8			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CGTAGTTTAACATTTCTTCTT	0.299																																					p.V34I		Atlas-SNP	.											.	C3orf33	18	.	0			c.G100A						.						98	97	97					3																	155493583		1803	4058	5861	SO:0001583	missense	285315	exon4			GTTTAACATTTCT	AF115515	CCDS54659.1	3q25.31	2012-10-31			ENSG00000174928	ENSG00000174928			26434	protein-coding gene	gene with protein product						20680465	Standard	NM_173657		Approved	FLJ31139, AC3-33	uc003fal.1	Q6P1S2	OTTHUMG00000158496	ENST00000340171.2:c.229G>A	chr3.hg19:g.155493583C>T	ENSP00000342512:p.Val77Ile	181.0	0.0		95.0	19.0	NM_173657	A8K1H5|Q86YE6|Q8IXA7|Q96NB5	Missense_Mutation	SNP	ENST00000340171.2	hg19		.	.	.	.	.	.	.	.	.	.	C	14.99	2.700126	0.48307	.	.	ENSG00000174928	ENST00000534941;ENST00000340171;ENST00000537385	T;T	0.46451	0.87;0.87	5.45	4.58	0.56647	.	0.134283	0.50627	D	0.000114	T	0.53110	0.1776	L	0.48642	1.525	0.33971	D	0.646824	D	0.76494	0.999	D	0.66497	0.944	T	0.62576	-0.6825	10	0.29301	T	0.29	-4.7845	13.0044	0.58696	0.0:0.921:0.0:0.079	.	77	Q6P1S2	CC033_HUMAN	I	34;77;77	ENSP00000445446:V34I;ENSP00000342512:V77I	ENSP00000342512:V77I	V	-	1	0	C3orf33	156976277	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	3.477000	0.53151	1.298000	0.44778	0.655000	0.94253	GTT	.	.		0.299	C3orf33-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351167.1	NM_173657		T	155493583	C	T	155493583	3	4	50	1	0	0	0	0	1	0	0	0	2225	478	17	3	667	3	C3orf33	3	155493583	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10		155493583	42528847	15	6486										
SI	6476	hgsc.bcm.edu	37	chr3	164754186	164754186	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ttcagacttacctttagtttCtccatcatcccagaaaaagt	4	11	3	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr3:164754186C>T	ENST00000264382.3	-	22	2568	c.2506G>A	c.(2506-2508)Gaa>Aaa	p.E836K		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	836	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	CCTTTAGTTTCTCCATCATCC	0.348										HNSCC(35;0.089)																											p.E836K		Atlas-SNP	.											.	SI	500	.	0			c.G2506A						.						114	116	115					3																	164754186		2203	4299	6502	SO:0001583	missense	6476	exon22			TAGTTTCTCCATC	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.2506G>A	chr3.hg19:g.164754186C>T	ENSP00000264382:p.Glu836Lys	142.0	0.0		86.0	21.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	hg19	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.431714	0.62844	.	.	ENSG00000090402	ENST00000264382	D	0.90261	-2.64	4.52	4.52	0.55395	.	0.055638	0.64402	D	0.000001	D	0.89567	0.6752	M	0.77712	2.385	0.44067	D	0.996813	B	0.28378	0.209	B	0.29862	0.108	D	0.88537	0.3107	10	0.59425	D	0.04	.	10.1817	0.42972	0.0:0.9063:0.0:0.0937	.	836	P14410	SUIS_HUMAN	K	836	ENSP00000264382:E836K	ENSP00000264382:E836K	E	-	1	0	SI	166236880	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.974000	0.63771	2.484000	0.83849	0.650000	0.86243	GAA	.	.		0.348	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		T	164754186	C	T	164754186	3	4	50	1	0	0	0	0	1	0	0	0	14312	922	32	3	3085	3	SI	3	164754186	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	9260603	164754186	33268244	16	6487										
TRIM2	23321	hgsc.bcm.edu	37	chr4	154214187	154214187	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gccatgtgtcgggagtgcacGgagggggagcacgcagagca	19	9	0	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr4:154214187G>A	ENST00000437508.2	+	4	627	c.426G>A	c.(424-426)acG>acA	p.T142T	TRIM2_ENST00000338700.5_Silent_p.T169T|TRIM2_ENST00000494872.1_3'UTR	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	142					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		GGGAGTGCACGGAGGGGGAGC	0.557																																					p.T169T		Atlas-SNP	.											.	TRIM2	105	.	0			c.G507A						.						63	54	57					4																	154214187		2203	4300	6503	SO:0001819	synonymous_variant	23321	exon4			GTGCACGGAGGGG	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15974	protein-coding gene	gene with protein product		614141	"tripartite motif-containing 2"			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.426G>A	chr4.hg19:g.154214187G>A		179.0	0.0		110.0	32.0	NM_015271	D3DP09|O60272|Q9BSI9|Q9UFZ1	Silent	SNP	ENST00000437508.2	hg19	CCDS47147.1																																																																																			.	.		0.557	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1			A	154214187	G	A	154214187	2	1	50	1	0	0	0	0	0	0	0	1	16509	1103	39	1		1	TRIM2	4	154214187	Silent	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10		154214187	36940089	17	6488										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183664409	183664409	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tcatgggcaatgggcgaaggCgcagcatttcctgccccagt	13	12	1	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr4:183664409C>T	ENST00000511685.1	+	19	3589	c.3466C>T	c.(3466-3468)Cgc>Tgc	p.R1156C	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.R1156C			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1156					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TGGGCGAAGGCGCAGCATTTC	0.522																																					p.R1156C		Atlas-SNP	.											.	.	.	.	0			c.C3466T						.						77	80	79					4																	183664409		2040	4197	6237	SO:0001583	missense	55714	exon18			CGAAGGCGCAGCA	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.3466C>T	chr4.hg19:g.183664409C>T	ENSP00000424226:p.Arg1156Cys	139.0	0.0		135.0	43.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332184	0.81801	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.91011	-2.77;-2.77	5.45	5.45	0.79879	.	.	.	.	.	D	0.96030	0.8707	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.96158	0.9113	9	0.87932	D	0	.	19.4688	0.94954	0.0:1.0:0.0:0.0	.	1156	Q9P273	TEN3_HUMAN	C	1156	ENSP00000424226:R1156C;ENSP00000385276:R1156C	ENSP00000385276:R1156C	R	+	1	0	ODZ3	183901403	1.000000	0.71417	0.997000	0.53966	0.894000	0.52154	3.770000	0.55310	2.838000	0.97847	0.561000	0.74099	CGC	.	.		0.522	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183664409	C	T	183664409	3	4	50	1	0	0	0	0	1	0	0	0	10845	768	27	1	3536	1	ODZ3	4	183664409	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	29450222	183664409	7489867	18	6489										
NPR3	4883	hgsc.bcm.edu	37	chr5	32724927	32724927	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	cttcaacagctcttcctatgGtaactctgcttccactttcc	4	15	3	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr5:32724927G>T	ENST00000265074.8	+	2	1235		c.e2+1		NPR3_ENST00000434067.2_Splice_Site|NPR3_ENST00000415685.2_Splice_Site|NPR3_ENST00000415167.2_Splice_Site	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	TCTTCCTATGGTAACTCTGCT	0.498																																					.		Atlas-SNP	.											.	NPR3	65	.	0			c.244+1G>T						.						182	189	187					5																	32724927		2154	4261	6415	SO:0001630	splice_region_variant	4883	exon2			CCTATGGTAACTC		CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"guanylate cyclase C"	108962	"chromosome 5 open reading frame 23", "atrionatriuretic peptide receptor C", "natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)", "natriuretic peptide receptor C"	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.892+1G>T	chr5.hg19:g.32724927G>T		234.0	0.0		173.0	36.0	NM_001204376	A2RRD1|B4DT84|E7EPG9	Splice_Site	SNP	ENST00000265074.8	hg19	CCDS56357.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.604504	0.87157	.	.	ENSG00000113389	ENST00000509104;ENST00000434067;ENST00000415685;ENST00000265074;ENST00000415167	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7103	0.91653	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NPR3	32760684	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	8.553000	0.90686	2.472000	0.83506	0.655000	0.94253	.	.	.		0.498	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908	Intron	T	32724927	G	T	32724927	5	4	50	1	0	0	0	0	0	0	1	0	10605	1275	44	3	899	3	NPR3	5	32724927	Splice_Site	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10		32724927	148190333	19	6490										
GABRB2	2561	hgsc.bcm.edu	37	chr5	160721290	160721290	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ggccaaaactatgcctgggcAacccagctttccgatactgg	10	13	0	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr5:160721290A>T	ENST00000393959.1	-	10	1336	c.1337T>A	c.(1336-1338)tTg>tAg	p.L446*	GABRB2_ENST00000274547.2_Nonsense_Mutation_p.L446*|GABRB2_ENST00000517901.1_Nonsense_Mutation_p.L345*|GABRB2_ENST00000353437.6_Nonsense_Mutation_p.L408*|GABRB2_ENST00000517547.1_Nonsense_Mutation_p.L248*|GABRB2_ENST00000520240.1_Nonsense_Mutation_p.L408*			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	446					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ATGCCTGGGCAACCCAGCTTT	0.527																																					p.L446X		Atlas-SNP	.											.	GABRB2	161	.	0			c.T1337A						.						106	95	99					5																	160721290		2203	4300	6503	SO:0001587	stop_gained	2561	exon11			CTGGGCAACCCAG		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.1337T>A	chr5.hg19:g.160721290A>T	ENSP00000377531:p.Leu446*	231.0	0.0		135.0	39.0	NM_021911	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Nonsense_Mutation	SNP	ENST00000393959.1	hg19	CCDS4355.1	.	.	.	.	.	.	.	.	.	.	A	37	6.062430	0.97246	.	.	ENSG00000145864	ENST00000393959;ENST00000274547;ENST00000353437;ENST00000520240;ENST00000517901;ENST00000517547	.	.	.	5.49	5.49	0.81192	.	0.246852	0.24136	N	0.041210	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06757	T	0.87	.	15.5792	0.76418	1.0:0.0:0.0:0.0	.	.	.	.	X	446;446;408;408;345;248	.	ENSP00000274547:L446X	L	-	2	0	GABRB2	160653868	0.989000	0.36119	0.733000	0.30861	0.879000	0.50718	6.989000	0.76219	2.086000	0.62901	0.528000	0.53228	TTG	.	.		0.527	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1			T	160721290	A	T	160721290	4	4	50	1	0	0	0	0	0	1	0	0	6175	131	5	4	205	4	GABRB2	5	160721290	Nonsense_Mutation	SNP	A	TCGA-BD-A3ER-01A-11D-A20W-10	127996363	160721290	20193970	20	6491										
ZKSCAN4	387032	hgsc.bcm.edu	37	chr6	28219692	28219693	+	Silent	DNP	GG	GG	AT													0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	cttctccaccttcacggtcaGgagccccgtctggtcttctg							TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr6:28219692_28219693GG>AT	ENST00000377294.2	-	1	309_310	c.66_67CC>AT	c.(64-69)ctCCtg>ctATtg	p.22_23LL>LL	ZKSCAN4_ENST00000423974.2_Intron	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	22					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						TTCACGGTCAGGAGCCCCGTCT	0.634																																					p.L23L|p.L22L		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.C67T|c.C66A						.																																			SO:0001819	synonymous_variant	387032	exon1			CGGTCAGGAGCCC|GGTCAGGAGCCCC	AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"Zinc fingers, C2H2-type", "-", "-", "-"	13854	protein-coding gene	gene with protein product		611643	"zinc finger protein 307", "zinc finger protein 427"	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.66_67delinsAT	chr6.hg19:g.28219692_28219693delinsAT		91.0	0.0		74.0	21.0|20.0	NM_019110	B2RE32|Q5U7L4	Silent	SNP	ENST00000377294.2	hg19	CCDS4647.1																																																																																			.	.		0.634	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110		AT	28219693	GG	AT	28219692	2	1	50	1	0	0	0	0	0	0	0	1	17704	991	35	3		3	ZKSCAN4	6	28219692	Silent	DNP	GG	TCGA-BD-A3ER-01A-11D-A20W-10		28219692	142895375	21	6492										
UBE2CBP	90025	hgsc.bcm.edu	37	chr6	83728705	83728705	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	aacttacttttcattcctgcTtttgatgcatggctggtaga	8	8	1	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr6:83728705T>C	ENST00000369747.3	-	8	1119	c.997A>G	c.(997-999)Agc>Ggc	p.S333G		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	333					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										TCATTCCTGCTTTTGATGCAT	0.363																																					p.S333G		Atlas-SNP	.											.	.	.	.	0			c.A997G						.						112	111	111					6																	83728705		2203	4300	6503	SO:0001583	missense	90025	exon8			TCCTGCTTTTGAT	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"UBCH10 binding protein with a hect-like domain"	612495	"chromosome 6 open reading frame 157", "ubiquitin-conjugating enzyme E2C binding protein"	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.997A>G	chr6.hg19:g.83728705T>C	ENSP00000358762:p.Ser333Gly	115.0	0.0		71.0	22.0	NM_198920	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	hg19	CCDS34491.1	.	.	.	.	.	.	.	.	.	.	T	8.344	0.829345	0.16749	.	.	ENSG00000118420	ENST00000369747	T	0.31769	1.48	5.92	3.5	0.40072	.	0.363269	0.36134	N	0.002772	T	0.13756	0.0333	L	0.47716	1.5	0.80722	D	1	B;B	0.27013	0.125;0.166	B;B	0.34452	0.183;0.138	T	0.03933	-1.0991	10	0.31617	T	0.26	-5.8907	8.7172	0.34419	0.0:0.1527:0.0:0.8473	.	312;333	C9JRS1;Q7Z6J8	.;UB2CB_HUMAN	G	333	ENSP00000358762:S333G	ENSP00000358762:S333G	S	-	1	0	UBE2CBP	83785424	0.872000	0.30054	0.775000	0.31657	0.012000	0.07955	1.025000	0.30090	0.483000	0.27608	-0.276000	0.10085	AGC	.	.		0.363	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920		C	83728705	T	C	83728705	3	2	50	1	0	0	0	0	1	0	0	0	16862	1609	56	2	184	2	UBE2CBP	6	83728705	Missense_Mutation	SNP	T	TCGA-BD-A3ER-01A-11D-A20W-10	55509013	83728705	87386362	22	6493										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152668272	152668272	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tgcacgttttgtttaagtttCgcttgcaggtggtctgcaca	11	8	1	0	rs148493518	byFrequency	TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr6:152668272C>G	ENST00000367255.5	-	73	12601	c.12000G>C	c.(11998-12000)gcG>gcC	p.A4000A	SYNE1_ENST00000448038.1_Silent_p.A3929A|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000265368.4_Silent_p.A4000A|SYNE1_ENST00000423061.1_Silent_p.A3929A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4000					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GTTTAAGTTTCGCTTGCAGGT	0.473										HNSCC(10;0.0054)																											p.A4000A		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G12000C						.						181	153	163					6																	152668272		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon73			AAGTTTCGCTTGC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.12000G>C	chr6.hg19:g.152668272C>G		209.0	0.0		122.0	29.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	C|0.995;T|0.005		0.473	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152668272	C	G	152668272	2	3	50	1	0	0	0	0	0	0	0	1	15460	871	31	4		4	SYNE1	6	152668272	Silent	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	68939567	152668272	18446795	23	6494										
OGDH	4967	hgsc.bcm.edu	37	chr7	44741215	44741216	+	Splice_Site	INS	-	-	T													0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tttgatgagatgcttccaggINStgggtgtgagggagatgggc							TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr7:44741215_44741216insT	ENST00000222673.5	+	20	2674		c.e20+1		OGDH_ENST00000444676.1_Splice_Site|OGDH_ENST00000449767.1_Splice_Site|OGDH_ENST00000439616.2_Splice_Site|OGDH_ENST00000543843.1_Splice_Site|OGDH_ENST00000447398.1_Splice_Site	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)						2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	ATGCTTCCAGGTGGGTGTGAGG	0.495																																					.		Atlas-Indel,Pindel	.											.	OGDH	145	.	0			c.2632+1->T						.																																			SO:0001630	splice_region_variant	4967	exon20			.	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.2632+1->T	chr7.hg19:g.44741216_44741216dupT		110.0	0.0		76.0	20.0	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Splice_Site	INS	ENST00000222673.5	hg19	CCDS34627.1																																																																																			.	.		0.495	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1		Intron	T	44741216	-	T	44741215	8	5	50	1	0	1	1	0	0	0	1	0	10848	1275	44	0	2880	0	OGDH	7	44741215	Splice_Site	INS	-	TCGA-BD-A3ER-01A-11D-A20W-10		44741215	114397448	24	6495										
PCLO	27445	hgsc.bcm.edu	37	chr7	82585585	82585585	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	atcttcatcagcactcatttCtatgatttgttttcgaatga	5	8	5	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr7:82585585C>T	ENST00000333891.9	-	5	5021	c.4684G>A	c.(4684-4686)Gaa>Aaa	p.E1562K	PCLO_ENST00000423517.2_Missense_Mutation_p.E1562K	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GCACTCATTTCTATGATTTGT	0.428																																					p.E1562K		Atlas-SNP	.											.	PCLO	1506	.	0			c.G4684A						.						153	142	146					7																	82585585		1917	4133	6050	SO:0001583	missense	27445	exon5			TCATTTCTATGAT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.4684G>A	chr7.hg19:g.82585585C>T	ENSP00000334319:p.Glu1562Lys	110.0	0.0		68.0	12.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.732022	0.48939	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.20738	2.05;2.05	5.26	5.26	0.73747	.	.	.	.	.	T	0.29620	0.0739	M	0.73217	2.22	0.80722	D	1	P;P	0.38504	0.634;0.634	B;B	0.36845	0.234;0.234	T	0.17745	-1.0359	9	0.87932	D	0	.	18.8645	0.92285	0.0:1.0:0.0:0.0	.	1562;1562	Q9Y6V0-5;Q9Y6V0-6	.;.	K	1493;1562;1562	ENSP00000334319:E1562K;ENSP00000388393:E1562K	ENSP00000334319:E1562K	E	-	1	0	PCLO	82423521	1.000000	0.71417	0.715000	0.30552	0.997000	0.91878	5.943000	0.70211	2.458000	0.83093	0.655000	0.94253	GAA	.	.		0.428	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82585585	C	T	82585585	3	4	50	1	0	0	0	0	1	0	0	0	11592	922	32	3	10845	3	PCLO	7	82585585	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	37844370	82585585	76553078	25	6496										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84628841	84628841	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tcatttcctgcatgtgcttcCactttgggccccccttgttt	7	14	1	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr7:84628841C>A	ENST00000284136.6	-	17	2292	c.2249G>T	c.(2248-2250)tGg>tTg	p.W750L	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	750	Arg/Lys-rich (basic).				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CATGTGCTTCCACTTTGGGCC	0.488																																					p.W750L	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.G2249T						.						172	142	153					7																	84628841		2203	4300	6503	SO:0001583	missense	223117	exon17			TGCTTCCACTTTG	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.2249G>T	chr7.hg19:g.84628841C>A	ENSP00000284136:p.Trp750Leu	357.0	0.0		232.0	64.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	hg19	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745776	0.49151	.	.	ENSG00000153993	ENST00000284136	T	0.28666	1.6	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.35219	0.0924	M	0.73217	2.22	0.80722	D	1	P	0.36599	0.56	B	0.31547	0.132	T	0.11991	-1.0565	10	0.23891	T	0.37	.	20.3409	0.98764	0.0:1.0:0.0:0.0	.	750	O95025	SEM3D_HUMAN	L	750	ENSP00000284136:W750L	ENSP00000284136:W750L	W	-	2	0	SEMA3D	84466777	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.256000	0.78350	2.814000	0.96858	0.655000	0.94253	TGG	.	.		0.488	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		A	84628841	C	A	84628841	3	1	50	1	0	0	0	0	1	0	0	0	14042	595	21	3	88	3	SEMA3D	7	84628841	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	2043256	84628841	74509822	26	6497										
SPAM1	6677	hgsc.bcm.edu	37	chr7	123599552	123599552	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ttacagaaatcttgcttgctCctagacaattacatggagac	7	9	1	3	rs563527585		TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr7:123599552C>G	ENST00000439500.1	+	6	1672	c.1059C>G	c.(1057-1059)ctC>ctG	p.L353L	SPAM1_ENST00000402183.2_Silent_p.L353L|SPAM1_ENST00000223028.7_Silent_p.L353L|SPAM1_ENST00000340011.5_Silent_p.L353L|SPAM1_ENST00000460182.1_Silent_p.L353L	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	353					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CTTGCTTGCTCCTAGACAATT	0.348																																					p.L353L		Atlas-SNP	.											.	SPAM1	195	.	0			c.C1059G						.						57	55	56					7																	123599552		2203	4300	6503	SO:0001819	synonymous_variant	6677	exon5			CTTGCTCCTAGAC	L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.1059C>G	chr7.hg19:g.123599552C>G		76.0	0.0		49.0	14.0	NM_153189	Q8TC30	Silent	SNP	ENST00000439500.1	hg19	CCDS5791.1																																																																																			.	.		0.348	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			G	123599552	C	G	123599552	2	3	50	1	0	0	0	0	0	0	0	1	15001	842	30	4		4	SPAM1	7	123599552	Silent	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	38970711	123599552	35539111	27	6498										
EPHA1	2041	hgsc.bcm.edu	37	chr7	143094441	143094441	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	cacgctgcctctgctgcctcTgccgctgggctctcctgtgg	12	17	3	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr7:143094441T>A	ENST00000275815.3	-	10	1813	c.1727A>T	c.(1726-1728)cAg>cTg	p.Q576L		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	576					activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				CTGCTGCCTCTGCCGCTGGGC	0.662																																					p.Q576L		Atlas-SNP	.											.	EPHA1	193	.	0			c.A1727T						.						23	16	18					7																	143094441		1992	3862	5854	SO:0001583	missense	2041	exon10			TGCCTCTGCCGCT	M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1727A>T	chr7.hg19:g.143094441T>A	ENSP00000275815:p.Gln576Leu	103.0	0.0		42.0	13.0	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	hg19	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	T	4.980	0.181933	0.09495	.	.	ENSG00000146904	ENST00000275815	T	0.10668	2.85	5.24	-1.5	0.08691	.	1.170610	0.06380	N	0.715114	T	0.05090	0.0136	N	0.05078	-0.115	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41574	-0.9501	10	0.59425	D	0.04	.	4.6158	0.12427	0.1496:0.2942:0.0:0.5562	.	576	P21709	EPHA1_HUMAN	L	576	ENSP00000275815:Q576L	ENSP00000275815:Q576L	Q	-	2	0	EPHA1	142804563	0.000000	0.05858	0.000000	0.03702	0.298000	0.27526	-0.234000	0.09028	-0.212000	0.10109	-0.274000	0.10170	CAG	.	.		0.662	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			A	143094441	T	A	143094441	3	1	50	1	0	0	0	0	1	0	0	0	5167	1580	55	4	1239	4	EPHA1	7	143094441	Missense_Mutation	SNP	T	TCGA-BD-A3ER-01A-11D-A20W-10	19494889	143094441	16044222	28	6499										
UBE3C	9690	hgsc.bcm.edu	37	chr7	156974970	156974970	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	agatgttcaagaaagagtggTggagcaccctggcttttcta	12	7	2	3			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr7:156974970T>C	ENST00000348165.5	+	8	1299	c.939T>C	c.(937-939)ggT>ggC	p.G313G	UBE3C_ENST00000389103.4_Silent_p.G270G	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	313					protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		GAAAGAGTGGTGGAGCACCCT	0.418																																					p.G313G		Atlas-SNP	.											.	UBE3C	124	.	0			c.T939C						.						99	97	98					7																	156974970		2203	4300	6503	SO:0001819	synonymous_variant	9690	exon8			GAGTGGTGGAGCA	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.939T>C	chr7.hg19:g.156974970T>C		314.0	0.0		157.0	43.0	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Silent	SNP	ENST00000348165.5	hg19	CCDS34789.1																																																																																			.	.		0.418	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		C	156974970	T	C	156974970	2	2	50	1	0	0	0	0	0	0	0	1	16896	1683	59	2		2	UBE3C	7	156974970	Silent	SNP	T	TCGA-BD-A3ER-01A-11D-A20W-10	13880529	156974970	2163693	29	6500										
C9orf131	138724	hgsc.bcm.edu	37	chr9	35044763	35044763	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ggagaaatgtgcaacaaagaGaagttccccaaggccccagc	11	11	0	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr9:35044763G>T	ENST00000312292.5	+	2	2184	c.2137G>T	c.(2137-2139)Gaa>Taa	p.E713*	FLJ00273_ENST00000595331.1_5'Flank|C9orf131_ENST00000354479.5_Nonsense_Mutation_p.E640*|C9orf131_ENST00000421362.2_Nonsense_Mutation_p.E665*	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	713										cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			GCAACAAAGAGAAGTTCCCCA	0.572																																					p.E713X		Atlas-SNP	.											.	C9orf131	71	.	0			c.G2137T						.						64	62	63					9																	35044763		2203	4300	6503	SO:0001587	stop_gained	138724	exon2			CAAAGAGAAGTTC	BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.2137G>T	chr9.hg19:g.35044763G>T	ENSP00000308279:p.Glu713*	46.0	0.0		18.0	4.0	NM_203299	A6NLE6|E9PB26|Q86XC6|Q9UF74	Nonsense_Mutation	SNP	ENST00000312292.5	hg19	CCDS6572.2	.	.	.	.	.	.	.	.	.	.	G	35	5.530470	0.96446	.	.	ENSG00000174038	ENST00000421362;ENST00000354479;ENST00000312292;ENST00000435140	.	.	.	3.94	3.04	0.35103	.	0.672301	0.13014	N	0.420636	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-1.91	7.7894	0.29112	0.1131:0.0:0.8869:0.0	.	.	.	.	X	665;640;713;188	.	ENSP00000308279:E713X	E	+	1	0	C9orf131	35034763	0.002000	0.14202	0.027000	0.17364	0.592000	0.36648	0.269000	0.18589	1.246000	0.43901	-0.150000	0.13652	GAA	.	.		0.572	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299		T	35044763	G	T	35044763	4	4	50	1	0	0	0	0	0	1	0	0	2459	943	33	3	2159	3	C9orf131	9	35044763	Nonsense_Mutation	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10		35044763	106168668	30	6501										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137710559	137710559	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gccccatcggcccccaggggGcccctgggaagcccggaccg	15	19	0	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr9:137710559G>T	ENST00000371817.3	+	55	4702	c.4288G>T	c.(4288-4290)Gcc>Tcc	p.A1430S		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1430	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCCCCAGGGGGCCCCTGGGAA	0.701																																					p.A1430S		Atlas-SNP	.											.	COL5A1	323	.	0			c.G4288T						.						11	14	13					9																	137710559		2188	4282	6470	SO:0001583	missense	1289	exon55			CAGGGGGCCCCTG	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4288G>T	chr9.hg19:g.137710559G>T	ENSP00000360882:p.Ala1430Ser	113.0	0.0		90.0	7.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	13.79	2.340866	0.41498	.	.	ENSG00000130635	ENST00000371817	D	0.96104	-3.91	4.89	4.89	0.63831	.	0.239724	0.35151	U	0.003409	D	0.90239	0.6948	N	0.20845	0.615	0.34685	D	0.725133	B	0.14438	0.01	B	0.11329	0.006	D	0.89462	0.3737	10	0.32370	T	0.25	.	13.3043	0.60342	0.0:0.2932:0.7068:0.0	.	1430	P20908	CO5A1_HUMAN	S	1430	ENSP00000360882:A1430S	ENSP00000360882:A1430S	A	+	1	0	COL5A1	136850380	1.000000	0.71417	0.988000	0.46212	0.661000	0.39034	1.795000	0.38784	2.258000	0.74832	0.448000	0.29417	GCC	.	.		0.701	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		T	137710559	G	T	137710559	3	4	50	1	0	0	0	0	1	0	0	0	3698	1203	42	3	4506	3	COL5A1	9	137710559	Missense_Mutation	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10	102665796	137710559	3502872	31	6502										
DDX50	79009	hgsc.bcm.edu	37	chr10	70706314	70706314	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ggaagtcgctcaggaagtcgAcaagatggtagaagacgaag	15	6	1	3			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr10:70706314A>G	ENST00000373585.3	+	15	2249	c.2142A>G	c.(2140-2142)cgA>cgG	p.R714R		NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	714	Arg-rich.					membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						CAGGAAGTCGACAAGATGGTA	0.522																																					p.R714R		Atlas-SNP	.											.	DDX50	65	.	0			c.A2142G						.						74	75	75					10																	70706314		2203	4300	6503	SO:0001819	synonymous_variant	79009	exon15			AAGTCGACAAGAT	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.2142A>G	chr10.hg19:g.70706314A>G		121.0	0.0		72.0	8.0	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Silent	SNP	ENST00000373585.3	hg19	CCDS7283.1																																																																																			.	.		0.522	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		G	70706314	A	G	70706314	2	3	50	1	0	0	0	0	0	0	0	1	4370	262	10	2		2	DDX50	10	70706314	Silent	SNP	A	TCGA-BD-A3ER-01A-11D-A20W-10		70706314	64828433	32	6503										
OR52E6	390078	hgsc.bcm.edu	37	chr11	5863124	5863124	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ctgggtgtcgttagctatagGcattctttctgtcacaaaaa	9	8	3	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr11:5863124G>A	ENST00000329322.5	-	1	3	c.4C>T	c.(4-6)Cct>Tct	p.P2S	TRIM5_ENST00000380027.1_Intron|OR52E6_ENST00000379946.2_Missense_Mutation_p.P6S	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	2						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTAGCTATAGGCATTCTTTCT	0.423																																					p.P2S		Atlas-SNP	.											.	OR52E6	70	.	0			c.C4T						.						55	52	53					11																	5863124		2155	4284	6439	SO:0001583	missense	390078	exon1			CTATAGGCATTCT	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"GPCR / Class A : Olfactory receptors"	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.4C>T	chr11.hg19:g.5863124G>A	ENSP00000328878:p.Pro2Ser	116.0	0.0		73.0	24.0	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	hg19	CCDS53597.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.800645	0.00611	.	.	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.38240	9.91;1.15	3.34	-0.608	0.11611	.	2.039350	0.02356	N	0.076414	T	0.09069	0.0224	N	0.00191	-1.88	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13926	-1.0491	10	0.19147	T	0.46	.	3.8657	0.09015	0.5808:0.186:0.2332:0.0	.	2	Q96RD3	O52E6_HUMAN	S	2;6	ENSP00000328878:P2S;ENSP00000369279:P6S	ENSP00000328878:P2S	P	-	1	0	OR52E6	5819700	0.005000	0.15991	0.002000	0.10522	0.101000	0.19017	-0.718000	0.04980	-0.241000	0.09681	-0.499000	0.04595	CCT	.	.		0.423	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167		A	5863124	G	A	5863124	3	1	50	1	0	0	0	0	1	0	0	0	11126	1203	42	3	939	3	OR52E6	11	5863124	Missense_Mutation	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10		5863124	129143392	33	6504										
EPS8	2059	hgsc.bcm.edu	37	chr12	15776172	15776172	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tgtcctcagttcatccttatTgagagagaaaagttgtgcac	9	8	2	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr12:15776172T>C	ENST00000281172.5	-	20	2711	c.2275A>G	c.(2275-2277)Aat>Gat	p.N759D	EPS8_ENST00000540613.1_Missense_Mutation_p.N499D|EPS8_ENST00000543523.1_Missense_Mutation_p.N759D|EPS8_ENST00000543612.1_Missense_Mutation_p.N759D|EPS8_ENST00000542903.1_Missense_Mutation_p.N499D	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	759	Effector region. {ECO:0000250}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		TCATCCTTATTGAGAGAGAAA	0.383																																					p.N759D		Atlas-SNP	.											.	EPS8	70	.	0			c.A2275G						.						117	120	119					12																	15776172		2203	4300	6503	SO:0001583	missense	2059	exon20			CCTTATTGAGAGA	U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.2275A>G	chr12.hg19:g.15776172T>C	ENSP00000281172:p.Asn759Asp	139.0	0.0		86.0	17.0	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Missense_Mutation	SNP	ENST00000281172.5	hg19	CCDS31753.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.106196	0.77096	.	.	ENSG00000151491	ENST00000543523;ENST00000281172;ENST00000543612;ENST00000540613;ENST00000542903	T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11	5.66	5.66	0.87406	.	0.050677	0.85682	D	0.000000	T	0.30541	0.0768	M	0.75615	2.305	0.50813	D	0.999895	P	0.50156	0.932	B	0.42738	0.396	T	0.15752	-1.0426	10	0.56958	D	0.05	-30.8889	15.8893	0.79279	0.0:0.0:0.0:1.0	.	759	Q12929	EPS8_HUMAN	D	759;759;759;499;499	ENSP00000441867:N759D;ENSP00000281172:N759D;ENSP00000442388:N759D;ENSP00000441888:N499D;ENSP00000437806:N499D	ENSP00000281172:N759D	N	-	1	0	EPS8	15667439	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	7.344000	0.79328	2.153000	0.67306	0.528000	0.53228	AAT	.	.		0.383	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			C	15776172	T	C	15776172	3	2	50	1	0	0	0	0	1	0	0	0	5196	1812	63	2	201	2	EPS8	12	15776172	Missense_Mutation	SNP	T	TCGA-BD-A3ER-01A-11D-A20W-10		15776172	118075723	34	6505										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40692294	40692294	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tggagcagctcattttagaaGggtaagaaagagctcattaa	11	5	2	3			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr12:40692294G>C	ENST00000298910.7	+	24	3404	c.3346G>C	c.(3346-3348)Gga>Cga	p.G1116R	LRRK2_ENST00000343742.2_Splice_Site_p.G1116R	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1116					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CATTTTAGAAGGGTAAGAAAG	0.358																																					p.G1116R		Atlas-SNP	.											LRRK2_ENST00000298910,NS,carcinoma,0,2	LRRK2	763	.	0			c.G3346C						.						91	92	92					12																	40692294		2203	4300	6503	SO:0001630	splice_region_variant	120892	exon24			TTAGAAGGGTAAG	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.3347+1G>C	chr12.hg19:g.40692294G>C		104.0	0.0		62.0	16.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.227664	0.79576	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	T;T	0.26067	2.09;1.76	5.76	4.84	0.62591	.	0.110577	0.64402	D	0.000006	T	0.52517	0.1739	M	0.78285	2.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	T	0.53114	-0.8484	10	0.51188	T	0.08	.	16.2336	0.82360	0.0:0.0:0.8667:0.1333	.	1116;1116	E9PC85;Q5S007	.;LRRK2_HUMAN	R	1116	ENSP00000341930:G1116R;ENSP00000298910:G1116R	ENSP00000298910:G1116R	G	+	1	0	LRRK2	38978561	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.091000	0.76923	2.714000	0.92807	0.591000	0.81541	GGA	.	.		0.358	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	Missense_Mutation	C	40692294	G	C	40692294	5	2	50	1	0	0	0	0	0	0	1	0	9042	1014	35	4	3440	4	LRRK2	12	40692294	Splice_Site	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10	24916122	40692294	93159601	35	6506										
KRT2	3849	hgsc.bcm.edu	37	chr12	53038813	53038813	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gggctcatctttatctaaaaGagaaggtcacgctggaacca	10	9	4	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr12:53038813G>C	ENST00000309680.3	-	9	1931	c.1910C>G	c.(1909-1911)tCt>tGt	p.S637C		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	637	Tail.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		TTATCTAAAAGAGAAGGTCAC	0.542																																					p.S637C		Atlas-SNP	.											.	KRT2	94	.	0			c.C1910G						.						50	56	54					12																	53038813		2203	4300	6503	SO:0001583	missense	3849	exon9			CTAAAAGAGAAGG		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.1910C>G	chr12.hg19:g.53038813G>C	ENSP00000310861:p.Ser637Cys	70.0	0.0		29.0	9.0	NM_000423	Q4VAQ2	Missense_Mutation	SNP	ENST00000309680.3	hg19	CCDS8835.1	.	.	.	.	.	.	.	.	.	.	G	6.404	0.442643	0.12164	.	.	ENSG00000172867	ENST00000309680	D	0.83163	-1.69	3.87	3.87	0.44632	.	.	.	.	.	T	0.68007	0.2954	N	0.08118	0	0.32373	N	0.555547	B	0.21821	0.061	B	0.19148	0.024	T	0.72194	-0.4364	9	0.87932	D	0	.	11.5326	0.50618	0.0:0.0:1.0:0.0	.	637	P35908	K22E_HUMAN	C	637	ENSP00000310861:S637C	ENSP00000310861:S637C	S	-	2	0	KRT2	51325080	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	2.760000	0.47581	2.184000	0.69523	0.561000	0.74099	TCT	.	.		0.542	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		C	53038813	G	C	53038813	3	2	50	1	0	0	0	0	1	0	0	0	8466	942	33	4	13	4	KRT2	12	53038813	Missense_Mutation	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10	12346519	53038813	80813082	36	6507										
EP400	57634	hgsc.bcm.edu	37	chr12	132546658	132546658	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ctgtttgccttttctagacgCcgggaggctctgctcccgcc	11	15	2	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr12:132546658C>A	ENST00000333577.4	+	47	8105	c.7996C>A	c.(7996-7998)Ccg>Acg	p.P2666T	EP400_ENST00000389561.2_Missense_Mutation_p.P2630T|EP400_ENST00000332482.4_Missense_Mutation_p.P2593T|EP400_ENST00000330386.6_Missense_Mutation_p.P2549T|EP400_ENST00000389562.2_Missense_Mutation_p.P2629T			Q96L91	EP400_HUMAN	E1A binding protein p400	2666	Interaction with ZNF42. {ECO:0000250}.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		TTTCTAGACGCCGGGAGGCTC	0.612																																					p.P2630T		Atlas-SNP	.											.	EP400	370	.	0			c.C7888A						.						26	29	28					12																	132546658		2200	4299	6499	SO:0001583	missense	57634	exon46			TAGACGCCGGGAG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.7996C>A	chr12.hg19:g.132546658C>A	ENSP00000333602:p.Pro2666Thr	50.0	0.0		34.0	19.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	hg19		.	.	.	.	.	.	.	.	.	.	C	3.400	-0.122372	0.06795	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.89552	-2.53;-2.53;-2.53;-2.53;-2.53	4.8	-1.75	0.08031	.	0.307023	0.32503	N	0.006013	T	0.77928	0.4204	N	0.04508	-0.205	0.09310	N	1	P;P;D	0.69078	0.629;0.629;0.997	B;B;P	0.61275	0.331;0.331;0.886	T	0.73694	-0.3902	10	0.09084	T	0.74	.	3.923	0.09251	0.263:0.2513:0.0:0.4857	.	2630;2549;2629	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	T	2666;2630;2629;2593;2549;2630	ENSP00000333602:P2666T;ENSP00000374212:P2630T;ENSP00000374213:P2629T;ENSP00000331737:P2593T;ENSP00000330620:P2549T	ENSP00000330620:P2549T	P	+	1	0	EP400	131112611	0.185000	0.23213	0.011000	0.14972	0.220000	0.24768	0.602000	0.24134	-0.085000	0.12573	0.561000	0.74099	CCG	.	.		0.612	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132546658	C	A	132546658	3	1	50	1	0	0	0	0	1	0	0	0	5151	739	26	3	8063	3	EP400	12	132546658	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	79507845	132546658	1305237	37	6508										
BRCA2	90634	hgsc.bcm.edu	37	chr13	32972543	32972543	+	IGR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tccggctgcacagaaggcatTtcagccaccaaggagttgtg	12	11	1	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr13:32972543T>G	ENST00000380130.2	-	0	3046				BRCA2_ENST00000380152.3_Missense_Mutation_p.F3298C|BRCA2_ENST00000544455.1_Missense_Mutation_p.F3298C	NM_052818.2	NP_438169.2	Q5TBK1	N42L1_HUMAN	NEDD4 binding protein 2-like 1											large_intestine(1)|lung(2)|ovary(1)|skin(1)	5		Lung SC(185;0.0262)		all cancers(112;6.3e-06)|Epithelial(112;3.51e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00607)|BRCA - Breast invasive adenocarcinoma(63;0.0171)		CAGAAGGCATTTCAGCCACCA	0.403																																					p.F3298C		Atlas-SNP	.											.	BRCA2	812	.	0			c.T9893G						.						124	124	124					13																	32972543		2203	4300	6503	SO:0001628	intergenic_variant	675	exon27			AGGCATTTCAGCC	U50527	CCDS9345.2, CCDS41877.1	13q13.1	2008-11-05			ENSG00000139597	ENSG00000139597			25037	protein-coding gene	gene with protein product	"hypothetical gene CG018"					8812419	Standard	NM_052818		Approved	CG018	uc001uuc.3	Q5TBK1	OTTHUMG00000016697		chr13.hg19:g.32972543T>G		146.0	0.0		101.0	6.0	NM_000059	A4QN21|Q5TBK0	Missense_Mutation	SNP	ENST00000380130.2	hg19	CCDS9345.2	.	.	.	.	.	.	.	.	.	.	T	21.7	4.190851	0.78789	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.02323	4.34;4.34	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.15435	0.0372	M	0.76328	2.33	0.53688	D	0.999975	D	0.89917	1.0	D	0.97110	1.0	T	0.00116	-1.2036	10	0.87932	D	0	.	15.7412	0.77899	0.0:0.0:0.0:1.0	.	3298	P51587	BRCA2_HUMAN	C	3298	ENSP00000369497:F3298C;ENSP00000439902:F3298C	ENSP00000369497:F3298C	F	+	2	0	BRCA2	31870543	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	5.505000	0.66981	2.114000	0.64651	0.383000	0.25322	TTT	.	.		0.403	N4BP2L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052818		G	32972543	T	G	32972543	1	3	50	0	1	0	0	0	0	0	0	0	1501	1841	64	5		5	BRCA2	13	32972543	IGR	SNP	T	TCGA-BD-A3ER-01A-11D-A20W-10		32972543	82197335	38	6509										
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46619587	46619587	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	cactgggtcttcgggatgtgCtatcagatatagtcttggta	12	7	3	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr13:46619587C>T	ENST00000242848.4	-	2	404	c.56G>A	c.(55-57)aGc>aAc	p.S19N	ZC3H13_ENST00000282007.3_Missense_Mutation_p.S19N			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	19							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		TCGGGATGTGCTATCAGATAT	0.413																																					p.S19N	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-SNP	.											.	ZC3H13	197	.	0			c.G56A						.						225	231	229					13																	46619587		2203	4300	6503	SO:0001583	missense	23091	exon2			GATGTGCTATCAG	AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.56G>A	chr13.hg19:g.46619587C>T	ENSP00000242848:p.Ser19Asn	249.0	0.0		158.0	45.0	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	hg19		.	.	.	.	.	.	.	.	.	.	C	13.95	2.391079	0.42410	.	.	ENSG00000123200	ENST00000242848;ENST00000282007;ENST00000428921	T;T	0.35421	2.27;1.31	5.5	4.65	0.58169	.	0.000000	0.64402	D	0.000002	T	0.22781	0.0550	N	0.08118	0	0.80722	D	1	B;B	0.12013	0.003;0.005	B;B	0.17098	0.007;0.017	T	0.04930	-1.0917	10	0.87932	D	0	.	14.6561	0.68833	0.0:0.9295:0.0:0.0705	.	19;19	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	N	19	ENSP00000242848:S19N;ENSP00000282007:S19N	ENSP00000242848:S19N	S	-	2	0	ZC3H13	45517588	1.000000	0.71417	0.973000	0.42090	0.930000	0.56654	5.759000	0.68785	1.315000	0.45114	0.585000	0.79938	AGC	.	.		0.413	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		T	46619587	C	T	46619587	3	4	50	1	0	0	0	0	1	0	0	0	17580	797	28	3	4702	3	ZC3H13	13	46619587	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	13647044	46619587	68550291	39	6510										
NPAS3	64067	hgsc.bcm.edu	37	chr14	33684454	33684454	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	cgccggggaaaagaaaacttTgagttctatgaattggccaa	11	7	1	3			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr14:33684454T>G	ENST00000356141.4	+	3	207	c.207T>G	c.(205-207)ttT>ttG	p.F69L	NPAS3_ENST00000357798.5_Missense_Mutation_p.F39L|NPAS3_ENST00000551492.1_Missense_Mutation_p.F76L|NPAS3_ENST00000346562.2_Missense_Mutation_p.F39L|NPAS3_ENST00000548645.1_Missense_Mutation_p.F39L|NPAS3_ENST00000551008.1_5'UTR|NPAS3_ENST00000547068.1_5'UTR|NPAS3_ENST00000341321.4_Missense_Mutation_p.F69L			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	69	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		AAGAAAACTTTGAGTTCTATG	0.448																																					p.F69L		Atlas-SNP	.											.	NPAS3	266	.	0			c.T207G						.						83	87	86					14																	33684454		2203	4300	6503	SO:0001583	missense	64067	exon3			AAACTTTGAGTTC	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.207T>G	chr14.hg19:g.33684454T>G	ENSP00000348460:p.Phe69Leu	160.0	0.0		105.0	7.0	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	T	10.84	1.463063	0.26248	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000341321;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;D;T;T;T	0.97752	3.56;3.43;3.44;-4.52;3.43;3.42;3.29	5.96	4.82	0.62117	Helix-loop-helix DNA-binding (4);	0.000000	0.64402	D	0.000001	D	0.94470	0.8220	N	0.22421	0.69	0.58432	D	0.999994	B;B;B;B	0.24483	0.104;0.063;0.104;0.104	B;B;B;B	0.35931	0.074;0.034;0.214;0.153	D	0.90209	0.4263	10	0.11485	T	0.65	.	12.2222	0.54441	0.0:0.0663:0.0:0.9336	.	39;69;39;39	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	L	46;76;39;69;39;69;39	ENSP00000448373:F46L;ENSP00000450392:F76L;ENSP00000319610:F39L;ENSP00000344158:F69L;ENSP00000448916:F39L;ENSP00000348460:F69L;ENSP00000350446:F39L	ENSP00000344158:F69L	F	+	3	2	NPAS3	32754205	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.375000	0.44283	1.077000	0.40990	-0.264000	0.10439	TTT	.	.		0.448	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			G	33684454	T	G	33684454	3	3	50	1	0	0	0	0	1	0	0	0	10573	1809	63	5	217	5	NPAS3	14	33684454	Missense_Mutation	SNP	T	TCGA-BD-A3ER-01A-11D-A20W-10		33684454	73665086	40	6511										
RYR3	6263	hgsc.bcm.edu	37	chr15	33765652	33765652	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gtactccagtgcatcgccacCattcataaggagcagaggaa	10	11	1	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr15:33765652C>T	ENST00000389232.4	+	2	154	c.84C>T	c.(82-84)acC>acT	p.T28T	RYR3_ENST00000415757.3_Silent_p.T28T	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	28					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GCATCGCCACCATTCATAAGG	0.562																																					p.T28T		Atlas-SNP	.											.	RYR3	760	.	0			c.C84T						.						108	111	110					15																	33765652		2093	4215	6308	SO:0001819	synonymous_variant	6263	exon2			CGCCACCATTCAT		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.84C>T	chr15.hg19:g.33765652C>T		111.0	0.0		71.0	15.0	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.562	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33765652	C	T	33765652	2	4	50	1	0	0	0	0	0	0	0	1	13785	581	21	3		3	RYR3	15	33765652	Silent	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10		33765652	68765740	41	6512										
CORO7	79585	hgsc.bcm.edu	37	chr16	4414675	4414675	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	agtgtccgggaacaggtcctCgtggaactccacagcctggc	13	13	0	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr16:4414675C>A	ENST00000251166.4	-	13	1205	c.1060G>T	c.(1060-1062)Gag>Tag	p.E354*	CORO7-PAM16_ENST00000572467.1_Nonsense_Mutation_p.E354*|CORO7_ENST00000539968.1_Nonsense_Mutation_p.E134*|CORO7_ENST00000537233.2_Nonsense_Mutation_p.E336*|CORO7_ENST00000574025.1_Nonsense_Mutation_p.E269*|CORO7_ENST00000423908.2_Nonsense_Mutation_p.E186*	NM_024535.4	NP_078811.3	P57737	CORO7_HUMAN	coronin 7	354					actin filament polymerization (GO:0030041)|Golgi to endosome transport (GO:0006895)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)			breast(3)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|prostate(2)|skin(2)|urinary_tract(2)	23						AACAGGTCCTCGTGGAACTCC	0.692																																					p.E354X		Atlas-SNP	.											.	CORO7	73	.	0			c.G1060T						.						15	15	15					16																	4414675		2184	4286	6470	SO:0001587	stop_gained	79585	exon13			GGTCCTCGTGGAA	AK097238	CCDS10513.1, CCDS55982.1, CCDS58417.1	16p13.3	2013-01-10			ENSG00000262246	ENSG00000262246		"Coronins", "WD repeat domain containing"	26161	protein-coding gene	gene with protein product		611668				15327992	Standard	NM_024535		Approved	FLJ22021		P57737	OTTHUMG00000129465	ENST00000251166.4:c.1060G>T	chr16.hg19:g.4414675C>A	ENSP00000251166:p.Glu354*	126.0	0.0		113.0	27.0	NM_024535	B4DFD6|B4DL18|I3L416|Q17RK4	Nonsense_Mutation	SNP	ENST00000251166.4	hg19	CCDS10513.1	.	.	.	.	.	.	.	.	.	.	C	42	9.357909	0.99147	.	.	ENSG00000103426	ENST00000251166;ENST00000537233;ENST00000539968;ENST00000423908	.	.	.	5.31	4.35	0.52113	.	0.327478	0.26975	N	0.021542	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-24.1669	10.0778	0.42370	0.0:0.7845:0.1398:0.0757	.	.	.	.	X	354;269;134;186	.	ENSP00000251166:E354X	E	-	1	0	CORO7	4354676	0.712000	0.27916	0.897000	0.35233	0.614000	0.37383	1.568000	0.36418	1.224000	0.43551	0.455000	0.32223	GAG	.	.		0.692	CORO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251628.2	NM_024535		A	4414675	C	A	4414675	4	1	50	1	0	0	0	0	0	1	0	0	3761	893	31	1	1781	1	CORO7	16	4414675	Nonsense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10		4414675	85940078	42	6513										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77323286	77323286	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ggactgaccgggtctggaccCctcccccacaggtgactgtg	13	15	1	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr16:77323286C>T	ENST00000282849.5	-	22	3843	c.3425G>A	c.(3424-3426)gGg>gAg	p.G1142E	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1142	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GGTCTGGACCCCTCCCCCACA	0.537																																					p.G1142E		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G3425A						.						72	77	75					16																	77323286		2198	4300	6498	SO:0001583	missense	170692	exon22			TGGACCCCTCCCC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3425G>A	chr16.hg19:g.77323286C>T	ENSP00000282849:p.Gly1142Glu	86.0	0.0		46.0	11.0	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.861476	0.91433	.	.	ENSG00000140873	ENST00000282849	D	0.83673	-1.75	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.95614	0.8574	H	0.99211	4.47	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96936	0.9684	10	0.87932	D	0	.	19.632	0.95713	0.0:1.0:0.0:0.0	.	1142	Q8TE60	ATS18_HUMAN	E	1142	ENSP00000282849:G1142E	ENSP00000282849:G1142E	G	-	2	0	ADAMTS18	75880787	1.000000	0.71417	0.966000	0.40874	0.732000	0.41865	7.461000	0.80834	2.890000	0.99128	0.650000	0.86243	GGG	.	.		0.537	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			T	77323286	C	T	77323286	3	4	50	1	0	0	0	0	1	0	0	0	263	623	22	3	248	3	ADAMTS18	16	77323286	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10	72908611	77323286	13031467	43	6514										
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28386624	28386624	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	agaagccatctttcagaagtGggacagtgatggctcaggct	13	8	3	3			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr17:28386624G>A	ENST00000394835.3	+	14	2834	c.2642G>A	c.(2641-2643)tGg>tAg	p.W881*	EFCAB5_ENST00000536908.2_Intron|EFCAB5_ENST00000541045.1_Intron|EFCAB5_ENST00000378738.3_Nonsense_Mutation_p.W881*|AC104984.4_ENST00000583250.1_RNA|EFCAB5_ENST00000394832.2_Nonsense_Mutation_p.W881*|RNY4P13_ENST00000384284.1_RNA|EFCAB5_ENST00000320856.5_Intron	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	881	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TTTCAGAAGTGGGACAGTGAT	0.413																																					p.W881X		Atlas-SNP	.											.	EFCAB5	122	.	0			c.G2642A						.						102	101	101					17																	28386624		1854	4098	5952	SO:0001587	stop_gained	374786	exon14			AGAAGTGGGACAG	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.2642G>A	chr17.hg19:g.28386624G>A	ENSP00000378312:p.Trp881*	151.0	0.0		80.0	17.0	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Nonsense_Mutation	SNP	ENST00000394835.3	hg19	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	G	40	8.315218	0.98757	.	.	ENSG00000176927	ENST00000394835;ENST00000394832;ENST00000378738	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.9875	16.6453	0.85175	0.0:0.0:1.0:0.0	.	.	.	.	X	881	.	ENSP00000368012:W881X	W	+	2	0	EFCAB5	25410750	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.161000	0.71868	2.514000	0.84764	0.455000	0.32223	TGG	.	.		0.413	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		A	28386624	G	A	28386624	4	1	50	1	0	0	0	0	0	1	0	0	4940	1357	47	3	2696	3	EFCAB5	17	28386624	Nonsense_Mutation	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10		28386624	52808586	44	6515										
RNF213	57674	hgsc.bcm.edu	37	chr17	78321423	78321423	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gtgaagatctgcatggaaacAggcaagatggtgttgcttct	13	6	2	3			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr17:78321423A>T	ENST00000582970.1	+	29	9431	c.9288A>T	c.(9286-9288)acA>acT	p.T3096T	RNF213_ENST00000336301.6_Silent_p.T1169T|RNF213_ENST00000508628.2_Silent_p.T3145T	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3096					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCATGGAAACAGGCAAGATGG	0.522																																					p.T3096T		Atlas-SNP	.											.	RNF213	766	.	0			c.A9288T						.						91	88	89					17																	78321423		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon29			GGAAACAGGCAAG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.9288A>T	chr17.hg19:g.78321423A>T		69.0	0.0		60.0	17.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.		0.522	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78321423	A	T	78321423	2	4	50	1	0	0	0	0	0	0	0	1	13492	175	7	4		4	RNF213	17	78321423	Silent	SNP	A	TCGA-BD-A3ER-01A-11D-A20W-10	49934799	78321423	2873787	45	6516										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30795652	30795652	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ggtctttaaaaattgctgagCgtttactctgaaaaaaaata	7	5	2	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr18:30795652C>A	ENST00000383096.3	-	19	2122	c.1940G>T	c.(1939-1941)cGc>cTc	p.R647L	CCDC178_ENST00000579947.1_Missense_Mutation_p.R647L|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000406524.2_Missense_Mutation_p.R647L|CCDC178_ENST00000300227.8_Missense_Mutation_p.R609L|CCDC178_ENST00000583930.1_Missense_Mutation_p.R647L|CCDC178_ENST00000402325.1_Missense_Mutation_p.R647L|CCDC178_ENST00000403303.1_Missense_Mutation_p.R647L			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	647																	AATTGCTGAGCGTTTACTCTG	0.279																																					p.R647L		Atlas-SNP	.											.	.	.	.	0			c.G1940T						.						36	40	39					18																	30795652		2177	4285	6462	SO:0001583	missense	374864	exon18			GCTGAGCGTTTAC	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.1940G>T	chr18.hg19:g.30795652C>A	ENSP00000372576:p.Arg647Leu	270.0	0.0		132.0	32.0	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	hg19	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	C	5.477	0.272981	0.10349	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.15603	2.43;2.43;2.41;2.42;2.42	4.27	-0.0237	0.13942	.	.	.	.	.	T	0.10423	0.0255	L	0.48642	1.525	0.09310	N	1	B;B;P;P;P	0.39376	0.034;0.034;0.67;0.67;0.67	B;B;B;B;B	0.32762	0.066;0.024;0.152;0.093;0.093	T	0.23940	-1.0174	9	0.23302	T	0.38	15.0468	3.131	0.06423	0.1853:0.4525:0.0:0.3622	.	647;647;647;609;647	F8W7A7;Q5BJE1-3;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;.;CR034_HUMAN	L	647;647;609;647;647	ENSP00000385591:R647L;ENSP00000372576:R647L;ENSP00000300227:R609L;ENSP00000385867:R647L;ENSP00000385234:R647L	ENSP00000300227:R609L	R	-	2	0	C18orf34	29049650	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-0.708000	0.05035	-0.020000	0.14032	-0.210000	0.12710	CGC	.	.		0.279	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		A	30795652	C	A	30795652	3	1	50	1	0	0	0	0	1	0	0	0	1904	768	27	1	683	1	C18orf34	18	30795652	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10		30795652	47281596	46	6517										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43523169	43523169	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tcacaaactgcctatagcgtGctctattaaaggtttctaac	6	10	3	0			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr18:43523169G>A	ENST00000282041.5	-	9	1935	c.1901C>T	c.(1900-1902)gCa>gTa	p.A634V		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	634					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CCTATAGCGTGCTCTATTAAA	0.423																																					p.A634V		Atlas-SNP	.											.	EPG5	199	.	0			c.C1901T						.						147	144	145					18																	43523169		1885	4104	5989	SO:0001583	missense	57724	exon9			TAGCGTGCTCTAT	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.1901C>T	chr18.hg19:g.43523169G>A	ENSP00000282041:p.Ala634Val	186.0	0.0		106.0	24.0	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559236	0.65538	.	.	ENSG00000152223	ENST00000282041	T	0.10573	2.86	5.53	5.53	0.82687	.	0.732208	0.13797	N	0.362061	T	0.09555	0.0235	L	0.29908	0.895	0.48571	D	0.999675	P;P	0.36683	0.565;0.565	B;B	0.33690	0.168;0.168	T	0.19976	-1.0289	10	0.44086	T	0.13	-9.3772	12.7567	0.57339	0.0749:0.0:0.9251:0.0	.	634;634	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	V	634	ENSP00000282041:A634V	ENSP00000282041:A634V	A	-	2	0	EPG5	41777167	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.697000	0.68295	2.593000	0.87608	0.455000	0.32223	GCA	.	.		0.423	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		A	43523169	G	A	43523169	3	1	50	1	0	0	0	0	1	0	0	0	8258	1319	46	3	5982	3	KIAA1632	18	43523169	Missense_Mutation	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10	12727517	43523169	34554079	47	6518										
ZNF554	115196	hgsc.bcm.edu	37	chr19	2834344	2834344	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gctccaccctcacgcgccatCtgagaactcatactggagag	9	15	3	2			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr19:2834344C>T	ENST00000317243.5	+	5	1309	c.1111C>T	c.(1111-1113)Ctg>Ttg	p.L371L		NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	371					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACGCGCCATCTGAGAACTCA	0.552																																					p.L371L		Atlas-SNP	.											.	ZNF554	47	.	0			c.C1111T						.						44	49	48					19																	2834344		2167	4286	6453	SO:0001819	synonymous_variant	115196	exon5			CGCCATCTGAGAA	AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"Zinc fingers, C2H2-type", "-"	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.1111C>T	chr19.hg19:g.2834344C>T		29.0	0.0		31.0	9.0	NM_001102651	Q8NAT3|Q9BWN3	Silent	SNP	ENST00000317243.5	hg19	CCDS42462.1																																																																																			.	.		0.552	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303		T	2834344	C	T	2834344	2	4	50	1	0	0	0	0	0	0	0	1	18000	912	32	3		3	ZNF554	19	2834344	Silent	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10		2834344	56294639	48	6519										
UNC13A	23025	hgsc.bcm.edu	37	chr19	17756598	17756598	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	ttcacgcgggatttgatgtcGtcatcctcgtcccagacgcg	11	13	2	2	rs373430076		TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr19:17756598G>A	ENST00000519716.2	-	19	2240	c.2241C>T	c.(2239-2241)gaC>gaT	p.D747D	UNC13A_ENST00000552293.1_Silent_p.D747D|UNC13A_ENST00000550896.1_Silent_p.D745D|UNC13A_ENST00000252773.7_Silent_p.D747D|UNC13A_ENST00000428389.2_Silent_p.D835D|UNC13A_ENST00000551649.1_Silent_p.D747D	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	747	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)	p.D747D(1)|p.D835D(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						ATTTGATGTCGTCATCCTCGT	0.592													G|||	1	0.000199681	0	0.0014	5008	,	,		22421	0		0	False		,,,				2504	0				p.D747D		Atlas-SNP	.											UNC13A_ENST00000519716,NS,carcinoma,0,2	UNC13A	299	.	2	Substitution - coding silent(2)	kidney(2)	c.C2241T						.	G		0,4254		0,0,2127	72	73	72		2241	-1.1	1	19		72	1,8507		0,1,4253	no	coding-synonymous	UNC13A	NM_001080421.2		0,1,6380	AA,AG,GG		0.0118,0.0,0.0078		747/1704	17756598	1,12761	2127	4254	6381	SO:0001819	synonymous_variant	23025	exon18			GATGTCGTCATCC	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.2241C>T	chr19.hg19:g.17756598G>A		179.0	0.0		93.0	19.0	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	hg19	CCDS46013.2																																																																																			.	.		0.592	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17756598	G	A	17756598	2	1	50	1	0	0	0	0	0	0	0	1	16999	1136	40	1		1	UNC13A	19	17756598	Silent	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10	14922254	17756598	41372385	49	6520										
KRTAP27-1	643812	hgsc.bcm.edu	37	chr21	31709697	31709697	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tttctgattggcacgctgtcCtttcgcagggcctggaattg	12	10	1	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr21:31709697C>A	ENST00000382835.2	-	1	315	c.290G>T	c.(289-291)aGg>aTg	p.R97M		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	97						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						GCACGCTGTCCTTTCGCAGGG	0.493																																					p.R97M		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.G290T						.						135	134	135					21																	31709697		2203	4300	6503	SO:0001583	missense	643812	exon1			GCTGTCCTTTCGC	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"Keratin associated proteins"	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.290G>T	chr21.hg19:g.31709697C>A	ENSP00000372286:p.Arg97Met	291.0	0.0		188.0	46.0	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	hg19	CCDS33532.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.500420	0.44455	.	.	ENSG00000206107	ENST00000382835	T	0.03330	3.97	4.44	-0.893	0.10567	.	1.281970	0.05992	N	0.646271	T	0.10637	0.0260	L	0.44542	1.39	0.09310	N	1	D	0.76494	0.999	D	0.70487	0.969	T	0.36187	-0.9758	10	0.54805	T	0.06	-1.1352	7.6524	0.28356	0.0:0.4089:0.0:0.5911	.	97	Q3LI81	KR271_HUMAN	M	97	ENSP00000372286:R97M	ENSP00000372286:R97M	R	-	2	0	KRTAP27-1	30631568	0.000000	0.05858	0.006000	0.13384	0.019000	0.09904	-1.515000	0.02252	-0.162000	0.10964	0.591000	0.81541	AGG	.	.		0.493	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711		A	31709697	C	A	31709697	3	1	50	1	0	0	0	0	1	0	0	0	8553	681	24	3	337	3	KRTAP27-1	21	31709697	Missense_Mutation	SNP	C	TCGA-BD-A3ER-01A-11D-A20W-10		31709697	16420198	50	6521										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18370147	18370147	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	tgcttaggaaggagatagggGatctggtgctggctatcagg	17	5	2	1			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr22:18370147G>A	ENST00000441493.2	-	14	2298	c.1946C>T	c.(1945-1947)tCc>tTc	p.S649F	MICAL3_ENST00000429452.1_Missense_Mutation_p.S649F|MICAL3_ENST00000585038.1_Missense_Mutation_p.S649F|MICAL3_ENST00000400561.2_Missense_Mutation_p.S649F|MICAL3_ENST00000414725.2_Missense_Mutation_p.S649F|MICAL3_ENST00000383094.3_Missense_Mutation_p.S649F|MICAL3_ENST00000444520.1_Missense_Mutation_p.S649F|MICAL3_ENST00000207726.7_Missense_Mutation_p.S649F	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	649					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		GGAGATAGGGGATCTGGTGCT	0.527																																					p.S649F		Atlas-SNP	.											.	MICAL3	53	.	0			c.C1946T						.						175	155	161					22																	18370147		1568	3582	5150	SO:0001583	missense	57553	exon14			ATAGGGGATCTGG	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.1946C>T	chr22.hg19:g.18370147G>A	ENSP00000416015:p.Ser649Phe	310.0	0.0		205.0	12.0	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.220411	0.79464	.	.	ENSG00000093100;ENSG00000093100;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156	ENST00000441493;ENST00000429452;ENST00000400561;ENST00000444520;ENST00000414725;ENST00000383094;ENST00000207726	T;T;T;T;T;T;T	0.69561	-0.16;-0.41;-0.23;-0.23;-0.22;-0.22;-0.22	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.81009	0.4734	L	0.58669	1.825	0.80722	D	1	D;B;B;B;D	0.71674	0.998;0.14;0.172;0.079;0.998	D;B;B;B;D	0.78314	0.991;0.077;0.099;0.067;0.938	T	0.80817	-0.1213	10	0.87932	D	0	.	20.547	0.99278	0.0:0.0:1.0:0.0	.	649;649;649;649;649	B2RXJ5;Q7RTP6-3;Q7RTP6-2;Q7RTP6-4;Q7RTP6	.;.;.;.;MICA3_HUMAN	F	649	ENSP00000416015:S649F;ENSP00000414846:S649F;ENSP00000383406:S649F;ENSP00000410315:S649F;ENSP00000391827:S649F;ENSP00000372574:S649F;ENSP00000207726:S649F	ENSP00000207726:S649F	S	-	2	0	XXbac-B461K10.4;MICAL3	16750147	1.000000	0.71417	0.990000	0.47175	0.991000	0.79684	9.837000	0.99465	2.850000	0.98022	0.650000	0.86243	TCC	.	.		0.527	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			A	18370147	G	A	18370147	3	1	50	1	0	0	0	0	1	0	0	0	9580	1174	41	3	4875	3	MICAL3	22	18370147	Missense_Mutation	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10		18370147	32934419	51	6522										
TOB2	10766	hgsc.bcm.edu	37	chr22	41832827	41832827	+	Frame_Shift_Del	DEL	T	T	-													0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	gaaggaggcggtggtgaaggTgatgggctgagcggagcggg							TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chr22:41832827delT	ENST00000327492.3	-	2	1229	c.523delA	c.(523-525)accfs	p.T175fs		NM_016272.3	NP_057356.1	Q14106	TOB2_HUMAN	transducer of ERBB2, 2	175					female gamete generation (GO:0007292)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ossification (GO:0045778)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10						GTGGTGAAGGTGATGGGCTGA	0.632																																					p.T175fs		Atlas-Indel,Pindel	.											.	TOB2	30	.	0			c.524delC						.						61	60	61					22																	41832827		2203	4300	6503	SO:0001589	frameshift_variant	10766	exon2			.	D64109	CCDS14015.1	22q13.2	2010-02-26			ENSG00000183864	ENSG00000183864			11980	protein-coding gene	gene with protein product		607396		TROB2		10602502, 10591208	Standard	XM_005261315		Approved	TOBL, TOB4, bK223H9	uc003azz.1	Q14106	OTTHUMG00000150970	ENST00000327492.3:c.523delA	chr22.hg19:g.41832827delT	ENSP00000331305:p.Thr175fs	121.0	0.0		80.0	27.0	NM_016272	Q6FHR7|Q6PIT9|Q9BY97|Q9UBI0	Frame_Shift_Del	DEL	ENST00000327492.3	hg19	CCDS14015.1																																																																																			.	.		0.632	TOB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320699.1	NM_016272		-	41832827	T	-	41832827	7	5	50	1	0	1	0	1	0	0	0	0	16363	1696	59	0	515	0	TOB2	22	41832827	Frame_Shift_Del	DEL	T	TCGA-BD-A3ER-01A-11D-A20W-10	23462680	41832827	9471739	52	6523										
USP9Y	8287	hgsc.bcm.edu	37	chrY	14885659	14885659	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.113207547169811	6	1	1.93213828425096	1.77112676056338	1.9679186228482	0.102564102564103	0.617038875103394	0	agttaatgggggatgaaccaGacttggatcctgatattaat	11	5	0	3			TCGA-BD-A3ER-01A-11D-A20W-10	TCGA-BD-A3ER-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f571d60-db6d-4282-9998-16c1ae74dcce	9124e6e8-f6c3-47a4-af2a-beda990f56f0	g.chrY:14885659G>A	ENST00000338981.3	+	17	3076	c.2131G>A	c.(2131-2133)Gac>Aac	p.D711N	USP9Y_ENST00000426564.2_3'UTR	NM_004654.3	NP_004645.2	O00507	USP9Y_HUMAN	ubiquitin specific peptidase 9, Y-linked	711					BMP signaling pathway (GO:0030509)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)	co-SMAD binding (GO:0070410)|cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(8)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GGATGAACCAGACTTGGATCC	0.358																																					p.D711N		Atlas-SNP	.											.	USP9Y	49	.	0			c.G2131A						.						86	80	81					Y																	14885659		616	1963	2579	SO:0001583	missense	8287	exon17			GAACCAGACTTGG	Y13618	CCDS14781.1	Yq11.2	2010-04-09	2009-03-17		ENSG00000114374	ENSG00000114374		"Ubiquitin-specific peptidases"	12633	protein-coding gene	gene with protein product	"fat facets-like homolog (Drosophila)"	400005	"ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)"			8922996, 9384609, 19246359	Standard	NM_004654		Approved	DFFRY	uc004fst.1	O00507	OTTHUMG00000036469	ENST00000338981.3:c.2131G>A	chrY.hg19:g.14885659G>A	ENSP00000342812:p.Asp711Asn	190.0	0.0		110.0	9.0	NM_004654	O14601	Missense_Mutation	SNP	ENST00000338981.3	hg19	CCDS14781.1																																																																																			.	.		0.358	USP9Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088703.2	NM_004654		A	14885659	G	A	14885659	3	1	50	1	0	0	0	0	1	0	0	0	17106	942	33	3	2189	3	USP9Y	24	14885659	Missense_Mutation	SNP	G	TCGA-BD-A3ER-01A-11D-A20W-10		14885659	44487907	53	6524										
MFN2	9927	hgsc.bcm.edu	37	chr1	12069707	12069707	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttgacgtcacccgggagaacCtggagcaggaaattgccgcc	13	12	1	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:12069707C>G	ENST00000235329.5	+	18	2450	c.2128C>G	c.(2128-2130)Ctg>Gtg	p.L710V	MFN2_ENST00000444836.1_Missense_Mutation_p.L710V	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	710					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blastocyst formation (GO:0001825)|blood coagulation (GO:0007596)|camera-type eye morphogenesis (GO:0048593)|mitochondrial fusion (GO:0008053)|mitochondrial membrane organization (GO:0007006)|mitochondrion localization (GO:0051646)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of smooth muscle cell proliferation (GO:0048662)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to mitochondrion (GO:0006626)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intrinsic component of mitochondrial outer membrane (GO:0031306)|microtubule cytoskeleton (GO:0015630)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	20	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		CCGGGAGAACCTGGAGCAGGA	0.552																																					p.L710V		Atlas-SNP	.											.	MFN2	83	.	0			c.C2128G						.						87	87	87					1																	12069707		2203	4300	6503	SO:0001583	missense	9927	exon18			GAGAACCTGGAGC	AF036536	CCDS30587.1	1p36.22	2014-09-17			ENSG00000116688	ENSG00000116688			16877	protein-coding gene	gene with protein product		608507				12499352, 11181170	Standard	NM_014874		Approved	CPRP1, KIAA0214, MARF, CMT2A2	uc009vni.3	O95140	OTTHUMG00000002392	ENST00000235329.5:c.2128C>G	chr1.hg19:g.12069707C>G	ENSP00000235329:p.Leu710Val	182.0	0.0		95.0	13.0	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Missense_Mutation	SNP	ENST00000235329.5	hg19	CCDS30587.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.720056	0.68844	.	.	ENSG00000116688	ENST00000444836;ENST00000235329	D;D	0.98028	-4.67;-4.67	5.28	3.29	0.37713	Fzo/mitofusin HR2 domain (1);	0.000000	0.64402	D	0.000002	D	0.98532	0.9510	M	0.86805	2.84	0.54753	D	0.999983	D	0.76494	0.999	D	0.75484	0.986	D	0.98698	1.0699	10	0.56958	D	0.05	-18.7584	11.4724	0.50278	0.0:0.8368:0.0:0.1632	.	710	O95140	MFN2_HUMAN	V	710	ENSP00000416338:L710V;ENSP00000235329:L710V	ENSP00000235329:L710V	L	+	1	2	MFN2	11992294	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	3.655000	0.54460	1.466000	0.48025	0.655000	0.94253	CTG	.	.		0.552	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		G	12069707	C	G	12069707	3	3	51	1	0	0	0	0	1	0	0	0	9533	680	24	4	2190	4	MFN2	1	12069707	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10		12069707	237180914	1	6525										
PLA2G2F	64600	hgsc.bcm.edu	37	chr1	20474797	20474797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ccgtggcttcctcaatgtctActgccagggccccacgccca	9	18	2	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:20474797A>G	ENST00000375102.3	+	5	641	c.539A>G	c.(538-540)tAc>tGc	p.Y180C		NM_022819.3	NP_073730.3	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	137					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CTCAATGTCTACTGCCAGGGC	0.592																																					p.Y180C		Atlas-SNP	.											.	PLA2G2F	28	.	0			c.A539G						.						159	133	142					1																	20474797		2203	4300	6503	SO:0001583	missense	64600	exon5			ATGTCTACTGCCA	AL158172	CCDS204.2	1p35	2008-09-19			ENSG00000158786	ENSG00000158786	3.1.1.4		30040	protein-coding gene	gene with protein product						11112443	Standard	NM_022819		Approved		uc009vpp.1	Q9BZM2	OTTHUMG00000002704	ENST00000375102.3:c.539A>G	chr1.hg19:g.20474797A>G	ENSP00000364243:p.Tyr180Cys	318.0	0.0		119.0	40.0	NM_022819	Q5R385|Q8N217|Q9H506	Missense_Mutation	SNP	ENST00000375102.3	hg19	CCDS204.2	.	.	.	.	.	.	.	.	.	.	A	11.44	1.640221	0.29157	.	.	ENSG00000158786	ENST00000375102	D	0.82619	-1.63	5.19	2.71	0.32032	.	0.139574	0.33075	N	0.005320	D	0.85570	0.5727	M	0.64260	1.97	0.32874	D	0.509673	D	0.76494	0.999	P	0.60236	0.871	D	0.86411	0.1748	10	0.51188	T	0.08	-43.461	7.8437	0.29414	0.6695:0.0:0.0:0.3305	.	180	Q9BZM2-2	.	C	180	ENSP00000364243:Y180C	ENSP00000364243:Y180C	Y	+	2	0	PLA2G2F	20347384	1.000000	0.71417	0.997000	0.53966	0.024000	0.10985	1.478000	0.35442	0.802000	0.34089	-0.490000	0.04691	TAC	.	.		0.592	PLA2G2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007687.1	NM_022819		G	20474797	A	G	20474797	3	3	51	1	0	0	0	0	1	0	0	0	12008	391	14	2	557	2	PLA2G2F	1	20474797	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	8405090	20474797	228775824	2	6526										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35857909	35857909	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tgtagtatcattggcaagtgCccctgctgctcagcctacag	10	12	2	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:35857909C>A	ENST00000314607.6	+	16	2764	c.2684C>A	c.(2683-2685)gCc>gAc	p.A895D	ZMYM4_ENST00000373297.2_Missense_Mutation_p.A806D	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	895					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTGGCAAGTGCCCCTGCTGCT	0.443																																					p.A895D		Atlas-SNP	.											.	ZMYM4	143	.	0			c.C2684A						.						80	73	75					1																	35857909		2203	4300	6503	SO:0001583	missense	9202	exon16			CAAGTGCCCCTGC	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.2684C>A	chr1.hg19:g.35857909C>A	ENSP00000322915:p.Ala895Asp	225.0	0.0		226.0	95.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	hg19	CCDS389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.97|16.97	3.268431|3.268431	0.59540|0.59540	.|.	.|.	ENSG00000146463|ENSG00000146463	ENST00000314607;ENST00000373297|ENST00000457946	T;T|.	0.24151|.	1.87;1.88|.	4.79|4.79	4.79|4.79	0.61399|0.61399	.|.	0.278200|.	0.36409|.	N|.	0.002615|.	T|.	0.59059|.	0.2166|.	L|L	0.34521|0.34521	1.04|1.04	0.47374|0.47374	D|D	0.9994|0.9994	B|.	0.27380|.	0.177|.	B|.	0.31016|.	0.123|.	T|.	0.55451|.	-0.8139|.	10|.	0.52906|.	T|.	0.07|.	-1.1659|-1.1659	18.194|18.194	0.89815|0.89815	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	895|.	Q5VZL5|.	ZMYM4_HUMAN|.	D|X	895;806|554	ENSP00000322915:A895D;ENSP00000362394:A806D|.	ENSP00000322915:A895D|.	A|C	+|+	2|3	0|2	ZMYM4|ZMYM4	35630496|35630496	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	4.740000|4.740000	0.62087|0.62087	2.362000|2.362000	0.80069|0.80069	0.591000|0.591000	0.81541|0.81541	GCC|TGC	.	.		0.443	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		A	35857909	C	A	35857909	3	1	51	1	0	0	0	0	1	0	0	0	17717	739	26	3	2746	3	ZMYM4	1	35857909	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	15383112	35857909	213392712	3	6527										
GJA9	81025	hgsc.bcm.edu	37	chr1	39340262	39340262	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ggaacccgcctaccaatgagAttgttcgttagggacactac	10	11	0	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:39340262A>G	ENST00000360786.3	-	1	1761	c.1509T>C	c.(1507-1509)aaT>aaC	p.N503N	MYCBP_ENST00000489803.1_5'UTR|RP5-864K19.4_ENST00000443161.1_RNA|GJA9_ENST00000454994.2_Intron|MYCBP_ENST00000397572.2_5'Flank|GJA9_ENST00000357771.3_Silent_p.N503N|RP5-864K19.4_ENST00000456813.1_RNA|RP5-864K19.4_ENST00000433671.2_RNA			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	503					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			TACCAATGAGATTGTTCGTTA	0.463																																					p.N503N		Atlas-SNP	.											.	GJA9	55	.	0			c.T1509C						.						83	83	83					1																	39340262		2203	4300	6503	SO:0001819	synonymous_variant	81025	exon2			AATGAGATTGTTC	AF179597	CCDS432.1	1p34	2008-02-05	2007-11-06	2007-11-06	ENSG00000131233	ENSG00000131233		"Ion channels / Gap junction proteins (connexins)"	19155	protein-coding gene	gene with protein product	"connexin 59"	611923	"gap junction protein, alpha 10, 59kDa"	GJA10			Standard	NM_030772		Approved	CX59, CX58	uc021olr.1	P57773	OTTHUMG00000000482	ENST00000360786.3:c.1509T>C	chr1.hg19:g.39340262A>G		133.0	0.0		142.0	62.0	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Silent	SNP	ENST00000360786.3	hg19	CCDS432.1																																																																																			.	.		0.463	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772		G	39340262	A	G	39340262	2	3	51	1	0	0	0	0	0	0	0	1	6414	330	12	2		2	GJA9	1	39340262	Silent	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	3482353	39340262	209910359	4	6528										
C1orf87	127795	hgsc.bcm.edu	37	chr1	60505838	60505838	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tcatttgttgtcccacttggGctctggccaatatcctaaca	7	12	2	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:60505838G>T	ENST00000371201.3	-	5	605	c.498C>A	c.(496-498)agC>agA	p.S166R	C1orf87_ENST00000450089.2_Intron	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	166							calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						TCCCACTTGGGCTCTGGCCAA	0.453																																					p.S166R	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.C498A						.						70	76	74					1																	60505838		2203	4300	6503	SO:0001583	missense	127795	exon5			ACTTGGGCTCTGG	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"carcinoma-related EF-hand protein"					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.498C>A	chr1.hg19:g.60505838G>T	ENSP00000360244:p.Ser166Arg	56.0	0.0		87.0	44.0	NM_152377	Q6ZU07|Q8IVS0	Missense_Mutation	SNP	ENST00000371201.3	hg19	CCDS614.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.606602	0.00121	.	.	ENSG00000162598	ENST00000371201	T	0.15372	2.43	5.18	-3.85	0.04243	.	0.431851	0.22152	N	0.063912	T	0.01976	0.0062	N	0.00268	-1.735	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35375	-0.9791	10	0.02654	T	1	0.2181	1.9018	0.03269	0.1132:0.1984:0.3088:0.3796	.	166	Q8N0U7	CA087_HUMAN	R	166	ENSP00000360244:S166R	ENSP00000360244:S166R	S	-	3	2	C1orf87	60278426	0.030000	0.19436	0.003000	0.11579	0.006000	0.05464	-0.985000	0.03751	-0.514000	0.06488	-0.139000	0.14373	AGC	.	.		0.453	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377		T	60505838	G	T	60505838	3	4	51	1	0	0	0	0	1	0	0	0	2066	1194	42	3	1174	3	C1orf87	1	60505838	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	21165576	60505838	188744783	5	6529										
INADL	10207	hgsc.bcm.edu	37	chr1	62267337	62267337	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	accaccagctctctttctaaCtggagcagtggaaactgaaa	8	11	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:62267337C>G	ENST00000371158.2	+	12	1559	c.1445C>G	c.(1444-1446)aCt>aGt	p.T482S	INADL_ENST00000316485.6_Missense_Mutation_p.T482S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	482					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						CTCTTTCTAACTGGAGCAGTG	0.294																																					p.T482S		Atlas-SNP	.											.	INADL	179	.	0			c.C1445G						.						51	53	52					1																	62267337		2203	4300	6503	SO:0001583	missense	10207	exon12			TTCTAACTGGAGC	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.1445C>G	chr1.hg19:g.62267337C>G	ENSP00000360200:p.Thr482Ser	194.0	0.0		261.0	47.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	C	2.718	-0.267140	0.05754	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.12147	2.86;2.71	5.11	2.08	0.27032	.	0.655234	0.14864	N	0.293914	T	0.13884	0.0336	M	0.63428	1.95	0.35073	D	0.762682	B;B;B	0.13594	0.007;0.008;0.002	B;B;B	0.17722	0.019;0.006;0.008	T	0.21075	-1.0256	10	0.10111	T	0.7	.	11.0245	0.47736	0.0:0.5712:0.361:0.0677	.	482;482;482	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	S	482	ENSP00000360200:T482S;ENSP00000326199:T482S	ENSP00000255202:T482S	T	+	2	0	INADL	62039925	0.041000	0.20044	0.067000	0.19924	0.694000	0.40290	0.768000	0.26590	0.275000	0.22094	0.650000	0.86243	ACT	.	.		0.294	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62267337	C	G	62267337	3	3	51	1	0	0	0	0	1	0	0	0	7740	565	20	4	1487	4	INADL	1	62267337	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	1761499	62267337	186983284	6	6530										
CACHD1	57685	hgsc.bcm.edu	37	chr1	65139104	65139104	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	cctgtgcaacagcttcagtgAcagaacggtccagaggtttt	11	10	1	3			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:65139104A>G	ENST00000371073.2	+	19	2684	c.2684A>G	c.(2683-2685)gAc>gGc	p.D895G	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Missense_Mutation_p.D844G			Q5VU97	CAHD1_HUMAN	cache domain containing 1	895					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						AGCTTCAGTGACAGAACGGTC	0.433																																					p.D844G		Atlas-SNP	.											.	CACHD1	125	.	0			c.A2531G						.						136	135	135					1																	65139104		2203	4300	6503	SO:0001583	missense	57685	exon19			TCAGTGACAGAAC	AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.2684A>G	chr1.hg19:g.65139104A>G	ENSP00000360113:p.Asp895Gly	166.0	0.0		169.0	18.0	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	hg19		.	.	.	.	.	.	.	.	.	.	A	22.2	4.257173	0.80246	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.25749	1.78;1.79	5.14	5.14	0.70334	.	0.042716	0.85682	D	0.000000	T	0.35248	0.0925	L	0.55481	1.735	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.12192	-1.0557	10	0.52906	T	0.07	-32.509	14.955	0.71107	1.0:0.0:0.0:0.0	.	895	Q5VU97	CAHD1_HUMAN	G	895;844	ENSP00000360113:D895G;ENSP00000290039:D844G	ENSP00000290039:D844G	D	+	2	0	CACHD1	64911692	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	8.710000	0.91388	1.924000	0.55735	0.482000	0.46254	GAC	.	.		0.433	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		G	65139104	A	G	65139104	3	3	51	1	0	0	0	0	1	0	0	0	2539	275	10	2	2605	2	CACHD1	1	65139104	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	2871767	65139104	184111517	7	6531										
CYB561D1	284613	hgsc.bcm.edu	37	chr1	110038869	110038871	+	In_Frame_Del	DEL	AAT	AAT	-													0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tcctacttgccgaggaagaaAatggaaatgtgagttcctgc							TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:110038869_110038871delAAT	ENST00000420578.2	+	3	718_720	c.678_680delAAT	c.(676-681)aaaatg>aag	p.M227del	CYB561D1_ENST00000310611.4_3'UTR|CYB561D1_ENST00000496961.1_3'UTR|CYB561D1_ENST00000369868.3_In_Frame_Del_p.M249del|CYB561D1_ENST00000393709.3_In_Frame_Del_p.M170del|CYB561D1_ENST00000528785.1_In_Frame_Del_p.M227del|CYB561D1_ENST00000527072.1_3'UTR|CYB561D1_ENST00000533024.1_3'UTR|CYB561D1_ENST00000430195.2_3'UTR			Q8N8Q1	C56D1_HUMAN	cytochrome b561 family, member D1	227					oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|prostate(1)	5		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0422)|Epithelial(280;0.0655)|all cancers(265;0.0685)|READ - Rectum adenocarcinoma(129;0.0689)|LUSC - Lung squamous cell carcinoma(189;0.227)		CGAGGAAGAAAATGGAAATGTGA	0.498																																					p.248_249del		Atlas-Indel,Pindel	.											.	CYB561D1	13	.	0			c.743_745del						.																																			SO:0001651	inframe_deletion	284613	exon3			.	AK096354	CCDS800.1, CCDS44188.1, CCDS44189.1, CCDS44190.1, CCDS44191.1	1p13.2	2013-03-14	2013-03-14		ENSG00000174151	ENSG00000174151		"Cytochrome b genes"	26804	protein-coding gene	gene with protein product			"cytochrome b-561 domain containing 1"			23249217	Standard	NM_182580		Approved	FLJ39035, FLJ44753	uc010ovo.2	Q8N8Q1	OTTHUMG00000011051	ENST00000420578.2:c.678_680delAAT	chr1.hg19:g.110038869_110038871delAAT	ENSP00000413530:p.Met227del	201.0	0.0		127.0	45.0	NM_001134400	B4DH97|E9PCM8|Q52M36|Q5T6C2|Q5T6C3	In_Frame_Del	DEL	ENST00000420578.2	hg19	CCDS800.1																																																																																			.	.		0.498	CYB561D1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030384.1	NM_182580		-	110038871	AAT	-	110038869	7	5	51	1	0	1	0	1	0	0	0	0	4122	11	1	0	873	0	CYB561D1	1	110038869	In_Frame_Del	DEL	AAT	TCGA-BW-A5NO-01A-11D-A27I-10	44899765	110038869	139211752	8	6532										
SETDB1	9869	hgsc.bcm.edu	37	chr1	150900277	150900277	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gcagagctgcaacaggcagtGgttgaggaactgggtatctc	15	8	1	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:150900277G>A	ENST00000271640.5	+	2	277	c.87G>A	c.(85-87)gtG>gtA	p.V29V	SETDB1_ENST00000368963.1_Silent_p.V29V|SETDB1_ENST00000368962.2_Silent_p.V29V|SETDB1_ENST00000459773.1_3'UTR|SETDB1_ENST00000368969.4_Silent_p.V29V	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	29					bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			AACAGGCAGTGGTTGAGGAAC	0.498																																					p.V29V		Atlas-SNP	.											.	SETDB1	204	.	0			c.G87A						.						163	155	158					1																	150900277		2203	4300	6503	SO:0001819	synonymous_variant	9869	exon2			GGCAGTGGTTGAG	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.87G>A	chr1.hg19:g.150900277G>A		322.0	0.0		378.0	32.0	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Silent	SNP	ENST00000271640.5	hg19	CCDS44217.1																																																																																			.	.		0.498	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			A	150900277	G	A	150900277	2	1	51	1	0	0	0	0	0	0	0	1	14153	1335	47	3		3	SETDB1	1	150900277	Silent	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	40861408	150900277	98350344	9	6533										
GLT25D2	23127	hgsc.bcm.edu	37	chr1	183942845	183942845	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttctgcaatcagtagattgaGggtctgtggattagtcagga	13	5	4	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:183942845G>A	ENST00000361927.4	-	4	903	c.532C>T	c.(532-534)Ctc>Ttc	p.L178F	COLGALT2_ENST00000546159.1_Missense_Mutation_p.L178F	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	178					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										AGTAGATTGAGGGTCTGTGGA	0.413																																					p.L178F		Atlas-SNP	.											.	.	.	.	0			c.C532T						.						111	121	117					1																	183942845		2203	4300	6503	SO:0001583	missense	23127	exon4			GATTGAGGGTCTG	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.532C>T	chr1.hg19:g.183942845G>A	ENSP00000354960:p.Leu178Phe	69.0	0.0		79.0	7.0	NM_015101	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	hg19	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.143433	0.77888	.	.	ENSG00000198756	ENST00000546159;ENST00000361927	T;T	0.70399	-0.48;-0.48	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000001	D	0.83275	0.5219	M	0.88979	2.995	0.80722	D	1	P;P	0.51449	0.9;0.945	P;P	0.57502	0.73;0.822	D	0.86081	0.1544	10	0.72032	D	0.01	.	12.5454	0.56197	0.076:0.0:0.924:0.0	.	178;178	F5H3T5;Q8IYK4	.;GT252_HUMAN	F	178	ENSP00000439112:L178F;ENSP00000354960:L178F	ENSP00000354960:L178F	L	-	1	0	GLT25D2	182209468	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.705000	0.84606	2.535000	0.85469	0.585000	0.79938	CTC	.	.		0.413	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		A	183942845	G	A	183942845	3	1	51	1	0	0	0	0	1	0	0	0	6475	1000	35	3	1384	3	GLT25D2	1	183942845	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	33042568	183942845	65307776	10	6534										
CR1	1378	hgsc.bcm.edu	37	chr1	207791472	207791472	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	acattggaggacacgtatctCtatatcttcctgggatgaca	9	9	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:207791472C>A	ENST00000367049.4	+	42	6946	c.6946C>A	c.(6946-6948)Cta>Ata	p.L2316I	CR1_ENST00000400960.2_Missense_Mutation_p.L1866I|CR1_ENST00000367053.1_Missense_Mutation_p.L1866I|CR1_ENST00000367052.1_Missense_Mutation_p.L1866I|CR1_ENST00000367051.1_Missense_Mutation_p.L1866I	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1866					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ACACGTATCTCTATATCTTCC	0.473																																					p.L2316I		Atlas-SNP	.											.	CR1	354	.	0			c.C6946A						.						163	156	158					1																	207791472		1978	4163	6141	SO:0001583	missense	1378	exon42			GTATCTCTATATC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6946C>A	chr1.hg19:g.207791472C>A	ENSP00000356016:p.Leu2316Ile	293.0	0.0		212.0	87.0	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	hg19	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376066	0.24857	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11	4.19	0.355	0.16069	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.51991	0.1707	N	0.17838	0.53	0.09310	N	1	P;P	0.52842	0.555;0.956	B;P	0.53401	0.353;0.725	T	0.41998	-0.9477	9	0.30854	T	0.27	.	6.4999	0.22164	0.0:0.5995:0.0:0.4005	.	1866;2316	P17927;E9PDY4	CR1_HUMAN;.	I	1866;1866;1866;1866;2316	ENSP00000356019:L1866I;ENSP00000356018:L1866I;ENSP00000356020:L1866I;ENSP00000383744:L1866I;ENSP00000356016:L2316I	ENSP00000356016:L2316I	L	+	1	2	CR1	205858095	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.366000	0.20365	0.076000	0.16826	0.563000	0.77884	CTA	.	.		0.473	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		A	207791472	C	A	207791472	3	1	51	1	0	0	0	0	1	0	0	0	3842	912	32	3	7112	3	CR1	1	207791472	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	23848627	207791472	41459149	11	6535										
IARS2	55699	hgsc.bcm.edu	37	chr1	220307815	220307816	+	Frame_Shift_Del	DEL	TT	TT	-													0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gttggtttcagtcatccttaTtaacaagtgtggcagcaagg							TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr1:220307815_220307816delTT	ENST00000302637.5	+	15	2013_2014	c.1909_1910delTT	c.(1909-1911)ttafs	p.L637fs	snoU13_ENST00000459443.1_RNA|IARS2_ENST00000366922.1_Frame_Shift_Del_p.L565fs	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	637					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	GTCATCCTTATTAACAAGTGTG	0.416																																					p.636_637del		Atlas-Indel,Pindel	.											.	IARS2	106	.	0			c.1908_1909del						.																																			SO:0001589	frameshift_variant	55699	exon15			.	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.1909_1910delTT	chr1.hg19:g.220307815_220307816delTT	ENSP00000303279:p.Leu637fs	125.0	0.0		120.0	48.0	NM_018060	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Frame_Shift_Del	DEL	ENST00000302637.5	hg19	CCDS1523.1																																																																																			.	.		0.416	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		-	220307816	TT	-	220307815	7	5	51	1	0	1	0	1	0	0	0	0	7483	1490	52	0	1967	0	IARS2	1	220307815	Frame_Shift_Del	DEL	TT	TCGA-BW-A5NO-01A-11D-A27I-10	12516343	220307815	28942806	12	6536										
C2orf7	84279	hgsc.bcm.edu	37	chr2	73456048	73456048	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	atgatcaccgcccgcccgccGtgctcctggaccacccgagt	10	19	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:73456048G>A	ENST00000258083.2	-	4	388	c.321C>T	c.(319-321)caC>caT	p.H107H	PRADC1_ENST00000480093.1_Intron	NM_032319.1	NP_115695.1	Q9BSG0	PADC1_HUMAN	protease-associated domain containing 1	107	PA.					extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(1)|lung(2)	4						CCCGCCCGCCGTGCTCCTGGA	0.592																																					p.H107H		Atlas-SNP	.											.	PRADC1	15	.	0			c.C321T						.						30	29	29					2																	73456048		2203	4300	6503	SO:0001819	synonymous_variant	84279	exon4			CCCGCCGTGCTCC	BC005069	CCDS1924.1	2p13.2	2012-10-31	2011-04-15	2011-04-15	ENSG00000135617	ENSG00000135617			16047	protein-coding gene	gene with protein product	"protease-associated domain-containing glycoprotein 21 kDa"		"chromosome 2 open reading frame 7"	C2orf7		15498570	Standard	NM_032319		Approved	MGC13004, PAP21, hPAP21	uc002siy.3	Q9BSG0	OTTHUMG00000129773	ENST00000258083.2:c.321C>T	chr2.hg19:g.73456048G>A		120.0	0.0		28.0	10.0	NM_032319	Q2Z1P2	Silent	SNP	ENST00000258083.2	hg19	CCDS1924.1																																																																																			.	.		0.592	PRADC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251989.1	NM_032319		A	73456048	G	A	73456048	2	1	51	1	0	0	0	0	0	0	0	1	2191	1136	40	1		1	C2orf7	2	73456048	Silent	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10		73456048	169743325	13	6537										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141055500	141055500	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gactgtcttaccacagtttgGcccagtgaaacccagtgcac	9	13	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:141055500G>T	ENST00000389484.3	-	84	13815	c.12844C>A	c.(12844-12846)Cca>Aca	p.P4282T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4282	EGF-like 18. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCACAGTTTGGCCCAGTGAAA	0.433										TSP Lung(27;0.18)																											p.P4282T	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C12844A						.						115	120	118					2																	141055500		2203	4300	6503	SO:0001583	missense	53353	exon84			AGTTTGGCCCAGT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12844C>A	chr2.hg19:g.141055500G>T	ENSP00000374135:p.Pro4282Thr	361.0	0.0		257.0	24.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.172511	0.78452	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.92647	-3.08	6.08	6.08	0.98989	EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.071752	0.64402	D	0.000018	D	0.91928	0.7444	N	0.17764	0.52	0.47698	D	0.999494	D	0.62365	0.991	P	0.62089	0.898	D	0.88418	0.3026	10	0.15499	T	0.54	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	4282	Q9NZR2	LRP1B_HUMAN	T	4282;4220	ENSP00000374135:P4282T	ENSP00000374135:P4282T	P	-	1	0	LRP1B	140771970	1.000000	0.71417	0.988000	0.46212	0.741000	0.42261	6.548000	0.73896	2.894000	0.99253	0.655000	0.94253	CCA	.	.		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141055500	G	T	141055500	3	4	51	1	0	0	0	0	1	0	0	0	8964	1203	42	3	987	3	LRP1B	2	141055500	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	67599452	141055500	102143873	14	6538										
TBR1	10716	hgsc.bcm.edu	37	chr2	162276744	162276744	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	agatcacaacccttttgcaaAaggatttcgggataattatg	8	7	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:162276744A>T	ENST00000389554.3	+	5	1483	c.1166A>T	c.(1165-1167)aAa>aTa	p.K389I	TBR1_ENST00000410035.1_Missense_Mutation_p.K102I|AC009487.4_ENST00000444164.1_RNA|TBR1_ENST00000489530.1_3'UTR|AC009487.4_ENST00000437683.1_RNA	NM_006593.2	NP_006584.1	Q16650	TBR1_HUMAN	T-box, brain, 1	389					axon guidance (GO:0007411)|brain development (GO:0007420)|hindbrain development (GO:0030902)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of neuron projection development (GO:0010975)|specification of organ identity (GO:0010092)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(3)	30						CCTTTTGCAAAAGGATTTCGG	0.338																																					p.K389I		Atlas-SNP	.											.	TBR1	59	.	0			c.A1166T						.						120	119	120					2																	162276744		2203	4300	6503	SO:0001583	missense	10716	exon5			TTGCAAAAGGATT	U49250	CCDS33310.1	2q24.2	2011-06-13			ENSG00000136535	ENSG00000136535		"T-boxes"	11590	protein-coding gene	gene with protein product		604616				7619531	Standard	NM_006593		Approved		uc002ubw.1	Q16650	OTTHUMG00000153888	ENST00000389554.3:c.1166A>T	chr2.hg19:g.162276744A>T	ENSP00000374205:p.Lys389Ile	130.0	0.0		127.0	70.0	NM_006593	B0AZS4|B2R6G5|Q14DC5|Q53TH0|Q56A81	Missense_Mutation	SNP	ENST00000389554.3	hg19	CCDS33310.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386862	0.82902	.	.	ENSG00000136535	ENST00000389554;ENST00000539334;ENST00000411412;ENST00000410035	D;D;D	0.83837	-1.77;-1.77;-1.77	5.25	5.25	0.73442	p53-like transcription factor, DNA-binding (1);	0.106321	0.64402	D	0.000005	D	0.94522	0.8236	H	0.98256	4.185	0.80722	D	1	D	0.57571	0.98	D	0.78314	0.991	D	0.96502	0.9372	10	0.87932	D	0	.	15.4594	0.75342	1.0:0.0:0.0:0.0	.	389	Q16650	TBR1_HUMAN	I	389;102;124;102	ENSP00000374205:K389I;ENSP00000393934:K124I;ENSP00000387023:K102I	ENSP00000374205:K389I	K	+	2	0	TBR1	161984990	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.243000	0.95416	2.119000	0.64992	0.533000	0.62120	AAA	.	.		0.338	TBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332845.1	NM_006593		T	162276744	A	T	162276744	3	4	51	1	0	0	0	0	1	0	0	0	15662	14	1	4	1184	4	TBR1	2	162276744	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	21221244	162276744	80922629	15	6539										
SLC4A10	57282	hgsc.bcm.edu	37	chr2	162807235	162807235	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ggctggtttgttacgcctttAggtccaaacccatggtggac	12	10	0	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:162807235A>T	ENST00000446997.1	+	19	2511	c.2418A>T	c.(2416-2418)ttA>ttT	p.L806F	SLC4A10_ENST00000272716.5_Missense_Mutation_p.L776F|SLC4A10_ENST00000375514.5_Missense_Mutation_p.L787F|SLC4A10_ENST00000421911.1_Missense_Mutation_p.L806F|SLC4A10_ENST00000415876.2_Missense_Mutation_p.L776F	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	806					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	TTACGCCTTTAGGTCCAAACC	0.378																																					p.L806F		Atlas-SNP	.											.	SLC4A10	309	.	0			c.A2418T						.						98	90	93					2																	162807235		1851	4088	5939	SO:0001583	missense	57282	exon19			GCCTTTAGGTCCA		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.2418A>T	chr2.hg19:g.162807235A>T	ENSP00000393066:p.Leu806Phe	160.0	0.0		167.0	32.0	NM_001178015	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	hg19	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	A	4.771	0.143285	0.09083	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	5.83	0.663	0.17885	Bicarbonate transporter, C-terminal (1);	0.146510	0.47852	N	0.000206	T	0.74884	0.3775	L	0.31664	0.95	0.48288	D	0.99962	P;P;B	0.42973	0.796;0.796;0.01	P;P;B	0.57720	0.826;0.826;0.028	T	0.69577	-0.5108	10	0.02654	T	1	.	8.4372	0.32795	0.5221:0.0:0.4779:0.0	.	787;776;806	F8W675;Q6U841-2;Q6U841	.;.;S4A10_HUMAN	F	787;776;776;775;806;806;805	ENSP00000364664:L787F;ENSP00000395797:L776F;ENSP00000272716:L776F;ENSP00000393066:L806F;ENSP00000404486:L806F	ENSP00000272716:L776F	L	+	3	2	SLC4A10	162515481	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.257000	0.43240	0.115000	0.18071	0.477000	0.44152	TTA	.	.		0.378	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		T	162807235	A	T	162807235	3	4	51	1	0	0	0	0	1	0	0	0	14666	417	15	4	2577	4	SLC4A10	2	162807235	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	530491	162807235	80392138	16	6540										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166223741	166223741	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttttagactgtgtacggaagTtcaagtgttgtcagataagc	11	5	2	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:166223741T>C	ENST00000375437.2	+	19	3825	c.3535T>C	c.(3535-3537)Ttc>Ctc	p.F1179L	SCN2A_ENST00000283256.6_Missense_Mutation_p.F1179L|SCN2A_ENST00000357398.3_Missense_Mutation_p.F1179L|SCN2A_ENST00000375427.2_Missense_Mutation_p.F1179L	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1179					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGTACGGAAGTTCAAGTGTTG	0.348																																					p.F1179L		Atlas-SNP	.											.	SCN2A	589	.	0			c.T3535C						.						123	119	120					2																	166223741		2203	4300	6503	SO:0001583	missense	6326	exon18			CGGAAGTTCAAGT	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.3535T>C	chr2.hg19:g.166223741T>C	ENSP00000364586:p.Phe1179Leu	119.0	0.0		84.0	4.0	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	hg19	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.709472	0.89018	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1	6.07	6.07	0.98685	Sodium ion transport-associated (1);	0.075804	0.56097	D	0.000023	D	0.93785	0.8013	M	0.92923	3.36	0.53688	D	0.999975	P;P	0.52463	0.953;0.886	P;P	0.54759	0.76;0.758	D	0.94882	0.8040	10	0.72032	D	0.01	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	1179;1179	Q99250-2;Q99250	.;SCN2A_HUMAN	L	1179	ENSP00000364586:F1179L;ENSP00000349973:F1179L;ENSP00000283256:F1179L;ENSP00000364576:F1179L	ENSP00000283256:F1179L	F	+	1	0	SCN2A	165931987	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.217000	0.72218	2.326000	0.78906	0.533000	0.62120	TTC	.	.		0.348	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		C	166223741	T	C	166223741	3	2	51	1	0	0	0	0	1	0	0	0	13931	1725	60	2	3701	2	SCN2A	2	166223741	Missense_Mutation	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10	3416506	166223741	76975632	17	6541										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168105466	168105466	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttgcgcctcttataaaatctCattcatttccagagagttca	5	10	4	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:168105466C>A	ENST00000409195.1	+	9	7653	c.7564C>A	c.(7564-7566)Cat>Aat	p.H2522N	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.H2300N|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.H2522N|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2347				H -> P (in Ref. 8; CAD91146). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.H2522Y(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TATAAAATCTCATTCATTTCC	0.343																																					p.H2522N		Atlas-SNP	.											XIRP2,NS,carcinoma,0,1	XIRP2	914	.	1	Substitution - Missense(1)	cervix(1)	c.C7564A						.						95	91	92					2																	168105466		1816	4067	5883	SO:0001583	missense	129446	exon9			AAATCTCATTCAT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.7564C>A	chr2.hg19:g.168105466C>A	ENSP00000386840:p.His2522Asn	95.0	0.0		93.0	49.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676351	0.67928	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02631	4.22;4.22;4.22	5.97	5.09	0.68999	.	0.111234	0.64402	N	0.000012	T	0.05090	0.0136	M	0.67953	2.075	0.32606	N	0.525195	B;P;P	0.36412	0.417;0.552;0.552	B;B;B	0.33042	0.075;0.157;0.157	T	0.10941	-1.0608	10	0.27785	T	0.31	-11.6991	15.5358	0.76001	0.1394:0.8606:0.0:0.0	.	2347;2347;2300	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	N	2522;2522;2300	ENSP00000386840:H2522N;ENSP00000295237:H2522N;ENSP00000387255:H2300N	ENSP00000295237:H2522N	H	+	1	0	XIRP2	167813712	0.975000	0.34042	0.988000	0.46212	0.971000	0.66376	2.557000	0.45871	1.512000	0.48834	0.655000	0.94253	CAT	.	.		0.343	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168105466	C	A	168105466	3	1	51	1	0	0	0	0	1	0	0	0	17445	826	29	3	7594	3	XIRP2	2	168105466	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	1881725	168105466	75093907	18	6542										
TTN	7273	hgsc.bcm.edu	37	chr2	179404631	179404631	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tggtatggtaagtctgatgaCgccaccttgccttacaaaga	10	9	1	3	rs533651182		TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:179404631C>T	ENST00000591111.1	-	302	93462	c.93238G>A	c.(93238-93240)Gtc>Atc	p.V31080I	TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V23848I|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V32721I|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V30153I|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V23781I|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V23656I|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588244.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000585358.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31080	Ig-like 139.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V23656I(2)|p.V30153I(1)|p.V30151I(1)|p.V23848I(1)|p.V23781I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTCTGATGACGCCACCTTGC	0.398													C|||	1	0.000199681	0	0	5008	,	,		24212	0.001		0	False		,,,				2504	0				p.V32721I		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,0,4	TTN	18412	.	6	Substitution - Missense(6)	prostate(6)	c.G98161A						.						133	123	126					2																	179404631		1946	4154	6100	SO:0001583	missense	7273	exon352			TGATGACGCCACC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.93238G>A	chr2.hg19:g.179404631C>T	ENSP00000465570:p.Val31080Ile	172.0	0.0		127.0	55.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.74	3.464891	0.63513	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	6.17	6.17	0.99709	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.53238	0.1784	L	0.50333	1.59	0.49130	D	0.999752	D;D;D;D	0.55800	0.973;0.973;0.973;0.973	P;P;P;P	0.51101	0.586;0.586;0.586;0.659	T	0.51593	-0.8686	9	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	23656;23781;23848;31080	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	30153;23656;23848;23781;23653	ENSP00000343764:V30153I;ENSP00000434586:V23656I;ENSP00000340554:V23848I;ENSP00000352154:V23781I	ENSP00000340554:V23848I	V	-	1	0	TTN	179112877	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.026000	0.70873	2.941000	0.99782	0.655000	0.94253	GTC	.	.		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179404631	C	T	179404631	3	4	51	1	0	0	0	0	1	0	0	0	16750	536	19	1	9862	1	TTN	2	179404631	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	11299165	179404631	63794742	19	6543										
TTN	7273	hgsc.bcm.edu	37	chr2	179596523	179596523	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	acaaacttgaggatctgcagGctaaccagatgatcctgaat	9	9	1	4	rs372588069		TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:179596523G>A	ENST00000591111.1	-	56	16352	c.16128C>T	c.(16126-16128)agC>agT	p.S5376S	TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.S5693S|TTN_ENST00000342992.6_Silent_p.S4449S|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	12195	Ig-like 34.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGATCTGCAGGCTAACCAGAT	0.488																																					p.S5693S		Atlas-SNP	.											.	TTN	18412	.	0			c.C17079T						.						125	125	125					2																	179596523		1966	4160	6126	SO:0001819	synonymous_variant	7273	exon58			CTGCAGGCTAACC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.16128C>T	chr2.hg19:g.179596523G>A		134.0	0.0		111.0	24.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179596523	G	A	179596523	2	1	51	1	0	0	0	0	0	0	0	1	16750	1194	42	3		3	TTN	2	179596523	Silent	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	191892	179596523	63602850	20	6544										
CCDC141	285025	hgsc.bcm.edu	37	chr2	179718305	179718305	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tgcactctgtggaatattttCcaactcttacaactgtggca	7	10	2	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:179718305C>T	ENST00000420890.2	-	20	3224	c.3107G>A	c.(3106-3108)gGa>gAa	p.G1036E	CCDC141_ENST00000295723.5_Missense_Mutation_p.G461E	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	1036										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			GGAATATTTTCCAACTCTTAC	0.388																																					p.G1036E		Atlas-SNP	.											CCDC141_ENST00000420890,mucosal,malignant_melanoma,0,4	CCDC141	362	.	0			c.G3107A						.						111	111	111					2																	179718305		2203	4300	6503	SO:0001583	missense	285025	exon20			TATTTTCCAACTC	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.3107G>A	chr2.hg19:g.179718305C>T	ENSP00000395995:p.Gly1036Glu	50.0	0.0		57.0	12.0	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	hg19		.	.	.	.	.	.	.	.	.	.	C	17.39	3.377901	0.61735	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723	T;T;T	0.31247	1.5;1.5;1.5	5.85	5.85	0.93711	.	0.000000	0.51477	D	0.000090	T	0.29976	0.0750	L	0.34521	1.04	0.37079	D	0.898886	P	0.49358	0.923	P	0.47470	0.548	T	0.06972	-1.0797	10	0.22109	T	0.4	-12.8104	14.34	0.66619	0.0:0.9295:0.0:0.0704	.	461	Q6ZP82	CC141_HUMAN	E	1036;480;461	ENSP00000395995:G1036E;ENSP00000344627:G480E;ENSP00000295723:G461E	ENSP00000295723:G461E	G	-	2	0	CCDC141	179426550	0.998000	0.40836	0.998000	0.56505	0.960000	0.62799	3.951000	0.56684	2.768000	0.95171	0.655000	0.94253	GGA	.	.		0.388	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		T	179718305	C	T	179718305	3	4	51	1	0	0	0	0	1	0	0	0	2777	855	30	3	1261	3	CCDC141	2	179718305	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	121782	179718305	63481068	21	6545										
SGOL2	151246	hgsc.bcm.edu	37	chr2	201437093	201437093	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aatcccagctctttctactaGagataatgaaaatcaatgtg	6	8	3	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:201437093G>A	ENST00000357799.4	+	7	2122	c.2024G>A	c.(2023-2025)aGa>aAa	p.R675K		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	675					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)		p.R675T(1)		NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						CTTTCTACTAGAGATAATGAA	0.348																																					p.R675K		Atlas-SNP	.											SGOL2,NS,carcinoma,0,1	SGOL2	126	.	1	Substitution - Missense(1)	breast(1)	c.G2024A						.						59	55	56					2																	201437093		1818	4071	5889	SO:0001583	missense	151246	exon7			CTACTAGAGATAA	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.2024G>A	chr2.hg19:g.201437093G>A	ENSP00000350447:p.Arg675Lys	181.0	1.0		162.0	16.0	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	hg19	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.353050	0.00217	.	.	ENSG00000163535	ENST00000357799	T	0.12672	2.66	5.25	0.149	0.14863	.	1.035800	0.07584	N	0.920789	T	0.04452	0.0122	N	0.04090	-0.28	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.40251	-0.9573	10	0.02654	T	1	3.6971	3.3255	0.07066	0.2599:0.0:0.3698:0.3703	.	675;675;675	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	K	675	ENSP00000350447:R675K	ENSP00000350447:R675K	R	+	2	0	SGOL2	201145338	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.340000	0.02650	0.099000	0.17552	0.585000	0.79938	AGA	.	.		0.348	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		A	201437093	G	A	201437093	3	1	51	1	0	0	0	0	1	0	0	0	14232	942	33	3	2046	3	SGOL2	2	201437093	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	21718788	201437093	41762280	22	6546										
DYTN	391475	hgsc.bcm.edu	37	chr2	207527925	207527925	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tttcgcagagcatgctctgcAtttgtgtgacttctgtgact	10	9	2	3			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:207527925A>G	ENST00000452335.2	-	11	1451	c.1335T>C	c.(1333-1335)aaT>aaC	p.N445N		NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	445						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		CATGCTCTGCATTTGTGTGAC	0.463																																					p.N445N		Atlas-SNP	.											.	DYTN	168	.	0			c.T1335C						.						171	162	165					2																	207527925		2017	4191	6208	SO:0001819	synonymous_variant	391475	exon11			CTCTGCATTTGTG	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.1335T>C	chr2.hg19:g.207527925A>G		229.0	0.0		165.0	44.0	NM_001093730		Silent	SNP	ENST00000452335.2	hg19	CCDS46502.1																																																																																			.	.		0.463	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			G	207527925	A	G	207527925	2	3	51	1	0	0	0	0	0	0	0	1	4863	214	8	2		2	DYTN	2	207527925	Silent	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	6090832	207527925	35671448	23	6547										
SPAG16	79582	hgsc.bcm.edu	37	chr2	214727353	214727353	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gactgctgcttccatcccagGtcagtgcacaggacccctag	10	15	1	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:214727353G>T	ENST00000331683.5	+	11	1309		c.e11+1		SPAG16_ENST00000374309.3_Splice_Site	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16						cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		TCCATCCCAGGTCAGTGCACA	0.493																																					.		Atlas-SNP	.											.	SPAG16	134	.	0			c.1214+1G>T						.						91	76	81					2																	214727353		2203	4300	6503	SO:0001630	splice_region_variant	79582	exon11			TCCCAGGTCAGTG	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.1214+1G>T	chr2.hg19:g.214727353G>T		160.0	0.0		85.0	11.0	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Splice_Site	SNP	ENST00000331683.5	hg19	CCDS2396.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.986830	0.74589	.	.	ENSG00000144451	ENST00000331683;ENST00000374309;ENST00000451561	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7858	0.88538	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SPAG16	214435598	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	6.713000	0.74686	2.707000	0.92482	0.643000	0.83706	.	.	.		0.493	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	Intron	T	214727353	G	T	214727353	5	4	51	1	0	0	0	0	0	0	1	0	14993	1275	44	3	1273	3	SPAG16	2	214727353	Splice_Site	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	7199428	214727353	28472020	24	6548										
CYP27A1	1593	hgsc.bcm.edu	37	chr2	219679131	219679131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ctgtggtccccacaaactccCggatcatagaaaaggaaatt	8	11	1	1	rs573951598		TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr2:219679131C>T	ENST00000258415.4	+	7	1640	c.1213C>T	c.(1213-1215)Cgg>Tgg	p.R405W		NM_000784.3	NP_000775.1	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A, polypeptide 1	405			R -> Q (in CTX). {ECO:0000269|PubMed:9186905}.		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	cholestanetriol 26-monooxygenase activity (GO:0047749)|cholesterol 26-hydroxylase activity (GO:0031073)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(3)|urinary_tract(1)	26		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Chenodeoxycholic acid(DB06777)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Pegvisomant(DB00082)	CACAAACTCCCGGATCATAGA	0.547													C|||	1	0.000199681	0	0.0014	5008	,	,		19544	0		0	False		,,,				2504	0				p.R405W		Atlas-SNP	.											.	CYP27A1	52	.	0			c.C1213T	GRCh37	CM004249	CYP27A1	M		.						112	116	115					2																	219679131		2203	4300	6503	SO:0001583	missense	1593	exon7			AACTCCCGGATCA	BC017044	CCDS2423.1	2q35	2013-09-19	2003-01-14		ENSG00000135929	ENSG00000135929		"Cytochrome P450s"	2605	protein-coding gene	gene with protein product	"cerebrotendinous xanthomatosis"	606530	"cytochrome P450, subfamily XXVIIA (steroid 27-hydroxylase, cerebrotendinous xanthomatosis), polypeptide 1"	CYP27		2019602	Standard	NM_000784		Approved	CTX, CP27	uc002viz.4	Q02318	OTTHUMG00000048238	ENST00000258415.4:c.1213C>T	chr2.hg19:g.219679131C>T	ENSP00000258415:p.Arg405Trp	137.0	0.0		84.0	11.0	NM_000784	A8K303|Q6LDB4|Q86YQ6	Missense_Mutation	SNP	ENST00000258415.4	hg19	CCDS2423.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.877821	0.72294	.	.	ENSG00000135929	ENST00000258415	T	0.81078	-1.45	5.75	3.72	0.42706	.	0.000000	0.85682	D	0.000000	D	0.91955	0.7452	H	0.95611	3.695	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	D	0.93639	0.6963	10	0.87932	D	0	-32.2986	12.5615	0.56283	0.3668:0.6332:0.0:0.0	.	405	Q02318	CP27A_HUMAN	W	405	ENSP00000258415:R405W	ENSP00000258415:R405W	R	+	1	2	CYP27A1	219387375	0.440000	0.25618	0.948000	0.38648	0.810000	0.45777	1.129000	0.31381	1.372000	0.46190	0.561000	0.74099	CGG	.	.		0.547	CYP27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109734.4			T	219679131	C	T	219679131	3	4	51	1	0	0	0	0	1	0	0	0	4160	643	23	1	1239	1	CYP27A1	2	219679131	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	4951778	219679131	23520242	25	6549										
MTMR14	64419	hgsc.bcm.edu	37	chr3	9712791	9712791	+	Frame_Shift_Del	DEL	A	A	-													0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tgacatcaagctgcttcgatAcctgtcagtcaaatacatct							TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr3:9712791delA	ENST00000296003.4	+	6	736	c.614delA	c.(613-615)tacfs	p.Y205fs	MTMR14_ENST00000353332.5_Frame_Shift_Del_p.Y205fs|MTMR14_ENST00000351233.5_Frame_Shift_Del_p.Y205fs|MTMR14_ENST00000420925.1_Intron	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	205					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(2)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	21	Medulloblastoma(99;0.227)					CTGCTTCGATACCTGTCAGTC	0.453																																					p.Y205fs		Atlas-Indel,Pindel	.											.	MTMR14	43	.	0			c.613delT						.						132	128	129					3																	9712791		2020	4189	6209	SO:0001589	frameshift_variant	64419	exon6			.	BC001674	CCDS43043.1, CCDS43044.1, CCDS43045.1	3p26	2011-06-09	2006-12-18	2006-12-18	ENSG00000163719	ENSG00000163719		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	26190	protein-coding gene	gene with protein product	"egg-derived tyrosine phosphatase homolog (Drosophila)"	611089	"chromosome 3 open reading frame 29"	C3orf29		15186772	Standard	NM_022485		Approved	FLJ22405, FLJ90311, hJumpy, hEDTP	uc003brz.3	Q8NCE2	OTTHUMG00000155111	ENST00000296003.4:c.614delA	chr3.hg19:g.9712791delA	ENSP00000296003:p.Tyr205fs	148.0	0.0		145.0	66.0	NM_001077525	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Frame_Shift_Del	DEL	ENST00000296003.4	hg19	CCDS43043.1																																																																																			.	.		0.453	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485		-	9712791	A	-	9712791	7	5	51	1	0	1	0	1	0	0	0	0	9951	391	14	0	636	0	MTMR14	3	9712791	Frame_Shift_Del	DEL	A	TCGA-BW-A5NO-01A-11D-A27I-10		9712791	188309639	26	6550										
ERC2	26059	hgsc.bcm.edu	37	chr3	56183107	56183107	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ccattggcttttaacatctgGatctcatcctcaagatccct	5	13	3	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr3:56183107G>A	ENST00000288221.6	-	5	1458	c.1203C>T	c.(1201-1203)atC>atT	p.I401I		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	401						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		TTAACATCTGGATCTCATCCT	0.358																																					p.I401I		Atlas-SNP	.											.	ERC2	221	.	0			c.C1203T						.						130	124	126					3																	56183107		1872	4113	5985	SO:0001819	synonymous_variant	26059	exon5			CATCTGGATCTCA	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.1203C>T	chr3.hg19:g.56183107G>A		179.0	0.0		173.0	60.0	NM_015576	Q2T9F6|Q86TK4	Silent	SNP	ENST00000288221.6	hg19	CCDS46851.1	.	.	.	.	.	.	.	.	.	.	G	10.28	1.306145	0.23736	.	.	ENSG00000187672	ENST00000492584	.	.	.	5.82	4.95	0.65309	.	.	.	.	.	T	0.60728	0.2291	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59123	-0.7513	4	.	.	.	-9.2696	9.8606	0.41112	0.0735:0.0:0.7567:0.1699	.	.	.	.	F	40	.	.	S	-	2	0	ERC2	56158147	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.893000	0.39758	1.462000	0.47948	0.650000	0.86243	TCC	.	.		0.358	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		A	56183107	G	A	56183107	2	1	51	1	0	0	0	0	0	0	0	1	5213	1164	41	3		3	ERC2	3	56183107	Silent	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	46470316	56183107	141839323	27	6551										
LSAMP	4045	hgsc.bcm.edu	37	chr3	115805264	115805264	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	atcatagacatccaccttctGgattcggaggctgtattcca	8	11	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr3:115805264G>C	ENST00000490035.2	-	2	794	c.295C>G	c.(295-297)Cag>Gag	p.Q99E	LSAMP_ENST00000539563.1_Missense_Mutation_p.Q96E	NM_002338.3	NP_002329.2	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	99	Ig-like C2-type 1.				cell adhesion (GO:0007155)|locomotory exploration behavior (GO:0035641)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(1)|large_intestine(4)|lung(14)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		TCCACCTTCTGGATTCGGAGG	0.498																																					p.Q99E		Atlas-SNP	.											.	LSAMP	62	.	0			c.C295G						.						109	100	103					3																	115805264		2203	4300	6503	SO:0001583	missense	4045	exon2			CCTTCTGGATTCG	U41901	CCDS2982.1	3q13.2-q21	2013-01-11			ENSG00000185565	ENSG00000185565		"Immunoglobulin superfamily / I-set domain containing"	6705	protein-coding gene	gene with protein product	"IgLON family member 3"	603241				9615236	Standard	NM_002338		Approved	LAMP, IGLON3	uc003ebs.3	Q13449	OTTHUMG00000159308	ENST00000490035.2:c.295C>G	chr3.hg19:g.115805264G>C	ENSP00000419000:p.Gln99Glu	321.0	0.0		270.0	105.0	NM_002338	Q8IV49	Missense_Mutation	SNP	ENST00000490035.2	hg19	CCDS2982.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.663615	0.67700	.	.	ENSG00000185565	ENST00000333617;ENST00000490035;ENST00000539563;ENST00000474851	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	5.82	5.82	0.92795	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.73156	0.3551	N	0.25286	0.73	0.54753	D	0.999986	D;B	0.53885	0.963;0.21	D;B	0.71414	0.973;0.173	T	0.71652	-0.4528	10	0.38643	T	0.18	-10.8766	20.0925	0.97824	0.0:0.0:1.0:0.0	.	99;99	B2RCU8;Q13449	.;LSAMP_HUMAN	E	83;99;96;133	ENSP00000328455:Q83E;ENSP00000419000:Q99E;ENSP00000443429:Q96E;ENSP00000418506:Q133E	ENSP00000328455:Q83E	Q	-	1	0	LSAMP	117287954	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.839000	0.86812	2.751000	0.94390	0.555000	0.69702	CAG	.	.		0.498	LSAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354495.4	NM_002338		C	115805264	G	C	115805264	3	2	51	1	0	0	0	0	1	0	0	0	9057	1357	47	4	745	4	LSAMP	3	115805264	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	59622157	115805264	82217166	28	6552										
ADPRH	141	hgsc.bcm.edu	37	chr3	119306692	119306692	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gctagggctttatattctctCgggtcaaaagaagacactgt	10	8	2	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr3:119306692C>A	ENST00000478399.1	+	4	2446	c.1041C>A	c.(1039-1041)ctC>ctA	p.L347L	ADPRH_ENST00000478927.1_Silent_p.L347L|ADPRH_ENST00000465513.1_Silent_p.L347L|ADPRH_ENST00000357003.3_Silent_p.L347L|ADPRH_ENST00000471850.1_3'UTR			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	347					cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		TATATTCTCTCGGGTCAAAAG	0.403																																					p.L347L	GBM(133;579 1804 5989 9967 40052)	Atlas-SNP	.											.	ADPRH	33	.	0			c.C1041A						.						81	86	84					3																	119306692		2203	4300	6503	SO:0001819	synonymous_variant	141	exon5			TTCTCTCGGGTCA	L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843			269	protein-coding gene	gene with protein product		603081				8349667, 12070318	Standard	NM_001125		Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.1041C>A	chr3.hg19:g.119306692C>A		53.0	0.0		62.0	32.0	NM_001125	B2R8H1|D3DN83	Silent	SNP	ENST00000478399.1	hg19	CCDS2990.1																																																																																			.	.		0.403	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355199.1	NM_001125		A	119306692	C	A	119306692	2	1	51	1	0	0	0	0	0	0	0	1	331	871	31	1		1	ADPRH	3	119306692	Silent	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	3501428	119306692	78715738	29	6553										
AADACL2	344752	hgsc.bcm.edu	37	chr3	151475327	151475327	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gacttcaccattttatttacGtctaggtcttaggataagag	8	7	3	1	rs373909154		TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr3:151475327G>A	ENST00000356517.3	+	5	1260	c.1151G>A	c.(1150-1152)cGt>cAt	p.R384H	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_207365.3	NP_997248.2	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2	384						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(13)|skin(2)	24			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			TTTTATTTACGTCTAGGTCTT	0.333													G|||	1	0.000199681	8e-04	0	5008	,	,		19959	0		0	False		,,,				2504	0				p.R384H		Atlas-SNP	.											.	AADACL2	102	.	0			c.G1151A						.	G	HIS/ARG	0,4406		0,0,2203	81	84	83		1151	-3.5	0	3		83	1,8595	1.2+/-3.3	0,1,4297	no	missense	AADACL2	NM_207365.3	29	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	benign	384/402	151475327	1,13001	2203	4298	6501	SO:0001583	missense	344752	exon5			ATTTACGTCTAGG	BC065724	CCDS3161.2	3q25.1	2010-12-14			ENSG00000197953	ENSG00000197953			24427	protein-coding gene	gene with protein product							Standard	NM_207365		Approved	MGC72001	uc003ezc.3	Q6P093	OTTHUMG00000155914	ENST00000356517.3:c.1151G>A	chr3.hg19:g.151475327G>A	ENSP00000348911:p.Arg384His	144.0	0.0		148.0	16.0	NM_207365	Q5HYJ4	Missense_Mutation	SNP	ENST00000356517.3	hg19	CCDS3161.2	.	.	.	.	.	.	.	.	.	.	G	10.50	1.366462	0.24771	0.0	1.16E-4	ENSG00000197953	ENST00000356517	T	0.59638	0.25	5.15	-3.55	0.04639	.	1.518380	0.03127	N	0.164612	T	0.35595	0.0937	N	0.04018	-0.295	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.30208	-0.9986	10	0.39692	T	0.17	-15.833	11.3473	0.49567	0.5341:0.0:0.4659:0.0	.	384	Q6P093	ADCL2_HUMAN	H	384	ENSP00000348911:R384H	ENSP00000348911:R384H	R	+	2	0	AADACL2	152958017	0.000000	0.05858	0.000000	0.03702	0.119000	0.20118	0.295000	0.19065	-0.385000	0.07833	-0.964000	0.02622	CGT	.	.		0.333	AADACL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342288.3	NM_207365		A	151475327	G	A	151475327	3	1	51	1	0	0	0	0	1	0	0	0	11	1145	40	1	1169	1	AADACL2	3	151475327	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	32168635	151475327	46547103	30	6554										
GHSR	2693	hgsc.bcm.edu	37	chr3	172162985	172162985	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tagattctgtccaggcccgaGaactttcatctttcagagtg	9	10	4	3			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr3:172162985G>T	ENST00000241256.2	-	2	1109	c.1067C>A	c.(1066-1068)tCt>tAt	p.S356Y		NM_198407.2	NP_940799.1	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor	356					actin polymerization or depolymerization (GO:0008154)|adult feeding behavior (GO:0008343)|cellular response to insulin stimulus (GO:0032869)|decidualization (GO:0046697)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone secretion (GO:0030252)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin secretion (GO:0046676)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of appetite (GO:0032100)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of hindgut contraction (GO:0043134)|regulation of synapse assembly (GO:0051963)|response to food (GO:0032094)|response to hormone (GO:0009725)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|growth hormone secretagogue receptor activity (GO:0001616)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	33	Ovarian(172;0.00143)|Breast(254;0.197)		Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			CCAGGCCCGAGAACTTTCATC	0.463																																					p.S356Y	Esophageal Squamous(93;641 1401 20883 29581 34638)	Atlas-SNP	.											.	GHSR	104	.	0			c.C1067A						.						91	103	98					3																	172162985		2203	4300	6503	SO:0001583	missense	2693	exon2			GCCCGAGAACTTT	AY429112	CCDS3218.1, CCDS46959.1	3q26.31	2012-08-08			ENSG00000121853	ENSG00000121853		"GPCR / Class A : Ghrelin receptors"	4267	protein-coding gene	gene with protein product		601898				8688086	Standard	NM_198407		Approved		uc003fib.2	Q92847	OTTHUMG00000156946	ENST00000241256.2:c.1067C>A	chr3.hg19:g.172162985G>T	ENSP00000241256:p.Ser356Tyr	93.0	0.0		193.0	31.0	NM_198407	Q14D12|Q6ISR8|Q92848|Q96RJ7	Missense_Mutation	SNP	ENST00000241256.2	hg19	CCDS3218.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.777648	0.70107	.	.	ENSG00000121853	ENST00000241256	T	0.69175	-0.38	5.78	5.78	0.91487	.	0.113831	0.64402	D	0.000009	T	0.64583	0.2611	L	0.55481	1.735	0.80722	D	1	P	0.39920	0.695	B	0.36719	0.231	T	0.64080	-0.6491	10	0.36615	T	0.2	-11.1438	20.0039	0.97428	0.0:0.0:1.0:0.0	.	356	Q92847	GHSR_HUMAN	Y	356	ENSP00000241256:S356Y	ENSP00000241256:S356Y	S	-	2	0	GHSR	173645679	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.932000	0.63476	2.722000	0.93159	0.557000	0.71058	TCT	.	.		0.463	GHSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346728.1	NM_004122		T	172162985	G	T	172162985	3	4	51	1	0	0	0	0	1	0	0	0	6383	942	33	3	37	3	GHSR	3	172162985	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	20687658	172162985	25859445	31	6555										
DNAJC19	131118	hgsc.bcm.edu	37	chr3	180706002	180706002	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	agcaatggtcagtccaactgCtaccactgtactggcctggt	10	12	1	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr3:180706002C>A	ENST00000382564.2	-	2	189	c.19G>T	c.(19-21)Gca>Tca	p.A7S	DNAJC19_ENST00000491873.1_Intron|DNAJC19_ENST00000479269.1_5'UTR|DNAJC19_ENST00000486355.1_Missense_Mutation_p.A7S	NM_145261.3	NP_660304.1	Q96DA6	TIM14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 19	7					cellular protein metabolic process (GO:0044267)|genitalia development (GO:0048806)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				large_intestine(2)|lung(1)	3	all_cancers(143;3.12e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-36)|OV - Ovarian serous cystadenocarcinoma(80;1.55e-22)			AGTCCAACTGCTACCACTGTA	0.438																																					p.A7S		Atlas-SNP	.											.	DNAJC19	4	.	0			c.G19T						.						82	77	78					3																	180706002		2203	4300	6503	SO:0001583	missense	131118	exon2			CAACTGCTACCAC		CCDS33895.1, CCDS54684.1	3q26.33	2014-09-17			ENSG00000205981	ENSG00000205981		"Heat shock proteins / DNAJ (HSP40)"	30528	protein-coding gene	gene with protein product		608977				19564938	Standard	NM_145261		Approved	TIMM14, Tim14, Pam18	uc003fkt.3	Q96DA6	OTTHUMG00000158180	ENST00000382564.2:c.19G>T	chr3.hg19:g.180706002C>A	ENSP00000372005:p.Ala7Ser	250.0	0.0		217.0	24.0	NM_145261	B2R4B1|C9JBV1	Missense_Mutation	SNP	ENST00000382564.2	hg19	CCDS33895.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.816459	0.90790	.	.	ENSG00000205981	ENST00000382564	.	.	.	5.37	5.37	0.77165	.	0.095488	0.64402	D	0.000001	T	0.72914	0.3520	M	0.86953	2.85	0.80722	D	1	P	0.48694	0.914	P	0.46419	0.516	T	0.78687	-0.2107	9	0.59425	D	0.04	-23.9316	16.3905	0.83533	0.0:1.0:0.0:0.0	.	7	Q96DA6	TIM14_HUMAN	S	7	.	ENSP00000372005:A7S	A	-	1	0	DNAJC19	182188696	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.879000	0.69690	2.677000	0.91161	0.655000	0.94253	GCA	.	.		0.438	DNAJC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350336.1	NM_145261		A	180706002	C	A	180706002	3	1	51	1	0	0	0	0	1	0	0	0	4640	797	28	3	351	3	DNAJC19	3	180706002	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	8543017	180706002	17316428	32	6556										
KLB	152831	hgsc.bcm.edu	37	chr4	39439384	39439384	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	atacgagtgtttggttatacTgcctggtctctcctggatgg	12	8	1	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr4:39439384T>C	ENST00000257408.4	+	3	1471	c.1374T>C	c.(1372-1374)acT>acC	p.T458T		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	458	Glycosyl hydrolase-1 1.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						TTGGTTATACTGCCTGGTCTC	0.408																																					p.T458T		Atlas-SNP	.											.	KLB	95	.	0			c.T1374C						.						212	199	203					4																	39439384		2203	4300	6503	SO:0001819	synonymous_variant	152831	exon3			TTATACTGCCTGG	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.1374T>C	chr4.hg19:g.39439384T>C		155.0	0.0		123.0	11.0	NM_175737	Q2M3K8	Silent	SNP	ENST00000257408.4	hg19	CCDS3451.1																																																																																			.	.		0.408	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		C	39439384	T	C	39439384	2	2	51	1	0	0	0	0	0	0	0	1	8341	1567	55	2		2	KLB	4	39439384	Silent	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10		39439384	151714892	33	6557										
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54256750	54256750	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttaatggagttccactcttaGaggtagatttggattctttt	9	5	2	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr4:54256750G>C	ENST00000337488.6	+	7	654	c.460G>C	c.(460-462)Gag>Cag	p.E154Q	FIP1L1_ENST00000306932.6_Missense_Mutation_p.E139Q|FIP1L1_ENST00000507922.1_Missense_Mutation_p.E139Q|FIP1L1_ENST00000507166.1_Missense_Mutation_p.E154Q|FIP1L1_ENST00000358575.5_Missense_Mutation_p.E139Q	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	154	Necessary for stimulating PAPOLA activity.|Sufficient for interaction with CPSF4.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TCCACTCTTAGAGGTAGATTT	0.343			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.E154Q		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.G460C						.						113	113	113					4																	54256750		2203	4300	6503	SO:0001583	missense	81608	exon7			CTCTTAGAGGTAG	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.460G>C	chr4.hg19:g.54256750G>C	ENSP00000336752:p.Glu154Gln	57.0	0.0		61.0	11.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Missense_Mutation	SNP	ENST00000337488.6	hg19	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.081579	0.76528	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000507922;ENST00000306932;ENST00000507166	T	0.78816	-1.21	5.43	5.43	0.79202	Pre-mRNA polyadenylation factor Fip1 (1);	0.000000	0.64402	D	0.000001	D	0.84915	0.5578	L	0.48174	1.505	0.80722	D	1	D;D;P;D	0.89917	1.0;0.989;0.879;1.0	D;D;P;D	0.79108	0.992;0.979;0.855;0.992	T	0.83208	-0.0075	10	0.36615	T	0.2	-15.4454	19.2217	0.93799	0.0:0.0:1.0:0.0	.	139;139;154;139	G3XAD6;Q6UN15-3;Q6UN15;Q6UN15-4	.;.;FIP1_HUMAN;.	Q	154;139;139;139;154	ENSP00000423325:E154Q	ENSP00000302993:E139Q	E	+	1	0	FIP1L1	53951507	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.429000	0.97481	2.534000	0.85438	0.591000	0.81541	GAG	.	.		0.343	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		C	54256750	G	C	54256750	3	2	51	1	0	0	0	0	1	0	0	0	5904	943	33	4	486	4	FIP1L1	4	54256750	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	14817366	54256750	136897526	34	6558										
CENPE	1062	hgsc.bcm.edu	37	chr4	104065713	104065713	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tctatttcacacattttctcCtgagtctcattgacagctgt	5	11	4	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr4:104065713C>T	ENST00000265148.3	-	33	5009	c.4920G>A	c.(4918-4920)caG>caA	p.Q1640Q	CENPE_ENST00000380026.3_Silent_p.Q1615Q	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1640					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		ACATTTTCTCCTGAGTCTCAT	0.343																																					p.Q1640Q		Atlas-SNP	.											.	CENPE	253	.	0			c.G4920A						.						92	89	90					4																	104065713		2203	4299	6502	SO:0001819	synonymous_variant	1062	exon33			TTTCTCCTGAGTC	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.4920G>A	chr4.hg19:g.104065713C>T		40.0	0.0		37.0	21.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	hg19	CCDS34042.1																																																																																			.	.		0.343	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	104065713	C	T	104065713	2	4	51	1	0	0	0	0	0	0	0	1	3232	680	24	3		3	CENPE	4	104065713	Silent	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	49808963	104065713	87088563	35	6559										
NDST4	64579	hgsc.bcm.edu	37	chr4	115754838	115754838	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	atccatcacagtagctgggtCagatctcagctgctgtccat	9	12	3	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr4:115754838C>G	ENST00000264363.2	-	12	2998	c.2320G>C	c.(2320-2322)Gac>Cac	p.D774H		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	774	Heparan sulfate N-sulfotransferase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		GTAGCTGGGTCAGATCTCAGC	0.378																																					p.D774H		Atlas-SNP	.											.	NDST4	193	.	0			c.G2320C						.						73	70	71					4																	115754838		2203	4300	6503	SO:0001583	missense	64579	exon12			CTGGGTCAGATCT	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.2320G>C	chr4.hg19:g.115754838C>G	ENSP00000264363:p.Asp774His	192.0	0.0		104.0	9.0	NM_022569	Q2KHM8	Missense_Mutation	SNP	ENST00000264363.2	hg19	CCDS3706.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.336813	0.81801	.	.	ENSG00000138653	ENST00000264363	D	0.86097	-2.07	5.98	5.13	0.70059	Sulfotransferase domain (1);	0.046170	0.85682	D	0.000000	D	0.89441	0.6716	M	0.74258	2.255	0.49299	D	0.999773	P	0.39003	0.654	P	0.48334	0.574	D	0.90308	0.4335	10	0.87932	D	0	.	16.6677	0.85257	0.1308:0.8692:0.0:0.0	.	774	Q9H3R1	NDST4_HUMAN	H	774	ENSP00000264363:D774H	ENSP00000264363:D774H	D	-	1	0	NDST4	115974287	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.661000	0.68025	1.511000	0.48818	0.650000	0.86243	GAC	.	.		0.378	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		G	115754838	C	G	115754838	3	3	51	1	0	0	0	0	1	0	0	0	10267	826	29	4	310	4	NDST4	4	115754838	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	11689125	115754838	75399438	36	6560										
HHIP	64399	hgsc.bcm.edu	37	chr4	145567924	145567924	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gggaaagaaacgaagggagcGgagcaaggaggagaaggtgc	20	4	0	2	rs199961348		TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr4:145567924G>A	ENST00000296575.3	+	1	752	c.97G>A	c.(97-99)Gga>Aga	p.G33R	HHIP-AS1_ENST00000512359.1_RNA|HHIP_ENST00000434550.2_Missense_Mutation_p.G33R|HHIP-AS1_ENST00000503066.1_RNA|HHIP-AS1_ENST00000508269.1_RNA	NM_022475.2	NP_071920.1	Q96QV1	HHIP_HUMAN	hedgehog interacting protein	33					carbohydrate metabolic process (GO:0005975)|dorsal/ventral pattern formation (GO:0009953)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|negative regulation of signal transduction (GO:0009968)|negative regulation of smoothened signaling pathway (GO:0045879)|neuroblast proliferation (GO:0007405)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|skeletal system morphogenesis (GO:0048705)|smoothened signaling pathway (GO:0007224)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	hedgehog family protein binding (GO:0097108)|oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		CGAAGGGAGCGGAGCAAGGAG	0.567																																					p.G33R		Atlas-SNP	.											HHIP,caecum,carcinoma,0,1	HHIP	100	.	0			c.G97A						.						89	95	93					4																	145567924		2203	4300	6503	SO:0001583	missense	64399	exon1			GGGAGCGGAGCAA	AK024645	CCDS3762.1	4q31.21-q31.3	2008-08-29	2001-11-29		ENSG00000164161	ENSG00000164161			14866	protein-coding gene	gene with protein product		606178	"hedgehog-interacting protein"			11435703, 11731473	Standard	NM_022475		Approved	HIP, FLJ20992	uc003ijs.2	Q96QV1	OTTHUMG00000161428	ENST00000296575.3:c.97G>A	chr4.hg19:g.145567924G>A	ENSP00000296575:p.Gly33Arg	207.0	0.0		43.0	18.0	NM_022475	Q6PK09|Q8NCI7|Q9BXK3|Q9H1J4|Q9H7E7	Missense_Mutation	SNP	ENST00000296575.3	hg19	CCDS3762.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.788555	0.70337	.	.	ENSG00000164161	ENST00000296575;ENST00000434550	T;T	0.50813	3.31;0.73	5.11	4.2	0.49525	.	0.263715	0.43747	D	0.000538	T	0.48857	0.1523	N	0.19112	0.55	0.46336	D	0.998992	D;D	0.67145	0.973;0.996	B;P	0.58780	0.282;0.845	T	0.55198	-0.8178	10	0.66056	D	0.02	-13.8416	15.0244	0.71656	0.0:0.1426:0.8574:0.0	.	33;33	Q96QV1;Q96QV1-2	HHIP_HUMAN;.	R	33	ENSP00000296575:G33R;ENSP00000408587:G33R	ENSP00000296575:G33R	G	+	1	0	HHIP	145787374	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.720000	0.54933	2.373000	0.80994	0.650000	0.86243	GGA	.	.		0.567	HHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364887.2			A	145567924	G	A	145567924	3	1	51	1	0	0	0	0	1	0	0	0	7101	1117	39	1	99	1	HHIP	4	145567924	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	29813086	145567924	45586352	37	6561										
RAPGEF2	9693	hgsc.bcm.edu	37	chr4	160262813	160262813	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aaatttccctccttcagctcAgcactgtggaagttgcaaca	7	12	2	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr4:160262813A>T	ENST00000264431.4	+	14	2568	c.2149A>T	c.(2149-2151)Agc>Tgc	p.S717C		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	717	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		CCTTCAGCTCAGCACTGTGGA	0.373																																					p.S717C		Atlas-SNP	.											.	RAPGEF2	171	.	0			c.A2149T						.						86	80	82					4																	160262813		1894	4129	6023	SO:0001583	missense	9693	exon14			CAGCTCAGCACTG	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.2149A>T	chr4.hg19:g.160262813A>T	ENSP00000264431:p.Ser717Cys	257.0	0.0		172.0	45.0	NM_014247	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	hg19	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.577649	0.86645	.	.	ENSG00000109756	ENST00000264431	T	0.34667	1.35	5.76	5.76	0.90799	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.62221	0.2410	M	0.79614	2.46	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.66654	-0.5869	10	0.87932	D	0	.	16.3668	0.83335	1.0:0.0:0.0:0.0	.	717	Q9Y4G8	RPGF2_HUMAN	C	717	ENSP00000264431:S717C	ENSP00000264431:S717C	S	+	1	0	RAPGEF2	160482263	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	9.313000	0.96297	2.322000	0.78497	0.528000	0.53228	AGC	.	.		0.373	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		T	160262813	A	T	160262813	3	4	51	1	0	0	0	0	1	0	0	0	13059	188	7	4	2203	4	RAPGEF2	4	160262813	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	14694889	160262813	30891463	38	6562										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183650121	183650121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aacatttctctctacagatgGactcattgactgcatggatc	7	10	3	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr4:183650121G>A	ENST00000511685.1	+	14	2495	c.2372G>A	c.(2371-2373)gGa>gAa	p.G791E	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.G791E			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	791					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TCTACAGATGGACTCATTGAC	0.428																																					p.G791E		Atlas-SNP	.											.	.	.	.	0			c.G2372A						.						63	59	60					4																	183650121		1887	4118	6005	SO:0001583	missense	55714	exon13			CAGATGGACTCAT	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.2372G>A	chr4.hg19:g.183650121G>A	ENSP00000424226:p.Gly791Glu	168.0	0.0		106.0	6.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.341944	0.81911	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.12774	2.65;2.65	5.14	5.14	0.70334	.	.	.	.	.	T	0.40067	0.1102	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.66716	0.946	T	0.28870	-1.0030	9	0.87932	D	0	.	18.7873	0.91960	0.0:0.0:1.0:0.0	.	791	Q9P273	TEN3_HUMAN	E	791	ENSP00000424226:G791E;ENSP00000385276:G791E	ENSP00000385276:G791E	G	+	2	0	ODZ3	183887115	1.000000	0.71417	0.992000	0.48379	0.971000	0.66376	9.657000	0.98554	2.666000	0.90696	0.563000	0.77884	GGA	.	.		0.428	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183650121	G	A	183650121	3	1	51	1	0	0	0	0	1	0	0	0	10845	1174	41	3	2422	3	ODZ3	4	183650121	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	23387308	183650121	7504155	39	6563										
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7867391	7867391	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	atgtttggtgttcatccactTtttcagtacatgcctgcaag	8	9	2	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr5:7867391T>A	ENST00000264669.5	-	2	942	c.806A>T	c.(805-807)aAa>aTa	p.K269I	MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000341013.6_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000502509.1_Intron	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	269					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TTCATCCACTTTTTCAGTACA	0.358																																					p.K269I		Atlas-SNP	.											.	FASTKD3	88	.	0			c.A806T						.						83	93	89					5																	7867391		2202	4300	6502	SO:0001583	missense	79072	exon2			TCCACTTTTTCAG	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.806A>T	chr5.hg19:g.7867391T>A	ENSP00000264669:p.Lys269Ile	18.0	0.0		33.0	5.0	NM_024091	Q9BVD3	Missense_Mutation	SNP	ENST00000264669.5	hg19	CCDS3873.1	.	.	.	.	.	.	.	.	.	.	T	16.22	3.060923	0.55432	.	.	ENSG00000124279	ENST00000264669	T	0.30182	1.54	4.85	2.35	0.29111	.	0.536026	0.20873	N	0.084127	T	0.26268	0.0641	L	0.60455	1.87	0.09310	N	1	B	0.31910	0.346	B	0.30316	0.114	T	0.12167	-1.0558	10	0.37606	T	0.19	-12.9531	7.9617	0.30074	0.1359:0.0:0.1425:0.7215	.	269	Q14CZ7	FAKD3_HUMAN	I	269	ENSP00000264669:K269I	ENSP00000264669:K269I	K	-	2	0	FASTKD3	7920391	0.797000	0.28877	0.001000	0.08648	0.725000	0.41563	2.733000	0.47360	0.304000	0.22809	0.528000	0.53228	AAA	.	.		0.358	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		A	7867391	T	A	7867391	3	1	51	1	0	0	0	0	1	0	0	0	5695	1841	64	4	1206	4	FASTKD3	5	7867391	Missense_Mutation	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10		7867391	173047869	40	6564										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13871081	13871081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tgacaaccatccaggcctttGtctcagcagtcagggcgaac	10	13	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr5:13871081G>A	ENST00000265104.4	-	24	3733	c.3629C>T	c.(3628-3630)aCa>aTa	p.T1210I	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1210	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CCAGGCCTTTGTCTCAGCAGT	0.388									Kartagener syndrome																												p.T1210I		Atlas-SNP	.											.	DNAH5	868	.	0			c.C3629T						.						86	88	87					5																	13871081		2202	4300	6502	SO:0001583	missense	1767	exon24	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GCCTTTGTCTCAG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3629C>T	chr5.hg19:g.13871081G>A	ENSP00000265104:p.Thr1210Ile	325.0	0.0		235.0	100.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	7.080	0.570056	0.13560	.	.	ENSG00000039139	ENST00000265104	T	0.21031	2.03	5.84	4.07	0.47477	.	0.097795	0.64402	N	0.000002	T	0.14356	0.0347	L	0.39085	1.19	0.47819	D	0.999529	B	0.02656	0.0	B	0.06405	0.002	T	0.05989	-1.0852	10	0.06365	T	0.9	.	11.6947	0.51536	0.1845:0.0:0.8155:0.0	.	1210	Q8TE73	DYH5_HUMAN	I	1210	ENSP00000265104:T1210I	ENSP00000265104:T1210I	T	-	2	0	DNAH5	13924081	1.000000	0.71417	0.938000	0.37757	0.754000	0.42855	4.471000	0.60182	0.816000	0.34421	0.655000	0.94253	ACA	.	.		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13871081	G	A	13871081	3	1	51	1	0	0	0	0	1	0	0	0	4606	1377	48	3	10469	3	DNAH5	5	13871081	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	6003690	13871081	167044179	41	6565										
CDH9	1007	hgsc.bcm.edu	37	chr5	26902658	26902658	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	actgccctcctttacatcttCatctacttctatcaagtaag	3	13	5	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr5:26902658C>A	ENST00000231021.4	-	7	1352	c.1180G>T	c.(1180-1182)Gaa>Taa	p.E394*		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	394	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TTTACATCTTCATCTACTTCT	0.378																																					p.E394X	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.G1180T						.						127	121	123					5																	26902658		2203	4300	6503	SO:0001587	stop_gained	1007	exon7			CATCTTCATCTAC	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1180G>T	chr5.hg19:g.26902658C>A	ENSP00000231021:p.Glu394*	73.0	0.0		83.0	45.0	NM_016279	Q3B7I5	Nonsense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	38	6.871465	0.97901	.	.	ENSG00000113100	ENST00000231021	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2244	0.89913	0.0:1.0:0.0:0.0	.	.	.	.	X	394	.	.	E	-	1	0	CDH9	26938415	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.461000	0.80834	2.648000	0.89879	0.650000	0.86243	GAA	.	.		0.378	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26902658	C	A	26902658	4	1	51	1	0	0	0	0	0	1	0	0	3119	835	29	3	1213	3	CDH9	5	26902658	Nonsense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	13031577	26902658	154012602	42	6566										
EMB	133418	hgsc.bcm.edu	37	chr5	49699137	49699137	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aatagctcagcaccacaagcTcaatgtgttcttcactctcg	6	13	5	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr5:49699137T>A	ENST00000303221.5	-	6	967	c.752A>T	c.(751-753)gAg>gTg	p.E251V	EMB_ENST00000508934.1_Missense_Mutation_p.E197V|EMB_ENST00000514111.1_Missense_Mutation_p.E201V|EMB_ENST00000506190.1_5'UTR	NM_198449.2	NP_940851.1	Q6PCB8	EMB_HUMAN	embigin	251	Ig-like V-type 2.				cell adhesion (GO:0007155)|plasma membrane lactate transport (GO:0035879)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	organic cyclic compound binding (GO:0097159)			breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	15	Lung SC(58;0.218)	Lung NSC(810;0.0795)				CACCACAAGCTCAATGTGTTC	0.438																																					p.E251V		Atlas-SNP	.											.	EMB	42	.	0			c.A752T						.						114	101	106					5																	49699137		2203	4299	6502	SO:0001583	missense	133418	exon6			ACAAGCTCAATGT	BC059398	CCDS3953.1	5q11.1	2013-01-29	2010-06-24		ENSG00000170571	ENSG00000170571		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30465	protein-coding gene	gene with protein product		615669	"embigin homolog (mouse)"			9438341	Standard	NM_198449		Approved	MGC71745	uc003jom.3	Q6PCB8	OTTHUMG00000131161	ENST00000303221.5:c.752A>T	chr5.hg19:g.49699137T>A	ENSP00000302289:p.Glu251Val	378.0	0.0		269.0	85.0	NM_198449	B7Z6S3|B7Z902	Missense_Mutation	SNP	ENST00000303221.5	hg19	CCDS3953.1	.	.	.	.	.	.	.	.	.	.	T	14.40	2.524400	0.44969	.	.	ENSG00000170571	ENST00000303221;ENST00000510295;ENST00000508934;ENST00000514111	T;T;T	0.69561	-0.41;-0.41;-0.41	4.75	3.49	0.39957	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.557202	0.19547	N	0.111649	T	0.63827	0.2544	L	0.38531	1.155	0.09310	N	1	P;P	0.48589	0.912;0.698	P;B	0.52598	0.703;0.238	T	0.53479	-0.8433	9	.	.	.	-9.6347	9.434	0.38628	0.159:0.0:0.0:0.841	.	197;251	D6RDX7;Q6PCB8	.;EMB_HUMAN	V	251;223;197;201	ENSP00000302289:E251V;ENSP00000425215:E197V;ENSP00000426404:E201V	.	E	-	2	0	EMB	49734894	0.008000	0.16893	0.360000	0.25837	0.952000	0.60782	1.701000	0.37825	1.906000	0.55180	0.397000	0.26171	GAG	.	.		0.438	EMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253853.1	NM_198449		A	49699137	T	A	49699137	3	1	51	1	0	0	0	0	1	0	0	0	5087	1551	54	4	247	4	EMB	5	49699137	Missense_Mutation	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10	22796479	49699137	131216123	43	6567										
ATG10	83734	hgsc.bcm.edu	37	chr5	81548458	81548458	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttcatgactcctgtattaaaGaattctcagaaaatcaataa	4	7	3	3			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr5:81548458G>T	ENST00000282185.3	+	6	825	c.531G>T	c.(529-531)aaG>aaT	p.K177N	ATG10_ENST00000458350.3_Missense_Mutation_p.K177N|ATG10_ENST00000513634.1_Missense_Mutation_p.K177N|ATG10_ENST00000514253.2_Intron	NM_031482.4	NP_113670.1	Q9H0Y0	ATG10_HUMAN	autophagy related 10	177					autophagy (GO:0006914)|autophagy in response to ER overload (GO:0034263)|positive regulation of protein modification process (GO:0031401)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	Atg12 ligase activity (GO:0019777)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(2)	9		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)		CTGTATTAAAGAATTCTCAGA	0.343																																					p.K177N		Atlas-SNP	.											.	ATG10	23	.	0			c.G531T						.						71	73	72					5																	81548458		2203	4300	6503	SO:0001583	missense	83734	exon7			ATTAAAGAATTCT	AK024016	CCDS4057.1	5q14.1	2014-02-12	2012-06-06	2005-09-11	ENSG00000152348	ENSG00000152348			20315	protein-coding gene	gene with protein product		610800	"APG10 autophagy 10-like (S. cerevisiae)", "ATG10 autophagy related 10 homolog (S. cerevisiae)"	APG10L			Standard	NM_031482		Approved	DKFZP586I0418, FLJ13954	uc003khr.3	Q9H0Y0	OTTHUMG00000119041	ENST00000282185.3:c.531G>T	chr5.hg19:g.81548458G>T	ENSP00000282185:p.Lys177Asn	128.0	0.0		102.0	21.0	NM_001131028	B2RE09|Q6PIX1|Q9H842	Missense_Mutation	SNP	ENST00000282185.3	hg19	CCDS4057.1	.	.	.	.	.	.	.	.	.	.	G	8.910	0.958521	0.18507	.	.	ENSG00000152348	ENST00000282185;ENST00000458350;ENST00000513634	T;T;T	0.47177	1.88;1.88;0.85	5.86	3.84	0.44239	.	0.256554	0.39146	N	0.001459	T	0.28400	0.0702	L	0.36672	1.1	0.27748	N	0.944259	B;B	0.32245	0.112;0.361	B;B	0.27500	0.016;0.08	T	0.06041	-1.0849	10	0.19590	T	0.45	.	4.0965	0.09993	0.1451:0.0:0.6315:0.2234	.	177;177	D6RDX3;Q9H0Y0	.;ATG10_HUMAN	N	177	ENSP00000282185:K177N;ENSP00000404938:K177N;ENSP00000425225:K177N	ENSP00000282185:K177N	K	+	3	2	ATG10	81584214	1.000000	0.71417	1.000000	0.80357	0.188000	0.23474	0.467000	0.22035	2.776000	0.95493	0.655000	0.94253	AAG	.	.		0.343	ATG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239252.2	NM_001131028		T	81548458	G	T	81548458	3	4	51	1	0	0	0	0	1	0	0	0	1089	933	33	3	549	3	ATG10	5	81548458	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	31849321	81548458	99366802	44	6568										
PJA2	9867	hgsc.bcm.edu	37	chr5	108714875	108714875	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttgattcaatgctgaaccacAagtgggaatttctgtttcac	8	8	3	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr5:108714875A>C	ENST00000361189.2	-	4	552	c.313T>G	c.(313-315)Tgt>Ggt	p.C105G	PJA2_ENST00000361557.3_Missense_Mutation_p.C105G|PJA2_ENST00000511624.1_5'UTR	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	105					long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		GCTGAACCACAAGTGGGAATT	0.388																																					p.C105G		Atlas-SNP	.											.	PJA2	53	.	0			c.T313G						.						71	70	70					5																	108714875		2202	4300	6502	SO:0001583	missense	9867	exon4			AACCACAAGTGGG	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"RING-type (C3HC4) zinc fingers"	17481	protein-coding gene	gene with protein product			"ring finger protein 131", "praja ring finger 2"	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.313T>G	chr5.hg19:g.108714875A>C	ENSP00000354775:p.Cys105Gly	96.0	0.0		82.0	5.0	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	hg19	CCDS4099.1	.	.	.	.	.	.	.	.	.	.	A	1.976	-0.435255	0.04669	.	.	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.04502	3.61;3.61	6.16	5.0	0.66597	.	0.198971	0.45867	D	0.000336	T	0.05823	0.0152	L	0.56769	1.78	0.35734	D	0.818173	B	0.28820	0.224	B	0.29353	0.101	T	0.24835	-1.0149	10	0.12430	T	0.62	-5.1915	8.2722	0.31851	0.7292:0.1387:0.0:0.1321	.	105	O43164	PJA2_HUMAN	G	105	ENSP00000354775:C105G;ENSP00000355284:C105G	ENSP00000354775:C105G	C	-	1	0	PJA2	108742774	0.977000	0.34250	0.912000	0.35992	0.656000	0.38851	1.404000	0.34623	1.134000	0.42165	0.528000	0.53228	TGT	.	.		0.388	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819		C	108714875	A	C	108714875	3	2	51	1	0	0	0	0	1	0	0	0	11971	130	5	5	1841	5	PJA2	5	108714875	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	27166417	108714875	72200385	45	6569										
SYCP2L	221711	hgsc.bcm.edu	37	chr6	10924837	10924837	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tgatttgcagttcaacatatCacaagtttccattcaagctt	5	9	3	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr6:10924837C>T	ENST00000283141.6	+	15	1477	c.1181C>T	c.(1180-1182)tCa>tTa	p.S394L	SYCP2L_ENST00000543878.1_Missense_Mutation_p.S235L|RP11-637O19.3_ENST00000480294.1_3'UTR	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	394						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			TTCAACATATCACAAGTTtcc	0.299																																					p.S394L		Atlas-SNP	.											.	SYCP2L	101	.	0			c.C1181T						.						81	75	77					6																	10924837		1828	4087	5915	SO:0001583	missense	221711	exon15			ACATATCACAAGT	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 177"	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.1181C>T	chr6.hg19:g.10924837C>T	ENSP00000283141:p.Ser394Leu	69.0	0.0		103.0	33.0	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Missense_Mutation	SNP	ENST00000283141.6	hg19	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	C	0.244	-1.011153	0.02095	.	.	ENSG00000153157	ENST00000543878;ENST00000283141	T;T	0.39997	1.05;2.37	5.24	-0.363	0.12556	.	1.038270	0.07581	N	0.920251	T	0.08403	0.0209	N	0.17082	0.46	0.09310	N	1	B;B	0.14438	0.0;0.01	B;B	0.08055	0.001;0.003	T	0.36841	-0.9731	10	0.15952	T	0.53	-13.2427	7.7702	0.29004	0.0:0.4152:0.0:0.5848	.	235;394	B4DFB8;Q5T4T6	.;SYC2L_HUMAN	L	235;394	ENSP00000440676:S235L;ENSP00000283141:S394L	ENSP00000283141:S394L	S	+	2	0	SYCP2L	11032823	0.000000	0.05858	0.000000	0.03702	0.421000	0.31385	0.025000	0.13577	0.041000	0.15688	-0.140000	0.14226	TCA	.	.		0.299	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		T	10924837	C	T	10924837	3	4	51	1	0	0	0	0	1	0	0	0	15448	838	29	3	1239	3	SYCP2L	6	10924837	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10		10924837	160190230	46	6570										
HIST1H2BD	3017	hgsc.bcm.edu	37	chr6	26158526	26158526	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	agctattcagtgtatgtgtaCaaggtgctgaagcaggtcca	12	7	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr6:26158526C>G	ENST00000289316.2	+	1	153	c.129C>G	c.(127-129)taC>taG	p.Y43*	HIST1H2BD_ENST00000377777.4_Nonsense_Mutation_p.Y43*	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	43					chromatin organization (GO:0006325)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	24						TGTATGTGTACAAGGTGCTGA	0.557																																					p.Y43X		Atlas-SNP	.											.	HIST1H2BD	45	.	0			c.C129G						.						203	188	193					6																	26158526		2203	4300	6503	SO:0001587	stop_gained	3017	exon1			TGTGTACAAGGTG	M60751	CCDS4587.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158373	ENSG00000158373		"Histones / Replication-dependent"	4747	protein-coding gene	gene with protein product		602799	"H2B histone family, member B", "histone 1, H2bd"	H2BFB		1916825, 12408966	Standard	NM_021063		Approved	H2B/b	uc003ngr.3	P58876	OTTHUMG00000014426	ENST00000289316.2:c.129C>G	chr6.hg19:g.26158526C>G	ENSP00000289316:p.Tyr43*	201.0	0.0		104.0	13.0	NM_021063		Nonsense_Mutation	SNP	ENST00000289316.2	hg19	CCDS4587.1	.	.	.	.	.	.	.	.	.	.	.	28.1	4.892487	0.91889	.	.	ENSG00000158373	ENST00000377777;ENST00000289316	.	.	.	5.19	4.32	0.51571	.	0.000000	0.38058	N	0.001833	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.3013	0.43654	0.1345:0.7921:0.0:0.0733	.	.	.	.	X	43	.	ENSP00000289316:Y43X	Y	+	3	2	HIST1H2BD	26266505	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	3.212000	0.51145	1.523000	0.49018	0.650000	0.86243	TAC	.	.		0.557	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063		G	26158526	C	G	26158526	4	3	51	1	0	0	0	0	0	1	0	0	7152	489	17	4	131	4	HIST1H2BD	6	26158526	Nonsense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	15233689	26158526	144956541	47	6571										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33652419	33652419	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ctgcaaaactacctccagaaCcggaagtccacctcgcgggg	10	15	0	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr6:33652419C>A	ENST00000374316.5	+	39	6151	c.5091C>A	c.(5089-5091)aaC>aaA	p.N1697K	ITPR3_ENST00000605930.1_Missense_Mutation_p.N1697K			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1697					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	ACCTCCAGAACCGGAAGTCCA	0.637																																					p.N1697K		Atlas-SNP	.											.	ITPR3	409	.	0			c.C5091A						.						78	82	80					6																	33652419		2203	4300	6503	SO:0001583	missense	3710	exon38			CCAGAACCGGAAG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.5091C>A	chr6.hg19:g.33652419C>A	ENSP00000363435:p.Asn1697Lys	211.0	0.0		38.0	11.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	12.83	2.056825	0.36277	.	.	ENSG00000096433	ENST00000374316	D	0.89746	-2.56	5.05	3.23	0.37069	.	0.200004	0.51477	D	0.000099	T	0.67869	0.2939	L	0.38838	1.175	0.46113	D	0.998874	P	0.38922	0.651	B	0.33521	0.165	T	0.69235	-0.5198	10	0.09843	T	0.71	-35.198	10.6993	0.45918	0.0:0.8411:0.0:0.1589	.	1697	Q14573	ITPR3_HUMAN	K	1697	ENSP00000363435:N1697K	ENSP00000363435:N1697K	N	+	3	2	ITPR3	33760397	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	3.131000	0.50515	1.265000	0.44215	-0.136000	0.14681	AAC	.	.		0.637	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		A	33652419	C	A	33652419	3	1	51	1	0	0	0	0	1	0	0	0	7931	506	18	3	5241	3	ITPR3	6	33652419	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	7493893	33652419	137462648	48	6572										
BTBD9	114781	hgsc.bcm.edu	37	chr6	38565731	38565731	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aaattaccctgtgggcaggaAaacgtttcttttccaccacg	8	11	1	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr6:38565731A>G	ENST00000481247.1	-	2	291	c.140T>C	c.(139-141)tTt>tCt	p.F47S	BTBD9_ENST00000419706.2_5'Flank|BTBD9_ENST00000403056.1_Missense_Mutation_p.F47S|BTBD9_ENST00000314100.6_5'Flank	NM_001099272.1|NM_052893.1	NP_001092742.1|NP_443125.1	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9	47	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|circadian sleep/wake cycle, non-REM sleep (GO:0042748)|long-term memory (GO:0007616)|multicellular organismal iron ion homeostasis (GO:0060586)|regulation of synaptic vesicle endocytosis (GO:1900242)|sensory perception of temperature stimulus (GO:0050951)|serotonin metabolic process (GO:0042428)					breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	12						GTGGGCAGGAAAACGTTTCTT	0.398																																					p.F47S		Atlas-SNP	.											.	BTBD9	85	.	0			c.T140C						.						101	98	99					6																	38565731		1903	4118	6021	SO:0001583	missense	114781	exon3			GCAGGAAAACGTT		CCDS43458.1, CCDS47418.1, CCDS54998.1	6p21	2014-01-28			ENSG00000183826	ENSG00000183826		"BTB/POZ domain containing"	21228	protein-coding gene	gene with protein product		611237				11572484	Standard	NM_052893		Approved	KIAA1880, dJ322I12.1	uc010jwx.3	Q96Q07	OTTHUMG00000014634	ENST00000481247.1:c.140T>C	chr6.hg19:g.38565731A>G	ENSP00000418751:p.Phe47Ser	221.0	0.0		198.0	25.0	NM_052893	Q494V9|Q494W1|Q96M00	Missense_Mutation	SNP	ENST00000481247.1	hg19	CCDS47418.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.757767	0.89843	.	.	ENSG00000183826	ENST00000481247;ENST00000403056;ENST00000498633	T;T;T	0.71698	-0.59;-0.59;-0.59	5.36	5.36	0.76844	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	.	.	.	.	D	0.88299	0.6399	H	0.97491	4.015	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	D	0.92473	0.5987	9	0.87932	D	0	.	15.6385	0.76977	1.0:0.0:0.0:0.0	.	47	Q96Q07	BTBD9_HUMAN	S	47	ENSP00000418751:F47S;ENSP00000386121:F47S;ENSP00000419382:F47S	ENSP00000386121:F47S	F	-	2	0	BTBD9	38673709	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.610000	0.90902	2.164000	0.68074	0.533000	0.62120	TTT	.	.		0.398	BTBD9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040433.2	NM_152733		G	38565731	A	G	38565731	3	3	51	1	0	0	0	0	1	0	0	0	1550	14	1	2	1837	2	BTBD9	6	38565731	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	4913312	38565731	132549336	49	6573										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76024440	76024440	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gaggctagagtttccacattCtcctttggcaattttatctc	7	10	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr6:76024440C>A	ENST00000237172.7	-	5	1438	c.1108G>T	c.(1108-1110)Gaa>Taa	p.E370*	FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000393004.2_Nonsense_Mutation_p.E370*|FILIP1_ENST00000370020.1_Nonsense_Mutation_p.E271*	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	370										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						TTTCCACATTCTCCTTTGGCA	0.413																																					p.E370X		Atlas-SNP	.											.	FILIP1	173	.	0			c.G1108T						.						167	167	167					6																	76024440		2203	4300	6503	SO:0001587	stop_gained	27145	exon5			CACATTCTCCTTT	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.1108G>T	chr6.hg19:g.76024440C>A	ENSP00000237172:p.Glu370*	148.0	0.0		108.0	26.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Nonsense_Mutation	SNP	ENST00000237172.7	hg19	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	C	39	7.345240	0.98224	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-28.3168	20.0965	0.97849	0.0:1.0:0.0:0.0	.	.	.	.	X	370;370;271	.	ENSP00000237172:E370X	E	-	1	0	FILIP1	76081160	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.959000	0.70339	2.824000	0.97209	0.655000	0.94253	GAA	.	.		0.413	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76024440	C	A	76024440	4	1	51	1	0	0	0	0	0	1	0	0	5902	922	32	3	2541	3	FILIP1	6	76024440	Nonsense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	37458709	76024440	95090627	50	6574										
IFNGR1	3459	hgsc.bcm.edu	37	chr6	137522034	137522034	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttaccaaggacttgggtaatAttatgcttttttccttcaat	6	7	1	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr6:137522034A>G	ENST00000367739.4	-	6	966	c.845T>C	c.(844-846)aTa>aCa	p.I282T	IFNGR1_ENST00000543628.1_Missense_Mutation_p.I254T	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	282					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)			central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	CTTGGGTAATATTATGCTTTT	0.264																																					p.I282T		Atlas-SNP	.											.	IFNGR1	46	.	0			c.T845C						.						26	27	27					6																	137522034		2199	4289	6488	SO:0001583	missense	3459	exon6			GGTAATATTATGC		CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"Interferons", "CD molecules"	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.845T>C	chr6.hg19:g.137522034A>G	ENSP00000356713:p.Ile282Thr	117.0	0.0		152.0	9.0	NM_000416	B4DFT7|E1P587|Q53Y96	Missense_Mutation	SNP	ENST00000367739.4	hg19	CCDS5185.1	.	.	.	.	.	.	.	.	.	.	A	10.97	1.500852	0.26861	.	.	ENSG00000027697	ENST00000367739;ENST00000543628	T;T	0.71461	-0.57;-0.42	5.47	-4.44	0.03557	Interferon gamma receptor, poxvirus/mammal (1);	1.247580	0.05363	N	0.534128	T	0.24160	0.0585	L	0.29908	0.895	0.09310	N	1	B;B	0.12630	0.004;0.006	B;B	0.14578	0.003;0.011	T	0.04386	-1.0955	10	0.13470	T	0.59	-0.5488	0.542	0.00647	0.3193:0.1334:0.2856:0.2617	.	254;282	F5H5M7;P15260	.;INGR1_HUMAN	T	282;254	ENSP00000356713:I282T;ENSP00000443282:I254T	ENSP00000356713:I282T	I	-	2	0	IFNGR1	137563727	0.000000	0.05858	0.003000	0.11579	0.470000	0.32858	-0.665000	0.05286	-0.378000	0.07918	0.477000	0.44152	ATA	.	.		0.264	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1			G	137522034	A	G	137522034	3	3	51	1	0	0	0	0	1	0	0	0	7558	449	16	2	632	2	IFNGR1	6	137522034	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	61497594	137522034	33593033	51	6575										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84727158	84727158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttaagtcaaccagactgagtAgaaagatgtggtctttggct	11	6	2	4			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr7:84727158A>G	ENST00000284136.6	-	2	318	c.275T>C	c.(274-276)cTa>cCa	p.L92P	SEMA3D_ENST00000444867.1_Missense_Mutation_p.L92P	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	92	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CAGACTGAGTAGAAAGATGTG	0.363																																					p.L92P	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.T275C						.						112	116	114					7																	84727158		2203	4300	6503	SO:0001583	missense	223117	exon2			CTGAGTAGAAAGA	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.275T>C	chr7.hg19:g.84727158A>G	ENSP00000284136:p.Leu92Pro	178.0	0.0		159.0	16.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	hg19	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.313278	0.60414	.	.	ENSG00000153993	ENST00000284136;ENST00000444867	T;T	0.11063	2.81;2.81	5.56	5.56	0.83823	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.31040	0.0784	M	0.71581	2.175	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.76575	0.988;0.974	T	0.01998	-1.1232	10	0.72032	D	0.01	.	12.2542	0.54615	0.8729:0.0:0.0:0.1271	.	92;92	C9JYT6;O95025	.;SEM3D_HUMAN	P	92	ENSP00000284136:L92P;ENSP00000401366:L92P	ENSP00000284136:L92P	L	-	2	0	SEMA3D	84565094	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.320000	0.59203	2.241000	0.73720	0.482000	0.46254	CTA	.	.		0.363	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		G	84727158	A	G	84727158	3	3	51	1	0	0	0	0	1	0	0	0	14042	420	15	2	2122	2	SEMA3D	7	84727158	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10		84727158	74411505	52	6576										
LRRC4	64101	hgsc.bcm.edu	37	chr7	127670230	127670230	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tgctttcgatggggttgttgCgaagccagagctcccgcagc	14	11	0	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr7:127670230C>T	ENST00000249363.3	-	2	721	c.464G>A	c.(463-465)cGc>cAc	p.R155H	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	155					postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		GGGGTTGTTGCGAAGCCAGAG	0.587																																					p.R155H		Atlas-SNP	.											LRRC4,colon,carcinoma,0,1	LRRC4	72	.	0			c.G464A						.						71	75	74					7																	127670230		2203	4300	6503	SO:0001583	missense	64101	exon2			TTGTTGCGAAGCC	AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594		"Immunoglobulin superfamily / I-set domain containing"	15586	protein-coding gene	gene with protein product		610486	"leucine-rich repeat-containing 4"			12969517	Standard	NM_022143		Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.464G>A	chr7.hg19:g.127670230C>T	ENSP00000249363:p.Arg155His	81.0	0.0		30.0	16.0	NM_022143	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Missense_Mutation	SNP	ENST00000249363.3	hg19	CCDS5799.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.919311	0.73098	.	.	ENSG00000128594	ENST00000249363;ENST00000494115	D;D	0.91407	-2.84;-2.59	4.56	4.56	0.56223	.	0.000000	0.64402	D	0.000001	D	0.90428	0.7003	N	0.13235	0.315	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.91691	0.5366	10	0.54805	T	0.06	.	14.8699	0.70448	0.0:1.0:0.0:0.0	.	155	Q9HBW1	LRRC4_HUMAN	H	155;73	ENSP00000249363:R155H;ENSP00000418254:R73H	ENSP00000249363:R155H	R	-	2	0	LRRC4	127457466	0.984000	0.35163	1.000000	0.80357	0.999000	0.98932	7.600000	0.82769	2.316000	0.78162	0.655000	0.94253	CGC	.	.		0.587	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349170.1	NM_022143		T	127670230	C	T	127670230	3	4	51	1	0	0	0	0	1	0	0	0	9006	768	27	1	1501	1	LRRC4	7	127670230	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	42943072	127670230	31468433	53	6577										
DENND2A	27147	hgsc.bcm.edu	37	chr7	140301984	140301984	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	agaggacggcagataatcctCctgtccgtctgctctcctgc	10	14	2	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr7:140301984C>A	ENST00000275884.6	-	2	631	c.214G>T	c.(214-216)Gag>Tag	p.E72*	DENND2A_ENST00000496613.1_Nonsense_Mutation_p.E72*|DENND2A_ENST00000537639.1_Nonsense_Mutation_p.E72*|DENND2A_ENST00000492720.1_Nonsense_Mutation_p.E72*			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	72					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					AGATAATCCTCCTGTCCGTCT	0.542																																					p.E72X		Atlas-SNP	.											.	DENND2A	132	.	0			c.G214T						.						171	164	166					7																	140301984		1974	4173	6147	SO:0001587	stop_gained	27147	exon1			AATCCTCCTGTCC	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.214G>T	chr7.hg19:g.140301984C>A	ENSP00000275884:p.Glu72*	179.0	0.0		94.0	37.0	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Nonsense_Mutation	SNP	ENST00000275884.6	hg19	CCDS43659.1	.	.	.	.	.	.	.	.	.	.	C	35	5.489489	0.96323	.	.	ENSG00000146966	ENST00000275884;ENST00000537639;ENST00000496613;ENST00000492720;ENST00000491728;ENST00000489552;ENST00000477488	.	.	.	4.85	4.85	0.62838	.	0.753358	0.12727	N	0.444179	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-18.0874	18.1897	0.89803	0.0:1.0:0.0:0.0	.	.	.	.	X	72	.	ENSP00000275884:E72X	E	-	1	0	DENND2A	139948453	0.130000	0.22417	0.099000	0.21106	0.106000	0.19336	0.960000	0.29253	2.529000	0.85273	0.655000	0.94253	GAG	.	.		0.542	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		A	140301984	C	A	140301984	4	1	51	1	0	0	0	0	0	1	0	0	4431	864	30	3	2887	3	DENND2A	7	140301984	Nonsense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	12631754	140301984	18836679	54	6578										
LPL	4023	hgsc.bcm.edu	37	chr8	19809442	19809442	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tgggacaggatgtggcccggTttatcaactggatggaggta	16	6	1	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr8:19809442T>A	ENST00000311322.8	+	3	882	c.412T>A	c.(412-414)Ttt>Att	p.F138I		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	138					chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	TGTGGCCCGGTTTATCAACTG	0.512																																					p.F138I		Atlas-SNP	.											.	LPL	78	.	0			c.T412A						.						80	75	76					8																	19809442		2203	4300	6503	SO:0001583	missense	4023	exon3			GCCCGGTTTATCA		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.412T>A	chr8.hg19:g.19809442T>A	ENSP00000309757:p.Phe138Ile	192.0	0.0		73.0	7.0	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Missense_Mutation	SNP	ENST00000311322.8	hg19	CCDS6012.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.821748	0.90873	.	.	ENSG00000175445	ENST00000520959;ENST00000311322;ENST00000538071;ENST00000535763	D;D	0.91407	-2.84;-2.84	5.91	5.91	0.95273	Lipase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95143	0.8426	M	0.81112	2.525	0.40734	D	0.982770	D	0.89917	1.0	D	0.97110	1.0	D	0.95296	0.8399	8	.	.	.	-21.7104	14.2952	0.66308	0.0:0.0:0.0:1.0	.	138	P06858	LIPL_HUMAN	I	62;138;62;124	ENSP00000428496:F62I;ENSP00000309757:F138I	.	F	+	1	0	LPL	19853722	1.000000	0.71417	0.988000	0.46212	0.871000	0.50021	7.898000	0.87363	2.263000	0.75096	0.377000	0.23210	TTT	.	.		0.512	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3			A	19809442	T	A	19809442	3	1	51	1	0	0	0	0	1	0	0	0	8930	1725	60	4	422	4	LPL	8	19809442	Missense_Mutation	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10		19809442	126554580	55	6579										
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24256455	24256455	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tggtctgatggggataagatAaaggtggtgcccagcgcaag	16	6	1	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr8:24256455A>G	ENST00000256412.4	+	9	1051	c.831A>G	c.(829-831)atA>atG	p.I277M	ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.I198M|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.I198M|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	277	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		GGGATAAGATAAAGGTGGTGC	0.448																																					p.I277M	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.A831G						.						115	109	111					8																	24256455		2203	4300	6503	SO:0001583	missense	27299	exon9			TAAGATAAAGGTG	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.831A>G	chr8.hg19:g.24256455A>G	ENSP00000256412:p.Ile277Met	227.0	0.0		115.0	93.0	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	hg19	CCDS6044.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.372029	0.42003	.	.	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.72167	-0.63;-0.63;-0.63	5.88	-11.8	0.00035	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.64402	D	0.000001	T	0.81791	0.4897	M	0.89658	3.05	0.23138	N	0.998235	D	0.76494	0.999	D	0.83275	0.996	T	0.82112	-0.0618	10	0.87932	D	0	-28.8524	17.4048	0.87470	0.1484:0.751:0.0:0.1006	.	277	O15204	ADEC1_HUMAN	M	277;198;198	ENSP00000256412:I277M;ENSP00000442592:I198M;ENSP00000428993:I198M	ENSP00000256412:I277M	I	+	3	3	ADAMDEC1	24312400	0.005000	0.15991	0.864000	0.33941	0.030000	0.12068	-0.595000	0.05727	-1.379000	0.02118	-1.243000	0.01532	ATA	.	.		0.448	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		G	24256455	A	G	24256455	3	3	51	1	0	0	0	0	1	0	0	0	254	352	13	2	865	2	ADAMDEC1	8	24256455	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	4447013	24256455	122107567	56	6580										
RAB11FIP1	80223	hgsc.bcm.edu	37	chr8	37729417	37729417	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	cctgatctattctttcatcaTccgatgcgacttcaggaatg	7	11	5	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr8:37729417T>C	ENST00000330843.4	-	4	2915	c.2903A>G	c.(2902-2904)gAt>gGt	p.D968G	RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000523182.1_5'UTR|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000524118.1_Intron	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	968					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TCTTTCATCATCCGATGCGAC	0.453																																					p.D968G		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.A2903G						.						157	129	138					8																	37729417		2203	4300	6503	SO:0001583	missense	80223	exon4			TCATCATCCGATG	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.2903A>G	chr8.hg19:g.37729417T>C	ENSP00000331342:p.Asp968Gly	292.0	0.0		106.0	6.0	NM_001002814	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	hg19	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.092374	0.76756	.	.	ENSG00000156675	ENST00000330843	T	0.32272	1.46	5.33	5.33	0.75918	.	0.000000	0.56097	D	0.000036	T	0.43188	0.1236	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.937	T	0.20806	-1.0264	10	0.34782	T	0.22	-15.5954	13.8876	0.63717	0.0:0.0:0.0:1.0	.	297;968	Q67C35;Q6WKZ4	.;RFIP1_HUMAN	G	968	ENSP00000331342:D968G	ENSP00000331342:D968G	D	-	2	0	RAB11FIP1	37848575	1.000000	0.71417	0.760000	0.31359	0.797000	0.45037	4.528000	0.60580	2.016000	0.59253	0.533000	0.62120	GAT	.	.		0.453	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		C	37729417	T	C	37729417	3	2	51	1	0	0	0	0	1	0	0	0	12908	1435	50	2	960	2	RAB11FIP1	8	37729417	Missense_Mutation	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10	13472962	37729417	108634605	57	6581										
LRP12	29967	hgsc.bcm.edu	37	chr8	105509410	105509410	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	cacaacgattgtttttacaaTggaaatttcctggttggcaa	8	7	0	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr8:105509410T>G	ENST00000276654.5	-	5	1478	c.1370A>C	c.(1369-1371)cAt>cCt	p.H457P	LRP12_ENST00000518375.1_5'Flank|LRP12_ENST00000424843.2_Missense_Mutation_p.H438P	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	457	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			GTTTTTACAATGGAAATTTCC	0.423																																					p.H457P		Atlas-SNP	.											.	LRP12	124	.	0			c.A1370C						.						107	100	102					8																	105509410		2203	4300	6503	SO:0001583	missense	29967	exon5			TTACAATGGAAAT	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.1370A>C	chr8.hg19:g.105509410T>G	ENSP00000276654:p.His457Pro	155.0	0.0		96.0	13.0	NM_013437	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000276654.5	hg19	CCDS6303.1	.	.	.	.	.	.	.	.	.	.	T	18.27	3.587574	0.66105	.	.	ENSG00000147650	ENST00000424843;ENST00000276654;ENST00000523007	D;D;D	0.95447	-3.71;-3.71;-3.71	5.79	4.64	0.57946	.	0.090349	0.85682	D	0.000000	D	0.93815	0.8022	L	0.39514	1.22	0.80722	D	1	P;P	0.50710	0.799;0.938	P;P	0.49140	0.466;0.601	D	0.92986	0.6410	10	0.59425	D	0.04	-29.021	11.6199	0.51111	0.0:0.0693:0.0:0.9307	.	438;457	Q9Y561-2;Q9Y561	.;LRP12_HUMAN	P	438;457;46	ENSP00000399148:H438P;ENSP00000276654:H457P;ENSP00000429305:H46P	ENSP00000276654:H457P	H	-	2	0	LRP12	105578586	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	8.040000	0.89188	1.027000	0.39758	0.455000	0.32223	CAT	.	.		0.423	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		G	105509410	T	G	105509410	3	3	51	1	0	0	0	0	1	0	0	0	8963	1464	51	5	1221	5	LRP12	8	105509410	Missense_Mutation	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10	67779993	105509410	40854612	58	6582										
SLC30A8	169026	hgsc.bcm.edu	37	chr8	118175765	118175766	+	Nonsense_Mutation	DNP	GG	GG	AT													0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gacttctccatcttactcatGgaaggtaggagtgattttat							TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr8:118175765_118175766GG>AT	ENST00000456015.2	+	6	825_826	c.825_826GG>AT	c.(823-828)atGGaa>atATaa	p.275_276ME>I*	RN7SL826P_ENST00000479724.2_RNA|SLC30A8_ENST00000521243.1_Nonsense_Mutation_p.226_227ME>I*|SLC30A8_ENST00000427715.2_Nonsense_Mutation_p.226_227ME>I*|SLC30A8_ENST00000519688.1_Nonsense_Mutation_p.226_227ME>I*	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	275					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			TCTTACTCATGGAAGGTAGGAG	0.416																																					p.M275I|p.E276X	Ovarian(162;1202 1922 6011 16223 52092)	Atlas-SNP	.											.	SLC30A8	102	.	0			c.G825A|c.G826T						.																																			SO:0001587	stop_gained	169026	exon6			ACTCATGGAAGGT|CTCATGGAAGGTA		CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"Solute carriers"	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	Exception_encountered	chr8.hg19:g.118175765_118175766delinsAT	ENSP00000415011:p.M275_E276delinsI*	68.0|67.0	0.0		42.0	22.0	NM_173851	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000456015.2	hg19	CCDS6322.1																																																																																			.	.		0.416	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851		AT	118175766	GG	AT	118175765	4	1	51	1	0	0	0	0	0	1	0	0	14576	1348	47	3	847	3	SLC30A8	8	118175765	Nonsense_Mutation	DNP	GG	TCGA-BW-A5NO-01A-11D-A27I-10	12666355	118175765	28188257	59	6583										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767486	105767486	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gcaaagaaagataacaaaaaAgataaaaaggattcaaacaa	6	4	1	3			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr9:105767486A>T	ENST00000374798.3	+	5	643	c.573A>T	c.(571-573)aaA>aaT	p.K191N	CYLC2_ENST00000487798.1_Missense_Mutation_p.K191N	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	191	3 X approximate tandem repeats.|31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				ataacaaaaaagataaaaagg	0.358																																					p.K191N		Atlas-SNP	.											.	CYLC2	109	.	0			c.A573T						.						81	79	79					9																	105767486		2203	4300	6503	SO:0001583	missense	1539	exon5			CAAAAAAGATAAA	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.573A>T	chr9.hg19:g.105767486A>T	ENSP00000420256:p.Lys191Asn	130.0	0.0		166.0	44.0	NM_001340	B2R8F4|Q5VVJ9	Missense_Mutation	SNP	ENST00000374798.3	hg19	CCDS35085.1	.	.	.	.	.	.	.	.	.	.	A	10.39	1.336383	0.24253	.	.	ENSG00000155833	ENST00000374798;ENST00000487798	T;T	0.20200	2.09;2.09	4.3	-0.829	0.10796	.	0.757856	0.11228	N	0.585908	T	0.36635	0.0974	M	0.77820	2.39	0.09310	N	1	D	0.71674	0.998	D	0.69654	0.965	T	0.23368	-1.0190	10	0.72032	D	0.01	-1.1039	1.1135	0.01709	0.4985:0.1633:0.1898:0.1484	.	191	Q14093	CYLC2_HUMAN	N	191	ENSP00000420256:K191N;ENSP00000417674:K191N	ENSP00000420256:K191N	K	+	3	2	CYLC2	104807307	0.017000	0.18338	0.000000	0.03702	0.001000	0.01503	1.033000	0.30191	-0.017000	0.14103	-0.613000	0.04052	AAA	.	.		0.358	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		T	105767486	A	T	105767486	3	4	51	1	0	0	0	0	1	0	0	0	4144	69	3	4	591	4	CYLC2	9	105767486	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10		105767486	35445945	60	6584										
GARNL3	84253	hgsc.bcm.edu	37	chr9	130073954	130073954	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gtacttggcgaagaacagacGtgcacttagagaacccagaa	11	9	0	4			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr9:130073954G>A	ENST00000373387.4	+	3	611	c.259G>A	c.(259-261)Gtg>Atg	p.V87M	GARNL3_ENST00000435213.2_Missense_Mutation_p.V65M|GARNL3_ENST00000314904.5_Missense_Mutation_p.V87M	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	87					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						AAGAACAGACGTGCACTTAGA	0.413																																					p.V87M		Atlas-SNP	.											.	GARNL3	83	.	0			c.G259A						.						162	148	153					9																	130073954		2203	4300	6503	SO:0001583	missense	84253	exon3			ACAGACGTGCACT	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.259G>A	chr9.hg19:g.130073954G>A	ENSP00000362485:p.Val87Met	143.0	0.0		186.0	23.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	hg19	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	G	26.6	4.750394	0.89753	.	.	ENSG00000136895	ENST00000439286;ENST00000444677;ENST00000446764;ENST00000373399;ENST00000425970;ENST00000435213;ENST00000314904;ENST00000373387	T;T;T;D;D;D	0.88975	1.75;0.43;0.53;-2.45;-2.41;-2.45	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.92525	0.7626	M	0.64997	1.995	0.53005	D	0.999965	D;D	0.76494	0.999;0.999	P;P	0.62740	0.906;0.864	D	0.91781	0.5435	9	.	.	.	.	15.4761	0.75481	0.0:0.0:1.0:0.0	.	87;65	Q5VVW2;B7Z3Q6	GARL3_HUMAN;.	M	110;110;110;110;65;65;87;87	ENSP00000400579:V110M;ENSP00000411160:V110M;ENSP00000411329:V65M;ENSP00000396205:V65M;ENSP00000313970:V87M;ENSP00000362485:V87M	.	V	+	1	0	GARNL3	129113775	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.117000	0.89575	2.713000	0.92767	0.655000	0.94253	GTG	.	.		0.413	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		A	130073954	G	A	130073954	3	1	51	1	0	0	0	0	1	0	0	0	6249	1145	40	1	269	1	GARNL3	9	130073954	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	24306468	130073954	11139477	61	6585										
NUP188	23511	hgsc.bcm.edu	37	chr9	131764256	131764256	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gcaccaacggcacagcacagGtgagtgtcaggagcttgcca	13	12	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr9:131764256G>A	ENST00000372577.2	+	36	4158		c.e36+1		RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						CACAGCACAGGTGAGTGTCAG	0.577																																					.		Atlas-SNP	.											NUP188,colon,carcinoma,0,1	NUP188	140	.	0			c.4137+1G>A						.						56	49	52					9																	131764256		2203	4300	6503	SO:0001630	splice_region_variant	23511	exon36			GCACAGGTGAGTG	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.4137+1G>A	chr9.hg19:g.131764256G>A		134.0	0.0		49.0	7.0	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Splice_Site	SNP	ENST00000372577.2	hg19	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.053004	0.55218	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1107	0.86674	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NUP188	130804077	1.000000	0.71417	1.000000	0.80357	0.506000	0.33950	8.617000	0.90927	2.619000	0.88677	0.462000	0.41574	.	.	.		0.577	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		Intron	A	131764256	G	A	131764256	5	1	51	1	0	0	0	0	0	0	1	0	10767	1275	44	3	4280	3	NUP188	9	131764256	Splice_Site	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	1690302	131764256	9449175	62	6586										
ATP5C1	509	hgsc.bcm.edu	37	chr10	7839122	7839122	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gagctgaaaccagctcgaatAtatggattgggatctttagg	12	6	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr10:7839122A>G	ENST00000356708.7	+	3	283	c.204A>G	c.(202-204)atA>atG	p.I68M	ATP5C1_ENST00000493053.1_3'UTR|ATP5C1_ENST00000335698.4_Missense_Mutation_p.I68M|ATP5C1_ENST00000541227.1_Missense_Mutation_p.I21M	NM_001001973.1	NP_001001973.1	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	68					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	16						CAGCTCGAATATATGGATTGG	0.388																																					p.I68M	Melanoma(143;1012 1820 16249 30920 33158)	Atlas-SNP	.											.	ATP5C1	32	.	0			c.A204G						.						64	63	63					10																	7839122		2203	4300	6503	SO:0001583	missense	509	exon3			TCGAATATATGGA	D16561	CCDS7081.1, CCDS31142.1	10p14	2012-10-12			ENSG00000165629	ENSG00000165629		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	833	protein-coding gene	gene with protein product		108729		ATP5CL1, ATP5C		8168843, 8227057	Standard	NM_005174		Approved		uc001iju.3	P36542	OTTHUMG00000017639	ENST00000356708.7:c.204A>G	chr10.hg19:g.7839122A>G	ENSP00000349142:p.Ile68Met	88.0	0.0		93.0	28.0	NM_001001973	A8KA31|Q5VYP3|Q6I9V2|Q96AS8	Missense_Mutation	SNP	ENST00000356708.7	hg19	CCDS31142.1	.	.	.	.	.	.	.	.	.	.	A	6.042	0.376011	0.11466	.	.	ENSG00000165629	ENST00000356708;ENST00000335698;ENST00000541227	.	.	.	5.17	-4.02	0.04034	ATPase, F1 complex, gamma subunit domain (1);	0.168378	0.51477	D	0.000092	T	0.22322	0.0538	L	0.31926	0.97	0.23150	N	0.99822	B	0.12013	0.005	B	0.16722	0.016	T	0.07195	-1.0785	9	0.59425	D	0.04	-9.3782	2.2673	0.04082	0.2011:0.2738:0.3597:0.1654	.	68	P36542	ATPG_HUMAN	M	68;68;21	.	ENSP00000338568:I68M	I	+	3	3	ATP5C1	7879128	0.191000	0.23288	0.819000	0.32651	0.138000	0.21146	-0.484000	0.06528	-0.563000	0.06078	-0.912000	0.02778	ATA	.	.		0.388	ATP5C1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046708.1	NM_005174		G	7839122	A	G	7839122	3	3	51	1	0	0	0	0	1	0	0	0	1149	439	16	2	214	2	ATP5C1	10	7839122	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10		7839122	127695625	63	6587										
TAF3	83860	hgsc.bcm.edu	37	chr10	8006085	8006085	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttaagcactaaaggggacacGctagatgttgtgttattgga	12	5	0	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr10:8006085G>T	ENST00000344293.5	+	3	818	c.612G>T	c.(610-612)acG>acT	p.T204T		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	204					maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						AAGGGGACACGCTAGATGTTG	0.478																																					p.T204T		Atlas-SNP	.											TAF3,NS,carcinoma,0,1	TAF3	93	.	0			c.G612T						.						83	83	83					10																	8006085		1942	4143	6085	SO:0001819	synonymous_variant	83860	exon3			GGACACGCTAGAT	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"Zinc fingers, PHD-type"	17303	protein-coding gene	gene with protein product		606576	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.612G>T	chr10.hg19:g.8006085G>T		270.0	2.0		144.0	51.0	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Silent	SNP	ENST00000344293.5	hg19	CCDS41487.1																																																																																			.	.		0.478	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		T	8006085	G	T	8006085	2	4	51	1	0	0	0	0	0	0	0	1	15540	1074	38	1		1	TAF3	10	8006085	Silent	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	166963	8006085	127528662	64	6588										
MSMB	4477	hgsc.bcm.edu	37	chr10	51562361	51562361	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	atcgtggtggagaagaaggaCccaaaaaagacctgttctgt	12	7	1	3			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr10:51562361C>T	ENST00000358559.2	+	4	393	c.306C>T	c.(304-306)gaC>gaT	p.D102D	NCOA4_ENST00000430396.2_5'Flank|NCOA4_ENST00000452682.1_5'Flank|NCOA4_ENST00000414907.2_5'Flank|NCOA4_ENST00000438493.1_5'Flank|MSMB_ENST00000298239.6_Missense_Mutation_p.T67I|NCOA4_ENST00000374087.4_5'Flank	NM_002443.3	NP_002434.1	P08118	MSMB_HUMAN	microseminoprotein, beta-	102						extracellular space (GO:0005615)|nucleus (GO:0005634)				lung(4)|ovary(2)|prostate(1)	7						AGAAGAAGGACCCAAAAAAGA	0.463																																					p.T67I		Atlas-SNP	.											.	MSMB	16	.	0			c.C200T						.						185	161	169					10																	51562361		2203	4300	6503	SO:0001819	synonymous_variant	4477	exon3			GAAGGACCCAAAA	BC005257	CCDS73095.1, CCDS73096.1	10q11.2	2014-05-06			ENSG00000138294	ENSG00000263639			7372	protein-coding gene	gene with protein product		157145				1783399	Standard	NM_002443		Approved	PSP-94, PSP57, PSP94, IGBF, MSP, MSPB, PN44, PRPS, PSP	uc001jiq.3	P08118	OTTHUMG00000188315	ENST00000358559.2:c.306C>T	chr10.hg19:g.51562361C>T		101.0	0.0		98.0	7.0	NM_138634	B1API6|P11999|Q13125|Q6IAY9|Q9UC59	Missense_Mutation	SNP	ENST00000358559.2	hg19	CCDS7235.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.942139	0.53079	.	.	ENSG00000138294	ENST00000298239	T	0.24151	1.87	4.18	3.28	0.37604	.	.	.	.	.	T	0.33352	0.0860	.	.	.	0.09310	N	0.999999	D	0.59357	0.985	P	0.52066	0.689	T	0.10660	-1.0620	8	0.87932	D	0	-15.5935	8.0565	0.30608	0.0:0.891:0.0:0.109	.	67	P08118-2	.	I	67	ENSP00000298239:T67I	ENSP00000298239:T67I	T	+	2	0	MSMB	51232367	0.022000	0.18835	0.385000	0.26158	0.038000	0.13279	0.518000	0.22847	1.362000	0.46000	0.650000	0.86243	ACC	.	.		0.463	MSMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048034.1	NM_002443, NM_138634		T	51562361	C	T	51562361	2	4	51	1	0	0	0	0	0	0	0	1	9892	507	18	3		3	MSMB	10	51562361	Silent	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	43556276	51562361	83972386	65	6589										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55955547	55955547	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	agattccaggatatagccttGataactgggcattgtaaaat	9	6	0	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr10:55955547G>C	ENST00000320301.6	-	11	1595	c.1201C>G	c.(1201-1203)Caa>Gaa	p.Q401E	PCDH15_ENST00000414778.1_Missense_Mutation_p.Q406E|PCDH15_ENST00000395430.1_Missense_Mutation_p.Q401E|PCDH15_ENST00000409834.1_Missense_Mutation_p.Q5E|PCDH15_ENST00000437009.1_Missense_Mutation_p.Q401E|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395438.1_Missense_Mutation_p.Q401E|PCDH15_ENST00000373965.2_Missense_Mutation_p.Q401E|PCDH15_ENST00000395445.1_Missense_Mutation_p.Q401E|PCDH15_ENST00000373957.3_Missense_Mutation_p.Q379E|PCDH15_ENST00000395446.1_Missense_Mutation_p.Q401E|PCDH15_ENST00000395440.1_Missense_Mutation_p.Q401E|PCDH15_ENST00000361849.3_Missense_Mutation_p.Q401E|PCDH15_ENST00000395432.2_Missense_Mutation_p.Q364E|PCDH15_ENST00000395433.1_Missense_Mutation_p.Q379E|PCDH15_ENST00000373955.1_Missense_Mutation_p.Q401E	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	401	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				ATATAGCCTTGATAACTGGGC	0.423										HNSCC(58;0.16)																											p.Q406E		Atlas-SNP	.											.	PCDH15	1715	.	0			c.C1216G						.						149	137	141					10																	55955547		2203	4300	6503	SO:0001583	missense	65217	exon12			AGCCTTGATAACT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1201C>G	chr10.hg19:g.55955547G>C	ENSP00000322604:p.Gln401Glu	139.0	0.0		89.0	45.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	5.938	0.357123	0.11239	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.6;0.24;0.24;0.36;0.24;0.24;0.24;0.24;0.24;0.24;0.24;0.24	5.17	4.21	0.49690	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.39462	0.1079	N	0.15975	0.35	0.28074	N	0.932458	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.24426	0.093;0.048;0.021;0.024;0.057;0.103;0.093;0.002;0.005;0.005;0.002;0.002;0.003;0.002;0.048	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.26864	0.047;0.023;0.015;0.015;0.074;0.023;0.047;0.005;0.015;0.015;0.005;0.005;0.003;0.008;0.015	T	0.08953	-1.0697	9	0.09590	T	0.72	.	14.2196	0.65818	0.0:0.2383:0.7617:0.0	.	379;401;401;406;401;364;401;401;401;401;401;406;401;379;401	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	E	401;406;401;401;5;401;401;401;364;401;379;379;401;401;406;401;401	ENSP00000363076:Q401E;ENSP00000410304:Q406E;ENSP00000378826:Q401E;ENSP00000386693:Q5E;ENSP00000378832:Q401E;ENSP00000378833:Q401E;ENSP00000378827:Q401E;ENSP00000378820:Q364E;ENSP00000354950:Q401E;ENSP00000378821:Q379E;ENSP00000363068:Q379E;ENSP00000322604:Q401E;ENSP00000378818:Q401E;ENSP00000412628:Q401E;ENSP00000363066:Q401E	ENSP00000322604:Q401E	Q	-	1	0	PCDH15	55625553	1.000000	0.71417	1.000000	0.80357	0.614000	0.37383	5.246000	0.65411	2.426000	0.82243	0.591000	0.81541	CAA	.	.		0.423	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		C	55955547	G	C	55955547	3	2	51	1	0	0	0	0	1	0	0	0	11520	1299	45	4	6402	4	PCDH15	10	55955547	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	4393186	55955547	79579200	66	6590										
LDB3	11155	hgsc.bcm.edu	37	chr10	88478564	88478564	+	Frame_Shift_Del	DEL	C	C	-													0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aagaagccttttgggaacagCctcttccacatggaagacgg							TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr10:88478564delC	ENST00000361373.4	+	11	1959	c.1938delC	c.(1936-1938)agcfs	p.S646fs	LDB3_ENST00000352360.5_Frame_Shift_Del_p.S389fs|LDB3_ENST00000458213.2_Frame_Shift_Del_p.S536fs|LDB3_ENST00000429277.2_Frame_Shift_Del_p.S651fs|LDB3_ENST00000263066.6_Frame_Shift_Del_p.S536fs	NM_007078.2	NP_009009.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						TTGGGAACAGCCTCTTCCACA	0.582																																					p.S651fs		Atlas-Indel,Pindel	.											.	LDB3	164	.	0			c.1952delG						.						76	68	71					10																	88478564		2203	4300	6503	SO:0001589	frameshift_variant	11155	exon12			.	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"cypher", "oracle", "Z-band alternatively spliced PDZ motif protein"	605906	"cardiomyopathy, dilated 1C (autosomal dominant)"	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.1938delC	chr10.hg19:g.88478564delC	ENSP00000355296:p.Ser646fs	148.0	0.0		60.0	24.0	NM_001171610		Frame_Shift_Del	DEL	ENST00000361373.4	hg19	CCDS7377.1																																																																																			.	.		0.582	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2			-	88478564	C	-	88478564	7	5	51	1	0	1	0	1	0	0	0	0	8706	738	26	0	2316	0	LDB3	10	88478564	Frame_Shift_Del	DEL	C	TCGA-BW-A5NO-01A-11D-A27I-10	32523017	88478564	47056183	67	6591										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106959827	106959827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	actacaaatctatcttcagcCggcattgcaccaaggaggac	8	12	3	0	rs202188584		TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr10:106959827C>T	ENST00000369701.3	+	15	2307	c.2080C>T	c.(2080-2082)Cgg>Tgg	p.R694W	SORCS3_ENST00000369699.4_5'UTR	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	694					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.R694W(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TATCTTCAGCCGGCATTGCAC	0.532																																					p.R694W	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											SORCS3,colon,carcinoma,0,2	SORCS3	282	.	1	Substitution - Missense(1)	prostate(1)	c.C2080T						.						130	117	121					10																	106959827		2203	4300	6503	SO:0001583	missense	22986	exon15			TTCAGCCGGCATT	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.2080C>T	chr10.hg19:g.106959827C>T	ENSP00000358715:p.Arg694Trp	218.0	0.0		76.0	27.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.181442	0.78677	.	.	ENSG00000156395	ENST00000369701	T	0.29655	1.56	6.07	4.23	0.50019	VPS10 (1);	0.057204	0.64402	N	0.000002	T	0.58666	0.2138	M	0.91406	3.205	0.49798	D	0.999822	D	0.89917	1.0	D	0.68621	0.959	T	0.63435	-0.6638	9	.	.	.	.	8.3777	0.32453	0.1237:0.759:0.0:0.1173	.	694	Q9UPU3	SORC3_HUMAN	W	694	ENSP00000358715:R694W	.	R	+	1	2	SORCS3	106949817	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.203000	0.32284	0.903000	0.36546	0.650000	0.86243	CGG	.	.		0.532	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		T	106959827	C	T	106959827	3	4	51	1	0	0	0	0	1	0	0	0	14947	643	23	1	2138	1	SORCS3	10	106959827	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	18481263	106959827	28574920	68	6592										
OR51G1	79324	hgsc.bcm.edu	37	chr11	4944787	4944787	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tcaccaaagcgatgcacaagAgacaagccaatcatggggat	10	10	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr11:4944787A>G	ENST00000321961.2	-	1	850	c.783T>C	c.(781-783)tcT>tcC	p.S261S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGCACAAGAGACAAGCCAA	0.517																																					p.S261S		Atlas-SNP	.											OR51G1,NS,carcinoma,0,1	OR51G1	74	.	0			c.T783C						.						187	145	159					11																	4944787		2201	4298	6499	SO:0001819	synonymous_variant	79324	exon1			CACAAGAGACAAG	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"GPCR / Class A : Olfactory receptors"	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.783T>C	chr11.hg19:g.4944787A>G		199.0	0.0		113.0	9.0	NM_001005237	B9EGW8|Q6IFH6	Silent	SNP	ENST00000321961.2	hg19	CCDS31366.1																																																																																			.	.		0.517	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237		G	4944787	A	G	4944787	2	3	51	1	0	0	0	0	0	0	0	1	11107	291	11	2		2	OR51G1	11	4944787	Silent	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10		4944787	130061729	69	6593										
SLC17A6	57084	hgsc.bcm.edu	37	chr11	22380967	22380967	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tttctatttcagggttttcgGagctgccatacttcttacct	7	10	3	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr11:22380967G>T	ENST00000263160.3	+	4	904	c.467G>T	c.(466-468)gGa>gTa	p.G156V	CTD-2140G10.4_ENST00000534543.1_RNA	NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	156					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						AGGGTTTTCGGAGCTGCCATA	0.363																																					p.G156V		Atlas-SNP	.											.	SLC17A6	135	.	0			c.G467T						.						112	102	106					11																	22380967		2203	4300	6503	SO:0001583	missense	57084	exon4			TTTTCGGAGCTGC	AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"Solute carriers"	16703	protein-coding gene	gene with protein product	"vesicular glutamate transporter 2", "differentiation-associated Na-dependent inorganic phosphate cotransporter"	607563	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.467G>T	chr11.hg19:g.22380967G>T	ENSP00000263160:p.Gly156Val	102.0	0.0		94.0	11.0	NM_020346	A6NKS2	Missense_Mutation	SNP	ENST00000263160.3	hg19	CCDS7856.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546401	0.86022	.	.	ENSG00000091664	ENST00000263160;ENST00000546171	T	0.55413	0.52	5.29	5.29	0.74685	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.72153	0.3425	M	0.73753	2.245	0.80722	D	1	P	0.51147	0.942	P	0.62298	0.9	T	0.73895	-0.3838	10	0.59425	D	0.04	.	19.2877	0.94085	0.0:0.0:1.0:0.0	.	156	Q9P2U8	VGLU2_HUMAN	V	156;44	ENSP00000263160:G156V	ENSP00000263160:G156V	G	+	2	0	SLC17A6	22337543	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.476000	0.97823	2.638000	0.89438	0.585000	0.79938	GGA	.	.		0.363	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		T	22380967	G	T	22380967	3	4	51	1	0	0	0	0	1	0	0	0	14436	1174	41	3	481	3	SLC17A6	11	22380967	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	17436180	22380967	112625549	70	6594										
CUL5	8065	hgsc.bcm.edu	37	chr11	107920728	107920728	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aacctttttgtcaactagagAttactttaatgggtaaacag	7	6	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr11:107920728A>T	ENST00000393094.2	+	4	962	c.346A>T	c.(346-348)Att>Ttt	p.I116F		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	116					calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		TCAACTAGAGATTACTTTAAT	0.328																																					p.I116F		Atlas-SNP	.											.	CUL5	71	.	0			c.A346T						.						79	81	80					11																	107920728		2201	4298	6499	SO:0001583	missense	8065	exon4			CTAGAGATTACTT	X81882	CCDS31668.1	11q22.3	2011-05-24			ENSG00000166266	ENSG00000166266			2556	protein-coding gene	gene with protein product		601741				8681378, 9037604	Standard	XM_005271682		Approved	VACM-1	uc001pjv.3	Q93034	OTTHUMG00000166369	ENST00000393094.2:c.346A>T	chr11.hg19:g.107920728A>T	ENSP00000376808:p.Ile116Phe	113.0	0.0		124.0	11.0	NM_003478	A8K960|O14766|Q9BZC6	Missense_Mutation	SNP	ENST00000393094.2	hg19	CCDS31668.1	.	.	.	.	.	.	.	.	.	.	A	16.95	3.264608	0.59431	.	.	ENSG00000166266	ENST00000393094	T	0.29397	1.57	5.83	4.71	0.59529	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.049975	0.85682	D	0.000000	T	0.21347	0.0514	N	0.14661	0.345	0.58432	D	0.999998	B	0.28378	0.209	B	0.33392	0.163	T	0.07252	-1.0782	10	0.72032	D	0.01	-10.0695	11.0632	0.47959	0.9269:0.0:0.0731:0.0	.	116	Q93034	CUL5_HUMAN	F	116	ENSP00000376808:I116F	ENSP00000376808:I116F	I	+	1	0	CUL5	107425938	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.054000	0.76649	1.056000	0.40484	0.533000	0.62120	ATT	.	.		0.328	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1			T	107920728	A	T	107920728	3	4	51	1	0	0	0	0	1	0	0	0	4061	333	12	4	360	4	CUL5	11	107920728	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	85539761	107920728	27085788	71	6595										
ZNF202	7753	hgsc.bcm.edu	37	chr11	123601551	123601551	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tttcaccatcagaattccctCttcttcccaaagatcctggt	4	14	4	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr11:123601551C>T	ENST00000529691.1	-	2	265	c.46G>A	c.(46-48)Gag>Aag	p.E16K	ZNF202_ENST00000336139.4_Missense_Mutation_p.E16K|ZNF202_ENST00000530393.1_Missense_Mutation_p.E16K			O95125	ZN202_HUMAN	zinc finger protein 202	16					lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		AGAATTCCCTCTTCTTCCCAA	0.522																																					p.E16K		Atlas-SNP	.											.	ZNF202	72	.	0			c.G46A						.						90	93	92					11																	123601551		2202	4299	6501	SO:0001583	missense	7753	exon4			TTCCCTCTTCTTC	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"Zinc fingers, C2H2-type", "-", "-", "-"	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.46G>A	chr11.hg19:g.123601551C>T	ENSP00000433881:p.Glu16Lys	168.0	0.0		96.0	21.0	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	hg19	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.532450	0.85812	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691;ENST00000533463;ENST00000528306	T;T;T;T	0.07114	3.22;3.22;3.22;3.26	4.7	4.7	0.59300	.	0.000000	0.49916	D	0.000132	T	0.12092	0.0294	N	0.08118	0	0.38108	D	0.937467	D	0.63880	0.993	D	0.68192	0.956	T	0.30416	-0.9979	10	0.72032	D	0.01	-21.7671	13.0223	0.58796	0.0:1.0:0.0:0.0	.	16	O95125	ZN202_HUMAN	K	16	ENSP00000337724:E16K;ENSP00000432504:E16K;ENSP00000433881:E16K;ENSP00000431223:E16K	ENSP00000337724:E16K	E	-	1	0	ZNF202	123106761	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.368000	0.44222	2.438000	0.82558	0.555000	0.69702	GAG	.	.		0.522	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		T	123601551	C	T	123601551	3	4	51	1	0	0	0	0	1	0	0	0	17778	922	32	3	1924	3	ZNF202	11	123601551	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	15680823	123601551	11404965	72	6596										
TAS2R10	50839	hgsc.bcm.edu	37	chr12	10978718	10978718	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	cagaaaaattcttgaaatagCtaagccggtgagaataaagc	9	6	1	3			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr12:10978718C>T	ENST00000240619.2	-	1	239	c.151G>A	c.(151-153)Gct>Act	p.A51T		NM_023921.1	NP_076410.1	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	51					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						CTTGAAATAGCTAAGCCGGTG	0.338																																					p.A51T		Atlas-SNP	.											.	TAS2R10	44	.	0			c.G151A						.						51	51	51					12																	10978718		2203	4300	6503	SO:0001583	missense	50839	exon1			AAATAGCTAAGCC	AF227136	CCDS8634.1	12p13	2012-08-22			ENSG00000121318	ENSG00000121318		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14918	protein-coding gene	gene with protein product		604791				10761934, 10766242	Standard	NM_023921		Approved	T2R10, TRB2	uc001qyy.1	Q9NYW0	OTTHUMG00000168508	ENST00000240619.2:c.151G>A	chr12.hg19:g.10978718C>T	ENSP00000240619:p.Ala51Thr	98.0	0.0		91.0	35.0	NM_023921	Q3MIM9|Q6NTD9	Missense_Mutation	SNP	ENST00000240619.2	hg19	CCDS8634.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.734965	0.69189	.	.	ENSG00000121318	ENST00000240619	T	0.56103	0.48	4.34	3.42	0.39159	.	0.175500	0.34133	N	0.004233	T	0.78541	0.4299	H	0.96365	3.81	0.29517	N	0.85379	D	0.67145	0.996	D	0.71656	0.974	T	0.78135	-0.2322	10	0.87932	D	0	.	11.3133	0.49377	0.1834:0.8166:0.0:0.0	.	51	Q9NYW0	T2R10_HUMAN	T	51	ENSP00000240619:A51T	ENSP00000240619:A51T	A	-	1	0	TAS2R10	10869985	0.009000	0.17119	0.947000	0.38551	0.833000	0.47200	0.388000	0.20735	1.113000	0.41760	0.591000	0.81541	GCT	.	.		0.338	TAS2R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399934.1			T	10978718	C	T	10978718	3	4	51	1	0	0	0	0	1	0	0	0	15581	797	28	3	776	3	TAS2R10	12	10978718	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10		10978718	122873177	73	6597										
EPS8	2059	hgsc.bcm.edu	37	chr12	15813579	15813579	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttccttttacctttcttgttTttcttccttttagaaagctc	3	10	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr12:15813579T>C	ENST00000281172.5	-	10	1342	c.906A>G	c.(904-906)aaA>aaG	p.K302K	EPS8_ENST00000543612.1_Silent_p.K302K|EPS8_ENST00000542903.1_Silent_p.K42K|EPS8_ENST00000543523.1_Silent_p.K302K|EPS8_ENST00000540613.1_Silent_p.K42K	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	302					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		CTTTCTTGTTTTTCTTCCTTT	0.383																																					p.K302K		Atlas-SNP	.											.	EPS8	70	.	0			c.A906G						.						114	110	111					12																	15813579		2203	4300	6503	SO:0001819	synonymous_variant	2059	exon10			CTTGTTTTTCTTC	U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.906A>G	chr12.hg19:g.15813579T>C		71.0	0.0		75.0	15.0	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Silent	SNP	ENST00000281172.5	hg19	CCDS31753.1																																																																																			.	.		0.383	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			C	15813579	T	C	15813579	2	2	51	1	0	0	0	0	0	0	0	1	5196	1838	64	2		2	EPS8	12	15813579	Silent	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10	4834861	15813579	118038316	74	6598										
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72017915	72017915	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ccagtgcactttggcatcttCcagtaaatatgtgcagctga	9	10	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr12:72017915C>T	ENST00000378743.3	-	23	4833	c.4475G>A	c.(4474-4476)gGa>gAa	p.G1492E		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1492					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TTGGCATCTTCCAGTAAATAT	0.393																																					p.G1492E		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.G4475A						.						169	161	163					12																	72017915		1841	4090	5931	SO:0001583	missense	196441	exon23			CATCTTCCAGTAA	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.4475G>A	chr12.hg19:g.72017915C>T	ENSP00000368017:p.Gly1492Glu	59.0	0.0		80.0	5.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	hg19	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.791081	0.90367	.	.	ENSG00000133858	ENST00000378743	T	0.33216	1.42	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.48696	0.1514	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.47129	-0.9141	10	0.62326	D	0.03	.	19.1586	0.93522	0.0:1.0:0.0:0.0	.	1492	O60293	ZC3H1_HUMAN	E	1492	ENSP00000368017:G1492E	ENSP00000368017:G1492E	G	-	2	0	ZFC3H1	70304182	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.907000	0.75724	2.520000	0.84964	0.655000	0.94253	GGA	.	.		0.393	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		T	72017915	C	T	72017915	3	4	51	1	0	0	0	0	1	0	0	0	17648	855	30	3	1546	3	ZFC3H1	12	72017915	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	56204336	72017915	61833980	75	6599										
TMTC2	160335	hgsc.bcm.edu	37	chr12	83290361	83290361	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ggactcaagactgcgatcagGaatggagactggcagaatga	14	7	2	4			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr12:83290361G>A	ENST00000321196.3	+	3	2126	c.1419G>A	c.(1417-1419)agG>agA	p.R473R	TMTC2_ENST00000549919.1_Silent_p.R467R|TMTC2_ENST00000548305.1_Silent_p.R473R	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	473					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						CTGCGATCAGGAATGGAGACT	0.373																																					p.R473R		Atlas-SNP	.											.	TMTC2	100	.	0			c.G1419A						.						66	63	64					12																	83290361		2203	4300	6503	SO:0001819	synonymous_variant	160335	exon3			GATCAGGAATGGA	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.1419G>A	chr12.hg19:g.83290361G>A		60.0	0.0		124.0	17.0	NM_152588	B2RCU7|Q8N2K8	Silent	SNP	ENST00000321196.3	hg19	CCDS9025.1																																																																																			.	.		0.373	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		A	83290361	G	A	83290361	2	1	51	1	0	0	0	0	0	0	0	1	16276	1165	41	3		3	TMTC2	12	83290361	Silent	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	11272446	83290361	50561534	76	6600										
ACACB	32	hgsc.bcm.edu	37	chr12	109629713	109629713	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	cttgaacgtggccgatgcgaTgttcagaacgtgcatgacag	13	9	1	3			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr12:109629713T>A	ENST00000338432.7	+	15	2476	c.2357T>A	c.(2356-2358)aTg>aAg	p.M786K	ACACB_ENST00000377854.5_Missense_Mutation_p.M786K|ACACB_ENST00000377848.3_Missense_Mutation_p.M786K			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	786					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GCCGATGCGATGTTCAGAACG	0.527																																					p.M786K		Atlas-SNP	.											.	ACACB	330	.	0			c.T2357A						.						140	117	125					12																	109629713		2203	4300	6503	SO:0001583	missense	32	exon14			ATGCGATGTTCAG	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.2357T>A	chr12.hg19:g.109629713T>A	ENSP00000341044:p.Met786Lys	242.0	0.0		187.0	35.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	T	8.773	0.926303	0.18056	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	D;D;D	0.95001	-3.56;-3.56;-3.58	5.32	2.91	0.33838	.	0.428494	0.29106	N	0.013140	T	0.80639	0.4661	N	0.03608	-0.345	0.58432	D	0.999999	B	0.13594	0.008	B	0.12156	0.007	T	0.65154	-0.6237	10	0.13853	T	0.58	.	1.0907	0.01662	0.1633:0.1474:0.1703:0.519	.	786	O00763	ACACB_HUMAN	K	786;786;786;17	ENSP00000341044:M786K;ENSP00000367079:M786K;ENSP00000367085:M786K	ENSP00000341044:M786K	M	+	2	0	ACACB	108114096	0.280000	0.24249	0.464000	0.27143	0.946000	0.59487	0.601000	0.24119	0.322000	0.23283	-0.354000	0.07668	ATG	.	.		0.527	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		A	109629713	T	A	109629713	3	1	51	1	0	0	0	0	1	0	0	0	107	1464	51	4	2411	4	ACACB	12	109629713	Missense_Mutation	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10	26339352	109629713	24222182	77	6601										
OAS2	4939	hgsc.bcm.edu	37	chr12	113444385	113444385	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	taaaggatttaattcgcctgGtgaagcactggtacaaagag	11	6	0	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr12:113444385G>T	ENST00000342315.4	+	8	1850	c.1636G>T	c.(1636-1638)Gtg>Ttg	p.V546L	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Missense_Mutation_p.V546L	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	546	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						AATTCGCCTGGTGAAGCACTG	0.478																																					p.V546L	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.G1636T						.						114	114	114					12																	113444385		2203	4300	6503	SO:0001583	missense	4939	exon8			CGCCTGGTGAAGC	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"2'-5'-oligoadenylate synthetase 2 (69-71 kD)"			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.1636G>T	chr12.hg19:g.113444385G>T	ENSP00000342278:p.Val546Leu	132.0	0.0		118.0	43.0	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	hg19	CCDS31906.1	.	.	.	.	.	.	.	.	.	.	.	12.62	1.992513	0.35131	.	.	ENSG00000111335	ENST00000342315;ENST00000392583	T;T	0.58940	0.3;0.3	4.62	-0.611	0.11601	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	0.965401	0.08458	N	0.942784	T	0.52075	0.1712	M	0.71871	2.18	0.80722	D	1	B;B	0.22683	0.073;0.043	B;B	0.20184	0.028;0.012	T	0.51309	-0.8722	10	0.62326	D	0.03	-34.4184	4.4805	0.11764	0.3754:0.1605:0.4641:0.0	.	546;546	P29728;P29728-2	OAS2_HUMAN;.	L	546	ENSP00000342278:V546L;ENSP00000376362:V546L	ENSP00000342278:V546L	V	+	1	0	OAS2	111928768	1.000000	0.71417	0.976000	0.42696	0.690000	0.40134	0.806000	0.27126	-0.048000	0.13401	-0.140000	0.14226	GTG	.	.		0.478	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1			T	113444385	G	T	113444385	3	4	51	1	0	0	0	0	1	0	0	0	10809	1261	44	3	1737	3	OAS2	12	113444385	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	3814672	113444385	20407510	78	6602										
TBX3	6926	hgsc.bcm.edu	37	chr12	115118767	115118767	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	catccactgttccccagtagCggggctgtccgggtgaatgt	13	12	0	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr12:115118767C>A	ENST00000257566.3	-	2	963	c.574G>T	c.(574-576)Gct>Tct	p.A192S	TBX3_ENST00000349155.2_Missense_Mutation_p.A192S	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	192					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		TCCCCAGTAGCGGGGCTGTCC	0.463																																					p.A192S		Atlas-SNP	.											.	TBX3	106	.	0			c.G574T						.						112	108	109					12																	115118767		2203	4300	6503	SO:0001583	missense	6926	exon2			CAGTAGCGGGGCT	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.574G>T	chr12.hg19:g.115118767C>A	ENSP00000257566:p.Ala192Ser	368.0	1.0		299.0	113.0	NM_005996	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	hg19	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	C	32	5.174696	0.94807	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.88046	-2.33;-2.33	5.81	5.81	0.92471	Transcription factor, T-box, conserved site (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.90335	0.6976	L	0.33137	0.985	0.80722	D	1	B;P;D	0.64830	0.221;0.856;0.994	P;P;D	0.87578	0.581;0.86;0.998	D	0.88813	0.3293	10	0.35671	T	0.21	.	19.0715	0.93140	0.0:1.0:0.0:0.0	.	192;192;192	B4E3A6;O15119-2;O15119	.;.;TBX3_HUMAN	S	192	ENSP00000257567:A192S;ENSP00000257566:A192S	ENSP00000257566:A192S	A	-	1	0	TBX3	113603150	1.000000	0.71417	0.504000	0.27639	0.962000	0.63368	7.487000	0.81328	2.756000	0.94617	0.655000	0.94253	GCT	.	.		0.463	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		A	115118767	C	A	115118767	3	1	51	1	0	0	0	0	1	0	0	0	15674	768	27	1	1685	1	TBX3	12	115118767	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	1674382	115118767	18733128	79	6603										
CIT	11113	hgsc.bcm.edu	37	chr12	120222843	120222843	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ccatggagctagtcttggcaGgggagtccagacccgacaca	13	12	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr12:120222843G>T	ENST00000261833.7	-	11	1374	c.1322C>A	c.(1321-1323)cCt>cAt	p.P441H	CIT_ENST00000392521.2_Missense_Mutation_p.P441H|CIT_ENST00000537607.1_5'Flank	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	441					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		AGTCTTGGCAGGGGAGTCCAG	0.498																																					p.P441H		Atlas-SNP	.											.	CIT	535	.	0			c.C1322A						.						93	83	86					12																	120222843		2203	4300	6503	SO:0001583	missense	11113	exon11			TTGGCAGGGGAGT	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.1322C>A	chr12.hg19:g.120222843G>T	ENSP00000261833:p.Pro441His	149.0	0.0		107.0	5.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.6|21.6	4.174650|4.174650	0.78452|0.78452	.|.	.|.	ENSG00000122966|ENSG00000122966	ENST00000392520|ENST00000392521;ENST00000261833	.|T;T	.|0.64438	.|-0.1;-0.09	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.69106|0.69106	0.3074|0.3074	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|D;D	.|0.63880	.|0.993;0.988	.|D;P	.|0.68943	.|0.961;0.887	T|T	0.72211|0.72211	-0.4359|-0.4359	5|10	.|0.66056	.|D	.|0.02	.|.	20.1379|20.1379	0.98040|0.98040	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|441;441	.|Q2M5E1;O14578	.|.;CTRO_HUMAN	M|H	69|441	.|ENSP00000376306:P441H;ENSP00000261833:P441H	.|ENSP00000261833:P441H	L|P	-|-	1|2	2|0	CIT|CIT	118707226|118707226	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.869000|9.869000	0.99810|0.99810	2.779000|2.779000	0.95612|0.95612	0.655000|0.655000	0.94253|0.94253	CTG|CCT	.	.		0.498	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120222843	G	T	120222843	3	4	51	1	0	0	0	0	1	0	0	0	3440	1000	35	3	4909	3	CIT	12	120222843	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	5104076	120222843	13629052	80	6604										
FREM2	341640	hgsc.bcm.edu	37	chr13	39266353	39266353	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttcacagtgactgatggcacCcatacagacttctatgtttt	7	10	2	3			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr13:39266353C>A	ENST00000280481.7	+	1	5088	c.4872C>A	c.(4870-4872)acC>acA	p.T1624T		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1624					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CTGATGGCACCCATACAGACT	0.428																																					p.T1624T		Atlas-SNP	.											.	FREM2	385	.	0			c.C4872A						.						105	102	103					13																	39266353		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			TGGCACCCATACA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.4872C>A	chr13.hg19:g.39266353C>A		204.0	0.0		111.0	22.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.428	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39266353	C	A	39266353	2	1	51	1	0	0	0	0	0	0	0	1	6053	610	22	3		3	FREM2	13	39266353	Silent	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10		39266353	75903525	81	6605										
OXA1L	5018	hgsc.bcm.edu	37	chr14	23235798	23235798	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	caagctccgttctcttttacCgcctgatctgcggctacaat	7	14	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr14:23235798C>T	ENST00000285848.5	+	1	68	c.68C>T	c.(67-69)cCg>cTg	p.P23L	OXA1L_ENST00000604262.1_5'Flank|CTD-2555K7.2_ENST00000554857.1_RNA|CTD-2555K7.2_ENST00000553792.1_RNA|OXA1L_ENST00000412791.1_5'Flank|OXA1L_ENST00000358043.5_5'Flank|CTD-2555K7.2_ENST00000554730.1_RNA	NM_005015.3	NP_005006.3	Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	0					aerobic respiration (GO:0009060)|mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex I biogenesis (GO:0097031)|negative regulation of ATPase activity (GO:0032780)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|protein complex assembly (GO:0006461)|protein insertion into membrane (GO:0051205)|protein tetramerization (GO:0051262)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	mitochondrial ribosome binding (GO:0097177)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|skin(2)	19	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		TCTCTTTTACCGCCTGATCTG	0.502																																					p.P23L		Atlas-SNP	.											.	OXA1L	49	.	0			c.C68T						.						114	120	118					14																	23235798		2203	4300	6503	SO:0001583	missense	5018	exon1			TTTTACCGCCTGA		CCDS9573.1	14q11.2	2009-05-26			ENSG00000155463	ENSG00000155463			8526	protein-coding gene	gene with protein product		601066				8586451, 19349278	Standard	NM_005015		Approved	MGC133129, OXA1	uc001wgn.2	Q15070	OTTHUMG00000028691	ENST00000285848.5:c.68C>T	chr14.hg19:g.23235798C>T	ENSP00000285848:p.Pro23Leu	195.0	0.0		84.0	4.0	NM_005015	B4DPA2	Missense_Mutation	SNP	ENST00000285848.5	hg19	CCDS9573.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.949540	0.53186	.	.	ENSG00000155463	ENST00000285848	T	0.38560	1.13	4.67	-0.937	0.10415	.	.	.	.	.	T	0.18002	0.0432	N	0.08118	0	0.19575	N	0.999964	B	0.12013	0.005	B	0.06405	0.002	T	0.20907	-1.0261	9	0.87932	D	0	-2.781	0.6373	0.00804	0.3124:0.3264:0.173:0.1883	.	23	Q2M1J6	.	L	23	ENSP00000285848:P23L	ENSP00000285848:P23L	P	+	2	0	OXA1L	22305638	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.524000	0.06222	-0.063000	0.13065	-0.182000	0.12963	CCG	.	.		0.502	OXA1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071630.2	NM_005015		T	23235798	C	T	23235798	3	4	51	1	0	0	0	0	1	0	0	0	11337	652	23	1	70	1	OXA1L	14	23235798	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10		23235798	84113742	82	6606										
SFRS5	6430	hgsc.bcm.edu	37	chr14	70237779	70237779	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aactttctggaaaggaaataAatgggagaaaaataaaatta	8	2	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr14:70237779A>T	ENST00000553521.1	+	8	1961	c.508A>T	c.(508-510)Aat>Tat	p.N170Y	SRSF5_ENST00000557154.1_Missense_Mutation_p.N170Y|SRSF5_ENST00000394366.2_Missense_Mutation_p.N170Y|SRSF5_ENST00000553635.1_Missense_Mutation_p.N167Y|SRSF5_ENST00000556587.1_3'UTR			Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5	170	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|liver(1)	2						AAAGGAAATAAATGGGAGAAA	0.313																																					p.N170Y		Atlas-SNP	.											.	SRSF5	45	.	0			c.A508T						.						91	95	94					14																	70237779		2203	4300	6503	SO:0001583	missense	6430	exon7			GAAATAAATGGGA	AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10787	protein-coding gene	gene with protein product	"SR splicing factor 5"	600914	"splicing factor, arginine/serine-rich 5"	SFRS5		7686911, 20516191	Standard	XM_005267998		Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.508A>T	chr14.hg19:g.70237779A>T	ENSP00000452123:p.Asn170Tyr	84.0	0.0		92.0	46.0	NM_001039465	O14797|Q16662|Q49AD6|Q6FGE0	Missense_Mutation	SNP	ENST00000553521.1	hg19	CCDS32109.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.069402	0.76301	.	.	ENSG00000100650	ENST00000553521;ENST00000394366;ENST00000557154;ENST00000553635	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	5.78	5.78	0.91487	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	M	0.71036	2.16	0.80722	D	1	P;D	0.76494	0.539;0.999	B;D	0.72982	0.281;0.979	T	0.19257	-1.0311	10	0.48119	T	0.1	.	16.1021	0.81178	1.0:0.0:0.0:0.0	.	167;170	Q13243-3;Q13243	.;SRSF5_HUMAN	Y	170;170;170;167	ENSP00000452123:N170Y;ENSP00000377892:N170Y;ENSP00000451088:N170Y;ENSP00000451391:N167Y	ENSP00000377892:N170Y	N	+	1	0	SRSF5	69307532	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.060000	0.93907	2.210000	0.71456	0.533000	0.62120	AAT	.	.		0.313	SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412456.1	NM_001039465		T	70237779	A	T	70237779	3	4	51	1	0	0	0	0	1	0	0	0	14195	14	1	4	530	4	SFRS5	14	70237779	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	47001981	70237779	37111761	83	6607										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92436115	92436115	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aacatctgagatgggtttcaGaagaagatgcccgggcccac	12	10	2	4			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr14:92436115G>C	ENST00000267622.4	-	21	6215	c.5842C>G	c.(5842-5844)Ctg>Gtg	p.L1948V		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1948					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		ATGGGTTTCAGAAGAAGATGC	0.483			T	PDGFRB	AML																																p.L1948V	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.C5842G						.						69	72	71					14																	92436115		2203	4300	6503	SO:0001583	missense	9321	exon21			GTTTCAGAAGAAG	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.5842C>G	chr14.hg19:g.92436115G>C	ENSP00000267622:p.Leu1948Val	270.0	0.0		221.0	9.0	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	hg19	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.22|16.22	3.062776|3.062776	0.55432|0.55432	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.05717|.	3.4|.	5.78|5.78	-11.3|-11.3	0.00108|0.00108	.|.	0.047609|.	0.85682|.	D|.	0.000000|.	T|T	0.44138|0.44138	0.1279|0.1279	L|L	0.53249|0.53249	1.67|1.67	0.28291|0.28291	N|N	0.92355|0.92355	P;P|.	0.43024|.	0.775;0.798|.	B;P|.	0.47134|.	0.266;0.539|.	T|T	0.52426|0.52426	-0.8577|-0.8577	10|5	0.66056|.	D|.	0.02|.	.|.	14.066|14.066	0.64828|0.64828	0.1566:0.0:0.6817:0.1617|0.1566:0.0:0.6817:0.1617	.|.	1684;1948|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	V|C	1948;1684|1663	ENSP00000267622:L1948V|.	ENSP00000267622:L1948V|.	L|S	-|-	1|2	2|0	TRIP11|TRIP11	91505868|91505868	0.998000|0.998000	0.40836|0.40836	0.012000|0.012000	0.15200|0.15200	0.400000|0.400000	0.30750|0.30750	1.281000|1.281000	0.33214|0.33214	-1.792000|-1.792000	0.01259|0.01259	-0.253000|-0.253000	0.11424|0.11424	CTG|TCT	.	.		0.483	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			C	92436115	G	C	92436115	3	2	51	1	0	0	0	0	1	0	0	0	16570	933	33	4	101	4	TRIP11	14	92436115	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	22198336	92436115	14913425	84	6608										
EML1	2009	hgsc.bcm.edu	37	chr14	100361092	100361092	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	caagagactcaagctggaatGggtgtatcctttattcattg	10	7	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr14:100361092G>T	ENST00000262233.6	+	6	813	c.674G>T	c.(673-675)tGg>tTg	p.W225L	EML1_ENST00000327921.9_Missense_Mutation_p.W213L|EML1_ENST00000334192.4_Missense_Mutation_p.W244L	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	225	Tandem atypical propeller in EMLs.		W -> R (probable disease-associated mutation found in a patient with atypical heterotopia and mental retardation). {ECO:0000269|PubMed:24859200}.		brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				AAGCTGGAATGGGTGTATCCT	0.393																																					p.W244L		Atlas-SNP	.											.	EML1	97	.	0			c.G731T						.						97	89	92					14																	100361092		2203	4300	6503	SO:0001583	missense	2009	exon7			TGGAATGGGTGTA	AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"WD repeat domain containing"	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.674G>T	chr14.hg19:g.100361092G>T	ENSP00000262233:p.Trp225Leu	107.0	0.0		66.0	18.0	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	hg19	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.805609	0.90623	.	.	ENSG00000066629	ENST00000554479;ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138;ENST00000556714	T;T;T;T;T	0.63744	1.2;-0.06;-0.06;-0.06;1.2	5.32	5.32	0.75619	HELP (1);Quinonprotein alcohol dehydrogenase-like (1);	0.110450	0.64402	D	0.000003	T	0.78349	0.4269	M	0.81239	2.535	0.80722	D	1	P;D;D;P;P	0.57257	0.9;0.969;0.979;0.95;0.918	B;P;P;P;P	0.58130	0.407;0.538;0.833;0.487;0.543	T	0.81854	-0.0741	10	0.87932	D	0	-15.4215	18.9766	0.92740	0.0:0.0:1.0:0.0	.	213;213;225;244;244	F8W717;B7Z650;O00423;O00423-3;B3KXA3	.;.;EMAL1_HUMAN;.;.	L	212;213;225;244;244;194	ENSP00000451346:W212L;ENSP00000327384:W213L;ENSP00000262233:W225L;ENSP00000334314:W244L;ENSP00000452089:W194L	ENSP00000262233:W225L	W	+	2	0	EML1	99430845	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.471000	0.83476	0.585000	0.79938	TGG	.	.		0.393	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		T	100361092	G	T	100361092	3	4	51	1	0	0	0	0	1	0	0	0	5098	1357	47	3	757	3	EML1	14	100361092	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	7924977	100361092	6988448	85	6609										
EID1	399694	hgsc.bcm.edu	37	chr15	49170689	49170689	+	Intron	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gcgaggaatttgatgactggGaggacgactacgactatccc	13	9	0	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr15:49170689G>C	ENST00000332408.4	-	4	1269				SHC4_ENST00000396535.3_5'Flank|EID1_ENST00000530028.2_Missense_Mutation_p.E106Q|EID1_ENST00000558295.1_Intron|SHC4_ENST00000537958.1_5'Flank|EID1_ENST00000560490.1_Missense_Mutation_p.E84Q	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4						apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		TGATGACTGGGAGGACGACTA	0.597																																					p.E106Q		Atlas-SNP	.											.	EID1	16	.	0			c.G316C						.						40	43	42					15																	49170689		2044	4189	6233	SO:0001627	intron_variant	23741	exon1			GACTGGGAGGACG	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"SH2 domain containing"	16743	protein-coding gene	gene with protein product	"rai-like protein"						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.840+5755C>G	chr15.hg19:g.49170689G>C		124.0	0.0		50.0	4.0	NM_014335	Q6UXQ3|Q8IYW3	Missense_Mutation	SNP	ENST00000332408.4	hg19	CCDS10130.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.247181	0.80024	.	.	ENSG00000255302	ENST00000530028	T	0.39997	1.05	4.19	4.19	0.49359	.	.	.	.	.	T	0.43255	0.1239	L	0.36672	1.1	0.29774	N	0.83455	P	0.50272	0.933	P	0.52267	0.694	T	0.18241	-1.0343	9	0.26408	T	0.33	.	12.3392	0.55085	0.0:0.0:1.0:0.0	.	106	Q9Y6B2	EID1_HUMAN	Q	106	ENSP00000431162:E106Q	ENSP00000431162:E106Q	E	+	1	0	EID1	46957981	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.727000	0.54984	2.622000	0.88805	0.655000	0.94253	GAG	.	.		0.597	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349		C	49170689	G	C	49170689	1	2	51	0	1	0	0	0	0	0	0	0	4988	1175	41	4		4	EID1	15	49170689	Intron	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10		49170689	53360703	86	6610										
TP53	7157	hgsc.bcm.edu	37	chr17	7577142	7577142	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	cacctcaaagctgttccgtcCcagtagattaccactactca	5	15	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr17:7577142C>T	ENST00000269305.4	-	8	985	c.796G>A	c.(796-798)Gga>Aga	p.G266R	TP53_ENST00000445888.2_Missense_Mutation_p.G266R|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.G266R|TP53_ENST00000455263.2_Missense_Mutation_p.G266R|TP53_ENST00000420246.2_Missense_Mutation_p.G266R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	266	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G266R(46)|p.G266*(14)|p.0?(8)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G262_S269delGNLLGRNS(2)|p.G266fs*79(2)|p.N263fs*5(1)|p.G266T(1)|p.L265_K305del41(1)|p.G266_E271delGRNSFE(1)|p.E258fs*71(1)|p.G266fs*9(1)|p.L265_R267delLGR(1)|p.G266_N268delGRN(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGTTCCGTCCCAGTAGATTA	0.517		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.G266R	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,+1,1	TP53	33396	.	86	Substitution - Missense(47)|Substitution - Nonsense(14)|Deletion - In frame(8)|Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(3)|Insertion - Frameshift(1)	lung(16)|large_intestine(11)|ovary(8)|central_nervous_system(6)|urinary_tract(6)|oesophagus(6)|upper_aerodigestive_tract(5)|breast(5)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|stomach(3)|liver(2)|skin(2)|pancreas(2)|biliary_tract(1)|peritoneum(1)|salivary_gland(1)|endometrium(1)|eye(1)|pleura(1)	c.G796A						.						49	44	46					17																	7577142		2203	4300	6503	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TCCGTCCCAGTAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.796G>A	chr17.hg19:g.7577142C>T	ENSP00000269305:p.Gly266Arg	123.0	0.0		60.0	7.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.539769	0.85917	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99900	-7.63;-7.63;-7.63;-7.63;-7.63;-7.63	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99906	0.9955	M	0.92367	3.3	0.80722	D	1	D;D;D;D	0.89917	0.996;1.0;0.986;0.997	D;D;D;D	0.97110	0.978;1.0;0.962;0.958	D	0.96190	0.9137	10	0.87932	D	0	-13.0798	16.1198	0.81342	0.0:1.0:0.0:0.0	.	266;266;266;266	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	R	266;266;266;266;266;255;134	ENSP00000352610:G266R;ENSP00000269305:G266R;ENSP00000398846:G266R;ENSP00000391127:G266R;ENSP00000391478:G266R;ENSP00000425104:G134R	ENSP00000269305:G266R	G	-	1	0	TP53	7517867	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	7.587000	0.82613	2.667000	0.90743	0.462000	0.41574	GGA	.	.		0.517	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577142	C	T	7577142	3	4	51	1	0	0	0	0	1	0	0	0	16396	632	22	3	490	3	TP53	17	7577142	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10		7577142	73618068	87	6611										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27421037	27421037	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	cgggcctcctccacctcctcAtcccgactctccatctcctt	4	22	3	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr17:27421037A>T	ENST00000527372.1	-	31	4962	c.4782T>A	c.(4780-4782)gaT>gaA	p.D1594E	MYO18A_ENST00000354329.4_Missense_Mutation_p.D1594E|MYO18A_ENST00000529578.1_5'Flank|MYO18A_ENST00000533112.1_Intron|MYO18A_ENST00000531253.1_Missense_Mutation_p.D1594E|TIAF1_ENST00000408971.2_5'Flank	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1594					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CCACCTCCTCATCCCGACTCT	0.547																																					p.D1594E	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.T4782A						.						130	138	135					17																	27421037		2080	4201	6281	SO:0001583	missense	399687	exon31			CTCCTCATCCCGA	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.4782T>A	chr17.hg19:g.27421037A>T	ENSP00000437073:p.Asp1594Glu	108.0	0.0		63.0	29.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.04|12.04	1.817852|1.817852	0.32145|0.32145	.|.	.|.	ENSG00000196535|ENSG00000196535	ENST00000354329;ENST00000531253;ENST00000527372;ENST00000529799;ENST00000540575;ENST00000458428|ENST00000527859	T;T;T|.	0.72942|.	-0.7;-0.7;-0.7|.	5.28|5.28	1.82|1.82	0.25136|0.25136	Myosin tail (1);|.	0.093634|.	0.64402|.	D|.	0.000001|.	T|T	0.43831|0.43831	0.1265|0.1265	L|L	0.31065|0.31065	0.9|0.9	0.35492|0.35492	D|D	0.799096|0.799096	B;B;B|.	0.26258|.	0.096;0.096;0.145|.	B;B;B|.	0.28139|.	0.062;0.062;0.086|.	T|T	0.46898|0.46898	-0.9158|-0.9158	10|5	0.02654|.	T|.	1|.	.|.	10.198|10.198	0.43067|0.43067	0.6707:0.0:0.3293:0.0|0.6707:0.0:0.3293:0.0	.|.	1197;1594;1594|.	F8W6Y3;Q92614-4;Q92614|.	.;.;MY18A_HUMAN|.	E|K	1594;1594;1594;490;490;1197|22	ENSP00000346291:D1594E;ENSP00000434228:D1594E;ENSP00000437073:D1594E|.	ENSP00000346291:D1594E|.	D|M	-|-	3|2	2|0	MYO18A|MYO18A	24445163|24445163	0.358000|0.358000	0.24947|0.24947	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	-0.288000|-0.288000	0.08377|0.08377	0.341000|0.341000	0.23771|0.23771	0.533000|0.533000	0.62120|0.62120	GAT|ATG	.	.		0.547	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		T	27421037	A	T	27421037	3	4	51	1	0	0	0	0	1	0	0	0	10074	214	8	4	1430	4	MYO18A	17	27421037	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	19843895	27421037	53774173	88	6612										
SLFN13	146857	hgsc.bcm.edu	37	chr17	33770885	33770885	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ctggtctgcaaagtgaaggaCtgtcagatagactcaactga	11	8	3	4	rs370603090		TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr17:33770885C>T	ENST00000285013.6	-	4	1396	c.1121G>A	c.(1120-1122)aGt>aAt	p.S374N	SLFN13_ENST00000533791.1_Missense_Mutation_p.S374N|SLFN13_ENST00000534689.1_Missense_Mutation_p.S56N|SLFN13_ENST00000360502.2_Missense_Mutation_p.S56N|SLFN13_ENST00000526861.1_Missense_Mutation_p.S374N|SLFN13_ENST00000542635.1_Missense_Mutation_p.S374N	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	374						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		AAGTGAAGGACTGTCAGATAG	0.383																																					p.S374N		Atlas-SNP	.											.	SLFN13	79	.	0			c.G1121A						.	C	ASN/SER	1,4405		0,1,2202	96	91	93		1121	2.4	0	17		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLFN13	NM_144682.5	46	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign	374/898	33770885	2,13004	2203	4300	6503	SO:0001583	missense	146857	exon4			GAAGGACTGTCAG	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.1121G>A	chr17.hg19:g.33770885C>T	ENSP00000285013:p.Ser374Asn	83.0	0.0		183.0	51.0	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	hg19	CCDS32620.1	.	.	.	.	.	.	.	.	.	.	c	9.299	1.052517	0.19907	2.27E-4	1.16E-4	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689;ENST00000532210	T;T;T;T;T;T	0.65549	-0.16;3.86;-0.16;-0.16;3.86;2.17	3.4	2.37	0.29283	.	1.407560	0.04453	N	0.373034	T	0.59004	0.2162	L	0.55481	1.735	0.09310	N	1	P;B	0.36315	0.547;0.118	B;B	0.35510	0.204;0.05	T	0.50659	-0.8802	10	0.52906	T	0.07	.	8.4279	0.32739	0.0:0.7579:0.2421:0.0	.	56;374	Q68D06-2;Q68D06	.;SLN13_HUMAN	N	374;56;374;374;56;43	ENSP00000285013:S374N;ENSP00000353692:S56N;ENSP00000434439:S374N;ENSP00000444016:S374N;ENSP00000435442:S56N;ENSP00000435328:S43N	ENSP00000285013:S374N	S	-	2	0	SLFN13	30794998	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-0.470000	0.06639	0.702000	0.31825	0.514000	0.50259	AGT	.	.		0.383	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		T	33770885	C	T	33770885	3	4	51	1	0	0	0	0	1	0	0	0	14751	565	20	3	1584	3	SLFN13	17	33770885	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	6349848	33770885	47424325	89	6613										
TADA2A	6871	hgsc.bcm.edu	37	chr17	35836972	35836972	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tgctctattgaacgaatgtaAcaagcaaggaggcttaagac	10	7	1	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr17:35836972A>G	ENST00000394395.2	+	16	1390	c.1217A>G	c.(1216-1218)aAc>aGc	p.N406S	TADA2A_ENST00000225396.6_Missense_Mutation_p.N406S	NM_001166105.1	NP_001159577.1	O75478	TAD2A_HUMAN	transcriptional adaptor 2A	406	SWIRM. {ECO:0000255|PROSITE- ProRule:PRU00247}.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)|skin(1)	13						AACGAATGTAACAAGCAAGGA	0.423																																					p.N406S		Atlas-SNP	.											.	TADA2A	91	.	0			c.A1217G						.						165	169	167					17																	35836972		2203	4300	6503	SO:0001583	missense	6871	exon16			AATGTAACAAGCA	AK022767	CCDS11319.1, CCDS45656.1	17q12-q21	2014-04-10	2009-10-02	2009-10-02	ENSG00000108264	ENSG00000276234			11531	protein-coding gene	gene with protein product		602276	"transcriptional adaptor 2 (ADA2 homolog, yeast)-like"	TADA2L		8552087	Standard	XM_006722043		Approved	ADA2, hADA2, ADA2A	uc002hnt.3	O75478	OTTHUMG00000188469	ENST00000394395.2:c.1217A>G	chr17.hg19:g.35836972A>G	ENSP00000377918:p.Asn406Ser	111.0	0.0		159.0	24.0	NM_001488	A8MVD0|B3KMU9|Q9BVJ0|Q9UCW2|Q9UP49	Missense_Mutation	SNP	ENST00000394395.2	hg19	CCDS11319.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.441130	0.43326	.	.	ENSG00000108264	ENST00000394395;ENST00000428846;ENST00000225396	T;T	0.39997	1.05;1.05	5.93	4.85	0.62838	Homeodomain-like (1);SWIRM (2);	0.216662	0.53938	N	0.000049	T	0.17704	0.0425	N	0.03608	-0.345	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.07046	-1.0793	10	0.15066	T	0.55	-13.7652	7.7126	0.28686	0.7899:0.1402:0.0699:0.0	.	406	O75478	TAD2A_HUMAN	S	406;305;406	ENSP00000377918:N406S;ENSP00000225396:N406S	ENSP00000225396:N406S	N	+	2	0	TADA2A	32911085	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.943000	0.63554	1.075000	0.40932	0.455000	0.32223	AAC	.	.		0.423	TADA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256677.3	NM_001488		G	35836972	A	G	35836972	3	3	51	1	0	0	0	0	1	0	0	0	15525	43	2	2	1370	2	TADA2A	17	35836972	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	2066087	35836972	45358238	90	6614										
SC65	10609	hgsc.bcm.edu	37	chr17	39959557	39959557	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	accagcctcggcctcgtcacCcttggcatccggctcctgcc	9	20	1	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr17:39959557C>T	ENST00000355468.3	-	8	1739	c.1273G>A	c.(1273-1275)Ggt>Agt	p.G425S	LEPREL4_ENST00000393928.1_Missense_Mutation_p.G425S			Q92791	SC65_HUMAN	leprecan-like 4	425	Asp/Glu-rich (acidic).				synaptonemal complex assembly (GO:0007130)	condensed nuclear chromosome (GO:0000794)|nucleolus (GO:0005730)|synaptonemal complex (GO:0000795)		p.G425R(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	8						GCCTCGTCACCCTTGGCATCC	0.642																																					p.G425S		Atlas-SNP	.											LEPREL4,NS,carcinoma,0,1	LEPREL4	20	.	1	Substitution - Missense(1)	lung(1)	c.G1273A						.						159	120	133					17																	39959557		2203	4300	6503	SO:0001583	missense	10609	exon7			CGTCACCCTTGGC	BC001047	CCDS11408.1	17q12	2013-05-03	2002-08-29		ENSG00000141696	ENSG00000141696			16946	protein-coding gene	gene with protein product			"nucleolar autoantigen (55kD)", "rat synaptonemal complex protein"			8862517	Standard	NM_006455		Approved	SC65, NO55	uc002hxt.3	Q92791	OTTHUMG00000133501	ENST00000355468.3:c.1273G>A	chr17.hg19:g.39959557C>T	ENSP00000347649:p.Gly425Ser	217.0	1.0		11.0	6.0	NM_006455	Q53GI6|Q9H4F6	Missense_Mutation	SNP	ENST00000355468.3	hg19	CCDS11408.1	.	.	.	.	.	.	.	.	.	.	C	16.47	3.133210	0.56828	.	.	ENSG00000141696	ENST00000355468;ENST00000393928;ENST00000545545	T;T	0.38887	1.11;1.11	5.78	4.82	0.62117	.	0.056069	0.64402	D	0.000001	T	0.34571	0.0902	L	0.32530	0.975	0.47905	D	0.999542	P;P	0.40211	0.707;0.707	B;B	0.38655	0.278;0.278	T	0.24368	-1.0162	10	0.66056	D	0.02	-22.27	13.7062	0.62641	0.0:0.9256:0.0:0.0744	.	414;425	B4DVZ5;Q92791	.;SC65_HUMAN	S	425;425;414	ENSP00000347649:G425S;ENSP00000377505:G425S	ENSP00000347649:G425S	G	-	1	0	LEPREL4	37213083	1.000000	0.71417	0.996000	0.52242	0.476000	0.33039	4.606000	0.61126	1.486000	0.48398	0.638000	0.83543	GGT	.	.		0.642	LEPREL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257439.2			T	39959557	C	T	39959557	3	4	51	1	0	0	0	0	1	0	0	0	13882	623	22	3	48	3	SC65	17	39959557	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	4122585	39959557	41235653	91	6615										
C18orf8	29919	hgsc.bcm.edu	37	chr18	21089229	21089229	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tcttcataacagatcaaggaAtcgaattttaccaggtatta	6	7	3	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr18:21089229A>G	ENST00000269221.3	+	5	504	c.394A>G	c.(394-396)Atc>Gtc	p.I132V	C18orf8_ENST00000590868.1_Intron	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	132						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					AGATCAAGGAATCGAATTTTA	0.294																																					p.I132V		Atlas-SNP	.											.	C18orf8	58	.	0			c.A394G						.						61	60	60					18																	21089229		2203	4297	6500	SO:0001583	missense	29919	exon5			CAAGGAATCGAAT	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"colon cancer associated protein Mic1", "macrophage inhibitory cytokine 1"					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.394A>G	chr18.hg19:g.21089229A>G	ENSP00000269221:p.Ile132Val	144.0	0.0		145.0	21.0	NM_013326	Q9BU17|Q9Y5M0	Missense_Mutation	SNP	ENST00000269221.3	hg19	CCDS32803.1	.	.	.	.	.	.	.	.	.	.	A	4.842	0.156492	0.09236	.	.	ENSG00000141452	ENST00000269221	T	0.11495	2.77	5.78	5.78	0.91487	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.150314	0.64402	D	0.000014	T	0.08313	0.0207	L	0.33189	0.99	0.80722	D	1	B	0.26195	0.144	B	0.19148	0.024	T	0.08146	-1.0736	10	0.06236	T	0.91	-13.3161	14.9685	0.71213	1.0:0.0:0.0:0.0	.	132	Q96DM3	MIC1_HUMAN	V	132	ENSP00000269221:I132V	ENSP00000269221:I132V	I	+	1	0	C18orf8	19343227	1.000000	0.71417	0.907000	0.35723	0.992000	0.81027	5.618000	0.67722	2.333000	0.79357	0.533000	0.62120	ATC	.	.		0.294	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326		G	21089229	A	G	21089229	3	3	51	1	0	0	0	0	1	0	0	0	1909	101	4	2	412	2	C18orf8	18	21089229	Missense_Mutation	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10		21089229	56988019	92	6616										
EMR1	2015	hgsc.bcm.edu	37	chr19	6904085	6904085	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aagatccatcaacctgtggtCctaattctatctgcaccaat	5	12	3	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr19:6904085C>G	ENST00000312053.4	+	8	878	c.841C>G	c.(841-843)Cct>Gct	p.P281A	EMR1_ENST00000450315.3_Intron|EMR1_ENST00000381407.5_Missense_Mutation_p.P140A|EMR1_ENST00000250572.8_Missense_Mutation_p.P281A|EMR1_ENST00000381404.4_Missense_Mutation_p.P229A	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	281	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					AACCTGTGGTCCTAATTCTAT	0.473																																					p.P281A		Atlas-SNP	.											.	EMR1	153	.	0			c.C841G						.						100	95	97					19																	6904085		2203	4300	6503	SO:0001583	missense	2015	exon8			TGTGGTCCTAATT	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.841C>G	chr19.hg19:g.6904085C>G	ENSP00000311545:p.Pro281Ala	101.0	0.0		108.0	12.0	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	hg19	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	C	6.281	0.419898	0.11928	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407	D;D;D;D	0.91180	-2.8;-2.21;-2.8;-2.21	3.41	2.37	0.29283	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.87589	0.6215	L	0.43598	1.365	0.34071	D	0.658396	B;P;P;P	0.47545	0.065;0.897;0.863;0.722	B;P;P;P	0.52454	0.01;0.598;0.699;0.525	D	0.84479	0.0604	9	0.09590	T	0.72	.	6.8296	0.23902	0.0:0.8709:0.0:0.1291	.	140;281;229;281	B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;EMR1_HUMAN	A	281;281;229;281;140	ENSP00000311545:P281A;ENSP00000370811:P229A;ENSP00000250572:P281A;ENSP00000370814:P140A	ENSP00000250572:P281A	P	+	1	0	EMR1	6855085	0.022000	0.18835	0.004000	0.12327	0.008000	0.06430	0.984000	0.29565	1.020000	0.39573	0.650000	0.86243	CCT	.	.		0.473	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			G	6904085	C	G	6904085	3	3	51	1	0	0	0	0	1	0	0	0	5106	855	30	4	871	4	EMR1	19	6904085	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10		6904085	52224898	93	6617										
MUC16	94025	hgsc.bcm.edu	37	chr19	9018487	9018487	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gaacttcctggagccagggcGatgcatgtcctcctcatact	10	13	1	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr19:9018487G>A	ENST00000397910.4	-	24	37890	c.37687C>T	c.(37687-37689)Cgc>Tgc	p.R12563C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12565	SEA 4. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAGCCAGGGCGATGCATGTCC	0.547																																					p.R12563C		Atlas-SNP	.											.	MUC16	4315	.	0			c.C37687T						.						227	195	206					19																	9018487		2019	4190	6209	SO:0001583	missense	94025	exon24			CAGGGCGATGCAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.37687C>T	chr19.hg19:g.9018487G>A	ENSP00000381008:p.Arg12563Cys	305.0	0.0		177.0	12.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	3.562	-0.089368	0.07097	.	.	ENSG00000181143	ENST00000397910	T	0.29917	1.55	2.01	-0.51	0.11973	.	.	.	.	.	T	0.24851	0.0603	M	0.73962	2.25	.	.	.	B	0.32031	0.352	B	0.06405	0.002	T	0.28396	-1.0045	8	0.87932	D	0	.	2.7893	0.05383	0.1726:0.0:0.5576:0.2698	.	12563	B5ME49	.	C	12563	ENSP00000381008:R12563C	ENSP00000381008:R12563C	R	-	1	0	MUC16	8879487	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.521000	0.06245	-0.031000	0.13781	0.195000	0.17529	CGC	.	.		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9018487	G	A	9018487	3	1	51	1	0	0	0	0	1	0	0	0	9982	1058	37	1	6080	1	MUC16	19	9018487	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	2114402	9018487	50110496	94	6618										
MUC16	94025	hgsc.bcm.edu	37	chr19	9038131	9038131	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tggggagaatgtagaagtcaCtggagctgagaaaaaaagaa	14	3	1	4			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr19:9038131C>A	ENST00000397910.4	-	8	36348	c.36145G>T	c.(36145-36147)Gtg>Ttg	p.V12049L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12051	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTAGAAGTCACTGGAGCTGAG	0.448																																					p.V12049L		Atlas-SNP	.											.	MUC16	4315	.	0			c.G36145T						.						61	60	61					19																	9038131		1914	4124	6038	SO:0001583	missense	94025	exon8			AAGTCACTGGAGC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.36145G>T	chr19.hg19:g.9038131C>A	ENSP00000381008:p.Val12049Leu	103.0	0.0		114.0	8.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	C	5.978	0.364452	0.11296	.	.	ENSG00000181143	ENST00000397910	T	0.02032	4.49	2.3	1.25	0.21368	.	.	.	.	.	T	0.02342	0.0072	N	0.08118	0	.	.	.	P	0.43701	0.815	P	0.51777	0.679	T	0.44997	-0.9291	8	0.87932	D	0	.	4.9543	0.14031	0.0:0.8221:0.0:0.1779	.	12049	B5ME49	.	L	12049	ENSP00000381008:V12049L	ENSP00000381008:V12049L	V	-	1	0	MUC16	8899131	0.003000	0.15002	0.210000	0.23637	0.134000	0.20937	1.111000	0.31159	0.535000	0.28714	-0.474000	0.04947	GTG	.	.		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9038131	C	A	9038131	3	1	51	1	0	0	0	0	1	0	0	0	9982	565	20	3	7686	3	MUC16	19	9038131	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	19644	9038131	50090852	95	6619										
ILF3	3609	hgsc.bcm.edu	37	chr19	10791742	10791742	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	cagctccataaagtcctaggCatggaccctctgccttccaa	7	15	1	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr19:10791742C>T	ENST00000590261.1	+	9	1005	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G	ILF3_ENST00000420083.1_Silent_p.G335G|ILF3_ENST00000449870.1_Silent_p.G335G|ILF3_ENST00000589998.1_Silent_p.G335G|ILF3_ENST00000318511.3_Silent_p.G335G|ILF3_ENST00000250241.8_Silent_p.G335G|ILF3_ENST00000588657.1_Silent_p.G335G|ILF3_ENST00000592763.1_Silent_p.G335G|ILF3_ENST00000407004.3_Silent_p.G335G			Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3, 90kDa	335	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				defense response to virus (GO:0051607)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			AAGTCCTAGGCATGGACCCTC	0.607																																					p.G335G		Atlas-SNP	.											.	ILF3	99	.	0			c.C1005T						.						96	96	96					19																	10791742		2203	4300	6503	SO:0001819	synonymous_variant	3609	exon10			CCTAGGCATGGAC	U10324	CCDS12246.1, CCDS12247.1, CCDS45965.1, CCDS45966.1, CCDS45967.1	19p13.2	2012-08-10	2002-08-29		ENSG00000129351	ENSG00000129351			6038	protein-coding gene	gene with protein product	"M-phase phosphoprotein 4"	603182	"interleukin enhancer binding factor 3, 90kD"			7519613, 8885239	Standard	NM_012218		Approved	NF90, MPHOSPH4, MPP4, DRBP76, NFAR-1	uc002mpo.3	Q12906		ENST00000590261.1:c.1005C>T	chr19.hg19:g.10791742C>T		107.0	0.0		35.0	11.0	NM_017620	A8K6F2|G5E9M5|O43409|Q6P1X1|Q86XY7|Q99544|Q99545|Q9BZH4|Q9BZH5|Q9NQ95|Q9NQ96|Q9NQ97|Q9NQ98|Q9NQ99|Q9NQA0|Q9NQA1|Q9NQA2|Q9NRN2|Q9NRN3|Q9NRN4|Q9UMZ9|Q9UN00|Q9UN84|Q9UNA2	Silent	SNP	ENST00000590261.1	hg19	CCDS12246.1																																																																																			.	.		0.607	ILF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452074.1			T	10791742	C	T	10791742	2	4	51	1	0	0	0	0	0	0	0	1	7721	697	25	3		3	ILF3	19	10791742	Silent	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	1753611	10791742	48337241	96	6620										
OR7A10	390892	hgsc.bcm.edu	37	chr19	14952528	14952528	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aagtacatgggggtgtggagGtgggagtctgagattgtggc	20	3	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr19:14952528G>T	ENST00000248058.1	-	1	161	c.162C>A	c.(160-162)caC>caA	p.H54Q		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	54						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					GGGTGTGGAGGTGGGAGTCTG	0.532																																					p.H54Q		Atlas-SNP	.											.	OR7A10	33	.	0			c.C162A						.						76	71	72					19																	14952528		2203	4297	6500	SO:0001583	missense	390892	exon1			GTGGAGGTGGGAG		CCDS32936.1	19p13.1	2012-08-09						"GPCR / Class A : Olfactory receptors"	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.162C>A	chr19.hg19:g.14952528G>T	ENSP00000248058:p.His54Gln	126.0	0.0		112.0	8.0	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	hg19	CCDS32936.1	.	.	.	.	.	.	.	.	.	.	g	10.82	1.459410	0.26248	.	.	ENSG00000127515	ENST00000248058	T	0.00792	5.69	2.79	1.71	0.24356	GPCR, rhodopsin-like superfamily (1);	0.182647	0.25978	U	0.027084	T	0.01092	0.0036	L	0.41027	1.25	0.21897	N	0.999481	B	0.33135	0.399	B	0.40864	0.342	T	0.45160	-0.9280	10	0.62326	D	0.03	.	7.8633	0.29522	0.1346:0.0:0.8654:0.0	.	54	O76100	OR7AA_HUMAN	Q	54	ENSP00000248058:H54Q	ENSP00000248058:H54Q	H	-	3	2	OR7A10	14813528	0.017000	0.18338	0.998000	0.56505	0.865000	0.49528	-0.345000	0.07770	0.497000	0.27926	0.430000	0.28490	CAC	.	.		0.532	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190		T	14952528	G	T	14952528	3	4	51	1	0	0	0	0	1	0	0	0	11223	1252	44	3	771	3	OR7A10	19	14952528	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	4160786	14952528	44176455	97	6621										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17068704	17068704	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	atccatgtttcggggaagaaAgtcctttttctcttctctgt	8	9	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr19:17068704A>G	ENST00000443236.1	-	19	2407	c.2376T>C	c.(2374-2376)acT>acC	p.T792T	CPAMD8_ENST00000388925.4_3'UTR	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	745						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CGGGGAAGAAAGTCCTTTTTC	0.378																																					p.T792T		Atlas-SNP	.											.	CPAMD8	192	.	0			c.T2376C						.						203	190	194					19																	17068704		1894	4125	6019	SO:0001819	synonymous_variant	27151	exon19			GAAGAAAGTCCTT	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.2376T>C	chr19.hg19:g.17068704A>G		92.0	0.0		102.0	26.0	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	hg19	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	A	8.438	0.850216	0.17034	.	.	ENSG00000160111	ENST00000443236	T	0.26223	1.75	3.3	-1.65	0.08291	.	.	.	.	.	T	0.22360	0.0539	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.14282	-1.0478	5	.	.	.	.	5.2229	0.15377	0.4408:0.0:0.4215:0.1378	.	.	.	.	P	803	ENSP00000402505:L803P	.	L	-	2	0	CPAMD8	16929704	0.963000	0.33076	0.920000	0.36463	0.874000	0.50279	-0.133000	0.10451	-0.124000	0.11724	0.477000	0.44152	CTT	.	.		0.378	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		G	17068704	A	G	17068704	2	3	51	1	0	0	0	0	0	0	0	1	3797	59	3	2		2	CPAMD8	19	17068704	Silent	SNP	A	TCGA-BW-A5NO-01A-11D-A27I-10	2116176	17068704	42060279	98	6622										
HAUS8	93323	hgsc.bcm.edu	37	chr19	17160925	17160925	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ggtctcttcccagacttcctGgtttgccaaggctgcctctt	9	14	2	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr19:17160925G>C	ENST00000253669.5	-	11	1181	c.991C>G	c.(991-993)Cag>Gag	p.Q331E	HAUS8_ENST00000448593.2_Missense_Mutation_p.Q330E|CTD-2528A14.3_ENST00000598893.1_RNA|HAUS8_ENST00000593360.1_Missense_Mutation_p.Q270E			Q9BT25	HAUS8_HUMAN	HAUS augmin-like complex, subunit 8	331					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	12						CAGACTTCCTGGTTTGCCAAG	0.572																																					p.Q331E		Atlas-SNP	.											.	HAUS8	31	.	0			c.C991G						.						40	40	40					19																	17160925		2203	4300	6503	SO:0001583	missense	93323	exon11			CTTCCTGGTTTGC	BC004398	CCDS32948.1, CCDS46009.1	19p13.11	2013-10-11	2009-04-20	2009-04-20	ENSG00000131351	ENSG00000131351		"HAUS augmin-like complex subunits"	30532	protein-coding gene	gene with protein product		613434	"HEC1/NDC80 interacting, centrosome associated 1"	HICE1		19427217	Standard	XM_005260154		Approved	MGC20533, NY-SAR-48	uc002nfe.3	Q9BT25		ENST00000253669.5:c.991C>G	chr19.hg19:g.17160925G>C	ENSP00000253669:p.Gln331Glu	127.0	0.0		51.0	21.0	NM_033417	B4DJA7|C9JBZ4|Q49AC4|Q86WF0|Q96FX3	Missense_Mutation	SNP	ENST00000253669.5	hg19	CCDS32948.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.530033	0.45073	.	.	ENSG00000131351	ENST00000253669;ENST00000448593	T;T	0.78003	-1.14;-1.14	4.66	4.66	0.58398	.	0.000000	0.64402	D	0.000012	D	0.82898	0.5137	L	0.49778	1.585	0.50171	D	0.999859	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.63957	0.92;0.92;0.92	D	0.84790	0.0778	10	0.87932	D	0	-32.132	13.0611	0.59008	0.0:0.0:1.0:0.0	.	270;330;331	Q9BT25-2;C9JBZ4;Q9BT25	.;.;HAUS8_HUMAN	E	331;330	ENSP00000253669:Q331E;ENSP00000395298:Q330E	ENSP00000253669:Q331E	Q	-	1	0	HAUS8	17021925	1.000000	0.71417	0.977000	0.42913	0.089000	0.18198	4.814000	0.62627	2.145000	0.66743	0.655000	0.94253	CAG	.	.		0.572	HAUS8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463015.1	NM_001011699		C	17160925	G	C	17160925	3	2	51	1	0	0	0	0	1	0	0	0	6981	1357	47	4	245	4	HAUS8	19	17160925	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	92221	17160925	41968058	99	6623										
BIRC8	112401	hgsc.bcm.edu	37	chr19	53793408	53793408	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gttgtttatatattcatgtcCcttctcttctagcagatatt	5	8	3	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr19:53793408C>T	ENST00000426466.1	-	1	1467	c.220G>A	c.(220-222)Gga>Aga	p.G74R		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	74					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		TATTCATGTCCCTTCTCTTCT	0.428																																					p.G74R		Atlas-SNP	.											.	BIRC8	54	.	0			c.G220A						.						156	149	151					19																	53793408		2203	4300	6503	SO:0001583	missense	112401	exon1			CATGTCCCTTCTC	AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"Baculoviral IAP repeat containing"	14878	protein-coding gene	gene with protein product	"IAP-like protein 2", "inhibitor of apoptosis-like protein 2"		"baculoviral IAP repeat-containing 8"			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.220G>A	chr19.hg19:g.53793408C>T	ENSP00000412957:p.Gly74Arg	187.0	0.0		145.0	59.0	NM_033341	Q6IPY1|Q96RW5	Missense_Mutation	SNP	ENST00000426466.1	hg19	CCDS12863.1	.	.	.	.	.	.	.	.	.	.	C	13.36	2.214847	0.39102	.	.	ENSG00000163098	ENST00000426466	T	0.04119	3.7	0.502	0.502	0.16932	Baculoviral inhibition of apoptosis protein repeat (1);	.	.	.	.	T	0.17365	0.0417	M	0.80183	2.485	0.51233	D	0.999915	D	0.89917	1.0	D	0.87578	0.998	T	0.01889	-1.1253	9	0.87932	D	0	.	6.9506	0.24542	0.0:0.9999:0.0:1.0E-4	.	74	Q96P09	BIRC8_HUMAN	R	74	ENSP00000412957:G74R	ENSP00000412957:G74R	G	-	1	0	BIRC8	58485220	0.825000	0.29262	0.018000	0.16275	0.006000	0.05464	1.856000	0.39389	0.578000	0.29487	0.420000	0.28162	GGA	.	.		0.428	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341		T	53793408	C	T	53793408	3	4	51	1	0	0	0	0	1	0	0	0	1440	632	22	3	494	3	BIRC8	19	53793408	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10	36632483	53793408	5335575	100	6624										
RBL1	5933	hgsc.bcm.edu	37	chr20	35684006	35684006	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ttcctgaaccattacagtctCtagtattttataatacaaaa	3	8	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr20:35684006C>T	ENST00000373664.3	-	11	1483	c.1417G>A	c.(1417-1419)Gag>Aag	p.E473K	RBL1_ENST00000344359.3_Missense_Mutation_p.E473K	NM_002895.2	NP_002886.2	P28749	RBL1_HUMAN	retinoblastoma-like 1	473	Domain A.|Pocket; binds T and E1A.				chromatin modification (GO:0016568)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(7)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	42		Myeloproliferative disorder(115;0.00878)				ATTACAGTCTCTAGTATTTTA	0.373																																					p.E473K		Atlas-SNP	.											.	RBL1	114	.	0			c.G1417A						.						93	90	91					20																	35684006		2202	4298	6500	SO:0001583	missense	5933	exon11			CAGTCTCTAGTAT	L14812	CCDS13289.1, CCDS13290.1	20q11.23	2014-03-11	2014-03-11		ENSG00000080839	ENSG00000080839			9893	protein-coding gene	gene with protein product		116957				1833063	Standard	NM_183404		Approved	p107, cp107, PRB1	uc002xgi.3	P28749	OTTHUMG00000032406	ENST00000373664.3:c.1417G>A	chr20.hg19:g.35684006C>T	ENSP00000362768:p.Glu473Lys	59.0	0.0		99.0	12.0	NM_183404	A8K2W5|Q4VXA0|Q8N5K6|Q9H1L5|Q9H1M1	Missense_Mutation	SNP	ENST00000373664.3	hg19	CCDS13289.1	.	.	.	.	.	.	.	.	.	.	C	35	5.446589	0.96205	.	.	ENSG00000080839	ENST00000373664;ENST00000344359	D;D	0.90504	-2.68;-2.68	4.8	4.8	0.61643	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.048215	0.85682	D	0.000000	D	0.95408	0.8509	M	0.80028	2.48	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.977;0.998	D	0.95508	0.8583	10	0.56958	D	0.05	-28.3863	18.1082	0.89527	0.0:1.0:0.0:0.0	.	473;473	P28749-2;P28749	.;RBL1_HUMAN	K	473	ENSP00000362768:E473K;ENSP00000343646:E473K	ENSP00000343646:E473K	E	-	1	0	RBL1	35117420	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.569000	0.82380	2.526000	0.85167	0.650000	0.86243	GAG	.	.		0.373	RBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079067.2	NM_002895		T	35684006	C	T	35684006	3	4	51	1	0	0	0	0	1	0	0	0	13124	922	32	3	1846	3	RBL1	20	35684006	Missense_Mutation	SNP	C	TCGA-BW-A5NO-01A-11D-A27I-10		35684006	27341514	101	6625										
LBP	3929	hgsc.bcm.edu	37	chr20	36999383	36999383	+	Splice_Site	DEL	C	C	-													0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	cttcttctggcatttccaggCcactaatgtgtccgccacct							TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr20:36999383delC	ENST00000217407.2	+	11	1312	c.1151delC	c.(1150-1152)gcc>gc	p.A384fs		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	384					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				CATTTCCAGGCCACTAATGTG	0.502																																					p.A384fs		Atlas-INDEL	.											.	LBP	60	.	0			c.1150delG						.						145	132	136					20																	36999383		2203	4300	6503	SO:0001630	splice_region_variant	3929	exon11			.		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"BPI fold containing"	6517	protein-coding gene	gene with protein product	"BPI fold containing family D, member 2"	151990	"lipopolysaccharide-binding protein"			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.1150-1C>-	chr20.hg19:g.36999383delC		204.0	0.0		185.0	15.0	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Frame_Shift_Del	DEL	ENST00000217407.2	hg19	CCDS13304.1																																																																																			.	.		0.502	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	Frame_Shift_Del	-	36999383	C	-	36999383	8	5	51	1	0	1	0	1	0	0	1	0	8660	753	26	0	1193	0	LBP	20	36999383	Splice_Site	DEL	C	TCGA-BW-A5NO-01A-11D-A27I-10	1315377	36999383	26026137	102	6626										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19207465	19207465	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	ccagagctccggatcctttcTgcataccaggtagcgggcct	11	14	1	1			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr22:19207465T>A	ENST00000263200.10	-	18	2920	c.2848A>T	c.(2848-2850)Aga>Tga	p.R950*	CLTCL1_ENST00000427926.1_Nonsense_Mutation_p.R950*|CLTCL1_ENST00000353891.5_Nonsense_Mutation_p.R950*	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	950	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GGATCCTTTCTGCATACCAGG	0.537			T	?	ALCL																																p.R950X		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.A2848T						.						137	139	138					22																	19207465		2007	4159	6166	SO:0001587	stop_gained	8218	exon18			CCTTTCTGCATAC		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.2848A>T	chr22.hg19:g.19207465T>A	ENSP00000445677:p.Arg950*	150.0	0.0		106.0	37.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Nonsense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	T	38	7.179437	0.98118	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	.	.	.	4.03	2.96	0.34315	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.7955	10.6207	0.45478	0.0:0.0:0.1612:0.8388	.	.	.	.	X	950	.	ENSP00000445677:R950X	R	-	1	2	CLTCL1	17587465	1.000000	0.71417	0.765000	0.31456	0.270000	0.26580	2.367000	0.44213	0.569000	0.29329	0.383000	0.25322	AGA	.	.		0.537	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		A	19207465	T	A	19207465	4	1	51	1	0	0	0	0	0	1	0	0	3569	1588	55	4	2134	4	CLTCL1	22	19207465	Nonsense_Mutation	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10		19207465	32097101	103	6627										
C22orf29	79680	hgsc.bcm.edu	37	chr22	19839038	19839038	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	tcgaacagagcacttctagaTacagagttggacccagacac	9	11	1	4			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chr22:19839038T>C	ENST00000405640.1	-	2	1415	c.747A>G	c.(745-747)gtA>gtG	p.V249V	GNB1L_ENST00000329517.6_Intron|C22orf29_ENST00000484072.1_Intron|C22orf29_ENST00000328554.4_Silent_p.V249V|GNB1L_ENST00000403325.1_Intron|GNB1L_ENST00000405009.1_Intron|GNB1L_ENST00000460402.1_Intron|C22orf29_ENST00000407472.1_Silent_p.V249V			Q7L3V2	BOP_HUMAN	chromosome 22 open reading frame 29	249					mitochondrial outer membrane permeabilization (GO:0097345)|regulation of mitochondrial membrane potential (GO:0051881)	mitochondrion (GO:0005739)				NS(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	7	Colorectal(54;0.0993)					CACTTCTAGATACAGAGTTGG	0.597																																					p.V249V		Atlas-SNP	.											.	C22orf29	23	.	0			c.A747G						.						66	70	69					22																	19839038		2203	4300	6503	SO:0001819	synonymous_variant	79680	exon3			TCTAGATACAGAG	BX640998	CCDS13769.1	22q11.21	2006-07-05			ENSG00000215012	ENSG00000215012			26112	protein-coding gene	gene with protein product						12477932	Standard	NM_024627		Approved	FLJ21125	uc002zqh.3	Q7L3V2	OTTHUMG00000030314	ENST00000405640.1:c.747A>G	chr22.hg19:g.19839038T>C		77.0	0.0		17.0	8.0	NM_024627	A8K5E7|D3DX21|Q6MZM8|Q6N000|Q9H7A0	Silent	SNP	ENST00000405640.1	hg19	CCDS13769.1																																																																																			.	.		0.597	C22orf29-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317290.2	NM_024627		C	19839038	T	C	19839038	2	2	51	1	0	0	0	0	0	0	0	1	2143	1393	49	2		2	C22orf29	22	19839038	Silent	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10	631573	19839038	31465528	104	6628										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34961245	34961245	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	aggaagaaaaagctgctcaaGaaagcggccctattttccga	10	9	1	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chrX:34961245G>A	ENST00000329357.5	+	1	333	c.297G>A	c.(295-297)aaG>aaA	p.K99K		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	99										breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						AGCTGCTCAAGAAAGCGGCCC	0.527																																					p.K99K		Atlas-SNP	.											.	FAM47B	209	.	0			c.G297A						.						91	84	86					X																	34961245		2202	4300	6502	SO:0001819	synonymous_variant	170062	exon1			GCTCAAGAAAGCG	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.297G>A	chrX.hg19:g.34961245G>A		132.0	0.0		85.0	43.0	NM_152631	Q5JQN5|Q6PIG3	Silent	SNP	ENST00000329357.5	hg19	CCDS14236.1																																																																																			.	.		0.527	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		A	34961245	G	A	34961245	2	1	51	1	0	0	0	0	0	0	0	1	5578	933	33	3		3	FAM47B	23	34961245	Silent	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10		34961245	120309315	105	6629										
RPS6KA6	27330	hgsc.bcm.edu	37	chrX	83359655	83359655	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	caaggtaaacatatctaccaTcatcaaagacctacaaaaga	4	10	3	2			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chrX:83359655T>C	ENST00000262752.2	-	17	1473	c.1466A>G	c.(1465-1467)gAt>gGt	p.D489G	RPS6KA6_ENST00000543399.1_Missense_Mutation_p.D489G|RPS6KA6_ENST00000495332.1_5'UTR	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	489	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						ATATCTACCATCATCAAAGAC	0.294																																					p.D489G		Atlas-SNP	.											.	RPS6KA6	116	.	0			c.A1466G						.						58	51	53					X																	83359655		2202	4296	6498	SO:0001583	missense	27330	exon17			CTACCATCATCAA	AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.1466A>G	chrX.hg19:g.83359655T>C	ENSP00000262752:p.Asp489Gly	106.0	0.0		174.0	155.0	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	hg19	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.188453	0.78789	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.67345	-0.26;-0.26	5.2	5.2	0.72013	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.049214	0.85682	D	0.000000	T	0.73845	0.3639	L	0.46157	1.445	0.80722	D	1	P;P	0.51449	0.638;0.945	P;P	0.59221	0.688;0.854	T	0.76820	-0.2818	10	0.87932	D	0	.	14.1772	0.65549	0.0:0.0:0.0:1.0	.	489;489	B7ZL90;Q9UK32	.;KS6A6_HUMAN	G	489	ENSP00000262752:D489G;ENSP00000440830:D489G	ENSP00000262752:D489G	D	-	2	0	RPS6KA6	83246311	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	7.859000	0.86982	1.725000	0.51514	0.430000	0.28490	GAT	.	.		0.294	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		C	83359655	T	C	83359655	3	2	51	1	0	0	0	0	1	0	0	0	13670	1435	50	2	795	2	RPS6KA6	23	83359655	Missense_Mutation	SNP	T	TCGA-BW-A5NO-01A-11D-A27I-10	48398410	83359655	71910905	106	6630										
MAGEA12	4111	hgsc.bcm.edu	37	chrX	151900290	151900290	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0841121495327103	9	1	1.24733889528193	2.2174913693901	0.923954737245877	1	1	0	gatgtacaagtggccgatgcGgaccacttccaccacctcga	10	14	0	0			TCGA-BW-A5NO-01A-11D-A27I-10	TCGA-BW-A5NO-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81a8b064-e735-455f-b2db-af7ae11daac4	3033ae06-ebb4-4dbb-9f60-b9b9d5c72805	g.chrX:151900290G>T	ENST00000357916.4	-	2	666	c.511C>A	c.(511-513)Cgc>Agc	p.R171S	MAGEA12_ENST00000393900.3_Missense_Mutation_p.R171S|CSAG1_ENST00000452779.2_5'Flank|CSAG1_ENST00000370291.2_5'Flank|MAGEA12_ENST00000393869.3_Missense_Mutation_p.R171S|CSAG4_ENST00000361201.4_RNA|CSAG1_ENST00000370287.3_5'Flank	NM_005367.5	NP_005358.2	P43365	MAGAC_HUMAN	melanoma antigen family A, 12	171	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(5)|large_intestine(5)|liver(1)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					TGGCCGATGCGGACCACTTCC	0.542																																					p.R171S		Atlas-SNP	.											.	MAGEA12	125	.	0			c.C511A						.						160	149	153					X																	151900290		2203	4300	6503	SO:0001583	missense	4111	exon2			CGATGCGGACCAC		CCDS76048.1	Xq28	2009-03-13			ENSG00000213401	ENSG00000213401			6799	protein-coding gene	gene with protein product	"cancer/testis antigen family 1, member 12"	300177		MAGE12		8575766	Standard	NM_001166386		Approved	CT1.12	uc004fgc.3	P43365	OTTHUMG00000022650	ENST00000357916.4:c.511C>A	chrX.hg19:g.151900290G>T	ENSP00000350592:p.Arg171Ser	398.0	2.0		311.0	245.0	NM_005367	Q9NSD3	Missense_Mutation	SNP	ENST00000357916.4	hg19	CCDS14710.1	.	.	.	.	.	.	.	.	.	.	G	6.965	0.548028	0.13312	.	.	ENSG00000213401	ENST00000357916;ENST00000393869;ENST00000393900	T;T;T	0.04360	3.64;3.64;3.64	0.809	0.809	0.18725	.	0.370527	0.30210	N	0.010156	T	0.01558	0.0050	N	0.00996	-1.065	0.09310	N	1	B	0.02656	0.0	B	0.12837	0.008	T	0.46261	-0.9204	9	0.40728	T	0.16	.	.	.	.	.	171	P43365	MAGAC_HUMAN	S	171	ENSP00000350592:R171S;ENSP00000377447:R171S;ENSP00000377478:R171S	ENSP00000350592:R171S	R	-	1	0	MAGEA12	151650946	0.021000	0.18746	0.025000	0.17156	0.047000	0.14425	1.666000	0.37460	0.675000	0.31264	0.181000	0.17075	CGC	.	.		0.542	MAGEA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058764.1	NM_005367		T	151900290	G	T	151900290	3	4	51	1	0	0	0	0	1	0	0	0	9175	1116	39	1	437	1	MAGEA12	23	151900290	Missense_Mutation	SNP	G	TCGA-BW-A5NO-01A-11D-A27I-10	68540635	151900290	3370270	107	6631										
NRAS	4893	hgsc.bcm.edu	37	chr1	115256530	115256530	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	catggcactgtactcttcttGtccagctgtatccagtatgt	8	11	2	0	rs121913254		TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr1:115256530G>T	ENST00000369535.4	-	3	434	c.181C>A	c.(181-183)Caa>Aaa	p.Q61K		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61K(595)|p.Q61E(9)|p.Q61L(3)|p.Q61R(2)|p.G60>?(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACTCTTCTTGTCCAGCTGTA	0.458	Q61K(CHP212_AUTONOMIC_GANGLIA)|Q61K(HCC15_LUNG)|Q61K(HS936T_SKIN)|Q61K(HS944T_SKIN)|Q61K(HT1080_SOFT_TISSUE)|Q61K(HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(NCIH1299_LUNG)|Q61K(NCIH2087_LUNG)|Q61K(OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(SKNAS_AUTONOMIC_GANGLIA)|Q61K(SKNSH_AUTONOMIC_GANGLIA)|Q61K(TYKNU_OVARY)	50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																											p.Q61K		Atlas-SNP	.		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	NRAS,NS,haematopoietic_neoplasm,0,4	NRAS	3766	.	610	Substitution - Missense(609)|Complex(1)	skin(372)|haematopoietic_and_lymphoid_tissue(73)|thyroid(55)|NS(29)|large_intestine(28)|soft_tissue(16)|lung(12)|autonomic_ganglia(6)|liver(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|cervix(2)|endometrium(2)|pancreas(2)|meninges(1)|kidney(1)|biliary_tract(1)|stomach(1)|ovary(1)|bone(1)	c.C181A						.						180	156	164					1																	115256530		2203	4300	6503	SO:0001583	missense	4893	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CTTCTTGTCCAGC	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.181C>A	chr1.hg19:g.115256530G>T	ENSP00000358548:p.Gln61Lys	100.0	0.0		75.0	8.0	NM_002524	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	hg19	CCDS877.1	.	.	.	.	.	.	.	.	.	.	G	33	5.255564	0.95336	.	.	ENSG00000213281	ENST00000369535	D	0.83506	-1.73	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.91845	0.7419	H	0.95850	3.73	0.80722	D	1	P	0.51791	0.948	P	0.54759	0.76	D	0.93711	0.7024	10	0.62326	D	0.03	.	18.6626	0.91477	0.0:0.0:1.0:0.0	.	61	P01111	RASN_HUMAN	K	61	ENSP00000358548:Q61K	ENSP00000358548:Q61K	Q	-	1	0	NRAS	115058053	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.520000	0.98027	2.624000	0.88883	0.655000	0.94253	CAA	.	.		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		T	115256530	G	T	115256530	3	4	52	1	0	0	0	0	1	0	0	0	10649	1386	48	3	400	3	NRAS	1	115256530	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10		115256530	133994091	1	6632										
ITGA10	8515	hgsc.bcm.edu	37	chr1	145533439	145533439	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tgtttcttccatgcttttgcGgggtggacgccgcctgtttc	12	11	1	0	rs149835959		TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr1:145533439G>T	ENST00000369304.3	+	12	1497	c.1322G>T	c.(1321-1323)cGg>cTg	p.R441L	ITGA10_ENST00000539363.1_Missense_Mutation_p.R298L|ITGA10_ENST00000538811.1_Missense_Mutation_p.R310L	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	441					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ATGCTTTTGCGGGGTGGACGC	0.517																																					p.R441L		Atlas-SNP	.											.	ITGA10	131	.	0			c.G1322T						.						126	140	136					1																	145533439		2203	4300	6503	SO:0001583	missense	8515	exon12			TTTTGCGGGGTGG	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.1322G>T	chr1.hg19:g.145533439G>T	ENSP00000358310:p.Arg441Leu	37.0	0.0		77.0	8.0	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	7.337	0.620130	0.14193	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.71461	-0.57;-0.57;-0.57	5.04	-2.87	0.05700	.	0.474289	0.20350	N	0.094065	T	0.28200	0.0696	N	0.25992	0.78	0.29511	N	0.854225	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.13407	0.009;0.004;0.001;0.002	T	0.12066	-1.0562	10	0.30078	T	0.28	.	6.0533	0.19796	0.085:0.4521:0.3421:0.1208	.	407;310;298;441	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	L	441;407;298;310	ENSP00000358310:R441L;ENSP00000439894:R298L;ENSP00000440011:R310L	ENSP00000358310:R441L	R	+	2	0	ITGA10	144244796	0.055000	0.20627	0.874000	0.34290	0.991000	0.79684	0.211000	0.17474	-0.245000	0.09625	-0.150000	0.13652	CGG	.	G|1.000;A|0.000		0.517	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		T	145533439	G	T	145533439	3	4	52	1	0	0	0	0	1	0	0	0	7882	1116	39	1	1368	1	ITGA10	1	145533439	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	30276909	145533439	103717182	2	6633										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176759013	176759013	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cagctgcattcctgtggtgtGtgagccaccccctcctgtgt	11	14	0	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr1:176759013G>A	ENST00000367662.3	+	18	5948	c.4784G>A	c.(4783-4785)tGt>tAt	p.C1595Y		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1595	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CCTGTGGTGTGTGAGCCACCC	0.478																																					p.C1595Y		Atlas-SNP	.											.	PAPPA2	665	.	0			c.G4784A						.						120	122	121					1																	176759013		2008	4168	6176	SO:0001583	missense	60676	exon18			TGGTGTGTGAGCC	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.4784G>A	chr1.hg19:g.176759013G>A	ENSP00000356634:p.Cys1595Tyr	136.0	0.0		156.0	44.0	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	hg19	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.873071	0.72180	.	.	ENSG00000116183	ENST00000367662	D	0.84298	-1.83	5.51	5.51	0.81932	Complement control module (1);Sushi/SCR/CCP (2);	0.000000	0.85682	D	0.000000	D	0.93006	0.7774	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93836	0.7132	10	0.87932	D	0	-13.0656	16.3531	0.83224	0.0:0.0:1.0:0.0	.	1595	Q9BXP8	PAPP2_HUMAN	Y	1595	ENSP00000356634:C1595Y	ENSP00000356634:C1595Y	C	+	2	0	PAPPA2	175025636	1.000000	0.71417	0.999000	0.59377	0.851000	0.48451	6.743000	0.74848	2.582000	0.87167	0.557000	0.71058	TGT	.	.		0.478	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176759013	G	A	176759013	3	1	52	1	0	0	0	0	1	0	0	0	11442	1377	48	3	4903	3	PAPPA2	1	176759013	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	31225574	176759013	72491608	3	6634										
CRB1	23418	hgsc.bcm.edu	37	chr1	197297620	197297620	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	aaaacaattctacatgcaaaGatttttcaaaagacaatgat	4	6	2	3			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr1:197297620G>T	ENST00000367400.3	+	2	274	c.139G>T	c.(139-141)Gat>Tat	p.D47Y	CRB1_ENST00000535699.1_5'UTR|CRB1_ENST00000367399.2_Missense_Mutation_p.D47Y|CRB1_ENST00000538660.1_Missense_Mutation_p.D47Y	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	47	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TACATGCAAAGATTTTTCAAA	0.348																																					p.D47Y		Atlas-SNP	.											.	CRB1	284	.	0			c.G139T						.						59	60	60					1																	197297620		2203	4300	6503	SO:0001583	missense	23418	exon2			TGCAAAGATTTTT		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.139G>T	chr1.hg19:g.197297620G>T	ENSP00000356370:p.Asp47Tyr	104.0	0.0		173.0	7.0	NM_001257966	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	hg19	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.366945	0.24771	.	.	ENSG00000134376	ENST00000538660;ENST00000367400;ENST00000367399	D;D;D	0.92805	-3.11;-1.79;-2.29	5.43	-1.2	0.09554	Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.93051	0.7788	M	0.82923	2.615	0.09310	N	1	B;D;P;P	0.63046	0.087;0.992;0.468;0.744	B;P;B;B	0.56042	0.099;0.79;0.115;0.24	D	0.84706	0.0731	9	0.72032	D	0.01	.	2.8843	0.05657	0.3794:0.1059:0.4111:0.1036	.	47;47;47;72	B7Z5T2;P82279-3;P82279;Q59H36	.;.;CRUM1_HUMAN;.	Y	47	ENSP00000438091:D47Y;ENSP00000356370:D47Y;ENSP00000356369:D47Y	ENSP00000356369:D47Y	D	+	1	0	CRB1	195564243	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.152000	0.16302	-0.408000	0.07565	-0.140000	0.14226	GAT	.	.		0.348	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		T	197297620	G	T	197297620	3	4	52	1	0	0	0	0	1	0	0	0	3850	942	33	3	145	3	CRB1	1	197297620	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	20538607	197297620	51953001	4	6635										
IPO9	55705	hgsc.bcm.edu	37	chr1	201827625	201827625	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gcagcagccctggctgctgcAgccactcgacatttacaaga	10	14	0	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr1:201827625A>C	ENST00000361565.4	+	12	1341	c.1272A>C	c.(1270-1272)gcA>gcC	p.A424A		NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	424					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						TGGCTGCTGCAGCCACTCGAC	0.458																																					p.A424A		Atlas-SNP	.											.	IPO9	98	.	0			c.A1272C						.						71	84	79					1																	201827625		2202	4300	6502	SO:0001819	synonymous_variant	55705	exon12			TGCTGCAGCCACT	AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"Importins"	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.1272A>C	chr1.hg19:g.201827625A>C		210.0	0.0		246.0	72.0	NM_018085	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Silent	SNP	ENST00000361565.4	hg19	CCDS1415.1																																																																																			.	.		0.458	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085		C	201827625	A	C	201827625	2	2	52	1	0	0	0	0	0	0	0	1	7808	175	7	5		5	IPO9	1	201827625	Silent	SNP	A	TCGA-BW-A5NP-01A-11D-A27I-10	4530005	201827625	47422996	5	6636										
TMCC2	9911	hgsc.bcm.edu	37	chr1	205238236	205238236	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	atcctgaagatcaccgagcaGatcaagattgagcaggaggc	12	9	2	5			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr1:205238236G>A	ENST00000358024.3	+	3	1295	c.906G>A	c.(904-906)caG>caA	p.Q302Q	TMCC2_ENST00000330675.7_Silent_p.Q77Q|TMCC2_ENST00000329800.7_Silent_p.Q62Q|TMCC2_ENST00000545499.1_Silent_p.Q224Q|TMCC2_ENST00000495538.1_3'UTR	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	302						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			TCACCGAGCAGATCAAGATTG	0.597																																					p.Q302Q		Atlas-SNP	.											.	TMCC2	89	.	0			c.G906A						.						64	56	59					1																	205238236		2203	4300	6503	SO:0001819	synonymous_variant	9911	exon3			CGAGCAGATCAAG	AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"Transmembrane and coiled-coil domain containing"	24239	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 2"			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.906G>A	chr1.hg19:g.205238236G>A		367.0	0.0		491.0	82.0	NM_014858	A2RRH3|B7Z1P7|Q6ZN09	Silent	SNP	ENST00000358024.3	hg19	CCDS30984.1																																																																																			.	.		0.597	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858		A	205238236	G	A	205238236	2	1	52	1	0	0	0	0	0	0	0	1	16008	933	33	3		3	TMCC2	1	205238236	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	3410611	205238236	44012385	6	6637										
PGBD5	79605	hgsc.bcm.edu	37	chr1	230468774	230468774	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ttccgcgcgcggagcaagccGcagcagtaaatccctgaggg	14	13	0	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr1:230468774G>A	ENST00000525115.1	-	5	905	c.882C>T	c.(880-882)tgC>tgT	p.C294C	PGBD5_ENST00000530424.1_5'UTR|PGBD5_ENST00000321327.2_Silent_p.C393C|PGBD5_ENST00000391860.1_Silent_p.C248C			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	294						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		GGAGCAAGCCGCAGCAGTAAA	0.657																																					p.C363C		Atlas-SNP	.											PGBD5,NS,carcinoma,0,1	PGBD5	73	.	0			c.C1089T						.						32	34	33					1																	230468774		2201	4299	6500	SO:0001819	synonymous_variant	79605	exon5			CAAGCCGCAGCAG	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.882C>T	chr1.hg19:g.230468774G>A		44.0	0.0		57.0	34.0	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Silent	SNP	ENST00000525115.1	hg19																																																																																				.	.		0.657	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		A	230468774	G	A	230468774	2	1	52	1	0	0	0	0	0	0	0	1	11793	1079	38	1		1	PGBD5	1	230468774	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	25230538	230468774	18781847	7	6638										
ITSN2	50618	hgsc.bcm.edu	37	chr2	24535152	24535152	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gagggagaaccacaggcaacTgttggccttgaagcttcagt	13	9	1	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr2:24535152T>A	ENST00000355123.4	-	5	724	c.281A>T	c.(280-282)cAg>cTg	p.Q94L	ITSN2_ENST00000407704.1_5'UTR|ITSN2_ENST00000361999.3_Missense_Mutation_p.Q94L|ITSN2_ENST00000406921.3_Missense_Mutation_p.Q94L	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	94	EH 1. {ECO:0000255|PROSITE- ProRule:PRU00077}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACAGGCAACTGTTGGCCTTG	0.398																																					p.Q94L		Atlas-SNP	.											.	ITSN2	224	.	0			c.A281T						.						182	154	163					2																	24535152		2203	4300	6503	SO:0001583	missense	50618	exon5			GGCAACTGTTGGC	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.281A>T	chr2.hg19:g.24535152T>A	ENSP00000347244:p.Gln94Leu	299.0	0.0		308.0	62.0	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	hg19	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	T	12.71	2.019421	0.35606	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011;ENST00000443927	T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54	5.07	2.68	0.31781	EPS15 homology (EH) (2);EF-hand-like domain (1);	0.207467	0.23474	U	0.047797	T	0.27169	0.0666	L	0.43152	1.355	0.22305	N	0.999216	P;P;P;B	0.35793	0.521;0.521;0.521;0.109	B;B;B;B	0.40285	0.325;0.325;0.325;0.146	T	0.12734	-1.0536	10	0.52906	T	0.07	.	7.4711	0.27349	0.0:0.0781:0.3963:0.5256	.	94;94;94;94	Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3	.;.;.;ITSN2_HUMAN	L	94;94;94;93;94;94;80	ENSP00000354561:Q94L;ENSP00000347244:Q94L;ENSP00000370250:Q94L;ENSP00000384499:Q94L;ENSP00000391224:Q94L;ENSP00000391715:Q80L	ENSP00000347244:Q94L	Q	-	2	0	ITSN2	24388656	0.380000	0.25131	0.992000	0.48379	0.801000	0.45260	0.097000	0.15168	1.030000	0.39839	0.533000	0.62120	CAG	.	.		0.398	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		A	24535152	T	A	24535152	3	1	52	1	0	0	0	0	1	0	0	0	7936	1580	55	4	5007	4	ITSN2	2	24535152	Missense_Mutation	SNP	T	TCGA-BW-A5NP-01A-11D-A27I-10		24535152	218664221	8	6639										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54753649	54753649	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gggatgtcgacgactgggacAatgagaacagctctgcgcgg	16	9	1	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr2:54753649A>T	ENST00000356805.4	+	2	375	c.94A>T	c.(94-96)Aat>Tat	p.N32Y	AC092839.3_ENST00000433475.1_RNA	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	32	Actin-binding.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CGACTGGGACAATGAGAACAG	0.532																																					p.N32Y		Atlas-SNP	.											.	SPTBN1	378	.	0			c.A94T						.						153	137	142					2																	54753649		2203	4300	6503	SO:0001583	missense	6711	exon2			TGGGACAATGAGA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.94A>T	chr2.hg19:g.54753649A>T	ENSP00000349259:p.Asn32Tyr	137.0	0.0		128.0	64.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.997650	0.93227	.	.	ENSG00000115306	ENST00000356805;ENST00000389980	T;T	0.24723	1.84;1.84	5.77	5.77	0.91146	Calponin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.35101	-0.9802	10	0.30078	T	0.28	.	16.1043	0.81209	1.0:0.0:0.0:0.0	.	32	Q01082	SPTB2_HUMAN	Y	32	ENSP00000349259:N32Y;ENSP00000374630:N32Y	ENSP00000349259:N32Y	N	+	1	0	SPTBN1	54607153	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	9.310000	0.96267	2.201000	0.70794	0.528000	0.53228	AAT	.	.		0.532	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54753649	A	T	54753649	3	4	52	1	0	0	0	0	1	0	0	0	15134	130	5	4	96	4	SPTBN1	2	54753649	Missense_Mutation	SNP	A	TCGA-BW-A5NP-01A-11D-A27I-10	30218497	54753649	188445724	9	6640										
WDR33	55339	hgsc.bcm.edu	37	chr2	128477498	128477498	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	aggacccatatgaccttgagGaccagaactaccttgtggtc	10	11	0	3			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr2:128477498G>T	ENST00000322313.4	-	16	2259	c.2101C>A	c.(2101-2103)Cct>Act	p.P701T		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	701	Collagen-like.				mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TGACCTTGAGGACCAGAACTA	0.642																																					p.P701T		Atlas-SNP	.											.	WDR33	136	.	0			c.C2101A						.						68	76	73					2																	128477498		2203	4300	6503	SO:0001583	missense	55339	exon16			CTTGAGGACCAGA		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.2101C>A	chr2.hg19:g.128477498G>T	ENSP00000325377:p.Pro701Thr	52.0	0.0		33.0	13.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.582560	0.46006	.	.	ENSG00000136709	ENST00000322313	D	0.93366	-3.21	5.37	3.54	0.40534	.	0.000000	0.64402	D	0.000002	D	0.91164	0.7217	M	0.72624	2.21	0.80722	D	1	B	0.21520	0.057	B	0.22386	0.039	D	0.86195	0.1615	10	0.30854	T	0.27	-6.0816	10.4611	0.44581	0.0699:0.0:0.7958:0.1343	.	701	Q9C0J8	WDR33_HUMAN	T	701	ENSP00000325377:P701T	ENSP00000325377:P701T	P	-	1	0	WDR33	128193968	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	5.551000	0.67274	0.729000	0.32403	0.585000	0.79938	CCT	.	.		0.642	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		T	128477498	G	T	128477498	3	4	52	1	0	0	0	0	1	0	0	0	17302	1174	41	3	1937	3	WDR33	2	128477498	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	73723849	128477498	114721875	10	6641										
TTN	7273	hgsc.bcm.edu	37	chr2	179441674	179441674	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tctgtctaccattttgacagGttcagactgtacaggttctc	8	10	4	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr2:179441674G>T	ENST00000591111.1	-	274	64689	c.64465C>A	c.(64465-64467)Cct>Act	p.P21489T	TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P14257T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P23130T|TTN_ENST00000342992.6_Missense_Mutation_p.P20562T|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P14190T|TTN_ENST00000460472.2_Missense_Mutation_p.P14065T|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA			Q8WZ42	TITIN_HUMAN	titin	21489	Fibronectin type-III 55. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTTTGACAGGTTCAGACTGT	0.403																																					p.P23130T		Atlas-SNP	.											.	TTN	18412	.	0			c.C69388A						.						202	197	199					2																	179441674		1907	4111	6018	SO:0001583	missense	7273	exon324			TGACAGGTTCAGA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.64465C>A	chr2.hg19:g.179441674G>T	ENSP00000465570:p.Pro21489Thr	121.0	0.0		132.0	38.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.95	2.092455	0.36952	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65916	-0.18;0.01;-0.04;-0.05	5.72	4.83	0.62350	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.71745	0.3376	M	0.82517	2.595	0.58432	D	0.999999	D;D;D;P	0.55605	0.972;0.972;0.972;0.949	P;P;P;P	0.48304	0.573;0.573;0.573;0.476	T	0.78597	-0.2142	9	0.87932	D	0	.	15.4216	0.75015	0.0676:0.0:0.9324:0.0	.	14065;14190;14257;21489	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	20562;14065;14257;14190;14063	ENSP00000343764:P20562T;ENSP00000434586:P14065T;ENSP00000340554:P14257T;ENSP00000352154:P14190T	ENSP00000340554:P14257T	P	-	1	0	TTN	179149920	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	6.582000	0.74049	1.533000	0.49186	0.655000	0.94253	CCT	.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179441674	G	T	179441674	3	4	52	1	0	0	0	0	1	0	0	0	16750	1261	44	3	38747	3	TTN	2	179441674	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	50964176	179441674	63757699	11	6642										
TTN	7273	hgsc.bcm.edu	37	chr2	179485580	179485580	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gtctttttggagaatgatgtAttttgaactatcaaatatag	8	3	2	3			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr2:179485580A>G	ENST00000591111.1	-	197	41058	c.40834T>C	c.(40834-40836)Tac>Cac	p.Y13612H	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Y6380H|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.Y15253H|TTN_ENST00000342992.6_Missense_Mutation_p.Y12685H|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Y6313H|TTN_ENST00000460472.2_Missense_Mutation_p.Y6188H|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13612	Ig-like 92.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGAATGATGTATTTTGAACTA	0.388																																					p.Y15253H		Atlas-SNP	.											.	TTN	18412	.	0			c.T45757C						.						159	154	155					2																	179485580		1870	4087	5957	SO:0001583	missense	7273	exon247			TGATGTATTTTGA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.40834T>C	chr2.hg19:g.179485580A>G	ENSP00000465570:p.Tyr13612His	99.0	0.0		170.0	36.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.73	2.324146	0.41197	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.83	5.83	0.93111	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.80171	0.4574	M	0.66560	2.04	0.45995	D	0.998808	D;D;D;D	0.71674	0.998;0.998;0.998;0.998	D;D;D;D	0.68483	0.958;0.958;0.958;0.958	T	0.82248	-0.0551	9	0.87932	D	0	.	16.1968	0.82036	1.0:0.0:0.0:0.0	.	6188;6313;6380;13612	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	12685;6188;6380;6313;6188	ENSP00000343764:Y12685H;ENSP00000434586:Y6188H;ENSP00000340554:Y6380H;ENSP00000352154:Y6313H	ENSP00000340554:Y6380H	Y	-	1	0	TTN	179193825	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.281000	0.95811	2.225000	0.72522	0.533000	0.62120	TAC	.	.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179485580	A	G	179485580	3	3	52	1	0	0	0	0	1	0	0	0	16750	449	16	2	62400	2	TTN	2	179485580	Missense_Mutation	SNP	A	TCGA-BW-A5NP-01A-11D-A27I-10	43906	179485580	63713793	12	6643										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215862522	215862522	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ttggaagagaataagagacaCtggttaggaagctgtaaaac	12	4	0	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr2:215862522C>A	ENST00000272895.7	-	23	3410	c.3191G>T	c.(3190-3192)aGt>aTt	p.S1064I	ABCA12_ENST00000389661.4_Missense_Mutation_p.S746I	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1064					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ATAAGAGACACTGGTTAGGAA	0.363																																					p.S1064I	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.G3191T						.						76	74	75					2																	215862522		2203	4300	6503	SO:0001583	missense	26154	exon23			GAGACACTGGTTA	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.3191G>T	chr2.hg19:g.215862522C>A	ENSP00000272895:p.Ser1064Ile	188.0	0.0		220.0	83.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.601698	0.66445	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.83075	-1.68;-1.68	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.87989	0.6317	L	0.49126	1.545	0.80722	D	1	D;D	0.89917	1.0;0.991	D;D	0.77004	0.989;0.974	T	0.80558	-0.1329	10	0.06625	T	0.88	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1064;746	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	I	1064;746	ENSP00000272895:S1064I;ENSP00000374312:S746I	ENSP00000272895:S1064I	S	-	2	0	ABCA12	215570767	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.755000	0.68750	2.941000	0.99782	0.655000	0.94253	AGT	.	.		0.363	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		A	215862522	C	A	215862522	3	1	52	1	0	0	0	0	1	0	0	0	30	565	20	3	4720	3	ABCA12	2	215862522	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	36376942	215862522	27336851	13	6644										
FGD5	152273	hgsc.bcm.edu	37	chr3	14964028	14964028	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gacttctccctcaccctgcgGcgtcatcactgtcacgcctg	8	18	5	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:14964028G>A	ENST00000285046.5	+	15	3890	c.3780G>A	c.(3778-3780)cgG>cgA	p.R1260R	FGD5-AS1_ENST00000430166.1_RNA|FGD5_ENST00000476851.1_3'UTR|FGD5_ENST00000543601.1_Silent_p.R1019R	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	1260					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						TCACCCTGCGGCGTCATCACT	0.657																																					p.R1260R		Atlas-SNP	.											.	FGD5	248	.	0			c.G3780A						.						31	35	34					3																	14964028		2116	4222	6338	SO:0001819	synonymous_variant	152273	exon15			CCTGCGGCGTCAT	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.3780G>A	chr3.hg19:g.14964028G>A		90.0	0.0		113.0	18.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Silent	SNP	ENST00000285046.5	hg19	CCDS46767.1																																																																																			.	.		0.657	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		A	14964028	G	A	14964028	2	1	52	1	0	0	0	0	0	0	0	1	5844	1190	42	3		3	FGD5	3	14964028	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10		14964028	183058402	14	6645										
ITGA9	3680	hgsc.bcm.edu	37	chr3	37574884	37574884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cagcgcctcagtgtcacgacGgacagcagcctgtgaactgc	12	14	2	1	rs369791724		TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:37574884G>A	ENST00000264741.5	+	14	1709	c.1453G>A	c.(1453-1455)Gga>Aga	p.G485R	ITGA9_ENST00000422441.1_Missense_Mutation_p.G485R	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	485					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GTGTCACGACGGACAGCAGCC	0.567													G|||	1	0.000199681	0	0	5008	,	,		19891	0.001		0	False		,,,				2504	0				p.G485R		Atlas-SNP	.											.	ITGA9	98	.	0			c.G1453A						.						104	75	85					3																	37574884		2203	4300	6503	SO:0001583	missense	3680	exon14			CACGACGGACAGC	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.1453G>A	chr3.hg19:g.37574884G>A	ENSP00000264741:p.Gly485Arg	169.0	0.0		175.0	72.0	NM_002207	Q14638	Missense_Mutation	SNP	ENST00000264741.5	hg19	CCDS2669.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.870787	0.91587	.	.	ENSG00000144668	ENST00000422441;ENST00000264741	T;T	0.68765	-0.35;-0.35	6.07	6.07	0.98685	Integrin alpha-2 (1);	0.052596	0.85682	D	0.000000	T	0.75953	0.3920	L	0.56769	1.78	0.80722	D	1	P;D	0.63046	0.904;0.992	B;P	0.57960	0.37;0.83	T	0.76550	-0.2918	10	0.62326	D	0.03	.	15.7396	0.77882	0.0666:0.0:0.9334:0.0	.	485;485	Q13797;E9PDS3	ITA9_HUMAN;.	R	485	ENSP00000397258:G485R;ENSP00000264741:G485R	ENSP00000264741:G485R	G	+	1	0	ITGA9	37549888	1.000000	0.71417	0.485000	0.27403	0.985000	0.73830	6.637000	0.74304	2.884000	0.98904	0.655000	0.94253	GGA	.	.		0.567	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		A	37574884	G	A	37574884	3	1	52	1	0	0	0	0	1	0	0	0	7892	1117	39	1	1507	1	ITGA9	3	37574884	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	22610856	37574884	160447546	15	6646										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89456488	89456488	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	agcggcagtagcaattattcTcctcactgttgtcatctatg	8	10	4	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:89456488T>A	ENST00000336596.2	+	8	1889	c.1664T>A	c.(1663-1665)cTc>cAc	p.L555H	EPHA3_ENST00000494014.1_Missense_Mutation_p.L555H	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	555					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		GCAATTATTCTCCTCACTGTT	0.418										TSP Lung(6;0.00050)																											p.L555H		Atlas-SNP	.											.	EPHA3	501	.	0			c.T1664A						.						202	168	180					3																	89456488		2203	4300	6503	SO:0001583	missense	2042	exon8			TTATTCTCCTCAC	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1664T>A	chr3.hg19:g.89456488T>A	ENSP00000337451:p.Leu555His	178.0	0.0		142.0	74.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.335977	0.60853	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.15017	2.46;2.46	5.89	5.89	0.94794	.	0.057950	0.64402	D	0.000001	T	0.33962	0.0881	M	0.87547	2.89	0.80722	D	1	D	0.57257	0.979	P	0.46362	0.514	T	0.38802	-0.9644	9	.	.	.	.	16.3127	0.82898	0.0:0.0:0.0:1.0	.	555	P29320	EPHA3_HUMAN	H	555	ENSP00000337451:L555H;ENSP00000419190:L555H	.	L	+	2	0	EPHA3	89539178	1.000000	0.71417	0.998000	0.56505	0.215000	0.24574	7.677000	0.84024	2.246000	0.74042	0.533000	0.62120	CTC	.	.		0.418	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		A	89456488	T	A	89456488	3	1	52	1	0	0	0	0	1	0	0	0	5170	1551	54	4	1720	4	EPHA3	3	89456488	Missense_Mutation	SNP	T	TCGA-BW-A5NP-01A-11D-A27I-10	51881604	89456488	108565942	16	6647										
HHLA2	11148	hgsc.bcm.edu	37	chr3	108076864	108076864	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	atacaattatcaatgaatccCgattctcatggaacaaagag	6	8	2	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:108076864C>T	ENST00000357759.5	+	6	1273	c.859C>T	c.(859-861)Cga>Tga	p.R287*	HHLA2_ENST00000489514.2_Nonsense_Mutation_p.R287*|HHLA2_ENST00000491820.1_Nonsense_Mutation_p.R287*|HHLA2_ENST00000467761.1_Nonsense_Mutation_p.R287*|HHLA2_ENST00000467562.1_Nonsense_Mutation_p.R223*	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	287	Ig-like V-type 2.				positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)		p.R287R(2)		endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						CAATGAATCCCGATTCTCATG	0.378																																					p.R287X		Atlas-SNP	.											.	HHLA2	95	.	2	Substitution - coding silent(2)	lung(2)	c.C859T						.						154	150	151					3																	108076864		1846	4097	5943	SO:0001587	stop_gained	11148	exon6			GAATCCCGATTCT	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.859C>T	chr3.hg19:g.108076864C>T	ENSP00000350402:p.Arg287*	159.0	0.0		116.0	63.0	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Nonsense_Mutation	SNP	ENST00000357759.5	hg19	CCDS46883.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.8|23.8	4.460156|4.460156	0.84317|0.84317	.|.	.|.	ENSG00000114455|ENSG00000114455	ENST00000482099|ENST00000491820;ENST00000467562;ENST00000357759;ENST00000467761;ENST00000489514	.|.	.|.	.|.	5.31|5.31	0.291|0.291	0.15732|0.15732	.|.	.|0.727246	.|0.10700	.|N	.|0.644162	T|.	0.16428|.	0.0395|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.40590|.	-0.9555|.	3|.	.|0.02654	.|T	.|1	.|.	8.0163|8.0163	0.30383|0.30383	0.0:0.5511:0.0:0.4489|0.0:0.5511:0.0:0.4489	.|.	.|.	.|.	.|.	L|X	189|287;223;287;287;287	.|.	.|ENSP00000350402:R287X	P|R	+|+	2|1	0|2	HHLA2|HHLA2	109559554|109559554	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.021000|0.021000	0.10359|0.10359	-0.171000|-0.171000	0.09883|0.09883	-0.169000|-0.169000	0.10834|0.10834	-0.142000|-0.142000	0.14014|0.14014	CCG|CGA	.	.		0.378	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072		T	108076864	C	T	108076864	4	4	52	1	0	0	0	0	0	1	0	0	7104	644	23	1	873	1	HHLA2	3	108076864	Nonsense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	18620376	108076864	89945566	17	6648										
ZBED2	79413	hgsc.bcm.edu	37	chr3	111312778	111312778	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tgcagtggtgcccacgttgaCcccagggccacggctcacct	12	16	1	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:111312778C>A	ENST00000317012.4	-	2	1279	c.271G>T	c.(271-273)Gtc>Ttc	p.V91F	CD96_ENST00000438817.2_Intron|CD96_ENST00000352690.4_Intron|CD96_ENST00000283285.5_Intron	NM_024508.4	NP_078784.2	Q9BTP6	ZBED2_HUMAN	zinc finger, BED-type containing 2	91							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(1)|skin(2)	6						CCCACGTTGACCCCAGGGCCA	0.612																																					p.V91F		Atlas-SNP	.											.	ZBED2	22	.	0			c.G271T						.						66	65	66					3																	111312778		2203	4300	6503	SO:0001583	missense	79413	exon2			CGTTGACCCCAGG	BC003536	CCDS2960.2	3p13-q13.2	2013-05-03			ENSG00000177494	ENSG00000177494		"Zinc fingers, BED-type"	20710	protein-coding gene	gene with protein product		615246				23533661	Standard	NM_024508		Approved	MGC10796	uc003dxy.3	Q9BTP6	OTTHUMG00000074061	ENST00000317012.4:c.271G>T	chr3.hg19:g.111312778C>A	ENSP00000321370:p.Val91Phe	38.0	0.0		38.0	21.0	NM_024508	D3DN62	Missense_Mutation	SNP	ENST00000317012.4	hg19	CCDS2960.2	.	.	.	.	.	.	.	.	.	.	C	4.512	0.094990	0.08681	.	.	ENSG00000177494	ENST00000317012	.	.	.	4.66	2.72	0.32119	Zinc finger, BED-type predicted (3);	0.187693	0.24925	U	0.034509	T	0.10294	0.0252	N	0.01874	-0.695	0.09310	N	1	P	0.37985	0.613	B	0.39590	0.304	T	0.33727	-0.9857	9	0.02654	T	1	-11.6599	9.8009	0.40764	0.3683:0.6317:0.0:0.0	.	91	Q9BTP6	ZBED2_HUMAN	F	91	.	ENSP00000321370:V91F	V	-	1	0	ZBED2	112795468	0.626000	0.27120	0.339000	0.25562	0.927000	0.56198	0.390000	0.20768	1.134000	0.42165	0.467000	0.42956	GTC	.	.		0.612	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	NM_024508		A	111312778	C	A	111312778	3	1	52	1	0	0	0	0	1	0	0	0	17533	507	18	3	389	3	ZBED2	3	111312778	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	3235914	111312778	86709652	18	6649										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113375328	113375328	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cacttggtttaaacgtctgaCaatcagaaaggcggatatct	9	8	3	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:113375328C>A	ENST00000478658.1	-	5	5218	c.5201G>T	c.(5200-5202)tGt>tTt	p.C1734F	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.C1734F			Q68DE3	K2018_HUMAN	KIAA2018	1734						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						AAACGTCTGACAATCAGAAAG	0.408																																					p.C1734F		Atlas-SNP	.											.	KIAA2018	180	.	0			c.G5201T						.						113	107	109					3																	113375328		1867	4115	5982	SO:0001583	missense	205717	exon7			GTCTGACAATCAG	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.5201G>T	chr3.hg19:g.113375328C>A	ENSP00000420721:p.Cys1734Phe	225.0	0.0		179.0	22.0	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	hg19	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.233052	0.58777	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.44881	0.91;0.91	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.58411	-0.7641	10	0.87932	D	0	-8.1223	20.0313	0.97540	0.0:1.0:0.0:0.0	.	1734	Q68DE3	K2018_HUMAN	F	1734	ENSP00000320794:C1734F;ENSP00000420721:C1734F	ENSP00000320794:C1734F	C	-	2	0	KIAA2018	114858018	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.824000	0.75288	2.746000	0.94184	0.655000	0.94253	TGT	.	.		0.408	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		A	113375328	C	A	113375328	3	1	52	1	0	0	0	0	1	0	0	0	8277	478	17	3	1540	3	KIAA2018	3	113375328	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	2062550	113375328	84647102	19	6650										
ADCY5	111	hgsc.bcm.edu	37	chr3	123033087	123033087	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gtcagctacactcacctttaCgcaggagtagatcacagaca	8	12	3	2	rs372853437		TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:123033087C>T	ENST00000462833.1	-	12	3649	c.2437G>A	c.(2437-2439)Gta>Ata	p.V813I	ADCY5_ENST00000491190.1_Missense_Mutation_p.V446I|ADCY5_ENST00000309879.5_Missense_Mutation_p.V463I	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	813					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		CTCACCTTTACGCAGGAGTAG	0.572																																					p.V813I		Atlas-SNP	.											.	ADCY5	169	.	0			c.G2437A						.	C	ILE/VAL,ILE/VAL	0,4406		0,0,2203	107	82	90		1387,2437	1.7	1	3		90	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ADCY5	NM_001199642.1,NM_183357.2	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	463/912,813/1262	123033087	1,13005	2203	4300	6503	SO:0001583	missense	111	exon12			CCTTTACGCAGGA	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.2437G>A	chr3.hg19:g.123033087C>T	ENSP00000419361:p.Val813Ile	458.0	1.0		301.0	95.0	NM_183357	B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	hg19	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.357009	0.24598	0.0	1.16E-4	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879;ENST00000466617	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.64	1.67	0.24075	.	0.089397	0.47852	D	0.000202	T	0.27798	0.0684	N	0.26042	0.785	0.30553	N	0.765301	B;B	0.11235	0.004;0.001	B;B	0.08055	0.003;0.001	T	0.13845	-1.0494	10	0.22109	T	0.4	.	5.7627	0.18209	0.0:0.5899:0.1289:0.2812	.	813;446	O95622;B3KWA8	ADCY5_HUMAN;.	I	813;446;463;372	ENSP00000419361:V813I;ENSP00000418537:V446I;ENSP00000308685:V463I;ENSP00000420082:V372I	ENSP00000308685:V463I	V	-	1	0	ADCY5	124515777	0.997000	0.39634	0.997000	0.53966	0.890000	0.51754	1.114000	0.31196	0.335000	0.23614	-0.448000	0.05591	GTA	.	.		0.572	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		T	123033087	C	T	123033087	3	4	52	1	0	0	0	0	1	0	0	0	297	536	19	1	1388	1	ADCY5	3	123033087	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	9657759	123033087	74989343	20	6651										
CHST2	9435	hgsc.bcm.edu	37	chr3	142840620	142840620	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ggcgccactgctgcgagaccCggccctggacctcaaggtca	13	16	2	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:142840620C>T	ENST00000309575.3	+	2	2346	c.962C>T	c.(961-963)cCg>cTg	p.P321L		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	321					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						CTGCGAGACCCGGCCCTGGAC	0.652																																					p.P321L		Atlas-SNP	.											CHST2,colon,carcinoma,0,1	CHST2	67	.	0			c.C962T						.						19	21	21					3																	142840620		2201	4298	6499	SO:0001583	missense	9435	exon2			GAGACCCGGCCCT	BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"Sulfotransferases, membrane-bound"	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.962C>T	chr3.hg19:g.142840620C>T	ENSP00000307911:p.Pro321Leu	48.0	0.0		39.0	28.0	NM_004267	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	hg19	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.132158	0.77662	.	.	ENSG00000175040	ENST00000309575	D	0.83506	-1.73	4.38	4.38	0.52667	Sulfotransferase domain (1);	0.000000	0.64402	D	0.000001	D	0.92811	0.7714	M	0.91354	3.2	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94527	0.7732	10	0.72032	D	0.01	-12.6312	17.1075	0.86667	0.0:1.0:0.0:0.0	.	321	Q9Y4C5	CHST2_HUMAN	L	321	ENSP00000307911:P321L	ENSP00000307911:P321L	P	+	2	0	CHST2	144323310	1.000000	0.71417	0.997000	0.53966	0.599000	0.36880	7.638000	0.83328	2.269000	0.75478	0.407000	0.27541	CCG	.	.		0.652	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		T	142840620	C	T	142840620	3	4	52	1	0	0	0	0	1	0	0	0	3406	652	23	1	964	1	CHST2	3	142840620	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	19807533	142840620	55181810	21	6652										
SLC33A1	9197	hgsc.bcm.edu	37	chr3	155571528	155571528	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tcccgccaagcccaggggaaTaccctgaagcacgtaaagaa	10	13	0	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:155571528T>C	ENST00000392845.3	-	1	639	c.259A>G	c.(259-261)Att>Gtt	p.I87V	SLC33A1_ENST00000460729.1_5'Flank|SLC33A1_ENST00000359479.3_Missense_Mutation_p.I87V			O00400	ACATN_HUMAN	solute carrier family 33 (acetyl-CoA transporter), member 1	87					acetyl-CoA transport (GO:0015876)|cell death (GO:0008219)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	acetyl-CoA transporter activity (GO:0008521)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	22			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CCCAGGGGAATACCCTGAAGC	0.493																																					p.I87V		Atlas-SNP	.											.	SLC33A1	57	.	0			c.A259G						.						55	58	57					3																	155571528		2203	4300	6503	SO:0001583	missense	9197	exon1			GGGGAATACCCTG	D88152	CCDS3173.1	3q25.31	2013-05-22		2002-12-06	ENSG00000169359	ENSG00000169359		"Solute carriers"	95	protein-coding gene	gene with protein product		603690	"acetyl-Coenzyme A transporter", "spastic paraplegia 42 (autosomal dominant)"	ACATN, SPG42		9096318, 19061983	Standard	NM_004733		Approved	AT-1, AT1	uc003fao.2	O00400	OTTHUMG00000158481	ENST00000392845.3:c.259A>G	chr3.hg19:g.155571528T>C	ENSP00000376587:p.Ile87Val	117.0	0.0		101.0	60.0	NM_004733	B2R5Q2|D3DNK4	Missense_Mutation	SNP	ENST00000392845.3	hg19	CCDS3173.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.077772	0.76528	.	.	ENSG00000169359	ENST00000392845;ENST00000359479	T;T	0.71341	-0.56;-0.56	5.57	5.57	0.84162	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.72162	0.3426	L	0.43554	1.36	0.80722	D	1	P	0.35894	0.526	P	0.47786	0.557	T	0.66814	-0.5828	10	0.18276	T	0.48	-20.143	16.0862	0.81056	0.0:0.0:0.0:1.0	.	87	O00400	ACATN_HUMAN	V	87	ENSP00000376587:I87V;ENSP00000352456:I87V	ENSP00000352456:I87V	I	-	1	0	SLC33A1	157054222	1.000000	0.71417	0.993000	0.49108	0.955000	0.61496	6.013000	0.70776	2.251000	0.74343	0.529000	0.55759	ATT	.	.		0.493	SLC33A1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351130.3	NM_004733		C	155571528	T	C	155571528	3	2	52	1	0	0	0	0	1	0	0	0	14581	1406	49	2	1414	2	SLC33A1	3	155571528	Missense_Mutation	SNP	T	TCGA-BW-A5NP-01A-11D-A27I-10	12730908	155571528	42450902	22	6653										
NAALADL2	254827	hgsc.bcm.edu	37	chr3	174951769	174951769	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gatgacatggaaatttcaaaGaagattaagactcagtggac	10	5	2	4			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:174951769G>T	ENST00000454872.1	+	3	722	c.594G>T	c.(592-594)aaG>aaT	p.K198N	NAALADL2-AS2_ENST00000424690.1_RNA|NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	198						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		AAATTTCAAAGAAGATTAAGA	0.343																																					p.K198N		Atlas-SNP	.											.	NAALADL2	86	.	0			c.G594T						.						67	63	64					3																	174951769		1851	4098	5949	SO:0001583	missense	254827	exon3			TTCAAAGAAGATT		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"glutamate carboxypeptidase II-type non-peptidase homologue"	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.594G>T	chr3.hg19:g.174951769G>T	ENSP00000404705:p.Lys198Asn	69.0	0.0		64.0	16.0	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	hg19	CCDS46960.1	.	.	.	.	.	.	.	.	.	.	G	13.83	2.353996	0.41700	.	.	ENSG00000177694	ENST00000454872;ENST00000316366	T	0.39406	1.08	5.87	4.96	0.65561	.	0.111451	0.40469	N	0.001089	T	0.28764	0.0713	N	0.24115	0.695	0.32796	N	0.500579	B;P	0.39216	0.053;0.664	B;B	0.36885	0.061;0.235	T	0.33777	-0.9855	10	0.20519	T	0.43	-16.9894	14.0831	0.64937	0.076:0.0:0.924:0.0	.	181;198	Q58DX5-2;Q58DX5	.;NADL2_HUMAN	N	198;5	ENSP00000404705:K198N	ENSP00000314951:K5N	K	+	3	2	NAALADL2	176434463	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	3.215000	0.51169	1.411000	0.46957	-0.355000	0.07637	AAG	.	.		0.343	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015		T	174951769	G	T	174951769	3	4	52	1	0	0	0	0	1	0	0	0	10139	933	33	3	604	3	NAALADL2	3	174951769	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	19380241	174951769	23070661	23	6654										
CCDC39	339829	hgsc.bcm.edu	37	chr3	180361989	180361989	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tcatttattttggtcataagGgactgtttttcatcactgtt	7	6	4	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr3:180361989G>A	ENST00000442201.2	-	12	1703	c.1584C>T	c.(1582-1584)tcC>tcT	p.S528S	CCDC39_ENST00000273654.4_Silent_p.S612S	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	528					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TGGTCATAAGGGACTGTTTTT	0.294																																					p.S528S		Atlas-SNP	.											.	CCDC39	242	.	0			c.C1584T						.						147	130	135					3																	180361989		1627	3637	5264	SO:0001819	synonymous_variant	339829	exon12			CATAAGGGACTGT	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.1584C>T	chr3.hg19:g.180361989G>A		29.0	0.0		20.0	7.0	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	hg19	CCDS46964.1																																																																																			.	.		0.294	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		A	180361989	G	A	180361989	2	1	52	1	0	0	0	0	0	0	0	1	2813	1219	43	3		3	CCDC39	3	180361989	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	5410220	180361989	17660441	24	6655										
TMPRSS11D	9407	hgsc.bcm.edu	37	chr4	68691558	68691558	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	acatcattacttattattctGacctgtccttgccttagctc	4	12	2	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr4:68691558G>A	ENST00000283916.6	-	9	1085	c.987C>T	c.(985-987)gtC>gtT	p.V329V	TMPRSS11D_ENST00000545541.1_Silent_p.V212V|UBA6-AS1_ENST00000500538.2_RNA	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	329	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)|respiratory gaseous exchange (GO:0007585)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						TTATTATTCTGACCTGTCCTT	0.403																																					p.V329V		Atlas-SNP	.											.	TMPRSS11D	68	.	0			c.C987T						.						214	187	196					4																	68691558		2203	4300	6503	SO:0001819	synonymous_variant	9407	exon9			TATTCTGACCTGT	AB002134	CCDS3518.1	4q13.2	2010-04-13			ENSG00000153802	ENSG00000153802		"Serine peptidases / Transmembrane"	24059	protein-coding gene	gene with protein product	"airway trypsin like protease"	605369				9565616, 9070615	Standard	XM_005265710		Approved		uc003hdq.3	O60235	OTTHUMG00000129300	ENST00000283916.6:c.987C>T	chr4.hg19:g.68691558G>A		141.0	0.0		130.0	31.0	NM_004262	Q08AF6	Silent	SNP	ENST00000283916.6	hg19	CCDS3518.1	.	.	.	.	.	.	.	.	.	.	G	8.381	0.837554	0.16891	.	.	ENSG00000153802	ENST00000514868	.	.	.	5.88	3.98	0.46160	.	.	.	.	.	T	0.55721	0.1938	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52909	-0.8512	4	.	.	.	.	6.4866	0.22093	0.1025:0.3111:0.5864:0.0	.	.	.	.	L	54	.	.	S	-	2	0	TMPRSS11D	68374153	0.848000	0.29623	0.413000	0.26509	0.314000	0.28054	1.265000	0.33027	1.407000	0.46875	0.555000	0.69702	TCA	.	.		0.403	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3	NM_004262		A	68691558	G	A	68691558	2	1	52	1	0	0	0	0	0	0	0	1	16256	1277	45	3		3	TMPRSS11D	4	68691558	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10		68691558	122462718	25	6656										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90816255	90816256	+	Missense_Mutation	DNP	CC	CC	AA													0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ctatgccttctgcttcagttCctccaaataaaatacaaagt							TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr4:90816255_90816256CC>AA	ENST00000394980.1	+	2	452_453	c.133_134CC>AA	c.(133-135)CCt>AAt	p.P45N	MMRN1_ENST00000264790.2_Missense_Mutation_p.P45N|MMRN1_ENST00000394981.1_Missense_Mutation_p.P45N			Q13201	MMRN1_HUMAN	multimerin 1	45					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		TGCTTCAGTTCCTCCAAATAAA	0.45																																					p.P45T|p.P45H		Atlas-SNP	.											MMRN1,NS,carcinoma,0,1|.	MMRN1	174	.	0			c.C133A|c.C134A						.																																			SO:0001583	missense	22915	exon1			TCAGTTCCTCCAA|CAGTTCCTCCAAA	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	Exception_encountered	chr4.hg19:g.90816255_90816256delinsAA	ENSP00000378431:p.Pro45Asn	76.0|77.0	0.0		32.0	21.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	hg19	CCDS3635.1																																																																																			.	.		0.45	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		AA	90816256	CC	AA	90816255	3	1	52	1	0	0	0	0	1	0	0	0	9679	855	30	3	135	3	MMRN1	4	90816255	Missense_Mutation	DNP	CC	TCGA-BW-A5NP-01A-11D-A27I-10	22124697	90816255	100338021	26	6657										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123193335	123193335	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gagttcggagccctacagagCcaacatgtaaagttgtgttt	11	8	0	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr4:123193335C>G	ENST00000264501.4	+	48	8594	c.8221C>G	c.(8221-8223)Cca>Gca	p.P2741A	KIAA1109_ENST00000455637.1_Missense_Mutation_p.P2741A|KIAA1109_ENST00000388738.3_Missense_Mutation_p.P2741A			Q2LD37	K1109_HUMAN	KIAA1109	2741					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CCCTACAGAGCCAACATGTAA	0.373																																					p.P2741A		Atlas-SNP	.											.	KIAA1109	424	.	0			c.C8221G						.						81	76	78					4																	123193335		1887	4108	5995	SO:0001583	missense	84162	exon46			ACAGAGCCAACAT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.8221C>G	chr4.hg19:g.123193335C>G	ENSP00000264501:p.Pro2741Ala	182.0	0.0		102.0	34.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	15.41|15.41|15.41	2.825378|2.825378|2.825378	0.50739|0.50739|0.50739	.|.|.	.|.|.	ENSG00000138688|ENSG00000138688|ENSG00000138688	ENST00000419325|ENST00000264501;ENST00000388738;ENST00000455637|ENST00000446180	.|T;T;T|.	.|0.22743|.	.|2.53;2.53;1.94|.	5.87|5.87|5.87	5.0|5.0|5.0	0.66597|0.66597|0.66597	.|.|.	.|0.150088|.	.|0.44285|.	.|D|.	.|0.000476|.	T|T|T	0.62405|0.62405|0.62405	0.2425|0.2425|0.2425	L|L|L	0.43152|0.43152|0.43152	1.355|1.355|1.355	0.45837|0.45837|0.45837	D|D|D	0.998701|0.998701|0.998701	.|B;B;B|.	.|0.32507|.	.|0.373;0.001;0.0|.	.|B;B;B|.	.|0.33121|.	.|0.158;0.002;0.001|.	T|T|T	0.57015|0.57015|0.57015	-0.7883|-0.7883|-0.7883	5|10|5	.|0.27082|.	.|T|.	.|0.32|.	.|.|.	17.0681|17.0681|17.0681	0.86564|0.86564|0.86564	0.0:0.8735:0.1265:0.0|0.0:0.8735:0.1265:0.0|0.0:0.8735:0.1265:0.0	.|.|.	.|2741;2740;2741|.	.|Q2LD37-6;Q2LD37-2;Q2LD37|.	.|.;.;K1109_HUMAN|.	G|A|R	698|2741|1313	.|ENSP00000264501:P2741A;ENSP00000373390:P2741A;ENSP00000389925:P2741A|.	.|ENSP00000264501:P2741A|.	A|P|S	+|+|+	2|1|3	0|0|2	KIAA1109|KIAA1109|KIAA1109	123412785|123412785|123412785	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	2.948000|2.948000|2.948000	0.49066|0.49066|0.49066	2.785000|2.785000|2.785000	0.95823|0.95823|0.95823	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GCC|CCA|AGC	.	.		0.373	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123193335	C	G	123193335	3	3	52	1	0	0	0	0	1	0	0	0	8217	739	26	4	8403	4	KIAA1109	4	123193335	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	32377080	123193335	67960941	27	6658										
HPGD	3248	hgsc.bcm.edu	37	chr4	175439184	175439184	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cactccagcattattgaccaAaatgtccagtcttccaaagt	5	12	1	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr4:175439184A>T	ENST00000296522.6	-	3	708	c.262T>A	c.(262-264)Ttg>Atg	p.L88M	HPGD_ENST00000422112.2_Intron|HPGD_ENST00000542498.1_Missense_Mutation_p.L88M|HPGD_ENST00000296521.7_Missense_Mutation_p.L88M|HPGD_ENST00000504433.1_Missense_Mutation_p.L88M|HPGD_ENST00000541923.1_Intron|HPGD_ENST00000510901.1_De_novo_Start_InFrame	NM_000860.5|NM_001145816.2|NM_001256301.1|NM_001256307.1	NP_000851.2|NP_001139288.1|NP_001243230.1|NP_001243236.1	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)	88					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|ductus arteriosus closure (GO:0097070)|female pregnancy (GO:0007565)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|ovulation (GO:0030728)|parturition (GO:0007567)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|thrombin receptor signaling pathway (GO:0070493)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|catalytic activity (GO:0003824)|NAD binding (GO:0051287)|NAD+ binding (GO:0070403)|prostaglandin E receptor activity (GO:0004957)|protein homodimerization activity (GO:0042803)			kidney(1)|lung(3)|prostate(3)	7		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)		TTATTGACCAAAATGTCCAGT	0.279																																					p.L88M		Atlas-SNP	.											.	HPGD	19	.	0			c.T262A						.						66	65	65					4																	175439184		2202	4293	6495	SO:0001583	missense	3248	exon3			TGACCAAAATGTC		CCDS3821.1, CCDS54821.1, CCDS58933.1, CCDS58934.1, CCDS58935.1	4q34-q35	2011-09-14			ENSG00000164120	ENSG00000164120	1.1.1.141	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	5154	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 36C, member 1"	601688				19027726	Standard	NM_000860		Approved	SDR36C1	uc003itu.3	P15428	OTTHUMG00000160772	ENST00000296522.6:c.262T>A	chr4.hg19:g.175439184A>T	ENSP00000296522:p.Leu88Met	129.0	0.0		86.0	7.0	NM_000860	B4DTA4|B4DU74|B4DV57|D3DP43|E7EV11|O00749|Q06F08|Q12998	Missense_Mutation	SNP	ENST00000296522.6	hg19	CCDS3821.1	.	.	.	.	.	.	.	.	.	.	A	15.91	2.972067	0.53614	.	.	ENSG00000164120	ENST00000296522;ENST00000296521;ENST00000542498;ENST00000504433	D;D;D;D	0.90133	-2.05;-2.62;-2.62;-2.62	5.98	4.8	0.61643	NAD(P)-binding domain (1);	0.209202	0.40144	N	0.001173	D	0.92113	0.7500	M	0.64567	1.98	0.39808	D	0.972665	D;P;B;P;B	0.52996	0.957;0.884;0.401;0.551;0.401	P;P;B;B;P	0.57468	0.821;0.725;0.416;0.351;0.521	D	0.91946	0.5567	10	0.66056	D	0.02	.	8.4713	0.32986	0.8486:0.0:0.1514:0.0	.	88;88;88;88;88	O00749;E9PBZ2;Q12998;B4DV57;P15428	.;.;.;.;PGDH_HUMAN	M	88	ENSP00000296522:L88M;ENSP00000296521:L88M;ENSP00000443644:L88M;ENSP00000420892:L88M	ENSP00000296521:L88M	L	-	1	2	HPGD	175675759	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.602000	0.36783	1.086000	0.41228	0.482000	0.46254	TTG	.	.		0.279	HPGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362228.3			T	175439184	A	T	175439184	3	4	52	1	0	0	0	0	1	0	0	0	7343	11	1	4	558	4	HPGD	4	175439184	Missense_Mutation	SNP	A	TCGA-BW-A5NP-01A-11D-A27I-10	52245849	175439184	15715092	28	6659										
GPR98	84059	hgsc.bcm.edu	37	chr5	90000211	90000211	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ttctgtatgacataggggtcGttgaatacaacattgtttgt	10	5	1	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr5:90000211G>A	ENST00000405460.2	+	36	8388	c.8292G>A	c.(8290-8292)tcG>tcA	p.S2764S		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2764	Calx-beta 19. {ECO:0000305|PubMed:11606593}.		S -> L (in dbSNP:rs16869016). {ECO:0000269|PubMed:14740321}.		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CATAGGGGTCGTTGAATACAA	0.363																																					p.S2764S		Atlas-SNP	.											.	GPR98	605	.	0			c.G8292A						.						152	130	137					5																	90000211		1851	4096	5947	SO:0001819	synonymous_variant	84059	exon36			GGGGTCGTTGAAT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.8292G>A	chr5.hg19:g.90000211G>A		224.0	0.0		239.0	16.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	G	0.058	-1.231959	0.01505	.	.	ENSG00000164199	ENST00000509621	.	.	.	4.89	-5.82	0.02333	.	.	.	.	.	T	0.15869	0.0382	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.28427	-1.0044	4	.	.	.	.	0.8004	0.01074	0.2652:0.3195:0.2073:0.208	.	.	.	.	H	330	.	.	R	+	2	0	GPR98	90035967	0.000000	0.05858	0.077000	0.20336	0.055000	0.15305	-1.032000	0.03574	-0.598000	0.05806	-0.290000	0.09829	CGT	.	.		0.363	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90000211	G	A	90000211	2	1	52	1	0	0	0	0	0	0	0	1	6730	1132	40	1		1	GPR98	5	90000211	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10		90000211	90915049	29	6660										
CLK4	57396	hgsc.bcm.edu	37	chr5	178039797	178039797	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	aaaacaagtctttaacttacCattttagaattatatttgac	3	6	1	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr5:178039797C>T	ENST00000316308.4	-	8	1089	c.921G>A	c.(919-921)atG>atA	p.M307I		NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	307	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		TTTAACTTACCATTTTAGAAT	0.279																																					p.M307I		Atlas-SNP	.											.	CLK4	103	.	0			c.G921A						.						49	56	53					5																	178039797		2194	4285	6479	SO:0001630	splice_region_variant	57396	exon8			ACTTACCATTTTA	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.921+1G>A	chr5.hg19:g.178039797C>T		116.0	0.0		119.0	6.0	NM_020666		Missense_Mutation	SNP	ENST00000316308.4	hg19	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.522495	0.44866	.	.	ENSG00000113240	ENST00000316308;ENST00000536763	T	0.66280	-0.2	5.41	5.41	0.78517	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.159072	0.64402	D	0.000002	T	0.52240	0.1722	L	0.33245	0.995	0.80722	D	1	B;B;B	0.21381	0.055;0.001;0.001	B;B;B	0.23150	0.044;0.006;0.006	T	0.45308	-0.9270	9	.	.	.	.	16.7018	0.85351	0.0:1.0:0.0:0.0	.	307;307;307	B7ZL31;B9EG64;Q9HAZ1	.;.;CLK4_HUMAN	I	307	ENSP00000316948:M307I	.	M	-	3	0	CLK4	177972403	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.949000	0.70257	2.527000	0.85204	0.650000	0.86243	ATG	.	.		0.279	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2		Missense_Mutation	T	178039797	C	T	178039797	5	4	52	1	0	0	0	0	0	0	1	0	3541	608	21	3	548	3	CLK4	5	178039797	Splice_Site	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	88039586	178039797	2875463	30	6661										
DSP	1832	hgsc.bcm.edu	37	chr6	7580848	7580848	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cttgatgatgctgccaaaacCatccaggataaaaacaagga	8	9	0	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr6:7580848C>T	ENST00000379802.3	+	23	4766	c.4425C>T	c.(4423-4425)acC>acT	p.T1475T	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1475	Central fibrous rod domain.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		CTGCCAAAACCATCCAGGATA	0.423																																					p.T1475T		Atlas-SNP	.											.	DSP	306	.	0			c.C4425T						.						100	96	97					6																	7580848		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon23			CAAAACCATCCAG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.4425C>T	chr6.hg19:g.7580848C>T		180.0	0.0		224.0	81.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.423	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7580848	C	T	7580848	2	4	52	1	0	0	0	0	0	0	0	1	4783	581	21	3		3	DSP	6	7580848	Silent	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10		7580848	163534219	31	6662										
DHX16	8449	hgsc.bcm.edu	37	chr6	30638843	30638843	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tcttccctttctcagaagccTcttcctcctcttcttcctca	2	18	6	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr6:30638843T>G	ENST00000376442.3	-	2	611	c.416A>C	c.(415-417)gAg>gCg	p.E139A		NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	139					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						CTCAGAAGCCTCTTCCTCCTC	0.502																																					p.E139A		Atlas-SNP	.											.	DHX16	119	.	0			c.A416C						.						207	167	182					6																	30638843		1511	2709	4220	SO:0001583	missense	8449	exon2			GAAGCCTCTTCCT	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"DEAH-boxes"	2739	protein-coding gene	gene with protein product		603405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.416A>C	chr6.hg19:g.30638843T>G	ENSP00000365625:p.Glu139Ala	155.0	0.0		197.0	17.0	NM_003587	O60322|Q5JP45|Q969X7|Q96QC1	Missense_Mutation	SNP	ENST00000376442.3	hg19	CCDS4685.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.448304	0.43429	.	.	ENSG00000204560	ENST00000376442;ENST00000415603	T;T	0.65364	-0.15;2.03	4.66	1.79	0.24919	.	0.234953	0.41500	D	0.000867	T	0.19366	0.0465	N	0.14661	0.345	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.04781	-1.0927	10	0.24483	T	0.36	.	5.4915	0.16779	0.1798:0.0:0.1607:0.6594	.	79;139	B4DZ28;O60231	.;DHX16_HUMAN	A	139;79	ENSP00000365625:E139A;ENSP00000399101:E79A	ENSP00000365625:E139A	E	-	2	0	DHX16	30746822	0.039000	0.19947	0.932000	0.37286	0.953000	0.61014	0.660000	0.25009	0.646000	0.30693	0.455000	0.32223	GAG	.	.		0.502	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		G	30638843	T	G	30638843	3	3	52	1	0	0	0	0	1	0	0	0	4504	1551	54	5	2785	5	DHX16	6	30638843	Missense_Mutation	SNP	T	TCGA-BW-A5NP-01A-11D-A27I-10	23057995	30638843	140476224	32	6663										
MDC1	9656	hgsc.bcm.edu	37	chr6	30672574	30672574	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ggctcaggggtaacaggctgGtctgtggaggtggaaggctg	20	6	2	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr6:30672574G>T	ENST00000376406.3	-	10	5033	c.4386C>A	c.(4384-4386)gaC>gaA	p.D1462E	MDC1_ENST00000376405.2_Missense_Mutation_p.D1198E|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1462	Interaction with the PRKDC complex.|Pro-rich.				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						TAACAGGCTGGTCTGTGGAGG	0.572								Other conserved DNA damage response genes																													p.D1462E		Atlas-SNP	.											.	MDC1	218	.	0			c.C4386A						.						114	126	122					6																	30672574		2203	4299	6502	SO:0001583	missense	9656	exon10			AGGCTGGTCTGTG	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.4386C>A	chr6.hg19:g.30672574G>T	ENSP00000365588:p.Asp1462Glu	126.0	0.0		158.0	52.0	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	hg19	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	G	9.412	1.080756	0.20309	.	.	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.16597	2.33;2.33	4.46	-2.91	0.05631	.	.	.	.	.	T	0.04048	0.0113	L	0.47716	1.5	0.09310	N	1	P;B	0.35575	0.51;0.003	B;B	0.42738	0.396;0.01	T	0.35076	-0.9803	9	0.10111	T	0.7	0.1944	0.8896	0.01252	0.1925:0.1513:0.2357:0.4205	.	1198;1462	Q14676-2;Q14676	.;MDC1_HUMAN	E	1462;1198;1175;1028	ENSP00000365588:D1462E;ENSP00000365587:D1198E	ENSP00000365587:D1198E	D	-	3	2	MDC1	30780553	0.001000	0.12720	0.015000	0.15790	0.045000	0.14185	0.045000	0.14013	-0.321000	0.08627	0.449000	0.29647	GAC	.	.		0.572	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		T	30672574	G	T	30672574	3	4	52	1	0	0	0	0	1	0	0	0	9412	1252	44	3	1907	3	MDC1	6	30672574	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	33731	30672574	140442493	33	6664										
TMEM184A	202915	hgsc.bcm.edu	37	chr7	1594988	1594988	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ggtgaggaagagccagggggCcccctgggagctgttcccca	17	12	0	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr7:1594988C>T	ENST00000297477.5	-	2	449	c.133G>A	c.(133-135)Gcc>Acc	p.A45T		NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	45					germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		AGCCAGGGGGCCCCCTGGGAG	0.706																																					p.A45T		Atlas-SNP	.											.	TMEM184A	35	.	0			c.G133A						.						20	29	26					7																	1594988		1936	4104	6040	SO:0001583	missense	202915	exon2			AGGGGGCCCCCTG		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.133G>A	chr7.hg19:g.1594988C>T	ENSP00000297477:p.Ala45Thr	53.0	0.0		58.0	32.0	NM_001097620	Q8TBQ6	Missense_Mutation	SNP	ENST00000297477.5	hg19	CCDS43537.1	.	.	.	.	.	.	.	.	.	.	C	2.199	-0.383394	0.04966	.	.	ENSG00000164855	ENST00000297477;ENST00000319010;ENST00000414730;ENST00000441933;ENST00000431208	T;T;T;T;T	0.46819	1.49;0.86;0.89;0.88;0.88	4.45	1.5	0.22942	.	891.613000	0.01644	U	0.024206	T	0.29882	0.0747	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.13899	-1.0492	10	0.14656	T	0.56	-9.0747	5.3605	0.16085	0.0:0.5298:0.1503:0.32	.	45	Q6ZMB5	T184A_HUMAN	T	45	ENSP00000297477:A45T;ENSP00000325945:A45T;ENSP00000398382:A45T;ENSP00000389092:A45T;ENSP00000403499:A45T	ENSP00000297477:A45T	A	-	1	0	TMEM184A	1561514	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.959000	0.01518	0.415000	0.25817	0.462000	0.41574	GCC	.	.		0.706	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689		T	1594988	C	T	1594988	3	4	52	1	0	0	0	0	1	0	0	0	16119	739	26	3	1140	3	TMEM184A	7	1594988	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10		1594988	157543675	34	6665										
MGC87042	256227	hgsc.bcm.edu	37	chr7	22532994	22532994	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ctgtaggatcgcctcattgcGtaagacagagtataaattgc	10	8	1	2	rs571881121		TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr7:22532994G>A	ENST00000406890.2	-	3	583	c.489C>T	c.(487-489)taC>taT	p.Y163Y	STEAP1B_ENST00000404369.4_Silent_p.Y182Y	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	163						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						GCCTCATTGCGTAAGACAGAG	0.388													g|||	1	0.000199681	0	0	5008	,	,		19769	0		0	False		,,,				2504	0.001				p.Y182Y		Atlas-SNP	.											STEAP1B,colon,carcinoma,0,2	STEAP1B	22	.	0			c.C546T						.						153	121	131					7																	22532994		692	1591	2283	SO:0001819	synonymous_variant	256227	exon3			CATTGCGTAAGAC		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.489C>T	chr7.hg19:g.22532994G>A		156.0	0.0		189.0	18.0	NM_001164460	B5MCI2	Silent	SNP	ENST00000406890.2	hg19	CCDS55094.1																																																																																			.	.		0.388	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2			A	22532994	G	A	22532994	2	1	52	1	0	0	0	0	0	0	0	1	9563	1140	40	1		1	MGC87042	7	22532994	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	20938006	22532994	136605669	35	6666										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48567919	48567919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tttctctaacttcaggacatGctatcatcaggactcccatg	6	12	4	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr7:48567919G>A	ENST00000435803.1	+	55	14356	c.14332G>A	c.(14332-14334)Gct>Act	p.A4778T	ABCA13_ENST00000544596.1_Missense_Mutation_p.A508T	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4778	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TTCAGGACATGCTATCATCAG	0.438																																					p.A4778T		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G14332A						.						78	72	74					7																	48567919		1969	4181	6150	SO:0001583	missense	154664	exon55			GGACATGCTATCA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.14332G>A	chr7.hg19:g.48567919G>A	ENSP00000411096:p.Ala4778Thr	69.0	0.0		77.0	14.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	12.23	1.875737	0.33162	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.93906	-3.31;-3.31;-3.31	5.73	2.94	0.34122	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.262385	0.26927	N	0.021788	D	0.90823	0.7118	M	0.74467	2.265	0.09310	N	1	B;P;P	0.38129	0.089;0.558;0.619	B;B;B	0.33890	0.073;0.128;0.172	T	0.83164	-0.0097	10	0.56958	D	0.05	.	9.4262	0.38581	0.2215:0.0:0.7785:0.0	.	508;2480;4778	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	T	4778;551;508	ENSP00000411096:A4778T;ENSP00000391042:A551T;ENSP00000442634:A508T	ENSP00000391042:A551T	A	+	1	0	ABCA13	48538465	0.649000	0.27322	0.001000	0.08648	0.005000	0.04900	2.880000	0.48530	0.334000	0.23590	0.655000	0.94253	GCT	.	.		0.438	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48567919	G	A	48567919	3	1	52	1	0	0	0	0	1	0	0	0	31	1319	46	3	14379	3	ABCA13	7	48567919	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	26034925	48567919	110570744	36	6667										
CCDC132	55610	hgsc.bcm.edu	37	chr7	92926471	92926471	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	aactaggttgatgcaagttgGagaagaattttgtggtagca	13	3	0	3			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr7:92926471G>T	ENST00000305866.5	+	16	1405	c.1277G>T	c.(1276-1278)gGa>gTa	p.G426V	CCDC132_ENST00000541136.1_Missense_Mutation_p.G237V|CCDC132_ENST00000317751.6_Missense_Mutation_p.G157V|CCDC132_ENST00000544910.1_Missense_Mutation_p.G396V|CCDC132_ENST00000535481.1_Missense_Mutation_p.G146V	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	426						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			ATGCAAGTTGGAGAAGAATTT	0.318																																					p.G426V		Atlas-SNP	.											.	CCDC132	136	.	0			c.G1277T						.						78	74	75					7																	92926471		1804	4069	5873	SO:0001583	missense	55610	exon16			AAGTTGGAGAAGA	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1277G>T	chr7.hg19:g.92926471G>T	ENSP00000307666:p.Gly426Val	90.0	0.0		94.0	4.0	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.8|23.8	4.455281|4.455281	0.84209|0.84209	.|.	.|.	ENSG00000004766|ENSG00000004766	ENST00000458707|ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751	.|T	.|0.70282	.|-0.47	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|D	.|0.85392	.|0.5686	M|M	0.82056|0.82056	2.57|2.57	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.87578	.|0.998;0.998;0.994	.|D	.|0.87385	.|0.2359	.|10	.|0.87932	.|D	.|0	-14.4067|-14.4067	18.8207|18.8207	0.92096|0.92096	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|146;396;426	.|B4DS55;F5H5U7;Q96JG6	.|.;.;CC132_HUMAN	X|V	213|426;396;237;146;157	.|ENSP00000325582:G157V	.|ENSP00000307666:G426V	E|G	+|+	1|2	0|0	CCDC132|CCDC132	92764407|92764407	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.711000|9.711000	0.98735|0.98735	2.525000|2.525000	0.85131|0.85131	0.557000|0.557000	0.71058|0.71058	GAG|GGA	.	.		0.318	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		T	92926471	G	T	92926471	3	4	52	1	0	0	0	0	1	0	0	0	2769	1174	41	3	1381	3	CCDC132	7	92926471	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	44358552	92926471	66212192	37	6668										
SLC26A3	1811	hgsc.bcm.edu	37	chr7	107423494	107423494	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gtactcccagcaaatcctctGaatactccacagactatgtt	5	13	1	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr7:107423494G>A	ENST00000340010.5	-	10	1348	c.1164C>T	c.(1162-1164)ttC>ttT	p.F388F	SLC26A3_ENST00000422236.2_Silent_p.F353F	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	388					anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						CAAATCCTCTGAATACTCCAC	0.463																																					p.F388F		Atlas-SNP	.											.	SLC26A3	120	.	0			c.C1164T						.						129	123	125					7																	107423494		2203	4300	6503	SO:0001819	synonymous_variant	1811	exon10			TCCTCTGAATACT	L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"Solute carriers"	3018	protein-coding gene	gene with protein product		126650	"congenital chloride diarrhea", "solute carrier family 26, member 3"	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.1164C>T	chr7.hg19:g.107423494G>A		179.0	0.0		166.0	64.0	NM_000111		Silent	SNP	ENST00000340010.5	hg19	CCDS5748.1																																																																																			.	.		0.463	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111		A	107423494	G	A	107423494	2	1	52	1	0	0	0	0	0	0	0	1	14533	1281	45	3		3	SLC26A3	7	107423494	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	14497023	107423494	51715169	38	6669										
KIAA1147	57189	hgsc.bcm.edu	37	chr7	141373871	141373872	+	Frame_Shift_Ins	INS	-	-	TC													0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cagggctaacctcaccttcaINStctcagggtacatgtatcgg							TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr7:141373871_141373872insTC	ENST00000536163.1	-	4	675_676	c.676_677insGA	c.(676-678)atgfs	p.M226fs	KIAA1147_ENST00000482493.1_Frame_Shift_Ins_p.M135fs	NM_001080392.1	NP_001073861.1	A4D1U4	LCHN_HUMAN	KIAA1147	226										breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|ovary(1)|skin(1)	12	Melanoma(164;0.0171)					CCTCACCTTCATCTCAGGGTAC	0.465																																					p.M226fs		Atlas-INDEL	.											.	KIAA1147	32	.	0			c.677_678insGA						.																																			SO:0001589	frameshift_variant	57189	exon4			.	AB032973	CCDS47726.1	7q34	2012-10-04			ENSG00000257093	ENSG00000257093			29472	protein-coding gene	gene with protein product							Standard	NM_001080392		Approved	LCHN	uc003vwk.3	A4D1U4	OTTHUMG00000157539	ENST00000536163.1:c.675_676dupGA	chr7.hg19:g.141373874_141373875dupTC	ENSP00000445768:p.Met226fs	129.0	0.0		128.0	60.0	NM_001080392	Q9ULS3	Frame_Shift_Ins	INS	ENST00000536163.1	hg19	CCDS47726.1																																																																																			.	.		0.465	KIAA1147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349104.1			TC	141373872	-	TC	141373871	7	5	52	1	0	1	1	0	0	0	0	0	8219	217	8	0	714	0	KIAA1147	7	141373871	Frame_Shift_Ins	INS	-	TCGA-BW-A5NP-01A-11D-A27I-10	33950377	141373871	17764792	39	6670										
ASAP1	50807	hgsc.bcm.edu	37	chr8	131181257	131181257	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cattatataaatcagcagccAgtttttcaatgtactgtttc	5	8	2	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr8:131181257A>C	ENST00000518721.1	-	10	1030	c.803T>G	c.(802-804)cTg>cGg	p.L268R	ASAP1_ENST00000357668.1_Missense_Mutation_p.L268R	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	268					cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						ATCAGCAGCCAGTTTTTCAAT	0.279																																					p.L268R		Atlas-SNP	.											.	ASAP1	133	.	0			c.T803G						.						61	67	65					8																	131181257		2200	4292	6492	SO:0001583	missense	50807	exon10			GCAGCCAGTTTTT	AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.803T>G	chr8.hg19:g.131181257A>C	ENSP00000429900:p.Leu268Arg	94.0	0.0		96.0	34.0	NM_018482	B2RNV3	Missense_Mutation	SNP	ENST00000518721.1	hg19	CCDS6362.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.313543	0.81358	.	.	ENSG00000153317	ENST00000343135;ENST00000357668;ENST00000518721;ENST00000524367	T;T;T	0.08102	3.13;3.13;3.13	5.91	5.91	0.95273	.	0.167754	0.40818	N	0.001007	T	0.32010	0.0815	M	0.81497	2.545	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.975;0.975;0.998	T	0.04522	-1.0945	10	0.87932	D	0	.	15.1723	0.72884	1.0:0.0:0.0:0.0	.	268;268;268	B2RNV3;Q9ULH1;Q9ULH1-2	.;ASAP1_HUMAN;.	R	268;268;268;238	ENSP00000350297:L268R;ENSP00000429900:L268R;ENSP00000430588:L238R	ENSP00000344591:L268R	L	-	2	0	ASAP1	131250439	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.533000	0.90617	2.254000	0.74563	0.533000	0.62120	CTG	.	.		0.279	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		C	131181257	A	C	131181257	3	2	52	1	0	0	0	0	1	0	0	0	1010	188	7	5	2670	5	ASAP1	8	131181257	Missense_Mutation	SNP	A	TCGA-BW-A5NP-01A-11D-A27I-10		131181257	15182765	40	6671										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2039815	2039815	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cagcagcagcagcagcagcaGcaacagcagccgcagcagca	12	15	0	0	rs574062756	byFrequency	TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr9:2039815G>A	ENST00000382203.1	+	4	914	c.705G>A	c.(703-705)caG>caA	p.Q235Q	RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000349721.2_Silent_p.Q235Q|SMARCA2_ENST00000357248.2_Silent_p.Q235Q|SMARCA2_ENST00000491574.1_3'UTR|SMARCA2_ENST00000382194.1_Silent_p.Q235Q			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	235	Poly-Gln.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		agcagcagcagcaacagcagc	0.587													G|||	41	0.0081869	0.0151	0.0029	5008	,	,		10366	0.0089		0	False		,,,				2504	0.0102				p.Q235Q		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G705A						.						10	13	12					9																	2039815		2161	4205	6366	SO:0001819	synonymous_variant	6595	exon4			GCAGCAGCAACAG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.705G>A	chr9.hg19:g.2039815G>A		35.0	0.0		27.0	5.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	hg19	CCDS34977.1																																																																																			.	.		0.587	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2039815	G	A	2039815	2	1	52	1	0	0	0	0	0	0	0	1	14784	962	34	3		3	SMARCA2	9	2039815	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10		2039815	139173616	41	6672										
TEX10	54881	hgsc.bcm.edu	37	chr9	103092435	103092435	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	atctatgttattggagagaaCtgtgcaatgcttgatgctag	11	5	1	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr9:103092435C>G	ENST00000374902.4	-	6	1443	c.1267G>C	c.(1267-1269)Gtt>Ctt	p.V423L	TEX10_ENST00000535814.1_Missense_Mutation_p.V426L|TEX10_ENST00000537512.1_Missense_Mutation_p.V358L	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	423						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		TTGGAGAGAACTGTGCAATGC	0.378																																					p.V426L		Atlas-SNP	.											.	TEX10	99	.	0			c.G1276C						.						130	125	127					9																	103092435		2203	4300	6503	SO:0001583	missense	54881	exon6			AGAGAACTGTGCA	AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"testis expressed gene 10", "testis expressed sequence 10"			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.1267G>C	chr9.hg19:g.103092435C>G	ENSP00000364037:p.Val423Leu	72.0	0.0		65.0	29.0	NM_001161584	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Missense_Mutation	SNP	ENST00000374902.4	hg19	CCDS6748.1	.	.	.	.	.	.	.	.	.	.	C	2.350	-0.349090	0.05208	.	.	ENSG00000136891	ENST00000535814;ENST00000374902;ENST00000444730;ENST00000429235;ENST00000537512	T;T;T	0.64085	-0.08;-0.08;-0.08	5.18	2.87	0.33458	Armadillo-type fold (1);	0.436379	0.26481	N	0.024128	T	0.40719	0.1128	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.12630	0.0;0.0;0.006;0.0	B;B;B;B	0.13407	0.0;0.001;0.009;0.0	T	0.17806	-1.0357	10	0.11485	T	0.65	-1.5738	4.1519	0.10242	0.1489:0.1667:0.0:0.6843	.	358;426;291;423	B7Z9D5;B4DYV2;E7ERG2;Q9NXF1	.;.;.;TEX10_HUMAN	L	426;423;291;68;358	ENSP00000444555:V426L;ENSP00000364037:V423L;ENSP00000438120:V358L	ENSP00000364037:V423L	V	-	1	0	TEX10	102132256	0.006000	0.16342	0.763000	0.31416	0.928000	0.56348	0.091000	0.15046	0.403000	0.25479	-0.302000	0.09304	GTT	.	.		0.378	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746		G	103092435	C	G	103092435	3	3	52	1	0	0	0	0	1	0	0	0	15787	565	20	4	1562	4	TEX10	9	103092435	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	101052620	103092435	38120996	42	6673										
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139395193	139395193	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ttgtgcaggctggcgccctgGtagatgaagtcggagatgac	16	8	0	4			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr9:139395193G>A	ENST00000277541.6	-	31	5820	c.5745C>T	c.(5743-5745)taC>taT	p.Y1915Y		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1915					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGGCGCCCTGGTAGATGAAGT	0.692			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.Y1915Y		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.C5745T						.						56	70	65					9																	139395193		2134	4259	6393	SO:0001819	synonymous_variant	4851	exon31			GCCCTGGTAGATG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5745C>T	chr9.hg19:g.139395193G>A		5.0	0.0		8.0	5.0	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	hg19	CCDS43905.1																																																																																			.	.		0.692	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139395193	G	A	139395193	2	1	52	1	0	0	0	0	0	0	0	1	10556	1256	44	3		3	NOTCH1	9	139395193	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	36302758	139395193	1818238	43	6674										
ASB13	79754	hgsc.bcm.edu	37	chr10	5683746	5683746	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gtctcactttcgtagtactcGaagcacttggcgggagcgct	12	11	1	0	rs144206251		TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr10:5683746G>A	ENST00000357700.6	-	5	722	c.696C>T	c.(694-696)ttC>ttT	p.F232F	ASB13_ENST00000479033.1_5'UTR	NM_024701.3	NP_078977.2	Q8WXK3	ASB13_HUMAN	ankyrin repeat and SOCS box containing 13	232	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					NS(1)|endometrium(3)|lung(3)|ovary(1)	8				GBM - Glioblastoma multiforme(2;9.59e-09)		CGTAGTACTCGAAGCACTTGG	0.637																																					p.F232F		Atlas-SNP	.											ASB13,NS,carcinoma,0,1	ASB13	26	.	0			c.C696T						.						69	67	68					10																	5683746		2203	4300	6503	SO:0001819	synonymous_variant	79754	exon5			GTACTCGAAGCAC	AK091935	CCDS7070.1	10p15.1	2013-01-10	2011-01-25		ENSG00000196372	ENSG00000196372		"Ankyrin repeat domain containing"	19765	protein-coding gene	gene with protein product		615055	"ankyrin repeat and SOCS box-containing 13"			12076535	Standard	NM_024701		Approved	FLJ13134, MGC19879	uc001iig.2	Q8WXK3	OTTHUMG00000017603	ENST00000357700.6:c.696C>T	chr10.hg19:g.5683746G>A		117.0	1.0		92.0	59.0	NM_024701	A8K7Q6|D3DRR2|Q96EP7|Q9H8Z1	Silent	SNP	ENST00000357700.6	hg19	CCDS7070.1																																																																																			.	G|1.000;T|0.000		0.637	ASB13-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046564.1			A	5683746	G	A	5683746	2	1	52	1	0	0	0	0	0	0	0	1	1017	1049	37	1		1	ASB13	10	5683746	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10		5683746	129851001	44	6675										
GHITM	27069	hgsc.bcm.edu	37	chr10	85902445	85902445	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	aacaagaattgggatccggcGtgggagaactggccaagaac	14	8	0	3			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr10:85902445G>A	ENST00000372134.3	+	3	357	c.164G>A	c.(163-165)cGt>cAt	p.R55H	RP11-338I21.1_ENST00000606511.1_RNA	NM_014394.2	NP_055209.2	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein	55					apoptotic process (GO:0006915)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(2)	10						GGGATCCGGCGTGGGAGAACT	0.393																																					p.R55H		Atlas-SNP	.											GHITM,NS,adenocarcinoma,0,1	GHITM	30	.	0			c.G164A						.						90	93	92					10																	85902445		1893	4119	6012	SO:0001583	missense	27069	exon3			TCCGGCGTGGGAG	AB009685	CCDS41542.1	10q23.1	2008-02-01			ENSG00000165678	ENSG00000165678			17281	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 5"					8619474, 9110174	Standard	NM_014394		Approved	HSPC282, PTD010, DERP2, My021, TMBIM5	uc001kcs.1	Q9H3K2	OTTHUMG00000018637	ENST00000372134.3:c.164G>A	chr10.hg19:g.85902445G>A	ENSP00000361207:p.Arg55His	96.0	0.0		128.0	8.0	NM_014394	A8K9Z9|D3DWE0|O95894|Q5VT95|Q9H0P2	Missense_Mutation	SNP	ENST00000372134.3	hg19	CCDS41542.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.815186	0.70912	.	.	ENSG00000165678	ENST00000372134;ENST00000538477;ENST00000436406;ENST00000339736	.	.	.	5.86	5.86	0.93980	.	0.046469	0.85682	D	0.000000	T	0.77811	0.4186	M	0.79258	2.445	0.58432	D	0.999993	D	0.76494	0.999	P	0.59643	0.861	T	0.77048	-0.2732	9	0.44086	T	0.13	-17.4394	18.9591	0.92671	0.0:0.0:1.0:0.0	.	55	Q9H3K2	GHITM_HUMAN	H	55;42;55;55	.	ENSP00000342214:R55H	R	+	2	0	GHITM	85892425	1.000000	0.71417	0.979000	0.43373	0.990000	0.78478	6.477000	0.73591	2.765000	0.95021	0.655000	0.94253	CGT	.	.		0.393	GHITM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049125.1	NM_014394		A	85902445	G	A	85902445	3	1	52	1	0	0	0	0	1	0	0	0	6378	1145	40	1	170	1	GHITM	10	85902445	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	80218699	85902445	49632302	45	6676										
FEN1	2237	hgsc.bcm.edu	37	chr11	61563319	61563319	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cccagtgaggcagaggccagCtgtgctgccctggtgaaggc	16	12	0	3			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr11:61563319C>T	ENST00000305885.2	+	2	899	c.486C>T	c.(484-486)agC>agT	p.S162S	FADS2_ENST00000574708.1_Intron	NM_004111.5	NP_004102.1			flap structure-specific endonuclease 1											endometrium(1)|large_intestine(4)|lung(1)|ovary(1)	7						CAGAGGCCAGCTGTGCTGCCC	0.572								Editing and processing nucleases																													p.S162S		Atlas-SNP	.											.	FEN1	15	.	0			c.C486T						.						62	62	62					11																	61563319		2202	4299	6501	SO:0001819	synonymous_variant	2237	exon2			GGCCAGCTGTGCT	L37374	CCDS8010.1	11q12	2013-05-08			ENSG00000168496	ENSG00000168496			3650	protein-coding gene	gene with protein product	"maturation factor-1", "DNase IV"	600393		RAD2		7774922	Standard	NM_004111		Approved	FEN-1, MF1	uc001nsg.3	P39748	OTTHUMG00000168162	ENST00000305885.2:c.486C>T	chr11.hg19:g.61563319C>T		94.0	0.0		69.0	23.0	NM_004111		Silent	SNP	ENST00000305885.2	hg19	CCDS8010.1																																																																																			.	.		0.572	FEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398526.1	NM_004111		T	61563319	C	T	61563319	2	4	52	1	0	0	0	0	0	0	0	1	5820	796	28	3		3	FEN1	11	61563319	Silent	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10		61563319	73443197	46	6677										
CNIH2	254263	hgsc.bcm.edu	37	chr11	66050237	66050239	+	Missense_Mutation	TNP	TGC	TGC	CTT													0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	aaaacatcgaacgcatctgcTgcctcctgaggaaggtcagt							TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	T|G|C	T|G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr11:66050237_66050239TGC>CTT	ENST00000311445.6	+	3	442_444	c.184_186TGC>CTT	c.(184-186)TGC>CTT	p.C62L	CNIH2_ENST00000528852.1_Missense_Mutation_p.C62L|YIF1A_ENST00000526497.1_5'Flank|CNIH2_ENST00000530519.1_3'UTR	NM_182553.2	NP_872359.1	Q6PI25	CNIH2_HUMAN	cornichon family AMPA receptor auxiliary protein 2	62					intracellular signal transduction (GO:0035556)|localization within membrane (GO:0051668)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	5						ACGCATCTGCTGCCTCCTGAGGA	0.635											OREG0021100	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C62R|p.C62F|p.C62C		Atlas-SNP	.											.	CNIH2	15	.	0			c.T184C|c.G185T|c.C186T						.																																			SO:0001583	missense	254263	exon3			ATCTGCTGCCTCC|TCTGCTGCCTCCT|CTGCTGCCTCCTG	BC047953	CCDS8131.1	11q13.2	2013-08-28	2013-08-28		ENSG00000174871	ENSG00000174871			28744	protein-coding gene	gene with protein product		611288	"cornichon homolog 2 (Drosophila)"			12477932	Standard	NM_182553		Approved	MGC50896, Cnil, CNIH-2	uc001ohi.2	Q6PI25	OTTHUMG00000166919	ENST00000311445.6:c.184_186TGC>CTT	chr11.hg19:g.66050237TGC>CTT	ENSP00000310003:p.Cys62Leu	156.0|154.0|154.0	0.0	1088	68.0|68.0|69.0	10.0	NM_182553		Missense_Mutation|Missense_Mutation|Silent	SNP	ENST00000311445.6	hg19	CCDS8131.1																																																																																			.	.		0.635	CNIH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391892.1	NM_182553		CTT	66050239	TGC	CTT	66050237	3	2	52	1	0	0	0	0	1	0	0	0	3605	1580	55	2	194	2	CNIH2	11	66050237	Missense_Mutation	TNP	TGC	TCGA-BW-A5NP-01A-11D-A27I-10	4486918	66050237	68956279	47	6678										
KRTAP5-7	440050	hgsc.bcm.edu	37	chr11	71238736	71238762	+	In_Frame_Del	DEL	CTGCTGTTCCTCAGGCTGTGGGTCATC	CTGCTGTTCCTCAGGCTGTGGGTCATC	-													0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tccagctgctgtaagccctgCtgctgttcctcaggctgtgg					rs533945918|rs79842834	byFrequency	TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	CTGCTGTTCCTCAGGCTGTGGGTCATC	CTGCTGTTCCTCAGGCTGTGGGTCATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr11:71238736_71238762delCTGCTGTTCCTCAGGCTGTGGGTCATC	ENST00000398536.4	+	1	424_450	c.390_416delCTGCTGTTCCTCAGGCTGTGGGTCATC	c.(388-417)tgctgctgttcctcaggctgtgggtcatcc>tgc	p.CCSSGCGSS131del		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	131	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.G137W(1)		breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						gtaagccctgctgctgttcctcaggctgtgggtcatcctgctgccag	0.604																																					p.130_139del		Atlas-INDEL	.											.	KRTAP5-7	23	.	1	Substitution - Missense(1)	lung(1)	c.389_415del						.																																			SO:0001651	inframe_deletion	440050	exon1			.	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"Keratin associated proteins"	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.390_416delCTGCTGTTCCTCAGGCTGTGGGTCATC	chr11.hg19:g.71238736_71238762delCTGCTGTTCCTCAGGCTGTGGGTCATC	ENSP00000417330:p.Cys131_Ser139del	174.0	0.0		147.0	13.0	NM_001012503	B2RNM3|Q701N5	In_Frame_Del	DEL	ENST00000398536.4	hg19	CCDS41682.1																																																																																			.	.		0.604	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1			-	71238762	CTGCTGTTCCTCAGGCTGTGGGTCATC	-	71238736	7	5	52	1	0	1	0	1	0	0	0	0	8575	805	28	0	392	0	KRTAP5-7	11	71238736	In_Frame_Del	DEL	CTGCTGTTCCTCAGGCTGTGGGTCATC	TCGA-BW-A5NP-01A-11D-A27I-10	5188499	71238736	63767780	48	6679										
PGR	5241	hgsc.bcm.edu	37	chr11	100996842	100996842	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ttaaacaaatcttctgaggtAatgactcgaagctgtattgt	8	6	2	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr11:100996842A>C	ENST00000325455.5	-	2	3138	c.1685T>G	c.(1684-1686)tTa>tGa	p.L562*	PGR_ENST00000534013.1_De_novo_Start_OutOfFrame|PGR_ENST00000263463.5_Nonsense_Mutation_p.L562*	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	562	Modulating, Pro-Rich.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	CTTCTGAGGTAATGACTCGAA	0.433																																					p.L562X	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.T1685G						.						84	72	76					11																	100996842		2203	4300	6503	SO:0001587	stop_gained	5241	exon2			TGAGGTAATGACT	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"Nuclear hormone receptors"	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.1685T>G	chr11.hg19:g.100996842A>C	ENSP00000325120:p.Leu562*	112.0	0.0		102.0	19.0	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Nonsense_Mutation	SNP	ENST00000325455.5	hg19	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	A	37	6.158621	0.97334	.	.	ENSG00000082175	ENST00000325455;ENST00000263463;ENST00000537623	.	.	.	5.55	5.55	0.83447	.	0.085158	0.47852	D	0.000217	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7017	0.77547	1.0:0.0:0.0:0.0	.	.	.	.	X	562	.	ENSP00000263463:L562X	L	-	2	0	PGR	100502052	0.983000	0.35010	0.720000	0.30636	0.280000	0.26924	7.553000	0.82203	2.096000	0.63516	0.528000	0.53228	TTA	.	.		0.433	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			C	100996842	A	C	100996842	4	2	52	1	0	0	0	0	0	1	0	0	11814	372	13	5	1144	5	PGR	11	100996842	Nonsense_Mutation	SNP	A	TCGA-BW-A5NP-01A-11D-A27I-10	29758106	100996842	34009674	49	6680										
APOA5	116519	hgsc.bcm.edu	37	chr11	116661338	116661338	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cagctcctgcacgtggcgccCgatgccgctcaccaggctct	11	18	2	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr11:116661338C>T	ENST00000227665.4	-	3	641	c.607G>A	c.(607-609)Ggg>Agg	p.G203R	APOA5_ENST00000542499.1_Missense_Mutation_p.G203R|ZNF259_ENST00000227322.3_5'Flank			Q6Q788	APOA5_HUMAN	apolipoprotein A-V	203					acylglycerol homeostasis (GO:0055090)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|organ regeneration (GO:0031100)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)	chylomicron (GO:0042627)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|lipase activator activity (GO:0060229)|lipase binding (GO:0035473)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|lipoprotein particle receptor binding (GO:0070325)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylcholine binding (GO:0031210)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	14	all_hematologic(175;0.0487)	all_cancers(61;3.31e-09)|all_epithelial(67;8.03e-06)|Breast(348;0.0126)|Melanoma(852;0.0153)|Acute lymphoblastic leukemia(157;0.0257)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0433)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;4.93e-06)|all cancers(92;0.000123)|OV - Ovarian serous cystadenocarcinoma(223;0.149)		ACGTGGCGCCCGATGCCGCTC	0.697																																					p.G203R		Atlas-SNP	.											.	APOA5	34	.	0			c.G607A						.						14	18	17					11																	116661338		2181	4258	6439	SO:0001583	missense	116519	exon4			GGCGCCCGATGCC	AF202889	CCDS8376.2	11q23	2013-01-24			ENSG00000110243	ENSG00000110243		"Apolipoproteins"	17288	protein-coding gene	gene with protein product		606368				11588264, 11577099	Standard	NM_001166598		Approved	RAP3, APOA-V	uc009yzf.3	Q6Q788	OTTHUMG00000046116	ENST00000227665.4:c.607G>A	chr11.hg19:g.116661338C>T	ENSP00000227665:p.Gly203Arg	7.0	0.0		5.0	4.0	NM_001166598	B0YIV9|Q3MIK6|Q6UWK9|Q9UBJ3	Missense_Mutation	SNP	ENST00000227665.4	hg19	CCDS8376.2	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429703	0.62844	.	.	ENSG00000110243	ENST00000227665;ENST00000542499	T;T	0.73789	-0.78;-0.78	4.84	1.92	0.25849	Apolipoprotein/apolipophorin (1);	0.268049	0.26727	N	0.022812	T	0.68174	0.2972	M	0.78223	2.4	0.30936	N	0.726384	B;B	0.27971	0.196;0.068	B;B	0.23852	0.049;0.049	T	0.60712	-0.7209	10	0.14656	T	0.56	-16.5259	9.2766	0.37703	0.0:0.506:0.415:0.079	.	200;203	B0YIW1;Q6Q788	.;APOA5_HUMAN	R	203	ENSP00000227665:G203R;ENSP00000445002:G203R	ENSP00000227665:G203R	G	-	1	0	APOA5	116166548	0.969000	0.33509	0.987000	0.45799	0.916000	0.54674	1.766000	0.38491	0.234000	0.21139	-0.172000	0.13284	GGG	.	.		0.697	APOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106285.2			T	116661338	C	T	116661338	3	4	52	1	0	0	0	0	1	0	0	0	784	652	23	1	497	1	APOA5	11	116661338	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	15664496	116661338	18345178	50	6681										
OR10G8	219869	hgsc.bcm.edu	37	chr11	123900967	123900967	+	Frame_Shift_Del	DEL	T	T	-													0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ctcgggctgctttgtcctgaTagtgctgtcctatgtgtcca							TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr11:123900967delT	ENST00000431524.1	+	1	671	c.638delT	c.(637-639)atafs	p.I213fs		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		TTTGTCCTGATAGTGCTGTCC	0.552																																					p.I213X		Pindel	.											.	OR10G8	132	.	0			c.637delA						.						188	163	172					11																	123900967		2201	4299	6500	SO:0001589	frameshift_variant	219869	exon1			.	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"GPCR / Class A : Olfactory receptors"	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.638delT	chr11.hg19:g.123900967delT	ENSP00000389072:p.Ile213fs	352.0	0.0		295.0	35.0	NM_001004464	B2RNJ3|Q6IEV2	Frame_Shift_Del	DEL	ENST00000431524.1	hg19	CCDS31704.1																																																																																			.	.		0.552	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464		-	123900967	T	-	123900967	7	5	52	1	0	1	0	1	0	0	0	0	10912	1406	49	0	640	0	OR10G8	11	123900967	Frame_Shift_Del	DEL	T	TCGA-BW-A5NP-01A-11D-A27I-10	7239629	123900967	11105549	51	6682										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48389497	48389498	+	In_Frame_Ins	INS	-	-	CACCAGGTT													0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cgtgctggtactcacagagaINScaccaggttcaccaggttca							TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr12:48389497_48389498insCACCAGGTT	ENST00000380518.3	-	10	867_868	c.703_704insAACCTGGTG	c.(703-705)gtc>gAACCTGGTGtc	p.234_235insEPG	COL2A1_ENST00000337299.6_In_Frame_Ins_p.165_166insEPG	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	234	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	ACTCACAGAGAcaccaggttca	0.525																																					p.V235delinsEPGV		Atlas-INDEL	.											.	COL2A1	368	.	0			c.704_705insAACCTGGTG						.																																			SO:0001652	inframe_insertion	1280	exon10			.	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.695_703dupAACCTGGTG	chr12.hg19:g.48389498_48389506dupCACCAGGTT	ENSP00000369889:p.Glu232_Gly234dup	291.0	0.0		217.0	19.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	In_Frame_Ins	INS	ENST00000380518.3	hg19	CCDS41778.1																																																																																			.	.		0.525	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		CACCAGGTT	48389498	-	CACCAGGTT	48389497	7	5	52	1	0	1	1	0	0	0	0	0	3689	275	10	0	3939	0	COL2A1	12	48389497	In_Frame_Ins	INS	-	TCGA-BW-A5NP-01A-11D-A27I-10		48389497	85462398	52	6683										
AQP5	362	hgsc.bcm.edu	37	chr12	50358790	50358790	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	accaggttttctgggtagggCccatcgtgggggcggtcctg	17	10	1	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr12:50358790C>T	ENST00000293599.6	+	4	776	c.628C>T	c.(628-630)Ccc>Tcc	p.P210S	RP11-469H8.6_ENST00000552379.1_RNA|RP11-469H8.6_ENST00000550214.1_RNA|AQP6_ENST00000551733.1_5'Flank|RP11-469H8.6_ENST00000550530.1_RNA	NM_001651.2	NP_001642.1	P55064	AQP5_HUMAN	aquaporin 5	210					camera-type eye morphogenesis (GO:0048593)|carbon dioxide transport (GO:0015670)|excretion (GO:0007588)|odontogenesis (GO:0042476)|pancreatic juice secretion (GO:0030157)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)			large_intestine(1)|lung(3)	4						CTGGGTAGGGCCCATCGTGGG	0.617																																					p.P210S		Atlas-SNP	.											.	AQP5	19	.	0			c.C628T						.						82	84	83					12																	50358790		2203	4300	6503	SO:0001583	missense	362	exon4			GTAGGGCCCATCG	U46569	CCDS8793.1	12q13	2013-09-10				ENSG00000161798		"Ion channels / Aquaporins"	638	protein-coding gene	gene with protein product		600442				8621489, 23830519	Standard	NM_001651		Approved		uc001rvo.3	P55064	OTTHUMG00000169710	ENST00000293599.6:c.628C>T	chr12.hg19:g.50358790C>T	ENSP00000293599:p.Pro210Ser	151.0	0.0		82.0	49.0	NM_001651	Q6FGW8	Missense_Mutation	SNP	ENST00000293599.6	hg19	CCDS8793.1	.	.	.	.	.	.	.	.	.	.	C	17.69	3.452005	0.63290	.	.	ENSG00000161798	ENST00000293599	D	0.96522	-4.04	5.03	5.03	0.67393	Aquaporin-like (2);	0.094674	0.45867	D	0.000340	D	0.98792	0.9593	H	0.99325	4.515	0.54753	D	0.999989	P	0.48503	0.911	P	0.56474	0.799	D	0.99445	1.0939	10	0.87932	D	0	9.2576	16.2949	0.82765	0.0:1.0:0.0:0.0	.	210	P55064	AQP5_HUMAN	S	210	ENSP00000293599:P210S	ENSP00000293599:P210S	P	+	1	0	AQP5	48645057	1.000000	0.71417	0.996000	0.52242	0.869000	0.49853	5.116000	0.64661	2.536000	0.85505	0.555000	0.69702	CCC	.	.		0.617	AQP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405542.2	NM_001651		T	50358790	C	T	50358790	3	4	52	1	0	0	0	0	1	0	0	0	829	739	26	3	642	3	AQP5	12	50358790	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	1969293	50358790	83493105	53	6684										
FLT1	2321	hgsc.bcm.edu	37	chr13	28964106	28964106	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tgctaatactgtagtgcattGttctgttattaactgtccgc	8	8	1	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr13:28964106G>C	ENST00000282397.4	-	13	2047	c.1796C>G	c.(1795-1797)aCa>aGa	p.T599R	FLT1_ENST00000541932.1_Missense_Mutation_p.T599R	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	599	Ig-like C2-type 6.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GTAGTGCATTGTTCTGTTATT	0.418																																					p.T599R		Atlas-SNP	.											.	FLT1	393	.	0			c.C1796G						.						281	238	253					13																	28964106		2203	4300	6503	SO:0001583	missense	2321	exon13			TGCATTGTTCTGT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1796C>G	chr13.hg19:g.28964106G>C	ENSP00000282397:p.Thr599Arg	230.0	0.0		238.0	27.0	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	hg19	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.003303	0.35320	.	.	ENSG00000102755	ENST00000282397;ENST00000541932	T;T	0.75477	-0.94;-0.38	6.06	5.21	0.72293	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.255299	0.39834	N	0.001243	T	0.72938	0.3523	M	0.66939	2.045	0.80722	D	1	B;B;B	0.31209	0.313;0.313;0.02	B;B;B	0.32090	0.14;0.14;0.018	T	0.69409	-0.5153	10	0.17832	T	0.49	.	17.4133	0.87493	0.0:0.1246:0.8754:0.0	.	599;599;599	P17948-3;P17948-2;P17948	.;.;VGFR1_HUMAN	R	599	ENSP00000282397:T599R;ENSP00000437631:T599R	ENSP00000282397:T599R	T	-	2	0	FLT1	27862106	1.000000	0.71417	0.528000	0.27938	0.963000	0.63663	5.072000	0.64389	1.545000	0.49373	0.650000	0.86243	ACA	.	.		0.418	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	28964106	G	C	28964106	3	2	52	1	0	0	0	0	1	0	0	0	5949	1377	48	4	2477	4	FLT1	13	28964106	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10		28964106	86205772	54	6685										
MGA	23269	hgsc.bcm.edu	37	chr15	42054412	42054412	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gcacaaaaaagaaaaaagaaGatgggatcagatgagtttga	11	3	1	6			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr15:42054412G>A	ENST00000570161.1	+	21	7596	c.7596G>A	c.(7594-7596)aaG>aaA	p.K2532K	MGA_ENST00000389936.4_Silent_p.K2493K|MGA_ENST00000545763.1_Silent_p.K2323K|MGA_ENST00000219905.7_Silent_p.K2532K|MGA_ENST00000566586.1_Silent_p.K2323K			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GAAAAAAGAAGATGGGATCAG	0.373																																					p.K2532K		Atlas-SNP	.											.	MGA	264	.	0			c.G7596A						.						72	71	72					15																	42054412		1872	4113	5985	SO:0001819	synonymous_variant	23269	exon22			AAAGAAGATGGGA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7596G>A	chr15.hg19:g.42054412G>A		188.0	1.0		170.0	94.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.373	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42054412	G	A	42054412	2	1	52	1	0	0	0	0	0	0	0	1	9549	933	33	3		3	MGA	15	42054412	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10		42054412	60476980	55	6686										
DUOX2	50506	hgsc.bcm.edu	37	chr15	45387780	45387780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gatggccctctccaaacggtCcatcaaggtacagctgccaa	9	14	2	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr15:45387780C>T	ENST00000603300.1	-	31	4296	c.4094G>A	c.(4093-4095)gGa>gAa	p.G1365E	DUOX2_ENST00000389039.6_Missense_Mutation_p.G1365E	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1365	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		TCCAAACGGTCCATCAAGGTA	0.567																																					p.G1365E		Atlas-SNP	.											.	DUOX2	137	.	0			c.G4094A						.						74	71	72					15																	45387780		2198	4298	6496	SO:0001583	missense	50506	exon31			AACGGTCCATCAA	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"EF-hand domain containing"	13273	protein-coding gene	gene with protein product	"dual oxidase-like domains 2", "nicotinamide adenine dinucleotide phosphate oxidase", "flavoprotein NADPH oxidase", "NADPH thyroid oxidase 2", "NADH/NADPH thyroid oxidase p138-tox", "NADPH oxidase/peroxidase DUOX2"	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.4094G>A	chr15.hg19:g.45387780C>T	ENSP00000475084:p.Gly1365Glu	127.0	0.0		87.0	39.0	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	hg19	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	C	32	5.139334	0.94560	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.84	5.84	0.93424	Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.90065	0.6897	H	0.96720	3.87	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.92740	0.6207	9	0.87932	D	0	-8.9646	19.116	0.93340	0.0:1.0:0.0:0.0	.	1365	Q9NRD8	DUOX2_HUMAN	E	1365	.	ENSP00000373691:G1365E	G	-	2	0	DUOX2	43175072	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.811000	0.86092	2.768000	0.95171	0.561000	0.74099	GGA	.	.		0.567	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		T	45387780	C	T	45387780	3	4	52	1	0	0	0	0	1	0	0	0	4803	855	30	3	568	3	DUOX2	15	45387780	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	3333368	45387780	57143612	56	6687										
SCAPER	49855	hgsc.bcm.edu	37	chr15	77025616	77025616	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tttcttcctgtcttctctgaCgctcttcctgtagctcatta	5	13	5	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr15:77025616C>T	ENST00000563290.1	-	16	2071	c.1976G>A	c.(1975-1977)cGt>cAt	p.R659H	SCAPER_ENST00000538941.2_Missense_Mutation_p.R413H|SCAPER_ENST00000324767.7_Missense_Mutation_p.R659H			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	659	Glu-rich.					endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						TCTTCTCTGACGCTCTTCCTG	0.393																																					p.R659H		Atlas-SNP	.											SCAPER,colon,carcinoma,0,1	SCAPER	160	.	0			c.G1976A						.						129	116	120					15																	77025616		1903	4136	6039	SO:0001583	missense	49855	exon15			CTCTGACGCTCTT	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.1976G>A	chr15.hg19:g.77025616C>T	ENSP00000454973:p.Arg659His	117.0	0.0		109.0	44.0	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	hg19	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	C	34	5.298994	0.95574	.	.	ENSG00000140386	ENST00000324767;ENST00000538941;ENST00000303521	T;T	0.48201	0.91;0.82	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.71048	0.3294	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73081	-0.4095	10	0.72032	D	0.01	.	19.7152	0.96115	0.0:1.0:0.0:0.0	.	680;413	Q9BY12-2;F5H7X8	.;.	H	659;413;681	ENSP00000326924:R659H;ENSP00000442190:R413H	ENSP00000303560:R681H	R	-	2	0	SCAPER	74812671	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.657000	0.67996	2.653000	0.90120	0.650000	0.86243	CGT	.	.		0.393	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		T	77025616	C	T	77025616	3	4	52	1	0	0	0	0	1	0	0	0	13893	536	19	1	2294	1	SCAPER	15	77025616	Missense_Mutation	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10	31637836	77025616	25505776	57	6688										
AXIN1	8312	hgsc.bcm.edu	37	chr16	347721	347721	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cactgacaggcgcacgctcaCctgtgggcgaggccatcact	12	15	2	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr16:347721C>T	ENST00000262320.3	-	6	2156		c.e6+1		AXIN1_ENST00000354866.3_Splice_Site|AXIN1_ENST00000481769.1_5'Flank	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1						activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CGCACGCTCACCTGTGGGCGA	0.642																																					.		Atlas-SNP	.											.	AXIN1	290	.	0			c.1784+1G>A						.						19	20	19					16																	347721		2201	4297	6498	SO:0001630	splice_region_variant	8312	exon7			CGCTCACCTGTGG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1784+1G>A	chr16.hg19:g.347721C>T		16.0	0.0		7.0	7.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Splice_Site	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.981479	0.34942	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5709	0.91135	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AXIN1	287722	1.000000	0.71417	0.999000	0.59377	0.173000	0.22820	4.880000	0.63107	2.477000	0.83638	0.472000	0.43445	.	.	.		0.642	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		Intron	T	347721	C	T	347721	5	4	52	1	0	0	0	0	0	0	1	0	1236	521	18	3	827	3	AXIN1	16	347721	Splice_Site	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10		347721	90007032	58	6689										
BTBD12	84464	hgsc.bcm.edu	37	chr16	3642739	3642739	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gctcagagctaaggccaggaGgaaggccagtgtccgcagtg	16	10	1	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr16:3642739G>T	ENST00000294008.3	-	11	2928	c.2288C>A	c.(2287-2289)cCt>cAt	p.P763H		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	763	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.|Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						AAGGCCAGGAGGAAGGCCAGT	0.602								Direct reversal of damage																													p.P763H		Atlas-SNP	.											.	SLX4	173	.	0			c.C2288A						.						61	56	57					16																	3642739		2197	4300	6497	SO:0001583	missense	84464	exon11			CCAGGAGGAAGGC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2288C>A	chr16.hg19:g.3642739G>T	ENSP00000294008:p.Pro763His	131.0	0.0		54.0	4.0	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	hg19	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	G	15.51	2.855052	0.51376	.	.	ENSG00000188827	ENST00000294008	T	0.23147	1.92	5.61	5.61	0.85477	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.431990	0.23826	N	0.044192	T	0.60637	0.2284	M	0.89715	3.055	0.22199	N	0.99929	D	0.89917	1.0	D	0.77557	0.99	T	0.60419	-0.7267	10	0.87932	D	0	.	18.196	0.89822	0.0:0.0:1.0:0.0	.	763	Q8IY92	SLX4_HUMAN	H	763	ENSP00000294008:P763H	ENSP00000294008:P763H	P	-	2	0	SLX4	3582740	0.400000	0.25295	0.012000	0.15200	0.006000	0.05464	2.817000	0.48034	2.652000	0.90054	0.655000	0.94253	CCT	.	.		0.602	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		T	3642739	G	T	3642739	3	4	52	1	0	0	0	0	1	0	0	0	1542	1000	35	3	3236	3	BTBD12	16	3642739	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	3295018	3642739	86712014	59	6690										
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76482022	76482022	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	aattcaaaaccatgcagagtGatgggattctactccacagg	9	9	2	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr16:76482022G>C	ENST00000476707.1	+	4	800	c.661G>C	c.(661-663)Gat>Cat	p.D221H	CNTNAP4_ENST00000377504.4_Missense_Mutation_p.D217H|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.D217H|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.D193H			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	218	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						CATGCAGAGTGATGGGATTCT	0.363																																					p.D193H		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.G577C						.						87	88	87					16																	76482022		2198	4300	6498	SO:0001583	missense	85445	exon5			CAGAGTGATGGGA	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.661G>C	chr16.hg19:g.76482022G>C	ENSP00000417628:p.Asp221His	146.0	0.0		77.0	70.0	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.68	3.873469	0.72180	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	5.11	5.11	0.69529	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.41396	D	0.000885	D	0.89248	0.6661	.	.	.	0.41837	D	0.990101	P;D;P;P	0.56521	0.755;0.976;0.755;0.924	P;P;P;D	0.63192	0.489;0.872;0.507;0.912	D	0.90583	0.4531	9	0.87932	D	0	.	18.7371	0.91759	0.0:0.0:1.0:0.0	.	193;221;193;218	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	H	217;217;193;221	ENSP00000306893:D217H;ENSP00000439733:D217H;ENSP00000418741:D193H;ENSP00000417628:D221H	ENSP00000306893:D217H	D	+	1	0	CNTNAP4	75039523	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	2.291000	0.43540	2.654000	0.90174	0.563000	0.77884	GAT	.	.		0.363	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		C	76482022	G	C	76482022	3	2	52	1	0	0	0	0	1	0	0	0	3651	1290	45	4	683	4	CNTNAP4	16	76482022	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	72839283	76482022	13872731	60	6691										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18055202	18055202	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	atgaagcggccagaccctcaTgaggaggccctgatgatcct	12	12	1	5			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr17:18055202T>A	ENST00000205890.5	+	41	8168	c.7830T>A	c.(7828-7830)caT>caA	p.H2610Q	MYO15A_ENST00000418233.3_5'Flank|MYO15A_ENST00000585180.1_5'Flank	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2610	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CAGACCCTCATGAGGAGGCCC	0.592																																					p.H2610Q		Atlas-SNP	.											.	MYO15A	268	.	0			c.T7830A						.						40	44	43					17																	18055202		1989	4166	6155	SO:0001583	missense	51168	exon40			CCCTCATGAGGAG	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.7830T>A	chr17.hg19:g.18055202T>A	ENSP00000205890:p.His2610Gln	183.0	0.0		139.0	39.0	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.159376	0.57368	.	.	ENSG00000091536	ENST00000205890	D	0.88896	-2.44	5.24	-3.08	0.05347	.	.	.	.	.	D	0.90748	0.7096	M	0.61703	1.905	0.80722	D	1	D	0.69078	0.997	P	0.60789	0.879	D	0.88022	0.2769	9	0.56958	D	0.05	.	12.6386	0.56696	0.0:0.4057:0.0:0.5943	.	2610	Q9UKN7	MYO15_HUMAN	Q	2610	ENSP00000205890:H2610Q	ENSP00000205890:H2610Q	H	+	3	2	MYO15A	17995927	0.000000	0.05858	0.865000	0.33974	0.964000	0.63967	-2.442000	0.01014	-1.109000	0.02996	-0.215000	0.12644	CAT	.	.		0.592	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		A	18055202	T	A	18055202	3	1	52	1	0	0	0	0	1	0	0	0	10072	1461	51	4	7984	4	MYO15A	17	18055202	Missense_Mutation	SNP	T	TCGA-BW-A5NP-01A-11D-A27I-10		18055202	63140008	61	6692										
SOST	50964	hgsc.bcm.edu	37	chr17	41836014	41836014	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tcggggatgatttccgtggcAtcattcttgaacgcctgcca	11	11	2	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr17:41836014A>T	ENST00000301691.2	-	1	142	c.96T>A	c.(94-96)gaT>gaA	p.D32E		NM_025237.2	NP_079513.1	Q9BQB4	SOST_HUMAN	sclerostin	32					cellular response to parathyroid hormone stimulus (GO:0071374)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000054)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|response to mechanical stimulus (GO:0009612)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|transcription factor binding (GO:0008134)			large_intestine(2)|lung(3)|prostate(1)	6		Breast(137;0.00725)		UCEC - Uterine corpus endometrioid carcinoma (308;0.177)|BRCA - Breast invasive adenocarcinoma(366;0.0741)		TTTCCGTGGCATCATTCTTGA	0.627																																					p.D32E		Atlas-SNP	.											.	SOST	19	.	0			c.T96A						.						91	82	85					17																	41836014		2203	4300	6503	SO:0001583	missense	50964	exon1			CGTGGCATCATTC	AF326736	CCDS11468.1	17q12-q21	2014-06-28	2010-04-28			ENSG00000167941			13771	protein-coding gene	gene with protein product		605740	"sclerosteosis"			11179006, 11181578	Standard	NM_025237		Approved	VBCH	uc002iec.1	Q9BQB4		ENST00000301691.2:c.96T>A	chr17.hg19:g.41836014A>T	ENSP00000301691:p.Asp32Glu	100.0	0.0		71.0	25.0	NM_025237	Q495N9	Missense_Mutation	SNP	ENST00000301691.2	hg19	CCDS11468.1	.	.	.	.	.	.	.	.	.	.	A	19.73	3.881328	0.72294	.	.	ENSG00000167941	ENST00000301691	D	0.83506	-1.73	4.36	-1.16	0.09678	.	0.000000	0.85682	D	0.000000	D	0.87067	0.6085	M	0.68317	2.08	0.44214	D	0.997045	D	0.62365	0.991	D	0.74023	0.982	D	0.84361	0.0538	10	0.87932	D	0	-4.4389	9.5227	0.39145	0.5418:0.0:0.4582:0.0	.	32	Q9BQB4	SOST_HUMAN	E	32	ENSP00000301691:D32E	ENSP00000301691:D32E	D	-	3	2	SOST	39191540	0.951000	0.32395	0.955000	0.39395	0.965000	0.64279	0.206000	0.17375	-0.452000	0.07087	0.454000	0.30748	GAT	.	.		0.627	SOST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453502.1	NM_025237		T	41836014	A	T	41836014	3	4	52	1	0	0	0	0	1	0	0	0	14953	214	8	4	553	4	SOST	17	41836014	Missense_Mutation	SNP	A	TCGA-BW-A5NP-01A-11D-A27I-10	23780812	41836014	39359196	62	6693										
DTNA	1837	hgsc.bcm.edu	37	chr18	32428268	32428268	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	tgttcttaatagcatgcttgAgagttcaaaccggcttgatg	10	7	2	2	rs374916548		TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr18:32428268A>G	ENST00000399113.3	+	13	1274	c.1274A>G	c.(1273-1275)gAg>gGg	p.E425G	DTNA_ENST00000597674.1_Missense_Mutation_p.E47G|DTNA_ENST00000595022.1_Missense_Mutation_p.E365G|DTNA_ENST00000269190.7_Missense_Mutation_p.E426G|DTNA_ENST00000556414.3_Missense_Mutation_p.E77G|DTNA_ENST00000399121.5_Missense_Mutation_p.E365G|DTNA_ENST00000399097.3_Missense_Mutation_p.E73G|DTNA_ENST00000596745.1_Intron|DTNA_ENST00000348997.5_Missense_Mutation_p.E422G|DTNA_ENST00000599844.1_Missense_Mutation_p.E47G|DTNA_ENST00000601125.1_Missense_Mutation_p.E47G|DTNA_ENST00000598334.1_Missense_Mutation_p.E365G|DTNA_ENST00000598774.1_Missense_Mutation_p.E368G|DTNA_ENST00000591182.1_Missense_Mutation_p.E73G|DTNA_ENST00000444659.1_Missense_Mutation_p.E425G|DTNA_ENST00000283365.9_Missense_Mutation_p.E368G|DTNA_ENST00000269191.6_Missense_Mutation_p.E425G|DTNA_ENST00000598142.1_Missense_Mutation_p.E368G|DTNA_ENST00000269192.7_Missense_Mutation_p.E134G|DTNA_ENST00000597599.1_Missense_Mutation_p.E365G			Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	425	Syntrophin-binding region.				neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						AGCATGCTTGAGAGTTCAAAC	0.438																																					p.E425G		Atlas-SNP	.											.	DTNA	321	.	0			c.A1274G						.	A	,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	0,4406		0,0,2203	105	97	100		,140,218,1103,1265,1103,1274,1274,230,344,401,1094,1094,1094,1094	5.4	1	18		100	2,8598	2.2+/-6.3	0,2,4298	no	intron,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	DTNA	NM_001198945.1,NM_032981.4,NM_032980.3,NM_032979.4,NM_032978.6,NM_032975.3,NM_001391.5,NM_001390.4,NM_001198944.1,NM_001198943.1,NM_001198942.1,NM_001198941.1,NM_001198940.1,NM_001198939.1,NM_001198938.1	,98,98,98,98,98,98,98,98,98,98,98,98,98,98	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	,47/193,73/392,368/514,422/568,368/687,425/571,425/744,77/396,115/434,134/453,365/511,365/684,365/691,365/725	32428268	2,13004	2203	4300	6503	SO:0001583	missense	1837	exon13			TGCTTGAGAGTTC	U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769			3057	protein-coding gene	gene with protein product	"dystrophin-related protein 3"	601239				8081380, 15834686	Standard	NM_001390		Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399113.3:c.1274A>G	chr18.hg19:g.32428268A>G	ENSP00000382064:p.Glu425Gly	87.0	0.0		45.0	42.0	NM_001390	A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	Missense_Mutation	SNP	ENST00000399113.3	hg19	CCDS59311.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.563243	0.65538	0.0	2.33E-4	ENSG00000134769	ENST00000399119;ENST00000283365;ENST00000399114;ENST00000269190;ENST00000399097;ENST00000348997;ENST00000399121;ENST00000444659;ENST00000269191;ENST00000399113;ENST00000269192;ENST00000450377;ENST00000556414	D;D;D;D;D;D;D;D;D	0.83163	-1.64;-1.69;-1.69;-1.66;-1.69;-1.69;-1.69;-1.69;-1.64	5.39	5.39	0.77823	.	0.287902	0.38897	N	0.001537	T	0.74038	0.3664	L	0.33485	1.01	0.47819	D	0.999527	B;B;B;P;B;B;B;B;B;P;B;B;B;B	0.41008	0.057;0.375;0.007;0.735;0.05;0.246;0.0;0.0;0.246;0.454;0.0;0.136;0.001;0.081	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.35727	0.096;0.197;0.01;0.209;0.089;0.138;0.001;0.004;0.157;0.138;0.001;0.04;0.004;0.046	T	0.73672	-0.3909	10	0.27785	T	0.31	-6.0175	15.4146	0.74956	1.0:0.0:0.0:0.0	.	77;134;115;47;425;425;365;368;73;422;365;376;368;368	B4DIU8;B4DIR0;B7Z3X3;Q9Y4J8-8;Q9Y4J8;Q9Y4J8-3;A8K541;F5H5C1;Q9Y4J8-6;Q9Y4J8-4;E9PEH8;Q59GK7;Q9Y4J8-2;Q9Y4J8-5	.;.;.;.;DTNA_HUMAN;.;.;.;.;.;.;.;.;.	G	368;368;365;426;73;422;425;425;425;425;134;73;77	ENSP00000283365:E368G;ENSP00000269190:E426G;ENSP00000336682:E422G;ENSP00000382072:E425G;ENSP00000405819:E425G;ENSP00000269191:E425G;ENSP00000382064:E425G;ENSP00000269192:E134G;ENSP00000452255:E77G	ENSP00000269190:E426G	E	+	2	0	DTNA	30682266	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	8.490000	0.90464	2.048000	0.60808	0.528000	0.53228	GAG	.	.		0.438	DTNA-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255422.2	NM_001390		G	32428268	A	G	32428268	3	3	52	1	0	0	0	0	1	0	0	0	4790	304	11	2	1359	2	DTNA	18	32428268	Missense_Mutation	SNP	A	TCGA-BW-A5NP-01A-11D-A27I-10		32428268	45648980	63	6694										
GTF2F1	2962	hgsc.bcm.edu	37	chr19	6381584	6381584	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	cccttgggcccctcctcctgCtgcggcgccttggccttgct	11	19	0	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr19:6381584C>T	ENST00000394456.5	-	8	1343	c.879G>A	c.(877-879)caG>caA	p.Q293Q	PSPN_ENST00000597721.1_5'Flank|GTF2F1_ENST00000429701.2_Silent_p.Q208Q	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	293	Glu-rich.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						CCTCCTCCTGCTGCGGCGCCT	0.677																																					p.Q293Q		Atlas-SNP	.											.	GTF2F1	39	.	0			c.G879A						.						43	45	44					19																	6381584		2202	4300	6502	SO:0001819	synonymous_variant	2962	exon8			CTCCTGCTGCGGC		CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"General transcription factors"	4652	protein-coding gene	gene with protein product		189968	"general transcription factor IIF, polypeptide 1 (74kD subunit)"			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.879G>A	chr19.hg19:g.6381584C>T		15.0	0.0		9.0	6.0	NM_002096	B2RCS0|Q9BWN0	Silent	SNP	ENST00000394456.5	hg19	CCDS12165.1																																																																																			.	.		0.677	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096		T	6381584	C	T	6381584	2	4	52	1	0	0	0	0	0	0	0	1	6867	796	28	3		3	GTF2F1	19	6381584	Silent	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10		6381584	52747399	64	6695										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42839240	42839240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ttgggacgtgcctgtgacctGcacctgtgggagaaccaggg	16	10	0	2			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr19:42839240G>A	ENST00000251268.6	+	4	612	c.612G>A	c.(610-612)ctG>ctA	p.L204L	MEGF8_ENST00000334370.4_Silent_p.L204L	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	204					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CCTGTGACCTGCACCTGTGGG	0.627																																					p.L204L		Atlas-SNP	.											.	MEGF8	358	.	0			c.G612A						.						33	38	36					19																	42839240		2050	4198	6248	SO:0001819	synonymous_variant	1954	exon4			TGACCTGCACCTG	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.612G>A	chr19.hg19:g.42839240G>A		104.0	0.0		54.0	8.0	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	hg19																																																																																				.	.		0.627	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		A	42839240	G	A	42839240	2	1	52	1	0	0	0	0	0	0	0	1	9472	1306	46	3		3	MEGF8	19	42839240	Silent	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	36457656	42839240	16289743	65	6696										
ZNF321	399669	hgsc.bcm.edu	37	chr19	53432442	53432442	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gcctttgatcatgtcggtctGtactaccagtcaactctttg	8	11	4	1			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr19:53432442G>A	ENST00000391777.3	-	4	537	c.416C>T	c.(415-417)aCa>aTa	p.T139I	ZNF816_ENST00000549216.1_Missense_Mutation_p.T70I|ZNF816_ENST00000434371.2_Missense_Mutation_p.T139I|ZNF816-ZNF321P_ENST00000313956.4_RNA			Q8N8H1	ZN321_HUMAN	zinc finger protein 321, pseudogene	70										endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						ATGTCGGTCTGTACTACCAGT	0.423																																					p.T139I		Atlas-SNP	.											.	.	.	.	0			c.C416T						.						191	189	190					19																	53432442		2203	4300	6503	SO:0001583	missense	100529240	exon4			CGGTCTGTACTAC	AK096828		19q13.4	2013-01-08	2011-04-19	2011-04-19	ENSG00000221874	ENSG00000221874			13827	pseudogene	pseudogene			"zinc finger protein 321"	ZNF321			Standard	NR_037805		Approved	MGC35402		Q8N8H1	OTTHUMG00000167760	ENST00000391777.3:c.416C>T	chr19.hg19:g.53432442G>A	ENSP00000375656:p.Thr139Ile	174.0	0.0		148.0	72.0	NM_001202473	B7ZB38|Q68DZ0|Q86SS5	Missense_Mutation	SNP	ENST00000391777.3	hg19	CCDS56101.1	.	.	.	.	.	.	.	.	.	.	g	6.659	0.490103	0.12702	.	.	ENSG00000180257;ENSG00000180257;ENSG00000221874	ENST00000549216;ENST00000434371;ENST00000391777	T;T;T	0.01947	4.54;5.79;5.79	1.66	-3.13	0.05266	.	.	.	.	.	T	0.02380	0.0073	L	0.54323	1.7	0.09310	N	1	B	0.34161	0.439	B	0.35727	0.209	T	0.40496	-0.9560	9	0.35671	T	0.21	.	2.7181	0.05193	0.0:0.3377:0.2635:0.3988	.	70	Q8N8H1	ZN321_HUMAN	I	70;139;139	ENSP00000449832:T70I;ENSP00000438519:T139I;ENSP00000375656:T139I	ENSP00000375656:T139I	T	-	2	0	ZNF321P;ZNF816	58124254	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-2.623000	0.00876	-0.438000	0.07232	0.134000	0.15878	ACA	.	.		0.423	ZNF321P-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000396130.1	NR_037805		A	53432442	G	A	53432442	3	1	52	1	0	0	0	0	1	0	0	0	17855	1377	48	3	289	3	ZNF321	19	53432442	Missense_Mutation	SNP	G	TCGA-BW-A5NP-01A-11D-A27I-10	10593202	53432442	5696541	66	6697										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41427743	41427743	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	gtctgctgttgcttgcttaaCgtatctgaagtccgggtatt	11	8	2	1	rs374386822		TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chr21:41427743C>A	ENST00000400454.1	-	29	5421	c.4944G>T	c.(4942-4944)acG>acT	p.T1648T		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1648					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GCTTGCTTAACGTATCTGAAG	0.448																																					p.T1648T	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.G4944T						.						194	187	189					21																	41427743		1938	4133	6071	SO:0001819	synonymous_variant	1826	exon29			GCTTAACGTATCT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4944G>T	chr21.hg19:g.41427743C>A		225.0	0.0		152.0	79.0	NM_001271534	O60468	Silent	SNP	ENST00000400454.1	hg19	CCDS42929.1																																																																																			.	.		0.448	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41427743	C	A	41427743	2	1	52	1	0	0	0	0	0	0	0	1	4770	523	19	1		1	DSCAM	21	41427743	Silent	SNP	C	TCGA-BW-A5NP-01A-11D-A27I-10		41427743	6702152	67	6698										
BCORL1	63035	hgsc.bcm.edu	37	chrX	129147853	129147853	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	catcttccggcccaccttctAcccccaccctcatccccgcc	3	25	3	0			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chrX:129147853A>G	ENST00000218147.7	+	4	1302	c.1105A>G	c.(1105-1107)Acc>Gcc	p.T369A	BCORL1_ENST00000303743.5_Missense_Mutation_p.T369A|BCORL1_ENST00000540052.1_Missense_Mutation_p.T369A|BCORL1_ENST00000359304.2_Missense_Mutation_p.T369A			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	369	Pro-rich.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						cccaccttctacccccaccct	0.677																																					p.T369A		Atlas-SNP	.											.	BCORL1	213	.	0			c.A1105G						.						25	23	23					X																	129147853		2055	4017	6072	SO:0001583	missense	63035	exon3			CCTTCTACCCCCA	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.1105A>G	chrX.hg19:g.129147853A>G	ENSP00000218147:p.Thr369Ala	32.0	0.0		21.0	12.0	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Missense_Mutation	SNP	ENST00000218147.7	hg19	CCDS14616.1	.	.	.	.	.	.	.	.	.	.	A	11.60	1.685650	0.29962	.	.	ENSG00000085185	ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052	T;T;T;T	0.39592	1.07;1.44;1.07;1.07	4.34	3.19	0.36642	.	0.000000	0.34484	N	0.003931	T	0.17323	0.0416	N	0.08118	0	0.20873	N	0.999839	B;B	0.16603	0.018;0.005	B;B	0.10450	0.005;0.001	T	0.09037	-1.0693	9	.	.	.	-15.7686	3.5577	0.07870	0.4758:0.3139:0.2103:0.0	.	369;369	Q5H9F3-2;Q5H9F3	.;BCORL_HUMAN	A	369	ENSP00000218147:T369A;ENSP00000307541:T369A;ENSP00000352253:T369A;ENSP00000437775:T369A	.	T	+	1	0	BCORL1	128975534	0.000000	0.05858	0.870000	0.34147	0.922000	0.55478	0.013000	0.13310	1.715000	0.51383	0.425000	0.28330	ACC	.	.		0.677	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		G	129147853	A	G	129147853	3	3	52	1	0	0	0	0	1	0	0	0	1387	391	14	2	1115	2	BCORL1	23	129147853	Missense_Mutation	SNP	A	TCGA-BW-A5NP-01A-11D-A27I-10		129147853	26122707	68	6699										
BCORL1	63035	hgsc.bcm.edu	37	chrX	129162763	129162763	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.072463768115942	5	1	0.927857142857143	1.62375	0.838064516129032	0.265734265734266	0.917767417767419	0	ggaagagccagcctgccttgAaaattcagaaaagccatcag	10	10	2	3			TCGA-BW-A5NP-01A-11D-A27I-10	TCGA-BW-A5NP-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c00925b-7328-4db0-b930-04aab2d80719	600ba105-b0f1-4fba-b1ec-0bbfe622e6cf	g.chrX:129162763A>T	ENST00000218147.7	+	8	4429	c.4232A>T	c.(4231-4233)gAa>gTa	p.E1411V	BCORL1_ENST00000303743.5_Missense_Mutation_p.E1411V|BCORL1_ENST00000540052.1_Missense_Mutation_p.E1411V|BCORL1_ENST00000359304.2_Missense_Mutation_p.E1281V			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	1411					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						GCCTGCCTTGAAAATTCAGAA	0.488											OREG0019921	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E1411V		Atlas-SNP	.											.	BCORL1	213	.	0			c.A4232T						.						83	78	80					X																	129162763		2203	4300	6503	SO:0001583	missense	63035	exon7			GCCTTGAAAATTC	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.4232A>T	chrX.hg19:g.129162763A>T	ENSP00000218147:p.Glu1411Val	199.0	0.0	1570	174.0	91.0	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Missense_Mutation	SNP	ENST00000218147.7	hg19	CCDS14616.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.89|17.89	3.498805|3.498805	0.64298|0.64298	.|.	.|.	ENSG00000085185|ENSG00000085185	ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052;ENST00000456822|ENST00000441294	T;T;T;T;T|.	0.48836|.	0.8;1.2;0.92;0.8;1.26|.	5.89|5.89	3.19|3.19	0.36642|0.36642	.|.	0.000000|.	0.37857|.	N|.	0.001919|.	T|.	0.41119|.	0.1145|.	L|L	0.46819|0.46819	1.47|1.47	0.09310|0.09310	N|N	0.999999|0.999999	P;D;D|.	0.71674|.	0.718;0.998;0.997|.	B;D;D|.	0.66351|.	0.346;0.943;0.939|.	T|.	0.23154|.	-1.0196|.	10|.	0.62326|.	D|.	0.03|.	-5.8609|-5.8609	9.3443|9.3443	0.38098|0.38098	0.8197:0.0:0.1803:0.0|0.8197:0.0:0.1803:0.0	.|.	1281;1411;1411|.	Q5H9F3-2;Q5H9F3-3;Q5H9F3|.	.;.;BCORL_HUMAN|.	V|C	1411;1411;1281;1411;1011|716	ENSP00000218147:E1411V;ENSP00000307541:E1411V;ENSP00000352253:E1281V;ENSP00000437775:E1411V;ENSP00000399483:E1011V|.	ENSP00000218147:E1411V|.	E|X	+|+	2|3	0|0	BCORL1|BCORL1	128990444|128990444	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.996000|0.996000	0.88848|0.88848	2.822000|2.822000	0.48073|0.48073	0.838000|0.838000	0.34948|0.34948	0.486000|0.486000	0.48141|0.48141	GAA|TGA	.	.		0.488	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		T	129162763	A	T	129162763	3	4	52	1	0	0	0	0	1	0	0	0	1387	246	9	4	4258	4	BCORL1	23	129162763	Missense_Mutation	SNP	A	TCGA-BW-A5NP-01A-11D-A27I-10	14910	129162763	26107797	69	6700										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27106299	27106300	+	Frame_Shift_Ins	INS	-	-	CTGGA													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	agaccccactgtgtacccttINSctggactggcaggattctct					rs372543523		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:27106299_27106300insCTGGA	ENST00000324856.7	+	20	6281_6282	c.5910_5911insCTGGA	c.(5911-5913)ctgfs	p.-1972fs	ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.-300fs|ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.-1755fs|ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.-1589fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)						androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TGTGTACCCTTCTGGACTGGCA	0.515			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.L1970fs		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.5910_5911insCTGGA						.																																			SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5911_5915dupCTGGA	chr1.hg19:g.27106300_27106304dupCTGGA	ENSP00000320485:p.Asp1972fs	103.0	0.0		106.0	22.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.515	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		CTGGA	27106300	-	CTGGA	27106299	7	5	53	1	0	1	1	0	0	0	0	0	913	1770	62	0	5988	0	ARID1A	1	27106299	Frame_Shift_Ins	INS	-	TCGA-BW-A5NQ-01A-11D-A27I-10		27106299	222144322	1	6701										
DOCK7	85440	hgsc.bcm.edu	37	chr1	62995020	62995020	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tagatacaacatggccactcGagcctttatctgagggtcag	10	10	2	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:62995020G>C	ENST00000340370.5	-	29	3633	c.3616C>G	c.(3616-3618)Cga>Gga	p.R1206G	DOCK7_ENST00000251157.5_Missense_Mutation_p.R1237G	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1237					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						ATGGCCACTCGAGCCTTTATC	0.403																																					p.R1237G		Atlas-SNP	.											.	DOCK7	184	.	0			c.C3709G						.						101	96	97					1																	62995020		2203	4300	6503	SO:0001583	missense	85440	exon30			CCACTCGAGCCTT		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.3616C>G	chr1.hg19:g.62995020G>C	ENSP00000340742:p.Arg1206Gly	94.0	0.0		117.0	6.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	hg19	CCDS30734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.43|18.43	3.621592|3.621592	0.66787|0.66787	.|.	.|.	ENSG00000116641|ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441|ENST00000454575	T;T|.	0.18338|.	2.22;2.22|.	5.84|5.84	3.89|3.89	0.44902|0.44902	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74419|0.74419	0.3714|0.3714	M|M	0.78285|0.78285	2.405|2.405	0.80722|0.80722	D|D	1|1	P;D;P;P;P;P|.	0.54207|.	0.802;0.965;0.702;0.702;0.706;0.862|.	B;P;B;B;B;P|.	0.54965|.	0.326;0.765;0.355;0.355;0.325;0.702|.	T|T	0.76599|0.76599	-0.2900|-0.2900	10|5	0.87932|.	D|.	0|.	.|.	14.668|14.668	0.68924|0.68924	0.0:0.0:0.6248:0.3752|0.0:0.0:0.6248:0.3752	.|.	1237;1237;1206;1206;1206;1237|.	Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6|.	DOCK7_HUMAN;.;.;.;.;.|.	G|W	1237;1237;1206;65|408	ENSP00000251157:R1237G;ENSP00000340742:R1206G|.	ENSP00000251157:R1237G|.	R|S	-|-	1|2	2|0	DOCK7|DOCK7	62767608|62767608	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.815000|0.815000	0.46073|0.46073	3.076000|3.076000	0.50081|0.50081	1.435000|1.435000	0.47434|0.47434	0.591000|0.591000	0.81541|0.81541	CGA|TCG	.	.		0.403	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		C	62995020	G	C	62995020	3	2	53	1	0	0	0	0	1	0	0	0	4694	1066	37	4	2797	4	DOCK7	1	62995020	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	35888721	62995020	186255601	2	6702										
DPYD	1806	hgsc.bcm.edu	37	chr1	97981322	97981322	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tggtgagggcaaaaccccatCcagcttcaaaagctcttcga	9	12	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:97981322C>A	ENST00000370192.3	-	13	1800	c.1700G>T	c.(1699-1701)gGa>gTa	p.G567V		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	567					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	AAAACCCCATCCAGCTTCAAA	0.363																																					p.G567V		Atlas-SNP	.											.	DPYD	219	.	0			c.G1700T						.						54	54	54					1																	97981322		2202	4300	6502	SO:0001583	missense	1806	exon13			CCCCATCCAGCTT	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1700G>T	chr1.hg19:g.97981322C>A	ENSP00000359211:p.Gly567Val	61.0	0.0		72.0	18.0	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.508698	0.85282	.	.	ENSG00000188641	ENST00000370192	D	0.83755	-1.76	5.37	5.37	0.77165	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.93546	0.7940	H	0.95004	3.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94713	0.7894	10	0.87932	D	0	-17.4008	19.4624	0.94922	0.0:1.0:0.0:0.0	.	567	Q12882	DPYD_HUMAN	V	567	ENSP00000359211:G567V	ENSP00000359211:G567V	G	-	2	0	DPYD	97753910	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	7.356000	0.79445	2.677000	0.91161	0.585000	0.79938	GGA	.	.		0.363	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		A	97981322	C	A	97981322	3	1	53	1	0	0	0	0	1	0	0	0	4747	855	30	3	1421	3	DPYD	1	97981322	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	34986302	97981322	151269299	3	6703										
LPPR5	163404	hgsc.bcm.edu	37	chr1	99358645	99358645	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atatcatgtgacttctgcgaAggcagtgatgtggttctgca	12	7	3	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:99358645A>G	ENST00000263177.4	-	6	1170	c.949T>C	c.(949-951)Ttc>Ctc	p.F317L	LPPR5_ENST00000370188.3_Missense_Mutation_p.F312L	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		317						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										ACTTCTGCGAAGGCAGTGATG	0.373																																					p.F317L		Atlas-SNP	.											.	.	.	.	0			c.T949C						.						112	106	108					1																	99358645		2203	4300	6503	SO:0001583	missense	0	exon6			CTGCGAAGGCAGT																												ENST00000263177.4:c.949T>C	chr1.hg19:g.99358645A>G	ENSP00000263177:p.Phe317Leu	116.0	0.0		115.0	52.0	NM_001037317	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Missense_Mutation	SNP	ENST00000263177.4	hg19	CCDS30778.1	.	.	.	.	.	.	.	.	.	.	A	12.21	1.868340	0.32977	.	.	ENSG00000117598	ENST00000370188;ENST00000263177	T;T	0.27890	1.65;1.64	5.61	5.61	0.85477	.	0.184679	0.47093	D	0.000251	T	0.08935	0.0221	N	0.22421	0.69	0.47994	D	0.999564	B;B	0.31351	0.32;0.1	B;B	0.26517	0.07;0.022	T	0.08493	-1.0719	10	0.11182	T	0.66	.	14.9872	0.71356	1.0:0.0:0.0:0.0	.	312;317	Q32ZL2-2;Q32ZL2	.;LPPR5_HUMAN	L	312;317	ENSP00000359207:F312L;ENSP00000263177:F317L	ENSP00000263177:F317L	F	-	1	0	AL161744.1	99131233	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.758000	0.74929	2.120000	0.65058	0.455000	0.32223	TTC	.	.		0.373	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1			G	99358645	A	G	99358645	3	3	53	1	0	0	0	0	1	0	0	0	8937	72	3	2	20	2	LPPR5	1	99358645	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	1377323	99358645	149891976	4	6704										
FLG	2312	hgsc.bcm.edu	37	chr1	152282032	152282032	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gccctgtgcgtccatgggcgGactcagactgttcatgagtg	14	11	2	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:152282032G>C	ENST00000368799.1	-	3	5365	c.5330C>G	c.(5329-5331)tCc>tGc	p.S1777C	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1777	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S1777Y(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCATGGGCGGACTCAGACTG	0.607									Ichthyosis																												p.S1777C		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	.	1	Substitution - Missense(1)	lung(1)	c.C5330G						.						205	212	209					1																	152282032		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGGCGGACTCAG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5330C>G	chr1.hg19:g.152282032G>C	ENSP00000357789:p.Ser1777Cys	365.0	0.0		434.0	99.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.454490	0.26161	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01745	4.66	4.64	0.35	0.16037	.	.	.	.	.	T	0.03348	0.0097	M	0.83483	2.645	0.09310	N	1	D	0.69078	0.997	D	0.73708	0.981	T	0.28681	-1.0036	9	0.87932	D	0	0.0123	5.0931	0.14720	0.1923:0.3131:0.4945:0.0	.	1777	P20930	FILA_HUMAN	C	1777;12	ENSP00000357789:S1777C	ENSP00000271820:S12C	S	-	2	0	FLG	150548656	0.001000	0.12720	0.000000	0.03702	0.036000	0.12997	0.682000	0.25335	-0.114000	0.11936	-0.259000	0.10710	TCC	.	.		0.607	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152282032	G	C	152282032	3	2	53	1	0	0	0	0	1	0	0	0	5930	1174	41	4	6859	4	FLG	1	152282032	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	52923387	152282032	96968589	5	6705										
TRIM46	80128	hgsc.bcm.edu	37	chr1	155148663	155148663	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	acccctggggcacccagaagGcccagcatgagcccaccctg	11	18	0	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:155148663G>T	ENST00000334634.4	+	3	625	c.625G>T	c.(625-627)Gcc>Tcc	p.A209S	TRIM46_ENST00000368385.4_Missense_Mutation_p.A209S|TRIM46_ENST00000368383.3_Missense_Mutation_p.A209S|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000543729.1_Missense_Mutation_p.A216S|TRIM46_ENST00000545012.1_Missense_Mutation_p.A83S|KRTCAP2_ENST00000295682.4_5'Flank|TRIM46_ENST00000392451.2_Missense_Mutation_p.A209S|TRIM46_ENST00000368382.1_Missense_Mutation_p.A186S|RP11-201K10.3_ENST00000473363.2_Intron|KRTCAP2_ENST00000490672.1_5'Flank	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	209						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CACCCAGAAGGCCCAGCATGA	0.652																																					p.A209S		Atlas-SNP	.											.	TRIM46	79	.	0			c.G625T						.						37	38	38					1																	155148663		2202	4298	6500	SO:0001583	missense	80128	exon3			CAGAAGGCCCAGC		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19019	protein-coding gene	gene with protein product		600986	"tripartite motif-containing 46"				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.625G>T	chr1.hg19:g.155148663G>T	ENSP00000334657:p.Ala209Ser	44.0	0.0		50.0	25.0	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	hg19	CCDS1097.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.943409	0.92593	.	.	ENSG00000163462	ENST00000543729;ENST00000430513;ENST00000368385;ENST00000545012;ENST00000392451;ENST00000368383;ENST00000368382;ENST00000334634	T;T;T;T;T;T;T	0.68624	0.71;0.4;-0.34;0.64;0.33;0.08;0.14	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.82444	0.5038	M	0.88377	2.95	0.54753	D	0.999989	D;D;D;D;D	0.89917	0.996;1.0;0.999;1.0;0.999	D;D;D;D;D	0.91635	0.986;0.999;0.987;0.999;0.994	D	0.85594	0.1248	10	0.87932	D	0	.	16.6522	0.85219	0.0:0.0:1.0:0.0	.	196;209;186;209;209	F5H5Z2;Q5VT61;B1AVQ4;Q7Z4K8;Q7Z4K8-2	.;.;.;TRI46_HUMAN;.	S	216;196;209;83;209;209;186;209	ENSP00000442719:A216S;ENSP00000357369:A209S;ENSP00000440254:A83S;ENSP00000376245:A209S;ENSP00000357367:A209S;ENSP00000357366:A186S;ENSP00000334657:A209S	ENSP00000334657:A209S	A	+	1	0	TRIM46	153415287	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.344000	0.97050	2.596000	0.87737	0.561000	0.74099	GCC	.	.		0.652	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058		T	155148663	G	T	155148663	3	4	53	1	0	0	0	0	1	0	0	0	16536	1203	42	3	635	3	TRIM46	1	155148663	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	2866631	155148663	94101958	6	6706										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155385687	155385687	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gctggggtttcagaaggactGggaatctcaactggtgcttc	14	8	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:155385687G>T	ENST00000368346.3	-	6	6495	c.5856C>A	c.(5854-5856)ccC>ccA	p.P1952P	snoU13_ENST00000458873.1_RNA|ASH1L_ENST00000392403.3_Silent_p.P1952P			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1952					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CAGAAGGACTGGGAATCTCAA	0.388																																					p.P1952P		Atlas-SNP	.											.	ASH1L	279	.	0			c.C5856A						.						75	75	75					1																	155385687		2203	4300	6503	SO:0001819	synonymous_variant	55870	exon6			AGGACTGGGAATC	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.5856C>A	chr1.hg19:g.155385687G>T		59.0	0.0		89.0	4.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.		0.388	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		T	155385687	G	T	155385687	2	4	53	1	0	0	0	0	0	0	0	1	1041	1335	47	3		3	ASH1L	1	155385687	Silent	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	237024	155385687	93864934	7	6707										
C1orf129	80133	hgsc.bcm.edu	37	chr1	170967421	170967421	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atattcctcactgaagtgagTtttgtagactgtgaacagct	9	7	1	4			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:170967421T>C	ENST00000367758.3	+	15	1701	c.1602T>C	c.(1600-1602)agT>agC	p.S534S	MROH9_ENST00000367759.4_Intron	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	534																	CTGAAGTGAGTTTTGTAGACT	0.393																																					p.S534S		Atlas-SNP	.											.	.	.	.	0			c.T1602C						.						186	167	173					1																	170967421		1846	4085	5931	SO:0001819	synonymous_variant	80133	exon15			AGTGAGTTTTGTA	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"maestro heat-like repeat containing"	26287	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 129"	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.1602T>C	chr1.hg19:g.170967421T>C		79.0	0.0		83.0	4.0	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Silent	SNP	ENST00000367758.3	hg19	CCDS41436.1																																																																																			.	.		0.393	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		C	170967421	T	C	170967421	2	2	53	1	0	0	0	0	0	0	0	1	1998	1722	60	2		2	C1orf129	1	170967421	Silent	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	15581734	170967421	78283200	8	6708										
RGL1	23179	hgsc.bcm.edu	37	chr1	183891363	183891363	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	attgtctttgcagttgacgaGccaggataaaacccccgctg	10	11	1	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:183891363G>A	ENST00000360851.3	+	17	2190	c.2012G>A	c.(2011-2013)aGc>aAc	p.S671N	RGL1_ENST00000304685.4_Missense_Mutation_p.S706N|RGL1_ENST00000536277.1_Missense_Mutation_p.S669N|RGL1_ENST00000539189.1_Missense_Mutation_p.S642N			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	671	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						CAGTTGACGAGCCAGGATAAA	0.517											OREG0014047	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S706N		Atlas-SNP	.											.	RGL1	91	.	0			c.G2117A						.						70	64	66					1																	183891363		2203	4300	6503	SO:0001583	missense	23179	exon18			TGACGAGCCAGGA	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.2012G>A	chr1.hg19:g.183891363G>A	ENSP00000354097:p.Ser671Asn	140.0	0.0	1987	131.0	17.0	NM_015149	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	hg19		.	.	.	.	.	.	.	.	.	.	G	13.40	2.224580	0.39300	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000360851;ENST00000539189	T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85	5.29	5.29	0.74685	Ras-association (3);	0.087292	0.85682	D	0.000000	T	0.37461	0.1004	L	0.33245	0.995	0.43647	D	0.996058	B;B;B;B	0.17465	0.01;0.022;0.008;0.022	B;B;B;B	0.23716	0.02;0.048;0.028;0.028	T	0.12967	-1.0527	10	0.22109	T	0.4	.	13.2635	0.60120	0.0778:0.0:0.9222:0.0	.	642;669;671;706	F5H6U6;B7Z2W5;Q9NZL6;Q5SXQ6	.;.;RGL1_HUMAN;.	N	706;706;669;671;642	ENSP00000303192:S706N;ENSP00000356501:S706N;ENSP00000438662:S669N;ENSP00000354097:S671N;ENSP00000437355:S642N	ENSP00000303192:S706N	S	+	2	0	RGL1	182157986	1.000000	0.71417	1.000000	0.80357	0.416000	0.31233	3.166000	0.50785	2.614000	0.88457	0.655000	0.94253	AGC	.	.		0.517	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149		A	183891363	G	A	183891363	3	1	53	1	0	0	0	0	1	0	0	0	13291	971	34	3	2183	3	RGL1	1	183891363	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	12923942	183891363	65359258	9	6709										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186120388	186120388	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atattaatgatgttgaatttGgaattgctttccttaatgcc	7	5	0	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:186120388G>C	ENST00000271588.4	+	94	14894	c.14665G>C	c.(14665-14667)Gga>Cga	p.G4889R	HMCN1_ENST00000367492.2_Missense_Mutation_p.G4889R	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4889	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGTTGAATTTGGAATTGCTTT	0.393																																					p.G4889R		Atlas-SNP	.											.	HMCN1	797	.	0			c.G14665C						.						141	141	141					1																	186120388		2203	4300	6503	SO:0001583	missense	83872	exon94			GAATTTGGAATTG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.14665G>C	chr1.hg19:g.186120388G>C	ENSP00000271588:p.Gly4889Arg	86.0	0.0		85.0	22.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.792151	0.90453	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.32023	1.47;1.47	5.13	5.13	0.70059	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.000000	0.85682	D	0.000000	T	0.60327	0.2260	M	0.81341	2.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.66388	-0.5936	10	0.87932	D	0	.	18.5888	0.91200	0.0:0.0:1.0:0.0	.	4889	Q96RW7	HMCN1_HUMAN	R	4889	ENSP00000271588:G4889R;ENSP00000356462:G4889R	ENSP00000271588:G4889R	G	+	1	0	HMCN1	184387011	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.373000	0.80994	0.655000	0.94253	GGA	.	.		0.393	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186120388	G	C	186120388	3	2	53	1	0	0	0	0	1	0	0	0	7229	1349	47	4	15039	4	HMCN1	1	186120388	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	2229025	186120388	63130233	10	6710										
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204197269	204197269	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	agggcgcaggagatttcaatCcgcttctcctgctcctgcag	11	13	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:204197269C>A	ENST00000272203.3	-	21	3289	c.2973G>T	c.(2971-2973)cgG>cgT	p.R991R	PLEKHA6_ENST00000414478.1_Silent_p.R1011R	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	991										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			AGATTTCAATCCGCTTCTCCT	0.657																																					p.R991R		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.G2973T						.						44	43	44					1																	204197269		2203	4300	6503	SO:0001819	synonymous_variant	22874	exon21			TTCAATCCGCTTC	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2973G>T	chr1.hg19:g.204197269C>A		59.0	0.0		84.0	31.0	NM_014935	A7MD51|Q5VTI6	Silent	SNP	ENST00000272203.3	hg19	CCDS1444.1																																																																																			.	.		0.657	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		A	204197269	C	A	204197269	2	1	53	1	0	0	0	0	0	0	0	1	12069	842	30	3		3	PLEKHA6	1	204197269	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	18076881	204197269	45053352	11	6711										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247588695	247588695	+	Frame_Shift_Del	DEL	C	C	-													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	caaagggccatggactatttCcccaagattgagatcaatct							TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:247588695delC	ENST00000336119.3	+	3	2696	c.1950delC	c.(1948-1950)ttcfs	p.F650fs	NLRP3_ENST00000348069.2_Frame_Shift_Del_p.F650fs|NLRP3_ENST00000391827.2_Frame_Shift_Del_p.F650fs|NLRP3_ENST00000366496.2_Frame_Shift_Del_p.F650fs|NLRP3_ENST00000391828.3_Frame_Shift_Del_p.F650fs|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000366497.2_Frame_Shift_Del_p.F650fs	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	650					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			TGGACTATTTCCCCAAGATTG	0.493																																					p.F650fs		Atlas-Indel,Pindel	.											.	NLRP3	286	.	0			c.1949delT						.						94	80	85					1																	247588695		2203	4300	6503	SO:0001589	frameshift_variant	114548	exon3			.	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1950delC	chr1.hg19:g.247588695delC	ENSP00000337383:p.Phe650fs	253.0	0.0		236.0	96.0	NM_004895	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Frame_Shift_Del	DEL	ENST00000336119.3	hg19	CCDS1632.1																																																																																			.	.		0.493	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		-	247588695	C	-	247588695	7	5	53	1	0	1	0	1	0	0	0	0	10487	854	30	0	1960	0	NLRP3	1	247588695	Frame_Shift_Del	DEL	C	TCGA-BW-A5NQ-01A-11D-A27I-10	43391426	247588695	1661926	12	6712										
TPO	7173	hgsc.bcm.edu	37	chr2	1437304	1437304	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gagtgattgcccgagcagcaGagataatggaaacatcaata	11	7	1	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:1437304G>A	ENST00000345913.4	+	4	365	c.274G>A	c.(274-276)Gag>Aag	p.E92K	TPO_ENST00000329066.4_Missense_Mutation_p.E92K|TPO_ENST00000346956.3_Missense_Mutation_p.E92K|TPO_ENST00000497517.2_Intron|TPO_ENST00000349624.3_Missense_Mutation_p.E92K|TPO_ENST00000539820.1_Missense_Mutation_p.E92K|TPO_ENST00000337415.3_Missense_Mutation_p.E92K|TPO_ENST00000382201.3_Missense_Mutation_p.E92K|TPO_ENST00000382269.3_Missense_Mutation_p.E92K|TPO_ENST00000382198.1_Missense_Mutation_p.E92K	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	92					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CCGAGCAGCAGAGATAATGGA	0.458																																					p.E92K		Atlas-SNP	.											.	TPO	224	.	0			c.G274A						.						119	107	111					2																	1437304		2203	4300	6503	SO:0001583	missense	7173	exon4			GCAGCAGAGATAA		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.274G>A	chr2.hg19:g.1437304G>A	ENSP00000318820:p.Glu92Lys	210.0	0.0		156.0	8.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.942694	0.53079	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	4.26	4.26	0.50523	.	0.000000	0.85682	D	0.000000	D	0.83238	0.5211	M	0.78637	2.42	0.35311	D	0.78387	D;D;D;D;D	0.89917	1.0;0.974;1.0;1.0;0.999	D;P;D;D;D	0.97110	0.988;0.854;1.0;0.988;0.962	D	0.89140	0.3516	10	0.72032	D	0.01	-30.1919	13.9712	0.64242	0.0:0.0:1.0:0.0	.	92;92;92;92;92	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	K	92;92;92;92;92;92;92;92;92;92;21	ENSP00000371704:E92K;ENSP00000337263:E92K;ENSP00000318820:E92K;ENSP00000263886:E92K;ENSP00000332044:E92K;ENSP00000444840:E92K;ENSP00000329869:E92K;ENSP00000371636:E92K;ENSP00000390994:E92K;ENSP00000371633:E92K;ENSP00000405788:E21K	ENSP00000329869:E92K	E	+	1	0	TPO	1416311	1.000000	0.71417	0.256000	0.24389	0.138000	0.21146	5.001000	0.63946	2.076000	0.62316	0.563000	0.77884	GAG	.	.		0.458	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		A	1437304	G	A	1437304	3	1	53	1	0	0	0	0	1	0	0	0	16425	943	33	3	284	3	TPO	2	1437304	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10		1437304	241762069	13	6713										
RTN4	57142	hgsc.bcm.edu	37	chr2	55252314	55252314	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gttttttctcagcttctttcAcaagaactttgggtttaact	6	8	3	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:55252314A>G	ENST00000337526.6	-	3	3164	c.2921T>C	c.(2920-2922)gTg>gCg	p.V974A	RTN4_ENST00000405240.1_Missense_Mutation_p.V768A|RTN4_ENST00000404909.1_Missense_Mutation_p.V768A|RTN4_ENST00000354474.6_Missense_Mutation_p.V742A|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357376.3_Missense_Mutation_p.V768A|RTN4_ENST00000394611.2_Missense_Mutation_p.V768A|RTN4_ENST00000357732.4_Intron	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	974					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						AGCTTCTTTCACAAGAACTTT	0.413																																					p.V974A		Atlas-SNP	.											.	RTN4	189	.	0			c.T2921C						.						141	138	139					2																	55252314		2203	4300	6503	SO:0001583	missense	57142	exon3			TCTTTCACAAGAA	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.2921T>C	chr2.hg19:g.55252314A>G	ENSP00000337838:p.Val974Ala	66.0	0.0		68.0	17.0	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	hg19	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	A	0.492	-0.874843	0.02550	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.26	5.51	-4.23	0.03789	.	1.271090	0.05534	N	0.564520	T	0.11665	0.0284	L	0.60455	1.87	0.09310	N	1	B	0.26318	0.146	B	0.21546	0.035	T	0.34800	-0.9814	10	0.09338	T	0.73	3.2446	1.0858	0.01652	0.2259:0.2147:0.3289:0.2305	.	974	Q9NQC3	RTN4_HUMAN	A	768;768;974;768;768;742	ENSP00000384471:V768A;ENSP00000349944:V768A;ENSP00000337838:V974A;ENSP00000378109:V768A;ENSP00000385650:V768A;ENSP00000346465:V742A	ENSP00000337838:V974A	V	-	2	0	RTN4	55105818	0.994000	0.37717	0.068000	0.19968	0.488000	0.33401	0.667000	0.25112	-0.678000	0.05224	-0.250000	0.11733	GTG	.	.		0.413	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			G	55252314	A	G	55252314	3	3	53	1	0	0	0	0	1	0	0	0	13743	159	6	2	723	2	RTN4	2	55252314	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	53815010	55252314	187947059	14	6714										
TBC1D8	11138	hgsc.bcm.edu	37	chr2	101648734	101648734	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	aagggggtctgtttaccgatCactcggtggttgaagtaatc	13	7	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:101648734C>G	ENST00000376840.4	-	11	1886	c.1887G>C	c.(1885-1887)gtG>gtC	p.V629V	TBC1D8_ENST00000409318.1_Silent_p.V644V			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	629	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						GTTTACCGATCACTCGGTGGT	0.532																																					p.V629V		Atlas-SNP	.											.	TBC1D8	169	.	0			c.G1887C						.						71	76	74					2																	101648734		2098	4243	6341	SO:0001819	synonymous_variant	11138	exon11			ACCGATCACTCGG	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"BUB2-like protein 1", "vascular Rab-GAP/TBC-containing protein"					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.1887G>C	chr2.hg19:g.101648734C>G		159.0	0.0		114.0	24.0	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	hg19	CCDS46375.1																																																																																			.	.		0.532	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063		G	101648734	C	G	101648734	2	3	53	1	0	0	0	0	0	0	0	1	15640	813	29	4		4	TBC1D8	2	101648734	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	46396420	101648734	141550639	15	6715										
B3GALT1	8708	hgsc.bcm.edu	37	chr2	168725799	168725799	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ttccttttcttgttatcctcAtcagcaccactcacaaggaa	4	13	4	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:168725799A>T	ENST00000392690.3	+	1	342	c.250A>T	c.(250-252)Atc>Ttc	p.I84F	AC016723.4_ENST00000430546.1_RNA|B3GALT1_ENST00000305861.1_Missense_Mutation_p.I84F|AC016723.4_ENST00000436982.2_RNA			Q9Y5Z6	B3GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	84					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			cervix(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18						TGTTATCCTCATCAGCACCAC	0.433																																					p.I84F		Atlas-SNP	.											.	B3GALT1	51	.	0			c.A250T						.						76	77	77					2																	168725799		2203	4300	6503	SO:0001583	missense	8708	exon2			ATCCTCATCAGCA	E07739	CCDS2227.1	2q24.3	2013-02-19			ENSG00000172318	ENSG00000172318		"Beta 3-glycosyltransferases"	916	protein-coding gene	gene with protein product		603093				9582303	Standard	NM_020981		Approved	beta3Gal-T1	uc002udz.1	Q9Y5Z6	OTTHUMG00000132163	ENST00000392690.3:c.250A>T	chr2.hg19:g.168725799A>T	ENSP00000376456:p.Ile84Phe	109.0	0.0		76.0	15.0	NM_020981	D3DPB8|Q53SS2	Missense_Mutation	SNP	ENST00000392690.3	hg19	CCDS2227.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.095921	0.76870	.	.	ENSG00000172318	ENST00000305861;ENST00000392690	T;T	0.50813	0.73;0.73	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.67683	0.2919	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	T	0.70149	-0.4951	10	0.87932	D	0	-27.9029	16.8061	0.85666	1.0:0.0:0.0:0.0	.	84	Q9Y5Z6	B3GT1_HUMAN	F	84	ENSP00000303740:I84F;ENSP00000376456:I84F	ENSP00000303740:I84F	I	+	1	0	B3GALT1	168434045	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.305000	0.96197	2.367000	0.80283	0.528000	0.53228	ATC	.	.		0.433	B3GALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255211.2	NM_020981		T	168725799	A	T	168725799	3	4	53	1	0	0	0	0	1	0	0	0	1247	217	8	4	252	4	B3GALT1	2	168725799	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	67077065	168725799	74473574	16	6716										
ITGAV	3685	hgsc.bcm.edu	37	chr2	187540572	187540572	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	aaatcagaatcattcctattCtctgaagtcgtctgcttcat	5	10	5	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:187540572C>A	ENST00000261023.3	+	28	3120	c.2846C>A	c.(2845-2847)tCt>tAt	p.S949Y	ITGAV_ENST00000433736.2_Missense_Mutation_p.S903Y|AC017101.10_ENST00000453665.1_RNA|ITGAV_ENST00000374907.3_Missense_Mutation_p.S913Y	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	949					angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)	p.S949Y(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	CATTCCTATTCTCTGAAGTCG	0.333																																					p.S949Y	Melanoma(58;108 1995 6081)	Atlas-SNP	.											ITGAV,rectum,carcinoma,0,1	ITGAV	124	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2846A						.						67	68	68					2																	187540572		2203	4299	6502	SO:0001583	missense	3685	exon28			CCTATTCTCTGAA		CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"CD molecules", "Integrins"	6150	protein-coding gene	gene with protein product		193210	"antigen identified by monoclonal antibody L230", "vitronectin receptor", "integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.2846C>A	chr2.hg19:g.187540572C>A	ENSP00000261023:p.Ser949Tyr	125.0	0.0		103.0	26.0	NM_002210	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Missense_Mutation	SNP	ENST00000261023.3	hg19	CCDS2292.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.96|18.96	3.733361|3.733361	0.69189|0.69189	.|.	.|.	ENSG00000138448|ENSG00000138448	ENST00000430709|ENST00000261023;ENST00000374907;ENST00000433736	.|T;T;T	.|0.50001	.|0.76;0.76;0.76	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	.|0.219770	.|0.40385	.|N	.|0.001110	T|T	0.61135|0.61135	0.2323|0.2323	L|L	0.59436|0.59436	1.845|1.845	0.42832|0.42832	D|D	0.994024|0.994024	.|P;D;P	.|0.54047	.|0.924;0.964;0.956	.|P;P;P	.|0.55824	.|0.459;0.785;0.459	T|T	0.64786|0.64786	-0.6325|-0.6325	5|10	.|0.62326	.|D	.|0.03	.|.	18.2525|18.2525	0.90009|0.90009	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|903;913;949	.|E7EWZ6;P06756-2;P06756	.|.;.;ITAV_HUMAN	I|Y	100|949;913;903	.|ENSP00000261023:S949Y;ENSP00000364042:S913Y;ENSP00000404291:S903Y	.|ENSP00000261023:S949Y	L|S	+|+	1|2	0|0	ITGAV|ITGAV	187248817|187248817	0.994000|0.994000	0.37717|0.37717	0.999000|0.999000	0.59377|0.59377	0.967000|0.967000	0.64934|0.64934	4.557000|4.557000	0.60782|0.60782	2.547000|2.547000	0.85894|0.85894	0.563000|0.563000	0.77884|0.77884	CTC|TCT	.	.		0.333	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		A	187540572	C	A	187540572	3	1	53	1	0	0	0	0	1	0	0	0	7897	913	32	3	3007	3	ITGAV	2	187540572	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	18814773	187540572	55658801	17	6717										
ZSWIM2	151112	hgsc.bcm.edu	37	chr2	187693382	187693382	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tgatagatgaatgatgtctcTgtttgaaacagactgatgtg	11	4	1	7			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:187693382T>C	ENST00000295131.2	-	9	1270	c.1231A>G	c.(1231-1233)Aga>Gga	p.R411G		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	411					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			ATGATGTCTCTGTTTGAAACA	0.348																																					p.R411G		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.A1231G						.						81	80	81					2																	187693382		2203	4300	6503	SO:0001583	missense	151112	exon9			TGTCTCTGTTTGA	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1231A>G	chr2.hg19:g.187693382T>C	ENSP00000295131:p.Arg411Gly	57.0	0.0		52.0	16.0	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	hg19	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	T	5.928	0.355220	0.11239	.	.	ENSG00000163012	ENST00000295131	T	0.24151	1.87	5.3	0.13	0.14746	.	0.887848	0.09682	N	0.769573	T	0.13798	0.0334	N	0.22421	0.69	0.09310	N	1	B	0.14012	0.009	B	0.12156	0.007	T	0.33343	-0.9872	10	0.24483	T	0.36	0.7174	3.6817	0.08313	0.1647:0.3355:0.0:0.4999	.	411	Q8NEG5	ZSWM2_HUMAN	G	411	ENSP00000295131:R411G	ENSP00000295131:R411G	R	-	1	2	ZSWIM2	187401627	0.000000	0.05858	0.053000	0.19242	0.219000	0.24729	0.295000	0.19065	0.073000	0.16731	0.482000	0.46254	AGA	.	.		0.348	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		C	187693382	T	C	187693382	3	2	53	1	0	0	0	0	1	0	0	0	18256	1588	55	2	674	2	ZSWIM2	2	187693382	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	152810	187693382	55505991	18	6718										
SDPR	8436	hgsc.bcm.edu	37	chr2	192701015	192701015	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ttttctgcatggctttctccCtctcggactttcttccgccc	6	16	4	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:192701015C>T	ENST00000304141.4	-	2	1241	c.912G>A	c.(910-912)gaG>gaA	p.E304E		NM_004657.5	NP_004648.1			serum deprivation response											NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			GGCTTTCTCCCTCTCGGACTT	0.483																																					p.E304E		Atlas-SNP	.											.	SDPR	67	.	0			c.G912A						.						98	106	103					2																	192701015		2203	4300	6503	SO:0001819	synonymous_variant	8436	exon2			TTCTCCCTCTCGG	AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"phosphatidylserine binding protein"	606728	"serum deprivation response (phosphatidylserine-binding protein)", "serum deprivation response (phosphatidylserine binding protein)"			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.912G>A	chr2.hg19:g.192701015C>T		94.0	0.0		76.0	19.0	NM_004657		Silent	SNP	ENST00000304141.4	hg19	CCDS2313.1																																																																																			.	.		0.483	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657		T	192701015	C	T	192701015	2	4	53	1	0	0	0	0	0	0	0	1	13985	680	24	3		3	SDPR	2	192701015	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	5007633	192701015	50498358	19	6719										
HECW2	57520	hgsc.bcm.edu	37	chr2	197080657	197080657	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gggccgttactccctcggagTgaagcaaatccttcataggg	12	11	1	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:197080657T>A	ENST00000260983.3	-	28	4721	c.4539A>T	c.(4537-4539)tcA>tcT	p.S1513S	HECW2_ENST00000409111.1_Silent_p.S1157S|snoU13_ENST00000459047.1_RNA	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1513	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						TCCCTCGGAGTGAAGCAAATC	0.443																																					p.S1513S		Atlas-SNP	.											.	HECW2	239	.	0			c.A4539T						.						76	76	76					2																	197080657		2203	4300	6503	SO:0001819	synonymous_variant	57520	exon28			TCGGAGTGAAGCA	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.4539A>T	chr2.hg19:g.197080657T>A		43.0	0.0		58.0	21.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Silent	SNP	ENST00000260983.3	hg19	CCDS33354.1																																																																																			.	.		0.443	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		A	197080657	T	A	197080657	2	1	53	1	0	0	0	0	0	0	0	1	7052	1683	59	4		4	HECW2	2	197080657	Silent	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	4379642	197080657	46118716	20	6720										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238255172	238255172	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tcctgggtagccagggtctcCcttctgtccaactatccctg	9	15	2	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:238255172C>A	ENST00000295550.4	-	32	7518	c.7066G>T	c.(7066-7068)Gga>Tga	p.G2356*	COL6A3_ENST00000409809.1_Nonsense_Mutation_p.G2150*|COL6A3_ENST00000353578.4_Nonsense_Mutation_p.G2150*|COL6A3_ENST00000472056.1_Nonsense_Mutation_p.G1749*|COL6A3_ENST00000347401.3_Nonsense_Mutation_p.G2155*|COL6A3_ENST00000346358.4_Nonsense_Mutation_p.G2156*	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2356	Collagen-like 5.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CCAGGGTCTCCCTTCTGTCCA	0.512																																					p.G2356X		Atlas-SNP	.											.	COL6A3	608	.	0			c.G7066T						.						102	99	100					2																	238255172		2203	4300	6503	SO:0001587	stop_gained	1293	exon32			GGTCTCCCTTCTG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7066G>T	chr2.hg19:g.238255172C>A	ENSP00000295550:p.Gly2356*	102.0	0.0		91.0	21.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Nonsense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	50	16.720992	0.99870	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	.	.	.	5.23	5.23	0.72850	.	0.000000	0.52532	D	0.000075	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.197	0.93693	0.0:1.0:0.0:0.0	.	.	.	.	X	2356;2155;2150;1749;2150;2156	.	ENSP00000295550:G2356X	G	-	1	0	COL6A3	237919911	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.233000	0.78125	2.605000	0.88082	0.655000	0.94253	GGA	.	.		0.512	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238255172	C	A	238255172	4	1	53	1	0	0	0	0	0	1	0	0	3703	632	22	3	2519	3	COL6A3	2	238255172	Nonsense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	41174515	238255172	4944201	21	6721										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266113	41266113	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	cctggactctggaatccattCtggtgccactaccacagctc	8	15	2	0	rs121913416|rs121913403		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr3:41266113C>T	ENST00000349496.5	+	3	390	c.110C>T	c.(109-111)tCt>tTt	p.S37F	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S30F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S37F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S37F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S37F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S37F(172)|p.S37C(141)|p.A5_A80del(53)|p.S37Y(31)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGAATCCATTCTGGTGCCACT	0.498	S37C(JHUEM2_ENDOMETRIUM)|S37C(SNU398_LIVER)|S37F(HUTU80_SMALL_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S37F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	474	Substitution - Missense(344)|Deletion - In frame(102)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(145)|endometrium(64)|stomach(38)|skin(34)|ovary(33)|central_nervous_system(28)|pancreas(28)|large_intestine(22)|pituitary(22)|lung(21)|biliary_tract(15)|thyroid(4)|soft_tissue(4)|urinary_tract(4)|small_intestine(3)|oesophagus(3)|adrenal_gland(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)|breast(1)	c.C110T						.						93	78	83					3																	41266113		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TCCATTCTGGTGC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.110C>T	chr3.hg19:g.41266113C>T	ENSP00000344456:p.Ser37Phe	253.0	0.0		257.0	96.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.513375	0.85389	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75297	-0.3367	10	0.87932	D	0	-15.9763	19.9596	0.97236	0.0:1.0:0.0:0.0	.	37	P35222	CTNB1_HUMAN	F	30;37;37;37;37;30;37;37;37	ENSP00000400508:S30F;ENSP00000385604:S37F;ENSP00000412219:S37F;ENSP00000379486:S37F;ENSP00000344456:S37F;ENSP00000411226:S30F;ENSP00000379488:S37F;ENSP00000409302:S37F;ENSP00000401599:S37F	ENSP00000344456:S37F	S	+	2	0	CTNNB1	41241117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266113	C	T	41266113	3	4	53	1	0	0	0	0	1	0	0	0	4018	913	32	3	116	3	CTNNB1	3	41266113	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10		41266113	156756317	22	6722										
FLNB	2317	hgsc.bcm.edu	37	chr3	58116537	58116537	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	caagattgccggccccgggcTgggctcaggcgtccgagccc	15	16	1	1	rs80356511		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr3:58116537T>A	ENST00000295956.4	+	25	4457	c.4292T>A	c.(4291-4293)cTg>cAg	p.L1431Q	FLNB_ENST00000490882.1_Missense_Mutation_p.L1431Q|FLNB_ENST00000493452.1_Missense_Mutation_p.L1262Q|FLNB_ENST00000358537.3_Missense_Mutation_p.L1431Q|FLNB_ENST00000357272.4_Missense_Mutation_p.L1431Q|FLNB_ENST00000348383.5_Missense_Mutation_p.L1431Q|FLNB_ENST00000429972.2_Missense_Mutation_p.L1431Q|FLNB_ENST00000419752.2_Missense_Mutation_p.L1262Q	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1431	Interaction with FBLP1.		L -> R (in LRS). {ECO:0000269|PubMed:16801345}.		actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GGCCCCGGGCTGGGCTCAGGC	0.637																																					p.L1431Q		Atlas-SNP	.											.	FLNB	430	.	0			c.T4292A	GRCh37	CM070931	FLNB	M	rs80356511	.						30	31	31					3																	58116537		2203	4300	6503	SO:0001583	missense	2317	exon25			CCGGGCTGGGCTC	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.4292T>A	chr3.hg19:g.58116537T>A	ENSP00000295956:p.Leu1431Gln	109.0	0.0		101.0	20.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.847091	0.91277	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24	5.51	5.51	0.81932	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.289256	0.34362	N	0.004037	D	0.95809	0.8636	H	0.97340	3.985	0.58432	D	0.999998	D;D;D;D;D;D	0.71674	0.984;0.996;0.974;0.998;0.987;0.987	P;D;D;D;D;D	0.71184	0.847;0.972;0.944;0.971;0.936;0.936	D	0.97172	0.9845	10	0.62326	D	0.03	.	15.6399	0.76989	0.0:0.0:0.0:1.0	.	1431;1431;1262;1262;1431;1431	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	Q	1431;1431;1431;1431;1431;1431;1262;1262	ENSP00000295956:L1431Q;ENSP00000420213:L1431Q;ENSP00000351339:L1431Q;ENSP00000415599:L1431Q;ENSP00000232447:L1431Q;ENSP00000349819:L1431Q;ENSP00000418510:L1262Q;ENSP00000414532:L1262Q	ENSP00000295956:L1431Q	L	+	2	0	FLNB	58091577	1.000000	0.71417	0.954000	0.39281	0.994000	0.84299	8.040000	0.89188	2.103000	0.63969	0.533000	0.62120	CTG	.	.		0.637	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		A	58116537	T	A	58116537	3	1	53	1	0	0	0	0	1	0	0	0	5942	1580	55	4	4390	4	FLNB	3	58116537	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	16850424	58116537	139905893	23	6723										
KY	339855	hgsc.bcm.edu	37	chr3	134338015	134338015	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	cattctctcgaagaggccagCatagccatcacagttggtct	9	12	3	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr3:134338015C>A	ENST00000423778.2	-	8	746	c.685G>T	c.(685-687)Gct>Tct	p.A229S	KY_ENST00000508041.1_5'UTR|KY_ENST00000508956.1_Missense_Mutation_p.A208S|KY_ENST00000503669.1_Missense_Mutation_p.A229S	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	229					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						AAGAGGCCAGCATAGCCATCA	0.562																																					p.A229S		Atlas-SNP	.											.	KY	92	.	0			c.G685T						.						149	154	152					3																	134338015		2116	4237	6353	SO:0001583	missense	339855	exon8			GGCCAGCATAGCC	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.685G>T	chr3.hg19:g.134338015C>A	ENSP00000397598:p.Ala229Ser	176.0	0.0		206.0	53.0	NM_178554	B7Z1S4|Q6ZT15	Missense_Mutation	SNP	ENST00000423778.2	hg19	CCDS46920.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.124822	0.56613	.	.	ENSG00000174611	ENST00000508956;ENST00000423778;ENST00000503669;ENST00000310263	T;T;T	0.39787	1.06;1.06;1.06	4.61	3.7	0.42460	.	0.152126	0.43260	N	0.000592	T	0.45856	0.1363	N	0.25992	0.78	0.39035	D	0.960024	P;D;D	0.52996	0.955;0.957;0.957	P;P;P	0.59595	0.717;0.86;0.728	T	0.42172	-0.9467	10	0.37606	T	0.19	-6.4357	13.6599	0.62361	0.156:0.844:0.0:0.0	.	208;229;229	Q8NBH2-3;B4DGA7;Q8NBH2-4	.;.;.	S	208;229;229;229	ENSP00000421297:A208S;ENSP00000397598:A229S;ENSP00000426777:A229S	ENSP00000309520:A229S	A	-	1	0	KY	135820705	0.996000	0.38824	0.780000	0.31762	0.518000	0.34316	3.716000	0.54904	0.869000	0.35703	0.462000	0.41574	GCT	.	.		0.562	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554		A	134338015	C	A	134338015	3	1	53	1	0	0	0	0	1	0	0	0	8595	710	25	3	1316	3	KY	3	134338015	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	76221478	134338015	63684415	24	6724										
VEPH1	79674	hgsc.bcm.edu	37	chr3	157146119	157146120	+	Frame_Shift_Ins	INS	-	-	T													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gtactttttacctcgagttgINSttttttctttgctgctacat							TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr3:157146119_157146120insT	ENST00000362010.2	-	5	994_995	c.687_688insA	c.(685-690)aaacaafs	p.Q230fs	VEPH1_ENST00000469007.1_5'UTR|VEPH1_ENST00000543418.1_Frame_Shift_Ins_p.Q230fs|VEPH1_ENST00000392832.2_Frame_Shift_Ins_p.Q230fs|VEPH1_ENST00000392833.2_Frame_Shift_Ins_p.Q230fs	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	230						plasma membrane (GO:0005886)		p.K229N(1)		autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			ACCTCGAGTTGTTTTTTCTTTG	0.431																																					p.Q230fs		Atlas-INDEL	.											.	VEPH1	129	.	1	Substitution - Missense(1)	large_intestine(1)	c.688_689insA						.																																			SO:0001589	frameshift_variant	79674	exon5			.	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"Pleckstrin homology (PH) domain containing"	25735	protein-coding gene	gene with protein product		609594	"ventricular zone expressed PH domain homolog 1 (zebrafish)"			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.688dupA	chr3.hg19:g.157146125_157146125dupT	ENSP00000354919:p.Gln230fs	122.0	0.0		132.0	40.0	NM_024621	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Frame_Shift_Ins	INS	ENST00000362010.2	hg19	CCDS3179.1																																																																																			.	.		0.431	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621		T	157146120	-	T	157146119	7	5	53	1	0	1	1	0	0	0	0	0	17169	1386	48	0	1853	0	VEPH1	3	157146119	Frame_Shift_Ins	INS	-	TCGA-BW-A5NQ-01A-11D-A27I-10	22808104	157146119	40876311	25	6725										
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193159259	193159259	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ccctcttagaacttacctttGgcagtaggctgctgaaatgt	9	10	1	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr3:193159259G>T	ENST00000342695.4	-	20	2757	c.2435C>A	c.(2434-2436)cCa>cAa	p.P812Q	ATP13A4_ENST00000392443.3_Missense_Mutation_p.P793Q	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	812						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		ACTTACCTTTGGCAGTAGGCT	0.388																																					p.P812Q		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C2435A						.						135	124	128					3																	193159259		2203	4300	6503	SO:0001583	missense	84239	exon20			ACCTTTGGCAGTA	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"ATPases / P-type"	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.2435C>A	chr3.hg19:g.193159259G>T	ENSP00000339182:p.Pro812Gln	164.0	0.0		149.0	64.0	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	hg19	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	G	19.55	3.848075	0.71603	.	.	ENSG00000127249	ENST00000392443;ENST00000342695	D;D	0.85773	-1.74;-2.03	6.03	6.03	0.97812	HAD-like domain (2);	0.078821	0.53938	D	0.000042	D	0.86977	0.6063	L	0.40543	1.245	0.80722	D	1	P;P;P	0.49358	0.923;0.68;0.923	P;P;P	0.56865	0.808;0.615;0.808	D	0.86580	0.1853	10	0.52906	T	0.07	-12.8445	14.0229	0.64568	0.0:0.0:0.8489:0.1511	.	793;812;812	B7WPN9;Q4VNC1-2;Q4VNC1	.;.;AT134_HUMAN	Q	793;812	ENSP00000376238:P793Q;ENSP00000339182:P812Q	ENSP00000339182:P812Q	P	-	2	0	ATP13A4	194641953	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.763000	0.62257	2.854000	0.98071	0.655000	0.94253	CCA	.	.		0.388	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		T	193159259	G	T	193159259	3	4	53	1	0	0	0	0	1	0	0	0	1126	1348	47	3	1199	3	ATP13A4	3	193159259	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	36013140	193159259	4863171	26	6726										
ZNF595	152687	hgsc.bcm.edu	37	chr4	59340	59340	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	caggaactcgtaacattcagGgatgtggccatagaattctc	10	9	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr4:59340G>T	ENST00000509152.2	+	2	206	c.21G>T	c.(19-21)agG>agT	p.R7S	ZNF595_ENST00000339368.6_3'UTR|ZNF595_ENST00000526473.2_Missense_Mutation_p.R7S			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	7	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TAACATTCAGGGATGTGGCCA	0.418																																					p.R7S		Atlas-SNP	.											.	.	.	.	0			c.G21T						.						358	385	376					4																	59340		2203	4300	6503	SO:0001583	missense	255403	exon2			ATTCAGGGATGTG	BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"Zinc fingers, C2H2-type", "-"	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.21G>T	chr4.hg19:g.59340G>T	ENSP00000434858:p.Arg7Ser	328.0	0.0		308.0	18.0	NM_001039127		Missense_Mutation	SNP	ENST00000509152.2	hg19		.	.	.	.	.	.	.	.	.	.	G	11.89	1.773554	0.31411	.	.	ENSG00000197701	ENST00000509152;ENST00000526473	T;T	0.01787	4.64;4.64	1.26	1.26	0.21427	Krueppel-associated box (4);	.	.	.	.	T	0.01835	0.0058	.	.	.	0.24906	N	0.992073	B	0.26775	0.159	B	0.30179	0.112	T	0.45425	-0.9262	8	0.72032	D	0.01	.	4.5605	0.12158	0.0:0.0:0.6249:0.3751	.	7	Q8IYB9	ZN595_HUMAN	S	7	ENSP00000434858:R7S;ENSP00000437878:R7S	ENSP00000434858:R7S	R	+	3	2	ZNF595	49340	0.920000	0.31207	0.528000	0.27938	0.224000	0.24922	0.731000	0.26058	0.655000	0.30866	0.484000	0.47621	AGG	.	.		0.418	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000357817.2	NM_182524		T	59340	G	T	59340	3	4	53	1	0	0	0	0	1	0	0	0	18040	1223	43	3	27	3	ZNF595	4	59340	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10		59340	191094936	27	6727										
SORCS2	57537	hgsc.bcm.edu	37	chr4	7726889	7726889	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gggtccccacagcccccctgCaggccctctacctggaggtg	12	18	1	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr4:7726889C>T	ENST00000507866.2	+	20	2729	c.2620C>T	c.(2620-2622)Cag>Tag	p.Q874*	SORCS2_ENST00000329016.9_Nonsense_Mutation_p.Q702*	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	874	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						AGCCCCCCTGCAGGCCCTCTA	0.552																																					p.Q874X		Atlas-SNP	.											.	SORCS2	98	.	0			c.C2620T						.						77	80	79					4																	7726889		1926	4118	6044	SO:0001587	stop_gained	57537	exon20			CCCCTGCAGGCCC	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2620C>T	chr4.hg19:g.7726889C>T	ENSP00000422185:p.Gln874*	61.0	0.0		56.0	12.0	NM_020777	Q9P2L7	Nonsense_Mutation	SNP	ENST00000507866.2	hg19	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	C	37	6.109498	0.97291	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	.	.	.	3.41	3.41	0.39046	.	0.367852	0.24752	U	0.035899	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	14.8181	0.70050	0.0:1.0:0.0:0.0	.	.	.	.	X	874;702	.	ENSP00000329124:Q702X	Q	+	1	0	SORCS2	7777789	1.000000	0.71417	1.000000	0.80357	0.378000	0.30076	6.721000	0.74728	1.465000	0.48006	0.453000	0.30009	CAG	.	.		0.552	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		T	7726889	C	T	7726889	4	4	53	1	0	0	0	0	0	1	0	0	14946	711	25	3	2698	3	SORCS2	4	7726889	Nonsense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	7667549	7726889	183427387	28	6728										
PDS5A	23244	hgsc.bcm.edu	37	chr4	39876002	39876002	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tggtgtggagtacccctcttTgctttttgatgtaaaatggg	12	6	1	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr4:39876002T>A	ENST00000303538.8	-	20	2723	c.2184A>T	c.(2182-2184)gcA>gcT	p.A728A		NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						TACCCCTCTTTGCTTTTTGAT	0.358																																					p.A728A		Atlas-SNP	.											.	PDS5A	114	.	0			c.A2184T						.						127	116	119					4																	39876002		1822	4085	5907	SO:0001819	synonymous_variant	23244	exon20			CCTCTTTGCTTTT	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.2184A>T	chr4.hg19:g.39876002T>A		55.0	0.0		69.0	14.0	NM_001100399		Silent	SNP	ENST00000303538.8	hg19	CCDS47045.1																																																																																			.	.		0.358	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		A	39876002	T	A	39876002	2	1	53	1	0	0	0	0	0	0	0	1	11700	1799	63	4		4	PDS5A	4	39876002	Silent	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	32149113	39876002	151278274	29	6729										
TIGD2	166815	hgsc.bcm.edu	37	chr4	90035516	90035516	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tgagcaaaagccttccagtaAgagtagaaaaacagaactga	9	7	0	5			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr4:90035516A>G	ENST00000317005.2	+	1	1549	c.1391A>G	c.(1390-1392)aAg>aGg	p.K464R	RP11-84C13.1_ENST00000603357.1_lincRNA|FAM13A_ENST00000502459.1_5'Flank	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	464						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	14		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)		CCTTCCAGTAAGAGTAGAAAA	0.453																																					p.K464R		Atlas-SNP	.											.	TIGD2	36	.	0			c.A1391G						.						51	50	51					4																	90035516		2203	4300	6503	SO:0001583	missense	166815	exon1			CCAGTAAGAGTAG	AK027653	CCDS3633.1	4q21.3	2013-02-21			ENSG00000180346	ENSG00000180346			18333	protein-coding gene	gene with protein product		612973					Standard	NM_145715		Approved		uc003hsk.3	Q4W5G0	OTTHUMG00000130946	ENST00000317005.2:c.1391A>G	chr4.hg19:g.90035516A>G	ENSP00000317170:p.Lys464Arg	96.0	0.0		81.0	15.0	NM_145715		Missense_Mutation	SNP	ENST00000317005.2	hg19	CCDS3633.1	.	.	.	.	.	.	.	.	.	.	A	9.901	1.206835	0.22205	.	.	ENSG00000180346	ENST00000317005	T	0.23754	1.89	4.49	3.31	0.37934	.	0.319358	0.22518	N	0.059011	T	0.13670	0.0331	L	0.36672	1.1	0.09310	N	1	P	0.35656	0.514	B	0.24394	0.053	T	0.11641	-1.0579	10	0.27785	T	0.31	-6.4638	5.2949	0.15747	0.868:0.0:0.132:0.0	.	464	Q4W5G0	TIGD2_HUMAN	R	464	ENSP00000317170:K464R	ENSP00000317170:K464R	K	+	2	0	TIGD2	90254539	0.910000	0.30920	0.133000	0.22050	0.912000	0.54170	3.019000	0.49635	1.881000	0.54492	0.383000	0.25322	AAG	.	.		0.453	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715		G	90035516	A	G	90035516	3	3	53	1	0	0	0	0	1	0	0	0	15911	72	3	2	1393	2	TIGD2	4	90035516	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	50159514	90035516	101118760	30	6730										
ELF2	1998	hgsc.bcm.edu	37	chr4	139983133	139983133	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atatgcctttttctctctgaGtccatttaatatacctggga	6	9	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr4:139983133G>T	ENST00000394235.2	-	8	1158	c.656C>A	c.(655-657)aCt>aAt	p.T219N	ELF2_ENST00000379550.1_Missense_Mutation_p.T231N|ELF2_ENST00000379549.2_Missense_Mutation_p.T142N|ELF2_ENST00000510408.1_Missense_Mutation_p.T159N|ELF2_ENST00000265495.4_Missense_Mutation_p.T219N|ELF2_ENST00000358635.3_Missense_Mutation_p.T171N|ELF2_ENST00000515489.1_5'Flank	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)											endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					TTCTCTCTGAGTCCATTTAAT	0.363																																					p.R171K		Atlas-SNP	.											.	ELF2	43	.	0			c.G512A						.						94	88	90					4																	139983133		2203	4300	6503	SO:0001583	missense	1998	exon5			CTCTGAGTCCATT	AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.656C>A	chr4.hg19:g.139983133G>T	ENSP00000377782:p.Thr219Asn	67.0	0.0		61.0	4.0	NM_006874		Missense_Mutation	SNP	ENST00000394235.2	hg19	CCDS3744.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474008	0.84640	.	.	ENSG00000109381	ENST00000358635;ENST00000394235;ENST00000379550;ENST00000265495;ENST00000379549;ENST00000540754;ENST00000510408;ENST00000420916;ENST00000512627	T;T;T;T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35	5.62	5.62	0.85841	.	0.043583	0.85682	D	0.000000	T	0.75243	0.3823	M	0.85777	2.775	0.80722	D	1	P;D;P;P;D	0.56746	0.933;0.977;0.934;0.861;0.957	P;P;P;P;P	0.62813	0.857;0.907;0.892;0.846;0.9	T	0.77035	-0.2737	9	.	.	.	.	19.661	0.95871	0.0:0.0:1.0:0.0	.	34;219;142;159;171	B7Z8R4;Q15723-1;E9PCX3;B7Z720;Q15723-3	.;.;.;.;.	N	171;219;231;219;142;34;159;142;130	ENSP00000351458:T171N;ENSP00000377782:T219N;ENSP00000368868:T231N;ENSP00000265495:T219N;ENSP00000368867:T142N;ENSP00000426997:T159N;ENSP00000397796:T142N;ENSP00000426087:T130N	.	T	-	2	0	ELF2	140202583	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.835000	0.86780	2.659000	0.90383	0.655000	0.94253	ACT	.	.		0.363	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874		T	139983133	G	T	139983133	3	4	53	1	0	0	0	0	1	0	0	0	5056	1029	36	3	1101	3	ELF2	4	139983133	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	49947617	139983133	51171143	31	6731										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11384929	11384929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gctggtggatgggcgaggagGagatggtggactgcacggtg	22	5	0	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:11384929G>A	ENST00000304623.8	-	7	1214	c.1025C>T	c.(1024-1026)tCc>tTc	p.S342F	CTNND2_ENST00000359640.2_Missense_Mutation_p.S342F|CTNND2_ENST00000495388.2_5'Flank|CTNND2_ENST00000458100.2_Intron|CTNND2_ENST00000511377.1_Missense_Mutation_p.S251F|CTNND2_ENST00000503622.1_Intron	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	342					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GGGCGAGGAGGAGATGGTGGA	0.667																																					p.S342F		Atlas-SNP	.											.	CTNND2	289	.	0			c.C1025T						.						88	84	85					5																	11384929		2200	4299	6499	SO:0001583	missense	1501	exon7			GAGGAGGAGATGG	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.1025C>T	chr5.hg19:g.11384929G>A	ENSP00000307134:p.Ser342Phe	26.0	0.0		28.0	9.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.189372	0.78789	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377	T;T;T	0.79653	-1.23;-1.29;-1.25	4.19	4.19	0.49359	.	0.567752	0.16119	N	0.228731	T	0.80248	0.4588	L	0.43152	1.355	0.80722	D	1	P	0.49961	0.93	P	0.48030	0.564	T	0.82906	-0.0225	10	0.72032	D	0.01	-9.6331	16.1132	0.81278	0.0:0.0:1.0:0.0	.	342	Q9UQB3	CTND2_HUMAN	F	342;342;251	ENSP00000307134:S342F;ENSP00000352661:S342F;ENSP00000426510:S251F	ENSP00000307134:S342F	S	-	2	0	CTNND2	11437929	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.165000	0.71891	1.882000	0.54519	0.462000	0.41574	TCC	.	.		0.667	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11384929	G	A	11384929	3	1	53	1	0	0	0	0	1	0	0	0	4022	1174	41	3	2716	3	CTNND2	5	11384929	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10		11384929	169530331	32	6732										
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41042223	41042223	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atcccccagttggttgggagCagtcagaaactccttaatct	9	11	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:41042223C>A	ENST00000399564.4	-	19	2374	c.1924G>T	c.(1924-1926)Gct>Tct	p.A642S	MROH2B_ENST00000506092.2_Missense_Mutation_p.A197S	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	642																	TGGTTGGGAGCAGTCAGAAAC	0.433																																					p.A642S		Atlas-SNP	.											.	.	.	.	0			c.G1924T						.						60	55	56					5																	41042223		1840	4092	5932	SO:0001583	missense	133558	exon19			TGGGAGCAGTCAG		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.1924G>T	chr5.hg19:g.41042223C>A	ENSP00000382476:p.Ala642Ser	87.0	0.0		80.0	32.0	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	hg19	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.560902	0.27827	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.01369	4.97;5.22	5.79	-1.24	0.09435	Armadillo-type fold (1);	0.543746	0.16865	N	0.196343	T	0.01092	0.0036	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.49082	-0.8976	10	0.10636	T	0.68	.	4.9854	0.14187	0.5785:0.2413:0.0:0.1802	.	642	Q7Z745	HTRB2_HUMAN	S	197;347;642	ENSP00000441504:A197S;ENSP00000382476:A642S	ENSP00000296803:A347S	A	-	1	0	HEATR7B2	41077980	0.003000	0.15002	0.680000	0.29994	0.658000	0.38924	-0.139000	0.10358	0.053000	0.16036	0.460000	0.39030	GCT	.	.		0.433	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		A	41042223	C	A	41042223	3	1	53	1	0	0	0	0	1	0	0	0	7044	710	25	3	2929	3	HEATR7B2	5	41042223	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	29657294	41042223	139873037	33	6733										
BDP1	55814	hgsc.bcm.edu	37	chr5	70840961	70840961	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gccctgcacacttggtttggAtaggggtcttggtgaaaatt	13	7	1	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:70840961A>T	ENST00000358731.4	+	32	6922	c.6659A>T	c.(6658-6660)gAt>gTt	p.D2220V	BDP1_ENST00000380675.2_Missense_Mutation_p.D356V	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2220					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.D2220V(1)		NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		CTTGGTTTGGATAGGGGTCTT	0.463																																					p.D2220V		Atlas-SNP	.											BDP1,NS,carcinoma,0,1	BDP1	204	.	1	Substitution - Missense(1)	lung(1)	c.A6659T						.						115	109	111					5																	70840961		1845	4098	5943	SO:0001583	missense	55814	exon32			GTTTGGATAGGGG	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.6659A>T	chr5.hg19:g.70840961A>T	ENSP00000351575:p.Asp2220Val	101.0	0.0		82.0	17.0	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	hg19	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	A	9.541	1.113418	0.20795	.	.	ENSG00000145734	ENST00000358731;ENST00000451951;ENST00000380675;ENST00000545546	T;T	0.45276	3.83;0.9	4.11	-8.22	0.01037	.	1.627000	0.03383	N	0.200682	T	0.32224	0.0822	L	0.44542	1.39	0.09310	N	1	P;P	0.38020	0.615;0.615	B;B	0.37091	0.124;0.241	T	0.44406	-0.9330	10	0.62326	D	0.03	.	7.8518	0.29459	0.5454:0.3054:0.1492:0.0	.	2220;2220	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	V	2220;1768;356;356	ENSP00000351575:D2220V;ENSP00000370050:D356V	ENSP00000351575:D2220V	D	+	2	0	BDP1	70876717	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-0.446000	0.06837	-2.571000	0.00468	-0.899000	0.02877	GAT	.	.		0.463	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		T	70840961	A	T	70840961	3	4	53	1	0	0	0	0	1	0	0	0	1395	333	12	4	6785	4	BDP1	5	70840961	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	29798738	70840961	110074299	34	6734										
GPR98	84059	hgsc.bcm.edu	37	chr5	89943506	89943506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ttggaagtagacagcagagcAtatccatatttgttaatgaa	9	5	0	3			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:89943506A>G	ENST00000405460.2	+	17	3310	c.3214A>G	c.(3214-3216)Ata>Gta	p.I1072V		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1072	Calx-beta 8. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ACAGCAGAGCATATCCATATT	0.383																																					p.I1072V		Atlas-SNP	.											.	GPR98	605	.	0			c.A3214G						.						144	138	140					5																	89943506		1871	4103	5974	SO:0001583	missense	84059	exon17			CAGAGCATATCCA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.3214A>G	chr5.hg19:g.89943506A>G	ENSP00000384582:p.Ile1072Val	128.0	0.0		107.0	52.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.954|8.954	0.968848|0.968848	0.18659|0.18659	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000504142|ENST00000405460;ENST00000296619;ENST00000399043	.|T	.|0.27890	.|1.64	5.49|5.49	-3.41|-3.41	0.04839|0.04839	.|Na-Ca exchanger/integrin-beta4 (2);	.|0.194186	.|0.53938	.|N	.|0.000058	T|T	0.25865|0.25865	0.0630|0.0630	L|L	0.60904|0.60904	1.88|1.88	0.46149|0.46149	D|D	0.998891|0.998891	.|B	.|0.31655	.|0.334	.|B	.|0.41510	.|0.359	T|T	0.13495|0.13495	-1.0507|-1.0507	5|10	.|0.49607	.|T	.|0.09	.|.	0.5087|0.5087	0.00591|0.00591	0.4146:0.1961:0.1777:0.2116|0.4146:0.1961:0.1777:0.2116	.|.	.|1072	.|Q8WXG9	.|GPR98_HUMAN	R|V	660|1072	.|ENSP00000384582:I1072V	.|ENSP00000296619:I1072V	H|I	+|+	2|1	0|0	GPR98|GPR98	89979262|89979262	0.003000|0.003000	0.15002|0.15002	0.000000|0.000000	0.03702|0.03702	0.376000|0.376000	0.30014|0.30014	0.019000|0.019000	0.13444|0.13444	-0.904000|-0.904000	0.03876|0.03876	0.528000|0.528000	0.53228|0.53228	CAT|ATA	.	.		0.383	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	89943506	A	G	89943506	3	3	53	1	0	0	0	0	1	0	0	0	6730	217	8	2	3280	2	GPR98	5	89943506	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	19102545	89943506	90971754	35	6735										
KCNN2	3781	hgsc.bcm.edu	37	chr5	113798833	113798833	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ctctccattggttatggtgaCatggtacctaacacatactg	8	10	1	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:113798833C>T	ENST00000512097.3	+	5	2107	c.1089C>T	c.(1087-1089)gaC>gaT	p.D363D	KCNN2_ENST00000503706.1_Silent_p.D15D|KCNN2_ENST00000264773.3_Silent_p.D363D|KCNN2_ENST00000507750.1_3'UTR			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	363					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	GTTATGGTGACATGGTACCTA	0.383																																					p.D363D		Atlas-SNP	.											.	KCNN2	144	.	0			c.C1089T						.						303	259	274					5																	113798833		2202	4300	6502	SO:0001819	synonymous_variant	3781	exon4			TGGTGACATGGTA	AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.1089C>T	chr5.hg19:g.113798833C>T		283.0	0.0		306.0	62.0	NM_021614	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Silent	SNP	ENST00000512097.3	hg19	CCDS4114.1																																																																																			.	.		0.383	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614		T	113798833	C	T	113798833	2	4	53	1	0	0	0	0	0	0	0	1	8088	477	17	3		3	KCNN2	5	113798833	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	23855327	113798833	67116427	36	6736										
AFF4	27125	hgsc.bcm.edu	37	chr5	132269980	132269980	+	Frame_Shift_Del	DEL	G	G	-													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atggactcctgtccgtccatGggccgcacataggcagtggg					rs200345107		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:132269980delG	ENST00000265343.5	-	3	1156	c.777delC	c.(775-777)cccfs	p.P259fs	AFF4_ENST00000491831.1_5'UTR|AFF4_ENST00000378595.3_Frame_Shift_Del_p.P259fs	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	259	Ser-rich.				spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTCCGTCCATGGGCCGCACAT	0.507																																					p.M260fs	Ovarian(126;889 1733 2942 10745 11605)	Pindel	.											.	AFF4	120	.	0			c.778delA						.						168	151	157					5																	132269980		2203	4300	6503	SO:0001589	frameshift_variant	27125	exon3			.	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.777delC	chr5.hg19:g.132269980delG	ENSP00000265343:p.Pro259fs	274.0	0.0		368.0	86.0	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Frame_Shift_Del	DEL	ENST00000265343.5	hg19	CCDS4164.1																																																																																			.	.		0.507	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		-	132269980	G	-	132269980	7	5	53	1	0	1	0	1	0	0	0	0	359	1335	47	0	2790	0	AFF4	5	132269980	Frame_Shift_Del	DEL	G	TCGA-BW-A5NQ-01A-11D-A27I-10	18471147	132269980	48645280	37	6737										
FAT2	2196	hgsc.bcm.edu	37	chr5	150885501	150885501	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atctccagggggaaggggaaGcccccatagaggccattagg	15	10	1	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:150885501G>A	ENST00000261800.5	-	23	12687	c.12675C>T	c.(12673-12675)ggC>ggT	p.G4225G		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	4225					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGAAGGGGAAGCCCCCATAGA	0.622																																					p.G4225G		Atlas-SNP	.											.	FAT2	465	.	0			c.C12675T						.						93	111	105					5																	150885501		2202	4300	6502	SO:0001819	synonymous_variant	2196	exon23			GGGGAAGCCCCCA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.12675C>T	chr5.hg19:g.150885501G>A		19.0	0.0		32.0	8.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	9.683	1.149935	0.21371	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.02	1.19	0.21007	.	.	.	.	.	T	0.53334	0.1790	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39251	-0.9623	4	.	.	.	.	6.2156	0.20653	0.2732:0.0:0.6077:0.1191	.	.	.	.	F	998	.	.	L	-	1	0	FAT2	150865694	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	1.567000	0.36407	-0.073000	0.12842	0.561000	0.74099	CTT	.	.		0.622	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150885501	G	A	150885501	2	1	53	1	0	0	0	0	0	0	0	1	5698	958	34	3		3	FAT2	5	150885501	Silent	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	18615521	150885501	30029759	38	6738										
LCP2	3937	hgsc.bcm.edu	37	chr5	169689858	169689859	+	Frame_Shift_Ins	INS	-	-	T													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gtcttaccttcccgctggaaINStcgagggctgcaagacagga							TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:169689858_169689859insT	ENST00000046794.5	-	12	1420_1421	c.805_806insA	c.(805-807)attfs	p.I269fs	LCP2_ENST00000521416.1_Frame_Shift_Ins_p.I64fs	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	269					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TCCCGCTGGAATCGAGGGCTGC	0.426																																					p.I269fs		Atlas-INDEL	.											.	LCP2	133	.	0			c.806_807insA						.																																			SO:0001589	frameshift_variant	3937	exon12			.		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.806dupA	chr5.hg19:g.169689859_169689859dupT	ENSP00000046794:p.Ile269fs	179.0	0.0		194.0	30.0	NM_005565	A8KA25|Q53XV4	Frame_Shift_Ins	INS	ENST00000046794.5	hg19	CCDS47339.1																																																																																			.	.		0.426	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		T	169689859	-	T	169689858	7	5	53	1	0	1	1	0	0	0	0	0	8701	101	4	0	835	0	LCP2	5	169689858	Frame_Shift_Ins	INS	-	TCGA-BW-A5NQ-01A-11D-A27I-10	18804357	169689858	11225402	39	6739	29	2								
LCP2	3937	hgsc.bcm.edu	37	chr5	169689860	169689860	+	Silent	SNP	C	C	T													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tcttaccttcccgctggaatCgagggctgcaagacaggagg					rs373086683		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:169689860C>T	ENST00000046794.5	-	12	1419	c.804G>A	c.(802-804)tcG>tcA	p.S268S	LCP2_ENST00000521416.1_Silent_p.S63S	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	268					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		CCGCTGGAATCGAGGGCTGCA	0.423																																					p.S268S		Atlas-SNP	.											.	LCP2	133	.	0			c.G804A						.						135	133	134					5																	169689860		1973	4157	6130	SO:0001819	synonymous_variant	3937	exon12			TGGAATCGAGGGC		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.804G>A	chr5.hg19:g.169689860C>T		175.0	0.0		195.0	31.0	NM_005565	A8KA25|Q53XV4	Silent	SNP	ENST00000046794.5	hg19	CCDS47339.1																																																																																			.	.		0.423	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		T	169689860	C	T	169689860	2	4	53	1	0	0	0	0	0	0	0	1	8701	871	31	1		1	LCP2	5	169689860	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	2	169689860	11225400	40	6740	29	2								
HRH2	3274	hgsc.bcm.edu	37	chr5	175110734	175110734	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	agcaggaacgagaccagcaaGggcaatcataccacctctaa	9	12	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:175110734G>A	ENST00000231683.2	+	1	2271	c.498G>A	c.(496-498)aaG>aaA	p.K166K	HRH2_ENST00000377291.2_Silent_p.K166K	NM_022304.2	NP_071640.1	P25021	HRH2_HUMAN	histamine receptor H2	166					digestive tract development (GO:0048565)|epithelial cell morphogenesis (GO:0003382)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|gastrin-induced gastric acid secretion (GO:0001698)|gland development (GO:0048732)|histamine-induced gastric acid secretion (GO:0001697)|immune response (GO:0006955)|memory (GO:0007613)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(10)|ovary(1)	22	all_cancers(89;0.00805)|Renal(175;0.000269)|Lung NSC(126;0.00419)|all_lung(126;0.00711)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Colorectal(1;0.0154)|COAD - Colon adenocarcinoma(1;0.149)	Amitriptyline(DB00321)|Asenapine(DB06216)|Betazole(DB00272)|Cimetidine(DB00501)|Doxepin(DB01142)|Epinastine(DB00751)|Famotidine(DB00927)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Methantheline(DB00940)|Nizatidine(DB00585)|Olanzapine(DB00334)|Ranitidine(DB00863)|Roxatidine acetate(DB08806)|Tolazoline(DB00797)	AGACCAGCAAGGGCAATCATA	0.527																																					p.K166K		Atlas-SNP	.											.	HRH2	108	.	0			c.G498A						.						114	94	101					5																	175110734		2203	4300	6503	SO:0001819	synonymous_variant	3274	exon2			CAGCAAGGGCAAT		CCDS4395.1, CCDS47344.1	5q35	2012-08-08			ENSG00000113749	ENSG00000113749		"GPCR / Class A : Histamine receptors"	5183	protein-coding gene	gene with protein product		142703				1714721	Standard	NM_022304		Approved		uc003mdc.4	P25021	OTTHUMG00000130660	ENST00000231683.2:c.498G>A	chr5.hg19:g.175110734G>A		206.0	0.0		218.0	14.0	NM_001131055	B5BUP7|Q14464|Q7Z5R9	Silent	SNP	ENST00000231683.2	hg19	CCDS4395.1																																																																																			.	.		0.527	HRH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253151.1			A	175110734	G	A	175110734	2	1	53	1	0	0	0	0	0	0	0	1	7365	991	35	3		3	HRH2	5	175110734	Silent	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	5420874	175110734	5804526	41	6741										
CCHCR1	54535	hgsc.bcm.edu	37	chr6	31113531	31113531	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	cggttgttgaggctgggaagCtgggcggcagccccttccac	16	12	0	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr6:31113531C>A	ENST00000376266.5	-	11	1490	c.1368G>T	c.(1366-1368)caG>caT	p.Q456H	CCHCR1_ENST00000451521.2_Missense_Mutation_p.Q509H|CCHCR1_ENST00000396268.3_Missense_Mutation_p.Q545H|CCHCR1_ENST00000396263.2_Intron	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	456					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						GGCTGGGAAGCTGGGCGGCAG	0.622																																					p.Q545H		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G1635T						.						92	80	84					6																	31113531		1511	2709	4220	SO:0001583	missense	54535	exon11			GGGAAGCTGGGCG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"chromosome 6 open reading frame 18"	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1368G>T	chr6.hg19:g.31113531C>A	ENSP00000365442:p.Gln456His	92.0	0.0		78.0	25.0	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	hg19	CCDS4695.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.350144	0.41599	.	.	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000440185;ENST00000451521	T;T;T	0.03951	3.75;3.75;3.75	4.83	3.0	0.34707	.	0.610314	0.15113	N	0.279871	T	0.03178	0.0093	L	0.43152	1.355	0.19775	N	0.999951	P;P;P;D;P	0.54397	0.771;0.794;0.771;0.966;0.545	P;P;P;P;B	0.52267	0.606;0.601;0.606;0.694;0.371	T	0.37979	-0.9682	10	0.66056	D	0.02	-10.0625	6.7147	0.23296	0.0:0.7204:0.1804:0.0991	.	456;456;456;509;545	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	H	545;456;456;509	ENSP00000379566:Q545H;ENSP00000365442:Q456H;ENSP00000401039:Q509H	ENSP00000365442:Q456H	Q	-	3	2	CCHCR1	31221510	0.987000	0.35691	0.953000	0.39169	0.250000	0.25880	1.342000	0.33919	0.534000	0.28695	0.549000	0.68633	CAG	.	.		0.622	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052		A	31113531	C	A	31113531	3	1	53	1	0	0	0	0	1	0	0	0	2879	796	28	3	1012	3	CCHCR1	6	31113531	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10		31113531	140001536	42	6742										
BVES	11149	hgsc.bcm.edu	37	chr6	105573357	105573357	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tttcaaggtttggatcatgcAaaactgtccagttagtcttc	8	8	3	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr6:105573357A>T	ENST00000314641.5	-	4	664	c.448T>A	c.(448-450)Tgc>Agc	p.C150S	BVES_ENST00000446408.2_Missense_Mutation_p.C150S|BVES_ENST00000336775.5_Missense_Mutation_p.C150S	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	150					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)			NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				TGGATCATGCAAAACTGTCCA	0.433																																					p.C150S		Atlas-SNP	.											.	BVES	33	.	0			c.T448A						.						158	156	156					6																	105573357		2203	4300	6503	SO:0001583	missense	11149	exon4			TCATGCAAAACTG	AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"popeye domain containing 1"	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.448T>A	chr6.hg19:g.105573357A>T	ENSP00000313172:p.Cys150Ser	136.0	0.0		161.0	54.0	NM_001199563	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Missense_Mutation	SNP	ENST00000314641.5	hg19	CCDS5051.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.614998	0.87359	.	.	ENSG00000112276	ENST00000314641;ENST00000336775;ENST00000446408	T;T;T	0.27402	1.67;1.67;1.67	5.76	5.76	0.90799	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.081344	0.85682	D	0.000000	T	0.26702	0.0653	L	0.40543	1.245	0.80722	D	1	D	0.63046	0.992	P	0.60117	0.869	T	0.04723	-1.0931	10	0.08837	T	0.75	-14.7206	16.0458	0.80720	1.0:0.0:0.0:0.0	.	150	Q8NE79	POPD1_HUMAN	S	150	ENSP00000313172:C150S;ENSP00000337259:C150S;ENSP00000397310:C150S	ENSP00000313172:C150S	C	-	1	0	BVES	105680050	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.830000	0.92063	2.192000	0.70111	0.533000	0.62120	TGC	.	.		0.433	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147		T	105573357	A	T	105573357	3	4	53	1	0	0	0	0	1	0	0	0	1577	130	5	4	654	4	BVES	6	105573357	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	74459826	105573357	65541710	43	6743										
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143095836	143095836	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atcagtttctccagaccttgAggtagctttttgtcctagag	9	9	2	3			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr6:143095836A>C	ENST00000367604.1	-	4	679	c.40T>G	c.(40-42)Tca>Gca	p.S14A	HIVEP2_ENST00000012134.2_Missense_Mutation_p.S14A|HIVEP2_ENST00000367603.2_Missense_Mutation_p.S14A			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	14					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		CCAGACCTTGAGGTAGCTTTT	0.463																																					p.S14A	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.T40G						.						190	177	181					6																	143095836		1953	4169	6122	SO:0001583	missense	3097	exon5			ACCTTGAGGTAGC	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.40T>G	chr6.hg19:g.143095836A>C	ENSP00000356576:p.Ser14Ala	177.0	0.0		237.0	89.0	NM_006734	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	hg19	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.763817	0.49574	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02446	4.29;4.29;4.29	5.56	5.56	0.83823	.	0.256825	0.39834	N	0.001244	T	0.02533	0.0077	L	0.60455	1.87	0.29347	N	0.865594	P	0.43788	0.817	B	0.41764	0.366	T	0.16129	-1.0413	10	0.66056	D	0.02	-12.2929	16.0068	0.80367	1.0:0.0:0.0:0.0	.	14	P31629	ZEP2_HUMAN	A	14	ENSP00000356576:S14A;ENSP00000356575:S14A;ENSP00000012134:S14A	ENSP00000012134:S14A	S	-	1	0	HIVEP2	143137529	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.110000	0.50352	2.240000	0.73641	0.528000	0.53228	TCA	.	.		0.463	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			C	143095836	A	C	143095836	3	2	53	1	0	0	0	0	1	0	0	0	7196	304	11	5	7324	5	HIVEP2	6	143095836	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	37522479	143095836	28019231	44	6744										
GNAI1	2770	hgsc.bcm.edu	37	chr7	79833109	79833109	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tagagtgaaaactacaggaaTtgttgaaacccattttactt	7	6	0	3			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr7:79833109T>C	ENST00000351004.3	+	5	924	c.551T>C	c.(550-552)aTt>aCt	p.I184T	GNAI1_ENST00000457358.2_Missense_Mutation_p.I132T	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	184					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						ACTACAGGAATTGTTGAAACC	0.299																																					p.I184T		Atlas-SNP	.											.	GNAI1	44	.	0			c.T551C						.						72	68	69					7																	79833109		2201	4298	6499	SO:0001583	missense	2770	exon5			CAGGAATTGTTGA	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"Gi1 protein alpha subunit"	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.551T>C	chr7.hg19:g.79833109T>C	ENSP00000343027:p.Ile184Thr	102.0	0.0		150.0	40.0	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Missense_Mutation	SNP	ENST00000351004.3	hg19	CCDS5595.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.712836	0.89112	.	.	ENSG00000127955	ENST00000351004;ENST00000418742;ENST00000457358	D;D;D	0.91011	-2.77;-2.77;-2.77	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.96972	0.9011	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98188	1.0461	9	.	.	.	.	16.2652	0.82574	0.0:0.0:0.0:1.0	.	184	P63096	GNAI1_HUMAN	T	184;132;132	ENSP00000343027:I184T;ENSP00000389435:I132T;ENSP00000410572:I132T	.	I	+	2	0	GNAI1	79671045	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.949000	0.87791	2.241000	0.73720	0.528000	0.53228	ATT	.	.		0.299	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		C	79833109	T	C	79833109	3	2	53	1	0	0	0	0	1	0	0	0	6512	1493	52	2	569	2	GNAI1	7	79833109	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10		79833109	79305554	45	6745										
KIAA1324L	222223	hgsc.bcm.edu	37	chr7	86526919	86526919	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	cccacaggaaatagaacgtaCacccatcacaggtacctgct	7	14	1	1	rs553991387		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr7:86526919C>T	ENST00000450689.2	-	19	2773	c.2588G>A	c.(2587-2589)tGt>tAt	p.C863Y	KIAA1324L_ENST00000444627.1_Missense_Mutation_p.C792Y|KIAA1324L_ENST00000416314.1_Missense_Mutation_p.C696Y|KIAA1324L_ENST00000297222.6_Missense_Mutation_p.C623Y	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	863						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					ATAGAACGTACACCCATCACA	0.453																																					p.C863Y		Atlas-SNP	.											.	KIAA1324L	225	.	0			c.G2588A						.						97	84	88					7																	86526919		2203	4300	6503	SO:0001583	missense	222223	exon19			AACGTACACCCAT	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.2588G>A	chr7.hg19:g.86526919C>T	ENSP00000413445:p.Cys863Tyr	98.0	0.0		122.0	30.0	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Missense_Mutation	SNP	ENST00000450689.2	hg19	CCDS47632.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.728619	0.89390	.	.	ENSG00000164659	ENST00000450689;ENST00000297222;ENST00000444627;ENST00000416314	T;T;T;T	0.16324	2.35;2.35;2.35;2.35	5.59	5.59	0.84812	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.49218	0.1544	M	0.85630	2.765	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.54302	-0.8314	10	0.87932	D	0	.	18.5874	0.91196	0.0:1.0:0.0:0.0	.	863;623;696	A8MWY0;A8MWY0-2;B4DJV3	K132L_HUMAN;.;.	Y	863;623;792;696	ENSP00000413445:C863Y;ENSP00000297222:C623Y;ENSP00000397377:C792Y;ENSP00000402390:C696Y	ENSP00000297222:C623Y	C	-	2	0	KIAA1324L	86364855	1.000000	0.71417	0.941000	0.38009	0.980000	0.70556	7.818000	0.86416	2.642000	0.89623	0.650000	0.86243	TGT	.	.		0.453	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		T	86526919	C	T	86526919	3	4	53	1	0	0	0	0	1	0	0	0	8233	478	17	3	517	3	KIAA1324L	7	86526919	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	6693810	86526919	72611744	46	6746										
CPA4	51200	hgsc.bcm.edu	37	chr7	129951882	129951882	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gattcccccttcccaggacaAggtggcgaggcttgcggcca	13	14	0	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr7:129951882A>T	ENST00000222482.4	+	10	1026	c.998A>T	c.(997-999)aAg>aTg	p.K333M	CPA4_ENST00000493259.1_Missense_Mutation_p.K229M|CPA4_ENST00000445470.2_Missense_Mutation_p.K300M	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	333					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					TCCCAGGACAAGGTGGCGAGG	0.537																																					p.K333M		Atlas-SNP	.											.	CPA4	47	.	0			c.A998T						.						72	65	67					7																	129951882		2203	4300	6503	SO:0001583	missense	51200	exon10			AGGACAAGGTGGC	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"carboxypeptidase A3"	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.998A>T	chr7.hg19:g.129951882A>T	ENSP00000222482:p.Lys333Met	99.0	0.0		127.0	34.0	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	hg19	CCDS5818.1	.	.	.	.	.	.	.	.	.	.	A	6.952	0.545519	0.13312	.	.	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.11277	2.79;2.79;2.79	6.02	2.32	0.28847	Peptidase M14, carboxypeptidase A (2);	1.293600	0.04827	N	0.438014	T	0.12646	0.0307	L	0.48935	1.535	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.17098	0.017;0.008	T	0.36383	-0.9750	10	0.54805	T	0.06	.	6.6356	0.22881	0.4876:0.2615:0.0:0.251	.	300;333	B7Z576;Q9UI42	.;CBPA4_HUMAN	M	300;333;138;229	ENSP00000412947:K300M;ENSP00000222482:K333M;ENSP00000419660:K229M	ENSP00000222482:K333M	K	+	2	0	CPA4	129739118	0.000000	0.05858	0.129000	0.21949	0.068000	0.16541	-0.060000	0.11712	0.158000	0.19367	-1.139000	0.01908	AAG	.	.		0.537	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352		T	129951882	A	T	129951882	3	4	53	1	0	0	0	0	1	0	0	0	3794	72	3	4	1036	4	CPA4	7	129951882	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	43424963	129951882	29186781	47	6747										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113240991	113240991	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atcaatgagcttacctttgtTtataaagataaaatccaaat	4	6	1	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr8:113240991T>G	ENST00000297405.5	-	70	11202	c.10958A>C	c.(10957-10959)aAa>aCa	p.K3653T	CSMD3_ENST00000343508.3_Missense_Mutation_p.K3613T|CSMD3_ENST00000455883.2_Missense_Mutation_p.K3484T|CSMD3_ENST00000352409.3_Missense_Mutation_p.K3583T	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3653						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTACCTTTGTTTATAAAGATA	0.299										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.K3653T		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A10958C						.						64	70	68					8																	113240991		2203	4295	6498	SO:0001583	missense	114788	exon70			CTTTGTTTATAAA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10958A>C	chr8.hg19:g.113240991T>G	ENSP00000297405:p.Lys3653Thr	37.0	0.0		33.0	19.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.688300	0.88639	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.41400	1.35;1.34;1.43;1.0;1.39	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.65739	0.2720	M	0.73962	2.25	0.54753	D	0.999988	D;D;D	0.89917	1.0;0.999;0.988	D;D;P	0.85130	0.997;0.994;0.693	T	0.69304	-0.5180	10	0.72032	D	0.01	.	16.2119	0.82168	0.0:0.0:0.0:1.0	.	3484;3653;3613	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	T	3613;3653;2923;3484;3583	ENSP00000345799:K3613T;ENSP00000297405:K3653T;ENSP00000341558:K2923T;ENSP00000412263:K3484T;ENSP00000343124:K3583T	ENSP00000297405:K3653T	K	-	2	0	CSMD3	113310167	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.997000	0.88414	2.288000	0.76882	0.482000	0.46254	AAA	.	.		0.299	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113240991	T	G	113240991	3	3	53	1	0	0	0	0	1	0	0	0	3948	1841	64	5	173	5	CSMD3	8	113240991	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10		113240991	33123031	48	6748										
TG	7038	hgsc.bcm.edu	37	chr8	133906037	133906037	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ttctcggttccctctgggggAgagtttcctggtggccaagg	15	10	2	1	rs61736740		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr8:133906037A>T	ENST00000220616.4	+	11	2904	c.2864A>T	c.(2863-2865)gAg>gTg	p.E955V	TG_ENST00000377869.1_Missense_Mutation_p.E955V	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	955	Thyroglobulin type-1 8. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CCTCTGGGGGAGAGTTTCCTG	0.582																																					p.E955V		Atlas-SNP	.											.	TG	416	.	0			c.A2864T						.						126	118	120					8																	133906037		2203	4300	6503	SO:0001583	missense	7038	exon11			TGGGGGAGAGTTT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.2864A>T	chr8.hg19:g.133906037A>T	ENSP00000220616:p.Glu955Val	236.0	1.0		247.0	109.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	a	14.62	2.589216	0.46110	.	.	ENSG00000042832	ENST00000377869;ENST00000220616	T;T	0.65916	-0.18;-0.18	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000015	T	0.54127	0.1839	L	0.46157	1.445	0.28834	N	0.896988	B	0.20671	0.047	B	0.21708	0.036	T	0.56068	-0.8040	10	0.72032	D	0.01	.	9.279	0.37716	0.8392:0.0:0.0:0.1608	.	955	P01266	THYG_HUMAN	V	955	ENSP00000367100:E955V;ENSP00000220616:E955V	ENSP00000220616:E955V	E	+	2	0	TG	133975219	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	3.711000	0.54868	1.950000	0.56595	0.313000	0.20887	GAG	.	A|0.987;C|0.013		0.582	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133906037	A	T	133906037	3	4	53	1	0	0	0	0	1	0	0	0	15828	304	11	4	2906	4	TG	8	133906037	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	20665046	133906037	12457985	49	6749										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5922603	5922603	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gatgaacaatgttgttctgtAcctttctgttgaagtggtgg	12	5	2	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr9:5922603A>G	ENST00000399933.3	-	8	3392	c.3393T>C	c.(3391-3393)ggT>ggC	p.G1131G	KIAA2026_ENST00000381461.2_Silent_p.G1101G	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1131										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		GTTGTTCTGTACCTTTCTGTT	0.368																																					p.G1131G		Atlas-SNP	.											.	KIAA2026	231	.	0			c.T3393C						.						129	123	125					9																	5922603		1883	4111	5994	SO:0001819	synonymous_variant	158358	exon8			TTCTGTACCTTTC	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.3393T>C	chr9.hg19:g.5922603A>G		105.0	0.0		93.0	36.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	hg19																																																																																				.	.		0.368	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		G	5922603	A	G	5922603	2	3	53	1	0	0	0	0	0	0	0	1	8279	378	14	2		2	KIAA2026	9	5922603	Silent	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10		5922603	135290828	50	6750										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113312196	113312196	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tgtagcaggtaacagtgctcCtcctttggggtggaagccat	13	9	0	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr9:113312196C>T	ENST00000401783.2	-	2	1056	c.720G>A	c.(718-720)gaG>gaA	p.E240E	SVEP1_ENST00000374469.1_Silent_p.E217E|SVEP1_ENST00000374461.1_Silent_p.E217E|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000302728.8_Silent_p.E240E	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	240	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						AACAGTGCTCCTCCTTTGGGG	0.478																																					p.E240E		Atlas-SNP	.											.	SVEP1	326	.	0			c.G720A						.						94	89	91					9																	113312196		1945	4144	6089	SO:0001819	synonymous_variant	79987	exon2			GTGCTCCTCCTTT	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.720G>A	chr9.hg19:g.113312196C>T		207.0	0.0		189.0	38.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.		0.478	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113312196	C	T	113312196	2	4	53	1	0	0	0	0	0	0	0	1	15435	680	24	3		3	SVEP1	9	113312196	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	107389593	113312196	27901235	51	6751										
NLRP14	338323	hgsc.bcm.edu	37	chr11	7064361	7064361	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ctgtttagcatgtgccaagtCcccctagtgtgctgggccgc	12	13	0	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:7064361C>G	ENST00000299481.4	+	4	1450	c.1104C>G	c.(1102-1104)gtC>gtG	p.V368V		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	368	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		TGTGCCAAGTCCCCCTAGTGT	0.453																																					p.V368V		Atlas-SNP	.											.	NLRP14	187	.	0			c.C1104G						.						131	130	131					11																	7064361		2201	4296	6497	SO:0001819	synonymous_variant	338323	exon4			CCAAGTCCCCCTA	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.1104C>G	chr11.hg19:g.7064361C>G		77.0	0.0		102.0	15.0	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	hg19	CCDS7776.1																																																																																			.	.		0.453	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		G	7064361	C	G	7064361	2	3	53	1	0	0	0	0	0	0	0	1	10485	842	30	4		4	NLRP14	11	7064361	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10		7064361	127942155	52	6752										
MRGPRX1	259249	hgsc.bcm.edu	37	chr11	18955438	18955438	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ccaccttcatccacctcagaCgcgtcctgcagagccctctg	7	19	3	2	rs374955450		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:18955438C>A	ENST00000302797.3	-	1	1118	c.894G>T	c.(892-894)gcG>gcT	p.A298A	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'Flank	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	298				AS -> TP (in Ref. 2; AAL86880). {ECO:0000305}.	acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CCACCTCAGACGCGTCCTGCA	0.562																																					p.A298A		Atlas-SNP	.											.	MRGPRX1	84	.	0			c.G894T						.						72	68	69					11																	18955438		2194	4286	6480	SO:0001819	synonymous_variant	259249	exon1			CTCAGACGCGTCC		CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"GPCR / Class A : Orphans"	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.894G>T	chr11.hg19:g.18955438C>A		67.0	0.0		89.0	22.0	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Silent	SNP	ENST00000302797.3	hg19	CCDS7846.1																																																																																			.	.		0.562	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199		A	18955438	C	A	18955438	2	1	53	1	0	0	0	0	0	0	0	1	9775	523	19	1		1	MRGPRX1	11	18955438	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	11891077	18955438	116051078	53	6753										
NELL1	4745	hgsc.bcm.edu	37	chr11	20699518	20699518	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	cctgaccttcagatggatatCgtcaccgagcttgaccttgt	9	12	2	3	rs146112225		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:20699518C>A	ENST00000357134.5	+	2	248	c.96C>A	c.(94-96)atC>atA	p.I32I	NELL1_ENST00000532434.1_Silent_p.I32I|NELL1_ENST00000325319.5_Silent_p.I32I|NELL1_ENST00000298925.5_Silent_p.I60I	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	32					cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						AGATGGATATCGTCACCGAGC	0.473																																					p.I32I		Atlas-SNP	.											.	NELL1	179	.	0			c.C96A						.						176	161	166					11																	20699518		2203	4300	6503	SO:0001819	synonymous_variant	4745	exon2			GGATATCGTCACC	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.96C>A	chr11.hg19:g.20699518C>A		178.0	0.0		231.0	79.0	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	hg19	CCDS7855.1																																																																																			.	C|1.000;T|0.000		0.473	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		A	20699518	C	A	20699518	2	1	53	1	0	0	0	0	0	0	0	1	10342	874	31	1		1	NELL1	11	20699518	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	1744080	20699518	114306998	54	6754										
OR5W2	390148	hgsc.bcm.edu	37	chr11	55681596	55681596	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tgtcatatgtatcaaagcatCtgctattcccaccagataaa	5	10	3	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:55681596C>T	ENST00000344514.1	-	1	462	c.463G>A	c.(463-465)Gat>Aat	p.D155N		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						ATCAAAGCATCTGCTATTCCC	0.448																																					p.D155N	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.G463A						.						81	71	74					11																	55681596		2201	4296	6497	SO:0001583	missense	390148	exon1			AAGCATCTGCTAT	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"GPCR / Class A : Olfactory receptors"	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.463G>A	chr11.hg19:g.55681596C>T	ENSP00000342448:p.Asp155Asn	77.0	0.0		83.0	35.0	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	hg19	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	C	0.115	-1.133505	0.01756	.	.	ENSG00000187612	ENST00000344514	T	0.36520	1.25	5.01	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41712	D	0.000824	T	0.10551	0.0258	N	0.01656	-0.775	0.09310	N	1	B	0.14012	0.009	B	0.24269	0.052	T	0.40001	-0.9586	10	0.02654	T	1	.	5.6206	0.17455	0.1968:0.7044:0.0:0.0987	.	155	Q8NH69	OR5W2_HUMAN	N	155	ENSP00000342448:D155N	ENSP00000342448:D155N	D	-	1	0	OR5W2	55438172	0.000000	0.05858	0.192000	0.23308	0.115000	0.19883	-1.037000	0.03557	2.311000	0.77944	0.549000	0.68633	GAT	.	.		0.448	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		T	55681596	C	T	55681596	3	4	53	1	0	0	0	0	1	0	0	0	11194	913	32	3	471	3	OR5W2	11	55681596	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	34982078	55681596	79324920	55	6755										
ENDOD1	23052	hgsc.bcm.edu	37	chr11	94861677	94861677	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ccaaagaggacagctttaccCattctcccttagcagtgatg	8	12	1	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:94861677C>G	ENST00000278505.4	+	2	555	c.437C>G	c.(436-438)cCa>cGa	p.P146R		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	146						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				CAGCTTTACCCATTCTCCCTT	0.483																																					p.P146R		Atlas-SNP	.											.	ENDOD1	26	.	0			c.C437G						.						122	120	121					11																	94861677		2016	4189	6205	SO:0001583	missense	23052	exon2			TTTACCCATTCTC	BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.437C>G	chr11.hg19:g.94861677C>G	ENSP00000278505:p.Pro146Arg	262.0	0.0		254.0	81.0	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	hg19	CCDS41699.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.669913	0.29693	.	.	ENSG00000149218	ENST00000278505	T	0.80566	-1.39	5.52	4.41	0.53225	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.137701	0.47455	D	0.000235	D	0.89832	0.6829	M	0.87971	2.92	0.32620	N	0.523472	D	0.89917	1.0	D	0.74023	0.982	D	0.92133	0.5714	10	0.72032	D	0.01	-2.9771	13.1853	0.59677	0.0:0.9112:0.0:0.0888	.	146	O94919	ENDD1_HUMAN	R	146	ENSP00000278505:P146R	ENSP00000278505:P146R	P	+	2	0	ENDOD1	94501325	0.964000	0.33143	0.907000	0.35723	0.027000	0.11550	2.173000	0.42472	2.591000	0.87537	0.455000	0.32223	CCA	.	.		0.483	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036		G	94861677	C	G	94861677	3	3	53	1	0	0	0	0	1	0	0	0	5116	594	21	4	443	4	ENDOD1	11	94861677	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	39180081	94861677	40144839	56	6756										
RAB39	54734	hgsc.bcm.edu	37	chr11	107799388	107799388	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tgcaccgcttcacccagggcCgcttccccgggctgcgctcc	11	20	1	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:107799388C>T	ENST00000320578.2	+	1	160	c.94C>T	c.(94-96)Cgc>Tgc	p.R32C	SLC35F2_ENST00000525071.1_5'Flank|SLC35F2_ENST00000429869.1_5'Flank	NM_017516.1	NP_059986.1	Q14964	RB39A_HUMAN	RAB39A, member RAS oncogene family	32					phagosome acidification (GO:0090383)|phagosome-lysosome fusion (GO:0090385)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)										CACCCAGGGCCGCTTCCCCGG	0.662																																					p.R32C		Atlas-SNP	.											.	.	.	.	0			c.C94T						.						41	39	40					11																	107799388		2201	4298	6499	SO:0001583	missense	54734	exon1			CAGGGCCGCTTCC	X99962	CCDS8338.1	11q22.3	2011-11-22	2011-11-22	2011-11-22	ENSG00000179331	ENSG00000179331		"RAB, member RAS oncogene"	16521	protein-coding gene	gene with protein product	"rab-related GTP-binding protein"		"RAB39, member RAS oncogene family"	RAB39		9119394	Standard	NM_017516		Approved		uc001pjt.3	Q14964	OTTHUMG00000166367	ENST00000320578.2:c.94C>T	chr11.hg19:g.107799388C>T	ENSP00000322594:p.Arg32Cys	15.0	0.0		19.0	8.0	NM_017516	A8KAA4|Q8N6W2	Missense_Mutation	SNP	ENST00000320578.2	hg19	CCDS8338.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.986337	0.74589	.	.	ENSG00000179331	ENST00000320578	T	0.77750	-1.12	4.61	4.61	0.57282	Small GTP-binding protein domain (1);	0.000000	0.51477	D	0.000097	T	0.78916	0.4359	M	0.78223	2.4	0.80722	D	1	B	0.11235	0.004	B	0.04013	0.001	T	0.78211	-0.2292	10	0.66056	D	0.02	.	16.7242	0.85417	0.0:1.0:0.0:0.0	.	32	Q14964	RB39A_HUMAN	C	32	ENSP00000322594:R32C	ENSP00000322594:R32C	R	+	1	0	RAB39	107304598	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.923000	0.48868	2.548000	0.85928	0.555000	0.69702	CGC	.	.		0.662	RAB39A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389423.1	NM_017516		T	107799388	C	T	107799388	3	4	53	1	0	0	0	0	1	0	0	0	12944	652	23	1	96	1	RAB39	11	107799388	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	12937711	107799388	27207128	57	6757										
APOA4	337	hgsc.bcm.edu	37	chr11	116693445	116693445	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ggcattgttgctcagctggcTgaagtagtcccacatcaccg	11	12	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:116693445T>C	ENST00000357780.3	-	2	220	c.106A>G	c.(106-108)Agc>Ggc	p.S36G		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	36	13 X 22 AA approximate tandem repeats.				cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		CTCAGCTGGCTGAAGTAGTCC	0.567																																					p.S36G		Atlas-SNP	.											.	APOA4	51	.	0			c.A106G						.						176	150	159					11																	116693445		2201	4296	6497	SO:0001583	missense	337	exon2			GCTGGCTGAAGTA		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"Apolipoproteins"	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.106A>G	chr11.hg19:g.116693445T>C	ENSP00000350425:p.Ser36Gly	97.0	0.0		119.0	41.0	NM_000482	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	hg19	CCDS31681.1	.	.	.	.	.	.	.	.	.	.	T	19.93	3.917991	0.73098	.	.	ENSG00000110244	ENST00000357780	T	0.75821	-0.97	5.19	4.04	0.47022	Apolipoprotein/apolipophorin (1);	1.228650	0.05431	N	0.545956	T	0.80934	0.4719	M	0.75264	2.295	0.24514	N	0.994196	D	0.53885	0.963	P	0.50825	0.651	T	0.62282	-0.6887	10	0.51188	T	0.08	-11.9228	8.5031	0.33170	0.426:0.0:0.0:0.574	.	36	P06727	APOA4_HUMAN	G	36	ENSP00000350425:S36G	ENSP00000350425:S36G	S	-	1	0	APOA4	116198655	0.940000	0.31905	0.999000	0.59377	0.996000	0.88848	1.306000	0.33505	0.957000	0.37930	0.533000	0.62120	AGC	.	.		0.567	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482		C	116693445	T	C	116693445	3	2	53	1	0	0	0	0	1	0	0	0	783	1580	55	2	1092	2	APOA4	11	116693445	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	8894057	116693445	18313071	58	6758										
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1993990	1993990	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ctcgtagtcctccacggcgcCgtcgctgatgagcatgatgg	13	13	0	3	rs375148197		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr12:1993990C>A	ENST00000382722.5	-	11	1578	c.1216G>T	c.(1216-1218)Ggc>Tgc	p.G406C	CACNA2D4_ENST00000585708.1_Missense_Mutation_p.G342C|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.G406C|CACNA2D4_ENST00000585732.1_Missense_Mutation_p.G322C|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.G406C|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.G342C	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	406	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		TCCACGGCGCCGTCGCTGATG	0.577																																					p.G406C	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.G1216T						.						48	55	53					12																	1993990		2055	4189	6244	SO:0001583	missense	93589	exon11			CGGCGCCGTCGCT	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"Calcium channel subunits"	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.1216G>T	chr12.hg19:g.1993990C>A	ENSP00000372169:p.Gly406Cys	197.0	0.0		184.0	42.0	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	hg19	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.785734	0.70337	.	.	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.33216	1.42	5.4	5.4	0.78164	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	T	0.66307	0.2776	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.74771	-0.3552	10	0.87932	D	0	.	19.178	0.93611	0.0:1.0:0.0:0.0	.	406;406	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	C	342;406;406	ENSP00000372169:G406C	ENSP00000280663:G406C	G	-	1	0	CACNA2D4	1864251	1.000000	0.71417	0.465000	0.27155	0.257000	0.26127	7.818000	0.86416	2.528000	0.85240	0.511000	0.50034	GGC	.	.		0.577	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			A	1993990	C	A	1993990	3	1	53	1	0	0	0	0	1	0	0	0	2553	652	23	1	2309	1	CACNA2D4	12	1993990	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10		1993990	131857905	59	6759										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70986132	70986132	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ctgacagtaacttgataaagTcgaccggggactaactcttt	9	9	1	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr12:70986132T>C	ENST00000261266.5	-	5	1085	c.1056A>G	c.(1054-1056)cgA>cgG	p.R352R	PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550358.1_Silent_p.R570R|PTPRB_ENST00000538708.1_Silent_p.R352R|PTPRB_ENST00000551525.1_Silent_p.R569R|PTPRB_ENST00000451516.2_Silent_p.R352R|PTPRB_ENST00000550857.1_Silent_p.R352R|PTPRB_ENST00000334414.6_Silent_p.R570R	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	352	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CTTGATAAAGTCGACCGGGGA	0.463																																					p.R570R		Atlas-SNP	.											.	PTPRB	676	.	0			c.A1710G						.						94	91	92					12																	70986132		1932	4140	6072	SO:0001819	synonymous_variant	5787	exon7			ATAAAGTCGACCG	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1056A>G	chr12.hg19:g.70986132T>C		114.0	0.0		97.0	11.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.463	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			C	70986132	T	C	70986132	2	2	53	1	0	0	0	0	0	0	0	1	12811	1654	58	2		2	PTPRB	12	70986132	Silent	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	68992142	70986132	62865763	60	6760										
TAOK3	51347	hgsc.bcm.edu	37	chr12	118639243	118639243	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ggtcaatgaggacacgtagtGgccggtctcgtcgaacaaag	14	9	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr12:118639243G>A	ENST00000392533.3	-	12	1335	c.845C>T	c.(844-846)cCa>cTa	p.P282L	TAOK3_ENST00000419821.2_Missense_Mutation_p.P282L	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	282					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GACACGTAGTGGCCGGTCTCG	0.403																																					p.P282L		Atlas-SNP	.											.	TAOK3	151	.	0			c.C845T						.						100	92	95					12																	118639243		2203	4300	6503	SO:0001583	missense	51347	exon12			CGTAGTGGCCGGT	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.845C>T	chr12.hg19:g.118639243G>A	ENSP00000376317:p.Pro282Leu	82.0	0.0		107.0	44.0	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Missense_Mutation	SNP	ENST00000392533.3	hg19	CCDS9188.1	.	.	.	.	.	.	.	.	.	.	G	18.56	3.649689	0.67358	.	.	ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000538601	D;D;D	0.85411	-1.98;-1.98;-1.98	4.65	4.65	0.58169	Protein kinase-like domain (1);	0.070349	0.64402	D	0.000015	D	0.83399	0.5246	L	0.56396	1.775	0.80722	D	1	B	0.25772	0.134	B	0.23716	0.048	T	0.81536	-0.0888	10	0.44086	T	0.13	.	17.703	0.88301	0.0:0.0:1.0:0.0	.	282	Q9H2K8	TAOK3_HUMAN	L	282;282;180	ENSP00000416374:P282L;ENSP00000376317:P282L;ENSP00000437389:P180L	ENSP00000376317:P282L	P	-	2	0	TAOK3	117123626	1.000000	0.71417	0.874000	0.34290	0.936000	0.57629	9.564000	0.98151	2.401000	0.81631	0.591000	0.81541	CCA	.	.		0.403	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281		A	118639243	G	A	118639243	3	1	53	1	0	0	0	0	1	0	0	0	15564	1348	47	3	1891	3	TAOK3	12	118639243	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	47653111	118639243	15212652	61	6761										
NBEA	26960	hgsc.bcm.edu	37	chr13	35692392	35692392	+	Nonsense_Mutation	SNP	C	C	T													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gggtcaaggaagatgaacttCagagtatattaaattaccta							TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr13:35692392C>T	ENST00000400445.3	+	15	2644	c.2110C>T	c.(2110-2112)Cag>Tag	p.Q704*	NBEA_ENST00000310336.4_Nonsense_Mutation_p.Q704*|NBEA_ENST00000379939.2_Nonsense_Mutation_p.Q704*|NBEA_ENST00000540320.1_Nonsense_Mutation_p.Q704*	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	704					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AGATGAACTTCAGAGTATATT	0.239																																					p.Q704X		Atlas-SNP	.											.	NBEA	340	.	0			c.C2110T						.						51	45	47					13																	35692392		1785	4049	5834	SO:0001587	stop_gained	26960	exon15			GAACTTCAGAGTA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.2110C>T	chr13.hg19:g.35692392C>T	ENSP00000383295:p.Gln704*	111.0	0.0		54.0	13.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Nonsense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	45	11.441239	0.99561	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	.	.	.	4.29	4.29	0.51040	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	16.7133	0.85391	0.0:1.0:0.0:0.0	.	.	.	.	X	704	.	ENSP00000308534:Q704X	Q	+	1	0	NBEA	34590392	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.345000	0.79337	1.929000	0.55896	0.460000	0.39030	CAG	.	.		0.239	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35692392	C	T	35692392	4	4	53	1	0	0	0	0	0	1	0	0	10196	827	29	3	2168	3	NBEA	13	35692392	Nonsense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10		35692392	79477486	62	6762	30	2								
NBEA	26960	hgsc.bcm.edu	37	chr13	35692394	35692394	+	Missense_Mutation	SNP	G	G	C													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gtcaaggaagatgaacttcaGagtatattaaattacctact					rs376099257		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr13:35692394G>C	ENST00000400445.3	+	15	2646	c.2112G>C	c.(2110-2112)caG>caC	p.Q704H	NBEA_ENST00000310336.4_Missense_Mutation_p.Q704H|NBEA_ENST00000379939.2_Missense_Mutation_p.Q704H|NBEA_ENST00000540320.1_Missense_Mutation_p.Q704H	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	704					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ATGAACTTCAGAGTATATTAA	0.244																																					p.Q704H		Atlas-SNP	.											.	NBEA	340	.	0			c.G2112C						.						52	46	48					13																	35692394		1785	4050	5835	SO:0001583	missense	26960	exon15			ACTTCAGAGTATA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.2112G>C	chr13.hg19:g.35692394G>C	ENSP00000383295:p.Gln704His	112.0	0.0		56.0	13.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.893891	0.52121	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	4.29	4.29	0.51040	.	0.000000	0.64402	D	0.000001	T	0.67524	0.2902	M	0.67953	2.075	0.80722	D	1	D	0.65815	0.995	D	0.77557	0.99	T	0.68089	-0.5501	10	0.45353	T	0.12	.	11.3759	0.49728	0.0896:0.0:0.9104:0.0	.	704	Q5T321	.	H	704	ENSP00000440951:Q704H;ENSP00000383295:Q704H;ENSP00000369271:Q704H;ENSP00000308534:Q704H	ENSP00000308534:Q704H	Q	+	3	2	NBEA	34590394	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.357000	0.34090	1.929000	0.55896	0.460000	0.39030	CAG	.	.		0.244	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		C	35692394	G	C	35692394	3	2	53	1	0	0	0	0	1	0	0	0	10196	933	33	4	2170	4	NBEA	13	35692394	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	2	35692394	79477484	63	6763	30	2								
NBEA	26960	hgsc.bcm.edu	37	chr13	35734090	35734090	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tattgatgcaggaagtataaTttcagatactgaaaggtctg	10	4	2	3			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr13:35734090T>G	ENST00000400445.3	+	22	4316	c.3782T>G	c.(3781-3783)aTt>aGt	p.I1261S	NBEA_ENST00000310336.4_Missense_Mutation_p.I1261S|NBEA_ENST00000379939.2_Missense_Mutation_p.I1261S|NBEA_ENST00000540320.1_Missense_Mutation_p.I1261S	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1261					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GGAAGTATAATTTCAGATACT	0.378																																					p.I1261S		Atlas-SNP	.											.	NBEA	340	.	0			c.T3782G						.						40	42	42					13																	35734090		1839	4074	5913	SO:0001583	missense	26960	exon22			GTATAATTTCAGA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.3782T>G	chr13.hg19:g.35734090T>G	ENSP00000383295:p.Ile1261Ser	38.0	0.0		62.0	22.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	T	12.38	1.920176	0.33908	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	5.8	5.8	0.92144	.	0.542704	0.19638	N	0.109515	T	0.34395	0.0896	N	0.19112	0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12734	-1.0536	10	0.18710	T	0.47	.	16.134	0.81465	0.0:0.0:0.0:1.0	.	1261	Q5T321	.	S	1261	ENSP00000440951:I1261S;ENSP00000383295:I1261S;ENSP00000369271:I1261S;ENSP00000308534:I1261S	ENSP00000308534:I1261S	I	+	2	0	NBEA	34632090	0.997000	0.39634	0.994000	0.49952	0.995000	0.86356	4.731000	0.62022	2.216000	0.71823	0.528000	0.53228	ATT	.	.		0.378	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35734090	T	G	35734090	3	3	53	1	0	0	0	0	1	0	0	0	10196	1493	52	5	3868	5	NBEA	13	35734090	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	41696	35734090	79435788	64	6764										
ARHGEF7	8874	hgsc.bcm.edu	37	chr13	111932983	111932983	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	aaacgaaggtcacgtctgtgGgaaaccccaccataaagcct	9	12	2	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr13:111932983G>A	ENST00000375741.2	+	16	1997	c.1747G>A	c.(1747-1749)Gga>Aga	p.G583R	ARHGEF7_ENST00000375723.1_Missense_Mutation_p.G405R|ARHGEF7_ENST00000218789.5_Missense_Mutation_p.G405R|ARHGEF7_ENST00000370623.3_Missense_Mutation_p.G490R|ARHGEF7_ENST00000375739.2_Missense_Mutation_p.G533R|ARHGEF7_ENST00000544132.1_3'UTR|ARHGEF7_ENST00000426073.2_Missense_Mutation_p.G405R|ARHGEF7_ENST00000317133.5_Missense_Mutation_p.G562R|ARHGEF7_ENST00000375736.4_Missense_Mutation_p.G405R|ARHGEF7_ENST00000478679.1_Missense_Mutation_p.G327R|ARHGEF7_ENST00000375737.5_Missense_Mutation_p.G480R	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	583					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CACGTCTGTGGGAAACCCCAC	0.542																																					p.G583R		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.G1747A						.						210	158	176					13																	111932983		2203	4300	6503	SO:0001583	missense	8874	exon16			TCTGTGGGAAACC	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.1747G>A	chr13.hg19:g.111932983G>A	ENSP00000364893:p.Gly583Arg	120.0	0.0		119.0	32.0	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Missense_Mutation	SNP	ENST00000375741.2	hg19	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	G	3.869	-0.028348	0.07589	.	.	ENSG00000102606	ENST00000317133;ENST00000375741;ENST00000375739;ENST00000370623;ENST00000545635;ENST00000466143;ENST00000218789;ENST00000375736;ENST00000426073;ENST00000375737;ENST00000375723;ENST00000478679	T;T;T;T;T;T;T;T;T;T;T	0.60672	0.75;0.76;0.76;0.72;0.74;0.71;0.72;0.72;0.76;0.7;0.17	4.91	0.798	0.18660	.	0.334721	0.33092	N	0.005291	T	0.37461	0.1004	N	0.24115	0.695	0.09310	N	0.999999	B;B;B;B;B	0.25850	0.044;0.105;0.068;0.136;0.07	B;B;B;B;B	0.30716	0.025;0.045;0.093;0.056;0.119	T	0.18524	-1.0334	10	0.39692	T	0.17	.	4.3244	0.11032	0.338:0.0:0.5151:0.1469	.	327;480;533;583;562	E9PDQ5;B7Z6G2;Q14155-2;Q14155;Q14155-3	.;.;.;ARHG7_HUMAN;.	R	562;583;533;490;560;405;405;405;405;480;405;327	ENSP00000325994:G562R;ENSP00000364893:G583R;ENSP00000364891:G533R;ENSP00000359657:G490R;ENSP00000418067:G405R;ENSP00000218789:G405R;ENSP00000364888:G405R;ENSP00000397068:G405R;ENSP00000364889:G480R;ENSP00000364875:G405R;ENSP00000417596:G327R	ENSP00000218789:G405R	G	+	1	0	ARHGEF7	110730984	0.981000	0.34729	0.001000	0.08648	0.005000	0.04900	2.237000	0.43061	-0.199000	0.10317	-0.188000	0.12872	GGA	.	.		0.542	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511		A	111932983	G	A	111932983	3	1	53	1	0	0	0	0	1	0	0	0	911	1233	43	3	1809	3	ARHGEF7	13	111932983	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	76198893	111932983	3236895	65	6765										
NDRG2	57447	hgsc.bcm.edu	37	chr14	21487891	21487892	+	Missense_Mutation	DNP	GA	GA	TG													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gtatcaactcagaatttccaGagagctcttcctgaaggaga							TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr14:21487891_21487892GA>TG	ENST00000556147.1	-	10	1562_1563	c.622_623TC>CA	c.(622-624)TCt>CAt	p.S208H	NDRG2_ENST00000350792.3_Missense_Mutation_p.S194H|NDRG2_ENST00000397853.3_Missense_Mutation_p.S208H|NDRG2_ENST00000397856.3_Missense_Mutation_p.S194H|NDRG2_ENST00000397847.2_Missense_Mutation_p.S208H|NDRG2_ENST00000397855.3_Missense_Mutation_p.S165H|NDRG2_ENST00000397858.1_Missense_Mutation_p.S208H|NDRG2_ENST00000397851.2_Missense_Mutation_p.S208H|NDRG2_ENST00000298687.5_Missense_Mutation_p.S208H|NDRG2_ENST00000553503.1_Missense_Mutation_p.S194H|NDRG2_ENST00000298684.5_Missense_Mutation_p.S165H|NDRG2_ENST00000360463.3_Missense_Mutation_p.S194H|NDRG2_ENST00000554143.1_Missense_Mutation_p.S194H|NDRG2_ENST00000554104.1_Missense_Mutation_p.S121H|NDRG2_ENST00000555158.1_Missense_Mutation_p.S194H|NDRG2_ENST00000403829.3_Missense_Mutation_p.S204H|NDRG2_ENST00000554277.1_5'UTR|NDRG2_ENST00000397844.2_Missense_Mutation_p.S194H			Q9UN36	NDRG2_HUMAN	NDRG family member 2	208					cell differentiation (GO:0030154)|negative regulation of cytokine production (GO:0001818)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of platelet-derived growth factor production (GO:0090361)|regulation of vascular endothelial growth factor production (GO:0010574)|substantia nigra development (GO:0021762)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)				breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	23	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		AGAATTTCCAGAGAGCTCTTCC	0.401																																					p.S208Y|p.S208P		Atlas-SNP	.											.	NDRG2	37	.	0			c.C623A|c.T622C						.																																			SO:0001583	missense	57447	exon10			TTTCCAGAGAGCT|TTCCAGAGAGCTC	AB033074	CCDS9564.1, CCDS9565.1, CCDS61384.1, CCDS61386.1, CCDS73613.1	14q11.2	2008-07-09			ENSG00000165795	ENSG00000165795			14460	protein-coding gene	gene with protein product		605272				10831399	Standard	NM_201535		Approved	KIAA1248, SYLD	uc001vyx.3	Q9UN36	OTTHUMG00000029619	ENST00000556147.1:c.622_623delinsTG	chr14.hg19:g.21487891_21487892delinsTG	ENSP00000451712:p.Ser208His	72.0|71.0	0.0		87.0	27.0	NM_201537	B3KUE3|B4DE86|B7WP11|B7WPD5|D3DS07|D3DS10|Q567T1|Q68DW2|Q86U08|Q86U46|Q96FD3|Q96FT0|Q96JU0|Q96PN0|Q9BQH5|Q9ULH2	Missense_Mutation	SNP	ENST00000556147.1	hg19	CCDS9565.1																																																																																			.	.		0.401	NDRG2-013	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411717.1			TG	21487892	GA	TG	21487891	3	4	53	1	0	0	0	0	1	0	0	0	10261	942	33	3	520	3	NDRG2	14	21487891	Missense_Mutation	DNP	GA	TCGA-BW-A5NQ-01A-11D-A27I-10		21487891	85861649	66	6766										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64554464	64554464	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atctagaagacctgtcaataAtttttgaaacagatgaatta	6	5	2	5			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr14:64554464A>C	ENST00000344113.4	+	58	11772	c.11560A>C	c.(11560-11562)Att>Ctt	p.I3854L	SYNE2_ENST00000358025.3_Missense_Mutation_p.I3854L|SYNE2_ENST00000554584.1_Missense_Mutation_p.I3887L|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.I488L|SYNE2_ENST00000357395.3_Missense_Mutation_p.I239L|SYNE2_ENST00000394768.2_Missense_Mutation_p.I239L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3854					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		CCTGTCAATAATTTTTGAAAC	0.333																																					p.I3854L		Atlas-SNP	.											.	SYNE2	577	.	0			c.A11560C						.						82	88	86					14																	64554464		2202	4300	6502	SO:0001583	missense	23224	exon58			TCAATAATTTTTG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.11560A>C	chr14.hg19:g.64554464A>C	ENSP00000341781:p.Ile3854Leu	107.0	0.0		110.0	34.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.777228	0.49786	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.34275	1.37;3.93;1.37;1.37;1.37;3.93	5.36	5.36	0.76844	.	0.115504	0.38778	N	0.001576	T	0.35098	0.0920	M	0.68317	2.08	0.80722	D	1	P;B;B;B	0.35507	0.506;0.402;0.372;0.183	B;B;B;B	0.32211	0.131;0.142;0.062;0.069	T	0.23797	-1.0178	10	0.46703	T	0.11	.	10.8822	0.46946	0.859:0.0:0.0:0.141	.	239;3888;3854;3854	Q8WXH0-7;D4YW74;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	L	3854;239;3854;3887;3887;488;239	ENSP00000350719:I3854L;ENSP00000349969:I239L;ENSP00000341781:I3854L;ENSP00000452570:I3887L;ENSP00000450831:I488L;ENSP00000378249:I239L	ENSP00000261678:I3887L	I	+	1	0	SYNE2	63624217	0.959000	0.32827	0.933000	0.37362	0.875000	0.50365	2.139000	0.42149	2.024000	0.59613	0.482000	0.46254	ATT	.	.		0.333	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		C	64554464	A	C	64554464	3	2	53	1	0	0	0	0	1	0	0	0	15461	101	4	5	11786	5	SYNE2	14	64554464	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	43066573	64554464	42795076	67	6767										
EML5	161436	hgsc.bcm.edu	37	chr14	89206879	89206879	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ccgtcttaccaaagacacctCgttttggggtcagagcattt	9	11	2	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr14:89206879C>T	ENST00000380664.5	-	5	562	c.563G>A	c.(562-564)cGa>cAa	p.R188Q	EML5_ENST00000554922.1_Missense_Mutation_p.R188Q|EML5_ENST00000352093.5_Missense_Mutation_p.R188Q			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	188						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AAAGACACCTCGTTTTGGGGT	0.368																																					p.R188Q		Atlas-SNP	.											.	EML5	141	.	0			c.G563A						.						143	135	138					14																	89206879		1860	4102	5962	SO:0001583	missense	161436	exon5			ACACCTCGTTTTG	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.563G>A	chr14.hg19:g.89206879C>T	ENSP00000370039:p.Arg188Gln	121.0	0.0		125.0	35.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	34	5.331765	0.95733	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.21734	1.99;1.99;1.99	5.21	5.21	0.72293	WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.35278	0.0926	L	0.52364	1.645	0.53005	D	0.999962	D	0.71674	0.998	P	0.59703	0.862	T	0.04268	-1.0964	10	0.11485	T	0.65	-7.7252	18.7549	0.91828	0.0:1.0:0.0:0.0	.	188	Q05BV3	EMAL5_HUMAN	Q	188	ENSP00000451998:R188Q;ENSP00000298315:R188Q;ENSP00000370039:R188Q	ENSP00000298315:R188Q	R	-	2	0	EML5	88276632	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.412000	0.80091	2.417000	0.82017	0.591000	0.81541	CGA	.	.		0.368	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89206879	C	T	89206879	3	4	53	1	0	0	0	0	1	0	0	0	5102	884	31	1	5526	1	EML5	14	89206879	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	24652415	89206879	18142661	68	6768										
ZNF839	55778	hgsc.bcm.edu	37	chr14	102792471	102792471	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ctggtggggctccatatcgcCagccctcagctgctcagggt	13	14	2	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr14:102792471C>T	ENST00000558850.1	+	2	440	c.90C>T	c.(88-90)gcC>gcT	p.A30A	ZNF839_ENST00000262236.5_Silent_p.A30A|ZNF839_ENST00000559185.1_Silent_p.A30A|ZNF839_ENST00000442396.2_Silent_p.A146A	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	30							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TCCATATCGCCAGCCCTCAGC	0.582																																					p.A146A		Atlas-SNP	.											.	ZNF839	41	.	0			c.C438T						.						39	45	43					14																	102792471		1944	4154	6098	SO:0001819	synonymous_variant	55778	exon2			TATCGCCAGCCCT	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 131"	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.90C>T	chr14.hg19:g.102792471C>T		98.0	0.0		67.0	14.0	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	hg19	CCDS58336.1																																																																																			.	.		0.582	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335		T	102792471	C	T	102792471	2	4	53	1	0	0	0	0	0	0	0	1	18203	581	21	3		3	ZNF839	14	102792471	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	13585592	102792471	4557069	69	6769										
MKRN3	7681	hgsc.bcm.edu	37	chr15	23812394	23812394	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gagatgagttacccttctctGaggaccagtgggacttgctt	12	9	1	3			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr15:23812394G>T	ENST00000314520.3	+	1	1941	c.1465G>T	c.(1465-1467)Gag>Tag	p.E489*	RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000568252.1_Intron|MKRN3_ENST00000564592.1_Intron|MKRN3_ENST00000568945.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	489					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.E489*(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		ACCCTTCTCTGAGGACCAGTG	0.453																																					p.E489X		Atlas-SNP	.											MKRN3,NS,carcinoma,0,1	MKRN3	155	.	1	Substitution - Nonsense(1)	lung(1)	c.G1465T						.						149	141	144					15																	23812394		2203	4300	6503	SO:0001587	stop_gained	7681	exon1			TTCTCTGAGGACC	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"RING-type (C3HC4) zinc fingers"	7114	protein-coding gene	gene with protein product	"zinc finger protein 127"	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.1465G>T	chr15.hg19:g.23812394G>T	ENSP00000313881:p.Glu489*	121.0	0.0		124.0	40.0	NM_005664		Nonsense_Mutation	SNP	ENST00000314520.3	hg19	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	G	36	5.955527	0.97145	.	.	ENSG00000179455	ENST00000314520	.	.	.	4.09	-0.159	0.13379	.	0.358986	0.23431	N	0.048259	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	3.643	0.08174	0.3435:0.1888:0.4677:0.0	.	.	.	.	X	489	.	ENSP00000313881:E489X	E	+	1	0	MKRN3	21363487	1.000000	0.71417	0.006000	0.13384	0.292000	0.27327	4.316000	0.59178	-0.008000	0.14320	0.563000	0.77884	GAG	.	.		0.453	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664		T	23812394	G	T	23812394	4	4	53	1	0	0	0	0	0	1	0	0	9617	1291	45	3	1467	3	MKRN3	15	23812394	Nonsense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10		23812394	78718998	70	6770										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51756896	51756896	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atggggtattttcaggttctAgcattgctttatttcgaaga	10	5	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr15:51756896A>C	ENST00000251076.5	-	32	8068	c.7781T>G	c.(7780-7782)cTa>cGa	p.L2594R	DMXL2_ENST00000449909.3_Missense_Mutation_p.L1958R|DMXL2_ENST00000543779.2_Missense_Mutation_p.L2595R|RP11-707P17.1_ENST00000561007.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2594						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TTCAGGTTCTAGCATTGCTTT	0.398																																					p.L2595R		Atlas-SNP	.											.	DMXL2	262	.	0			c.T7784G						.						87	82	84					15																	51756896		2196	4293	6489	SO:0001583	missense	23312	exon32			GGTTCTAGCATTG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.7781T>G	chr15.hg19:g.51756896A>C	ENSP00000251076:p.Leu2594Arg	120.0	0.0		65.0	15.0	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.792617	0.90453	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909;ENST00000436119	T;T;T	0.37584	1.34;1.35;1.19	5.55	5.55	0.83447	.	0.153974	0.44285	D	0.000465	T	0.59514	0.2199	M	0.81942	2.565	0.53688	D	0.999974	P;D;P;D	0.67145	0.929;0.996;0.857;0.99	P;P;P;P	0.60415	0.724;0.823;0.451;0.874	T	0.65676	-0.6110	10	0.87932	D	0	.	15.8527	0.78947	1.0:0.0:0.0:0.0	.	2595;1958;2594;2595	F5GWF1;B2RTR3;Q8TDJ6;B7ZMH3	.;.;DMXL2_HUMAN;.	R	2594;2595;1958;139	ENSP00000251076:L2594R;ENSP00000441858:L2595R;ENSP00000400855:L1958R	ENSP00000251076:L2594R	L	-	2	0	DMXL2	49544188	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.761000	0.91691	2.330000	0.79161	0.477000	0.44152	CTA	.	.		0.398	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		C	51756896	A	C	51756896	3	2	53	1	0	0	0	0	1	0	0	0	4597	420	15	5	1377	5	DMXL2	15	51756896	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	27944502	51756896	50774496	71	6771										
SGK269	79834	hgsc.bcm.edu	37	chr15	77471864	77471864	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tgctcttagcaacatcagcaTctggaggaatggcataaagc	10	9	3	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr15:77471864T>C	ENST00000560626.2	-	4	2880	c.2405A>G	c.(2404-2406)gAt>gGt	p.D802G	PEAK1_ENST00000312493.4_Missense_Mutation_p.D802G|PEAK1_ENST00000558305.1_Missense_Mutation_p.D802G			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	802	Pro-rich.				cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										AACATCAGCATCTGGAGGAAT	0.512																																					p.D802G		Atlas-SNP	.											.	.	.	.	0			c.A2405G						.						82	84	83					15																	77471864		2013	4187	6200	SO:0001583	missense	0	exon5			TCAGCATCTGGAG		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.2405A>G	chr15.hg19:g.77471864T>C	ENSP00000452796:p.Asp802Gly	122.0	0.0		87.0	19.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	T	12.78	2.040023	0.35989	.	.	ENSG00000173517	ENST00000312493	T	0.72725	-0.68	5.78	3.17	0.36434	.	0.181563	0.31415	N	0.007693	T	0.55529	0.1926	N	0.20986	0.625	0.44918	D	0.997935	B	0.11235	0.004	B	0.10450	0.005	T	0.55088	-0.8195	10	0.72032	D	0.01	-3.4663	10.6403	0.45590	0.0:0.1508:0.0:0.8492	.	802	Q9H792	PEAK1_HUMAN	G	802	ENSP00000309230:D802G	ENSP00000309230:D802G	D	-	2	0	AC087465.1	75258919	1.000000	0.71417	0.564000	0.28396	0.538000	0.34931	3.785000	0.55424	1.031000	0.39867	0.533000	0.62120	GAT	.	.		0.512	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			C	77471864	T	C	77471864	3	2	53	1	0	0	0	0	1	0	0	0	14226	1435	50	2	2851	2	SGK269	15	77471864	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	25714968	77471864	25059528	72	6772										
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79382797	79382799	+	In_Frame_Del	DEL	AGG	AGG	-													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ccttgcgcgccagcagtcccAgggacgcgacgtggccatca							TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr15:79382797_79382799delAGG	ENST00000419573.3	-	1	316_318	c.42_44delCCT	c.(40-45)tccctg>tcg	p.L15del	RASGRF1_ENST00000558480.2_In_Frame_Del_p.L15del	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	15					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CAGCAGTCCCAGGGACGCGACGT	0.635																																					p.15_15del		Atlas-INDEL	.											.	RASGRF1	168	.	0			c.43_45del						.																																			SO:0001651	inframe_deletion	5923	exon1			.	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.42_44delCCT	chr15.hg19:g.79382797_79382799delAGG	ENSP00000405963:p.Leu15del	94.0	0.0		55.0	10.0	NM_001145648	F8VPA5|H0YKF2|J3KQP9|Q16027	In_Frame_Del	DEL	ENST00000419573.3	hg19	CCDS10309.1																																																																																			.	.		0.635	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		-	79382799	AGG	-	79382797	7	5	53	1	0	1	0	1	0	0	0	0	13087	188	7	0	3889	0	RASGRF1	15	79382797	In_Frame_Del	DEL	AGG	TCGA-BW-A5NQ-01A-11D-A27I-10	1910933	79382797	23148595	73	6773										
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1384728	1384728	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ctgcacctgggcaccgccatCggcttcgcaggggccatctg	13	16	1	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr16:1384728C>A	ENST00000324385.5	+	1	224	c.66C>A	c.(64-66)atC>atA	p.I22I	BAIAP3_ENST00000562208.1_Intron|BAIAP3_ENST00000421665.2_5'Flank|BAIAP3_ENST00000397488.2_Intron|BAIAP3_ENST00000397489.1_5'UTR|BAIAP3_ENST00000426824.3_Intron|BAIAP3_ENST00000568887.1_Intron	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	22					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				GCACCGCCATCGGCTTCGCAG	0.662																																					p.I22I		Atlas-SNP	.											.	BAIAP3	88	.	0			c.C66A						.						8	9	9					16																	1384728		2113	4180	6293	SO:0001819	synonymous_variant	8938	exon1			CGCCATCGGCTTC	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.66C>A	chr16.hg19:g.1384728C>A		99.0	0.0		79.0	35.0	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Silent	SNP	ENST00000324385.5	hg19	CCDS10434.1																																																																																			.	.		0.662	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			A	1384728	C	A	1384728	2	1	53	1	0	0	0	0	0	0	0	1	1304	874	31	1		1	BAIAP3	16	1384728	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10		1384728	88970025	74	6774										
TP53	7157	hgsc.bcm.edu	37	chr17	7578275	7578275	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ttccactcggataagatgctGaggaggggccagacctaaga	13	9	0	4			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr17:7578275G>A	ENST00000269305.4	-	6	763	c.574C>T	c.(574-576)Cag>Tag	p.Q192*	TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q192*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000445888.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q192*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	192	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Q -> H (in sporadic cancers; somatic mutation).|Q -> K (in a sporadic cancer; somatic mutation).|Q -> L (in sporadic cancers; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q192*(83)|p.0?(8)|p.Q99*(6)|p.?(6)|p.Q60*(6)|p.P191del(4)|p.P191delP(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.G187fs*16(2)|p.P59delP(2)|p.P98delP(2)|p.P191fs*6(1)|p.A189_Q192>E(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P191_Q192delPQ(1)|p.Q192K(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.Q192del(1)|p.Q192fs*16(1)|p.L188_P191del(1)|p.Q192fs*30(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATAAGATGCTGAGGAGGGGCC	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Q192X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	144	Substitution - Nonsense(95)|Deletion - In frame(19)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - deletion inframe(6)|Unknown(6)|Insertion - Frameshift(1)|Complex - frameshift(1)|Substitution - Missense(1)	breast(26)|ovary(20)|urinary_tract(15)|lung(12)|upper_aerodigestive_tract(10)|skin(8)|biliary_tract(7)|oesophagus(7)|large_intestine(6)|kidney(6)|stomach(5)|haematopoietic_and_lymphoid_tissue(5)|liver(5)|bone(4)|central_nervous_system(3)|pancreas(2)|cervix(1)|endometrium(1)|eye(1)	c.C574T						.						89	80	83					17																	7578275		2203	4300	6503	SO:0001587	stop_gained	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGCTGAGGAGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.574C>T	chr17.hg19:g.7578275G>A	ENSP00000269305:p.Gln192*	167.0	0.0		113.0	47.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.269040	0.40095	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.41	3.36	0.38483	.	0.242461	0.43260	D	0.000594	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-22.6404	8.6971	0.34303	0.0:0.1484:0.545:0.3066	.	.	.	.	X	192;192;192;192;192;192;181;99;60;99;60	.	ENSP00000269305:Q192X	Q	-	1	0	TP53	7519000	1.000000	0.71417	0.987000	0.45799	0.035000	0.12851	2.163000	0.42377	0.732000	0.32470	0.655000	0.94253	CAG	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578275	G	A	7578275	4	1	53	1	0	0	0	0	0	1	0	0	16396	1299	45	3	720	3	TP53	17	7578275	Nonsense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10		7578275	73616935	75	6775										
MAP2K4	6416	hgsc.bcm.edu	37	chr17	12013730	12013731	+	In_Frame_Ins	INS	-	-	ATT													0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	acttaaaagaaaacttgaaaINSattattcacagaggtgggta							TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr17:12013730_12013731insATT	ENST00000353533.5	+	6	735_736	c.672_673insATT	c.(673-675)att>ATTatt	p.225_225I>II	MAP2K4_ENST00000415385.3_In_Frame_Ins_p.236_236I>II|MAP2K4_ENST00000581941.1_3'UTR	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		AAAACTTGAAAATTATTCACAG	0.322			"D, Mis, N"		"pancreatic, breast, colorectal"																																p.K224delinsKI		Atlas-INDEL	.		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	MAP2K4	176	.	11	Whole gene deletion(10)|Unknown(1)	ovary(4)|breast(4)|biliary_tract(1)|large_intestine(1)|pancreas(1)	c.672_673insATT						.																																			SO:0001652	inframe_insertion	6416	exon6			.	L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.676_678dupATT	chr17.hg19:g.12013734_12013736dupATT	ENSP00000262445:p.Ile226dup	103.0	0.0		48.0	14.0	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	In_Frame_Ins	INS	ENST00000353533.5	hg19	CCDS11162.1																																																																																			.	.		0.322	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			ATT	12013731	-	ATT	12013730	7	5	53	1	0	1	1	0	0	0	0	0	9248	11	1	0	694	0	MAP2K4	17	12013730	In_Frame_Ins	INS	-	TCGA-BW-A5NQ-01A-11D-A27I-10	4435455	12013730	69181480	76	6776										
PIGS	94005	hgsc.bcm.edu	37	chr17	26888556	26888556	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	acatggcctgggccacctggActatgcggcggccaatgatg	14	12	0	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr17:26888556A>T	ENST00000308360.7	-	6	935	c.560T>A	c.(559-561)gTc>gAc	p.V187D	PIGS_ENST00000543734.1_Missense_Mutation_p.V126D|PIGS_ENST00000395346.2_Missense_Mutation_p.V179D|PIGS_ENST00000465444.1_5'UTR	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	187					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					GGCCACCTGGACTATGCGGCG	0.597																																					p.V187D		Atlas-SNP	.											.	PIGS	42	.	0			c.T560A						.						81	64	70					17																	26888556		2203	4300	6503	SO:0001583	missense	94005	exon6			ACCTGGACTATGC		CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"Phosphatidylinositol glycan anchor biosynthesis"	14937	protein-coding gene	gene with protein product	"GPI transamidase subunit"	610271	"phosphatidylinositol glycan, class S"				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.560T>A	chr17.hg19:g.26888556A>T	ENSP00000309430:p.Val187Asp	144.0	0.0		130.0	49.0	NM_033198	Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	hg19	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.662267	0.29515	.	.	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.43294	0.95;0.95;0.95	5.68	3.27	0.37495	.	0.552930	0.21428	N	0.074703	T	0.28532	0.0706	L	0.34521	1.04	0.39722	D	0.971482	B;B	0.16802	0.019;0.016	B;B	0.20384	0.026;0.029	T	0.06954	-1.0798	10	0.14656	T	0.56	-3.8239	9.2515	0.37557	0.4912:0.0:0.0:0.5088	.	187;179	Q96S52;Q96S52-2	PIGS_HUMAN;.	D	179;187;126	ENSP00000378755:V179D;ENSP00000309430:V187D;ENSP00000438447:V126D	ENSP00000309430:V187D	V	-	2	0	PIGS	23912683	0.170000	0.23016	0.494000	0.27515	0.961000	0.63080	0.457000	0.21875	0.930000	0.37217	0.533000	0.62120	GTC	.	.		0.597	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198		T	26888556	A	T	26888556	3	4	53	1	0	0	0	0	1	0	0	0	11907	275	10	4	1135	4	PIGS	17	26888556	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	14874826	26888556	54306654	77	6777										
MED13	9969	hgsc.bcm.edu	37	chr17	60038954	60038954	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	aaaacatatacttacatcagGacttctaagggcagtttcca	6	9	2	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr17:60038954G>T	ENST00000397786.2	-	22	5327	c.5251C>A	c.(5251-5253)Cct>Act	p.P1751T		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1751					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CTTACATCAGGACTTCTAAGG	0.408																																					p.P1751T		Atlas-SNP	.											.	MED13	181	.	0			c.C5251A						.						99	96	97					17																	60038954		1870	4098	5968	SO:0001583	missense	9969	exon22			CATCAGGACTTCT	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.5251C>A	chr17.hg19:g.60038954G>T	ENSP00000380888:p.Pro1751Thr	87.0	0.0		81.0	31.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.074063	0.76415	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	D	0.82619	-1.63	5.34	4.37	0.52481	.	0.051925	0.85682	D	0.000000	T	0.80008	0.4545	L	0.33485	1.01	0.80722	D	1	B	0.29936	0.262	B	0.41440	0.357	T	0.78122	-0.2327	10	0.40728	T	0.16	0.261	13.4147	0.60961	0.0755:0.0:0.9245:0.0	.	1751	Q9UHV7	MED13_HUMAN	T	1751;1750	ENSP00000380888:P1751T	ENSP00000262436:P1750T	P	-	1	0	MED13	57393736	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.399000	0.79935	2.496000	0.84212	0.591000	0.81541	CCT	.	.		0.408	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		T	60038954	G	T	60038954	3	4	53	1	0	0	0	0	1	0	0	0	9439	1174	41	3	1309	3	MED13	17	60038954	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	33150398	60038954	21156256	78	6778										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6958645	6958645	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	cacaggattgttctcatccaAttggacagtgataattctaa	7	8	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr18:6958645A>G	ENST00000389658.3	-	55	7888	c.7795T>C	c.(7795-7797)Ttg>Ctg	p.L2599L	RP11-781P6.1_ENST00000584722.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2599	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTCTCATCCAATTGGACAGTG	0.363																																					p.L2599L		Atlas-SNP	.											.	LAMA1	458	.	0			c.T7795C						.						80	71	74					18																	6958645		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon55			CATCCAATTGGAC	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.7795T>C	chr18.hg19:g.6958645A>G		98.0	0.0		89.0	24.0	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.363	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	6958645	A	G	6958645	2	3	53	1	0	0	0	0	0	0	0	1	8614	98	4	2		2	LAMA1	18	6958645	Silent	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10		6958645	71118603	79	6779										
TAF4B	6875	hgsc.bcm.edu	37	chr18	23854650	23854650	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gtggctgtgccaaccagtgtCgtcacagttactcctggaaa	11	11	1	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr18:23854650C>T	ENST00000269142.5	+	4	1619	c.621C>T	c.(619-621)gtC>gtT	p.V207V	TAF4B_ENST00000578121.1_Silent_p.V207V|TAF4B_ENST00000400466.2_Silent_p.V207V	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	207					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			CAACCAGTGTCGTCACAGTTA	0.413																																					p.V207V		Atlas-SNP	.											.	TAF4B	71	.	0			c.C621T						.						117	112	113					18																	23854650		1896	4119	6015	SO:0001819	synonymous_variant	6875	exon4			CAGTGTCGTCACA	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.621C>T	chr18.hg19:g.23854650C>T		187.0	0.0		129.0	21.0	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	hg19	CCDS42421.1																																																																																			.	.		0.413	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		T	23854650	C	T	23854650	2	4	53	1	0	0	0	0	0	0	0	1	15542	871	31	1		1	TAF4B	18	23854650	Silent	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10	16896005	23854650	54222598	80	6780										
ELAVL1	1994	hgsc.bcm.edu	37	chr19	8032602	8032602	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	aacctgggggtttatgaccaTtgaaactggtaattgcctct	10	8	1	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:8032602T>C	ENST00000407627.2	-	5	632	c.503A>G	c.(502-504)aAt>aGt	p.N168S	ELAVL1_ENST00000351593.5_Missense_Mutation_p.N195S|ELAVL1_ENST00000593807.1_Intron|ELAVL1_ENST00000596459.1_Missense_Mutation_p.N168S	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	168	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						TTTATGACCATTGAAACTGGT	0.493																																					p.N168S		Atlas-SNP	.											.	ELAVL1	44	.	0			c.A503G						.						148	117	128					19																	8032602		2203	4300	6503	SO:0001583	missense	1994	exon5			TGACCATTGAAAC	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"RNA binding motif (RRM) containing"	3312	protein-coding gene	gene with protein product	"embryonic lethal, abnormal vision, drosophila, homolog-like 1", "Hu antigen R"	603466	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.503A>G	chr19.hg19:g.8032602T>C	ENSP00000385269:p.Asn168Ser	146.0	0.0		146.0	46.0	NM_001419	B4DVB8|Q53XN6|Q9BTT1	Missense_Mutation	SNP	ENST00000407627.2	hg19	CCDS12193.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.546629	0.86022	.	.	ENSG00000066044	ENST00000407627;ENST00000351593	T;T	0.09163	3.01;3.01	6.17	6.17	0.99709	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.23611	0.0571	M	0.72894	2.215	0.80722	D	1	D	0.61697	0.99	P	0.51135	0.66	T	0.00501	-1.1702	10	0.59425	D	0.04	.	14.7743	0.69713	0.0:0.0:0.0:1.0	.	168	Q15717	ELAV1_HUMAN	S	168;195	ENSP00000385269:N168S;ENSP00000264073:N195S	ENSP00000264073:N195S	N	-	2	0	ELAVL1	7938602	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.493	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419		C	8032602	T	C	8032602	3	2	53	1	0	0	0	0	1	0	0	0	5051	1493	52	2	485	2	ELAVL1	19	8032602	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10		8032602	51096381	81	6781										
FBN3	84467	hgsc.bcm.edu	37	chr19	8196686	8196686	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tacagtggccgttcacgcagAtgccgggcgtctggcactcg	14	13	2	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:8196686A>G	ENST00000600128.1	-	15	2156	c.1742T>C	c.(1741-1743)aTc>aCc	p.I581T	FBN3_ENST00000601739.1_Missense_Mutation_p.I581T|FBN3_ENST00000270509.2_Missense_Mutation_p.I581T			Q75N90	FBN3_HUMAN	fibrillin 3	581	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GTTCACGCAGATGCCGGGCGT	0.672																																					p.I581T		Atlas-SNP	.											.	FBN3	300	.	0			c.T1742C						.						24	26	25					19																	8196686		2203	4300	6503	SO:0001583	missense	84467	exon14			ACGCAGATGCCGG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.1742T>C	chr19.hg19:g.8196686A>G	ENSP00000470498:p.Ile581Thr	42.0	0.0		54.0	8.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	a	14.18	2.458988	0.43634	.	.	ENSG00000142449	ENST00000270509	D	0.86865	-2.18	2.92	2.92	0.33932	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.82917	0.5141	L	0.35793	1.09	0.42019	D	0.990978	P	0.48089	0.905	P	0.47299	0.543	T	0.80703	-0.1264	10	0.37606	T	0.19	.	10.9744	0.47456	1.0:0.0:0.0:0.0	.	581	Q75N90	FBN3_HUMAN	T	581	ENSP00000270509:I581T	ENSP00000270509:I581T	I	-	2	0	FBN3	8102686	1.000000	0.71417	0.625000	0.29200	0.037000	0.13140	6.212000	0.72188	0.961000	0.38030	0.155000	0.16302	ATC	.	.		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		G	8196686	A	G	8196686	3	3	53	1	0	0	0	0	1	0	0	0	5712	333	12	2	6887	2	FBN3	19	8196686	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10	164084	8196686	50932297	82	6782										
MUC16	94025	hgsc.bcm.edu	37	chr19	9015640	9015640	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ccagactctgcaggactctcTctgtggtgttgaacttcctg	10	12	3	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:9015640T>G	ENST00000397910.4	-	29	38386	c.38183A>C	c.(38182-38184)gAg>gCg	p.E12728A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12730	SEA 5. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGGACTCTCTCTGTGGTGTT	0.542																																					p.E12728A		Atlas-SNP	.											.	MUC16	4315	.	0			c.A38183C						.						186	166	173					19																	9015640		2024	4164	6188	SO:0001583	missense	94025	exon29			ACTCTCTCTGTGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.38183A>C	chr19.hg19:g.9015640T>G	ENSP00000381008:p.Glu12728Ala	201.0	0.0		172.0	58.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	9.701	1.154433	0.21371	.	.	ENSG00000181143	ENST00000397910	T	0.29397	1.57	3.34	2.27	0.28462	.	.	.	.	.	T	0.52885	0.1762	M	0.88310	2.945	.	.	.	D	0.57899	0.981	D	0.62955	0.909	T	0.63646	-0.6590	8	0.87932	D	0	.	5.6416	0.17567	0.0:0.1464:0.0:0.8536	.	12728	B5ME49	.	A	12728	ENSP00000381008:E12728A	ENSP00000381008:E12728A	E	-	2	0	MUC16	8876640	0.024000	0.19004	0.002000	0.10522	0.013000	0.08279	2.372000	0.44257	1.274000	0.44362	0.254000	0.18369	GAG	.	.		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9015640	T	G	9015640	3	3	53	1	0	0	0	0	1	0	0	0	9982	1551	54	5	5564	5	MUC16	19	9015640	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	818954	9015640	50113343	83	6783										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14024108	14024108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gatgcggcgctacgatcgggGgcttaaagtaagtgggcaga	17	7	0	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:14024108G>A	ENST00000318003.7	+	5	747	c.506G>A	c.(505-507)gGg>gAg	p.G169E	CC2D1A_ENST00000589606.1_Missense_Mutation_p.G169E	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	169					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			TACGATCGGGGGCTTAAAGTA	0.602																																					p.G169E		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G506A						.						25	31	29					19																	14024108		1964	4142	6106	SO:0001583	missense	54862	exon5			ATCGGGGGCTTAA	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.506G>A	chr19.hg19:g.14024108G>A	ENSP00000313601:p.Gly169Glu	86.0	0.0		86.0	30.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	hg19	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710151	0.68730	.	.	ENSG00000132024	ENST00000318003;ENST00000254346;ENST00000389233	D	0.91068	-2.78	4.8	4.8	0.61643	Domain of unknown function DM14 (1);	0.056252	0.64402	D	0.000001	D	0.95287	0.8471	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94511	0.7718	10	0.36615	T	0.2	-26.0657	16.7813	0.85563	0.0:0.0:1.0:0.0	.	169;169	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	E	169;7;144	ENSP00000313601:G169E	ENSP00000254346:G7E	G	+	2	0	CC2D1A	13885108	1.000000	0.71417	0.926000	0.36857	0.200000	0.23975	7.883000	0.87264	2.494000	0.84150	0.561000	0.74099	GGG	.	.		0.602	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		A	14024108	G	A	14024108	3	1	53	1	0	0	0	0	1	0	0	0	2728	1232	43	3	524	3	CC2D1A	19	14024108	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	5008468	14024108	45104875	84	6784										
ZNF714	148206	hgsc.bcm.edu	37	chr19	21299717	21299717	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gcaaatgtgaacatgagaatTtacagttaagaaaaggctcc	9	6	0	3			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:21299717T>G	ENST00000596143.1	+	5	572	c.247T>G	c.(247-249)Tta>Gta	p.L83V	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	83					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						ACATGAGAATTTACAGTTAAG	0.373																																					p.L83V		Atlas-SNP	.											.	ZNF714	121	.	0			c.T247G						.						63	63	63					19																	21299717		2199	4298	6497	SO:0001583	missense	148206	exon5			GAGAATTTACAGT	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.247T>G	chr19.hg19:g.21299717T>G	ENSP00000472368:p.Leu83Val	171.0	0.0		177.0	51.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	9.034	0.987923	0.18966	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.601	-0.984	0.10259	.	.	.	.	.	T	0.54271	0.1848	M	0.72894	2.215	0.09310	N	1	D;D	0.63880	0.971;0.993	P;D	0.73708	0.721;0.981	T	0.42582	-0.9443	8	0.48119	T	0.1	.	3.8304	0.08871	0.3218:0.0:0.0:0.6781	.	83;83	Q96N38-2;A6NEM4	.;.	V	83	.	ENSP00000291770:L83V	L	+	1	2	ZNF714	21091557	0.007000	0.16637	0.005000	0.12908	0.008000	0.06430	0.095000	0.15127	-0.425000	0.07371	-0.714000	0.03626	TTA	.	.		0.373	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		G	21299717	T	G	21299717	3	3	53	1	0	0	0	0	1	0	0	0	18133	1838	64	5	257	5	ZNF714	19	21299717	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	7275609	21299717	37829266	85	6785										
CCNE1	898	hgsc.bcm.edu	37	chr19	30311721	30311721	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	aactcttttacagcttattgGgatttcatctttatttattg	5	6	3	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:30311721G>C	ENST00000262643.3	+	7	854	c.575G>C	c.(574-576)gGg>gCg	p.G192A	CCNE1_ENST00000444983.2_Missense_Mutation_p.G177A|CCNE1_ENST00000357943.5_Intron	NM_001238.2	NP_001229.1	P24864	CCNE1_HUMAN	cyclin E1	192					androgen receptor signaling pathway (GO:0030521)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|Wnt signaling pathway (GO:0016055)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|kinase activity (GO:0016301)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|skin(1)	20	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			CAGCTTATTGGGATTTCATCT	0.348			A		serous ovarian																																p.G192A		Atlas-SNP	.		Dom	yes		19	19q12	898	cyclin E1		E	.	CCNE1	49	.	0			c.G575C						.						69	72	71					19																	30311721		2203	4300	6503	SO:0001583	missense	898	exon7			TTATTGGGATTTC	M73812	CCDS12419.1	19q12	2014-07-03			ENSG00000105173	ENSG00000105173			1589	protein-coding gene	gene with protein product	"cyclin Es", "cyclin Et"	123837		CCNE		1833066	Standard	NM_001238		Approved		uc002nsn.3	P24864	OTTHUMG00000177626	ENST00000262643.3:c.575G>C	chr19.hg19:g.30311721G>C	ENSP00000262643:p.Gly192Ala	117.0	0.0		89.0	22.0	NM_001238	A8K684|Q14091|Q8NFG1|Q92501|Q9UD21	Missense_Mutation	SNP	ENST00000262643.3	hg19	CCDS12419.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.919889	0.92249	.	.	ENSG00000105173	ENST00000262643;ENST00000444983	T;T	0.11604	2.76;2.76	5.97	5.97	0.96955	Cyclin, N-terminal (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.38665	0.1049	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.08848	-1.0702	10	0.87932	D	0	.	19.4017	0.94632	0.0:0.0:1.0:0.0	.	192	P24864	CCNE1_HUMAN	A	192;177	ENSP00000262643:G192A;ENSP00000410179:G177A	ENSP00000262643:G192A	G	+	2	0	CCNE1	35003561	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	9.860000	0.99555	2.835000	0.97688	0.591000	0.81541	GGG	.	.		0.348	CCNE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438138.1	NM_001238		C	30311721	G	C	30311721	3	2	53	1	0	0	0	0	1	0	0	0	2922	1232	43	4	597	4	CCNE1	19	30311721	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	9012004	30311721	28817262	86	6786										
C19orf55	148137	hgsc.bcm.edu	37	chr19	36256039	36256039	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tcccttctcggagaccttcaTccctgactccagcaagggcc	8	17	2	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:36256039T>C	ENST00000544099.1	+	7	794	c.731T>C	c.(730-732)aTc>aCc	p.I244T	C19orf55_ENST00000396908.4_Missense_Mutation_p.I244T			Q2NL68	PRSR3_HUMAN		244	Ser-rich.									cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GAGACCTTCATCCCTGACTCC	0.627																																					p.I244T		Atlas-SNP	.											.	C19orf55	39	.	0			c.T731C						.						87	90	89					19																	36256039		2107	4242	6349	SO:0001583	missense	148137	exon7			CCTTCATCCCTGA																												ENST00000544099.1:c.731T>C	chr19.hg19:g.36256039T>C	ENSP00000467267:p.Ile244Thr	79.0	0.0		68.0	15.0	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Missense_Mutation	SNP	ENST00000544099.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.013	-1.610108	0.00835	.	.	ENSG00000167595	ENST00000396908;ENST00000301165	T;T	0.40476	1.03;1.03	4.42	-5.24	0.02789	.	1.025080	0.07815	N	0.958850	T	0.10937	0.0267	N	0.02802	-0.49	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28964	-1.0027	10	0.02654	T	1	-2.4375	0.3981	0.00421	0.2784:0.2354:0.1297:0.3565	.	244	E5RFB9	.	T	244;243	ENSP00000380116:I244T;ENSP00000301165:I243T	ENSP00000301165:I243T	I	+	2	0	C19orf55	40947879	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	-0.856000	0.04290	-0.671000	0.05274	-0.379000	0.06801	ATC	.	.		0.627	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2			C	36256039	T	C	36256039	3	2	53	1	0	0	0	0	1	0	0	0	1939	1435	50	2	757	2	C19orf55	19	36256039	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	5944318	36256039	22872944	87	6787										
DYRK1B	9149	hgsc.bcm.edu	37	chr19	40316849	40316849	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gttcatctcacagtctgtgaTagggggcccagggcccccac	12	14	3	1			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:40316849T>C	ENST00000593685.1	-	10	1957	c.1489A>G	c.(1489-1491)Atc>Gtc	p.I497V	DYRK1B_ENST00000430012.2_Missense_Mutation_p.I457V|DYRK1B_ENST00000348817.3_Missense_Mutation_p.I469V|DYRK1B_ENST00000597639.1_Missense_Mutation_p.I469V|DYRK1B_ENST00000323039.5_Missense_Mutation_p.I497V			Q9Y463	DYR1B_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1B	497	Interaction with RANBP9.				adipose tissue development (GO:0060612)|myoblast fusion (GO:0007520)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(7)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	24	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)		Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)			CAGTCTGTGATAGGGGGCCCA	0.622																																					p.I497V		Atlas-SNP	.											.	DYRK1B	114	.	0			c.A1489G						.						51	55	53					19																	40316849		2203	4300	6503	SO:0001583	missense	9149	exon10			CTGTGATAGGGGG	Y17999	CCDS12543.1, CCDS12544.1, CCDS46075.1	19q13.2	2012-10-02			ENSG00000105204	ENSG00000105204	2.7.12.1		3092	protein-coding gene	gene with protein product	"minibrain-related kinase"	604556				9918863	Standard	XM_005259395		Approved	MIRK	uc002omj.3	Q9Y463		ENST00000593685.1:c.1489A>G	chr19.hg19:g.40316849T>C	ENSP00000469863:p.Ile497Val	46.0	0.0		32.0	7.0	NM_004714	O75258|O75788|O75789	Missense_Mutation	SNP	ENST00000593685.1	hg19	CCDS12543.1	.	.	.	.	.	.	.	.	.	.	T	3.615	-0.078772	0.07141	.	.	ENSG00000105204	ENST00000323039;ENST00000348817;ENST00000430012	T;T;T	0.55052	0.56;0.54;0.55	4.18	0.313	0.15842	.	0.664334	0.13789	N	0.362640	T	0.19765	0.0475	N	0.03608	-0.345	0.20975	N	0.999813	P;B;B	0.36086	0.536;0.007;0.003	B;B;B	0.34038	0.174;0.003;0.007	T	0.10917	-1.0609	10	0.16896	T	0.51	.	2.2481	0.04036	0.2223:0.2714:0.0:0.5063	.	457;497;469	Q9Y463-2;Q9Y463;Q9Y463-3	.;DYR1B_HUMAN;.	V	497;469;457	ENSP00000312789:I497V;ENSP00000221803:I469V;ENSP00000403182:I457V	ENSP00000312789:I497V	I	-	1	0	DYRK1B	45008689	0.984000	0.35163	0.997000	0.53966	0.991000	0.79684	0.829000	0.27449	0.445000	0.26639	0.379000	0.24179	ATC	.	.		0.622	DYRK1B-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462874.2	NM_004714		C	40316849	T	C	40316849	3	2	53	1	0	0	0	0	1	0	0	0	4857	1406	49	2	408	2	DYRK1B	19	40316849	Missense_Mutation	SNP	T	TCGA-BW-A5NQ-01A-11D-A27I-10	4060810	40316849	18812134	88	6788										
ERG	2078	hgsc.bcm.edu	37	chr21	39817538	39817538	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	gtcctcactcacaactgataAggcttcctgaatgcccaaag	7	13	2	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr21:39817538A>C	ENST00000417133.2	-	4	231	c.46T>G	c.(46-48)Tta>Gta	p.L16V	ERG_ENST00000398907.1_Missense_Mutation_p.L9V|ERG_ENST00000429727.2_Missense_Mutation_p.L9V|ERG_ENST00000398910.1_Missense_Mutation_p.L16V|ERG_ENST00000398905.1_Missense_Mutation_p.L9V|ERG_ENST00000398919.2_Missense_Mutation_p.L16V|ERG_ENST00000442448.1_Missense_Mutation_p.L16V|ERG_ENST00000398911.1_Missense_Mutation_p.L16V|ERG_ENST00000453032.2_Intron|ERG_ENST00000288319.7_Missense_Mutation_p.L9V|ERG_ENST00000398897.1_Intron	NM_001136154.1|NM_001243432.1	NP_001129626.1|NP_001230361.1	Q12809	KCNH2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog	0					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)		EWSR1/ERG(178)|NDRG1/ERG(5)|TMPRSS2/ERG(3582)|FUS/ERG(167)|SLC45A3/ERG(50)	lung(2)|ovary(1)|skin(1)	4		Prostate(19;3.6e-06)			Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	ACAACTGATAAGGCTTCCTGA	0.478			T	"EWSR1, TMPRSS2, ELF4, FUS, HERPUD1, NDRG1"	"Ewing sarcoma, prostate, AML"																																p.L16V	Esophageal Squamous(130;336 1700 3010 3083 40589)	Atlas-SNP	.		Dom	yes		21	21q22.3	2078	v-ets erythroblastosis virus E26 oncogene like (avian)		"M, E, L"	.	ERG	78	.	0			c.T46G						.						87	71	77					21																	39817538		2203	4300	6503	SO:0001583	missense	2078	exon4			CTGATAAGGCTTC		CCDS13657.1, CCDS13658.1, CCDS46648.1, CCDS46649.1, CCDS58789.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157554	ENSG00000157554			3446	protein-coding gene	gene with protein product	"v-ets avian erythroblastosis virus E26 oncogene related", "transcriptional regulator ERG (transforming protein ERG)", "v-ets erythroblastosis virus E26 oncogene like", "TMPRSS2-ERG prostate cancer specific"	165080	"v-ets avian erythroblastosis virus E26 oncogene related"			3274086	Standard	NM_001136154		Approved	erg-3, p55	uc002yxa.3	P11308	OTTHUMG00000090767	ENST00000417133.2:c.46T>G	chr21.hg19:g.39817538A>C	ENSP00000414150:p.Leu16Val	248.0	0.0		291.0	56.0	NM_001243432	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000417133.2	hg19	CCDS46648.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.891027	0.52014	.	.	ENSG00000157554	ENST00000398905;ENST00000398907;ENST00000288319;ENST00000398911;ENST00000417133;ENST00000398910;ENST00000442448;ENST00000398919;ENST00000429727	T;T;T;T;T;T;T;T	0.37915	1.54;1.48;1.35;1.38;1.17;1.37;1.38;1.17	5.77	-3.5	0.04710	.	0.000000	0.64402	D	0.000003	T	0.50990	0.1648	M	0.64404	1.975	0.26945	N	0.966165	D;D;D;D;D	0.89917	0.998;1.0;1.0;0.999;0.998	D;D;D;D;D	0.91635	0.996;0.998;0.999;0.996;0.996	T	0.53151	-0.8479	10	0.87932	D	0	.	13.5166	0.61543	0.4795:0.0:0.5205:0.0	.	9;16;16;16;9	B4E3C5;P11308;P11308-6;P11308-1;P11308-4	.;ERG_HUMAN;.;.;.	V	9;9;9;16;16;16;16;16;9	ENSP00000381877:L9V;ENSP00000381879:L9V;ENSP00000288319:L9V;ENSP00000381882:L16V;ENSP00000414150:L16V;ENSP00000381881:L16V;ENSP00000394694:L16V;ENSP00000381891:L16V	ENSP00000288319:L9V	L	-	1	2	ERG	38739408	0.103000	0.21917	0.003000	0.11579	0.778000	0.44026	0.645000	0.24782	-0.664000	0.05324	-0.993000	0.02533	TTA	.	.		0.478	ERG-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207532.2	NM_182918		C	39817538	A	C	39817538	3	2	53	1	0	0	0	0	1	0	0	0	5224	69	3	5	1450	5	ERG	21	39817538	Missense_Mutation	SNP	A	TCGA-BW-A5NQ-01A-11D-A27I-10		39817538	8312357	89	6789										
TXN2	25828	hgsc.bcm.edu	37	chr22	36876748	36876748	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	atattgtccgggctgggttgGgtgttacagtcaggccacca	14	9	1	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr22:36876748G>A	ENST00000216185.2	-	2	603	c.137C>T	c.(136-138)cCc>cTc	p.P46L	TXN2_ENST00000416967.1_5'UTR|TXN2_ENST00000403313.1_Missense_Mutation_p.P46L|TXN2_ENST00000487725.1_5'UTR			Q99757	THIOM_HUMAN	thioredoxin 2	46					cell redox homeostasis (GO:0045454)|cellular response to nutrient levels (GO:0031669)|glycerol ether metabolic process (GO:0006662)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)	dendrite (GO:0030425)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)	protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|lung(1)|prostate(1)	3						GGCTGGGTTGGGTGTTACAGT	0.547																																					p.P46L		Atlas-SNP	.											.	TXN2	15	.	0			c.C137T						.						155	132	140					22																	36876748		2203	4300	6503	SO:0001583	missense	25828	exon2			GGGTTGGGTGTTA	U78678	CCDS13928.1	22q13.1	2008-06-11			ENSG00000100348	ENSG00000100348			17772	protein-coding gene	gene with protein product		609063				9006939, 17220299	Standard	NM_012473		Approved	MT-TRX	uc003apk.1	Q99757	OTTHUMG00000150596	ENST00000216185.2:c.137C>T	chr22.hg19:g.36876748G>A	ENSP00000216185:p.Pro46Leu	113.0	0.0		66.0	15.0	NM_012473	Q5JZA0|Q6FH60|Q9UH29	Missense_Mutation	SNP	ENST00000216185.2	hg19	CCDS13928.1	.	.	.	.	.	.	.	.	.	.	g	2.067	-0.413949	0.04799	.	.	ENSG00000100348	ENST00000216185;ENST00000403313	T;T	0.12672	2.66;2.66	5.36	-1.28	0.09318	.	0.254450	0.39407	N	0.001368	T	0.12860	0.0312	M	0.69823	2.125	0.26776	N	0.969698	B	0.02656	0.0	B	0.01281	0.0	T	0.16988	-1.0384	10	0.39692	T	0.17	-23.1098	6.5833	0.22607	0.2285:0.3384:0.4331:0.0	.	46	Q99757	THIOM_HUMAN	L	46	ENSP00000216185:P46L;ENSP00000385393:P46L	ENSP00000216185:P46L	P	-	2	0	TXN2	35206694	0.000000	0.05858	0.305000	0.25099	0.037000	0.13140	-0.025000	0.12413	-0.092000	0.12417	-0.738000	0.03535	CCC	.	.		0.547	TXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319016.1	NM_012473		A	36876748	G	A	36876748	3	1	53	1	0	0	0	0	1	0	0	0	16806	1232	43	3	375	3	TXN2	22	36876748	Missense_Mutation	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10		36876748	14427818	90	6790										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73960550	73960550	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	ccttccccaaggcccaatctCcagaaagtcccttttgactt	5	16	1	2			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chrX:73960550C>A	ENST00000055682.6	-	3	4453	c.3842G>T	c.(3841-3843)gGa>gTa	p.G1281V		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1281					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						GGCCCAATCTCCAGAAAGTCC	0.517																																					p.G1281V		Atlas-SNP	.											.	KIAA2022	262	.	0			c.G3842T						.						88	73	78					X																	73960550		2203	4300	6503	SO:0001583	missense	340533	exon3			CAATCTCCAGAAA		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.3842G>T	chrX.hg19:g.73960550C>A	ENSP00000055682:p.Gly1281Val	53.0	0.0		44.0	22.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	C	14.56	2.570404	0.45798	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.30714	1.52;1.52	5.11	3.33	0.38152	.	0.503490	0.23414	N	0.048438	T	0.28034	0.0691	L	0.29908	0.895	0.80722	D	1	P	0.45827	0.867	P	0.47206	0.541	T	0.02844	-1.1103	10	0.87932	D	0	-1.3178	9.7619	0.40537	0.0:0.7849:0.1373:0.0778	.	1281	Q5QGS0	K2022_HUMAN	V	1281	ENSP00000362567:G1281V;ENSP00000055682:G1281V	ENSP00000055682:G1281V	G	-	2	0	KIAA2022	73877275	0.999000	0.42202	0.992000	0.48379	0.915000	0.54546	2.181000	0.42547	0.538000	0.28769	0.600000	0.82982	GGA	.	.		0.517	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		A	73960550	C	A	73960550	3	1	53	1	0	0	0	0	1	0	0	0	8278	855	30	3	716	3	KIAA2022	23	73960550	Missense_Mutation	SNP	C	TCGA-BW-A5NQ-01A-11D-A27I-10		73960550	81310010	91	6791										
RAP2C	57826	hgsc.bcm.edu	37	chrX	131348421	131348421	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0555555555555556	5	1	1.17509892594686	0.851946721311475	1.29820452771272	0.265734265734266	0.917767417767419	0	tttcctactaggattagtggGactttttcatatctcttcac	6	9	3	0			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chrX:131348421G>C	ENST00000342983.2	-	3	1073	c.327C>G	c.(325-327)gtC>gtG	p.V109V	RAP2C_ENST00000460462.1_5'UTR|RAP2C-AS1_ENST00000421483.2_RNA|RAP2C_ENST00000370874.1_Silent_p.V109V	NM_001271187.1|NM_021183.4	NP_001258116.1|NP_067006.3	Q9Y3L5	RAP2C_HUMAN	RAP2C, member of RAS oncogene family	109					GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|positive regulation of protein autophosphorylation (GO:0031954)|Rap protein signal transduction (GO:0032486)|regulation of protein tyrosine kinase activity (GO:0061097)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	8	Acute lymphoblastic leukemia(192;0.000127)					GGATTAGTGGGACTTTTTCAT	0.393																																					p.V109V		Atlas-SNP	.											.	RAP2C	22	.	0			c.C327G						.						91	72	78					X																	131348421		2203	4300	6503	SO:0001819	synonymous_variant	57826	exon3			TAGTGGGACTTTT	BC051467	CCDS14632.1, CCDS76024.1	Xq25	2014-05-09			ENSG00000123728	ENSG00000123728			21165	protein-coding gene	gene with protein product							Standard	NM_001271186		Approved	DKFZp313B211	uc004ewp.4	Q9Y3L5	OTTHUMG00000022424	ENST00000342983.2:c.327C>G	chrX.hg19:g.131348421G>C		104.0	0.0		71.0	33.0	NM_021183	B3KWD6|Q5H9H9|Q9BTS0	Silent	SNP	ENST00000342983.2	hg19	CCDS14632.1																																																																																			.	.		0.393	RAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058312.1	NM_021183		C	131348421	G	C	131348421	2	2	53	1	0	0	0	0	0	0	0	1	13057	1161	41	4		4	RAP2C	23	131348421	Silent	SNP	G	TCGA-BW-A5NQ-01A-11D-A27I-10	57387871	131348421	23922139	92	6792										
DFFB	1677	hgsc.bcm.edu	37	chr1	3786299	3786300	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gacagaggagccaagggcggINScagccgcctctgcacaccgg					rs374397595		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:3786299_3786300insC	ENST00000378209.3	+	5	964_965	c.641_642insC	c.(640-645)ggcagcfs	p.S215fs	DFFB_ENST00000338895.3_Frame_Shift_Ins_p.S215fs	NM_004402.2	NP_004393.1	O76075	DFFB_HUMAN	DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase)	215					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			endometrium(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		GCCAAGGGCGGCAGCCGCCTCT	0.649																																					p.G214fs		Atlas-INDEL	.											.	DFFB	30	.	0			c.641_642insC						.																																			SO:0001589	frameshift_variant	1677	exon5			.		CCDS52.1, CCDS72693.1	1p36.3	2014-03-06	2002-08-29		ENSG00000169598	ENSG00000169598			2773	protein-coding gene	gene with protein product		601883				9108473, 9560346	Standard	NM_004402		Approved	CAD, CPAN, DFF-40, DFF40	uc001alc.3	O76075	OTTHUMG00000003525	ENST00000378209.3:c.642dupC	chr1.hg19:g.3786300_3786300dupC	ENSP00000367454:p.Ser215fs	100.0	0.0		198.0	13.0	NM_004402	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Frame_Shift_Ins	INS	ENST00000378209.3	hg19	CCDS52.1																																																																																			.	.		0.649	DFFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009821.2	NM_001282669		C	3786300	-	C	3786299	7	5	54	1	0	1	1	0	0	0	0	0	4455	1203	42	0	659	0	DFFB	1	3786299	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10		3786299	245464322	1	6793										
CASZ1	54897	hgsc.bcm.edu	37	chr1	10713557	10713558	+	Frame_Shift_Ins	INS	-	-	G													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ggtggtgccgggacagaggcINSggcagccacgggggctgagt					rs576823495		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:10713557_10713558insG	ENST00000377022.3	-	11	2873_2874	c.2556_2557insC	c.(2554-2559)gccgccfs	p.A853fs	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Frame_Shift_Ins_p.A853fs	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	853					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GGGACAGAGGCGGCAGCCACGG	0.678																																					p.A853fs		Atlas-INDEL	.											.	CASZ1	150	.	0			c.2557_2558insC						.																																			SO:0001589	frameshift_variant	54897	exon11			.	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.2557dupC	chr1.hg19:g.10713559_10713559dupG	ENSP00000366221:p.Ala853fs	82.0	0.0		186.0	11.0	NM_017766	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Frame_Shift_Ins	INS	ENST00000377022.3	hg19	CCDS41246.1																																																																																			.	.		0.678	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		G	10713558	-	G	10713557	7	5	54	1	0	1	1	0	0	0	0	0	2687	768	27	0	2770	0	CASZ1	1	10713557	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	6927258	10713557	238537064	2	6794										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27087894	27087898	+	Frame_Shift_Del	DEL	GCCAC	GCCAC	-													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ggcaaccagatgccacctcgGccacccagtggccagtcgga							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	GCCAC	GCCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:27087894_27087898delGCCAC	ENST00000324856.7	+	6	2552_2556	c.2181_2185delGCCAC	c.(2179-2187)cggccacccfs	p.PP728fs	RN7SL501P_ENST00000578818.1_RNA|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.PP345fs|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.PP728fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	728					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.R727fs*12(1)|p.P728fs(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TGCCACCTCGGCCACCCAGTGGCCA	0.522			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.727_728del		Atlas-Indel,Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.,1	ARID1A	842	.	2	Deletion - Frameshift(1)|Complex(1)	ovary(1)|liver(1)	c.2180_2184del						.																																			SO:0001589	frameshift_variant	8289	exon6			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2181_2185delGCCAC	chr1.hg19:g.27087894_27087898delGCCAC	ENSP00000320485:p.Pro728fs	322.0	0.0		200.0	70.0	NM_139135	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.522	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27087898	GCCAC	-	27087894	7	5	54	1	0	1	0	1	0	0	0	0	913	1190	42	0	2203	0	ARID1A	1	27087894	Frame_Shift_Del	DEL	GCCAC	TCGA-CC-5258-01A-01D-A12Z-10	16374337	27087894	222162727	3	6795										
BAI2	576	hgsc.bcm.edu	37	chr1	32207068	32207068	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gggcactgaggagacagcggCggctggcagaccctgcaggg	19	11	0	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:32207068C>A	ENST00000373658.3	-	11	2041	c.1700G>T	c.(1699-1701)cGc>cTc	p.R567L	BAI2_ENST00000373655.2_Missense_Mutation_p.R567L|BAI2_ENST00000398542.1_Missense_Mutation_p.R500L|BAI2_ENST00000398556.3_Missense_Mutation_p.R515L|BAI2_ENST00000440175.2_Missense_Mutation_p.R209L|BAI2_ENST00000398547.1_Missense_Mutation_p.R500L|BAI2_ENST00000398538.1_Missense_Mutation_p.R555L|BAI2_ENST00000527361.1_Missense_Mutation_p.R567L|BAI2_ENST00000257070.4_Missense_Mutation_p.R567L	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	567					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GAGACAGCGGCGGCTGGCAGA	0.632																																					p.R567L		Atlas-SNP	.											.	BAI2	128	.	0			c.G1700T						.						16	18	17					1																	32207068		2200	4295	6495	SO:0001583	missense	576	exon11			CAGCGGCGGCTGG	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.1700G>T	chr1.hg19:g.32207068C>A	ENSP00000362762:p.Arg567Leu	61.0	0.0		132.0	72.0	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	hg19	CCDS346.2	.	.	.	.	.	.	.	.	.	.	C	33	5.195741	0.94960	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538;ENST00000420125	T;T;T;T;T;T;T;T;T;T	0.69561	1.27;1.45;-0.41;-0.41;1.69;-0.41;-0.41;-0.41;-0.41;-0.41	5.38	5.38	0.77491	GPCR, family 2, extracellular hormone receptor domain (2);	0.000000	0.43579	D	0.000544	T	0.81245	0.4782	M	0.68317	2.08	0.58432	D	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;0.999;1.0	T	0.82623	-0.0366	10	0.87932	D	0	.	18.2761	0.90084	0.0:1.0:0.0:0.0	.	567;555;209;500;567;567	O60241-4;O60241-3;B4DKC3;A2A3C1;O60241-2;O60241	.;.;.;.;.;BAI2_HUMAN	L	515;500;567;567;500;567;567;209;555;505	ENSP00000381564:R515L;ENSP00000381555:R500L;ENSP00000362762:R567L;ENSP00000362759:R567L;ENSP00000381550:R500L;ENSP00000257070:R567L;ENSP00000435397:R567L;ENSP00000391071:R209L;ENSP00000381548:R555L;ENSP00000410921:R505L	ENSP00000257070:R567L	R	-	2	0	BAI2	31979655	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.645000	0.83430	2.694000	0.91930	0.555000	0.69702	CGC	.	.		0.632	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		A	32207068	C	A	32207068	3	1	54	1	0	0	0	0	1	0	0	0	1299	768	27	1	3149	1	BAI2	1	32207068	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	5119174	32207068	217043553	4	6796										
ARTN	9048	hgsc.bcm.edu	37	chr1	44402421	44402421	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ccgcctctccgccaccgcctGcggctgcctgggctgagggc	14	19	1	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:44402421G>T	ENST00000372359.5	+	5	1429	c.647G>T	c.(646-648)tGc>tTc	p.C216F	ARTN_ENST00000438616.3_Missense_Mutation_p.C233F|ARTN_ENST00000372354.3_Missense_Mutation_p.C216F|ARTN_ENST00000498139.2_Missense_Mutation_p.C224F|ARTN_ENST00000414809.3_Missense_Mutation_p.C224F	NM_057091.2	NP_476432.2	Q5T4W7	ARTN_HUMAN	artemin	216					axon guidance (GO:0007411)|induction of positive chemotaxis (GO:0050930)|lymphocyte migration into lymphoid organs (GO:0097021)|neuroblast proliferation (GO:0007405)|peripheral nervous system development (GO:0007422)|Peyer's patch morphogenesis (GO:0061146)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	receptor binding (GO:0005102)					Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)				GCCACCGCCTGCGGCTGCCTG	0.677																																					p.C224F		Atlas-SNP	.											.	ARTN	6	.	0			c.G671T						.						11	12	11					1																	44402421		2127	4174	6301	SO:0001583	missense	9048	exon4			CCGCCTGCGGCTG	AF109401	CCDS501.1, CCDS502.1	1p33-p32	2014-01-30			ENSG00000117407	ENSG00000117407		"Endogenous ligands"	727	protein-coding gene	gene with protein product	"neublastin", "neurotrophic factor"	603886				9883723	Standard	NM_057090		Approved	NBN, EVN, ENOVIN	uc001ckt.3	Q5T4W7	OTTHUMG00000007705	ENST00000372359.5:c.647G>T	chr1.hg19:g.44402421G>T	ENSP00000361434:p.Cys216Phe	21.0	0.0		59.0	28.0	NM_001136215	D3DPY1|D3DPY3|O95441|O96030|Q6P6A3	Missense_Mutation	SNP	ENST00000372359.5	hg19	CCDS501.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611251	0.66558	.	.	ENSG00000117407	ENST00000372359;ENST00000414809;ENST00000498139;ENST00000372354;ENST00000438616	D;D;D;D;D	0.99582	-6.22;-6.22;-6.22;-6.22;-6.22	4.33	4.33	0.51752	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99507	0.9824	M	0.71036	2.16	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	D	0.98198	1.0466	10	0.87932	D	0	-19.3201	16.4443	0.83913	0.0:0.0:1.0:0.0	.	233;224;216	Q5T4W7-2;Q5T4W7-3;Q5T4W7	.;.;ARTN_HUMAN	F	216;224;224;216;233	ENSP00000361434:C216F;ENSP00000387435:C224F;ENSP00000436727:C224F;ENSP00000361429:C216F;ENSP00000391998:C233F	ENSP00000361429:C216F	C	+	2	0	ARTN	44175008	1.000000	0.71417	1.000000	0.80357	0.373000	0.29922	9.232000	0.95325	1.980000	0.57719	0.478000	0.44815	TGC	.	.		0.677	ARTN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000020713.2	NM_057090		T	44402421	G	T	44402421	3	4	54	1	0	0	0	0	1	0	0	0	1001	1319	46	3	768	3	ARTN	1	44402421	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	12195353	44402421	204848200	5	6797										
AMPD1	270	hgsc.bcm.edu	37	chr1	115220086	115220086	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tgcggccatagatggacaggCggggctcagcatgctggtac	16	10	1	1	rs121912682	byFrequency	TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:115220086C>A	ENST00000520113.2	-	10	1388	c.1373G>T	c.(1372-1374)cGc>cTc	p.R458L	AMPD1_ENST00000353928.6_Missense_Mutation_p.R425L|AMPD1_ENST00000369538.3_Missense_Mutation_p.R454L			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	458			R -> H (in MMDD; loss of activity). {ECO:0000269|PubMed:11102975}.		IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	GATGGACAGGCGGGGCTCAGC	0.572																																					p.R458L		Atlas-SNP	.											.	AMPD1	223	.	0			c.G1373T	GRCh37	CM002933	AMPD1	M	rs121912682	.						98	84	89					1																	115220086		2203	4300	6503	SO:0001583	missense	270	exon10			GACAGGCGGGGCT	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.1373G>T	chr1.hg19:g.115220086C>A	ENSP00000430075:p.Arg458Leu	96.0	0.0		143.0	21.0	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	hg19	CCDS876.2	.	.	.	.	.	.	.	.	.	.	C	36	5.636488	0.96693	.	.	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.82711	-1.64;-1.64;-1.64	5.85	5.85	0.93711	Adenosine/AMP deaminase (1);	0.000000	0.85682	D	0.000000	D	0.93996	0.8077	H	0.95365	3.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.94872	0.8031	10	0.87932	D	0	-15.6719	20.1775	0.98187	0.0:1.0:0.0:0.0	.	454;425	Q5TF02;P23109	.;AMPD1_HUMAN	L	458;454;425	ENSP00000430075:R458L;ENSP00000358551:R454L;ENSP00000316520:R425L	ENSP00000316520:R425L	R	-	2	0	AMPD1	115021609	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.771000	0.95319	0.561000	0.74099	CGC	.	C|0.999;T|0.001		0.572	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			A	115220086	C	A	115220086	3	1	54	1	0	0	0	0	1	0	0	0	585	768	27	1	997	1	AMPD1	1	115220086	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	70817665	115220086	134030535	6	6798										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117122413	117122413	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gcgggagtcctggctggagcGggacacgatgctacagtcca	16	11	0	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:117122413G>A	ENST00000369486.3	-	10	3700	c.2935C>T	c.(2935-2937)Cgc>Tgc	p.R979C	IGSF3_ENST00000369483.1_Missense_Mutation_p.R999C|IGSF3_ENST00000318837.6_Missense_Mutation_p.R999C	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	979	Ig-like C2-type 8.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		TGGCTGGAGCGGGACACGATG	0.592																																					p.R999C		Atlas-SNP	.											IGSF3_ENST00000369483,NS,carcinoma,0,2	IGSF3	294	.	0			c.C2995T						.						37	36	36					1																	117122413		2203	4300	6503	SO:0001583	missense	3321	exon11			TGGAGCGGGACAC	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.2935C>T	chr1.hg19:g.117122413G>A	ENSP00000358498:p.Arg979Cys	71.0	0.0		121.0	56.0	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.651009	0.88056	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.22539	1.95;1.95;1.95	4.67	4.67	0.58626	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.218972	0.42172	D	0.000759	T	0.26484	0.0647	L	0.50333	1.59	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	P;P	0.59288	0.791;0.855	T	0.01225	-1.1413	10	0.56958	D	0.05	-36.4972	15.1177	0.72416	0.0:0.0:1.0:0.0	.	979;999	O75054;A6NJZ6	IGSF3_HUMAN;.	C	979;999;999	ENSP00000358498:R979C;ENSP00000358495:R999C;ENSP00000321184:R999C	ENSP00000321184:R999C	R	-	1	0	IGSF3	116923936	1.000000	0.71417	0.991000	0.47740	0.991000	0.79684	8.151000	0.89636	2.421000	0.82119	0.462000	0.41574	CGC	.	.		0.592	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		A	117122413	G	A	117122413	3	1	54	1	0	0	0	0	1	0	0	0	7610	1116	39	1	657	1	IGSF3	1	117122413	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	1902327	117122413	132128208	7	6799										
OTUD7B	56957	hgsc.bcm.edu	37	chr1	149916120	149916120	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	aggtggcatatggtggtaggCccccgacacatggaccccct	13	13	0	0	rs376252200		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:149916120C>A	ENST00000369135.4	-	12	2462	c.2168G>T	c.(2167-2169)gGc>gTc	p.G723V		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	723					mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			TGGTGGTAGGCCCCCGACACA	0.652																																					p.G723V		Atlas-SNP	.											.	OTUD7B	76	.	0			c.G2168T						.	C	VAL/GLY	0,3914		0,0,1957	28	32	31		2168	4.4	0.9	1		31	1,8265		0,1,4132	no	missense	OTUD7B	NM_020205.2	109	0,1,6089	AA,AC,CC		0.0121,0.0,0.0082	possibly-damaging	723/844	149916120	1,12179	1957	4133	6090	SO:0001583	missense	56957	exon12			GGTAGGCCCCCGA	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"OTU domain containing"	16683	protein-coding gene	gene with protein product		611748	"zinc finger, A20 domain containing 1", "OTU domain containing 7B"	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.2168G>T	chr1.hg19:g.149916120C>A	ENSP00000358131:p.Gly723Val	43.0	0.0		51.0	22.0	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Missense_Mutation	SNP	ENST00000369135.4	hg19	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	C	10.67	1.414535	0.25465	0.0	1.21E-4	ENSG00000163113	ENST00000369135;ENST00000543330	T	0.32023	1.47	4.37	4.37	0.52481	.	0.306666	0.35151	N	0.003409	T	0.09598	0.0236	L	0.34521	1.04	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.09292	-1.0681	9	.	.	.	-31.7542	8.1151	0.30937	0.0:0.8922:0.0:0.1078	.	723	Q6GQQ9	OTU7B_HUMAN	V	723	ENSP00000358131:G723V	.	G	-	2	0	OTUD7B	148182744	0.434000	0.25570	0.918000	0.36340	0.688000	0.40055	1.197000	0.32211	2.272000	0.75746	0.455000	0.32223	GGC	.	.		0.652	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205		A	149916120	C	A	149916120	3	1	54	1	0	0	0	0	1	0	0	0	11328	739	26	3	367	3	OTUD7B	1	149916120	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	32793707	149916120	99334501	8	6800										
OR10J5	127385	hgsc.bcm.edu	37	chr1	159505721	159505721	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ttaggaaaaccacaaagaggGttatctgatgctttccaaag	9	7	1	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:159505721G>T	ENST00000334857.2	-	1	121	c.77C>A	c.(76-78)aCc>aAc	p.T26N		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	26						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					CACAAAGAGGGTTATCTGATG	0.388																																					p.T26N		Atlas-SNP	.											.	OR10J5	68	.	0			c.C77A						.						96	92	93					1																	159505721		2203	4300	6503	SO:0001583	missense	127385	exon1			AAGAGGGTTATCT		CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"GPCR / Class A : Olfactory receptors"	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.77C>A	chr1.hg19:g.159505721G>T	ENSP00000334441:p.Thr26Asn	118.0	0.0		152.0	31.0	NM_001004469	B9EH35|Q6IFH2	Missense_Mutation	SNP	ENST00000334857.2	hg19	CCDS30910.1	.	.	.	.	.	.	.	.	.	.	G	12.97	2.097148	0.37048	.	.	ENSG00000184155	ENST00000334857	T	0.00438	7.42	4.43	3.52	0.40303	.	.	.	.	.	T	0.00241	0.0007	M	0.75085	2.285	0.09310	N	1	P	0.52692	0.955	P	0.50231	0.635	T	0.46830	-0.9163	9	0.30078	T	0.28	.	6.9396	0.24486	0.2056:0.0:0.7944:0.0	.	26	Q8NHC4	O10J5_HUMAN	N	26	ENSP00000334441:T26N	ENSP00000334441:T26N	T	-	2	0	OR10J5	157772345	0.000000	0.05858	0.867000	0.34043	0.504000	0.33889	0.240000	0.18042	1.208000	0.43306	0.557000	0.71058	ACC	.	.		0.388	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469		T	159505721	G	T	159505721	3	4	54	1	0	0	0	0	1	0	0	0	10921	1261	44	3	854	3	OR10J5	1	159505721	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	9589601	159505721	89744900	9	6801										
RFWD2	64326	hgsc.bcm.edu	37	chr1	175956209	175956209	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	aagtcttagaaagtcctttaTagtacaggtagagagagtta	10	4	1	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:175956209T>C	ENST00000367669.3	-	18	2517	c.2003A>G	c.(2002-2004)tAt>tGt	p.Y668C	RFWD2_ENST00000308769.8_Missense_Mutation_p.Y644C	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	668					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						AAGTCCTTTATAGTACAGGTA	0.299																																					p.Y668C	Ovarian(134;1413 1765 5706 35534 51541)	Atlas-SNP	.											.	RFWD2	67	.	0			c.A2003G						.						59	59	59					1																	175956209		2203	4300	6503	SO:0001583	missense	64326	exon18			CCTTTATAGTACA	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	17440	protein-coding gene	gene with protein product		608067	"ring finger and WD repeat domain 2"			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.2003A>G	chr1.hg19:g.175956209T>C	ENSP00000356641:p.Tyr668Cys	179.0	0.0		202.0	45.0	NM_022457	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Missense_Mutation	SNP	ENST00000367669.3	hg19	CCDS30944.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962913	0.53507	.	.	ENSG00000143207	ENST00000367665;ENST00000367669;ENST00000367666;ENST00000308769	T;T;T	0.70399	-0.48;-0.48;-0.48	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.85969	0.5821	M	0.87269	2.87	0.80722	D	1	B;D;B;D;D	0.76494	0.067;0.98;0.169;0.999;0.98	B;D;B;D;D	0.77557	0.114;0.941;0.091;0.99;0.941	D	0.88357	0.2985	10	0.72032	D	0.01	-15.7895	15.8017	0.78456	0.0:0.0:0.0:1.0	.	443;428;644;668;668	Q8NHY2-3;B1AMD2;Q8NHY2-2;Q8NHY2;Q504W6	.;.;.;RFWD2_HUMAN;.	C	443;668;503;644	ENSP00000356641:Y668C;ENSP00000356638:Y503C;ENSP00000310943:Y644C	ENSP00000310943:Y644C	Y	-	2	0	RFWD2	174222832	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.268000	0.78473	2.261000	0.74972	0.533000	0.62120	TAT	.	.		0.299	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457		C	175956209	T	C	175956209	3	2	54	1	0	0	0	0	1	0	0	0	13275	1406	49	2	204	2	RFWD2	1	175956209	Missense_Mutation	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	16450488	175956209	73294412	10	6802										
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222705320	222705320	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tttgttacctgcttcatcttCagcaaaggagatgatgaact	8	8	3	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:222705320C>G	ENST00000343410.6	-	6	1769	c.1711G>C	c.(1711-1713)Gaa>Caa	p.E571Q		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	571					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		GCTTCATCTTCAGCAAAGGAG	0.433																																					p.E571Q		Atlas-SNP	.											.	HHIPL2	122	.	0			c.G1711C						.						84	81	82					1																	222705320		2203	4300	6503	SO:0001583	missense	79802	exon6			CATCTTCAGCAAA	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"KIAA1822-like"	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1711G>C	chr1.hg19:g.222705320C>G	ENSP00000342118:p.Glu571Gln	91.0	0.0		62.0	25.0	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	hg19	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999179	0.74818	.	.	ENSG00000143512	ENST00000343410	T	0.11169	2.8	5.0	4.09	0.47781	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.052062	0.64402	D	0.000001	T	0.23688	0.0573	L	0.43757	1.38	0.52099	D	0.999942	D	0.89917	1.0	D	0.97110	1.0	T	0.00581	-1.1660	10	0.39692	T	0.17	-18.8979	12.8232	0.57704	0.0:0.9204:0.0:0.0796	.	571	Q6UWX4	HIPL2_HUMAN	Q	571	ENSP00000342118:E571Q	ENSP00000342118:E571Q	E	-	1	0	HHIPL2	220771943	1.000000	0.71417	0.994000	0.49952	0.982000	0.71751	5.694000	0.68272	1.091000	0.41335	0.591000	0.81541	GAA	.	.		0.433	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		G	222705320	C	G	222705320	3	3	54	1	0	0	0	0	1	0	0	0	7103	835	29	4	479	4	HHIPL2	1	222705320	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	46749111	222705320	26545301	11	6803										
RBM34	23029	hgsc.bcm.edu	37	chr1	235318339	235318339	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	aagtatttttctatctgctaCtttaacaccaggttgagaat	6	7	2	1	rs200657743		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:235318339C>A	ENST00000408888.3	-	4	684	c.454G>T	c.(454-456)Gta>Tta	p.V152L	RBM34_ENST00000366606.3_Missense_Mutation_p.V147L			P42696	RBM34_HUMAN	RNA binding motif protein 34	152						nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			CTATCTGCTACTTTAACACCA	0.368																																					p.V152L		Atlas-SNP	.											.	RBM34	41	.	0			c.G454T						.						188	159	168					1																	235318339		1819	4089	5908	SO:0001583	missense	23029	exon4			CTGCTACTTTAAC		CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739		"RNA binding motif (RRM) containing"	28965	protein-coding gene	gene with protein product						7788527, 15134903	Standard	NM_015014		Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.454G>T	chr1.hg19:g.235318339C>A	ENSP00000386226:p.Val152Leu	662.0	1.0		694.0	308.0	NM_001161533	A8K8J7|Q8N2Z8|Q9H5A1	Missense_Mutation	SNP	ENST00000408888.3	hg19	CCDS41477.2	.	.	.	.	.	.	.	.	.	.	C	1.089	-0.664488	0.03428	.	.	ENSG00000188739	ENST00000408888;ENST00000366606;ENST00000400947;ENST00000447801;ENST00000429912	T;T;T	0.14391	2.51;2.51;2.63	5.67	0.267	0.15622	.	1.363850	0.04381	N	0.360761	T	0.15003	0.0362	M	0.64997	1.995	0.09310	N	1	B;B	0.33171	0.4;0.01	B;B	0.26969	0.075;0.005	T	0.35201	-0.9798	10	0.27785	T	0.31	-1.4571	8.9883	0.36008	0.0:0.5752:0.0:0.4248	.	152;152	P42696-2;P42696	.;RBM34_HUMAN	L	152;147;181;150;181	ENSP00000386226:V152L;ENSP00000355565:V147L;ENSP00000400000:V150L	ENSP00000355565:V147L	V	-	1	0	RBM34	233384962	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.038000	0.12144	0.091000	0.17302	0.655000	0.94253	GTA	.	.		0.368	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100146.1	NM_015014		A	235318339	C	A	235318339	3	1	54	1	0	0	0	0	1	0	0	0	13146	565	20	3	891	3	RBM34	1	235318339	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	12613019	235318339	13932282	12	6804										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245772747	245772747	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	aggagaacctgcgggacctgCtgtcggaggtggccacgggc	18	11	0	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr1:245772747C>G	ENST00000407071.2	+	8	2271	c.1831C>G	c.(1831-1833)Ctg>Gtg	p.L611V	KIF26B_ENST00000366518.4_Missense_Mutation_p.L230V	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	611	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GCGGGACCTGCTGTCGGAGGT	0.637																																					p.L611V		Atlas-SNP	.											.	KIF26B	343	.	0			c.C1831G						.						16	21	20					1																	245772747		1971	4134	6105	SO:0001583	missense	55083	exon8			GACCTGCTGTCGG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.1831C>G	chr1.hg19:g.245772747C>G	ENSP00000385545:p.Leu611Val	55.0	0.0		132.0	23.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.917892	0.52546	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	D;D	0.87887	-2.31;-2.31	5.4	3.51	0.40186	Kinesin, motor domain (4);	.	.	.	.	D	0.93690	0.7984	M	0.90425	3.115	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93431	0.6785	9	0.87932	D	0	.	10.4968	0.44783	0.0:0.7695:0.0:0.2305	.	230;611	B7WPD9;Q2KJY2	.;KI26B_HUMAN	V	611;230;227	ENSP00000385545:L611V;ENSP00000355475:L230V	ENSP00000355475:L230V	L	+	1	2	KIF26B	243839370	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	2.697000	0.47060	0.746000	0.32786	0.650000	0.86243	CTG	.	.		0.637	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		G	245772747	C	G	245772747	3	3	54	1	0	0	0	0	1	0	0	0	8304	796	28	4	1861	4	KIF26B	1	245772747	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	10454408	245772747	3477874	13	6805										
SFRS7	6432	hgsc.bcm.edu	37	chr2	38976737	38976737	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gtcccttttcgccacactcaTagcatctatcatttggatca	5	13	4	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr2:38976737T>C	ENST00000313117.6	-	3	557	c.320A>G	c.(319-321)tAt>tGt	p.Y107C	SRSF7_ENST00000409276.1_Missense_Mutation_p.Y107C|SRSF7_ENST00000446327.2_Missense_Mutation_p.Y107C|GEMIN6_ENST00000409011.1_5'Flank	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	107					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GCCACACTCATAGCATCTATC	0.458																																					p.Y107C		Atlas-SNP	.											.	SRSF7	29	.	0			c.A320G						.						149	141	144					2																	38976737		2203	4300	6503	SO:0001583	missense	6432	exon3			CACTCATAGCATC	L41887	CCDS33183.1, CCDS56115.1	2p22.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000115875	ENSG00000115875		"Zinc fingers, CCHC domain containing", "Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10789	protein-coding gene	gene with protein product	"SR splicing factor 7"	600572	"splicing factor, arginine/serine-rich 7 (35kD)", "splicing factor, arginine/serine-rich 7, 35kDa"	SFRS7		8013463, 20516191	Standard	NM_001031684		Approved	9G8, ZCRB2, HSSG1, AAG3, RBM37, ZCCHC20	uc002rqz.3	Q16629	OTTHUMG00000102076	ENST00000313117.6:c.320A>G	chr2.hg19:g.38976737T>C	ENSP00000325905:p.Tyr107Cys	282.0	1.0		529.0	188.0	NM_001195446	B4DLU6|G5E9M3|Q564D3	Missense_Mutation	SNP	ENST00000313117.6	hg19	CCDS33183.1	.	.	.	.	.	.	.	.	.	.	T	18.42	3.621157	0.66787	.	.	ENSG00000115875	ENST00000313117;ENST00000446327;ENST00000409276	T;T;T	0.78003	-1.14;-1.14;-1.14	5.93	4.75	0.60458	Zinc finger, CCHC retroviral-type (1);Zinc finger, CCHC-type (2);	0.000000	0.64402	D	0.000004	D	0.89047	0.6604	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.90120	0.4198	10	0.87932	D	0	.	12.3223	0.54991	0.1269:0.0:0.0:0.8731	.	107;107	G5E9M3;Q16629	.;SRSF7_HUMAN	C	107	ENSP00000325905:Y107C;ENSP00000402264:Y107C;ENSP00000386806:Y107C	ENSP00000325905:Y107C	Y	-	2	0	SRSF7	38830241	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.677000	0.84024	1.024000	0.39682	0.533000	0.62120	TAT	.	.		0.458	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684		C	38976737	T	C	38976737	3	2	54	1	0	0	0	0	1	0	0	0	14197	1406	49	2	420	2	SFRS7	2	38976737	Missense_Mutation	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10		38976737	204222636	14	6806										
MTIF2	4528	hgsc.bcm.edu	37	chr2	55470647	55470647	+	Frame_Shift_Del	DEL	G	G	-													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tttctaaaaaccgtagaattGatctcttcttccacagtaga							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr2:55470647delG	ENST00000263629.4	-	12	1784	c.1469delC	c.(1468-1470)tcafs	p.S490fs	MTIF2_ENST00000403721.1_Frame_Shift_Del_p.S490fs|MTIF2_ENST00000394600.3_Frame_Shift_Del_p.S490fs	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	490					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						CCGTAGAATTGATCTCTTCTT	0.363																																					p.S490fs		Atlas-Indel,Pindel	.											.	MTIF2	64	.	0			c.1470delA						.						174	171	172					2																	55470647		2203	4300	6503	SO:0001589	frameshift_variant	4528	exon12			.	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1469delC	chr2.hg19:g.55470647delG	ENSP00000263629:p.Ser490fs	784.0	0.0		612.0	80.0	NM_002453	D6W5D0	Frame_Shift_Del	DEL	ENST00000263629.4	hg19	CCDS1853.1																																																																																			.	.		0.363	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		-	55470647	G	-	55470647	7	5	54	1	0	1	0	1	0	0	0	0	9943	1294	45	0	734	0	MTIF2	2	55470647	Frame_Shift_Del	DEL	G	TCGA-CC-5258-01A-01D-A12Z-10	16493910	55470647	187728726	15	6807										
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55582881	55582881	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ccgctcttcagagagttctaTgatagtctagaaatacacac	7	10	4	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr2:55582881T>C	ENST00000436346.1	-	8	1475	c.634A>G	c.(634-636)Ata>Gta	p.I212V	CCDC88A_ENST00000413716.2_Missense_Mutation_p.I212V|CCDC88A_ENST00000263630.8_Missense_Mutation_p.I212V|CCDC88A_ENST00000336838.6_Missense_Mutation_p.I212V	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	212					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						GAGAGTTCTATGATAGTCTAG	0.423																																					p.I212V		Atlas-SNP	.											CCDC88A_ENST00000336838,NS,carcinoma,0,2	CCDC88A	336	.	0			c.A634G						.						62	52	55					2																	55582881		2203	4300	6503	SO:0001583	missense	55704	exon8			GTTCTATGATAGT	AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.634A>G	chr2.hg19:g.55582881T>C	ENSP00000410608:p.Ile212Val	75.0	0.0		78.0	30.0	NM_018084	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	hg19		.	.	.	.	.	.	.	.	.	.	T	2.571	-0.299616	0.05532	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716;ENST00000430086	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;2.34	5.05	-6.62	0.01813	.	0.490245	0.16762	N	0.200562	T	0.19087	0.0458	N	0.17082	0.46	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.42344	-0.9457	10	0.02654	T	1	-1.1238	15.1743	0.72899	0.0:0.567:0.0:0.4329	.	212;212;212	B7ZM78;Q3V6T2-2;Q3V6T2-3	.;.;.	V	212;212;212;212;137	ENSP00000338728:I212V;ENSP00000263630:I212V;ENSP00000410608:I212V;ENSP00000404431:I212V;ENSP00000399237:I137V	ENSP00000263630:I212V	I	-	1	0	CCDC88A	55436385	0.000000	0.05858	0.028000	0.17463	0.985000	0.73830	-0.362000	0.07602	-1.480000	0.01865	0.482000	0.46254	ATA	.	.		0.423	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		C	55582881	T	C	55582881	3	2	54	1	0	0	0	0	1	0	0	0	2865	1464	51	2	5081	2	CCDC88A	2	55582881	Missense_Mutation	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	112234	55582881	187616492	16	6808										
SLC5A7	60482	hgsc.bcm.edu	37	chr2	108622601	108622601	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tgtccttcctggcagctttcGggtgcctggtgatggccatc	13	12	0	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr2:108622601G>A	ENST00000264047.2	+	7	1114	c.838G>A	c.(838-840)Ggg>Agg	p.G280R	SLC5A7_ENST00000540517.1_Missense_Mutation_p.G175R|SLC5A7_ENST00000409059.1_Missense_Mutation_p.G280R	NM_021815.2	NP_068587.1	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (sodium/choline cotransporter), member 7	280					acetylcholine biosynthetic process (GO:0008292)|cell death (GO:0008219)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	choline binding (GO:0033265)|choline transmembrane transporter activity (GO:0015220)|choline:sodium symporter activity (GO:0005307)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	49					Choline(DB00122)	GGCAGCTTTCGGGTGCCTGGT	0.522																																					p.G280R		Atlas-SNP	.											.	SLC5A7	109	.	0			c.G838A						.						109	94	99					2																	108622601		2203	4300	6503	SO:0001583	missense	60482	exon7			GCTTTCGGGTGCC	AF276871	CCDS2074.1	2q12	2013-07-19	2013-07-19		ENSG00000115665	ENSG00000115665		"Solute carriers"	14025	protein-coding gene	gene with protein product		608761	"solute carrier family 5 (choline transporter), member 7"			11027560	Standard	NM_021815		Approved	hCHT, CHT1	uc002tdv.3	Q9GZV3	OTTHUMG00000130959	ENST00000264047.2:c.838G>A	chr2.hg19:g.108622601G>A	ENSP00000264047:p.Gly280Arg	101.0	0.0		156.0	59.0	NM_021815	Q53TF2	Missense_Mutation	SNP	ENST00000264047.2	hg19	CCDS2074.1	.	.	.	.	.	.	.	.	.	.	G	33	5.207259	0.95033	.	.	ENSG00000115665	ENST00000409059;ENST00000540517;ENST00000264047	D;D;D	0.88201	-2.35;-2.35;-2.35	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.95934	0.8676	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.96084	0.9056	10	0.66056	D	0.02	-14.1517	19.8703	0.96847	0.0:0.0:1.0:0.0	.	280	Q9GZV3	SC5A7_HUMAN	R	280;175;280	ENSP00000387346:G280R;ENSP00000445351:G175R;ENSP00000264047:G280R	ENSP00000264047:G280R	G	+	1	0	SLC5A7	107989033	1.000000	0.71417	0.993000	0.49108	0.896000	0.52359	9.810000	0.99221	2.770000	0.95276	0.650000	0.86243	GGG	.	.		0.522	SLC5A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253562.1			A	108622601	G	A	108622601	3	1	54	1	0	0	0	0	1	0	0	0	14685	1116	39	1	860	1	SLC5A7	2	108622601	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	53039720	108622601	134576772	17	6809										
POLR1B	84172	hgsc.bcm.edu	37	chr2	113300082	113300083	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ggtggccacatggatcctggINScagccggtggcggaacctgc							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr2:113300082_113300083insC	ENST00000263331.5	+	1	591_592	c.11_12insC	c.(10-15)ggcagcfs	p.S5fs	POLR1B_ENST00000417433.2_Frame_Shift_Ins_p.S5fs|POLR1B_ENST00000409894.3_Frame_Shift_Ins_p.S5fs|POLR1B_ENST00000537335.1_5'UTR|POLR1B_ENST00000541869.1_Frame_Shift_Ins_p.S43fs	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	5					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						ATGGATCCTGGCAGCCGGTGGC	0.644																																					p.G4fs	Ovarian(16;256 576 9537 23969 41147)	Atlas-INDEL	.											.	POLR1B	95	.	0			c.11_12insC						.																																			SO:0001589	frameshift_variant	84172	exon1			.	AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"RNA polymerase subunits"	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.12dupC	chr2.hg19:g.113300083_113300083dupC	ENSP00000263331:p.Ser5fs	64.0	0.0		149.0	10.0	NM_019014	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Frame_Shift_Ins	INS	ENST00000263331.5	hg19	CCDS2097.1																																																																																			.	.		0.644	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014		C	113300083	-	C	113300082	7	5	54	1	0	1	1	0	0	0	0	0	12219	1203	42	0	13	0	POLR1B	2	113300082	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	4677481	113300082	129899291	18	6810										
TFCP2L1	29842	hgsc.bcm.edu	37	chr2	121989435	121989436	+	Frame_Shift_Ins	INS	-	-	CC													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ccacatggatgcccgtggggINSccctgccggtagactcggtg							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr2:121989435_121989436insCC	ENST00000263707.5	-	13	1404_1405	c.1307_1308insGG	c.(1306-1308)ggcfs	p.G436fs		NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1	436					cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					TGCCCGTGGGGCCCTGCCGGTA	0.634																																					p.G436fs		Atlas-INDEL	.											.,1	TFCP2L1	54	.	0			c.1308_1309insGG						.																																			SO:0001589	frameshift_variant	29842	exon13			.	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.1306_1307dupGG	chr2.hg19:g.121989436_121989437dupCC	ENSP00000263707:p.Gly436fs	53.0	0.0		145.0	14.0	NM_014553	Q4ZG43	Frame_Shift_Ins	INS	ENST00000263707.5	hg19	CCDS2134.1																																																																																			.	.		0.634	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553		CC	121989436	-	CC	121989435	7	5	54	1	0	1	1	0	0	0	0	0	15811	1190	42	0	143	0	TFCP2L1	2	121989435	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	8689353	121989435	121209938	19	6811										
KYNU	8942	hgsc.bcm.edu	37	chr2	143718192	143718192	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cttgtgcctaacttgatttaGggggaagaaaccttaagaat	10	6	0	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr2:143718192G>A	ENST00000264170.4	+	8	840		c.e8-1		KYNU_ENST00000375773.2_Splice_Site|KYNU_ENST00000409512.1_Splice_Site	NM_003937.2	NP_003928.1			kynureninase											large_intestine(10)|liver(1)|lung(18)|prostate(3)|skin(4)	36				BRCA - Breast invasive adenocarcinoma(221;0.072)		ACTTGATTTAGGGGGAAGAAA	0.363																																					.		Atlas-SNP	.											.	KYNU	110	.	0			c.583-1G>A						.						82	83	82					2																	143718192		2203	4300	6503	SO:0001630	splice_region_variant	8942	exon9			GATTTAGGGGGAA	U57721	CCDS2183.1, CCDS33299.1	2q22.2	2010-11-23	2010-11-23		ENSG00000115919	ENSG00000115919	3.7.1.3		6469	protein-coding gene	gene with protein product	"L-kynurenine hydrolase"	605197	"kynureninase (L-kynurenine hydrolase)"			8706755, 9180257	Standard	NM_001199241		Approved		uc002tvl.3	Q16719	OTTHUMG00000131829	ENST00000264170.4:c.583-1G>A	chr2.hg19:g.143718192G>A		74.0	0.0		48.0	12.0	NM_001199241		Splice_Site	SNP	ENST00000264170.4	hg19	CCDS2183.1	.	.	.	.	.	.	.	.	.	.	G	18.77	3.695405	0.68386	.	.	ENSG00000115919	ENST00000264170;ENST00000375773;ENST00000409512	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0789	0.93173	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KYNU	143434662	1.000000	0.71417	0.999000	0.59377	0.683000	0.39861	9.360000	0.97119	2.668000	0.90789	0.644000	0.83932	.	.	.		0.363	KYNU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254772.1	NM_001032998	Intron	A	143718192	G	A	143718192	5	1	54	1	0	0	0	0	0	0	1	0	8596	1014	35	3	608	3	KYNU	2	143718192	Splice_Site	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	21728757	143718192	99481181	20	6812										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166211045	166211045	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tgtagaaaaatatgtcgtggAtgaaagtgattacatgtcat	10	3	1	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr2:166211045A>G	ENST00000375437.2	+	17	3553	c.3263A>G	c.(3262-3264)gAt>gGt	p.D1088G	SCN2A_ENST00000375427.2_Missense_Mutation_p.D1088G|SCN2A_ENST00000283256.6_Missense_Mutation_p.D1088G|SCN2A_ENST00000357398.3_Missense_Mutation_p.D1088G	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1088					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TATGTCGTGGATGAAAGTGAT	0.373																																					p.D1088G		Atlas-SNP	.											.	SCN2A	589	.	0			c.A3263G						.						113	111	112					2																	166211045		2203	4300	6503	SO:0001583	missense	6326	exon16			TCGTGGATGAAAG	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.3263A>G	chr2.hg19:g.166211045A>G	ENSP00000364586:p.Asp1088Gly	309.0	0.0		305.0	95.0	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	hg19	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.193601	0.38707	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	5.26	5.26	0.73747	Sodium ion transport-associated (1);	0.172626	0.41001	D	0.000972	D	0.88239	0.6383	M	0.77616	2.38	0.34725	D	0.729149	B;P	0.47545	0.01;0.897	B;P	0.53760	0.015;0.734	D	0.91929	0.5553	10	0.40728	T	0.16	.	15.1655	0.72821	1.0:0.0:0.0:0.0	.	1088;1088	Q99250-2;Q99250	.;SCN2A_HUMAN	G	1088	ENSP00000364586:D1088G;ENSP00000349973:D1088G;ENSP00000283256:D1088G;ENSP00000364576:D1088G	ENSP00000283256:D1088G	D	+	2	0	SCN2A	165919291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.903000	0.56318	1.981000	0.57761	0.482000	0.46254	GAT	.	.		0.373	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		G	166211045	A	G	166211045	3	3	54	1	0	0	0	0	1	0	0	0	13931	333	12	2	3421	2	SCN2A	2	166211045	Missense_Mutation	SNP	A	TCGA-CC-5258-01A-01D-A12Z-10	22492853	166211045	76988328	21	6813										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1371531	1371532	+	Missense_Mutation	DNP	GA	GA	AT													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cttttgttcaagttggtgggGatattgttatcggatgcaaa							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr3:1371531_1371532GA>AT	ENST00000446702.2	+	11	1903_1904	c.1276_1277GA>AT	c.(1276-1278)GAt>ATt	p.D426I	CNTN6_ENST00000350110.2_Missense_Mutation_p.D426I|CNTN6_ENST00000539053.1_Missense_Mutation_p.D354I			Q9UQ52	CNTN6_HUMAN	contactin 6	426	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.D426N(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AGTTGGTGGGGATATTGTTATC	0.371																																					p.D426N|p.D426V		Atlas-SNP	.											CNTN6,colon,carcinoma,0,1|.	CNTN6	245	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1276A|c.A1277T						.																																			SO:0001583	missense	27255	exon11			GGTGGGGATATTG|GTGGGGATATTGT	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	Exception_encountered	chr3.hg19:g.1371531_1371532delinsAT	ENSP00000407822:p.Asp426Ile	519.0|516.0	1.0		177.0|175.0	63.0|60.0	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	hg19	CCDS2557.1																																																																																			.	.		0.371	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		AT	1371532	GA	AT	1371531	3	1	54	1	0	0	0	0	1	0	0	0	3647	1174	41	3	1314	3	CNTN6	3	1371531	Missense_Mutation	DNP	GA	TCGA-CC-5258-01A-01D-A12Z-10		1371531	196650899	22	6814										
PDCD6IP	10015	hgsc.bcm.edu	37	chr3	33840383	33840383	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	agctgcgccgcgccgcagtcGgtcgtccgctggacaagcac	14	16	0	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr3:33840383G>A	ENST00000307296.3	+	1	540	c.163G>A	c.(163-165)Ggt>Agt	p.G55S	RP11-10C24.3_ENST00000604982.1_lincRNA|RP11-10C24.1_ENST00000605513.1_lincRNA|PDCD6IP_ENST00000457054.2_Missense_Mutation_p.G55S			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	55	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						CGCCGCAGTCGGTCGTCCGCT	0.701																																					p.G55S		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.G163A						.						6	8	8					3																	33840383		2064	4021	6085	SO:0001583	missense	10015	exon1			GCAGTCGGTCGTC	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.163G>A	chr3.hg19:g.33840383G>A	ENSP00000307387:p.Gly55Ser	14.0	0.0		41.0	26.0	NM_013374	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	hg19	CCDS2660.1	.	.	.	.	.	.	.	.	.	.	G	16.46	3.128482	0.56721	.	.	ENSG00000170248	ENST00000307296;ENST00000457054;ENST00000413073	T;T;T	0.17213	2.29;2.29;2.29	5.65	4.78	0.61160	BRO1 domain (3);	0.000000	0.85682	D	0.000000	T	0.23886	0.0578	M	0.73372	2.23	0.80722	D	1	B;B;P	0.37997	0.004;0.0;0.614	B;B;B	0.41202	0.006;0.002;0.35	T	0.03335	-1.1047	10	0.17832	T	0.49	-2.2186	14.4391	0.67303	0.0718:0.0:0.9282:0.0	.	55;55;55	C5MQH7;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	S	55	ENSP00000307387:G55S;ENSP00000411825:G55S;ENSP00000406693:G55S	ENSP00000307387:G55S	G	+	1	0	PDCD6IP	33815387	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.893000	0.75649	1.383000	0.46405	0.591000	0.81541	GGT	.	.		0.701	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			A	33840383	G	A	33840383	3	1	54	1	0	0	0	0	1	0	0	0	11633	1116	39	1	165	1	PDCD6IP	3	33840383	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	32468852	33840383	164182047	23	6815										
PRSS50	29122	hgsc.bcm.edu	37	chr3	46757122	46757123	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cgcacgctgaccatccagggINSccaccgccgagccacggctt							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr3:46757122_46757123insC	ENST00000460241.1	-	8	2042_2043	c.372_373insG	c.(370-375)tggcccfs	p.P125fs	PRSS50_ENST00000315170.7_Frame_Shift_Ins_p.P125fs			Q9UI38	TSP50_HUMAN	protease, serine, 50	125	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						ACCATCCAGGGCCACCGCCGAG	0.629																																					p.P125fs	Pancreas(41;915 1239 11561 17469)	Atlas-INDEL	.											.	PRSS50	35	.	0			c.373_374insG						.																																			SO:0001589	frameshift_variant	29122	exon3			.	AF100707	CCDS2745.1	3p21.31	2011-05-24			ENSG00000206549	ENSG00000206549		"Serine peptidases / Serine peptidases"	17910	protein-coding gene	gene with protein product	"cancer/testis antigen 20", "testes specific protease 50"	607950				10397268	Standard	NM_013270		Approved	TSP50, CT20	uc003cqe.1	Q9UI38	OTTHUMG00000164067	ENST00000460241.1:c.373dupG	chr3.hg19:g.46757124_46757124dupC	ENSP00000418875:p.Pro125fs	97.0	0.0		246.0	29.0	NM_013270		Frame_Shift_Ins	INS	ENST00000460241.1	hg19	CCDS2745.1																																																																																			.	.		0.629	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1			C	46757123	-	C	46757122	7	5	54	1	0	1	1	0	0	0	0	0	12643	1203	42	0	800	0	PRSS50	3	46757122	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	12916739	46757122	151265308	24	6816										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48691751	48691752	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gccattatttgcgacaaaagINSccgccatgtccactcggcgg							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr3:48691751_48691752insC	ENST00000164024.4	-	7	5402_5403	c.5122_5123insG	c.(5122-5124)gctfs	p.A1708fs	CELSR3_ENST00000544264.1_Frame_Shift_Ins_p.A1708fs	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1708	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TGCGACAAAAGCCGCCATGTCC	0.584																																					p.A1708fs		Atlas-INDEL	.											.	CELSR3	237	.	0			c.5123_5124insG						.																																			SO:0001589	frameshift_variant	1951	exon7			.	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.5123dupG	chr3.hg19:g.48691753_48691753dupC	ENSP00000164024:p.Ala1708fs	73.0	0.0		154.0	12.0	NM_001407	O75092	Frame_Shift_Ins	INS	ENST00000164024.4	hg19	CCDS2775.1																																																																																			.	.		0.584	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		C	48691752	-	C	48691751	7	5	54	1	0	1	1	0	0	0	0	0	3225	971	34	0	4931	0	CELSR3	3	48691751	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	1934629	48691751	149330679	25	6817										
SEMA3F	6405	hgsc.bcm.edu	37	chr3	50222142	50222143	+	Frame_Shift_Ins	INS	-	-	G													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cgtgtaccctctgcagcggcINSggcccctggtagtccgcaca					rs145958913|rs546599637		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr3:50222142_50222143insG	ENST00000002829.3	+	13	1835_1836	c.1351_1352insG	c.(1351-1353)cggfs	p.R451fs	SEMA3F_ENST00000434342.1_Frame_Shift_Ins_p.R420fs|SEMA3F_ENST00000413852.1_Frame_Shift_Ins_p.R352fs	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	451	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		TCTGCAGCGGCGGCCCCTGGTA	0.599																																					p.R451fs		Atlas-INDEL	.											.	SEMA3F	62	.	0			c.1351_1352insG						.																																			SO:0001589	frameshift_variant	6405	exon13			.	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10728	protein-coding gene	gene with protein product	"sema IV"	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.1353dupG	chr3.hg19:g.50222144_50222144dupG	ENSP00000002829:p.Arg451fs	40.0	0.0		121.0	22.0	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Frame_Shift_Ins	INS	ENST00000002829.3	hg19	CCDS2811.1																																																																																			.	.		0.599	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186		G	50222143	-	G	50222142	7	5	54	1	0	1	1	0	0	0	0	0	14044	759	27	0	1397	0	SEMA3F	3	50222142	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	1530391	50222142	147800288	26	6818										
TLR9	54106	hgsc.bcm.edu	37	chr3	52255499	52255499	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gaagctggcgcgcaagagacCactgacccggtccgtgtggg	16	12	0	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr3:52255499C>T	ENST00000360658.2	-	2	3466	c.2833G>A	c.(2833-2835)Ggt>Agt	p.G945S	TLR9_ENST00000494383.1_Nonsense_Mutation_p.W1098*|TLR9_ENST00000597542.1_Missense_Mutation_p.G969S	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	945	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	CGCAAGAGACCACTGACCCGG	0.662																																					p.G945S		Atlas-SNP	.											.	TLR9	72	.	0			c.G2833A						.						38	42	40					3																	52255499		2201	4298	6499	SO:0001583	missense	54106	exon2			AGAGACCACTGAC	AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"CD molecules"	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.2833G>A	chr3.hg19:g.52255499C>T	ENSP00000353874:p.Gly945Ser	20.0	0.0		54.0	15.0	NM_017442	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	hg19	CCDS2848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.1|22.1	4.248815|4.248815	0.80024|0.80024	.|.	.|.	ENSG00000239732|ENSG00000173366	ENST00000360658|ENST00000494383	T|.	0.07216|.	3.21|.	5.81|5.81	4.0|4.0	0.46444|0.46444	Toll/interleukin-1 receptor homology (TIR) domain (3);|.	0.000000|.	0.42172|.	D|.	0.000750|.	T|.	0.62011|.	0.2393|.	L|L	0.61036|0.61036	1.89|1.89	0.52099|0.52099	D|D	0.999945|0.999945	P;D|.	0.89917|.	0.889;1.0|.	B;D|.	0.97110|.	0.435;1.0|.	T|.	0.58329|.	-0.7655|.	10|.	0.66056|.	D|.	0.02|.	.|.	9.2959|9.2959	0.37815|0.37815	0.1441:0.7797:0.0:0.0763|0.1441:0.7797:0.0:0.0763	.|.	1042;945|.	B4E0A1;Q9NR96|.	.;TLR9_HUMAN|.	S|X	945|1098	ENSP00000353874:G945S|.	ENSP00000353874:G945S|.	G|W	-|-	1|2	0|0	TLR9|RP11-330H6.5	52230539|52230539	0.994000|0.994000	0.37717|0.37717	0.241000|0.241000	0.24154|0.24154	0.835000|0.835000	0.47333|0.47333	3.218000|3.218000	0.51192|0.51192	0.783000|0.783000	0.33636|0.33636	0.591000|0.591000	0.81541|0.81541	GGT|TGG	.	.		0.662	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1			T	52255499	C	T	52255499	3	4	54	1	0	0	0	0	1	0	0	0	15973	594	21	3	269	3	TLR9	3	52255499	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	2033357	52255499	145766931	27	6819										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173996955	173996955	+	Frame_Shift_Del	DEL	C	C	-													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gatataatgttaggagtgaaCcaaggggaagggttaaaatt							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr3:173996955delC	ENST00000457714.1	+	6	1593	c.1164delC	c.(1162-1164)aacfs	p.N388fs	NLGN1_ENST00000361589.4_Frame_Shift_Del_p.N388fs|NLGN1_ENST00000401917.3_Frame_Shift_Del_p.N428fs|NLGN1_ENST00000466350.1_3'UTR|NLGN1_ENST00000545397.1_Frame_Shift_Del_p.N388fs	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	405					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TAGGAGTGAACCAAGGGGAAG	0.368																																					p.N388fs		Atlas-Indel,Pindel	.											.	NLGN1	209	.	0			c.1163delA						.						138	144	142					3																	173996955		2203	4300	6503	SO:0001589	frameshift_variant	22871	exon6			.	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.1164delC	chr3.hg19:g.173996955delC	ENSP00000392500:p.Asn388fs	228.0	0.0		131.0	38.0	NM_014932	Q9UPT2	Frame_Shift_Del	DEL	ENST00000457714.1	hg19	CCDS3222.1																																																																																			.	.		0.368	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		-	173996955	C	-	173996955	7	5	54	1	0	1	0	1	0	0	0	0	10470	506	18	0	1178	0	NLGN1	3	173996955	Frame_Shift_Del	DEL	C	TCGA-CC-5258-01A-01D-A12Z-10	121741456	173996955	24025475	28	6820										
FGFRL1	53834	hgsc.bcm.edu	37	chr4	1015991	1015991	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ttcctcggtcccacccgcagGccccccaaagatggcggaca	10	18	0	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr4:1015991G>T	ENST00000398484.2	+	4	660	c.80G>T	c.(79-81)gGc>gTc	p.G27V	FGFRL1_ENST00000510644.1_Splice_Site_p.G27V|FGFRL1_ENST00000264748.6_Splice_Site_p.G27V|FGFRL1_ENST00000504138.1_Splice_Site_p.G27V			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	27					diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCACCCGCAGGCCCCCCAAAG	0.741																																					p.G27V		Atlas-SNP	.											.	FGFRL1	77	.	0			c.G80T						.						5	6	5					4																	1015991		1971	3964	5935	SO:0001630	splice_region_variant	53834	exon3			CCGCAGGCCCCCC		CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418		"Immunoglobulin superfamily / I-set domain containing"	3693	protein-coding gene	gene with protein product		605830					Standard	NM_021923		Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.80-1G>T	chr4.hg19:g.1015991G>T		39.0	0.0		78.0	20.0	NM_001004356	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Missense_Mutation	SNP	ENST00000398484.2	hg19	CCDS3344.1	.	.	.	.	.	.	.	.	.	.	g	12.76	2.033972	0.35893	.	.	ENSG00000127418	ENST00000398484;ENST00000510644;ENST00000504138;ENST00000512174;ENST00000507339;ENST00000264748	T;T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.4;0.03;-0.67	4.62	3.71	0.42584	Immunoglobulin-like fold (1);	0.000000	0.85682	U	0.000000	T	0.62097	0.2400	L	0.49778	1.585	0.80722	D	1	B	0.27732	0.187	B	0.26969	0.075	T	0.59830	-0.7380	9	.	.	.	.	12.1552	0.54072	0.0:0.0:0.828:0.1719	.	27	Q8N441	FGRL1_HUMAN	V	27	ENSP00000381498:G27V;ENSP00000425025:G27V;ENSP00000423091:G27V;ENSP00000426740:G27V;ENSP00000424037:G27V;ENSP00000264748:G27V	.	G	+	2	0	FGFRL1	1005991	1.000000	0.71417	0.999000	0.59377	0.145000	0.21501	6.390000	0.73204	2.109000	0.64355	0.457000	0.33378	GGC	.	.		0.741	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923	Missense_Mutation	T	1015991	G	T	1015991	5	4	54	1	0	0	0	0	0	0	1	0	5877	1217	42	3	86	3	FGFRL1	4	1015991	Splice_Site	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10		1015991	190138285	29	6821										
TLR1	7096	hgsc.bcm.edu	37	chr4	38798989	38798990	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	atacagaaaggctgctaaagINSctgccacatccaggaaggtc							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr4:38798989_38798990insC	ENST00000502213.2	-	3	1692_1693	c.1463_1464insG	c.(1462-1464)agcfs	p.S488fs	TLR1_ENST00000308979.2_Frame_Shift_Ins_p.S488fs|TLR1_ENST00000510552.1_5'Flank			Q15399	TLR1_HUMAN	toll-like receptor 1	488					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						GGCTGCTAAAGCTGCCACATCC	0.401																																					p.S488fs	GBM(5;216 373 40795 46382)	Atlas-INDEL	.											.	TLR1	70	.	0			c.1464_1465insG						.																																			SO:0001589	frameshift_variant	7096	exon4			.	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1464dupG	chr4.hg19:g.38798990_38798990dupC	ENSP00000421259:p.Ser488fs	258.0	0.0		256.0	27.0	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Frame_Shift_Ins	INS	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.		0.401	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			C	38798990	-	C	38798989	7	5	54	1	0	1	1	0	0	0	0	0	15964	962	34	0	900	0	TLR1	4	38798989	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	37782998	38798989	152355287	30	6822										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62849309	62849309	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	agtagactacaggagttatgGaacagataaagtgtaagttt	11	3	0	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr4:62849309G>T	ENST00000514591.1	+	18	3349	c.3020G>T	c.(3019-3021)gGa>gTa	p.G1007V	LPHN3_ENST00000509896.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000545650.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000514157.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000508946.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000508693.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000507625.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000506720.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000507164.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000511324.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000506746.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000506700.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000504896.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000514996.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000512091.2_Missense_Mutation_p.G1007V			Q9HAR2	LPHN3_HUMAN	latrophilin 3	994					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						AGGAGTTATGGAACAGATAAA	0.383																																					p.G1007V		Atlas-SNP	.											.	LPHN3	800	.	0			c.G3020T						.						179	172	174					4																	62849309		1865	4120	5985	SO:0001583	missense	23284	exon16			GTTATGGAACAGA	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.3020G>T	chr4.hg19:g.62849309G>T	ENSP00000422533:p.Gly1007Val	260.0	0.0		192.0	100.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.5|25.5	4.645391|4.645391	0.87859|0.87859	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996|ENST00000502815	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.47869|.	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83|.	5.82|5.82	5.82|5.82	0.92795|0.92795	GPCR, family 2-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84270|0.84270	0.5435|0.5435	M|M	0.86502|0.86502	2.82|2.82	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	D|D	0.85057|0.85057	0.0932|0.0932	10|5	0.87932|.	D|.	0|.	.|.	20.099|20.099	0.97865|0.97865	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1007;994;1007|.	E9PE04;Q9HAR2;Q9HAR2-2|.	.;LPHN3_HUMAN;.|.	V|C	1007;1007;1075;1075;1007;1007;994;1007;1075;1075;1075;1007;1007;1007;1075;1075;1007|464	ENSP00000423388:G1007V;ENSP00000422533:G1007V;ENSP00000423787:G1075V;ENSP00000425033:G1075V;ENSP00000424120:G1007V;ENSP00000439831:G1007V;ENSP00000421476:G1075V;ENSP00000424030:G1075V;ENSP00000421372:G1075V;ENSP00000425201:G1007V;ENSP00000423434:G1007V;ENSP00000421627:G1007V;ENSP00000420931:G1075V;ENSP00000425884:G1075V;ENSP00000424258:G1007V|.	ENSP00000280009:G1007V|.	G|W	+|+	2|3	0|0	LPHN3|LPHN3	62531904|62531904	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	9.869000|9.869000	0.99810|0.99810	2.752000|2.752000	0.94435|0.94435	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.	.		0.383	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			T	62849309	G	T	62849309	3	4	54	1	0	0	0	0	1	0	0	0	8926	1174	41	3	3082	3	LPHN3	4	62849309	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	24050320	62849309	128304967	31	6823										
UGT2A1	10941	hgsc.bcm.edu	37	chr4	70455333	70455333	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ggctttacaggttgatcatgGtgaattcttgataacctcat	9	7	3	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr4:70455333G>T	ENST00000503640.1	-	6	1396	c.1341C>A	c.(1339-1341)caC>caA	p.H447Q	UGT2A2_ENST00000457664.2_Missense_Mutation_p.H456Q|UGT2A1_ENST00000512704.1_Missense_Mutation_p.H403Q|UGT2A1_ENST00000502343.1_5'UTR|UGT2A1_ENST00000514019.1_Missense_Mutation_p.H613Q|UGT2A1_ENST00000286604.4_Missense_Mutation_p.H447Q	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	447					cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						GTTGATCATGGTGAATTCTTG	0.398																																					p.H613Q		Atlas-SNP	.											.	UGT2A1	131	.	0			c.C1839A						.						99	104	103					4																	70455333		2203	4300	6503	SO:0001583	missense	10941	exon7			ATCATGGTGAATT	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"UDP glucuronosyltransferases"	12542	protein-coding gene	gene with protein product		604716	"UDP glycosyltransferase 2 family, polypeptide A1", "UDP glucuronosyltransferase 2 family, polypeptide A1"			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.1341C>A	chr4.hg19:g.70455333G>T	ENSP00000424478:p.His447Gln	328.0	1.0		289.0	139.0	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	hg19	CCDS3529.1	.	.	.	.	.	.	.	.	.	.	G	16.04	3.009498	0.54361	.	.	ENSG00000173610	ENST00000457664;ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57;-0.57	4.65	-2.05	0.07321	.	0.050572	0.85682	N	0.000000	T	0.75953	0.3920	M	0.69358	2.11	.	.	.	P;D;D;D;B	0.89917	0.476;0.988;1.0;0.999;0.134	B;P;D;D;B	0.87578	0.159;0.863;0.998;0.994;0.112	T	0.74645	-0.3596	9	0.49607	T	0.09	.	5.8441	0.18652	0.5368:0.0:0.3295:0.1337	.	613;613;403;456;447	E9PDM7;B4E2F4;D6RFW5;Q9Y4X1-2;Q9Y4X1	.;.;.;.;UD2A1_HUMAN	Q	456;447;403;613;447	ENSP00000387888:H456Q;ENSP00000424478:H447Q;ENSP00000421432:H403Q;ENSP00000425497:H613Q;ENSP00000286604:H447Q	ENSP00000286604:H447Q	H	-	3	2	UGT2A1	70489922	0.999000	0.42202	0.946000	0.38457	0.956000	0.61745	0.520000	0.22878	-0.616000	0.05671	0.579000	0.79373	CAC	.	.		0.398	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798		T	70455333	G	T	70455333	3	4	54	1	0	0	0	0	1	0	0	0	16968	1252	44	3	246	3	UGT2A1	4	70455333	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	7606024	70455333	120698943	32	6824										
PLK4	10733	hgsc.bcm.edu	37	chr4	128806961	128806961	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tttctaacctcctactgactCgtaatatgaacatcaagatt	4	10	2	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr4:128806961C>T	ENST00000270861.5	+	5	710	c.436C>T	c.(436-438)Cgt>Tgt	p.R146C	PLK4_ENST00000515069.1_Missense_Mutation_p.R146C|PLK4_ENST00000507249.1_Missense_Mutation_p.R146C|PLK4_ENST00000513090.1_Missense_Mutation_p.R114C|PLK4_ENST00000514379.1_Missense_Mutation_p.R105C	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	146	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs35232579). {ECO:0000269|PubMed:17344846}.		centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						CCTACTGACTCGTAATATGAA	0.418																																					p.R146C	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											PLK4,NS,carcinoma,0,1	PLK4	65	.	0			c.C436T						.						186	172	177					4																	128806961		2203	4300	6503	SO:0001583	missense	10733	exon5			CTGACTCGTAATA	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.436C>T	chr4.hg19:g.128806961C>T	ENSP00000270861:p.Arg146Cys	223.0	0.0		327.0	114.0	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	hg19	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.342200	0.61073	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249;ENST00000514379	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23	6.03	3.23	0.37069	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.197045	0.51477	D	0.000093	T	0.67850	0.2937	L	0.51853	1.615	0.23440	N	0.997677	D;D	0.76494	0.999;0.999	P;P	0.58970	0.827;0.849	T	0.59241	-0.7491	10	0.72032	D	0.01	-7.3389	3.6812	0.08310	0.2627:0.437:0.2236:0.0768	.	114;146	O00444-2;O00444	.;PLK4_HUMAN	C	146;146;114;146;105	ENSP00000270861:R146C;ENSP00000421774:R146C;ENSP00000427554:R114C;ENSP00000423412:R146C;ENSP00000423582:R105C	ENSP00000270861:R146C	R	+	1	0	PLK4	129026411	1.000000	0.71417	0.023000	0.16930	0.988000	0.76386	4.517000	0.60503	0.865000	0.35603	0.655000	0.94253	CGT	.	.		0.418	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			T	128806961	C	T	128806961	3	4	54	1	0	0	0	0	1	0	0	0	12107	884	31	1	454	1	PLK4	4	128806961	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	58351628	128806961	62347315	33	6825										
PDE4D	5144	hgsc.bcm.edu	37	chr5	58882174	58882174	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ccatatccaggaatgccttcTaaagggaaaattattcacgt	7	9	2	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr5:58882174T>C	ENST00000340635.6	-	1	631				PDE4D_ENST00000360047.5_Missense_Mutation_p.R10G|PDE4D_ENST00000546160.1_Intron|PDE4D_ENST00000502575.1_Intron|PDE4D_ENST00000507116.1_Intron|PDE4D_ENST00000502484.2_Intron	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific						adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	GAATGCCTTCTAAAGGGAAAA	0.353																																					p.R10G		Atlas-SNP	.											.	PDE4D	345	.	0			c.A28G						.						258	253	254					5																	58882174		1864	4103	5967	SO:0001627	intron_variant	5144	exon1			GCCTTCTAAAGGG		CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"Phosphodiesterases"	8783	protein-coding gene	gene with protein product	"phosphodiesterase E3 dunce homolog (Drosophila)"	600129	"phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.455+306820A>G	chr5.hg19:g.58882174T>C		221.0	0.0		166.0	78.0	NM_006203	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Missense_Mutation	SNP	ENST00000340635.6	hg19	CCDS47213.1	.	.	.	.	.	.	.	.	.	.	T	9.961	1.222890	0.22457	.	.	ENSG00000113448	ENST00000360047	T	0.67865	-0.29	5.64	5.64	0.86602	.	.	.	.	.	T	0.73745	0.3626	.	.	.	0.80722	D	1	P	0.43662	0.814	P	0.51701	0.677	T	0.76119	-0.3076	8	0.62326	D	0.03	.	11.9443	0.52920	0.0:0.0:0.1448:0.8552	.	9	Q08499-2	.	G	10	ENSP00000353152:R10G	ENSP00000353152:R10G	R	-	1	2	PDE4D	58917931	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.288000	0.43514	2.367000	0.80283	0.528000	0.53228	AGA	.	.		0.353	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3			C	58882174	T	C	58882174	1	2	54	0	1	0	0	0	0	0	0	0	11651	1530	53	2		2	PDE4D	5	58882174	Intron	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10		58882174	122033086	34	6826										
GPR98	84059	hgsc.bcm.edu	37	chr5	89953983	89953983	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	attcattcttaaactagtttCtgtatatggaggagctcgta	8	6	3	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr5:89953983C>T	ENST00000405460.2	+	21	4736	c.4640C>T	c.(4639-4641)tCt>tTt	p.S1547F		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1547					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AAACTAGTTTCTGTATATGGA	0.363																																					p.S1547F		Atlas-SNP	.											.	GPR98	605	.	0			c.C4640T						.						99	100	99					5																	89953983		1825	4082	5907	SO:0001583	missense	84059	exon21			TAGTTTCTGTATA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.4640C>T	chr5.hg19:g.89953983C>T	ENSP00000384582:p.Ser1547Phe	214.0	0.0		223.0	30.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	14.81	2.646393	0.47258	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.30714	1.52	5.86	5.86	0.93980	.	0.099573	0.64402	D	0.000001	T	0.43765	0.1262	L	0.27053	0.805	0.80722	D	1	D	0.71674	0.998	D	0.68943	0.961	T	0.35226	-0.9797	10	0.87932	D	0	.	17.1393	0.86748	0.0:0.874:0.126:0.0	.	1547	Q8WXG9	GPR98_HUMAN	F	1547	ENSP00000384582:S1547F	ENSP00000296619:S1547F	S	+	2	0	GPR98	89989739	1.000000	0.71417	1.000000	0.80357	0.049000	0.14656	4.622000	0.61240	2.771000	0.95319	0.650000	0.86243	TCT	.	.		0.363	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	89953983	C	T	89953983	3	4	54	1	0	0	0	0	1	0	0	0	6730	913	32	3	4722	3	GPR98	5	89953983	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	31071809	89953983	90961277	35	6827										
RHOBTB3	22836	hgsc.bcm.edu	37	chr5	95091309	95091309	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ctgacattcaggattccagtAtcatccgaactacccaggat	7	12	2	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr5:95091309A>G	ENST00000379982.3	+	6	1400	c.892A>G	c.(892-894)Atc>Gtc	p.I298V	GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	298	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		GGATTCCAGTATCATCCGAAC	0.448																																					p.I298V		Atlas-SNP	.											.	RHOBTB3	43	.	0			c.A892G						.						104	94	98					5																	95091309		2203	4300	6503	SO:0001583	missense	22836	exon6			TCCAGTATCATCC	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"BTB/POZ domain containing"	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.892A>G	chr5.hg19:g.95091309A>G	ENSP00000369318:p.Ile298Val	271.0	0.0		167.0	28.0	NM_014899	A0PJA4|A8K1W9|Q8IW06	Missense_Mutation	SNP	ENST00000379982.3	hg19	CCDS4077.1	.	.	.	.	.	.	.	.	.	.	A	6.328	0.428644	0.11987	.	.	ENSG00000164292	ENST00000379982	T	0.62498	0.02	6.08	4.95	0.65309	BTB/POZ-like (2);BTB/POZ (1);	0.249082	0.42172	D	0.000751	T	0.35219	0.0924	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25710	-1.0124	10	0.10111	T	0.7	-27.8358	7.9112	0.29791	0.8235:0.0:0.1765:0.0	.	298	O94955	RHBT3_HUMAN	V	298	ENSP00000369318:I298V	ENSP00000369318:I298V	I	+	1	0	RHOBTB3	95117065	0.085000	0.21516	0.977000	0.42913	0.886000	0.51366	0.966000	0.29331	2.333000	0.79357	0.482000	0.46254	ATC	.	.		0.448	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899		G	95091309	A	G	95091309	3	3	54	1	0	0	0	0	1	0	0	0	13350	449	16	2	914	2	RHOBTB3	5	95091309	Missense_Mutation	SNP	A	TCGA-CC-5258-01A-01D-A12Z-10	5137326	95091309	85823951	36	6828										
PCBD2	84105	hgsc.bcm.edu	37	chr5	134246024	134246024	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tgaaatgtgttctcttcataGtcatcaggtactcacaggtt	8	8	5	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr5:134246024G>C	ENST00000512783.1	+	2	104		c.e2-1		PCBD2_ENST00000510013.1_Splice_Site|PCBD2_ENST00000254908.6_Splice_Site			Q9H0N5	PHS2_HUMAN	pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2						positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein homotetramerization (GO:0051289)|tetrahydrobiopterin biosynthetic process (GO:0006729)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	4-alpha-hydroxytetrahydrobiopterin dehydratase activity (GO:0008124)|phenylalanine 4-monooxygenase activity (GO:0004505)			kidney(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TCTCTTCATAGTCATCAGGTA	0.408																																					.		Atlas-SNP	.											.	PCBD2	3	.	0			c.85-1G>C						.						109	102	104					5																	134246024		1929	4148	6077	SO:0001630	splice_region_variant	84105	exon2			TTCATAGTCATCA	AF499009	CCDS43364.1	5q31.1	2008-02-05	2006-01-10			ENSG00000132570			24474	protein-coding gene	gene with protein product		609836	"6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2"			15182178, 11980910	Standard	NM_032151		Approved	DCOHM, DCOH2	uc010jdz.3	Q9H0N5		ENST00000512783.1:c.85-1G>C	chr5.hg19:g.134246024G>C		103.0	0.0		125.0	23.0	NM_032151	Q8TD40	Splice_Site	SNP	ENST00000512783.1	hg19	CCDS43364.1	.	.	.	.	.	.	.	.	.	.	G	9.558	1.117736	0.20877	.	.	ENSG00000132570	ENST00000254908;ENST00000512783	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8022	0.88591	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PCBD2	134273923	1.000000	0.71417	0.175000	0.22980	0.033000	0.12548	6.318000	0.72866	2.710000	0.92621	0.563000	0.77884	.	.	.		0.408	PCBD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371578.1	NM_032151	Intron	C	134246024	G	C	134246024	5	2	54	1	0	0	0	0	0	0	1	0	11508	1043	36	4	90	4	PCBD2	5	134246024	Splice_Site	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	39154715	134246024	46669236	37	6829										
FOXI1	2299	hgsc.bcm.edu	37	chr5	169535204	169535204	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	agcagtctcccggtggacagCcccaagaccacggagcctca	11	16	2	1	rs35678180	byFrequency	TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr5:169535204C>A	ENST00000306268.6	+	2	787	c.726C>A	c.(724-726)agC>agA	p.S242R	FOXI1_ENST00000449804.2_Intron			Q12951	FOXI1_HUMAN	forkhead box I1	242					embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGGTGGACAGCCCCAAGACCA	0.592									Pendred syndrome																												p.S242R		Atlas-SNP	.											.	FOXI1	70	.	0			c.C726A						.						56	62	60					5																	169535204		2203	4300	6503	SO:0001583	missense	2299	exon2	Familial Cancer Database	Goiter-Deafness syndrome	GGACAGCCCCAAG	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.726C>A	chr5.hg19:g.169535204C>A	ENSP00000304286:p.Ser242Arg	57.0	0.0		113.0	25.0	NM_012188	Q14518|Q66SR7|Q8N6L8	Missense_Mutation	SNP	ENST00000306268.6	hg19	CCDS4372.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.949135	0.34377	.	.	ENSG00000168269	ENST00000306268	D	0.94280	-3.39	4.91	3.01	0.34805	.	0.246213	0.41605	D	0.000858	D	0.94997	0.8381	M	0.81682	2.555	0.80722	D	1	D	0.59357	0.985	P	0.58077	0.832	D	0.93602	0.6931	10	0.41790	T	0.15	.	10.1849	0.42991	0.0:0.826:0.0:0.174	.	242	Q12951	FOXI1_HUMAN	R	242	ENSP00000304286:S242R	ENSP00000304286:S242R	S	+	3	2	FOXI1	169467782	1.000000	0.71417	0.997000	0.53966	0.015000	0.08874	1.094000	0.30951	0.987000	0.38709	0.455000	0.32223	AGC	.	C|0.995;T|0.005		0.592	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		A	169535204	C	A	169535204	3	1	54	1	0	0	0	0	1	0	0	0	6017	738	26	3	732	3	FOXI1	5	169535204	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	35289180	169535204	11380056	38	6830										
DBN1	1627	hgsc.bcm.edu	37	chr5	176895871	176895871	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	atgctgcaagcttgaggtcaTcggagccatcttcatatgtg	11	9	3	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr5:176895871T>A	ENST00000309007.5	-	2	335	c.116A>T	c.(115-117)gAt>gTt	p.D39V	DBN1_ENST00000292385.5_Missense_Mutation_p.D41V|DBN1_ENST00000393565.1_Missense_Mutation_p.D39V	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	39	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTTGAGGTCATCGGAGCCATC	0.607																																					p.D41V		Atlas-SNP	.											.	DBN1	122	.	0			c.A122T						.						183	159	167					5																	176895871		2203	4300	6503	SO:0001583	missense	1627	exon3			AGGTCATCGGAGC		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.116A>T	chr5.hg19:g.176895871T>A	ENSP00000308532:p.Asp39Val	101.0	0.0		176.0	23.0	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	hg19	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.098996	0.76870	.	.	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000477391;ENST00000514833	T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16	3.76	3.76	0.43208	Actin-binding, cofilin/tropomyosin type (3);	0.137801	0.47093	D	0.000241	T	0.56790	0.2009	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.987	T	0.62220	-0.6900	10	0.87932	D	0	-21.9146	12.4455	0.55649	0.0:0.0:0.0:1.0	.	39;41	Q16643;Q16643-2	DREB_HUMAN;.	V	39;41;39;39;39	ENSP00000308532:D39V;ENSP00000292385:D41V;ENSP00000377195:D39V;ENSP00000422854:D39V;ENSP00000421465:D39V	ENSP00000292385:D41V	D	-	2	0	DBN1	176828477	1.000000	0.71417	0.994000	0.49952	0.827000	0.46813	5.052000	0.64263	1.941000	0.56285	0.450000	0.29827	GAT	.	.		0.607	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		A	176895871	T	A	176895871	3	1	54	1	0	0	0	0	1	0	0	0	4254	1435	50	4	1885	4	DBN1	5	176895871	Missense_Mutation	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	7360667	176895871	4019389	39	6831										
JARID2	3720	hgsc.bcm.edu	37	chr6	15507624	15507624	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	caataacacagggtccatccTgcgtcacctcggtgctgtgc	10	14	1	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr6:15507624T>A	ENST00000341776.2	+	11	2952	c.2708T>A	c.(2707-2709)cTg>cAg	p.L903Q	JARID2_ENST00000541660.1_Missense_Mutation_p.L865Q|JARID2_ENST00000474854.1_3'UTR|JARID2_ENST00000397311.3_Missense_Mutation_p.L731Q	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	903	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				GGGTCCATCCTGCGTCACCTC	0.587																																					p.L903Q		Atlas-SNP	.											.	JARID2	135	.	0			c.T2708A						.						154	127	136					6																	15507624		2203	4300	6503	SO:0001583	missense	3720	exon11			CCATCCTGCGTCA	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.2708T>A	chr6.hg19:g.15507624T>A	ENSP00000341280:p.Leu903Gln	71.0	0.0		155.0	49.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	hg19	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.945874	0.92593	.	.	ENSG00000008083	ENST00000341776;ENST00000397311;ENST00000541660	T;T;T	0.57752	0.38;0.38;0.38	5.36	5.36	0.76844	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	T	0.69433	0.3110	M	0.83012	2.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.76024	-0.3110	10	0.87932	D	0	-10.9955	15.3324	0.74223	0.0:0.0:0.0:1.0	.	865;903	F5H590;Q92833	.;JARD2_HUMAN	Q	903;731;865	ENSP00000341280:L903Q;ENSP00000380478:L731Q;ENSP00000444623:L865Q	ENSP00000341280:L903Q	L	+	2	0	JARID2	15615603	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.930000	0.87610	2.028000	0.59812	0.477000	0.44152	CTG	.	.		0.587	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		A	15507624	T	A	15507624	3	1	54	1	0	0	0	0	1	0	0	0	7954	1580	55	4	2750	4	JARID2	6	15507624	Missense_Mutation	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10		15507624	155607443	40	6832										
OR11A1	26531	hgsc.bcm.edu	37	chr6	29395051	29395051	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ggtagcaaattgccaggtagCggtcatatgccatgacagcc	12	10	1	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr6:29395051C>T	ENST00000377149.1	-	5	840	c.368G>A	c.(367-369)cGc>cAc	p.R123H	OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377148.1_Missense_Mutation_p.R123H|OR11A1_ENST00000377147.2_Missense_Mutation_p.R123H			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						TGCCAGGTAGCGGTCATATGC	0.537																																					p.R123H		Atlas-SNP	.											.	OR11A1	30	.	0			c.G368A						.						64	70	68					6																	29395051		1510	2709	4219	SO:0001583	missense	26531	exon1			AGGTAGCGGTCAT		CCDS34363.1	6p22.2-p21.31	2014-02-19	2002-02-28		ENSG00000204694	ENSG00000204694		"GPCR / Class A : Olfactory receptors"	8176	protein-coding gene	gene with protein product			"olfactory receptor, family 11, subfamily A, member 2"	OR11A2			Standard	XM_005249001		Approved	hs6M1-18	uc003nmg.3	Q9GZK7	OTTHUMG00000031225	ENST00000377149.1:c.368G>A	chr6.hg19:g.29395051C>T	ENSP00000366354:p.Arg123His	77.0	0.0		94.0	34.0	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	hg19	CCDS34363.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638066	0.47153	.	.	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.77489	-1.1;-1.1;-1.1	3.78	2.9	0.33743	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38436	N	0.001686	D	0.84969	0.5590	M	0.88906	2.99	0.35989	D	0.836566	D	0.89917	1.0	D	0.87578	0.998	D	0.86849	0.2022	10	0.87932	D	0	-20.52	10.1326	0.42687	0.0:0.8986:0.0:0.1014	.	123	Q9GZK7	O11A1_HUMAN	H	123	ENSP00000366353:R123H;ENSP00000366354:R123H;ENSP00000366352:R123H	ENSP00000366352:R123H	R	-	2	0	OR11A1	29503030	0.966000	0.33281	0.949000	0.38748	0.086000	0.17979	5.138000	0.64795	0.785000	0.33685	0.405000	0.27470	CGC	.	.		0.537	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1			T	29395051	C	T	29395051	3	4	54	1	0	0	0	0	1	0	0	0	10933	768	27	1	583	1	OR11A1	6	29395051	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	13887427	29395051	141720016	41	6833										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51732778	51732778	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gggtttccatagaagcaagaAtgtgacttctgtttttccca	9	8	1	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr6:51732778A>G	ENST00000371117.3	-	48	7891	c.7616T>C	c.(7615-7617)aTt>aCt	p.I2539T	PKHD1_ENST00000340994.4_Missense_Mutation_p.I2539T	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2539					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGAAGCAAGAATGTGACTTCT	0.428																																					p.I2539T		Atlas-SNP	.											.	PKHD1	927	.	0			c.T7616C						.						91	84	86					6																	51732778		2203	4299	6502	SO:0001583	missense	5314	exon48			GCAAGAATGTGAC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.7616T>C	chr6.hg19:g.51732778A>G	ENSP00000360158:p.Ile2539Thr	155.0	0.0		126.0	39.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.145150	0.57044	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87334	-2.04;-2.24	5.67	5.67	0.87782	.	0.329660	0.29253	N	0.012689	D	0.83059	0.5172	L	0.54323	1.7	0.23620	N	0.997277	P;P;P	0.47545	0.799;0.897;0.651	B;P;B	0.47470	0.276;0.548;0.115	T	0.79914	-0.1602	10	0.72032	D	0.01	.	15.0934	0.72215	1.0:0.0:0.0:0.0	.	2539;2539;2539	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	T	2539	ENSP00000360158:I2539T;ENSP00000341097:I2539T	ENSP00000341097:I2539T	I	-	2	0	PKHD1	51840737	0.980000	0.34600	0.928000	0.36995	0.811000	0.45836	6.060000	0.71141	2.165000	0.68154	0.482000	0.46254	ATT	.	.		0.428	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51732778	A	G	51732778	3	3	54	1	0	0	0	0	1	0	0	0	11980	101	4	2	4727	2	PKHD1	6	51732778	Missense_Mutation	SNP	A	TCGA-CC-5258-01A-01D-A12Z-10	22337727	51732778	119382289	42	6834										
GFRAL	389400	hgsc.bcm.edu	37	chr6	55263983	55263983	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	atgattttctttcagattatCcaaccctgtctaatgtcaaa	4	9	4	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr6:55263983C>A	ENST00000340465.2	+	7	1044	c.958C>A	c.(958-960)Cca>Aca	p.P320T		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	320					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			TTCAGATTATCCAACCCTGTC	0.294																																					p.P320T		Atlas-SNP	.											.	GFRAL	91	.	0			c.C958A						.						36	35	36					6																	55263983		2203	4289	6492	SO:0001583	missense	389400	exon7			GATTATCCAACCC	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.958C>A	chr6.hg19:g.55263983C>A	ENSP00000343636:p.Pro320Thr	648.0	1.0		489.0	149.0	NM_207410	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	hg19	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	C	3.374	-0.127832	0.06753	.	.	ENSG00000187871	ENST00000340465	T	0.30981	1.51	5.79	1.61	0.23674	.	1.656770	0.03636	N	0.238747	T	0.07279	0.0184	L	0.27053	0.805	0.09310	N	1	B	0.27625	0.183	B	0.22386	0.039	T	0.23154	-1.0196	10	0.25751	T	0.34	-0.8127	5.5127	0.16890	0.1501:0.5985:0.0:0.2513	.	320	Q6UXV0	GFRAL_HUMAN	T	320	ENSP00000343636:P320T	ENSP00000343636:P320T	P	+	1	0	GFRAL	55371942	0.112000	0.22096	0.208000	0.23602	0.032000	0.12392	0.767000	0.26575	0.378000	0.24764	-0.150000	0.13652	CCA	.	.		0.294	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		A	55263983	C	A	55263983	3	1	54	1	0	0	0	0	1	0	0	0	6359	855	30	3	984	3	GFRAL	6	55263983	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	3531205	55263983	115851084	43	6835										
REV3L	5980	hgsc.bcm.edu	37	chr6	111678241	111678241	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ttattatatttgcaatttcaTgaaaaagtgccttctcatca	4	7	3	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr6:111678241T>A	ENST00000358835.3	-	19	7614	c.7160A>T	c.(7159-7161)cAt>cTt	p.H2387L	REV3L_ENST00000435970.1_Missense_Mutation_p.H2309L|REV3L_ENST00000368802.3_Missense_Mutation_p.H2387L|REV3L_ENST00000368805.1_Missense_Mutation_p.H2387L			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2387					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TGCAATTTCATGAAAAAGTGC	0.323								DNA polymerases (catalytic subunits)																													p.H2387L		Atlas-SNP	.											.	REV3L	386	.	0			c.A7160T						.						90	99	96					6																	111678241		2203	4300	6503	SO:0001583	missense	5980	exon18			ATTTCATGAAAAA	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.7160A>T	chr6.hg19:g.111678241T>A	ENSP00000351697:p.His2387Leu	260.0	0.0		182.0	52.0	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	T	16.23	3.065852	0.55539	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	T;T;T;T	0.08720	3.06;3.06;3.06;3.06	5.93	5.93	0.95920	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.188610	0.47455	D	0.000229	T	0.01800	0.0057	N	0.02247	-0.625	0.39361	D	0.965926	B	0.06786	0.001	B	0.01281	0.0	T	0.49312	-0.8953	10	0.44086	T	0.13	-0.8613	16.3766	0.83401	0.0:0.0:0.0:1.0	.	2387	O60673	DPOLZ_HUMAN	L	2387;2387;2387;2309;460	ENSP00000357792:H2387L;ENSP00000357795:H2387L;ENSP00000351697:H2387L;ENSP00000402003:H2309L	ENSP00000351697:H2387L	H	-	2	0	REV3L	111784934	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.213000	0.77950	2.263000	0.75096	0.533000	0.62120	CAT	.	.		0.323	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111678241	T	A	111678241	3	1	54	1	0	0	0	0	1	0	0	0	13255	1464	51	4	2292	4	REV3L	6	111678241	Missense_Mutation	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	56414258	111678241	59436826	44	6836										
UTRN	7402	hgsc.bcm.edu	37	chr6	144758707	144758707	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	atgtccctttctaggcttttAtgatggaactgactgcacac	8	10	1	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr6:144758707A>G	ENST00000367545.3	+	10	1066	c.1066A>G	c.(1066-1068)Atg>Gtg	p.M356V		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	356	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		CTAGGCTTTTATGATGGAACT	0.423																																					p.M356V		Atlas-SNP	.											.	UTRN	327	.	0			c.A1066G						.						60	59	60					6																	144758707		2203	4300	6503	SO:0001583	missense	7402	exon10			GCTTTTATGATGG	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.1066A>G	chr6.hg19:g.144758707A>G	ENSP00000356515:p.Met356Val	64.0	0.0		56.0	22.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.188889	0.78789	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.48522	0.81	5.45	5.45	0.79879	.	0.000000	0.64402	D	0.000010	T	0.64438	0.2598	M	0.80508	2.5	0.80722	D	1	D	0.65815	0.995	D	0.77004	0.989	T	0.70846	-0.4761	10	0.72032	D	0.01	.	15.5234	0.75881	1.0:0.0:0.0:0.0	.	356	P46939	UTRO_HUMAN	V	356	ENSP00000356515:M356V	ENSP00000356499:M356V	M	+	1	0	UTRN	144800400	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.339000	0.96797	2.072000	0.62099	0.533000	0.62120	ATG	.	.		0.423	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			G	144758707	A	G	144758707	3	3	54	1	0	0	0	0	1	0	0	0	17118	449	16	2	1104	2	UTRN	6	144758707	Missense_Mutation	SNP	A	TCGA-CC-5258-01A-01D-A12Z-10	33080466	144758707	26356360	45	6837										
KCND2	3751	hgsc.bcm.edu	37	chr7	119914945	119914945	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ctcagcagtatttctttgacCgtgacccagacatcttccgc	7	14	3	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr7:119914945C>A	ENST00000331113.4	+	1	1224	c.259C>A	c.(259-261)Cgt>Agt	p.R87S		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	87	Interaction with KCNIP1. {ECO:0000250}.				action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	TTTCTTTGACCGTGACCCAGA	0.527																																					p.R87S		Atlas-SNP	.											.	KCND2	194	.	0			c.C259A						.						134	137	136					7																	119914945		2203	4300	6503	SO:0001583	missense	3751	exon1			TTTGACCGTGACC	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.259C>A	chr7.hg19:g.119914945C>A	ENSP00000333496:p.Arg87Ser	82.0	0.0		144.0	65.0	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	hg19	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049908	0.75846	.	.	ENSG00000184408	ENST00000331113	D	0.90133	-2.62	5.51	5.51	0.81932	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.97235	0.9096	H	0.98646	4.29	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.98281	1.0508	9	.	.	.	.	14.2875	0.66256	0.1486:0.8514:0.0:0.0	.	87	Q9NZV8	KCND2_HUMAN	S	87	ENSP00000333496:R87S	.	R	+	1	0	KCND2	119702181	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.930000	0.70104	2.603000	0.88011	0.655000	0.94253	CGT	.	.		0.527	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		A	119914945	C	A	119914945	3	1	54	1	0	0	0	0	1	0	0	0	8028	652	23	1	261	1	KCND2	7	119914945	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10		119914945	39223718	46	6838										
ASB15	142685	hgsc.bcm.edu	37	chr7	123270025	123270025	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tatcaattctctcagttctgTgagtttattacagttccttg	6	8	4	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr7:123270025T>C	ENST00000451558.1	+	13	1967	c.1446T>C	c.(1444-1446)tgT>tgC	p.C482C	ASB15_ENST00000275699.3_Silent_p.C482C|ASB15_ENST00000434204.1_Silent_p.C482C|ASB15_ENST00000540573.1_Silent_p.C482C|ASB15_ENST00000451215.1_Silent_p.C482C			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	482					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						CTCAGTTCTGTGAGTTTATTA	0.308																																					p.C482C		Atlas-SNP	.											.	ASB15	94	.	0			c.T1446C						.						115	116	116					7																	123270025		2203	4300	6503	SO:0001819	synonymous_variant	142685	exon9			GTTCTGTGAGTTT	AF403033	CCDS34742.1	7q31.31	2013-01-10	2011-01-25		ENSG00000146809	ENSG00000146809		"Ankyrin repeat domain containing"	19767	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 15"			12076535	Standard	XM_005250149		Approved	FLJ43370	uc003vkw.1	Q8WXK1	OTTHUMG00000157114	ENST00000451558.1:c.1446T>C	chr7.hg19:g.123270025T>C		143.0	0.0		133.0	52.0	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Silent	SNP	ENST00000451558.1	hg19	CCDS34742.1																																																																																			.	.		0.308	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1			C	123270025	T	C	123270025	2	2	54	1	0	0	0	0	0	0	0	1	1019	1702	59	2		2	ASB15	7	123270025	Silent	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	3355080	123270025	35868638	47	6839										
ZYX	7791	hgsc.bcm.edu	37	chr7	143080154	143080155	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ctaacacccagccccgagggINScccccagcctcatctccggc							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr7:143080154_143080155insC	ENST00000322764.5	+	5	1107_1108	c.762_763insC	c.(763-765)cccfs	p.P255fs	ZYX_ENST00000449423.2_Frame_Shift_Ins_p.P168fs|AC093673.5_ENST00000429630.1_RNA|ZYX_ENST00000477373.1_3'UTR|ZYX_ENST00000392910.2_Frame_Shift_Ins_p.P98fs	NM_001010972.1|NM_003461.4	NP_001010972.1|NP_003452.1	Q15942	ZYX_HUMAN	zyxin	255					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|integrin-mediated signaling pathway (GO:0007229)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)	17	Melanoma(164;0.205)					AGCCCCGAGGGCCCCCAGCCTC	0.599																																					p.G254fs		Atlas-INDEL	.											.	ZYX	46	.	0			c.762_763insC						.																																			SO:0001589	frameshift_variant	7791	exon5			.	X95735	CCDS5883.1	7q32	2010-02-26			ENSG00000159840	ENSG00000159840			13200	protein-coding gene	gene with protein product		602002				8917469, 8940160	Standard	XM_005250052		Approved		uc003wcx.3	Q15942	OTTHUMG00000023822	ENST00000322764.5:c.767dupC	chr7.hg19:g.143080159_143080159dupC	ENSP00000324422:p.Pro255fs	99.0	0.0		204.0	14.0	NM_003461	A4D2G6|Q6I9S4	Frame_Shift_Ins	INS	ENST00000322764.5	hg19	CCDS5883.1																																																																																			.	.		0.599	ZYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156296.2	NM_003461		C	143080155	-	C	143080154	7	5	54	1	0	1	1	0	0	0	0	0	18269	1190	42	0	776	0	ZYX	7	143080154	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	19810129	143080154	16058509	48	6840										
TTPA	7274	hgsc.bcm.edu	37	chr8	63973866	63973866	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cttcagacttcattataaaaTttgtccattcctgacaaatg	4	9	2	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr8:63973866T>C	ENST00000260116.4	-	5	813	c.782A>G	c.(781-783)aAt>aGt	p.N261S	TTPA_ENST00000521138.1_Intron	NM_000370.3	NP_000361.1	P49638	TTPA_HUMAN	tocopherol (alpha) transfer protein	261					embryonic placenta development (GO:0001892)|intermembrane transport (GO:0046909)|intracellular pH reduction (GO:0051452)|lipid metabolic process (GO:0006629)|negative regulation of cell death (GO:0060548)|negative regulation of establishment of blood-brain barrier (GO:0090212)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|response to toxic substance (GO:0009636)|transport (GO:0006810)|vitamin E metabolic process (GO:0042360)|vitamin transport (GO:0051180)	cytosol (GO:0005829)|late endosome (GO:0005770)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)	15	Breast(64;0.0716)	all_cancers(86;0.145)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.123)			Vitamin E(DB00163)	CATTATAAAATTTGTCCATTC	0.373																																					p.N261S		Atlas-SNP	.											.	TTPA	29	.	0			c.A782G						.						79	79	79					8																	63973866		2203	4300	6503	SO:0001583	missense	7274	exon5			ATAAAATTTGTCC	BC058000	CCDS6178.1	8q12.3	2007-07-18	2007-07-16			ENSG00000137561			12404	protein-coding gene	gene with protein product		600415	"ataxia (Friedreich-like) with vitamin E deficiency"	AVED		7719340, 7887897	Standard	NM_000370		Approved		uc003xux.2	P49638		ENST00000260116.4:c.782A>G	chr8.hg19:g.63973866T>C	ENSP00000260116:p.Asn261Ser	186.0	0.0		357.0	69.0	NM_000370	Q71V64	Missense_Mutation	SNP	ENST00000260116.4	hg19	CCDS6178.1	.	.	.	.	.	.	.	.	.	.	T	9.479	1.097706	0.20552	.	.	ENSG00000137561	ENST00000260116	D	0.84070	-1.8	5.86	5.86	0.93980	Cellular retinaldehyde-binding/triple function, C-terminal (2);	0.361985	0.34223	N	0.004144	T	0.70945	0.3282	N	0.25647	0.755	0.30101	N	0.807391	B	0.10296	0.003	B	0.04013	0.001	T	0.59789	-0.7388	10	0.10111	T	0.7	.	12.4132	0.55480	0.0:0.0:0.1399:0.8601	.	261	P49638	TTPA_HUMAN	S	261	ENSP00000260116:N261S	ENSP00000260116:N261S	N	-	2	0	TTPA	64136420	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.218000	0.58554	2.367000	0.80283	0.528000	0.53228	AAT	.	.		0.373	TTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378460.1	NM_000370		C	63973866	T	C	63973866	3	2	54	1	0	0	0	0	1	0	0	0	16751	1493	52	2	58	2	TTPA	8	63973866	Missense_Mutation	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10		63973866	82390156	49	6841										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110460575	110460575	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gctcagccatgtccacagttGtatttgagtacccgcttaat	8	11	1	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr8:110460575G>C	ENST00000378402.5	+	39	6084	c.5980G>C	c.(5980-5982)Gta>Cta	p.V1994L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1994	IPT/TIG 12.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GTCCACAGTTGTATTTGAGTA	0.398										HNSCC(38;0.096)																											p.V1994L		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G5980C						.						77	76	76					8																	110460575		1930	4153	6083	SO:0001583	missense	93035	exon39			ACAGTTGTATTTG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5980G>C	chr8.hg19:g.110460575G>C	ENSP00000367655:p.Val1994Leu	103.0	0.0		232.0	13.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	7.036	0.561583	0.13498	.	.	ENSG00000205038	ENST00000378402	T	0.75938	-0.98	5.63	2.85	0.33270	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.694656	0.13897	N	0.355149	T	0.66015	0.2747	M	0.68317	2.08	0.09310	N	1	B	0.18863	0.031	B	0.22880	0.042	T	0.50725	-0.8794	10	0.13108	T	0.6	.	4.6974	0.12811	0.2566:0.1591:0.5843:0.0	.	1994	Q86WI1	PKHL1_HUMAN	L	1994	ENSP00000367655:V1994L	ENSP00000367655:V1994L	V	+	1	0	PKHD1L1	110529751	0.000000	0.05858	0.012000	0.15200	0.290000	0.27261	0.347000	0.20014	0.734000	0.32515	0.585000	0.79938	GTA	.	.		0.398	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110460575	G	C	110460575	3	2	54	1	0	0	0	0	1	0	0	0	11981	1377	48	4	6134	4	PKHD1L1	8	110460575	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	46486709	110460575	35903447	50	6842										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113662479	113662479	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	acctgtatcctgaatcacaaCtaaatgaaacagtagagcca	6	10	1	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr8:113662479C>A	ENST00000297405.5	-	19	3348	c.3104G>T	c.(3103-3105)aGt>aTt	p.S1035I	CSMD3_ENST00000455883.2_Missense_Mutation_p.S931I|CSMD3_ENST00000352409.3_Missense_Mutation_p.S1035I|CSMD3_ENST00000343508.3_Missense_Mutation_p.S995I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1035	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TGAATCACAACTAAATGAAAC	0.448										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S1035I		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G3104T						.						145	142	143					8																	113662479		2203	4300	6503	SO:0001583	missense	114788	exon19			TCACAACTAAATG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3104G>T	chr8.hg19:g.113662479C>A	ENSP00000297405:p.Ser1035Ile	287.0	0.0		567.0	50.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.585164	0.86748	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22	5.88	5.88	0.94601	Complement control module (2);Sushi/SCR/CCP (3);	0.293249	0.33938	N	0.004411	T	0.80768	0.4686	M	0.73753	2.245	0.43798	D	0.99634	B;B;P	0.49090	0.257;0.146;0.919	B;B;P	0.57846	0.271;0.148;0.828	T	0.80665	-0.1281	10	0.59425	D	0.04	.	20.2228	0.98330	0.0:1.0:0.0:0.0	.	931;1035;995	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	I	995;1035;375;931;1035	ENSP00000345799:S995I;ENSP00000297405:S1035I;ENSP00000341558:S375I;ENSP00000412263:S931I;ENSP00000343124:S1035I	ENSP00000297405:S1035I	S	-	2	0	CSMD3	113731655	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.854000	0.62918	2.789000	0.95967	0.655000	0.94253	AGT	.	.		0.448	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113662479	C	A	113662479	3	1	54	1	0	0	0	0	1	0	0	0	3948	565	20	3	8231	3	CSMD3	8	113662479	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	3201904	113662479	32701543	51	6843										
ASAP1	50807	hgsc.bcm.edu	37	chr8	131164981	131164981	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	taaattaagaaacatacttaCtgtggcatgtgagatggtca	9	5	1	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr8:131164981C>T	ENST00000518721.1	-	13	1308		c.e13+1		ASAP1_ENST00000357668.1_Splice_Site	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1						cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						AACATACTTACTGTGGCATGT	0.413																																					.		Atlas-SNP	.											.	ASAP1	133	.	0			c.1059+1G>A						.						226	198	207					8																	131164981		2203	4300	6503	SO:0001630	splice_region_variant	50807	exon15			TACTTACTGTGGC	AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.1080+1G>A	chr8.hg19:g.131164981C>T		175.0	0.0		364.0	61.0	NM_001247996	B2RNV3	Splice_Site	SNP	ENST00000518721.1	hg19	CCDS6362.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.861874	0.51482	.	.	ENSG00000153317	ENST00000343135;ENST00000357668;ENST00000524124;ENST00000518721	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5795	0.84711	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ASAP1	131234163	1.000000	0.71417	0.991000	0.47740	0.361000	0.29550	7.047000	0.76599	2.572000	0.86782	0.655000	0.94253	.	.	.		0.413	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482	Intron	T	131164981	C	T	131164981	5	4	54	1	0	0	0	0	0	0	1	0	1010	579	20	3	2380	3	ASAP1	8	131164981	Splice_Site	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	17502502	131164981	15199041	52	6844										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139895383	139895384	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gcagcagcatccagaggaggINSccagccacagcgttccctcg							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr8:139895383_139895384insC	ENST00000303045.6	-	2	478_479	c.32_33insG	c.(31-33)ggcfs	p.G11fs	COL22A1_ENST00000435777.1_Frame_Shift_Ins_p.G11fs	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	11					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.G11D(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TCCAGAGGAGGCCAGCCACAGC	0.663										HNSCC(7;0.00092)																											p.G11fs		Atlas-INDEL	.											.	COL22A1	390	.	1	Substitution - Missense(1)	endometrium(1)	c.33_34insG						.																																			SO:0001589	frameshift_variant	169044	exon2			.	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.33dupG	chr8.hg19:g.139895385_139895385dupC	ENSP00000303153:p.Gly11fs	25.0	0.0		107.0	15.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Frame_Shift_Ins	INS	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.663	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		C	139895384	-	C	139895383	7	5	54	1	0	1	1	0	0	0	0	0	3683	1190	42	0	5103	0	COL22A1	8	139895383	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	8730402	139895383	6468639	53	6845										
DDX58	23586	hgsc.bcm.edu	37	chr9	32457172	32457178	+	Frame_Shift_Del	DEL	TTCCACT	TTCCACT	-													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tcttctcaaaatgaaagtccTtccacttcgagtacagtgtc							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	TTCCACT	TTCCACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr9:32457172_32457178delTTCCACT	ENST00000379883.2	-	18	2877_2883	c.2720_2726delAGTGGAA	c.(2719-2727)aagtggaagfs	p.KWK907fs	DDX58_ENST00000379882.1_Frame_Shift_Del_p.KWK862fs|DDX58_ENST00000542096.1_Frame_Shift_Del_p.KWK836fs|DDX58_ENST00000379868.1_Frame_Shift_Del_p.KWK704fs	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	907	Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		ATGAAAGTCCTTCCACTTCGAGTACAG	0.391																																					p.907_909del		Atlas-Indel,Pindel	.											.	DDX58	82	.	0			c.2721_2727del						.																																			SO:0001589	frameshift_variant	23586	exon18			.	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2720_2726delAGTGGAA	chr9.hg19:g.32457172_32457178delTTCCACT	ENSP00000369213:p.Lys907fs	246.0	0.0		106.0	22.0	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Frame_Shift_Del	DEL	ENST00000379883.2	hg19	CCDS6526.1																																																																																			.	.		0.391	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		-	32457178	TTCCACT	-	32457172	7	5	54	1	0	1	0	1	0	0	0	0	4377	1609	56	0	55	0	DDX58	9	32457172	Frame_Shift_Del	DEL	TTCCACT	TCGA-CC-5258-01A-01D-A12Z-10		32457172	108756259	54	6846										
OLFM1	10439	hgsc.bcm.edu	37	chr9	138011770	138011770	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cgagctaccccaagcgcagcGccggggaggccttcatcatc	12	16	2	0	rs1130517		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr9:138011770G>A	ENST00000371793.3	+	6	1455	c.1204G>A	c.(1204-1206)Gcc>Acc	p.A402T	OLFM1_ENST00000252854.4_Missense_Mutation_p.A384T|OLFM1_ENST00000371796.3_Missense_Mutation_p.A375T	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	402	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		CAAGCGCAGCGCCGGGGAGGC	0.617																																					p.A384T		Atlas-SNP	.											.	OLFM1	57	.	0			c.G1150A						.						73	63	66					9																	138011770		2203	4300	6503	SO:0001583	missense	10439	exon6			CGCAGCGCCGGGG	AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558			17187	protein-coding gene	gene with protein product	"pancortin"	605366				9039501	Standard	NM_006334		Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371793.3:c.1204G>A	chr9.hg19:g.138011770G>A	ENSP00000360858:p.Ala402Thr	35.0	0.0		55.0	32.0	NM_014279	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	hg19		.	.	.	.	.	.	.	.	.	.	G	31	5.084437	0.94100	.	.	ENSG00000130558	ENST00000252854;ENST00000371796;ENST00000371793	D;D;D	0.90385	-2.66;-2.66;-2.66	4.7	4.7	0.59300	Olfactomedin-like (3);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	D	0.96043	0.8711	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.96926	0.9677	10	0.72032	D	0.01	.	17.6361	0.88122	0.0:0.0:1.0:0.0	.	402;384	Q99784;Q6IMJ8	NOE1_HUMAN;.	T	384;375;402	ENSP00000252854:A384T;ENSP00000360861:A375T;ENSP00000360858:A402T	ENSP00000252854:A384T	A	+	1	0	OLFM1	137151591	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.571000	0.98176	2.166000	0.68216	0.491000	0.48974	GCC	.	.		0.617	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279		A	138011770	G	A	138011770	3	1	54	1	0	0	0	0	1	0	0	0	10861	1087	38	1	1182	1	OLFM1	9	138011770	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	105554598	138011770	3201661	55	6847										
GPRIN2	9721	hgsc.bcm.edu	37	chr10	47000008	47000008	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tccagcctggaggaggtgccGtcccctgtgcgggatgtgcg	17	12	0	0	rs111800394		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr10:47000008G>T	ENST00000374317.1	+	3	1401	c.1128G>T	c.(1126-1128)ccG>ccT	p.P376P	GPRIN2_ENST00000374314.4_Silent_p.P376P	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	376										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						AGGAGGTGCCGTCCCCTGTGC	0.657																																					p.P376P		Atlas-SNP	.											.	GPRIN2	94	.	0			c.G1128T						.						164	140	148					10																	47000008		2203	4300	6503	SO:0001819	synonymous_variant	9721	exon3			GGTGCCGTCCCCT	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"KIAA0514"	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.1128G>T	chr10.hg19:g.47000008G>T		78.0	0.0		221.0	23.0	NM_014696	Q5SVF0	Silent	SNP	ENST00000374317.1	hg19	CCDS31192.1																																																																																			.	G|0.500;A|0.500		0.657	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		T	47000008	G	T	47000008	2	4	54	1	0	0	0	0	0	0	0	1	6739	1132	40	1		1	GPRIN2	10	47000008	Silent	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10		47000008	88534739	56	6848										
KIF20B	9585	hgsc.bcm.edu	37	chr10	91477208	91477209	+	Frame_Shift_Del	DEL	AC	AC	-													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	atattcactgttaaaatattAcagattgaagattctgaaat							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr10:91477208_91477209delAC	ENST00000371728.3	+	10	1145_1146	c.1080_1081delAC	c.(1078-1083)ttacagfs	p.Q361fs	KIF20B_ENST00000394289.2_Frame_Shift_Del_p.Q361fs|KIF20B_ENST00000260753.4_Frame_Shift_Del_p.Q361fs|KIF20B_ENST00000416354.1_Frame_Shift_Del_p.Q361fs	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	361	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						TTAAAATATTACAGATTGAAGA	0.257																																					p.360_360del		Atlas-Indel,Pindel	.											.	KIF20B	191	.	0			c.1079_1080del						.																																			SO:0001589	frameshift_variant	9585	exon10			.	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.1080_1081delAC	chr10.hg19:g.91477208_91477209delAC	ENSP00000360793:p.Gln361fs	603.0	0.0		311.0	50.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Frame_Shift_Del	DEL	ENST00000371728.3	hg19																																																																																				.	.		0.257	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		-	91477209	AC	-	91477208	7	5	54	1	0	1	0	1	0	0	0	0	8296	388	14	0	1114	0	KIF20B	10	91477208	Frame_Shift_Del	DEL	AC	TCGA-CC-5258-01A-01D-A12Z-10	44477200	91477208	44057539	57	6849										
TLL2	7093	hgsc.bcm.edu	37	chr10	98145959	98145960	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cattcagcttggtaatgaaaINSccgccacaggccactgcacg					rs374446747		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr10:98145959_98145960insC	ENST00000357947.3	-	15	2090_2091	c.1865_1866insG	c.(1864-1866)ggtfs	p.G622fs		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	622	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		TGGTAATGAAACCGCCACAGGC	0.545																																					p.G622fs		Atlas-INDEL	.											.	TLL2	122	.	0			c.1866_1867insG						.																																			SO:0001589	frameshift_variant	7093	exon15			.	AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.1866dupG	chr10.hg19:g.98145961_98145961dupC	ENSP00000350630:p.Gly622fs	40.0	0.0		98.0	13.0	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Frame_Shift_Ins	INS	ENST00000357947.3	hg19	CCDS7449.1																																																																																			.	.		0.545	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			C	98145960	-	C	98145959	7	5	54	1	0	1	1	0	0	0	0	0	15961	30	2	0	1209	0	TLL2	10	98145959	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	6668751	98145959	37388788	58	6850										
SFRP5	6425	hgsc.bcm.edu	37	chr10	99531159	99531160	+	Frame_Shift_Ins	INS	-	-	A													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gcagcatctcaggccaggggINSaagccgtaggcctccatgag							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr10:99531159_99531160insA	ENST00000266066.3	-	1	549_550	c.431_432insT	c.(430-432)ttcfs	p.F144fs		NM_003015.3	NP_003006.2	Q5T4F7	SFRP5_HUMAN	secreted frizzled-related protein 5	144	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cell differentiation (GO:0030154)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|establishment or maintenance of cell polarity (GO:0007163)|gonad development (GO:0008406)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of Wnt signaling pathway involved in digestive tract morphogenesis (GO:2000057)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|post-anal tail morphogenesis (GO:0036342)|signal transduction (GO:0007165)|vasculature development (GO:0001944)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			large_intestine(1)|lung(4)	5		Colorectal(252;0.234)		Epithelial(162;4.98e-10)|all cancers(201;3.58e-08)		CAGGCCAGGGGAAGCCGTAGGC	0.698																																					p.F144fs		Atlas-INDEL	.											.	SFRP5	32	.	0			c.432_433insT						.																																			SO:0001589	frameshift_variant	6425	exon1			.	AF017988	CCDS7472.1	10q24	2008-07-10			ENSG00000120057	ENSG00000120057		"Secreted frizzled-related proteins"	10779	protein-coding gene	gene with protein product	"secreted apoptosis related protein 3"	604158				9391078	Standard	NM_003015		Approved	SARP3	uc001kor.4	Q5T4F7	OTTHUMG00000018866	ENST00000266066.3:c.432dupT	chr10.hg19:g.99531161_99531161dupA	ENSP00000266066:p.Phe144fs	39.0	0.0		132.0	10.0	NM_003015	O14780|Q86TH7	Frame_Shift_Ins	INS	ENST00000266066.3	hg19	CCDS7472.1																																																																																			.	.		0.698	SFRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049742.1	NM_003015		A	99531160	-	A	99531159	7	5	54	1	0	1	1	0	0	0	0	0	14179	1165	41	0	533	0	SFRP5	10	99531159	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	1385200	99531159	36003588	59	6851										
NFKB2	4791	hgsc.bcm.edu	37	chr10	104157402	104157403	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gtgatggctccttctccctgINScccctgaagccagtcatctc							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr10:104157402_104157403insC	ENST00000369966.3	+	8	871_872	c.621_622insC	c.(622-624)cccfs	p.P208fs	NFKB2_ENST00000189444.6_Frame_Shift_Ins_p.P208fs|NFKB2_ENST00000428099.1_Frame_Shift_Ins_p.P208fs	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	208	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	CCTTCTCCCTGCCCCTGAAGCC	0.579			T	IGH@	B-NHL																																p.L207fs		Atlas-INDEL	.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	.	NFKB2	48	.	0			c.621_622insC						.																																			SO:0001589	frameshift_variant	4791	exon8			.	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"Ankyrin repeat domain containing"	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.625dupC	chr10.hg19:g.104157406_104157406dupC	ENSP00000358983:p.Pro208fs	134.0	0.0		218.0	15.0	NM_002502	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Frame_Shift_Ins	INS	ENST00000369966.3	hg19	CCDS41564.1																																																																																			.	.		0.579	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			C	104157403	-	C	104157402	7	5	54	1	0	1	1	0	0	0	0	0	10385	1306	46	0	647	0	NFKB2	10	104157402	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	4626243	104157402	31377345	60	6852										
CHST15	51363	hgsc.bcm.edu	37	chr10	125769678	125769678	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tcagctctcacgtcgtcttcCacgcaaacgcctcatccgcg	7	18	4	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr10:125769678C>T	ENST00000346248.5	-	8	2315	c.1673G>A	c.(1672-1674)tGg>tAg	p.W558*	CHST15_ENST00000435907.1_Nonsense_Mutation_p.W558*	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	558					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						CGTCGTCTTCCACGCAAACGC	0.562																																					p.W558X		Atlas-SNP	.											.	CHST15	134	.	0			c.G1673A						.						65	65	65					10																	125769678		2203	4300	6503	SO:0001587	stop_gained	51363	exon8			GTCTTCCACGCAA	AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"Sulfotransferases, membrane-bound"	18137	protein-coding gene	gene with protein product	"B cell RAG associated protein", "N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1673G>A	chr10.hg19:g.125769678C>T	ENSP00000333947:p.Trp558*	37.0	0.0		94.0	34.0	NM_015892	O60338|O60474|Q86VM4	Nonsense_Mutation	SNP	ENST00000346248.5	hg19	CCDS7638.1	.	.	.	.	.	.	.	.	.	.	C	43	10.455762	0.99408	.	.	ENSG00000182022	ENST00000346248;ENST00000435907	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.112	19.2238	0.93810	0.0:1.0:0.0:0.0	.	.	.	.	X	558	.	ENSP00000333947:W558X	W	-	2	0	CHST15	125759668	1.000000	0.71417	0.997000	0.53966	0.875000	0.50365	6.984000	0.76186	2.543000	0.85770	0.563000	0.77884	TGG	.	.		0.562	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892		T	125769678	C	T	125769678	4	4	54	1	0	0	0	0	0	1	0	0	3405	595	21	3	16	3	CHST15	10	125769678	Nonsense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	21612276	125769678	9765069	61	6853										
OR10A3	26496	hgsc.bcm.edu	37	chr11	7960259	7960259	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ccaatgagatcagtttcttgGtttcgggtgagtagccagat	12	7	2	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr11:7960259G>C	ENST00000360759.3	-	1	882	c.809C>G	c.(808-810)aCc>aGc	p.T270S		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	270					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAGTTTCTTGGTTTCGGGTGA	0.453																																					p.T270S		Atlas-SNP	.											.	OR10A3	54	.	0			c.C809G						.						197	179	185					11																	7960259		2201	4296	6497	SO:0001583	missense	26496	exon1			TTCTTGGTTTCGG	BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"GPCR / Class A : Olfactory receptors"	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.809C>G	chr11.hg19:g.7960259G>C	ENSP00000353988:p.Thr270Ser	335.0	0.0		210.0	72.0	NM_001003745	B9EH39|Q6IF58|Q96R11	Missense_Mutation	SNP	ENST00000360759.3	hg19	CCDS31421.1	.	.	.	.	.	.	.	.	.	.	G	0.429	-0.904393	0.02453	.	.	ENSG00000170683	ENST00000360759	T	0.00054	8.8	4.65	1.46	0.22682	GPCR, rhodopsin-like superfamily (1);	0.370076	0.19214	N	0.119853	T	0.00073	0.0002	N	0.04018	-0.295	0.09310	N	1	B	0.09022	0.002	B	0.21708	0.036	T	0.02437	-1.1159	10	0.09084	T	0.74	.	8.9595	0.35838	0.0:0.4598:0.3828:0.1574	.	270	P58181	O10A3_HUMAN	S	270	ENSP00000353988:T270S	ENSP00000353988:T270S	T	-	2	0	OR10A3	7916835	0.000000	0.05858	0.998000	0.56505	0.501000	0.33797	0.019000	0.13444	0.671000	0.31185	-0.234000	0.12200	ACC	.	.		0.453	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745		C	7960259	G	C	7960259	3	2	54	1	0	0	0	0	1	0	0	0	10900	1261	44	4	138	4	OR10A3	11	7960259	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10		7960259	127046257	62	6854										
NAT10	55226	hgsc.bcm.edu	37	chr11	34137375	34137375	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gtctttctttgttaggatgtGcattccaggtacagaactga	10	7	2	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr11:34137375G>A	ENST00000257829.3	+	6	707	c.501G>A	c.(499-501)gtG>gtA	p.V167V	NAT10_ENST00000527971.1_Silent_p.V167V|NAT10_ENST00000531159.2_Silent_p.V95V	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	167						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				GTTAGGATGTGCATTCCAGGT	0.463																																					p.V167V		Atlas-SNP	.											.	NAT10	78	.	0			c.G501A						.						191	191	191					11																	34137375		2202	4298	6500	SO:0001819	synonymous_variant	55226	exon6			GGATGTGCATTCC	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.501G>A	chr11.hg19:g.34137375G>A		311.0	0.0		215.0	63.0	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Silent	SNP	ENST00000257829.3	hg19	CCDS7889.1																																																																																			.	.		0.463	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		A	34137375	G	A	34137375	2	1	54	1	0	0	0	0	0	0	0	1	10183	1306	46	3		3	NAT10	11	34137375	Silent	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	26177116	34137375	100869141	63	6855										
C1QTNF4	114900	hgsc.bcm.edu	37	chr11	47611682	47611682	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gtgaaggagaagaagtaggcGccgggcagacggcagcggaa	19	7	0	4			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr11:47611682G>A	ENST00000302514.3	-	2	1197	c.681C>T	c.(679-681)ggC>ggT	p.G227G		NM_031909.2	NP_114115.2	Q9BXJ3	C1QT4_HUMAN	C1q and tumor necrosis factor related protein 4	227	C1q 2. {ECO:0000255|PROSITE- ProRule:PRU00368}.					extracellular space (GO:0005615)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						AGAAGTAGGCGCCGGGCAGAC	0.647																																					p.G227G		Atlas-SNP	.											.	C1QTNF4	19	.	0			c.C681T						.						11	15	13					11																	47611682		2161	4273	6434	SO:0001819	synonymous_variant	114900	exon2			GTAGGCGCCGGGC	AF329838	CCDS7942.1	11q11	2008-07-18				ENSG00000172247			14346	protein-coding gene	gene with protein product	"complement-c1q tumor necrosis factor-related protein 4"	614911				16094384	Standard	NM_031909		Approved	CTRP4, ZACRP4	uc001ngc.2	Q9BXJ3		ENST00000302514.3:c.681C>T	chr11.hg19:g.47611682G>A		14.0	0.0		42.0	13.0	NM_031909	Q8IV25	Silent	SNP	ENST00000302514.3	hg19	CCDS7942.1																																																																																			.	.		0.647	C1QTNF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391772.1	NM_031909		A	47611682	G	A	47611682	2	1	54	1	0	0	0	0	0	0	0	1	1967	1074	38	1		1	C1QTNF4	11	47611682	Silent	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	13474307	47611682	87394834	64	6856										
OR8K5	219453	hgsc.bcm.edu	37	chr11	55927260	55927260	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	agcaaaggaacatcatcacaGtaaaaatgactgatgacatt	7	7	2	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr11:55927260G>T	ENST00000313447.1	-	1	533	c.534C>A	c.(532-534)taC>taA	p.Y178*		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	178						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				CATCATCACAGTAAAAATGAC	0.358																																					p.Y178X		Atlas-SNP	.											.	OR8K5	82	.	0			c.C534A						.						93	94	94					11																	55927260		2201	4296	6497	SO:0001587	stop_gained	219453	exon1			ATCACAGTAAAAA	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"GPCR / Class A : Olfactory receptors"	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.534C>A	chr11.hg19:g.55927260G>T	ENSP00000323853:p.Tyr178*	141.0	0.0		107.0	28.0	NM_001004058	Q6IFB5	Nonsense_Mutation	SNP	ENST00000313447.1	hg19	CCDS31521.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759194	0.49468	.	.	ENSG00000181752	ENST00000313447	.	.	.	4.18	1.08	0.20341	.	0.000000	0.51477	D	0.000095	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	8.6385	0.33964	0.2774:0.0:0.7226:0.0	.	.	.	.	X	178	.	ENSP00000323853:Y178X	Y	-	3	2	OR8K5	55683836	0.002000	0.14202	0.990000	0.47175	0.832000	0.47134	0.090000	0.15025	0.120000	0.18254	-0.254000	0.11334	TAC	.	.		0.358	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058		T	55927260	G	T	55927260	4	4	54	1	0	0	0	0	0	1	0	0	11254	1024	36	3	392	3	OR8K5	11	55927260	Nonsense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	8315578	55927260	79079256	65	6857										
SYVN1	84447	hgsc.bcm.edu	37	chr11	64900941	64900941	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tccctgagccctgaactcacTgccatgctggggctggactt	11	14	1	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr11:64900941T>C	ENST00000377190.3	-	2	226	c.132A>G	c.(130-132)gcA>gcG	p.A44A	SYVN1_ENST00000526060.1_Splice_Site_p.A44A|SYVN1_ENST00000307289.6_Splice_Site_p.A44A|SYVN1_ENST00000526121.1_5'Flank|SYVN1_ENST00000294256.8_Splice_Site_p.A44A	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	44					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						CTGAACTCACTGCCATGCTGG	0.627																																					p.A44A		Atlas-SNP	.											.	SYVN1	55	.	0			c.A132G						.						73	70	71					11																	64900941		2201	4297	6498	SO:0001630	splice_region_variant	84447	exon2			ACTCACTGCCATG	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"RING-type (C3HC4) zinc fingers"	20738	protein-coding gene	gene with protein product	"HMG-coA reductase degradation 1 homolog (S. cerevisiae)"	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.132+1A>G	chr11.hg19:g.64900941T>C		44.0	0.0		82.0	28.0	NM_172230	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Silent	SNP	ENST00000377190.3	hg19	CCDS31605.1																																																																																			.	.		0.627	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431	Silent	C	64900941	T	C	64900941	5	2	54	1	0	0	0	0	0	0	1	0	15502	1594	55	2	1781	2	SYVN1	11	64900941	Splice_Site	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	8973681	64900941	70105575	66	6858										
CADM1	23705	hgsc.bcm.edu	37	chr11	115085443	115085443	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	atgaacaggttgggcccagaCagtacggcgtgttgaggcat	15	8	0	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr11:115085443C>G	ENST00000452722.3	-	7	899	c.879G>C	c.(877-879)ctG>ctC	p.L293L	CADM1_ENST00000331581.6_Silent_p.L293L|CADM1_ENST00000537058.1_Silent_p.L293L|CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000536727.1_Silent_p.L293L|CADM1_ENST00000542447.2_Silent_p.L293L	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		TGGGCCCAGACAGTACGGCGT	0.473																																					p.L293L		Atlas-SNP	.											.	CADM1	74	.	0			c.G879C						.						259	222	234					11																	115085443		2201	4296	6497	SO:0001819	synonymous_variant	23705	exon7			CCCAGACAGTACG	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5951	protein-coding gene	gene with protein product	"nectin-like 2"	605686	"tumor suppressor in lung cancer 1", "immunoglobulin superfamily, member 4"	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.879G>C	chr11.hg19:g.115085443C>G		389.0	0.0		171.0	25.0	NM_014333		Silent	SNP	ENST00000452722.3	hg19	CCDS8373.1	.	.	.	.	.	.	.	.	.	.	C	7.913	0.736960	0.15574	.	.	ENSG00000182985	ENST00000545380	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	T	0.71333	0.3327	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69468	-0.5137	4	.	.	.	.	15.1897	0.73035	0.0:0.8597:0.1403:0.0	.	.	.	.	L	292	.	.	V	-	1	0	CADM1	114590653	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.578000	0.36525	2.660000	0.90430	0.655000	0.94253	GTC	.	.		0.473	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		G	115085443	C	G	115085443	2	3	54	1	0	0	0	0	0	0	0	1	2568	465	17	4		4	CADM1	11	115085443	Silent	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	50184502	115085443	19921073	67	6859										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133814256	133814256	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tgccttatcatgaagactggCccggcctgggggaatagagc	14	10	1	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr11:133814256C>A	ENST00000321016.8	-	3	498	c.268G>T	c.(268-270)Gcc>Tcc	p.A90S	IGSF9B_ENST00000533871.2_Missense_Mutation_p.A90S			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	90	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		TGAAGACTGGCCCGGCCTGGG	0.577																																					p.A90S		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G268T						.						52	55	54					11																	133814256		1991	4159	6150	SO:0001583	missense	22997	exon3			GACTGGCCCGGCC	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.268G>T	chr11.hg19:g.133814256C>A	ENSP00000317980:p.Ala90Ser	74.0	0.0		148.0	39.0	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	23.6	4.431127	0.83776	.	.	ENSG00000080854	ENST00000321016;ENST00000527648;ENST00000533160;ENST00000526663	T;T;T;T	0.27890	1.64;1.64;1.64;1.92	5.69	5.69	0.88448	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000008	T	0.38188	0.1031	N	0.25380	0.74	0.54753	D	0.999987	B	0.33318	0.408	P	0.46144	0.505	T	0.27020	-1.0086	10	0.66056	D	0.02	.	19.8208	0.96592	0.0:1.0:0.0:0.0	.	90	Q9UPX0	TUTLB_HUMAN	S	90;90;80;137	ENSP00000317980:A90S;ENSP00000436576:A90S;ENSP00000434026:A80S;ENSP00000435989:A137S	ENSP00000317980:A90S	A	-	1	0	IGSF9B	133319466	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	4.713000	0.61895	2.688000	0.91661	0.563000	0.77884	GCC	.	.		0.577	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133814256	C	A	133814256	3	1	54	1	0	0	0	0	1	0	0	0	7615	739	26	3	3849	3	IGSF9B	11	133814256	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	18728813	133814256	1192260	68	6860										
VAMP1	6843	hgsc.bcm.edu	37	chr12	6575091	6575091	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tcctgcctgcaaggcatcagCtcggtcatccagctctgaca	9	15	3	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr12:6575091C>G	ENST00000396308.3	-	3	350	c.205G>C	c.(205-207)Gct>Cct	p.A69P	VAMP1_ENST00000361716.3_Missense_Mutation_p.A69P|TAPBPL_ENST00000545700.1_3'UTR|VAMP1_ENST00000400911.3_Missense_Mutation_p.A69P|VAMP1_ENST00000535180.1_Missense_Mutation_p.A69P|VAMP1_ENST00000544432.1_5'UTR	NM_014231.3|NM_199245.1	NP_055046.1|NP_954740.1	P23763	VAMP1_HUMAN	vesicle-associated membrane protein 1 (synaptobrevin 1)	69	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				neurotransmitter secretion (GO:0007269)|SNARE complex assembly (GO:0035493)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuron projection (GO:0043005)|synapse (GO:0045202)				endometrium(1)|large_intestine(1)|prostate(1)	3					Botulinum Toxin Type B(DB00042)	AAGGCATCAGCTCGGTCATCC	0.512											OREG0021627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A69P		Atlas-SNP	.											.	VAMP1	6	.	0			c.G205C						.						132	108	116					12																	6575091		2203	4300	6503	SO:0001583	missense	6843	exon3			CATCAGCTCGGTC		CCDS31731.1, CCDS41740.1, CCDS44809.1, CCDS73422.1	12p	2013-02-13			ENSG00000139190	ENSG00000139190		"Vesicle-associated membrane proteins"	12642	protein-coding gene	gene with protein product		185880		SYB1		1976629	Standard	XM_006719011		Approved	VAMP-1	uc001qok.3	P23763	OTTHUMG00000168269	ENST00000396308.3:c.205G>C	chr12.hg19:g.6575091C>G	ENSP00000379602:p.Ala69Pro	124.0	0.0	635	240.0	90.0	NM_014231	A8MVP3|D3DUR3|O75468|Q15857|Q6FG94|Q8IVC9	Missense_Mutation	SNP	ENST00000396308.3	hg19	CCDS41740.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.609022	0.87258	.	.	ENSG00000139190	ENST00000400911;ENST00000361716;ENST00000535180;ENST00000355479;ENST00000396308;ENST00000396943;ENST00000539047	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.77	5.77	0.91146	Synaptobrevin (4);	0.000000	0.85682	D	0.000000	T	0.73513	0.3596	H	0.94771	3.58	0.80722	D	1	B;B;B	0.31100	0.2;0.238;0.308	B;B;P	0.44946	0.317;0.445;0.465	T	0.77175	-0.2684	10	0.87932	D	0	.	19.9983	0.97395	0.0:1.0:0.0:0.0	.	69;69;69	P23763-3;P23763;P23763-2	.;VAMP1_HUMAN;.	P	69	ENSP00000383702:A69P;ENSP00000355122:A69P;ENSP00000444181:A69P;ENSP00000379602:A69P	ENSP00000347664:A69P	A	-	1	0	VAMP1	6445352	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.747000	0.85070	2.724000	0.93272	0.561000	0.74099	GCT	.	.		0.512	VAMP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399078.1			G	6575091	C	G	6575091	3	3	54	1	0	0	0	0	1	0	0	0	17127	797	28	4	192	4	VAMP1	12	6575091	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10		6575091	127276804	69	6861										
LRP6	4040	hgsc.bcm.edu	37	chr12	12291266	12291266	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cattaacacttactgtattcTtgaaggttcagctcctttac	5	10	2	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr12:12291266T>C	ENST00000261349.4	-	16	3676	c.3600A>G	c.(3598-3600)caA>caG	p.Q1200Q	BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000543091.1_Silent_p.Q1200Q	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1200	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TACTGTATTCTTGAAGGTTCA	0.358																																					p.Q1200Q		Atlas-SNP	.											.	LRP6	170	.	0			c.A3600G						.						177	162	167					12																	12291266		2203	4300	6503	SO:0001819	synonymous_variant	4040	exon16			GTATTCTTGAAGG	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.3600A>G	chr12.hg19:g.12291266T>C		258.0	0.0		186.0	61.0	NM_002336	Q17RZ2	Silent	SNP	ENST00000261349.4	hg19	CCDS8647.1																																																																																			.	.		0.358	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			C	12291266	T	C	12291266	2	2	54	1	0	0	0	0	0	0	0	1	8971	1606	56	2		2	LRP6	12	12291266	Silent	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	5716175	12291266	121560629	70	6862										
IFLTD1	160492	hgsc.bcm.edu	37	chr12	25801457	25801457	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tctggactctggaaacaccgAtgtctcctgctctcactggc	9	14	4	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr12:25801457A>T	ENST00000445693.1	-	1	31	c.29T>A	c.(28-30)aTc>aAc	p.I10N		NM_001145727.2	NP_001139199.1	Q8N9Z9	LMTD1_HUMAN		0				R -> K (in Ref. 1; BAC04132). {ECO:0000305}.	cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GGAAACACCGATGTCTCCTGC	0.488																																					p.I10N		Atlas-SNP	.											.	IFLTD1	121	.	0			c.T29A						.						242	215	223					12																	25801457		692	1591	2283	SO:0001583	missense	160492	exon1			ACACCGATGTCTC																												ENST00000445693.1:c.29T>A	chr12.hg19:g.25801457A>T	ENSP00000407043:p.Ile10Asn	255.0	0.0		228.0	78.0	NM_001145727	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000445693.1	hg19	CCDS44847.1	.	.	.	.	.	.	.	.	.	.	A	9.613	1.131801	0.21041	.	.	ENSG00000152936	ENST00000445693	T	0.14266	2.52	3.84	-3.21	0.05140	.	.	.	.	.	T	0.08179	0.0204	.	.	.	0.09310	N	0.999996	P	0.39157	0.662	B	0.34242	0.178	T	0.22243	-1.0222	8	0.66056	D	0.02	.	5.5128	0.16890	0.3756:0.1724:0.452:0.0	.	10	Q8N9Z9-3	.	N	10	ENSP00000407043:I10N	ENSP00000407043:I10N	I	-	2	0	IFLTD1	25692724	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.532000	0.06164	-0.529000	0.06358	-0.323000	0.08544	ATC	.	.		0.488	IFLTD1-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402280.1			T	25801457	A	T	25801457	3	4	54	1	0	0	0	0	1	0	0	0	7539	333	12	4	1324	4	IFLTD1	12	25801457	Missense_Mutation	SNP	A	TCGA-CC-5258-01A-01D-A12Z-10	13510191	25801457	108050438	71	6863										
DENND5B	160518	hgsc.bcm.edu	37	chr12	31562239	31562239	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gaagcagaaatagtccacagCattgagagaaagaaggtggt	13	5	0	4			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr12:31562239C>T	ENST00000389082.5	-	14	3025	c.2761G>A	c.(2761-2763)Gct>Act	p.A921T	DENND5B_ENST00000536562.1_Missense_Mutation_p.A956T|DENND5B_ENST00000306833.6_Missense_Mutation_p.A956T	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	921	RUN 1. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TAGTCCACAGCATTGAGAGAA	0.413																																					p.A921T		Atlas-SNP	.											.	DENND5B	114	.	0			c.G2761A						.						62	62	62					12																	31562239		1865	4101	5966	SO:0001583	missense	160518	exon14			CCACAGCATTGAG	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.2761G>A	chr12.hg19:g.31562239C>T	ENSP00000373734:p.Ala921Thr	155.0	0.0		116.0	41.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	hg19	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.935931	0.52972	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562	T;T;T	0.35789	1.29;1.29;1.29	4.5	4.5	0.54988	RUN (3);	0.067075	0.64402	D	0.000014	T	0.36026	0.0952	L	0.52126	1.63	0.51767	D	0.999939	B;B	0.31730	0.2;0.337	B;B	0.33254	0.16;0.156	T	0.16837	-1.0389	10	0.30854	T	0.27	-21.1322	17.4537	0.87600	0.0:1.0:0.0:0.0	.	921;956	Q6ZUT9;G3V1S3	DEN5B_HUMAN;.	T	921;956;956	ENSP00000373734:A921T;ENSP00000306482:A956T;ENSP00000444889:A956T	ENSP00000306482:A956T	A	-	1	0	DENND5B	31453506	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.589000	0.61006	2.328000	0.79073	0.558000	0.71614	GCT	.	.		0.413	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		T	31562239	C	T	31562239	3	4	54	1	0	0	0	0	1	0	0	0	4439	710	25	3	1095	3	DENND5B	12	31562239	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	5760782	31562239	102289656	72	6864										
OR6C65	403282	hgsc.bcm.edu	37	chr12	55794609	55794610	+	Frame_Shift_Ins	INS	-	-	T													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	atgcttccatggcccaagtaINSttttttttaattcttttggg							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr12:55794609_55794610insT	ENST00000379665.2	+	1	396_397	c.297_298insT	c.(298-300)tttfs	p.F100fs		NM_001005518.1	NP_001005518.1	A6NJZ3	O6C65_HUMAN	olfactory receptor, family 6, subfamily C, member 65	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L102fs*1(1)		cervix(1)|endometrium(2)|large_intestine(3)|lung(9)	15						TGGCCCAAGTATTTTTTTTAAT	0.356																																					p.V99fs		Atlas-Indel,Pindel	.											.	OR6C65	44	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.297_298insT						.																																			SO:0001589	frameshift_variant	403282	exon1			.		CCDS31821.1	12q13.2	2013-09-23			ENSG00000205328	ENSG00000205328		"GPCR / Class A : Olfactory receptors"	31295	protein-coding gene	gene with protein product							Standard	NM_001005518		Approved		uc010spl.2	A6NJZ3	OTTHUMG00000169955	ENST00000379665.2:c.305dupT	chr12.hg19:g.55794617_55794617dupT	ENSP00000368986:p.Phe100fs	122.0	0.0		140.0	44.0	NM_001005518	B2RNH9	Frame_Shift_Ins	INS	ENST00000379665.2	hg19	CCDS31821.1																																																																																			.	.		0.356	OR6C65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406674.1			T	55794610	-	T	55794609	7	5	54	1	0	1	1	0	0	0	0	0	11204	436	16	0	299	0	OR6C65	12	55794609	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	24232370	55794609	78057286	73	6865										
ATP5B	506	hgsc.bcm.edu	37	chr12	57038650	57038650	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	agtctcaggaccaacaggaaTtttgattggtgcaccagaat	10	8	1	2	rs11542649		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr12:57038650T>C	ENST00000262030.3	-	3	450	c.400A>G	c.(400-402)Att>Gtt	p.I134V	ATP5B_ENST00000550162.1_5'Flank|ATP5B_ENST00000552919.1_Missense_Mutation_p.I134V|SNORD59A_ENST00000384304.1_RNA	NM_001686.3	NP_001677.2	P06576	ATPB_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide	134					angiogenesis (GO:0001525)|ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|osteoblast differentiation (GO:0001649)|proton transport (GO:0015992)|regulation of intracellular pH (GO:0051453)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial nucleoid (GO:0042645)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase, catalytic core (GO:0005754)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCAACAGGAATTTTGATTGGT	0.428																																					p.I134V		Atlas-SNP	.											.	ATP5B	48	.	0			c.A400G						.						124	114	117					12																	57038650		2203	4300	6503	SO:0001583	missense	506	exon3			CAGGAATTTTGAT	M27132	CCDS8924.1	12p13.3	2012-10-12			ENSG00000110955	ENSG00000110955	3.6.3.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	830	protein-coding gene	gene with protein product		102910		ATPSB		2687158	Standard	NM_001686		Approved		uc001slr.3	P06576	OTTHUMG00000170291	ENST00000262030.3:c.400A>G	chr12.hg19:g.57038650T>C	ENSP00000262030:p.Ile134Val	381.0	0.0		562.0	161.0	NM_001686	A8K4X0|Q14283	Missense_Mutation	SNP	ENST00000262030.3	hg19	CCDS8924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.80|12.80	2.047170|2.047170	0.36085|0.36085	.|.	.|.	ENSG00000110955|ENSG00000110955	ENST00000262030;ENST00000552919;ENST00000551020|ENST00000552959	T;T;T|.	0.79247|.	-1.25;-1.25;-1.25|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.35998|0.35998	0.0951|0.0951	N|N	0.04320|0.04320	-0.23|-0.23	0.80722|0.80722	D|D	1|1	B|.	0.06786|.	0.001|.	B|.	0.08055|.	0.003|.	T|T	0.32824|0.32824	-0.9892|-0.9892	10|5	0.02654|.	T|.	1|.	-17.1497|-17.1497	15.0669|15.0669	0.72002|0.72002	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs11542649;rs11542649|rs11542649;rs11542649	134|.	P06576|.	ATPB_HUMAN|.	V|S	134;134;73|70	ENSP00000262030:I134V;ENSP00000450297:I134V;ENSP00000446677:I73V|.	ENSP00000262030:I134V|.	I|N	-|-	1|2	0|0	ATP5B|ATP5B	55324917|55324917	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.549000|7.549000	0.82163|0.82163	2.248000|2.248000	0.74166|0.74166	0.460000|0.460000	0.39030|0.39030	ATT|AAT	.	T|1.000;|0.000		0.428	ATP5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408380.1	NM_001686		C	57038650	T	C	57038650	3	2	54	1	0	0	0	0	1	0	0	0	1148	1493	52	2	1221	2	ATP5B	12	57038650	Missense_Mutation	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	1244041	57038650	76813245	74	6866										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120580635	120580635	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ccactgcaggcaccttgttgGactgggcagttccaaagtta	11	11	0	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr12:120580635G>A	ENST00000300648.6	-	43	5618	c.5606C>T	c.(5605-5607)tCc>tTc	p.S1869F		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1869					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CACCTTGTTGGACTGGGCAGT	0.537																																					p.S1869F		Atlas-SNP	.											.	GCN1L1	207	.	0			c.C5606T						.						141	145	143					12																	120580635		2060	4201	6261	SO:0001583	missense	10985	exon43			TTGTTGGACTGGG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.5606C>T	chr12.hg19:g.120580635G>A	ENSP00000300648:p.Ser1869Phe	140.0	0.0		199.0	63.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.750913	0.89753	.	.	ENSG00000089154	ENST00000300648	T	0.50548	0.74	5.97	5.97	0.96955	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68476	0.3005	M	0.64997	1.995	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.67110	-0.5753	10	0.59425	D	0.04	.	20.4238	0.99064	0.0:0.0:1.0:0.0	.	1869	Q92616	GCN1L_HUMAN	F	1869	ENSP00000300648:S1869F	ENSP00000300648:S1869F	S	-	2	0	GCN1L1	119065018	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.209000	0.95087	2.828000	0.97474	0.655000	0.94253	TCC	.	.		0.537	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			A	120580635	G	A	120580635	3	1	54	1	0	0	0	0	1	0	0	0	6307	1174	41	3	2473	3	GCN1L1	12	120580635	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	63541985	120580635	13271260	75	6867										
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130927134	130927134	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ccccagcgtgcttgccaaccGcgactcgttgtcctgcacaa	9	17	0	0	rs549158714		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr12:130927134G>T	ENST00000261655.4	-	8	875	c.712C>A	c.(712-714)Cgg>Agg	p.R238R	RIMBP2_ENST00000536002.1_Silent_p.R146R|RIMBP2_ENST00000535703.1_Silent_p.R146R	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	238					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CTTGCCAACCGCGACTCGTTG	0.587																																					p.R238R		Atlas-SNP	.											RIMBP2,rectum,carcinoma,0,3	RIMBP2	220	.	0			c.C712A						.						130	129	129					12																	130927134		2203	4300	6503	SO:0001819	synonymous_variant	23504	exon8			CCAACCGCGACTC	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.712C>A	chr12.hg19:g.130927134G>T		217.0	0.0		428.0	152.0	NM_015347	Q96ID2	Silent	SNP	ENST00000261655.4	hg19	CCDS31925.1																																																																																			.	.		0.587	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		T	130927134	G	T	130927134	2	4	54	1	0	0	0	0	0	0	0	1	13378	1086	38	1		1	RIMBP2	12	130927134	Silent	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	10346499	130927134	2924761	76	6868										
LNX2	222484	hgsc.bcm.edu	37	chr13	28143356	28143356	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tcattctcaatctctgcttgAgttctactagttttccttct	4	11	5	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr13:28143356A>C	ENST00000316334.3	-	3	594	c.465T>G	c.(463-465)acT>acG	p.T155T		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	155					protein homooligomerization (GO:0051260)		zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		TCTCTGCTTGAGTTCTACTAG	0.463																																					p.T155T		Atlas-SNP	.											.	LNX2	70	.	0			c.T465G						.						208	212	211					13																	28143356		2203	4300	6503	SO:0001819	synonymous_variant	222484	exon3			TGCTTGAGTTCTA	AL138699	CCDS9323.1	13q12.2	2013-01-09	2004-01-22	2004-01-23	ENSG00000139517	ENSG00000139517		"RING-type (C3HC4) zinc fingers"	20421	protein-coding gene	gene with protein product		609733	"PDZ domain containing ring finger 1"	PDZRN1			Standard	NM_153371		Approved	MGC46315	uc001url.4	Q8N448	OTTHUMG00000016634	ENST00000316334.3:c.465T>G	chr13.hg19:g.28143356A>C		290.0	0.0		136.0	68.0	NM_153371	Q5W0P0|Q6ZMH2|Q96SH4	Silent	SNP	ENST00000316334.3	hg19	CCDS9323.1																																																																																			.	.		0.463	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2			C	28143356	A	C	28143356	2	2	54	1	0	0	0	0	0	0	0	1	8875	291	11	5		5	LNX2	13	28143356	Silent	SNP	A	TCGA-CC-5258-01A-01D-A12Z-10		28143356	87026522	77	6869										
POSTN	10631	hgsc.bcm.edu	37	chr13	38158220	38158220	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ggtggtttgctgttttccagCcagctcaataacttgtttgg	11	8	1	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr13:38158220C>T	ENST00000379747.4	-	9	1246	c.1129G>A	c.(1129-1131)Gct>Act	p.A377T	POSTN_ENST00000379743.4_Missense_Mutation_p.A377T|POSTN_ENST00000541481.1_Missense_Mutation_p.A377T|POSTN_ENST00000379742.4_Missense_Mutation_p.A377T|POSTN_ENST00000379749.4_Missense_Mutation_p.A377T|POSTN_ENST00000541179.1_Missense_Mutation_p.A377T	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	377	FAS1 3. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TGTTTTCCAGCCAGCTCAATA	0.428																																					p.A377T		Atlas-SNP	.											.	POSTN	161	.	0			c.G1129A						.						109	86	94					13																	38158220		2203	4300	6503	SO:0001583	missense	10631	exon9			TTCCAGCCAGCTC	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1129G>A	chr13.hg19:g.38158220C>T	ENSP00000369071:p.Ala377Thr	100.0	0.0		86.0	18.0	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	hg19	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.504838	0.85176	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.91631	-2.86;-2.88;-2.88;-2.88;-2.88;-2.88	5.81	5.81	0.92471	FAS1 domain (2);	0.326694	0.36167	N	0.002744	D	0.93324	0.7872	L	0.52905	1.665	0.32023	N	0.600508	B;B;B;P;P;B;B	0.39920	0.425;0.411;0.136;0.695;0.51;0.38;0.136	B;B;B;P;B;B;B	0.51297	0.248;0.431;0.171;0.665;0.349;0.322;0.171	D	0.90345	0.4362	10	0.13853	T	0.58	-4.8705	20.0912	0.97820	0.0:1.0:0.0:0.0	.	377;377;377;377;377;377;377	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	T	377	ENSP00000437959:A377T;ENSP00000369073:A377T;ENSP00000369071:A377T;ENSP00000369067:A377T;ENSP00000369066:A377T;ENSP00000437953:A377T	ENSP00000369066:A377T	A	-	1	0	POSTN	37056220	0.999000	0.42202	1.000000	0.80357	0.970000	0.65996	1.325000	0.33724	2.746000	0.94184	0.591000	0.81541	GCT	.	.		0.428	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		T	38158220	C	T	38158220	3	4	54	1	0	0	0	0	1	0	0	0	12268	739	26	3	1441	3	POSTN	13	38158220	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	10014864	38158220	77011658	78	6870										
FNDC3A	22862	hgsc.bcm.edu	37	chr13	49710511	49710511	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tccaactttagagatgaacgAtctagtaaaacatatgaacg	7	7	1	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr13:49710511A>G	ENST00000492622.2	+	6	839	c.534A>G	c.(532-534)cgA>cgG	p.R178R	FNDC3A_ENST00000398316.3_Silent_p.R122R|FNDC3A_ENST00000541916.1_Silent_p.R178R	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	178					fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		GAGATGAACGATCTAGTAAAA	0.378																																					p.R178R		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A534G						.						69	66	67					13																	49710511		2203	4300	6503	SO:0001819	synonymous_variant	22862	exon6			TGAACGATCTAGT	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"Fibronectin type III domain containing"	20296	protein-coding gene	gene with protein product		615794	"fibronectin type III domain containing 3"	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.534A>G	chr13.hg19:g.49710511A>G		241.0	1.0		133.0	59.0	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Silent	SNP	ENST00000492622.2	hg19	CCDS41886.1																																																																																			.	.		0.378	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		G	49710511	A	G	49710511	2	3	54	1	0	0	0	0	0	0	0	1	5977	320	12	2		2	FNDC3A	13	49710511	Silent	SNP	A	TCGA-CC-5258-01A-01D-A12Z-10	11552291	49710511	65459367	79	6871										
SPRY2	10253	hgsc.bcm.edu	37	chr13	80911451	80911451	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cctagcagtctctgttcagaGgagctgctgctggtacttgt	12	10	2	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr13:80911451G>C	ENST00000377102.1	-	2	1367	c.390C>G	c.(388-390)tcC>tcG	p.S130S	SPRY2_ENST00000377104.3_Silent_p.S130S|SPRY2_ENST00000540649.1_Silent_p.S130S			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	130	Poly-Ser.				bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of mitotic spindle orientation (GO:0000132)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inner ear morphogenesis (GO:0042472)|lung growth (GO:0060437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|sensory perception of sound (GO:0007605)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase inhibitor activity (GO:0030291)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	12	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		TCTGTTCAGAGGAGCTGCTGC	0.567																																					p.S130S		Atlas-SNP	.											.	SPRY2	28	.	0			c.C390G						.						109	99	102					13																	80911451		2203	4300	6503	SO:0001819	synonymous_variant	10253	exon2			TTCAGAGGAGCTG	AF039843	CCDS9463.1	13q31.1	2008-05-14	2001-11-28		ENSG00000136158	ENSG00000136158			11270	protein-coding gene	gene with protein product		602466	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005842		Approved	hSPRY2	uc001vlj.3	O43597	OTTHUMG00000017140	ENST00000377102.1:c.390C>G	chr13.hg19:g.80911451G>C		87.0	0.0		183.0	26.0	NM_005842	B2R9J9|Q5T6Z7	Silent	SNP	ENST00000377102.1	hg19	CCDS9463.1																																																																																			.	.		0.567	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1			C	80911451	G	C	80911451	2	2	54	1	0	0	0	0	0	0	0	1	15121	987	35	4		4	SPRY2	13	80911451	Silent	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	31200940	80911451	34258427	80	6872										
OR4K14	122740	hgsc.bcm.edu	37	chr14	20483095	20483095	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	atgagtttttgatcactaagGaaatccctgatcatcttggg	9	7	3	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr14:20483095G>T	ENST00000305045.2	-	1	257	c.258C>A	c.(256-258)ttC>ttA	p.F86L		NM_001004712.1	NP_001004712.1	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K, member 14	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(20)|skin(6)	37	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)		GATCACTAAGGAAATCCCTGA	0.507																																					p.F86L		Atlas-SNP	.											.	OR4K14	86	.	0			c.C258A						.						97	88	91					14																	20483095		2203	4300	6503	SO:0001583	missense	122740	exon1			ACTAAGGAAATCC		CCDS32027.1	14q11.2	2013-09-23			ENSG00000169484	ENSG00000169484		"GPCR / Class A : Olfactory receptors"	15352	protein-coding gene	gene with protein product							Standard	NM_001004712		Approved		uc010tky.2	Q8NGD5	OTTHUMG00000170780	ENST00000305045.2:c.258C>A	chr14.hg19:g.20483095G>T	ENSP00000305011:p.Phe86Leu	102.0	0.0		116.0	29.0	NM_001004712	Q6IEU1|Q96R71	Missense_Mutation	SNP	ENST00000305045.2	hg19	CCDS32027.1	.	.	.	.	.	.	.	.	.	.	.	9.728	1.161402	0.21538	.	.	ENSG00000169484	ENST00000305045	T	0.00912	5.55	4.04	-3.11	0.05299	GPCR, rhodopsin-like superfamily (1);	0.326573	0.22055	N	0.065245	T	0.00524	0.0017	N	0.10782	0.045	0.24601	N	0.993775	B	0.16802	0.019	B	0.17979	0.02	T	0.44817	-0.9303	10	0.02654	T	1	.	10.7225	0.46048	0.6162:0.0:0.3838:0.0	.	86	Q8NGD5	OR4KE_HUMAN	L	86	ENSP00000305011:F86L	ENSP00000305011:F86L	F	-	3	2	OR4K14	19552935	0.000000	0.05858	0.518000	0.27811	0.852000	0.48524	-2.379000	0.01067	-1.033000	0.03299	-0.438000	0.05819	TTC	.	.		0.507	OR4K14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410343.1			T	20483095	G	T	20483095	3	4	54	1	0	0	0	0	1	0	0	0	11078	1165	41	3	677	3	OR4K14	14	20483095	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10		20483095	86866445	81	6873										
PARP2	10038	hgsc.bcm.edu	37	chr14	20820469	20820469	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tgagaaggtgcctggaaaatAtgatatgctacagatggact	12	5	0	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr14:20820469A>G	ENST00000250416.5	+	7	629	c.602A>G	c.(601-603)tAt>tGt	p.Y201C	PARP2_ENST00000429687.3_Missense_Mutation_p.Y188C|PARP2_ENST00000527915.1_Missense_Mutation_p.Y201C	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	201					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		CCTGGAAAATATGATATGCTA	0.343								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.Y201C		Atlas-SNP	.											PARP2_ENST00000250416,NS,carcinoma,0,2	PARP2	92	.	0			c.A602G						.						107	97	100					14																	20820469		1842	4097	5939	SO:0001583	missense	10038	exon7			GAAAATATGATAT	AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484		"Poly (ADP-ribose) polymerases"	272	protein-coding gene	gene with protein product		607725	"ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2", "poly (ADP-ribose) polymerase family, member 2"	ADPRTL2		10329013, 18353725	Standard	NM_005484		Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000250416.5:c.602A>G	chr14.hg19:g.20820469A>G	ENSP00000250416:p.Tyr201Cys	72.0	0.0		99.0	27.0	NM_005484	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Missense_Mutation	SNP	ENST00000250416.5	hg19	CCDS41910.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.223462	0.79464	.	.	ENSG00000129484	ENST00000429687;ENST00000250416;ENST00000527915	T;T;T	0.33654	1.4;1.4;1.4	5.53	5.53	0.82687	WGR domain (1);	0.000000	0.85682	D	0.000000	T	0.59756	0.2217	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.63937	-0.6524	10	0.87932	D	0	-13.683	14.635	0.68682	1.0:0.0:0.0:0.0	.	188;201	Q9UGN5-2;Q9UGN5	.;PARP2_HUMAN	C	188;201;201	ENSP00000392972:Y188C;ENSP00000250416:Y201C;ENSP00000432283:Y201C	ENSP00000250416:Y201C	Y	+	2	0	PARP2	19890309	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.600000	0.82769	2.106000	0.64143	0.460000	0.39030	TAT	.	.		0.343	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2			G	20820469	A	G	20820469	3	3	54	1	0	0	0	0	1	0	0	0	11470	449	16	2	628	2	PARP2	14	20820469	Missense_Mutation	SNP	A	TCGA-CC-5258-01A-01D-A12Z-10	337374	20820469	86529071	82	6874										
PRKCH	5583	hgsc.bcm.edu	37	chr14	61997206	61997206	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	atgagatgctctgtggtcacGcgccttttgaggcagagaac	13	9	2	3			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr14:61997206G>T	ENST00000332981.5	+	12	2039	c.1654G>T	c.(1654-1656)Gcg>Tcg	p.A552S	PRKCH_ENST00000555082.1_Missense_Mutation_p.A391S|RP11-47I22.4_ENST00000556347.1_Silent_p.T56T	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	552	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		CTGTGGTCACGCGCCTTTTGA	0.552																																					p.A552S	Melanoma(135;863 1779 8064 14443 26348)	Atlas-SNP	.											PRKCH,colon,carcinoma,-1,1	PRKCH	89	.	0			c.G1654T						.						225	180	195					14																	61997206		2203	4300	6503	SO:0001583	missense	5583	exon12			GGTCACGCGCCTT	M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.1654G>T	chr14.hg19:g.61997206G>T	ENSP00000329127:p.Ala552Ser	155.0	0.0		163.0	26.0	NM_006255	B4DJN5|Q16246|Q8NE03	Missense_Mutation	SNP	ENST00000332981.5	hg19	CCDS9752.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.588420	0.28357	.	.	ENSG00000027075	ENST00000555185;ENST00000332981;ENST00000555082	T;T;T	0.65549	-0.16;1.88;1.88	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000011	T	0.62877	0.2464	N	0.17345	0.48	0.80722	D	1	D	0.53312	0.959	D	0.67548	0.952	T	0.54364	-0.8305	10	0.02654	T	1	.	19.6972	0.96030	0.0:0.0:1.0:0.0	.	552	P24723	KPCL_HUMAN	S	120;552;391	ENSP00000451871:A120S;ENSP00000329127:A552S;ENSP00000450981:A391S	ENSP00000329127:A552S	A	+	1	0	PRKCH	61066959	1.000000	0.71417	0.268000	0.24571	0.241000	0.25554	4.418000	0.59828	2.663000	0.90544	0.650000	0.86243	GCG	.	.		0.552	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255		T	61997206	G	T	61997206	3	4	54	1	0	0	0	0	1	0	0	0	12525	1087	38	1	1700	1	PRKCH	14	61997206	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	41176737	61997206	45352334	83	6875										
LTBP2	4053	hgsc.bcm.edu	37	chr14	74995708	74995708	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	actcgctgccccatgctttgCccacgcggctgcagcagcat	10	17	0	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr14:74995708C>A	ENST00000261978.4	-	11	2491	c.2105G>T	c.(2104-2106)gGc>gTc	p.G702V	LTBP2_ENST00000556690.1_Missense_Mutation_p.G702V	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	702	TB 2.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CCATGCTTTGCCCACGCGGCT	0.637																																					p.G702V		Atlas-SNP	.											LTBP2,NS,carcinoma,0,1	LTBP2	158	.	0			c.G2105T						.						32	26	28					14																	74995708		2201	4299	6500	SO:0001583	missense	4053	exon11			GCTTTGCCCACGC		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.2105G>T	chr14.hg19:g.74995708C>A	ENSP00000261978:p.Gly702Val	97.0	1.0		190.0	80.0	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	hg19	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.809856	0.90707	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	D;D	0.96104	-3.91;-3.91	5.35	5.35	0.76521	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.42964	D	0.000637	D	0.98030	0.9351	M	0.91510	3.215	0.80722	D	1	D	0.67145	0.996	D	0.63597	0.916	D	0.98626	1.0669	10	0.72032	D	0.01	.	18.0607	0.89377	0.0:1.0:0.0:0.0	.	702	Q14767	LTBP2_HUMAN	V	702	ENSP00000261978:G702V;ENSP00000451477:G702V	ENSP00000261978:G702V	G	-	2	0	LTBP2	74065461	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.287000	0.65645	2.804000	0.96469	0.650000	0.86243	GGC	.	.		0.637	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		A	74995708	C	A	74995708	3	1	54	1	0	0	0	0	1	0	0	0	9083	739	26	3	3464	3	LTBP2	14	74995708	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	12998502	74995708	32353832	84	6876										
C14orf174	161394	hgsc.bcm.edu	37	chr14	77844990	77844990	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tctagagttaccagatgaaaCcaaaccaagggagacacatg	9	9	1	4			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr14:77844990C>T	ENST00000216471.4	+	1	1515	c.1229C>T	c.(1228-1230)aCc>aTc	p.T410I	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	410										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CCAGATGAAACCAAACCAAGG	0.438																																					p.T410I		Atlas-SNP	.											.	SAMD15	60	.	0			c.C1229T						.						78	75	76					14																	77844990		2203	4300	6503	SO:0001583	missense	161394	exon1			ATGAAACCAAACC	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"Sterile alpha motif (SAM) domain containing"	18631	protein-coding gene	gene with protein product			"family with sequence similarity 15, member A", "chromosome 14 open reading frame 174"	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.1229C>T	chr14.hg19:g.77844990C>T	ENSP00000216471:p.Thr410Ile	295.0	0.0		417.0	84.0	NM_001010860	Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	hg19	CCDS32126.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.877404	0.33162	.	.	ENSG00000100583	ENST00000216471	T	0.18810	2.19	5.6	1.71	0.24356	.	1.066930	0.07477	N	0.903237	T	0.10895	0.0266	N	0.12182	0.205	0.09310	N	1	B	0.32245	0.361	B	0.29942	0.109	T	0.31752	-0.9932	10	0.39692	T	0.17	2.4634	4.0072	0.09607	0.1648:0.5723:0.0:0.2628	.	410	Q9P1V8	SAM15_HUMAN	I	410	ENSP00000216471:T410I	ENSP00000216471:T410I	T	+	2	0	SAMD15	76914743	0.000000	0.05858	0.001000	0.08648	0.304000	0.27724	0.083000	0.14871	0.045000	0.15804	0.555000	0.69702	ACC	.	.		0.438	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		T	77844990	C	T	77844990	3	4	54	1	0	0	0	0	1	0	0	0	1761	507	18	3	1231	3	C14orf174	14	77844990	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	2849282	77844990	29504550	85	6877										
TGM7	116179	hgsc.bcm.edu	37	chr15	43571883	43571883	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gaagggcttctgggtaccacCcccatgcagcagggcctgtg	14	13	1	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr15:43571883C>T	ENST00000452443.2	-	10	1622	c.1618G>A	c.(1618-1620)Ggt>Agt	p.G540S		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	540					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	TGGGTACCACCCCCATGCAGC	0.642																																					p.G540S		Atlas-SNP	.											.	TGM7	86	.	0			c.G1618A						.						93	94	94					15																	43571883		2202	4299	6501	SO:0001583	missense	116179	exon10			TACCACCCCCATG	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1618G>A	chr15.hg19:g.43571883C>T	ENSP00000389466:p.Gly540Ser	32.0	0.0		70.0	21.0	NM_052955		Missense_Mutation	SNP	ENST00000452443.2	hg19	CCDS32213.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.607287	0.46527	.	.	ENSG00000159495	ENST00000452443	T	0.68331	-0.32	4.69	4.69	0.59074	Transglutaminase, C-terminal (1);Immunoglobulin-like fold (1);	0.121727	0.56097	D	0.000026	T	0.71702	0.3371	M	0.78801	2.425	0.19300	N	0.999973	D	0.59767	0.986	P	0.48304	0.573	T	0.69323	-0.5175	10	0.59425	D	0.04	-12.9329	13.0102	0.58727	0.0:1.0:0.0:0.0	.	540	Q96PF1	TGM7_HUMAN	S	540	ENSP00000389466:G540S	ENSP00000389466:G540S	G	-	1	0	TGM7	41359175	0.137000	0.22531	0.076000	0.20297	0.693000	0.40251	1.492000	0.35594	2.427000	0.82271	0.655000	0.94253	GGT	.	.		0.642	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		T	43571883	C	T	43571883	3	4	54	1	0	0	0	0	1	0	0	0	15850	623	22	3	530	3	TGM7	15	43571883	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10		43571883	58959509	86	6878										
LEO1	123169	hgsc.bcm.edu	37	chr15	52258056	52258056	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tctcttcatcagacagctgtGgttgttcttcatcatcagaa	7	10	7	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr15:52258056G>C	ENST00000299601.5	-	2	764	c.704C>G	c.(703-705)cCa>cGa	p.P235R	LEO1_ENST00000315141.5_Missense_Mutation_p.P235R	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	235	Asp-rich.				endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		AGACAGCTGTGGTTGTTCTTC	0.423																																					p.P235R	Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)	Atlas-SNP	.											.	LEO1	46	.	0			c.C704G						.						246	246	246					15																	52258056		2195	4293	6488	SO:0001583	missense	123169	exon2			AGCTGTGGTTGTT	AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.704C>G	chr15.hg19:g.52258056G>C	ENSP00000299601:p.Pro235Arg	545.0	0.0		563.0	96.0	NM_138792	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	hg19	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.003248	0.35320	.	.	ENSG00000166477	ENST00000299601;ENST00000315141	.	.	.	4.84	4.84	0.62591	.	0.261206	0.40818	N	0.001011	T	0.42517	0.1206	N	0.16478	0.41	0.80722	D	1	B;B	0.11235	0.004;0.001	B;B	0.09377	0.004;0.001	T	0.24835	-1.0149	9	0.18276	T	0.48	.	18.1449	0.89651	0.0:0.0:1.0:0.0	.	235;235	Q8WVC0-2;Q8WVC0	.;LEO1_HUMAN	R	235	.	ENSP00000299601:P235R	P	-	2	0	LEO1	50045348	0.997000	0.39634	0.555000	0.28281	0.965000	0.64279	3.722000	0.54948	2.509000	0.84616	0.655000	0.94253	CCA	.	.		0.423	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792		C	52258056	G	C	52258056	3	2	54	1	0	0	0	0	1	0	0	0	8735	1348	47	4	1340	4	LEO1	15	52258056	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	8686173	52258056	50273336	87	6879										
TTLL13	440307	hgsc.bcm.edu	37	chr15	90799374	90799374	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	aggccctctctgcacatagcTatggggacttccagtcctac	9	14	1	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr15:90799374T>A	ENST00000339615.5	+	6	840	c.550T>A	c.(550-552)Tat>Aat	p.Y184N	TTLL13_ENST00000438251.1_Splice_Site_p.Y184N|RP11-697E2.6_ENST00000561573.1_Intron	NM_001029964.2	NP_001025135.2			tubulin tyrosine ligase-like family, member 13											NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)	16	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)			TGCACATAGCTATGGGGACTT	0.547																																					p.Y184N		Atlas-SNP	.											.	TTLL13	44	.	0			c.T550A						.						80	77	78					15																	90799374		2199	4298	6497	SO:0001630	splice_region_variant	440307	exon6			CATAGCTATGGGG	BC036668		15q26.1	2013-02-14				ENSG00000213471		"Tubulin tyrosine ligase-like family"	32484	protein-coding gene	gene with protein product						15890843	Standard	NR_104604		Approved	FLJ46079, MGC33417	uc002bpd.1	A6NNM8		ENST00000339615.5:c.549-1T>A	chr15.hg19:g.90799374T>A		51.0	0.0		70.0	29.0	NM_001029964		Missense_Mutation	SNP	ENST00000339615.5	hg19	CCDS32328.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.172795	0.57584	.	.	ENSG00000213471	ENST00000438251;ENST00000339615	T;T	0.06142	3.34;3.34	5.18	5.18	0.71444	.	0.369213	0.26586	N	0.023546	T	0.22975	0.0555	M	0.83603	2.65	0.80722	D	1	P	0.45594	0.862	P	0.55455	0.776	T	0.00478	-1.1715	10	0.56958	D	0.05	.	14.3636	0.66789	0.0:0.0:0.0:1.0	.	184	A6NNM8-2	.	N	184	ENSP00000413362:Y184N;ENSP00000345294:Y184N	ENSP00000345294:Y184N	Y	+	1	0	TTLL13	88600378	1.000000	0.71417	0.963000	0.40424	0.267000	0.26476	5.619000	0.67729	2.184000	0.69523	0.459000	0.35465	TAT	.	.		0.547	TTLL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435854.1	NM_001029964	Missense_Mutation	A	90799374	T	A	90799374	5	1	54	1	0	0	0	0	0	0	1	0	16741	1536	53	4	568	4	TTLL13	15	90799374	Splice_Site	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	38541318	90799374	11732018	88	6880										
CIITA	4261	hgsc.bcm.edu	37	chr16	11001148	11001149	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gccctgacgctcctccgggaINSccggccacttcttctcagtc							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr16:11001148_11001149insC	ENST00000324288.8	+	11	1932_1933	c.1799_1800insC	c.(1798-1803)gaccggfs	p.R601fs	CIITA_ENST00000381835.5_Intron|CIITA_ENST00000537380.1_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	601	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						CTCCTCCGGGACCGGCCACTTC	0.624			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.D600fs		Atlas-INDEL	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.1799_1800insC						.																																			SO:0001589	frameshift_variant	4261	exon11			.	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.1801dupC	chr16.hg19:g.11001150_11001150dupC	ENSP00000316328:p.Arg601fs	108.0	0.0		171.0	12.0	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Frame_Shift_Ins	INS	ENST00000324288.8	hg19	CCDS10544.1																																																																																			.	.		0.624	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		C	11001149	-	C	11001148	7	5	54	1	0	1	1	0	0	0	0	0	3430	275	10	0	1841	0	CIITA	16	11001148	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10		11001148	79353605	89	6881										
SLC12A3	6559	hgsc.bcm.edu	37	chr16	56920341	56920341	+	Frame_Shift_Del	DEL	C	C	-													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cctggtggactttgtgggcaCcttcacccggaacctcagcc							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr16:56920341delC	ENST00000563236.1	+	16	2016	c.1991delC	c.(1990-1992)accfs	p.T664fs	SLC12A3_ENST00000262502.5_Frame_Shift_Del_p.T663fs|SLC12A3_ENST00000438926.2_Frame_Shift_Del_p.T664fs|SLC12A3_ENST00000566786.1_Frame_Shift_Del_p.T663fs			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	664					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	TTTGTGGGCACCTTCACCCGG	0.657																																					p.T664fs		Atlas-Indel,Pindel	.											.	SLC12A3	99	.	0			c.1990delA						.						55	55	55					16																	56920341		2198	4300	6498	SO:0001589	frameshift_variant	6559	exon16			.		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"Solute carriers"	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.1991delC	chr16.hg19:g.56920341delC	ENSP00000456149:p.Thr664fs	46.0	0.0		73.0	38.0	NM_001126108	A8MSJ2|C9JNN9	Frame_Shift_Del	DEL	ENST00000563236.1	hg19	CCDS58464.1																																																																																			.	.		0.657	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			-	56920341	C	-	56920341	7	5	54	1	0	1	0	1	0	0	0	0	14399	507	18	0	2053	0	SLC12A3	16	56920341	Frame_Shift_Del	DEL	C	TCGA-CC-5258-01A-01D-A12Z-10	45919193	56920341	33434412	90	6882										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70884513	70884513	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ttgcagatcaaattaaagttCacatctccttcctgctttgg	6	10	3	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr16:70884513C>G	ENST00000393567.2	-	74	12639	c.12489G>C	c.(12487-12489)gtG>gtC	p.V4163V	RNU6ATAC25P_ENST00000408798.1_RNA	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4163					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				AATTAAAGTTCACATCTCCTT	0.428																																					p.V4163V		Atlas-SNP	.											.	HYDIN	788	.	0			c.G12489C						.						75	65	68					16																	70884513		1856	4104	5960	SO:0001819	synonymous_variant	54768	exon74			AAAGTTCACATCT	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.12489G>C	chr16.hg19:g.70884513C>G		173.0	0.0		68.0	34.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	hg19	CCDS59269.1																																																																																			.	.		0.428	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			G	70884513	C	G	70884513	2	3	54	1	0	0	0	0	0	0	0	1	7476	813	29	4		4	HYDIN	16	70884513	Silent	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	13964172	70884513	19470240	91	6883										
GPS2	2874	hgsc.bcm.edu	37	chr17	7216697	7216697	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ctcctgcatgggatgttatcAcctgtctgagtgggctgaaa	12	9	2	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr17:7216697A>G	ENST00000380728.2	-	8	1025		c.e8+1		RP11-542C16.2_ENST00000575474.1_Splice_Site|GPS2_ENST00000389167.5_Splice_Site|GPS2_ENST00000391950.3_Splice_Site			Q13227	GPS2_HUMAN	G protein pathway suppressor 2						cell cycle (GO:0007049)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase inhibitor activity (GO:0005095)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(4)	24		Prostate(122;0.157)				GGATGTTATCACCTGTCTGAG	0.557											OREG0024133	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	GPS2	44	.	0			c.724+2T>C						.						99	102	101					17																	7216697		2203	4300	6503	SO:0001630	splice_region_variant	2874	exon9			GTTATCACCTGTC	U28963	CCDS11100.1	17p13.1	2006-04-29			ENSG00000132522	ENSG00000132522			4550	protein-coding gene	gene with protein product		601935				8943324	Standard	NM_004489		Approved		uc002gfx.1	Q13227	OTTHUMG00000102198	ENST00000380728.2:c.724+1T>C	chr17.hg19:g.7216697A>G		97.0	0.0	640	98.0	51.0	NM_004489	B4DXA1|Q6FHM8	Splice_Site	SNP	ENST00000380728.2	hg19	CCDS11100.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.044178	0.55110	.	.	ENSG00000132522	ENST00000391950;ENST00000380728;ENST00000389167;ENST00000315601	.	.	.	3.67	3.67	0.42095	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6611	0.45702	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GPS2	7157421	0.999000	0.42202	1.000000	0.80357	0.958000	0.62258	4.623000	0.61247	1.899000	0.54978	0.523000	0.50628	.	.	.		0.557	GPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220048.4	NM_004489	Intron	G	7216697	A	G	7216697	5	3	54	1	0	0	0	0	0	0	1	0	6742	173	6	2	273	2	GPS2	17	7216697	Splice_Site	SNP	A	TCGA-CC-5258-01A-01D-A12Z-10		7216697	73978513	92	6884										
TP53	7157	hgsc.bcm.edu	37	chr17	7577150	7577150	+	Frame_Shift_Del	DEL	T	T	-													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	agctgttccgtcccagtagaTtaccactactcaggatagga							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr17:7577150delT	ENST00000269305.4	-	8	977	c.788delA	c.(787-789)aatfs	p.N263fs	TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Frame_Shift_Del_p.N263fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.N263fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.N263fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.N263fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	263	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		GN -> PD (in a sporadic cancer; somatic mutation).|N -> D (in sporadic cancers; somatic mutation).|N -> H (in sporadic cancers; somatic mutation).|N -> I (in sporadic cancers; somatic mutation).|N -> K (in a sporadic cancer; somatic mutation).|N -> S (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.N263I(2)|p.G262_S269delGNLLGRNS(2)|p.N263fs*5(1)|p.E258fs*71(1)|p.S261_L264>R(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCCCAGTAGATTACCACTACT	0.517		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.N263fs	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53,colon,carcinoma,-1,1	TP53	33396	.	21	Whole gene deletion(8)|Deletion - In frame(4)|Unknown(3)|Deletion - Frameshift(3)|Substitution - Missense(2)|Complex - deletion inframe(1)	bone(4)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|lung(2)|ovary(2)|eye(1)|urinary_tract(1)|stomach(1)	c.789delT						.						43	39	40					17																	7577150		2203	4299	6502	SO:0001589	frameshift_variant	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.788delA	chr17.hg19:g.7577150delT	ENSP00000269305:p.Asn263fs	65.0	0.0		70.0	33.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.517	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7577150	T	-	7577150	7	5	54	1	0	1	0	1	0	0	0	0	16396	1493	52	0	498	0	TP53	17	7577150	Frame_Shift_Del	DEL	T	TCGA-CC-5258-01A-01D-A12Z-10	360453	7577150	73618060	93	6885										
ALOX15B	247	hgsc.bcm.edu	37	chr17	7950032	7950032	+	Frame_Shift_Del	DEL	C	C	-													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cctgcacatcaacacactcgCccgggagctgcttatcgtgc					rs140152561		TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr17:7950032delC	ENST00000380183.4	+	9	1386	c.1247delC	c.(1246-1248)gccfs	p.A416fs	ALOX15B_ENST00000380173.2_Intron|ALOX15B_ENST00000573359.1_Intron|ALOX15B_ENST00000572022.1_Frame_Shift_Del_p.A416fs	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	416	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						AACACACTCGCCCGGGAGCTG	0.602																																					p.A416fs		Atlas-INDEL	.											.	ALOX15B	66	.	0			c.1246delG						.						66	55	59					17																	7950032		2203	4300	6503	SO:0001589	frameshift_variant	247	exon9			.	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"Arachidonate lipoxygenases"	434	protein-coding gene	gene with protein product		603697	"arachidonate 15-lipoxygenase, second type"			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1247delC	chr17.hg19:g.7950032delC	ENSP00000369530:p.Ala416fs	54.0	0.0		64.0	11.0	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Frame_Shift_Del	DEL	ENST00000380183.4	hg19	CCDS11128.1																																																																																			.	.		0.602	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2			-	7950032	C	-	7950032	7	5	54	1	0	1	0	1	0	0	0	0	539	739	26	0	1281	0	ALOX15B	17	7950032	Frame_Shift_Del	DEL	C	TCGA-CC-5258-01A-01D-A12Z-10	372882	7950032	73245178	94	6886										
PIGS	94005	hgsc.bcm.edu	37	chr17	26898507	26898508	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tgtagccgcagccccggcggINSccgccatgctagcttccggc							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr17:26898507_26898508insC	ENST00000308360.7	-	1	382_383	c.7_8insG	c.(7-9)gccfs	p.A3fs	PIGS_ENST00000395346.2_5'UTR|RP11-192H23.5_ENST00000585189.1_RNA|PIGS_ENST00000543734.1_5'UTR	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	3					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					AGCCCCGGCGGCCGCCATGCTA	0.688																																					p.A3fs		Atlas-INDEL	.											.	PIGS	42	.	0			c.8_9insG						.																																			SO:0001589	frameshift_variant	94005	exon1			.		CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"Phosphatidylinositol glycan anchor biosynthesis"	14937	protein-coding gene	gene with protein product	"GPI transamidase subunit"	610271	"phosphatidylinositol glycan, class S"				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.8dupG	chr17.hg19:g.26898509_26898509dupC	ENSP00000309430:p.Ala3fs	90.0	0.0		215.0	19.0	NM_033198	Q6UVX6	Frame_Shift_Ins	INS	ENST00000308360.7	hg19	CCDS11235.1																																																																																			.	.		0.688	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198		C	26898508	-	C	26898507	7	5	54	1	0	1	1	0	0	0	0	0	11907	1203	42	0	1707	0	PIGS	17	26898507	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	18948475	26898507	54296703	95	6887										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26967658	26967658	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tctggcagctgctggagaagGaataggccaggcagagttgg	17	7	1	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr17:26967658G>A	ENST00000528896.2	-	8	884	c.810C>T	c.(808-810)ttC>ttT	p.F270F	KIAA0100_ENST00000389003.3_Silent_p.F127F|KIAA0100_ENST00000544884.1_Silent_p.F127F	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	270						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					GCTGGAGAAGGAATAGGCCAG	0.448																																					p.F270F		Atlas-SNP	.											.	KIAA0100	175	.	0			c.C810T						.						128	120	123					17																	26967658		2203	4300	6503	SO:0001819	synonymous_variant	9703	exon8			GAGAAGGAATAGG	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.810C>T	chr17.hg19:g.26967658G>A		251.0	0.0		372.0	127.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Silent	SNP	ENST00000528896.2	hg19	CCDS32595.1																																																																																			.	.		0.448	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		A	26967658	G	A	26967658	2	1	54	1	0	0	0	0	0	0	0	1	8163	1165	41	3		3	KIAA0100	17	26967658	Silent	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	69151	26967658	54227552	96	6888										
LYZL6	57151	hgsc.bcm.edu	37	chr17	34266279	34266279	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ctccagctgcagcacctgggCcaagtcacagcgactgatga	11	14	1	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr17:34266279C>T	ENST00000585556.1	-	2	416	c.82G>A	c.(82-84)Gcc>Acc	p.A28T	LYZL6_ENST00000492340.2_5'Flank|LYZL6_ENST00000293274.4_Missense_Mutation_p.A28T|LYZL6_ENST00000394523.3_Missense_Mutation_p.A28T			O75951	LYZL6_HUMAN	lysozyme-like 6	28					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	12				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGCACCTGGGCCAAGTCACAG	0.562																																					p.A28T		Atlas-SNP	.											.	LYZL6	18	.	0			c.G82A						.						107	100	103					17																	34266279		2203	4300	6503	SO:0001583	missense	57151	exon1			CCTGGGCCAAGTC	AF088219, AY742214	CCDS11302.1	17q11.2	2014-04-10			ENSG00000161572	ENSG00000275722			29614	protein-coding gene	gene with protein product		612751				10213461	Standard	NM_020426		Approved	LYC1, PRO1485, TKAL754	uc002hkj.2	O75951	OTTHUMG00000188400	ENST00000585556.1:c.82G>A	chr17.hg19:g.34266279C>T	ENSP00000468094:p.Ala28Thr	84.0	0.0		59.0	28.0	NM_020426	Q6UW30	Missense_Mutation	SNP	ENST00000585556.1	hg19	CCDS11302.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.396060	0.83011	.	.	ENSG00000161572	ENST00000293274;ENST00000394523	T;T	0.54675	0.56;0.56	5.29	5.29	0.74685	Lysozyme-like domain (1);	0.270354	0.30455	N	0.009588	T	0.72187	0.3429	M	0.81112	2.525	0.44807	D	0.997812	D	0.65815	0.995	D	0.65573	0.936	T	0.75786	-0.3195	10	0.72032	D	0.01	-7.5879	14.8301	0.70142	0.0:1.0:0.0:0.0	.	28	O75951	LYZL6_HUMAN	T	28	ENSP00000293274:A28T;ENSP00000378031:A28T	ENSP00000293274:A28T	A	-	1	0	LYZL6	31290392	0.996000	0.38824	0.959000	0.39883	0.729000	0.41735	2.433000	0.44793	2.646000	0.89796	0.655000	0.94253	GCC	.	.		0.562	LYZL6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256578.2	NM_020426		T	34266279	C	T	34266279	3	4	54	1	0	0	0	0	1	0	0	0	9143	739	26	3	380	3	LYZL6	17	34266279	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	7298621	34266279	46928931	97	6889										
ACACA	31	hgsc.bcm.edu	37	chr17	35538246	35538246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ggtcacatatggagtattgaTtaacattccatgcagtggtc	10	7	1	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr17:35538246T>C	ENST00000394406.2	-	40	4907	c.4717A>G	c.(4717-4719)Atc>Gtc	p.I1573V	ACACA_ENST00000335166.5_Missense_Mutation_p.I1495V|ACACA_ENST00000360679.3_Missense_Mutation_p.I1515V|ACACA_ENST00000353139.5_Missense_Mutation_p.I1610V	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1573					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	GGAGTATTGATTAACATTCCA	0.408																																					p.I1610V	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.A4828G						.						204	187	193					17																	35538246		2203	4300	6503	SO:0001583	missense	31	exon40			TATTGATTAACAT	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.4717A>G	chr17.hg19:g.35538246T>C	ENSP00000377928:p.Ile1573Val	345.0	0.0		224.0	112.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	hg19	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.777983	0.31502	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166;ENST00000427330	D;D;D;D	0.94497	-3.44;-3.43;-3.44;-3.43	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.88782	0.6530	L	0.31476	0.935	0.80722	D	1	B;P;B;B	0.39480	0.296;0.675;0.015;0.026	B;B;B;B	0.37601	0.101;0.254;0.016;0.035	D	0.87674	0.2543	10	0.02654	T	1	-15.0967	15.6571	0.77150	0.0:0.0:0.0:1.0	.	321;1610;1573;1515	F8W6G0;Q13085-4;Q13085;Q13085-2	.;.;ACACA_HUMAN;.	V	1610;1515;1573;1597;1495;321	ENSP00000344789:I1610V;ENSP00000353898:I1515V;ENSP00000377928:I1573V;ENSP00000335323:I1495V	ENSP00000335323:I1495V	I	-	1	0	ACACA	32612359	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.993000	0.88291	2.161000	0.67846	0.528000	0.53228	ATC	.	.		0.408	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		C	35538246	T	C	35538246	3	2	54	1	0	0	0	0	1	0	0	0	106	1493	52	2	2391	2	ACACA	17	35538246	Missense_Mutation	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	1271967	35538246	45656964	98	6890										
HEATR6	63897	hgsc.bcm.edu	37	chr17	58156056	58156056	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ccagcagggcgcgccgcctaCctccggggccacgccactgc	13	20	0	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr17:58156056C>T	ENST00000184956.6	-	1	236		c.e1+1		HEATR6_ENST00000585712.1_Splice_Site|CTD-2319I12.2_ENST00000589740.1_lincRNA|HEATR6_ENST00000585976.1_Splice_Site	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6								poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			GCGCCGCCTACCTCCGGGGCC	0.711																																					.		Atlas-SNP	.											.	HEATR6	98	.	0			c.219+1G>A						.						8	7	7					17																	58156056		2071	4060	6131	SO:0001630	splice_region_variant	63897	exon2			CGCCTACCTCCGG	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"amplified in breast cancer 1"					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.219+1G>A	chr17.hg19:g.58156056C>T		14.0	0.0		38.0	14.0	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Splice_Site	SNP	ENST00000184956.6	hg19	CCDS11623.1	.	.	.	.	.	.	.	.	.	.	.	16.87	3.240773	0.58995	.	.	ENSG00000068097	ENST00000184956	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6658	0.62393	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HEATR6	55510838	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	4.277000	0.58939	2.479000	0.83701	0.558000	0.71614	.	.	.		0.711	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070	Intron	T	58156056	C	T	58156056	5	4	54	1	0	0	0	0	0	0	1	0	7042	521	18	3	3405	3	HEATR6	17	58156056	Splice_Site	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	22617810	58156056	23039154	99	6891										
ASPSCR1	79058	hgsc.bcm.edu	37	chr17	79954362	79954363	+	Frame_Shift_Ins	INS	-	-	G													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tgggctcgtcagcgtcggctINSggccaggcagccgccagcgc							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr17:79954362_79954363insG	ENST00000306739.4	+	7	670_671	c.573_574insG	c.(574-576)ggcfs	p.G192fs	ASPSCR1_ENST00000306729.7_Frame_Shift_Ins_p.G192fs|ASPSCR1_ENST00000580534.1_Frame_Shift_Ins_p.G115fs	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	192					glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			CAGCGTCGGCTGGCCAGGCAGC	0.668			T	TFE3	alveolar soft part sarcoma																																p.A191fs		Atlas-INDEL	.		Dom	yes		17	17q25	79058	"alveolar soft part sarcoma chromosome region, candidate 1"		M	.	ASPSCR1	27	.	0			c.573_574insG						.																																			SO:0001589	frameshift_variant	79058	exon7			.	AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"UBX domain containing"	13825	protein-coding gene	gene with protein product	"UBX domain protein 9"	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.575dupG	chr17.hg19:g.79954364_79954364dupG	ENSP00000302176:p.Gly192fs	43.0	0.0		79.0	10.0	NM_024083	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Frame_Shift_Ins	INS	ENST00000306739.4	hg19	CCDS11796.1																																																																																			.	.		0.668	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083		G	79954363	-	G	79954362	7	5	54	1	0	1	1	0	0	0	0	0	1059	1567	55	0	599	0	ASPSCR1	17	79954362	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	21798306	79954362	1240848	100	6892										
PTPRM	5797	hgsc.bcm.edu	37	chr18	8088802	8088802	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ttgaatcaaactgacaatacCgtgacagtcatgctgaaacc	7	10	2	4			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr18:8088802C>T	ENST00000332175.8	+	11	2846	c.1809C>T	c.(1807-1809)acC>acT	p.T603T	PTPRM_ENST00000400060.4_Silent_p.T603T|PTPRM_ENST00000400053.4_Silent_p.T541T|PTPRM_ENST00000580170.1_Silent_p.T603T|PTPRM_ENST00000444013.1_Silent_p.T390T|PTPRM_ENST00000578571.1_3'UTR	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	603	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.T603T(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CTGACAATACCGTGACAGTCA	0.463																																					p.T603T		Atlas-SNP	.											PTPRM,NS,carcinoma,0,1	PTPRM	185	.	1	Substitution - coding silent(1)	breast(1)	c.C1809T						.						123	108	113					18																	8088802		2203	4300	6503	SO:0001819	synonymous_variant	5797	exon11			CAATACCGTGACA	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.1809C>T	chr18.hg19:g.8088802C>T		123.0	1.0		67.0	29.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	hg19	CCDS11840.1																																																																																			.	.		0.463	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	8088802	C	T	8088802	2	4	54	1	0	0	0	0	0	0	0	1	12821	639	23	1		1	PTPRM	18	8088802	Silent	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10		8088802	69988446	101	6893										
DYM	54808	hgsc.bcm.edu	37	chr18	46860102	46860102	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	taaagtagaaacataccatgGacctcgcatcaaatacttgt	6	9	1	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr18:46860102G>A	ENST00000269445.6	-	7	1073	c.616C>T	c.(616-618)Cca>Tca	p.P206S	DYM_ENST00000442713.2_Intron|DYM_ENST00000578396.1_Missense_Mutation_p.P51S	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	206					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						ACATACCATGGACCTCGCATC	0.373																																					p.P206S		Atlas-SNP	.											.	DYM	52	.	0			c.C616T						.						103	99	100					18																	46860102		2203	4300	6503	SO:0001583	missense	54808	exon7			ACCATGGACCTCG	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.616C>T	chr18.hg19:g.46860102G>A	ENSP00000269445:p.Pro206Ser	80.0	0.0		80.0	12.0	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	hg19	CCDS11937.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.997369	0.35226	.	.	ENSG00000141627	ENST00000269445	D	0.81499	-1.5	4.43	4.43	0.53597	.	0.260980	0.39475	N	0.001351	T	0.69949	0.3168	N	0.16790	0.44	0.44771	D	0.997773	B;B	0.10296	0.003;0.002	B;B	0.11329	0.006;0.006	T	0.66164	-0.5992	10	0.45353	T	0.12	.	18.0098	0.89219	0.0:0.0:1.0:0.0	.	28;206	Q9NXS9;Q7RTS9	.;DYM_HUMAN	S	206	ENSP00000269445:P206S	ENSP00000269445:P206S	P	-	1	0	DYM	45114100	1.000000	0.71417	0.999000	0.59377	0.670000	0.39368	6.997000	0.76270	2.424000	0.82194	0.454000	0.30748	CCA	.	.		0.373	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		A	46860102	G	A	46860102	3	1	54	1	0	0	0	0	1	0	0	0	4842	1174	41	3	1437	3	DYM	18	46860102	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	38771300	46860102	31217146	102	6894										
GMIP	51291	hgsc.bcm.edu	37	chr19	19740822	19740822	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gacgtccgggcagcaggtggCcctgggcacagcctcgctgt	16	14	0	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr19:19740822C>T	ENST00000203556.4	-	21	3000	c.2863G>A	c.(2863-2865)Gcc>Acc	p.A955T	LPAR2_ENST00000407877.3_5'Flank|LPAR2_ENST00000542587.1_5'Flank|LPAR2_ENST00000589311.1_5'Flank|GMIP_ENST00000445806.2_Missense_Mutation_p.A926T|GMIP_ENST00000587238.1_Missense_Mutation_p.A929T|LPAR2_ENST00000586703.1_5'Flank	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	955					intracellular signal transduction (GO:0035556)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						CAGCAGGTGGCCCTGGGCACA	0.627																																					p.A955T		Atlas-SNP	.											.	GMIP	55	.	0			c.G2863A						.						17	17	17					19																	19740822		2203	4300	6503	SO:0001583	missense	51291	exon21			AGGTGGCCCTGGG	AF132541	CCDS12408.1, CCDS74318.1	19p13.11	2011-09-07				ENSG00000089639		"Rho GTPase activating proteins"	24852	protein-coding gene	gene with protein product		609694				12093360, 16086184	Standard	XM_005259927		Approved	ARHGAP46	uc002nnd.3	Q9P107		ENST00000203556.4:c.2863G>A	chr19.hg19:g.19740822C>T	ENSP00000203556:p.Ala955Thr	90.0	0.0		182.0	38.0	NM_016573	A0AVN9|B7ZLZ0	Missense_Mutation	SNP	ENST00000203556.4	hg19	CCDS12408.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.863421	0.51482	.	.	ENSG00000089639	ENST00000203556;ENST00000445806	T;T	0.21543	2.0;2.0	5.11	-1.89	0.07689	.	0.424132	0.17523	N	0.171189	T	0.09158	0.0226	N	0.17082	0.46	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.40308	-0.9570	10	0.08179	T	0.78	-7.6898	9.0822	0.36558	0.0:0.4364:0.0:0.5636	.	926;929;955	E7ERB7;B7ZLZ0;Q9P107	.;.;GMIP_HUMAN	T	955;926	ENSP00000203556:A955T;ENSP00000397075:A926T	ENSP00000203556:A955T	A	-	1	0	GMIP	19601822	0.000000	0.05858	0.006000	0.13384	0.922000	0.55478	-0.356000	0.07661	-0.126000	0.11682	0.561000	0.74099	GCC	.	.		0.627	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573		T	19740822	C	T	19740822	3	4	54	1	0	0	0	0	1	0	0	0	6499	739	26	3	53	3	GMIP	19	19740822	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10		19740822	39388161	103	6895										
ZNF99	7652	hgsc.bcm.edu	37	chr19	22942280	22942281	+	Frame_Shift_Ins	INS	-	-	T													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	atatttgttacactgaaataINStttttccctgggtagttgtc					rs564678369	byFrequency	TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr19:22942280_22942281insT	ENST00000596209.1	-	4	520_521	c.430_431insA	c.(430-432)atafs	p.I144fs	ZNF99_ENST00000397104.3_Frame_Shift_Ins_p.I165fs	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	144					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I165V(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				ACACTGAAATATTTTTCCCTGG	0.282																																					p.I144fs		Atlas-Indel,Pindel	.											.	ZNF99	273	.	1	Substitution - Missense(1)	ovary(1)	c.431_432insA						.																																			SO:0001589	frameshift_variant	7652	exon4			.	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.431dupA	chr19.hg19:g.22942285_22942285dupT	ENSP00000472969:p.Ile144fs	320.0	0.0		158.0	51.0	NM_001080409	M0R335	Frame_Shift_Ins	INS	ENST00000596209.1	hg19	CCDS59369.1																																																																																			.	.		0.282	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		T	22942281	-	T	22942280	7	5	54	1	0	1	1	0	0	0	0	0	18219	449	16	0	2634	0	ZNF99	19	22942280	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10	3201458	22942280	36186703	104	6896										
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927076	23927076	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gttagaagctttgccacattTttcacactggtagggttttt	9	7	1	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr19:23927076T>C	ENST00000402377.3	-	4	1417	c.1276A>G	c.(1276-1278)Aaa>Gaa	p.K426E	ZNF681_ENST00000395385.3_Missense_Mutation_p.K357E	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	426					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTGCCACATTTTTCACACTGG	0.378																																					p.K426E		Atlas-SNP	.											.	ZNF681	76	.	0			c.A1276G						.						74	78	77					19																	23927076		2203	4300	6503	SO:0001583	missense	148213	exon4			CACATTTTTCACA	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1276A>G	chr19.hg19:g.23927076T>C	ENSP00000384000:p.Lys426Glu	161.0	0.0		134.0	47.0	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	hg19	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	0.001	-3.293486	0.00019	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.07444	3.19;3.19	1.51	-3.01	0.05463	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01730	0.0055	N	0.00894	-1.105	0.09310	N	1	B	0.14805	0.011	B	0.08055	0.003	T	0.45731	-0.9241	9	0.02654	T	1	.	4.3373	0.11092	0.0:0.5774:0.2273:0.1952	.	426	Q96N22	ZN681_HUMAN	E	426;357	ENSP00000384000:K426E;ENSP00000378783:K357E	ENSP00000378783:K357E	K	-	1	0	ZNF681	23718916	0.000000	0.05858	0.262000	0.24481	0.016000	0.09150	-1.519000	0.02243	-0.127000	0.11661	-0.736000	0.03550	AAA	.	.		0.378	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		C	23927076	T	C	23927076	3	2	54	1	0	0	0	0	1	0	0	0	18103	1850	64	2	665	2	ZNF681	19	23927076	Missense_Mutation	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	984796	23927076	35201907	105	6897										
MLL4	9757	hgsc.bcm.edu	37	chr19	36214013	36214013	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	gttctggagggaccctggccCacacaccccggcgctcactg	12	17	2	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr19:36214013C>A	ENST00000222270.7	+	6	2839	c.2839C>A	c.(2839-2841)Cac>Aac	p.H947N	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.H947N	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	947					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GACCCTGGCCCACACACCCCG	0.662																																					p.H947N		Atlas-SNP	.											.	MLL4	229	.	0			c.C2839A						.						42	52	49					19																	36214013		2097	4211	6308	SO:0001583	missense	8085	exon6			CTGGCCCACACAC	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.2839C>A	chr19.hg19:g.36214013C>A	ENSP00000222270:p.His947Asn	35.0	0.0		46.0	7.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.718681	0.30503	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.83075	-1.68;-1.68	5.82	4.73	0.59995	.	0.337529	0.21381	N	0.075480	T	0.74703	0.3751	L	0.36672	1.1	0.26207	N	0.979354	B	0.23735	0.09	B	0.18871	0.023	T	0.62909	-0.6754	10	0.32370	T	0.25	.	12.9635	0.58472	0.1618:0.8382:0.0:0.0	.	947	Q9UMN6	MLL4_HUMAN	N	947	ENSP00000222270:H947N;ENSP00000398837:H947N	ENSP00000222270:H947N	H	+	1	0	AD000671.1	40905853	0.006000	0.16342	0.998000	0.56505	0.963000	0.63663	0.956000	0.29202	2.757000	0.94681	0.655000	0.94253	CAC	.	.		0.662	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		A	36214013	C	A	36214013	3	1	54	1	0	0	0	0	1	0	0	0	9632	594	21	3	2861	3	MLL4	19	36214013	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	12286937	36214013	22914970	106	6898										
TGFB1	7040	hgsc.bcm.edu	37	chr19	41850671	41850671	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cctccacggctcaaccactgCcgcacaactccggtgacatc	7	19	1	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr19:41850671C>A	ENST00000221930.5	-	3	1481	c.615G>T	c.(613-615)cgG>cgT	p.R205R		NM_000660.4	NP_000651.3	P01137	TGFB1_HUMAN	transforming growth factor, beta 1	205	Arm domain. {ECO:0000250}.				active induction of host immune response by virus (GO:0046732)|adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains (GO:0002460)|aging (GO:0007568)|ATP biosynthetic process (GO:0006754)|blood coagulation (GO:0007596)|branch elongation involved in mammary gland duct branching (GO:0060751)|cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cell-cell junction organization (GO:0045216)|cellular calcium ion homeostasis (GO:0006874)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation (GO:0002062)|common-partner SMAD protein phosphorylation (GO:0007182)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|defense response to fungus, incompatible interaction (GO:0009817)|digestive tract development (GO:0048565)|embryo development (GO:0009790)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|evasion or tolerance of host defenses by virus (GO:0019049)|extracellular matrix assembly (GO:0085029)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|face morphogenesis (GO:0060325)|female pregnancy (GO:0007565)|frontal suture morphogenesis (GO:0060364)|germ cell migration (GO:0008354)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|lens fiber cell differentiation (GO:0070306)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymph node development (GO:0048535)|macrophage derived foam cell differentiation (GO:0010742)|mammary gland branching involved in thelarche (GO:0060744)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|modulation by virus of host morphology or physiology (GO:0019048)|mononuclear cell proliferation (GO:0032943)|myelination (GO:0042552)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA replication (GO:0008156)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of extracellular matrix disassembly (GO:0010716)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of ossification (GO:0030279)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|ossification involved in bone remodeling (GO:0043932)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|phosphate-containing compound metabolic process (GO:0006796)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NAD+ ADP-ribosyltransferase activity (GO:1901666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of odontogenesis (GO:0042482)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein secretion (GO:0050714)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein export from nucleus (GO:0006611)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|receptor catabolic process (GO:0032801)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of binding (GO:0051098)|regulation of blood vessel remodeling (GO:0060312)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of cartilage development (GO:0061035)|regulation of cell migration (GO:0030334)|regulation of DNA binding (GO:0051101)|regulation of miRNA metabolic process (GO:2000628)|regulation of protein import into nucleus (GO:0042306)|regulation of sodium ion transport (GO:0002028)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulatory T cell differentiation (GO:0045066)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to laminar fluid shear stress (GO:0034616)|response to progesterone (GO:0032570)|response to radiation (GO:0009314)|response to vitamin D (GO:0033280)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|T cell homeostasis (GO:0043029)|tolerance induction to self antigen (GO:0002513)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|viral life cycle (GO:0019058)	axon (GO:0030424)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	antigen binding (GO:0003823)|cytokine activity (GO:0005125)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)	8					Hyaluronidase(DB00070)	TCAACCACTGCCGCACAACTC	0.557																																					p.R205R		Atlas-SNP	.											.	TGFB1	27	.	0			c.G615T						.						117	81	93					19																	41850671		2203	4300	6503	SO:0001819	synonymous_variant	7040	exon3			CCACTGCCGCACA	X02812	CCDS33031.1	19q13.1	2014-01-30	2007-02-16			ENSG00000105329		"Endogenous ligands"	11766	protein-coding gene	gene with protein product	"Camurati-Engelmann disease", "prepro-transforming growth factor beta-1"	190180		TGFB, DPD1		10631145, 10843814	Standard	NM_000660		Approved	CED, TGFbeta	uc002oqh.2	P01137		ENST00000221930.5:c.615G>T	chr19.hg19:g.41850671C>A		57.0	0.0		71.0	19.0	NM_000660	A8K792|Q9UCG4	Silent	SNP	ENST00000221930.5	hg19	CCDS33031.1																																																																																			.	.		0.557	TGFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463500.2			A	41850671	C	A	41850671	2	1	54	1	0	0	0	0	0	0	0	1	15831	726	26	3		3	TGFB1	19	41850671	Silent	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	5636658	41850671	17278312	107	6899										
GIPR	2696	hgsc.bcm.edu	37	chr19	46185002	46185002	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cacaggtgcagtcggagatcCgccgtggctggcaccactgc	14	14	0	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr19:46185002C>A	ENST00000590918.1	+	14	1309	c.1210C>A	c.(1210-1212)Cgc>Agc	p.R404S	GIPR_ENST00000304207.8_Missense_Mutation_p.R368S|GIPR_ENST00000263281.3_3'UTR	NM_000164.2	NP_000155.1	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	404					activation of adenylate cyclase activity (GO:0007190)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|endocrine pancreas development (GO:0031018)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|response to axon injury (GO:0048678)|response to calcium ion (GO:0051592)|response to fatty acid (GO:0070542)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gastric inhibitory peptide receptor activity (GO:0016519)|peptide hormone binding (GO:0017046)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|kidney(2)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	12		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)		GTCGGAGATCCGCCGTGGCTG	0.771																																					p.R404S		Atlas-SNP	.											.	GIPR	36	.	0			c.C1210A						.						8	11	10					19																	46185002		2118	4158	6276	SO:0001583	missense	2696	exon14			GAGATCCGCCGTG		CCDS12671.1	19q13.2-q13.3	2012-08-10				ENSG00000010310		"GPCR / Class B : Glucagon receptors"	4271	protein-coding gene	gene with protein product		137241				7490109	Standard	NM_000164		Approved		uc002pcu.1	P48546		ENST00000590918.1:c.1210C>A	chr19.hg19:g.46185002C>A	ENSP00000467494:p.Arg404Ser	3.0	0.0		22.0	11.0	NM_000164	B7WP14|B7ZKQ0|Q14401|Q16400|Q52M04|Q9UPI1	Missense_Mutation	SNP	ENST00000590918.1	hg19	CCDS12671.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.774468	0.90108	.	.	ENSG00000010310	ENST00000263281;ENST00000304207	T	0.65178	-0.14	5.2	5.2	0.72013	.	0.155416	0.31909	N	0.006861	T	0.63058	0.2479	M	0.62723	1.935	0.41404	D	0.987691	P;D	0.54601	0.943;0.967	B;P	0.45138	0.343;0.471	T	0.68247	-0.5459	10	0.56958	D	0.05	.	14.0841	0.64944	0.0:1.0:0.0:0.0	.	368;404	B7WP14;P48546	.;GIPR_HUMAN	S	404;368	ENSP00000305321:R368S	ENSP00000263281:R404S	R	+	1	0	GIPR	50876842	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.304000	0.65744	2.705000	0.92388	0.561000	0.74099	CGC	.	.		0.771	GIPR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459640.1			A	46185002	C	A	46185002	3	1	54	1	0	0	0	0	1	0	0	0	6403	652	23	1	1260	1	GIPR	19	46185002	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	4334331	46185002	12943981	108	6900										
ZNF677	342926	hgsc.bcm.edu	37	chr19	53747099	53747099	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ctgggcagggtccaggcactCccactcctcttgagagaatt	11	13	1	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr19:53747099C>G	ENST00000598513.1	-	4	217	c.67G>C	c.(67-69)Gag>Cag	p.E23Q	ZNF677_ENST00000599012.1_Missense_Mutation_p.E23Q|ZNF677_ENST00000594681.1_Missense_Mutation_p.E23Q|ZNF677_ENST00000601828.1_Missense_Mutation_p.E23Q|ZNF677_ENST00000601413.1_Missense_Mutation_p.E23Q|ZNF677_ENST00000333952.4_Missense_Mutation_p.E23Q|ZNF677_ENST00000598806.1_Missense_Mutation_p.E23Q|CTD-2245F17.6_ENST00000596041.1_RNA	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	23	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		TCCAGGCACTCCCACTCCTCT	0.468																																					p.E23Q		Atlas-SNP	.											.	ZNF677	94	.	0			c.G67C						.						101	94	97					19																	53747099		2203	4300	6503	SO:0001583	missense	342926	exon4			GGCACTCCCACTC	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.67G>C	chr19.hg19:g.53747099C>G	ENSP00000469391:p.Glu23Gln	153.0	0.0		134.0	45.0	NM_182609		Missense_Mutation	SNP	ENST00000598513.1	hg19	CCDS12861.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.941521	0.53079	.	.	ENSG00000197928	ENST00000416063;ENST00000333952	T	0.01918	4.56	2.02	2.02	0.26589	Krueppel-associated box (4);	0.225060	0.22744	N	0.056176	T	0.07052	0.0179	L	0.53780	1.695	0.25115	N	0.990686	D	0.76494	0.999	D	0.87578	0.998	T	0.26710	-1.0095	10	0.21014	T	0.42	.	10.0974	0.42484	0.0:1.0:0.0:0.0	.	23	Q86XU0	ZN677_HUMAN	Q	23	ENSP00000334394:E23Q	ENSP00000334394:E23Q	E	-	1	0	ZNF677	58438911	0.169000	0.23002	0.941000	0.38009	0.871000	0.50021	0.249000	0.18216	1.449000	0.47699	0.561000	0.74099	GAG	.	.		0.468	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		G	53747099	C	G	53747099	3	3	54	1	0	0	0	0	1	0	0	0	18099	864	30	4	1695	4	ZNF677	19	53747099	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	7562097	53747099	5381884	109	6901										
CTCFL	140690	hgsc.bcm.edu	37	chr20	56098886	56098887	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tgctgcaggctctgccggggINScccttcctcaagccacagca							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr20:56098886_56098887insC	ENST00000608263.1	-	1	1036_1037	c.375_376insG	c.(373-378)gggcccfs	p.P126fs	CTCFL_ENST00000423479.3_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000609232.1_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000432255.2_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000243914.3_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000433949.3_Intron|CTCFL_ENST00000608440.1_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000608425.1_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000422869.2_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000371196.2_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000429804.3_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000608158.1_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000481655.2_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000539382.1_Intron	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	126					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			CTCTGCCGGGGCCCTTCCTCAA	0.579																																					p.P126fs		Atlas-INDEL	.											.	CTCFL	97	.	0			c.376_377insG						.																																			SO:0001589	frameshift_variant	140690	exon1			.		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.376dupG	chr20.hg19:g.56098889_56098889dupC	ENSP00000476783:p.Pro126fs	83.0	0.0		139.0	11.0	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Frame_Shift_Ins	INS	ENST00000608263.1	hg19	CCDS13459.1																																																																																			.	.		0.579	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		C	56098887	-	C	56098886	7	5	54	1	0	1	1	0	0	0	0	0	4003	1203	42	0	1655	0	CTCFL	20	56098886	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10		56098886	6926634	110	6902										
PTTG1IP	754	hgsc.bcm.edu	37	chr21	46281119	46281120	+	Frame_Shift_Ins	INS	-	-	A													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	agagctcaatttacaaagggINSaagccggtggcaagacgctt							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr21:46281119_46281120insA	ENST00000330938.3	-	3	455_456	c.235_236insT	c.(235-237)tccfs	p.S79fs	PTTG1IP_ENST00000445724.2_Intron|PTTG1IP_ENST00000397886.3_Frame_Shift_Ins_p.S58fs|PTTG1IP_ENST00000397887.3_Frame_Shift_Ins_p.S79fs|PTTG1IP_ENST00000494690.1_5'UTR	NM_004339.3	NP_004330.1	P53801	PTTG_HUMAN	pituitary tumor-transforming 1 interacting protein	79	PSI.				multicellular organismal development (GO:0007275)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)			ovary(1)|prostate(1)	2				Colorectal(79;0.0659)		TTTACAAAGGGAAGCCGGTGGC	0.431																																					p.S79fs		Atlas-INDEL	.											.	PTTG1IP	22	.	0			c.236_237insT						.																																			SO:0001589	frameshift_variant	754	exon3			.	AF149785	CCDS13715.1, CCDS68221.1	21q22.3	2008-07-04			ENSG00000183255	ENSG00000183255			13524	protein-coding gene	gene with protein product		603784		C21orf3, C21orf1		9570958, 10830953	Standard	NM_004339		Approved	PBF	uc002zgb.2	P53801	OTTHUMG00000090254	ENST00000330938.3:c.236dupT	chr21.hg19:g.46281121_46281121dupA	ENSP00000328325:p.Ser79fs	99.0	0.0		182.0	17.0	NM_004339	B2RDP7|D3DSL9|Q9NS09	Frame_Shift_Ins	INS	ENST00000330938.3	hg19	CCDS13715.1																																																																																			.	.		0.431	PTTG1IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206553.1			A	46281120	-	A	46281119	7	5	54	1	0	1	1	0	0	0	0	0	12835	1174	41	0	322	0	PTTG1IP	21	46281119	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10		46281119	1848776	111	6903										
PCNT	5116	hgsc.bcm.edu	37	chr21	47850032	47850032	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cagcgtgcagaagctcctggCggcggagcagactgtagtgc	16	11	0	2			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr21:47850032C>T	ENST00000359568.5	+	36	7906	c.7799C>T	c.(7798-7800)gCg>gTg	p.A2600V	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2600					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AAGCTCCTGGCGGCGGAGCAG	0.562																																					p.A2600V		Atlas-SNP	.											.	PCNT	283	.	0			c.C7799T						.						101	95	97					21																	47850032		2203	4300	6503	SO:0001583	missense	5116	exon36			TCCTGGCGGCGGA	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7799C>T	chr21.hg19:g.47850032C>T	ENSP00000352572:p.Ala2600Val	166.0	0.0		315.0	55.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.589419	0.00864	.	.	ENSG00000160299	ENST00000359568	T	0.01464	4.86	4.32	-2.5	0.06384	.	.	.	.	.	T	0.00724	0.0024	N	0.01576	-0.805	0.09310	N	1	B;B	0.17852	0.006;0.024	B;B	0.08055	0.003;0.003	T	0.47983	-0.9074	9	0.17832	T	0.49	.	6.886	0.24199	0.0:0.3494:0.1207:0.5299	.	2482;2600	O95613-2;O95613	.;PCNT_HUMAN	V	2600	ENSP00000352572:A2600V	ENSP00000352572:A2600V	A	+	2	0	PCNT	46674460	0.003000	0.15002	0.023000	0.16930	0.207000	0.24258	0.099000	0.15210	-0.578000	0.05959	0.462000	0.41574	GCG	.	.		0.562	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47850032	C	T	47850032	3	4	54	1	0	0	0	0	1	0	0	0	11599	768	27	1	7941	1	PCNT	21	47850032	Missense_Mutation	SNP	C	TCGA-CC-5258-01A-01D-A12Z-10	1568913	47850032	279863	112	6904										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38119347	38119347	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	ccacgtctcaggcttctcctGcccaaagggacactgctcag	9	16	3	0			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chr22:38119347G>A	ENST00000406386.3	+	7	1039	c.784G>A	c.(784-786)Gcc>Acc	p.A262T		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	262					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GGCTTCTCCTGCCCAAAGGGA	0.607																																					p.A262T		Atlas-SNP	.											.	TRIOBP	262	.	0			c.G784A						.						70	81	77					22																	38119347		2122	4238	6360	SO:0001583	missense	11078	exon7			TCTCCTGCCCAAA	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.784G>A	chr22.hg19:g.38119347G>A	ENSP00000384312:p.Ala262Thr	62.0	0.0		122.0	30.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.255830	0.39896	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.27720	1.65	3.91	-2.33	0.06724	.	.	.	.	.	T	0.13200	0.0320	N	0.08118	0	0.18873	N	0.999984	B	0.18013	0.025	B	0.13407	0.009	T	0.27088	-1.0084	9	0.33141	T	0.24	.	6.9194	0.24378	0.1743:0.4047:0.421:0.0	.	262	Q9H2D6	TARA_HUMAN	T	262	ENSP00000384312:A262T	ENSP00000384312:A262T	A	+	1	0	TRIOBP	36449293	0.000000	0.05858	0.510000	0.27712	0.006000	0.05464	0.005000	0.13129	-0.146000	0.11274	-0.370000	0.07254	GCC	.	.		0.607	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			A	38119347	G	A	38119347	3	1	54	1	0	0	0	0	1	0	0	0	16568	1319	46	3	802	3	TRIOBP	22	38119347	Missense_Mutation	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10		38119347	13185219	113	6905										
ZBED1	9189	hgsc.bcm.edu	37	chrX	2406709	2406710	+	Frame_Shift_Ins	INS	-	-	C													0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	tgtccctaatgccaaagaaaINSccgccgctgacgccatcccc							TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chrX:2406709_2406710insC	ENST00000381223.4	-	2	2254_2255	c.2051_2052insG	c.(2050-2052)ggtfs	p.G684fs	ZBED1_ENST00000381218.3_Frame_Shift_Ins_p.G684fs|DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381222.2_Frame_Shift_Ins_p.G684fs|ZBED1_ENST00000515319.1_Intron	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	684					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)			endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGCCAAAGAAACCGCCGCTGAC	0.604																																					p.G684fs		Atlas-INDEL	.											.	ZBED1	64	.	0			c.2052_2053insG						.																																			SO:0001589	frameshift_variant	9189	exon2			.	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"Pseudoautosomal regions / PAR1", "Zinc fingers, BED-type"	447	protein-coding gene	gene with protein product		300178	"Ac-like transposable element"	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.2052dupG	chrX.hg19:g.2406711_2406711dupC	ENSP00000370621:p.Gly684fs	141.0	0.0		194.0	16.0	NM_001171135	Q96BY4	Frame_Shift_Ins	INS	ENST00000381223.4	hg19	CCDS14118.1																																																																																			.	.		0.604	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729		C	2406710	-	C	2406709	7	5	54	1	0	1	1	0	0	0	0	0	17532	30	2	0	36	0	ZBED1	23	2406709	Frame_Shift_Ins	INS	-	TCGA-CC-5258-01A-01D-A12Z-10		2406709	152863851	114	6906										
PAGE2	203569	hgsc.bcm.edu	37	chrX	55117891	55117891	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cactaaagtgctggaagcagGtttgttattcatttaagatg	10	5	1	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chrX:55117891G>A	ENST00000374968.4	+	4	423		c.e4+1		PAGE2_ENST00000374965.1_Splice_Site	NM_207339.2	NP_997222.1	Q7Z2X7	PAGE2_HUMAN	P antigen family, member 2 (prostate associated)											endometrium(1)|large_intestine(2)|lung(1)|ovary(2)	6						CTGGAAGCAGGTTTGTTATTC	0.383																																					.		Atlas-SNP	.											.	PAGE2	26	.	0			c.319+1G>A						.						94	108	104					X																	55117891		2172	4296	6468	SO:0001630	splice_region_variant	203569	exon4			AAGCAGGTTTGTT	BC054022	CCDS14367.1	Xp11.22	2009-06-17			ENSG00000234068	ENSG00000234068			31804	protein-coding gene	gene with protein product		300738	"G antigen, family C, 2"	GAGEC2		9724777	Standard	NM_207339		Approved	MGC62094, PAGE-2, CT16.4		Q7Z2X7	OTTHUMG00000021648	ENST00000374968.4:c.319+1G>A	chrX.hg19:g.55117891G>A		321.0	0.0		334.0	104.0	NM_207339	Q5JRK7|Q5JRK8	Splice_Site	SNP	ENST00000374968.4	hg19	CCDS14367.1	.	.	.	.	.	.	.	.	.	.	g	2.931	-0.221059	0.06061	.	.	ENSG00000234068	ENST00000374968;ENST00000374965	.	.	.	1.13	1.13	0.20643	.	.	.	.	.	.	.	.	.	.	.	0.21473	N	0.999673	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.3082	0.15815	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PAGE2	55134616	0.973000	0.33851	0.014000	0.15608	0.012000	0.07955	1.535000	0.36061	0.862000	0.35528	0.287000	0.19450	.	.	.		0.383	PAGE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056857.1	NM_207339	Intron	A	55117891	G	A	55117891	5	1	54	1	0	0	0	0	0	0	1	0	11399	1275	44	3	330	3	PAGE2	23	55117891	Splice_Site	SNP	G	TCGA-CC-5258-01A-01D-A12Z-10	52711182	55117891	100152669	115	6907										
NAP1L3	4675	hgsc.bcm.edu	37	chrX	92927476	92927476	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0258620689655172	3	1	0.533492822966507	1.22865013774105	0.250280583613917	1	1	0	cttttatgagtctctcttacTgcagcccttgccttagcctc	6	14	2	1			TCGA-CC-5258-01A-01D-A12Z-10	TCGA-CC-5258-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53feb92e-977d-4591-aaa1-7172f3e42965	04203961-a51c-4ee4-af73-8007d37a0113	g.chrX:92927476T>A	ENST00000373079.3	-	1	1091	c.828A>T	c.(826-828)gcA>gcT	p.A276A	FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000355813.5_5'Flank|NAP1L3_ENST00000475430.2_Silent_p.A269A|FAM133A_ENST00000332647.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	276					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.A276A(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						TCTCTCTTACTGCAGCCCTTG	0.448																																					p.A276A		Atlas-SNP	.											.	NAP1L3	81	.	1	Substitution - coding silent(1)	lung(1)	c.A828T						.						116	108	111					X																	92927476		2203	4300	6503	SO:0001819	synonymous_variant	4675	exon1			TCTTACTGCAGCC		CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.828A>T	chrX.hg19:g.92927476T>A		133.0	0.0		231.0	166.0	NM_004538	B2RCM0|O60788	Silent	SNP	ENST00000373079.3	hg19	CCDS14465.1																																																																																			.	.		0.448	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538		A	92927476	T	A	92927476	2	1	54	1	0	0	0	0	0	0	0	1	10167	1567	55	4		4	NAP1L3	23	92927476	Silent	SNP	T	TCGA-CC-5258-01A-01D-A12Z-10	37809585	92927476	62343084	116	6908										
AKR7A3	22977	hgsc.bcm.edu	37	chr1	19615114	19615136	+	Frame_Shift_Del	DEL	TGCGGCGCTGGTGGGCGCGTCCA	TGCGGCGCTGGTGGGCGCGTCCA	-													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tccaggaaggcgcgcgtgacTgcggcgctggtgggcgcgtc					rs552561219		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	TGCGGCGCTGGTGGGCGCGTCCA	TGCGGCGCTGGTGGGCGCGTCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:19615114_19615136delTGCGGCGCTGGTGGGCGCGTCCA	ENST00000361640.4	-	1	608_630	c.68_90delTGGACGCGCCCACCAGCGCCGCA	c.(67-90)atggacgcgcccaccagcgccgcafs	p.MDAPTSAA23fs		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	23					cellular aldehyde metabolic process (GO:0006081)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)	13		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CGCGCGTGACTGCGGCGCTGGTGGGCGCGTCCATGCGGCGCCC	0.722																																					p.23_31del		Pindel	.											.	AKR7A3	30	.	0			c.69_91del						.			11,4179		0,11,2084						-1.4	0			14	63,8041		2,59,3991	no	frameshift	AKR7A3	NM_012067.2		2,70,6075	A1A1,A1R,RR		0.7774,0.2625,0.6019				74,12220				SO:0001589	frameshift_variant	22977	exon1			.	AF040639	CCDS193.1	1p36.13	2008-05-14			ENSG00000162482	ENSG00000162482		"Aldo-keto reductases"	390	protein-coding gene	gene with protein product		608477				10383892	Standard	NM_012067		Approved		uc001bbv.1	O95154	OTTHUMG00000002523	ENST00000361640.4:c.68_90delTGGACGCGCCCACCAGCGCCGCA	chr1.hg19:g.19615114_19615136delTGCGGCGCTGGTGGGCGCGTCCA	ENSP00000355377:p.Met23fs	0.0	0.0		10.0	10.0	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Frame_Shift_Del	DEL	ENST00000361640.4	hg19	CCDS193.1																																																																																			.	.		0.722	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067		-	19615136	TGCGGCGCTGGTGGGCGCGTCCA	-	19615114	7	5	55	1	0	1	0	1	0	0	0	0	476	1567	55	0	933	0	AKR7A3	1	19615114	Frame_Shift_Del	DEL	TGCGGCGCTGGTGGGCGCGTCCA	TCGA-CC-5259-01A-31D-A20W-10		19615114	229635507	1	6909										
MED18	54797	hgsc.bcm.edu	37	chr1	28657195	28657195	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tggaggcacctccagtcaccAtgatgcctgtcactgggggc	13	13	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:28657195A>G	ENST00000373842.4	+	2	231	c.22A>G	c.(22-24)Atg>Gtg	p.M8V	MED18_ENST00000479574.1_3'UTR|MED18_ENST00000398997.2_Missense_Mutation_p.M8V	NM_001127350.1|NM_017638.2	NP_001120822.1|NP_060108.2	Q9BUE0	MED18_HUMAN	mediator complex subunit 18	8						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Lung NSC(340;0.000818)|all_lung(284;0.000996)|Renal(390;0.00357)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0557)|Ovarian(437;0.113)		OV - Ovarian serous cystadenocarcinoma(117;2.36e-22)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0141)|READ - Rectum adenocarcinoma(331;0.0649)		TCCAGTCACCATGATGCCTGT	0.493																																					p.M8V		Atlas-SNP	.											.	MED18	30	.	0			c.A22G						.						142	120	128					1																	28657195		2203	4300	6503	SO:0001583	missense	54797	exon2			GTCACCATGATGC	BC002694	CCDS322.1	1p35.3	2007-07-30	2007-07-30		ENSG00000130772	ENSG00000130772			25944	protein-coding gene	gene with protein product		612384	"mediator of RNA polymerase II transcription, subunit 18 homolog (S. cerevisiae)"			15175163	Standard	NM_001127350		Approved	FLJ20045, p28b	uc009vtg.3	Q9BUE0	OTTHUMG00000003537	ENST00000373842.4:c.22A>G	chr1.hg19:g.28657195A>G	ENSP00000362948:p.Met8Val	159.0	0.0		137.0	113.0	NM_017638	D3DPM1|Q9NXU9	Missense_Mutation	SNP	ENST00000373842.4	hg19	CCDS322.1	.	.	.	.	.	.	.	.	.	.	A	10.59	1.392142	0.25118	.	.	ENSG00000130772	ENST00000373842;ENST00000398997	.	.	.	5.45	5.45	0.79879	.	0.098154	0.64402	D	0.000001	T	0.15176	0.0366	N	0.02011	-0.69	0.24283	N	0.995197	B	0.02656	0.0	B	0.01281	0.0	T	0.12192	-1.0557	9	0.12103	T	0.63	-20.0887	14.4943	0.67674	1.0:0.0:0.0:0.0	.	8	Q9BUE0	MED18_HUMAN	V	8	.	ENSP00000362948:M8V	M	+	1	0	MED18	28529782	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.062000	0.71155	2.072000	0.62099	0.533000	0.62120	ATG	.	.		0.493	MED18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009856.1	NM_017638		G	28657195	A	G	28657195	3	3	55	1	0	0	0	0	1	0	0	0	9445	217	8	2	24	2	MED18	1	28657195	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	9042081	28657195	220593426	2	6910										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42048714	42048714	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gccggctggcgcttcagcatCcgggggtgggaggtaaacac	17	11	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:42048714C>G	ENST00000372583.1	-	4	2640	c.1755G>C	c.(1753-1755)cgG>cgC	p.R585R	HIVEP3_ENST00000372584.1_Silent_p.R585R|HIVEP3_ENST00000247584.5_Silent_p.R585R|HIVEP3_ENST00000429157.2_Silent_p.R585R	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	585	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GCTTCAGCATCCGGGGGTGGG	0.602																																					p.R585R		Atlas-SNP	.											.	HIVEP3	235	.	0			c.G1755C						.						50	52	52					1																	42048714		2203	4300	6503	SO:0001819	synonymous_variant	59269	exon4			CAGCATCCGGGGG	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.1755G>C	chr1.hg19:g.42048714C>G		115.0	0.0		91.0	68.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.		0.602	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		G	42048714	C	G	42048714	2	3	55	1	0	0	0	0	0	0	0	1	7197	842	30	4		4	HIVEP3	1	42048714	Silent	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	13391519	42048714	207201907	3	6911										
SLC44A5	204962	hgsc.bcm.edu	37	chr1	75683603	75683603	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	attttaaacatttgaattaaTgcaataattaaagatccaaa	3	4	0	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:75683603T>G	ENST00000370855.5	-	18	1685	c.1572A>C	c.(1570-1572)gcA>gcC	p.A524A	SLC44A5_ENST00000535611.1_Silent_p.A394A|SLC44A5_ENST00000370859.3_Silent_p.A524A	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	524					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						TTTGAATTAATGCAATAATTA	0.303																																					p.A524A		Atlas-SNP	.											.	SLC44A5	231	.	0			c.A1572C						.						55	59	58					1																	75683603		2201	4299	6500	SO:0001819	synonymous_variant	204962	exon18			AATTAATGCAATA	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.1572A>C	chr1.hg19:g.75683603T>G		126.0	0.0		102.0	71.0	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Silent	SNP	ENST00000370855.5	hg19	CCDS667.1																																																																																			.	.		0.303	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		G	75683603	T	G	75683603	2	3	55	1	0	0	0	0	0	0	0	1	14654	1451	51	5		5	SLC44A5	1	75683603	Silent	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	33634889	75683603	173567018	4	6912										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144923732	144923732	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tggattttttcctggagttcTgccaagtgggaatcagatac	11	7	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:144923732T>A	ENST00000369354.3	-	6	915	c.726A>T	c.(724-726)gcA>gcT	p.A242A	PDE4DIP_ENST00000313382.9_Silent_p.A308A|PDE4DIP_ENST00000369359.4_Silent_p.A379A|PDE4DIP_ENST00000479408.2_Silent_p.A29A|PDE4DIP_ENST00000530740.1_Silent_p.A379A|PDE4DIP_ENST00000313431.9_Silent_p.A405A|PDE4DIP_ENST00000369351.3_Silent_p.A242A|PDE4DIP_ENST00000529945.1_Silent_p.A405A|PDE4DIP_ENST00000369349.3_Silent_p.A242A|PDE4DIP_ENST00000369356.4_Silent_p.A242A			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	242					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CCTGGAGTTCTGCCAAGTGGG	0.443			T	PDGFRB	MPD																																p.A405A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A1215T						.						368	330	343					1																	144923732		2203	4300	6503	SO:0001819	synonymous_variant	9659	exon2			GAGTTCTGCCAAG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.726A>T	chr1.hg19:g.144923732T>A		410.0	0.0		448.0	125.0	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	hg19	CCDS30824.1																																																																																			.	.		0.443	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		A	144923732	T	A	144923732	2	1	55	1	0	0	0	0	0	0	0	1	11652	1567	55	4		4	PDE4DIP	1	144923732	Silent	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	69240129	144923732	104326889	5	6913										
TCHH	7062	hgsc.bcm.edu	37	chr1	152081179	152081179	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cctgactgcgcagttcctgtTcgcggaattttctgtcacgc	10	13	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:152081179T>A	ENST00000368804.1	-	2	4513	c.4514A>T	c.(4513-4515)gAa>gTa	p.E1505V		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1505	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAGTTCCTGTTCGCGGAATTT	0.552																																					p.E1505V		Atlas-SNP	.											.	TCHH	275	.	0			c.A4514T						.						89	88	88					1																	152081179		1891	4112	6003	SO:0001583	missense	7062	exon3			TCCTGTTCGCGGA	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.4514A>T	chr1.hg19:g.152081179T>A	ENSP00000357794:p.Glu1505Val	122.0	0.0		198.0	33.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	N	6.759	0.508834	0.12883	.	.	ENSG00000159450	ENST00000368804	T	0.06849	3.25	2.47	1.31	0.21738	.	.	.	.	.	T	0.02767	0.0083	M	0.66939	2.045	0.09310	N	1	D	0.59357	0.985	B	0.40659	0.336	T	0.38950	-0.9637	9	0.29301	T	0.29	.	3.6795	0.08305	0.0:0.2176:0.0:0.7824	.	1505	Q07283	TRHY_HUMAN	V	1505	ENSP00000357794:E1505V	ENSP00000357794:E1505V	E	-	2	0	TCHH	150347803	0.043000	0.20138	0.001000	0.08648	0.016000	0.09150	0.903000	0.28475	0.102000	0.17638	0.332000	0.21555	GAA	.	.		0.552	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		A	152081179	T	A	152081179	3	1	55	1	0	0	0	0	1	0	0	0	15715	1783	62	4	1321	4	TCHH	1	152081179	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	7157447	152081179	97169442	6	6914										
PGLYRP4	57115	hgsc.bcm.edu	37	chr1	153318651	153318651	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	acctgtttagcttgtgttttGttccaggaggaatcacctgc	10	9	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:153318651G>T	ENST00000359650.5	-	3	130	c.66C>A	c.(64-66)aaC>aaA	p.N22K	PGLYRP4_ENST00000368739.3_Missense_Mutation_p.N22K|PGLYRP4_ENST00000490266.1_5'UTR	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	22					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.N22K(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTTGTGTTTTGTTCCAGGAGG	0.473																																					p.N22K		Atlas-SNP	.											PGLYRP4,NS,carcinoma,0,1	PGLYRP4	45	.	1	Substitution - Missense(1)	breast(1)	c.C66A						.						238	237	237					1																	153318651		2203	4300	6503	SO:0001583	missense	57115	exon3			TGTTTTGTTCCAG	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I beta precursor"	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.66C>A	chr1.hg19:g.153318651G>T	ENSP00000352672:p.Asn22Lys	229.0	0.0		302.0	141.0	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	hg19	CCDS30871.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.396225	0.25205	.	.	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.05139	3.5;3.49	3.25	-2.58	0.06228	.	.	.	.	.	T	0.00784	0.0026	N	0.08118	0	0.09310	N	1	P;P	0.38078	0.617;0.483	B;B	0.34242	0.178;0.086	T	0.44967	-0.9293	9	0.59425	D	0.04	-0.4372	0.9398	0.01353	0.2075:0.3901:0.1892:0.2132	.	22;22	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	K	22	ENSP00000357728:N22K;ENSP00000352672:N22K	ENSP00000352672:N22K	N	-	3	2	PGLYRP4	151585275	0.000000	0.05858	0.000000	0.03702	0.489000	0.33432	-0.142000	0.10311	-0.471000	0.06891	0.462000	0.41574	AAC	.	.		0.473	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393		T	153318651	G	T	153318651	3	4	55	1	0	0	0	0	1	0	0	0	11805	1368	48	3	1083	3	PGLYRP4	1	153318651	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	1237472	153318651	95931970	7	6915										
EFNA4	1945	hgsc.bcm.edu	37	chr1	155039354	155039354	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	caggctatgagtcctgccagGcagagggcccccgggcctac	14	15	0	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:155039354G>T	ENST00000368409.3	+	2	355	c.262G>T	c.(262-264)Gca>Tca	p.A88S	EFNA3_ENST00000556931.1_Intron|EFNA3_ENST00000505139.1_Intron|EFNA4_ENST00000359751.4_Missense_Mutation_p.A88S|EFNA4_ENST00000427683.2_Missense_Mutation_p.A88S	NM_005227.2	NP_005218.1	P52798	EFNA4_HUMAN	ephrin-A4	88	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|bone remodeling (GO:0046849)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|osteoclast differentiation (GO:0030316)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|transmembrane-ephrin receptor activity (GO:0005005)			breast(1)|endometrium(1)|large_intestine(1)|ovary(1)	4	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			GTCCTGCCAGGCAGAGGGCCC	0.617																																					p.A88S		Atlas-SNP	.											.	EFNA4	11	.	0			c.G262T						.						45	49	47					1																	155039354		2203	4300	6503	SO:0001583	missense	1945	exon2			TGCCAGGCAGAGG	AJ006352	CCDS1089.1, CCDS41407.1, CCDS44237.1	1q21-q22	2011-03-09			ENSG00000243364	ENSG00000243364		"Ephrins"	3224	protein-coding gene	gene with protein product		601380		EPLG4		8660976	Standard	NM_182690		Approved	LERK4		P52798	OTTHUMG00000035309	ENST00000368409.3:c.262G>T	chr1.hg19:g.155039354G>T	ENSP00000357394:p.Ala88Ser	172.0	0.0		236.0	82.0	NM_182690	C9JHJ8|G3XAK2|O95457|Q5SR71|Q6FI57	Missense_Mutation	SNP	ENST00000368409.3	hg19	CCDS1089.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.492044	0.44352	.	.	ENSG00000243364	ENST00000368409;ENST00000359751;ENST00000427683	T;T;T	0.43688	0.94;0.94;0.94	5.31	4.33	0.51752	Cupredoxin (2);	0.120943	0.53938	D	0.000048	T	0.26268	0.0641	N	0.20766	0.605	0.80722	D	1	P;P;B	0.40602	0.723;0.476;0.244	P;B;B	0.49708	0.62;0.1;0.099	T	0.05666	-1.0871	10	0.46703	T	0.11	-31.9773	11.0938	0.48132	0.0:0.1871:0.8129:0.0	.	88;88;88	P52798-2;P52798;G3XAK2	.;EFNA4_HUMAN;.	S	88	ENSP00000357394:A88S;ENSP00000352789:A88S;ENSP00000414378:A88S	ENSP00000352789:A88S	A	+	1	0	EFNA4	153305978	0.023000	0.18921	0.768000	0.31515	0.628000	0.37860	1.436000	0.34980	2.489000	0.83994	0.561000	0.74099	GCA	.	.		0.617	EFNA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000085421.2	NM_005227		T	155039354	G	T	155039354	3	4	55	1	0	0	0	0	1	0	0	0	4955	1203	42	3	268	3	EFNA4	1	155039354	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	1720703	155039354	94211267	8	6916										
CD5L	922	hgsc.bcm.edu	37	chr1	157804417	157804417	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tttgcggcccggaggctccaGcctgtctggcacacggtata	13	13	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:157804417G>A	ENST00000368174.4	-	4	594	c.498C>T	c.(496-498)ggC>ggT	p.G166G	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	166	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GGAGGCTCCAGCCTGTCTGGC	0.612																																					p.G166G		Atlas-SNP	.											.	CD5L	112	.	0			c.C498T						.						94	92	93					1																	157804417		2203	4300	6503	SO:0001819	synonymous_variant	922	exon4			GCTCCAGCCTGTC	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.498C>T	chr1.hg19:g.157804417G>A		92.0	0.0		128.0	57.0	NM_005894	A8K7M5|Q6UX63	Silent	SNP	ENST00000368174.4	hg19	CCDS1171.1																																																																																			.	.		0.612	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		A	157804417	G	A	157804417	2	1	55	1	0	0	0	0	0	0	0	1	3029	958	34	3		3	CD5L	1	157804417	Silent	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	2765063	157804417	91446204	9	6917										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158590172	158590172	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cagggagacacagtgcacagGctctgacaagttttcttcca	10	11	2	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:158590172G>T	ENST00000368147.4	-	44	6385	c.6205C>A	c.(6205-6207)Cct>Act	p.P2069T		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2069					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CAGTGCACAGGCTCTGACAAG	0.468																																					p.P2069T		Atlas-SNP	.											SPTA1,NS,carcinoma,0,1	SPTA1	720	.	0			c.C6205A						.						84	78	80					1																	158590172		1924	4149	6073	SO:0001583	missense	6708	exon44			GCACAGGCTCTGA	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6205C>A	chr1.hg19:g.158590172G>T	ENSP00000357129:p.Pro2069Thr	307.0	0.0		423.0	36.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.914933	0.52546	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48836	0.8;0.8	5.05	3.16	0.36331	.	0.000000	0.31989	N	0.006747	T	0.49508	0.1561	M	0.72353	2.195	0.46774	D	0.999195	D	0.55605	0.972	D	0.68039	0.955	T	0.48091	-0.9065	10	0.33141	T	0.24	.	8.7768	0.34767	0.0795:0.0:0.7705:0.1501	.	2069	P02549	SPTA1_HUMAN	T	2069;2066	ENSP00000357130:P2069T;ENSP00000357129:P2066T	ENSP00000357129:P2066T	P	-	1	0	SPTA1	156856796	1.000000	0.71417	0.967000	0.41034	0.468000	0.32798	5.990000	0.70595	0.697000	0.31718	0.585000	0.79938	CCT	.	.		0.468	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158590172	G	T	158590172	3	4	55	1	0	0	0	0	1	0	0	0	15131	1203	42	3	1090	3	SPTA1	1	158590172	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	785755	158590172	90660449	10	6918										
HSPA6	3310	hgsc.bcm.edu	37	chr1	161495008	161495008	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agctgccatcgcctatgggcTggaccggcggggcgcgggag	19	12	0	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:161495008T>A	ENST00000309758.4	+	1	973	c.560T>A	c.(559-561)cTg>cAg	p.L187Q	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	187					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCCTATGGGCTGGACCGGCGG	0.647																																					p.L187Q		Atlas-SNP	.											.	HSPA6	53	.	0			c.T560A						.						28	35	33					1																	161495008		2202	4297	6499	SO:0001583	missense	3310	exon1			ATGGGCTGGACCG		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"Heat shock proteins / HSP70"	5239	protein-coding gene	gene with protein product		140555	"heat shock 70kD protein 6 (HSP70B')"			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.560T>A	chr1.hg19:g.161495008T>A	ENSP00000310219:p.Leu187Gln	267.0	0.0		314.0	120.0	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	hg19	CCDS1231.1	.	.	.	.	.	.	.	.	.	.	.	15.66	2.899944	0.52227	.	.	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.01685	4.69	3.3	3.3	0.37823	.	0.000000	0.31577	U	0.007407	T	0.13457	0.0326	H	0.99732	4.735	0.53688	D	0.999973	D	0.89917	1.0	D	0.87578	0.998	T	0.09596	-1.0667	10	0.87932	D	0	-31.2204	9.6319	0.39785	0.0:0.0:0.0:1.0	.	187	P17066	HSP76_HUMAN	Q	187;163	ENSP00000310219:L187Q	ENSP00000310219:L187Q	L	+	2	0	HSPA6	159761632	1.000000	0.71417	0.748000	0.31131	0.440000	0.31957	6.802000	0.75175	1.351000	0.45789	0.398000	0.26397	CTG	.	.		0.647	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155		A	161495008	T	A	161495008	3	1	55	1	0	0	0	0	1	0	0	0	7424	1580	55	4	562	4	HSPA6	1	161495008	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	2904836	161495008	87755613	11	6919										
GLT25D2	23127	hgsc.bcm.edu	37	chr1	183933105	183933105	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gtctgatggggcttcaggggGatgggcaggtagccatagtg	19	6	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:183933105G>C	ENST00000361927.4	-	6	1253	c.882C>G	c.(880-882)atC>atG	p.I294M	COLGALT2_ENST00000546159.1_Missense_Mutation_p.I294M|COLGALT2_ENST00000367520.3_Missense_Mutation_p.I31M	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	294					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										GCTTCAGGGGGATGGGCAGGT	0.522																																					p.I294M		Atlas-SNP	.											.	.	.	.	0			c.C882G						.						155	122	133					1																	183933105		2203	4300	6503	SO:0001583	missense	23127	exon6			CAGGGGGATGGGC	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.882C>G	chr1.hg19:g.183933105G>C	ENSP00000354960:p.Ile294Met	244.0	0.0		286.0	129.0	NM_015101	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	hg19	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.761698	0.31228	.	.	ENSG00000198756	ENST00000546159;ENST00000361927;ENST00000367520	T;T	0.26223	1.75;1.75	5.74	3.86	0.44501	.	0.224837	0.44688	N	0.000438	T	0.08626	0.0214	N	0.01352	-0.895	0.36125	D	0.84576	B;B;B	0.25772	0.134;0.027;0.015	B;B;B	0.23275	0.045;0.027;0.007	T	0.12091	-1.0561	10	0.51188	T	0.08	.	7.3064	0.26451	0.1508:0.3373:0.5119:0.0	.	294;294;31	F5H3T5;Q8IYK4;Q5SXQ3	.;GT252_HUMAN;.	M	294;294;31	ENSP00000439112:I294M;ENSP00000354960:I294M	ENSP00000354960:I294M	I	-	3	3	GLT25D2	182199728	0.994000	0.37717	1.000000	0.80357	0.996000	0.88848	0.316000	0.19469	0.766000	0.33244	0.655000	0.94253	ATC	.	.		0.522	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		C	183933105	G	C	183933105	3	2	55	1	0	0	0	0	1	0	0	0	6475	1164	41	4	1026	4	GLT25D2	1	183933105	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	22438097	183933105	65317516	12	6920										
RGS18	64407	hgsc.bcm.edu	37	chr1	192128370	192128370	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agctaaggaaaaaagaaataGactaagtcttcttgtgcaga	9	5	2	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:192128370G>C	ENST00000367460.3	+	2	321	c.140G>C	c.(139-141)aGa>aCa	p.R47T	RGS18_ENST00000481707.1_3'UTR	NM_130782.2	NP_570138.1	Q9NS28	RGS18_HUMAN	regulator of G-protein signaling 18	47					G-protein coupled receptor signaling pathway (GO:0007186)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			kidney(1)|large_intestine(2)|lung(15)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AAAAGAAATAGACTAAGTCTT	0.378																																					p.R47T		Atlas-SNP	.											.	RGS18	54	.	0			c.G140C						.						49	52	51					1																	192128370		2203	4299	6502	SO:0001583	missense	64407	exon2			GAAATAGACTAAG	AF268036	CCDS1374.1	1q31.2	2008-02-05	2007-08-14		ENSG00000150681	ENSG00000150681		"Regulators of G-protein signaling"	14261	protein-coding gene	gene with protein product		607192	"regulator of G-protein signalling 18"			11042171	Standard	NM_130782		Approved	RGS13	uc001gsg.3	Q9NS28	OTTHUMG00000035592	ENST00000367460.3:c.140G>C	chr1.hg19:g.192128370G>C	ENSP00000356430:p.Arg47Thr	81.0	0.0		141.0	15.0	NM_130782	B2RD23	Missense_Mutation	SNP	ENST00000367460.3	hg19	CCDS1374.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.541478	0.45280	.	.	ENSG00000150681	ENST00000367460	T	0.58060	0.36	5.88	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.71986	0.3405	M	0.83774	2.66	0.53688	D	0.999974	D	0.76494	0.999	D	0.66716	0.946	T	0.76599	-0.2900	10	0.87932	D	0	.	12.1049	0.53807	0.0796:0.0:0.9204:0.0	.	47	Q9NS28	RGS18_HUMAN	T	47	ENSP00000356430:R47T	ENSP00000356430:R47T	R	+	2	0	RGS18	190394993	0.975000	0.34042	0.783000	0.31826	0.153000	0.21895	5.789000	0.69029	1.493000	0.48517	-0.145000	0.13849	AGA	.	.		0.378	RGS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086382.1	NM_130782		C	192128370	G	C	192128370	3	2	55	1	0	0	0	0	1	0	0	0	13315	942	33	4	146	4	RGS18	1	192128370	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	8195265	192128370	57122251	13	6921										
TROVE2	6738	hgsc.bcm.edu	37	chr1	193046176	193046176	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tgctgctttttataaaacatTtaaggtagtgatatgatttt	7	3	0	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:193046176T>G	ENST00000367446.3	+	5	1292	c.1082T>G	c.(1081-1083)tTt>tGt	p.F361C	TROVE2_ENST00000367444.3_Missense_Mutation_p.F361C|TROVE2_ENST00000460715.2_3'UTR|TROVE2_ENST00000416058.2_Missense_Mutation_p.F86C|TROVE2_ENST00000432079.1_Missense_Mutation_p.F86C|TROVE2_ENST00000400968.2_Missense_Mutation_p.F361C|TROVE2_ENST00000367443.1_Missense_Mutation_p.F361C|TROVE2_ENST00000367445.3_Missense_Mutation_p.F361C|TROVE2_ENST00000367441.1_Missense_Mutation_p.F361C	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2	361	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.|VWFA-like domain. {ECO:0000250}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)			biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						TATAAAACATTTAAGGTAGTG	0.294																																					p.F361C		Atlas-SNP	.											.	TROVE2	50	.	0			c.T1082G						.						53	49	50					1																	193046176		1824	4079	5903	SO:0001583	missense	6738	exon5			AAACATTTAAGGT	BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.1082T>G	chr1.hg19:g.193046176T>G	ENSP00000356416:p.Phe361Cys	90.0	0.0		154.0	64.0	NM_004600	B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Missense_Mutation	SNP	ENST00000367446.3	hg19	CCDS1379.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.985311	0.74474	.	.	ENSG00000116747	ENST00000400968;ENST00000416058;ENST00000367446;ENST00000367443;ENST00000367445;ENST00000367444;ENST00000367441	T;T;T;T;T;T;T	0.17213	2.29;2.29;2.29;2.29;2.29;2.29;2.29	5.81	5.81	0.92471	TROVE (2);	0.095324	0.64402	D	0.000001	T	0.49029	0.1533	M	0.89095	3.005	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.99;0.99;0.998;0.998	T	0.54118	-0.8341	10	0.42905	T	0.14	-17.0419	15.8769	0.79170	0.0:0.0:0.0:1.0	.	361;361;361;361	Q5LJ99;Q5LJ98;Q5LJA0;P10155	.;.;.;RO60_HUMAN	C	361;86;361;361;361;361;361	ENSP00000383752:F361C;ENSP00000411421:F86C;ENSP00000356416:F361C;ENSP00000356413:F361C;ENSP00000356415:F361C;ENSP00000356414:F361C;ENSP00000356411:F361C	ENSP00000356411:F361C	F	+	2	0	TROVE2	191312799	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	6.480000	0.73604	2.234000	0.73211	0.524000	0.50904	TTT	.	.		0.294	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	NM_004600		G	193046176	T	G	193046176	3	3	55	1	0	0	0	0	1	0	0	0	16591	1841	64	5	1096	5	TROVE2	1	193046176	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	917806	193046176	56204445	14	6922										
WDR64	128025	hgsc.bcm.edu	37	chr1	241946598	241946598	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tcaagcagctgctttcctggCgtgctcattctttggaaatt	9	10	3	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:241946598C>T	ENST00000366552.2	+	22	2797	c.2590C>T	c.(2590-2592)Cgt>Tgt	p.R864C	WDR64_ENST00000437684.2_Missense_Mutation_p.R697C	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	864										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GCTTTCCTGGCGTGCTCATTC	0.373																																					p.R864C		Atlas-SNP	.											.	WDR64	234	.	0			c.C2590T						.						70	66	67					1																	241946598		2203	4300	6503	SO:0001583	missense	128025	exon22			TCCTGGCGTGCTC	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.2590C>T	chr1.hg19:g.241946598C>T	ENSP00000355510:p.Arg864Cys	98.0	0.0		139.0	14.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	hg19		.	.	.	.	.	.	.	.	.	.	C	23.1	4.370414	0.82573	.	.	ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635	T;T;T	0.51071	0.72;0.88;0.72	5.66	5.66	0.87406	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.102421	0.43416	D	0.000562	T	0.73257	0.3564	M	0.87180	2.865	0.41243	D	0.986658	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.986	T	0.78170	-0.2308	10	0.87932	D	0	-6.1842	16.6706	0.85266	0.0:1.0:0.0:0.0	.	864;417	B1ANS9;D1MPS4	WDR64_HUMAN;.	C	864;697;468	ENSP00000355510:R864C;ENSP00000402446:R697C;ENSP00000406656:R468C	ENSP00000355510:R864C	R	+	1	0	WDR64	240013221	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.839000	0.39220	2.690000	0.91761	0.655000	0.94253	CGT	.	.		0.373	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		T	241946598	C	T	241946598	3	4	55	1	0	0	0	0	1	0	0	0	17330	768	27	1	2676	1	WDR64	1	241946598	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	48900422	241946598	7304023	15	6923										
EXO1	9156	hgsc.bcm.edu	37	chr1	242024779	242024779	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aaatacttttgaacagatcgAtgactacaatccagacactg	6	9	0	4			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr1:242024779A>G	ENST00000366548.3	+	10	1609	c.1016A>G	c.(1015-1017)gAt>gGt	p.D339G	EXO1_ENST00000518483.1_Missense_Mutation_p.D339G|EXO1_ENST00000348581.5_Missense_Mutation_p.D339G	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	339	Interaction with MSH3.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			GAACAGATCGATGACTACAAT	0.343								Editing and processing nucleases																													p.D339G		Atlas-SNP	.											.	EXO1	103	.	0			c.A1016G						.						79	79	79					1																	242024779		2203	4300	6503	SO:0001583	missense	9156	exon8			AGATCGATGACTA	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1016A>G	chr1.hg19:g.242024779A>G	ENSP00000355506:p.Asp339Gly	61.0	0.0		95.0	43.0	NM_006027	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	hg19	CCDS1620.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.708908	0.89018	.	.	ENSG00000174371	ENST00000366548;ENST00000348581;ENST00000518483	T;T;T	0.34667	1.35;1.35;1.35	5.1	5.1	0.69264	-3&apos (1); exonuclease, C-terminal domain (1);5&apos (1);	0.054032	0.64402	D	0.000001	T	0.58104	0.2099	M	0.74647	2.275	0.80722	D	1	D;D;D	0.67145	0.986;0.996;0.969	P;D;P	0.66847	0.897;0.947;0.861	T	0.59279	-0.7484	10	0.40728	T	0.16	-11.5482	14.8368	0.70190	1.0:0.0:0.0:0.0	.	339;339;339	A8K5H6;Q9UQ84-4;Q9UQ84	.;.;EXO1_HUMAN	G	339	ENSP00000355506:D339G;ENSP00000311873:D339G;ENSP00000430251:D339G	ENSP00000311873:D339G	D	+	2	0	EXO1	240091402	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	8.834000	0.92094	2.057000	0.61298	0.533000	0.62120	GAT	.	.		0.343	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027		G	242024779	A	G	242024779	3	3	55	1	0	0	0	0	1	0	0	0	5302	333	12	2	1042	2	EXO1	1	242024779	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	78181	242024779	7225842	16	6924										
CRIM1	51232	hgsc.bcm.edu	37	chr2	36691797	36691797	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gatgtctttgaatgtgttaaTggtacgtggggtttctcttg	13	4	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr2:36691797T>C	ENST00000280527.2	+	5	1357	c.990T>C	c.(988-990)aaT>aaC	p.N330N		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	330					insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				AATGTGTTAATGGTACGTGGG	0.507																																					p.N330N		Atlas-SNP	.											.	CRIM1	88	.	0			c.T990C						.						318	295	303					2																	36691797		2203	4300	6503	SO:0001630	splice_region_variant	51232	exon5			TGTTAATGGTACG	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"cysteine-rich motor neuron 1"	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.991+1T>C	chr2.hg19:g.36691797T>C		294.0	0.0		268.0	83.0	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Silent	SNP	ENST00000280527.2	hg19	CCDS1783.1																																																																																			.	.		0.507	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441	Silent	C	36691797	T	C	36691797	5	2	55	1	0	0	0	0	0	0	1	0	3875	1478	51	2	1008	2	CRIM1	2	36691797	Splice_Site	SNP	T	TCGA-CC-5259-01A-31D-A20W-10		36691797	206507576	17	6925										
TBC1D8	11138	hgsc.bcm.edu	37	chr2	101670763	101670763	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tcgggttcctcctcctgctcGgcgagcctgctgctggtctc	12	16	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr2:101670763G>A	ENST00000376840.4	-	4	392	c.393C>T	c.(391-393)gcC>gcT	p.A131A	TBC1D8_ENST00000409318.1_Silent_p.A146A			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	131					blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						CCTCCTGCTCGGCGAGCCTGC	0.602																																					p.A131A		Atlas-SNP	.											.	TBC1D8	169	.	0			c.C393T						.						22	25	24					2																	101670763		2022	4195	6217	SO:0001819	synonymous_variant	11138	exon4			CTGCTCGGCGAGC	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"BUB2-like protein 1", "vascular Rab-GAP/TBC-containing protein"					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.393C>T	chr2.hg19:g.101670763G>A		64.0	0.0		87.0	14.0	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	hg19	CCDS46375.1																																																																																			.	.		0.602	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063		A	101670763	G	A	101670763	2	1	55	1	0	0	0	0	0	0	0	1	15640	1103	39	1		1	TBC1D8	2	101670763	Silent	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	64978966	101670763	141528610	18	6926										
CXCR4	7852	hgsc.bcm.edu	37	chr2	136872834	136872834	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gtgtgacagcttggagatgaTaatgcaatagcaggacagga	14	5	0	3	rs374458307		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr2:136872834T>A	ENST00000241393.3	-	2	768	c.664A>T	c.(664-666)Atc>Ttc	p.I222F	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Missense_Mutation_p.I226F	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	222					activation of MAPK activity (GO:0000187)|ameboidal cell migration (GO:0001667)|apoptotic process (GO:0006915)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular response to cytokine stimulus (GO:0071345)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|inflammatory response (GO:0006954)|motor neuron axon guidance (GO:0008045)|myelin maintenance (GO:0043217)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|neutrophil activation (GO:0042119)|patterning of blood vessels (GO:0001569)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of chemotaxis (GO:0050920)|response to hypoxia (GO:0001666)|response to virus (GO:0009615)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)|myosin light chain binding (GO:0032027)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)|Plerixafor(DB06809)	TTGGAGATGATAATGCAATAG	0.517																																					p.I226F		Atlas-SNP	.											.	CXCR4	51	.	0			c.A676T						.						163	152	156					2																	136872834		2203	4300	6503	SO:0001583	missense	7852	exon1			AGATGATAATGCA	AF005058	CCDS33295.1, CCDS46420.1	2q21	2014-09-17	2002-08-22		ENSG00000121966	ENSG00000121966		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	2561	protein-coding gene	gene with protein product		162643	"chemokine (C-X-C motif), receptor 4 (fusin)"			9599023, 9379028	Standard	NM_001008540		Approved	LESTR, NPY3R, HM89, NPYY3R, D2S201E, fusin, HSY3RR, NPYR, CD184	uc002tuz.3	P61073	OTTHUMG00000153583	ENST00000241393.3:c.664A>T	chr2.hg19:g.136872834T>A	ENSP00000241393:p.Ile222Phe	133.0	0.0		126.0	85.0	NM_001008540	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Missense_Mutation	SNP	ENST00000241393.3	hg19	CCDS46420.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.738980	0.69304	.	.	ENSG00000121966	ENST00000409817;ENST00000241393;ENST00000537957	T;T	0.57436	0.4;0.4	6.17	6.17	0.99709	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.84379	0.5459	H	0.98786	4.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	D	0.90701	0.4620	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	222;226	P61073;P61073-2	CXCR4_HUMAN;.	F	226;222;92	ENSP00000386884:I226F;ENSP00000241393:I222F	ENSP00000241393:I222F	I	-	1	0	CXCR4	136589304	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.289000	0.72696	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.517	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1			A	136872834	T	A	136872834	3	1	55	1	0	0	0	0	1	0	0	0	4095	1406	49	4	398	4	CXCR4	2	136872834	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	35202071	136872834	106326539	19	6927										
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172700890	172700890	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	taagctcacctggagaaactGcgtgaattctgtgtagttaa	10	7	2	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr2:172700890G>A	ENST00000422440.2	-	5	491	c.454C>T	c.(454-456)Cag>Tag	p.Q152*	SLC25A12_ENST00000392592.4_Nonsense_Mutation_p.Q45*|SLC25A12_ENST00000472748.1_5'UTR	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	152	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	TGGAGAAACTGCGTGAATTCT	0.333																																					p.Q152X		Atlas-SNP	.											.	SLC25A12	59	.	0			c.C454T						.						147	162	157					2																	172700890		2203	4300	6503	SO:0001587	stop_gained	8604	exon5			GAAACTGCGTGAA	Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"Solute carriers", "EF-hand domain containing"	10982	protein-coding gene	gene with protein product		603667	"solute carrier family 25 (mitochondrial carrier, Aralar), member 12"			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.454C>T	chr2.hg19:g.172700890G>A	ENSP00000388658:p.Gln152*	85.0	0.0		77.0	49.0	NM_003705	B3KR64|Q96AM8	Nonsense_Mutation	SNP	ENST00000422440.2	hg19	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.372544	0.42003	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	.	.	.	5.8	5.8	0.92144	.	0.185538	0.48286	D	0.000198	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-8.4178	15.5404	0.76039	0.0:0.1374:0.8626:0.0	.	.	.	.	X	152;45	.	ENSP00000376371:Q45X	Q	-	1	0	SLC25A12	172409136	1.000000	0.71417	0.999000	0.59377	0.848000	0.48234	7.884000	0.87274	2.744000	0.94065	0.655000	0.94253	CAG	.	.		0.333	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		A	172700890	G	A	172700890	4	1	55	1	0	0	0	0	0	1	0	0	14489	1328	46	3	1638	3	SLC25A12	2	172700890	Nonsense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	35828056	172700890	70498483	20	6928										
PTH2R	5746	hgsc.bcm.edu	37	chr2	209345847	209345847	+	Frame_Shift_Del	DEL	G	G	-													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agttctagctaccaaaatctGggagaccaatgcagttgggc					rs151296979		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr2:209345847delG	ENST00000272847.2	+	10	1247	c.1034delG	c.(1033-1035)tggfs	p.W345fs	AC019185.4_ENST00000424628.1_RNA|PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	345					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)	p.W345L(2)		breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	ACCAAAATCTGGGAGACCAAT	0.358																																					p.W345fs		Atlas-Indel,Pindel	.											.	PTH2R	92	.	2	Substitution - Missense(2)	lung(2)	c.1033delT						.						101	99	99					2																	209345847		2203	4300	6503	SO:0001589	frameshift_variant	5746	exon10			.	BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"GPCR / Class B : Parathyroid hormone receptors"	9609	protein-coding gene	gene with protein product		601469	"parathyroid hormone receptor 2"	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1034delG	chr2.hg19:g.209345847delG	ENSP00000272847:p.Trp345fs	209.0	0.0		252.0	161.0	NM_005048	Q8N429	Frame_Shift_Del	DEL	ENST00000272847.2	hg19	CCDS2383.1																																																																																			.	.		0.358	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048		-	209345847	G	-	209345847	7	5	55	1	0	1	0	1	0	0	0	0	12773	1357	47	0	1072	0	PTH2R	2	209345847	Frame_Shift_Del	DEL	G	TCGA-CC-5259-01A-31D-A20W-10	36644957	209345847	33853526	21	6929										
C2orf62	375307	hgsc.bcm.edu	37	chr2	219225314	219225314	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agttcctcatcctccccatgGaacggaagatgagtttgctg	10	11	1	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr2:219225314G>T	ENST00000289388.3	+	5	423	c.394G>T	c.(394-396)Gaa>Taa	p.E132*	C2orf62_ENST00000481940.1_3'UTR|AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		132					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTCCCCATGGAACGGAAGAT	0.552																																					p.E132X		Atlas-SNP	.											.	C2orf62	28	.	0			c.G394T						.						99	83	88					2																	219225314		2203	4300	6503	SO:0001587	stop_gained	375307	exon5			CCCATGGAACGGA																												ENST00000289388.3:c.394G>T	chr2.hg19:g.219225314G>T	ENSP00000289388:p.Glu132*	39.0	0.0		53.0	34.0	NM_198559		Nonsense_Mutation	SNP	ENST00000289388.3	hg19	CCDS2414.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696440	0.30142	.	.	ENSG00000158428	ENST00000289388	.	.	.	4.36	3.48	0.39840	.	0.187935	0.44285	D	0.000479	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-3.8436	8.0276	0.30446	0.111:0.0:0.889:0.0	.	.	.	.	X	132	.	ENSP00000289388:E132X	E	+	1	0	C2orf62	218933558	1.000000	0.71417	0.815000	0.32552	0.192000	0.23643	3.157000	0.50716	1.047000	0.40274	-0.148000	0.13756	GAA	.	.		0.552	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			T	219225314	G	T	219225314	4	4	55	1	0	0	0	0	0	1	0	0	2183	1175	41	3	412	3	C2orf62	2	219225314	Nonsense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	9879467	219225314	23974059	22	6930										
ZNF142	7701	hgsc.bcm.edu	37	chr2	219508734	219508734	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gggcagtgtgggcagcggaaGgctcgcccctctccctggat	16	13	1	0	rs185508464	byFrequency	TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr2:219508734G>T	ENST00000449707.1	-	8	2926	c.2505C>A	c.(2503-2505)gcC>gcA	p.A835A	ZNF142_ENST00000411696.2_Silent_p.A835A	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	835					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGCAGCGGAAGGCTCGCCCCT	0.612																																					p.A835A	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.C2505A						.						153	162	159					2																	219508734		2079	4197	6276	SO:0001819	synonymous_variant	7701	exon8			GCGGAAGGCTCGC	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.2505C>A	chr2.hg19:g.219508734G>T		114.0	0.0		114.0	30.0	NM_001105537	Q92510	Silent	SNP	ENST00000449707.1	hg19	CCDS42817.1																																																																																			.	G|0.998;A|0.002		0.612	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		T	219508734	G	T	219508734	2	4	55	1	0	0	0	0	0	0	0	1	17746	987	35	3		3	ZNF142	2	219508734	Silent	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	283420	219508734	23690639	23	6931										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222365784	222365784	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tgtcagctctgaaaaagcctCggtcacaggtgcacgaggtg	13	10	3	1	rs375924623		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr2:222365784C>T	ENST00000281821.2	-	4	973	c.932G>A	c.(931-933)cGa>cAa	p.R311Q	EPHA4_ENST00000409938.1_Missense_Mutation_p.R311Q|EPHA4_ENST00000409854.1_Missense_Mutation_p.R311Q|EPHA4_ENST00000392071.4_Missense_Mutation_p.R260Q	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	311	Cys-rich.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GAAAAAGCCTCGGTCACAGGT	0.532																																					p.R311Q		Atlas-SNP	.											EPHA4_ENST00000281821,colon,carcinoma,0,2	EPHA4	263	.	0			c.G932A						.	C	GLN/ARG	0,4406		0,0,2203	147	124	131		932	6.1	1	2		131	1,8599	1.2+/-3.3	0,1,4299	no	missense	EPHA4	NM_004438.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	311/987	222365784	1,13005	2203	4300	6503	SO:0001583	missense	2043	exon4			AAGCCTCGGTCAC	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.932G>A	chr2.hg19:g.222365784C>T	ENSP00000281821:p.Arg311Gln	62.0	0.0		56.0	12.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.75|15.75	2.926449|2.926449	0.52759|0.52759	0.0|0.0	1.16E-4|1.16E-4	ENSG00000116106|ENSG00000116106	ENST00000441679|ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071	.|T;T;T;T	.|0.62232	.|0.04;0.04;0.04;0.04	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	.|0.060275	.|0.64402	.|D	.|0.000004	T|T	0.44456|0.44456	0.1294|0.1294	N|N	0.12746|0.12746	0.255|0.255	0.45962|0.45962	D|D	0.998785|0.998785	.|B	.|0.27910	.|0.193	.|B	.|0.21151	.|0.033	T|T	0.34403|0.34403	-0.9830|-0.9830	5|10	.|0.24483	.|T	.|0.36	.|.	16.8423|16.8423	0.85972|0.85972	0.0:0.8718:0.1281:0.0|0.0:0.8718:0.1281:0.0	.|.	.|311	.|P54764	.|EPHA4_HUMAN	K|Q	48|311;311;311;260	.|ENSP00000281821:R311Q;ENSP00000386276:R311Q;ENSP00000386829:R311Q;ENSP00000375923:R260Q	.|ENSP00000281821:R311Q	E|R	-|-	1|2	0|0	EPHA4|EPHA4	222074028|222074028	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.743000|3.743000	0.55104|0.55104	2.884000|2.884000	0.98904|0.98904	0.655000|0.655000	0.94253|0.94253	GAG|CGA	.	.		0.532	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222365784	C	T	222365784	3	4	55	1	0	0	0	0	1	0	0	0	5171	884	31	1	2084	1	EPHA4	2	222365784	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	2857050	222365784	20833589	24	6932										
FBXO36	130888	hgsc.bcm.edu	37	chr2	230787284	230787284	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ctgtaggacaaggcccgccgCctagcaaagactattaccag	10	13	0	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr2:230787284C>G	ENST00000283946.3	+	1	73	c.55C>G	c.(55-57)Cct>Gct	p.P19A	TRIP12_ENST00000389044.4_5'Flank|TRIP12_ENST00000283943.5_5'Flank|TRIP12_ENST00000389045.3_5'Flank|TRIP12_ENST00000409677.1_5'Flank|FBXO36_ENST00000373652.3_5'UTR|FBXO36_ENST00000409992.1_Missense_Mutation_p.P19A|TRIP12_ENST00000543084.1_5'Flank	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	19										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		AGGCCCGCCGCCTAGCAAAGA	0.622																																					p.P19A		Atlas-SNP	.											.	FBXO36	22	.	0			c.C55G						.						56	54	55					2																	230787284		2203	4300	6503	SO:0001583	missense	130888	exon1			CCGCCGCCTAGCA	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"F-boxes /  "other""	27020	protein-coding gene	gene with protein product		609105	"F-box only protein 36"			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.55C>G	chr2.hg19:g.230787284C>G	ENSP00000283946:p.Pro19Ala	248.0	0.0		205.0	41.0	NM_174899	B3KVQ6|Q53TE6|Q8WWD4	Missense_Mutation	SNP	ENST00000283946.3	hg19	CCDS2472.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.547149	0.27652	.	.	ENSG00000153832	ENST00000283946;ENST00000409992	T	0.66460	-0.21	4.07	4.07	0.47477	.	0.174193	0.37304	N	0.002152	T	0.77130	0.4085	M	0.85945	2.785	0.40447	D	0.980105	D;P	0.69078	0.997;0.805	P;B	0.52881	0.712;0.201	T	0.83180	-0.0089	10	0.87932	D	0	0.0812	13.2649	0.60128	0.0:1.0:0.0:0.0	.	19;19	Q8NEA4;B8ZZQ1	FBX36_HUMAN;.	A	19	ENSP00000283946:P19A	ENSP00000283946:P19A	P	+	1	0	FBXO36	230495528	1.000000	0.71417	0.962000	0.40283	0.150000	0.21749	2.762000	0.47597	2.113000	0.64589	0.655000	0.94253	CCT	.	.		0.622	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899		G	230787284	C	G	230787284	3	3	55	1	0	0	0	0	1	0	0	0	5753	739	26	4	57	4	FBXO36	2	230787284	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	8421500	230787284	12412089	25	6933										
PSMD1	5707	hgsc.bcm.edu	37	chr2	231937074	231937074	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gaactgttggcacccctattGcttctgtgcctggatccact	9	13	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr2:231937074G>T	ENST00000308696.6	+	7	988	c.826G>T	c.(826-828)Gct>Tct	p.A276S	PSMD1_ENST00000409643.1_Missense_Mutation_p.A276S|PSMD1_ENST00000373635.4_Missense_Mutation_p.A276S	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	276					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	CACCCCTATTGCTTCTGTGCC	0.398																																					p.A276S		Atlas-SNP	.											.	PSMD1	77	.	0			c.G826T						.						159	162	161					2																	231937074		2203	4300	6503	SO:0001583	missense	5707	exon7			CCTATTGCTTCTG	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.826G>T	chr2.hg19:g.231937074G>T	ENSP00000309474:p.Ala276Ser	104.0	0.0		113.0	18.0	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	hg19	CCDS2482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.02|16.02	3.005039|3.005039	0.54254|0.54254	.|.	.|.	ENSG00000173692|ENSG00000173692	ENST00000308696;ENST00000373635;ENST00000409643|ENST00000444007	.|.	.|.	.|.	5.98|5.98	5.09|5.09	0.68999|0.68999	Armadillo-type fold (1);|.	0.095545|.	0.64402|.	D|.	0.000001|.	T|T	0.45196|0.45196	0.1330|0.1330	N|N	0.11341|0.11341	0.13|0.13	0.45867|0.45867	D|D	0.998725|0.998725	B;B|.	0.06786|.	0.0;0.001|.	B;B|.	0.06405|.	0.0;0.002|.	T|T	0.40194|0.40194	-0.9576|-0.9576	9|5	0.08179|.	T|.	0.78|.	-9.7803|-9.7803	15.5537|15.5537	0.76173|0.76173	0.0:0.2607:0.7393:0.0|0.0:0.2607:0.7393:0.0	.|.	276;276|.	Q99460;Q99460-2|.	PSMD1_HUMAN;.|.	S|F	276|127	.|.	ENSP00000309474:A276S|.	A|C	+|+	1|2	0|0	PSMD1|PSMD1	231645318|231645318	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.991000|0.991000	0.79684|0.79684	4.854000|4.854000	0.62918|0.62918	1.506000|1.506000	0.48736|0.48736	0.650000|0.650000	0.86243|0.86243	GCT|TGC	.	.		0.398	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			T	231937074	G	T	231937074	3	4	55	1	0	0	0	0	1	0	0	0	12704	1319	46	3	852	3	PSMD1	2	231937074	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	1149790	231937074	11262299	26	6934										
SCN11A	11280	hgsc.bcm.edu	37	chr3	38888226	38888226	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cttggccaccccaaagctagAcaagtctccattgcaaagag	8	13	1	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr3:38888226A>T	ENST00000302328.3	-	26	5533	c.5335T>A	c.(5335-5337)Tct>Act	p.S1779T	SCN11A_ENST00000456224.3_Missense_Mutation_p.S1741T|SCN11A_ENST00000450244.1_Missense_Mutation_p.S1779T	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1779					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCAAAGCTAGACAAGTCTCCA	0.532																																					p.S1779T		Atlas-SNP	.											.	SCN11A	296	.	0			c.T5335A						.						160	141	148					3																	38888226		2203	4300	6503	SO:0001583	missense	11280	exon26			AGCTAGACAAGTC	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.5335T>A	chr3.hg19:g.38888226A>T	ENSP00000307599:p.Ser1779Thr	211.0	0.0		191.0	99.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	hg19	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	A	0.176	-1.067032	0.01934	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224	D;D;D	0.96168	-3.93;-3.93;-3.88	5.02	-9.2	0.00682	.	1.461070	0.04665	N	0.409654	D	0.87589	0.6215	N	0.20766	0.605	0.09310	N	1	B	0.17667	0.023	B	0.18263	0.021	T	0.77843	-0.2437	10	0.18710	T	0.47	.	7.767	0.28986	0.2719:0.0945:0.5404:0.0932	.	1779	Q9UI33	SCNBA_HUMAN	T	1779;1779;1741	ENSP00000307599:S1779T;ENSP00000400945:S1779T;ENSP00000416757:S1741T	ENSP00000307599:S1779T	S	-	1	0	SCN11A	38863230	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-1.003000	0.03682	-1.944000	0.01038	-1.162000	0.01777	TCT	.	.		0.532	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		T	38888226	A	T	38888226	3	4	55	1	0	0	0	0	1	0	0	0	13928	275	10	4	44	4	SCN11A	3	38888226	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10		38888226	159134204	27	6935										
ARIH2	10425	hgsc.bcm.edu	37	chr3	49006060	49006060	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agaattgagagagaaatacaGgcgctacctcttcagggact	11	8	2	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr3:49006060G>C	ENST00000356401.4	+	7	971	c.632G>C	c.(631-633)aGg>aCg	p.R211T	ARIH2_ENST00000449376.1_Missense_Mutation_p.R211T|ARIH2_ENST00000490095.1_3'UTR	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	211					developmental cell growth (GO:0048588)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organismal development (GO:0007275)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R211M(1)		cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		GAGAAATACAGGCGCTACCTC	0.512																																					p.R211T		Atlas-SNP	.											ARIH2,NS,carcinoma,0,1	ARIH2	32	.	1	Substitution - Missense(1)	lung(1)	c.G632C						.						166	162	163					3																	49006060		2203	4300	6503	SO:0001583	missense	10425	exon7			AATACAGGCGCTA	AF099149	CCDS2780.1	3p21	2013-10-03	2013-10-03		ENSG00000177479	ENSG00000177479			690	protein-coding gene	gene with protein product	"all-trans retinoic acid inducible RING finger"	605615	"ariadne (Drosophila) homolog 2", "ariadne homolog 2 (Drosophila)"			10422847, 24058416	Standard	XM_005264798		Approved	TRIAD1	uc003cvb.3	O95376	OTTHUMG00000133547	ENST00000356401.4:c.632G>C	chr3.hg19:g.49006060G>C	ENSP00000348769:p.Arg211Thr	177.0	0.0		145.0	19.0	NM_006321	Q9HBZ6|Q9UEM9	Missense_Mutation	SNP	ENST00000356401.4	hg19	CCDS2780.1	.	.	.	.	.	.	.	.	.	.	G	32	5.180134	0.94846	.	.	ENSG00000177479	ENST00000356401;ENST00000449376;ENST00000444790;ENST00000395481	T;T	0.80480	-1.38;-1.38	5.95	5.95	0.96441	Zinc finger, C6HC-type (2);	0.000000	0.85682	D	0.000000	D	0.86310	0.5902	L	0.42744	1.35	0.80722	D	1	D;D;P	0.59357	0.979;0.985;0.618	P;D;P	0.72338	0.76;0.977;0.447	T	0.81353	-0.0971	10	0.21540	T	0.41	.	20.3931	0.98965	0.0:0.0:1.0:0.0	.	218;211;211	B3KMG5;Q53ET9;O95376	.;.;ARI2_HUMAN	T	211;211;210;35	ENSP00000348769:R211T;ENSP00000403222:R211T	ENSP00000348769:R211T	R	+	2	0	ARIH2	48981064	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.604000	0.82830	2.824000	0.97209	0.655000	0.94253	AGG	.	.		0.512	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257525.1	NM_006321		C	49006060	G	C	49006060	3	2	55	1	0	0	0	0	1	0	0	0	924	1000	35	4	650	4	ARIH2	3	49006060	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	10117834	49006060	149016370	28	6936										
PHLDB2	90102	hgsc.bcm.edu	37	chr3	111603106	111603106	+	Frame_Shift_Del	DEL	C	C	-													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ctattctggctcctatttaaCcctctcacaacctgtgcctg							TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr3:111603106delC	ENST00000431670.2	+	2	593	c.182delC	c.(181-183)accfs	p.T61fs	PHLDB2_ENST00000393925.3_Frame_Shift_Del_p.T61fs|PHLDB2_ENST00000478922.1_Frame_Shift_Del_p.T61fs|PHLDB2_ENST00000477695.1_Frame_Shift_Del_p.T61fs|PHLDB2_ENST00000393923.3_Frame_Shift_Del_p.T88fs|PHLDB2_ENST00000481953.1_Frame_Shift_Del_p.T61fs|PHLDB2_ENST00000412622.1_Frame_Shift_Del_p.T61fs	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	61						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						TCCTATTTAACCCTCTCACAA	0.483																																					p.T88fs		Atlas-INDEL	.											.	PHLDB2	449	.	0			c.262delA						.						141	146	144					3																	111603106		2203	4300	6503	SO:0001589	frameshift_variant	90102	exon3			.		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"Pleckstrin homology (PH) domain containing"	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.182delC	chr3.hg19:g.111603106delC	ENSP00000405405:p.Thr61fs	101.0	0.0		109.0	66.0	NM_001134437	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Frame_Shift_Del	DEL	ENST00000431670.2	hg19	CCDS46886.1																																																																																			.	.		0.483	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		-	111603106	C	-	111603106	7	5	55	1	0	1	0	1	0	0	0	0	11861	507	18	0	269	0	PHLDB2	3	111603106	Frame_Shift_Del	DEL	C	TCGA-CC-5259-01A-31D-A20W-10	62597046	111603106	86419324	29	6937	31	3								
PHLDB2	90102	hgsc.bcm.edu	37	chr3	111603108	111603109	+	Frame_Shift_Del	DEL	CT	CT	-													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	attctggctcctatttaaccCtctcacaacctgtgcctgca							TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr3:111603108_111603109delCT	ENST00000431670.2	+	2	595_596	c.184_185delCT	c.(184-186)ctcfs	p.L62fs	PHLDB2_ENST00000393925.3_Frame_Shift_Del_p.L62fs|PHLDB2_ENST00000478922.1_Frame_Shift_Del_p.L62fs|PHLDB2_ENST00000477695.1_Frame_Shift_Del_p.L62fs|PHLDB2_ENST00000393923.3_Frame_Shift_Del_p.L89fs|PHLDB2_ENST00000481953.1_Frame_Shift_Del_p.L62fs|PHLDB2_ENST00000412622.1_Frame_Shift_Del_p.L62fs	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	62						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						CTATTTAACCCTCTCACAACCT	0.48																																					p.88_89del		Pindel	.											.	PHLDB2	449	.	0			c.264_265del						.																																			SO:0001589	frameshift_variant	90102	exon3			.		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"Pleckstrin homology (PH) domain containing"	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.184_185delCT	chr3.hg19:g.111603110_111603111delCT	ENSP00000405405:p.Leu62fs	0.0	0.0		43.0	43.0	NM_001134437	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Frame_Shift_Del	DEL	ENST00000431670.2	hg19	CCDS46886.1																																																																																			.	.		0.48	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		-	111603109	CT	-	111603108	7	5	55	1	0	1	0	1	0	0	0	0	11861	681	24	0	271	0	PHLDB2	3	111603108	Frame_Shift_Del	DEL	CT	TCGA-CC-5259-01A-31D-A20W-10	2	111603108	86419322	30	6938	31	3								
PHLDB2	90102	hgsc.bcm.edu	37	chr3	111603109	111603109	+	Missense_Mutation	SNP	T	T	G													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ttctggctcctatttaacccTctcacaacctgtgcctgcaa							TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr3:111603109T>G	ENST00000431670.2	+	2	596	c.185T>G	c.(184-186)cTc>cGc	p.L62R	PHLDB2_ENST00000393925.3_Missense_Mutation_p.L62R|PHLDB2_ENST00000478922.1_Missense_Mutation_p.L62R|PHLDB2_ENST00000477695.1_Missense_Mutation_p.L62R|PHLDB2_ENST00000393923.3_Missense_Mutation_p.L89R|PHLDB2_ENST00000481953.1_Missense_Mutation_p.L62R|PHLDB2_ENST00000412622.1_Missense_Mutation_p.L62R	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	62						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						TATTTAACCCTCTCACAACCT	0.478																																					p.L89R		Atlas-SNP	.											.	PHLDB2	449	.	0			c.T266G						.						141	146	144					3																	111603109		2203	4300	6503	SO:0001583	missense	90102	exon3			TAACCCTCTCACA		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"Pleckstrin homology (PH) domain containing"	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.185T>G	chr3.hg19:g.111603109T>G	ENSP00000405405:p.Leu62Arg	100.0	0.0		111.0	68.0	NM_001134437	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Missense_Mutation	SNP	ENST00000431670.2	hg19	CCDS46886.1	.	.	.	.	.	.	.	.	.	.	T	19.64	3.865890	0.71949	.	.	ENSG00000144824	ENST00000359729;ENST00000393923;ENST00000431670;ENST00000412622;ENST00000498699;ENST00000478922;ENST00000477695;ENST00000393925;ENST00000481953	T;T;T;T;T;T	0.50001	0.76;0.88;0.79;0.81;0.88;0.79	5.87	5.87	0.94306	.	0.063315	0.64402	D	0.000005	T	0.65154	0.2664	L	0.56769	1.78	0.43919	D	0.996567	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.994;0.999;0.999;0.998	T	0.67573	-0.5636	10	0.87932	D	0	.	14.0962	0.65023	0.0:0.0:0.0:1.0	.	62;62;62;62;89	Q86SQ0;G5E9V3;E9PDY7;Q86SQ0-2;Q86SQ0-3	PHLB2_HUMAN;.;.;.;.	R	89;89;62;62;62;62;62;62;62	ENSP00000377500:L89R;ENSP00000405405:L62R;ENSP00000405292:L62R;ENSP00000418296:L62R;ENSP00000377502:L62R;ENSP00000418319:L62R	ENSP00000352764:L89R	L	+	2	0	PHLDB2	113085799	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.259000	0.65485	2.371000	0.80710	0.533000	0.62120	CTC	.	.		0.478	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		G	111603109	T	G	111603109	3	3	55	1	0	0	0	0	1	0	0	0	11861	1551	54	5	272	5	PHLDB2	3	111603109	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	1	111603109	86419321	31	6939	31	3								
TMPRSS7	344805	hgsc.bcm.edu	37	chr3	111794166	111794166	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	acatgccctttctccaccaaAgcctgcagcaggagttcctc	7	16	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr3:111794166A>G	ENST00000452346.2	+	15	1786		c.e15-1		TMPRSS7_ENST00000419127.1_Splice_Site			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7						proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TCTCCACCAAAGCCTGCAGCA	0.532																																					.		Atlas-SNP	.											.	TMPRSS7	126	.	0			c.1406-2A>G						.						77	82	80					3																	111794166		1960	4153	6113	SO:0001630	splice_region_variant	344805	exon13			CACCAAAGCCTGC	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.1784-1A>G	chr3.hg19:g.111794166A>G		109.0	0.0		104.0	6.0	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Splice_Site	SNP	ENST00000452346.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.78	3.217759	0.58560	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1495	0.72687	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMPRSS7	113276856	1.000000	0.71417	0.994000	0.49952	0.557000	0.35523	4.074000	0.57577	2.210000	0.71456	0.533000	0.62120	.	.	.		0.532	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599	Intron	G	111794166	A	G	111794166	5	3	55	1	0	0	0	0	0	0	1	0	16267	86	3	2	1450	2	TMPRSS7	3	111794166	Splice_Site	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	191057	111794166	86228264	32	6940										
CP	1356	hgsc.bcm.edu	37	chr3	148927024	148927024	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ttctgttactctcctggaagTcttcgttgtctttgtcaact	7	10	5	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr3:148927024T>A	ENST00000264613.6	-	4	1017	c.755A>T	c.(754-756)gAc>gTc	p.D252V		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	252	F5/8 type A 1.|Plastocyanin-like 2.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CTCCTGGAAGTCTTCGTTGTC	0.373																																					p.D252V		Atlas-SNP	.											.	CP	112	.	0			c.A755T						.						238	224	229					3																	148927024		2203	4300	6503	SO:0001583	missense	1356	exon4			TGGAAGTCTTCGT	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.755A>T	chr3.hg19:g.148927024T>A	ENSP00000264613:p.Asp252Val	261.0	0.0		240.0	119.0	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	hg19	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.138204	0.56936	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98876	-5.2;-5.2	5.5	4.27	0.50696	Cupredoxin (2);Multicopper oxidase, type 1 (1);	0.215379	0.47093	D	0.000253	D	0.98163	0.9393	M	0.63208	1.945	0.80722	D	1	P;P;P	0.51791	0.948;0.948;0.907	P;P;P	0.55999	0.664;0.789;0.664	D	0.97231	0.9884	10	0.25106	T	0.35	-22.3529	12.199	0.54313	0.0:0.0:0.1424:0.8576	.	252;252;252	A8K5A4;P00450;Q1L857	.;CERU_HUMAN;.	V	252;35	ENSP00000264613:D252V;ENSP00000420545:D35V	ENSP00000264613:D252V	D	-	2	0	CP	150409714	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	4.683000	0.61679	2.064000	0.61679	0.528000	0.53228	GAC	.	.		0.373	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		A	148927024	T	A	148927024	3	1	55	1	0	0	0	0	1	0	0	0	3789	1667	58	4	2506	4	CP	3	148927024	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	37132858	148927024	49095406	33	6941										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ctacacgagatcctctctctGaaatcactgagcaggagaaa	8	11	3	4	rs121913273		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E542K	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,carcinoma,0,2	PIK3CA	8460	.	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)	c.G1624A						.						56	56	56					3																	178936082		1809	4069	5878	SO:0001583	missense	5290	exon10			CTCTCTGAAATCA		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	chr3.hg19:g.178936082G>A	ENSP00000263967:p.Glu542Lys	331.0	0.0		361.0	157.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	.	.		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178936082	G	A	178936082	3	1	55	1	0	0	0	0	1	0	0	0	11922	1291	45	3	1658	3	PIK3CA	3	178936082	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	30009058	178936082	19086348	34	6942										
DLG1	1739	hgsc.bcm.edu	37	chr3	197023346	197023346	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aaggtgcaatgctctctgggTatctgagaagaaaaagcaga	12	6	2	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr3:197023346T>A	ENST00000419354.1	-	3	308	c.22A>T	c.(22-24)Acc>Tcc	p.T8S	DLG1_ENST00000314062.3_Missense_Mutation_p.T8S|DLG1-AS1_ENST00000430666.1_RNA|DLG1_ENST00000392382.2_Missense_Mutation_p.T8S|DLG1_ENST00000357674.4_Missense_Mutation_p.T8S|DLG1_ENST00000422288.1_Missense_Mutation_p.T8S|MIR4797_ENST00000577559.1_RNA|DLG1-AS1_ENST00000414529.1_RNA|DLG1_ENST00000485409.1_5'UTR|DLG1_ENST00000346964.2_Missense_Mutation_p.T8S|DLG1_ENST00000448528.2_Missense_Mutation_p.T8S|DLG1_ENST00000450955.1_Missense_Mutation_p.T8S			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	8	L27. {ECO:0000255|PROSITE- ProRule:PRU00365}.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		GCTCTCTGGGTATCTGAGAAG	0.363																																					p.T8S		Atlas-SNP	.											.	DLG1	120	.	0			c.A22T						.						116	116	116					3																	197023346		2203	4300	6503	SO:0001583	missense	1739	exon3			TCTGGGTATCTGA	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"discs large homolog 1", "presynaptic protein SAP97", "synapse-associated protein 97"	601014	"discs, large (Drosophila) homolog 1"			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.22A>T	chr3.hg19:g.197023346T>A	ENSP00000407531:p.Thr8Ser	81.0	0.0		116.0	49.0	NM_001204386	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	hg19	CCDS43194.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.491614	0.64074	.	.	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000422288;ENST00000448528;ENST00000392382;ENST00000450955;ENST00000456699;ENST00000392380;ENST00000419553;ENST00000436682;ENST00000412364;ENST00000434148	T;T;T;T;T;T;T;T;T;T;T	0.47869	2.55;2.51;2.48;2.55;2.48;2.55;2.52;2.51;0.85;0.83;0.84	5.02	5.02	0.67125	L27 (2);L27-1 (1);	0.067727	0.64402	D	0.000016	T	0.40886	0.1135	L	0.36672	1.1	0.49582	D	0.999809	B;B;B;B	0.29988	0.264;0.073;0.149;0.264	B;B;B;B	0.32211	0.124;0.088;0.142;0.124	T	0.41556	-0.9502	10	0.66056	D	0.02	.	13.338	0.60528	0.0:0.0:0.0:1.0	.	8;8;8;8	Q12959-4;Q12959-3;Q12959;Q12959-2	.;.;DLG1_HUMAN;.	S	8	ENSP00000345731:T8S;ENSP00000350303:T8S;ENSP00000321087:T8S;ENSP00000407531:T8S;ENSP00000413238:T8S;ENSP00000391732:T8S;ENSP00000376187:T8S;ENSP00000411278:T8S;ENSP00000396474:T8S;ENSP00000376185:T8S;ENSP00000414189:T8S	ENSP00000321087:T8S	T	-	1	0	DLG1	198507743	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.546000	0.53656	2.185000	0.69588	0.528000	0.53228	ACC	.	.		0.363	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087		A	197023346	T	A	197023346	3	1	55	1	0	0	0	0	1	0	0	0	4556	1638	57	4	2892	4	DLG1	3	197023346	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	18087264	197023346	999084	35	6943										
C4orf44	345222	hgsc.bcm.edu	37	chr4	3251094	3251094	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gggcccgcaactggacggacGccgagatgcgcggcctcatg	16	14	1	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr4:3251094G>T	ENST00000438480.2	+	1	1892	c.145G>T	c.(145-147)Gcc>Tcc	p.A49S	MSANTD1_ENST00000510580.1_Missense_Mutation_p.A49S|MSANTD1_ENST00000507492.1_Missense_Mutation_p.A36S	NM_001042690.1	NP_001036155.1	Q6ZTZ1	MSD1_HUMAN	Myb/SANT-like DNA-binding domain containing 1	49	Myb-like.									endometrium(1)|lung(2)	3						CTGGACGGACGCCGAGATGCG	0.682																																					p.A49S		Atlas-SNP	.											.	MSANTD1	14	.	0			c.G145T						.						19	20	20					4																	3251094		2162	4263	6425	SO:0001583	missense	345222	exon1			ACGGACGCCGAGA		CCDS47003.1	4p16.2	2012-03-02	2012-03-02	2012-03-02	ENSG00000188981	ENSG00000188981			33741	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 44"	C4orf44			Standard	NM_001042690		Approved	LOC345222	uc003ggs.3	Q6ZTZ1	OTTHUMG00000159977	ENST00000438480.2:c.145G>T	chr4.hg19:g.3251094G>T	ENSP00000411584:p.Ala49Ser	66.0	0.0		90.0	29.0	NM_001042690	C9J6V0	Missense_Mutation	SNP	ENST00000438480.2	hg19	CCDS47003.1	.	.	.	.	.	.	.	.	.	.	G	16.99	3.273875	0.59649	.	.	ENSG00000188981	ENST00000507492;ENST00000438480;ENST00000510580	T;T;T	0.42900	0.96;0.96;0.96	4.68	4.68	0.58851	.	0.362337	0.26220	N	0.025629	T	0.26268	0.0641	N	0.03324	-0.35	0.38826	D	0.955738	P;P	0.35242	0.492;0.492	B;B	0.41174	0.349;0.24	T	0.20974	-1.0259	10	0.16896	T	0.51	.	16.5959	0.84796	0.0:0.0:1.0:0.0	.	49;49	D6RD98;Q6ZTZ1	.;CD044_HUMAN	S	36;49;49	ENSP00000423547:A36S;ENSP00000411584:A49S;ENSP00000420966:A49S	ENSP00000411584:A49S	A	+	1	0	C4orf44	3220892	1.000000	0.71417	0.388000	0.26195	0.965000	0.64279	4.970000	0.63742	2.140000	0.66376	0.591000	0.81541	GCC	.	.		0.682	MSANTD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370924.1	NM_001012982		T	3251094	G	T	3251094	3	4	55	1	0	0	0	0	1	0	0	0	2274	1087	38	1	147	1	C4orf44	4	3251094	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10		3251094	187903182	36	6944										
KCTD8	386617	hgsc.bcm.edu	37	chr4	44177224	44177224	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gtgactttgtcatgtttcctAtcttcatgttcttgtttagg	8	7	4	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr4:44177224A>T	ENST00000360029.3	-	2	1288	c.1005T>A	c.(1003-1005)gaT>gaA	p.D335E		NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	335					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						CATGTTTCCTATCTTCATGTT	0.398										HNSCC(17;0.042)																											p.D335E		Atlas-SNP	.											.	KCTD8	96	.	0			c.T1005A						.						116	109	111					4																	44177224		2203	4300	6503	SO:0001583	missense	386617	exon2			TTTCCTATCTTCA	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.1005T>A	chr4.hg19:g.44177224A>T	ENSP00000353129:p.Asp335Glu	116.0	0.0		113.0	53.0	NM_198353	A2RU39	Missense_Mutation	SNP	ENST00000360029.3	hg19	CCDS3467.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.231|9.231	1.035724|1.035724	0.19590|0.19590	.|.	.|.	ENSG00000183783|ENSG00000183783	ENST00000360029|ENST00000515268	T|.	0.36157|.	1.27|.	4.65|4.65	-4.54|-4.54	0.03452|0.03452	.|.	0.123995|.	0.35772|.	N|.	0.002991|.	T|T	0.16599|0.16599	0.0399|0.0399	N|N	0.14661|0.14661	0.345|0.345	0.22888|0.22888	N|N	0.998602|0.998602	B|.	0.09022|.	0.002|.	B|.	0.08055|.	0.003|.	T|T	0.28299|0.28299	-1.0048|-1.0048	10|5	0.02654|.	T|.	1|.	.|.	5.3121|5.3121	0.15835|0.15835	0.1932:0.1054:0.5168:0.1846|0.1932:0.1054:0.5168:0.1846	.|.	335|.	Q6ZWB6|.	KCTD8_HUMAN|.	E|K	335|71	ENSP00000353129:D335E|.	ENSP00000353129:D335E|.	D|I	-|-	3|2	2|0	KCTD8|KCTD8	43871981|43871981	0.395000|0.395000	0.25254|0.25254	0.953000|0.953000	0.39169|0.39169	0.950000|0.950000	0.60333|0.60333	-0.597000|-0.597000	0.05713|0.05713	-0.945000|-0.945000	0.03681|0.03681	-0.334000|-0.334000	0.08254|0.08254	GAT|ATA	.	.		0.398	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			T	44177224	A	T	44177224	3	4	55	1	0	0	0	0	1	0	0	0	8124	446	16	4	420	4	KCTD8	4	44177224	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	40926130	44177224	146977052	37	6945										
TECRL	253017	hgsc.bcm.edu	37	chr4	65274943	65274943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agttggtcttagagggcccgCtgagagtacaagttttgaca	13	7	1	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr4:65274943C>T	ENST00000381210.3	-	1	237	c.127G>A	c.(127-129)Gcg>Acg	p.A43T	TECRL_ENST00000507440.1_Missense_Mutation_p.A43T	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	43					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(2)|kidney(5)|large_intestine(7)|lung(30)|prostate(1)|skin(1)|stomach(1)	47						AGAGGGCCCGCTGAGAGTACA	0.388																																					p.A43T		Atlas-SNP	.											.	TECRL	106	.	0			c.G127A						.						84	85	84					4																	65274943		2203	4300	6503	SO:0001583	missense	253017	exon1			GGCCCGCTGAGAG	AL833108	CCDS33990.1	4q13.1	2009-07-21			ENSG00000205678	ENSG00000205678			27365	protein-coding gene	gene with protein product	"glycoprotein, synaptic 2-like"					12477932	Standard	NM_001010874		Approved	GPSN2L, SRD5A2L2, DKFZp313D0829, DKFZp313B2333, TERL	uc003hcv.3	Q5HYJ1	OTTHUMG00000160680	ENST00000381210.3:c.127G>A	chr4.hg19:g.65274943C>T	ENSP00000370607:p.Ala43Thr	123.0	0.0		123.0	12.0	NM_001010874		Missense_Mutation	SNP	ENST00000381210.3	hg19	CCDS33990.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.830169	0.32329	.	.	ENSG00000205678	ENST00000507440;ENST00000381210;ENST00000509536	T;T;T	0.46063	0.88;0.88;0.88	4.99	4.99	0.66335	.	0.250003	0.34531	N	0.003888	T	0.46560	0.1399	M	0.72118	2.19	0.31191	N	0.700919	P;P	0.46987	0.72;0.888	B;B	0.42163	0.275;0.378	T	0.62282	-0.6887	10	0.72032	D	0.01	-0.9371	15.3559	0.74425	0.0:1.0:0.0:0.0	.	43;43	Q6IN47;Q5HYJ1	.;TECRL_HUMAN	T	43	ENSP00000426043:A43T;ENSP00000370607:A43T;ENSP00000422497:A43T	ENSP00000370607:A43T	A	-	1	0	TECRL	64957538	1.000000	0.71417	0.876000	0.34364	0.015000	0.08874	1.694000	0.37752	2.471000	0.83476	0.655000	0.94253	GCG	.	.		0.388	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874		T	65274943	C	T	65274943	3	4	55	1	0	0	0	0	1	0	0	0	15761	797	28	3	1012	3	TECRL	4	65274943	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	21097719	65274943	125879333	38	6946										
UBE2D3	7323	hgsc.bcm.edu	37	chr4	103722609	103722609	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ttatttcactagaaatatttAcctttagaaattgttaaagc	4	5	1	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr4:103722609A>C	ENST00000453744.2	-	6	818		c.e6+1		UBE2D3_ENST00000394803.5_Splice_Site|UBE2D3_ENST00000507845.1_Splice_Site|UBE2D3_ENST00000349311.8_Splice_Site|UBE2D3_ENST00000338145.3_Splice_Site|UBE2D3_ENST00000502404.1_Splice_Site|UBE2D3_ENST00000394801.4_Splice_Site|UBE2D3_ENST00000394804.2_Splice_Site|UBE2D3_ENST00000343106.5_Splice_Site|UBE2D3_ENST00000504211.1_Splice_Site|UBE2D3_ENST00000350435.7_Splice_Site|UBE2D3_ENST00000357194.6_Splice_Site|UBE2D3_ENST00000321805.7_Splice_Site|UBE2D3_ENST00000505207.1_Splice_Site	NM_181891.1	NP_871620.1	P61077	UB2D3_HUMAN	ubiquitin-conjugating enzyme E2D 3						apoptotic process (GO:0006915)|BMP signaling pathway (GO:0030509)|cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|lung(3)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)		AGAAATATTTACCTTTAGAAA	0.308																																					.		Atlas-SNP	.											.	UBE2D3	25	.	0			c.304+2T>G						.						57	61	60					4																	103722609		2203	4290	6493	SO:0001630	splice_region_variant	7323	exon7			ATATTTACCTTTA	U39318	CCDS3659.1, CCDS3660.1, CCDS3661.1, CCDS75172.1	4q24	2011-05-19	2011-05-19		ENSG00000109332	ENSG00000109332		"Ubiquitin-conjugating enzymes E2"	12476	protein-coding gene	gene with protein product		602963	"ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)"			8530467	Standard	NM_181886		Approved	UbcH5C	uc003hwl.3	P61077	OTTHUMG00000131119	ENST00000453744.2:c.304+1T>G	chr4.hg19:g.103722609A>C		274.0	0.0		239.0	180.0	NM_003340	A6NJ93|A6NJB1|A6NM99|P47986|Q6IB88|Q6NXS4|Q8N924	Splice_Site	SNP	ENST00000453744.2	hg19	CCDS3660.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.151496	0.78001	.	.	ENSG00000109332	ENST00000453744;ENST00000394801;ENST00000394803;ENST00000394804;ENST00000343106;ENST00000321805;ENST00000350435;ENST00000338145;ENST00000349311;ENST00000504211;ENST00000357194;ENST00000505207;ENST00000507845;ENST00000502404	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4591	0.75339	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBE2D3	103941719	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.030000	0.93725	2.105000	0.64084	0.477000	0.44152	.	.	.		0.308	UBE2D3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253791.2	NM_181893	Intron	C	103722609	A	C	103722609	5	2	55	1	0	0	0	0	0	0	1	0	16865	405	14	5	202	5	UBE2D3	4	103722609	Splice_Site	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	38447666	103722609	87431667	39	6947										
SPATA5	166378	hgsc.bcm.edu	37	chr4	123978434	123978445	+	Splice_Site	DEL	AAAGGGGCAGGT	AAAGGGGCAGGT	-													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	actggatgccttagcagttgAaaggggcaggtaagaagtat							TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	AAAGGGGCAGGT	AAAGGGGCAGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr4:123978434_123978445delAAAGGGGCAGGT	ENST00000274008.4	+	13	2273_2282	c.2204_2213delAAAGGGGCAGGT	c.(2203-2214)gaaaggggcagg>gg	p.ERGR735del	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	735					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						TTAGCAGTTGAAAGGGGCAGGTAAGAAGTATT	0.349																																					p.735_738del		Atlas-Indel,Pindel	.											.	SPATA5	62	.	0			c.2203_2213del						.																																			SO:0001630	splice_region_variant	166378	exon13			.	AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"ATPases / AAA-type"	18119	protein-coding gene	gene with protein product	"ATPase family gene 2 homolog (S. cerevisiae)"	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.2213+1AAAGGGGCAGGT>-	chr4.hg19:g.123978434_123978445delAAAGGGGCAGGT		178.0	0.0		146.0	39.0	NM_145207	C9JT97|Q86XW1|Q8NI20|Q8TDL7	Frame_Shift_Del	DEL	ENST00000274008.4	hg19	CCDS3730.1																																																																																			.	.		0.349	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	NM_145207	In_Frame_Del	-	123978445	AAAGGGGCAGGT	-	123978434	8	5	55	1	0	1	0	1	0	0	1	0	15026	246	9	0	2254	0	SPATA5	4	123978434	Splice_Site	DEL	AAAGGGGCAGGT	TCGA-CC-5259-01A-31D-A20W-10	20255825	123978434	67175842	40	6948										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153273838	153273838	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ggcaacaaaactccacagtaAaggcaaatgcagctcagtat	8	10	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr4:153273838A>T	ENST00000281708.4	-	3	1731				FBXW7_ENST00000263981.5_Silent_p.L15L|FBXW7_ENST00000603841.1_Intron|FBXW7_ENST00000296555.5_Intron|FBXW7_ENST00000603548.1_Intron	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase						cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)			NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CTCCACAGTAAAGGCAAATGC	0.458			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																p.L15L		Atlas-SNP	.		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	.	FBXW7	2157	.	0			c.T45A						.						73	69	70					4																	153273838		2203	4300	6503	SO:0001627	intron_variant	55294	exon1			ACAGTAAAGGCAA	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.502-2562T>A	chr4.hg19:g.153273838A>T		55.0	0.0		57.0	17.0	NM_018315	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	hg19	CCDS3777.1																																																																																			.	.		0.458	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153273838	A	T	153273838	1	4	55	0	1	0	0	0	0	0	0	0	5777	1	1	4		4	FBXW7	4	153273838	Intron	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	29295404	153273838	37880438	41	6949										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155243495	155243495	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aacattacctgaatattaacAactgcctgtccttgaagagg	7	9	0	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr4:155243495A>T	ENST00000357232.4	-	13	2798	c.2799T>A	c.(2797-2799)gtT>gtA	p.V933V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	933	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GAATATTAACAACTGCCTGTC	0.363																																					p.V933V		Atlas-SNP	.											.	DCHS2	594	.	0			c.T2799A						.						152	138	143					4																	155243495		2203	4300	6503	SO:0001819	synonymous_variant	54798	exon13			ATTAACAACTGCC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.2799T>A	chr4.hg19:g.155243495A>T		85.0	0.0		110.0	48.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	hg19	CCDS3785.1																																																																																			.	.		0.363	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		T	155243495	A	T	155243495	2	4	55	1	0	0	0	0	0	0	0	1	4290	117	5	4		4	DCHS2	4	155243495	Silent	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	1969657	155243495	35910781	42	6950										
VEGFC	7424	hgsc.bcm.edu	37	chr4	177605084	177605085	+	Frame_Shift_Del	DEL	AT	AT	-													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aaacagtacaatcttagctcAtcatttgtggtcttttccaa					rs3062984|rs398108361|rs5864401|rs397710947|rs201525483	byFrequency	TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr4:177605084_177605085delAT	ENST00000280193.2	-	7	1670_1671	c.1255_1256delAT	c.(1255-1257)atgfs	p.M419fs	RP11-313E19.2_ENST00000509194.1_RNA|RP11-313E19.2_ENST00000504017.1_RNA	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	0					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)			biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		ATCTTAGCTCATCATTTGTGGT	0.436																																					p.419_419del		Atlas-INDEL	.											.	VEGFC	94	.	0			c.1256_1257del						.																																			SO:0001589	frameshift_variant	7424	exon7			.	BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"vascular endothelial growth factor-related protein"	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.1255_1256delAT	chr4.hg19:g.177605084_177605085delAT	ENSP00000280193:p.Met419fs	85.0	0.0		103.0	49.0	NM_005429	B2R9Q8	Frame_Shift_Del	DEL	ENST00000280193.2	hg19	CCDS43285.1																																																																																			.	.		0.436	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		-	177605085	AT	-	177605084	7	5	55	1	0	1	0	1	0	0	0	0	17167	217	8	0	10	0	VEGFC	4	177605084	Frame_Shift_Del	DEL	AT	TCGA-CC-5259-01A-31D-A20W-10	22361589	177605084	13549192	43	6951	32	2								
VEGFC	7424	hgsc.bcm.edu	37	chr4	177605087	177605087	+	Missense_Mutation	SNP	A	A	C													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cagtacaatcttagctcatcAtttgtggtcttttccaatat							TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr4:177605087A>C	ENST00000280193.2	-	7	1668	c.1253T>G	c.(1252-1254)aTg>aGg	p.M418R	RP11-313E19.2_ENST00000509194.1_RNA|RP11-313E19.2_ENST00000504017.1_RNA	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	418					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)			biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		TTAGCTCATCATTTGTGGTCT	0.433																																					p.M418R		Atlas-SNP	.											.	VEGFC	94	.	0			c.T1253G						.						130	119	122					4																	177605087		1871	4101	5972	SO:0001583	missense	7424	exon7			CTCATCATTTGTG	BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"vascular endothelial growth factor-related protein"	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.1253T>G	chr4.hg19:g.177605087A>C	ENSP00000280193:p.Met418Arg	84.0	0.0		108.0	8.0	NM_005429	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	hg19	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	A	0.014	-1.591238	0.00864	.	.	ENSG00000150630	ENST00000280193	.	.	.	.	.	.	.	0.901625	0.09679	N	0.770027	T	0.26593	0.0650	N	0.24115	0.695	0.09310	N	1	B	0.20368	0.044	B	0.19946	0.027	T	0.29458	-1.0011	7	0.87932	D	0	.	.	.	.	.	418	P49767	VEGFC_HUMAN	R	418	.	ENSP00000280193:M418R	M	-	2	0	VEGFC	177842081	0.001000	0.12720	0.018000	0.16275	0.076000	0.17211	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	ATG	.	.		0.433	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		C	177605087	A	C	177605087	3	2	55	1	0	0	0	0	1	0	0	0	17167	217	8	5	13	5	VEGFC	4	177605087	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	3	177605087	13549189	44	6952	32	2								
MYO10	4651	hgsc.bcm.edu	37	chr5	16761637	16761637	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tctgttcttctccaagatacCtcggacatcatattgcacct	5	13	4	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr5:16761637C>A	ENST00000513610.1	-	17	2129	c.1675G>T	c.(1675-1677)Ggt>Tgt	p.G559C		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	559	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						TCCAAGATACCTCGGACATCA	0.393																																					p.G559C		Atlas-SNP	.											.	MYO10	198	.	0			c.G1675T						.						99	96	97					5																	16761637		1841	4092	5933	SO:0001583	missense	4651	exon17			AGATACCTCGGAC	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.1675G>T	chr5.hg19:g.16761637C>A	ENSP00000421280:p.Gly559Cys	59.0	0.0		53.0	29.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	hg19	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.896607	0.91962	.	.	ENSG00000145555	ENST00000513610;ENST00000513882	T;T	0.76060	-0.99;-0.99	5.82	5.82	0.92795	Myosin head, motor domain (2);	.	.	.	.	D	0.92681	0.7674	H	0.98936	4.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.95040	0.8177	9	0.87932	D	0	.	20.1143	0.97922	0.0:1.0:0.0:0.0	.	200;559	Q69YP8;Q9HD67	.;MYO10_HUMAN	C	559;570	ENSP00000421280:G559C;ENSP00000421309:G570C	ENSP00000421280:G559C	G	-	1	0	MYO10	16814637	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.763000	0.85283	2.765000	0.95021	0.650000	0.86243	GGT	.	.		0.393	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16761637	C	A	16761637	3	1	55	1	0	0	0	0	1	0	0	0	10071	681	24	3	4601	3	MYO10	5	16761637	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10		16761637	164153623	45	6953										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38350697	38350697	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agggcggctgagctctcctcGgcatgtcaccactttgtccc	11	15	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr5:38350697G>C	ENST00000354891.3	+	4	732	c.386G>C	c.(385-387)cGg>cCg	p.R129P	EGFLAM_ENST00000322350.5_Missense_Mutation_p.R129P	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	129	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					AGCTCTCCTCGGCATGTCACC	0.478																																					p.R129P	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.G386C						.						87	80	82					5																	38350697		2203	4300	6503	SO:0001583	missense	133584	exon4			CTCCTCGGCATGT	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.386G>C	chr5.hg19:g.38350697G>C	ENSP00000346964:p.Arg129Pro	74.0	0.0		75.0	23.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	hg19	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	g	16.05	3.012545	0.54468	.	.	ENSG00000164318	ENST00000354891;ENST00000322350	T;T	0.53640	0.61;0.61	4.92	-4.65	0.03339	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.256111	0.36200	N	0.002729	T	0.49029	0.1533	L	0.60455	1.87	0.31311	N	0.687192	D;D	0.56521	0.96;0.976	P;P	0.57324	0.662;0.818	T	0.55673	-0.8104	10	0.72032	D	0.01	-29.3369	7.2105	0.25931	0.5367:0.0:0.3513:0.112	.	129;129	Q63HQ2;Q63HQ2-2	EGFLA_HUMAN;.	P	129	ENSP00000346964:R129P;ENSP00000313084:R129P	ENSP00000313084:R129P	R	+	2	0	EGFLAM	38386454	0.000000	0.05858	0.079000	0.20413	0.843000	0.47879	-0.806000	0.04525	-0.955000	0.03636	0.462000	0.41574	CGG	.	.		0.478	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		C	38350697	G	C	38350697	3	2	55	1	0	0	0	0	1	0	0	0	4968	1116	39	4	400	4	EGFLAM	5	38350697	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	21589060	38350697	142564563	46	6954										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118469442	118469442	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aaaacatgctgatggttctcTgaatcagtggctggtcagtt	11	7	3	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr5:118469442T>A	ENST00000311085.8	+	12	1903	c.1823T>A	c.(1822-1824)cTg>cAg	p.L608Q	DMXL1_ENST00000539542.1_Missense_Mutation_p.L608Q	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	608										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GATGGTTCTCTGAATCAGTGG	0.338																																					p.L608Q		Atlas-SNP	.											.	DMXL1	268	.	0			c.T1823A						.						95	95	95					5																	118469442		2202	4300	6502	SO:0001583	missense	1657	exon12			GTTCTCTGAATCA	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.1823T>A	chr5.hg19:g.118469442T>A	ENSP00000309690:p.Leu608Gln	176.0	0.0		194.0	52.0	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.985608	0.74589	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.28069	1.63;2.49	5.43	5.43	0.79202	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.57140	0.2033	M	0.78049	2.395	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.59804	-0.7385	9	.	.	.	-5.6682	15.4658	0.75400	0.0:0.0:0.0:1.0	.	608;608	F5H269;Q9Y485	.;DMXL1_HUMAN	Q	608	ENSP00000309690:L608Q;ENSP00000439479:L608Q	.	L	+	2	0	DMXL1	118497341	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	2.072000	0.62099	0.482000	0.46254	CTG	.	.		0.338	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		A	118469442	T	A	118469442	3	1	55	1	0	0	0	0	1	0	0	0	4596	1580	55	4	1869	4	DMXL1	5	118469442	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	80118745	118469442	62445818	47	6955										
FBN2	2201	hgsc.bcm.edu	37	chr5	127714494	127714494	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ttgcttggtaggagtcctctGgaatccagcatgacatttac	10	9	1	1	rs199720456		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr5:127714494G>T	ENST00000508053.1	-	18	2667	c.1693C>A	c.(1693-1695)Cag>Aag	p.Q565K	FBN2_ENST00000511489.1_5'Flank|FBN2_ENST00000262464.4_Missense_Mutation_p.Q565K|FBN2_ENST00000508989.1_Missense_Mutation_p.Q532K			P35556	FBN2_HUMAN	fibrillin 2	565	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GGAGTCCTCTGGAATCCAGCA	0.408																																					p.Q565K		Atlas-SNP	.											.	FBN2	858	.	0			c.C1693A						.						102	96	98					5																	127714494		2203	4300	6503	SO:0001583	missense	2201	exon12			TCCTCTGGAATCC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.1693C>A	chr5.hg19:g.127714494G>T	ENSP00000424571:p.Gln565Lys	102.0	0.0		89.0	31.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	G	19.43	3.826368	0.71143	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.87179	-2.22;-2.22;-2.22	4.26	4.26	0.50523	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.111526	0.41605	D	0.000851	D	0.84247	0.5430	N	0.12502	0.225	0.46901	D	0.999248	D;P	0.55800	0.973;0.865	P;P	0.58013	0.831;0.824	T	0.80957	-0.1150	10	0.15499	T	0.54	.	17.9883	0.89161	0.0:0.0:1.0:0.0	.	532;565	D6RJI3;P35556	.;FBN2_HUMAN	K	565;565;532	ENSP00000262464:Q565K;ENSP00000424571:Q565K;ENSP00000425596:Q532K	ENSP00000262464:Q565K	Q	-	1	0	FBN2	127742393	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.330000	0.79181	2.654000	0.90174	0.655000	0.94253	CAG	.	G|0.999;A|0.001		0.408	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127714494	G	T	127714494	3	4	55	1	0	0	0	0	1	0	0	0	5711	1357	47	3	7261	3	FBN2	5	127714494	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	9245052	127714494	53200766	48	6956										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139892497	139892497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gcatgagatacatagcaacaAttacagataaggtaagttta	8	5	0	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr5:139892497A>G	ENST00000360839.2	+	23	4343	c.4189A>G	c.(4189-4191)Att>Gtt	p.I1397V	ANKHD1_ENST00000297183.6_Missense_Mutation_p.I1397V|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.I1397V	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1397						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATAGCAACAATTACAGATAA	0.318																																					p.I1397V		Atlas-SNP	.											.	ANKHD1	233	.	0			c.A4189G						.						110	115	113					5																	139892497		2202	4300	6502	SO:0001583	missense	54882	exon23			GCAACAATTACAG	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.4189A>G	chr5.hg19:g.139892497A>G	ENSP00000354085:p.Ile1397Val	179.0	0.0		201.0	125.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.081916	0.36758	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000235510;ENST00000421134;ENST00000412116;ENST00000431508;ENST00000532219	T;T;T;T;T;T	0.66099	-0.1;-0.14;-0.04;-0.19;1.71;-0.14	5.2	5.2	0.72013	.	0.052621	0.64402	D	0.000001	T	0.49745	0.1575	L	0.39633	1.23	0.52099	D	0.999942	B;B;B;B;P;B	0.35507	0.112;0.021;0.104;0.021;0.506;0.123	B;B;B;B;B;B	0.27796	0.023;0.01;0.051;0.004;0.083;0.034	T	0.48801	-0.9003	10	0.23302	T	0.38	.	15.4127	0.74941	1.0:0.0:0.0:0.0	.	1397;608;1397;1416;1397;1397	E9PF56;E7ET58;Q8IWZ3-4;E9PDP5;Q8IWZ2;Q8IWZ3	.;.;.;.;.;ANKH1_HUMAN	V	1397;1430;1397;1397;931;608;1416;550;53;1397	ENSP00000354085:I1397V;ENSP00000297183:I1397V;ENSP00000394489:I1416V;ENSP00000405602:I550V;ENSP00000393204:I53V;ENSP00000432016:I1397V	ENSP00000432016:I1397V	I	+	1	0	ANKHD1-EIF4EBP3;ANKHD1	139872681	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.385000	0.79763	2.106000	0.64143	0.456000	0.33151	ATT	.	.		0.318	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		G	139892497	A	G	139892497	3	3	55	1	0	0	0	0	1	0	0	0	628	101	4	2	4385	2	ANKHD1	5	139892497	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	12178003	139892497	41022763	49	6957										
KIF4B	285643	hgsc.bcm.edu	37	chr5	154395188	154395188	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gacagcaaagaagaatgtcaAccaagccaagctgagtgagc	11	9	1	4			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr5:154395188A>G	ENST00000435029.4	+	1	1929	c.1769A>G	c.(1768-1770)aAc>aGc	p.N590S		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	590					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AAGAATGTCAACCAAGCCAAG	0.418																																					p.N590S		Atlas-SNP	.											.	KIF4B	307	.	0			c.A1769G						.						84	86	85					5																	154395188		2203	4300	6503	SO:0001583	missense	285643	exon1			ATGTCAACCAAGC	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"Kinesins"	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.1769A>G	chr5.hg19:g.154395188A>G	ENSP00000387875:p.Asn590Ser	145.0	0.0		157.0	7.0	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	hg19	CCDS47324.1	.	.	.	.	.	.	.	.	.	.	a	8.860	0.946671	0.18356	.	.	ENSG00000226650	ENST00000435029	T	0.68765	-0.35	1.2	-0.14	0.13456	.	.	.	.	.	T	0.48909	0.1526	L	0.33710	1.025	0.44966	D	0.997981	B	0.33345	0.409	B	0.37480	0.251	T	0.19128	-1.0315	9	0.15066	T	0.55	.	5.2328	0.15432	0.7022:0.2978:0.0:0.0	.	590	Q2VIQ3	KIF4B_HUMAN	S	590	ENSP00000387875:N590S	ENSP00000387875:N590S	N	+	2	0	KIF4B	154375381	1.000000	0.71417	0.988000	0.46212	0.566000	0.35808	2.228000	0.42981	-0.035000	0.13691	-0.460000	0.05396	AAC	.	.		0.418	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			G	154395188	A	G	154395188	3	3	55	1	0	0	0	0	1	0	0	0	8313	43	2	2	1771	2	KIF4B	5	154395188	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	14502691	154395188	26520072	50	6958										
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178505747	178505747	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ggacatttttatagaagaaaCatctcagggaatggtaaaga	10	4	1	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr5:178505747C>A	ENST00000315475.6	+	5	620	c.314C>A	c.(313-315)aCa>aAa	p.T105K		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	105					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		ATAGAAGAAACATCTCAGGGA	0.388																																					p.T105K		Atlas-SNP	.											.	ZNF354C	77	.	0			c.C314A						.						70	73	72					5																	178505747		2203	4300	6503	SO:0001583	missense	30832	exon5			AAGAAACATCTCA		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"Zinc fingers, C2H2-type", "-"	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.314C>A	chr5.hg19:g.178505747C>A	ENSP00000324064:p.Thr105Lys	153.0	0.0		168.0	19.0	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	hg19	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	C	0.246	-1.009890	0.02095	.	.	ENSG00000177932	ENST00000315475	T	0.04809	3.55	4.09	-0.353	0.12594	.	.	.	.	.	T	0.02807	0.0084	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.48163	-0.9059	9	0.06099	T	0.92	-0.8541	3.0714	0.06231	0.3007:0.4563:0.1477:0.0953	.	105	Q86Y25	Z354C_HUMAN	K	105	ENSP00000324064:T105K	ENSP00000324064:T105K	T	+	2	0	ZNF354C	178438353	0.182000	0.23173	0.001000	0.08648	0.049000	0.14656	0.596000	0.24044	0.086000	0.17137	0.591000	0.81541	ACA	.	.		0.388	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			A	178505747	C	A	178505747	3	1	55	1	0	0	0	0	1	0	0	0	17881	478	17	3	328	3	ZNF354C	5	178505747	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	24110559	178505747	2409513	51	6959										
SLC35B3	51000	hgsc.bcm.edu	37	chr6	8430331	8430332	+	Frame_Shift_Ins	INS	-	-	T													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	attcaatgctttcagagttaINStttttgttggtttcctggac							TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr6:8430331_8430332insT	ENST00000379660.4	-	3	511_512	c.62_63insA	c.(61-63)aatfs	p.N21fs	SLC35B3_ENST00000339306.5_Frame_Shift_Ins_p.N21fs|SLC35B3_ENST00000426876.1_Frame_Shift_Ins_p.N87fs	NM_001142540.1|NM_001142541.1|NM_015948.3	NP_001136012.1|NP_001136013.1|NP_057032.2	Q9H1N7	S35B3_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B3	21					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(1)|prostate(1)	15	Ovarian(93;0.0569)					TTTCAGAGTTATTTTTGTTGGT	0.342																																					p.N21fs	Melanoma(83;700 1353 9357 11478 30548)	Pindel	.											.	SLC35B3	38	.	0			c.63_64insA						.																																			SO:0001589	frameshift_variant	51000	exon3			.	AF132953	CCDS4508.1	6p24.3	2013-07-17	2013-07-17	2003-09-10	ENSG00000124786	ENSG00000124786		"Solute carriers"	21601	protein-coding gene	gene with protein product	"3' phosphoadenosine 5' phosphosulfate transporter 2"	610845	"chromosome 6 open reading frame 196", "solute carrier family 35, member B3"	C6orf196		10810093	Standard	XM_005249156		Approved	CGI-19, dJ453H5.1, PAPST2	uc010joe.3	Q9H1N7	OTTHUMG00000014224	ENST00000379660.4:c.63dupA	chr6.hg19:g.8430336_8430336dupT	ENSP00000368981:p.Asn21fs	0.0	0.0		10.0	10.0	NM_001142540	A6NKX9|Q1XH11|Q6MZJ0|Q7Z662|Q9Y308	Frame_Shift_Ins	INS	ENST00000379660.4	hg19	CCDS4508.1																																																																																			.	.		0.342	SLC35B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039802.1	NM_015948		T	8430332	-	T	8430331	7	5	55	1	0	1	1	0	0	0	0	0	14592	446	16	0	1178	0	SLC35B3	6	8430331	Frame_Shift_Ins	INS	-	TCGA-CC-5259-01A-31D-A20W-10		8430331	162684736	52	6960										
MAK	4117	hgsc.bcm.edu	37	chr6	10818123	10818123	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gaggttttctttcatatattCaaatataaaataaagatggt	6	3	3	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr6:10818123C>A	ENST00000313243.2	-	4	620	c.238G>T	c.(238-240)Gaa>Taa	p.E80*	RP11-637O19.3_ENST00000480294.1_Intron|MAK_ENST00000536370.1_Nonsense_Mutation_p.E80*|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000538030.1_Nonsense_Mutation_p.E80*|MAK_ENST00000354489.2_Nonsense_Mutation_p.E80*|MAK_ENST00000474039.1_Nonsense_Mutation_p.E80*			P20794	MAK_HUMAN	male germ cell-associated kinase	80	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				TTCATATATTCAAATATAAAA	0.274																																					p.E80X		Atlas-SNP	.											.	MAK	47	.	0			c.G238T						.						24	27	26					6																	10818123		2173	4260	6433	SO:0001587	stop_gained	4117	exon4			TATATTCAAATAT		CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.238G>T	chr6.hg19:g.10818123C>A	ENSP00000313021:p.Glu80*	139.0	0.0		150.0	54.0	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Nonsense_Mutation	SNP	ENST00000313243.2	hg19	CCDS4516.1	.	.	.	.	.	.	.	.	.	.	C	38	7.207121	0.98136	.	.	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030;ENST00000536370	.	.	.	5.75	4.88	0.63580	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.1843	0.72986	0.0:0.9315:0.0:0.0685	.	.	.	.	X	80	.	ENSP00000313021:E80X	E	-	1	0	MAK	10926109	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.893000	0.69798	2.716000	0.92895	0.655000	0.94253	GAA	.	.		0.274	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906		A	10818123	C	A	10818123	4	1	55	1	0	0	0	0	0	1	0	0	9206	835	29	3	1677	3	MAK	6	10818123	Nonsense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	2387792	10818123	160296944	53	6961										
HLA-DPB1	3115	hgsc.bcm.edu	37	chr6	33048530	33048530	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ggagagatacatctacaaccGggaggagttcgcgcgcttcg	14	10	1	1	rs41561114		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr6:33048530G>A	ENST00000418931.2	+	2	298	c.182G>A	c.(181-183)cGg>cAg	p.R61Q	HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.R61Q	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	61	Beta-1.		R -> P (in allele DPB1*14:02 and allele DPB1*21:02; dbSNP:rs41561114).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						ATCTACAACCGGGAGGAGTTC	0.622																																					p.R61Q		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.G182A						.						69	70	69					6																	33048530		1511	2709	4220	SO:0001583	missense	3115	exon2			ACAACCGGGAGGA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.182G>A	chr6.hg19:g.33048530G>A	ENSP00000408146:p.Arg61Gln	71.0	0.0		100.0	10.0	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	hg19	CCDS4765.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.621|6.621	0.483043|0.483043	0.12581|0.12581	.|.	.|.	ENSG00000223865|ENSG00000223865	ENST00000416804|ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835	.|T;T;T	.|0.00297	.|8.23;8.23;8.23	4.02|4.02	-1.36|-1.36	0.09085|0.09085	.|MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);	.|0.371038	.|0.26688	.|N	.|0.023012	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.39020|0.39020	1.185|1.185	0.09310|0.09310	N|N	1|1	.|B;B	.|0.24186	.|0.099;0.041	.|B;B	.|0.15052	.|0.012;0.007	T|T	0.52064|0.52064	-0.8625|-0.8625	5|10	.|0.02654	.|T	.|1	.|.	4.6263|4.6263	0.12479|0.12479	0.3495:0.2843:0.3663:0.0|0.3495:0.2843:0.3663:0.0	.|.	.|71;61	.|Q59GY1;P04440	.|.;DPB1_HUMAN	R|Q	28|61;61;61;38	.|ENSP00000408146:R61Q;ENSP00000439674:R61Q;ENSP00000412654:R38Q	.|ENSP00000389210:R61Q	G|R	+|+	1|2	0|0	HLA-DPB1|HLA-DPB1	33156508|33156508	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.004000|0.004000	0.04260|0.04260	-0.107000|-0.107000	0.10873|0.10873	-0.425000|-0.425000	0.07371|0.07371	-0.855000|-0.855000	0.03028|0.03028	GGG|CGG	.	.		0.622	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121		A	33048530	G	A	33048530	3	1	55	1	0	0	0	0	1	0	0	0	7212	1116	39	1	188	1	HLA-DPB1	6	33048530	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	22230407	33048530	138066537	54	6962										
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33411166	33411166	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aggtcccccaggcggccatgGagggggcggtggccatggcc	19	13	0	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr6:33411166G>C	ENST00000418600.2	+	15	2938	c.2837G>C	c.(2836-2838)gGa>gCa	p.G946A	SYNGAP1_ENST00000428982.2_Missense_Mutation_p.G887A|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.G946A	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	946					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GGCGGCCATGGAGGGGGCGGT	0.657																																					p.G946A		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.G2837C						.						86	93	91					6																	33411166		2202	4299	6501	SO:0001583	missense	8831	exon15			GCCATGGAGGGGG	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.2837G>C	chr6.hg19:g.33411166G>C	ENSP00000403636:p.Gly946Ala	104.0	0.0		123.0	71.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	hg19	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	G	1.835	-0.468821	0.04445	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	D;D;D	0.86562	-2.14;-2.14;-2.14	4.53	2.69	0.31865	.	0.953693	0.08554	N	0.928610	T	0.54431	0.1858	N	0.08118	0	0.23787	N	0.996849	P;P;P	0.38827	0.649;0.597;0.597	B;B;B	0.35727	0.209;0.133;0.133	T	0.46830	-0.9163	10	0.15066	T	0.55	.	10.7869	0.46411	0.0:0.3736:0.6264:0.0	.	946;946;946	Q96PV0;Q96PV0-2;Q96PV0-4	SYGP1_HUMAN;.;.	A	946;946;932;887	ENSP00000293748:G946A;ENSP00000403636:G946A;ENSP00000412475:G887A	ENSP00000293748:G946A	G	+	2	0	SYNGAP1	33519144	1.000000	0.71417	0.395000	0.26283	0.941000	0.58515	1.951000	0.40333	0.507000	0.28148	0.491000	0.48974	GGA	.	.		0.657	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		C	33411166	G	C	33411166	3	2	55	1	0	0	0	0	1	0	0	0	15462	1174	41	4	2895	4	SYNGAP1	6	33411166	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	362636	33411166	137703901	55	6963										
C6orf138	442213	hgsc.bcm.edu	37	chr6	48036326	48036326	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gactggagccctctgcgaagCacctgccgcagcatcctcca	10	17	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr6:48036326C>G	ENST00000339488.4	-	1	99	c.66G>C	c.(64-66)gtG>gtC	p.V22V	PTCHD4_ENST00000543600.1_Silent_p.V5V	NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	22						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										CTCTGCGAAGCACCTGCCGCA	0.622																																					p.V22V		Atlas-SNP	.											.	.	.	.	0			c.G66C						.						7	9	8					6																	48036326		1922	4070	5992	SO:0001819	synonymous_variant	442213	exon1			GCGAAGCACCTGC		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 138"	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.66G>C	chr6.hg19:g.48036326C>G		78.0	0.0		127.0	61.0	NM_001013732	B0QZ29|B4DRK3|Q5T884	Silent	SNP	ENST00000339488.4	hg19	CCDS34473.2	.	.	.	.	.	.	.	.	.	.	C	5.538	0.284247	0.10513	.	.	ENSG00000244694	ENST00000398738	.	.	.	4.54	3.64	0.41730	.	.	.	.	.	T	0.62841	0.2461	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63695	-0.6579	4	.	.	.	.	15.602	0.76631	0.0:0.824:0.176:0.0	.	.	.	.	P	22	.	.	A	-	1	0	C6orf138	48144285	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.890000	0.48609	2.061000	0.61500	0.442000	0.29010	GCT	.	.		0.622	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		G	48036326	C	G	48036326	2	3	55	1	0	0	0	0	0	0	0	1	2334	697	25	4		4	C6orf138	6	48036326	Silent	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	14625160	48036326	123078741	56	6964										
TINAG	27283	hgsc.bcm.edu	37	chr6	54186162	54186162	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ttcgttcagaattaattgaaCaggtcaataaaggagactat	8	5	2	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr6:54186162C>T	ENST00000259782.4	+	3	583	c.487C>T	c.(487-489)Cag>Tag	p.Q163*	TINAG_ENST00000370864.3_Nonsense_Mutation_p.Q145*|TINAG_ENST00000486436.1_3'UTR|TINAG_ENST00000370869.3_Nonsense_Mutation_p.Q159*	NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	163					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			ATTAATTGAACAGGTCAATAA	0.388																																					p.Q163X		Atlas-SNP	.											.	TINAG	102	.	0			c.C487T						.						128	117	121					6																	54186162		2203	4300	6503	SO:0001587	stop_gained	27283	exon3			ATTGAACAGGTCA	AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.487C>T	chr6.hg19:g.54186162C>T	ENSP00000259782:p.Gln163*	49.0	0.0		44.0	26.0	NM_014464	Q5T467|Q9UJW1|Q9ULZ4	Nonsense_Mutation	SNP	ENST00000259782.4	hg19	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	C	17.62	3.435287	0.62955	.	.	ENSG00000137251	ENST00000370869;ENST00000259782;ENST00000370864	.	.	.	5.79	1.25	0.21368	.	1.259680	0.05190	N	0.502868	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	4.6647	0.12659	0.3102:0.494:0.0:0.1958	.	.	.	.	X	159;163;145	.	ENSP00000259782:Q163X	Q	+	1	0	TINAG	54294121	0.012000	0.17670	0.025000	0.17156	0.639000	0.38242	0.221000	0.17680	0.290000	0.22444	-0.309000	0.09137	CAG	.	.		0.388	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		T	54186162	C	T	54186162	4	4	55	1	0	0	0	0	0	1	0	0	15936	479	17	3	497	3	TINAG	6	54186162	Nonsense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	6149836	54186162	116928905	57	6965										
KCNQ5	56479	hgsc.bcm.edu	37	chr6	73879546	73879546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tatcagtggaagacctcaccCcaccacttaaaactgtcatt	5	13	3	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr6:73879546C>T	ENST00000370398.1	+	11	1655	c.1546C>T	c.(1546-1548)Cca>Tca	p.P516S	KCNQ5_ENST00000355194.4_Missense_Mutation_p.P516S|KCNQ5_ENST00000355635.3_Missense_Mutation_p.P517S|KCNQ5_ENST00000414165.2_Intron|KCNQ5_ENST00000342056.2_Missense_Mutation_p.P535S|KCNQ5_ENST00000402622.2_Missense_Mutation_p.P526S|KCNQ5_ENST00000403813.2_Missense_Mutation_p.P507S	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	516					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	AGACCTCACCCCACCACTTAA	0.398																																					p.P535S	GBM(142;1375 1859 14391 23261 44706)	Atlas-SNP	.											.	KCNQ5	153	.	0			c.C1603T						.						158	125	136					6																	73879546		2203	4300	6503	SO:0001583	missense	56479	exon12			CTCACCCCACCAC	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.1546C>T	chr6.hg19:g.73879546C>T	ENSP00000359425:p.Pro516Ser	150.0	0.0		195.0	98.0	NM_001160133	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	hg19	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	C	19.66	3.869182	0.72065	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000402622;ENST00000355635;ENST00000403813	D;D;D;D;D;D	0.99637	-6.29;-6.29;-6.29;-6.29;-6.29;-6.29	5.46	4.59	0.56863	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.056594	0.64402	D	0.000001	D	0.98975	0.9651	L	0.37850	1.14	0.80722	D	1	P;P;P;D	0.56287	0.832;0.875;0.849;0.975	P;P;P;P	0.59546	0.495;0.627;0.493;0.859	D	0.99116	1.0848	10	0.52906	T	0.07	.	16.2663	0.82581	0.0:0.8669:0.1331:0.0	.	526;535;507;516	Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82	.;.;.;KCNQ5_HUMAN	S	535;535;516;516;526;517;507	ENSP00000345055:P535S;ENSP00000347326:P516S;ENSP00000359425:P516S;ENSP00000385501:P526S;ENSP00000347853:P517S;ENSP00000384453:P507S	ENSP00000345055:P535S	P	+	1	0	KCNQ5	73936267	0.992000	0.36948	1.000000	0.80357	0.996000	0.88848	2.585000	0.46111	1.431000	0.47355	0.655000	0.94253	CCA	.	.		0.398	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		T	73879546	C	T	73879546	3	4	55	1	0	0	0	0	1	0	0	0	8095	623	22	3	1649	3	KCNQ5	6	73879546	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	19693384	73879546	97235521	58	6966										
IFNGR1	3459	hgsc.bcm.edu	37	chr6	137519200	137519200	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tttggaatcttctgttggtcTataaccaatcaaggactctt	7	8	5	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr6:137519200T>A	ENST00000367739.4	-	7	1559	c.1438A>T	c.(1438-1440)Aga>Tga	p.R480*	IFNGR1_ENST00000543628.1_Nonsense_Mutation_p.R452*	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	480					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)			central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	TCTGTTGGTCTATAACCAATC	0.388																																					p.R480X		Atlas-SNP	.											.	IFNGR1	46	.	0			c.A1438T						.						100	100	100					6																	137519200		2203	4300	6503	SO:0001587	stop_gained	3459	exon7			TTGGTCTATAACC		CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"Interferons", "CD molecules"	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.1438A>T	chr6.hg19:g.137519200T>A	ENSP00000356713:p.Arg480*	137.0	0.0		161.0	88.0	NM_000416	B4DFT7|E1P587|Q53Y96	Nonsense_Mutation	SNP	ENST00000367739.4	hg19	CCDS5185.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.517931	0.64634	.	.	ENSG00000027697	ENST00000367739;ENST00000543628	.	.	.	6.03	3.46	0.39613	.	0.131846	0.48286	D	0.000182	.	.	.	.	.	.	0.18873	N	0.999988	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.6577	10.9029	0.47062	0.0:0.0:0.3146:0.6854	.	.	.	.	X	480;452	.	ENSP00000356713:R480X	R	-	1	2	IFNGR1	137560893	0.940000	0.31905	0.061000	0.19648	0.267000	0.26476	2.670000	0.46833	1.066000	0.40716	0.533000	0.62120	AGA	.	.		0.388	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1			A	137519200	T	A	137519200	4	1	55	1	0	0	0	0	0	1	0	0	7558	1530	53	4	35	4	IFNGR1	6	137519200	Nonsense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	63639654	137519200	33595867	59	6967										
ACAT2	39	hgsc.bcm.edu	37	chr6	160184055	160184055	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tggctccggaagatgtgtctGaggtcatctttggacatgtc	13	8	3	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr6:160184055G>T	ENST00000367048.4	+	2	1920	c.160G>T	c.(160-162)Gag>Tag	p.E54*	SOD2_ENST00000535372.1_5'Flank|SOD2_ENST00000546087.1_5'Flank|ACAT2_ENST00000541436.1_Nonsense_Mutation_p.E83*	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	54					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		AGATGTGTCTGAGGTCATCTT	0.502																																					p.E54X		Atlas-SNP	.											.	ACAT2	32	.	0			c.G160T						.						158	152	154					6																	160184055		2203	4300	6503	SO:0001587	stop_gained	39	exon2			GTGTCTGAGGTCA	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	100678	"acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)", "acetyl-Coenzyme A acetyltransferase 2"			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.160G>T	chr6.hg19:g.160184055G>T	ENSP00000356015:p.Glu54*	214.0	0.0		224.0	55.0	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Nonsense_Mutation	SNP	ENST00000367048.4	hg19	CCDS5268.1	.	.	.	.	.	.	.	.	.	.	G	39	7.334209	0.98217	.	.	ENSG00000120437	ENST00000367048;ENST00000541436	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-5.9042	19.5715	0.95421	0.0:0.0:1.0:0.0	.	.	.	.	X	54;83	.	ENSP00000356015:E54X	E	+	1	0	ACAT2	160104045	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.247000	0.95444	2.704000	0.92352	0.555000	0.69702	GAG	.	.		0.502	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891		T	160184055	G	T	160184055	4	4	55	1	0	0	0	0	0	1	0	0	122	1291	45	3	166	3	ACAT2	6	160184055	Nonsense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	22664855	160184055	10931012	60	6968										
T	6862	hgsc.bcm.edu	37	chr6	166571945	166571945	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aggaagagggcgccgagaccGgatgggtgaggggtgtgtag	22	5	0	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr6:166571945G>A	ENST00000296946.2	-	9	1634	c.1166C>T	c.(1165-1167)cCg>cTg	p.P389L	T_ENST00000366871.3_Missense_Mutation_p.P331L	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	389					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		CGCCGAGACCGGATGGGTGAG	0.726									Chordoma, Familial Clustering of																												p.P389L		Atlas-SNP	.											.	T	77	.	0			c.C1166T						.						44	53	50					6																	166571945		2202	4298	6500	SO:0001583	missense	6862	exon9	Familial Cancer Database		GAGACCGGATGGG	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"T-boxes"	11515	protein-coding gene	gene with protein product		601397	"T brachyury (mouse) homolog"			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.1166C>T	chr6.hg19:g.166571945G>A	ENSP00000296946:p.Pro389Leu	117.0	0.0		151.0	48.0	NM_003181	E7ERD6|Q4KMP4	Missense_Mutation	SNP	ENST00000296946.2	hg19	CCDS5290.1	.	.	.	.	.	.	.	.	.	.	G	5.921	0.353923	0.11182	.	.	ENSG00000164458	ENST00000366876;ENST00000296946;ENST00000366871	D;D	0.83419	-1.68;-1.72	4.71	2.86	0.33363	.	1.373470	0.04839	N	0.440181	T	0.63651	0.2529	L	0.54323	1.7	0.19575	N	0.999966	B;B;B	0.26547	0.152;0.001;0.044	B;B;B	0.10450	0.005;0.0;0.003	T	0.53092	-0.8487	10	0.12103	T	0.63	.	13.9359	0.64026	0.0:0.3165:0.6835:0.0	.	331;389;331	E7ERD6;O15178;Q4KMP4	.;BRAC_HUMAN;.	L	389;389;331	ENSP00000296946:P389L;ENSP00000355836:P331L	ENSP00000296946:P389L	P	-	2	0	T	166491935	0.815000	0.29118	0.000000	0.03702	0.001000	0.01503	4.591000	0.61019	0.459000	0.27016	-0.176000	0.13171	CCG	.	.		0.726	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181		A	166571945	G	A	166571945	3	1	55	1	0	0	0	0	1	0	0	0	15503	1116	39	1	145	1	T	6	166571945	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	6387890	166571945	4543122	61	6969										
CARD11	84433	hgsc.bcm.edu	37	chr7	2968238	2968238	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cacctgccacccacctgcgaTggggcgcgtcctccttgtag	11	17	0	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr7:2968238T>C	ENST00000396946.4	-	13	2151	c.1748A>G	c.(1747-1749)cAt>cGt	p.H583R		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	583					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CCACCTGCGATGGGGCGCGTC	0.662			Mis		DLBCL																																p.H583R		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.A1748G						.						80	66	71					7																	2968238		2203	4300	6503	SO:0001583	missense	84433	exon13			CTGCGATGGGGCG	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1748A>G	chr7.hg19:g.2968238T>C	ENSP00000380150:p.His583Arg	57.0	0.0		27.0	9.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	t	0.643	-0.812527	0.02798	.	.	ENSG00000198286	ENST00000396946;ENST00000355508	T;T	0.42513	0.97;0.97	4.96	0.974	0.19715	.	0.475226	0.21916	N	0.067239	T	0.19565	0.0470	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.19148	0.024	T	0.18650	-1.0330	10	0.25751	T	0.34	-9.5868	7.9574	0.30051	0.1313:0.0:0.4092:0.4595	.	583	Q9BXL7	CAR11_HUMAN	R	583;54	ENSP00000380150:H583R;ENSP00000347695:H54R	ENSP00000347695:H54R	H	-	2	0	CARD11	2934764	0.962000	0.33011	0.008000	0.14137	0.833000	0.47200	1.739000	0.38217	-0.068000	0.12953	0.454000	0.30748	CAT	.	.		0.662	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		C	2968238	T	C	2968238	3	2	55	1	0	0	0	0	1	0	0	0	2647	1464	51	2	1768	2	CARD11	7	2968238	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10		2968238	156170425	62	6970										
ADCY1	107	hgsc.bcm.edu	37	chr7	45688359	45688359	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agactgaccatgcccactgcTgtgtggagatgggactcgac	13	11	0	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr7:45688359T>A	ENST00000297323.7	+	5	1133	c.1111T>A	c.(1111-1113)Tgt>Agt	p.C371S	ADCY1_ENST00000432715.1_Missense_Mutation_p.C146S	NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	371					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TGCCCACTGCTGTGTGGAGAT	0.562																																					p.C371S		Atlas-SNP	.											.	ADCY1	187	.	0			c.T1111A						.						115	89	97					7																	45688359		2203	4300	6503	SO:0001583	missense	107	exon5			CACTGCTGTGTGG	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.1111T>A	chr7.hg19:g.45688359T>A	ENSP00000297323:p.Cys371Ser	266.0	0.0		184.0	75.0	NM_021116	A4D2L8|Q75MI1	Missense_Mutation	SNP	ENST00000297323.7	hg19	CCDS34631.1	.	.	.	.	.	.	.	.	.	.	T	17.32	3.359538	0.61403	.	.	ENSG00000164742	ENST00000432715;ENST00000297323;ENST00000545300	D;D	0.84442	-1.85;-1.85	4.34	4.34	0.51931	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.86184	0.5872	M	0.64630	1.985	0.80722	D	1	D;P	0.56287	0.975;0.805	P;P	0.51101	0.659;0.585	D	0.86083	0.1545	10	0.45353	T	0.12	.	11.5212	0.50551	0.0:0.0:0.0:1.0	.	371;146	Q08828;C9J1J0	ADCY1_HUMAN;.	S	146;371;371	ENSP00000392721:C146S;ENSP00000297323:C371S	ENSP00000297323:C371S	C	+	1	0	ADCY1	45654884	1.000000	0.71417	0.997000	0.53966	0.944000	0.59088	7.277000	0.78572	1.820000	0.53075	0.459000	0.35465	TGT	.	.		0.562	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		A	45688359	T	A	45688359	3	1	55	1	0	0	0	0	1	0	0	0	292	1580	55	4	1129	4	ADCY1	7	45688359	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	42720121	45688359	113450304	63	6971										
ADCY1	107	hgsc.bcm.edu	37	chr7	45717579	45717579	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	acaggtacatcagccgcctcTtagaagcccgccagacagag	10	14	2	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr7:45717579T>A	ENST00000297323.7	+	9	1739	c.1717T>A	c.(1717-1719)Tta>Ata	p.L573I		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	573					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CAGCCGCCTCTTAGAAGCCCG	0.507																																					p.L573I		Atlas-SNP	.											.	ADCY1	187	.	0			c.T1717A						.						75	82	80					7																	45717579		2203	4300	6503	SO:0001583	missense	107	exon9			CGCCTCTTAGAAG	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.1717T>A	chr7.hg19:g.45717579T>A	ENSP00000297323:p.Leu573Ile	222.0	0.0		180.0	61.0	NM_021116	A4D2L8|Q75MI1	Missense_Mutation	SNP	ENST00000297323.7	hg19	CCDS34631.1	.	.	.	.	.	.	.	.	.	.	T	7.392	0.631051	0.14322	.	.	ENSG00000164742	ENST00000297323;ENST00000545300	T	0.74526	-0.85	5.24	-4.52	0.03472	.	0.063315	0.64402	D	0.000015	T	0.29158	0.0725	N	0.00648	-1.295	0.31492	N	0.665802	B	0.02656	0.0	B	0.04013	0.001	T	0.50021	-0.8876	10	0.02654	T	1	.	6.9609	0.24597	0.181:0.6385:0.0:0.1804	.	573	Q08828	ADCY1_HUMAN	I	573	ENSP00000297323:L573I	ENSP00000297323:L573I	L	+	1	2	ADCY1	45684104	1.000000	0.71417	0.905000	0.35620	0.991000	0.79684	4.295000	0.59049	-0.584000	0.05913	-0.290000	0.09829	TTA	.	.		0.507	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		A	45717579	T	A	45717579	3	1	55	1	0	0	0	0	1	0	0	0	292	1606	56	4	1751	4	ADCY1	7	45717579	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	29220	45717579	113421084	64	6972										
GRM3	2913	hgsc.bcm.edu	37	chr7	86416221	86416221	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aacaaacgcaaccacaggcgCgtctgcgacaagcacctggc	10	15	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr7:86416221C>T	ENST00000361669.2	+	3	2212	c.1113C>T	c.(1111-1113)cgC>cgT	p.R371R	GRM3_ENST00000394720.2_Silent_p.R369R|AC005009.2_ENST00000452471.1_RNA|AC005009.2_ENST00000418031.1_RNA|GRM3_ENST00000536043.1_Silent_p.R243R|GRM3_ENST00000439827.1_Silent_p.R371R|GRM3_ENST00000546348.1_Intron	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	371					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					ACCACAGGCGCGTCTGCGACA	0.567																																					p.R371R	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.C1113T						.						101	85	90					7																	86416221		2203	4300	6503	SO:0001819	synonymous_variant	2913	exon3			CAGGCGCGTCTGC		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.1113C>T	chr7.hg19:g.86416221C>T		95.0	0.0		88.0	36.0	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Silent	SNP	ENST00000361669.2	hg19	CCDS5600.1																																																																																			.	.		0.567	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			T	86416221	C	T	86416221	2	4	55	1	0	0	0	0	0	0	0	1	6807	755	27	1		1	GRM3	7	86416221	Silent	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	40698642	86416221	72722442	65	6973										
SAMD9	54809	hgsc.bcm.edu	37	chr7	92732475	92732475	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agtgaatgatgcgtactccaCagtagttcccacattcgatg	9	10	0	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr7:92732475C>A	ENST00000379958.2	-	3	3205	c.2936G>T	c.(2935-2937)tGt>tTt	p.C979F		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	979						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			GCGTACTCCACAGTAGTTCCC	0.388																																					p.C979F		Atlas-SNP	.											.	SAMD9	239	.	0			c.G2936T						.						126	123	124					7																	92732475		2203	4300	6503	SO:0001583	missense	54809	exon2			ACTCCACAGTAGT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.2936G>T	chr7.hg19:g.92732475C>A	ENSP00000369292:p.Cys979Phe	147.0	0.0		122.0	47.0	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	hg19	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.937307	0.00484	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.23147	1.92;2.73	4.88	-0.5	0.12012	.	0.628283	0.14950	N	0.288966	T	0.15435	0.0372	L	0.36672	1.1	0.09310	N	1	B	0.27971	0.196	B	0.14023	0.01	T	0.14008	-1.0488	10	0.59425	D	0.04	-0.0689	5.7348	0.18061	0.0:0.4519:0.1363:0.4119	.	979	Q5K651	SAMD9_HUMAN	F	979	ENSP00000369292:C979F;ENSP00000414529:C979F	ENSP00000369292:C979F	C	-	2	0	SAMD9	92570411	0.107000	0.21998	0.085000	0.20634	0.234000	0.25298	1.266000	0.33039	0.012000	0.14892	-0.208000	0.12717	TGT	.	.		0.388	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		A	92732475	C	A	92732475	3	1	55	1	0	0	0	0	1	0	0	0	13841	478	17	3	1837	3	SAMD9	7	92732475	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	6316254	92732475	66406188	66	6974										
RELN	5649	hgsc.bcm.edu	37	chr7	103292164	103292164	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gggaggtggggtccagcacaGatctcaggtaagcattcagt	15	8	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr7:103292164G>T	ENST00000428762.1	-	15	1995	c.1836C>A	c.(1834-1836)atC>atA	p.I612I	RELN_ENST00000343529.5_Silent_p.I612I|RELN_ENST00000424685.2_Silent_p.I612I	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	612					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GTCCAGCACAGATCTCAGGTA	0.468																																					p.I612I	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C1836A						.						82	67	72					7																	103292164		2203	4300	6503	SO:0001819	synonymous_variant	5649	exon15			AGCACAGATCTCA		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.1836C>A	chr7.hg19:g.103292164G>T		104.0	0.0		76.0	42.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	hg19	CCDS47680.1																																																																																			.	.		0.468	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103292164	G	T	103292164	2	4	55	1	0	0	0	0	0	0	0	1	13235	932	33	3		3	RELN	7	103292164	Silent	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	10559689	103292164	55846499	67	6975										
PRSS37	136242	hgsc.bcm.edu	37	chr7	141537672	141537672	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	acacttaccactgttttcttGgctccagtccaaacctgaga	6	13	1	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr7:141537672G>T	ENST00000350549.3	-	3	789	c.418C>A	c.(418-420)Caa>Aaa	p.Q140K	PRSS37_ENST00000438520.1_Missense_Mutation_p.Q140K	NM_001008270.2|NM_001171951.1	NP_001008271.2|NP_001165422.1	A4D1T9	PRS37_HUMAN	protease, serine, 37	140	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				binding of sperm to zona pellucida (GO:0007339)|cell migration (GO:0016477)|protein maturation (GO:0051604)	extracellular region (GO:0005576)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(3)	15						CTGTTTTCTTGGCTCCAGTCC	0.522																																					p.Q140K		Atlas-SNP	.											.	PRSS37	42	.	0			c.C418A						.						154	140	145					7																	141537672		2203	4300	6503	SO:0001583	missense	136242	exon3			TTTCTTGGCTCCA		CCDS34764.1	7q34	2010-05-07			ENSG00000165076	ENSG00000165076		"Serine peptidases / Serine peptidases"	29211	protein-coding gene	gene with protein product							Standard	NM_001008270		Approved		uc003vws.2	A4D1T9	OTTHUMG00000157174	ENST00000350549.3:c.418C>A	chr7.hg19:g.141537672G>T	ENSP00000297767:p.Gln140Lys	214.0	0.0		175.0	78.0	NM_001171951	B2RPB5	Missense_Mutation	SNP	ENST00000350549.3	hg19	CCDS34764.1	.	.	.	.	.	.	.	.	.	.	G	4.507	0.094009	0.08632	.	.	ENSG00000165076	ENST00000350549;ENST00000438520	D;D	0.87729	-2.29;-2.29	5.65	3.73	0.42828	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.018330	0.07832	N	0.961480	T	0.77961	0.4209	L	0.28400	0.85	0.28473	N	0.915302	B;B	0.06786	0.001;0.001	B;B	0.17979	0.02;0.02	T	0.62412	-0.6860	10	0.05620	T	0.96	.	8.8757	0.35343	0.0825:0.0:0.7604:0.1571	.	140;140	B7ZMK3;A4D1T9	.;PRS37_HUMAN	K	140	ENSP00000297767:Q140K;ENSP00000414461:Q140K	ENSP00000297767:Q140K	Q	-	1	0	PRSS37	141184141	1.000000	0.71417	0.978000	0.43139	0.025000	0.11179	1.465000	0.35299	1.632000	0.50472	-0.140000	0.14226	CAA	.	.		0.522	PRSS37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347763.1	NM_001008270		T	141537672	G	T	141537672	3	4	55	1	0	0	0	0	1	0	0	0	12638	1357	47	3	301	3	PRSS37	7	141537672	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	38245508	141537672	17600991	68	6976										
LRRC61	65999	hgsc.bcm.edu	37	chr7	150034607	150034789	+	Stop_Codon_Del	DEL	CTGCCGGCAGTTCCAGGACACACTGCAGGAGTGCTGGGACCTGGACCGCCAGGCCAGCGACAGCCTGGCCCAGGCGGAGCAGGTACTCAGCTCTGCGGGCCCCACCTCTTCCTTCGTCTTCTGAACGTGGCCTATGGCCCAGGACAGCCTGGCAGGTGGCCTCGCTGCCCCCAGTTCCCCTCT	CTGCCGGCAGTTCCAGGACACACTGCAGGAGTGCTGGGACCTGGACCGCCAGGCCAGCGACAGCCTGGCCCAGGCGGAGCAGGTACTCAGCTCTGCGGGCCCCACCTCTTCCTTCGTCTTCTGAACGTGGCCTATGGCCCAGGACAGCCTGGCAGGTGGCCTCGCTGCCCCCAGTTCCCCTCT	-													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agctccatcctggaggaggcCtgccggcagttccaggacac					rs560834038|rs529699133|rs138347257|rs75914222|rs573247336|rs368294440|rs565347229|rs376663448|rs546648175|rs148701145|rs368650752|rs111309260|rs149223172|rs374204901|rs376071210	byFrequency	TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	CTGCCGGCAGTTCCAGGACACACTGCAGGAGTGCTGGGACCTGGACCGCCAGGCCAGCGACAGCCTGGCCCAGGCGGAGCAGGTACTCAGCTCTGCGGGCCCCACCTCTTCCTTCGTCTTCTGAACGTGGCCTATGGCCCAGGACAGCCTGGCAGGTGGCCTCGCTGCCCCCAGTTCCCCTCT	CTGCCGGCAGTTCCAGGACACACTGCAGGAGTGCTGGGACCTGGACCGCCAGGCCAGCGACAGCCTGGCCCAGGCGGAGCAGGTACTCAGCTCTGCGGGCCCCACCTCTTCCTTCGTCTTCTGAACGTGGCCTATGGCCCAGGACAGCCTGGCAGGTGGCCTCGCTGCCCCCAGTTCCCCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr7:150034607_150034789delCTGCCGGCAGTTCCAGGACACACTGCAGGAGTGCTGGGACCTGGACCGCCAGGCCAGCGACAGCCTGGCCCAGGCGGAGCAGGTACTCAGCTCTGCGGGCCCCACCTCTTCCTTCGTCTTCTGAACGTGGCCTATGGCCCAGGACAGCCTGGCAGGTGGCCTCGCTGCCCCCAGTTCCCCTCT	ENST00000359623.4	+	0	1245_1427				LRRC61_ENST00000493307.1_Stop_Codon_Del|LRRC61_ENST00000323078.7_Stop_Codon_Del	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61											endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			TGGAGGAGGCCTGCCGGCAGTTCCAGGACACACTGCAGGAGTGCTGGGACCTGGACCGCCAGGCCAGCGACAGCCTGGCCCAGGCGGAGCAGGTACTCAGCTCTGCGGGCCCCACCTCTTCCTTCGTCTTCTGAACGTGGCCTATGGCCCAGGACAGCCTGGCAGGTGGCCTCGCTGCCCCCAGTTCCCCTCTCTGCCCCCAC	0.663																																					p.219_260del		Pindel	.											.	LRRC61	17	.	0			c.656_1278del						.																																			SO:0001567	stop_retained_variant	65999	exon2			.	BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	Exception_encountered	chr7.hg19:g.150034607_150034789delCTGCCGGCAGTTCCAGGACACACTGCAGGAGTGCTGGGACCTGGACCGCCAGGCCAGCGACAGCCTGGCCCAGGCGGAGCAGGTACTCAGCTCTGCGGGCCCCACCTCTTCCTTCGTCTTCTGAACGTGGCCTATGGCCCAGGACAGCCTGGCAGGTGGCCTCGCTGCCCCCAGTTCCCCTCT	ENSP00000352642:p.*260Cysext*1	0.0	0.0		23.0	23.0	NM_023942	B3KUW0|D3DWY8	Frame_Shift_Del	DEL	ENST00000359623.4	hg19	CCDS5901.1																																																																																			.	.		0.663	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942		-	150034789	CTGCCGGCAGTTCCAGGACACACTGCAGGAGTGCTGGGACCTGGACCGCCAGGCCAGCGACAGCCTGGCCCAGGCGGAGCAGGTACTCAGCTCTGCGGGCCCCACCTCTTCCTTCGTCTTCTGAACGTGGCCTATGGCCCAGGACAGCCTGGCAGGTGGCCTCGCTGCCCCCAGTTCCCCTCT	-	150034607	7	5	55	1	0	1	0	1	0	0	0	0	9026	668	24	0	659	0	LRRC61	7	150034607	Stop_Codon_Del	DEL	CTGCCGGCAGTTCCAGGACACACTGCAGGAGTGCTGGGACCTGGACCGCCAGGCCAGCGACAGCCTGGCCCAGGCGGAGCAGGTACTCAGCTCTGCGGGCCCCACCTCTTCCTTCGTCTTCTGAACGTGGCCTATGGCCCAGGACAGCCTGGCAGGTGGCCTCGCTGCCCCCAGTTCCCCTCT	TCGA-CC-5259-01A-31D-A20W-10	8496935	150034607	9104056	69	6977										
PIWIL2	55124	hgsc.bcm.edu	37	chr8	22146165	22146165	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ctgtgcattcccttctacaaTgttgttttccgtcggtaaga	8	10	1	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr8:22146165T>C	ENST00000454009.2	+	8	1481	c.972T>C	c.(970-972)aaT>aaC	p.N324N	PIWIL2_ENST00000356766.6_Silent_p.N324N|PIWIL2_ENST00000521356.1_Silent_p.N324N	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	324					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		CCTTCTACAATGTTGTTTTCC	0.388																																					p.N324N		Atlas-SNP	.											.	PIWIL2	100	.	0			c.T972C						.						135	113	121					8																	22146165		2203	4300	6503	SO:0001819	synonymous_variant	55124	exon8			CTACAATGTTGTT	AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"Argonaute/PIWI family"	17644	protein-coding gene	gene with protein product	"Hiwi-like", "cancer/testis antigen 80"	610312	"piwi-like 2 (Drosophila)"			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.972T>C	chr8.hg19:g.22146165T>C		185.0	0.0		188.0	105.0	NM_001135721	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Silent	SNP	ENST00000454009.2	hg19	CCDS6029.1																																																																																			.	.		0.388	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1			C	22146165	T	C	22146165	2	2	55	1	0	0	0	0	0	0	0	1	11967	1461	51	2		2	PIWIL2	8	22146165	Silent	SNP	T	TCGA-CC-5259-01A-31D-A20W-10		22146165	124217857	70	6978										
IDO2	169355	hgsc.bcm.edu	37	chr8	39873103	39873103	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gataagaccttggagtcaatCcttcacccacgtggttagga	10	10	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr8:39873103C>A	ENST00000389060.4	+	10	1206	c.1206C>A	c.(1204-1206)atC>atA	p.I402I	IDO2_ENST00000343295.4_3'UTR|IDO2_ENST00000502986.2_Silent_p.I415I			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	402					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						TGGAGTCAATCCTTCACCCAC	0.577																																					p.I415I		Atlas-SNP	.											.	IDO2	78	.	0			c.C1245A						.						90	89	89					8																	39873103		1979	4158	6137	SO:0001819	synonymous_variant	169355	exon11			GTCAATCCTTCAC	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"indoleamine-pyrrole 2,3 dioxygenase-like 1"	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.1206C>A	chr8.hg19:g.39873103C>A		95.0	0.0		92.0	39.0	NM_194294	A4UD41	Silent	SNP	ENST00000389060.4	hg19																																																																																				.	.		0.577	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294		A	39873103	C	A	39873103	2	1	55	1	0	0	0	0	0	0	0	1	7511	845	30	3		3	IDO2	8	39873103	Silent	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	17726938	39873103	106490919	71	6979										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52322116	52322116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ggacaccaagtcattgtaccGgaattctgaaaggcaagcgg	12	9	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr8:52322116G>A	ENST00000356297.4	-	17	2168	c.2068C>T	c.(2068-2070)Cgg>Tgg	p.R690W	PXDNL_ENST00000543296.1_Missense_Mutation_p.R690W	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	690					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TCATTGTACCGGAATTCTGAA	0.617																																					p.R690W		Atlas-SNP	.											.	PXDNL	414	.	0			c.C2068T						.						26	29	28					8																	52322116		2027	4177	6204	SO:0001583	missense	137902	exon17			TGTACCGGAATTC		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2068C>T	chr8.hg19:g.52322116G>A	ENSP00000348645:p.Arg690Trp	121.0	0.0		108.0	56.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	6.283	0.420284	0.11928	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.66460	-0.19;-0.21	3.59	-0.81	0.10860	.	.	.	.	.	T	0.51126	0.1656	L	0.49350	1.555	0.24931	N	0.991916	B	0.29212	0.237	B	0.16722	0.016	T	0.27773	-1.0064	8	.	.	.	.	4.912	0.13827	0.2831:0.1567:0.5602:0.0	.	690	A1KZ92	PXDNL_HUMAN	W	690	ENSP00000348645:R690W;ENSP00000444865:R690W	.	R	-	1	2	PXDNL	52484669	1.000000	0.71417	0.022000	0.16811	0.151000	0.21798	2.869000	0.48444	-0.517000	0.06461	0.462000	0.41574	CGG	.	.		0.617	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52322116	G	A	52322116	3	1	55	1	0	0	0	0	1	0	0	0	12863	1115	39	1	2351	1	PXDNL	8	52322116	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	12449013	52322116	94041906	72	6980										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53540730	53540730	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	caaatctcccacctgaaaacTgaataaagaaatgcaatttt	4	9	1	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr8:53540730T>G	ENST00000025008.5	-	22	5023		c.e22-2		RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000435644.2_Splice_Site|RB1CC1_ENST00000539297.1_Splice_Site	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1						autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				ACCTGAAAACTGAATAAAGAA	0.313																																					.	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.4500-2A>C						.						82	84	83					8																	53540730		2203	4300	6503	SO:0001630	splice_region_variant	9821	exon23			GAAAACTGAATAA	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.4500-2A>C	chr8.hg19:g.53540730T>G		51.0	0.0		75.0	22.0	NM_014781	Q86YR4|Q8WVU9|Q92601	Splice_Site	SNP	ENST00000025008.5	hg19	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.319238	0.81469	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000519912;ENST00000539297	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4755	0.75474	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RB1CC1	53703283	1.000000	0.71417	0.936000	0.37596	0.955000	0.61496	7.698000	0.84413	2.050000	0.60909	0.482000	0.46254	.	.	.		0.313	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	Intron	G	53540730	T	G	53540730	5	3	55	1	0	0	0	0	0	0	1	0	13114	1594	55	5	298	5	RB1CC1	8	53540730	Splice_Site	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	1218614	53540730	92823292	73	6981										
CA8	767	hgsc.bcm.edu	37	chr8	61193683	61193683	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tcggggaaggcgacggtatcTtcgatgaagctcaggtccgc	15	10	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr8:61193683T>A	ENST00000317995.4	-	1	288	c.24A>T	c.(22-24)gaA>gaT	p.E8D		NM_004056.4	NP_004047.3	P35219	CAH8_HUMAN	carbonic anhydrase VIII	8					one-carbon metabolic process (GO:0006730)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasm (GO:0005737)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|prostate(2)|skin(1)	16		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)			Zonisamide(DB00909)	CGACGGTATCTTCGATGAAGC	0.677																																					p.E8D		Atlas-SNP	.											.	CA8	31	.	0			c.A24T						.						71	56	61					8																	61193683		2186	4290	6476	SO:0001583	missense	767	exon1			GGTATCTTCGATG	L04656	CCDS6174.1	8q12.1	2012-08-21			ENSG00000178538	ENSG00000178538		"Carbonic anhydrases"	1382	protein-coding gene	gene with protein product		114815		CALS		17219437	Standard	NM_004056		Approved	CARP	uc003xtz.1	P35219	OTTHUMG00000165325	ENST00000317995.4:c.24A>T	chr8.hg19:g.61193683T>A	ENSP00000314407:p.Glu8Asp	44.0	0.0		44.0	19.0	NM_004056	A8K0A5|B3KQZ7|Q32MY2	Missense_Mutation	SNP	ENST00000317995.4	hg19	CCDS6174.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.101451	0.76983	.	.	ENSG00000178538	ENST00000317995	T	0.67865	-0.29	3.64	-4.2	0.03823	.	0.284967	0.32769	N	0.005663	T	0.47469	0.1447	L	0.36672	1.1	0.38712	D	0.953245	B	0.02656	0.0	B	0.01281	0.0	T	0.05937	-1.0855	10	0.87932	D	0	.	6.8076	0.23786	0.1449:0.5382:0.0:0.3169	.	8	P35219	CAH8_HUMAN	D	8	ENSP00000314407:E8D	ENSP00000314407:E8D	E	-	3	2	CA8	61356237	0.412000	0.25392	0.988000	0.46212	0.716000	0.41182	-0.663000	0.05299	-0.644000	0.05465	0.379000	0.24179	GAA	.	.		0.677	CA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383445.1			A	61193683	T	A	61193683	3	1	55	1	0	0	0	0	1	0	0	0	2525	1606	56	4	880	4	CA8	8	61193683	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	7652953	61193683	85170339	74	6982										
PREX2	80243	hgsc.bcm.edu	37	chr8	69104009	69104009	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	caaactccacatccaaagctGcctatgtagataaggtaaaa	6	10	0	1	rs202233704		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr8:69104009G>T	ENST00000288368.4	+	36	4676	c.4399G>T	c.(4399-4401)Gcc>Tcc	p.A1467S		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1467					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						ATCCAAAGCTGCCTATGTAGA	0.313																																					p.A1467S		Atlas-SNP	.											PREX2,colon,carcinoma,0,1	PREX2	614	.	0			c.G4399T						.						98	98	98					8																	69104009		2203	4300	6503	SO:0001583	missense	80243	exon36			AAAGCTGCCTATG	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4399G>T	chr8.hg19:g.69104009G>T	ENSP00000288368:p.Ala1467Ser	233.0	0.0		445.0	26.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201109	0.58234	.	.	ENSG00000046889	ENST00000288368	T	0.59638	0.25	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.54334	0.1852	L	0.44542	1.39	0.58432	D	0.999999	B	0.28900	0.227	B	0.29353	0.101	T	0.55786	-0.8086	10	0.72032	D	0.01	.	18.7115	0.91658	0.0:0.0:1.0:0.0	.	1467	Q70Z35	PREX2_HUMAN	S	1467	ENSP00000288368:A1467S	ENSP00000288368:A1467S	A	+	1	0	PREX2	69266563	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.173000	0.77612	2.729000	0.93468	0.650000	0.86243	GCC	.	G|1.000;A|0.000		0.313	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	69104009	G	T	69104009	3	4	55	1	0	0	0	0	1	0	0	0	12489	1319	46	3	4770	3	PREX2	8	69104009	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	7910326	69104009	77260013	75	6983										
FABP9	646480	hgsc.bcm.edu	37	chr8	82371529	82371529	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tcaacactaatagttactgtCggtttcactaaccctgccat	5	12	2	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr8:82371529C>A	ENST00000379071.2	-	2	172	c.117G>T	c.(115-117)ccG>ccT	p.P39P	RP11-157I4.4_ENST00000524085.2_RNA	NM_001080526.1	NP_001073995.1	Q0Z7S8	FABP9_HUMAN	fatty acid binding protein 9, testis	39					acrosome assembly (GO:0001675)	acrosomal vesicle (GO:0001669)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	6			Epithelial(68;0.186)			TAGTTACTGTCGGTTTCACTA	0.423																																					p.P39P		Atlas-SNP	.											.	FABP9	15	.	0			c.G117T						.						137	133	134					8																	82371529		2203	4300	6503	SO:0001819	synonymous_variant	646480	exon2			TACTGTCGGTTTC			8q21.13	2013-03-01			ENSG00000205186	ENSG00000205186		"Fatty acid binding protein family"	3563	protein-coding gene	gene with protein product						7958448	Standard	NM_001080526		Approved	PERF, T-FABP, PERF15	uc011lfo.2	Q0Z7S8	OTTHUMG00000164601	ENST00000379071.2:c.117G>T	chr8.hg19:g.82371529C>A		150.0	0.0		249.0	59.0	NM_001080526		Silent	SNP	ENST00000379071.2	hg19																																																																																				.	.		0.423	FABP9-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379367.2	NM_001080526		A	82371529	C	A	82371529	2	1	55	1	0	0	0	0	0	0	0	1	5368	871	31	1		1	FABP9	8	82371529	Silent	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	13267520	82371529	63992493	76	6984										
OXR1	55074	hgsc.bcm.edu	37	chr8	107719001	107719001	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aaactgatttaaataatcttGaaatggccattaaggaagat	7	4	1	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr8:107719001G>T	ENST00000442977.2	+	8	1354	c.1255G>T	c.(1255-1257)Gaa>Taa	p.E419*	OXR1_ENST00000445937.1_Nonsense_Mutation_p.E418*|OXR1_ENST00000517566.2_Nonsense_Mutation_p.E418*|OXR1_ENST00000531443.1_Nonsense_Mutation_p.E418*|OXR1_ENST00000312046.6_Nonsense_Mutation_p.E411*|OXR1_ENST00000497705.1_Nonsense_Mutation_p.E351*|OXR1_ENST00000452423.2_5'UTR	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	419					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			AAATAATCTTGAAATGGCCAT	0.348																																					p.E419X		Atlas-SNP	.											.	OXR1	190	.	0			c.G1255T						.						74	77	76					8																	107719001		2203	4300	6503	SO:0001587	stop_gained	55074	exon8			AATCTTGAAATGG	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 3"	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.1255G>T	chr8.hg19:g.107719001G>T	ENSP00000405424:p.Glu419*	80.0	0.0		177.0	19.0	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Nonsense_Mutation	SNP	ENST00000442977.2	hg19	CCDS56548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.44|17.44	3.389482|3.389482	0.61956|0.61956	.|.	.|.	ENSG00000164830|ENSG00000164830	ENST00000445937;ENST00000531443;ENST00000517566;ENST00000442977;ENST00000497705;ENST00000312046|ENST00000519415	.|T	.|0.17213	.|2.29	5.76|5.76	4.89|4.89	0.63831|0.63831	.|.	0.726780|.	0.13942|.	N|.	0.352159|.	.|T	.|0.20780	.|0.0500	.|.	.|.	.|.	0.21697|0.21697	N|N	0.999584|0.999584	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.12811	.|-1.0533	.|6	0.52906|0.49607	T|T	0.07|0.09	-16.4775|-16.4775	9.0489|9.0489	0.36363|0.36363	0.137:0.1233:0.7396:0.0|0.137:0.1233:0.7396:0.0	.|.	.|.	.|.	.|.	X|F	418;418;418;419;351;411|131	.|ENSP00000430701:L131F	ENSP00000311026:E411X|ENSP00000430701:L131F	E|L	+|+	1|3	0|2	OXR1|OXR1	107788177|107788177	0.988000|0.988000	0.35896|0.35896	0.017000|0.017000	0.16124|0.16124	0.558000|0.558000	0.35554|0.35554	3.043000|3.043000	0.49823|0.49823	1.446000|1.446000	0.47643|0.47643	0.591000|0.591000	0.81541|0.81541	GAA|TTG	.	.		0.348	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		T	107719001	G	T	107719001	4	4	55	1	0	0	0	0	0	1	0	0	11343	1291	45	3	1485	3	OXR1	8	107719001	Nonsense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	25347472	107719001	38645021	77	6985										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116599692	116599692	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ctcctctttgatggtggataTggcatgaccgtcctcttcgc	10	12	2	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr8:116599692T>A	ENST00000220888.5	-	4	2356	c.2197A>T	c.(2197-2199)Ata>Tta	p.I733L	TRPS1_ENST00000519076.1_Missense_Mutation_p.I487L|TRPS1_ENST00000520276.1_Missense_Mutation_p.I737L|TRPS1_ENST00000395715.3_Missense_Mutation_p.I746L|TRPS1_ENST00000519674.1_Missense_Mutation_p.I733L			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	733	Mediates interaction with GLI3.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			ATGGTGGATATGGCATGACCG	0.493									Langer-Giedion syndrome																												p.I746L		Atlas-SNP	.											.	TRPS1	516	.	0			c.A2236T						.						175	178	177					8																	116599692		2011	4170	6181	SO:0001583	missense	7227	exon5	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	TGGATATGGCATG	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2197A>T	chr8.hg19:g.116599692T>A	ENSP00000220888:p.Ile733Leu	267.0	0.0		465.0	84.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	T	10.38	1.333963	0.24253	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276;ENST00000519674	D;D;D;D;T	0.98264	-4.83;-4.81;-4.78;-4.81;1.0	5.86	-6.22	0.02058	.	1.038030	0.07571	N	0.918556	D	0.94000	0.8078	N	0.14661	0.345	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.001;0.0;0.002	T	0.82566	-0.0393	10	0.49607	T	0.09	.	14.7677	0.69651	0.0:0.3719:0.0:0.6281	.	737;733;746	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	L	746;733;487;737;733	ENSP00000379065:I746L;ENSP00000220888:I733L;ENSP00000428910:I487L;ENSP00000428680:I737L;ENSP00000429174:I733L	ENSP00000220888:I733L	I	-	1	0	TRPS1	116668867	0.000000	0.05858	0.000000	0.03702	0.414000	0.31173	-0.779000	0.04659	-1.580000	0.01644	-0.242000	0.12053	ATA	.	.		0.493	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		A	116599692	T	A	116599692	3	1	55	1	0	0	0	0	1	0	0	0	16608	1464	51	4	1660	4	TRPS1	8	116599692	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	8880691	116599692	29764330	78	6986										
PIP5K1B	8395	hgsc.bcm.edu	37	chr9	71491629	71491629	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	accccagcacatcactacccAgactttagatttaagacata	4	13	1	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr9:71491629A>T	ENST00000265382.3	+	6	542	c.237A>T	c.(235-237)ccA>ccT	p.P79P	PIP5K1B_ENST00000541509.1_Silent_p.P79P	NM_003558.2	NP_003549.1	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, beta	79	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			breast(1)|large_intestine(2)|stomach(1)	4				Lung(182;0.133)		ATCACTACCCAGACTTTAGAT	0.383																																					p.P79P		Atlas-SNP	.											.	PIP5K1B	40	.	0			c.A237T						.						123	123	123					9																	71491629		2203	4300	6503	SO:0001819	synonymous_variant	8395	exon6			CTACCCAGACTTT	U78579	CCDS6624.1, CCDS65063.1	9q13	2008-02-05			ENSG00000107242	ENSG00000107242			8995	protein-coding gene	gene with protein product		602745				9177790, 8841185	Standard	NM_003558		Approved	STM7, MSS4	uc004agu.4	O14986	OTTHUMG00000019976	ENST00000265382.3:c.237A>T	chr9.hg19:g.71491629A>T		102.0	0.0		127.0	57.0	NM_003558	A8K9L9|B4DIG7|P78518|P78519|Q5T5K6|Q5T5K8|Q5T5K9|Q5VZ00|Q7KYT5|Q8NHQ5|Q92749	Silent	SNP	ENST00000265382.3	hg19	CCDS6624.1																																																																																			.	.		0.383	PIP5K1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052561.2	NM_003558		T	71491629	A	T	71491629	2	4	55	1	0	0	0	0	0	0	0	1	11949	175	7	4		4	PIP5K1B	9	71491629	Silent	SNP	A	TCGA-CC-5259-01A-31D-A20W-10		71491629	69721802	79	6987										
SCAI	286205	hgsc.bcm.edu	37	chr9	127734043	127734043	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ccataggcctctgcgcatgcTtgacaatccagagacaaata	8	12	1	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr9:127734043T>A	ENST00000336505.6	-	16	1538	c.1480A>T	c.(1480-1482)Agc>Tgc	p.S494C	SCAI_ENST00000373549.4_Missense_Mutation_p.S517C	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	494					negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						CTGCGCATGCTTGACAATCCA	0.418																																					p.S517C		Atlas-SNP	.											.	SCAI	84	.	0			c.A1549T						.						136	123	127					9																	127734043		1861	4098	5959	SO:0001583	missense	286205	exon17			GCATGCTTGACAA	AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 126"	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.1480A>T	chr9.hg19:g.127734043T>A	ENSP00000336756:p.Ser494Cys	147.0	0.0		197.0	93.0	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Missense_Mutation	SNP	ENST00000336505.6	hg19	CCDS48017.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.176984	0.78564	.	.	ENSG00000173611	ENST00000336505;ENST00000373549	T;T	0.48522	0.81;0.81	4.95	4.95	0.65309	.	0.037833	0.85682	D	0.000000	T	0.66819	0.2828	M	0.71036	2.16	0.53688	D	0.999972	D;D	0.76494	0.999;0.999	D;D	0.79784	0.993;0.992	T	0.70421	-0.4876	10	0.62326	D	0.03	-9.8697	14.1109	0.65121	0.0:0.0:0.0:1.0	.	494;517	Q8N9R8;Q8N9R8-2	SCAI_HUMAN;.	C	494;517	ENSP00000336756:S494C;ENSP00000362650:S517C	ENSP00000336756:S494C	S	-	1	0	SCAI	126773864	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.309000	0.78937	1.996000	0.58369	0.533000	0.62120	AGC	.	.		0.418	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690		A	127734043	T	A	127734043	3	1	55	1	0	0	0	0	1	0	0	0	13884	1609	56	4	352	4	SCAI	9	127734043	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	56242414	127734043	13479388	80	6988										
CRAT	1384	hgsc.bcm.edu	37	chr9	131859581	131859581	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ccttccgcagcagctccaccTtctggtgctcctagagtggt	10	15	1	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr9:131859581T>A	ENST00000318080.2	-	12	1769	c.1475A>T	c.(1474-1476)aAg>aTg	p.K492M	RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	492					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	CAGCTCCACCTTCTGGTGCTC	0.612																																					p.K492M		Atlas-SNP	.											.	CRAT	43	.	0			c.A1475T						.						46	32	37					9																	131859581		2197	4286	6483	SO:0001583	missense	1384	exon12			TCCACCTTCTGGT	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"carnitine acetyltransferase"			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.1475A>T	chr9.hg19:g.131859581T>A	ENSP00000315013:p.Lys492Met	45.0	0.0		67.0	27.0	NM_000755	Q5T952|Q9BW16	Missense_Mutation	SNP	ENST00000318080.2	hg19	CCDS6919.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.0|25.0	4.589550|4.589550	0.86851|0.86851	.|.	.|.	ENSG00000095321|ENSG00000095321	ENST00000455396|ENST00000351352;ENST00000318080	.|D	.|0.91237	.|-2.81	5.69|5.69	4.53|4.53	0.55603|0.55603	.|.	.|0.096905	.|0.64402	.|D	.|0.000002	D|D	0.95743|0.95743	0.8615|0.8615	M|M	0.92268|0.92268	3.29|3.29	0.80722|0.80722	D|D	1|1	.|D	.|0.65815	.|0.995	.|D	.|0.73380	.|0.98	D|D	0.95297|0.95297	0.8400|0.8400	5|10	.|0.72032	.|D	.|0.01	-35.4726|-35.4726	9.8793|9.8793	0.41222|0.41222	0.0:0.0781:0.0:0.9219|0.0:0.0781:0.0:0.9219	.|.	.|492	.|P43155	.|CACP_HUMAN	D|M	90|411;492	.|ENSP00000315013:K492M	.|ENSP00000315013:K492M	E|K	-|-	3|2	2|0	CRAT|CRAT	130899402|130899402	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.955000|0.955000	0.61496|0.61496	4.103000|4.103000	0.57783|0.57783	0.944000|0.944000	0.37579|0.37579	0.528000|0.528000	0.53228|0.53228	GAA|AAG	.	.		0.612	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1			A	131859581	T	A	131859581	3	1	55	1	0	0	0	0	1	0	0	0	3849	1609	56	4	417	4	CRAT	9	131859581	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	4125538	131859581	9353850	81	6989										
MAMDC4	158056	hgsc.bcm.edu	37	chr9	139749459	139749459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gttcctgcagactctggggcCcggcgccccccgggcccccg	14	20	1	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr9:139749459C>T	ENST00000317446.2	+	10	1144	c.1094C>T	c.(1093-1095)cCc>cTc	p.P365L	MAMDC4_ENST00000445819.1_Missense_Mutation_p.P365L|MAMDC4_ENST00000485732.1_3'UTR	NM_206920.2	NP_996803.2			MAM domain containing 4											breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	19	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		ACTCTggggcccggcgccccc	0.692																																					p.P365L		Atlas-SNP	.											.	MAMDC4	117	.	0			c.C1094T						.						13	16	15					9																	139749459		2174	4271	6445	SO:0001583	missense	158056	exon10			TGGGGCCCGGCGC	AL834531	CCDS7010.1	9q34.3	2013-10-21			ENSG00000177943	ENSG00000177943			24083	protein-coding gene	gene with protein product	"apical early endosomal glycoprotein precursor", "endotubin"					7829488	Standard	NM_206920		Approved	AEGP, DKFZp434M1411	uc004cjs.3	Q6UXC1	OTTHUMG00000020951	ENST00000317446.2:c.1094C>T	chr9.hg19:g.139749459C>T	ENSP00000319388:p.Pro365Leu	42.0	0.0		74.0	37.0	NM_206920		Missense_Mutation	SNP	ENST00000317446.2	hg19	CCDS7010.1	.	.	.	.	.	.	.	.	.	.	.	2.063	-0.414851	0.04766	.	.	ENSG00000177943	ENST00000317446;ENST00000445819	T;T	0.02015	4.5;4.5	4.65	3.73	0.42828	.	0.379178	0.22542	N	0.058715	T	0.01940	0.0061	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.46527	-0.9185	10	0.26408	T	0.33	-6.3944	6.7173	0.23310	0.0:0.7777:0.0:0.2223	.	365	Q6UXC1-2	.	L	365	ENSP00000319388:P365L;ENSP00000411339:P365L	ENSP00000319388:P365L	P	+	2	0	MAMDC4	138869280	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.039000	0.12124	0.930000	0.37217	0.561000	0.74099	CCC	.	.		0.692	MAMDC4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254642.3	NM_206920		T	139749459	C	T	139749459	3	4	55	1	0	0	0	0	1	0	0	0	9213	623	22	3	1132	3	MAMDC4	9	139749459	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	7889878	139749459	1463972	82	6990										
NET1	10276	hgsc.bcm.edu	37	chr10	5494450	5494450	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agatgctggacatcaccatgAaggagtctctcaccaccagg	10	12	3	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr10:5494450A>G	ENST00000355029.4	+	5	635	c.493A>G	c.(493-495)Aag>Gag	p.K165E	NET1_ENST00000380359.3_Missense_Mutation_p.K111E|NET1_ENST00000542715.1_5'UTR	NM_001047160.2	NP_001040625.1	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming 1	165					apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|myoblast migration (GO:0051451)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|kidney(2)|large_intestine(9)|lung(5)|prostate(2)|skin(1)	23						CATCACCATGAAGGAGTCTCT	0.527																																					p.K165E		Atlas-SNP	.											.	NET1	82	.	0			c.A493G						.						97	84	89					10																	5494450		2203	4300	6503	SO:0001583	missense	10276	exon5			ACCATGAAGGAGT	AJ010046	CCDS7067.1, CCDS41483.1	10p15	2013-01-10	2008-09-12		ENSG00000173848	ENSG00000173848		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14592	protein-coding gene	gene with protein product		606450				8649828	Standard	NR_073040		Approved	ARHGEF8, NET1A	uc001iia.4	Q7Z628	OTTHUMG00000017596	ENST00000355029.4:c.493A>G	chr10.hg19:g.5494450A>G	ENSP00000347134:p.Lys165Glu	109.0	0.0		146.0	8.0	NM_001047160	Q12773|Q96D82|Q99903|Q9UEN6	Missense_Mutation	SNP	ENST00000355029.4	hg19	CCDS41483.1	.	.	.	.	.	.	.	.	.	.	A	12.03	1.816307	0.32145	.	.	ENSG00000173848	ENST00000355029;ENST00000380359	T;T	0.67523	-0.27;-0.27	5.54	5.54	0.83059	Dbl homology (DH) domain (1);	0.000000	0.43919	D	0.000520	T	0.63283	0.2498	M	0.65498	2.005	0.80722	D	1	B;B	0.25521	0.128;0.066	B;B	0.24394	0.053;0.053	T	0.59747	-0.7396	10	0.15499	T	0.54	-29.0071	14.5067	0.67758	1.0:0.0:0.0:0.0	.	111;165	Q5SQI7;Q7Z628	.;ARHG8_HUMAN	E	165;111	ENSP00000347134:K165E;ENSP00000369717:K111E	ENSP00000347134:K165E	K	+	1	0	NET1	5484450	1.000000	0.71417	0.999000	0.59377	0.211000	0.24417	7.306000	0.78905	2.093000	0.63338	0.533000	0.62120	AAG	.	.		0.527	NET1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046553.3	NM_005863		G	5494450	A	G	5494450	3	3	55	1	0	0	0	0	1	0	0	0	10347	247	9	2	608	2	NET1	10	5494450	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10		5494450	130040297	83	6991										
PLXDC2	84898	hgsc.bcm.edu	37	chr10	20453406	20453406	+	Frame_Shift_Del	DEL	T	T	-													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tttttttccagattcctgtcTtggtcacacagataagttca							TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr10:20453406delT	ENST00000377252.4	+	7	1634	c.793delT	c.(793-795)ttgfs	p.L265fs	PLXDC2_ENST00000377238.2_3'UTR|PLXDC2_ENST00000377242.3_Frame_Shift_Del_p.L216fs	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	265					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						GATTCCTGTCTTGGTCACACA	0.408																																					p.V264fs		Atlas-Indel,Pindel	.											.	PLXDC2	108	.	0			c.792delC						.						111	90	97					10																	20453406		2203	4300	6503	SO:0001589	frameshift_variant	84898	exon7			.	AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"tumor endothelial marker 7-related precursor"	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.793delT	chr10.hg19:g.20453406delT	ENSP00000366460:p.Leu265fs	86.0	0.0		103.0	43.0	NM_032812	Q96E59|Q96PD9|Q96SU9	Frame_Shift_Del	DEL	ENST00000377252.4	hg19	CCDS7132.1																																																																																			.	.		0.408	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		-	20453406	T	-	20453406	7	5	55	1	0	1	0	1	0	0	0	0	12127	1606	56	0	819	0	PLXDC2	10	20453406	Frame_Shift_Del	DEL	T	TCGA-CC-5259-01A-31D-A20W-10	14958956	20453406	115081341	84	6992										
ARMC3	219681	hgsc.bcm.edu	37	chr10	23244747	23244747	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tgatgtcaggtgaggaaaatAaaacaaccctccttgaactt	8	8	1	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr10:23244747A>G	ENST00000298032.5	+	4	262	c.178A>G	c.(178-180)Aaa>Gaa	p.K60E	ARMC3_ENST00000376528.4_5'UTR|ARMC3_ENST00000464017.1_3'UTR|ARMC3_ENST00000409049.3_Missense_Mutation_p.K60E|ARMC3_ENST00000409983.3_Missense_Mutation_p.K60E	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	60						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TGAGGAAAATAAAACAACCCT	0.378																																					p.K60E		Atlas-SNP	.											.	ARMC3	102	.	0			c.A178G						.						122	122	122					10																	23244747		2203	4300	6503	SO:0001583	missense	219681	exon4			GAAAATAAAACAA	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"Armadillo repeat containing"	30964	protein-coding gene	gene with protein product	"cancer/testis antigen 81"	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.178A>G	chr10.hg19:g.23244747A>G	ENSP00000298032:p.Lys60Glu	43.0	0.0		64.0	19.0	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Missense_Mutation	SNP	ENST00000298032.5	hg19	CCDS7142.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.604019	0.87157	.	.	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000376523;ENST00000409049	T;T;T	0.72505	-0.66;-0.66;-0.66	5.36	5.36	0.76844	Armadillo-like helical (1);Armadillo-type fold (1);	0.092218	0.64402	D	0.000001	T	0.82217	0.4989	M	0.63843	1.955	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.979;0.999	D	0.84109	0.0400	10	0.72032	D	0.01	-20.9279	15.659	0.77169	1.0:0.0:0.0:0.0	.	60;60	Q5W041-4;Q5W041	.;ARMC3_HUMAN	E	60	ENSP00000298032:K60E;ENSP00000386943:K60E;ENSP00000387288:K60E	ENSP00000298032:K60E	K	+	1	0	ARMC3	23284753	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	8.077000	0.89505	2.165000	0.68154	0.533000	0.62120	AAA	.	.		0.378	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		G	23244747	A	G	23244747	3	3	55	1	0	0	0	0	1	0	0	0	952	363	13	2	188	2	ARMC3	10	23244747	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	2791341	23244747	112290000	85	6993										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27324233	27324233	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ttaggttagacacatcaaaaTtcattttgtcctgtaaacga	6	7	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr10:27324233T>C	ENST00000376087.4	-	24	3311	c.3146A>G	c.(3145-3147)aAt>aGt	p.N1049S	ANKRD26_ENST00000436985.2_Missense_Mutation_p.N1065S|ANKRD26_ENST00000376070.3_Missense_Mutation_p.N606S	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1048					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CACATCAAAATTCATTTTGTC	0.338																																					p.N1049S		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A3146G						.						96	89	92					10																	27324233		1856	4093	5949	SO:0001583	missense	22852	exon24			TCAAAATTCATTT	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3146A>G	chr10.hg19:g.27324233T>C	ENSP00000365255:p.Asn1049Ser	126.0	0.0		155.0	69.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	hg19	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	T	5.645	0.303739	0.10678	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.14893	2.47;2.47;2.47	5.7	3.26	0.37387	.	0.098954	0.41194	D	0.000926	T	0.16300	0.0392	L	0.49640	1.575	0.09310	N	1	B;B;P	0.36282	0.136;0.084;0.546	B;B;B	0.34722	0.053;0.024;0.188	T	0.06954	-1.0798	10	0.52906	T	0.07	.	11.0481	0.47870	0.0:0.0:0.2962:0.7038	.	1049;1048;1065	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	S	606;1049;1065	ENSP00000365238:N606S;ENSP00000365255:N1049S;ENSP00000405112:N1065S	ENSP00000365238:N606S	N	-	2	0	ANKRD26	27364239	1.000000	0.71417	0.010000	0.14722	0.060000	0.15804	1.619000	0.36965	0.385000	0.24970	0.482000	0.46254	AAT	.	.		0.338	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			C	27324233	T	C	27324233	3	2	55	1	0	0	0	0	1	0	0	0	654	1493	52	2	2030	2	ANKRD26	10	27324233	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	4079486	27324233	108210514	86	6994										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55996688	55996688	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aacaataatggggttcagttCttcctgaaaaaaaaattaag	7	5	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr10:55996688C>A	ENST00000320301.6	-	9	1274	c.880G>T	c.(880-882)Gaa>Taa	p.E294*	PCDH15_ENST00000395446.1_Nonsense_Mutation_p.E294*|PCDH15_ENST00000395432.2_Nonsense_Mutation_p.E257*|PCDH15_ENST00000395433.1_Nonsense_Mutation_p.E272*|PCDH15_ENST00000414778.1_Nonsense_Mutation_p.E299*|PCDH15_ENST00000373965.2_Nonsense_Mutation_p.E294*|PCDH15_ENST00000373955.1_Nonsense_Mutation_p.E294*|PCDH15_ENST00000395438.1_Nonsense_Mutation_p.E294*|PCDH15_ENST00000361849.3_Nonsense_Mutation_p.E294*|PCDH15_ENST00000373957.3_Nonsense_Mutation_p.E272*|PCDH15_ENST00000395440.1_Nonsense_Mutation_p.E294*|PCDH15_ENST00000395430.1_Nonsense_Mutation_p.E294*|PCDH15_ENST00000395445.1_Nonsense_Mutation_p.E294*|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000437009.1_Nonsense_Mutation_p.E294*|PCDH15_ENST00000395442.1_Nonsense_Mutation_p.E294*	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	294	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GGGTTCAGTTCTTCCTGAAAA	0.398										HNSCC(58;0.16)																											p.E299X		Atlas-SNP	.											.	PCDH15	1715	.	0			c.G895T						.						142	138	140					10																	55996688		2203	4300	6503	SO:0001587	stop_gained	65217	exon10			TCAGTTCTTCCTG	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.880G>T	chr10.hg19:g.55996688C>A	ENSP00000322604:p.Glu294*	129.0	0.0		156.0	42.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Nonsense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	40	8.166969	0.98686	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	.	.	.	5.19	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	9.0928	0.36621	0.0:0.7692:0.1483:0.0825	.	.	.	.	X	294;299;294;294;294;294;294;294;257;294;272;272;294;294;299;294;294	.	ENSP00000322604:E294X	E	-	1	0	PCDH15	55666694	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	3.046000	0.49846	1.189000	0.43028	0.650000	0.86243	GAA	.	.		0.398	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55996688	C	A	55996688	4	1	55	1	0	0	0	0	0	1	0	0	11520	922	32	3	6731	3	PCDH15	10	55996688	Nonsense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	28672455	55996688	79538059	87	6995										
SYNPO2L	79933	hgsc.bcm.edu	37	chr10	75414002	75414002	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	caagagctggtccctctctcGgagtcctgctctgccagcct	10	16	2	1	rs543087941		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr10:75414002G>A	ENST00000394810.2	-	2	291	c.142C>T	c.(142-144)Cga>Tga	p.R48*	RP11-464F9.21_ENST00000606726.1_RNA|RP11-464F9.21_ENST00000607450.1_RNA	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	48	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					TCCCTCTCTCGGAGTCCTGCT	0.532																																					p.R48X		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.C142T						.						111	97	101					10																	75414002		692	1591	2283	SO:0001587	stop_gained	79933	exon2			TCTCTCGGAGTCC	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.142C>T	chr10.hg19:g.75414002G>A	ENSP00000378289:p.Arg48*	175.0	0.0		143.0	14.0	NM_001114133	A5PKV9|Q68A20	Nonsense_Mutation	SNP	ENST00000394810.2	hg19	CCDS44438.1	.	.	.	.	.	.	.	.	.	.	G	36	5.964151	0.97151	.	.	ENSG00000166317	ENST00000372872;ENST00000394810	.	.	.	5.31	4.32	0.51571	.	0.201703	0.32819	U	0.005619	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-0.8396	5.8295	0.18572	0.1296:0.0:0.6637:0.2067	.	.	.	.	X	48	.	ENSP00000361963:R48X	R	-	1	2	SYNPO2L	75084008	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.961000	0.40432	2.495000	0.84180	0.455000	0.32223	CGA	.	.		0.532	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875		A	75414002	G	A	75414002	4	1	55	1	0	0	0	0	0	1	0	0	15473	1124	39	1	2907	1	SYNPO2L	10	75414002	Nonsense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	19417314	75414002	60120745	88	6996										
SLC18A2	6571	hgsc.bcm.edu	37	chr10	119001223	119001223	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ccatggccctgagcgagctgGcgctggtccgctggctgcag	16	14	0	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr10:119001223G>C	ENST00000298472.5	+	2	162	c.19G>C	c.(19-21)Gcg>Ccg	p.A7P	RP11-501J20.5_ENST00000425264.1_RNA|SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	7					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	GAGCGAGCTGGCGCTGGTCCG	0.706																																					p.A7P		Atlas-SNP	.											.	SLC18A2	58	.	0			c.G19C						.						19	19	19					10																	119001223		2202	4299	6501	SO:0001583	missense	6571	exon2			GAGCTGGCGCTGG	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"Solute carriers"	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.19G>C	chr10.hg19:g.119001223G>C	ENSP00000298472:p.Ala7Pro	86.0	0.0		61.0	38.0	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Missense_Mutation	SNP	ENST00000298472.5	hg19	CCDS7599.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.281161	0.59758	.	.	ENSG00000165646	ENST00000298472	T	0.03889	3.77	5.09	4.19	0.49359	.	0.768875	0.12583	N	0.456298	T	0.02848	0.0085	N	0.04508	-0.205	0.09310	N	1	B	0.33448	0.412	B	0.30855	0.121	T	0.44997	-0.9291	10	0.56958	D	0.05	-7.9427	10.0113	0.41988	0.1614:0.0:0.8386:0.0	.	7	Q05940	VMAT2_HUMAN	P	7	ENSP00000298472:A7P	ENSP00000298472:A7P	A	+	1	0	SLC18A2	118991213	0.796000	0.28864	0.993000	0.49108	0.990000	0.78478	1.140000	0.31516	1.148000	0.42385	0.563000	0.77884	GCG	.	.		0.706	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054		C	119001223	G	C	119001223	3	2	55	1	0	0	0	0	1	0	0	0	14441	1203	42	4	21	4	SLC18A2	10	119001223	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	43587221	119001223	16533524	89	6997										
DOCK1	1793	hgsc.bcm.edu	37	chr10	128798514	128798514	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gcgtgggtcgcatggagctgAgggacaacaacaccaggaaa	15	9	0	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr10:128798514A>T	ENST00000280333.6	+	10	1037	c.928A>T	c.(928-930)Agg>Tgg	p.R310W	RP11-223P11.3_ENST00000595456.1_RNA|RP11-223P11.3_ENST00000594614.1_RNA|RP11-223P11.3_ENST00000594559.1_RNA|RP11-223P11.3_ENST00000601242.1_RNA|RP11-223P11.3_ENST00000601826.1_RNA	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	310					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		CATGGAGCTGAGGGACAACAA	0.463																																					p.R310W		Atlas-SNP	.											.	DOCK1	188	.	0			c.A928T						.						90	95	93					10																	128798514		1940	4156	6096	SO:0001583	missense	1793	exon10			GAGCTGAGGGACA	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.928A>T	chr10.hg19:g.128798514A>T	ENSP00000280333:p.Arg310Trp	132.0	0.0		125.0	46.0	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	hg19		.	.	.	.	.	.	.	.	.	.	A	19.65	3.867809	0.72065	.	.	ENSG00000150760	ENST00000280333	T	0.18016	2.24	4.0	4.0	0.46444	.	0.000000	0.85682	D	0.000000	T	0.26085	0.0636	L	0.34521	1.04	0.44719	D	0.997719	D;D	0.69078	0.993;0.997	D;D	0.64321	0.924;0.924	T	0.01617	-1.1311	10	0.87932	D	0	.	10.5292	0.44967	0.7123:0.2877:0.0:0.0	.	310;310	B2RUU3;Q14185	.;DOCK1_HUMAN	W	310	ENSP00000280333:R310W	ENSP00000280333:R310W	R	+	1	2	DOCK1	128688504	0.969000	0.33509	1.000000	0.80357	0.997000	0.91878	0.818000	0.27295	2.043000	0.60533	0.533000	0.62120	AGG	.	.		0.463	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		T	128798514	A	T	128798514	3	4	55	1	0	0	0	0	1	0	0	0	4686	295	11	4	966	4	DOCK1	10	128798514	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	9797291	128798514	6736233	90	6998										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135009191	135009191	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ctgtgtactgtgtggccgccGttctgtggaccgcagccaag	14	12	1	0	rs541722509		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr10:135009191G>A	ENST00000304613.3	+	10	1621	c.1600G>A	c.(1600-1602)Gtt>Att	p.V534I	KNDC1_ENST00000368572.2_Missense_Mutation_p.V534I|KNDC1_ENST00000368571.2_Missense_Mutation_p.V469I			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	534	KIND 2. {ECO:0000255|PROSITE- ProRule:PRU00709}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TGTGGCCGCCGTTCTGTGGAC	0.667													G|||	1	0.000199681	8e-04	0	5008	,	,		15057	0		0	False		,,,				2504	0				p.V534I		Atlas-SNP	.											.	KNDC1	155	.	0			c.G1600A						.						48	44	45					10																	135009191		2202	4300	6502	SO:0001583	missense	85442	exon10			GCCGCCGTTCTGT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.1600G>A	chr10.hg19:g.135009191G>A	ENSP00000304437:p.Val534Ile	346.0	0.0		257.0	65.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.494320	0.26774	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.41400	1.0;1.0;1.0	4.63	2.32	0.28847	KIND (2);	0.189090	0.34067	N	0.004291	T	0.24851	0.0603	L	0.45581	1.43	0.38564	D	0.949782	P;B	0.45428	0.858;0.221	B;B	0.32928	0.155;0.051	T	0.08806	-1.0704	10	0.32370	T	0.25	-39.5659	4.8812	0.13681	0.3953:0.0:0.6047:0.0	.	469;534	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	I	534;534;469	ENSP00000304437:V534I;ENSP00000357561:V534I;ENSP00000357560:V469I	ENSP00000304437:V534I	V	+	1	0	KNDC1	134859181	0.108000	0.22018	0.624000	0.29186	0.129000	0.20672	1.040000	0.30278	1.085000	0.41206	0.306000	0.20318	GTT	.	.		0.667	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	135009191	G	A	135009191	3	1	55	1	0	0	0	0	1	0	0	0	8435	1145	40	1	1638	1	KNDC1	10	135009191	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	6210677	135009191	525556	91	6999										
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468094	56468094	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tggtattcttctgtctacacCccaaagatcctagtgacctg	7	12	3	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr11:56468094C>A	ENST00000312153.1	+	1	231	c.231C>A	c.(229-231)acC>acA	p.T77T		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	77						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						CTGTCTACACCCCAAAGATCC	0.468																																					p.T77T		Atlas-SNP	.											.	.	.	.	0			c.C231A						.						146	136	139					11																	56468094		2201	4296	6497	SO:0001819	synonymous_variant	504191	exon1			CTACACCCCAAAG	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"GPCR / Class A : Olfactory receptors"	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.231C>A	chr11.hg19:g.56468094C>A		199.0	0.0		234.0	53.0	NM_001013358	Q6IEU9|Q8NGQ0	Silent	SNP	ENST00000312153.1	hg19	CCDS31536.1																																																																																			.	.		0.468	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		A	56468094	C	A	56468094	2	1	55	1	0	0	0	0	0	0	0	1	11259	610	22	3		3	OR9G1	11	56468094	Silent	SNP	C	TCGA-CC-5259-01A-31D-A20W-10		56468094	78538422	92	7000										
C11orf9	745	hgsc.bcm.edu	37	chr11	61547380	61547380	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tgcagggaaccatcattgccCtggtggtggtcatggccttc	13	11	2	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr11:61547380C>G	ENST00000278836.5	+	17	2410	c.2314C>G	c.(2314-2316)Ctg>Gtg	p.L772V	MYRF_ENST00000389602.4_Missense_Mutation_p.L163V|MYRF_ENST00000327797.1_Missense_Mutation_p.L418V|TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000265460.5_Missense_Mutation_p.L763V	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	772					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CATCATTGCCCTGGTGGTGGT	0.597																																					p.L772V		Atlas-SNP	.											.	.	.	.	0			c.C2314G						.						87	83	84					11																	61547380		2202	4299	6501	SO:0001583	missense	745	exon17			ATTGCCCTGGTGG		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"myelin gene regulatory factor"	608329	"chromosome 11 open reading frame 9"	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.2314C>G	chr11.hg19:g.61547380C>G	ENSP00000278836:p.Leu772Val	296.0	0.0		270.0	129.0	NM_001127392	O43582|Q9P1Q6	Missense_Mutation	SNP	ENST00000278836.5	hg19	CCDS44622.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.140041	0.56936	.	.	ENSG00000124920	ENST00000278836;ENST00000265460;ENST00000327797;ENST00000389602	T;T;T;T	0.58940	0.58;0.53;0.3;0.3	5.23	5.23	0.72850	.	0.181349	0.38111	N	0.001816	T	0.73481	0.3592	M	0.80616	2.505	0.58432	D	0.999992	D;D;P	0.71674	0.998;0.965;0.908	D;P;P	0.65773	0.938;0.837;0.656	T	0.76767	-0.2838	10	0.87932	D	0	-19.1061	10.5217	0.44922	0.0:0.8656:0.0:0.1344	.	163;763;772	B4DHB2;Q9Y2G1-2;Q9Y2G1	.;.;MRF_HUMAN	V	772;763;418;163	ENSP00000278836:L772V;ENSP00000265460:L763V;ENSP00000333261:L418V;ENSP00000374253:L163V	ENSP00000265460:L763V	L	+	1	2	C11orf9	61303956	0.966000	0.33281	1.000000	0.80357	0.993000	0.82548	1.787000	0.38704	2.610000	0.88304	0.563000	0.77884	CTG	.	.		0.597	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		G	61547380	C	G	61547380	3	3	55	1	0	0	0	0	1	0	0	0	1673	680	24	4	2403	4	C11orf9	11	61547380	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	5079286	61547380	73459136	93	7001										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62292811	62292811	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ggcatgctgaatttgggcatTttcactttgggcatttttag	11	6	1	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr11:62292811T>A	ENST00000378024.4	-	5	9352	c.9078A>T	c.(9076-9078)aaA>aaT	p.K3026N	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3026					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				ATTTGGGCATTTTCACTTTGG	0.547																																					p.K3026N		Atlas-SNP	.											.	AHNAK	532	.	0			c.A9078T						.						190	199	196					11																	62292811		2202	4299	6501	SO:0001583	missense	79026	exon5			GGGCATTTTCACT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.9078A>T	chr11.hg19:g.62292811T>A	ENSP00000367263:p.Lys3026Asn	165.0	0.0		162.0	67.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	13.65	2.299384	0.40694	.	.	ENSG00000124942	ENST00000378024	T	0.01538	4.79	3.97	-0.0249	0.13937	.	.	.	.	.	T	0.08133	0.0203	M	0.85197	2.74	0.31884	N	0.618068	D	0.65815	0.995	D	0.79784	0.993	T	0.08166	-1.0735	9	0.35671	T	0.21	.	5.7294	0.18030	0.0:0.339:0.1383:0.5226	.	3026	Q09666	AHNK_HUMAN	N	3026	ENSP00000367263:K3026N	ENSP00000367263:K3026N	K	-	3	2	AHNAK	62049387	0.802000	0.28943	0.990000	0.47175	0.589000	0.36550	-0.152000	0.10159	-0.219000	0.10003	0.242000	0.17961	AAA	.	.		0.547	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62292811	T	A	62292811	3	1	55	1	0	0	0	0	1	0	0	0	414	1838	64	4	8714	4	AHNAK	11	62292811	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	745431	62292811	72713705	94	7002										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66463896	66463896	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ggttggcatcaaagaggctgCgggccttggcttgggtggtg	19	7	1	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr11:66463896C>T	ENST00000533211.1	-	21	4461	c.4130G>A	c.(4129-4131)cGc>cAc	p.R1377H	SPTBN2_ENST00000309996.2_Missense_Mutation_p.R1377H|SPTBN2_ENST00000529997.1_Missense_Mutation_p.R1377H			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1377					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						AAAGAGGCTGCGGGCCTTGGC	0.632																																					p.R1377H		Atlas-SNP	.											SPTBN2,NS,carcinoma,0,1	SPTBN2	188	.	0			c.G4130A						.						83	89	87					11																	66463896		2200	4295	6495	SO:0001583	missense	6712	exon20			AGGCTGCGGGCCT	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.4130G>A	chr11.hg19:g.66463896C>T	ENSP00000432568:p.Arg1377His	48.0	0.0		66.0	23.0	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.781893	0.90282	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.49432	0.78;0.78;0.78	4.85	4.85	0.62838	.	0.066599	0.64402	D	0.000004	T	0.62233	0.2411	M	0.75085	2.285	0.47994	D	0.999566	D	0.69078	0.997	P	0.60236	0.871	T	0.65685	-0.6108	10	0.66056	D	0.02	.	10.4728	0.44646	0.0:0.9098:0.0:0.0902	.	1377	O15020	SPTN2_HUMAN	H	1377	ENSP00000432568:R1377H;ENSP00000311489:R1377H;ENSP00000433593:R1377H	ENSP00000311489:R1377H	R	-	2	0	SPTBN2	66220472	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.599000	0.46231	2.531000	0.85337	0.557000	0.71058	CGC	.	.		0.632	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		T	66463896	C	T	66463896	3	4	55	1	0	0	0	0	1	0	0	0	15135	768	27	1	3114	1	SPTBN2	11	66463896	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	4171085	66463896	68542620	95	7003										
B3GNT6	192134	hgsc.bcm.edu	37	chr11	76751585	76751585	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cagcggccacgagggcatccTggcccttcggcgtgcagctt	14	15	0	0	rs11292199		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr11:76751585T>C	ENST00000354301.5	+	4	1076	c.988T>C	c.(988-990)Tgg>Cgg	p.W330R	B3GNT6_ENST00000421061.1_Splice_Site|B3GNT6_ENST00000533140.1_Silent_p.P330P	NM_138706.3	NP_619651.3	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						GAGGGCATCCTGGCCCTTCGG	0.697																																					.		Atlas-SNP	.											.,2	B3GNT6	27	.	0			c.988+1T>C						.						6	5	6					11																	76751585		1175	2610	3785	SO:0001630	splice_region_variant	192134	exon3			GCATCCTGGCCCT	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"Beta 3-glycosyltransferases"	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000354301.5:c.988-1T>C	chr11.hg19:g.76751585T>C		6.0	0.0		13.0	4.0	NM_138706	Q4TTN0	Splice_Site	SNP	ENST00000354301.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.007|0.007	-1.936685|-1.936685	0.00484|0.00484	.|.	.|.	ENSG00000198488|ENSG00000198488	ENST00000354301;ENST00000421061|ENST00000354301	.|T	.|0.24538	.|1.85	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.11024	.|0.0269	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.26916	.|-1.0089	.|4	.|0.02654	.|T	.|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|R	-1|330	.|ENSP00000346256:W330R	.|ENSP00000346256:W330R	.|W	+|+	.|1	.|0	B3GNT6|B3GNT6	76429233|76429233	0.988000|0.988000	0.35896|0.35896	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	0.000000|0.000000	0.12993|0.12993	0.000000|0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	.|TGG	.	.		0.697	B3GNT6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_138706	Missense_Mutation	C	76751585	T	C	76751585	5	2	55	1	0	0	0	0	0	0	1	0	1261	1567	55	2	992	2	B3GNT6	11	76751585	Splice_Site	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	10287689	76751585	58254931	96	7004										
PCF11	51585	hgsc.bcm.edu	37	chr11	82879771	82879771	+	Frame_Shift_Del	DEL	G	G	-													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gatgggtcaccaggacaaatGgggggaggaggccctttgag							TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr11:82879771delG	ENST00000298281.4	+	8	2846	c.2394delG	c.(2392-2394)atgfs	p.M798fs		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	798	Gly-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						CAGGACAAATGGGGGGAGGAG	0.522																																					p.M798fs		Atlas-Indel,Pindel	.											.	PCF11	220	.	0			c.2393delT						.						57	57	57					11																	82879771		1904	4105	6009	SO:0001589	frameshift_variant	51585	exon8			.	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.2394delG	chr11.hg19:g.82879771delG	ENSP00000298281:p.Met798fs	80.0	0.0		117.0	16.0	NM_015885	A6H8W7|O43671|Q6P0X8	Frame_Shift_Del	DEL	ENST00000298281.4	hg19	CCDS44689.1																																																																																			.	.		0.522	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		-	82879771	G	-	82879771	7	5	55	1	0	1	0	1	0	0	0	0	11582	1348	47	0	2424	0	PCF11	11	82879771	Frame_Shift_Del	DEL	G	TCGA-CC-5259-01A-31D-A20W-10	6128186	82879771	52126745	97	7005										
NCAM1	4684	hgsc.bcm.edu	37	chr11	113078628	113078628	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	acgatagttcccagctgaccAtcaaaaaggtggataagaac	9	9	1	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr11:113078628A>G	ENST00000533760.1	+	7	1065	c.466A>G	c.(466-468)Atc>Gtc	p.I156V	NCAM1_ENST00000316851.7_Missense_Mutation_p.I264V|NCAM1_ENST00000401611.2_Missense_Mutation_p.I273V|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	274	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CCAGCTGACCATCAAAAAGGT	0.488																																					p.I274V		Atlas-SNP	.											.	NCAM1	372	.	0			c.A820G						.						71	71	71					11																	113078628		2037	4204	6241	SO:0001583	missense	4684	exon8			CTGACCATCAAAA		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.466A>G	chr11.hg19:g.113078628A>G	ENSP00000473281:p.Ile156Val	75.0	0.0		95.0	37.0	NM_001242608	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.363	1.068409	0.20067	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.77750	-1.12;-1.12	5.71	4.57	0.56435	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.085585	0.85682	D	0.000000	T	0.70002	0.3174	.	.	.	0.80722	D	1	B;B;B;B;B	0.27286	0.136;0.122;0.087;0.133;0.174	B;B;B;B;B	0.34385	0.102;0.058;0.096;0.132;0.181	T	0.62358	-0.6871	9	0.22109	T	0.4	-10.0213	12.1467	0.54028	0.8716:0.0:0.0:0.1284	.	274;274;274;274;274	P13591-5;P13591-1;P13591;P13591-3;P13591-6	.;.;NCAM1_HUMAN;.;.	V	156;273;264	ENSP00000384055:I273V;ENSP00000318472:I264V	ENSP00000318472:I264V	I	+	1	0	NCAM1	112583838	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.979000	0.76154	0.970000	0.38263	0.533000	0.62120	ATC	.	.		0.488	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		G	113078628	A	G	113078628	3	3	55	1	0	0	0	0	1	0	0	0	10211	217	8	2	847	2	NCAM1	11	113078628	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	30198857	113078628	21927888	98	7006										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117301488	117301488	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ccacgtttttgccccggtccGcatcctggggcttgggtggt	14	13	0	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr11:117301488G>A	ENST00000321322.6	-	32	5817	c.5816C>T	c.(5815-5817)gCg>gTg	p.A1939V	DSCAML1_ENST00000527706.1_Missense_Mutation_p.A1669V	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1879					axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GCCCCGGTCCGCATCCTGGGG	0.657																																					p.A1939V		Atlas-SNP	.											.	DSCAML1	286	.	0			c.C5816T						.						179	154	163					11																	117301488		2201	4296	6497	SO:0001583	missense	57453	exon32			CGGTCCGCATCCT		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.5816C>T	chr11.hg19:g.117301488G>A	ENSP00000315465:p.Ala1939Val	140.0	0.0		152.0	9.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	G	13.76	2.333384	0.41297	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.60299	0.23;0.2	5.04	4.09	0.47781	.	.	.	.	.	T	0.37348	0.1000	N	0.08118	0	0.31442	N	0.671895	B	0.09022	0.002	B	0.10450	0.005	T	0.32693	-0.9897	9	0.35671	T	0.21	.	12.3343	0.55058	0.0:0.3658:0.6342:0.0	.	1879	Q8TD84	DSCL1_HUMAN	V	1669;1939;1646	ENSP00000434335:A1669V;ENSP00000315465:A1939V	ENSP00000315465:A1939V	A	-	2	0	DSCAML1	116806698	0.998000	0.40836	0.955000	0.39395	0.979000	0.70002	2.957000	0.49137	2.628000	0.89032	0.591000	0.81541	GCG	.	.		0.657	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		A	117301488	G	A	117301488	3	1	55	1	0	0	0	0	1	0	0	0	4771	1087	38	1	533	1	DSCAML1	11	117301488	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	4222860	117301488	17705028	99	7007										
STAT6	6778	hgsc.bcm.edu	37	chr12	57493655	57493655	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	attgagaagaaggctagtaaCgtactgtttgctgatgaagc	12	5	0	4			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr12:57493655C>T	ENST00000300134.3	-	15	1964	c.1639G>A	c.(1639-1641)Gtt>Att	p.V547I	STAT6_ENST00000543873.2_Missense_Mutation_p.V547I|STAT6_ENST00000454075.3_Missense_Mutation_p.V547I|STAT6_ENST00000537215.2_Missense_Mutation_p.V437I|STAT6_ENST00000556155.1_Missense_Mutation_p.V547I|STAT6_ENST00000538913.2_Missense_Mutation_p.V437I	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	547	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						AGGCTAGTAACGTACTGTTTG	0.557																																					p.V547I		Atlas-SNP	.											.	STAT6	69	.	0			c.G1639A						.						100	92	95					12																	57493655		2203	4300	6503	SO:0001583	missense	6778	exon15			TAGTAACGTACTG	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"SH2 domain containing"	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.1639G>A	chr12.hg19:g.57493655C>T	ENSP00000300134:p.Val547Ile	185.0	0.0		169.0	43.0	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	hg19	CCDS8931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.61|18.61	3.660387|3.660387	0.67586|0.67586	.|.	.|.	ENSG00000166888|ENSG00000166888	ENST00000553533|ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516;ENST00000555375	.|D;D;D;D;D;D;D	.|0.89196	.|-2.48;-2.48;-2.48;-2.48;-2.48;-2.48;-2.48	4.92|4.92	4.92|4.92	0.64577|0.64577	.|SH2 motif (4);	.|0.144343	.|0.46758	.|D	.|0.000268	D|D	0.88500|0.88500	0.6453|0.6453	L|L	0.27053|0.27053	0.805|0.805	0.42281|0.42281	D|D	0.992096|0.992096	.|D;P	.|0.58268	.|0.982;0.916	.|P;B	.|0.55785	.|0.784;0.387	D|D	0.90164|0.90164	0.4230|0.4230	5|10	.|0.72032	.|D	.|0.01	-23.5551|-23.5551	15.645|15.645	0.77042|0.77042	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|547;547	.|A8K4S9;P42226	.|.;STAT6_HUMAN	H|I	265|547;437;437;547;547;437;547;437;547;113	.|ENSP00000300134:V547I;ENSP00000445409:V437I;ENSP00000438451:V547I;ENSP00000451742:V547I;ENSP00000444530:V437I;ENSP00000401486:V547I;ENSP00000450921:V113I	.|ENSP00000300134:V547I	R|V	-|-	2|1	0|0	STAT6|STAT6	55779922|55779922	0.319000|0.319000	0.24607|0.24607	0.996000|0.996000	0.52242|0.52242	0.499000|0.499000	0.33736|0.33736	2.478000|2.478000	0.45189|0.45189	2.550000|2.550000	0.86006|0.86006	0.655000|0.655000	0.94253|0.94253	CGT|GTT	.	.		0.557	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		T	57493655	C	T	57493655	3	4	55	1	0	0	0	0	1	0	0	0	15285	536	19	1	936	1	STAT6	12	57493655	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10		57493655	76358240	100	7008										
GEFT	115557	hgsc.bcm.edu	37	chr12	58008160	58008160	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gtctgaaagatcctgattggCtggctcagctattcatcaaa	9	9	4	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr12:58008160C>T	ENST00000286494.4	+	7	1163	c.703C>T	c.(703-705)Ctg>Ttg	p.L235L	AC025165.8_ENST00000356672.3_RNA|AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000610219.1_RNA|ARHGEF25_ENST00000333972.7_Silent_p.L274L|AC025165.8_ENST00000593846.1_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	235	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						TCCTGATTGGCTGGCTCAGCT	0.547																																					p.L274L		Atlas-SNP	.											.	ARHGEF25	111	.	0			c.C820T						.						74	80	78					12																	58008160		2203	4300	6503	SO:0001819	synonymous_variant	115557	exon8			GATTGGCTGGCTC		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"Rho guanine nucleotide exchange factors"	30275	protein-coding gene	gene with protein product	"RAC/CDC42 exchange factor"	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.703C>T	chr12.hg19:g.58008160C>T		149.0	0.0		152.0	12.0	NM_001111270	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Silent	SNP	ENST00000286494.4	hg19	CCDS8947.1																																																																																			.	.		0.547	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483		T	58008160	C	T	58008160	2	4	55	1	0	0	0	0	0	0	0	1	6336	796	28	3		3	GEFT	12	58008160	Silent	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	514505	58008160	75843735	101	7009										
HELB	92797	hgsc.bcm.edu	37	chr12	66703544	66703544	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aagttggatagcattttgtcAgtgtgagtctcttctccagc	10	8	3	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr12:66703544A>T	ENST00000247815.4	+	4	895	c.836A>T	c.(835-837)cAg>cTg	p.Q279L		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	279					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		GCATTTTGTCAGTGTGAGTCT	0.383																																					p.Q279L		Atlas-SNP	.											.	HELB	90	.	0			c.A836T						.						166	164	164					12																	66703544		2203	4300	6503	SO:0001583	missense	92797	exon4			TTTGTCAGTGTGA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.836A>T	chr12.hg19:g.66703544A>T	ENSP00000247815:p.Gln279Leu	147.0	0.0		156.0	101.0	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	hg19	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	A	13.33	2.204879	0.38905	.	.	ENSG00000127311	ENST00000247815	T	0.13657	2.57	6.17	6.17	0.99709	.	0.063541	0.64402	D	0.000004	T	0.17789	0.0427	L	0.57536	1.79	0.35484	D	0.79843	P	0.42692	0.787	B	0.39217	0.294	T	0.14615	-1.0466	9	.	.	.	-15.0315	16.8222	0.85835	1.0:0.0:0.0:0.0	.	279	Q8NG08	HELB_HUMAN	L	279	ENSP00000247815:Q279L	.	Q	+	2	0	HELB	64989811	1.000000	0.71417	0.985000	0.45067	0.021000	0.10359	4.177000	0.58276	2.371000	0.80710	0.533000	0.62120	CAG	.	.		0.383	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1			T	66703544	A	T	66703544	3	4	55	1	0	0	0	0	1	0	0	0	7054	188	7	4	850	4	HELB	12	66703544	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	8695384	66703544	67148351	102	7010										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80730730	80730730	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tctggactttgttttaagaaGttaaatgtgacaacacccat	7	7	1	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr12:80730730G>C	ENST00000547103.1	+	41	4749	c.4743G>C	c.(4741-4743)aaG>aaC	p.K1581N	OTOGL_ENST00000458043.2_Missense_Mutation_p.K1593N			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1581	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						GTTTTAAGAAGTTAAATGTGA	0.294																																					p.K1593N		Atlas-SNP	.											.	OTOGL	235	.	0			c.G4779C						.						32	29	30					12																	80730730		1785	4042	5827	SO:0001583	missense	283310	exon41			TAAGAAGTTAAAT	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.4743G>C	chr12.hg19:g.80730730G>C	ENSP00000447211:p.Lys1581Asn	81.0	0.0		116.0	61.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.413|8.413	0.844612|0.844612	0.16963|0.16963	.|.	.|.	ENSG00000165899|ENSG00000165899	ENST00000547103;ENST00000458043|ENST00000298820	T;T|.	0.60171|.	0.21;0.21|.	4.92|4.92	3.05|3.05	0.35203|0.35203	.|.	.|.	.|.	.|.	.|.	T|T	0.52224|0.52224	0.1721|0.1721	M|M	0.65975|0.65975	2.015|2.015	0.27367|0.27367	N|N	0.955805|0.955805	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.44772|0.44772	-0.9306|-0.9306	7|5	0.17832|.	T|.	0.49|.	.|.	8.6387|8.6387	0.33964|0.33964	0.2833:0.0:0.7167:0.0|0.2833:0.0:0.7167:0.0	.|.	.|.	.|.	.|.	N|T	1581;1593|36	ENSP00000447211:K1581N;ENSP00000400895:K1593N|.	ENSP00000400895:K1593N|.	K|S	+|+	3|2	2|0	OTOGL|OTOGL	79254861|79254861	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.742000|0.742000	0.42306|0.42306	1.783000|1.783000	0.38664|0.38664	1.187000|1.187000	0.43000|0.43000	-0.218000|-0.218000	0.12543|0.12543	AAG|AGT	.	.		0.294	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		C	80730730	G	C	80730730	3	2	55	1	0	0	0	0	1	0	0	0	1709	1020	36	4	4941	4	C12orf64	12	80730730	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	14027186	80730730	53121165	103	7011										
ANO4	121601	hgsc.bcm.edu	37	chr12	101381353	101381353	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agcaggtttcggagatggttAcctaagaagccaatgaggct	13	7	0	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr12:101381353A>T	ENST00000392977.3	+	8	849	c.639A>T	c.(637-639)ttA>ttT	p.L213F	ANO4_ENST00000538618.1_3'UTR|ANO4_ENST00000299222.9_5'UTR|ANO4_ENST00000392979.3_Missense_Mutation_p.L178F			Q32M45	ANO4_HUMAN	anoctamin 4	213					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						GGAGATGGTTACCTAAGAAGC	0.502										HNSCC(74;0.22)	OREG0022059	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L178F		Atlas-SNP	.											.	ANO4	183	.	0			c.A534T						.						262	251	255					12																	101381353		2203	4300	6503	SO:0001583	missense	121601	exon7			ATGGTTACCTAAG	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.639A>T	chr12.hg19:g.101381353A>T	ENSP00000376703:p.Leu213Phe	87.0	0.0	1358	86.0	47.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	hg19		.	.	.	.	.	.	.	.	.	.	A	17.37	3.371406	0.61624	.	.	ENSG00000151572	ENST00000392979;ENST00000392977	T;T	0.70986	-0.52;-0.53	5.33	5.33	0.75918	.	0.000000	0.56097	D	0.000028	T	0.71550	0.3353	L	0.34521	1.04	0.80722	D	1	P;P	0.50443	0.893;0.935	P;P	0.57324	0.482;0.818	T	0.72121	-0.4386	10	0.45353	T	0.12	.	11.2781	0.49178	0.9269:0.0:0.0731:0.0	.	213;178	Q32M45;Q32M45-2	ANO4_HUMAN;.	F	178;213	ENSP00000376705:L178F;ENSP00000376703:L213F	ENSP00000376703:L213F	L	+	3	2	ANO4	99905484	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.443000	0.35057	2.020000	0.59435	0.533000	0.62120	TTA	.	.		0.502	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		T	101381353	A	T	101381353	3	4	55	1	0	0	0	0	1	0	0	0	699	388	14	4	556	4	ANO4	12	101381353	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	20650623	101381353	32470542	104	7012										
STAB2	55576	hgsc.bcm.edu	37	chr12	104149204	104149204	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ggactatggacctagacccaAcaagagtgaaatgtgggatg	13	7	0	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr12:104149204A>G	ENST00000388887.2	+	62	7043	c.6839A>G	c.(6838-6840)aAc>aGc	p.N2280S	RP11-341G23.4_ENST00000551299.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CCTAGACCCAACAAGAGTGAA	0.577																																					p.N2280S		Atlas-SNP	.											.	STAB2	370	.	0			c.A6839G						.						149	127	135					12																	104149204		2203	4300	6503	SO:0001583	missense	55576	exon62			GACCCAACAAGAG	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.6839A>G	chr12.hg19:g.104149204A>G	ENSP00000373539:p.Asn2280Ser	149.0	0.0		156.0	86.0	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.351579	0.61183	.	.	ENSG00000136011	ENST00000388887;ENST00000258495	T	0.31510	1.49	5.26	5.26	0.73747	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.112845	0.64402	D	0.000020	T	0.34221	0.0890	M	0.65975	2.015	0.44523	D	0.997477	B	0.33494	0.414	B	0.30716	0.119	T	0.23084	-1.0198	10	0.59425	D	0.04	.	15.2305	0.73383	1.0:0.0:0.0:0.0	.	2280	Q8WWQ8	STAB2_HUMAN	S	2280;967	ENSP00000373539:N2280S	ENSP00000258495:N967S	N	+	2	0	STAB2	102673334	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.606000	0.90888	1.989000	0.58080	0.529000	0.55759	AAC	.	.		0.577	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			G	104149204	A	G	104149204	3	3	55	1	0	0	0	0	1	0	0	0	15253	43	2	2	7085	2	STAB2	12	104149204	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	2767851	104149204	29702691	105	7013										
HPD	3242	hgsc.bcm.edu	37	chr12	122287654	122287654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tccaggcaagaattggccgaTgtagttcatcttctccacca	8	12	3	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr12:122287654T>C	ENST00000289004.4	-	8	492	c.457A>G	c.(457-459)Atc>Gtc	p.I153V	HPD_ENST00000543869.2_5'UTR|HPD_ENST00000543163.1_Missense_Mutation_p.I114V	NM_002150.2	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase	153					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|urinary_tract(1)	18	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	AATTGGCCGATGTAGTTCATC	0.597																																					p.I153V		Atlas-SNP	.											.	HPD	46	.	0			c.A457G						.						143	115	125					12																	122287654		2203	4300	6503	SO:0001583	missense	3242	exon8			GGCCGATGTAGTT	BC014790	CCDS9224.1, CCDS53839.1	12q24.31	2013-09-19			ENSG00000158104	ENSG00000158104	1.13.11.27		5147	protein-coding gene	gene with protein product	"glyoxalase domain containing 3"	609695		PPD			Standard	NM_001171993		Approved	4-HPPD, 4HPPD, GLOD3	uc001ubj.3	P32754	OTTHUMG00000169081	ENST00000289004.4:c.457A>G	chr12.hg19:g.122287654T>C	ENSP00000289004:p.Ile153Val	140.0	0.0		165.0	36.0	NM_002150	A8K461|B3KQ63|Q13234	Missense_Mutation	SNP	ENST00000289004.4	hg19	CCDS9224.1	.	.	.	.	.	.	.	.	.	.	T	9.290	1.050298	0.19827	.	.	ENSG00000158104	ENST00000289004;ENST00000545969;ENST00000543163	T;T	0.61859	0.07;0.07	5.41	3.06	0.35304	.	0.408106	0.28493	N	0.015146	T	0.35189	0.0923	N	0.08118	0	0.09310	N	0.999992	B	0.02656	0.0	B	0.01281	0.0	T	0.27571	-1.0070	10	0.59425	D	0.04	-18.68	9.8108	0.40822	0.0:0.1404:0.0:0.8596	.	153	P32754	HPPD_HUMAN	V	153;150;114	ENSP00000289004:I153V;ENSP00000441677:I114V	ENSP00000289004:I153V	I	-	1	0	HPD	120772037	0.992000	0.36948	0.304000	0.25085	0.059000	0.15707	2.117000	0.41939	0.360000	0.24265	-0.274000	0.10170	ATC	.	.		0.597	HPD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402184.1	NM_002150		C	122287654	T	C	122287654	3	2	55	1	0	0	0	0	1	0	0	0	7341	1464	51	2	752	2	HPD	12	122287654	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	18138450	122287654	11564241	106	7014										
PCDH9	5101	hgsc.bcm.edu	37	chr13	67801363	67801363	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	atgaaatgggacctctctttCaataaaacagatcactttgc	6	9	3	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr13:67801363C>A	ENST00000377865.2	-	1	1344	c.1210G>T	c.(1210-1212)Gaa>Taa	p.E404*	PCDH9_ENST00000544246.1_Nonsense_Mutation_p.E404*|PCDH9_ENST00000328454.5_Nonsense_Mutation_p.E404*|PCDH9_ENST00000456367.1_Nonsense_Mutation_p.E404*|PCDH9_ENST00000377861.3_Nonsense_Mutation_p.E404*			Q9HC56	PCDH9_HUMAN	protocadherin 9	404	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		ACCTCTCTTTCAATAAAACAG	0.378																																					p.E404X		Atlas-SNP	.											.	PCDH9	252	.	0			c.G1210T						.						91	88	89					13																	67801363		2203	4300	6503	SO:0001587	stop_gained	5101	exon2			CTCTTTCAATAAA	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1210G>T	chr13.hg19:g.67801363C>A	ENSP00000367096:p.Glu404*	108.0	0.0		71.0	62.0	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Nonsense_Mutation	SNP	ENST00000377865.2	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831922	0.91036	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	404	.	ENSP00000332060:E404X	E	-	1	0	PCDH9	66699364	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.920000	0.70017	2.941000	0.99782	0.655000	0.94253	GAA	.	.		0.378	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		A	67801363	C	A	67801363	4	1	55	1	0	0	0	0	0	1	0	0	11527	835	29	3	2519	3	PCDH9	13	67801363	Nonsense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10		67801363	47368515	107	7015										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94079314	94079314	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aaaggccttcaacacggtcaAgcgacacctgtacgtcttac	8	13	3	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr14:94079314A>T	ENST00000393151.2	+	27	3926	c.3926A>T	c.(3925-3927)aAg>aTg	p.K1309M	UNC79_ENST00000555664.1_Missense_Mutation_p.K1309M|UNC79_ENST00000256339.4_Missense_Mutation_p.K1132M|UNC79_ENST00000553484.1_Missense_Mutation_p.K1331M			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1309					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AACACGGTCAAGCGACACCTG	0.478																																					p.K1132M		Atlas-SNP	.											.	UNC79	366	.	0			c.A3395T						.						140	116	124					14																	94079314		2203	4300	6503	SO:0001583	missense	57578	exon27			CGGTCAAGCGACA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.3926A>T	chr14.hg19:g.94079314A>T	ENSP00000376858:p.Lys1309Met	136.0	0.0		104.0	84.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	A	22.9	4.350711	0.82132	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.19250	2.16;2.16;2.17;2.16	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.32645	0.0836	N	0.22421	0.69	0.50171	D	0.999859	D	0.89917	1.0	D	0.85130	0.997	T	0.06499	-1.0823	10	0.34782	T	0.22	-23.6572	15.7162	0.77670	1.0:0.0:0.0:0.0	.	1331	C9JQL1	.	M	1132;1309;1331;1309;1331	ENSP00000256339:K1132M;ENSP00000450868:K1309M;ENSP00000451360:K1331M;ENSP00000376858:K1309M	ENSP00000256339:K1132M	K	+	2	0	KIAA1409	93149067	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.115000	0.64714	0.528000	0.53228	AAG	.	.		0.478	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94079314	A	T	94079314	3	4	55	1	0	0	0	0	1	0	0	0	8239	72	3	4	3489	4	KIAA1409	14	94079314	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10		94079314	13270226	108	7016										
DUOX1	53905	hgsc.bcm.edu	37	chr15	45427708	45427708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gctggctggacggcagcgccAtctatggttcctcgcattcc	12	14	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr15:45427708A>G	ENST00000321429.4	+	7	939	c.532A>G	c.(532-534)Atc>Gtc	p.I178V	DUOX1_ENST00000389037.3_Missense_Mutation_p.I178V	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	178	Peroxidase-like; mediates peroxidase activity.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CGGCAGCGCCATCTATGGTTC	0.721																																					p.I178V		Atlas-SNP	.											.	DUOX1	125	.	0			c.A532G						.						7	6	6					15																	45427708		2080	4145	6225	SO:0001583	missense	53905	exon7			AGCGCCATCTATG	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.532A>G	chr15.hg19:g.45427708A>G	ENSP00000317997:p.Ile178Val	126.0	0.0		44.0	22.0	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	hg19	CCDS32221.1	.	.	.	.	.	.	.	.	.	.	.	18.04	3.534987	0.64972	.	.	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	T;T	0.66460	-0.21;-0.21	3.8	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.71476	0.3344	L	0.43923	1.385	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	T	0.66504	-0.5907	10	0.19147	T	0.46	-29.7211	10.8148	0.46569	1.0:0.0:0.0:0.0	.	178	Q9NRD9	DUOX1_HUMAN	V	178	ENSP00000317997:I178V;ENSP00000373689:I178V	ENSP00000317997:I178V	I	+	1	0	DUOX1	43215000	1.000000	0.71417	1.000000	0.80357	0.345000	0.29048	6.982000	0.76173	1.708000	0.51301	0.455000	0.32223	ATC	.	.		0.721	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		G	45427708	A	G	45427708	3	3	55	1	0	0	0	0	1	0	0	0	4802	217	8	2	550	2	DUOX1	15	45427708	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10		45427708	57103684	109	7017										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51828802	51828802	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gacttatcagcaaaagtgacTgcccactgatttaaagaacc	7	10	1	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr15:51828802T>A	ENST00000251076.5	-	12	2162	c.1875A>T	c.(1873-1875)gcA>gcT	p.A625A	DMXL2_ENST00000543779.2_Silent_p.A625A|DMXL2_ENST00000449909.3_Silent_p.A625A	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	625						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		CAAAAGTGACTGCCCACTGAT	0.413																																					p.A625A		Atlas-SNP	.											.	DMXL2	262	.	0			c.A1875T						.						124	115	118					15																	51828802		2195	4293	6488	SO:0001819	synonymous_variant	23312	exon12			AGTGACTGCCCAC	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.1875A>T	chr15.hg19:g.51828802T>A		165.0	1.0		94.0	69.0	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	hg19	CCDS10141.1																																																																																			.	.		0.413	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		A	51828802	T	A	51828802	2	1	55	1	0	0	0	0	0	0	0	1	4597	1567	55	4		4	DMXL2	15	51828802	Silent	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	6401094	51828802	50702590	110	7018										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52622690	52622690	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ctggggatatgttctccatcTggcccactttatgagaagta	10	9	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr15:52622690T>A	ENST00000399231.3	-	34	4583	c.4340A>T	c.(4339-4341)cAg>cTg	p.Q1447L	MYO5A_ENST00000399233.2_Missense_Mutation_p.Q1444L|MYO5A_ENST00000358212.6_Missense_Mutation_p.Q1472L|MYO5A_ENST00000553916.1_Missense_Mutation_p.Q1445L|MYO5A_ENST00000356338.6_Missense_Mutation_p.Q1420L	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1447					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GTTCTCCATCTGGCCCACTTT	0.403																																					p.Q1447L		Atlas-SNP	.											.	MYO5A	145	.	0			c.A4340T						.						129	116	120					15																	52622690		1840	4075	5915	SO:0001583	missense	4644	exon34			TCCATCTGGCCCA		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.4340A>T	chr15.hg19:g.52622690T>A	ENSP00000382177:p.Gln1447Leu	192.0	0.0		154.0	101.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	hg19	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	T	19.16	3.773455	0.69992	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05	5.45	5.45	0.79879	.	0.842110	0.10855	N	0.626743	T	0.15132	0.0365	L	0.27053	0.805	0.80722	D	1	B;B;P	0.43352	0.006;0.005;0.804	B;B;B	0.33392	0.013;0.003;0.163	T	0.16630	-1.0396	10	0.24483	T	0.36	.	15.5017	0.75703	0.0:0.0:0.0:1.0	.	177;1447;1420	B5LY56;Q9Y4I1;Q9Y4I1-2	.;MYO5A_HUMAN;.	L	1447;954;1444;1420;1472;1050;1445	ENSP00000382177:Q1447L;ENSP00000382179:Q1444L;ENSP00000348693:Q1420L;ENSP00000350945:Q1472L;ENSP00000451109:Q1445L	ENSP00000348693:Q1420L	Q	-	2	0	MYO5A	50409982	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.841000	0.48223	2.068000	0.61886	0.455000	0.32223	CAG	.	.		0.403	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		A	52622690	T	A	52622690	3	1	55	1	0	0	0	0	1	0	0	0	10087	1580	55	4	1259	4	MYO5A	15	52622690	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	793888	52622690	49908702	111	7019										
TRAF7	84231	hgsc.bcm.edu	37	chr16	2225896	2225896	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gacgtctggtggcagcgtctActccattgctgtgacaaatc	11	11	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr16:2225896A>T	ENST00000326181.6	+	18	1820	c.1688A>T	c.(1687-1689)tAc>tTc	p.Y563F		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	563					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						GGCAGCGTCTACTCCATTGCT	0.577																																					p.Y563F		Atlas-SNP	.											TRAF7,NS,meningioma,0,1	TRAF7	158	.	0			c.A1688T						.						150	114	126					16																	2225896		2197	4300	6497	SO:0001583	missense	84231	exon18			GCGTCTACTCCAT	AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"RING-type (C3HC4) zinc fingers", "WD repeat domain containing"	20456	protein-coding gene	gene with protein product		606692	"ring finger and WD repeat domain 1", "TNF receptor-associated factor 7"	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.1688A>T	chr16.hg19:g.2225896A>T	ENSP00000318944:p.Tyr563Phe	195.0	1.0		217.0	87.0	NM_032271	Q9H073	Missense_Mutation	SNP	ENST00000326181.6	hg19	CCDS10461.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.665593	0.88251	.	.	ENSG00000131653	ENST00000326181	T	0.18502	2.21	5.01	3.91	0.45181	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.34454	0.0898	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.02774	-1.1112	10	0.40728	T	0.16	-47.6465	9.6466	0.39872	0.9169:0.0:0.0831:0.0	.	563	Q6Q0C0	TRAF7_HUMAN	F	563	ENSP00000318944:Y563F	ENSP00000318944:Y563F	Y	+	2	0	TRAF7	2165897	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.770000	0.68873	2.026000	0.59711	0.459000	0.35465	TAC	.	.		0.577	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271		T	2225896	A	T	2225896	3	4	55	1	0	0	0	0	1	0	0	0	16461	391	14	4	1754	4	TRAF7	16	2225896	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10		2225896	88128857	112	7020										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21061288	21061288	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tctgtcttgccagtcccagcTggaccctctggagcaccccc	9	18	3	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr16:21061288T>A	ENST00000261383.3	-	30	4289	c.4290A>T	c.(4288-4290)ccA>ccT	p.P1430P	DNAH3_ENST00000415178.1_Silent_p.P1430P	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1430	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CAGTCCCAGCTGGACCCTCTG	0.522																																					p.P1430P		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A4290T						.						179	162	168					16																	21061288		2201	4300	6501	SO:0001819	synonymous_variant	55567	exon30			CCCAGCTGGACCC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.4290A>T	chr16.hg19:g.21061288T>A		65.0	0.0		62.0	25.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	hg19	CCDS10594.1																																																																																			.	.		0.522	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21061288	T	A	21061288	2	1	55	1	0	0	0	0	0	0	0	1	4605	1567	55	4		4	DNAH3	16	21061288	Silent	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	18835392	21061288	69293465	113	7021										
RAP1GAP2	23108	hgsc.bcm.edu	37	chr17	2929754	2929754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ggccatggaggagggcgacaGtggggtaggtgtgccccgtc	20	9	0	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr17:2929754G>A	ENST00000254695.8	+	21	2066	c.1976G>A	c.(1975-1977)aGt>aAt	p.S659N	RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.S644N|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.S659N|RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.S640N	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	659	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						GAGGGCGACAGTGGGGTAGGT	0.642																																					p.S659N		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.G1976A						.						17	21	20					17																	2929754		2035	4084	6119	SO:0001583	missense	23108	exon21			GCGACAGTGGGGT	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 4", "GTPase activating Rap/RanGAP domain-like 4"	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1976G>A	chr17.hg19:g.2929754G>A	ENSP00000254695:p.Ser659Asn	144.0	0.0		119.0	98.0	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	hg19	CCDS45573.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.856625	0.51376	.	.	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.89050	-2.46;-2.46;-2.46;-2.46	5.42	3.18	0.36537	.	0.191310	0.56097	D	0.000031	D	0.85678	0.5752	L	0.41236	1.265	0.28868	N	0.895103	B;B	0.30973	0.302;0.201	B;B	0.35971	0.215;0.107	T	0.81927	-0.0709	10	0.54805	T	0.06	-20.0906	15.1305	0.72520	0.0:0.0:0.7457:0.2542	.	644;659	Q684P5-2;Q684P5	.;RPGP2_HUMAN	N	659;644;640;659	ENSP00000254695:S659N;ENSP00000389824:S644N;ENSP00000439688:S640N;ENSP00000444890:S659N	ENSP00000254695:S659N	S	+	2	0	RAP1GAP2	2876504	1.000000	0.71417	0.914000	0.36105	0.923000	0.55619	3.901000	0.56303	1.277000	0.44412	0.462000	0.41574	AGT	.	.		0.642	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2			A	2929754	G	A	2929754	3	1	55	1	0	0	0	0	1	0	0	0	13053	1029	36	3	2058	3	RAP1GAP2	17	2929754	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10		2929754	78265456	114	7022										
TP53	7157	hgsc.bcm.edu	37	chr17	7579312	7579312	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agcccctcagggcaactgacCgtgcaagtcacagacttggc	11	14	2	2	rs55863639		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr17:7579312C>A	ENST00000269305.4	-	4	564	c.375G>T	c.(373-375)acG>acT	p.T125T	TP53_ENST00000455263.2_Splice_Site_p.T125T|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Splice_Site_p.T125T|TP53_ENST00000413465.2_Splice_Site_p.T125T|TP53_ENST00000445888.2_Splice_Site_p.T125T|TP53_ENST00000359597.4_Splice_Site_p.T125T	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	125	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		T -> A (in a sporadic cancer; somatic mutation).|T -> K (in sporadic cancers; somatic mutation).|T -> M (in sporadic cancers; somatic mutation).|T -> P (in a sporadic cancer; somatic mutation).|T -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.T125T(51)|p.0?(8)|p.?(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCAACTGACCGTGCAAGTCA	0.537		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.T125T	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_upper_lobe,carcinoma,0,1	TP53	33396	.	66	Substitution - coding silent(51)|Whole gene deletion(8)|Deletion - Frameshift(3)|Unknown(2)|Deletion - In frame(1)|Insertion - In frame(1)	lung(21)|haematopoietic_and_lymphoid_tissue(14)|large_intestine(8)|upper_aerodigestive_tract(7)|bone(4)|central_nervous_system(3)|biliary_tract(3)|stomach(1)|liver(1)|urinary_tract(1)|kidney(1)|ovary(1)|pancreas(1)	c.G375T	GRCh37	CS004351|CS011573|CS971913	TP53	S	rs55863639	.						66	61	63					17																	7579312		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ACTGACCGTGCAA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.375+1G>T	chr17.hg19:g.7579312C>A		157.0	0.0		159.0	124.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.537	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Silent	A	7579312	C	A	7579312	5	1	55	1	0	0	0	0	0	0	1	0	16396	666	23	1	927	1	TP53	17	7579312	Splice_Site	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	4649558	7579312	73615898	115	7023										
KRTAP4-2	85291	hgsc.bcm.edu	37	chr17	39334191	39334191	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cacacagcagctgggacggcAgcaggtggtcctgcagcaag	15	12	0	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr17:39334191A>T	ENST00000377726.2	-	1	269	c.226T>A	c.(226-228)Tgc>Agc	p.C76S		NM_033062.3	NP_149051	Q9BYR5	KRA42_HUMAN	keratin associated protein 4-2	76	20 X 5 AA repeats OF C-C-[GRQVS]-[SPT]- [VSTQ].					keratin filament (GO:0045095)				kidney(2)|lung(4)|upper_aerodigestive_tract(1)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			CTGGGACGGCAGCAGGTGGTC	0.667																																					p.C76S		Atlas-SNP	.											.	KRTAP4-2	93	.	0			c.T226A						.						43	49	47					17																	39334191		2203	4298	6501	SO:0001583	missense	85291	exon1			GACGGCAGCAGGT	AJ406934	CCDS11384.1	17q21.2	2013-06-25			ENSG00000244537	ENSG00000244537		"Keratin associated proteins"	18900	protein-coding gene	gene with protein product						11279113	Standard	NM_033062		Approved	KAP4.2	uc002hwd.3	Q9BYR5	OTTHUMG00000133437	ENST00000377726.2:c.226T>A	chr17.hg19:g.39334191A>T	ENSP00000366955:p.Cys76Ser	74.0	0.0		85.0	66.0	NM_033062	A0JP64	Missense_Mutation	SNP	ENST00000377726.2	hg19	CCDS11384.1	.	.	.	.	.	.	.	.	.	.	.	12.70	2.016391	0.35606	.	.	ENSG00000244537	ENST00000377726;ENST00000458321	T	0.02890	4.12	4.82	2.54	0.30619	.	0.000000	0.48286	U	0.000195	T	0.10465	0.0256	M	0.89478	3.035	0.31244	N	0.694795	D	0.63880	0.993	P	0.57620	0.824	T	0.07424	-1.0773	10	0.54805	T	0.06	.	3.2153	0.06696	0.6362:0.0:0.1903:0.1735	.	76	Q9BYR5	KRA42_HUMAN	S	76;193	ENSP00000366955:C76S	ENSP00000366955:C76S	C	-	1	0	KRTAP4-2	36587717	1.000000	0.71417	0.909000	0.35828	0.019000	0.09904	5.626000	0.67777	0.184000	0.20083	0.421000	0.28195	TGC	.	.		0.667	KRTAP4-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257305.1			T	39334191	A	T	39334191	3	4	55	1	0	0	0	0	1	0	0	0	8560	188	7	4	188	4	KRTAP4-2	17	39334191	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	31754879	39334191	41861019	116	7024										
KRT34	3885	hgsc.bcm.edu	37	chr17	39535916	39535916	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tcaggacctggttcaggtccAcagtgggggcagtgtccacc	14	12	2	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr17:39535916A>G	ENST00000394001.1	-	4	812	c.782T>C	c.(781-783)gTg>gCg	p.V261A		NM_021013.3	NP_066293.2	O76011	KRT34_HUMAN	keratin 34	261	Linker 12.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Breast(137;0.000496)				GTTCAGGTCCACAGTGGGGGC	0.577																																					p.V261A		Atlas-SNP	.											.	KRT34	71	.	0			c.T782C						.						98	77	84					17																	39535916		2203	4300	6503	SO:0001583	missense	3885	exon4			AGGTCCACAGTGG	Y16790	CCDS11390.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131737	ENSG00000131737		"-", "Intermediate filaments type I, keratins (acidic)"	6452	protein-coding gene	gene with protein product	"hard keratin type I 4"	602763	"keratin, hair, acidic, 4"	KRTHA4		2431943, 9756910, 16831889	Standard	NM_021013		Approved	Ha-4	uc002hwm.3	O76011	OTTHUMG00000133436	ENST00000394001.1:c.782T>C	chr17.hg19:g.39535916A>G	ENSP00000377570:p.Val261Ala	188.0	0.0		126.0	89.0	NM_021013	Q8IUT8|Q8N4W2	Missense_Mutation	SNP	ENST00000394001.1	hg19	CCDS11390.1	.	.	.	.	.	.	.	.	.	.	a	10.74	1.434655	0.25813	.	.	ENSG00000131737	ENST00000394001;ENST00000251648	.	.	.	4.6	4.6	0.57074	Filament (1);	0.000000	0.56097	D	0.000031	T	0.53077	0.1774	M	0.85197	2.74	0.28351	N	0.92092	B	0.33826	0.427	B	0.40940	0.344	T	0.60989	-0.7153	9	0.87932	D	0	.	4.3741	0.11262	0.7165:0.0:0.0955:0.188	.	261	O76011	KRT34_HUMAN	A	219;261	.	ENSP00000251648:V261A	V	-	2	0	KRT34	36789442	0.015000	0.18098	0.974000	0.42286	0.072000	0.16883	2.166000	0.42406	1.830000	0.53286	0.491000	0.48974	GTG	.	.		0.577	KRT34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257304.3	NM_021013		G	39535916	A	G	39535916	3	3	55	1	0	0	0	0	1	0	0	0	8480	159	6	2	544	2	KRT34	17	39535916	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	201725	39535916	41659294	117	7025										
CYB561	1534	hgsc.bcm.edu	37	chr17	61513455	61513455	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gcaaagatgtgcagcagcccGtgcaggaccttggtggtgcg	16	10	0	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr17:61513455G>T	ENST00000392976.1	-	3	560	c.261C>A	c.(259-261)caC>caA	p.H87Q	CYB561_ENST00000392975.2_Missense_Mutation_p.H87Q|CYB561_ENST00000582997.1_Missense_Mutation_p.H94Q|CYB561_ENST00000582034.1_Missense_Mutation_p.H58Q|CYB561_ENST00000448884.2_Missense_Mutation_p.H87Q|CYB561_ENST00000581573.1_Missense_Mutation_p.H87Q|CYB561_ENST00000584031.1_Missense_Mutation_p.H87Q|CYB561_ENST00000542042.1_Missense_Mutation_p.H154Q|CYB561_ENST00000582297.1_Missense_Mutation_p.H87Q|CYB561_ENST00000581163.1_5'UTR|CYB561_ENST00000360793.3_Missense_Mutation_p.H87Q	NM_001017916.1	NP_001017916.1	P49447	CY561_HUMAN	cytochrome b561	87	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				electron transport chain (GO:0022900)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|transmembrane electron transfer carrier (GO:0022865)			lung(2)|ovary(1)|prostate(1)	4				READ - Rectum adenocarcinoma(1115;0.0689)		GCAGCAGCCCGTGCAGGACCT	0.617																																					p.H87Q		Atlas-SNP	.											CYB561,NS,malignant_melanoma,0,1	CYB561	15	.	0			c.C261A						.						146	117	127					17																	61513455		2203	4300	6503	SO:0001583	missense	1534	exon3			CAGCCCGTGCAGG		CCDS11636.1	17q23.3	2013-03-14	2013-03-14		ENSG00000008283	ENSG00000008283		"Cytochrome b genes"	2571	protein-coding gene	gene with protein product	"ferric-chelate reductase 2", "cytochrome b561 family, member A1"	600019				7959749, 23249217	Standard	XM_005257091		Approved	FRRS2, CYB561A1	uc002jas.3	P49447		ENST00000392976.1:c.261C>A	chr17.hg19:g.61513455G>T	ENSP00000376702:p.His87Gln	116.0	0.0		99.0	58.0	NM_001915	B2RE96|B7Z775|D3DU11|Q5BJG9|Q9BU05|Q9BWR9	Missense_Mutation	SNP	ENST00000392976.1	hg19	CCDS11636.1	.	.	.	.	.	.	.	.	.	.	G	6.059	0.379146	0.11466	.	.	ENSG00000008283	ENST00000360793;ENST00000392976;ENST00000392975;ENST00000448884;ENST00000542042	D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75	4.87	-2.18	0.07037	Cytochrome b561, eukaryote (1);Cytochrome b561/ferric reductase transmembrane (2);	0.158856	0.56097	D	0.000037	D	0.91181	0.7222	M	0.93283	3.4	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.91635	0.999;0.999;0.974;0.996	D	0.89871	0.4023	10	0.87932	D	0	-10.7002	10.3904	0.44164	0.3942:0.0:0.6058:0.0	.	87;87;154;87	B7Z775;B3KTA1;F5H757;P49447	.;.;.;CY561_HUMAN	Q	87;87;87;87;154	ENSP00000354028:H87Q;ENSP00000376702:H87Q;ENSP00000376701:H87Q;ENSP00000400350:H87Q;ENSP00000442773:H154Q	ENSP00000354028:H87Q	H	-	3	2	CYB561	58867187	0.974000	0.33945	0.978000	0.43139	0.024000	0.10985	-0.034000	0.12225	-0.364000	0.08088	-1.149000	0.01842	CAC	.	.		0.617	CYB561-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444843.1	NM_001915		T	61513455	G	T	61513455	3	4	55	1	0	0	0	0	1	0	0	0	4121	1136	40	1	510	1	CYB561	17	61513455	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	21977539	61513455	19681755	118	7026										
CCDC47	57003	hgsc.bcm.edu	37	chr17	61829358	61829358	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tgattcgctccttctctgctCtttttttctcctcccgccga	5	16	3	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr17:61829358C>A	ENST00000225726.5	-	12	1695	c.1313G>T	c.(1312-1314)aGa>aTa	p.R438I	CCDC47_ENST00000582252.1_Missense_Mutation_p.R438I|CCDC47_ENST00000403162.3_Missense_Mutation_p.R438I|RP11-51F16.8_ENST00000580553.1_Nonsense_Mutation_p.E34*	NM_020198.2	NP_064583.2	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47	438					calcium ion homeostasis (GO:0055074)|ER overload response (GO:0006983)|osteoblast differentiation (GO:0001649)|post-embryonic development (GO:0009791)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	18						CTTCTCTGCTCTTTTTTTCTC	0.463																																					p.R438I		Atlas-SNP	.											.	CCDC47	34	.	0			c.G1313T						.						141	137	139					17																	61829358		2203	4300	6503	SO:0001583	missense	57003	exon12			TCTGCTCTTTTTT	AF226054	CCDS11643.1	17q23.3	2005-12-19				ENSG00000108588			24856	protein-coding gene	gene with protein product						12477932	Standard	NM_020198		Approved	GK001	uc002jbs.4	Q96A33		ENST00000225726.5:c.1313G>T	chr17.hg19:g.61829358C>A	ENSP00000225726:p.Arg438Ile	156.0	0.0		126.0	75.0	NM_020198	B2RAS8|D3DU20|Q96D00|Q96JZ7|Q9H3E4|Q9NRG3	Missense_Mutation	SNP	ENST00000225726.5	hg19	CCDS11643.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.116551	0.56505	.	.	ENSG00000108588	ENST00000225726;ENST00000403162	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.83184	0.5199	M	0.81497	2.545	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.85130	0.994;0.997	D	0.84786	0.0776	9	0.62326	D	0.03	-14.4897	18.3164	0.90223	0.0:1.0:0.0:0.0	.	438;438	Q96A33-2;Q96A33	.;CCD47_HUMAN	I	438	.	ENSP00000225726:R438I	R	-	2	0	CCDC47	59183090	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.809000	0.86057	2.566000	0.86566	0.563000	0.77884	AGA	.	.		0.463	CCDC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444016.2	NM_020198		A	61829358	C	A	61829358	3	1	55	1	0	0	0	0	1	0	0	0	2820	913	32	3	146	3	CCDC47	17	61829358	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	315903	61829358	19365852	119	7027										
DOT1L	84444	hgsc.bcm.edu	37	chr19	2214500	2214500	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gctgcgaggagctgcagctgGactgggccacgctgtcgctg	17	12	0	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:2214500G>T	ENST00000398665.3	+	19	1864	c.1828G>T	c.(1828-1830)Gac>Tac	p.D610Y	AC004490.1_ENST00000585593.1_RNA|DOT1L_ENST00000608122.1_3'UTR	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	610					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTGCAGCTGGACTGGGCCAC	0.642																																					p.D610Y		Atlas-SNP	.											.	DOT1L	205	.	0			c.G1828T						.						33	37	36					19																	2214500		2128	4247	6375	SO:0001583	missense	84444	exon19			CAGCTGGACTGGG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.1828G>T	chr19.hg19:g.2214500G>T	ENSP00000381657:p.Asp610Tyr	172.0	0.0		384.0	18.0	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.2|25.2	4.614498|4.614498	0.87359|0.87359	.|.	.|.	ENSG00000104885|ENSG00000104885	ENST00000398665;ENST00000221482|ENST00000440640	T|.	0.37915|.	1.17|.	4.99|4.99	4.99|4.99	0.66335|0.66335	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74535|0.74535	0.3729|0.3729	M|M	0.70275|0.70275	2.135|2.135	0.58432|0.58432	D|D	0.999995|0.999995	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.74648|0.74648	-0.3595|-0.3595	10|5	0.87932|.	D|.	0|.	-46.4337|-46.4337	17.278|17.278	0.87121|0.87121	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	610|.	Q8TEK3-2|.	.|.	Y|C	610|396	ENSP00000381657:D610Y|.	ENSP00000221482:D610Y|.	D|W	+|+	1|3	0|0	DOT1L|DOT1L	2165500|2165500	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	9.083000|9.083000	0.94067|0.94067	2.309000|2.309000	0.77851|0.77851	0.561000|0.561000	0.74099|0.74099	GAC|TGG	.	.		0.642	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2214500	G	T	2214500	3	4	55	1	0	0	0	0	1	0	0	0	4711	1174	41	3	1902	3	DOT1L	19	2214500	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10		2214500	56914483	120	7028										
C19orf29	58509	hgsc.bcm.edu	37	chr19	3612206	3612206	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ttgggcggtgggttgtcaaaGtcgtagtgcgtctggttgta	17	5	2	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:3612206G>A	ENST00000429344.2	-	10	2044	c.1992C>T	c.(1990-1992)gaC>gaT	p.D664D	CACTIN_ENST00000221899.3_Silent_p.D596D|CACTIN_ENST00000248420.5_Silent_p.D664D|CACTIN-AS1_ENST00000592274.1_RNA	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	664					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										GGTTGTCAAAGTCGTAGTGCG	0.587																																					p.D664D		Atlas-SNP	.											.	.	.	.	0			c.C1992T						.						133	149	143					19																	3612206		2170	4265	6435	SO:0001819	synonymous_variant	58509	exon10			GTCAAAGTCGTAG	BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"NY REN 24 antigen", "functional spliceosome-associated protein c", "cactin homolog (Drosophila)"		"chromosome 19 open reading frame 29"	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.1992C>T	chr19.hg19:g.3612206G>A		274.0	0.0		617.0	456.0	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Silent	SNP	ENST00000429344.2	hg19	CCDS45920.1	.	.	.	.	.	.	.	.	.	.	G	8.361	0.833183	0.16820	.	.	ENSG00000226800	ENST00000447295	.	.	.	4.02	2.97	0.34412	.	.	.	.	.	T	0.48333	0.1494	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25467	-1.0131	5	0.18710	T	0.47	.	7.592	0.28027	0.2018:0.0:0.7982:0.0	.	.	.	.	I	160	.	ENSP00000412459:V160I	V	+	1	0	C19orf29OS	3563206	1.000000	0.71417	0.999000	0.59377	0.003000	0.03518	6.183000	0.72002	1.036000	0.39998	-0.152000	0.13540	GTC	.	.		0.587	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2			A	3612206	G	A	3612206	2	1	55	1	0	0	0	0	0	0	0	1	1920	1020	36	3		3	C19orf29	19	3612206	Silent	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	1397706	3612206	55516777	121	7029										
TMEM146	257062	hgsc.bcm.edu	37	chr19	5772804	5772804	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gtgcctgtgtcctaggtggcGaaaagacagtttccaggagg	15	8	0	1	rs369818912		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:5772804G>A	ENST00000381624.3	+	20	1830	c.1769G>A	c.(1768-1770)cGa>cAa	p.R590Q	CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	590					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											CCTAGGTGGCGAAAAGACAGT	0.612																																					p.R590Q		Atlas-SNP	.											.	.	.	.	0			c.G1769A						.	G	GLN/ARG	0,4260		0,0,2130	83	87	86		1769	-4.8	0	19		86	1,8481		0,1,4240	no	missense	TMEM146	NM_152784.3	43	0,1,6370	AA,AG,GG		0.0118,0.0,0.0078	benign	590/799	5772804	1,12741	2130	4241	6371	SO:0001583	missense	257062	exon20			GGTGGCGAAAAGA	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.1769G>A	chr19.hg19:g.5772804G>A	ENSP00000371037:p.Arg590Gln	156.0	0.0		209.0	65.0	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	hg19	CCDS12149.2	.	.	.	.	.	.	.	.	.	.	G	8.770	0.925745	0.18056	0.0	1.18E-4	ENSG00000174898	ENST00000381624;ENST00000309164;ENST00000381613	T	0.23552	1.9	3.01	-4.75	0.03239	.	2.340000	0.02425	N	0.082989	T	0.20618	0.0496	L	0.51422	1.61	0.09310	N	1	B	0.27351	0.176	B	0.15870	0.014	T	0.25537	-1.0129	10	0.62326	D	0.03	-1.6801	4.7864	0.13227	0.3131:0.0:0.5153:0.1716	.	590	Q86XM0	TM146_HUMAN	Q	590;261;259	ENSP00000371037:R590Q	ENSP00000310546:R261Q	R	+	2	0	TMEM146	5723804	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.497000	0.02289	-0.914000	0.03827	-1.267000	0.01435	CGA	.	.		0.612	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		A	5772804	G	A	5772804	3	1	55	1	0	0	0	0	1	0	0	0	16075	1058	37	1	1847	1	TMEM146	19	5772804	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	2160598	5772804	53356179	122	7030										
MUC16	94025	hgsc.bcm.edu	37	chr19	9065780	9065780	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tgaggggttgatatggcaacAgttgtatcctcctgggtgga	15	6	0	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:9065780A>T	ENST00000397910.4	-	3	21869	c.21666T>A	c.(21664-21666)acT>acA	p.T7222T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7224	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATATGGCAACAGTTGTATCCT	0.488																																					p.T7222T		Atlas-SNP	.											.	MUC16	4315	.	0			c.T21666A						.						217	206	209					19																	9065780		2037	4184	6221	SO:0001819	synonymous_variant	94025	exon3			GGCAACAGTTGTA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21666T>A	chr19.hg19:g.9065780A>T		270.0	1.0		153.0	106.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9065780	A	T	9065780	2	4	55	1	0	0	0	0	0	0	0	1	9982	175	7	4		4	MUC16	19	9065780	Silent	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	3292976	9065780	50063203	123	7031										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23544469	23544469	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gttaaatgctttgccacattCttcacacttgtaaggtttct	6	9	3	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:23544469C>T	ENST00000300619.7	-	4	1517	c.1312G>A	c.(1312-1314)Gaa>Aaa	p.E438K	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Missense_Mutation_p.E406K	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	438					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TTGCCACATTCTTCACACTTG	0.338																																					p.E438K		Atlas-SNP	.											.	ZNF91	349	.	0			c.G1312A						.						24	26	25					19																	23544469		2043	4215	6258	SO:0001583	missense	7644	exon4			CACATTCTTCACA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1312G>A	chr19.hg19:g.23544469C>T	ENSP00000300619:p.Glu438Lys	62.0	0.0		51.0	9.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	9.646	1.140215	0.21205	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.07327	3.2;3.2	1.47	-2.08	0.07254	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11024	0.0269	L	0.28192	0.835	0.09310	N	1	D;D	0.61080	0.984;0.989	P;P	0.56474	0.799;0.729	T	0.32107	-0.9919	9	0.62326	D	0.03	.	9.4396	0.38659	0.0:0.5941:0.4059:0.0	.	406;438	Q05481-2;Q05481	.;ZNF91_HUMAN	K	438;406	ENSP00000300619:E438K;ENSP00000380272:E406K	ENSP00000300619:E438K	E	-	1	0	ZNF91	23336309	0.000000	0.05858	0.027000	0.17364	0.021000	0.10359	-0.241000	0.08940	-0.034000	0.13713	-1.027000	0.02421	GAA	.	.		0.338	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		T	23544469	C	T	23544469	3	4	55	1	0	0	0	0	1	0	0	0	18215	922	32	3	2267	3	ZNF91	19	23544469	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	14478689	23544469	35584514	124	7032										
PEPD	5184	hgsc.bcm.edu	37	chr19	34001941	34001941	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ggctgctccttactttcccaTccaggtggcatggctggcag	12	13	0	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:34001941T>A	ENST00000244137.7	-	3	355	c.322A>T	c.(322-324)Atg>Ttg	p.M108L	PEPD_ENST00000436370.3_Intron|PEPD_ENST00000397032.4_Missense_Mutation_p.M108L	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	108				M -> I (in Ref. 3; BAF83445). {ECO:0000305}.	cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					TACTTTCCCATCCAGGTGGCA	0.617																																					p.M108L		Atlas-SNP	.											.	PEPD	48	.	0			c.A322T						.						34	37	36					19																	34001941		2015	4172	6187	SO:0001583	missense	5184	exon3			TTCCCATCCAGGT	BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"prolidase"	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.322A>T	chr19.hg19:g.34001941T>A	ENSP00000244137:p.Met108Leu	64.0	0.0		88.0	30.0	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Missense_Mutation	SNP	ENST00000244137.7	hg19	CCDS42544.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.664193	0.47572	.	.	ENSG00000124299	ENST00000244137;ENST00000397032	T;T	0.75821	-0.97;-0.97	4.9	4.9	0.64082	Peptidase M24B, X-Pro dipeptidase/aminopeptidase P N-terminal (1);	0.037944	0.85682	D	0.000000	T	0.68742	0.3034	L	0.46741	1.465	0.80722	D	1	B;B	0.17852	0.024;0.004	B;B	0.26969	0.075;0.011	T	0.64495	-0.6394	10	0.30078	T	0.28	-41.6574	13.6423	0.62257	0.0:0.0:0.0:1.0	.	108;108	A8MX47;P12955	.;PEPD_HUMAN	L	108	ENSP00000244137:M108L;ENSP00000380226:M108L	ENSP00000244137:M108L	M	-	1	0	PEPD	38693781	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.482000	0.66833	1.971000	0.57363	0.397000	0.26171	ATG	.	.		0.617	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285		A	34001941	T	A	34001941	3	1	55	1	0	0	0	0	1	0	0	0	11737	1435	50	4	1211	4	PEPD	19	34001941	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	10457472	34001941	25127042	125	7033										
ZNF567	163081	hgsc.bcm.edu	37	chr19	37210908	37210908	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	atatttgtaatgaatgtgggAaatccttctcccagaagaca	8	7	1	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:37210908A>T	ENST00000536254.2	+	6	1504	c.1282A>T	c.(1282-1284)Aaa>Taa	p.K428*	ZNF567_ENST00000392163.2_Nonsense_Mutation_p.K397*|ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000360729.4_Nonsense_Mutation_p.K397*|ZNF567_ENST00000588311.1_Nonsense_Mutation_p.K397*|ZNF567_ENST00000585696.1_Nonsense_Mutation_p.K397*			Q8N184	ZN567_HUMAN	zinc finger protein 567	428					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TGAATGTGGGAAATCCTTCTC	0.408																																					p.K397X		Atlas-SNP	.											.	ZNF567	61	.	0			c.A1189T						.						54	58	57					19																	37210908		2203	4300	6503	SO:0001587	stop_gained	163081	exon4			TGTGGGAAATCCT	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"Zinc fingers, C2H2-type", "-"	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.1282A>T	chr19.hg19:g.37210908A>T	ENSP00000441838:p.Lys428*	39.0	0.0		97.0	10.0	NM_152603	B3KX49|Q6N044	Nonsense_Mutation	SNP	ENST00000536254.2	hg19		.	.	.	.	.	.	.	.	.	.	A	36	5.785643	0.96937	.	.	ENSG00000189042	ENST00000536254;ENST00000378686;ENST00000360729;ENST00000423498;ENST00000392163	.	.	.	4.88	4.88	0.63580	.	0.000000	0.48286	D	0.000200	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.7584	0.57350	1.0:0.0:0.0:0.0	.	.	.	.	X	428;372;397;427;397	.	ENSP00000353957:K397X	K	+	1	0	ZNF567	41902748	1.000000	0.71417	0.758000	0.31321	0.973000	0.67179	8.427000	0.90275	2.176000	0.68965	0.459000	0.35465	AAA	.	.		0.408	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603		T	37210908	A	T	37210908	4	4	55	1	0	0	0	0	0	1	0	0	18013	247	9	4	1199	4	ZNF567	19	37210908	Nonsense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	3208967	37210908	21918075	126	7034										
ZNF224	7767	hgsc.bcm.edu	37	chr19	44611314	44611314	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gagatcagcacttaatagtcAtcgcatgatccacacaggag	9	10	2	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:44611314A>T	ENST00000336976.6	+	6	1255	c.1001A>T	c.(1000-1002)cAt>cTt	p.H334L	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	334					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				CTTAATAGTCATCGCATGATC	0.433																																					p.H334L		Atlas-SNP	.											.	ZNF224	70	.	0			c.A1001T						.						166	163	164					19																	44611314		2203	4300	6503	SO:0001583	missense	7767	exon6			ATAGTCATCGCAT	AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"Zinc fingers, C2H2-type", "-"	13017	protein-coding gene	gene with protein product		194555	"zinc finger protein 255", "zinc finger protein 27"	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.1001A>T	chr19.hg19:g.44611314A>T	ENSP00000337368:p.His334Leu	74.0	0.0		175.0	44.0	NM_013398	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Missense_Mutation	SNP	ENST00000336976.6	hg19	CCDS33046.1	.	.	.	.	.	.	.	.	.	.	a	19.03	3.746934	0.69418	.	.	ENSG00000186019	ENST00000336976	D	0.86865	-2.18	2.95	2.95	0.34219	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.95790	0.8630	H	0.98965	4.385	0.31912	N	0.614539	D	0.76494	0.999	D	0.81914	0.995	D	0.94367	0.7592	9	0.87932	D	0	.	10.9531	0.47341	1.0:0.0:0.0:0.0	.	334	Q9NZL3	ZN224_HUMAN	L	334	ENSP00000337368:H334L	ENSP00000337368:H334L	H	+	2	0	ZNF224	49303154	1.000000	0.71417	0.019000	0.16419	0.298000	0.27526	8.373000	0.90131	1.592000	0.50018	0.482000	0.46254	CAT	.	.		0.433	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398		T	44611314	A	T	44611314	3	4	55	1	0	0	0	0	1	0	0	0	17793	217	8	4	1015	4	ZNF224	19	44611314	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	7400406	44611314	14517669	127	7035										
BCL3	602	hgsc.bcm.edu	37	chr19	45260278	45260278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agtcactgttccccagacacCgctccacctggctgtgatca	8	16	2	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:45260278C>T	ENST00000164227.5	+	4	768	c.524C>T	c.(523-525)cCg>cTg	p.P175L		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	175					antimicrobial humoral response (GO:0019730)|cellular response to DNA damage stimulus (GO:0006974)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|protein import into nucleus, translocation (GO:0000060)|regulation of apoptotic process (GO:0042981)|regulation of DNA binding (GO:0051101)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to UV-C (GO:0010225)|response to virus (GO:0009615)|spleen development (GO:0048536)|T-helper 1 type immune response (GO:0042088)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	Bcl3-Bcl10 complex (GO:0032996)|Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)				CCCCAGACACCGCTCCACCTG	0.622			T	IGH@	CLL																																p.P175L		Atlas-SNP	.		Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	.	BCL3	28	.	0			c.C524T						.						32	20	24					19																	45260278		2146	4186	6332	SO:0001583	missense	602	exon4			AGACACCGCTCCA	M31732	CCDS12642.2	19q13.1-q13.2	2013-01-10			ENSG00000069399	ENSG00000069399		"Ankyrin repeat domain containing"	998	protein-coding gene	gene with protein product	"B-cell lymphoma 3-encoded protein", "B-cell leukemia/lymphoma 3", "chronic lymphatic leukemia protein"	109560		D19S37, BCL4		1501714, 2180580	Standard	NM_005178		Approved		uc010xxe.2	P20749	OTTHUMG00000151517	ENST00000164227.5:c.524C>T	chr19.hg19:g.45260278C>T	ENSP00000164227:p.Pro175Leu	210.0	0.0		537.0	101.0	NM_005178		Missense_Mutation	SNP	ENST00000164227.5	hg19	CCDS12642.2	.	.	.	.	.	.	.	.	.	.	C	25.3	4.627946	0.87560	.	.	ENSG00000069399	ENST00000403534;ENST00000164227	T	0.71698	-0.59	4.95	4.95	0.65309	Ankyrin repeat-containing domain (3);	0.000000	0.42682	D	0.000680	D	0.85331	0.5672	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87585	0.2487	10	0.62326	D	0.03	-13.5552	15.6745	0.77303	0.0:1.0:0.0:0.0	.	175	P20749	BCL3_HUMAN	L	135;175	ENSP00000164227:P175L	ENSP00000164227:P175L	P	+	2	0	BCL3	49952118	1.000000	0.71417	0.879000	0.34478	0.981000	0.71138	6.265000	0.72534	2.276000	0.75962	0.462000	0.41574	CCG	.	.		0.622	BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1	NM_005178		T	45260278	C	T	45260278	3	4	55	1	0	0	0	0	1	0	0	0	1375	652	23	1	538	1	BCL3	19	45260278	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	648964	45260278	13868705	128	7036										
CEACAM18	729767	hgsc.bcm.edu	37	chr19	51981868	51981868	+	5'Flank	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ggctgtgtctctggagggacCcctcctcctggaggacccca	13	15	1	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:51981868C>A	ENST00000396477.4	+	0	0				CEACAM18_ENST00000451626.1_Missense_Mutation_p.P52H	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18											breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CTGGAGGGACCCCTCCTCCTG	0.627																																					p.P52H		Atlas-SNP	.											.	CEACAM18	96	.	0			c.C155A						.						30	35	34					19																	51981868		1984	4147	6131	SO:0001631	upstream_gene_variant	729767	exon2			AGGGACCCCTCCT			19q13.41	2013-01-29				ENSG00000213822		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9			chr19.hg19:g.51981868C>A	Exception_encountered	82.0	0.0		203.0	32.0	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	hg19		.	.	.	.	.	.	.	.	.	.	.	12.26	1.883505	0.33255	.	.	ENSG00000213822	ENST00000451626	T	0.05580	3.42	2.6	-1.17	0.09648	.	.	.	.	.	T	0.03477	0.0100	N	0.08118	0	0.09310	N	1	B	0.15719	0.014	B	0.11329	0.006	T	0.42137	-0.9469	9	0.62326	D	0.03	.	8.2875	0.31937	0.665:0.335:0.0:0.0	.	52	A8MTB9	CEA18_HUMAN	H	52	ENSP00000402203:P52H	ENSP00000402203:P52H	P	+	2	0	CEACAM18	56673680	0.020000	0.18652	0.002000	0.10522	0.011000	0.07611	-0.102000	0.10956	-0.143000	0.11334	-0.181000	0.13052	CCC	.	.		0.627	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2			A	51981868	C	A	51981868	1	1	55	0	1	0	0	0	0	0	0	0	3191	623	22	3		3	CEACAM18	19	51981868	5'Flank	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	6721590	51981868	7147115	129	7037										
ZNF135	7694	hgsc.bcm.edu	37	chr19	58578450	58578450	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gtggaaaaagggagaagccaGacctaaatgttttacagaaa	11	5	0	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr19:58578450G>C	ENST00000313434.5	+	5	699	c.598G>C	c.(598-600)Gac>Cac	p.D200H	RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000359978.6_Missense_Mutation_p.D212H|ZNF135_ENST00000511556.1_Missense_Mutation_p.D212H|ZNF135_ENST00000401053.4_Missense_Mutation_p.D224H|ZNF135_ENST00000506786.1_Missense_Mutation_p.D158H|ZNF135_ENST00000439855.2_Missense_Mutation_p.D200H	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	200					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		GGAGAAGCCAGACCTAAATGT	0.453																																					p.D224H		Atlas-SNP	.											.	ZNF135	159	.	0			c.G670C						.						71	70	70					19																	58578450		2203	4300	6503	SO:0001583	missense	7694	exon4			AAGCCAGACCTAA	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"Zinc fingers, C2H2-type", "-"	12919	protein-coding gene	gene with protein product		604077	"zinc finger protein 61", "zinc finger protein 135 (clone pHZ-17)"	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.598G>C	chr19.hg19:g.58578450G>C	ENSP00000321406:p.Asp200His	50.0	0.0		110.0	34.0	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.302|0.302	-0.973322|-0.973322	0.02215|0.02215	.|.	.|.	ENSG00000176293|ENSG00000176293	ENST00000504540;ENST00000401053;ENST00000359978;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786|ENST00000391699	T;T;T;T;T;T|.	0.06528|.	3.39;3.46;3.41;3.41;3.39;3.29|.	3.07|3.07	-0.607|-0.607	0.11615|0.11615	.|.	.|.	.|.	.|.	.|.	T|T	0.17874|0.17874	0.0429|0.0429	N|N	0.11560|0.11560	0.145|0.145	0.09310|0.09310	N|N	1|1	B;P;B|.	0.37731|.	0.003;0.607;0.01|.	B;B;B|.	0.25759|.	0.001;0.063;0.003|.	T|T	0.30794|0.30794	-0.9966|-0.9966	9|5	0.31617|.	T|.	0.26|.	.|.	8.121|8.121	0.30971|0.30971	0.1218:0.6271:0.2511:0.0|0.1218:0.6271:0.2511:0.0	.|.	212;200;212|.	E9PEV2;P52742;Q8N1I7|.	.;ZN135_HUMAN;.|.	H|H	212;224;212;200;200;212;158|217	ENSP00000441410:D224H;ENSP00000369437:D212H;ENSP00000444828:D200H;ENSP00000321406:D200H;ENSP00000422074:D212H;ENSP00000427691:D158H|.	ENSP00000321406:D200H|.	D|Q	+|+	1|3	0|2	ZNF135|ZNF135	63270262|63270262	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.106000|0.106000	0.19336|0.19336	-0.230000|-0.230000	0.09083|0.09083	-0.026000|-0.026000	0.13895|0.13895	-0.312000|-0.312000	0.09012|0.09012	GAC|CAG	.	.		0.453	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		C	58578450	G	C	58578450	3	2	55	1	0	0	0	0	1	0	0	0	17740	942	33	4	801	4	ZNF135	19	58578450	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	6596582	58578450	550533	130	7038										
CBFA2T2	9139	hgsc.bcm.edu	37	chr20	32207387	32207387	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agccacaaactttccccttcGtccttttgtgattccatttc	4	14	0	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr20:32207387G>T	ENST00000346541.3	+	5	1049	c.512G>T	c.(511-513)cGt>cTt	p.R171L	CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000344201.3_Missense_Mutation_p.R142L|CBFA2T2_ENST00000397800.1_Missense_Mutation_p.R142L|CBFA2T2_ENST00000359606.3_Missense_Mutation_p.R181L|CBFA2T2_ENST00000375279.2_Missense_Mutation_p.R171L|CBFA2T2_ENST00000492345.1_Missense_Mutation_p.R142L|CBFA2T2_ENST00000397798.2_Missense_Mutation_p.R142L|CBFA2T2_ENST00000342704.6_Missense_Mutation_p.R162L	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	171	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						TTTCCCCTTCGTCCTTTTGTG	0.338																																					p.R171L	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-SNP	.											CBFA2T2_ENST00000342704,colon,carcinoma,0,2	CBFA2T2	93	.	0			c.G512T						.						84	86	85					20																	32207387		2203	4300	6503	SO:0001583	missense	9139	exon5			CCCTTCGTCCTTT	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"Zinc fingers, MYND-type"	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.512G>T	chr20.hg19:g.32207387G>T	ENSP00000262653:p.Arg171Leu	123.0	0.0		137.0	62.0	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Missense_Mutation	SNP	ENST00000346541.3	hg19	CCDS13221.1	.	.	.	.	.	.	.	.	.	.	G	32	5.186916	0.94923	.	.	ENSG00000078699	ENST00000375279;ENST00000342704;ENST00000417366;ENST00000344201;ENST00000346541;ENST00000397800;ENST00000397798;ENST00000359606	T;T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.4	5.4	0.78164	TAFH/NHR1 (3);	0.000000	0.85682	D	0.000000	T	0.71358	0.3330	M	0.77820	2.39	0.80722	D	1	D;D	0.62365	0.991;0.989	D;D	0.80764	0.994;0.99	T	0.74907	-0.3504	10	0.87932	D	0	-0.6716	19.1707	0.93576	0.0:0.0:1.0:0.0	.	171;162	O43439;F8W6D7	MTG8R_HUMAN;.	L	171;162;162;142;171;142;142;181	ENSP00000364428:R171L;ENSP00000345810:R162L;ENSP00000408352:R162L;ENSP00000341865:R142L;ENSP00000262653:R171L;ENSP00000380902:R142L;ENSP00000380900:R142L;ENSP00000352622:R181L	ENSP00000345810:R162L	R	+	2	0	CBFA2T2	31671048	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.568000	0.82369	2.522000	0.85027	0.650000	0.86243	CGT	.	.		0.338	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		T	32207387	G	T	32207387	3	4	55	1	0	0	0	0	1	0	0	0	2699	1145	40	1	564	1	CBFA2T2	20	32207387	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10		32207387	30818133	131	7039										
KCNS1	3787	hgsc.bcm.edu	37	chr20	43727336	43727336	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	caaaggtttcagtgctcctcCctgcggacaccagaagggcg	12	13	1	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr20:43727336C>T	ENST00000306117.1	-	4	473	c.77G>A	c.(76-78)gGg>gAg	p.G26E	KCNS1_ENST00000537075.1_Splice_Site_p.G26E	NM_002251.3	NP_002242.2	Q96KK3	KCNS1_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1	26					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(1)|lung(3)|ovary(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				AGTGCTCCTCCCTGCGGACAC	0.652																																					p.G26E		Atlas-SNP	.											.	KCNS1	30	.	0			c.G77A						.						7	8	8					20																	43727336		1995	4160	6155	SO:0001630	splice_region_variant	3787	exon4			CTCCTCCCTGCGG	AF043473	CCDS13342.1	20q12	2011-07-05			ENSG00000124134	ENSG00000124134		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6300	protein-coding gene	gene with protein product		602905				9305895, 16382104	Standard	NM_002251		Approved	Kv9.1	uc002xnc.3	Q96KK3	OTTHUMG00000033079	ENST00000306117.1:c.77-1G>A	chr20.hg19:g.43727336C>T		47.0	0.0		52.0	18.0	NM_002251	A2RUL9|B7ZM31|O43652|Q6DJU6	Missense_Mutation	SNP	ENST00000306117.1	hg19	CCDS13342.1	.	.	.	.	.	.	.	.	.	.	C	11.47	1.648526	0.29336	.	.	ENSG00000124134	ENST00000306117;ENST00000537075	D;D	0.96200	-3.94;-3.94	3.5	2.54	0.30619	.	27.440700	0.04882	U	0.447800	D	0.89643	0.6774	N	0.08118	0	0.09310	N	1	B	0.32010	0.351	B	0.35278	0.199	T	0.81581	-0.0867	10	0.18710	T	0.47	.	9.8096	0.40815	0.0:0.8919:0.0:0.1081	.	26	Q96KK3	KCNS1_HUMAN	E	26	ENSP00000307694:G26E;ENSP00000445595:G26E	ENSP00000307694:G26E	G	-	2	0	KCNS1	43160750	0.565000	0.26610	0.004000	0.12327	0.048000	0.14542	0.941000	0.29005	0.753000	0.32945	0.655000	0.94253	GGG	.	.		0.652	KCNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080507.3	NM_002251	Missense_Mutation	T	43727336	C	T	43727336	5	4	55	1	0	0	0	0	0	0	1	0	8097	637	22	3	1511	3	KCNS1	20	43727336	Splice_Site	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	11519949	43727336	19298184	132	7040										
KCNG1	3755	hgsc.bcm.edu	37	chr20	49621256	49621256	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gaacttgctgggcgcctgaaTgagccgcaggaggaactcca	14	11	0	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr20:49621256T>C	ENST00000371571.4	-	3	1147	c.862A>G	c.(862-864)Att>Gtt	p.I288V	KCNG1_ENST00000506387.1_5'UTR|RP5-955M13.4_ENST00000424566.1_RNA	NM_002237.3	NP_002228.2	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G, member 1	288					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GGCGCCTGAATGAGCCGCAGG	0.642																																					p.I288V		Atlas-SNP	.											.	KCNG1	86	.	0			c.A862G						.						21	20	21					20																	49621256		2198	4295	6493	SO:0001583	missense	3755	exon3			CCTGAATGAGCCG	AF033383	CCDS13436.1	20q13	2011-07-05			ENSG00000026559	ENSG00000026559		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6248	protein-coding gene	gene with protein product		603788		KCNG		9434767, 16382104	Standard	NM_002237		Approved	Kv6.1, kH2, K13	uc002xwa.4	Q9UIX4	OTTHUMG00000032745	ENST00000371571.4:c.862A>G	chr20.hg19:g.49621256T>C	ENSP00000360626:p.Ile288Val	196.0	0.0		256.0	113.0	NM_002237	A8K3S4|O43528|Q5JXL5|Q9BRC1	Missense_Mutation	SNP	ENST00000371571.4	hg19	CCDS13436.1	.	.	.	.	.	.	.	.	.	.	T	8.742	0.919312	0.17982	.	.	ENSG00000026559	ENST00000371571	D	0.98455	-4.94	4.88	1.3	0.21679	Ion transport (1);	0.317848	0.38217	N	0.001775	D	0.93452	0.7911	N	0.17764	0.52	0.80722	D	1	B	0.12013	0.005	B	0.20577	0.03	D	0.86058	0.1530	9	.	.	.	.	8.1685	0.31241	0.0:0.2938:0.0:0.7062	.	288	Q9UIX4	KCNG1_HUMAN	V	288	ENSP00000360626:I288V	.	I	-	1	0	KCNG1	49054663	1.000000	0.71417	0.972000	0.41901	0.397000	0.30659	2.119000	0.41958	0.305000	0.22832	0.260000	0.18958	ATT	.	.		0.642	KCNG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079726.4	NM_002237		C	49621256	T	C	49621256	3	2	55	1	0	0	0	0	1	0	0	0	8036	1464	51	2	683	2	KCNG1	20	49621256	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	5893920	49621256	13404264	133	7041										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58467120	58467121	+	Frame_Shift_Ins	INS	-	-	T													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cttttctatgactttgcacaINStttttgctagcagatggatt							TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr20:58467120_58467121insT	ENST00000357552.3	-	24	2513_2514	c.2288_2289insA	c.(2287-2289)aatfs	p.N763fs	SYCP2_ENST00000371001.2_Frame_Shift_Ins_p.N763fs			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	763					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			GACTTTGCACATTTTTGCTAGC	0.322																																					p.N763fs		Atlas-Indel,Pindel	.											.	SYCP2	204	.	0			c.2289_2290insA						.																																			SO:0001589	frameshift_variant	10388	exon23			.	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.2289dupA	chr20.hg19:g.58467125_58467125dupT	ENSP00000350162:p.Asn763fs	150.0	0.0		195.0	15.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Frame_Shift_Ins	INS	ENST00000357552.3	hg19	CCDS13482.1																																																																																			.	.		0.322	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		T	58467121	-	T	58467120	7	5	55	1	0	1	1	0	0	0	0	0	15447	214	8	0	2391	0	SYCP2	20	58467120	Frame_Shift_Ins	INS	-	TCGA-CC-5259-01A-31D-A20W-10	8845864	58467120	4558400	134	7042										
C20orf177	63939	hgsc.bcm.edu	37	chr20	58519115	58519115	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ccgagaagcagcctcacagcTgtcacccagcctactgaaga	9	15	2	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr20:58519115T>A	ENST00000358293.3	+	5	532	c.117T>A	c.(115-117)gcT>gcA	p.A39A	FAM217B_ENST00000360816.3_Silent_p.A39A|FAM217B_ENST00000469084.1_Intron	NM_001190826.1	NP_001177755.1	Q9NTX9	F217B_HUMAN	family with sequence similarity 217, member B	39																	GCCTCACAGCTGTCACCCAGC	0.493																																					p.A39A		Atlas-SNP	.											.	.	.	.	0			c.T117A						.						48	49	49					20																	58519115		2203	4300	6503	SO:0001819	synonymous_variant	63939	exon4			CACAGCTGTCACC	AL109928	CCDS13484.1	20q13.33	2012-02-07	2012-02-07	2012-02-07	ENSG00000196227	ENSG00000196227			16170	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 177"	C20orf177			Standard	NM_022106		Approved	dJ551D2.5	uc002ybc.3	Q9NTX9	OTTHUMG00000032873	ENST00000358293.3:c.117T>A	chr20.hg19:g.58519115T>A		136.0	0.0		189.0	62.0	NM_022106	B3KWH1|Q9NTA3	Silent	SNP	ENST00000358293.3	hg19	CCDS13484.1																																																																																			.	.		0.493	FAM217B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268139.1	NM_022106		A	58519115	T	A	58519115	2	1	55	1	0	0	0	0	0	0	0	1	2098	1567	55	4		4	C20orf177	20	58519115	Silent	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	51995	58519115	4506405	135	7043										
COL9A3	1299	hgsc.bcm.edu	37	chr20	61467861	61467861	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cagcgagcagcgcatcagggAgctgtgtggggggatgatca	18	8	2	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr20:61467861A>T	ENST00000343916.3	+	29	1583	c.1580A>T	c.(1579-1581)gAg>gTg	p.E527V	COL9A3_ENST00000462700.1_Intron	NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	527	Nonhelical region 3 (NC3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					CGCATCAGGGAGCTGTGTGGG	0.672																																					p.E527V		Atlas-SNP	.											.	COL9A3	70	.	0			c.A1580T						.						30	35	33					20																	61467861		2201	4300	6501	SO:0001583	missense	1299	exon29			TCAGGGAGCTGTG	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2219	protein-coding gene	gene with protein product	"collagen type IX proteoglycan"	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.1580A>T	chr20.hg19:g.61467861A>T	ENSP00000341640:p.Glu527Val	99.0	0.0		81.0	26.0	NM_001853	Q13681|Q9H4G9|Q9UPE2	Missense_Mutation	SNP	ENST00000343916.3	hg19	CCDS13505.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.098468	0.76870	.	.	ENSG00000092758	ENST00000343916	D	0.94232	-3.38	4.33	3.18	0.36537	.	0.171760	0.49916	D	0.000125	D	0.94712	0.8294	L	0.56340	1.77	0.58432	D	0.999999	D;D	0.76494	0.999;0.995	D;P	0.80764	0.994;0.593	D	0.93053	0.6467	10	0.45353	T	0.12	.	10.8599	0.46821	0.8414:0.1586:0.0:0.0	.	30;527	Q9BT15;Q14050	.;CO9A3_HUMAN	V	527	ENSP00000341640:E527V	ENSP00000341640:E527V	E	+	2	0	COL9A3	60938306	1.000000	0.71417	0.998000	0.56505	0.905000	0.53344	6.513000	0.73742	0.589000	0.29677	0.459000	0.35465	GAG	.	.		0.672	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853		T	61467861	A	T	61467861	3	4	55	1	0	0	0	0	1	0	0	0	3711	304	11	4	1694	4	COL9A3	20	61467861	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	2948746	61467861	1557659	136	7044										
SIK1	150094	hgsc.bcm.edu	37	chr21	44838314	44838314	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cagcagcccctgagtggccgGggtgccactgagccccgcgg	16	16	0	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr21:44838314G>A	ENST00000270162.6	-	12	1702	c.1570C>T	c.(1570-1572)Ccg>Tcg	p.P524S		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	524					cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	TGAGTGGCCGGGGTGCCACTG	0.701																																					p.P524S		Atlas-SNP	.											.	SIK1	65	.	0			c.C1570T						.						19	22	21					21																	44838314		2199	4297	6496	SO:0001583	missense	150094	exon12			TGGCCGGGGTGCC	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"myocardial SNF1-like kinase"	605705	"SNF1-like kinase"	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.1570C>T	chr21.hg19:g.44838314G>A	ENSP00000270162:p.Pro524Ser	52.0	0.0		55.0	39.0	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	hg19	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.574741	0.00887	.	.	ENSG00000142178	ENST00000270162	T	0.71341	-0.56	4.79	3.91	0.45181	.	0.314575	0.29314	N	0.012505	T	0.48768	0.1518	L	0.29908	0.895	0.09310	N	1	B	0.23442	0.085	B	0.16722	0.016	T	0.28839	-1.0031	10	0.07644	T	0.81	.	4.4526	0.11628	0.2351:0.1812:0.5837:0.0	.	524	P57059	SIK1_HUMAN	S	524	ENSP00000270162:P524S	ENSP00000270162:P524S	P	-	1	0	SIK1	43662742	1.000000	0.71417	0.460000	0.27093	0.001000	0.01503	1.862000	0.39448	1.013000	0.39391	-0.137000	0.14449	CCG	.	.		0.701	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		A	44838314	G	A	44838314	3	1	55	1	0	0	0	0	1	0	0	0	14332	1232	43	3	793	3	SIK1	21	44838314	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10		44838314	3291581	137	7045										
DRG1	4733	hgsc.bcm.edu	37	chr22	31799026	31799026	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	atgttttaggttttgatgtgGccaagacaggtgatgctcga	13	5	0	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr22:31799026G>T	ENST00000331457.4	+	3	339	c.178G>T	c.(178-180)Gcc>Tcc	p.A60S	DRG1_ENST00000433341.1_3'UTR	NM_004147.3	NP_004138.1	Q9Y295	DRG1_HUMAN	developmentally regulated GTP binding protein 1	60					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|polysome (GO:0005844)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	11						TTTTGATGTGGCCAAGACAGG	0.423																																					p.A60S		Atlas-SNP	.											.	DRG1	28	.	0			c.G178T						.						261	234	243					22																	31799026		2203	4300	6503	SO:0001583	missense	4733	exon3			GATGTGGCCAAGA	AJ005940	CCDS13897.1	22q12.2	2010-02-26	2001-11-28		ENSG00000185721	ENSG00000185721			3029	protein-coding gene	gene with protein product		603952	"developmentally regulated GTP-binding protein 1"	NEDD3		7929244, 1449490	Standard	NM_004147		Approved		uc003aku.3	Q9Y295	OTTHUMG00000030792	ENST00000331457.4:c.178G>T	chr22.hg19:g.31799026G>T	ENSP00000329715:p.Ala60Ser	417.0	0.0		277.0	13.0	NM_004147	B2RDS8|Q6FGP8|Q8WW69|Q9UGF2	Missense_Mutation	SNP	ENST00000331457.4	hg19	CCDS13897.1	.	.	.	.	.	.	.	.	.	.	G	15.96	2.986392	0.53934	.	.	ENSG00000185721	ENST00000331457	T	0.44482	0.92	5.49	5.49	0.81192	.	0.097640	0.64402	D	0.000001	T	0.40791	0.1131	L	0.56340	1.77	0.80722	D	1	B	0.15141	0.012	B	0.10450	0.005	T	0.23868	-1.0176	10	0.15952	T	0.53	-27.4646	18.7282	0.91722	0.0:0.0:1.0:0.0	.	60	Q9Y295	DRG1_HUMAN	S	60	ENSP00000329715:A60S	ENSP00000329715:A60S	A	+	1	0	DRG1	30129026	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.937000	0.92936	2.734000	0.93682	0.655000	0.94253	GCC	.	.		0.423	DRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075680.5	NM_004147		T	31799026	G	T	31799026	3	4	55	1	0	0	0	0	1	0	0	0	4763	1203	42	3	188	3	DRG1	22	31799026	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10		31799026	19505540	138	7046										
PHF5A	84844	hgsc.bcm.edu	37	chr22	41863491	41863491	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cactccttacaataataggcAtcagagaccccaggtcctcc	6	15	1	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr22:41863491A>G	ENST00000216252.3	-	3	275	c.204T>C	c.(202-204)gaT>gaC	p.D68D	ACO2_ENST00000216254.4_5'Flank|ACO2_ENST00000396512.3_5'Flank|PHF5A_ENST00000491254.1_5'UTR	NM_032758.3	NP_116147.1	Q7RTV0	PHF5A_HUMAN	PHD finger protein 5A	68					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of transcription, DNA-templated (GO:0045893)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|U12-type spliceosomal complex (GO:0005689)|U2 snRNP (GO:0005686)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(1)	4						AATAATAGGCATCAGAGACCC	0.493																																					p.D68D	Ovarian(15;130 571 1826 2981 46141)	Atlas-SNP	.											.	PHF5A	6	.	0			c.T204C						.						95	77	83					22																	41863491		2203	4300	6503	SO:0001819	synonymous_variant	84844	exon3			ATAGGCATCAGAG	BC007321	CCDS14016.1	22q13.2	2014-02-14			ENSG00000100410	ENSG00000100410		"Zinc fingers, PHD-type"	18000	protein-coding gene	gene with protein product	"splicing factor 3b, subunit 7"					12054543, 12234937, 18076038	Standard	NM_032758		Approved	MGC1346, SF3b14b, INI, bK223H9.2, Rds3, SAP14b, SF3B7	uc003bab.3	Q7RTV0	OTTHUMG00000150966	ENST00000216252.3:c.204T>C	chr22.hg19:g.41863491A>G		171.0	0.0		141.0	99.0	NM_032758	Q9UH06	Silent	SNP	ENST00000216252.3	hg19	CCDS14016.1																																																																																			.	.		0.493	PHF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320686.1	NM_032758		G	41863491	A	G	41863491	2	3	55	1	0	0	0	0	0	0	0	1	11846	214	8	2		2	PHF5A	22	41863491	Silent	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	10064465	41863491	9441075	139	7047										
CCDC134	79879	hgsc.bcm.edu	37	chr22	42209427	42209427	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	aggcgtcttcaaccaggggcCccactcgcccatcctcagcc	9	19	3	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chr22:42209427C>T	ENST00000255784.5	+	5	574	c.470C>T	c.(469-471)cCc>cTc	p.P157L	CCDC134_ENST00000402061.3_Intron	NM_024821.2	NP_079097.1	Q9H6E4	CC134_HUMAN	coiled-coil domain containing 134	157						extracellular region (GO:0005576)|membrane (GO:0016020)				large_intestine(1)|lung(2)|ovary(2)|skin(1)	6						AACCAGGGGCCCCACTCGCCC	0.577																																					p.P157L		Atlas-SNP	.											.	CCDC134	19	.	0			c.C470T						.						51	49	50					22																	42209427		2203	4300	6503	SO:0001583	missense	79879	exon5			AGGGGCCCCACTC	AL021453	CCDS33654.1	22q13.2	2010-12-24			ENSG00000100147	ENSG00000100147			26185	protein-coding gene	gene with protein product						18087676	Standard	NM_024821		Approved	FLJ22349	uc003bbh.1	Q9H6E4	OTTHUMG00000151262	ENST00000255784.5:c.470C>T	chr22.hg19:g.42209427C>T	ENSP00000255784:p.Pro157Leu	187.0	1.0		166.0	128.0	NM_024821		Missense_Mutation	SNP	ENST00000255784.5	hg19	CCDS33654.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.922042	0.52653	.	.	ENSG00000100147	ENST00000255784	.	.	.	5.51	4.44	0.53790	.	0.167589	0.52532	D	0.000063	T	0.57710	0.2072	L	0.50333	1.59	0.58432	D	0.999998	B	0.32467	0.372	B	0.30855	0.121	T	0.62737	-0.6791	9	0.56958	D	0.05	-18.8769	16.9734	0.86306	0.0:0.8728:0.1272:0.0	.	157	Q9H6E4	CC134_HUMAN	L	157	.	ENSP00000255784:P157L	P	+	2	0	CCDC134	40539373	0.955000	0.32602	1.000000	0.80357	0.346000	0.29079	5.626000	0.67777	2.746000	0.94184	0.655000	0.94253	CCC	.	.		0.577	CCDC134-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321964.1	NM_024821		T	42209427	C	T	42209427	3	4	55	1	0	0	0	0	1	0	0	0	2770	623	22	3	484	3	CCDC134	22	42209427	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	345936	42209427	9095139	140	7048										
EGFL6	25975	hgsc.bcm.edu	37	chrX	13645318	13645318	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gtaacaatgccctggcatggGagaagaccacgagtgaggat	14	8	0	3			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:13645318G>C	ENST00000361306.1	+	11	1731	c.1474G>C	c.(1474-1476)Gag>Cag	p.E492Q	EGFL6_ENST00000380602.3_Missense_Mutation_p.E493Q	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	492	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						CCTGGCATGGGAGAAGACCAC	0.438																																					p.E493Q		Atlas-SNP	.											.	EGFL6	111	.	0			c.G1477C						.						140	129	133					X																	13645318		2203	4300	6503	SO:0001583	missense	25975	exon11			GCATGGGAGAAGA	AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"MAM and EGF domain containing"	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.1474G>C	chrX.hg19:g.13645318G>C	ENSP00000355126:p.Glu492Gln	117.0	0.0		126.0	58.0	NM_001167890	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Missense_Mutation	SNP	ENST00000361306.1	hg19	CCDS14155.1	.	.	.	.	.	.	.	.	.	.	G	16.02	3.004762	0.54254	.	.	ENSG00000198759	ENST00000361306;ENST00000380602	T;T	0.02216	4.39;4.39	4.76	3.89	0.44902	Concanavalin A-like lectin/glucanase (1);MAM domain (2);	0.052439	0.64402	D	0.000001	T	0.09291	0.0229	M	0.62088	1.915	0.47547	D	0.999454	D;D	0.89917	0.996;1.0	D;D	0.91635	0.991;0.999	T	0.09952	-1.0651	10	0.33141	T	0.24	.	12.2856	0.54791	0.0852:0.0:0.9148:0.0	.	493;492	Q8IUX8-2;Q8IUX8	.;EGFL6_HUMAN	Q	492;493	ENSP00000355126:E492Q;ENSP00000369976:E493Q	ENSP00000355126:E492Q	E	+	1	0	EGFL6	13555239	1.000000	0.71417	0.977000	0.42913	0.775000	0.43874	5.076000	0.64413	0.805000	0.34159	0.544000	0.68410	GAG	.	.		0.438	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507		C	13645318	G	C	13645318	3	2	55	1	0	0	0	0	1	0	0	0	4965	1175	41	4	1519	4	EGFL6	23	13645318	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10		13645318	141625242	141	7049										
RAI2	10742	hgsc.bcm.edu	37	chrX	17819079	17819079	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cagggggaggctcggatttcCggtgggctgccactgacagg	18	10	0	1	rs140631545		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:17819079C>T	ENST00000545871.1	-	3	1512	c.1052G>A	c.(1051-1053)cGg>cAg	p.R351Q	RAI2_ENST00000415486.3_Missense_Mutation_p.R301Q|RAI2_ENST00000360011.1_Missense_Mutation_p.R351Q|RAI2_ENST00000331511.1_Missense_Mutation_p.R351Q|RAI2_ENST00000451717.1_Missense_Mutation_p.R351Q	NM_001172739.1|NM_001172743.1	NP_001166210|NP_001166214	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	351					embryo development (GO:0009790)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	22	Hepatocellular(33;0.183)					CTCGGATTTCCGGTGGGCTGC	0.552																																					p.R351Q		Atlas-SNP	.											.	RAI2	66	.	0			c.G1052A						.		GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,3835		0,0,1632,571	62	60	60		902,1052,1052,1052	5.3	1	X	dbSNP_134	60	1,6727		0,1,2427,1872	no	missense,missense,missense,missense	RAI2	NM_001172732.1,NM_001172739.1,NM_001172743.1,NM_021785.4	43,43,43,43	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	probably-damaging,probably-damaging,probably-damaging,probably-damaging	301/481,351/531,351/531,351/531	17819079	1,10562	2203	4300	6503	SO:0001583	missense	10742	exon3			GATTTCCGGTGGG	Z93242	CCDS14183.1, CCDS55374.1	Xp22	2008-02-05			ENSG00000131831	ENSG00000131831			9835	protein-coding gene	gene with protein product		300217				10049581, 10394933	Standard	NR_033348		Approved		uc010nfa.3	Q9Y5P3	OTTHUMG00000021209	ENST00000545871.1:c.1052G>A	chrX.hg19:g.17819079C>T	ENSP00000444210:p.Arg351Gln	132.0	0.0		149.0	12.0	NM_001172739	B1B1K2|B4DQM9|E7EMN4|Q8N6X7	Missense_Mutation	SNP	ENST00000545871.1	hg19	CCDS14183.1	.	.	.	.	.	.	.	.	.	.	c	18.38	3.611504	0.66558	0.0	1.49E-4	ENSG00000131831	ENST00000331511;ENST00000360011;ENST00000545871;ENST00000451717;ENST00000415486	T;T;T;T;T	0.38077	1.18;1.18;1.18;1.18;1.16	5.29	5.29	0.74685	.	0.074690	0.49305	D	0.000142	T	0.54532	0.1864	L	0.55481	1.735	0.37167	D	0.902861	D;D	0.89917	1.0;1.0	D;D	0.66847	0.947;0.947	T	0.62364	-0.6870	10	0.72032	D	0.01	-24.2176	15.8108	0.78561	0.0:1.0:0.0:0.0	.	301;351	E7EMN4;Q9Y5P3	.;RAI2_HUMAN	Q	351;351;351;351;301	ENSP00000333456:R351Q;ENSP00000353106:R351Q;ENSP00000444210:R351Q;ENSP00000401323:R351Q;ENSP00000392578:R301Q	ENSP00000333456:R351Q	R	-	2	0	RAI2	17729000	0.979000	0.34478	0.999000	0.59377	0.942000	0.58702	2.626000	0.46460	2.457000	0.83068	0.597000	0.82753	CGG	.	C|1.000;T|0.000		0.552	RAI2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055937.1	NM_021785		T	17819079	C	T	17819079	3	4	55	1	0	0	0	0	1	0	0	0	13024	652	23	1	544	1	RAI2	23	17819079	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	4173761	17819079	137451481	142	7050										
MAGEB18	286514	hgsc.bcm.edu	37	chrX	26157856	26157856	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ccaaagatttggtgcagctaAagtacctggagtaccagcaa	10	9	0	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:26157856A>T	ENST00000325250.1	+	2	941	c.754A>T	c.(754-756)Aag>Tag	p.K252*		NM_173699.3	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	252	Interaction with LNX1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(17)|skin(2)|stomach(1)|urinary_tract(2)	33						GGTGCAGCTAAAGTACCTGGA	0.478																																					p.K252X		Atlas-SNP	.											.	MAGEB18	67	.	0			c.A754T						.						75	66	69					X																	26157856		2202	4300	6502	SO:0001587	stop_gained	286514	exon2			CAGCTAAAGTACC	AK057361	CCDS14216.1	Xp21.3	2008-02-05			ENSG00000176774	ENSG00000176774			28515	protein-coding gene	gene with protein product							Standard	NM_173699		Approved	MGC33889	uc004dbq.2	Q96M61	OTTHUMG00000021282	ENST00000325250.1:c.754A>T	chrX.hg19:g.26157856A>T	ENSP00000314543:p.Lys252*	245.0	0.0		251.0	79.0	NM_173699		Nonsense_Mutation	SNP	ENST00000325250.1	hg19	CCDS14216.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.655368	0.88056	.	.	ENSG00000176774	ENST00000325250	.	.	.	4.56	2.12	0.27331	.	0.218142	0.46442	D	0.000281	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.9674	0.09437	0.6776:0.2115:0.1109:0.0	.	.	.	.	X	252	.	ENSP00000314543:K252X	K	+	1	0	MAGEB18	26067777	0.512000	0.26186	0.007000	0.13788	0.631000	0.37964	1.631000	0.37092	0.326000	0.23384	0.486000	0.48141	AAG	.	.		0.478	MAGEB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056120.1	NM_173699		T	26157856	A	T	26157856	4	4	55	1	0	0	0	0	0	1	0	0	9184	15	1	4	756	4	MAGEB18	23	26157856	Nonsense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	8338777	26157856	129112704	143	7051										
BCOR	54880	hgsc.bcm.edu	37	chrX	39922123	39922123	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	gcttctcgctgttgtcggtgTatttctgcagcagggaggca	14	9	2	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:39922123T>A	ENST00000378444.4	-	9	4277	c.4049A>T	c.(4048-4050)tAc>tTc	p.Y1350F	BCOR_ENST00000342274.4_Missense_Mutation_p.Y1316F|BCOR_ENST00000378463.1_Missense_Mutation_p.Y193F|BCOR_ENST00000397354.3_Missense_Mutation_p.Y1316F|BCOR_ENST00000378455.4_Missense_Mutation_p.Y1298F	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1350					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GTTGTCGGTGTATTTCTGCAG	0.527			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.Y1350F		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.A4049T						.						128	100	109					X																	39922123		2202	4300	6502	SO:0001583	missense	54880	exon9			TCGGTGTATTTCT	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.4049A>T	chrX.hg19:g.39922123T>A	ENSP00000367705:p.Tyr1350Phe	373.0	1.0		341.0	118.0	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	hg19	CCDS48093.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.61|13.61	2.289061|2.289061	0.40494|0.40494	.|.	.|.	ENSG00000183337|ENSG00000183337	ENST00000427012|ENST00000413905;ENST00000378463;ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000442018	.|T;T;T;T;T;T;T	.|0.70164	.|-0.41;0.98;1.04;1.01;1.01;1.01;-0.46	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	.|.	.|.	.|.	.|.	T|T	0.52208|0.52208	0.1720|0.1720	N|N	0.19112|0.19112	0.55|0.55	0.43457|0.43457	D|D	0.995655|0.995655	.|B;B;B	.|0.16166	.|0.007;0.016;0.016	.|B;B;B	.|0.15484	.|0.013;0.006;0.013	T|T	0.48281|0.48281	-0.9049|-0.9049	5|9	.|0.37606	.|T	.|0.19	-14.861|-14.861	14.0817|14.0817	0.64929|0.64929	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1298;1350;1316	.|Q6W2J9-4;Q6W2J9;Q6W2J9-2	.|.;BCOR_HUMAN;.	S|F	45|220;193;1298;1316;1350;1316;23	.|ENSP00000408006:Y220F;ENSP00000367724:Y193F;ENSP00000367716:Y1298F;ENSP00000380512:Y1316F;ENSP00000367705:Y1350F;ENSP00000345923:Y1316F;ENSP00000387552:Y23F	.|ENSP00000345923:Y1316F	T|Y	-|-	1|2	0|0	BCOR|BCOR	39807067|39807067	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.923000|0.923000	0.55619|0.55619	1.531000|1.531000	0.36018|0.36018	1.900000|1.900000	0.55004|0.55004	0.486000|0.486000	0.48141|0.48141	ACA|TAC	.	.		0.527	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		A	39922123	T	A	39922123	3	1	55	1	0	0	0	0	1	0	0	0	1386	1638	57	4	1246	4	BCOR	23	39922123	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	13764267	39922123	115348437	144	7052										
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49126933	49126933	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	acccagcgcgctacgtcccgCgcagcccgccgtgggcagga	14	18	0	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:49126933C>T	ENST00000055335.6	+	1	617	c.601C>T	c.(601-603)Cgc>Tgc	p.R201C	PPP1R3F_ENST00000438316.1_Intron|PPP1R3F_ENST00000495799.1_Intron|PPP1R3F_ENST00000466508.1_Intron|LL0XNC01-7P3.1_ENST00000602455.1_lincRNA	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	201	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CTACGTCCCGCGCAGCCCGCC	0.711																																					p.R201C		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.C601T						.						9	9	9					X																	49126933		2081	4086	6167	SO:0001583	missense	89801	exon1			GTCCCGCGCAGCC		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14944	protein-coding gene	gene with protein product			"protein phosphatase 1, regulatory (inhibitor) subunit 3F"			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.601C>T	chrX.hg19:g.49126933C>T	ENSP00000055335:p.Arg201Cys	28.0	0.0		36.0	14.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	hg19	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	c	16.97	3.268552	0.59540	.	.	ENSG00000049769	ENST00000055335	T	0.56776	0.44	3.68	2.7	0.31948	Putative phosphatase regulatory subunit (2);	0.000000	0.37219	N	0.002193	T	0.52256	0.1723	N	0.17082	0.46	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.56667	-0.7941	10	0.72032	D	0.01	-7.7459	9.6531	0.39910	0.0:0.7885:0.2115:0.0	.	201	Q6ZSY5	PPR3F_HUMAN	C	201	ENSP00000055335:R201C	ENSP00000055335:R201C	R	+	1	0	PPP1R3F	49013877	0.998000	0.40836	1.000000	0.80357	0.899000	0.52679	0.676000	0.25247	1.779000	0.52309	0.525000	0.51046	CGC	.	.		0.711	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		T	49126933	C	T	49126933	3	4	55	1	0	0	0	0	1	0	0	0	12387	768	27	1	603	1	PPP1R3F	23	49126933	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	9204810	49126933	106143627	145	7053										
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54780134	54780134	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agtccccagggtgcccattcAgtgtgaagcagatcttctct	10	12	3	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:54780134A>T	ENST00000218436.6	-	11	3331	c.3302T>A	c.(3301-3303)cTg>cAg	p.L1101Q		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1101					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										GTGCCCATTCAGTGTGAAGCA	0.498																																					p.L1101Q		Atlas-SNP	.											.	.	.	.	0			c.T3302A						.						109	90	96					X																	54780134		2203	4300	6503	SO:0001583	missense	347365	exon11			CCATTCAGTGTGA	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3302T>A	chrX.hg19:g.54780134A>T	ENSP00000218436:p.Leu1101Gln	145.0	0.0		168.0	82.0	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	hg19	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	A	11.65	1.702214	0.30232	.	.	ENSG00000102313	ENST00000218436	T	0.02682	4.2	3.25	3.25	0.37280	.	1.157720	0.06647	U	0.762144	T	0.06096	0.0158	L	0.34521	1.04	0.09310	N	1	D	0.55385	0.971	P	0.51355	0.667	T	0.48636	-0.9018	10	0.87932	D	0	.	10.1393	0.42725	1.0:0.0:0.0:0.0	.	1101	Q6UXX5	ITH5L_HUMAN	Q	1101	ENSP00000218436:L1101Q	ENSP00000218436:L1101Q	L	-	2	0	ITIH5L	54796859	0.510000	0.26171	0.381000	0.26106	0.439000	0.31926	6.608000	0.74168	0.984000	0.38629	0.341000	0.21757	CTG	.	.		0.498	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		T	54780134	A	T	54780134	3	4	55	1	0	0	0	0	1	0	0	0	7917	188	7	4	651	4	ITIH5L	23	54780134	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	5653201	54780134	100490426	146	7054										
ZMYM3	9203	hgsc.bcm.edu	37	chrX	70467743	70467743	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ttagtgaagtcctgtttgtaCagcagcacacagcctggaaa	10	9	0	1	rs200745411		TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:70467743C>T	ENST00000353904.2	-	12	2176	c.1989G>A	c.(1987-1989)ctG>ctA	p.L663L	ZMYM3_ENST00000314425.5_Silent_p.L663L|ZMYM3_ENST00000373988.1_Silent_p.L665L|ZMYM3_ENST00000489332.1_5'UTR|ZMYM3_ENST00000373984.3_Silent_p.L665L|ZMYM3_ENST00000373998.1_Silent_p.L663L	NM_005096.3	NP_005087.1	Q14202	ZMYM3_HUMAN	zinc finger, MYM-type 3	663					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(7)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(17)|ovary(1)|prostate(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(35;0.156)					CCTGTTTGTACAGCAGCACAC	0.517																																					p.L663L		Atlas-SNP	.											.	ZMYM3	137	.	0			c.G1989A						.						53	38	43					X																	70467743		2203	4299	6502	SO:0001819	synonymous_variant	9203	exon12			TTTGTACAGCAGC	AB002383	CCDS14409.1, CCDS55443.1, CCDS55444.1	Xq13.1	2013-01-08	2005-12-19	2005-12-19	ENSG00000147130	ENSG00000147130		"Zinc fingers, MYM type"	13054	protein-coding gene	gene with protein product		300061	"zinc finger protein 261"	ZNF261		10486218	Standard	NM_201599		Approved	ZNF198L2, DXS6673E, KIAA0385, MYM	uc004dzh.2	Q14202	OTTHUMG00000021799	ENST00000353904.2:c.1989G>A	chrX.hg19:g.70467743C>T		190.0	0.0		204.0	67.0	NM_005096	D3DVV3|O15089|Q96E26	Silent	SNP	ENST00000353904.2	hg19	CCDS14409.1																																																																																			.	.		0.517	ZMYM3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057154.1	NM_201599		T	70467743	C	T	70467743	2	4	55	1	0	0	0	0	0	0	0	1	17716	465	17	3		3	ZMYM3	23	70467743	Silent	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	15687609	70467743	84802817	147	7055										
TAF1	6872	hgsc.bcm.edu	37	chrX	70617219	70617219	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tttatcgcacgtttcgagatGaagaggggaaagagtatgtt	13	4	0	4			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:70617219G>A	ENST00000373790.4	+	23	3571	c.3520G>A	c.(3520-3522)Gaa>Aaa	p.E1174K	TAF1_ENST00000276072.3_Missense_Mutation_p.E1195K|TAF1_ENST00000423759.1_Missense_Mutation_p.E1195K|TAF1_ENST00000449580.1_Missense_Mutation_p.E1174K	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1174					cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GTTTCGAGATGAAGAGGGGAA	0.468																																					p.E1195K		Atlas-SNP	.											.	TAF1	439	.	0			c.G3583A						.						185	130	149					X																	70617219		2203	4300	6503	SO:0001583	missense	6872	exon23			CGAGATGAAGAGG		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.3520G>A	chrX.hg19:g.70617219G>A	ENSP00000362895:p.Glu1174Lys	520.0	1.0		569.0	217.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	25.2|25.2	4.613278|4.613278	0.87359|0.87359	.|.	.|.	ENSG00000147133|ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072|ENST00000483985	T;T;T;T|.	0.18174|.	2.23;2.23;2.23;2.23|.	4.91|4.91	4.91|4.91	0.64330|0.64330	.|.	0.193008|.	0.53938|.	D|.	0.000054|.	T|T	0.68933|0.68933	0.3055|0.3055	L|L	0.49571|0.49571	1.57|1.57	0.80722|0.80722	D|D	1|1	B;P;P|.	0.45348|.	0.029;0.774;0.856|.	B;B;P|.	0.47645|.	0.096;0.351;0.553|.	T|T	0.66709|0.66709	-0.5855|-0.5855	10|5	0.10902|.	T|.	0.67|.	.|.	17.5217|17.5217	0.87789|0.87789	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1174;1174;1195|.	P21675-4;P21675;P21675-2|.	.;TAF1_HUMAN;.|.	K|I	1174;1174;1195;1195|84	ENSP00000362895:E1174K;ENSP00000389000:E1174K;ENSP00000406549:E1195K;ENSP00000276072:E1195K|.	ENSP00000276072:E1195K|.	E|M	+|+	1|3	0|0	TAF1|TAF1	70533944|70533944	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.198000|9.198000	0.94994|0.94994	2.322000|2.322000	0.78497|0.78497	0.449000|0.449000	0.29647|0.29647	GAA|ATG	.	.		0.468	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70617219	G	A	70617219	3	1	55	1	0	0	0	0	1	0	0	0	15528	1291	45	3	3673	3	TAF1	23	70617219	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	149476	70617219	84653341	148	7056										
ATP7A	538	hgsc.bcm.edu	37	chrX	77244075	77244075	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	cagtttagatactgggacacTggagaaaaagtcaggagctt	12	6	1	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:77244075T>C	ENST00000341514.6	+	3	613	c.458T>C	c.(457-459)cTg>cCg	p.L153P	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Missense_Mutation_p.L153P	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	153					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ACTGGGACACTGGAGAAAAAG	0.433																																					p.L153P		Atlas-SNP	.											.	ATP7A	248	.	0			c.T458C						.						118	115	116					X																	77244075		2203	4295	6498	SO:0001583	missense	538	exon3			GGACACTGGAGAA	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.458T>C	chrX.hg19:g.77244075T>C	ENSP00000345728:p.Leu153Pro	199.0	0.0		237.0	89.0	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	hg19	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	T	4.813	0.151205	0.09185	.	.	ENSG00000165240	ENST00000343533;ENST00000341514;ENST00000400860;ENST00000355691	D;D	0.96232	-3.94;-3.95	5.21	2.77	0.32553	.	0.564178	0.17117	N	0.186409	D	0.86518	0.5952	N	0.04880	-0.145	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.74957	-0.3487	10	0.31617	T	0.26	-14.8364	0.1137	0.00058	0.2617:0.2487:0.2365:0.2531	.	153;163	Q04656;Q59HD1	ATP7A_HUMAN;.	P	153;153;153;163	ENSP00000343026:L153P;ENSP00000345728:L153P	ENSP00000345728:L153P	L	+	2	0	ATP7A	77130731	0.094000	0.21725	0.961000	0.40146	0.769000	0.43574	0.391000	0.20784	0.611000	0.30052	0.486000	0.48141	CTG	.	.		0.433	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		C	77244075	T	C	77244075	3	2	55	1	0	0	0	0	1	0	0	0	1190	1580	55	2	464	2	ATP7A	23	77244075	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	6626856	77244075	78026485	149	7057										
RPS6KA6	27330	hgsc.bcm.edu	37	chrX	83389790	83389790	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	taataagaaaatctgcatacCtgttaatttgatatgtccta	5	6	1	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:83389790C>T	ENST00000262752.2	-	8	653	c.646G>A	c.(646-648)Gat>Aat	p.D216N	RPS6KA6_ENST00000543399.1_Splice_Site_p.D216N	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	216	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						ATCTGCATACCTGTTAATTTG	0.239																																					p.D216N		Atlas-SNP	.											.	RPS6KA6	116	.	0			c.G646A						.						37	36	36					X																	83389790		2181	4236	6417	SO:0001630	splice_region_variant	27330	exon8			GCATACCTGTTAA	AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.646+1G>A	chrX.hg19:g.83389790C>T		109.0	0.0		144.0	47.0	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	hg19	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.108502	0.77096	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	D;D	0.92965	-3.14;-3.14	4.62	3.73	0.42828	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97359	0.9136	H	0.97465	4.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.97620	1.0135	9	.	.	.	.	13.2717	0.60164	0.1599:0.8401:0.0:0.0	.	216;216	B7ZL90;Q9UK32	.;KS6A6_HUMAN	N	216	ENSP00000262752:D216N;ENSP00000440830:D216N	.	D	-	1	0	RPS6KA6	83276446	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	5.358000	0.66064	0.714000	0.32081	0.523000	0.50628	GAT	.	.		0.239	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496	Missense_Mutation	T	83389790	C	T	83389790	5	4	55	1	0	0	0	0	0	0	1	0	13670	695	24	3	1651	3	RPS6KA6	23	83389790	Splice_Site	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	6145715	83389790	71880770	150	7058										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86873049	86873049	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tctcataaagcagctccatcCttcaaactgcttagggattc	6	12	2	0			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:86873049C>A	ENST00000373119.4	+	4	987	c.842C>A	c.(841-843)cCt>cAt	p.P281H	KLHL4_ENST00000373114.4_Missense_Mutation_p.P281H	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	281						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.P281H(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						CAGCTCCATCCTTCAAACTGC	0.423																																					p.P281H		Atlas-SNP	.											.	KLHL4	263	.	1	Substitution - Missense(1)	ovary(1)	c.C842A						.						106	87	93					X																	86873049		2203	4300	6503	SO:0001583	missense	56062	exon4			TCCATCCTTCAAA	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.842C>A	chrX.hg19:g.86873049C>A	ENSP00000362211:p.Pro281His	335.0	0.0		343.0	155.0	NM_019117	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	hg19	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.356767	0.82243	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.77358	-1.09;-1.06	4.74	4.74	0.60224	.	0.061530	0.64402	D	0.000003	D	0.89753	0.6806	M	0.89715	3.055	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.72075	0.946;0.976	D	0.92014	0.5620	10	0.66056	D	0.02	.	15.9642	0.79952	0.0:1.0:0.0:0.0	.	281;281	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	H	281	ENSP00000362211:P281H;ENSP00000362206:P281H	ENSP00000362206:P281H	P	+	2	0	KLHL4	86759705	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.243000	0.78219	1.960000	0.56953	0.502000	0.49764	CCT	.	.		0.423	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			A	86873049	C	A	86873049	3	1	55	1	0	0	0	0	1	0	0	0	8400	681	24	3	856	3	KLHL4	23	86873049	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	3483259	86873049	68397511	151	7059										
ARMCX3	51566	hgsc.bcm.edu	37	chrX	100880696	100880696	+	Frame_Shift_Del	DEL	A	A	-													0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	agtatcagcacatgcttgctAattccatttctgactttttt							TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:100880696delA	ENST00000341189.4	+	5	1593	c.727delA	c.(727-729)aatfs	p.N243fs	ARMCX3_ENST00000537169.1_Frame_Shift_Del_p.N243fs|ARMCX3_ENST00000471229.2_Frame_Shift_Del_p.N243fs|ARMCX3-AS1_ENST00000454228.1_RNA|RP4-545K15.5_ENST00000564612.1_RNA	NM_016607.3	NP_057691.1	Q9UH62	ARMX3_HUMAN	armadillo repeat containing, X-linked 3	243					cellular protein localization (GO:0034613)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of mitochondrial outer membrane (GO:0031307)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11						CATGCTTGCTAATTCCATTTC	0.388																																					p.A242fs		Atlas-Indel,Pindel	.											.	ARMCX3	33	.	0			c.726delT						.						92	81	85					X																	100880696		2203	4300	6503	SO:0001589	frameshift_variant	51566	exon5			.	AY359079	CCDS14489.1	Xq22.1	2014-03-21			ENSG00000102401	ENSG00000102401		"Armadillo repeat containing"	24065	protein-coding gene	gene with protein product		300364				11162520, 11042152, 19304657, 16221301, 22569362	Standard	NM_016607		Approved	ALEX3, GASP6	uc004eia.1	Q9UH62	OTTHUMG00000022035	ENST00000341189.4:c.727delA	chrX.hg19:g.100880696delA	ENSP00000340672:p.Asn243fs	160.0	0.0		175.0	89.0	NM_177948	Q53HC6|Q7LCF5|Q9NPE4	Frame_Shift_Del	DEL	ENST00000341189.4	hg19	CCDS14489.1																																																																																			.	.		0.388	ARMCX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057568.2	NM_016607		-	100880696	A	-	100880696	7	5	55	1	0	1	0	1	0	0	0	0	961	362	13	0	729	0	ARMCX3	23	100880696	Frame_Shift_Del	DEL	A	TCGA-CC-5259-01A-31D-A20W-10	14007647	100880696	54389864	152	7060										
SAGE1	55511	hgsc.bcm.edu	37	chrX	134989876	134989876	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	ccagatgctaccatcactcaCaatgtctgtgaagagagagt	9	10	3	4			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:134989876C>A	ENST00000370709.3	+	9	1035	c.1035C>A	c.(1033-1035)caC>caA	p.H345Q	SAGE1_ENST00000324447.3_Missense_Mutation_p.H345Q|SAGE1_ENST00000537770.1_Intron|SAGE1_ENST00000535938.1_Missense_Mutation_p.H345Q			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	345						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					CCATCACTCACAATGTCTGTG	0.448																																					p.H345Q		Atlas-SNP	.											.	SAGE1	160	.	0			c.C1035A						.						117	92	100					X																	134989876		2203	4300	6503	SO:0001583	missense	55511	exon10			CACTCACAATGTC	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.1035C>A	chrX.hg19:g.134989876C>A	ENSP00000359743:p.His345Gln	215.0	0.0		235.0	97.0	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	hg19	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	C	0.038	-1.297685	0.01364	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000370709	T;T;T	0.35236	1.32;1.32;1.32	1.53	-1.46	0.08800	.	.	.	.	.	T	0.12732	0.0309	N	0.04880	-0.145	0.09310	N	1	B	0.14012	0.009	B	0.04013	0.001	T	0.31280	-0.9949	9	0.07813	T	0.8	.	4.6613	0.12643	0.0:0.3751:0.0:0.6249	.	345	Q9NXZ1	SAGE1_HUMAN	Q	345	ENSP00000323191:H345Q;ENSP00000445959:H345Q;ENSP00000359743:H345Q	ENSP00000323191:H345Q	H	+	3	2	SAGE1	134817542	0.000000	0.05858	0.002000	0.10522	0.064000	0.16182	-2.065000	0.01386	-0.570000	0.06022	0.149000	0.16113	CAC	.	.		0.448	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		A	134989876	C	A	134989876	3	1	55	1	0	0	0	0	1	0	0	0	13824	477	17	3	1069	3	SAGE1	23	134989876	Missense_Mutation	SNP	C	TCGA-CC-5259-01A-31D-A20W-10	34109180	134989876	20280684	153	7061										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140983104	140983104	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tgtgctttcccgacttgcacTgtgggagtctgaaggacctg	13	10	1	1			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:140983104T>C	ENST00000298296.1	+	5	959	c.959T>C	c.(958-960)cTg>cCg	p.L320P	MAGEC3_ENST00000544766.1_5'UTR|MAGEC3_ENST00000483584.1_3'UTR|MAGEC3_ENST00000448920.1_Missense_Mutation_p.L72P|MAGEC3_ENST00000443323.2_Intron|MAGEC3_ENST00000536088.1_Intron|MAGEC3_ENST00000409007.1_5'Flank	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	320	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					CGACTTGCACTGTGGGAGTCT	0.592																																					p.L320P		Atlas-SNP	.											.	MAGEC3	228	.	0			c.T959C						.						123	112	116					X																	140983104		2203	4300	6503	SO:0001583	missense	139081	exon5			TTGCACTGTGGGA	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.959T>C	chrX.hg19:g.140983104T>C	ENSP00000298296:p.Leu320Pro	329.0	1.0		337.0	132.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	hg19	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	N	0.095	-1.160694	0.01686	.	.	ENSG00000165509	ENST00000298296;ENST00000448920	T;T	0.48522	3.59;0.81	0.688	-1.38	0.09027	.	.	.	.	.	T	0.20740	0.0499	N	0.03608	-0.345	0.19300	N	0.999976	B	0.09022	0.002	B	0.01281	0.0	T	0.16070	-1.0415	8	0.87932	D	0	.	.	.	.	.	320	Q8TD91	MAGC3_HUMAN	P	320;72	ENSP00000298296:L320P;ENSP00000395092:L72P	ENSP00000298296:L320P	L	+	2	0	MAGEC3	140810770	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.873000	0.01637	-0.401000	0.07644	-0.632000	0.03989	CTG	.	.		0.592	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		C	140983104	T	C	140983104	3	2	55	1	0	0	0	0	1	0	0	0	9191	1580	55	2	977	2	MAGEC3	23	140983104	Missense_Mutation	SNP	T	TCGA-CC-5259-01A-31D-A20W-10	5993228	140983104	14287456	154	7062										
CNGA2	1260	hgsc.bcm.edu	37	chrX	150912895	150912895	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	acagttctggaaaccaagatGaaacagaacaatgaagatga	9	6	1	6			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:150912895G>T	ENST00000329903.4	+	6	1953	c.1920G>T	c.(1918-1920)atG>atT	p.M640I		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	640					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					AAACCAAGATGAAACAGAACA	0.552																																					p.M640I		Atlas-SNP	.											.	CNGA2	136	.	0			c.G1920T						.						97	85	89					X																	150912895		2203	4300	6503	SO:0001583	missense	1260	exon7			CAAGATGAAACAG	S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.1920G>T	chrX.hg19:g.150912895G>T	ENSP00000328478:p.Met640Ile	124.0	0.0		111.0	8.0	NM_005140	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	hg19	CCDS14701.1	.	.	.	.	.	.	.	.	.	.	G	9.999	1.232890	0.22626	.	.	ENSG00000183862	ENST00000329903	D	0.97016	-4.21	5.5	5.5	0.81552	.	0.158195	0.64402	D	0.000018	D	0.92848	0.7725	L	0.40543	1.245	0.30921	N	0.727989	B	0.02656	0.0	B	0.01281	0.0	D	0.89095	0.3485	10	0.36615	T	0.2	.	10.8688	0.46870	0.0:0.0:0.8122:0.1878	.	640	Q16280	CNGA2_HUMAN	I	640	ENSP00000328478:M640I	ENSP00000328478:M640I	M	+	3	0	CNGA2	150663551	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	2.963000	0.49184	2.297000	0.77311	0.529000	0.55759	ATG	.	.		0.552	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		T	150912895	G	T	150912895	3	4	55	1	0	0	0	0	1	0	0	0	3599	1290	45	3	1942	3	CNGA2	23	150912895	Missense_Mutation	SNP	G	TCGA-CC-5259-01A-31D-A20W-10	9929791	150912895	4357665	155	7063										
NSDHL	50814	hgsc.bcm.edu	37	chrX	152018893	152018893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0326797385620915	5	1	0.816723250465447	1.15597752373571	0.683077627662011	1	1	0	tggcaagaggatatgctgtcAatgtatttgatatccagcaa	10	6	1	2			TCGA-CC-5259-01A-31D-A20W-10	TCGA-CC-5259-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e2280d-a133-4737-b089-f4aab5b894a3	17b4c09e-50c8-408e-999f-5b31e55417fe	g.chrX:152018893A>G	ENST00000370274.3	+	3	387	c.193A>G	c.(193-195)Aat>Gat	p.N65D	NSDHL_ENST00000440023.1_Missense_Mutation_p.N65D	NM_015922.2	NP_057006.1	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	65					cholesterol biosynthetic process (GO:0006695)|hair follicle development (GO:0001942)|labyrinthine layer blood vessel development (GO:0060716)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity (GO:0047012)			NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(5)	15	Acute lymphoblastic leukemia(192;6.56e-05)					ATATGCTGTCAATGTATTTGA	0.527																																					p.N65D		Atlas-SNP	.											.	NSDHL	33	.	0			c.A193G						.						237	215	223					X																	152018893		2203	4300	6503	SO:0001583	missense	50814	exon3			GCTGTCAATGTAT	X96621	CCDS14717.1	Xq28	2011-09-14			ENSG00000147383	ENSG00000147383	1.1.1.170	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	13398	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 31E, member 1"	300275				10710235, 12837764, 19027726	Standard	NM_015922		Approved	XAP104, H105e3, SDR31E1	uc004fgs.1	Q15738	OTTHUMG00000024185	ENST00000370274.3:c.193A>G	chrX.hg19:g.152018893A>G	ENSP00000359297:p.Asn65Asp	240.0	0.0		229.0	102.0	NM_015922	D3DWT6|O00344	Missense_Mutation	SNP	ENST00000370274.3	hg19	CCDS14717.1	.	.	.	.	.	.	.	.	.	.	a	14.18	2.458422	0.43634	.	.	ENSG00000147383	ENST00000370274;ENST00000440023;ENST00000432467	D;D;D	0.84223	-1.82;-1.82;-1.82	5.51	5.51	0.81932	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.141053	0.64402	D	0.000008	D	0.87051	0.6081	L	0.57536	1.79	0.41478	D	0.988143	D	0.55172	0.97	P	0.53401	0.725	D	0.86723	0.1943	10	0.40728	T	0.16	1.7125	12.4744	0.55805	1.0:0.0:0.0:0.0	.	65	Q15738	NSDHL_HUMAN	D	65	ENSP00000359297:N65D;ENSP00000391854:N65D;ENSP00000396266:N65D	ENSP00000359297:N65D	N	+	1	0	NSDHL	151769549	1.000000	0.71417	0.805000	0.32314	0.414000	0.31173	4.393000	0.59665	1.852000	0.53769	0.433000	0.28618	AAT	.	.		0.527	NSDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060927.1	NM_015922		G	152018893	A	G	152018893	3	3	55	1	0	0	0	0	1	0	0	0	10679	130	5	2	199	2	NSDHL	23	152018893	Missense_Mutation	SNP	A	TCGA-CC-5259-01A-31D-A20W-10	1105998	152018893	3251667	156	7064										
MACF1	23499	hgsc.bcm.edu	37	chr1	39907974	39907974	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ctctgggagaacctgggtgaGaaaattgcccaccgacaggt	13	10	1	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr1:39907974G>T	ENST00000372915.3	+	75	18714	c.18627G>T	c.(18625-18627)gaG>gaT	p.E6209D	MACF1_ENST00000567887.1_Missense_Mutation_p.E6347D|MACF1_ENST00000539005.1_Missense_Mutation_p.E4121D|MACF1_ENST00000564288.1_Missense_Mutation_p.E6310D|MACF1_ENST00000289893.4_Missense_Mutation_p.E4753D|MACF1_ENST00000545844.1_Missense_Mutation_p.E4251D|MACF1_ENST00000317713.7_Missense_Mutation_p.E4251D|MACF1_ENST00000361689.2_Missense_Mutation_p.E4251D			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6209					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACCTGGGTGAGAAAATTGCCC	0.438																																					p.E4251D		Atlas-SNP	.											.	MACF1	909	.	0			c.G12753T						.						46	48	47					1																	39907974		2203	4300	6503	SO:0001583	missense	23499	exon73			GGGTGAGAAAATT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18627G>T	chr1.hg19:g.39907974G>T	ENSP00000362006:p.Glu6209Asp	128.0	0.0		123.0	39.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.61|12.61	1.989737|1.989737	0.35131|0.35131	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.53640|.	0.61;0.61;0.61;0.61;0.61;0.61|.	6.03|6.03	0.646|0.646	0.17789|0.17789	.|.	0.090504|0.090504	0.47852|0.47852	D|D	0.000217|0.000217	T|.	0.26448|.	0.0646|.	N|N	0.11927|0.11927	0.2|0.2	0.80722|0.80722	D|D	1|1	B;B|.	0.32800|.	0.27;0.385|.	B;B|.	0.38842|.	0.241;0.283|.	T|.	0.09335|.	-1.0679|.	10|.	0.34782|0.07175	T|T	0.22|0.84	.|.	6.3831|6.3831	0.21546|0.21546	0.4178:0.1188:0.4634:0.0|0.4178:0.1188:0.4634:0.0	.|.	6209;4251|.	Q9UPN3;F8W8Q1|.	MACF1_HUMAN;.|.	D|X	4251;6209;4251;4251;4121;4753|3255	ENSP00000439537:E4251D;ENSP00000362006:E6209D;ENSP00000354573:E4251D;ENSP00000313438:E4251D;ENSP00000444364:E4121D;ENSP00000289893:E4753D|.	ENSP00000289893:E4753D|ENSP00000362016:E3255X	E|E	+|+	3|1	2|0	MACF1|MACF1	39680561|39680561	0.969000|0.969000	0.33509|0.33509	0.995000|0.995000	0.50966|0.50966	0.993000|0.993000	0.82548|0.82548	0.116000|0.116000	0.15561|0.15561	-0.132000|-0.132000	0.11557|0.11557	0.655000|0.655000	0.94253|0.94253	GAG|GAA	.	.		0.438	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39907974	G	T	39907974	3	4	56	1	0	0	0	0	1	0	0	0	9153	933	33	3	19190	3	MACF1	1	39907974	Missense_Mutation	SNP	G	TCGA-CC-5260-01A-01D-A12Z-10		39907974	209342647	1	7065										
C1orf83	127428	hgsc.bcm.edu	37	chr1	54520147	54520148	+	Frame_Shift_Ins	INS	-	-	T													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ccagaatagccctcagaagaINSaagattctggaggaaaggtt							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr1:54520147_54520148insT	ENST00000234827.1	+	2	252_253	c.52_53insT	c.(52-54)aaafs	p.K18fs	TCEANC2_ENST00000371331.1_Frame_Shift_Ins_p.K48fs|TMEM59_ENST00000234831.5_5'Flank|TCEANC2_ENST00000498272.1_3'UTR|TMEM59_ENST00000371337.3_5'Flank|TMEM59_ENST00000371341.1_5'Flank|MIR4781_ENST00000585250.1_RNA	NM_153035.1	NP_694580.1	Q96MN5	TEAN2_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing 2	18					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|lung(3)|pancreas(1)	5						CCCTCAGAAGAAAGATTCTGGA	0.485																																					p.K18fs		Atlas-Indel,Pindel	.											.	TCEANC2	17	.	0			c.52_53insT						.																																			SO:0001589	frameshift_variant	127428	exon2			.	AK056674	CCDS587.1	1p32.3	2011-01-25	2011-01-25	2011-01-25	ENSG00000116205	ENSG00000116205			26494	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 83"	C1orf83		12477932	Standard	NM_153035		Approved	FLJ32112	uc001cwt.1	Q96MN5	OTTHUMG00000008434	Exception_encountered	chr1.hg19:g.54520147_54520148insT	ENSP00000234827:p.Lys18fs	110.0	0.0		151.0	43.0	NM_153035	Q5T702|Q8N8N2	Frame_Shift_Ins	INS	ENST00000234827.1	hg19	CCDS587.1																																																																																			.	.		0.485	TCEANC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023245.1	NM_153035		T	54520148	-	T	54520147	7	5	56	1	0	1	1	0	0	0	0	0	2062	247	9	0	54	0	C1orf83	1	54520147	Frame_Shift_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10	14612173	54520147	194730474	2	7066										
STXBP3	6814	hgsc.bcm.edu	37	chr1	109339272	109339272	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	agaaaatttggacaggttgaTccagaatgtaaagatagaaa	10	3	0	5			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr1:109339272T>A	ENST00000370008.3	+	15	1330	c.1280T>A	c.(1279-1281)aTc>aAc	p.I427N		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	427					blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		GACAGGTTGATCCAGAATGTA	0.358																																					p.I427N		Atlas-SNP	.											.	STXBP3	44	.	0			c.T1280A						.						137	134	135					1																	109339272		2203	4300	6503	SO:0001583	missense	6814	exon15			GGTTGATCCAGAA	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1280T>A	chr1.hg19:g.109339272T>A	ENSP00000359025:p.Ile427Asn	230.0	0.0		208.0	62.0	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	hg19	CCDS790.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.422713	0.83559	.	.	ENSG00000116266	ENST00000370008	T	0.79141	-1.24	5.44	5.44	0.79542	.	0.149746	0.64402	D	0.000017	T	0.77758	0.4178	M	0.78049	2.395	0.58432	D	0.999996	B	0.27765	0.188	B	0.40101	0.319	T	0.80462	-0.1372	10	0.72032	D	0.01	-1.0014	15.4851	0.75560	0.0:0.0:0.0:1.0	.	427	O00186	STXB3_HUMAN	N	427	ENSP00000359025:I427N	ENSP00000359025:I427N	I	+	2	0	STXBP3	109140795	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.999000	0.76283	2.060000	0.61445	0.383000	0.25322	ATC	.	.		0.358	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		A	109339272	T	A	109339272	3	1	56	1	0	0	0	0	1	0	0	0	15369	1435	50	4	1338	4	STXBP3	1	109339272	Missense_Mutation	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10	54819125	109339272	139911349	3	7067										
KPRP	448834	hgsc.bcm.edu	37	chr1	152732812	152732812	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	tcactgaacagcaccgctctCggagcaccagcagatgcctt	9	15	2	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr1:152732812C>T	ENST00000606109.1	+	1	776	c.748C>T	c.(748-750)Cgg>Tgg	p.R250W	KPRP_ENST00000368773.1_Missense_Mutation_p.R250W			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	250						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCACCGCTCTCGGAGCACCAG	0.607																																					p.R250W		Atlas-SNP	.											.	KPRP	152	.	0			c.C748T						.						52	58	56					1																	152732812		2203	4300	6503	SO:0001583	missense	448834	exon2			CGCTCTCGGAGCA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.748C>T	chr1.hg19:g.152732812C>T	ENSP00000475216:p.Arg250Trp	58.0	0.0		82.0	26.0	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	hg19	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.609401	0.28623	.	.	ENSG00000203786	ENST00000368773	T	0.13657	2.57	5.56	2.67	0.31697	.	0.921332	0.08935	N	0.872419	T	0.02848	0.0085	N	0.19112	0.55	0.09310	N	1	B	0.23650	0.089	B	0.21546	0.035	T	0.46048	-0.9219	10	0.87932	D	0	-0.0836	5.188	0.15195	0.1647:0.6645:0.0:0.1708	.	250	Q5T749	KPRP_HUMAN	W	250	ENSP00000357762:R250W	ENSP00000357762:R250W	R	+	1	2	KPRP	150999436	0.106000	0.21978	0.010000	0.14722	0.008000	0.06430	1.379000	0.34340	0.390000	0.25115	-0.140000	0.14226	CGG	.	.		0.607	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		T	152732812	C	T	152732812	3	4	56	1	0	0	0	0	1	0	0	0	8445	875	31	1	750	1	KPRP	1	152732812	Missense_Mutation	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10	43393540	152732812	96517809	4	7068										
CD1E	913	hgsc.bcm.edu	37	chr1	158325699	158325699	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	tgccatgtctcaggattctaCccaaagcccgtgtgggtgat	11	11	2	1			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr1:158325699C>T	ENST00000368167.3	+	4	947	c.708C>T	c.(706-708)taC>taT	p.Y236Y	CD1E_ENST00000368163.3_Silent_p.Y236Y|CD1E_ENST00000444681.2_Silent_p.Y137Y|CD1E_ENST00000368161.3_Silent_p.Y236Y|CD1E_ENST00000368155.3_Silent_p.Y146Y|CD1E_ENST00000368166.3_Silent_p.Y47Y|CD1E_ENST00000368165.3_Silent_p.Y146Y|CD1E_ENST00000368160.3_Silent_p.Y236Y|CD1E_ENST00000434258.1_Silent_p.Y234Y|CD1E_ENST00000368164.3_Silent_p.Y47Y|CD1E_ENST00000368156.1_Silent_p.Y146Y|CD1E_ENST00000368157.1_Silent_p.Y47Y|CD1E_ENST00000368154.1_Silent_p.Y47Y|CD1E_ENST00000452291.2_Silent_p.Y47Y	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	236	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					CAGGATTCTACCCAAAGCCCG	0.607																																					p.Y236Y		Atlas-SNP	.											.	CD1E	129	.	0			c.C708T						.						74	73	74					1																	158325699		2203	4298	6501	SO:0001819	synonymous_variant	913	exon4			ATTCTACCCAAAG	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1638	protein-coding gene	gene with protein product		188411	"CD1E antigen, e polypeptide", "CD1e antigen"			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.708C>T	chr1.hg19:g.158325699C>T		273.0	0.0		320.0	14.0	NM_001042584	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Silent	SNP	ENST00000368167.3	hg19	CCDS41417.1	.	.	.	.	.	.	.	.	.	.	C	9.848	1.193006	0.21954	.	.	ENSG00000158488	ENST00000368162	.	.	.	4.83	0.315	0.15852	.	.	.	.	.	T	0.38081	0.1027	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25222	-1.0138	4	.	.	.	-10.221	6.8541	0.24030	0.0:0.5054:0.0:0.4946	.	.	.	.	S	6	.	.	P	+	1	0	CD1E	156592323	0.070000	0.21116	0.886000	0.34754	0.996000	0.88848	-0.738000	0.04871	-0.099000	0.12263	0.563000	0.77884	CCC	.	.		0.607	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		T	158325699	C	T	158325699	2	4	56	1	0	0	0	0	0	0	0	1	2980	518	18	3		3	CD1E	1	158325699	Silent	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10	5592887	158325699	90924922	5	7069										
ABCG5	64240	hgsc.bcm.edu	37	chr2	44053584	44053584	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	attcggttcctgcgagccagTtccaccaggaggacgacaat	11	12	0	0			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr2:44053584T>G	ENST00000260645.1	-	6	850	c.711A>C	c.(709-711)gaA>gaC	p.E237D	ABCG5_ENST00000543989.1_Intron|ABCG5_ENST00000405322.1_Intron	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	237	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	TGCGAGCCAGTTCCACCAGGA	0.532																																					p.E237D		Atlas-SNP	.											.	ABCG5	72	.	0			c.A711C						.						146	126	133					2																	44053584		2203	4300	6503	SO:0001583	missense	64240	exon6			AGCCAGTTCCACC	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"ATP binding cassette transporters / subfamily G"	13886	protein-coding gene	gene with protein product	"sterolin 1"	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.711A>C	chr2.hg19:g.44053584T>G	ENSP00000260645:p.Glu237Asp	150.0	0.0		184.0	61.0	NM_022436	Q2T9G2|Q96QZ2|Q96QZ3	Missense_Mutation	SNP	ENST00000260645.1	hg19	CCDS1814.1	.	.	.	.	.	.	.	.	.	.	T	11.50	1.657373	0.29425	.	.	ENSG00000138075	ENST00000260645	T	0.42131	0.98	5.56	2.31	0.28768	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.300661	0.40222	N	0.001146	T	0.25344	0.0616	N	0.20845	0.615	0.80722	D	1	P	0.46395	0.877	B	0.43194	0.411	T	0.02560	-1.1141	10	0.13853	T	0.58	.	9.2504	0.37551	0.0:0.6013:0.0:0.3987	.	237	Q9H222	ABCG5_HUMAN	D	237	ENSP00000260645:E237D	ENSP00000260645:E237D	E	-	3	2	ABCG5	43907088	1.000000	0.71417	0.985000	0.45067	0.195000	0.23768	1.080000	0.30779	0.689000	0.31550	-0.242000	0.12053	GAA	.	.		0.532	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436		G	44053584	T	G	44053584	3	3	56	1	0	0	0	0	1	0	0	0	71	1722	60	5	1276	5	ABCG5	2	44053584	Missense_Mutation	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10		44053584	199145789	6	7070										
CCDC104	112942	hgsc.bcm.edu	37	chr2	55772122	55772124	+	In_Frame_Del	DEL	AAG	AAG	-													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	attgcttgcagagaaactcaAagaagaagttattaataagt					rs528334905		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr2:55772122_55772124delAAG	ENST00000349456.4	+	10	1155_1157	c.1007_1009delAAG	c.(1006-1011)aaagaa>aaa	p.E338del	CCDC104_ENST00000339012.3_In_Frame_Del_p.E363del|CCDC104_ENST00000407816.3_In_Frame_Del_p.E309del			Q96G28	CFA36_HUMAN		338										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(2)|lung(1)|ovary(2)	14			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GAGAAACTCAAAGAAGAAGTTAT	0.286																																					p.336_336del		Atlas-Indel,Pindel	.											.	CCDC104	35	.	0			c.1006_1008del						.			3,4253		0,3,2125						5.7	1			35	0,8244		0,0,4122	no	coding	CCDC104	NM_080667.5		0,3,6247	A1A1,A1R,RR		0.0,0.0705,0.024				3,12497				SO:0001651	inframe_deletion	112942	exon10			.																												ENST00000349456.4:c.1007_1009delAAG	chr2.hg19:g.55772128_55772130delAAG	ENSP00000295117:p.Glu338del	439.0	0.0		259.0	59.0	NM_080667	Q53SF0|Q53ST9|Q6UY34	In_Frame_Del	DEL	ENST00000349456.4	hg19	CCDS1854.2																																																																																			.	.		0.286	CCDC104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319610.2			-	55772124	AAG	-	55772122	7	5	56	1	0	1	0	1	0	0	0	0	2741	14	1	0	1045	0	CCDC104	2	55772122	In_Frame_Del	DEL	AAG	TCGA-CC-5260-01A-01D-A12Z-10	11718538	55772122	187427251	7	7071										
CHRNA1	1134	hgsc.bcm.edu	37	chr2	175624066	175624066	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ctggctaagttacctgtttcAgacgcacattggttgtcacg	10	10	2	1			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr2:175624066A>T	ENST00000261007.5	-	3	293	c.227T>A	c.(226-228)cTg>cAg	p.L76Q	CHRNA1_ENST00000409542.1_Missense_Mutation_p.L76Q|CHRNA1_ENST00000409323.1_Missense_Mutation_p.L76Q|CHRNA1_ENST00000409219.1_Missense_Mutation_p.L76Q|CHRNA1_ENST00000348749.5_Missense_Mutation_p.L76Q|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	76					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	TACCTGTTTCAGACGCACATT	0.428																																					p.L76Q		Atlas-SNP	.											.	CHRNA1	92	.	0			c.T227A						.						106	101	102					2																	175624066		2203	4300	6503	SO:0001583	missense	1134	exon3			TGTTTCAGACGCA	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1955	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 1 (muscle)"	100690	"cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.227T>A	chr2.hg19:g.175624066A>T	ENSP00000261007:p.Leu76Gln	216.0	0.0		247.0	78.0	NM_001039523	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	hg19	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.883238	0.91740	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219;ENST00000409323	D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58	5.95	5.95	0.96441	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.93245	0.7848	M	0.92738	3.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.997;1.0	D	0.94649	0.7837	10	0.87932	D	0	.	16.4101	0.83708	1.0:0.0:0.0:0.0	.	76;76;76	G5E9G9;Q53SH4;P02708	.;.;ACHA_HUMAN	Q	76	ENSP00000261008:L76Q;ENSP00000261007:L76Q;ENSP00000387026:L76Q;ENSP00000386611:L76Q;ENSP00000386684:L76Q	ENSP00000261007:L76Q	L	-	2	0	CHRNA1	175332312	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.277000	0.95755	2.280000	0.76307	0.460000	0.39030	CTG	.	.		0.428	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			T	175624066	A	T	175624066	3	4	56	1	0	0	0	0	1	0	0	0	3383	188	7	4	1253	4	CHRNA1	2	175624066	Missense_Mutation	SNP	A	TCGA-CC-5260-01A-01D-A12Z-10	119851944	175624066	67575307	8	7072										
IDH1	3417	hgsc.bcm.edu	37	chr2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ttgatccccataagcatgacGacctatgatgataggtttta	8	8	0	4	rs121913499		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000446179.1_Missense_Mutation_p.R132C|IDH1_ENST00000345146.2_Missense_Mutation_p.R132C	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																p.R132C	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	IDH1,NS,haematopoietic_neoplasm,0,788	IDH1	6310	.	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)	c.C394T						.						81	74	76					2																	209113113		2203	4300	6503	SO:0001583	missense	3417	exon4			CATGACGACCTAT		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>T	chr2.hg19:g.209113113G>A	ENSP00000390265:p.Arg132Cys	267.0	0.0		294.0	87.0	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	hg19	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT	.	.		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			A	209113113	G	A	209113113	3	1	56	1	0	0	0	0	1	0	0	0	7503	1058	37	1	878	1	IDH1	2	209113113	Missense_Mutation	SNP	G	TCGA-CC-5260-01A-01D-A12Z-10	33489047	209113113	34086260	9	7073										
USP37	57695	hgsc.bcm.edu	37	chr2	219423315	219423315	+	Frame_Shift_Del	DEL	T	T	-													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	caaaggatccttctttccacTttgtaatcccagtctgcata							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr2:219423315delT	ENST00000258399.3	-	4	474	c.62delA	c.(61-63)aagfs	p.K21fs	USP37_ENST00000454775.1_Frame_Shift_Del_p.K21fs|USP37_ENST00000418019.1_Frame_Shift_Del_p.K21fs|USP37_ENST00000338465.5_Frame_Shift_Del_p.K21fs|USP37_ENST00000415516.1_Intron	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	21					G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		TTCTTTCCACTTTGTAATCCC	0.343																																					p.K21fs		Atlas-Indel,Pindel	.											.	USP37	76	.	0			c.63delG						.						169	179	176					2																	219423315		2203	4300	6503	SO:0001589	frameshift_variant	57695	exon4			.	AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"Ubiquitin-specific peptidases"	20063	protein-coding gene	gene with protein product			"ubiquitin specific protease 37"			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.62delA	chr2.hg19:g.219423315delT	ENSP00000258399:p.Lys21fs	328.0	0.0		299.0	86.0	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Frame_Shift_Del	DEL	ENST00000258399.3	hg19	CCDS2418.1																																																																																			.	.		0.343	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		-	219423315	T	-	219423315	7	5	56	1	0	1	0	1	0	0	0	0	17083	1609	56	0	2969	0	USP37	2	219423315	Frame_Shift_Del	DEL	T	TCGA-CC-5260-01A-01D-A12Z-10	10310202	219423315	23776058	10	7074										
BAP1	8314	hgsc.bcm.edu	37	chr3	52437456	52437456	+	Frame_Shift_Del	DEL	C	C	-													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	cagcgccaggggactcagcaCcccatcctcagccaggtgca							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr3:52437456delC	ENST00000460680.1	-	13	2176	c.1705delG	c.(1705-1707)gtgfs	p.V569fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.V551fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GGACTCAGCACCCCATCCTCA	0.617			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.V569fs	GBM(101;493 1458 7992 21037 25532)	Atlas-INDEL	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.1706delT						.						60	56	58					3																	52437456		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon13			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1705delG	chr3.hg19:g.52437456delC	ENSP00000417132:p.Val569fs	47.0	0.0		53.0	19.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.617	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52437456	C	-	52437456	7	5	56	1	0	1	0	1	0	0	0	0	1311	507	18	0	504	0	BAP1	3	52437456	Frame_Shift_Del	DEL	C	TCGA-CC-5260-01A-01D-A12Z-10		52437456	145584974	11	7075										
TMPRSS7	344805	hgsc.bcm.edu	37	chr3	111797619	111797619	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ctccctcgttctgcagcaagCggaggtagagctcattgatc	11	12	2	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr3:111797619C>T	ENST00000452346.2	+	17	2258	c.2255C>T	c.(2254-2256)gCg>gTg	p.A752V	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.A626V			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	752	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CTGCAGCAAGCGGAGGTAGAG	0.463																																					p.A626V		Atlas-SNP	.											.	TMPRSS7	126	.	0			c.C1877T						.						112	111	112					3																	111797619		1942	4131	6073	SO:0001583	missense	344805	exon15			AGCAAGCGGAGGT	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.2255C>T	chr3.hg19:g.111797619C>T	ENSP00000398236:p.Ala752Val	218.0	0.0		231.0	64.0	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	hg19		.	.	.	.	.	.	.	.	.	.	C	35	5.518493	0.96416	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	T;T	0.58940	0.3;0.3	5.79	5.79	0.91817	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	T	0.54647	0.1871	N	0.02765	-0.5	0.58432	D	0.999997	D;D	0.89917	1.0;0.996	D;P	0.80764	0.994;0.794	T	0.64968	-0.6282	10	0.39692	T	0.17	.	16.9482	0.86236	0.0:1.0:0.0:0.0	.	752;626	Q7RTY8;Q7RTY8-2	TMPS7_HUMAN;.	V	752;740;726;626	ENSP00000398236:A752V;ENSP00000411645:A626V	ENSP00000411645:A626V	A	+	2	0	TMPRSS7	113280309	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.884000	0.75600	2.716000	0.92895	0.655000	0.94253	GCG	.	.		0.463	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		T	111797619	C	T	111797619	3	4	56	1	0	0	0	0	1	0	0	0	16267	768	27	1	1931	1	TMPRSS7	3	111797619	Missense_Mutation	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10	59360163	111797619	86224811	12	7076										
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122629075	122629075	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ggcttgggtagtaagtagtcGtgtacacattggtctgctgc	14	7	1	0	rs369693926		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr3:122629075G>A	ENST00000357599.3	-	23	3757	c.3371C>T	c.(3370-3372)aCg>aTg	p.T1124M	SEMA5B_ENST00000195173.4_3'UTR|SEMA5B_ENST00000451055.2_Missense_Mutation_p.T1178M	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	1124					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GTAAGTAGTCGTGTACACATT	0.542																																					p.T1178M		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C3533T						.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	206	173	184		3371	5.1	1	3		184	0,8600		0,0,4300	no	missense	SEMA5B	NM_001031702.2	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1124/1152	122629075	1,13005	2203	4300	6503	SO:0001583	missense	54437	exon23			GTAGTCGTGTACA	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.3371C>T	chr3.hg19:g.122629075G>A	ENSP00000350215:p.Thr1124Met	620.0	0.0		705.0	231.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	hg19	CCDS35491.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.7|22.7	4.323460|4.323460	0.81580|0.81580	2.27E-4|2.27E-4	0.0|0.0	ENSG00000082684|ENSG00000082684	ENST00000451541|ENST00000357599;ENST00000418793;ENST00000451055	.|T;T	.|0.37584	.|1.19;1.23	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	.|0.052354	.|0.85682	.|D	.|0.000000	.|T	.|0.48786	.|0.1519	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.72338	.|0.977;0.95	.|T	.|0.46693	.|-0.9173	.|10	.|0.52906	.|T	.|0.07	.|.	17.1675|17.1675	0.86820|0.86820	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1030;1124	.|D3YTI7;Q9P283	.|.;SEM5B_HUMAN	X|M	170|1124;1030;1178	.|ENSP00000350215:T1124M;ENSP00000389588:T1178M	.|ENSP00000350215:T1124M	R|T	-|-	1|2	2|0	SEMA5B|SEMA5B	124111765|124111765	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.981000|0.981000	0.71138|0.71138	9.263000|9.263000	0.95617|0.95617	2.643000|2.643000	0.89663|0.89663	0.650000|0.650000	0.86243|0.86243	CGA|ACG	.	.		0.542	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		A	122629075	G	A	122629075	3	1	56	1	0	0	0	0	1	0	0	0	14053	1145	40	1	88	1	SEMA5B	3	122629075	Missense_Mutation	SNP	G	TCGA-CC-5260-01A-01D-A12Z-10	10831456	122629075	75393355	13	7077										
CCDC48	79825	hgsc.bcm.edu	37	chr3	128758638	128758639	+	Frame_Shift_Ins	INS	-	-	C													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	gttgcggagacagccctcggINScaccagcctctgcagcagct							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr3:128758638_128758639insC	ENST00000480450.1	+	8	1744_1745	c.1744_1745insC	c.(1744-1746)gcafs	p.A582fs	EFCC1_ENST00000436022.2_Frame_Shift_Ins_p.A145fs			Q9HA90	EFCC1_HUMAN	EF-hand and coiled-coil domain containing 1	582	Poly-Ala.						calcium ion binding (GO:0005509)										ACAGCCCTCGGCACCAGCCTCT	0.658																																					p.A582fs		Atlas-INDEL	.											.	.	.	.	0			c.1744_1745insC						.																																			SO:0001589	frameshift_variant	79825	exon8			.	AK022119	CCDS3054.1, CCDS3054.2	3q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000114654	ENSG00000114654		"EF-hand domain containing"	25692	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 73", "coiled-coil domain containing 48"	C3orf73, CCDC48			Standard	NM_024768		Approved	FLJ12057	uc011bkt.2	Q9HA90	OTTHUMG00000158996	ENST00000480450.1:c.1745dupC	chr3.hg19:g.128758639_128758639dupC	ENSP00000420075:p.Ala582fs	151.0	0.0		172.0	14.0	NM_024768	A8MYE2	Frame_Shift_Ins	INS	ENST00000480450.1	hg19	CCDS3054.2																																																																																			.	.		0.658	EFCC1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352832.1	NM_024768		C	128758639	-	C	128758638	7	5	56	1	0	1	1	0	0	0	0	0	2821	1203	42	0	1774	0	CCDC48	3	128758638	Frame_Shift_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10	6129563	128758638	69263792	14	7078										
ZNF518B	85460	hgsc.bcm.edu	37	chr4	10446101	10446101	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	agtcctttcagaattctttaAttccaaaggcttatccccag	5	11	2	1			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr4:10446101A>T	ENST00000326756.3	-	3	2290	c.1852T>A	c.(1852-1854)Tta>Ata	p.L618I		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	618					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						GAATTCTTTAATTCCAAAGGC	0.398																																					p.L618I		Atlas-SNP	.											.	ZNF518B	116	.	0			c.T1852A						.						144	144	144					4																	10446101		2203	4300	6503	SO:0001583	missense	85460	exon3			TCTTTAATTCCAA	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.1852T>A	chr4.hg19:g.10446101A>T	ENSP00000317614:p.Leu618Ile	403.0	1.0		293.0	77.0	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	hg19	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	A	17.67	3.446832	0.63178	.	.	ENSG00000178163	ENST00000326756	T	0.01902	4.57	6.06	-10.4	0.00318	.	0.495160	0.13666	N	0.371205	T	0.02267	0.0070	L	0.42245	1.32	0.09310	N	1	P	0.42456	0.78	B	0.36666	0.23	T	0.09552	-1.0669	10	0.51188	T	0.08	-0.1159	20.4514	0.99126	0.1311:0.0867:0.7822:0.0	.	618	Q9C0D4	Z518B_HUMAN	I	618	ENSP00000317614:L618I	ENSP00000317614:L618I	L	-	1	2	ZNF518B	10055199	0.000000	0.05858	0.000000	0.03702	0.599000	0.36880	-0.202000	0.09451	-1.789000	0.01264	-0.250000	0.11733	TTA	.	.		0.398	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		T	10446101	A	T	10446101	3	4	56	1	0	0	0	0	1	0	0	0	17978	98	4	4	1376	4	ZNF518B	4	10446101	Missense_Mutation	SNP	A	TCGA-CC-5260-01A-01D-A12Z-10		10446101	180708175	15	7079										
AMTN	401138	hgsc.bcm.edu	37	chr4	71396955	71396955	+	Frame_Shift_Del	DEL	C	C	-													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	tgacgactttgcagtgaccaCccctgcaggcatccaaagga							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr4:71396955delC	ENST00000339336.4	+	8	687	c.557delC	c.(556-558)accfs	p.T186fs	AMTN_ENST00000504451.1_Frame_Shift_Del_p.T185fs	NM_212557.2	NP_997722.1	Q6UX39	AMTN_HUMAN	amelotin	186					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|odontogenesis of dentin-containing tooth (GO:0042475)	basal lamina (GO:0005605)|cell-cell junction (GO:0005911)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)|skin(1)	19			Lung(101;0.235)			GCAGTGACCACCCCTGCAGGC	0.552																																					p.T186fs		Atlas-INDEL	.											.	AMTN	28	.	0			c.556delA						.						69	56	61					4																	71396955		2203	4300	6503	SO:0001589	frameshift_variant	401138	exon8			.	AY358528	CCDS3542.1, CCDS68716.1	4q13.3	2006-12-12			ENSG00000187689	ENSG00000187689			33188	protein-coding gene	gene with protein product		610912				16304441	Standard	NM_001286731		Approved	UNQ689, RSTI689	uc003hfk.1	Q6UX39	OTTHUMG00000129906	ENST00000339336.4:c.557delC	chr4.hg19:g.71396955delC	ENSP00000341013:p.Thr186fs	184.0	0.0		202.0	14.0	NM_212557	Q0P503|Q0P506	Frame_Shift_Del	DEL	ENST00000339336.4	hg19	CCDS3542.1																																																																																			.	.		0.552	AMTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252157.1	NM_212557		-	71396955	C	-	71396955	7	5	56	1	0	1	0	1	0	0	0	0	590	507	18	0	583	0	AMTN	4	71396955	Frame_Shift_Del	DEL	C	TCGA-CC-5260-01A-01D-A12Z-10	60950854	71396955	119757321	16	7080										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	74043114	74043115	+	Frame_Shift_Ins	INS	-	-	C													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	acctgcagcttctagtaaagINScttccagtctagcctgtgtt							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr4:74043114_74043115insC	ENST00000358602.4	-	2	645_646	c.529_530insG	c.(529-531)gctfs	p.A177fs	ANKRD17_ENST00000330838.6_Frame_Shift_Ins_p.A177fs|ANKRD17_ENST00000509867.2_Frame_Shift_Ins_p.A64fs	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	177					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTCTAGTAAAGCTTCCAGTCTA	0.391																																					p.A177fs		Atlas-INDEL	.											.	ANKRD17	214	.	0			c.530_531insG						.																																			SO:0001589	frameshift_variant	26057	exon2			.	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.530dupG	chr4.hg19:g.74043115_74043115dupC	ENSP00000351416:p.Ala177fs	158.0	0.0		129.0	10.0	NM_198889	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Frame_Shift_Ins	INS	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.391	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		C	74043115	-	C	74043114	7	5	56	1	0	1	1	0	0	0	0	0	646	971	34	0	7413	0	ANKRD17	4	74043114	Frame_Shift_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10	2646159	74043114	117111162	17	7081										
GYPA	2994	hgsc.bcm.edu	37	chr4	145039884	145039884	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	tacctggttcagagaaatgaTgggcaagttgtaccctttct	10	8	2	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr4:145039884T>A	ENST00000283126.7	-	1	93				GYPA_ENST00000360771.4_Missense_Mutation_p.H85L|RP11-673E1.4_ENST00000506982.1_RNA|GYPA_ENST00000324022.10_Missense_Mutation_p.H52L|GYPA_ENST00000512789.1_Missense_Mutation_p.H20L|GYPA_ENST00000503627.1_Intron|GYPA_ENST00000535709.1_Missense_Mutation_p.H59L|GYPA_ENST00000512064.1_Intron|GYPA_ENST00000504786.1_Missense_Mutation_p.H53L			P06028	GLPB_HUMAN	glycophorin B (MNS blood group)							integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|skin(1)	4	all_hematologic(180;0.158)					AGAGAAATGATGGGCAAGTTG	0.313																																					p.H85L		Atlas-SNP	.											GYPA,right_upper_lobe,carcinoma,0,1	GYPA	27	.	0			c.A254T						.						109	109	109					4																	145039884		2203	4300	6503	SO:0001627	intron_variant	2993	exon4			AAATGATGGGCAA		CCDS54809.1	4q31.21	2014-09-17	2006-02-23			ENSG00000250361		"CD molecules", "Blood group antigens"	4703	protein-coding gene	gene with protein product		111740	"glycophorin B (includes Ss blood group)", "glycophorin B (Ss blood group)"	MNS			Standard	NM_002100		Approved	GPB, SS, CD235b		P06028		ENST00000283126.7:c.37+21867A>T	chr4.hg19:g.145039884T>A		722.0	0.0		370.0	87.0	NM_002099	B8Q174|E2QBW7|Q0VAF4|Q58HE9|Q58HF0|Q58HF1|Q9UCH7	Missense_Mutation	SNP	ENST00000283126.7	hg19		.	.	.	.	.	.	.	.	.	.	T	9.261	1.043323	0.19748	.	.	ENSG00000170180	ENST00000360771;ENST00000324022;ENST00000535709;ENST00000512789;ENST00000504786;ENST00000394119	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	3.94	1.33	0.21861	.	0.000000	0.42682	D	0.000668	T	0.35711	0.0941	M	0.68952	2.095	0.09310	N	1	D;D;D;B;D	0.89917	0.996;0.992;0.999;0.007;1.0	D;D;D;B;D	0.72338	0.934;0.912;0.955;0.022;0.977	T	0.08743	-1.0707	10	0.87932	D	0	-13.6461	4.5091	0.11903	0.1971:0.0:0.2052:0.5976	.	52;20;53;85;85	B8Q185;Q13030;E7EQF3;P02724;Q16336	.;.;.;GLPA_HUMAN;.	L	85;52;59;20;53;53	ENSP00000354003:H85L;ENSP00000324483:H52L;ENSP00000445398:H59L;ENSP00000425193:H20L;ENSP00000425549:H53L	ENSP00000324483:H52L	H	-	2	0	GYPA	145259334	0.029000	0.19370	0.000000	0.03702	0.001000	0.01503	1.046000	0.30354	0.288000	0.22398	0.482000	0.46254	CAT	.	.		0.313	GYPB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002100		A	145039884	T	A	145039884	1	1	56	0	1	0	0	0	0	0	0	0	6917	1464	51	4		4	GYPA	4	145039884	Intron	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10	70996770	145039884	46114392	18	7082										
GZMK	3003	hgsc.bcm.edu	37	chr5	54320547	54320548	+	Frame_Shift_Ins	INS	-	-	C													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	tcattccaggccatttatggINScctccatccagtatggcgga							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr5:54320547_54320548insC	ENST00000231009.2	+	2	194_195	c.124_125insC	c.(124-126)gccfs	p.A42fs	CTD-2313F11.1_ENST00000608929.1_RNA|CTD-2313F11.1_ENST00000596137.1_RNA|CTD-2313F11.1_ENST00000607910.1_RNA|CTD-2313F11.1_ENST00000595218.1_RNA|CTD-2313F11.1_ENST00000609699.1_RNA|CTD-2313F11.1_ENST00000371487.3_RNA|CTD-2313F11.1_ENST00000608466.1_RNA|CTD-2313F11.1_ENST00000596909.2_RNA|ESM1_ENST00000598310.1_5'Flank	NM_002104.2	NP_002095.1	P49863	GRAK_HUMAN	granzyme K (granzyme 3; tryptase II)	42	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)	15		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				GCCATTTATGGCCTCCATCCAG	0.46																																					p.A42fs		Atlas-INDEL	.											.	GZMK	39	.	0			c.124_125insC						.																																			SO:0001589	frameshift_variant	3003	exon2			.	BC035802	CCDS3964.1	5q11.2	2008-05-15	2005-08-17		ENSG00000113088	ENSG00000113088			4711	protein-coding gene	gene with protein product		600784	"granzyme K (serine protease, granzyme 3; tryptase II)"			7758581	Standard	NM_002104		Approved	TRYP2, PRSS	uc003jpl.1	P49863	OTTHUMG00000097009	ENST00000231009.2:c.126dupC	chr5.hg19:g.54320549_54320549dupC	ENSP00000231009:p.Ala42fs	159.0	0.0		174.0	11.0	NM_002104	B2R563	Frame_Shift_Ins	INS	ENST00000231009.2	hg19	CCDS3964.1																																																																																			.	.		0.46	GZMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214098.1	NM_002104		C	54320548	-	C	54320547	7	5	56	1	0	1	1	0	0	0	0	0	6927	1203	42	0	130	0	GZMK	5	54320547	Frame_Shift_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10		54320547	126594713	19	7083										
FAM53C	51307	hgsc.bcm.edu	37	chr5	137681062	137681062	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	tgtcaccttgcccacctcagCgccgcttctccctgtcaccc	6	21	4	0			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr5:137681062C>T	ENST00000239906.5	+	4	1113	c.685C>T	c.(685-687)Cgc>Tgc	p.R229C	FAM53C_ENST00000507506.1_3'UTR|FAM53C_ENST00000513056.1_Intron|RP11-256P1.1_ENST00000504539.1_RNA|FAM53C_ENST00000434981.2_Missense_Mutation_p.R229C	NM_016605.2	NP_057689.1	Q9NYF3	FA53C_HUMAN	family with sequence similarity 53, member C	229										breast(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CCCACCTCAGCGCCGCTTCTC	0.677																																					p.R229C		Atlas-SNP	.											.	FAM53C	35	.	0			c.C685T						.						85	97	93					5																	137681062		2203	4300	6503	SO:0001583	missense	51307	exon4			CCTCAGCGCCGCT	AF251040	CCDS4204.1	5q31	2008-02-05	2004-11-24	2004-11-26	ENSG00000120709	ENSG00000120709			1336	protein-coding gene	gene with protein product		609372	"chromosome 5 open reading frame 6"	C5orf6		11087669, 11161817	Standard	NM_001135647		Approved		uc003lcv.3	Q9NYF3	OTTHUMG00000129201	ENST00000239906.5:c.685C>T	chr5.hg19:g.137681062C>T	ENSP00000239906:p.Arg229Cys	29.0	0.0		49.0	14.0	NM_001135647	B2RDJ5|D3DQB9	Missense_Mutation	SNP	ENST00000239906.5	hg19	CCDS4204.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.929458	0.73327	.	.	ENSG00000120709	ENST00000434981;ENST00000239906	T;T	0.57907	0.37;0.37	5.55	5.55	0.83447	.	0.252298	0.39834	N	0.001253	T	0.70937	0.3281	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	P	0.62298	0.9	T	0.70156	-0.4949	9	.	.	.	-9.4919	18.4386	0.90656	0.0:1.0:0.0:0.0	.	229	Q9NYF3	FA53C_HUMAN	C	229	ENSP00000403705:R229C;ENSP00000239906:R229C	.	R	+	1	0	FAM53C	137708961	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.135000	0.50546	2.894000	0.99253	0.655000	0.94253	CGC	.	.		0.677	FAM53C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251278.2	NM_016605		T	137681062	C	T	137681062	3	4	56	1	0	0	0	0	1	0	0	0	5589	768	27	1	695	1	FAM53C	5	137681062	Missense_Mutation	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10	83360515	137681062	43234198	20	7084										
ZNF192	7745	hgsc.bcm.edu	37	chr6	28121267	28121268	+	In_Frame_Ins	INS	-	-	AAA													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	agagaatccacactggggagINSaagccatatcagtgcaatca					rs200152195	byFrequency	TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr6:28121267_28121268insAAA	ENST00000330236.6	+	6	1393_1394	c.1209_1210insAAA	c.(1210-1212)aag>AAAaag	p.404_404K>KK	ZKSCAN8_ENST00000457389.2_In_Frame_Ins_p.404_404K>KK	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	404					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										ACACTGGGGAGAAGCCATATCA	0.48																																					p.E403delinsEK		Atlas-INDEL	.											.	.	.	.	0			c.1209_1210insAAA						.																																			SO:0001652	inframe_insertion	7745	exon6			.		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"Zinc fingers, C2H2-type", "-", "-", "-"	12983	protein-coding gene	gene with protein product		602240	"zinc finger protein 192"	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	Exception_encountered	chr6.hg19:g.28121267_28121268insAAA	ENSP00000332750:p.Lys404dup	83.0	0.0		106.0	13.0	NM_006298	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	In_Frame_Ins	INS	ENST00000330236.6	hg19	CCDS4645.1																																																																																			.	.		0.48	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2			AAA	28121268	-	AAA	28121267	7	5	56	1	0	1	1	0	0	0	0	0	17771	933	33	0	1227	0	ZNF192	6	28121267	In_Frame_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10		28121267	142993800	21	7085										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75806972	75806973	+	Frame_Shift_Ins	INS	-	-	G													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	cacatttagttcttaccggcINSggccctggtgggcccctggg							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr6:75806972_75806973insG	ENST00000322507.8	-	59	8882_8883	c.8573_8574insC	c.(8572-8574)ccgfs	p.P2858fs	COL12A1_ENST00000511023.1_5'UTR|COL12A1_ENST00000345356.6_Frame_Shift_Ins_p.P1694fs|COL12A1_ENST00000416123.2_Frame_Shift_Ins_p.P2782fs|COL12A1_ENST00000483888.2_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2858	Collagen-like 3.|Triple-helical region (COL2) with 1 imperfection.			P -> R (in Ref. 1; AAC51244). {ECO:0000305}.	cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTCTTACCGGCGGCCCTGGTGG	0.475																																					p.P2858fs		Atlas-INDEL	.											.	COL12A1	385	.	0			c.8574_8575insC						.																																			SO:0001589	frameshift_variant	1303	exon59			.	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.8574dupC	chr6.hg19:g.75806974_75806974dupG	ENSP00000325146:p.Pro2858fs	137.0	0.0		171.0	20.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Frame_Shift_Ins	INS	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.475	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		G	75806973	-	G	75806972	7	5	56	1	0	1	1	0	0	0	0	0	3671	755	27	0	649	0	COL12A1	6	75806972	Frame_Shift_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10	47685705	75806972	95308095	22	7086										
HOXA10	3206	hgsc.bcm.edu	37	chr7	27213355	27213356	+	Frame_Shift_Ins	INS	-	-	G													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ggcggcgggccccgcgggaaINSgggagccagttcggcggcgg							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr7:27213355_27213356insG	ENST00000283921.4	-	1	569_570	c.570_571insC	c.(568-573)cccttcfs	p.F191fs	RP1-170O19.20_ENST00000465941.1_Intron|HOXA-AS4_ENST00000523790.1_RNA|HOXA-AS4_ENST00000519694.1_RNA|HOXA10_ENST00000521421.1_5'Flank|RP1-170O19.20_ENST00000470747.4_Intron|HOXA10_ENST00000396344.4_Intron|HOXA-AS4_ENST00000519935.1_RNA	NM_018951.3	NP_061824.3	P31260	HXA10_HUMAN	homeobox A10	191					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|male gonad development (GO:0008584)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	9						CCCCGCGGGAAGGGAGCCAGTT	0.673																																					p.F191fs		Atlas-INDEL	.											.	HOXA10	55	.	0			c.571_572insC						.																																			SO:0001589	frameshift_variant	3206	exon1			.		CCDS5410.2	7p15.2	2011-06-20	2005-12-22		ENSG00000253293	ENSG00000253293		"Homeoboxes / ANTP class : HOXL subclass"	5100	protein-coding gene	gene with protein product		142957	"homeo box A10"	HOX1H, HOX1		1973146, 1358459	Standard	NR_037939		Approved		uc011jzm.2	P31260	OTTHUMG00000023436	ENST00000283921.4:c.571dupC	chr7.hg19:g.27213358_27213358dupG	ENSP00000283921:p.Phe191fs	17.0	0.0		97.0	10.0	NM_018951	O43370|O43605|Q15949|Q504T1	Frame_Shift_Ins	INS	ENST00000283921.4	hg19	CCDS5410.2																																																																																			.	.		0.673	HOXA10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358724.2			G	27213356	-	G	27213355	7	5	56	1	0	1	1	0	0	0	0	0	7298	72	3	0	669	0	HOXA10	7	27213355	Frame_Shift_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10		27213355	131925308	23	7087										
TYW1	55253	hgsc.bcm.edu	37	chr7	66582482	66582482	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ttactaaggaacctcgagccGgttactcagctgtatgtcag	10	10	2	0	rs13221716		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr7:66582482G>A	ENST00000359626.5	+	13	1739	c.1575G>A	c.(1573-1575)ccG>ccA	p.P525P		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	525					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				ACCTCGAGCCGGTTACTCAGC	0.398																																					p.P525P		Atlas-SNP	.											.	TYW1	71	.	0			c.G1575A						.						73	72	72					7																	66582482		2203	4300	6503	SO:0001819	synonymous_variant	55253	exon13			CGAGCCGGTTACT	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"	611243	"radical S-adenosyl methionine and flavodoxin domains 1"	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1575G>A	chr7.hg19:g.66582482G>A		186.0	0.0		198.0	8.0	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	hg19	CCDS5538.1																																																																																			.	.		0.398	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264		A	66582482	G	A	66582482	2	1	56	1	0	0	0	0	0	0	0	1	16833	1103	39	1		1	TYW1	7	66582482	Silent	SNP	G	TCGA-CC-5260-01A-01D-A12Z-10	39369127	66582482	92556181	24	7088										
CHPF2	54480	hgsc.bcm.edu	37	chr7	150934562	150934562	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	caccacactctcgctttgagGtgctgggctgggactacttc	11	13	1	1	rs139379425	byFrequency	TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr7:150934562G>A	ENST00000035307.2	+	4	2627	c.1114G>A	c.(1114-1116)Gtg>Atg	p.V372M	MIR671_ENST00000390183.1_RNA|RP4-548D19.3_ENST00000607902.1_RNA|CHPF2_ENST00000495645.1_Missense_Mutation_p.V364M	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	372					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						TCGCTTTGAGGTGCTGGGCTG	0.637																																					p.V372M		Atlas-SNP	.											.	CHPF2	52	.	0			c.G1114A						.						81	81	81					7																	150934562		2203	4300	6503	SO:0001583	missense	54480	exon4			TTTGAGGTGCTGG	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.1114G>A	chr7.hg19:g.150934562G>A	ENSP00000035307:p.Val372Met	97.0	0.0		236.0	62.0	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	hg19	CCDS34779.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025532	0.75390	.	.	ENSG00000033100	ENST00000495645;ENST00000035307;ENST00000377851	T;T	0.25579	1.79;1.79	5.63	5.63	0.86233	.	0.058009	0.64402	D	0.000002	T	0.49047	0.1534	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.81914	0.995;0.925	T	0.45381	-0.9265	10	0.62326	D	0.03	-22.7659	14.3202	0.66482	0.0:0.1479:0.8521:0.0	.	372;364	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	M	364;372;372	ENSP00000418914:V364M;ENSP00000035307:V372M	ENSP00000035307:V372M	V	+	1	0	CHPF2	150565495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.884000	0.87274	2.652000	0.90054	0.655000	0.94253	GTG	.	G|1.000;T|0.000		0.637	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015		A	150934562	G	A	150934562	3	1	56	1	0	0	0	0	1	0	0	0	3371	1261	44	3	1128	3	CHPF2	7	150934562	Missense_Mutation	SNP	G	TCGA-CC-5260-01A-01D-A12Z-10	84352080	150934562	8204101	25	7089										
TNKS	8658	hgsc.bcm.edu	37	chr8	9627614	9627614	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ttgtttttttctttttccttAgacaaatgctcttctgtaga	5	7	3	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr8:9627614A>T	ENST00000310430.6	+	26	3766		c.e26-1		TNKS_ENST00000518281.1_Splice_Site	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase						mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		CTTTTTCCTTAGACAAATGCT	0.373																																					.		Atlas-SNP	.											.	TNKS	198	.	0			c.3741-2A>T						.						45	48	47					8																	9627614		2202	4300	6502	SO:0001630	splice_region_variant	8658	exon26			TTCCTTAGACAAA	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.3741-1A>T	chr8.hg19:g.9627614A>T		28.0	0.0		38.0	21.0	NM_003747	O95272|Q4G0F2	Splice_Site	SNP	ENST00000310430.6	hg19	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914815	0.72983	.	.	ENSG00000173273	ENST00000310430;ENST00000518281	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7698	0.78157	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TNKS	9665024	1.000000	0.71417	0.990000	0.47175	0.930000	0.56654	9.287000	0.95975	2.189000	0.69895	0.533000	0.62120	.	.	.		0.373	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	Intron	T	9627614	A	T	9627614	5	4	56	1	0	0	0	0	0	0	1	0	16334	434	15	4	3841	4	TNKS	8	9627614	Splice_Site	SNP	A	TCGA-CC-5260-01A-01D-A12Z-10		9627614	136736408	26	7090										
RAB11FIP1	80223	hgsc.bcm.edu	37	chr8	37756823	37756823	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	cgtacttctccttgcccaccTggatcaccgcgtacgcgtcg	9	17	2	0			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr8:37756823T>A	ENST00000330843.4	-	1	149	c.137A>T	c.(136-138)cAg>cTg	p.Q46L	RAB11FIP1_ENST00000522727.1_5'UTR|RAB11FIP1_ENST00000287263.4_Missense_Mutation_p.Q46L	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	46	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			CTTGCCCACCTGGATCACCGC	0.731																																					p.Q46L		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.A137T						.						14	17	16					8																	37756823		2192	4286	6478	SO:0001583	missense	80223	exon1			CCCACCTGGATCA	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.137A>T	chr8.hg19:g.37756823T>A	ENSP00000331342:p.Gln46Leu	24.0	0.0		79.0	26.0	NM_025151	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	hg19	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	t	31	5.069606	0.93950	.	.	ENSG00000156675	ENST00000287263;ENST00000330843;ENST00000343853	T;T	0.69806	-0.43;-0.43	5.05	5.05	0.67936	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.335659	0.25948	N	0.027275	T	0.75398	0.3844	M	0.71581	2.175	0.80722	D	1	P;D	0.54772	0.763;0.968	B;P	0.56960	0.3;0.81	T	0.77555	-0.2544	10	0.56958	D	0.05	-11.3897	11.0281	0.47757	0.0:0.0:0.2031:0.7969	.	46;46	Q6WKZ4-3;Q6WKZ4	.;RFIP1_HUMAN	L	46	ENSP00000287263:Q46L;ENSP00000331342:Q46L	ENSP00000287263:Q46L	Q	-	2	0	RAB11FIP1	37875981	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.035000	0.57297	1.902000	0.55061	0.524000	0.50904	CAG	.	.		0.731	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		A	37756823	T	A	37756823	3	1	56	1	0	0	0	0	1	0	0	0	12908	1580	55	4	3738	4	RAB11FIP1	8	37756823	Missense_Mutation	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10	28129209	37756823	108607199	27	7091										
MMP16	4325	hgsc.bcm.edu	37	chr8	89180036	89180036	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	agagctgtccccatggaaacCagatgcaaaaataatggtta	9	8	0	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr8:89180036C>T	ENST00000286614.6	-	4	852	c.571G>A	c.(571-573)Ggt>Agt	p.G191S	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	191					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	CCATGGAAACCAGATGCAAAA	0.443																																					p.G191S		Atlas-SNP	.											.	MMP16	176	.	0			c.G571A						.						89	80	83					8																	89180036		2203	4300	6503	SO:0001583	missense	4325	exon4			GGAAACCAGATGC	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.571G>A	chr8.hg19:g.89180036C>T	ENSP00000286614:p.Gly191Ser	188.0	0.0		135.0	33.0	NM_005941	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	hg19	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	C	36	5.750365	0.96890	.	.	ENSG00000156103	ENST00000286614	T	0.21543	2.0	5.91	5.91	0.95273	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.085161	0.85682	D	0.000000	T	0.49541	0.1563	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.35500	-0.9786	10	0.52906	T	0.07	.	20.3829	0.98937	0.0:1.0:0.0:0.0	.	191;191	P51512-2;P51512	.;MMP16_HUMAN	S	191	ENSP00000286614:G191S	ENSP00000286614:G191S	G	-	1	0	MMP16	89249152	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.751000	0.85126	2.823000	0.97156	0.644000	0.83932	GGT	.	.		0.443	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		T	89180036	C	T	89180036	3	4	56	1	0	0	0	0	1	0	0	0	9664	594	21	3	1436	3	MMP16	8	89180036	Missense_Mutation	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10	51423213	89180036	57183986	28	7092										
TMC1	117531	hgsc.bcm.edu	37	chr9	75355074	75355074	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	agtgaaaatgaaggggctctTgggaaaggaaaaggaaaacg	15	3	1	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr9:75355074T>A	ENST00000297784.5	+	9	942	c.402T>A	c.(400-402)ctT>ctA	p.L134L	TMC1_ENST00000340019.3_Silent_p.L134L|TMC1_ENST00000396237.3_Silent_p.L134L	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	134	Arg/Asp/Glu/Lys-rich (highly charged).				auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						AAGGGGCTCTTGGGAAAGGAA	0.373																																					p.L134L	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.T402A						.						103	106	105					9																	75355074		2203	4300	6503	SO:0001819	synonymous_variant	117531	exon9			GGCTCTTGGGAAA	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"transmembrane, cochlear expressed, 1"	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.402T>A	chr9.hg19:g.75355074T>A		271.0	0.0		275.0	67.0	NM_138691	A8MVZ2|B1AM91	Silent	SNP	ENST00000297784.5	hg19	CCDS6643.1																																																																																			.	.		0.373	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1			A	75355074	T	A	75355074	2	1	56	1	0	0	0	0	0	0	0	1	15999	1799	63	4		4	TMC1	9	75355074	Silent	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10		75355074	65858357	29	7093										
HEMGN	55363	hgsc.bcm.edu	37	chr9	100693389	100693389	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ggtgccagtgctttctccacTatttccttttctatctgtgg	8	11	3	0	rs201990544	byFrequency	TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr9:100693389T>C	ENST00000259456.3	-	4	431	c.288A>G	c.(286-288)atA>atG	p.I96M		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	96				IV -> M (in Ref. 6; AAH48324). {ECO:0000305}.	cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				NS(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|skin(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(62;0.0559)				CTTTCTCCACTATTTCCTTTT	0.458																																					p.I96M		Atlas-SNP	.											.	HEMGN	55	.	0			c.A288G						.						154	145	148					9																	100693389		2203	4300	6503	SO:0001583	missense	55363	exon3			CTCCACTATTTCC	AF228713	CCDS6731.1	9q22.33	2014-01-21			ENSG00000136929	ENSG00000136929			17509	protein-coding gene	gene with protein product		610715					Standard	NM_018437		Approved	EDAG, CT155, NDR	uc004axy.4	Q9BXL5	OTTHUMG00000020336	ENST00000259456.3:c.288A>G	chr9.hg19:g.100693389T>C	ENSP00000259456:p.Ile96Met	197.0	0.0		166.0	21.0	NM_197978	Q6XAR3|Q86XY5|Q9NPC0	Missense_Mutation	SNP	ENST00000259456.3	hg19	CCDS6731.1	.	.	.	.	.	.	.	.	.	.	T	9.069	0.996436	0.19043	.	.	ENSG00000136929	ENST00000375112;ENST00000259456	.	.	.	4.84	-0.593	0.11667	.	1.389330	0.04154	N	0.321907	T	0.16685	0.0401	N	0.05124	-0.11	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.14643	-1.0465	9	0.29301	T	0.29	5.0598	2.682	0.05096	0.3468:0.3265:0.0:0.3267	.	96	Q9BXL5	HEMGN_HUMAN	M	96	.	ENSP00000259456:I96M	I	-	3	3	HEMGN	99733210	0.000000	0.05858	0.000000	0.03702	0.176000	0.22953	-0.528000	0.06193	0.015000	0.14971	-1.251000	0.01509	ATA	.	.		0.458	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978		C	100693389	T	C	100693389	3	2	56	1	0	0	0	0	1	0	0	0	7059	1512	53	2	1174	2	HEMGN	9	100693389	Missense_Mutation	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10	25338315	100693389	40520042	30	7094										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123177407	123177407	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ctaaacgctttctcaaagttCgaatttcctgtatgtgttcc	6	10	1	0			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr9:123177407C>T	ENST00000349780.4	-	28	4387	c.4208G>A	c.(4207-4209)cGa>cAa	p.R1403Q	CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.R1362Q|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.R1371Q|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.R1403Q	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1403					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.R1403Q(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TCTCAAAGTTCGAATTTCCTG	0.348																																					p.R1403Q		Atlas-SNP	.											CDK5RAP2,NS,carcinoma,0,2	CDK5RAP2	157	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4208A						.						130	120	123					9																	123177407		2203	4300	6503	SO:0001583	missense	55755	exon28			AAAGTTCGAATTT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.4208G>A	chr9.hg19:g.123177407C>T	ENSP00000343818:p.Arg1403Gln	209.0	0.0		280.0	32.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	hg19	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.045848	0.93685	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000416449;ENST00000425647;ENST00000345313	T;T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3;1.3	5.97	5.97	0.96955	.	0.000000	0.43747	D	0.000528	T	0.60287	0.2257	M	0.64997	1.995	0.42278	D	0.99208	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.997;0.999;0.999;0.998;0.998;0.997	T	0.60326	-0.7285	10	0.87932	D	0	.	18.6193	0.91316	0.0:1.0:0.0:0.0	.	413;1172;1371;1403;1403;797	Q5JTU8;Q6MZT4;Q96SN8-2;Q96SN8-4;Q96SN8;B1AMJ5	.;.;.;.;CK5P2_HUMAN;.	Q	1371;1362;1403;1403;797;413;1175	ENSP00000354065:R1371Q;ENSP00000352258:R1362Q;ENSP00000343818:R1403Q;ENSP00000353317:R1403Q;ENSP00000400395:R797Q;ENSP00000409941:R413Q	ENSP00000341695:R1175Q	R	-	2	0	CDK5RAP2	122217228	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.941000	0.70195	2.836000	0.97738	0.655000	0.94253	CGA	.	.		0.348	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		T	123177407	C	T	123177407	3	4	56	1	0	0	0	0	1	0	0	0	3148	884	31	1	1517	1	CDK5RAP2	9	123177407	Missense_Mutation	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10	22484018	123177407	18036024	31	7095										
MAPKAP1	79109	hgsc.bcm.edu	37	chr9	128230302	128230302	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	acagagcaggtcggaatcgaTtgagatgggtttctgcttaa	13	6	1	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr9:128230302T>C	ENST00000373498.1	-	9	1362	c.1294A>G	c.(1294-1296)Atc>Gtc	p.I432V	MAPKAP1_ENST00000373511.2_Missense_Mutation_p.I385V|MAPKAP1_ENST00000394063.1_Missense_Mutation_p.I240V|MAPKAP1_ENST00000350766.3_Missense_Mutation_p.I396V|MAPKAP1_ENST00000373503.3_Missense_Mutation_p.I240V|MAPKAP1_ENST00000373497.5_Missense_Mutation_p.I145V|MAPKAP1_ENST00000483937.1_5'UTR|MAPKAP1_ENST00000265960.3_Missense_Mutation_p.I432V			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	432					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						TCGGAATCGATTGAGATGGGT	0.453																																					p.I432V		Atlas-SNP	.											.	MAPKAP1	68	.	0			c.A1294G						.						205	196	199					9																	128230302		2203	4300	6503	SO:0001583	missense	79109	exon10			AATCGATTGAGAT	M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487			18752	protein-coding gene	gene with protein product	"stress-activated protein kinase-interacting 1"	610558				15363842	Standard	NM_001006620		Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000373498.1:c.1294A>G	chr9.hg19:g.128230302T>C	ENSP00000362597:p.Ile432Val	384.0	0.0		394.0	30.0	NM_001006617	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Missense_Mutation	SNP	ENST00000373498.1	hg19	CCDS35140.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.097275	0.56075	.	.	ENSG00000119487	ENST00000373511;ENST00000350766;ENST00000373503;ENST00000373498;ENST00000265960;ENST00000394063;ENST00000373497;ENST00000420643	.	.	.	6.07	3.72	0.42706	.	0.000000	0.85682	D	0.000000	T	0.64735	0.2625	M	0.65975	2.015	0.52099	D	0.999941	D;D;P;D	0.58268	0.971;0.971;0.936;0.982	P;P;P;P	0.57283	0.795;0.816;0.698;0.817	T	0.60454	-0.7260	9	0.15952	T	0.53	-3.9461	10.8112	0.46549	0.0:0.1281:0.0:0.8719	.	145;385;396;432	B7Z5E5;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7	.;.;.;SIN1_HUMAN	V	385;396;240;432;432;240;145;204	.	ENSP00000265960:I432V	I	-	1	0	MAPKAP1	127270123	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.298000	0.72763	0.523000	0.28482	0.533000	0.62120	ATC	.	.		0.453	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1			C	128230302	T	C	128230302	3	2	56	1	0	0	0	0	1	0	0	0	9297	1493	52	2	286	2	MAPKAP1	9	128230302	Missense_Mutation	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10	5052895	128230302	12983129	32	7096										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55839135	55839135	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	tgtgatgatcagaatgtagcGatcagtgctttccctgtcca	10	9	2	3	rs573043647		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr10:55839135G>A	ENST00000320301.6	-	17	2441	c.2047C>T	c.(2047-2049)Cgc>Tgc	p.R683C	PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395430.1_Missense_Mutation_p.R683C|PCDH15_ENST00000373957.3_Missense_Mutation_p.R661C|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000409834.1_Missense_Mutation_p.R294C|PCDH15_ENST00000395446.1_Missense_Mutation_p.R683C|PCDH15_ENST00000395445.1_Missense_Mutation_p.R690C|PCDH15_ENST00000414778.1_Missense_Mutation_p.R688C|PCDH15_ENST00000395432.2_Missense_Mutation_p.R646C|PCDH15_ENST00000373955.1_Missense_Mutation_p.R683C|PCDH15_ENST00000395438.1_Missense_Mutation_p.R683C|PCDH15_ENST00000437009.1_Missense_Mutation_p.R612C|PCDH15_ENST00000373965.2_Missense_Mutation_p.R690C|PCDH15_ENST00000395433.1_Missense_Mutation_p.R661C|PCDH15_ENST00000361849.3_Missense_Mutation_p.R683C	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	683	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				AGAATGTAGCGATCAGTGCTT	0.428										HNSCC(58;0.16)			G|||	1	0.000199681	0	0	5008	,	,		18679	0		0.001	False		,,,				2504	0				p.R688C		Atlas-SNP	.											PCDH15_ENST00000417177,caecum,carcinoma,+1,3	PCDH15	1715	.	0			c.C2062T						.						259	232	241					10																	55839135		2203	4300	6503	SO:0001583	missense	65217	exon18			TGTAGCGATCAGT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.2047C>T	chr10.hg19:g.55839135G>A	ENSP00000322604:p.Arg683Cys	264.0	1.0		151.0	61.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.763231	0.89932	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58940	0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.3;0.63	5.9	5.9	0.94986	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.72779	0.3503	L	0.45744	1.44	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;0.999;0.998;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.999;0.978;0.978;0.964;0.973;0.978;0.999;0.935;0.964;0.964;0.935;0.935;0.931;0.959;0.964	T	0.73225	-0.4050	9	0.87932	D	0	.	19.8634	0.96793	0.0:0.0:1.0:0.0	.	661;683;683;688;612;646;683;683;690;690;683;688;683;661;683	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	C	690;688;683;683;294;690;683;646;683;661;661;683;683;688;612;683	ENSP00000363076:R690C;ENSP00000410304:R688C;ENSP00000378826:R683C;ENSP00000386693:R294C;ENSP00000378832:R690C;ENSP00000378833:R683C;ENSP00000378820:R646C;ENSP00000354950:R683C;ENSP00000378821:R661C;ENSP00000363068:R661C;ENSP00000322604:R683C;ENSP00000378818:R683C;ENSP00000412628:R612C;ENSP00000363066:R683C	ENSP00000322604:R683C	R	-	1	0	PCDH15	55509141	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.963000	0.63694	2.800000	0.96347	0.591000	0.81541	CGC	.	.		0.428	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55839135	G	A	55839135	3	1	56	1	0	0	0	0	1	0	0	0	11520	1058	37	1	5507	1	PCDH15	10	55839135	Missense_Mutation	SNP	G	TCGA-CC-5260-01A-01D-A12Z-10		55839135	79695612	33	7097										
MKI67	4288	hgsc.bcm.edu	37	chr10	129901092	129901092	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ctcttggttcccgtgacgctTccatctttgccacctcccct	6	18	2	1			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr10:129901092T>A	ENST00000368654.3	-	13	9387	c.9012A>T	c.(9010-9012)ggA>ggT	p.G3004G	MKI67_ENST00000368653.3_Silent_p.G2644G	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3004					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CCGTGACGCTTCCATCTTTGC	0.572																																					p.G3004G		Atlas-SNP	.											.	MKI67	363	.	0			c.A9012T						.						88	80	83					10																	129901092		2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			GACGCTTCCATCT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.9012A>T	chr10.hg19:g.129901092T>A		107.0	0.0		73.0	32.0	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	hg19	CCDS7659.1																																																																																			.	.		0.572	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		A	129901092	T	A	129901092	2	1	56	1	0	0	0	0	0	0	0	1	9607	1770	62	4		4	MKI67	10	129901092	Silent	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10	74061957	129901092	5633655	34	7098										
OR8H2	390151	hgsc.bcm.edu	37	chr11	55872687	55872687	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	tccgcctggacctccagcttCacactcccatgtattttttc	5	16	1	0			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:55872687C>T	ENST00000313503.1	+	1	169	c.169C>T	c.(169-171)Cac>Tac	p.H57Y		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	57						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H57Y(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					CCTCCAGCTTCACACTCCCAT	0.423										HNSCC(53;0.14)																											p.H57Y		Atlas-SNP	.											OR8H2,NS,carcinoma,0,1	OR8H2	117	.	1	Substitution - Missense(1)	lung(1)	c.C169T						.						264	239	248					11																	55872687		2201	4293	6494	SO:0001583	missense	390151	exon1			CAGCTTCACACTC	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"GPCR / Class A : Olfactory receptors"	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.169C>T	chr11.hg19:g.55872687C>T	ENSP00000323982:p.His57Tyr	301.0	1.0		302.0	33.0	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	hg19	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	c	13.22	2.172220	0.38315	.	.	ENSG00000181767	ENST00000313503	T	0.15952	2.38	3.58	3.58	0.41010	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000030	T	0.42517	0.1206	M	0.90542	3.125	0.30664	N	0.754128	D	0.76494	0.999	D	0.70487	0.969	T	0.51108	-0.8747	10	0.87932	D	0	.	6.5232	0.22287	0.1797:0.7187:0.0:0.1016	.	57	Q8N162	OR8H2_HUMAN	Y	57	ENSP00000323982:H57Y	ENSP00000323982:H57Y	H	+	1	0	OR8H2	55629263	0.976000	0.34144	0.954000	0.39281	0.234000	0.25298	2.543000	0.45752	1.952000	0.56665	0.440000	0.28878	CAC	.	.		0.423	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200		T	55872687	C	T	55872687	3	4	56	1	0	0	0	0	1	0	0	0	11247	826	29	3	171	3	OR8H2	11	55872687	Missense_Mutation	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10		55872687	79133829	35	7099										
SUV420H1	51111	hgsc.bcm.edu	37	chr11	67957441	67957441	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	cttcagggtgtccttccccgTgtgctgtaattttgattgat	10	9	1	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:67957441T>A	ENST00000304363.4	-	2	456	c.103A>T	c.(103-105)Acg>Tcg	p.T35S	SUV420H1_ENST00000402789.1_Missense_Mutation_p.T35S|SUV420H1_ENST00000401547.2_Missense_Mutation_p.T35S|SUV420H1_ENST00000402185.2_Missense_Mutation_p.T35S|SUV420H1_ENST00000405515.1_Missense_Mutation_p.T35S	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	35					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TCCTTCCCCGTGTGCTGTAAT	0.453																																					p.T35S		Atlas-SNP	.											.	SUV420H1	125	.	0			c.A103T						.						370	320	337					11																	67957441		2200	4294	6494	SO:0001583	missense	51111	exon2			TCCCCGTGTGCTG	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.103A>T	chr11.hg19:g.67957441T>A	ENSP00000305899:p.Thr35Ser	538.0	0.0		462.0	122.0	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Missense_Mutation	SNP	ENST00000304363.4	hg19	CCDS31623.1	.	.	.	.	.	.	.	.	.	.	T	5.134	0.210418	0.09757	.	.	ENSG00000110066	ENST00000304363;ENST00000401547;ENST00000405515;ENST00000402789;ENST00000402185;ENST00000434573	T;T;T;T;T;T	0.40476	1.04;1.04;1.04;1.04;1.03;1.04	5.77	-11.5	0.00074	.	1.182760	0.05656	N	0.586013	T	0.19967	0.0480	L	0.29908	0.895	0.18873	N	0.999987	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.002;0.001	T	0.06463	-1.0825	10	0.08179	T	0.78	0.5301	5.4972	0.16809	0.3645:0.3961:0.1218:0.1176	.	35;35;35;35	B7WNX0;B5MCB3;Q4FZB7-2;Q4FZB7	.;.;.;SV421_HUMAN	S	35	ENSP00000305899:T35S;ENSP00000385965:T35S;ENSP00000385640:T35S;ENSP00000385005:T35S;ENSP00000384724:T35S;ENSP00000402921:T35S	ENSP00000305899:T35S	T	-	1	0	SUV420H1	67714017	0.000000	0.05858	0.002000	0.10522	0.950000	0.60333	-3.146000	0.00584	-4.185000	0.00066	-0.386000	0.06593	ACG	.	.		0.453	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		A	67957441	T	A	67957441	3	1	56	1	0	0	0	0	1	0	0	0	15429	1696	59	4	2602	4	SUV420H1	11	67957441	Missense_Mutation	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10	12084754	67957441	67049075	36	7100										
KRTAP5-11	440051	hgsc.bcm.edu	37	chr11	71293866	71293867	+	Frame_Shift_Ins	INS	-	-	C													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	cagagccacagcctccagaaINScagccacagcagcccatgat							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:71293866_71293867insC	ENST00000398530.1	-	1	54_55	c.17_18insG	c.(16-18)tgtfs	p.C6fs	KRTAP5-11_ENST00000526239.1_Intron|AP000867.1_ENST00000343767.3_Intron	NM_001005405.2	NP_001005405.1	Q6L8G4	KR511_HUMAN	keratin associated protein 5-11	6						keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						AGCCTCCAGAACAGCCACAGCA	0.644																																					p.C6fs		Atlas-INDEL	.											.	KRTAP5-11	36	.	0			c.18_19insG						.																																			SO:0001589	frameshift_variant	440051	exon1			.	AB126080	CCDS41685.1	11q13.4	2008-11-06			ENSG00000204571	ENSG00000204571		"Keratin associated proteins"	23606	protein-coding gene	gene with protein product						15144888	Standard	NM_001005405		Approved	KRTAP5.11, KRTAP5-6	uc001oqu.3	Q6L8G4	OTTHUMG00000057586	ENST00000398530.1:c.18dupG	chr11.hg19:g.71293867_71293867dupC	ENSP00000381541:p.Cys6fs	224.0	0.0		300.0	22.0	NM_001005405		Frame_Shift_Ins	INS	ENST00000398530.1	hg19	CCDS41685.1																																																																																			.	.		0.644	KRTAP5-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127969.1	NM_001005405		C	71293867	-	C	71293866	7	5	56	1	0	1	1	0	0	0	0	0	8569	41	2	0	456	0	KRTAP5-11	11	71293866	Frame_Shift_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10	3336425	71293866	63712650	37	7101										
LRTOMT	25906	hgsc.bcm.edu	37	chr11	71819726	71819726	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	atcagctgagtcgggcagacCtggtgctcctggcacaccgg	14	13	1	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:71819726C>A	ENST00000227618.4	-	0	886				LRTOMT_ENST00000439209.1_3'UTR|LRTOMT_ENST00000419228.1_Missense_Mutation_p.L171M|LRTOMT_ENST00000307198.7_Missense_Mutation_p.L211M|ANAPC15_ENST00000543015.1_5'Flank|ANAPC15_ENST00000543050.1_Intron|ANAPC15_ENST00000502597.2_Intron|LRTOMT_ENST00000435085.1_Missense_Mutation_p.L211M	NM_001278487.1|NM_001278491.1|NM_014042.2	NP_001265416.1|NP_001265420.1|NP_054761.1	P60006	APC15_HUMAN	anaphase promoting complex subunit 15						mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	anaphase-promoting complex (GO:0005680)|intracellular (GO:0005622)											TCGGGCAGACCTGGTGCTCCT	0.652																																					p.L211M		Atlas-SNP	.											.	LRTOMT	20	.	0			c.C631A						.						54	51	52					11																	71819726		692	1591	2283	SO:0001628	intergenic_variant	220074	exon9			GCAGACCTGGTGC	AL080071	CCDS8210.1, CCDS60880.1	11q13.4	2012-10-17	2012-05-31	2012-05-31	ENSG00000110200	ENSG00000110200		"Anaphase promoting complex subunits"	24531	protein-coding gene	gene with protein product		614717	"chromosome 11 open reading frame 51"	C11orf51		21926987	Standard	NM_014042		Approved	HSPC020, DKFZP564M082, APC15	uc001orw.3	P60006	OTTHUMG00000167865		chr11.hg19:g.71819726C>A		28.0	0.0		36.0	9.0	NM_001145309	G3V1Q3|Q9CXK2|Q9Y269	Missense_Mutation	SNP	ENST00000227618.4	hg19	CCDS8210.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687934	0.29962	.	.	ENSG00000184154	ENST00000419228;ENST00000435085;ENST00000307198	T;T;T	0.29142	1.58;1.58;1.58	5.17	3.21	0.36854	.	.	.	.	.	T	0.39384	0.1076	L	0.44542	1.39	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.75020	0.985;0.974	T	0.14090	-1.0485	9	0.18710	T	0.47	-3.6591	7.6386	0.28280	0.0:0.6301:0.0:0.3699	.	211;171	Q8WZ04;Q8WZ04-2	TOMT_HUMAN;.	M	171;211;211	ENSP00000392233:L171M;ENSP00000409789:L211M;ENSP00000305742:L211M	ENSP00000305742:L171M	L	+	1	2	LRTOMT	71497374	0.483000	0.25956	0.988000	0.46212	0.915000	0.54546	0.730000	0.26043	0.647000	0.30713	-0.144000	0.13903	CTG	.	.		0.652	ANAPC15-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396695.1	NM_014042		A	71819726	C	A	71819726	1	1	56	0	1	0	0	0	0	0	0	0	9055	680	24	3		3	LRTOMT	11	71819726	IGR	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10	525860	71819726	63186790	38	7102										
PICALM	8301	hgsc.bcm.edu	37	chr11	85712084	85712084	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	atgcacaaacttacctttaaAgctttcaaacgtgcctgttc	5	11	1	0			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:85712084A>G	ENST00000393346.3	-	10	1159	c.1011T>C	c.(1009-1011)gcT>gcC	p.A337A	PICALM_ENST00000356360.5_Silent_p.A337A|PICALM_ENST00000532317.1_Silent_p.A337A|PICALM_ENST00000526033.1_Silent_p.A337A|PICALM_ENST00000528398.1_Silent_p.A286A			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	337					axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				TTACCTTTAAAGCTTTCAAAC	0.423			T	"MLLT10, MLL"	"TALL, AML, "																																p.A337A		Atlas-SNP	.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	.	PICALM	82	.	0			c.T1011C						.						269	245	253					11																	85712084		2203	4299	6502	SO:0001819	synonymous_variant	8301	exon10			CTTTAAAGCTTTC	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.1011T>C	chr11.hg19:g.85712084A>G		520.0	0.0		584.0	158.0	NM_007166	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Silent	SNP	ENST00000393346.3	hg19	CCDS8272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.46|11.46	1.645177|1.645177	0.29246|0.29246	.|.	.|.	ENSG00000073921|ENSG00000073921	ENST00000529760;ENST00000530542|ENST00000529016	.|.	.|.	.|.	5.83|5.83	4.68|4.68	0.58851|0.58851	.|.	.|.	.|.	.|.	.|.	T|T	0.63546|0.63546	0.2520|0.2520	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.60606|0.60606	-0.7230|-0.7230	4|4	.|.	.|.	.|.	-10.6027|-10.6027	11.9757|11.9757	0.53089|0.53089	0.8663:0.0:0.0:0.1337|0.8663:0.0:0.0:0.1337	.|.	.|.	.|.	.|.	L|P	40|34	.|.	.|.	F|L	-|-	1|2	0|0	PICALM|PICALM	85389732|85389732	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.021000|2.021000	0.41020|0.41020	0.992000|0.992000	0.38840|0.38840	0.533000|0.533000	0.62120|0.62120	TTT|CTT	.	.		0.423	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166		G	85712084	A	G	85712084	2	3	56	1	0	0	0	0	0	0	0	1	11889	59	3	2		2	PICALM	11	85712084	Silent	SNP	A	TCGA-CC-5260-01A-01D-A12Z-10	13892358	85712084	49294432	39	7103										
PRMT8	56341	hgsc.bcm.edu	37	chr12	3702274	3702274	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ctgccttgcagcgagacctcGatttcacagtagacttggat	10	11	1	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr12:3702274G>A	ENST00000382622.3	+	10	1501	c.1111G>A	c.(1111-1113)Gat>Aat	p.D371N	PRMT8_ENST00000261252.4_3'UTR|PRMT8_ENST00000452611.2_Missense_Mutation_p.D362N	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	371	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			GCGAGACCTCGATTTCACAGT	0.532																																					p.D371N		Atlas-SNP	.											.	PRMT8	97	.	0			c.G1111A						.						99	82	87					12																	3702274		2203	4300	6503	SO:0001583	missense	56341	exon10			GACCTCGATTTCA	AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"Protein arginine methyltransferases"	5188	protein-coding gene	gene with protein product		610086	"HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)", "HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.1111G>A	chr12.hg19:g.3702274G>A	ENSP00000372067:p.Asp371Asn	108.0	0.0		126.0	15.0	NM_019854	B2RDP0|Q8TBJ8	Missense_Mutation	SNP	ENST00000382622.3	hg19	CCDS8521.2	.	.	.	.	.	.	.	.	.	.	G	21.8	4.199887	0.79015	.	.	ENSG00000111218	ENST00000452611;ENST00000382622	D;D	0.86627	-2.15;-2.15	5.22	5.22	0.72569	.	0.044150	0.85682	D	0.000000	D	0.86389	0.5921	L	0.54965	1.715	0.80722	D	1	P;B	0.47841	0.901;0.41	B;B	0.44044	0.439;0.133	D	0.87923	0.2705	10	0.59425	D	0.04	.	16.2763	0.82644	0.0:0.0:1.0:0.0	.	362;371	Q9NR22-2;Q9NR22	.;ANM8_HUMAN	N	362;371	ENSP00000414507:D362N;ENSP00000372067:D371N	ENSP00000372067:D371N	D	+	1	0	PRMT8	3572535	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.732000	0.98816	2.445000	0.82738	0.313000	0.20887	GAT	.	.		0.532	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854		A	3702274	G	A	3702274	3	1	56	1	0	0	0	0	1	0	0	0	12554	1058	37	1	1149	1	PRMT8	12	3702274	Missense_Mutation	SNP	G	TCGA-CC-5260-01A-01D-A12Z-10		3702274	130149621	40	7104										
POU6F1	5463	hgsc.bcm.edu	37	chr12	51589910	51589911	+	Frame_Shift_Ins	INS	-	-	C													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	gctttgggctggtgctggggINSccgccacactagctgagttc							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr12:51589910_51589911insC	ENST00000389243.4	-	8	1030_1031	c.91_92insG	c.(91-93)gccfs	p.A31fs	POU6F1_ENST00000333640.10_Frame_Shift_Ins_p.A31fs|POU6F1_ENST00000550824.1_Frame_Shift_Ins_p.A31fs			Q14863	PO6F1_HUMAN	POU class 6 homeobox 1	31	Gln/Pro-rich.				brain development (GO:0007420)|heart development (GO:0007507)|muscle organ development (GO:0007517)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	11						TGGTGCTGGGGCCGCCACACTA	0.629																																					p.A31fs		Atlas-INDEL	.											.	POU6F1	31	.	0			c.92_93insG						.																																			SO:0001589	frameshift_variant	5463	exon3			.	AL832881	CCDS31803.1	12q13.13	2011-06-20	2007-07-13			ENSG00000184271		"Homeoboxes / POU class"	9224	protein-coding gene	gene with protein product			"POU domain, class 6, transcription factor 1"			7908264	Standard	NM_002702		Approved	BRN5, MPOU, TCFB1	uc001rxz.3	Q14863		ENST00000389243.4:c.92dupG	chr12.hg19:g.51589912_51589912dupC	ENSP00000373895:p.Ala31fs	58.0	0.0		116.0	13.0	NM_002702	Q15944|Q6DK47|Q7Z7P6	Frame_Shift_Ins	INS	ENST00000389243.4	hg19	CCDS31803.1																																																																																			.	.		0.629	POU6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405126.1	NM_002702		C	51589911	-	C	51589910	7	5	56	1	0	1	1	0	0	0	0	0	12293	1203	42	0	829	0	POU6F1	12	51589910	Frame_Shift_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10	47887636	51589910	82261985	41	7105										
PCDH20	64881	hgsc.bcm.edu	37	chr13	61987587	61987587	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	gcattttccgggacccacacCgagatctgggaaacagggaa	12	11	1	1	rs201107730		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr13:61987587C>T	ENST00000409186.1	-	5	2750	c.645G>A	c.(643-645)tcG>tcA	p.S215S	PCDH20_ENST00000409204.4_Silent_p.S215S			Q8N6Y1	PCD20_HUMAN	protocadherin 20	215	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.S188S(1)|p.S215S(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		GGACCCACACCGAGATCTGGG	0.527																																					p.S215S		Atlas-SNP	.											PCDH20_ENST00000409186,caecum,carcinoma,0,2	PCDH20	265	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G645A						.						110	99	102					13																	61987587		2203	4300	6503	SO:0001819	synonymous_variant	64881	exon2			CCACACCGAGATC	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.645G>A	chr13.hg19:g.61987587C>T		107.0	1.0		92.0	20.0	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Silent	SNP	ENST00000409186.1	hg19	CCDS9442.2																																																																																			.	C|1.000;A|0.000		0.527	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		T	61987587	C	T	61987587	2	4	56	1	0	0	0	0	0	0	0	1	11524	639	23	1		1	PCDH20	13	61987587	Silent	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10		61987587	53182291	42	7106										
C14orf101	54916	hgsc.bcm.edu	37	chr14	57075883	57075883	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ttctctgctggtttgctgccCtatgtccaccttcccatctc	6	16	2	0			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr14:57075883C>G	ENST00000261556.6	+	6	818	c.696C>G	c.(694-696)ccC>ccG	p.P232P	TMEM260_ENST00000538838.1_Silent_p.P232P|TMEM260_ENST00000536419.1_5'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	232						integral component of membrane (GO:0016021)											GTTTGCTGCCCTATGTCCACC	0.478																																					p.P232P		Atlas-SNP	.											.	.	.	.	0			c.C696G						.						309	295	300					14																	57075883		2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			GCTGCCCTATGTC	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 101"	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.696C>G	chr14.hg19:g.57075883C>G		582.0	0.0		610.0	133.0	NM_017799	A8KAN4|B3KPF5|Q86XE1	Silent	SNP	ENST00000261556.6	hg19	CCDS9727.2																																																																																			.	.		0.478	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799		G	57075883	C	G	57075883	2	3	56	1	0	0	0	0	0	0	0	1	1736	668	24	4		4	C14orf101	14	57075883	Silent	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10		57075883	50273657	43	7107										
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42110257	42110257	+	Frame_Shift_Del	DEL	A	A	-													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	gaagctgtttaaagggtcacAgggtgaggacggcacactca							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr15:42110257delA	ENST00000456763.2	+	18	2169	c.1973delA	c.(1972-1974)cagfs	p.Q658fs	MAPKBP1_ENST00000514566.1_Frame_Shift_Del_p.Q652fs|MAPKBP1_ENST00000221214.6_Frame_Shift_Del_p.Q535fs|MAPKBP1_ENST00000457542.2_Frame_Shift_Del_p.Q652fs|MAPKBP1_ENST00000260357.7_Frame_Shift_Del_p.Q491fs	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	658										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		AAAGGGTCACAGGGTGAGGAC	0.527																																					p.Q658fs		Atlas-Indel,Pindel	.											.	MAPKBP1	120	.	0			c.1972delC						.						116	119	118					15																	42110257		2203	4300	6503	SO:0001589	frameshift_variant	23005	exon18			.	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.1973delA	chr15.hg19:g.42110257delA	ENSP00000393099:p.Gln658fs	147.0	0.0		192.0	45.0	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Frame_Shift_Del	DEL	ENST00000456763.2	hg19	CCDS45239.1																																																																																			.	.		0.527	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		-	42110257	A	-	42110257	7	5	56	1	0	1	0	1	0	0	0	0	9301	188	7	0	2039	0	MAPKBP1	15	42110257	Frame_Shift_Del	DEL	A	TCGA-CC-5260-01A-01D-A12Z-10		42110257	60421135	44	7108										
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79063584	79063584	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	gcgggacctcgtcgtggccaCctgcctccctgtggatggtg	15	14	0	0			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr15:79063584C>T	ENST00000388820.4	-	16	2648	c.2438G>A	c.(2437-2439)gGt>gAt	p.G813D	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	813					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GTCGTGGCCACCTGCCTCCCT	0.652																																					p.G813D		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.G2438A						.						44	33	37					15																	79063584		2196	4291	6487	SO:0001583	missense	11173	exon16			TGGCCACCTGCCT	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.2438G>A	chr15.hg19:g.79063584C>T	ENSP00000373472:p.Gly813Asp	142.0	0.0		208.0	39.0	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	hg19	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.568149	0.00133	.	.	ENSG00000136378	ENST00000388820	T	0.58506	0.33	3.28	-1.88	0.07713	.	0.734180	0.12442	N	0.468536	T	0.14356	0.0347	N	0.00496	-1.435	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29549	-1.0008	10	0.02654	T	1	.	1.6689	0.02808	0.1567:0.1053:0.189:0.549	.	813	Q9UKP4	ATS7_HUMAN	D	813	ENSP00000373472:G813D	ENSP00000373472:G813D	G	-	2	0	ADAMTS7	76850639	0.004000	0.15560	0.000000	0.03702	0.019000	0.09904	1.364000	0.34171	-0.341000	0.08376	-0.768000	0.03414	GGT	.	.		0.652	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		T	79063584	C	T	79063584	3	4	56	1	0	0	0	0	1	0	0	0	271	507	18	3	2658	3	ADAMTS7	15	79063584	Missense_Mutation	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10	36953327	79063584	23467808	45	7109										
CDH1	999	hgsc.bcm.edu	37	chr16	68856129	68856129	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	cattcagtacaacgacccaaGtgggtacctgagttttattt	8	9	1	1			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr16:68856129G>A	ENST00000261769.5	+	12	2127		c.e12+1		CDH1_ENST00000422392.2_Splice_Site|RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_Splice_Site	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)						adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		AACGACCCAAGTGGGTACCTG	0.488			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												.		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	CDH1,NS,carcinoma,0,2	CDH1	535	.	0			c.1936+1G>A						.						72	60	64					16																	68856129		2198	4300	6498	SO:0001630	splice_region_variant	999	exon12	Familial Cancer Database	HDGC	ACCCAAGTGGGTA	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1936+1G>A	chr16.hg19:g.68856129G>A		82.0	0.0		89.0	17.0	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Splice_Site	SNP	ENST00000261769.5	hg19	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.025419	0.35701	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000422392	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4194	0.90584	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDH1	67413630	1.000000	0.71417	0.540000	0.28089	0.048000	0.14542	7.958000	0.87877	2.697000	0.92050	0.632000	0.83419	.	.	.		0.488	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	Intron	A	68856129	G	A	68856129	5	1	56	1	0	0	0	0	0	0	1	0	3097	1043	36	3	1983	3	CDH1	16	68856129	Splice_Site	SNP	G	TCGA-CC-5260-01A-01D-A12Z-10		68856129	21498624	46	7110										
SGCA	6442	hgsc.bcm.edu	37	chr17	48244792	48244792	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	gctacacccacttgtgggccGtgtctttgtgcacaccttgg	11	13	1	0	rs371675217		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr17:48244792G>T	ENST00000262018.3	+	2	137	c.101G>T	c.(100-102)cGt>cTt	p.R34L	SGCA_ENST00000543315.1_Missense_Mutation_p.R34L|SGCA_ENST00000513942.1_Intron|SGCA_ENST00000451235.2_5'UTR|SGCA_ENST00000344627.6_Missense_Mutation_p.R34L|RP11-893F2.14_ENST00000572855.1_RNA	NM_000023.2	NP_000014.1	Q16586	SGCA_HUMAN	sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein)	34			R -> C (in LGMD2D). {ECO:0000269|PubMed:9192266}.|R -> H (in LGMD2D). {ECO:0000269|PubMed:7663524}.		muscle contraction (GO:0006936)|muscle organ development (GO:0007517)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						CTTGTGGGCCGTGTCTTTGTG	0.642																																					p.R34L		Atlas-SNP	.											SGCA,colon,carcinoma,0,1	SGCA	35	.	0			c.G101T	GRCh37	CM951149	SGCA	M		.						104	87	92					17																	48244792		2203	4300	6503	SO:0001583	missense	6442	exon2			TGGGCCGTGTCTT	L34355	CCDS32679.1, CCDS45729.1	17q21	2014-09-17	2002-08-29		ENSG00000108823	ENSG00000108823			10805	protein-coding gene	gene with protein product	"50kD DAG", "Sarcoglycan, alpha (50kD dystrophin-associated glycoprotein; adhalin)", "adhalin (limb girdle muscular dystrophy 2D)"	600119	"sarcoglycan, alpha (50kD dystrophin-associated glycoprotein)"	ADL		7937874	Standard	NM_000023		Approved	SCARMD1, LGMD2D, adhalin, DMDA2, A2	uc002iqi.3	Q16586	OTTHUMG00000162024	ENST00000262018.3:c.101G>T	chr17.hg19:g.48244792G>T	ENSP00000262018:p.Arg34Leu	130.0	0.0		219.0	51.0	NM_001135697	A6NEB8|A8K3K7|Q13710|Q13712	Missense_Mutation	SNP	ENST00000262018.3	hg19	CCDS32679.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857415	0.51376	.	.	ENSG00000108823	ENST00000344627;ENST00000262018;ENST00000543315	D;D;D	0.98531	-4.98;-4.98;-4.98	4.47	4.47	0.54385	Dystroglycan-type cadherin-like (1);Cadherin-like (1);	0.144240	0.43579	D	0.000544	D	0.95990	0.8694	L	0.46157	1.445	0.80722	D	1	B;B	0.28636	0.218;0.004	B;B	0.26864	0.074;0.007	D	0.95008	0.8149	10	0.42905	T	0.14	-15.278	12.9801	0.58559	0.0:0.0:1.0:0.0	.	34;34	Q16586-2;Q16586	.;SGCA_HUMAN	L	34	ENSP00000345522:R34L;ENSP00000262018:R34L;ENSP00000444539:R34L	ENSP00000262018:R34L	R	+	2	0	SGCA	45599791	0.584000	0.26766	0.960000	0.40013	0.753000	0.42808	2.894000	0.48640	2.184000	0.69523	0.407000	0.27541	CGT	.	.		0.642	SGCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366841.1	NM_000023		T	48244792	G	T	48244792	3	4	56	1	0	0	0	0	1	0	0	0	14214	1145	40	1	107	1	SGCA	17	48244792	Missense_Mutation	SNP	G	TCGA-CC-5260-01A-01D-A12Z-10		48244792	32950418	47	7111										
C18orf8	29919	hgsc.bcm.edu	37	chr18	21104108	21104109	+	Frame_Shift_Ins	INS	-	-	C													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	tgtaggtcctgctgccgtgaINSccagccagtctcctgttcca							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr18:21104108_21104109insC	ENST00000269221.3	+	11	1086_1087	c.976_977insC	c.(976-978)accfs	p.T326fs	C18orf8_ENST00000590868.1_Frame_Shift_Ins_p.T278fs	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	326						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TGCTGCCGTGACCAGCCAGTCT	0.46																																					p.T326fs		Atlas-INDEL	.											.	C18orf8	58	.	0			c.976_977insC						.																																			SO:0001589	frameshift_variant	29919	exon11			.	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"colon cancer associated protein Mic1", "macrophage inhibitory cytokine 1"					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.978dupC	chr18.hg19:g.21104110_21104110dupC	ENSP00000269221:p.Thr326fs	155.0	0.0		170.0	10.0	NM_013326	Q9BU17|Q9Y5M0	Frame_Shift_Ins	INS	ENST00000269221.3	hg19	CCDS32803.1																																																																																			.	.		0.46	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326		C	21104109	-	C	21104108	7	5	56	1	0	1	1	0	0	0	0	0	1909	275	10	0	1018	0	C18orf8	18	21104108	Frame_Shift_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10		21104108	56973140	48	7112										
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38610466	38610466	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	gacgaggagaccacatcttcCtacaggcgacagagggttct	12	11	2	2			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr19:38610466C>T	ENST00000222345.6	+	9	3321	c.2812C>T	c.(2812-2814)Cta>Tta	p.L938L		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	938					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CCACATCTTCCTACAGGCGAC	0.532																																					p.L938L		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.C2812T						.						44	47	46					19																	38610466		2203	4300	6503	SO:0001819	synonymous_variant	23094	exon9			ATCTTCCTACAGG	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.2812C>T	chr19.hg19:g.38610466C>T		47.0	0.0		76.0	31.0	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	hg19	CCDS33007.1																																																																																			.	.		0.532	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		T	38610466	C	T	38610466	2	4	56	1	0	0	0	0	0	0	0	1	14346	680	24	3		3	SIPA1L3	19	38610466	Silent	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10		38610466	20518517	49	7113										
EPN1	29924	hgsc.bcm.edu	37	chr19	56206198	56206199	+	Frame_Shift_Del	DEL	TG	TG	-													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	gctgtgggcagccccccaccTgcagccacaccaactcccac							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr19:56206198_56206199delTG	ENST00000270460.6	+	10	1682_1683	c.1371_1372delTG	c.(1369-1374)cctgcafs	p.A459fs	EPN1_ENST00000411543.2_Frame_Shift_Del_p.A545fs|AC010525.6_ENST00000587937.1_lincRNA|EPN1_ENST00000085079.7_Frame_Shift_Del_p.A433fs|AC010525.4_ENST00000585559.1_RNA|AC010525.7_ENST00000589698.1_lincRNA	NM_001130072.1	NP_001123544.1	Q9Y6I3	EPN1_HUMAN	epsin 1	459	Ala/Gly/Pro-rich.				embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|female pregnancy (GO:0007565)|in utero embryonic development (GO:0001701)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|Notch signaling pathway (GO:0007219)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	17		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)		GCCCCCCACCTGCAGCCACACC	0.693																																					p.543_543del		Atlas-INDEL	.											.	EPN1	98	.	0			c.1628_1629del						.																																			SO:0001589	frameshift_variant	29924	exon10			.	AF073727	CCDS46198.1, CCDS46199.1, CCDS46200.1	19q13.42	2014-08-12			ENSG00000063245	ENSG00000063245			21604	protein-coding gene	gene with protein product		607262				9723620, 10557078	Standard	NM_001130072		Approved		uc002qlx.3	Q9Y6I3	OTTHUMG00000180911	ENST00000270460.6:c.1371_1372delTG	chr19.hg19:g.56206198_56206199delTG	ENSP00000270460:p.Ala459fs	71.0	0.0		105.0	11.0	NM_001130071	Q86ST3|Q9HA18	Frame_Shift_Del	DEL	ENST00000270460.6	hg19	CCDS46199.1																																																																																			.	.		0.693	EPN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453610.1	NM_013333		-	56206199	TG	-	56206198	7	5	56	1	0	1	0	1	0	0	0	0	5187	1567	55	0	1746	0	EPN1	19	56206198	Frame_Shift_Del	DEL	TG	TCGA-CC-5260-01A-01D-A12Z-10	17595732	56206198	2922785	50	7114										
CBS	875	hgsc.bcm.edu	37	chr21	44492127	44492128	+	Frame_Shift_Ins	INS	-	-	G													0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	gatgtggggactcggaggcaINSggccggcccagctgccaggt							TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr21:44492127_44492128insG	ENST00000398165.3	-	3	435_436	c.176_177insC	c.(175-177)cctfs	p.P59fs	CBS_ENST00000544202.1_5'Flank|CBS_ENST00000352178.5_Frame_Shift_Ins_p.P59fs|CBS_ENST00000398158.1_Frame_Shift_Ins_p.P59fs|CBS_ENST00000359624.3_Frame_Shift_Ins_p.P59fs|CBS_ENST00000398168.1_Frame_Shift_Ins_p.P59fs|CBS_ENST00000470912.1_5'UTR	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	59					cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	ACTCGGAGGCAGGCCGGCCCAG	0.624																																					p.P59fs		Atlas-INDEL	.											.	CBS	85	.	0			c.177_178insC						.																																			SO:0001589	frameshift_variant	875	exon3			.	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.177dupC	chr21.hg19:g.44492129_44492129dupG	ENSP00000381231:p.Pro59fs	123.0	0.0		191.0	13.0	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Frame_Shift_Ins	INS	ENST00000398165.3	hg19	CCDS13693.1																																																																																			.	.		0.624	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071		G	44492128	-	G	44492127	7	5	56	1	0	1	1	0	0	0	0	0	2713	175	7	0	1538	0	CBS	21	44492127	Frame_Shift_Ins	INS	-	TCGA-CC-5260-01A-01D-A12Z-10		44492127	3637768	51	7115										
KRTAP10-11	386678	hgsc.bcm.edu	37	chr21	46066650	46066650	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	ccagccggcttgctgcacctCctccccctgccagcaggcct	9	21	0	0			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr21:46066650C>G	ENST00000334670.8	+	1	320	c.275C>G	c.(274-276)tCc>tGc	p.S92C	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	92	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						TGCTGCACCTCCTCCCcctgc	0.657																																					p.S92C		Atlas-SNP	.											.	KRTAP10-11	36	.	0			c.C275G						.						85	87	86					21																	46066650		2203	4298	6501	SO:0001583	missense	386678	exon1			GCACCTCCTCCCC	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"Keratin associated proteins"	20528	protein-coding gene	gene with protein product			"keratin associated protein 10-11"	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.275C>G	chr21.hg19:g.46066650C>G	ENSP00000334197:p.Ser92Cys	191.0	0.0		247.0	23.0	NM_198692	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	hg19	CCDS42962.1	.	.	.	.	.	.	.	.	.	.	c	9.733	1.162758	0.21538	.	.	ENSG00000243489	ENST00000334670	T	0.00695	5.83	3.57	0.12	0.14691	.	.	.	.	.	T	0.01627	0.0052	M	0.80422	2.495	0.09310	N	1	B	0.12013	0.005	B	0.12837	0.008	T	0.28713	-1.0035	9	0.49607	T	0.09	.	12.8421	0.57809	0.0:0.4303:0.5697:0.0	.	92	P60412	KR10B_HUMAN	C	92	ENSP00000334197:S92C	ENSP00000334197:S92C	S	+	2	0	KRTAP10-11	44891078	0.000000	0.05858	0.018000	0.16275	0.822000	0.46500	0.194000	0.17135	0.008000	0.14787	0.456000	0.33151	TCC	.	.		0.657	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692		G	46066650	C	G	46066650	3	3	56	1	0	0	0	0	1	0	0	0	8516	855	30	4	277	4	KRTAP10-11	21	46066650	Missense_Mutation	SNP	C	TCGA-CC-5260-01A-01D-A12Z-10	1574523	46066650	2063245	52	7116										
GPR82	27197	hgsc.bcm.edu	37	chrX	41586732	41586732	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	aaatttcgccagcccaacttTgctagaaaactatgcattta	5	10	0	1			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chrX:41586732T>A	ENST00000302548.4	+	3	693	c.453T>A	c.(451-453)ttT>ttA	p.F151L	CASK_ENST00000361962.4_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378154.1_Intron|CASK_ENST00000378163.1_Intron	NM_080817.4	NP_543007.1	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	151						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	10						AGCCCAACTTTGCTAGAAAAC	0.388																																					p.F151L		Atlas-SNP	.											.	GPR82	52	.	0			c.T453A						.						49	50	50					X																	41586732		2202	4299	6501	SO:0001583	missense	27197	exon3			CAACTTTGCTAGA	AF411111	CCDS14259.1	Xp11.4	2012-08-21			ENSG00000171657	ENSG00000171657		"GPCR / Class A : Orphans"	4533	protein-coding gene	gene with protein product		300748				11574155	Standard	NM_080817		Approved		uc004dft.3	Q96P67	OTTHUMG00000021373	ENST00000302548.4:c.453T>A	chrX.hg19:g.41586732T>A	ENSP00000303549:p.Phe151Leu	182.0	0.0		100.0	13.0	NM_080817	Q5VT13	Missense_Mutation	SNP	ENST00000302548.4	hg19	CCDS14259.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336319	0.60963	.	.	ENSG00000171657	ENST00000302548	T	0.35236	1.32	5.73	2.07	0.26955	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000005	T	0.46014	0.1371	L	0.54323	1.7	0.31162	N	0.704282	D	0.69078	0.997	D	0.80764	0.994	T	0.48091	-0.9065	10	0.12430	T	0.62	-14.8389	8.3659	0.32387	0.0:0.3226:0.0:0.6774	.	151	Q96P67	GPR82_HUMAN	L	151	ENSP00000303549:F151L	ENSP00000303549:F151L	F	+	3	2	GPR82	41471676	1.000000	0.71417	0.949000	0.38748	0.948000	0.59901	1.063000	0.30567	0.015000	0.14971	-0.323000	0.08544	TTT	.	.		0.388	GPR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056261.1	NM_080817		A	41586732	T	A	41586732	3	1	56	1	0	0	0	0	1	0	0	0	6720	1809	63	4	455	4	GPR82	23	41586732	Missense_Mutation	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10		41586732	113683828	53	7117										
SMC1A	8243	hgsc.bcm.edu	37	chrX	53409455	53409455	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.424376731301939	0	0.474303405572755	1	1	0	tgctattgcgggacagggccTtatagatctcatcaatgttg	11	8	2	1			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chrX:53409455T>A	ENST00000322213.4	-	21	3384	c.3257A>T	c.(3256-3258)aAg>aTg	p.K1086M	SMC1A_ENST00000469129.1_5'UTR	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	1086					DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						GGACAGGGCCTTATAGATCTC	0.522																																					p.K1086M		Atlas-SNP	.											.	SMC1A	112	.	0			c.A3257T						.						76	61	66					X																	53409455		2203	4300	6503	SO:0001583	missense	8243	exon21			AGGGCCTTATAGA	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"Structural maintenance of chromosomes proteins"	11111	protein-coding gene	gene with protein product		300040	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.3257A>T	chrX.hg19:g.53409455T>A	ENSP00000323421:p.Lys1086Met	137.0	0.0		139.0	38.0	NM_006306	O14995|Q16351|Q2M228	Missense_Mutation	SNP	ENST00000322213.4	hg19	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.226692	0.79576	.	.	ENSG00000072501	ENST00000322213	T	0.79845	-1.31	5.45	5.45	0.79879	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.91905	0.7437	M	0.93939	3.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93744	0.7053	10	0.87932	D	0	.	13.6717	0.62430	0.0:0.0:0.0:1.0	.	1086	Q14683	SMC1A_HUMAN	M	1086	ENSP00000323421:K1086M	ENSP00000323421:K1086M	K	-	2	0	SMC1A	53426180	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.162000	0.71874	1.940000	0.56252	0.486000	0.48141	AAG	.	.		0.522	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		A	53409455	T	A	53409455	3	1	56	1	0	0	0	0	1	0	0	0	14796	1609	56	4	464	4	SMC1A	23	53409455	Missense_Mutation	SNP	T	TCGA-CC-5260-01A-01D-A12Z-10	11822723	53409455	101861105	54	7118										
KCNQ4	9132	hgsc.bcm.edu	37	chr1	41285601	41285602	+	Frame_Shift_Ins	INS	-	-	G													0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	accgcacacatggctgggcaINSgggtcctggctgctggcttc							TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr1:41285601_41285602insG	ENST00000347132.5	+	6	971_972	c.889_890insG	c.(889-891)aggfs	p.R297fs	KCNQ4_ENST00000509682.2_Frame_Shift_Ins_p.R297fs|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	297					inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	ATGGCTGGGCAGGGTCCTGGCT	0.594																																					p.R297fs		Atlas-INDEL	.											.	KCNQ4	58	.	0			c.889_890insG						.																																			SO:0001589	frameshift_variant	9132	exon6			.	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.892dupG	chr1.hg19:g.41285604_41285604dupG	ENSP00000262916:p.Arg297fs	163.0	0.0		155.0	10.0	NM_004700	O96025	Frame_Shift_Ins	INS	ENST00000347132.5	hg19	CCDS456.1																																																																																			.	.		0.594	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700		G	41285602	-	G	41285601	7	5	57	1	0	1	1	0	0	0	0	0	8094	179	7	0	911	0	KCNQ4	1	41285601	Frame_Shift_Ins	INS	-	TCGA-CC-5261-01A-01D-A12Z-10		41285601	207965020	1	7119										
ANKRD34A	284615	hgsc.bcm.edu	37	chr1	145474788	145474788	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	cctgctggggggcttccagaGtctaggtgggcctggggagc	19	10	1	1			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr1:145474788G>T	ENST00000323397.4	+	4	2753	c.1460G>T	c.(1459-1461)aGt>aTt	p.S487I	LIX1L_ENST00000369308.3_5'Flank|RP11-315I20.1_ENST00000600340.1_RNA	NM_001039888.2	NP_001034977.1	Q69YU3	AN34A_HUMAN	ankyrin repeat domain 34A	487						cytoplasm (GO:0005737)				endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	20	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGCTTCCAGAGTCTAGGTGGG	0.627																																					p.S487I		Atlas-SNP	.											.	ANKRD34A	52	.	0			c.G1460T						.						14	16	15					1																	145474788		2202	4299	6501	SO:0001583	missense	284615	exon4			TCCAGAGTCTAGG	AK128050	CCDS72874.1	1q21.1	2013-01-10	2007-11-20	2007-11-20	ENSG00000181039	ENSG00000272031		"Ankyrin repeat domain containing"	27639	protein-coding gene	gene with protein product			"ankyrin repeat domain 34"	ANKRD34			Standard	NM_001039888		Approved		uc001enq.1	Q69YU3	OTTHUMG00000013740	ENST00000323397.4:c.1460G>T	chr1.hg19:g.145474788G>T	ENSP00000314103:p.Ser487Ile	35.0	0.0		125.0	28.0	NM_001039888	B3KSU3	Missense_Mutation	SNP	ENST00000323397.4	hg19	CCDS30829.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.567226	0.45694	.	.	ENSG00000181039	ENST00000323397	T	0.72394	-0.65	4.95	4.95	0.65309	.	0.817225	0.11261	N	0.582578	T	0.40645	0.1125	N	0.22421	0.69	0.36766	D	0.883537	P	0.45126	0.851	B	0.35688	0.208	T	0.49204	-0.8964	10	0.87932	D	0	-8.3853	9.2048	0.37282	0.0957:0.0:0.9043:0.0	.	487	Q69YU3	AN34A_HUMAN	I	487	ENSP00000314103:S487I	ENSP00000314103:S487I	S	+	2	0	ANKRD34A	144186145	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.040000	0.49799	2.563000	0.86464	0.650000	0.86243	AGT	.	.		0.627	ANKRD34A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038512.1			T	145474788	G	T	145474788	3	4	57	1	0	0	0	0	1	0	0	0	662	1029	36	3	1462	3	ANKRD34A	1	145474788	Missense_Mutation	SNP	G	TCGA-CC-5261-01A-01D-A12Z-10	104189187	145474788	103775833	2	7120										
OR10R2	343406	hgsc.bcm.edu	37	chr1	158450031	158450031	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	actgttgtgctcttcaaatgTtcttcttccttggttttgcc	7	10	4	0			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr1:158450031T>C	ENST00000368152.1	+	1	364	c.364T>C	c.(364-366)Ttc>Ctc	p.F122L	RP11-144L1.4_ENST00000426251.1_RNA|RP11-144L1.4_ENST00000419738.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					TCTTCAAATGTTCTTCTTCCT	0.453																																					p.F122L		Atlas-SNP	.											.	OR10R2	81	.	0			c.T364C						.						401	335	357					1																	158450031		2203	4300	6503	SO:0001583	missense	343406	exon1			CAAATGTTCTTCT	AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"GPCR / Class A : Olfactory receptors"	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.364T>C	chr1.hg19:g.158450031T>C	ENSP00000357134:p.Phe122Leu	396.0	0.0		657.0	53.0	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	hg19	CCDS30898.1	.	.	.	.	.	.	.	.	.	.	t	21.6	4.174090	0.78452	.	.	ENSG00000198965	ENST00000368152	T	0.02067	4.47	4.48	4.48	0.54585	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.03477	0.0100	M	0.68728	2.09	0.36402	D	0.863218	P	0.50943	0.94	P	0.52424	0.698	T	0.41360	-0.9513	9	0.52906	T	0.07	.	12.8873	0.58051	0.0:0.0:0.0:1.0	.	122	Q8NGX6	O10R2_HUMAN	L	122	ENSP00000357134:F122L	ENSP00000357134:F122L	F	+	1	0	OR10R2	156716655	0.999000	0.42202	1.000000	0.80357	0.931000	0.56810	3.223000	0.51231	1.847000	0.53656	0.533000	0.62120	TTC	.	.		0.453	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472		C	158450031	T	C	158450031	3	2	57	1	0	0	0	0	1	0	0	0	10926	1725	60	2	366	2	OR10R2	1	158450031	Missense_Mutation	SNP	T	TCGA-CC-5261-01A-01D-A12Z-10	12975243	158450031	90800590	3	7121										
ATP1A2	477	hgsc.bcm.edu	37	chr1	160106761	160106761	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	tgccagcatcgtggtggtgcAgtgggctgacctcatcatct	13	11	3	1			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr1:160106761A>T	ENST00000361216.3	+	20	2869	c.2780A>T	c.(2779-2781)cAg>cTg	p.Q927L	ATP1A2_ENST00000392233.3_Missense_Mutation_p.Q927L	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	927					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			GTGGTGGTGCAGTGGGCTGAC	0.607																																					p.Q927L		Atlas-SNP	.											.	ATP1A2	167	.	0			c.A2780T						.						184	144	157					1																	160106761		2203	4300	6503	SO:0001583	missense	477	exon20			TGGTGCAGTGGGC	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.2780A>T	chr1.hg19:g.160106761A>T	ENSP00000354490:p.Gln927Leu	116.0	0.0		286.0	52.0	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	hg19	CCDS1196.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	26.6|26.6	4.754991|4.754991	0.89843|0.89843	.|.	.|.	ENSG00000018625|ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000435866|ENST00000447527	D;D|.	0.97256|.	-4.31;-4.31|.	4.65|4.65	4.65|4.65	0.58169|0.58169	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);|.	0.060913|.	0.64402|.	D|.	0.000003|.	D|D	0.86251|0.86251	0.5888|0.5888	H|H	0.98295|0.98295	4.195|4.195	0.80722|0.80722	D|D	1|1	D;D|.	0.58268|.	0.977;0.982|.	D;D|.	0.67900|.	0.924;0.954|.	D|D	0.90695|0.90695	0.4616|0.4616	10|5	0.87932|.	D|.	0|.	.|.	12.3814|12.3814	0.55309|0.55309	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	827;927|.	F5GXJ7;P50993|.	.;AT1A2_HUMAN|.	L|C	927;927;630|621	ENSP00000354490:Q927L;ENSP00000376066:Q927L|.	ENSP00000354490:Q927L|.	Q|S	+|+	2|1	0|0	ATP1A2|ATP1A2	158373385|158373385	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	9.084000|9.084000	0.94076|0.94076	2.073000|2.073000	0.62155|0.62155	0.529000|0.529000	0.55759|0.55759	CAG|AGT	.	.		0.607	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		T	160106761	A	T	160106761	3	4	57	1	0	0	0	0	1	0	0	0	1129	188	7	4	2858	4	ATP1A2	1	160106761	Missense_Mutation	SNP	A	TCGA-CC-5261-01A-01D-A12Z-10	1656730	160106761	89143860	4	7122										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245862258	245862258	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	agaggatcgccgaggtccgcGcgaagtacgagtggctgatg	17	9	0	2			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr1:245862258G>A	ENST00000407071.2	+	14	6537	c.6097G>A	c.(6097-6099)Gcg>Acg	p.A2033T	KIF26B_ENST00000366518.4_Missense_Mutation_p.A1652T	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	2033					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			CGAGGTCCGCGCGAAGTACGA	0.567																																					p.A2033T		Atlas-SNP	.											.	KIF26B	343	.	0			c.G6097A						.						73	80	78					1																	245862258		2105	4222	6327	SO:0001583	missense	55083	exon14			GTCCGCGCGAAGT	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.6097G>A	chr1.hg19:g.245862258G>A	ENSP00000385545:p.Ala2033Thr	76.0	0.0		172.0	8.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.458239	0.84317	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	D;D	0.82433	-1.61;-1.6	5.82	5.82	0.92795	.	.	.	.	.	D	0.90352	0.6981	M	0.65975	2.015	0.58432	D	0.999999	D	0.89917	1.0	D	0.66602	0.945	D	0.90525	0.4491	9	0.87932	D	0	.	20.099	0.97865	0.0:0.0:1.0:0.0	.	2033	Q2KJY2	KI26B_HUMAN	T	2033;1652;1649	ENSP00000385545:A2033T;ENSP00000355475:A1652T	ENSP00000355475:A1652T	A	+	1	0	KIF26B	243928881	1.000000	0.71417	0.991000	0.47740	0.678000	0.39670	9.838000	0.99474	2.752000	0.94435	0.655000	0.94253	GCG	.	.		0.567	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245862258	G	A	245862258	3	1	57	1	0	0	0	0	1	0	0	0	8304	1087	38	1	6151	1	KIF26B	1	245862258	Missense_Mutation	SNP	G	TCGA-CC-5261-01A-01D-A12Z-10	85755497	245862258	3388363	5	7123										
MAP3K2	10746	hgsc.bcm.edu	37	chr2	128075798	128075798	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	aacttgcttaacagccaattCtcttcctgtatcaacatcat	3	12	3	0			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr2:128075798C>A	ENST00000409947.1	-	13	1423	c.1141G>T	c.(1141-1143)Gaa>Taa	p.E381*	MAP3K2_ENST00000344908.5_Nonsense_Mutation_p.E381*|RNU6-1147P_ENST00000363380.1_RNA			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	381	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.E381*(1)		central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	ACAGCCAATTCTCTTCCTGTA	0.438																																					p.E381X		Atlas-SNP	.											MAP3K2_ENST00000409947,NS,carcinoma,0,5	MAP3K2	78	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1141T						.						109	106	107					2																	128075798		1862	4093	5955	SO:0001587	stop_gained	10746	exon12			CCAATTCTCTTCC	AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6854	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 2"	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.1141G>T	chr2.hg19:g.128075798C>A	ENSP00000387246:p.Glu381*	118.0	0.0		114.0	13.0	NM_006609	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Nonsense_Mutation	SNP	ENST00000409947.1	hg19	CCDS46404.1	.	.	.	.	.	.	.	.	.	.	C	39	7.772382	0.98480	.	.	ENSG00000169967	ENST00000409947;ENST00000344908	.	.	.	5.69	4.81	0.61882	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	16.6685	0.85259	0.0:0.8701:0.1299:0.0	.	.	.	.	X	381	.	ENSP00000343463:E381X	E	-	1	0	MAP3K2	127792268	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	7.734000	0.84928	1.389000	0.46526	-0.291000	0.09656	GAA	.	.		0.438	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609		A	128075798	C	A	128075798	4	1	57	1	0	0	0	0	0	1	0	0	9259	922	32	3	738	3	MAP3K2	2	128075798	Nonsense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		128075798	115123575	6	7124										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209190043	209190043	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	ggttgtccacagcacctaggCtgtacaatcaagctaagagg	11	10	1	1			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr2:209190043C>T	ENST00000264380.4	+	20	2666	c.2508C>T	c.(2506-2508)ggC>ggT	p.G836G		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	836					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						AGCACCTAGGCTGTACAATCA	0.398																																					p.G836G		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.C2508T						.						80	74	76					2																	209190043		2203	4300	6503	SO:0001819	synonymous_variant	200576	exon20			CCTAGGCTGTACA	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.2508C>T	chr2.hg19:g.209190043C>T		153.0	0.0		158.0	23.0	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	hg19	CCDS2382.1																																																																																			.	.		0.398	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		T	209190043	C	T	209190043	2	4	57	1	0	0	0	0	0	0	0	1	11933	784	28	3		3	PIKFYVE	2	209190043	Silent	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10	81114245	209190043	34009330	7	7125										
XRCC5	7520	hgsc.bcm.edu	37	chr2	217012804	217012813	+	Splice_Site	DEL	TTTCCAACAG	TTTCCAACAG	-													0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	aaatccttactttttccaacAgtgtctgctgcacagagctt							TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	TTTCCAACAG	TTTCCAACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr2:217012804_217012813delTTTCCAACAG	ENST00000392133.3	+	16	1937_1945	c.1476_1484delTTTCCAACAG	c.(1474-1485)catttccaacag>cag	p.HFQ492fs	XRCC5_ENST00000392132.2_Splice_Site_p.HFQ492fs			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	492	Pro-rich.				brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to fatty acid (GO:0071398)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|hematopoietic stem cell differentiation (GO:0060218)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of type I interferon production (GO:0032481)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|kidney(3)|large_intestine(8)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		TTTTTCCAACAGTGTCTGCTGCACAGAGCT	0.438								Non-homologous end-joining																													.		Atlas-Indel,Pindel	.											.	XRCC5	64	.	0			.						.																																			SO:0001630	splice_region_variant	7520	.			.	AF039597	CCDS2402.1	2q35	2008-07-31	2008-07-31		ENSG00000079246	ENSG00000079246			12833	protein-coding gene	gene with protein product	"Ku autoantigen, 80kDa"	194364	"X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)"			9636207, 9214634	Standard	NM_021141		Approved	KU80, KARP-1, Ku86, KUB2	uc002vfy.3	P13010	OTTHUMG00000133059	ENST00000392133.3:c.1477-1TTTCCAACAG>-	chr2.hg19:g.217012804_217012813delTTTCCAACAG		305.0	0.0		289.0	22.0	.	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Splice_Site	DEL	ENST00000392133.3	hg19	CCDS2402.1																																																																																			.	.		0.438	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141	Frame_Shift_Del	-	217012813	TTTCCAACAG	-	217012804	8	5	57	1	0	1	0	1	0	0	1	0	17471	202	7	0	1529	0	XRCC5	2	217012804	Splice_Site	DEL	TTTCCAACAG	TCGA-CC-5261-01A-01D-A12Z-10	7822761	217012804	26186569	8	7126										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38150949	38150949	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	ctgacccatctggccctcccTtgtcacgtgtcaggcatgaa	9	15	3	2			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr3:38150949T>A	ENST00000308059.6	+	22	3177	c.3156T>A	c.(3154-3156)ccT>ccA	p.P1052P	DLEC1_ENST00000452631.2_Silent_p.P1052P|DLEC1_ENST00000346219.3_Silent_p.P1052P					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		TGGCCCTCCCTTGTCACGTGT	0.562																																					p.P1052P		Atlas-SNP	.											.	DLEC1	278	.	0			c.T3156A						.						95	95	95					3																	38150949		1902	4128	6030	SO:0001819	synonymous_variant	9940	exon22			CCTCCCTTGTCAC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.3156T>A	chr3.hg19:g.38150949T>A		65.0	0.0		78.0	11.0	NM_007337		Silent	SNP	ENST00000308059.6	hg19	CCDS2672.2																																																																																			.	.		0.562	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		A	38150949	T	A	38150949	2	1	57	1	0	0	0	0	0	0	0	1	4554	1596	56	4		4	DLEC1	3	38150949	Silent	SNP	T	TCGA-CC-5261-01A-01D-A12Z-10		38150949	159871481	9	7127										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77607249	77607250	+	Missense_Mutation	DNP	TC	TC	AT													0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	tttacttttccgggtagagaTccaagagcaacaattcaaga							TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr3:77607249_77607250TC>AT	ENST00000461745.1	+	9	2286_2287	c.1386_1387TC>AT	c.(1384-1389)gaTCca>gaATca	p.462_463DP>ES	ROBO2_ENST00000487694.3_Missense_Mutation_p.478_479DP>ES|ROBO2_ENST00000332191.8_Missense_Mutation_p.462_463DP>ES	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	462	Ig-like C2-type 5.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CGGGTAGAGATCCAAGAGCAAC	0.406																																					p.D462E|p.P463S		Atlas-SNP	.											.	ROBO2	527	.	0			c.T1386A|c.C1387T						.																																			SO:0001583	missense	6092	exon9			TAGAGATCCAAGA|AGAGATCCAAGAG	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	Exception_encountered	chr3.hg19:g.77607249_77607250delinsAT	ENSP00000417164:p.D462_P463delinsES	114.0|116.0	0.0		165.0|163.0	65.0|64.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1																																																																																			.	.		0.406	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		AT	77607250	TC	AT	77607249	3	1	57	1	0	0	0	0	1	0	0	0	13529	1432	50	4	1422	4	ROBO2	3	77607249	Missense_Mutation	DNP	TC	TCGA-CC-5261-01A-01D-A12Z-10	39456300	77607249	120415181	10	7128										
GTPBP8	29083	hgsc.bcm.edu	37	chr3	112711969	112711969	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	aagtcagagtctccaaaaaaCcagtatgttgaagtttttaa	7	6	2	2			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr3:112711969C>A	ENST00000383678.2	+	2	515	c.433C>A	c.(433-435)Cca>Aca	p.P145T	GTPBP8_ENST00000467752.1_Missense_Mutation_p.P34T|GTPBP8_ENST00000383677.3_Intron|GTPBP8_ENST00000473129.1_5'UTR|RP11-484K9.4_ENST00000609673.1_RNA	NM_014170.2	NP_054889.2	Q8N3Z3	GTPB8_HUMAN	GTP-binding protein 8 (putative)	145	EngB-type G.				barrier septum assembly (GO:0000917)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	6						CTCCAAAAAACCAGTATGTTG	0.333																																					p.P145T		Atlas-SNP	.											.	GTPBP8	22	.	0			c.C433A						.						97	97	97					3																	112711969		2203	4300	6503	SO:0001583	missense	29083	exon2			AAAAAACCAGTAT	BC037163	CCDS33820.1, CCDS33821.1	3q13.2	2008-02-05			ENSG00000163607	ENSG00000163607			25007	protein-coding gene	gene with protein product							Standard	NM_014170		Approved	HSPC135	uc003dzn.3	Q8N3Z3	OTTHUMG00000159268	ENST00000383678.2:c.433C>A	chr3.hg19:g.112711969C>A	ENSP00000373176:p.Pro145Thr	360.0	0.0		284.0	17.0	NM_014170	A6NE99|A6NN11|A8K0P6|Q5I0Y4	Missense_Mutation	SNP	ENST00000383678.2	hg19	CCDS33820.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.5|22.5	4.301768|4.301768	0.81136|0.81136	.|.	.|.	ENSG00000163607|ENSG00000163607	ENST00000305485|ENST00000383678;ENST00000467752	.|T;T	.|0.22743	.|1.94;1.94	5.65|5.65	5.65|5.65	0.86999|0.86999	.|GTP-binding domain, HSR1-related (1);	1.009650|.	0.07954|.	N|.	0.981389|.	T|T	0.59046|0.59046	0.2165|0.2165	H|H	0.95470|0.95470	3.675|3.675	0.80722|0.80722	D|D	1|1	.|D	.|0.59767	.|0.986	.|P	.|0.62885	.|0.908	T|T	0.72141|0.72141	-0.4380|-0.4380	7|9	0.52906|0.87932	T|D	0.07|0	-28.0696|-28.0696	18.5031|18.5031	0.90889|0.90889	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|145	.|Q8N3Z3	.|GTPB8_HUMAN	K|T	168|145;34	.|ENSP00000373176:P145T;ENSP00000417632:P34T	ENSP00000303802:N168K|ENSP00000373176:P145T	N|P	+|+	3|1	2|0	GTPBP8|GTPBP8	114194659|114194659	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.902000|0.902000	0.53008|0.53008	6.916000|6.916000	0.75776|0.75776	2.661000|2.661000	0.90470|0.90470	0.467000|0.467000	0.42956|0.42956	AAC|CCA	.	.		0.333	GTPBP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354260.2	NM_014170		A	112711969	C	A	112711969	3	1	57	1	0	0	0	0	1	0	0	0	6893	507	18	3	439	3	GTPBP8	3	112711969	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10	35104720	112711969	85310461	11	7129										
CPZ	8532	hgsc.bcm.edu	37	chr4	8605903	8605903	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	agttctccagccgccccggcCagcacgagctgagtgagtgc	13	15	1	2			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr4:8605903C>T	ENST00000360986.4	+	4	871	c.697C>T	c.(697-699)Cag>Tag	p.Q233*	CPZ_ENST00000382480.2_Nonsense_Mutation_p.Q96*|CPZ_ENST00000315782.6_Nonsense_Mutation_p.Q222*|CPZ_ENST00000429646.2_5'UTR	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	233					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CCGCCCCGGCCAGCACGAGCT	0.692																																					p.Q233X		Atlas-SNP	.											.	CPZ	95	.	0			c.C697T						.						9	10	9					4																	8605903		2179	4266	6445	SO:0001587	stop_gained	8532	exon4			CCCGGCCAGCACG	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.697C>T	chr4.hg19:g.8605903C>T	ENSP00000354255:p.Gln233*	55.0	0.0		88.0	46.0	NM_001014447	O00520|Q96MX2	Nonsense_Mutation	SNP	ENST00000360986.4	hg19	CCDS33953.1	.	.	.	.	.	.	.	.	.	.	C	38	6.749772	0.97809	.	.	ENSG00000109625	ENST00000360986;ENST00000382480;ENST00000315782	.	.	.	3.86	3.86	0.44501	.	0.477193	0.23416	N	0.048414	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-25.9624	15.9374	0.79723	0.0:1.0:0.0:0.0	.	.	.	.	X	233;96;222	.	ENSP00000315074:Q222X	Q	+	1	0	CPZ	8656803	0.923000	0.31300	1.000000	0.80357	0.884000	0.51177	1.265000	0.33027	1.973000	0.57446	0.555000	0.69702	CAG	.	.		0.692	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		T	8605903	C	T	8605903	4	4	57	1	0	0	0	0	0	1	0	0	3841	595	21	3	711	3	CPZ	4	8605903	Nonsense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		8605903	182548373	12	7130										
FBN2	2201	hgsc.bcm.edu	37	chr5	127873149	127873149	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gccttcagagcctgctgtagCggaccgaacctgttgcggcg	14	13	1	1			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr5:127873149C>A	ENST00000508053.1	-	7	1122	c.148G>T	c.(148-150)Gct>Tct	p.A50S	FBN2_ENST00000508989.1_Missense_Mutation_p.A50S|FBN2_ENST00000262464.4_Missense_Mutation_p.A50S			P35556	FBN2_HUMAN	fibrillin 2	50					anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CCTGCTGTAGCGGACCGAACC	0.736																																					p.A50S		Atlas-SNP	.											.	FBN2	858	.	0			c.G148T						.						13	16	15					5																	127873149		2191	4290	6481	SO:0001583	missense	2201	exon1			CTGTAGCGGACCG	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.148G>T	chr5.hg19:g.127873149C>A	ENSP00000424571:p.Ala50Ser	17.0	0.0		51.0	16.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	13.35	2.210148	0.39003	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989;ENST00000502468	D;D;D;T	0.85773	-1.82;-1.82;-2.03;-0.59	4.92	4.92	0.64577	.	0.000000	0.51477	D	0.000091	T	0.69806	0.3152	N	0.08118	0	0.25687	N	0.98574	P;P;P;B	0.47034	0.777;0.789;0.889;0.358	B;B;B;B	0.41236	0.241;0.17;0.351;0.122	T	0.63708	-0.6576	10	0.29301	T	0.29	.	10.8968	0.47027	0.0:0.911:0.0:0.089	.	50;50;50;50	P35556-2;E9PHW4;D6RJI3;P35556	.;.;.;FBN2_HUMAN	S	50	ENSP00000262464:A50S;ENSP00000424571:A50S;ENSP00000425596:A50S;ENSP00000424753:A50S	ENSP00000262464:A50S	A	-	1	0	FBN2	127901048	0.615000	0.27026	0.991000	0.47740	0.144000	0.21451	1.017000	0.29989	2.431000	0.82371	0.591000	0.81541	GCT	.	.		0.736	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127873149	C	A	127873149	3	1	57	1	0	0	0	0	1	0	0	0	5711	768	27	1	8850	1	FBN2	5	127873149	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		127873149	53042111	13	7131										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148407322	148407322	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gtccagagaggagctgcaggCgctcggcaaagggcaggacc	17	11	0	1	rs138040787		TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr5:148407322C>T	ENST00000515425.1	-	11	2074	c.1973G>A	c.(1972-1974)cGc>cAc	p.R658H	SH3TC2_ENST00000512049.1_Missense_Mutation_p.R651H|SH3TC2_ENST00000394358.2_Missense_Mutation_p.R543H|SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000538184.1_Missense_Mutation_p.R205H	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	658			R -> C (in CMT4C; heterozygous in one German patient with affected sibling). {ECO:0000269|PubMed:14574644}.		cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCTGCAGGCGCTCGGCAAA	0.617																																					p.R658H		Atlas-SNP	.											.	SH3TC2	178	.	0			c.G1973A						.	C	HIS/ARG	0,4406		0,0,2203	47	54	52		1973	6.2	1	5	dbSNP_134	52	3,8597	3.0+/-9.4	0,3,4297	yes	missense	SH3TC2	NM_024577.3	29	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	possibly-damaging	658/1289	148407322	3,13003	2203	4300	6503	SO:0001583	missense	79628	exon11			TGCAGGCGCTCGG	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.1973G>A	chr5.hg19:g.148407322C>T	ENSP00000423660:p.Arg658His	46.0	0.0		60.0	14.0	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.938799	0.52972	0.0	3.49E-4	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049;ENST00000394358	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	6.16	6.16	0.99307	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.59459	0.2195	M	0.67700	2.07	0.54753	D	0.999983	P;D;D;D	0.58268	0.896;0.982;0.982;0.982	B;B;B;B	0.41571	0.189;0.36;0.36;0.36	T	0.62817	-0.6774	10	0.44086	T	0.13	-17.8698	11.6865	0.51490	0.0:0.8957:0.0:0.1043	.	543;651;658;658	C9JLC3;Q14CC0;E9PDF1;Q8TF17	.;.;.;S3TC2_HUMAN	H	205;658;651;543	ENSP00000441427:R205H;ENSP00000423660:R658H;ENSP00000421860:R651H;ENSP00000377886:R543H	ENSP00000377886:R543H	R	-	2	0	SH3TC2	148387515	0.996000	0.38824	0.985000	0.45067	0.827000	0.46813	3.263000	0.51546	2.937000	0.99478	0.650000	0.86243	CGC	.	C|1.000;T|0.000		0.617	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		T	148407322	C	T	148407322	3	4	57	1	0	0	0	0	1	0	0	0	14277	768	27	1	1921	1	SH3TC2	5	148407322	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10	20534173	148407322	32507938	14	7132										
PRSS16	10279	hgsc.bcm.edu	37	chr6	27218849	27218849	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	tctcattttcgcgtcggtcgCctcctccgccccggtgcggg	12	17	1	0			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr6:27218849C>T	ENST00000230582.3	+	6	635	c.620C>T	c.(619-621)gCc>gTc	p.A207V	PRSS16_ENST00000421826.2_Intron	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	207					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						GCGTCGGTCGCCTCCTCCGCC	0.642																																					p.A207V	NSCLC(178;1118 2105 17078 23587 44429)	Atlas-SNP	.											.	PRSS16	66	.	0			c.C620T						.						68	77	74					6																	27218849		2203	4300	6503	SO:0001583	missense	10279	exon6			CGGTCGCCTCCTC	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"Serine peptidases / Serine peptidases"	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.620C>T	chr6.hg19:g.27218849C>T	ENSP00000230582:p.Ala207Val	69.0	0.0		115.0	26.0	NM_005865	O75416	Missense_Mutation	SNP	ENST00000230582.3	hg19	CCDS4623.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.398981	0.83120	.	.	ENSG00000112812	ENST00000230582;ENST00000343467	T	0.26660	1.72	3.87	3.87	0.44632	.	0.000000	0.85682	D	0.000000	T	0.45597	0.1350	M	0.86740	2.835	0.51482	D	0.999928	D;P	0.69078	0.997;0.736	D;B	0.79108	0.992;0.367	T	0.50206	-0.8855	10	0.62326	D	0.03	-11.4193	11.6135	0.51074	0.0:1.0:0.0:0.0	.	207;207	C9JI59;Q9NQE7	.;TSSP_HUMAN	V	207	ENSP00000230582:A207V	ENSP00000230582:A207V	A	+	2	0	PRSS16	27326828	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	2.658000	0.46733	2.456000	0.83038	0.563000	0.77884	GCC	.	.		0.642	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2			T	27218849	C	T	27218849	3	4	57	1	0	0	0	0	1	0	0	0	12628	739	26	3	642	3	PRSS16	6	27218849	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		27218849	143896218	15	7133										
C6orf136	221545	hgsc.bcm.edu	37	chr6	30615170	30615170	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gcggagcgcgcgctgggttcCgcgcaggcgcagagacaccc	17	15	0	1	rs372110822	byFrequency	TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr6:30615170C>T	ENST00000376473.5	+	1	231				AL662800.2_ENST00000583820.1_RNA|C6orf136_ENST00000376471.4_Intron|C6orf136_ENST00000493705.1_Intron|C6orf136_ENST00000293604.6_Silent_p.S54S|C6orf136_ENST00000528347.2_5'Flank	NM_001109938.2	NP_001103408.1	Q5SQH8	CF136_HUMAN	chromosome 6 open reading frame 136							mitochondrion (GO:0005739)				endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						CGCTGGGTTCCGCGCAGGCGC	0.746													C|||	11	0.00219649	0	0	5008	,	,		10938	0.0109		0	False		,,,				2504	0				p.S54S		Atlas-SNP	.											.	C6orf136	31	.	0			c.C162T						.						2	3	3					6																	30615170		487	1257	1744	SO:0001627	intron_variant	221545	exon1			GGGTTCCGCGCAG	BC016167	CCDS4684.1, CCDS43443.1, CCDS4684.2, CCDS54979.1	6p21.32	2012-02-06			ENSG00000204564	ENSG00000204564			21301	protein-coding gene	gene with protein product							Standard	NM_001109938		Approved	Em:AB023049.8	uc003nqx.4	Q5SQH8	OTTHUMG00000031221	ENST00000376473.5:c.72+90C>T	chr6.hg19:g.30615170C>T		1.0	0.0		16.0	5.0	NM_001161376	A9R9P9|F8VX15|Q5SU01|Q6ZSB7|Q8TB84	Silent	SNP	ENST00000376473.5	hg19	CCDS43443.1																																																																																			.	.		0.746	C6orf136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076457.4	NM_145029		T	30615170	C	T	30615170	1	4	57	0	1	0	0	0	0	0	0	0	2333	639	23	1		1	C6orf136	6	30615170	Intron	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10	3396321	30615170	140499897	16	7134										
ALDH8A1	64577	hgsc.bcm.edu	37	chr6	135265052	135265052	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gtgagcgctcctgggggctgCgggatgaccagctgggaaag	19	9	0	2	rs200812012		TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr6:135265052C>T	ENST00000265605.2	-	2	259	c.191G>A	c.(190-192)cGc>cAc	p.R64H	ALDH8A1_ENST00000367845.2_Missense_Mutation_p.R64H|ALDH8A1_ENST00000367847.2_Missense_Mutation_p.R64H|RP11-349J5.2_ENST00000416448.2_RNA	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	64					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		CTGGGGGCTGCGGGATGACCA	0.592																																					p.R64H		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.G191A						.						45	49	47					6																	135265052		2203	4300	6503	SO:0001583	missense	64577	exon2			GGGCTGCGGGATG	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"Aldehyde dehydrogenases"	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.191G>A	chr6.hg19:g.135265052C>T	ENSP00000265605:p.Arg64His	33.0	0.0		41.0	27.0	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	hg19	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	c	11.91	1.780245	0.31502	.	.	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	T;T;T	0.76186	-1.0;-1.0;1.53	6.07	0.0747	0.14396	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.550434	0.19098	N	0.122762	T	0.38612	0.1047	L	0.41710	1.295	0.09310	N	1	B;B;B	0.17038	0.02;0.016;0.02	B;B;B	0.13407	0.009;0.005;0.009	T	0.29088	-1.0023	10	0.59425	D	0.04	.	2.1588	0.03819	0.1224:0.3694:0.1202:0.388	.	64;64;64	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	H	64	ENSP00000265605:R64H;ENSP00000356819:R64H;ENSP00000356821:R64H	ENSP00000265605:R64H	R	-	2	0	ALDH8A1	135306745	0.004000	0.15560	0.525000	0.27900	0.798000	0.45092	0.448000	0.21726	0.476000	0.27440	-0.235000	0.12190	CGC	.	.		0.592	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			T	135265052	C	T	135265052	3	4	57	1	0	0	0	0	1	0	0	0	505	768	27	1	1296	1	ALDH8A1	6	135265052	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10	104649882	135265052	35850015	17	7135										
NMBR	4829	hgsc.bcm.edu	37	chr6	142396836	142396836	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	ccatttagtaaaacagaattGgtcaccatgttcttagcatt	6	8	2	1			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr6:142396836G>C	ENST00000258042.1	-	3	1262	c.1122C>G	c.(1120-1122)acC>acG	p.T374T	NMBR_ENST00000480652.1_Intron	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	374					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)			breast(2)|central_nervous_system(3)|endometrium(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;9.93e-06)|GBM - Glioblastoma multiforme(68;0.0013)		AAACAGAATTGGTCACCATGT	0.443																																					p.T374T		Atlas-SNP	.											.	NMBR	62	.	0			c.C1122G						.						117	106	110					6																	142396836		2203	4300	6503	SO:0001819	synonymous_variant	4829	exon3			AGAATTGGTCACC		CCDS5196.1	6q24.1	2014-02-21			ENSG00000135577	ENSG00000135577		"GPCR / Class A : Bombesin receptors"	7843	protein-coding gene	gene with protein product	"bombesin receptor 1"	162341					Standard	NM_002511		Approved	BB1	uc003qiu.3	P28336	OTTHUMG00000015704	ENST00000258042.1:c.1122C>G	chr6.hg19:g.142396836G>C		168.0	0.0		169.0	46.0	NM_002511	E9KL38|Q5VUK8	Silent	SNP	ENST00000258042.1	hg19	CCDS5196.1																																																																																			.	.		0.443	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1			C	142396836	G	C	142396836	2	2	57	1	0	0	0	0	0	0	0	1	10496	1335	47	4		4	NMBR	6	142396836	Silent	SNP	G	TCGA-CC-5261-01A-01D-A12Z-10	7131784	142396836	28718231	18	7136										
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72903721	72903721	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	tgctggcacgttactgatgaTctaggttaaaaagaaacaaa	9	6	1	3			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr7:72903721T>C	ENST00000339594.4	-	6	1032	c.694A>G	c.(694-696)Atc>Gtc	p.I232V	BAZ1B_ENST00000404251.1_Splice_Site_p.I232V	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	232	Mediates the tyrosine-protein kinase activity.				cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				TTACTGATGATCTAGGTTAAA	0.393																																					p.I232V	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.A694G						.						108	94	99					7																	72903721		2203	4300	6503	SO:0001630	splice_region_variant	9031	exon6			TGATGATCTAGGT	AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.694-1A>G	chr7.hg19:g.72903721T>C		269.0	0.0		214.0	12.0	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	hg19	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	T	4.518	0.096070	0.08681	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.57436	0.4;0.4	5.88	4.72	0.59763	.	0.113674	0.64402	N	0.000009	T	0.25865	0.0630	N	0.08118	0	0.38723	D	0.953488	B	0.02656	0.0	B	0.04013	0.001	T	0.14727	-1.0462	10	0.05721	T	0.95	-9.0796	8.3585	0.32344	0.0:0.1502:0.0:0.8498	.	232	Q9UIG0	BAZ1B_HUMAN	V	232	ENSP00000342434:I232V;ENSP00000385442:I232V	ENSP00000342434:I232V	I	-	1	0	BAZ1B	72541657	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.480000	0.53172	1.050000	0.40346	0.533000	0.62120	ATC	.	.		0.393	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	Missense_Mutation	C	72903721	T	C	72903721	5	2	57	1	0	0	0	0	0	0	1	0	1330	1449	50	2	3813	2	BAZ1B	7	72903721	Splice_Site	SNP	T	TCGA-CC-5261-01A-01D-A12Z-10		72903721	86234942	19	7137										
GALNTL5	168391	hgsc.bcm.edu	37	chr7	151664464	151664464	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	aaagccaggagcctctgtcaGcttggtcccctggaaaaaaa	10	11	2	0			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr7:151664464G>A	ENST00000392800.2	+	2	387	c.133G>A	c.(133-135)Gct>Act	p.A45T	GALNTL5_ENST00000431418.2_Missense_Mutation_p.A45T	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	45					spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		GCCTCTGTCAGCTTGGTCCCC	0.428																																					p.A45T		Atlas-SNP	.											.	GALNTL5	87	.	0			c.G133A						.						62	63	63					7																	151664464		2203	4300	6503	SO:0001583	missense	168391	exon2			CTGTCAGCTTGGT	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"Glycosyltransferase family 2 domain containing"	21725	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 5"	615133	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.133G>A	chr7.hg19:g.151664464G>A	ENSP00000376548:p.Ala45Thr	264.0	0.0		203.0	12.0	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	hg19	CCDS5929.1	.	.	.	.	.	.	.	.	.	.	G	9.617	1.132789	0.21041	.	.	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.59224	0.28;0.28	4.33	-8.67	0.00863	.	1.962090	0.02605	N	0.101470	T	0.33323	0.0859	N	0.22421	0.69	0.09310	N	1	B	0.22604	0.072	B	0.18871	0.023	T	0.11567	-1.0582	10	0.21014	T	0.42	.	2.7292	0.05222	0.5072:0.2096:0.1778:0.1054	.	45	Q7Z4T8	GLTL5_HUMAN	T	45	ENSP00000392582:A45T;ENSP00000376548:A45T	ENSP00000376548:A45T	A	+	1	0	GALNTL5	151295397	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-1.359000	0.02602	-1.821000	0.01213	0.650000	0.86243	GCT	.	.		0.428	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292		A	151664464	G	A	151664464	3	1	57	1	0	0	0	0	1	0	0	0	6232	971	34	3	135	3	GALNTL5	7	151664464	Missense_Mutation	SNP	G	TCGA-CC-5261-01A-01D-A12Z-10	78760743	151664464	7474199	20	7138										
C8orf34	116328	hgsc.bcm.edu	37	chr8	69434170	69434170	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	aagaagcaaaaatgaccaatGggaaagtgaagatagtggct	12	4	0	4			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr8:69434170G>T	ENST00000539993.1	+	6	1193	c.644G>T	c.(643-645)tGg>tTg	p.W215L	C8orf34_ENST00000518698.1_Missense_Mutation_p.W301L|C8orf34_ENST00000337103.4_Missense_Mutation_p.W190L|C8orf34_ENST00000349492.3_3'UTR|C8orf34_ENST00000348340.2_Missense_Mutation_p.W215L			Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	215										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(12)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	36			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			AATGACCAATGGGAAAGTGAA	0.418																																					p.W301L		Atlas-SNP	.											.	C8orf34	170	.	0			c.G902T						.						101	97	98					8																	69434170		2203	4300	6503	SO:0001583	missense	116328	exon6			ACCAATGGGAAAG	AB056652	CCDS6203.1, CCDS6203.2	8q13	2009-10-01			ENSG00000165084	ENSG00000165084			30905	protein-coding gene	gene with protein product	"vestibule 1"						Standard	NM_052958		Approved	vest-1, VEST1	uc010lyz.3	Q49A92	OTTHUMG00000164438	ENST00000539993.1:c.644G>T	chr8.hg19:g.69434170G>T	ENSP00000438159:p.Trp215Leu	128.0	0.0		95.0	7.0	NM_052958	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	Missense_Mutation	SNP	ENST00000539993.1	hg19		.	.	.	.	.	.	.	.	.	.	G	24.8	4.568212	0.86439	.	.	ENSG00000165084	ENST00000518698;ENST00000539993;ENST00000348340;ENST00000337103	T;T;T	0.44482	0.92;0.95;0.95	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.62913	0.2467	L	0.60455	1.87	0.50039	D	0.999845	P;D	0.71674	0.952;0.998	P;D	0.80764	0.6;0.994	T	0.57825	-0.7744	9	.	.	.	-6.5266	19.961	0.97250	0.0:0.0:1.0:0.0	.	215;215	Q49A92;Q49A92-3	CH034_HUMAN;.	L	301;215;215;190	ENSP00000427820:W301L;ENSP00000438159:W215L;ENSP00000337174:W190L	.	W	+	2	0	C8orf34	69596724	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.551000	0.73909	2.783000	0.95769	0.655000	0.94253	TGG	.	.		0.418	C8orf34-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_052958		T	69434170	G	T	69434170	3	4	57	1	0	0	0	0	1	0	0	0	2424	1357	47	3	587	3	C8orf34	8	69434170	Missense_Mutation	SNP	G	TCGA-CC-5261-01A-01D-A12Z-10		69434170	76929852	21	7139										
TRHR	7201	hgsc.bcm.edu	37	chr8	110131528	110131528	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	ccaacagagaaacctgctaaCtacagtgtggccctaaatta	7	11	0	1			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr8:110131528C>G	ENST00000518632.1	+	3	1392	c.1041C>G	c.(1039-1041)aaC>aaG	p.N347K	TRHR_ENST00000311762.2_Missense_Mutation_p.N347K			P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	347					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thyrotropin-releasing hormone receptor activity (GO:0004997)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(12)|prostate(4)|skin(4)|urinary_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			AACCTGCTAACTACAGTGTGG	0.473																																					p.N347K		Atlas-SNP	.											.	TRHR	74	.	0			c.C1041G						.						151	144	146					8																	110131528		2203	4299	6502	SO:0001583	missense	7201	exon2			TGCTAACTACAGT		CCDS6311.1	8q23.1	2013-09-20			ENSG00000174417	ENSG00000174417			12299	protein-coding gene	gene with protein product		188545				8128317	Standard	NM_003301		Approved		uc003ymz.4	P34981	OTTHUMG00000164910	ENST00000518632.1:c.1041C>G	chr8.hg19:g.110131528C>G	ENSP00000430711:p.Asn347Lys	163.0	0.0		222.0	27.0	NM_003301	Q2M339	Missense_Mutation	SNP	ENST00000518632.1	hg19	CCDS6311.1	.	.	.	.	.	.	.	.	.	.	C	2.612	-0.290575	0.05568	.	.	ENSG00000174417	ENST00000518632;ENST00000311762	T;T	0.57436	0.4;0.4	5.86	4.99	0.66335	.	0.338377	0.38492	N	0.001661	T	0.34077	0.0885	L	0.31207	0.915	0.45307	D	0.998304	B	0.06786	0.001	B	0.06405	0.002	T	0.14811	-1.0459	10	0.13470	T	0.59	-10.856	5.968	0.19336	0.0:0.6717:0.1587:0.1696	.	347	P34981	TRFR_HUMAN	K	347	ENSP00000430711:N347K;ENSP00000309818:N347K	ENSP00000309818:N347K	N	+	3	2	TRHR	110200704	0.449000	0.25689	0.996000	0.52242	0.928000	0.56348	0.646000	0.24797	1.492000	0.48499	0.585000	0.79938	AAC	.	.		0.473	TRHR-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380892.1			G	110131528	C	G	110131528	3	3	57	1	0	0	0	0	1	0	0	0	16495	564	20	4	1047	4	TRHR	8	110131528	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10	40697358	110131528	36232494	22	7140										
CYP11B2	1585	hgsc.bcm.edu	37	chr8	143994118	143994118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	aggcggcattgcgacccagcGagtagaggaaaacctgtacc	13	11	0	1			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr8:143994118G>A	ENST00000323110.2	-	8	1228	c.1226C>T	c.(1225-1227)tCg>tTg	p.S409L		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	409					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	GCGACCCAGCGAGTAGAGGAA	0.622									Familial Hyperaldosteronism type I																												p.S409L		Atlas-SNP	.											.	CYP11B2	107	.	0			c.C1226T						.						93	90	91					8																	143994118		2203	4300	6503	SO:0001583	missense	1585	exon8	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	CCCAGCGAGTAGA	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"Cytochrome P450s"	2592	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	124080	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.1226C>T	chr8.hg19:g.143994118G>A	ENSP00000325822:p.Ser409Leu	92.0	0.0		106.0	15.0	NM_000498	B0ZBE4|Q16726	Missense_Mutation	SNP	ENST00000323110.2	hg19	CCDS6393.1	.	.	.	.	.	.	.	.	.	.	.	19.93	3.918803	0.73098	.	.	ENSG00000179142	ENST00000323110	T	0.69435	-0.4	3.52	3.52	0.40303	.	0.442635	0.19241	N	0.119173	T	0.66366	0.2782	L	0.56769	1.78	0.33867	D	0.63453	P	0.47106	0.89	P	0.46659	0.523	T	0.75439	-0.3317	10	0.36615	T	0.2	.	12.9218	0.58237	0.0:0.0:1.0:0.0	.	409	P19099	C11B2_HUMAN	L	409	ENSP00000325822:S409L	ENSP00000325822:S409L	S	-	2	0	CYP11B2	143991120	0.678000	0.27586	0.156000	0.22583	0.007000	0.05969	4.006000	0.57083	1.937000	0.56155	0.563000	0.77884	TCG	.	.		0.622	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1			A	143994118	G	A	143994118	3	1	57	1	0	0	0	0	1	0	0	0	4148	1059	37	1	293	1	CYP11B2	8	143994118	Missense_Mutation	SNP	G	TCGA-CC-5261-01A-01D-A12Z-10	33862590	143994118	2369904	23	7141										
CPXM2	119587	hgsc.bcm.edu	37	chr10	125639753	125639753	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	tgacatcttcacgggccacaCggacactgtgatcatcgttg	10	12	3	2			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr10:125639753C>A	ENST00000241305.3	-	2	531	c.377G>T	c.(376-378)cGt>cTt	p.R126L	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	126					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		ACGGGCCACACGGACACTGTG	0.542																																					p.R126L		Atlas-SNP	.											.	CPXM2	120	.	0			c.G377T						.						217	205	209					10																	125639753		2203	4300	6503	SO:0001583	missense	119587	exon2			GCCACACGGACAC	AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase"					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.377G>T	chr10.hg19:g.125639753C>A	ENSP00000241305:p.Arg126Leu	207.0	0.0		203.0	61.0	NM_198148	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	hg19	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	C	2.986	-0.209163	0.06140	.	.	ENSG00000121898	ENST00000241305;ENST00000418782	D	0.96073	-3.9	3.76	-2.33	0.06724	.	1.253220	0.05575	N	0.571736	D	0.87787	0.6265	N	0.08118	0	0.21762	N	0.999554	B	0.23650	0.089	B	0.20184	0.028	T	0.78170	-0.2308	10	0.46703	T	0.11	-1.6276	7.4296	0.27120	0.0:0.4323:0.318:0.2497	.	126	Q8N436	CPXM2_HUMAN	L	126	ENSP00000241305:R126L	ENSP00000241305:R126L	R	-	2	0	CPXM2	125629743	0.000000	0.05858	0.001000	0.08648	0.137000	0.21094	-0.230000	0.09083	-0.448000	0.07128	-0.211000	0.12701	CGT	.	.		0.542	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		A	125639753	C	A	125639753	3	1	57	1	0	0	0	0	1	0	0	0	3840	536	19	1	1945	1	CPXM2	10	125639753	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		125639753	9894994	24	7142										
BRSK2	9024	hgsc.bcm.edu	37	chr11	1472640	1472640	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gtccaacctgacaccagagtCgtccccagagtaagtggccc	10	15	0	3			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr11:1472640C>T	ENST00000528841.1	+	15	1919	c.1535C>T	c.(1534-1536)tCg>tTg	p.S512L	BRSK2_ENST00000528710.1_Missense_Mutation_p.S452L|BRSK2_ENST00000544817.1_Missense_Mutation_p.S207L|BRSK2_ENST00000308230.5_Missense_Mutation_p.S534L|BRSK2_ENST00000526678.1_Missense_Mutation_p.S534L|BRSK2_ENST00000382179.1_Missense_Mutation_p.S558L|BRSK2_ENST00000308219.9_Missense_Mutation_p.S512L|BRSK2_ENST00000531197.1_Missense_Mutation_p.S512L			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	512					actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		ACACCAGAGTCGTCCCCAGAG	0.637																																					p.S558L		Atlas-SNP	.											.	BRSK2	97	.	0			c.C1673T						.						87	100	95					11																	1472640		2144	4234	6378	SO:0001583	missense	9024	exon15			CAGAGTCGTCCCC	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"serine/threonine kinase 29"	609236	"chromsosome 11 open reading frame 7"	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.1535C>T	chr11.hg19:g.1472640C>T	ENSP00000432000:p.Ser512Leu	43.0	0.0		50.0	20.0	NM_001256630	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	hg19	CCDS58107.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.209415	0.58343	.	.	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678;ENST00000528710;ENST00000382179;ENST00000544817	T;T;T;T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15	3.81	3.81	0.43845	.	0.000000	0.64402	U	0.000001	T	0.76666	0.4019	M	0.80847	2.515	0.58432	D	0.999993	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.998;0.999;0.972;0.978	T	0.81850	-0.0743	10	0.87932	D	0	.	15.8948	0.79326	0.0:1.0:0.0:0.0	.	534;558;512;512;512	Q8IWQ3-4;Q8IWQ3-5;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;.;BRSK2_HUMAN;.	L	512;512;534;512;534;452;558;207	ENSP00000310697:S512L;ENSP00000431152:S512L;ENSP00000310805:S534L;ENSP00000432000:S512L;ENSP00000433370:S534L;ENSP00000433235:S452L;ENSP00000371614:S558L;ENSP00000445168:S207L	ENSP00000310697:S512L	S	+	2	0	BRSK2	1429216	1.000000	0.71417	0.821000	0.32701	0.078000	0.17371	4.560000	0.60802	1.981000	0.57761	0.462000	0.41574	TCG	.	.		0.637	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		T	1472640	C	T	1472640	3	4	57	1	0	0	0	0	1	0	0	0	1526	893	31	1	1593	1	BRSK2	11	1472640	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		1472640	133533876	25	7143										
NBEA	26960	hgsc.bcm.edu	37	chr13	36046548	36046548	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gccttgcaggcccagtggttCtcagcacccctgcccagctc	10	18	1	0	rs371213802		TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr13:36046548C>T	ENST00000400445.3	+	41	6994	c.6460C>T	c.(6460-6462)Ctc>Ttc	p.L2154F	NBEA_ENST00000379939.2_Missense_Mutation_p.L2151F|NBEA_ENST00000310336.4_Missense_Mutation_p.L2154F|NBEA_ENST00000540320.1_Missense_Mutation_p.L2154F	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2154					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CCCAGTGGTTCTCAGCACCCC	0.572																																					p.L2154F		Atlas-SNP	.											.	NBEA	340	.	0			c.C6460T						.						57	60	59					13																	36046548		1997	4162	6159	SO:0001583	missense	26960	exon41			GTGGTTCTCAGCA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.6460C>T	chr13.hg19:g.36046548C>T	ENSP00000383295:p.Leu2154Phe	22.0	0.0		32.0	12.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	19.23	3.788096	0.70337	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.51	5.51	0.81932	PH-BEACH domain (1);	0.000000	0.85682	D	0.000000	T	0.49729	0.1574	L	0.51853	1.615	0.80722	D	1	B;B	0.29531	0.024;0.247	B;B	0.22880	0.019;0.042	T	0.47005	-0.9150	10	0.45353	T	0.12	.	19.4328	0.94778	0.0:1.0:0.0:0.0	.	2154;2151	Q8NFP9;Q5T321	NBEA_HUMAN;.	F	2154;2154;2151;2154;781	ENSP00000440951:L2154F;ENSP00000383295:L2154F;ENSP00000369271:L2151F;ENSP00000308534:L2154F	ENSP00000308534:L2154F	L	+	1	0	NBEA	34944548	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.697000	0.61782	2.584000	0.87258	0.563000	0.77884	CTC	.	.		0.572	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	36046548	C	T	36046548	3	4	57	1	0	0	0	0	1	0	0	0	10196	913	32	3	6622	3	NBEA	13	36046548	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		36046548	79123330	26	7144										
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42303780	42303780	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	agctttgtcagcctcatctaCtaccagaatatgacccaact	5	13	3	2			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr13:42303780C>G	ENST00000379310.3	-	23	2604	c.2536G>C	c.(2536-2538)Gta>Cta	p.V846L	VWA8_ENST00000281496.6_Missense_Mutation_p.V846L	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	846						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										GCCTCATCTACTACCAGAATA	0.338																																					p.V846L		Atlas-SNP	.											.	.	.	.	0			c.G2536C						.						143	137	139					13																	42303780		2203	4300	6503	SO:0001583	missense	23078	exon23			CATCTACTACCAG	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.2536G>C	chr13.hg19:g.42303780C>G	ENSP00000368612:p.Val846Leu	297.0	0.0		227.0	24.0	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	hg19	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.380281	0.61845	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	T;T	0.17691	2.26;2.26	5.55	3.84	0.44239	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.354917	0.30011	N	0.010636	T	0.13286	0.0322	N	0.12527	0.23	0.44956	D	0.997976	P	0.44429	0.835	P	0.49477	0.612	T	0.13045	-1.0524	10	0.30078	T	0.28	.	8.537	0.33368	0.0:0.6565:0.0:0.3435	.	846	A3KMH1	K0564_HUMAN	L	750;846;846	ENSP00000368612:V846L;ENSP00000281496:V846L	ENSP00000251030:V750L	V	-	1	0	KIAA0564	41201780	0.947000	0.32204	0.493000	0.27502	0.945000	0.59286	1.660000	0.37397	0.908000	0.36671	0.655000	0.94253	GTA	.	.		0.338	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		G	42303780	C	G	42303780	3	3	57	1	0	0	0	0	1	0	0	0	8194	565	20	4	3277	4	KIAA0564	13	42303780	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10	6257232	42303780	72866098	27	7145										
VPS39	23339	hgsc.bcm.edu	37	chr15	42492106	42492106	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gcacttaccaacgtccttccGaatcctatagagaagaagat	7	11	0	3			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr15:42492106G>A	ENST00000348544.4	-	2	126	c.127C>T	c.(127-129)Cgg>Tgg	p.R43W	MIR627_ENST00000384979.1_RNA|VPS39_ENST00000568357.1_5'UTR|VPS39_ENST00000318006.5_Missense_Mutation_p.R43W			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	43	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		ACGTCCTTCCGAATCCTATAG	0.348																																					p.R43W		Atlas-SNP	.											.	VPS39	53	.	0			c.C127T						.						71	71	71					15																	42492106		2203	4299	6502	SO:0001583	missense	23339	exon2			CCTTCCGAATCCT	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.127C>T	chr15.hg19:g.42492106G>A	ENSP00000335193:p.Arg43Trp	180.0	0.0		162.0	29.0	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Missense_Mutation	SNP	ENST00000348544.4	hg19	CCDS10083.1	.	.	.	.	.	.	.	.	.	.	G	19.53	3.845655	0.71603	.	.	ENSG00000166887	ENST00000318006;ENST00000348544	T;T	0.18338	2.22;2.22	4.88	3.96	0.45880	Citron-like (2);	0.058692	0.64402	D	0.000004	T	0.24236	0.0587	L	0.34521	1.04	0.36010	D	0.837962	P;P	0.49185	0.92;0.902	P;P	0.55222	0.771;0.502	T	0.23547	-1.0185	10	0.66056	D	0.02	-19.6016	12.9477	0.58382	0.0:0.0:0.5939:0.4061	.	43;43	Q96JC1;Q96JC1-2	VPS39_HUMAN;.	W	43	ENSP00000326534:R43W;ENSP00000335193:R43W	ENSP00000326534:R43W	R	-	1	2	VPS39	40279398	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.597000	0.54031	1.403000	0.46800	0.563000	0.77884	CGG	.	.		0.348	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		A	42492106	G	A	42492106	3	1	57	1	0	0	0	0	1	0	0	0	17224	1057	37	1	2596	1	VPS39	15	42492106	Missense_Mutation	SNP	G	TCGA-CC-5261-01A-01D-A12Z-10		42492106	60039286	28	7146										
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79069906	79069906	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	atgtccttggcaggagggtcGtccaggcacaggccccaccc	13	15	0	0	rs377763034		TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr15:79069906G>A	ENST00000388820.4	-	9	1557	c.1347C>T	c.(1345-1347)gaC>gaT	p.D449D	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	449	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CAGGAGGGTCGTCCAGGCACA	0.647																																					p.D449D		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C1347T						.	A		0,4380		0,0,2190	58	48	52		1347	-8	0.1	15		52	1,8583		0,1,4291	no	coding-synonymous	ADAMTS7	NM_014272.3		0,1,6481	AA,AG,GG		0.0116,0.0,0.0077		449/1687	79069906	1,12963	2190	4292	6482	SO:0001819	synonymous_variant	11173	exon9			AGGGTCGTCCAGG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.1347C>T	chr15.hg19:g.79069906G>A		55.0	0.0		61.0	17.0	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	hg19	CCDS32303.1																																																																																			.	.		0.647	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		A	79069906	G	A	79069906	2	1	57	1	0	0	0	0	0	0	0	1	271	1136	40	1		1	ADAMTS7	15	79069906	Silent	SNP	G	TCGA-CC-5261-01A-01D-A12Z-10	36577800	79069906	23461486	29	7147										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89350737	89350737	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	ccttttctgctttattcgaaCggtctttctcttctcggaaa	6	11	4	0	rs370690185		TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr16:89350737C>T	ENST00000301030.4	-	9	2673	c.2213G>A	c.(2212-2214)cGt>cAt	p.R738H	ANKRD11_ENST00000378330.2_Missense_Mutation_p.R738H	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	738	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TTTATTCGAACGGTCTTTCTC	0.373																																					p.R738H		Atlas-SNP	.											.	ANKRD11	195	.	0			c.G2213A						.	C	HIS/ARG	0,4396		0,0,2198	57	58	57		2213	5.7	0.7	16		57	2,8596	2.2+/-6.3	0,2,4297	no	missense	ANKRD11	NM_013275.4	29	0,2,6495	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	738/2664	89350737	2,12992	2198	4299	6497	SO:0001583	missense	29123	exon9			TTCGAACGGTCTT	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.2213G>A	chr16.hg19:g.89350737C>T	ENSP00000301030:p.Arg738His	578.0	0.0		426.0	206.0	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.517965	0.44763	0.0	2.33E-4	ENSG00000167522	ENST00000301030;ENST00000378330;ENST00000330736	T;T	0.41400	1.0;1.0	5.7	5.7	0.88788	.	0.081220	0.49305	D	0.000148	T	0.41282	0.1152	L	0.56769	1.78	0.80722	D	1	P;P	0.52463	0.953;0.921	B;B	0.38194	0.267;0.137	T	0.49428	-0.8941	10	0.72032	D	0.01	.	17.3282	0.87255	0.0:1.0:0.0:0.0	.	357;738	Q7Z5E5;Q6UB99	.;ANR11_HUMAN	H	738;738;357	ENSP00000301030:R738H;ENSP00000367581:R738H	ENSP00000301030:R738H	R	-	2	0	ANKRD11	87878238	0.998000	0.40836	0.708000	0.30435	0.064000	0.16182	4.014000	0.57145	2.696000	0.92011	0.561000	0.74099	CGT	.	.		0.373	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		T	89350737	C	T	89350737	3	4	57	1	0	0	0	0	1	0	0	0	639	536	19	1	5798	1	ANKRD11	16	89350737	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		89350737	1004016	30	7148										
ABR	29	hgsc.bcm.edu	37	chr17	973210	973210	+	Splice_Site	SNP	C	C	G													0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	cctggactcacacactcaccCtgcagaggtcttcttcagct							TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr17:973210C>G	ENST00000302538.5	-	9	1161	c.1015G>C	c.(1015-1017)Ggg>Cgg	p.G339R	ABR_ENST00000574437.1_Splice_Site_p.G293R|ABR_ENST00000536794.2_Splice_Site_p.G121R|ABR_ENST00000291107.2_Splice_Site_p.G302R|ABR_ENST00000544583.2_Splice_Site_p.G293R	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	339	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CACACTCACCCTGCAGAGGTC	0.652																																					p.G339R	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.G1015C						.						56	49	51					17																	973210		2203	4300	6503	SO:0001630	splice_region_variant	29	exon9			CTCACCCTGCAGA	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	81	protein-coding gene	gene with protein product		600365	"active BCR-related gene"			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.1016+1G>C	chr17.hg19:g.973210C>G		69.0	0.0		94.0	35.0	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Missense_Mutation	SNP	ENST00000302538.5	hg19	CCDS10999.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.408485	0.83340	.	.	ENSG00000159842	ENST00000302538;ENST00000544583;ENST00000291107;ENST00000536794;ENST00000382259	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.77	5.77	0.91146	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.57888	0.2084	M	0.72353	2.195	0.80722	D	1	D;D;D;D	0.89917	0.996;0.974;1.0;0.996	D;P;D;D	0.97110	0.978;0.78;1.0;0.978	T	0.58446	-0.7635	10	0.72032	D	0.01	.	18.9737	0.92725	0.0:1.0:0.0:0.0	.	121;223;302;339	B7Z683;Q6ZT60;Q12979-2;Q12979	.;.;.;ABR_HUMAN	R	339;293;302;121;223	ENSP00000303909:G339R;ENSP00000442048:G293R;ENSP00000291107:G302R;ENSP00000437429:G121R	ENSP00000291107:G302R	G	-	1	0	ABR	919960	1.000000	0.71417	0.965000	0.40720	0.347000	0.29111	7.800000	0.85949	2.735000	0.93741	0.555000	0.69702	GGG	.	.		0.652	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4		Missense_Mutation	G	973210	C	G	973210	5	3	57	1	0	0	0	0	0	0	1	0	99	695	24	4	1624	4	ABR	17	973210	Splice_Site	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		973210	80222000	31	7149	33	2								
ABR	29	hgsc.bcm.edu	37	chr17	973214	973214	+	Silent	SNP	A	A	T													0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gactcacacactcaccctgcAgaggtcttcttcagcttggc							TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr17:973214A>T	ENST00000302538.5	-	9	1157	c.1011T>A	c.(1009-1011)tcT>tcA	p.S337S	ABR_ENST00000574437.1_Silent_p.S291S|ABR_ENST00000536794.2_Silent_p.S119S|ABR_ENST00000291107.2_Silent_p.S300S|ABR_ENST00000544583.2_Silent_p.S291S	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	337	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CTCACCCTGCAGAGGTCTTCT	0.652																																					p.S337S	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.T1011A						.						59	52	55					17																	973214		2203	4300	6503	SO:0001819	synonymous_variant	29	exon9			CCCTGCAGAGGTC	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	81	protein-coding gene	gene with protein product		600365	"active BCR-related gene"			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.1011T>A	chr17.hg19:g.973214A>T		70.0	0.0		101.0	41.0	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Silent	SNP	ENST00000302538.5	hg19	CCDS10999.1																																																																																			.	.		0.652	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			T	973214	A	T	973214	2	4	57	1	0	0	0	0	0	0	0	1	99	175	7	4		4	ABR	17	973214	Silent	SNP	A	TCGA-CC-5261-01A-01D-A12Z-10	4	973214	80221996	32	7150	33	2								
SP6	80320	hgsc.bcm.edu	37	chr17	45924716	45924716	+	Frame_Shift_Del	DEL	G	G	-													0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	tcgcgtttgcctttgcccccGgggggctccactgcgccgcc							TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr17:45924716delG	ENST00000536300.1	-	2	1411	c.1080delC	c.(1078-1080)cccfs	p.P360fs	SP6_ENST00000342234.2_Frame_Shift_Del_p.P360fs	NM_001258248.1	NP_001245177.1	Q3SY56	SP6_HUMAN	Sp6 transcription factor	360					positive regulation of cell proliferation (GO:0008284)|regulation of odontogenesis (GO:0042481)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(5)|prostate(1)|skin(1)	8						CTTTGCCCCCGGGGGGCTCCA	0.721																																					p.G361fs		Pindel	.											.	SP6	26	.	0			c.1081delG						.						8	11	10					17																	45924716		2159	4244	6403	SO:0001589	frameshift_variant	80320	exon2			.		CCDS11520.1	17q21.32	2013-01-08			ENSG00000189120	ENSG00000189120		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	14530	protein-coding gene	gene with protein product	"epiprofin"	608613				11087666, 14551215	Standard	NM_001258248		Approved	KLF14, Epfn	uc002img.2	Q3SY56	OTTHUMG00000132067	ENST00000536300.1:c.1080delC	chr17.hg19:g.45924716delG	ENSP00000438209:p.Pro360fs	36.0	0.0		105.0	22.0	NM_199262	B3KXS4	Frame_Shift_Del	DEL	ENST00000536300.1	hg19	CCDS11520.1																																																																																			.	.		0.721	SP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441395.1	NM_199262		-	45924716	G	-	45924716	7	5	57	1	0	1	0	1	0	0	0	0	14983	1103	39	0	54	0	SP6	17	45924716	Frame_Shift_Del	DEL	G	TCGA-CC-5261-01A-01D-A12Z-10	44951502	45924716	35270494	33	7151										
TAF4B	6875	hgsc.bcm.edu	37	chr18	23807168	23807168	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gcggccctaggctgcctgctCctcagatagtcgccgtgaaa	12	14	1	2			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr18:23807168C>T	ENST00000269142.5	+	1	1269	c.271C>T	c.(271-273)Cct>Tct	p.P91S	TAF4B_ENST00000400466.2_Missense_Mutation_p.P91S|TAF4B_ENST00000578121.1_Missense_Mutation_p.P91S	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	91					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			GCTGCCTGCTCCTCAGATAGT	0.607																																					p.P91S		Atlas-SNP	.											.	TAF4B	71	.	0			c.C271T						.						80	86	84					18																	23807168		1977	4162	6139	SO:0001583	missense	6875	exon1			CCTGCTCCTCAGA	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.271C>T	chr18.hg19:g.23807168C>T	ENSP00000269142:p.Pro91Ser	155.0	0.0		200.0	33.0	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	hg19	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.553495	0.27739	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.36340	1.26;1.49;1.26	4.7	3.81	0.43845	.	0.258920	0.30940	N	0.008579	T	0.44435	0.1293	L	0.59436	1.845	0.26207	N	0.979353	P;D	0.69078	0.924;0.997	P;P	0.57911	0.603;0.829	T	0.22695	-1.0209	10	0.30854	T	0.27	-9.6706	7.8075	0.29211	0.0:0.8871:0.0:0.1129	.	91;91	Q92750;A4PBF7	TAF4B_HUMAN;.	S	91	ENSP00000389365:P91S;ENSP00000269142:P91S;ENSP00000383314:P91S	ENSP00000269142:P91S	P	+	1	0	TAF4B	22061166	1.000000	0.71417	0.932000	0.37286	0.735000	0.41995	2.181000	0.42547	2.140000	0.66376	0.455000	0.32223	CCT	.	.		0.607	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		T	23807168	C	T	23807168	3	4	57	1	0	0	0	0	1	0	0	0	15542	855	30	3	273	3	TAF4B	18	23807168	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		23807168	54270080	34	7152										
SBNO2	22904	hgsc.bcm.edu	37	chr19	1113608	1113609	+	Frame_Shift_Ins	INS	-	-	C													0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	actggcagttcccggcccagINSccgccgcactttgtccagca							TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr19:1113608_1113609insC	ENST00000361757.3	-	19	2409_2410	c.2172_2173insG	c.(2170-2175)cggctgfs	p.L725fs	SBNO2_ENST00000587024.1_Frame_Shift_Ins_p.L715fs|SBNO2_ENST00000438103.2_Frame_Shift_Ins_p.L668fs	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	725					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCCGGCCCAGCCGCCGCACTT	0.703																																					p.L725fs		Atlas-INDEL	.											.	SBNO2	112	.	0			c.2173_2174insG						.																																			SO:0001589	frameshift_variant	22904	exon19			.	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.2173dupG	chr19.hg19:g.1113610_1113610dupC	ENSP00000354733:p.Leu725fs	69.0	0.0		148.0	10.0	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Frame_Shift_Ins	INS	ENST00000361757.3	hg19	CCDS45894.1																																																																																			.	.		0.703	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		C	1113609	-	C	1113608	7	5	57	1	0	1	1	0	0	0	0	0	13878	962	34	0	1983	0	SBNO2	19	1113608	Frame_Shift_Ins	INS	-	TCGA-CC-5261-01A-01D-A12Z-10		1113608	58015375	35	7153										
LBP	3929	hgsc.bcm.edu	37	chr20	36999419	36999419	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	caccttgaccttcaataccaGcaagatcactgggttcctga	7	13	2	3			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr20:36999419G>A	ENST00000217407.2	+	11	1348	c.1187G>A	c.(1186-1188)aGc>aAc	p.S396N		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	396					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				TTCAATACCAGCAAGATCACT	0.502																																					p.S396N		Atlas-SNP	.											.	LBP	60	.	0			c.G1187A						.						165	146	153					20																	36999419		2203	4300	6503	SO:0001583	missense	3929	exon11			ATACCAGCAAGAT		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"BPI fold containing"	6517	protein-coding gene	gene with protein product	"BPI fold containing family D, member 2"	151990	"lipopolysaccharide-binding protein"			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.1187G>A	chr20.hg19:g.36999419G>A	ENSP00000217407:p.Ser396Asn	135.0	0.0		233.0	22.0	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	hg19	CCDS13304.1	.	.	.	.	.	.	.	.	.	.	G	5.785	0.329173	0.10956	.	.	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.09538	2.97	4.87	1.41	0.22369	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.297164	0.34484	N	0.003938	T	0.06280	0.0162	L	0.28014	0.82	0.22127	N	0.999342	B	0.14012	0.009	B	0.25405	0.06	T	0.44559	-0.9320	10	0.09843	T	0.71	-10.8147	6.6596	0.23007	0.1187:0.3223:0.559:0.0	.	396	P18428	LBP_HUMAN	N	396	ENSP00000217407:S396N	ENSP00000217407:S396N	S	+	2	0	LBP	36432833	0.999000	0.42202	0.999000	0.59377	0.582000	0.36321	1.820000	0.39032	0.121000	0.18284	-0.300000	0.09419	AGC	.	.		0.502	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139		A	36999419	G	A	36999419	3	1	57	1	0	0	0	0	1	0	0	0	8660	971	34	3	1229	3	LBP	20	36999419	Missense_Mutation	SNP	G	TCGA-CC-5261-01A-01D-A12Z-10		36999419	26026101	36	7154										
DGCR6L	85359	hgsc.bcm.edu	37	chr22	20302911	20302911	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	cccccgccttctccagtgtgCtctgctggtcagccaccttc	8	19	3	0	rs573329481		TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chr22:20302911C>T	ENST00000248879.3	-	4	552	c.461G>A	c.(460-462)aGc>aAc	p.S154N	XXbac-B444P24.13_ENST00000608275.1_RNA|DGCR6L_ENST00000405465.3_Missense_Mutation_p.S116N	NM_033257.3	NP_150282.2	Q9BY27	DGC6L_HUMAN	DiGeorge syndrome critical region gene 6-like	154						nucleus (GO:0005634)				endometrium(1)|kidney(1)|lung(2)|stomach(1)	5	Colorectal(54;0.0993)					CTCCAGTGTGCTCTGCTGGTC	0.677													.|||	1	0.000199681	8e-04	0	5008	,	,		16282	0		0	False		,,,				2504	0				p.S154N		Atlas-SNP	.											.	DGCR6L	9	.	0			c.G461A						.						95	79	84					22																	20302911		2203	4299	6502	SO:0001583	missense	85359	exon4			AGTGTGCTCTGCT	AF228708	CCDS13778.1	22q11.21	2013-02-19			ENSG00000128185	ENSG00000128185			18551	protein-coding gene	gene with protein product		609459				11157784	Standard	NM_033257		Approved	FLJ10666	uc002zrx.3	Q9BY27	OTTHUMG00000150583	ENST00000248879.3:c.461G>A	chr22.hg19:g.20302911C>T	ENSP00000248879:p.Ser154Asn	91.0	0.0		134.0	10.0	NM_033257	A8K1N7|B3KMC0|D3DX29|Q9BW33	Missense_Mutation	SNP	ENST00000248879.3	hg19	CCDS13778.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.693723	0.48202	.	.	ENSG00000128185	ENST00000248879;ENST00000405465	T;T	0.35048	1.33;1.33	2.04	2.04	0.26737	.	0.089386	0.85682	D	0.000000	T	0.34861	0.0912	N	0.16602	0.42	0.36620	D	0.875729	P;D	0.59357	0.489;0.985	B;D	0.67231	0.265;0.95	T	0.30563	-0.9974	10	0.39692	T	0.17	-31.2466	6.6364	0.22885	0.0:0.6984:0.3015:0.0	.	154;154	B3KMC0;Q9BY27	.;DGC6L_HUMAN	N	154;116	ENSP00000248879:S154N;ENSP00000386052:S116N	ENSP00000248879:S154N	S	-	2	0	DGCR6L	18682911	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.798000	0.38814	1.463000	0.47967	0.461000	0.40582	AGC	.	.		0.677	DGCR6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318970.3	NM_033257		T	20302911	C	T	20302911	3	4	57	1	0	0	0	0	1	0	0	0	4465	797	28	3	209	3	DGCR6L	22	20302911	Missense_Mutation	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10		20302911	31001655	37	7155										
POLA1	5422	hgsc.bcm.edu	37	chrX	24741360	24741360	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gtgaaaaatatcgagcgaacGctttacttccttccccgtga	8	11	0	2			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chrX:24741360G>A	ENST00000379059.3	+	11	1173	c.1158G>A	c.(1156-1158)acG>acA	p.T386T	POLA1_ENST00000379068.3_Silent_p.T392T	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	386					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	TCGAGCGAACGCTTTACTTCC	0.423																																					p.T386T		Atlas-SNP	.											.	POLA1	117	.	0			c.G1158A						.						183	166	172					X																	24741360		2203	4300	6503	SO:0001819	synonymous_variant	5422	exon11			GCGAACGCTTTAC		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1158G>A	chrX.hg19:g.24741360G>A		175.0	1.0		194.0	131.0	NM_016937	Q86UQ7	Silent	SNP	ENST00000379059.3	hg19	CCDS14214.1																																																																																			.	.		0.423	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		A	24741360	G	A	24741360	2	1	57	1	0	0	0	0	0	0	0	1	12196	1074	38	1		1	POLA1	23	24741360	Silent	SNP	G	TCGA-CC-5261-01A-01D-A12Z-10		24741360	130529200	38	7156										
HTATSF1	27336	hgsc.bcm.edu	37	chrX	135593320	135593320	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.363131313131313	0	0.443827160493827	1	1	0	gaatctgaagagggctgcccCaaaagagggtttgaaggcag	15	7	1	4			TCGA-CC-5261-01A-01D-A12Z-10	TCGA-CC-5261-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2f143d6-ba07-4ff0-960d-b29c3c716665	5ad24cf2-db35-428a-a10f-50b2decbe482	g.chrX:135593320C>G	ENST00000218364.4	+	9	1590	c.1416C>G	c.(1414-1416)ccC>ccG	p.P472P	HTATSF1_ENST00000535601.1_Silent_p.P472P	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	472	Asp/Glu-rich (acidic).|Mediates interaction with the P-TEFb complex.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					AGGGCTGCCCCAAAAGAGGGT	0.443																																					p.P472P		Atlas-SNP	.											.	HTATSF1	66	.	0			c.C1416G						.						45	50	48					X																	135593320		2187	4280	6467	SO:0001819	synonymous_variant	27336	exon10			CTGCCCCAAAAGA	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"RNA binding motif (RRM) containing"	5276	protein-coding gene	gene with protein product		300346	"HIV TAT specific factor 1"			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.1416C>G	chrX.hg19:g.135593320C>G		66.0	0.0		72.0	14.0	NM_001163280	D3DWG9|Q59G06|Q99730	Silent	SNP	ENST00000218364.4	hg19	CCDS14657.1																																																																																			.	.		0.443	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		G	135593320	C	G	135593320	2	3	57	1	0	0	0	0	0	0	0	1	7442	581	21	4		4	HTATSF1	23	135593320	Silent	SNP	C	TCGA-CC-5261-01A-01D-A12Z-10	110851960	135593320	19677240	39	7157										
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19166175	19166175	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ccgggtagaagaggatcatgTagcacttggggccgaagtag	16	7	1	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:19166175T>C	ENST00000375371.3	-	6	2459	c.2438A>G	c.(2437-2439)tAc>tGc	p.Y813C		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	813					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	GAGGATCATGTAGCACTTGGG	0.597																																					p.Y813C		Atlas-SNP	.											.	TAS1R2	134	.	0			c.A2438G						.						105	83	91					1																	19166175		2203	4300	6503	SO:0001583	missense	80834	exon6			ATCATGTAGCACT		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14905	protein-coding gene	gene with protein product		606226	"G protein-coupled receptor 71"	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.2438A>G	chr1.hg19:g.19166175T>C	ENSP00000364520:p.Tyr813Cys	259.0	0.0		266.0	29.0	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	hg19	CCDS187.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.197509	0.58126	.	.	ENSG00000179002	ENST00000375371	D	0.90324	-2.65	5.05	2.66	0.31614	GPCR, family 3, C-terminal (2);	0.323941	0.22278	N	0.062173	D	0.93387	0.7891	M	0.74467	2.265	0.47065	D	0.999308	D	0.89917	1.0	D	0.97110	1.0	D	0.90878	0.4751	10	0.87932	D	0	.	5.6203	0.17453	0.1509:0.0849:0.0:0.7642	.	813	Q8TE23	TS1R2_HUMAN	C	813	ENSP00000364520:Y813C	ENSP00000364520:Y813C	Y	-	2	0	TAS1R2	19038762	1.000000	0.71417	0.981000	0.43875	0.925000	0.55904	1.822000	0.39052	0.254000	0.21573	-0.351000	0.07748	TAC	.	.		0.597	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			C	19166175	T	C	19166175	3	2	58	1	0	0	0	0	1	0	0	0	15578	1638	57	2	85	2	TAS1R2	1	19166175	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10		19166175	230084446	1	7158										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22222416	22222416	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gaggcctgcagcaacttaccCatctggaagtccccgctgcc	10	16	1	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:22222416C>T	ENST00000374695.3	-	3	322	c.243G>A	c.(241-243)atG>atA	p.M81I		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	81	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCAACTTACCCATCTGGAAGT	0.587																																					p.M81I		Atlas-SNP	.											.	HSPG2	311	.	0			c.G243A						.						53	55	55					1																	22222416		2203	4300	6503	SO:0001630	splice_region_variant	3339	exon3			CTTACCCATCTGG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.244+1G>A	chr1.hg19:g.22222416C>T		108.0	0.0		94.0	18.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	16.73	3.203750	0.58234	.	.	ENSG00000142798	ENST00000374695;ENST00000412328;ENST00000439717	T;T;T	0.74947	-0.89;0.56;0.95	4.72	4.72	0.59763	SEA (2);	0.155231	0.30704	N	0.009052	T	0.73281	0.3567	N	0.12182	0.205	0.33492	D	0.588755	D;B	0.67145	0.996;0.022	D;B	0.76071	0.987;0.01	T	0.79070	-0.1954	10	0.42905	T	0.14	.	13.0666	0.59036	0.0:1.0:0.0:0.0	.	60;81	Q5SZI5;P98160	.;PGBM_HUMAN	I	81;60;47	ENSP00000363827:M81I;ENSP00000405412:M60I;ENSP00000395884:M47I	ENSP00000363827:M81I	M	-	3	0	HSPG2	22095003	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.530000	0.53539	2.452000	0.82932	0.643000	0.83706	ATG	.	.		0.587	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	Missense_Mutation	T	22222416	C	T	22222416	5	4	58	1	0	0	0	0	0	0	1	0	7439	608	21	3	13312	3	HSPG2	1	22222416	Splice_Site	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	3056241	22222416	227028205	2	7159										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27099008	27099008	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cagcgggatcaggatctatgCaggggccccagactccccag	13	14	2	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:27099008C>T	ENST00000324856.7	+	13	3795	c.3424C>T	c.(3424-3426)Cag>Tag	p.Q1142*	ARID1A_ENST00000540690.1_5'Flank|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q759*|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q1142*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1142					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.Q1142*(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGGATCTATGCAGGGGCCCCA	0.527			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Q1142X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	ARID1A,NS,carcinoma,0,1	ARID1A	842	.	1	Substitution - Nonsense(1)	liver(1)	c.C3424T						.						77	75	76					1																	27099008		2203	4300	6503	SO:0001587	stop_gained	8289	exon13			TCTATGCAGGGGC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3424C>T	chr1.hg19:g.27099008C>T	ENSP00000320485:p.Gln1142*	207.0	0.0		248.0	45.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.328846|9.328846	0.99138|0.99138	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000430799|ENST00000324856;ENST00000457599;ENST00000374152	.|.	.|.	.|.	5.16|5.16	5.16|5.16	0.70880|0.70880	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.74786|.	0.3762|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.73180|.	-0.4064|.	4|.	.|0.40728	.|T	.|0.16	-6.7363|-6.7363	18.8418|18.8418	0.92188|0.92188	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	V|X	39|1142;1142;759	.|.	.|ENSP00000320485:Q1142X	A|Q	+|+	2|1	0|0	ARID1A|ARID1A	26971595|26971595	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.320000|7.320000	0.79064|0.79064	2.690000|2.690000	0.91761|0.91761	0.655000|0.655000	0.94253|0.94253	GCA|CAG	.	.		0.527	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27099008	C	T	27099008	4	4	58	1	0	0	0	0	0	1	0	0	913	711	25	3	3474	3	ARID1A	1	27099008	Nonsense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	4876592	27099008	222151613	3	7160										
GNL2	29889	hgsc.bcm.edu	37	chr1	38034740	38034740	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	caaagttctgccgaactcgtGtgagaatctgctgcatctct	9	11	3	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:38034740G>T	ENST00000373062.3	-	13	1678	c.1580C>A	c.(1579-1581)aCa>aAa	p.T527K	GNL2_ENST00000462812.1_5'UTR	NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	527					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				CCGAACTCGTGTGAGAATCTG	0.473																																					p.T527K		Atlas-SNP	.											.	GNL2	58	.	0			c.C1580A						.						169	154	159					1																	38034740		2203	4300	6503	SO:0001583	missense	29889	exon13			ACTCGTGTGAGAA	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.1580C>A	chr1.hg19:g.38034740G>T	ENSP00000362153:p.Thr527Lys	344.0	0.0		369.0	15.0	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	hg19	CCDS421.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.773041	0.31411	.	.	ENSG00000134697	ENST00000373062	T	0.20881	2.04	6.17	6.17	0.99709	.	0.311804	0.39407	N	0.001367	T	0.10809	0.0264	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22452	-1.0216	10	0.05959	T	0.93	-11.4385	20.8794	0.99867	0.0:0.0:1.0:0.0	.	527	Q13823	NOG2_HUMAN	K	527	ENSP00000362153:T527K	ENSP00000362153:T527K	T	-	2	0	GNL2	37807327	0.997000	0.39634	0.152000	0.22495	0.952000	0.60782	7.722000	0.84778	2.941000	0.99782	0.655000	0.94253	ACA	.	.		0.473	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285		T	38034740	G	T	38034740	3	4	58	1	0	0	0	0	1	0	0	0	6544	1377	48	3	631	3	GNL2	1	38034740	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	10935732	38034740	211215881	4	7161										
PTPRF	5792	hgsc.bcm.edu	37	chr1	44069658	44069658	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ccagtgctggcggagaggaaCgggcgcatcatcagctacac	14	12	2	1	rs368237069		TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:44069658C>T	ENST00000359947.4	+	16	3175	c.2835C>T	c.(2833-2835)aaC>aaT	p.N945N	PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000372413.3_Silent_p.N936N|PTPRF_ENST00000372414.3_Silent_p.N945N|PTPRF_ENST00000422171.2_Silent_p.N293N|PTPRF_ENST00000438120.1_Silent_p.N936N	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	945	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CGGAGAGGAACGGGCGCATCA	0.597																																					p.N945N		Atlas-SNP	.											.	PTPRF	172	.	0			c.C2835T						.	C	,	0,4406		0,0,2203	87	73	78		2835,2808	-3.5	0.6	1		78	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	945/1908,936/1899	44069658	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon16			GAGGAACGGGCGC	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.2835C>T	chr1.hg19:g.44069658C>T		117.0	0.0		119.0	28.0	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	hg19	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.152|0.152	-1.090406|-1.090406	0.01873|0.01873	0.0|0.0	1.16E-4|1.16E-4	ENSG00000142949|ENSG00000142949	ENST00000414879|ENST00000429895	.|.	.|.	.|.	5.19|5.19	-3.5|-3.5	0.04710|0.04710	.|.	.|.	.|.	.|.	.|.	T|T	0.65923|0.65923	0.2738|0.2738	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.62742|0.62742	-0.6790|-0.6790	4|4	.|.	.|.	.|.	.|.	16.0217|16.0217	0.80503|0.80503	0.0:0.402:0.0:0.598|0.0:0.402:0.0:0.598	.|.	.|.	.|.	.|.	W|M	359|591	.|.	.|.	R|T	+|+	1|2	2|0	PTPRF|PTPRF	43842245|43842245	0.004000|0.004000	0.15560|0.15560	0.636000|0.636000	0.29352|0.29352	0.179000|0.179000	0.23085|0.23085	-1.164000|-1.164000	0.03135|0.03135	-1.372000|-1.372000	0.02137|0.02137	-2.048000|-2.048000	0.00412|0.00412	CGG|ACG	.	.		0.597	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44069658	C	T	44069658	2	4	58	1	0	0	0	0	0	0	0	1	12816	535	19	1		1	PTPRF	1	44069658	Silent	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	6034918	44069658	205180963	5	7162										
TESK2	10420	hgsc.bcm.edu	37	chr1	45810698	45810699	+	Frame_Shift_Ins	INS	-	-	TG													0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tggagcagtccatagcctcaINStgggcttgagcagctggtag							TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:45810698_45810699insTG	ENST00000372086.3	-	11	1929_1930	c.1529_1530insCA	c.(1528-1530)catfs	p.H510fs	TESK2_ENST00000538496.1_Frame_Shift_Ins_p.H427fs|TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000372084.1_Frame_Shift_Ins_p.H481fs|TESK2_ENST00000341771.6_Frame_Shift_Ins_p.H481fs	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	510					actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					CCATAGCCTCATGGGCTTGAGC	0.569																																					p.H510fs		Atlas-Indel,Pindel	.											.	TESK2	60	.	0			c.1530_1531insCA						.																																			SO:0001589	frameshift_variant	10420	exon11			.	AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.1528_1529dupCA	chr1.hg19:g.45810699_45810700dupTG	ENSP00000361158:p.His510fs	148.0	0.0		151.0	21.0	NM_007170	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Frame_Shift_Ins	INS	ENST00000372086.3	hg19	CCDS41323.1																																																																																			.	.		0.569	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170		TG	45810699	-	TG	45810698	7	5	58	1	0	1	1	0	0	0	0	0	15783	214	8	0	189	0	TESK2	1	45810698	Frame_Shift_Ins	INS	-	TCGA-CC-5262-01A-01D-A12Z-10	1741040	45810698	203439923	6	7163										
SH3GLB1	51100	hgsc.bcm.edu	37	chr1	87189994	87189994	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tttttcttttctatatttatAgaaagaaaggaaactattgc	5	4	2	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:87189994A>G	ENST00000370558.4	+	5	801		c.e5-1		SH3GLB1_ENST00000482504.1_Splice_Site|SH3GLB1_ENST00000535010.1_Splice_Site	NM_001206651.1|NM_001206653.1|NM_016009.4	NP_001193580.1|NP_001193582.1|NP_057093.1	Q9Y371	SHLB1_HUMAN	SH3-domain GRB2-like endophilin B1						'de novo' posttranslational protein folding (GO:0051084)|apoptotic process (GO:0006915)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|protein complex (GO:0043234)	fatty acid binding (GO:0005504)|identical protein binding (GO:0042802)|lysophosphatidic acid acyltransferase activity (GO:0042171)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|stomach(1)	11		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)		CTATATTTATAGAAAGAAAGG	0.299																																					.		Atlas-SNP	.											.	SH3GLB1	57	.	0			c.178-2A>G						.						14	17	16					1																	87189994		2163	4260	6423	SO:0001630	splice_region_variant	51100	exon4			ATTTATAGAAAGA	AF263293	CCDS710.1, CCDS55612.1, CCDS55613.1, CCDS72819.1	1p22.3	2012-04-17	2001-12-04		ENSG00000097033	ENSG00000097033		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	10833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 70"	609287	"SH3-domain, GRB2-like, endophilin B1"			11161816, 11259440	Standard	NM_016009		Approved	CGI-61, KIAA0491, Bif-1, PPP1R70	uc001dly.3	Q9Y371	OTTHUMG00000010257	ENST00000370558.4:c.478-1A>G	chr1.hg19:g.87189994A>G		254.0	0.0		452.0	93.0	NM_001206653	B4E182|Q5H8U5|Q9H3Z0|Q9NR47|Q9NYA9	Splice_Site	SNP	ENST00000370558.4	hg19	CCDS710.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.355713	0.61293	.	.	ENSG00000097033	ENST00000212369;ENST00000535010;ENST00000482504	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7857	0.78300	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SH3GLB1	86962582	1.000000	0.71417	0.996000	0.52242	0.645000	0.38454	8.618000	0.90932	2.142000	0.66516	0.528000	0.53228	.	.	.		0.299	SH3GLB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028287.2	NM_016009	Intron	G	87189994	A	G	87189994	5	3	58	1	0	0	0	0	0	0	1	0	14268	434	15	2	494	2	SH3GLB1	1	87189994	Splice_Site	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	41379296	87189994	162060627	7	7164										
LCE1C	353133	hgsc.bcm.edu	37	chr1	152777757	152777757	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cctcccccagaactgcagcaTcccccagagctggagccaca	8	19	0	2	rs565723067		TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:152777757T>A	ENST00000607093.1	-	1	197	c.198A>T	c.(196-198)ggA>ggT	p.G66G	LCE1C_ENST00000368768.1_Silent_p.G66G			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	66	Gly-rich.				keratinization (GO:0031424)					NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1)	9	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AACTGCAGCATCCCCCAGAGC	0.672													G|||	1	0.000199681	0	0	5008	,	,		13167	0.001		0	False		,,,				2504	0				p.G66G		Atlas-SNP	.											LCE1C,NS,carcinoma,0,3	LCE1C	40	.	0			c.A198T						.						41	47	45					1																	152777757		2203	4300	6503	SO:0001819	synonymous_variant	353133	exon2			GCAGCATCCCCCA		CCDS1026.1	1q21.3	2008-02-05			ENSG00000197084	ENSG00000197084		"Late cornified envelopes"	29464	protein-coding gene	gene with protein product		612605				11698679	Standard	NM_001276331		Approved	LEP3	uc001fap.1	Q5T751	OTTHUMG00000012445	ENST00000607093.1:c.198A>T	chr1.hg19:g.152777757T>A		182.0	1.0		150.0	19.0	NM_178351		Silent	SNP	ENST00000607093.1	hg19	CCDS1026.1																																																																																			.	.		0.672	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351		A	152777757	T	A	152777757	2	1	58	1	0	0	0	0	0	0	0	1	8670	1422	50	4		4	LCE1C	1	152777757	Silent	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	65587763	152777757	96472864	8	7165										
OR6Y1	391112	hgsc.bcm.edu	37	chr1	158517119	158517119	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cgggcataggtgaaaagtgtCatggaatagaagagaattac	13	4	1	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:158517119C>A	ENST00000302617.3	-	1	776	c.777G>T	c.(775-777)atG>atT	p.M259I		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					TGAAAAGTGTCATGGAATAGA	0.502																																					p.M259I		Atlas-SNP	.											.	OR6Y1	73	.	0			c.G777T						.						196	187	190					1																	158517119		2203	4300	6503	SO:0001583	missense	391112	exon1			AAGTGTCATGGAA	BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"GPCR / Class A : Olfactory receptors"	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.777G>T	chr1.hg19:g.158517119C>A	ENSP00000304807:p.Met259Ile	146.0	0.0		184.0	32.0	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	hg19	CCDS30899.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376146	0.24857	.	.	ENSG00000197532	ENST00000302617	T	0.00076	8.76	5.34	-10.7	0.00240	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43416	D	0.000575	T	0.00012	0.0000	N	0.04355	-0.22	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.54589	-0.8271	10	0.87932	D	0	.	2.1765	0.03864	0.1944:0.2246:0.4023:0.1787	.	259	Q8NGX8	OR6Y1_HUMAN	I	259	ENSP00000304807:M259I	ENSP00000304807:M259I	M	-	3	0	OR6Y1	156783743	0.000000	0.05858	0.015000	0.15790	0.929000	0.56500	-3.880000	0.00343	-3.438000	0.00163	-0.238000	0.12139	ATG	.	.		0.502	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		A	158517119	C	A	158517119	3	1	58	1	0	0	0	0	1	0	0	0	11222	826	29	3	202	3	OR6Y1	1	158517119	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	5739362	158517119	90733502	9	7166										
ATP1A2	477	hgsc.bcm.edu	37	chr1	160104352	160104352	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gcatcatatcagagggtaacGagactgtggaggacattgca	13	7	2	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:160104352G>T	ENST00000361216.3	+	14	1995	c.1906G>T	c.(1906-1908)Gag>Tag	p.E636*	ATP1A2_ENST00000392233.3_Nonsense_Mutation_p.E636*	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	636					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			AGAGGGTAACGAGACTGTGGA	0.557																																					p.E636X		Atlas-SNP	.											.	ATP1A2	167	.	0			c.G1906T						.						149	121	130					1																	160104352		2203	4300	6503	SO:0001587	stop_gained	477	exon14			GGTAACGAGACTG	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.1906G>T	chr1.hg19:g.160104352G>T	ENSP00000354490:p.Glu636*	196.0	0.0		223.0	11.0	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Nonsense_Mutation	SNP	ENST00000361216.3	hg19	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	G	38	6.723119	0.97788	.	.	ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000435866	.	.	.	5.0	5.0	0.66597	.	0.103551	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	17.4432	0.87570	0.0:0.0:1.0:0.0	.	.	.	.	X	636;636;339	.	ENSP00000354490:E636X	E	+	1	0	ATP1A2	158370976	1.000000	0.71417	0.985000	0.45067	0.366000	0.29705	9.813000	0.99286	2.467000	0.83353	0.561000	0.74099	GAG	.	.		0.557	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		T	160104352	G	T	160104352	4	4	58	1	0	0	0	0	0	1	0	0	1129	1059	37	1	1960	1	ATP1A2	1	160104352	Nonsense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	1587233	160104352	89146269	10	7167										
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173570862	173570863	+	Nonsense_Mutation	DNP	GC	GC	TT													0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aggtagtcagctggctgcccGcagagtaaatcaggtctgtt							TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:173570862_173570863GC>TT	ENST00000367714.3	-	2	475_476	c.53_54GC>AA	c.(52-54)tGC>tAA	p.C18*	SLC9C2_ENST00000536496.1_Intron|RP3-436N22.3_ENST00000431459.1_RNA	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	18					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										CTGGCTGCCCGCAGAGTAAATC	0.426																																					p.C18X|p.C18Y		Atlas-SNP	.											.	.	.	.	0			c.C54A|c.G53A						.																																			SO:0001587	stop_gained	284525	exon2			CTGCCCGCAGAGT|TGCCCGCAGAGTA	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.53_54delinsTT	chr1.hg19:g.173570862_173570863delinsTT	ENSP00000356687:p.Cys18*	305.0|302.0	0.0		425.0|429.0	66.0|69.0	NM_178527	Q86UF3	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000367714.3	hg19	CCDS1308.1																																																																																			.	.		0.426	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		TT	173570863	GC	TT	173570862	4	4	58	1	0	0	0	0	0	1	0	0	14726	1079	38	1	3428	1	SLC9A11	1	173570862	Nonsense_Mutation	DNP	GC	TCGA-CC-5262-01A-01D-A12Z-10	13466510	173570862	75679759	11	7168										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177250229	177250229	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aataggtggaagactttcttTgagacagttcatgtttacct	9	6	2	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:177250229T>A	ENST00000361539.4	+	8	2229	c.1917T>A	c.(1915-1917)ttT>ttA	p.F639L	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	639					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											AGACTTTCTTTGAGACAGTTC	0.498																																					p.F639L		Atlas-SNP	.											.	FAM5B	191	.	0			c.T1917A						.						63	63	63					1																	177250229		2203	4300	6503	SO:0001583	missense	57795	exon8			TTTCTTTGAGACA		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1917T>A	chr1.hg19:g.177250229T>A	ENSP00000354481:p.Phe639Leu	177.0	0.0		259.0	41.0	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	hg19	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	T	18.81	3.703514	0.68501	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.18338	2.22	5.16	1.63	0.23807	.	0.000000	0.85682	D	0.000000	T	0.35189	0.0923	M	0.69823	2.125	0.58432	D	0.999991	D;D	0.76494	0.999;0.993	D;D	0.80764	0.994;0.956	T	0.04347	-1.0958	10	0.72032	D	0.01	-12.2269	8.3636	0.32374	0.0:0.233:0.0:0.767	.	534;639	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	L	392;639	ENSP00000354481:F639L	ENSP00000354481:F639L	F	+	3	2	FAM5B	175516852	0.989000	0.36119	1.000000	0.80357	0.983000	0.72400	0.180000	0.16860	0.304000	0.22809	0.260000	0.18958	TTT	.	.		0.498	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		A	177250229	T	A	177250229	3	1	58	1	0	0	0	0	1	0	0	0	5601	1809	63	4	1943	4	FAM5B	1	177250229	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	3679367	177250229	72000392	12	7169										
SERTAD4	56256	hgsc.bcm.edu	37	chr1	210415122	210415122	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ggtttatggctcaagactgcCcttaccgaaaacgaccacgg	10	12	1	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:210415122C>G	ENST00000367012.3	+	4	741	c.511C>G	c.(511-513)Cct>Gct	p.P171A	SERTAD4_ENST00000490620.1_3'UTR	NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	171						nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		TCAAGACTGCCCTTACCGAAA	0.473																																					p.P171A		Atlas-SNP	.											.	SERTAD4	53	.	0			c.C511G						.						185	189	188					1																	210415122		2203	4300	6503	SO:0001583	missense	56256	exon4			GACTGCCCTTACC	BC012083	CCDS1494.1	1q32.1-q41	2008-02-05			ENSG00000082497	ENSG00000082497			25236	protein-coding gene	gene with protein product						12477932	Standard	NM_019605		Approved	DJ667H12.2	uc001hhy.3	Q9NUC0	OTTHUMG00000036391	ENST00000367012.3:c.511C>G	chr1.hg19:g.210415122C>G	ENSP00000355979:p.Pro171Ala	138.0	0.0		200.0	30.0	NM_019605	B2RD32	Missense_Mutation	SNP	ENST00000367012.3	hg19	CCDS1494.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315944	0.60524	.	.	ENSG00000082497	ENST00000367012	.	.	.	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000001	T	0.68238	0.2979	L	0.29908	0.895	0.43230	D	0.995122	D	0.76494	0.999	D	0.78314	0.991	T	0.70139	-0.4954	9	0.66056	D	0.02	-20.4626	19.861	0.96785	0.0:1.0:0.0:0.0	.	171	Q9NUC0	SRTD4_HUMAN	A	171	.	ENSP00000355979:P171A	P	+	1	0	SERTAD4	208481745	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	5.884000	0.69729	2.767000	0.95098	0.655000	0.94253	CCT	.	.		0.473	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1	NM_019605		G	210415122	C	G	210415122	3	3	58	1	0	0	0	0	1	0	0	0	14138	623	22	4	521	4	SERTAD4	1	210415122	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	33164893	210415122	38835499	13	7170										
SMYD2	56950	hgsc.bcm.edu	37	chr1	214501025	214501025	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gtgacctacaaagggaccctGgcagaagtcagagctgtaca	12	10	1	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:214501025G>T	ENST00000366957.5	+	7	685	c.663G>T	c.(661-663)ctG>ctT	p.L221L	SMYD2_ENST00000415093.2_Silent_p.L221L|SMYD2_ENST00000491455.1_3'UTR	NM_020197.2	NP_064582.2	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	221	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|RNA polymerase II core binding (GO:0000993)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		AAGGGACCCTGGCAGAAGTCA	0.483											OREG0004276	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.L221L		Atlas-SNP	.											.	SMYD2	40	.	0			c.G663T						.						114	114	114					1																	214501025		2203	4300	6503	SO:0001819	synonymous_variant	56950	exon7			GACCCTGGCAGAA	AF226053	CCDS31022.1	1q32.3	2011-07-01			ENSG00000143499	ENSG00000143499		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	20982	protein-coding gene	gene with protein product		610663					Standard	NM_020197		Approved	HSKM-B, ZMYND14, KMT3C	uc021pix.1	Q9NRG4	OTTHUMG00000037066	ENST00000366957.5:c.663G>T	chr1.hg19:g.214501025G>T		149.0	0.0	2221	187.0	65.0	NM_020197	B2R9P9|I6L9H7|Q4V765|Q5VSH9|Q96AI4	Silent	SNP	ENST00000366957.5	hg19	CCDS31022.1																																																																																			.	.		0.483	SMYD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089998.1	NM_020197		T	214501025	G	T	214501025	2	4	58	1	0	0	0	0	0	0	0	1	14837	1335	47	3		3	SMYD2	1	214501025	Silent	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	4085903	214501025	34749596	14	7171										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228465514	228465514	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aagatgcaggagagatccaaTttgtagccgaaaatgcagaa	11	6	0	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:228465514T>C	ENST00000422127.1	+	25	6858	c.6814T>C	c.(6814-6816)Ttt>Ctt	p.F2272L	RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000284548.11_Missense_Mutation_p.F2272L|RP5-1139B12.3_ENST00000602529.1_RNA|OBSCN_ENST00000359599.6_Missense_Mutation_p.F1119L|OBSCN_ENST00000570156.2_Missense_Mutation_p.F2701L|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2272					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGAGATCCAATTTGTAGCCGA	0.612																																					p.F2701L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T8101C						.						69	71	70					1																	228465514		1923	4133	6056	SO:0001583	missense	84033	exon30			ATCCAATTTGTAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.6814T>C	chr1.hg19:g.228465514T>C	ENSP00000409493:p.Phe2272Leu	230.0	0.0		328.0	34.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.502149	0.44455	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.63580	0.35;-0.05;0.09	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000001	T	0.77212	0.4097	M	0.83384	2.64	0.80722	D	1	D;D	0.76494	0.986;0.999	D;D	0.85130	0.965;0.997	T	0.76044	-0.3103	10	0.13470	T	0.59	.	13.406	0.60913	0.0:0.0:0.0:1.0	.	2272;2272	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	L	2272;2272;1119	ENSP00000284548:F2272L;ENSP00000409493:F2272L;ENSP00000352613:F1119L	ENSP00000284548:F2272L	F	+	1	0	OBSCN	226532137	1.000000	0.71417	0.857000	0.33713	0.127000	0.20565	5.395000	0.66291	1.754000	0.51921	0.379000	0.24179	TTT	.	.		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228465514	T	C	228465514	3	2	58	1	0	0	0	0	1	0	0	0	10821	1493	52	2	6908	2	OBSCN	1	228465514	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	13964489	228465514	20785107	15	7172										
CAPN9	10753	hgsc.bcm.edu	37	chr1	230914798	230914798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ccgatgccctggaggaagacGcgatccacaaatgggaggtg	15	10	0	1	rs145648359	byFrequency	TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:230914798G>A	ENST00000271971.2	+	9	1146	c.1033G>A	c.(1033-1035)Gcg>Acg	p.A345T	CAPN9_ENST00000354537.1_Missense_Mutation_p.A319T|RP11-99J16__A.2_ENST00000412344.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000452640.1_RNA|CAPN9_ENST00000366666.2_Missense_Mutation_p.A282T	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	345	Domain III.				digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)	p.A319T(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				GGAGGAAGACGCGATCCACAA	0.577													G|||	7	0.00139776	0	0	5008	,	,		16239	0		0	False		,,,				2504	0.0072				p.A345T		Atlas-SNP	.											CAPN9,colon,carcinoma,0,1	CAPN9	116	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1033A						.	G	THR/ALA,THR/ALA	4,4402	8.1+/-20.4	0,4,2199	84	71	75		1033,955	-2.6	0	1	dbSNP_134	75	0,8600		0,0,4300	yes	missense,missense	CAPN9	NM_006615.2,NM_016452.1	58,58	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	benign,benign	345/691,319/665	230914798	4,13002	2203	4300	6503	SO:0001583	missense	10753	exon9			GAAGACGCGATCC	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"EF-hand domain containing"	1486	protein-coding gene	gene with protein product	"novel calpain large subunit-4"	606401	"calpain 9 (nCL-4)"			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1033G>A	chr1.hg19:g.230914798G>A	ENSP00000271971:p.Ala345Thr	85.0	1.0		116.0	24.0	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	hg19	CCDS1586.1	.	.	.	.	.	.	.	.	.	.	G	0.678	-0.799307	0.02841	9.08E-4	0.0	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	T;T;T	0.15952	2.38;2.38;2.38	5.24	-2.63	0.06133	Peptidase C2, calpain, catalytic domain (1);	0.446021	0.27455	N	0.019297	T	0.06600	0.0169	N	0.10733	0.035	0.22620	N	0.998922	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.08055	0.002;0.003;0.001	T	0.40403	-0.9565	10	0.11485	T	0.65	.	11.9229	0.52801	0.5965:0.0:0.4035:0.0	.	282;319;345	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	T	345;319;282	ENSP00000271971:A345T;ENSP00000346538:A319T;ENSP00000355626:A282T	ENSP00000271971:A345T	A	+	1	0	CAPN9	228981421	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.274000	0.18680	-0.278000	0.09180	-0.244000	0.11960	GCG	.	G|1.000;A|0.000		0.577	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615		A	230914798	G	A	230914798	3	1	58	1	0	0	0	0	1	0	0	0	2634	1087	38	1	1067	1	CAPN9	1	230914798	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	2449284	230914798	18335823	16	7173										
OR2L13	284521	hgsc.bcm.edu	37	chr1	248263522	248263522	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cttctacaccatccttacccCcatgctcaatcccattatct	1	18	3	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr1:248263522C>A	ENST00000358120.2	+	2	990	c.845C>A	c.(844-846)cCc>cAc	p.P282H	OR2L13_ENST00000366478.2_Missense_Mutation_p.P282H			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			ATCCTTACCCCCATGCTCAAT	0.468																																					p.P282H		Atlas-SNP	.											.	OR2L13	261	.	0			c.C845A						.						78	79	79					1																	248263522		2203	4300	6503	SO:0001583	missense	284521	exon3			TTACCCCCATGCT	BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"GPCR / Class A : Olfactory receptors"	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.845C>A	chr1.hg19:g.248263522C>A	ENSP00000350836:p.Pro282His	113.0	0.0		181.0	25.0	NM_175911	Q5VUR5	Missense_Mutation	SNP	ENST00000358120.2	hg19	CCDS1637.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.239329	0.58995	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	T;T	0.00349	7.99;7.99	4.21	4.21	0.49690	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	D	0.000472	T	0.01592	0.0051	H	0.98682	4.3	0.32703	N	0.512541	D	0.89917	1.0	D	0.69479	0.964	T	0.02610	-1.1134	10	0.87932	D	0	.	15.4907	0.75602	0.0:1.0:0.0:0.0	.	282	Q8N349	OR2LD_HUMAN	H	282	ENSP00000355434:P282H;ENSP00000350836:P282H	ENSP00000350836:P282H	P	+	2	0	OR2L13	246330145	0.543000	0.26434	1.000000	0.80357	0.604000	0.37047	4.213000	0.58520	2.138000	0.66242	0.650000	0.86243	CCC	.	.		0.468	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911		A	248263522	C	A	248263522	3	1	58	1	0	0	0	0	1	0	0	0	11015	623	22	3	847	3	OR2L13	1	248263522	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	17348724	248263522	987099	17	7174										
PXDN	7837	hgsc.bcm.edu	37	chr2	1664717	1664717	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ttccgggccacacactcataGcgacctgcgtctgcagggcc	11	16	2	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr2:1664717G>T	ENST00000252804.4	-	14	1823	c.1773C>A	c.(1771-1773)cgC>cgA	p.R591R		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	591	Ig-like C2-type 4.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		CACACTCATAGCGACCTGCGT	0.537																																					p.R591R		Atlas-SNP	.											.	PXDN	255	.	0			c.C1773A						.						96	100	99					2																	1664717		2050	4187	6237	SO:0001819	synonymous_variant	7837	exon14			CTCATAGCGACCT	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1773C>A	chr2.hg19:g.1664717G>T		74.0	0.0		98.0	12.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	hg19	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	G	1.380	-0.583679	0.03827	.	.	ENSG00000130508	ENST00000433670	.	.	.	5.05	0.832	0.18867	.	.	.	.	.	T	0.50854	0.1640	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37244	-0.9714	4	.	.	.	-29.5186	4.9067	0.13802	0.2737:0.0:0.4738:0.2525	.	.	.	.	D	587	.	.	A	-	2	0	PXDN	1643724	0.997000	0.39634	0.998000	0.56505	0.031000	0.12232	0.331000	0.19733	0.249000	0.21456	0.591000	0.81541	GCT	.	.		0.537	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1664717	G	T	1664717	2	4	58	1	0	0	0	0	0	0	0	1	12862	958	34	3		3	PXDN	2	1664717	Silent	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10		1664717	241534656	18	7175										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33174004	33174004	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ggcccctggctcccagaggtGcaccaaacgtaagttgccat	11	14	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr2:33174004G>C	ENST00000404816.2	+	2	910	c.557G>C	c.(556-558)tGc>tCc	p.C186S	LTBP1_ENST00000354476.3_Missense_Mutation_p.C186S			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	186					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				TCCCAGAGGTGCACCAAACGT	0.572																																					p.C186S		Atlas-SNP	.											.	LTBP1	317	.	0			c.G557C						.						150	125	134					2																	33174004		2203	4300	6503	SO:0001583	missense	4052	exon2			AGAGGTGCACCAA		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.557G>C	chr2.hg19:g.33174004G>C	ENSP00000386043:p.Cys186Ser	144.0	0.0		189.0	38.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333177	0.81801	.	.	ENSG00000049323	ENST00000404816;ENST00000354476	D;D	0.91011	-2.76;-2.77	5.7	5.7	0.88788	.	.	.	.	.	D	0.92008	0.7468	N	0.24115	0.695	0.80722	D	1	D	0.67145	0.996	D	0.77557	0.99	D	0.93154	0.6552	9	0.87932	D	0	.	17.6293	0.88102	0.0:0.0:1.0:0.0	.	186	Q14766-4	.	S	186	ENSP00000386043:C186S;ENSP00000346467:C186S	ENSP00000346467:C186S	C	+	2	0	LTBP1	33027508	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.282000	0.78630	2.683000	0.91414	0.655000	0.94253	TGC	.	.		0.572	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		C	33174004	G	C	33174004	3	2	58	1	0	0	0	0	1	0	0	0	9082	1319	46	4	563	4	LTBP1	2	33174004	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	31509287	33174004	210025369	19	7176										
BCL11A	53335	hgsc.bcm.edu	37	chr2	60688381	60688381	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gaaggcctcgctgaagtgctGcatggagctgagcaccatgc	14	11	0	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr2:60688381G>T	ENST00000335712.6	-	4	1893	c.1666C>A	c.(1666-1668)Cag>Aag	p.Q556K	BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000538214.1_Missense_Mutation_p.Q522K|BCL11A_ENST00000358510.4_Missense_Mutation_p.Q522K|BCL11A_ENST00000537768.1_Missense_Mutation_p.Q225K|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000356842.4_Missense_Mutation_p.Q556K	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	556					B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			CTGAAGTGCTGCATGGAGCTG	0.697			T	IGH@	B-CLL																																p.Q556K		Atlas-SNP	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.C1666A						.						24	23	23					2																	60688381		2200	4291	6491	SO:0001583	missense	53335	exon4			AGTGCTGCATGGA	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"Zinc fingers, C2H2-type"	13221	protein-coding gene	gene with protein product		606557	"ecotropic viral integration site 9"	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.1666C>A	chr2.hg19:g.60688381G>T	ENSP00000338774:p.Gln556Lys	73.0	0.0		58.0	9.0	NM_018014	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	hg19	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018947	0.35606	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000537768;ENST00000335712;ENST00000358510	T;T;T;T;T	0.08370	3.1;3.37;3.24;3.4;3.31	5.69	5.69	0.88448	.	0.198852	0.34628	N	0.003804	T	0.11281	0.0275	L	0.58101	1.795	0.80722	D	1	P;B;B;B;P	0.37914	0.554;0.139;0.058;0.01;0.611	B;B;B;B;B	0.30646	0.107;0.038;0.037;0.004;0.118	T	0.05632	-1.0873	10	0.35671	T	0.21	-3.0658	19.4143	0.94688	0.0:0.0:1.0:0.0	.	522;225;522;556;556	F5H2Y4;B4DT16;Q9H165-6;Q9H165;D9YZV9	.;.;.;BC11A_HUMAN;.	K	556;581;522;225;556;522	ENSP00000349300:Q556K;ENSP00000438303:Q522K;ENSP00000443712:Q225K;ENSP00000338774:Q556K;ENSP00000351307:Q522K	ENSP00000338774:Q556K	Q	-	1	0	BCL11A	60541885	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.863000	0.87023	2.690000	0.91761	0.555000	0.69702	CAG	.	.		0.697	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		T	60688381	G	T	60688381	3	4	58	1	0	0	0	0	1	0	0	0	1363	1328	46	3	951	3	BCL11A	2	60688381	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	27514377	60688381	182510992	20	7177										
PROM2	150696	hgsc.bcm.edu	37	chr2	95952937	95952937	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ctgaaaggagagctgcctgcCtgggcagccaggatcctgag	15	11	0	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr2:95952937C>T	ENST00000317620.9	+	19	2284	c.2151C>T	c.(2149-2151)gcC>gcT	p.A717A	PROM2_ENST00000403131.2_Silent_p.A717A|PROM2_ENST00000317668.4_Silent_p.A717A|PROM2_ENST00000542147.1_Silent_p.A668A	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	717					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						AGCTGCCTGCCTGGGCAGCCA	0.602																																					p.A717A		Atlas-SNP	.											.	PROM2	78	.	0			c.C2151T						.						55	54	54					2																	95952937		2203	4300	6503	SO:0001819	synonymous_variant	150696	exon19			GCCTGCCTGGGCA	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.2151C>T	chr2.hg19:g.95952937C>T		85.0	0.0		100.0	23.0	NM_001165977	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Silent	SNP	ENST00000317620.9	hg19	CCDS2012.1																																																																																			.	.		0.602	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707		T	95952937	C	T	95952937	2	4	58	1	0	0	0	0	0	0	0	1	12568	668	24	3		3	PROM2	2	95952937	Silent	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	35264556	95952937	147246436	21	7178										
CCDC93	54520	hgsc.bcm.edu	37	chr2	118716046	118716046	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tctggactttcttcagctgaTagctcagactgctgtggaaa	10	9	4	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr2:118716046T>G	ENST00000376300.2	-	12	1037	c.900A>C	c.(898-900)ctA>ctC	p.L300L	CCDC93_ENST00000460781.1_5'UTR|CCDC93_ENST00000319432.5_Silent_p.L299L	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	300										breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						CTTCAGCTGATAGCTCAGACT	0.433																																					p.L300L		Atlas-SNP	.											.	CCDC93	70	.	0			c.A900C						.						107	97	100					2																	118716046		2203	4300	6503	SO:0001819	synonymous_variant	54520	exon12			AGCTGATAGCTCA	BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.900A>C	chr2.hg19:g.118716046T>G		282.0	0.0		365.0	73.0	NM_019044	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Silent	SNP	ENST00000376300.2	hg19	CCDS2121.2																																																																																			.	.		0.433	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044		G	118716046	T	G	118716046	2	3	58	1	0	0	0	0	0	0	0	1	2874	1393	49	5		5	CCDC93	2	118716046	Silent	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	22763109	118716046	124483327	22	7179										
MBD5	55777	hgsc.bcm.edu	37	chr2	149247524	149247524	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	agccccagaggggagcgaaaCaggtggaagtacgaggaatt	16	7	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr2:149247524C>A	ENST00000407073.1	+	12	4621	c.3624C>A	c.(3622-3624)aaC>aaA	p.N1208K	MBD5_ENST00000404807.1_Missense_Mutation_p.N1441K	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1208					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		GGGAGCGAAACAGGTGGAAGT	0.478																																					p.N1208K		Atlas-SNP	.											.	MBD5	164	.	0			c.C3624A						.						112	108	109					2																	149247524		2203	4300	6503	SO:0001583	missense	55777	exon12			GCGAAACAGGTGG	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.3624C>A	chr2.hg19:g.149247524C>A	ENSP00000386049:p.Asn1208Lys	107.0	0.0		109.0	11.0	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	hg19	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.878778	0.33162	.	.	ENSG00000204406	ENST00000407073;ENST00000404807	T;T	0.49139	0.83;0.79	6.01	6.01	0.97437	.	0.000000	0.64402	D	0.000001	T	0.33876	0.0878	N	0.14661	0.345	0.34009	D	0.651207	B;B	0.27732	0.187;0.11	B;B	0.25140	0.058;0.04	T	0.47623	-0.9103	10	0.62326	D	0.03	-7.5334	15.6336	0.76933	0.0:0.9327:0.0:0.0673	.	1441;1208	E9PHH0;Q9P267	.;MBD5_HUMAN	K	1208;1441	ENSP00000386049:N1208K;ENSP00000384672:N1441K	ENSP00000384672:N1441K	N	+	3	2	MBD5	148963994	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.163000	0.31798	2.860000	0.98153	0.655000	0.94253	AAC	.	.		0.478	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			A	149247524	C	A	149247524	3	1	58	1	0	0	0	0	1	0	0	0	9356	477	17	3	3650	3	MBD5	2	149247524	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	30531478	149247524	93951849	23	7180										
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172749745	172749745	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	atgtttcttaactcatgaggAtcccctcgcttagttgtctg	8	10	3	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr2:172749745A>T	ENST00000422440.2	-	2	73	c.36T>A	c.(34-36)gaT>gaA	p.D12E	SLC25A12_ENST00000472748.1_5'UTR|SLC25A12_ENST00000392592.4_5'UTR	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	12					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	ACTCATGAGGATCCCCTCGCT	0.378																																					p.D12E		Atlas-SNP	.											.	SLC25A12	59	.	0			c.T36A						.						138	135	136					2																	172749745		2203	4300	6503	SO:0001583	missense	8604	exon2			ATGAGGATCCCCT	Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"Solute carriers", "EF-hand domain containing"	10982	protein-coding gene	gene with protein product		603667	"solute carrier family 25 (mitochondrial carrier, Aralar), member 12"			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.36T>A	chr2.hg19:g.172749745A>T	ENSP00000388658:p.Asp12Glu	264.0	0.0		333.0	56.0	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	hg19	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	A	14.10	2.433694	0.43224	.	.	ENSG00000115840	ENST00000422440	D	0.87179	-2.22	5.48	3.01	0.34805	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.85932	0.5812	M	0.82323	2.585	0.80722	D	1	B	0.15141	0.012	B	0.15484	0.013	T	0.80500	-0.1355	10	0.66056	D	0.02	-14.2562	7.4461	0.27211	0.8246:0.0:0.1754:0.0	.	12	O75746	CMC1_HUMAN	E	12	ENSP00000388658:D12E	ENSP00000263812:D12E	D	-	3	2	SLC25A12	172457991	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.646000	0.37249	0.347000	0.23924	0.533000	0.62120	GAT	.	.		0.378	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		T	172749745	A	T	172749745	3	4	58	1	0	0	0	0	1	0	0	0	14489	330	12	4	2068	4	SLC25A12	2	172749745	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	23502221	172749745	70449628	24	7181										
RAPH1	65059	hgsc.bcm.edu	37	chr2	204354662	204354662	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aggtgccatgtttcaatgtaTgtcggctaacaggcaatttc	10	8	1	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr2:204354662T>C	ENST00000319170.5	-	4	676	c.377A>G	c.(376-378)cAt>cGt	p.H126R	RAPH1_ENST00000418114.1_Missense_Mutation_p.H126R|RAPH1_ENST00000419464.1_Missense_Mutation_p.H126R|RAPH1_ENST00000453034.1_Missense_Mutation_p.H126R|RAPH1_ENST00000374489.2_Missense_Mutation_p.H126R|RAPH1_ENST00000457812.1_Missense_Mutation_p.H126R|RAPH1_ENST00000423104.1_Missense_Mutation_p.H126R|RAPH1_ENST00000374488.2_Missense_Mutation_p.H126R|RAPH1_ENST00000308091.4_Missense_Mutation_p.H126R|RAPH1_ENST00000374493.3_Missense_Mutation_p.H126R|RAPH1_ENST00000439222.1_Missense_Mutation_p.H126R	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	126					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTTCAATGTATGTCGGCTAAC	0.448																																					p.H126R		Atlas-SNP	.											.	RAPH1	118	.	0			c.A377G						.						244	233	237					2																	204354662		2203	4300	6503	SO:0001583	missense	65059	exon4			AATGTATGTCGGC	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.377A>G	chr2.hg19:g.204354662T>C	ENSP00000316543:p.His126Arg	433.0	0.0		569.0	34.0	NM_213589	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	hg19	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	T	1.353	-0.590863	0.03799	.	.	ENSG00000173166	ENST00000457812;ENST00000319170;ENST00000374493;ENST00000374489;ENST00000374488;ENST00000308091;ENST00000439222;ENST00000419464;ENST00000423104;ENST00000453034;ENST00000432342;ENST00000418114;ENST00000413201;ENST00000428637	T;T;T;T;T;T;T;T;T;T;T	0.41758	1.01;1.01;1.0;1.02;1.02;0.99;1.02;1.01;1.02;0.99;1.01	5.51	5.51	0.81932	.	0.144549	0.32015	N	0.006717	T	0.21427	0.0516	N	0.14661	0.345	0.24486	N	0.994321	B;B;B	0.20671	0.0;0.008;0.047	B;B;B	0.19148	0.001;0.007;0.024	T	0.18745	-1.0327	10	0.13108	T	0.6	-10.9074	6.1481	0.20296	0.2423:0.0:0.1499:0.6078	.	126;126;126	Q70E73-6;C9K0J5;Q70E73	.;.;RAPH1_HUMAN	R	126	ENSP00000392854:H126R;ENSP00000316543:H126R;ENSP00000363617:H126R;ENSP00000363613:H126R;ENSP00000363612:H126R;ENSP00000311293:H126R;ENSP00000411138:H126R;ENSP00000390578:H126R;ENSP00000397751:H126R;ENSP00000406662:H126R;ENSP00000396711:H126R	ENSP00000311293:H126R	H	-	2	0	RAPH1	204062907	0.976000	0.34144	0.903000	0.35520	0.280000	0.26924	2.211000	0.42825	2.074000	0.62210	0.528000	0.53228	CAT	.	.		0.448	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		C	204354662	T	C	204354662	3	2	58	1	0	0	0	0	1	0	0	0	13065	1464	51	2	3590	2	RAPH1	2	204354662	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	31604917	204354662	38844711	25	7182										
CPS1	1373	hgsc.bcm.edu	37	chr2	211456588	211456589	+	Frame_Shift_Ins	INS	-	-	A													0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ctgttttgaatatcacaaacINSaaacaggctttcattactgc							TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr2:211456588_211456589insA	ENST00000233072.5	+	10	1177_1178	c.981_982insA	c.(982-984)aaafs	p.K328fs	CPS1_ENST00000430249.2_Frame_Shift_Ins_p.K334fs|CPS1_ENST00000451903.2_5'Flank	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	328	Glutamine amidotransferase type-1.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	ATATCACAAACAAACAGGCTTT	0.396																																					p.N333fs		Atlas-Indel,Pindel	.											.	CPS1	485	.	0			c.999_1000insA						.																																			SO:0001589	frameshift_variant	1373	exon11			.	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.984dupA	chr2.hg19:g.211456591_211456591dupA	ENSP00000233072:p.Lys328fs	179.0	0.0		261.0	50.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Frame_Shift_Ins	INS	ENST00000233072.5	hg19	CCDS2393.1																																																																																			.	.		0.396	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			A	211456589	-	A	211456588	7	5	58	1	0	1	1	0	0	0	0	0	3825	477	17	0	1041	0	CPS1	2	211456588	Frame_Shift_Ins	INS	-	TCGA-CC-5262-01A-01D-A12Z-10	7101926	211456588	31742785	26	7183										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41274899	41274899	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cttgttcagaactgtctttgGactctcaggaatctttcaga	8	9	5	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:41274899G>C	ENST00000349496.5	+	8	1429	c.1149G>C	c.(1147-1149)tgG>tgC	p.W383C	CTNNB1_ENST00000453024.1_Missense_Mutation_p.W376C|CTNNB1_ENST00000396185.3_Missense_Mutation_p.W383C|CTNNB1_ENST00000396183.3_Missense_Mutation_p.W383C|CTNNB1_ENST00000405570.1_Missense_Mutation_p.W383C	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	383					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.W383C(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACTGTCTTTGGACTCTCAGGA	0.418		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.W383C	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,malignant_melanoma,0,2	CTNNB1	4904	.	1	Substitution - Missense(1)	liver(1)	c.G1149C						.						105	96	99					3																	41274899		2203	4300	6503	SO:0001583	missense	1499	exon8	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TCTTTGGACTCTC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1149G>C	chr3.hg19:g.41274899G>C	ENSP00000344456:p.Trp383Cys	194.0	0.0		260.0	56.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.148323	0.78001	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88;-0.88	5.72	5.72	0.89469	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85544	0.5721	M	0.76002	2.32	0.80722	D	1	P;D	0.57899	0.93;0.981	P;P	0.62435	0.558;0.902	D	0.85389	0.1124	10	0.52906	T	0.07	-7.7281	19.8737	0.96861	0.0:0.0:1.0:0.0	.	311;383	B4DSW9;P35222	.;CTNB1_HUMAN	C	383;383;383;376;383	ENSP00000385604:W383C;ENSP00000379486:W383C;ENSP00000344456:W383C;ENSP00000411226:W376C;ENSP00000379488:W383C	ENSP00000344456:W383C	W	+	3	0	CTNNB1	41249903	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.687000	0.91594	0.655000	0.94253	TGG	.	.		0.418	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41274899	G	C	41274899	3	2	58	1	0	0	0	0	1	0	0	0	4018	1183	41	4	1175	4	CTNNB1	3	41274899	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10		41274899	156747531	27	7184										
CCDC13	152206	hgsc.bcm.edu	37	chr3	42787466	42787466	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cgacccctccaggtccctggCgaagataggagctgctgaac	12	14	0	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:42787466C>A	ENST00000310232.6	-	7	857	c.774G>T	c.(772-774)tcG>tcT	p.S258S	CCDC13-AS1_ENST00000418161.1_RNA|CCDC13-AS1_ENST00000446950.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	258										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						AGGTCCCTGGCGAAGATAGGA	0.507																																					p.S258S		Atlas-SNP	.											CCDC13,colon,carcinoma,0,1	CCDC13	71	.	0			c.G774T						.						90	88	89					3																	42787466		2203	4300	6503	SO:0001819	synonymous_variant	152206	exon7			CCCTGGCGAAGAT	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.774G>T	chr3.hg19:g.42787466C>A		77.0	0.0		107.0	14.0	NM_144719		Silent	SNP	ENST00000310232.6	hg19	CCDS2705.1																																																																																			.	.		0.507	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		A	42787466	C	A	42787466	2	1	58	1	0	0	0	0	0	0	0	1	2767	755	27	1		1	CCDC13	3	42787466	Silent	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	1512567	42787466	155234964	28	7185										
MAP4	4134	hgsc.bcm.edu	37	chr3	47957722	47957722	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ctggaggcagacatacgttcTtgatgagaactacttctgtt	10	8	2	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:47957722T>G	ENST00000360240.6	-	7	2113	c.1595A>C	c.(1594-1596)aAg>aCg	p.K532T	MAP4_ENST00000395734.3_Missense_Mutation_p.K532T|MAP4_ENST00000426837.2_Missense_Mutation_p.K549T|MAP4_ENST00000383737.4_Intron	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	532	17 X 14 AA tandem repeats.				cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	ACATACGTTCTTGATGAGAAC	0.517																																					p.K532T		Atlas-SNP	.											.	MAP4	176	.	0			c.A1595C						.						136	124	128					3																	47957722		2203	4300	6503	SO:0001583	missense	4134	exon7			ACGTTCTTGATGA		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1595A>C	chr3.hg19:g.47957722T>G	ENSP00000353375:p.Lys532Thr	345.0	0.0		393.0	85.0	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	hg19	CCDS33750.1	.	.	.	.	.	.	.	.	.	.	T	13.28	2.191320	0.38707	.	.	ENSG00000047849	ENST00000395734;ENST00000426837;ENST00000360240	T;T;T	0.08193	3.19;3.12;3.19	3.69	2.53	0.30540	.	.	.	.	.	T	0.23210	0.0561	M	0.75777	2.31	0.21553	N	0.999649	D;D;P	0.89917	0.969;1.0;0.862	P;D;P	0.91635	0.711;0.999;0.451	T	0.05321	-1.0892	9	0.46703	T	0.11	-2.7446	5.2803	0.15673	0.0:0.2304:0.0:0.7696	.	509;532;532	C9JFC3;P27816-6;P27816	.;.;MAP4_HUMAN	T	532;549;532	ENSP00000379083:K532T;ENSP00000407602:K549T;ENSP00000353375:K532T	ENSP00000353375:K532T	K	-	2	0	MAP4	47932726	0.005000	0.15991	0.014000	0.15608	0.286000	0.27126	0.842000	0.27627	0.774000	0.33427	0.460000	0.39030	AAG	.	.		0.517	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375		G	47957722	T	G	47957722	3	3	58	1	0	0	0	0	1	0	0	0	9267	1609	56	5	3274	5	MAP4	3	47957722	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	5170256	47957722	150064708	29	7186										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57438657	57438657	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	taagcatattttacattgcaAttaatgatacgaactcgggc	7	7	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:57438657A>G	ENST00000351747.2	-	25	3810	c.3630T>C	c.(3628-3630)aaT>aaC	p.N1210N		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1210	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TTACATTGCAATTAATGATAC	0.373																																					p.N1210N		Atlas-SNP	.											.	DNAH12	182	.	0			c.T3630C						.						170	166	167					3																	57438657		692	1591	2283	SO:0001819	synonymous_variant	201625	exon25			ATTGCAATTAATG	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.3630T>C	chr3.hg19:g.57438657A>G		112.0	0.0		134.0	30.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Silent	SNP	ENST00000351747.2	hg19																																																																																				.	.		0.373	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		G	57438657	A	G	57438657	2	3	58	1	0	0	0	0	0	0	0	1	4602	98	4	2		2	DNAH12	3	57438657	Silent	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	9480935	57438657	140583773	30	7187										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57443514	57443514	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tcttccacttgaatgagccaCttttccacagcaccccgcgc	6	17	1	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:57443514C>T	ENST00000351747.2	-	22	3381	c.3201G>A	c.(3199-3201)aaG>aaA	p.K1067K		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1067	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						GAATGAGCCACTTTTCCACAG	0.498																																					p.K1067K		Atlas-SNP	.											.	DNAH12	182	.	0			c.G3201A						.						65	60	61					3																	57443514		692	1591	2283	SO:0001819	synonymous_variant	201625	exon22			GAGCCACTTTTCC	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.3201G>A	chr3.hg19:g.57443514C>T		127.0	0.0		175.0	42.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Silent	SNP	ENST00000351747.2	hg19																																																																																				.	.		0.498	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		T	57443514	C	T	57443514	2	4	58	1	0	0	0	0	0	0	0	1	4602	564	20	3		3	DNAH12	3	57443514	Silent	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	4857	57443514	140578916	31	7188										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64599095	64599095	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	catagatgttggcttggtctCagggtcacacattctatcat	9	9	4	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:64599095C>G	ENST00000498707.1	-	22	3622	c.3280G>C	c.(3280-3282)Gag>Cag	p.E1094Q	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.E1066Q	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1094	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		GGCTTGGTCTCAGGGTCACAC	0.488																																					p.E1094Q		Atlas-SNP	.											ADAMTS9,bladder,carcinoma,0,1	ADAMTS9	206	.	0			c.G3280C						.						109	105	106					3																	64599095		2203	4300	6503	SO:0001583	missense	56999	exon22			TGGTCTCAGGGTC	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.3280G>C	chr3.hg19:g.64599095C>G	ENSP00000418735:p.Glu1094Gln	153.0	0.0		162.0	34.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581437	0.28180	.	.	ENSG00000163638	ENST00000295903;ENST00000498707	T;T	0.55413	0.52;0.52	6.06	5.18	0.71444	.	0.186809	0.37623	N	0.002008	T	0.40979	0.1139	L	0.35644	1.08	0.80722	D	1	B;B;B	0.16166	0.007;0.016;0.015	B;B;B	0.19148	0.024;0.017;0.024	T	0.22556	-1.0213	10	0.14656	T	0.56	.	12.3259	0.55011	0.0:0.8147:0.1202:0.0651	.	1066;1094;1094	B7ZVX9;Q9P2N4-1;Q9P2N4	.;.;ATS9_HUMAN	Q	1066;1094	ENSP00000295903:E1066Q;ENSP00000418735:E1094Q	ENSP00000295903:E1066Q	E	-	1	0	ADAMTS9	64574135	0.978000	0.34361	0.978000	0.43139	0.918000	0.54935	2.148000	0.42235	1.529000	0.49120	0.655000	0.94253	GAG	.	.		0.488	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			G	64599095	C	G	64599095	3	3	58	1	0	0	0	0	1	0	0	0	273	835	29	4	2599	4	ADAMTS9	3	64599095	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	7155581	64599095	133423335	32	7189										
GPR149	344758	hgsc.bcm.edu	37	chr3	154055824	154055824	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ttatcacaaatttcaagaacCtccaagtgtattttcacact	3	10	3	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:154055824C>T	ENST00000389740.2	-	4	1959	c.1860G>A	c.(1858-1860)gaG>gaA	p.E620E		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	620					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTTCAAGAACCTCCAAGTGTA	0.413																																					p.E620E		Atlas-SNP	.											.	GPR149	134	.	0			c.G1860A						.						101	95	97					3																	154055824		1873	4120	5993	SO:0001819	synonymous_variant	344758	exon4			AAGAACCTCCAAG	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1860G>A	chr3.hg19:g.154055824C>T		457.0	0.0		513.0	49.0	NM_001038705		Silent	SNP	ENST00000389740.2	hg19	CCDS43162.1																																																																																			.	.		0.413	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		T	154055824	C	T	154055824	2	4	58	1	0	0	0	0	0	0	0	1	6662	680	24	3		3	GPR149	3	154055824	Silent	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	89456729	154055824	43966606	33	7190										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164906413	164906414	+	Missense_Mutation	DNP	CG	CG	TT													0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gtactcatacacatgacccaCgggaggggccttctctggag					rs372406969|rs34531905		TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:164906413_164906414CG>TT	ENST00000475390.1	-	2	2648_2649	c.2205_2206CG>AA	c.(2203-2208)ccCGtg>ccAAtg	p.V736M	SLITRK3_ENST00000241274.3_Missense_Mutation_p.V736M			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	736					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						ACATGACCCACGGGAGGGGCCT	0.569										HNSCC(40;0.11)																											p.V736M|p.P735P		Atlas-SNP	.											.	SLITRK3	263	.	0			c.G2206A|c.C2205A						.																																			SO:0001583	missense	22865	exon2			GACCCACGGGAGG|ACCCACGGGAGGG	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.2205_2206delinsTT	chr3.hg19:g.164906413_164906414delinsTT	ENSP00000420091:p.Val736Met	100.0	0.0		109.0|110.0	20.0	NM_014926	Q1RMY6	Missense_Mutation|Silent	SNP	ENST00000475390.1	hg19	CCDS3197.1																																																																																			.	.		0.569	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		TT	164906414	CG	TT	164906413	3	4	58	1	0	0	0	0	1	0	0	0	14759	536	19	1	731	1	SLITRK3	3	164906413	Missense_Mutation	DNP	CG	TCGA-CC-5262-01A-01D-A12Z-10	10850589	164906413	33116017	34	7191										
PHC3	80012	hgsc.bcm.edu	37	chr3	169820663	169820663	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cacgatgcccaagactttgaTtatcaggcttacgattccaa	7	11	1	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:169820663T>A	ENST00000494943.1	-	13	2560	c.2492A>T	c.(2491-2493)aAt>aTt	p.N831I	PHC3_ENST00000467570.1_Missense_Mutation_p.N790I|PHC3_ENST00000495893.2_Missense_Mutation_p.N843I			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	831					multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			AAGACTTTGATTATCAGGCTT	0.398																																					p.N843I		Atlas-SNP	.											.	PHC3	113	.	0			c.A2528T						.						53	52	53					3																	169820663		1901	4103	6004	SO:0001583	missense	80012	exon13			CTTTGATTATCAG		CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"Sterile alpha motif (SAM) domain containing"	15682	protein-coding gene	gene with protein product	"early development regulator 3", "polyhomeotic like 3"		"polyhomeotic like 3 (Drosophila)"			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.2492A>T	chr3.hg19:g.169820663T>A	ENSP00000420271:p.Asn831Ile	248.0	0.0		297.0	44.0	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Missense_Mutation	SNP	ENST00000494943.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.79|16.79	3.221259|3.221259	0.58560|0.58560	.|.	.|.	ENSG00000173889|ENSG00000173889	ENST00000484068|ENST00000494943;ENST00000495893;ENST00000467570	.|T;T	.|0.32988	.|1.43;1.43	5.47|5.47	4.32|4.32	0.51571|0.51571	.|.	.|0.249898	.|0.35349	.|N	.|0.003267	T|T	0.24160|0.24160	0.0585|0.0585	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	D|D	1|1	.|P;B;B	.|0.40794	.|0.729;0.031;0.318	.|B;B;B	.|0.39531	.|0.302;0.011;0.092	T|T	0.03103|0.03103	-1.1072|-1.1072	5|10	.|0.44086	.|T	.|0.13	-11.691|-11.691	6.117|6.117	0.20132|0.20132	0.0:0.306:0.0:0.694|0.0:0.306:0.0:0.694	.|.	.|790;831;843	.|E7EX82;Q8NDX5;Q8NDX5-7	.|.;PHC3_HUMAN;.	F|I	9|831;843;790	.|ENSP00000420271:N831I;ENSP00000420294:N843I	.|ENSP00000419089:N790I	I|N	-|-	1|2	0|0	PHC3|PHC3	171303357|171303357	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.813000|2.813000	0.48002|0.48002	0.925000|0.925000	0.37094|0.37094	0.528000|0.528000	0.53228|0.53228	ATC|AAT	.	.		0.398	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947		A	169820663	T	A	169820663	3	1	58	1	0	0	0	0	1	0	0	0	11827	1493	52	4	471	4	PHC3	3	169820663	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	4914250	169820663	28201767	35	7192										
SPATA16	83893	hgsc.bcm.edu	37	chr3	172835457	172835457	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tgcttgtgtttatctttggaAcaagctgatcatgatagatc	9	6	2	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:172835457A>C	ENST00000351008.3	-	2	248	c.65T>G	c.(64-66)gTt>gGt	p.V22G		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	22					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			TATCTTTGGAACAAGCTGATC	0.443																																					p.V22G		Atlas-SNP	.											.	SPATA16	111	.	0			c.T65G						.						207	192	197					3																	172835457		2203	4300	6503	SO:0001583	missense	83893	exon2			TTTGGAACAAGCT	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.65T>G	chr3.hg19:g.172835457A>C	ENSP00000341765:p.Val22Gly	698.0	1.0		783.0	165.0	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	hg19	CCDS3221.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.031980	0.35893	.	.	ENSG00000144962	ENST00000351008	T	0.18960	2.18	5.55	3.23	0.37069	.	0.443465	0.19004	N	0.125255	T	0.10852	0.0265	N	0.24115	0.695	0.41590	D	0.988794	P	0.34724	0.465	B	0.28011	0.085	T	0.09997	-1.0649	10	0.87932	D	0	-5.6764	4.1813	0.10376	0.6402:0.1898:0.17:0.0	.	22	Q9BXB7	SPT16_HUMAN	G	22	ENSP00000341765:V22G	ENSP00000341765:V22G	V	-	2	0	SPATA16	174318151	0.000000	0.05858	1.000000	0.80357	0.909000	0.53808	0.514000	0.22786	2.096000	0.63516	0.528000	0.53228	GTT	.	.		0.443	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955		C	172835457	A	C	172835457	3	2	58	1	0	0	0	0	1	0	0	0	15016	43	2	5	1684	5	SPATA16	3	172835457	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	3014794	172835457	25186973	36	7193										
RTP1	132112	hgsc.bcm.edu	37	chr3	186915400	186915400	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ggaaattgccttccctcactActgacgagaccatgtgtaaa	8	11	1	2	rs41469544		TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:186915400A>T	ENST00000312295.4	+	1	127	c.97A>T	c.(97-99)Act>Tct	p.T33S	RP11-208N14.4_ENST00000356133.3_RNA	NM_153708.2	NP_714919.2	P59025	RTP1_HUMAN	receptor (chemosensory) transporter protein 1	33					protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)			breast(2)|endometrium(4)|large_intestine(5)|lung(6)|ovary(3)|skin(2)	22	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		TTCCCTCACTACTGACGAGAC	0.527																																					p.T33S		Atlas-SNP	.											.	RTP1	51	.	0			c.A97T						.						142	137	138					3																	186915400		2203	4300	6503	SO:0001583	missense	132112	exon1			CTCACTACTGACG	BC034744	CCDS3287.2	3q27.3	2014-02-20	2006-11-21		ENSG00000175077	ENSG00000175077		"Receptor transporter proteins"	28580	protein-coding gene	gene with protein product	"receptor transporting protein 1", "zinc finger, 3CxxC-type 1"	609137	"receptor transporter protein 1"			16271481, 15550249, 16720576	Standard	NM_153708		Approved	MGC35450, Z3CXXC1	uc003frg.3	P59025	OTTHUMG00000149886	ENST00000312295.4:c.97A>T	chr3.hg19:g.186915400A>T	ENSP00000311712:p.Thr33Ser	244.0	0.0		255.0	46.0	NM_153708		Missense_Mutation	SNP	ENST00000312295.4	hg19	CCDS3287.2	.	.	.	.	.	.	.	.	.	.	A	10.88	1.474956	0.26511	.	.	ENSG00000175077	ENST00000312295	T	0.14516	2.5	5.16	-2.65	0.06095	.	0.443969	0.21260	N	0.077491	T	0.03095	0.0091	N	0.00926	-1.1	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.45745	-0.9240	10	0.13853	T	0.58	.	8.8419	0.35146	0.2575:0.6046:0.0:0.1379	.	33	P59025	RTP1_HUMAN	S	33	ENSP00000311712:T33S	ENSP00000311712:T33S	T	+	1	0	RTP1	188398094	0.001000	0.12720	0.661000	0.29709	0.716000	0.41182	-1.007000	0.03667	-0.161000	0.10983	0.533000	0.62120	ACT	.	.		0.527	RTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313731.2	NM_153708		T	186915400	A	T	186915400	3	4	58	1	0	0	0	0	1	0	0	0	13748	391	14	4	99	4	RTP1	3	186915400	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	14079943	186915400	11107030	37	7194										
C3orf59	151963	hgsc.bcm.edu	37	chr3	192516896	192516896	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cccaaaagtggttctccatgAgccagctctgggccactgca	10	14	2	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr3:192516896A>T	ENST00000392452.2	-	2	1075	c.755T>A	c.(754-756)cTc>cAc	p.L252H		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	252							protein complex binding (GO:0032403)			endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						GTTCTCCATGAGCCAGCTCTG	0.483																																					p.L252H		Atlas-SNP	.											.	MB21D2	75	.	0			c.T755A						.						75	71	72					3																	192516896		2203	4300	6503	SO:0001583	missense	151963	exon2			TCCATGAGCCAGC	AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 59"	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.755T>A	chr3.hg19:g.192516896A>T	ENSP00000376246:p.Leu252His	107.0	0.0		99.0	19.0	NM_178496	Q86VD8	Missense_Mutation	SNP	ENST00000392452.2	hg19	CCDS3302.2	.	.	.	.	.	.	.	.	.	.	A	18.42	3.620664	0.66787	.	.	ENSG00000180611	ENST00000392452	T	0.09255	3.0	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.29126	0.0724	M	0.67953	2.075	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.05649	-1.0872	10	0.15499	T	0.54	-17.2311	15.0511	0.71872	1.0:0.0:0.0:0.0	.	252	Q8IYB1	M21D2_HUMAN	H	252	ENSP00000376246:L252H	ENSP00000376246:L252H	L	-	2	0	MB21D2	193999590	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.145000	0.66743	0.533000	0.62120	CTC	.	.		0.483	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496		T	192516896	A	T	192516896	3	4	58	1	0	0	0	0	1	0	0	0	2239	304	11	4	724	4	C3orf59	3	192516896	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	5601496	192516896	5505534	38	7195										
EVC2	132884	hgsc.bcm.edu	37	chr4	5578157	5578157	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ctgcaccagctggtcctccaGcttcctctccaactcctgga	7	18	1	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr4:5578157G>A	ENST00000344408.5	-	18	3135	c.3082C>T	c.(3082-3084)Ctg>Ttg	p.L1028L	EVC2_ENST00000344938.1_Silent_p.L1028L|EVC2_ENST00000310917.2_Silent_p.L948L	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	1028					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TGGTCCTCCAGCTTCCTCTCC	0.642																																					p.L1028L		Atlas-SNP	.											.	EVC2	202	.	0			c.C3082T						.						20	19	19					4																	5578157		2202	4300	6502	SO:0001819	synonymous_variant	132884	exon18			CCTCCAGCTTCCT	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.3082C>T	chr4.hg19:g.5578157G>A		47.0	0.0		54.0	20.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Silent	SNP	ENST00000344408.5	hg19	CCDS3382.2																																																																																			.	.		0.642	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		A	5578157	G	A	5578157	2	1	58	1	0	0	0	0	0	0	0	1	5288	962	34	3		3	EVC2	4	5578157	Silent	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10		5578157	185576119	39	7196										
C4orf23	152992	hgsc.bcm.edu	37	chr4	8469997	8469997	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	caagtggttttgcaagtagcGaatttactgttaggtggaaa	12	4	0	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr4:8469997G>A	ENST00000389737.4	+	9	1851	c.1851G>A	c.(1849-1851)gcG>gcA	p.A617A	TRMT44_ENST00000513449.2_Silent_p.A376A	NM_152544.2	NP_689757.2	Q8IYL2	TRM44_HUMAN	tRNA methyltransferase 44 homolog (S. cerevisiae)	617					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										TGCAAGTAGCGAATTTACTGT	0.478																																					p.A617A		Atlas-SNP	.											.	TRMT44	7	.	0			c.G1851A						.						71	77	75					4																	8469997		2203	4300	6503	SO:0001819	synonymous_variant	152992	exon9			AGTAGCGAATTTA	AK093044	CCDS3402.1, CCDS3402.2	4p16.1	2012-06-12	2012-06-12	2012-06-12	ENSG00000155275	ENSG00000155275			26653	protein-coding gene	gene with protein product	"tRNA methyltransferase 44 homolog (S. cerevisiae)"	614309	"chromosome 4 open reading frame 23", "methyltransferase like 19"	C4orf23, METTL19		21658913	Standard	NM_152544		Approved	FLJ35725, TRM44	uc003glg.2	Q8IYL2	OTTHUMG00000160935	ENST00000389737.4:c.1851G>A	chr4.hg19:g.8469997G>A		138.0	0.0		145.0	13.0	NM_152544	Q8NA95	Silent	SNP	ENST00000389737.4	hg19	CCDS3402.2																																																																																			.	.		0.478	TRMT44-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359197.2	NM_152544		A	8469997	G	A	8469997	2	1	58	1	0	0	0	0	0	0	0	1	2258	1045	37	1		1	C4orf23	4	8469997	Silent	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	2891840	8469997	182684279	40	7197										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85707240	85707240	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ccaaatgacactttctcctcTggtactaatgacacagggga	8	11	2	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr4:85707240T>C	ENST00000295888.4	-	24	4361	c.3954A>G	c.(3952-3954)ccA>ccG	p.P1318P	WDFY3_ENST00000322366.6_Silent_p.P1318P	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1318					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CTTTCTCCTCTGGTACTAATG	0.413																																					p.P1318P		Atlas-SNP	.											.	WDFY3	314	.	0			c.A3954G						.						132	120	124					4																	85707240		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon24			CTCCTCTGGTACT	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.3954A>G	chr4.hg19:g.85707240T>C		207.0	0.0		244.0	44.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.		0.413	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		C	85707240	T	C	85707240	2	2	58	1	0	0	0	0	0	0	0	1	17285	1567	55	2		2	WDFY3	4	85707240	Silent	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	77237243	85707240	105447036	41	7198										
ABCE1	6059	hgsc.bcm.edu	37	chr4	146029198	146029198	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tggcgccttatcaattgtcaAtctaccaagcaacttggaaa	7	10	3	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr4:146029198A>G	ENST00000296577.4	+	4	736	c.221A>G	c.(220-222)aAt>aGt	p.N74S	OTUD4_ENST00000455611.2_5'Flank|ABCE1_ENST00000502803.1_Intron	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	74	4Fe-4S ferredoxin-type 2. {ECO:0000255|PROSITE-ProRule:PRU00711}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					TCAATTGTCAATCTACCAAGC	0.328																																					p.N74S		Atlas-SNP	.											.	ABCE1	47	.	0			c.A221G						.						86	80	82					4																	146029198		2203	4300	6503	SO:0001583	missense	6059	exon4			TTGTCAATCTACC	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"ATP binding cassette transporters / subfamily E"	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.221A>G	chr4.hg19:g.146029198A>G	ENSP00000296577:p.Asn74Ser	86.0	0.0		152.0	26.0	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Missense_Mutation	SNP	ENST00000296577.4	hg19	CCDS34071.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.343082	0.82022	.	.	ENSG00000164163	ENST00000296577;ENST00000502586	D	0.91180	-2.8	5.31	5.31	0.75309	4Fe-4S ferredoxin, iron-sulpur binding domain (1);	0.000000	0.85682	D	0.000000	D	0.92424	0.7595	L	0.39397	1.21	0.80722	D	1	D	0.67145	0.996	D	0.64595	0.927	D	0.93155	0.6553	10	0.62326	D	0.03	-22.293	15.5552	0.76187	1.0:0.0:0.0:0.0	.	74	P61221	ABCE1_HUMAN	S	74	ENSP00000296577:N74S	ENSP00000296577:N74S	N	+	2	0	ABCE1	146248648	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	9.203000	0.95033	2.131000	0.65755	0.477000	0.44152	AAT	.	.		0.328	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940		G	146029198	A	G	146029198	3	3	58	1	0	0	0	0	1	0	0	0	64	101	4	2	231	2	ABCE1	4	146029198	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	60321958	146029198	45125078	42	7199										
SH3D19	152503	hgsc.bcm.edu	37	chr4	152058972	152058972	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tatctatcttctccagaagaTaaacaatttctccagaagtg	5	9	4	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr4:152058972T>A	ENST00000409252.2	-	14	2275	c.1568A>T	c.(1567-1569)tAt>tTt	p.Y523F	SH3D19_ENST00000455740.1_Missense_Mutation_p.Y500F|SH3D19_ENST00000304527.4_Missense_Mutation_p.Y523F|SH3D19_ENST00000424281.1_Missense_Mutation_p.Y464F|SH3D19_ENST00000514152.1_Missense_Mutation_p.Y500F|SH3D19_ENST00000409598.4_Missense_Mutation_p.Y500F|RP11-372K14.2_ENST00000603472.1_RNA|SH3D19_ENST00000427414.2_Missense_Mutation_p.Y464F			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	523	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cytoskeleton organization (GO:0007010)|membrane organization (GO:0061024)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of cell morphogenesis (GO:0022604)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(1)|skin(3)|urinary_tract(1)	20	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				CTCCAGAAGATAAACAATTTC	0.353																																					p.Y523F		Atlas-SNP	.											.	SH3D19	54	.	0			c.A1568T						.						71	69	70					4																	152058972		2203	4300	6503	SO:0001583	missense	152503	exon15			AGAAGATAAACAA	BX647422	CCDS34077.2, CCDS47143.1, CCDS47144.1	4q31.3	2009-03-05	2009-03-05	2009-03-05	ENSG00000109686	ENSG00000109686			30418	protein-coding gene	gene with protein product	"EEN binding protein"	608674				12477932	Standard	NM_001009555		Approved	DKFZp434D0215, EVE1, EBP, Kryn, SH3P19	uc010ipl.1	Q5HYK7	OTTHUMG00000154051	ENST00000409252.2:c.1568A>T	chr4.hg19:g.152058972T>A	ENSP00000386848:p.Tyr523Phe	95.0	0.0		134.0	30.0	NM_001009555	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Missense_Mutation	SNP	ENST00000409252.2	hg19	CCDS34077.2	.	.	.	.	.	.	.	.	.	.	T	16.33	3.092865	0.56075	.	.	ENSG00000109686	ENST00000409598;ENST00000304527;ENST00000455740;ENST00000424281;ENST00000427414;ENST00000409252;ENST00000514152	T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85	5.39	5.39	0.77823	Src homology-3 domain (4);	0.740258	0.12576	N	0.456916	T	0.44829	0.1312	L	0.35249	1.045	0.44899	D	0.997913	B;B;B;B	0.30526	0.171;0.142;0.257;0.283	B;B;B;B	0.40329	0.229;0.146;0.103;0.326	T	0.26360	-1.0105	10	0.29301	T	0.29	-11.9087	11.626	0.51145	0.0:0.0715:0.0:0.9285	.	523;500;464;278	Q5HYK7;Q5HYK7-2;Q5HYK7-3;B3KY23	SH319_HUMAN;.;.;.	F	500;523;500;464;464;523;500	ENSP00000387030:Y500F;ENSP00000302913:Y523F;ENSP00000416708:Y500F;ENSP00000404542:Y464F;ENSP00000415694:Y464F;ENSP00000386848:Y523F;ENSP00000423449:Y500F	ENSP00000302913:Y523F	Y	-	2	0	SH3D19	152278422	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.313000	0.43735	2.165000	0.68154	0.528000	0.53228	TAT	.	.		0.353	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555		A	152058972	T	A	152058972	3	1	58	1	0	0	0	0	1	0	0	0	14264	1406	49	4	832	4	SH3D19	4	152058972	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	6029774	152058972	39095304	43	7200										
GPM6A	2823	hgsc.bcm.edu	37	chr4	176556173	176556173	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cggcaggcgtctttcacataGgcccagttggcagacagaac	12	12	2	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr4:176556173G>A	ENST00000280187.7	-	8	765	c.720C>T	c.(718-720)gcC>gcT	p.A240A	GPM6A_ENST00000506894.1_Silent_p.A229A|GPM6A_ENST00000393658.2_Silent_p.A240A|GPM6A_ENST00000515090.1_Silent_p.A233A|GPM6A_ENST00000506219.1_5'UTR	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	240					neural retina development (GO:0003407)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|positive regulation of filopodium assembly (GO:0051491)|stem cell differentiation (GO:0048863)|synapse assembly (GO:0007416)	axonal growth cone (GO:0044295)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium channel activity (GO:0005262)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		CTTTCACATAGGCCCAGTTGG	0.438																																					p.A240A		Atlas-SNP	.											.	GPM6A	70	.	0			c.C720T						.						81	75	77					4																	176556173		2203	4300	6503	SO:0001819	synonymous_variant	2823	exon7			CACATAGGCCCAG		CCDS3824.1, CCDS54822.1, CCDS58936.1	4q34	2008-08-29				ENSG00000150625			4460	protein-coding gene	gene with protein product		601275		GPM6		8661015, 18574501	Standard	NM_005277		Approved		uc003iug.4	P51674		ENST00000280187.7:c.720C>T	chr4.hg19:g.176556173G>A		141.0	0.0		216.0	41.0	NM_201591	B7Z642|E9PHI5|Q92602	Silent	SNP	ENST00000280187.7	hg19	CCDS3824.1																																																																																			.	.		0.438	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1			A	176556173	G	A	176556173	2	1	58	1	0	0	0	0	0	0	0	1	6623	987	35	3		3	GPM6A	4	176556173	Silent	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	24497201	176556173	14598103	44	7201										
PPIP5K2	23262	hgsc.bcm.edu	37	chr5	102494240	102494240	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	caaaatatatgcctctgatgAaggacgagtccagatgactg	10	8	1	4			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr5:102494240A>T	ENST00000358359.3	+	16	2209	c.1700A>T	c.(1699-1701)gAa>gTa	p.E567V	PPIP5K2_ENST00000321521.9_Missense_Mutation_p.E567V|PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000414217.1_Missense_Mutation_p.E567V	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	567					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GCCTCTGATGAAGGACGAGTC	0.323																																					p.E567V		Atlas-SNP	.											.	PPIP5K2	98	.	0			c.A1700T						.						132	126	128					5																	102494240		2203	4300	6503	SO:0001583	missense	23262	exon15			CTGATGAAGGACG	AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"histidine acid phosphatase domain containing 1"	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.1700A>T	chr5.hg19:g.102494240A>T	ENSP00000351126:p.Glu567Val	343.0	0.0		544.0	108.0	NM_015216	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	hg19		.	.	.	.	.	.	.	.	.	.	A	25.9	4.689326	0.88735	.	.	ENSG00000145725	ENST00000321521;ENST00000358359;ENST00000451606;ENST00000414217	T;T;T	0.36157	1.27;1.27;1.27	5.28	5.28	0.74379	.	0.158377	0.42964	D	0.000637	T	0.69780	0.3149	M	0.93854	3.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79208	-0.1898	10	0.87932	D	0	.	15.5032	0.75716	1.0:0.0:0.0:0.0	.	567;567	O43314-2;O43314	.;VIP2_HUMAN	V	567	ENSP00000313070:E567V;ENSP00000351126:E567V;ENSP00000416016:E567V	ENSP00000313070:E567V	E	+	2	0	PPIP5K2	102522139	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.901000	0.92560	2.118000	0.64928	0.472000	0.43445	GAA	.	.		0.323	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		T	102494240	A	T	102494240	3	4	58	1	0	0	0	0	1	0	0	0	12345	246	9	4	1758	4	PPIP5K2	5	102494240	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10		102494240	78421020	45	7202										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237567	140237567	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gactgactcgccacgccagcGcctactggtgctggtgaagg	14	13	0	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr5:140237567G>T	ENST00000307360.5	+	1	1934	c.1934G>T	c.(1933-1935)cGc>cTc	p.R645L	PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	645	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACGCCAGCGCCTACTGGTG	0.672																																					p.R645L		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1934T						.						23	29	26					5																	140237567		1321	2287	3608	SO:0001583	missense	56139	exon1			GCCAGCGCCTACT	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1934G>T	chr5.hg19:g.140237567G>T	ENSP00000304234:p.Arg645Leu	211.0	0.0		121.0	26.0	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	hg19	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	G	7.331	0.618979	0.14129	.	.	ENSG00000250120	ENST00000307360	T	0.52983	0.64	3.49	2.51	0.30379	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.45796	0.1360	L	0.42487	1.325	0.22017	N	0.999412	B;B	0.33120	0.209;0.398	B;B	0.43838	0.082;0.433	T	0.45440	-0.9261	9	0.72032	D	0.01	.	6.368	0.21465	0.1534:0.0:0.6774:0.1691	.	645;645	Q9Y5I2-3;Q9Y5I2	.;PCDAA_HUMAN	L	645	ENSP00000304234:R645L	ENSP00000304234:R645L	R	+	2	0	PCDHA10	140217751	0.000000	0.05858	1.000000	0.80357	0.031000	0.12232	0.204000	0.17335	1.932000	0.55993	0.491000	0.48974	CGC	.	.		0.672	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140237567	G	T	140237567	3	4	58	1	0	0	0	0	1	0	0	0	11529	1087	38	1	1936	1	PCDHA10	5	140237567	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	37743327	140237567	40677693	46	7203										
RANBP17	64901	hgsc.bcm.edu	37	chr5	170305242	170305242	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gtcaacttttattagaacaaGgaacagtaagtatttggtaa	8	4	1	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr5:170305242G>C	ENST00000523189.1	+	2	324	c.160G>C	c.(160-162)Gga>Cga	p.G54R		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	54					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ATTAGAACAAGGAACAGTAAG	0.358			T	TRD@	ALL																																p.G54R		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.G160C						.						96	94	94					5																	170305242		2203	4300	6503	SO:0001583	missense	64901	exon2			GAACAAGGAACAG	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.160G>C	chr5.hg19:g.170305242G>C	ENSP00000427975:p.Gly54Arg	283.0	0.0		304.0	58.0	NM_022897	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	hg19	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.134705	0.56828	.	.	ENSG00000204764	ENST00000523189	T	0.67345	-0.26	5.35	5.35	0.76521	Armadillo-type fold (1);Importin-beta, N-terminal (2);	0.000000	0.45867	D	0.000325	D	0.83285	0.5221	M	0.79805	2.47	0.49051	D	0.999741	B;D	0.89917	0.356;1.0	B;D	0.97110	0.248;1.0	D	0.85224	0.1028	10	0.66056	D	0.02	-14.6699	18.6626	0.91477	0.0:0.0:1.0:0.0	.	54;104	Q9H2T7;B4DQG2	RBP17_HUMAN;.	R	54	ENSP00000427975:G54R	ENSP00000373770:G54R	G	+	1	0	RANBP17	170237820	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.478000	0.60230	2.492000	0.84095	0.563000	0.77884	GGA	.	.		0.358	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		C	170305242	G	C	170305242	3	2	58	1	0	0	0	0	1	0	0	0	13042	1001	35	4	166	4	RANBP17	5	170305242	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	30067675	170305242	10610018	47	7204										
C6orf138	442213	hgsc.bcm.edu	37	chr6	47846352	47846352	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tttttatacattgtgttcggGtgtgctcagttgctaataca	9	6	1	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr6:47846352G>T	ENST00000339488.4	-	3	2261	c.2228C>A	c.(2227-2229)aCc>aAc	p.T743N		NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	743						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										TTGTGTTCGGGTGTGCTCAGT	0.408																																					p.T743N		Atlas-SNP	.											.	.	.	.	0			c.C2228A						.						104	94	98					6																	47846352		2203	4300	6503	SO:0001583	missense	442213	exon3			GTTCGGGTGTGCT		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 138"	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.2228C>A	chr6.hg19:g.47846352G>T	ENSP00000341914:p.Thr743Asn	252.0	0.0		251.0	51.0	NM_001013732	B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	hg19	CCDS34473.2	.	.	.	.	.	.	.	.	.	.	G	17.16	3.318435	0.60524	.	.	ENSG00000244694	ENST00000339488	D	0.91843	-2.92	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	D	0.88526	0.6460	L	0.59436	1.845	0.80722	D	1	P	0.38729	0.644	B	0.36186	0.219	D	0.87706	0.2563	10	0.39692	T	0.17	.	20.5211	0.99222	0.0:0.0:1.0:0.0	.	743	Q6ZW05	CF138_HUMAN	N	743	ENSP00000341914:T743N	ENSP00000341914:T743N	T	-	2	0	C6orf138	47954311	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.861000	0.98227	0.650000	0.86243	ACC	.	.		0.408	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		T	47846352	G	T	47846352	3	4	58	1	0	0	0	0	1	0	0	0	2334	1261	44	3	316	3	C6orf138	6	47846352	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10		47846352	123268715	48	7205										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75853093	75853093	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gagtttcagatcctgaggtcTgggtaaaggcactagagaag	14	6	2	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr6:75853093T>A	ENST00000322507.8	-	26	5011	c.4702A>T	c.(4702-4704)Aga>Tga	p.R1568*	COL12A1_ENST00000416123.2_Nonsense_Mutation_p.R1568*|COL12A1_ENST00000483888.2_Nonsense_Mutation_p.R1568*|COL12A1_ENST00000345356.6_Nonsense_Mutation_p.R404*	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1568	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TCCTGAGGTCTGGGTAAAGGC	0.423																																					p.R1568X		Atlas-SNP	.											.	COL12A1	385	.	0			c.A4702T						.						105	96	99					6																	75853093		1885	4115	6000	SO:0001587	stop_gained	1303	exon26			GAGGTCTGGGTAA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4702A>T	chr6.hg19:g.75853093T>A	ENSP00000325146:p.Arg1568*	128.0	0.0		214.0	32.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Nonsense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	43|43	10.391375|10.391375	0.99396|0.99396	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000419671|ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	.|.	.|.	.|.	5.81|5.81	-2.39|-2.39	0.06602|0.06602	.|.	.|0.343561	.|0.29775	.|N	.|0.011223	T|.	0.04048|.	0.0113|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.36040|.	-0.9764|.	3|.	.|0.02654	.|T	.|1	.|.	6.2577|6.2577	0.20884|0.20884	0.0:0.2859:0.4523:0.2617|0.0:0.2859:0.4523:0.2617	.|.	.|.	.|.	.|.	L|X	309|1568;1568;404;1568;1568	.|.	.|ENSP00000325146:R1568X	Q|R	-|-	2|1	0|2	COL12A1|COL12A1	75909813|75909813	0.990000|0.990000	0.36364|0.36364	0.953000|0.953000	0.39169|0.39169	0.994000|0.994000	0.84299|0.84299	1.068000|1.068000	0.30629|0.30629	-0.120000|-0.120000	0.11809|0.11809	0.533000|0.533000	0.62120|0.62120	CAG|AGA	.	.		0.423	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75853093	T	A	75853093	4	1	58	1	0	0	0	0	0	1	0	0	3671	1588	55	4	4653	4	COL12A1	6	75853093	Nonsense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	28006741	75853093	95261974	49	7206										
RWDD2A	112611	hgsc.bcm.edu	37	chr6	83904246	83904249	+	Frame_Shift_Del	DEL	CAAG	CAAG	-													0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tgttttctatgtttcctaacCaaggagaagtaaaacttgaa							TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	CAAG	CAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr6:83904246_83904249delCAAG	ENST00000369724.4	+	2	281_284	c.76_79delCAAG	c.(76-81)caaggafs	p.QG26fs	RWDD2A_ENST00000539997.1_Splice_Site|PGM3_ENST00000283977.4_5'Flank|PGM3_ENST00000506587.1_5'Flank|PGM3_ENST00000513973.1_5'Flank|PGM3_ENST00000512866.1_5'Flank	NM_033411.3	NP_219479.2	Q9UIY3	RWD2A_HUMAN	RWD domain containing 2A	26	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.									cervix(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	5		all_cancers(76;2.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00217)		BRCA - Breast invasive adenocarcinoma(397;0.045)		GTTTCCTAACCAAGGAGAAGTAAA	0.441																																					p.25_26del		Atlas-Indel,Pindel	.											.	RWDD2A	12	.	0			c.75_78del						.																																			SO:0001589	frameshift_variant	112611	exon2			.	BC010930	CCDS4998.1	6q15	2012-12-07	2007-07-17	2007-07-17	ENSG00000013392	ENSG00000013392			21385	protein-coding gene	gene with protein product			"RWD domain containing 2"	RWDD2			Standard	NM_033411		Approved	MGC13523, dJ747H23.2	uc003pjx.4	Q9UIY3	OTTHUMG00000015109	ENST00000369724.4:c.76_79delCAAG	chr6.hg19:g.83904246_83904249delCAAG	ENSP00000358739:p.Gln26fs	123.0	0.0		130.0	16.0	NM_033411	B4DIQ3|E1P548|Q2M3R3|Q96FH1	Frame_Shift_Del	DEL	ENST00000369724.4	hg19	CCDS4998.1																																																																																			.	.		0.441	RWDD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041348.2	NM_033411		-	83904249	CAAG	-	83904246	7	5	58	1	0	1	0	1	0	0	0	0	13770	595	21	0	78	0	RWDD2A	6	83904246	Frame_Shift_Del	DEL	CAAG	TCGA-CC-5262-01A-01D-A12Z-10	8051153	83904246	87210821	50	7207										
TBX18	9096	hgsc.bcm.edu	37	chr6	85446949	85446950	+	Missense_Mutation	DNP	GG	GG	AT													0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gatgtgctgtatcggttgagGgtgaggcctgagcgggcaca							TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr6:85446949_85446950GG>AT	ENST00000369663.5	-	8	1614_1615	c.1277_1278CC>AT	c.(1276-1278)aCC>aAT	p.T426N	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	426					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		ATCGGTTGAGGGTGAGGCCTGA	0.609																																					p.T426T|p.T426N		Atlas-SNP	.											.	TBX18	131	.	0			c.C1278T|c.C1277A						.																																			SO:0001583	missense	9096	exon8			GTTGAGGGTGAGG|TTGAGGGTGAGGC	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"T-boxes"	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1277_1278delinsAT	chr6.hg19:g.85446949_85446950delinsAT	ENSP00000358677:p.Thr426Asn	195.0	0.0		189.0|192.0	30.0|31.0	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Silent|Missense_Mutation	SNP	ENST00000369663.5	hg19	CCDS34495.1																																																																																			.	.		0.609	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508		AT	85446950	GG	AT	85446949	3	1	58	1	0	0	0	0	1	0	0	0	15668	1219	43	3	549	3	TBX18	6	85446949	Missense_Mutation	DNP	GG	TCGA-CC-5262-01A-01D-A12Z-10	1542703	85446949	85668118	51	7208										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18833076	18833076	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tggcctcaggagagctgaagGtgaggtccgggttgcattaa	16	7	1	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr7:18833076G>A	ENST00000432645.2	+	16	2313		c.e16+1		HDAC9_ENST00000401921.1_Splice_Site|HDAC9_ENST00000406451.4_Splice_Site|HDAC9_ENST00000441542.2_Splice_Site	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9						B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	AGAGCTGAAGGTGAGGTCCGG	0.512																																					.		Atlas-SNP	.											HDAC9_ENST00000262069,NS,carcinoma,0,2	HDAC9	560	.	0			c.2313+1G>A						.						47	49	48					7																	18833076		2094	4221	6315	SO:0001630	splice_region_variant	9734	exon17			CTGAAGGTGAGGT	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.2313+1G>A	chr7.hg19:g.18833076G>A		155.0	0.0		157.0	33.0	NM_178423	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Splice_Site	SNP	ENST00000432645.2	hg19	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.295392	0.60086	.	.	ENSG00000048052	ENST00000406451;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000341009	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4736	0.94973	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HDAC9	18799601	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.724000	0.84798	2.609000	0.88269	0.655000	0.94253	.	.	.		0.512	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		Intron	A	18833076	G	A	18833076	5	1	58	1	0	0	0	0	0	0	1	0	7023	1275	44	3	2436	3	HDAC9	7	18833076	Splice_Site	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10		18833076	140305587	52	7209										
MGC87042	256227	hgsc.bcm.edu	37	chr7	22533400	22533400	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	catcagcatgggctgtttgcTgcaaatgcaaaagcacaggt	11	9	1	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr7:22533400T>A	ENST00000406890.2	-	3	179		c.e3-2		STEAP1B_ENST00000404369.4_Missense_Mutation_p.Q47L	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B							integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						GGCTGTTTGCTGCAAATGCAA	0.418																																					p.Q47L		Atlas-SNP	.											.	STEAP1B	22	.	0			c.A140T						.						75	56	62					7																	22533400		692	1591	2283	SO:0001630	splice_region_variant	256227	exon3			GTTTGCTGCAAAT		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.85-2A>T	chr7.hg19:g.22533400T>A		498.0	0.0		574.0	114.0	NM_001164460	B5MCI2	Missense_Mutation	SNP	ENST00000406890.2	hg19	CCDS55094.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	8.812|8.812	0.935492|0.935492	0.18206|0.18206	.|.	.|.	ENSG00000105889|ENSG00000105889	ENST00000406890|ENST00000404369;ENST00000424363;ENST00000439708	.|T;T;T	.|0.11712	.|2.89;2.95;2.75	1.06|1.06	1.06|1.06	0.20224|0.20224	.|.	.|.	.|.	.|.	.|.	.|T	.|0.07863	.|0.0197	L|L	0.40543|0.40543	1.245|1.245	0.19575|0.19575	N|N	0.999965|0.999965	.|B	.|0.28233	.|0.204	.|B	.|0.21151	.|0.033	.|T	.|0.33752	.|-0.9856	.|8	.|.	.|.	.|.	.|0.4639	6.3811|6.3811	0.21536|0.21536	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|47	.|B5MCI2	.|.	.|L	-1|47	.|ENSP00000384370:Q47L;ENSP00000416608:Q47L;ENSP00000408954:Q47L	.|.	.|Q	-|-	.|2	.|0	STEAP1B|STEAP1B	22499925|22499925	1.000000|1.000000	0.71417|0.71417	0.418000|0.418000	0.26571|0.26571	0.098000|0.098000	0.18820|0.18820	2.590000|2.590000	0.46154|0.46154	0.759000|0.759000	0.33084|0.33084	0.102000|0.102000	0.15555|0.15555	.|CAG	.	.		0.418	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		Intron	A	22533400	T	A	22533400	5	1	58	1	0	0	0	0	0	0	1	0	9563	1594	55	4	937	4	MGC87042	7	22533400	Splice_Site	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	3700324	22533400	136605263	53	7210										
PON1	5444	hgsc.bcm.edu	37	chr7	94947702	94947702	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tctcggagagcattaagtcgTgttctgtgggggagaaagaa	15	5	2	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr7:94947702T>G	ENST00000222381.3	-	2	309	c.78A>C	c.(76-78)acA>acC	p.T26T	PON1_ENST00000542556.1_Intron	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	26					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	CATTAAGTCGTGTTCTGTGGG	0.393																																					p.T26T	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											.	PON1	55	.	0			c.A78C						.						78	81	80					7																	94947702		2203	4300	6503	SO:0001819	synonymous_variant	5444	exon2			AAGTCGTGTTCTG	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"Paraoxonases"	9204	protein-coding gene	gene with protein product	"esterase A", "arylesterase 1"	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.78A>C	chr7.hg19:g.94947702T>G		148.0	0.0		145.0	26.0	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Silent	SNP	ENST00000222381.3	hg19	CCDS5638.1																																																																																			.	.		0.393	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446		G	94947702	T	G	94947702	2	3	58	1	0	0	0	0	0	0	0	1	12257	1683	59	5		5	PON1	7	94947702	Silent	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	72414302	94947702	64190961	54	7211										
DLX6	1750	hgsc.bcm.edu	37	chr7	96639126	96639126	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aggtgaagatatggtttcagAacaaacgctctaagtttaag	10	5	2	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr7:96639126A>T	ENST00000518156.2	+	3	1079	c.649A>T	c.(649-651)Aac>Tac	p.N217Y	DLX6-AS1_ENST00000430404.2_RNA|DLX6_ENST00000555308.1_Missense_Mutation_p.N89Y|DLX6-AS1_ENST00000430027.3_RNA|DLX6-AS2_ENST00000606174.1_RNA|DLX6_ENST00000493273.2_3'UTR|DLX6-AS1_ENST00000452769.2_RNA|DLX6-AS1_ENST00000437541.1_RNA|DLX6-AS1_ENST00000458352.2_RNA|DLX6_ENST00000007660.5_Missense_Mutation_p.N189Y|DLX6-AS1_ENST00000605417.1_RNA|DLX6-AS1_ENST00000437331.2_RNA			P56179	DLX6_HUMAN	distal-less homeobox 6	99					anatomical structure formation involved in morphogenesis (GO:0048646)|embryonic limb morphogenesis (GO:0030326)|epithelial cell differentiation (GO:0030855)|head development (GO:0060322)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|palate development (GO:0060021)|positive regulation of epithelial cell proliferation (GO:0050679)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(2)|urinary_tract(1)	12	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					ATGGTTTCAGAACAAACGCTC	0.502																																					p.N217Y		Atlas-SNP	.											.	DLX6	37	.	0			c.A649T						.						99	98	98					7																	96639126		2011	4195	6206	SO:0001583	missense	1750	exon3			TTTCAGAACAAAC		CCDS47647.1, CCDS47647.2	7q21.3	2011-06-20	2005-12-22		ENSG00000006377	ENSG00000006377		"Homeoboxes / ANTP class : NKL subclass"	2919	protein-coding gene	gene with protein product		600030	"distal-less homeo box 6"			7907794	Standard	NM_005222		Approved		uc022ahu.1	P56179	OTTHUMG00000154201	ENST00000518156.2:c.649A>T	chr7.hg19:g.96639126A>T	ENSP00000428480:p.Asn217Tyr	190.0	0.0		246.0	33.0	NM_005222	A4D1I2|B3KSQ0|J3KR92|Q3ZAR6|Q9UPL2	Missense_Mutation	SNP	ENST00000518156.2	hg19	CCDS47647.2	.	.	.	.	.	.	.	.	.	.	A	23.7	4.447881	0.84101	.	.	ENSG00000006377	ENST00000518156;ENST00000007660;ENST00000555308	D;D;D	0.99369	-5.78;-5.78;-5.78	5.24	5.24	0.73138	.	0.083122	0.85682	D	0.000000	D	0.99684	0.9881	H	0.98936	4.375	0.80722	D	1	D	0.69078	0.997	D	0.72075	0.976	D	0.97232	0.9885	10	0.87932	D	0	-22.1374	15.2972	0.73919	1.0:0.0:0.0:0.0	.	189	P56179-2	.	Y	217;189;89	ENSP00000428480:N217Y;ENSP00000007660:N189Y;ENSP00000451635:N89Y	ENSP00000007660:N189Y	N	+	1	0	DLX6	96477062	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.081000	0.94049	2.206000	0.71126	0.533000	0.62120	AAC	.	.		0.502	DLX6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334373.4	NM_005222		T	96639126	A	T	96639126	3	4	58	1	0	0	0	0	1	0	0	0	4577	246	9	4	659	4	DLX6	7	96639126	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	1691424	96639126	62499537	55	7212										
IQUB	154865	hgsc.bcm.edu	37	chr7	123092919	123092919	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cagcactggaacctgagaaaAatagttcttagccaggatat	9	8	1	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr7:123092919A>T	ENST00000466202.1	-	13	2830	c.2254T>A	c.(2254-2256)Ttt>Att	p.F752I	IQUB_ENST00000324698.6_Missense_Mutation_p.F752I	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	752					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)				breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						ACCTGAGAAAAATAGTTCTTA	0.343																																					p.F752I		Atlas-SNP	.											.	IQUB	117	.	0			c.T2254A						.						99	94	96					7																	123092919		2203	4300	6503	SO:0001583	missense	154865	exon13			GAGAAAAATAGTT	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.2254T>A	chr7.hg19:g.123092919A>T	ENSP00000417769:p.Phe752Ile	300.0	0.0		359.0	76.0	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	hg19	CCDS5787.1	.	.	.	.	.	.	.	.	.	.	A	34	5.398149	0.96030	.	.	ENSG00000164675	ENST00000466202;ENST00000324698	T;T	0.30448	1.53;1.53	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.61602	0.2360	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67772	-0.5584	10	0.87932	D	0	.	16.4197	0.83754	1.0:0.0:0.0:0.0	.	752	Q8NA54	IQUB_HUMAN	I	752	ENSP00000417769:F752I;ENSP00000324882:F752I	ENSP00000324882:F752I	F	-	1	0	IQUB	122880155	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.002000	0.88514	2.278000	0.76064	0.467000	0.42956	TTT	.	.		0.343	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827		T	123092919	A	T	123092919	3	4	58	1	0	0	0	0	1	0	0	0	7829	14	1	4	125	4	IQUB	7	123092919	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	26453793	123092919	36045744	56	7213										
METTL2B	55798	hgsc.bcm.edu	37	chr7	128119312	128119312	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tggctttttaccgaattcccTgagctggcacctagccaaaa	8	12	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr7:128119312T>G	ENST00000262432.8	+	3	340	c.303T>G	c.(301-303)ccT>ccG	p.P101P	METTL2B_ENST00000480046.1_Silent_p.P36P|RP11-212P7.3_ENST00000462662.1_RNA	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	101					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						CCGAATTCCCTGAGCTGGCAC	0.388																																					p.P101P		Atlas-SNP	.											.	METTL2B	34	.	0			c.T303G						.						60	61	61					7																	128119312		2203	4300	6503	SO:0001819	synonymous_variant	55798	exon3			ATTCCCTGAGCTG	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"methyltransferase like 2"	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.303T>G	chr7.hg19:g.128119312T>G		565.0	0.0		713.0	130.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Silent	SNP	ENST00000262432.8	hg19	CCDS5803.2																																																																																			.	.		0.388	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396		G	128119312	T	G	128119312	2	3	58	1	0	0	0	0	0	0	0	1	9509	1567	55	5		5	METTL2B	7	128119312	Silent	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	5026393	128119312	31019351	57	7214										
HTR5A	3361	hgsc.bcm.edu	37	chr7	154862969	154862969	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tgccagctttggatcgcgtgCgacgtgctttgctgcacggc	14	12	0	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr7:154862969C>T	ENST00000287907.2	+	1	936	c.360C>T	c.(358-360)tgC>tgT	p.C120C	HTR5A-AS1_ENST00000395731.2_Silent_p.S15S|HTR5A-AS1_ENST00000543018.1_Silent_p.S15S|HTR5A-AS1_ENST00000493904.1_5'UTR	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	120					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	GGATCGCGTGCGACGTGCTTT	0.667																																					p.C120C		Atlas-SNP	.											.	HTR5A	114	.	0			c.C360T						.						63	49	53					7																	154862969		2203	4300	6503	SO:0001819	synonymous_variant	3361	exon1			CGCGTGCGACGTG		CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5300	protein-coding gene	gene with protein product		601305	"5-hydroxytryptamine (serotonin) receptor 5A"			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.360C>T	chr7.hg19:g.154862969C>T		33.0	0.0		40.0	8.0	NM_024012	Q2M2D2	Silent	SNP	ENST00000287907.2	hg19	CCDS5936.1																																																																																			.	.		0.667	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012		T	154862969	C	T	154862969	2	4	58	1	0	0	0	0	0	0	0	1	7459	776	27	1		1	HTR5A	7	154862969	Silent	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	26743657	154862969	4275694	58	7215										
STC1	6781	hgsc.bcm.edu	37	chr8	23712004	23712004	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gttgcagaagcactgatcacCagcaccagaagcactgctga	10	12	1	4			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr8:23712004C>T	ENST00000290271.2	-	1	316	c.33G>A	c.(31-33)ctG>ctA	p.L11L	STC1_ENST00000524323.1_5'Flank	NM_003155.2	NP_003146.1	P52823	STC1_HUMAN	stanniocalcin 1	11					bone development (GO:0060348)|cellular calcium ion homeostasis (GO:0006874)|cellular response to cAMP (GO:0071320)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hypoxia (GO:0071456)|chondrocyte proliferation (GO:0035988)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endothelial cell morphogenesis (GO:0001886)|growth plate cartilage axis specification (GO:0003421)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of renal phosphate excretion (GO:1903403)|ossification (GO:0001503)|positive regulation of calcium ion import (GO:0090280)|regulation of anion transport (GO:0044070)|regulation of cardiac muscle cell contraction (GO:0086004)|response to vitamin D (GO:0033280)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26		Prostate(55;0.055)|Breast(100;0.116)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		CACTGATCACCAGCACCAGAA	0.512																																					p.L11L		Atlas-SNP	.											.	STC1	49	.	0			c.G33A						.						130	136	134					8																	23712004		2203	4300	6503	SO:0001819	synonymous_variant	6781	exon1			GATCACCAGCACC		CCDS6043.1	8p22-p12	2008-06-23			ENSG00000159167	ENSG00000159167			11373	protein-coding gene	gene with protein product		601185		STC		9480753	Standard	NM_003155		Approved		uc003xdw.1	P52823	OTTHUMG00000097853	ENST00000290271.2:c.33G>A	chr8.hg19:g.23712004C>T		233.0	0.0		273.0	67.0	NM_003155	B4DN22|Q71UE5	Silent	SNP	ENST00000290271.2	hg19	CCDS6043.1																																																																																			.	.		0.512	STC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215143.1			T	23712004	C	T	23712004	2	4	58	1	0	0	0	0	0	0	0	1	15290	581	21	3		3	STC1	8	23712004	Silent	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10		23712004	122652018	59	7216										
IMPAD1	54928	hgsc.bcm.edu	37	chr8	57876515	57876515	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cccctagggcttttaagatgGcattaccagcacatatatcc	7	12	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr8:57876515G>C	ENST00000262644.4	-	5	1175	c.917C>G	c.(916-918)gCc>gGc	p.A306G		NM_017813.4	NP_060283.3	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	306					chondrocyte development (GO:0002063)|chondroitin sulfate metabolic process (GO:0030204)|embryonic digit morphogenesis (GO:0042733)|endochondral ossification (GO:0001958)|inositol biosynthetic process (GO:0006021)|phosphatidylinositol phosphorylation (GO:0046854)|post-embryonic development (GO:0009791)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|3'-nucleotidase activity (GO:0008254)|inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)	p.A306G(1)		kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)				TTTTAAGATGGCATTACCAGC	0.433																																					p.A306G		Atlas-SNP	.											IMPAD1,colon,carcinoma,0,1	IMPAD1	27	.	1	Substitution - Missense(1)	large_intestine(1)	c.C917G						.						68	63	65					8																	57876515		2203	4300	6503	SO:0001583	missense	54928	exon5			AAGATGGCATTAC		CCDS6169.1	8q12.1	2013-05-16			ENSG00000104331	ENSG00000104331			26019	protein-coding gene	gene with protein product		614010				21549340	Standard	NM_017813		Approved	FLJ20421, IMPA3, gPAPP	uc003xte.4	Q9NX62	OTTHUMG00000164415	ENST00000262644.4:c.917C>G	chr8.hg19:g.57876515G>C	ENSP00000262644:p.Ala306Gly	260.0	0.0		320.0	69.0	NM_017813	Q6NVY7	Missense_Mutation	SNP	ENST00000262644.4	hg19	CCDS6169.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.595039	0.86953	.	.	ENSG00000104331	ENST00000262644	T	0.57107	0.42	5.32	5.32	0.75619	Inositol monophosphatase, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.76990	0.4065	M	0.87547	2.89	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80238	-0.1465	10	0.54805	T	0.06	-27.5718	17.9675	0.89103	0.0:0.0:1.0:0.0	.	306	Q9NX62	IMPA3_HUMAN	G	306	ENSP00000262644:A306G	ENSP00000262644:A306G	A	-	2	0	IMPAD1	58039069	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.336000	0.96533	2.480000	0.83734	0.585000	0.79938	GCC	.	.		0.433	IMPAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378665.1	NM_017813		C	57876515	G	C	57876515	3	2	58	1	0	0	0	0	1	0	0	0	7734	1203	42	4	166	4	IMPAD1	8	57876515	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	34164511	57876515	88487507	60	7217										
NCOA2	10499	hgsc.bcm.edu	37	chr8	71068895	71068895	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gctgagtgggggaggattcaTattaactggggagttttgca	16	4	1	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr8:71068895T>C	ENST00000452400.2	-	11	1886	c.1705A>G	c.(1705-1707)Atg>Gtg	p.M569V	NCOA2_ENST00000524223.1_5'UTR	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	569					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			GGAGGATTCATATTAACTGGG	0.507			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.M569V		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.A1705G						.						97	96	96					8																	71068895		1879	4123	6002	SO:0001583	missense	10499	exon11			GATTCATATTAAC	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.1705A>G	chr8.hg19:g.71068895T>C	ENSP00000399968:p.Met569Val	153.0	0.0		164.0	28.0	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	hg19	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	T	10.89	1.477833	0.26511	.	.	ENSG00000140396	ENST00000452400	T	0.01474	4.85	5.93	4.71	0.59529	.	0.084489	0.85682	D	0.000000	T	0.01870	0.0059	N	0.25647	0.755	0.80722	D	1	B	0.13145	0.007	B	0.08055	0.003	T	0.58713	-0.7588	10	0.41790	T	0.15	.	12.874	0.57980	0.0:0.0:0.1356:0.8644	.	569	Q15596	NCOA2_HUMAN	V	569	ENSP00000399968:M569V	ENSP00000399968:M569V	M	-	1	0	NCOA2	71231449	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.139000	0.58024	2.263000	0.75096	0.533000	0.62120	ATG	.	.		0.507	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			C	71068895	T	C	71068895	3	2	58	1	0	0	0	0	1	0	0	0	10238	1406	49	2	2741	2	NCOA2	8	71068895	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	13192380	71068895	75295127	61	7218										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110432768	110432768	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aatgcccaagagaagacttcCtgcattagcaaataaaggaa	8	8	0	2	rs547689763		TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr8:110432768C>A	ENST00000378402.5	+	23	2650	c.2546C>A	c.(2545-2547)cCt>cAt	p.P849H		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	849					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AGAAGACTTCCTGCATTAGCA	0.333										HNSCC(38;0.096)																											p.P849H		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.C2546A						.						65	58	60					8																	110432768		1798	4076	5874	SO:0001583	missense	93035	exon23			GACTTCCTGCATT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.2546C>A	chr8.hg19:g.110432768C>A	ENSP00000367655:p.Pro849His	176.0	0.0		334.0	107.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.876361	0.51801	.	.	ENSG00000205038	ENST00000378402	D	0.87103	-2.21	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.85902	0.5805	M	0.69823	2.125	0.30531	N	0.767401	B	0.27951	0.195	B	0.18561	0.022	D	0.85213	0.1022	10	0.87932	D	0	.	14.9728	0.71246	0.0:1.0:0.0:0.0	.	849	Q86WI1	PKHL1_HUMAN	H	849	ENSP00000367655:P849H	ENSP00000367655:P849H	P	+	2	0	PKHD1L1	110501944	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.944000	0.56629	2.610000	0.88304	0.585000	0.79938	CCT	.	.		0.333	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110432768	C	A	110432768	3	1	58	1	0	0	0	0	1	0	0	0	11981	681	24	3	2636	3	PKHD1L1	8	110432768	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	39363873	110432768	35931254	62	7219										
HAS2	3037	hgsc.bcm.edu	37	chr8	122627257	122627257	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	actgctgaggaatgagatccAggaatcgtacttgtttaaaa	10	6	0	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr8:122627257A>T	ENST00000303924.4	-	4	1288	c.751T>A	c.(751-753)Tgg>Agg	p.W251R		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	251					atrioventricular canal development (GO:0036302)|bone morphogenesis (GO:0060349)|cellular response to fluid shear stress (GO:0071498)|cellular response to interleukin-1 (GO:0071347)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|endocardial cushion to mesenchymal transition (GO:0090500)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|hyaluronan biosynthetic process (GO:0030213)|kidney development (GO:0001822)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	hyaluronan synthase activity (GO:0050501)		HAS2/PLAG1(10)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			AATGAGATCCAGGAATCGTAC	0.378																																					p.W251R		Atlas-SNP	.											.	HAS2	87	.	0			c.T751A						.						61	60	60					8																	122627257		2203	4300	6503	SO:0001583	missense	3037	exon4			AGATCCAGGAATC	U54804	CCDS6335.1	8q24.12	2013-02-22			ENSG00000170961	ENSG00000170961	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4819	protein-coding gene	gene with protein product		601636				9169154	Standard	NM_005328		Approved		uc003yph.2	Q92819	OTTHUMG00000164953	ENST00000303924.4:c.751T>A	chr8.hg19:g.122627257A>T	ENSP00000306991:p.Trp251Arg	94.0	0.0		174.0	28.0	NM_005328	Q32MM3	Missense_Mutation	SNP	ENST00000303924.4	hg19	CCDS6335.1	.	.	.	.	.	.	.	.	.	.	A	16.54	3.151941	0.57151	.	.	ENSG00000170961	ENST00000303924;ENST00000443194	T	0.59083	0.29	5.73	5.73	0.89815	.	0.049569	0.85682	D	0.000000	T	0.78622	0.4312	M	0.86343	2.81	0.80722	D	1	D	0.63046	0.992	D	0.66497	0.944	T	0.82557	-0.0398	10	0.72032	D	0.01	-9.8245	16.3143	0.82909	1.0:0.0:0.0:0.0	.	251	Q92819	HAS2_HUMAN	R	251	ENSP00000306991:W251R	ENSP00000306991:W251R	W	-	1	0	HAS2	122696438	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.275000	0.95738	2.313000	0.78055	0.454000	0.30748	TGG	.	.		0.378	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328		T	122627257	A	T	122627257	3	4	58	1	0	0	0	0	1	0	0	0	6971	188	7	4	911	4	HAS2	8	122627257	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	12194489	122627257	23736765	63	7220										
FAM83H	286077	hgsc.bcm.edu	37	chr8	144812668	144812668	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cagtgcatccaccgccaggcGgtagtactctttgtagtgag	12	11	1	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr8:144812668G>A	ENST00000388913.3	-	2	210	c.85C>T	c.(85-87)Cgc>Tgc	p.R29C	MIR4664_ENST00000583819.1_RNA	NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	29					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			ACCGCCAGGCGGTAGTACTCT	0.672																																					p.R29C		Atlas-SNP	.											.	FAM83H	68	.	0			c.C85T						.						23	25	24					8																	144812668		1994	4148	6142	SO:0001583	missense	286077	exon2			CCAGGCGGTAGTA	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.85C>T	chr8.hg19:g.144812668G>A	ENSP00000373565:p.Arg29Cys	30.0	0.0		29.0	11.0	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	hg19	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	g	19.47	3.833196	0.71258	.	.	ENSG00000180921	ENST00000388913	T	0.35421	1.31	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.67534	0.2903	M	0.90705	3.14	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76465	-0.2949	10	0.87932	D	0	.	16.8086	0.85712	0.0:0.0:1.0:0.0	.	29	Q6ZRV2	FA83H_HUMAN	C	29	ENSP00000373565:R29C	ENSP00000373565:R29C	R	-	1	0	FAM83H	144884656	1.000000	0.71417	1.000000	0.80357	0.482000	0.33219	6.340000	0.72973	2.285000	0.76669	0.478000	0.44815	CGC	.	.		0.672	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		A	144812668	G	A	144812668	3	1	58	1	0	0	0	0	1	0	0	0	5648	1116	39	1	3470	1	FAM83H	8	144812668	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	22185411	144812668	1551354	64	7221										
RANBP6	26953	hgsc.bcm.edu	37	chr9	6012698	6012698	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gtagcaatgacattttttttGgttttggaatttgcacactt	8	5	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr9:6012698G>T	ENST00000259569.5	-	1	2920	c.2910C>A	c.(2908-2910)acC>acA	p.T970T	RANBP6_ENST00000485372.1_5'Flank	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	970					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.K971fs*1(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		CATTTTTTTTGGTTTTGGAAT	0.368																																					p.T970T		Atlas-SNP	.											.	RANBP6	127	.	1	Insertion - Frameshift(1)	NS(1)	c.C2910A						.						108	101	104					9																	6012698		2203	4300	6503	SO:0001819	synonymous_variant	26953	exon1			TTTTTTGGTTTTG	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.2910C>A	chr9.hg19:g.6012698G>T		252.0	0.0		313.0	13.0	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Silent	SNP	ENST00000259569.5	hg19	CCDS6467.1																																																																																			.	.		0.368	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		T	6012698	G	T	6012698	2	4	58	1	0	0	0	0	0	0	0	1	13046	1335	47	3		3	RANBP6	9	6012698	Silent	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10		6012698	135200733	65	7222										
ACO1	48	hgsc.bcm.edu	37	chr9	32418350	32418350	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gttcccaggcttttcacaacAtgcggattattccccctggc	8	14	1	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr9:32418350A>G	ENST00000309951.6	+	6	637	c.499A>G	c.(499-501)Atg>Gtg	p.M167V	ACO1_ENST00000379923.1_Missense_Mutation_p.M167V|ACO1_ENST00000541043.1_Missense_Mutation_p.M68V	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	167					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		TTTTCACAACATGCGGATTAT	0.463																																					p.M167V		Atlas-SNP	.											.	ACO1	149	.	0			c.A499G						.						74	77	76					9																	32418350		2203	4300	6503	SO:0001583	missense	48	exon6			CACAACATGCGGA	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.499A>G	chr9.hg19:g.32418350A>G	ENSP00000309477:p.Met167Val	365.0	0.0		379.0	62.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	hg19	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.034436	0.35893	.	.	ENSG00000122729	ENST00000432017;ENST00000309951;ENST00000379923;ENST00000379921;ENST00000541043	T;T;T	0.15603	2.41;2.41;2.41	6.16	6.16	0.99307	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 (1);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (3);	0.000000	0.85682	D	0.000000	T	0.12135	0.0295	N	0.11560	0.145	0.80722	D	1	B;B	0.20052	0.041;0.006	B;B	0.20384	0.029;0.008	T	0.09079	-1.0691	10	0.87932	D	0	-13.5172	15.7887	0.78332	1.0:0.0:0.0:0.0	.	203;167	Q59FI0;P21399	.;ACOC_HUMAN	V	203;167;167;167;68	ENSP00000309477:M167V;ENSP00000369255:M167V;ENSP00000438733:M68V	ENSP00000309477:M167V	M	+	1	0	ACO1	32408350	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.770000	0.55310	2.367000	0.80283	0.528000	0.53228	ATG	.	.		0.463	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		G	32418350	A	G	32418350	3	3	58	1	0	0	0	0	1	0	0	0	146	217	8	2	517	2	ACO1	9	32418350	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	26405652	32418350	108795081	66	7223										
KIAA1958	158405	hgsc.bcm.edu	37	chr9	115336637	115336638	+	Frame_Shift_Ins	INS	-	-	AGACACAGACTAGCCCTGTTGAA													0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tataatcggggtgccctctgINSagacacagactagccctgtt							TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr9:115336637_115336638insAGACACAGACTAGCCCTGTTGAA	ENST00000337530.6	+	2	573_574	c.277_278insAGACACAGACTAGCCCTGTTGAA	c.(277-279)gagfs	p.E93fs	KIAA1958_ENST00000374244.3_Frame_Shift_Ins_p.E93fs|KIAA1958_ENST00000536272.1_Frame_Shift_Ins_p.E93fs	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	93										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						GGTGCCCTCTGAGACACAGACT	0.49																																					p.E93fs		Pindel	.											.	KIAA1958	52	.	0			c.277_278insAGACACAGACTAGCCCTGTTGAA						.																																			SO:0001589	frameshift_variant	158405	exon2			.	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.278_300dupAGACACAGACTAGCCCTGTTGAA	chr9.hg19:g.115336637_115336638insAGACACAGACTAGCCCTGTTGAA	ENSP00000336940:p.Glu93fs	136.0	0.0		140.0	15.0	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Frame_Shift_Ins	INS	ENST00000337530.6	hg19	CCDS35108.1																																																																																			.	.		0.49	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465		AGACACAGACTAGCCCTGTTGAA	115336638	-	AGACACAGACTAGCCCTGTTGAA	115336637	7	5	58	1	0	1	1	0	0	0	0	0	8273	1291	45	0	279	0	KIAA1958	9	115336637	Frame_Shift_Ins	INS	-	TCGA-CC-5262-01A-01D-A12Z-10	82918287	115336637	25876794	67	7224										
C10orf71	118461	hgsc.bcm.edu	37	chr10	50533357	50533357	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	catcgacacccactaacacaCggggcacacgtgtgaagtgc	10	14	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr10:50533357C>A	ENST00000374144.3	+	3	3055	c.2767C>A	c.(2767-2769)Cgg>Agg	p.R923R	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	923										endometrium(1)	1						CACTAACACACGGGGCACACG	0.592																																					p.R923R		Atlas-SNP	.											.	C10orf71	179	.	0			c.C2767A						.						18	17	17					10																	50533357		692	1591	2283	SO:0001819	synonymous_variant	118461	exon3			AACACACGGGGCA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.2767C>A	chr10.hg19:g.50533357C>A		75.0	0.0		90.0	22.0	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	hg19	CCDS44387.1																																																																																			.	.		0.592	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		A	50533357	C	A	50533357	2	1	58	1	0	0	0	0	0	0	0	1	1616	527	19	1		1	C10orf71	10	50533357	Silent	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10		50533357	85001390	68	7225										
PRF1	5551	hgsc.bcm.edu	37	chr10	72358776	72358776	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tgcgcagggcagtgagggccGatatgcggccacccagctcc	15	14	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr10:72358776G>T	ENST00000441259.1	-	3	861	c.701C>A	c.(700-702)tCg>tAg	p.S234*	PRF1_ENST00000373209.2_Nonsense_Mutation_p.S234*	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	234	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						AGTGAGGGCCGATATGCGGCC	0.652			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.S234X		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.C701A						.						62	54	57					10																	72358776		2203	4300	6503	SO:0001587	stop_gained	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AGGGCCGATATGC	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"Perforin", "perforin 1 (preforming protein)"	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.701C>A	chr10.hg19:g.72358776G>T	ENSP00000398568:p.Ser234*	98.0	0.0		77.0	11.0	NM_001083116	B2R6X4|Q59F57|Q86WX7	Nonsense_Mutation	SNP	ENST00000441259.1	hg19	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	G	37	6.189954	0.97362	.	.	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	.	.	.	5.76	3.91	0.45181	.	0.761983	0.12600	N	0.454757	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-2.7514	9.6964	0.40161	0.0777:0.142:0.7803:0.0	.	.	.	.	X	234	.	ENSP00000316746:S234X	S	-	2	0	PRF1	72028782	0.000000	0.05858	0.004000	0.12327	0.739000	0.42172	0.434000	0.21494	0.768000	0.33290	0.655000	0.94253	TCG	.	.		0.652	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		T	72358776	G	T	72358776	4	4	58	1	0	0	0	0	0	1	0	0	12490	1059	37	1	970	1	PRF1	10	72358776	Nonsense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	21825419	72358776	63175971	69	7226										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72468471	72468471	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gtgctgctggtggtggacgaCtcggtggttcgcttccatgg	17	9	0	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr10:72468471C>G	ENST00000373207.1	+	4	807	c.807C>G	c.(805-807)gaC>gaG	p.D269E	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.D269E	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	269	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						TGGTGGACGACTCGGTGGTTC	0.612																																					p.D269E		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.C807G						.						146	116	126					10																	72468471		2203	4300	6503	SO:0001583	missense	140766	exon4			GGACGACTCGGTG	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.807C>G	chr10.hg19:g.72468471C>G	ENSP00000362303:p.Asp269Glu	130.0	0.0		123.0	31.0	NM_080722	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	hg19	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951517	0.73787	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	D;D	0.86432	-2.12;-2.12	4.48	3.57	0.40892	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.85695	0.5756	N	0.25647	0.755	0.39518	D	0.968479	D;D	0.64830	0.987;0.994	P;D	0.67231	0.9;0.95	T	0.81256	-0.1015	10	0.15499	T	0.54	.	9.4147	0.38514	0.0:0.8244:0.0:0.1756	.	269;269	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	E	269	ENSP00000362304:D269E;ENSP00000362303:D269E	ENSP00000362303:D269E	D	+	3	2	ADAMTS14	72138477	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	3.168000	0.50801	1.094000	0.41399	0.491000	0.48974	GAC	.	.		0.612	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		G	72468471	C	G	72468471	3	3	58	1	0	0	0	0	1	0	0	0	259	564	20	4	821	4	ADAMTS14	10	72468471	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	109695	72468471	63066276	70	7227										
MGEA5	10724	hgsc.bcm.edu	37	chr10	103550822	103550822	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	caaagcagtaatccaggctgAgggaaagcagccctcctact	10	12	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr10:103550822A>T	ENST00000361464.3	-	14	2680	c.2285T>A	c.(2284-2286)cTc>cAc	p.L762H	MGEA5_ENST00000439817.1_Missense_Mutation_p.L709H|MGEA5_ENST00000482611.1_5'UTR|MGEA5_ENST00000357797.5_Missense_Mutation_p.L695H	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	762					aging (GO:0007568)|dATP metabolic process (GO:0046060)|glycoprotein catabolic process (GO:0006516)|N-acetylglucosamine metabolic process (GO:0006044)|necrotic cell death (GO:0070265)|negative regulation of cardiac muscle adaptation (GO:0010616)|negative regulation of protein glycosylation (GO:0060051)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cell killing (GO:0031343)|positive regulation of DNA metabolic process (GO:0051054)|positive regulation of glucose import (GO:0046326)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of proteolysis (GO:0045862)|protein targeting to membrane (GO:0006612)|response to steroid hormone (GO:0048545)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	23		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		ATCCAGGCTGAGGGAAAGCAG	0.418																																					p.L762H		Atlas-SNP	.											.	MGEA5	53	.	0			c.T2285A						.						73	72	72					10																	103550822		2203	4300	6503	SO:0001583	missense	10724	exon14			AGGCTGAGGGAAA	AF036144	CCDS7520.1, CCDS44471.1	10q24.1-q24.3	2008-08-01			ENSG00000198408	ENSG00000198408			7056	protein-coding gene	gene with protein product	"nuclear cytoplasmic O-GlcNAcase and acetyltransferase"	604039				9811929, 16356930	Standard	NM_012215		Approved	MEA5, NCOAT, OGA	uc001ktv.2	O60502	OTTHUMG00000018939	ENST00000361464.3:c.2285T>A	chr10.hg19:g.103550822A>T	ENSP00000354850:p.Leu762His	234.0	0.0		289.0	60.0	NM_012215	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Missense_Mutation	SNP	ENST00000361464.3	hg19	CCDS7520.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.104450	0.56291	.	.	ENSG00000198408	ENST00000439817;ENST00000361464;ENST00000357797	T;T;T	0.54866	0.55;0.55;0.55	5.77	5.77	0.91146	Acyl-CoA N-acyltransferase (2);	0.066272	0.64402	D	0.000008	T	0.46132	0.1377	L	0.45285	1.41	0.80722	D	1	B;B;B	0.27932	0.016;0.028;0.194	B;B;B	0.28385	0.007;0.026;0.089	T	0.48258	-0.9051	10	0.87932	D	0	-6.3828	11.4753	0.50295	0.8658:0.0:0.0:0.1342	.	709;695;762	E9PGF9;O60502-2;O60502	.;.;NCOAT_HUMAN	H	709;762;695	ENSP00000409973:L709H;ENSP00000354850:L762H;ENSP00000350445:L695H	ENSP00000350445:L695H	L	-	2	0	MGEA5	103540812	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	6.904000	0.75708	2.326000	0.78906	0.533000	0.62120	CTC	.	.		0.418	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215		T	103550822	A	T	103550822	3	4	58	1	0	0	0	0	1	0	0	0	9564	304	11	4	477	4	MGEA5	10	103550822	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	31082351	103550822	31983925	71	7228										
INPP5F	22876	hgsc.bcm.edu	37	chr10	121556404	121556404	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ttctagtggctctcatttcaCgccgaagtaggcacagagca	10	11	3	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr10:121556404C>T	ENST00000361976.2	+	7	1013	c.847C>T	c.(847-849)Cgc>Tgc	p.R283C	INPP5F_ENST00000369083.3_Missense_Mutation_p.R283C	NM_014937.3	NP_055752.1	Q01968	OCRL_HUMAN	inositol polyphosphate-5-phosphatase F	0	5-phosphatase.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(9)|lung(5)|ovary(5)|pancreas(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		TCTCATTTCACGCCGAAGTAG	0.483																																					p.R283C		Atlas-SNP	.											.	INPP5F	112	.	0			c.C847T						.						61	55	57					10																	121556404		2203	4300	6503	SO:0001583	missense	22876	exon7			ATTTCACGCCGAA	AB023183	CCDS7616.1, CCDS58098.1	10q26.13	2009-02-03			ENSG00000198825	ENSG00000198825			17054	protein-coding gene	gene with protein product		609389				10231032, 11274189	Standard	NM_014937		Approved	SAC2, KIAA0966, hSac2	uc001leo.3	Q9Y2H2	OTTHUMG00000019158	ENST00000361976.2:c.847C>T	chr10.hg19:g.121556404C>T	ENSP00000354519:p.Arg283Cys	211.0	0.0		319.0	67.0	NM_014937	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000361976.2	hg19	CCDS7616.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.490270	0.84962	.	.	ENSG00000198825	ENST00000361976;ENST00000369083	T;T	0.77358	-1.09;-1.09	5.7	5.7	0.88788	Synaptojanin, N-terminal (2);	0.099000	0.64402	D	0.000002	D	0.92662	0.7668	H	0.96861	3.895	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.94539	0.7743	10	0.87932	D	0	-5.5853	19.8339	0.96646	0.0:1.0:0.0:0.0	.	283	Q9Y2H2	SAC2_HUMAN	C	283	ENSP00000354519:R283C;ENSP00000358079:R283C	ENSP00000354519:R283C	R	+	1	0	INPP5F	121546394	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.426000	0.66476	2.701000	0.92244	0.655000	0.94253	CGC	.	.		0.483	INPP5F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050679.1	NM_014937		T	121556404	C	T	121556404	3	4	58	1	0	0	0	0	1	0	0	0	7767	536	19	1	873	1	INPP5F	10	121556404	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	18005582	121556404	13978343	72	7229										
TACC2	10579	hgsc.bcm.edu	37	chr10	123843041	123843041	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ccagtgggagcatatctgccGcacgcagagctgccctgggg	15	13	1	1	rs201912981	byFrequency	TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr10:123843041G>T	ENST00000369005.1	+	4	1366	c.1026G>T	c.(1024-1026)ccG>ccT	p.P342P	TACC2_ENST00000453444.2_Silent_p.P342P|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Silent_p.P342P|TACC2_ENST00000515603.1_Silent_p.P342P|TACC2_ENST00000334433.3_Silent_p.P342P	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	342					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CATATCTGCCGCACGCAGAGC	0.632																																					p.P342P		Atlas-SNP	.											.	TACC2	271	.	0			c.G1026T						.						31	37	35					10																	123843041		2199	4297	6496	SO:0001819	synonymous_variant	10579	exon4			TCTGCCGCACGCA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.1026G>T	chr10.hg19:g.123843041G>T		83.0	0.0		80.0	18.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	G|0.999;A|0.001		0.632	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123843041	G	T	123843041	2	4	58	1	0	0	0	0	0	0	0	1	15517	1074	38	1		1	TACC2	10	123843041	Silent	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	2286637	123843041	11691706	73	7230										
KIF18A	81930	hgsc.bcm.edu	37	chr11	28116264	28116264	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gcatttgtaaaggtgtaacaTtgttagatacatcactccag	8	7	1	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr11:28116264T>G	ENST00000263181.6	-	3	699	c.409A>C	c.(409-411)Atg>Ctg	p.M137L		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	137	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						AGGTGTAACATTGTTAGATAC	0.388																																					p.M137L		Atlas-SNP	.											.	KIF18A	92	.	0			c.A409C						.						193	172	179					11																	28116264		2202	4299	6501	SO:0001583	missense	81930	exon3			GTAACATTGTTAG	AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"Kinesins"	29441	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 99"	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.409A>C	chr11.hg19:g.28116264T>G	ENSP00000263181:p.Met137Leu	226.0	0.0		277.0	46.0	NM_031217	Q4VPE3|Q86VS5|Q9H0F3	Missense_Mutation	SNP	ENST00000263181.6	hg19	CCDS7867.1	.	.	.	.	.	.	.	.	.	.	T	17.30	3.355496	0.61293	.	.	ENSG00000121621	ENST00000263181	T	0.72282	-0.64	5.58	4.43	0.53597	Kinesin, motor domain (4);	0.034657	0.85682	N	0.000000	T	0.59676	0.2211	L	0.33293	1	0.80722	D	1	B	0.21381	0.055	B	0.26969	0.075	T	0.52200	-0.8607	10	0.27082	T	0.32	.	11.9799	0.53113	0.13:0.0:0.0:0.87	.	137	Q8NI77	KI18A_HUMAN	L	137	ENSP00000263181:M137L	ENSP00000263181:M137L	M	-	1	0	KIF18A	28072840	1.000000	0.71417	0.988000	0.46212	0.950000	0.60333	5.139000	0.64801	0.929000	0.37192	0.529000	0.55759	ATG	.	.		0.388	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217		G	28116264	T	G	28116264	3	3	58	1	0	0	0	0	1	0	0	0	8289	1493	52	5	2347	5	KIF18A	11	28116264	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10		28116264	106890252	74	7231										
ELMOD1	55531	hgsc.bcm.edu	37	chr11	107518278	107518278	+	Frame_Shift_Del	DEL	C	C	-													0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ttggtttccaaggtgatgatCctaaaacagactttcgagga							TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr11:107518278delC	ENST00000265840.7	+	7	770	c.505delC	c.(505-507)cctfs	p.P169fs	ELMOD1_ENST00000443271.2_Frame_Shift_Del_p.P169fs|ELMOD1_ENST00000531234.1_Frame_Shift_Del_p.P163fs	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	169	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)	cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)			endometrium(2)|large_intestine(5)|liver(2)|lung(7)|pancreas(2)|prostate(1)	19		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		AGGTGATGATCCTAAAACAGA	0.403																																					p.D168fs		Atlas-Indel,Pindel	.											.	ELMOD1	40	.	0			c.504delT						.						128	122	124					11																	107518278		1854	4109	5963	SO:0001589	frameshift_variant	55531	exon7			.	AL359601	CCDS44723.1, CCDS44724.1	11q23.1	2012-10-15	2006-01-20		ENSG00000110675	ENSG00000110675			25334	protein-coding gene	gene with protein product		615456	"ELMO domain containing 1"			12477932	Standard	NM_018712		Approved	DKFZp547C176	uc010rvs.2	Q8N336	OTTHUMG00000166361	ENST00000265840.7:c.505delC	chr11.hg19:g.107518278delC	ENSP00000265840:p.Pro169fs	153.0	0.0		173.0	41.0	NM_018712	B4E167|G5E9S5|Q9NPW3	Frame_Shift_Del	DEL	ENST00000265840.7	hg19	CCDS44723.1																																																																																			.	.		0.403	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389406.1	NM_018712		-	107518278	C	-	107518278	7	5	58	1	0	1	0	1	0	0	0	0	5070	855	30	0	527	0	ELMOD1	11	107518278	Frame_Shift_Del	DEL	C	TCGA-CC-5262-01A-01D-A12Z-10	79402014	107518278	27488238	75	7232										
EI24	9538	hgsc.bcm.edu	37	chr11	125448940	125448940	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gacatgctcttcaaccttttGctgcaggctcttttcctcat	6	13	4	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr11:125448940G>T	ENST00000278903.6	+	7	779	c.537G>T	c.(535-537)ttG>ttT	p.L179F	EI24_ENST00000530985.1_3'UTR|STT3A-AS1_ENST00000532714.1_RNA|STT3A-AS1_ENST00000530526.1_RNA|EI24_ENST00000343678.4_Missense_Mutation_p.L179F	NM_004879.3	NP_004870.3	O14681	EI24_HUMAN	etoposide induced 2.4	179					apoptotic process (GO:0006915)|autophagy (GO:0006914)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of cell growth (GO:0030308)|neuromuscular process controlling balance (GO:0050885)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|response to drug (GO:0042493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(1)|lung(9)|ovary(1)	11	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)		TCAACCTTTTGCTGCAGGCTC	0.438																																					p.L179F		Atlas-SNP	.											.	EI24	33	.	0			c.G537T						.						68	57	61					11																	125448940		1863	4107	5970	SO:0001583	missense	9538	exon7			CCTTTTGCTGCAG	AF010313	CCDS73410.1	11q24.2	2012-11-19	2012-11-16		ENSG00000149547	ENSG00000149547			13276	protein-coding gene	gene with protein product	"ectopic P-granules autophagy protein 4 homolog (C. elegans)"	605170	"etoposide induced 2.4 mRNA"			10594026, 9305847	Standard	NM_001290135		Approved	PIG8, TP53I8, EPG4	uc001qcb.3	O14681	OTTHUMG00000165851	ENST00000278903.6:c.537G>T	chr11.hg19:g.125448940G>T	ENSP00000278903:p.Leu179Phe	152.0	0.0		179.0	15.0	NM_001007277	A8K7D6|B4DKL6|Q9BUQ1	Missense_Mutation	SNP	ENST00000278903.6	hg19		.	.	.	.	.	.	.	.	.	.	G	18.77	3.693754	0.68386	.	.	ENSG00000149547	ENST00000278903;ENST00000343678;ENST00000527842	.	.	.	5.25	4.32	0.51571	.	0.065455	0.64402	D	0.000007	T	0.77452	0.4132	M	0.79693	2.465	0.58432	D	0.999998	D;D;D;D	0.76494	0.999;0.993;0.999;0.999	D;D;D;D	0.91635	0.999;0.992;0.998;0.999	T	0.79361	-0.1835	9	0.72032	D	0.01	-5.9291	10.3522	0.43943	0.1498:0.0:0.8502:0.0	.	165;179;179;179	B4DKL6;E9PM05;A6NES3;O14681	.;.;.;EI24_HUMAN	F	179	.	ENSP00000278903:L179F	L	+	3	2	EI24	124954150	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	0.577000	0.23758	2.615000	0.88500	0.650000	0.86243	TTG	.	.		0.438	EI24-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_004879		T	125448940	G	T	125448940	3	4	58	1	0	0	0	0	1	0	0	0	4987	1310	46	3	559	3	EI24	11	125448940	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	17930662	125448940	9557576	76	7233										
A2ML1	144568	hgsc.bcm.edu	37	chr12	9027104	9027104	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aaaccagcaaccatcaaggtCtatgactactacctaccagg	6	13	2	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr12:9027104C>T	ENST00000299698.7	+	34	4485	c.4305C>T	c.(4303-4305)gtC>gtT	p.V1435V	A2ML1_ENST00000539547.1_Silent_p.V944V	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						CCATCAAGGTCTATGACTACT	0.468																																					p.V1435V		Atlas-SNP	.											.	A2ML1	199	.	0			c.C4305T						.						118	115	116					12																	9027104		2009	4169	6178	SO:0001819	synonymous_variant	144568	exon34			CAAGGTCTATGAC	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.4305C>T	chr12.hg19:g.9027104C>T		92.0	0.0		97.0	26.0	NM_144670		Silent	SNP	ENST00000299698.7	hg19	CCDS8596.2																																																																																			.	.		0.468	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		T	9027104	C	T	9027104	2	4	58	1	0	0	0	0	0	0	0	1	5	900	32	3		3	A2ML1	12	9027104	Silent	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10		9027104	124824791	77	7234										
WBP11	51729	hgsc.bcm.edu	37	chr12	14943652	14943652	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tcgtcctctgaaaattcctcTacttcccgtccctcctcagg	5	17	3	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr12:14943652T>C	ENST00000261167.2	-	10	1280	c.1047A>G	c.(1045-1047)gtA>gtG	p.V349V		NM_016312.2	NP_057396.1	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	349					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein phosphatase type 1 regulator activity (GO:0008599)|single-stranded DNA binding (GO:0003697)|WW domain binding (GO:0050699)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)	30						AAAATTCCTCTACTTCCCGTC	0.403																																					p.V349V		Atlas-SNP	.											.	WBP11	66	.	0			c.A1047G						.						144	136	139					12																	14943652		2203	4300	6503	SO:0001819	synonymous_variant	51729	exon10			TTCCTCTACTTCC	AB029309	CCDS8666.1	12p12.3	2014-06-13			ENSG00000084463	ENSG00000084463			16461	protein-coding gene	gene with protein product	"splicing factor, PQBP1 and PP1 interacting", "protein phosphatase 1, regulatory subunit 165"					10593949	Standard	NM_016312		Approved	NPWBP, SIPP1, PPP1R165	uc001rci.3	Q9Y2W2	OTTHUMG00000168737	ENST00000261167.2:c.1047A>G	chr12.hg19:g.14943652T>C		308.0	0.0		372.0	67.0	NM_016312	Q96AY8	Silent	SNP	ENST00000261167.2	hg19	CCDS8666.1																																																																																			.	.		0.403	WBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400850.1	NM_016312		C	14943652	T	C	14943652	2	2	58	1	0	0	0	0	0	0	0	1	17273	1509	53	2		2	WBP11	12	14943652	Silent	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	5916548	14943652	118908243	78	7235										
SYT10	341359	hgsc.bcm.edu	37	chr12	33592365	33592365	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aagatgcccgagcacttctcCcactccacctggccggcgaa	9	17	1	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr12:33592365C>T	ENST00000228567.3	-	1	389	c.93G>A	c.(91-93)tgG>tgA	p.W31*	SYT10_ENST00000535526.1_5'UTR	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	31					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					AGCACTTCTCCCACTCCACCT	0.652																																					p.W31X		Atlas-SNP	.											.	SYT10	109	.	0			c.G93A						.						176	164	168					12																	33592365		2203	4300	6503	SO:0001587	stop_gained	341359	exon1			CTTCTCCCACTCC	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"Synaptotagmins"	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.93G>A	chr12.hg19:g.33592365C>T	ENSP00000228567:p.Trp31*	130.0	0.0		144.0	12.0	NM_198992	Q495U2	Nonsense_Mutation	SNP	ENST00000228567.3	hg19	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	C	41	8.953365	0.99016	.	.	ENSG00000110975	ENST00000228567	.	.	.	4.41	4.41	0.53225	.	0.210963	0.24117	U	0.041392	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	16.4521	0.83994	0.0:1.0:0.0:0.0	.	.	.	.	X	31	.	ENSP00000228567:W31X	W	-	3	0	SYT10	33483632	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.118000	0.50414	2.376000	0.81061	0.655000	0.94253	TGG	.	.		0.652	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992		T	33592365	C	T	33592365	4	4	58	1	0	0	0	0	0	1	0	0	15481	624	22	3	1506	3	SYT10	12	33592365	Nonsense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	18648713	33592365	100259530	79	7236										
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42858905	42858905	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	agaatcagaggcatggacgtCttcaccaagactgcacgttt	10	10	3	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr12:42858905C>G	ENST00000455697.1	-	7	1216	c.931G>C	c.(931-933)Gac>Cac	p.D311H	PRICKLE1_ENST00000345127.3_Missense_Mutation_p.D311H|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.D311H|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.D311H|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.D311H	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	311	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		GCATGGACGTCTTCACCAAGA	0.507																																					p.D311H		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.G931C						.						111	109	110					12																	42858905		2203	4300	6503	SO:0001583	missense	144165	exon7			GGACGTCTTCACC	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.931G>C	chr12.hg19:g.42858905C>G	ENSP00000401060:p.Asp311His	148.0	0.0		150.0	40.0	NM_001144882	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	hg19	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.572585	0.86542	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	5.33	5.33	0.75918	Zinc finger, LIM-type (1);	0.000000	0.85682	D	0.000000	T	0.78842	0.4347	M	0.67953	2.075	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.80233	-0.1467	10	0.72032	D	0.01	-7.7765	19.3834	0.94546	0.0:1.0:0.0:0.0	.	311	Q96MT3	PRIC1_HUMAN	H	311	ENSP00000401060:D311H;ENSP00000398947:D311H;ENSP00000448359:D311H;ENSP00000345064:D311H;ENSP00000449819:D311H	ENSP00000345064:D311H	D	-	1	0	PRICKLE1	41145172	1.000000	0.71417	0.995000	0.50966	0.847000	0.48162	7.776000	0.85560	2.641000	0.89580	0.650000	0.86243	GAC	.	.		0.507	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			G	42858905	C	G	42858905	3	3	58	1	0	0	0	0	1	0	0	0	12498	913	32	4	1572	4	PRICKLE1	12	42858905	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	9266540	42858905	90992990	80	7237										
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105538197	105538197	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ctctttttttctctctgaatCcaattcggtttttcaatcgt	4	10	4	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr12:105538197C>A	ENST00000332180.5	+	21	2230	c.2143C>A	c.(2143-2145)Cca>Aca	p.P715T		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						CTCTCTGAATCCAATTCGGTT	0.373																																					p.P715T		Atlas-SNP	.											.	KIAA1033	83	.	0			c.C2143A						.						121	117	118					12																	105538197		1804	4078	5882	SO:0001583	missense	23325	exon21			CTGAATCCAATTC	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.2143C>A	chr12.hg19:g.105538197C>A	ENSP00000328062:p.Pro715Thr	367.0	0.0		422.0	75.0	NM_015275		Missense_Mutation	SNP	ENST00000332180.5	hg19	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	C	33	5.272716	0.95429	.	.	ENSG00000136051	ENST00000332180	T	0.49720	0.77	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.69949	0.3168	M	0.81614	2.55	0.80722	D	1	D;D	0.59767	0.986;0.986	P;P	0.59761	0.863;0.863	T	0.71758	-0.4496	10	0.72032	D	0.01	.	20.5934	0.99428	0.0:1.0:0.0:0.0	.	716;715	B7ZKT9;Q2M389	.;WASH7_HUMAN	T	715	ENSP00000328062:P715T	ENSP00000328062:P715T	P	+	1	0	KIAA1033	104062327	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.749000	0.85096	2.872000	0.98467	0.650000	0.86243	CCA	.	.		0.373	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		A	105538197	C	A	105538197	3	1	58	1	0	0	0	0	1	0	0	0	8215	855	30	3	2225	3	KIAA1033	12	105538197	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	62679292	105538197	28313698	81	7238										
PAN3	255967	hgsc.bcm.edu	37	chr13	28794510	28794510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ccctgctactgctggattagCgccaggtaagttgagtaact	11	10	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr13:28794510C>T	ENST00000380958.3	+	6	1147	c.995C>T	c.(994-996)gCg>gTg	p.A332V	PAN3_ENST00000399613.1_Missense_Mutation_p.A132V	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit											endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		GCTGGATTAGCGCCAGGTAAG	0.423																																					p.A332V		Atlas-SNP	.											.	PAN3	123	.	0			c.C995T						.						162	163	163					13																	28794510		2203	4300	6503	SO:0001583	missense	255967	exon6			GATTAGCGCCAGG	AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.995C>T	chr13.hg19:g.28794510C>T	ENSP00000370345:p.Ala332Val	86.0	0.0		127.0	27.0	NM_175854		Missense_Mutation	SNP	ENST00000380958.3	hg19	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	C	18.99	3.740449	0.69304	.	.	ENSG00000152520	ENST00000380958;ENST00000399613	T;T	0.47869	0.83;0.87	5.6	5.6	0.85130	.	0.050294	0.85682	D	0.000000	T	0.35098	0.0920	N	0.19112	0.55	0.80722	D	1	P;P;B	0.51791	0.948;0.669;0.44	B;B;B	0.39503	0.301;0.036;0.016	T	0.11567	-1.0582	10	0.29301	T	0.29	-13.567	19.6153	0.95632	0.0:1.0:0.0:0.0	.	332;332;278	Q58A45-4;Q58A45;Q58A45-3	.;PAN3_HUMAN;.	V	332;132	ENSP00000370345:A332V;ENSP00000382522:A132V	ENSP00000370345:A332V	A	+	2	0	PAN3	27692510	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	5.642000	0.67888	2.630000	0.89119	0.555000	0.69702	GCG	.	.		0.423	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854		T	28794510	C	T	28794510	3	4	58	1	0	0	0	0	1	0	0	0	11424	768	27	1	1017	1	PAN3	13	28794510	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10		28794510	86375368	82	7239										
OR4N5	390437	hgsc.bcm.edu	37	chr14	20612277	20612277	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ccgctacatcgccatctgccGgcctttacactattcaacca	5	17	2	0	rs139546094		TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr14:20612277G>A	ENST00000333629.1	+	1	383	c.383G>A	c.(382-384)cGg>cAg	p.R128Q	RNA5SP381_ENST00000516076.1_RNA	NM_001004724.1	NP_001004724.1	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N, member 5	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(23)|ovary(1)|skin(2)|urinary_tract(1)	29	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)		GCCATCTGCCGGCCTTTACAC	0.488																																					p.R128Q		Atlas-SNP	.											.	OR4N5	72	.	0			c.G383A						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	165	161	163		383	-0.2	0	14	dbSNP_134	163	0,8600		0,0,4300	no	missense	OR4N5	NM_001004724.1	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	128/309	20612277	1,13005	2203	4300	6503	SO:0001583	missense	390437	exon1			TCTGCCGGCCTTT		CCDS32031.1	14q11.2	2013-09-23			ENSG00000184394	ENSG00000184394		"GPCR / Class A : Olfactory receptors"	15358	protein-coding gene	gene with protein product							Standard	NM_001004724		Approved		uc010tla.2	Q8IXE1	OTTHUMG00000170784	ENST00000333629.1:c.383G>A	chr14.hg19:g.20612277G>A	ENSP00000332110:p.Arg128Gln	347.0	0.0		416.0	100.0	NM_001004724	Q6IF11	Missense_Mutation	SNP	ENST00000333629.1	hg19	CCDS32031.1	.	.	.	.	.	.	.	.	.	.	G	4.710	0.131999	0.08981	2.27E-4	0.0	ENSG00000184394	ENST00000333629	T	0.00392	7.58	4.0	-0.184	0.13280	GPCR, rhodopsin-like superfamily (1);	0.597438	0.13923	N	0.353453	T	0.00210	0.0006	L	0.28014	0.82	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.34104	-0.9842	10	0.54805	T	0.06	.	7.4878	0.27443	0.5469:0.0:0.4531:0.0	.	128	Q8IXE1	OR4N5_HUMAN	Q	128	ENSP00000332110:R128Q	ENSP00000332110:R128Q	R	+	2	0	OR4N5	19682117	0.000000	0.05858	0.000000	0.03702	0.158000	0.22134	-0.209000	0.09358	-0.147000	0.11254	-0.136000	0.14681	CGG	.	G|1.000;A|0.000		0.488	OR4N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410347.1			A	20612277	G	A	20612277	3	1	58	1	0	0	0	0	1	0	0	0	11088	1116	39	1	385	1	OR4N5	14	20612277	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10		20612277	86737263	83	7240										
ADAM10	102	hgsc.bcm.edu	37	chr15	58902701	58902701	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gcacagaccctgtactggcaCaagttgatgggtccactgga	12	11	0	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr15:58902701C>A	ENST00000260408.3	-	14	2263	c.1820G>T	c.(1819-1821)tGt>tTt	p.C607F	ADAM10_ENST00000396140.2_Missense_Mutation_p.C306F|ADAM10_ENST00000402627.1_Intron|ADAM10_ENST00000561288.1_Intron	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	607	Cys-rich.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		TGTACTGGCACAAGTTGATGG	0.438																																					p.C607F		Atlas-SNP	.											.	ADAM10	59	.	0			c.G1820T						.						60	58	59					15																	58902701		2192	4292	6484	SO:0001583	missense	102	exon14			CTGGCACAAGTTG	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"ADAM metallopeptidase domain containing", "CD molecules"	188	protein-coding gene	gene with protein product		602192	"a disintegrin and metalloproteinase domain 10"			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.1820G>T	chr15.hg19:g.58902701C>A	ENSP00000260408:p.Cys607Phe	96.0	0.0		115.0	23.0	NM_001110	B4DU28|Q10742|Q92650	Missense_Mutation	SNP	ENST00000260408.3	hg19	CCDS10167.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.592056	0.86953	.	.	ENSG00000137845	ENST00000260408;ENST00000396136;ENST00000396140	T;T	0.33654	1.4;2.82	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.69233	0.3088	M	0.90198	3.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.75921	-0.3147	10	0.87932	D	0	-18.8648	19.4747	0.94982	0.0:1.0:0.0:0.0	.	306;426;607	B4DU28;A8MY20;O14672	.;.;ADA10_HUMAN	F	607;426;306	ENSP00000260408:C607F;ENSP00000379444:C306F	ENSP00000260408:C607F	C	-	2	0	ADAM10	56689993	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.445000	0.80570	2.666000	0.90696	0.655000	0.94253	TGT	.	.		0.438	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110		A	58902701	C	A	58902701	3	1	58	1	0	0	0	0	1	0	0	0	234	478	17	3	438	3	ADAM10	15	58902701	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10		58902701	43628691	84	7241										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75983035	75983035	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cgttcagaaacccatcgactGacaacgtggcccagccctct	8	16	2	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr15:75983035G>A	ENST00000308508.5	-	3	463	c.371C>T	c.(370-372)tCa>tTa	p.S124L		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	124	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCCATCGACTGACAACGTGGC	0.632																																					p.S124L		Atlas-SNP	.											.	CSPG4	175	.	0			c.C371T						.						64	65	65					15																	75983035		2197	4294	6491	SO:0001583	missense	1464	exon3			TCGACTGACAACG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.371C>T	chr15.hg19:g.75983035G>A	ENSP00000312506:p.Ser124Leu	225.0	0.0		260.0	58.0	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	hg19	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	15.27	2.783403	0.49891	.	.	ENSG00000173546	ENST00000308508	T	0.78126	-1.15	4.76	2.73	0.32206	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.348037	0.23646	N	0.045972	T	0.64746	0.2626	L	0.38838	1.175	0.37045	D	0.897329	B	0.02656	0.0	B	0.08055	0.003	T	0.61168	-0.7117	10	0.31617	T	0.26	.	8.3308	0.32184	0.0889:0.1572:0.7538:0.0	.	124	Q6UVK1	CSPG4_HUMAN	L	124	ENSP00000312506:S124L	ENSP00000312506:S124L	S	-	2	0	CSPG4	73770090	0.999000	0.42202	0.198000	0.23420	0.011000	0.07611	2.949000	0.49074	0.998000	0.38996	0.555000	0.69702	TCA	.	.		0.632	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		A	75983035	G	A	75983035	3	1	58	1	0	0	0	0	1	0	0	0	3962	1294	45	3	6629	3	CSPG4	15	75983035	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	17080334	75983035	26548357	85	7242										
LRRC28	123355	hgsc.bcm.edu	37	chr15	99796167	99796167	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tgggatatattcagtcatggCgtccgaactttgtaagacga	11	7	2	1	rs539126226		TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr15:99796167C>T	ENST00000301981.3	+	2	245	c.5C>T	c.(4-6)gCg>gTg	p.A2V	LRRC28_ENST00000442993.2_Missense_Mutation_p.A2V|LRRC28_ENST00000559399.1_3'UTR|LRRC28_ENST00000422500.2_Missense_Mutation_p.A2V|LRRC28_ENST00000447360.2_Missense_Mutation_p.A2V|LRRC28_ENST00000558879.1_Missense_Mutation_p.A2V|AC022819.1_ENST00000581052.1_RNA|LRRC28_ENST00000331450.5_Missense_Mutation_p.A2V	NM_144598.2	NP_653199.2	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	2										endometrium(2)|large_intestine(3)|lung(6)|prostate(1)	12	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			TCAGTCATGGCGTCCGAACTT	0.378																																					p.A2V		Atlas-SNP	.											.	LRRC28	38	.	0			c.C5T						.						92	87	88					15																	99796167		2197	4297	6494	SO:0001583	missense	123355	exon2			TCATGGCGTCCGA	AK091588	CCDS10380.1, CCDS66873.1	15q26.3	2004-06-29			ENSG00000168904	ENSG00000168904			28355	protein-coding gene	gene with protein product						12975309	Standard	XM_005254861		Approved	MGC24976, FLJ34269, FLJ45242	uc002bva.1	Q86X40	OTTHUMG00000149854	ENST00000301981.3:c.5C>T	chr15.hg19:g.99796167C>T	ENSP00000304923:p.Ala2Val	141.0	0.0		191.0	19.0	NM_144598	A8KA22|Q6UY49|Q6ZSS6	Missense_Mutation	SNP	ENST00000301981.3	hg19	CCDS10380.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.155429	0.78114	.	.	ENSG00000168904	ENST00000301981;ENST00000447360;ENST00000422500;ENST00000442993;ENST00000331450	T;T;T;T	0.53206	0.78;0.63;1.45;0.86	5.78	5.78	0.91487	.	0.050961	0.85682	D	0.000000	T	0.56587	0.1995	N	0.19112	0.55	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;0.999	D;D;D;D	0.76071	0.986;0.987;0.981;0.98	T	0.58498	-0.7626	10	0.51188	T	0.08	.	19.0086	0.92863	0.0:1.0:0.0:0.0	.	2;2;2;2	B4DHL3;Q8WUS2;Q86X40-2;Q86X40	.;.;.;LRC28_HUMAN	V	2	ENSP00000304923:A2V;ENSP00000404520:A2V;ENSP00000398606:A2V;ENSP00000404206:A2V	ENSP00000304923:A2V	A	+	2	0	LRRC28	97613690	1.000000	0.71417	0.953000	0.39169	0.798000	0.45092	5.554000	0.67294	2.729000	0.93468	0.650000	0.86243	GCG	.	.		0.378	LRRC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313546.1	NM_144598		T	99796167	C	T	99796167	3	4	58	1	0	0	0	0	1	0	0	0	8991	768	27	1	7	1	LRRC28	15	99796167	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	23813132	99796167	2735225	86	7243										
STUB1	339123	hgsc.bcm.edu	37	chr16	732214	732214	+	3'UTR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	caagatcagctttgagctgaTgcgggagccgtgcatcacgc	13	11	2	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr16:732214T>C	ENST00000293882.4	-	0	1584				JMJD8_ENST00000609261.1_3'UTR|JMJD8_ENST00000412368.2_3'UTR|LA16c-313D11.9_ENST00000571933.1_RNA|STUB1_ENST00000564370.1_Missense_Mutation_p.M168T|STUB1_ENST00000219548.4_Missense_Mutation_p.M240T|JMJD8_ENST00000454700.1_3'UTR|STUB1_ENST00000565677.1_Missense_Mutation_p.M168T|LA16c-313D11.9_ENST00000567091.1_RNA			Q96S16	JMJD8_HUMAN	jumonji domain containing 8							extracellular vesicular exosome (GO:0070062)				breast(1)	1						TTTGAGCTGATGCGGGAGCCG	0.637																																					p.M240T		Atlas-SNP	.											.	STUB1	26	.	0			c.T719C						.						87	76	79					16																	732214		2201	4297	6498	SO:0001624	3_prime_UTR_variant	10273	exon6			AGCTGATGCGGGA		CCDS45369.1	16p13.3	2008-07-28	2008-07-28	2008-07-28		ENSG00000161999			14148	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 20"	C16orf20			Standard	NM_001005920		Approved		uc002ciw.1	Q96S16		ENST00000293882.4:c.*580A>G	chr16.hg19:g.732214T>C		96.0	0.0		56.0	22.0	NM_005861	B2RNS7|D3DU58|Q4PKE3|Q4VBY1|Q6GMW5|Q71RB8	Missense_Mutation	SNP	ENST00000293882.4	hg19		.	.	.	.	.	.	.	.	.	.	T	18.29	3.590335	0.66105	.	.	ENSG00000103266	ENST00000219548	T	0.34859	1.34	4.3	4.3	0.51218	Zinc finger, RING/FYVE/PHD-type (1);U box domain (2);	0.000000	0.85682	D	0.000000	T	0.68824	0.3043	H	0.94658	3.565	0.80722	D	1	D	0.69078	0.997	D	0.87578	0.998	T	0.78560	-0.2157	10	0.87932	D	0	-32.0609	13.1338	0.59397	0.0:0.0:0.0:1.0	.	240	Q9UNE7	CHIP_HUMAN	T	240	ENSP00000219548:M240T	ENSP00000219548:M240T	M	+	2	0	STUB1	672215	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.775000	0.85489	1.947000	0.56498	0.449000	0.29647	ATG	.	.		0.637	JMJD8-201	KNOWN	basic	protein_coding	protein_coding		NM_001005920		C	732214	T	C	732214	1	2	58	0	1	0	0	0	0	0	0	0	15350	1464	51	2		2	STUB1	16	732214	3'UTR	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10		732214	89622539	87	7244										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21031159	21031159	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tgacaggccttcacctaattCcatttcctcctcttctactg	4	15	3	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr16:21031159C>T	ENST00000261383.3	-	41	5808	c.5809G>A	c.(5809-5811)Gaa>Aaa	p.E1937K	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1937					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TCACCTAATTCCATTTCCTCC	0.483																																					p.E1937K		Atlas-SNP	.											.	DNAH3	1142	.	0			c.G5809A						.						85	79	81					16																	21031159		2201	4300	6501	SO:0001583	missense	55567	exon41			CTAATTCCATTTC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.5809G>A	chr16.hg19:g.21031159C>T	ENSP00000261383:p.Glu1937Lys	481.0	0.0		434.0	93.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	9.251	1.040814	0.19669	.	.	ENSG00000158486	ENST00000261383	T	0.26957	1.7	5.46	5.46	0.80206	.	0.640158	0.15150	N	0.277762	T	0.16471	0.0396	N	0.16790	0.44	0.80722	D	1	P	0.37781	0.608	B	0.35413	0.202	T	0.07578	-1.0765	10	0.09338	T	0.73	.	16.8701	0.86038	0.0:1.0:0.0:0.0	.	1937	Q8TD57	DYH3_HUMAN	K	1937	ENSP00000261383:E1937K	ENSP00000261383:E1937K	E	-	1	0	DNAH3	20938660	0.875000	0.30112	0.065000	0.19835	0.078000	0.17371	2.276000	0.43408	2.597000	0.87782	0.558000	0.71614	GAA	.	.		0.483	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	21031159	C	T	21031159	3	4	58	1	0	0	0	0	1	0	0	0	4605	864	30	3	6628	3	DNAH3	16	21031159	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	20298945	21031159	69323594	88	7245										
POLR2A	5430	hgsc.bcm.edu	37	chr17	7404887	7404887	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	atgagctggagcccaccccaGggaacactctgcggcagacg	13	14	1	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr17:7404887G>T	ENST00000322644.6	+	14	2587	c.2188G>T	c.(2188-2190)Ggg>Tgg	p.G730W		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	730					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				GCCCACCCCAGGGAACACTCT	0.537																																					p.G730W		Atlas-SNP	.											.	POLR2A	157	.	0			c.G2188T						.						71	70	70					17																	7404887		2203	4300	6503	SO:0001583	missense	5430	exon14			ACCCCAGGGAACA			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.2188G>T	chr17.hg19:g.7404887G>T	ENSP00000314949:p.Gly730Trp	88.0	0.0		96.0	34.0	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.879958	0.72294	.	.	ENSG00000181222	ENST00000535204;ENST00000322644	T	0.79653	-1.29	6.17	4.21	0.49690	RNA polymerase Rpb1, domain 4 (1);	0.000000	0.85682	D	0.000000	D	0.94162	0.8127	H	0.99634	4.67	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95088	0.8219	10	0.87932	D	0	-12.5474	12.2619	0.54655	0.1385:0.0:0.8615:0.0	.	730	P24928	RPB1_HUMAN	W	686;730	ENSP00000314949:G730W	ENSP00000314949:G730W	G	+	1	0	SLC35G6	7345611	1.000000	0.71417	0.935000	0.37517	0.935000	0.57460	9.639000	0.98448	0.955000	0.37878	-0.140000	0.14226	GGG	.	.		0.537	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		T	7404887	G	T	7404887	3	4	58	1	0	0	0	0	1	0	0	0	12223	1000	35	3	2242	3	POLR2A	17	7404887	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10		7404887	73790323	89	7246										
TEKT3	64518	hgsc.bcm.edu	37	chr17	15211984	15211984	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ttcccctcccaccttaccgtAgctgagccatgtctcggcac	7	18	1	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr17:15211984A>T	ENST00000395930.1	-	8	1439	c.1253T>A	c.(1252-1254)cTa>cAa	p.L418Q	TEKT3_ENST00000338696.2_Missense_Mutation_p.L418Q|TEKT3_ENST00000462175.1_5'Flank|RNU6-799P_ENST00000363567.1_RNA	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	418					cilium morphogenesis (GO:0060271)|regulation of fertilization (GO:0080154)|sperm motility (GO:0030317)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				endometrium(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	23				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		ACCTTACCGTAGCTGAGCCAT	0.592																																					p.L418Q		Atlas-SNP	.											.	TEKT3	64	.	0			c.T1253A						.						162	130	141					17																	15211984		2203	4300	6503	SO:0001583	missense	64518	exon8			TACCGTAGCTGAG	AF334676	CCDS11169.1	17p12	2011-05-23			ENSG00000125409	ENSG00000125409			14293	protein-coding gene	gene with protein product		612683				11381029, 14735490	Standard	NM_031898		Approved	FLJ32828	uc002gon.3	Q9BXF9	OTTHUMG00000058965	ENST00000395930.1:c.1253T>A	chr17.hg19:g.15211984A>T	ENSP00000379263:p.Leu418Gln	163.0	0.0		110.0	20.0	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Missense_Mutation	SNP	ENST00000395930.1	hg19	CCDS11169.1	.	.	.	.	.	.	.	.	.	.	A	4.479	0.088802	0.08583	.	.	ENSG00000125409	ENST00000395930;ENST00000338696	T;T	0.02472	4.28;4.28	5.31	5.31	0.75309	.	0.180261	0.49916	D	0.000126	T	0.07098	0.0180	L	0.42245	1.32	0.09310	N	0.999999	P	0.52463	0.953	P	0.54431	0.752	T	0.33752	-0.9856	10	0.28530	T	0.3	.	14.7337	0.69402	1.0:0.0:0.0:0.0	.	418	Q9BXF9	TEKT3_HUMAN	Q	418	ENSP00000379263:L418Q;ENSP00000343995:L418Q	ENSP00000343995:L418Q	L	-	2	0	TEKT3	15152709	0.931000	0.31567	0.040000	0.18447	0.008000	0.06430	8.241000	0.89816	2.142000	0.66516	0.533000	0.62120	CTA	.	.		0.592	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898		T	15211984	A	T	15211984	3	4	58	1	0	0	0	0	1	0	0	0	15769	420	15	4	227	4	TEKT3	17	15211984	Missense_Mutation	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	7807097	15211984	65983226	90	7247										
NAGLU	4669	hgsc.bcm.edu	37	chr17	40696106	40696106	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cagggcatccctttccaacaGcaccagtttgacaaaaatgt	7	12	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr17:40696106G>A	ENST00000225927.2	+	6	2183	c.2082G>A	c.(2080-2082)caG>caA	p.Q694Q	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	694					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	CTTTCCAACAGCACCAGTTTG	0.602																																					p.Q694Q		Atlas-SNP	.											.	NAGLU	36	.	0			c.G2082A						.						50	46	47					17																	40696106		2203	4300	6503	SO:0001819	synonymous_variant	4669	exon6			CCAACAGCACCAG		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"Sanfilippo disease IIIB"	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.2082G>A	chr17.hg19:g.40696106G>A		70.0	0.0		63.0	16.0	NM_000263		Silent	SNP	ENST00000225927.2	hg19	CCDS11427.1																																																																																			.	.		0.602	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		A	40696106	G	A	40696106	2	1	58	1	0	0	0	0	0	0	0	1	10152	962	34	3		3	NAGLU	17	40696106	Silent	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	25484122	40696106	40499104	91	7248										
RSAD1	55316	hgsc.bcm.edu	37	chr17	48557383	48557383	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aggctaatcctacttcagctCcgggctccagactggcagag	11	13	1	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr17:48557383C>G	ENST00000258955.2	+	3	497	c.412C>G	c.(412-414)Ccg>Gcg	p.P138A		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	138					porphyrin-containing compound biosynthetic process (GO:0006779)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|coproporphyrinogen oxidase activity (GO:0004109)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TACTTCAGCTCCGGGCTCCAG	0.617											OREG0024566	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P138A		Atlas-SNP	.											.	RSAD1	36	.	0			c.C412G						.						60	66	64					17																	48557383		2203	4300	6503	SO:0001583	missense	55316	exon3			TCAGCTCCGGGCT	AK002026	CCDS11569.1	17q21.33	2004-11-08			ENSG00000136444	ENSG00000136444			25634	protein-coding gene	gene with protein product						12477932	Standard	NM_018346		Approved	FLJ11164	uc002iqw.1	Q9HA92	OTTHUMG00000162126	ENST00000258955.2:c.412C>G	chr17.hg19:g.48557383C>G	ENSP00000258955:p.Pro138Ala	144.0	0.0	955	131.0	20.0	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Missense_Mutation	SNP	ENST00000258955.2	hg19	CCDS11569.1	.	.	.	.	.	.	.	.	.	.	C	6.757	0.508464	0.12883	.	.	ENSG00000136444	ENST00000258955	T	0.22539	1.95	4.64	1.29	0.21616	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);Radical SAM (1);	0.455201	0.23424	N	0.048323	T	0.07683	0.0193	N	0.03983	-0.305	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.14023	0.01;0.001	T	0.22417	-1.0217	10	0.62326	D	0.03	-1.4563	3.8695	0.09030	0.2145:0.3296:0.3721:0.0837	.	138;138	B4DEV9;Q9HA92	.;RSAD1_HUMAN	A	138	ENSP00000258955:P138A	ENSP00000258955:P138A	P	+	1	0	RSAD1	45912382	0.033000	0.19621	0.658000	0.29665	0.026000	0.11368	1.111000	0.31159	0.544000	0.28883	0.491000	0.48974	CCG	.	.		0.617	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346		G	48557383	C	G	48557383	3	3	58	1	0	0	0	0	1	0	0	0	13709	855	30	4	422	4	RSAD1	17	48557383	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	7861277	48557383	32637827	92	7249										
MRC2	9902	hgsc.bcm.edu	37	chr17	60744895	60744895	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ggccgagcccacccctccagGtgagccagggactgtgccgc	14	17	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr17:60744895G>T	ENST00000303375.5	+	6	1519		c.e6+1			NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2						collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						ACCCCTCCAGGTGAGCCAGGG	0.687																																					.		Atlas-SNP	.											.	MRC2	126	.	0			c.1117+1G>T						.						39	36	37					17																	60744895		2203	4300	6503	SO:0001630	splice_region_variant	9902	exon6			CTCCAGGTGAGCC	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.1117+1G>T	chr17.hg19:g.60744895G>T		34.0	0.0		32.0	7.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Splice_Site	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686684	0.88639	.	.	ENSG00000011028	ENST00000303375	.	.	.	4.69	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9212	0.70838	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MRC2	58098627	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.534000	0.90620	2.425000	0.82216	0.462000	0.41574	.	.	.		0.687	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		Intron	T	60744895	G	T	60744895	5	4	58	1	0	0	0	0	0	0	1	0	9767	1275	44	3	1140	3	MRC2	17	60744895	Splice_Site	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	12187512	60744895	20450315	93	7250										
STRADA	92335	hgsc.bcm.edu	37	chr17	61788154	61788154	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aaaagtggctcgatatggcaCgatattgggatggttgaaga	14	4	0	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr17:61788154C>A	ENST00000336174.6	-	7	503	c.391G>T	c.(391-393)Gtg>Ttg	p.V131L	STRADA_ENST00000447001.3_Missense_Mutation_p.V87L|RP11-51F16.8_ENST00000580553.1_3'UTR|STRADA_ENST00000245865.5_Missense_Mutation_p.V73L|STRADA_ENST00000582137.1_Missense_Mutation_p.V102L|STRADA_ENST00000392950.4_Missense_Mutation_p.V94L|STRADA_ENST00000580039.1_5'UTR|STRADA_ENST00000579340.1_Missense_Mutation_p.V73L|STRADA_ENST00000375840.4_Missense_Mutation_p.V73L	NM_001003787.2	NP_001003787.1	Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha	131	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|protein export from nucleus (GO:0006611)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|prostate(2)	13						CGATATGGCACGATATTGGGA	0.483																																					p.V131L		Atlas-SNP	.											.	STRADA	27	.	0			c.G391T						.						150	120	130					17																	61788154		2203	4300	6503	SO:0001583	missense	92335	exon7			ATGGCACGATATT	AF308302	CCDS11642.1, CCDS32703.1, CCDS42367.1, CCDS54156.1, CCDS58585.1	17q23.3	2014-09-04			ENSG00000266173	ENSG00000266173			30172	protein-coding gene	gene with protein product	"STE20-like pseudokinase"	608626				12805220, 17921699	Standard	NM_153335		Approved	NY-BR-96, LYK5, Stlk, STRAD	uc002jbm.3	Q7RTN6	OTTHUMG00000178908	ENST00000336174.6:c.391G>T	chr17.hg19:g.61788154C>A	ENSP00000336655:p.Val131Leu	127.0	0.0		156.0	28.0	NM_001003787	B4DDE3|B4DW17|J3KTC9|Q5JPI2|Q7Z4K9|Q8NC31|Q8NCF1|Q9H272	Missense_Mutation	SNP	ENST00000336174.6	hg19	CCDS32703.1	.	.	.	.	.	.	.	.	.	.	C	12.69	2.014291	0.35511	.	.	ENSG00000125695	ENST00000336174;ENST00000375840;ENST00000447001;ENST00000392950;ENST00000245865	T;T;T;T	0.70164	-0.46;-0.46;-0.46;1.24	4.97	1.9	0.25705	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.446177	0.23635	N	0.046087	T	0.39784	0.1091	N	0.11023	0.085	0.37101	D	0.8999	B;B;B;B;B;B;B	0.14438	0.0;0.003;0.004;0.0;0.001;0.01;0.001	B;B;B;B;B;B;B	0.16289	0.001;0.005;0.009;0.002;0.001;0.015;0.005	T	0.37244	-0.9714	10	0.05436	T	0.98	.	10.8638	0.46842	0.0:0.6327:0.2905:0.0768	.	102;87;73;73;94;94;131	B4DW17;B4DDE3;Q5JPI2;Q86YC8;Q7RTN6-2;Q7RTN6-3;Q7RTN6	.;.;.;.;.;.;STRAA_HUMAN	L	131;73;87;94;93	ENSP00000336655:V131L;ENSP00000365000:V73L;ENSP00000398841:V87L;ENSP00000376677:V94L	ENSP00000245865:V93L	V	-	1	0	STRADA	59141886	1.000000	0.71417	0.971000	0.41717	0.949000	0.60115	2.178000	0.42519	0.295000	0.22570	0.561000	0.74099	GTG	.	.		0.483	STRADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443894.1			A	61788154	C	A	61788154	3	1	58	1	0	0	0	0	1	0	0	0	15339	536	19	1	990	1	STRADA	17	61788154	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	1043259	61788154	19407056	94	7251										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62018994	62018994	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gttggggtcacagtctggggGcccgctgttgaggatggggt	20	7	2	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr17:62018994G>T	ENST00000435607.1	-	24	4724	c.4648C>A	c.(4648-4650)Ccc>Acc	p.P1550T	SCN4A_ENST00000578147.1_Missense_Mutation_p.P1550T	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1550					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAGTCTGGGGGCCCGCTGTTG	0.602																																					p.P1550T		Atlas-SNP	.											.	SCN4A	205	.	0			c.C4648A						.						30	35	34					17																	62018994		2125	4249	6374	SO:0001583	missense	6329	exon24			CTGGGGGCCCGCT	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.4648C>A	chr17.hg19:g.62018994G>T	ENSP00000396320:p.Pro1550Thr	115.0	0.0		92.0	21.0	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	g	16.51	3.144501	0.57044	.	.	ENSG00000007314	ENST00000435607	D	0.97279	-4.32	3.9	3.9	0.45041	Ion transport (1);	0.165679	0.53938	D	0.000044	D	0.98210	0.9408	M	0.88979	2.995	0.52501	D	0.999958	D	0.63880	0.993	P	0.58928	0.848	D	0.98956	1.0796	10	0.66056	D	0.02	.	15.4266	0.75055	0.0:0.0:1.0:0.0	.	1550	P35499	SCN4A_HUMAN	T	1550	ENSP00000396320:P1550T	ENSP00000396320:P1550T	P	-	1	0	SCN4A	59372726	1.000000	0.71417	1.000000	0.80357	0.711000	0.40976	4.067000	0.57527	2.177000	0.69029	0.556000	0.70494	CCC	.	.		0.602	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62018994	G	T	62018994	3	4	58	1	0	0	0	0	1	0	0	0	13935	1203	42	3	866	3	SCN4A	17	62018994	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	230840	62018994	19176216	95	7252										
RPTOR	57521	hgsc.bcm.edu	37	chr17	78704429	78704429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tgggcagcccgtcgatcttcGtctacgactgctccaatgct	10	14	2	0			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr17:78704429G>A	ENST00000306801.3	+	5	939	c.577G>A	c.(577-579)Gtc>Atc	p.V193I	RPTOR_ENST00000544334.2_Missense_Mutation_p.V193I|RPTOR_ENST00000570891.1_Missense_Mutation_p.V193I|RPTOR_ENST00000537330.1_Missense_Mutation_p.V8I	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	193					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.V193I(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						GTCGATCTTCGTCTACGACTG	0.537																																					p.V193I		Atlas-SNP	.											RPTOR,caecum,carcinoma,-1,1	RPTOR	122	.	1	Substitution - Missense(1)	lung(1)	c.G577A						.						136	98	111					17																	78704429		2203	4300	6503	SO:0001583	missense	57521	exon5			ATCTTCGTCTACG		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.577G>A	chr17.hg19:g.78704429G>A	ENSP00000307272:p.Val193Ile	134.0	0.0		131.0	16.0	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	hg19	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.697643	0.68386	.	.	ENSG00000141564	ENST00000537330;ENST00000306801;ENST00000544334	T;T	0.57436	0.4;0.5	4.77	4.77	0.60923	.	0.000000	0.64402	D	0.000001	T	0.69115	0.3075	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	0.981;0.995;1.0	D;P;D	0.65010	0.931;0.686;0.927	T	0.66172	-0.5990	10	0.25106	T	0.35	.	17.9664	0.89100	0.0:0.0:1.0:0.0	.	193;8;193	F5H7J5;F5GXV9;Q8N122	.;.;RPTOR_HUMAN	I	8;193;193	ENSP00000307272:V193I;ENSP00000442479:V193I	ENSP00000307272:V193I	V	+	1	0	RPTOR	76319024	1.000000	0.71417	0.978000	0.43139	0.373000	0.29922	9.534000	0.98061	2.445000	0.82738	0.655000	0.94253	GTC	.	.		0.537	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		A	78704429	G	A	78704429	3	1	58	1	0	0	0	0	1	0	0	0	13680	1145	40	1	595	1	RPTOR	17	78704429	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	16685435	78704429	2490781	96	7253										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43532588	43532588	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gcgatgatagctgaaaacttTcacttgatctgcacagatac	8	9	2	4			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr18:43532588T>C	ENST00000282041.5	-	3	1064	c.1030A>G	c.(1030-1032)Aaa>Gaa	p.K344E		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	344					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CTGAAAACTTTCACTTGATCT	0.413																																					p.K344E		Atlas-SNP	.											.	EPG5	199	.	0			c.A1030G						.						88	86	86					18																	43532588		1893	4118	6011	SO:0001583	missense	57724	exon3			AAACTTTCACTTG	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.1030A>G	chr18.hg19:g.43532588T>C	ENSP00000282041:p.Lys344Glu	341.0	0.0		430.0	71.0	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	T	28.0	4.883644	0.91740	.	.	ENSG00000152223	ENST00000282041	T	0.80824	-1.42	5.59	5.59	0.84812	.	0.257192	0.45126	D	0.000391	D	0.87669	0.6235	L	0.56769	1.78	0.54753	D	0.999983	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.87245	0.2269	10	0.44086	T	0.13	-19.4113	16.065	0.80865	0.0:0.0:0.0:1.0	.	344;344	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	E	344	ENSP00000282041:K344E	ENSP00000282041:K344E	K	-	1	0	EPG5	41786586	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.782000	0.68973	2.257000	0.74773	0.460000	0.39030	AAA	.	.		0.413	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43532588	T	C	43532588	3	2	58	1	0	0	0	0	1	0	0	0	8258	1792	62	2	6877	2	KIAA1632	18	43532588	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10		43532588	34544660	97	7254										
LRG1	116844	hgsc.bcm.edu	37	chr19	4538064	4538064	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tttgggcctgaagccaacgaTagaggtcgctcaggttctgg	14	9	2	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr19:4538064T>C	ENST00000306390.6	-	2	1392	c.932A>G	c.(931-933)tAt>tGt	p.Y311C	PLIN5_ENST00000381848.3_5'Flank|CTB-50L17.14_ENST00000586020.1_Intron|PLIN5_ENST00000586133.1_5'Flank|LRG1_ENST00000586883.1_5'Flank	NM_052972.2	NP_443204.1	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1	311	LRRCT.				brown fat cell differentiation (GO:0050873)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				NS(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGCCAACGATAGAGGTCGCT	0.602																																					p.Y311C		Atlas-SNP	.											.	LRG1	25	.	0			c.A932G						.						74	68	70					19																	4538064		2203	4300	6503	SO:0001583	missense	116844	exon2			CAACGATAGAGGT		CCDS12130.1	19p13.3	2013-09-20			ENSG00000171236	ENSG00000171236			29480	protein-coding gene	gene with protein product	"leucine rich alpha 2 glycoprotein"	611289				3856868, 12223515	Standard	NM_052972		Approved	LRG	uc002mau.3	P02750	OTTHUMG00000182010	ENST00000306390.6:c.932A>G	chr19.hg19:g.4538064T>C	ENSP00000302621:p.Tyr311Cys	91.0	0.0		101.0	15.0	NM_052972	Q8N4F5|Q96QZ4	Missense_Mutation	SNP	ENST00000306390.6	hg19	CCDS12130.1	.	.	.	.	.	.	.	.	.	.	.	9.954	1.221030	0.22457	.	.	ENSG00000171236	ENST00000306390;ENST00000538589	T	0.02323	4.34	5.24	-8.8	0.00817	Cysteine-rich flanking region, C-terminal (1);	1.160920	0.06603	N	0.754204	T	0.01661	0.0053	N	0.25201	0.72	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44682	-0.9312	10	0.38643	T	0.18	2.0E-4	2.1433	0.03780	0.5087:0.2058:0.1036:0.1819	.	311	P02750	A2GL_HUMAN	C	311;294	ENSP00000302621:Y311C	ENSP00000302621:Y311C	Y	-	2	0	LRG1	4489064	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.425000	0.02446	-2.408000	0.00573	-0.301000	0.09380	TAT	.	.		0.602	LRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458654.2	NM_052972		C	4538064	T	C	4538064	3	2	58	1	0	0	0	0	1	0	0	0	8951	1406	49	2	115	2	LRG1	19	4538064	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10		4538064	54590919	98	7255										
MUC16	94025	hgsc.bcm.edu	37	chr19	9020787	9020787	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	gagagaggtcagtctgcagcCagagtacagagggccaacac	14	10	2	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr19:9020787C>A	ENST00000397910.4	-	20	37518	c.37315G>T	c.(37315-37317)Ggc>Tgc	p.G12439C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12441	SEA 3. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGTCTGCAGCCAGAGTACAGA	0.547																																					p.G12439C		Atlas-SNP	.											.	MUC16	4315	.	0			c.G37315T						.						169	146	153					19																	9020787		2017	4175	6192	SO:0001583	missense	94025	exon20			TGCAGCCAGAGTA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.37315G>T	chr19.hg19:g.9020787C>A	ENSP00000381008:p.Gly12439Cys	325.0	0.0		327.0	71.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	9.665	1.145184	0.21288	.	.	ENSG00000181143	ENST00000397910	T	0.39997	1.05	3.19	2.1	0.27182	.	.	.	.	.	T	0.64594	0.2612	M	0.86953	2.85	.	.	.	D	0.89917	1.0	D	0.79108	0.992	T	0.73525	-0.3955	8	0.87932	D	0	.	8.8964	0.35467	0.0:0.7699:0.2301:0.0	.	12439	B5ME49	.	C	12439	ENSP00000381008:G12439C	ENSP00000381008:G12439C	G	-	1	0	MUC16	8881787	0.010000	0.17322	0.133000	0.22050	0.290000	0.27261	0.228000	0.17814	0.573000	0.29400	0.455000	0.32223	GGC	.	.		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9020787	C	A	9020787	3	1	58	1	0	0	0	0	1	0	0	0	9982	594	21	3	6468	3	MUC16	19	9020787	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10	4482723	9020787	50108196	99	7256										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15297927	15297927	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	cggtcccacctgtggtcccaGaagggcagcggcagaggtac	15	13	0	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr19:15297927G>T	ENST00000263388.2	-	11	1904	c.1829C>A	c.(1828-1830)tCt>tAt	p.S610Y		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	610	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TGTGGTCCCAGAAGGGCAGCG	0.652																																					p.S610Y		Atlas-SNP	.											.	NOTCH3	340	.	0			c.C1829A						.						28	28	28					19																	15297927		2203	4300	6503	SO:0001583	missense	4854	exon11			GTCCCAGAAGGGC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1829C>A	chr19.hg19:g.15297927G>T	ENSP00000263388:p.Ser610Tyr	217.0	0.0		173.0	35.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.544100	0.45280	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.91894	-2.93	4.51	3.45	0.39498	EGF (1);EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.89921	0.6855	L	0.46670	1.46	0.42160	D	0.991598	B;B	0.28178	0.202;0.043	B;B	0.40410	0.328;0.128	D	0.88658	0.3187	9	0.87932	D	0	.	6.5569	0.22466	0.0956:0.0:0.7233:0.1811	.	613;610	Q59FL3;Q9UM47	.;NOTC3_HUMAN	Y	610;612	ENSP00000263388:S610Y	ENSP00000263388:S610Y	S	-	2	0	NOTCH3	15158927	0.000000	0.05858	0.962000	0.40283	0.968000	0.65278	0.318000	0.19504	2.215000	0.71742	0.655000	0.94253	TCT	.	.		0.652	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		T	15297927	G	T	15297927	3	4	58	1	0	0	0	0	1	0	0	0	10559	942	33	3	5228	3	NOTCH3	19	15297927	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10	6277140	15297927	43831056	100	7257										
CD22	933	hgsc.bcm.edu	37	chr19	35823581	35823581	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tagatggtgacctggaaagcTtcatcctgttccacaatcct	8	11	1	2			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr19:35823581T>C	ENST00000085219.5	+	3	232	c.166T>C	c.(166-168)Ttc>Ctc	p.F56L	CD22_ENST00000536635.2_Missense_Mutation_p.F56L|CD22_ENST00000544992.2_Missense_Mutation_p.F56L|CD22_ENST00000270311.6_5'UTR|CD22_ENST00000594250.1_Missense_Mutation_p.F56L|CD22_ENST00000341773.6_Missense_Mutation_p.F56L|CD22_ENST00000419549.2_5'UTR|U62631.5_ENST00000597110.1_RNA|CD22_ENST00000595419.1_3'UTR	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	56	Ig-like V-type.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CCTGGAAAGCTTCATCCTGTT	0.507																																					p.F56L	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.T166C						.						87	86	86					19																	35823581		2203	4300	6503	SO:0001583	missense	933	exon3			GAAAGCTTCATCC	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1643	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 2"	107266	"CD22 antigen"			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.166T>C	chr19.hg19:g.35823581T>C	ENSP00000085219:p.Phe56Leu	165.0	0.0		230.0	44.0	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	hg19	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	T	6.397	0.441309	0.12164	.	.	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	5.42	-5.26	0.02772	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.128640	0.06779	N	0.784875	T	0.08846	0.0219	N	0.02721	-0.515	0.09310	N	0.999992	B;B;B;B	0.18968	0.0;0.032;0.0;0.001	B;B;B;B	0.20767	0.001;0.031;0.001;0.001	T	0.24764	-1.0151	10	0.12103	T	0.63	.	1.1372	0.01758	0.2629:0.4005:0.1254:0.2112	.	56;56;56;56	F5GYU4;F5H7U3;P20273;P20273-2	.;.;CD22_HUMAN;.	L	56	ENSP00000085219:F56L;ENSP00000442279:F56L;ENSP00000339349:F56L;ENSP00000441237:F56L	ENSP00000085219:F56L	F	+	1	0	CD22	40515421	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.830000	0.00744	-1.149000	0.02843	-0.461000	0.05368	TTC	.	.		0.507	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		C	35823581	T	C	35823581	3	2	58	1	0	0	0	0	1	0	0	0	2987	1609	56	2	172	2	CD22	19	35823581	Missense_Mutation	SNP	T	TCGA-CC-5262-01A-01D-A12Z-10	20525654	35823581	23305402	101	7258										
ZNF221	7638	hgsc.bcm.edu	37	chr19	44471487	44471487	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tcatttacatcagtaagtctAtgtgggagaaaagccatata	8	6	3	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr19:44471487A>C	ENST00000251269.5	+	6	2161	c.1833A>C	c.(1831-1833)ctA>ctC	p.L611L	ZNF221_ENST00000592350.1_Silent_p.L611L|ZNF221_ENST00000587682.1_Silent_p.L611L	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	611					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				CAGTAAGTCTATGTGGGAGAA	0.438																																					p.L611L		Atlas-SNP	.											.	ZNF221	59	.	0			c.A1833C						.						60	61	61					19																	44471487		2203	4300	6503	SO:0001819	synonymous_variant	7638	exon6			AAGTCTATGTGGG	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1833A>C	chr19.hg19:g.44471487A>C		66.0	0.0		98.0	18.0	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Silent	SNP	ENST00000251269.5	hg19	CCDS12633.1																																																																																			.	.		0.438	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			C	44471487	A	C	44471487	2	2	58	1	0	0	0	0	0	0	0	1	17790	436	16	5		5	ZNF221	19	44471487	Silent	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	8647906	44471487	14657496	102	7259										
LILRB4	11006	hgsc.bcm.edu	37	chr19	55175420	55175420	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	tccatgacagaggactatgcAgggagataccgctgttacta	11	9	0	3			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr19:55175420A>T	ENST00000391736.1	+	5	594	c.279A>T	c.(277-279)gcA>gcT	p.A93A	LILRB4_ENST00000391734.3_Silent_p.A93A|LILRB4_ENST00000270452.2_Silent_p.A93A|LILRB4_ENST00000430952.2_Silent_p.A93A|LILRB4_ENST00000391733.3_Silent_p.A93A	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	93	Ig-like C2-type 1.				immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		AGGACTATGCAGGGAGATACC	0.572																																					p.A93A		Atlas-SNP	.											LILRB4,NS,carcinoma,+1,1	LILRB4	86	.	0			c.A279T						.						283	246	259					19																	55175420		2203	4300	6503	SO:0001819	synonymous_variant	11006	exon3			CTATGCAGGGAGA	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.279A>T	chr19.hg19:g.55175420A>T		557.0	0.0		549.0	102.0	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Silent	SNP	ENST00000391736.1	hg19	CCDS12902.1																																																																																			.	.		0.572	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3			T	55175420	A	T	55175420	2	4	58	1	0	0	0	0	0	0	0	1	8802	175	7	4		4	LILRB4	19	55175420	Silent	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	10703933	55175420	3953563	103	7260										
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45194931	45194931	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ttgctggcaaactcagtgaaGaaggcgatgaccacagtgat	12	8	1	4			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr20:45194931G>T	ENST00000279027.4	-	11	1449	c.1431C>A	c.(1429-1431)ttC>ttA	p.F477L	SLC13A3_ENST00000435032.1_Missense_Mutation_p.F62L|SLC13A3_ENST00000396360.1_Missense_Mutation_p.F395L|SLC13A3_ENST00000472148.1_Missense_Mutation_p.F395L|SLC13A3_ENST00000290317.5_Missense_Mutation_p.F430L|SLC13A3_ENST00000413164.2_Missense_Mutation_p.F427L|SLC13A3_ENST00000495082.1_Missense_Mutation_p.F430L	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	477					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	ACTCAGTGAAGAAGGCGATGA	0.617																																					p.F477L		Atlas-SNP	.											.	SLC13A3	88	.	0			c.C1431A						.						113	113	113					20																	45194931		2203	4300	6503	SO:0001583	missense	64849	exon11			AGTGAAGAAGGCG	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1431C>A	chr20.hg19:g.45194931G>T	ENSP00000279027:p.Phe477Leu	140.0	0.0		139.0	19.0	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	hg19	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.383865	0.25031	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000435032;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082	T;T;T;T;T;T;T	0.02472	4.28;4.28;4.28;4.28;4.28;4.28;4.28	5.09	5.09	0.68999	.	0.158141	0.64402	D	0.000020	T	0.02418	0.0074	N	0.20766	0.605	0.80722	D	1	B;B;B;B;B;B	0.13594	0.002;0.004;0.004;0.002;0.005;0.008	B;B;B;B;B;B	0.18871	0.013;0.022;0.009;0.014;0.023;0.015	T	0.56444	-0.7978	10	0.23891	T	0.37	-21.8466	10.668	0.45741	0.0:0.2046:0.6644:0.131	.	427;62;395;430;379;477	B4DIR8;B4E181;Q8WWT9-3;F6WI18;B4DF27;Q8WWT9	.;.;.;.;.;S13A3_HUMAN	L	430;395;62;477;395;427;430	ENSP00000290317:F430L;ENSP00000379648:F395L;ENSP00000403394:F62L;ENSP00000279027:F477L;ENSP00000420177:F395L;ENSP00000415852:F427L;ENSP00000419621:F430L	ENSP00000279027:F477L	F	-	3	2	SLC13A3	44628338	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	2.992000	0.49417	2.365000	0.80145	0.561000	0.74099	TTC	.	.		0.617	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			T	45194931	G	T	45194931	3	4	58	1	0	0	0	0	1	0	0	0	14408	933	33	3	389	3	SLC13A3	20	45194931	Missense_Mutation	SNP	G	TCGA-CC-5262-01A-01D-A12Z-10		45194931	17830589	104	7261										
SFI1	9814	hgsc.bcm.edu	37	chr22	31979928	31979928	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aaaggaaagagagctgctccCcttactgcatgctgcctggg	12	11	0	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chr22:31979928C>A	ENST00000400288.2	+	13	1421	c.1316C>A	c.(1315-1317)cCc>cAc	p.P439H	SFI1_ENST00000432498.1_Missense_Mutation_p.P408H|SFI1_ENST00000443326.1_Missense_Mutation_p.P357H|SFI1_ENST00000400289.1_Missense_Mutation_p.P357H|SFI1_ENST00000443011.1_Missense_Mutation_p.P286H|SFI1_ENST00000540643.1_Missense_Mutation_p.P384H|SFI1_ENST00000414585.1_Missense_Mutation_p.P286H	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	439					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GAGCTGCTCCCCTTACTGCAT	0.512																																					p.P439H		Atlas-SNP	.											.	SFI1	78	.	0			c.C1316A						.						142	144	144					22																	31979928		1995	4173	6168	SO:0001583	missense	9814	exon13			TGCTCCCCTTACT	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.1316C>A	chr22.hg19:g.31979928C>A	ENSP00000383145:p.Pro439His	109.0	0.0		151.0	29.0	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	hg19	CCDS43004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.01|16.01	3.002487|3.002487	0.54254|0.54254	.|.	.|.	ENSG00000198089|ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000443326;ENST00000421060;ENST00000414585;ENST00000443011;ENST00000400289;ENST00000400288;ENST00000417682|ENST00000425671	T;T;T;T;T;T;T;T|.	0.58940|.	2.98;3.0;0.3;0.3;0.3;0.3;0.3;2.44|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.406771|0.406771	0.27096|0.27096	N|N	0.020949|0.020949	T|T	0.33206|0.33206	0.0855|0.0855	N|N	0.08118|0.08118	0|0	0.19945|0.19945	N|N	0.999944|0.999944	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.91635|.	0.982;0.972;0.999;0.982;0.999;0.996|.	T|T	0.41324|0.41324	-0.9515|-0.9515	10|7	0.72032|0.87932	D|D	0.01|0	.|.	15.9221|15.9221	0.79583|0.79583	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	384;357;357;408;439;415|.	A8K8P3-9;A8K8P3-10;A8K8P3-3;A8K8P3-2;A8K8P3;A8K8P3-5|.	.;.;.;.;SFI1_HUMAN;.|.	H|T	408;384;357;415;286;286;357;439;54|13	ENSP00000402679:P408H;ENSP00000443025:P384H;ENSP00000416469:P357H;ENSP00000397148:P286H;ENSP00000401199:P286H;ENSP00000383146:P357H;ENSP00000383145:P439H;ENSP00000398871:P54H|.	ENSP00000383145:P439H|ENSP00000416931:P13T	P|P	+|+	2|1	0|0	SFI1|SFI1	30309928|30309928	0.055000|0.055000	0.20627|0.20627	0.466000|0.466000	0.27168|0.27168	0.227000|0.227000	0.25037|0.25037	4.205000|4.205000	0.58466|0.58466	2.832000|2.832000	0.97577|0.97577	0.655000|0.655000	0.94253|0.94253	CCC|CCT	.	.		0.512	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		A	31979928	C	A	31979928	3	1	58	1	0	0	0	0	1	0	0	0	14171	623	22	3	1362	3	SFI1	22	31979928	Missense_Mutation	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10		31979928	19324638	105	7262										
MED14	9282	hgsc.bcm.edu	37	chrX	40572166	40572166	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aatcactacttatgatttacCtcctgtttccttatcctcaa	2	12	2	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chrX:40572166C>T	ENST00000324817.1	-	6	899	c.781G>A	c.(781-783)Gat>Aat	p.D261N		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	261	Interaction with STAT2.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TATGATTTACCTCCTGTTTCC	0.373																																					p.D261N		Atlas-SNP	.											.	MED14	108	.	0			c.G781A						.						69	54	59					X																	40572166		2203	4300	6503	SO:0001630	splice_region_variant	9282	exon6			ATTTACCTCCTGT	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.781+1G>A	chrX.hg19:g.40572166C>T		268.0	0.0		357.0	140.0	NM_004229	Q4KMR7|Q9UNB3	Missense_Mutation	SNP	ENST00000324817.1	hg19	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.968760	0.74131	.	.	ENSG00000180182	ENST00000324817	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.53594	0.1806	L	0.38953	1.18	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.47824	-0.9087	8	.	.	.	.	18.1915	0.89808	0.0:1.0:0.0:0.0	.	261	O60244	MED14_HUMAN	N	261	.	.	D	-	1	0	MED14	40457110	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.397000	0.79903	2.321000	0.78463	0.594000	0.82650	GAT	.	.		0.373	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229	Missense_Mutation	T	40572166	C	T	40572166	5	4	58	1	0	0	0	0	0	0	1	0	9441	695	24	3	3687	3	MED14	23	40572166	Splice_Site	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10		40572166	114698394	106	7263										
PHF16	9767	hgsc.bcm.edu	37	chrX	46844301	46844301	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	ccaggatgctccaggatgaaAcgccataggcctgtcagcag	12	12	1	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chrX:46844301A>G	ENST00000218343.4	+	2	304	c.6A>G	c.(4-6)aaA>aaG	p.K2K	PHF16_ENST00000397189.1_Silent_p.K2K	NM_014735.3	NP_055550.1														NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						CCAGGATGAAACGCCATAGGC	0.483																																					p.K2K		Atlas-SNP	.											.	PHF16	72	.	0			c.A6G						.						138	118	125					X																	46844301		2203	4300	6503	SO:0001819	synonymous_variant	9767	exon2			GATGAAACGCCAT																												ENST00000218343.4:c.6A>G	chrX.hg19:g.46844301A>G		209.0	0.0		215.0	67.0	NM_001077445		Silent	SNP	ENST00000218343.4	hg19	CCDS14271.1																																																																																			.	.		0.483	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			G	46844301	A	G	46844301	2	3	58	1	0	0	0	0	0	0	0	1	11836	40	2	2		2	PHF16	23	46844301	Silent	SNP	A	TCGA-CC-5262-01A-01D-A12Z-10	6272135	46844301	108426259	107	7264										
RPS4Y2	140032	hgsc.bcm.edu	37	chrY	22941543	22941543	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0462962962962963	5	1	1.03135888501742	1.60433604336043	0.833020637898687	1	1	0	aggatttccaacatttttgtCattggcaatgtaagacttgc	8	7	1	1			TCGA-CC-5262-01A-01D-A12Z-10	TCGA-CC-5262-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93083c92-9303-48e6-aa25-4bb4ba6764b5	48faa33d-3094-4b3b-8c61-d29f392591ff	g.chrY:22941543C>T	ENST00000288666.5	+	6	681	c.681C>T	c.(679-681)gtC>gtT	p.V227V		NM_001039567.2	NP_001034656.1	Q8TD47	RS4Y2_HUMAN	ribosomal protein S4, Y-linked 2	227					translation (GO:0006412)	ribosome (GO:0005840)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			lung(2)	2						ACATTTTTGTCATTGGCAATG	0.418																																					p.V227V		Atlas-SNP	.											.	RPS4Y2	3	.	0			c.C681T						.						134	126	128					Y																	22941543		618	1974	2592	SO:0001819	synonymous_variant	140032	exon6			TTTTGTCATTGGC	AF497481	CCDS44028.1	Yq11.223	2006-02-22	2006-02-22	2006-02-22	ENSG00000157828	ENSG00000157828		"S ribosomal proteins"	18501	protein-coding gene	gene with protein product		400030	"ribosomal protein S4, Y-linked 2 pseudogene"	RPS4Y2P		12815422	Standard	NM_001039567		Approved		uc011nbb.2	Q8TD47	OTTHUMG00000036540	ENST00000288666.5:c.681C>T	chrY.hg19:g.22941543C>T		339.0	0.0		305.0	128.0	NM_001039567	A6NIR6	Silent	SNP	ENST00000288666.5	hg19	CCDS44028.1																																																																																			.	.		0.418	RPS4Y2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088873.1			T	22941543	C	T	22941543	2	4	58	1	0	0	0	0	0	0	0	1	13662	813	29	3		3	RPS4Y2	24	22941543	Silent	SNP	C	TCGA-CC-5262-01A-01D-A12Z-10		22941543	36432023	108	7265										
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21231426	21231426	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ggttcgggtccgatcttttgGtttcttccatgtctttggta	11	8	3	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:21231426G>A	ENST00000264211.8	-	9	1728	c.1534C>T	c.(1534-1536)Cca>Tca	p.P512S	EIF4G3_ENST00000374937.3_Missense_Mutation_p.P518S|EIF4G3_ENST00000374933.3_5'UTR|EIF4G3_ENST00000602326.1_Missense_Mutation_p.P518S|EIF4G3_ENST00000400422.1_Missense_Mutation_p.P512S|EIF4G3_ENST00000544689.1_Missense_Mutation_p.P55S|EIF4G3_ENST00000374935.3_Missense_Mutation_p.P232S|EIF4G3_ENST00000536266.1_Missense_Mutation_p.P116S	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	512					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		CGATCTTTTGGTTTCTTCCAT	0.408																																					p.P518S		Atlas-SNP	.											.	EIF4G3	300	.	0			c.C1552T						.						240	209	220					1																	21231426		2203	4300	6503	SO:0001583	missense	8672	exon13			CTTTTGGTTTCTT	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.1534C>T	chr1.hg19:g.21231426G>A	ENSP00000264211:p.Pro512Ser	372.0	0.0		393.0	144.0	NM_001198802	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	hg19	CCDS214.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.427611	0.62733	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000374937;ENST00000536266;ENST00000374933;ENST00000544689	T;T;T;T;T;D	0.87029	2.06;2.06;2.21;2.06;2.06;-2.2	5.44	4.5	0.54988	.	0.053329	0.85682	D	0.000000	T	0.74114	0.3674	N	0.08118	0	0.80722	D	1	P;B;B;P;B	0.48589	0.847;0.278;0.04;0.912;0.232	B;B;B;B;B	0.37480	0.219;0.057;0.029;0.251;0.108	T	0.78743	-0.2085	10	0.52906	T	0.07	-5.6273	15.4333	0.75121	0.0:0.0:0.8557:0.1442	.	707;232;116;518;512	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	S	512;708;512;232;518;116;55;55	ENSP00000264211:P512S;ENSP00000383274:P512S;ENSP00000364071:P232S;ENSP00000364073:P518S;ENSP00000444693:P116S;ENSP00000444401:P55S	ENSP00000264211:P512S	P	-	1	0	EIF4G3	21104013	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.553000	0.67287	1.371000	0.46172	0.557000	0.71058	CCA	.	.		0.408	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		A	21231426	G	A	21231426	3	1	59	1	0	0	0	0	1	0	0	0	5040	1261	44	3	3315	3	EIF4G3	1	21231426	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10		21231426	228019195	1	7266										
CCDC21	64793	hgsc.bcm.edu	37	chr1	26570728	26570729	+	Frame_Shift_Ins	INS	-	-	G													0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	agttatctcggagccctttcINSggagccgcttcagccgctgt					rs368381610		TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:26570728_26570729insG	ENST00000252992.4	+	3	258_259	c.127_128insG	c.(127-129)cggfs	p.R43fs	CEP85_ENST00000451429.2_Intron	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	43						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						GGAGCCCTTTCGGAGCCGCTTC	0.51																																					p.R43fs		Atlas-INDEL	.											.	CEP85	61	.	0			c.127_128insG						.																																			SO:0001589	frameshift_variant	64793	exon3			.	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"coiled-coil domain containing 21"	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.129dupG	chr1.hg19:g.26570730_26570730dupG	ENSP00000252992:p.Arg43fs	196.0	0.0		282.0	20.0	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Frame_Shift_Ins	INS	ENST00000252992.4	hg19	CCDS277.1																																																																																			.	.		0.51	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778		G	26570729	-	G	26570728	7	5	59	1	0	1	1	0	0	0	0	0	2798	875	31	0	133	0	CCDC21	1	26570728	Frame_Shift_Ins	INS	-	TCGA-CC-5263-01A-01D-A12Z-10	5339302	26570728	222679893	2	7267										
CYP4A22	284541	hgsc.bcm.edu	37	chr1	47610101	47610101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gaagatcaagaggaagaggcActtggattttctggacatcc	12	7	2	3			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:47610101A>G	ENST00000371891.3	+	7	894	c.863A>G	c.(862-864)cAc>cGc	p.H288R	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000371890.3_Silent_p.A236A|CYP4A22_ENST00000294337.3_Missense_Mutation_p.H288R|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	288						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGGAAGAGGCACTTGGATTTT	0.507																																					p.H288R	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.A863G						.						165	156	159					1																	47610101		2203	4300	6503	SO:0001583	missense	284541	exon7			AGAGGCACTTGGA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"Cytochrome P450s"	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.863A>G	chr1.hg19:g.47610101A>G	ENSP00000360958:p.His288Arg	325.0	1.0		435.0	176.0	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	hg19	CCDS30707.1	.	.	.	.	.	.	.	.	.	.	a	8.716	0.913237	0.17907	.	.	ENSG00000162365	ENST00000371891;ENST00000294337	T;T	0.66280	-0.2;-0.2	1.51	1.51	0.23008	.	0.394484	0.30704	N	0.009050	T	0.29882	0.0747	N	0.02275	-0.615	0.30176	N	0.800886	B	0.13594	0.008	B	0.20577	0.03	T	0.15492	-1.0435	10	0.26408	T	0.33	.	5.6291	0.17499	0.8494:0.0:0.1506:0.0	.	288	Q5TCH4	CP4AM_HUMAN	R	288	ENSP00000360958:H288R;ENSP00000294337:H288R	ENSP00000294337:H288R	H	+	2	0	CYP4A22	47382688	0.988000	0.35896	0.620000	0.29132	0.329000	0.28539	4.808000	0.62583	0.702000	0.31825	0.163000	0.16589	CAC	.	.		0.507	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213		G	47610101	A	G	47610101	3	3	59	1	0	0	0	0	1	0	0	0	4186	159	6	2	889	2	CYP4A22	1	47610101	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	21039373	47610101	201640520	3	7268										
PTGER3	5733	hgsc.bcm.edu	37	chr1	71512812	71512812	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gcgcccgctcgacggccatgGcgctggcgatgaacaacgag	15	14	0	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:71512812G>A	ENST00000306666.5	-	1	659	c.449C>T	c.(448-450)gCc>gTc	p.A150V	PTGER3_ENST00000460330.1_Missense_Mutation_p.A150V|PTGER3_ENST00000370924.4_Missense_Mutation_p.A150V|PTGER3_ENST00000356595.4_Missense_Mutation_p.A150V|PTGER3_ENST00000351052.5_Missense_Mutation_p.A150V|PTGER3_ENST00000354608.5_Missense_Mutation_p.A150V|PTGER3_ENST00000370932.2_Missense_Mutation_p.A150V|PTGER3_ENST00000370931.3_Missense_Mutation_p.A150V|PTGER3_ENST00000414819.1_Missense_Mutation_p.A150V|ZRANB2-AS1_ENST00000450461.1_RNA	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	150					cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	GACGGCCATGGCGCTGGCGAT	0.662																																					p.A150V		Atlas-SNP	.											.	PTGER3	246	.	0			c.C449T						.						14	15	14					1																	71512812		2194	4281	6475	SO:0001583	missense	5733	exon1			GCCATGGCGCTGG	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.449C>T	chr1.hg19:g.71512812G>A	ENSP00000302313:p.Ala150Val	24.0	0.0		51.0	24.0	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Missense_Mutation	SNP	ENST00000306666.5	hg19	CCDS657.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146958	0.77888	.	.	ENSG00000050628	ENST00000370931;ENST00000370932;ENST00000351052;ENST00000460330;ENST00000370934;ENST00000354608;ENST00000356595;ENST00000414819;ENST00000306666;ENST00000370924	T;T;T;T;T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14	4.9	3.99	0.46301	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.41282	0.1152	L	0.59912	1.85	0.80722	D	1	D;D;D;D;D;D;D;D	0.76494	0.997;0.997;0.997;0.999;0.999;0.993;0.996;0.997	D;D;D;D;D;P;P;D	0.70487	0.943;0.943;0.962;0.969;0.969;0.906;0.906;0.943	T	0.22173	-1.0224	10	0.28530	T	0.3	-18.8832	13.4836	0.61353	0.0758:0.0:0.9242:0.0	.	150;150;150;150;150;150;150;150	Q147U0;Q6TTN3;F5H821;B1AK19;Q147X8;P43115-3;P43115-4;P43115	.;.;.;.;.;.;.;PE2R3_HUMAN	V	150	ENSP00000359969:A150V;ENSP00000359970:A150V;ENSP00000280208:A150V;ENSP00000418073:A150V;ENSP00000346624:A150V;ENSP00000349003:A150V;ENSP00000401423:A150V;ENSP00000302313:A150V;ENSP00000359962:A150V	ENSP00000302313:A150V	A	-	2	0	PTGER3	71285400	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.371000	0.66150	1.282000	0.44496	0.462000	0.41574	GCC	.	.		0.662	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957		A	71512812	G	A	71512812	3	1	59	1	0	0	0	0	1	0	0	0	12757	1203	42	3	1042	3	PTGER3	1	71512812	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	23902711	71512812	177737809	4	7269										
STXBP3	6814	hgsc.bcm.edu	37	chr1	109340799	109340799	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	aaaccgttaagaaaggatcgGtctgcagaagaaacttttca	9	7	2	3	rs374868665		TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:109340799G>T	ENST00000370008.3	+	16	1439	c.1389G>T	c.(1387-1389)cgG>cgT	p.R463R		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	463					blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		GAAAGGATCGGTCTGCAGAAG	0.333																																					p.R463R		Atlas-SNP	.											.	STXBP3	44	.	0			c.G1389T						.						113	123	119					1																	109340799		2203	4300	6503	SO:0001819	synonymous_variant	6814	exon16			GGATCGGTCTGCA	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1389G>T	chr1.hg19:g.109340799G>T		536.0	1.0		598.0	245.0	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Silent	SNP	ENST00000370008.3	hg19	CCDS790.1																																																																																			.	.		0.333	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		T	109340799	G	T	109340799	2	4	59	1	0	0	0	0	0	0	0	1	15369	1248	44	3		3	STXBP3	1	109340799	Silent	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	37827987	109340799	139909822	5	7270										
SYT6	148281	hgsc.bcm.edu	37	chr1	114646254	114646254	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gtgatgtccatcgccttgagGttccgacacttaatcactgt	9	11	1	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:114646254G>T	ENST00000610222.1	-	4	1307	c.1161C>A	c.(1159-1161)aaC>aaA	p.N387K	SYT6_ENST00000609117.1_Missense_Mutation_p.N302K|SYT6_ENST00000607941.1_Missense_Mutation_p.N302K|SYT6_ENST00000369547.1_Missense_Mutation_p.N302K|SYT6_ENST00000393296.1_Missense_Mutation_p.N387K			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	387	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCGCCTTGAGGTTCCGACACT	0.537																																					p.N302K		Atlas-SNP	.											.	SYT6	66	.	0			c.C906A						.						144	113	124					1																	114646254		2203	4300	6503	SO:0001583	missense	148281	exon4			CTTGAGGTTCCGA		CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"Synaptotagmins"	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.1161C>A	chr1.hg19:g.114646254G>T	ENSP00000476396:p.Asn387Lys	76.0	0.0		83.0	39.0	NM_205848	B1AMB8|B3KPK1	Missense_Mutation	SNP	ENST00000610222.1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.53	3.844182	0.71488	.	.	ENSG00000134207	ENST00000369547;ENST00000393296;ENST00000369546;ENST00000369545	T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86	5.71	3.82	0.43975	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.75488	0.3856	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.71870	0.975	T	0.77600	-0.2527	10	0.87932	D	0	.	6.7243	0.23348	0.4015:0.0:0.5985:0.0	.	387	Q5T7P8	SYT6_HUMAN	K	302;387;302;387	ENSP00000358560:N302K;ENSP00000376974:N387K;ENSP00000358559:N302K;ENSP00000358558:N387K	ENSP00000358558:N387K	N	-	3	2	SYT6	114447777	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.247000	0.43151	0.738000	0.32606	0.561000	0.74099	AAC	.	.		0.537	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848		T	114646254	G	T	114646254	3	4	59	1	0	0	0	0	1	0	0	0	15493	1252	44	3	387	3	SYT6	1	114646254	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	5305455	114646254	134604367	6	7271										
NUP210L	91181	hgsc.bcm.edu	37	chr1	154033436	154033436	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	acctttacatcagggtggttAtagatggtggcattctcagg	12	7	2	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:154033436A>G	ENST00000368559.3	-	19	2801	c.2730T>C	c.(2728-2730)taT>taC	p.Y910Y	NUP210L_ENST00000271854.3_Silent_p.Y910Y	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	910					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CAGGGTGGTTATAGATGGTGG	0.358																																					p.Y910Y		Atlas-SNP	.											.	NUP210L	181	.	0			c.T2730C						.						107	101	103					1																	154033436		1869	4114	5983	SO:0001819	synonymous_variant	91181	exon19			GTGGTTATAGATG	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2730T>C	chr1.hg19:g.154033436A>G		262.0	0.0		324.0	118.0	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Silent	SNP	ENST00000368559.3	hg19	CCDS41399.1																																																																																			.	.		0.358	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		G	154033436	A	G	154033436	2	3	59	1	0	0	0	0	0	0	0	1	10770	456	16	2		2	NUP210L	1	154033436	Silent	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	39387182	154033436	95217185	7	7272										
PMVK	10654	hgsc.bcm.edu	37	chr1	154904884	154904884	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gaggacagcacagacatcagCtccaagtctgcaggacaggg	13	11	2	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:154904884C>G	ENST00000368467.3	-	2	408	c.103G>C	c.(103-105)Gct>Cct	p.A35P		NM_006556.3	NP_006547.1	Q15126	PMVK_HUMAN	phosphomevalonate kinase	35					cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|response to cholesterol (GO:0070723)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|phosphomevalonate kinase activity (GO:0004631)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.142)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CAGACATCAGCTCCAAGTCTG	0.562																																					p.A35P		Atlas-SNP	.											.	PMVK	17	.	0			c.G103C						.						102	91	95					1																	154904884		2203	4300	6503	SO:0001583	missense	10654	exon2			CATCAGCTCCAAG	L77213	CCDS1073.1	1q21.3	2012-09-20			ENSG00000163344	ENSG00000163344	2.7.4.2		9141	protein-coding gene	gene with protein product		607622				8663599, 10191291	Standard	NM_006556		Approved	PMK, PMKA, HUMPMKI	uc001ffq.3	Q15126	OTTHUMG00000037415	ENST00000368467.3:c.103G>C	chr1.hg19:g.154904884C>G	ENSP00000357452:p.Ala35Pro	179.0	0.0		259.0	14.0	NM_006556	Q5TZW9	Missense_Mutation	SNP	ENST00000368467.3	hg19	CCDS1073.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.580194	0.46006	.	.	ENSG00000163344	ENST00000368467	T	0.45276	0.9	4.59	2.71	0.32032	.	0.312350	0.31404	N	0.007710	T	0.10121	0.0248	N	0.21097	0.63	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16808	-1.0390	10	0.30854	T	0.27	-0.5485	6.3066	0.21141	0.0:0.7829:0.0:0.2171	.	35	Q15126	PMVK_HUMAN	P	35	ENSP00000357452:A35P	ENSP00000357452:A35P	A	-	1	0	PMVK	153171508	0.005000	0.15991	0.009000	0.14445	0.846000	0.48090	0.682000	0.25335	1.283000	0.44513	0.561000	0.74099	GCT	.	.		0.562	PMVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091088.1	NM_006556		G	154904884	C	G	154904884	3	3	59	1	0	0	0	0	1	0	0	0	12153	797	28	4	491	4	PMVK	1	154904884	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	871448	154904884	94345737	8	7273										
MNDA	4332	hgsc.bcm.edu	37	chr1	158817665	158817665	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ttcaactgagaacagttgacCgcaagctgaaactggtgtgt	11	8	1	3	rs139902913		TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:158817665C>A	ENST00000368141.4	+	6	1396	c.1135C>A	c.(1135-1137)Cgc>Agc	p.R379S		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	379	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					AACAGTTGACCGCAAGCTGAA	0.443																																					p.R379S		Atlas-SNP	.											.	MNDA	147	.	0			c.C1135A						.						130	123	125					1																	158817665		2203	4300	6503	SO:0001583	missense	4332	exon6			GTTGACCGCAAGC	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.1135C>A	chr1.hg19:g.158817665C>A	ENSP00000357123:p.Arg379Ser	127.0	0.0		145.0	58.0	NM_002432		Missense_Mutation	SNP	ENST00000368141.4	hg19	CCDS1177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.250|0.250	-1.007183|-1.007183	0.02112|0.02112	.|.	.|.	ENSG00000163563|ENSG00000163563	ENST00000438394|ENST00000368141	.|T	.|0.21543	.|2.0	3.76|3.76	-7.52|-7.52	0.01341|0.01341	.|HIN-200/IF120x (1);Nucleic acid-binding, OB-fold (1);	.|3.094270	.|0.01403	.|N	.|0.013692	T|T	0.01870|0.01870	0.0059|0.0059	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	.|P	.|0.34724	.|0.465	.|B	.|0.28849	.|0.095	T|T	0.30119|0.30119	-0.9989|-0.9989	5|10	.|0.10902	.|T	.|0.67	9.6375|9.6375	1.2349|1.2349	0.01951|0.01951	0.2408:0.3124:0.2874:0.1594|0.2408:0.3124:0.2874:0.1594	.|.	.|379	.|P41218	.|MNDA_HUMAN	Q|S	84|379	.|ENSP00000357123:R379S	.|ENSP00000357123:R379S	P|R	+|+	2|1	0|0	MNDA|MNDA	157084289|157084289	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.008000|0.008000	0.06430|0.06430	-2.155000|-2.155000	0.01284|0.01284	-2.488000|-2.488000	0.00518|0.00518	-0.440000|-0.440000	0.05779|0.05779	CCG|CGC	.	C|1.000;T|0.000		0.443	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		A	158817665	C	A	158817665	3	1	59	1	0	0	0	0	1	0	0	0	9685	652	23	1	1153	1	MNDA	1	158817665	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	3912781	158817665	90432956	9	7274										
TBX19	9095	hgsc.bcm.edu	37	chr1	168262484	168262484	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gctccttccctgaaacccagTtcatagccgtgactgcctat	7	15	1	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:168262484T>C	ENST00000367821.3	+	3	622	c.571T>C	c.(571-573)Ttc>Ctc	p.F191L		NM_005149.2	NP_005140.1	O60806	TBX19_HUMAN	T-box 19	191					anatomical structure morphogenesis (GO:0009653)|cell fate commitment (GO:0045165)|pituitary gland development (GO:0021983)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(11)|prostate(2)|skin(2)|urinary_tract(1)	34	all_hematologic(923;0.215)					TGAAACCCAGTTCATAGCCGT	0.468																																					p.F191L		Atlas-SNP	.											.	TBX19	68	.	0			c.T571C						.						91	70	77					1																	168262484		2203	4300	6503	SO:0001583	missense	9095	exon3			ACCCAGTTCATAG	AJ010277	CCDS1272.1	1q23-q24	2008-02-05			ENSG00000143178	ENSG00000143178		"T-boxes"	11596	protein-coding gene	gene with protein product	"TBS 19"	604614				9888994	Standard	NM_005149		Approved	dj747L4.1, TPIT	uc001gfl.3	O60806	OTTHUMG00000034648	ENST00000367821.3:c.571T>C	chr1.hg19:g.168262484T>C	ENSP00000356795:p.Phe191Leu	67.0	0.0		126.0	52.0	NM_005149	Q52M53	Missense_Mutation	SNP	ENST00000367821.3	hg19	CCDS1272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.122564|5.122564	0.94429|0.94429	.|.	.|.	ENSG00000143178|ENSG00000143178	ENST00000367821;ENST00000367828|ENST00000431969	D|.	0.93189|.	-3.18|.	5.02|5.02	5.02|5.02	0.67125|0.67125	p53-like transcription factor, DNA-binding (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86422|0.86422	0.5929|0.5929	H|H	0.98199|0.98199	4.17|4.17	0.49582|.	D|.	0.999803|.	D;D|.	0.71674|.	0.998;0.99|.	D;P|.	0.64877|.	0.93;0.841|.	D|D	0.91584|0.91584	0.5281|0.5281	9|4	0.72032|.	D|.	0.01|.	.|.	14.4281|14.4281	0.67230|0.67230	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	191;122|.	O60806;B3KRD9|.	TBX19_HUMAN;.|.	L|A	191;131|123	ENSP00000356795:F191L|.	ENSP00000356795:F191L|.	F|V	+|+	1|2	0|0	TBX19|TBX19	166529108|166529108	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.507000|7.507000	0.81676|0.81676	1.884000|1.884000	0.54569|0.54569	0.460000|0.460000	0.39030|0.39030	TTC|GTT	.	.		0.468	TBX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083825.1	NM_005149		C	168262484	T	C	168262484	3	2	59	1	0	0	0	0	1	0	0	0	15669	1725	60	2	581	2	TBX19	1	168262484	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	9444819	168262484	80988137	10	7275										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179603595	179603595	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cggaaatttgtgtttagttcAgtcagataagaaaatagaag	10	3	2	3			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:179603595A>T	ENST00000367614.1	+	8	1489	c.1130A>T	c.(1129-1131)cAg>cTg	p.Q377L	TDRD5_ENST00000294848.8_Missense_Mutation_p.Q377L|TDRD5_ENST00000444136.1_Missense_Mutation_p.Q377L	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	377					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						TGTTTAGTTCAGTCAGATAAG	0.383																																					p.Q377L		Atlas-SNP	.											.	TDRD5	149	.	0			c.A1130T						.						101	101	101					1																	179603595		2203	4300	6503	SO:0001583	missense	163589	exon8			TAGTTCAGTCAGA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1130A>T	chr1.hg19:g.179603595A>T	ENSP00000356586:p.Gln377Leu	183.0	0.0		183.0	73.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	A	9.612	1.131531	0.21041	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.12774	2.65;2.65;2.83	5.24	2.72	0.32119	.	0.626135	0.16158	N	0.226908	T	0.12689	0.0308	L	0.54323	1.7	0.29136	N	0.879299	B;B	0.12013	0.005;0.002	B;B	0.09377	0.004;0.002	T	0.12344	-1.0551	10	0.27785	T	0.31	-2.8607	8.2597	0.31777	0.687:0.0:0.0:0.313	.	377;377	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	L	377	ENSP00000356586:Q377L;ENSP00000294848:Q377L;ENSP00000406052:Q377L	ENSP00000294848:Q377L	Q	+	2	0	TDRD5	177870218	0.997000	0.39634	0.996000	0.52242	0.864000	0.49448	1.718000	0.38001	0.910000	0.36722	0.533000	0.62120	CAG	.	.		0.383	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		T	179603595	A	T	179603595	3	4	59	1	0	0	0	0	1	0	0	0	15748	188	7	4	1156	4	TDRD5	1	179603595	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	11341111	179603595	69647026	11	7276										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245847619	245847619	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	atcgcgcacatctcggccgcGgtcgggagctacgcggagac	15	14	1	1	rs201075952		TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:245847619G>A	ENST00000407071.2	+	11	2783	c.2343G>A	c.(2341-2343)gcG>gcA	p.A781A	KIF26B_ENST00000366518.4_Silent_p.A400A	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	781	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TCTCGGCCGCGGTCGGGAGCT	0.577													G|||	1	0.000199681	0	0	5008	,	,		18869	0		0.001	False		,,,				2504	0				p.A781A		Atlas-SNP	.											.	KIF26B	343	.	0			c.G2343A						.						56	61	59					1																	245847619		2060	4183	6243	SO:0001819	synonymous_variant	55083	exon11			GGCCGCGGTCGGG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2343G>A	chr1.hg19:g.245847619G>A		68.0	0.0		124.0	42.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	G|0.999;A|0.001		0.577	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245847619	G	A	245847619	2	1	59	1	0	0	0	0	0	0	0	1	8304	1103	39	1		1	KIF26B	1	245847619	Silent	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	66244024	245847619	3403002	12	7277										
SCCPDH	51097	hgsc.bcm.edu	37	chr1	246923373	246923373	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gaattggaaggcaacttctcAtaaaagtaagtaagatttta	8	4	1	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr1:246923373A>T	ENST00000366510.3	+	8	1304	c.928A>T	c.(928-930)Ata>Tta	p.I310L		NM_016002.2	NP_057086.2	Q8NBX0	SCPDL_HUMAN	saccharopine dehydrogenase (putative)	310						lipid particle (GO:0005811)|membrane (GO:0016020)|midbody (GO:0030496)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(9)|ovary(1)	17	all_cancers(71;6.8e-05)|all_epithelial(71;7.93e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0545)|Lung NSC(105;0.0618)	all_cancers(173;0.0343)	OV - Ovarian serous cystadenocarcinoma(106;0.00323)	GBM - Glioblastoma multiforme(49;0.0896)		GCAACTTCTCATAAAAGTAAG	0.308																																					p.I310L		Atlas-SNP	.											.	SCCPDH	37	.	0			c.A928T						.						175	162	167					1																	246923373		2203	4300	6503	SO:0001583	missense	51097	exon8			CTTCTCATAAAAG		CCDS31084.1	1q44	2009-11-06			ENSG00000143653	ENSG00000143653			24275	protein-coding gene	gene with protein product						10810093	Standard	NM_016002		Approved	CGI-49, NET11	uc001ibr.3	Q8NBX0	OTTHUMG00000040221	ENST00000366510.3:c.928A>T	chr1.hg19:g.246923373A>T	ENSP00000355467:p.Ile310Leu	854.0	1.0		934.0	323.0	NM_016002	Q8TAR0|Q9Y363	Missense_Mutation	SNP	ENST00000366510.3	hg19	CCDS31084.1	.	.	.	.	.	.	.	.	.	.	A	4.955	0.177422	0.09443	.	.	ENSG00000143653	ENST00000366510;ENST00000366509	T	0.43688	0.94	5.43	1.28	0.21552	.	0.216134	0.53938	D	0.000052	T	0.15262	0.0368	N	0.01529	-0.815	0.46298	D	0.998973	B	0.06786	0.001	B	0.14578	0.011	T	0.05068	-1.0908	10	0.26408	T	0.33	.	9.7998	0.40757	0.7365:0.0:0.2635:0.0	.	310	Q8NBX0	SCPDL_HUMAN	L	310;141	ENSP00000355467:I310L	ENSP00000355466:I141L	I	+	1	0	SCCPDH	244989996	0.988000	0.35896	1.000000	0.80357	0.998000	0.95712	1.425000	0.34859	0.396000	0.25283	0.533000	0.62120	ATA	.	.		0.308	SCCPDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096902.2	NM_016002		T	246923373	A	T	246923373	3	4	59	1	0	0	0	0	1	0	0	0	13900	217	8	4	958	4	SCCPDH	1	246923373	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	1075754	246923373	2327248	13	7278										
TET3	200424	hgsc.bcm.edu	37	chr2	74327943	74327943	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gtttgccgagctgcccagccAggctgttcccacagacgccc	11	17	0	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr2:74327943A>T	ENST00000409262.3	+	9	3623	c.3623A>T	c.(3622-3624)cAg>cTg	p.Q1208L		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	1208					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CTGCCCAGCCAGGCTGTTCCC	0.642																																					p.Q1208L		Atlas-SNP	.											.	TET3	101	.	0			c.A3623T						.						20	23	22					2																	74327943		2075	4210	6285	SO:0001583	missense	200424	exon9			CCAGCCAGGCTGT		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.3623A>T	chr2.hg19:g.74327943A>T	ENSP00000386869:p.Gln1208Leu	46.0	0.0		69.0	27.0	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	ENST00000409262.3	hg19	CCDS46339.1	.	.	.	.	.	.	.	.	.	.	A	12.22	1.871563	0.33069	.	.	ENSG00000187605	ENST00000409262;ENST00000233310	T	0.12039	2.72	4.91	3.74	0.42951	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	0.364872	0.23811	N	0.044329	T	0.14830	0.0358	L	0.41961	1.31	0.37416	D	0.913455	B	0.31413	0.322	B	0.37198	0.243	T	0.09596	-1.0667	10	0.51188	T	0.08	.	10.5629	0.45156	0.6928:0.3072:0.0:0.0	.	1208	O43151	TET3_HUMAN	L	1208	ENSP00000386869:Q1208L	ENSP00000233310:Q1208L	Q	+	2	0	TET3	74181451	0.829000	0.29322	1.000000	0.80357	0.986000	0.74619	2.472000	0.45136	0.977000	0.38444	0.533000	0.62120	CAG	.	.		0.642	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			T	74327943	A	T	74327943	3	4	59	1	0	0	0	0	1	0	0	0	15786	188	7	4	3657	4	TET3	2	74327943	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10		74327943	168871430	14	7279										
NR4A2	4929	hgsc.bcm.edu	37	chr2	157186659	157186659	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ctgagaagcggggctggctcCttgaggcgaggacccatact	15	11	0	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr2:157186659C>T	ENST00000339562.4	-	3	402	c.40G>A	c.(40-42)Gga>Aga	p.G14R	NR4A2_ENST00000409108.2_Missense_Mutation_p.G14R|NR4A2_ENST00000429376.1_Intron|NR4A2_ENST00000409572.1_Missense_Mutation_p.G14R|NR4A2_ENST00000426264.1_Intron|NR4A2_ENST00000539077.1_Missense_Mutation_p.G25R	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	14					adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						GGGCTGGCTCCTTGAGGCGAG	0.517																																					p.G14R		Atlas-SNP	.											.	NR4A2	82	.	0			c.G40A						.						48	51	50					2																	157186659		2203	4300	6503	SO:0001583	missense	4929	exon3			TGGCTCCTTGAGG	X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"Nuclear hormone receptors"	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.40G>A	chr2.hg19:g.157186659C>T	ENSP00000344479:p.Gly14Arg	122.0	0.0		147.0	38.0	NM_006186	Q16311|Q53RZ2|Q6NXU0	Missense_Mutation	SNP	ENST00000339562.4	hg19	CCDS2201.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.003131	0.74932	.	.	ENSG00000153234	ENST00000339562;ENST00000409572;ENST00000539077;ENST00000409108;ENST00000424077	D;D;D;D;D	0.93859	-3.04;-3.04;-3.02;-3.3;-1.75	5.43	5.43	0.79202	.	0.214284	0.48286	D	0.000187	D	0.95007	0.8384	L	0.42245	1.32	0.80722	D	1	D	0.63880	0.993	D	0.64237	0.923	D	0.95066	0.8200	10	0.66056	D	0.02	.	19.0129	0.92881	0.0:1.0:0.0:0.0	.	14	P43354	NR4A2_HUMAN	R	14;14;25;14;14	ENSP00000344479:G14R;ENSP00000386747:G14R;ENSP00000444925:G25R;ENSP00000386993:G14R;ENSP00000406808:G14R	ENSP00000344479:G14R	G	-	1	0	NR4A2	156894905	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.825000	0.97269	0.655000	0.94253	GGA	.	.		0.517	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2			T	157186659	C	T	157186659	3	4	59	1	0	0	0	0	1	0	0	0	10642	690	24	3	1780	3	NR4A2	2	157186659	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	82858716	157186659	86012714	15	7280										
HOXD4	3233	hgsc.bcm.edu	37	chr2	177017653	177017653	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tggccaaagaccaccacacgGacctgacgaccttatagaag	9	13	0	3			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr2:177017653G>C	ENST00000306324.3	+	2	1163	c.751G>C	c.(751-753)Gac>Cac	p.D251H	HOXD3_ENST00000468418.3_5'UTR|MIR10B_ENST00000385011.1_RNA	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	251					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		CCACCACACGGACCTGACGAC	0.627																																					p.D251H		Atlas-SNP	.											.	HOXD4	32	.	0			c.G751C						.						70	77	75					2																	177017653		2203	4300	6503	SO:0001583	missense	3233	exon2			CACACGGACCTGA		CCDS2269.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170166	ENSG00000170166		"Homeoboxes / ANTP class : HOXL subclass"	5138	protein-coding gene	gene with protein product		142981	"homeo box D4"	HOX4B, HOX4		1973146, 1358459	Standard	NM_014621		Approved		uc002uks.3	P09016	OTTHUMG00000132515	ENST00000306324.3:c.751G>C	chr2.hg19:g.177017653G>C	ENSP00000302548:p.Asp251His	86.0	0.0		138.0	52.0	NM_014621	B2R9R3|Q96AU0	Missense_Mutation	SNP	ENST00000306324.3	hg19	CCDS2269.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.988556	0.74589	.	.	ENSG00000170166	ENST00000306324	D	0.91011	-2.77	5.67	5.67	0.87782	.	1.924890	0.02868	N	0.131199	D	0.95529	0.8547	L	0.60455	1.87	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	D	0.85832	0.1392	10	0.87932	D	0	.	19.7626	0.96329	0.0:0.0:1.0:0.0	.	251	P09016	HXD4_HUMAN	H	251	ENSP00000302548:D251H	ENSP00000302548:D251H	D	+	1	0	HOXD4	176725899	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.914000	0.87478	2.676000	0.91093	0.561000	0.74099	GAC	.	.		0.627	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2			C	177017653	G	C	177017653	3	2	59	1	0	0	0	0	1	0	0	0	7333	1174	41	4	757	4	HOXD4	2	177017653	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	19830994	177017653	66181720	16	7281										
TTN	7273	hgsc.bcm.edu	37	chr2	179419703	179419703	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tttgatgagtatagatgcgaGgtccgtggtattttcaacac	11	6	1	3			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr2:179419703G>A	ENST00000591111.1	-	281	83784	c.83560C>T	c.(83560-83562)Ctc>Ttc	p.L27854F	TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L20622F|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L29495F|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L20555F|TTN_ENST00000460472.2_Missense_Mutation_p.L20430F|TTN_ENST00000342992.6_Missense_Mutation_p.L26927F|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27854	Ig-like 130.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATAGATGCGAGGTCCGTGGTA	0.438																																					p.L29495F		Atlas-SNP	.											.	TTN	18412	.	0			c.C88483T						.						86	81	82					2																	179419703		1915	4125	6040	SO:0001583	missense	7273	exon331			ATGCGAGGTCCGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.83560C>T	chr2.hg19:g.179419703G>A	ENSP00000465570:p.Leu27854Phe	150.0	0.0		198.0	79.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.36	3.370558	0.61624	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.66	4.76	0.60689	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.49184	0.1542	N	0.25144	0.715	0.31858	N	0.62137	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.003;0.003;0.003	T	0.54057	-0.8350	9	0.87932	D	0	.	4.5974	0.12336	0.1759:0.0:0.6327:0.1914	.	20430;20555;20622;27854	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	F	26927;20430;20622;20555;20427	ENSP00000343764:L26927F;ENSP00000434586:L20430F;ENSP00000340554:L20622F;ENSP00000352154:L20555F	ENSP00000340554:L20622F	L	-	1	0	TTN	179127949	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.150000	0.64869	1.462000	0.47948	0.655000	0.94253	CTC	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179419703	G	A	179419703	3	1	59	1	0	0	0	0	1	0	0	0	16750	1000	35	3	19624	3	TTN	2	179419703	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	2402050	179419703	63779670	17	7282										
NCL	4691	hgsc.bcm.edu	37	chr2	232325414	232325414	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tcttcctcctcctcatcatcTtcatcatcatcatcttcatc	0	17	10	0	rs540030591|rs139777351|rs371359723|rs199689485|rs527711138|rs368566589	byFrequency	TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr2:232325414T>A	ENST00000322723.4	-	4	1017	c.777A>T	c.(775-777)gaA>gaT	p.E259D	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	259	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CCtcatcatcttcatcatcat	0.438																																					p.E259D		Atlas-SNP	.											.	NCL	80	.	0			c.A777T						.						229	194	206					2																	232325414		2203	4300	6503	SO:0001583	missense	4691	exon4			ATCATCTTCATCA		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.777A>T	chr2.hg19:g.232325414T>A	ENSP00000318195:p.Glu259Asp	350.0	0.0		432.0	44.0	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	hg19	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	T	0.028	-1.357543	0.01245	.	.	ENSG00000115053	ENST00000322723;ENST00000392033	T	0.23552	1.9	4.93	-9.86	0.00473	.	1.633390	0.02710	N	0.112777	T	0.06554	0.0168	N	0.03608	-0.345	0.19945	N	0.999949	B	0.02656	0.0	B	0.08055	0.003	T	0.26677	-1.0096	10	0.02654	T	1	0.5096	0.6058	0.00752	0.2352:0.1751:0.2128:0.3769	.	259	P19338	NUCL_HUMAN	D	259;151	ENSP00000318195:E259D	ENSP00000318195:E259D	E	-	3	2	NCL	232033658	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.197000	0.00276	-4.228000	0.00063	-3.370000	0.00041	GAA	.	.		0.438	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		A	232325414	T	A	232325414	3	1	59	1	0	0	0	0	1	0	0	0	10235	1606	56	4	1399	4	NCL	2	232325414	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	52905711	232325414	10873959	18	7283										
TTC21A	199223	hgsc.bcm.edu	37	chr3	39171742	39171742	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gacactttccccaccagcccGagaaggccctggaggtctat	10	15	1	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr3:39171742G>T	ENST00000431162.2	+	17	2367	c.2233G>T	c.(2233-2235)Gag>Tag	p.E745*	TTC21A_ENST00000440121.1_Nonsense_Mutation_p.E697*|TTC21A_ENST00000301819.6_Nonsense_Mutation_p.E746*			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	745										NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CCACCAGCCCGAGAAGGCCCT	0.582																																					p.E745X		Atlas-SNP	.											.	TTC21A	96	.	0			c.G2233T						.						44	45	45					3																	39171742		1914	4118	6032	SO:0001587	stop_gained	199223	exon17			CAGCCCGAGAAGG	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"Tetratricopeptide (TTC) repeat domain containing"	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.2233G>T	chr3.hg19:g.39171742G>T	ENSP00000398211:p.Glu745*	77.0	0.0		63.0	42.0	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Nonsense_Mutation	SNP	ENST00000431162.2	hg19	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	38	7.162369	0.98107	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	.	.	.	4.85	4.85	0.62838	.	0.159354	0.38217	N	0.001765	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-28.9477	17.1263	0.86715	0.0:0.0:1.0:0.0	.	.	.	.	X	746;728;745;697	.	ENSP00000301819:E746X	E	+	1	0	TTC21A	39146746	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.872000	0.75536	2.414000	0.81942	0.563000	0.77884	GAG	.	.		0.582	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		T	39171742	G	T	39171742	4	4	59	1	0	0	0	0	0	1	0	0	16702	1059	37	1	2302	1	TTC21A	3	39171742	Nonsense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10		39171742	158850688	19	7284										
ZIC4	84107	hgsc.bcm.edu	37	chr3	147120535	147120535	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ttgactctttaagagtgtttCggtaaagccgtaatcgtttc	9	7	1	2	rs148365070		TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr3:147120535C>G	ENST00000383075.3	-	2	562	c.50G>C	c.(49-51)cGa>cCa	p.R17P	ZIC4_ENST00000484399.1_Missense_Mutation_p.R17P|ZIC4_ENST00000491672.1_Missense_Mutation_p.R17P|ZIC4_ENST00000425731.3_Missense_Mutation_p.R55P|ZIC4_ENST00000525172.2_Missense_Mutation_p.R67P|ZIC4_ENST00000473123.1_Missense_Mutation_p.R17P	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	17						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						AAGAGTGTTTCGGTAAAGCCG	0.353																																					p.R67P		Atlas-SNP	.											ZIC4_ENST00000525172,NS,carcinoma,0,4	ZIC4	174	.	0			c.G200C						.						152	139	143					3																	147120535		1854	4089	5943	SO:0001583	missense	84107	exon2			GTGTTTCGGTAAA	AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"Zinc fingers, C2H2-type"	20393	protein-coding gene	gene with protein product		608948	"zinc finger protein of the cerebellum 4"				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.50G>C	chr3.hg19:g.147120535C>G	ENSP00000372553:p.Arg17Pro	181.0	0.0		191.0	65.0	NM_001168378	A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Missense_Mutation	SNP	ENST00000383075.3	hg19	CCDS43160.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.825324	0.71143	.	.	ENSG00000174963	ENST00000383075;ENST00000425731;ENST00000525172;ENST00000484399;ENST00000473123;ENST00000491672;ENST00000462748;ENST00000484586;ENST00000463250	T;T;T;T;T;T;T	0.38077	2.63;2.43;2.39;2.63;2.63;1.16;2.48	6.06	5.19	0.71726	.	0.670270	0.12134	N	0.496457	T	0.33411	0.0862	L	0.27053	0.805	0.80722	D	1	P;P	0.43094	0.766;0.799	P;B	0.44811	0.461;0.423	T	0.08330	-1.0727	10	0.87932	D	0	.	11.3963	0.49843	0.0:0.8625:0.0:0.1375	.	67;17	B7Z2L2;Q8N9L1	.;ZIC4_HUMAN	P	17;55;67;17;17;17;17;17;17	ENSP00000372553:R17P;ENSP00000397695:R55P;ENSP00000435509:R67P;ENSP00000417855:R17P;ENSP00000420775:R17P;ENSP00000418277:R17P;ENSP00000420627:R17P	ENSP00000372553:R17P	R	-	2	0	ZIC4	148603225	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.965000	0.40471	1.576000	0.49790	0.655000	0.94253	CGA	.	C|0.999;T|0.001		0.353	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1			G	147120535	C	G	147120535	3	3	59	1	0	0	0	0	1	0	0	0	17696	884	31	4	970	4	ZIC4	3	147120535	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	107948793	147120535	50901895	20	7285										
ABCC5	10057	hgsc.bcm.edu	37	chr3	183667834	183667834	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	aggaaccacgggaagactccTgcgatcattcccacacagaa	9	13	1	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr3:183667834T>A	ENST00000334444.6	-	21	3264	c.3024A>T	c.(3022-3024)gcA>gcT	p.A1008A	ABCC5_ENST00000265586.6_Silent_p.A1008A	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	1008	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	GGAAGACTCCTGCGATCATTC	0.517																																					p.A1008A		Atlas-SNP	.											.	ABCC5	142	.	0			c.A3024T						.						59	67	64					3																	183667834		2067	4220	6287	SO:0001819	synonymous_variant	10057	exon21			GACTCCTGCGATC	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.3024A>T	chr3.hg19:g.183667834T>A		105.0	0.0		143.0	45.0	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	hg19	CCDS43176.1																																																																																			.	.		0.517	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		A	183667834	T	A	183667834	2	1	59	1	0	0	0	0	0	0	0	1	56	1567	55	4		4	ABCC5	3	183667834	Silent	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	36547299	183667834	14354596	21	7286										
ZNF141	7700	hgsc.bcm.edu	37	chr4	367384	367397	+	Frame_Shift_Del	DEL	AAAAATTCATACTG	AAAAATTCATACTG	-													0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	agggtcctgaatgaacataaAaaaattcatactggagagaa					rs544940326		TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	AAAAATTCATACTG	AAAAATTCATACTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr4:367384_367397delAAAAATTCATACTG	ENST00000240499.7	+	4	1307_1320	c.1158_1171delAAAAATTCATACTG	c.(1156-1173)aaaaaaattcatactggafs	p.KIHTG387fs	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	387					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						ATGAACATAAAAAAATTCATACTGGAGAGAAACC	0.411																																					p.386_390del		Atlas-Indel,Pindel	.											.	ZNF141	48	.	0			c.1157_1170del						.																																			SO:0001589	frameshift_variant	7700	exon4			.	L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"Zinc fingers, C2H2-type", "-"	12926	protein-coding gene	gene with protein product		194648	"zinc finger protein 141 (clone pHZ-44)"	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.1158_1171delAAAAATTCATACTG	chr4.hg19:g.367384_367397delAAAAATTCATACTG	ENSP00000240499:p.Lys387fs	111.0	0.0		125.0	17.0	NM_003441	Q6DK07	Frame_Shift_Del	DEL	ENST00000240499.7	hg19	CCDS33931.1																																																																																			.	.		0.411	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441		-	367397	AAAAATTCATACTG	-	367384	7	5	59	1	0	1	0	1	0	0	0	0	17745	11	1	0	1172	0	ZNF141	4	367384	Frame_Shift_Del	DEL	AAAAATTCATACTG	TCGA-CC-5263-01A-01D-A12Z-10		367384	190786892	22	7287										
CEP135	9662	hgsc.bcm.edu	37	chr4	56846403	56846403	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	aaaatatatggaagatatacAgtccaatgttaaattattga	6	3	0	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr4:56846403A>T	ENST00000257287.4	+	12	1692	c.1568A>T	c.(1567-1569)cAg>cTg	p.Q523L		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	523					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					GAAGATATACAGTCCAATGTT	0.289																																					p.Q523L		Atlas-SNP	.											.	CEP135	115	.	0			c.A1568T						.						71	74	73					4																	56846403		2203	4296	6499	SO:0001583	missense	9662	exon12			ATATACAGTCCAA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.1568A>T	chr4.hg19:g.56846403A>T	ENSP00000257287:p.Gln523Leu	502.0	0.0		432.0	168.0	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	hg19	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.387832	0.82902	.	.	ENSG00000174799	ENST00000257287	T	0.57273	0.41	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.73187	0.3555	M	0.78801	2.425	0.58432	D	0.999995	D	0.89917	1.0	D	0.80764	0.994	T	0.74553	-0.3627	10	0.46703	T	0.11	.	16.2813	0.82687	1.0:0.0:0.0:0.0	.	523	Q66GS9	CP135_HUMAN	L	523	ENSP00000257287:Q523L	ENSP00000257287:Q523L	Q	+	2	0	CEP135	56541160	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.121000	0.71602	2.244000	0.73946	0.533000	0.62120	CAG	.	.		0.289	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		T	56846403	A	T	56846403	3	4	59	1	0	0	0	0	1	0	0	0	3249	188	7	4	1610	4	CEP135	4	56846403	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	56479019	56846403	134307873	23	7288										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123274094	123274094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	atcatcgacactggcctggaGtattgaaggtggtatcagga	13	7	2	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr4:123274094G>A	ENST00000264501.4	+	81	14258	c.13885G>A	c.(13885-13887)Gta>Ata	p.V4629I	KIAA1109_ENST00000388738.3_Missense_Mutation_p.V4629I			Q2LD37	K1109_HUMAN	KIAA1109	4629					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CTGGCCTGGAGTATTGAAGGT	0.418																																					p.V4629I		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G13885A						.						163	156	158					4																	123274094		1998	4182	6180	SO:0001583	missense	84162	exon79			CCTGGAGTATTGA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.13885G>A	chr4.hg19:g.123274094G>A	ENSP00000264501:p.Val4629Ile	121.0	0.0		152.0	52.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.741024	0.89573	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707;ENST00000431755	T;T;T	0.50277	0.75;0.75;0.75	5.98	5.98	0.97165	Fragile site-associated protein, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.64327	0.2588	L	0.47716	1.5	0.80722	D	1	D;D	0.69078	0.99;0.997	D;D	0.79108	0.98;0.992	T	0.55939	-0.8061	10	0.32370	T	0.25	.	20.4581	0.99154	0.0:0.0:1.0:0.0	.	4628;4629	Q2LD37-4;Q2LD37	.;K1109_HUMAN	I	4629;4629;1298;230	ENSP00000264501:V4629I;ENSP00000373390:V4629I;ENSP00000410874:V1298I	ENSP00000264501:V4629I	V	+	1	0	KIAA1109	123493544	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	9.869000	0.99810	2.835000	0.97688	0.650000	0.86243	GTA	.	.		0.418	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123274094	G	A	123274094	3	1	59	1	0	0	0	0	1	0	0	0	8217	1029	36	3	14199	3	KIAA1109	4	123274094	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	66427691	123274094	67880182	24	7289										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158262498	158262499	+	Missense_Mutation	DNP	GC	GC	AA													0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cctacacggctaacttagctGccttcctgactgtagagagg							TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr4:158262498_158262499GC>AA	ENST00000264426.9	+	12	2206_2207	c.1927_1928GC>AA	c.(1927-1929)GCc>AAc	p.A643N	GRIA2_ENST00000393815.2_Missense_Mutation_p.A596N|GRIA2_ENST00000507898.1_Missense_Mutation_p.A596N|GRIA2_ENST00000449365.1_Missense_Mutation_p.A596N|GRIA2_ENST00000296526.7_Missense_Mutation_p.A643N	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	643					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TAACTTAGCTGCCTTCCTGACT	0.455																																					p.A643T|p.A643D		Atlas-SNP	.											.	GRIA2	358	.	0			c.G1927A|c.C1928A						.																																			SO:0001583	missense	2891	exon12			TTAGCTGCCTTCC|TAGCTGCCTTCCT		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	Exception_encountered	chr4.hg19:g.158262498_158262499delinsAA	ENSP00000264426:p.Ala643Asn	639.0|634.0	1.0|2.0		608.0|600.0	231.0|227.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1																																																																																			.	.		0.455	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			AA	158262499	GC	AA	158262498	3	1	59	1	0	0	0	0	1	0	0	0	6777	1319	46	3	1973	3	GRIA2	4	158262498	Missense_Mutation	DNP	GC	TCGA-CC-5263-01A-01D-A12Z-10	34988404	158262498	32891778	25	7290										
SLC1A3	6507	hgsc.bcm.edu	37	chr5	36684073	36684073	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cctgcccactgacgacatcaCgctcatcatcgcggtggact	9	16	3	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr5:36684073C>T	ENST00000265113.4	+	9	1873	c.1397C>T	c.(1396-1398)aCg>aTg	p.T466M	SLC1A3_ENST00000381918.3_Intron|CTD-2353F22.1_ENST00000510740.1_RNA	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	466					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GACGACATCACGCTCATCATC	0.597																																					p.T466M		Atlas-SNP	.											.	SLC1A3	88	.	0			c.C1397T						.						171	143	153					5																	36684073		2203	4300	6503	SO:0001583	missense	6507	exon9			ACATCACGCTCAT		CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"Solute carriers"	10941	protein-coding gene	gene with protein product	"glutamate transporter variant EAAT1ex9skip"	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.1397C>T	chr5.hg19:g.36684073C>T	ENSP00000265113:p.Thr466Met	173.0	0.0		383.0	87.0	NM_004172	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	hg19	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732405	0.89482	.	.	ENSG00000079215	ENST00000265113;ENST00000427100	T	0.59502	0.26	5.74	5.74	0.90152	.	0.047302	0.85682	D	0.000000	T	0.80592	0.4652	M	0.87097	2.86	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	T	0.83127	-0.0115	10	0.87932	D	0	-17.5109	19.9326	0.97124	0.0:1.0:0.0:0.0	.	466	P43003	EAA1_HUMAN	M	466;414	ENSP00000265113:T466M	ENSP00000265113:T466M	T	+	2	0	SLC1A3	36719830	1.000000	0.71417	0.993000	0.49108	0.975000	0.68041	5.969000	0.70422	2.720000	0.93068	0.650000	0.86243	ACG	.	.		0.597	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172		T	36684073	C	T	36684073	3	4	59	1	0	0	0	0	1	0	0	0	14448	536	19	1	1444	1	SLC1A3	5	36684073	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10		36684073	144231187	26	7291										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38427282	38427282	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tgacacaggcagcaaagactTcctgtccatcaacttggcag	9	12	1	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr5:38427282T>A	ENST00000354891.3	+	14	2328	c.1982T>A	c.(1981-1983)tTc>tAc	p.F661Y	EGFLAM_ENST00000336740.6_Missense_Mutation_p.F427Y|EGFLAM-AS1_ENST00000508986.1_RNA|EGFLAM_ENST00000397202.2_Missense_Mutation_p.F27Y|EGFLAM_ENST00000322350.5_Missense_Mutation_p.F661Y	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	661	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					AGCAAAGACTTCCTGTCCATC	0.537																																					p.F661Y	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.T1982A						.						154	153	153					5																	38427282		2203	4300	6503	SO:0001583	missense	133584	exon14			AAGACTTCCTGTC	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.1982T>A	chr5.hg19:g.38427282T>A	ENSP00000346964:p.Phe661Tyr	104.0	0.0		165.0	43.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	hg19	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.004289	0.93287	.	.	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000397202;ENST00000339580	T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.31	5.76	5.76	0.90799	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.88804	0.6536	M	0.70275	2.135	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.993	D;D;D	0.91635	0.999;0.999;0.946	D	0.88418	0.3026	10	0.42905	T	0.14	-10.3947	16.0677	0.80897	0.0:0.0:0.0:1.0	.	427;661;661	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	Y	661;661;427;27;427	ENSP00000346964:F661Y;ENSP00000313084:F661Y;ENSP00000337607:F427Y;ENSP00000380385:F27Y	ENSP00000313084:F661Y	F	+	2	0	EGFLAM	38463039	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.635000	0.83286	2.201000	0.70794	0.533000	0.62120	TTC	.	.		0.537	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		A	38427282	T	A	38427282	3	1	59	1	0	0	0	0	1	0	0	0	4968	1783	62	4	2050	4	EGFLAM	5	38427282	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	1743209	38427282	142487978	27	7292										
GPR98	84059	hgsc.bcm.edu	37	chr5	89910835	89910835	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	aaatgttactgcaattgtatCggtaagaaattattatagct	7	4	0	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr5:89910835C>A	ENST00000405460.2	+	2	302	c.206C>A	c.(205-207)tCg>tAg	p.S69*		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	69	Calx-beta 1. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GCAATTGTATCGGTAAGAAAT	0.308																																					p.S69X		Atlas-SNP	.											.	GPR98	605	.	0			c.C206A						.						46	41	43					5																	89910835		1804	4056	5860	SO:0001630	splice_region_variant	84059	exon2			TTGTATCGGTAAG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.207+1C>A	chr5.hg19:g.89910835C>A		227.0	0.0		109.0	63.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Nonsense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.034704	0.93575	.	.	ENSG00000164199	ENST00000508842;ENST00000405460;ENST00000296619;ENST00000399043	.	.	.	5.98	5.98	0.97165	.	0.167402	0.48286	D	0.000194	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	15.2005	0.73132	0.1408:0.8592:0.0:0.0	.	.	.	.	X	73;69;69;69	.	ENSP00000296619:S69X	S	+	2	0	GPR98	89946591	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.714000	0.47202	2.838000	0.97847	0.591000	0.81541	TCG	.	.		0.308	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	Nonsense_Mutation	A	89910835	C	A	89910835	5	1	59	1	0	0	0	0	0	0	1	0	6730	898	31	1	212	1	GPR98	5	89910835	Splice_Site	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	51483553	89910835	91004425	28	7293										
RNF182	221687	hgsc.bcm.edu	37	chr6	13977395	13977395	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	actgcggagtctcaggcctcTgatgagctggagtgcaaaat	13	9	2	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr6:13977395T>C	ENST00000488300.1	+	3	568	c.45T>C	c.(43-45)tcT>tcC	p.S15S	RNF182_ENST00000537663.1_Silent_p.S15S|RNF182_ENST00000537388.1_Silent_p.S15S|RNF182_ENST00000544682.1_Silent_p.S15S	NM_152737.3	NP_689950.1	Q8N6D2	RN182_HUMAN	ring finger protein 182	15					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|large_intestine(7)|liver(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(50;0.00405)|Ovarian(93;0.0964)	all_hematologic(90;0.135)	Epithelial(50;0.195)			CTCAGGCCTCTGATGAGCTGG	0.463																																					p.S15S		Atlas-SNP	.											.	RNF182	51	.	0			c.T45C						.						113	114	114					6																	13977395		2203	4300	6503	SO:0001819	synonymous_variant	221687	exon4			GGCCTCTGATGAG	AK090576	CCDS4531.1	6p23	2013-01-09			ENSG00000180537	ENSG00000180537		"RING-type (C3HC4) zinc fingers"	28522	protein-coding gene	gene with protein product						12477932	Standard	NM_152737		Approved	MGC33993	uc003nbg.3	Q8N6D2	OTTHUMG00000014280	ENST00000488300.1:c.45T>C	chr6.hg19:g.13977395T>C		113.0	0.0		193.0	85.0	NM_001165032	B2RDG2|Q8NBG3	Silent	SNP	ENST00000488300.1	hg19	CCDS4531.1																																																																																			.	.		0.463	RNF182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039911.2	NM_152737		C	13977395	T	C	13977395	2	2	59	1	0	0	0	0	0	0	0	1	13481	1567	55	2		2	RNF182	6	13977395	Silent	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10		13977395	157137672	29	7294										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76024218	76024218	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ggtgcactcagatttactctTgctaaatgcttcttccaatt	6	10	3	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr6:76024218T>A	ENST00000237172.7	-	5	1660	c.1330A>T	c.(1330-1332)Aag>Tag	p.K444*	FILIP1_ENST00000393004.2_Nonsense_Mutation_p.K444*|FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Nonsense_Mutation_p.K345*	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	444										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GATTTACTCTTGCTAAATGCT	0.408																																					p.K444X		Atlas-SNP	.											.	FILIP1	173	.	0			c.A1330T						.						141	142	142					6																	76024218		2203	4300	6503	SO:0001587	stop_gained	27145	exon5			TACTCTTGCTAAA	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.1330A>T	chr6.hg19:g.76024218T>A	ENSP00000237172:p.Lys444*	457.0	1.0		662.0	328.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Nonsense_Mutation	SNP	ENST00000237172.7	hg19	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	T	38	6.803656	0.97849	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	.	.	.	5.65	3.07	0.35406	.	0.221173	0.45867	D	0.000329	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.2141	12.2983	0.54860	0.0:0.0:0.2768:0.7232	.	.	.	.	X	444;444;345	.	ENSP00000237172:K444X	K	-	1	0	FILIP1	76080938	0.800000	0.28916	1.000000	0.80357	0.942000	0.58702	0.942000	0.29017	1.057000	0.40506	0.533000	0.62120	AAG	.	.		0.408	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76024218	T	A	76024218	4	1	59	1	0	0	0	0	0	1	0	0	5902	1821	63	4	2319	4	FILIP1	6	76024218	Nonsense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	62046823	76024218	95090849	30	7295										
CITED2	10370	hgsc.bcm.edu	37	chr6	139694674	139694675	+	Missense_Mutation	DNP	CG	CG	TT													0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cctgcagcagggtgcaaatcCggcatgtagtggttgtgggg							TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr6:139694674_139694675CG>TT	ENST00000367651.2	-	2	622_623	c.407_408CG>AA	c.(406-408)cCG>cAA	p.P136Q	CITED2_ENST00000536159.1_Missense_Mutation_p.P136Q|CITED2_ENST00000537332.1_Missense_Mutation_p.P136Q	NM_006079.4	NP_006070.2	Q99967	CITE2_HUMAN	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	136					adrenal cortex formation (GO:0035802)|bone morphogenesis (GO:0060349)|cardiac neural crest cell development involved in heart development (GO:0061308)|cell aging (GO:0007569)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|cranial nerve morphogenesis (GO:0021602)|decidualization (GO:0046697)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endocardial cushion development (GO:0003197)|erythrocyte development (GO:0048821)|granulocyte differentiation (GO:0030851)|heart development (GO:0007507)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|left/right axis specification (GO:0070986)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|peripheral nervous system development (GO:0007422)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of gene expression (GO:0010628)|positive regulation of male gonad development (GO:2000020)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|pulmonary artery morphogenesis (GO:0061156)|regulation of organ formation (GO:0003156)|regulation of RNA biosynthetic process (GO:2001141)|response to estrogen (GO:0043627)|response to fluid shear stress (GO:0034405)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sex determination (GO:0007530)|skeletal muscle cell differentiation (GO:0035914)|spleen development (GO:0048536)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|LBD domain binding (GO:0050693)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(4)	5	Breast(32;0.226)			GBM - Glioblastoma multiforme(68;0.000171)|OV - Ovarian serous cystadenocarcinoma(155;0.00134)		GGTGCAAATCCGGCATGTAGTG	0.624																																					p.P141P|p.P141Q	NSCLC(98;1219 1550 33720 43229 49330)	Atlas-SNP	.											.	CITED2	16	.	0			c.G423A|c.C422A						.																																			SO:0001583	missense	10370	exon2			CAAATCCGGCATG|AAATCCGGCATGT	U65093	CCDS5195.1, CCDS75530.1	6q23.3	2008-08-29			ENSG00000164442	ENSG00000164442			1987	protein-coding gene	gene with protein product		602937				8901575, 10552932	Standard	NM_006079		Approved	MRG1	uc021zfz.2	Q99967	OTTHUMG00000015691	ENST00000367651.2:c.407_408delinsTT	chr6.hg19:g.139694674_139694675delinsTT	ENSP00000356623:p.Pro136Gln	154.0	0.0		288.0|291.0	141.0|145.0	NM_001168389	O95426|Q5VTF4	Silent|Missense_Mutation	SNP	ENST00000367651.2	hg19	CCDS5195.1																																																																																			.	.		0.624	CITED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042463.1			TT	139694675	CG	TT	139694674	3	4	59	1	0	0	0	0	1	0	0	0	3442	639	23	1	408	1	CITED2	6	139694674	Missense_Mutation	DNP	CG	TCGA-CC-5263-01A-01D-A12Z-10	63670456	139694674	31420393	31	7296										
SASH1	23328	hgsc.bcm.edu	37	chr6	148867236	148867236	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gcgggacgtcgccgccaacaTggaccagatccgggtgaagc	15	13	0	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr6:148867236T>A	ENST00000367467.3	+	19	3909	c.3434T>A	c.(3433-3435)aTg>aAg	p.M1145K		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	1145					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GCCGCCAACATGGACCAGATC	0.602																																					p.M1145K		Atlas-SNP	.											.	SASH1	123	.	0			c.T3434A						.						71	64	66					6																	148867236		2203	4300	6503	SO:0001583	missense	23328	exon19			CCAACATGGACCA	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.3434T>A	chr6.hg19:g.148867236T>A	ENSP00000356437:p.Met1145Lys	57.0	0.0		104.0	51.0	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	hg19	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.028284	0.75390	.	.	ENSG00000111961	ENST00000367467;ENST00000537769	T	0.41065	1.01	5.46	5.46	0.80206	.	0.229371	0.64402	D	0.000020	T	0.17195	0.0413	N	0.24115	0.695	0.51767	D	0.999936	P	0.36048	0.534	B	0.28553	0.091	T	0.11084	-1.0602	10	0.87932	D	0	-18.4612	15.5466	0.76108	0.0:0.0:0.0:1.0	.	1145	O94885	SASH1_HUMAN	K	1145;555	ENSP00000356437:M1145K	ENSP00000356437:M1145K	M	+	2	0	SASH1	148908929	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.519000	0.81809	2.077000	0.62373	0.533000	0.62120	ATG	.	.		0.602	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		A	148867236	T	A	148867236	3	1	59	1	0	0	0	0	1	0	0	0	13863	1464	51	4	3508	4	SASH1	6	148867236	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	9172562	148867236	22247831	32	7297										
NOX3	50508	hgsc.bcm.edu	37	chr6	155718096	155718096	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	aagaacacgccaatactgctGctgcagtaggggtaagaaaa	11	8	0	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr6:155718096G>T	ENST00000159060.2	-	13	1683	c.1581C>A	c.(1579-1581)agC>agA	p.S527R		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	527					detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		CAATACTGCTGCTGCAGTAGG	0.458																																					p.S527R		Atlas-SNP	.											.	NOX3	93	.	0			c.C1581A						.						60	62	61					6																	155718096		2203	4300	6503	SO:0001630	splice_region_variant	50508	exon13			ACTGCTGCTGCAG	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.1581-1C>A	chr6.hg19:g.155718096G>T		77.0	0.0		159.0	38.0	NM_015718	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	hg19	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.899972	0.33535	.	.	ENSG00000074771	ENST00000159060	D	0.95001	-3.58	5.53	5.53	0.82687	Ferric reductase, NAD binding (1);	0.089605	0.48767	D	0.000164	D	0.91637	0.7357	L	0.27975	0.815	0.46149	D	0.998891	D	0.56746	0.977	P	0.62298	0.9	D	0.89533	0.3787	10	0.21540	T	0.41	.	12.0236	0.53358	0.0788:0.0:0.9212:0.0	.	527	Q9HBY0	NOX3_HUMAN	R	527	ENSP00000159060:S527R	ENSP00000159060:S527R	S	-	3	2	NOX3	155759788	1.000000	0.71417	1.000000	0.80357	0.500000	0.33767	3.888000	0.56204	2.608000	0.88229	0.561000	0.74099	AGC	.	.		0.458	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		Missense_Mutation	T	155718096	G	T	155718096	5	4	59	1	0	0	0	0	0	0	1	0	10566	1333	46	3	129	3	NOX3	6	155718096	Splice_Site	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	6850860	155718096	15396971	33	7298										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160454027	160454027	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tgttttatttgaatgtctgtGgagaaactgaaatacagttc	9	4	1	3			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr6:160454027G>T	ENST00000356956.1	+	9	1247	c.1099G>T	c.(1099-1101)Gga>Tga	p.G367*		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	367					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	GAATGTCTGTGGAGAAACTGA	0.338																																					p.G367X		Atlas-SNP	.											.	IGF2R	251	.	0			c.G1099T						.						92	97	96					6																	160454027		2203	4300	6503	SO:0001587	stop_gained	3482	exon9			GTCTGTGGAGAAA	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.1099G>T	chr6.hg19:g.160454027G>T	ENSP00000349437:p.Gly367*	143.0	0.0		197.0	59.0	NM_000876	Q7Z7G9|Q96PT5	Nonsense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	36	5.629446	0.96671	.	.	ENSG00000197081	ENST00000356956	.	.	.	4.81	4.81	0.61882	.	0.113164	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-17.0764	16.4499	0.83976	0.0:0.0:1.0:0.0	.	.	.	.	X	367	.	ENSP00000349437:G367X	G	+	1	0	IGF2R	160374017	1.000000	0.71417	0.459000	0.27081	0.120000	0.20174	4.843000	0.62838	2.386000	0.81285	0.655000	0.94253	GGA	.	.		0.338	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		T	160454027	G	T	160454027	4	4	59	1	0	0	0	0	0	1	0	0	7585	1349	47	3	1133	3	IGF2R	6	160454027	Nonsense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	4735931	160454027	10661040	34	7299										
PDE10A	10846	hgsc.bcm.edu	37	chr6	165846593	165846593	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	acgagtccctgattccagtcCagtacctcttggaaatcgtt	8	12	1	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr6:165846593C>G	ENST00000366882.1	-	8	686	c.532G>C	c.(532-534)Gga>Cga	p.G178R	PDE10A_ENST00000539869.2_Missense_Mutation_p.G188R|PDE10A_ENST00000354448.4_Missense_Mutation_p.G178R			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	178	GAF 1.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	GATTCCAGTCCAGTACCTCTT	0.388																																					p.G188R	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											.	PDE10A	154	.	0			c.G562C						.						94	90	91					6																	165846593		2203	4300	6503	SO:0001583	missense	10846	exon7			CCAGTCCAGTACC	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.532G>C	chr6.hg19:g.165846593C>G	ENSP00000355847:p.Gly178Arg	231.0	0.0		323.0	84.0	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	hg19		.	.	.	.	.	.	.	.	.	.	C	27.8	4.867217	0.91511	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.69435	-0.4;-0.4	5.89	5.89	0.94794	GAF (2);	0.000000	0.85682	D	0.000000	T	0.79364	0.4433	M	0.68952	2.095	0.80722	D	1	D;P	0.89917	1.0;0.86	D;P	0.97110	1.0;0.643	T	0.79475	-0.1788	10	0.72032	D	0.01	.	20.2508	0.98407	0.0:1.0:0.0:0.0	.	188;178	Q9ULW9;Q9Y233	.;PDE10_HUMAN	R	178;206;188;178;177	ENSP00000355847:G178R;ENSP00000346435:G178R	ENSP00000341187:G188R	G	-	1	0	PDE10A	165766583	1.000000	0.71417	0.927000	0.36925	0.842000	0.47809	7.538000	0.82048	2.788000	0.95919	0.585000	0.79938	GGA	.	.		0.388	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			G	165846593	C	G	165846593	3	3	59	1	0	0	0	0	1	0	0	0	11639	603	21	4	1871	4	PDE10A	6	165846593	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	5392566	165846593	5268474	35	7300										
AOAH	313	hgsc.bcm.edu	37	chr7	36633945	36633945	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gggtgcacaaagacacttacCcaacagtggagtccagaaat	10	10	0	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr7:36633945C>T	ENST00000258749.5	-	12	1337	c.938G>A	c.(937-939)gGa>gAa	p.G313E	AOAH_ENST00000535891.1_Splice_Site_p.G281E|AOAH_ENST00000538464.1_Splice_Site_p.G35E|AOAH_ENST00000431169.1_Splice_Site_p.G313E	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	313					inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						AGACACTTACCCAACAGTGGA	0.448																																					p.G313E		Atlas-SNP	.											.	AOAH	79	.	0			c.G938A						.						133	127	129					7																	36633945		2203	4300	6503	SO:0001630	splice_region_variant	313	exon12			ACTTACCCAACAG	BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.938+1G>A	chr7.hg19:g.36633945C>T		146.0	0.0		213.0	12.0	NM_001637	A4D1Y5|B7Z490|Q53F13	Missense_Mutation	SNP	ENST00000258749.5	hg19	CCDS5448.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.741165	0.30865	.	.	ENSG00000136250	ENST00000538464;ENST00000535891;ENST00000258749;ENST00000431169;ENST00000544647	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.05	4.17	0.49024	Esterase, SGNH hydrolase-type (1);Lipase, GDSL (1);	0.736603	0.12841	N	0.434811	T	0.26666	0.0652	.	.	.	0.39287	D	0.964669	P;P;B	0.51057	0.849;0.941;0.166	P;P;B	0.49192	0.602;0.577;0.138	T	0.03315	-1.1049	8	.	.	.	-9.2314	9.0872	0.36587	0.0:0.9015:0.0:0.0985	.	281;313;313	B7Z490;C9J8T1;P28039	.;.;AOAH_HUMAN	E	35;281;313;313;313	ENSP00000439283:G35E;ENSP00000441101:G281E;ENSP00000258749:G313E;ENSP00000405683:G313E	.	G	-	2	0	AOAH	36600470	0.966000	0.33281	0.779000	0.31741	0.003000	0.03518	2.282000	0.43461	1.360000	0.45960	0.557000	0.71058	GGA	.	.		0.448	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	Missense_Mutation	T	36633945	C	T	36633945	5	4	59	1	0	0	0	0	0	0	1	0	726	637	22	3	1170	3	AOAH	7	36633945	Splice_Site	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10		36633945	122504718	36	7301										
TPST1	8460	hgsc.bcm.edu	37	chr7	65751568	65751568	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tatcaaaatgggttgggaagAtaccgccagatgttttacaa	10	6	1	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr7:65751568A>G	ENST00000304842.5	+	3	1341	c.916A>G	c.(916-918)Ata>Gta	p.I306V	TPST1_ENST00000480281.1_3'UTR	NM_003596.3	NP_003587.1	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1	306					inflammatory response (GO:0006954)|peptidyl-tyrosine sulfation (GO:0006478)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			NS(1)|biliary_tract(1)|breast(1)|kidney(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						GGTTGGGAAGATACCGCCAGA	0.413																																					p.I306V		Atlas-SNP	.											.	TPST1	25	.	0			c.A916G						.						140	124	130					7																	65751568		2203	4300	6503	SO:0001583	missense	8460	exon3			GGGAAGATACCGC	AF038009	CCDS5533.1	7q11.21	2012-12-13			ENSG00000169902	ENSG00000169902	2.8.2.20	"Sulfotransferases, membrane-bound"	12020	protein-coding gene	gene with protein product	"transport and golgi organization 13 homolog A (Drosophila)"	603125				9501187	Standard	NM_003596		Approved	TANGO13A	uc003tuw.3	O60507	OTTHUMG00000023871	ENST00000304842.5:c.916A>G	chr7.hg19:g.65751568A>G	ENSP00000302413:p.Ile306Val	139.0	0.0		147.0	68.0	NM_003596	A4D2M0|Q6FGM7	Missense_Mutation	SNP	ENST00000304842.5	hg19	CCDS5533.1	.	.	.	.	.	.	.	.	.	.	A	17.36	3.370232	0.61624	.	.	ENSG00000169902	ENST00000304842;ENST00000544114	T	0.45276	0.9	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.55033	0.1895	M	0.86740	2.835	0.80722	D	1	P;P	0.40834	0.73;0.467	B;B	0.43445	0.42;0.175	T	0.61108	-0.7129	10	0.42905	T	0.14	-21.5617	14.8826	0.70545	1.0:0.0:0.0:0.0	.	306;306	F5H7U7;O60507	.;TPST1_HUMAN	V	306	ENSP00000302413:I306V	ENSP00000302413:I306V	I	+	1	0	TPST1	65389003	1.000000	0.71417	0.997000	0.53966	0.900000	0.52787	8.266000	0.89871	2.123000	0.65237	0.383000	0.25322	ATA	.	.		0.413	TPST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251705.2	NM_003596		G	65751568	A	G	65751568	3	3	59	1	0	0	0	0	1	0	0	0	16442	333	12	2	922	2	TPST1	7	65751568	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	29117623	65751568	93387095	37	7302										
CALN1	83698	hgsc.bcm.edu	37	chr7	71571275	71571275	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	agaacccgaaaggcctctcgGatttctacaatggaaaagca	9	10	2	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr7:71571275G>T	ENST00000329008.5	-	3	421	c.123C>A	c.(121-123)atC>atA	p.I41I	CALN1_ENST00000405452.2_Silent_p.I41I|CALN1_ENST00000412588.1_Silent_p.I83I|CALN1_ENST00000395276.2_Silent_p.I41I|CALN1_ENST00000431984.1_Silent_p.I41I|CALN1_ENST00000395275.2_Silent_p.I83I	NM_001017440.2	NP_001017440.1	Q9BXU9	CABP8_HUMAN	calneuron 1	41	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(6)|lung(19)|skin(2)	32		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				AGGCCTCTCGGATTTCTACAA	0.522																																					p.I83I		Atlas-SNP	.											.	CALN1	92	.	0			c.C249A						.						48	50	49					7																	71571275		2203	4300	6503	SO:0001819	synonymous_variant	83698	exon4			CTCTCGGATTTCT	AF282250	CCDS5541.1, CCDS47603.1	7q11	2013-01-10			ENSG00000183166	ENSG00000183166		"EF-hand domain containing"	13248	protein-coding gene	gene with protein product	"calcium-binding protein CABP8"	607176				11286509	Standard	NM_031468		Approved		uc003twb.4	Q9BXU9	OTTHUMG00000023787	ENST00000329008.5:c.123C>A	chr7.hg19:g.71571275G>T		45.0	0.0		56.0	20.0	NM_031468	J3KQA7	Silent	SNP	ENST00000329008.5	hg19	CCDS5541.1																																																																																			.	.		0.522	CALN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320044.2	NM_031468		T	71571275	G	T	71571275	2	4	59	1	0	0	0	0	0	0	0	1	2593	1164	41	3		3	CALN1	7	71571275	Silent	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	5819707	71571275	87567388	38	7303										
YWHAG	7532	hgsc.bcm.edu	37	chr7	75959524	75959524	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	agaaggtttcgttcctcattCgacagtggctcattcagctc	9	11	3	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr7:75959524C>G	ENST00000307630.3	-	2	336	c.114G>C	c.(112-114)tcG>tcC	p.S38S		NM_012479.3	NP_036611.2	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma	38					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of neuron differentiation (GO:0045664)|regulation of signal transduction (GO:0009966)|regulation of synaptic plasticity (GO:0048167)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	insulin-like growth factor receptor binding (GO:0005159)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)|protein kinase C inhibitor activity (GO:0008426)			endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8						GTTCCTCATTCGACAGTGGCT	0.502																																					p.S38S		Atlas-SNP	.											.	YWHAG	24	.	0			c.G114C						.						76	58	64					7																	75959524		2203	4300	6503	SO:0001819	synonymous_variant	7532	exon2			CTCATTCGACAGT	AF142498	CCDS5584.1	7q11.23	2014-06-13	2013-12-03		ENSG00000170027	ENSG00000170027			12852	protein-coding gene	gene with protein product	"14-3-3 gamma", "protein phosphatase 1, regulatory subunit 170"	605356	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide"			10486217, 10433554	Standard	NM_012479		Approved	PPP1R170	uc011kgj.1	P61981	OTTHUMG00000022862	ENST00000307630.3:c.114G>C	chr7.hg19:g.75959524C>G		36.0	0.0		56.0	27.0	NM_012479	O70457|P35214|Q6FH52|Q9UDP2|Q9UN99	Silent	SNP	ENST00000307630.3	hg19	CCDS5584.1																																																																																			.	.		0.502	YWHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253002.1	NM_012479		G	75959524	C	G	75959524	2	3	59	1	0	0	0	0	0	0	0	1	17518	871	31	4		4	YWHAG	7	75959524	Silent	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	4388249	75959524	83179139	39	7304										
MCM7	4176	hgsc.bcm.edu	37	chr7	99693701	99693701	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	agccagcaccagggccccacCctctaaggtcagttctccac	8	18	3	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr7:99693701C>A	ENST00000303887.5	-	11	1936	c.1291G>T	c.(1291-1293)Ggt>Tgt	p.G431C	MCM7_ENST00000343023.6_Intron|MCM7_ENST00000354230.3_Missense_Mutation_p.G255C|MIR25_ENST00000384816.1_RNA|MIR93_ENST00000385024.1_RNA|MIR106B_ENST00000385301.1_RNA	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	431	MCM.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGGGCCCCACCCTCTAAGGTC	0.607																																					p.G431C		Atlas-SNP	.											.	MCM7	136	.	0			c.G1291T						.						57	54	55					7																	99693701		2203	4300	6503	SO:0001583	missense	4176	exon11			CCCCACCCTCTAA		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.1291G>T	chr7.hg19:g.99693701C>A	ENSP00000307288:p.Gly431Cys	69.0	0.0		94.0	35.0	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	hg19	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.254289	0.80135	.	.	ENSG00000166508	ENST00000303887;ENST00000542483;ENST00000362082;ENST00000354230	T;T	0.11495	2.77;2.77	5.02	4.13	0.48395	ATPase, AAA+ type, core (1);	0.109029	0.64402	D	0.000007	T	0.48909	0.1526	H	0.98370	4.215	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67821	-0.5571	10	0.87932	D	0	-23.2828	12.4978	0.55937	0.1682:0.8318:0.0:0.0	.	431	P33993	MCM7_HUMAN	C	431;368;324;255	ENSP00000307288:G431C;ENSP00000346171:G255C	ENSP00000307288:G431C	G	-	1	0	MCM7	99531637	1.000000	0.71417	0.988000	0.46212	0.914000	0.54420	7.604000	0.82830	1.302000	0.44855	0.655000	0.94253	GGT	.	.		0.607	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			A	99693701	C	A	99693701	3	1	59	1	0	0	0	0	1	0	0	0	9401	623	22	3	888	3	MCM7	7	99693701	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	23734177	99693701	59444962	40	7305										
FGF20	26281	hgsc.bcm.edu	37	chr8	16853235	16853235	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cacacctctaatactgaccaGtcccactgccacactgatga	5	16	1	3			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr8:16853235G>T	ENST00000180166.5	-	2	467	c.319C>A	c.(319-321)Ctg>Atg	p.L107M		NM_019851.2	NP_062825.1	Q9NP95	FGF20_HUMAN	fibroblast growth factor 20	107					cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of cardiac muscle cell proliferation (GO:0060043)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	11				Colorectal(111;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		ATACTGACCAGTCCCACTGCC	0.338																																					p.L107M		Atlas-SNP	.											.	FGF20	16	.	0			c.C319A						.						113	107	109					8																	16853235		2203	4300	6503	SO:0001583	missense	26281	exon2			TGACCAGTCCCAC	AB030648	CCDS5998.1	8p22	2008-05-15			ENSG00000078579	ENSG00000078579			3677	protein-coding gene	gene with protein product		605558				10913340	Standard	NM_019851		Approved		uc003wxc.1	Q9NP95	OTTHUMG00000096964	ENST00000180166.5:c.319C>A	chr8.hg19:g.16853235G>T	ENSP00000180166:p.Leu107Met	152.0	0.0		103.0	56.0	NM_019851	B2RPH5	Missense_Mutation	SNP	ENST00000180166.5	hg19	CCDS5998.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.97|17.97	3.518782|3.518782	0.64634|0.64634	.|.	.|.	ENSG00000078579|ENSG00000078579	ENST00000180166|ENST00000381981	T|.	0.68479|.	-0.33|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67088|0.67088	0.2856|0.2856	L|L	0.58302|0.58302	1.8|1.8	0.58432|0.58432	D|D	0.999998|0.999998	B|.	0.32693|.	0.38|.	B|.	0.39971|.	0.315|.	T|T	0.68511|0.68511	-0.5389|-0.5389	10|6	0.66056|0.87932	D|D	0.02|0	.|.	13.4923|13.4923	0.61402|0.61402	0.0714:0.0:0.9286:0.0|0.0714:0.0:0.9286:0.0	.|.	107|.	Q9NP95|.	FGF20_HUMAN|.	M|N	107|75	ENSP00000180166:L107M|.	ENSP00000180166:L107M|ENSP00000371411:T75N	L|T	-|-	1|2	2|0	FGF20|FGF20	16897606|16897606	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	3.808000|3.808000	0.55598|0.55598	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	CTG|ACT	.	.		0.338	FGF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214030.1			T	16853235	G	T	16853235	3	4	59	1	0	0	0	0	1	0	0	0	5857	1020	36	3	324	3	FGF20	8	16853235	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10		16853235	129510787	41	7306										
PPP2R4	5524	hgsc.bcm.edu	37	chr9	131909700	131909700	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ccctgtgatccagcacttcaAgttcgggagcctgctgccca	10	15	1	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr9:131909700A>G	ENST00000337738.1	+	11	1301	c.1034A>G	c.(1033-1035)aAg>aGg	p.K345R	PPP2R4_ENST00000348141.5_Missense_Mutation_p.K316R|PPP2R4_ENST00000434095.1_Missense_Mutation_p.K48R|PPP2R4_ENST00000347048.4_Missense_Mutation_p.K91R|PPP2R4_ENST00000419582.1_Missense_Mutation_p.K48R|PPP2R4_ENST00000393370.2_Missense_Mutation_p.K310R|PPP2R4_ENST00000355007.3_Missense_Mutation_p.K268R|PPP2R4_ENST00000357197.4_Missense_Mutation_p.K281R|PPP2R4_ENST00000358994.4_Missense_Mutation_p.K310R|PPP2R4_ENST00000423100.1_Missense_Mutation_p.K48R|PPP2R4_ENST00000435132.1_Missense_Mutation_p.K48R|PPP2R4_ENST00000414510.1_Missense_Mutation_p.K48R|PPP2R4_ENST00000432651.1_Missense_Mutation_p.K48R	NM_178001.2	NP_821068.1	Q15257	PTPA_HUMAN	protein phosphatase 2A activator, regulatory subunit 4	345					ATP catabolic process (GO:0006200)|mitotic spindle organization in nucleus (GO:0030472)|negative regulation of phosphoprotein phosphatase activity (GO:0032515)|negative regulation of protein dephosphorylation (GO:0035308)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein dephosphorylation (GO:0035307)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of phosphoprotein phosphatase activity (GO:0043666)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	ATP binding (GO:0005524)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein tyrosine phosphatase activator activity (GO:0008160)|receptor binding (GO:0005102)			breast(3)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12		Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		CAGCACTTCAAGTTCGGGAGC	0.632																																					p.K345R	Colon(158;2158 2504 4450 20433)	Atlas-SNP	.											.	PPP2R4	32	.	0			c.A1034G						.						90	71	78					9																	131909700		2203	4300	6503	SO:0001583	missense	5524	exon11			ACTTCAAGTTCGG	X73478	CCDS6920.1, CCDS65156.1, CCDS75917.1	9q34	2010-06-18	2007-01-22		ENSG00000119383	ENSG00000119383		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9308	protein-coding gene	gene with protein product	"phosphotyrosyl phosphatase activator", "PP2A phosphatase activator"	600756	"protein phosphatase 2A, regulatory subunit B' (PR 53)"			8530035	Standard	NM_021131		Approved	PTPA, PR53	uc004bxm.2	Q15257	OTTHUMG00000020774	ENST00000337738.1:c.1034A>G	chr9.hg19:g.131909700A>G	ENSP00000337448:p.Lys345Arg	43.0	0.0		87.0	44.0	NM_178001	A2A347|A9IZU4|B4DXM4|Q15258|Q53GZ3|Q5TZQ2|Q9BUK1|Q9NNZ7|Q9NNZ8|Q9NNZ9	Missense_Mutation	SNP	ENST00000337738.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.87	2.365001	0.41902	.	.	ENSG00000119383	ENST00000358994;ENST00000393370;ENST00000337738;ENST00000348141;ENST00000347048;ENST00000357197;ENST00000355007;ENST00000423100;ENST00000414510;ENST00000419582;ENST00000432651;ENST00000435132;ENST00000434095	T;T;T;T;T;T;T;T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61	5.16	4.02	0.46733	.	0.045098	0.85682	D	0.000000	T	0.19765	0.0475	N	0.17248	0.465	0.80722	D	1	B;B;B;B;B	0.15473	0.0;0.013;0.001;0.001;0.001	B;B;B;B;B	0.28465	0.005;0.09;0.004;0.012;0.002	T	0.05305	-1.0893	10	0.25106	T	0.35	.	9.9436	0.41596	0.9199:0.0:0.0801:0.0	.	281;91;268;345;310	Q15257-3;Q68CR8;Q15257-4;Q15257;Q15257-2	.;.;.;PTPA_HUMAN;.	R	310;310;345;316;91;281;268;48;48;48;48;48;48	ENSP00000351885:K310R;ENSP00000377036:K310R;ENSP00000337448:K345R;ENSP00000335200:K316R;ENSP00000337412:K91R;ENSP00000349726:K281R;ENSP00000347109:K268R;ENSP00000408316:K48R;ENSP00000408726:K48R;ENSP00000394001:K48R;ENSP00000416661:K48R;ENSP00000387726:K48R;ENSP00000411604:K48R	ENSP00000337448:K345R	K	+	2	0	PPP2R4	130949521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.960000	0.76036	0.812000	0.34326	0.459000	0.35465	AAG	.	.		0.632	PPP2R4-201	KNOWN	basic	protein_coding	protein_coding		NM_021131		G	131909700	A	G	131909700	3	3	59	1	0	0	0	0	1	0	0	0	12403	72	3	2	1076	2	PPP2R4	9	131909700	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10		131909700	9303731	42	7307										
MASTL	84930	hgsc.bcm.edu	37	chr10	27459791	27459791	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tacaagagagtaaccaaaaaAtgttaggtcctcctttggag	9	7	0	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr10:27459791A>T	ENST00000375940.4	+	8	1960	c.1903A>T	c.(1903-1905)Atg>Ttg	p.M635L	MASTL_ENST00000342386.6_Missense_Mutation_p.M635L|MASTL_ENST00000375946.4_Missense_Mutation_p.M635L|MASTL_ENST00000477034.1_3'UTR			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	635	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TAACCAAAAAATGTTAGGTCC	0.383																																					p.M635L		Atlas-SNP	.											.	MASTL	81	.	0			c.A1903T						.						63	61	62					10																	27459791		2203	4300	6503	SO:0001583	missense	84930	exon8			CAAAAAATGTTAG	BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.1903A>T	chr10.hg19:g.27459791A>T	ENSP00000365107:p.Met635Leu	110.0	0.0		139.0	49.0	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	hg19	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	A	7.795	0.712418	0.15306	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.21734	1.99;1.99;1.99	5.28	2.83	0.33086	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.539261	0.22682	N	0.056939	T	0.14399	0.0348	L	0.48362	1.52	0.23401	N	0.997751	B;B;B	0.22211	0.066;0.04;0.066	B;B;B	0.20577	0.03;0.013;0.03	T	0.33979	-0.9847	10	0.05959	T	0.93	-13.5015	8.4168	0.32676	0.6766:0.0:0.3234:0.0	.	635;635;635	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	L	635	ENSP00000365113:M635L;ENSP00000343446:M635L;ENSP00000365107:M635L	ENSP00000343446:M635L	M	+	1	0	MASTL	27499797	0.182000	0.23173	0.986000	0.45419	0.824000	0.46624	0.604000	0.24164	0.891000	0.36235	0.482000	0.46254	ATG	.	.		0.383	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		T	27459791	A	T	27459791	3	4	59	1	0	0	0	0	1	0	0	0	9337	101	4	4	1933	4	MASTL	10	27459791	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10		27459791	108074956	43	7308										
ERCC6	2074	hgsc.bcm.edu	37	chr10	50732464	50732464	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cccctggaactgcaaagcccTcttctggagtttcttgatgt	9	12	3	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr10:50732464T>A	ENST00000355832.5	-	5	1090	c.1012A>T	c.(1012-1014)Agg>Tgg	p.R338W	ERCC6-PGBD3_ENST00000515869.1_Missense_Mutation_p.R338W|PGBD3_ENST00000374127.3_5'Flank|PGBD3_ENST00000603152.1_Missense_Mutation_p.R338W|ERCC6-PGBD3_ENST00000447839.2_Missense_Mutation_p.R338W	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	338					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TGCAAAGCCCTCTTCTGGAGT	0.488								Direct reversal of damage;Nucleotide excision repair (NER)																													p.K338X		Atlas-SNP	.											.	ERCC6	162	.	0			c.A1012T						.						111	107	109					10																	50732464		2203	4300	6503	SO:0001583	missense	2074	exon5			AAGCCCTCTTCTG	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.1012A>T	chr10.hg19:g.50732464T>A	ENSP00000348089:p.Arg338Trp	736.0	2.0		985.0	364.0	NM_000124	D3DX94|Q5W0L9	Nonsense_Mutation	SNP	ENST00000355832.5	hg19	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.699856	0.88924	.	.	ENSG00000225830;ENSG00000258838;ENSG00000258838	ENST00000355832;ENST00000515869;ENST00000447839	D;T;T	0.83755	-1.76;3.17;3.17	6.03	3.58	0.41010	.	.	.	.	.	D	0.87273	0.6136	L	0.57536	1.79	0.80722	D	1	D;D	0.76494	0.999;0.979	D;P	0.64321	0.924;0.699	D	0.87592	0.2491	9	0.66056	D	0.02	-22.645	11.924	0.52808	0.0:0.0:0.4892:0.5108	.	338;338	E7EV46;Q03468	.;ERCC6_HUMAN	W	338	ENSP00000348089:R338W;ENSP00000423550:R338W;ENSP00000387966:R338W	ENSP00000348089:R338W	R	-	1	2	ERCC6;RP11-123B3.6	50402470	0.996000	0.38824	0.994000	0.49952	0.996000	0.88848	4.072000	0.57563	1.091000	0.41335	0.533000	0.62120	AGG	.	.		0.488	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		A	50732464	T	A	50732464	3	1	59	1	0	0	0	0	1	0	0	0	5219	1550	54	4	3537	4	ERCC6	10	50732464	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	23272673	50732464	84802283	44	7309										
PDE3B	5140	hgsc.bcm.edu	37	chr11	14665851	14665851	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gcgctgctcccccttctgccGggcgcgcctctcgctgggcg	14	19	2	0	rs534967735	byFrequency	TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr11:14665851G>T	ENST00000282096.4	+	1	583	c.230G>T	c.(229-231)cGg>cTg	p.R77L	PDE3B_ENST00000455098.2_Missense_Mutation_p.R77L|PDE3B_ENST00000534317.1_3'UTR|PSMA1_ENST00000418988.2_5'Flank	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	77					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	CCCTTCTGCCGGGCGCGCCTC	0.761													G|||	2	0.000399361	8e-04	0	5008	,	,		12360	0.001		0	False		,,,				2504	0				p.R77L		Atlas-SNP	.											.	PDE3B	98	.	0			c.G230T						.						6	6	6					11																	14665851		2032	3990	6022	SO:0001583	missense	5140	exon1			TCTGCCGGGCGCG	U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"Phosphodiesterases"	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.230G>T	chr11.hg19:g.14665851G>T	ENSP00000282096:p.Arg77Leu	0.0	0.0		17.0	11.0	NM_000922	B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	ENST00000282096.4	hg19	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.690888	0.29962	.	.	ENSG00000152270	ENST00000282096;ENST00000455098	T;T	0.61742	0.11;0.08	3.83	0.529	0.17095	.	2.626090	0.03438	N	0.208919	T	0.39009	0.1062	N	0.14661	0.345	0.23936	N	0.99642	B;B;B	0.31077	0.307;0.084;0.307	B;B;B	0.22880	0.042;0.022;0.042	T	0.27123	-1.0083	10	0.36615	T	0.2	.	8.2155	0.31509	0.0868:0.2956:0.6175:0.0	.	77;77;77	B7ZM37;Q13370;A7E2E5	.;PDE3B_HUMAN;.	L	77	ENSP00000282096:R77L;ENSP00000388644:R77L	ENSP00000282096:R77L	R	+	2	0	PDE3B	14622427	0.982000	0.34865	0.907000	0.35723	0.890000	0.51754	1.060000	0.30530	0.130000	0.18549	0.313000	0.20887	CGG	.	.		0.761	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922		T	14665851	G	T	14665851	3	4	59	1	0	0	0	0	1	0	0	0	11647	1116	39	1	232	1	PDE3B	11	14665851	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10		14665851	120340665	45	7310										
OR10V1	390201	hgsc.bcm.edu	37	chr11	59481145	59481145	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ttagccaggaaaaagtacatGggggtgtggagggaatgatt	16	3	0	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr11:59481145G>T	ENST00000307552.2	-	1	192	c.174C>A	c.(172-174)ccC>ccA	p.P58P	STX3_ENST00000300150.7_5'UTR	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, member 1	58						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|liver(1)|lung(10)|skin(1)	16						AAAAGTACATGGGGGTGTGGA	0.448																																					p.P58P		Atlas-SNP	.											.	OR10V1	40	.	0			c.C174A						.						61	65	63					11																	59481145		2201	4295	6496	SO:0001819	synonymous_variant	390201	exon1			GTACATGGGGGTG	AB065807	CCDS31565.1	11q12.1	2012-08-09			ENSG00000172289	ENSG00000172289		"GPCR / Class A : Olfactory receptors"	15136	protein-coding gene	gene with protein product							Standard	NM_001005324		Approved		uc001nof.1	Q8NGI7	OTTHUMG00000167406	ENST00000307552.2:c.174C>A	chr11.hg19:g.59481145G>T		167.0	0.0		231.0	10.0	NM_001005324	Q6IFD9|Q96R50	Silent	SNP	ENST00000307552.2	hg19	CCDS31565.1																																																																																			.	.		0.448	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324		T	59481145	G	T	59481145	2	4	59	1	0	0	0	0	0	0	0	1	10929	1335	47	3		3	OR10V1	11	59481145	Silent	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	44815294	59481145	75525371	46	7311										
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	668557	668557	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	caaggagttccgagaccgctGgggcggggaagactgggagc	19	9	0	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr12:668557G>A	ENST00000266383.5	+	19	2871	c.2858G>A	c.(2857-2859)tGg>tAg	p.W953*		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	953					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			CGAGACCGCTGGGGCGGGGAA	0.617																																					p.W953X		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G2858A						.						88	94	92					12																	668557		2203	4300	6503	SO:0001587	stop_gained	283358	exon19			ACCGCTGGGGCGG	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.2858G>A	chr12.hg19:g.668557G>A	ENSP00000266383:p.Trp953*	69.0	0.0		93.0	34.0	NM_173593	Q6ZNC1|Q8N7T6	Nonsense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	G	41	8.958160	0.99016	.	.	ENSG00000139044	ENST00000266383	.	.	.	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.6164	18.2881	0.90120	0.0:0.0:1.0:0.0	.	.	.	.	X	953	.	ENSP00000266383:W953X	W	+	2	0	B4GALNT3	538818	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.809000	0.86057	2.383000	0.81215	0.462000	0.41574	TGG	.	.		0.617	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		A	668557	G	A	668557	4	1	59	1	0	0	0	0	0	1	0	0	1268	1357	47	3	2932	3	B4GALNT3	12	668557	Nonsense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10		668557	133183338	47	7312										
KRT78	196374	hgsc.bcm.edu	37	chr12	53237937	53237937	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	atctcttggtgtagctgagaGatctggactttcgtttcctg	11	8	2	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr12:53237937G>A	ENST00000304620.4	-	6	1050	c.987C>T	c.(985-987)atC>atT	p.I329I	KRT78_ENST00000359499.4_Silent_p.I219I	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	329	Coil 2.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						GTAGCTGAGAGATCTGGACTT	0.517																																					p.I329I		Atlas-SNP	.											.	KRT78	41	.	0			c.C987T						.						203	187	193					12																	53237937		2203	4300	6503	SO:0001819	synonymous_variant	196374	exon6			CTGAGAGATCTGG	AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"-", "Intermediate filaments type II, keratins (basic)"	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.987C>T	chr12.hg19:g.53237937G>A		289.0	0.0		402.0	152.0	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Silent	SNP	ENST00000304620.4	hg19	CCDS8840.1																																																																																			.	.		0.517	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352		A	53237937	G	A	53237937	2	1	59	1	0	0	0	0	0	0	0	1	8500	932	33	3		3	KRT78	12	53237937	Silent	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	52569380	53237937	80613958	48	7313										
OR6C75	390323	hgsc.bcm.edu	37	chr12	55759521	55759521	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gtaacactgatggtcaccttGacattagttattctctccta	6	10	2	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr12:55759521G>T	ENST00000343399.3	+	1	627	c.627G>T	c.(625-627)ttG>ttT	p.L209F		NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C, member 75	209						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)	25						TGGTCACCTTGACATTAGTTA	0.408																																					p.L209F		Atlas-SNP	.											.	OR6C75	67	.	0			c.G627T						.						147	129	135					12																	55759521		2203	4300	6503	SO:0001583	missense	390323	exon1			CACCTTGACATTA		CCDS31820.1	12q13.2	2013-09-23			ENSG00000187857	ENSG00000187857		"GPCR / Class A : Olfactory receptors"	31304	protein-coding gene	gene with protein product							Standard	NM_001005497		Approved		uc010spk.2	A6NL08	OTTHUMG00000169886	ENST00000343399.3:c.627G>T	chr12.hg19:g.55759521G>T	ENSP00000368987:p.Leu209Phe	406.0	1.0		466.0	174.0	NM_001005497		Missense_Mutation	SNP	ENST00000343399.3	hg19	CCDS31820.1	.	.	.	.	.	.	.	.	.	.	g	15.12	2.740123	0.49045	.	.	ENSG00000187857	ENST00000343399	T	0.40476	1.03	5.22	-0.481	0.12082	GPCR, rhodopsin-like superfamily (1);	0.201247	0.23896	N	0.043482	T	0.32224	0.0822	L	0.28274	0.84	0.09310	N	0.999996	P	0.45011	0.848	P	0.50825	0.651	T	0.15464	-1.0436	10	0.72032	D	0.01	.	3.0854	0.06276	0.2711:0.4368:0.1802:0.1119	.	209	A6NL08	O6C75_HUMAN	F	209	ENSP00000368987:L209F	ENSP00000368987:L209F	L	+	3	2	OR6C75	54045788	0.000000	0.05858	0.904000	0.35570	0.966000	0.64601	-2.394000	0.01054	-0.010000	0.14271	0.632000	0.83419	TTG	.	.		0.408	OR6C75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406418.1			T	55759521	G	T	55759521	3	4	59	1	0	0	0	0	1	0	0	0	11208	1281	45	3	629	3	OR6C75	12	55759521	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	2521584	55759521	78092374	49	7314										
KL	9365	hgsc.bcm.edu	37	chr13	33638123	33638123	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ccatgaaacattacaggaaaAttattgacagcaatggtttc	7	7	0	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr13:33638123A>G	ENST00000380099.3	+	5	2847	c.2839A>G	c.(2839-2841)Att>Gtt	p.I947V	KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	947	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TTACAGGAAAATTATTGACAG	0.453																																					p.I947V		Atlas-SNP	.											.	KL	106	.	0			c.A2839G						.						124	124	124					13																	33638123		2203	4300	6503	SO:0001583	missense	9365	exon5			AGGAAAATTATTG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.2839A>G	chr13.hg19:g.33638123A>G	ENSP00000369442:p.Ile947Val	322.0	0.0		225.0	51.0	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	hg19	CCDS9347.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.707815	0.48412	.	.	ENSG00000133116	ENST00000380099	T	0.27890	1.64	5.52	4.32	0.51571	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.111045	0.64402	D	0.000011	T	0.32071	0.0817	L	0.48260	1.515	0.50313	D	0.999868	P	0.41597	0.756	P	0.44647	0.456	T	0.02179	-1.1200	10	0.28530	T	0.3	-10.3003	12.5759	0.56363	0.8611:0.1389:0.0:0.0	.	947	Q9UEF7	KLOT_HUMAN	V	947	ENSP00000369442:I947V	ENSP00000369442:I947V	I	+	1	0	KL	32536123	1.000000	0.71417	0.817000	0.32601	0.948000	0.59901	6.653000	0.74382	0.893000	0.36288	0.533000	0.62120	ATT	.	.		0.453	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			G	33638123	A	G	33638123	3	3	59	1	0	0	0	0	1	0	0	0	8340	101	4	2	2857	2	KL	13	33638123	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10		33638123	81531755	50	7315										
MAB21L1	4081	hgsc.bcm.edu	37	chr13	36050192	36050193	+	Missense_Mutation	DNP	GG	GG	TT													0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cagacttcccggatagttttGgcaatggcagctttcctggc							TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr13:36050192_36050193GG>TT	ENST00000379919.4	-	1	639_640	c.83_84CC>AA	c.(82-84)gCC>gAA	p.A28E	NBEA_ENST00000537702.1_5'Flank|NBEA_ENST00000310336.4_Intron|NBEA_ENST00000400445.3_Intron|NBEA_ENST00000540320.1_Intron|NBEA_ENST00000379939.2_Intron	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)	28					anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		GGATAGTTTTGGCAATGGCAGC	0.51																																					p.A28A|p.A28D		Atlas-SNP	.											.	MAB21L1	52	.	0			c.C84A|c.C83A						.																																			SO:0001583	missense	4081	exon1			AGTTTTGGCAATG|GTTTTGGCAATGG	BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"mab-21 (C. elegans)-like 1"			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.83_84delinsTT	chr13.hg19:g.36050192_36050193delinsTT	ENSP00000369251:p.Ala28Glu	82.0	0.0		56.0	35.0|34.0	NM_005584	Q6I9T5	Silent|Missense_Mutation	SNP	ENST00000379919.4	hg19	CCDS9353.1																																																																																			.	.		0.51	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584		TT	36050193	GG	TT	36050192	3	4	59	1	0	0	0	0	1	0	0	0	9150	1335	47	3	999	3	MAB21L1	13	36050192	Missense_Mutation	DNP	GG	TCGA-CC-5263-01A-01D-A12Z-10	2412069	36050192	79119686	51	7316										
NALCN	259232	hgsc.bcm.edu	37	chr13	101717813	101717813	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ggagcctctccatttcgtagCacatgtgcttaaacaggagc	10	11	1	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr13:101717813C>T	ENST00000251127.6	-	40	4628	c.4547G>A	c.(4546-4548)tGc>tAc	p.C1516Y		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1516					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CATTTCGTAGCACATGTGCTT	0.592																																					p.C1516Y		Atlas-SNP	.											.	NALCN	431	.	0			c.G4547A						.						175	135	149					13																	101717813		2203	4300	6503	SO:0001583	missense	259232	exon40			TCGTAGCACATGT	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.4547G>A	chr13.hg19:g.101717813C>T	ENSP00000251127:p.Cys1516Tyr	64.0	0.0		130.0	42.0	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.751465	0.89753	.	.	ENSG00000102452	ENST00000251127	D	0.97906	-4.6	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.98333	0.9447	L	0.55213	1.73	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.99647	1.0990	10	0.87932	D	0	.	19.8625	0.96789	0.0:1.0:0.0:0.0	.	1516	Q8IZF0	NALCN_HUMAN	Y	1516	ENSP00000251127:C1516Y	ENSP00000251127:C1516Y	C	-	2	0	NALCN	100515814	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.487000	0.81328	2.689000	0.91719	0.655000	0.94253	TGC	.	.		0.592	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		T	101717813	C	T	101717813	3	4	59	1	0	0	0	0	1	0	0	0	10157	710	25	3	689	3	NALCN	13	101717813	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	65667621	101717813	13452065	52	7317										
CHD8	57680	hgsc.bcm.edu	37	chr14	21878045	21878045	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tgggtgccttgactgaatccGtttaaattctcgaatcttgc	9	9	2	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr14:21878045G>A	ENST00000557364.1	-	11	2592	c.2329C>T	c.(2329-2331)Cgg>Tgg	p.R777W	CHD8_ENST00000430710.3_Missense_Mutation_p.R498W|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000399982.2_Missense_Mutation_p.R777W			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	777	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		GACTGAATCCGTTTAAATTCT	0.393																																					p.R777W		Atlas-SNP	.											.	CHD8	339	.	0			c.C2329T						.						146	135	138					14																	21878045		1865	4097	5962	SO:0001583	missense	57680	exon10			GAATCCGTTTAAA	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.2329C>T	chr14.hg19:g.21878045G>A	ENSP00000451601:p.Arg777Trp	331.0	0.0		311.0	30.0	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	hg19	CCDS53885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.85|18.85	3.712158|3.712158	0.68730|0.68730	.|.	.|.	ENSG00000100888|ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364|ENST00000555935	T;T;T|.	0.74002|.	-0.8;-0.8;-0.8|.	5.0|5.0	4.08|4.08	0.47627|0.47627	.|.	0.138303|.	0.48286|.	D|.	0.000189|.	T|T	0.58293|0.58293	0.2112|0.2112	L|L	0.42245|0.42245	1.32|1.32	0.48452|0.48452	D|D	0.999657|0.999657	D|.	0.76494|.	0.999|.	D|.	0.65987|.	0.94|.	T|T	0.55068|0.55068	-0.8198|-0.8198	10|5	0.87932|.	D|.	0|.	-16.3856|-16.3856	13.372|13.372	0.60719|0.60719	0.0:0.0:0.8411:0.1589|0.0:0.0:0.8411:0.1589	.|.	498|.	Q9HCK8-2|.	.|.	W|M	498;777;497;777|2	ENSP00000406288:R498W;ENSP00000382863:R777W;ENSP00000451601:R777W|.	ENSP00000262707:R497W|.	R|T	-|-	1|2	2|0	CHD8|CHD8	20947885|20947885	0.052000|0.052000	0.20516|0.20516	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.639000|1.639000	0.37176|0.37176	1.270000|1.270000	0.44297|0.44297	0.655000|0.655000	0.94253|0.94253	CGG|ACG	.	.		0.393	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		A	21878045	G	A	21878045	3	1	59	1	0	0	0	0	1	0	0	0	3333	1144	40	1	5528	1	CHD8	14	21878045	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10		21878045	85471495	53	7318										
ITPK1	3705	hgsc.bcm.edu	37	chr14	93483123	93483123	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	acgtccagggggccctgctcCtcgatcggccggctaaggtt	14	14	0	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr14:93483123C>T	ENST00000267615.6	-	4	317	c.144G>A	c.(142-144)gaG>gaA	p.E48E	ITPK1_ENST00000556954.1_5'UTR|ITPK1_ENST00000556603.2_Silent_p.E48E|ITPK1_ENST00000354313.3_Silent_p.E48E|ITPK1_ENST00000555495.1_5'UTR			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	48					blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		GGCCCTGCTCCTCGATCGGCC	0.582																																					p.E48E		Atlas-SNP	.											.	ITPK1	53	.	0			c.G144A						.						110	91	98					14																	93483123		2203	4300	6503	SO:0001819	synonymous_variant	3705	exon4			CTGCTCCTCGATC	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.144G>A	chr14.hg19:g.93483123C>T		47.0	0.0		71.0	34.0	NM_001142593	Q9BTL6|Q9H2E7	Silent	SNP	ENST00000267615.6	hg19	CCDS9907.1																																																																																			.	.		0.582	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		T	93483123	C	T	93483123	2	4	59	1	0	0	0	0	0	0	0	1	7925	680	24	3		3	ITPK1	14	93483123	Silent	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	71605078	93483123	13866417	54	7319										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94088075	94088075	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	aaagctacgctctttcaaacAaaaatctcttgatataggga	6	8	3	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr14:94088075A>G	ENST00000393151.2	+	30	4496	c.4496A>G	c.(4495-4497)cAa>cGa	p.Q1499R	UNC79_ENST00000555664.1_Missense_Mutation_p.Q1499R|UNC79_ENST00000553484.1_Missense_Mutation_p.Q1521R|UNC79_ENST00000256339.4_Missense_Mutation_p.Q1322R			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1499					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TCTTTCAAACAAAAATCTCTT	0.433																																					p.Q1322R		Atlas-SNP	.											.	UNC79	366	.	0			c.A3965G						.						81	80	81					14																	94088075		2203	4300	6503	SO:0001583	missense	57578	exon30			TCAAACAAAAATC	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4496A>G	chr14.hg19:g.94088075A>G	ENSP00000376858:p.Gln1499Arg	149.0	0.0		182.0	63.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	A	18.97	3.735305	0.69189	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.26373	1.79;1.74;1.8;1.79	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	L	0.32530	0.975	0.48185	D	0.999609	D	0.63046	0.992	D	0.72982	0.979	T	0.29549	-1.0008	10	0.87932	D	0	-16.0344	16.4728	0.84119	1.0:0.0:0.0:0.0	.	1521	C9JQL1	.	R	1322;1499;1521;1499;1521	ENSP00000256339:Q1322R;ENSP00000450868:Q1499R;ENSP00000451360:Q1521R;ENSP00000376858:Q1499R	ENSP00000256339:Q1322R	Q	+	2	0	KIAA1409	93157828	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.962000	0.93254	2.296000	0.77279	0.482000	0.46254	CAA	.	.		0.433	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		G	94088075	A	G	94088075	3	3	59	1	0	0	0	0	1	0	0	0	8239	130	5	2	4071	2	KIAA1409	14	94088075	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	604952	94088075	13261465	55	7320										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52638630	52638630	+	Frame_Shift_Del	DEL	A	A	-													0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tcattttttgtacatcttccAaaagtattgtggaatctgtc							TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr15:52638630delA	ENST00000399231.3	-	30	4130	c.3887delT	c.(3886-3888)ttgfs	p.L1296fs	MYO5A_ENST00000553916.1_Frame_Shift_Del_p.L1296fs|MYO5A_ENST00000399233.2_Frame_Shift_Del_p.L1293fs|MYO5A_ENST00000356338.6_Frame_Shift_Del_p.L1296fs|MYO5A_ENST00000358212.6_Frame_Shift_Del_p.L1296fs	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1296					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		TACATCTTCCAAAAGTATTGT	0.299																																					p.L1296fs		Atlas-Indel,Pindel	.											.	MYO5A	145	.	0			c.3888delG						.						170	156	160					15																	52638630		1829	4073	5902	SO:0001589	frameshift_variant	4644	exon30			.		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.3887delT	chr15.hg19:g.52638630delA	ENSP00000382177:p.Leu1296fs	278.0	0.0		269.0	107.0	NM_001142495	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Frame_Shift_Del	DEL	ENST00000399231.3	hg19	CCDS42037.1																																																																																			.	.		0.299	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		-	52638630	A	-	52638630	7	5	59	1	0	1	0	1	0	0	0	0	10087	131	5	0	1728	0	MYO5A	15	52638630	Frame_Shift_Del	DEL	A	TCGA-CC-5263-01A-01D-A12Z-10		52638630	49892762	56	7321										
OR4F15	390649	hgsc.bcm.edu	37	chr15	102359072	102359072	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tctgttcactgtttggaaacAttcttctggtggtctagcca	9	9	5	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr15:102359072A>T	ENST00000332238.4	+	1	707	c.683A>T	c.(682-684)cAt>cTt	p.H228L		NM_001001674.1	NP_001001674.1	Q8NGB8	O4F15_HUMAN	olfactory receptor, family 4, subfamily F, member 15	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(10)	19	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			GTTTGGAAACATTCTTCTGGT	0.463																																					p.H228L		Atlas-SNP	.											.	OR4F15	42	.	0			c.A683T						.						280	242	255					15																	102359072		2203	4300	6503	SO:0001583	missense	390649	exon1			GGAAACATTCTTC	BK004405	CCDS32342.1	15q26.3	2012-08-09				ENSG00000182854		"GPCR / Class A : Olfactory receptors"	15078	protein-coding gene	gene with protein product							Standard	NM_001001674		Approved		uc010uts.2	Q8NGB8		ENST00000332238.4:c.683A>T	chr15.hg19:g.102359072A>T	ENSP00000333184:p.His228Leu	611.0	0.0		989.0	257.0	NM_001001674	B2RNQ5|Q6IF57|Q96R70	Missense_Mutation	SNP	ENST00000332238.4	hg19	CCDS32342.1	.	.	.	.	.	.	.	.	.	.	.	8.090	0.774339	0.16051	.	.	ENSG00000182854	ENST00000332238	T	0.00042	8.84	5.57	4.46	0.54185	GPCR, rhodopsin-like superfamily (1);	0.095904	0.46442	D	0.000294	T	0.00073	0.0002	N	0.03324	-0.35	0.09310	N	1	B	0.20368	0.044	B	0.23852	0.049	T	0.02026	-1.1227	9	.	.	.	.	9.5446	0.39273	0.9181:0.0:0.0819:0.0	.	228	Q8NGB8	O4F15_HUMAN	L	228	ENSP00000333184:H228L	.	H	+	2	0	OR4F15	100176595	0.000000	0.05858	0.202000	0.23494	0.201000	0.24016	-0.249000	0.08842	1.134000	0.42165	0.528000	0.53228	CAT	.	.		0.463	OR4F15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417594.1	NM_001001674		T	102359072	A	T	102359072	3	4	59	1	0	0	0	0	1	0	0	0	11070	217	8	4	685	4	OR4F15	15	102359072	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	49720442	102359072	172320	57	7322										
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15126797	15126797	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tccatgctggactcctgaagAagttaaatgaactggaatct	9	8	1	3			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr16:15126797A>T	ENST00000396410.4	+	18	1748	c.1651A>T	c.(1651-1653)Aag>Tag	p.K551*	PDXDC1_ENST00000450288.2_Nonsense_Mutation_p.K523*|PDXDC1_ENST00000447912.2_Nonsense_Mutation_p.K460*|PDXDC1_ENST00000569715.1_Nonsense_Mutation_p.K524*|PDXDC1_ENST00000325823.7_Nonsense_Mutation_p.K536*|PDXDC1_ENST00000563679.1_Nonsense_Mutation_p.K569*|PDXDC1_ENST00000535621.2_Intron	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	551					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACTCCTGAAGAAGTTAAATGA	0.408																																					p.K551X		Atlas-SNP	.											.	PDXDC1	59	.	0			c.A1651T						.						94	100	98					16																	15126797		2197	4300	6497	SO:0001587	stop_gained	23042	exon18			CTGAAGAAGTTAA	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.1651A>T	chr16.hg19:g.15126797A>T	ENSP00000379691:p.Lys551*	124.0	0.0		138.0	52.0	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Nonsense_Mutation	SNP	ENST00000396410.4	hg19	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	A	38	6.906433	0.97924	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000396410;ENST00000450288	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.7462	14.9371	0.70964	1.0:0.0:0.0:0.0	.	.	.	.	X	536;460;551;523	.	ENSP00000322807:K536X	K	+	1	0	PDXDC1	15034298	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.142000	0.77339	2.131000	0.65755	0.533000	0.62120	AAG	.	.		0.408	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		T	15126797	A	T	15126797	4	4	59	1	0	0	0	0	0	1	0	0	11705	247	9	4	1721	4	PDXDC1	16	15126797	Nonsense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10		15126797	75227956	58	7323										
LAT	27040	hgsc.bcm.edu	37	chr16	29001267	29001267	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cttacagccgccctgagttcCcaggaggcagaggaagtgga	14	11	0	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr16:29001267C>A	ENST00000360872.5	+	10	801	c.723C>A	c.(721-723)tcC>tcA	p.S241S	LAT_ENST00000395456.2_Silent_p.S212S|LAT_ENST00000395461.3_Silent_p.S248S|LAT_ENST00000564277.1_Silent_p.S211S|LAT_ENST00000354453.4_Silent_p.S231S|RP11-264B17.5_ENST00000561471.1_RNA|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000454369.2_Silent_p.S211S|LAT_ENST00000566177.1_Silent_p.S240S			O43561	LAT_HUMAN	linker for activation of T cells	241					blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|gene expression (GO:0010467)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lymphocyte homeostasis (GO:0002260)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|regulation of T cell activation (GO:0050863)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(2)|lung(3)|urinary_tract(1)	6		Hepatocellular(780;0.244)				CCCTGAGTTCCCAGGAGGCAG	0.632																																					p.S248S		Atlas-SNP	.											.	LAT	22	.	0			c.C744A						.						71	68	69					16																	29001267		2197	4300	6497	SO:0001819	synonymous_variant	27040	exon12			GAGTTCCCAGGAG	AF036905	CCDS10647.1, CCDS32425.1, CCDS45455.1, CCDS53999.1	16q13	2011-11-01			ENSG00000213658	ENSG00000213658			18874	protein-coding gene	gene with protein product	"linker for activation of T cells, transmembrane adaptor"	602354				9489702	Standard	NM_014387		Approved	LAT1	uc010vdj.2	O43561	OTTHUMG00000131761	ENST00000360872.5:c.723C>A	chr16.hg19:g.29001267C>A		95.0	0.0		161.0	53.0	NM_001014989	B7WPI0|C7C5T6|G5E9K3|O43919	Silent	SNP	ENST00000360872.5	hg19	CCDS10647.1																																																																																			.	.		0.632	LAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254688.2			A	29001267	C	A	29001267	2	1	59	1	0	0	0	0	0	0	0	1	8653	610	22	3		3	LAT	16	29001267	Silent	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	13874470	29001267	61353486	59	7324										
MYLK3	91807	hgsc.bcm.edu	37	chr16	46766546	46766546	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gcctgtcatcagcatctcccCaggagtatccatctcttgta	7	14	4	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr16:46766546C>T	ENST00000394809.4	-	4	1151	c.1036G>A	c.(1036-1038)Ggg>Agg	p.G346R	MYLK3_ENST00000536476.1_Missense_Mutation_p.G5R	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	346					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				AGCATCTCCCCAGGAGTATCC	0.607																																					p.G346R		Atlas-SNP	.											.	MYLK3	82	.	0			c.G1036A						.						20	15	17					16																	46766546		2011	4016	6027	SO:0001583	missense	91807	exon4			TCTCCCCAGGAGT	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.1036G>A	chr16.hg19:g.46766546C>T	ENSP00000378288:p.Gly346Arg	8.0	0.0		18.0	14.0	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	hg19	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	C	9.418	1.082352	0.20309	.	.	ENSG00000140795	ENST00000394809;ENST00000536476	T;T	0.68765	-0.35;-0.35	5.51	3.57	0.40892	.	0.470755	0.15827	N	0.242698	T	0.51635	0.1686	L	0.34521	1.04	0.32663	N	0.517819	B;B	0.24533	0.105;0.105	B;B	0.20184	0.028;0.028	T	0.54153	-0.8336	10	0.30078	T	0.28	.	8.1388	0.31071	0.0:0.8171:0.0:0.1829	.	346;346	B5BUL9;Q32MK0	.;MYLK3_HUMAN	R	346;5	ENSP00000378288:G346R;ENSP00000439297:G5R	ENSP00000378288:G346R	G	-	1	0	MYLK3	45324047	0.104000	0.21937	0.653000	0.29593	0.055000	0.15305	0.836000	0.27545	0.685000	0.31468	0.655000	0.94253	GGG	.	.		0.607	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		T	46766546	C	T	46766546	3	4	59	1	0	0	0	0	1	0	0	0	10067	594	21	3	1463	3	MYLK3	16	46766546	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	17765279	46766546	43588207	60	7325										
DVL2	1856	hgsc.bcm.edu	37	chr17	7129551	7129551	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	actcactgccactgccggacTtggactcgggggcccgctcc	12	17	1	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:7129551T>G	ENST00000005340.5	-	15	2126	c.1844A>C	c.(1843-1845)aAg>aCg	p.K615T	MIR324_ENST00000362183.1_RNA|DVL2_ENST00000574642.1_5'Flank|DVL2_ENST00000575458.1_Missense_Mutation_p.K609T	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	615					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						ACTGCCGGACTTGGACTCGGG	0.726																																					p.K615T		Atlas-SNP	.											.	DVL2	49	.	0			c.A1844C						.						24	31	29					17																	7129551		2200	4296	6496	SO:0001583	missense	1856	exon15			CCGGACTTGGACT	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"Dishevelled homologs"	3086	protein-coding gene	gene with protein product		602151	"dishevelled 2 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 2 (Drosophila)"			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.1844A>C	chr17.hg19:g.7129551T>G	ENSP00000005340:p.Lys615Thr	14.0	0.0		25.0	14.0	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	hg19	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	T	11.61	1.690114	0.29962	.	.	ENSG00000004975	ENST00000005340	T	0.04234	3.67	5.49	4.35	0.52113	Dishevelled C-terminal (1);	0.397637	0.27586	N	0.018707	T	0.04318	0.0119	L	0.38175	1.15	0.36357	D	0.86045	B;B	0.18013	0.025;0.025	B;B	0.16289	0.015;0.015	T	0.35151	-0.9800	10	0.14252	T	0.57	-26.9546	10.3546	0.43956	0.0:0.0:0.1647:0.8353	.	609;615	B4DLQ0;O14641	.;DVL2_HUMAN	T	615	ENSP00000005340:K615T	ENSP00000005340:K615T	K	-	2	0	DVL2	7070275	0.884000	0.30299	1.000000	0.80357	0.961000	0.63080	1.600000	0.36762	2.080000	0.62538	0.533000	0.62120	AAG	.	.		0.726	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422		G	7129551	T	G	7129551	3	3	59	1	0	0	0	0	1	0	0	0	4838	1609	56	5	370	5	DVL2	17	7129551	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10		7129551	74065659	61	7326										
TP53	7157	hgsc.bcm.edu	37	chr17	7577107	7577107	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gtgcgccggtctctcccaggAcaggcacaaacacgcacctc	10	17	1	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:7577107A>T	ENST00000269305.4	-	8	1020	c.831T>A	c.(829-831)tgT>tgA	p.C277*	TP53_ENST00000359597.4_Nonsense_Mutation_p.C277*|TP53_ENST00000445888.2_Nonsense_Mutation_p.C277*|TP53_ENST00000420246.2_Nonsense_Mutation_p.C277*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.C277*|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	277	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in an osteosarcoma with no family history; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.C277*(8)|p.C277C(4)|p.?(2)|p.P278fs*28(2)|p.C277W(2)|p.A276_R283delACPGRDRR(1)|p.C275fs*20(1)|p.A276fs*64(1)|p.L265_K305del41(1)|p.F270_D281del12(1)|p.A276_C277delAC(1)|p.V274_P278del(1)|p.C277_P278insXXXXXXX(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTCTCCCAGGACAGGCACAAA	0.547		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.C277X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,-1,2	TP53	33396	.	38	Substitution - Nonsense(8)|Whole gene deletion(8)|Deletion - In frame(7)|Deletion - Frameshift(4)|Substitution - coding silent(4)|Insertion - Frameshift(2)|Unknown(2)|Substitution - Missense(2)|Insertion - In frame(1)	upper_aerodigestive_tract(6)|breast(6)|urinary_tract(5)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|stomach(3)|central_nervous_system(2)|oesophagus(2)|lung(2)|biliary_tract(1)|large_intestine(1)|ovary(1)|prostate(1)	c.T831A	GRCh37	CM065496	TP53	M		.						72	62	65					17																	7577107		2203	4300	6503	SO:0001587	stop_gained	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CCCAGGACAGGCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.831T>A	chr17.hg19:g.7577107A>T	ENSP00000269305:p.Cys277*	87.0	0.0		65.0	47.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	37	6.040834	0.97226	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.13	1.53	0.23141	.	0.044315	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.0792	7.7422	0.28848	0.6581:0.0:0.3419:0.0	.	.	.	.	X	277;277;277;277;277;266;145	.	ENSP00000269305:C277X	C	-	3	2	TP53	7517832	0.987000	0.35691	1.000000	0.80357	0.977000	0.68977	0.281000	0.18810	0.383000	0.24910	0.379000	0.24179	TGT	.	.		0.547	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577107	A	T	7577107	4	4	59	1	0	0	0	0	0	1	0	0	16396	273	10	4	455	4	TP53	17	7577107	Nonsense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	447556	7577107	73618103	62	7327										
CRLF3	51379	hgsc.bcm.edu	37	chr17	29119458	29119458	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	atgttttaatatctacttgcCtgaatgttaatgtctgccca	6	8	2	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:29119458C>T	ENST00000324238.6	-	6	1083	c.959G>A	c.(958-960)aGa>aAa	p.R320K	CRLF3_ENST00000577725.1_Intron|CTD-2349P21.9_ENST00000580085.1_lincRNA|CRLF3_ENST00000544695.1_Splice_Site_p.R204K	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	320					G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				ATCTACTTGCCTGAATGTTAA	0.418																																					p.R320K	Pancreas(30;346 881 29244 33464 41299)	Atlas-SNP	.											.	CRLF3	36	.	0			c.G959A						.						114	110	112					17																	29119458		2203	4300	6503	SO:0001630	splice_region_variant	51379	exon6			ACTTGCCTGAATG	AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.959+1G>A	chr17.hg19:g.29119458C>T		116.0	0.0		131.0	46.0	NM_015986	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Missense_Mutation	SNP	ENST00000324238.6	hg19	CCDS32607.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957192	0.53293	.	.	ENSG00000176390	ENST00000324238;ENST00000544695	T;T	0.60171	0.21;0.21	5.49	5.49	0.81192	.	0.565711	0.21304	N	0.076745	T	0.44159	0.1280	N	0.17082	0.46	0.43798	D	0.996349	B	0.16396	0.017	B	0.10450	0.005	T	0.28964	-1.0027	9	.	.	.	-5.7154	19.3434	0.94355	0.0:1.0:0.0:0.0	.	320	Q8IUI8	CRLF3_HUMAN	K	320;204	ENSP00000318804:R320K;ENSP00000444188:R204K	.	R	-	2	0	CRLF3	26143584	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.595000	0.54016	2.560000	0.86352	0.591000	0.81541	AGA	.	.		0.418	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444354.1		Missense_Mutation	T	29119458	C	T	29119458	5	4	59	1	0	0	0	0	0	0	1	0	3890	695	24	3	381	3	CRLF3	17	29119458	Splice_Site	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	21542351	29119458	52075752	63	7328										
KRT28	162605	hgsc.bcm.edu	37	chr17	38955214	38955214	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gtctggcattatcaatctgcAgaatgacattagcattagta	8	7	3	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:38955214A>G	ENST00000306658.7	-	2	553	c.488T>C	c.(487-489)cTg>cCg	p.L163P		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				ATCAATCTGCAGAATGACATT	0.328																																					p.L163P	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.T488C						.						111	114	113					17																	38955214		2203	4299	6502	SO:0001583	missense	162605	exon2			ATCTGCAGAATGA	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"-", "Intermediate filaments type I, keratins (acidic)"	30842	protein-coding gene	gene with protein product			"keratin 25D"	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.488T>C	chr17.hg19:g.38955214A>G	ENSP00000305263:p.Leu163Pro	595.0	0.0		783.0	217.0	NM_181535		Missense_Mutation	SNP	ENST00000306658.7	hg19	CCDS11376.1	.	.	.	.	.	.	.	.	.	.	A	19.71	3.877625	0.72294	.	.	ENSG00000173908	ENST00000306658	T	0.73789	-0.78	5.36	5.36	0.76844	Filament (1);	0.000000	0.47093	D	0.000254	D	0.91250	0.7242	H	0.98005	4.125	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94285	0.7523	10	0.87932	D	0	.	14.8194	0.70059	1.0:0.0:0.0:0.0	.	163	Q7Z3Y7	K1C28_HUMAN	P	163	ENSP00000305263:L163P	ENSP00000305263:L163P	L	-	2	0	KRT28	36208740	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.494000	0.90477	2.162000	0.67917	0.533000	0.62120	CTG	.	.		0.328	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535		G	38955214	A	G	38955214	3	3	59	1	0	0	0	0	1	0	0	0	8474	188	7	2	934	2	KRT28	17	38955214	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	9835756	38955214	42239996	64	7329										
FAM134C	162427	hgsc.bcm.edu	37	chr17	40733882	40733889	+	Frame_Shift_Del	DEL	CAGAAGTT	CAGAAGTT	-													0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tgactcagctccgactggtcCagaagttcaaagtcatcccc					rs546107864		TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	CAGAAGTT	CAGAAGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:40733882_40733889delCAGAAGTT	ENST00000309428.5	-	9	1402_1409	c.1343_1350delAACTTCTG	c.(1342-1350)gaacttctgfs	p.ELL448fs	FAM134C_ENST00000543197.1_Frame_Shift_Del_p.ELL253fs|FAM134C_ENST00000585894.1_Frame_Shift_Del_p.ELL351fs	NM_178126.3	NP_835227.1	Q86VR2	F134C_HUMAN	family with sequence similarity 134, member C	448						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.134)		CCGACTGGTCCAGAAGTTCAAAGTCATC	0.572																																					p.448_451del		Atlas-Indel,Pindel	.											.	FAM134C	26	.	0			c.1344_1351del						.																																			SO:0001589	frameshift_variant	162427	exon9			.	BC049370	CCDS11432.1	17q21.2	2007-05-01							27258	protein-coding gene	gene with protein product						12477932	Standard	NM_178126		Approved	DKFZp686B1036, FLJ33806	uc002ial.2	Q86VR2		ENST00000309428.5:c.1343_1350delAACTTCTG	chr17.hg19:g.40733882_40733889delCAGAAGTT	ENSP00000309432:p.Glu448fs	47.0	0.0		97.0	22.0	NM_178126	B3KR75	Frame_Shift_Del	DEL	ENST00000309428.5	hg19	CCDS11432.1																																																																																			.	.		0.572	FAM134C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450536.1	NM_178126		-	40733889	CAGAAGTT	-	40733882	7	5	59	1	0	1	0	1	0	0	0	0	5452	581	21	0	54	0	FAM134C	17	40733882	Frame_Shift_Del	DEL	CAGAAGTT	TCGA-CC-5263-01A-01D-A12Z-10	1778668	40733882	40461328	65	7330										
MPP2	4355	hgsc.bcm.edu	37	chr17	41958848	41958848	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gccaccagttggcatcatccTggtttacgatctggagcaag	11	11	2	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:41958848T>G	ENST00000461854.1	-	8	948	c.863A>C	c.(862-864)cAg>cCg	p.Q288P	MPP2_ENST00000520305.1_Missense_Mutation_p.Q125P|MPP2_ENST00000523501.1_Missense_Mutation_p.Q253P|MPP2_ENST00000377184.3_Missense_Mutation_p.Q281P|MPP2_ENST00000536246.1_Missense_Mutation_p.Q253P|MPP2_ENST00000473246.1_5'Flank|MPP2_ENST00000518766.1_Missense_Mutation_p.Q309P|MPP2_ENST00000269095.4_Missense_Mutation_p.Q264P			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	288	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(4)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		GGCATCATCCTGGTTTACGAT	0.617																																					p.Q264P		Atlas-SNP	.											.	MPP2	67	.	0			c.A791C						.						93	84	87					17																	41958848		2203	4300	6503	SO:0001583	missense	4355	exon7			TCATCCTGGTTTA		CCDS11471.1, CCDS62206.1, CCDS62207.1, CCDS62208.1, CCDS62209.1, CCDS62210.1	17q12-q21	2008-07-18			ENSG00000108852	ENSG00000108852			7220	protein-coding gene	gene with protein product	"MAGUK p55 subfamily member 2", "discs large, homolog 2"	600723		DLG2		7590743	Standard	NM_001278370		Approved	DKFZp761D0712	uc002ieo.1	Q14168	OTTHUMG00000133840	ENST00000461854.1:c.863A>C	chr17.hg19:g.41958848T>G	ENSP00000428286:p.Gln288Pro	55.0	0.0		105.0	30.0	NM_005374	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000461854.1	hg19		.	.	.	.	.	.	.	.	.	.	t	19.91	3.914920	0.72983	.	.	ENSG00000108852	ENST00000377184;ENST00000269095;ENST00000461854;ENST00000520305;ENST00000523501;ENST00000536246;ENST00000518766	T;T;T;T;T;T;T	0.08546	3.08;3.08;3.08;3.08;3.08;3.08;3.08	5.1	4.02	0.46733	.	.	.	.	.	T	0.26593	0.0650	M	0.81682	2.555	0.58432	D	0.99999	D;D	0.63046	0.992;0.991	D;P	0.69142	0.962;0.894	T	0.01039	-1.1472	9	0.87932	D	0	.	9.17	0.37074	0.0:0.0861:0.0:0.9139	.	309;281	E7EV80;Q14168-3	.;.	P	281;264;288;125;253;253;309	ENSP00000366389:Q281P;ENSP00000269095:Q264P;ENSP00000428286:Q288P;ENSP00000428136:Q125P;ENSP00000430540:Q253P;ENSP00000438012:Q253P;ENSP00000428182:Q309P	ENSP00000269095:Q264P	Q	-	2	0	MPP2	39314374	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	3.296000	0.51802	0.964000	0.38108	0.454000	0.30748	CAG	.	.		0.617	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374		G	41958848	T	G	41958848	3	3	59	1	0	0	0	0	1	0	0	0	9743	1580	55	5	895	5	MPP2	17	41958848	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	1224966	41958848	39236362	66	7331										
HOXB9	3219	hgsc.bcm.edu	37	chr17	46703431	46703431	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	aggctcccggacgcgtgcggGctcagcggcgcccaggaggc	18	15	1	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:46703431G>A	ENST00000311177.5	-	1	408	c.201C>T	c.(199-201)agC>agT	p.S67S	HOXB-AS4_ENST00000480386.1_RNA|HOXB9_ENST00000550387.1_Silent_p.S67S|HOXB7_ENST00000567101.2_Intron	NM_024017.4	NP_076922.1	P17482	HXB9_HUMAN	homeobox B9	67					anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|embryonic skeletal system development (GO:0048706)|mammary gland development (GO:0030879)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(1)|large_intestine(1)|liver(1)|lung(6)|prostate(1)	12						ACGCGTGCGGGCTCAGCGGCG	0.736																																					p.S67S		Atlas-SNP	.											.	HOXB9	19	.	0			c.C201T						.						4	6	5					17																	46703431		2030	4035	6065	SO:0001819	synonymous_variant	3219	exon1			GTGCGGGCTCAGC		CCDS11534.1	17q21.32	2011-06-20	2005-12-22		ENSG00000170689	ENSG00000170689		"Homeoboxes / ANTP class : HOXL subclass"	5120	protein-coding gene	gene with protein product		142964	"homeo box B9"	HOX2E, HOX2		1973146, 1358459	Standard	NM_024017		Approved		uc002inx.3	P17482	OTTHUMG00000159907	ENST00000311177.5:c.201C>T	chr17.hg19:g.46703431G>A		2.0	0.0		15.0	10.0	NM_024017	B2RDB7|Q9H1I1	Silent	SNP	ENST00000311177.5	hg19	CCDS11534.1																																																																																			.	.		0.736	HOXB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358101.2			A	46703431	G	A	46703431	2	1	59	1	0	0	0	0	0	0	0	1	7317	1194	42	3		3	HOXB9	17	46703431	Silent	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	4744583	46703431	34491779	67	7332										
ITGA3	3675	hgsc.bcm.edu	37	chr17	48165169	48165170	+	Frame_Shift_Ins	INS	-	-	G													0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gccgaaatcgagctgtggctINSggtgctggtggccgtgggtg							TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:48165169_48165170insG	ENST00000320031.8	+	24	3311_3312	c.2981_2982insG	c.(2980-2985)ctggtgfs	p.V995fs	ITGA3_ENST00000007722.7_Frame_Shift_Ins_p.V995fs	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	995					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						GAGCTGTGGCTGGTGCTGGTGG	0.644																																					p.L994fs		Atlas-INDEL	.											.	ITGA3	128	.	0			c.2981_2982insG						.																																			SO:0001589	frameshift_variant	3675	exon24			.	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"CD molecules", "Integrins"	6139	protein-coding gene	gene with protein product		605025	"antigen identified by monoclonal antibody J143"	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.2983dupG	chr17.hg19:g.48165171_48165171dupG	ENSP00000315190:p.Val995fs	69.0	0.0		165.0	12.0	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Frame_Shift_Ins	INS	ENST00000320031.8	hg19	CCDS11558.1																																																																																			.	.		0.644	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		G	48165170	-	G	48165169	7	5	59	1	0	1	1	0	0	0	0	0	7886	1580	55	0	3075	0	ITGA3	17	48165169	Frame_Shift_Ins	INS	-	TCGA-CC-5263-01A-01D-A12Z-10	1461738	48165169	33030041	68	7333										
CLTC	1213	hgsc.bcm.edu	37	chr17	57759022	57759022	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	acttaggtcttaattgagcaTattggaaacttggatcgggc	11	6	1	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:57759022T>C	ENST00000269122.3	+	21	3538	c.3264T>C	c.(3262-3264)caT>caC	p.H1088H	CLTC_ENST00000393043.1_Silent_p.H1088H|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	1088	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TAATTGAGCATATTGGAAACT	0.388			T	"ALK, TFE3"	"ALCL, renal "																																p.H1088H		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.T3264C						.						103	99	101					17																	57759022		2203	4300	6503	SO:0001819	synonymous_variant	1213	exon21			TGAGCATATTGGA	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.3264T>C	chr17.hg19:g.57759022T>C		147.0	0.0		179.0	93.0	NM_004859	D3DU00|Q6N0A0|Q86TF2	Silent	SNP	ENST00000269122.3	hg19	CCDS32696.1																																																																																			.	.		0.388	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		C	57759022	T	C	57759022	2	2	59	1	0	0	0	0	0	0	0	1	3568	1403	49	2		2	CLTC	17	57759022	Silent	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	9593853	57759022	23436188	69	7334										
KIF19	124602	hgsc.bcm.edu	37	chr17	72343926	72343926	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tcccatccaggactctctggGaggaaacagccgcacagtga	11	13	1	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:72343926G>A	ENST00000389916.4	+	9	1073	c.935G>A	c.(934-936)gGa>gAa	p.G312E		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	312	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GACTCTCTGGGAGGAAACAGC	0.637																																					p.G312E		Atlas-SNP	.											.	KIF19	102	.	0			c.G935A						.						80	46	58					17																	72343926		2202	4286	6488	SO:0001583	missense	124602	exon9			CTCTGGGAGGAAA	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.935G>A	chr17.hg19:g.72343926G>A	ENSP00000374566:p.Gly312Glu	26.0	0.0		50.0	13.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	G	19.95	3.921765	0.73213	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.76448	-1.02;-1.02	5.68	5.68	0.88126	Kinesin, motor domain (4);	.	.	.	.	D	0.90920	0.7146	M	0.91090	3.175	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.969;0.969	D;D;D;P	0.91635	0.98;0.999;0.918;0.891	D	0.92383	0.5915	9	0.87932	D	0	.	18.629	0.91352	0.0:0.0:1.0:0.0	.	312;270;270;312	Q2TAC6;F8VW50;Q2TAC6-3;Q2TAC6-2	KIF19_HUMAN;.;.;.	E	270;312	ENSP00000449134:G270E;ENSP00000374566:G312E	ENSP00000374566:G312E	G	+	2	0	KIF19	69855521	1.000000	0.71417	0.995000	0.50966	0.292000	0.27327	9.336000	0.96533	2.705000	0.92388	0.556000	0.70494	GGA	.	.		0.637	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		A	72343926	G	A	72343926	3	1	59	1	0	0	0	0	1	0	0	0	8291	1174	41	3	969	3	KIF19	17	72343926	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	14584904	72343926	8851284	70	7335										
FASN	2194	hgsc.bcm.edu	37	chr17	80039104	80039104	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	agcgtgagttgccgcacctcGcgcacggacagcaccaggtt	13	14	0	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr17:80039104G>A	ENST00000306749.2	-	38	6749	c.6531C>T	c.(6529-6531)cgC>cgT	p.R2177R	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2177	Acyl carrier. {ECO:0000255|PROSITE- ProRule:PRU00258}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GCCGCACCTCGCGCACGGACA	0.682																																					p.R2177R	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C6531T						.						27	24	25					17																	80039104		2188	4286	6474	SO:0001819	synonymous_variant	2194	exon38			CACCTCGCGCACG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6531C>T	chr17.hg19:g.80039104G>A		43.0	0.0		113.0	68.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.682	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80039104	G	A	80039104	2	1	59	1	0	0	0	0	0	0	0	1	5691	1074	38	1		1	FASN	17	80039104	Silent	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	7695178	80039104	1156106	71	7336										
MPPE1	65258	hgsc.bcm.edu	37	chr18	11889442	11889442	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	accttcagctgtacatgactTgggtgtctgaacattttctg	9	9	3	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr18:11889442T>A	ENST00000588072.1	-	5	1659	c.438A>T	c.(436-438)ccA>ccT	p.P146P	MPPE1_ENST00000399978.2_Silent_p.P146P|MPPE1_ENST00000317235.7_Silent_p.P146P|MPPE1_ENST00000344987.7_Silent_p.P146P|MPPE1_ENST00000309976.9_Silent_p.P146P	NM_023075.5	NP_075563.3	Q53F39	MPPE1_HUMAN	metallophosphoesterase 1	146					ER to Golgi vesicle-mediated transport (GO:0006888)|GPI anchor biosynthetic process (GO:0006506)	cis-Golgi network (GO:0005801)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GPI anchor binding (GO:0034235)|manganese ion binding (GO:0030145)|phosphoric diester hydrolase activity (GO:0008081)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5						GTACATGACTTGGGTGTCTGA	0.488																																					p.P146P		Atlas-SNP	.											.	MPPE1	21	.	0			c.A438T						.						127	108	114					18																	11889442		2203	4300	6503	SO:0001819	synonymous_variant	65258	exon4			ATGACTTGGGTGT	BC002877	CCDS11853.1, CCDS56054.1	18p11.21	2004-04-30			ENSG00000154889	ENSG00000154889			15988	protein-coding gene	gene with protein product		611900				11978971	Standard	NM_001242904		Approved		uc002kqf.3	Q53F39	OTTHUMG00000131661	ENST00000588072.1:c.438A>T	chr18.hg19:g.11889442T>A		135.0	0.0		203.0	50.0	NM_001242904	B0YJ39|B0YJ40|B0YJ41|B5ME53|B7WNJ3|D3DUI5|D3DUI7|Q6GMP1|Q8TAD6|Q8TE26|Q8WZ32|Q9BU58|Q9H958|Q9HAI4	Silent	SNP	ENST00000588072.1	hg19	CCDS11853.1																																																																																			.	.		0.488	MPPE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254562.2	NM_023075		A	11889442	T	A	11889442	2	1	59	1	0	0	0	0	0	0	0	1	9749	1799	63	4		4	MPPE1	18	11889442	Silent	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10		11889442	66187806	72	7337										
SYT4	6860	hgsc.bcm.edu	37	chr18	40854035	40854035	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	aaaagagcttcggggttgcaTtctccagatcagaaggactg	12	8	2	3			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr18:40854035T>A	ENST00000255224.3	-	2	727	c.359A>T	c.(358-360)aAt>aTt	p.N120I	SYT4_ENST00000586678.1_Intron|SYT4_ENST00000590752.1_Missense_Mutation_p.N102I	NM_020783.3	NP_065834.1	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	120					exocytosis (GO:0006887)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of vesicle fusion (GO:0031339)|neurotransmitter secretion (GO:0007269)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44						CGGGGTTGCATTCTCCAGATC	0.433																																					p.N120I	NSCLC(85;81 1419 2855 22820 35912)	Atlas-SNP	.											.	SYT4	162	.	0			c.A359T						.						118	116	117					18																	40854035		2203	4298	6501	SO:0001583	missense	6860	exon2			GTTGCATTCTCCA	BC036538	CCDS11922.1	18q12.3	2013-01-21			ENSG00000132872	ENSG00000132872		"Synaptotagmins"	11512	protein-coding gene	gene with protein product		600103				8058779	Standard	NM_020783		Approved	KIAA1342, HsT1192	uc002law.3	Q9H2B2	OTTHUMG00000132610	ENST00000255224.3:c.359A>T	chr18.hg19:g.40854035T>A	ENSP00000255224:p.Asn120Ile	207.0	0.0		329.0	105.0	NM_020783	B4DEU3|Q9P2K4	Missense_Mutation	SNP	ENST00000255224.3	hg19	CCDS11922.1	.	.	.	.	.	.	.	.	.	.	T	7.314	0.615635	0.14129	.	.	ENSG00000132872	ENST00000255224	T	0.37235	1.21	5.87	2.2	0.27929	.	0.335126	0.36002	N	0.002846	T	0.27489	0.0675	L	0.44542	1.39	0.33493	D	0.589003	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.25222	-1.0138	10	0.28530	T	0.3	.	9.812	0.40828	0.0:0.1939:0.0:0.8061	.	102;120	B4DEU3;Q9H2B2	.;SYT4_HUMAN	I	120	ENSP00000255224:N120I	ENSP00000255224:N120I	N	-	2	0	SYT4	39108033	1.000000	0.71417	0.949000	0.38748	0.606000	0.37113	3.844000	0.55873	0.206000	0.20587	0.533000	0.62120	AAT	.	.		0.433	SYT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255851.2	NM_020783		A	40854035	T	A	40854035	3	1	59	1	0	0	0	0	1	0	0	0	15491	1493	52	4	930	4	SYT4	18	40854035	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	28964593	40854035	37223213	73	7338										
ABCA7	10347	hgsc.bcm.edu	37	chr19	1051263	1051263	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	aggatgtggggctggtctccAagcagagtgtgcagactcgc	16	9	1	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr19:1051263A>T	ENST00000263094.6	+	20	3025	c.2794A>T	c.(2794-2796)Aag>Tag	p.K932*	ABCA7_ENST00000433129.1_Nonsense_Mutation_p.K932*|ABCA7_ENST00000435683.2_Nonsense_Mutation_p.K794*	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	932	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTGGTCTCCAAGCAGAGTGT	0.642																																					p.K932X		Atlas-SNP	.											.	ABCA7	174	.	0			c.A2794T						.						51	49	50					19																	1051263		2190	4288	6478	SO:0001587	stop_gained	10347	exon20			GTCTCCAAGCAGA	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.2794A>T	chr19.hg19:g.1051263A>T	ENSP00000263094:p.Lys932*	53.0	0.0		85.0	27.0	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Nonsense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	A	43	10.507155	0.99418	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7119	0.51630	1.0:0.0:0.0:0.0	.	.	.	.	X	932	.	ENSP00000263094:K932X	K	+	1	0	ABCA7	1002263	1.000000	0.71417	0.622000	0.29159	0.789000	0.44602	8.712000	0.91403	1.665000	0.50811	0.374000	0.22700	AAG	.	.		0.642	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1051263	A	T	1051263	4	4	59	1	0	0	0	0	0	1	0	0	37	131	5	4	2868	4	ABCA7	19	1051263	Nonsense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10		1051263	58077720	74	7339										
KHSRP	8570	hgsc.bcm.edu	37	chr19	6416830	6416830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gggaccccaattgccttggcCtcttcctcggcctcggcccc	10	19	1	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr19:6416830C>T	ENST00000398148.3	-	13	1338	c.1246G>A	c.(1246-1248)Ggc>Agc	p.G416S	MIR3940_ENST00000579148.1_RNA	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	416	Gly-rich.				gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						TTGCCTTGGCCTCTTCCTCGG	0.662																																					p.G416S	Colon(55;593 1006 2067 9135 22980)	Atlas-SNP	.											.	KHSRP	51	.	0			c.G1246A						.						17	20	19					19																	6416830		1939	4123	6062	SO:0001583	missense	8570	exon13			CTTGGCCTCTTCC	U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247			6316	protein-coding gene	gene with protein product	"FUSE binding protein 2"	603445				9136930, 8940189	Standard	NM_003685		Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945		ENST00000398148.3:c.1246G>A	chr19.hg19:g.6416830C>T	ENSP00000381216:p.Gly416Ser	31.0	0.0		34.0	14.0	NM_003685	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Missense_Mutation	SNP	ENST00000398148.3	hg19	CCDS45936.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.637286	0.87760	.	.	ENSG00000088247	ENST00000398148;ENST00000201886	T	0.54071	0.59	5.53	4.48	0.54585	.	0.000000	0.85682	D	0.000000	T	0.61565	0.2357	L	0.48642	1.525	0.58432	D	0.999999	D	0.61080	0.989	P	0.61722	0.893	T	0.60042	-0.7340	10	0.37606	T	0.19	.	13.5826	0.61911	0.0:0.9229:0.0:0.0771	.	416	Q92945	FUBP2_HUMAN	S	416	ENSP00000381216:G416S	ENSP00000201886:G416S	G	-	1	0	KHSRP	6367830	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	5.811000	0.69187	1.301000	0.44836	0.655000	0.94253	GGC	.	.		0.662	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1			T	6416830	C	T	6416830	3	4	59	1	0	0	0	0	1	0	0	0	8160	681	24	3	921	3	KHSRP	19	6416830	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	5365567	6416830	52712153	75	7340										
MUC16	94025	hgsc.bcm.edu	37	chr19	9045799	9045799	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ggcatctctgatggtatcaaGgtcatagtggtgcctgtgac	13	8	3	2	rs375775766		TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr19:9045799G>C	ENST00000397910.4	-	5	36035	c.35832C>G	c.(35830-35832)acC>acG	p.T11944T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11946	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATGGTATCAAGGTCATAGTGG	0.473																																					p.T11944T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C35832G						.						167	158	161					19																	9045799		1958	4151	6109	SO:0001819	synonymous_variant	94025	exon5			TATCAAGGTCATA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.35832C>G	chr19.hg19:g.9045799G>C		313.0	0.0		455.0	148.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9045799	G	C	9045799	2	2	59	1	0	0	0	0	0	0	0	1	9982	987	35	4		4	MUC16	19	9045799	Silent	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10	2628969	9045799	50083184	76	7341										
ABHD8	79575	hgsc.bcm.edu	37	chr19	17412326	17412326	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gggcttgacctctacaaaggTgtagccatcgctggactcga	12	11	1	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr19:17412326T>A	ENST00000247706.3	-	2	339	c.100A>T	c.(100-102)Acc>Tcc	p.T34S	MRPL34_ENST00000595444.1_Intron|MRPL34_ENST00000600434.1_Intron|MRPL34_ENST00000594999.1_5'Flank	NM_024527.4	NP_078803.4	Q96I13	ABHD8_HUMAN	abhydrolase domain containing 8	34							hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	9						TCTACAAAGGTGTAGCCATCG	0.672																																					p.T34S	Ovarian(156;1368 2543 15275 41187)	Atlas-SNP	.											.	ABHD8	26	.	0			c.A100T						.						18	22	21					19																	17412326		2192	4278	6470	SO:0001583	missense	79575	exon2			CAAAGGTGTAGCC	AK021805	CCDS12355.1	19p13.12	2010-12-09			ENSG00000127220	ENSG00000127220		"Abhydrolase domain containing"	23759	protein-coding gene	gene with protein product						12477932	Standard	NM_024527		Approved	FLJ11743, MGC14280, MGC2512	uc002ngb.4	Q96I13		ENST00000247706.3:c.100A>T	chr19.hg19:g.17412326T>A	ENSP00000247706:p.Thr34Ser	26.0	0.0		49.0	23.0	NM_024527	Q9HAE9	Missense_Mutation	SNP	ENST00000247706.3	hg19	CCDS12355.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.551576	0.27739	.	.	ENSG00000127220	ENST00000247706	T	0.30182	1.54	5.24	3.0	0.34707	.	0.386165	0.29722	N	0.011368	T	0.11452	0.0279	N	0.08118	0	0.27073	N	0.963261	B	0.02656	0.0	B	0.04013	0.001	T	0.20907	-1.0261	10	0.17832	T	0.49	-39.906	1.8784	0.03223	0.1671:0.0899:0.1743:0.5688	.	34	Q96I13	ABHD8_HUMAN	S	34	ENSP00000247706:T34S	ENSP00000247706:T34S	T	-	1	0	ABHD8	17273326	1.000000	0.71417	0.971000	0.41717	0.986000	0.74619	2.101000	0.41787	0.253000	0.21552	0.402000	0.26972	ACC	.	.		0.672	ABHD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462937.1	NM_024527		A	17412326	T	A	17412326	3	1	59	1	0	0	0	0	1	0	0	0	87	1696	59	4	1235	4	ABHD8	19	17412326	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	8366527	17412326	41716657	77	7342										
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927768	23927768	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cttcacatttgtagaaatttActctagtacaaattatttta	3	6	2	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr19:23927768A>T	ENST00000402377.3	-	4	725	c.584T>A	c.(583-585)gTa>gAa	p.V195E	ZNF681_ENST00000395385.3_Missense_Mutation_p.V126E	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	195					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				GTAGAAATTTACTCTAGTACA	0.279																																					p.V195E		Atlas-SNP	.											.	ZNF681	76	.	0			c.T584A						.						22	23	23					19																	23927768		2197	4290	6487	SO:0001583	missense	148213	exon4			AAATTTACTCTAG	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.584T>A	chr19.hg19:g.23927768A>T	ENSP00000384000:p.Val195Glu	280.0	0.0		202.0	77.0	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	hg19	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	0.012	-1.690277	0.00738	.	.	ENSG00000196172	ENST00000402377;ENST00000395385;ENST00000528059;ENST00000531570	T;T;T;T	0.22539	2.83;2.83;1.95;6.31	1.39	-2.77	0.05877	.	.	.	.	.	T	0.03608	0.0103	N	0.00403	-1.54	0.26265	N	0.978515	B	0.13145	0.007	B	0.17433	0.018	T	0.40813	-0.9543	9	0.02654	T	1	.	4.9577	0.14050	0.3414:0.0:0.0:0.6586	.	195	Q96N22	ZN681_HUMAN	E	195;126;126;126	ENSP00000384000:V195E;ENSP00000378783:V126E;ENSP00000433806:V126E;ENSP00000435824:V126E	ENSP00000378783:V126E	V	-	2	0	ZNF681	23719608	0.000000	0.05858	0.009000	0.14445	0.009000	0.06853	0.407000	0.21049	-0.383000	0.07858	-0.732000	0.03574	GTA	.	.		0.279	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		T	23927768	A	T	23927768	3	4	59	1	0	0	0	0	1	0	0	0	18103	391	14	4	1357	4	ZNF681	19	23927768	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10	6515442	23927768	35201215	78	7343										
ZNF230	7773	hgsc.bcm.edu	37	chr19	44514563	44514563	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gaacaaggtgatgtcccctcCcaggttgaggcaggactatc	12	11	0	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr19:44514563C>G	ENST00000429154.2	+	5	600	c.372C>G	c.(370-372)tcC>tcG	p.S124S		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	124	KRNB.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				ATGTCCCCTCCCAGGTTGAGG	0.433																																					p.S124S	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.C372G						.						102	96	98					19																	44514563		2203	4300	6503	SO:0001819	synonymous_variant	7773	exon5			CCCCTCCCAGGTT	U95044	CCDS33044.1	19q13.31	2013-01-08				ENSG00000159882		"Zinc fingers, C2H2-type", "-"	13024	protein-coding gene	gene with protein product							Standard	NM_006300		Approved	FDZF2	uc002oyb.1	Q9UIE0		ENST00000429154.2:c.372C>G	chr19.hg19:g.44514563C>G		193.0	0.0		134.0	95.0	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Silent	SNP	ENST00000429154.2	hg19	CCDS33044.1																																																																																			.	.		0.433	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1			G	44514563	C	G	44514563	2	3	59	1	0	0	0	0	0	0	0	1	17799	610	22	4		4	ZNF230	19	44514563	Silent	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	20586795	44514563	14614420	79	7344										
PPP1R12C	54776	hgsc.bcm.edu	37	chr19	55606963	55606963	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cgcctggagaagggggcctcTtcaagctgctgggagaagga	17	9	2	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr19:55606963T>C	ENST00000263433.3	-	10	1251	c.1236A>G	c.(1234-1236)gaA>gaG	p.E412E	PPP1R12C_ENST00000435544.2_Silent_p.E338E|PPP1R12C_ENST00000376393.2_Silent_p.E412E	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		AGGGGGCCTCTTCAAGCTGCT	0.592																																					p.E412E		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.A1236G						.						9	11	10					19																	55606963		2192	4275	6467	SO:0001819	synonymous_variant	54776	exon10			GGCCTCTTCAAGC	AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14947	protein-coding gene	gene with protein product	"myosin-binding subunit 85"	613245	"leukocyte receptor cluster (LRC) member 3", "protein phosphatase 1, regulatory (inhibitor) subunit 12C"	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.1236A>G	chr19.hg19:g.55606963T>C		25.0	0.0		54.0	18.0	NM_017607		Silent	SNP	ENST00000263433.3	hg19	CCDS12916.1																																																																																			.	.		0.592	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607		C	55606963	T	C	55606963	2	2	59	1	0	0	0	0	0	0	0	1	12368	1606	56	2		2	PPP1R12C	19	55606963	Silent	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	11092400	55606963	3522020	80	7345										
PTPRH	5794	hgsc.bcm.edu	37	chr19	55716907	55716907	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ggggacctcccaggtcagggCgatggagctgttggtctgag	18	9	2	1	rs144055741	byFrequency	TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr19:55716907C>A	ENST00000376350.3	-	4	428	c.406G>T	c.(406-408)Gcc>Tcc	p.A136S	PTPRH_ENST00000263434.5_Intron|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	136	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CAGGTCAGGGCGATGGAGCTG	0.592																																					p.A136S		Atlas-SNP	.											.	PTPRH	139	.	0			c.G406T						.						106	86	93					19																	55716907		2203	4300	6503	SO:0001583	missense	5794	exon4			TCAGGGCGATGGA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.406G>T	chr19.hg19:g.55716907C>A	ENSP00000365528:p.Ala136Ser	255.0	0.0		396.0	156.0	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	hg19	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	c	0.017	-1.509536	0.00984	.	.	ENSG00000080031	ENST00000376350	T	0.55413	0.52	4.23	2.09	0.27110	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.265460	0.06178	N	0.678911	T	0.28764	0.0713	N	0.04162	-0.26	0.29679	N	0.841854	B	0.14438	0.01	B	0.10450	0.005	T	0.26780	-1.0093	10	0.08599	T	0.76	.	9.1546	0.36985	0.0:0.1011:0.0:0.8989	.	136	Q9HD43	PTPRH_HUMAN	S	136	ENSP00000365528:A136S	ENSP00000365528:A136S	A	-	1	0	PTPRH	60408719	0.733000	0.28132	0.086000	0.20670	0.000000	0.00434	0.023000	0.13533	0.177000	0.19895	-2.885000	0.00097	GCC	.	C|1.000;T|0.000		0.592	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			A	55716907	C	A	55716907	3	1	59	1	0	0	0	0	1	0	0	0	12818	768	27	1	3009	1	PTPRH	19	55716907	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	109944	55716907	3412076	81	7346										
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3669214	3669214	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gcaacaccactggtcagcccAggggtggggcacaggttgag	16	11	1	1			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr20:3669214A>T	ENST00000344754.4	-	21	5122	c.5123T>A	c.(5122-5124)cTg>cAg	p.L1708Q	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.W1684R	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1708					cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						TGGTCAGCCCAGGGGTGGGGC	0.577																																					p.L1708Q		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.T5123A						.						57	45	49					20																	3669214		2201	4297	6498	SO:0001583	missense	6614	exon21			CAGCCCAGGGGTG	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.5123T>A	chr20.hg19:g.3669214A>T	ENSP00000341141:p.Leu1708Gln	81.0	0.0		107.0	44.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	hg19	CCDS13060.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.06|15.06	2.720618|2.720618	0.48728|0.48728	.|.	.|.	ENSG00000088827|ENSG00000088827	ENST00000344754|ENST00000202578	T|T	0.24151|0.22134	1.87|1.97	4.76|4.76	2.43|2.43	0.29744|0.29744	.|.	.|.	.|.	.|.	.|.	T|T	0.12347|0.12347	0.0300|0.0300	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B|B	0.20550|0.02656	0.046|0.0	B|B	0.14578|0.01281	0.011|0.0	T|T	0.26780|0.26780	-1.0093|-1.0093	9|9	0.87932|0.87932	D|D	0|0	.|.	4.1782|4.1782	0.10362|0.10362	0.7253:0.0:0.0972:0.1776|0.7253:0.0:0.0972:0.1776	.|.	1708|1684	Q9BZZ2|Q9BZZ2-3	SN_HUMAN|.	Q|R	1708|1684	ENSP00000341141:L1708Q|ENSP00000202578:W1684R	ENSP00000341141:L1708Q|ENSP00000202578:W1684R	L|W	-|-	2|1	0|0	SIGLEC1|SIGLEC1	3617214|3617214	0.003000|0.003000	0.15002|0.15002	0.505000|0.505000	0.27651|0.27651	0.028000|0.028000	0.11728|0.11728	1.202000|1.202000	0.32271|0.32271	0.374000|0.374000	0.24650|0.24650	0.454000|0.454000	0.30748|0.30748	CTG|TGG	.	.		0.577	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		T	3669214	A	T	3669214	3	4	59	1	0	0	0	0	1	0	0	0	14320	188	7	4	10	4	SIGLEC1	20	3669214	Missense_Mutation	SNP	A	TCGA-CC-5263-01A-01D-A12Z-10		3669214	59356306	82	7347										
ELMO2	63916	hgsc.bcm.edu	37	chr20	45004003	45004003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cagttcaaatatgatgtcccTttgagcctgcgaggtgaaac	10	9	1	3			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr20:45004003T>C	ENST00000290246.6	-	13	1131	c.937A>G	c.(937-939)Agg>Ggg	p.R313G	ELMO2_ENST00000439931.2_Missense_Mutation_p.R325G|ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000454865.2_Missense_Mutation_p.R45G|ELMO2_ENST00000396391.1_Missense_Mutation_p.R313G|ELMO2_ENST00000352077.2_Missense_Mutation_p.R311G|ELMO2_ENST00000372176.1_Missense_Mutation_p.R225G|ELMO2_ENST00000445496.2_Missense_Mutation_p.R130G	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	313	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				ATGATGTCCCTTTGAGCCTGC	0.502																																					p.R313G		Atlas-SNP	.											.	ELMO2	51	.	0			c.A937G						.						112	78	90					20																	45004003		2203	4300	6503	SO:0001583	missense	63916	exon12			TGTCCCTTTGAGC	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"Engulfment and cell motility proteins"	17233	protein-coding gene	gene with protein product		606421	"engulfment and cell motility 2 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.937A>G	chr20.hg19:g.45004003T>C	ENSP00000290246:p.Arg313Gly	152.0	0.0		206.0	76.0	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Missense_Mutation	SNP	ENST00000290246.6	hg19	CCDS13398.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.756808	0.69648	.	.	ENSG00000062598	ENST00000290246;ENST00000372176;ENST00000396391;ENST00000439931;ENST00000445496;ENST00000454865;ENST00000352077;ENST00000425546;ENST00000450812	T;T;T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.73	4.81	3.67	0.42095	Terpene synthase-like (1);Engulfment/cell motility, ELMO (2);	0.000000	0.85682	D	0.000000	T	0.53642	0.1809	M	0.62723	1.935	0.80722	D	1	P;D;D;D;P	0.67145	0.785;0.996;0.985;0.974;0.943	P;D;P;P;P	0.72625	0.636;0.978;0.83;0.908;0.867	T	0.54214	-0.8327	10	0.66056	D	0.02	-14.8006	10.8249	0.46627	0.0:0.0:0.1588:0.8412	.	325;45;313;130;313	B4DRL5;B4DZ20;E9PBG2;B7Z1S8;Q96JJ3	.;.;.;.;ELMO2_HUMAN	G	313;225;313;325;130;45;311;101;313	ENSP00000290246:R313G;ENSP00000361249:R225G;ENSP00000379673:R313G;ENSP00000396519:R325G;ENSP00000409920:R130G;ENSP00000415641:R45G;ENSP00000326172:R311G;ENSP00000388962:R101G;ENSP00000416181:R313G	ENSP00000290246:R313G	R	-	1	2	ELMO2	44437410	1.000000	0.71417	0.995000	0.50966	0.776000	0.43924	4.964000	0.63701	0.828000	0.34709	0.454000	0.30748	AGG	.	.		0.502	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086		C	45004003	T	C	45004003	3	2	59	1	0	0	0	0	1	0	0	0	5068	1608	56	2	1265	2	ELMO2	20	45004003	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	41334789	45004003	18021517	83	7348										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58444857	58444857	+	Frame_Shift_Del	DEL	C	C	-													0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	atagtcccacacttacctctCttttgctttgtatataattt							TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr20:58444857delC	ENST00000357552.3	-	36	3962	c.3737delG	c.(3736-3738)agafs	p.R1246fs	SYCP2_ENST00000371001.2_Frame_Shift_Del_p.R1246fs			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	1246					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ACTTACCTCTCTTTTGCTTTG	0.299																																					p.R1246fs		Atlas-Indel,Pindel	.											.	SYCP2	204	.	0			c.3738delA						.						109	105	107					20																	58444857		2199	4296	6495	SO:0001589	frameshift_variant	10388	exon35			.	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.3737delG	chr20.hg19:g.58444857delC	ENSP00000350162:p.Arg1246fs	279.0	0.0		195.0	70.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Frame_Shift_Del	DEL	ENST00000357552.3	hg19	CCDS13482.1																																																																																			.	.		0.299	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		-	58444857	C	-	58444857	7	5	59	1	0	1	0	1	0	0	0	0	15447	913	32	0	895	0	SYCP2	20	58444857	Frame_Shift_Del	DEL	C	TCGA-CC-5263-01A-01D-A12Z-10	13440854	58444857	4580663	84	7349										
NPBWR2	2832	hgsc.bcm.edu	37	chr20	62737266	62737266	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	ggggttcaggcacgagttggCgtagctgaggctggtgatga	19	6	1	3			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr20:62737266C>T	ENST00000369768.1	-	1	1258	c.919G>A	c.(919-921)Gcc>Acc	p.A307T		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	307					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					CACGAGTTGGCGTAGCTGAGG	0.597																																					p.A307T		Atlas-SNP	.											.	NPBWR2	36	.	0			c.G919A						.						197	132	154					20																	62737266		2202	4298	6500	SO:0001583	missense	2832	exon1			AGTTGGCGTAGCT	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"GPCR / Class A : Neuropeptide receptors : W/B"	4530	protein-coding gene	gene with protein product		600731	"G protein-coupled receptor 8"	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.919G>A	chr20.hg19:g.62737266C>T	ENSP00000358783:p.Ala307Thr	71.0	0.0		73.0	28.0	NM_005286	Q6NWQ6|Q9H4K3	Missense_Mutation	SNP	ENST00000369768.1	hg19	CCDS13557.1	.	.	.	.	.	.	.	.	.	.	C	6.535	0.467050	0.12402	.	.	ENSG00000125522	ENST00000369768	T	0.37915	1.17	3.43	0.189	0.15119	GPCR, rhodopsin-like superfamily (1);	0.224693	0.35262	N	0.003338	T	0.19525	0.0469	L	0.33137	0.985	0.39667	D	0.970707	B	0.29766	0.256	B	0.26310	0.068	T	0.18366	-1.0339	10	0.06236	T	0.91	.	9.5523	0.39317	0.0:0.7615:0.0:0.2385	.	307	P48146	NPBW2_HUMAN	T	307	ENSP00000358783:A307T	ENSP00000358783:A307T	A	-	1	0	NPBWR2	62207710	0.975000	0.34042	0.272000	0.24630	0.688000	0.40055	1.370000	0.34238	0.104000	0.17725	0.491000	0.48974	GCC	.	.		0.597	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286		T	62737266	C	T	62737266	3	4	59	1	0	0	0	0	1	0	0	0	10578	768	27	1	85	1	NPBWR2	20	62737266	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	4292409	62737266	288254	85	7350										
DNAJC28	54943	hgsc.bcm.edu	37	chr21	34860757	34860757	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	tcaggatgggaacaattaaaTtaaaatcattaattcgcttg	7	5	2	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr21:34860757T>A	ENST00000314399.3	-	2	1382	c.944A>T	c.(943-945)aAt>aTt	p.N315I	DNAJC28_ENST00000381947.3_Missense_Mutation_p.N315I|DNAJC28_ENST00000402202.1_Missense_Mutation_p.N315I	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	315										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						AACAATTAAATTAAAATCATT	0.348																																					p.N315I		Atlas-SNP	.											.	DNAJC28	47	.	0			c.A944T						.						83	79	80					21																	34860757		2203	4300	6503	SO:0001583	missense	54943	exon2			ATTAAATTAAAAT	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"Heat shock proteins / DNAJ (HSP40)"	1297	protein-coding gene	gene with protein product	"Orf28"		"chromosome 21 open reading frame 55"	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.944A>T	chr21.hg19:g.34860757T>A	ENSP00000320303:p.Asn315Ile	402.0	0.0		535.0	37.0	NM_001040192	D3DSF2	Missense_Mutation	SNP	ENST00000314399.3	hg19	CCDS13626.1	.	.	.	.	.	.	.	.	.	.	T	19.95	3.921477	0.73213	.	.	ENSG00000177692	ENST00000381947;ENST00000314399;ENST00000402202	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.79816	0.4511	M	0.80183	2.485	0.53688	D	0.999979	D	0.89917	1.0	D	0.87578	0.998	T	0.83136	-0.0111	9	0.87932	D	0	-25.7443	14.8401	0.70217	0.0:0.0:0.0:1.0	.	315	Q9NX36	DJC28_HUMAN	I	315	.	ENSP00000320303:N315I	N	-	2	0	DNAJC28	33782627	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.094000	0.76944	2.050000	0.60909	0.528000	0.53228	AAT	.	.		0.348	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3			A	34860757	T	A	34860757	3	1	59	1	0	0	0	0	1	0	0	0	4648	1493	52	4	226	4	DNAJC28	21	34860757	Missense_Mutation	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10		34860757	13269138	86	7351										
ST13	6767	hgsc.bcm.edu	37	chr22	41223190	41223190	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	atgccccctcccattccaggCattcctccgggaaaattacc	6	17	0	0	rs710193	byFrequency	TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr22:41223190C>A	ENST00000216218.3	-	11	1372	c.891G>T	c.(889-891)atG>atT	p.M297I		NM_003932.3	NP_003923.2	P50502	F10A1_HUMAN	suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein)	297	Gly/Met/Pro-rich.		M -> I (in dbSNP:rs710193).		chaperone cofactor-dependent protein refolding (GO:0070389)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	dATP binding (GO:0032564)|protein binding, bridging (GO:0030674)			cervix(1)|large_intestine(1)|lung(3)|skin(1)	6						CCATTCCAGGCATTCCTCCGG	0.458																																					p.M297I		Atlas-SNP	.											.	ST13	16	.	0			c.G891T						.						53	58	56					22																	41223190		2203	4298	6501	SO:0001583	missense	6767	exon11			TCCAGGCATTCCT		CCDS14006.1	22q13.2	2013-01-10	2001-11-29		ENSG00000100380	ENSG00000100380		"Tetratricopeptide (TTC) repeat domain containing"	11343	protein-coding gene	gene with protein product	"progesterone receptor-associated p48 protein"	606796	"suppression of tumorigenicity 13 (colon carcinoma) (Hsp70-interacting protein)"			9925927, 8721986	Standard	NM_003932		Approved	SNC6, HSPABP1, HIP, P48, FAM10A1	uc003aze.3	P50502	OTTHUMG00000151201	ENST00000216218.3:c.891G>T	chr22.hg19:g.41223190C>A	ENSP00000216218:p.Met297Ile	39.0	0.0		49.0	20.0	NM_003932	O14999|Q2TU77	Missense_Mutation	SNP	ENST00000216218.3	hg19	CCDS14006.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.812778	0.32053	.	.	ENSG00000100380	ENST00000216218	D	0.84730	-1.89	5.01	5.01	0.66863	.	0.135171	0.64402	D	0.000003	D	0.85396	0.5687	M	0.80746	2.51	0.43803	D	0.996355	B;B	0.27765	0.188;0.188	B;B	0.31101	0.124;0.124	T	0.82544	-0.0404	10	0.26408	T	0.33	.	13.9913	0.64369	0.1521:0.8479:0.0:0.0	.	287;297	B4E0U6;P50502	.;F10A1_HUMAN	I	297	ENSP00000216218:M297I	ENSP00000216218:M297I	M	-	3	0	ST13	39553136	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.292000	0.51772	2.340000	0.79590	0.555000	0.69702	ATG	.	C|0.940;T|0.060		0.458	ST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321759.1	NM_003932		A	41223190	C	A	41223190	3	1	59	1	0	0	0	0	1	0	0	0	15225	710	25	3	226	3	ST13	22	41223190	Missense_Mutation	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10		41223190	10081376	87	7352										
ZC3H7B	23264	hgsc.bcm.edu	37	chr22	41739420	41739420	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gtgtccaccctgcccataggCccccgggctggcgactacac	11	18	0	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr22:41739420C>T	ENST00000352645.4	+	13	1556	c.1299C>T	c.(1297-1299)ggC>ggT	p.G433G	ZC3H7B_ENST00000351589.4_Splice_Site_p.G433G	NM_017590.4	NP_060060.3	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	449					viral process (GO:0016032)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						TGCCCATAGGCCCCCGGGCTG	0.622																																					p.G433G		Atlas-SNP	.											.	ZC3H7B	82	.	0			c.C1299T						.						55	57	56					22																	41739420		2203	4298	6501	SO:0001630	splice_region_variant	23264	exon13			CATAGGCCCCCGG		CCDS14013.1	22q13.2	2013-01-10		2005-08-09	ENSG00000100403	ENSG00000100403		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30869	protein-coding gene	gene with protein product						10470851, 11230166	Standard	NM_017590		Approved	RoXaN, FLJ13787, DKFZp434K0920, KIAA1031	uc003azw.4	Q9UGR2	OTTHUMG00000150969	ENST00000352645.4:c.1298-1C>T	chr22.hg19:g.41739420C>T		50.0	0.0		108.0	36.0	NM_017590	A7YY88|B2RCA4|Q5TFX9|Q8TBT9|Q9H8B6|Q9UGQ9|Q9UGR0|Q9UGR1|Q9UK03|Q9UPW9	Silent	SNP	ENST00000352645.4	hg19	CCDS14013.1																																																																																			.	.		0.622	ZC3H7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320696.1	NM_017590	Silent	T	41739420	C	T	41739420	5	4	59	1	0	0	0	0	0	0	1	0	17588	753	26	3	1345	3	ZC3H7B	22	41739420	Splice_Site	SNP	C	TCGA-CC-5263-01A-01D-A12Z-10	516230	41739420	9565146	88	7353										
CRELD2	79174	hgsc.bcm.edu	37	chr22	50315943	50315980	+	Intron	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-													0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	cgattcttacgcccctcagcAgtcaggaccggcctctccga					rs377640443|rs562885075|rs542695980|rs113299196|rs7410276|rs12160965|rs386822607|rs386822606|rs564615833|rs368043307|rs71805922|rs386822608|rs73891177	byFrequency	TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chr22:50315943_50315980delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	ENST00000328268.4	+	6	666				CRELD2_ENST00000403427.3_Intron|CRELD2_ENST00000404488.3_Splice_Site_p.PQQSGPASPILTR198fs|CRELD2_ENST00000444954.1_Intron|CRELD2_ENST00000407217.3_Intron	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2							endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		GCCCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCGCCTTGCTGTCTGTCTCT	0.618																																					p.198_207del		Atlas-INDEL	.											.	CRELD2	57	.	0			c.593_620del						.																																			SO:0001627	intron_variant	79174	exon6			.	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.593-280CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG>-	chr22.hg19:g.50315943_50315980delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG		57.0	0.0		112.0	32.0	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Frame_Shift_Del	DEL	ENST00000328268.4	hg19	CCDS14082.1																																																																																			.	.		0.618	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324		-	50315980	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-	50315943	6	5	59	0	1	1	0	1	0	0	0	0	3869	202	7	0		0	CRELD2	22	50315943	Intron	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	TCGA-CC-5263-01A-01D-A12Z-10	8576523	50315943	988623	89	7354										
ARAF	369	hgsc.bcm.edu	37	chrX	47428285	47428285	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	gtggcccggcagactgcccaGggcatggagtgagcctccca	15	14	0	2			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chrX:47428285G>T	ENST00000377045.4	+	11	1439	c.1245G>T	c.(1243-1245)caG>caT	p.Q415H		NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	415	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	AGACTGCCCAGGGCATGGAGT	0.657											OREG0019759	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q418H		Atlas-SNP	.											.	ARAF	67	.	0			c.G1254T						.						29	24	26					X																	47428285		2203	4300	6503	SO:0001583	missense	369	exon11			TGCCCAGGGCATG	X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"v-raf murine sarcoma 3611 viral oncogene homolog 1"	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.1245G>T	chrX.hg19:g.47428285G>T	ENSP00000366244:p.Gln415His	62.0	0.0	946	106.0	84.0	NM_001256196	P07557|Q5H9B2|Q5H9B3	Missense_Mutation	SNP	ENST00000377045.4	hg19	CCDS35232.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990746	0.74589	.	.	ENSG00000078061	ENST00000377045	D	0.83163	-1.69	5.33	4.47	0.54385	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85366	0.5680	L	0.41356	1.27	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.84916	0.0851	10	0.87932	D	0	.	7.5126	0.27583	0.1992:0.0:0.8008:0.0	.	415;281	P10398;B4DV85	ARAF_HUMAN;.	H	415	ENSP00000366244:Q415H	ENSP00000366244:Q415H	Q	+	3	2	ARAF	47313229	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.143000	0.64826	1.008000	0.39264	0.422000	0.28245	CAG	.	.		0.657	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1			T	47428285	G	T	47428285	3	4	59	1	0	0	0	0	1	0	0	0	837	991	35	3	1283	3	ARAF	23	47428285	Missense_Mutation	SNP	G	TCGA-CC-5263-01A-01D-A12Z-10		47428285	107842275	90	7355										
OPHN1	4983	hgsc.bcm.edu	37	chrX	67283856	67283856	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.010989010989011	1	1	0.266999376169682	0	0.355999168226242	1	1	0	aacttccccacgtccacctcTgggcagggctccaacttgcc	8	18	1	0			TCGA-CC-5263-01A-01D-A12Z-10	TCGA-CC-5263-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b3dc66b5-ad21-46ef-bea2-13b364e8f7ee	e354902e-c055-43ca-ad8a-29b0cd8fd07d	g.chrX:67283856T>A	ENST00000355520.5	-	21	2639	c.1998A>T	c.(1996-1998)ccA>ccT	p.P666P	OPHN1_ENST00000484842.1_5'UTR|OPHN1_ENST00000540071.1_Intron	NM_002547.2	NP_002538.1	O60890	OPHN1_HUMAN	oligophrenin 1	666	Pro-rich.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|negative regulation of proteasomal protein catabolic process (GO:1901799)|nervous system development (GO:0007399)|regulation of endocytosis (GO:0030100)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|substrate-dependent cell migration, cell extension (GO:0006930)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|terminal bouton (GO:0043195)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|skin(2)	31						CGTCCACCTCTGGGCAGGGCT	0.582																																					p.P666P		Atlas-SNP	.											.	OPHN1	75	.	0			c.A1998T						.						84	69	74					X																	67283856		2203	4300	6503	SO:0001819	synonymous_variant	4983	exon21			CACCTCTGGGCAG	AJ001189	CCDS14388.1	Xq12	2011-07-04			ENSG00000079482	ENSG00000079482		"Rho GTPase activating proteins"	8148	protein-coding gene	gene with protein product		300127	"mental retardation, X-linked 60"	MRX60		9195162, 9582072	Standard	NM_002547		Approved	OPN1, ARHGAP41	uc004dww.4	O60890	OTTHUMG00000021744	ENST00000355520.5:c.1998A>T	chrX.hg19:g.67283856T>A		114.0	0.0		216.0	168.0	NM_002547	B9EIP8|Q5JQ81|Q6PCC1|Q8WX47	Silent	SNP	ENST00000355520.5	hg19	CCDS14388.1																																																																																			.	.		0.582	OPHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057011.1	NM_002547		A	67283856	T	A	67283856	2	1	59	1	0	0	0	0	0	0	0	1	10884	1567	55	4		4	OPHN1	23	67283856	Silent	SNP	T	TCGA-CC-5263-01A-01D-A12Z-10	19855571	67283856	87986704	91	7356										
PRDM16	63976	hgsc.bcm.edu	37	chr1	3342300	3342300	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gcacctcaagaagcacgagcAcgagaacgcaccaggtgggc	13	13	1	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr1:3342300A>T	ENST00000270722.5	+	13	3144	c.3095A>T	c.(3094-3096)cAc>cTc	p.H1032L	PRDM16_ENST00000378398.3_Missense_Mutation_p.H1032L|PRDM16_ENST00000378391.2_Missense_Mutation_p.H1032L|PRDM16_ENST00000442529.2_Missense_Mutation_p.H1031L|PRDM16_ENST00000511072.1_Missense_Mutation_p.H1033L|PRDM16_ENST00000514189.1_Missense_Mutation_p.H1032L|PRDM16_ENST00000441472.2_Missense_Mutation_p.H1031L|PRDM16_ENST00000512462.1_3'UTR			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	1032	Interaction with CTBP1 and CTBP2. {ECO:0000250}.|Mediates interaction with SKI and regulation of TGF-beta signaling.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AAGCACGAGCACGAGAACGCA	0.667			T	EVI1	"MDS, AML"																																p.H1032L		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.A3095T						.						60	69	66					1																	3342300		2112	4203	6315	SO:0001583	missense	63976	exon13			ACGAGCACGAGAA	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.3095A>T	chr1.hg19:g.3342300A>T	ENSP00000270722:p.His1032Leu	44.0	0.0		114.0	38.0	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	hg19	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	A	15.43	2.831560	0.50845	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.14893	2.47;2.47;2.47;2.47;2.47;2.47;2.47;2.47;2.47	4.02	4.02	0.46733	Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	U	0.000113	T	0.36690	0.0976	M	0.68317	2.08	0.54753	D	0.99998	D;D;P;P	0.55800	0.973;0.971;0.904;0.951	D;P;P;P	0.64042	0.921;0.908;0.674;0.812	T	0.19224	-1.0312	10	0.72032	D	0.01	.	12.9149	0.58200	1.0:0.0:0.0:0.0	.	1032;1032;1031;1031	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	L	1033;1032;1031;1031;1032;1032;1032;848;848;840	ENSP00000426975:H1033L;ENSP00000367651:H1032L;ENSP00000407968:H1031L;ENSP00000405253:H1031L;ENSP00000367643:H1032L;ENSP00000421400:H1032L;ENSP00000270722:H1032L;ENSP00000422504:H848L;ENSP00000425796:H840L	ENSP00000270722:H1032L	H	+	2	0	PRDM16	3332160	1.000000	0.71417	0.998000	0.56505	0.946000	0.59487	7.051000	0.76627	1.451000	0.47736	0.379000	0.24179	CAC	.	.		0.667	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		T	3342300	A	T	3342300	3	4	60	1	0	0	0	0	1	0	0	0	12469	159	6	4	3145	4	PRDM16	1	3342300	Missense_Mutation	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10		3342300	245908321	1	7357										
SRM	6723	hgsc.bcm.edu	37	chr1	11119332	11119332	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	caggttggcgatcatctcctGgtaggagaactcgtctctct	11	11	4	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr1:11119332G>A	ENST00000376957.2	-	2	318	c.238C>T	c.(238-240)Cag>Tag	p.Q80*		NM_003132.2	NP_003123.2	P19623	SPEE_HUMAN	spermidine synthase	80	PABS.				cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)|spermidine synthase activity (GO:0004766)			large_intestine(1)|lung(1)|urinary_tract(1)	3	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.228)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)	S-Adenosylmethionine(DB00118)	ATCATCTCCTGGTAGGAGAAC	0.637																																					p.Q80X		Atlas-SNP	.											.	SRM	18	.	0			c.C238T						.						116	101	106					1																	11119332		2203	4300	6503	SO:0001587	stop_gained	6723	exon2			TCTCCTGGTAGGA	BC033106	CCDS125.1	1p36-p22	2010-11-08			ENSG00000116649	ENSG00000116649	2.5.1.16		11296	protein-coding gene	gene with protein product		182891		SRML1		2344393	Standard	NM_003132		Approved	SPS1	uc001arz.1	P19623	OTTHUMG00000002119	ENST00000376957.2:c.238C>T	chr1.hg19:g.11119332G>A	ENSP00000366156:p.Gln80*	98.0	0.0		337.0	95.0	NM_003132	B1AKP9|Q15511	Nonsense_Mutation	SNP	ENST00000376957.2	hg19	CCDS125.1	.	.	.	.	.	.	.	.	.	.	G	37	6.242829	0.97408	.	.	ENSG00000116649	ENST00000376957	.	.	.	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.289	0.66265	0.0:0.0:1.0:0.0	.	.	.	.	X	80	.	ENSP00000366156:Q80X	Q	-	1	0	SRM	11041919	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.865000	0.92300	2.191000	0.70037	0.448000	0.29417	CAG	.	.		0.637	SRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006056.1	NM_003132		A	11119332	G	A	11119332	4	1	60	1	0	0	0	0	0	1	0	0	15166	1357	47	3	698	3	SRM	1	11119332	Nonsense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	7777032	11119332	238131289	2	7358										
TMEM82	388595	hgsc.bcm.edu	37	chr1	16073479	16073479	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gctggacctgctgggcatccTtgtctccctactgggcgagc	13	14	1	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr1:16073479T>A	ENST00000375782.1	+	5	1013	c.875T>A	c.(874-876)cTt>cAt	p.L292H	RP11-169K16.4_ENST00000418525.1_RNA	NM_001013641.1	NP_001013663.1	A0PJX8	TMM82_HUMAN	transmembrane protein 82	292	Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|lung(5)|prostate(1)|skin(1)	13		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGGCATCCTTGTCTCCCTA	0.672																																					p.L292H		Atlas-SNP	.											.	TMEM82	30	.	0			c.T875A						.						99	87	91					1																	16073479		2203	4300	6503	SO:0001583	missense	388595	exon5			GCATCCTTGTCTC		CCDS30608.1	1p36.13	2008-02-05				ENSG00000162460			32350	protein-coding gene	gene with protein product							Standard	NM_001013641		Approved		uc001axc.4	A0PJX8		ENST00000375782.1:c.875T>A	chr1.hg19:g.16073479T>A	ENSP00000364938:p.Leu292His	159.0	0.0		400.0	114.0	NM_001013641	B2RP27|Q5VVD4	Missense_Mutation	SNP	ENST00000375782.1	hg19	CCDS30608.1	.	.	.	.	.	.	.	.	.	.	T	14.68	2.608396	0.46527	.	.	ENSG00000162460	ENST00000375782	T	0.54279	0.58	4.8	3.67	0.42095	.	0.709482	0.13524	N	0.381498	T	0.58892	0.2154	L	0.38175	1.15	0.21627	N	0.999612	D	0.71674	0.998	D	0.63192	0.912	T	0.48559	-0.9025	10	0.72032	D	0.01	-4.3264	9.972	0.41761	0.0:0.0812:0.0:0.9188	.	292	A0PJX8	TMM82_HUMAN	H	292	ENSP00000364938:L292H	ENSP00000364938:L292H	L	+	2	0	TMEM82	15946066	0.439000	0.25610	0.002000	0.10522	0.114000	0.19823	4.145000	0.58065	0.862000	0.35528	0.379000	0.24179	CTT	.	.		0.672	TMEM82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008471.2	NM_001013641		A	16073479	T	A	16073479	3	1	60	1	0	0	0	0	1	0	0	0	16221	1609	56	4	893	4	TMEM82	1	16073479	Missense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	4954147	16073479	233177142	3	7359										
FBXO42	54455	hgsc.bcm.edu	37	chr1	16577289	16577289	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	cttgtaccacggtatgcaggCtggtttcaggaggtccaacc	12	11	1	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr1:16577289C>A	ENST00000375592.3	-	10	2246	c.2030G>T	c.(2029-2031)aGc>aTc	p.S677I		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	677										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		GGTATGCAGGCTGGTTTCAGG	0.458																																					p.S677I		Atlas-SNP	.											.	FBXO42	53	.	0			c.G2030T						.						186	178	181					1																	16577289		2203	4300	6503	SO:0001583	missense	54455	exon10			TGCAGGCTGGTTT	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"F-boxes /  "other""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.2030G>T	chr1.hg19:g.16577289C>A	ENSP00000364742:p.Ser677Ile	236.0	0.0		393.0	133.0	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Missense_Mutation	SNP	ENST00000375592.3	hg19	CCDS30613.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103104	0.76983	.	.	ENSG00000037637	ENST00000375592	T	0.03745	3.82	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.07458	0.0188	N	0.08118	0	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.60949	-0.7161	10	0.23891	T	0.37	-16.1142	18.7865	0.91957	0.0:1.0:0.0:0.0	.	677	Q6P3S6	FBX42_HUMAN	I	677	ENSP00000364742:S677I	ENSP00000364742:S677I	S	-	2	0	FBXO42	16449876	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.587000	0.82613	2.767000	0.95098	0.655000	0.94253	AGC	.	.		0.458	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			A	16577289	C	A	16577289	3	1	60	1	0	0	0	0	1	0	0	0	5759	797	28	3	127	3	FBXO42	1	16577289	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	503810	16577289	232673332	4	7360										
RCC1	1104	hgsc.bcm.edu	37	chr1	28863318	28863318	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tgggccttggagagggtgctGaggagaagagcatacccacc	16	9	0	4	rs547058163		TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr1:28863318G>A	ENST00000373833.6	+	12	1282	c.997G>A	c.(997-999)Gag>Aag	p.E333K	RCC1_ENST00000373831.3_Missense_Mutation_p.E364K|RCC1_ENST00000398958.2_Missense_Mutation_p.E333K|RCC1_ENST00000373832.1_Missense_Mutation_p.E333K			P18754	RCC1_HUMAN	regulator of chromosome condensation 1	333					chromosome segregation (GO:0007059)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of Ran GTPase activity (GO:0032853)|regulation of mitosis (GO:0007088)|spindle assembly (GO:0051225)|viral process (GO:0016032)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosomal DNA binding (GO:0031492)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		AGAGGGTGCTGAGGAGAAGAG	0.607													G|||	1	0.000199681	0	0.0014	5008	,	,		18363	0		0	False		,,,				2504	0				p.E364K		Atlas-SNP	.											.	RCC1	61	.	0			c.G1090A						.						126	121	123					1																	28863318		2203	4300	6503	SO:0001583	missense	1104	exon10			GGTGCTGAGGAGA	X12654	CCDS323.1, CCDS41295.1	1p35.3	2008-08-18	2005-05-09	2005-05-09	ENSG00000180198	ENSG00000180198			1913	protein-coding gene	gene with protein product		179710	"chromosome condensation 1"	CHC1		7851910	Standard	NM_001048199		Approved		uc001bqf.2	P18754	OTTHUMG00000003645	ENST00000373833.6:c.997G>A	chr1.hg19:g.28863318G>A	ENSP00000362939:p.Glu333Lys	97.0	0.0		264.0	149.0	NM_001048194	Q16269|Q6NT97	Missense_Mutation	SNP	ENST00000373833.6	hg19	CCDS323.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271718	0.59649	.	.	ENSG00000180198	ENST00000398958;ENST00000373833;ENST00000373832;ENST00000373831;ENST00000411533	T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37	5.8	5.8	0.92144	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.045916	0.85682	D	0.000000	T	0.79913	0.4528	L	0.35288	1.05	0.58432	D	0.999994	B;P;P	0.42871	0.007;0.792;0.592	B;P;B	0.50314	0.005;0.637;0.392	T	0.73965	-0.3816	10	0.15066	T	0.55	-27.0717	18.6252	0.91334	0.0:0.0:1.0:0.0	.	364;350;333	P18754-2;E9PAT9;P18754	.;.;RCC1_HUMAN	K	333;333;333;364;350	ENSP00000381931:E333K;ENSP00000362939:E333K;ENSP00000362938:E333K;ENSP00000362937:E364K;ENSP00000413644:E350K	ENSP00000362937:E364K	E	+	1	0	RCC1	28735905	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.620000	0.67736	2.741000	0.93983	0.655000	0.94253	GAG	.	.		0.607	RCC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010323.3	NM_001269		A	28863318	G	A	28863318	3	1	60	1	0	0	0	0	1	0	0	0	13188	1291	45	3	1124	3	RCC1	1	28863318	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	12286029	28863318	220387303	5	7361										
RBM8A	9939	hgsc.bcm.edu	37	chr1	145508934	145508934	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	aggggtatactctagttgaaTatgaaacatacaaggaagcc	10	6	1	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr1:145508934T>C	ENST00000330165.8	+	5	430	c.361T>C	c.(361-363)Tat>Cat	p.Y121H	RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RBM8A_ENST00000369307.3_Missense_Mutation_p.Y120H|RP11-315I20.1_ENST00000447686.2_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|GNRHR2_ENST00000312753.5_RNA|RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000596355.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA	NM_005105.3	NP_005096.1	Q9Y5S9	RBM8A_HUMAN	RNA binding motif protein 8A	121	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TCTAGTTGAATATGAAACATA	0.453																																					p.Y121H		Atlas-SNP	.											.	RBM8A	18	.	0			c.T361C						.						71	73	72					1																	145508934		2203	4300	6503	SO:0001583	missense	9939	exon5			GTTGAATATGAAA	AF127761	CCDS72872.1	1q21.1	2013-02-12			ENSG00000131795			"RNA binding motif (RRM) containing"	9905	protein-coding gene	gene with protein product		605313		RBM8		11004516, 11013075	Standard	NM_005105		Approved	ZNRP, BOV-1A, BOV-1B, BOV-1C, RBM8B, Y14	uc001ent.2	Q9Y5S9	OTTHUMG00000013736	ENST00000330165.8:c.361T>C	chr1.hg19:g.145508934T>C	ENSP00000333001:p.Tyr121His	215.0	0.0		483.0	184.0	NM_005105	B3KQI9|Q6FHD1|Q6IQ40|Q9GZX8|Q9NZI4	Missense_Mutation	SNP	ENST00000330165.8	hg19	CCDS916.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.091281	0.76756	.	.	ENSG00000131795	ENST00000330165;ENST00000369307	T;T	0.78924	-1.22;-1.22	4.17	4.17	0.49024	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.64402	D	0.000001	D	0.89986	0.6874	H	0.98089	4.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.91837	0.5480	10	0.87932	D	0	-15.6879	9.5232	0.39149	0.0:0.0:0.0:1.0	.	120;121	Q9Y5S9-2;Q9Y5S9	.;RBM8A_HUMAN	H	121;120	ENSP00000333001:Y121H;ENSP00000358313:Y120H	ENSP00000333001:Y121H	Y	+	1	0	RBM8A	144220291	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	6.909000	0.75735	1.755000	0.51935	0.459000	0.35465	TAT	.	.		0.453	RBM8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038503.2	NM_005105		C	145508934	T	C	145508934	3	2	60	1	0	0	0	0	1	0	0	0	13161	1406	49	2	379	2	RBM8A	1	145508934	Missense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	116645616	145508934	103741687	6	7362										
KISS1	3814	hgsc.bcm.edu	37	chr1	204159887	204159887	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ggtgcacggcaggctctgctCcccgggggccaggaggccca	17	15	1	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr1:204159887C>A	ENST00000367194.4	-	3	290	c.142G>T	c.(142-144)Gag>Tag	p.E48*		NM_002256.3	NP_002247.3	Q15726	KISS1_HUMAN	KiSS-1 metastasis-suppressor	48					cytoskeleton organization (GO:0007010)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of luteinizing hormone secretion (GO:0033686)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of synaptic transmission (GO:0050806)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				large_intestine(1)|lung(1)|ovary(1)	3	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)	Breast(1374;9.42e-05)	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.069)|Kidney(21;0.0934)|Epithelial(59;0.239)	Colorectal(1306;0.0129)		AGGCTCTGCTCCCCGGGGGCC	0.687																																					p.E48X		Atlas-SNP	.											.	KISS1	6	.	0			c.G142T						.						10	12	11					1																	204159887		1449	3362	4811	SO:0001587	stop_gained	3814	exon3			TCTGCTCCCCGGG	U43527	CCDS41454.1	1q32	2014-01-30			ENSG00000170498	ENSG00000170498		"Endogenous ligands"	6341	protein-coding gene	gene with protein product	"prepro-kisspeptin", "kisspeptin"	603286				9192814, 9806840	Standard	NM_002256		Approved		uc001har.3	Q15726	OTTHUMG00000036060	ENST00000367194.4:c.142G>T	chr1.hg19:g.204159887C>A	ENSP00000356162:p.Glu48*	26.0	0.0		101.0	50.0	NM_002256	A8K6N0|Q9HBP1	Nonsense_Mutation	SNP	ENST00000367194.4	hg19	CCDS41454.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.276141	0.59649	.	.	ENSG00000170498	ENST00000367194	.	.	.	4.87	2.97	0.34412	.	0.660246	0.12998	N	0.421909	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-14.1018	12.0686	0.53603	0.0:0.6678:0.3322:0.0	.	.	.	.	X	48	.	ENSP00000356162:E48X	E	-	1	0	KISS1	202426510	0.594000	0.26849	0.005000	0.12908	0.003000	0.03518	1.169000	0.31871	0.557000	0.29117	-0.121000	0.15023	GAG	.	.		0.687	KISS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087892.1	NM_002256		A	204159887	C	A	204159887	4	1	60	1	0	0	0	0	0	1	0	0	8336	864	30	3	278	3	KISS1	1	204159887	Nonsense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	58650953	204159887	45090734	7	7363										
LAMB3	3914	hgsc.bcm.edu	37	chr1	209789918	209789918	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ctcacccagcatggaactctGacccaaccggtccttcaact	6	17	3	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr1:209789918G>A	ENST00000356082.4	-	22	3414	c.3280C>T	c.(3280-3282)Cag>Tag	p.Q1094*	LAMB3_ENST00000391911.1_Nonsense_Mutation_p.Q1094*|LAMB3_ENST00000367030.3_Nonsense_Mutation_p.Q1094*	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	1094	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		ATGGAACTCTGACCCAACCGG	0.488																																					p.Q1094X		Atlas-SNP	.											.	LAMB3	136	.	0			c.C3280T						.						157	149	151					1																	209789918		2203	4300	6503	SO:0001587	stop_gained	3914	exon22			AACTCTGACCCAA	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.3280C>T	chr1.hg19:g.209789918G>A	ENSP00000348384:p.Gln1094*	166.0	0.0		631.0	221.0	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Nonsense_Mutation	SNP	ENST00000356082.4	hg19	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	G	31	5.094827	0.94197	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	.	.	.	3.91	2.95	0.34219	.	1.007520	0.07981	U	0.985576	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.4611	0.21956	0.0:0.2041:0.5857:0.2102	.	.	.	.	X	1094	.	ENSP00000348384:Q1094X	Q	-	1	0	LAMB3	207856541	0.028000	0.19301	0.007000	0.13788	0.185000	0.23345	2.092000	0.41700	0.810000	0.34279	0.449000	0.29647	CAG	.	.		0.488	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		A	209789918	G	A	209789918	4	1	60	1	0	0	0	0	0	1	0	0	8621	1299	45	3	246	3	LAMB3	1	209789918	Nonsense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	5630031	209789918	39460703	8	7364										
EXO1	9156	hgsc.bcm.edu	37	chr1	242045224	242045224	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tctggggactctaggaatctGattgcaatattaagttactt	9	6	3	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr1:242045224G>A	ENST00000366548.3	+	14	2709	c.2116G>A	c.(2116-2118)Gat>Aat	p.D706N	EXO1_ENST00000348581.5_Missense_Mutation_p.D706N|EXO1_ENST00000518483.1_Missense_Mutation_p.D706N	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	706	Interaction with MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			CTAGGAATCTGATTGCAATAT	0.303								Editing and processing nucleases																													p.D706N		Atlas-SNP	.											.	EXO1	103	.	0			c.G2116A						.						53	52	53					1																	242045224		2203	4296	6499	SO:0001583	missense	9156	exon12			GAATCTGATTGCA	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.2116G>A	chr1.hg19:g.242045224G>A	ENSP00000355506:p.Asp706Asn	467.0	1.0		210.0	77.0	NM_006027	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	hg19	CCDS1620.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.078429	0.36662	.	.	ENSG00000174371	ENST00000366548;ENST00000348581;ENST00000518483	T;T;T	0.39229	1.22;1.22;1.09	4.77	4.77	0.60923	.	0.312666	0.36134	N	0.002774	T	0.51381	0.1671	M	0.71581	2.175	0.39135	D	0.961937	D;P;D	0.56521	0.976;0.921;0.976	P;P;P	0.51742	0.477;0.678;0.601	T	0.51576	-0.8688	10	0.28530	T	0.3	-37.7005	13.4964	0.61428	0.0:0.0:1.0:0.0	.	705;706;706	A8K5H6;Q9UQ84-4;Q9UQ84	.;.;EXO1_HUMAN	N	706	ENSP00000355506:D706N;ENSP00000311873:D706N;ENSP00000430251:D706N	ENSP00000311873:D706N	D	+	1	0	EXO1	240111847	1.000000	0.71417	0.998000	0.56505	0.498000	0.33706	4.550000	0.60733	2.636000	0.89361	0.655000	0.94253	GAT	.	.		0.303	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027		A	242045224	G	A	242045224	3	1	60	1	0	0	0	0	1	0	0	0	5302	1290	45	3	2158	3	EXO1	1	242045224	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	32255306	242045224	7205397	9	7365										
ADAM17	6868	hgsc.bcm.edu	37	chr2	9667941	9667941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gtggttctctgtctactaacCcttttgggagcaactcttca	8	11	4	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr2:9667941C>T	ENST00000310823.3	-	5	775	c.593G>A	c.(592-594)gGg>gAg	p.G198E	ADAM17_ENST00000497134.1_Missense_Mutation_p.G198E	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	198					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		GTCTACTAACCCTTTTGGGAG	0.343																																					p.G198E		Atlas-SNP	.											.	ADAM17	61	.	0			c.G593A						.						144	144	144					2																	9667941		2203	4299	6502	SO:0001583	missense	6868	exon5			ACTAACCCTTTTG	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.593G>A	chr2.hg19:g.9667941C>T	ENSP00000309968:p.Gly198Glu	155.0	0.0		92.0	28.0	NM_003183	O60226	Missense_Mutation	SNP	ENST00000310823.3	hg19	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	C	7.292	0.611305	0.14066	.	.	ENSG00000151694	ENST00000310823;ENST00000497134;ENST00000538558	T;T	0.63096	2.12;-0.02	5.48	3.68	0.42216	.	0.596963	0.18368	N	0.143352	T	0.56848	0.2013	L	0.31664	0.95	0.38154	D	0.938826	D;B;D;B	0.62365	0.991;0.0;0.991;0.0	P;B;P;B	0.55965	0.788;0.001;0.788;0.001	T	0.55302	-0.8162	10	0.02654	T	1	.	12.0942	0.53744	0.0:0.8601:0.0:0.1399	.	198;198;198;198	A8K1B4;B2RNB2;Q6P5T8;P78536	.;.;.;ADA17_HUMAN	E	198	ENSP00000309968:G198E;ENSP00000418728:G198E	ENSP00000309968:G198E	G	-	2	0	ADAM17	9585392	0.991000	0.36638	0.065000	0.19835	0.187000	0.23431	2.793000	0.47845	0.786000	0.33708	-0.373000	0.07131	GGG	.	.		0.343	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			T	9667941	C	T	9667941	3	4	60	1	0	0	0	0	1	0	0	0	238	623	22	3	1941	3	ADAM17	2	9667941	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10		9667941	233531432	10	7366										
TRMT61B	55006	hgsc.bcm.edu	37	chr2	29092901	29092901	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	aggttttccagtgacgaaagAcatccagtcccaatgtccga	9	11	0	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr2:29092901A>G	ENST00000306108.5	-	1	266	c.243T>C	c.(241-243)tgT>tgC	p.C81C		NM_017910.3	NP_060380.3	Q9BVS5	TR61B_HUMAN	tRNA methyltransferase 61 homolog B (S. cerevisiae)	81					mitochondrial tRNA methylation (GO:0070901)|protein homooligomerization (GO:0051260)	mitochondrion (GO:0005739)|tRNA (m1A) methyltransferase complex (GO:0031515)	tRNA (adenine-N1-)-methyltransferase activity (GO:0016429)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	13						GTGACGAAAGACATCCAGTCC	0.602																																					p.C81C		Atlas-SNP	.											.	TRMT61B	28	.	0			c.T243C						.						87	87	87					2																	29092901		2203	4300	6503	SO:0001819	synonymous_variant	55006	exon1			CGAAAGACATCCA	BC010365	CCDS1768.1	2p23.2	2009-01-09			ENSG00000171103	ENSG00000171103			26070	protein-coding gene	gene with protein product						11230166	Standard	NM_017910		Approved	FLJ20628	uc002rmm.3	Q9BVS5	OTTHUMG00000128433	ENST00000306108.5:c.243T>C	chr2.hg19:g.29092901A>G		86.0	0.0		311.0	152.0	NM_017910	Q9H0Q9|Q9NWS7	Silent	SNP	ENST00000306108.5	hg19	CCDS1768.1																																																																																			.	.		0.602	TRMT61B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250224.1	NM_017910		G	29092901	A	G	29092901	2	3	60	1	0	0	0	0	0	0	0	1	16585	273	10	2		2	TRMT61B	2	29092901	Silent	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	19424960	29092901	214106472	11	7367										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141250227	141250227	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	agtgctaattttccttatctCatgatgatcagcaagaatta	6	7	2	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr2:141250227C>T	ENST00000389484.3	-	57	10041	c.9070G>A	c.(9070-9072)Gag>Aag	p.E3024K		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3024					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TTCCTTATCTCATGATGATCA	0.343										TSP Lung(27;0.18)																											p.E3024K	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G9070A						.						206	182	190					2																	141250227		2203	4300	6503	SO:0001583	missense	53353	exon57			TTATCTCATGATG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.9070G>A	chr2.hg19:g.141250227C>T	ENSP00000374135:p.Glu3024Lys	113.0	0.0		59.0	15.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.602309	0.66445	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91180	-2.8	5.11	5.11	0.69529	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.91126	0.7206	L	0.55103	1.725	0.51233	D	0.999912	D	0.61697	0.99	P	0.54759	0.76	D	0.88043	0.2782	10	0.06099	T	0.92	.	18.5004	0.90879	0.0:1.0:0.0:0.0	.	3024	Q9NZR2	LRP1B_HUMAN	K	3024;2962	ENSP00000374135:E3024K	ENSP00000374135:E3024K	E	-	1	0	LRP1B	140966697	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.674000	0.61612	2.373000	0.80994	0.460000	0.39030	GAG	.	.		0.343	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141250227	C	T	141250227	3	4	60	1	0	0	0	0	1	0	0	0	8964	835	29	3	4869	3	LRP1B	2	141250227	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	112157326	141250227	101949146	12	7368										
FAM124B	79843	hgsc.bcm.edu	37	chr2	225266346	225266346	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	agtatttcacaggactggccCgttcagacacctgaaagagc	10	11	2	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr2:225266346C>G	ENST00000409685.3	-	1	405	c.140G>C	c.(139-141)cGg>cCg	p.R47P	FAM124B_ENST00000243806.2_Missense_Mutation_p.R47P|FAM124B_ENST00000389874.3_Missense_Mutation_p.R47P	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	47										endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		AGGACTGGCCCGTTCAGACAC	0.572																																					p.R47P		Atlas-SNP	.											FAM124B_ENST00000409685,NS,carcinoma,0,2	FAM124B	71	.	0			c.G140C						.						47	49	49					2																	225266346		2203	4300	6503	SO:0001583	missense	79843	exon1			CTGGCCCGTTCAG	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.140G>C	chr2.hg19:g.225266346C>G	ENSP00000386895:p.Arg47Pro	59.0	0.0		65.0	53.0	NM_024785	A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	hg19	CCDS46527.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695087	0.68386	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	T;T;T	0.55052	0.54;0.54;0.54	5.81	5.81	0.92471	.	0.052994	0.64402	D	0.000001	T	0.76637	0.4015	M	0.83603	2.65	0.58432	D	0.999998	D;D	0.89917	0.986;1.0	D;D	0.79784	0.927;0.993	T	0.78398	-0.2219	10	0.66056	D	0.02	-33.1611	20.0628	0.97684	0.0:1.0:0.0:0.0	.	47;47	Q9H5Z6;Q9H5Z6-2	F124B_HUMAN;.	P	47	ENSP00000374524:R47P;ENSP00000386895:R47P;ENSP00000243806:R47P	ENSP00000243806:R47P	R	-	2	0	FAM124B	224974590	0.968000	0.33430	0.386000	0.26170	0.075000	0.17131	7.294000	0.78760	2.745000	0.94114	0.655000	0.94253	CGG	.	.		0.572	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		G	225266346	C	G	225266346	3	3	60	1	0	0	0	0	1	0	0	0	5431	652	23	4	1326	4	FAM124B	2	225266346	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	84016119	225266346	17933027	13	7369										
GLB1	2720	hgsc.bcm.edu	37	chr3	33106973	33106973	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	acctgcactgttataactggCcctccattctgatagaggag	9	11	1	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr3:33106973C>T	ENST00000307377.8	-	3	382	c.322G>A	c.(322-324)Gcc>Acc	p.A108T	GLB1_ENST00000399402.3_Silent_p.G148G|GLB1_ENST00000445488.2_Silent_p.G226G|GLB1_ENST00000307363.5_Silent_p.G178G	NM_001135602.1	NP_001129074	P16278	BGAL_HUMAN	galactosidase, beta 1	0					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)	beta-galactosidase activity (GO:0004565)|galactoside binding (GO:0016936)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	21		Melanoma(143;0.104)				TTATAACTGGCCCTCCATTCT	0.468																																					p.A108T		Atlas-SNP	.											.	GLB1	51	.	0			c.G322A						.						57	63	61					3																	33106973		1941	4117	6058	SO:0001583	missense	2720	exon3			AACTGGCCCTCCA	M22590	CCDS43061.1, CCDS43062.1, CCDS46785.1	3p22.3	2012-10-02			ENSG00000170266	ENSG00000170266	3.2.1.23		4298	protein-coding gene	gene with protein product		611458	"elastin receptor 1, 67kDa", "elastin receptor 1 (67kD)"	ELNR1		110522, 3143362	Standard	NM_000404		Approved	EBP	uc003cfi.1	P16278	OTTHUMG00000155781	ENST00000307377.8:c.322G>A	chr3.hg19:g.33106973C>T	ENSP00000305920:p.Ala108Thr	314.0	0.0		428.0	230.0	NM_001135602	B2R7H8|B7Z6B0|P16279	Missense_Mutation	SNP	ENST00000307377.8	hg19	CCDS46785.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.500002	0.44455	.	.	ENSG00000170266	ENST00000307377	D	0.97924	-4.61	6.01	-1.38	0.09027	.	.	.	.	.	D	0.93419	0.7901	.	.	.	0.80722	D	1	B	0.21071	0.051	B	0.19946	0.027	T	0.82786	-0.0285	8	0.54805	T	0.06	-19.1601	1.3747	0.02218	0.1315:0.2644:0.2826:0.3215	.	108	E7EQ29	.	T	108	ENSP00000305920:A108T	ENSP00000305920:A108T	A	-	1	0	GLB1	33081977	0.003000	0.15002	0.825000	0.32803	0.980000	0.70556	-1.147000	0.03188	-0.611000	0.05709	0.650000	0.86243	GCC	.	.		0.468	GLB1-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341571.1	NM_000404		T	33106973	C	T	33106973	3	4	60	1	0	0	0	0	1	0	0	0	6435	739	26	3	1547	3	GLB1	3	33106973	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10		33106973	164915457	14	7370										
SLC22A14	9389	hgsc.bcm.edu	37	chr3	38347844	38347844	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	atcctggcagtgggcccccaCctgtccaaagctgagcagct	11	15	0	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr3:38347844C>T	ENST00000273173.4	+	1	418	c.327C>T	c.(325-327)caC>caT	p.H109H	RNU6-235P_ENST00000362644.1_RNA|SLC22A14_ENST00000448498.1_Silent_p.H109H	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	109					organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		TGGGCCCCCACCTGTCCAAAG	0.532																																					p.H109H		Atlas-SNP	.											.	SLC22A14	64	.	0			c.C327T						.						108	100	103					3																	38347844		2203	4300	6503	SO:0001819	synonymous_variant	9389	exon1			CCCCCACCTGTCC	AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"Solute carriers"	8495	protein-coding gene	gene with protein product		604048	"organic cationic transporter-like 4", "solute carrier family 22 (organic cation transporter), member 14"	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.327C>T	chr3.hg19:g.38347844C>T		115.0	0.0		273.0	20.0	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Silent	SNP	ENST00000273173.4	hg19	CCDS2677.1																																																																																			.	.		0.532	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803		T	38347844	C	T	38347844	2	4	60	1	0	0	0	0	0	0	0	1	14460	506	18	3		3	SLC22A14	3	38347844	Silent	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	5240871	38347844	159674586	15	7371										
FAM116A	201627	hgsc.bcm.edu	37	chr3	57678508	57678509	+	Splice_Site	DNP	CC	CC	AA													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	aagggcggggccgggcctcaCctccacggcctggcccagct							TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr3:57678508_57678509CC>AA	ENST00000311128.5	-	1	307_308	c.237_238GG>TT	c.(235-240)gaGGta>gaTTta	p.79_80EV>DL	RP11-755B10.3_ENST00000465933.1_lincRNA	NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	79					positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										CCGGGCCTCACCTCCACGGCCT	0.752																																					.|p.E79D		Atlas-SNP	.											.	.	.	.	0			c.237+1G>T|c.G237T						.																																			SO:0001630	splice_region_variant	201627	exon2|exon1			GCCTCACCTCCAC|CCTCACCTCCACG	AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839		"DENN/MADD domain containing"	26635	protein-coding gene	gene with protein product			"family with sequence similarity 116, member A"	FAM116A		21330364	Standard	NM_152678		Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.237_238delinsAA	chr3.hg19:g.57678508_57678509delinsAA		16.0|17.0	0.0		48.0|52.0	29.0|31.0	NM_152678	Q7Z5T4|Q8N235|Q8TEG8	Splice_Site|Missense_Mutation	SNP	ENST00000311128.5	hg19	CCDS33773.1																																																																																			.	.		0.752	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351594.1	NM_152678	Missense_Mutation	AA	57678509	CC	AA	57678508	5	1	60	1	0	0	0	0	0	0	1	0	5412	521	18	3	1668	3	FAM116A	3	57678508	Splice_Site	DNP	CC	TCGA-CC-5264-01A-01D-A12Z-10	19330664	57678508	140343922	16	7372										
KY	339855	hgsc.bcm.edu	37	chr3	134369796	134369796	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	agcgttgatgtccttcttcaGctccatgatgccgcctcctt	8	14	2	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr3:134369796G>A	ENST00000423778.2	-	1	68	c.7C>T	c.(7-9)Ctg>Ttg	p.L3L	KY_ENST00000508956.1_Silent_p.L3L|KY_ENST00000503669.1_Silent_p.L3L	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	3					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						TCCTTCTTCAGCTCCATGATG	0.652																																					p.L3L		Atlas-SNP	.											.	KY	92	.	0			c.C7T						.						56	62	60					3																	134369796		2111	4225	6336	SO:0001819	synonymous_variant	339855	exon1			TCTTCAGCTCCAT	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.7C>T	chr3.hg19:g.134369796G>A		138.0	0.0		325.0	85.0	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	hg19	CCDS46920.1																																																																																			.	.		0.652	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554		A	134369796	G	A	134369796	2	1	60	1	0	0	0	0	0	0	0	1	8595	962	34	3		3	KY	3	134369796	Silent	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	76691288	134369796	63652634	17	7373										
PLS1	5357	hgsc.bcm.edu	37	chr3	142405170	142405170	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	cttaatcagattgcccctaaAggtggggaagatggacctgc	12	9	1	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr3:142405170A>T	ENST00000337777.3	+	9	1146	c.933A>T	c.(931-933)aaA>aaT	p.K311N	PLS1_ENST00000497002.1_Missense_Mutation_p.K311N|PLS1_ENST00000457734.2_Missense_Mutation_p.K311N	NM_002670.2	NP_002661.2	Q14651	PLSI_HUMAN	plastin 1	311	Actin-binding 1.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	27						TTGCCCCTAAAGGTGGGGAAG	0.343																																					p.K311N		Atlas-SNP	.											.	PLS1	71	.	0			c.A933T						.						133	130	131					3																	142405170		2203	4300	6503	SO:0001583	missense	5357	exon9			CCCTAAAGGTGGG	L20826	CCDS3125.1	3q23	2013-01-10	2010-02-10		ENSG00000120756	ENSG00000120756		"EF-hand domain containing"	9090	protein-coding gene	gene with protein product		602734	"plastin 1 (I isoform)"			8139549	Standard	NM_002670		Approved	I-plastin, Plastin-1	uc003euz.3	Q14651	OTTHUMG00000159292	ENST00000337777.3:c.933A>T	chr3.hg19:g.142405170A>T	ENSP00000336831:p.Lys311Asn	87.0	0.0		116.0	32.0	NM_001172312	A8K2Q1|D3DNG3|Q8NEG6	Missense_Mutation	SNP	ENST00000337777.3	hg19	CCDS3125.1	.	.	.	.	.	.	.	.	.	.	A	15.96	2.987374	0.53934	.	.	ENSG00000120756	ENST00000457734;ENST00000476044;ENST00000337777;ENST00000497002	D;D;D;D	0.95238	-3.65;-3.65;-3.65;-3.65	5.36	2.96	0.34315	Calponin homology domain (5);	0.284737	0.43919	D	0.000501	D	0.89660	0.6779	L	0.55103	1.725	0.54753	D	0.999981	P	0.37997	0.614	B	0.30782	0.12	D	0.84497	0.0614	10	0.37606	T	0.19	-24.6923	7.8338	0.29358	0.8282:0.0:0.1718:0.0	.	311	Q14651	PLSI_HUMAN	N	311;232;311;311	ENSP00000387890:K311N;ENSP00000417481:K232N;ENSP00000336831:K311N;ENSP00000418700:K311N	ENSP00000336831:K311N	K	+	3	2	PLS1	143887860	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	3.565000	0.53798	0.464000	0.27142	0.533000	0.62120	AAA	.	.		0.343	PLS1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354435.1	NM_002670		T	142405170	A	T	142405170	3	4	60	1	0	0	0	0	1	0	0	0	12116	69	3	4	963	4	PLS1	3	142405170	Missense_Mutation	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	8035374	142405170	55617260	18	7374										
KCNAB1	7881	hgsc.bcm.edu	37	chr3	156009791	156009791	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gagctccaccgcccccaatgTggtgaacgcagcccgggcca	12	17	0	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr3:156009791T>A	ENST00000490337.1	+	2	339				KCNAB1_ENST00000302490.8_Missense_Mutation_p.V32E|KCNAB1_ENST00000471742.1_Intron|KCNAB1_ENST00000389634.5_Missense_Mutation_p.V32E|KCNAB1_ENST00000389636.5_Intron	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1						learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GCCCCCAATGTGGTGAACGCA	0.572																																					p.V32E		Atlas-SNP	.											.	KCNAB1	176	.	0			c.T95A						.						68	64	65					3																	156009791		2203	4300	6503	SO:0001627	intron_variant	7881	exon1			CCAATGTGGTGAA	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.276-129614T>A	chr3.hg19:g.156009791T>A		141.0	0.0		313.0	27.0	NM_172159	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	hg19	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.915197	0.52546	.	.	ENSG00000169282	ENST00000302490;ENST00000389634	T;T	0.09163	3.34;3.01	4.89	3.73	0.42828	.	0.000000	0.85682	D	0.000000	T	0.06188	0.0160	N	0.22421	0.69	0.58432	D	0.999998	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.26121	-1.0112	10	0.09084	T	0.74	.	8.2737	0.31860	0.0:0.1663:0.0:0.8337	.	32;32	F8W6W4;B3KPZ4	.;.	E	32	ENSP00000305858:V32E;ENSP00000374285:V32E	ENSP00000305858:V32E	V	+	2	0	KCNAB1	157492485	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.019000	0.70818	0.722000	0.32252	0.377000	0.23210	GTG	.	.		0.572	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		A	156009791	T	A	156009791	1	1	60	0	1	0	0	0	0	0	0	0	8018	1696	59	4		4	KCNAB1	3	156009791	Intron	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	13604621	156009791	42012639	19	7375										
UBXN7	26043	hgsc.bcm.edu	37	chr3	196134222	196134222	+	Frame_Shift_Del	DEL	T	T	-													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ctgccatttccagattattgTtgcacgcttcaagcatatgt							TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr3:196134222delT	ENST00000296328.4	-	2	190	c.116delA	c.(115-117)aacfs	p.N41fs	UBXN7_ENST00000535858.1_Intron|UBXN7_ENST00000428095.1_Intron	NM_015562.1	NP_056377.1	O94888	UBXN7_HUMAN	UBX domain protein 7	41						Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|nucleus (GO:0005634)	transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						CAGATTATTGTTGCACGCTTC	0.403																																					p.N39fs		Atlas-Indel,Pindel	.											.	UBXN7	43	.	0			c.117delC						.						190	175	180					3																	196134222		1903	4118	6021	SO:0001589	frameshift_variant	26043	exon2			.	AB018337	CCDS43191.1	3q29	2012-07-06	2008-07-25	2008-07-25	ENSG00000163960	ENSG00000163960		"UBX domain containing"	29119	protein-coding gene	gene with protein product			"UBX domain containing 7"	UBXD7		9872452, 22537386	Standard	NM_015562		Approved	KIAA0794	uc003fwm.4	O94888	OTTHUMG00000155639	ENST00000296328.4:c.116delA	chr3.hg19:g.196134222delT	ENSP00000296328:p.Asn41fs	196.0	0.0		278.0	93.0	NM_015562	D3DXB3|Q6ZP77|Q86X20|Q8N327	Frame_Shift_Del	DEL	ENST00000296328.4	hg19	CCDS43191.1																																																																																			.	.		0.403	UBXN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340938.2	XM_087353		-	196134222	T	-	196134222	7	5	60	1	0	1	0	1	0	0	0	0	16933	1725	60	0	1393	0	UBXN7	3	196134222	Frame_Shift_Del	DEL	T	TCGA-CC-5264-01A-01D-A12Z-10	40124431	196134222	1888208	20	7376										
TLR1	7096	hgsc.bcm.edu	37	chr4	38799406	38799406	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gaaaaatccaaatgcaggaaCgggctaattttggatgggca	12	6	0	0	rs375416156		TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr4:38799406C>A	ENST00000502213.2	-	3	1276	c.1047G>T	c.(1045-1047)ccG>ccT	p.P349P	TLR1_ENST00000308979.2_Silent_p.P349P			Q15399	TLR1_HUMAN	toll-like receptor 1	349					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						AATGCAGGAACGGGCTAATTT	0.363																																					p.P349P	GBM(5;216 373 40795 46382)	Atlas-SNP	.											TLR1,right_upper_lobe,carcinoma,0,1	TLR1	70	.	0			c.G1047T						.						57	59	58					4																	38799406		2203	4300	6503	SO:0001819	synonymous_variant	7096	exon4			CAGGAACGGGCTA	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1047G>T	chr4.hg19:g.38799406C>A		84.0	0.0		79.0	16.0	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.		0.363	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			A	38799406	C	A	38799406	2	1	60	1	0	0	0	0	0	0	0	1	15964	523	19	1		1	TLR1	4	38799406	Silent	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10		38799406	152354870	21	7377										
YIPF7	285525	hgsc.bcm.edu	37	chr4	44631480	44631480	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ggtccagtgaggtccgtttcAttcataatgctgccatctac	9	11	3	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr4:44631480A>G	ENST00000332990.5	-	4	454	c.438T>C	c.(436-438)aaT>aaC	p.N146N	YIPF7_ENST00000415895.4_Silent_p.N122N	NM_182592.2	NP_872398.2	Q8N8F6	YIPF7_HUMAN	Yip1 domain family, member 7	146						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(1)	12						GGTCCGTTTCATTCATAATGC	0.423																																					p.N146N		Atlas-SNP	.											.	YIPF7	33	.	0			c.T438C						.						83	90	88					4																	44631480		1904	4115	6019	SO:0001819	synonymous_variant	285525	exon4			CGTTTCATTCATA	AK096895	CCDS54766.1	4p13	2008-08-07			ENSG00000177752	ENSG00000177752		"Yip1 domain family"	26825	protein-coding gene	gene with protein product							Standard	NM_182592		Approved	FLJ39576, FinGER9	uc021xnx.1	Q8N8F6	OTTHUMG00000160467	ENST00000332990.5:c.438T>C	chr4.hg19:g.44631480A>G		158.0	0.0		104.0	58.0	NM_182592	Q3SY21|Q3SY22	Silent	SNP	ENST00000332990.5	hg19	CCDS54766.1	.	.	.	.	.	.	.	.	.	.	A	7.318	0.616431	0.14129	.	.	ENSG00000177752	ENST00000415895	.	.	.	5.31	0.122	0.14702	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-9.4527	5.1453	0.14981	0.5627:0.0:0.3108:0.1265	.	.	.	.	R	123	.	.	X	-	1	0	YIPF7	44326237	0.869000	0.29996	0.998000	0.56505	0.826000	0.46750	0.083000	0.14871	-0.097000	0.12307	-0.425000	0.05940	TGA	.	.		0.423	YIPF7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_182592		G	44631480	A	G	44631480	2	3	60	1	0	0	0	0	0	0	0	1	17498	214	8	2		2	YIPF7	4	44631480	Silent	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	5832074	44631480	146522796	22	7378										
GABRA4	2557	hgsc.bcm.edu	37	chr4	46930408	46930408	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ccgatggaggaggagtagctGacaacttcccagtagcccct	12	12	0	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr4:46930408G>T	ENST00000264318.3	-	9	2481	c.1499C>A	c.(1498-1500)tCa>tAa	p.S500*		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	500					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	AGGAGTAGCTGACAACTTCCC	0.468																																					p.S500X	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											.	GABRA4	129	.	0			c.C1499A						.						166	155	158					4																	46930408		2203	4300	6503	SO:0001587	stop_gained	2557	exon9			GTAGCTGACAACT		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4078	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 4"	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.1499C>A	chr4.hg19:g.46930408G>T	ENSP00000264318:p.Ser500*	196.0	1.0		99.0	63.0	NM_000809	Q8IYR7	Nonsense_Mutation	SNP	ENST00000264318.3	hg19	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	G	42	9.806889	0.99268	.	.	ENSG00000109158	ENST00000264318	.	.	.	5.82	5.82	0.92795	.	1.208420	0.05585	N	0.573544	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	17.2702	0.87099	0.0:0.0:1.0:0.0	.	.	.	.	X	500	.	ENSP00000264318:S500X	S	-	2	0	GABRA4	46625165	1.000000	0.71417	0.016000	0.15963	0.002000	0.02628	5.713000	0.68415	2.765000	0.95021	0.650000	0.86243	TCA	.	.		0.468	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			T	46930408	G	T	46930408	4	4	60	1	0	0	0	0	0	1	0	0	6171	1294	45	3	169	3	GABRA4	4	46930408	Nonsense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	2298928	46930408	144223868	23	7379										
KIT	3815	hgsc.bcm.edu	37	chr4	55599301	55599301	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ggtcggatcacaaagatttgTgattttggtctagccagaga	12	6	2	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr4:55599301T>A	ENST00000288135.5	+	17	2524	c.2427T>A	c.(2425-2427)tgT>tgA	p.C809*		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	809	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAAAGATTTGTGATTTTGGTC	0.388		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.C809X		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT	7396	.	0			c.T2427A						.						131	133	132					4																	55599301		2203	4300	6503	SO:0001587	stop_gained	3815	exon17	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	GATTTGTGATTTT	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2427T>A	chr4.hg19:g.55599301T>A	ENSP00000288135:p.Cys809*	174.0	0.0		82.0	17.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Nonsense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	T	38	7.059608	0.98036	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	.	.	.	5.62	-2.43	0.06522	.	0.000000	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.0215	0.47720	0.0:0.4074:0.0:0.5926	.	.	.	.	X	809;805	.	ENSP00000288135:C809X	C	+	3	2	KIT	55294058	1.000000	0.71417	0.991000	0.47740	0.967000	0.64934	1.047000	0.30367	-0.392000	0.07751	-0.361000	0.07541	TGT	.	.		0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			A	55599301	T	A	55599301	4	1	60	1	0	0	0	0	0	1	0	0	8338	1702	59	4	2493	4	KIT	4	55599301	Nonsense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	8668893	55599301	135554975	24	7380										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123268886	123268886	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gacagagcctaaaatccccaGcttccataagatcaaggagt	8	11	1	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr4:123268886G>C	ENST00000264501.4	+	76	13454	c.13081G>C	c.(13081-13083)Gct>Cct	p.A4361P	KIAA1109_ENST00000388738.3_Missense_Mutation_p.A4361P			Q2LD37	K1109_HUMAN	KIAA1109	4361					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AAAATCCCCAGCTTCCATAAG	0.448																																					p.A4361P		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G13081C						.						122	122	122					4																	123268886		2020	4169	6189	SO:0001583	missense	84162	exon74			TCCCCAGCTTCCA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.13081G>C	chr4.hg19:g.123268886G>C	ENSP00000264501:p.Ala4361Pro	138.0	0.0		60.0	17.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.215852|5.215852	0.95104|0.95104	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707|ENST00000306802	T;T;T|.	0.33654|.	2.39;2.39;1.4|.	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58119|0.58119	0.2100|0.2100	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.85130|.	0.997;0.996|.	T|T	0.48210|0.48210	-0.9055|-0.9055	10|5	0.33141|.	T|.	0.24|.	.|.	20.8598|20.8598	0.99761|0.99761	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	4360;4361|.	Q2LD37-4;Q2LD37|.	.;K1109_HUMAN|.	P|H	4361;4361;1030|736	ENSP00000264501:A4361P;ENSP00000373390:A4361P;ENSP00000410874:A1030P|.	ENSP00000264501:A4361P|.	A|Q	+|+	1|3	0|2	KIAA1109|KIAA1109	123488336|123488336	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.211000|7.211000	0.77933|0.77933	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GCT|CAG	.	.		0.448	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123268886	G	C	123268886	3	2	60	1	0	0	0	0	1	0	0	0	8217	971	34	4	13375	4	KIAA1109	4	123268886	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	67669585	123268886	67885390	25	7381										
FAM198B	51313	hgsc.bcm.edu	37	chr4	159048703	159048703	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tacactttatcaagaaacagAgactgaagaagtttctgccg	8	8	2	4			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr4:159048703A>T	ENST00000296530.8	-	5	2037	c.1416T>A	c.(1414-1416)tcT>tcA	p.S472S	FAM198B_ENST00000393807.5_Silent_p.S480S|FAM198B_ENST00000585682.1_Silent_p.S472S	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	472						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(14)|skin(2)|urinary_tract(1)	26						CAAGAAACAGAGACTGAAGAA	0.363																																					p.S480S		Atlas-SNP	.											.	FAM198B	134	.	0			c.T1440A						.						95	96	96					4																	159048703		2203	4300	6503	SO:0001819	synonymous_variant	51313	exon6			AAACAGAGACTGA		CCDS3798.1, CCDS34087.1	4q32.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000164125	ENSG00000164125			25312	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 18"	C4orf18		12975309	Standard	NM_001031700		Approved	FLJ38155, DKFZp434L142	uc003ipr.4	Q6UWH4	OTTHUMG00000161537	ENST00000296530.8:c.1416T>A	chr4.hg19:g.159048703A>T		134.0	0.0		76.0	64.0	NM_001031700	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Silent	SNP	ENST00000296530.8	hg19	CCDS3798.1																																																																																			.	.		0.363	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613		T	159048703	A	T	159048703	2	4	60	1	0	0	0	0	0	0	0	1	5534	291	11	4		4	FAM198B	4	159048703	Silent	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	35779817	159048703	32105573	26	7382										
HAND2	9464	hgsc.bcm.edu	37	chr4	174450187	174450187	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ggcccgggggcccggcgcccGgcggcacccccccgtaatgg	17	19	0	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr4:174450187G>T	ENST00000359562.4	-	1	1193	c.254C>A	c.(253-255)cCg>cAg	p.P85Q	HAND2-AS1_ENST00000515376.1_RNA|HAND2-AS1_ENST00000512209.2_RNA|HAND2-AS1_ENST00000507571.1_RNA|HAND2-AS1_ENST00000515310.1_RNA|HAND2-AS1_ENST00000512246.1_RNA|HAND2-AS1_ENST00000511196.1_RNA|HAND2-AS1_ENST00000510268.1_RNA|HAND2-AS1_ENST00000509640.1_RNA|HAND2-AS1_ENST00000510339.1_RNA|HAND2-AS1_ENST00000504740.1_RNA|HAND2-AS1_ENST00000512943.1_RNA|HAND2-AS1_ENST00000510221.1_RNA|HAND2-AS1_ENST00000507062.1_RNA|HAND2-AS1_ENST00000504429.1_RNA|HAND2-AS1_ENST00000502896.1_RNA|HAND2-AS1_ENST00000503198.1_RNA|HAND2-AS1_ENST00000514673.1_RNA|HAND2-AS1_ENST00000505817.1_RNA|HAND2-AS1_ENST00000509866.1_RNA|HAND2-AS1_ENST00000515350.1_RNA|HAND2-AS1_ENST00000508534.1_RNA|HAND2-AS1_ENST00000502941.1_RNA|HAND2-AS1_ENST00000512099.1_RNA|HAND2-AS1_ENST00000515741.1_RNA|HAND2-AS1_ENST00000511728.1_RNA|HAND2-AS1_ENST00000515345.1_RNA|HAND2-AS1_ENST00000508887.1_RNA|HAND2-AS1_ENST00000505032.1_RNA|HAND2-AS1_ENST00000505621.1_RNA|HAND2-AS1_ENST00000503309.1_RNA|HAND2-AS1_ENST00000507322.1_RNA|HAND2-AS1_ENST00000512929.1_RNA|HAND2_ENST00000505300.1_5'UTR|HAND2-AS1_ENST00000507636.1_RNA|HAND2-AS1_ENST00000503474.1_RNA|HAND2-AS1_ENST00000514431.1_RNA|HAND2-AS1_ENST00000502334.1_RNA	NM_021973.2	NP_068808.1	P61296	HAND2_HUMAN	heart and neural crest derivatives expressed 2	85					adult heart development (GO:0007512)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic process involved in heart morphogenesis (GO:0003278)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cardiac right ventricle formation (GO:0003219)|cartilage morphogenesis (GO:0060536)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|coronary artery morphogenesis (GO:0060982)|embryonic digit morphogenesis (GO:0042733)|heart development (GO:0007507)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mesenchymal cell proliferation (GO:0010463)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural crest cell development (GO:0014032)|noradrenergic neuron differentiation (GO:0003357)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peripheral nervous system neuron development (GO:0048935)|positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis (GO:2000764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process (GO:2000763)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|sympathetic nervous system development (GO:0048485)|thymus development (GO:0048538)|tongue development (GO:0043586)|visceral serous pericardium development (GO:0061032)	nuclear chromatin (GO:0000790)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|E-box binding (GO:0070888)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	13		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.37e-18)|Epithelial(43;5.5e-17)|OV - Ovarian serous cystadenocarcinoma(60;3.3e-10)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		cccggcgcccggcggcacccc	0.751																																					p.P85Q		Atlas-SNP	.											.	HAND2	25	.	0			c.C254A						.						5	6	6					4																	174450187		1696	3627	5323	SO:0001583	missense	9464	exon1			GCGCCCGGCGGCA	AF087941	CCDS3819.1	4q34.1	2014-08-12			ENSG00000164107	ENSG00000164107		"Basic helix-loop-helix proteins"	4808	protein-coding gene	gene with protein product		602407				9878849	Standard	NM_021973		Approved	dHand, Thing2, Hed, bHLHa26	uc003ith.1	P61296	OTTHUMG00000160775	ENST00000359562.4:c.254C>A	chr4.hg19:g.174450187G>T	ENSP00000352565:p.Pro85Gln	7.0	0.0		22.0	22.0	NM_021973	B6ECG9|O95300|O95301|P97833|Q494T1	Missense_Mutation	SNP	ENST00000359562.4	hg19	CCDS3819.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.986756	0.35036	.	.	ENSG00000164107	ENST00000359562;ENST00000535864	D	0.96856	-4.15	3.89	3.89	0.44902	.	0.197781	0.43747	D	0.000540	D	0.93602	0.7957	N	0.08118	0	0.42338	D	0.992326	D;P	0.71674	0.998;0.938	D;P	0.65010	0.931;0.535	D	0.90729	0.4641	10	0.13470	T	0.59	-13.708	12.475	0.55807	0.0:0.1699:0.8301:0.0	.	85;85	B6ECG9;P61296	.;HAND2_HUMAN	Q	85;33	ENSP00000352565:P85Q	ENSP00000352565:P85Q	P	-	2	0	HAND2	174686762	1.000000	0.71417	0.996000	0.52242	0.810000	0.45777	7.307000	0.78920	2.002000	0.58637	0.462000	0.41574	CCG	.	.		0.751	HAND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362241.3			T	174450187	G	T	174450187	3	4	60	1	0	0	0	0	1	0	0	0	6959	1116	39	1	407	1	HAND2	4	174450187	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	15401484	174450187	16704089	27	7383										
ZDHHC11	79844	hgsc.bcm.edu	37	chr5	837587	837587	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	atactcaaaggtggtcatctTcttggcctctggaaagggaa	11	8	5	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr5:837587T>A	ENST00000283441.8	-	6	1176	c.793A>T	c.(793-795)Aag>Tag	p.K265*	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Nonsense_Mutation_p.K265*	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	265						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GTGGTCATCTTCTTGGCCTCT	0.502																																					p.K265X		Atlas-SNP	.											.	ZDHHC11	97	.	0			c.A793T						.						141	156	151					5																	837587		2203	4300	6503	SO:0001587	stop_gained	79844	exon6			TCATCTTCTTGGC	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"Zinc fingers, DHHC-type"	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.793A>T	chr5.hg19:g.837587T>A	ENSP00000283441:p.Lys265*	491.0	0.0		1986.0	262.0	NM_024786	Q6UWR9	Nonsense_Mutation	SNP	ENST00000283441.8	hg19	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	t	22.4	4.283359	0.80803	.	.	ENSG00000188818	ENST00000424784;ENST00000283441;ENST00000511193	.	.	.	1.51	1.51	0.23008	.	5.581290	0.00993	U	0.003555	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-8.4861	5.2664	0.15601	0.0:0.0:0.0:1.0	.	.	.	.	X	265;265;40	.	ENSP00000283441:K265X	K	-	1	0	ZDHHC11	890587	0.001000	0.12720	0.015000	0.15790	0.028000	0.11728	0.036000	0.13819	0.979000	0.38497	0.315000	0.21342	AAG	.	.		0.502	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786		A	837587	T	A	837587	4	1	60	1	0	0	0	0	0	1	0	0	17616	1792	62	4	473	4	ZDHHC11	5	837587	Nonsense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10		837587	180077673	28	7384										
RAI14	26064	hgsc.bcm.edu	37	chr5	34826481	34826482	+	Frame_Shift_Ins	INS	-	-	C													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	aaattgaaggaggccttgaaINScagcctctcccagctctcct							TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr5:34826481_34826482insC	ENST00000265109.3	+	16	2983_2984	c.2696_2697insC	c.(2695-2700)aacagcfs	p.S900fs	RAI14_ENST00000503673.1_Frame_Shift_Ins_p.S900fs|RAI14_ENST00000515799.1_Frame_Shift_Ins_p.S903fs|RAI14_ENST00000397449.1_Frame_Shift_Ins_p.S893fs|RAI14_ENST00000428746.2_Frame_Shift_Ins_p.S900fs|RAI14_ENST00000512629.1_Frame_Shift_Ins_p.S871fs|RAI14_ENST00000506376.1_Frame_Shift_Ins_p.S892fs	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	900						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GAGGCCTTGAACAGCCTCTCCC	0.485																																					p.N902fs		Atlas-INDEL	.											RAI14,NS,carcinoma,0,1	RAI14	100	.	0			c.2705_2706insC						.																																			SO:0001589	frameshift_variant	26064	exon18			.	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.2697dupC	chr5.hg19:g.34826482_34826482dupC	ENSP00000265109:p.Ser900fs	86.0	0.0		298.0	19.0	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Frame_Shift_Ins	INS	ENST00000265109.3	hg19	CCDS34142.1																																																																																			.	.		0.485	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		C	34826482	-	C	34826481	7	5	60	1	0	1	1	0	0	0	0	0	13023	43	2	0	2819	0	RAI14	5	34826481	Frame_Shift_Ins	INS	-	TCGA-CC-5264-01A-01D-A12Z-10	33988894	34826481	146088779	29	7385										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37186475	37186475	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gtcctcaggatagggaaatgCtttcacgaaaatttctgcta	9	8	3	0	rs373443151		TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr5:37186475C>A	ENST00000508244.1	-	23	4195	c.4102G>T	c.(4102-4104)Gca>Tca	p.A1368S	C5orf42_ENST00000425232.2_Missense_Mutation_p.A1368S|C5orf42_ENST00000274258.7_Missense_Mutation_p.A249S			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1368						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TAGGGAAATGCTTTCACGAAA	0.328																																					p.A1368S		Atlas-SNP	.											.	C5orf42	422	.	0			c.G4102T						.						96	97	97					5																	37186475		2203	4300	6503	SO:0001583	missense	65250	exon24			GAAATGCTTTCAC		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.4102G>T	chr5.hg19:g.37186475C>A	ENSP00000421690:p.Ala1368Ser	217.0	0.0		567.0	136.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	32	5.112367	0.94339	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.31769	1.56;1.56;1.48;1.51	5.31	5.31	0.75309	.	0.236801	0.28671	N	0.014530	T	0.44095	0.1277	N	0.24115	0.695	0.41303	D	0.987056	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.37478	-0.9704	10	0.45353	T	0.12	.	18.9261	0.92546	0.0:1.0:0.0:0.0	.	1368;249	E9PH94;Q9H799	.;CE042_HUMAN	S	1368;1368;249;416;249	ENSP00000421690:A1368S;ENSP00000389014:A1368S;ENSP00000274258:A249S;ENSP00000424223:A416S	ENSP00000274258:A249S	A	-	1	0	C5orf42	37222232	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.738000	0.68613	2.624000	0.88883	0.655000	0.94253	GCA	.	.		0.328	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37186475	C	A	37186475	3	1	60	1	0	0	0	0	1	0	0	0	2303	797	28	3	5607	3	C5orf42	5	37186475	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	2359994	37186475	143728785	30	7386										
ERAP2	64167	hgsc.bcm.edu	37	chr5	96219543	96219543	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	aacccaggcacgcatggcttTcccttgctttgatgaaccgt	9	13	0	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr5:96219543T>C	ENST00000437043.3	+	3	1334	c.623T>C	c.(622-624)tTc>tCc	p.F208S	ERAP2_ENST00000379904.4_Missense_Mutation_p.F208S|CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000510309.1_Missense_Mutation_p.F208S	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	208					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		CGCATGGCTTTCCCTTGCTTT	0.443																																					p.F208S		Atlas-SNP	.											.	ERAP2	77	.	0			c.T623C						.						93	86	89					5																	96219543		2203	4300	6503	SO:0001583	missense	64167	exon3			TGGCTTTCCCTTG	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"leukocyte-derived arginine aminopeptidase"	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.623T>C	chr5.hg19:g.96219543T>C	ENSP00000400376:p.Phe208Ser	250.0	0.0		175.0	149.0	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	hg19	CCDS4086.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.532548	0.85812	.	.	ENSG00000164308	ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904;ENST00000510309	T;T;T;T;T	0.08370	3.65;3.65;3.65;3.1;3.65	5.13	3.97	0.46021	Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	0.069403	0.56097	D	0.000023	T	0.44912	0.1316	H	0.99130	4.44	0.35165	D	0.771068	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.69000	-0.5261	10	0.87932	D	0	.	9.8751	0.41197	0.0:0.0827:0.0:0.9173	.	208;208	Q6P179-3;Q6P179	.;ERAP2_HUMAN	S	208	ENSP00000400376:F208S;ENSP00000421175:F208S;ENSP00000421849:F208S;ENSP00000369235:F208S;ENSP00000425758:F208S	ENSP00000369235:F208S	F	+	2	0	ERAP2	96245299	1.000000	0.71417	0.981000	0.43875	0.985000	0.73830	4.610000	0.61155	0.901000	0.36495	0.455000	0.32223	TTC	.	.		0.443	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350		C	96219543	T	C	96219543	3	2	60	1	0	0	0	0	1	0	0	0	5206	1783	62	2	629	2	ERAP2	5	96219543	Missense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	59033068	96219543	84695717	31	7387										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148411195	148411195	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ctcagtctgcttatcacttcCcagggccaacagggagcatc	9	14	3	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr5:148411195C>A	ENST00000515425.1	-	9	1158	c.1057G>T	c.(1057-1059)Gga>Tga	p.G353*	SH3TC2_ENST00000513340.1_5'UTR|SH3TC2_ENST00000394358.2_Nonsense_Mutation_p.G238*|SH3TC2_ENST00000512049.1_Nonsense_Mutation_p.G346*|SH3TC2_ENST00000538184.1_5'UTR	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	353					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTATCACTTCCCAGGGCCAAC	0.527																																					p.G353X		Atlas-SNP	.											.	SH3TC2	178	.	0			c.G1057T						.						160	128	139					5																	148411195		2203	4300	6503	SO:0001587	stop_gained	79628	exon9			CACTTCCCAGGGC	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.1057G>T	chr5.hg19:g.148411195C>A	ENSP00000423660:p.Gly353*	103.0	0.0		153.0	131.0	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Nonsense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.865918	0.91511	.	.	ENSG00000169247	ENST00000515425;ENST00000512049;ENST00000394358	.	.	.	5.53	4.66	0.58398	.	0.208186	0.44097	D	0.000488	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	9.565	0.39394	0.1737:0.7505:0.0:0.0758	.	.	.	.	X	353;346;238	.	ENSP00000377886:G238X	G	-	1	0	SH3TC2	148391388	0.677000	0.27577	0.719000	0.30619	0.397000	0.30659	1.260000	0.32968	1.468000	0.48064	0.563000	0.77884	GGA	.	.		0.527	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		A	148411195	C	A	148411195	4	1	60	1	0	0	0	0	0	1	0	0	14277	632	22	3	2845	3	SH3TC2	5	148411195	Nonsense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	52191652	148411195	32504065	32	7388										
RANBP17	64901	hgsc.bcm.edu	37	chr5	170610173	170610173	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ttccttaacttctattacttAtatccttttaaaaaaacttg	1	8	1	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr5:170610173A>G	ENST00000523189.1	+	17	2032	c.1868A>G	c.(1867-1869)tAt>tGt	p.Y623C	RANBP17_ENST00000521759.1_Intron	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	623					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCTATTACTTATATCCTTTTA	0.269			T	TRD@	ALL																																p.Y623C		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.A1868G						.						27	31	30					5																	170610173		2190	4280	6470	SO:0001583	missense	64901	exon17			TTACTTATATCCT	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.1868A>G	chr5.hg19:g.170610173A>G	ENSP00000427975:p.Tyr623Cys	288.0	0.0		56.0	44.0	NM_022897	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	hg19	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.267783	0.59540	.	.	ENSG00000204764	ENST00000523189;ENST00000534916	T	0.67523	-0.27	5.49	5.49	0.81192	Armadillo-type fold (1);	1.051830	0.07457	N	0.899966	T	0.78666	0.4319	M	0.74546	2.27	0.45295	D	0.998296	D	0.63046	0.992	P	0.54401	0.751	T	0.70324	-0.4903	10	0.41790	T	0.15	-13.0125	14.103	0.65070	1.0:0.0:0.0:0.0	.	623	Q9H2T7	RBP17_HUMAN	C	623;53	ENSP00000427975:Y623C	ENSP00000427975:Y623C	Y	+	2	0	RANBP17	170542778	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.839000	0.86812	2.194000	0.70268	0.533000	0.62120	TAT	.	.		0.269	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		G	170610173	A	G	170610173	3	3	60	1	0	0	0	0	1	0	0	0	13042	449	16	2	1934	2	RANBP17	5	170610173	Missense_Mutation	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	22198978	170610173	10305087	33	7389										
OR2W1	26692	hgsc.bcm.edu	37	chr6	29012335	29012335	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	aggatgagaggtgtgaggacAattataatgcctaaagcgaa	13	4	0	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr6:29012335A>T	ENST00000377175.1	-	1	682	c.618T>A	c.(616-618)atT>atA	p.I206I		NM_030903.3	NP_112165.1	Q9Y3N9	OR2W1_HUMAN	olfactory receptor, family 2, subfamily W, member 1	206						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|skin(1)	23						GTGTGAGGACAATTATAATGC	0.413																																					p.I206I		Atlas-SNP	.											.	OR2W1	36	.	0			c.T618A						.						148	150	150					6																	29012335		1511	2709	4220	SO:0001819	synonymous_variant	26692	exon1			GAGGACAATTATA	AL035402	CCDS4656.1	6p22.1	2012-08-09			ENSG00000204704	ENSG00000204704		"GPCR / Class A : Olfactory receptors"	8281	protein-coding gene	gene with protein product							Standard	NM_030903		Approved	hs6M1-15	uc003nlw.2	Q9Y3N9	OTTHUMG00000031048	ENST00000377175.1:c.618T>A	chr6.hg19:g.29012335A>T		226.0	0.0		257.0	77.0	NM_030903	B0S7Y5|Q5JNZ1|Q6IEU0|Q96R17|Q9GZL0|Q9GZL1	Silent	SNP	ENST00000377175.1	hg19	CCDS4656.1																																																																																			.	.		0.413	OR2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076053.2			T	29012335	A	T	29012335	2	4	60	1	0	0	0	0	0	0	0	1	11041	126	5	4		4	OR2W1	6	29012335	Silent	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10		29012335	142102732	34	7390										
NFYA	4800	hgsc.bcm.edu	37	chr6	41065105	41065106	+	Frame_Shift_Ins	INS	-	-	A													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ttgtctctaggatccaaaccINSaagccgatgaagaagcaatg					rs79078414		TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr6:41065105_41065106insA	ENST00000341376.6	+	10	1201_1202	c.1000_1001insA	c.(1000-1002)caafs	p.Q334fs	OARD1_ENST00000480585.1_Intron|NFYA_ENST00000353205.5_Frame_Shift_Ins_p.Q305fs	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	334					cellular lipid metabolic process (GO:0044255)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	9	Ovarian(28;0.0418)|Colorectal(47;0.196)					GGATCCAAACCAAGCCGATGAA	0.45																																					p.Q334fs		Atlas-INDEL	.											.	NFYA	33	.	0			c.1000_1001insA						.																																			SO:0001589	frameshift_variant	4800	exon10			.		CCDS4849.1, CCDS4850.1	6p21.3	2008-11-11			ENSG00000001167	ENSG00000001167			7804	protein-coding gene	gene with protein product		189903				1774067, 9612081	Standard	NM_002505		Approved	HAP2, CBF-B, NF-YA	uc003opo.3	P23511	OTTHUMG00000014669	ENST00000341376.6:c.1002dupA	chr6.hg19:g.41065107_41065107dupA	ENSP00000345702:p.Gln334fs	144.0	0.0		264.0	16.0	NM_002505	Q8IXU0	Frame_Shift_Ins	INS	ENST00000341376.6	hg19	CCDS4849.1																																																																																			.	.		0.45	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040496.1			A	41065106	-	A	41065105	7	5	60	1	0	1	1	0	0	0	0	0	10398	595	21	0	1034	0	NFYA	6	41065105	Frame_Shift_Ins	INS	-	TCGA-CC-5264-01A-01D-A12Z-10	12052770	41065105	130049962	35	7391										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138550956	138550956	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	acctacacgccaacatttgaTctgaatgggagtgccgtgct	10	11	1	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr6:138550956T>C	ENST00000251691.4	+	5	553	c.387T>C	c.(385-387)gaT>gaC	p.D129D		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CAACATTTGATCTGAATGGGA	0.443																																					p.D129D		Atlas-SNP	.											.	KIAA1244	236	.	0			c.T387C						.						194	159	171					6																	138550956		2203	4300	6503	SO:0001819	synonymous_variant	57221	exon5			ATTTGATCTGAAT	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.387T>C	chr6.hg19:g.138550956T>C		302.0	0.0		406.0	181.0	NM_020340		Silent	SNP	ENST00000251691.4	hg19	CCDS5189.2																																																																																			.	.		0.443	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		C	138550956	T	C	138550956	2	2	60	1	0	0	0	0	0	0	0	1	8226	1432	50	2		2	KIAA1244	6	138550956	Silent	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	97485851	138550956	32564111	36	7392										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157502282	157502282	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gacctgttccgactctacgtCtgcgtcaaagagatcggggg	13	11	3	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr6:157502282C>G	ENST00000350026.5	+	11	3277	c.3276C>G	c.(3274-3276)gtC>gtG	p.V1092V	ARID1B_ENST00000275248.4_Silent_p.V1087V|ARID1B_ENST00000367148.1_Silent_p.V1145V|ARID1B_ENST00000346085.5_Silent_p.V1105V|ARID1B_ENST00000478761.2_3'UTR	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1092	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.		V -> I. {ECO:0000269|PubMed:22405089}.		chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GACTCTACGTCTGCGTCAAAG	0.537																																					p.V1105V		Atlas-SNP	.											.	ARID1B	320	.	0			c.C3315G						.						57	56	56					6																	157502282		2203	4296	6499	SO:0001819	synonymous_variant	57492	exon12			CTACGTCTGCGTC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3276C>G	chr6.hg19:g.157502282C>G		40.0	0.0		111.0	40.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	hg19	CCDS5251.2																																																																																			.	.		0.537	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		G	157502282	C	G	157502282	2	3	60	1	0	0	0	0	0	0	0	1	914	900	32	4		4	ARID1B	6	157502282	Silent	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	18951326	157502282	13612785	37	7393										
HEATR2	54919	hgsc.bcm.edu	37	chr7	769380	769381	+	Frame_Shift_Ins	INS	-	-	C													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gcactggaaggtccgtgtggINSccgccattgaagccacaggc							TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr7:769380_769381insC	ENST00000297440.6	+	2	696_697	c.676_677insC	c.(676-678)gccfs	p.A226fs	PRKAR1B_ENST00000537384.1_5'Flank|PRKAR1B_ENST00000403562.1_5'Flank|HEATR2_ENST00000313147.5_Frame_Shift_Ins_p.A226fs|HEATR2_ENST00000438961.1_3'UTR|PRKAR1B_ENST00000488474.1_5'Flank	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	226						cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		GGTCCGTGTGGCCGCCATTGAA	0.599																																					p.A226fs		Atlas-INDEL	.											.	HEATR2	62	.	0			c.676_677insC						.																																			SO:0001589	frameshift_variant	54919	exon2			.	AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.678dupC	chr7.hg19:g.769382_769382dupC	ENSP00000297440:p.Ala226fs	56.0	0.0		226.0	15.0	NM_017802	Q69YL1|Q96FI9|Q9NX75	Frame_Shift_Ins	INS	ENST00000297440.6	hg19	CCDS34580.1																																																																																			.	.		0.599	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802		C	769381	-	C	769380	7	5	60	1	0	1	1	0	0	0	0	0	7037	1203	42	0	682	0	HEATR2	7	769380	Frame_Shift_Ins	INS	-	TCGA-CC-5264-01A-01D-A12Z-10		769380	158369283	38	7394										
SHFM1	7979	hgsc.bcm.edu	37	chr7	96324155	96324155	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ctacattgtcatcatcccaaTtatcctcccagacatgtgca	4	14	2	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr7:96324155T>G	ENST00000248566.2	-	2	252	c.125A>C	c.(124-126)aAt>aCt	p.N42T	SHFM1_ENST00000417009.1_Missense_Mutation_p.N42T|SHFM1_ENST00000444799.1_Missense_Mutation_p.N42T|SHFM1_ENST00000413065.1_Missense_Mutation_p.N42T	NM_006304.1	NP_006295.1	P60896	DSS1_HUMAN	split hand/foot malformation (ectrodactyly) type 1	42	Asp/Glu-rich (highly acidic).				double-strand break repair via homologous recombination (GO:0000724)	proteasome complex (GO:0000502)		p.N42S(1)		breast(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5	all_cancers(62;4.24e-09)|all_epithelial(64;5.59e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0353)|Lung NSC(181;0.0987)					ATCATCCCAATTATCCTCCCA	0.343								Homologous recombination																													p.N42T		Atlas-SNP	.											SHFM1,NS,carcinoma,0,1	SHFM1	12	.	1	Substitution - Missense(1)	prostate(1)	c.A125C						.						181	177	178					7																	96324155		2203	4300	6503	SO:0001583	missense	7979	exon2			TCCCAATTATCCT	U41515	CCDS5646.1	7q21.3	2010-04-22			ENSG00000127922	ENSG00000127922			10845	protein-coding gene	gene with protein product	"deleted in split-hand/foot 1"	601285		SHFD1		1895319, 8733122	Standard	NM_006304		Approved	DSS1, Shfdg1, ECD, SEM1, SHSF1	uc003uoi.3	P60896	OTTHUMG00000150680	ENST00000248566.2:c.125A>C	chr7.hg19:g.96324155T>G	ENSP00000248566:p.Asn42Thr	143.0	0.0		147.0	17.0	NM_006304	Q13437|Q61067	Missense_Mutation	SNP	ENST00000248566.2	hg19	CCDS5646.1	.	.	.	.	.	.	.	.	.	.	T	17.36	3.370713	0.61624	.	.	ENSG00000127922	ENST00000417009;ENST00000444799;ENST00000413065;ENST00000248566	T;T;T;T	0.48836	0.8;0.8;0.8;0.8	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.68879	0.3049	.	.	.	0.80722	D	1	D;P	0.76494	0.999;0.807	D;P	0.81914	0.995;0.728	T	0.72574	-0.4252	9	0.56958	D	0.05	.	15.1597	0.72775	0.0:0.0:0.0:1.0	.	42;42	F2Z309;P60896	.;DSS1_HUMAN	T	42	ENSP00000416322:N42T;ENSP00000390049:N42T;ENSP00000409481:N42T;ENSP00000248566:N42T	ENSP00000248566:N42T	N	-	2	0	SHFM1	96162091	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.815000	0.86186	2.202000	0.70862	0.528000	0.53228	AAT	.	.		0.343	SHFM1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319595.1	NM_006304		G	96324155	T	G	96324155	3	3	60	1	0	0	0	0	1	0	0	0	14293	1493	52	5	95	5	SHFM1	7	96324155	Missense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	95554775	96324155	62814508	39	7395										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107836240	107836240	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	agaggagacccaaagaaggcAcagtctagtaaagcaggcct	12	9	1	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr7:107836240A>G	ENST00000425651.2	-	12	1427	c.1428T>C	c.(1426-1428)tgT>tgC	p.C476C	NRCAM_ENST00000379022.4_Silent_p.C476C|NRCAM_ENST00000413765.2_Silent_p.C457C|NRCAM_ENST00000379028.3_Silent_p.C476C|NRCAM_ENST00000379024.4_Silent_p.C457C|NRCAM_ENST00000351718.4_Silent_p.C470C	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	476	Ig-like 5.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CAAAGAAGGCACAGTCTAGTA	0.413																																					p.C476C		Atlas-SNP	.											.	NRCAM	267	.	0			c.T1428C						.						138	119	126					7																	107836240		2203	4300	6503	SO:0001819	synonymous_variant	4897	exon12			GAAGGCACAGTCT		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.1428T>C	chr7.hg19:g.107836240A>G		223.0	0.0		359.0	177.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	hg19	CCDS47686.1																																																																																			.	.		0.413	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		G	107836240	A	G	107836240	2	3	60	1	0	0	0	0	0	0	0	1	10653	157	6	2		2	NRCAM	7	107836240	Silent	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	11512085	107836240	51302423	40	7396										
PNPLA8	50640	hgsc.bcm.edu	37	chr7	108155899	108155899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	acttcttgcattactaaggaGgtaaatatatatatctacag	6	6	2	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr7:108155899G>A	ENST00000422087.1	-	4	443	c.37C>T	c.(37-39)Ctc>Ttc	p.L13F	PNPLA8_ENST00000257694.8_Missense_Mutation_p.L13F|PNPLA8_ENST00000426128.2_Missense_Mutation_p.L13F|PNPLA8_ENST00000453144.1_Intron|PNPLA8_ENST00000388728.5_Missense_Mutation_p.L13F|PNPLA8_ENST00000436062.1_Missense_Mutation_p.L13F|PNPLA8_ENST00000483879.1_Intron	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	13					arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						TTACTAAGGAGGTAAATATAT	0.338																																					p.L13F		Atlas-SNP	.											.	PNPLA8	82	.	0			c.C37T						.						60	56	58					7																	108155899		2202	4300	6502	SO:0001583	missense	50640	exon2			TAAGGAGGTAAAT	AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"Patatin-like phospholipase domain containing"	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.37C>T	chr7.hg19:g.108155899G>A	ENSP00000410804:p.Leu13Phe	87.0	0.0		82.0	43.0	NM_001256008	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Missense_Mutation	SNP	ENST00000422087.1	hg19	CCDS34733.1	.	.	.	.	.	.	.	.	.	.	G	9.319	1.057455	0.19907	.	.	ENSG00000135241	ENST00000426128;ENST00000257694;ENST00000388728;ENST00000422087;ENST00000436062;ENST00000427008;ENST00000415498	D;D;D;D;D	0.98493	-3.77;-4.96;-3.77;-4.96;-4.96	5.26	2.4	0.29515	.	0.649498	0.14456	N	0.318482	D	0.94676	0.8283	L	0.46157	1.445	0.25488	N	0.987675	B	0.11235	0.004	B	0.09377	0.004	D	0.85450	0.1160	10	0.12430	T	0.62	.	4.4129	0.11441	0.4079:0.0:0.4435:0.1486	.	13	Q9NP80	PLPL8_HUMAN	F	13	ENSP00000394988:L13F;ENSP00000257694:L13F;ENSP00000373380:L13F;ENSP00000410804:L13F;ENSP00000406779:L13F	ENSP00000257694:L13F	L	-	1	0	PNPLA8	107943135	0.993000	0.37304	1.000000	0.80357	0.977000	0.68977	0.170000	0.16663	0.565000	0.29255	0.460000	0.39030	CTC	.	.		0.338	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		A	108155899	G	A	108155899	3	1	60	1	0	0	0	0	1	0	0	0	12180	1000	35	3	2347	3	PNPLA8	7	108155899	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	319659	108155899	50982764	41	7397										
AASS	10157	hgsc.bcm.edu	37	chr7	121756964	121756964	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gaaacttcttttaattcatgGggctccacatattcacaagg	7	9	3	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr7:121756964G>C	ENST00000393376.1	-	6	830	c.735C>G	c.(733-735)ccC>ccG	p.P245P	AASS_ENST00000417368.2_Silent_p.P245P|AASS_ENST00000473553.1_Intron			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	245	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TTAATTCATGGGGCTCCACAT	0.333																																					p.P245P		Atlas-SNP	.											.	AASS	123	.	0			c.C735G						.						76	84	81					7																	121756964		2203	4300	6503	SO:0001819	synonymous_variant	10157	exon7			TTCATGGGGCTCC	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.735C>G	chr7.hg19:g.121756964G>C		94.0	0.0		118.0	19.0	NM_005763	O95462	Silent	SNP	ENST00000393376.1	hg19	CCDS5783.1																																																																																			.	.		0.333	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		C	121756964	G	C	121756964	2	2	60	1	0	0	0	0	0	0	0	1	24	1219	43	4		4	AASS	7	121756964	Silent	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	13601065	121756964	37381699	42	7398										
TACC1	6867	hgsc.bcm.edu	37	chr8	38678084	38678084	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	cttaacaagcagtgacttttGttctcccactggtaatcacg	7	11	2	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr8:38678084G>C	ENST00000317827.4	+	3	1701	c.1322G>C	c.(1321-1323)tGt>tCt	p.C441S	TACC1_ENST00000522752.1_Intron|TACC1_ENST00000520973.1_Missense_Mutation_p.C246S|TACC1_ENST00000519416.1_Missense_Mutation_p.C246S|TACC1_ENST00000348567.4_Intron|TACC1_ENST00000518415.1_Missense_Mutation_p.C396S|TACC1_ENST00000520340.1_Missense_Mutation_p.C405S|TACC1_ENST00000520615.1_Missense_Mutation_p.C246S|TACC1_ENST00000443286.2_Missense_Mutation_p.C457S|TACC1_ENST00000276520.8_Intron|TACC1_ENST00000520611.1_5'UTR|TACC1_ENST00000330691.6_Intron|TACC1_ENST00000379931.3_Missense_Mutation_p.C441S	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	441	SPAZ 2.				cell cycle (GO:0007049)|cell division (GO:0051301)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				breast(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(3)	17		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			AGTGACTTTTGTTCTCCCACT	0.468																																					p.C441S		Atlas-SNP	.											.	TACC1	98	.	0			c.G1322C						.						158	171	167					8																	38678084		2203	4300	6503	SO:0001583	missense	6867	exon3			ACTTTTGTTCTCC	AF049910	CCDS6109.1, CCDS47845.1, CCDS55224.1	8p11	2012-12-20			ENSG00000147526	ENSG00000147526			11522	protein-coding gene	gene with protein product		605301					Standard	NM_006283		Approved		uc010lwp.3	O75410	OTTHUMG00000164018	ENST00000317827.4:c.1322G>C	chr8.hg19:g.38678084G>C	ENSP00000321703:p.Cys441Ser	16.0	0.0		60.0	10.0	NM_006283	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Missense_Mutation	SNP	ENST00000317827.4	hg19	CCDS6109.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.022|9.022	0.985143|0.985143	0.18889|0.18889	.|.	.|.	ENSG00000147526|ENSG00000147526	ENST00000519416;ENST00000520615;ENST00000443388;ENST00000443286;ENST00000518415;ENST00000522904;ENST00000317827;ENST00000379931;ENST00000520973|ENST00000521866;ENST00000518809	T;T;T;T;T;T;T;T|.	0.09538|.	3.01;3.01;3.15;3.15;2.97;3.17;3.15;3.0|.	5.5|5.5	3.53|3.53	0.40419|0.40419	.|.	0.473755|.	0.24750|.	N|.	0.035919|.	T|T	0.54143|0.54143	0.1840|0.1840	L|L	0.53249|0.53249	1.67|1.67	0.33831|0.33831	D|D	0.630281|0.630281	P;B;B;B;P;B;B;B|.	0.43352|.	0.804;0.007;0.007;0.281;0.546;0.026;0.012;0.034|.	B;B;B;B;B;B;B;B|.	0.39840|.	0.311;0.005;0.005;0.081;0.221;0.014;0.01;0.031|.	T|T	0.61720|0.61720	-0.7005|-0.7005	10|5	0.09338|.	T|.	0.73|.	8.3026|8.3026	9.9902|9.9902	0.41865|0.41865	0.1706:0.0:0.8294:0.0|0.1706:0.0:0.8294:0.0	.|.	246;246;246;457;441;441;246;396|.	B7Z3G3;E7EVI4;B4DH49;B4E302;O75410-2;O75410;E7ET87;O75410-7|.	.;.;.;.;.;TACC1_HUMAN;.;.|.	S|L	246;246;246;457;396;413;441;441;246|216;79	ENSP00000428687:C246S;ENSP00000428450:C246S;ENSP00000393647:C457S;ENSP00000428706:C396S;ENSP00000430355:C413S;ENSP00000321703:C441S;ENSP00000369263:C441S;ENSP00000430959:C246S|.	ENSP00000321703:C441S|.	C|V	+|+	2|1	0|0	TACC1|TACC1	38797241|38797241	0.989000|0.989000	0.36119|0.36119	0.957000|0.957000	0.39632|0.39632	0.939000|0.939000	0.58152|0.58152	2.094000|2.094000	0.41719|0.41719	0.564000|0.564000	0.29238|0.29238	0.655000|0.655000	0.94253|0.94253	TGT|GTT	.	.		0.468	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376768.1	NM_006283		C	38678084	G	C	38678084	3	2	60	1	0	0	0	0	1	0	0	0	15516	1377	48	4	1332	4	TACC1	8	38678084	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10		38678084	107685938	43	7399										
ZMAT4	79698	hgsc.bcm.edu	37	chr8	40683185	40683185	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ataaatcctgatcaatatcgGaggacttcatcaggctacaa	7	9	3	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr8:40683185G>A	ENST00000297737.6	-	2	157	c.11C>T	c.(10-12)tCc>tTc	p.S4F	ZMAT4_ENST00000523823.1_5'UTR|ZMAT4_ENST00000315769.7_Missense_Mutation_p.S4F	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	4						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			ATCAATATCGGAGGACTTCAT	0.443																																					p.S4F		Atlas-SNP	.											.	ZMAT4	47	.	0			c.C11T						.						44	37	39					8																	40683185		2186	4262	6448	SO:0001583	missense	79698	exon2			ATATCGGAGGACT	AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061		"Zinc fingers, matrin-type"	25844	protein-coding gene	gene with protein product						12477932	Standard	NM_024645		Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.11C>T	chr8.hg19:g.40683185G>A	ENSP00000297737:p.Ser4Phe	35.0	0.0		87.0	37.0	NM_024645	Q8WUT8	Missense_Mutation	SNP	ENST00000297737.6	hg19	CCDS34885.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.428304	0.43122	.	.	ENSG00000165061	ENST00000315769;ENST00000297737;ENST00000519406	T;T;T	0.46819	0.86;0.87;0.87	5.37	5.37	0.77165	.	0.174304	0.50627	D	0.000101	T	0.48169	0.1485	N	0.08118	0	0.46376	D	0.999019	P;P	0.48694	0.914;0.855	D;B	0.63703	0.917;0.36	T	0.57142	-0.7862	10	0.72032	D	0.01	-16.5024	14.9923	0.71399	0.0:0.0:1.0:0.0	.	4;4	Q9H898-2;Q9H898	.;ZMAT4_HUMAN	F	4	ENSP00000319785:S4F;ENSP00000297737:S4F;ENSP00000428423:S4F	ENSP00000297737:S4F	S	-	2	0	ZMAT4	40802342	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.339000	0.72969	2.692000	0.91855	0.591000	0.81541	TCC	.	.		0.443	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376950.1	NM_024645		A	40683185	G	A	40683185	3	1	60	1	0	0	0	0	1	0	0	0	17709	1174	41	3	702	3	ZMAT4	8	40683185	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	2005101	40683185	105680837	44	7400										
OPRK1	4986	hgsc.bcm.edu	37	chr8	54147486	54147486	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ccacgctcatcatggtcaagGtgaagatgctggtgaacatg	12	9	3	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr8:54147486G>C	ENST00000265572.3	-	3	740	c.443C>G	c.(442-444)aCc>aGc	p.T148S	OPRK1_ENST00000520287.1_Missense_Mutation_p.T148S|OPRK1_ENST00000524278.1_Missense_Mutation_p.T59S|RP11-162D9.3_ENST00000524425.1_RNA	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	148					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)			NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CATGGTCAAGGTGAAGATGCT	0.483																																					p.T148S		Atlas-SNP	.											.	OPRK1	90	.	0			c.C443G						.						140	113	122					8																	54147486		2203	4300	6503	SO:0001583	missense	4986	exon3			GTCAAGGTGAAGA		CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"GPCR / Class A : Opioid receptors"	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.443C>G	chr8.hg19:g.54147486G>C	ENSP00000265572:p.Thr148Ser	99.0	0.0		225.0	64.0	NM_000912	E5RHC9|Q499G4	Missense_Mutation	SNP	ENST00000265572.3	hg19	CCDS6152.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.379661	0.82682	.	.	ENSG00000082556	ENST00000265572;ENST00000524278;ENST00000520287;ENST00000396798	T;T;T	0.19532	2.14;2.14;2.14	5.95	5.95	0.96441	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.49270	0.1547	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.35847	-0.9772	10	0.12430	T	0.62	.	20.3732	0.98896	0.0:0.0:1.0:0.0	.	148	P41145	OPRK_HUMAN	S	148;59;148;134	ENSP00000265572:T148S;ENSP00000430923:T59S;ENSP00000429706:T148S	ENSP00000265572:T148S	T	-	2	0	OPRK1	54310039	1.000000	0.71417	0.990000	0.47175	0.997000	0.91878	9.711000	0.98735	2.809000	0.96659	0.650000	0.86243	ACC	.	.		0.483	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1			C	54147486	G	C	54147486	3	2	60	1	0	0	0	0	1	0	0	0	10894	1261	44	4	707	4	OPRK1	8	54147486	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	13464301	54147486	92216536	45	7401										
PREX2	80243	hgsc.bcm.edu	37	chr8	68934295	68934295	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	acaagtttcgtatctatgatGaatattgtagtaaccatgag	8	5	1	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr8:68934295G>C	ENST00000288368.4	+	4	638	c.361G>C	c.(361-363)Gaa>Caa	p.E121Q	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	121	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TATCTATGATGAATATTGTAG	0.294																																					p.E121Q		Atlas-SNP	.											.	PREX2	614	.	0			c.G361C						.						108	106	107					8																	68934295		2202	4300	6502	SO:0001583	missense	80243	exon4			TATGATGAATATT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.361G>C	chr8.hg19:g.68934295G>C	ENSP00000288368:p.Glu121Gln	75.0	0.0		43.0	16.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	31	5.067046	0.93898	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.64085	-0.08	6.04	6.04	0.98038	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.75781	0.3896	L	0.45051	1.395	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.999	D;D;D	0.91635	0.999;0.981;0.979	T	0.75739	-0.3212	10	0.87932	D	0	.	20.5948	0.99439	0.0:0.0:1.0:0.0	.	121;121;121	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	Q	121	ENSP00000288368:E121Q	ENSP00000288368:E121Q	E	+	1	0	PREX2	69096849	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.452000	0.97615	2.873000	0.98535	0.563000	0.77884	GAA	.	.		0.294	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		C	68934295	G	C	68934295	3	2	60	1	0	0	0	0	1	0	0	0	12489	1291	45	4	375	4	PREX2	8	68934295	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	14786809	68934295	77429727	46	7402										
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88886016	88886016	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	agaggagggatcccagctatGaatctggacctttttcctct	10	10	2	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr8:88886016G>A	ENST00000319675.3	-	1	280	c.184C>T	c.(184-186)Cat>Tat	p.H62Y		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	62										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						TCCCAGCTATGAATCTGGACC	0.512																																					p.H62Y		Atlas-SNP	.											.	DCAF4L2	187	.	0			c.C184T						.						129	119	123					8																	88886016		2203	4300	6503	SO:0001583	missense	138009	exon1			AGCTATGAATCTG	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.184C>T	chr8.hg19:g.88886016G>A	ENSP00000316496:p.His62Tyr	199.0	0.0		544.0	271.0	NM_152418		Missense_Mutation	SNP	ENST00000319675.3	hg19	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	G	6.232	0.410986	0.11812	.	.	ENSG00000176566	ENST00000319675	T	0.78126	-1.15	1.92	0.997	0.19851	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.410508	0.30101	N	0.010409	T	0.49525	0.1562	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37663	-0.9696	10	0.42905	T	0.14	.	4.8635	0.13596	0.2101:0.0:0.7899:0.0	.	62	Q8NA75	DC4L2_HUMAN	Y	62	ENSP00000316496:H62Y	ENSP00000316496:H62Y	H	-	1	0	DCAF4L2	88955132	1.000000	0.71417	0.005000	0.12908	0.018000	0.09664	0.673000	0.25203	-0.061000	0.13110	-0.444000	0.05651	CAT	.	.		0.512	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		A	88886016	G	A	88886016	3	1	60	1	0	0	0	0	1	0	0	0	4274	1290	45	3	1007	3	DCAF4L2	8	88886016	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	19951721	88886016	57478006	47	7403										
OR13D1	286365	hgsc.bcm.edu	37	chr9	107457698	107457698	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	aataaagaggtcaaagaggcTgtaaagaaagtcctgagcag	12	5	1	4			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr9:107457698T>A	ENST00000318763.5	+	1	1039	c.996T>A	c.(994-996)gcT>gcA	p.A332A		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	332						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						TCAAAGAGGCTGTAAAGAAAG	0.403																																					p.A332A		Atlas-SNP	.											.	OR13D1	42	.	0			c.T996A						.						70	72	72					9																	107457698		2203	4300	6503	SO:0001819	synonymous_variant	286365	exon1			AGAGGCTGTAAAG		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"GPCR / Class A : Olfactory receptors"	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.996T>A	chr9.hg19:g.107457698T>A		122.0	0.0		131.0	36.0	NM_001004484	B9EIS1|Q6IFL1	Silent	SNP	ENST00000318763.5	hg19	CCDS35094.1																																																																																			.	.		0.403	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1			A	107457698	T	A	107457698	2	1	60	1	0	0	0	0	0	0	0	1	10949	1567	55	4		4	OR13D1	9	107457698	Silent	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10		107457698	33755733	48	7404										
ZNF462	58499	hgsc.bcm.edu	37	chr9	109687219	109687219	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tccaagttttcgcccatgtcTtaccctcagatgaagccgaa	7	13	2	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr9:109687219T>G	ENST00000277225.5	+	3	1315	c.1026T>G	c.(1024-1026)tcT>tcG	p.S342S	ZNF462_ENST00000441147.2_5'Flank|ZNF462_ENST00000457913.1_Silent_p.S342S			Q96JM2	ZN462_HUMAN	zinc finger protein 462	342					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						CGCCCATGTCTTACCCTCAGA	0.488																																					p.S342S		Atlas-SNP	.											.	ZNF462	322	.	0			c.T1026G						.						75	70	71					9																	109687219		2203	4300	6503	SO:0001819	synonymous_variant	58499	exon3			CATGTCTTACCCT	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.1026T>G	chr9.hg19:g.109687219T>G		54.0	0.0		197.0	35.0	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	hg19	CCDS35096.1																																																																																			.	.		0.488	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		G	109687219	T	G	109687219	2	3	60	1	0	0	0	0	0	0	0	1	17941	1596	56	5		5	ZNF462	9	109687219	Silent	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	2229521	109687219	31526212	49	7405										
PKN3	29941	hgsc.bcm.edu	37	chr9	131476850	131476850	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tctccctacagtaatttcctGcccaagaagacccccttggg	7	15	1	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr9:131476850G>A	ENST00000291906.4	+	12	1884	c.1491G>A	c.(1489-1491)ctG>ctA	p.L497L		NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	497	Pro-rich.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						GTAATTTCCTGCCCAAGAAGA	0.592																																					p.L497L		Atlas-SNP	.											.	PKN3	62	.	0			c.G1491A						.						69	70	70					9																	131476850		2203	4300	6503	SO:0001819	synonymous_variant	29941	exon12			TTTCCTGCCCAAG	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.1491G>A	chr9.hg19:g.131476850G>A		89.0	0.0		275.0	111.0	NM_013355	Q9UM03	Silent	SNP	ENST00000291906.4	hg19	CCDS6908.1																																																																																			.	.		0.592	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		A	131476850	G	A	131476850	2	1	60	1	0	0	0	0	0	0	0	1	11990	1306	46	3		3	PKN3	9	131476850	Silent	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	21789631	131476850	9736581	50	7406										
LAMC3	10319	hgsc.bcm.edu	37	chr9	133948175	133948175	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	acctggaggcagtgctggagTcctcggaagaggagattctg	16	8	1	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr9:133948175T>A	ENST00000361069.4	+	19	3503	c.3370T>A	c.(3370-3372)Tcc>Acc	p.S1124T	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1124	Domain II and I.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		AGTGCTGGAGTCCTCGGAAGA	0.637																																					p.S1124T		Atlas-SNP	.											.	LAMC3	167	.	0			c.T3370A						.						32	34	34					9																	133948175		2203	4300	6503	SO:0001583	missense	10319	exon19			CTGGAGTCCTCGG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.3370T>A	chr9.hg19:g.133948175T>A	ENSP00000354360:p.Ser1124Thr	94.0	0.0		283.0	127.0	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	hg19	CCDS6938.1	.	.	.	.	.	.	.	.	.	.	T	4.268	0.048908	0.08243	.	.	ENSG00000050555	ENST00000361069;ENST00000355048	T	0.27557	1.66	4.97	2.46	0.29980	.	0.420127	0.27122	N	0.020825	T	0.26846	0.0657	M	0.70595	2.14	0.23559	N	0.997413	B	0.33345	0.409	B	0.30646	0.118	T	0.23190	-1.0195	10	0.10111	T	0.7	.	9.8917	0.41294	0.0:0.0:0.3313:0.6687	.	1124	Q9Y6N6	LAMC3_HUMAN	T	1124	ENSP00000354360:S1124T	ENSP00000347156:S1124T	S	+	1	0	LAMC3	132937996	0.960000	0.32886	0.553000	0.28255	0.932000	0.56968	1.458000	0.35223	0.278000	0.22164	0.454000	0.30748	TCC	.	.		0.637	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059		A	133948175	T	A	133948175	3	1	60	1	0	0	0	0	1	0	0	0	8625	1667	58	4	3444	4	LAMC3	9	133948175	Missense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	2471325	133948175	7265256	51	7407										
QSOX2	169714	hgsc.bcm.edu	37	chr9	139108510	139108511	+	Frame_Shift_Ins	INS	-	-	C													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	cctgtccaggggaaggctggINSccagccactcctgcagcatc							TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr9:139108510_139108511insC	ENST00000358701.5	-	9	1181_1182	c.1144_1145insG	c.(1144-1146)gccfs	p.A382fs		NM_181701.3	NP_859052.3	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2	382					cell redox homeostasis (GO:0045454)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	thiol oxidase activity (GO:0016972)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)		GGGAAGGCTGGCCAGCCACTCC	0.624																																					p.A382fs		Atlas-INDEL	.											.	QSOX2	63	.	0			c.1145_1146insG						.																																			SO:0001589	frameshift_variant	169714	exon9			.	AJ318051	CCDS35178.1	9q34.3	2008-02-05	2007-04-23	2007-04-23	ENSG00000165661	ENSG00000165661			30249	protein-coding gene	gene with protein product		612860	"quiescin Q6-like 1"	QSCN6L1		12176051	Standard	NM_181701		Approved	SOXN, DKFZp762A2013	uc010nbi.2	Q6ZRP7	OTTHUMG00000020923	ENST00000358701.5:c.1145dupG	chr9.hg19:g.139108512_139108512dupC	ENSP00000351536:p.Ala382fs	33.0	0.0		119.0	13.0	NM_181701	A2CEE0|A6NLB0|Q5TB37|Q7Z7B6|Q86VV7|Q8N3G2	Frame_Shift_Ins	INS	ENST00000358701.5	hg19	CCDS35178.1																																																																																			.	.		0.624	QSOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055046.2	NM_181701		C	139108511	-	C	139108510	7	5	60	1	0	1	1	0	0	0	0	0	12899	1203	42	0	967	0	QSOX2	9	139108510	Frame_Shift_Ins	INS	-	TCGA-CC-5264-01A-01D-A12Z-10	5160335	139108510	2104921	52	7408										
MCM10	55388	hgsc.bcm.edu	37	chr10	13239672	13239672	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	aggccaggttcttacaaaaaCaaacccaaacagcattaaga	6	10	1	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr10:13239672C>T	ENST00000484800.2	+	15	2130	c.2027C>T	c.(2026-2028)aCa>aTa	p.T676I	MCM10_ENST00000378694.1_Missense_Mutation_p.T675I|MCM10_ENST00000378714.3_Missense_Mutation_p.T675I			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	676					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						CTTACAAAAACAAACCCAAAC	0.408																																					p.T676I		Atlas-SNP	.											.	MCM10	76	.	0			c.C2027T						.						95	88	90					10																	13239672		2203	4300	6503	SO:0001583	missense	55388	exon15			CAAAAACAAACCC	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.2027C>T	chr10.hg19:g.13239672C>T	ENSP00000418268:p.Thr676Ile	148.0	0.0		287.0	118.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	hg19	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	C	8.838	0.941562	0.18281	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.29655	1.56;1.56;1.56	5.23	2.32	0.28847	Replication factor Mcm10 (1);	0.398558	0.30859	N	0.008728	T	0.19167	0.0460	L	0.34521	1.04	0.26907	N	0.966989	B;B;B	0.12630	0.006;0.004;0.005	B;B;B	0.17098	0.017;0.004;0.007	T	0.14671	-1.0464	10	0.40728	T	0.16	0.2019	4.1158	0.10081	0.1306:0.5994:0.1265:0.1435	.	675;675;676	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	I	675;676;676;675	ENSP00000367986:T675I;ENSP00000418268:T676I;ENSP00000367966:T675I	ENSP00000354945:T676I	T	+	2	0	MCM10	13279678	0.807000	0.29009	0.994000	0.49952	0.761000	0.43186	0.511000	0.22739	0.283000	0.22279	0.655000	0.94253	ACA	.	.		0.408	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		T	13239672	C	T	13239672	3	4	60	1	0	0	0	0	1	0	0	0	9394	478	17	3	2081	3	MCM10	10	13239672	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10		13239672	122295075	53	7409										
CCDC6	8030	hgsc.bcm.edu	37	chr10	61572436	61572436	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tgcttcttcagccgttccacTtcattctttaaaaacctgat	4	12	4	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr10:61572436T>G	ENST00000263102.6	-	5	1035	c.804A>C	c.(802-804)gaA>gaC	p.E268D		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	268						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		GCCGTTCCACTTCATTCTTTA	0.438			T	RET	NSCLC																																p.E268D		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	CCDC6	44	.	0			c.A804C						.						102	103	103					10																	61572436		2203	4300	6503	SO:0001583	missense	8030	exon5			TTCCACTTCATTC	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"	601985	"DNA segment on chromosome 10 (unique) 170"	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.804A>C	chr10.hg19:g.61572436T>G	ENSP00000263102:p.Glu268Asp	153.0	0.0		96.0	82.0	NM_005436	Q15250|Q6GSG7	Missense_Mutation	SNP	ENST00000263102.6	hg19	CCDS7257.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.505999	0.64410	.	.	ENSG00000108091	ENST00000263102	D	0.94138	-3.36	5.82	1.51	0.23008	.	0.043090	0.85682	D	0.000000	D	0.95408	0.8509	M	0.74467	2.265	0.58432	D	0.999999	D	0.57257	0.979	D	0.74023	0.982	D	0.94158	0.7412	10	0.72032	D	0.01	-13.4153	9.9544	0.41657	0.0:0.2609:0.0:0.7391	.	268	Q16204	CCDC6_HUMAN	D	268	ENSP00000263102:E268D	ENSP00000263102:E268D	E	-	3	2	CCDC6	61242442	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	0.690000	0.25451	0.374000	0.24650	0.528000	0.53228	GAA	.	.		0.438	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436		G	61572436	T	G	61572436	3	3	60	1	0	0	0	0	1	0	0	0	2832	1606	56	5	640	5	CCDC6	10	61572436	Missense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	48332764	61572436	73962311	54	7410										
OR10A2	341276	hgsc.bcm.edu	37	chr11	6891293	6891293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ggctgaatgcttcctcctggCtaccatggcatatgaccgct	10	13	0	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr11:6891293C>T	ENST00000307322.4	+	1	370	c.308C>T	c.(307-309)gCt>gTt	p.A103V		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TTCCTCCTGGCTACCATGGCA	0.542																																					p.A103V		Atlas-SNP	.											.	OR10A2	55	.	0			c.C308T						.						119	116	117					11																	6891293		2201	4296	6497	SO:0001583	missense	341276	exon1			TCCTGGCTACCAT	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"GPCR / Class A : Olfactory receptors"	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.308C>T	chr11.hg19:g.6891293C>T	ENSP00000303862:p.Ala103Val	134.0	0.0		265.0	114.0	NM_001004460	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	hg19	CCDS31415.1	.	.	.	.	.	.	.	.	.	.	c	13.52	2.261735	0.39995	.	.	ENSG00000170790	ENST00000307322	T	0.02015	4.5	4.19	4.19	0.49359	GPCR, rhodopsin-like superfamily (1);	0.104975	0.42420	D	0.000708	T	0.04588	0.0125	M	0.64676	1.99	0.32945	D	0.519008	P	0.41748	0.761	B	0.41332	0.354	T	0.05683	-1.0870	10	0.87932	D	0	.	14.4844	0.67606	0.0:1.0:0.0:0.0	.	103	Q9H208	O10A2_HUMAN	V	103	ENSP00000303862:A103V	ENSP00000303862:A103V	A	+	2	0	OR10A2	6847869	0.047000	0.20315	0.988000	0.46212	0.360000	0.29518	2.781000	0.47750	2.330000	0.79161	0.650000	0.86243	GCT	.	.		0.542	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460		T	6891293	C	T	6891293	3	4	60	1	0	0	0	0	1	0	0	0	10899	797	28	3	310	3	OR10A2	11	6891293	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10		6891293	128115223	55	7411										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43833853	43833853	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tttccattgaaaagaaaattCccttcagcgtcagataatgc	6	9	2	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr12:43833853C>A	ENST00000389420.3	-	17	2309	c.2310G>T	c.(2308-2310)ggG>ggT	p.G770G	ADAMTS20_ENST00000395541.2_5'Flank|ADAMTS20_ENST00000553158.1_Silent_p.G770G	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	770	Spacer.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		AAAGAAAATTCCCTTCAGCGT	0.294																																					p.G770G		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.G2310T						.						33	27	29					12																	43833853		2189	4275	6464	SO:0001819	synonymous_variant	80070	exon17			AAAATTCCCTTCA	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2310G>T	chr12.hg19:g.43833853C>A		45.0	0.0		38.0	16.0	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.		0.294	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		A	43833853	C	A	43833853	2	1	60	1	0	0	0	0	0	0	0	1	266	842	30	3		3	ADAMTS20	12	43833853	Silent	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10		43833853	90018042	56	7412										
SCN8A	6334	hgsc.bcm.edu	37	chr12	52056826	52056826	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tacggggacatcccccaaggCctggttgcagttcccctgga	12	14	0	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr12:52056826C>T	ENST00000354534.6	+	2	403	c.225C>T	c.(223-225)ggC>ggT	p.G75G	SCN8A_ENST00000550891.1_Silent_p.G75G|SCN8A_ENST00000545061.1_Silent_p.G75G	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	75					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	TCCCCCAAGGCCTGGTTGCAG	0.552																																					p.G75G		Atlas-SNP	.											.	SCN8A	331	.	0			c.C225T						.						126	128	127					12																	52056826		2005	4158	6163	SO:0001819	synonymous_variant	6334	exon2			CCAAGGCCTGGTT	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10596	protein-coding gene	gene with protein product		600702	"sodium channel, voltage gated, type VIII, alpha polypeptide"	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.225C>T	chr12.hg19:g.52056826C>T		151.0	0.0		254.0	123.0	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Silent	SNP	ENST00000354534.6	hg19	CCDS44891.1																																																																																			.	.		0.552	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		T	52056826	C	T	52056826	2	4	60	1	0	0	0	0	0	0	0	1	13939	726	26	3		3	SCN8A	12	52056826	Silent	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	8222973	52056826	81795069	57	7413										
KRT6C	286887	hgsc.bcm.edu	37	chr12	52863028	52863028	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tccacccaggcctaagccacTgccgacaccgctggcaccgc	9	20	0	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr12:52863028T>A	ENST00000252250.6	-	9	1560	c.1513A>T	c.(1513-1515)Agt>Tgt	p.S505C		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	505	Tail.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		CCTAAGCCACTGCCGACACCG	0.602																																					p.S505C		Atlas-SNP	.											.	KRT6C	55	.	0			c.A1513T						.						45	43	44					12																	52863028		2203	4299	6502	SO:0001583	missense	286887	exon9			AGCCACTGCCGAC	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"-", "Intermediate filaments type II, keratins (basic)"	20406	protein-coding gene	gene with protein product		612315	"keratin 6E"	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.1513A>T	chr12.hg19:g.52863028T>A	ENSP00000252250:p.Ser505Cys	72.0	0.0		135.0	29.0	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	hg19	CCDS8829.1	.	.	.	.	.	.	.	.	.	.	T	8.854	0.945401	0.18356	.	.	ENSG00000170465	ENST00000252250;ENST00000411979	D	0.87809	-2.3	3.17	-0.525	0.11917	.	0.508870	0.18334	N	0.144390	T	0.80752	0.4683	L	0.61218	1.895	0.19945	N	0.999943	B	0.09022	0.002	B	0.09377	0.004	T	0.67393	-0.5682	10	0.39692	T	0.17	.	4.9899	0.14209	0.1383:0.3436:0.0:0.5181	.	505	P48668	K2C6C_HUMAN	C	505;490	ENSP00000252250:S505C	ENSP00000252250:S505C	S	-	1	0	KRT6C	51149295	0.000000	0.05858	0.009000	0.14445	0.126000	0.20510	-2.726000	0.00808	0.020000	0.15106	-0.660000	0.03859	AGT	.	.		0.602	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086		A	52863028	T	A	52863028	3	1	60	1	0	0	0	0	1	0	0	0	8491	1580	55	4	185	4	KRT6C	12	52863028	Missense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	806202	52863028	80988867	58	7414										
HOXC8	3224	hgsc.bcm.edu	37	chr12	54405067	54405067	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ggaaaaaggagaacaacaagGataaactgccgggagcccga	13	8	0	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr12:54405067G>T	ENST00000040584.4	+	2	868	c.631G>T	c.(631-633)Gat>Tat	p.D211Y	RP11-834C11.12_ENST00000513209.1_Intron	NM_022658.3	NP_073149.1	P31273	HXC8_HUMAN	homeobox C8	211					anterior/posterior pattern specification (GO:0009952)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	8						GAACAACAAGGATAAACTGCC	0.488																																					p.D211Y	GBM(197;701 2226 7002 18822 41696)	Atlas-SNP	.											.	HOXC8	15	.	0			c.G631T						.						79	86	84					12																	54405067		2203	4300	6503	SO:0001583	missense	3224	exon2			AACAAGGATAAAC	X99680	CCDS8870.1	12q13.13	2011-06-20	2005-12-22			ENSG00000037965		"Homeoboxes / ANTP class : HOXL subclass"	5129	protein-coding gene	gene with protein product		142970	"homeo box C8"	HOX3, HOX3A		1973146, 1358459	Standard	NM_022658		Approved		uc001ser.3	P31273		ENST00000040584.4:c.631G>T	chr12.hg19:g.54405067G>T	ENSP00000040584:p.Asp211Tyr	43.0	0.0		146.0	33.0	NM_022658	A8K4J4|O15221|O15362	Missense_Mutation	SNP	ENST00000040584.4	hg19	CCDS8870.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.957836	0.73902	.	.	ENSG00000037965	ENST00000040584	D	0.91237	-2.81	5.16	5.16	0.70880	Homeobox (1);	0.000000	0.85682	D	0.000000	D	0.91324	0.7264	N	0.19112	0.55	0.80722	D	1	D	0.67145	0.996	D	0.67725	0.953	D	0.92922	0.6356	10	0.87932	D	0	.	17.7934	0.88562	0.0:0.0:1.0:0.0	.	211	P31273	HXC8_HUMAN	Y	211	ENSP00000040584:D211Y	ENSP00000040584:D211Y	D	+	1	0	HOXC8	52691334	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.567000	0.86603	0.650000	0.86243	GAT	.	.		0.488	HOXC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358957.2			T	54405067	G	T	54405067	3	4	60	1	0	0	0	0	1	0	0	0	7325	1174	41	3	637	3	HOXC8	12	54405067	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	1542039	54405067	79446828	59	7415										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124829344	124829344	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ccggctcttcaggctctcctCgtagcaggcacgttccagtg	11	15	3	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr12:124829344C>T	ENST00000405201.1	-	32	4513	c.4513G>A	c.(4513-4515)Gag>Aag	p.E1505K	NCOR2_ENST00000404621.1_Missense_Mutation_p.E1495K|NCOR2_ENST00000429285.2_Missense_Mutation_p.E1495K|NCOR2_ENST00000356219.3_Missense_Mutation_p.E1512K|NCOR2_ENST00000404121.2_Missense_Mutation_p.E1066K|NCOR2_ENST00000397355.1_Missense_Mutation_p.E1496K			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1513					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		AGGCTCTCCTCGTAGCAGGCA	0.716																																					p.E1505K		Atlas-SNP	.											NCOR2_ENST00000405201,NS,carcinoma,0,2	NCOR2	475	.	0			c.G4513A						.						12	16	15					12																	124829344		1871	3961	5832	SO:0001583	missense	9612	exon34			TCTCCTCGTAGCA	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.4513G>A	chr12.hg19:g.124829344C>T	ENSP00000384018:p.Glu1505Lys	17.0	0.0		72.0	18.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	C	15.87	2.960726	0.53400	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285	T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53	4.36	4.36	0.52297	.	0.121187	0.53938	D	0.000049	T	0.69984	0.3172	M	0.75264	2.295	0.58432	D	0.999995	D;D;D	0.76494	0.998;0.998;0.999	P;P;P	0.61201	0.824;0.771;0.885	T	0.76258	-0.3025	10	0.87932	D	0	-14.6558	16.8679	0.86033	0.0:1.0:0.0:0.0	.	1495;1496;1505	C9J0Q5;C9J239;C9JFD3	.;.;.	K	1505;1495;1512;1496;1504;1066;1495	ENSP00000384018:E1505K;ENSP00000384202:E1495K;ENSP00000348551:E1512K;ENSP00000380513:E1496K;ENSP00000385618:E1066K;ENSP00000400281:E1495K	ENSP00000348551:E1512K	E	-	1	0	NCOR2	123395297	1.000000	0.71417	0.634000	0.29324	0.084000	0.17831	6.657000	0.74402	1.982000	0.57802	0.484000	0.47621	GAG	.	.		0.716	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		T	124829344	C	T	124829344	3	4	60	1	0	0	0	0	1	0	0	0	10245	893	31	1	3095	1	NCOR2	12	124829344	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	70424277	124829344	9022551	60	7416										
MAP4K5	11183	hgsc.bcm.edu	37	chr14	50915494	50915494	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ttaaaaatgaattcttaccaTttcatctcgtgcttctgttt	4	8	4	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr14:50915494T>C	ENST00000013125.4	-	15	1390	c.1072A>G	c.(1072-1074)Atg>Gtg	p.M358V	RP11-406H23.2_ENST00000555257.1_lincRNA	NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	358					activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					ATTCTTACCATTTCATCTCGT	0.284																																					p.M358V		Atlas-SNP	.											.	MAP4K5	48	.	0			c.A1072G						.						82	76	78					14																	50915494		1801	4063	5864	SO:0001583	missense	11183	exon15			TTACCATTTCATC	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6867	protein-coding gene	gene with protein product	"germinal center kinase-related"	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.1072A>G	chr14.hg19:g.50915494T>C	ENSP00000013125:p.Met358Val	200.0	0.0		39.0	29.0	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	hg19		.	.	.	.	.	.	.	.	.	.	T	10.38	1.334513	0.24253	.	.	ENSG00000012983	ENST00000013125	T	0.12879	2.64	5.79	4.64	0.57946	Protein kinase-like domain (1);	0.091042	0.64402	N	0.000001	T	0.13586	0.0329	L	0.51422	1.61	0.45528	D	0.998486	B;B;B	0.22480	0.0;0.036;0.07	B;B;B	0.22753	0.0;0.041;0.016	T	0.05649	-1.0872	10	0.24483	T	0.36	.	10.9645	0.47403	0.0:0.0742:0.0:0.9258	.	32;358;358	B3KWC4;B2R928;Q9Y4K4	.;.;M4K5_HUMAN	V	358	ENSP00000013125:M358V	ENSP00000013125:M358V	M	-	1	0	MAP4K5	49985244	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.266000	0.51569	0.996000	0.38943	0.533000	0.62120	ATG	.	.		0.284	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575		C	50915494	T	C	50915494	3	2	60	1	0	0	0	0	1	0	0	0	9272	1493	52	2	1540	2	MAP4K5	14	50915494	Missense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10		50915494	56434046	61	7417										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68238928	68238928	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ggaatgtatactggagatacCtgggaggcagagccagaggt	16	6	0	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr14:68238928C>T	ENST00000347230.4	-	28	5459		c.e28-1		ZFYVE26_ENST00000555452.1_Splice_Site	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26						cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CTGGAGATACCTGGGAGGCAG	0.473																																					.		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.5321-1G>A						.						24	25	25					14																	68238928		2203	4299	6502	SO:0001630	splice_region_variant	23503	exon29			AGATACCTGGGAG	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.5321-1G>A	chr14.hg19:g.68238928C>T		148.0	0.0		90.0	71.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Splice_Site	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.042641	0.75732	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	.	.	.	5.98	5.98	0.97165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1626	0.86807	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZFYVE26	67308681	1.000000	0.71417	0.996000	0.52242	0.842000	0.47809	3.813000	0.55636	2.838000	0.97847	0.655000	0.94253	.	.	.		0.473	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	Intron	T	68238928	C	T	68238928	5	4	60	1	0	0	0	0	0	0	1	0	17683	695	24	3	2359	3	ZFYVE26	14	68238928	Splice_Site	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	17323434	68238928	39110612	62	7418										
VWA3A	146177	hgsc.bcm.edu	37	chr16	22126725	22126725	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	cctgatggaggcagcaacctGctacaagctctgaagaagat	11	10	1	4	rs368919567	byFrequency	TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr16:22126725G>A	ENST00000389398.5	+	9	843	c.747G>A	c.(745-747)ctG>ctA	p.L249L	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	249						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		GCAGCAACCTGCTACAAGCTC	0.493													G|||	5	0.000998403	0	0	5008	,	,		17217	0		0	False		,,,				2504	0.0051				p.L249L		Atlas-SNP	.											.	VWA3A	115	.	0			c.G747A						.						38	40	40					16																	22126725		1936	4132	6068	SO:0001819	synonymous_variant	146177	exon9			CAACCTGCTACAA	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.747G>A	chr16.hg19:g.22126725G>A		98.0	0.0		173.0	79.0	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Silent	SNP	ENST00000389398.5	hg19	CCDS45441.1																																																																																			.	.		0.493	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			A	22126725	G	A	22126725	2	1	60	1	0	0	0	0	0	0	0	1	17255	1306	46	3		3	VWA3A	16	22126725	Silent	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10		22126725	68228028	63	7419										
ZNF668	79759	hgsc.bcm.edu	37	chr16	31072640	31072640	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gggccggagctccgggtgtgAgcgctcgtgccgacgcagca	18	13	0	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr16:31072640A>T	ENST00000538906.1	-	3	2393	c.1609T>A	c.(1609-1611)Tca>Aca	p.S537T	ZNF668_ENST00000394983.2_Missense_Mutation_p.S537T|ZNF668_ENST00000426488.2_Missense_Mutation_p.S560T|ZNF668_ENST00000300849.4_Missense_Mutation_p.S537T|ZNF668_ENST00000535577.1_Missense_Mutation_p.S537T|ZNF668_ENST00000539836.3_Missense_Mutation_p.S560T|ZNF668_ENST00000417110.2_5'Flank	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	537					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						TCCGGGTGTGAGCGCTCGTGC	0.667																																					p.S560T	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.T1678A						.						39	39	39					16																	31072640		2197	4300	6497	SO:0001583	missense	79759	exon4			GGTGTGAGCGCTC		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"Zinc fingers, C2H2-type"	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.1609T>A	chr16.hg19:g.31072640A>T	ENSP00000440149:p.Ser537Thr	51.0	0.0		147.0	28.0	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Missense_Mutation	SNP	ENST00000538906.1	hg19	CCDS10701.1	.	.	.	.	.	.	.	.	.	.	A	12.98	2.100316	0.37048	.	.	ENSG00000167394	ENST00000539836;ENST00000535577;ENST00000538906;ENST00000394983;ENST00000300849	T;T;T;T;T	0.16073	2.37;2.37;2.37;2.37;2.37	5.04	3.92	0.45320	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.340229	0.27275	N	0.020117	T	0.08492	0.0211	N	0.10760	0.04	0.28473	N	0.915336	B	0.17268	0.021	B	0.18561	0.022	T	0.19745	-1.0296	10	0.33940	T	0.23	-14.3349	8.5754	0.33595	0.6922:0.0:0.0:0.3078	.	537	Q96K58	ZN668_HUMAN	T	560;537;537;537;537	ENSP00000442573:S560T;ENSP00000441349:S537T;ENSP00000440149:S537T;ENSP00000378434:S537T;ENSP00000300849:S537T	ENSP00000300849:S537T	S	-	1	0	ZNF668	30980141	0.056000	0.20664	1.000000	0.80357	0.970000	0.65996	0.209000	0.17435	0.905000	0.36596	0.459000	0.35465	TCA	.	.		0.667	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706		T	31072640	A	T	31072640	3	4	60	1	0	0	0	0	1	0	0	0	18090	304	11	4	254	4	ZNF668	16	31072640	Missense_Mutation	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	8945915	31072640	59282113	64	7420										
TSNAXIP1	80152	hgsc.bcm.edu	37	chr16	67859123	67859123	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tgtaagatcctcatcgcagaCctgaatgagctgcggtacca	10	11	1	4			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr16:67859123C>A	ENST00000562787.1	-	0	2345				TSNAXIP1_ENST00000388833.3_Missense_Mutation_p.D200E|TSNAXIP1_ENST00000562321.1_3'UTR|TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.D185E|TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.D254E	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T						chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		TCATCGCAGACCTGAATGAGC	0.542																																					p.D200E		Atlas-SNP	.											.	TSNAXIP1	66	.	0			c.C600A						.						100	104	103					16																	67859123		2077	4215	6292	SO:0001628	intergenic_variant	55815	exon7			CGCAGACCTGAAT	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3			chr16.hg19:g.67859123C>A		68.0	0.0		165.0	69.0	NM_018430	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	hg19	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	C	15.29	2.789254	0.49997	.	.	ENSG00000102904	ENST00000415766;ENST00000388833	T;T	0.00940	5.52;5.52	6.07	2.75	0.32379	.	0.271819	0.32736	N	0.005713	T	0.02119	0.0066	L	0.55834	1.745	0.30239	N	0.795175	D;B;B	0.65815	0.995;0.197;0.197	P;B;B	0.58873	0.847;0.062;0.062	T	0.31641	-0.9936	10	0.59425	D	0.04	-20.5441	3.1841	0.06594	0.367:0.4221:0.0:0.2109	.	185;254;200	E7ENJ7;B4DXD0;Q2TAA8	.;.;TXIP1_HUMAN	E	185;200	ENSP00000411472:D185E;ENSP00000373485:D200E	ENSP00000373485:D200E	D	+	3	2	TSNAXIP1	66416624	1.000000	0.71417	1.000000	0.80357	0.362000	0.29581	0.649000	0.24843	0.888000	0.36160	0.655000	0.94253	GAC	.	.		0.542	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		A	67859123	C	A	67859123	1	1	60	0	1	0	0	0	0	0	0	0	16647	506	18	3		3	TSNAXIP1	16	67859123	IGR	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	36786483	67859123	22495630	65	7421										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72831362	72831363	+	Missense_Mutation	DNP	TG	TG	GC													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gggccagcgtttgtgcttgtTgttgttgttgttgttgttgt					rs568545014	byFrequency	TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr16:72831362_72831363TG>GC	ENST00000268489.5	-	9	5890_5891	c.5218_5219CA>GC	c.(5218-5220)CAa>GCa	p.Q1740A	ZFHX3_ENST00000397992.5_Missense_Mutation_p.Q826A	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1740	Poly-Gln.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TTGTGCttgttgttgttgttgt	0.53																																					p.Q1740P|p.Q1740E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.A5219C|c.C5218G						.																																			SO:0001583	missense	463	exon9			GCTTGTTGTTGTT|CTTGTTGTTGTTG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.5218_5219delinsGC	chr16.hg19:g.72831362_72831363delinsGC	ENSP00000268489:p.Gln1740Ala	106.0|105.0	0.0		407.0|404.0	19.0|21.0	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.53	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		GC	72831363	TG	GC	72831362	3	3	60	1	0	0	0	0	1	0	0	0	17649	1812	63	5	5900	5	ZFHX3	16	72831362	Missense_Mutation	DNP	TG	TCGA-CC-5264-01A-01D-A12Z-10	4972239	72831362	17523391	66	7422										
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85687939	85687940	+	Frame_Shift_Del	DEL	CG	CG	-													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	acgcctcattgtggagccccCgctccctcaggagaaggcag							TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr16:85687939_85687940delCG	ENST00000253458.7	+	4	658_659	c.482_483delCG	c.(481-483)ccgfs	p.P161fs	GSE1_ENST00000405402.2_Frame_Shift_Del_p.P57fs|GSE1_ENST00000393243.1_Frame_Shift_Del_p.P88fs	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	161																	GTGGAGCCCCCGCTCCCTCAGG	0.673																																					p.161_161del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.481_482del						.																																			SO:0001589	frameshift_variant	23199	exon4			.	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.482_483delCG	chr16.hg19:g.85687939_85687940delCG	ENSP00000253458:p.Pro161fs	93.0	0.0		147.0	121.0	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Frame_Shift_Del	DEL	ENST00000253458.7	hg19	CCDS10952.1																																																																																			.	.		0.673	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		-	85687940	CG	-	85687939	7	5	60	1	0	1	0	1	0	0	0	0	8168	652	23	0	496	0	KIAA0182	16	85687939	Frame_Shift_Del	DEL	CG	TCGA-CC-5264-01A-01D-A12Z-10	12856577	85687939	4666814	67	7423										
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6360967	6360970	+	Frame_Shift_Del	DEL	AGGC	AGGC	-													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gcccacaatgaagatctgggAggcaggcaggcccagcacgc							TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	AGGC	AGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr17:6360967_6360970delAGGC	ENST00000262483.8	-	19	2650_2653	c.2563_2566delGCCT	c.(2563-2568)gcctccfs	p.AS855fs	PITPNM3_ENST00000576664.1_5'UTR|PITPNM3_ENST00000421306.3_Frame_Shift_Del_p.AS819fs	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	855					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		AAGATCTGGGAGGCAGGCAGGCCC	0.613																																					p.855_856del		Atlas-Indel,Pindel	.											.	PITPNM3	91	.	0			c.2564_2567del						.																																			SO:0001589	frameshift_variant	83394	exon19			.	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.2563_2566delGCCT	chr17.hg19:g.6360975_6360978delAGGC	ENSP00000262483:p.Ala855fs	52.0	0.0		54.0	41.0	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Frame_Shift_Del	DEL	ENST00000262483.8	hg19	CCDS11076.1																																																																																			.	.		0.613	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		-	6360970	AGGC	-	6360967	7	5	60	1	0	1	0	1	0	0	0	0	11961	304	11	0	366	0	PITPNM3	17	6360967	Frame_Shift_Del	DEL	AGGC	TCGA-CC-5264-01A-01D-A12Z-10		6360967	74834243	68	7424										
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319829	21319829	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ccgtgacgaggaggatgaggCggacggagaccaggacggcc	19	10	0	3	rs541946650	byFrequency	TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr17:21319829C>A	ENST00000583088.1	+	3	2070	c.1175C>A	c.(1174-1176)gCg>gAg	p.A392E	KCNJ12_ENST00000331718.5_Missense_Mutation_p.A392E	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	392					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GAGGATGAGGCGGACGGAGAC	0.657										Prostate(3;0.18)																											p.A392E		Atlas-SNP	.											.	.	.	.	0			c.C1175A						.						62	59	60					17																	21319829		2203	4300	6503	SO:0001583	missense	100134444	exon3			ATGAGGCGGACGG	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1175C>A	chr17.hg19:g.21319829C>A	ENSP00000463778:p.Ala392Glu	25.0	0.0		100.0	21.0	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	hg19	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.504482	0.00992	.	.	ENSG00000184185	ENST00000331718	D	0.86694	-2.16	5.83	-1.89	0.07689	.	0.777035	0.12187	N	0.491524	T	0.51007	0.1649	N	0.00583	-1.355	0.24571	N	0.993925	B	0.02656	0.0	B	0.04013	0.001	T	0.55309	-0.8161	10	0.02654	T	1	.	1.7021	0.02874	0.3082:0.1572:0.0873:0.4473	.	392	Q14500	IRK12_HUMAN	E	392	ENSP00000328150:A392E	ENSP00000328150:A392E	A	+	2	0	KCNJ12	21260422	0.126000	0.22350	0.009000	0.14445	0.375000	0.29983	0.559000	0.23485	-0.590000	0.05866	-0.136000	0.14681	GCG	.	.		0.657	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21319829	C	A	21319829	3	1	60	1	0	0	0	0	1	0	0	0	8055	768	27	1	1177	1	KCNJ12	17	21319829	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	14958862	21319829	59875381	69	7425										
GJC1	10052	hgsc.bcm.edu	37	chr17	42883077	42883077	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gatggattctcctcctacagCtgtaaggacgatccggaaga	11	10	1	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr17:42883077C>G	ENST00000426548.1	-	3	378	c.109G>C	c.(109-111)Gct>Cct	p.A37P	GJC1_ENST00000330514.4_Missense_Mutation_p.A37P|GJC1_ENST00000590758.1_Missense_Mutation_p.A37P|GJC1_ENST00000592524.1_Missense_Mutation_p.A37P	NM_001080383.1|NM_005497.3	NP_001073852.1|NP_005488.2	P36383	CXG1_HUMAN	gap junction protein, gamma 1, 45kDa	37					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle tissue development (GO:0048738)|cell development (GO:0048468)|cell-cell junction assembly (GO:0007043)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vasculogenesis (GO:0001570)|visual perception (GO:0007601)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion channel activity (GO:0005216)			NS(1)|kidney(1)|large_intestine(5)|liver(1)|lung(10)|prostate(1)	19		Prostate(33;0.0959)				CCTCCTACAGCTGTAAGGACG	0.483																																					p.A37P		Atlas-SNP	.											.	GJC1	45	.	0			c.G109C						.						108	89	95					17																	42883077		2203	4300	6503	SO:0001583	missense	10052	exon3			CTACAGCTGTAAG	U03493	CCDS11487.1	17q21.31	2008-02-04	2007-11-06	2007-11-06		ENSG00000182963		"Ion channels / Gap junction proteins (connexins)"	4280	protein-coding gene	gene with protein product	"connexin 45"	608655	"gap junction protein, alpha 7, 45kDa"	GJA7		7966354	Standard	NM_005497		Approved	CX45	uc002ihl.3	P36383		ENST00000426548.1:c.109G>C	chr17.hg19:g.42883077C>G	ENSP00000411528:p.Ala37Pro	139.0	0.0		230.0	96.0	NM_005497	B3KW68|Q4VAY0	Missense_Mutation	SNP	ENST00000426548.1	hg19	CCDS11487.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.230285	0.79688	.	.	ENSG00000182963	ENST00000426548;ENST00000330514	D;D	0.99194	-5.54;-5.54	5.26	5.26	0.73747	Connexin, N-terminal (1);	0.056597	0.64402	D	0.000001	D	0.99299	0.9755	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99357	1.0916	10	0.66056	D	0.02	.	17.8787	0.88833	0.0:1.0:0.0:0.0	.	37	P36383	CXG1_HUMAN	P	37	ENSP00000411528:A37P;ENSP00000333193:A37P	ENSP00000333193:A37P	A	-	1	0	GJC1	40238603	1.000000	0.71417	0.996000	0.52242	0.971000	0.66376	7.818000	0.86416	2.458000	0.83093	0.455000	0.32223	GCT	.	.		0.483	GJC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448661.1	NM_005497		G	42883077	C	G	42883077	3	3	60	1	0	0	0	0	1	0	0	0	6422	797	28	4	1085	4	GJC1	17	42883077	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	21563248	42883077	38312133	70	7426										
DNAH17	9489	hgsc.bcm.edu	37	chr17	76421607	76421607	+	IGR	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gttgaagaagccggccagccAcacggtggtgggcagggcaa	17	10	0	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr17:76421607A>T	ENST00000262764.6	+	0	2201				DNAH17_ENST00000585328.1_Missense_Mutation_p.W4316R|DNAH17_ENST00000389840.5_Missense_Mutation_p.W4344R|DNAH17_ENST00000586052.1_5'UTR|AC061992.1_ENST00000600087.1_5'Flank	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			CCGGCCAGCCACACGGTGGTG	0.592																																					p.W4321R	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	DNAH17	347	.	0			c.T12961A						.						44	44	44					17																	76421607		2203	4300	6503	SO:0001628	intergenic_variant	8632	exon80			CCAGCCACACGGT		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			chr17.hg19:g.76421607A>T		31.0	0.0		100.0	12.0	NM_173628	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Missense_Mutation	SNP	ENST00000262764.6	hg19	CCDS42391.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.681642	0.88542	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.12569	2.67	4.85	4.85	0.62838	.	0.000000	0.51477	D	0.000095	T	0.59932	0.2230	H	0.99870	4.87	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.80018	-0.1558	10	0.87932	D	0	.	14.6095	0.68507	1.0:0.0:0.0:0.0	.	4316	E7EUM8	.	R	4316;4344	ENSP00000374490:W4344R	ENSP00000300671:W4316R	W	-	1	0	DNAH17	73933202	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.208000	0.95075	2.027000	0.59764	0.482000	0.46254	TGG	.	.		0.592	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419		T	76421607	A	T	76421607	1	4	60	0	1	0	0	0	0	0	0	0	4603	159	6	4		4	DNAH17	17	76421607	IGR	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	33538530	76421607	4773603	71	7427										
ENGASE	64772	hgsc.bcm.edu	37	chr17	77075702	77075702	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	gaccaacactgcccacaggcAtggggtctgcgtgctgggta	14	12	1	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr17:77075702A>G	ENST00000579016.1	+	4	548	c.548A>G	c.(547-549)cAt>cGt	p.H183R	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	183						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						GCCCACAGGCATGGGGTCTGC	0.597																																					p.H183R		Atlas-SNP	.											.	ENGASE	55	.	0			c.A548G						.						79	96	90					17																	77075702		2125	4219	6344	SO:0001583	missense	64772	exon4			ACAGGCATGGGGT	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.548A>G	chr17.hg19:g.77075702A>G	ENSP00000462333:p.His183Arg	65.0	0.0		197.0	82.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	hg19	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	A	13.24	2.178780	0.38511	.	.	ENSG00000167280	ENST00000311595;ENST00000545583	.	.	.	5.22	5.22	0.72569	Glycoside hydrolase, family 85 (1);	0.162195	0.53938	D	0.000042	T	0.69378	0.3104	M	0.75085	2.285	0.80722	D	1	B;B	0.19817	0.031;0.039	B;B	0.29176	0.037;0.099	T	0.70189	-0.4940	9	0.72032	D	0.01	-7.8611	13.9551	0.64142	1.0:0.0:0.0:0.0	.	183;183	Q8NFI3;Q8NFI3-3	ENASE_HUMAN;.	R	183	.	ENSP00000308158:H183R	H	+	2	0	ENGASE	74587297	1.000000	0.71417	0.907000	0.35723	0.551000	0.35334	8.455000	0.90355	2.091000	0.63221	0.533000	0.62120	CAT	.	.		0.597	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		G	77075702	A	G	77075702	3	3	60	1	0	0	0	0	1	0	0	0	5120	217	8	2	562	2	ENGASE	17	77075702	Missense_Mutation	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	654095	77075702	4119508	72	7428										
LRRC45	201255	hgsc.bcm.edu	37	chr17	79982609	79982609	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	aggggccgaggctctgggaaAactcctccaacagaacaagt	12	11	1	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr17:79982609A>G	ENST00000306688.3	+	3	665	c.323A>G	c.(322-324)aAa>aGa	p.K108R	STRA13_ENST00000306704.6_5'Flank|STRA13_ENST00000392359.3_5'Flank|STRA13_ENST00000584347.1_5'Flank|STRA13_ENST00000583767.1_5'Flank|LRRC45_ENST00000583383.1_3'UTR|STRA13_ENST00000580435.1_5'Flank	NM_144999.2	NP_659436.1	Q96CN5	LRC45_HUMAN	leucine rich repeat containing 45	108						centrosome (GO:0005813)				lung(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	5	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GCTCTGGGAAAACTCCTCCAA	0.612																																					p.K108R		Atlas-SNP	.											.	LRRC45	22	.	0			c.A323G						.						56	61	60					17																	79982609		2202	4299	6501	SO:0001583	missense	201255	exon3			TGGGAAAACTCCT	BC014109	CCDS11797.1	17q25.3	2005-08-09				ENSG00000169683			28302	protein-coding gene	gene with protein product						12477932	Standard	NM_144999		Approved	MGC20806	uc002kde.3	Q96CN5		ENST00000306688.3:c.323A>G	chr17.hg19:g.79982609A>G	ENSP00000306760:p.Lys108Arg	51.0	0.0		108.0	46.0	NM_144999		Missense_Mutation	SNP	ENST00000306688.3	hg19	CCDS11797.1	.	.	.	.	.	.	.	.	.	.	A	12.43	1.936767	0.34189	.	.	ENSG00000169683	ENST00000306688	T	0.53640	0.61	3.36	2.26	0.28386	.	0.282465	0.32343	N	0.006239	T	0.35393	0.0930	L	0.41961	1.31	0.36463	D	0.86679	P	0.35745	0.518	B	0.35182	0.197	T	0.28650	-1.0037	9	.	.	.	-5.6332	8.5755	0.33597	0.9045:0.0:0.0955:0.0	.	108	Q96CN5	LRC45_HUMAN	R	108	ENSP00000306760:K108R	.	K	+	2	0	LRRC45	77575898	1.000000	0.71417	0.688000	0.30117	0.835000	0.47333	2.765000	0.47621	0.480000	0.27534	0.379000	0.24179	AAA	.	.		0.612	LRRC45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442058.1	NM_144999		G	79982609	A	G	79982609	3	3	60	1	0	0	0	0	1	0	0	0	9011	14	1	2	333	2	LRRC45	17	79982609	Missense_Mutation	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	2906907	79982609	1212601	73	7429										
MBD3	53615	hgsc.bcm.edu	37	chr19	1578491	1578491	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	cagcatgtcggccatcagcgCctcctccagccgcttccgca	9	19	1	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr19:1578491C>A	ENST00000434436.3	-	6	853	c.724G>T	c.(724-726)Gcg>Tcg	p.A242S	MBD3_ENST00000156825.1_Missense_Mutation_p.A242S|MBD3_ENST00000590550.2_Missense_Mutation_p.A186S|UQCR11_ENST00000585937.1_3'UTR|MBD3_ENST00000585967.1_5'Flank|MBD3_ENST00000592012.1_Missense_Mutation_p.A210S	NM_001281453.1	NP_001268382.1	O95983	MBD3_HUMAN	methyl-CpG binding domain protein 3	242					ATP-dependent chromatin remodeling (GO:0043044)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|tissue development (GO:0009888)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)			central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	8		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.179)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCATCAGCGCCTCCTCCAGC	0.667																																					p.A242S		Atlas-SNP	.											.	MBD3	22	.	0			c.G724T						.						70	72	71					19																	1578491		2203	4300	6503	SO:0001583	missense	53615	exon6			TCAGCGCCTCCTC	AF072247	CCDS12072.1, CCDS62481.1	19p13	2008-07-17				ENSG00000071655			6918	protein-coding gene	gene with protein product		603573				9774669, 10441743	Standard	NM_001281454		Approved		uc002ltl.1	O95983		ENST00000434436.3:c.724G>T	chr19.hg19:g.1578491C>A	ENSP00000412302:p.Ala242Ser	39.0	0.0		98.0	20.0	NM_003926	A8K4B7|D6W5Z2|Q6PIL9|Q6PJZ9|Q86XF4	Missense_Mutation	SNP	ENST00000434436.3	hg19	CCDS12072.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.024505	0.93518	.	.	ENSG00000071655	ENST00000434436;ENST00000156825	D	0.99194	-5.54	4.32	4.32	0.51571	.	0.000000	0.85682	D	0.000000	D	0.99290	0.9752	M	0.86864	2.845	0.58432	D	0.999998	D;D	0.67145	0.996;0.995	D;D	0.77557	0.99;0.988	D	0.98948	1.0793	10	0.87932	D	0	-40.5947	15.3787	0.74633	0.0:1.0:0.0:0.0	.	210;242	O95983-2;O95983	.;MBD3_HUMAN	S	210;242	ENSP00000156825:A242S	ENSP00000156825:A242S	A	-	1	0	MBD3	1529491	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.542000	0.82095	1.950000	0.56595	0.313000	0.20887	GCG	.	.		0.667	MBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449658.2	NM_003926		A	1578491	C	A	1578491	3	1	60	1	0	0	0	0	1	0	0	0	9353	739	26	3	155	3	MBD3	19	1578491	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10		1578491	57550492	74	7430										
LONP1	9361	hgsc.bcm.edu	37	chr19	5699211	5699211	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	cggagctggctaacggcaatGaactcctgcagacagaggca	13	11	0	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr19:5699211G>A	ENST00000360614.3	-	10	1669	c.1512C>T	c.(1510-1512)ttC>ttT	p.F504F	LONP1_ENST00000585374.1_Silent_p.F390F|LONP1_ENST00000593119.1_Silent_p.F440F|LONP1_ENST00000590729.1_Silent_p.F374F|LONP1_ENST00000540670.2_Silent_p.F308F	NM_004793.2	NP_004784.2			lon peptidase 1, mitochondrial											breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TAACGGCAATGAACTCCTGCA	0.637																																					p.S504S		Atlas-SNP	.											.	LONP1	66	.	0			c.C1512T						.						36	37	37					19																	5699211		2203	4300	6503	SO:0001819	synonymous_variant	9361	exon10			GGCAATGAACTCC	U02389	CCDS12148.1, CCDS62507.1, CCDS62508.1	19p13.2	2014-01-28	2006-10-20	2006-10-20	ENSG00000196365	ENSG00000196365		"ATPases / AAA-type", "Serine peptidases / Serine peptidases"	9479	protein-coding gene	gene with protein product		605490	"protease, serine, 15"	PRSS15		8248235, 8119403	Standard	NM_004793		Approved	LonHS, hLON, PIM1	uc002mcx.4	P36776		ENST00000360614.3:c.1512C>T	chr19.hg19:g.5699211G>A		22.0	0.0		43.0	27.0	NM_004793		Silent	SNP	ENST00000360614.3	hg19	CCDS12148.1																																																																																			.	.		0.637	LONP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451662.1	NM_004793		A	5699211	G	A	5699211	2	1	60	1	0	0	0	0	0	0	0	1	8901	1281	45	3		3	LONP1	19	5699211	Silent	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	4120720	5699211	53429772	75	7431										
ZNF565	147929	hgsc.bcm.edu	37	chr19	36673862	36673862	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ctttccgcattccttacactCgtagggtttctcaccagtgt	7	13	1	0	rs373289614	byFrequency	TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr19:36673862C>A	ENST00000355114.5	-	5	1852	c.1126G>T	c.(1126-1128)Gag>Tag	p.E376*	ZNF565_ENST00000392173.2_Nonsense_Mutation_p.E336*|ZNF565_ENST00000304116.5_Nonsense_Mutation_p.E336*			Q8N9K5	ZN565_HUMAN	zinc finger protein 565	376					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(4)|lung(4)|ovary(1)|skin(2)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)			TCCTTACACTCGTAGGGTTTC	0.478																																					p.E336X		Atlas-SNP	.											.	ZNF565	46	.	0			c.G1006T						.						74	66	69					19																	36673862		2203	4300	6503	SO:0001587	stop_gained	147929	exon5			TACACTCGTAGGG	AK094310	CCDS12491.1	19q13.12	2013-09-20			ENSG00000196357	ENSG00000196357		"Zinc fingers, C2H2-type", "-"	26726	protein-coding gene	gene with protein product		614275					Standard	NM_001042474		Approved	FLJ36991	uc002odn.3	Q8N9K5	OTTHUMG00000180508	ENST00000355114.5:c.1126G>T	chr19.hg19:g.36673862C>A	ENSP00000347234:p.Glu376*	94.0	0.0		163.0	49.0	NM_001042474	B3KQ35|Q6NUS2	Nonsense_Mutation	SNP	ENST00000355114.5	hg19		.	.	.	.	.	.	.	.	.	.	c	12.69	2.013646	0.35511	.	.	ENSG00000196357	ENST00000392173;ENST00000304116;ENST00000355114	.	.	.	4.7	2.51	0.30379	.	0.000000	0.37623	N	0.002020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	3.5117	0.07710	0.1745:0.5636:0.1691:0.0927	.	.	.	.	X	336;336;376	.	ENSP00000306869:E336X	E	-	1	0	ZNF565	41365702	0.000000	0.05858	0.997000	0.53966	0.013000	0.08279	-2.003000	0.01463	0.679000	0.31345	-0.142000	0.14014	GAG	.	.		0.478	ZNF565-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000451697.1	NM_152477		A	36673862	C	A	36673862	4	1	60	1	0	0	0	0	0	1	0	0	18011	893	31	1	497	1	ZNF565	19	36673862	Nonsense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	30974651	36673862	22455121	76	7432										
ZFP36	7538	hgsc.bcm.edu	37	chr19	39898413	39898413	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	cgctgagccctgacgtgcccGtgccatccgaccatggaggg	14	15	0	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr19:39898413G>T	ENST00000248673.3	+	2	113	c.55G>T	c.(55-57)Gtg>Ttg	p.V19L	ZFP36_ENST00000597629.1_Missense_Mutation_p.V25L|ZFP36_ENST00000594045.1_3'UTR|MIR4530_ENST00000581459.1_RNA	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	19					3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of inflammatory response (GO:0050728)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of tumor necrosis factor production (GO:0032680)|response to starvation (GO:0042594)|RNA destabilization (GO:0050779)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|AU-rich element binding (GO:0017091)|C-C chemokine binding (GO:0019957)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(5)|pancreas(1)	7	all_cancers(60;6.54e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.53e-06)|Ovarian(47;0.0512)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TGACGTGCCCGTGCCATCCGA	0.672																																					p.V25L	NSCLC(67;1164 1324 12056 21056 30097)	Atlas-SNP	.											.	ZFP36	19	.	0			c.G73T						.						95	106	102					19																	39898413		2202	4298	6500	SO:0001583	missense	7538	exon2			GTGCCCGTGCCAT	M63625	CCDS12534.1, CCDS12534.2	19q13.1	2012-11-27	2012-11-27			ENSG00000128016		"RING-type (C3HC4) zinc fingers"	12862	protein-coding gene	gene with protein product		190700	"zinc finger protein 36, C3H type, homolog (mouse)"			1699942	Standard	NM_003407		Approved	RNF162A, TIS11, G0S24, TTP, NUP475, tristetraprolin	uc002olh.2	P26651		ENST00000248673.3:c.55G>T	chr19.hg19:g.39898413G>T	ENSP00000248673:p.Val19Leu	24.0	0.0		72.0	18.0	NM_003407	B2RA54	Missense_Mutation	SNP	ENST00000248673.3	hg19		.	.	.	.	.	.	.	.	.	.	G	0.765	-0.767704	0.02974	.	.	ENSG00000128016	ENST00000248673	T	0.17370	2.28	3.88	-3.28	0.05033	.	6.637530	0.02098	U	0.053685	T	0.07188	0.0182	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22487	-1.0215	10	0.15066	T	0.55	.	2.8173	0.05459	0.2725:0.3503:0.2862:0.091	.	19	P26651	TTP_HUMAN	L	19	ENSP00000248673:V19L	ENSP00000248673:V19L	V	+	1	0	ZFP36	44590253	0.004000	0.15560	0.009000	0.14445	0.012000	0.07955	1.431000	0.34925	-0.273000	0.09246	-0.362000	0.07510	GTG	.	.		0.672	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	39898413	G	T	39898413	3	4	60	1	0	0	0	0	1	0	0	0	17660	1145	40	1	61	1	ZFP36	19	39898413	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	3224551	39898413	19230570	77	7433										
B9D2	80776	hgsc.bcm.edu	37	chr19	41860879	41860879	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	caagctggcagcggccaaagCtgtcctgggaccacacctgg	13	14	0	0			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr19:41860879C>A	ENST00000243578.3	-	4	473	c.254G>T	c.(253-255)aGc>aTc	p.S85I	CTC-435M10.3_ENST00000604424.1_Intron|TGFB1_ENST00000221930.5_5'Flank|TMEM91_ENST00000539627.1_Intron|TMEM91_ENST00000604123.1_Intron	NM_030578.3	NP_085055.2	Q9BPU9	B9D2_HUMAN	B9 protein domain 2	85	B9. {ECO:0000255|PROSITE- ProRule:PRU00713}.				cilium assembly (GO:0042384)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)	gamma-tubulin binding (GO:0043015)			large_intestine(1)|ovary(1)	2						GCGGCCAAAGCTGTCCTGGGA	0.652																																					p.S85I		Atlas-SNP	.											.	B9D2	9	.	0			c.G254T						.						11	12	12					19																	41860879		2198	4289	6487	SO:0001583	missense	80776	exon4			CCAAAGCTGTCCT	BC004157	CCDS12579.1	19q13.2	2014-01-28				ENSG00000123810			28636	protein-coding gene	gene with protein product		611951				21763481	Standard	NM_030578		Approved	MGC4093, MKS10	uc002oqj.2	Q9BPU9		ENST00000243578.3:c.254G>T	chr19.hg19:g.41860879C>A	ENSP00000243578:p.Ser85Ile	32.0	0.0		72.0	43.0	NM_030578		Missense_Mutation	SNP	ENST00000243578.3	hg19	CCDS12579.1	.	.	.	.	.	.	.	.	.	.	c	12.43	1.935294	0.34189	.	.	ENSG00000123810	ENST00000243578	T	0.72167	-0.63	4.04	2.93	0.34026	.	0.260739	0.36555	N	0.002532	T	0.61324	0.2338	M	0.62723	1.935	0.40152	D	0.976961	B	0.13145	0.007	B	0.10450	0.005	T	0.56347	-0.7994	10	0.20519	T	0.43	.	7.5486	0.27781	0.1623:0.5428:0.2949:0.0	.	85	Q9BPU9	B9D2_HUMAN	I	85	ENSP00000243578:S85I	ENSP00000243578:S85I	S	-	2	0	B9D2	46552719	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.127000	0.42035	2.081000	0.62600	0.457000	0.33378	AGC	.	.		0.652	B9D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463489.1	NM_030578		A	41860879	C	A	41860879	3	1	60	1	0	0	0	0	1	0	0	0	1278	797	28	3	277	3	B9D2	19	41860879	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	1962466	41860879	17268104	78	7434										
KDELR1	10945	hgsc.bcm.edu	37	chr19	48886580	48886580	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	aaactcaacttcttccccttTaggactgtgaggagagaaaa	8	9	2	2			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr19:48886580T>C	ENST00000330720.2	-	5	803	c.609A>G	c.(607-609)ctA>ctG	p.L203L	KDELR1_ENST00000597017.1_Silent_p.L141L	NM_006801.2	NP_006792.1	P24390	ERD21_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1	203					intracellular protein transport (GO:0006886)|protein retention in ER lumen (GO:0006621)|vesicle-mediated transport (GO:0016192)	cis-Golgi network (GO:0005801)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	KDEL sequence binding (GO:0005046)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|pancreas(1)|urinary_tract(1)	11		all_epithelial(76;2.48e-06)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Prostate(7;0.122)|Breast(70;0.203)		all cancers(93;0.000114)|OV - Ovarian serous cystadenocarcinoma(262;0.000136)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.0145)		TCTTCCCCTTTAGGACTGTGA	0.622																																					p.L203L		Atlas-SNP	.											.	KDELR1	26	.	0			c.A609G						.						31	24	26					19																	48886580		2144	4148	6292	SO:0001819	synonymous_variant	10945	exon5			CCCCTTTAGGACT	X55885	CCDS12718.1	19q13.3	2008-05-02				ENSG00000105438			6304	protein-coding gene	gene with protein product		131235				2172835	Standard	NM_006801		Approved	ERD2.1, ERD2, HDEL	uc002pjb.1	P24390		ENST00000330720.2:c.609A>G	chr19.hg19:g.48886580T>C		49.0	0.0		107.0	56.0	NM_006801	B2R6N4|Q54A39|Q8NBW7	Silent	SNP	ENST00000330720.2	hg19	CCDS12718.1																																																																																			.	.		0.622	KDELR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465708.1			C	48886580	T	C	48886580	2	2	60	1	0	0	0	0	0	0	0	1	8128	1741	61	2		2	KDELR1	19	48886580	Silent	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	7025701	48886580	10242403	79	7435										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55493601	55493601	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	ggaagagctggcctggagatAgcaaagaggtccaggttatg	16	6	0	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr19:55493601A>T	ENST00000543010.1	+	6	678	c.535A>T	c.(535-537)Agc>Tgc	p.S179C	NLRP2_ENST00000537859.1_Missense_Mutation_p.S157C|NLRP2_ENST00000263437.6_Missense_Mutation_p.S176C|NLRP2_ENST00000427260.2_Missense_Mutation_p.S156C|NLRP2_ENST00000448584.2_Missense_Mutation_p.S179C|NLRP2_ENST00000339757.7_Missense_Mutation_p.S157C|NLRP2_ENST00000538819.1_Missense_Mutation_p.S155C|NLRP2_ENST00000391721.4_Missense_Mutation_p.S155C	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	179					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GCCTGGAGATAGCAAAGAGGT	0.507																																					p.S179C		Atlas-SNP	.											.	NLRP2	161	.	0			c.A535T						.						160	172	168					19																	55493601		2203	4300	6503	SO:0001583	missense	55655	exon6			GGAGATAGCAAAG	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.535A>T	chr19.hg19:g.55493601A>T	ENSP00000445135:p.Ser179Cys	104.0	0.0		239.0	124.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	A	10.88	1.475578	0.26511	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.74737	-0.82;-0.74;-0.77;-0.82;-0.77;-0.87;-0.74;0.5	2.05	-2.01	0.07410	.	1.244490	0.06057	N	0.657629	T	0.68933	0.3055	N	0.24115	0.695	0.09310	N	1	D;D;D;D;D	0.76494	0.991;0.998;0.996;0.995;0.999	P;P;P;P;P	0.61722	0.706;0.893;0.784;0.846;0.864	T	0.56432	-0.7980	10	0.54805	T	0.06	.	0.136	0.00078	0.3483:0.2418:0.1717:0.2383	.	156;157;176;155;179	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	C	179;155;157;179;157;156;155;176	ENSP00000445135:S179C;ENSP00000375601:S155C;ENSP00000344074:S157C;ENSP00000409370:S179C;ENSP00000440601:S157C;ENSP00000402474:S156C;ENSP00000441133:S155C;ENSP00000263437:S176C	ENSP00000263437:S176C	S	+	1	0	NLRP2	60185413	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.155000	0.10115	-0.629000	0.05575	0.402000	0.26972	AGC	.	.		0.507	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		T	55493601	A	T	55493601	3	4	60	1	0	0	0	0	1	0	0	0	10486	420	15	4	553	4	NLRP2	19	55493601	Missense_Mutation	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10	6607021	55493601	3635382	80	7436										
ZIK1	284307	hgsc.bcm.edu	37	chr19	58101688	58101688	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	attgaagccctttcgcaaatGggaggttggaaaggaccttc	12	8	0	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr19:58101688G>T	ENST00000597850.1	+	4	724	c.509G>T	c.(508-510)tGg>tTg	p.W170L	ZIK1_ENST00000307468.4_3'UTR|ZIK1_ENST00000599456.1_Missense_Mutation_p.W115L|ZIK1_ENST00000536878.2_Missense_Mutation_p.W157L	NM_001010879.2	NP_001010879.2	Q3SY52	ZIK1_HUMAN	zinc finger protein interacting with K protein 1	170					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	34		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TTTCGCAAATGGGAGGTTGGA	0.502																																					p.W170L		Atlas-SNP	.											.	ZIK1	94	.	0			c.G509T						.						74	69	71					19																	58101688		2203	4300	6503	SO:0001583	missense	284307	exon4			GCAAATGGGAGGT	AK092538	CCDS33135.1	19q13.43	2013-01-08	2012-12-07		ENSG00000171649	ENSG00000171649		"Zinc fingers, C2H2-type", "-"	33104	protein-coding gene	gene with protein product			"zinc finger protein interacting with K protein 1 homolog (mouse)"				Standard	XM_005258769		Approved	ZNF762	uc002qpg.3	Q3SY52		ENST00000597850.1:c.509G>T	chr19.hg19:g.58101688G>T	ENSP00000472867:p.Trp170Leu	83.0	0.0		147.0	49.0	NM_001010879	O43339|Q3SY51|Q3SY53	Missense_Mutation	SNP	ENST00000597850.1	hg19	CCDS33135.1	.	.	.	.	.	.	.	.	.	.	G	2.446	-0.327465	0.05350	.	.	ENSG00000171649	ENST00000536878;ENST00000356724;ENST00000307468	T	0.04654	3.58	2.97	-5.94	0.02247	.	.	.	.	.	T	0.01254	0.0041	N	0.01048	-1.04	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44982	-0.9292	9	0.27785	T	0.31	.	1.8751	0.03217	0.4707:0.136:0.2556:0.1377	.	157;170	F5H435;Q3SY52	.;ZIK1_HUMAN	L	157;151;170	ENSP00000438487:W157L	ENSP00000303820:W170L	W	+	2	0	ZIK1	62793500	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-0.344000	0.07780	-1.595000	0.01613	-1.626000	0.00786	TGG	.	.		0.502	ZIK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466791.1	NM_001010879		T	58101688	G	T	58101688	3	4	60	1	0	0	0	0	1	0	0	0	17698	1357	47	3	523	3	ZIK1	19	58101688	Missense_Mutation	SNP	G	TCGA-CC-5264-01A-01D-A12Z-10	2608087	58101688	1027295	81	7437										
ADRA1D	146	hgsc.bcm.edu	37	chr20	4202228	4202229	+	Missense_Mutation	DNP	GC	GC	TT													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	attcgtaggcctggcaggtgGcgccctcggccacctcgtgt					rs371559421		TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr20:4202228_4202229GC>TT	ENST00000379453.4	-	2	1776_1777	c.1660_1661GC>AA	c.(1660-1662)GCc>AAc	p.A554N		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	554				KPPSAFREWRLLGPFRRPTTQLRAKVSSLSHKIRAGGAQRA EAACAQRSEVEAVSLGVPHEVAEGATCQAYELADYSNLRET DI -> SHPAPSASGGCWGRSGDPRPSCAPKSPACRTRSPP GARSAQRQRAPSAQRWRLCP (in Ref. 1). {ECO:0000305}.	adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			endometrium(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	14					Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	CTGGCAGGTGGCGCCCTCGGCC	0.688																																					p.A554D|p.A554T		Atlas-SNP	.											.	ADRA1D	36	.	0			c.C1661A|c.G1660A						.																																			SO:0001583	missense	146	exon2			CAGGTGGCGCCCT|AGGTGGCGCCCTC	U03864	CCDS13079.1	20p13	2012-08-08	2012-05-09		ENSG00000171873	ENSG00000171873		"GPCR / Class A : Adrenoceptors : alpha"	280	protein-coding gene	gene with protein product		104219	"adrenergic, alpha-1D-, receptor"			8039425	Standard	NM_000678		Approved	ADRA1R, ADRA1A, ADRA1	uc002wkr.2	P25100	OTTHUMG00000031779	ENST00000379453.4:c.1660_1661delinsTT	chr20.hg19:g.4202228_4202229delinsTT	ENSP00000368766:p.Ala554Asn	62.0|60.0	0.0		236.0	102.0	NM_000678	Q9NPY0	Missense_Mutation	SNP	ENST00000379453.4	hg19	CCDS13079.1																																																																																			.	.		0.688	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678		TT	4202229	GC	TT	4202228	3	4	60	1	0	0	0	0	1	0	0	0	336	1203	42	3	61	3	ADRA1D	20	4202228	Missense_Mutation	DNP	GC	TCGA-CC-5264-01A-01D-A12Z-10		4202228	58823292	82	7438										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39792450	39792451	+	Frame_Shift_Ins	INS	-	-	T													0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	acaaccctctttcccactacINStggatctcctcctcgcacaa							TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr20:39792450_39792451insT	ENST00000373271.1	+	10	1392_1393	c.987_988insT	c.(988-990)tggfs	p.W330fs	PLCG1_ENST00000244007.3_Frame_Shift_Ins_p.W330fs|PLCG1_ENST00000373272.2_Frame_Shift_Ins_p.W330fs	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	330	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				TTTCCCACTACTGGATCTCCTC	0.559																																					p.Y329fs		Atlas-Indel,Pindel	.											.	PLCG1	111	.	0			c.987_988insT						.																																			SO:0001589	frameshift_variant	5335	exon10			.	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.988dupT	chr20.hg19:g.39792451_39792451dupT	ENSP00000362368:p.Trp330fs	112.0	0.0		353.0	140.0	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Frame_Shift_Ins	INS	ENST00000373271.1	hg19	CCDS13314.1																																																																																			.	.		0.559	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		T	39792451	-	T	39792450	7	5	60	1	0	1	1	0	0	0	0	0	12044	576	20	0	1025	0	PLCG1	20	39792450	Frame_Shift_Ins	INS	-	TCGA-CC-5264-01A-01D-A12Z-10	35590222	39792450	23233070	83	7439										
BMP7	655	hgsc.bcm.edu	37	chr20	55840845	55840845	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	cagaggggggccctgggtacTgaagacggccttgtaggggt	19	8	0	3			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chr20:55840845T>A	ENST00000395863.3	-	1	839	c.334A>T	c.(334-336)Agt>Tgt	p.S112C	BMP7_ENST00000450594.2_Missense_Mutation_p.S112C|BMP7_ENST00000395864.3_Missense_Mutation_p.S112C|RP4-813D12.3_ENST00000412321.1_lincRNA	NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	112					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of an epithelial tube (GO:0048754)|cartilage development (GO:0051216)|cellular response to hypoxia (GO:0071456)|dendrite development (GO:0016358)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint morphogenesis (GO:0060272)|epithelial cell differentiation (GO:0030855)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|mesenchymal cell differentiation (GO:0048762)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|mesonephros development (GO:0001823)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephros development (GO:0001656)|monocyte aggregation (GO:0070487)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis (GO:0072040)|negative regulation of mitosis (GO:0045839)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of dendrite development (GO:1900006)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of removal of superoxide radicals (GO:2000121)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|steroid hormone mediated signaling pathway (GO:0043401)|ureteric bud development (GO:0001657)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	heparin binding (GO:0008201)			endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			CCCTGGGTACTGAAGACGGCC	0.647																																					p.S112C		Atlas-SNP	.											.	BMP7	60	.	0			c.A334T						.						24	24	24					20																	55840845		2202	4299	6501	SO:0001583	missense	655	exon1			GGGTACTGAAGAC		CCDS13455.1	20q13	2014-01-30	2008-05-22		ENSG00000101144	ENSG00000101144		"Bone morphogenetic proteins", "Endogenous ligands"	1074	protein-coding gene	gene with protein product	"osteogenic protein 1"	112267				1427904	Standard	NM_001719		Approved	OP-1	uc010gip.1	P18075	OTTHUMG00000032812	ENST00000395863.3:c.334A>T	chr20.hg19:g.55840845T>A	ENSP00000379204:p.Ser112Cys	61.0	0.0		177.0	79.0	NM_001719	Q9H512|Q9NTQ7	Missense_Mutation	SNP	ENST00000395863.3	hg19	CCDS13455.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.595492	0.46318	.	.	ENSG00000101144	ENST00000395863;ENST00000395864;ENST00000450594	T;T;T	0.68479	-0.33;-0.33;-0.33	5.04	5.04	0.67666	Transforming growth factor-beta, N-terminal (1);	0.090404	0.85682	D	0.000000	T	0.69958	0.3169	L	0.49126	1.545	0.38758	D	0.954257	D;B;B	0.54601	0.967;0.21;0.049	P;B;B	0.51055	0.657;0.057;0.051	T	0.76321	-0.3002	10	0.72032	D	0.01	.	14.7775	0.69740	0.0:0.0:0.0:1.0	.	112;112;112	B1AKZ9;P18075;B1AL00	.;BMP7_HUMAN;.	C	112	ENSP00000379204:S112C;ENSP00000379205:S112C;ENSP00000398687:S112C	ENSP00000379204:S112C	S	-	1	0	BMP7	55274252	1.000000	0.71417	0.996000	0.52242	0.978000	0.69477	2.865000	0.48412	1.873000	0.54277	0.402000	0.26972	AGT	.	.		0.647	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079831.2			A	55840845	T	A	55840845	3	1	60	1	0	0	0	0	1	0	0	0	1465	1580	55	4	989	4	BMP7	20	55840845	Missense_Mutation	SNP	T	TCGA-CC-5264-01A-01D-A12Z-10	16048395	55840845	7184675	84	7440										
TLR7	51284	hgsc.bcm.edu	37	chrX	12904609	12904609	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tgtcccaaaacttcttggccAaagaaattggggatgctaaa	9	8	1	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chrX:12904609A>G	ENST00000380659.3	+	3	1121	c.982A>G	c.(982-984)Aaa>Gaa	p.K328E		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	328					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	CTTCTTGGCCAAAGAAATTGG	0.418																																					p.K328E		Atlas-SNP	.											.	TLR7	125	.	0			c.A982G						.						72	71	72					X																	12904609		2203	4299	6502	SO:0001583	missense	51284	exon3			TTGGCCAAAGAAA	AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.982A>G	chrX.hg19:g.12904609A>G	ENSP00000370034:p.Lys328Glu	86.0	0.0		95.0	82.0	NM_016562	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	hg19	CCDS14151.1	.	.	.	.	.	.	.	.	.	.	A	14.36	2.511550	0.44660	.	.	ENSG00000196664	ENST00000380659	T	0.02395	4.31	5.65	5.65	0.86999	.	0.186695	0.46145	D	0.000308	T	0.03959	0.0111	L	0.46157	1.445	0.34566	D	0.712874	B	0.16396	0.017	B	0.19946	0.027	T	0.17715	-1.0360	10	0.44086	T	0.13	.	10.1847	0.42991	0.8494:0.0:0.0:0.1506	.	328	Q9NYK1	TLR7_HUMAN	E	328	ENSP00000370034:K328E	ENSP00000370034:K328E	K	+	1	0	TLR7	12814530	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	6.094000	0.71431	1.891000	0.54761	0.486000	0.48141	AAA	.	.		0.418	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		G	12904609	A	G	12904609	3	3	60	1	0	0	0	0	1	0	0	0	15971	131	5	2	988	2	TLR7	23	12904609	Missense_Mutation	SNP	A	TCGA-CC-5264-01A-01D-A12Z-10		12904609	142365951	85	7441										
MORF4L2	9643	hgsc.bcm.edu	37	chrX	102931737	102931737	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0930232558139535	8	1	2.11507936507937	1.85069444444444	2.22083333333333	0.153434800493624	0.751940625889747	0	tgcttgttctttctggtcttCctcacggatcctgaaggggg	12	10	4	1			TCGA-CC-5264-01A-01D-A12Z-10	TCGA-CC-5264-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ebf24cf-16a5-4dd3-b594-062b8d626dc3	b864a5b7-de17-4b12-b93e-4246ea56a3d6	g.chrX:102931737C>A	ENST00000441076.2	-	4	523	c.219G>T	c.(217-219)agG>agT	p.R73S	MORF4L2_ENST00000451301.1_Missense_Mutation_p.R73S|MORF4L2_ENST00000423833.2_Missense_Mutation_p.R73S|MORF4L2_ENST00000433176.2_Missense_Mutation_p.R73S|MORF4L2_ENST00000360458.1_Missense_Mutation_p.R73S|MORF4L2_ENST00000492116.1_5'UTR|MORF4L2_ENST00000422154.2_Missense_Mutation_p.R73S	NM_001142419.1|NM_012286.2	NP_001135891.1|NP_036418.1	Q15014	MO4L2_HUMAN	mortality factor 4 like 2	73					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA repair (GO:0006281)|positive regulation of striated muscle cell differentiation (GO:0051155)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)	13						TTCTGGTCTTCCTCACGGATC	0.567																																					p.R73S		Atlas-SNP	.											.	MORF4L2	35	.	0			c.G219T						.						66	57	60					X																	102931737		2203	4300	6503	SO:0001583	missense	9643	exon5			GGTCTTCCTCACG	AF100620	CCDS14512.1	Xq22	2010-11-24			ENSG00000123562	ENSG00000123562			16849	protein-coding gene	gene with protein product	"MORF-related gene X"	300409				9891081, 7584026	Standard	NM_012286		Approved	KIAA0026, MRGX	uc011msa.2	Q15014	OTTHUMG00000022104	ENST00000441076.2:c.219G>T	chrX.hg19:g.102931737C>A	ENSP00000391969:p.Arg73Ser	82.0	0.0		219.0	206.0	NM_001142422	B3KP92|D3DXA5|Q567V0|Q8J026	Missense_Mutation	SNP	ENST00000441076.2	hg19	CCDS14512.1	.	.	.	.	.	.	.	.	.	.	C	9.773	1.173156	0.21704	.	.	ENSG00000123562	ENST00000360458;ENST00000433176;ENST00000422154;ENST00000451301;ENST00000372619;ENST00000441076;ENST00000423833;ENST00000434230;ENST00000418819;ENST00000442614	T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55	4.52	3.66	0.41972	.	0.109692	0.38837	N	0.001545	T	0.15089	0.0364	N	0.24115	0.695	0.34938	D	0.749982	B	0.26081	0.141	B	0.18263	0.021	T	0.15607	-1.0431	10	0.07482	T	0.82	-16.8622	7.308	0.26459	0.0:0.8813:0.0:0.1187	.	73	Q15014	MO4L2_HUMAN	S	73;73;73;73;55;73;73;73;73;73	ENSP00000353643:R73S;ENSP00000415476:R73S;ENSP00000394417:R73S;ENSP00000410532:R73S;ENSP00000391969:R73S;ENSP00000416120:R73S	ENSP00000353643:R73S	R	-	3	2	MORF4L2	102818393	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.687000	0.46976	1.244000	0.43870	0.600000	0.82982	AGG	.	.		0.567	MORF4L2-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057732.1	NM_012286		A	102931737	C	A	102931737	3	1	60	1	0	0	0	0	1	0	0	0	9716	854	30	3	651	3	MORF4L2	23	102931737	Missense_Mutation	SNP	C	TCGA-CC-5264-01A-01D-A12Z-10	90027128	102931737	52338823	86	7442										
PLEKHG5	57449	hgsc.bcm.edu	37	chr1	6530878	6530878	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	cagcgggtacttggtgagccGctggtggggtttggccagca	18	9	0	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr1:6530878G>A	ENST00000400915.3	-	15	1693	c.1627C>T	c.(1627-1629)Cgg>Tgg	p.R543W	PLEKHG5_ENST00000400913.1_Missense_Mutation_p.R487W|PLEKHG5_ENST00000377728.3_Missense_Mutation_p.R487W|PLEKHG5_ENST00000535355.1_Missense_Mutation_p.R556W|PLEKHG5_ENST00000377737.2_Missense_Mutation_p.R487W|PLEKHG5_ENST00000537245.1_Missense_Mutation_p.R566W|PLEKHG5_ENST00000377725.1_Missense_Mutation_p.R487W|PLEKHG5_ENST00000377740.3_Missense_Mutation_p.R564W|PLEKHG5_ENST00000377732.1_Missense_Mutation_p.R524W|PLEKHG5_ENST00000377748.1_Missense_Mutation_p.R564W|PLEKHG5_ENST00000544978.1_Missense_Mutation_p.R487W|PLEKHG5_ENST00000340850.5_Missense_Mutation_p.R487W	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	543	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		TTGGTGAGCCGCTGGTGGGGT	0.677																																					p.R566W		Atlas-SNP	.											.	PLEKHG5	66	.	0			c.C1696T						.						17	15	16					1																	6530878		2200	4290	6490	SO:0001583	missense	57449	exon15			TGAGCCGCTGGTG	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"Pleckstrin homology (PH) domain containing"	29105	protein-coding gene	gene with protein product	"synectin-binding guanine exchange factor"	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.1627C>T	chr1.hg19:g.6530878G>A	ENSP00000383706:p.Arg543Trp	52.0	0.0		75.0	47.0	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Missense_Mutation	SNP	ENST00000400915.3	hg19	CCDS41241.1	.	.	.	.	.	.	.	.	.	.	g	18.42	3.620802	0.66787	.	.	ENSG00000171680	ENST00000377748;ENST00000340850;ENST00000400913;ENST00000400915;ENST00000377740;ENST00000377732;ENST00000377728;ENST00000377725;ENST00000535355;ENST00000377737;ENST00000535966;ENST00000537245;ENST00000544978	D;D;D;D;D;D;D;D;D;D;D;D	0.88124	-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34	4.55	3.52	0.40303	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.95233	0.8454	H	0.96547	3.84	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.96472	0.9349	10	0.87932	D	0	-29.4198	13.9756	0.64271	0.0:0.0:0.8375:0.1625	.	556;487;564;564;543	F5GZ21;O94827-4;Q5SY18;O94827-2;O94827	.;.;.;.;PKHG5_HUMAN	W	564;487;487;543;564;524;487;487;556;487;393;566;487	ENSP00000366977:R564W;ENSP00000344570:R487W;ENSP00000383704:R487W;ENSP00000383706:R543W;ENSP00000366969:R564W;ENSP00000366961:R524W;ENSP00000366957:R487W;ENSP00000366954:R487W;ENSP00000441445:R556W;ENSP00000366966:R487W;ENSP00000439625:R566W;ENSP00000437710:R487W	ENSP00000344570:R487W	R	-	1	2	PLEKHG5	6453465	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.438000	0.52871	2.069000	0.61940	0.457000	0.33378	CGG	.	.		0.677	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631		A	6530878	G	A	6530878	3	1	61	1	0	0	0	0	1	0	0	0	12082	1086	38	1	1593	1	PLEKHG5	1	6530878	Missense_Mutation	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10		6530878	242719743	1	7443										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27107084	27107085	+	Frame_Shift_Ins	INS	-	-	GC													0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	actagtgtggacatgatgcgINSgcgggctgcccgcgcgctgc					rs142878055		TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr1:27107084_27107085insGC	ENST00000324856.7	+	20	7066_7067	c.6695_6696insGC	c.(6694-6699)cggcggfs	p.RR2232fs	ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.RR560fs|ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.RR1849fs|ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.RR2015fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2232					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.M2231fs*32(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GACATGATGCGGCGGGCTGCCC	0.594			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.R2232fs		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	1	Deletion - Frameshift(1)	liver(1)	c.6695_6696insGC						.																																			SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.6696_6697dupGC	chr1.hg19:g.27107085_27107086dupGC	ENSP00000320485:p.Arg2232fs	18.0	0.0		22.0	13.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.594	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		GC	27107085	-	GC	27107084	7	5	61	1	0	1	1	0	0	0	0	0	913	1116	39	0	6773	0	ARID1A	1	27107084	Frame_Shift_Ins	INS	-	TCGA-CC-A123-01A-11D-A12Z-10	20576206	27107084	222143537	2	7444										
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77333366	77333366	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	aaagaggtgcccaaaatgaaGaccctgatggtgagtcagtt	12	7	1	5			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr1:77333366G>A	ENST00000477717.1	+	1	241	c.6G>A	c.(4-6)aaG>aaA	p.K2K	ST6GALNAC5_ENST00000496845.1_3'UTR	NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	2					glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						CCAAAATGAAGACCCTGATGG	0.617																																					p.K2K		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.G6A						.						78	83	81					1																	77333366		2203	4300	6503	SO:0001819	synonymous_variant	81849	exon1			AATGAAGACCCTG		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.6G>A	chr1.hg19:g.77333366G>A		115.0	0.0		118.0	52.0	NM_030965	B1AK82	Silent	SNP	ENST00000477717.1	hg19	CCDS673.1																																																																																			.	.		0.617	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		A	77333366	G	A	77333366	2	1	61	1	0	0	0	0	0	0	0	1	15242	933	33	3		3	ST6GALNAC5	1	77333366	Silent	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10	50226282	77333366	171917255	3	7445										
LCE1E	353135	hgsc.bcm.edu	37	chr1	152759968	152759968	+	Frame_Shift_Del	DEL	G	G	-													0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gcagctgtggctccagctctGggggctgctgcagctctggg							TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr1:152759968delG	ENST00000368770.3	+	2	246	c.193delG	c.(193-195)gggfs	p.G66fs	LCE1E_ENST00000368771.1_Frame_Shift_Del_p.G66fs	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	66	Cys-rich.				keratinization (GO:0031424)					lung(5)|stomach(1)	6	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCAGCTCTGGGGGCTGCTG	0.657																																					p.S64fs		Atlas-Indel,Pindel	.											.	LCE1E	26	.	0			c.192delT						.						36	45	42					1																	152759968		2203	4299	6502	SO:0001589	frameshift_variant	353135	exon2			.	BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"Late cornified envelopes"	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.193delG	chr1.hg19:g.152759968delG	ENSP00000357759:p.Gly66fs	111.0	0.0		146.0	39.0	NM_178353	D3DV30	Frame_Shift_Del	DEL	ENST00000368770.3	hg19	CCDS1024.1																																																																																			.	.		0.657	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353		-	152759968	G	-	152759968	7	5	61	1	0	1	0	1	0	0	0	0	8672	1348	47	0	195	0	LCE1E	1	152759968	Frame_Shift_Del	DEL	G	TCGA-CC-A123-01A-11D-A12Z-10	75426602	152759968	96490653	4	7446										
C1orf104	23623	hgsc.bcm.edu	37	chr1	155290718	155290718	+	5'UTR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	tcccctcccgctctgtgcccCgccgggcggggaccgtggga	15	18	1	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr1:155290718C>A	ENST00000368352.5	+	0	1				RUSC1-AS1_ENST00000450199.1_RNA|RUSC1_ENST00000368354.3_5'UTR|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000543656.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1						positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			CTCTGTGCCCCGCCGGGCGGG	0.726																																					p.G188W		Atlas-SNP	.											.	.	.	.	0			c.G562T						.						17	21	20					1																	155290718		1882	4080	5962	SO:0001623	5_prime_UTR_variant	284618	exon2			GTGCCCCGCCGGG	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.-151C>A	chr1.hg19:g.155290718C>A		18.0	0.0		41.0	13.0	NM_001039517	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Missense_Mutation	SNP	ENST00000368352.5	hg19	CCDS41410.1																																																																																			.	.		0.726	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			A	155290718	C	A	155290718	1	1	61	0	1	0	0	0	0	0	0	0	1980	652	23	1		1	C1orf104	1	155290718	5'UTR	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	2530750	155290718	93959903	5	7447										
ADAM17	6868	hgsc.bcm.edu	37	chr2	9676045	9676045	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gggctagaaccctagagtcaGgctcaccttaagagaaaaaa	10	9	2	3			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr2:9676045G>T	ENST00000310823.3	-	4	550	c.368C>A	c.(367-369)cCt>cAt	p.P123H	ADAM17_ENST00000497134.1_Missense_Mutation_p.P123H	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	123					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		CCTAGAGTCAGGCTCACCTTA	0.308																																					p.P123H		Atlas-SNP	.											.	ADAM17	61	.	0			c.C368A						.						46	46	46					2																	9676045		2202	4298	6500	SO:0001583	missense	6868	exon4			GAGTCAGGCTCAC	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.368C>A	chr2.hg19:g.9676045G>T	ENSP00000309968:p.Pro123His	122.0	0.0		108.0	8.0	NM_003183	O60226	Missense_Mutation	SNP	ENST00000310823.3	hg19	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	G	8.093	0.775049	0.16051	.	.	ENSG00000151694	ENST00000310823;ENST00000497134;ENST00000538558	T;T	0.09630	2.96;2.96	5.33	4.33	0.51752	Peptidase M12B, propeptide (1);	0.224065	0.45867	D	0.000325	T	0.06234	0.0161	N	0.11201	0.11	0.28723	N	0.902895	B;B;B;B	0.22480	0.07;0.006;0.07;0.006	B;B;B;B	0.23419	0.046;0.013;0.046;0.013	T	0.17745	-1.0359	10	0.35671	T	0.21	.	10.7755	0.46348	0.0:0.0:0.6408:0.3592	.	123;123;123;123	A8K1B4;B2RNB2;Q6P5T8;P78536	.;.;.;ADA17_HUMAN	H	123	ENSP00000309968:P123H;ENSP00000418728:P123H	ENSP00000309968:P123H	P	-	2	0	ADAM17	9593496	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	4.259000	0.58828	2.642000	0.89623	0.557000	0.71058	CCT	.	.		0.308	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			T	9676045	G	T	9676045	3	4	61	1	0	0	0	0	1	0	0	0	238	1000	35	3	2170	3	ADAM17	2	9676045	Missense_Mutation	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10		9676045	233523328	6	7448										
MYCN	4613	hgsc.bcm.edu	37	chr2	16082220	16082220	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ccacgtccaccatgccgggcAtgatctgcaagaacccagac	9	16	1	3			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr2:16082220A>G	ENST00000281043.3	+	2	331	c.34A>G	c.(34-36)Atg>Gtg	p.M12V	MYCNOS_ENST00000439180.1_RNA|MYCNOS_ENST00000453400.1_RNA|MYCNOS_ENST00000420452.1_RNA|MYCNOS_ENST00000448719.1_RNA|MYCNOS_ENST00000419083.1_RNA	NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	12					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			CATGCCGGGCATGATCTGCAA	0.637			A		neuroblastoma																																p.M12V		Atlas-SNP	.		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	.	MYCN	63	.	0			c.A34G						.						51	52	51					2																	16082220		2203	4300	6503	SO:0001583	missense	4613	exon2			CCGGGCATGATCT	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.34A>G	chr2.hg19:g.16082220A>G	ENSP00000281043:p.Met12Val	162.0	0.0		268.0	120.0	NM_005378	Q53XS5|Q6LDT9	Missense_Mutation	SNP	ENST00000281043.3	hg19	CCDS1687.1	.	.	.	.	.	.	.	.	.	.	A	12.23	1.875283	0.33162	.	.	ENSG00000134323	ENST00000281043;ENST00000426211	T	0.17854	2.25	3.38	1.96	0.26148	Transcription regulator Myc, N-terminal (1);	0.591738	0.18420	U	0.141775	T	0.15652	0.0377	L	0.57536	1.79	0.29984	N	0.817415	B	0.21225	0.053	B	0.27076	0.076	T	0.10567	-1.0624	10	0.54805	T	0.06	-13.8999	3.5969	0.08009	0.6554:0.0:0.1599:0.1847	.	12	P04198	MYCN_HUMAN	V	12	ENSP00000281043:M12V	ENSP00000281043:M12V	M	+	1	0	MYCN	15999671	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	3.202000	0.51067	1.313000	0.45069	0.459000	0.35465	ATG	.	.		0.637	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		G	16082220	A	G	16082220	3	3	61	1	0	0	0	0	1	0	0	0	10030	217	8	2	36	2	MYCN	2	16082220	Missense_Mutation	SNP	A	TCGA-CC-A123-01A-11D-A12Z-10	6406175	16082220	227117153	7	7449										
C2orf89	129293	hgsc.bcm.edu	37	chr2	85066338	85066338	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	aaagggccttcacccgcttcCctattctctcattccgcttg	6	16	3	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr2:85066338C>G	ENST00000409520.2	-	4	968	c.926G>C	c.(925-927)gGg>gCg	p.G309A	TRABD2A_ENST00000409133.1_Missense_Mutation_p.G309A|TRABD2A_ENST00000335459.5_Missense_Mutation_p.G260A	NM_001277053.1	NP_001263982.1	Q86V40	TIKI1_HUMAN	TraB domain containing 2A	309					head development (GO:0060322)|metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|Wnt-protein binding (GO:0017147)	p.G260E(1)									CACCCGCTTCCCTATTCTCTC	0.512																																					p.Y260S		Atlas-SNP	.											C2orf89_ENST00000335459,extremity,malignant_melanoma,0,1	.	.	.	1	Substitution - Missense(1)	skin(1)	c.A779C						.						89	90	89					2																	85066338		1899	4122	6021	SO:0001583	missense	129293	exon3			CGCTTCCCTATTC	BC049209	CCDS46349.1, CCDS62946.1	2p11.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000186854	ENSG00000186854			27013	protein-coding gene	gene with protein product		614912	"chromosome 2 open reading frame 89"	C2orf89		12477932	Standard	NM_001080824		Approved		uc010ysl.3	Q86V40	OTTHUMG00000152922	ENST00000409520.2:c.926G>C	chr2.hg19:g.85066338C>G	ENSP00000387075:p.Gly309Ala	130.0	0.0		193.0	23.0	NM_001080824	B4DKK8|I6UMB9	Missense_Mutation	SNP	ENST00000409520.2	hg19		.	.	.	.	.	.	.	.	.	.	C	7.394	0.631466	0.14322	.	.	ENSG00000186854	ENST00000335459;ENST00000409520;ENST00000409133	T;T;T	0.27402	2.06;1.67;1.67	3.75	2.87	0.33458	.	0.180079	0.35466	N	0.003197	T	0.15349	0.0370	.	.	.	0.41223	D	0.986528	P;B;P	0.43542	0.81;0.08;0.783	B;B;B	0.42030	0.303;0.083;0.373	T	0.12041	-1.0563	9	0.02654	T	1	.	8.9389	0.35718	0.0:0.887:0.0:0.113	.	309;309;260	Q86V40;C9IYB5;Q86V40-2	CB089_HUMAN;.;.	A	260;309;309	ENSP00000335004:G260A;ENSP00000387075:G309A;ENSP00000387183:G309A	ENSP00000335004:G260A	G	-	2	0	C2orf89	84919849	0.992000	0.36948	0.801000	0.32222	0.790000	0.44656	2.910000	0.48766	0.797000	0.33971	0.563000	0.77884	GGG	.	.		0.512	TRABD2A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001080824		G	85066338	C	G	85066338	3	3	61	1	0	0	0	0	1	0	0	0	2205	623	22	4	607	4	C2orf89	2	85066338	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	68984118	85066338	158133035	8	7450										
TTN	7273	hgsc.bcm.edu	37	chr2	179472788	179472788	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gcttgtgtcagtgactcttgGgataggtggcccaggaggag	17	7	2	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr2:179472788G>A	ENST00000591111.1	-	226	48027	c.47803C>T	c.(47803-47805)Cca>Tca	p.P15935S	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P15008S|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P8703S|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P17576S|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P8636S|TTN_ENST00000460472.2_Missense_Mutation_p.P8511S|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15935	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTGACTCTTGGGATAGGTGGC	0.423																																					p.P17576S		Atlas-SNP	.											.	TTN	18412	.	0			c.C52726T						.						70	69	70					2																	179472788		1857	4095	5952	SO:0001583	missense	7273	exon276			CTCTTGGGATAGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.47803C>T	chr2.hg19:g.179472788G>A	ENSP00000465570:p.Pro15935Ser	120.0	0.0		172.0	78.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.88	2.070362	0.36566	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	6.17	6.17	0.99709	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79644	0.4481	M	0.92649	3.33	0.80722	D	1	D;D;D;D	0.63046	0.984;0.984;0.984;0.992	P;P;P;D	0.63283	0.85;0.85;0.85;0.913	T	0.82882	-0.0237	9	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	8511;8636;8703;15935	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	15008;8511;8703;8636;8511	ENSP00000343764:P15008S;ENSP00000434586:P8511S;ENSP00000340554:P8703S;ENSP00000352154:P8636S	ENSP00000340554:P8703S	P	-	1	0	TTN	179181033	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.134000	0.57990	2.941000	0.99782	0.655000	0.94253	CCA	.	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179472788	G	A	179472788	3	1	61	1	0	0	0	0	1	0	0	0	16750	1232	43	3	55315	3	TTN	2	179472788	Missense_Mutation	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10	94406450	179472788	63726585	9	7451										
BRPF1	7862	hgsc.bcm.edu	37	chr3	9776191	9776191	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	tggatgtggtgtcagaggatGaggaagcccccgaggaggcc	18	8	1	2			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr3:9776191G>A	ENST00000457855.1	+	1	378	c.367G>A	c.(367-369)Gag>Aag	p.E123K	BRPF1_ENST00000424362.1_Missense_Mutation_p.E123K|BRPF1_ENST00000302054.3_Missense_Mutation_p.E123K|BRPF1_ENST00000433861.2_Missense_Mutation_p.E123K|BRPF1_ENST00000383829.2_Missense_Mutation_p.E123K			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	123	Interaction with KAT6A and KAT6B.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					GTCAGAGGATGAGGAAGCCCC	0.562																																					p.E123K		Atlas-SNP	.											.	BRPF1	104	.	0			c.G367A						.						82	85	84					3																	9776191		2203	4300	6503	SO:0001583	missense	7862	exon2			GAGGATGAGGAAG	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"peregrin", "bromodomain-containing protein, 140kD"	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.367G>A	chr3.hg19:g.9776191G>A	ENSP00000410210:p.Glu123Lys	88.0	0.0		116.0	72.0	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	hg19	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	G	34	5.350093	0.95830	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.73	5.73	0.89815	Enhancer of polycomb-like, N-terminal (1);	0.145914	0.64402	D	0.000007	T	0.61148	0.2324	L	0.48362	1.52	0.80722	D	1	P;B;B;P	0.48016	0.904;0.384;0.226;0.582	P;B;B;P	0.57548	0.823;0.419;0.343;0.7	T	0.60622	-0.7227	10	0.66056	D	0.02	.	19.4877	0.95037	0.0:0.0:1.0:0.0	.	123;123;123;123	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	K	123	ENSP00000402485:E123K;ENSP00000398863:E123K;ENSP00000373340:E123K;ENSP00000306297:E123K;ENSP00000410210:E123K	ENSP00000306297:E123K	E	+	1	0	BRPF1	9751191	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.476000	0.97823	2.709000	0.92574	0.563000	0.77884	GAG	.	.		0.562	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		A	9776191	G	A	9776191	3	1	61	1	0	0	0	0	1	0	0	0	1522	1291	45	3	369	3	BRPF1	3	9776191	Missense_Mutation	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10		9776191	188246239	10	7452										
PRRT3	285368	hgsc.bcm.edu	37	chr3	9988526	9988526	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ccctggggtccgcgacccaaCgacgcagccgagccccaggc	13	19	0	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr3:9988526C>A	ENST00000412055.1	-	4	2460	c.2331G>T	c.(2329-2331)tcG>tcT	p.S777S	PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	777						integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						CGCGACCCAACGACGCAGCCG	0.706																																					p.S777S		Atlas-SNP	.											.	PRRT3	35	.	0			c.G2331T						.						4	5	5					3																	9988526		1846	3911	5757	SO:0001819	synonymous_variant	285368	exon4			ACCCAACGACGCA	AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"Proline-rich transmembrane proteins"	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.2331G>T	chr3.hg19:g.9988526C>A		2.0	0.0		12.0	11.0	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Silent	SNP	ENST00000412055.1	hg19	CCDS43049.1																																																																																			.	.		0.706	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351		A	9988526	C	A	9988526	2	1	61	1	0	0	0	0	0	0	0	1	12623	523	19	1		1	PRRT3	3	9988526	Silent	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	212335	9988526	188033904	11	7453										
ZCWPW2	152098	hgsc.bcm.edu	37	chr3	28566047	28566047	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	tgcagcccagaagctcctgcAggcagtctgtttgaaaacca	10	12	1	2			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr3:28566047A>T	ENST00000383768.2	+	10	1127	c.939A>T	c.(937-939)gcA>gcT	p.A313A	ZCWPW2_ENST00000421010.1_Silent_p.A313A			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	313							zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						AAGCTCCTGCAGGCAGTCTGT	0.323																																					p.A313A		Atlas-SNP	.											.	ZCWPW2	49	.	0			c.A939T						.						123	137	132					3																	28566047		2202	4298	6500	SO:0001819	synonymous_variant	152098	exon9			TCCTGCAGGCAGT	BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.939A>T	chr3.hg19:g.28566047A>T		323.0	0.0		326.0	79.0	NM_001040432		Silent	SNP	ENST00000383768.2	hg19	CCDS33723.1	.	.	.	.	.	.	.	.	.	.	A	0.886	-0.727137	0.03158	.	.	ENSG00000206559	ENST00000419130	.	.	.	6.03	2.3	0.28687	.	.	.	.	.	T	0.26774	0.0655	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.22173	-1.0224	4	.	.	.	-0.4976	5.1998	0.15258	0.7241:0.0:0.1444:0.1315	.	.	.	.	W	198	.	.	R	+	1	2	ZCWPW2	28541051	0.424000	0.25490	0.000000	0.03702	0.150000	0.21749	0.679000	0.25291	0.153000	0.19213	-0.290000	0.09829	AGG	.	.		0.323	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384		T	28566047	A	T	28566047	2	4	61	1	0	0	0	0	0	0	0	1	17613	175	7	4		4	ZCWPW2	3	28566047	Silent	SNP	A	TCGA-CC-A123-01A-11D-A12Z-10	18577521	28566047	169456383	12	7454										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37366808	37366808	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	aaagctagaggttgacttgaAtaagtctctgaaggaaaata	10	4	1	4			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr3:37366808A>G	ENST00000361924.2	+	14	3805	c.3431A>G	c.(3430-3432)aAt>aGt	p.N1144S	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.N1166S	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1144	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GTTGACTTGAATAAGTCTCTG	0.398																																					p.N1166S		Atlas-SNP	.											.	GOLGA4	173	.	0			c.A3497G						.						43	44	44					3																	37366808		2203	4298	6501	SO:0001583	missense	2803	exon15			ACTTGAATAAGTC	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.3431A>G	chr3.hg19:g.37366808A>G	ENSP00000354486:p.Asn1144Ser	207.0	0.0		225.0	123.0	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	hg19	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	A	1.943	-0.443090	0.04604	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.25250	1.81;1.82;1.83	5.12	-4.11	0.03928	.	1.537750	0.04263	N	0.340658	T	0.14570	0.0352	N	0.25380	0.74	0.09310	N	1	B;B;B;B	0.15473	0.013;0.005;0.005;0.001	B;B;B;B	0.14578	0.011;0.007;0.007;0.002	T	0.25710	-1.0124	10	0.11485	T	0.65	.	6.3196	0.21211	0.2917:0.3749:0.3334:0.0	.	1144;1144;1166;1144	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	S	1144;1166;1015	ENSP00000354486:N1144S;ENSP00000349305:N1166S;ENSP00000405842:N1015S	ENSP00000349305:N1166S	N	+	2	0	GOLGA4	37341812	0.050000	0.20438	0.005000	0.12908	0.432000	0.31715	0.397000	0.20883	-0.518000	0.06452	-0.290000	0.09829	AAT	.	.		0.398	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		G	37366808	A	G	37366808	3	3	61	1	0	0	0	0	1	0	0	0	6563	101	4	2	3555	2	GOLGA4	3	37366808	Missense_Mutation	SNP	A	TCGA-CC-A123-01A-11D-A12Z-10	8800761	37366808	160655622	13	7455										
KALRN	8997	hgsc.bcm.edu	37	chr3	124044866	124044867	+	Frame_Shift_Ins	INS	-	-	TC													0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ccgcatcatgtccgtggcttINScccgcctctctgaggccggt					rs201405841		TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr3:124044866_124044867insTC	ENST00000240874.3	+	7	1283_1284	c.1126_1127insTC	c.(1126-1128)tccfs	p.S376fs	KALRN_ENST00000460856.1_Frame_Shift_Ins_p.S376fs|KALRN_ENST00000360013.3_Frame_Shift_Ins_p.S376fs	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	376					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GTCCGTGGCTTCCCGCCTCTCT	0.535																																					p.S376fs		Atlas-INDEL	.											.,2	KALRN	556	.	0			c.1126_1127insTC						.																																			SO:0001589	frameshift_variant	8997	exon7			.	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	Exception_encountered	chr3.hg19:g.124044866_124044867insTC	ENSP00000240874:p.Ser376fs	107.0	0.0		241.0	25.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Frame_Shift_Ins	INS	ENST00000240874.3	hg19	CCDS3027.1																																																																																			.	.		0.535	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		TC	124044867	-	TC	124044866	7	5	61	1	0	1	1	0	0	0	0	0	7984	1783	62	0	1152	0	KALRN	3	124044866	Frame_Shift_Ins	INS	-	TCGA-CC-A123-01A-11D-A12Z-10	86678058	124044866	73977564	14	7456										
GMPS	8833	hgsc.bcm.edu	37	chr3	155643090	155643090	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	aagaggatcaggagaagctgAtgcaaattaccagtctgcat	11	7	2	3			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr3:155643090A>T	ENST00000496455.2	+	12	1830	c.1495A>T	c.(1495-1497)Atg>Ttg	p.M499L	GMPS_ENST00000295920.7_Missense_Mutation_p.M400L	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase	499					glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|GMP synthase (glutamine-hydrolyzing) activity (GO:0003922)|GMP synthase activity (GO:0003921)|pyrophosphatase activity (GO:0016462)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamine(DB00130)	GGAGAAGCTGATGCAAATTAC	0.408			T	MLL	AML																																p.M499L	Ovarian(153;896 1876 4149 15499 28134)	Atlas-SNP	.		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	.	GMPS	70	.	0			c.A1495T						.						111	111	111					3																	155643090		1913	4133	6046	SO:0001583	missense	8833	exon12			AAGCTGATGCAAA	U10860	CCDS46941.1	3q25.31	2013-06-18	2013-06-18		ENSG00000163655	ENSG00000163655	6.3.5.2		4378	protein-coding gene	gene with protein product	"GMP synthase"	600358	"guanine monphosphate synthetase"			8089153, 9195163	Standard	NM_003875		Approved		uc003faq.3	P49915	OTTHUMG00000158551	ENST00000496455.2:c.1495A>T	chr3.hg19:g.155643090A>T	ENSP00000419851:p.Met499Leu	643.0	1.0		1011.0	681.0	NM_003875	A8K639|B4DXV7|F8W720	Missense_Mutation	SNP	ENST00000496455.2	hg19	CCDS46941.1	.	.	.	.	.	.	.	.	.	.	A	12.17	1.858086	0.32791	.	.	ENSG00000163655	ENST00000496455;ENST00000295920;ENST00000537975;ENST00000541628	.	.	.	5.76	4.61	0.57282	GMP synthase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.27933	0.0688	N	0.05306	-0.075	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07616	-1.0763	9	0.09338	T	0.73	-17.9133	11.5552	0.50743	0.9307:0.0:0.0693:0.0	.	400;499	F8W720;P49915	.;GUAA_HUMAN	L	499;400;448;499	.	ENSP00000295920:M400L	M	+	1	0	GMPS	157125784	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.210000	0.95106	1.018000	0.39521	0.533000	0.62120	ATG	.	.		0.408	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351260.2			T	155643090	A	T	155643090	3	4	61	1	0	0	0	0	1	0	0	0	6506	333	12	4	1541	4	GMPS	3	155643090	Missense_Mutation	SNP	A	TCGA-CC-A123-01A-11D-A12Z-10	31598224	155643090	42379340	15	7457										
CCDC39	339829	hgsc.bcm.edu	37	chr3	180381668	180381668	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	actgtacctgtgtaattgagAgctcttgcttaacatttttg	8	7	1	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr3:180381668A>C	ENST00000442201.2	-	2	316	c.197T>G	c.(196-198)cTc>cGc	p.L66R	CCDC39_ENST00000273654.4_Missense_Mutation_p.L150R	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	66					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TGTAATTGAGAGCTCTTGCTT	0.343																																					p.L66R		Atlas-SNP	.											.	CCDC39	242	.	0			c.T197G						.						138	129	131					3																	180381668		1842	4096	5938	SO:0001583	missense	339829	exon2			ATTGAGAGCTCTT	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.197T>G	chr3.hg19:g.180381668A>C	ENSP00000405708:p.Leu66Arg	137.0	0.0		168.0	13.0	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	hg19	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.100024	0.76983	.	.	ENSG00000145075	ENST00000273654;ENST00000442201;ENST00000471307	D	0.82167	-1.58	6.07	6.07	0.98685	.	0.303342	0.40064	N	0.001199	D	0.84492	0.5484	L	0.60455	1.87	0.34811	D	0.737735	P	0.40180	0.705	P	0.46172	0.506	D	0.89722	0.3920	10	0.59425	D	0.04	-3.9915	14.0082	0.64478	1.0:0.0:0.0:0.0	.	66	Q9UFE4	CCD39_HUMAN	R	150;66;48	ENSP00000418702:L48R	ENSP00000273654:L150R	L	-	2	0	CCDC39	181864362	0.976000	0.34144	0.122000	0.21767	0.954000	0.61252	6.156000	0.71840	2.330000	0.79161	0.477000	0.44152	CTC	.	.		0.343	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		C	180381668	A	C	180381668	3	2	61	1	0	0	0	0	1	0	0	0	2813	304	11	5	2704	5	CCDC39	3	180381668	Missense_Mutation	SNP	A	TCGA-CC-A123-01A-11D-A12Z-10	24738578	180381668	17640762	16	7458										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55260049	55260057	+	In_Frame_Del	DEL	CAATGTTGA	CAATGTTGA	-													0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ctctgcttctacccagacttCaatgttgacaaaatacacag							TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	CAATGTTGA	CAATGTTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr5:55260049_55260057delCAATGTTGA	ENST00000381298.2	-	6	887_895	c.575_583delTCAACATTG	c.(574-585)gtcaacattgaa>gaa	p.VNI192del	IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000502326.3_In_Frame_Del_p.VNI192del|IL6ST_ENST00000522633.2_In_Frame_Del_p.VNI192del|IL6ST_ENST00000336909.5_In_Frame_Del_p.VNI192del|IL6ST_ENST00000381287.4_In_Frame_Del_p.VNI192del|IL6ST_ENST00000536319.1_In_Frame_Del_p.VNI192del|IL6ST_ENST00000396816.1_In_Frame_Del_p.STL50del|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000381294.3_In_Frame_Del_p.VNI192del|IL6ST_ENST00000577363.1_5'UTR	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	192	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)	p.N193delN(1)		breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				ACCCAGACTTCAATGTTGACAAAATACAC	0.378			O		hepatocellular ca																																p.192_195del		Atlas-Indel,Pindel	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	1	Deletion - In frame(1)	liver(1)	c.576_584del						.																																			SO:0001651	inframe_deletion	3572	exon6			.	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.575_583delTCAACATTG	chr5.hg19:g.55260049_55260057delCAATGTTGA	ENSP00000370698:p.Val192_Ile194del	296.0	0.0		271.0	73.0	NM_002184	A0N0L4|Q5FC04|Q9UQ41	In_Frame_Del	DEL	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.		0.378	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		-	55260057	CAATGTTGA	-	55260049	7	5	61	1	0	1	0	1	0	0	0	0	7712	835	29	0	2221	0	IL6ST	5	55260049	In_Frame_Del	DEL	CAATGTTGA	TCGA-CC-A123-01A-11D-A12Z-10		55260049	125655211	17	7459										
RASA1	5921	hgsc.bcm.edu	37	chr5	86637134	86637134	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	aagaagatccacatgaaggaAaaatgtgagtttgtgttaat	10	3	0	4			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr5:86637134A>T	ENST00000274376.6	+	6	1609	c.1045A>T	c.(1045-1047)Aaa>Taa	p.K349*	RASA1_ENST00000456692.2_Nonsense_Mutation_p.K172*|RASA1_ENST00000506290.1_Nonsense_Mutation_p.K183*|RASA1_ENST00000512763.1_Nonsense_Mutation_p.K182*	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	349					blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		ACATGAAGGAAAAATGTGAGT	0.234																																					p.K349X		Atlas-SNP	.											.	RASA1	213	.	0			c.A1045T						.						8	9	8					5																	86637134		1184	2214	3398	SO:0001587	stop_gained	5921	exon6			GAAGGAAAAATGT		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.1045A>T	chr5.hg19:g.86637134A>T	ENSP00000274376:p.Lys349*	167.0	0.0		145.0	49.0	NM_002890	B2R6W3|Q9UDI1	Nonsense_Mutation	SNP	ENST00000274376.6	hg19	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	A	44	10.633254	0.99441	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	.	.	.	5.01	5.01	0.66863	.	0.045776	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.6756	0.68978	1.0:0.0:0.0:0.0	.	.	.	.	X	349;382;172;182;183	.	ENSP00000274376:K349X	K	+	1	0	RASA1	86672890	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.121000	0.94375	2.016000	0.59253	0.533000	0.62120	AAA	.	.		0.234	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		T	86637134	A	T	86637134	4	4	61	1	0	0	0	0	0	1	0	0	13075	15	1	4	1079	4	RASA1	5	86637134	Nonsense_Mutation	SNP	A	TCGA-CC-A123-01A-11D-A12Z-10	31377085	86637134	94278126	18	7460										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141036086	141036086	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ctcactttcttctccttgagCagcagcaggcagcggccacg	10	15	3	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr5:141036086C>A	ENST00000239440.4	-	27	3839	c.3774G>T	c.(3772-3774)ctG>ctT	p.L1258L	ARAP3_ENST00000508305.1_Silent_p.L1089L|ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000513878.1_Silent_p.L920L	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1258	PH 3. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						TCTCCTTGAGCAGCAGCAGGC	0.647																																					p.L1258L		Atlas-SNP	.											.	ARAP3	139	.	0			c.G3774T						.						19	21	20					5																	141036086		2203	4300	6503	SO:0001819	synonymous_variant	64411	exon27			CTTGAGCAGCAGC	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3774G>T	chr5.hg19:g.141036086C>A		86.0	0.0		92.0	35.0	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	hg19	CCDS4266.1																																																																																			.	.		0.647	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		A	141036086	C	A	141036086	2	1	61	1	0	0	0	0	0	0	0	1	840	697	25	3		3	ARAP3	5	141036086	Silent	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	54398952	141036086	39879174	19	7461										
B3GAT2	135152	hgsc.bcm.edu	37	chr6	71603895	71603895	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	taccagccaacaactttgccGttttccaccagcggacgttc	7	15	0	0	rs371527631		TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr6:71603895G>A	ENST00000230053.6	-	2	1280	c.672C>T	c.(670-672)aaC>aaT	p.N224N		NM_080742.2	NP_542780.1	Q9NPZ5	B3GA2_HUMAN	beta-1,3-glucuronyltransferase 2	224					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						CAACTTTGCCGTTTTCCACCA	0.572																																					p.N224N		Atlas-SNP	.											.	B3GAT2	33	.	0			c.C672T						.						107	86	93					6																	71603895		2203	4300	6503	SO:0001819	synonymous_variant	135152	exon2			TTTGCCGTTTTCC	AB075843	CCDS4974.1	6q12	2014-07-08	2014-07-08		ENSG00000112309	ENSG00000112309	2.4.1.135	"Beta-1,3-glucuronyltransferases"	922	protein-coding gene	gene with protein product	"glucuronosyltransferase S", "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2"	607497				12383500	Standard	NM_080742		Approved	GlcAT-S	uc003pfv.3	Q9NPZ5	OTTHUMG00000014997	ENST00000230053.6:c.672C>T	chr6.hg19:g.71603895G>A		61.0	0.0		67.0	18.0	NM_080742	Q5JS09|Q8TF38|Q96NK4	Silent	SNP	ENST00000230053.6	hg19	CCDS4974.1																																																																																			.	.		0.572	B3GAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041150.2	NM_080742		A	71603895	G	A	71603895	2	1	61	1	0	0	0	0	0	0	0	1	1254	1136	40	1		1	B3GAT2	6	71603895	Silent	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10		71603895	99511172	20	7462										
HDAC2	3066	hgsc.bcm.edu	37	chr6	114264582	114264582	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ttctttgctcctttcttatgAtcagccacatttcttcgacc	4	13	4	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr6:114264582A>T	ENST00000519065.1	-	12	1687	c.1311T>A	c.(1309-1311)gaT>gaA	p.D437E	HDAC2_ENST00000368632.2_Missense_Mutation_p.D407E|HDAC2_ENST00000398283.2_Missense_Mutation_p.D531E|HDAC2_ENST00000519108.1_Missense_Mutation_p.D407E			Q92769	HDAC2_HUMAN	histone deacetylase 2	437					ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	ctttcttATGATCAGCCACAT	0.378																																					p.D437E		Atlas-SNP	.											.	HDAC2	102	.	0			c.T1311A						.						168	156	160					6																	114264582		1866	4104	5970	SO:0001583	missense	3066	exon12			CTTATGATCAGCC	U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.1311T>A	chr6.hg19:g.114264582A>T	ENSP00000430432:p.Asp437Glu	198.0	0.0		194.0	71.0	NM_001527	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Missense_Mutation	SNP	ENST00000519065.1	hg19	CCDS43493.2	.	.	.	.	.	.	.	.	.	.	A	14.99	2.700563	0.48307	.	.	ENSG00000196591	ENST00000519065;ENST00000398283;ENST00000519108;ENST00000368632	T;T;T;T	0.73047	-0.69;-0.71;-0.69;-0.69	6.16	3.79	0.43588	.	0.073236	0.56097	N	0.000032	T	0.30198	0.0757	N	0.16098	0.37	0.42098	D	0.99132	B;B	0.19583	0.0;0.037	B;B	0.18263	0.001;0.021	T	0.09773	-1.0659	10	0.14656	T	0.56	-45.4507	10.4506	0.44520	0.8697:0.0:0.1303:0.0	.	407;437	B3KRS5;Q92769	.;HDAC2_HUMAN	E	437;531;407;407	ENSP00000430432:D437E;ENSP00000381331:D531E;ENSP00000430008:D407E;ENSP00000357621:D407E	ENSP00000357621:D407E	D	-	3	2	HDAC2	114371275	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.696000	0.47052	0.567000	0.29293	-0.256000	0.11100	GAT	.	.		0.378	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2			T	114264582	A	T	114264582	3	4	61	1	0	0	0	0	1	0	0	0	7016	330	12	4	167	4	HDAC2	6	114264582	Missense_Mutation	SNP	A	TCGA-CC-A123-01A-11D-A12Z-10	42660687	114264582	56850485	21	7463										
MTRF1L	54516	hgsc.bcm.edu	37	chr6	153316373	153316374	+	Frame_Shift_Ins	INS	-	-	TT													0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gatgtaaacaacattgcctcINSctgacctccaactcctgcag							TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr6:153316373_153316374insTT	ENST00000367233.5	-	3	419_420	c.420_421insAA	c.(418-423)caggagfs	p.E141fs	MTRF1L_ENST00000367230.1_Intron|MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367231.5_Frame_Shift_Ins_p.E141fs	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	141						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		AACATTGCCTCCTGACCTCCAA	0.342																																					p.E141fs		Atlas-INDEL	.											.	MTRF1L	21	.	0			c.421_422insAA						.																																			SO:0001589	frameshift_variant	54516	exon3			.	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.420_421insAA	chr6.hg19:g.153316373_153316374insTT	ENSP00000356202:p.Glu141fs	360.0	0.0		339.0	32.0	NM_001114184	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Frame_Shift_Ins	INS	ENST00000367233.5	hg19	CCDS5243.1																																																																																			.	.		0.342	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041		TT	153316374	-	TT	153316373	7	5	61	1	0	1	1	0	0	0	0	0	9969	864	30	0	741	0	MTRF1L	6	153316373	Frame_Shift_Ins	INS	-	TCGA-CC-A123-01A-11D-A12Z-10	39051791	153316373	17798694	22	7464										
HECW1	23072	hgsc.bcm.edu	37	chr7	43484350	43484350	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gcaggctgcagctgcgggccTcggtgaagagaaaaagcagg	17	9	0	2			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr7:43484350T>A	ENST00000395891.2	+	11	2184	c.1579T>A	c.(1579-1581)Tcg>Acg	p.S527T	HECW1_ENST00000453890.1_Missense_Mutation_p.S527T	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	527					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						GCTGCGGGCCTCGGTGAAGAG	0.652																																					p.S527T		Atlas-SNP	.											.	HECW1	540	.	0			c.T1579A						.						26	34	31					7																	43484350		2132	4229	6361	SO:0001583	missense	23072	exon11			CGGGCCTCGGTGA	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.1579T>A	chr7.hg19:g.43484350T>A	ENSP00000379228:p.Ser527Thr	58.0	0.0		73.0	20.0	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	hg19	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	T	2.333	-0.353009	0.05173	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.30448	1.53;1.54	5.32	4.15	0.48705	.	.	.	.	.	T	0.19644	0.0472	L	0.27053	0.805	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20505	-1.0273	9	0.30854	T	0.27	.	5.9688	0.19340	0.2829:0.0:0.1247:0.5924	.	527;527	B4DH42;Q76N89	.;HECW1_HUMAN	T	527	ENSP00000379228:S527T;ENSP00000407774:S527T	ENSP00000265522:S527T	S	+	1	0	HECW1	43450875	0.002000	0.14202	0.029000	0.17559	0.126000	0.20510	0.651000	0.24873	0.838000	0.34948	0.533000	0.62120	TCG	.	.		0.652	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43484350	T	A	43484350	3	1	61	1	0	0	0	0	1	0	0	0	7051	1551	54	4	1613	4	HECW1	7	43484350	Missense_Mutation	SNP	T	TCGA-CC-A123-01A-11D-A12Z-10		43484350	115654313	23	7465										
MYO1G	64005	hgsc.bcm.edu	37	chr7	45005391	45005391	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	cgcaccttgtgtctccggaaCcagcgcatgatggtgtagat	12	11	1	2			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr7:45005391C>T	ENST00000258787.7	-	17	2362	c.2226G>A	c.(2224-2226)tgG>tgA	p.W742*		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	742						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						GTCTCCGGAACCAGCGCATGA	0.672																																					p.W742X		Atlas-SNP	.											.	MYO1G	86	.	0			c.G2226A						.						52	52	52					7																	45005391		2203	4300	6503	SO:0001587	stop_gained	64005	exon17			CCGGAACCAGCGC	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"Myosins / Myosin superfamily : Class I"	13880	protein-coding gene	gene with protein product	"minor histocompatibility antigen HA-2"	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.2226G>A	chr7.hg19:g.45005391C>T	ENSP00000258787:p.Trp742*	16.0	0.0		23.0	14.0	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Nonsense_Mutation	SNP	ENST00000258787.7	hg19	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	C	39	7.449687	0.98292	.	.	ENSG00000136286	ENST00000258787	.	.	.	3.96	0.357	0.16079	.	0.485344	0.15512	U	0.258512	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	.	14.1344	0.65276	0.0:0.2823:0.7177:0.0	.	.	.	.	X	742	.	ENSP00000258787:W742X	W	-	3	0	MYO1G	44971916	0.998000	0.40836	1.000000	0.80357	0.976000	0.68499	1.310000	0.33551	0.233000	0.21120	0.462000	0.41574	TGG	.	.		0.672	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2			T	45005391	C	T	45005391	4	4	61	1	0	0	0	0	0	1	0	0	10083	508	18	3	854	3	MYO1G	7	45005391	Nonsense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	1521041	45005391	114133272	24	7466										
ASNS	440	hgsc.bcm.edu	37	chr7	97498423	97498423	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	catagcactcagacactgaaCagaaaggcaatcatcactgc	7	12	3	3			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr7:97498423C>G	ENST00000394309.3	-	3	517	c.46G>C	c.(46-48)Gtt>Ctt	p.V16L	ASNS_ENST00000422745.1_Intron|ASNS_ENST00000437628.1_Intron|ASNS_ENST00000455086.1_Intron|ASNS_ENST00000444334.1_Intron|ASNS_ENST00000394308.3_Missense_Mutation_p.V16L|ASNS_ENST00000175506.4_Missense_Mutation_p.V16L	NM_133436.3	NP_597680.2	P08243	ASNS_HUMAN	asparagine synthetase (glutamine-hydrolyzing)	16	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|asparagine biosynthetic process (GO:0006529)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular protein metabolic process (GO:0044267)|cellular response to glucose starvation (GO:0042149)|cellular response to hormone stimulus (GO:0032870)|endoplasmic reticulum unfolded protein response (GO:0030968)|glutamine metabolic process (GO:0006541)|L-asparagine biosynthetic process (GO:0070981)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|positive regulation of mitotic cell cycle (GO:0045931)|response to amino acid (GO:0043200)|response to follicle-stimulating hormone (GO:0032354)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)|ATP binding (GO:0005524)|cofactor binding (GO:0048037)			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	AGACACTGAACAGAAAGGCAA	0.433																																					p.V16L	Melanoma(70;6 1280 3108 3799 51123)|GBM(6;275 291 425 9929 27738)	Atlas-SNP	.											.	ASNS	97	.	0			c.G46C						.						75	65	68					7																	97498423		2203	4300	6503	SO:0001583	missense	440	exon3			ACTGAACAGAAAG	M27396	CCDS5652.1, CCDS55131.1, CCDS55132.1	7q21.3	2012-10-02	2010-05-07		ENSG00000070669	ENSG00000070669	6.3.5.4		753	protein-coding gene	gene with protein product		108370	"asparagine synthetase"				Standard	NM_001673		Approved		uc003uov.4	P08243	OTTHUMG00000022892	ENST00000394309.3:c.46G>C	chr7.hg19:g.97498423C>G	ENSP00000377846:p.Val16Leu	221.0	0.0		186.0	55.0	NM_133436	A4D1I8|B4DXZ1|B7ZAA9|D6W5R3|E9PCI3|E9PCX6|P08184|Q15666|Q549T9|Q96HD0	Missense_Mutation	SNP	ENST00000394309.3	hg19	CCDS5652.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.291929	0.23564	.	.	ENSG00000070669	ENST00000175506;ENST00000394309;ENST00000394308;ENST00000442734;ENST00000437657;ENST00000448127;ENST00000451771;ENST00000414884	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.29	4.29	0.51040	Glutamine amidotransferase, type II (1);	0.222920	0.36778	N	0.002411	T	0.29093	0.0723	L	0.29908	0.895	0.53688	D	0.999972	B	0.25235	0.121	B	0.20767	0.031	T	0.07385	-1.0775	10	0.11182	T	0.66	-10.6197	14.6248	0.68614	0.0:1.0:0.0:0.0	.	16	P08243	ASNS_HUMAN	L	16	ENSP00000175506:V16L;ENSP00000377846:V16L;ENSP00000377845:V16L;ENSP00000400422:V16L	ENSP00000175506:V16L	V	-	1	0	ASNS	97336359	1.000000	0.71417	0.996000	0.52242	0.961000	0.63080	4.424000	0.59868	2.120000	0.65058	0.555000	0.69702	GTT	.	.		0.433	ASNS-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333645.1	NM_001673, NM_183356		G	97498423	C	G	97498423	3	3	61	1	0	0	0	0	1	0	0	0	1048	478	17	4	1683	4	ASNS	7	97498423	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	52493032	97498423	61640240	25	7467										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113662399	113662399	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	tgagttattaccatcacaggTtggaagtggatgactccacc	10	9	1	2			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr8:113662399T>C	ENST00000297405.5	-	19	3428	c.3184A>G	c.(3184-3186)Acc>Gcc	p.T1062A	CSMD3_ENST00000455883.2_Missense_Mutation_p.T958A|CSMD3_ENST00000352409.3_Missense_Mutation_p.T1062A|CSMD3_ENST00000343508.3_Missense_Mutation_p.T1022A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1062	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CCATCACAGGTTGGAAGTGGA	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.T1062A		Atlas-SNP	.											CSMD3_ENST00000343508,colon,carcinoma,0,2	CSMD3	2325	.	0			c.A3184G						.						99	97	97					8																	113662399		2203	4300	6503	SO:0001583	missense	114788	exon19			CACAGGTTGGAAG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3184A>G	chr8.hg19:g.113662399T>C	ENSP00000297405:p.Thr1062Ala	143.0	1.0		363.0	84.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.238031	0.39598	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.88	5.88	0.94601	Complement control module (2);Sushi/SCR/CCP (3);	0.068119	0.56097	D	0.000023	T	0.65481	0.2695	L	0.58810	1.83	0.29851	N	0.828449	P;P;B	0.39903	0.694;0.604;0.09	P;P;B	0.45712	0.452;0.491;0.096	T	0.63537	-0.6615	10	0.21540	T	0.41	.	16.2824	0.82697	0.0:0.0:0.0:1.0	.	958;1062;1022	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	A	1022;1062;402;958;1062	ENSP00000345799:T1022A;ENSP00000297405:T1062A;ENSP00000341558:T402A;ENSP00000412263:T958A;ENSP00000343124:T1062A	ENSP00000297405:T1062A	T	-	1	0	CSMD3	113731575	1.000000	0.71417	0.921000	0.36526	0.277000	0.26821	5.115000	0.64655	2.250000	0.74265	0.533000	0.62120	ACC	.	.		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113662399	T	C	113662399	3	2	61	1	0	0	0	0	1	0	0	0	3948	1725	60	2	8151	2	CSMD3	8	113662399	Missense_Mutation	SNP	T	TCGA-CC-A123-01A-11D-A12Z-10		113662399	32701623	26	7468										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116616801	116616801	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	tgctgcttgccataatgttcTagcagtttaagtgagctaga	10	7	1	2			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr8:116616801T>A	ENST00000220888.5	-	3	1515	c.1356A>T	c.(1354-1356)ctA>ctT	p.L452L	TRPS1_ENST00000519076.1_Intron|TRPS1_ENST00000395715.3_Silent_p.L465L|TRPS1_ENST00000519674.1_Silent_p.L452L|TRPS1_ENST00000520276.1_Silent_p.L456L			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	452					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CATAATGTTCTAGCAGTTTAA	0.448									Langer-Giedion syndrome																												p.L465L		Atlas-SNP	.											.	TRPS1	516	.	0			c.A1395T						.						55	53	54					8																	116616801		1942	4147	6089	SO:0001819	synonymous_variant	7227	exon4	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	ATGTTCTAGCAGT	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.1356A>T	chr8.hg19:g.116616801T>A		106.0	0.0		238.0	63.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	hg19																																																																																				.	.		0.448	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		A	116616801	T	A	116616801	2	1	61	1	0	0	0	0	0	0	0	1	16608	1509	53	4		4	TRPS1	8	116616801	Silent	SNP	T	TCGA-CC-A123-01A-11D-A12Z-10	2954402	116616801	29747221	27	7469										
OC90	729330	hgsc.bcm.edu	37	chr8	133053841	133053841	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	aaccatagtcttcaaagtctCgggggcagagaccagccaca	10	12	3	1	rs372434452		TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr8:133053841C>A	ENST00000443356.2	-	5	361	c.275G>T	c.(274-276)cGa>cTa	p.R92L	OC90_ENST00000262283.5_Missense_Mutation_p.R288L|OC90_ENST00000254627.3_Missense_Mutation_p.R92L|OC90_ENST00000603859.1_Missense_Mutation_p.R92L			Q02509	OC90_HUMAN	otoconin 90	92	Phospholipase A2-like 1.				lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			TTCAAAGTCTCGGGGGCAGAG	0.527																																					p.R92L		Atlas-SNP	.											.	OC90	163	.	0			c.G275T						.						46	47	47					8																	133053841		1998	4165	6163	SO:0001583	missense	729330	exon5			AAGTCTCGGGGGC	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.275G>T	chr8.hg19:g.133053841C>A	ENSP00000390050:p.Arg92Leu	151.0	0.0		270.0	85.0	NM_001080399	B4DNG8	Missense_Mutation	SNP	ENST00000443356.2	hg19		.	.	.	.	.	.	.	.	.	.	C	20.9	4.073290	0.76415	.	.	ENSG00000253117;ENSG00000253117;ENSG00000258417	ENST00000254627;ENST00000443356;ENST00000262283	T;T;T	0.23552	1.9;1.9;1.9	5.88	4.9	0.64082	Phospholipase A2 (3);	0.204155	0.39909	N	0.001230	T	0.26011	0.0634	N	0.04880	-0.145	0.34035	D	0.654297	D;D	0.89917	1.0;1.0	D;D	0.78314	0.985;0.991	T	0.27331	-1.0077	10	0.35671	T	0.21	-24.1919	10.1278	0.42661	0.0:0.8788:0.0:0.1212	.	92;92	Q02509-2;Q02509	.;OC90_HUMAN	L	92;92;288	ENSP00000254627:R92L;ENSP00000390050:R92L;ENSP00000262283:R288L	ENSP00000254627:R92L	R	-	2	0	RP11-240B13.2;OC90	133123023	0.991000	0.36638	0.998000	0.56505	0.991000	0.79684	2.905000	0.48727	2.790000	0.95986	0.591000	0.81541	CGA	.	.		0.527	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399		A	133053841	C	A	133053841	3	1	61	1	0	0	0	0	1	0	0	0	10823	884	31	1	1198	1	OC90	8	133053841	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	16437040	133053841	13310181	28	7470										
LCN2	3934	hgsc.bcm.edu	37	chr9	130912582	130912582	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ctcagagaagacaaagacccGcaaaagatgtatgccaccat	8	11	1	4			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr9:130912582G>A	ENST00000373017.1	+	3	441	c.204G>A	c.(202-204)ccG>ccA	p.P68P	LCN2_ENST00000470902.1_Intron|LCN2_ENST00000372998.1_Silent_p.P68P|LCN2_ENST00000540948.1_Silent_p.P68P|LCN2_ENST00000277480.2_Silent_p.P68P|LCN2_ENST00000373013.2_Silent_p.P68P			P80188	NGAL_HUMAN	lipocalin 2	68					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|small molecule binding (GO:0036094)|transporter activity (GO:0005215)			central_nervous_system(1)|lung(3)|prostate(2)|skin(1)|urinary_tract(1)	8						ACAAAGACCCGCAAAAGATGT	0.512																																					p.P68P		Atlas-SNP	.											.	LCN2	12	.	0			c.G204A						.						168	144	152					9																	130912582		2203	4300	6503	SO:0001819	synonymous_variant	3934	exon2			AGACCCGCAAAAG		CCDS6892.1	9q34	2011-10-24	2007-12-18		ENSG00000148346	ENSG00000148346		"Lipocalins"	6526	protein-coding gene	gene with protein product	"oncogene 24p3", "neutrophil gelatinase-associated lipocalin", "siderocalin"	600181	"lipocalin 2 (oncogene 24p3)"			7683678	Standard	NM_005564		Approved	NGAL, 24p3	uc004bto.1	P80188	OTTHUMG00000020734	ENST00000373017.1:c.204G>A	chr9.hg19:g.130912582G>A		178.0	0.0		232.0	111.0	NM_005564	A6NII8|B4DWV4|B7ZAA2|P30150|Q5SYV9|Q5SYW0|Q6FGL5|Q92683	Silent	SNP	ENST00000373017.1	hg19	CCDS6892.1																																																																																			.	.		0.512	LCN2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054375.1	NM_005564		A	130912582	G	A	130912582	2	1	61	1	0	0	0	0	0	0	0	1	8693	1074	38	1		1	LCN2	9	130912582	Silent	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10		130912582	10300849	29	7471										
C9orf96	169436	hgsc.bcm.edu	37	chr9	136269044	136269044	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	agcccggcccctttctgcagGctgcatcaaggagcagcagt	12	14	2	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr9:136269044G>T	ENST00000371957.3	+	16	1711	c.1604G>T	c.(1603-1605)gGc>gTc	p.G535V	C9orf96_ENST00000371955.1_Splice_Site_p.G68V	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		535							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CTTTCTGCAGGCTGCATCAAG	0.667																																					p.G535V		Atlas-SNP	.											.	C9orf96	77	.	0			c.G1604T						.						39	43	42					9																	136269044		2203	4300	6503	SO:0001630	splice_region_variant	169436	exon16			CTGCAGGCTGCAT																												ENST00000371957.3:c.1604-1G>T	chr9.hg19:g.136269044G>T		34.0	0.0		49.0	14.0	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	hg19	CCDS35169.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.021670	0.54576	.	.	ENSG00000198870	ENST00000371957;ENST00000371955	T;T	0.51071	0.72;0.76	5.13	4.23	0.50019	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.63780	0.2540	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.63256	-0.6678	9	.	.	.	.	12.6603	0.56809	0.0803:0.0:0.9197:0.0	.	535	Q8NE28	SGK71_HUMAN	V	535;68	ENSP00000361025:G535V;ENSP00000361023:G68V	.	G	+	2	0	C9orf96	135258865	1.000000	0.71417	1.000000	0.80357	0.301000	0.27625	5.846000	0.69444	1.134000	0.42165	0.561000	0.74099	GGC	.	.		0.667	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		Missense_Mutation	T	136269044	G	T	136269044	5	4	61	1	0	0	0	0	0	0	1	0	2510	1217	42	3	1666	3	C9orf96	9	136269044	Splice_Site	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10	5356462	136269044	4944387	30	7472										
TUBB8	347688	hgsc.bcm.edu	37	chr10	94784	94784	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	acgttgatgcgctccagctgCaggtggctgtccccgtggta	14	12	0	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr10:94784C>A	ENST00000309812.4	-	2	188	c.126G>T	c.(124-126)ctG>ctT	p.L42L	TUBB8_ENST00000447903.2_5'UTR|TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000332708.5_Intron	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	42					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		GCTCCAGCTGCAGGTGGCTGT	0.647																																					p.L42L	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.G126T						.						30	27	28					10																	94784		2199	4298	6497	SO:0001819	synonymous_variant	347688	exon2			CAGCTGCAGGTGG	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"Tubulins"	20773	protein-coding gene	gene with protein product	"class VIII beta-tubulin"						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.126G>T	chr10.hg19:g.94784C>A		38.0	0.0		63.0	30.0	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	hg19	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	C	2.674	-0.276995	0.05679	.	.	ENSG00000173876	ENST00000272035	.	.	.	0.109	0.109	0.14578	.	.	.	.	.	T	0.59459	0.2195	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59193	-0.7500	5	0.87932	D	0	.	5.9913	0.19465	0.0:0.9994:0.0:6.0E-4	.	.	.	.	F	17	.	ENSP00000272035:C17F	C	-	2	0	RP11-631M21.2	84784	1.000000	0.71417	0.021000	0.16686	0.021000	0.10359	0.879000	0.28146	0.181000	0.19994	0.184000	0.17185	TGC	.	.		0.647	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987		A	94784	C	A	94784	2	1	61	1	0	0	0	0	0	0	0	1	16776	697	25	3		3	TUBB8	10	94784	Silent	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10		94784	135439963	31	7473										
PCDH15	65217	hgsc.bcm.edu	37	chr10	56106175	56106177	+	In_Frame_Del	DEL	CAT	CAT	-													0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ctctatctgtccatttggtcCatcatctatatctgtagctc							TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr10:56106175_56106177delCAT	ENST00000320301.6	-	6	936_938	c.542_544delATG	c.(541-546)gatgga>gga	p.D181del	PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000414778.1_In_Frame_Del_p.D186del|PCDH15_ENST00000395430.1_In_Frame_Del_p.D181del|PCDH15_ENST00000395433.1_In_Frame_Del_p.D159del|PCDH15_ENST00000361849.3_In_Frame_Del_p.D181del|PCDH15_ENST00000373955.1_In_Frame_Del_p.D181del|PCDH15_ENST00000395440.1_In_Frame_Del_p.D181del|PCDH15_ENST00000437009.1_In_Frame_Del_p.D181del|PCDH15_ENST00000373965.2_In_Frame_Del_p.D181del|PCDH15_ENST00000395438.1_In_Frame_Del_p.D181del|AC013737.1_ENST00000583830.1_RNA|PCDH15_ENST00000395432.2_In_Frame_Del_p.D181del|PCDH15_ENST00000395446.1_In_Frame_Del_p.D181del|PCDH15_ENST00000373957.3_In_Frame_Del_p.D159del|PCDH15_ENST00000395445.1_In_Frame_Del_p.D181del|PCDH15_ENST00000395442.1_In_Frame_Del_p.D181del	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	181	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CCATTTGGTCCATCATCTATATC	0.315										HNSCC(58;0.16)																											p.186_187del		Atlas-Indel,Pindel	.											.	PCDH15	1715	.	0			c.558_560del						.																																			SO:0001651	inframe_deletion	65217	exon7			.	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.542_544delATG	chr10.hg19:g.56106178_56106180delCAT	ENSP00000322604:p.Asp181del	134.0	0.0		158.0	62.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	In_Frame_Del	DEL	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.		0.315	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		-	56106177	CAT	-	56106175	7	5	61	1	0	1	0	1	0	0	0	0	11520	603	21	0	7079	0	PCDH15	10	56106175	In_Frame_Del	DEL	CAT	TCGA-CC-A123-01A-11D-A12Z-10	56011391	56106175	79428572	32	7474										
USP54	159195	hgsc.bcm.edu	37	chr10	75277370	75277370	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	tgctgtggggcagatgactcTggagatagtgatgagtgtga	17	4	1	6			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr10:75277370T>C	ENST00000339859.4	-	19	2914	c.2814A>G	c.(2812-2814)ccA>ccG	p.P938P	RP11-137L10.6_ENST00000600206.1_RNA|RP11-137L10.6_ENST00000593790.1_RNA|USP54_ENST00000497106.1_5'UTR|USP54_ENST00000394811.2_Silent_p.P26P|USP54_ENST00000422491.2_Silent_p.P120P|RP11-137L10.6_ENST00000595069.1_RNA|USP54_ENST00000428547.1_Silent_p.P788P|USP54_ENST00000408019.1_Silent_p.P938P|RP11-137L10.6_ENST00000597958.1_RNA			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	938					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					CAGATGACTCTGGAGATAGTG	0.517																																					p.P938P	Colon(195;880 2046 8854 25025 38456)	Atlas-SNP	.											.	USP54	178	.	0			c.A2814G						.						77	71	73					10																	75277370		2203	4300	6503	SO:0001819	synonymous_variant	159195	exon18			TGACTCTGGAGAT	AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"Ubiquitin-specific peptidases"	23513	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 29", "ubiquitin specific protease 54"	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.2814A>G	chr10.hg19:g.75277370T>C		170.0	0.0		260.0	137.0	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Silent	SNP	ENST00000339859.4	hg19	CCDS7329.2																																																																																			.	.		0.517	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		C	75277370	T	C	75277370	2	2	61	1	0	0	0	0	0	0	0	1	17100	1567	55	2		2	USP54	10	75277370	Silent	SNP	T	TCGA-CC-A123-01A-11D-A12Z-10	19171195	75277370	60257377	33	7475										
NLRP6	171389	hgsc.bcm.edu	37	chr11	281055	281055	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	acgggccccggttgcagggcGacctgcgcaatctgtgccgc	15	15	1	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr11:281055G>C	ENST00000312165.5	+	4	1321	c.1321G>C	c.(1321-1323)Gac>Cac	p.D441H	NLRP6_ENST00000534750.1_Missense_Mutation_p.D441H	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	441	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		GTTGCAGGGCGACCTGCGCAA	0.657																																					p.D441H		Atlas-SNP	.											.	NLRP6	4	.	0			c.G1321C						.						57	65	62					11																	281055		2202	4296	6498	SO:0001583	missense	171389	exon4			CAGGGCGACCTGC	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"Nucleotide-binding domain and leucine rich repeat containing"	22944	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"	609650	"NACHT, leucine rich repeat and PYD containing 6"	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.1321G>C	chr11.hg19:g.281055G>C	ENSP00000309767:p.Asp441His	44.0	0.0		72.0	17.0	NM_138329	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	hg19	CCDS7693.1	.	.	.	.	.	.	.	.	.	.	G	1.891	-0.455583	0.04540	.	.	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.75154	-0.91;-0.9	3.26	1.21	0.21127	NACHT nucleoside triphosphatase (1);	0.195037	0.25338	N	0.031390	T	0.49525	0.1562	N	0.04508	-0.205	0.09310	N	1	B;P	0.45240	0.007;0.854	B;B	0.43274	0.002;0.414	T	0.46638	-0.9177	10	0.30854	T	0.27	.	7.304	0.26436	0.0:0.186:0.6225:0.1915	.	441;441	E9PJZ8;P59044	.;NALP6_HUMAN	H	441	ENSP00000433617:D441H;ENSP00000309767:D441H	ENSP00000309767:D441H	D	+	1	0	NLRP6	271055	0.000000	0.05858	0.068000	0.19968	0.563000	0.35712	0.153000	0.16323	0.327000	0.23409	0.455000	0.32223	GAC	.	.		0.657	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		C	281055	G	C	281055	3	2	61	1	0	0	0	0	1	0	0	0	10490	1058	37	4	1335	4	NLRP6	11	281055	Missense_Mutation	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10		281055	134725461	34	7476										
BBOX1	8424	hgsc.bcm.edu	37	chr11	27137031	27137031	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	agtgcaagacaaaatcgatgCaaacaatgtggcttacacaa	8	8	0	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr11:27137031C>A	ENST00000529202.1	+	5	905	c.566C>A	c.(565-567)gCa>gAa	p.A189E	BBOX1_ENST00000528583.1_Missense_Mutation_p.A189E|RP11-1L12.3_ENST00000525302.1_RNA|RP11-1L12.3_ENST00000526061.1_RNA|BBOX1_ENST00000525090.1_Missense_Mutation_p.A189E|BBOX1_ENST00000263182.3_Missense_Mutation_p.A189E|BBOX1_ENST00000527505.1_3'UTR|RP11-1L12.3_ENST00000530430.1_RNA			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	189					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	AAAATCGATGCAAACAATGTG	0.413																																					p.A189E		Atlas-SNP	.											.	BBOX1	46	.	0			c.C566A						.						142	122	129					11																	27137031		2202	4298	6500	SO:0001583	missense	8424	exon6			TCGATGCAAACAA	AF082868	CCDS7862.1	11p	2008-02-01			ENSG00000129151	ENSG00000129151	1.14.11.1		964	protein-coding gene	gene with protein product		603312		BBOX		9753662	Standard	XM_005253159		Approved	gamma-BBH, G-BBH, BBH	uc001mre.1	O75936	OTTHUMG00000166121	ENST00000529202.1:c.566C>A	chr11.hg19:g.27137031C>A	ENSP00000435781:p.Ala189Glu	43.0	0.0		67.0	24.0	NM_003986	B2R8L7|D3DQZ1|Q6IBJ2	Missense_Mutation	SNP	ENST00000529202.1	hg19	CCDS7862.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.573696	0.86542	.	.	ENSG00000129151	ENST00000529202;ENST00000263182;ENST00000528583;ENST00000525090	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.90631	0.7062	M	0.82716	2.605	0.80722	D	1	D	0.76494	0.999	D	0.65323	0.934	D	0.89287	0.3616	10	0.28530	T	0.3	.	17.4422	0.87568	0.0:1.0:0.0:0.0	.	189	O75936	BODG_HUMAN	E	189	ENSP00000435781:A189E;ENSP00000263182:A189E;ENSP00000434918:A189E;ENSP00000433772:A189E	ENSP00000263182:A189E	A	+	2	0	BBOX1	27093607	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.173000	0.77612	2.457000	0.83068	0.655000	0.94253	GCA	.	.		0.413	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986		A	27137031	C	A	27137031	3	1	61	1	0	0	0	0	1	0	0	0	1334	710	25	3	580	3	BBOX1	11	27137031	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	26855976	27137031	107869485	35	7477										
EFCAB4B	84766	hgsc.bcm.edu	37	chr12	3736844	3736844	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gccacctgagagttgtccacAttcaacgtcttcacacggta	8	13	3	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr12:3736844A>C	ENST00000440314.2	-	16	2237	c.1764T>G	c.(1762-1764)aaT>aaG	p.N588K		NM_001144958.1	NP_001138430.1	Q9BSW2	EFC4B_HUMAN		0					activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			AGTTGTCCACATTCAACGTCT	0.597																																					p.N588K		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.T1764G						.						83	74	77					12																	3736844		692	1591	2283	SO:0001583	missense	84766	exon16			GTCCACATTCAAC																												ENST00000440314.2:c.1764T>G	chr12.hg19:g.3736844A>C	ENSP00000409382:p.Asn588Lys	46.0	0.0		59.0	15.0	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000440314.2	hg19	CCDS44803.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.701751	0.00725	.	.	ENSG00000130038	ENST00000440314	T	0.76060	-0.99	5.47	-10.7	0.00240	.	1.384710	0.03987	N	0.294258	T	0.46718	0.1407	.	.	.	0.53688	D	0.999979	B	0.06786	0.001	B	0.08055	0.003	T	0.13575	-1.0504	9	0.07644	T	0.81	.	8.7676	0.34713	0.2645:0.0:0.4938:0.2417	.	588	Q9BSW2-2	.	K	588	ENSP00000409382:N588K	ENSP00000409382:N588K	N	-	3	2	EFCAB4B	3607105	0.000000	0.05858	0.001000	0.08648	0.124000	0.20399	-3.893000	0.00340	-1.703000	0.01409	-0.924000	0.02725	AAT	.	.		0.597	EFCAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398640.2			C	3736844	A	C	3736844	3	2	61	1	0	0	0	0	1	0	0	0	4939	214	8	5	451	5	EFCAB4B	12	3736844	Missense_Mutation	SNP	A	TCGA-CC-A123-01A-11D-A12Z-10		3736844	130115051	36	7478										
CCND2	894	hgsc.bcm.edu	37	chr12	4383263	4383263	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	agggccgtgcgggaccgcaaCctgctccgagacgaccgcgt	15	15	0	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr12:4383263C>A	ENST00000261254.3	+	1	326	c.57C>A	c.(55-57)aaC>aaA	p.N19K	RP11-264F23.3_ENST00000539135.1_RNA|RP11-264F23.4_ENST00000537370.1_RNA	NM_001759.3	NP_001750.1	P30279	CCND2_HUMAN	cyclin D2	19					cell cycle (GO:0007049)|cell division (GO:0051301)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of protein phosphorylation (GO:0001934)	chromatin (GO:0000785)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17			all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)			GGGACCGCAACCTGCTCCGAG	0.677			T	IGL@	"NHL,CLL"																																p.N19K		Atlas-SNP	.		Dom	yes		12	12p13	894	cyclin D2		L	.	CCND2	50	.	0			c.C57A						.						51	43	45					12																	4383263		2203	4300	6503	SO:0001583	missense	894	exon1			CCGCAACCTGCTC	AF518005	CCDS8524.1	12p13	2008-08-04			ENSG00000118971	ENSG00000118971			1583	protein-coding gene	gene with protein product	"G1/S-specific cyclin D2"	123833				1386335	Standard	NM_001759		Approved		uc001qmo.3	P30279	OTTHUMG00000168123	ENST00000261254.3:c.57C>A	chr12.hg19:g.4383263C>A	ENSP00000261254:p.Asn19Lys	42.0	0.0		75.0	18.0	NM_001759	A8K531|Q13955|Q5U035	Missense_Mutation	SNP	ENST00000261254.3	hg19	CCDS8524.1	.	.	.	.	.	.	.	.	.	.	C	7.907	0.735734	0.15574	.	.	ENSG00000118971	ENST00000261254	T	0.07908	3.15	4.17	4.17	0.49024	Cyclin-like (1);	0.158028	0.56097	D	0.000038	T	0.10508	0.0257	M	0.81497	2.545	0.50813	D	0.999897	B	0.28713	0.22	B	0.21708	0.036	T	0.05194	-1.0900	10	0.07030	T	0.85	.	11.653	0.51301	0.0:0.8204:0.1796:0.0	.	19	P30279	CCND2_HUMAN	K	19	ENSP00000261254:N19K	ENSP00000261254:N19K	N	+	3	2	CCND2	4253524	1.000000	0.71417	1.000000	0.80357	0.603000	0.37013	1.240000	0.32731	2.127000	0.65507	0.491000	0.48974	AAC	.	.		0.677	CCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398287.1	NM_001759		A	4383263	C	A	4383263	3	1	61	1	0	0	0	0	1	0	0	0	2919	506	18	3	59	3	CCND2	12	4383263	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	646419	4383263	129468632	37	7479										
TMTC2	160335	hgsc.bcm.edu	37	chr12	83250808	83250808	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gccgtgctatcaagactaatCaggaccttctcccagaaact	7	13	3	2			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr12:83250808C>T	ENST00000321196.3	+	2	810	c.103C>T	c.(103-105)Cag>Tag	p.Q35*	TMTC2_ENST00000549919.1_Nonsense_Mutation_p.Q29*|TMTC2_ENST00000548305.1_Nonsense_Mutation_p.Q35*	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	35					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						CAAGACTAATCAGGACCTTCT	0.393																																					p.Q35X		Atlas-SNP	.											.	TMTC2	100	.	0			c.C103T						.						108	118	115					12																	83250808		2203	4300	6503	SO:0001587	stop_gained	160335	exon2			ACTAATCAGGACC	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.103C>T	chr12.hg19:g.83250808C>T	ENSP00000322300:p.Gln35*	134.0	0.0		158.0	57.0	NM_152588	B2RCU7|Q8N2K8	Nonsense_Mutation	SNP	ENST00000321196.3	hg19	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	C	43	10.100441	0.99337	.	.	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.393	19.0404	0.92997	0.0:1.0:0.0:0.0	.	.	.	.	X	35;35;29	.	ENSP00000322300:Q35X	Q	+	1	0	TMTC2	81774939	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	CAG	.	.		0.393	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		T	83250808	C	T	83250808	4	4	61	1	0	0	0	0	0	1	0	0	16276	827	29	3	109	3	TMTC2	12	83250808	Nonsense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	78867545	83250808	50601087	38	7480										
OR4Q3	441669	hgsc.bcm.edu	37	chr14	20215599	20215599	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ttggcttgatgaaaaaagaaCaagattctaatgtgacagaa	9	4	1	6			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr14:20215599C>G	ENST00000331723.1	+	1	13	c.13C>G	c.(13-15)Caa>Gaa	p.Q5E		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	5						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GAAAAAAGAACAAGATTCTAA	0.318																																					p.Q5E		Atlas-SNP	.											.	OR4Q3	117	.	0			c.C13G						.						100	101	101					14																	20215599		2203	4300	6503	SO:0001583	missense	441669	exon1			AAAGAACAAGATT	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"GPCR / Class A : Olfactory receptors"	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.13C>G	chr14.hg19:g.20215599C>G	ENSP00000330049:p.Gln5Glu	869.0	0.0		822.0	172.0	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	hg19	CCDS32020.1	.	.	.	.	.	.	.	.	.	.	.	3.049	-0.195873	0.06259	.	.	ENSG00000182652	ENST00000331723	T	0.00573	6.48	4.32	3.17	0.36434	.	0.345098	0.20123	U	0.098754	T	0.00468	0.0015	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49303	-0.8954	10	0.87932	D	0	.	9.088	0.36592	0.8096:0.1903:0.0:0.0	.	5	Q8NH05	OR4Q3_HUMAN	E	5	ENSP00000330049:Q5E	ENSP00000330049:Q5E	Q	+	1	0	OR4Q3	19285439	0.980000	0.34600	0.060000	0.19600	0.276000	0.26787	0.927000	0.28818	0.695000	0.31675	-0.598000	0.04106	CAA	.	.		0.318	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2			G	20215599	C	G	20215599	3	3	61	1	0	0	0	0	1	0	0	0	11090	479	17	4	15	4	OR4Q3	14	20215599	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10		20215599	87133941	39	7481										
OR4N5	390437	hgsc.bcm.edu	37	chr14	20612767	20612767	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gttatttatacgcttcgcaaCcaggaggtgaaagcttccat	9	9	0	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr14:20612767C>A	ENST00000333629.1	+	1	873	c.873C>A	c.(871-873)aaC>aaA	p.N291K	RNA5SP381_ENST00000516076.1_RNA	NM_001004724.1	NP_001004724.1	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N, member 5	291						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(23)|ovary(1)|skin(2)|urinary_tract(1)	29	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)		CGCTTCGCAACCAGGAGGTGA	0.413																																					p.N291K		Atlas-SNP	.											.	OR4N5	72	.	0			c.C873A						.						90	90	90					14																	20612767		2203	4300	6503	SO:0001583	missense	390437	exon1			TCGCAACCAGGAG		CCDS32031.1	14q11.2	2013-09-23			ENSG00000184394	ENSG00000184394		"GPCR / Class A : Olfactory receptors"	15358	protein-coding gene	gene with protein product							Standard	NM_001004724		Approved		uc010tla.2	Q8IXE1	OTTHUMG00000170784	ENST00000333629.1:c.873C>A	chr14.hg19:g.20612767C>A	ENSP00000332110:p.Asn291Lys	106.0	0.0		130.0	65.0	NM_001004724	Q6IF11	Missense_Mutation	SNP	ENST00000333629.1	hg19	CCDS32031.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.836518	0.50951	.	.	ENSG00000184394	ENST00000333629	T	0.50001	0.76	4.0	-1.13	0.09775	.	0.000000	0.47852	D	0.000203	T	0.62768	0.2455	H	0.94542	3.55	0.27766	N	0.94364	D	0.60160	0.987	P	0.51742	0.678	T	0.62426	-0.6857	10	0.87932	D	0	.	8.5173	0.33253	0.0:0.5099:0.0:0.4901	.	291	Q8IXE1	OR4N5_HUMAN	K	291	ENSP00000332110:N291K	ENSP00000332110:N291K	N	+	3	2	OR4N5	19682607	0.000000	0.05858	0.996000	0.52242	0.990000	0.78478	-0.654000	0.05354	-0.121000	0.11787	0.655000	0.94253	AAC	.	.		0.413	OR4N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410347.1			A	20612767	C	A	20612767	3	1	61	1	0	0	0	0	1	0	0	0	11088	506	18	3	875	3	OR4N5	14	20612767	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	397168	20612767	86736773	40	7482										
DDHD1	80821	hgsc.bcm.edu	37	chr14	53540463	53540463	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ttttaaataaatatacctccAtcaagagtaagttttgaccg	5	7	1	2			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr14:53540463A>G	ENST00000323669.5	-	5	1391	c.1392T>C	c.(1390-1392)gaT>gaC	p.D464D	DDHD1_ENST00000395606.1_Silent_p.D471D|DDHD1_ENST00000357758.3_Silent_p.D464D	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	464					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					ATATACCTCCATCAAGAGTAA	0.323																																					p.D471D		Atlas-SNP	.											.	DDHD1	202	.	0			c.T1413C						.						63	66	65					14																	53540463		2203	4300	6503	SO:0001819	synonymous_variant	80821	exon6			ACCTCCATCAAGA	AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"phosphatidic acid-preferring phospholipase A1"	614603	"spastic paraplegia 28 (autosomal recessive)"	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.1392T>C	chr14.hg19:g.53540463A>G		214.0	0.0		191.0	77.0	NM_001160147	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Silent	SNP	ENST00000323669.5	hg19	CCDS53895.1																																																																																			.	.		0.323	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1			G	53540463	A	G	53540463	2	3	61	1	0	0	0	0	0	0	0	1	4328	214	8	2		2	DDHD1	14	53540463	Silent	SNP	A	TCGA-CC-A123-01A-11D-A12Z-10	32927696	53540463	53809077	41	7483										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64520042	64520042	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gataagttatacaaagttctCcaaaacatggtattagaact	6	6	1	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr14:64520042C>T	ENST00000344113.4	+	48	9623	c.9411C>T	c.(9409-9411)ctC>ctT	p.L3137L	SYNE2_ENST00000554584.1_Silent_p.L3170L|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000358025.3_Silent_p.L3137L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3137					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ACAAAGTTCTCCAAAACATGG	0.294																																					p.L3137L		Atlas-SNP	.											.	SYNE2	577	.	0			c.C9411T						.						42	42	42					14																	64520042		1818	4066	5884	SO:0001819	synonymous_variant	23224	exon48			AGTTCTCCAAAAC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.9411C>T	chr14.hg19:g.64520042C>T		213.0	0.0		169.0	68.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.294	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64520042	C	T	64520042	2	4	61	1	0	0	0	0	0	0	0	1	15461	842	30	3		3	SYNE2	14	64520042	Silent	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	10979579	64520042	42829498	42	7484										
POMT2	29954	hgsc.bcm.edu	37	chr14	77746417	77746417	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gtcattgacccctgagaagcGtaggccctgtggaatagaga	13	9	1	3	rs148466370		TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr14:77746417G>A	ENST00000261534.4	-	17	1934	c.1732C>T	c.(1732-1734)Cgc>Tgc	p.R578C		NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	578						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		CCTGAGAAGCGTAGGCCCTGT	0.597																																					p.R578C		Atlas-SNP	.											POMT2,colon,carcinoma,0,1	POMT2	47	.	0			c.C1732T						.	G	CYS/ARG	0,4406		0,0,2203	118	97	104		1732	5.7	1	14	dbSNP_134	104	1,8599	1.2+/-3.3	0,1,4299	yes	missense	POMT2	NM_013382.5	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	578/751	77746417	1,13005	2203	4300	6503	SO:0001583	missense	29954	exon17			AGAAGCGTAGGCC	AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.1732C>T	chr14.hg19:g.77746417G>A	ENSP00000261534:p.Arg578Cys	74.0	0.0		96.0	37.0	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	hg19	CCDS9857.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.346254	0.82022	0.0	1.16E-4	ENSG00000009830	ENST00000261534	D	0.92397	-3.03	5.67	5.67	0.87782	.	0.051252	0.85682	D	0.000000	D	0.94837	0.8332	M	0.81942	2.565	0.80722	D	1	D	0.69078	0.997	P	0.53360	0.724	D	0.93847	0.7142	10	0.38643	T	0.18	-12.6745	19.7763	0.96395	0.0:0.0:1.0:0.0	.	578	Q9UKY4	POMT2_HUMAN	C	578	ENSP00000261534:R578C	ENSP00000261534:R578C	R	-	1	0	POMT2	76816170	1.000000	0.71417	1.000000	0.80357	0.745000	0.42441	7.115000	0.77110	2.687000	0.91594	0.563000	0.77884	CGC	.	G|1.000;A|0.000		0.597	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382		A	77746417	G	A	77746417	3	1	61	1	0	0	0	0	1	0	0	0	12255	1145	40	1	540	1	POMT2	14	77746417	Missense_Mutation	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10	13226375	77746417	29603123	43	7485										
CHRNB4	1143	hgsc.bcm.edu	37	chr15	78927919	78927919	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ttttcctccgcattggccacGcggcagttccctgagaaaac	9	14	0	1	rs552677379		TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr15:78927919G>C	ENST00000261751.3	-	2	177	c.66C>G	c.(64-66)cgC>cgG	p.R22R	CHRNB4_ENST00000412074.2_Silent_p.R22R|CHRNB4_ENST00000560511.1_5'UTR	NM_000750.3	NP_000741.1	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4 (neuronal)	22					action potential (GO:0001508)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|regulation of neurotransmitter secretion (GO:0046928)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			endometrium(7)|kidney(1)|lung(13)|prostate(1)	22					Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)	CATTGGCCACGCGGCAGTTCC	0.587																																					p.R22R		Atlas-SNP	.											CHRNB4,NS,carcinoma,0,2	CHRNB4	59	.	0			c.C66G						.						247	234	239					15																	78927919		2196	4293	6489	SO:0001819	synonymous_variant	1143	exon2			GGCCACGCGGCAG	U48861	CCDS10306.1, CCDS58392.1	15q24	2012-02-11	2012-02-07		ENSG00000117971	ENSG00000117971		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1964	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 4 (neuronal)"	118509	"cholinergic receptor, nicotinic, beta polypeptide 4"			2004777	Standard	NM_000750		Approved		uc002bed.1	P30926	OTTHUMG00000143860	ENST00000261751.3:c.66C>G	chr15.hg19:g.78927919G>C		49.0	0.0		123.0	108.0	NM_000750	A4FTX5|E9PHE8|Q16607|Q4VBA5|Q8WXC8|Q9BQR4	Silent	SNP	ENST00000261751.3	hg19	CCDS10306.1																																																																																			.	.		0.587	CHRNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290108.1			C	78927919	G	C	78927919	2	2	61	1	0	0	0	0	0	0	0	1	3395	1074	38	4		4	CHRNB4	15	78927919	Silent	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10		78927919	23603473	44	7486										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88472662	88472662	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	atcattgcatctggcccatgGgccctgcaagagcatgggga	13	11	2	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr15:88472662G>T	ENST00000360948.2	-	16	2054	c.1893C>A	c.(1891-1893)gcC>gcA	p.A631A	NTRK3_ENST00000542733.2_Silent_p.A533A|NTRK3_ENST00000355254.2_Silent_p.A631A|NTRK3_ENST00000557856.1_Silent_p.A623A|NTRK3_ENST00000357724.2_Silent_p.A623A|NTRK3_ENST00000394480.2_Silent_p.A631A|NTRK3_ENST00000558676.1_Silent_p.A623A	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	631	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CTGGCCCATGGGCCCTGCAAG	0.592			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.A631A		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.C1893A						.						38	37	37					15																	88472662		2201	4299	6500	SO:0001819	synonymous_variant	4916	exon17			CCCATGGGCCCTG	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1893C>A	chr15.hg19:g.88472662G>T		51.0	0.0		74.0	39.0	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	ENST00000360948.2	hg19	CCDS32322.1																																																																																			.	.		0.592	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				T	88472662	G	T	88472662	2	4	61	1	0	0	0	0	0	0	0	1	10717	1219	43	3		3	NTRK3	15	88472662	Silent	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10	9544743	88472662	14058730	45	7487										
IL21R	50615	hgsc.bcm.edu	37	chr16	27448870	27448870	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gcagcctccacaggtcggccCacaatgccacgcatgccacc	9	19	0	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr16:27448870C>A	ENST00000337929.3	+	4	687	c.214C>A	c.(214-216)Cac>Aac	p.H72N	IL21R_ENST00000395755.1_Missense_Mutation_p.H72N|IL21R_ENST00000395754.4_Missense_Mutation_p.H72N|IL21R_ENST00000564089.1_Missense_Mutation_p.H72N	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	72	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						CAGGTCGGCCCACAATGCCAC	0.557			T	BCL6	NHL																																p.H94N		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.C280A						.						131	100	111					16																	27448870		2197	4300	6497	SO:0001583	missense	50615	exon5			TCGGCCCACAATG	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.214C>A	chr16.hg19:g.27448870C>A	ENSP00000338010:p.His72Asn	37.0	0.0		38.0	27.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	hg19	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.711849	0.30322	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	D;D;D	0.95885	-3.84;-3.84;-3.84	4.65	4.65	0.58169	Fibronectin, type III (1);	0.407180	0.21333	N	0.076263	D	0.93138	0.7815	M	0.66939	2.045	0.37177	D	0.903308	P	0.37276	0.589	B	0.35813	0.211	D	0.92638	0.6122	10	0.14656	T	0.56	-17.6511	13.3953	0.60849	0.0:1.0:0.0:0.0	.	72	Q9HBE5	IL21R_HUMAN	N	72	ENSP00000338010:H72N;ENSP00000379104:H72N;ENSP00000379103:H72N	ENSP00000338010:H72N	H	+	1	0	IL21R	27356371	0.045000	0.20229	0.811000	0.32455	0.038000	0.13279	0.197000	0.17197	2.271000	0.75665	0.650000	0.86243	CAC	.	.		0.557	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		A	27448870	C	A	27448870	3	1	61	1	0	0	0	0	1	0	0	0	7680	594	21	3	224	3	IL21R	16	27448870	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10		27448870	62905883	46	7488										
ZDHHC1	29800	hgsc.bcm.edu	37	chr16	67432171	67432171	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ctccctgtgaacccccttggCctcctgtggtgggcggtgct	13	15	0	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr16:67432171C>G	ENST00000348579.2	-	8	1212	c.871G>C	c.(871-873)Gcc>Ccc	p.A291P	ZDHHC1_ENST00000566075.1_5'Flank	NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	291					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		ACCCCCTTGGCCTCCTGTGGT	0.637																																					p.A291P		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.G871C						.						121	106	111					16																	67432171		2198	4300	6498	SO:0001583	missense	29800	exon8			CCTTGGCCTCCTG	U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"Zinc fingers, DHHC-type"	17916	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 1"	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.871G>C	chr16.hg19:g.67432171C>G	ENSP00000340299:p.Ala291Pro	74.0	0.0		92.0	74.0	NM_013304	O15461	Missense_Mutation	SNP	ENST00000348579.2	hg19	CCDS10836.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.529073	0.44969	.	.	ENSG00000159714	ENST00000348579	T	0.37752	1.18	5.46	4.49	0.54785	.	1.706460	0.02790	N	0.121901	T	0.28632	0.0709	L	0.27053	0.805	0.32577	N	0.528965	B	0.15473	0.013	B	0.12156	0.007	T	0.30297	-0.9983	10	0.30078	T	0.28	.	5.4746	0.16688	0.1477:0.6332:0.1425:0.0765	.	291	Q8WTX9	ZDHC1_HUMAN	P	291	ENSP00000340299:A291P	ENSP00000340299:A291P	A	-	1	0	ZDHHC1	65989672	0.994000	0.37717	1.000000	0.80357	0.861000	0.49209	0.541000	0.23207	1.260000	0.44134	0.407000	0.27541	GCC	.	.		0.637	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304		G	67432171	C	G	67432171	3	3	61	1	0	0	0	0	1	0	0	0	17615	739	26	4	602	4	ZDHHC1	16	67432171	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	39983301	67432171	22922582	47	7489										
OR1A2	26189	hgsc.bcm.edu	37	chr17	3101458	3101458	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	cattactatgcatcattgtcTcctatgttcaggtcttttcc	5	11	4	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr17:3101458T>C	ENST00000381951.1	+	1	646	c.646T>C	c.(646-648)Tcc>Ccc	p.S216P		NM_012352.1	NP_036484.1	Q9Y585	OR1A2_HUMAN	olfactory receptor, family 1, subfamily A, member 2	216					positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(4)|stomach(2)	18						CATCATTGTCTCCTATGTTCA	0.448																																					p.S216P		Atlas-SNP	.											OR1A2,NS,neuroblastoma,0,1	OR1A2	52	.	0			c.T646C						.						233	201	212					17																	3101458		2203	4300	6503	SO:0001583	missense	26189	exon1			ATTGTCTCCTATG	AF155225	CCDS11021.1	17p13.3	2012-08-09			ENSG00000172150	ENSG00000172150		"GPCR / Class A : Olfactory receptors"	8180	protein-coding gene	gene with protein product						10673334	Standard	NM_012352		Approved	OR17-6	uc002fvd.1	Q9Y585	OTTHUMG00000090638	ENST00000381951.1:c.646T>C	chr17.hg19:g.3101458T>C	ENSP00000371377:p.Ser216Pro	620.0	0.0		354.0	32.0	NM_012352	Q3KPH3|Q6IFM0|Q6NTD8|Q96R86	Missense_Mutation	SNP	ENST00000381951.1	hg19	CCDS11021.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.686963	0.48097	.	.	ENSG00000172150	ENST00000381951	T	0.46819	0.86	4.09	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000159	T	0.77458	0.4133	H	0.96576	3.845	0.38894	D	0.957189	D	0.89917	1.0	D	0.91635	0.999	D	0.85604	0.1254	10	0.87932	D	0	.	12.3223	0.54991	0.0:0.0:0.0:1.0	.	216	Q9Y585	OR1A2_HUMAN	P	216	ENSP00000371377:S216P	ENSP00000371377:S216P	S	+	1	0	OR1A2	3048208	1.000000	0.71417	0.871000	0.34182	0.066000	0.16364	6.986000	0.76200	1.850000	0.53721	0.496000	0.49642	TCC	.	.		0.448	OR1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207293.1	NM_012352		C	3101458	T	C	3101458	3	2	61	1	0	0	0	0	1	0	0	0	10959	1551	54	2	648	2	OR1A2	17	3101458	Missense_Mutation	SNP	T	TCGA-CC-A123-01A-11D-A12Z-10		3101458	78093752	48	7490										
ELAC2	60528	hgsc.bcm.edu	37	chr17	12896302	12896302	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	catctcctcgatgtcgccagCaaacagggctttcagtgggg	12	12	2	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr17:12896302C>G	ENST00000338034.4	-	24	2553	c.2314G>C	c.(2314-2316)Gct>Cct	p.A772P	ELAC2_ENST00000395962.2_Missense_Mutation_p.A753P|ELAC2_ENST00000426905.3_Missense_Mutation_p.A732P|RP11-597M12.1_ENST00000582915.1_RNA	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	772					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						ATGTCGCCAGCAAACAGGGCT	0.602																																					p.A772P		Atlas-SNP	.											.	ELAC2	48	.	0			c.G2314C						.						67	68	68					17																	12896302		2203	4300	6503	SO:0001583	missense	60528	exon24			CGCCAGCAAACAG	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"tRNase Z (long form)"	605367	"elaC (E. coli) homolog 2", "elaC homolog 2 (E. coli)"			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.2314G>C	chr17.hg19:g.12896302C>G	ENSP00000337445:p.Ala772Pro	16.0	0.0		25.0	19.0	NM_018127	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Missense_Mutation	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.060295	0.55432	.	.	ENSG00000006744	ENST00000426905;ENST00000338034;ENST00000395962	T;T;T	0.66099	0.25;-0.18;-0.19	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.78547	0.4300	M	0.69523	2.12	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;0.999;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D;D	0.87578	0.991;0.979;0.998;0.961;0.995;0.995;0.996;0.983	T	0.78823	-0.2052	10	0.51188	T	0.08	-22.3167	16.9478	0.86235	0.0:1.0:0.0:0.0	.	732;755;753;570;772;532;757;400	B4DPL9;E9PGJ0;G5E9D5;E7ES68;Q9BQ52;B3KSU9;B4DT15;Q9BQ52-3	.;.;.;.;RNZ2_HUMAN;.;.;.	P	732;772;753	ENSP00000405223:A732P;ENSP00000337445:A772P;ENSP00000379291:A753P	ENSP00000337445:A772P	A	-	1	0	ELAC2	12837027	1.000000	0.71417	0.991000	0.47740	0.866000	0.49608	7.138000	0.77305	2.593000	0.87608	0.655000	0.94253	GCT	.	.		0.602	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5			G	12896302	C	G	12896302	3	3	61	1	0	0	0	0	1	0	0	0	5049	710	25	4	170	4	ELAC2	17	12896302	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	9794844	12896302	68298908	49	7491										
GAS2L2	246176	hgsc.bcm.edu	37	chr17	34072948	34072948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ctgtcctgggacttccacttGtagcaccaggaaagctcctt	9	13	0	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr17:34072948G>A	ENST00000254466.6	-	6	1595	c.1568C>T	c.(1567-1569)aCa>aTa	p.T523I	GAS2L2_ENST00000587565.1_Missense_Mutation_p.T507I	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	523					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACTTCCACTTGTAGCACCAGG	0.612																																					p.T523I		Atlas-SNP	.											.	GAS2L2	94	.	0			c.C1568T						.						39	42	41					17																	34072948		2203	4300	6503	SO:0001583	missense	246176	exon6			CCACTTGTAGCAC	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1568C>T	chr17.hg19:g.34072948G>A	ENSP00000254466:p.Thr523Ile	14.0	0.0		27.0	9.0	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	hg19	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	G	9.843	1.191464	0.21954	.	.	ENSG00000132139	ENST00000254466	T	0.17854	2.25	5.19	0.539	0.17156	.	0.954354	0.08595	N	0.922406	T	0.07548	0.0190	N	0.08118	0	0.09310	N	1	B	0.18610	0.029	B	0.14023	0.01	T	0.36016	-0.9765	10	0.41790	T	0.15	0.014	2.5366	0.04716	0.0934:0.2048:0.4125:0.2893	.	523	Q8NHY3	GA2L2_HUMAN	I	523	ENSP00000254466:T523I	ENSP00000254466:T523I	T	-	2	0	GAS2L2	31097061	0.000000	0.05858	0.003000	0.11579	0.010000	0.07245	-1.180000	0.03088	0.313000	0.23062	0.655000	0.94253	ACA	.	.		0.612	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		A	34072948	G	A	34072948	3	1	61	1	0	0	0	0	1	0	0	0	6255	1377	48	3	1078	3	GAS2L2	17	34072948	Missense_Mutation	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10	21176646	34072948	47122262	50	7492										
FKBP10	60681	hgsc.bcm.edu	37	chr17	39969300	39969301	+	Frame_Shift_Ins	INS	-	-	C													0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ggcaccatgttccccgcgggINScccccccagccacagcctcc							TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr17:39969300_39969301insC	ENST00000321562.4	+	1	118_119	c.14_15insC	c.(13-18)ggccccfs	p.GP5fs	LEPREL4_ENST00000355468.3_5'Flank|LEPREL4_ENST00000393928.1_5'Flank	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	5					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)		TTCCCCGCGGGCCCCCCCAGCC	0.748																																					p.G5fs		Atlas-INDEL	.											.,2	FKBP10	57	.	0			c.14_15insC						.																																			SO:0001589	frameshift_variant	60681	exon1			.	AB045981	CCDS11409.1	17q21.2	2014-09-17	2002-08-29		ENSG00000141756	ENSG00000141756		"EF-hand domain containing"	18169	protein-coding gene	gene with protein product		607063	"FK506 binding protein 10 (65 kDa)"			11071917, 18786928	Standard	NM_021939		Approved	hFKBP65, FLJ22041, FKBP6, FLJ20683, FLJ23833	uc002hxv.2	Q96AY3	OTTHUMG00000133497	ENST00000321562.4:c.21dupC	chr17.hg19:g.39969307_39969307dupC	ENSP00000317232:p.Gly5fs	28.0	0.0		104.0	10.0	NM_021939	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Frame_Shift_Ins	INS	ENST00000321562.4	hg19	CCDS11409.1																																																																																			.	.		0.748	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939		C	39969301	-	C	39969300	7	5	61	1	0	1	1	0	0	0	0	0	5910	1203	42	0	16	0	FKBP10	17	39969300	Frame_Shift_Ins	INS	-	TCGA-CC-A123-01A-11D-A12Z-10	5896352	39969300	41225910	51	7493										
STRADA	92335	hgsc.bcm.edu	37	chr17	61784645	61784645	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gctgagccacggcagaacctTgacactgtacttgggaaaat	11	10	0	3			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr17:61784645T>C	ENST00000336174.6	-	9	827	c.715A>G	c.(715-717)Aag>Gag	p.K239E	STRADA_ENST00000580039.1_5'UTR|STRADA_ENST00000375840.4_Missense_Mutation_p.K181E|STRADA_ENST00000245865.5_Missense_Mutation_p.K181E|STRADA_ENST00000447001.3_Missense_Mutation_p.K195E|STRADA_ENST00000582137.1_Missense_Mutation_p.K210E|STRADA_ENST00000579340.1_Intron|RP11-51F16.8_ENST00000580553.1_3'UTR|STRADA_ENST00000392950.4_Missense_Mutation_p.K202E	NM_001003787.2	NP_001003787.1	Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|protein export from nucleus (GO:0006611)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|prostate(2)	13						GGCAGAACCTTGACACTGTAC	0.592																																					p.K239E		Atlas-SNP	.											.	STRADA	27	.	0			c.A715G						.						103	93	96					17																	61784645		2203	4300	6503	SO:0001583	missense	92335	exon9			GAACCTTGACACT	AF308302	CCDS11642.1, CCDS32703.1, CCDS42367.1, CCDS54156.1, CCDS58585.1	17q23.3	2014-09-04			ENSG00000266173	ENSG00000266173			30172	protein-coding gene	gene with protein product	"STE20-like pseudokinase"	608626				12805220, 17921699	Standard	NM_153335		Approved	NY-BR-96, LYK5, Stlk, STRAD	uc002jbm.3	Q7RTN6	OTTHUMG00000178908	ENST00000336174.6:c.715A>G	chr17.hg19:g.61784645T>C	ENSP00000336655:p.Lys239Glu	29.0	0.0		73.0	48.0	NM_001003787	B4DDE3|B4DW17|J3KTC9|Q5JPI2|Q7Z4K9|Q8NC31|Q8NCF1|Q9H272	Missense_Mutation	SNP	ENST00000336174.6	hg19	CCDS32703.1	.	.	.	.	.	.	.	.	.	.	t	15.82	2.946124	0.53079	.	.	ENSG00000125695	ENST00000336174;ENST00000375840;ENST00000447001;ENST00000392950;ENST00000245865	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.13	5.46	5.46	0.80206	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.041428	0.85682	D	0.000000	T	0.73321	0.3572	L	0.45051	1.395	0.80722	D	1	P;P;P;B;P;P;P	0.47302	0.893;0.838;0.801;0.043;0.763;0.873;0.837	P;B;B;B;B;B;P	0.46389	0.478;0.222;0.266;0.024;0.242;0.306;0.515	T	0.76405	-0.2971	10	0.59425	D	0.04	.	15.8442	0.78874	0.0:0.0:0.0:1.0	.	210;195;181;181;202;202;239	B4DW17;B4DDE3;Q5JPI2;Q86YC8;Q7RTN6-2;Q7RTN6-3;Q7RTN6	.;.;.;.;.;.;STRAA_HUMAN	E	239;181;195;202;201	ENSP00000336655:K239E;ENSP00000365000:K181E;ENSP00000398841:K195E;ENSP00000376677:K202E	ENSP00000245865:K201E	K	-	1	0	STRADA	59138377	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	7.652000	0.83633	2.197000	0.70478	0.454000	0.30748	AAG	.	.		0.592	STRADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443894.1			C	61784645	T	C	61784645	3	2	61	1	0	0	0	0	1	0	0	0	15339	1821	63	2	658	2	STRADA	17	61784645	Missense_Mutation	SNP	T	TCGA-CC-A123-01A-11D-A12Z-10	21815345	61784645	19410565	52	7494										
LMAN1	3998	hgsc.bcm.edu	37	chr18	57026472	57026472	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gacccctttgcctggatcccGccatcttggattctggaacg	10	14	2	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr18:57026472G>A	ENST00000251047.5	-	1	722	c.5C>T	c.(4-6)gCg>gTg	p.A2V	RP11-27G24.1_ENST00000591331.1_lincRNA	NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	2					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	CCTGGATCCCGCCATCTTGGA	0.697																																					p.A2V		Atlas-SNP	.											.	LMAN1	57	.	0			c.C5T						.						30	37	35					18																	57026472		2202	4300	6502	SO:0001583	missense	3998	exon1			GATCCCGCCATCT	X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"endoplasmic reticulum-golgi intermediate compartment protein 53"	601567	"coagulation factor V-factor VIII combined deficiency"	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.5C>T	chr18.hg19:g.57026472G>A	ENSP00000251047:p.Ala2Val	52.0	0.0		39.0	27.0	NM_005570	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Missense_Mutation	SNP	ENST00000251047.5	hg19	CCDS11974.1	.	.	.	.	.	.	.	.	.	.	G	35	5.520706	0.96416	.	.	ENSG00000074695	ENST00000251047	T	0.58940	0.3	3.94	3.94	0.45596	.	0.152793	0.44483	D	0.000447	T	0.57504	0.2058	N	0.08118	0	0.43107	D	0.994802	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	T	0.67027	-0.5774	10	0.51188	T	0.08	-14.6621	16.1379	0.81502	0.0:0.0:1.0:0.0	.	2;2	B4DVV0;P49257	.;LMAN1_HUMAN	V	2	ENSP00000251047:A2V	ENSP00000251047:A2V	A	-	2	0	LMAN1	55177452	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.624000	0.74243	2.190000	0.69967	0.561000	0.74099	GCG	.	.		0.697	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570		A	57026472	G	A	57026472	3	1	61	1	0	0	0	0	1	0	0	0	8845	1087	38	1	1579	1	LMAN1	18	57026472	Missense_Mutation	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10		57026472	21050776	53	7495										
AP3D1	8943	hgsc.bcm.edu	37	chr19	2120931	2120931	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	cccgttccgctgggtgctgcTggccagcaggtgtgcactgt	15	13	0	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr19:2120931T>G	ENST00000345016.5	-	14	1642	c.1411A>C	c.(1411-1413)Agc>Cgc	p.S471R	AP3D1_ENST00000356926.4_Missense_Mutation_p.S380R|AP3D1_ENST00000350812.6_Missense_Mutation_p.S302R|AP3D1_ENST00000355272.6_Missense_Mutation_p.S471R|AP3D1_ENST00000590683.1_5'Flank	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	471					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGTGCTGCTGGCCAGCAGG	0.657																																					p.S471R		Atlas-SNP	.											AP3D1,colon,carcinoma,0,1	AP3D1	81	.	0			c.A1411C						.						43	48	47					19																	2120931		2180	4276	6456	SO:0001583	missense	8943	exon14			TGCTGCTGGCCAG	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.1411A>C	chr19.hg19:g.2120931T>G	ENSP00000344055:p.Ser471Arg	38.0	0.0		66.0	24.0	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	hg19	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.968519	0.74131	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	T;T;T;T	0.63255	2.16;-0.03;1.56;-0.03	4.67	4.67	0.58626	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.045388	0.85682	D	0.000000	T	0.72676	0.3490	M	0.68952	2.095	0.58432	D	0.999997	D;P;D	0.69078	0.958;0.629;0.997	P;B;D	0.64042	0.563;0.439;0.921	T	0.70135	-0.4955	10	0.21014	T	0.42	-28.7632	13.2693	0.60152	0.0:0.0:0.0:1.0	.	471;471;380	O14617-5;O14617;G5E988	.;AP3D1_HUMAN;.	R	380;471;471;471;302	ENSP00000349398:S380R;ENSP00000344055:S471R;ENSP00000347416:S471R;ENSP00000342321:S302R	ENSP00000341579:S471R	S	-	1	0	AP3D1	2071931	1.000000	0.71417	1.000000	0.80357	0.635000	0.38103	4.650000	0.61440	1.753000	0.51906	0.379000	0.24179	AGC	.	.		0.657	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1			G	2120931	T	G	2120931	3	3	61	1	0	0	0	0	1	0	0	0	746	1580	55	5	2276	5	AP3D1	19	2120931	Missense_Mutation	SNP	T	TCGA-CC-A123-01A-11D-A12Z-10		2120931	57008052	54	7496										
YIPF2	78992	hgsc.bcm.edu	37	chr19	11034659	11034659	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	cacgcatagcagtagatgctGatgcctgccacggtcactgg	12	12	1	2			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr19:11034659G>A	ENST00000586748.1	-	7	673	c.501C>T	c.(499-501)atC>atT	p.I167I	YIPF2_ENST00000253031.2_Silent_p.I167I|YIPF2_ENST00000590329.1_Silent_p.I128I			Q9BWQ6	YIPF2_HUMAN	Yip1 domain family, member 2	167						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				cervix(1)|endometrium(1)|lung(3)|ovary(2)	7						AGTAGATGCTGATGCCTGCCA	0.677																																					p.I167I		Atlas-SNP	.											.	YIPF2	13	.	0			c.C501T						.						35	37	37					19																	11034659		2203	4297	6500	SO:0001819	synonymous_variant	78992	exon7			GATGCTGATGCCT	BC013014	CCDS12251.1	19p13.2	2008-02-05				ENSG00000130733		"Yip1 domain family"	28476	protein-coding gene	gene with protein product						12477932	Standard	NM_024029		Approved	MGC3262, FinGER2	uc002mqc.3	Q9BWQ6		ENST00000586748.1:c.501C>T	chr19.hg19:g.11034659G>A		27.0	0.0		22.0	10.0	NM_024029		Silent	SNP	ENST00000586748.1	hg19	CCDS12251.1																																																																																			.	.		0.677	YIPF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453045.1	NM_024029		A	11034659	G	A	11034659	2	1	61	1	0	0	0	0	0	0	0	1	17493	1280	45	3		3	YIPF2	19	11034659	Silent	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10	8913728	11034659	48094324	55	7497										
RFX1	5989	hgsc.bcm.edu	37	chr19	14092957	14092957	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gggggcgagtgcacctgctgGgtaccatggaccgtcaggga	18	10	1	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr19:14092957G>A	ENST00000254325.4	-	5	831	c.597C>T	c.(595-597)acC>acT	p.T199T		NM_002918.4	NP_002909.4	P22670	RFX1_HUMAN	regulatory factor X, 1 (influences HLA class II expression)	199					immune response (GO:0006955)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)			GCACCTGCTGGGTACCATGGA	0.642																																					p.T199T		Atlas-SNP	.											.	RFX1	63	.	0			c.C597T						.						55	50	52					19																	14092957		2203	4300	6503	SO:0001819	synonymous_variant	5989	exon5			CTGCTGGGTACCA		CCDS12301.1	19p13.1	2008-07-17				ENSG00000132005			9982	protein-coding gene	gene with protein product	"trans-acting regulatory factor 1", "enhancer factor C", "MHC class II regulatory factor RFX"	600006				1505960, 8289803	Standard	NM_002918		Approved	EF-C	uc002mxv.3	P22670		ENST00000254325.4:c.597C>T	chr19.hg19:g.14092957G>A		87.0	0.0		103.0	50.0	NM_002918		Silent	SNP	ENST00000254325.4	hg19	CCDS12301.1																																																																																			.	.		0.642	RFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458510.1	NM_002918		A	14092957	G	A	14092957	2	1	61	1	0	0	0	0	0	0	0	1	13277	1219	43	3		3	RFX1	19	14092957	Silent	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10	3058298	14092957	45036026	56	7498										
NPHS1	4868	hgsc.bcm.edu	37	chr19	36339602	36339602	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	agccaccatcgtagcagaacCcgcgggcgactggacttgct	12	14	0	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr19:36339602C>T	ENST00000378910.5	-	9	1106	c.1107G>A	c.(1105-1107)cgG>cgA	p.R369R	NPHS1_ENST00000353632.6_Silent_p.R369R|NPHS1_ENST00000591817.1_5'Flank	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	369	Ig-like C2-type 4.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTAGCAGAACCCGCGGGCGAC	0.597																																					p.R369R		Atlas-SNP	.											.	NPHS1	165	.	0			c.G1107A						.						55	51	53					19																	36339602		2203	4300	6503	SO:0001819	synonymous_variant	4868	exon9			CAGAACCCGCGGG		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.1107G>A	chr19.hg19:g.36339602C>T		63.0	0.0		197.0	50.0	NM_004646	A6NDH2|C3RX61	Silent	SNP	ENST00000378910.5	hg19	CCDS32996.1																																																																																			.	.		0.597	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			T	36339602	C	T	36339602	2	4	61	1	0	0	0	0	0	0	0	1	10591	610	22	3		3	NPHS1	19	36339602	Silent	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	22246645	36339602	22789381	57	7499										
ZNF234	10780	hgsc.bcm.edu	37	chr19	44661606	44661606	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	attcaccagctgatccatacCggtgagaaaccatacaaatg	7	11	1	2	rs182811010	byFrequency	TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr19:44661606C>G	ENST00000426739.2	+	6	1695	c.1437C>G	c.(1435-1437)acC>acG	p.T479T	ZNF234_ENST00000592437.1_Silent_p.T479T	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	479					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)	23		Prostate(69;0.0435)				TGATCCATACCGGTGAGAAAC	0.433																																					p.T479T		Atlas-SNP	.											.	ZNF234	132	.	0			c.C1437G						.						82	83	82					19																	44661606		2045	4225	6270	SO:0001819	synonymous_variant	10780	exon6			CCATACCGGTGAG	X78927	CCDS46101.1	19q13	2013-01-08				ENSG00000263002		"Zinc fingers, C2H2-type", "-"	13027	protein-coding gene	gene with protein product		604750		ZNF269		7865130	Standard	NM_006630		Approved	HZF4	uc002oyl.4	Q14588		ENST00000426739.2:c.1437C>G	chr19.hg19:g.44661606C>G		126.0	0.0		148.0	42.0	NM_006630	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Silent	SNP	ENST00000426739.2	hg19	CCDS46101.1																																																																																			.	C|0.999;T|0.001		0.433	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2			G	44661606	C	G	44661606	2	3	61	1	0	0	0	0	0	0	0	1	17802	639	23	4		4	ZNF234	19	44661606	Silent	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	8322004	44661606	14467377	58	7500										
CCDC8	83987	hgsc.bcm.edu	37	chr19	46914871	46914942	+	In_Frame_Del	DEL	CTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCT	CTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCT	-													0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ttatctgtaacctctgacccCtggtcagctggggcctccgc					rs367620133|rs145734886|rs370755857|rs34186470|rs540532754|rs538950740|rs75175362	byFrequency	TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	CTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCT	CTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr19:46914871_46914942delCTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCT	ENST00000307522.3	-	1	1899_1970	c.1126_1197delAGGTCACAGGGCACAGATAACCACAGGGAAGAGGCTGCAGATAATCAGAGGGCGGAGGCCCCAGCTGACCAG	c.(1126-1197)aggtcacagggcacagataaccacagggaagaggctgcagataatcagagggcggaggccccagctgaccagdel	p.RSQGTDNHREEAADNQRAEAPADQ376del		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	376					microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.A393V(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;4.66e-05)|all cancers(93;0.000582)|Epithelial(262;0.00428)|GBM - Glioblastoma multiforme(486;0.0421)		CCTCTGACCCCTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCTCTGGTCAGCT	0.603																																					p.376_400del		Pindel	.											.	CCDC8	56	.	1	Substitution - Missense(1)	large_intestine(1)	c.1127_1198del						.																																			SO:0001651	inframe_deletion	83987	exon1			.	BC025243	CCDS12685.1	19q13.33	2012-04-17			ENSG00000169515	ENSG00000169515		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25367	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 20"	614145				11230166	Standard	NM_032040		Approved	DKFZp564K0322, 3M3, PPP1R20	uc002pep.3	Q9H0W5	OTTHUMG00000162348	ENST00000307522.3:c.1126_1197delAGGTCACAGGGCACAGATAACCACAGGGAAGAGGCTGCAGATAATCAGAGGGCGGAGGCCCCAGCTGACCAG	chr19.hg19:g.46914871_46914942delCTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCT	ENSP00000303158:p.Arg376_Gln399del	190.0	0.0		302.0	16.0	NM_032040	Q8TB26	In_Frame_Del	DEL	ENST00000307522.3	hg19	CCDS12685.1																																																																																			.	.		0.603	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	NM_032040		-	46914942	CTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCT	-	46914871	7	5	61	1	0	1	0	1	0	0	0	0	2855	680	24	0	423	0	CCDC8	19	46914871	In_Frame_Del	DEL	CTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCT	TCGA-CC-A123-01A-11D-A12Z-10	2253265	46914871	12214112	59	7501			1	8		2	2	19	N	CTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCT_C	3.953827e-05
CCDC8	83987	hgsc.bcm.edu	37	chr19	46914889	46914889	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ccctggtcagctggggcctcCgccctctgattatctgcagc	11	16	3	1	rs538950740		TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr19:46914889C>T	ENST00000307522.3	-	1	1952	c.1179G>A	c.(1177-1179)gcG>gcA	p.A393A		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	393					microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;4.66e-05)|all cancers(93;0.000582)|Epithelial(262;0.00428)|GBM - Glioblastoma multiforme(486;0.0421)		CTGGGGCCTCCGCCCTCTGAT	0.582																																					p.A393A		Atlas-SNP	.											.	CCDC8	56	.	0			c.G1179A						.						121	114	116					19																	46914889		2203	4300	6503	SO:0001819	synonymous_variant	83987	exon1			GGCCTCCGCCCTC	BC025243	CCDS12685.1	19q13.33	2012-04-17			ENSG00000169515	ENSG00000169515		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25367	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 20"	614145				11230166	Standard	NM_032040		Approved	DKFZp564K0322, 3M3, PPP1R20	uc002pep.3	Q9H0W5	OTTHUMG00000162348	ENST00000307522.3:c.1179G>A	chr19.hg19:g.46914889C>T		182.0	0.0		325.0	141.0	NM_032040	Q8TB26	Silent	SNP	ENST00000307522.3	hg19	CCDS12685.1	.	.	.	.	.	.	.	.	.	.	C	4.719	0.133637	0.09032	.	.	ENSG00000169515	ENST00000540252	.	.	.	3.03	-0.331	0.12679	.	.	.	.	.	T	0.19485	0.0468	.	.	.	0.18873	N	0.999984	.	.	.	.	.	.	T	0.30736	-0.9968	5	0.16896	T	0.51	.	5.7112	0.17935	0.0:0.4164:0.0:0.5836	.	.	.	.	Q	240	.	ENSP00000441180:R240Q	R	-	2	0	CCDC8	51606729	0.000000	0.05858	0.009000	0.14445	0.012000	0.07955	-0.684000	0.05173	-0.134000	0.11516	-0.811000	0.03165	CGG	.	.		0.582	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	NM_032040		T	46914889	C	T	46914889	2	4	61	1	0	0	0	0	0	0	0	1	2855	639	23	1		1	CCDC8	19	46914889	Silent	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	18	46914889	12214094	60	7502			1	8		2	2	19	N	CTGGTCAGCTGGGGCCTCCGCCCTCTGATTATCTGCAGCCTCTTCCCTGTGGTTATCTGTGCCCTGTGACCT_C	3.953827e-05
JPH2	57158	hgsc.bcm.edu	37	chr20	42815335	42815335	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	catcatcaaagtcgaagcggCccccactcatctcatcatag	6	15	5	0			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr20:42815335C>A	ENST00000372980.3	-	1	883	c.11G>T	c.(10-12)gGc>gTc	p.G4V	JPH2_ENST00000342272.3_Missense_Mutation_p.G4V	NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	4	Gly-rich.				calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			GTCGAAGCGGCCCCCACTCAT	0.662																																					p.G4V		Atlas-SNP	.											.	JPH2	86	.	0			c.G11T						.						36	36	36					20																	42815335		2203	4300	6503	SO:0001583	missense	57158	exon1			AAGCGGCCCCCAC	AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.11G>T	chr20.hg19:g.42815335C>A	ENSP00000362071:p.Gly4Val	9.0	0.0		15.0	11.0	NM_175913	E1P5X1|O95913|Q5JY74|Q9UJN4	Missense_Mutation	SNP	ENST00000372980.3	hg19	CCDS13325.1	.	.	.	.	.	.	.	.	.	.	c	18.13	3.555108	0.65425	.	.	ENSG00000149596	ENST00000372980;ENST00000342272	D;T	0.84442	-1.85;-0.44	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	D	0.96116	0.8734	H	0.99454	4.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.98667	1.0686	10	0.87932	D	0	.	17.4267	0.87528	0.0:1.0:0.0:0.0	.	4;4	Q9BR39-2;Q9BR39	.;JPH2_HUMAN	V	4	ENSP00000362071:G4V;ENSP00000344590:G4V	ENSP00000344590:G4V	G	-	2	0	JPH2	42248749	1.000000	0.71417	1.000000	0.80357	0.353000	0.29299	7.387000	0.79785	2.100000	0.63781	0.556000	0.70494	GGC	.	.		0.662	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1			A	42815335	C	A	42815335	3	1	61	1	0	0	0	0	1	0	0	0	7970	739	26	3	2114	3	JPH2	20	42815335	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10		42815335	20210185	61	7503										
CDH26	60437	hgsc.bcm.edu	37	chr20	58560154	58560154	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	gtggatgtgcaagaaggcaaCaaccacaggcctgcatttac	11	10	0	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr20:58560154C>A	ENST00000244047.5	+	7	1118	c.807C>A	c.(805-807)aaC>aaA	p.N269K	CDH26_ENST00000348616.4_Missense_Mutation_p.N269K			Q8IXH8	CAD26_HUMAN	cadherin 26	269	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			AAGAAGGCAACAACCACAGGC	0.557																																					p.N269K		Atlas-SNP	.											.	CDH26	229	.	0			c.C807A						.						60	53	55					20																	58560154		2203	4300	6503	SO:0001583	missense	60437	exon7			AGGCAACAACCAC	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"Cadherins / Major cadherins"	15902	protein-coding gene	gene with protein product			"cadherin-like 26"				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.807C>A	chr20.hg19:g.58560154C>A	ENSP00000244047:p.Asn269Lys	41.0	0.0		80.0	20.0	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	hg19		.	.	.	.	.	.	.	.	.	.	C	11.55	1.672713	0.29693	.	.	ENSG00000124215	ENST00000244047;ENST00000348616	T;T	0.75477	-0.94;-0.94	4.44	2.46	0.29980	.	0.103168	0.64402	D	0.000005	D	0.89269	0.6667	H	0.98005	4.125	0.23572	N	0.997382	D	0.89917	1.0	D	0.97110	1.0	T	0.80365	-0.1413	10	0.87932	D	0	.	7.0596	0.25119	0.0:0.7294:0.1739:0.0967	.	269	Q8IXH8-4	.	K	269	ENSP00000244047:N269K;ENSP00000339390:N269K	ENSP00000244047:N269K	N	+	3	2	CDH26	57993549	1.000000	0.71417	0.004000	0.12327	0.035000	0.12851	1.796000	0.38794	0.316000	0.23135	0.591000	0.81541	AAC	.	.		0.557	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980		A	58560154	C	A	58560154	3	1	61	1	0	0	0	0	1	0	0	0	3112	477	17	3	833	3	CDH26	20	58560154	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10	15744819	58560154	4465366	62	7504										
CHAF1B	8208	hgsc.bcm.edu	37	chr21	37785409	37785409	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	aacccaagaccccagcagccCcggcacgactccccctcagg	8	21	1	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr21:37785409C>A	ENST00000314103.5	+	12	1440	c.1289C>A	c.(1288-1290)cCc>cAc	p.P430H		NM_005441.2	NP_005432.1	Q13112	CAF1B_HUMAN	chromatin assembly factor 1, subunit B (p60)	430					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(2)	20						CCCAGCAGCCCCGGCACGACT	0.632																																					p.P430H		Atlas-SNP	.											.	CHAF1B	47	.	0			c.C1289A						.						36	38	38					21																	37785409		2203	4300	6503	SO:0001583	missense	8208	exon12			GCAGCCCCGGCAC	U20980	CCDS13644.1	21q22.2	2013-01-10			ENSG00000159259	ENSG00000159259		"WD repeat domain containing"	1911	protein-coding gene	gene with protein product	"M-phase phosphoprotein 7", "Chromatin assembly factor I, p60 subunit", "human chromatin assembly factor-I p60 subunit"	601245				7600578, 8792829	Standard	NM_005441		Approved	CAF1P60, CAF-1, CAF1, CAF1A, MPP7, MPHOSPH7	uc002yvj.3	Q13112	OTTHUMG00000086606	ENST00000314103.5:c.1289C>A	chr21.hg19:g.37785409C>A	ENSP00000315700:p.Pro430His	35.0	0.0		54.0	20.0	NM_005441	Q99548	Missense_Mutation	SNP	ENST00000314103.5	hg19	CCDS13644.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789568	0.70337	.	.	ENSG00000159259	ENST00000314103	T	0.52295	0.67	5.19	5.19	0.71726	.	0.308479	0.35040	N	0.003500	T	0.46580	0.1400	L	0.29908	0.895	0.31766	N	0.632729	D	0.58620	0.983	P	0.51487	0.671	T	0.55392	-0.8148	10	0.46703	T	0.11	-22.6419	14.1135	0.65137	0.0:0.9251:0.0:0.0749	.	430	Q13112	CAF1B_HUMAN	H	430	ENSP00000315700:P430H	ENSP00000315700:P430H	P	+	2	0	CHAF1B	36707279	0.714000	0.27936	0.484000	0.27391	0.325000	0.28411	2.033000	0.41136	2.407000	0.81776	0.558000	0.71614	CCC	.	.		0.632	CHAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194616.2	NM_005441		A	37785409	C	A	37785409	3	1	61	1	0	0	0	0	1	0	0	0	3314	623	22	3	1331	3	CHAF1B	21	37785409	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10		37785409	10344486	63	7505										
IL17REL	400935	hgsc.bcm.edu	37	chr22	50439551	50439551	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	cgtacacgcaggagcatcgcGcagccgtcagaggggacaca	14	13	1	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chr22:50439551G>C	ENST00000389983.2	-	4	333	c.69C>G	c.(67-69)tgC>tgG	p.C23W	IL17REL_ENST00000341280.5_Missense_Mutation_p.C23W	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	23										endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GGAGCATCGCGCAGCCGTCAG	0.652																																					p.C23W		Atlas-SNP	.											.	IL17REL	21	.	0			c.C69G						.						41	33	35					22																	50439551		2194	4295	6489	SO:0001583	missense	400935	exon4			CATCGCGCAGCCG	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.69C>G	chr22.hg19:g.50439551G>C	ENSP00000374633:p.Cys23Trp	43.0	0.0		78.0	46.0	NM_001001694	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	hg19	CCDS33679.1	.	.	.	.	.	.	.	.	.	.	g	12.74	2.028950	0.35797	.	.	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.34072	1.38;1.38	3.16	-0.348	0.12613	.	0.155416	0.43747	U	0.000535	T	0.47432	0.1445	L	0.59436	1.845	0.09310	N	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.27157	-1.0082	10	0.87932	D	0	.	5.7491	0.18136	0.4071:0.0:0.5929:0.0	.	23	Q6ZVW7	I17EL_HUMAN	W	23	ENSP00000374633:C23W;ENSP00000342520:C23W	ENSP00000342520:C23W	C	-	3	2	IL17REL	48781678	0.022000	0.18835	0.020000	0.16555	0.006000	0.05464	-0.109000	0.10840	0.093000	0.17368	-0.144000	0.13903	TGC	.	.		0.652	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694		C	50439551	G	C	50439551	3	2	61	1	0	0	0	0	1	0	0	0	7653	1079	38	4	985	4	IL17REL	22	50439551	Missense_Mutation	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10		50439551	865015	64	7506										
GPR64	10149	hgsc.bcm.edu	37	chrX	19017392	19017392	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	atactgcattgttgttgatcCagcagctggagtttgtggag	13	6	0	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chrX:19017392C>A	ENST00000379869.3	-	26	2499	c.2336G>T	c.(2335-2337)tGg>tTg	p.W779L	GPR64_ENST00000379876.1_Missense_Mutation_p.W755L|GPR64_ENST00000354791.3_Missense_Mutation_p.W763L|GPR64_ENST00000379878.3_Missense_Mutation_p.W763L|GPR64_ENST00000357991.3_Missense_Mutation_p.W776L|GPR64_ENST00000356606.4_Missense_Mutation_p.W765L|GPR64_ENST00000340581.3_Missense_Mutation_p.W660L|GPR64_ENST00000360279.4_Missense_Mutation_p.W757L|GPR64_ENST00000357544.3_Missense_Mutation_p.W749L|GPR64_ENST00000379873.2_Missense_Mutation_p.W779L	NM_001079858.2|NM_005756.3	NP_001073327.1|NP_005747.2	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64	779					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)|spermatogenesis (GO:0007283)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(18)|stomach(1)|urinary_tract(1)	42	Hepatocellular(33;0.183)					GTTGTTGATCCAGCAGCTGGA	0.398																																					p.W779L		Atlas-SNP	.											.	GPR64	102	.	0			c.G2336T						.						93	95	94					X																	19017392		2203	4300	6503	SO:0001583	missense	10149	exon26			TTGATCCAGCAGC	X81892	CCDS14191.1, CCDS43921.1, CCDS43922.1, CCDS43923.1, CCDS55376.1, CCDS55377.1, CCDS55378.1, CCDS55379.1	Xp22.13	2014-08-08			ENSG00000173698	ENSG00000173698		"-", "GPCR / Class B : Orphans"	4516	protein-coding gene	gene with protein product	"epididymal protein 6"	300572				9739419, 9150425	Standard	NM_005756		Approved	HE6, TM7LN2, EDDM6	uc004cyx.3	Q8IZP9	OTTHUMG00000021223	ENST00000379869.3:c.2336G>T	chrX.hg19:g.19017392C>A	ENSP00000369198:p.Trp779Leu	152.0	0.0		209.0	20.0	NM_001184834	B1AWB3|B1AWB4|B1AWB6|B1AWB7|O00406|Q14CE0|Q8IWT2|Q8IZE4|Q8IZE5|Q8IZE6|Q8IZE7|Q8IZP3|Q8IZP4	Missense_Mutation	SNP	ENST00000379869.3	hg19	CCDS43923.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.654407	0.88056	.	.	ENSG00000173698	ENST00000379873;ENST00000379878;ENST00000354791;ENST00000379876;ENST00000357544;ENST00000379869;ENST00000360279;ENST00000357991;ENST00000356606;ENST00000340581	D;D;D;D;D;D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62;-1.62;-1.62;-1.62;-1.62;-1.62	5.88	5.88	0.94601	GPCR, family 2-like (1);	0.000000	0.52532	D	0.000079	D	0.94466	0.8219	H	0.96015	3.755	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.89917	0.997;0.963;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;P;D;D;D;D;D;D;D;D;D	0.97110	0.992;0.8;0.999;0.998;0.998;1.0;0.999;1.0;1.0;0.999;1.0	D	0.95826	0.8854	10	0.87932	D	0	.	19.1599	0.93526	0.0:1.0:0.0:0.0	.	660;741;749;755;763;779;757;765;776;779;763	Q14CE0;Q8IZP9-8;Q8IZP9-7;Q8IZP9-5;Q8IZP9-3;Q8IZP9-9;Q8IZP9-6;Q8IZP9-4;Q8IZP9-2;Q8IZP9;Q14CE1	.;.;.;.;.;.;.;.;.;GPR64_HUMAN;.	L	779;763;763;755;749;779;757;776;765;660	ENSP00000369202:W779L;ENSP00000369207:W763L;ENSP00000346845:W763L;ENSP00000369205:W755L;ENSP00000350152:W749L;ENSP00000369198:W779L;ENSP00000353421:W757L;ENSP00000350680:W776L;ENSP00000349015:W765L;ENSP00000344972:W660L	ENSP00000344972:W660L	W	-	2	0	GPR64	18927313	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.407000	0.80029	2.475000	0.83589	0.594000	0.82650	TGG	.	.		0.398	GPR64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055970.2			A	19017392	C	A	19017392	3	1	61	1	0	0	0	0	1	0	0	0	6713	595	21	3	733	3	GPR64	23	19017392	Missense_Mutation	SNP	C	TCGA-CC-A123-01A-11D-A12Z-10		19017392	136253168	65	7507										
RLIM	51132	hgsc.bcm.edu	37	chrX	73811891	73811891	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	ctgagtcgctatcactgtacAtaaaatagcttaactcacca	5	11	2	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chrX:73811891A>T	ENST00000332687.6	-	4	1477	c.1259T>A	c.(1258-1260)aTg>aAg	p.M420K	RLIM_ENST00000349225.2_Missense_Mutation_p.M420K	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	420					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ATCACTGTACATAAAATAGCT	0.428																																					p.M420K	Esophageal Squamous(169;1899 1923 14997 18818 32118)	Atlas-SNP	.											.	RLIM	90	.	0			c.T1259A						.						97	90	93					X																	73811891		2203	4300	6503	SO:0001583	missense	51132	exon5			CTGTACATAAAAT	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1259T>A	chrX.hg19:g.73811891A>T	ENSP00000328059:p.Met420Lys	160.0	0.0		185.0	88.0	NM_183353	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	hg19	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.429224	0.43122	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.10477	2.87;2.87	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.34250	0.0891	M	0.79693	2.465	0.80722	D	1	D	0.60160	0.987	D	0.66196	0.942	T	0.15925	-1.0420	10	0.87932	D	0	-1.959	14.696	0.69121	1.0:0.0:0.0:0.0	.	420	Q9NVW2	RNF12_HUMAN	K	420	ENSP00000328059:M420K;ENSP00000253571:M420K	ENSP00000328059:M420K	M	-	2	0	RLIM	73728616	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.903000	0.92573	1.851000	0.53745	0.486000	0.48141	ATG	.	.		0.428	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		T	73811891	A	T	73811891	3	4	61	1	0	0	0	0	1	0	0	0	13405	217	8	4	619	4	RLIM	23	73811891	Missense_Mutation	SNP	A	TCGA-CC-A123-01A-11D-A12Z-10	54794499	73811891	81458669	66	7508										
RAB40A	142684	hgsc.bcm.edu	37	chrX	102755566	102755566	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	cgagatggctgtacggggacTcagctgcaccatcctgcagg	14	12	1	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chrX:102755566T>A	ENST00000372633.1	-	1	2237	c.119A>T	c.(118-120)gAg>gTg	p.E40V	LL0XNC01-250H12.3_ENST00000445990.1_RNA|RAB40A_ENST00000304236.1_Missense_Mutation_p.E40V			Q8WXH6	RB40A_HUMAN	RAB40A, member RAS oncogene family	40					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	12						GTACGGGGACTCAGCTGCACC	0.622																																					p.E40V		Atlas-SNP	.											.	RAB40A	30	.	0			c.A119T						.						118	105	109					X																	102755566		2203	4300	6503	SO:0001583	missense	142684	exon3			GGGGACTCAGCTG	AF132748	CCDS35357.1	Xq22.1	2009-08-25			ENSG00000172476	ENSG00000172476		"RAB, member RAS oncogene"	18283	protein-coding gene	gene with protein product						11697911	Standard	NM_080879		Approved	RAR2A, Rar-2	uc004ekk.3	Q8WXH6	OTTHUMG00000022100	ENST00000372633.1:c.119A>T	chrX.hg19:g.102755566T>A	ENSP00000361716:p.Glu40Val	236.0	0.0		281.0	104.0	NM_080879	O00407|Q17RQ5|Q6DK06|Q8TF06	Missense_Mutation	SNP	ENST00000372633.1	hg19	CCDS35357.1	.	.	.	.	.	.	.	.	.	.	.	16.52	3.146237	0.57044	.	.	ENSG00000172476	ENST00000372633;ENST00000304236	T;T	0.76968	-1.06;-1.06	1.53	1.53	0.23141	Small GTP-binding protein domain (1);	0.000000	0.47455	U	0.000231	T	0.55816	0.1944	N	0.17345	0.48	0.58432	D	0.999995	P	0.39352	0.669	B	0.34931	0.192	T	0.50110	-0.8866	10	0.39692	T	0.17	.	6.8887	0.24216	0.0:0.0:0.0:1.0	.	40	Q8WXH6	RB40A_HUMAN	V	40	ENSP00000361716:E40V;ENSP00000305648:E40V	ENSP00000305648:E40V	E	-	2	0	RAB40A	102642222	1.000000	0.71417	0.017000	0.16124	0.029000	0.11900	5.041000	0.64196	0.580000	0.29522	0.235000	0.17854	GAG	.	.		0.622	RAB40A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057714.1			A	102755566	T	A	102755566	3	1	61	1	0	0	0	0	1	0	0	0	12954	1551	54	4	718	4	RAB40A	23	102755566	Missense_Mutation	SNP	T	TCGA-CC-A123-01A-11D-A12Z-10	28943675	102755566	52514994	67	7509										
FRMD7	90167	hgsc.bcm.edu	37	chrX	131212315	131212315	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	4	1	1.2224281742354	0	1.86959603118356	0.0285714285714286	0.304738562091504	0	cttgaatgttacatacaaatGcatcttccaaatttgggtct	6	8	2	1			TCGA-CC-A123-01A-11D-A12Z-10	TCGA-CC-A123-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b962e0d4-7df3-46f3-82a3-9a9a6bf09d4b	69282336-dc29-494e-a63e-b8aef9c80bed	g.chrX:131212315G>A	ENST00000298542.4	-	12	1905	c.1730C>T	c.(1729-1731)gCa>gTa	p.A577V	FRMD7_ENST00000464296.1_Missense_Mutation_p.A562V|FRMD7_ENST00000370879.1_Missense_Mutation_p.A457V	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	577					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					ACATACAAATGCATCTTCCAA	0.423																																					p.A577V		Atlas-SNP	.											.	FRMD7	69	.	0			c.C1730T						.						126	113	117					X																	131212315		2203	4300	6503	SO:0001583	missense	90167	exon12			ACAAATGCATCTT	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"nystagmus 1, congenital"	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1730C>T	chrX.hg19:g.131212315G>A	ENSP00000298542:p.Ala577Val	202.0	0.0		245.0	113.0	NM_194277	C0LLJ3|Q5JX99	Missense_Mutation	SNP	ENST00000298542.4	hg19	CCDS35397.1	.	.	.	.	.	.	.	.	.	.	G	3.190	-0.166006	0.06461	.	.	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	D;D;D	0.87809	-2.3;-1.96;-2.06	5.26	2.15	0.27550	.	0.822948	0.10736	N	0.640041	T	0.78329	0.4266	L	0.31752	0.955	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.60255	-0.7299	10	0.21540	T	0.41	.	9.0464	0.36349	0.3562:0.0:0.6438:0.0	.	562;577	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	V	457;577;562	ENSP00000359916:A457V;ENSP00000298542:A577V;ENSP00000417996:A562V	ENSP00000298542:A577V	A	-	2	0	FRMD7	131039996	0.643000	0.27269	0.926000	0.36857	0.064000	0.16182	1.180000	0.32005	0.275000	0.22094	-0.197000	0.12766	GCA	.	.		0.423	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		A	131212315	G	A	131212315	3	1	61	1	0	0	0	0	1	0	0	0	6063	1319	46	3	418	3	FRMD7	23	131212315	Missense_Mutation	SNP	G	TCGA-CC-A123-01A-11D-A12Z-10	28456749	131212315	24058245	68	7510										
SCNN1D	6339	hgsc.bcm.edu	37	chr1	1222261	1222262	+	Frame_Shift_Ins	INS	-	-	C													0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gccgccctctccgccactgtINScccccgccacgagcccccct							TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr1:1222261_1222262insC	ENST00000338555.2	+	5	1677_1678	c.533_534insC	c.(532-537)gtccccfs	p.VP178fs	SCNN1D_ENST00000379116.5_Frame_Shift_Ins_p.VP342fs|SCNN1D_ENST00000325425.8_Frame_Shift_Ins_p.VP244fs|SCNN1D_ENST00000400928.3_Frame_Shift_Ins_p.VP178fs			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	178					ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	TCCGCCACTGTCCCCCGCCACG	0.644																																					p.V342fs		Atlas-INDEL	.											.	SCNN1D	60	.	0			c.1025_1026insC						.																																			SO:0001589	frameshift_variant	6339	exon8			.	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10601	protein-coding gene	gene with protein product		601328	"sodium channel, nonvoltage-gated 1, delta", "sodium channel, non-voltage-gated 1, delta"			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.538dupC	chr1.hg19:g.1222266_1222266dupC	ENSP00000339504:p.Val178fs	131.0	0.0		171.0	12.0	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Frame_Shift_Ins	INS	ENST00000338555.2	hg19																																																																																				.	.		0.644	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978		C	1222262	-	C	1222261	7	5	62	1	0	1	1	0	0	0	0	0	13944	1667	58	0	749	0	SCNN1D	1	1222261	Frame_Shift_Ins	INS	-	TCGA-CC-A1HT-01A-11D-A12Z-10		1222261	248028360	1	7511										
MTOR	2475	hgsc.bcm.edu	37	chr1	11264717	11264718	+	Frame_Shift_Ins	INS	-	-	C													0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gctcagccgtctcagccattINSccagccagtcatctttggag							TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr1:11264717_11264718insC	ENST00000361445.4	-	26	3920_3921	c.3844_3845insG	c.(3844-3846)gaafs	p.E1282fs		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1282					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCTCAGCCATTCCAGCCAGTCA	0.589																																					p.E1282fs		Atlas-INDEL	.											.	MTOR	327	.	0			c.3845_3846insG						.																																			SO:0001589	frameshift_variant	2475	exon26			.	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.3845dupG	chr1.hg19:g.11264719_11264719dupC	ENSP00000354558:p.Glu1282fs	191.0	0.0		210.0	13.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Frame_Shift_Ins	INS	ENST00000361445.4	hg19	CCDS127.1																																																																																			.	.		0.589	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		C	11264718	-	C	11264717	7	5	62	1	0	1	1	0	0	0	0	0	9963	1783	62	0	3936	0	MTOR	1	11264717	Frame_Shift_Ins	INS	-	TCGA-CC-A1HT-01A-11D-A12Z-10	10042456	11264717	237985904	2	7512										
NRD1	4898	hgsc.bcm.edu	37	chr1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	catcatcttcttcttcttccTccacctcctcttcttcttca	0	18	9	0	rs62648104		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr1:52306079T>A	ENST00000354831.7	-	2	638	c.449A>T	c.(448-450)gAg>gTg	p.E150V	NRD1_ENST00000539524.1_Missense_Mutation_p.E18V|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_Missense_Mutation_p.E18V|NRD1_ENST00000352171.7_Missense_Mutation_p.E150V	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).|Poly-Glu.				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcttcttcctccacctcctc	0.378																																					p.E150V		Atlas-SNP	.											.	NRD1	89	.	0			c.A449T						.						163	138	146					1																	52306079		2203	4300	6503	SO:0001583	missense	4898	exon2			TCTTCCTCCACCT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.449A>T	chr1.hg19:g.52306079T>A	ENSP00000346890:p.Glu150Val	311.0	0.0		314.0	44.0	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	3.056	-0.194350	0.06259	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.38240	1.31;3.15;1.15;1.22	5.25	2.92	0.33932	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.525899	0.19688	N	0.108344	T	0.18341	0.0440	N	0.14661	0.345	0.09310	N	1	B;B;B	0.23650	0.062;0.089;0.01	B;B;B	0.17098	0.017;0.007;0.007	T	0.14755	-1.0461	10	0.38643	T	0.18	-0.0317	5.1939	0.15225	0.0:0.1704:0.2022:0.6274	rs62648104	150;150;150	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	V	150;150;18;150;18	ENSP00000262679:E150V;ENSP00000346890:E150V;ENSP00000444416:E18V;ENSP00000442262:E18V	ENSP00000262679:E150V	E	-	2	0	NRD1	52078667	0.129000	0.22400	0.012000	0.15200	0.145000	0.21501	0.870000	0.28010	0.317000	0.23160	0.454000	0.30748	GAG	.	T|0.024;A|0.976		0.378	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		A	52306079	T	A	52306079	3	1	62	1	0	0	0	0	1	0	0	0	10654	1551	54	4	3338	4	NRD1	1	52306079	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	41041362	52306079	196944542	3	7513										
SEMA6C	10500	hgsc.bcm.edu	37	chr1	151108527	151108527	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	aggctgatgggtgacaggtgGtacagcggggtccagcagcg	19	8	0	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr1:151108527G>T	ENST00000341697.3	-	13	2910	c.1219C>A	c.(1219-1221)Cca>Aca	p.P407T				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	407	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GTGACAGGTGGTACAGCGGGG	0.572																																					p.P407T		Atlas-SNP	.											.	SEMA6C	70	.	0			c.C1219A						.						128	120	123					1																	151108527		2203	4300	6503	SO:0001583	missense	10500	exon13			CAGGTGGTACAGC	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"Semaphorins"	10740	protein-coding gene	gene with protein product	"m-Sema Y2"	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.1219C>A	chr1.hg19:g.151108527G>T	ENSP00000344148:p.Pro407Thr	284.0	0.0		452.0	170.0	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	hg19	CCDS984.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.658586	0.67586	.	.	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697	T;T;T;T	0.10005	2.92;2.92;2.92;2.92	5.35	5.35	0.76521	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.056339	0.64402	D	0.000001	T	0.24160	0.0585	M	0.68593	2.085	0.47308	D	0.999387	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.996;0.998;0.999	T	0.00533	-1.1685	10	0.59425	D	0.04	.	16.5625	0.84570	0.0:0.0:1.0:0.0	.	407;367;407;407	B4DZD4;Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;.;SEM6C_HUMAN	T	407;367;407;407	ENSP00000357910:P407T;ENSP00000357908:P367T;ENSP00000357909:P407T;ENSP00000344148:P407T	ENSP00000344148:P407T	P	-	1	0	SEMA6C	149375151	1.000000	0.71417	1.000000	0.80357	0.720000	0.41350	3.325000	0.52030	2.526000	0.85167	0.561000	0.74099	CCA	.	.		0.572	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		T	151108527	G	T	151108527	3	4	62	1	0	0	0	0	1	0	0	0	14056	1261	44	3	1701	3	SEMA6C	1	151108527	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	98802448	151108527	98142094	4	7514										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158623173	158623173	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tcttctgacatagacagctgGgacaatgccctgatgatcag	10	10	3	4			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr1:158623173G>T	ENST00000368147.4	-	22	3259	c.3079C>A	c.(3079-3081)Cca>Aca	p.P1027T		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1027	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TAGACAGCTGGGACAATGCCC	0.552																																					p.P1027T		Atlas-SNP	.											.	SPTA1	720	.	0			c.C3079A						.						90	93	92					1																	158623173		2048	4175	6223	SO:0001583	missense	6708	exon22			CAGCTGGGACAAT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3079C>A	chr1.hg19:g.158623173G>T	ENSP00000357129:p.Pro1027Thr	201.0	0.0		232.0	97.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	18.06	3.540463	0.65085	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	D;D	0.90504	-2.68;-2.68	5.15	5.15	0.70609	Src homology-3 domain (4);Spectrin alpha chain, SH3 domain (1);	0.000000	0.31976	N	0.006762	D	0.97043	0.9034	H	0.97758	4.07	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.97467	1.0038	10	0.54805	T	0.06	.	17.367	0.87367	0.0:0.0:1.0:0.0	.	1027	P02549	SPTA1_HUMAN	T	1027	ENSP00000357130:P1027T;ENSP00000357129:P1027T	ENSP00000357129:P1027T	P	-	1	0	SPTA1	156889797	1.000000	0.71417	1.000000	0.80357	0.188000	0.23474	8.882000	0.92420	2.692000	0.91855	0.655000	0.94253	CCA	.	.		0.552	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158623173	G	T	158623173	3	4	62	1	0	0	0	0	1	0	0	0	15131	1232	43	3	4304	3	SPTA1	1	158623173	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	7514646	158623173	90627448	5	7515										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185970862	185970862	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ttctcagaagtactttaacaTtgatgtgctaggtaagaaat	8	5	1	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr1:185970862T>A	ENST00000271588.4	+	28	4566	c.4337T>A	c.(4336-4338)aTt>aAt	p.I1446N	HMCN1_ENST00000367492.2_Missense_Mutation_p.I1446N	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1446	Ig-like C2-type 11.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TACTTTAACATTGATGTGCTA	0.353																																					p.I1446N		Atlas-SNP	.											.	HMCN1	797	.	0			c.T4337A						.						49	52	51					1																	185970862		2203	4298	6501	SO:0001583	missense	83872	exon28			TTAACATTGATGT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.4337T>A	chr1.hg19:g.185970862T>A	ENSP00000271588:p.Ile1446Asn	234.0	0.0		189.0	46.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.429619	0.83776	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.78816	-1.21;-1.21	5.82	5.82	0.92795	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.370573	0.29868	N	0.010988	D	0.86752	0.6008	M	0.77486	2.375	0.23487	N	0.997577	D	0.60160	0.987	P	0.60173	0.87	T	0.81756	-0.0787	10	0.87932	D	0	.	16.1839	0.81934	0.0:0.0:0.0:1.0	.	1446	Q96RW7	HMCN1_HUMAN	N	1446	ENSP00000271588:I1446N;ENSP00000356462:I1446N	ENSP00000271588:I1446N	I	+	2	0	HMCN1	184237485	0.972000	0.33761	0.708000	0.30435	0.982000	0.71751	7.344000	0.79328	2.222000	0.72286	0.533000	0.62120	ATT	.	.		0.353	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	185970862	T	A	185970862	3	1	62	1	0	0	0	0	1	0	0	0	7229	1493	52	4	4447	4	HMCN1	1	185970862	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	27347689	185970862	63279759	6	7516										
OR2B11	127623	hgsc.bcm.edu	37	chr1	247614391	247614391	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	agagcccccttcatatctttAtttctcagggtgtaggtgaa	9	9	3	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr1:247614391A>G	ENST00000318749.6	-	1	917	c.894T>C	c.(892-894)aaT>aaC	p.N298N		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			TCATATCTTTATTTCTCAGGG	0.473																																					p.N298N		Atlas-SNP	.											.	OR2B11	102	.	0			c.T894C						.						186	200	195					1																	247614391		2203	4300	6503	SO:0001819	synonymous_variant	127623	exon1			ATCTTTATTTCTC		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"GPCR / Class A : Olfactory receptors"	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.894T>C	chr1.hg19:g.247614391A>G		202.0	0.0		186.0	28.0	NM_001004492	B2RP03	Silent	SNP	ENST00000318749.6	hg19	CCDS31090.1																																																																																			.	.		0.473	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492		G	247614391	A	G	247614391	2	3	62	1	0	0	0	0	0	0	0	1	10997	446	16	2		2	OR2B11	1	247614391	Silent	SNP	A	TCGA-CC-A1HT-01A-11D-A12Z-10	61643529	247614391	1636230	7	7517										
ACP1	52	hgsc.bcm.edu	37	chr2	277013	277013	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	aaaagtaatcaagttaaaacCtgcaaagctaaaattgaact	5	6	1	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr2:277013C>T	ENST00000272065.5	+	5	420	c.327C>T	c.(325-327)acC>acT	p.T109T	ACP1_ENST00000484464.1_3'UTR|ACP1_ENST00000272067.6_Silent_p.T109T	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble	109						cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	AAGTTAAAACCTGCAAAGCTA	0.313																																					p.T109T		Atlas-SNP	.											.	ACP1	42	.	0			c.C327T						.						60	63	62					2																	277013		2201	4300	6501	SO:0001819	synonymous_variant	52	exon5			TAAAACCTGCAAA	M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"Protein tyrosine phosphatases / Class II Cys-based PTPs"	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.327C>T	chr2.hg19:g.277013C>T		277.0	0.0		241.0	39.0	NM_007099	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Silent	SNP	ENST00000272065.5	hg19	CCDS1639.1																																																																																			.	.		0.313	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3			T	277013	C	T	277013	2	4	62	1	0	0	0	0	0	0	0	1	162	668	24	3		3	ACP1	2	277013	Silent	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10		277013	242922360	8	7518										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1812887	1812887	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gatggtcagcatctgctctcCagaaagctttgccttcttca	8	12	5	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr2:1812887C>T	ENST00000399161.2	-	22	3880	c.3133G>A	c.(3133-3135)Gga>Aga	p.G1045R	MYT1L_ENST00000428368.2_Missense_Mutation_p.G1043R|MYT1L_ENST00000407844.1_Missense_Mutation_p.G41R	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1045					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		ATCTGCTCTCCAGAAAGCTTT	0.592																																					p.G1043R		Atlas-SNP	.											.	MYT1L	241	.	0			c.G3127A						.						116	123	121					2																	1812887		2147	4245	6392	SO:0001583	missense	23040	exon22			GCTCTCCAGAAAG	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.3133G>A	chr2.hg19:g.1812887C>T	ENSP00000382114:p.Gly1045Arg	197.0	0.0		170.0	26.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	C	29.7	5.029396	0.93518	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000407844;ENST00000399157;ENST00000428368	T;T;T	0.48201	0.82;1.62;0.82	5.24	5.24	0.73138	.	0.108901	0.64402	D	0.000007	T	0.63189	0.2490	M	0.62723	1.935	0.80722	D	1	P;D;D	0.63880	0.587;0.988;0.993	B;P;P	0.57776	0.221;0.676;0.827	T	0.64202	-0.6463	10	0.49607	T	0.09	-16.9142	18.8228	0.92105	0.0:1.0:0.0:0.0	.	41;1045;1043	Q9UL68-3;Q9UL68;Q9UL68-4	.;MYT1L_HUMAN;.	R	1045;991;41;99;1043	ENSP00000382114:G1045R;ENSP00000382111:G99R;ENSP00000396103:G1043R	ENSP00000295067:G991R	G	-	1	0	MYT1L	1791894	1.000000	0.71417	0.837000	0.33122	0.967000	0.64934	4.754000	0.62191	2.439000	0.82584	0.655000	0.94253	GGA	.	.		0.592	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		T	1812887	C	T	1812887	3	4	62	1	0	0	0	0	1	0	0	0	10116	603	21	3	443	3	MYT1L	2	1812887	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	1535874	1812887	241386486	9	7519										
TTC27	55622	hgsc.bcm.edu	37	chr2	32859027	32859027	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gggccccctgttgacttacaCcctcaggactttttgtcatc	8	14	2	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr2:32859027C>T	ENST00000317907.4	+	3	582	c.351C>T	c.(349-351)caC>caT	p.H117H	MIR4765_ENST00000585007.1_RNA	NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	117										breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						TTGACTTACACCCTCAGGACT	0.363																																					p.H117H		Atlas-SNP	.											.	TTC27	71	.	0			c.C351T						.						130	128	128					2																	32859027		2203	4300	6503	SO:0001819	synonymous_variant	55622	exon3			CTTACACCCTCAG	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.351C>T	chr2.hg19:g.32859027C>T		456.0	0.0		461.0	74.0	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Silent	SNP	ENST00000317907.4	hg19	CCDS33176.1																																																																																			.	.		0.363	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		T	32859027	C	T	32859027	2	4	62	1	0	0	0	0	0	0	0	1	16710	506	18	3		3	TTC27	2	32859027	Silent	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	31046140	32859027	210340346	10	7520										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141812802	141812802	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gccccctggcattccatatgGatcgacttcacatgcatggc	9	14	1	0	rs545142973		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr2:141812802G>A	ENST00000389484.3	-	10	2406	c.1435C>T	c.(1435-1437)Cca>Tca	p.P479S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	479	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATTCCATATGGATCGACTTCA	0.433										TSP Lung(27;0.18)																											p.P479S	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C1435T						.						100	89	93					2																	141812802		2203	4300	6503	SO:0001583	missense	53353	exon10			CATATGGATCGAC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1435C>T	chr2.hg19:g.141812802G>A	ENSP00000374135:p.Pro479Ser	167.0	0.0		167.0	22.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118079	0.37339	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.89681	-2.55	5.45	4.56	0.56223	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);Epidermal growth factor-like (1);	0.370906	0.25349	U	0.031320	T	0.78253	0.4254	N	0.12746	0.255	0.25272	N	0.989504	B	0.06786	0.001	B	0.04013	0.001	T	0.56195	-0.8019	10	0.09084	T	0.74	.	15.8587	0.79005	0.0:0.1406:0.8594:0.0	.	479	Q9NZR2	LRP1B_HUMAN	S	479;417	ENSP00000374135:P479S	ENSP00000374135:P479S	P	-	1	0	LRP1B	141529272	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.527000	0.45615	1.268000	0.44264	0.557000	0.71058	CCA	.	.		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141812802	G	A	141812802	3	1	62	1	0	0	0	0	1	0	0	0	8964	1174	41	3	12692	3	LRP1B	2	141812802	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	108953775	141812802	101386571	11	7521										
COBLL1	22837	hgsc.bcm.edu	37	chr2	165551580	165551580	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tctgtttggatggcagtttcTttcacattctcatgagtgtg	10	7	4	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr2:165551580T>A	ENST00000392717.2	-	13	2554	c.2550A>T	c.(2548-2550)aaA>aaT	p.K850N	COBLL1_ENST00000194871.6_Missense_Mutation_p.K879N|COBLL1_ENST00000342193.4_Missense_Mutation_p.K812N|COBLL1_ENST00000375458.2_Missense_Mutation_p.K774N|COBLL1_ENST00000409184.3_Missense_Mutation_p.K812N			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	850						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						TGGCAGTTTCTTTCACATTCT	0.423																																					p.K812N		Atlas-SNP	.											.	COBLL1	122	.	0			c.A2436T						.						147	145	146					2																	165551580		2203	4300	6503	SO:0001583	missense	22837	exon12			AGTTTCTTTCACA	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.2550A>T	chr2.hg19:g.165551580T>A	ENSP00000376478:p.Lys850Asn	396.0	0.0		324.0	60.0	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.71	3.199731	0.58126	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	6.04	1.36	0.22044	.	0.144833	0.48767	D	0.000166	T	0.48804	0.1520	L	0.46157	1.445	0.32112	N	0.589155	P;P;D	0.58268	0.893;0.948;0.982	P;P;P	0.58331	0.567;0.649;0.837	T	0.53620	-0.8413	9	0.32370	T	0.25	-10.6926	6.1571	0.20344	0.1249:0.1933:0.0:0.6817	.	850;879;812	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	N	774;812;812;850;879	.	ENSP00000194871:K879N	K	-	3	2	COBLL1	165259826	0.158000	0.22850	0.990000	0.47175	0.986000	0.74619	-0.280000	0.08468	0.140000	0.18849	0.460000	0.39030	AAA	.	.		0.423	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		A	165551580	T	A	165551580	3	1	62	1	0	0	0	0	1	0	0	0	3656	1606	56	4	1076	4	COBLL1	2	165551580	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	23738778	165551580	77647793	12	7522										
TTN	7273	hgsc.bcm.edu	37	chr2	179395002	179395002	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tccagatggcagttggccggGgttctccagtagccttaact	12	11	1	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr2:179395002G>C	ENST00000591111.1	-	308	101641	c.101417C>G	c.(101416-101418)cCc>cGc	p.P33806R	TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P26382R|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P26574R|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000587576.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P26507R|TTN_ENST00000342992.6_Missense_Mutation_p.P32879R|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P35447R|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000442329.2_RNA			Q8WZ42	TITIN_HUMAN	titin	33806	Ig-like 149.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTTGGCCGGGGTTCTCCAGT	0.378																																					p.P35447R		Atlas-SNP	.											.	TTN	18412	.	0			c.C106340G						.						97	90	92					2																	179395002		1822	4080	5902	SO:0001583	missense	7273	exon358			GGCCGGGGTTCTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.101417C>G	chr2.hg19:g.179395002G>C	ENSP00000465570:p.Pro33806Arg	131.0	0.0		134.0	21.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	8.740	0.918832	0.17982	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83	5.14	5.14	0.70334	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89111	0.6622	H	0.96269	3.795	0.39327	D	0.965345	D;D;D;D	0.59767	0.986;0.986;0.986;0.986	P;P;P;P	0.61800	0.859;0.859;0.859;0.894	D	0.92802	0.6257	9	0.87932	D	0	.	14.1191	0.65175	0.0:0.0:1.0:0.0	.	26382;26507;26574;33806	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	R	32879;26382;26574;26507;26379	ENSP00000343764:P32879R;ENSP00000434586:P26382R;ENSP00000340554:P26574R;ENSP00000352154:P26507R	ENSP00000340554:P26574R	P	-	2	0	TTN	179103248	1.000000	0.71417	0.993000	0.49108	0.157000	0.22087	5.191000	0.65110	2.406000	0.81754	0.491000	0.48974	CCC	.	.		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179395002	G	C	179395002	3	2	62	1	0	0	0	0	1	0	0	0	16750	1232	43	4	1659	4	TTN	2	179395002	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	13843422	179395002	63804371	13	7523										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207170909	207170909	+	Frame_Shift_Del	DEL	C	C	-													0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tgcagtcagtggttgacagaCccccagtggctgtcacagaa							TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr2:207170909delC	ENST00000374423.3	+	5	2043	c.1657delC	c.(1657-1659)cccfs	p.P554fs		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	554							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GGTTGACAGACCCCCAGTGGC	0.433																																					p.R552fs		Pindel	.											.	ZDBF2	531	.	0			c.1656delA						.						100	94	96					2																	207170909		1865	4113	5978	SO:0001589	frameshift_variant	57683	exon5			.	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.1657delC	chr2.hg19:g.207170909delC	ENSP00000363545:p.Pro554fs	99.0	0.0		98.0	10.0	NM_020923	Q6ZNP7|Q6ZSN8	Frame_Shift_Del	DEL	ENST00000374423.3	hg19	CCDS46501.1																																																																																			.	.		0.433	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		-	207170909	C	-	207170909	7	5	62	1	0	1	0	1	0	0	0	0	17614	507	18	0	1667	0	ZDBF2	2	207170909	Frame_Shift_Del	DEL	C	TCGA-CC-A1HT-01A-11D-A12Z-10	27775907	207170909	36028464	14	7524										
TNP1	7141	hgsc.bcm.edu	37	chr2	217724619	217724619	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	cctccccatccctcactcacCgtcatcgccccgtttcctac	3	23	3	0			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr2:217724619C>A	ENST00000236979.2	-	1	168	c.139G>T	c.(139-141)Gcc>Tcc	p.A47S	AC007563.5_ENST00000607591.1_RNA|AC007563.5_ENST00000447289.1_RNA	NM_003284.3	NP_003275.1	P09430	STP1_HUMAN	transition protein 1 (during histone to protamine replacement)	47					chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|fertilization, exchange of chromosomal proteins (GO:0035042)|multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|sexual reproduction (GO:0019953)|single strand break repair (GO:0000012)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|spermatid nucleus elongation (GO:0007290)	male germ cell nucleus (GO:0001673)|nucleosome (GO:0000786)	DNA binding (GO:0003677)			large_intestine(1)|lung(1)|stomach(1)	3		Renal(207;0.0822)		Epithelial(149;8.97e-07)|all cancers(144;2.46e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTCACTCACCGTCATCGCCC	0.552																																					p.A47S		Atlas-SNP	.											.	TNP1	10	.	0			c.G139T						.						218	196	203					2																	217724619		2203	4300	6503	SO:0001630	splice_region_variant	7141	exon1			ACTCACCGTCATC		CCDS2406.1	2q35-q36	2008-06-03			ENSG00000118245	ENSG00000118245			11951	protein-coding gene	gene with protein product		190231				2249851	Standard	NM_003284		Approved		uc002vgk.3	P09430	OTTHUMG00000133057	ENST00000236979.2:c.139+1G>T	chr2.hg19:g.217724619C>A		221.0	0.0		226.0	37.0	NM_003284		Missense_Mutation	SNP	ENST00000236979.2	hg19	CCDS2406.1	.	.	.	.	.	.	.	.	.	.	C	11.69	1.714696	0.30413	.	.	ENSG00000118245	ENST00000236979	.	.	.	5.55	4.67	0.58626	.	0.123073	0.37437	N	0.002085	T	0.34221	0.0890	.	.	.	0.29839	N	0.829379	B	0.21225	0.053	B	0.25405	0.06	T	0.24512	-1.0158	7	.	.	.	-7.7748	11.7343	0.51757	0.1755:0.8245:0.0:0.0	.	47	P09430	STP1_HUMAN	S	47	.	.	A	-	1	0	TNP1	217432864	0.980000	0.34600	0.998000	0.56505	0.660000	0.38997	1.224000	0.32539	1.569000	0.49696	0.655000	0.94253	GCC	.	.		0.552	TNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256673.1	NM_003284	Missense_Mutation	A	217724619	C	A	217724619	5	1	62	1	0	0	0	0	0	0	1	0	16348	666	23	1	36	1	TNP1	2	217724619	Splice_Site	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	10553710	217724619	25474754	15	7525										
PRRT3	285368	hgsc.bcm.edu	37	chr3	9991578	9991578	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tcagcaggggcgtggcggacAtcagagttcctgtgactgtc	15	10	2	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr3:9991578A>G	ENST00000412055.1	-	2	351	c.222T>C	c.(220-222)gaT>gaC	p.D74D	PRRT3_ENST00000411976.2_Silent_p.D74D|PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	74						integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						CGTGGCGGACATCAGAGTTCC	0.627																																					p.D74D		Atlas-SNP	.											.	PRRT3	35	.	0			c.T222C						.						53	60	57					3																	9991578		2009	4178	6187	SO:0001819	synonymous_variant	285368	exon2			GCGGACATCAGAG	AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"Proline-rich transmembrane proteins"	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.222T>C	chr3.hg19:g.9991578A>G		90.0	0.0		120.0	25.0	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Silent	SNP	ENST00000412055.1	hg19	CCDS43049.1																																																																																			.	.		0.627	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351		G	9991578	A	G	9991578	2	3	62	1	0	0	0	0	0	0	0	1	12623	214	8	2		2	PRRT3	3	9991578	Silent	SNP	A	TCGA-CC-A1HT-01A-11D-A12Z-10		9991578	188030852	16	7526										
VGLL4	9686	hgsc.bcm.edu	37	chr3	11606425	11606426	+	Frame_Shift_Del	DEL	GC	GC	-													0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ggctcatggtgggggccacaGcgcgctcgatggggctgcgg					rs145391722		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr3:11606425_11606426delGC	ENST00000413604.1	-	3	515_516	c.145_146delGC	c.(145-147)gctfs	p.A49fs	VGLL4_ENST00000273038.3_Frame_Shift_Del_p.A108fs|VGLL4_ENST00000404339.1_Frame_Shift_Del_p.A113fs|VGLL4_ENST00000430365.2_Frame_Shift_Del_p.A114fs|VGLL4_ENST00000451674.2_Frame_Shift_Del_p.A28fs|VGLL4_ENST00000424529.2_Frame_Shift_Del_p.A24fs			Q14135	VGLL4_HUMAN	vestigial-like family member 4	108					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|endometrium(1)|large_intestine(1)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)		GGGGGCCACAGCGCGCTCGATG	0.653																																					p.114_114del		Atlas-INDEL	.											.	VGLL4	47	.	0			c.341_342del						.																																			SO:0001589	frameshift_variant	9686	exon3			.	D50911	CCDS2606.1, CCDS46754.1, CCDS46755.1, CCDS46756.1, CCDS68342.1, CCDS68343.1	3p25.2	2014-03-03	2014-03-03		ENSG00000144560	ENSG00000144560			28966	protein-coding gene	gene with protein product			"vestigial like 4 (Drosophila)"			8590280, 15140898	Standard	NM_001284390		Approved	KIAA0121	uc010hdx.1	Q14135	OTTHUMG00000129739	ENST00000413604.1:c.145_146delGC	chr3.hg19:g.11606429_11606430delGC	ENSP00000404624:p.Ala49fs	80.0	0.0		104.0	11.0	NM_001128219	B4DTS7|J3KN68|Q7L5V0|Q9BQ78	Frame_Shift_Del	DEL	ENST00000413604.1	hg19																																																																																				.	.		0.653	VGLL4-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000339139.2	NM_014667		-	11606426	GC	-	11606425	7	5	62	1	0	1	0	1	0	0	0	0	17176	971	34	0	561	0	VGLL4	3	11606425	Frame_Shift_Del	DEL	GC	TCGA-CC-A1HT-01A-11D-A12Z-10	1614847	11606425	186416005	17	7527										
C3orf23	285343	hgsc.bcm.edu	37	chr3	44449032	44449032	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	catttctagtatacaaatggTggattgttgtaagagacttc	9	5	1	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr3:44449032T>G	ENST00000342649.4	+	11	1776	c.1349T>G	c.(1348-1350)gTg>gGg	p.V450G	TCAIM_ENST00000417237.1_Missense_Mutation_p.V450G	NM_001282913.1|NM_173826.3	NP_001269842.1|NP_776187.2	Q8N3R3	TCAIM_HUMAN	T cell activation inhibitor, mitochondrial	450						mitochondrion (GO:0005739)											ATACAAATGGTGGATTGTTGT	0.358																																					p.V450G		Atlas-SNP	.											.	.	.	.	0			c.T1349G						.						103	106	105					3																	44449032		2203	4300	6503	SO:0001583	missense	285343	exon11			AAATGGTGGATTG		CCDS2712.1, CCDS43076.1	3p21.33-p21.32	2012-08-22	2012-08-22	2012-08-22	ENSG00000179152	ENSG00000179152			25241	protein-coding gene	gene with protein product	"tolerance associated gene-1"		"chromosome 3 open reading frame 23"	C3orf23		12477932	Standard	NM_001029840		Approved	DKFZp313N0621, TOAG-1	uc003cnd.4	Q8N3R3	OTTHUMG00000133049	ENST00000342649.4:c.1349T>G	chr3.hg19:g.44449032T>G	ENSP00000341539:p.Val450Gly	376.0	0.0		362.0	56.0	NM_173826	A8K9P1|Q0P5T9|Q495R1|Q495R3|Q4G0M4|Q6GMU8	Missense_Mutation	SNP	ENST00000342649.4	hg19	CCDS2712.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.212411	0.79240	.	.	ENSG00000179152	ENST00000417237;ENST00000342649	T;T	0.54279	0.58;0.58	6.07	1.07	0.20283	.	0.227073	0.42420	D	0.000718	T	0.42017	0.1184	L	0.36672	1.1	0.58432	D	0.999992	P	0.38078	0.617	B	0.39738	0.308	T	0.29882	-0.9997	10	0.87932	D	0	.	9.7349	0.40382	0.0:0.255:0.0:0.745	.	450	Q8N3R3	CC023_HUMAN	G	450	ENSP00000402581:V450G;ENSP00000341539:V450G	ENSP00000341539:V450G	V	+	2	0	C3orf23	44424036	1.000000	0.71417	0.878000	0.34440	0.990000	0.78478	3.661000	0.54503	-0.035000	0.13691	0.533000	0.62120	GTG	.	.		0.358	TCAIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256655.2	NM_173826		G	44449032	T	G	44449032	3	3	62	1	0	0	0	0	1	0	0	0	2218	1696	59	5	1439	5	C3orf23	3	44449032	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	32842607	44449032	153573398	18	7528										
PIK3CB	5291	hgsc.bcm.edu	37	chr3	138426053	138426053	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ttttattctctggaaatttaAcatgcaaagctgttgcattt	6	6	1	0			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr3:138426053A>G	ENST00000477593.1	-	10	1551	c.1478T>C	c.(1477-1479)gTt>gCt	p.V493A	PIK3CB_ENST00000289153.2_Missense_Mutation_p.V493A|PIK3CB_ENST00000544716.1_Intron			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	493	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	TGGAAATTTAACATGCAAAGC	0.313																																					p.V493A		Atlas-SNP	.											.	PIK3CB	103	.	0			c.T1478C						.						107	106	106					3																	138426053		2203	4300	6503	SO:0001583	missense	5291	exon9			AATTTAACATGCA		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.1478T>C	chr3.hg19:g.138426053A>G	ENSP00000418143:p.Val493Ala	256.0	0.0		265.0	34.0	NM_006219	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	hg19	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	A	12.41	1.930360	0.34096	.	.	ENSG00000051382	ENST00000477593;ENST00000289153	T;T	0.73789	-0.78;-0.78	5.84	4.67	0.58626	C2 calcium/lipid-binding domain, CaLB (1);	0.830341	0.11251	N	0.583632	T	0.73552	0.3601	L	0.52011	1.625	0.80722	D	1	B;B	0.29270	0.08;0.24	B;B	0.36092	0.142;0.217	T	0.68758	-0.5324	10	0.87932	D	0	-6.1165	11.9542	0.52973	0.932:0.0:0.068:0.0	.	493;97	P42338;B4DZI3	PK3CB_HUMAN;.	A	493	ENSP00000418143:V493A;ENSP00000289153:V493A	ENSP00000289153:V493A	V	-	2	0	PIK3CB	139908743	1.000000	0.71417	0.572000	0.28498	0.194000	0.23727	8.690000	0.91272	1.024000	0.39682	0.482000	0.46254	GTT	.	.		0.313	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			G	138426053	A	G	138426053	3	3	62	1	0	0	0	0	1	0	0	0	11923	43	2	2	1788	2	PIK3CB	3	138426053	Missense_Mutation	SNP	A	TCGA-CC-A1HT-01A-11D-A12Z-10	93977021	138426053	59596377	19	7529										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140401304	140401304	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gcctttgcttctcctttcagCtccaagactgccctgcgcac	7	17	2	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr3:140401304C>A	ENST00000286349.3	+	2	533	c.342C>A	c.(340-342)tcC>tcA	p.S114S		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	114						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						CTCCTTTCAGCTCCAAGACTG	0.537																																					p.S114S		Atlas-SNP	.											.	TRIM42	143	.	0			c.C342A						.						62	64	63					3																	140401304		2203	4300	6503	SO:0001630	splice_region_variant	287015	exon2			TTTCAGCTCCAAG	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.342-1C>A	chr3.hg19:g.140401304C>A		111.0	0.0		118.0	15.0	NM_152616	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	hg19	CCDS3113.1																																																																																			.	.		0.537	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616	Silent	A	140401304	C	A	140401304	5	1	62	1	0	0	0	0	0	0	1	0	16532	811	28	3	348	3	TRIM42	3	140401304	Splice_Site	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	1975251	140401304	57621126	20	7530										
CP	1356	hgsc.bcm.edu	37	chr3	148923993	148923993	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ttttctttagtgaagatgtcTataccagagggagcatagtt	10	5	2	3	rs201036476		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr3:148923993T>C	ENST00000264613.6	-	6	1432	c.1170A>G	c.(1168-1170)atA>atG	p.I390M		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	390	F5/8 type A 2.|Plastocyanin-like 3.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	TGAAGATGTCTATACCAGAGG	0.393																																					p.I390M		Atlas-SNP	.											.	CP	112	.	0			c.A1170G						.						124	124	124					3																	148923993		2203	4300	6503	SO:0001583	missense	1356	exon6			GATGTCTATACCA	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1170A>G	chr3.hg19:g.148923993T>C	ENSP00000264613:p.Ile390Met	267.0	0.0		253.0	62.0	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	hg19	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	T	2.831	-0.242725	0.05906	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98947	-5.26;-5.26	5.08	1.05	0.20165	Cupredoxin (2);	0.594800	0.17372	N	0.176645	D	0.94265	0.8158	L	0.31294	0.92	0.09310	N	0.999997	B;B;B;B	0.32245	0.2;0.2;0.2;0.361	B;B;B;B	0.28232	0.059;0.059;0.059;0.087	D	0.89158	0.3528	10	0.33940	T	0.23	-8.5659	2.7669	0.05322	0.1192:0.1462:0.1234:0.6113	.	390;390;390;390	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	M	390;173	ENSP00000264613:I390M;ENSP00000420545:I173M	ENSP00000264613:I390M	I	-	3	3	CP	150406683	0.067000	0.21026	0.012000	0.15200	0.145000	0.21501	0.290000	0.18975	0.077000	0.16863	-0.316000	0.08728	ATA	.	T|0.999;C|0.001		0.393	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		C	148923993	T	C	148923993	3	2	62	1	0	0	0	0	1	0	0	0	3789	1512	53	2	2083	2	CP	3	148923993	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	8522689	148923993	49098437	21	7531										
MME	4311	hgsc.bcm.edu	37	chr3	154890002	154890002	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ttttcttgaactttgcacagGtattgtgtctttcttgattg	8	6	3	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr3:154890002G>T	ENST00000460393.1	+	21	2196		c.e21+1		MME-AS1_ENST00000484721.1_RNA|MME_ENST00000360490.2_Splice_Site|MME_ENST00000462745.1_Splice_Site|MME_ENST00000492661.1_Splice_Site|MME_ENST00000493237.1_Splice_Site	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase						angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	CTTTGCACAGGTATTGTGTCT	0.328																																					.		Atlas-SNP	.											.	MME	133	.	0			c.2076+1G>T						.						89	96	94					3																	154890002		2203	4298	6501	SO:0001630	splice_region_variant	4311	exon21			GCACAGGTATTGT		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.2076+1G>T	chr3.hg19:g.154890002G>T		1098.0	0.0		827.0	132.0	NM_000902	A8K6U6|D3DNJ9|Q3MIX4	Splice_Site	SNP	ENST00000460393.1	hg19	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110435	0.77210	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2626	0.93974	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MME	156372696	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.666000	0.98612	2.544000	0.85801	0.585000	0.79938	.	.	.		0.328	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902	Intron	T	154890002	G	T	154890002	5	4	62	1	0	0	0	0	0	0	1	0	9654	1275	44	3	2155	3	MME	3	154890002	Splice_Site	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	5966009	154890002	43132428	22	7532										
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184045645	184045645	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tccagtgcgtgcaggagctgGcctcaccctccttgctcttc	10	16	2	0			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr3:184045645G>A	ENST00000346169.2	+	26	4079	c.3808G>A	c.(3808-3810)Gcc>Acc	p.A1270T	EIF4G1_ENST00000435046.2_Missense_Mutation_p.A1074T|EIF4G1_ENST00000427845.1_Missense_Mutation_p.A1184T|EIF4G1_ENST00000424196.1_Missense_Mutation_p.A1277T|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000392537.2_Missense_Mutation_p.A1183T|EIF4G1_ENST00000350481.5_Missense_Mutation_p.A1106T|EIF4G1_ENST00000434061.2_Missense_Mutation_p.A1075T|EIF4G1_ENST00000342981.4_Missense_Mutation_p.A1271T|EIF4G1_ENST00000352767.3_Missense_Mutation_p.A1277T|EIF4G1_ENST00000382330.3_Missense_Mutation_p.A1277T|EIF4G1_ENST00000411531.1_Missense_Mutation_p.A1231T|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000319274.6_Missense_Mutation_p.A1270T|EIF4G1_ENST00000414031.1_Missense_Mutation_p.A1230T|EIF4G1_ENST00000441154.1_Missense_Mutation_p.A1107T	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1270	MI. {ECO:0000255|PROSITE- ProRule:PRU00698}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GCAGGAGCTGGCCTCACCCTC	0.617																																					p.A1277T		Atlas-SNP	.											.	EIF4G1	151	.	0			c.G3829A						.						88	74	79					3																	184045645		2203	4300	6503	SO:0001583	missense	1981	exon27			GAGCTGGCCTCAC	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.3808G>A	chr3.hg19:g.184045645G>A	ENSP00000316879:p.Ala1270Thr	106.0	0.0		109.0	33.0	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	hg19	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.916641	0.73098	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000382330;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000441154;ENST00000434061;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55	6.17	4.37	0.52481	Initiation factor eIF-4 gamma, MA3 (3);Armadillo-type fold (1);	0.221143	0.47852	D	0.000219	T	0.24392	0.0591	L	0.40543	1.245	0.30116	N	0.806153	P;P;P	0.40931	0.733;0.733;0.733	B;B;B	0.43052	0.406;0.406;0.406	T	0.09357	-1.0678	10	0.16420	T	0.52	-5.3456	6.6418	0.22913	0.1259:0.0:0.6099:0.2642	.	1277;1271;1270	E9PFM1;D3DNT2;Q04637	.;.;IF4G1_HUMAN	T	1270;1230;1183;1277;1106;1277;1184;1271;1270;1277;1231;1107;1075;1074	ENSP00000316879:A1270T;ENSP00000391935:A1230T;ENSP00000376320:A1183T;ENSP00000371767:A1277T;ENSP00000317600:A1106T;ENSP00000338020:A1277T;ENSP00000407682:A1184T;ENSP00000343450:A1271T;ENSP00000323737:A1270T;ENSP00000416255:A1277T;ENSP00000395974:A1231T;ENSP00000399858:A1107T;ENSP00000411826:A1075T;ENSP00000404754:A1074T	ENSP00000323737:A1270T	A	+	1	0	EIF4G1	185528339	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.505000	0.53356	0.923000	0.37045	-0.169000	0.13324	GCC	.	.		0.617	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		A	184045645	G	A	184045645	3	1	62	1	0	0	0	0	1	0	0	0	5038	1203	42	3	3902	3	EIF4G1	3	184045645	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	29155643	184045645	13976785	23	7533										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66361224	66361224	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ggacatttgccgcagctctgGatgtgaggtgaggctttgaa	15	7	1	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr4:66361224G>A	ENST00000273854.3	-	4	1548	c.948C>T	c.(946-948)atC>atT	p.I316I	EPHA5_ENST00000511294.1_Silent_p.I316I|EPHA5_ENST00000432638.2_Intron|EPHA5_ENST00000354839.4_Silent_p.I316I	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	316	Cys-rich.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CGCAGCTCTGGATGTGAGGTG	0.448										TSP Lung(17;0.13)																											p.I316I		Atlas-SNP	.											.	EPHA5	315	.	0			c.C948T						.						130	131	131					4																	66361224		2203	4300	6503	SO:0001819	synonymous_variant	2044	exon4			GCTCTGGATGTGA	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.948C>T	chr4.hg19:g.66361224G>A		216.0	0.0		208.0	37.0	NM_004439	Q7Z3F2	Silent	SNP	ENST00000273854.3	hg19	CCDS3513.1																																																																																			.	.		0.448	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		A	66361224	G	A	66361224	2	1	62	1	0	0	0	0	0	0	0	1	5172	1164	41	3		3	EPHA5	4	66361224	Silent	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10		66361224	124793052	24	7534										
MUC7	4589	hgsc.bcm.edu	37	chr4	71346814	71346814	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tccatctgtgactttcccatCagcttccaccaaaattacta	3	14	2	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr4:71346814C>T	ENST00000304887.5	+	3	543	c.353C>T	c.(352-354)tCa>tTa	p.S118L	MUC7_ENST00000456088.1_Missense_Mutation_p.S118L|MUC7_ENST00000413702.1_Missense_Mutation_p.S118L|MUC7_ENST00000514512.1_3'UTR	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	118	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			ACTTTCCCATCAGCTTCCACC	0.428																																					p.S118L		Atlas-SNP	.											.	MUC7	91	.	0			c.C353T						.						122	115	118					4																	71346814		2203	4300	6503	SO:0001583	missense	4589	exon4			TCCCATCAGCTTC	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"Mucins"	7518	protein-coding gene	gene with protein product		158375	"mucin 7, salivary"			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.353C>T	chr4.hg19:g.71346814C>T	ENSP00000302021:p.Ser118Leu	171.0	0.0		160.0	31.0	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	hg19	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.704882	0.30232	.	.	ENSG00000171195	ENST00000413702;ENST00000505411;ENST00000456088;ENST00000304887	T;T;T;T	0.54479	0.58;0.57;0.58;0.58	3.44	2.57	0.30868	.	.	.	.	.	T	0.52256	0.1723	N	0.24115	0.695	0.09310	N	1	D	0.65815	0.995	P	0.61003	0.882	T	0.39035	-0.9633	9	0.37606	T	0.19	-2.6315	10.1996	0.43075	0.2007:0.7993:0.0:0.0	.	118	Q8TAX7	MUC7_HUMAN	L	118	ENSP00000407422:S118L;ENSP00000427594:S118L;ENSP00000400585:S118L;ENSP00000302021:S118L	ENSP00000302021:S118L	S	+	2	0	MUC7	71381403	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	1.245000	0.32790	0.991000	0.38814	-0.181000	0.13052	TCA	.	.		0.428	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		T	71346814	C	T	71346814	3	4	62	1	0	0	0	0	1	0	0	0	9990	838	29	3	359	3	MUC7	4	71346814	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	4985590	71346814	119807462	25	7535										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79328918	79328918	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	cccccaccagcaccttcaccCagcaggacatcaatgaaggc	7	18	2	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr4:79328918C>T	ENST00000325942.6	+	31	4671	c.4231C>T	c.(4231-4233)Cag>Tag	p.Q1411*	FRAS1_ENST00000264895.6_Nonsense_Mutation_p.Q1411*	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1411					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CACCTTCACCCAGCAGGACAT	0.582																																					p.Q1411X		Atlas-SNP	.											.	FRAS1	779	.	0			c.C4231T						.						77	84	82					4																	79328918		2123	4238	6361	SO:0001587	stop_gained	80144	exon31			TTCACCCAGCAGG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.4231C>T	chr4.hg19:g.79328918C>T	ENSP00000326330:p.Gln1411*	162.0	0.0		207.0	27.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Nonsense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	C	47	13.622374	0.99753	.	.	ENSG00000138759	ENST00000325942;ENST00000264895	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	18.7528	0.91821	0.0:1.0:0.0:0.0	.	.	.	.	X	1411	.	ENSP00000264895:Q1411X	Q	+	1	0	FRAS1	79547942	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.264000	0.78432	2.671000	0.90904	0.585000	0.79938	CAG	.	.		0.582	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			T	79328918	C	T	79328918	4	4	62	1	0	0	0	0	0	1	0	0	6050	595	21	3	4353	3	FRAS1	4	79328918	Nonsense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	7982104	79328918	111825358	26	7536										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79455713	79455713	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gaaggtgttcctaatggatcCcaatacatctgatatgtcac	8	9	2	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr4:79455713C>T	ENST00000264895.6	+	71	11476	c.11036C>T	c.(11035-11037)cCc>cTc	p.P3679L		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3675					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CTAATGGATCCCAATACATCT	0.453																																					p.P3679L		Atlas-SNP	.											.	FRAS1	779	.	0			c.C11036T						.						131	118	122					4																	79455713		1896	4124	6020	SO:0001583	missense	80144	exon71			TGGATCCCAATAC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11036C>T	chr4.hg19:g.79455713C>T	ENSP00000264895:p.Pro3679Leu	133.0	0.0		133.0	20.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.401489	0.83120	.	.	ENSG00000138759	ENST00000264895	T	0.14516	2.5	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.39332	0.1074	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.28106	-1.0054	10	0.87932	D	0	.	18.4025	0.90522	0.0:1.0:0.0:0.0	.	3679	E9PHH6	.	L	3679	ENSP00000264895:P3679L	ENSP00000264895:P3679L	P	+	2	0	FRAS1	79674737	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	7.667000	0.83888	2.336000	0.79503	0.591000	0.81541	CCC	.	.		0.453	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79455713	C	T	79455713	3	4	62	1	0	0	0	0	1	0	0	0	6050	623	22	3	11393	3	FRAS1	4	79455713	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	126795	79455713	111698563	27	7537										
BANK1	55024	hgsc.bcm.edu	37	chr4	102712095	102712095	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	cggaccccgccccctgcggcCcagcgcccccaggtgggtag	14	20	0	0			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr4:102712095C>T	ENST00000322953.4	+	1	332	c.58C>T	c.(58-60)Cca>Tca	p.P20S	BANK1_ENST00000508653.1_Missense_Mutation_p.P20S|BANK1_ENST00000504592.1_Intron|BANK1_ENST00000428908.1_Missense_Mutation_p.P20S	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	20	Interaction with ITPR2.				B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		CCCCTGCGGCCCAGCGCCCCC	0.726																																					p.P20S		Atlas-SNP	.											.	BANK1	95	.	0			c.C58T						.						2	3	3					4																	102712095		1668	3561	5229	SO:0001583	missense	55024	exon1			TGCGGCCCAGCGC	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.58C>T	chr4.hg19:g.102712095C>T	ENSP00000320509:p.Pro20Ser	4.0	0.0		22.0	13.0	NM_001127507	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	hg19	CCDS34038.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.287454	0.23478	.	.	ENSG00000153064	ENST00000322953;ENST00000428908;ENST00000508653	T;T;T	0.48201	0.82;1.35;1.35	3.43	2.59	0.31030	.	0.400535	0.18627	N	0.135696	T	0.29914	0.0748	N	0.24115	0.695	0.21740	N	0.999568	B;B	0.22909	0.077;0.077	B;B	0.22152	0.038;0.021	T	0.15292	-1.0442	10	0.41790	T	0.15	.	6.645	0.22931	0.0:0.8703:0.0:0.1297	.	20;20	Q8NDB2-4;Q8NDB2	.;BANK1_HUMAN	S	20	ENSP00000320509:P20S;ENSP00000412748:P20S;ENSP00000422314:P20S	ENSP00000320509:P20S	P	+	1	0	BANK1	102931118	0.002000	0.14202	0.716000	0.30569	0.619000	0.37552	1.155000	0.31700	1.015000	0.39444	0.591000	0.81541	CCA	.	.		0.726	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		T	102712095	C	T	102712095	3	4	62	1	0	0	0	0	1	0	0	0	1309	623	22	3	60	3	BANK1	4	102712095	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	23256382	102712095	88442181	28	7538										
TACR3	6870	hgsc.bcm.edu	37	chr4	104640417	104640417	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	cgtagatgaaattgaccaacGtgttgaaggcggccatggag	14	7	0	4			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr4:104640417G>T	ENST00000304883.2	-	1	556	c.416C>A	c.(415-417)aCg>aAg	p.T139K		NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	139					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		ATTGACCAACGTGTTGAAGGC	0.537																																					p.T139K		Atlas-SNP	.											.	TACR3	102	.	0			c.C416A						.						110	100	104					4																	104640417		2203	4300	6503	SO:0001583	missense	6870	exon1			ACCAACGTGTTGA	M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"GPCR / Class A : Tachykinin receptors"	11528	protein-coding gene	gene with protein product	"neurokinin beta receptor"	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.416C>A	chr4.hg19:g.104640417G>T	ENSP00000303325:p.Thr139Lys	128.0	0.0		128.0	17.0	NM_001059	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	hg19	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	G	31	5.082663	0.94050	.	.	ENSG00000169836	ENST00000304883	T	0.19806	2.12	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.120864	0.56097	D	0.000032	T	0.51924	0.1703	M	0.82716	2.605	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.58075	-0.7700	10	0.72032	D	0.01	.	17.8687	0.88804	0.0:0.0:1.0:0.0	.	139	P29371	NK3R_HUMAN	K	139	ENSP00000303325:T139K	ENSP00000303325:T139K	T	-	2	0	TACR3	104859866	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	9.398000	0.97281	2.446000	0.82766	0.591000	0.81541	ACG	.	.		0.537	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		T	104640417	G	T	104640417	3	4	62	1	0	0	0	0	1	0	0	0	15522	1145	40	1	1001	1	TACR3	4	104640417	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	1928322	104640417	86513859	29	7539										
NDST3	9348	hgsc.bcm.edu	37	chr4	119154261	119154261	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gaggaggtacagttctttaaTagaaataactaccacagggg	11	6	1	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr4:119154261T>C	ENST00000296499.5	+	9	2317	c.1914T>C	c.(1912-1914)aaT>aaC	p.N638N	NDST3_ENST00000433996.2_Intron	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	638	Heparan sulfate N-sulfotransferase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						AGTTCTTTAATAGAAATAACT	0.368																																					p.N638N		Atlas-SNP	.											.	NDST3	107	.	0			c.T1914C						.						100	100	100					4																	119154261		2203	4300	6503	SO:0001819	synonymous_variant	9348	exon9			CTTTAATAGAAAT	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.1914T>C	chr4.hg19:g.119154261T>C		234.0	0.0		238.0	45.0	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Silent	SNP	ENST00000296499.5	hg19	CCDS3708.1																																																																																			.	.		0.368	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		C	119154261	T	C	119154261	2	2	62	1	0	0	0	0	0	0	0	1	10266	1403	49	2		2	NDST3	4	119154261	Silent	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	14513844	119154261	72000015	30	7540										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155226013	155226013	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gctggacaatgaagggaatcCcccatctcgtactagtactg	10	11	1	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr4:155226013C>A	ENST00000357232.4	-	17	4047	c.4048G>T	c.(4048-4050)Gga>Tga	p.G1350*		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1350	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GAAGGGAATCCCCCATCTCGT	0.418																																					p.G1350X		Atlas-SNP	.											.	DCHS2	594	.	0			c.G4048T						.						57	54	55					4																	155226013		2203	4300	6503	SO:0001587	stop_gained	54798	exon17			GGAATCCCCCATC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4048G>T	chr4.hg19:g.155226013C>A	ENSP00000349768:p.Gly1350*	409.0	0.0		314.0	47.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Nonsense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	43	9.986833	0.99312	.	.	ENSG00000197410	ENST00000357232	.	.	.	5.88	5.88	0.94601	.	0.084158	0.49305	D	0.000146	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.2441	0.98394	0.0:1.0:0.0:0.0	.	.	.	.	X	1350	.	ENSP00000349768:G1350X	G	-	1	0	DCHS2	155445463	0.996000	0.38824	0.375000	0.26029	0.049000	0.14656	3.986000	0.56937	2.774000	0.95407	0.655000	0.94253	GGA	.	.		0.418	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155226013	C	A	155226013	4	1	62	1	0	0	0	0	0	1	0	0	4290	632	22	3	4738	3	DCHS2	4	155226013	Nonsense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	36071752	155226013	35928263	31	7541										
SLC9A3	6550	hgsc.bcm.edu	37	chr5	488534	488535	+	Frame_Shift_Ins	INS	-	-	C													0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	caggacggccaccgggtccaINScagccgccatgaggctgcca							TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr5:488534_488535insC	ENST00000264938.3	-	3	580_581	c.571_572insG	c.(571-573)gtgfs	p.V191fs	SLC9A3_ENST00000514375.1_Frame_Shift_Ins_p.V191fs	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	191					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CACCGGGTCCACAGCCGCCATG	0.649																																					p.V191fs		Atlas-INDEL	.											.	SLC9A3	89	.	0			c.572_573insG						.																																			SO:0001589	frameshift_variant	6550	exon3			.		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.572dupG	chr5.hg19:g.488535_488535dupC	ENSP00000264938:p.Val191fs	94.0	0.0		135.0	11.0	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Frame_Shift_Ins	INS	ENST00000264938.3	hg19	CCDS3855.1																																																																																			.	.		0.649	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		C	488535	-	C	488534	7	5	62	1	0	1	1	0	0	0	0	0	14728	159	6	0	1992	0	SLC9A3	5	488534	Frame_Shift_Ins	INS	-	TCGA-CC-A1HT-01A-11D-A12Z-10		488534	180426726	32	7542										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140210049	140210049	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	aaggcggagaatcaggatttAaatgaagatcatgatgccaa	11	5	2	4			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr5:140210049A>G	ENST00000529310.1	+	1	2487	c.2373A>G	c.(2371-2373)ttA>ttG	p.L791L	PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	791					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCAGGATTTAAATGAAGATC	0.368																																					p.L791L		Atlas-SNP	.											.	PCDHA6	442	.	0			c.A2373G						.						60	64	63					5																	140210049		2203	4300	6503	SO:0001819	synonymous_variant	56142	exon1			GGATTTAAATGAA	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.2373A>G	chr5.hg19:g.140210049A>G		133.0	0.0		153.0	12.0	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	hg19	CCDS47281.1																																																																																			.	.		0.368	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		G	140210049	A	G	140210049	2	3	62	1	0	0	0	0	0	0	0	1	11537	359	13	2		2	PCDHA6	5	140210049	Silent	SNP	A	TCGA-CC-A1HT-01A-11D-A12Z-10	139721515	140210049	40705211	33	7543										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140432442	140432442	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	cctatatcttgactgttcgaGaaaacaacagtcctgcggtt	8	10	1	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr5:140432442G>A	ENST00000306549.3	+	1	1464	c.1387G>A	c.(1387-1389)Gaa>Aaa	p.E463K		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	463	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GACTGTTCGAGAAAACAACAG	0.413																																					p.E463K		Atlas-SNP	.											.	PCDHB1	148	.	0			c.G1387A						.						76	75	75					5																	140432442		2203	4300	6503	SO:0001583	missense	29930	exon1			GTTCGAGAAAACA	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1387G>A	chr5.hg19:g.140432442G>A	ENSP00000307234:p.Glu463Lys	146.0	0.0		147.0	23.0	NM_013340	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	hg19	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.631364	0.87660	.	.	ENSG00000171815	ENST00000306549	T	0.76316	-1.01	6.17	6.17	0.99709	Cadherin (4);Cadherin-like (1);	0.000000	0.45606	D	0.000356	D	0.94453	0.8215	H	0.99770	4.765	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.96165	0.9118	10	0.87932	D	0	.	20.4898	0.99202	0.0:0.0:1.0:0.0	.	463	Q9Y5F3	PCDB1_HUMAN	K	463	ENSP00000307234:E463K	ENSP00000307234:E463K	E	+	1	0	PCDHB1	140412626	1.000000	0.71417	0.998000	0.56505	0.878000	0.50629	6.688000	0.74557	2.941000	0.99782	0.655000	0.94253	GAA	.	.		0.413	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		A	140432442	G	A	140432442	3	1	62	1	0	0	0	0	1	0	0	0	11543	943	33	3	1389	3	PCDHB1	5	140432442	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	222393	140432442	40482818	34	7544										
PCDHGA6	56109	hgsc.bcm.edu	37	chr5	140753695	140753695	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	cagcgcagcgagcaggtcctGctcctcacgctcctggggac	13	16	1	0	rs376765941		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr5:140753695G>T	ENST00000517434.1	+	1	45	c.45G>T	c.(43-45)ctG>ctT	p.L15L	PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	15					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCAGGTCCTGCTCCTCACGC	0.597																																					p.L15L		Atlas-SNP	.											.	PCDHGA6	219	.	0			c.G45T						.	G	,,,,,,,,,	1,3989		0,1,1994	14	17	16		,,,,,45,,,,45	1	0	5		16	0,8370		0,0,4185	no	intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,coding-synonymous	PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032086.1	,,,,,,,,,	0,1,6179	TT,TG,GG		0.0,0.0251,0.0081	,,,,,,,,,	,,,,,15/933,,,,15/819	140753695	1,12359	1995	4185	6180	SO:0001819	synonymous_variant	56109	exon1			GGTCCTGCTCCTC	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"Cadherins / Protocadherins : Clustered"	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.45G>T	chr5.hg19:g.140753695G>T		122.0	0.0		176.0	47.0	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Silent	SNP	ENST00000517434.1	hg19	CCDS54926.1																																																																																			.	.		0.597	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		T	140753695	G	T	140753695	2	4	62	1	0	0	0	0	0	0	0	1	11567	1306	46	3		3	PCDHGA6	5	140753695	Silent	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	321253	140753695	40161565	35	7545										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38781906	38781906	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	atcttgcaattcctaatgtgGtaagtattattaaatacact	5	6	1	0			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr6:38781906G>T	ENST00000359357.3	+	23	2936		c.e23+1		DNAH8_ENST00000449981.2_Splice_Site|DNAH8_ENST00000441566.1_Splice_Site			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8						cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TCCTAATGTGGTAAGTATTAT	0.323																																					.		Atlas-SNP	.											.	DNAH8	1239	.	0			c.3333+1G>T						.						93	103	100					6																	38781906		2203	4299	6502	SO:0001630	splice_region_variant	1769	exon25			AATGTGGTAAGTA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.2682+1G>T	chr6.hg19:g.38781906G>T		147.0	0.0		146.0	21.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Splice_Site	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	G	21.0	4.079767	0.76528	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.803	0.85618	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAH8	38889884	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.832000	0.69337	2.503000	0.84419	0.655000	0.94253	.	.	.		0.323	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	Intron	T	38781906	G	T	38781906	5	4	62	1	0	0	0	0	0	0	1	0	4609	1275	44	3	2765	3	DNAH8	6	38781906	Splice_Site	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10		38781906	132333161	36	7546										
EPHA7	2045	hgsc.bcm.edu	37	chr6	94124469	94124469	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	aactctgtttgttgtgctttAgaatccagcagtagtactga	9	7	1	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr6:94124469A>T	ENST00000369303.4	-	2	298	c.114T>A	c.(112-114)tcT>tcA	p.S38S	EPHA7_ENST00000369297.1_Silent_p.S38S	NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	38	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		GTTGTGCTTTAGAATCCAGCA	0.323																																					p.S38S		Atlas-SNP	.											.	EPHA7	251	.	0			c.T114A						.						93	90	91					6																	94124469		2203	4298	6501	SO:0001819	synonymous_variant	2045	exon2			TGCTTTAGAATCC	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.114T>A	chr6.hg19:g.94124469A>T		97.0	0.0		71.0	10.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Silent	SNP	ENST00000369303.4	hg19	CCDS5031.1																																																																																			.	.		0.323	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			T	94124469	A	T	94124469	2	4	62	1	0	0	0	0	0	0	0	1	5174	407	15	4		4	EPHA7	6	94124469	Silent	SNP	A	TCGA-CC-A1HT-01A-11D-A12Z-10	55342563	94124469	76990598	37	7547										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152674871	152674871	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ctgtatgcagtcacttcttcGtgccacttctgaaatgacaa	7	11	3	2	rs201704617		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr6:152674871G>T	ENST00000367255.5	-	68	11536	c.10935C>A	c.(10933-10935)caC>caA	p.H3645Q	SYNE1_ENST00000341594.5_Missense_Mutation_p.H3616Q|SYNE1_ENST00000423061.1_Missense_Mutation_p.H3630Q|SYNE1_ENST00000448038.1_Missense_Mutation_p.H3630Q|SYNE1_ENST00000265368.4_Missense_Mutation_p.H3645Q	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3645					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCACTTCTTCGTGCCACTTCT	0.438										HNSCC(10;0.0054)																											p.H3645Q		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C10935A						.						131	117	122					6																	152674871		2203	4300	6503	SO:0001583	missense	23345	exon68			TTCTTCGTGCCAC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.10935C>A	chr6.hg19:g.152674871G>T	ENSP00000356224:p.His3645Gln	122.0	0.0		132.0	21.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	11.54	1.670013	0.29693	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	5.75	-11.5	0.00074	.	0.095986	0.45867	N	0.000325	T	0.06096	0.0158	L	0.43923	1.385	0.80722	D	1	B;B;B;B	0.16396	0.002;0.002;0.002;0.017	B;B;B;B	0.15052	0.008;0.008;0.008;0.012	T	0.28138	-1.0053	10	0.21014	T	0.42	.	8.2456	0.31686	0.4341:0.2698:0.2961:0.0	.	3645;3645;3645;3630	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	Q	3645;3630;3645;3630;3616	ENSP00000356224:H3645Q;ENSP00000396024:H3630Q;ENSP00000265368:H3645Q;ENSP00000390975:H3630Q;ENSP00000341887:H3616Q	ENSP00000265368:H3645Q	H	-	3	2	SYNE1	152716564	0.200000	0.23398	0.321000	0.25320	0.811000	0.45836	-0.313000	0.08103	-1.959000	0.01018	-0.290000	0.09829	CAC	.	G|0.999;A|0.001		0.438	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152674871	G	T	152674871	3	4	62	1	0	0	0	0	1	0	0	0	15460	1136	40	1	15847	1	SYNE1	6	152674871	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	58550402	152674871	18440196	38	7548										
INTS1	26173	hgsc.bcm.edu	37	chr7	1517435	1517435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	cccagccaggggctcctcctCctgcagcagcagggagctca	12	17	1	0			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr7:1517435C>T	ENST00000404767.3	-	34	4853	c.4768G>A	c.(4768-4770)Gag>Aag	p.E1590K	INTS1_ENST00000389470.4_Missense_Mutation_p.E1789K	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	1590					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GGCTCCTCCTCCTGCAGCAGC	0.687																																					p.E1590K		Atlas-SNP	.											.	INTS1	145	.	0			c.G4768A						.						26	33	30					7																	1517435		2068	4183	6251	SO:0001583	missense	26173	exon34			CCTCCTCCTGCAG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.4768G>A	chr7.hg19:g.1517435C>T	ENSP00000385722:p.Glu1590Lys	93.0	0.0		165.0	21.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.697416	0.30142	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.52295	0.75;0.67	4.46	3.01	0.34805	.	0.197549	0.52532	D	0.000077	T	0.34164	0.0888	L	0.32530	0.975	0.37088	D	0.899313	B	0.09022	0.002	B	0.08055	0.003	T	0.18178	-1.0345	10	0.36615	T	0.2	.	9.7376	0.40397	0.0:0.8534:0.0:0.1466	.	1590	Q8N201	INT1_HUMAN	K	1590;1789	ENSP00000385722:E1590K;ENSP00000374121:E1789K	ENSP00000374121:E1789K	E	-	1	0	INTS1	1483961	1.000000	0.71417	0.943000	0.38184	0.923000	0.55619	5.424000	0.66464	0.441000	0.26529	0.561000	0.74099	GAG	.	.		0.687	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			T	1517435	C	T	1517435	3	4	62	1	0	0	0	0	1	0	0	0	7784	864	30	3	1864	3	INTS1	7	1517435	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10		1517435	157621228	39	7549										
ITGB8	3696	hgsc.bcm.edu	37	chr7	20445703	20445703	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	aggaattgtatgcaatgcctTcaccctcacaatttgtctca	6	11	3	0			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr7:20445703T>A	ENST00000222573.4	+	12	2616	c.1932T>A	c.(1930-1932)ctT>ctA	p.L644L	ITGB8_ENST00000537992.1_Silent_p.L509L	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	644					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						TGCAATGCCTTCACCCTCACA	0.383																																					p.L644L		Atlas-SNP	.											.	ITGB8	159	.	0			c.T1932A						.						133	118	123					7																	20445703		2203	4300	6503	SO:0001819	synonymous_variant	3696	exon12			ATGCCTTCACCCT		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.1932T>A	chr7.hg19:g.20445703T>A		145.0	0.0		141.0	25.0	NM_002214	A4D133|B4DHD4	Silent	SNP	ENST00000222573.4	hg19	CCDS5370.1																																																																																			.	.		0.383	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		A	20445703	T	A	20445703	2	1	62	1	0	0	0	0	0	0	0	1	7910	1770	62	4		4	ITGB8	7	20445703	Silent	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	18928268	20445703	138692960	40	7550										
PDE1C	5137	hgsc.bcm.edu	37	chr7	31877505	31877505	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	cttctggctgctgcagagcaGtcttcattgctttgatttgt	10	9	3	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr7:31877505G>A	ENST00000396191.1	-	10	1516	c.1061C>T	c.(1060-1062)aCt>aTt	p.T354I	PDE1C_ENST00000396184.3_Missense_Mutation_p.T354I|PDE1C_ENST00000321453.7_Missense_Mutation_p.T354I|PDE1C_ENST00000396182.2_Missense_Mutation_p.T354I|PDE1C_ENST00000396193.1_Missense_Mutation_p.T414I	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	354	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.T354I(2)|p.T414I(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	CTGCAGAGCAGTCTTCATTGC	0.433																																					p.T414I		Atlas-SNP	.											PDE1C_ENST00000396193,NS,carcinoma,0,3	PDE1C	465	.	3	Substitution - Missense(3)	lung(3)	c.C1241T						.						191	184	187					7																	31877505		2203	4300	6503	SO:0001583	missense	5137	exon11			AGAGCAGTCTTCA	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1061C>T	chr7.hg19:g.31877505G>A	ENSP00000379494:p.Thr354Ile	109.0	1.0		117.0	11.0	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	hg19	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.953691	0.53293	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05	5.53	4.59	0.56863	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.090141	0.64402	D	0.000001	T	0.73079	0.3541	M	0.66297	2.02	0.43021	D	0.994577	B;B;B	0.24920	0.016;0.017;0.114	B;B;B	0.21917	0.037;0.009;0.03	T	0.74087	-0.3778	10	0.87932	D	0	.	8.4074	0.32622	0.0:0.1284:0.5786:0.293	.	354;414;354	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	I	414;354;354;354;354	ENSP00000379496:T414I;ENSP00000379494:T354I;ENSP00000318105:T354I;ENSP00000379487:T354I;ENSP00000379485:T354I	ENSP00000318105:T354I	T	-	2	0	PDE1C	31844030	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	5.689000	0.68234	2.603000	0.88011	0.655000	0.94253	ACT	.	.		0.433	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			A	31877505	G	A	31877505	3	1	62	1	0	0	0	0	1	0	0	0	11644	1029	36	3	875	3	PDE1C	7	31877505	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	11431802	31877505	127261158	41	7551										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87196165	87196165	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ccagcctatctcctgtcgcaTtatagcatgaaaaaactgtt	6	11	1	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr7:87196165T>A	ENST00000265724.3	-	7	883	c.466A>T	c.(466-468)Atg>Ttg	p.M156L	ABCB1_ENST00000543898.1_Intron	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	156	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	TCCTGTCGCATTATAGCATGA	0.428																																					p.M156L		Atlas-SNP	.											.	ABCB1	263	.	0			c.A466T						.						135	138	137					7																	87196165		2203	4300	6503	SO:0001583	missense	5243	exon7			GTCGCATTATAGC	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.466A>T	chr7.hg19:g.87196165T>A	ENSP00000265724:p.Met156Leu	147.0	0.0		133.0	23.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	hg19	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	T	6.733	0.504023	0.12822	.	.	ENSG00000085563	ENST00000265724	D	0.86769	-2.17	5.91	4.69	0.59074	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.259797	0.51477	D	0.000087	T	0.61375	0.2342	N	0.00605	-1.335	0.80722	D	1	B	0.10296	0.003	B	0.17433	0.018	T	0.64947	-0.6287	10	0.02654	T	1	-34.9453	12.3263	0.55013	0.0:0.0:0.322:0.678	.	156	P08183	MDR1_HUMAN	L	156	ENSP00000265724:M156L	ENSP00000265724:M156L	M	-	1	0	ABCB1	87034101	0.987000	0.35691	0.919000	0.36401	0.941000	0.58515	1.562000	0.36353	2.269000	0.75478	0.533000	0.62120	ATG	.	.		0.428	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		A	87196165	T	A	87196165	3	1	62	1	0	0	0	0	1	0	0	0	40	1493	52	4	3468	4	ABCB1	7	87196165	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	55318660	87196165	71942498	42	7552										
SLC13A1	6561	hgsc.bcm.edu	37	chr7	122787291	122787291	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	caccaatggtagaagagtagGcaatgcacaaacacgtaagt	10	8	0	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr7:122787291G>C	ENST00000194130.2	-	7	773	c.734C>G	c.(733-735)gCc>gGc	p.A245G	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	245					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	AGAAGAGTAGGCAATGCACAA	0.413																																					p.A245G		Atlas-SNP	.											.	SLC13A1	110	.	0			c.C734G						.						242	184	204					7																	122787291		2203	4300	6503	SO:0001583	missense	6561	exon7			GAGTAGGCAATGC		CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"Solute carriers"	10916	protein-coding gene	gene with protein product		606193	"solute carrier family 13 (sodium/sulphate symporters), member 1"			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.734C>G	chr7.hg19:g.122787291G>C	ENSP00000194130:p.Ala245Gly	163.0	0.0		168.0	29.0	NM_022444	Q9H5Z0	Missense_Mutation	SNP	ENST00000194130.2	hg19	CCDS5786.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.720452	0.89205	.	.	ENSG00000081800	ENST00000194130	T	0.03094	4.05	5.0	5.0	0.66597	.	0.107097	0.64402	D	0.000006	T	0.18841	0.0452	M	0.85777	2.775	0.80722	D	1	D;D	0.55800	0.973;0.973	P;P	0.62382	0.901;0.901	T	0.00512	-1.1696	10	0.51188	T	0.08	.	15.81	0.78552	0.0:0.0:1.0:0.0	.	245;245	A4D0X1;Q9BZW2	.;S13A1_HUMAN	G	245	ENSP00000194130:A245G	ENSP00000194130:A245G	A	-	2	0	SLC13A1	122574527	1.000000	0.71417	0.995000	0.50966	0.968000	0.65278	8.354000	0.90080	2.337000	0.79520	0.563000	0.77884	GCC	.	.		0.413	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		C	122787291	G	C	122787291	3	2	62	1	0	0	0	0	1	0	0	0	14406	1203	42	4	1089	4	SLC13A1	7	122787291	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	35591126	122787291	36351372	43	7553										
NUP205	23165	hgsc.bcm.edu	37	chr7	135269705	135269705	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	atcaggaagaattttatattCgcagagtccataatctcatc	6	8	2	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr7:135269705C>T	ENST00000285968.6	+	8	1194	c.1168C>T	c.(1168-1170)Cgc>Tgc	p.R390C	NUP205_ENST00000440390.2_Missense_Mutation_p.R184C	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	390					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						ATTTTATATTCGCAGAGTCCA	0.348																																					p.R390C		Atlas-SNP	.											.	NUP205	198	.	0			c.C1168T						.						56	55	55					7																	135269705		2203	4300	6503	SO:0001583	missense	23165	exon8			TATATTCGCAGAG	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.1168C>T	chr7.hg19:g.135269705C>T	ENSP00000285968:p.Arg390Cys	161.0	0.0		153.0	18.0	NM_015135	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	hg19	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.848444	0.91277	.	.	ENSG00000155561	ENST00000285968;ENST00000440390	T;T	0.35605	1.3;1.3	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.64204	0.2577	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.66901	-0.5806	10	0.66056	D	0.02	-27.8968	19.44	0.94815	0.0:1.0:0.0:0.0	.	390	Q92621	NU205_HUMAN	C	390;184	ENSP00000285968:R390C;ENSP00000401983:R184C	ENSP00000285968:R390C	R	+	1	0	NUP205	134920245	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	7.818000	0.86416	2.586000	0.87340	0.591000	0.81541	CGC	.	.		0.348	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			T	135269705	C	T	135269705	3	4	62	1	0	0	0	0	1	0	0	0	10768	884	31	1	1198	1	NUP205	7	135269705	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	12482414	135269705	23868958	44	7554										
DPP6	1804	hgsc.bcm.edu	37	chr7	154263941	154263941	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ttttaggaatcattaagagcCatcagatatgaaatatctcc	6	7	3	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr7:154263941C>T	ENST00000377770.3	+	5	708	c.567C>T	c.(565-567)gcC>gcT	p.A189A	DPP6_ENST00000332007.3_Silent_p.A127A|DPP6_ENST00000404039.1_Silent_p.A125A|DPP6_ENST00000427557.1_Silent_p.A127A|DPP6_ENST00000406326.1_Silent_p.A189A|DPP6_ENST00000496611.1_3'UTR			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	189					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			CATTAAGAGCCATCAGATATG	0.308																																					p.A189A	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.C567T						.						67	68	68					7																	154263941		1794	4055	5849	SO:0001819	synonymous_variant	1804	exon5			AAGAGCCATCAGA	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.567C>T	chr7.hg19:g.154263941C>T		185.0	0.0		127.0	15.0	NM_130797		Silent	SNP	ENST00000377770.3	hg19																																																																																				.	.		0.308	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		T	154263941	C	T	154263941	2	4	62	1	0	0	0	0	0	0	0	1	4732	581	21	3		3	DPP6	7	154263941	Silent	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	18994236	154263941	4874722	45	7555										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3081364	3081364	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gacaaaataacacctgctggGcccgtcagattccctccaca	7	15	1	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr8:3081364G>T	ENST00000520002.1	-	29	4929	c.4374C>A	c.(4372-4374)ggC>ggA	p.G1458G	CSMD1_ENST00000539096.1_Silent_p.G1457G|CSMD1_ENST00000537824.1_Silent_p.G1457G|CSMD1_ENST00000602723.1_Silent_p.G1458G|CSMD1_ENST00000400186.3_Silent_p.G1458G|CSMD1_ENST00000542608.1_Silent_p.G1457G|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602557.1_Silent_p.G1458G			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1458	CUB 9. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CACCTGCTGGGCCCGTCAGAT	0.507																																					p.G1457G		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C4371A						.						56	61	59					8																	3081364		1901	4123	6024	SO:0001819	synonymous_variant	64478	exon28			TGCTGGGCCCGTC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4374C>A	chr8.hg19:g.3081364G>T		188.0	0.0		169.0	18.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.22	1.288916	0.23478	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.08	-0.301	0.12800	.	.	.	.	.	T	0.44307	0.1287	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24297	-1.0164	4	.	.	.	.	4.2458	0.10670	0.1348:0.2292:0.5181:0.1179	.	.	.	.	T	938	.	.	P	-	1	0	CSMD1	3068771	1.000000	0.71417	0.821000	0.32701	0.974000	0.67602	1.471000	0.35365	-0.041000	0.13558	0.650000	0.86243	CCC	.	.		0.507	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3081364	G	T	3081364	2	4	62	1	0	0	0	0	0	0	0	1	3946	1190	42	3		3	CSMD1	8	3081364	Silent	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10		3081364	143282658	46	7556										
MYBL1	4603	hgsc.bcm.edu	37	chr8	67492397	67492397	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	aagttctagagtctctgcaaAttctgggatggtctgcaaag	11	7	4	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr8:67492397A>G	ENST00000522677.3	-	9	1482	c.1072T>C	c.(1072-1074)Ttt>Ctt	p.F358L	MYBL1_ENST00000524176.2_Missense_Mutation_p.F358L|MYBL1_ENST00000517885.1_Intron	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	358	Negative regulatory domain. {ECO:0000250}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			GTCTCTGCAAATTCTGGGATG	0.388																																					p.F358L		Atlas-SNP	.											.	MYBL1	73	.	0			c.T1072C						.						59	56	57					8																	67492397		1857	4100	5957	SO:0001583	missense	4603	exon9			CTGCAAATTCTGG	X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.1072T>C	chr8.hg19:g.67492397A>G	ENSP00000429633:p.Phe358Leu	111.0	0.0		206.0	20.0	NM_001080416	E7EW29|Q495F9	Missense_Mutation	SNP	ENST00000522677.3	hg19	CCDS47867.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.784089	0.70222	.	.	ENSG00000185697	ENST00000522677;ENST00000524176	T;T	0.22134	2.42;1.97	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.39145	0.1067	L	0.48986	1.54	0.80722	D	1	D;D;P	0.76494	0.999;0.969;0.714	D;D;B	0.68765	0.96;0.914;0.288	T	0.06285	-1.0835	10	0.34782	T	0.22	-15.6715	15.3103	0.74026	1.0:0.0:0.0:0.0	.	358;357;358	Q495F9;Q495G0;P10243	.;.;MYBA_HUMAN	L	358	ENSP00000429633:F358L;ENSP00000428011:F358L	ENSP00000429633:F358L	F	-	1	0	MYBL1	67654951	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	8.546000	0.90661	2.007000	0.58848	0.533000	0.62120	TTT	.	.		0.388	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		G	67492397	A	G	67492397	3	3	62	1	0	0	0	0	1	0	0	0	10018	101	4	2	1218	2	MYBL1	8	67492397	Missense_Mutation	SNP	A	TCGA-CC-A1HT-01A-11D-A12Z-10	64411033	67492397	78871625	47	7557										
DDX31	64794	hgsc.bcm.edu	37	chr9	135537950	135537950	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tggagaaaacattttttgtgCgttccccttaaaagtcctct	7	9	1	1	rs367667543		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr9:135537950C>T	ENST00000372159.3	-	2	674	c.523G>A	c.(523-525)Gca>Aca	p.A175T	DDX31_ENST00000544003.1_Missense_Mutation_p.A79T|DDX31_ENST00000372153.1_Missense_Mutation_p.A175T|DDX31_ENST00000480876.1_5'UTR|DDX31_ENST00000310532.2_Missense_Mutation_p.A175T|DDX31_ENST00000438527.3_Missense_Mutation_p.A46T	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	175						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		ATTTTTTGTGCGTTCCCCTTA	0.428																																					p.A175T		Atlas-SNP	.											.	DDX31	76	.	0			c.G523A						.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	174	171	172		523,523	-7.7	0	9		172	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	DDX31	NM_138620.1,NM_022779.7	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	175/586,175/852	135537950	1,13005	2203	4300	6503	SO:0001583	missense	64794	exon2			TTTGTGCGTTCCC	AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"DEAD-boxes", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16715	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 25"		"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.523G>A	chr9.hg19:g.135537950C>T	ENSP00000361232:p.Ala175Thr	319.0	0.0		271.0	22.0	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Missense_Mutation	SNP	ENST00000372159.3	hg19	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	c	3.149	-0.174630	0.06421	0.0	1.16E-4	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000372153;ENST00000438527;ENST00000310532;ENST00000544003	T;T;T;T;T	0.47869	4.37;3.92;4.34;3.5;0.83	5.6	-7.73	0.01245	.	1.174590	0.05861	N	0.622977	T	0.15998	0.0385	N	0.08118	0	0.09310	N	1	B;B;B	0.23891	0.093;0.003;0.002	B;B;B	0.14578	0.011;0.003;0.0	T	0.18871	-1.0323	10	0.09843	T	0.71	0.329	0.3822	0.00396	0.2246:0.2316:0.2547:0.2891	.	175;175;175	Q9H8H2-2;Q9H8H2-3;Q9H8H2	.;.;DDX31_HUMAN	T	175;175;175;46;175;79	ENSP00000361232:A175T;ENSP00000361226:A175T;ENSP00000387730:A46T;ENSP00000310539:A175T;ENSP00000442425:A79T	ENSP00000310539:A175T	A	-	1	0	DDX31	134527771	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.965000	0.03829	-0.997000	0.03450	-0.285000	0.09966	GCA	.	.		0.428	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620		T	135537950	C	T	135537950	3	4	62	1	0	0	0	0	1	0	0	0	4358	768	27	1	2115	1	DDX31	9	135537950	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10		135537950	5675481	48	7558										
EPC1	80314	hgsc.bcm.edu	37	chr10	32582635	32582635	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	catcttcagaatccaaatcaTaatcaggctgttcagcatcc	5	12	5	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr10:32582635T>C	ENST00000263062.8	-	3	613	c.344A>G	c.(343-345)tAt>tGt	p.Y115C	EPC1_ENST00000319778.6_Missense_Mutation_p.Y115C|EPC1_ENST00000375110.2_Missense_Mutation_p.Y65C	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	115					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				ATCCAAATCATAATCAGGCTG	0.378																																					p.Y115C		Atlas-SNP	.											.	EPC1	74	.	0			c.A344G						.						55	50	52					10																	32582635		2203	4300	6503	SO:0001583	missense	80314	exon3			AAATCATAATCAG	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.344A>G	chr10.hg19:g.32582635T>C	ENSP00000263062:p.Tyr115Cys	210.0	0.0		260.0	37.0	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Missense_Mutation	SNP	ENST00000263062.8	hg19	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.397618	0.83120	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	D;D;D	0.82255	-1.59;-1.59;-1.59	5.67	5.67	0.87782	Enhancer of polycomb-like, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92655	0.7666	M	0.89601	3.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.997;1.0;1.0	D	0.94069	0.7333	10	0.87932	D	0	-10.2067	15.9001	0.79365	0.0:0.0:0.0:1.0	.	115;65;115;115	B8XCX7;Q9H2F5-3;Q9H2F5-2;Q9H2F5	.;.;.;EPC1_HUMAN	C	65;115;115	ENSP00000364251:Y65C;ENSP00000318559:Y115C;ENSP00000263062:Y115C	ENSP00000263062:Y115C	Y	-	2	0	EPC1	32622641	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.040000	0.89188	2.162000	0.67917	0.383000	0.25322	TAT	.	.		0.378	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			C	32582635	T	C	32582635	3	2	62	1	0	0	0	0	1	0	0	0	5162	1406	49	2	2218	2	EPC1	10	32582635	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10		32582635	102952112	49	7559										
ANO9	338440	hgsc.bcm.edu	37	chr11	418530	418530	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tccagaaccttgttcttcacCgactgagggatgtcgggcac	11	12	2	2	rs369737399		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr11:418530C>T	ENST00000332826.6	-	23	2274	c.2190G>A	c.(2188-2190)tcG>tcA	p.S730S	SIGIRR_ENST00000397632.3_5'Flank|SIGIRR_ENST00000382520.2_5'Flank|SIGIRR_ENST00000332725.3_5'Flank	NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	730					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						TGTTCTTCACCGACTGAGGGA	0.637																																					p.S730S		Atlas-SNP	.											.	ANO9	61	.	0			c.G2190A						.	C		0,4406		0,0,2203	112	100	104		2190	-7.1	0	11		104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ANO9	NM_001012302.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		730/783	418530	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	338440	exon23			CTTCACCGACTGA	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	20679	protein-coding gene	gene with protein product			"tumor protein p53 inducible protein 5", "transmembrane protein 16J"	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.2190G>A	chr11.hg19:g.418530C>T		139.0	0.0		137.0	15.0	NM_001012302	B3KUC4|B4E134|Q8TEN4	Silent	SNP	ENST00000332826.6	hg19	CCDS31326.1																																																																																			.	.		0.637	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302		T	418530	C	T	418530	2	4	62	1	0	0	0	0	0	0	0	1	704	639	23	1		1	ANO9	11	418530	Silent	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10		418530	134587986	50	7560										
OR5D13	390142	hgsc.bcm.edu	37	chr11	55541610	55541610	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ccattatgaagatgcgatctGcaagtgggcgccagaaaact	11	9	1	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr11:55541610G>A	ENST00000361760.1	+	1	697	c.697G>A	c.(697-699)Gca>Aca	p.A233T		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				GATGCGATCTGCAAGTGGGCG	0.418																																					p.A233T		Atlas-SNP	.											.	OR5D13	96	.	0			c.G697A						.						133	120	124					11																	55541610		2200	4296	6496	SO:0001583	missense	390142	exon1			CGATCTGCAAGTG	BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"GPCR / Class A : Olfactory receptors"	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.697G>A	chr11.hg19:g.55541610G>A	ENSP00000354800:p.Ala233Thr	170.0	0.0		189.0	17.0	NM_001001967	Q6IF68|Q6IFC9	Missense_Mutation	SNP	ENST00000361760.1	hg19	CCDS31507.1	.	.	.	.	.	.	.	.	.	.	G	8.180	0.793602	0.16327	.	.	ENSG00000198877	ENST00000361760	T	0.00174	8.62	3.82	-0.775	0.10988	GPCR, rhodopsin-like superfamily (1);	0.514144	0.14326	N	0.326681	T	0.00109	0.0003	N	0.20357	0.565	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.12553	-1.0543	10	0.28530	T	0.3	-0.3088	3.2185	0.06707	0.471:0.0:0.2483:0.2807	.	233	Q8NGL4	OR5DD_HUMAN	T	233	ENSP00000354800:A233T	ENSP00000354800:A233T	A	+	1	0	OR5D13	55298186	0.000000	0.05858	0.004000	0.12327	0.015000	0.08874	-0.680000	0.05197	0.230000	0.21059	0.486000	0.48141	GCA	.	.		0.418	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967		A	55541610	G	A	55541610	3	1	62	1	0	0	0	0	1	0	0	0	11163	1319	46	3	699	3	OR5D13	11	55541610	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	55123080	55541610	79464906	51	7561										
FAM111B	374393	hgsc.bcm.edu	37	chr11	58893210	58893210	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tgaaaatctagattatgccaTtttaaaactaaaagaaaatg	5	4	1	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr11:58893210T>G	ENST00000343597.3	+	4	1831	c.1640T>G	c.(1639-1641)aTt>aGt	p.I547S	FAM111B_ENST00000529618.1_Missense_Mutation_p.I517S|FAM111B_ENST00000411426.1_Missense_Mutation_p.I517S	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	547							catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						GATTATGCCATTTTAAAACTA	0.378																																					p.I547S		Atlas-SNP	.											.	FAM111B	84	.	0			c.T1640G						.						92	90	90					11																	58893210		2201	4295	6496	SO:0001583	missense	374393	exon4			ATGCCATTTTAAA	BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.1640T>G	chr11.hg19:g.58893210T>G	ENSP00000341565:p.Ile547Ser	90.0	0.0		69.0	14.0	NM_198947	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	hg19	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	T	16.36	3.102341	0.56183	.	.	ENSG00000189057	ENST00000411426;ENST00000529618;ENST00000343597	D;D;D	0.90069	-2.61;-2.61;-2.61	4.63	4.63	0.57726	Peptidase cysteine/serine, trypsin-like (1);	0.233245	0.28940	N	0.013644	D	0.93207	0.7836	M	0.77313	2.365	0.27418	N	0.954369	D	0.63046	0.992	D	0.65987	0.94	D	0.87986	0.2746	10	0.87932	D	0	.	11.667	0.51379	0.0:0.0:0.0:1.0	.	547	Q6SJ93	F111B_HUMAN	S	517;517;547	ENSP00000393855:I517S;ENSP00000432875:I517S;ENSP00000341565:I547S	ENSP00000341565:I547S	I	+	2	0	FAM111B	58649786	0.281000	0.24258	0.851000	0.33527	0.453000	0.32348	5.032000	0.64140	1.958000	0.56883	0.533000	0.62120	ATT	.	.		0.378	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		G	58893210	T	G	58893210	3	3	62	1	0	0	0	0	1	0	0	0	5405	1493	52	5	1646	5	FAM111B	11	58893210	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	3351600	58893210	76113306	52	7562										
C11orf9	745	hgsc.bcm.edu	37	chr11	61537931	61537931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	catggggcaggggctggtgcCcactgatcttcaccacaccc	12	15	2	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr11:61537931C>T	ENST00000278836.5	+	5	770	c.674C>T	c.(673-675)cCc>cTc	p.P225L	TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000265460.5_Missense_Mutation_p.P216L	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	225	Pro-rich.				central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GGGCTGGTGCCCACTGATCTT	0.652																																					p.P225L		Atlas-SNP	.											.	.	.	.	0			c.C674T						.						13	12	12					11																	61537931		2180	4256	6436	SO:0001583	missense	745	exon5			TGGTGCCCACTGA		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"myelin gene regulatory factor"	608329	"chromosome 11 open reading frame 9"	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.674C>T	chr11.hg19:g.61537931C>T	ENSP00000278836:p.Pro225Leu	278.0	0.0		363.0	37.0	NM_001127392	O43582|Q9P1Q6	Missense_Mutation	SNP	ENST00000278836.5	hg19	CCDS44622.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.156698	0.78114	.	.	ENSG00000124920	ENST00000278836;ENST00000265460	T;T	0.36520	1.25;1.28	4.35	4.35	0.52113	.	0.247105	0.41294	D	0.000915	T	0.44095	0.1277	N	0.24115	0.695	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.62184	0.899;0.895	T	0.45160	-0.9280	10	0.51188	T	0.08	-29.57	17.4499	0.87589	0.0:1.0:0.0:0.0	.	216;225	Q9Y2G1-2;Q9Y2G1	.;MRF_HUMAN	L	225;216	ENSP00000278836:P225L;ENSP00000265460:P216L	ENSP00000265460:P216L	P	+	2	0	C11orf9	61294507	0.979000	0.34478	0.977000	0.42913	0.972000	0.66771	5.193000	0.65120	2.430000	0.82344	0.491000	0.48974	CCC	.	.		0.652	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		T	61537931	C	T	61537931	3	4	62	1	0	0	0	0	1	0	0	0	1673	623	22	3	715	3	C11orf9	11	61537931	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	2644721	61537931	73468585	53	7563										
GAB2	9846	hgsc.bcm.edu	37	chr11	77932827	77932828	+	Splice_Site	INS	-	-	G													0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ctggagttgaaggtgtggctINSgttgtgggaaggaagagtta					rs145840199		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr11:77932827_77932828insG	ENST00000361507.4	-	8	1744		c.e8-2		GAB2_ENST00000340149.2_Splice_Site	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2						cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			AAGGTGTGGCTGTTGTGGGAAG	0.584																																					.		Atlas-INDEL	.											.	GAB2	63	.	0			c.1659-2->C						.																																			SO:0001630	splice_region_variant	9846	exon9			.	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"Pleckstrin homology (PH) domain containing"	14458	protein-coding gene	gene with protein product	"Grb2-associated binder 2"	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.1659-2->C	chr11.hg19:g.77932828_77932828dupG		353.0	0.0		336.0	22.0	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Splice_Site	INS	ENST00000361507.4	hg19	CCDS8259.1																																																																																			.	.		0.584	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491	Intron	G	77932828	-	G	77932827	8	5	62	1	0	1	1	0	0	0	1	0	6157	1594	55	0	385	0	GAB2	11	77932827	Splice_Site	INS	-	TCGA-CC-A1HT-01A-11D-A12Z-10	16394896	77932827	57073689	54	7564										
FAT3	120114	hgsc.bcm.edu	37	chr11	92085831	92085831	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	cccaggtgactgcaacagacGcagatattggttccaatgga	11	10	0	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr11:92085831G>T	ENST00000298047.6	+	1	570	c.553G>T	c.(553-555)Gca>Tca	p.A185S	FAT3_ENST00000409404.2_Missense_Mutation_p.A185S|FAT3_ENST00000541502.1_Missense_Mutation_p.A185S|FAT3_ENST00000525166.1_Missense_Mutation_p.A35S			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	185	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A185T(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TGCAACAGACGCAGATATTGG	0.428										TCGA Ovarian(4;0.039)																											p.A185S		Atlas-SNP	.											FAT3_ENST00000409404,NS,carcinoma,0,2	FAT3	1822	.	2	Substitution - Missense(2)	endometrium(2)	c.G553T						.						60	60	60					11																	92085831		1866	4110	5976	SO:0001583	missense	120114	exon1			ACAGACGCAGATA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.553G>T	chr11.hg19:g.92085831G>T	ENSP00000298047:p.Ala185Ser	108.0	0.0		86.0	14.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	21.6	4.180161	0.78564	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	5.26	5.26	0.73747	.	.	.	.	.	T	0.74696	0.3750	M	0.67397	2.05	0.54753	D	0.999981	D	0.89917	1.0	D	0.91635	0.999	T	0.73084	-0.4094	9	0.39692	T	0.17	.	18.2264	0.89918	0.0:0.0:1.0:0.0	.	185	Q8TDW7-3	.	S	185;185;185;35	ENSP00000298047:A185S;ENSP00000387040:A185S;ENSP00000443786:A185S;ENSP00000432586:A35S	ENSP00000298047:A185S	A	+	1	0	FAT3	91725479	1.000000	0.71417	0.998000	0.56505	0.797000	0.45037	9.787000	0.99055	2.607000	0.88179	0.655000	0.94253	GCA	.	.		0.428	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92085831	G	T	92085831	3	4	62	1	0	0	0	0	1	0	0	0	5699	1087	38	1	555	1	FAT3	11	92085831	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	14153004	92085831	42920685	55	7565										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105842667	105842667	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tgtaaaccttgccgttttgaAactcagtgaggcaggcgtct	11	9	2	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr11:105842667A>C	ENST00000530497.1	+	14	2321	c.2321A>C	c.(2320-2322)aAa>aCa	p.K774T	GRIA4_ENST00000393127.2_Intron|RNU6-277P_ENST00000516272.1_RNA|GRIA4_ENST00000525187.1_Intron|GRIA4_ENST00000282499.5_Missense_Mutation_p.K774T|GRIA4_ENST00000533094.1_Intron			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	774					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		GCCGTTTTGAAACTCAGTGAG	0.383																																					p.K774T		Atlas-SNP	.											.	GRIA4	380	.	0			c.A2321C						.						91	89	90					11																	105842667		2201	4299	6500	SO:0001583	missense	2893	exon15			TTTTGAAACTCAG	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.2321A>C	chr11.hg19:g.105842667A>C	ENSP00000435775:p.Lys774Thr	164.0	0.0		201.0	40.0	NM_000829	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	hg19	CCDS8333.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.3|20.3	3.963841|3.963841	0.74131|0.74131	.|.	.|.	ENSG00000152578|ENSG00000152578	ENST00000539249|ENST00000282499;ENST00000530497	.|T;T	.|0.40225	.|1.04;1.04	5.55|5.55	5.55|5.55	0.83447|0.83447	.|Ionotropic glutamate receptor (2);	.|0.000000	.|0.64402	.|D	.|0.000002	T|T	0.43144|0.43144	0.1234|0.1234	L|L	0.37850|0.37850	1.14|1.14	0.80722|0.80722	D|D	1|1	.|P	.|0.46395	.|0.877	.|P	.|0.46885	.|0.53	T|T	0.43228|0.43228	-0.9404|-0.9404	6|10	0.16896|0.87932	T|D	0.51|0	.|.	15.7049|15.7049	0.77569|0.77569	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|774	.|P48058	.|GRIA4_HUMAN	D|T	117|774	.|ENSP00000282499:K774T;ENSP00000435775:K774T	ENSP00000440835:E117D|ENSP00000282499:K774T	E|K	+|+	3|2	2|0	GRIA4|GRIA4	105347877|105347877	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.307000|9.307000	0.96226|0.96226	2.117000|2.117000	0.64856|0.64856	0.533000|0.533000	0.62120|0.62120	GAA|AAA	.	.		0.383	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			C	105842667	A	C	105842667	3	2	62	1	0	0	0	0	1	0	0	0	6779	14	1	5	2531	5	GRIA4	11	105842667	Missense_Mutation	SNP	A	TCGA-CC-A1HT-01A-11D-A12Z-10	13756836	105842667	29163849	56	7566										
NTF3	4908	hgsc.bcm.edu	37	chr12	5603521	5603521	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gcagatattttgaaaaacaaGctctccaagcagatggtgga	10	7	1	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr12:5603521G>A	ENST00000331010.6	+	1	224	c.141G>A	c.(139-141)aaG>aaA	p.K47K	NTF3_ENST00000423158.3_Silent_p.K60K|NTF3_ENST00000535299.1_Intron	NM_002527.4	NP_002518.1	P20783	NTF3_HUMAN	neurotrophin 3	47					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell-cell signaling (GO:0007267)|enteric nervous system development (GO:0048484)|epidermis development (GO:0008544)|glial cell fate determination (GO:0007403)|induction of positive chemotaxis (GO:0050930)|mechanoreceptor differentiation (GO:0042490)|myelination (GO:0042552)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive chemotaxis (GO:0050918)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of synaptic transmission (GO:0050804)|signal transduction (GO:0007165)|smooth muscle cell differentiation (GO:0051145)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular region (GO:0005576)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(3)|upper_aerodigestive_tract(1)	22						TGAAAAACAAGCTCTCCAAGC	0.517																																					p.K60K	GBM(194;1104 2182 8339 9578 18493)	Atlas-SNP	.											.	NTF3	50	.	0			c.G180A						.						88	91	90					12																	5603521		2203	4300	6503	SO:0001819	synonymous_variant	4908	exon2			AAACAAGCTCTCC		CCDS8538.1, CCDS44806.1	12p13	2014-01-30			ENSG00000185652	ENSG00000185652		"Endogenous ligands"	8023	protein-coding gene	gene with protein product		162660				1889806	Standard	NM_002527		Approved	NGF2	uc001qnk.4	P20783	OTTHUMG00000168649	ENST00000331010.6:c.141G>A	chr12.hg19:g.5603521G>A		68.0	0.0		54.0	10.0	NM_001102654	B7Z1T5|Q6FH50	Silent	SNP	ENST00000331010.6	hg19	CCDS8538.1																																																																																			.	.		0.517	NTF3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400486.1			A	5603521	G	A	5603521	2	1	62	1	0	0	0	0	0	0	0	1	10705	962	34	3		3	NTF3	12	5603521	Silent	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10		5603521	128248374	57	7567										
SLC2A14	144195	hgsc.bcm.edu	37	chr12	7967043	7967043	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	atcctcaaaagtcctgccacGggtctcagggactttgaaga	10	11	2	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr12:7967043G>A	ENST00000543909.1	-	16	2191	c.1432C>T	c.(1432-1434)Cgt>Tgt	p.R478C	SLC2A14_ENST00000340749.5_Missense_Mutation_p.R455C|SLC2A14_ENST00000539924.1_Missense_Mutation_p.R493C|SLC2A14_ENST00000431042.2_Missense_Mutation_p.R455C|SLC2A14_ENST00000542505.1_Missense_Mutation_p.R119C|SLC2A14_ENST00000535295.1_Missense_Mutation_p.R369C|SLC2A14_ENST00000396589.2_Missense_Mutation_p.R478C|SLC2A14_ENST00000542546.1_Missense_Mutation_p.R369C			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	478					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		GTCCTGCCACGGGTCTCAGGG	0.498													G|||	1	0.000199681	8e-04	0	5008	,	,		-128	0		0	False		,,,				2504	0				p.R478C		Atlas-SNP	.											.	SLC2A14	78	.	0			c.C1432T						.						79	71	74					12																	7967043		2203	4300	6503	SO:0001583	missense	144195	exon12			TGCCACGGGTCTC	AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"Solute carriers"	18301	protein-coding gene	gene with protein product		611039	"solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.1432C>T	chr12.hg19:g.7967043G>A	ENSP00000440480:p.Arg478Cys	202.0	0.0		195.0	15.0	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	hg19	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.567354	0.45694	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000542505;ENST00000396589;ENST00000535295;ENST00000542546;ENST00000539924	T;T;T;T;T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82;-0.82;-0.82;-0.82;-0.82	3.81	1.64	0.23874	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.264168	0.34484	N	0.003935	T	0.74794	0.3763	M	0.88906	2.99	0.43191	D	0.995025	P;B;B;B	0.37276	0.589;0.435;0.381;0.108	B;B;B;B	0.36244	0.168;0.12;0.073;0.22	T	0.76141	-0.3068	10	0.87932	D	0	.	8.9369	0.35706	0.0:0.0:0.4245:0.5754	.	493;369;455;478	B7ZAC3;B7Z844;Q8TDB8-2;Q8TDB8	.;.;.;GTR14_HUMAN	C	455;478;455;119;478;369;369;493	ENSP00000340450:R455C;ENSP00000440480:R478C;ENSP00000407287:R455C;ENSP00000438484:R119C;ENSP00000379834:R478C;ENSP00000440492:R369C;ENSP00000443903:R369C;ENSP00000445929:R493C	ENSP00000340450:R455C	R	-	1	0	SLC2A14	7858310	0.997000	0.39634	0.999000	0.59377	0.989000	0.77384	3.098000	0.50259	0.643000	0.30638	0.460000	0.39030	CGT	.	.		0.498	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		A	7967043	G	A	7967043	3	1	62	1	0	0	0	0	1	0	0	0	14558	1116	39	1	134	1	SLC2A14	12	7967043	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	2363522	7967043	125884852	58	7568										
DENND5B	160518	hgsc.bcm.edu	37	chr12	31605091	31605092	+	Frame_Shift_Ins	INS	-	-	T													0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	cagagaagcagagaggtccaINSttttttccacagccacacca							TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr12:31605091_31605092insT	ENST00000389082.5	-	5	1675_1676	c.1411_1412insA	c.(1411-1413)atgfs	p.M471fs	DENND5B_ENST00000354285.4_Frame_Shift_Ins_p.M493fs|DENND5B_ENST00000306833.6_Frame_Shift_Ins_p.M506fs|snoU13_ENST00000458765.1_RNA|DENND5B_ENST00000536562.1_Frame_Shift_Ins_p.M506fs	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	471					positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						AGAGAGGTCCATTTTTTCCACA	0.47																																					p.M471fs		Atlas-Indel,Pindel	.											.	DENND5B	114	.	0			c.1412_1413insA						.																																			SO:0001589	frameshift_variant	160518	exon5			.	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.1412dupA	chr12.hg19:g.31605097_31605097dupT	ENSP00000373734:p.Met471fs	227.0	0.0		269.0	42.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Frame_Shift_Ins	INS	ENST00000389082.5	hg19	CCDS44857.1																																																																																			.	.		0.47	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		T	31605092	-	T	31605091	7	5	62	1	0	1	1	0	0	0	0	0	4439	217	8	0	2480	0	DENND5B	12	31605091	Frame_Shift_Ins	INS	-	TCGA-CC-A1HT-01A-11D-A12Z-10	23638048	31605091	102246804	59	7569										
FLT1	2321	hgsc.bcm.edu	37	chr13	28883065	28883065	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	acttgaaagcatttacgtatCtaatgaagaaacagaaagaa	7	5	1	5			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr13:28883065C>G	ENST00000282397.4	-	28	3887		c.e28-1		FLT1_ENST00000543394.1_Splice_Site|FLT1_ENST00000540678.1_Splice_Site	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1						blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATTTACGTATCTAATGAAGAA	0.403																																					.		Atlas-SNP	.											.	FLT1	393	.	0			c.3636-1G>C						.						79	67	71					13																	28883065		2203	4300	6503	SO:0001630	splice_region_variant	2321	exon29			ACGTATCTAATGA	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.3636-1G>C	chr13.hg19:g.28883065C>G		71.0	0.0		67.0	8.0	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Splice_Site	SNP	ENST00000282397.4	hg19	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.703649	0.48412	.	.	ENSG00000102755	ENST00000282397;ENST00000543394;ENST00000540678	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8181	0.78621	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FLT1	27781065	1.000000	0.71417	0.996000	0.52242	0.583000	0.36354	4.400000	0.59709	2.551000	0.86045	0.561000	0.74099	.	.	.		0.403	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		Intron	G	28883065	C	G	28883065	5	3	62	1	0	0	0	0	0	0	1	0	5949	927	32	4	393	4	FLT1	13	28883065	Splice_Site	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10		28883065	86286813	60	7570										
DACH1	1602	hgsc.bcm.edu	37	chr13	72204825	72204825	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ctgcattggtagcagcagcaGctgctgcagcggctgctgtc	14	12	0	0			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr13:72204825G>T	ENST00000359684.2	-	3	994	c.995C>A	c.(994-996)gCt>gAt	p.A332D	DACH1_ENST00000305425.4_Missense_Mutation_p.A332D|DACH1_ENST00000354591.4_Intron|DACH1_ENST00000313174.7_Missense_Mutation_p.A332D			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	332	Interaction with SIX6 and HDAC3. {ECO:0000250}.|Poly-Ala.				cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		agcagcagcagctgctgcagc	0.373																																					p.A332D		Atlas-SNP	.											.	DACH1	123	.	0			c.C995A						.						99	89	92					13																	72204825		1802	4069	5871	SO:0001583	missense	1602	exon3			GCAGCAGCTGCTG	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.995C>A	chr13.hg19:g.72204825G>T	ENSP00000352712:p.Ala332Asp	100.0	0.0		118.0	39.0	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Missense_Mutation	SNP	ENST00000359684.2	hg19		.	.	.	.	.	.	.	.	.	.	G	32	5.168386	0.94768	.	.	ENSG00000165659	ENST00000305425;ENST00000313174;ENST00000359684;ENST00000377826	T;T;T	0.36520	1.25;1.35;1.29	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.57489	0.2057	L	0.47716	1.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.53802	-0.8387	10	0.72032	D	0.01	-10.5268	20.4702	0.99162	0.0:0.0:1.0:0.0	.	330;330	Q9UI36-3;Q9UI36-2	.;.	D	332	ENSP00000304994:A332D;ENSP00000318506:A332D;ENSP00000352712:A332D	ENSP00000304994:A332D	A	-	2	0	DACH1	71102826	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.357000	0.97099	2.937000	0.99478	0.650000	0.86243	GCT	.	.		0.373	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		T	72204825	G	T	72204825	3	4	62	1	0	0	0	0	1	0	0	0	4222	971	34	3	1167	3	DACH1	13	72204825	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	43321760	72204825	42965053	61	7571										
KIAA0831	22863	hgsc.bcm.edu	37	chr14	55848812	55848812	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gtgatcgtcacagacccatcGtcctgagaggtaagttgtcc	11	11	1	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr14:55848812G>A	ENST00000247178.5	-	6	780	c.745C>T	c.(745-747)Cga>Tga	p.R249*		NM_014924.4	NP_055739.2	Q6ZNE5	BAKOR_HUMAN	autophagy related 14	249					autophagic vacuole assembly (GO:0000045)|endosome to lysosome transport (GO:0008333)|positive regulation of autophagy (GO:0010508)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|pre-autophagosomal structure membrane (GO:0034045)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(2)	13						CAGACCCATCGTCCTGAGAGG	0.537																																					p.R249X		Atlas-SNP	.											.	ATG14	36	.	0			c.C745T						.						189	158	169					14																	55848812		2203	4300	6503	SO:0001587	stop_gained	22863	exon6			CCCATCGTCCTGA	AB020638	CCDS32087.1	14q22.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000126775	ENSG00000126775			19962	protein-coding gene	gene with protein product	"Barkor", "beclin 1-associated autophagy-related key regulator"	613515	"KIAA0831", "ATG14 autophagy related 14 homolog (S. cerevisiae)"	KIAA0831		18843052	Standard	NM_014924		Approved	ATG14L	uc001xbx.2	Q6ZNE5	OTTHUMG00000172129	ENST00000247178.5:c.745C>T	chr14.hg19:g.55848812G>A	ENSP00000247178:p.Arg249*	429.0	0.0		397.0	83.0	NM_014924	A6NJE4|A8K9U5|B7ZWP5|O94920|Q32MK7|Q32MK8	Nonsense_Mutation	SNP	ENST00000247178.5	hg19	CCDS32087.1	.	.	.	.	.	.	.	.	.	.	g	21.6	4.173478	0.78452	.	.	ENSG00000126775	ENST00000247178	.	.	.	5.87	-2.25	0.06888	.	0.054032	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.4068	12.222	0.54439	0.0779:0.0:0.4422:0.4799	.	.	.	.	X	249	.	ENSP00000247178:R249X	R	-	1	2	ATG14	54918565	0.981000	0.34729	0.231000	0.23993	0.631000	0.37964	1.067000	0.30616	-0.286000	0.09076	-0.142000	0.14014	CGA	.	.		0.537	ATG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416992.1	NM_014924		A	55848812	G	A	55848812	4	1	62	1	0	0	0	0	0	1	0	0	8204	1153	40	1	753	1	KIAA0831	14	55848812	Nonsense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10		55848812	51500728	62	7572										
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43749109	43749109	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ggatactatcattttcagcaGgaacaaatttagaattgaga	8	5	2	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr15:43749109G>C	ENST00000263801.3	-	12	1934	c.1682C>G	c.(1681-1683)cCt>cGt	p.P561R	TP53BP1_ENST00000605155.1_5'Flank|TP53BP1_ENST00000382039.3_Missense_Mutation_p.P566R|TP53BP1_ENST00000382044.4_Missense_Mutation_p.P566R|TP53BP1_ENST00000450115.2_Missense_Mutation_p.P566R	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	561					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		ATTTTCAGCAGGAACAAATTT	0.413								Other conserved DNA damage response genes																													p.P566R		Atlas-SNP	.											.	TP53BP1	157	.	0			c.C1697G						.						147	134	139					15																	43749109		2201	4298	6499	SO:0001583	missense	7158	exon12			TCAGCAGGAACAA	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.1682C>G	chr15.hg19:g.43749109G>C	ENSP00000263801:p.Pro561Arg	204.0	0.0		174.0	34.0	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	hg19	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	G	8.830	0.939737	0.18281	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.16597	2.33;2.33;2.33;2.33;2.33	5.04	3.13	0.36017	.	0.321644	0.29995	N	0.010668	T	0.13200	0.0320	L	0.38838	1.175	0.31601	N	0.652675	B;B;B;B	0.09022	0.002;0.001;0.001;0.001	B;B;B;B	0.09377	0.004;0.001;0.003;0.003	T	0.05971	-1.0853	10	0.51188	T	0.08	-1.3124	8.7541	0.34635	0.0775:0.2843:0.6381:0.0	.	566;561;566;566	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	R	561;566;566;566;566	ENSP00000263801:P561R;ENSP00000371475:P566R;ENSP00000371470:P566R;ENSP00000393497:P566R;ENSP00000388028:P566R	ENSP00000263801:P561R	P	-	2	0	TP53BP1	41536401	0.048000	0.20356	1.000000	0.80357	0.663000	0.39108	1.628000	0.37060	0.609000	0.30018	0.563000	0.77884	CCT	.	.		0.413	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			C	43749109	G	C	43749109	3	2	62	1	0	0	0	0	1	0	0	0	16398	1000	35	4	4304	4	TP53BP1	15	43749109	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10		43749109	58782283	63	7573										
BNC1	646	hgsc.bcm.edu	37	chr15	83926506	83926506	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ctcgacccttcacagttcccAtcactgtcctccataagcac	4	18	2	0			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr15:83926506A>G	ENST00000345382.2	-	5	2758	c.2673T>C	c.(2671-2673)gaT>gaC	p.D891D	RP11-382A20.4_ENST00000565495.1_RNA|BNC1_ENST00000569704.1_Silent_p.D884D	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	891					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						CACAGTTCCCATCACTGTCCT	0.557																																					p.D891D		Atlas-SNP	.											.	BNC1	149	.	0			c.T2673C						.						186	147	160					15																	83926506		2203	4300	6503	SO:0001819	synonymous_variant	646	exon5			GTTCCCATCACTG	L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"Zinc fingers, C2H2-type"	1081	protein-coding gene	gene with protein product		601930	"basonuclin"	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.2673T>C	chr15.hg19:g.83926506A>G		84.0	0.0		90.0	23.0	NM_001717	Q15840	Silent	SNP	ENST00000345382.2	hg19	CCDS10324.1																																																																																			.	.		0.557	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		G	83926506	A	G	83926506	2	3	62	1	0	0	0	0	0	0	0	1	1474	214	8	2		2	BNC1	15	83926506	Silent	SNP	A	TCGA-CC-A1HT-01A-11D-A12Z-10	40177397	83926506	18604886	64	7574										
NR2F2	7026	hgsc.bcm.edu	37	chr15	96875607	96875608	+	Frame_Shift_Del	DEL	CG	CG	-													0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	aagtcgagcggcaagcactaCggccagttcacgtgcgaggg							TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr15:96875607_96875608delCG	ENST00000394166.3	+	1	1662_1663	c.273_274delCG	c.(271-276)tacggcfs	p.YG91fs	NR2F2_ENST00000421109.2_Intron|NR2F2_ENST00000453270.2_5'Flank|NR2F2_ENST00000394171.2_5'Flank|MIR1469_ENST00000410719.1_RNA	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	91					anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			GCAAGCACTACGGCCAGTTCAC	0.653																																					p.91_91del		Atlas-Indel,Pindel	.											.	NR2F2	35	.	0			c.272_273del						.																																			SO:0001589	frameshift_variant	7026	exon1			.	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"Nuclear hormone receptors"	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.273_274delCG	chr15.hg19:g.96875607_96875608delCG	ENSP00000377721:p.Tyr91fs	100.0	0.0		100.0	15.0	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Frame_Shift_Del	DEL	ENST00000394166.3	hg19	CCDS10375.1																																																																																			.	.		0.653	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			-	96875608	CG	-	96875607	7	5	62	1	0	1	0	1	0	0	0	0	10637	547	19	0	322	0	NR2F2	15	96875607	Frame_Shift_Del	DEL	CG	TCGA-CC-A1HT-01A-11D-A12Z-10	12949101	96875607	5655785	65	7575										
SOLH	6650	hgsc.bcm.edu	37	chr16	601376	601376	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ctacgagagcctgggcctgcGcccccggcatgcctactcca	11	18	0	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr16:601376G>A	ENST00000219611.2	+	8	2504	c.2141G>A	c.(2140-2142)cGc>cAc	p.R714H	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	714	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CTGGGCCTGCGCCCCCGGCAT	0.682																																					p.R714H		Atlas-SNP	.											.	SOLH	47	.	0			c.G2141A						.						52	61	58					16																	601376		2200	4297	6497	SO:0001583	missense	6650	exon8			GCCTGCGCCCCCG	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"small optic lobes (Drosophila) homolog", "small optic lobes homolog (Drosophila)"	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.2141G>A	chr16.hg19:g.601376G>A	ENSP00000219611:p.Arg714His	28.0	0.0		44.0	7.0	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	hg19	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	g	29.2	4.989237	0.93106	.	.	ENSG00000103326	ENST00000219611	D	0.87809	-2.3	5.36	5.36	0.76844	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.85682	D	0.000000	D	0.91774	0.7398	L	0.49256	1.55	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92401	0.5929	10	0.72032	D	0.01	.	17.6567	0.88180	0.0:0.0:1.0:0.0	.	714	O75808	CAN15_HUMAN	H	714	ENSP00000219611:R714H	ENSP00000219611:R714H	R	+	2	0	SOLH	541377	1.000000	0.71417	0.995000	0.50966	0.793000	0.44817	9.745000	0.98856	2.509000	0.84616	0.556000	0.70494	CGC	.	.		0.682	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		A	601376	G	A	601376	3	1	62	1	0	0	0	0	1	0	0	0	14940	1087	38	1	2159	1	SOLH	16	601376	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10		601376	89753377	66	7576										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70884548	70884548	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ctttggtgtgaagaaaatatCaattgggaacctggttgggg	14	4	1	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr16:70884548C>T	ENST00000393567.2	-	74	12604	c.12454G>A	c.(12454-12456)Gat>Aat	p.D4152N	RNU6ATAC25P_ENST00000408798.1_RNA	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4152					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				AAGAAAATATCAATTGGGAAC	0.398																																					p.D4152N		Atlas-SNP	.											.	HYDIN	788	.	0			c.G12454A						.						53	47	49					16																	70884548		1846	4095	5941	SO:0001583	missense	54768	exon74			AAATATCAATTGG	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.12454G>A	chr16.hg19:g.70884548C>T	ENSP00000377197:p.Asp4152Asn	162.0	0.0		134.0	20.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	hg19	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.997662	0.54147	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00882	5.58	5.56	4.6	0.57074	.	0.982987	0.08228	U	0.978048	T	0.01835	0.0058	L	0.56769	1.78	0.80722	D	1	P	0.42337	0.776	P	0.48598	0.583	T	0.60352	-0.7280	10	0.12430	T	0.62	.	4.0023	0.09585	0.2125:0.6206:0.0:0.1669	.	4151	F8WD23	.	N	4152;4151	ENSP00000377197:D4152N	ENSP00000313052:D4151N	D	-	1	0	HYDIN	69442049	0.988000	0.35896	1.000000	0.80357	0.936000	0.57629	1.568000	0.36418	2.615000	0.88500	0.511000	0.50034	GAT	.	.		0.398	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70884548	C	T	70884548	3	4	62	1	0	0	0	0	1	0	0	0	7476	826	29	3	2963	3	HYDIN	16	70884548	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	70283172	70884548	19470205	67	7577										
TP53	7157	hgsc.bcm.edu	37	chr17	7578555	7578555	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ttgttgagggcaggggagtaCtgtaggaagaggaaggagac	19	3	0	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr17:7578555C>T	ENST00000269305.4	-	5	565		c.e5-1		TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(39)|p.0?(8)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGGGGAGTACTGTAGGAAGA	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,58	TP53	33396	.	51	Unknown(39)|Whole gene deletion(8)|Deletion - Frameshift(3)|Insertion - In frame(1)	ovary(9)|pancreas(6)|bone(5)|upper_aerodigestive_tract(4)|liver(4)|lung(4)|breast(4)|large_intestine(3)|central_nervous_system(3)|oesophagus(3)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|endometrium(1)|urinary_tract(1)|autonomic_ganglia(1)	c.376-1G>A						.						42	42	42					17																	7578555		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGAGTACTGTAGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.376-1G>A	chr17.hg19:g.7578555C>T		56.0	0.0		50.0	8.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.431133	0.62844	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	.	.	.	4.87	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4246	0.50003	0.0:0.9094:0.0:0.0906	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519280	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	7.639000	0.83342	1.359000	0.45940	0.655000	0.94253	.	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	T	7578555	C	T	7578555	5	4	62	1	0	0	0	0	0	0	1	0	16396	579	20	3	923	3	TP53	17	7578555	Splice_Site	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10		7578555	73616655	68	7578										
KRT14	3861	hgsc.bcm.edu	37	chr17	39742690	39742690	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ggcctcctccagagcacgcaCcttgtccaggtaggaggcca	12	15	0	1	rs61027685		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr17:39742690C>T	ENST00000167586.6	-	1	483	c.397G>A	c.(397-399)Gtg>Atg	p.V133M		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	133	Coil 1A.|Rod.		V -> A (in dbSNP:rs642601).|V -> L (in WC-EBS and K-EBS; dbSNP:rs61027685). {ECO:0000269|PubMed:14987259, ECO:0000269|PubMed:16786515}.		aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				AGAGCACGCACCTTGTCCAGG	0.582																																					p.V133M		Atlas-SNP	.											.	KRT14	65	.	0			c.G397A	GRCh37	CM044653|CM055346|CM070974	KRT14	M	rs61027685	.						136	142	140					17																	39742690		2203	4296	6499	SO:0001583	missense	3861	exon1			CACGCACCTTGTC	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"-", "Intermediate filaments type I, keratins (acidic)"	6416	protein-coding gene	gene with protein product	"epidermolysis bullosa simplex, Dowling-Meara, Koebner"	148066	"keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.397G>A	chr17.hg19:g.39742690C>T	ENSP00000167586:p.Val133Met	200.0	0.0		225.0	48.0	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Missense_Mutation	SNP	ENST00000167586.6	hg19	CCDS11400.1	.	.	.	.	.	.	.	.	.	.	C	32	5.121927	0.94429	.	.	ENSG00000186847	ENST00000167586	D	0.95885	-3.84	4.98	4.98	0.66077	Filament (1);	0.000000	0.47455	D	0.000240	D	0.98598	0.9531	H	0.97659	4.05	0.80722	D	1	D	0.61080	0.989	D	0.67382	0.951	D	0.99601	1.0978	10	0.66056	D	0.02	.	18.6154	0.91300	0.0:1.0:0.0:0.0	.	133	P02533	K1C14_HUMAN	M	133	ENSP00000167586:V133M	ENSP00000167586:V133M	V	-	1	0	KRT14	36996216	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.757000	0.85209	2.472000	0.83506	0.448000	0.29417	GTG	.	.		0.582	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526		T	39742690	C	T	39742690	3	4	62	1	0	0	0	0	1	0	0	0	8460	507	18	3	1053	3	KRT14	17	39742690	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	32164135	39742690	41452520	69	7579										
CNTD1	124817	hgsc.bcm.edu	37	chr17	40961398	40961398	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tgaaggttgtggggcatttgCagagcatcactggtattgcc	14	7	1	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr17:40961398C>A	ENST00000588408.1	+	7	1114	c.838C>A	c.(838-840)Cag>Aag	p.Q280K	CNTD1_ENST00000588527.1_Missense_Mutation_p.Q197K|CNTD1_ENST00000315066.5_3'UTR	NM_173478.2	NP_775749.2	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1	280										central_nervous_system(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		GGGGCATTTGCAGAGCATCAC	0.438																																					p.Q280K		Atlas-SNP	.											.	CNTD1	22	.	0			c.C838A						.						135	128	130					17																	40961398		2203	4300	6503	SO:0001583	missense	124817	exon7			CATTTGCAGAGCA	AK097456	CCDS11440.1	17q21.31	2014-07-03	2006-03-31	2006-03-31	ENSG00000176563	ENSG00000176563			26847	protein-coding gene	gene with protein product			"cyclin N-terminal domain containing"	CNTD		24891606	Standard	NM_173478		Approved	FLJ40137	uc002ibm.4	Q8N815		ENST00000588408.1:c.838C>A	chr17.hg19:g.40961398C>A	ENSP00000465204:p.Gln280Lys	207.0	0.0		220.0	42.0	NM_173478	Q658Q6|Q8NEP1	Missense_Mutation	SNP	ENST00000588408.1	hg19	CCDS11440.1	.	.	.	.	.	.	.	.	.	.	C	5.742	0.321308	0.10845	.	.	ENSG00000176563	ENST00000315066	.	.	.	6.03	6.03	0.97812	.	0.192857	0.56097	D	0.000034	T	0.37679	0.1012	L	0.36672	1.1	0.32552	N	0.532304	B	0.23937	0.094	B	0.19666	0.026	T	0.35525	-0.9785	9	0.02654	T	1	-7.9759	12.2136	0.54394	0.132:0.7405:0.1275:0.0	.	280	Q8N815	CNTD1_HUMAN	K	280	.	ENSP00000316647:Q280K	Q	+	1	0	CNTD1	38214924	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	2.324000	0.43831	2.868000	0.98415	0.555000	0.69702	CAG	.	.		0.438	CNTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452398.1	NM_173478		A	40961398	C	A	40961398	3	1	62	1	0	0	0	0	1	0	0	0	3637	711	25	3	864	3	CNTD1	17	40961398	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	1218708	40961398	40233812	70	7580										
AXIN2	8313	hgsc.bcm.edu	37	chr17	63545764	63545765	+	Frame_Shift_Del	DEL	CT	CT	-													0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gataaggattaacaggatcgCtcctcttgaaggacctatgg							TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr17:63545764_63545765delCT	ENST00000375702.5	-	2	937_938	c.829_830delAG	c.(829-831)agcfs	p.S277fs	AXIN2_ENST00000307078.5_Frame_Shift_Del_p.S277fs|CTD-2535L24.2_ENST00000577662.1_3'UTR			Q9Y2T1	AXIN2_HUMAN	axin 2	277					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						AACAGGATCGCTCCTCTTGAAG	0.51									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																												p.277_277del		Atlas-Indel,Pindel	.											AXIN2,rectum,carcinoma,0,1	AXIN2	92	.	0			c.830_831del						.																																			SO:0001589	frameshift_variant	8313	exon3	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	.	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"conductin", "axil"	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.829_830delAG	chr17.hg19:g.63545764_63545765delCT	ENSP00000364854:p.Ser277fs	123.0	0.0		92.0	14.0	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Frame_Shift_Del	DEL	ENST00000375702.5	hg19																																																																																				.	.		0.51	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		-	63545765	CT	-	63545764	7	5	62	1	0	1	0	1	0	0	0	0	1237	797	28	0	1737	0	AXIN2	17	63545764	Frame_Shift_Del	DEL	CT	TCGA-CC-A1HT-01A-11D-A12Z-10	22584366	63545764	17649446	71	7581										
CDR2L	30850	hgsc.bcm.edu	37	chr17	72998268	72998268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tgctccgggagaagcgggaaCgcaggcgtaccatccacacc	13	14	0	1	rs529209429		TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr17:72998268C>T	ENST00000337231.5	+	4	863	c.451C>T	c.(451-453)Cgc>Tgc	p.R151C		NM_014603.2	NP_055418.2	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like	151												all_lung(278;0.226)					GAAGCGGGAACGCAGGCGTAC	0.642													C|||	1	0.000199681	0	0	5008	,	,		17825	0		0.001	False		,,,				2504	0				p.R151C		Atlas-SNP	.											HUMPPA,NS,carcinoma,0,1	.	.	.	0			c.C451T						.						67	49	56					17																	72998268		2203	4299	6502	SO:0001583	missense	30850	exon4			CGGGAACGCAGGC		CCDS11710.2	17q25.1	2006-03-28			ENSG00000109089	ENSG00000109089			29999	protein-coding gene	gene with protein product	"paraneoplastic antigen"						Standard	NM_014603		Approved	HUMPPA	uc002jml.4	Q86X02	OTTHUMG00000150435	ENST00000337231.5:c.451C>T	chr17.hg19:g.72998268C>T	ENSP00000336587:p.Arg151Cys	39.0	0.0		80.0	18.0	NM_014603	B4DFA7|Q15175	Missense_Mutation	SNP	ENST00000337231.5	hg19	CCDS11710.2	.	.	.	.	.	.	.	.	.	.	C	23.7	4.448746	0.84101	.	.	ENSG00000109089	ENST00000337231	T	0.50813	0.73	5.22	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.67970	0.2950	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71938	-0.4441	10	0.72032	D	0.01	-24.4178	13.7862	0.63110	0.2953:0.7047:0.0:0.0	.	151	Q86X02	CDR2L_HUMAN	C	151	ENSP00000336587:R151C	ENSP00000336587:R151C	R	+	1	0	CDR2L	70509863	0.949000	0.32298	0.984000	0.44739	0.996000	0.88848	1.774000	0.38573	2.609000	0.88269	0.563000	0.77884	CGC	.	.		0.642	CDR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318080.1	NM_014603		T	72998268	C	T	72998268	3	4	62	1	0	0	0	0	1	0	0	0	3175	536	19	1	465	1	CDR2L	17	72998268	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	9452504	72998268	8196942	72	7582										
LLGL2	3993	hgsc.bcm.edu	37	chr17	73569581	73569581	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ggcttctacctgatctcaccCtcggagtttgagcgcttctc	9	14	3	2	rs144386071	byFrequency	TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr17:73569581C>G	ENST00000392550.3	+	21	2862	c.2745C>G	c.(2743-2745)ccC>ccG	p.P915P	LLGL2_ENST00000577200.1_Silent_p.P915P|LLGL2_ENST00000167462.5_Silent_p.P915P	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	915					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			TGATCTCACCCTCGGAGTTTG	0.637																																					p.P915P		Atlas-SNP	.											.	LLGL2	155	.	0			c.C2745G						.						90	93	92					17																	73569581		2203	4299	6502	SO:0001819	synonymous_variant	3993	exon21			CTCACCCTCGGAG	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"WD repeat domain containing"	6629	protein-coding gene	gene with protein product			"lethal giant larvae (Drosophila) homolog 2"				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2745C>G	chr17.hg19:g.73569581C>G		224.0	0.0		254.0	40.0	NM_004524	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	hg19	CCDS32733.1																																																																																			.	C|0.997;T|0.003		0.637	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		G	73569581	C	G	73569581	2	3	62	1	0	0	0	0	0	0	0	1	8843	668	24	4		4	LLGL2	17	73569581	Silent	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	571313	73569581	7625629	73	7583										
ARHGEF18	23370	hgsc.bcm.edu	37	chr19	7505118	7505118	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tggataacgagctgctgaccTccaagatcctgtctgtgctg	11	11	1	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr19:7505118T>A	ENST00000359920.6	+	1	545	c.292T>A	c.(292-294)Tcc>Acc	p.S98T	ARHGEF18_ENST00000319670.9_Intron|CTD-2207O23.3_ENST00000593531.1_Intron	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	98					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				GCTGCTGACCTCCAAGATCCT	0.637																																					p.S98T		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.T292A						.						27	33	31					19																	7505118		692	1591	2283	SO:0001583	missense	23370	exon1			CTGACCTCCAAGA	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	17090	protein-coding gene	gene with protein product	"Rho-specific guanine nucleotide exchange factor p114"		"rho/rac guanine nucleotide exchange factor (GEF) 18"			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.292T>A	chr19.hg19:g.7505118T>A	ENSP00000352995:p.Ser98Thr	109.0	0.0		111.0	17.0	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	hg19	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	T	15.32	2.799354	0.50208	.	.	ENSG00000104880	ENST00000359920	T	0.34275	1.37	5.43	4.41	0.53225	.	0.178690	0.27008	N	0.021398	T	0.22360	0.0539	N	0.17082	0.46	0.80722	D	1	B	0.13145	0.007	B	0.09377	0.004	T	0.03403	-1.1040	10	0.38643	T	0.18	-15.3691	10.0409	0.42158	0.1508:0.0:0.0:0.8492	.	98	Q6ZSZ5	ARHGI_HUMAN	T	98	ENSP00000352995:S98T	ENSP00000352995:S98T	S	+	1	0	ARHGEF18	7411118	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.697000	0.47060	0.877000	0.35895	0.459000	0.35465	TCC	.	.		0.637	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		A	7505118	T	A	7505118	3	1	62	1	0	0	0	0	1	0	0	0	901	1551	54	4	294	4	ARHGEF18	19	7505118	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10		7505118	51623865	74	7584										
MUC16	94025	hgsc.bcm.edu	37	chr19	9024161	9024161	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gctggagagggaggatggagTccctgaggttctgagatcca	17	7	1	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr19:9024161T>A	ENST00000397910.4	-	18	37314	c.37111A>T	c.(37111-37113)Act>Tct	p.T12371S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12373					cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAGGATGGAGTCCCTGAGGTT	0.468																																					p.T12371S		Atlas-SNP	.											.	MUC16	4315	.	0			c.A37111T						.						78	75	76					19																	9024161		1910	4124	6034	SO:0001583	missense	94025	exon18			ATGGAGTCCCTGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.37111A>T	chr19.hg19:g.9024161T>A	ENSP00000381008:p.Thr12371Ser	254.0	0.0		241.0	21.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	8.766	0.924672	0.18056	.	.	ENSG00000181143	ENST00000397910	T	0.01998	4.51	1.58	-1.68	0.08212	.	.	.	.	.	T	0.01905	0.0060	L	0.45137	1.4	.	.	.	P	0.35481	0.504	B	0.26614	0.071	T	0.37572	-0.9700	8	0.87932	D	0	.	4.7752	0.13175	0.0:0.4639:0.0:0.5361	.	12371	B5ME49	.	S	12371	ENSP00000381008:T12371S	ENSP00000381008:T12371S	T	-	1	0	MUC16	8885161	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-4.046000	0.00306	-0.479000	0.06813	0.172000	0.16884	ACT	.	.		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9024161	T	A	9024161	3	1	62	1	0	0	0	0	1	0	0	0	9982	1667	58	4	6680	4	MUC16	19	9024161	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	1519043	9024161	50104822	75	7585										
MUC16	94025	hgsc.bcm.edu	37	chr19	9048324	9048324	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ggtcactgccctggaactagTgaccagaggggtcaccactc	12	13	2	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr19:9048324T>G	ENST00000397910.4	-	5	33510	c.33307A>C	c.(33307-33309)Act>Cct	p.T11103P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11105	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGGAACTAGTGACCAGAGGG	0.522																																					p.T11103P		Atlas-SNP	.											.	MUC16	4315	.	0			c.A33307C						.						75	68	70					19																	9048324		1918	4137	6055	SO:0001583	missense	94025	exon5			AACTAGTGACCAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33307A>C	chr19.hg19:g.9048324T>G	ENSP00000381008:p.Thr11103Pro	158.0	0.0		136.0	21.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	6.256	0.415281	0.11870	.	.	ENSG00000181143	ENST00000397910	T	0.02579	4.24	3.02	-2.62	0.06152	.	.	.	.	.	T	0.03651	0.0104	L	0.47716	1.5	.	.	.	B	0.31383	0.321	B	0.37304	0.246	T	0.34378	-0.9831	8	0.87932	D	0	.	5.8554	0.18716	0.0:0.1169:0.5372:0.3459	.	11103	B5ME49	.	P	11103	ENSP00000381008:T11103P	ENSP00000381008:T11103P	T	-	1	0	MUC16	8909324	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.936000	0.03946	-0.713000	0.04981	0.398000	0.26397	ACT	.	.		0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9048324	T	G	9048324	3	3	62	1	0	0	0	0	1	0	0	0	9982	1696	59	5	10536	5	MUC16	19	9048324	Missense_Mutation	SNP	T	TCGA-CC-A1HT-01A-11D-A12Z-10	24163	9048324	50080659	76	7586										
ZNF253	56242	hgsc.bcm.edu	37	chr19	20002465	20002465	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	atggacttaaccaatgtttgAcaactacccagaaagaaata	6	8	0	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr19:20002465A>T	ENST00000589717.1	+	4	501	c.409A>T	c.(409-411)Aca>Tca	p.T137S	AC011477.1_ENST00000578823.1_RNA|ZNF253_ENST00000355650.4_Missense_Mutation_p.T61S|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	137					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCAATGTTTGACAACTACCCA	0.323																																					p.T137S		Atlas-SNP	.											.	ZNF253	99	.	0			c.A409T						.						56	58	57					19																	20002465		2139	4275	6414	SO:0001583	missense	56242	exon4			TGTTTGACAACTA	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"Zinc fingers, C2H2-type", "-"	13497	protein-coding gene	gene with protein product		606954	"zinc finger protein 411"	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.409A>T	chr19.hg19:g.20002465A>T	ENSP00000468720:p.Thr137Ser	236.0	0.0		163.0	27.0	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Missense_Mutation	SNP	ENST00000589717.1	hg19	CCDS42532.1	.	.	.	.	.	.	.	.	.	.	a	0.054	-1.242289	0.01481	.	.	ENSG00000256771	ENST00000355650	.	.	.	1.4	-2.81	0.05805	.	.	.	.	.	T	0.14399	0.0348	L	0.31420	0.93	0.09310	N	1	P	0.40144	0.704	B	0.34093	0.175	T	0.10823	-1.0613	7	.	.	.	.	2.2207	0.03971	0.3458:0.2228:0.0:0.4315	.	137	O75346	ZN253_HUMAN	S	137	.	.	T	+	1	0	ZNF253	19863465	0.003000	0.15002	0.043000	0.18650	0.043000	0.13939	1.039000	0.30266	-0.987000	0.03494	-1.020000	0.02445	ACA	.	.		0.323	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047		T	20002465	A	T	20002465	3	4	62	1	0	0	0	0	1	0	0	0	17812	275	10	4	423	4	ZNF253	19	20002465	Missense_Mutation	SNP	A	TCGA-CC-A1HT-01A-11D-A12Z-10	10954141	20002465	39126518	77	7587										
TRIM28	10155	hgsc.bcm.edu	37	chr19	59059680	59059680	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	gatctacttccagctgcaccGggccctcaagatgattgtgg	11	12	2	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr19:59059680G>A	ENST00000253024.5	+	8	1410	c.1121G>A	c.(1120-1122)cGg>cAg	p.R374Q	TRIM28_ENST00000341753.6_Missense_Mutation_p.R292Q	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28	374	Interaction with MAGEC2.|Leucine zipper alpha helical coiled-coil region.|RBCC domain.				convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CAGCTGCACCGGGCCCTCAAG	0.542																																					p.R374Q		Atlas-SNP	.											.	TRIM28	46	.	0			c.G1121A						.						74	74	74					19																	59059680		2203	4300	6503	SO:0001583	missense	10155	exon8			TGCACCGGGCCCT		CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	16384	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 157"	601742	"tripartite motif-containing 28"			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.1121G>A	chr19.hg19:g.59059680G>A	ENSP00000253024:p.Arg374Gln	121.0	0.0		129.0	34.0	NM_005762	O00677|Q7Z632|Q93040|Q96IM1	Missense_Mutation	SNP	ENST00000253024.5	hg19	CCDS12985.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.931134	0.52866	.	.	ENSG00000130726	ENST00000253024;ENST00000341753	T;T	0.67698	-0.07;-0.28	5.64	4.61	0.57282	B-box, C-terminal (1);	0.235442	0.36303	N	0.002665	T	0.49218	0.1544	L	0.32530	0.975	0.36324	D	0.858459	P;P	0.42161	0.772;0.663	B;B	0.28385	0.089;0.041	T	0.62129	-0.6919	10	0.49607	T	0.09	-21.1432	12.4604	0.55729	0.0812:0.0:0.9188:0.0	.	292;374	Q13263-2;Q13263	.;TIF1B_HUMAN	Q	374;292	ENSP00000253024:R374Q;ENSP00000342232:R292Q	ENSP00000253024:R374Q	R	+	2	0	TRIM28	63751492	0.810000	0.29049	0.997000	0.53966	0.994000	0.84299	3.464000	0.53057	1.540000	0.49301	0.655000	0.94253	CGG	.	.		0.542	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467074.1	NM_005762		A	59059680	G	A	59059680	3	1	62	1	0	0	0	0	1	0	0	0	16517	1116	39	1	1151	1	TRIM28	19	59059680	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10	39057215	59059680	69303	78	7588										
TGM3	7053	hgsc.bcm.edu	37	chr20	2321189	2321189	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	tctcctgcaacaagttccctGcaatcaaggccatgttgtcc	7	14	2	0			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr20:2321189G>T	ENST00000381458.5	+	13	2107	c.2044G>T	c.(2044-2046)Gca>Tca	p.A682S		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	682					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	CAAGTTCCCTGCAATCAAGGC	0.592																																					p.A682S		Atlas-SNP	.											.	TGM3	105	.	0			c.G2044T						.						137	100	113					20																	2321189		2203	4300	6503	SO:0001583	missense	7053	exon13			TTCCCTGCAATCA	L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"Transglutaminases"	11779	protein-coding gene	gene with protein product	"E polypeptide, protein-glutamine-gamma-glutamyltransferase"	600238	"transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.2044G>T	chr20.hg19:g.2321189G>T	ENSP00000370867:p.Ala682Ser	122.0	0.0		141.0	12.0	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	hg19	CCDS33435.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.920268	0.73098	.	.	ENSG00000125780	ENST00000381458	T	0.28666	1.6	4.68	4.68	0.58851	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.361836	0.28241	N	0.016067	T	0.47691	0.1459	L	0.57536	1.79	0.35900	D	0.830321	D	0.55800	0.973	D	0.66979	0.948	T	0.51818	-0.8657	10	0.29301	T	0.29	-5.3995	12.9733	0.58525	0.0:0.0:1.0:0.0	.	682	Q08188	TGM3_HUMAN	S	682	ENSP00000370867:A682S	ENSP00000370867:A682S	A	+	1	0	TGM3	2269189	0.522000	0.26266	0.819000	0.32651	0.871000	0.50021	3.691000	0.54720	2.427000	0.82271	0.655000	0.94253	GCA	.	.		0.592	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245		T	2321189	G	T	2321189	3	4	62	1	0	0	0	0	1	0	0	0	15846	1319	46	3	2094	3	TGM3	20	2321189	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10		2321189	60704331	79	7589										
SPATA2	9825	hgsc.bcm.edu	37	chr20	48523374	48523374	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	acataataaacaaaagggccCgtgtaggtctagaagggagg	13	6	1	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr20:48523374C>A	ENST00000422556.1	-	3	694	c.345G>T	c.(343-345)acG>acT	p.T115T	SPATA2_ENST00000289431.5_Silent_p.T115T|SPATA2_ENST00000543716.1_5'UTR	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	115					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	20	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			CAAAAGGGCCCGTGTAGGTCT	0.488																																					p.T115T		Atlas-SNP	.											.	SPATA2	36	.	0			c.G345T						.																																			SO:0001819	synonymous_variant	9825	exon3			AGGGCCCGTGTAG	AB018300	CCDS13422.1	20q13.13	2014-06-13			ENSG00000158480	ENSG00000158480			14681	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 145"	607662					Standard	NM_001135773		Approved	KIAA0757, PD1, tamo, PPP1R145	uc002xuw.3	Q9UM82	OTTHUMG00000032704	ENST00000422556.1:c.345G>T	chr20.hg19:g.48523374C>A		186.0	0.0		242.0	22.0	NM_006038	E1P626|O94857	Silent	SNP	ENST00000422556.1	hg19	CCDS13422.1																																																																																			.	.		0.488	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038		A	48523374	C	A	48523374	2	1	62	1	0	0	0	0	0	0	0	1	15020	639	23	1		1	SPATA2	20	48523374	Silent	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	46202185	48523374	14502146	80	7590										
CSNK1E	1454	hgsc.bcm.edu	37	chr22	38696748	38696748	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ccaatgcccaggtgcgtgttGatggaagcgtagcgggccgt	16	10	0	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chr22:38696748G>C	ENST00000396832.1	-	5	806	c.546C>G	c.(544-546)atC>atG	p.I182M	CSNK1E_ENST00000403904.1_Missense_Mutation_p.I182M|CSNK1E_ENST00000400206.2_Missense_Mutation_p.I182M|CSNK1E_ENST00000359867.3_Missense_Mutation_p.I182M|CSNK1E_ENST00000405675.3_Missense_Mutation_p.I182M|CSNK1E_ENST00000413574.2_Missense_Mutation_p.I182M|CSNK1E_ENST00000498529.1_5'Flank	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	182	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein localization (GO:0034613)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Melanoma(58;0.045)					GGTGCGTGTTGATGGAAGCGT	0.662																																					p.I182M	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)	Atlas-SNP	.											.	CSNK1E	143	.	0			c.C546G						.						88	78	81					22																	38696748		2203	4300	6503	SO:0001583	missense	1454	exon5			CGTGTTGATGGAA		CCDS13970.1	22q13.1	2013-01-17			ENSG00000213923	ENSG00000213923			2453	protein-coding gene	gene with protein product		600863				7797465, 10535959	Standard	NM_001894		Approved	HCKIE, CKIE, CKIepsilon	uc003avk.3	P49674	OTTHUMG00000151135	ENST00000396832.1:c.546C>G	chr22.hg19:g.38696748G>C	ENSP00000380044:p.Ile182Met	353.0	0.0		289.0	77.0	NM_001894		Missense_Mutation	SNP	ENST00000396832.1	hg19	CCDS13970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.364562|5.364562	0.95877|0.95877	.|.	.|.	ENSG00000213923|ENSG00000213923	ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904;ENST00000413574;ENST00000405675;ENST00000430335|ENST00000451964	T;T;T;T;T;T;T|.	0.65178|.	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14|.	4.92|4.92	3.91|3.91	0.45181|0.45181	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.095385|.	0.64402|.	D|.	0.000001|.	T|.	0.74268|.	0.3694|.	M|M	0.88310|0.88310	2.945|2.945	0.80722|0.80722	D|D	1|1	D;P;D|.	0.63880|.	0.992;0.873;0.993|.	D;D;D|.	0.77557|.	0.984;0.966;0.99|.	T|.	0.75758|.	-0.3205|.	10|.	0.45353|.	T|.	0.12|.	.|.	5.7528|5.7528	0.18156|0.18156	0.1617:0.0:0.6809:0.1574|0.1617:0.0:0.6809:0.1574	.|.	182;182;182|.	B0QY35;B0QY34;P49674|.	.;.;KC1E_HUMAN|.	M|X	182|120	ENSP00000352929:I182M;ENSP00000380044:I182M;ENSP00000383067:I182M;ENSP00000384074:I182M;ENSP00000407235:I182M;ENSP00000384426:I182M;ENSP00000412335:I182M|.	ENSP00000352929:I182M|.	I|S	-|-	3|2	3|0	CSNK1E|CSNK1E	37026694|37026694	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.933000|0.933000	0.57130|0.57130	2.454000|2.454000	0.44979|0.44979	1.449000|1.449000	0.47699|0.47699	0.561000|0.561000	0.74099|0.74099	ATC|TCA	.	.		0.662	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894		C	38696748	G	C	38696748	3	2	62	1	0	0	0	0	1	0	0	0	3955	1280	45	4	728	4	CSNK1E	22	38696748	Missense_Mutation	SNP	G	TCGA-CC-A1HT-01A-11D-A12Z-10		38696748	12607818	81	7591										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140985121	140985121	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	caaccactcctatttctttgAagacacattagacctcacct	3	14	2	3			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chrX:140985121A>G	ENST00000298296.1	+	7	1577	c.1577A>G	c.(1576-1578)gAa>gGa	p.E526G	MAGEC3_ENST00000544766.1_Missense_Mutation_p.E228G|MAGEC3_ENST00000409007.1_Missense_Mutation_p.E228G|MAGEC3_ENST00000443323.2_Missense_Mutation_p.E148G|MAGEC3_ENST00000536088.1_Missense_Mutation_p.E228G	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	526	MAGE 2. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					TATTTCTTTGAAGACACATTA	0.438																																					p.E526G		Atlas-SNP	.											.	MAGEC3	228	.	0			c.A1577G						.						152	144	147					X																	140985121		2203	4300	6503	SO:0001583	missense	139081	exon7			TCTTTGAAGACAC	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1577A>G	chrX.hg19:g.140985121A>G	ENSP00000298296:p.Glu526Gly	75.0	0.0		44.0	22.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	hg19	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	a	5.460	0.269946	0.10349	.	.	ENSG00000165509	ENST00000298296;ENST00000536088;ENST00000443323;ENST00000544766;ENST00000409007	T;T;T;T;T	0.04603	3.59;3.59;3.59;3.59;3.59	1.25	-2.5	0.06384	.	.	.	.	.	T	0.02418	0.0074	N	0.08118	0	0.09310	N	1	P;P	0.49253	0.921;0.49	B;B	0.42188	0.218;0.379	T	0.37865	-0.9687	9	0.59425	D	0.04	.	4.071	0.09882	0.5973:0.0:0.0:0.4027	.	526;228	Q8TD91;Q3SYA7	MAGC3_HUMAN;.	G	526;228;148;228;228	ENSP00000298296:E526G;ENSP00000441107:E228G;ENSP00000438254:E148G;ENSP00000440444:E228G;ENSP00000386566:E228G	ENSP00000298296:E526G	E	+	2	0	MAGEC3	140812787	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.807000	0.04520	-1.029000	0.03317	-1.111000	0.02071	GAA	.	.		0.438	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		G	140985121	A	G	140985121	3	3	62	1	0	0	0	0	1	0	0	0	9191	246	9	2	1832	2	MAGEC3	23	140985121	Missense_Mutation	SNP	A	TCGA-CC-A1HT-01A-11D-A12Z-10		140985121	14285439	82	7592										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151821044	151821044	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	agacggagtcagctctctccCcatcaccccagcgcaggccc	9	19	3	1			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chrX:151821044C>A	ENST00000370306.2	+	9	1219	c.1199C>A	c.(1198-1200)cCc>cAc	p.P400H		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	400					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AGCTCTCTCCCCATCACCCCA	0.582																																					p.P400H		Atlas-SNP	.											.	GABRQ	131	.	0			c.C1199A						.						74	68	70					X																	151821044		2203	4300	6503	SO:0001583	missense	55879	exon9			CTCTCCCCATCAC	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1199C>A	chrX.hg19:g.151821044C>A	ENSP00000359329:p.Pro400His	159.0	0.0		169.0	66.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	hg19	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.279283	0.59758	.	.	ENSG00000147402	ENST00000370306	D	0.85629	-2.01	4.59	-0.767	0.11016	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.485053	0.15556	N	0.256196	T	0.74558	0.3732	L	0.46157	1.445	0.09310	N	1	B	0.12013	0.005	B	0.20767	0.031	T	0.62576	-0.6825	10	0.56958	D	0.05	.	0.591	0.00728	0.1747:0.3097:0.1684:0.3472	.	400	Q9UN88	GBRT_HUMAN	H	400	ENSP00000359329:P400H	ENSP00000359329:P400H	P	+	2	0	GABRQ	151571700	0.000000	0.05858	0.000000	0.03702	0.480000	0.33159	0.034000	0.13776	-0.294000	0.08973	0.600000	0.82982	CCC	.	.		0.582	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		A	151821044	C	A	151821044	3	1	62	1	0	0	0	0	1	0	0	0	6183	623	22	3	1233	3	GABRQ	23	151821044	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	10835923	151821044	3449516	83	7593										
MPP1	4354	hgsc.bcm.edu	37	chrX	154013425	154013425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	agctgactgagccatacttgCcactcgcctggtaggaaaag	11	11	0	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chrX:154013425C>T	ENST00000369534.3	-	7	832	c.685G>A	c.(685-687)Gca>Aca	p.A229T	MPP1_ENST00000462825.1_5'UTR|MPP1_ENST00000413259.3_Missense_Mutation_p.A199T|MPP1_ENST00000393531.1_Missense_Mutation_p.A209T	NM_001166460.1|NM_001166461.1|NM_002436.3	NP_001159932.1|NP_001159933.1|NP_002427.1	Q00013	EM55_HUMAN	membrane protein, palmitoylated 1, 55kDa	229					nucleotide phosphorylation (GO:0046939)|regulation of neutrophil chemotaxis (GO:0090022)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(9)|ovary(2)|prostate(1)	21	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GCCATACTTGCCACTCGCCTG	0.557																																					p.A229T		Atlas-SNP	.											.	MPP1	52	.	0			c.G685A						.						71	60	64					X																	154013425		2203	4300	6503	SO:0001583	missense	4354	exon7			TACTTGCCACTCG		CCDS14762.1, CCDS55544.1, CCDS55545.1	Xq28	2008-03-04	2002-08-29		ENSG00000130830	ENSG00000130830			7219	protein-coding gene	gene with protein product		305360	"membrane protein, palmitoylated 1 (55kD)"	DXS552E		1713685	Standard	NM_002436		Approved	PEMP	uc004fmp.2	Q00013	OTTHUMG00000024244	ENST00000369534.3:c.685G>A	chrX.hg19:g.154013425C>T	ENSP00000358547:p.Ala229Thr	65.0	0.0		70.0	30.0	NM_002436	B4DZV5|G3XAI1|Q2TSB6|Q5J7V5	Missense_Mutation	SNP	ENST00000369534.3	hg19	CCDS14762.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372189	0.61624	.	.	ENSG00000130830	ENST00000369534;ENST00000413259;ENST00000393531;ENST00000453245;ENST00000393529;ENST00000428488	D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	5.56	5.56	0.83823	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	D	0.91754	0.7392	M	0.83312	2.635	0.54753	D	0.999988	D;P;D;P;P	0.89917	1.0;0.784;1.0;0.863;0.784	D;P;D;P;P	0.85130	0.996;0.465;0.997;0.666;0.465	D	0.92891	0.6331	10	0.87932	D	0	.	16.9479	0.86235	0.0:1.0:0.0:0.0	.	212;199;103;209;229	B4E325;B4DZV5;C9J9J4;G3XAI1;Q00013	.;.;.;.;EM55_HUMAN	T	229;199;209;103;183;126	ENSP00000358547:A229T;ENSP00000400155:A199T;ENSP00000377165:A209T;ENSP00000410888:A103T;ENSP00000377163:A183T;ENSP00000391701:A126T	ENSP00000358547:A229T	A	-	1	0	MPP1	153666619	1.000000	0.71417	0.805000	0.32314	0.040000	0.13550	7.146000	0.77373	2.313000	0.78055	0.600000	0.82982	GCA	.	.		0.557	MPP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061191.3	NM_002436		T	154013425	C	T	154013425	3	4	62	1	0	0	0	0	1	0	0	0	9742	739	26	3	739	3	MPP1	23	154013425	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	2192381	154013425	1257135	84	7594										
IL9R	3581	hgsc.bcm.edu	37	chrX	155239667	155239667	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	5	1	0.882386689615605	2.05890227576975	0.638969671790611	1	1	0	ggaccaggctcccggggaacCtgagctcagaggatgtgctg	16	11	1	2			TCGA-CC-A1HT-01A-11D-A12Z-10	TCGA-CC-A1HT-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b25a78f-20dc-4ccc-b4c0-f9885d16725d	0255f601-3be9-4059-9d36-7f666977eff0	g.chrX:155239667C>A	ENST00000244174.5	+	9	1338	c.1159C>A	c.(1159-1161)Ctg>Atg	p.L387M	IL9R_ENST00000540897.1_3'UTR|IL9R_ENST00000424344.3_Missense_Mutation_p.L366M|IL9R_ENST00000369423.2_3'UTR	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	387					cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)			NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCCGGGGAACCTGAGCTCAGA	0.647																																					p.L387M		Atlas-SNP	.											.	IL9R	73	.	0			c.C1159A						.						18	33	28					X																	155239667		2128	4267	6395	SO:0001583	missense	3581	exon9			GGGAACCTGAGCT	M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"Pseudoautosomal regions / PAR2", "Interleukins and interleukin receptors", "CD molecules"	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.1159C>A	chrX.hg19:g.155239667C>A	ENSP00000244174:p.Leu387Met	247.0	0.0		330.0	38.0	NM_002186	B9ZVT0|Q14634|Q8WWU1|Q96TF0	Missense_Mutation	SNP	ENST00000244174.5	hg19	CCDS14771.4	.	.	.	.	.	.	.	.	.	.	c	6.810	0.518491	0.13005	.	.	ENSG00000124334	ENST00000244174;ENST00000424344	T;T	0.10860	2.83;2.83	0.971	0.0097	0.14080	.	2.975570	0.01806	U	0.033170	T	0.17365	0.0417	.	.	.	0.09310	N	1	D	0.60160	0.987	P	0.55391	0.775	T	0.09292	-1.0681	9	0.38643	T	0.18	.	3.0994	0.06320	0.0:0.6516:0.0:0.3484	.	387	Q01113	IL9R_HUMAN	M	387;366	ENSP00000244174:L387M;ENSP00000388918:L366M	ENSP00000244174:L387M	L	+	1	2	IL9R	154892861	0.000000	0.05858	0.003000	0.11579	0.052000	0.14988	-0.626000	0.05527	-0.069000	0.12931	0.287000	0.19450	CTG	.	.		0.647	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	NM_002186		A	155239667	C	A	155239667	3	1	62	1	0	0	0	0	1	0	0	0	7717	680	24	3	1193	3	IL9R	23	155239667	Missense_Mutation	SNP	C	TCGA-CC-A1HT-01A-11D-A12Z-10	1226242	155239667	30893	85	7595										
MEGF6	1953	hgsc.bcm.edu	37	chr1	3425655	3425655	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tcaccaaacttctctgtgagCgtgtgttcgccccgcaactc	8	15	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:3425655C>T	ENST00000356575.4	-	12	1738	c.1512G>A	c.(1510-1512)acG>acA	p.T504T	MEGF6_ENST00000294599.4_Silent_p.T399T	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	504						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		TCTCTGTGAGCGTGTGTTCGC	0.672																																					p.T504T	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.G1512A						.						15	18	17					1																	3425655		1958	4117	6075	SO:0001819	synonymous_variant	1953	exon12			TGTGAGCGTGTGT	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"EGF-like-domain, multiple 3"	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.1512G>A	chr1.hg19:g.3425655C>T		114.0	0.0		138.0	41.0	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	hg19	CCDS41237.1																																																																																			.	.		0.672	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		T	3425655	C	T	3425655	2	4	63	1	0	0	0	0	0	0	0	1	9471	755	27	1		1	MEGF6	1	3425655	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10		3425655	245824966	1	7596										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32158742	32158742	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gtggaccaggcaggccccgcTcacctttccctccctgagag	11	17	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:32158742T>A	ENST00000373672.3	-	13	1538	c.1022A>T	c.(1021-1023)gAg>gTg	p.E341V	COL16A1_ENST00000271069.6_Missense_Mutation_p.E341V|COL16A1_ENST00000373668.3_Missense_Mutation_p.E341V	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	341	Nonhelical region 10 (NC10).				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CAGGCCCCGCTCACCTTTCCC	0.632																																					p.E341V	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.A1022T						.						35	37	37					1																	32158742		1928	4122	6050	SO:0001583	missense	1307	exon13			CCCCGCTCACCTT	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.1022A>T	chr1.hg19:g.32158742T>A	ENSP00000362776:p.Glu341Val	125.0	0.0		113.0	18.0	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497511	0.44455	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668;ENST00000373667	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	4.92	4.92	0.64577	.	0.150748	0.41938	D	0.000790	D	0.93223	0.7841	M	0.62266	1.93	0.38037	D	0.93533	P;P;P	0.49185	0.92;0.7;0.801	B;B;P	0.48704	0.341;0.383;0.587	D	0.94418	0.7638	10	0.62326	D	0.03	.	12.3899	0.55352	0.0:0.0:0.0:1.0	.	341;341;341	A6NCT7;Q07092;Q07092-2	.;COGA1_HUMAN;.	V	341;341;341;60	ENSP00000362776:E341V;ENSP00000271069:E341V;ENSP00000362772:E341V;ENSP00000362771:E60V	ENSP00000271069:E341V	E	-	2	0	COL16A1	31931329	1.000000	0.71417	0.965000	0.40720	0.658000	0.38924	4.988000	0.63863	1.996000	0.58369	0.379000	0.24179	GAG	.	.		0.632	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		A	32158742	T	A	32158742	3	1	63	1	0	0	0	0	1	0	0	0	3675	1551	54	4	4028	4	COL16A1	1	32158742	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	28733087	32158742	217091879	2	7597										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34498286	34498286	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gctgcactaacaatggtggcTggcagctgaaagcctgtgag	14	9	0	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:34498286T>G	ENST00000373381.4	-	3	602	c.426A>C	c.(424-426)ccA>ccC	p.P142P		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	102	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CAATGGTGGCTGGCAGCTGAA	0.527																																					p.P102P		Atlas-SNP	.											.	CSMD2	946	.	0			c.A306C						.						79	62	68					1																	34498286		2203	4300	6503	SO:0001819	synonymous_variant	114784	exon3			GGTGGCTGGCAGC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.426A>C	chr1.hg19:g.34498286T>G		83.0	0.0		93.0	12.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	hg19																																																																																				.	.		0.527	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		G	34498286	T	G	34498286	2	3	63	1	0	0	0	0	0	0	0	1	3947	1567	55	5		5	CSMD2	1	34498286	Silent	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	2339544	34498286	214752335	3	7598										
CNN3	1266	hgsc.bcm.edu	37	chr1	95364951	95364951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ctggctcctttattagtgccCatctgcagactaattgtggt	9	10	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:95364951C>T	ENST00000370206.4	-	6	1007	c.624G>A	c.(622-624)atG>atA	p.M208I	CNN3_ENST00000394202.4_Missense_Mutation_p.M162I|CNN3_ENST00000538964.1_Missense_Mutation_p.M208I|CNN3_ENST00000487539.1_5'UTR|CNN3_ENST00000545882.1_Missense_Mutation_p.M167I	NM_001839.3	NP_001830.1	Q15417	CNN3_HUMAN	calponin 3, acidic	208					actomyosin structure organization (GO:0031032)|epithelial cell differentiation (GO:0030855)	focal adhesion (GO:0005925)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|stomach(1)|urinary_tract(2)	18		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)		TATTAGTGCCCATCTGCAGAC	0.408																																					p.M208I		Atlas-SNP	.											.	CNN3	23	.	0			c.G624A						.						131	123	126					1																	95364951		2203	4300	6503	SO:0001583	missense	1266	exon6			AGTGCCCATCTGC	BC025372	CCDS30775.1, CCDS65592.1, CCDS65593.1	1p22-p21	2010-07-08			ENSG00000117519	ENSG00000117519			2157	protein-coding gene	gene with protein product		602374				8526917	Standard	NM_001839		Approved		uc001dqz.4	Q15417	OTTHUMG00000010783	ENST00000370206.4:c.624G>A	chr1.hg19:g.95364951C>T	ENSP00000359225:p.Met208Ile	128.0	0.0		67.0	15.0	NM_001839	B4DFK6|B4DP09|F8WA86|Q6FHA7	Missense_Mutation	SNP	ENST00000370206.4	hg19	CCDS30775.1	.	.	.	.	.	.	.	.	.	.	C	31	5.069592	0.93950	.	.	ENSG00000117519	ENST00000370206;ENST00000538964;ENST00000394202;ENST00000545882;ENST00000415017	T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.81069	0.4746	M	0.93978	3.48	0.80722	D	1	D;D	0.71674	0.998;0.963	D;D	0.69824	0.944;0.966	D	0.84795	0.0781	10	0.72032	D	0.01	-15.6579	20.2279	0.98344	0.0:1.0:0.0:0.0	.	162;208	F8WA86;Q15417	.;CNN3_HUMAN	I	208;208;162;167;167	ENSP00000359225:M208I;ENSP00000437665:M208I;ENSP00000377752:M162I;ENSP00000440081:M167I;ENSP00000401452:M167I	ENSP00000359225:M208I	M	-	3	0	CNN3	95137539	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.778000	0.95560	0.655000	0.94253	ATG	.	.		0.408	CNN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029702.2	NM_001839		T	95364951	C	T	95364951	3	4	63	1	0	0	0	0	1	0	0	0	3613	594	21	3	373	3	CNN3	1	95364951	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	60866665	95364951	153885670	4	7599										
FNDC7	163479	hgsc.bcm.edu	37	chr1	109273448	109273448	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	acactcatcaaaaccactgcCtcctaggatgcatcacatgt	5	14	3	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:109273448C>T	ENST00000370017.3	+	9	2054	c.1777C>T	c.(1777-1779)Ctc>Ttc	p.L593F	FNDC7_ENST00000271311.2_Missense_Mutation_p.L594F	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	593	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		AAACCACTGCCTCCTAGGATG	0.468																																					p.L593F		Atlas-SNP	.											.	FNDC7	113	.	0			c.C1777T						.						166	132	144					1																	109273448		2203	4300	6503	SO:0001583	missense	163479	exon9			CACTGCCTCCTAG		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"Fibronectin type III domain containing"	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.1777C>T	chr1.hg19:g.109273448C>T	ENSP00000359034:p.Leu593Phe	106.0	0.0		98.0	18.0	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	hg19	CCDS44185.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.1|20.1	3.935704|3.935704	0.73442|0.73442	.|.	.|.	ENSG00000143107|ENSG00000143107	ENST00000370017;ENST00000271311|ENST00000445274	D;D|.	0.99051|.	-5.37;-5.37|.	6.05|6.05	3.97|3.97	0.46021|0.46021	Fibronectin, type III (3);|.	0.195956|.	0.46442|.	D|.	0.000290|.	T|T	0.63105|0.63105	0.2483|0.2483	M|M	0.63843|0.63843	1.955|1.955	0.46279|0.46279	D|D	0.998968|0.998968	D;D|.	0.58620|.	0.983;0.969|.	P;P|.	0.59595|.	0.86;0.73|.	T|T	0.64685|0.64685	-0.6349|-0.6349	10|5	0.44086|.	T|.	0.13|.	-16.7176|-16.7176	16.7121|16.7121	0.85388|0.85388	0.2468:0.7532:0.0:0.0|0.2468:0.7532:0.0:0.0	.|.	594;593|.	Q5VTL7;E9PAZ5|.	FNDC7_HUMAN;.|.	F|L	593;594|368	ENSP00000359034:L593F;ENSP00000271311:L594F|.	ENSP00000271311:L594F|.	L|P	+|+	1|2	0|0	FNDC7|FNDC7	109074971|109074971	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.941000|0.941000	0.58515|0.58515	5.661000|5.661000	0.68025|0.68025	1.530000|1.530000	0.49136|0.49136	0.655000|0.655000	0.94253|0.94253	CTC|CCT	.	.		0.468	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532		T	109273448	C	T	109273448	3	4	63	1	0	0	0	0	1	0	0	0	5981	681	24	3	1811	3	FNDC7	1	109273448	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	13908497	109273448	139977173	5	7600										
DCLRE1B	64858	hgsc.bcm.edu	37	chr1	114454510	114454510	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	acggccccactgggattttcAgtgcacttaaggtctacaga	10	11	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:114454510A>G	ENST00000369563.3	+	4	1742	c.1296A>G	c.(1294-1296)tcA>tcG	p.S432S	DCLRE1B_ENST00000466480.1_Intron	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	432					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGGGATTTTCAGTGCACTTAA	0.463								Other identified genes with known or suspected DNA repair function																													p.S432S		Atlas-SNP	.											.	DCLRE1B	36	.	0			c.A1296G						.						171	189	183					1																	114454510		2203	4300	6503	SO:0001819	synonymous_variant	64858	exon4			ATTTTCAGTGCAC	BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"APOLLO", "PSO2 homolog (S. cerevisiae)"	609683	"DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.1296A>G	chr1.hg19:g.114454510A>G		117.0	0.0		102.0	18.0	NM_022836	Q9H9E5	Silent	SNP	ENST00000369563.3	hg19	CCDS866.1																																																																																			.	.		0.463	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836		G	114454510	A	G	114454510	2	3	63	1	0	0	0	0	0	0	0	1	4297	175	7	2		2	DCLRE1B	1	114454510	Silent	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	5181062	114454510	134796111	6	7601										
C1orf92	149499	hgsc.bcm.edu	37	chr1	156901780	156901780	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	accgagatgggaaagttttcAtgcctgggaacaaggtcctt	12	8	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:156901780A>G	ENST00000337428.7	+	13	1556	c.1402A>G	c.(1402-1404)Atg>Gtg	p.M468V	LRRC71_ENST00000490146.1_3'UTR|ARHGEF11_ENST00000487682.1_5'Flank	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	468										endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						GAAAGTTTTCATGCCTGGGAA	0.552																																					p.M468V		Atlas-SNP	.											.	LRRC71	33	.	0			c.A1402G						.						78	83	81					1																	156901780		2046	4181	6227	SO:0001583	missense	149499	exon13			GTTTTCATGCCTG	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 92"	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.1402A>G	chr1.hg19:g.156901780A>G	ENSP00000336661:p.Met468Val	210.0	0.0		187.0	16.0	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	hg19	CCDS44249.1	.	.	.	.	.	.	.	.	.	.	A	9.998	1.232562	0.22626	.	.	ENSG00000160838	ENST00000337428	T	0.17854	2.25	5.68	-1.36	0.09085	.	0.216602	0.32819	N	0.005616	T	0.03348	0.0097	L	0.27053	0.805	0.23483	N	0.997586	B;B	0.24920	0.01;0.114	B;B	0.27262	0.004;0.078	T	0.37384	-0.9708	10	0.48119	T	0.1	-32.5944	6.0254	0.19652	0.2605:0.2118:0.0:0.5277	.	468;254	Q8N4P6;Q8N4P6-2	LRC71_HUMAN;.	V	468	ENSP00000336661:M468V	ENSP00000336661:M468V	M	+	1	0	LRRC71	155168404	0.997000	0.39634	0.999000	0.59377	0.949000	0.60115	0.329000	0.19698	0.046000	0.15833	-0.490000	0.04691	ATG	.	.		0.552	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702		G	156901780	A	G	156901780	3	3	63	1	0	0	0	0	1	0	0	0	2071	217	8	2	1452	2	C1orf92	1	156901780	Missense_Mutation	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	42447270	156901780	92348841	7	7602										
DDR2	4921	hgsc.bcm.edu	37	chr1	162688873	162688873	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gatgatcctgattcccagaaTgctcttggtgctgttcctgc	10	11	1	3			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:162688873T>C	ENST00000367922.3	+	4	458	c.20T>C	c.(19-21)aTg>aCg	p.M7T	DDR2_ENST00000367921.3_Missense_Mutation_p.M7T	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	7					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	ATTCCCAGAATGCTCTTGGTG	0.448																																					p.M7T	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											.	DDR2	228	.	0			c.T20C						.						205	178	187					1																	162688873		2203	4300	6503	SO:0001583	missense	4921	exon4			CCAGAATGCTCTT	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"discoidin domain receptor family, member 2"	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.20T>C	chr1.hg19:g.162688873T>C	ENSP00000356899:p.Met7Thr	118.0	0.0		64.0	15.0	NM_001014796	Q7Z730	Missense_Mutation	SNP	ENST00000367922.3	hg19	CCDS1241.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.611739	0.28712	.	.	ENSG00000162733	ENST00000446985;ENST00000415555;ENST00000542391;ENST00000367922;ENST00000367921	D;D;D;D	0.97688	-4.22;-4.49;-1.67;-1.67	4.25	3.12	0.35913	.	1.126930	0.06488	N	0.734009	D	0.91307	0.7259	L	0.36672	1.1	0.25662	N	0.985988	B	0.02656	0.0	B	0.06405	0.002	D	0.84515	0.0624	9	0.62326	D	0.03	.	6.3202	0.21213	0.0:0.1125:0.0:0.8875	.	7	Q16832	DDR2_HUMAN	T	7	ENSP00000400309:M7T;ENSP00000391310:M7T;ENSP00000356899:M7T;ENSP00000356898:M7T	ENSP00000356898:M7T	M	+	2	0	DDR2	160955497	1.000000	0.71417	0.993000	0.49108	0.970000	0.65996	1.360000	0.34125	0.796000	0.33947	0.383000	0.25322	ATG	.	.		0.448	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		C	162688873	T	C	162688873	3	2	63	1	0	0	0	0	1	0	0	0	4339	1464	51	2	22	2	DDR2	1	162688873	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	5787093	162688873	86561748	8	7603										
MFSD4	148808	hgsc.bcm.edu	37	chr1	205568282	205568282	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ttccaggctcagggcagctaTagtttcctggtctgtggcgt	13	10	2	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:205568282T>C	ENST00000367147.4	+	9	1485	c.1392T>C	c.(1390-1392)taT>taC	p.Y464Y	MFSD4_ENST00000478555.1_3'UTR|MFSD4_ENST00000536357.1_Silent_p.Y377Y|MFSD4_ENST00000539267.1_Nonstop_Mutation_p.*441Q	NM_181644.4	NP_857595.3	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing 4	464					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			AGGGCAGCTATAGTTTCCTGG	0.483																																					p.Y464Y		Atlas-SNP	.											.	MFSD4	46	.	0			c.T1392C						.						438	386	404					1																	205568282		2203	4300	6503	SO:0001819	synonymous_variant	148808	exon9			CAGCTATAGTTTC	BC036549	CCDS1455.1	1q32.1	2008-02-05			ENSG00000174514	ENSG00000174514			25433	protein-coding gene	gene with protein product							Standard	NM_181644		Approved	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004	uc001hcv.4	Q8N468	OTTHUMG00000037197	ENST00000367147.4:c.1392T>C	chr1.hg19:g.205568282T>C		369.0	0.0		317.0	73.0	NM_181644	B7Z8X3|Q6UY25|Q8NAY0|Q8TCP4	Silent	SNP	ENST00000367147.4	hg19	CCDS1455.1	.	.	.	.	.	.	.	.	.	.	T	13.37	2.215492	0.39102	.	.	ENSG00000174514	ENST00000539267	.	.	.	5.64	-3.36	0.04913	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.5828	15.7076	0.77598	0.0:0.817:0.0:0.183	.	.	.	.	Q	441	.	.	X	+	1	0	MFSD4	203834905	1.000000	0.71417	0.985000	0.45067	0.992000	0.81027	0.873000	0.28052	-0.496000	0.06650	-0.376000	0.06991	TAG	.	.		0.483	MFSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090391.1	NM_181644		C	205568282	T	C	205568282	2	2	63	1	0	0	0	0	0	0	0	1	9542	1413	49	2		2	MFSD4	1	205568282	Silent	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	42879409	205568282	43682339	9	7604										
ZNF496	84838	hgsc.bcm.edu	37	chr1	247464447	247464447	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ggggaggctgcgctgcttctCtgtggggctccccagctctt	15	13	2	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:247464447C>A	ENST00000294753.4	-	9	1602	c.1138G>T	c.(1138-1140)Gag>Tag	p.E380*	ZNF496_ENST00000366498.2_Nonsense_Mutation_p.E416*|ZNF496_ENST00000462139.1_5'UTR	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	380					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			CGCTGCTTCTCTGTGGGGCTC	0.632																																					p.E380X		Atlas-SNP	.											ZNF496,right_lower_lobe,carcinoma,0,1	ZNF496	80	.	0			c.G1138T						.						31	38	35					1																	247464447		2203	4296	6499	SO:0001587	stop_gained	84838	exon9			GCTTCTCTGTGGG	BC007263	CCDS1631.1	1q44	2013-01-09			ENSG00000162714	ENSG00000162714		"Zinc fingers, C2H2-type", "-", "-", "-"	23713	protein-coding gene	gene with protein product		613911				12477932	Standard	NM_032752		Approved	ZKSCAN17, MGC15548, ZSCAN49	uc001ico.3	Q96IT1	OTTHUMG00000041164	ENST00000294753.4:c.1138G>T	chr1.hg19:g.247464447C>A	ENSP00000294753:p.Glu380*	190.0	0.0		154.0	47.0	NM_032752	Q8TBS2	Nonsense_Mutation	SNP	ENST00000294753.4	hg19	CCDS1631.1	.	.	.	.	.	.	.	.	.	.	C	37	6.432110	0.97564	.	.	ENSG00000162714	ENST00000294753;ENST00000366498	.	.	.	3.88	1.99	0.26369	.	0.757625	0.11666	N	0.541327	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-10.814	5.0192	0.14352	0.0:0.6497:0.0:0.3503	.	.	.	.	X	380;416	.	ENSP00000294753:E380X	E	-	1	0	ZNF496	245531070	0.001000	0.12720	0.022000	0.16811	0.021000	0.10359	1.225000	0.32551	0.983000	0.38602	0.591000	0.81541	GAG	.	.		0.632	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752		A	247464447	C	A	247464447	4	1	63	1	0	0	0	0	0	1	0	0	17960	922	32	3	629	3	ZNF496	1	247464447	Nonsense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	41896165	247464447	1786174	10	7605										
TRIM58	25893	hgsc.bcm.edu	37	chr1	248039390	248039390	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	actgggaggttctggtgggaGaaggagcagagtggggttta	20	3	1	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:248039390G>A	ENST00000366481.3	+	6	1108	c.1060G>A	c.(1060-1062)Gaa>Aaa	p.E354K	OR2W3_ENST00000537741.1_Intron	NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	354	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TCTGGTGGGAGAAGGAGCAGA	0.572																																					p.E354K		Atlas-SNP	.											.	TRIM58	143	.	0			c.G1060A						.						110	100	103					1																	248039390		2203	4300	6503	SO:0001583	missense	25893	exon6			GTGGGAGAAGGAG	AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	24150	protein-coding gene	gene with protein product			"tripartite motif-containing 58"				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.1060G>A	chr1.hg19:g.248039390G>A	ENSP00000355437:p.Glu354Lys	206.0	0.0		193.0	11.0	NM_015431	Q6B0H9	Missense_Mutation	SNP	ENST00000366481.3	hg19	CCDS1636.1	.	.	.	.	.	.	.	.	.	.	G	9.325	1.058964	0.19987	.	.	ENSG00000162722	ENST00000366481	T	0.61040	0.14	4.05	3.12	0.35913	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.828799	0.10839	N	0.628397	T	0.43255	0.1239	L	0.28054	0.825	0.80722	D	1	B	0.06786	0.001	B	0.12837	0.008	T	0.18618	-1.0331	10	0.23891	T	0.37	.	10.462	0.44585	0.0976:0.0:0.9024:0.0	.	354	Q8NG06	TRI58_HUMAN	K	354	ENSP00000355437:E354K	ENSP00000355437:E354K	E	+	1	0	TRIM58	246106013	1.000000	0.71417	0.089000	0.20774	0.062000	0.15995	5.895000	0.69814	1.288000	0.44600	0.650000	0.86243	GAA	.	.		0.572	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431		A	248039390	G	A	248039390	3	1	63	1	0	0	0	0	1	0	0	0	16546	943	33	3	1082	3	TRIM58	1	248039390	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	574943	248039390	1211231	11	7606										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125555776	125555776	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tcatcctcagctatttacacAgattcagctccatccaagga	5	13	3	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr2:125555776A>T	ENST00000431078.1	+	19	3457	c.3093A>T	c.(3091-3093)acA>acT	p.T1031T		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	1031	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CTATTTACACAGATTCAGCTC	0.438																																					p.T1031T		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.A3093T						.						148	142	144					2																	125555776		1946	4150	6096	SO:0001819	synonymous_variant	129684	exon19			TTACACAGATTCA	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.3093A>T	chr2.hg19:g.125555776A>T		243.0	0.0		199.0	53.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	hg19	CCDS46401.1																																																																																			.	.		0.438	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125555776	A	T	125555776	2	4	63	1	0	0	0	0	0	0	0	1	3652	175	7	4		4	CNTNAP5	2	125555776	Silent	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10		125555776	117643597	12	7607										
IWS1	55677	hgsc.bcm.edu	37	chr2	128247424	128247424	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	atacctgttcattcttcgtcGttgaggcatctgttctagat	8	9	4	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr2:128247424G>A	ENST00000295321.4	-	11	2402	c.2143C>T	c.(2143-2145)Cga>Tga	p.R715*	AC010976.2_ENST00000454503.2_RNA|AC010976.2_ENST00000598065.1_RNA|AC010976.2_ENST00000595561.1_RNA|AC010976.2_ENST00000596439.1_RNA|AC010976.2_ENST00000599001.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	715	Interaction with SUPT6H and ALYREF.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		ATTCTTCGTCGTTGAGGCATC	0.413																																					p.R715X		Atlas-SNP	.											.	IWS1	61	.	0			c.C2143T						.						401	344	363					2																	128247424		2203	4300	6503	SO:0001587	stop_gained	55677	exon11			TTCGTCGTTGAGG	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.2143C>T	chr2.hg19:g.128247424G>A	ENSP00000295321:p.Arg715*	348.0	0.0		268.0	41.0	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Nonsense_Mutation	SNP	ENST00000295321.4	hg19	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	G	39	7.512099	0.98329	.	.	ENSG00000163166	ENST00000295321;ENST00000433551	.	.	.	5.03	3.16	0.36331	.	0.133236	0.50627	D	0.000119	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.7877	13.711	0.62667	0.0:0.0:0.7186:0.2814	.	.	.	.	X	715;668	.	ENSP00000295321:R715X	R	-	1	2	IWS1	127963894	1.000000	0.71417	0.989000	0.46669	0.943000	0.58893	2.581000	0.46077	0.480000	0.27534	0.563000	0.77884	CGA	.	.		0.413	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		A	128247424	G	A	128247424	4	1	63	1	0	0	0	0	0	1	0	0	7940	1153	40	1	332	1	IWS1	2	128247424	Nonsense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	2691648	128247424	114951949	13	7608										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171259467	171259467	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	acatcgccaatgagcaaatcCagtactatttcaatcagcat	5	11	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr2:171259467C>G	ENST00000408978.4	+	19	2382	c.2239C>G	c.(2239-2241)Cag>Gag	p.Q747E	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.Q747E|MYO3B_ENST00000334231.6_Missense_Mutation_p.Q756E	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	747	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TGAGCAAATCCAGTACTATTT	0.413																																					p.Q747E		Atlas-SNP	.											.	MYO3B	320	.	0			c.C2239G						.						125	114	117					2																	171259467		1872	4107	5979	SO:0001583	missense	140469	exon19			CAAATCCAGTACT		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2239C>G	chr2.hg19:g.171259467C>G	ENSP00000386213:p.Gln747Glu	126.0	0.0		102.0	16.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	hg19	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.879044	0.91740	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	6.02	6.02	0.97574	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.93446	0.7909	H	0.98629	4.285	0.80722	D	1	D;D;D	0.76494	0.982;0.999;0.997	D;D;D	0.72075	0.91;0.975;0.976	D	0.95115	0.8241	10	0.87932	D	0	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	747;747;747	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	E	747;747;746;756;756	ENSP00000386497:Q747E;ENSP00000386213:Q747E;ENSP00000446237:Q756E;ENSP00000335100:Q756E	ENSP00000314213:Q746E	Q	+	1	0	MYO3B	170967713	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.788000	0.85771	2.865000	0.98341	0.655000	0.94253	CAG	.	.		0.413	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			G	171259467	C	G	171259467	3	3	63	1	0	0	0	0	1	0	0	0	10086	595	21	4	2313	4	MYO3B	2	171259467	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	43012043	171259467	71939906	14	7609										
NUP210	23225	hgsc.bcm.edu	37	chr3	13383318	13383318	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cacttgcagttagactggtcTggccgatggccacaccgcgg	13	13	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:13383318T>A	ENST00000254508.5	-	23	3240	c.3158A>T	c.(3157-3159)cAg>cTg	p.Q1053L	NUP210_ENST00000485755.1_5'Flank	NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1053					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TAGACTGGTCTGGCCGATGGC	0.522																																					p.Q1053L		Atlas-SNP	.											.	NUP210	182	.	0			c.A3158T						.						151	126	134					3																	13383318		2203	4300	6503	SO:0001583	missense	23225	exon23			CTGGTCTGGCCGA	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.3158A>T	chr3.hg19:g.13383318T>A	ENSP00000254508:p.Gln1053Leu	217.0	0.0		193.0	57.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	T	17.82	3.482924	0.63962	.	.	ENSG00000132182	ENST00000254508	T	0.04917	3.53	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.19406	0.0466	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.13602	-1.0503	10	0.02654	T	1	-17.7609	14.8389	0.70209	0.0:0.0:0.0:1.0	.	1053	Q8TEM1	PO210_HUMAN	L	1053	ENSP00000254508:Q1053L	ENSP00000254508:Q1053L	Q	-	2	0	NUP210	13358318	1.000000	0.71417	1.000000	0.80357	0.023000	0.10783	7.073000	0.76784	2.147000	0.66899	0.455000	0.32223	CAG	.	.		0.522	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		A	13383318	T	A	13383318	3	1	63	1	0	0	0	0	1	0	0	0	10769	1580	55	4	2577	4	NUP210	3	13383318	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10		13383318	184639112	15	7610										
SCN5A	6331	hgsc.bcm.edu	37	chr3	38645542	38645542	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gaacgtggcttcatagaagtCctgctgaggccacgggtgag	15	9	1	3			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:38645542C>T	ENST00000333535.4	-	12	1700	c.1551G>A	c.(1549-1551)agG>agA	p.R517R	SCN5A_ENST00000425664.1_Silent_p.R517R|SCN5A_ENST00000451551.2_Silent_p.R517R|SCN5A_ENST00000413689.1_Silent_p.R517R|SCN5A_ENST00000423572.2_Silent_p.R517R|SCN5A_ENST00000414099.2_Silent_p.R517R|SCN5A_ENST00000455624.2_Silent_p.R517R|SCN5A_ENST00000443581.1_Silent_p.R517R|SCN5A_ENST00000450102.2_Silent_p.R517R|SCN5A_ENST00000449557.2_Silent_p.R517R			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	517					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	TCATAGAAGTCCTGCTGAGGC	0.537																																					p.R517R		Atlas-SNP	.											.	SCN5A	634	.	0			c.G1551A						.						27	28	28					3																	38645542		2040	4209	6249	SO:0001819	synonymous_variant	6331	exon12			AGAAGTCCTGCTG	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1551G>A	chr3.hg19:g.38645542C>T		101.0	0.0		107.0	16.0	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	hg19	CCDS46796.1																																																																																			.	.		0.537	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		T	38645542	C	T	38645542	2	4	63	1	0	0	0	0	0	0	0	1	13937	854	30	3		3	SCN5A	3	38645542	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	25262224	38645542	159376888	16	7611										
SCN11A	11280	hgsc.bcm.edu	37	chr3	38991632	38991632	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	aagtcttccagaggctttccTatgagctcacgaggaatgtc	10	10	2	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:38991632T>A	ENST00000302328.3	-	1	420	c.222A>T	c.(220-222)atA>atT	p.I74I	SCN11A_ENST00000444237.2_Silent_p.I74I|SCN11A_ENST00000450244.1_Silent_p.I74I|SCN11A_ENST00000456224.3_Silent_p.I74I	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	74					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GAGGCTTTCCTATGAGCTCAC	0.562																																					p.I74I		Atlas-SNP	.											.	SCN11A	296	.	0			c.A222T						.						100	102	101					3																	38991632		2203	4300	6503	SO:0001819	synonymous_variant	11280	exon1			CTTTCCTATGAGC	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.222A>T	chr3.hg19:g.38991632T>A		170.0	0.0		152.0	26.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.		0.562	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		A	38991632	T	A	38991632	2	1	63	1	0	0	0	0	0	0	0	1	13928	1512	53	4		4	SCN11A	3	38991632	Silent	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	346090	38991632	159030798	17	7612										
GPR128	84873	hgsc.bcm.edu	37	chr3	100354665	100354810	+	Splice_Site	DEL	CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	-													0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	acacttccagaaatgcttcaCctgaggtaaaactcacagag					rs78754646|rs1520652|rs569801502|rs79409266|rs183117613|rs201699644|rs573702880|rs548009741|rs532138567|rs529836893|rs1718281|rs188782193	byFrequency	TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:100354665_100354810delCCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	ENST00000273352.3	+	5	860_865	c.592_597delCCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	c.(592-597)cctgagdel	p.PE198fs	GPR128_ENST00000475887.1_5'UTR	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	198					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.?(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						AAATGCTTCACCTGAGGTAAAACTCACAGAGCtttaaaaaaaattttttttttatttttaGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTGCATAGCACTC	0.358																																					p.197_199del	Pancreas(87;185 1975 7223 18722)	Pindel	.											.	GPR128	126	.	1	Unknown(1)	kidney(1)	c.591_597del						.																																			SO:0001630	splice_region_variant	84873	exon5			.	AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"-", "GPCR / Class B : Orphans"	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.597+1CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG>-	chr3.hg19:g.100354665_100354810delCCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG		47.0	0.0		42.0	15.0	NM_032787	Q14D94|Q86SQ2	Frame_Shift_Del	DEL	ENST00000273352.3	hg19	CCDS2938.1																																																																																			.	.		0.358	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1		Frame_Shift_Del	-	100354810	CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	-	100354665	8	5	63	1	0	1	0	1	0	0	1	0	6649	507	18	0	610	0	GPR128	3	100354665	Splice_Site	DEL	CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	TCGA-CC-A3M9-01A-11D-A20W-10	61363033	100354665	97667765	18	7613										
POLQ	10721	hgsc.bcm.edu	37	chr3	121179064	121179064	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ttcaagctgagagtagtcagCagccagtattgaaccacctg	10	10	2	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:121179064C>A	ENST00000264233.5	-	25	7113	c.6985G>T	c.(6985-6987)Gct>Tct	p.A2329S		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2329					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		GAGTAGTCAGCAGCCAGTATT	0.398								DNA polymerases (catalytic subunits)																													p.A2329S	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G6985T						.						75	71	72					3																	121179064		2203	4300	6503	SO:0001583	missense	10721	exon25			AGTCAGCAGCCAG	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.6985G>T	chr3.hg19:g.121179064C>A	ENSP00000264233:p.Ala2329Ser	159.0	0.0		155.0	24.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.047027	0.93740	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	D	0.97352	-4.35	5.6	5.6	0.85130	DNA-directed DNA polymerase, family A, palm domain (2);	0.111909	0.64402	D	0.000011	D	0.98501	0.9500	M	0.79693	2.465	0.44908	D	0.997926	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	D	0.99338	1.0911	10	0.72032	D	0.01	.	19.6126	0.95616	0.0:1.0:0.0:0.0	.	2329;1501	O75417;O75417-2	DPOLQ_HUMAN;.	S	1952;2329;2465	ENSP00000264233:A2329S	ENSP00000264233:A2329S	A	-	1	0	POLQ	122661754	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.172000	0.77604	2.630000	0.89119	0.591000	0.81541	GCT	.	.		0.398	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121179064	C	A	121179064	3	1	63	1	0	0	0	0	1	0	0	0	12217	710	25	3	811	3	POLQ	3	121179064	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	20824399	121179064	76843366	19	7614										
MGLL	11343	hgsc.bcm.edu	37	chr3	127413989	127413989	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tggatgccgaagcacaccttCagccctgcccggcagatcag	11	15	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:127413989C>T	ENST00000434178.2	-	7	1511	c.615G>A	c.(613-615)ctG>ctA	p.L205L	MGLL_ENST00000265052.5_Silent_p.L215L|MGLL_ENST00000398104.1_Silent_p.L205L|MGLL_ENST00000398101.3_Silent_p.L179L|MGLL_ENST00000453507.2_Silent_p.L185L|MGLL_ENST00000476682.1_5'UTR			Q99685	MGLL_HUMAN	monoglyceride lipase	205					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						AGCACACCTTCAGCCCTGCCC	0.612																																					p.L215L		Atlas-SNP	.											.	MGLL	19	.	0			c.G645A						.						49	54	52					3																	127413989		2067	4195	6262	SO:0001819	synonymous_variant	11343	exon7			CACCTTCAGCCCT	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.615G>A	chr3.hg19:g.127413989C>T		232.0	0.0		165.0	36.0	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	ENST00000434178.2	hg19	CCDS43148.1																																																																																			.	.		0.612	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283		T	127413989	C	T	127413989	2	4	63	1	0	0	0	0	0	0	0	1	9565	813	29	3		3	MGLL	3	127413989	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	6234925	127413989	70608441	20	7615										
WDR49	151790	hgsc.bcm.edu	37	chr3	167277892	167277892	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tgccagtcaaaagccgagtcTcatttgcatcaagggccata	9	11	3	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:167277892T>A	ENST00000308378.3	-	5	916	c.611A>T	c.(610-612)gAg>gTg	p.E204V	WDR49_ENST00000453925.2_Missense_Mutation_p.E257V|WDR49_ENST00000479765.1_Intron|WDR49_ENST00000476376.1_Missense_Mutation_p.E29V	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	204										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						AAGCCGAGTCTCATTTGCATC	0.448																																					p.E204V		Atlas-SNP	.											.	WDR49	188	.	0			c.A611T						.						189	172	178					3																	167277892		2203	4300	6503	SO:0001583	missense	151790	exon5			CGAGTCTCATTTG	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.611A>T	chr3.hg19:g.167277892T>A	ENSP00000311343:p.Glu204Val	222.0	0.0		152.0	44.0	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	hg19	CCDS3201.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.514|9.514	1.106465|1.106465	0.20632|0.20632	.|.	.|.	ENSG00000174776|ENSG00000174776	ENST00000308378;ENST00000476376;ENST00000453925;ENST00000466760|ENST00000472600	T;T;T;T|.	0.60424|.	1.51;1.22;2.09;0.19|.	4.94|4.94	3.77|3.77	0.43336|0.43336	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.308110|.	0.34700|.	N|.	0.003745|.	T|.	0.50034|.	0.1592|.	L|L	0.52905|0.52905	1.665|1.665	0.26302|0.26302	N|N	0.977969|0.977969	P;P|.	0.50369|.	0.934;0.829|.	P;P|.	0.47346|.	0.541;0.544|.	T|.	0.38520|.	-0.9657|.	10|.	0.72032|.	D|.	0.01|.	.|.	11.3497|11.3497	0.49581|0.49581	0.0:0.0:0.1526:0.8474|0.0:0.0:0.1526:0.8474	.|.	257;204|.	E7EQK3;Q8IV35|.	.;WDR49_HUMAN|.	V|X	204;29;257;97|269	ENSP00000311343:E204V;ENSP00000420508:E29V;ENSP00000410863:E257V;ENSP00000418718:E97V|.	ENSP00000311343:E204V|.	E|R	-|-	2|1	0|2	WDR49|WDR49	168760586|168760586	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.483000|0.483000	0.33249|0.33249	2.697000|2.697000	0.47060|0.47060	0.839000|0.839000	0.34971|0.34971	-0.338000|-0.338000	0.08134|0.08134	GAG|AGA	.	.		0.448	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		A	167277892	T	A	167277892	3	1	63	1	0	0	0	0	1	0	0	0	17317	1551	54	4	1526	4	WDR49	3	167277892	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	39863903	167277892	30744538	21	7616										
HNRNPD	3184	hgsc.bcm.edu	37	chr4	83278019	83278020	+	Frame_Shift_Ins	INS	-	-	C													0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gttgctgttgctgatattgtINStccttcgacatggctacttt							TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr4:83278019_83278020insC	ENST00000313899.7	-	6	1059_1060	c.782_783insG	c.(781-783)gaafs	p.E261fs	HNRNPD_ENST00000352301.4_Frame_Shift_Ins_p.E242fs|HNRNPD_ENST00000508119.1_5'UTR|HNRNPD_ENST00000541060.1_Frame_Shift_Ins_p.E107fs|HNRNPD_ENST00000543098.1_Frame_Shift_Ins_p.E209fs|HNRNPD_ENST00000353341.4_Frame_Shift_Ins_p.E261fs	NM_031370.2	NP_112738.1	Q14103	HNRPD_HUMAN	heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)	261	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				circadian regulation of translation (GO:0097167)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|regulation of circadian rhythm (GO:0042752)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	7						GCTGATATTGTTCCTTCGACAT	0.366																																					p.E261fs		Atlas-INDEL	.											.	HNRNPD	23	.	0			c.783_784insG						.																																			SO:0001589	frameshift_variant	3184	exon6			.	AF026126	CCDS3590.1, CCDS3591.1, CCDS3592.1	4q21	2013-02-12	2002-08-29	2008-04-18	ENSG00000138668	ENSG00000138668		"RNA binding motif (RRM) containing"	5036	protein-coding gene	gene with protein product		601324	"heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA-binding protein 1, 37kD)"	AUF1, HNRPD		9615222	Standard	NM_001003810		Approved		uc003hmm.1	Q14103	OTTHUMG00000130290	ENST00000313899.7:c.782_783insG	chr4.hg19:g.83278019_83278020insC	ENSP00000313199:p.Glu261fs	175.0	0.0		132.0	23.0	NM_002138	A8K9J2|P07029|Q01858|Q14100|Q14101|Q14102|Q4W5A1|Q9UCE8|Q9UCE9	Frame_Shift_Ins	INS	ENST00000313899.7	hg19	CCDS3592.1																																																																																			.	.		0.366	HNRNPD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252630.2	NM_031370		C	83278020	-	C	83278019	7	5	63	1	0	1	1	0	0	0	0	0	7273	1722	60	0	296	0	HNRNPD	4	83278019	Frame_Shift_Ins	INS	-	TCGA-CC-A3M9-01A-11D-A20W-10		83278019	107876257	22	7617										
MAPKSP1	8649	hgsc.bcm.edu	37	chr4	100808468	100808468	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tttacctttaataacaggtaCtccatctctatctgacacaa	3	11	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr4:100808468C>A	ENST00000499666.2	-	4	280	c.88G>T	c.(88-90)Gta>Tta	p.V30L	LAMTOR3_ENST00000226522.8_Missense_Mutation_p.V30L|LAMTOR3_ENST00000515100.1_5'UTR	NM_001243736.1|NM_021970.3	NP_001230665.1|NP_068805.1	Q9UHA4	LTOR3_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	30					cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Ragulator complex (GO:0071986)				endometrium(1)|large_intestine(1)|lung(1)	3						ATAACAGGTACTCCATCTCTA	0.289																																					p.V30L		Atlas-SNP	.											.	LAMTOR3	6	.	0			c.G88T						.						54	50	51					4																	100808468		2202	4296	6498	SO:0001583	missense	8649	exon4			CAGGTACTCCATC	AF201947	CCDS3652.1, CCDS58920.1	4q24-q26	2012-02-28	2011-02-15	2011-02-15	ENSG00000109270	ENSG00000109270			15606	protein-coding gene	gene with protein product	"MEK partner 1"	603296	"mitogen-activated protein kinase kinase 1 interacting protein 1", "MAPK scaffold protein 1"	MAP2K1IP1, MAPKSP1		9733512, 15016825	Standard	NM_021970		Approved	MP1, MAPBP, Ragulator3	uc003hvg.2	Q9UHA4	OTTHUMG00000131050	ENST00000499666.2:c.88G>T	chr4.hg19:g.100808468C>A	ENSP00000424183:p.Val30Leu	214.0	0.0		143.0	42.0	NM_021970	B2R4A1|J3KMX4|Q9H364	Missense_Mutation	SNP	ENST00000499666.2	hg19	CCDS3652.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.571581	0.65765	.	.	ENSG00000109270	ENST00000499666;ENST00000226522	.	.	.	4.72	4.72	0.59763	.	0.122073	0.56097	D	0.000040	T	0.72843	0.3511	M	0.87827	2.91	0.80722	D	1	B;B	0.28208	0.203;0.008	B;B	0.26864	0.074;0.009	T	0.76990	-0.2754	9	0.87932	D	0	.	18.0646	0.89387	0.0:1.0:0.0:0.0	.	30;30	Q53FH6;Q9UHA4	.;LTOR3_HUMAN	L	30	.	ENSP00000226522:V30L	V	-	1	0	LAMTOR3	101027491	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.137000	0.77295	2.343000	0.79666	0.467000	0.42956	GTA	.	.		0.289	LAMTOR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253698.2	NM_021970		A	100808468	C	A	100808468	3	1	63	1	0	0	0	0	1	0	0	0	9302	565	20	3	302	3	MAPKSP1	4	100808468	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	17530449	100808468	90345808	23	7618										
TET2	54790	hgsc.bcm.edu	37	chr4	106155167	106155168	+	Frame_Shift_Ins	INS	-	-	T													0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ttcctgataccatcacctccINScatttgccagacagaacctc							TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr4:106155167_106155168insT	ENST00000540549.1	+	3	928_929	c.68_69insT	c.(67-72)cccattfs	p.I24fs	TET2_ENST00000380013.4_Frame_Shift_Ins_p.I24fs|TET2_ENST00000394764.1_Frame_Shift_Ins_p.I24fs|TET2_ENST00000305737.2_Frame_Shift_Ins_p.I24fs|TET2_ENST00000513237.1_Frame_Shift_Ins_p.I45fs|TET2_ENST00000413648.2_Frame_Shift_Ins_p.I24fs|TET2_ENST00000545826.1_Frame_Shift_Ins_p.I24fs			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	24					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		CCATCACCTCCCATTTGCCAGA	0.52			"Mis N, F"		MDS																																p.P23fs		Atlas-INDEL	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.68_69insT						.																																			SO:0001589	frameshift_variant	54790	exon3			.	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	Exception_encountered	chr4.hg19:g.106155167_106155168insT	ENSP00000442788:p.Ile24fs	89.0	0.0		47.0	11.0	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Ins	INS	ENST00000540549.1	hg19	CCDS47120.1																																																																																			.	.		0.52	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106155168	-	T	106155167	7	5	63	1	0	1	1	0	0	0	0	0	15785	623	22	0	70	0	TET2	4	106155167	Frame_Shift_Ins	INS	-	TCGA-CC-A3M9-01A-11D-A20W-10	5346699	106155167	84999109	24	7619	34	2								
TET2	54790	hgsc.bcm.edu	37	chr4	106155168	106155169	+	Frame_Shift_Ins	INS	-	-	CA													0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tcctgataccatcacctcccINSatttgccagacagaacctct							TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr4:106155168_106155169insCA	ENST00000540549.1	+	3	929_930	c.69_70insCA	c.(70-72)attfs	p.I24fs	TET2_ENST00000380013.4_Frame_Shift_Ins_p.I24fs|TET2_ENST00000394764.1_Frame_Shift_Ins_p.I24fs|TET2_ENST00000305737.2_Frame_Shift_Ins_p.I24fs|TET2_ENST00000513237.1_Frame_Shift_Ins_p.I45fs|TET2_ENST00000413648.2_Frame_Shift_Ins_p.I24fs|TET2_ENST00000545826.1_Frame_Shift_Ins_p.I24fs			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	24					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		CATCACCTCCCATTTGCCAGAC	0.515			"Mis N, F"		MDS																																p.P23fs		Atlas-INDEL	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.69_70insCA						.																																			SO:0001589	frameshift_variant	54790	exon3			.	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	Exception_encountered	chr4.hg19:g.106155168_106155169insCA	ENSP00000442788:p.Ile24fs	92.0	0.0		48.0	11.0	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Ins	INS	ENST00000540549.1	hg19	CCDS47120.1																																																																																			.	.		0.515	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		CA	106155169	-	CA	106155168	7	5	63	1	0	1	1	0	0	0	0	0	15785	581	21	0	71	0	TET2	4	106155168	Frame_Shift_Ins	INS	-	TCGA-CC-A3M9-01A-11D-A20W-10	1	106155168	84999108	25	7620	34	2								
PDCD6	10016	hgsc.bcm.edu	37	chr5	306821	306821	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tcttccgcacgtacgaccggGacaactccgggatgatcgat	11	13	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:306821G>C	ENST00000264933.4	+	4	413	c.313G>C	c.(313-315)Gac>Cac	p.D105H	AHRR_ENST00000505113.1_Intron|PDCD6_ENST00000511482.1_3'UTR|PDCD6_ENST00000505221.1_Intron|AHRR_ENST00000512529.1_Intron|AHRR_ENST00000316418.5_Intron|PDCD6_ENST00000507528.1_Missense_Mutation_p.D105H	NM_001267556.1|NM_001267558.1|NM_013232.3	NP_001254485.1|NP_001254487.1|NP_037364.1	O75340	PDCD6_HUMAN	programmed cell death 6	105	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)			breast(2)|endometrium(1)|large_intestine(4)|lung(1)	8			Epithelial(17;0.00193)|OV - Ovarian serous cystadenocarcinoma(19;0.00489)|all cancers(22;0.00511)|Lung(60;0.113)			GTACGACCGGGACAACTCCGG	0.542																																					p.D105H		Atlas-SNP	.											.	PDCD6	24	.	0			c.G313C						.						148	120	129					5																	306821		2203	4300	6503	SO:0001583	missense	10016	exon4			GACCGGGACAACT	AF035606	CCDS3854.1, CCDS58940.1, CCDS58941.1, CCDS75222.1, CCDS75223.1	5p15.33	2013-01-10			ENSG00000249915	ENSG00000249915		"EF-hand domain containing"	8765	protein-coding gene	gene with protein product	"apoptosis-linked gene-2"	601057				8560270	Standard	NM_013232		Approved	ALG-2, PEF1B	uc003jat.1	O75340	OTTHUMG00000090283	ENST00000264933.4:c.313G>C	chr5.hg19:g.306821G>C	ENSP00000264933:p.Asp105His	184.0	0.0		220.0	30.0	NM_001267556	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Missense_Mutation	SNP	ENST00000264933.4	hg19	CCDS3854.1	.	.	.	.	.	.	.	.	.	.	g	18.39	3.612557	0.66672	.	.	ENSG00000249915	ENST00000264933;ENST00000507528	T;T	0.46063	0.88;0.88	5.53	5.53	0.82687	EF-hand-like domain (1);	.	.	.	.	T	0.80166	0.4573	H	0.99261	4.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88520	0.3095	9	0.87932	D	0	.	16.9576	0.86263	0.0:0.0:1.0:0.0	.	105;105	Q2YDC2;O75340	.;PDCD6_HUMAN	H	105	ENSP00000264933:D105H;ENSP00000423815:D105H	ENSP00000264933:D105H	D	+	1	0	PDCD6	359821	1.000000	0.71417	1.000000	0.80357	0.178000	0.23041	8.839000	0.92120	2.599000	0.87857	0.650000	0.86243	GAC	.	.		0.542	PDCD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206609.2	NM_013232		C	306821	G	C	306821	3	2	63	1	0	0	0	0	1	0	0	0	11632	1174	41	4	327	4	PDCD6	5	306821	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10		306821	180608439	26	7621										
EXOC3	11336	hgsc.bcm.edu	37	chr5	464493	464493	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	caccgtggaagactatttcaAcgattttgccaaaattaaaa	6	8	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:464493A>G	ENST00000512944.1	+	10	1931	c.1742A>G	c.(1741-1743)aAc>aGc	p.N581S	CTD-2228K2.5_ENST00000510714.1_5'Flank|EXOC3_ENST00000315013.5_Missense_Mutation_p.N581S	NM_007277.4	NP_009208.2	O60645	EXOC3_HUMAN	exocyst complex component 3	592					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|secretory granule membrane (GO:0030667)				breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(13)|ovary(1)|urinary_tract(1)	23		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			GACTATTTCAACGATTTTGCC	0.443																																					p.N581S		Atlas-SNP	.											.	EXOC3	54	.	0			c.A1742G						.						147	149	149					5																	464493		1961	4130	6091	SO:0001583	missense	11336	exon10			ATTTCAACGATTT	BC034427	CCDS54830.1	5p15.33	2013-01-22	2005-11-01	2005-11-01	ENSG00000180104	ENSG00000180104			30378	protein-coding gene	gene with protein product		608186	"SEC6-like 1 (S. cerevisiae)"	SEC6L1		8619474	Standard	XM_005248238		Approved	Sec6p	uc003jba.3	O60645	OTTHUMG00000162205	ENST00000512944.1:c.1742A>G	chr5.hg19:g.464493A>G	ENSP00000425587:p.Asn581Ser	85.0	0.0		74.0	7.0	NM_007277	Q6P2E8|Q8TEN6|Q8WUW0|Q96DI4	Missense_Mutation	SNP	ENST00000512944.1	hg19	CCDS54830.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.748380	0.49257	.	.	ENSG00000180104	ENST00000512944;ENST00000315013;ENST00000340158	T;T	0.06608	3.28;3.28	4.92	3.75	0.43078	.	0.046651	0.85682	N	0.000000	T	0.05456	0.0144	L	0.45137	1.4	0.58432	D	0.999999	B	0.02656	0.0	B	0.12156	0.007	T	0.21484	-1.0244	10	0.07813	T	0.8	-28.488	9.0643	0.36453	0.911:0.0:0.089:0.0	.	592	O60645	EXOC3_HUMAN	S	581;581;476	ENSP00000425587:N581S;ENSP00000323377:N581S	ENSP00000323377:N581S	N	+	2	0	EXOC3	517493	1.000000	0.71417	0.845000	0.33349	0.611000	0.37282	4.533000	0.60615	0.829000	0.34733	0.533000	0.62120	AAC	.	.		0.443	EXOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367882.1	NM_007277		G	464493	A	G	464493	3	3	63	1	0	0	0	0	1	0	0	0	5305	43	2	2	1776	2	EXOC3	5	464493	Missense_Mutation	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	157672	464493	180450767	27	7622										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71491475	71491475	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	aagtacccaagaaggaagagTctgtcaagaaagattctgtt	10	6	3	4			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:71491475T>C	ENST00000296755.7	+	5	2591	c.2293T>C	c.(2293-2295)Tct>Cct	p.S765P		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	765	Lys-rich (highly basic, contains many KKEE and KKEI/V repeats).				axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		GAAGGAAGAGTCTGTCAAGAA	0.443																																					p.S765P	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T2293C						.						78	85	83					5																	71491475		2203	4300	6503	SO:0001583	missense	4131	exon5			GAAGAGTCTGTCA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.2293T>C	chr5.hg19:g.71491475T>C	ENSP00000296755:p.Ser765Pro	116.0	0.0		82.0	12.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.552924	0.00138	.	.	ENSG00000131711	ENST00000296755	T	0.25579	1.79	5.63	-9.33	0.00639	.	0.731439	0.13093	N	0.414380	T	0.07818	0.0196	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12967	-1.0527	10	0.21014	T	0.42	2.3708	5.3613	0.16089	0.0741:0.185:0.2202:0.5208	.	639;765	A2BDK6;P46821	.;MAP1B_HUMAN	P	765	ENSP00000296755:S765P	ENSP00000296755:S765P	S	+	1	0	MAP1B	71527231	0.000000	0.05858	0.000000	0.03702	0.354000	0.29330	-4.608000	0.00209	-2.962000	0.00289	-1.139000	0.01908	TCT	.	.		0.443	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		C	71491475	T	C	71491475	3	2	63	1	0	0	0	0	1	0	0	0	9237	1667	58	2	2311	2	MAP1B	5	71491475	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	71026982	71491475	109423785	28	7623										
EPB41L4A	64097	hgsc.bcm.edu	37	chr5	111600669	111600669	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	aacaaaccggtactcagataCatatcctgcagtatgtttat	6	9	1	1	rs370791654		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:111600669C>A	ENST00000261486.5	-	6	754	c.478G>T	c.(478-480)Gta>Tta	p.V160L		NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	160	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TACTCAGATACATATCCTGCA	0.338																																					p.V160L		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.G478T						.						167	153	157					5																	111600669		1826	4095	5921	SO:0001583	missense	64097	exon6			CAGATACATATCC	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.478G>T	chr5.hg19:g.111600669C>A	ENSP00000261486:p.Val160Leu	75.0	0.0		85.0	13.0	NM_022140	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	hg19	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.368726	0.82463	.	.	ENSG00000129595	ENST00000261486	T	0.68903	-0.36	5.46	5.46	0.80206	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.64402	D	0.000001	T	0.71409	0.3336	N	0.17723	0.515	0.40048	D	0.975742	D	0.89917	1.0	D	0.85130	0.997	T	0.71724	-0.4506	10	0.34782	T	0.22	.	18.0769	0.89430	0.0:1.0:0.0:0.0	.	160	Q9HCS5	E41LA_HUMAN	L	160	ENSP00000261486:V160L	ENSP00000261486:V160L	V	-	1	0	EPB41L4A	111628568	0.999000	0.42202	0.840000	0.33206	0.687000	0.40016	4.437000	0.59955	2.568000	0.86640	0.650000	0.86243	GTA	.	.		0.338	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			A	111600669	C	A	111600669	3	1	63	1	0	0	0	0	1	0	0	0	5157	478	17	3	1654	3	EPB41L4A	5	111600669	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	40109194	111600669	69314591	29	7624										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112899131	112899131	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tcccattgctgattttcttaTgaaagctcctgaacctccac	5	13	1	3	rs559215760	byFrequency	TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:112899131T>C	ENST00000161863.4	+	19	2597	c.2384T>C	c.(2383-2385)aTg>aCg	p.M795T		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	795					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GATTTTCTTATGAAAGCTCCT	0.313													T|||	2	0.000399361	0	0	5008	,	,		14416	0.002		0	False		,,,				2504	0				p.M795T		Atlas-SNP	.											.	YTHDC2	118	.	0			c.T2384C						.						73	75	74					5																	112899131		2202	4300	6502	SO:0001583	missense	64848	exon19			TTCTTATGAAAGC	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.2384T>C	chr5.hg19:g.112899131T>C	ENSP00000161863:p.Met795Thr	104.0	0.0		124.0	17.0	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	T	5.363	0.252250	0.10185	.	.	ENSG00000047188	ENST00000161863;ENST00000511372	T	0.02395	4.31	5.31	5.31	0.75309	.	0.143832	0.64402	D	0.000004	T	0.02156	0.0067	N	0.05124	-0.11	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.59129	-0.7512	10	0.39692	T	0.17	.	15.2608	0.73621	0.0:0.0:0.0:1.0	.	795	Q9H6S0	YTDC2_HUMAN	T	795;705	ENSP00000161863:M795T	ENSP00000161863:M795T	M	+	2	0	YTHDC2	112927030	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.975000	0.56859	2.020000	0.59435	0.523000	0.50628	ATG	.	.		0.313	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		C	112899131	T	C	112899131	3	2	63	1	0	0	0	0	1	0	0	0	17512	1464	51	2	2458	2	YTHDC2	5	112899131	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	1298462	112899131	68016129	30	7625										
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125821443	125821443	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	aatgtccgatgcttcaccatAttcttatattctatgcaatt	4	9	3	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:125821443A>G	ENST00000285689.3	+	11	1497	c.1036A>G	c.(1036-1038)Att>Gtt	p.I346V	RP11-517I3.1_ENST00000512500.1_RNA|GRAMD3_ENST00000502348.1_Missense_Mutation_p.I237V|GRAMD3_ENST00000515200.1_Missense_Mutation_p.I324V|GRAMD3_ENST00000511134.1_Missense_Mutation_p.I330V|GRAMD3_ENST00000544396.1_Missense_Mutation_p.I242V|GRAMD3_ENST00000513040.1_Missense_Mutation_p.I361V|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000543198.1_Missense_Mutation_p.I324V|GRAMD3_ENST00000542322.1_Missense_Mutation_p.I354V	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	346						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		GCTTCACCATATTCTTATATT	0.348																																					p.I361V		Atlas-SNP	.											.	GRAMD3	30	.	0			c.A1081G						.						121	110	114					5																	125821443		2203	4300	6503	SO:0001583	missense	65983	exon11			CACCATATTCTTA	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"HCV NS3 transactivated protein 2"					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.1036A>G	chr5.hg19:g.125821443A>G	ENSP00000285689:p.Ile346Val	52.0	0.0		39.0	6.0	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	hg19	CCDS4136.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.38|10.38	1.334276|1.334276	0.24253|0.24253	.|.	.|.	ENSG00000155324|ENSG00000155324	ENST00000543367|ENST00000513040;ENST00000285689;ENST00000515200;ENST00000542322;ENST00000544396;ENST00000543198;ENST00000502348;ENST00000511134	.|T;T;T;T;T;T;T;T	.|0.34472	.|1.36;1.38;1.43;1.38;1.47;1.45;1.47;1.42	5.94|5.94	3.53|3.53	0.40419|0.40419	.|.	0.227191|0.227191	0.45126|0.45126	D|N	0.000396|0.000396	T|T	0.31918|0.31918	0.0812|0.0812	M|M	0.65975|0.65975	2.015|2.015	0.33672|0.33672	D|D	0.611053|0.611053	.|B;B;B;B;B	.|0.28900	.|0.151;0.028;0.145;0.227;0.151	.|B;B;B;B;B	.|0.27887	.|0.036;0.015;0.026;0.084;0.036	T|T	0.35943|0.35943	-0.9768|-0.9768	7|10	0.42905|0.22109	T|T	0.14|0.4	.|.	7.5781|7.5781	0.27948|0.27948	0.7867:0.1415:0.0719:0.0|0.7867:0.1415:0.0719:0.0	.|.	.|330;242;354;361;346	.|B7Z8T2;B7Z1F2;B7Z3R1;B7Z6D8;Q96HH9	.|.;.;.;.;GRAM3_HUMAN	M|V	281|361;346;324;354;242;324;237;330	.|ENSP00000426120:I361V;ENSP00000285689:I346V;ENSP00000426143:I324V;ENSP00000441876:I354V;ENSP00000444049:I242V;ENSP00000442902:I324V;ENSP00000427596:I237V;ENSP00000426088:I330V	ENSP00000445954:I281M|ENSP00000285689:I346V	I|I	+|+	3|1	3|0	GRAMD3|GRAMD3	125849342|125849342	0.662000|0.662000	0.27439|0.27439	0.997000|0.997000	0.53966|0.53966	0.256000|0.256000	0.26092|0.26092	0.989000|0.989000	0.29629|0.29629	0.487000|0.487000	0.27698|0.27698	-0.379000|-0.379000	0.06801|0.06801	ATA|ATT	.	.		0.348	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927		G	125821443	A	G	125821443	3	3	63	1	0	0	0	0	1	0	0	0	6760	449	16	2	1292	2	GRAMD3	5	125821443	Missense_Mutation	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	12922312	125821443	55093817	31	7626										
HSPA4	3308	hgsc.bcm.edu	37	chr5	132400692	132400692	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ggcttgcatttcttttggtcCtaagaatcgttcaattggag	10	7	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:132400692C>T	ENST00000304858.2	+	2	417	c.128C>T	c.(127-129)cCt>cTt	p.P43L		NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	43					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTTTTGGTCCTAAGAATCGT	0.348																																					p.P43L	Colon(114;1299 1588 6063 12302 48757)	Atlas-SNP	.											.	HSPA4	68	.	0			c.C128T						.						189	190	189					5																	132400692		2203	4300	6503	SO:0001583	missense	3308	exon2			TTGGTCCTAAGAA	AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"Heat shock proteins / HSP70"	5237	protein-coding gene	gene with protein product	"hsp70 RY"	601113	"heat shock 70kD protein 4"			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.128C>T	chr5.hg19:g.132400692C>T	ENSP00000302961:p.Pro43Leu	183.0	0.0		209.0	32.0	NM_002154	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	hg19	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542968	0.65198	.	.	ENSG00000170606	ENST00000304858;ENST00000321956;ENST00000537974	T	0.01034	5.42	5.69	5.69	0.88448	.	0.160713	0.56097	D	0.000029	T	0.02012	0.0063	L	0.61218	1.895	0.80722	D	1	B	0.23442	0.085	B	0.22152	0.038	T	0.60707	-0.7210	10	0.35671	T	0.21	-3.324	19.8209	0.96592	0.0:1.0:0.0:0.0	.	43	P34932	HSP74_HUMAN	L	43	ENSP00000302961:P43L	ENSP00000302961:P43L	P	+	2	0	HSPA4	132428591	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.473000	0.81007	2.688000	0.91661	0.650000	0.86243	CCT	.	.		0.348	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431		T	132400692	C	T	132400692	3	4	63	1	0	0	0	0	1	0	0	0	7421	681	24	3	134	3	HSPA4	5	132400692	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	6579249	132400692	48514568	32	7627										
PCDHGB7	56099	hgsc.bcm.edu	37	chr5	140798233	140798233	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	agagtgaaggccactgaccaGgacgagggcatcaactcaga	13	10	2	4			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:140798233G>A	ENST00000398594.2	+	1	807	c.807G>A	c.(805-807)caG>caA	p.Q269Q	PCDHGA8_ENST00000398604.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	269	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACTGACCAGGACGAGGGCA	0.522																																					p.Q269Q		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.G807A						.						56	58	57					5																	140798233		2053	4195	6248	SO:0001819	synonymous_variant	56099	exon1			TGACCAGGACGAG	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.807G>A	chr5.hg19:g.140798233G>A		37.0	0.0		41.0	5.0	NM_018927	Q9UN63	Silent	SNP	ENST00000398594.2	hg19	CCDS47293.1																																																																																			.	.		0.522	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		A	140798233	G	A	140798233	2	1	63	1	0	0	0	0	0	0	0	1	11577	991	35	3		3	PCDHGB7	5	140798233	Silent	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	8397541	140798233	40117027	33	7628										
ARHGAP26	23092	hgsc.bcm.edu	37	chr5	142435642	142435642	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	agtttcaaagaagtttcatcAaagcagcaagtaagtctttt	7	6	4	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:142435642A>T	ENST00000274498.4	+	16	1801	c.1423A>T	c.(1423-1425)Aaa>Taa	p.K475*	ARHGAP26_ENST00000378004.3_Nonsense_Mutation_p.K475*	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	475	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGTTTCATCAAAGCAGCAAG	0.338																																					p.K475X		Atlas-SNP	.											.	ARHGAP26	57	.	0			c.A1423T						.						161	156	158					5																	142435642		2203	4300	6503	SO:0001587	stop_gained	23092	exon16			TTCATCAAAGCAG	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.1423A>T	chr5.hg19:g.142435642A>T	ENSP00000274498:p.Lys475*	59.0	0.0		51.0	8.0	NM_015071	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Nonsense_Mutation	SNP	ENST00000274498.4	hg19	CCDS4277.1	.	.	.	.	.	.	.	.	.	.	A	44	10.908573	0.99487	.	.	ENSG00000145819	ENST00000274498;ENST00000378004;ENST00000418668	.	.	.	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	16.2666	0.82588	1.0:0.0:0.0:0.0	.	.	.	.	X	475;475;48	.	ENSP00000274498:K475X	K	+	1	0	ARHGAP26	142415835	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.136000	0.89610	2.320000	0.78422	0.528000	0.53228	AAA	.	.		0.338	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071		T	142435642	A	T	142435642	4	4	63	1	0	0	0	0	0	1	0	0	875	131	5	4	1485	4	ARHGAP26	5	142435642	Nonsense_Mutation	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	1637409	142435642	38479618	34	7629										
GRM4	2914	hgsc.bcm.edu	37	chr6	34029743	34029743	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	caggaggcggcggatgatctTgtcgaactcgcctgccttgg	15	11	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr6:34029743T>A	ENST00000538487.2	-	4	1242	c.799A>T	c.(799-801)Aag>Tag	p.K267*	GRM4_ENST00000544773.2_Nonsense_Mutation_p.K98*|GRM4_ENST00000374181.4_Nonsense_Mutation_p.K267*|GRM4_ENST00000455714.2_Nonsense_Mutation_p.K127*|GRM4_ENST00000535756.1_Nonsense_Mutation_p.K134*|GRM4_ENST00000374177.3_Nonsense_Mutation_p.K198*|GRM4_ENST00000609222.1_Nonsense_Mutation_p.K134*|GRM4_ENST00000545715.1_5'UTR	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	267					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						CGGATGATCTTGTCGAACTCG	0.637																																					p.K267X		Atlas-SNP	.											.	GRM4	317	.	0			c.A799T						.						138	118	125					6																	34029743		2203	4300	6503	SO:0001587	stop_gained	2914	exon4			TGATCTTGTCGAA	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.799A>T	chr6.hg19:g.34029743T>A	ENSP00000440556:p.Lys267*	214.0	0.0		170.0	55.0	NM_001256811	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Nonsense_Mutation	SNP	ENST00000538487.2	hg19	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	T	37	6.533798	0.97641	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	.	.	.	4.01	4.01	0.46588	.	0.145987	0.45126	D	0.000398	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9967	0.58650	0.0:0.0:0.0:1.0	.	.	.	.	X	267;198;134;98;267;127	.	ENSP00000363292:K198X	K	-	1	0	GRM4	34137721	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.790000	0.85794	1.799000	0.52666	0.433000	0.28618	AAG	.	.		0.637	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			A	34029743	T	A	34029743	4	1	63	1	0	0	0	0	0	1	0	0	6808	1821	63	4	1971	4	GRM4	6	34029743	Nonsense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10		34029743	137085324	35	7630										
PRSS35	167681	hgsc.bcm.edu	37	chr6	84233541	84233541	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	aagagacaggtgtatggcacCgacagcaggttcagcatctt	12	9	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr6:84233541C>A	ENST00000369700.3	+	2	558	c.381C>A	c.(379-381)acC>acA	p.T127T	PRSS35_ENST00000536636.1_Silent_p.T127T	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	127	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		TGTATGGCACCGACAGCAGGT	0.463																																					p.T127T		Atlas-SNP	.											.	PRSS35	60	.	0			c.C381A						.						94	88	90					6																	84233541		2203	4300	6503	SO:0001819	synonymous_variant	167681	exon2			TGGCACCGACAGC	BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"Serine peptidases / Serine peptidases"	21387	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 158"	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.381C>A	chr6.hg19:g.84233541C>A		210.0	0.0		157.0	10.0	NM_153362	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	hg19	CCDS4999.1																																																																																			.	.		0.463	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362		A	84233541	C	A	84233541	2	1	63	1	0	0	0	0	0	0	0	1	12636	639	23	1		1	PRSS35	6	84233541	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	50203798	84233541	86881526	36	7631										
FAM54A	113115	hgsc.bcm.edu	37	chr6	136562631	136562631	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	atttccacaattgctgcaatCtgagagcgaagaaaagtcag	9	8	2	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr6:136562631C>G	ENST00000420702.1	-	5	854	c.465G>C	c.(463-465)caG>caC	p.Q155H	MTFR2_ENST00000451457.2_Missense_Mutation_p.Q155H	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	155					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											TTGCTGCAATCTGAGAGCGAA	0.358																																					p.Q155H		Atlas-SNP	.											.	.	.	.	0			c.G465C						.						98	91	94					6																	136562631		2203	4300	6503	SO:0001583	missense	113115	exon5			TGCAATCTGAGAG	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"DUF729 domain containing 1", "family with sequence similarity 54, member A"	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.465G>C	chr6.hg19:g.136562631C>G	ENSP00000395232:p.Gln155His	155.0	0.0		149.0	10.0	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Missense_Mutation	SNP	ENST00000420702.1	hg19	CCDS5176.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.568702	0.65651	.	.	ENSG00000146410	ENST00000451457;ENST00000420702;ENST00000418509	T;T;T	0.70282	-0.47;-0.47;-0.47	5.59	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.80691	0.4671	M	0.87547	2.89	0.49051	D	0.999746	D	0.89917	1.0	D	0.97110	1.0	D	0.84097	0.0393	10	0.87932	D	0	-12.3202	9.8347	0.40963	0.0:0.8405:0.0:0.1595	.	155	Q6P444	FA54A_HUMAN	H	155;155;112	ENSP00000407010:Q155H;ENSP00000395232:Q155H;ENSP00000410861:Q112H	ENSP00000410861:Q112H	Q	-	3	2	FAM54A	136604324	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.406000	0.34646	1.367000	0.46095	0.462000	0.41574	CAG	.	.		0.358	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419		G	136562631	C	G	136562631	3	3	63	1	0	0	0	0	1	0	0	0	5590	912	32	4	708	4	FAM54A	6	136562631	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	52329090	136562631	34552436	37	7632										
INTS1	26173	hgsc.bcm.edu	37	chr7	1529320	1529320	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gaggttcggaggctggtaccTggaaggcaggggcgccccga	19	10	0	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:1529320T>A	ENST00000404767.3	-	17	2251		c.e17-2		INTS1_ENST00000389470.4_Splice_Site	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1						inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GGCTGGTACCTGGAAGGCAGG	0.677																																					.		Atlas-SNP	.											.	INTS1	145	.	0			c.2166-2A>T						.						27	30	29					7																	1529320		2032	4159	6191	SO:0001630	splice_region_variant	26173	exon18			GGTACCTGGAAGG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.2166-2A>T	chr7.hg19:g.1529320T>A		79.0	0.0		65.0	9.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Splice_Site	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.740938	0.49151	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4533	0.75294	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	INTS1	1495846	1.000000	0.71417	0.937000	0.37676	0.268000	0.26511	7.512000	0.81728	2.051000	0.60960	0.529000	0.55759	.	.	.		0.677	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		Intron	A	1529320	T	A	1529320	5	1	63	1	0	0	0	0	0	0	1	0	7784	1594	55	4	4536	4	INTS1	7	1529320	Splice_Site	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10		1529320	157609343	38	7633										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94057038	94057038	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tctacagggctgaccagcctCgctcagcaccttctctcaga	8	16	4	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:94057038C>A	ENST00000297268.6	+	49	3838	c.3367C>A	c.(3367-3369)Cgc>Agc	p.R1123S		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1123				Missing (in Ref. 17; CAA23761). {ECO:0000305}.	blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TGACCAGCCTCGCTCAGCACC	0.552										HNSCC(75;0.22)																											p.R1123S		Atlas-SNP	.											.	COL1A2	240	.	0			c.C3367A						.						98	97	98					7																	94057038		2203	4300	6503	SO:0001583	missense	1278	exon49			CAGCCTCGCTCAG	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3367C>A	chr7.hg19:g.94057038C>A	ENSP00000297268:p.Arg1123Ser	123.0	0.0		87.0	26.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.145829	0.37923	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.89196	-2.48	5.71	5.71	0.89125	.	0.000000	0.56097	D	0.000040	D	0.87204	0.6119	N	0.11427	0.14	0.32726	N	0.509689	D	0.60160	0.987	D	0.67725	0.953	D	0.84882	0.0831	10	0.17369	T	0.5	.	15.7376	0.77859	0.0:1.0:0.0:0.0	.	1123	P08123	CO1A2_HUMAN	S	1123;1124	ENSP00000297268:R1123S	ENSP00000297268:R1123S	R	+	1	0	COL1A2	93894974	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.549000	0.53681	2.873000	0.98535	0.561000	0.74099	CGC	.	.		0.552	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		A	94057038	C	A	94057038	3	1	63	1	0	0	0	0	1	0	0	0	3680	884	31	1	3561	1	COL1A2	7	94057038	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	92527718	94057038	65081625	39	7634										
TRIM4	89122	hgsc.bcm.edu	37	chr7	99490170	99490171	+	Frame_Shift_Ins	INS	-	-	T													0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gtttccctgaggtgaaaacgINSttttttcccagaacacaggg							TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:99490170_99490171insT	ENST00000355947.2	-	7	1247_1248	c.1118_1119insA	c.(1117-1119)aacfs	p.N373fs	TRIM4_ENST00000349062.2_Frame_Shift_Ins_p.N347fs	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	373	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein trimerization (GO:0070206)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				AGGTGAAAACGTTTTTTCCCAG	0.46																																					p.N373fs		Atlas-INDEL	.											.	TRIM4	33	.	0			c.1119_1120insA						.																																			SO:0001589	frameshift_variant	89122	exon7			.	AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16275	protein-coding gene	gene with protein product	"tripartite motif protein TRIM4", "tripartite motif protein 4"		"tripartite motif-containing 4"			11331580	Standard	NM_033017		Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.1119dupA	chr7.hg19:g.99490176_99490176dupT	ENSP00000348216:p.Asn373fs	139.0	0.0		139.0	18.0	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Frame_Shift_Ins	INS	ENST00000355947.2	hg19	CCDS5679.1																																																																																			.	.		0.46	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017		T	99490171	-	T	99490170	7	5	63	1	0	1	1	0	0	0	0	0	16529	1136	40	0	387	0	TRIM4	7	99490170	Frame_Shift_Ins	INS	-	TCGA-CC-A3M9-01A-11D-A20W-10	5433132	99490170	59648493	40	7635										
LRWD1	222229	hgsc.bcm.edu	37	chr7	102113247	102113247	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ggcagccctgcaggcccccaCacaggtactgcccggctcac	11	19	1	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:102113247C>T	ENST00000292616.5	+	14	1951	c.1799C>T	c.(1798-1800)aCa>aTa	p.T600I	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	600					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						CAGGCCCCCACACAGGTACTG	0.667																																					p.T600I		Atlas-SNP	.											.	LRWD1	41	.	0			c.C1799T						.						25	27	27					7																	102113247		2203	4299	6502	SO:0001583	missense	222229	exon14			CCCCCACACAGGT	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"WD repeat domain containing"	21769	protein-coding gene	gene with protein product	"origin recognition complex associated", "centromere protein 33"	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.1799C>T	chr7.hg19:g.102113247C>T	ENSP00000292616:p.Thr600Ile	110.0	0.0		141.0	6.0	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Missense_Mutation	SNP	ENST00000292616.5	hg19	CCDS34715.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.550|8.550	0.875249|0.875249	0.17395|0.17395	.|.	.|.	ENSG00000161036|ENSG00000161036	ENST00000488689;ENST00000468175|ENST00000292616	.|T	.|0.62498	.|0.02	4.85|4.85	1.8|1.8	0.24995|0.24995	.|.	.|0.144056	.|0.64402	.|D	.|0.000006	T|T	0.66703|0.66703	0.2816|0.2816	M|M	0.61703|0.61703	1.905|1.905	0.20489|0.20489	N|N	0.999896|0.999896	.|D	.|0.60160	.|0.987	.|P	.|0.55871	.|0.786	T|T	0.57871|0.57871	-0.7736|-0.7736	5|10	.|0.62326	.|D	.|0.03	-6.3954|-6.3954	8.4157|8.4157	0.32670|0.32670	0.0:0.6243:0.2923:0.0835|0.0:0.6243:0.2923:0.0835	.|.	.|600	.|Q9UFC0	.|LRWD1_HUMAN	Y|I	211;186|600	.|ENSP00000292616:T600I	.|ENSP00000292616:T600I	H|T	+|+	1|2	0|0	LRWD1|LRWD1	101900252|101900252	0.000000|0.000000	0.05858|0.05858	0.033000|0.033000	0.17914|0.17914	0.113000|0.113000	0.19764|0.19764	0.329000|0.329000	0.19698|0.19698	0.730000|0.730000	0.32425|0.32425	0.561000|0.561000	0.74099|0.74099	CAC|ACA	.	.		0.667	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892		T	102113247	C	T	102113247	3	4	63	1	0	0	0	0	1	0	0	0	9056	478	17	3	1853	3	LRWD1	7	102113247	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	2623077	102113247	57025416	41	7636										
CFTR	1080	hgsc.bcm.edu	37	chr7	117243675	117243675	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	caccagttcgtattatgtgtTttacatttacgtgggagtag	10	6	0	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:117243675T>A	ENST00000003084.6	+	17	2879	c.2747T>A	c.(2746-2748)tTt>tAt	p.F916Y	CFTR_ENST00000454343.1_Missense_Mutation_p.F855Y|AC000111.6_ENST00000456270.1_RNA	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	916	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	TATTATGTGTTTTACATTTAC	0.408									Cystic Fibrosis																												p.F916Y		Atlas-SNP	.											.	CFTR	171	.	0			c.T2747A						.						219	186	197					7																	117243675		2203	4300	6503	SO:0001583	missense	1080	exon17	Familial Cancer Database	CF	ATGTGTTTTACAT	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.2747T>A	chr7.hg19:g.117243675T>A	ENSP00000003084:p.Phe916Tyr	243.0	0.0		118.0	11.0	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	hg19	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.416019	0.83449	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.94576	-3.46;-3.46;-3.46	5.82	5.82	0.92795	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.294147	0.42682	D	0.000666	D	0.95143	0.8426	M	0.72118	2.19	0.42193	D	0.991737	P	0.34412	0.453	B	0.42959	0.403	D	0.95242	0.8352	10	0.72032	D	0.01	-7.0964	16.179	0.81887	0.0:0.0:0.0:1.0	.	916	P13569	CFTR_HUMAN	Y	916;855;886	ENSP00000003084:F916Y;ENSP00000403677:F855Y;ENSP00000389119:F886Y	ENSP00000003084:F916Y	F	+	2	0	CFTR	117030911	1.000000	0.71417	0.943000	0.38184	0.506000	0.33950	7.990000	0.88215	2.232000	0.73038	0.477000	0.44152	TTT	.	.		0.408	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		A	117243675	T	A	117243675	3	1	63	1	0	0	0	0	1	0	0	0	3296	1841	64	4	2813	4	CFTR	7	117243675	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	15130428	117243675	41894988	42	7637										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117432538	117432538	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cttggcacgaagctgttcccGctcagtgtcaaactcagaga	10	12	3	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:117432538G>A	ENST00000160373.3	-	4	803	c.712C>T	c.(712-714)Cgg>Tgg	p.R238W	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	238					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		AGCTGTTCCCGCTCAGTGTCA	0.453																																					p.R238W		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.C712T						.						130	106	114					7																	117432538		2203	4300	6503	SO:0001583	missense	83992	exon4			GTTCCCGCTCAGT		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.712C>T	chr7.hg19:g.117432538G>A	ENSP00000160373:p.Arg238Trp	233.0	0.0		232.0	28.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.405680	0.42715	.	.	ENSG00000077063	ENST00000160373	T	0.77098	-1.07	5.77	1.35	0.21983	.	0.000000	0.85682	D	0.000000	D	0.89223	0.6654	M	0.90650	3.135	0.53688	D	0.999979	D	0.89917	1.0	D	0.97110	1.0	D	0.91072	0.4893	10	0.72032	D	0.01	-16.092	15.4882	0.75584	0.0:0.0:0.5666:0.4333	.	238	Q8WZ74	CTTB2_HUMAN	W	238	ENSP00000160373:R238W	ENSP00000160373:R238W	R	-	1	2	CTTNBP2	117219774	0.995000	0.38212	0.033000	0.17914	0.401000	0.30781	2.190000	0.42630	0.362000	0.24319	0.650000	0.86243	CGG	.	.		0.453	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		A	117432538	G	A	117432538	3	1	63	1	0	0	0	0	1	0	0	0	4047	1086	38	1	4359	1	CTTNBP2	7	117432538	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	188863	117432538	41706125	43	7638										
SLC13A4	26266	hgsc.bcm.edu	37	chr7	135377154	135377154	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	atcaggatgaagaaaaatccAgtcaccatttctgggtagct	9	8	3	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:135377154A>G	ENST00000354042.4	-	11	1826	c.1137T>C	c.(1135-1137)acT>acC	p.T379T	C7orf73_ENST00000422968.1_3'UTR	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	379					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						AGAAAAATCCAGTCACCATTT	0.418																																					p.T379T		Atlas-SNP	.											.	SLC13A4	56	.	0			c.T1137C						.						57	64	61					7																	135377154		2203	4300	6503	SO:0001819	synonymous_variant	26266	exon11			AAATCCAGTCACC	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1137T>C	chr7.hg19:g.135377154A>G		86.0	0.0		81.0	17.0	NM_012450	A4D1Q4|Q8N631	Silent	SNP	ENST00000354042.4	hg19	CCDS5840.1																																																																																			.	.		0.418	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		G	135377154	A	G	135377154	2	3	63	1	0	0	0	0	0	0	0	1	14409	175	7	2		2	SLC13A4	7	135377154	Silent	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	17944616	135377154	23761509	44	7639										
TRIM24	8805	hgsc.bcm.edu	37	chr7	138239638	138239638	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tcagaggcaacaggtgcaacGgaggccagcacctgtgggtt	15	10	1	1	rs201288398		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:138239638G>A	ENST00000343526.4	+	9	1672	c.1457G>A	c.(1456-1458)cGg>cAg	p.R486Q	TRIM24_ENST00000497516.1_Intron|TRIM24_ENST00000415680.2_Intron			O15164	TIF1A_HUMAN	tripartite motif containing 24	486					calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						CAGGTGCAACGGAGGCCAGCA	0.517																																					p.R486Q	Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)	Atlas-SNP	.											.	TRIM24	131	.	0			c.G1457A						.						95	99	98					7																	138239638		2203	4300	6503	SO:0001583	missense	8805	exon9			TGCAACGGAGGCC	AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	11812	protein-coding gene	gene with protein product		603406	"transcriptional intermediary factor 1", "tripartite motif-containing 24"	TIF1		9115274, 9191165	Standard	NM_003852		Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.1457G>A	chr7.hg19:g.138239638G>A	ENSP00000340507:p.Arg486Gln	244.0	0.0		129.0	11.0	NM_015905	A4D1R7|A4D1R8|O95854	Missense_Mutation	SNP	ENST00000343526.4	hg19	CCDS5847.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.256006	0.39896	.	.	ENSG00000122779	ENST00000343526;ENST00000536822	T	0.75154	-0.91	5.54	5.54	0.83059	.	0.269417	0.35585	N	0.003110	T	0.76666	0.4019	N	0.25144	0.715	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	T	0.70132	-0.4956	10	0.10902	T	0.67	-17.1036	19.0694	0.93126	0.0:0.0:1.0:0.0	.	486	O15164	TIF1A_HUMAN	Q	486;397	ENSP00000340507:R486Q	ENSP00000340507:R486Q	R	+	2	0	TRIM24	137890178	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.022000	0.64078	2.602000	0.87976	0.557000	0.71058	CGG	.	G|0.999;T|0.001		0.517	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341814.1	NM_015905		A	138239638	G	A	138239638	3	1	63	1	0	0	0	0	1	0	0	0	16513	1116	39	1	1491	1	TRIM24	7	138239638	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	2862484	138239638	20899025	45	7640										
JHDM1D	80853	hgsc.bcm.edu	37	chr7	139791731	139791731	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ctgccattacttatctggcaCgcccccgaagtcaggtttga	9	13	2	1	rs376853003		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:139791731C>T	ENST00000397560.2	-	19	2701	c.2604G>A	c.(2602-2604)gcG>gcA	p.A868A	Y_RNA_ENST00000515919.1_RNA	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		868					histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					TTATCTGGCACGCCCCCGAAG	0.493																																					p.A868A		Atlas-SNP	.											.	JHDM1D	54	.	0			c.G2604A						.	C		0,3824		0,0,1912	110	106	107		2604	-11.2	0	7		107	1,8249		0,1,4124	no	coding-synonymous	JHDM1D	NM_030647.1		0,1,6036	TT,TC,CC		0.0121,0.0,0.0083		868/942	139791731	1,12073	1912	4125	6037	SO:0001819	synonymous_variant	80853	exon19			CTGGCACGCCCCC																												ENST00000397560.2:c.2604G>A	chr7.hg19:g.139791731C>T		201.0	0.0		181.0	9.0	NM_030647	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Silent	SNP	ENST00000397560.2	hg19	CCDS43658.1																																																																																			.	.		0.493	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1			T	139791731	C	T	139791731	2	4	63	1	0	0	0	0	0	0	0	1	7957	523	19	1		1	JHDM1D	7	139791731	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	1552093	139791731	19346932	46	7641										
NOS3	4846	hgsc.bcm.edu	37	chr7	150708074	150708074	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tgtgccctgcttcatccgggGgtaagtgagatggaagactt	14	8	1	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:150708074G>C	ENST00000297494.3	+	23	3341	c.2984G>C	c.(2983-2985)gGg>gCg	p.G995A	ATG9B_ENST00000494791.1_5'Flank|NOS3_ENST00000461406.1_Splice_Site_p.G789A|NOS3_ENST00000477227.1_3'UTR	NM_000603.4	NP_000594.2	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTCATCCGGGGGTAAGTGAGA	0.622																																					p.G995A		Atlas-SNP	.											.	NOS3	131	.	0			c.G2984C						.						36	34	35					7																	150708074		2203	4300	6503	SO:0001630	splice_region_variant	4846	exon23			TCCGGGGGTAAGT		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000297494.3:c.2984+1G>C	chr7.hg19:g.150708074G>C		78.0	0.0		48.0	10.0	NM_000603	Q495E5	Missense_Mutation	SNP	ENST00000297494.3	hg19	CCDS5912.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.60|14.60	2.583779|2.583779	0.46006|0.46006	.|.	.|.	ENSG00000164867|ENSG00000164867	ENST00000297494;ENST00000461406|ENST00000475017	T;T|.	0.32023|.	1.47;1.47|.	4.61|4.61	4.61|4.61	0.57282|0.57282	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);|.	0.000000|.	0.56097|.	D|.	0.000031|.	T|T	0.33933|0.33933	0.0880|0.0880	N|N	0.03154|0.03154	-0.405|-0.405	0.80722|0.80722	D|D	1|1	B;B|.	0.19200|.	0.034;0.0|.	B;B|.	0.22601|.	0.04;0.002|.	T|T	0.24799|0.24799	-1.0150|-1.0150	10|5	0.35671|.	T|.	0.21|.	-5.9629|-5.9629	14.9693|14.9693	0.71220|0.71220	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	789;995|.	E7ESA7;P29474|.	.;NOS3_HUMAN|.	A|L	995;789|289	ENSP00000297494:G995A;ENSP00000417143:G789A|.	ENSP00000297494:G995A|.	G|V	+|+	2|1	0|0	NOS3|NOS3	150339007|150339007	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.720000|0.720000	0.41350|0.41350	5.241000|5.241000	0.65384|0.65384	2.377000|2.377000	0.81083|0.81083	0.491000|0.491000	0.48974|0.48974	GGG|GTC	.	.		0.622	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603	Missense_Mutation	C	150708074	G	C	150708074	5	2	63	1	0	0	0	0	0	0	1	0	10553	1246	43	4	3352	4	NOS3	7	150708074	Splice_Site	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	10916343	150708074	8430589	47	7642										
MLL3	58508	hgsc.bcm.edu	37	chr7	151970873	151970873	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	aggtgccggctcctgcagcaCaaggataatgatacatctgg	12	10	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:151970873C>A	ENST00000262189.6	-	7	1147	c.929G>T	c.(928-930)tGt>tTt	p.C310F	KMT2C_ENST00000355193.2_Missense_Mutation_p.C310F	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	310					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.C310S(2)									TCCTGCAGCACAAGGATAATG	0.448																																					p.C310F		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,2	MLL3	1564	.	2	Substitution - Missense(2)	endometrium(2)	c.G929T						.						215	200	205					7																	151970873		2203	4300	6503	SO:0001583	missense	58508	exon7			GCAGCACAAGGAT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.929G>T	chr7.hg19:g.151970873C>A	ENSP00000262189:p.Cys310Phe	472.0	0.0		394.0	18.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.366743	0.61513	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.94330	-3.4;-3.4	4.87	4.87	0.63330	Zinc finger, PHD-type (1);	0.000000	0.48767	D	0.000161	D	0.97907	0.9312	H	0.96460	3.825	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.99379	1.0922	10	0.87932	D	0	.	18.3752	0.90433	0.0:1.0:0.0:0.0	.	310	Q8NEZ4	MLL3_HUMAN	F	310	ENSP00000262189:C310F;ENSP00000347325:C310F	ENSP00000262189:C310F	C	-	2	0	MLL3	151601806	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.752000	0.85141	2.423000	0.82170	0.650000	0.86243	TGT	.	.		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151970873	C	A	151970873	3	1	63	1	0	0	0	0	1	0	0	0	9631	478	17	3	14018	3	MLL3	7	151970873	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	1262799	151970873	7167790	48	7643										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2799992	2799992	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	acagatggtgtttctgcagtAcctgtgtttgtagaggtaaa	12	5	1	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:2799992A>C	ENST00000520002.1	-	70	11094		c.e70+1		CSMD1_ENST00000400186.3_Splice_Site|CSMD1_ENST00000602557.1_Splice_Site|CSMD1_ENST00000537824.1_Splice_Site|CSMD1_ENST00000542608.1_Splice_Site|CSMD1_ENST00000602723.1_Splice_Site			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1							integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TTTCTGCAGTACCTGTGTTTG	0.428																																					.		Atlas-SNP	.											.	CSMD1	1469	.	0			c.10535+2T>G						.						48	47	47					8																	2799992		1888	4123	6011	SO:0001630	splice_region_variant	64478	exon70			TGCAGTACCTGTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.10538+1T>G	chr8.hg19:g.2799992A>C		51.0	0.0		41.0	23.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Splice_Site	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	A	28.0	4.884016	0.91814	.	.	ENSG00000183117	ENST00000335551;ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8993	0.79359	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CSMD1	2787399	1.000000	0.71417	0.997000	0.53966	0.962000	0.63368	9.023000	0.93683	2.150000	0.67090	0.523000	0.50628	.	.	.		0.428	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	Intron	C	2799992	A	C	2799992	5	2	63	1	0	0	0	0	0	0	1	0	3946	405	14	5	165	5	CSMD1	8	2799992	Splice_Site	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10		2799992	143564030	49	7644										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3443701	3443701	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ctccaagcagcgagcgtctcTgtaactctctgacaggtgat	10	12	2	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:3443701T>C	ENST00000520002.1	-	10	1737	c.1182A>G	c.(1180-1182)acA>acG	p.T394T	CSMD1_ENST00000400186.3_Silent_p.T394T|CSMD1_ENST00000602557.1_Silent_p.T394T|CSMD1_ENST00000537824.1_Silent_p.T393T|CSMD1_ENST00000542608.1_Silent_p.T393T|CSMD1_ENST00000602723.1_Silent_p.T394T|CSMD1_ENST00000539096.1_Silent_p.T393T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	394	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CGAGCGTCTCTGTAACTCTCT	0.478																																					p.T393T		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A1179G						.						47	46	46					8																	3443701		1928	4135	6063	SO:0001819	synonymous_variant	64478	exon9			CGTCTCTGTAACT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.1182A>G	chr8.hg19:g.3443701T>C		79.0	0.0		75.0	21.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19																																																																																				.	.		0.478	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		C	3443701	T	C	3443701	2	2	63	1	0	0	0	0	0	0	0	1	3946	1567	55	2		2	CSMD1	8	3443701	Silent	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	643709	3443701	142920321	50	7645										
CHRNB3	1142	hgsc.bcm.edu	37	chr8	42587427	42587427	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cgttcaccacagatcttcttCcacgtaccaccccatggccc	5	19	3	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:42587427C>T	ENST00000289957.2	+	5	1105	c.977C>T	c.(976-978)tCc>tTc	p.S326F		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	326					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	AGATCTTCTTCCACGTACCAC	0.453																																					p.S326F		Atlas-SNP	.											.	CHRNB3	74	.	0			c.C977T						.						297	248	265					8																	42587427		2203	4300	6503	SO:0001583	missense	1142	exon5			CTTCTTCCACGTA	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.977C>T	chr8.hg19:g.42587427C>T	ENSP00000289957:p.Ser326Phe	300.0	0.0		438.0	176.0	NM_000749	Q15827	Missense_Mutation	SNP	ENST00000289957.2	hg19	CCDS6134.1	.	.	.	.	.	.	.	.	.	.	c	14.61	2.587081	0.46110	.	.	ENSG00000147432	ENST00000289957	T	0.71934	-0.61	5.85	5.85	0.93711	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.055024	0.64402	D	0.000001	D	0.83418	0.5250	M	0.79011	2.435	0.28985	N	0.888397	P	0.51057	0.941	D	0.65140	0.932	T	0.80348	-0.1420	10	0.87932	D	0	.	15.3155	0.74074	0.0:0.9317:0.0:0.0683	.	326	Q05901	ACHB3_HUMAN	F	326	ENSP00000289957:S326F	ENSP00000289957:S326F	S	+	2	0	CHRNB3	42706584	0.839000	0.29477	0.108000	0.21378	0.117000	0.20001	6.067000	0.71193	2.778000	0.95560	0.650000	0.86243	TCC	.	.		0.453	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			T	42587427	C	T	42587427	3	4	63	1	0	0	0	0	1	0	0	0	3394	855	30	3	995	3	CHRNB3	8	42587427	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	39143726	42587427	103776595	51	7646										
CRISPLD1	83690	hgsc.bcm.edu	37	chr8	75932132	75932132	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cagtctgctaattccttcacAgtctctaaagtaacaggtta	6	10	3	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:75932132A>G	ENST00000262207.4	+	11	1623	c.1155A>G	c.(1153-1155)acA>acG	p.T385T	CRISPLD1_ENST00000523524.1_Silent_p.T197T|CRISPLD1_ENST00000517786.1_Silent_p.T199T	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	385					face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)		p.V386fs*5(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			ATTCCTTCACAGTCTCTAAAG	0.323																																					p.T385T		Atlas-SNP	.											.,1	CRISPLD1	94	.	1	Insertion - Frameshift(1)	prostate(1)	c.A1155G						.						150	145	147					8																	75932132		2203	4300	6503	SO:0001819	synonymous_variant	83690	exon11			CTTCACAGTCTCT	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.1155A>G	chr8.hg19:g.75932132A>G		211.0	0.0		165.0	56.0	NM_031461	B2RA60|B7Z929	Silent	SNP	ENST00000262207.4	hg19	CCDS6219.1																																																																																			.	.		0.323	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		G	75932132	A	G	75932132	2	3	63	1	0	0	0	0	0	0	0	1	3884	175	7	2		2	CRISPLD1	8	75932132	Silent	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	33344705	75932132	70431890	52	7647										
PMP2	5375	hgsc.bcm.edu	37	chr8	82357106	82357106	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	aattcctggcctagcttgaaGgagatttctgtatttttaaa	8	6	1	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:82357106G>C	ENST00000256103.2	-	2	328	c.192C>G	c.(190-192)tcC>tcG	p.S64S	PMP2_ENST00000519260.1_Intron|RP11-157I4.4_ENST00000524085.2_RNA	NM_002677.3	NP_002668.1	P02689	MYP2_HUMAN	peripheral myelin protein 2	64					membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cholesterol binding (GO:0015485)|fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			Epithelial(68;0.186)			CTAGCTTGAAGGAGATTTCTG	0.393																																					p.S64S		Atlas-SNP	.											PMP2,right_lower_lobe,carcinoma,0,1	PMP2	21	.	0			c.C192G						.						138	137	137					8																	82357106		2203	4300	6503	SO:0001819	synonymous_variant	5375	exon2			CTTGAAGGAGATT	X62167	CCDS6229.1	8q21.3-q22.1	2013-03-01			ENSG00000147588	ENSG00000147588		"Fatty acid binding protein family"	9117	protein-coding gene	gene with protein product		170715				1720307, 8288226	Standard	NM_002677		Approved	MP2, FABP8, M-FABP	uc003ycb.1	P02689	OTTHUMG00000164600	ENST00000256103.2:c.192C>G	chr8.hg19:g.82357106G>C		117.0	0.0		104.0	13.0	NM_002677	Q6FHL4	Silent	SNP	ENST00000256103.2	hg19	CCDS6229.1																																																																																			.	.		0.393	PMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379365.1	NM_002677		C	82357106	G	C	82357106	2	2	63	1	0	0	0	0	0	0	0	1	12147	987	35	4		4	PMP2	8	82357106	Silent	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	6424974	82357106	64006916	53	7648										
ATP6V0D2	245972	hgsc.bcm.edu	37	chr8	87165053	87165053	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ttctttcctcaggtacaaatGaatgtgctggcattcaacag	8	9	3	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:87165053G>T	ENST00000285393.3	+	8	1042	c.900G>T	c.(898-900)atG>atT	p.M300I	CTD-3118D11.2_ENST00000522679.1_RNA|CTD-3118D11.2_ENST00000524253.1_RNA	NM_152565.1	NP_689778.1	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2	300					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen ion transmembrane transporter activity (GO:0015078)			breast(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|prostate(1)	27						AGGTACAAATGAATGTGCTGG	0.358																																					p.M300I		Atlas-SNP	.											ATP6V0D2,NS,carcinoma,0,1	ATP6V0D2	61	.	0			c.G900T						.						158	146	151					8																	87165053		2203	4300	6503	SO:0001583	missense	245972	exon8			ACAAATGAATGTG	AY079172	CCDS6241.1	8q21.3	2014-01-28	2006-01-20	2002-05-24	ENSG00000147614	ENSG00000147614		"ATPases / V-type"	18266	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal 38kD, V0 subunit d isoform 2", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 2", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D2"			12384298	Standard	NM_152565		Approved	FLJ38708, VMA6, ATP6D2	uc003ydp.1	Q8N8Y2	OTTHUMG00000163637	ENST00000285393.3:c.900G>T	chr8.hg19:g.87165053G>T	ENSP00000285393:p.Met300Ile	84.0	0.0		64.0	21.0	NM_152565		Missense_Mutation	SNP	ENST00000285393.3	hg19	CCDS6241.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.852908	0.32699	.	.	ENSG00000147614	ENST00000285393	T	0.28454	1.61	6.06	5.16	0.70880	.	0.181318	0.51477	N	0.000092	T	0.20495	0.0493	N	0.16656	0.425	0.41711	D	0.989459	B	0.02656	0.0	B	0.08055	0.003	T	0.03433	-1.1037	10	0.33940	T	0.23	-3.548	13.4993	0.61445	0.0786:0.0:0.9214:0.0	.	300	Q8N8Y2	VA0D2_HUMAN	I	300	ENSP00000285393:M300I	ENSP00000285393:M300I	M	+	3	0	ATP6V0D2	87234169	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	5.454000	0.66651	1.481000	0.48307	-0.355000	0.07637	ATG	.	.		0.358	ATP6V0D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374651.1	NM_152565		T	87165053	G	T	87165053	3	4	63	1	0	0	0	0	1	0	0	0	1174	1290	45	3	930	3	ATP6V0D2	8	87165053	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	4807947	87165053	59198969	54	7649										
CNGB3	54714	hgsc.bcm.edu	37	chr8	87755800	87755800	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gacgagaactttgttcattcTcattgttctctcctataggc	7	10	3	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:87755800T>A	ENST00000320005.5	-	1	103	c.56A>T	c.(55-57)gAg>gTg	p.E19V	RP11-386D6.1_ENST00000519041.1_RNA|CNGB3_ENST00000519777.1_5'UTR	NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	19					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						TTGTTCATTCTCATTGTTCTC	0.433																																					p.E19V		Atlas-SNP	.											.	CNGB3	176	.	0			c.A56T						.						316	263	281					8																	87755800		2203	4300	6503	SO:0001583	missense	54714	exon1			TCATTCTCATTGT	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2153	protein-coding gene	gene with protein product		605080	"achromatopsia (rod monochromacy) 3", "achromatopsia (rod monochromacy) 1"	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.56A>T	chr8.hg19:g.87755800T>A	ENSP00000316605:p.Glu19Val	397.0	0.0		285.0	120.0	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	hg19	CCDS6244.1	.	.	.	.	.	.	.	.	.	.	T	17.28	3.349232	0.61183	.	.	ENSG00000170289	ENST00000320005	T	0.31247	1.5	5.96	4.79	0.61399	.	0.741096	0.11364	N	0.571597	T	0.33644	0.0870	L	0.40543	1.245	0.09310	N	0.999992	D	0.58620	0.983	P	0.49140	0.601	T	0.13495	-1.0507	10	0.62326	D	0.03	.	9.1158	0.36758	0.0:0.0893:0.0:0.9107	.	19	Q9NQW8	CNGB3_HUMAN	V	19	ENSP00000316605:E19V	ENSP00000316605:E19V	E	-	2	0	CNGB3	87824916	0.024000	0.19004	0.048000	0.18961	0.022000	0.10575	1.538000	0.36094	1.042000	0.40150	-0.417000	0.06048	GAG	.	.		0.433	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		A	87755800	T	A	87755800	3	1	63	1	0	0	0	0	1	0	0	0	3603	1551	54	4	2445	4	CNGB3	8	87755800	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	590747	87755800	58608222	55	7650										
SNTB1	6641	hgsc.bcm.edu	37	chr8	121644855	121644855	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tccttgctccttaggatcacCgtgtgcttagcatctggaga	10	11	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:121644855C>T	ENST00000395601.3	-	4	1239	c.825G>A	c.(823-825)acG>acA	p.T275T	SNTB1_ENST00000517992.1_Silent_p.T275T|SNTB1_ENST00000519177.1_5'UTR	NM_021021.3	NP_066301.1	Q13884	SNTB1_HUMAN	syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)	275	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|protein complex (GO:0043234)|synapse (GO:0045202)		p.T275T(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(6)	24	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			TTAGGATCACCGTGTGCTTAG	0.532																																					p.T275T		Atlas-SNP	.											SNTB1,colon,NS,0,1	SNTB1	54	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G825A						.						112	102	105					8																	121644855		2203	4300	6503	SO:0001819	synonymous_variant	6641	exon3			GATCACCGTGTGC	AF028828	CCDS6334.1	8q23-q24	2013-01-10	2002-08-29		ENSG00000172164	ENSG00000172164		"Pleckstrin homology (PH) domain containing"	11168	protein-coding gene	gene with protein product	"tax interaction protein 43"	600026	"syntrophin, beta 1 (dystrophin-associated protein A1, 59kD, basic component 1)"	SNT2B1		8183929, 9482110	Standard	NM_021021		Approved	59-DAP, A1B, BSYN2, TIP-43, SNT2	uc010mdg.3	Q13884	OTTHUMG00000165041	ENST00000395601.3:c.825G>A	chr8.hg19:g.121644855C>T		131.0	0.0		96.0	5.0	NM_021021	A8K9E0|O14912|Q4KMG8	Silent	SNP	ENST00000395601.3	hg19	CCDS6334.1																																																																																			.	.		0.532	SNTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381535.1	NM_021021		T	121644855	C	T	121644855	2	4	63	1	0	0	0	0	0	0	0	1	14887	639	23	1		1	SNTB1	8	121644855	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	33889055	121644855	24719167	56	7651										
ZHX1	11244	hgsc.bcm.edu	37	chr8	124266621	124266621	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tgtaagcactgattactcttTgaatttctctggttgtacct	7	8	2	2	rs373764646		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:124266621T>C	ENST00000522655.1	-	3	2106	c.1566A>G	c.(1564-1566)tcA>tcG	p.S522S	ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000395571.3_Silent_p.S522S|ZHX1_ENST00000297857.2_Silent_p.S522S|ZHX1_ENST00000522595.1_5'Flank			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	522	Required for interaction with NFYA.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			GATTACTCTTTGAATTTCTCT	0.388																																					p.S522S		Atlas-SNP	.											.	ZHX1	89	.	0			c.A1566G						.						140	136	138					8																	124266621		2203	4300	6503	SO:0001819	synonymous_variant	11244	exon3			ACTCTTTGAATTT	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	12871	protein-coding gene	gene with protein product		604764	"zinc-fingers and homeoboxes 1"			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.1566A>G	chr8.hg19:g.124266621T>C		100.0	0.0		54.0	20.0	NM_007222	Q8IWD8	Silent	SNP	ENST00000522655.1	hg19	CCDS6342.1	.	.	.	.	.	.	.	.	.	.	T	4.702	0.130447	0.08981	.	.	ENSG00000165156	ENST00000520474	.	.	.	5.19	-3.42	0.04825	.	.	.	.	.	T	0.39091	0.1065	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38672	-0.9650	4	.	.	.	-11.7049	2.1581	0.03818	0.103:0.1917:0.1954:0.51	.	.	.	.	R	207	.	.	Q	-	2	0	ZHX1	124335802	0.111000	0.22076	0.997000	0.53966	0.989000	0.77384	-0.744000	0.04839	-0.144000	0.11314	-0.388000	0.06559	CAA	.	.		0.388	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1			C	124266621	T	C	124266621	2	2	63	1	0	0	0	0	0	0	0	1	17690	1799	63	2		2	ZHX1	8	124266621	Silent	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	2621766	124266621	22097401	57	7652										
PRSS3	5646	hgsc.bcm.edu	37	chr9	33796749	33796749	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tggctcccacttctgcggtgGctccctcatcagcgaacagt	10	15	3	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr9:33796749G>A	ENST00000361005.5	+	2	320	c.320G>A	c.(319-321)gGc>gAc	p.G107D	PRSS3_ENST00000379405.3_Missense_Mutation_p.G50D|PRSS3_ENST00000429677.3_Missense_Mutation_p.G43D|PRSS3_ENST00000342836.4_Missense_Mutation_p.G64D|RP11-133O22.6_ENST00000454429.2_RNA	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	107	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			TTCTGCGGTGGCTCCCTCATC	0.572																																					p.G107D		Atlas-SNP	.											.	PRSS3	79	.	0			c.G320A						.						125	128	127					9																	33796749		2203	4300	6503	SO:0001583	missense	5646	exon2			GCGGTGGCTCCCT		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"Serine peptidases / Serine peptidases"	9486	protein-coding gene	gene with protein product	"mesotrypsin"	613578	"protease, serine, 4 (trypsin 4, brain)", "protease, serine, 3 (mesotrypsin)"	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.320G>A	chr9.hg19:g.33796749G>A	ENSP00000354280:p.Gly107Asp	229.0	0.0		174.0	21.0	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	hg19	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816339	0.50527	.	.	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	T;D;D;T;D	0.98280	-1.46;-1.53;-4.84;-1.46;-4.84	3.21	3.21	0.36854	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.99149	0.9706	H	0.98068	4.14	0.58432	D	0.999999	D;D;D	0.60575	0.958;0.988;0.958	P;P;P	0.59948	0.866;0.842;0.866	D	0.98834	1.0752	10	0.72032	D	0.01	.	12.3047	0.54895	0.0:0.0:1.0:0.0	.	50;107;64	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	D	107;62;64;43;50	ENSP00000354280:G107D;ENSP00000401249:G62D;ENSP00000340889:G64D;ENSP00000401828:G43D;ENSP00000368715:G50D	ENSP00000340889:G64D	G	+	2	0	PRSS3	33786749	1.000000	0.71417	0.928000	0.36995	0.040000	0.13550	8.524000	0.90579	1.538000	0.49270	0.306000	0.20318	GGC	.	.		0.572	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771		A	33796749	G	A	33796749	3	1	63	1	0	0	0	0	1	0	0	0	12634	1203	42	3	370	3	PRSS3	9	33796749	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10		33796749	107416682	58	7653										
DAB2IP	153090	hgsc.bcm.edu	37	chr9	124535287	124535287	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ccagctgttggcaccgctctCcttccagaaccctgtgtacc	8	17	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr9:124535287C>G	ENST00000408936.3	+	12	2662	c.2480C>G	c.(2479-2481)tCc>tGc	p.S827C	DAB2IP_ENST00000259371.2_Missense_Mutation_p.S799C|DAB2IP_ENST00000309989.1_Missense_Mutation_p.S703C			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	827	Necessary for interaction with AKT1.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						GCACCGCTCTCCTTCCAGAAC	0.706																																					p.S799C		Atlas-SNP	.											.	DAB2IP	150	.	0			c.C2396G						.						29	29	29					9																	124535287		2158	4217	6375	SO:0001583	missense	153090	exon12			CGCTCTCCTTCCA	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.2480C>G	chr9.hg19:g.124535287C>G	ENSP00000386183:p.Ser827Cys	148.0	0.0		98.0	28.0	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Missense_Mutation	SNP	ENST00000408936.3	hg19		.	.	.	.	.	.	.	.	.	.	C	21.7	4.184906	0.78677	.	.	ENSG00000136848	ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.59018	0.2163	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.997;1.0	T	0.66011	-0.6029	10	0.87932	D	0	.	16.9563	0.86260	0.0:1.0:0.0:0.0	.	827;799	Q5VWQ8;G3XA90	DAB2P_HUMAN;.	C	799;827;736;703	ENSP00000259371:S799C;ENSP00000386183:S827C;ENSP00000362887:S736C;ENSP00000310827:S703C	ENSP00000259371:S799C	S	+	2	0	DAB2IP	123575108	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.409000	0.80053	2.317000	0.78254	0.462000	0.41574	TCC	.	.		0.706	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		G	124535287	C	G	124535287	3	3	63	1	0	0	0	0	1	0	0	0	4221	855	30	4	2442	4	DAB2IP	9	124535287	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	90738538	124535287	16678144	59	7654										
GPR158	57512	hgsc.bcm.edu	37	chr10	25861801	25861801	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gcctcattgaccgctgggacTacatgacagcagttggtatg	12	10	1	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr10:25861801T>A	ENST00000376351.3	+	7	2097	c.1738T>A	c.(1738-1740)Tac>Aac	p.Y580N		NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	580					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CCGCTGGGACTACATGACAGC	0.423																																					p.Y580N		Atlas-SNP	.											.	GPR158	255	.	0			c.T1738A						.						132	104	114					10																	25861801		2203	4300	6503	SO:0001583	missense	57512	exon7			TGGGACTACATGA	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.1738T>A	chr10.hg19:g.25861801T>A	ENSP00000365529:p.Tyr580Asn	201.0	0.0		102.0	17.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.625518	0.87560	.	.	ENSG00000151025	ENST00000376351	D	0.88354	-2.37	5.67	5.67	0.87782	GPCR, family 3, C-terminal (2);	0.098369	0.44483	D	0.000447	D	0.94909	0.8354	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95517	0.8591	10	0.72032	D	0.01	.	15.9002	0.79369	0.0:0.0:0.0:1.0	.	580	Q5T848	GP158_HUMAN	N	580	ENSP00000365529:Y580N	ENSP00000365529:Y580N	Y	+	1	0	GPR158	25901807	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.161000	0.67846	0.455000	0.32223	TAC	.	.		0.423	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		A	25861801	T	A	25861801	3	1	63	1	0	0	0	0	1	0	0	0	6671	1522	53	4	1764	4	GPR158	10	25861801	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10		25861801	109672946	60	7655										
GDF2	2658	hgsc.bcm.edu	37	chr10	48413759	48413759	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gcacgatagcgtgtttcgtcGgcgtcacatcgtcagccaag	12	12	2	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr10:48413759G>A	ENST00000249598.1	-	2	1268	c.1109C>T	c.(1108-1110)cCg>cTg	p.P370L		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	370					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						GTGTTTCGTCGGCGTCACATC	0.587																																					p.P370L		Atlas-SNP	.											.	GDF2	77	.	0			c.C1109T						.						128	105	113					10																	48413759		2203	4300	6503	SO:0001583	missense	2658	exon2			TTCGTCGGCGTCA	AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"Endogenous ligands"	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.1109C>T	chr10.hg19:g.48413759G>A	ENSP00000249598:p.Pro370Leu	162.0	0.0		141.0	18.0	NM_016204	Q5VSQ9|Q9Y571	Missense_Mutation	SNP	ENST00000249598.1	hg19	CCDS7219.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.752802	0.69648	.	.	ENSG00000128802	ENST00000249598	D	0.88046	-2.33	5.62	5.62	0.85841	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.94115	0.8113	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94522	0.7728	10	0.87932	D	0	.	18.6283	0.91349	0.0:0.0:1.0:0.0	.	370	Q9UK05	GDF2_HUMAN	L	370	ENSP00000249598:P370L	ENSP00000249598:P370L	P	-	2	0	GDF2	48033765	1.000000	0.71417	0.336000	0.25522	0.329000	0.28539	9.710000	0.98732	2.652000	0.90054	0.585000	0.79938	CCG	.	.		0.587	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204		A	48413759	G	A	48413759	3	1	63	1	0	0	0	0	1	0	0	0	6322	1116	39	1	184	1	GDF2	10	48413759	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	22551958	48413759	87120988	61	7656										
KIF11	3832	hgsc.bcm.edu	37	chr10	94369152	94369152	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ttttggtcagagaggagtgaTaattaaaggtttagaagaaa	12	1	1	4			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr10:94369152T>C	ENST00000260731.3	+	6	674	c.584T>C	c.(583-585)aTa>aCa	p.I195T		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	195	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)			breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGAGGAGTGATAATTAAAGGT	0.388																																					p.I195T	Colon(47;212 1003 2764 4062 8431)	Atlas-SNP	.											.	KIF11	58	.	0			c.T584C						.						174	188	183					10																	94369152		2203	4300	6503	SO:0001583	missense	3832	exon6			GAGTGATAATTAA	X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"Kinesins"	6388	protein-coding gene	gene with protein product		148760	"kinesin-like 1"	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.584T>C	chr10.hg19:g.94369152T>C	ENSP00000260731:p.Ile195Thr	91.0	0.0		60.0	9.0	NM_004523	A0AV49|B2RMV3|Q15716|Q5VWX0	Missense_Mutation	SNP	ENST00000260731.3	hg19	CCDS7422.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.886183	0.72410	.	.	ENSG00000138160	ENST00000260731	T	0.64991	-0.13	5.54	5.54	0.83059	Kinesin, motor domain (4);	0.107041	0.64402	D	0.000006	T	0.56307	0.1976	N	0.17631	0.505	0.58432	D	0.999995	P	0.39022	0.655	P	0.45377	0.478	T	0.59674	-0.7410	10	0.48119	T	0.1	.	15.8422	0.78857	0.0:0.0:0.0:1.0	.	195	P52732	KIF11_HUMAN	T	195	ENSP00000260731:I195T	ENSP00000260731:I195T	I	+	2	0	KIF11	94359132	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.796000	0.62496	2.323000	0.78572	0.528000	0.53228	ATA	.	.		0.388	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523		C	94369152	T	C	94369152	3	2	63	1	0	0	0	0	1	0	0	0	8281	1406	49	2	606	2	KIF11	10	94369152	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	45955393	94369152	41165595	62	7657										
HSPA12A	259217	hgsc.bcm.edu	37	chr10	118458224	118458224	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	actttcttgccatttgctgcCgtcaggtctgtatccatggt	9	11	3	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr10:118458224C>A	ENST00000369209.3	-	5	572	c.468G>T	c.(466-468)acG>acT	p.T156T		NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	156						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32				all cancers(201;0.0158)		CATTTGCTGCCGTCAGGTCTG	0.493																																					p.T156T		Atlas-SNP	.											.	HSPA12A	81	.	0			c.G468T						.						142	135	137					10																	118458224		1949	4157	6106	SO:0001819	synonymous_variant	259217	exon5			TGCTGCCGTCAGG	AB007877	CCDS41569.1	10q25.3	2011-09-02	2002-08-29		ENSG00000165868	ENSG00000165868		"Heat shock proteins / HSP70"	19022	protein-coding gene	gene with protein product		610701	"heat shock 70kD protein 12A"			12552099	Standard	NM_025015		Approved	FLJ13874, KIAA0417	uc001lct.3	O43301	OTTHUMG00000019107	ENST00000369209.3:c.468G>T	chr10.hg19:g.118458224C>A		124.0	0.0		89.0	28.0	NM_025015		Silent	SNP	ENST00000369209.3	hg19	CCDS41569.1																																																																																			.	.		0.493	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015		A	118458224	C	A	118458224	2	1	63	1	0	0	0	0	0	0	0	1	7413	639	23	1		1	HSPA12A	10	118458224	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	24089072	118458224	17076523	63	7658										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124377713	124377713	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	catgtcagccccaggaaatgCccagtttggccagggctcag	12	13	2	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr10:124377713C>A	ENST00000338354.3	+	38	4791	c.4685C>A	c.(4684-4686)gCc>gAc	p.A1562D	DMBT1_ENST00000368956.2_Missense_Mutation_p.A934D|DMBT1_ENST00000359586.6_Missense_Mutation_p.A413D|DMBT1_ENST00000344338.3_Missense_Mutation_p.A1552D|DMBT1_ENST00000368955.3_Missense_Mutation_p.A1552D|DMBT1_ENST00000368909.3_Missense_Mutation_p.A1562D|DMBT1_ENST00000330163.4_Missense_Mutation_p.A934D			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1562	SRCR 12. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCAGGAAATGCCCAGTTTGGC	0.612																																					p.A1562D	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.C4685A						.						160	164	163					10																	124377713		1960	4163	6123	SO:0001583	missense	1755	exon38			GAAATGCCCAGTT		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.4685C>A	chr10.hg19:g.124377713C>A	ENSP00000342210:p.Ala1562Asp	100.0	0.0		66.0	21.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	C	16.99	3.272970	0.59649	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;-0.06;-0.06	4.12	3.21	0.36854	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.760730	0.04550	U	0.389673	D	0.82719	0.5098	M	0.86028	2.79	0.37016	D	0.895959	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999;0.999	D;D;D;D;D;D	0.91635	0.967;0.988;0.999;0.991;0.951;0.97	T	0.69495	-0.5130	10	0.72032	D	0.01	.	12.2281	0.54472	0.0:0.9153:0.0:0.0847	.	413;811;1691;934;1552;1562	F8WEF7;Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;DMBT1_HUMAN	D	1562;1691;1562;1562;1562;1562;934;1552;934;934;1562;1552;934;413	ENSP00000342210:A1562D;ENSP00000343175:A1552D;ENSP00000327747:A934D;ENSP00000357905:A1562D;ENSP00000357951:A1552D;ENSP00000357952:A934D;ENSP00000352593:A413D	ENSP00000331522:A934D	A	+	2	0	DMBT1	124367703	0.981000	0.34729	0.061000	0.19648	0.427000	0.31564	2.975000	0.49281	0.862000	0.35528	0.549000	0.68633	GCC	.	.		0.612	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124377713	C	A	124377713	3	1	63	1	0	0	0	0	1	0	0	0	4579	739	26	3	4835	3	DMBT1	10	124377713	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	5919489	124377713	11157034	64	7659										
SYT8	90019	hgsc.bcm.edu	37	chr11	1858034	1858034	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ctctccggtacgtgcccagcTcaggccggctgaccgtggtg	14	15	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:1858034T>A	ENST00000381968.3	+	7	903	c.775T>A	c.(775-777)Tca>Aca	p.S259T	SYT8_ENST00000535046.1_3'UTR|TNNI2_ENST00000381911.1_5'Flank|TNNI2_ENST00000252898.7_5'Flank|SYT8_ENST00000341958.3_Missense_Mutation_p.S245T|TNNI2_ENST00000381906.1_5'Flank	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	259	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosome reaction (GO:0007340)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CGTGCCCAGCTCAGGCCGGCT	0.672																																					p.S259T		Atlas-SNP	.											.	SYT8	29	.	0			c.T775A						.						36	38	37					11																	1858034		2200	4298	6498	SO:0001583	missense	90019	exon7			CCCAGCTCAGGCC	AL137708	CCDS7726.2	11p15.5	2013-01-21			ENSG00000149043	ENSG00000149043		"Synaptotagmins"	19264	protein-coding gene	gene with protein product		607719				7791877	Standard	XM_005253216		Approved	DKFZp434K0322	uc001lue.1	Q8NBV8	OTTHUMG00000009026	ENST00000381968.3:c.775T>A	chr11.hg19:g.1858034T>A	ENSP00000371394:p.Ser259Thr	107.0	0.0		94.0	11.0	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	hg19	CCDS7726.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	9.247|9.247	1.039737|1.039737	0.19669|0.19669	.|.	.|.	ENSG00000149043|ENSG00000149043	ENST00000381978|ENST00000381968;ENST00000341958	.|T;T	.|0.07567	.|3.18;3.18	2.97|2.97	1.68|1.68	0.24146|0.24146	.|C2 membrane targeting protein (1);C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	.|.	.|.	.|.	.|.	T|T	0.04452|0.04452	0.0122|0.0122	N|N	0.16708|0.16708	0.43|0.43	0.18873|0.18873	N|N	0.999988|0.999988	.|B;B	.|0.26483	.|0.15;0.15	.|B;B	.|0.17722	.|0.019;0.019	T|T	0.36065|0.36065	-0.9763|-0.9763	5|9	.|0.44086	.|T	.|0.13	.|.	3.5396|3.5396	0.07806|0.07806	0.4358:0.0:0.1724:0.3917|0.4358:0.0:0.1724:0.3917	.|.	.|259;245	.|Q8NBV8;A6NCR4	.|SYT8_HUMAN;.	H|T	257|259;245	.|ENSP00000371394:S259T;ENSP00000343691:S245T	.|ENSP00000343691:S245T	L|S	+|+	2|1	0|0	SYT8|SYT8	1814610|1814610	0.001000|0.001000	0.12720|0.12720	0.879000|0.879000	0.34478|0.34478	0.447000|0.447000	0.32167|0.32167	0.421000|0.421000	0.21280|0.21280	1.368000|1.368000	0.46115|0.46115	0.260000|0.260000	0.18958|0.18958	CTC|TCA	.	.		0.672	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4			A	1858034	T	A	1858034	3	1	63	1	0	0	0	0	1	0	0	0	15495	1551	54	4	801	4	SYT8	11	1858034	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10		1858034	133148482	65	7660										
TNNT3	7140	hgsc.bcm.edu	37	chr11	1955638	1955638	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gaagaagaagaaagctctgtCttccatgggagccaactaca	10	9	2	3			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:1955638C>T	ENST00000397301.1	+	13	484	c.476C>T	c.(475-477)tCt>tTt	p.S159F	TNNT3_ENST00000446240.1_Missense_Mutation_p.S129F|TNNT3_ENST00000360603.3_Missense_Mutation_p.S142F|TNNT3_ENST00000381548.3_Missense_Mutation_p.S150F|TNNT3_ENST00000493234.1_3'UTR|TNNT3_ENST00000381589.3_Missense_Mutation_p.S146F|TNNT3_ENST00000381558.1_Missense_Mutation_p.S140F|TNNT3_ENST00000397304.2_Missense_Mutation_p.S129F|TNNT3_ENST00000278317.6_Missense_Mutation_p.S148F|TNNT3_ENST00000381549.3_Missense_Mutation_p.S140F|TNNT3_ENST00000381561.4_Missense_Mutation_p.S151F|TNNT3_ENST00000381579.3_Missense_Mutation_p.S140F			P45378	TNNT3_HUMAN	troponin T type 3 (skeletal, fast)	159					ATP catabolic process (GO:0006200)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)|regulation of striated muscle contraction (GO:0006942)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium-dependent protein binding (GO:0048306)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)			breast(2)|endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(4)|stomach(1)	19		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00253)|Lung(200;0.0333)|LUSC - Lung squamous cell carcinoma(625;0.0826)		AAAGCTCTGTCTTCCATGGGA	0.592																																					p.S148F		Atlas-SNP	.											.	TNNT3	68	.	0			c.C443T						.						104	95	98					11																	1955638		2202	4298	6500	SO:0001583	missense	7140	exon12			CTCTGTCTTCCAT	M21984	CCDS7727.1, CCDS41594.1, CCDS41595.1, CCDS41596.1	11p15.5	2014-09-17	2005-09-12		ENSG00000130595	ENSG00000130595			11950	protein-coding gene	gene with protein product	"troponin-T3, skeletal, fast"	600692	"troponin T3, skeletal, fast"			8172653	Standard	NM_001042782		Approved	AMCD2B, DA2B, FSSV, DKFZp779M2348	uc001lup.4	P45378	OTTHUMG00000012475	ENST00000397301.1:c.476C>T	chr11.hg19:g.1955638C>T	ENSP00000380468:p.Ser159Phe	82.0	0.0		92.0	14.0	NM_006757	A8MQ76|A8MSW1|B3KPX3|B7WP64|B7ZL26|B7ZVV9|Q12975|Q12976|Q12977|Q12978|Q17RG9|Q6FH29|Q6N056|Q86TH6	Missense_Mutation	SNP	ENST00000397301.1	hg19		.	.	.	.	.	.	.	.	.	.	.	23.9	4.472056	0.84533	.	.	ENSG00000130595	ENST00000278317;ENST00000544980;ENST00000397309;ENST00000381561;ENST00000381548;ENST00000360603;ENST00000381549;ENST00000381589;ENST00000381579;ENST00000381557;ENST00000453458;ENST00000381563;ENST00000344578;ENST00000381558;ENST00000397301;ENST00000397304;ENST00000446240	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98996	-1.57;-1.57;-1.57;-1.57;-1.57;-1.57;-1.57;-1.57;-5.31;-1.57;-1.57;-1.57;-1.57;-1.57;-1.57	4.66	4.66	0.58398	.	0.115083	0.64402	D	0.000013	D	0.99351	0.9772	M	0.87971	2.92	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.992;0.992;0.992;0.994;0.997	D	0.98903	1.0777	10	0.87932	D	0	-24.9044	17.9291	0.88992	0.0:1.0:0.0:0.0	.	148;140;146;140;159	P45378-2;P45378-7;P45378-6;P45378-4;P45378	.;.;.;.;TNNT3_HUMAN	F	148;44;160;151;150;142;140;146;140;134;129;151;135;140;159;129;129	ENSP00000278317:S148F;ENSP00000370973:S151F;ENSP00000370960:S150F;ENSP00000353815:S142F;ENSP00000370961:S140F;ENSP00000371001:S146F;ENSP00000370991:S140F;ENSP00000370969:S134F;ENSP00000415614:S129F;ENSP00000370975:S151F;ENSP00000344870:S135F;ENSP00000370970:S140F;ENSP00000380468:S159F;ENSP00000380471:S129F;ENSP00000413203:S129F	ENSP00000278317:S148F	S	+	2	0	TNNT3	1912214	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	5.663000	0.68038	2.314000	0.78098	0.313000	0.20887	TCT	.	.		0.592	TNNT3-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000142920.3	NM_006757		T	1955638	C	T	1955638	3	4	63	1	0	0	0	0	1	0	0	0	16347	913	32	3	526	3	TNNT3	11	1955638	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	97604	1955638	133050878	66	7661										
STK33	65975	hgsc.bcm.edu	37	chr11	8496345	8496345	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gacatttccaccaccaaaacTggaggaacccttgttttgct	7	12	0	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:8496345T>C	ENST00000447869.1	-	1	1026	c.108A>G	c.(106-108)ccA>ccG	p.P36P	STK33_ENST00000358872.3_Intron|STK33_ENST00000396672.1_Silent_p.P36P|STK33_ENST00000534493.1_5'UTR|STK33_ENST00000396673.1_Silent_p.P36P|STK33_ENST00000315204.1_Silent_p.P36P			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	36					protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		CCACCAAAACTGGAGGAACCC	0.368																																					p.P36P		Atlas-SNP	.											.	STK33	147	.	0			c.A108G						.						135	138	137					11																	8496345		2201	4296	6497	SO:0001819	synonymous_variant	65975	exon3			CAAAACTGGAGGA	AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.108A>G	chr11.hg19:g.8496345T>C		140.0	0.0		92.0	21.0	NM_030906	Q658S6|Q8NEF5	Silent	SNP	ENST00000447869.1	hg19	CCDS7789.1																																																																																			.	.		0.368	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906		C	8496345	T	C	8496345	2	2	63	1	0	0	0	0	0	0	0	1	15315	1567	55	2		2	STK33	11	8496345	Silent	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	6540707	8496345	126510171	67	7662										
RBM14	10432	hgsc.bcm.edu	37	chr11	66384504	66384504	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tcttcgagcgccgcggacgcGtcatcgagtgtgacgtggtg	16	11	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:66384504G>T	ENST00000310137.4	+	1	452	c.313G>T	c.(313-315)Gtc>Ttc	p.V105F	RBM14_ENST00000409738.4_Missense_Mutation_p.V105F|RBM4_ENST00000503028.2_5'UTR|RBM14_ENST00000393979.3_Missense_Mutation_p.V105F|RBM14-RBM4_ENST00000412278.2_Missense_Mutation_p.V105F|RBM14-RBM4_ENST00000500635.2_Missense_Mutation_p.V105F|RNU4-39P_ENST00000362455.1_RNA|RBM4_ENST00000514361.3_Missense_Mutation_p.V105F|RBM14-RBM4_ENST00000511114.1_3'UTR|RBM14_ENST00000409372.1_Missense_Mutation_p.V105F|RBM14_ENST00000443702.1_Missense_Mutation_p.V105F	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	105	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CCGCGGACGCGTCATCGAGTG	0.662																																					p.V105F		Atlas-SNP	.											.	RBM14	59	.	0			c.G313T						.						43	51	48					11																	66384504		2159	4218	6377	SO:0001583	missense	10432	exon1			GGACGCGTCATCG	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"RNA binding motif (RRM) containing"	14219	protein-coding gene	gene with protein product	"coactivator activator", "SYT interacting protein"	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.313G>T	chr11.hg19:g.66384504G>T	ENSP00000311747:p.Val105Phe	73.0	0.0		76.0	9.0	NM_001198837	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	hg19	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.989364	0.93106	.	.	ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000248643;ENSG00000248643	ENST00000310137;ENST00000393979;ENST00000409372;ENST00000443702;ENST00000409738;ENST00000412278;ENST00000500635	T;T;T;T;T;T;T	0.79554	-1.28;-1.28;2.05;2.05;2.05;2.05;2.05	5.18	4.25	0.50352	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.256789	0.32563	N	0.005936	D	0.90995	0.7168	M	0.91768	3.24	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.992;1.0	D	0.92334	0.5876	10	0.87932	D	0	-11.3981	12.6918	0.56978	0.0:0.0:0.8335:0.1665	.	105;105;105;105	B0LM41;Q96PK6-2;Q2PYN1;Q96PK6	.;.;.;RBM14_HUMAN	F	105	ENSP00000311747:V105F;ENSP00000377548:V105F;ENSP00000386518:V105F;ENSP00000414650:V105F;ENSP00000386995:V105F;ENSP00000388552:V105F;ENSP00000421279:V105F	ENSP00000311747:V105F	V	+	1	0	RBM14;RBM14-RBM4	66141080	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.213000	0.77950	1.157000	0.42530	0.555000	0.69702	GTC	.	.		0.662	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		T	66384504	G	T	66384504	3	4	63	1	0	0	0	0	1	0	0	0	13130	1145	40	1	315	1	RBM14	11	66384504	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	57888159	66384504	68622012	68	7663										
FOLR4	390243	hgsc.bcm.edu	37	chr11	94040391	94040391	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cgctgtgccaggaggactgtGaggagtggtgggaagactgt	19	6	0	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:94040391G>A	ENST00000440961.2	+	3	432	c.388G>A	c.(388-390)Gag>Aag	p.E130K		NM_001199206.1	NP_001186135.1	A6ND01	JUNO_HUMAN	folate receptor 4, delta (putative)	137					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14						GGAGGACTGTGAGGAGTGGTG	0.567																																					p.E137K		Atlas-SNP	.											.	FOLR4	31	.	0			c.G409A						.						102	110	108					11																	94040391		2195	4292	6487	SO:0001583	missense	390243	exon3			GACTGTGAGGAGT			11q14	2014-07-23	2012-12-07		ENSG00000183560	ENSG00000183560			32565	protein-coding gene	gene with protein product		615737	"folate receptor 4 (delta) homolog (mouse)"			11111049, 24739963	Standard	NM_001199206		Approved	Folbp3, JUNO	uc021qou.1	A6ND01		ENST00000440961.2:c.388G>A	chr11.hg19:g.94040391G>A	ENSP00000416935:p.Glu130Lys	162.0	0.0		112.0	12.0	NM_001199206		Missense_Mutation	SNP	ENST00000440961.2	hg19		.	.	.	.	.	.	.	.	.	.	G	17.51	3.406533	0.62399	.	.	ENSG00000183560	ENST00000440961	T	0.76316	-1.01	4.67	1.75	0.24633	.	0.501919	0.22175	N	0.063598	T	0.74854	0.3771	M	0.77313	2.365	0.09310	N	1	P	0.40553	0.721	B	0.42030	0.373	T	0.66356	-0.5944	10	0.49607	T	0.09	-13.7692	5.5608	0.17142	0.1814:0.0:0.6554:0.1633	.	130	A6ND01-2	.	K	130	ENSP00000416935:E130K	ENSP00000416935:E130K	E	+	1	0	FOLR4	93680039	0.985000	0.35326	0.877000	0.34402	0.990000	0.78478	2.373000	0.44266	0.681000	0.31386	0.491000	0.48974	GAG	.	.		0.567	FOLR4-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000396420.1	NM_001080486		A	94040391	G	A	94040391	3	1	63	1	0	0	0	0	1	0	0	0	5992	1291	45	3	398	3	FOLR4	11	94040391	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	27655887	94040391	40966125	69	7664										
C11orf87	399947	hgsc.bcm.edu	37	chr11	109294862	109294862	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ctgtgctcctccgcctccacCgccagcctccagtccccaag	7	22	0	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:109294862C>A	ENST00000327419.6	+	2	906	c.503C>A	c.(502-504)cCg>cAg	p.P168Q	RP11-708B6.2_ENST00000532929.1_RNA|RP11-708B6.2_ENST00000532992.1_RNA	NM_207645.3	NP_997528.2	Q6NUJ2	CK087_HUMAN	chromosome 11 open reading frame 87	168						integral component of membrane (GO:0016021)		p.P168L(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17						CCGCCTCCACCGCCAGCCTCC	0.652																																					p.P168Q		Atlas-SNP	.											C11orf87,rectum,carcinoma,0,2	C11orf87	37	.	1	Substitution - Missense(1)	large_intestine(1)	c.C503A						.						40	42	41					11																	109294862		2201	4298	6499	SO:0001583	missense	399947	exon2			CTCCACCGCCAGC	AB096240, BC035798	CCDS31672.1	11q22.3	2013-12-13	2013-12-13	2013-12-13	ENSG00000185742	ENSG00000185742			33788	protein-coding gene	gene with protein product	"neuronal integral membrane protein 1"					12477932	Standard	NM_207645		Approved	LOH11CR1A, LOC399947, NEURIM1	uc010rwb.2	Q6NUJ2		ENST00000327419.6:c.503C>A	chr11.hg19:g.109294862C>A	ENSP00000331581:p.Pro168Gln	71.0	0.0		64.0	19.0	NM_207645	B4E169	Missense_Mutation	SNP	ENST00000327419.6	hg19	CCDS31672.1	.	.	.	.	.	.	.	.	.	.	C	7.918	0.737911	0.15574	.	.	ENSG00000185742	ENST00000327419	.	.	.	3.42	0.388	0.16264	.	.	.	.	.	T	0.12050	0.0293	N	0.08118	0	0.23249	N	0.998049	B	0.30146	0.27	B	0.22386	0.039	T	0.19031	-1.0318	8	0.40728	T	0.16	-5.3732	3.1802	0.06582	0.186:0.4978:0.0:0.3162	.	168	Q6NUJ2	CK087_HUMAN	Q	168	.	ENSP00000331581:P168Q	P	+	2	0	C11orf87	108800072	0.000000	0.05858	0.934000	0.37439	0.983000	0.72400	0.007000	0.13174	0.095000	0.17434	-0.123000	0.14984	CCG	.	.		0.652	C11orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390403.1	NM_207645		A	109294862	C	A	109294862	3	1	63	1	0	0	0	0	1	0	0	0	1671	652	23	1	505	1	C11orf87	11	109294862	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	15254471	109294862	25711654	70	7665										
LHX5	64211	hgsc.bcm.edu	37	chr12	113901064	113901064	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ccgctgtagccgctggtgccGctcattgggaagggcgggct	17	12	1	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr12:113901064G>T	ENST00000261731.3	-	5	1713	c.1140C>A	c.(1138-1140)agC>agA	p.S380R		NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	380					cell proliferation in forebrain (GO:0021846)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|forebrain neuron differentiation (GO:0021879)|hippocampus development (GO:0021766)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						CGCTGGTGCCGCTCATTGGGA	0.751																																					p.S380R		Atlas-SNP	.											.	LHX5	39	.	0			c.C1140A						.						3	6	5					12																	113901064		1712	3364	5076	SO:0001583	missense	64211	exon5			GGTGCCGCTCATT	AF291181	CCDS9171.1	12q24.13	2014-01-15			ENSG00000089116	ENSG00000089116		"Homeoboxes / LIM class"	14216	protein-coding gene	gene with protein product		605992					Standard	NM_022363		Approved		uc001tvj.1	Q9H2C1	OTTHUMG00000169552	ENST00000261731.3:c.1140C>A	chr12.hg19:g.113901064G>T	ENSP00000261731:p.Ser380Arg	20.0	0.0		34.0	14.0	NM_022363	Q32MA4	Missense_Mutation	SNP	ENST00000261731.3	hg19	CCDS9171.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.462281	0.43736	.	.	ENSG00000089116	ENST00000261731	D	0.90900	-2.75	4.08	2.23	0.28157	.	0.269330	0.24856	N	0.035041	T	0.81823	0.4904	L	0.40543	1.245	0.45261	D	0.998267	P	0.45715	0.865	B	0.35971	0.215	T	0.74604	-0.3610	10	0.29301	T	0.29	.	7.7318	0.28791	0.2635:0.0:0.7365:0.0	.	380	Q9H2C1	LHX5_HUMAN	R	380	ENSP00000261731:S380R	ENSP00000261731:S380R	S	-	3	2	LHX5	112385447	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.399000	0.44495	0.324000	0.23333	-0.258000	0.10820	AGC	.	.		0.751	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363		T	113901064	G	T	113901064	3	4	63	1	0	0	0	0	1	0	0	0	8783	1078	38	1	72	1	LHX5	12	113901064	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10		113901064	19950831	71	7666										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121432040	121432040	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ccaacctcgtcacggaggtgCgtgtctacaactggtttgcc	11	13	2	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr12:121432040C>G	ENST00000257555.6	+	4	1013	c.787C>G	c.(787-789)Cgt>Ggt	p.R263G	HNF1A_ENST00000543427.1_Missense_Mutation_p.R146G|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_Missense_Mutation_p.R263G|HNF1A_ENST00000402929.1_Missense_Mutation_p.R263G|HNF1A_ENST00000400024.2_Missense_Mutation_p.R263G|HNF1A_ENST00000541395.1_Missense_Mutation_p.R263G			P20823	HNF1A_HUMAN	HNF1 homeobox A	263	Interaction with DNA.		R -> C (in MODY3; expected to interfere with DNA binding). {ECO:0000269|PubMed:9287053}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R263C(2)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CACGGAGGTGCGTGTCTACAA	0.647									Hepatic Adenoma, Familial Clustering of																												p.R263G		Atlas-SNP	.											HNF1A,NS,other,-1,2	HNF1A	302	.	2	Substitution - Missense(2)	liver(2)	c.C787G	GRCh37	CM971458	HNF1A	M		.						41	40	40					12																	121432040		2203	4300	6503	SO:0001583	missense	6927	exon4	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	GAGGTGCGTGTCT	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.787C>G	chr12.hg19:g.121432040C>G	ENSP00000257555:p.Arg263Gly	111.0	0.0		61.0	5.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316878	0.81469	.	.	ENSG00000135100	ENST00000257555;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89	4.84	4.84	0.62591	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000003	D	0.96747	0.8938	L	0.60455	1.87	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;0.997	D;D;D;D	0.81914	0.994;0.995;0.988;0.983	D	0.97136	0.9821	10	0.87932	D	0	-10.9955	13.6154	0.62105	0.1555:0.8445:0.0:0.0	.	263;263;263;263	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	G	263;263;263;263;146;263;263;263;263;263	ENSP00000257555:R263G;ENSP00000439721:R146G;ENSP00000443112:R263G;ENSP00000438804:R263G	ENSP00000257555:R263G	R	+	1	0	HNF1A	119916423	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.985000	0.49362	2.245000	0.73994	0.409000	0.27619	CGT	.	.		0.647	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		G	121432040	C	G	121432040	3	3	63	1	0	0	0	0	1	0	0	0	7260	768	27	4	801	4	HNF1A	12	121432040	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	7530976	121432040	12419855	72	7667										
GOLGA3	2802	hgsc.bcm.edu	37	chr12	133384623	133384623	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ggaatctcctggccgttgacCatatagggggtgtcctgcgt	14	10	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr12:133384623C>A	ENST00000450791.2	-	4	1215	c.1032G>T	c.(1030-1032)atG>atT	p.M344I	GOLGA3_ENST00000456883.2_Missense_Mutation_p.M344I|GOLGA3_ENST00000204726.3_Missense_Mutation_p.M344I|GOLGA3_ENST00000545875.1_Missense_Mutation_p.M344I|GOLGA3_ENST00000537452.1_Missense_Mutation_p.M344I			Q08378	GOGA3_HUMAN	golgin A3	344					intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GGCCGTTGACCATATAGGGGG	0.612																																					p.M344I		Atlas-SNP	.											.	GOLGA3	234	.	0			c.G1032T						.						90	77	81					12																	133384623		2203	4300	6503	SO:0001583	missense	2802	exon5			GTTGACCATATAG	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"SY2/SY10 protein", "Golgi complex-associated protein of 170 kD"	602581	"golgi autoantigen, golgin subfamily a, 3"			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.1032G>T	chr12.hg19:g.133384623C>A	ENSP00000410378:p.Met344Ile	124.0	0.0		103.0	30.0	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	hg19	CCDS9281.1	.	.	.	.	.	.	.	.	.	.	c	1.100	-0.661288	0.03454	.	.	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.73	4.83	0.62350	.	0.618093	0.17067	N	0.188325	T	0.19846	0.0477	L	0.36672	1.1	0.33105	D	0.539808	B;B;B	0.10296	0.003;0.001;0.002	B;B;B	0.11329	0.006;0.006;0.003	T	0.17623	-1.0363	10	0.21014	T	0.42	.	3.9634	0.09421	0.2206:0.6184:0.0:0.161	.	344;344;344	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	I	344	ENSP00000204726:M344I;ENSP00000410378:M344I;ENSP00000409303:M344I;ENSP00000442143:M344I;ENSP00000442603:M344I	ENSP00000204726:M344I	M	-	3	0	GOLGA3	131894696	0.964000	0.33143	0.048000	0.18961	0.006000	0.05464	0.276000	0.18716	2.707000	0.92482	0.645000	0.84053	ATG	.	.		0.612	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895		A	133384623	C	A	133384623	3	1	63	1	0	0	0	0	1	0	0	0	6562	594	21	3	3682	3	GOLGA3	12	133384623	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	11952583	133384623	467272	73	7668										
UCHL3	7347	hgsc.bcm.edu	37	chr13	76140947	76140947	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gcctgtggaacaattggactGattcatgctattgcaaacaa	9	8	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr13:76140947G>A	ENST00000377595.3	+	4	330	c.300G>A	c.(298-300)ctG>ctA	p.L100L	RP11-29G8.3_ENST00000563635.1_RNA	NM_001270952.1|NM_006002.4	NP_001257881.1|NP_005993.1	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)	100					protein catabolic process (GO:0030163)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(2)|lung(3)|skin(1)	7				GBM - Glioblastoma multiforme(99;0.0125)		CAATTGGACTGATTCATGCTA	0.338																																					p.L100L		Atlas-SNP	.											.	UCHL3	9	.	0			c.G300A						.						130	124	126					13																	76140947		2203	4300	6503	SO:0001819	synonymous_variant	7347	exon4			TGGACTGATTCAT	M30496	CCDS9453.1, CCDS73586.1	13q21.33	2008-02-05			ENSG00000118939	ENSG00000118939	3.2.1.15		12515	protein-coding gene	gene with protein product		603090				2530630	Standard	NM_001270952		Approved		uc001vjq.4	P15374	OTTHUMG00000017090	ENST00000377595.3:c.300G>A	chr13.hg19:g.76140947G>A		102.0	0.0		54.0	8.0	NM_006002	B2R970|Q5TBK8|Q6IBE9	Silent	SNP	ENST00000377595.3	hg19	CCDS9453.1																																																																																			.	.		0.338	UCHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045292.2	NM_006002		A	76140947	G	A	76140947	2	1	63	1	0	0	0	0	0	0	0	1	16936	1277	45	3		3	UCHL3	13	76140947	Silent	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10		76140947	39028931	74	7669										
C14orf166B	145497	hgsc.bcm.edu	37	chr14	77311222	77311222	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	caattctctgatgtaggaggGgagcacctgggccagatgct	14	9	1	2	rs374431496		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr14:77311222G>A	ENST00000393774.3	+	7	829	c.705G>A	c.(703-705)ggG>ggA	p.G235G	C14orf166B_ENST00000450042.2_3'UTR	NM_194287.2	NP_919263.2														breast(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(1)	18			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		ATGTAGGAGGGGAGCACCTGG	0.478																																					p.G235G	Ovarian(165;1056 1958 32571 36789 48728)	Atlas-SNP	.											.	C14orf166B	52	.	0			c.G705A						.	G		0,4406		0,0,2203	50	50	50		705	-7.4	0	14		50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C14orf166B	NM_194287.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		235/489	77311222	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	145497	exon7			AGGAGGGGAGCAC																												ENST00000393774.3:c.705G>A	chr14.hg19:g.77311222G>A		67.0	0.0		51.0	17.0	NM_194287		Silent	SNP	ENST00000393774.3	hg19	CCDS9853.2																																																																																			.	.		0.478	C14orf166B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316592.1			A	77311222	G	A	77311222	2	1	63	1	0	0	0	0	0	0	0	1	1759	1219	43	3		3	C14orf166B	14	77311222	Silent	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10		77311222	30038318	75	7670										
NRXN3	9369	hgsc.bcm.edu	37	chr14	79269978	79269978	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ggcagaggcatccatcctgaGctatgatggtagcatgtaca	12	9	0	3			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr14:79269978G>A	ENST00000554719.1	+	6	1432	c.941G>A	c.(940-942)aGc>aAc	p.S314N	NRXN3_ENST00000335750.5_Missense_Mutation_p.S314N	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	0					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TCCATCCTGAGCTATGATGGT	0.493																																					p.S314N		Atlas-SNP	.											.	NRXN3	342	.	0			c.G941A						.						178	134	149					14																	79269978		2203	4300	6503	SO:0001583	missense	9369	exon6			TCCTGAGCTATGA	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.941G>A	chr14.hg19:g.79269978G>A	ENSP00000451648:p.Ser314Asn	130.0	0.0		107.0	27.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	hg19	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.831635	0.71258	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750	T;T	0.80304	-1.36;-1.36	5.91	5.91	0.95273	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.207171	0.51477	D	0.000086	D	0.90147	0.6921	.	.	.	0.43338	D	0.995381	D;D	0.76494	0.996;0.999	D;D	0.73380	0.978;0.98	D	0.89074	0.3471	8	.	.	.	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	687;314	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	N	687;685;314;314	ENSP00000451648:S314N;ENSP00000338349:S314N	.	S	+	2	0	NRXN3	78339731	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	6.265000	0.72534	2.793000	0.96121	0.655000	0.94253	AGC	.	.		0.493	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250		A	79269978	G	A	79269978	3	1	63	1	0	0	0	0	1	0	0	0	10676	971	34	3	955	3	NRXN3	14	79269978	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	1958756	79269978	28079562	76	7671										
KIF26A	26153	hgsc.bcm.edu	37	chr14	104642658	104642658	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	aacctggggtccgtgccctgGggaagtggctgcagtggccc	17	12	0	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr14:104642658G>T	ENST00000423312.2	+	12	3533	c.3533G>T	c.(3532-3534)gGg>gTg	p.G1178V	KIF26A_ENST00000315264.7_Missense_Mutation_p.G1039V	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1178					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		CCGTGCCCTGGGGAAGTGGCT	0.721																																					p.G1178V		Atlas-SNP	.											.	KIF26A	84	.	0			c.G3533T						.						8	10	9					14																	104642658		1708	3820	5528	SO:0001583	missense	26153	exon12			GCCCTGGGGAAGT	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"Kinesins"	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.3533G>T	chr14.hg19:g.104642658G>T	ENSP00000388241:p.Gly1178Val	83.0	0.0		107.0	34.0	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	hg19	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	G	0.517	-0.863862	0.02590	.	.	ENSG00000066735	ENST00000423312;ENST00000315264	T;T	0.78481	-1.18;-1.17	3.52	-1.71	0.08133	.	.	.	.	.	T	0.67748	0.2926	M	0.64404	1.975	0.09310	N	1	B	0.22003	0.063	B	0.14578	0.011	T	0.57004	-0.7885	9	0.48119	T	0.1	.	2.8448	0.05540	0.1081:0.4273:0.2229:0.2418	.	1178	Q9ULI4	KI26A_HUMAN	V	1178;1039	ENSP00000388241:G1178V;ENSP00000325452:G1039V	ENSP00000325452:G1039V	G	+	2	0	KIF26A	103712411	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	-0.682000	0.05185	-0.127000	0.11661	-0.657000	0.03884	GGG	.	.		0.721	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			T	104642658	G	T	104642658	3	4	63	1	0	0	0	0	1	0	0	0	8303	1232	43	3	3579	3	KIF26A	14	104642658	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	25372680	104642658	2706882	77	7672										
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48500027	48500027	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gagagcagtgcagctgcagaTgacaatactgacccaccaca	10	12	0	4			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr15:48500027T>A	ENST00000558405.1	+	1	125	c.111T>A	c.(109-111)gaT>gaA	p.D37E	SLC12A1_ENST00000330289.6_Missense_Mutation_p.D37E|SLC12A1_ENST00000396577.3_Missense_Mutation_p.D37E|SLC12A1_ENST00000561031.1_Missense_Mutation_p.D37E|SLC12A1_ENST00000380993.3_Missense_Mutation_p.D37E			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	37					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CAGCTGCAGATGACAATACTG	0.433																																					p.D37E		Atlas-SNP	.											.	SLC12A1	243	.	0			c.T111A						.						76	72	73					15																	48500027		2198	4297	6495	SO:0001583	missense	6557	exon2			TGCAGATGACAAT		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.111T>A	chr15.hg19:g.48500027T>A	ENSP00000453409:p.Asp37Glu	120.0	0.0		83.0	25.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.422|3.422	-0.117977|-0.117977	0.06838|0.06838	.|.	.|.	ENSG00000074803|ENSG00000074803	ENST00000380993;ENST00000396577;ENST00000330289|ENST00000546071	D;D;D|.	0.91180|.	-1.89;-1.89;-2.8|.	5.45|5.45	-4.87|-4.87	0.03123|0.03123	.|.	1.652850|.	0.03156|.	N|.	0.168601|.	T|T	0.19248|0.19248	0.0462|0.0462	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.14012|.	0.0;0.009|.	B;B|.	0.12156|.	0.001;0.007|.	T|T	0.39292|0.39292	-0.9621|-0.9621	10|6	0.24483|0.56958	T|D	0.36|0.05	.|.	9.3696|9.3696	0.38246|0.38246	0.0:0.4299:0.2772:0.2929|0.0:0.4299:0.2772:0.2929	.|.	37;37|.	Q8IUN5;Q13621|.	.;S12A1_HUMAN|.	E|K	37|11	ENSP00000370381:D37E;ENSP00000379822:D37E;ENSP00000331550:D37E|.	ENSP00000331550:D37E|ENSP00000441148:M11K	D|M	+|+	3|2	2|0	SLC12A1|SLC12A1	46287319|46287319	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-0.804000|-0.804000	0.04535|0.04535	-0.488000|-0.488000	0.06726|0.06726	0.460000|0.460000	0.39030|0.39030	GAT|ATG	.	.		0.433	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			A	48500027	T	A	48500027	3	1	63	1	0	0	0	0	1	0	0	0	14397	1461	51	4	113	4	SLC12A1	15	48500027	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10		48500027	54031365	78	7673										
SHC4	399694	hgsc.bcm.edu	37	chr15	49135766	49135766	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gtatctcgctgggactgcacCcctcttggatggacattacc	10	13	2	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr15:49135766C>T	ENST00000332408.4	-	10	1751	c.1323G>A	c.(1321-1323)ggG>ggA	p.G441G	SHC4_ENST00000537958.1_Silent_p.G155G|SHC4_ENST00000396535.3_Silent_p.G198G	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	441	CH1.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		GGGACTGCACCCCTCTTGGAT	0.388																																					p.G441G		Atlas-SNP	.											.	SHC4	70	.	0			c.G1323A						.						122	111	114					15																	49135766		2197	4295	6492	SO:0001819	synonymous_variant	399694	exon10			CTGCACCCCTCTT	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"SH2 domain containing"	16743	protein-coding gene	gene with protein product	"rai-like protein"						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.1323G>A	chr15.hg19:g.49135766C>T		183.0	0.0		186.0	57.0	NM_203349	Q6UXQ3|Q8IYW3	Silent	SNP	ENST00000332408.4	hg19	CCDS10130.1																																																																																			.	.		0.388	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349		T	49135766	C	T	49135766	2	4	63	1	0	0	0	0	0	0	0	1	14288	610	22	3		3	SHC4	15	49135766	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	635739	49135766	53395626	79	7674										
UBE2Q2	92912	hgsc.bcm.edu	37	chr15	76165791	76165791	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tatagaagacttagatcactAtgagatgaaggaagaagagc	11	4	1	7			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr15:76165791A>G	ENST00000267938.4	+	5	852	c.470A>G	c.(469-471)tAt>tGt	p.Y157C	UBE2Q2_ENST00000338677.4_Missense_Mutation_p.Y157C|UBE2Q2_ENST00000561851.1_Missense_Mutation_p.Y141C|UBE2Q2_ENST00000569423.1_Missense_Mutation_p.Y122C	NM_173469.2	NP_775740.1	Q8WVN8	UB2Q2_HUMAN	ubiquitin-conjugating enzyme E2Q family member 2	157	Glu-rich.				protein K48-linked ubiquitination (GO:0070936)	cytoplasm (GO:0005737)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	12						TTAGATCACTATGAGATGAAG	0.313																																					p.Y157C		Atlas-SNP	.											.	UBE2Q2	26	.	0			c.A470G						.						71	71	71					15																	76165791		2197	4294	6491	SO:0001583	missense	92912	exon5			ATCACTATGAGAT	BC017708	CCDS10286.1, CCDS45309.1, CCDS66839.1	15q24.2	2010-05-12	2008-05-02		ENSG00000140367	ENSG00000140367		"Ubiquitin-conjugating enzymes E2"	19248	protein-coding gene	gene with protein product		612501	"ubiquitin-conjugating enzyme E2Q (putative) 2"			16300736	Standard	NM_001145335		Approved	DKFZp762C143	uc002bbg.2	Q8WVN8	OTTHUMG00000142839	ENST00000267938.4:c.470A>G	chr15.hg19:g.76165791A>G	ENSP00000267938:p.Tyr157Cys	183.0	0.0		130.0	20.0	NM_173469	B7Z3Q2|H3BRG2|Q8N4G6|Q96J08	Missense_Mutation	SNP	ENST00000267938.4	hg19	CCDS10286.1	.	.	.	.	.	.	.	.	.	.	A	14.70	2.614236	0.46631	.	.	ENSG00000140367	ENST00000338677;ENST00000267938;ENST00000426727	.	.	.	4.41	4.41	0.53225	.	0.192041	0.44902	D	0.000401	T	0.60663	0.2286	M	0.67953	2.075	0.53688	D	0.999973	B;B;B;B	0.17465	0.022;0.01;0.009;0.012	B;B;B;B	0.17979	0.02;0.019;0.01;0.014	T	0.61997	-0.6947	9	0.51188	T	0.08	.	13.5368	0.61652	1.0:0.0:0.0:0.0	.	141;157;141;157	E9PHD0;C9JX13;B7Z3Q2;Q8WVN8	.;.;.;UB2Q2_HUMAN	C	157;157;141	.	ENSP00000267938:Y157C	Y	+	2	0	UBE2Q2	73952846	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.158000	0.94723	1.933000	0.56026	0.519000	0.50382	TAT	.	.		0.313	UBE2Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286475.1	NM_173469		G	76165791	A	G	76165791	3	3	63	1	0	0	0	0	1	0	0	0	16885	449	16	2	624	2	UBE2Q2	15	76165791	Missense_Mutation	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	27030025	76165791	26365601	80	7675										
ACAN	176	hgsc.bcm.edu	37	chr15	89417182	89417182	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cagtgcacagaggggtttgtCcagcgccacatgcccaccat	11	14	0	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr15:89417182C>A	ENST00000561243.1	+	16	7443	c.7443C>A	c.(7441-7443)gtC>gtA	p.V2481V	ACAN_ENST00000352105.7_Intron|ACAN_ENST00000439576.2_Silent_p.V2481V|ACAN_ENST00000559004.1_Silent_p.V2443V			P16112	PGCA_HUMAN	aggrecan	2366					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			AGGGGTTTGTCCAGCGCCACA	0.637																																					p.V2481V		Atlas-SNP	.											.	ACAN	220	.	0			c.C7443A						.						44	55	51					15																	89417182		2153	4241	6394	SO:0001819	synonymous_variant	176	exon17			GTTTGTCCAGCGC	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.7443C>A	chr15.hg19:g.89417182C>A		107.0	0.0		95.0	9.0	NM_013227	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.637	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		A	89417182	C	A	89417182	2	1	63	1	0	0	0	0	0	0	0	1	117	842	30	3		3	ACAN	15	89417182	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	13251391	89417182	13114210	81	7676										
KIF22	3835	hgsc.bcm.edu	37	chr16	29811026	29811026	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cgcttctacctagacacagtCtccgcactcaactttgctgc	6	16	3	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr16:29811026C>T	ENST00000160827.4	+	7	1108	c.1068C>T	c.(1066-1068)gtC>gtT	p.V356V	KIF22_ENST00000569382.2_Silent_p.V288V|KIF22_ENST00000400750.2_5'UTR|KIF22_ENST00000563263.1_3'UTR|KIF22_ENST00000400751.5_Silent_p.V288V|KIF22_ENST00000561482.1_Silent_p.V288V	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22	356	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA repair (GO:0006281)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)			endometrium(1)|large_intestine(1)|lung(11)|skin(1)	14						TAGACACAGTCTCCGCACTCA	0.562																																					p.V356V		Atlas-SNP	.											.	KIF22	29	.	0			c.C1068T						.						58	42	47					16																	29811026		2197	4296	6493	SO:0001819	synonymous_variant	3835	exon7			CACAGTCTCCGCA	D38751	CCDS10653.1, CCDS58444.1	16p11.2	2008-03-03	2003-01-09	2003-01-10	ENSG00000079616	ENSG00000079616		"Kinesins"	6391	protein-coding gene	gene with protein product		603213	"kinesin-like 4"	KNSL4		8599929, 11416179	Standard	NM_007317		Approved	Kid, OBP-1, OBP-2	uc002dts.4	Q14807	OTTHUMG00000097771	ENST00000160827.4:c.1068C>T	chr16.hg19:g.29811026C>T		225.0	0.0		124.0	22.0	NM_007317	B2R5M0|B7Z265|O60845|O94814|Q53F58|Q9BT46	Silent	SNP	ENST00000160827.4	hg19	CCDS10653.1																																																																																			.	.		0.562	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2			T	29811026	C	T	29811026	2	4	63	1	0	0	0	0	0	0	0	1	8299	900	32	3		3	KIF22	16	29811026	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10		29811026	60543727	82	7677										
CDH11	1009	hgsc.bcm.edu	37	chr16	65038624	65038624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	agacccagccacgcttggagCgctgtagcacctgcccctcc	10	18	0	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr16:65038624C>T	ENST00000268603.4	-	3	764	c.149G>A	c.(148-150)cGc>cAc	p.R50H	CDH11_ENST00000394156.3_Missense_Mutation_p.R50H|CDH11_ENST00000569624.1_5'UTR|CDH11_ENST00000566827.1_Intron	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	50					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R50L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		ACGCTTGGAGCGCTGTAGCAC	0.642			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.R50H		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	CDH11_ENST00000394156,NS,carcinoma,-1,2	CDH11	260	.	1	Substitution - Missense(1)	lung(1)	c.G149A						.						55	44	48					16																	65038624		2202	4300	6502	SO:0001583	missense	1009	exon3			TTGGAGCGCTGTA	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.149G>A	chr16.hg19:g.65038624C>T	ENSP00000268603:p.Arg50His	109.0	0.0		95.0	19.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	hg19	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	C	36	5.617948	0.96649	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000536902	T;T	0.00585	6.39;6.39	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.02533	0.0077	L	0.58810	1.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.59193	-0.7500	10	0.87932	D	0	.	18.6407	0.91394	0.0:1.0:0.0:0.0	.	50;50	P55287-2;P55287	.;CAD11_HUMAN	H	50	ENSP00000268603:R50H;ENSP00000377711:R50H	ENSP00000268603:R50H	R	-	2	0	CDH11	63596125	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.250000	0.78287	2.662000	0.90505	0.591000	0.81541	CGC	.	.		0.642	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		T	65038624	C	T	65038624	3	4	63	1	0	0	0	0	1	0	0	0	3099	768	27	1	2285	1	CDH11	16	65038624	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	35227598	65038624	25316129	83	7678										
WWP2	11060	hgsc.bcm.edu	37	chr16	69959360	69959360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gtgcttcgactgaccatgatCccctgggccccctccctcct	8	19	0	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr16:69959360C>T	ENST00000359154.2	+	11	1308	c.1207C>T	c.(1207-1209)Ccc>Tcc	p.P403S	WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Missense_Mutation_p.P403S|WWP2_ENST00000356003.2_Missense_Mutation_p.P403S|WWP2_ENST00000568684.1_5'UTR|WWP2_ENST00000542271.1_Missense_Mutation_p.P287S	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	403					cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TGACCATGATCCCCTGGGCCC	0.522																																					p.P403S		Atlas-SNP	.											.	WWP2	88	.	0			c.C1207T						.						354	351	352					16																	69959360		2198	4300	6498	SO:0001583	missense	11060	exon11			CATGATCCCCTGG	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.1207C>T	chr16.hg19:g.69959360C>T	ENSP00000352069:p.Pro403Ser	129.0	0.0		157.0	40.0	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	hg19	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	C	35	5.547943	0.96488	.	.	ENSG00000198373	ENST00000359154;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.31247	1.52;1.52;1.52;1.5	5.65	5.65	0.86999	WW/Rsp5/WWP (2);	0.096147	0.64402	D	0.000001	T	0.33847	0.0877	M	0.63428	1.95	0.80722	D	1	B	0.33103	0.397	B	0.28709	0.093	T	0.07404	-1.0774	9	.	.	.	.	19.7358	0.96202	0.0:1.0:0.0:0.0	.	403	O00308	WWP2_HUMAN	S	403;403;403;290;287	ENSP00000352069:P403S;ENSP00000396871:P403S;ENSP00000348283:P403S;ENSP00000445616:P287S	.	P	+	1	0	WWP2	68516861	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.802000	0.85969	2.660000	0.90430	0.557000	0.71058	CCC	.	.		0.522	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014		T	69959360	C	T	69959360	3	4	63	1	0	0	0	0	1	0	0	0	17431	855	30	3	1249	3	WWP2	16	69959360	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	4920736	69959360	20395393	84	7679										
FOXL1	2300	hgsc.bcm.edu	37	chr16	86612389	86612389	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gcctcgcccatgctgtatctGtacggtcccgagagacccgg	12	15	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr16:86612389G>C	ENST00000320241.3	+	1	275	c.60G>C	c.(58-60)ctG>ctC	p.L20L		NM_005250.2	NP_005241.1	Q12952	FOXL1_HUMAN	forkhead box L1	20					heart development (GO:0007507)|multicellular organismal development (GO:0007275)|organ morphogenesis (GO:0009887)|Peyer's patch morphogenesis (GO:0061146)|proteoglycan biosynthetic process (GO:0030166)|regulation of Wnt signaling pathway (GO:0030111)|transcription, DNA-templated (GO:0006351)|visceral mesoderm-endoderm interaction involved in midgut development (GO:0007495)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(2)|prostate(3)|skin(1)|urinary_tract(1)	15						TGCTGTATCTGTACGGTCCCG	0.706																																					p.L20L	NSCLC(163;308 2020 10889 11476 18208)	Atlas-SNP	.											.	FOXL1	39	.	0			c.G60C						.						35	39	38					16																	86612389		2195	4295	6490	SO:0001819	synonymous_variant	2300	exon1			GTATCTGTACGGT	AF315075	CCDS10959.1	16q24	2014-07-15			ENSG00000176678	ENSG00000176678		"Forkhead boxes"	3817	protein-coding gene	gene with protein product		603252		FKHL11		7957066	Standard	NM_005250		Approved	FREAC7, FKH6	uc002fjr.3	Q12952	OTTHUMG00000137653	ENST00000320241.3:c.60G>C	chr16.hg19:g.86612389G>C		115.0	0.0		96.0	11.0	NM_005250	Q17RR1|Q9H242	Silent	SNP	ENST00000320241.3	hg19	CCDS10959.1																																																																																			.	.		0.706	FOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269105.2	NM_005250		C	86612389	G	C	86612389	2	2	63	1	0	0	0	0	0	0	0	1	6024	1364	48	4		4	FOXL1	16	86612389	Silent	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	16653029	86612389	3742364	85	7680										
OR3A3	8392	hgsc.bcm.edu	37	chr17	3324438	3324438	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tctactgtgacctcccacagCtcttccagctctcctgctcc	5	19	3	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:3324438C>T	ENST00000291231.1	+	1	577	c.577C>T	c.(577-579)Ctc>Ttc	p.L193F		NM_012373.2	NP_036505.2	P47888	OR3A3_HUMAN	olfactory receptor, family 3, subfamily A, member 3	193				L -> V (in Ref. 7; AAA18351). {ECO:0000305}.	signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(1)	9						CCTCCCACAGCTCTTCCAGCT	0.552																																					p.L193F		Atlas-SNP	.											.	OR3A3	20	.	0			c.C577T						.						76	72	74					17																	3324438		2203	4297	6500	SO:0001583	missense	8392	exon1			CCACAGCTCTTCC	U04688	CCDS11025.1	17p13.3	2012-08-09			ENSG00000159961	ENSG00000159961		"GPCR / Class A : Olfactory receptors"	8284	protein-coding gene	gene with protein product				OR3A6, OR3A7, OR3A8P		8004088, 9500546	Standard	NM_012373		Approved	OR17-201, OR17-137, OR17-16	uc010vrd.2	P47888	OTTHUMG00000090649	ENST00000291231.1:c.577C>T	chr17.hg19:g.3324438C>T	ENSP00000291231:p.Leu193Phe	262.0	0.0		311.0	13.0	NM_012373	Q2VPE4|Q6IFM6|Q9P1Q4|Q9UBE7	Missense_Mutation	SNP	ENST00000291231.1	hg19	CCDS11025.1	.	.	.	.	.	.	.	.	.	.	.	13.48	2.248630	0.39797	.	.	ENSG00000159961	ENST00000291231	T	0.00231	8.49	2.52	2.52	0.30459	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00580	0.0019	M	0.90759	3.145	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.43228	-0.9404	9	0.72032	D	0.01	.	5.1894	0.15201	0.2316:0.5421:0.2263:0.0	.	193	P47888	OR3A3_HUMAN	F	193	ENSP00000291231:L193F	ENSP00000291231:L193F	L	+	1	0	OR3A3	3271188	0.000000	0.05858	0.997000	0.53966	0.989000	0.77384	-0.558000	0.05978	1.692000	0.51112	0.650000	0.86243	CTC	.	.		0.552	OR3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207309.1			T	3324438	C	T	3324438	3	4	63	1	0	0	0	0	1	0	0	0	11048	797	28	3	579	3	OR3A3	17	3324438	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10		3324438	77870772	86	7681										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000420246.2_Missense_Mutation_p.R249S|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R249S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	211.0	0.0		203.0	103.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	63	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	4253096	7577534	73617676	87	7682										
MYH2	4620	hgsc.bcm.edu	37	chr17	10432947	10432947	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ttgactttgtcctcctctgcCtgcaggtcatccagggtctg	10	13	3	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:10432947C>T	ENST00000245503.5	-	24	3435	c.3051G>A	c.(3049-3051)caG>caA	p.Q1017Q	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000532183.2_Intron|MYH2_ENST00000397183.2_Silent_p.Q1017Q	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1017					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CCTCCTCTGCCTGCAGGTCAT	0.478																																					p.Q1017Q		Atlas-SNP	.											.	MYH2	390	.	0			c.G3051A						.						169	162	165					17																	10432947		2203	4297	6500	SO:0001819	synonymous_variant	4620	exon24			CTCTGCCTGCAGG		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.3051G>A	chr17.hg19:g.10432947C>T		335.0	0.0		362.0	166.0	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	hg19	CCDS11156.1																																																																																			.	.		0.478	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		T	10432947	C	T	10432947	2	4	63	1	0	0	0	0	0	0	0	1	10044	680	24	3		3	MYH2	17	10432947	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	2855413	10432947	70762263	88	7683										
CCDC55	84081	hgsc.bcm.edu	37	chr17	28511699	28511699	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	agttcaaaaaacagaataccAcaagagaaatgcattcttca	5	8	3	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:28511699A>G	ENST00000247026.5	+	7	747	c.684A>G	c.(682-684)ccA>ccG	p.P228P	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	228					developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						ACAGAATACCACAAGAGAAAT	0.368																																					p.P228P		Atlas-SNP	.											.	NSRP1	49	.	0			c.A684G						.						60	59	59					17																	28511699		2203	4300	6503	SO:0001819	synonymous_variant	84081	exon7			AATACCACAAGAG	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"coiled-coil domain containing 55"	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.684A>G	chr17.hg19:g.28511699A>G		145.0	0.0		280.0	15.0	NM_032141	Q6FI71	Silent	SNP	ENST00000247026.5	hg19	CCDS11255.1																																																																																			.	.		0.368	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141		G	28511699	A	G	28511699	2	3	63	1	0	0	0	0	0	0	0	1	2827	146	6	2		2	CCDC55	17	28511699	Silent	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	18078752	28511699	52683511	89	7684										
OSBPL7	114881	hgsc.bcm.edu	37	chr17	45885990	45885990	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tgctcgatccttctcttctgGgcctcagcggcctgtatgtt	10	13	3	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:45885990G>A	ENST00000007414.3	-	22	2525	c.2334C>T	c.(2332-2334)gcC>gcT	p.A778A	OSBPL7_ENST00000392507.3_Silent_p.A778A	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	778					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						TTCTCTTCTGGGCCTCAGCGG	0.597																																					p.A778A		Atlas-SNP	.											.	OSBPL7	65	.	0			c.C2334T						.						258	230	240					17																	45885990		2203	4300	6503	SO:0001819	synonymous_variant	114881	exon22			CTTCTGGGCCTCA	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.2334C>T	chr17.hg19:g.45885990G>A		305.0	0.0		237.0	33.0	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	hg19	CCDS11515.1																																																																																			.	.		0.597	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		A	45885990	G	A	45885990	2	1	63	1	0	0	0	0	0	0	0	1	11291	1219	43	3		3	OSBPL7	17	45885990	Silent	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	17374291	45885990	35309220	90	7685										
SLC16A6	9120	hgsc.bcm.edu	37	chr17	66267772	66267772	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gaggctgtatctccagccaaTgcgctccttcagagccatga	10	13	2	2	rs139961659		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:66267772T>C	ENST00000327268.4	-	6	693	c.529A>G	c.(529-531)Att>Gtt	p.I177V	ARSG_ENST00000448504.2_Intron|SLC16A6_ENST00000580666.1_Missense_Mutation_p.I177V	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	177					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	CTCCAGCCAATGCGCTCCTTC	0.473																																					p.I177V		Atlas-SNP	.											.	SLC16A6	56	.	0			c.A529G						.	T	VAL/ILE,VAL/ILE,	1,4405	2.1+/-5.4	0,1,2202	44	43	44		529,529,	0.9	0	17	dbSNP_134	44	0,8600		0,0,4300	no	missense,missense,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	29,29,	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign,	177/524,177/524,	66267772	1,13005	2203	4300	6503	SO:0001583	missense	9120	exon6			AGCCAATGCGCTC	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"Solute carriers"	10927	protein-coding gene	gene with protein product		603880	"solute carrier family 16 (monocarboxylic acid transporters), member 6", "solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.529A>G	chr17.hg19:g.66267772T>C	ENSP00000319991:p.Ile177Val	93.0	0.0		95.0	19.0	NM_001174166	Q6P1X3	Missense_Mutation	SNP	ENST00000327268.4	hg19	CCDS11675.1	.	.	.	.	.	.	.	.	.	.	T	8.162	0.789772	0.16258	2.27E-4	0.0	ENSG00000108932	ENST00000327268	T	0.36699	1.24	4.33	0.903	0.19296	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.248067	0.40469	N	0.001095	T	0.30947	0.0781	L	0.55834	1.745	0.26325	N	0.9776	B	0.20459	0.045	B	0.26693	0.072	T	0.26258	-1.0108	10	0.52906	T	0.07	.	7.6143	0.28148	0.0:0.2577:0.0:0.7423	.	177	O15403	MOT7_HUMAN	V	177	ENSP00000319991:I177V	ENSP00000319991:I177V	I	-	1	0	SLC16A6	63779367	0.998000	0.40836	0.002000	0.10522	0.871000	0.50021	3.060000	0.49955	-0.043000	0.13513	0.397000	0.26171	ATT	.	T|1.000;C|0.000		0.473	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694		C	66267772	T	C	66267772	3	2	63	1	0	0	0	0	1	0	0	0	14427	1464	51	2	1050	2	SLC16A6	17	66267772	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	20381782	66267772	14927438	91	7686										
TMC6	11322	hgsc.bcm.edu	37	chr17	76113656	76113656	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gccgcctccaggtggcgcacCcacaccctgccggcctcgta	11	20	0	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:76113656C>A	ENST00000590602.1	-	17	2250	c.2091G>T	c.(2089-2091)tgG>tgT	p.W697C	TMC6_ENST00000306591.7_Intron|TMC6_ENST00000322933.4_Missense_Mutation_p.W276C|TMC6_ENST00000322914.3_Missense_Mutation_p.W697C|TMC6_ENST00000392467.3_Missense_Mutation_p.W697C|TMC6_ENST00000591436.1_Missense_Mutation_p.W276C|TMC6_ENST00000592076.1_Intron			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	697					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GGTGGCGCACCCACACCCTGC	0.667																																					p.W697C		Atlas-SNP	.											.	TMC6	42	.	0			c.G2091T						.						12	13	13					17																	76113656		2186	4266	6452	SO:0001583	missense	11322	exon17			GCGCACCCACACC	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"epidermodysplasia verruciformis 1"	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.2091G>T	chr17.hg19:g.76113656C>A	ENSP00000465261:p.Trp697Cys	86.0	0.0		67.0	20.0	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	hg19	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476388	0.44044	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000322933	T;T;T	0.71934	-0.3;-0.3;-0.61	3.69	3.69	0.42338	.	0.204709	0.45606	D	0.000343	T	0.82042	0.4951	M	0.79693	2.465	0.80722	D	1	P;D	0.76494	0.801;0.999	P;D	0.69654	0.447;0.965	D	0.84070	0.0379	10	0.66056	D	0.02	-12.8777	11.0062	0.47635	0.1865:0.8135:0.0:0.0	.	697;276	Q7Z403;Q7Z403-3	TMC6_HUMAN;.	C	697;697;276	ENSP00000313408:W697C;ENSP00000376260:W697C;ENSP00000313479:W276C	ENSP00000313408:W697C	W	-	3	0	TMC6	73625251	1.000000	0.71417	1.000000	0.80357	0.178000	0.23041	5.227000	0.65305	1.894000	0.54839	0.555000	0.69702	TGG	.	.		0.667	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			A	76113656	C	A	76113656	3	1	63	1	0	0	0	0	1	0	0	0	16004	624	22	3	342	3	TMC6	17	76113656	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	9845884	76113656	5081554	92	7687										
NDC80	10403	hgsc.bcm.edu	37	chr18	2610833	2610833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ttgcaacgtctgttagagatGgttgctacacatgttgggtc	12	7	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:2610833G>A	ENST00000261597.4	+	16	1946	c.1764G>A	c.(1762-1764)atG>atA	p.M588I		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	588	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						TGTTAGAGATGGTTGCTACAC	0.373																																					p.M588I		Atlas-SNP	.											.	NDC80	62	.	0			c.G1764A						.						169	149	156					18																	2610833		2203	4300	6503	SO:0001583	missense	10403	exon16			AGAGATGGTTGCT	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1764G>A	chr18.hg19:g.2610833G>A	ENSP00000261597:p.Met588Ile	213.0	0.0		174.0	22.0	NM_006101	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	hg19	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.425834	0.25726	.	.	ENSG00000080986	ENST00000261597	T	0.46451	0.87	5.43	4.5	0.54988	.	0.264830	0.45606	D	0.000348	T	0.31702	0.0805	L	0.44542	1.39	0.30725	N	0.74784	B	0.20164	0.042	B	0.13407	0.009	T	0.15752	-1.0426	10	0.32370	T	0.25	-6.95	8.2722	0.31851	0.0842:0.1595:0.7563:0.0	.	588	O14777	NDC80_HUMAN	I	588	ENSP00000261597:M588I	ENSP00000261597:M588I	M	+	3	0	NDC80	2600833	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	1.917000	0.39996	2.547000	0.85894	0.650000	0.86243	ATG	.	.		0.373	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101		A	2610833	G	A	2610833	3	1	63	1	0	0	0	0	1	0	0	0	10251	1348	47	3	1822	3	NDC80	18	2610833	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10		2610833	75466415	93	7688										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7023225	7023225	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cagcacacctttcacagtggGcgccatctgtgttccccagg	10	15	2	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:7023225G>T	ENST00000389658.3	-	19	2732	c.2639C>A	c.(2638-2640)gCc>gAc	p.A880D		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	880	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTCACAGTGGGCGCCATCTGT	0.602																																					p.A880D		Atlas-SNP	.											.	LAMA1	458	.	0			c.C2639A						.						94	70	78					18																	7023225		2203	4300	6503	SO:0001583	missense	284217	exon19			CAGTGGGCGCCAT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2639C>A	chr18.hg19:g.7023225G>T	ENSP00000374309:p.Ala880Asp	122.0	0.0		119.0	10.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	G	5.205	0.223300	0.09863	.	.	ENSG00000101680	ENST00000389658	T	0.61158	0.13	5.47	4.56	0.56223	EGF-like, laminin (4);	0.881961	0.09731	N	0.763140	T	0.39545	0.1082	N	0.04260	-0.245	0.09310	N	1	P	0.40970	0.734	P	0.46049	0.502	T	0.12041	-1.0563	10	0.32370	T	0.25	.	5.852	0.18697	0.0736:0.3403:0.4635:0.1226	.	880	P25391	LAMA1_HUMAN	D	880	ENSP00000374309:A880D	ENSP00000374309:A880D	A	-	2	0	LAMA1	7013225	0.000000	0.05858	0.952000	0.39060	0.605000	0.37080	0.226000	0.17776	2.578000	0.87016	0.643000	0.83706	GCC	.	.		0.602	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	7023225	G	T	7023225	3	4	63	1	0	0	0	0	1	0	0	0	8614	1203	42	3	6768	3	LAMA1	18	7023225	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	4412392	7023225	71054023	94	7689										
CEP192	55125	hgsc.bcm.edu	37	chr18	13049219	13049219	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tagtatgtctgatacttgggAtttatctttgcccaaagaac	8	7	2	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:13049219A>T	ENST00000325971.8	+	14	2234	c.641A>T	c.(640-642)gAt>gTt	p.D214V	CEP192_ENST00000506447.1_Missense_Mutation_p.D810V|CEP192_ENST00000430049.2_Missense_Mutation_p.D335V			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	214					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GATACTTGGGATTTATCTTTG	0.383																																					p.D810V		Atlas-SNP	.											.	CEP192	340	.	0			c.A2429T						.						103	101	102					18																	13049219		2203	4300	6503	SO:0001583	missense	55125	exon16			CTTGGGATTTATC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.641A>T	chr18.hg19:g.13049219A>T	ENSP00000317156:p.Asp214Val	72.0	0.0		80.0	11.0	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	A	19.16	3.774142	0.69992	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.07908	3.15;3.17;3.17	5.27	5.27	0.74061	.	0.000000	0.49305	D	0.000160	T	0.25419	0.0618	M	0.62723	1.935	0.52501	D	0.999957	D;D;D	0.76494	0.99;0.996;0.999	P;D;D	0.71656	0.901;0.931;0.974	T	0.00485	-1.1711	10	0.41790	T	0.15	-12.6436	15.4964	0.75653	1.0:0.0:0.0:0.0	.	335;810;214	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	V	810;214;214;335	ENSP00000427550:D810V;ENSP00000317156:D214V;ENSP00000389190:D335V	ENSP00000317156:D214V	D	+	2	0	CEP192	13039219	0.999000	0.42202	1.000000	0.80357	0.900000	0.52787	3.468000	0.53086	2.131000	0.65755	0.528000	0.53228	GAT	.	.		0.383	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		T	13049219	A	T	13049219	3	4	63	1	0	0	0	0	1	0	0	0	3253	333	12	4	2487	4	CEP192	18	13049219	Missense_Mutation	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	6025994	13049219	65028029	95	7690										
ABHD3	171586	hgsc.bcm.edu	37	chr18	19263896	19263896	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cttaccaagagattctccccCgccactcctctgttgttaaa	5	15	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:19263896C>T	ENST00000289119.2	-	4	679	c.540G>A	c.(538-540)gcG>gcA	p.A180A	ABHD3_ENST00000578270.1_5'UTR|RP11-13N13.6_ENST00000578583.1_RNA|MIR320C1_ENST00000408566.1_RNA|ABHD3_ENST00000579875.1_Intron|ABHD3_ENST00000580981.1_Intron	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	180						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						GATTCTCCCCCGCCACTCCTC	0.279																																					p.A180A		Atlas-SNP	.											.	ABHD3	32	.	0			c.G540A						.						67	75	72					18																	19263896		2203	4294	6497	SO:0001819	synonymous_variant	171586	exon4			CTCCCCCGCCACT	AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201		"Abhydrolase domain containing"	18718	protein-coding gene	gene with protein product		612197					Standard	NM_138340		Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.540G>A	chr18.hg19:g.19263896C>T		189.0	0.0		193.0	46.0	NM_138340	B0YIV0|B7Z5C2|O43411	Silent	SNP	ENST00000289119.2	hg19	CCDS32802.1																																																																																			.	.		0.279	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1			T	19263896	C	T	19263896	2	4	63	1	0	0	0	0	0	0	0	1	83	639	23	1		1	ABHD3	18	19263896	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	6214677	19263896	58813352	96	7691										
KIAA1328	57536	hgsc.bcm.edu	37	chr18	34646878	34646878	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cagtagaaaaagcactctccAgtgttcatctgtggaactgg	10	9	3	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:34646878A>G	ENST00000280020.5	+	7	624	c.602A>G	c.(601-603)cAg>cGg	p.Q201R	KIAA1328_ENST00000591619.1_Missense_Mutation_p.Q197R|KIAA1328_ENST00000435985.2_5'UTR|KIAA1328_ENST00000586501.1_5'UTR|KIAA1328_ENST00000543923.1_Missense_Mutation_p.Q93R|KIAA1328_ENST00000586135.1_5'UTR	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	201										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		AGCACTCTCCAGTGTTCATCT	0.413																																					p.Q201R		Atlas-SNP	.											.	KIAA1328	39	.	0			c.A602G						.						65	61	62					18																	34646878		1873	4103	5976	SO:0001583	missense	57536	exon7			CTCTCCAGTGTTC	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.602A>G	chr18.hg19:g.34646878A>G	ENSP00000280020:p.Gln201Arg	166.0	0.0		142.0	33.0	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Missense_Mutation	SNP	ENST00000280020.5	hg19	CCDS45855.1	.	.	.	.	.	.	.	.	.	.	A	8.462	0.855430	0.17106	.	.	ENSG00000150477	ENST00000543923;ENST00000280020;ENST00000383055	T;T	0.41065	1.01;2.32	6.17	-12.3	0.00002	.	0.832930	0.10897	N	0.622016	T	0.21145	0.0509	N	0.20986	0.625	0.09310	N	0.999991	B;B	0.14438	0.01;0.002	B;B	0.11329	0.006;0.004	T	0.36625	-0.9740	10	0.09590	T	0.72	.	16.9504	0.86244	0.7855:0.1442:0.0702:0.0	.	201;201	A8K8C3;Q86T90	.;K1328_HUMAN	R	93;201;201	ENSP00000441359:Q93R;ENSP00000280020:Q201R	ENSP00000280020:Q201R	Q	+	2	0	KIAA1328	32900876	0.000000	0.05858	0.000000	0.03702	0.792000	0.44763	-0.845000	0.04340	-2.876000	0.00321	-0.408000	0.06270	CAG	.	.		0.413	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776		G	34646878	A	G	34646878	3	3	63	1	0	0	0	0	1	0	0	0	8234	188	7	2	628	2	KIAA1328	18	34646878	Missense_Mutation	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	15382982	34646878	43430370	97	7692										
DCC	1630	hgsc.bcm.edu	37	chr18	51025767	51025767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	accaagcagaaccatccccaCagcttgtgttcgaccaactc	6	16	0	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:51025767C>T	ENST00000442544.2	+	27	4614	c.3998C>T	c.(3997-3999)aCa>aTa	p.T1333I	DCC_ENST00000581580.1_Missense_Mutation_p.T966I|RP11-671P2.1_ENST00000582064.1_RNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1333					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		ACCATCCCCACAGCTTGTGTT	0.532																																					p.T1333I		Atlas-SNP	.											.	DCC	360	.	0			c.C3998T						.						238	181	200					18																	51025767		2203	4300	6503	SO:0001583	missense	1630	exon27			TCCCCACAGCTTG	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.3998C>T	chr18.hg19:g.51025767C>T	ENSP00000389140:p.Thr1333Ile	171.0	0.0		84.0	9.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599054	0.46318	.	.	ENSG00000187323	ENST00000442544	T	0.49432	0.78	6.17	6.17	0.99709	Neogenin, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.68897	0.3051	M	0.65498	2.005	0.53005	D	0.999961	D	0.67145	0.996	D	0.70227	0.968	T	0.68198	-0.5472	10	0.72032	D	0.01	-6.4138	19.6509	0.95805	0.0:1.0:0.0:0.0	.	1333	P43146	DCC_HUMAN	I	1333	ENSP00000389140:T1333I	ENSP00000389140:T1333I	T	+	2	0	DCC	49279765	1.000000	0.71417	0.969000	0.41365	0.971000	0.66376	6.259000	0.72494	2.941000	0.99782	0.655000	0.94253	ACA	.	.		0.532	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	51025767	C	T	51025767	3	4	63	1	0	0	0	0	1	0	0	0	4284	478	17	3	4104	3	DCC	18	51025767	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	16378889	51025767	27051481	98	7693										
SEMA6B	10501	hgsc.bcm.edu	37	chr19	4550257	4550257	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gcgctggaggcattgtactgCatcccgggggctgcgcagca	16	12	0	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:4550257C>T	ENST00000586582.1	-	12	1459	c.1149G>A	c.(1147-1149)atG>atA	p.M383I	SEMA6B_ENST00000301293.3_Missense_Mutation_p.M383I|SEMA6B_ENST00000586965.1_Missense_Mutation_p.M383I	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	383	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		CATTGTACTGCATCCCGGGGG	0.622																																					p.M383I		Atlas-SNP	.											.	SEMA6B	51	.	0			c.G1149A						.						61	53	56					19																	4550257		2203	4300	6503	SO:0001583	missense	10501	exon12			GTACTGCATCCCG	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"Semaphorins"	10739	protein-coding gene	gene with protein product	"Sema VIb", "semaphorin Z", "semaphorin VIB"	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.1149G>A	chr19.hg19:g.4550257C>T	ENSP00000467290:p.Met383Ile	138.0	0.0		107.0	26.0	NM_032108	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	hg19	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	.	6.001	0.368594	0.11352	.	.	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.10382	2.88	2.6	1.5	0.22942	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.264529	0.37095	U	0.002241	T	0.08403	0.0209	L	0.39147	1.195	0.22446	N	0.9991	B;B	0.19445	0.036;0.008	B;B	0.29524	0.103;0.065	T	0.34825	-0.9813	10	0.20519	T	0.43	.	6.3431	0.21335	0.209:0.5869:0.2041:0.0	.	383;383	B4DT36;Q9H3T3	.;SEM6B_HUMAN	I	383	ENSP00000301293:M383I	ENSP00000301292:M383I	M	-	3	0	SEMA6B	4501257	0.000000	0.05858	0.925000	0.36789	0.541000	0.35023	-0.102000	0.10956	0.640000	0.30582	0.478000	0.44815	ATG	.	.		0.622	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108		T	4550257	C	T	4550257	3	4	63	1	0	0	0	0	1	0	0	0	14055	710	25	3	1541	3	SEMA6B	19	4550257	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10		4550257	54578726	99	7694										
MUC16	94025	hgsc.bcm.edu	37	chr19	9011461	9011461	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	agacggtggctgcagatggcAtccattccagtggctgcccc	13	13	0	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:9011461A>G	ENST00000397910.4	-	36	38975	c.38772T>C	c.(38770-38772)gaT>gaC	p.D12924D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12926	SEA 6. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGCAGATGGCATCCATTCCAG	0.542																																					p.D12924D		Atlas-SNP	.											.	MUC16	4315	.	0			c.T38772C						.						149	133	138					19																	9011461		1933	4133	6066	SO:0001819	synonymous_variant	94025	exon36			GATGGCATCCATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.38772T>C	chr19.hg19:g.9011461A>G		241.0	0.0		154.0	12.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9011461	A	G	9011461	2	3	63	1	0	0	0	0	0	0	0	1	9982	214	8	2		2	MUC16	19	9011461	Silent	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	4461204	9011461	50117522	100	7695										
ZNF878	729747	hgsc.bcm.edu	37	chr19	12155914	12155914	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cacacacactgctttcatatGattgtactccaggagttttc	6	11	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:12155914G>A	ENST00000547628.1	-	4	439	c.302C>T	c.(301-303)tCa>tTa	p.S101L	CTD-2006C1.2_ENST00000591838.1_RNA|ZNF878_ENST00000602107.1_Missense_Mutation_p.S148L|CTD-2006C1.10_ENST00000547473.1_Intron|CTD-2006C1.2_ENST00000591898.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA	NM_001080404.2	NP_001073873.2	C9JN71	ZN878_HUMAN	zinc finger protein 878	101					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						GCTTTCATATGATTGTACTCC	0.433																																					p.S101L		Atlas-SNP	.											.	ZNF878	172	.	0			c.C302T						.						66	62	63					19																	12155914		2018	4219	6237	SO:0001583	missense	729747	exon4			TCATATGATTGTA		CCDS45984.1, CCDS45984.2	19p13.2	2013-01-08				ENSG00000257446		"Zinc fingers, C2H2-type", "-"	37246	protein-coding gene	gene with protein product							Standard	NM_001080404		Approved		uc021upl.1	C9JN71		ENST00000547628.1:c.302C>T	chr19.hg19:g.12155914G>A	ENSP00000447931:p.Ser101Leu	142.0	0.0		124.0	31.0	NM_001080404		Missense_Mutation	SNP	ENST00000547628.1	hg19	CCDS45984.2	.	.	.	.	.	.	.	.	.	.	G	6.743	0.505917	0.12883	.	.	ENSG00000257446;ENSG00000232371	ENST00000547628;ENST00000440730	T	0.06687	3.27	1.3	1.3	0.21679	.	.	.	.	.	T	0.11922	0.0290	L	0.40543	1.245	0.09310	N	1	D	0.60575	0.988	P	0.53313	0.723	T	0.20140	-1.0284	9	0.44086	T	0.13	.	8.094	0.30818	0.0:0.0:1.0:0.0	.	101	C9JN71	ZN878_HUMAN	L	101;148	ENSP00000447931:S101L	ENSP00000447931:S101L	S	-	2	0	AC022415.4;ZNF878	12016914	0.000000	0.05858	0.003000	0.11579	0.025000	0.11179	0.400000	0.20932	0.675000	0.31264	0.313000	0.20887	TCA	.	.		0.433	ZNF878-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403723.1	NM_001080404		A	12155914	G	A	12155914	3	1	63	1	0	0	0	0	1	0	0	0	18211	1294	45	3	1297	3	ZNF878	19	12155914	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	3144453	12155914	46973069	101	7696										
ZNF709	163051	hgsc.bcm.edu	37	chr19	12575313	12575313	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	acactgtttacattcataggGtttctctccagtgtgaattc	7	9	2	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:12575313G>A	ENST00000397732.3	-	4	1594	c.1423C>T	c.(1423-1425)Ccc>Tcc	p.P475S	CTD-3105H18.18_ENST00000598753.1_Intron|ZNF709_ENST00000428311.1_Missense_Mutation_p.P475S	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	475					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|upper_aerodigestive_tract(3)	6						CATTCATAGGGTTTCTCTCCA	0.403																																					p.P475S	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											.	ZNF709	80	.	0			c.C1423T						.						90	96	94					19																	12575313		2203	4300	6503	SO:0001583	missense	163051	exon4			CATAGGGTTTCTC	AK095600	CCDS42504.1	19p13.2	2013-01-08			ENSG00000242852	ENSG00000242852		"Zinc fingers, C2H2-type", "-"	20629	protein-coding gene	gene with protein product							Standard	NM_152601		Approved	FLJ38281	uc002mtv.4	Q8N972	OTTHUMG00000156406	ENST00000397732.3:c.1423C>T	chr19.hg19:g.12575313G>A	ENSP00000380840:p.Pro475Ser	51.0	0.0		42.0	8.0	NM_152601	A8K4E6	Missense_Mutation	SNP	ENST00000397732.3	hg19	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.449384	0.84101	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	T;T	0.16743	2.32;2.32	3.05	3.05	0.35203	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33772	N	0.004580	T	0.32645	0.0836	L	0.53780	1.695	0.31497	N	0.665273	D	0.89917	1.0	D	0.80764	0.994	T	0.19516	-1.0303	10	0.66056	D	0.02	.	10.1848	0.42991	0.0:0.2053:0.7947:0.0	.	475	Q8N972	ZN709_HUMAN	S	475	ENSP00000380840:P475S;ENSP00000404127:P475S	ENSP00000404127:P475S	P	-	1	0	ZNF709;CTD-2192J16.17	12436313	0.554000	0.26522	0.121000	0.21740	0.998000	0.95712	2.607000	0.46300	2.032000	0.59987	0.591000	0.81541	CCC	.	.		0.403	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		A	12575313	G	A	12575313	3	1	63	1	0	0	0	0	1	0	0	0	18128	1261	44	3	506	3	ZNF709	19	12575313	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	419399	12575313	46553670	102	7697										
U2AF1L4	199746	hgsc.bcm.edu	37	chr19	36236067	36236067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gtgaagccgggagcaccggtCcccgtgccggcagaccccga	15	16	0	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:36236067C>T	ENST00000412391.2	-	2	104	c.91G>A	c.(91-93)Gac>Aac	p.D31N	PSENEN_ENST00000587708.2_5'UTR|AC002398.9_ENST00000591613.2_5'Flank|IGFLR1_ENST00000344990.3_5'Flank|U2AF1L4_ENST00000292879.5_Missense_Mutation_p.D31N|IGFLR1_ENST00000246532.1_5'Flank|IGFLR1_ENST00000588992.1_5'Flank|AC002398.11_ENST00000591091.1_RNA|AC002398.11_ENST00000585365.1_RNA|U2AF1L4_ENST00000588100.1_5'UTR|PSENEN_ENST00000222266.2_5'Flank|U2AF1L4_ENST00000378975.3_Missense_Mutation_p.D31N|AD000671.6_ENST00000589807.1_Missense_Mutation_p.D31N|IGFLR1_ENST00000592537.1_5'Flank|PSENEN_ENST00000591949.1_5'Flank			Q8WU68	U2AF4_HUMAN	U2 small nuclear RNA auxiliary factor 1-like 4	31					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GAGCACCGGTCCCCGTGCCGG	0.622																																					p.D31N		Atlas-SNP	.											.	U2AF1L4	34	.	0			c.G91A						.						37	44	42					19																	36236067		2203	4300	6503	SO:0001583	missense	199746	exon2			ACCGGTCCCCGTG	BC021186, AY569437	CCDS12473.1, CCDS42551.1	19q13.13	2013-02-12	2006-04-12	2006-04-12		ENSG00000161265		"RNA binding motif (RRM) containing"	23020	protein-coding gene	gene with protein product		601080	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 3", "U2 small nuclear RNA auxiliary factor 1-like 3"	U2AF1L3		8586425, 11739736	Standard	NM_001040425		Approved	MGC33901, U2af26	uc002obf.3	Q8WU68		ENST00000412391.2:c.91G>A	chr19.hg19:g.36236067C>T	ENSP00000397645:p.Asp31Asn	78.0	0.0		56.0	19.0	NM_144987	A6NKI8|Q56UU3	Missense_Mutation	SNP	ENST00000412391.2	hg19		.	.	.	.	.	.	.	.	.	.	C	18.77	3.695790	0.68386	.	.	ENSG00000161265	ENST00000292879;ENST00000378975;ENST00000412391	T;T;T	0.48201	0.82;0.82;0.82	5.19	3.09	0.35607	.	0.673695	0.14230	N	0.332819	T	0.57814	0.2079	.	.	.	0.80722	D	1	P;P	0.49862	0.929;0.918	P;P	0.55303	0.729;0.773	T	0.56195	-0.8019	9	0.56958	D	0.05	-2.2858	9.2691	0.37659	0.0:0.8267:0.0:0.1733	.	31;31	Q8WU68-2;Q8WU68-3	.;.	N	31	ENSP00000292879:D31N;ENSP00000368258:D31N;ENSP00000397645:D31N	ENSP00000292879:D31N	D	-	1	0	U2AF1L4	40927907	1.000000	0.71417	1.000000	0.80357	0.085000	0.17905	3.562000	0.53777	0.780000	0.33566	0.643000	0.83706	GAC	.	.		0.622	U2AF1L4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144987		T	36236067	C	T	36236067	3	4	63	1	0	0	0	0	1	0	0	0	16837	855	30	3	595	3	U2AF1L4	19	36236067	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	23660754	36236067	22892916	103	7698										
PSMC4	5704	hgsc.bcm.edu	37	chr19	40485836	40485836	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gagaatgcacctgccatcatCttcatagacgagattgatgc	9	10	3	4			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:40485836C>G	ENST00000157812.2	+	7	984	c.786C>G	c.(784-786)atC>atG	p.I262M	PSMC4_ENST00000455878.2_Missense_Mutation_p.I231M	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	262					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTGCCATCATCTTCATAGACG	0.572																																					p.I262M	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.C786G						.						71	69	69					19																	40485836		2203	4300	6503	SO:0001583	missense	5704	exon7			CATCATCTTCATA	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9551	protein-coding gene	gene with protein product	"protease 26S subunit 6", "Tat-binding protein 7", "MB67 interacting protein"	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.786C>G	chr19.hg19:g.40485836C>G	ENSP00000157812:p.Ile262Met	188.0	0.0		161.0	34.0	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Missense_Mutation	SNP	ENST00000157812.2	hg19	CCDS12547.1	.	.	.	.	.	.	.	.	.	.	c	11.95	1.792327	0.31685	.	.	ENSG00000013275	ENST00000157812;ENST00000455878	D;D	0.95949	-3.86;-3.86	6.06	2.25	0.28309	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.046718	0.85682	D	0.000000	D	0.97068	0.9042	M	0.88241	2.94	0.54753	D	0.999985	P;D	0.63046	0.596;0.992	P;D	0.80764	0.498;0.994	D	0.95386	0.8477	10	0.66056	D	0.02	-9.3148	4.3152	0.10990	0.2766:0.5069:0.1348:0.0817	.	231;262	P43686-2;P43686	.;PRS6B_HUMAN	M	262;231	ENSP00000157812:I262M;ENSP00000413869:I231M	ENSP00000157812:I262M	I	+	3	3	PSMC4	45177676	1.000000	0.71417	1.000000	0.80357	0.027000	0.11550	3.832000	0.55783	0.849000	0.35215	-0.176000	0.13171	ATC	.	.		0.572	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503		G	40485836	C	G	40485836	3	3	63	1	0	0	0	0	1	0	0	0	12701	903	32	4	812	4	PSMC4	19	40485836	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	4249769	40485836	18643147	104	7699										
LYPD3	27076	hgsc.bcm.edu	37	chr19	43969676	43969676	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	agcagcagcagcagccagccTgcagtccagatcatggcctg	12	14	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:43969676T>A	ENST00000244333.3	-	1	136	c.48A>T	c.(46-48)gcA>gcT	p.A16A		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	16					cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				GCAGCCAGCCTGCAGTCCAGA	0.692																																					p.A16A		Atlas-SNP	.											.	LYPD3	24	.	0			c.A48T						.						94	82	86					19																	43969676		2203	4300	6503	SO:0001819	synonymous_variant	27076	exon1			CCAGCCTGCAGTC	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.48A>T	chr19.hg19:g.43969676T>A		64.0	0.0		56.0	12.0	NM_014400	Q9UJ74	Silent	SNP	ENST00000244333.3	hg19	CCDS12620.1																																																																																			.	.		0.692	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		A	43969676	T	A	43969676	2	1	63	1	0	0	0	0	0	0	0	1	9120	1567	55	4		4	LYPD3	19	43969676	Silent	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	3483840	43969676	15159307	105	7700										
KLC3	147700	hgsc.bcm.edu	37	chr19	45853937	45853937	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tcactctccaagatccgtgaGtctatcaggcgaggaagtga	11	10	4	3			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:45853937G>A	ENST00000391946.2	+	11	1413	c.1311G>A	c.(1309-1311)gaG>gaA	p.E437E	KLC3_ENST00000470402.1_Silent_p.E451E|ERCC2_ENST00000391945.4_3'UTR|KLC3_ENST00000585434.1_Silent_p.E436E	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	437					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		AGATCCGTGAGTCTATCAGGC	0.682																																					p.E437E		Atlas-SNP	.											.	KLC3	37	.	0			c.G1311A						.						21	26	24					19																	45853937		1938	4126	6064	SO:0001819	synonymous_variant	147700	exon11			CCGTGAGTCTATC	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"Tetratricopeptide (TTC) repeat domain containing"	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.1311G>A	chr19.hg19:g.45853937G>A		184.0	0.0		159.0	37.0	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Silent	SNP	ENST00000391946.2	hg19	CCDS12660.2																																																																																			.	.		0.682	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275		A	45853937	G	A	45853937	2	1	63	1	0	0	0	0	0	0	0	1	8344	1020	36	3		3	KLC3	19	45853937	Silent	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	1884261	45853937	13275046	106	7701										
ERCC1	2067	hgsc.bcm.edu	37	chr19	45924624	45924624	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ggtgtccacagtgggaaggcTctgtgtagatcggaataagg	16	6	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:45924624T>C	ENST00000300853.3	-	3	724	c.133A>G	c.(133-135)Agc>Ggc	p.S45G	ERCC1_ENST00000589165.1_Missense_Mutation_p.S45G|ERCC1_ENST00000340192.7_Missense_Mutation_p.S45G|ERCC1_ENST00000591636.1_Missense_Mutation_p.S45G|ERCC1_ENST00000013807.5_Missense_Mutation_p.S45G|ERCC1_ENST00000423698.2_Intron	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	45					cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		GTGGGAAGGCTCTGTGTAGAT	0.622								Nucleotide excision repair (NER)																													p.S45G		Atlas-SNP	.											.	ERCC1	46	.	0			c.A133G						.						67	64	65					19																	45924624		2203	4300	6503	SO:0001583	missense	2067	exon3			GAAGGCTCTGTGT		CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.133A>G	chr19.hg19:g.45924624T>C	ENSP00000300853:p.Ser45Gly	74.0	0.0		74.0	10.0	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Missense_Mutation	SNP	ENST00000300853.3	hg19	CCDS12662.1	.	.	.	.	.	.	.	.	.	.	T	11.47	1.649248	0.29336	.	.	ENSG00000012061	ENST00000300853;ENST00000340192;ENST00000013807	T;T;T	0.48522	0.84;0.83;0.81	4.25	3.21	0.36854	.	0.868449	0.10211	N	0.702162	T	0.31420	0.0796	N	0.24115	0.695	0.09310	N	1	B;B;B	0.26318	0.146;0.049;0.02	B;B;B	0.22152	0.038;0.016;0.016	T	0.19712	-1.0297	10	0.34782	T	0.22	-6.0974	6.72	0.23325	0.0:0.1103:0.0:0.8897	.	45;45;45	Q7Z7F5;Q96S40;P07992	.;.;ERCC1_HUMAN	G	45	ENSP00000300853:S45G;ENSP00000345203:S45G;ENSP00000013807:S45G	ENSP00000013807:S45G	S	-	1	0	ERCC1	50616464	0.519000	0.26242	0.009000	0.14445	0.068000	0.16541	1.701000	0.37825	0.753000	0.32945	0.402000	0.26972	AGC	.	.		0.622	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983		C	45924624	T	C	45924624	3	2	63	1	0	0	0	0	1	0	0	0	5214	1551	54	2	921	2	ERCC1	19	45924624	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	70687	45924624	13204359	107	7702										
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47569634	47569634	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tactggcaaaagggggaggcCgtggggtcgaagcctttaaa	16	7	0	0			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:47569634C>A	ENST00000253048.5	-	15	3928	c.3891G>T	c.(3889-3891)acG>acT	p.T1297T	ZC3H4_ENST00000594019.1_5'UTR	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	1297							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		AGGGGGAGGCCGTGGGGTCGA	0.627																																					p.T1297T		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G3891T						.						9	11	10					19																	47569634		1904	4069	5973	SO:0001819	synonymous_variant	23211	exon15			GGAGGCCGTGGGG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"Zinc fingers, CCCH-type domain containing"	17808	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 7"	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.3891G>T	chr19.hg19:g.47569634C>A		73.0	0.0		64.0	12.0	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	hg19	CCDS42582.1																																																																																			.	.		0.627	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			A	47569634	C	A	47569634	2	1	63	1	0	0	0	0	0	0	0	1	17585	639	23	1		1	ZC3H4	19	47569634	Silent	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	1645010	47569634	11559349	108	7703										
KCNA7	3743	hgsc.bcm.edu	37	chr19	49574011	49574011	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tgcttggacagaccaggaggCgtaccagcagctcaaaggag	14	10	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:49574011C>A	ENST00000221444.1	-	2	1035	c.680G>T	c.(679-681)cGc>cTc	p.R227L		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	227					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	GACCAGGAGGCGTACCAGCAG	0.527																																					p.R227L	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											.	KCNA7	30	.	0			c.G680T						.						146	106	119					19																	49574011		2203	4300	6503	SO:0001583	missense	3743	exon2			AGGAGGCGTACCA	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.680G>T	chr19.hg19:g.49574011C>A	ENSP00000221444:p.Arg227Leu	83.0	0.0		67.0	20.0	NM_031886	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	hg19	CCDS12755.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.349632	0.61183	.	.	ENSG00000104848	ENST00000221444	D	0.98684	-5.07	4.49	4.49	0.54785	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	H	0.98818	4.34	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.97677	1.0170	10	0.87932	D	0	.	16.3041	0.82841	0.0:1.0:0.0:0.0	.	227	Q96RP8	KCNA7_HUMAN	L	227	ENSP00000221444:R227L	ENSP00000221444:R227L	R	-	2	0	KCNA7	54265823	1.000000	0.71417	0.954000	0.39281	0.149000	0.21700	7.811000	0.86092	2.234000	0.73211	0.313000	0.20887	CGC	.	.		0.527	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886		A	49574011	C	A	49574011	3	1	63	1	0	0	0	0	1	0	0	0	8017	768	27	1	694	1	KCNA7	19	49574011	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	2004377	49574011	9554972	109	7704										
FPR1	2357	hgsc.bcm.edu	37	chr19	52249985	52249985	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	agccgaaaggccaatgtcctCccatggccttcctgaccatg	9	15	0	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:52249985C>A	ENST00000595042.1	-	3	404	c.263G>T	c.(262-264)gGa>gTa	p.G88V	FPR1_ENST00000304748.4_Missense_Mutation_p.G88V	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	88					activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	CCAATGTCCTCCCATGGCCTT	0.507																																					p.G88V		Atlas-SNP	.											.	FPR1	64	.	0			c.G263T						.						137	105	116					19																	52249985		2203	4300	6503	SO:0001583	missense	2357	exon3			TGTCCTCCCATGG	M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"GPCR / Class A : Formyl peptide receptors"	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.263G>T	chr19.hg19:g.52249985C>A	ENSP00000471493:p.Gly88Val	204.0	0.0		183.0	35.0	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	hg19	CCDS12839.1	.	.	.	.	.	.	.	.	.	.	.	7.804	0.714234	0.15306	.	.	ENSG00000171051	ENST00000304748	T	0.37058	1.22	3.72	2.68	0.31781	GPCR, rhodopsin-like superfamily (1);	0.745223	0.12330	N	0.478436	T	0.44244	0.1284	L	0.58810	1.83	0.40445	D	0.980084	P	0.37276	0.589	P	0.50896	0.653	T	0.26916	-1.0089	10	0.27785	T	0.31	.	6.5403	0.22377	0.0:0.7644:0.0:0.2356	.	88	P21462	FPR1_HUMAN	V	88	ENSP00000302707:G88V	ENSP00000302707:G88V	G	-	2	0	FPR1	56941797	0.000000	0.05858	0.002000	0.10522	0.031000	0.12232	-0.015000	0.12634	0.844000	0.35094	0.563000	0.77884	GGA	.	.		0.507	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029		A	52249985	C	A	52249985	3	1	63	1	0	0	0	0	1	0	0	0	6046	855	30	3	793	3	FPR1	19	52249985	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	2675974	52249985	6878998	110	7705										
ZNF880	400713	hgsc.bcm.edu	37	chr19	52887146	52887146	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	atgccggaaacaagtctcttAaaaatcaacttggattaacc	6	9	2	0	rs398101268|rs34470614		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:52887146A>T	ENST00000422689.2	+	4	328	c.313A>T	c.(313-315)Aaa>Taa	p.K105*	ZNF880_ENST00000424032.2_3'UTR	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	105					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						CAAGTCTCTTAAAAATCAACT	0.368																																					p.K105X		Atlas-SNP	.											.	ZNF880	45	.	0			c.A313T						.						61	45	50					19																	52887146		690	1569	2259	SO:0001587	stop_gained	400713	exon4			TCTCTTAAAAATC	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"Zinc fingers, C2H2-type", "-"	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.313A>T	chr19.hg19:g.52887146A>T	ENSP00000406318:p.Lys105*	93.0	0.0		109.0	6.0	NM_001145434	B4DNA6	Nonsense_Mutation	SNP	ENST00000422689.2	hg19	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	A	8.517	0.867766	0.17250	.	.	ENSG00000221923	ENST00000422689	.	.	.	1.6	-2.54	0.06307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.7816	0.03033	0.4842:0.0:0.2398:0.276	.	.	.	.	X	105	.	ENSP00000406318:K105X	K	+	1	0	ZNF880	57578958	0.000000	0.05858	0.006000	0.13384	0.124000	0.20399	-1.231000	0.02939	-0.761000	0.04670	0.368000	0.22195	AAA	.	.		0.368	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434		T	52887146	A	T	52887146	4	4	63	1	0	0	0	0	0	1	0	0	18212	363	13	4	327	4	ZNF880	19	52887146	Nonsense_Mutation	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	637161	52887146	6241837	111	7706										
C19orf51	352909	hgsc.bcm.edu	37	chr19	55670500	55670500	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	cctgaggctgagccagaaccTctgagagtgaacctggagac	13	11	1	6			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:55670500T>C	ENST00000524407.2	-	12	1589	c.1556A>G	c.(1555-1557)gAg>gGg	p.E519G	CTD-2587H24.5_ENST00000591665.1_RNA|TNNI3_ENST00000590463.1_5'Flank|DNAAF3_ENST00000455045.1_Missense_Mutation_p.E465G|DNAAF3_ENST00000587789.2_5'UTR|DNAAF3_ENST00000391720.4_Missense_Mutation_p.E566G|DNAAF3_ENST00000527223.2_Missense_Mutation_p.E586G|CTD-2587H24.4_ENST00000587871.1_Intron|TNNI3_ENST00000588882.1_5'Flank|TNNI3_ENST00000344887.5_5'Flank			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	519					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											AGCCAGAACCTCTGAGAGTGA	0.617																																					p.E586G		Atlas-SNP	.											.	.	.	.	0			c.A1757G						.						25	27	27					19																	55670500		1857	4113	5970	SO:0001583	missense	352909	exon12			AGAACCTCTGAGA	AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"chromosome 19 open reading frame 51", "ciliary dyskinesia, primary 2"	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.1556A>G	chr19.hg19:g.55670500T>C	ENSP00000432046:p.Glu519Gly	168.0	0.0		133.0	31.0	NM_001256714	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Missense_Mutation	SNP	ENST00000524407.2	hg19	CCDS59422.1	.	.	.	.	.	.	.	.	.	.	t	12.02	1.813756	0.32053	.	.	ENSG00000167646	ENST00000301249;ENST00000455045;ENST00000391720	T;T	0.20069	2.13;2.1	3.77	2.71	0.32032	.	0.416306	0.17608	N	0.168190	T	0.16171	0.0389	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.33612	0.419;0.253;0.16;0.16	B;B;B;B	0.36244	0.22;0.128;0.128;0.128	T	0.15235	-1.0444	10	0.72032	D	0.01	-6.6568	8.6882	0.34251	0.0:0.0:0.1928:0.8072	.	586;465;539;519	E9PAX5;E3W9A1;Q8N9W5-3;Q8N9W5	.;.;.;CS051_HUMAN	G	586;465;566	ENSP00000394343:E465G;ENSP00000375600:E566G	ENSP00000301249:E586G	E	-	2	0	C19orf51	60362312	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.064000	0.11636	0.776000	0.33473	0.454000	0.30748	GAG	.	.		0.617	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837		C	55670500	T	C	55670500	3	2	63	1	0	0	0	0	1	0	0	0	1935	1551	54	2	73	2	C19orf51	19	55670500	Missense_Mutation	SNP	T	TCGA-CC-A3M9-01A-11D-A20W-10	2783354	55670500	3458483	112	7707										
PHF20	51230	hgsc.bcm.edu	37	chr20	34515736	34515736	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gtgctggcagcatggggtctGcatgggattactggaagaaa	16	6	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr20:34515736G>T	ENST00000374012.3	+	14	2168	c.2039G>T	c.(2038-2040)tGc>tTc	p.C680F	PHF20_ENST00000439301.1_3'UTR|RNU6-937P_ENST00000384325.1_RNA			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	680					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					CATGGGGTCTGCATGGGATTA	0.438																																					p.C680F		Atlas-SNP	.											.	PHF20	94	.	0			c.G2039T						.						149	146	147					20																	34515736		2203	4300	6503	SO:0001583	missense	51230	exon14			GGGTCTGCATGGG	AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"Tudor domain containing", "Zinc fingers, PHD-type"	16098	protein-coding gene	gene with protein product	"tudor domain containing 20A"	610335	"chromosome 20 open reading frame 104"	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.2039G>T	chr20.hg19:g.34515736G>T	ENSP00000363124:p.Cys680Phe	120.0	0.0		139.0	50.0	NM_016436	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	hg19	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875229	0.91664	.	.	ENSG00000025293	ENST00000374012	D	0.99252	-5.63	5.91	5.91	0.95273	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.99746	0.9899	H	0.98965	4.385	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97171	0.9844	10	0.87932	D	0	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	680	Q9BVI0	PHF20_HUMAN	F	680	ENSP00000363124:C680F	ENSP00000363124:C680F	C	+	2	0	PHF20	33979150	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.296000	0.96104	2.793000	0.96121	0.655000	0.94253	TGC	.	.		0.438	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		T	34515736	G	T	34515736	3	4	63	1	0	0	0	0	1	0	0	0	11840	1319	46	3	2089	3	PHF20	20	34515736	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10		34515736	28509784	113	7708										
MATN4	8785	hgsc.bcm.edu	37	chr20	43933399	43933399	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gctgcgggagctgtcaatcaCgaacaccagatccaggggcc	13	13	2	1	rs114313957	byFrequency	TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr20:43933399C>T	ENST00000372754.1	-	2	120	c.112G>A	c.(112-114)Gtg>Atg	p.V38M	RBPJL_ENST00000372741.3_5'Flank|MATN4_ENST00000342716.4_Missense_Mutation_p.V38M|MATN4_ENST00000360607.6_Missense_Mutation_p.V38M|MATN4_ENST00000372751.4_Intron|MATN4_ENST00000537548.1_Missense_Mutation_p.V38M|RBPJL_ENST00000343694.3_5'Flank|MATN4_ENST00000372756.1_Missense_Mutation_p.V38M|RBPJL_ENST00000372743.1_5'Flank|MATN4_ENST00000353917.5_Missense_Mutation_p.V38M			O95460	MATN4_HUMAN	matrilin 4	38	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CTGTCAATCACGAACACCAGA	0.642																																					p.V38M		Atlas-SNP	.											.	MATN4	57	.	0			c.G112A						.						25	22	23					20																	43933399		2198	4284	6482	SO:0001583	missense	8785	exon3			CAATCACGAACAC	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.112G>A	chr20.hg19:g.43933399C>T	ENSP00000361840:p.Val38Met	88.0	0.0		116.0	28.0	NM_030592	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Missense_Mutation	SNP	ENST00000372754.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.12	2.141067	0.37825	.	.	ENSG00000124159	ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132	D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	4.2	2.1	0.27182	.	0.567187	0.14655	N	0.306376	D	0.82912	0.5140	M	0.67700	2.07	0.80722	D	1	B;B;B	0.28512	0.032;0.097;0.214	B;B;B	0.28139	0.023;0.086;0.086	T	0.79588	-0.1741	10	0.54805	T	0.06	.	4.952	0.14019	0.0:0.6284:0.1751:0.1964	.	38;38;38	A6NNA4;O95460-4;O95460-2	.;.;.	M	38	ENSP00000361840:V38M;ENSP00000361842:V38M;ENSP00000243983:V38M;ENSP00000353819:V38M;ENSP00000343164:V38M;ENSP00000440328:V38M	ENSP00000255132:V38M	V	-	1	0	MATN4	43366813	0.999000	0.42202	0.988000	0.46212	0.975000	0.68041	1.406000	0.34646	0.943000	0.37553	0.462000	0.41574	GTG	.	C|0.987;G|0.013		0.642	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1			T	43933399	C	T	43933399	3	4	63	1	0	0	0	0	1	0	0	0	9345	536	19	1	1665	1	MATN4	20	43933399	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	9417663	43933399	19092121	114	7709										
DSCR3	10311	hgsc.bcm.edu	37	chr21	38597864	38597864	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gctatatcctgcagagcttcAgcgggaagttctccgtgatg	12	10	2	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr21:38597864A>T	ENST00000309117.6	-	8	1112	c.875T>A	c.(874-876)cTg>cAg	p.L292Q	AP001432.14_ENST00000440629.1_lincRNA|DSCR3_ENST00000398998.1_Missense_Mutation_p.L244Q|DSCR3_ENST00000399000.3_5'UTR|DSCR3_ENST00000476950.1_Missense_Mutation_p.L265Q|DSCR3_ENST00000399001.1_Missense_Mutation_p.L167Q|DSCR3_ENST00000539844.1_Missense_Mutation_p.L215Q|DSCR3_ENST00000288304.5_Missense_Mutation_p.L248Q	NM_006052.1	NP_006043.1	O14972	DSCR3_HUMAN	Down syndrome critical region gene 3	292						nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9						GCAGAGCTTCAGCGGGAAGTT	0.527																																					p.L292Q		Atlas-SNP	.											.	DSCR3	21	.	0			c.T875A						.						82	75	78					21																	38597864		2203	4300	6503	SO:0001583	missense	10311	exon8			AGCTTCAGCGGGA	D87343	CCDS33553.1	21q22.2	2008-05-22			ENSG00000157538	ENSG00000157538			3044	protein-coding gene	gene with protein product		605298				9399594	Standard	NM_006052		Approved	DCRA	uc002ywf.1	O14972	OTTHUMG00000086659	ENST00000309117.6:c.875T>A	chr21.hg19:g.38597864A>T	ENSP00000311399:p.Leu292Gln	120.0	0.0		106.0	20.0	NM_006052	B2R6T8|B7Z6B1|D3DSH4|Q2TAY6	Missense_Mutation	SNP	ENST00000309117.6	hg19	CCDS33553.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.854712	0.91355	.	.	ENSG00000157538	ENST00000309117;ENST00000288304;ENST00000539844;ENST00000399001;ENST00000476950;ENST00000398998	.	.	.	4.99	4.99	0.66335	.	0.000000	0.64402	D	0.000002	T	0.77089	0.4079	M	0.70275	2.135	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.995;1.0	D;D;D;D	0.69142	0.931;0.962;0.947;0.927	T	0.80469	-0.1369	9	0.87932	D	0	-6.6983	14.973	0.71249	1.0:0.0:0.0:0.0	.	167;215;265;292	A8MY26;B7Z606;B7Z6B1;O14972	.;.;.;DSCR3_HUMAN	Q	292;248;215;167;265;244	.	ENSP00000288304:L248Q	L	-	2	0	DSCR3	37519734	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.338000	0.90038	2.001000	0.58596	0.533000	0.62120	CTG	.	.		0.527	DSCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194807.1			T	38597864	A	T	38597864	3	4	63	1	0	0	0	0	1	0	0	0	4773	188	7	4	22	4	DSCR3	21	38597864	Missense_Mutation	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10		38597864	9532031	115	7710										
CDC45	8318	hgsc.bcm.edu	37	chr22	19492928	19492929	+	Frame_Shift_Ins	INS	-	-	C													0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	tgtcctgcagcgccacgtttINScccgccacaaccaccggaac							TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr22:19492928_19492929insC	ENST00000407835.1	+	11	1004_1005	c.748_749insC	c.(748-750)tccfs	p.S250fs	CDC45_ENST00000404724.3_Frame_Shift_Ins_p.S204fs|CDC45_ENST00000437685.2_Frame_Shift_Ins_p.S282fs|CDC45_ENST00000263201.1_Frame_Shift_Ins_p.S250fs			O75419	CDC45_HUMAN	cell division cycle 45	250					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						GCGCCACGTTTCCCGCCACAAC	0.55																																					p.S282fs		Atlas-INDEL	.											.	CDC45	48	.	0			c.844_845insC						.																																			SO:0001589	frameshift_variant	8318	exon11			.	AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"human CDC45"	603465	"CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like", "CDC45 cell division cycle 45-like (S. cerevisiae)", "cell division cycle 45 homolog (S. cerevisiae)"	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.751dupC	chr22.hg19:g.19492931_19492931dupC	ENSP00000385240:p.Ser250fs	125.0	0.0		130.0	10.0	NM_001178010	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Frame_Shift_Ins	INS	ENST00000407835.1	hg19	CCDS13762.1																																																																																			.	.		0.55	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504		C	19492929	-	C	19492928	7	5	63	1	0	1	1	0	0	0	0	0	3083	1783	62	0	886	0	CDC45	22	19492928	Frame_Shift_Ins	INS	-	TCGA-CC-A3M9-01A-11D-A20W-10		19492928	31811638	116	7711										
SSTR3	6753	hgsc.bcm.edu	37	chr22	37602722	37602722	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	caggctgcgtgatctggctgAcccggccgttcatctccttc	11	15	3	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr22:37602722A>T	ENST00000328544.3	-	2	1654	c.1121T>A	c.(1120-1122)gTc>gAc	p.V374D	SSTR3_ENST00000402501.1_Missense_Mutation_p.V374D	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	374					cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	GATCTGGCTGACCCGGCCGTT	0.677																																					p.V374D		Atlas-SNP	.											.	SSTR3	42	.	0			c.T1121A						.						45	42	43					22																	37602722		2203	4300	6503	SO:0001583	missense	6753	exon2			TGGCTGACCCGGC		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"GPCR / Class A : Somatostatin receptors"	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.1121T>A	chr22.hg19:g.37602722A>T	ENSP00000330138:p.Val374Asp	89.0	0.0		58.0	16.0	NM_001051	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	hg19	CCDS13944.1	.	.	.	.	.	.	.	.	.	.	A	14.82	2.648189	0.47258	.	.	ENSG00000183473	ENST00000328544;ENST00000402501	T;T	0.72505	-0.66;-0.66	5.33	5.33	0.75918	.	1.359230	0.05115	N	0.489532	T	0.70684	0.3252	L	0.54323	1.7	0.50813	D	0.99989	P	0.48407	0.91	B	0.43575	0.424	T	0.58515	-0.7623	10	0.24483	T	0.36	.	11.6877	0.51497	1.0:0.0:0.0:0.0	.	374	P32745	SSR3_HUMAN	D	374	ENSP00000330138:V374D;ENSP00000384904:V374D	ENSP00000330138:V374D	V	-	2	0	SSTR3	35932668	1.000000	0.71417	0.795000	0.32087	0.863000	0.49368	3.695000	0.54749	2.008000	0.58898	0.482000	0.46254	GTC	.	.		0.677	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1			T	37602722	A	T	37602722	3	4	63	1	0	0	0	0	1	0	0	0	15214	275	10	4	139	4	SSTR3	22	37602722	Missense_Mutation	SNP	A	TCGA-CC-A3M9-01A-11D-A20W-10	18109794	37602722	13701844	117	7712										
PCDH19	57526	hgsc.bcm.edu	37	chrX	99551540	99551540	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	gggaggtgacagggctaatcGcctcacagccattgcctgcc	13	13	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chrX:99551540G>T	ENST00000373034.4	-	6	4857	c.3182C>A	c.(3181-3183)gCg>gAg	p.A1061E	PCDH19_ENST00000420881.2_Missense_Mutation_p.A1013E|PCDH19_ENST00000464981.1_5'Flank|PCDH19_ENST00000255531.7_Missense_Mutation_p.A1014E	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	1061					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						AGGGCTAATCGCCTCACAGCC	0.607																																					p.A1061E		Atlas-SNP	.											.	PCDH19	269	.	0			c.C3182A						.						53	56	55					X																	99551540		2137	4232	6369	SO:0001583	missense	57526	exon6			CTAATCGCCTCAC	AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.3182C>A	chrX.hg19:g.99551540G>T	ENSP00000362125:p.Ala1061Glu	65.0	0.0		46.0	22.0	NM_001184880	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	hg19	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.007882	0.54361	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.55234	0.53;0.73;0.53	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.66277	0.2773	L	0.51422	1.61	0.80722	D	1	D;B;B	0.76494	0.999;0.388;0.269	D;B;B	0.81914	0.995;0.299;0.157	T	0.58836	-0.7566	10	0.12430	T	0.62	.	18.9069	0.92466	0.0:0.0:1.0:0.0	.	1061;1014;1013	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	E	1013;1061;1014	ENSP00000400327:A1013E;ENSP00000362125:A1061E;ENSP00000255531:A1014E	ENSP00000255531:A1014E	A	-	2	0	PCDH19	99438196	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.087000	0.94110	2.413000	0.81919	0.600000	0.82982	GCG	.	.		0.607	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		T	99551540	G	T	99551540	3	4	63	1	0	0	0	0	1	0	0	0	11523	1087	38	1	268	1	PCDH19	23	99551540	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10		99551540	55719020	118	7713										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135314089	135314089	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	caccacaggcgacacgtccaCgctcaccacagggaatgagt	10	15	1	1			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chrX:135314089C>G	ENST00000316077.9	-	8	1247	c.1027G>C	c.(1027-1029)Gtg>Ctg	p.V343L	MAP7D3_ENST00000370661.1_Missense_Mutation_p.V308L|MAP7D3_ENST00000495432.1_5'Flank|MAP7D3_ENST00000370663.5_Missense_Mutation_p.V325L	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	343					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					GACACGTCCACGCTCACCACA	0.567																																					p.V343L		Atlas-SNP	.											.	MAP7D3	102	.	0			c.G1027C						.						103	107	106					X																	135314089		2186	4252	6438	SO:0001583	missense	79649	exon8			CGTCCACGCTCAC	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1027G>C	chrX.hg19:g.135314089C>G	ENSP00000318086:p.Val343Leu	114.0	0.0		101.0	55.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	hg19	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	C	9.134	1.012172	0.19277	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.07800	3.16;3.16;3.16;3.16	4.19	0.94	0.19513	.	.	.	.	.	T	0.04634	0.0126	L	0.27053	0.805	0.09310	N	1	B;B;B;B	0.28439	0.212;0.068;0.212;0.032	B;B;B;B	0.22386	0.039;0.02;0.039;0.034	T	0.42085	-0.9472	9	0.27785	T	0.31	-0.1196	2.2736	0.04096	0.1892:0.3311:0.3653:0.1144	.	325;302;343;308	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	L	308;343;325;302	ENSP00000359695:V308L;ENSP00000318086:V343L;ENSP00000359697:V325L;ENSP00000359694:V302L	ENSP00000318086:V343L	V	-	1	0	MAP7D3	135141755	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-5.194000	0.00142	0.291000	0.22468	-0.229000	0.12294	GTG	.	.		0.567	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			G	135314089	C	G	135314089	3	3	63	1	0	0	0	0	1	0	0	0	9278	536	19	4	1647	4	MAP7D3	23	135314089	Missense_Mutation	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	35762549	135314089	19956471	119	7714										
MAGEC2	51438	hgsc.bcm.edu	37	chrX	141291370	141291370	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	ctagtgtatatgtgaaagagGactcactgtctggcaggccc	12	9	2	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chrX:141291370G>A	ENST00000247452.3	-	3	751	c.404C>T	c.(403-405)tCc>tTc	p.S135F		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	135	Interaction with TRIM28.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					TGTGAAAGAGGACTCACTGTC	0.522										HNSCC(46;0.14)																											p.S135F		Atlas-SNP	.											.	MAGEC2	102	.	0			c.C404T						.						103	102	102					X																	141291370		2203	4300	6503	SO:0001583	missense	51438	exon3			AAAGAGGACTCAC	AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"cancer/testis antigen 10"	300468	"melanoma antigen, family E, 1, cancer/testis specific"	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.404C>T	chrX.hg19:g.141291370G>A	ENSP00000354660:p.Ser135Phe	38.0	0.0		35.0	16.0	NM_016249	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Missense_Mutation	SNP	ENST00000247452.3	hg19	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	4.658	0.122303	0.08931	.	.	ENSG00000046774	ENST00000247452	T	0.02863	4.13	1.13	1.13	0.20643	.	.	.	.	.	T	0.03564	0.0102	L	0.53617	1.68	0.09310	N	1	B	0.14012	0.009	B	0.15484	0.013	T	0.35748	-0.9776	9	0.54805	T	0.06	.	5.306	0.15803	0.0:0.0:1.0:0.0	.	135	Q9UBF1	MAGC2_HUMAN	F	135	ENSP00000354660:S135F	ENSP00000354660:S135F	S	-	2	0	MAGEC2	141119036	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.273000	0.18662	0.861000	0.35504	0.458000	0.33432	TCC	.	.		0.522	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		A	141291370	G	A	141291370	3	1	63	1	0	0	0	0	1	0	0	0	9190	1174	41	3	721	3	MAGEC2	23	141291370	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10	5977281	141291370	13979190	120	7715										
TMEM185A	84548	hgsc.bcm.edu	37	chrX	148693147	148693147	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	aggcatagatgaggaatttaCtaggagaaaagtaaaacgat	11	3	0	3	rs376945268		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chrX:148693147C>A	ENST00000316916.8	-	2	343		c.e2-1		TMEM185A_ENST00000507237.1_Splice_Site|TMEM185A_ENST00000536359.1_Intron	NM_032508.2	NP_115897.1	Q8NFB2	T185A_HUMAN	transmembrane protein 185A							dendrite (GO:0030425)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(10)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					GAGGAATTTACTAGGAGAAAA	0.423																																					.		Atlas-SNP	.											.	TMEM185A	26	.	0			c.39-1G>T						.	C	,	1,3834		0,1,1631,571	122	123	123		,	5.1	1	X		123	0,6727		0,0,2428,1871	no	intron,splice-3	TMEM185A	NM_001174092.1,NM_032508.2	,	0,1,4059,2442	AA,AC,CC,C		0.0,0.0261,0.0095	,	,	148693147	1,10561	2203	4299	6502	SO:0001630	splice_region_variant	84548	exon3			AATTTACTAGGAG	AF353675	CCDS14689.1, CCDS55523.1, CCDS76041.1	Xq28	2014-01-28	2007-02-05	2007-02-05	ENSG00000155984	ENSG00000269556			17125	protein-coding gene	gene with protein product		300031	"chromosome X open reading frame 13", "family with sequence similarity 11, member A"	CXorf13, FAM11A		12404111	Standard	NM_032508		Approved		uc022cgl.1	Q8NFB2	OTTHUMG00000022625	ENST00000316916.8:c.39-1G>T	chrX.hg19:g.148693147C>A		60.0	0.0		56.0	32.0	NM_032508	B3KTZ3|Q3SYH1|Q96CW3|Q96KE8	Splice_Site	SNP	ENST00000316916.8	hg19	CCDS14689.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.437393	0.62955	2.61E-4	0.0	ENSG00000155984	ENST00000316916;ENST00000507237	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6197	0.84927	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM185A	148500948	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.249000	0.78278	2.126000	0.65437	0.600000	0.82982	.	.	.		0.423	TMEM185A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058710.4	NM_032508	Intron	A	148693147	C	A	148693147	5	1	63	1	0	0	0	0	0	0	1	0	16122	579	20	3	1038	3	TMEM185A	23	148693147	Splice_Site	SNP	C	TCGA-CC-A3M9-01A-11D-A20W-10	7401777	148693147	6577413	121	7716										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	4966401	4966401	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0826446280991736	10	1	1.47017543859649	2.00478468899522	1.31938821412506	0.213756898640463	0.813584930539721	0	agatggtggctttcctcaaaGatccagtactgctattttgc	9	9	1	2			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chrY:4966401G>C	ENST00000333703.4	+	5	1262	c.749G>C	c.(748-750)aGa>aCa	p.R250T	PCDH11Y_ENST00000215473.6_Missense_Mutation_p.R261T|PCDH11Y_ENST00000362095.5_Missense_Mutation_p.R261T	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	261	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R250K(2)|p.R261K(1)		autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						TTTCCTCAAAGATCCAGTACT	0.393																																					p.R261T		Atlas-SNP	.											.	PCDH11Y	163	.	3	Substitution - Missense(3)	large_intestine(3)	c.G782C						.																																			SO:0001583	missense	83259	exon2			CTCAAAGATCCAG	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000333703.4:c.749G>C	chrY.hg19:g.4966401G>C	ENSP00000330552:p.Arg250Thr	284.0	0.0		162.0	21.0	NM_032972	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000333703.4	hg19	CCDS14776.1																																																																																			.	.		0.393	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	NM_032973		C	4966401	G	C	4966401	3	2	63	1	0	0	0	0	1	0	0	0	11518	942	33	4	824	4	PCDH11Y	24	4966401	Missense_Mutation	SNP	G	TCGA-CC-A3M9-01A-11D-A20W-10		4966401	54407165	122	7717										
KIAA2013	90231	hgsc.bcm.edu	37	chr1	11983301	11983301	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggtcagcctccacaggtcagAgagctgcaggatctgctgga	14	11	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:11983301A>G	ENST00000376572.3	-	2	1464	c.1279T>C	c.(1279-1281)Tct>Cct	p.S427P	KIAA2013_ENST00000376576.3_Missense_Mutation_p.S427P	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	427						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CACAGGTCAGAGAGCTGCAGG	0.647																																					p.S427P		Atlas-SNP	.											.	KIAA2013	25	.	0			c.T1279C						.						22	22	22					1																	11983301		2202	4300	6502	SO:0001583	missense	90231	exon2			GGTCAGAGAGCTG	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.1279T>C	chr1.hg19:g.11983301A>G	ENSP00000365756:p.Ser427Pro	161.0	0.0		89.0	4.0	NM_138346	Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Missense_Mutation	SNP	ENST00000376572.3	hg19	CCDS141.1	.	.	.	.	.	.	.	.	.	.	A	11.08	1.533212	0.27387	.	.	ENSG00000116685	ENST00000376572;ENST00000376576	.	.	.	5.52	3.1	0.35709	.	0.594816	0.17241	N	0.181556	T	0.32194	0.0821	L	0.38175	1.15	0.09310	N	0.999998	B;B	0.34264	0.446;0.163	B;B	0.34038	0.17;0.174	T	0.08597	-1.0714	9	0.29301	T	0.29	-14.3534	11.823	0.52250	0.7114:0.2886:0.0:0.0	.	427;427	Q8IYS2-2;Q8IYS2	.;K2013_HUMAN	P	427	.	ENSP00000365756:S427P	S	-	1	0	KIAA2013	11905888	0.838000	0.29461	0.107000	0.21349	0.885000	0.51271	2.858000	0.48356	0.431000	0.26258	0.528000	0.53228	TCT	.	.		0.647	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1	NM_138346		G	11983301	A	G	11983301	3	3	64	1	0	0	0	0	1	0	0	0	8276	304	11	2	633	2	KIAA2013	1	11983301	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10		11983301	237267320	1	7718										
IGSF21	84966	hgsc.bcm.edu	37	chr1	18691796	18691796	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgcgagctccggccccctacAggacagcaggcccttccgca	11	18	0	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:18691796A>G	ENST00000251296.1	+	6	1003	c.620A>G	c.(619-621)cAg>cGg	p.Q207R		NM_032880.4	NP_116269.3	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	207						extracellular region (GO:0005576)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	40		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		GGCCCCCTACAGGACAGCAGG	0.602																																					p.Q207R		Atlas-SNP	.											.	IGSF21	87	.	0			c.A620G						.						48	54	52					1																	18691796		2203	4300	6503	SO:0001583	missense	84966	exon6			CCCTACAGGACAG	AK075316	CCDS184.1	1p36.13	2013-01-29			ENSG00000117154	ENSG00000117154		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28246	protein-coding gene	gene with protein product						12477932	Standard	NM_032880		Approved	MGC15730, RP11-121A23.1	uc001bau.2	Q96ID5	OTTHUMG00000002432	ENST00000251296.1:c.620A>G	chr1.hg19:g.18691796A>G	ENSP00000251296:p.Gln207Arg	135.0	0.0		68.0	4.0	NM_032880	Q8NBR8	Missense_Mutation	SNP	ENST00000251296.1	hg19	CCDS184.1	.	.	.	.	.	.	.	.	.	.	A	5.218	0.225751	0.09916	.	.	ENSG00000117154	ENST00000251296	T	0.29917	1.55	4.63	2.19	0.27852	.	0.374960	0.29609	N	0.011676	T	0.14485	0.0350	N	0.19112	0.55	0.28472	N	0.915381	B	0.02656	0.0	B	0.04013	0.001	T	0.25467	-1.0131	10	0.13108	T	0.6	-10.6533	4.7798	0.13197	0.7072:0.1906:0.1022:0.0	.	207	Q96ID5	IGS21_HUMAN	R	207	ENSP00000251296:Q207R	ENSP00000251296:Q207R	Q	+	2	0	IGSF21	18564383	0.968000	0.33430	0.979000	0.43373	0.780000	0.44128	1.073000	0.30691	0.216000	0.20781	0.379000	0.24179	CAG	.	.		0.602	IGSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006924.1	NM_032880		G	18691796	A	G	18691796	3	3	64	1	0	0	0	0	1	0	0	0	7608	188	7	2	642	2	IGSF21	1	18691796	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	6708495	18691796	230558825	2	7719										
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19186095	19186095	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aagtccgagttctcagccggCtcagccaggacccataggag	12	13	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:19186095C>G	ENST00000375371.3	-	1	81	c.60G>C	c.(58-60)gaG>gaC	p.E20D	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	20					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	TCTCAGCCGGCTCAGCCAGGA	0.577																																					p.E20D		Atlas-SNP	.											.	TAS1R2	134	.	0			c.G60C						.						120	111	114					1																	19186095		2203	4300	6503	SO:0001583	missense	80834	exon1			AGCCGGCTCAGCC		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14905	protein-coding gene	gene with protein product		606226	"G protein-coupled receptor 71"	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.60G>C	chr1.hg19:g.19186095C>G	ENSP00000364520:p.Glu20Asp	186.0	0.0		135.0	90.0	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	hg19	CCDS187.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.866326	0.32977	.	.	ENSG00000179002	ENST00000375371	D	0.88896	-2.44	4.47	2.58	0.30949	.	.	.	.	.	T	0.79511	0.4458	L	0.40543	1.245	0.09310	N	1	P	0.38922	0.651	B	0.32677	0.15	T	0.64241	-0.6454	9	0.14656	T	0.56	.	7.1459	0.25583	0.0:0.7855:0.0:0.2145	.	20	Q8TE23	TS1R2_HUMAN	D	20	ENSP00000364520:E20D	ENSP00000364520:E20D	E	-	3	2	TAS1R2	19058682	0.000000	0.05858	0.001000	0.08648	0.082000	0.17680	0.321000	0.19558	0.446000	0.26666	0.313000	0.20887	GAG	.	.		0.577	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			G	19186095	C	G	19186095	3	3	64	1	0	0	0	0	1	0	0	0	15578	796	28	4	2483	4	TAS1R2	1	19186095	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	494299	19186095	230064526	3	7720										
SRRM1	10250	hgsc.bcm.edu	37	chr1	24997900	24997900	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcagatcaggaaggaggtggAaagaaaaagaagaaaaagaa	13	2	2	5			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:24997900A>G	ENST00000323848.9	+	16	2739	c.2424A>G	c.(2422-2424)ggA>ggG	p.G808G	SRRM1_ENST00000374389.4_Silent_p.G817G|SRRM1_ENST00000447431.2_Silent_p.G820G|SRRM1_ENST00000479034.1_3'UTR	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	808					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		AAGGAGGTGGAaagaaaaaga	0.358																																					p.G808G	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.A2424G						.						40	42	41					1																	24997900		2203	4300	6503	SO:0001819	synonymous_variant	10250	exon16			AGGTGGAAAGAAA	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.2424A>G	chr1.hg19:g.24997900A>G		100.0	0.0		66.0	4.0	NM_005839	O60585|Q5VVN4	Silent	SNP	ENST00000323848.9	hg19	CCDS255.1																																																																																			.	.		0.358	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		G	24997900	A	G	24997900	2	3	64	1	0	0	0	0	0	0	0	1	15183	233	9	2		2	SRRM1	1	24997900	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5811805	24997900	224252721	4	7721										
SLFNL1	200172	hgsc.bcm.edu	37	chr1	41481866	41481866	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccatcatcagcgccttcatcTtctcttccagcttgcccagc	5	18	5	0	rs558283454	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:41481866T>A	ENST00000359345.1	-	4	3712	c.1136A>T	c.(1135-1137)aAg>aTg	p.K379M	SLFNL1_ENST00000372613.2_Missense_Mutation_p.K331M|SLFNL1_ENST00000302946.8_Missense_Mutation_p.K379M|SLFNL1_ENST00000372611.1_Missense_Mutation_p.K320M|SLFNL1_ENST00000397197.2_Missense_Mutation_p.K331M|SLFNL1_ENST00000439569.2_Missense_Mutation_p.K379M	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	379							ATP binding (GO:0005524)			endometrium(3)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				CGCCTTCATCTTCTCTTCCAG	0.637																																					p.K379M		Atlas-SNP	.											.	SLFNL1	37	.	0			c.A1136T						.						93	85	88					1																	41481866		2203	4300	6503	SO:0001583	missense	200172	exon6			TTCATCTTCTCTT	BC022037	CCDS460.1, CCDS72766.1	1p34.2	2008-02-05			ENSG00000171790	ENSG00000171790			26313	protein-coding gene	gene with protein product							Standard	NM_144990		Approved	FLJ23878	uc001cgm.2	Q499Z3	OTTHUMG00000005719	ENST00000359345.1:c.1136A>T	chr1.hg19:g.41481866T>A	ENSP00000352299:p.Lys379Met	138.0	0.0		176.0	12.0	NM_001168247	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	hg19	CCDS460.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.414547	0.42817	.	.	ENSG00000171790	ENST00000302946;ENST00000372613;ENST00000372611;ENST00000359345;ENST00000439569;ENST00000397197	T;T;T;T;T;T	0.32515	1.45;1.7;1.55;1.45;1.45;1.7	5.25	-2.72	0.05968	.	0.516811	0.17718	N	0.164340	T	0.27063	0.0663	N	0.24115	0.695	0.22827	N	0.998686	P;P;P	0.49696	0.927;0.83;0.881	P;P;P	0.53062	0.717;0.508;0.525	T	0.28364	-1.0046	10	0.72032	D	0.01	-45.9013	10.1794	0.42959	0.0:0.3847:0.0:0.6153	.	331;320;379	Q499Z3-3;Q499Z3-2;Q499Z3	.;.;SLNL1_HUMAN	M	379;331;320;379;379;331	ENSP00000304401:K379M;ENSP00000361696:K331M;ENSP00000361694:K320M;ENSP00000352299:K379M;ENSP00000398938:K379M;ENSP00000380381:K331M	ENSP00000304401:K379M	K	-	2	0	SLFNL1	41254453	0.000000	0.05858	0.632000	0.29296	0.291000	0.27294	-0.048000	0.11944	-0.239000	0.09710	-1.545000	0.00906	AAG	.	.		0.637	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990		A	41481866	T	A	41481866	3	1	64	1	0	0	0	0	1	0	0	0	14753	1609	56	4	91	4	SLFNL1	1	41481866	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	16483966	41481866	207768755	5	7722										
CCDC30	728621	hgsc.bcm.edu	37	chr1	43076653	43076653	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttcaatgtttttcagcatgTcaaaagcaaccaggaattgt	7	7	3	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:43076653T>C	ENST00000340612.4	+	9	1388	c.1388T>C	c.(1387-1389)gTc>gCc	p.V463A	CCDC30_ENST00000390640.4_Missense_Mutation_p.V252A|CCDC30_ENST00000428554.2_Missense_Mutation_p.V463A|CCDC30_ENST00000507855.1_Missense_Mutation_p.V252A|CCDC30_ENST00000342022.4_Missense_Mutation_p.V463A			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	463						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						TTTCAGCATGTCAAAAGCAAC	0.348																																					p.V463A		Atlas-SNP	.											.	CCDC30	78	.	0			c.T1388C						.						92	88	89					1																	43076653		2203	4300	6503	SO:0001583	missense	728621	exon10			AGCATGTCAAAAG	AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"prefoldin 6-like"					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1388T>C	chr1.hg19:g.43076653T>C	ENSP00000340378:p.Val463Ala	82.0	0.0		65.0	4.0	NM_001080850	Q14F06|Q5VVM5	Missense_Mutation	SNP	ENST00000340612.4	hg19	CCDS30690.1	.	.	.	.	.	.	.	.	.	.	T	11.46	1.646364	0.29246	.	.	ENSG00000186409	ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	5.68	5.68	0.88126	.	0.833727	0.10772	N	0.635922	T	0.33962	0.0881	L	0.40543	1.245	0.19775	N	0.999952	B;P	0.42871	0.341;0.792	B;B	0.37601	0.116;0.254	T	0.11567	-1.0582	10	0.18710	T	0.47	.	12.3251	0.55007	0.0:0.0:0.0:1.0	.	463;252	Q5VVM6;Q5VVM6-2	CCD30_HUMAN;.	A	463;252;463;463;252	ENSP00000397035:V463A;ENSP00000426711:V252A;ENSP00000340378:V463A;ENSP00000339280:V463A;ENSP00000375051:V252A	ENSP00000340378:V463A	V	+	2	0	CCDC30	42849240	0.636000	0.27207	0.784000	0.31847	0.131000	0.20780	0.634000	0.24614	2.156000	0.67533	0.460000	0.39030	GTC	.	.		0.348	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030		C	43076653	T	C	43076653	3	2	64	1	0	0	0	0	1	0	0	0	2807	1667	58	2	1422	2	CCDC30	1	43076653	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1594787	43076653	206173968	6	7723										
WDR65	149465	hgsc.bcm.edu	37	chr1	43649297	43649297	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	caggataacactcaggtgtgTgtcactggaaatgggatgtt	13	6	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:43649297T>C	ENST00000372492.4	+	4	834	c.510T>C	c.(508-510)tgT>tgC	p.C170C	WDR65_ENST00000528956.1_Silent_p.C170C	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		170										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTCAGGTGTGTGTCACTGGAA	0.413																																					p.C170C		Atlas-SNP	.											.	WDR65	76	.	0			c.T510C						.						84	86	85					1																	43649297		2203	4300	6503	SO:0001819	synonymous_variant	149465	exon4			GGTGTGTGTCACT																												ENST00000372492.4:c.510T>C	chr1.hg19:g.43649297T>C		87.0	0.0		119.0	5.0	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	hg19																																																																																				.	.		0.413	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			C	43649297	T	C	43649297	2	2	64	1	0	0	0	0	0	0	0	1	17331	1702	59	2		2	WDR65	1	43649297	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	572644	43649297	205601324	7	7724										
TESK2	10420	hgsc.bcm.edu	37	chr1	45811552	45811552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctggtctaatctcttaccccTggctgtgggctgcagcttcc	10	14	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:45811552T>C	ENST00000372086.3	-	10	1394	c.994A>G	c.(994-996)Agg>Ggg	p.R332G	TESK2_ENST00000538496.1_Missense_Mutation_p.R249G|TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000372084.1_Missense_Mutation_p.R303G|TESK2_ENST00000341771.6_Missense_Mutation_p.R303G	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	332					actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					CTCTTACCCCTGGCTGTGGGC	0.557																																					p.R332G		Atlas-SNP	.											.	TESK2	60	.	0			c.A994G						.						95	96	95					1																	45811552		1915	4127	6042	SO:0001583	missense	10420	exon10			TACCCCTGGCTGT	AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.994A>G	chr1.hg19:g.45811552T>C	ENSP00000361158:p.Arg332Gly	104.0	0.0		110.0	5.0	NM_007170	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Missense_Mutation	SNP	ENST00000372086.3	hg19	CCDS41323.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.904575	0.33628	.	.	ENSG00000070759	ENST00000372084;ENST00000372086;ENST00000372083;ENST00000341771;ENST00000538496	T;T;T;T	0.75260	-0.16;-0.65;-0.16;-0.92	5.67	5.67	0.87782	Protein kinase-like domain (1);	0.409870	0.25572	N	0.029742	T	0.51295	0.1666	N	0.03608	-0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.50457	-0.8826	10	0.37606	T	0.19	.	10.8885	0.46981	0.0:0.0:0.1574:0.8426	.	303;332	Q96S53-3;Q96S53	.;TESK2_HUMAN	G	303;332;316;303;249	ENSP00000361156:R303G;ENSP00000361158:R332G;ENSP00000343940:R303G;ENSP00000441746:R249G	ENSP00000343940:R303G	R	-	1	2	TESK2	45584139	0.997000	0.39634	0.856000	0.33681	0.442000	0.32017	5.878000	0.69682	2.168000	0.68352	0.529000	0.55759	AGG	.	.		0.557	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170		C	45811552	T	C	45811552	3	2	64	1	0	0	0	0	1	0	0	0	15783	1579	55	2	729	2	TESK2	1	45811552	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2162255	45811552	203439069	8	7725										
DMBX1	127343	hgsc.bcm.edu	37	chr1	46976674	46976674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cctgcagaaggaacagctccAgaagcagaaggaggctgagg	15	9	0	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:46976674A>G	ENST00000360032.3	+	3	415	c.401A>G	c.(400-402)cAg>cGg	p.Q134R	DMBX1_ENST00000371956.4_Missense_Mutation_p.Q139R	NM_172225.1	NP_757379.1			diencephalon/mesencephalon homeobox 1											endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)					GAACAGCTCCAGAAGCAGAAG	0.647																																					p.Q139R		Atlas-SNP	.											.	DMBX1	50	.	0			c.A416G						.						41	49	47					1																	46976674		2203	4300	6503	SO:0001583	missense	127343	exon3			AGCTCCAGAAGCA	AB037699	CCDS536.1	1p34.1	2011-06-20	2004-03-29	2004-03-30	ENSG00000197587	ENSG00000197587		"Homeoboxes / PRD class"	19026	protein-coding gene	gene with protein product		607410	"orthodenticle homolog 3 (Drosophila)"	OTX3			Standard	NM_147192		Approved	PAXB	uc001cpx.3	Q8NFW5	OTTHUMG00000007982	ENST00000360032.3:c.401A>G	chr1.hg19:g.46976674A>G	ENSP00000353132:p.Gln134Arg	124.0	0.0		117.0	43.0	NM_147192		Missense_Mutation	SNP	ENST00000360032.3	hg19	CCDS536.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.279998	0.80692	.	.	ENSG00000197587	ENST00000371956;ENST00000360032	D;D	0.93906	-3.21;-3.31	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.94551	0.8245	L	0.55990	1.75	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.79784	0.985;0.993	D	0.92307	0.5854	10	0.09590	T	0.72	.	13.9043	0.63823	1.0:0.0:0.0:0.0	.	139;134	Q8NFW5;Q8NFW5-2	DMBX1_HUMAN;.	R	139;134	ENSP00000361024:Q139R;ENSP00000353132:Q134R	ENSP00000353132:Q134R	Q	+	2	0	DMBX1	46749261	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.333000	0.96459	1.894000	0.54839	0.482000	0.46254	CAG	.	.		0.647	DMBX1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021895.1			G	46976674	A	G	46976674	3	3	64	1	0	0	0	0	1	0	0	0	4580	188	7	2	426	2	DMBX1	1	46976674	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1165122	46976674	202273947	9	7726										
CDKN2C	1031	hgsc.bcm.edu	37	chr1	51436144	51436144	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgtaaacgtcaatgcacaaaAtggatttggaaggactgcgc	11	7	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:51436144A>G	ENST00000262662.1	+	3	2138	c.104A>G	c.(103-105)aAt>aGt	p.N35S	CDKN2C_ENST00000396148.1_Missense_Mutation_p.N35S|CDKN2C_ENST00000371761.3_Missense_Mutation_p.N35S			P42773	CDN2C_HUMAN	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	35					cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|oligodendrocyte differentiation (GO:0048709)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)	p.0?(11)		central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|thyroid(1)	23				GBM - Glioblastoma multiforme(3;3.61e-13)|all cancers(3;0.00151)		AATGCACAAAATGGATTTGGA	0.488			D		"glioma, MM"																																p.N35S	Melanoma(47;50 1155 4767 22863 47597)	Atlas-SNP	.		Rec	yes		1	1p32	1031	"cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)"		"O, L"	.	CDKN2C	24	.	11	Whole gene deletion(11)	central_nervous_system(6)|haematopoietic_and_lymphoid_tissue(4)|thyroid(1)	c.A104G						.						104	106	105					1																	51436144		2203	4300	6503	SO:0001583	missense	1031	exon2			CACAAAATGGATT	BC000598	CCDS555.1	1p32.3	2013-01-10			ENSG00000123080	ENSG00000123080		"Ankyrin repeat domain containing"	1789	protein-coding gene	gene with protein product		603369				8001816, 9636670	Standard	NM_001262		Approved	INK4C, p18	uc001csg.3	P42773	OTTHUMG00000008046	ENST00000262662.1:c.104A>G	chr1.hg19:g.51436144A>G	ENSP00000262662:p.Asn35Ser	89.0	0.0		94.0	4.0	NM_001262	Q8TB83	Missense_Mutation	SNP	ENST00000262662.1	hg19	CCDS555.1	.	.	.	.	.	.	.	.	.	.	A	17.83	3.486198	0.63962	.	.	ENSG00000123080	ENST00000262662;ENST00000396148;ENST00000371761	T;T;T	0.68765	-0.35;-0.35;-0.35	5.23	4.07	0.47477	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.69682	0.3138	M	0.79258	2.445	0.52099	D	0.999946	P	0.49559	0.925	P	0.45681	0.49	T	0.72906	-0.4150	10	0.62326	D	0.03	-6.7408	11.3684	0.49686	0.8641:0.0:0.0:0.1359	.	35	P42773	CDN2C_HUMAN	S	35	ENSP00000262662:N35S;ENSP00000379452:N35S;ENSP00000360826:N35S	ENSP00000262662:N35S	N	+	2	0	CDKN2C	51208732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.939000	0.87685	0.965000	0.38133	0.533000	0.62120	AAT	.	.		0.488	CDKN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022058.1	NM_001262		G	51436144	A	G	51436144	3	3	64	1	0	0	0	0	1	0	0	0	3167	101	4	2	106	2	CDKN2C	1	51436144	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	4459470	51436144	197814477	10	7727										
NRD1	4898	hgsc.bcm.edu	37	chr1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	catcatcttcttcttcttccTccacctcctcttcttcttca	0	18	9	0	rs62648104		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:52306079T>A	ENST00000354831.7	-	2	638	c.449A>T	c.(448-450)gAg>gTg	p.E150V	NRD1_ENST00000352171.7_Missense_Mutation_p.E150V|NRD1_ENST00000544028.1_Missense_Mutation_p.E18V|NRD1_ENST00000539524.1_Missense_Mutation_p.E18V|NRD1_ENST00000485608.1_5'UTR	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).|Poly-Glu.				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcttcttcctccacctcctc	0.378																																					p.E150V		Atlas-SNP	.											.	NRD1	89	.	0			c.A449T						.						163	138	146					1																	52306079		2203	4300	6503	SO:0001583	missense	4898	exon2			TCTTCCTCCACCT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.449A>T	chr1.hg19:g.52306079T>A	ENSP00000346890:p.Glu150Val	235.0	0.0		233.0	36.0	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	3.056	-0.194350	0.06259	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.38240	1.31;3.15;1.15;1.22	5.25	2.92	0.33932	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.525899	0.19688	N	0.108344	T	0.18341	0.0440	N	0.14661	0.345	0.09310	N	1	B;B;B	0.23650	0.062;0.089;0.01	B;B;B	0.17098	0.017;0.007;0.007	T	0.14755	-1.0461	10	0.38643	T	0.18	-0.0317	5.1939	0.15225	0.0:0.1704:0.2022:0.6274	rs62648104	150;150;150	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	V	150;150;18;150;18	ENSP00000262679:E150V;ENSP00000346890:E150V;ENSP00000444416:E18V;ENSP00000442262:E18V	ENSP00000262679:E150V	E	-	2	0	NRD1	52078667	0.129000	0.22400	0.012000	0.15200	0.145000	0.21501	0.870000	0.28010	0.317000	0.23160	0.454000	0.30748	GAG	.	T|0.024;A|0.976		0.378	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		A	52306079	T	A	52306079	3	1	64	1	0	0	0	0	1	0	0	0	10654	1551	54	4	3338	4	NRD1	1	52306079	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	869935	52306079	196944542	11	7728										
ACADM	34	hgsc.bcm.edu	37	chr1	76216192	76216192	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttggatgaagctaccaagtaTgccctggaaaggaaaacttt	10	7	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:76216192T>C	ENST00000370841.4	+	10	1343	c.906T>C	c.(904-906)taT>taC	p.Y302Y	ACADM_ENST00000481374.1_3'UTR|ACADM_ENST00000420607.2_Silent_p.Y306Y|ACADM_ENST00000541113.1_Silent_p.Y266Y|ACADM_ENST00000370834.5_Silent_p.Y335Y|ACADM_ENST00000543667.1_Silent_p.Y113Y	NM_000016.4|NM_001127328.1	NP_000007.1|NP_001120800.1	P11310	ACADM_HUMAN	acyl-CoA dehydrogenase, C-4 to C-12 straight chain	302					cardiac muscle cell differentiation (GO:0055007)|carnitine biosynthetic process (GO:0045329)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|glycogen biosynthetic process (GO:0005978)|liver development (GO:0001889)|medium-chain fatty acid catabolic process (GO:0051793)|medium-chain fatty acid metabolic process (GO:0051791)|oxidation-reduction process (GO:0055114)|post-embryonic development (GO:0009791)|regulation of gluconeogenesis (GO:0006111)|response to cold (GO:0009409)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|identical protein binding (GO:0042802)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)			breast(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	18					Flavin adenine dinucleotide(DB03147)	CTACCAAGTATGCCCTGGAAA	0.333																																					p.Y306Y		Atlas-SNP	.											.	ACADM	50	.	0			c.T918C						.						66	73	71					1																	76216192		2203	4300	6503	SO:0001819	synonymous_variant	34	exon10			CAAGTATGCCCTG	M16827	CCDS668.1, CCDS44165.1, CCDS65562.1, CCDS72807.1	1p31	2014-09-17	2010-04-30		ENSG00000117054	ENSG00000117054	1.3.99.3		89	protein-coding gene	gene with protein product		607008	"acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain"			3035565	Standard	NM_000016		Approved	MCAD, MCADH, ACAD1	uc009wbp.3	P11310	OTTHUMG00000009784	ENST00000370841.4:c.906T>C	chr1.hg19:g.76216192T>C		75.0	0.0		86.0	4.0	NM_001127328	Q5T4U4|Q9NYF1	Silent	SNP	ENST00000370841.4	hg19	CCDS668.1																																																																																			.	.		0.333	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1			C	76216192	T	C	76216192	2	2	64	1	0	0	0	0	0	0	0	1	113	1471	51	2		2	ACADM	1	76216192	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	23910113	76216192	173034429	12	7729										
GBP5	115362	hgsc.bcm.edu	37	chr1	89728392	89728392	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tctttttttccgtctctgtgAgagcctggtcagtctgtaat	9	9	4	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:89728392A>G	ENST00000370459.3	-	9	1566	c.1439T>C	c.(1438-1440)cTc>cCc	p.L480P	GBP5_ENST00000471171.1_5'Flank|RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000343435.5_Missense_Mutation_p.L480P			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	480						cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		CGTCTCTGTGAGAGCCTGGTC	0.383																																					p.L480P		Atlas-SNP	.											.	GBP5	65	.	0			c.T1439C						.						80	81	81					1																	89728392		2203	4300	6503	SO:0001583	missense	115362	exon10			TCTGTGAGAGCCT	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.1439T>C	chr1.hg19:g.89728392A>G	ENSP00000359488:p.Leu480Pro	102.0	0.0		75.0	4.0	NM_052942	B2RCE1|Q86TM5	Missense_Mutation	SNP	ENST00000370459.3	hg19	CCDS722.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.372748	0.82573	.	.	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	T;T;T	0.72725	-0.68;-0.68;-0.68	4.86	4.86	0.63082	Guanylate-binding protein, C-terminal (3);	0.000000	0.64402	D	0.000001	D	0.84070	0.5391	M	0.90922	3.16	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87593	0.2492	10	0.87932	D	0	-17.0177	12.8668	0.57944	1.0:0.0:0.0:0.0	.	480	Q96PP8	GBP5_HUMAN	P	480	ENSP00000340396:L480P;ENSP00000359488:L480P;ENSP00000403010:L480P	ENSP00000340396:L480P	L	-	2	0	GBP5	89500980	1.000000	0.71417	0.997000	0.53966	0.295000	0.27426	4.243000	0.58721	2.198000	0.70561	0.524000	0.50904	CTC	.	.		0.383	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942		G	89728392	A	G	89728392	3	3	64	1	0	0	0	0	1	0	0	0	6285	304	11	2	333	2	GBP5	1	89728392	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	13512200	89728392	159522229	13	7730										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103491481	103491481	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttagtagccactgtcctcaTcttctttttgaaattggatt	6	8	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:103491481T>C	ENST00000370096.3	-	6	1210				COL11A1_ENST00000353414.4_Intron|COL11A1_ENST00000358392.2_Missense_Mutation_p.M270V|COL11A1_ENST00000512756.1_Intron	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1						cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		ACTGTCCTCATCTTCTTTTTG	0.333																																					p.M270V		Atlas-SNP	.											COL11A1,NS,carcinoma,0,1	COL11A1	972	.	0			c.A808G						.						108	116	113					1																	103491481		2202	4300	6502	SO:0001627	intron_variant	1301	exon6			TCCTCATCTTCTT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.897+290A>G	chr1.hg19:g.103491481T>C		63.0	0.0		35.0	2.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	6.480	0.456688	0.12283	.	.	ENSG00000060718	ENST00000358392;ENST00000427239	T;T	0.70986	-0.5;-0.53	5.54	5.54	0.83059	.	3.549350	0.00424	N	0.000067	T	0.39332	0.1074	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.00400	-1.1763	10	0.16896	T	0.51	.	15.6738	0.77300	0.0:0.0:0.0:1.0	.	270	P12107-2	.	V	270	ENSP00000351163:M270V;ENSP00000408640:M270V	ENSP00000351163:M270V	M	-	1	0	COL11A1	103264069	1.000000	0.71417	0.931000	0.37212	0.990000	0.78478	5.758000	0.68776	2.109000	0.64355	0.523000	0.50628	ATG	.	.		0.333	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		C	103491481	T	C	103491481	1	2	64	0	1	0	0	0	0	0	0	0	3669	1435	50	2		2	COL11A1	1	103491481	Intron	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	13763089	103491481	145759140	14	7731										
ADORA3	140	hgsc.bcm.edu	37	chr1	112033360	112033360	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aactggaatgatagaatgcaCccagggagcccaggaattct	11	9	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:112033360C>T	ENST00000369716.4	-	2	508	c.375G>A	c.(373-375)ggG>ggA	p.G125G	RNU6-792P_ENST00000363490.1_RNA|ADORA3_ENST00000369717.4_Silent_p.G44G	NM_020683.6	NP_065734.5	P33765	AA3R_HUMAN	adenosine A3 receptor	250					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)	p.G125G(1)		NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	ATAGAATGCACCCAGGGAGCC	0.448																																					p.G125G		Atlas-SNP	.											ADORA3_ENST00000369716,NS,carcinoma,0,1	ADORA3	104	.	1	Substitution - coding silent(1)	ovary(1)	c.G375A						.						101	95	97					1																	112033360		2203	4300	6503	SO:0001819	synonymous_variant	140	exon2			AATGCACCCAGGG	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"GPCR / Class A : Adenosine receptors", "Immunoglobulin superfamily / V-set domain containing"	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000369716.4:c.375G>A	chr1.hg19:g.112033360C>T		29.0	0.0		43.0	2.0	NM_020683	A2A3P4|Q6UWU0|Q9BYZ1	Silent	SNP	ENST00000369716.4	hg19	CCDS838.1																																																																																			.	.		0.448	ADORA3-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157679.1	NM_000677, NM_020683		T	112033360	C	T	112033360	2	4	64	1	0	0	0	0	0	0	0	1	329	494	18	3		3	ADORA3	1	112033360	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	8541879	112033360	137217261	15	7732										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120458918	120458919	+	Frame_Shift_Ins	INS	-	-	AA													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gataaagttactgaactctcINSagacagttggaccttctcac							TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:120458918_120458919insAA	ENST00000256646.2	-	34	6645_6646	c.6426_6427insTT	c.(6424-6429)tctgagfs	p.E2143fs		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2143					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACTGAACTCTCAGACAGTTGGA	0.485			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.E2143fs		Atlas-Indel,Pindel	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.6427_6428insTT						.																																			SO:0001589	frameshift_variant	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	.	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.6426_6427insTT	chr1.hg19:g.120458918_120458919insAA	ENSP00000256646:p.Glu2143fs	217.0	0.0		216.0	49.0	NM_024408	Q5T3X7|Q99734|Q9H240	Frame_Shift_Ins	INS	ENST00000256646.2	hg19	CCDS908.1																																																																																			.	.		0.485	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		AA	120458919	-	AA	120458918	7	5	64	1	0	1	1	0	0	0	0	0	10557	835	29	0	992	0	NOTCH2	1	120458918	Frame_Shift_Ins	INS	-	TCGA-CC-A3MA-01A-11D-A20W-10	8425558	120458918	128791703	16	7733										
OLFML2B	25903	hgsc.bcm.edu	37	chr1	161989875	161989875	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tggaggcccccgcattgatcCtctggcaggcatcccggccc	12	17	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:161989875C>A	ENST00000294794.3	-	2	695	c.272G>T	c.(271-273)aGg>aTg	p.R91M	OLFML2B_ENST00000367940.2_Missense_Mutation_p.R91M	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	91					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			CGCATTGATCCTCTGGCAGGC	0.592																																					p.R91M		Atlas-SNP	.											.	OLFML2B	114	.	0			c.G272T						.						80	81	80					1																	161989875		2203	4300	6503	SO:0001583	missense	25903	exon2			TTGATCCTCTGGC	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.272G>T	chr1.hg19:g.161989875C>A	ENSP00000294794:p.Arg91Met	127.0	0.0		223.0	49.0	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	hg19	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.391902	0.83011	.	.	ENSG00000162745	ENST00000294794;ENST00000367940	T;T	0.49720	0.77;0.77	4.5	4.5	0.54988	.	.	.	.	.	T	0.52613	0.1745	L	0.55213	1.73	0.38414	D	0.945999	D;D	0.76494	0.997;0.999	P;P	0.61201	0.781;0.885	T	0.58662	-0.7597	8	0.87932	D	0	.	15.0948	0.72226	0.0:1.0:0.0:0.0	.	91;91	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	M	91	ENSP00000294794:R91M;ENSP00000356917:R91M	ENSP00000294794:R91M	R	-	2	0	OLFML2B	160256499	1.000000	0.71417	0.942000	0.38095	0.789000	0.44602	6.931000	0.75863	2.487000	0.83934	0.561000	0.74099	AGG	.	.		0.592	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		A	161989875	C	A	161989875	3	1	64	1	0	0	0	0	1	0	0	0	10867	681	24	3	2008	3	OLFML2B	1	161989875	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	41530957	161989875	87260746	17	7734										
CEP350	9857	hgsc.bcm.edu	37	chr1	179972310	179972310	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgttactggtatgtattaggTttcaacccttcagagaccaa	8	8	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:179972310T>C	ENST00000367607.3	+	7	1438	c.1020T>C	c.(1018-1020)ggT>ggC	p.G340G		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	340					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						ATGTATTAGGTTTCAACCCTT	0.343																																					p.G340G		Atlas-SNP	.											.	CEP350	418	.	0			c.T1020C						.						76	71	72					1																	179972310		2203	4300	6503	SO:0001630	splice_region_variant	9857	exon7			ATTAGGTTTCAAC	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.1019-1T>C	chr1.hg19:g.179972310T>C		68.0	0.0		117.0	5.0	NM_014810	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	hg19	CCDS1336.1																																																																																			.	.		0.343	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	Silent	C	179972310	T	C	179972310	5	2	64	1	0	0	0	0	0	0	1	0	3256	1739	60	2	1042	2	CEP350	1	179972310	Splice_Site	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	17982435	179972310	69278311	18	7735										
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186919790	186919790	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttttgttttcttttcacagaAaatattaccacaaagcatat	3	7	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:186919790A>G	ENST00000367466.3	+	13	1418	c.1266A>G	c.(1264-1266)gaA>gaG	p.E422E	PLA2G4A_ENST00000442353.2_Splice_Site_p.E362E	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	422	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	TTTTCACAGAAAATATTACCA	0.348																																					p.E422E		Atlas-SNP	.											PLA2G4A,NS,carcinoma,0,1	PLA2G4A	125	.	0			c.A1266G						.						41	41	41					1																	186919790		2203	4300	6503	SO:0001630	splice_region_variant	5321	exon13			CACAGAAAATATT	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.1265-1A>G	chr1.hg19:g.186919790A>G		38.0	0.0		73.0	3.0	NM_024420	B1AKG4|Q29R80	Silent	SNP	ENST00000367466.3	hg19	CCDS1372.1																																																																																			.	.		0.348	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420	Silent	G	186919790	A	G	186919790	5	3	64	1	0	0	0	0	0	0	1	0	12010	28	1	2	1312	2	PLA2G4A	1	186919790	Splice_Site	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	6947480	186919790	62330831	19	7736										
ZBTB41	360023	hgsc.bcm.edu	37	chr1	197169179	197169179	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aaaattctgatgtgtaaagaAattcaagcaaatgctgaaaa	7	4	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:197169179A>G	ENST00000367405.4	-	1	493	c.425T>C	c.(424-426)tTt>tCt	p.F142S	ZBTB41_ENST00000467322.1_5'UTR|CRB1_ENST00000535699.1_5'Flank	NM_194314.2	NP_919290.2	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	142	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(11)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	40						TGTGTAAAGAAATTCAAGCAA	0.343																																					p.F142S		Atlas-SNP	.											.	ZBTB41	116	.	0			c.T425C						.						48	47	47					1																	197169179		2203	4300	6503	SO:0001583	missense	360023	exon1			TAAAGAAATTCAA		CCDS30960.1	1q31.3	2013-01-08			ENSG00000177888	ENSG00000177888		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	24819	protein-coding gene	gene with protein product							Standard	NM_194314		Approved	FRBZ1, FLJ36199, DKFZp686C06120, ZNF924	uc001gtx.1	Q5SVQ8	OTTHUMG00000036275	ENST00000367405.4:c.425T>C	chr1.hg19:g.197169179A>G	ENSP00000356375:p.Phe142Ser	42.0	0.0		83.0	4.0	NM_194314	A2RUA8|Q6MZT8|Q6ZR25|Q7Z4T1|Q8IZ99	Missense_Mutation	SNP	ENST00000367405.4	hg19	CCDS30960.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.835592	0.71373	.	.	ENSG00000177888	ENST00000367405	T	0.72394	-0.65	4.77	4.77	0.60923	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.44902	D	0.000411	D	0.82412	0.5031	M	0.75777	2.31	0.53688	D	0.99997	D	0.76494	0.999	D	0.67231	0.95	D	0.85099	0.0956	10	0.87932	D	0	.	14.2994	0.66336	1.0:0.0:0.0:0.0	.	142	Q5SVQ8	ZBT41_HUMAN	S	142	ENSP00000356375:F142S	ENSP00000356375:F142S	F	-	2	0	ZBTB41	195435802	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.957000	0.93082	1.755000	0.51935	0.254000	0.18369	TTT	.	.		0.343	ZBTB41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088249.2	NM_194314		G	197169179	A	G	197169179	3	3	64	1	0	0	0	0	1	0	0	0	17558	14	1	2	2344	2	ZBTB41	1	197169179	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	10249389	197169179	52081442	20	7737										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204401382	204401382	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cggcagaggaaaacatcactGattcggccagagctcttgag	12	10	2	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:204401382G>C	ENST00000367187.3	-	28	4657	c.4101C>G	c.(4099-4101)atC>atG	p.I1367M	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.I1339M|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1367	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			AAACATCACTGATTCGGCCAG	0.517																																					p.I1367M		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C4101G						.						131	130	130					1																	204401382		2203	4300	6503	SO:0001583	missense	5287	exon28			ATCACTGATTCGG	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4101C>G	chr1.hg19:g.204401382G>C	ENSP00000356155:p.Ile1367Met	184.0	0.0		360.0	81.0	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	hg19	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.686187	0.47991	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.45276	0.9;0.9	6.08	4.18	0.49190	Phox homologous domain (5);	0.104907	0.64402	D	0.000005	T	0.64182	0.2575	M	0.82823	2.61	0.40977	D	0.984742	P;B	0.52463	0.953;0.331	P;P	0.59357	0.856;0.448	T	0.71823	-0.4476	10	0.87932	D	0	.	15.3304	0.74203	0.0:0.0:0.744:0.256	.	1339;1367	F5GWN5;O00750	.;P3C2B_HUMAN	M	1367;1339	ENSP00000356155:I1367M;ENSP00000400561:I1339M	ENSP00000356155:I1367M	I	-	3	3	PIK3C2B	202668005	1.000000	0.71417	0.727000	0.30756	0.312000	0.27988	4.878000	0.63093	0.880000	0.35969	-0.181000	0.13052	ATC	.	.		0.517	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		C	204401382	G	C	204401382	3	2	64	1	0	0	0	0	1	0	0	0	11919	1280	45	4	831	4	PIK3C2B	1	204401382	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	7232203	204401382	44849239	21	7738										
WDR26	80232	hgsc.bcm.edu	37	chr1	224621626	224621626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tggcggcggagggggcggaaGgcaggagcccattggcgtgg	23	8	0	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:224621626G>A	ENST00000414423.2	-	1	375	c.182C>T	c.(181-183)cCt>cTt	p.P61L	WDR26_ENST00000295024.6_5'UTR|WDR26_ENST00000366852.2_Missense_Mutation_p.P61L	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	61						cytoplasm (GO:0005737)|nucleus (GO:0005634)				biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		GGGGGCGGAAGGCAGGAGCCC	0.697																																					p.P61L		Atlas-SNP	.											.	WDR26	104	.	0			c.C182T						.						15	22	20					1																	224621626		692	1588	2280	SO:0001583	missense	80232	exon1			GCGGAAGGCAGGA	AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"WD repeat domain containing"	21208	protein-coding gene	gene with protein product	"GID complex subunit 7 homolog (S. cerevisiae)"						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.182C>T	chr1.hg19:g.224621626G>A	ENSP00000408108:p.Pro61Leu	1.0	0.0		4.0	4.0	NM_001115113	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Missense_Mutation	SNP	ENST00000414423.2	hg19	CCDS31037.2	.	.	.	.	.	.	.	.	.	.	G	21.4	4.147928	0.78001	.	.	ENSG00000162923	ENST00000414423;ENST00000366852	T;D	0.83992	0.77;-1.79	3.93	3.93	0.45458	.	.	.	.	.	T	0.74612	0.3739	N	0.08118	0	0.46521	D	0.999086	.	.	.	.	.	.	T	0.78871	-0.2033	7	0.62326	D	0.03	.	13.7722	0.63034	0.0:0.0:1.0:0.0	.	.	.	.	L	61	ENSP00000408108:P61L;ENSP00000355817:P61L	ENSP00000355817:P61L	P	-	2	0	WDR26	222688249	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	3.385000	0.52485	1.748000	0.51833	0.555000	0.69702	CCT	.	.		0.697	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160		A	224621626	G	A	224621626	3	1	64	1	0	0	0	0	1	0	0	0	17298	1000	35	3	1859	3	WDR26	1	224621626	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	20220244	224621626	24628995	22	7739										
ITPKB	3707	hgsc.bcm.edu	37	chr1	226923808	226923808	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aggggctgcccccaagcaagCccagcgttggggaccctccc	13	17	0	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr1:226923808C>T	ENST00000272117.3	-	1	1351	c.1352G>A	c.(1351-1353)gGc>gAc	p.G451D	ITPKB_ENST00000429204.1_Missense_Mutation_p.G451D|ITPKB_ENST00000366784.1_Missense_Mutation_p.G451D			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	451					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				CCCAAGCAAGCCCAGCGTTGG	0.692																																					p.G451D	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.G1352A						.						23	28	26					1																	226923808		2190	4295	6485	SO:0001583	missense	3707	exon2			AGCAAGCCCAGCG	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"inositol 1,4,5-trisphosphate 3-kinase B"			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1352G>A	chr1.hg19:g.226923808C>T	ENSP00000272117:p.Gly451Asp	55.0	0.0		84.0	4.0	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	hg19	CCDS1555.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072740	0.76415	.	.	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.47177	0.96;0.96;0.85	4.91	4.91	0.64330	.	0.357050	0.24415	N	0.038733	T	0.50701	0.1631	L	0.27053	0.805	0.21933	N	0.999462	D	0.69078	0.997	D	0.63597	0.916	T	0.40079	-0.9582	10	0.14656	T	0.56	-23.278	15.4562	0.75314	0.0:1.0:0.0:0.0	.	451	P27987	IP3KB_HUMAN	D	451	ENSP00000272117:G451D;ENSP00000411152:G451D;ENSP00000355748:G451D	ENSP00000272117:G451D	G	-	2	0	ITPKB	224990431	0.000000	0.05858	0.639000	0.29394	0.820000	0.46376	0.640000	0.24705	2.707000	0.92482	0.484000	0.47621	GGC	.	.		0.692	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		T	226923808	C	T	226923808	3	4	64	1	0	0	0	0	1	0	0	0	7927	739	26	3	1516	3	ITPKB	1	226923808	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	2302182	226923808	22326813	23	7740										
APOB	338	hgsc.bcm.edu	37	chr2	21250701	21250701	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcaaactcttcacacttaccTcgatgaggtcagctgaagca	7	12	4	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:21250701T>C	ENST00000233242.1	-	14	2193	c.2066A>G	c.(2065-2067)gAg>gGg	p.E689G	APOB_ENST00000399256.4_Splice_Site_p.E689G	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	689					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACACTTACCTCGATGAGGTC	0.438																																					p.E689G		Atlas-SNP	.											.	APOB	761	.	0			c.A2066G						.						76	82	80					2																	21250701		2202	4300	6502	SO:0001630	splice_region_variant	338	exon14			CTTACCTCGATGA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.2067+1A>G	chr2.hg19:g.21250701T>C		92.0	0.0		98.0	4.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.439747	0.83885	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.39406	1.08;1.08	5.73	5.73	0.89815	Vitellinogen, open beta-sheet, subdomain 1 (1);Lipid transport protein, beta-sheet shell (1);Vitellinogen, open beta-sheet (1);	0.000000	0.85682	D	0.000000	T	0.68357	0.2992	M	0.83953	2.67	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.73487	-0.3967	10	0.87932	D	0	.	16.3259	0.82979	0.0:0.0:0.0:1.0	.	689	P04114	APOB_HUMAN	G	689	ENSP00000233242:E689G;ENSP00000382200:E689G	ENSP00000233242:E689G	E	-	2	0	APOB	21104206	1.000000	0.71417	0.999000	0.59377	0.590000	0.36582	6.489000	0.73641	2.319000	0.78375	0.533000	0.62120	GAG	.	.		0.438	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		Missense_Mutation	C	21250701	T	C	21250701	5	2	64	1	0	0	0	0	0	0	1	0	785	1565	54	2	11689	2	APOB	2	21250701	Splice_Site	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		21250701	221948672	24	7741										
PPM1G	5496	hgsc.bcm.edu	37	chr2	27608639	27608639	+	Missense_Mutation	SNP	T	T	A													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcttcatcagctactttttcTttttcatcttcatcctcagt							TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:27608639T>A	ENST00000344034.4	-	4	648	c.384A>T	c.(382-384)aaA>aaT	p.K128N	PPM1G_ENST00000350803.4_Missense_Mutation_p.K128N	NM_177983.2	NP_817092.1	O15355	PPM1G_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1G	128					cell cycle arrest (GO:0007050)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					CTACTTTTTCTTTTTCATCTT	0.393																																					p.K128N		Atlas-SNP	.											.	PPM1G	42	.	0			c.A384T						.						160	155	157					2																	27608639		2203	4300	6503	SO:0001583	missense	5496	exon4			TTTTTCTTTTTCA	Y13936	CCDS1752.1	2p23.3	2012-04-17	2010-03-05		ENSG00000115241	ENSG00000115241	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9278	protein-coding gene	gene with protein product	"PP2C, gamma", "protein phosphatase 2C, gamma isoform"	605119	"protein phosphatase 1G (formerly 2C), magnesium-dependent, gamma isoform"			9276438	Standard	NM_177983		Approved	PP2CG, PP2Cgamma	uc002rkl.4	O15355	OTTHUMG00000097788	ENST00000344034.4:c.384A>T	chr2.hg19:g.27608639T>A	ENSP00000342778:p.Lys128Asn	149.0	0.0		166.0	26.0	NM_177983		Missense_Mutation	SNP	ENST00000344034.4	hg19	CCDS1752.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.115052	0.37339	.	.	ENSG00000115241	ENST00000344034;ENST00000350803;ENST00000544412	T;T	0.48201	0.82;0.82	5.75	3.4	0.38934	Protein phosphatase 2C-like (4);	0.252181	0.41097	D	0.000947	T	0.34774	0.0909	L	0.52364	1.645	0.42093	D	0.991308	P	0.35011	0.48	B	0.28638	0.092	T	0.10382	-1.0632	10	0.39692	T	0.17	-13.5374	6.391	0.21587	0.0:0.3351:0.0:0.6649	.	128	O15355	PPM1G_HUMAN	N	128;128;111	ENSP00000342778:K128N;ENSP00000264714:K128N	ENSP00000342778:K128N	K	-	3	2	PPM1G	27462143	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.406000	0.34646	0.448000	0.26722	-1.139000	0.01908	AAA	.	.		0.393	PPM1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215032.1	NM_002707		A	27608639	T	A	27608639	3	1	64	1	0	0	0	0	1	0	0	0	12352	1606	56	4	1284	4	PPM1G	2	27608639	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	6357938	27608639	215590734	25	7742	35	2								
PPM1G	5496	hgsc.bcm.edu	37	chr2	27608641	27608641	+	Missense_Mutation	SNP	T	T	C													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttcatcagctactttttcttTttcatcttcatcctcagtgg							TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:27608641T>C	ENST00000344034.4	-	4	646	c.382A>G	c.(382-384)Aaa>Gaa	p.K128E	PPM1G_ENST00000350803.4_Missense_Mutation_p.K128E	NM_177983.2	NP_817092.1	O15355	PPM1G_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1G	128					cell cycle arrest (GO:0007050)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					ACTTTTTCTTTTTCATCTTCA	0.398																																					p.K128E		Atlas-SNP	.											.	PPM1G	42	.	0			c.A382G						.						160	155	156					2																	27608641		2203	4300	6503	SO:0001583	missense	5496	exon4			TTTCTTTTTCATC	Y13936	CCDS1752.1	2p23.3	2012-04-17	2010-03-05		ENSG00000115241	ENSG00000115241	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9278	protein-coding gene	gene with protein product	"PP2C, gamma", "protein phosphatase 2C, gamma isoform"	605119	"protein phosphatase 1G (formerly 2C), magnesium-dependent, gamma isoform"			9276438	Standard	NM_177983		Approved	PP2CG, PP2Cgamma	uc002rkl.4	O15355	OTTHUMG00000097788	ENST00000344034.4:c.382A>G	chr2.hg19:g.27608641T>C	ENSP00000342778:p.Lys128Glu	152.0	0.0		168.0	25.0	NM_177983		Missense_Mutation	SNP	ENST00000344034.4	hg19	CCDS1752.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.009702	0.54361	.	.	ENSG00000115241	ENST00000344034;ENST00000350803;ENST00000544412	T;T	0.46063	0.88;0.88	5.75	5.75	0.90469	Protein phosphatase 2C-like (4);	0.252181	0.41097	D	0.000947	T	0.38427	0.1040	L	0.52364	1.645	0.38452	D	0.946972	B	0.30326	0.276	B	0.27796	0.083	T	0.30534	-0.9975	10	0.33141	T	0.24	-13.5374	14.8904	0.70604	0.0:0.0:0.0:1.0	.	128	O15355	PPM1G_HUMAN	E	128;128;111	ENSP00000342778:K128E;ENSP00000264714:K128E	ENSP00000342778:K128E	K	-	1	0	PPM1G	27462145	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.167000	0.42415	2.201000	0.70794	0.533000	0.62120	AAA	.	.		0.398	PPM1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215032.1	NM_002707		C	27608641	T	C	27608641	3	2	64	1	0	0	0	0	1	0	0	0	12352	1850	64	2	1286	2	PPM1G	2	27608641	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2	27608641	215590732	26	7743	35	2								
LHCGR	3973	hgsc.bcm.edu	37	chr2	48915345	48915345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	caccacattgagaatcaggaTggttaatatatagacttgtg	9	6	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:48915345T>C	ENST00000294954.7	-	11	1612	c.1591A>G	c.(1591-1593)Atc>Gtc	p.I531V	LHCGR_ENST00000344775.3_Missense_Mutation_p.I469V|LHCGR_ENST00000403273.1_3'UTR|LHCGR_ENST00000401907.1_Intron|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000405626.1_Missense_Mutation_p.I504V	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	531					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	AGAATCAGGATGGTTAATATA	0.393																																					p.I531V		Atlas-SNP	.											.	LHCGR	154	.	0			c.A1591G						.						111	113	112					2																	48915345		2203	4300	6503	SO:0001583	missense	3973	exon11			TCAGGATGGTTAA		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"GPCR / Class A : Gonadotropin and TSH receptors"	6585	protein-coding gene	gene with protein product		152790	"hypergonadotropic hypogonadism"	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.1591A>G	chr2.hg19:g.48915345T>C	ENSP00000294954:p.Ile531Val	113.0	0.0		87.0	4.0	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	hg19	CCDS1842.1	.	.	.	.	.	.	.	.	.	.	T	8.373	0.835702	0.16820	.	.	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000405626	T;T;T	0.71934	-0.61;-0.61;-0.61	5.68	4.46	0.54185	GPCR, rhodopsin-like superfamily (1);	0.251853	0.42682	D	0.000665	T	0.61311	0.2337	N	0.11201	0.11	0.45161	D	0.998173	P	0.50272	0.933	P	0.53912	0.737	T	0.60214	-0.7307	9	.	.	.	.	11.7903	0.52065	0.0:0.0:0.1466:0.8534	.	531	P22888	LSHR_HUMAN	V	469;531;504	ENSP00000344301:I469V;ENSP00000294954:I531V;ENSP00000386033:I504V	.	I	-	1	0	LHCGR	48768849	0.993000	0.37304	1.000000	0.80357	0.980000	0.70556	0.852000	0.27764	2.176000	0.68965	0.477000	0.44152	ATC	.	.		0.393	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3		C	48915345	T	C	48915345	3	2	64	1	0	0	0	0	1	0	0	0	8771	1464	51	2	512	2	LHCGR	2	48915345	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	21306704	48915345	194284028	27	7744										
EFEMP1	2202	hgsc.bcm.edu	37	chr2	56145028	56145028	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agctacaaccccggtggttgCccctgaggttccttctgctg	11	14	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:56145028C>T	ENST00000394555.2	-	4	724	c.289G>A	c.(289-291)Gca>Aca	p.A97T	EFEMP1_ENST00000394554.1_Missense_Mutation_p.A97T|EFEMP1_ENST00000424836.2_Missense_Mutation_p.A39T|EFEMP1_ENST00000355426.3_Missense_Mutation_p.A97T	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	97					epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CCGGTGGTTGCCCCTGAGGTT	0.557																																					p.A97T	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.G289A						.						97	97	97					2																	56145028		2203	4300	6503	SO:0001583	missense	2202	exon4			TGGTTGCCCCTGA	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"Fibulins"	3218	protein-coding gene	gene with protein product	"fibulin 3"	601548	"fibrillin-like", "EGF-containing fibulin-like extracellular matrix protein 1"	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.289G>A	chr2.hg19:g.56145028C>T	ENSP00000378058:p.Ala97Thr	217.0	0.0		199.0	78.0	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Missense_Mutation	SNP	ENST00000394555.2	hg19	CCDS1857.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.797549	0.31777	.	.	ENSG00000115380	ENST00000394555;ENST00000394554;ENST00000424836;ENST00000355426;ENST00000438672;ENST00000439193;ENST00000440439	D;D;T;D;T;T;T	0.83591	-1.74;-1.74;-1.28;-1.74;-1.23;-1.25;-1.12	5.34	-0.879	0.10613	.	0.646499	0.13744	N	0.365742	T	0.64450	0.2599	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.53816	-0.8385	10	0.48119	T	0.1	.	9.9113	0.41408	0.0:0.5395:0.0:0.4605	.	39;97	B4DW75;Q12805	.;FBLN3_HUMAN	T	97;97;39;97;97;97;97	ENSP00000378058:A97T;ENSP00000378057:A97T;ENSP00000399145:A39T;ENSP00000347596:A97T;ENSP00000392055:A97T;ENSP00000408195:A97T;ENSP00000398345:A97T	ENSP00000347596:A97T	A	-	1	0	EFEMP1	55998532	0.000000	0.05858	0.002000	0.10522	0.802000	0.45316	-0.396000	0.07278	-0.104000	0.12154	0.650000	0.86243	GCA	.	.		0.557	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2			T	56145028	C	T	56145028	3	4	64	1	0	0	0	0	1	0	0	0	4943	739	26	3	1224	3	EFEMP1	2	56145028	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	7229683	56145028	187054345	28	7745										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84806671	84806671	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtgctaaattttatgcttccTcgtcaaagcaagaaaaaagt	7	7	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:84806671T>C	ENST00000237449.6	+	13	2105	c.2097T>C	c.(2095-2097)ccT>ccC	p.P699P	DNAH6_ENST00000398278.2_Silent_p.P699P|DNAH6_ENST00000389394.3_Silent_p.P699P			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	699	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTATGCTTCCTCGTCAAAGCA	0.328																																					p.P699P		Atlas-SNP	.											.	DNAH6	194	.	0			c.T2097C						.						108	104	106					2																	84806671		2203	4300	6503	SO:0001819	synonymous_variant	1768	exon14			GCTTCCTCGTCAA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.2097T>C	chr2.hg19:g.84806671T>C		81.0	0.0		90.0	4.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.328	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		C	84806671	T	C	84806671	2	2	64	1	0	0	0	0	0	0	0	1	4607	1538	54	2		2	DNAH6	2	84806671	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	28661643	84806671	158392702	29	7746										
CLASP1	23332	hgsc.bcm.edu	37	chr2	122159109	122159109	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgacatctagagccttttgaActtttgcttgcacagatcca	7	10	1	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:122159109A>G	ENST00000263710.4	-	28	3265	c.2876T>C	c.(2875-2877)gTt>gCt	p.V959A	CLASP1_ENST00000545861.1_Missense_Mutation_p.V705A|CLASP1_ENST00000397587.3_Missense_Mutation_p.V938A|CLASP1_ENST00000541859.1_Missense_Mutation_p.V715A|CLASP1_ENST00000455322.2_Missense_Mutation_p.V954A|CLASP1_ENST00000409078.3_Missense_Mutation_p.V931A|CLASP1_ENST00000541377.1_Missense_Mutation_p.V937A	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	959					axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					AGCCTTTTGAACTTTTGCTTG	0.348																																					p.V959A		Atlas-SNP	.											.	CLASP1	135	.	0			c.T2876C						.						248	244	245					2																	122159109		1853	4095	5948	SO:0001583	missense	23332	exon27			TTTTGAACTTTTG	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"multiple asters 1"	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.2876T>C	chr2.hg19:g.122159109A>G	ENSP00000263710:p.Val959Ala	95.0	0.0		122.0	5.0	NM_015282	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	hg19		.	.	.	.	.	.	.	.	.	.	A	28.2	4.900940	0.92035	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55;0.55	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68641	0.3023	L	0.55103	1.725	0.58432	D	0.999998	D;D;D	0.67145	0.994;0.992;0.996	D;D;D	0.75484	0.97;0.945;0.986	T	0.71527	-0.4566	10	0.87932	D	0	-1.8452	16.0303	0.80572	1.0:0.0:0.0:0.0	.	931;938;959	E7EUA5;F5GWS0;Q7Z460	.;.;CLAP1_HUMAN	A	959;954;938;937;715;931;705	ENSP00000263710:V959A;ENSP00000389372:V954A;ENSP00000380717:V938A;ENSP00000441625:V937A;ENSP00000441770:V715A;ENSP00000386442:V931A;ENSP00000438620:V705A	ENSP00000263710:V959A	V	-	2	0	CLASP1	121875579	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.859000	0.92264	2.243000	0.73865	0.482000	0.46254	GTT	.	.		0.348	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		G	122159109	A	G	122159109	3	3	64	1	0	0	0	0	1	0	0	0	3456	43	2	2	1792	2	CLASP1	2	122159109	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	37352438	122159109	121040264	30	7747										
UGGT1	56886	hgsc.bcm.edu	37	chr2	128930206	128930206	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttcagacaatagttttgctaAgggtccaatcgcaaaatttt	7	7	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:128930206A>G	ENST00000259253.6	+	29	3211	c.3164A>G	c.(3163-3165)aAg>aGg	p.K1055R	UGGT1_ENST00000375990.3_Missense_Mutation_p.K1031R	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1055					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						AGTTTTGCTAAGGGTCCAATC	0.383																																					p.K1055R		Atlas-SNP	.											.	UGGT1	126	.	0			c.A3164G						.						140	134	136					2																	128930206		2203	4300	6503	SO:0001583	missense	56886	exon29			TTGCTAAGGGTCC	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.3164A>G	chr2.hg19:g.128930206A>G	ENSP00000259253:p.Lys1055Arg	83.0	0.0		97.0	4.0	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	hg19	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	A	13.33	2.204200	0.38905	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.30714	1.52;1.52	5.81	3.26	0.37387	.	0.337771	0.31246	N	0.007983	T	0.16128	0.0388	N	0.05230	-0.09	0.29449	N	0.858624	B	0.20988	0.05	B	0.35770	0.21	T	0.28554	-1.0040	9	.	.	.	.	7.1817	0.25776	0.5488:0.3374:0.0:0.1138	.	1055	Q9NYU2	UGGG1_HUMAN	R	1031;1055	ENSP00000365158:K1031R;ENSP00000259253:K1055R	.	K	+	2	0	UGGT1	128646676	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.994000	0.63901	0.999000	0.39023	0.482000	0.46254	AAG	.	.		0.383	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		G	128930206	A	G	128930206	3	3	64	1	0	0	0	0	1	0	0	0	16956	72	3	2	3278	2	UGGT1	2	128930206	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	6771097	128930206	114269167	31	7748										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141092035	141092035	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atcatacctgtgggtctctgTaagttcttttgtactaaaat	7	7	3	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:141092035T>C	ENST00000389484.3	-	79	13181	c.12210A>G	c.(12208-12210)ttA>ttG	p.L4070L		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4070					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGGGTCTCTGTAAGTTCTTTT	0.378										TSP Lung(27;0.18)																											p.L4070L	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A12210G						.						164	152	156					2																	141092035		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon79			TCTCTGTAAGTTC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12210A>G	chr2.hg19:g.141092035T>C		288.0	0.0		252.0	94.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	9.331	1.060628	0.19987	.	.	ENSG00000168702	ENST00000437977	.	.	.	6.08	-1.42	0.08913	.	.	.	.	.	T	0.51449	0.1675	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43458	-0.9390	4	.	.	.	.	6.9361	0.24466	0.0:0.3497:0.208:0.4423	.	.	.	.	C	302	.	.	Y	-	2	0	LRP1B	140808505	1.000000	0.71417	0.985000	0.45067	0.938000	0.57974	0.736000	0.26130	-0.136000	0.11475	0.482000	0.46254	TAC	.	.		0.378	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141092035	T	C	141092035	2	2	64	1	0	0	0	0	0	0	0	1	8964	1635	57	2		2	LRP1B	2	141092035	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	12161829	141092035	102107338	32	7749										
TTN	7273	hgsc.bcm.edu	37	chr2	179628973	179628973	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gacagtgtcctgaagcggggTgatgatggcaggtggataaa	17	5	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:179628973T>C	ENST00000591111.1	-	43	10269	c.10045A>G	c.(10045-10047)Acc>Gcc	p.T3349A	TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.T3349A|TTN_ENST00000589042.1_Missense_Mutation_p.T3349A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T3303A|TTN_ENST00000342992.6_Missense_Mutation_p.T3349A|TTN_ENST00000359218.5_Missense_Mutation_p.T3303A|TTN_ENST00000460472.2_Missense_Mutation_p.T3303A			Q8WZ42	TITIN_HUMAN	titin	13665	Ig-like 20.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGAAGCGGGGTGATGATGGCA	0.458																																					p.T3349A		Atlas-SNP	.											.	TTN	18412	.	0			c.A10045G						.						86	83	84					2																	179628973		2203	4300	6503	SO:0001583	missense	7273	exon43			GCGGGGTGATGAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10045A>G	chr2.hg19:g.179628973T>C	ENSP00000465570:p.Thr3349Ala	123.0	0.0		93.0	6.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.91	2.675966	0.47886	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28	5.69	0.208	0.15221	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50188	0.1601	L	0.34521	1.04	0.20703	N	0.999866	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.09377	0.001;0.001;0.001;0.001;0.004	T	0.44711	-0.9310	9	0.87932	D	0	.	4.3501	0.11151	0.2248:0.1916:0.0:0.5837	.	3303;3303;3303;3349;3349	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	A	3349;3303;3303;3303;3303;3349	ENSP00000343764:T3349A;ENSP00000434586:T3303A;ENSP00000340554:T3303A;ENSP00000352154:T3303A;ENSP00000354117:T3349A	ENSP00000340554:T3303A	T	-	1	0	TTN	179337218	0.997000	0.39634	0.748000	0.31131	0.966000	0.64601	0.563000	0.23547	0.079000	0.16929	0.533000	0.62120	ACC	.	.		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179628973	T	C	179628973	3	2	64	1	0	0	0	0	1	0	0	0	16750	1696	59	2	101223	2	TTN	2	179628973	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	38536938	179628973	63570400	33	7750										
TMEFF2	23671	hgsc.bcm.edu	37	chr2	193056689	193056689	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggtgttggtgtcacagaggaAgagatcattttctctgtcat	12	6	4	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:193056689A>G	ENST00000272771.5	-	2	1383	c.199T>C	c.(199-201)Ttc>Ctc	p.F67L	TMEFF2_ENST00000409056.3_Missense_Mutation_p.F67L|TMEFF2_ENST00000392314.1_Missense_Mutation_p.F67L	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2	67						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(12)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			TCACAGAGGAAGAGATCATTT	0.348																																					p.F67L	Pancreas(50;1277 1381 28487 47072)	Atlas-SNP	.											.	TMEFF2	54	.	0			c.T199C						.						91	87	89					2																	193056689		2203	4300	6503	SO:0001583	missense	23671	exon2			AGAGGAAGAGATC	AB017269	CCDS2314.1	2q32.3	2010-05-04			ENSG00000144339	ENSG00000144339			11867	protein-coding gene	gene with protein product	"transmembrane protein TENB2", "tomoregulin", "cancer/testis antigen family 120, member 2"	605734				10903839	Standard	NM_016192		Approved	TENB2, HPP1, TR, TPEF, CT120.2	uc002utc.3	Q9UIK5	OTTHUMG00000132723	ENST00000272771.5:c.199T>C	chr2.hg19:g.193056689A>G	ENSP00000272771:p.Phe67Leu	86.0	0.0		91.0	4.0	NM_016192	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Missense_Mutation	SNP	ENST00000272771.5	hg19	CCDS2314.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.137932	0.77775	.	.	ENSG00000144339	ENST00000392314;ENST00000272771;ENST00000409056	T;T;T	0.67865	0.34;0.33;-0.29	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.76198	0.3954	L	0.54323	1.7	0.58432	D	0.999999	D;P	0.71674	0.998;0.863	D;P	0.63283	0.913;0.53	T	0.72972	-0.4129	10	0.27785	T	0.31	-15.4577	16.5655	0.84588	1.0:0.0:0.0:0.0	.	67;67	Q9UIK5-3;Q9UIK5	.;TEFF2_HUMAN	L	67	ENSP00000376128:F67L;ENSP00000272771:F67L;ENSP00000386871:F67L	ENSP00000272771:F67L	F	-	1	0	TMEFF2	192764934	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.801000	0.75170	2.302000	0.77476	0.533000	0.62120	TTC	.	.		0.348	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192		G	193056689	A	G	193056689	3	3	64	1	0	0	0	0	1	0	0	0	16029	72	3	2	961	2	TMEFF2	2	193056689	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	13427716	193056689	50142684	34	7751										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196750895	196750895	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gagtaagtttctcgatcattTctctcctttagtttgacttc	6	9	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:196750895T>C	ENST00000312428.6	-	34	5608	c.5508A>G	c.(5506-5508)agA>agG	p.R1836R		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1836					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CTCGATCATTTCTCTCCTTTA	0.398																																					p.R1836R		Atlas-SNP	.											.	DNAH7	512	.	0			c.A5508G						.						154	154	154					2																	196750895		1878	4111	5989	SO:0001819	synonymous_variant	56171	exon34			ATCATTTCTCTCC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.5508A>G	chr2.hg19:g.196750895T>C		58.0	0.0		100.0	4.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.398	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196750895	T	C	196750895	2	2	64	1	0	0	0	0	0	0	0	1	4608	1780	62	2		2	DNAH7	2	196750895	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	3694206	196750895	46448478	35	7752										
STK17B	9262	hgsc.bcm.edu	37	chr2	197021354	197021354	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtagattttgatatacattgTctaaccacagcaaattttcc	5	8	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:197021354T>C	ENST00000263955.4	-	3	430	c.144A>G	c.(142-144)agA>agG	p.R48R	RP11-347P5.1_ENST00000606818.1_RNA|STK17B_ENST00000409228.1_Silent_p.R48R	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	48	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(10)	15			OV - Ovarian serous cystadenocarcinoma(117;0.141)			ATATACATTGTCTAACCACAG	0.348																																					p.R48R		Atlas-SNP	.											.	STK17B	28	.	0			c.A144G						.						85	88	87					2																	197021354		2203	4300	6503	SO:0001819	synonymous_variant	9262	exon3			ACATTGTCTAACC	AB011421	CCDS2315.1	2q33.1	2008-02-05	2007-02-12		ENSG00000081320	ENSG00000081320			11396	protein-coding gene	gene with protein product	"death-associated protein kinase-related 2"	604727	"serine/threonine kinase 17b (apoptosis-inducing)"			9786912	Standard	NM_004226		Approved	DRAK2	uc002utk.3	O94768	OTTHUMG00000132735	ENST00000263955.4:c.144A>G	chr2.hg19:g.197021354T>C		102.0	0.0		98.0	4.0	NM_004226		Silent	SNP	ENST00000263955.4	hg19	CCDS2315.1																																																																																			.	.		0.348	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2			C	197021354	T	C	197021354	2	2	64	1	0	0	0	0	0	0	0	1	15306	1664	58	2		2	STK17B	2	197021354	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	270459	197021354	46178019	36	7753										
SGOL2	151246	hgsc.bcm.edu	37	chr2	201437542	201437542	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	taattcctgaaaccaaccaaAtatatgagaatgataacaaa	4	7	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:201437542A>G	ENST00000357799.4	+	7	2571	c.2473A>G	c.(2473-2475)Ata>Gta	p.I825V		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	825					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						AACCAACCAAATATATGAGAA	0.323																																					p.I825V		Atlas-SNP	.											.	SGOL2	126	.	0			c.A2473G						.						90	87	88					2																	201437542		1830	4085	5915	SO:0001583	missense	151246	exon7			AACCAAATATATG	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.2473A>G	chr2.hg19:g.201437542A>G	ENSP00000350447:p.Ile825Val	116.0	0.0		119.0	5.0	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	hg19	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	A	0.141	-1.101785	0.01828	.	.	ENSG00000163535	ENST00000357799	T	0.14766	2.48	5.0	1.3	0.21679	.	0.530450	0.18477	N	0.140028	T	0.13927	0.0337	M	0.69823	2.125	0.09310	N	1	B;B;B	0.20887	0.049;0.018;0.007	B;B;B	0.10450	0.005;0.005;0.003	T	0.21245	-1.0251	10	0.31617	T	0.26	-0.2792	6.9476	0.24528	0.7311:0.0:0.2689:0.0	.	825;825;825	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	V	825	ENSP00000350447:I825V	ENSP00000350447:I825V	I	+	1	0	SGOL2	201145787	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.168000	0.09925	0.136000	0.18733	-0.359000	0.07587	ATA	.	.		0.323	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		G	201437542	A	G	201437542	3	3	64	1	0	0	0	0	1	0	0	0	14232	101	4	2	2495	2	SGOL2	2	201437542	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	4416188	201437542	41761831	37	7754										
NCL	4691	hgsc.bcm.edu	37	chr2	232325414	232325414	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcttcctcctcctcatcatcTtcatcatcatcatcttcatc	0	17	10	0	rs540030591|rs139777351|rs371359723|rs199689485|rs527711138|rs368566589	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:232325414T>A	ENST00000322723.4	-	4	1017	c.777A>T	c.(775-777)gaA>gaT	p.E259D	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	259	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CCtcatcatcttcatcatcat	0.438																																					p.E259D		Atlas-SNP	.											.	NCL	80	.	0			c.A777T						.						229	194	206					2																	232325414		2203	4300	6503	SO:0001583	missense	4691	exon4			ATCATCTTCATCA		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.777A>T	chr2.hg19:g.232325414T>A	ENSP00000318195:p.Glu259Asp	209.0	0.0		206.0	18.0	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	hg19	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	T	0.028	-1.357543	0.01245	.	.	ENSG00000115053	ENST00000322723;ENST00000392033	T	0.23552	1.9	4.93	-9.86	0.00473	.	1.633390	0.02710	N	0.112777	T	0.06554	0.0168	N	0.03608	-0.345	0.19945	N	0.999949	B	0.02656	0.0	B	0.08055	0.003	T	0.26677	-1.0096	10	0.02654	T	1	0.5096	0.6058	0.00752	0.2352:0.1751:0.2128:0.3769	.	259	P19338	NUCL_HUMAN	D	259;151	ENSP00000318195:E259D	ENSP00000318195:E259D	E	-	3	2	NCL	232033658	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.197000	0.00276	-4.228000	0.00063	-3.370000	0.00041	GAA	.	.		0.438	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		A	232325414	T	A	232325414	3	1	64	1	0	0	0	0	1	0	0	0	10235	1606	56	4	1399	4	NCL	2	232325414	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	30887872	232325414	10873959	38	7755										
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233684562	233684562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggctctgcgtcgccagcgggAgcaagaaattgcattaaggc	14	10	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:233684562A>G	ENST00000409547.1	+	23	2707	c.2396A>G	c.(2395-2397)gAg>gGg	p.E799G	GIGYF2_ENST00000409196.3_Missense_Mutation_p.E793G|GIGYF2_ENST00000409451.3_Missense_Mutation_p.E820G|GIGYF2_ENST00000373563.4_Missense_Mutation_p.E799G|GIGYF2_ENST00000373566.3_Missense_Mutation_p.E821G|GIGYF2_ENST00000409480.1_Missense_Mutation_p.E821G|GIGYF2_ENST00000452341.2_Missense_Mutation_p.E630G	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	799	Gln-rich.|Glu-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		CGCCAGCGGGAGCAAGAAATT	0.478																																					p.E820G		Atlas-SNP	.											.	GIGYF2	288	.	0			c.A2459G						.						53	57	55					2																	233684562		2203	4300	6503	SO:0001583	missense	26058	exon23			AGCGGGAGCAAGA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2396A>G	chr2.hg19:g.233684562A>G	ENSP00000386537:p.Glu799Gly	79.0	0.0		87.0	6.0	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	A	19.09	3.760744	0.69763	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	T;T;T;T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03;-1.03;-1.03;-1.03	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	D	0.85517	0.5715	L	0.56769	1.78	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.998;0.998;0.998	D;D;D;D	0.83275	0.996;0.979;0.979;0.979	D	0.86381	0.1729	10	0.54805	T	0.06	-9.0267	14.7797	0.69756	1.0:0.0:0.0:0.0	.	630;820;799;793	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	G	821;799;821;799;793;820;793;630	ENSP00000362667:E821G;ENSP00000362664:E799G;ENSP00000386765:E821G;ENSP00000386537:E799G;ENSP00000387070:E793G;ENSP00000387170:E820G;ENSP00000410297:E793G;ENSP00000411505:E630G	ENSP00000362664:E799G	E	+	2	0	GIGYF2	233392806	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	5.494000	0.66905	1.891000	0.54761	0.379000	0.24179	GAG	.	.		0.478	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		G	233684562	A	G	233684562	3	3	64	1	0	0	0	0	1	0	0	0	6386	304	11	2	2540	2	GIGYF2	2	233684562	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1359148	233684562	9514811	39	7756										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238244875	238244875	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	actggttttgcagcagcagcAgcggggggtcttacagctgc	15	10	1	0	rs398102314		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:238244875A>G	ENST00000295550.4	-	40	9320	c.8868T>C	c.(8866-8868)gcT>gcC	p.A2956A	COL6A3_ENST00000346358.4_Silent_p.A2756A|COL6A3_ENST00000409809.1_Silent_p.A2750A|COL6A3_ENST00000353578.4_Silent_p.A2750A|COL6A3_ENST00000347401.3_Silent_p.A2755A|COL6A3_ENST00000472056.1_Silent_p.A2349A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2956	Ala-rich.|Nonhelical region.			Missing (in Ref. 1; CAA36267). {ECO:0000305}.	axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CAGCAGCAGCAGCGGGGGGTC	0.617																																					p.A2956A		Atlas-SNP	.											.,7	COL6A3	608	.	0			c.T8868C						.						37	41	40					2																	238244875		2199	4298	6497	SO:0001819	synonymous_variant	1293	exon40			AGCAGCAGCGGGG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8868T>C	chr2.hg19:g.238244875A>G		73.0	0.0		65.0	3.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.		0.617	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238244875	A	G	238244875	2	3	64	1	0	0	0	0	0	0	0	1	3703	175	7	2		2	COL6A3	2	238244875	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	4560313	238244875	4954498	40	7757										
CAPN10	11132	hgsc.bcm.edu	37	chr2	241534647	241534647	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gggcccgggcactggtgggtGacagtcatacttcgtggagc	17	10	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:241534647G>T	ENST00000391984.2	+	7	1400	c.1204G>T	c.(1204-1206)Gac>Tac	p.D402Y	CAPN10_ENST00000270364.7_Intron|CAPN10_ENST00000354082.4_Missense_Mutation_p.D402Y|CAPN10_ENST00000352879.4_Intron|CAPN10_ENST00000391982.2_Missense_Mutation_p.D402Y|CAPN10_ENST00000404753.3_Missense_Mutation_p.D402Y	NM_023083.3	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10	402	Domain III 1.				actin cytoskeleton reorganization (GO:0031532)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to insulin stimulus (GO:0032869)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin secretion (GO:0032024)|positive regulation of intracellular transport (GO:0032388)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteolysis (GO:0006508)|type B pancreatic cell apoptotic process (GO:0097050)	cell (GO:0005623)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cytoskeletal protein binding (GO:0008092)|SNARE binding (GO:0000149)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|urinary_tract(1)	27		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)		ACTGGTGGGTGACAGTCATAC	0.657																																					p.D402Y		Atlas-SNP	.											.	CAPN10	105	.	0			c.G1204T						.						40	44	42					2																	241534647		2203	4299	6502	SO:0001583	missense	11132	exon7			GTGGGTGACAGTC	AF089088	CCDS33420.1, CCDS42838.1	2q37.3	2008-05-22			ENSG00000142330	ENSG00000142330			1477	protein-coding gene	gene with protein product		605286				11017071, 11018080	Standard	NM_023083		Approved		uc002vzk.2	Q9HC96	OTTHUMG00000133358	ENST00000391984.2:c.1204G>T	chr2.hg19:g.241534647G>T	ENSP00000375844:p.Asp402Tyr	222.0	0.0		293.0	72.0	NM_023085	A8MVS7|Q4ZFV1|Q8NCD4|Q96IG4|Q96JI2|Q9HC89|Q9HC90|Q9HC91|Q9HC92|Q9HC93|Q9HC94|Q9HC95	Missense_Mutation	SNP	ENST00000391984.2	hg19	CCDS42838.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.480577	0.44044	.	.	ENSG00000142330	ENST00000391984;ENST00000391982;ENST00000404753;ENST00000354082	T;D;T;D	0.88431	1.02;-2.38;1.02;-1.9	4.38	-1.87	0.07737	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.770342	0.11744	N	0.533774	D	0.86560	0.5962	L	0.54323	1.7	0.09310	N	1	P;B;P;B	0.50272	0.889;0.307;0.933;0.307	B;B;P;B	0.49421	0.434;0.232;0.61;0.232	T	0.77915	-0.2409	10	0.87932	D	0	.	5.5588	0.17131	0.4988:0.147:0.3542:0.0	.	402;402;402;402	B7Z6G3;B7WPF5;Q9HC96-3;Q9HC96	.;.;.;CAN10_HUMAN	Y	402	ENSP00000375844:D402Y;ENSP00000375842:D402Y;ENSP00000384422:D402Y;ENSP00000270362:D402Y	ENSP00000270362:D402Y	D	+	1	0	CAPN10	241183320	0.005000	0.15991	0.000000	0.03702	0.010000	0.07245	1.184000	0.32053	-0.289000	0.09038	0.655000	0.94253	GAC	.	.		0.657	CAPN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257191.3	NM_023083		T	241534647	G	T	241534647	3	4	64	1	0	0	0	0	1	0	0	0	2625	1290	45	3	1230	3	CAPN10	2	241534647	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	3289772	241534647	1664726	41	7758										
NEU4	129807	hgsc.bcm.edu	37	chr2	242756278	242756278	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tctgctgtgtggccagccgtGacgccggcctctcgtggggc	16	14	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr2:242756278G>T	ENST00000391969.2	+	4	1102	c.391G>T	c.(391-393)Gac>Tac	p.D131Y	NEU4_ENST00000404257.1_Missense_Mutation_p.D143Y|NEU4_ENST00000325935.6_Missense_Mutation_p.D144Y|NEU4_ENST00000407683.1_Missense_Mutation_p.D131Y|NEU4_ENST00000405370.1_Missense_Mutation_p.D131Y	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	131					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		GGCCAGCCGTGACGCCGGCCT	0.711																																					p.D144Y		Atlas-SNP	.											.	NEU4	39	.	0			c.G430T						.						6	8	7					2																	242756278		2038	4048	6086	SO:0001583	missense	129807	exon3			AGCCGTGACGCCG	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.391G>T	chr2.hg19:g.242756278G>T	ENSP00000375830:p.Asp131Tyr	2.0	0.0		38.0	18.0	NM_001167599	A8K056|J3KNJ5|Q96D64	Missense_Mutation	SNP	ENST00000391969.2	hg19	CCDS54442.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.391018	0.62066	.	.	ENSG00000204099	ENST00000407683;ENST00000405370;ENST00000472793;ENST00000423583;ENST00000404257;ENST00000391969;ENST00000325935;ENST00000420288	D;D;D;D;D;D;D	0.96459	-4.02;-4.02;-4.02;-4.02;-4.02;-4.02;-4.02	4.57	4.57	0.56435	Neuraminidase (2);	0.000000	0.85682	D	0.000000	D	0.98658	0.9550	M	0.94142	3.5	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99851	1.1072	10	0.87932	D	0	-42.3075	17.3295	0.87258	0.0:0.0:1.0:0.0	.	143;143;131	A8K211;Q8WWR8-2;Q8WWR8	.;.;NEUR4_HUMAN	Y	131;131;141;131;143;131;144;131	ENSP00000385402:D131Y;ENSP00000384804:D131Y;ENSP00000397860:D131Y;ENSP00000385149:D143Y;ENSP00000375830:D131Y;ENSP00000320318:D144Y;ENSP00000388707:D131Y	ENSP00000320318:D144Y	D	+	1	0	NEU4	242404951	1.000000	0.71417	0.528000	0.27938	0.028000	0.11728	6.298000	0.72763	2.077000	0.62373	0.462000	0.41574	GAC	.	.		0.711	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741		T	242756278	G	T	242756278	3	4	64	1	0	0	0	0	1	0	0	0	10353	1290	45	3	440	3	NEU4	2	242756278	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	1221631	242756278	443095	42	7759										
TRNT1	51095	hgsc.bcm.edu	37	chr3	3189269	3189269	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cacaaaattggatttgaggtTgaagatcgcaaaagaggaga	12	4	0	5			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:3189269T>C	ENST00000251607.6	+	7	1040	c.938T>C	c.(937-939)tTg>tCg	p.L313S	TRNT1_ENST00000280591.6_Missense_Mutation_p.L293S	NM_182916.2	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	313					protein targeting to mitochondrion (GO:0006626)|tRNA 3'-end processing (GO:0042780)|tRNA 3'-terminal CCA addition (GO:0001680)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity (GO:0052929)|CTP:3'-cytidine-tRNA cytidylyltransferase activity (GO:0052928)|CTP:tRNA cytidylyltransferase activity (GO:0052927)|tRNA adenylyltransferase activity (GO:0004810)|tRNA binding (GO:0000049)			breast(2)|endometrium(3)|large_intestine(4)|lung(2)|urinary_tract(1)	12				Epithelial(13;0.00226)|OV - Ovarian serous cystadenocarcinoma(96;0.00592)|all cancers(10;0.011)		GATTTGAGGTTGAAGATCGCA	0.333																																					p.L313S		Atlas-SNP	.											.	TRNT1	34	.	0			c.T938C						.						87	93	91					3																	3189269		2203	4300	6503	SO:0001583	missense	51095	exon7			TGAGGTTGAAGAT	AF151805	CCDS2561.2	3p25.1	2002-05-30			ENSG00000072756	ENSG00000072756	2.7.7.25		17341	protein-coding gene	gene with protein product		612907				10810093, 11504732	Standard	NM_182916		Approved	MtCCA, CGI-47, CCA1	uc003bpp.4	Q96Q11	OTTHUMG00000090259	ENST00000251607.6:c.938T>C	chr3.hg19:g.3189269T>C	ENSP00000251607:p.Leu313Ser	148.0	0.0		102.0	5.0	NM_182916	A8K2Z6|B7WP13|C9JKA2|Q8ND57|Q9BS97|Q9Y362	Missense_Mutation	SNP	ENST00000251607.6	hg19	CCDS2561.2	.	.	.	.	.	.	.	.	.	.	T	23.7	4.445521	0.84101	.	.	ENSG00000072756	ENST00000251607;ENST00000280591	T;T	0.54866	0.55;0.59	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000001	T	0.73297	0.3569	M	0.80183	2.485	0.80722	D	1	P;D	0.76494	0.86;0.999	P;D	0.69654	0.661;0.965	T	0.77760	-0.2467	10	0.87932	D	0	-2.0847	15.5464	0.76104	0.0:0.0:0.0:1.0	.	293;313	Q96Q11-2;Q96Q11	.;TRNT1_HUMAN	S	313;293	ENSP00000251607:L313S;ENSP00000280591:L293S	ENSP00000251607:L313S	L	+	2	0	TRNT1	3164269	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.424000	0.80242	2.155000	0.67459	0.533000	0.62120	TTG	.	.		0.333	TRNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337616.1			C	3189269	T	C	3189269	3	2	64	1	0	0	0	0	1	0	0	0	16588	1821	63	2	960	2	TRNT1	3	3189269	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		3189269	194833161	43	7760										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9106232	9106232	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cttgctttccgcactgatgcTctctgcatggtacatgtggt	10	11	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:9106232T>C	ENST00000383836.3	-	5	947	c.520A>G	c.(520-522)Agc>Ggc	p.S174G	SRGAP3_ENST00000360413.3_Missense_Mutation_p.S174G|SRGAP3_ENST00000433332.3_5'UTR	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	174	F-BAR domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GCACTGATGCTCTCTGCATGG	0.557			T	RAF1	pilocytic astrocytoma																																p.S174G		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.A520G						.						146	111	123					3																	9106232		2203	4300	6503	SO:0001583	missense	9901	exon5			TGATGCTCTCTGC	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.520A>G	chr3.hg19:g.9106232T>C	ENSP00000373347:p.Ser174Gly	180.0	0.0		101.0	5.0	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.586067	0.86748	.	.	ENSG00000196220	ENST00000383836;ENST00000360413;ENST00000544908	T;T	0.14391	2.51;2.51	4.9	4.9	0.64082	.	0.041576	0.85682	N	0.000000	T	0.38799	0.1054	M	0.83012	2.62	0.58432	D	0.999995	D;B;P;P	0.58268	0.982;0.135;0.949;0.915	D;B;P;P	0.67548	0.952;0.12;0.731;0.543	T	0.27400	-1.0075	10	0.42905	T	0.14	.	14.5406	0.67990	0.0:0.0:0.0:1.0	.	174;43;174;174	C7TPG7;Q9ULR4;O43295-2;O43295	.;.;.;SRGP2_HUMAN	G	174;174;54	ENSP00000373347:S174G;ENSP00000353587:S174G	ENSP00000353587:S174G	S	-	1	0	SRGAP3	9081232	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.822000	0.86651	1.982000	0.57802	0.333000	0.21579	AGC	.	.		0.557	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			C	9106232	T	C	9106232	3	2	64	1	0	0	0	0	1	0	0	0	15162	1551	54	2	2886	2	SRGAP3	3	9106232	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	5916963	9106232	188916198	44	7761										
ZNF860	344787	hgsc.bcm.edu	37	chr3	32031946	32031946	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aaccttacaagtgtaatgagTgtggcaagaccttccatcac	8	10	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:32031946T>C	ENST00000360311.4	+	2	1924	c.1375T>C	c.(1375-1377)Tgt>Cgt	p.C459R		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	459					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						GTGTAATGAGTGTGGCAAGAC	0.398																																					p.C459R		Atlas-SNP	.											.	ZNF860	96	.	0			c.T1375C						.						44	69	62					3																	32031946		692	1591	2283	SO:0001583	missense	344787	exon2			AATGAGTGTGGCA	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"Zinc fingers, C2H2-type", "-"	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1375T>C	chr3.hg19:g.32031946T>C	ENSP00000373274:p.Cys459Arg	49.0	0.0		33.0	4.0	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	hg19	CCDS46784.1	.	.	.	.	.	.	.	.	.	.	t	7.117	0.577209	0.13686	.	.	ENSG00000197385	ENST00000360311	D	0.85955	-2.05	0.336	-0.672	0.11377	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93122	0.7810	H	0.97707	4.06	0.36032	D	0.839491	D	0.63046	0.992	D	0.79108	0.992	D	0.88221	0.2897	8	.	.	.	.	4.0308	0.09708	0.0:0.2849:0.0:0.7151	.	459	A6NHJ4	ZN860_HUMAN	R	459	ENSP00000373274:C459R	.	C	+	1	0	ZNF860	32006950	0.999000	0.42202	0.005000	0.12908	0.005000	0.04900	3.829000	0.55760	-0.993000	0.03467	-1.026000	0.02426	TGT	.	.		0.398	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1			C	32031946	T	C	32031946	3	2	64	1	0	0	0	0	1	0	0	0	18209	1696	59	2	1377	2	ZNF860	3	32031946	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	22925714	32031946	165990484	45	7762										
ZNF662	389114	hgsc.bcm.edu	37	chr3	42954744	42954744	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccatcctgagcaggtggaagAgccattaaacctgaaactgc	10	11	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:42954744A>G	ENST00000541208.1	+	4	572	c.203A>G	c.(202-204)gAg>gGg	p.E68G	ZNF662_ENST00000440367.2_Missense_Mutation_p.E68G|ZNF662_ENST00000430067.2_3'UTR|KRBOX1_ENST00000426937.1_Intron|ZNF662_ENST00000328199.6_Intron|ZNF662_ENST00000422021.1_Intron			Q6ZS27	ZN662_HUMAN	zinc finger protein 662	68					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.217)		CAGGTGGAAGAGCCATTAAAC	0.473																																					p.E68G		Atlas-SNP	.											.	ZNF662	112	.	0			c.A203G						.						95	97	96					3																	42954744		2203	4300	6503	SO:0001583	missense	389114	exon4			TGGAAGAGCCATT	AK127779	CCDS2708.1, CCDS46807.1	3p22.1	2013-01-08			ENSG00000182983	ENSG00000182983		"Zinc fingers, C2H2-type", "-"	31930	protein-coding gene	gene with protein product							Standard	NM_207404		Approved	FLJ45880	uc003cmk.2	Q6ZS27	OTTHUMG00000133041	ENST00000541208.1:c.203A>G	chr3.hg19:g.42954744A>G	ENSP00000446208:p.Glu68Gly	127.0	0.0		62.0	4.0	NM_207404	A1A4T9|F8W7S8|Q6ZNF8|Q6ZQW8	Missense_Mutation	SNP	ENST00000541208.1	hg19	CCDS2708.1	.	.	.	.	.	.	.	.	.	.	A	7.478	0.648042	0.14516	.	.	ENSG00000182983	ENST00000440367;ENST00000541208	T;T	0.49720	0.77;0.77	3.46	3.46	0.39613	.	.	.	.	.	T	0.48822	0.1521	L	0.34521	1.04	0.21527	N	0.999654	D	0.69078	0.997	P	0.60682	0.878	T	0.25813	-1.0121	9	0.22706	T	0.39	.	8.4924	0.33108	1.0:0.0:0.0:0.0	.	68	Q6ZS27	ZN662_HUMAN	G	68	ENSP00000405047:E68G;ENSP00000446208:E68G	ENSP00000405047:E68G	E	+	2	0	ZNF662	42929748	0.992000	0.36948	0.447000	0.26932	0.016000	0.09150	2.013000	0.40942	1.575000	0.49775	0.460000	0.39030	GAG	.	.		0.473	ZNF662-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256646.4	NM_207404		G	42954744	A	G	42954744	3	3	64	1	0	0	0	0	1	0	0	0	18086	304	11	2	400	2	ZNF662	3	42954744	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	10922798	42954744	155067686	46	7763										
FYCO1	79443	hgsc.bcm.edu	37	chr3	46021198	46021198	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggctgcttgctcagcttaccTctgagatagacttgacaaag	10	10	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:46021198T>C	ENST00000296137.2	-	4	492	c.287A>G	c.(286-288)gAg>gGg	p.E96G	FYCO1_ENST00000535325.1_Splice_Site_p.E96G	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	96	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TCAGCTTACCTCTGAGATAGA	0.498																																					p.E96G		Atlas-SNP	.											.	FYCO1	115	.	0			c.A287G						.						192	164	174					3																	46021198		2203	4300	6503	SO:0001630	splice_region_variant	79443	exon4			CTTACCTCTGAGA	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.288+1A>G	chr3.hg19:g.46021198T>C		210.0	0.0		125.0	5.0	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	T	18.28	3.590006	0.66105	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.12255	2.7;2.7	5.36	5.36	0.76844	RUN (2);	0.000000	0.85682	D	0.000000	T	0.32734	0.0839	L	0.53249	1.67	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.83275	0.981;0.996	T	0.02797	-1.1109	10	0.72032	D	0.01	-31.7368	13.9155	0.63895	0.0:0.0:0.0:1.0	.	96;96	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	G	96	ENSP00000296137:E96G;ENSP00000441178:E96G	ENSP00000296137:E96G	E	-	2	0	FYCO1	45996202	1.000000	0.71417	0.994000	0.49952	0.197000	0.23852	7.699000	0.84547	2.033000	0.60031	0.397000	0.26171	GAG	.	.		0.498	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	Missense_Mutation	C	46021198	T	C	46021198	5	2	64	1	0	0	0	0	0	0	1	0	6133	1565	54	2	4209	2	FYCO1	3	46021198	Splice_Site	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	3066454	46021198	152001232	47	7764										
P4HTM	54681	hgsc.bcm.edu	37	chr3	49041657	49041657	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tacctggctctaccagggtgAgggtgcccaccacatcatgc	11	14	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:49041657A>G	ENST00000383729.4	+	5	1222	c.851A>G	c.(850-852)gAg>gGg	p.E284G	WDR6_ENST00000395474.3_5'Flank|P4HTM_ENST00000343546.4_Missense_Mutation_p.E284G	NM_177939.2	NP_808808.1	Q9NXG6	P4HTM_HUMAN	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	284						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21					Vitamin C(DB00126)	TACCAGGGTGAGGGTGCCCAC	0.597																																					p.E284G		Atlas-SNP	.											.	P4HTM	71	.	0			c.A851G						.						35	24	28					3																	49041657		2062	3995	6057	SO:0001583	missense	54681	exon5			AGGGTGAGGGTGC		CCDS2781.2, CCDS43089.1	3p21.31	2009-01-14			ENSG00000178467	ENSG00000178467			28858	protein-coding gene	gene with protein product	"Prolyl hydroxlase domain-containing 4", "hypoxia inducible factor prolyl 4 hydroxylase"	614584				12163023, 17726031	Standard	XR_245139		Approved	P4H-TM, PHD4, PH4, HIFPH4, FLJ20262, EGLN4, PH-4	uc003cvh.3	Q9NXG6	OTTHUMG00000074057	ENST00000383729.4:c.851A>G	chr3.hg19:g.49041657A>G	ENSP00000373235:p.Glu284Gly	96.0	0.0		35.0	4.0	NM_177938	Q6PAG6|Q8TCJ9|Q8WV55|Q96F22|Q9BW77	Missense_Mutation	SNP	ENST00000383729.4	hg19	CCDS43089.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.7|26.7	4.764168|4.764168	0.89932|0.89932	.|.	.|.	ENSG00000178467|ENSG00000178467	ENST00000383729;ENST00000343546|ENST00000444213	T|.	0.79554|.	-1.28|.	5.76|5.76	5.76|5.76	0.90799|0.90799	Prolyl 4-hydroxylase, alpha subunit (1);|.	0.101208|.	0.64402|.	D|.	0.000001|.	T|.	0.69691|.	0.3139|.	L|L	0.54323|0.54323	1.7|1.7	0.44221|0.44221	D|D	0.997055|0.997055	D;D|.	0.60575|.	0.988;0.979|.	P;P|.	0.58721|.	0.844;0.702|.	T|.	0.67562|.	-0.5639|.	10|.	0.72032|.	D|.	0.01|.	-24.9026|-24.9026	16.0766|16.0766	0.80971|0.80971	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	284;284|.	Q9NXG6-3;Q9NXG6|.	.;P4HTM_HUMAN|.	G|W	284|213	ENSP00000373235:E284G|.	ENSP00000341422:E284G|.	E|X	+|+	2|3	0|0	P4HTM|P4HTM	49016661|49016661	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.034000|4.034000	0.57289|0.57289	2.202000|2.202000	0.70862|0.70862	0.533000|0.533000	0.62120|0.62120	GAG|TGA	.	.		0.597	P4HTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157211.1	NM_177938		G	49041657	A	G	49041657	3	3	64	1	0	0	0	0	1	0	0	0	11369	304	11	2	869	2	P4HTM	3	49041657	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	3020459	49041657	148980773	48	7765										
C3orf63	23272	hgsc.bcm.edu	37	chr3	56667646	56667646	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgaactcggaaagccgtttcAtcttctcttgtgttgaaaag	9	8	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:56667646A>G	ENST00000493960.2	-	18	3183	c.3173T>C	c.(3172-3174)aTg>aCg	p.M1058T	FAM208A_ENST00000431842.2_Missense_Mutation_p.M621T|FAM208A_ENST00000355628.5_Missense_Mutation_p.M997T	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1058							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						AAGCCGTTTCATCTTCTCTTG	0.343																																					p.M1058T		Atlas-SNP	.											.	FAM208A	113	.	0			c.T3173C						.						110	119	116					3																	56667646		2203	4300	6503	SO:0001583	missense	23272	exon18			CGTTTCATCTTCT	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 63"	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.3173T>C	chr3.hg19:g.56667646A>G	ENSP00000417509:p.Met1058Thr	38.0	0.0		26.0	4.0	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	A	12.34	1.909510	0.33721	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.12774	2.65;2.89;2.9	5.76	5.76	0.90799	.	0.391146	0.30401	N	0.009705	T	0.15003	0.0362	L	0.59436	1.845	0.33387	D	0.575673	B;B;B;B	0.32467	0.332;0.372;0.218;0.224	B;B;B;B	0.31869	0.137;0.098;0.104;0.101	T	0.16364	-1.0405	10	0.32370	T	0.25	-2.4445	10.6901	0.45867	0.9288:0.0:0.0712:0.0	.	1058;997;621;1058	Q9UK61-3;Q9UK61-4;Q9UK61-2;Q9UK61	.;.;.;F208A_HUMAN	T	621;1058;997	ENSP00000399410:M621T;ENSP00000417509:M1058T;ENSP00000347845:M997T	ENSP00000347845:M997T	M	-	2	0	C3orf63	56642686	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.725000	0.61979	2.323000	0.78572	0.528000	0.53228	ATG	.	.		0.343	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		G	56667646	A	G	56667646	3	3	64	1	0	0	0	0	1	0	0	0	2241	217	8	2	1927	2	C3orf63	3	56667646	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	7625989	56667646	141354784	49	7766										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57343779	57343779	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtttggagcctccctgggtgAggagcaaggactcaaagagg	16	8	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:57343779A>G	ENST00000351747.2	-	53	8576	c.8396T>C	c.(8395-8397)cTc>cCc	p.L2799P	DNAH12_ENST00000344804.4_Missense_Mutation_p.L386P	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	2799					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TCCCTGGGTGAGGAGCAAGGA	0.418																																					p.L2799P		Atlas-SNP	.											.	DNAH12	182	.	0			c.T8396C						.						166	159	161					3																	57343779		692	1591	2283	SO:0001583	missense	201625	exon53			TGGGTGAGGAGCA	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.8396T>C	chr3.hg19:g.57343779A>G	ENSP00000295937:p.Leu2799Pro	150.0	0.0		93.0	4.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	hg19		.	.	.	.	.	.	.	.	.	.	A	19.78	3.891740	0.72524	.	.	ENSG00000174844	ENST00000351747;ENST00000466540;ENST00000344804	T;T;T	0.08984	3.03;3.03;3.03	5.92	5.92	0.95590	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.38878	0.1057	M	0.92219	3.285	0.58432	D	0.999995	P;D	0.76494	0.886;0.999	P;D	0.79784	0.785;0.993	T	0.49532	-0.8930	10	0.66056	D	0.02	.	15.5337	0.75986	1.0:0.0:0.0:0.0	.	386;2799	Q6ZR08-2;Q6ZR08	.;DYH12_HUMAN	P	2799;444;386	ENSP00000295937:L2799P;ENSP00000420359:L444P;ENSP00000340464:L386P	ENSP00000340464:L386P	L	-	2	0	DNAH12	57318819	1.000000	0.71417	0.998000	0.56505	0.480000	0.33159	7.343000	0.79319	2.255000	0.74692	0.533000	0.62120	CTC	.	.		0.418	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		G	57343779	A	G	57343779	3	3	64	1	0	0	0	0	1	0	0	0	4602	304	11	2	910	2	DNAH12	3	57343779	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	676133	57343779	140678651	50	7767										
SLMAP	7871	hgsc.bcm.edu	37	chr3	57846497	57846497	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aaacataactatgagacaacAgccaaagagtccctgaggcg	9	10	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:57846497A>G	ENST00000428312.1	+	8	853	c.759A>G	c.(757-759)acA>acG	p.T253T	SLMAP_ENST00000295951.3_Silent_p.T253T|SLMAP_ENST00000449503.2_Silent_p.T253T|SLMAP_ENST00000295952.3_Silent_p.T253T|SLMAP_ENST00000383718.3_Silent_p.T253T|SLMAP_ENST00000416870.1_5'UTR			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	253					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)				endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		ATGAGACAACAGCCAAAGAGT	0.308																																					p.T253T		Atlas-SNP	.											.	SLMAP	46	.	0			c.A759G						.						37	43	41					3																	57846497		2201	4298	6499	SO:0001819	synonymous_variant	7871	exon8			GACAACAGCCAAA	AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"Sarcolemmal-associated protein"	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.759A>G	chr3.hg19:g.57846497A>G		158.0	0.0		115.0	5.0	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Silent	SNP	ENST00000428312.1	hg19																																																																																				.	.		0.308	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159		G	57846497	A	G	57846497	2	3	64	1	0	0	0	0	0	0	0	1	14764	175	7	2		2	SLMAP	3	57846497	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	502718	57846497	140175933	51	7768										
TMF1	7110	hgsc.bcm.edu	37	chr3	69079080	69079080	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtgactccatggaagacatcTgaattttgttagcaaggagt	11	6	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:69079080T>C	ENST00000398559.2	-	11	2696	c.2480A>G	c.(2479-2481)cAg>cGg	p.Q827R	CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000601511.1_RNA|CTD-2013N24.2_ENST00000597366.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000599467.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.Q830R|CTD-2013N24.2_ENST00000596732.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	827					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		GGAAGACATCTGAATTTTGTT	0.423																																					p.Q827R		Atlas-SNP	.											.	TMF1	77	.	0			c.A2480G						.						156	154	155					3																	69079080		1890	4120	6010	SO:0001583	missense	7110	exon11			GACATCTGAATTT		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.2480A>G	chr3.hg19:g.69079080T>C	ENSP00000381567:p.Gln827Arg	132.0	0.0		77.0	4.0	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	hg19	CCDS43105.1	.	.	.	.	.	.	.	.	.	.	T	13.86	2.362304	0.41902	.	.	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248	T;T	0.43294	0.95;0.95	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.35038	0.0918	L	0.34521	1.04	0.80722	D	1	P;P	0.42518	0.782;0.726	B;B	0.43413	0.419;0.259	T	0.08889	-1.0700	10	0.07644	T	0.81	-10.1573	15.8852	0.79241	0.0:0.0:0.0:1.0	.	830;827	P82094-2;P82094	.;TMF1_HUMAN	R	827;830;743	ENSP00000381567:Q827R;ENSP00000438706:Q830R	ENSP00000348582:Q743R	Q	-	2	0	TMF1	69161770	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	7.694000	0.84235	2.146000	0.66826	0.477000	0.44152	CAG	.	.		0.423	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		C	69079080	T	C	69079080	3	2	64	1	0	0	0	0	1	0	0	0	16243	1580	55	2	829	2	TMF1	3	69079080	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	11232583	69079080	128943350	52	7769										
CNTN3	5067	hgsc.bcm.edu	37	chr3	74418520	74418520	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tctccaattaatctgaggtaTgggactaagaagaaaatcgt	9	6	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:74418520T>C	ENST00000263665.6	-	7	793	c.766A>G	c.(766-768)Ata>Gta	p.I256V		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	256	Ig-like C2-type 3.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		ATCTGAGGTATGGGACTAAGA	0.383																																					p.I256V		Atlas-SNP	.											.	CNTN3	174	.	0			c.A766G						.						43	43	43					3																	74418520		2203	4298	6501	SO:0001583	missense	5067	exon7			GAGGTATGGGACT	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.766A>G	chr3.hg19:g.74418520T>C	ENSP00000263665:p.Ile256Val	184.0	0.0		81.0	4.0	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	hg19	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	T	0.670	-0.802436	0.02841	.	.	ENSG00000113805	ENST00000263665	T	0.65916	-0.18	5.2	-1.46	0.08800	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.272223	0.35708	N	0.003023	T	0.25975	0.0633	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30357	-0.9981	10	0.02654	T	1	.	6.2168	0.20659	0.0:0.5523:0.1122:0.3355	.	256	Q9P232	CNTN3_HUMAN	V	256	ENSP00000263665:I256V	ENSP00000263665:I256V	I	-	1	0	CNTN3	74501210	0.867000	0.29959	0.051000	0.19133	0.992000	0.81027	1.719000	0.38011	-0.721000	0.04929	0.482000	0.46254	ATA	.	.		0.383	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		C	74418520	T	C	74418520	3	2	64	1	0	0	0	0	1	0	0	0	3644	1464	51	2	2384	2	CNTN3	3	74418520	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	5339440	74418520	123603910	53	7770										
PROS1	5627	hgsc.bcm.edu	37	chr3	93611837	93611837	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtgattttggatgtatgttcAttcttaagctgaacttcaat	8	5	3	2	rs199469491	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:93611837A>G	ENST00000394236.3	-	10	1411	c.1095T>C	c.(1093-1095)aaT>aaC	p.N365N	PROS1_ENST00000407433.1_Silent_p.N234N	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	365	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)			endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	ATGTATGTTCATTCTTAAGCT	0.398																																					p.N365N		Atlas-SNP	.											.	PROS1	126	.	0			c.T1095C						.						130	120	124					3																	93611837		2203	4300	6503	SO:0001819	synonymous_variant	5627	exon10			ATGTTCATTCTTA		CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.1095T>C	chr3.hg19:g.93611837A>G		371.0	0.0		421.0	172.0	NM_000313	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Silent	SNP	ENST00000394236.3	hg19	CCDS2923.1																																																																																			.	A|0.999;C|0.001		0.398	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313		G	93611837	A	G	93611837	2	3	64	1	0	0	0	0	0	0	0	1	12570	214	8	2		2	PROS1	3	93611837	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	19193317	93611837	104410593	54	7771										
OR5H6	79295	hgsc.bcm.edu	37	chr3	97983495	97983495	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aatttttttcccttgtaaccActgtaaccacagaatgtttt	4	9	0	1	rs398062605|rs74203917|rs149984587	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:97983495A>C	ENST00000383696.2	+	1	408	c.367A>C	c.(367-369)Act>Cct	p.T123P	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						CCTTGTAACCACTGTAACCAC	0.383																																					p.T123P		Atlas-SNP	.											.	OR5H6	89	.	0			c.A367C						.						93	59	71					3																	97983495		2195	4251	6446	SO:0001583	missense	79295	exon1			GTAACCACTGTAA	BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"GPCR / Class A : Olfactory receptors"	14767	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily H, member 6"				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.367A>C	chr3.hg19:g.97983495A>C	ENSP00000373196:p.Thr123Pro	125.0	0.0		126.0	6.0	NM_001005479	Q6IF88	Missense_Mutation	SNP	ENST00000383696.2	hg19	CCDS33800.1	.	.	.	.	.	.	.	.	.	.	-	4.810	0.150643	0.09185	.	.	ENSG00000230301	ENST00000383696	T	0.00479	7.12	2.19	-3.59	0.04583	GPCR, rhodopsin-like superfamily (1);	0.914442	0.09287	N	0.822835	T	0.00241	0.0007	N	0.24115	0.695	0.09310	N	1	B	0.31435	0.323	B	0.27887	0.084	T	0.37337	-0.9710	10	0.72032	D	0.01	.	3.1801	0.06582	0.522:0.0:0.1327:0.3452	.	123	Q8NGV6	OR5H6_HUMAN	P	123	ENSP00000373196:T123P	ENSP00000373196:T123P	T	+	1	0	OR5H6	99466185	0.000000	0.05858	0.011000	0.14972	0.001000	0.01503	-1.002000	0.03686	-0.512000	0.06505	-1.140000	0.01884	ACT	.	.		0.383	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2			C	97983495	A	C	97983495	3	2	64	1	0	0	0	0	1	0	0	0	11172	159	6	5	369	5	OR5H6	3	97983495	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	4371658	97983495	100038935	55	7772										
HCLS1	3059	hgsc.bcm.edu	37	chr3	121351335	121351335	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gggctcaggctcaggctctgCttcgtacactggctcttcct	11	14	4	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:121351335C>G	ENST00000314583.3	-	12	1175	c.1084G>C	c.(1084-1086)Gca>Cca	p.A362P	HCLS1_ENST00000428394.2_Missense_Mutation_p.A325P|HCLS1_ENST00000473883.1_5'UTR	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	362					actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		tcaggctcTGCTTCGTACACT	0.597																																					p.A362P		Atlas-SNP	.											HCLS1,NS,carcinoma,0,1	HCLS1	78	.	0			c.G1084C						.						116	111	112					3																	121351335		2203	4300	6503	SO:0001583	missense	3059	exon12			GCTCTGCTTCGTA		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"cortactin-like"	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.1084G>C	chr3.hg19:g.121351335C>G	ENSP00000320176:p.Ala362Pro	103.0	0.0		134.0	10.0	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Missense_Mutation	SNP	ENST00000314583.3	hg19	CCDS3003.1	.	.	.	.	.	.	.	.	.	.	C	0.018	-1.474350	0.01044	.	.	ENSG00000180353	ENST00000314583;ENST00000428394	T;T	0.22743	1.95;1.94	5.06	1.08	0.20341	.	600.137000	0.00166	N	0.000000	T	0.10465	0.0256	N	0.04880	-0.145	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.20306	-1.0279	10	0.25106	T	0.35	2.8309	3.4017	0.07325	0.1646:0.4235:0.3199:0.0919	rs34277781	325;362	E7EVW7;P14317	.;HCLS1_HUMAN	P	362;325	ENSP00000320176:A362P;ENSP00000387645:A325P	ENSP00000320176:A362P	A	-	1	0	HCLS1	122834025	0.013000	0.17824	0.324000	0.25361	0.111000	0.19643	0.495000	0.22483	0.715000	0.32103	0.655000	0.94253	GCA	.	.		0.597	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335		G	121351335	C	G	121351335	3	3	64	1	0	0	0	0	1	0	0	0	7004	797	28	4	388	4	HCLS1	3	121351335	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	23367840	121351335	76671095	56	7773										
KLF15	28999	hgsc.bcm.edu	37	chr3	126071499	126071499	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atgctactgccgctgcccccGccactgcccagcgtggcctg	11	19	0	0	rs376071138	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:126071499G>A	ENST00000296233.3	-	2	497	c.267C>T	c.(265-267)ggC>ggT	p.G89G	KLF15_ENST00000509675.1_5'Flank	NM_014079.3	NP_054798.1	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	89					cardiac muscle hypertrophy in response to stress (GO:0014898)|cellular response to peptide (GO:1901653)|glial cell differentiation (GO:0010001)|glomerular visceral epithelial cell differentiation (GO:0072112)|glucose transport (GO:0015758)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(7)|ovary(2)|skin(2)	12				GBM - Glioblastoma multiforme(114;0.147)		CGCTGCCCCCGCCACTGCCCA	0.672													G|||	3	0.000599042	0	0.0043	5008	,	,		16334	0		0	False		,,,				2504	0				p.G89G		Atlas-SNP	.											.	KLF15	40	.	0			c.C267T						.	G		2,4374		0,2,2186	8	9	8		267	-6.8	0	3		8	2,8524		0,2,4261	no	coding-synonymous	KLF15	NM_014079.3		0,4,6447	AA,AG,GG		0.0235,0.0457,0.031		89/417	126071499	4,12898	2188	4263	6451	SO:0001819	synonymous_variant	28999	exon2			GCCCCCGCCACTG	AB029254	CCDS3036.1	3q21.3	2013-01-08			ENSG00000163884	ENSG00000163884		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	14536	protein-coding gene	gene with protein product	"kidney-enriched Kruppel-like factor"	606465				10982849	Standard	NM_014079		Approved	KKLF	uc011bkk.1	Q9UIH9	OTTHUMG00000162689	ENST00000296233.3:c.267C>T	chr3.hg19:g.126071499G>A		64.0	0.0		130.0	60.0	NM_014079		Silent	SNP	ENST00000296233.3	hg19	CCDS3036.1																																																																																			.	.		0.672	KLF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370096.1	NM_014079		A	126071499	G	A	126071499	2	1	64	1	0	0	0	0	0	0	0	1	8352	1074	38	1		1	KLF15	3	126071499	Silent	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	4720164	126071499	71950931	57	7774										
PODXL2	50512	hgsc.bcm.edu	37	chr3	127379378	127379378	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gaggaagaagaggaagaggaAgaggaggagagggagaagga	22	0	0	6			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:127379378A>G	ENST00000342480.6	+	3	546	c.507A>G	c.(505-507)gaA>gaG	p.E169E		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	169	Glu-rich.				leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						aggaagaggaagaggaggaga	0.552																																					p.E169E		Atlas-SNP	.											.	PODXL2	53	.	0			c.A507G						.						55	60	58					3																	127379378		2203	4300	6503	SO:0001819	synonymous_variant	50512	exon3			AGAGGAAGAGGAG	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"endoglycan"					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.507A>G	chr3.hg19:g.127379378A>G		68.0	0.0		72.0	4.0	NM_015720	Q6UVY4|Q8WUV6	Silent	SNP	ENST00000342480.6	hg19	CCDS3044.1																																																																																			.	.		0.552	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		G	127379378	A	G	127379378	2	3	64	1	0	0	0	0	0	0	0	1	12190	69	3	2		2	PODXL2	3	127379378	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1307879	127379378	70643052	58	7775										
TMCC1	23023	hgsc.bcm.edu	37	chr3	129546658	129546658	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aaacttacccgctccgcagtTccctcctctcctggtagaca	6	17	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:129546658T>C	ENST00000393238.3	-	3	904	c.564A>G	c.(562-564)ggA>ggG	p.G188G	TMCC1_ENST00000426664.2_Silent_p.G74G	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	188						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						GCTCCGCAGTTCCCTCCTCTC	0.448																																					p.G188G		Atlas-SNP	.											.	TMCC1	105	.	0			c.A564G						.						44	46	45					3																	129546658		2203	4300	6503	SO:0001819	synonymous_variant	23023	exon3			CGCAGTTCCCTCC	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.564A>G	chr3.hg19:g.129546658T>C		58.0	0.0		80.0	5.0	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Silent	SNP	ENST00000393238.3	hg19	CCDS33855.1																																																																																			.	.		0.448	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		C	129546658	T	C	129546658	2	2	64	1	0	0	0	0	0	0	0	1	16007	1770	62	2		2	TMCC1	3	129546658	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2167280	129546658	68475772	59	7776										
PIK3R4	30849	hgsc.bcm.edu	37	chr3	130449233	130449233	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttccatattaagattttttaActgtactaattccaggaatc	4	7	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:130449233A>G	ENST00000356763.3	-	5	2061	c.1504T>C	c.(1504-1506)Tta>Cta	p.L502L		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	502					innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						AGATTTTTTAACTGTACTAAT	0.303																																					p.L502L		Atlas-SNP	.											.	PIK3R4	145	.	0			c.T1504C						.						73	77	75					3																	130449233		2203	4296	6499	SO:0001819	synonymous_variant	30849	exon5			TTTTTAACTGTAC	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.1504T>C	chr3.hg19:g.130449233A>G		85.0	0.0		86.0	4.0	NM_014602	Q2TBF4	Silent	SNP	ENST00000356763.3	hg19	CCDS3067.1																																																																																			.	.		0.303	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		G	130449233	A	G	130449233	2	3	64	1	0	0	0	0	0	0	0	1	11930	40	2	2		2	PIK3R4	3	130449233	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	902575	130449233	67573197	60	7777										
SERPINI1	5274	hgsc.bcm.edu	37	chr3	167506954	167506954	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cttctctttgctggttctgcAaagtatggctacaggggcca	11	10	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:167506954A>G	ENST00000295777.5	+	2	469	c.38A>G	c.(37-39)cAa>cGa	p.Q13R	SERPINI1_ENST00000446050.2_Missense_Mutation_p.Q13R	NM_005025.4	NP_005016.1	Q99574	NEUS_HUMAN	serpin peptidase inhibitor, clade I (neuroserpin), member 1	13					cell death (GO:0008219)|central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|peripheral nervous system development (GO:0007422)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(7)|skin(2)	20						CTGGTTCTGCAAAGTATGGCT	0.368																																					p.Q13R		Atlas-SNP	.											.	SERPINI1	52	.	0			c.A38G						.						75	77	76					3																	167506954		2203	4300	6503	SO:0001583	missense	5274	exon2			TTCTGCAAAGTAT	Z81326	CCDS3203.1	3q26.1	2014-02-18	2005-08-18		ENSG00000163536	ENSG00000163536		"Serine (or cysteine) peptidase inhibitors"	8943	protein-coding gene	gene with protein product		602445	"serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1"	PI12		24172014	Standard	NM_005025		Approved	neuroserpin	uc003ffa.4	Q99574	OTTHUMG00000158450	ENST00000295777.5:c.38A>G	chr3.hg19:g.167506954A>G	ENSP00000295777:p.Gln13Arg	67.0	0.0		75.0	4.0	NM_005025	A8K217|D3DNP1|Q6AHZ4	Missense_Mutation	SNP	ENST00000295777.5	hg19	CCDS3203.1	.	.	.	.	.	.	.	.	.	.	A	1.702	-0.501211	0.04261	.	.	ENSG00000163536	ENST00000472941;ENST00000446050;ENST00000295777;ENST00000472747	T;D;D;T	0.83837	-0.98;-1.77;-1.77;-1.47	5.23	0.972	0.19704	Serpin domain (1);	0.645510	0.17376	N	0.176474	T	0.72819	0.3508	L	0.29908	0.895	0.80722	D	1	B	0.16802	0.019	B	0.16722	0.016	T	0.62272	-0.6889	10	0.24483	T	0.36	.	14.3299	0.66548	0.5344:0.4656:0.0:0.0	.	13	Q99574	NEUS_HUMAN	R	13	ENSP00000420133:Q13R;ENSP00000397373:Q13R;ENSP00000295777:Q13R;ENSP00000420561:Q13R	ENSP00000295777:Q13R	Q	+	2	0	SERPINI1	168989648	0.998000	0.40836	0.680000	0.29994	0.024000	0.10985	0.840000	0.27600	0.319000	0.23209	0.533000	0.62120	CAA	.	.		0.368	SERPINI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351056.1			G	167506954	A	G	167506954	3	3	64	1	0	0	0	0	1	0	0	0	14133	130	5	2	40	2	SERPINI1	3	167506954	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	37057721	167506954	30515476	61	7778										
GOLIM4	27333	hgsc.bcm.edu	37	chr3	167747641	167747641	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cagggccatctctcttgccaCctgctgctgctgctgttcct	9	16	2	0	rs550869030	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:167747641C>G	ENST00000470487.1	-	10	2049	c.1360G>C	c.(1360-1362)Gtg>Ctg	p.V454L	GOLIM4_ENST00000309027.4_Missense_Mutation_p.V426L	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	454	Gln-rich.|Glu-rich.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TCTCTTGCCACctgctgctgc	0.637																																					p.V454L		Atlas-SNP	.											.,1	GOLIM4	71	.	0			c.G1360C						.						36	36	36					3																	167747641		2203	4300	6503	SO:0001583	missense	27333	exon10			TTGCCACCTGCTG	U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"golgi phosphoprotein 4"	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.1360G>C	chr3.hg19:g.167747641C>G	ENSP00000417354:p.Val454Leu	75.0	0.0		67.0	7.0	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	hg19	CCDS3204.1	.	.	.	.	.	.	.	.	.	.	G	2.085	-0.409763	0.04799	.	.	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	2.99	0.777	0.18538	.	1.358100	0.04855	N	0.443063	T	0.08268	0.0206	N	0.00237	-1.79	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19257	-1.0311	9	0.25751	T	0.34	-0.0494	5.721	0.17986	0.0:0.4155:0.3727:0.2118	.	426;454	F8W785;O00461	.;GOLI4_HUMAN	L	454;426	.	ENSP00000309893:V426L	V	-	1	0	GOLIM4	169230335	0.153000	0.22777	1.000000	0.80357	0.639000	0.38242	2.640000	0.46579	0.120000	0.18254	-0.223000	0.12442	GTG	.	.		0.637	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2			G	167747641	C	G	167747641	3	3	64	1	0	0	0	0	1	0	0	0	6574	507	18	4	758	4	GOLIM4	3	167747641	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	240687	167747641	30274789	62	7779										
KLHL24	54800	hgsc.bcm.edu	37	chr3	183381420	183381420	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgtgctctaaggaatgacatTcttgtttcaggtaaatatag	9	5	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr3:183381420T>C	ENST00000454652.2	+	5	1481	c.1095T>C	c.(1093-1095)atT>atC	p.I365I	KLHL24_ENST00000476808.1_Silent_p.I365I|KLHL24_ENST00000242810.6_Silent_p.I365I	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24	365						cell projection (GO:0042995)|cytoplasm (GO:0005737)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			GGAATGACATTCTTGTTTCAG	0.348																																					p.I365I		Atlas-SNP	.											.	KLHL24	56	.	0			c.T1095C						.						84	81	82					3																	183381420		2203	4300	6503	SO:0001819	synonymous_variant	54800	exon4			TGACATTCTTGTT		CCDS3246.1	3q27.1	2013-02-22	2013-02-22		ENSG00000114796	ENSG00000114796		"Kelch-like", "BTB/POZ domain containing"	25947	protein-coding gene	gene with protein product		611295	"kelch-like 24 (Drosophila)"				Standard	XM_005247552		Approved	DRE1, FLJ20059	uc003flv.3	Q6TFL4	OTTHUMG00000156911	ENST00000454652.2:c.1095T>C	chr3.hg19:g.183381420T>C		95.0	0.0		71.0	4.0	NM_017644	A5PLN8|Q9H620|Q9NXT9	Silent	SNP	ENST00000454652.2	hg19	CCDS3246.1																																																																																			.	.		0.348	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	NM_017644		C	183381420	T	C	183381420	2	2	64	1	0	0	0	0	0	0	0	1	8388	1771	62	2		2	KLHL24	3	183381420	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	15633779	183381420	14641010	63	7780										
FBXL5	26234	hgsc.bcm.edu	37	chr4	15629615	15629615	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atggagtaaacgtttttccaTttgtgcaatgctgatagcaa	9	6	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:15629615T>C	ENST00000341285.3	-	7	1058	c.934A>G	c.(934-936)Atg>Gtg	p.M312V	FBXL5_ENST00000412094.2_Missense_Mutation_p.M295V|FBXL5_ENST00000382358.4_Missense_Mutation_p.M186V	NM_001193534.1|NM_001193535.1|NM_012161.3	NP_001180463.1|NP_001180464.1|NP_036293.1	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5	312					iron ion homeostasis (GO:0055072)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	iron ion binding (GO:0005506)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13						CGTTTTTCCATTTGTGCAATG	0.353																																					p.M312V		Atlas-SNP	.											.	FBXL5	52	.	0			c.A934G						.						133	120	124					4																	15629615		2202	4300	6502	SO:0001583	missense	26234	exon7			TTTCCATTTGTGC	AF174591	CCDS3415.1, CCDS54745.1	4p15.33	2011-06-09			ENSG00000118564	ENSG00000118564		"F-boxes / Leucine-rich repeats"	13602	protein-coding gene	gene with protein product		605655				10531035	Standard	NM_012161		Approved	FBL4, FBL5, FLR1	uc003goc.2	Q9UKA1	OTTHUMG00000097097	ENST00000341285.3:c.934A>G	chr4.hg19:g.15629615T>C	ENSP00000344866:p.Met312Val	86.0	0.0		82.0	4.0	NM_012161	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Missense_Mutation	SNP	ENST00000341285.3	hg19	CCDS3415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.92|12.92	2.082100|2.082100	0.36758|0.36758	.|.	.|.	ENSG00000118564|ENSG00000118564	ENST00000341285;ENST00000412094;ENST00000382358|ENST00000513163	T;T;T|.	0.28069|.	1.63;1.63;1.63|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.130156|.	0.64402|.	D|.	0.000005|.	T|T	0.36690|0.36690	0.0976|0.0976	N|N	0.22421|0.22421	0.69|0.69	0.29150|0.29150	N|N	0.87841|0.87841	B;B|.	0.22480|.	0.07;0.042|.	B;B|.	0.21151|.	0.033;0.015|.	T|T	0.29882|0.29882	-0.9997|-0.9997	10|5	0.20046|.	T|.	0.44|.	-9.9694|-9.9694	14.4046|14.4046	0.67073|0.67073	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	295;312|.	Q9UKA1-2;Q9UKA1|.	.;FBXL5_HUMAN|.	V|S	312;295;186|232	ENSP00000344866:M312V;ENSP00000408679:M295V;ENSP00000371795:M186V|.	ENSP00000344866:M312V|.	M|N	-|-	1|2	0|0	FBXL5|FBXL5	15238713|15238713	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.992000|0.992000	0.81027|0.81027	3.413000|3.413000	0.52686|0.52686	2.138000|2.138000	0.66242|0.66242	0.377000|0.377000	0.23210|0.23210	ATG|AAT	.	.		0.353	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2			C	15629615	T	C	15629615	3	2	64	1	0	0	0	0	1	0	0	0	5730	1493	52	2	1161	2	FBXL5	4	15629615	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		15629615	175524661	64	7781										
CORIN	10699	hgsc.bcm.edu	37	chr4	47685795	47685795	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cacagtcatcatatccatcaCacacaaggctgtaattaagg	6	11	3	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:47685795C>T	ENST00000273857.4	-	7	973	c.974G>A	c.(973-975)tGt>tAt	p.C325Y	CORIN_ENST00000505909.1_Missense_Mutation_p.C325Y|CORIN_ENST00000504584.1_Missense_Mutation_p.C325Y|CORIN_ENST00000502252.1_Missense_Mutation_p.C258Y|CORIN_ENST00000508498.1_Missense_Mutation_p.C186Y	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	325	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						ATATCCATCACACACAAGGCT	0.398																																					p.C325Y		Atlas-SNP	.											.	CORIN	154	.	0			c.G974A						.						131	123	126					4																	47685795		2203	4300	6503	SO:0001583	missense	10699	exon7			CCATCACACACAA	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"Serine peptidases / Transmembrane"	19012	protein-coding gene	gene with protein product		605236	"corin, serine protease"			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.974G>A	chr4.hg19:g.47685795C>T	ENSP00000273857:p.Cys325Tyr	60.0	0.0		67.0	4.0	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	hg19	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.759066	0.89843	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252;ENST00000505909;ENST00000504584	D;D;D;D;D	0.99755	-6.64;-6.64;-6.64;-6.64;-6.64	5.83	5.83	0.93111	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99900	0.9952	H	0.98738	4.315	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;1.0;1.0;1.0	D	0.96361	0.9266	10	0.87932	D	0	.	20.1133	0.97917	0.0:1.0:0.0:0.0	.	325;325;258;186;325	B7Z4R1;B4E2W9;B4E1Y7;B4DZA3;Q9Y5Q5	.;.;.;.;CORIN_HUMAN	Y	325;186;258;325;325	ENSP00000273857:C325Y;ENSP00000425597:C186Y;ENSP00000424212:C258Y;ENSP00000425401:C325Y;ENSP00000423216:C325Y	ENSP00000273857:C325Y	C	-	2	0	CORIN	47380552	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	7.163000	0.77524	2.762000	0.94881	0.591000	0.81541	TGT	.	.		0.398	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2			T	47685795	C	T	47685795	3	4	64	1	0	0	0	0	1	0	0	0	3754	478	17	3	2218	3	CORIN	4	47685795	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	32056180	47685795	143468481	65	7782										
FRYL	285527	hgsc.bcm.edu	37	chr4	48545872	48545872	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtttctacaagtctggagagAacatcagaaagtgtagttgc	11	6	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:48545872A>G	ENST00000503238.1	-	41	5543	c.5544T>C	c.(5542-5544)gtT>gtC	p.V1848V	FRYL_ENST00000537810.1_Silent_p.V1848V|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Silent_p.V1848V|FRYL_ENST00000507873.2_5'UTR			O94915	FRYL_HUMAN	FRY-like	1848					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GTCTGGAGAGAACATCAGAAA	0.443																																					p.V1848V		Atlas-SNP	.											.	FRYL	242	.	0			c.T5544C						.						90	88	89					4																	48545872		1866	4109	5975	SO:0001819	synonymous_variant	285527	exon44			GGAGAGAACATCA	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.5544T>C	chr4.hg19:g.48545872A>G		68.0	0.0		90.0	4.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	A	8.997	0.979145	0.18812	.	.	ENSG00000075539	ENST00000514617	.	.	.	5.46	-1.56	0.08532	.	.	.	.	.	T	0.49847	0.1581	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41016	-0.9532	4	.	.	.	.	5.3753	0.16162	0.5375:0.2533:0.2092:0.0	.	.	.	.	P	718	.	.	S	-	1	0	FRYL	48240629	1.000000	0.71417	0.997000	0.53966	0.778000	0.44026	0.968000	0.29357	-0.088000	0.12506	0.533000	0.62120	TCT	.	.		0.443	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			G	48545872	A	G	48545872	2	3	64	1	0	0	0	0	0	0	0	1	6072	233	9	2		2	FRYL	4	48545872	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	860077	48545872	142608404	66	7783										
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54265931	54265931	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aactggaaactcagagaaagAaactgcccttccatctacaa	6	11	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:54265931A>G	ENST00000337488.6	+	10	934	c.740A>G	c.(739-741)gAa>gGa	p.E247G	FIP1L1_ENST00000507922.1_Missense_Mutation_p.E232G|FIP1L1_ENST00000507166.1_Missense_Mutation_p.E247G|FIP1L1_ENST00000358575.5_Missense_Mutation_p.E232G|FIP1L1_ENST00000306932.6_Missense_Mutation_p.E209G	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	247	Necessary for stimulating PAPOLA activity.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TCAGAGAAAGAAACTGCCCTT	0.373			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.E247G		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.A740G						.						169	163	165					4																	54265931		2203	4300	6503	SO:0001583	missense	81608	exon10			AGAAAGAAACTGC	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.740A>G	chr4.hg19:g.54265931A>G	ENSP00000336752:p.Glu247Gly	108.0	0.0		87.0	5.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Missense_Mutation	SNP	ENST00000337488.6	hg19	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.539816	0.85917	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000507922;ENST00000306932;ENST00000507166	T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72	5.38	5.38	0.77491	.	0.068969	0.64402	D	0.000013	T	0.58595	0.2133	L	0.43152	1.355	0.58432	D	0.99999	D;D;D;D;D;D	0.69078	0.994;0.997;0.99;0.969;0.983;0.983	P;D;P;P;P;P	0.64687	0.854;0.928;0.718;0.723;0.791;0.858	T	0.54938	-0.8218	10	0.32370	T	0.25	-13.739	15.6962	0.77502	1.0:0.0:0.0:0.0	.	232;51;232;209;247;232	G3XAD6;B4DTW7;B4DIR3;Q6UN15-3;Q6UN15;Q6UN15-4	.;.;.;.;FIP1_HUMAN;.	G	247;232;232;209;247	ENSP00000336752:E247G;ENSP00000351383:E232G;ENSP00000425456:E232G;ENSP00000302993:E209G;ENSP00000423325:E247G	ENSP00000302993:E209G	E	+	2	0	FIP1L1	53960688	1.000000	0.71417	0.992000	0.48379	0.963000	0.63663	5.426000	0.66476	2.168000	0.68352	0.533000	0.62120	GAA	.	.		0.373	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		G	54265931	A	G	54265931	3	3	64	1	0	0	0	0	1	0	0	0	5904	246	9	2	778	2	FIP1L1	4	54265931	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5720059	54265931	136888345	67	7784										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62936570	62936570	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tagttcctccaaacaaagatGggacccctcccgagggaagt	10	12	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:62936570G>A	ENST00000514591.1	+	25	4683	c.4354G>A	c.(4354-4356)Ggg>Agg	p.G1452R	LPHN3_ENST00000504896.1_3'UTR|LPHN3_ENST00000514157.1_3'UTR|LPHN3_ENST00000512091.2_3'UTR|LPHN3_ENST00000511324.1_3'UTR|LPHN3_ENST00000506720.1_Missense_Mutation_p.G1563R|RP11-84A1.3_ENST00000509461.1_RNA|LPHN3_ENST00000508693.1_3'UTR|LPHN3_ENST00000508946.1_Missense_Mutation_p.G1495R|LPHN3_ENST00000507625.1_Missense_Mutation_p.G1511R|RP11-84A1.3_ENST00000506704.1_RNA|LPHN3_ENST00000509896.1_3'UTR|LPHN3_ENST00000514996.1_Missense_Mutation_p.G1486R|LPHN3_ENST00000506746.1_Missense_Mutation_p.G1554R|LPHN3_ENST00000507164.1_3'UTR|RP11-84A1.3_ENST00000504135.1_RNA|LPHN3_ENST00000506700.1_3'UTR|LPHN3_ENST00000545650.1_Missense_Mutation_p.G1452R			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1430					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						AAACAAAGATGGGACCCCTCC	0.483																																					p.G1452R		Atlas-SNP	.											.	LPHN3	800	.	0			c.G4354A						.						62	60	61					4																	62936570		692	1591	2283	SO:0001583	missense	23284	exon23			AAAGATGGGACCC	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.4354G>A	chr4.hg19:g.62936570G>A	ENSP00000422533:p.Gly1452Arg	90.0	0.0		83.0	32.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.69|19.69	3.874474|3.874474	0.72180|0.72180	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000514591;ENST00000545650;ENST00000295349;ENST00000507625;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996|ENST00000502815	T;T;T;T;T;T;T|.	0.71698|.	-0.57;-0.57;-0.59;-0.54;-0.55;-0.55;-0.54|.	5.5|5.5	5.5|5.5	0.81552|0.81552	GPCR, family 2, latrophilin, C-terminal (1);|.	0.112670|.	0.64402|.	D|.	0.000010|.	T|.	0.68540|.	0.3012|.	L|L	0.43923|0.43923	1.385|1.385	0.54753|0.54753	D|D	0.999981|0.999981	D;D|.	0.62365|.	0.966;0.991|.	P;D|.	0.64877|.	0.837;0.93|.	T|.	0.63730|.	-0.6571|.	10|.	0.87932|.	D|.	0|.	.|.	19.4053|19.4053	0.94646|0.94646	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1452;1430|.	E9PE04;Q9HAR2|.	.;LPHN3_HUMAN|.	R|X	1452;1452;1430;1511;1495;1563;1554;1486|900	ENSP00000422533:G1452R;ENSP00000439831:G1452R;ENSP00000421372:G1511R;ENSP00000421627:G1495R;ENSP00000420931:G1563R;ENSP00000425884:G1554R;ENSP00000424258:G1486R|.	ENSP00000295349:G1430R|.	G|W	+|+	1|2	0|0	LPHN3|LPHN3	62619165|62619165	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.990000|0.990000	0.78478|0.78478	9.416000|9.416000	0.97383|0.97383	2.607000|2.607000	0.88179|0.88179	0.591000|0.591000	0.81541|0.81541	GGG|TGG	.	.		0.483	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			A	62936570	G	A	62936570	3	1	64	1	0	0	0	0	1	0	0	0	8926	1348	47	3	4444	3	LPHN3	4	62936570	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	8670639	62936570	128217706	68	7785										
MTHFD2L	441024	hgsc.bcm.edu	37	chr4	75023925	75023925	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gagcgccggcgttgggcagaAgcacagcaccctccgtaagg	15	13	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:75023925A>G	ENST00000395759.2	+	1	97	c.70A>G	c.(70-72)Agc>Ggc	p.S24G	MTHFD2L_ENST00000331145.6_5'UTR|MTHFD2L_ENST00000325278.6_5'UTR|AC093677.1_ENST00000600169.1_Missense_Mutation_p.L54P|MTHFD2L_ENST00000461101.1_3'UTR|MTHFD2L_ENST00000433372.1_Intron	NM_001144978.1	NP_001138450.1	Q9H903	MTD2L_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	24					folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|tetrahydrofolate interconversion (GO:0035999)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NAD+) activity (GO:0004487)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)			central_nervous_system(1)|endometrium(1)|lung(4)|ovary(2)	8			all cancers(17;0.0101)|Lung(101;0.196)			GTTGGGCAGAAGCACAGCACC	0.746																																					p.S24G		Atlas-SNP	.											.	MTHFD2L	41	.	0			c.A70G						.						7	12	11					4																	75023925		673	1565	2238	SO:0001583	missense	441024	exon1			GGCAGAAGCACAG	BC065771	CCDS47075.1	4q13.3	2011-08-03			ENSG00000163738	ENSG00000163738			31865	protein-coding gene	gene with protein product		614047				21163947	Standard	NM_001144978		Approved	MGC72244	uc011cbk.2	Q9H903	OTTHUMG00000157135	ENST00000395759.2:c.70A>G	chr4.hg19:g.75023925A>G	ENSP00000379108:p.Ser24Gly	36.0	0.0		101.0	5.0	NM_001144978	Q6P079|Q8N560	Missense_Mutation	SNP	ENST00000395759.2	hg19	CCDS47075.1	.	.	.	.	.	.	.	.	.	.	A	9.307	1.054588	0.19907	.	.	ENSG00000163738	ENST00000395759	T	0.22945	1.93	2.18	-3.69	0.04450	Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain (1);	.	.	.	.	T	0.12050	0.0293	N	0.22421	0.69	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.36890	-0.9729	9	0.13853	T	0.58	.	5.2508	0.15521	0.2217:0.2008:0.5775:0.0	.	24;24	Q9H903;Q9H903-5	MTD2L_HUMAN;.	G	24	ENSP00000379108:S24G	ENSP00000379108:S24G	S	+	1	0	MTHFD2L	75242789	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.155000	0.03163	-0.982000	0.03515	-0.334000	0.08254	AGC	.	.		0.746	MTHFD2L-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004346		G	75023925	A	G	75023925	3	3	64	1	0	0	0	0	1	0	0	0	9939	72	3	2	72	2	MTHFD2L	4	75023925	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	12087355	75023925	116130351	69	7786										
ART3	419	hgsc.bcm.edu	37	chr4	77003153	77003153	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aaatgggcagcccgaaagacTcaaatctttctccctatgaa	7	11	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:77003153T>C	ENST00000355810.4	+	3	365	c.246T>C	c.(244-246)acT>acC	p.T82T	ART3_ENST00000349321.3_Silent_p.T82T|ART3_ENST00000341029.5_Silent_p.T82T|ART3_ENST00000513494.1_3'UTR	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	82					protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|stomach(1)	16			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			CCCGAAAGACTCAAATCTTTC	0.418																																					p.T82T		Atlas-SNP	.											.	ART3	34	.	0			c.T246C						.						77	78	78					4																	77003153		2203	4300	6503	SO:0001819	synonymous_variant	419	exon3			AAAGACTCAAATC	X95827	CCDS3575.1, CCDS47079.1, CCDS47080.1	4q21.1	2008-05-15			ENSG00000156219	ENSG00000156219			725	protein-coding gene	gene with protein product		603086				9119374	Standard	NM_001130017		Approved		uc003hjo.3	Q13508	OTTHUMG00000130110	ENST00000355810.4:c.246T>C	chr4.hg19:g.77003153T>C		62.0	0.0		61.0	4.0	NM_001130017	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Silent	SNP	ENST00000355810.4	hg19	CCDS47079.1																																																																																			.	.		0.418	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179		C	77003153	T	C	77003153	2	2	64	1	0	0	0	0	0	0	0	1	998	1538	54	2		2	ART3	4	77003153	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1979228	77003153	114151123	70	7787										
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77663055	77663055	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	catgtgaggtccaggtcatcTcccgccaccgcagacaagcg	11	15	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:77663055T>C	ENST00000296043.6	+	5	4682	c.3729T>C	c.(3727-3729)tcT>tcC	p.S1243S		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1243					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			CCAGGTCATCTCCCGCCACCG	0.662																																					p.S1243S		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T3729C						.						21	19	20					4																	77663055		2170	4244	6414	SO:0001819	synonymous_variant	57619	exon5			GTCATCTCCCGCC	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.3729T>C	chr4.hg19:g.77663055T>C		148.0	0.0		153.0	8.0	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	hg19	CCDS3579.2																																																																																			.	.		0.662	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		C	77663055	T	C	77663055	2	2	64	1	0	0	0	0	0	0	0	1	14310	1538	54	2		2	SHROOM3	4	77663055	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	659902	77663055	113491221	71	7788										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90844418	90844418	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcagcagcaaggctgtggtgAcccaggtcatagattgtaat	13	8	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:90844418A>G	ENST00000394980.1	+	5	1269	c.950A>G	c.(949-951)gAc>gGc	p.D317G	MMRN1_ENST00000264790.2_Missense_Mutation_p.D317G|MMRN1_ENST00000394981.1_Missense_Mutation_p.D283G|MMRN1_ENST00000508372.1_Missense_Mutation_p.D59G			Q13201	MMRN1_HUMAN	multimerin 1	317					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		GGCTGTGGTGACCCAGGTCAT	0.433																																					p.D317G		Atlas-SNP	.											.	MMRN1	174	.	0			c.A950G						.						159	160	160					4																	90844418		2203	4300	6503	SO:0001583	missense	22915	exon4			GTGGTGACCCAGG	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.950A>G	chr4.hg19:g.90844418A>G	ENSP00000378431:p.Asp317Gly	118.0	0.0		123.0	5.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	hg19	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.481750	0.44147	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000394981;ENST00000508372	T;T;T;T	0.73363	0.06;0.06;-0.74;-0.34	5.36	4.17	0.49024	.	0.304283	0.31507	N	0.007531	T	0.67249	0.2873	L	0.53249	1.67	0.25111	N	0.990715	B;B	0.17268	0.021;0.012	B;B	0.19946	0.027;0.004	T	0.58912	-0.7552	10	0.42905	T	0.14	.	8.5906	0.33686	0.8417:0.0:0.1583:0.0	.	283;317	Q13201-2;Q13201	.;MMRN1_HUMAN	G	317;317;283;59	ENSP00000378431:D317G;ENSP00000264790:D317G;ENSP00000378432:D283G;ENSP00000426461:D59G	ENSP00000264790:D317G	D	+	2	0	MMRN1	91063441	0.990000	0.36364	0.878000	0.34440	0.889000	0.51656	2.647000	0.46639	1.120000	0.41904	0.482000	0.46254	GAC	.	.		0.433	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		G	90844418	A	G	90844418	3	3	64	1	0	0	0	0	1	0	0	0	9679	275	10	2	964	2	MMRN1	4	90844418	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	13181363	90844418	100309858	72	7789										
GSTCD	79807	hgsc.bcm.edu	37	chr4	106650634	106650634	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cttgattggaatgttctcccTgcagcagtcagcccaaagga	10	11	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:106650634T>C	ENST00000515279.1	+	5	1438	c.1218T>C	c.(1216-1218)ccT>ccC	p.P406P	GSTCD_ENST00000360505.5_Silent_p.P406P|GSTCD_ENST00000507281.1_Silent_p.P319P|GSTCD_ENST00000394728.3_Silent_p.P406P|GSTCD_ENST00000394730.3_Silent_p.P319P|GSTCD_ENST00000515255.1_3'UTR			Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain containing	406						extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	14		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)		ATGTTCTCCCTGCAGCAGTCA	0.383																																					p.P406P		Atlas-SNP	.											.	GSTCD	69	.	0			c.T1218C						.						103	103	103					4																	106650634		2203	4300	6503	SO:0001819	synonymous_variant	79807	exon5			TCTCCCTGCAGCA	BC032942	CCDS3672.2, CCDS43257.1	4q24	2008-02-05	2006-05-09		ENSG00000138780	ENSG00000138780			25806	protein-coding gene	gene with protein product		615912	"Glutathione S-transferase, C-terminal domain containing"			12477932	Standard	NM_001031720		Approved	FLJ13273	uc003hxz.4	Q8NEC7	OTTHUMG00000131211	ENST00000515279.1:c.1218T>C	chr4.hg19:g.106650634T>C		96.0	0.0		95.0	4.0	NM_001031720	A8K8J0|A8MVD3|H9KV97|Q9H8S3	Silent	SNP	ENST00000515279.1	hg19	CCDS43257.1																																																																																			.	.		0.383	GSTCD-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363981.1	NM_024751		C	106650634	T	C	106650634	2	2	64	1	0	0	0	0	0	0	0	1	6844	1567	55	2		2	GSTCD	4	106650634	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	15806216	106650634	84503642	73	7790										
NAF1	92345	hgsc.bcm.edu	37	chr4	164058390	164058390	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcattcttccatgatgcatcTgatcccttatccctgagtgg	7	12	3	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:164058390T>C	ENST00000274054.2	-	6	1084	c.891A>G	c.(889-891)tcA>tcG	p.S297S	NAF1_ENST00000509434.1_Silent_p.S25S|NAF1_ENST00000422287.2_Silent_p.S297S	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	297					pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				ATGATGCATCTGATCCCTTAT	0.353																																					p.S297S		Atlas-SNP	.											.	NAF1	69	.	0			c.A891G						.						103	96	99					4																	164058390		2203	4300	6503	SO:0001819	synonymous_variant	92345	exon6			TGCATCTGATCCC		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"nuclear assembly factor 1 homolog (S. cerevisiae)"			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.891A>G	chr4.hg19:g.164058390T>C		144.0	0.0		69.0	4.0	NM_138386	D3DP28|E9PAZ2	Silent	SNP	ENST00000274054.2	hg19	CCDS3803.1																																																																																			.	.		0.353	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386		C	164058390	T	C	164058390	2	2	64	1	0	0	0	0	0	0	0	1	10149	1567	55	2		2	NAF1	4	164058390	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	57407756	164058390	27095886	74	7791										
KIAA1712	80817	hgsc.bcm.edu	37	chr4	175224972	175224972	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttgaattgtgtgatgaaaaAgcacaaggaattaagcagtc	10	4	0	3	rs143573166		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:175224972A>G	ENST00000503780.1	+	5	770	c.356A>G	c.(355-357)aAg>aGg	p.K119R	CEP44_ENST00000457424.2_Missense_Mutation_p.K119R|CEP44_ENST00000426172.1_Missense_Mutation_p.K119R|CEP44_ENST00000296519.4_Missense_Mutation_p.K119R	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	119						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)				endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						GTGATGAAAAAGCACAAGGAA	0.279																																					p.K119R		Atlas-SNP	.											.	CEP44	35	.	0			c.A356G						.						71	74	73					4																	175224972		2202	4300	6502	SO:0001583	missense	80817	exon5			TGAAAAAGCACAA	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"KIAA1712"	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.356A>G	chr4.hg19:g.175224972A>G	ENSP00000423153:p.Lys119Arg	166.0	0.0		96.0	4.0	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Missense_Mutation	SNP	ENST00000503780.1	hg19	CCDS34106.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.261564	0.39995	.	.	ENSG00000164118	ENST00000503780;ENST00000457424;ENST00000515299;ENST00000503053;ENST00000426172;ENST00000296519	T;T;T;T;T	0.50548	0.77;0.74;0.81;0.74;0.77	5.61	4.43	0.53597	.	0.049693	0.85682	D	0.000000	T	0.35068	0.0919	L	0.37897	1.145	0.42321	D	0.992254	P;P	0.45474	0.859;0.859	B;B	0.40782	0.34;0.34	T	0.08659	-1.0711	10	0.27082	T	0.32	.	9.4081	0.38473	0.8643:0.0:0.1357:0.0	.	119;119	Q9C0F1-2;Q9C0F1	.;CEP44_HUMAN	R	119	ENSP00000423153:K119R;ENSP00000389427:K119R;ENSP00000421128:K119R;ENSP00000408221:K119R;ENSP00000296519:K119R	ENSP00000296519:K119R	K	+	2	0	CEP44	175461547	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	3.650000	0.54424	2.263000	0.75096	0.528000	0.53228	AAG	.	A|1.000;C|0.000		0.279	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633		G	175224972	A	G	175224972	3	3	64	1	0	0	0	0	1	0	0	0	8262	72	3	2	366	2	KIAA1712	4	175224972	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	11166582	175224972	15929304	75	7792										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186544675	186544675	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctggatccgtaaaagctttcGgaggatgtgaaggaaaagtg	14	5	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr4:186544675G>A	ENST00000284776.7	-	13	2405	c.1896C>T	c.(1894-1896)tcC>tcT	p.S632S	SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000418609.1_Silent_p.S536S|SORBS2_ENST00000355634.5_Silent_p.S732S|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000431808.1_Silent_p.S632S	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	632					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		AAAAGCTTTCGGAGGATGTGA	0.557																																					p.S732S	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											SORBS2,NS,haematopoietic_neoplasm,0,1	SORBS2	300	.	0			c.C2196T						.						55	51	52					4																	186544675		2203	4300	6503	SO:0001819	synonymous_variant	8470	exon16			GCTTTCGGAGGAT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1896C>T	chr4.hg19:g.186544675G>A		59.0	0.0		45.0	2.0	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	hg19	CCDS3845.1																																																																																			.	.		0.557	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		A	186544675	G	A	186544675	2	1	64	1	0	0	0	0	0	0	0	1	14943	1103	39	1		1	SORBS2	4	186544675	Silent	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	11319703	186544675	4609601	76	7793										
CDH6	1004	hgsc.bcm.edu	37	chr5	31305284	31305284	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccacccccaacctcaagctcTtggactttgaaaagaagaaa	6	13	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:31305284T>C	ENST00000265071.2	+	7	1268	c.1003T>C	c.(1003-1005)Ttg>Ctg	p.L335L	CDH6_ENST00000514738.1_Silent_p.L280L	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	335	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CCTCAAGCTCTTGGACTTTGA	0.428																																					p.L335L		Atlas-SNP	.											.	CDH6	175	.	0			c.T1003C						.						71	73	72					5																	31305284		2203	4300	6503	SO:0001819	synonymous_variant	1004	exon7			AAGCTCTTGGACT	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"Cadherins / Major cadherins"	1765	protein-coding gene	gene with protein product	"K-Cadherin"	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.1003T>C	chr5.hg19:g.31305284T>C		61.0	0.0		54.0	5.0	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	hg19	CCDS3894.1																																																																																			.	.		0.428	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		C	31305284	T	C	31305284	2	2	64	1	0	0	0	0	0	0	0	1	3116	1606	56	2		2	CDH6	5	31305284	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		31305284	149609976	77	7794										
RANBP3L	202151	hgsc.bcm.edu	37	chr5	36301506	36301506	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtggctgctgccttttcttgGtatggtagtcatggtcctag	13	8	2	0	rs555708030		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:36301506G>A	ENST00000296604.3	-	1	498	c.13C>T	c.(13-15)Cca>Tca	p.P5S	RANBP3L_ENST00000502994.1_Missense_Mutation_p.P5S|RANBP3L_ENST00000515759.1_Missense_Mutation_p.P5S	NM_145000.3	NP_659437.3	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like	5					intracellular transport (GO:0046907)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	16	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			CCTTTTCTTGGTATGGTAGTC	0.557																																					p.P5S		Atlas-SNP	.											.	RANBP3L	41	.	0			c.C13T						.						136	125	129					5																	36301506		2203	4300	6503	SO:0001583	missense	202151	exon1			TTCTTGGTATGGT	BC047660	CCDS3918.1, CCDS54843.1	5p13.2	2008-02-05			ENSG00000164188	ENSG00000164188			26353	protein-coding gene	gene with protein product						12477932	Standard	NM_145000		Approved	FLJ25422	uc011cow.2	Q86VV4	OTTHUMG00000131110	ENST00000296604.3:c.13C>T	chr5.hg19:g.36301506G>A	ENSP00000296604:p.Pro5Ser	86.0	0.0		75.0	4.0	NM_001161429	B7Z866|E9PGP9|Q96LK2	Missense_Mutation	SNP	ENST00000296604.3	hg19	CCDS3918.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902078	0.33628	.	.	ENSG00000164188	ENST00000296604;ENST00000502994;ENST00000515759;ENST00000505865	T;T;T;T	0.42131	2.02;1.95;1.99;0.98	5.71	4.84	0.62591	.	0.994632	0.08147	N	0.990705	T	0.31544	0.0800	N	0.19112	0.55	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.06405	0.002;0.002	T	0.18366	-1.0339	10	0.44086	T	0.13	2.376	10.8368	0.46692	0.0869:0.0:0.9131:0.0	.	5;5	E9PGP9;Q86VV4	.;RNB3L_HUMAN	S	5	ENSP00000296604:P5S;ENSP00000421853:P5S;ENSP00000421149:P5S;ENSP00000427147:P5S	ENSP00000296604:P5S	P	-	1	0	RANBP3L	36337263	0.146000	0.22672	0.002000	0.10522	0.040000	0.13550	4.332000	0.59279	1.558000	0.49541	0.650000	0.86243	CCA	.	.		0.557	RANBP3L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253773.2	NM_145000		A	36301506	G	A	36301506	3	1	64	1	0	0	0	0	1	0	0	0	13045	1261	44	3	1519	3	RANBP3L	5	36301506	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	4996222	36301506	144613754	78	7795										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37183712	37183712	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ataacttttcatgatcttctTtctttgtaggattttctttc	4	7	5	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:37183712T>C	ENST00000508244.1	-	25	4664	c.4571A>G	c.(4570-4572)aAa>aGa	p.K1524R	C5orf42_ENST00000274258.7_Missense_Mutation_p.K405R|C5orf42_ENST00000425232.2_Missense_Mutation_p.K1524R			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1524						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			ATGATCTTCTTTCTTTGTAGG	0.303																																					p.K1524R		Atlas-SNP	.											.	C5orf42	422	.	0			c.A4571G						.						46	45	45					5																	37183712		2202	4296	6498	SO:0001583	missense	65250	exon26			TCTTCTTTCTTTG		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.4571A>G	chr5.hg19:g.37183712T>C	ENSP00000421690:p.Lys1524Arg	90.0	0.0		68.0	4.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	T	8.255	0.809778	0.16537	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5	4.53	3.36	0.38483	.	0.446903	0.18946	N	0.126810	T	0.47967	0.1474	N	0.14661	0.345	0.20196	N	0.999929	B;B	0.31459	0.184;0.324	B;B	0.30179	0.112;0.112	T	0.29579	-1.0007	10	0.10902	T	0.67	.	9.5851	0.39512	0.0:0.0849:0.0:0.9151	.	1524;405	E9PH94;Q9H799	.;CE042_HUMAN	R	1524;1524;405;572;405	ENSP00000421690:K1524R;ENSP00000389014:K1524R;ENSP00000274258:K405R;ENSP00000424223:K572R	ENSP00000274258:K405R	K	-	2	0	C5orf42	37219469	0.208000	0.23494	0.852000	0.33557	0.471000	0.32888	1.699000	0.37804	0.743000	0.32719	0.533000	0.62120	AAA	.	.		0.303	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37183712	T	C	37183712	3	2	64	1	0	0	0	0	1	0	0	0	2303	1841	64	2	5130	2	C5orf42	5	37183712	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	882206	37183712	143731548	79	7796										
FBXO4	26272	hgsc.bcm.edu	37	chr5	41941379	41941379	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agtggaatctaagcgtgcaaGatgattctcttttcagatct	9	7	4	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:41941379G>A	ENST00000281623.3	+	7	1216	c.1160G>A	c.(1159-1161)aGa>aAa	p.R387K	FBXO4_ENST00000509134.1_3'UTR	NM_012176.2	NP_036308.1	Q9UKT5	FBX4_HUMAN	F-box protein 4	387					positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|telomere maintenance (GO:0000723)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)	p.R387K(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(11)|prostate(1)|stomach(1)|urinary_tract(2)	27		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				AAGCGTGCAAGATGATTCTCT	0.413																																					p.R387K		Atlas-SNP	.											FBXO4,NS,carcinoma,0,1	FBXO4	42	.	1	Substitution - Missense(1)	lung(1)	c.G1160A						.						119	113	115					5																	41941379		2203	4300	6503	SO:0001583	missense	26272	exon7			GTGCAAGATGATT	AF129534	CCDS3938.1, CCDS3939.1, CCDS75238.1	5p12	2008-02-05	2004-06-15		ENSG00000151876	ENSG00000151876		"F-boxes /  "other""	13583	protein-coding gene	gene with protein product		609090	"F-box only protein 4"			10531035, 10531037	Standard	NM_033484		Approved	FBX4	uc003jmq.3	Q9UKT5	OTTHUMG00000094799	ENST00000281623.3:c.1160G>A	chr5.hg19:g.41941379G>A	ENSP00000281623:p.Arg387Lys	112.0	0.0		97.0	4.0	NM_012176	Q68CU8|Q86VT8|Q9UK98	Missense_Mutation	SNP	ENST00000281623.3	hg19	CCDS3938.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.728007	0.30593	.	.	ENSG00000151876	ENST00000281623	.	.	.	5.29	2.41	0.29592	.	0.391635	0.24757	N	0.035848	T	0.41213	0.1149	L	0.36672	1.1	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11867	-1.0570	9	0.18710	T	0.47	-23.5446	7.7053	0.28646	0.3786:0.0:0.6214:0.0	.	387	Q9UKT5	FBX4_HUMAN	K	387	.	ENSP00000281623:R387K	R	+	2	0	FBXO4	41977136	0.996000	0.38824	0.985000	0.45067	0.680000	0.39746	0.612000	0.24283	0.327000	0.23409	0.556000	0.70494	AGA	.	.		0.413	FBXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211614.1			A	41941379	G	A	41941379	3	1	64	1	0	0	0	0	1	0	0	0	5756	942	33	3	1212	3	FBXO4	5	41941379	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	4757667	41941379	138973881	80	7797										
ITGA1	3672	hgsc.bcm.edu	37	chr5	52214692	52214692	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctacagtgtgttttgatgtgAaattaaagtctaaagaagac	9	4	1	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:52214692A>G	ENST00000282588.6	+	16	2577	c.2119A>G	c.(2119-2121)Aaa>Gaa	p.K707E		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	707					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TTTTGATGTGAAATTAAAGTC	0.328																																					p.K707E		Atlas-SNP	.											.	ITGA1	112	.	0			c.A2119G						.						94	87	90					5																	52214692		2203	4299	6502	SO:0001583	missense	3672	exon16			GATGTGAAATTAA	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.2119A>G	chr5.hg19:g.52214692A>G	ENSP00000282588:p.Lys707Glu	81.0	0.0		90.0	5.0	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	hg19	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.264894	0.59431	.	.	ENSG00000213949	ENST00000282588	T	0.47869	0.83	5.51	5.51	0.81932	Integrin alpha-2 (1);	0.308515	0.35677	N	0.003055	T	0.36193	0.0958	L	0.38175	1.15	0.31469	N	0.668637	B	0.28258	0.205	B	0.29077	0.098	T	0.37979	-0.9682	10	0.13853	T	0.58	.	11.8599	0.52459	0.8542:0.1458:0.0:0.0	.	707	P56199	ITA1_HUMAN	E	707	ENSP00000282588:K707E	ENSP00000282588:K707E	K	+	1	0	ITGA1	52250449	0.998000	0.40836	0.997000	0.53966	0.992000	0.81027	3.299000	0.51826	2.210000	0.71456	0.533000	0.62120	AAA	.	.		0.328	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		G	52214692	A	G	52214692	3	3	64	1	0	0	0	0	1	0	0	0	7881	247	9	2	2181	2	ITGA1	5	52214692	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	10273313	52214692	128700568	81	7798										
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64466487	64466487	+	5'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctgtcacatttgctttcacaCtgctgcattgatggaggccg	10	11	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:64466487C>T	ENST00000314351.5	-	0	860							Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6							proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		TGCTTTCACACTGCTGCATTG	0.498																																					p.Q1067Q		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.G3201A						.						90	80	83					5																	64466487		2203	4300	6503	SO:0001623	5_prime_UTR_variant	11174	exon24			TTCACACTGCTGC	AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192		"ADAM metallopeptidases with thrombospondin type 1 motif"	222	protein-coding gene	gene with protein product	"a disintegrin and metalloproteinase with thrombospondin motifs 6"	605008	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6"			10464288	Standard	NM_197941		Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000314351.5:c.-462G>A	chr5.hg19:g.64466487C>T		106.0	0.0		98.0	4.0	NM_197941	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Silent	SNP	ENST00000314351.5	hg19																																																																																				.	.		0.498	ADAMTS6-006	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000157334.2	NM_197941		T	64466487	C	T	64466487	1	4	64	0	1	0	0	0	0	0	0	0	270	564	20	3		3	ADAMTS6	5	64466487	5'UTR	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	12251795	64466487	116448773	82	7799										
RASA1	5921	hgsc.bcm.edu	37	chr5	86665656	86665668	+	Frame_Shift_Del	DEL	AGCACTTTAGTGA	AGCACTTTAGTGA	-													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctgttttcagatagtagttcAgcactttagtgaagaacatt					rs528357903	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	AGCACTTTAGTGA	AGCACTTTAGTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:86665656_86665668delAGCACTTTAGTGA	ENST00000274376.6	+	12	2201_2213	c.1637_1649delAGCACTTTAGTGA	c.(1636-1650)cagcactttagtgaafs	p.QHFSE546fs	RASA1_ENST00000456692.2_Frame_Shift_Del_p.QHFSE369fs|RASA1_ENST00000512763.1_Frame_Shift_Del_p.QHFSE379fs|RASA1_ENST00000506290.1_Frame_Shift_Del_p.QHFSE380fs	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	546	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		ATAGTAGTTCAGCACTTTAGTGAAGAACATTAC	0.31																																					p.546_550del		Pindel	.											.	RASA1	213	.	0			c.1636_1648del						.																																			SO:0001589	frameshift_variant	5921	exon12			.		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.1637_1649delAGCACTTTAGTGA	chr5.hg19:g.86665656_86665668delAGCACTTTAGTGA	ENSP00000274376:p.Gln546fs	0.0	0.0		158.0	20.0	NM_002890	B2R6W3|Q9UDI1	Frame_Shift_Del	DEL	ENST00000274376.6	hg19	CCDS34200.1																																																																																			.	.		0.31	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		-	86665668	AGCACTTTAGTGA	-	86665656	7	5	64	1	0	1	0	1	0	0	0	0	13075	188	7	0	1695	0	RASA1	5	86665656	Frame_Shift_Del	DEL	AGCACTTTAGTGA	TCGA-CC-A3MA-01A-11D-A20W-10	22199169	86665656	94249604	83	7800	36	2								
RASA1	5921	hgsc.bcm.edu	37	chr5	86665661	86665661	+	Missense_Mutation	SNP	T	T	A													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttcagatagtagttcagcacTttagtgaagaacattacatc							TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:86665661T>A	ENST00000274376.6	+	12	2206	c.1642T>A	c.(1642-1644)Ttt>Att	p.F548I	RASA1_ENST00000456692.2_Missense_Mutation_p.F371I|RASA1_ENST00000512763.1_Missense_Mutation_p.F381I|RASA1_ENST00000506290.1_Missense_Mutation_p.F382I	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	548	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		AGTTCAGCACTTTAGTGAAGA	0.308																																					p.F548I		Atlas-SNP	.											.	RASA1	213	.	0			c.T1642A						.						64	64	64					5																	86665661		2203	4298	6501	SO:0001583	missense	5921	exon12			CAGCACTTTAGTG		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.1642T>A	chr5.hg19:g.86665661T>A	ENSP00000274376:p.Phe548Ile	203.0	0.0		142.0	10.0	NM_002890	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	hg19	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	T	19.32	3.805315	0.70682	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9	5.43	5.43	0.79202	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.59932	0.2230	N	0.10760	0.04	0.80722	D	1	P;P;P;P;P	0.36199	0.543;0.543;0.543;0.488;0.543	B;B;B;B;B	0.40256	0.304;0.324;0.324;0.217;0.304	T	0.62148	-0.6915	10	0.30078	T	0.28	.	15.4775	0.75497	0.0:0.0:0.0:1.0	.	382;381;382;371;548	E9PGC0;B4DTL2;B4DTX4;P20936-2;P20936	.;.;.;.;RASA1_HUMAN	I	548;581;371;381;382	ENSP00000274376:F548I;ENSP00000411221:F371I;ENSP00000422008:F381I;ENSP00000420905:F382I	ENSP00000274376:F548I	F	+	1	0	RASA1	86701417	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.643000	0.83403	2.066000	0.61787	0.533000	0.62120	TTT	.	.		0.308	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		A	86665661	T	A	86665661	3	1	64	1	0	0	0	0	1	0	0	0	13075	1609	56	4	1700	4	RASA1	5	86665661	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	5	86665661	94249599	84	7801	36	2								
RIOK2	55781	hgsc.bcm.edu	37	chr5	96514829	96514829	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	actttattacagccaccatgTttaaggctggctatagaagc	8	9	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:96514829T>C	ENST00000283109.3	-	2	203	c.135A>G	c.(133-135)aaA>aaG	p.K45K	CTD-2215E18.1_ENST00000509481.1_Intron|RIOK2_ENST00000508447.1_Silent_p.K45K	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	45							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		AGCCACCATGTTTAAGGCTGG	0.348																																					p.K45K		Atlas-SNP	.											.	RIOK2	82	.	0			c.A135G						.						84	81	82					5																	96514829		2203	4300	6503	SO:0001819	synonymous_variant	55781	exon2			ACCATGTTTAAGG	AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"RIO kinase 2 (yeast)"				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.135A>G	chr5.hg19:g.96514829T>C		51.0	0.0		48.0	4.0	NM_001159749	D6RDI3|Q9NUT0	Silent	SNP	ENST00000283109.3	hg19	CCDS4089.1																																																																																			.	.		0.348	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1	NM_018343		C	96514829	T	C	96514829	2	2	64	1	0	0	0	0	0	0	0	1	13393	1722	60	2		2	RIOK2	5	96514829	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	9849168	96514829	84400431	85	7802										
KLHL3	26249	hgsc.bcm.edu	37	chr5	136963985	136963985	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gatggagagagcagtcattaCctgcgttgcgccggcacatg	14	10	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:136963985C>A	ENST00000309755.4	-	13	2035		c.e13+1		KLHL3_ENST00000506491.1_Splice_Site|KLHL3_ENST00000506873.1_Splice_Site|KLHL3_ENST00000508657.1_Splice_Site|KLHL3_ENST00000541417.1_Splice_Site	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3						distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		GCAGTCATTACCTGCGTTGCG	0.532																																					.		Atlas-SNP	.											KLHL3,NS,carcinoma,0,1	KLHL3	54	.	0			c.1591+1G>T						.						208	180	190					5																	136963985		2203	4300	6503	SO:0001630	splice_region_variant	26249	exon14			TCATTACCTGCGT	AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"Kelch-like", "BTB/POZ domain containing"	6354	protein-coding gene	gene with protein product		605775	"kelch (Drosophila)-like 3", "kelch-like 3 (Drosophila)"			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.1591+1G>T	chr5.hg19:g.136963985C>A		99.0	0.0		93.0	42.0	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Splice_Site	SNP	ENST00000309755.4	hg19	CCDS4192.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.995012	0.74703	.	.	ENSG00000146021	ENST00000506491;ENST00000508657;ENST00000309755	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6787	0.95950	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KLHL3	136991884	1.000000	0.71417	1.000000	0.80357	0.706000	0.40770	7.651000	0.83577	2.884000	0.98904	0.655000	0.94253	.	.	.		0.532	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2		Intron	A	136963985	C	A	136963985	5	1	64	1	0	0	0	0	0	0	1	0	8392	521	18	3	183	3	KLHL3	5	136963985	Splice_Site	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	40449156	136963985	43951275	86	7803										
HBEGF	1839	hgsc.bcm.edu	37	chr5	139725515	139725515	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cctctcaaaaggtccagatcTgcctcttgcaagtcacggac	8	14	4	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:139725515T>C	ENST00000230990.6	-	2	503	c.201A>G	c.(199-201)gcA>gcG	p.A67A	CTC-329D1.3_ENST00000520443.1_RNA|HBEGF_ENST00000507104.1_Silent_p.A67A	NM_001945.2	NP_001936.1	Q99075	HBEGF_HUMAN	heparin-binding EGF-like growth factor	67					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|muscle organ development (GO:0007517)|negative regulation of elastin biosynthetic process (GO:0051545)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of wound healing (GO:0090303)|regulation of heart contraction (GO:0008016)|signal transduction (GO:0007165)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)	7			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTCCAGATCTGCCTCTTGCA	0.587											OREG0016844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A67A		Atlas-SNP	.											.	HBEGF	12	.	0			c.A201G						.						61	62	62					5																	139725515		2203	4300	6503	SO:0001819	synonymous_variant	1839	exon2			CAGATCTGCCTCT		CCDS4223.1	5q23	2012-10-02	2005-01-14	2005-01-14	ENSG00000113070	ENSG00000113070			3059	protein-coding gene	gene with protein product	"Diphtheria toxin receptor (heparin-binding EGF-like growth factor)", "heparin-binding epidermal growth factor"	126150	"diphtheria toxin receptor (heparin-binding epidermal growth factor-like growth factor)"	HEGFL, DTS, DTR		7590736, 12163414	Standard	NM_001945		Approved		uc003lfi.3	Q99075	OTTHUMG00000129496	ENST00000230990.6:c.201A>G	chr5.hg19:g.139725515T>C		188.0	0.0	1651	124.0	5.0	NM_001945	B2R821	Silent	SNP	ENST00000230990.6	hg19	CCDS4223.1																																																																																			.	.		0.587	HBEGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251665.2	NM_001945		C	139725515	T	C	139725515	2	2	64	1	0	0	0	0	0	0	0	1	6990	1567	55	2		2	HBEGF	5	139725515	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2761530	139725515	41189745	87	7804										
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140559337	140559337	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aatggctccgcgccctgcacCgagctggtgccccgggcggc	15	17	0	0	rs374710779		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:140559337C>T	ENST00000239444.2	+	1	1967	c.1722C>T	c.(1720-1722)acC>acT	p.T574T	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	574	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCCCTGCACCGAGCTGGTGC	0.701																																					p.T574T		Atlas-SNP	.											PCDHB8,NS,carcinoma,0,1	PCDHB8	199	.	0			c.C1722T						.						9	18	15					5																	140559337		2148	4213	6361	SO:0001819	synonymous_variant	56128	exon1			CTGCACCGAGCTG	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.1722C>T	chr5.hg19:g.140559337C>T		23.0	0.0		99.0	4.0	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	hg19	CCDS4250.1																																																																																			.	.		0.701	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		T	140559337	C	T	140559337	2	4	64	1	0	0	0	0	0	0	0	1	11557	639	23	1		1	PCDHB8	5	140559337	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	833822	140559337	40355923	88	7805										
HAVCR1	26762	hgsc.bcm.edu	37	chr5	156479571	156479571	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gttgtcgttggaacagtcgtCattggaacagtcgttgtcgt	13	7	1	0	rs6149307|rs386693994|rs183130208|rs141023871	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:156479571C>T	ENST00000339252.3	-	3	1006	c.474G>A	c.(472-474)atG>atA	p.M158I	HAVCR1_ENST00000425854.1_Missense_Mutation_p.M158I|HAVCR1_ENST00000522693.1_Missense_Mutation_p.M158I|HAVCR1_ENST00000544197.1_Missense_Mutation_p.M158I|HAVCR1_ENST00000523175.1_Missense_Mutation_p.M158I	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)			endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GAACAGTCGTCATTGGAACAG	0.488																																					p.M158I		Atlas-SNP	.											.	HAVCR1	84	.	0			c.G474A						.						413	302	340					5																	156479571		2079	3991	6070	SO:0001583	missense	26762	exon4			AGTCGTCATTGGA	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"Immunoglobulin superfamily / V-set domain containing"	17866	protein-coding gene	gene with protein product	"T-cell immunoglobulin mucin family member 1"	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.474G>A	chr5.hg19:g.156479571C>T	ENSP00000344844:p.Met158Ile	3.0	0.0		242.0	25.0	NM_001099414	O43656	Missense_Mutation	SNP	ENST00000339252.3	hg19	CCDS43392.1	.	.	.	.	.	.	.	.	.	.	C	2.575	-0.298775	0.05532	.	.	ENSG00000113249	ENST00000522693;ENST00000523175;ENST00000339252;ENST00000425854;ENST00000544197;ENST00000518745	T;T;T;T;T;T	0.13901	2.55;2.6;2.6;2.55;2.6;2.57	1.56	-3.12	0.05282	.	.	.	.	.	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.31392	-0.9945	7	0.62326	D	0.03	.	0.1239	0.00067	0.2901:0.1916:0.1631:0.3551	.	.	.	.	I	158	ENSP00000428524:M158I;ENSP00000427898:M158I;ENSP00000344844:M158I;ENSP00000403333:M158I;ENSP00000440258:M158I;ENSP00000428422:M158I	ENSP00000344844:M158I	M	-	3	0	HAVCR1	156412149	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.878000	0.28126	-1.479000	0.01867	-0.507000	0.04495	ATG	.	.		0.488	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1			T	156479571	C	T	156479571	3	4	64	1	0	0	0	0	1	0	0	0	6982	826	29	3	644	3	HAVCR1	5	156479571	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	15920234	156479571	24435689	89	7806										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167689611	167689611	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cagagggccctgggcacggcCtgggccaaggagcagcagaa	17	12	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr5:167689611C>G	ENST00000518659.1	+	29	8160	c.8121C>G	c.(8119-8121)gcC>gcG	p.A2707A	TENM2_ENST00000519204.1_Silent_p.A2586A|TENM2_ENST00000520394.1_Silent_p.A2468A|TENM2_ENST00000545108.1_Silent_p.A2706A|TENM2_ENST00000403607.2_Silent_p.A2531A	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2707					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TGGGCACGGCCTGGGCCAAGG	0.687																																					p.A2698A		Atlas-SNP	.											.	.	.	.	0			c.C8094G						.						11	12	12					5																	167689611		1984	4145	6129	SO:0001819	synonymous_variant	57451	exon29			CACGGCCTGGGCC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.8121C>G	chr5.hg19:g.167689611C>G		60.0	0.0		63.0	26.0	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	hg19																																																																																				.	.		0.687	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		G	167689611	C	G	167689611	2	3	64	1	0	0	0	0	0	0	0	1	10844	668	24	4		4	ODZ2	5	167689611	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	11210040	167689611	13225649	90	7807										
CAGE1	285782	hgsc.bcm.edu	37	chr6	7366104	7366104	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	taaaggttgtgattctatctTtatgtttcagtagctaagaa	8	4	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:7366104T>C	ENST00000512086.1	-	8	2207				CAGE1_ENST00000296742.7_Intron|CAGE1_ENST00000502583.1_Missense_Mutation_p.K673R|CAGE1_ENST00000379918.4_Missense_Mutation_p.K651R|CAGE1_ENST00000338150.4_Missense_Mutation_p.K673R			Q8TC20	CAGE1_HUMAN	cancer antigen 1											breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					GATTCTATCTTTATGTTTCAG	0.308																																					p.K673R		Atlas-SNP	.											.	CAGE1	165	.	0			c.A2018G						.						139	124	129					6																	7366104		692	1591	2283	SO:0001627	intron_variant	285782	exon8			CTATCTTTATGTT	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"cancer/testis antigen 95"	608304	"cancer/testis antigen 3"	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.2005-296A>G	chr6.hg19:g.7366104T>C		71.0	0.0		59.0	4.0	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Missense_Mutation	SNP	ENST00000512086.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.42	2.233347	0.39498	.	.	ENSG00000164304	ENST00000379918;ENST00000502583;ENST00000338150;ENST00000542431	T;T;T	0.35789	1.29;1.43;1.43	5.43	1.7	0.24286	.	0.196102	0.35739	N	0.003018	T	0.08179	0.0204	N	0.25890	0.77	0.27234	N	0.95932	B;B	0.24576	0.106;0.106	B;B	0.26969	0.075;0.045	T	0.33777	-0.9855	10	0.23302	T	0.38	-15.0625	6.6693	0.23060	0.0:0.2787:0.0:0.7213	.	673;673	Q8TC20-3;D6RCT9	.;.	R	651;673;673;673	ENSP00000369250:K651R;ENSP00000425493:K673R;ENSP00000338107:K673R	ENSP00000338107:K673R	K	-	2	0	CAGE1	7311103	1.000000	0.71417	0.986000	0.45419	0.819000	0.46315	0.434000	0.21494	0.341000	0.23771	0.460000	0.39030	AAA	.	.		0.308	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745		C	7366104	T	C	7366104	1	2	64	0	1	0	0	0	0	0	0	0	2574	1841	64	2		2	CAGE1	6	7366104	Intron	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		7366104	163748963	91	7808										
DSP	1832	hgsc.bcm.edu	37	chr6	7580098	7580098	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	accaccatcaaggagatatcCatgcaaaaagaggatgattc	8	9	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:7580098C>G	ENST00000379802.3	+	23	4016	c.3675C>G	c.(3673-3675)tcC>tcG	p.S1225S	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1225	Central fibrous rod domain.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AGGAGATATCCATGCAAAAAG	0.368																																					p.S1225S		Atlas-SNP	.											.	DSP	306	.	0			c.C3675G						.						75	72	73					6																	7580098		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon23			GATATCCATGCAA	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.3675C>G	chr6.hg19:g.7580098C>G		116.0	0.0		91.0	39.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.368	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		G	7580098	C	G	7580098	2	3	64	1	0	0	0	0	0	0	0	1	4783	581	21	4		4	DSP	6	7580098	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	213994	7580098	163534969	92	7809										
ALDH5A1	7915	hgsc.bcm.edu	37	chr6	24523152	24523152	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	taatgaaaaagcggtagaaaAggtaagtatattgtattatt	9	1	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:24523152A>G	ENST00000357578.3	+	7	1317	c.1172A>G	c.(1171-1173)aAg>aGg	p.K391R	ALDH5A1_ENST00000546278.1_Splice_Site_p.K303R|ALDH5A1_ENST00000348925.2_Splice_Site_p.K404R|ALDH5A1_ENST00000491546.1_Splice_Site_p.K363R	NM_001080.3	NP_001071.1	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5 family, member A1	391					acetate metabolic process (GO:0006083)|central nervous system development (GO:0007417)|galactosylceramide metabolic process (GO:0006681)|gamma-aminobutyric acid catabolic process (GO:0009450)|glucose metabolic process (GO:0006006)|glucosylceramide metabolic process (GO:0006678)|glutamate metabolic process (GO:0006536)|glutamine metabolic process (GO:0006541)|glutathione metabolic process (GO:0006749)|glycerophospholipid metabolic process (GO:0006650)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|respiratory electron transport chain (GO:0022904)|short-chain fatty acid metabolic process (GO:0046459)|succinate metabolic process (GO:0006105)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	protein homodimerization activity (GO:0042803)|succinate-semialdehyde dehydrogenase (NAD+) activity (GO:0004777)|succinate-semialdehyde dehydrogenase [NAD(P)+] activity (GO:0009013)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|skin(2)|urinary_tract(1)	20					Chlormerodrin(DB00534)|Succinic acid(DB00139)|Valproic Acid(DB00313)	GCGGTAGAAAAGGTAAGTATA	0.393																																					p.K404R		Atlas-SNP	.											ALDH5A1,colon,carcinoma,0,1	ALDH5A1	42	.	0			c.A1211G						.						79	82	81					6																	24523152		2203	4300	6503	SO:0001630	splice_region_variant	7915	exon8			TAGAAAAGGTAAG	L34820	CCDS4555.1, CCDS4556.1	6p22	2013-06-03	2008-07-31		ENSG00000112294	ENSG00000112294	1.2.1.24	"Aldehyde dehydrogenases"	408	protein-coding gene	gene with protein product	"succinate-semialdehyde dehydrogenase"	610045				7814412, 9059628	Standard	NM_001080		Approved	SSADH, SSDH	uc003nef.3	P51649	OTTHUMG00000014356	ENST00000357578.3:c.1173+1A>G	chr6.hg19:g.24523152A>G		30.0	0.0		30.0	2.0	NM_170740	B2RD26|G5E949|Q546H9|Q8N3W6	Missense_Mutation	SNP	ENST00000357578.3	hg19	CCDS4555.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.070766	0.76301	.	.	ENSG00000112294	ENST00000357578;ENST00000546278;ENST00000491546;ENST00000348925	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	5.2	5.2	0.72013	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.76608	0.4011	L	0.37466	1.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.80522	-0.1345	10	0.87932	D	0	-8.0048	15.5259	0.75905	1.0:0.0:0.0:0.0	.	391;404	P51649;G5E949	SSDH_HUMAN;.	R	391;303;363;404	ENSP00000350191:K391R;ENSP00000438193:K303R;ENSP00000417687:K363R;ENSP00000314649:K404R	ENSP00000314649:K404R	K	+	2	0	ALDH5A1	24631131	1.000000	0.71417	1.000000	0.80357	0.527000	0.34593	8.873000	0.92357	2.308000	0.77769	0.533000	0.62120	AAG	.	.		0.393	ALDH5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040007.2		Missense_Mutation	G	24523152	A	G	24523152	5	3	64	1	0	0	0	0	0	0	1	0	502	86	3	2	1241	2	ALDH5A1	6	24523152	Splice_Site	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	16943054	24523152	146591915	93	7810										
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31931312	31931312	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gctctttttgttgctggactCccgaggagccttccatacaa	9	12	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:31931312C>T	ENST00000375394.2	+	14	1639	c.1526C>T	c.(1525-1527)tCc>tTc	p.S509F	SKIV2L_ENST00000544581.1_Missense_Mutation_p.S316F	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	509					ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						TTGCTGGACTCCCGAGGAGCC	0.577																																					p.S509F		Atlas-SNP	.											.	SKIV2L	97	.	0			c.C1526T						.						40	43	42					6																	31931312		2203	4300	6503	SO:0001583	missense	6499	exon14			TGGACTCCCGAGG		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.1526C>T	chr6.hg19:g.31931312C>T	ENSP00000364543:p.Ser509Phe	136.0	0.0		102.0	5.0	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490153	0.64074	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.50813	0.81;0.73	5.25	5.25	0.73442	.	0.174960	0.49305	D	0.000141	T	0.47857	0.1468	M	0.80982	2.52	0.46396	D	0.999021	B	0.24651	0.108	B	0.33960	0.173	T	0.53885	-0.8375	10	0.72032	D	0.01	-9.5684	17.828	0.88672	0.0:1.0:0.0:0.0	.	509	Q15477	SKIV2_HUMAN	F	509;351;316	ENSP00000364543:S509F;ENSP00000442645:S316F	ENSP00000364543:S509F	S	+	2	0	SKIV2L	32039291	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.720000	0.61944	2.733000	0.93635	0.650000	0.86243	TCC	.	.		0.577	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			T	31931312	C	T	31931312	3	4	64	1	0	0	0	0	1	0	0	0	14374	855	30	3	1580	3	SKIV2L	6	31931312	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	7408160	31931312	139183755	94	7811										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32187547	32187547	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gaaccgccatgttcacagggActtgggccttgctgggctgg	15	11	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:32187547A>G	ENST00000375023.3	-	8	1470	c.1332T>C	c.(1330-1332)agT>agC	p.S444S		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	444	EGF-like 11; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GTTCACAGGGACTTGGGCCTT	0.612																																					p.S444S		Atlas-SNP	.											.	NOTCH4	201	.	0			c.T1332C						.						75	53	61					6																	32187547		1510	2709	4219	SO:0001819	synonymous_variant	4855	exon8			ACAGGGACTTGGG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.1332T>C	chr6.hg19:g.32187547A>G		151.0	0.0		118.0	5.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	hg19	CCDS34420.1																																																																																			.	.		0.612	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			G	32187547	A	G	32187547	2	3	64	1	0	0	0	0	0	0	0	1	10560	272	10	2		2	NOTCH4	6	32187547	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	256235	32187547	138927520	95	7812										
PTK7	5754	hgsc.bcm.edu	37	chr6	43097478	43097478	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gctacagggattgaggcaggTcctgtggtcctgaagcatcc	14	10	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:43097478T>C	ENST00000230419.4	+	3	602	c.381T>C	c.(379-381)ggT>ggC	p.G127G	PTK7_ENST00000471863.1_Silent_p.G127G|PTK7_ENST00000349241.2_Silent_p.G127G|PTK7_ENST00000345201.2_Silent_p.G127G|PTK7_ENST00000352931.2_Silent_p.G127G|PTK7_ENST00000481273.1_Silent_p.G135G	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	127					actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			TTGAGGCAGGTCCTGTGGTCC	0.607											OREG0017449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G135G		Atlas-SNP	.											.	PTK7	101	.	0			c.T405C						.						87	74	79					6																	43097478		2203	4300	6503	SO:0001819	synonymous_variant	5754	exon3			GGCAGGTCCTGTG	AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.381T>C	chr6.hg19:g.43097478T>C		134.0	0.0	913	85.0	4.0	NM_001270398	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Silent	SNP	ENST00000230419.4	hg19	CCDS4884.1																																																																																			.	.		0.607	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2			C	43097478	T	C	43097478	2	2	64	1	0	0	0	0	0	0	0	1	12778	1654	58	2		2	PTK7	6	43097478	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	10909931	43097478	128017589	96	7813										
MAD2L1BP	9587	hgsc.bcm.edu	37	chr6	43604135	43604135	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cagatttggagtggtatgagAagtccgaagaaactcacgcc	12	8	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:43604135A>G	ENST00000372171.4	+	2	121	c.64A>G	c.(64-66)Aag>Gag	p.K22E	MAD2L1BP_ENST00000508232.1_3'UTR|MAD2L1BP_ENST00000451025.2_Missense_Mutation_p.K54E	NM_014628.2	NP_055443.1	Q15013	MD2BP_HUMAN	MAD2L1 binding protein	22					mitotic cell cycle checkpoint (GO:0007093)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|large_intestine(1)|lung(3)	5	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000351)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			GTGGTATGAGAAGTCCGAAGA	0.468																																					p.K54E		Atlas-SNP	.											.	MAD2L1BP	12	.	0			c.A160G						.						78	77	77					6																	43604135		2203	4300	6503	SO:0001583	missense	9587	exon3			TATGAGAAGTCCG	BC002904	CCDS4904.1, CCDS47431.1	6p21.1	2003-06-23			ENSG00000124688	ENSG00000124688			21059	protein-coding gene	gene with protein product						7788527, 12456649	Standard	NM_014628		Approved	CMT2, KIAA0110, dJ261G23.1	uc003ovu.3	Q15013	OTTHUMG00000014747	ENST00000372171.4:c.64A>G	chr6.hg19:g.43604135A>G	ENSP00000361244:p.Lys22Glu	82.0	0.0		100.0	4.0	NM_001003690	B4DLV3|E9PAT7|Q6IBB1	Missense_Mutation	SNP	ENST00000372171.4	hg19	CCDS4904.1	.	.	.	.	.	.	.	.	.	.	A	17.24	3.338237	0.60963	.	.	ENSG00000124688	ENST00000451025;ENST00000372171	T	0.13657	2.57	5.69	1.77	0.24775	.	0.448313	0.20991	N	0.082034	T	0.02047	0.0064	N	0.14661	0.345	0.25502	N	0.987542	B;B	0.09022	0.001;0.002	B;B	0.08055	0.002;0.003	T	0.41698	-0.9494	10	0.66056	D	0.02	-0.8498	3.2583	0.06840	0.4998:0.2136:0.2865:0.0	.	22;54	Q15013;E9PAT7	MD2BP_HUMAN;.	E	54;22	ENSP00000410818:K54E	ENSP00000361244:K22E	K	+	1	0	MAD2L1BP	43712113	0.998000	0.40836	0.528000	0.27938	0.523000	0.34469	1.126000	0.31344	0.363000	0.24346	0.459000	0.35465	AAG	.	.		0.468	MAD2L1BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040692.2	NM_014628		G	43604135	A	G	43604135	3	3	64	1	0	0	0	0	1	0	0	0	9158	247	9	2	220	2	MAD2L1BP	6	43604135	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	506657	43604135	127510932	97	7814										
EYS	346007	hgsc.bcm.edu	37	chr6	64498005	64498005	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtccatgccttaccttgaaaAccatttttaaaatctgctcc	4	12	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:64498005A>G	ENST00000370621.3	-	39	8242	c.7716T>C	c.(7714-7716)ggT>ggC	p.G2572G	EYS_ENST00000370616.2_Silent_p.G2572G|EYS_ENST00000503581.1_Silent_p.G2572G|EYS_ENST00000486069.1_5'UTR			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2572	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TACCTTGAAAACCATTTTTAA	0.333																																					p.G2572G		Atlas-SNP	.											.	EYS	527	.	0			c.T7716C						.						124	102	109					6																	64498005		692	1591	2283	SO:0001819	synonymous_variant	346007	exon39			TTGAAAACCATTT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.7716T>C	chr6.hg19:g.64498005A>G		58.0	0.0		56.0	5.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	A	8.281	0.815531	0.16607	.	.	ENSG00000188107	ENST00000398580	.	.	.	4.1	-0.136	0.13473	.	.	.	.	.	T	0.34019	0.0883	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22277	-1.0221	4	.	.	.	.	4.9725	0.14123	0.2999:0.3246:0.3755:0.0	.	.	.	.	A	344	.	.	V	-	2	0	EYS	64555964	0.970000	0.33590	0.995000	0.50966	0.998000	0.95712	0.006000	0.13152	-0.216000	0.10048	0.533000	0.62120	GTT	.	.		0.333	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	64498005	A	G	64498005	2	3	64	1	0	0	0	0	0	0	0	1	5334	30	2	2		2	EYS	6	64498005	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	20893870	64498005	106617062	98	7815										
SENP6	26054	hgsc.bcm.edu	37	chr6	76388329	76388329	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aatctaaaatacaacttagaAgcaaacaagaatttcagttt	4	6	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:76388329A>G	ENST00000447266.2	+	15	2357	c.1879A>G	c.(1879-1881)Agc>Ggc	p.S627G	SENP6_ENST00000370014.3_Missense_Mutation_p.S627G|SENP6_ENST00000327284.8_Missense_Mutation_p.S620G|SENP6_ENST00000541192.1_Missense_Mutation_p.S223G|SENP6_ENST00000370010.2_Missense_Mutation_p.S620G	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	627					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				ACAACTTAGAAGCAAACAAGA	0.308																																					p.S627G		Atlas-SNP	.											.	SENP6	189	.	0			c.A1879G						.						95	90	92					6																	76388329		1796	4060	5856	SO:0001583	missense	26054	exon15			CTTAGAAGCAAAC		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.1879A>G	chr6.hg19:g.76388329A>G	ENSP00000402527:p.Ser627Gly	120.0	0.0		99.0	4.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	hg19	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.893688	0.52121	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000327284;ENST00000447266;ENST00000424947;ENST00000541192	T;T;T;T;T;T	0.30981	2.73;2.73;1.53;2.73;1.53;1.51	5.71	5.71	0.89125	.	0.629814	0.18288	N	0.145788	T	0.10852	0.0265	N	0.22421	0.69	0.25468	N	0.987859	B;B;B	0.20164	0.041;0.011;0.042	B;B;B	0.23574	0.047;0.015;0.046	T	0.12941	-1.0528	10	0.25106	T	0.35	-2.5798	15.9778	0.80083	1.0:0.0:0.0:0.0	.	620;627;620	Q9GZR1-2;Q9GZR1;F8W6D9	.;SENP6_HUMAN;.	G	620;627;620;627;517;223	ENSP00000359027:S620G;ENSP00000359031:S627G;ENSP00000321820:S620G;ENSP00000402527:S627G;ENSP00000391426:S517G;ENSP00000441715:S223G	ENSP00000321820:S620G	S	+	1	0	SENP6	76445049	1.000000	0.71417	0.562000	0.28370	0.911000	0.54048	6.379000	0.73154	2.173000	0.68751	0.533000	0.62120	AGC	.	.		0.308	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		G	76388329	A	G	76388329	3	3	64	1	0	0	0	0	1	0	0	0	14065	72	3	2	1937	2	SENP6	6	76388329	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	11890324	76388329	94726738	99	7816										
ME1	4199	hgsc.bcm.edu	37	chr6	84108172	84108172	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggcatgaatttctcaatgtcAgatgtcagcactctataaaa	7	8	4	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:84108172A>G	ENST00000369705.3	-	3	392	c.276T>C	c.(274-276)tcT>tcC	p.S92S	ME1_ENST00000541327.1_Intron|ME1_ENST00000543031.1_Silent_p.S17S	NM_002395.4	NP_002386.1	P48163	MAOX_HUMAN	malic enzyme 1, NADP(+)-dependent, cytosolic	92					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|malate metabolic process (GO:0006108)|NADP biosynthetic process (GO:0006741)|protein tetramerization (GO:0051262)|response to carbohydrate (GO:0009743)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|manganese ion binding (GO:0030145)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|oxaloacetate decarboxylase activity (GO:0008948)			NS(2)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)		TCTCAATGTCAGATGTCAGCA	0.363																																					p.S92S		Atlas-SNP	.											.	ME1	68	.	0			c.T276C						.						70	66	67					6																	84108172		2203	4300	6503	SO:0001819	synonymous_variant	4199	exon3			AATGTCAGATGTC	X77244	CCDS34492.1	6q12	2012-10-02			ENSG00000065833	ENSG00000065833	1.1.1.40		6983	protein-coding gene	gene with protein product		154250				8187880	Standard	NM_002395		Approved		uc003pjy.3	P48163	OTTHUMG00000015111	ENST00000369705.3:c.276T>C	chr6.hg19:g.84108172A>G		128.0	0.0		99.0	4.0	NM_002395	B4DZ70|Q16797|Q16855|Q53F72|Q5VWA2|Q9BWX8|Q9H1W3|Q9UIY4	Silent	SNP	ENST00000369705.3	hg19	CCDS34492.1																																																																																			.	.		0.363	ME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041350.1			G	84108172	A	G	84108172	2	3	64	1	0	0	0	0	0	0	0	1	9426	175	7	2		2	ME1	6	84108172	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	7719843	84108172	87006895	100	7817										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84371275	84371275	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtctgtaagaaaaagcctttTcattcaaatatctactatag	5	7	4	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:84371275T>C	ENST00000439399.2	-	5	714	c.398A>G	c.(397-399)gAa>gGa	p.E133G	SNAP91_ENST00000521743.1_Missense_Mutation_p.E133G|SNAP91_ENST00000369694.2_Missense_Mutation_p.E133G|SNAP91_ENST00000195649.6_Missense_Mutation_p.E133G|SNAP91_ENST00000521485.1_Missense_Mutation_p.E133G|SNAP91_ENST00000437520.1_Missense_Mutation_p.E133G|SNAP91_ENST00000520302.1_Missense_Mutation_p.E133G|SNAP91_ENST00000520213.1_Missense_Mutation_p.E133G|SNAP91_ENST00000428679.2_Missense_Mutation_p.E133G	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	133	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		AAAAGCCTTTTCATTCAAATA	0.328																																					p.E133G		Atlas-SNP	.											.	SNAP91	199	.	0			c.A398G						.						57	56	56					6																	84371275		1808	4070	5878	SO:0001583	missense	9892	exon5			GCCTTTTCATTCA	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.398A>G	chr6.hg19:g.84371275T>C	ENSP00000400459:p.Glu133Gly	134.0	0.0		72.0	4.0	NM_001242794	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.679502	0.88542	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000437520;ENST00000520302;ENST00000521743;ENST00000520213;ENST00000521931;ENST00000519779;ENST00000518309;ENST00000369690	T;T;T;T;T;T;T;T;T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21	5.13	5.13	0.70059	ENTH/VHS (2);ANTH (1);Epsin-like, N-terminal (2);	0.099801	0.64402	D	0.000002	T	0.65037	0.2653	H	0.94847	3.59	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.996;1.0	D;D;D;D	0.83275	0.996;0.995;0.921;0.995	T	0.77000	-0.2750	10	0.87932	D	0	-16.6735	15.2297	0.73378	0.0:0.0:0.0:1.0	.	133;133;133;133	O60641-3;E5RI02;O60641;E1P549	.;.;AP180_HUMAN;.	G	133	ENSP00000429776:E133G;ENSP00000358708:E133G;ENSP00000400459:E133G;ENSP00000195649:E133G;ENSP00000412492:E133G;ENSP00000413277:E133G;ENSP00000428511:E133G;ENSP00000428215:E133G;ENSP00000428026:E133G;ENSP00000430071:E133G;ENSP00000429429:E133G;ENSP00000430441:E133G;ENSP00000358704:E133G	ENSP00000195649:E133G	E	-	2	0	SNAP91	84427994	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.932000	0.87634	2.056000	0.61249	0.460000	0.39030	GAA	.	.		0.328	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			C	84371275	T	C	84371275	3	2	64	1	0	0	0	0	1	0	0	0	14848	1783	62	2	2421	2	SNAP91	6	84371275	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	263103	84371275	86743792	101	7818										
MANEA	79694	hgsc.bcm.edu	37	chr6	96052708	96052708	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tattgtttgttttaggttacTtttcacatagaaccatatag	6	5	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:96052708T>C	ENST00000358812.4	+	4	794	c.660T>C	c.(658-660)acT>acC	p.T220T	MANEA_ENST00000474553.1_3'UTR	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	220	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		TTTAGGTTACTTTTCACATAG	0.229																																					p.T220T		Atlas-SNP	.											.	MANEA	58	.	0			c.T660C						.						28	29	29					6																	96052708		2157	4207	6364	SO:0001819	synonymous_variant	79694	exon4			GGTTACTTTTCAC	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.660T>C	chr6.hg19:g.96052708T>C		171.0	0.0		92.0	4.0	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Silent	SNP	ENST00000358812.4	hg19	CCDS5032.1																																																																																			.	.		0.229	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641		C	96052708	T	C	96052708	2	2	64	1	0	0	0	0	0	0	0	1	9230	1596	56	2		2	MANEA	6	96052708	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	11681433	96052708	75062359	102	7819										
HACE1	57531	hgsc.bcm.edu	37	chr6	105244550	105244550	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	catgttttctcggaggtcttCattctgtgtcatttgaataa	8	7	5	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:105244550C>T	ENST00000262903.4	-	9	1072	c.796G>A	c.(796-798)Gaa>Aaa	p.E266K	HACE1_ENST00000369125.2_Missense_Mutation_p.E266K	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	266					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		CGGAGGTCTTCATTCTGTGTC	0.338																																					p.E266K		Atlas-SNP	.											.	HACE1	96	.	0			c.G796A						.						81	81	81					6																	105244550		2203	4298	6501	SO:0001583	missense	57531	exon9			GGTCTTCATTCTG	BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"Ankyrin repeat domain containing"	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.796G>A	chr6.hg19:g.105244550C>T	ENSP00000262903:p.Glu266Lys	114.0	0.0		44.0	23.0	NM_020771	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Missense_Mutation	SNP	ENST00000262903.4	hg19	CCDS5050.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.811993	0.90707	.	.	ENSG00000085382	ENST00000262903;ENST00000369125	T;T	0.36520	1.25;1.29	5.6	5.6	0.85130	.	0.093200	0.64402	D	0.000001	T	0.13415	0.0325	N	0.19112	0.55	0.58432	D	0.999999	P;P	0.34522	0.455;0.455	B;B	0.27076	0.076;0.076	T	0.05099	-1.0906	10	0.22109	T	0.4	.	19.6045	0.95575	0.0:1.0:0.0:0.0	.	266;266	E9PGP0;Q8IYU2	.;HACE1_HUMAN	K	266	ENSP00000262903:E266K;ENSP00000358121:E266K	ENSP00000262903:E266K	E	-	1	0	HACE1	105351243	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.400000	0.66320	2.623000	0.88846	0.585000	0.79938	GAA	.	.		0.338	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095		T	105244550	C	T	105244550	3	4	64	1	0	0	0	0	1	0	0	0	6949	835	29	3	1997	3	HACE1	6	105244550	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	9191842	105244550	65870517	103	7820										
AIM1	202	hgsc.bcm.edu	37	chr6	106960807	106960807	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcagagggaggtcgaagcagAgagctgggcagagcggccgg	21	8	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:106960807A>G	ENST00000369066.3	+	1	1078	c.591A>G	c.(589-591)agA>agG	p.R197R		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GTCGAAGCAGAGAGCTGGGCA	0.657																																					p.R197R		Atlas-SNP	.											.	AIM1	161	.	0			c.A591G						.						13	18	16					6																	106960807		2195	4289	6484	SO:0001819	synonymous_variant	202	exon1			AAGCAGAGAGCTG	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.591A>G	chr6.hg19:g.106960807A>G		81.0	0.0		79.0	4.0	NM_001624	Q6P2P0|Q9BTM3	Silent	SNP	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.		0.657	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			G	106960807	A	G	106960807	2	3	64	1	0	0	0	0	0	0	0	1	430	301	11	2		2	AIM1	6	106960807	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1716257	106960807	64154260	104	7821										
SNX3	8724	hgsc.bcm.edu	37	chr6	108544209	108544209	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	caaagtcactgtatcttcttCtaacagtagattctttcagc	5	10	6	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:108544209C>T	ENST00000230085.8	-	2	541	c.203G>A	c.(202-204)aGa>aAa	p.R68K	SNX3_ENST00000426155.2_Intron|SNX3_ENST00000368982.4_Missense_Mutation_p.R68K|SNX3_ENST00000349379.5_Missense_Mutation_p.R46K	NM_003795.4	NP_003786.1	O60493	SNX3_HUMAN	sorting nexin 3	68	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				hemoglobin biosynthetic process (GO:0042541)|intracellular protein transport (GO:0006886)|intralumenal vesicle formation (GO:0070676)|membrane invagination (GO:0010324)|negative regulation of early endosome to late endosome transport (GO:2000642)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein transport (GO:0051224)|negative regulation of viral entry into host cell (GO:0046597)|regulation of cellular protein metabolic process (GO:0032268)|regulation of intracellular protein transport (GO:0033157)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein phosphatase binding (GO:0019903)			large_intestine(1)	1		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0136)|Epithelial(106;0.0564)|OV - Ovarian serous cystadenocarcinoma(136;0.0717)|all cancers(137;0.0743)		GTATCTTCTTCTAACAGTAGA	0.328																																					p.R68K		Atlas-SNP	.											.	SNX3	11	.	0			c.G203A						.						85	78	80					6																	108544209		2203	4297	6500	SO:0001583	missense	8724	exon2			CTTCTTCTAACAG	AF034546	CCDS5064.1, CCDS5065.1, CCDS75501.1	6q21	2010-08-05			ENSG00000112335	ENSG00000112335		"Sorting nexins"	11174	protein-coding gene	gene with protein product		605930				9819414	Standard	XM_005267192		Approved	Grd19	uc003psh.3	O60493	OTTHUMG00000015323	ENST00000230085.8:c.203G>A	chr6.hg19:g.108544209C>T	ENSP00000230085:p.Arg68Lys	71.0	0.0		50.0	4.0	NM_003795	A8K0B1|E1P5E4|E1P5E5|O60718|Q4TT29|Q4TT31|Q5JXJ7|Q5JXJ8|Q96AP9|Q9C0J5|Q9NU45	Missense_Mutation	SNP	ENST00000230085.8	hg19	CCDS5064.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.044505	0.75732	.	.	ENSG00000112335	ENST00000230085;ENST00000349379;ENST00000368982	T;T;T	0.36699	1.24;1.24;1.24	6.08	6.08	0.98989	Phox homologous domain (5);	0.129957	0.64402	D	0.000004	T	0.31136	0.0787	M	0.64080	1.96	0.80722	D	1	B	0.09022	0.002	B	0.28991	0.097	T	0.06899	-1.0801	10	0.29301	T	0.29	-16.5963	20.6647	0.99678	0.0:1.0:0.0:0.0	.	68	O60493	SNX3_HUMAN	K	68;46;68	ENSP00000230085:R68K;ENSP00000296991:R46K;ENSP00000357978:R68K	ENSP00000230085:R68K	R	-	2	0	SNX3	108650902	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.800000	0.62524	2.890000	0.99128	0.655000	0.94253	AGA	.	.		0.328	SNX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041717.1			T	108544209	C	T	108544209	3	4	64	1	0	0	0	0	1	0	0	0	14914	913	32	3	297	3	SNX3	6	108544209	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	1583402	108544209	62570858	105	7822										
DCBLD1	285761	hgsc.bcm.edu	37	chr6	117861869	117861869	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aactttcgggacccagtgcaAaacaatttcatccctcccat	5	14	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:117861869A>G	ENST00000338728.5	+	10	1260	c.1140A>G	c.(1138-1140)caA>caG	p.Q380Q	DCBLD1_ENST00000296955.8_Silent_p.Q380Q|GOPC_ENST00000467125.1_Intron|DCBLD1_ENST00000534777.1_3'UTR|DCBLD1_ENST00000368503.4_Intron			Q8N8Z6	DCBD1_HUMAN	discoidin, CUB and LCCL domain containing 1	380	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_cancers(87;0.171)		GBM - Glioblastoma multiforme(226;0.0447)|OV - Ovarian serous cystadenocarcinoma(136;0.0921)|all cancers(137;0.125)		ACCCAGTGCAAAACAATTTCA	0.448																																					p.Q380Q		Atlas-SNP	.											.	DCBLD1	56	.	0			c.A1140G						.						133	133	133					6																	117861869		2203	4300	6503	SO:0001819	synonymous_variant	285761	exon10			AGTGCAAAACAAT	AK055462	CCDS34522.1	6q22.31	2003-06-20			ENSG00000164465	ENSG00000164465			21479	protein-coding gene	gene with protein product							Standard	NM_173674		Approved	MGC46341, dJ94G16.1	uc003pxs.3	Q8N8Z6	OTTHUMG00000015455	ENST00000338728.5:c.1140A>G	chr6.hg19:g.117861869A>G		131.0	0.0		95.0	4.0	NM_173674	Q5H992|Q8IYK5|Q8N7L9|Q96NH2	Silent	SNP	ENST00000338728.5	hg19																																																																																				.	.		0.448	DCBLD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000041979.2	NM_173674		G	117861869	A	G	117861869	2	3	64	1	0	0	0	0	0	0	0	1	4282	11	1	2		2	DCBLD1	6	117861869	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	9317660	117861869	53253198	106	7823										
HDDC2	51020	hgsc.bcm.edu	37	chr6	125619942	125619942	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgcattctgccatatcatgaAccagggctaggcgtacacat	9	11	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:125619942A>G	ENST00000398153.2	-	3	269	c.227T>C	c.(226-228)gTt>gCt	p.V76A	HDDC2_ENST00000608284.1_Missense_Mutation_p.V76A|HDDC2_ENST00000368377.4_Intron|HDDC2_ENST00000608295.1_Missense_Mutation_p.V76A	NM_016063.2	NP_057147.2	Q7Z4H3	HDDC2_HUMAN	HD domain containing 2	76	HD.					extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(4)	6			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0186)		CATATCATGAACCAGGGCTAG	0.403																																					p.V76A		Atlas-SNP	.											.	HDDC2	21	.	0			c.T227C						.						174	151	158					6																	125619942		1918	4165	6083	SO:0001583	missense	51020	exon3			TCATGAACCAGGG	AF151888	CCDS43503.1	6q13-q24.3	2008-02-05	2005-08-22	2005-08-22	ENSG00000111906	ENSG00000111906			21078	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 74"	C6orf74		10810093	Standard	NM_016063		Approved	CGI-130, dJ167O5.2	uc003qaa.1	Q7Z4H3	OTTHUMG00000015506	ENST00000398153.2:c.227T>C	chr6.hg19:g.125619942A>G	ENSP00000381220:p.Val76Ala	131.0	0.0		89.0	4.0	NM_016063	Q5TDQ4|Q6NZ49|Q9BTT2|Q9BV31|Q9Y3D1	Missense_Mutation	SNP	ENST00000398153.2	hg19	CCDS43503.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.922341	0.92319	.	.	ENSG00000111906	ENST00000398153	T	0.48836	0.8	5.53	5.53	0.82687	Metal-dependent phosphohydrolase, HD domain (1);Metal-dependent phosphohydrolase, HD subdomain (1);HD domain (1);	0.000000	0.64402	U	0.000001	T	0.67988	0.2952	M	0.92268	3.29	0.80722	D	1	D	0.59767	0.986	P	0.61328	0.887	T	0.77616	-0.2521	10	0.87932	D	0	.	14.9197	0.70829	1.0:0.0:0.0:0.0	.	76	Q7Z4H3	HDDC2_HUMAN	A	76	ENSP00000381220:V76A	ENSP00000381220:V76A	V	-	2	0	HDDC2	125661641	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.852000	0.92215	2.229000	0.72834	0.533000	0.62120	GTT	.	.		0.403	HDDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472493.1	NM_016063		G	125619942	A	G	125619942	3	3	64	1	0	0	0	0	1	0	0	0	7025	43	2	2	403	2	HDDC2	6	125619942	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	7758073	125619942	45495125	107	7824										
ENPP3	5169	hgsc.bcm.edu	37	chr6	132047295	132047295	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tatgtcagtggatttggaaaAgctatgaggatgcccatgtg	13	5	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:132047295A>G	ENST00000414305.1	+	21	2236	c.1908A>G	c.(1906-1908)aaA>aaG	p.K636K	ENPP3_ENST00000358229.5_Silent_p.K636K|ENPP3_ENST00000357639.3_Silent_p.K636K			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	636	Nuclease.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		GATTTGGAAAAGCTATGAGGA	0.448																																					p.K636K		Atlas-SNP	.											.	ENPP3	117	.	0			c.A1908G						.						173	162	166					6																	132047295		2203	4300	6503	SO:0001819	synonymous_variant	5169	exon20			TGGAAAAGCTATG	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.1908A>G	chr6.hg19:g.132047295A>G		156.0	0.0		98.0	4.0	NM_005021	Q5JTL3	Silent	SNP	ENST00000414305.1	hg19	CCDS5148.1																																																																																			.	.		0.448	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2			G	132047295	A	G	132047295	2	3	64	1	0	0	0	0	0	0	0	1	5133	69	3	2		2	ENPP3	6	132047295	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	6427353	132047295	39067772	108	7825										
ZC3H12D	340152	hgsc.bcm.edu	37	chr6	149783104	149783104	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agaaggtttctttatttccaTggctacaatgggaaaacaaa	8	6	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:149783104T>C	ENST00000409806.3	-	3	626	c.308A>G	c.(307-309)cAt>cGt	p.H103R	ZC3H12D_ENST00000409948.1_Missense_Mutation_p.H103R|ZC3H12D_ENST00000389942.5_Missense_Mutation_p.H103R|ZC3H12D_ENST00000542614.1_Missense_Mutation_p.H103R|ZC3H12D_ENST00000416573.2_Missense_Mutation_p.H103R			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	103					negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)		TTTATTTCCATGGCTACAATG	0.443																																					p.H103R		Atlas-SNP	.											.	ZC3H12D	21	.	0			c.A308G						.						46	46	46					6																	149783104		1914	4129	6043	SO:0001583	missense	340152	exon3			TTTCCATGGCTAC			6q25.1	2012-07-05	2005-06-30	2005-06-30	ENSG00000178199	ENSG00000178199		"Zinc fingers, CCCH-type domain containing"	21175	protein-coding gene	gene with protein product	"MCP induced protein 4"	611106	"chromosome 6 open reading frame 95"	C6orf95		18178554	Standard	NM_207360		Approved	dJ281H8.1, MCPIP4	uc010kid.3	A2A288	OTTHUMG00000015786	ENST00000409806.3:c.308A>G	chr6.hg19:g.149783104T>C	ENSP00000386616:p.His103Arg	94.0	0.0		41.0	4.0	NM_207360	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	Missense_Mutation	SNP	ENST00000409806.3	hg19		.	.	.	.	.	.	.	.	.	.	T	24.0	4.478196	0.84747	.	.	ENSG00000178199	ENST00000389942;ENST00000416573;ENST00000409806;ENST00000542614;ENST00000409948	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67	5.19	5.19	0.71726	Ribonuclease Zc3h12a-like (1);	0.000000	0.85682	D	0.000000	T	0.67439	0.2893	M	0.86420	2.815	0.53005	D	0.999969	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	T	0.74951	-0.3489	10	0.87932	D	0	-15.4523	15.2075	0.73190	0.0:0.0:0.0:1.0	.	103;103	A2A288;B7WNU7	ZC12D_HUMAN;.	R	103	ENSP00000374592:H103R;ENSP00000408686:H103R;ENSP00000386616:H103R;ENSP00000440813:H103R;ENSP00000387062:H103R	ENSP00000374592:H103R	H	-	2	0	ZC3H12D	149824797	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.388000	0.79795	2.187000	0.69744	0.460000	0.39030	CAT	.	.		0.443	ZC3H12D-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000286400.2	NM_207360		C	149783104	T	C	149783104	3	2	64	1	0	0	0	0	1	0	0	0	17579	1464	51	2	1291	2	ZC3H12D	6	149783104	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	17735809	149783104	21331963	109	7826										
KATNA1	11104	hgsc.bcm.edu	37	chr6	149959680	149959680	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctcactaatcataagaagacTcatgttcaactgtaagctaa	5	9	4	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:149959680T>C	ENST00000335647.5	-	1	48	c.4A>G	c.(4-6)Agt>Ggt	p.S2G	KATNA1_ENST00000335643.8_Missense_Mutation_p.S2G|KATNA1_ENST00000367411.2_Missense_Mutation_p.S2G					katanin p60 (ATPase containing) subunit A 1									p.S2G(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	12		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		ATAAGAAGACTCATGTTCAAC	0.328																																					p.S2G		Atlas-SNP	.											KATNA1,NS,carcinoma,0,1	KATNA1	34	.	1	Substitution - Missense(1)	lung(1)	c.A4G						.						124	130	128					6																	149959680		2203	4300	6503	SO:0001583	missense	11104	exon2			GAAGACTCATGTT	AF056022	CCDS5217.1, CCDS56456.1	6q24.3	2011-01-25	2011-01-25		ENSG00000186625	ENSG00000186625		"ATPases / AAA-type"	6216	protein-coding gene	gene with protein product		606696	"katanin p60 (ATPase-containing) subunit A 1"			9658175	Standard	NM_007044		Approved		uc003qms.3	O75449	OTTHUMG00000015787	ENST00000335647.5:c.4A>G	chr6.hg19:g.149959680T>C	ENSP00000335106:p.Ser2Gly	93.0	0.0		57.0	3.0	NM_007044		Missense_Mutation	SNP	ENST00000335647.5	hg19	CCDS5217.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.257679	0.80246	.	.	ENSG00000186625	ENST00000335647;ENST00000335643;ENST00000367411;ENST00000444282;ENST00000420200	D;D;D;D	0.96168	-3.48;-3.69;-3.48;-3.93	5.75	5.75	0.90469	.	0.075885	0.85682	D	0.000000	D	0.93400	0.7895	L	0.55481	1.735	0.58432	D	0.999998	P;P;P	0.45715	0.859;0.865;0.859	B;P;B	0.46940	0.403;0.532;0.403	D	0.92941	0.6372	9	.	.	.	.	16.1166	0.81309	0.0:0.0:0.0:1.0	.	2;2;2	A8K7S5;O75449-2;O75449	.;.;KTNA1_HUMAN	G	2	ENSP00000335106:S2G;ENSP00000335180:S2G;ENSP00000356381:S2G;ENSP00000390322:S2G	.	S	-	1	0	KATNA1	150001373	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.692000	0.84203	2.204000	0.70986	0.529000	0.55759	AGT	.	.		0.328	KATNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042641.2	NM_007044		C	149959680	T	C	149959680	3	2	64	1	0	0	0	0	1	0	0	0	7993	1551	54	2	1511	2	KATNA1	6	149959680	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	176576	149959680	21155387	110	7827										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151161732	151161732	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tatgtggaaatcaagtcagaAgaagatgagtcggagttgga	14	3	2	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:151161732A>G	ENST00000358517.2	+	16	4069	c.3858A>G	c.(3856-3858)gaA>gaG	p.E1286E	PLEKHG1_ENST00000367328.1_Silent_p.E1286E			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	1286							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		TCAAGTCAGAAGAAGATGAGT	0.388																																					p.E1286E		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.A3858G						.						107	109	109					6																	151161732		2203	4300	6503	SO:0001819	synonymous_variant	57480	exon17			GTCAGAAGAAGAT	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.3858A>G	chr6.hg19:g.151161732A>G		157.0	0.0		97.0	4.0	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	hg19	CCDS34552.1																																																																																			.	.		0.388	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			G	151161732	A	G	151161732	2	3	64	1	0	0	0	0	0	0	0	1	12077	69	3	2		2	PLEKHG1	6	151161732	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1202052	151161732	19953335	111	7828										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152763360	152763360	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgcacatctctcttctttgcTgagatccgctttgtcttttg	7	11	4	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:152763360T>C	ENST00000367255.5	-	31	4459	c.3858A>G	c.(3856-3858)tcA>tcG	p.S1286S	SYNE1_ENST00000341594.5_Silent_p.S1352S|SYNE1_ENST00000367248.3_Silent_p.S1276S|SYNE1_ENST00000265368.4_Silent_p.S1286S|SYNE1_ENST00000423061.1_Silent_p.S1293S|SYNE1_ENST00000448038.1_Silent_p.S1293S|SYNE1_ENST00000367253.4_Silent_p.S1286S|SYNE1_ENST00000413186.2_Silent_p.S1286S	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1286					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCTTCTTTGCTGAGATCCGCT	0.522										HNSCC(10;0.0054)																											p.S1293S		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A3879G						.						78	68	71					6																	152763360		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon31			CTTTGCTGAGATC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.3858A>G	chr6.hg19:g.152763360T>C		107.0	0.0		73.0	4.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.522	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152763360	T	C	152763360	2	2	64	1	0	0	0	0	0	0	0	1	15460	1567	55	2		2	SYNE1	6	152763360	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1601628	152763360	18351707	112	7829										
SLC22A3	6581	hgsc.bcm.edu	37	chr6	160857848	160857848	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aggaagttagtaatccatccTttttagatctggtgagaact	9	6	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr6:160857848T>C	ENST00000275300.2	+	6	1164	c.1012T>C	c.(1012-1014)Ttt>Ctt	p.F338L	SLC22A3_ENST00000392145.1_Missense_Mutation_p.F338L	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	338					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	TAATCCATCCTTTTTAGATCT	0.338																																					p.F338L		Atlas-SNP	.											.	SLC22A3	58	.	0			c.T1012C						.						114	103	107					6																	160857848		2203	4300	6503	SO:0001583	missense	6581	exon6			CCATCCTTTTTAG	AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477		"Solute carriers"	10967	protein-coding gene	gene with protein product		604842	"solute carrier family 22 (extraneuronal monoamine transporter), member 3"			9632645, 9933568	Standard	NM_021977		Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.1012T>C	chr6.hg19:g.160857848T>C	ENSP00000275300:p.Phe338Leu	130.0	0.0		100.0	4.0	NM_021977	Q5SYN6|Q9UP02	Missense_Mutation	SNP	ENST00000275300.2	hg19	CCDS5277.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.382332	0.42207	.	.	ENSG00000146477	ENST00000275300;ENST00000392145	T;T	0.56776	0.44;0.44	5.73	3.23	0.37069	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.288191	0.34676	N	0.003772	T	0.13713	0.0332	L	0.29908	0.895	0.30549	N	0.76569	B	0.10296	0.003	B	0.17722	0.019	T	0.23368	-1.0190	10	0.11182	T	0.66	.	5.2391	0.15462	0.298:0.0738:0.0:0.6282	.	338	O75751	S22A3_HUMAN	L	338	ENSP00000275300:F338L;ENSP00000375989:F338L	ENSP00000275300:F338L	F	+	1	0	SLC22A3	160777838	1.000000	0.71417	0.981000	0.43875	0.988000	0.76386	1.065000	0.30592	0.382000	0.24878	-0.438000	0.05819	TTT	.	.		0.338	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042953.1	NM_021977		C	160857848	T	C	160857848	3	2	64	1	0	0	0	0	1	0	0	0	14470	1609	56	2	1034	2	SLC22A3	6	160857848	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	8094488	160857848	10257219	113	7830										
LFNG	3955	hgsc.bcm.edu	37	chr7	2552910	2552911	+	Missense_Mutation	DNP	AG	AG	GA													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gatggatggatggatggatgAgtggagcccaacaccagctc					rs199517402		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:2552910_2552911AG>GA	ENST00000402506.1	+	2	293_294	c.167_168AG>GA	c.(166-168)gAG>gGA	p.E56G		NM_001166355.1	NP_001159827.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		tggatggatgagtggaGCCCAA	0.55																																					p.E56G|p.E56E		Atlas-SNP	.											.	LFNG	57	.	0			c.A167G|c.G168A						.																																			SO:0001583	missense	3955	exon2			TGGATGAGTGGAG|GGATGAGTGGAGC	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"Beta 3-glycosyltransferases"	6560	protein-coding gene	gene with protein product		602576	"lunatic fringe (Drosophila) homolog", "lunatic fringe homolog (Drosophila)"			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	Exception_encountered	chr7.hg19:g.2552910_2552911delinsGA	ENSP00000385764:p.Glu56Gly	94.0	0.0		110.0	6.0|5.0	NM_001166355	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Missense_Mutation|Silent	SNP	ENST00000402506.1	hg19	CCDS55081.1																																																																																			.	.		0.55	LFNG-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000325023.1	NM_002304		GA	2552911	AG	GA	2552910	3	3	64	1	0	0	0	0	1	0	0	0	8746	304	11	2	173	2	LFNG	7	2552910	Missense_Mutation	DNP	AG	TCGA-CC-A3MA-01A-11D-A20W-10		2552910	156585753	114	7831										
PAPOLB	56903	hgsc.bcm.edu	37	chr7	4900926	4900926	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atagtctgtagtgctaatctTgcaaataaaatatcaatctc	5	7	4	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:4900926T>C	ENST00000404991.1	-	1	699	c.513A>G	c.(511-513)gcA>gcG	p.A171A	RADIL_ENST00000536091.1_Intron|RADIL_ENST00000399583.3_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	171					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		GTGCTAATCTTGCAAATAAAA	0.368																																					p.A172A		Atlas-SNP	.											.	PAPOLB	93	.	0			c.A516G						.						62	63	63					7																	4900926		2013	4213	6226	SO:0001819	synonymous_variant	56903	exon1			TAATCTTGCAAAT	AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.513A>G	chr7.hg19:g.4900926T>C		67.0	0.0		54.0	4.0	NM_020144	Q75LH1|Q8NE14	Silent	SNP	ENST00000404991.1	hg19																																																																																				.	.		0.368	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144		C	4900926	T	C	4900926	2	2	64	1	0	0	0	0	0	0	0	1	11439	1799	63	2		2	PAPOLB	7	4900926	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2348016	4900926	154237737	115	7832										
BBS9	27241	hgsc.bcm.edu	37	chr7	33217138	33217138	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccaatgtcagatgaaattgaTgtatgaacataatcttcaga	7	6	3	5			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:33217138T>C	ENST00000242067.6	+	5	898	c.377T>C	c.(376-378)aTg>aCg	p.M126T	RNA5SP229_ENST00000410809.1_RNA|BBS9_ENST00000350941.3_Missense_Mutation_p.M126T|BBS9_ENST00000354265.4_Missense_Mutation_p.M126T|BBS9_ENST00000396127.2_Missense_Mutation_p.M126T|BBS9_ENST00000355070.2_Missense_Mutation_p.M126T|BBS9_ENST00000425508.2_Missense_Mutation_p.M81T	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	126					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			ATGAAATTGATGTATGAACAT	0.328									Bardet-Biedl syndrome																												p.M126T		Atlas-SNP	.											.	BBS9	194	.	0			c.T377C						.						170	160	163					7																	33217138		2203	4300	6503	SO:0001583	missense	27241	exon5	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AATTGATGTATGA		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"parathyroid hormone responsive B1 gene"	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.377T>C	chr7.hg19:g.33217138T>C	ENSP00000242067:p.Met126Thr	64.0	0.0		70.0	4.0	NM_014451	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Missense_Mutation	SNP	ENST00000242067.6	hg19	CCDS43566.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.011872	0.54468	.	.	ENSG00000122507	ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132;ENST00000396125;ENST00000425508;ENST00000442858;ENST00000537775	D;D;D;D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57;-1.57;-1.57	5.61	5.61	0.85477	.	0.088451	0.85682	D	0.000000	T	0.81574	0.4851	L	0.43152	1.355	0.51482	D	0.999929	P;P;B;P;B	0.38370	0.628;0.591;0.057;0.591;0.127	B;B;B;B;B	0.42827	0.236;0.399;0.085;0.399;0.147	T	0.81690	-0.0818	10	0.45353	T	0.12	-21.6	16.1045	0.81212	0.0:0.0:0.0:1.0	.	126;126;126;126;126	B3KQ86;Q3SYG4-2;E9PDC9;Q3SYG4-4;Q3SYG4	.;.;.;.;PTHB1_HUMAN	T	126;126;126;126;126;126;126;81;4;4	ENSP00000242067:M126T;ENSP00000313122:M126T;ENSP00000379433:M126T;ENSP00000347182:M126T;ENSP00000346214:M126T;ENSP00000405151:M81T;ENSP00000388646:M4T	ENSP00000242067:M126T	M	+	2	0	BBS9	33183663	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.434000	0.80377	2.267000	0.75376	0.533000	0.62120	ATG	.	.		0.328	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1			C	33217138	T	C	33217138	3	2	64	1	0	0	0	0	1	0	0	0	1342	1464	51	2	391	2	BBS9	7	33217138	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	28316212	33217138	125921525	116	7833										
MLXIPL	51085	hgsc.bcm.edu	37	chr7	73011792	73011792	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggagacactcctggggcaggAgggacggtggggaagggaaa	21	6	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:73011792A>G	ENST00000313375.3	-	9	1370	c.1323T>C	c.(1321-1323)ccT>ccC	p.P441P	MLXIPL_ENST00000395189.1_Silent_p.P348P|MLXIPL_ENST00000354613.1_Silent_p.P441P|MLXIPL_ENST00000429400.2_Silent_p.P441P|MLXIPL_ENST00000414749.2_Silent_p.P441P|MLXIPL_ENST00000434326.1_Silent_p.P348P	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	441					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				CTGGGGCAGGAGGGACGGTGG	0.667																																					p.P441P		Atlas-SNP	.											.	MLXIPL	54	.	0			c.T1323C						.						36	25	29					7																	73011792		2071	4074	6145	SO:0001819	synonymous_variant	51085	exon9			GGCAGGAGGGACG	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"carbohydrate response element binding protein"	605678	"Williams Beuren syndrome chromosome region 14"	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.1323T>C	chr7.hg19:g.73011792A>G		90.0	0.0		89.0	4.0	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Silent	SNP	ENST00000313375.3	hg19	CCDS5553.1																																																																																			.	.		0.667	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951		G	73011792	A	G	73011792	2	3	64	1	0	0	0	0	0	0	0	1	9646	291	11	2		2	MLXIPL	7	73011792	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	39794654	73011792	86126871	117	7834										
RFC2	5982	hgsc.bcm.edu	37	chr7	73646540	73646540	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tattttcatgtgagtgtatcCaatttcctgaaaaacaaacc	5	8	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:73646540C>T	ENST00000055077.3	-	11	1021	c.961G>A	c.(961-963)Gga>Aga	p.G321R	RFC2_ENST00000352131.3_Missense_Mutation_p.G287R	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	321					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						TGAGTGTATCCAATTTCCTGA	0.398																																					p.G321R		Atlas-SNP	.											.	RFC2	27	.	0			c.G961A						.						63	62	62					7																	73646540		2203	4300	6503	SO:0001583	missense	5982	exon11			TGTATCCAATTTC		CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"ATPases / AAA-type"	9970	protein-coding gene	gene with protein product	"activator 1"	600404	"replication factor C (activator 1) 2 (40kD)"			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.961G>A	chr7.hg19:g.73646540C>T	ENSP00000055077:p.Gly321Arg	77.0	0.0		91.0	4.0	NM_181471	B5BU07|D3DXG3|P32846|Q9BU93	Missense_Mutation	SNP	ENST00000055077.3	hg19	CCDS5568.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872914	0.91664	.	.	ENSG00000049541	ENST00000352131;ENST00000055077	T;T	0.50277	0.75;0.75	5.22	5.22	0.72569	Replication factor C (1);DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.66406	0.2786	M	0.89968	3.075	0.80722	D	1	B;B;P	0.44578	0.26;0.306;0.838	B;P;P	0.48189	0.322;0.451;0.57	T	0.75158	-0.3416	10	0.87932	D	0	.	17.7123	0.88325	0.0:1.0:0.0:0.0	.	287;287;321	P35250-2;Q75MT5;P35250	.;.;RFC2_HUMAN	R	287;321	ENSP00000275627:G287R;ENSP00000055077:G321R	ENSP00000055077:G321R	G	-	1	0	RFC2	73284476	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	7.322000	0.79097	2.610000	0.88304	0.650000	0.86243	GGA	.	.		0.398	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471		T	73646540	C	T	73646540	3	4	64	1	0	0	0	0	1	0	0	0	13260	603	21	3	107	3	RFC2	7	73646540	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	634748	73646540	85492123	118	7835										
PCLO	27445	hgsc.bcm.edu	37	chr7	82580361	82580361	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gatgctgtggttaaagtgggAacagagtctatcgtctcagc	13	7	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:82580361A>G	ENST00000333891.9	-	6	9880	c.9543T>C	c.(9541-9543)gtT>gtC	p.V3181V	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Silent_p.V3181V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTAAAGTGGGAACAGAGTCTA	0.433																																					p.V3181V		Atlas-SNP	.											.	PCLO	1506	.	0			c.T9543C						.						52	49	50					7																	82580361		1922	4153	6075	SO:0001819	synonymous_variant	27445	exon6			AGTGGGAACAGAG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.9543T>C	chr7.hg19:g.82580361A>G		90.0	0.0		100.0	4.0	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.433	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82580361	A	G	82580361	2	3	64	1	0	0	0	0	0	0	0	1	11592	233	9	2		2	PCLO	7	82580361	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	8933821	82580361	76558302	119	7836										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94035575	94035575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctttcagggacacaatggtcTggatggattgaagggacagc	14	7	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:94035575T>C	ENST00000297268.6	+	12	1025	c.554T>C	c.(553-555)cTg>cCg	p.L185P		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	185			Missing (in OI4). {ECO:0000269|PubMed:1642148}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CACAATGGTCTGGATGGATTG	0.378										HNSCC(75;0.22)																											p.L185P		Atlas-SNP	.											.	COL1A2	240	.	0			c.T554C						.						97	94	95					7																	94035575		2203	4300	6503	SO:0001583	missense	1278	exon12			ATGGTCTGGATGG	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.554T>C	chr7.hg19:g.94035575T>C	ENSP00000297268:p.Leu185Pro	68.0	0.0		91.0	4.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	T	12.67	2.006525	0.35415	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.94376	-3.41	5.34	2.92	0.33932	.	0.436644	0.23349	N	0.049146	D	0.89674	0.6783	N	0.04063	-0.285	0.58432	D	0.999999	B	0.23591	0.088	P	0.48425	0.577	T	0.82950	-0.0203	10	0.36615	T	0.2	.	10.2776	0.43519	0.0:0.1119:0.0:0.8881	.	185	P08123	CO1A2_HUMAN	P	185;186	ENSP00000297268:L185P	ENSP00000297268:L185P	L	+	2	0	COL1A2	93873511	1.000000	0.71417	0.999000	0.59377	0.883000	0.51084	4.530000	0.60595	0.516000	0.28340	-0.248000	0.11899	CTG	.	.		0.378	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		C	94035575	T	C	94035575	3	2	64	1	0	0	0	0	1	0	0	0	3680	1580	55	2	600	2	COL1A2	7	94035575	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	11455214	94035575	65103088	120	7837										
SLC26A5	375611	hgsc.bcm.edu	37	chr7	103050911	103050911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	acatggaggtgaagacatgcAcagctgctgcggtggtaaac	14	8	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:103050911A>G	ENST00000306312.3	-	7	917	c.656T>C	c.(655-657)gTg>gCg	p.V219A	SLC26A5_ENST00000393729.1_Missense_Mutation_p.V182A|SLC26A5_ENST00000356767.4_Missense_Mutation_p.V219A|SLC26A5_ENST00000393723.1_Missense_Mutation_p.V219A|SLC26A5_ENST00000393730.1_Missense_Mutation_p.V219A|SLC26A5_ENST00000354356.4_5'UTR|SLC26A5_ENST00000432958.2_Missense_Mutation_p.V219A|SLC26A5_ENST00000339444.6_Missense_Mutation_p.V219A|SLC26A5_ENST00000393727.1_Missense_Mutation_p.V219A|SLC26A5_ENST00000393735.2_Missense_Mutation_p.V219A	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	219					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						GAAGACATGCACAGCTGCTGC	0.418																																					p.V219A		Atlas-SNP	.											.	SLC26A5	231	.	0			c.T656C						.						72	70	71					7																	103050911		2203	4300	6503	SO:0001583	missense	375611	exon7			ACATGCACAGCTG	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.656T>C	chr7.hg19:g.103050911A>G	ENSP00000304783:p.Val219Ala	104.0	0.0		113.0	5.0	NM_206883	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Missense_Mutation	SNP	ENST00000306312.3	hg19	CCDS5733.1	.	.	.	.	.	.	.	.	.	.	A	17.58	3.424191	0.62733	.	.	ENSG00000170615	ENST00000339444;ENST00000356767;ENST00000393735;ENST00000306312;ENST00000393730;ENST00000432958;ENST00000393729;ENST00000393727;ENST00000393723	D;D;D;D;D;D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29;-3.29;-3.29;-3.29;-3.29;-3.29	5.72	5.72	0.89469	Sulphate transporter (1);	0.057214	0.64402	D	0.000001	D	0.92264	0.7546	M	0.66560	2.04	0.80722	D	1	B;P;B;P;B	0.36222	0.152;0.456;0.057;0.544;0.319	B;B;B;B;B	0.35688	0.189;0.208;0.037;0.132;0.132	D	0.91741	0.5404	10	0.44086	T	0.13	.	16.0046	0.80354	1.0:0.0:0.0:0.0	.	219;219;219;219;219	P58743;Q496J2;P58743-4;P58743-3;P58743-2	S26A5_HUMAN;.;.;.;.	A	219;219;219;219;219;219;182;219;219	ENSP00000342396:V219A;ENSP00000349210:V219A;ENSP00000377336:V219A;ENSP00000304783:V219A;ENSP00000377331:V219A;ENSP00000389733:V219A;ENSP00000377330:V182A;ENSP00000377328:V219A;ENSP00000377324:V219A	ENSP00000304783:V219A	V	-	2	0	SLC26A5	102838147	1.000000	0.71417	0.927000	0.36925	0.911000	0.54048	7.022000	0.76431	2.186000	0.69663	0.482000	0.46254	GTG	.	.		0.418	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		G	103050911	A	G	103050911	3	3	64	1	0	0	0	0	1	0	0	0	14535	159	6	2	1675	2	SLC26A5	7	103050911	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	9015336	103050911	56087752	121	7838										
RELN	5649	hgsc.bcm.edu	37	chr7	103162472	103162472	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agcagccaaacactcaccccActgaaatggagagccattcc	7	15	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:103162472A>G	ENST00000428762.1	-	48	7824	c.7665T>C	c.(7663-7665)agT>agC	p.S2555S	RELN_ENST00000424685.2_Silent_p.S2555S|RELN_ENST00000343529.5_Silent_p.S2555S	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2555					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CACTCACCCCACTGAAATGGA	0.478																																					p.S2555S	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T7665C						.						135	124	128					7																	103162472		2203	4300	6503	SO:0001819	synonymous_variant	5649	exon48			CACCCCACTGAAA		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.7665T>C	chr7.hg19:g.103162472A>G		57.0	0.0		75.0	4.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	hg19	CCDS47680.1																																																																																			.	.		0.478	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		G	103162472	A	G	103162472	2	3	64	1	0	0	0	0	0	0	0	1	13235	156	6	2		2	RELN	7	103162472	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	111561	103162472	55976191	122	7839										
MET	4233	hgsc.bcm.edu	37	chr7	116371722	116371722	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atgaccatattttattccagAcacttctgagaaattcatca	4	9	3	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:116371722A>G	ENST00000318493.6	+	3	1388	c.1201A>G	c.(1201-1203)Aca>Gca	p.T401A	MET_ENST00000436117.2_Splice_Site_p.T401A|MET_ENST00000495962.1_3'UTR|MET_ENST00000397752.3_Splice_Site_p.T401A			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TTTATTCCAGACACTTCTGAG	0.423			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.T401A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A1201G						.						73	66	68					7																	116371722		1862	4092	5954	SO:0001630	splice_region_variant	4233	exon3	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TTCCAGACACTTC	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1201-1A>G	chr7.hg19:g.116371722A>G		93.0	0.0		90.0	4.0	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	A	13.04	2.117647	0.37339	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.10288	2.89;2.89;2.89	5.71	5.71	0.89125	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.182658	0.46442	D	0.000294	T	0.10895	0.0266	L	0.43152	1.355	0.80722	D	1	B;B;B;B;B;B;B;B;B;B;B	0.22983	0.034;0.025;0.044;0.044;0.044;0.044;0.078;0.019;0.016;0.006;0.07	B;B;B;B;B;B;B;B;B;B;B	0.27262	0.026;0.065;0.026;0.04;0.065;0.04;0.057;0.078;0.013;0.026;0.046	T	0.16100	-1.0414	9	.	.	.	.	10.6403	0.45590	0.9196:0.0:0.0804:0.0	.	401;401;401;401;401;401;401;401;401;401;401	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;B5A939;B5A941;P08581-2;B5A942;P08581	.;.;.;.;.;.;.;.;.;.;MET_HUMAN	A	401	ENSP00000380860:T401A;ENSP00000317272:T401A;ENSP00000410980:T401A	.	T	+	1	0	MET	116158958	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.095000	0.57728	2.169000	0.68431	0.533000	0.62120	ACA	.	.		0.423	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		Missense_Mutation	G	116371722	A	G	116371722	5	3	64	1	0	0	0	0	0	0	1	0	9494	289	10	2	1207	2	MET	7	116371722	Splice_Site	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	13209250	116371722	42766941	123	7840										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128452197	128452197	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gagctttctcaagagctatgAcagcagcaccagtgccagtg	11	11	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:128452197A>G	ENST00000297788.4	+	13	2739	c.2372A>G	c.(2371-2373)gAc>gGc	p.D791G	CCDC136_ENST00000378685.4_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000464832.1_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	791	Ser-rich.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						AAGAGCTATGACAGCAGCACC	0.488																																					p.D791G		Atlas-SNP	.											.	CCDC136	170	.	0			c.A2372G						.						85	86	85					7																	128452197		2124	4238	6362	SO:0001583	missense	64753	exon13			GCTATGACAGCAG		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.2372A>G	chr7.hg19:g.128452197A>G	ENSP00000297788:p.Asp791Gly	110.0	0.0		103.0	5.0	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.27|15.27	2.785155|2.785155	0.49997|0.49997	.|.	.|.	ENSG00000128596|ENSG00000128596	ENST00000297788;ENST00000397697;ENST00000320524;ENST00000464672|ENST00000494552	T;T|.	0.50548|.	0.74;0.74|.	5.77|5.77	-2.62|-2.62	0.06152|0.06152	.|.	0.899797|.	0.09590|.	N|.	0.781606|.	T|T	0.37128|0.37128	0.0992|0.0992	M|M	0.63843|0.63843	1.955|1.955	0.09310|0.09310	N|N	1|1	B;B;B|.	0.06786|.	0.001;0.001;0.001|.	B;B;B|.	0.09377|.	0.004;0.004;0.001|.	T|T	0.40136|0.40136	-0.9579|-0.9579	10|5	0.46703|.	T|.	0.11|.	-0.7923|-0.7923	1.6647|1.6647	0.02799|0.02799	0.4178:0.139:0.309:0.1342|0.4178:0.139:0.309:0.1342	.|.	791;791;791|.	Q96JN2-4;Q96JN2-2;Q96JN2|.	.;.;CC136_HUMAN|.	G|A	791;791;791;382|668	ENSP00000297788:D791G;ENSP00000417991:D382G|.	ENSP00000297788:D791G|.	D|T	+|+	2|1	0|0	CCDC136|CCDC136	128239433|128239433	0.000000|0.000000	0.05858|0.05858	0.066000|0.066000	0.19879|0.19879	0.666000|0.666000	0.39218|0.39218	-0.072000|-0.072000	0.11486|0.11486	-0.347000|-0.347000	0.08299|0.08299	-0.250000|-0.250000	0.11733|0.11733	GAC|ACA	.	.		0.488	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		G	128452197	A	G	128452197	3	3	64	1	0	0	0	0	1	0	0	0	2772	275	10	2	2422	2	CCDC136	7	128452197	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	12080475	128452197	30686466	124	7841										
DGKI	9162	hgsc.bcm.edu	37	chr7	137374712	137374712	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aggctgaggggatgtgcaggAgccagatgctggaggcctgc	19	8	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:137374712A>G	ENST00000288490.5	-	2	438	c.438T>C	c.(436-438)gcT>gcC	p.A146A	DGKI_ENST00000424189.2_Silent_p.A146A|DGKI_ENST00000453654.2_Intron|DGKI_ENST00000446122.1_Silent_p.A146A	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	146					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						GATGTGCAGGAGCCAGATGCT	0.483																																					p.A146A		Atlas-SNP	.											.	DGKI	335	.	0			c.T438C						.						72	71	71					7																	137374712		2203	4300	6503	SO:0001819	synonymous_variant	9162	exon2			TGCAGGAGCCAGA	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.438T>C	chr7.hg19:g.137374712A>G		75.0	0.0		87.0	5.0	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	hg19	CCDS5845.1																																																																																			.	.		0.483	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		G	137374712	A	G	137374712	2	3	64	1	0	0	0	0	0	0	0	1	4473	291	11	2		2	DGKI	7	137374712	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	8922515	137374712	21763951	125	7842										
ZNF777	27153	hgsc.bcm.edu	37	chr7	149129992	149129992	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcctcctcttcttcctcctcGtcttgttcctctgtcttgat	4	16	5	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr7:149129992G>A	ENST00000247930.4	-	6	1694	c.1371C>T	c.(1369-1371)gaC>gaT	p.D457D		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	457	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			cttcctcctcGTCTTGTTCCT	0.582																																					p.D457D		Atlas-SNP	.											.	ZNF777	63	.	0			c.C1371T						.						11	12	12					7																	149129992		2132	4244	6376	SO:0001819	synonymous_variant	27153	exon6			CTCCTCGTCTTGT	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"Zinc fingers, C2H2-type", "-"	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.1371C>T	chr7.hg19:g.149129992G>A		141.0	0.0		143.0	63.0	NM_015694	Q8N2R2|Q8N659	Silent	SNP	ENST00000247930.4	hg19	CCDS43675.1																																																																																			.	.		0.582	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694		A	149129992	G	A	149129992	2	1	64	1	0	0	0	0	0	0	0	1	18165	1136	40	1		1	ZNF777	7	149129992	Silent	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	11755280	149129992	10008671	126	7843										
DLC1	10395	hgsc.bcm.edu	37	chr8	13357252	13357252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cattgttatcctcatcagaaAcatgcactagtgtttctgtg	7	9	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr8:13357252A>G	ENST00000276297.4	-	2	738	c.329T>C	c.(328-330)gTt>gCt	p.V110A	DLC1_ENST00000316609.5_Missense_Mutation_p.V110A|DLC1_ENST00000511869.1_Missense_Mutation_p.V110A	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	110					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						CTCATCAGAAACATGCACTAG	0.413																																					p.V110A		Atlas-SNP	.											.	DLC1	411	.	0			c.T329C						.						215	216	215					8																	13357252		2203	4300	6503	SO:0001583	missense	10395	exon2			TCAGAAACATGCA	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.329T>C	chr8.hg19:g.13357252A>G	ENSP00000276297:p.Val110Ala	91.0	0.0		89.0	4.0	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	hg19	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.787364	0.49997	.	.	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	T;T;T	0.33654	1.4;1.4;1.4	5.55	5.55	0.83447	.	0.182461	0.26742	N	0.022732	T	0.31949	0.0813	L	0.43923	1.385	0.19945	N	0.99994	P;P;B	0.46142	0.787;0.873;0.084	B;B;B	0.40782	0.164;0.34;0.03	T	0.38286	-0.9668	10	0.87932	D	0	.	11.1412	0.48404	0.8624:0.0:0.0:0.1376	.	110;110;110	E9PF76;Q96QB1-3;Q96QB1	.;.;RHG07_HUMAN	A	110	ENSP00000276297:V110A;ENSP00000321034:V110A;ENSP00000425878:V110A	ENSP00000276297:V110A	V	-	2	0	DLC1	13401623	0.952000	0.32445	0.983000	0.44433	0.976000	0.68499	3.749000	0.55150	2.250000	0.74265	0.533000	0.62120	GTT	.	.		0.413	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		G	13357252	A	G	13357252	3	3	64	1	0	0	0	0	1	0	0	0	4552	43	2	2	4410	2	DLC1	8	13357252	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10		13357252	133006770	127	7844										
PIWIL2	55124	hgsc.bcm.edu	37	chr8	22172606	22172606	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgtggcccagaagattttacTtcagattaactgtaaattgg	9	6	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr8:22172606T>C	ENST00000454009.2	+	18	2665	c.2156T>C	c.(2155-2157)cTt>cCt	p.L719P	PIWIL2_ENST00000356766.6_Missense_Mutation_p.L719P|PIWIL2_ENST00000521356.1_Missense_Mutation_p.L719P	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	719	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		AAGATTTTACTTCAGATTAAC	0.488																																					p.L719P		Atlas-SNP	.											.	PIWIL2	100	.	0			c.T2156C						.						139	135	137					8																	22172606		2203	4300	6503	SO:0001583	missense	55124	exon18			TTTTACTTCAGAT	AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"Argonaute/PIWI family"	17644	protein-coding gene	gene with protein product	"Hiwi-like", "cancer/testis antigen 80"	610312	"piwi-like 2 (Drosophila)"			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.2156T>C	chr8.hg19:g.22172606T>C	ENSP00000406956:p.Leu719Pro	158.0	0.0		92.0	4.0	NM_001135721	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Missense_Mutation	SNP	ENST00000454009.2	hg19	CCDS6029.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.369495	0.82463	.	.	ENSG00000197181	ENST00000356766;ENST00000521356;ENST00000454009	T;T;T	0.17691	2.26;2.26;2.26	5.75	5.75	0.90469	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.56124	0.1964	H	0.96547	3.84	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.99;0.994	T	0.71083	-0.4695	10	0.87932	D	0	-0.0015	15.3343	0.74238	0.0:0.0:0.0:1.0	.	719;719	E7ECA4;Q8TC59	.;PIWL2_HUMAN	P	719	ENSP00000349208:L719P;ENSP00000428267:L719P;ENSP00000406956:L719P	ENSP00000349208:L719P	L	+	2	0	PIWIL2	22228551	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.030000	0.76484	2.311000	0.77944	0.528000	0.53228	CTT	.	.		0.488	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1			C	22172606	T	C	22172606	3	2	64	1	0	0	0	0	1	0	0	0	11967	1609	56	2	2222	2	PIWIL2	8	22172606	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	8815354	22172606	124191416	128	7845										
ERLIN2	11160	hgsc.bcm.edu	37	chr8	37611578	37611578	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtttgaggggctagctgacaAgctaagctttggcttagaag	14	6	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr8:37611578A>G	ENST00000276461.5	+	12	1032	c.965A>G	c.(964-966)aAg>aGg	p.K322R	ERLIN2_ENST00000519638.1_Missense_Mutation_p.K322R	NM_007175.6	NP_009106.1	O94905	ERLN2_HUMAN	ER lipid raft associated 2	322					cell death (GO:0008219)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|lung(5)	7		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			CTAGCTGACAAGCTAAGCTTT	0.423																																					p.K322R		Atlas-SNP	.											.	ERLIN2	27	.	0			c.A965G						.						99	90	93					8																	37611578		2203	4300	6503	SO:0001583	missense	11160	exon12			CTGACAAGCTAAG	AY358108	CCDS6095.1, CCDS34879.1	8p11.2	2012-11-23	2007-01-26	2007-01-26	ENSG00000147475	ENSG00000147475			1356	protein-coding gene	gene with protein product		611605	"chromosome 8 open reading frame 2", "SPFH domain family, member 2"	C8orf2, SPFH2, Erlin-2		10449903, 15897872, 16835267	Standard	NM_007175		Approved	NET32, SPG18	uc003xke.4	O94905	OTTHUMG00000164005	ENST00000276461.5:c.965A>G	chr8.hg19:g.37611578A>G	ENSP00000276461:p.Lys322Arg	140.0	0.0		95.0	4.0	NM_007175	A0JLQ1|A8K5S9|B4DM38|D3DSW0|Q6NW21|Q86VS6|Q86W49	Missense_Mutation	SNP	ENST00000276461.5	hg19	CCDS6095.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.028138	0.35797	.	.	ENSG00000147475	ENST00000276461;ENST00000521644;ENST00000519638	T;T;T	0.64803	-0.12;-0.12;-0.12	5.99	4.81	0.61882	.	0.441828	0.26991	N	0.021461	T	0.36220	0.0959	N	0.04636	-0.2	0.28092	N	0.931759	B	0.09022	0.002	B	0.08055	0.003	T	0.19160	-1.0314	10	0.30078	T	0.28	-17.689	8.0033	0.30310	0.7875:0.138:0.0745:0.0	.	322	O94905	ERLN2_HUMAN	R	322	ENSP00000276461:K322R;ENSP00000429621:K322R;ENSP00000428112:K322R	ENSP00000276461:K322R	K	+	2	0	ERLIN2	37730736	1.000000	0.71417	1.000000	0.80357	0.572000	0.35998	3.250000	0.51445	1.054000	0.40438	0.533000	0.62120	AAG	.	.		0.423	ERLIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376712.2	NM_007175		G	37611578	A	G	37611578	3	3	64	1	0	0	0	0	1	0	0	0	5235	72	3	2	1046	2	ERLIN2	8	37611578	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	15438972	37611578	108752444	129	7846										
BRF2	25960	hgsc.bcm.edu	37	chr8	37702706	37702706	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cacgtatttggctggcacagAaggtgaagcttggaacagtt	13	7	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr8:37702706A>G	ENST00000412232.2	+	0	5651				BRF2_ENST00000220659.6_Missense_Mutation_p.S188P|BRF2_ENST00000520601.1_3'UTR	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124						central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			GCTGGCACAGAAGGTGAAGCT	0.498																																					p.S188P		Atlas-SNP	.											.	BRF2	33	.	0			c.T562C						.						76	79	78					8																	37702706		2203	4300	6503	SO:0001628	intergenic_variant	55290	exon4			GCACAGAAGGTGA	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182		chr8.hg19:g.37702706A>G		187.0	0.0		97.0	4.0	NM_018310	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	A	6.958	0.546617	0.13312	.	.	ENSG00000104221	ENST00000220659;ENST00000545765	.	.	.	5.27	2.74	0.32292	.	0.427833	0.27164	N	0.020631	T	0.36082	0.0954	L	0.44542	1.39	0.30998	N	0.720632	B	0.06786	0.001	B	0.08055	0.003	T	0.29397	-1.0013	9	0.40728	T	0.16	.	7.7416	0.28845	0.4195:0.4554:0.0:0.1251	.	188	Q9HAW0	BRF2_HUMAN	P	188;165	.	ENSP00000220659:S188P	S	-	1	0	BRF2	37821864	0.000000	0.05858	0.040000	0.18447	0.404000	0.30871	0.356000	0.20181	0.267000	0.21916	0.533000	0.62120	TCT	.	.		0.498	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			G	37702706	A	G	37702706	1	3	64	0	1	0	0	0	0	0	0	0	1513	246	9	2		2	BRF2	8	37702706	IGR	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	91128	37702706	108661316	130	7847										
SGK3	23678	hgsc.bcm.edu	37	chr8	67752280	67752280	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aacggtcctttcctgagcacAgagctaggttttacgctgct	10	11	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr8:67752280A>G	ENST00000396596.1	+	11	998	c.784A>G	c.(784-786)Aga>Gga	p.R262G	SGK3_ENST00000345714.4_Missense_Mutation_p.R262G|SGK3_ENST00000520976.1_Missense_Mutation_p.R262G|SGK3_ENST00000521435.1_3'UTR|C8orf44-SGK3_ENST00000519289.1_Missense_Mutation_p.R262G|SGK3_ENST00000522398.1_Missense_Mutation_p.R262G|SGK3_ENST00000521198.2_Missense_Mutation_p.R262G	NM_013257.4	NP_037389.4	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase family, member 3	262	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ion transmembrane transport (GO:0034220)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|phosphatidylinositol binding (GO:0035091)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	18	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TCCTGAGCACAGAGCTAGGTT	0.383																																					p.R262G		Atlas-SNP	.											.	SGK3	92	.	0			c.A784G						.						129	113	119					8																	67752280		2203	4300	6503	SO:0001583	missense	23678	exon11			GAGCACAGAGCTA		CCDS6195.1, CCDS6196.1	8q12	2008-07-28	2005-09-13	2005-09-13		ENSG00000104205			10812	protein-coding gene	gene with protein product		607591	"serum/glucocorticoid regulated kinase-like"	SGK2, SGKL		10585774, 10548550	Standard	NM_013257		Approved		uc003xwr.3	Q96BR1		ENST00000396596.1:c.784A>G	chr8.hg19:g.67752280A>G	ENSP00000379842:p.Arg262Gly	85.0	0.0		75.0	4.0	NM_001033578	A8K5W3|B3KQC2|Q9P1Q7|Q9UKG5	Missense_Mutation	SNP	ENST00000396596.1	hg19	CCDS6195.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.693556	0.48202	.	.	ENSG00000104205	ENST00000519289;ENST00000521198;ENST00000262211;ENST00000522398;ENST00000520976;ENST00000396596;ENST00000345714;ENST00000521152	T;T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	5.29	4.12	0.48240	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.74435	0.3716	L	0.60455	1.87	0.49582	D	0.999809	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80768	-0.1235	9	0.87932	D	0	.	12.3914	0.55360	0.8591:0.1409:0.0:0.0	.	262;262	Q96BR1-2;Q96BR1	.;SGK3_HUMAN	G	262;262;262;262;262;262;262;159	ENSP00000429022:R262G;ENSP00000430463:R262G;ENSP00000430256:R262G;ENSP00000430691:R262G;ENSP00000379842:R262G;ENSP00000331816:R262G;ENSP00000429565:R159G	ENSP00000262211:R262G	R	+	1	2	SGK3	67914834	1.000000	0.71417	0.997000	0.53966	0.090000	0.18270	7.234000	0.78134	0.813000	0.34350	-0.321000	0.08615	AGA	.	.		0.383	SGK3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379232.3			G	67752280	A	G	67752280	3	3	64	1	0	0	0	0	1	0	0	0	14227	180	7	2	822	2	SGK3	8	67752280	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	30049574	67752280	78611742	131	7848										
CSPP1	79848	hgsc.bcm.edu	37	chr8	68070772	68070772	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gacggcttgcagaacagaggGcacgaattcagcaggagtat	14	8	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr8:68070772G>A	ENST00000262210.5	+	18	2348	c.2317G>A	c.(2317-2319)Gca>Aca	p.A773T	CSPP1_ENST00000412460.1_Missense_Mutation_p.A428T|CSPP1_ENST00000521168.1_3'UTR	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	808					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			AGAACAGAGGGCACGAATTCa	0.398																																					p.A773T		Atlas-SNP	.											.	CSPP1	129	.	0			c.G2317A						.						60	59	60					8																	68070772		1859	4091	5950	SO:0001583	missense	79848	exon18			CAGAGGGCACGAA	AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.2317G>A	chr8.hg19:g.68070772G>A	ENSP00000262210:p.Ala773Thr	104.0	0.0		83.0	4.0	NM_024790	A6ND63|Q70F00|Q8TBC1	Missense_Mutation	SNP	ENST00000262210.5	hg19	CCDS43744.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.349532	0.82132	.	.	ENSG00000104218	ENST00000262210;ENST00000389042;ENST00000412460;ENST00000519668	T;T;T	0.43294	0.95;1.34;1.34	5.17	5.17	0.71159	.	0.350989	0.26851	N	0.022162	T	0.47210	0.1433	N	0.24115	0.695	0.39075	D	0.960788	D;D;D;D	0.89917	1.0;0.999;0.999;0.999	D;D;D;D	0.69479	0.964;0.935;0.935;0.935	T	0.39396	-0.9616	10	0.29301	T	0.29	-3.447	13.3954	0.60849	0.0788:0.0:0.9212:0.0	.	428;773;808;808	Q1MSJ5-2;Q1MSJ5-1;Q1MSJ5;F8W7C3	.;.;CSPP1_HUMAN;.	T	773;808;428;428	ENSP00000262210:A773T;ENSP00000415782:A428T;ENSP00000430092:A428T	ENSP00000262210:A773T	A	+	1	0	CSPP1	68233326	1.000000	0.71417	0.988000	0.46212	0.735000	0.41995	4.321000	0.59209	2.553000	0.86117	0.563000	0.77884	GCA	.	.		0.398	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		A	68070772	G	A	68070772	3	1	64	1	0	0	0	0	1	0	0	0	3964	1203	42	3	2500	3	CSPP1	8	68070772	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	318492	68070772	78293250	132	7849										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77766356	77766356	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atcacccaaaccagaacctgAgaagacttctccaaaacctg	5	14	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr8:77766356A>G	ENST00000521891.2	+	10	7647	c.7199A>G	c.(7198-7200)gAg>gGg	p.E2400G	ZFHX4_ENST00000518282.1_Missense_Mutation_p.E2374G|ZFHX4_ENST00000050961.6_Missense_Mutation_p.E2355G|ZFHX4_ENST00000455469.2_Missense_Mutation_p.E2355G	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2355	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CCAGAACCTGAGAAGACTTCT	0.552										HNSCC(33;0.089)																											p.E2400G		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A7199G						.						38	46	43					8																	77766356		1930	4135	6065	SO:0001583	missense	79776	exon10			AACCTGAGAAGAC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.7199A>G	chr8.hg19:g.77766356A>G	ENSP00000430497:p.Glu2400Gly	92.0	0.0		91.0	4.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	15.01	2.707427	0.48412	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.50001	0.76;0.8;0.77;0.77	5.23	5.23	0.72850	.	0.000000	0.44688	U	0.000429	T	0.38772	0.1053	L	0.38175	1.15	0.37762	D	0.926354	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.002	T	0.29458	-1.0011	10	0.23891	T	0.37	.	15.2884	0.73849	1.0:0.0:0.0:0.0	.	2355;2355;2400	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	G	2400;2384;2355;2355;2374	ENSP00000430497:E2400G;ENSP00000399605:E2355G;ENSP00000050961:E2355G;ENSP00000430848:E2374G	ENSP00000050961:E2355G	E	+	2	0	ZFHX4	77928911	1.000000	0.71417	0.992000	0.48379	0.865000	0.49528	6.539000	0.73856	2.197000	0.70478	0.528000	0.53228	GAG	.	.		0.552	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		G	77766356	A	G	77766356	3	3	64	1	0	0	0	0	1	0	0	0	17650	304	11	2	7233	2	ZFHX4	8	77766356	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	9695584	77766356	68597666	133	7850										
MATN2	4147	hgsc.bcm.edu	37	chr8	98943556	98943556	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gatcgtgacagatgggagacCtcaggactccgtggccgagg	16	10	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr8:98943556C>G	ENST00000520016.1	+	2	642	c.518C>G	c.(517-519)cCt>cGt	p.P173R	MATN2_ENST00000524308.1_Missense_Mutation_p.P173R|MATN2_ENST00000254898.5_Missense_Mutation_p.P173R|MATN2_ENST00000521689.1_Missense_Mutation_p.P173R|MATN2_ENST00000522025.2_Intron			O00339	MATN2_HUMAN	matrilin 2	173	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			GATGGGAGACCTCAGGACTCC	0.577																																					p.P173R		Atlas-SNP	.											.	MATN2	165	.	0			c.C518G						.						38	44	42					8																	98943556		2125	4241	6366	SO:0001583	missense	4147	exon3			GGAGACCTCAGGA	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.518C>G	chr8.hg19:g.98943556C>G	ENSP00000430487:p.Pro173Arg	73.0	0.0		95.0	18.0	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	hg19	CCDS55264.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.128974	0.77549	.	.	ENSG00000132561	ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000520016	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	5.82	5.82	0.92795	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000008	D	0.92747	0.7694	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.92955	0.6384	10	0.66056	D	0.02	-16.2546	20.1001	0.97870	0.0:1.0:0.0:0.0	.	173;173;173;173	E9PF03;O00339-2;O00339;Q8N2G3	.;.;MATN2_HUMAN;.	R	173	ENSP00000429977:P173R;ENSP00000254898:P173R;ENSP00000430221:P173R;ENSP00000430487:P173R	ENSP00000254898:P173R	P	+	2	0	MATN2	99012732	1.000000	0.71417	0.966000	0.40874	0.501000	0.33797	7.770000	0.85390	2.760000	0.94817	0.655000	0.94253	CCT	.	.		0.577	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			G	98943556	C	G	98943556	3	3	64	1	0	0	0	0	1	0	0	0	9343	681	24	4	524	4	MATN2	8	98943556	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	21177200	98943556	47420466	134	7851										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133492571	133492571	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cctcgtcgcggccgccgcccTccagcagcagggtcccgtct	12	20	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr8:133492571T>C	ENST00000388996.4	-	1	629	c.209A>G	c.(208-210)gAg>gGg	p.E70G	KCNQ3_ENST00000519445.1_Missense_Mutation_p.E70G	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	70					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GCCGCCGCCCTCCAGCAGCAG	0.721																																					p.E70G		Atlas-SNP	.											.	KCNQ3	164	.	0			c.A209G						.						12	15	14					8																	133492571		2193	4269	6462	SO:0001583	missense	3786	exon1			CCGCCCTCCAGCA	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.209A>G	chr8.hg19:g.133492571T>C	ENSP00000373648:p.Glu70Gly	1.0	0.0		73.0	4.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	hg19	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	T	8.542	0.873466	0.17322	.	.	ENSG00000184156	ENST00000388996;ENST00000519445;ENST00000542679	D;D	0.98958	-5.25;-5.27	4.33	3.17	0.36434	.	0.114902	0.33364	N	0.004990	D	0.91713	0.7380	N	0.08118	0	0.28278	N	0.924109	P;P	0.43477	0.808;0.808	B;B	0.33295	0.161;0.161	D	0.89366	0.3671	10	0.07644	T	0.81	-10.2153	7.7694	0.28999	0.0:0.0963:0.0:0.9037	.	70;70	E7ET42;O43525	.;KCNQ3_HUMAN	G	70;70;59	ENSP00000373648:E70G;ENSP00000428790:E70G	ENSP00000373648:E70G	E	-	2	0	KCNQ3	133561753	1.000000	0.71417	1.000000	0.80357	0.017000	0.09413	1.536000	0.36072	0.703000	0.31848	0.455000	0.32223	GAG	.	.		0.721	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		C	133492571	T	C	133492571	3	2	64	1	0	0	0	0	1	0	0	0	8093	1551	54	2	2469	2	KCNQ3	8	133492571	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	34549015	133492571	12871451	135	7852										
C8orf73	642475	hgsc.bcm.edu	37	chr8	144650754	144650754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cctgctggggtcatgcaggcGcagcagcagcggcacgagac	16	13	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr8:144650754G>A	ENST00000398882.3	-	10	1868	c.1612C>T	c.(1612-1614)Cgc>Tgc	p.R538C	MROH6_ENST00000534459.1_5'UTR|MROH6_ENST00000524906.1_5'UTR|MROH6_ENST00000533679.1_5'UTR|MROH6_ENST00000532704.1_5'Flank	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	538	Leu-rich.																TCATGCAGGCGCAGCAGCAGC	0.721																																					p.R538C		Atlas-SNP	.											.	.	.	.	0			c.C1612T						.						4	5	4					8																	144650754		1835	3855	5690	SO:0001583	missense	642475	exon10			GCAGGCGCAGCAG	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"maestro heat-like repeat containing"	27814	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 73"	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.1612C>T	chr8.hg19:g.144650754G>A	ENSP00000381857:p.Arg538Cys	1.0	0.0		17.0	5.0	NM_001100878	A8MWB1	Missense_Mutation	SNP	ENST00000398882.3	hg19	CCDS47928.1	.	.	.	.	.	.	.	.	.	.	g	18.79	3.699009	0.68501	.	.	ENSG00000204839	ENST00000398882	T	0.43294	0.95	4.89	4.89	0.63831	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.56572	0.1994	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.57825	-0.7744	9	0.54805	T	0.06	-48.715	15.5415	0.76052	0.0:0.0:1.0:0.0	.	538	A6NGR9	CH073_HUMAN	C	538	ENSP00000381857:R538C	ENSP00000381857:R538C	R	-	1	0	C8orf73	144721897	1.000000	0.71417	0.998000	0.56505	0.373000	0.29922	5.761000	0.68801	2.266000	0.75297	0.543000	0.68304	CGC	.	.		0.721	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		A	144650754	G	A	144650754	3	1	64	1	0	0	0	0	1	0	0	0	2437	1087	38	1	567	1	C8orf73	8	144650754	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	11158183	144650754	1713268	136	7853										
DOCK8	81704	hgsc.bcm.edu	37	chr9	441995	441995	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttaccaagcttcctgagatcTcacatagactagaggtaaga	8	9	1	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:441995T>C	ENST00000453981.1	+	42	5588	c.5476T>C	c.(5476-5478)Tca>Cca	p.S1826P	DOCK8_ENST00000432829.2_Missense_Mutation_p.S1758P|DOCK8_ENST00000469391.1_Missense_Mutation_p.S1726P|DOCK8_ENST00000382329.1_Missense_Mutation_p.S1293P			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1826	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TCCTGAGATCTCACATAGACT	0.398																																					p.S1826P		Atlas-SNP	.											.	DOCK8	401	.	0			c.T5476C						.						109	105	106					9																	441995		2203	4300	6503	SO:0001583	missense	81704	exon42			GAGATCTCACATA	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.5476T>C	chr9.hg19:g.441995T>C	ENSP00000408464:p.Ser1826Pro	50.0	0.0		51.0	4.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	T	24.0	4.481952	0.84747	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.19806	2.34;2.34;2.35;2.12	5.46	5.46	0.80206	.	0.118609	0.64402	D	0.000012	T	0.48077	0.1480	M	0.92604	3.325	0.80722	D	1	P;P;P	0.50943	0.866;0.94;0.94	P;P;P	0.52031	0.688;0.566;0.688	T	0.61466	-0.7057	10	0.62326	D	0.03	.	15.7119	0.77635	0.0:0.0:0.0:1.0	.	1726;1293;1826	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	P	1826;1794;1758;1726;1293	ENSP00000408464:S1826P;ENSP00000394888:S1758P;ENSP00000419438:S1726P;ENSP00000371766:S1293P	ENSP00000287364:S1794P	S	+	1	0	DOCK8	431995	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.778000	0.85637	2.291000	0.77112	0.533000	0.62120	TCA	.	.		0.398	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		C	441995	T	C	441995	3	2	64	1	0	0	0	0	1	0	0	0	4695	1551	54	2	5642	2	DOCK8	9	441995	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		441995	140771436	137	7854										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2039815	2039815	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cagcagcagcagcagcagcaGcaacagcagccgcagcagca	12	15	0	0	rs574062756	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:2039815G>A	ENST00000382203.1	+	4	914	c.705G>A	c.(703-705)caG>caA	p.Q235Q	SMARCA2_ENST00000491574.1_3'UTR|RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000357248.2_Silent_p.Q235Q|SMARCA2_ENST00000349721.2_Silent_p.Q235Q|SMARCA2_ENST00000382194.1_Silent_p.Q235Q			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	235	Poly-Gln.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		agcagcagcagcaacagcagc	0.587													G|||	41	0.0081869	0.0151	0.0029	5008	,	,		10366	0.0089		0	False		,,,				2504	0.0102				p.Q235Q		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G705A						.						10	13	12					9																	2039815		2161	4205	6366	SO:0001819	synonymous_variant	6595	exon4			GCAGCAGCAACAG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.705G>A	chr9.hg19:g.2039815G>A		94.0	0.0		97.0	6.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	hg19	CCDS34977.1																																																																																			.	.		0.587	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2039815	G	A	2039815	2	1	64	1	0	0	0	0	0	0	0	1	14784	962	34	3		3	SMARCA2	9	2039815	Silent	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	1597820	2039815	139173616	138	7855										
TLN1	7094	hgsc.bcm.edu	37	chr9	35700292	35700292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agcagcaacggccttggcggTtgccatggtgatacccttgg	14	11	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:35700292T>C	ENST00000314888.9	-	49	6909	c.6556A>G	c.(6556-6558)Acc>Gcc	p.T2186A	TLN1_ENST00000540444.1_Missense_Mutation_p.T2074A	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2186					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCCTTGGCGGTTGCCATGGTG	0.557																																					p.T2186A		Atlas-SNP	.											.	TLN1	185	.	0			c.A6556G						.						70	70	70					9																	35700292		2203	4300	6503	SO:0001583	missense	7094	exon49			TGGCGGTTGCCAT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.6556A>G	chr9.hg19:g.35700292T>C	ENSP00000316029:p.Thr2186Ala	138.0	0.0		100.0	4.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.846765	0.91277	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.69806	-0.43;-0.41	5.2	5.2	0.72013	.	0.051237	0.85682	D	0.000000	T	0.76126	0.3944	M	0.78916	2.43	0.80722	D	1	D	0.57899	0.981	P	0.53401	0.725	T	0.78211	-0.2292	10	0.44086	T	0.13	-13.177	14.7488	0.69508	0.0:0.0:0.0:1.0	.	2186	Q9Y490	TLN1_HUMAN	A	2186;2074	ENSP00000316029:T2186A;ENSP00000442981:T2074A	ENSP00000316029:T2186A	T	-	1	0	TLN1	35690292	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.967000	0.87967	1.972000	0.57404	0.533000	0.62120	ACC	.	.		0.557	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		C	35700292	T	C	35700292	3	2	64	1	0	0	0	0	1	0	0	0	15962	1725	60	2	1105	2	TLN1	9	35700292	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	33660477	35700292	105513139	139	7856										
GNE	10020	hgsc.bcm.edu	37	chr9	36246060	36246060	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gaatgatgctcatgtagtctTtgttcttggctgagagaagt	12	5	3	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:36246060T>C	ENST00000539815.1	-	2	624	c.584A>G	c.(583-585)aAa>aGa	p.K195R	GNE_ENST00000539208.1_Missense_Mutation_p.K136R|GNE_ENST00000377902.5_Missense_Mutation_p.K195R|GNE_ENST00000447283.2_Missense_Mutation_p.K195R|GNE_ENST00000543356.2_Missense_Mutation_p.K190R|GNE_ENST00000396594.3_Missense_Mutation_p.K226R			Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	195					carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)			endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			CATGTAGTCTTTGTTCTTGGC	0.458																																					p.K226R	GBM(184;106 2118 20004 35750 50727)	Atlas-SNP	.											.	GNE	141	.	0			c.A677G						.						142	124	130					9																	36246060		2203	4300	6503	SO:0001583	missense	10020	exon3			TAGTCTTTGTTCT	AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921			23657	protein-coding gene	gene with protein product		603824	"UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase"	IBM2		9305887, 9305888	Standard	NM_005476		Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539815.1:c.584A>G	chr9.hg19:g.36246060T>C	ENSP00000439155:p.Lys195Arg	81.0	0.0		93.0	4.0	NM_001128227	A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	Missense_Mutation	SNP	ENST00000539815.1	hg19	CCDS6602.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.927134	0.34002	.	.	ENSG00000159921	ENST00000377902;ENST00000396594;ENST00000339267;ENST00000539815;ENST00000543356;ENST00000539208;ENST00000447283	D;D;D;D;D	0.98978	-5.29;-5.29;-5.29;-5.29;-5.29	5.52	5.52	0.82312	.	0.094405	0.64402	D	0.000001	D	0.95544	0.8552	N	0.11560	0.145	0.38069	D	0.936301	B;B;B;B;B	0.10296	0.0;0.001;0.0;0.001;0.003	B;B;B;B;B	0.09377	0.001;0.001;0.001;0.002;0.004	D	0.94273	0.7512	10	0.23891	T	0.37	-20.9812	13.5913	0.61961	0.0:0.0:0.0:1.0	.	136;154;226;195;195	F5H499;Q9Y223-3;Q9Y223-2;Q9Y223;A7UNU7	.;.;.;GLCNE_HUMAN;.	R	195;226;190;195;167;136;195	ENSP00000367134:K195R;ENSP00000379839:K226R;ENSP00000439155:K195R;ENSP00000445117:K136R;ENSP00000414760:K195R	ENSP00000340770:K190R	K	-	2	0	GNE	36236060	0.998000	0.40836	1.000000	0.80357	0.956000	0.61745	2.672000	0.46850	2.106000	0.64143	0.383000	0.25322	AAA	.	.		0.458	GNE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052412.4	NM_005476		C	36246060	T	C	36246060	3	2	64	1	0	0	0	0	1	0	0	0	6530	1841	64	2	1624	2	GNE	9	36246060	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	545768	36246060	104967371	140	7857										
PTAR1	375743	hgsc.bcm.edu	37	chr9	72356709	72356709	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	actaatgaaaatgacataccTcacgttccatgcagtggtaa	7	9	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:72356709T>C	ENST00000340434.4	-	3	325	c.322A>G	c.(322-324)Agg>Ggg	p.R108G	PTAR1_ENST00000377200.5_Intron	NM_001099666.1	NP_001093136.1	Q7Z6K3	PTAR1_HUMAN	protein prenyltransferase alpha subunit repeat containing 1	108					protein prenylation (GO:0018342)		protein prenyltransferase activity (GO:0008318)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)	5						ATGACATACCTCACGTTCCAT	0.333																																					p.R108G		Atlas-SNP	.											.	PTAR1	46	.	0			c.A322G						.						82	76	77					9																	72356709		1875	4118	5993	SO:0001630	splice_region_variant	375743	exon3			CATACCTCACGTT	BC053622	CCDS47978.1	9q21.13	2008-10-01			ENSG00000188647	ENSG00000188647		"Prenyltransferase alpha subunit repeat containing"	30449	protein-coding gene	gene with protein product						12477932	Standard	NM_001099666		Approved		uc004ahj.4	Q7Z6K3	OTTHUMG00000019982	ENST00000340434.4:c.323+1A>G	chr9.hg19:g.72356709T>C		85.0	0.0		98.0	5.0	NM_001099666	Q5T7V5|Q5T7V6	Missense_Mutation	SNP	ENST00000340434.4	hg19	CCDS47978.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.270626	0.80469	.	.	ENSG00000188647	ENST00000340434	T	0.70749	-0.51	5.74	5.74	0.90152	Protein prenyltransferase (1);	.	.	.	.	T	0.77103	0.4081	M	0.70595	2.14	0.80722	D	1	D	0.58620	0.983	P	0.49683	0.619	T	0.80845	-0.1200	9	0.87932	D	0	.	16.0405	0.80679	0.0:0.0:0.0:1.0	.	108	Q7Z6K3	PTAR1_HUMAN	G	108	ENSP00000344299:R108G	ENSP00000344299:R108G	R	-	1	2	PTAR1	71546529	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.519000	0.60517	2.187000	0.69744	0.519000	0.50382	AGG	.	.		0.333	PTAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052582.4	NM_001099666	Missense_Mutation	C	72356709	T	C	72356709	5	2	64	1	0	0	0	0	0	0	1	0	12736	1565	54	2	910	2	PTAR1	9	72356709	Splice_Site	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	36110649	72356709	68856722	141	7858										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79834895	79834895	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cgtcccatatctgctaatgcCaaacttgtgatgaatcgccg	8	12	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:79834895C>T	ENST00000360280.3	+	11	1040	c.780C>T	c.(778-780)gcC>gcT	p.A260A	VPS13A_ENST00000376634.4_Silent_p.A260A|VPS13A_ENST00000357409.5_Silent_p.A260A|VPS13A_ENST00000376636.3_Silent_p.A260A	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	260					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CTGCTAATGCCAAACTTGTGA	0.318																																					p.A260A		Atlas-SNP	.											.	VPS13A	735	.	0			c.C780T						.						78	80	80					9																	79834895		2203	4299	6502	SO:0001819	synonymous_variant	23230	exon11			TAATGCCAAACTT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.780C>T	chr9.hg19:g.79834895C>T		93.0	0.0		75.0	4.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	hg19	CCDS6655.1																																																																																			.	.		0.318	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		T	79834895	C	T	79834895	2	4	64	1	0	0	0	0	0	0	0	1	17204	581	21	3		3	VPS13A	9	79834895	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	7478186	79834895	61378536	142	7859										
RASEF	158158	hgsc.bcm.edu	37	chr9	85627416	85627416	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttgacttacgcgttttgatTgttcttcgagctgaaagacc	9	8	1	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:85627416T>C	ENST00000376447.3	-	5	1036	c.776A>G	c.(775-777)cAa>cGa	p.Q259R		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	259					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(4)|liver(1)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						GCGTTTTGATTGTTCTTCGAG	0.328																																					p.Q259R		Atlas-SNP	.											.	RASEF	69	.	0			c.A776G						.						115	96	102					9																	85627416		2200	4298	6498	SO:0001583	missense	158158	exon5			TTTGATTGTTCTT	AK056176	CCDS6662.1	9q21.33	2014-05-09	2004-06-11	2004-06-16	ENSG00000165105	ENSG00000165105		"EF-hand domain containing", "RAB, member RAS oncogene"	26464	protein-coding gene	gene with protein product		611344	"RAB45, member RAS oncogene family"	RAB45		17448446	Standard	NM_152573		Approved	FLJ31614	uc004amo.2	Q8IZ41	OTTHUMG00000020100	ENST00000376447.3:c.776A>G	chr9.hg19:g.85627416T>C	ENSP00000365630:p.Gln259Arg	74.0	0.0		77.0	4.0	NM_152573	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	hg19	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	T	17.05	3.289356	0.59976	.	.	ENSG00000165105	ENST00000376447	T	0.61742	0.08	5.22	5.22	0.72569	.	0.122400	0.56097	D	0.000030	T	0.59238	0.2179	M	0.67953	2.075	0.80722	D	1	P	0.46142	0.873	B	0.42422	0.387	T	0.66763	-0.5841	10	0.87932	D	0	.	14.3933	0.66994	0.0:0.0:0.0:1.0	.	259	Q8IZ41	RASEF_HUMAN	R	259	ENSP00000365630:Q259R	ENSP00000365630:Q259R	Q	-	2	0	RASEF	84817236	1.000000	0.71417	0.974000	0.42286	0.874000	0.50279	5.042000	0.64202	2.093000	0.63338	0.528000	0.53228	CAA	.	.		0.328	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		C	85627416	T	C	85627416	3	2	64	1	0	0	0	0	1	0	0	0	13083	1812	63	2	1498	2	RASEF	9	85627416	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	5792521	85627416	55586015	143	7860										
IARS	3376	hgsc.bcm.edu	37	chr9	95050074	95050074	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgaaaaaaacccaacataccTtccactcagcagaatatctc	3	13	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:95050074T>C	ENST00000375643.3	-	4	661	c.395A>G	c.(394-396)aAg>aGg	p.K132R	IARS_ENST00000375629.3_5'UTR|IARS_ENST00000443024.2_Splice_Site_p.K132R|IARS_ENST00000447699.2_Splice_Site_p.K22R	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	132					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	CCAACATACCTTCCACTCAGC	0.383																																					p.K132R		Atlas-SNP	.											.	IARS	74	.	0			c.A395G						.						182	157	166					9																	95050074		2203	4300	6503	SO:0001630	splice_region_variant	3376	exon4			CATACCTTCCACT	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	5330	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 1, cytoplasmic"	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.396+1A>G	chr9.hg19:g.95050074T>C		143.0	0.0		136.0	6.0	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	hg19	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	T	1.235	-0.623029	0.03636	.	.	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000447699;ENST00000375660;ENST00000395554	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.79	0.578	0.17391	Rossmann-like alpha/beta/alpha sandwich fold (1);Aminoacyl-tRNA synthetase, class Ia (1);	0.486738	0.23583	N	0.046623	T	0.17959	0.0431	N	0.12920	0.275	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.17623	-1.0363	10	0.10902	T	0.67	-4.5741	11.094	0.48132	0.0:0.2823:0.0:0.7177	.	132	P41252	SYIC_HUMAN	R	132;132;22;132;132	ENSP00000364794:K132R;ENSP00000406448:K132R;ENSP00000415020:K22R;ENSP00000378922:K132R	ENSP00000364794:K132R	K	-	2	0	IARS	94089895	1.000000	0.71417	0.989000	0.46669	0.168000	0.22595	2.306000	0.43673	-0.415000	0.07484	-1.447000	0.01057	AAG	.	.		0.383	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161	Missense_Mutation	C	95050074	T	C	95050074	5	2	64	1	0	0	0	0	0	0	1	0	7482	1623	56	2	3517	2	IARS	9	95050074	Splice_Site	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	9422658	95050074	46163357	144	7861										
FAM22F	54754	hgsc.bcm.edu	37	chr9	97080944	97080944	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cttcttggacttgctggcagGagaaggtgatgggctgaggc	17	7	1	3	rs150455117	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:97080944G>C	ENST00000253262.4	-	7	2094	c.2074C>G	c.(2074-2076)Cct>Gct	p.P692A	NUTM2F_ENST00000341207.4_Missense_Mutation_p.P677A|NUTM2F_ENST00000335456.7_Intron	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	692																	TTGCTGGCAGGAGAAGGTGAT	0.607																																					p.P692A		Atlas-SNP	.											.	FAM22F	72	.	0			c.C2074G						.						21	19	20					9																	97080944		1843	4069	5912	SO:0001583	missense	54754	exon7			TGGCAGGAGAAGG		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"family with sequence similarity 22, member F"	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.2074C>G	chr9.hg19:g.97080944G>C	ENSP00000253262:p.Pro692Ala	377.0	0.0		390.0	17.0	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Missense_Mutation	SNP	ENST00000253262.4	hg19	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.581686	0.00879	.	.	ENSG00000130950	ENST00000253262;ENST00000341207;ENST00000375347	T;T	0.14640	2.49;2.52	1.52	-3.04	0.05412	Nuclear Testis protein, C-terminal (1);	2.077270	0.02242	N	0.065820	T	0.12561	0.0305	L	0.56769	1.78	0.09310	N	1	B	0.13594	0.008	B	0.16289	0.015	T	0.30621	-0.9972	10	0.09084	T	0.74	.	5.0244	0.14378	0.1751:0.5512:0.2738:0.0	.	692	A1L443	FA22F_HUMAN	A	692;677;526	ENSP00000253262:P692A;ENSP00000343865:P677A	ENSP00000253262:P692A	P	-	1	0	FAM22F	96120765	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.495000	0.06443	-1.287000	0.02381	-0.518000	0.04402	CCT	.	.		0.607	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561		C	97080944	G	C	97080944	3	2	64	1	0	0	0	0	1	0	0	0	5550	1174	41	4	200	4	FAM22F	9	97080944	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	2030870	97080944	44132487	145	7862										
IKBKAP	8518	hgsc.bcm.edu	37	chr9	111644428	111644428	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cctcaaagcttcttcccaggCagctccttctaacagcaaga	6	15	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:111644428C>T	ENST00000374647.5	-	30	3569	c.3262G>A	c.(3262-3264)Gcc>Acc	p.A1088T	IKBKAP_ENST00000467959.1_5'UTR|IKBKAP_ENST00000537196.1_Missense_Mutation_p.A739T	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	1088					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TCTTCCCAGGCAGCTCCTTCT	0.473																																					p.A1088T		Atlas-SNP	.											.	IKBKAP	122	.	0			c.G3262A						.						76	72	73					9																	111644428		2203	4300	6503	SO:0001583	missense	8518	exon30			CCCAGGCAGCTCC	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"Elongator acetyltransferase complex subunits"	5959	protein-coding gene	gene with protein product	"elongator acetyltransferase complex subunit 1"	603722	"dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.3262G>A	chr9.hg19:g.111644428C>T	ENSP00000363779:p.Ala1088Thr	93.0	0.0		94.0	4.0	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	hg19	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.209239	0.39003	.	.	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.36878	1.23;1.23	5.9	3.99	0.46301	.	0.416662	0.25119	N	0.032984	T	0.25901	0.0631	L	0.51422	1.61	0.27865	N	0.94025	B	0.31910	0.346	B	0.22386	0.039	T	0.07083	-1.0791	10	0.22706	T	0.39	-15.0669	8.4608	0.32927	0.1451:0.5873:0.2676:0.0	.	1088	O95163	ELP1_HUMAN	T	1088;739	ENSP00000363779:A1088T;ENSP00000439367:A739T	ENSP00000363779:A1088T	A	-	1	0	IKBKAP	110684249	0.281000	0.24258	1.000000	0.80357	0.959000	0.62525	0.071000	0.14594	2.788000	0.95919	0.650000	0.86243	GCC	.	.		0.473	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1			T	111644428	C	T	111644428	3	4	64	1	0	0	0	0	1	0	0	0	7619	710	25	3	768	3	IKBKAP	9	111644428	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	14563484	111644428	29569003	146	7863										
CTNNAL1	8727	hgsc.bcm.edu	37	chr9	111735058	111735058	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttaatgcttttagaaccacaTgatcagcatggtattttaat	6	6	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:111735058T>C	ENST00000325551.4	-	9	1330	c.1244A>G	c.(1243-1245)cAt>cGt	p.H415R	CTNNAL1_ENST00000488130.1_5'UTR|CTNNAL1_ENST00000325580.6_Intron|CTNNAL1_ENST00000374595.4_Missense_Mutation_p.H415R	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	415					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		TAGAACCACATGATCAGCATG	0.448																																					p.H415R		Atlas-SNP	.											.	CTNNAL1	51	.	0			c.A1244G						.						100	99	99					9																	111735058		2203	4300	6503	SO:0001583	missense	8727	exon9			ACCACATGATCAG	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.1244A>G	chr9.hg19:g.111735058T>C	ENSP00000320434:p.His415Arg	88.0	0.0		82.0	4.0	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	hg19	CCDS6775.1	.	.	.	.	.	.	.	.	.	.	T	19.04	3.749298	0.69533	.	.	ENSG00000119326	ENST00000374595;ENST00000325551	T;T	0.34667	1.35;1.35	6.03	4.9	0.64082	.	0.092956	0.85682	N	0.000000	T	0.45175	0.1329	M	0.65975	2.015	0.80722	D	1	D;P;D	0.53619	0.961;0.778;0.961	P;B;P	0.52514	0.701;0.299;0.701	T	0.33752	-0.9856	10	0.24483	T	0.36	-8.5087	10.1304	0.42676	0.0:0.078:0.0:0.922	.	415;415;415	B2RBI4;Q9UBT7-2;Q9UBT7	.;.;CTNL1_HUMAN	R	415	ENSP00000363723:H415R;ENSP00000320434:H415R	ENSP00000320434:H415R	H	-	2	0	CTNNAL1	110774879	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.735000	0.62051	1.108000	0.41662	0.533000	0.62120	CAT	.	.		0.448	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		C	111735058	T	C	111735058	3	2	64	1	0	0	0	0	1	0	0	0	4017	1464	51	2	1004	2	CTNNAL1	9	111735058	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	90630	111735058	29478373	147	7864										
ZBTB6	10773	hgsc.bcm.edu	37	chr9	125673934	125673934	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agaagactgacacaggtcagTgtgttggttgttgtttttca	12	5	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:125673934T>C	ENST00000373659.3	-	2	506	c.418A>G	c.(418-420)Act>Gct	p.T140A		NM_006626.5	NP_006617.1	Q15916	ZBTB6_HUMAN	zinc finger and BTB domain containing 6	140					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	11						CACAGGTCAGTGTGTTGGTTG	0.358																																					p.T140A		Atlas-SNP	.											.	ZBTB6	32	.	0			c.A418G						.						70	69	70					9																	125673934		2203	4300	6503	SO:0001583	missense	10773	exon2			GGTCAGTGTGTTG	X82018	CCDS6846.1	9q33.1-q33.3	2013-01-08	2006-04-10	2006-04-10	ENSG00000186130	ENSG00000186130		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16764	protein-coding gene	gene with protein product		605976	"zinc finger protein 482"	ZNF482		7958847	Standard	NM_006626		Approved	ZID	uc004bnh.4	Q15916	OTTHUMG00000020628	ENST00000373659.3:c.418A>G	chr9.hg19:g.125673934T>C	ENSP00000362763:p.Thr140Ala	75.0	0.0		55.0	4.0	NM_006626	A8K8N6	Missense_Mutation	SNP	ENST00000373659.3	hg19	CCDS6846.1	.	.	.	.	.	.	.	.	.	.	T	2.358	-0.347348	0.05208	.	.	ENSG00000186130	ENST00000373659	T	0.08546	3.08	5.96	-0.543	0.11851	.	0.764063	0.12114	N	0.498263	T	0.02012	0.0063	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45293	-0.9271	10	0.07644	T	0.81	.	1.5049	0.02484	0.18:0.3724:0.1373:0.3104	.	140	Q15916	ZBTB6_HUMAN	A	140	ENSP00000362763:T140A	ENSP00000362763:T140A	T	-	1	0	ZBTB6	124713755	0.004000	0.15560	0.988000	0.46212	0.992000	0.81027	-0.037000	0.12164	0.095000	0.17434	0.533000	0.62120	ACT	.	.		0.358	ZBTB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053962.1	NM_006626		C	125673934	T	C	125673934	3	2	64	1	0	0	0	0	1	0	0	0	17567	1696	59	2	860	2	ZBTB6	9	125673934	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	13938876	125673934	15539497	148	7865										
DOLPP1	57171	hgsc.bcm.edu	37	chr9	131847308	131847308	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtcttccccagcagatctccTtccttgggggcctggcactg	11	15	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:131847308T>C	ENST00000372546.4	+	3	216	c.184T>C	c.(184-186)Ttc>Ctc	p.F62L	DOLPP1_ENST00000540102.1_Intron|DOLPP1_ENST00000406974.3_Missense_Mutation_p.F62L	NM_020438.4	NP_065171.2	Q86YN1	DOPP1_HUMAN	dolichyldiphosphatase 1	62					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|lipid biosynthetic process (GO:0008610)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	dolichyldiphosphatase activity (GO:0047874)			endometrium(3)|kidney(2)|lung(7)|skin(1)	13						GCAGATCTCCTTCCTTGGGGG	0.617																																					p.F62L		Atlas-SNP	.											.	DOLPP1	17	.	0			c.T184C						.						51	54	53					9																	131847308		2203	4300	6503	SO:0001583	missense	57171	exon3			ATCTCCTTCCTTG	BC009493	CCDS6918.1, CCDS48039.1	9q34.1	2013-05-21	2013-05-21		ENSG00000167130	ENSG00000167130	3.6.1.43		29565	protein-coding gene	gene with protein product	"linked to Surfeit genes in Fugu rubripes 2"	614516	"dolichyl pyrophosphate phosphatase 1"			10369878, 12198133	Standard	NM_020438		Approved	LSFR2	uc004bxc.3	Q86YN1	OTTHUMG00000020771	ENST00000372546.4:c.184T>C	chr9.hg19:g.131847308T>C	ENSP00000361625:p.Phe62Leu	57.0	0.0		64.0	4.0	NM_001135917	A8K3U8|B0QZG4|Q96GF8|Q9Y3G1	Missense_Mutation	SNP	ENST00000372546.4	hg19	CCDS6918.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.714515	0.89112	.	.	ENSG00000167130	ENST00000372546;ENST00000406974	T;T	0.71461	-0.57;-0.57	5.44	5.44	0.79542	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77485	0.4137	L	0.51914	1.62	0.80722	D	1	P;D	0.59767	0.941;0.986	P;P	0.59357	0.676;0.856	T	0.78874	-0.2032	10	0.54805	T	0.06	-18.2171	14.3128	0.66426	0.0:0.0:0.0:1.0	.	62;62	B0QZG4;Q86YN1	.;DOPP1_HUMAN	L	62	ENSP00000361625:F62L;ENSP00000384043:F62L	ENSP00000361625:F62L	F	+	1	0	DOLPP1	130887129	1.000000	0.71417	0.906000	0.35671	0.868000	0.49771	7.186000	0.77722	2.061000	0.61500	0.402000	0.26972	TTC	.	.		0.617	DOLPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054548.4	NM_020438		C	131847308	T	C	131847308	3	2	64	1	0	0	0	0	1	0	0	0	4706	1609	56	2	194	2	DOLPP1	9	131847308	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	6173374	131847308	9366123	149	7866										
FAM78A	286336	hgsc.bcm.edu	37	chr9	134136640	134136640	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggggcccacgatggtgcaggTctctgtggtgttgccgtacc	16	11	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:134136640T>C	ENST00000372271.3	-	2	788	c.421A>G	c.(421-423)Acc>Gcc	p.T141A	FAM78A_ENST00000372269.3_Missense_Mutation_p.T138A|FAM78A_ENST00000247295.4_5'UTR	NM_033387.3	NP_203745.2	Q5JUQ0	FA78A_HUMAN	family with sequence similarity 78, member A	141										NS(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.15e-05)|Epithelial(140;0.000267)		ATGGTGCAGGTCTCTGTGGTG	0.602																																					p.T141A		Atlas-SNP	.											.	FAM78A	28	.	0			c.A421G						.						86	77	80					9																	134136640		2203	4300	6503	SO:0001583	missense	286336	exon2			TGCAGGTCTCTGT	AK095423	CCDS6941.2	9q34	2008-02-05	2005-07-18	2005-07-18	ENSG00000126882	ENSG00000126882			25465	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 59"	C9orf59		11214971	Standard	NM_033387		Approved	FLJ00024	uc004cak.3	Q5JUQ0	OTTHUMG00000020821	ENST00000372271.3:c.421A>G	chr9.hg19:g.134136640T>C	ENSP00000361345:p.Thr141Ala	76.0	0.0		69.0	4.0	NM_033387	Q86VQ9|Q9H7P4	Missense_Mutation	SNP	ENST00000372271.3	hg19	CCDS6941.2	.	.	.	.	.	.	.	.	.	.	T	21.1	4.094409	0.76870	.	.	ENSG00000126882	ENST00000372269;ENST00000372271;ENST00000464831	.	.	.	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.73528	0.3598	M	0.63843	1.955	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.75484	0.986;0.985	T	0.70114	-0.4961	9	0.18710	T	0.47	-35.1641	13.7403	0.62845	0.0:0.0:0.0:1.0	.	141;138	Q5JUQ0;Q5JUQ2	FA78A_HUMAN;.	A	138;141;110	.	ENSP00000361343:T138A	T	-	1	0	FAM78A	133126461	1.000000	0.71417	0.997000	0.53966	0.915000	0.54546	7.997000	0.88414	1.894000	0.54839	0.379000	0.24179	ACC	.	.		0.602	FAM78A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054720.1	NM_033387		C	134136640	T	C	134136640	3	2	64	1	0	0	0	0	1	0	0	0	5634	1667	58	2	434	2	FAM78A	9	134136640	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2289332	134136640	7076791	150	7867										
SEC16A	9919	hgsc.bcm.edu	37	chr9	139358965	139358965	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccgccagggccaaacctggcAcagacatgaggcactgaaaa	11	13	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr9:139358965A>G	ENST00000371706.3	-	7	3852	c.3819T>C	c.(3817-3819)tgT>tgC	p.C1273C	SEC16A_ENST00000290037.6_Silent_p.C1273C|SEC16A_ENST00000313050.7_Silent_p.C1451C|SEC16A_ENST00000431893.2_Silent_p.C1273C			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	1273					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		CAAACCTGGCACAGACATGAG	0.453																																					p.C1451C		Atlas-SNP	.											.	SEC16A	249	.	0			c.T4353C						.						72	76	75					9																	139358965		1901	4116	6017	SO:0001819	synonymous_variant	9919	exon9			CCTGGCACAGACA	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"KIAA0310"	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.3819T>C	chr9.hg19:g.139358965A>G		78.0	0.0		78.0	4.0	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	hg19																																																																																				.	.		0.453	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		G	139358965	A	G	139358965	2	3	64	1	0	0	0	0	0	0	0	1	14001	157	6	2		2	SEC16A	9	139358965	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5222325	139358965	1854466	151	7868										
ASB13	79754	hgsc.bcm.edu	37	chr10	5691033	5691033	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgcgcttccagattggccccGacgtcaataagaagcctcac	9	14	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:5691033G>A	ENST00000357700.6	-	4	443	c.417C>T	c.(415-417)gtC>gtT	p.V139V	ASB13_ENST00000479033.1_5'UTR	NM_024701.3	NP_078977.2	Q8WXK3	ASB13_HUMAN	ankyrin repeat and SOCS box containing 13	139					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					NS(1)|endometrium(3)|lung(3)|ovary(1)	8				GBM - Glioblastoma multiforme(2;9.59e-09)		GATTGGCCCCGACGTCAATAA	0.527																																					p.V139V		Atlas-SNP	.											.	ASB13	26	.	0			c.C417T						.						120	108	112					10																	5691033		2203	4300	6503	SO:0001819	synonymous_variant	79754	exon4			GGCCCCGACGTCA	AK091935	CCDS7070.1	10p15.1	2013-01-10	2011-01-25		ENSG00000196372	ENSG00000196372		"Ankyrin repeat domain containing"	19765	protein-coding gene	gene with protein product		615055	"ankyrin repeat and SOCS box-containing 13"			12076535	Standard	NM_024701		Approved	FLJ13134, MGC19879	uc001iig.2	Q8WXK3	OTTHUMG00000017603	ENST00000357700.6:c.417C>T	chr10.hg19:g.5691033G>A		98.0	0.0		105.0	61.0	NM_024701	A8K7Q6|D3DRR2|Q96EP7|Q9H8Z1	Silent	SNP	ENST00000357700.6	hg19	CCDS7070.1																																																																																			.	.		0.527	ASB13-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046564.1			A	5691033	G	A	5691033	2	1	64	1	0	0	0	0	0	0	0	1	1017	1045	37	1		1	ASB13	10	5691033	Silent	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10		5691033	129843714	152	7869										
UBE2D1	7321	hgsc.bcm.edu	37	chr10	60123367	60123367	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgcaaatcttttgtaatttcAgcctgatagcgcatatcaag	7	8	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:60123367A>G	ENST00000373910.4	+	4	347		c.e4-1			NM_001204880.1|NM_003338.4	NP_001191809.1|NP_003329.1	P51668	UB2D1_HUMAN	ubiquitin-conjugating enzyme E2D 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|BMP signaling pathway (GO:0030509)|cellular response to hypoxia (GO:0071456)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|prostate(1)|skin(2)	10						TTGTAATTTCAGCCTGATAGC	0.299																																					.		Atlas-SNP	.											.	UBE2D1	16	.	0			c.7-2A>G						.						102	95	98					10																	60123367		2203	4299	6502	SO:0001630	splice_region_variant	7321	exon3			AATTTCAGCCTGA	BC015997	CCDS7252.1, CCDS73139.1	10q21.1	2011-05-19	2011-05-19		ENSG00000072401	ENSG00000072401		"Ubiquitin-conjugating enzymes E2"	12474	protein-coding gene	gene with protein product		602961	"stimulator of Fe transport", "ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast)"	SFT		10072594, 8530467	Standard	NM_003338		Approved	UbcH5A, UBCH5, UBC4/5, E2(17)KB1	uc001jke.2	P51668	OTTHUMG00000018269	ENST00000373910.4:c.121-1A>G	chr10.hg19:g.60123367A>G		76.0	0.0		111.0	5.0	NM_001204880	A6NLF6|A8K786	Splice_Site	SNP	ENST00000373910.4	hg19	CCDS7252.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.649783	0.67358	.	.	ENSG00000072401	ENST00000373910	.	.	.	5.72	4.57	0.56435	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.251	0.49026	0.8465:0.1535:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UBE2D1	59793373	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.993000	0.93524	0.972000	0.38314	0.455000	0.32223	.	.	.		0.299	UBE2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048143.2	NM_003338	Intron	G	60123367	A	G	60123367	5	3	64	1	0	0	0	0	0	0	1	0	16863	202	7	2	133	2	UBE2D1	10	60123367	Splice_Site	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	54432334	60123367	75411380	153	7870										
MYST4	23522	hgsc.bcm.edu	37	chr10	76790247	76790247	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccaacctgactcctcctccaAtgaatctgccgccgcctctt	5	19	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:76790247A>G	ENST00000287239.4	+	18	6154	c.5665A>G	c.(5665-5667)Atg>Gtg	p.M1889V	KAT6B_ENST00000372725.1_Missense_Mutation_p.M1597V|KAT6B_ENST00000372714.1_Missense_Mutation_p.M1597V|KAT6B_ENST00000372724.1_Missense_Mutation_p.M1597V|KAT6B_ENST00000372711.1_Missense_Mutation_p.M1706V	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1889	Interaction with RUNX1 and RUNX2.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										TCCTCCTCCAATGAATCTGCC	0.557																																					p.M1889V		Atlas-SNP	.											.	.	.	.	0			c.A5665G						.						133	150	144					10																	76790247		2203	4300	6503	SO:0001583	missense	23522	exon18			CCTCCAATGAATC	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.5665A>G	chr10.hg19:g.76790247A>G	ENSP00000287239:p.Met1889Val	106.0	0.0		216.0	73.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	hg19	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.132500	0.37630	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.79749	-1.25;-1.25;-1.3;-1.25;-1.25	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000009	D	0.83769	0.5326	L	0.29908	0.895	0.42035	D	0.99104	P;P;D	0.53312	0.679;0.811;0.959	P;P;D	0.65443	0.65;0.879;0.935	D	0.86093	0.1551	10	0.72032	D	0.01	-10.0301	15.6712	0.77279	1.0:0.0:0.0:0.0	.	1706;1597;1889	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	V	1597;1597;1889;1597;1706	ENSP00000361810:M1597V;ENSP00000361809:M1597V;ENSP00000287239:M1889V;ENSP00000361799:M1597V;ENSP00000361796:M1706V	ENSP00000287239:M1889V	M	+	1	0	KAT6B	76460253	1.000000	0.71417	0.962000	0.40283	0.992000	0.81027	5.662000	0.68032	2.095000	0.63458	0.460000	0.39030	ATG	.	.		0.557	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		G	76790247	A	G	76790247	3	3	64	1	0	0	0	0	1	0	0	0	10114	101	4	2	5727	2	MYST4	10	76790247	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	16666880	76790247	58744500	154	7871										
ATAD1	84896	hgsc.bcm.edu	37	chr10	89544340	89544340	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cggtcagtgtcgaaggctgaAggttaataaatcgacagcct	12	8	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:89544340A>G	ENST00000308448.7	-	5	848	c.470T>C	c.(469-471)cTt>cCt	p.L157P	ATAD1_ENST00000400215.3_Missense_Mutation_p.L99P|ATAD1_ENST00000495903.1_5'UTR|ATAD1_ENST00000541004.1_Missense_Mutation_p.L157P|ATAD1_ENST00000328142.3_Missense_Mutation_p.L157P	NM_032810.2	NP_116199.2	Q8NBU5	ATAD1_HUMAN	ATPase family, AAA domain containing 1	157					ATP catabolic process (GO:0006200)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|positive regulation of receptor internalization (GO:0002092)	cell junction (GO:0030054)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			kidney(1)|large_intestine(4)|lung(4)|ovary(1)	10		all_cancers(4;6.78e-12)|Prostate(4;3.56e-12)|all_epithelial(4;5.58e-09)|Melanoma(5;0.0273)|Breast(4;0.0424)|all_hematologic(4;0.0846)|Colorectal(252;0.207)|Glioma(4;0.217)|all_neural(4;0.224)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00131)|GBM - Glioblastoma multiforme(1;1.1e-32)|Lung(2;1.4e-05)|LUSC - Lung squamous cell carcinoma(2;2.69e-05)|Colorectal(12;7.09e-05)|COAD - Colon adenocarcinoma(12;0.000261)|STAD - Stomach adenocarcinoma(243;0.235)		CGAAGGCTGAAGGTTAATAAA	0.463																																					p.L157P		Atlas-SNP	.											.	ATAD1	32	.	0			c.T470C						.						142	130	134					10																	89544340		2203	4300	6503	SO:0001583	missense	84896	exon5			GGCTGAAGGTTAA	AL834370	CCDS7386.1	10q23.31	2010-04-21		2007-02-08	ENSG00000138138	ENSG00000138138		"ATPases / AAA-type"	25903	protein-coding gene	gene with protein product		614452				12477932	Standard	NM_032810		Approved	FLJ14600	uc001kez.1	Q8NBU5	OTTHUMG00000018685	ENST00000308448.7:c.470T>C	chr10.hg19:g.89544340A>G	ENSP00000339017:p.Leu157Pro	108.0	0.0		89.0	5.0	NM_032810	D3DR26|Q6DKG1|Q6P4B9|Q8N3G1|Q8WYR9|Q969Y3	Missense_Mutation	SNP	ENST00000308448.7	hg19	CCDS7386.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.695430	0.88830	.	.	ENSG00000138138	ENST00000308448;ENST00000328142;ENST00000400215;ENST00000541004	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	5.35	5.35	0.76521	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.97195	0.9083	M	0.89968	3.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97875	1.0288	9	.	.	.	-20.4442	15.6409	0.77001	1.0:0.0:0.0:0.0	.	99;157	B4E2J1;Q8NBU5	.;ATAD1_HUMAN	P	157;157;99;157	ENSP00000339017:L157P;ENSP00000339016:L157P;ENSP00000412968:L99P;ENSP00000445500:L157P	.	L	-	2	0	ATAD1	89534320	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.151000	0.67156	0.460000	0.39030	CTT	.	.		0.463	ATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049235.1	NM_032810		G	89544340	A	G	89544340	3	3	64	1	0	0	0	0	1	0	0	0	1070	72	3	2	639	2	ATAD1	10	89544340	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	12754093	89544340	45990407	155	7872										
IFIT5	24138	hgsc.bcm.edu	37	chr10	91177501	91177501	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atttaacatcggctatgctaTcacagtgtatcggctggatg	10	8	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:91177501T>C	ENST00000371795.4	+	2	758	c.545T>C	c.(544-546)aTc>aCc	p.I182T	IFIT5_ENST00000416601.1_Intron	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	182					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						GGCTATGCTATCACAGTGTAT	0.443																																					p.I182T		Atlas-SNP	.											.	IFIT5	32	.	0			c.T545C						.						65	71	69					10																	91177501		2203	4300	6503	SO:0001583	missense	24138	exon2			ATGCTATCACAGT	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.545T>C	chr10.hg19:g.91177501T>C	ENSP00000360860:p.Ile182Thr	191.0	0.0		92.0	4.0	NM_012420	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Missense_Mutation	SNP	ENST00000371795.4	hg19	CCDS7403.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.289354	0.40494	.	.	ENSG00000152778	ENST00000371795	T	0.52754	0.65	6.03	6.03	0.97812	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.157599	0.53938	D	0.000056	T	0.37183	0.0994	L	0.49350	1.555	0.80722	D	1	B	0.32918	0.39	B	0.24541	0.054	T	0.27191	-1.0081	10	0.34782	T	0.22	-4.6845	8.8211	0.35027	0.0:0.1422:0.0:0.8578	.	182	Q13325	IFIT5_HUMAN	T	182	ENSP00000360860:I182T	ENSP00000360860:I182T	I	+	2	0	IFIT5	91167481	0.999000	0.42202	0.999000	0.59377	0.921000	0.55340	3.787000	0.55439	2.308000	0.77769	0.533000	0.62120	ATC	.	.		0.443	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		C	91177501	T	C	91177501	3	2	64	1	0	0	0	0	1	0	0	0	7534	1435	50	2	551	2	IFIT5	10	91177501	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1633161	91177501	44357246	156	7873										
IFIT5	24138	hgsc.bcm.edu	37	chr10	91177909	91177909	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggataaactaaaggttgatgAgctgatttcatctgctatat	9	5	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:91177909A>G	ENST00000371795.4	+	2	1166	c.953A>G	c.(952-954)gAg>gGg	p.E318G	IFIT5_ENST00000416601.1_Missense_Mutation_p.E270G	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	318					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						AAGGTTGATGAGCTGATTTCA	0.438																																					p.E318G		Atlas-SNP	.											.	IFIT5	32	.	0			c.A953G						.						140	133	136					10																	91177909		2203	4300	6503	SO:0001583	missense	24138	exon2			TTGATGAGCTGAT	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.953A>G	chr10.hg19:g.91177909A>G	ENSP00000360860:p.Glu318Gly	111.0	0.0		95.0	4.0	NM_012420	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Missense_Mutation	SNP	ENST00000371795.4	hg19	CCDS7403.1	.	.	.	.	.	.	.	.	.	.	A	12.82	2.053313	0.36181	.	.	ENSG00000152778	ENST00000371795;ENST00000416601	T;T	0.38887	1.11;1.11	6.03	3.6	0.41247	Tetratricopeptide-like helical (1);	0.463546	0.25219	N	0.032254	T	0.31949	0.0813	L	0.46157	1.445	0.24281	N	0.995206	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18618	-1.0331	10	0.16420	T	0.52	-7.3931	9.4161	0.38523	0.8431:0.0:0.1569:0.0	.	318;270	Q13325;B4DDV1	IFIT5_HUMAN;.	G	318;270	ENSP00000360860:E318G;ENSP00000414042:E270G	ENSP00000360860:E318G	E	+	2	0	IFIT5	91167889	0.097000	0.21791	0.545000	0.28153	0.884000	0.51177	2.149000	0.42244	1.042000	0.40150	0.533000	0.62120	GAG	.	.		0.438	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		G	91177909	A	G	91177909	3	3	64	1	0	0	0	0	1	0	0	0	7534	304	11	2	959	2	IFIT5	10	91177909	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	408	91177909	44356838	157	7874										
IDE	3416	hgsc.bcm.edu	37	chr10	94274762	94274762	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcttgtcttacatcaatgccTtcttggtttggtctagtctc	7	10	6	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:94274762T>C	ENST00000265986.6	-	5	755	c.699A>G	c.(697-699)gaA>gaG	p.E233E		NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	233					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	CATCAATGCCTTCTTGGTTTG	0.363																																					p.E233E		Atlas-SNP	.											.	IDE	77	.	0			c.A699G						.						183	190	188					10																	94274762		2203	4300	6503	SO:0001819	synonymous_variant	3416	exon5			AATGCCTTCTTGG	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.699A>G	chr10.hg19:g.94274762T>C		108.0	0.0		64.0	4.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Silent	SNP	ENST00000265986.6	hg19	CCDS7421.1																																																																																			.	.		0.363	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		C	94274762	T	C	94274762	2	2	64	1	0	0	0	0	0	0	0	1	7502	1606	56	2		2	IDE	10	94274762	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	3096853	94274762	41259985	158	7875										
CCNJ	54619	hgsc.bcm.edu	37	chr10	97816897	97816897	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtagctgctgcatgtgtggcTtcttcgaggattatacttcg	12	8	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:97816897T>C	ENST00000265992.5	+	5	967	c.600T>C	c.(598-600)gcT>gcC	p.A200A	CCNJ_ENST00000534974.1_Silent_p.A200A|ENTPD1-AS1_ENST00000458228.1_RNA|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000452728.1_RNA|CCNJ_ENST00000403870.3_Silent_p.A199A|ENTPD1-AS1_ENST00000451364.1_RNA|CCNJ_ENST00000465148.2_Silent_p.A211A|ENTPD1-AS1_ENST00000427846.1_RNA	NM_001134375.1|NM_001134376.1|NM_019084.4	NP_001127847.1|NP_001127848.1|NP_061957.2	Q5T5M9	CCNJ_HUMAN	cyclin J	200						nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	11				Epithelial(162;6.1e-08)|all cancers(201;2.32e-06)		CATGTGTGGCTTCTTCGAGGA	0.423																																					p.A211A		Atlas-SNP	.											.	CCNJ	27	.	0			c.T633C						.						245	213	224					10																	97816897		2203	4300	6503	SO:0001819	synonymous_variant	54619	exon5			TGTGGCTTCTTCG	AK001757	CCDS7445.1, CCDS44462.1, CCDS44463.1	10q23.33	2008-05-14			ENSG00000107443	ENSG00000107443			23434	protein-coding gene	gene with protein product						12477932	Standard	NM_019084		Approved	FLJ10895, bA690P14.1	uc010qoq.2	Q5T5M9	OTTHUMG00000018823	ENST00000265992.5:c.600T>C	chr10.hg19:g.97816897T>C		293.0	0.0		133.0	6.0	NM_001134375	B7Z4E7|Q86XL1|Q9NV69	Silent	SNP	ENST00000265992.5	hg19	CCDS7445.1																																																																																			.	.		0.423	CCNJ-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090166.3	NM_019084		C	97816897	T	C	97816897	2	2	64	1	0	0	0	0	0	0	0	1	2930	1596	56	2		2	CCNJ	10	97816897	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	3542135	97816897	37717850	159	7876										
SEC31B	25956	hgsc.bcm.edu	37	chr10	102256018	102256018	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cacatggccccacttacctgAgcacagtccctgggtagaaa	9	14	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:102256018A>G	ENST00000370345.3	-	18	2404	c.2307T>C	c.(2305-2307)gcT>gcC	p.A769A	SEC31B_ENST00000494350.1_5'Flank	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	769					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)		p.A769A(1)		NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CACTTACCTGAGCACAGTCCC	0.537																																					p.A769A		Atlas-SNP	.											SEC31B,colon,carcinoma,0,1	SEC31B	84	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2307C						.						86	73	77					10																	102256018		2203	4300	6503	SO:0001819	synonymous_variant	25956	exon18			TACCTGAGCACAG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.2307T>C	chr10.hg19:g.102256018A>G		127.0	0.0		96.0	4.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	ENST00000370345.3	hg19	CCDS7495.1																																																																																			.	.		0.537	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		G	102256018	A	G	102256018	2	3	64	1	0	0	0	0	0	0	0	1	14014	291	11	2		2	SEC31B	10	102256018	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	4439121	102256018	33278729	160	7877										
POLL	27343	hgsc.bcm.edu	37	chr10	103347044	103347044	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccctcctaggaatctttgcaAgtacttttgatgatgcatca	7	10	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:103347044A>G	ENST00000370162.3	-	2	568	c.74T>C	c.(73-75)cTt>cCt	p.L25P	POLL_ENST00000370169.1_Missense_Mutation_p.L25P|DPCD_ENST00000370151.4_5'Flank|DPCD_ENST00000470165.1_3'UTR|DPCD_ENST00000416979.2_5'UTR|DPCD_ENST00000370148.2_5'Flank|POLL_ENST00000370158.3_Silent_p.L9L|POLL_ENST00000436284.2_Intron|POLL_ENST00000370172.1_Intron|POLL_ENST00000456836.2_Silent_p.L7L|DPCD_ENST00000370147.1_5'Flank|POLL_ENST00000299206.4_Missense_Mutation_p.L25P|POLL_ENST00000339310.3_Silent_p.L7L	NM_001174084.1|NM_001174085.1|NM_013274.3	NP_001167555.1|NP_001167556.1|NP_037406.1	Q9UGP5	DPOLL_HUMAN	polymerase (DNA directed), lambda	25					DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|nucleotide-excision repair (GO:0006289)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		AATCTTTGCAAGTACTTTTGA	0.498								DNA polymerases (catalytic subunits)																													p.L25P		Atlas-SNP	.											.	POLL	43	.	0			c.T74C						.						212	192	199					10																	103347044		2203	4300	6503	SO:0001583	missense	27343	exon2			TTTGCAAGTACTT	AF161019	CCDS7513.1	10q23	2012-05-18			ENSG00000166169	ENSG00000166169		"DNA polymerases"	9184	protein-coding gene	gene with protein product		606343				17686665	Standard	NM_001174084		Approved		uc001kti.2	Q9UGP5	OTTHUMG00000018933	ENST00000370162.3:c.74T>C	chr10.hg19:g.103347044A>G	ENSP00000359181:p.Leu25Pro	125.0	0.0		86.0	4.0	NM_013274	D3DR76|Q5JQP5|Q6NUM2|Q9BTN8|Q9HA10|Q9HB35	Missense_Mutation	SNP	ENST00000370162.3	hg19	CCDS7513.1	.	.	.	.	.	.	.	.	.	.	A	5.172	0.217390	0.09810	.	.	ENSG00000166169	ENST00000299206;ENST00000370174;ENST00000370169;ENST00000370162;ENST00000370157;ENST00000415897;ENST00000413344;ENST00000430045	T;T;T;T;T	0.43688	2.75;2.75;2.75;2.27;0.94	5.18	1.6	0.23607	.	0.493920	0.20428	N	0.092535	T	0.28566	0.0707	L	0.48362	1.52	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.15464	-1.0436	10	0.33141	T	0.24	-0.3554	2.6016	0.04867	0.5349:0.0:0.2696:0.1955	.	25;25	Q9UGP5;A8K860	DPOLL_HUMAN;.	P	25	ENSP00000299206:L25P;ENSP00000359188:L25P;ENSP00000359181:L25P;ENSP00000400676:L25P;ENSP00000400517:L25P	ENSP00000299206:L25P	L	-	2	0	POLL	103337034	0.000000	0.05858	0.373000	0.26003	0.180000	0.23129	0.329000	0.19698	0.305000	0.22832	0.533000	0.62120	CTT	.	.		0.498	POLL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049946.1	NM_013274		G	103347044	A	G	103347044	3	3	64	1	0	0	0	0	1	0	0	0	12214	72	3	2	1685	2	POLL	10	103347044	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1091026	103347044	32187703	161	7878										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106865182	106865182	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctacctcacctgcaggatccAggaatgtgccgagacaacta	9	13	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:106865182A>G	ENST00000369701.3	+	7	1348	c.1121A>G	c.(1120-1122)cAg>cGg	p.Q374R		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	374					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TGCAGGATCCAGGAATGTGCC	0.478																																					p.Q374R	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.A1121G						.						139	111	120					10																	106865182		2203	4300	6503	SO:0001583	missense	22986	exon7			GGATCCAGGAATG	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1121A>G	chr10.hg19:g.106865182A>G	ENSP00000358715:p.Gln374Arg	167.0	0.0		92.0	4.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.991742	0.74703	.	.	ENSG00000156395	ENST00000369701	T	0.39787	1.06	5.43	5.43	0.79202	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.60766	0.2294	M	0.70595	2.14	0.46356	D	0.999	D	0.71674	0.998	D	0.67900	0.954	T	0.64516	-0.6389	10	0.66056	D	0.02	.	11.8572	0.52444	1.0:0.0:0.0:0.0	.	374	Q9UPU3	SORC3_HUMAN	R	374	ENSP00000358715:Q374R	ENSP00000358715:Q374R	Q	+	2	0	SORCS3	106855172	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	7.460000	0.80816	2.050000	0.60909	0.379000	0.24179	CAG	.	.		0.478	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		G	106865182	A	G	106865182	3	3	64	1	0	0	0	0	1	0	0	0	14947	188	7	2	1147	2	SORCS3	10	106865182	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	3518138	106865182	28669565	162	7879										
GPAM	57678	hgsc.bcm.edu	37	chr10	113940243	113940243	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gttcttacccagctctggggAgtgcaggagtaacaacatct	11	10	3	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:113940243A>G	ENST00000348367.4	-	4	410	c.213T>C	c.(211-213)acT>acC	p.T71T	GPAM_ENST00000480130.1_5'Flank|GPAM_ENST00000369425.1_Silent_p.T71T|GPAM_ENST00000423155.1_Silent_p.T71T			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	71					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		AGCTCTGGGGAGTGCAGGAGT	0.398																																					p.T71T	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.T213C						.						115	95	102					10																	113940243		2203	4300	6503	SO:0001819	synonymous_variant	57678	exon4			CTGGGGAGTGCAG	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"glycerol-3-phosphate acyltransferase 1, mitochondrial"	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.213T>C	chr10.hg19:g.113940243A>G		92.0	0.0		47.0	4.0	NM_001244949	Q5VW51|Q86TA3	Silent	SNP	ENST00000348367.4	hg19	CCDS7570.1																																																																																			.	.		0.398	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		G	113940243	A	G	113940243	2	3	64	1	0	0	0	0	0	0	0	1	6596	291	11	2		2	GPAM	10	113940243	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	7075061	113940243	21594504	163	7880										
VWA2	340706	hgsc.bcm.edu	37	chr10	116045937	116045937	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tggtctggagcctcgatggcAttcccttccgtggtggcccc	13	14	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:116045937A>G	ENST00000392982.3	+	11	1487	c.1237A>G	c.(1237-1239)Att>Gtt	p.I413V	VWA2_ENST00000603594.1_Missense_Mutation_p.I413V			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	413	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		CCTCGATGGCATTCCCTTCCG	0.697																																					p.I413V		Atlas-SNP	.											.	VWA2	64	.	0			c.A1237G						.						76	69	72					10																	116045937		2203	4300	6503	SO:0001583	missense	340706	exon11			GATGGCATTCCCT	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1237A>G	chr10.hg19:g.116045937A>G	ENSP00000376708:p.Ile413Val	115.0	0.0		72.0	4.0	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	hg19		.	.	.	.	.	.	.	.	.	.	A	0.011	-1.730903	0.00687	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	T	0.80123	-1.34	5.6	-5.49	0.02584	von Willebrand factor, type A (3);	0.762112	0.12551	N	0.459047	T	0.57902	0.2085	N	0.25060	0.705	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.08055	0.003;0.003;0.002	T	0.40232	-0.9574	10	0.29301	T	0.29	.	2.9749	0.05934	0.3066:0.3463:0.2545:0.0926	.	109;413;413	Q5GFL6-3;Q5GFL6;Q5GFL6-2	.;VWA2_HUMAN;.	V	413	ENSP00000376708:I413V	ENSP00000298715:I413V	I	+	1	0	VWA2	116035927	0.010000	0.17322	0.000000	0.03702	0.153000	0.21895	0.219000	0.17641	-0.875000	0.04022	-0.376000	0.06991	ATT	.	.		0.697	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		G	116045937	A	G	116045937	3	3	64	1	0	0	0	0	1	0	0	0	17254	217	8	2	1275	2	VWA2	10	116045937	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	2105694	116045937	19488810	164	7881										
FANK1	92565	hgsc.bcm.edu	37	chr10	127697829	127697829	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gaaatggccagagtttttgaCagacaggttgggatgctctt	13	6	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:127697829C>T	ENST00000368693.1	+	10	1070	c.966C>T	c.(964-966)gaC>gaT	p.D322D	FANK1_ENST00000368695.1_Silent_p.D316D|FANK1_ENST00000477963.1_3'UTR			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	322						cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				GAGTTTTTGACAGACAGGTTG	0.413																																					p.D322D		Atlas-SNP	.											.	FANK1	46	.	0			c.C966T						.						164	172	169					10																	127697829		2203	4300	6503	SO:0001819	synonymous_variant	92565	exon10			TTTTGACAGACAG	BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	23527	protein-coding gene	gene with protein product		611640	"fibronectin type 3 and ankyrin repeat domains 1"			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.966C>T	chr10.hg19:g.127697829C>T		106.0	0.0		58.0	5.0	NM_145235	Q6UXY9|Q6X7T6	Silent	SNP	ENST00000368693.1	hg19	CCDS31309.1																																																																																			.	.		0.413	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145235		T	127697829	C	T	127697829	2	4	64	1	0	0	0	0	0	0	0	1	5680	477	17	3		3	FANK1	10	127697829	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	11651892	127697829	7836918	165	7882										
MKI67	4288	hgsc.bcm.edu	37	chr10	129907660	129907660	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cagatggctgttttgctgcaTtctgtgcactgaagaacaca	10	9	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:129907660T>C	ENST00000368654.3	-	13	2819	c.2444A>G	c.(2443-2445)aAt>aGt	p.N815S	MKI67_ENST00000484853.1_5'Flank|MKI67_ENST00000368653.3_Missense_Mutation_p.N455S	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	815					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTTTGCTGCATTCTGTGCACT	0.398																																					p.N815S		Atlas-SNP	.											.	MKI67	363	.	0			c.A2444G						.						112	109	110					10																	129907660		2203	4300	6503	SO:0001583	missense	4288	exon13			GCTGCATTCTGTG	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.2444A>G	chr10.hg19:g.129907660T>C	ENSP00000357643:p.Asn815Ser	122.0	0.0		95.0	4.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	14.55	2.570049	0.45798	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01767	4.68;4.65	4.02	4.02	0.46733	.	0.896444	0.09569	N	0.784480	T	0.06005	0.0156	L	0.50333	1.59	0.09310	N	1	D;D;D	0.64830	0.994;0.994;0.989	P;P;P	0.61477	0.889;0.889;0.777	T	0.44314	-0.9336	10	0.39692	T	0.17	.	9.5304	0.39191	0.0:0.0:0.0:1.0	.	814;455;815	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	S	815;455;814;390	ENSP00000357643:N815S;ENSP00000357642:N455S	ENSP00000357641:N390S	N	-	2	0	MKI67	129797650	0.001000	0.12720	0.014000	0.15608	0.007000	0.05969	0.792000	0.26929	1.829000	0.53265	0.460000	0.39030	AAT	.	.		0.398	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		C	129907660	T	C	129907660	3	2	64	1	0	0	0	0	1	0	0	0	9607	1493	52	2	7338	2	MKI67	10	129907660	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2209831	129907660	5627087	166	7883										
TUBGCP2	10844	hgsc.bcm.edu	37	chr10	135111545	135111545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	catacacccatgctgggaagAtggggaggtgctggcctgaa	15	9	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr10:135111545A>G	ENST00000252936.3	-	4	566	c.527T>C	c.(526-528)aTc>aCc	p.I176T	TUBGCP2_ENST00000368563.2_Missense_Mutation_p.I176T|TUBGCP2_ENST00000543663.1_Missense_Mutation_p.I176T|TUBGCP2_ENST00000470829.1_5'Flank|TUBGCP2_ENST00000417178.2_Missense_Mutation_p.I46T|RP11-122K13.12_ENST00000424450.1_RNA			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	176					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		TGCTGGGAAGATGGGGAGGTG	0.473																																					p.I176T		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.T527C						.						188	168	175					10																	135111545		2203	4300	6503	SO:0001583	missense	10844	exon5			GGGAAGATGGGGA	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.527T>C	chr10.hg19:g.135111545A>G	ENSP00000252936:p.Ile176Thr	222.0	0.0		100.0	5.0	NM_006659	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Missense_Mutation	SNP	ENST00000252936.3	hg19	CCDS7676.1	.	.	.	.	.	.	.	.	.	.	A	9.146	1.015071	0.19355	.	.	ENSG00000130640	ENST00000252936;ENST00000417178;ENST00000368563;ENST00000543663	T;T;T;T	0.16073	2.63;2.37;2.63;2.63	5.24	4.12	0.48240	.	0.173608	0.50627	N	0.000110	T	0.06645	0.0170	N	0.03608	-0.345	0.20975	N	0.999812	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.38520	-0.9657	10	0.10377	T	0.69	-31.4391	9.9033	0.41362	0.919:0.0:0.081:0.0	.	176;176;176	F5H4L0;B7ZKL8;Q9BSJ2	.;.;GCP2_HUMAN	T	176;46;176;176	ENSP00000252936:I176T;ENSP00000395666:I46T;ENSP00000357551:I176T;ENSP00000446093:I176T	ENSP00000252936:I176T	I	-	2	0	TUBGCP2	134961535	0.999000	0.42202	0.789000	0.31954	0.790000	0.44656	4.100000	0.57762	0.962000	0.38057	0.459000	0.35465	ATC	.	.		0.473	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1			G	135111545	A	G	135111545	3	3	64	1	0	0	0	0	1	0	0	0	16781	333	12	2	2237	2	TUBGCP2	10	135111545	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5203885	135111545	423202	167	7884										
PSMD13	5719	hgsc.bcm.edu	37	chr11	248788	248788	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	taccatagtgtctgagcagcAggagagagccttcacgctgg	13	10	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:248788A>G	ENST00000532097.1	+	8	1085	c.581A>G	c.(580-582)cAg>cGg	p.Q194R	PSMD13_ENST00000352303.5_Missense_Mutation_p.Q194R|PSMD13_ENST00000431206.2_Missense_Mutation_p.Q196R	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	194					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		TCTGAGCAGCAGGAGAGAGCC	0.443																																					p.Q196R		Atlas-SNP	.											.	PSMD13	53	.	0			c.A587G						.						77	75	75					11																	248788		2203	4300	6503	SO:0001583	missense	5719	exon6			AGCAGCAGGAGAG	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"Proteasome (prosome, macropain) subunits"	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.581A>G	chr11.hg19:g.248788A>G	ENSP00000436186:p.Gln194Arg	119.0	0.0		72.0	4.0	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	hg19	CCDS7692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.87|11.87	1.768985|1.768985	0.31320|0.31320	.|.	.|.	ENSG00000185627|ENSG00000185627	ENST00000532097;ENST00000538343;ENST00000431206;ENST00000528906;ENST00000352303|ENST00000526783	T;T;T;T|.	0.18502|.	2.22;2.22;2.24;2.21|.	5.45|5.45	3.14|3.14	0.36123|0.36123	.|.	0.222920|.	0.47455|.	D|.	0.000236|.	T|T	0.51244|0.51244	0.1663|0.1663	L|L	0.38175|0.38175	1.15|1.15	0.52501|0.52501	D|D	0.999957|0.999957	B;B;B;B|.	0.13594|.	0.008;0.002;0.001;0.001|.	B;B;B;B|.	0.09377|.	0.004;0.003;0.002;0.002|.	T|T	0.35201|0.35201	-0.9798|-0.9798	10|5	0.11182|.	T|.	0.66|.	.|.	9.0653|9.0653	0.36460|0.36460	0.8486:0.0:0.1514:0.0|0.8486:0.0:0.1514:0.0	.|.	196;129;194;194|.	Q9UNM6-2;B4DJ66;B2RBM7;Q9UNM6|.	.;.;.;PSD13_HUMAN|.	R|G	194;129;196;156;194|105	ENSP00000436186:Q194R;ENSP00000396937:Q196R;ENSP00000433364:Q156R;ENSP00000333811:Q194R|.	ENSP00000333811:Q194R|.	Q|R	+|+	2|1	0|2	PSMD13|PSMD13	238788|238788	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	7.408000|7.408000	0.80041|0.80041	0.471000|0.471000	0.27319|0.27319	0.529000|0.529000	0.55759|0.55759	CAG|AGG	.	.		0.443	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817		G	248788	A	G	248788	3	3	64	1	0	0	0	0	1	0	0	0	12708	188	7	2	692	2	PSMD13	11	248788	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10		248788	134757728	168	7885										
IFITM3	10410	hgsc.bcm.edu	37	chr11	320723	320723	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gttgtggggcgcccccagcaCagccacctcgtgctcctcct	11	18	0	0	rs199582787	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:320723C>T	ENST00000399808.4	-	1	327	c.91G>A	c.(91-93)Gtg>Atg	p.V31M	RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.11_ENST00000602429.1_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.V10M|RP11-326C3.11_ENST00000602756.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.10_ENST00000534271.1_RNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.V10M	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	31					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		GCCCCCAGCACAGCCACCTCG	0.612																																					p.V31M		Atlas-SNP	.											IFITM3,brain,glioma,0,1	IFITM3	132	.	0			c.G91A						.						87	98	95					11																	320723		1967	4140	6107	SO:0001583	missense	10410	exon1			CCAGCACAGCCAC	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"interferon induced transmembrane protein 3 (1-8U)"			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.91G>A	chr11.hg19:g.320723C>T	ENSP00000382707:p.Val31Met	96.0	1.0		58.0	3.0	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	hg19	CCDS41585.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.526447	0.27299	.	.	ENSG00000142089	ENST00000399808;ENST00000270031;ENST00000526811	T;T	0.79454	-1.03;-1.27	4.61	-4.91	0.03085	.	11.488500	0.02440	N	0.084490	T	0.64516	0.2605	L	0.39147	1.195	0.09310	N	1	B	0.16802	0.019	B	0.15484	0.013	T	0.46400	-0.9194	10	0.13108	T	0.6	0.9022	6.4601	0.21952	0.1231:0.361:0.0:0.5159	.	31	Q01628	IFM3_HUMAN	M	31;15;10	ENSP00000382707:V31M;ENSP00000432108:V10M	ENSP00000372047:V15M	V	-	1	0	IFITM3	310723	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-1.638000	0.02013	-0.562000	0.06086	-1.790000	0.00627	GTG	.	.		0.612	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034		T	320723	C	T	320723	3	4	64	1	0	0	0	0	1	0	0	0	7537	478	17	3	318	3	IFITM3	11	320723	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	71935	320723	134685793	169	7886										
C11orf40	143501	hgsc.bcm.edu	37	chr11	4592711	4592712	+	Missense_Mutation	DNP	TT	TT	AG													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtagaacacgatccatacagTttttccctgcaaagacctgg					rs78543312|rs78387367		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:4592711_4592712TT>AG	ENST00000307616.1	-	4	594_595	c.595_596AA>CT	c.(595-597)AAc>CTc	p.N199L		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	199										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		atccatacagtttttccCTGCA	0.441																																					p.N199I|p.N199H		Atlas-SNP	.											.	C11orf40	37	.	0			c.A596T|c.A595C						.																																			SO:0001583	missense	143501	exon4			ATACAGTTTTTCC|TACAGTTTTTCCC		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.595_596delinsAG	chr11.hg19:g.4592711_4592712delinsAG	ENSP00000302918:p.Asn199Leu	155.0|154.0	0.0		133.0|130.0	10.0|7.0	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	hg19	CCDS31354.1																																																																																			.	.		0.441	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663		AG	4592712	TT	AG	4592711	3	1	64	1	0	0	0	0	1	0	0	0	1641	1725	60	4	60	4	C11orf40	11	4592711	Missense_Mutation	DNP	TT	TCGA-CC-A3MA-01A-11D-A20W-10	4271988	4592711	130413805	170	7887										
ARFIP2	23647	hgsc.bcm.edu	37	chr11	6501574	6501574	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgctccagcccatcatcttcAggaagctgcctggcttcgcc	9	16	3	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:6501574A>G	ENST00000254584.2	-	2	161	c.78T>C	c.(76-78)ccT>ccC	p.P26P	ARFIP2_ENST00000423813.2_Intron|ARFIP2_ENST00000525235.1_Silent_p.P26P|TIMM10B_ENST00000530751.1_5'Flank|ARFIP2_ENST00000396777.3_Silent_p.P26P|TIMM10B_ENST00000472836.1_5'Flank|TIMM10B_ENST00000254616.6_5'Flank|ARFIP2_ENST00000445086.2_Intron	NM_012402.3	NP_036534.1	P53365	ARFP2_HUMAN	ADP-ribosylation factor interacting protein 2	26					actin cytoskeleton organization (GO:0030036)|cellular component movement (GO:0006928)|lamellipodium assembly (GO:0030032)|ruffle organization (GO:0031529)|small GTPase mediated signal transduction (GO:0007264)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|Rac GTPase binding (GO:0048365)			endometrium(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(2)	15		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CATCATCTTCAGGAAGCTGCC	0.483																																					p.P26P	Melanoma(119;796 1674 9049 20480 24794)	Atlas-SNP	.											.	ARFIP2	23	.	0			c.T78C						.						69	59	62					11																	6501574		2201	4296	6497	SO:0001819	synonymous_variant	23647	exon2			ATCTTCAGGAAGC	BC000392	CCDS7765.1, CCDS55739.1, CCDS55740.1, CCDS73250.1	11p15	2008-08-01	2008-08-01		ENSG00000132254	ENSG00000132254			17160	protein-coding gene	gene with protein product	"arfaptin 2"	601638				8670882, 9038142	Standard	NM_012402		Approved	POR1	uc010ran.2	P53365	OTTHUMG00000133406	ENST00000254584.2:c.78T>C	chr11.hg19:g.6501574A>G		132.0	0.0		70.0	4.0	NM_012402	B4DX86|B4E306|D3DQT5	Silent	SNP	ENST00000254584.2	hg19	CCDS7765.1																																																																																			.	.		0.483	ARFIP2-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387044.1	NM_012402		G	6501574	A	G	6501574	2	3	64	1	0	0	0	0	0	0	0	1	855	175	7	2		2	ARFIP2	11	6501574	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1908863	6501574	128504942	171	7888										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6662744	6662744	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aggcacctggcaccccagccCccagcagcagcagcagcagc	11	19	0	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:6662744C>A	ENST00000299441.3	-	2	512	c.101G>T	c.(100-102)gGg>gTg	p.G34V		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	34					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACCCCAGCCCCcagcagcag	0.642																																					p.G34V		Atlas-SNP	.											.	DCHS1	277	.	0			c.G101T						.						8	8	8					11																	6662744		2165	4229	6394	SO:0001583	missense	8642	exon2			CCAGCCCCCAGCA	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.101G>T	chr11.hg19:g.6662744C>A	ENSP00000299441:p.Gly34Val	53.0	0.0		31.0	6.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.535676	0.45176	.	.	ENSG00000166341	ENST00000299441	T	0.54279	0.58	5.32	5.32	0.75619	.	0.000000	0.40554	N	0.001076	T	0.65176	0.2666	M	0.68952	2.095	0.47584	D	0.999464	D	0.64830	0.994	P	0.61328	0.887	T	0.60286	-0.7293	10	0.10902	T	0.67	.	16.1489	0.81599	0.0:1.0:0.0:0.0	.	34	Q96JQ0	PCD16_HUMAN	V	34	ENSP00000299441:G34V	ENSP00000299441:G34V	G	-	2	0	DCHS1	6619320	0.845000	0.29573	0.928000	0.36995	0.824000	0.46624	1.469000	0.35343	2.489000	0.83994	0.579000	0.79373	GGG	.	.		0.642	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6662744	C	A	6662744	3	1	64	1	0	0	0	0	1	0	0	0	4289	623	22	3	9875	3	DCHS1	11	6662744	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	161170	6662744	128343772	172	7889										
MRVI1	10335	hgsc.bcm.edu	37	chr11	10647928	10647928	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggccaggctgagggctgttcAgggccattttcccactgctg	14	12	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:10647928A>G	ENST00000436272.1	-	8	950	c.872T>C	c.(871-873)cTg>cCg	p.L291P	MRVI1_ENST00000424001.1_Missense_Mutation_p.L3P|MRVI1_ENST00000423302.2_Missense_Mutation_p.L318P|MRVI1_ENST00000558540.1_Missense_Mutation_p.L3P|MRVI1_ENST00000534266.2_Missense_Mutation_p.L3P|MRVI1_ENST00000527509.2_Missense_Mutation_p.L227P|MRVI1_ENST00000545852.1_Missense_Mutation_p.L3P|MRVI1_ENST00000421747.1_Missense_Mutation_p.L309P|MRVI1_ENST00000547195.1_Missense_Mutation_p.L227P|MRVI1_ENST00000541483.1_Intron|MRVI1_ENST00000552103.1_Missense_Mutation_p.L227P|MRVI1_ENST00000531107.1_Missense_Mutation_p.L310P			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	291					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		AGGGCTGTTCAGGGCCATTTT	0.572																																					p.L318P		Atlas-SNP	.											.	MRVI1	113	.	0			c.T953C						.						72	78	76					11																	10647928		1942	4138	6080	SO:0001583	missense	10335	exon9			CTGTTCAGGGCCA	AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"inositol 1,4,5-triphosphate-associated cGMP kinase substrate", "IP3R-associated cGMP kinase substrate"	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.872T>C	chr11.hg19:g.10647928A>G	ENSP00000412229:p.Leu291Pro	176.0	0.0		91.0	4.0	NM_130385	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Missense_Mutation	SNP	ENST00000436272.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.04	2.713778	0.48622	.	.	ENSG00000072952	ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000545852;ENST00000424001;ENST00000423302;ENST00000531107;ENST00000527509	T;T;T;T;T;T;T;T;T	0.35789	2.2;2.66;1.64;1.64;1.29;1.29;2.01;2.2;1.64	5.71	5.71	0.89125	.	0.230509	0.30556	N	0.009363	T	0.59348	0.2187	M	0.66939	2.045	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.60845	-0.7182	10	0.54805	T	0.06	-8.5711	15.9822	0.80121	1.0:0.0:0.0:0.0	.	291;310;309	Q9Y6F6;E9PQY6;Q9Y6F6-4	MRVI1_HUMAN;.;.	P	309;292;291;227;227;3;3;318;310;227	ENSP00000414598:L309P;ENSP00000412229:L291P;ENSP00000448278:L227P;ENSP00000446764:L227P;ENSP00000441971:L3P;ENSP00000401205:L3P;ENSP00000412130:L318P;ENSP00000432436:L310P;ENSP00000432067:L227P	ENSP00000307885:L292P	L	-	2	0	MRVI1	10604504	1.000000	0.71417	1.000000	0.80357	0.486000	0.33341	4.760000	0.62235	2.189000	0.69895	0.460000	0.39030	CTG	.	.		0.572	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		G	10647928	A	G	10647928	3	3	64	1	0	0	0	0	1	0	0	0	9862	188	7	2	1837	2	MRVI1	11	10647928	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	3985184	10647928	124358588	173	7890										
USP47	55031	hgsc.bcm.edu	37	chr11	11941963	11941963	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gattttgattatacaaccatGcataggattaaactgaatga	7	5	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:11941963G>A	ENST00000399455.2	+	11	1320	c.1200G>A	c.(1198-1200)atG>atA	p.M400I	USP47_ENST00000539466.1_5'UTR|USP47_ENST00000527733.1_Missense_Mutation_p.M380I|USP47_ENST00000339865.5_Missense_Mutation_p.M312I	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	400	USP.				base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		ATACAACCATGCATAGGATTA	0.338																																					p.M312I		Atlas-SNP	.											.	USP47	91	.	0			c.G936A						.						109	103	105					11																	11941963		1823	4075	5898	SO:0001583	missense	55031	exon9			AACCATGCATAGG	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.1200G>A	chr11.hg19:g.11941963G>A	ENSP00000382382:p.Met400Ile	102.0	0.0		58.0	4.0	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	hg19		.	.	.	.	.	.	.	.	.	.	G	25.9	4.687971	0.88639	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455;ENST00000535588	T;T;T	0.29917	1.55;1.55;1.55	5.5	5.5	0.81552	.	0.105200	0.85682	D	0.000000	T	0.47284	0.1437	L	0.55990	1.75	0.80722	D	1	P;P	0.47677	0.899;0.745	P;P	0.56865	0.808;0.6	T	0.11941	-1.0567	10	0.26408	T	0.33	.	18.9869	0.92775	0.0:0.0:1.0:0.0	.	380;312	E9PM46;Q96K76-2	.;.	I	312;380;400;400	ENSP00000339957:M312I;ENSP00000433146:M380I;ENSP00000382382:M400I	ENSP00000339957:M312I	M	+	3	0	USP47	11898539	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.062000	0.89475	2.591000	0.87537	0.563000	0.77884	ATG	.	.		0.338	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		A	11941963	G	A	11941963	3	1	64	1	0	0	0	0	1	0	0	0	17093	1319	46	3	970	3	USP47	11	11941963	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	1294035	11941963	123064553	174	7891										
NUCB2	4925	hgsc.bcm.edu	37	chr11	17352479	17352480	+	Missense_Mutation	DNP	CA	CA	TT													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agatggaacaaaaaaaattaCaacaaggaattcctccatca					rs189362726|rs535406012|rs3842269	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:17352479_17352480CA>TT	ENST00000529010.1	+	13	1423_1424	c.1204_1205CA>TT	c.(1204-1206)CAa>TTa	p.Q402L	NUCB2_ENST00000458064.2_Missense_Mutation_p.Q372L|NUCB2_ENST00000323688.6_Missense_Mutation_p.Q402L	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	402	Binds to necdin. {ECO:0000250}.		Missing. {ECO:0000269|PubMed:12087473, ECO:0000269|PubMed:14702039}.			cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AAAAAAATTACAACAAGGAATT	0.322																																					p.Q402X|p.Q402L		Atlas-SNP	.											.	NUCB2	31	.	0			c.C1204T|c.A1205T						.																																			SO:0001583	missense	4925	exon13			AAATTACAACAAG|AATTACAACAAGG	AF052642	CCDS41623.1	11p15.1	2013-01-10						"EF-hand domain containing"	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		Exception_encountered	chr11.hg19:g.17352479_17352480delinsTT	ENSP00000436455:p.Gln402Leu	1.0	0.0		16.0|14.0	6.0	NM_005013	A8K642|D3DQX5|Q8NFT5	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000529010.1	hg19	CCDS41623.1																																																																																			.	.		0.322	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013		TT	17352480	CA	TT	17352479	3	4	64	1	0	0	0	0	1	0	0	0	10728	479	17	3	1246	3	NUCB2	11	17352479	Missense_Mutation	DNP	CA	TCGA-CC-A3MA-01A-11D-A20W-10	5410516	17352479	117654037	175	7892										
SLC17A6	57084	hgsc.bcm.edu	37	chr11	22381052	22381052	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggatgtgtcatctttgtcagAatactgcagggacttgttga	12	6	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:22381052A>G	ENST00000263160.3	+	4	989	c.552A>G	c.(550-552)agA>agG	p.R184R	CTD-2140G10.4_ENST00000534543.1_RNA	NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	184					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						TCTTTGTCAGAATACTGCAGG	0.408																																					p.R184R		Atlas-SNP	.											.	SLC17A6	135	.	0			c.A552G						.						148	133	138					11																	22381052		2203	4300	6503	SO:0001819	synonymous_variant	57084	exon4			TGTCAGAATACTG	AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"Solute carriers"	16703	protein-coding gene	gene with protein product	"vesicular glutamate transporter 2", "differentiation-associated Na-dependent inorganic phosphate cotransporter"	607563	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.552A>G	chr11.hg19:g.22381052A>G		139.0	0.0		96.0	4.0	NM_020346	A6NKS2	Silent	SNP	ENST00000263160.3	hg19	CCDS7856.1																																																																																			.	.		0.408	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		G	22381052	A	G	22381052	2	3	64	1	0	0	0	0	0	0	0	1	14436	243	9	2		2	SLC17A6	11	22381052	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5028573	22381052	112625464	176	7893										
QSER1	79832	hgsc.bcm.edu	37	chr11	32977609	32977609	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcattgaaaatgcaaacaagAaggaatatgtcagagtgtgt	10	4	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:32977609A>G	ENST00000399302.2	+	7	4641	c.4306A>G	c.(4306-4308)Aag>Gag	p.K1436E	QSER1_ENST00000527788.1_Missense_Mutation_p.K1197E	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1436										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					TGCAAACAAGAAGGAATATGT	0.308																																					p.K1436E		Atlas-SNP	.											.	QSER1	153	.	0			c.A4306G						.						142	135	137					11																	32977609		1820	4069	5889	SO:0001583	missense	79832	exon7			AACAAGAAGGAAT	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.4306A>G	chr11.hg19:g.32977609A>G	ENSP00000382241:p.Lys1436Glu	115.0	0.0		71.0	4.0	NM_001076786	Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	hg19	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.279215	0.80692	.	.	ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788	T;T	0.31769	1.81;1.48	5.57	5.57	0.84162	.	0.000000	0.64402	D	0.000006	T	0.50069	0.1594	M	0.66939	2.045	0.42105	D	0.991359	D;D;D	0.67145	0.99;0.982;0.996	P;P;P	0.58266	0.768;0.628;0.836	T	0.54556	-0.8276	10	0.72032	D	0.01	.	15.7316	0.77810	1.0:0.0:0.0:0.0	.	1197;1197;1436	C9JJ88;Q2KHR3-2;Q2KHR3	.;.;QSER1_HUMAN	E	1436;1197;1197	ENSP00000382241:K1436E;ENSP00000432766:K1197E	ENSP00000078652:K1197E	K	+	1	0	QSER1	32934185	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.629000	0.67798	2.109000	0.64355	0.482000	0.46254	AAG	.	.		0.308	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		G	32977609	A	G	32977609	3	3	64	1	0	0	0	0	1	0	0	0	12897	247	9	2	4324	2	QSER1	11	32977609	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	10596557	32977609	102028907	177	7894										
NAT10	55226	hgsc.bcm.edu	37	chr11	34145347	34145347	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tacctccccaagccctgataAcctccatactctgtttgaat	4	15	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:34145347A>G	ENST00000257829.3	+	10	1159	c.953A>G	c.(952-954)aAc>aGc	p.N318S	NAT10_ENST00000527971.1_Intron|NAT10_ENST00000531159.2_Missense_Mutation_p.N246S	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	318						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				AGCCCTGATAACCTCCATACT	0.323																																					p.N318S		Atlas-SNP	.											.	NAT10	78	.	0			c.A953G						.						122	120	120					11																	34145347		2202	4298	6500	SO:0001583	missense	55226	exon10			CTGATAACCTCCA	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.953A>G	chr11.hg19:g.34145347A>G	ENSP00000257829:p.Asn318Ser	178.0	0.0		99.0	4.0	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	SNP	ENST00000257829.3	hg19	CCDS7889.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.556601	0.86231	.	.	ENSG00000135372	ENST00000257829;ENST00000531159	T;T	0.46819	0.86;0.86	5.36	5.36	0.76844	Domain of unknown function DUF699, exodeoxyribonuclease V alpha chain (1);	0.083040	0.85682	D	0.000000	T	0.63355	0.2504	M	0.64404	1.975	0.80722	D	1	D	0.63880	0.993	D	0.63033	0.91	T	0.63337	-0.6660	10	0.42905	T	0.14	-32.1786	15.3831	0.74676	1.0:0.0:0.0:0.0	.	318	Q9H0A0	NAT10_HUMAN	S	318;246	ENSP00000257829:N318S;ENSP00000433011:N246S	ENSP00000257829:N318S	N	+	2	0	NAT10	34101923	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.053000	0.93860	2.181000	0.69327	0.524000	0.50904	AAC	.	.		0.323	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		G	34145347	A	G	34145347	3	3	64	1	0	0	0	0	1	0	0	0	10183	43	2	2	987	2	NAT10	11	34145347	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1167738	34145347	100861169	178	7895										
EXT2	2132	hgsc.bcm.edu	37	chr11	44228357	44228357	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttccagattctctctggcccAaaatccgggttccattaaaa	6	12	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:44228357A>G	ENST00000343631.3	+	10	1639	c.1510A>G	c.(1510-1512)Aaa>Gaa	p.K504E	EXT2_ENST00000533608.1_Missense_Mutation_p.K504E|EXT2_ENST00000358681.4_Missense_Mutation_p.K514E|EXT2_ENST00000395673.3_Missense_Mutation_p.K537E			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	504					carbohydrate metabolic process (GO:0005975)|cell differentiation (GO:0030154)|cellular polysaccharide biosynthetic process (GO:0033692)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm formation (GO:0001707)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|lung(17)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	32						TCTCTGGCCCAAAATCCGGGT	0.388			"Mis, N, F, S"			"exostoses, osteosarcoma"			Hereditary Multiple Exostoses																												p.K537E		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	EXT2_ENST00000358681,NS,carcinoma,0,2	EXT2	129	.	0			c.A1609G						.						94	95	95					11																	44228357		2203	4299	6502	SO:0001583	missense	2132	exon10	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	TGGCCCAAAATCC		CCDS7908.1, CCDS53618.1, CCDS53619.1	11p12-p11	2014-09-17	2013-03-01		ENSG00000151348	ENSG00000151348	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3513	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608210	"exostoses (multiple) 2", "exostosin 2"			8162019, 9576285	Standard	NM_000401		Approved	SOTV	uc001mya.3	Q93063	OTTHUMG00000166498	ENST00000343631.3:c.1510A>G	chr11.hg19:g.44228357A>G	ENSP00000342656:p.Lys504Glu	67.0	0.0		39.0	2.0	NM_000401	B2R5Z6|C9JU51|J3KPT2|O15288	Missense_Mutation	SNP	ENST00000343631.3	hg19	CCDS7908.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.022363	0.54683	.	.	ENSG00000151348	ENST00000533608;ENST00000358681;ENST00000395673;ENST00000343631	D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0	5.81	3.44	0.39384	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.000000	0.85682	D	0.000000	T	0.79890	0.4524	L	0.33293	1	0.53688	D	0.999975	B;P;P;P;P	0.41978	0.174;0.642;0.589;0.767;0.767	B;P;B;P;P	0.46144	0.068;0.505;0.372;0.505;0.505	T	0.71836	-0.4472	10	0.10902	T	0.67	-27.0637	12.8389	0.57790	0.7435:0.2565:0.0:0.0	.	504;514;514;504;517	Q6NUL1;C9JU51;Q93063-2;Q93063;D3DR24	.;.;.;EXT2_HUMAN;.	E	504;514;537;504	ENSP00000431173:K504E;ENSP00000351509:K514E;ENSP00000379032:K537E;ENSP00000342656:K504E	ENSP00000342656:K504E	K	+	1	0	EXT2	44184933	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.182000	0.77689	0.434000	0.26340	-1.243000	0.01532	AAA	.	.		0.388	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401		G	44228357	A	G	44228357	3	3	64	1	0	0	0	0	1	0	0	0	5326	131	5	2	1744	2	EXT2	11	44228357	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	10083010	44228357	90778159	179	7896										
LRTOMT	25906	hgsc.bcm.edu	37	chr11	71819858	71819858	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctggtgcaccccgcttcttgCagtatgctaagagctgtggc	12	12	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:71819858C>A	ENST00000227618.4	-	0	886				ANAPC15_ENST00000502597.2_Intron|ANAPC15_ENST00000543050.1_Intron|LRTOMT_ENST00000435085.1_Missense_Mutation_p.Q255K|LRTOMT_ENST00000419228.1_Missense_Mutation_p.Q215K|LRTOMT_ENST00000307198.7_Missense_Mutation_p.Q255K|ANAPC15_ENST00000543015.1_5'Flank	NM_001278487.1|NM_001278491.1|NM_014042.2	NP_001265416.1|NP_001265420.1|NP_054761.1	P60006	APC15_HUMAN	anaphase promoting complex subunit 15						mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	anaphase-promoting complex (GO:0005680)|intracellular (GO:0005622)											CCGCTTCTTGCAGTATGCTAA	0.622																																					p.Q255K		Atlas-SNP	.											.	LRTOMT	20	.	0			c.C763A						.						75	67	69					11																	71819858		692	1591	2283	SO:0001628	intergenic_variant	220074	exon9			TTCTTGCAGTATG	AL080071	CCDS8210.1, CCDS60880.1	11q13.4	2012-10-17	2012-05-31	2012-05-31	ENSG00000110200	ENSG00000110200		"Anaphase promoting complex subunits"	24531	protein-coding gene	gene with protein product		614717	"chromosome 11 open reading frame 51"	C11orf51		21926987	Standard	NM_014042		Approved	HSPC020, DKFZP564M082, APC15	uc001orw.3	P60006	OTTHUMG00000167865		chr11.hg19:g.71819858C>A		108.0	0.0		125.0	45.0	NM_001145309	G3V1Q3|Q9CXK2|Q9Y269	Missense_Mutation	SNP	ENST00000227618.4	hg19	CCDS8210.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.704317	0.48412	.	.	ENSG00000184154	ENST00000419228;ENST00000435085;ENST00000307198	T;T;T	0.70282	-0.47;-0.47;-0.47	5.53	4.6	0.57074	.	.	.	.	.	T	0.51500	0.1678	N	0.12182	0.205	0.80722	D	1	P;P	0.39022	0.454;0.655	B;B	0.38264	0.266;0.269	T	0.51601	-0.8685	9	0.08599	T	0.76	-10.8557	15.9651	0.79966	0.0:0.8648:0.1352:0.0	.	255;215	Q8WZ04;Q8WZ04-2	TOMT_HUMAN;.	K	215;255;255	ENSP00000392233:Q215K;ENSP00000409789:Q255K;ENSP00000305742:Q255K	ENSP00000305742:Q215K	Q	+	1	0	LRTOMT	71497506	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	4.200000	0.58433	1.513000	0.48852	0.651000	0.88453	CAG	.	.		0.622	ANAPC15-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396695.1	NM_014042		A	71819858	C	A	71819858	1	1	64	0	1	0	0	0	0	0	0	0	9055	711	25	3		3	LRTOMT	11	71819858	IGR	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	27591501	71819858	63186658	180	7897										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103018563	103018563	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gaagactgtgattgatgatcTcatccagaagttatttgatc	9	6	1	6			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:103018563T>C	ENST00000375735.2	+	19	2909	c.2765T>C	c.(2764-2766)cTc>cCc	p.L922P	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.L922P	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	922	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		ATTGATGATCTCATCCAGAAG	0.303																																					p.L922P		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T2765C						.						120	116	117					11																	103018563		1839	4078	5917	SO:0001583	missense	79659	exon19			ATGATCTCATCCA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.2765T>C	chr11.hg19:g.103018563T>C	ENSP00000364887:p.Leu922Pro	41.0	0.0		64.0	4.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.393574	0.62066	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.28895	1.59;1.59	5.49	5.49	0.81192	.	0.385199	0.20577	U	0.089603	T	0.48295	0.1492	M	0.71581	2.175	0.80722	D	1	P;P	0.39576	0.679;0.619	P;P	0.51355	0.466;0.667	T	0.32929	-0.9888	10	0.29301	T	0.29	.	15.8882	0.79269	0.0:0.0:0.0:1.0	.	922;922	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	P	922	ENSP00000364887:L922P;ENSP00000381167:L922P	ENSP00000364887:L922P	L	+	2	0	DYNC2H1	102523773	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.619000	0.83057	2.220000	0.72140	0.528000	0.53228	CTC	.	.		0.303	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103018563	T	C	103018563	3	2	64	1	0	0	0	0	1	0	0	0	4848	1551	54	2	2839	2	DYNC2H1	11	103018563	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	31198705	103018563	31987953	181	7898										
SNX19	399979	hgsc.bcm.edu	37	chr11	130780180	130780180	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctgacctttaggaatgattcTaggaggctcttacgggcttc	11	9	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr11:130780180T>C	ENST00000265909.4	-	3	2468	c.1899A>G	c.(1897-1899)ctA>ctG	p.L633L	SNX19_ENST00000528555.1_Silent_p.L13L|SNX19_ENST00000530356.1_Silent_p.L13L|SNX19_ENST00000545537.1_5'UTR|SNX19_ENST00000539184.1_Silent_p.L76L|SNX19_ENST00000533214.1_Silent_p.L633L|SNX19_ENST00000534726.1_5'Flank|SNX19_ENST00000533318.1_5'UTR	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	633	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GGAATGATTCTAGGAGGCTCT	0.448																																					p.L633L		Atlas-SNP	.											SNX19,NS,carcinoma,0,1	SNX19	84	.	0			c.A1899G						.						91	91	91					11																	130780180		2201	4296	6497	SO:0001819	synonymous_variant	399979	exon3			TGATTCTAGGAGG	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1899A>G	chr11.hg19:g.130780180T>C		66.0	0.0		47.0	2.0	NM_014758	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	hg19	CCDS31721.1																																																																																			.	.		0.448	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		C	130780180	T	C	130780180	2	2	64	1	0	0	0	0	0	0	0	1	14905	1509	53	2		2	SNX19	11	130780180	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	27761617	130780180	4226336	182	7899										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2764398	2764398	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cccccaggccgtgctgctccTcttcaggtgggtccctgaag	12	16	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:2764398T>C	ENST00000347598.4	+	36	4370	c.4370T>C	c.(4369-4371)cTc>cCc	p.L1457P	CACNA1C_ENST00000402845.3_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399601.1_Missense_Mutation_p.L1409P|CACNA1C_ENST00000344100.3_Missense_Mutation_p.L1431P|CACNA1C_ENST00000399655.1_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399644.1_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399597.1_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399591.1_Missense_Mutation_p.L1398P|CACNA1C_ENST00000399637.1_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399629.1_Missense_Mutation_p.L1426P|CACNA1C_ENST00000399621.1_Missense_Mutation_p.L1409P|CACNA1C_ENST00000327702.7_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399649.1_Missense_Mutation_p.L1396P|CACNA1C_ENST00000406454.3_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399603.1_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399638.1_Missense_Mutation_p.L1437P|CACNA1C_ENST00000399641.1_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399634.1_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399606.1_Missense_Mutation_p.L1429P|CACNA1C_ENST00000399617.1_Missense_Mutation_p.L1409P|CACNA1C_ENST00000399595.1_Missense_Mutation_p.L1398P|CACNA1C_ENST00000335762.5_Missense_Mutation_p.L1434P	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1457					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GTGCTGCTCCTCTTCAGGTGG	0.532																																					p.L1457P		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.T4370C						.						77	81	80					12																	2764398		2124	4264	6388	SO:0001583	missense	775	exon36			TGCTCCTCTTCAG	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.4370T>C	chr12.hg19:g.2764398T>C	ENSP00000266376:p.Leu1457Pro	92.0	0.0		91.0	4.0	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.097917	0.76870	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97731	-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51;-4.51	3.96	3.96	0.45880	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99239	0.9735	H	0.98883	4.36	0.80722	D	1	D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.995;0.999;1.0;0.995;0.999;0.999;1.0;0.999;0.837;1.0;0.999;1.0;1.0;0.999;1.0;0.999;0.999;0.972;1.0;0.984;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;P;D;D;D;D;D	0.97110	0.932;0.998;0.996;0.949;0.998;0.996;0.996;0.997;0.832;0.999;0.996;0.996;1.0;1.0;0.999;0.998;0.996;0.914;0.999;0.843;0.996;0.999;0.999;0.996;0.996	D	0.98459	1.0595	10	0.87932	D	0	.	13.3114	0.60382	0.0:0.0:0.0:1.0	.	100;1431;1406;1457;1409;1409;1409;1426;1437;1409;1429;1409;1369;1457;1409;1409;1409;1398;1396;1398;1398;1409;1409;1409;1409	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	P	1434;1409;1409;1437;1409;1409;1409;1398;1409;1457;1429;1409;1431;1426;1409;1396;1409;1409;1409;1409;1409;1398;1239	ENSP00000336982:L1434P;ENSP00000382563:L1409P;ENSP00000382552:L1409P;ENSP00000382547:L1437P;ENSP00000382506:L1409P;ENSP00000382530:L1409P;ENSP00000382546:L1409P;ENSP00000382500:L1398P;ENSP00000382549:L1409P;ENSP00000266376:L1457P;ENSP00000382515:L1429P;ENSP00000382510:L1409P;ENSP00000341092:L1431P;ENSP00000382537:L1426P;ENSP00000329877:L1409P;ENSP00000382557:L1396P;ENSP00000385724:L1409P;ENSP00000382512:L1409P;ENSP00000382542:L1409P;ENSP00000382526:L1409P;ENSP00000385896:L1409P;ENSP00000382504:L1398P	ENSP00000323129:L1239P	L	+	2	0	CACNA1C	2634659	1.000000	0.71417	0.997000	0.53966	0.959000	0.62525	7.821000	0.86641	1.780000	0.52325	0.459000	0.35465	CTC	.	.		0.532	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		C	2764398	T	C	2764398	3	2	64	1	0	0	0	0	1	0	0	0	2542	1551	54	2	4686	2	CACNA1C	12	2764398	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		2764398	131087497	183	7900										
CLECL1	160365	hgsc.bcm.edu	37	chr12	9885707	9885707	+	Missense_Mutation	SNP	A	A	T													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttctgcaaagaaacttctgAtaagtaaattgagatggcaa					rs71929655|rs113575400|rs113222621|rs71045297|rs398070028		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:9885707A>T	ENST00000327839.3	-	1	188	c.154T>A	c.(154-156)Tca>Aca	p.S52T		NM_172004.3	NP_742001.1	Q8IZS7	CLCL1_HUMAN	C-type lectin-like 1	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.S52fs*26(1)		breast(1)|kidney(1)|large_intestine(4)|lung(3)	9						GAAACTTCTGATAAGTAAATT	0.403																																					p.S52T		Atlas-SNP	.											.,2	CLECL1	18	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.T154A						.						76	79	78					12																	9885707		2203	4300	6503	SO:0001583	missense	160365	exon1			CTTCTGATAAGTA	AF518873	CCDS8603.1, CCDS73441.1	12p13.31	2007-06-21				ENSG00000184293			24462	protein-coding gene	gene with protein product	"dendritic cell associated lectin 1"	607467				12421943	Standard	NM_172004		Approved	DCAL1	uc001qwi.3	Q8IZS7		ENST00000327839.3:c.154T>A	chr12.hg19:g.9885707A>T	ENSP00000331766:p.Ser52Thr	108.0	0.0		99.0	9.0	NM_001267701		Missense_Mutation	SNP	ENST00000327839.3	hg19	CCDS8603.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.803|7.803	0.714090|0.714090	0.15306|0.15306	.|.	.|.	ENSG00000184293|ENSG00000184293	ENST00000327839|ENST00000542530	T|.	0.54071|.	0.59|.	1.85|1.85	1.85|1.85	0.25348|0.25348	.|.	.|.	.|.	.|.	.|.	T|.	0.15739|.	0.0379|.	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|.	0.06786|.	0.001|.	B|.	0.01281|.	0.0|.	T|.	0.24799|.	-1.0150|.	8|.	.|.	.|.	.|.	.|.	4.4866|4.4866	0.11792|0.11792	0.1978:0.0:0.8022:0.0|0.1978:0.0:0.8022:0.0	.|.	52|.	Q8IZS7|.	CLCL1_HUMAN|.	T|X	52|3	ENSP00000331766:S52T|.	.|.	S|Y	-|-	1|3	0|2	CLECL1|CLECL1	9776974|9776974	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.036000|0.036000	0.12997|0.12997	-0.740000|-0.740000	0.04861|0.04861	0.333000|0.333000	0.23563|0.23563	-0.131000|-0.131000	0.14894|0.14894	TCA|TAT	.	T|1.000;|0.000		0.403	CLECL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399815.1	NM_172004		T	9885707	A	T	9885707	3	4	64	1	0	0	0	0	1	0	0	0	3525	333	12	4	357	4	CLECL1	12	9885707	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	7121309	9885707	123966188	184	7901	37	2								
CLECL1	160365	hgsc.bcm.edu	37	chr12	9885713	9885713	+	Missense_Mutation	SNP	A	A	T													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	caaagaaacttctgataagtAaattgagatggcaaatttcc					rs200639830		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:9885713A>T	ENST00000327839.3	-	1	182	c.148T>A	c.(148-150)Tac>Aac	p.Y50N		NM_172004.3	NP_742001.1	Q8IZS7	CLCL1_HUMAN	C-type lectin-like 1	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|kidney(1)|large_intestine(4)|lung(3)	9						TCTGATAAGTAAATTGAGATG	0.403																																					p.Y50N		Atlas-SNP	.											.	CLECL1	18	.	0			c.T148A						.						77	80	79					12																	9885713		2203	4300	6503	SO:0001583	missense	160365	exon1			ATAAGTAAATTGA	AF518873	CCDS8603.1, CCDS73441.1	12p13.31	2007-06-21				ENSG00000184293			24462	protein-coding gene	gene with protein product	"dendritic cell associated lectin 1"	607467				12421943	Standard	NM_172004		Approved	DCAL1	uc001qwi.3	Q8IZS7		ENST00000327839.3:c.148T>A	chr12.hg19:g.9885713A>T	ENSP00000331766:p.Tyr50Asn	110.0	0.0		103.0	9.0	NM_001267701		Missense_Mutation	SNP	ENST00000327839.3	hg19	CCDS8603.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.915|6.915	0.538458|0.538458	0.13250|0.13250	.|.	.|.	ENSG00000184293|ENSG00000184293	ENST00000542530|ENST00000327839	.|T	.|0.56275	.|0.47	1.86|1.86	0.666|0.666	0.17901|0.17901	.|.	.|.	.|.	.|.	.|.	T|T	0.21590|0.21590	0.0520|0.0520	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	.|P	.|0.51147	.|0.942	.|B	.|0.39217	.|0.294	T|T	0.08027|0.08027	-1.0742|-1.0742	5|8	.|.	.|.	.|.	.|.	3.7406|3.7406	0.08528|0.08528	0.7983:0.0:0.2017:0.0|0.7983:0.0:0.2017:0.0	.|.	.|50	.|Q8IZS7	.|CLCL1_HUMAN	L|N	1|50	.|ENSP00000331766:Y50N	.|.	F|Y	-|-	3|1	2|0	CLECL1|CLECL1	9776980|9776980	0.002000|0.002000	0.14202|0.14202	0.001000|0.001000	0.08648|0.08648	0.004000|0.004000	0.04260|0.04260	1.812000|1.812000	0.38952|0.38952	0.170000|0.170000	0.19704|0.19704	-0.463000|-0.463000	0.05309|0.05309	TTT|TAC	.	.		0.403	CLECL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399815.1	NM_172004		T	9885713	A	T	9885713	3	4	64	1	0	0	0	0	1	0	0	0	3525	362	13	4	363	4	CLECL1	12	9885713	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	6	9885713	123966182	185	7902	37	2								
SLCO1B3	28234	hgsc.bcm.edu	37	chr12	21068948	21068948	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cttttcacagaagggtctacTtgggcttatctatagcttta	8	8	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:21068948T>C	ENST00000381545.3	+	16	2095	c.1876T>C	c.(1876-1878)Ttg>Ctg	p.L626L	SLCO1B7_ENST00000554957.1_Intron|LST3_ENST00000381541.3_Intron|SLCO1B3_ENST00000553473.1_Intron|SLCO1B3_ENST00000261196.2_Silent_p.L626L|LST3_ENST00000540229.1_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	626					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	AAGGGTCTACTTGGGCTTATC	0.299																																					p.L626L		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.T1876C						.						77	77	77					12																	21068948		2201	4299	6500	SO:0001819	synonymous_variant	28234	exon16			GTCTACTTGGGCT		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1876T>C	chr12.hg19:g.21068948T>C		59.0	0.0		58.0	5.0	NM_019844	E7EMT8|Q5JAR4	Silent	SNP	ENST00000381545.3	hg19	CCDS8684.1																																																																																			.	.		0.299	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		C	21068948	T	C	21068948	2	2	64	1	0	0	0	0	0	0	0	1	14739	1606	56	2		2	SLCO1B3	12	21068948	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	11183235	21068948	112782947	186	7903										
IPO8	10526	hgsc.bcm.edu	37	chr12	30814173	30814173	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aacttcttcatattcatcacTttgaagaactttgccaaata	3	9	4	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:30814173T>C	ENST00000256079.4	-	16	2121	c.1783A>G	c.(1783-1785)Agt>Ggt	p.S595G	IPO8_ENST00000544829.1_Missense_Mutation_p.S390G	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	595					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)	p.S595C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TATTCATCACTTTGAAGAACT	0.328																																					p.S595G		Atlas-SNP	.											IPO8,NS,carcinoma,0,1	IPO8	105	.	1	Substitution - Missense(1)	lung(1)	c.A1783G						.						110	105	106					12																	30814173		2201	4300	6501	SO:0001583	missense	10526	exon16			CATCACTTTGAAG	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.1783A>G	chr12.hg19:g.30814173T>C	ENSP00000256079:p.Ser595Gly	70.0	0.0		45.0	2.0	NM_006390	B7Z7M3	Missense_Mutation	SNP	ENST00000256079.4	hg19	CCDS8719.1	.	.	.	.	.	.	.	.	.	.	T	16.56	3.156055	0.57259	.	.	ENSG00000133704	ENST00000256079;ENST00000545286;ENST00000544829	T;T	0.68025	-0.3;-0.3	4.42	4.42	0.53409	Armadillo-like helical (1);Armadillo-type fold (1);	0.042986	0.85682	D	0.000000	T	0.72423	0.3458	L	0.48642	1.525	0.80722	D	1	B;D;B	0.61697	0.055;0.99;0.026	B;P;B	0.58820	0.075;0.846;0.02	T	0.74100	-0.3774	10	0.49607	T	0.09	-11.8667	13.9505	0.64113	0.0:0.0:0.0:1.0	.	390;71;595	B7Z7M3;Q59F59;O15397	.;.;IPO8_HUMAN	G	595;71;390	ENSP00000256079:S595G;ENSP00000444520:S390G	ENSP00000256079:S595G	S	-	1	0	IPO8	30705440	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.424000	0.80242	1.748000	0.51833	0.402000	0.26972	AGT	.	.		0.328	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		C	30814173	T	C	30814173	3	2	64	1	0	0	0	0	1	0	0	0	7807	1609	56	2	1370	2	IPO8	12	30814173	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	9745225	30814173	103037722	187	7904										
ARID2	196528	hgsc.bcm.edu	37	chr12	46246364	46246376	+	Frame_Shift_Del	DEL	TCCCGACTCAGGA	TCCCGACTCAGGA	-													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggacatcaaatcatagcagtTcccgactcaggatcaaaagt							TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	TCCCGACTCAGGA	TCCCGACTCAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:46246364_46246376delTCCCGACTCAGGA	ENST00000334344.6	+	15	4630_4642	c.4458_4470delTCCCGACTCAGGA	c.(4456-4470)gttcccgactcaggafs	p.VPDSG1486fs	ARID2_ENST00000457135.1_Frame_Shift_Del_p.VPDSG94fs|ARID2_ENST00000444670.1_Frame_Shift_Del_p.VPDSG1096fs|ARID2_ENST00000422737.1_Frame_Shift_Del_p.VPDSG1337fs|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1486					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCATAGCAGTTCCCGACTCAGGATCAAAAGTAT	0.451			"N, S, F"		hepatocellular carcinoma																																p.1486_1490del		Atlas-Indel,Pindel	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.4457_4469del						.																																			SO:0001589	frameshift_variant	196528	exon15			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4458_4470delTCCCGACTCAGGA	chr12.hg19:g.46246364_46246376delTCCCGACTCAGGA	ENSP00000335044:p.Val1486fs	210.0	0.0		81.0	23.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.451	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		-	46246376	TCCCGACTCAGGA	-	46246364	7	5	64	1	0	1	0	1	0	0	0	0	915	1770	62	0	4516	0	ARID2	12	46246364	Frame_Shift_Del	DEL	TCCCGACTCAGGA	TCGA-CC-A3MA-01A-11D-A20W-10	15432191	46246364	87605531	188	7905										
TMEM106C	79022	hgsc.bcm.edu	37	chr12	48359893	48359893	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccaccctgaaaatcaggaacTccaacttctacacggtggca	7	14	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:48359893T>C	ENST00000429772.2	+	5	546	c.433T>C	c.(433-435)Tcc>Ccc	p.S145P	TMEM106C_ENST00000552561.1_Missense_Mutation_p.S145P|TMEM106C_ENST00000552546.1_Missense_Mutation_p.S74P|TMEM106C_ENST00000549288.1_Intron|TMEM106C_ENST00000449758.2_Missense_Mutation_p.S145P|TMEM106C_ENST00000256686.6_Missense_Mutation_p.S145P|TMEM106C_ENST00000550552.1_Missense_Mutation_p.S145P	NM_001143842.1	NP_001137314.1	Q9BVX2	T106C_HUMAN	transmembrane protein 106C	145						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	14		Acute lymphoblastic leukemia(13;0.11)		GBM - Glioblastoma multiforme(48;0.241)		AATCAGGAACTCCAACTTCTA	0.512																																					p.S145P		Atlas-SNP	.											.	TMEM106C	24	.	0			c.T433C						.						109	93	98					12																	48359893		2203	4300	6503	SO:0001583	missense	79022	exon5			AGGAACTCCAACT	BC000854	CCDS8758.1, CCDS44867.1	12q13.1	2005-12-19				ENSG00000134291			28775	protein-coding gene	gene with protein product							Standard	NM_024056		Approved	MGC5576	uc001rqr.3	Q9BVX2	OTTHUMG00000169892	ENST00000429772.2:c.433T>C	chr12.hg19:g.48359893T>C	ENSP00000400471:p.Ser145Pro	122.0	0.0		94.0	4.0	NM_001143843	B2R998|B7Z5M4|Q3B761	Missense_Mutation	SNP	ENST00000429772.2	hg19	CCDS8758.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.98|12.98	2.101176|2.101176	0.37048|0.37048	.|.	.|.	ENSG00000134291|ENSG00000134291	ENST00000547682|ENST00000256686;ENST00000552561;ENST00000546749;ENST00000552546;ENST00000550552;ENST00000429772;ENST00000449758;ENST00000548640	.|T;T;T;T;T;T;T;T	.|0.26518	.|1.73;3.67;1.73;3.67;1.73;3.67;1.73;1.73	4.68|4.68	3.52|3.52	0.40303|0.40303	.|.	.|0.129485	.|0.53938	.|D	.|0.000049	T|T	0.21509|0.21509	0.0518|0.0518	L|L	0.45137|0.45137	1.4|1.4	0.49687|0.49687	D|D	0.999811|0.999811	.|B;B	.|0.28605	.|0.217;0.181	.|B;B	.|0.30855	.|0.121;0.074	T|T	0.03887|0.03887	-1.0995|-1.0995	5|10	.|0.23302	.|T	.|0.38	1.8348|1.8348	11.2577|11.2577	0.49063|0.49063	0.0:0.0:0.1535:0.8465|0.0:0.0:0.1535:0.8465	.|.	.|145;145	.|Q9BVX2;Q9BVX2-2	.|T106C_HUMAN;.	P|P	31|145;145;9;74;145;145;145;74	.|ENSP00000256686:S145P;ENSP00000446657:S145P;ENSP00000446622:S9P;ENSP00000448268:S74P;ENSP00000449737:S145P;ENSP00000400471:S145P;ENSP00000402705:S145P;ENSP00000447254:S74P	.|ENSP00000256686:S145P	L|S	+|+	2|1	0|0	TMEM106C|TMEM106C	46646160|46646160	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.911000|0.911000	0.54048|0.54048	2.537000|2.537000	0.45702|0.45702	1.096000|1.096000	0.41439|0.41439	0.533000|0.533000	0.62120|0.62120	CTC|TCC	.	.		0.512	TMEM106C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406452.1	NM_024056		C	48359893	T	C	48359893	3	2	64	1	0	0	0	0	1	0	0	0	16037	1551	54	2	447	2	TMEM106C	12	48359893	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2113529	48359893	85492002	189	7906										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48372091	48372091	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	caccgacgggccaggcaagcCagggaatcctctctcaccac	10	17	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:48372091C>T	ENST00000380518.3	-	43	3150	c.2986G>A	c.(2986-2988)Ggc>Agc	p.G996S	COL2A1_ENST00000337299.6_Missense_Mutation_p.G927S|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	996	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CCAGGCAAGCCAGGGAATCCT	0.647																																					p.G996S		Atlas-SNP	.											.	COL2A1	368	.	0			c.G2986A						.						133	80	98					12																	48372091		2203	4300	6503	SO:0001583	missense	1280	exon43			GCAAGCCAGGGAA	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.2986G>A	chr12.hg19:g.48372091C>T	ENSP00000369889:p.Gly996Ser	143.0	0.0		91.0	4.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676915	0.67928	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	D;D	0.99527	-6.09;-6.09	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.99806	0.9916	H	0.99336	4.52	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.998	D	0.96694	0.9513	10	0.87932	D	0	.	18.8574	0.92259	0.0:1.0:0.0:0.0	.	927;996	P02458-1;P02458	.;CO2A1_HUMAN	S	996;927;927	ENSP00000369889:G996S;ENSP00000338213:G927S	ENSP00000338213:G927S	G	-	1	0	COL2A1	46658358	1.000000	0.71417	0.949000	0.38748	0.336000	0.28762	7.751000	0.85126	2.550000	0.86006	0.462000	0.41574	GGC	.	.		0.647	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		T	48372091	C	T	48372091	3	4	64	1	0	0	0	0	1	0	0	0	3689	594	21	3	1525	3	COL2A1	12	48372091	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	12198	48372091	85479804	190	7907										
ATF7	11016	hgsc.bcm.edu	37	chr12	53911113	53911113	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	acaggggctggagaacccgtTggctctgagctttccttggg	15	10	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:53911113T>C	ENST00000548446.2	-	12	1405	c.1293A>G	c.(1291-1293)ccA>ccG	p.P431P	ATF7_ENST00000328463.7_Silent_p.P431P|ATF7_ENST00000415113.1_Silent_p.P399P|ATF7_ENST00000546661.1_5'UTR|RP11-793H13.3_ENST00000548347.1_RNA|RP11-793H13.10_ENST00000591834.1_Intron|ATF7_ENST00000420353.2_Silent_p.P420P|ATF7_ENST00000456903.4_Silent_p.P420P			P17544	ATF7_HUMAN	activating transcription factor 7	431	Essential for binding adenovirus 2 E1A.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9					Pseudoephedrine(DB00852)	GAGAACCCGTTGGCTCTGAGC	0.557																																					p.P420P		Atlas-SNP	.											.	ATF7	51	.	0			c.A1260G						.						57	60	59					12																	53911113		1986	4167	6153	SO:0001819	synonymous_variant	11016	exon12			ACCCGTTGGCTCT	X52943	CCDS44906.1, CCDS58238.1	12q13	2013-01-10				ENSG00000170653		"basic leucine zipper proteins"	792	protein-coding gene	gene with protein product		606371				1694576, 11278933	Standard	NM_006856		Approved	ATFA	uc001sdz.3	P17544	OTTHUMG00000169776	ENST00000548446.2:c.1293A>G	chr12.hg19:g.53911113T>C		144.0	0.0		89.0	4.0	NM_006856	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Silent	SNP	ENST00000548446.2	hg19																																																																																				.	.		0.557	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059		C	53911113	T	C	53911113	2	2	64	1	0	0	0	0	0	0	0	1	1086	1799	63	2		2	ATF7	12	53911113	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	5539022	53911113	79940782	191	7908										
DTX3	196403	hgsc.bcm.edu	37	chr12	58001168	58001168	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctgggggagatccagaatgcCaagacattggagaagtgccg	15	8	0	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:58001168C>T	ENST00000548198.1	+	3	2026	c.522C>T	c.(520-522)gcC>gcT	p.A174A	DTX3_ENST00000548804.1_Silent_p.A174A|DTX3_ENST00000551632.1_Silent_p.A177A|ARHGEF25_ENST00000333972.7_5'Flank|DTX3_ENST00000337737.3_Silent_p.A174A			Q8N9I9	DTX3_HUMAN	deltex 3, E3 ubiquitin ligase	174					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(6)|urinary_tract(1)	12	Melanoma(17;0.122)					TCCAGAATGCCAAGACATTGG	0.632																																					p.A174A		Atlas-SNP	.											.	DTX3	27	.	0			c.C522T						.						21	23	22					12																	58001168		1917	4113	6030	SO:0001819	synonymous_variant	196403	exon5			GAATGCCAAGACA	AK094385	CCDS41800.1, CCDS66410.1	12q13.2	2014-01-28	2014-01-28			ENSG00000178498		"RING-type (C3HC4) zinc fingers"	24457	protein-coding gene	gene with protein product		613142	"deltex 3 homolog (Drosophila)", "deltex homolog 3 (Drosophila)"			12670957	Standard	XM_005268697		Approved	FLJ34766, RNF154	uc001sow.1	Q8N9I9		ENST00000548198.1:c.522C>T	chr12.hg19:g.58001168C>T		189.0	0.0		123.0	5.0	NM_178502	Q53ZZ2|Q8NAU6|Q8NDS8	Silent	SNP	ENST00000548198.1	hg19	CCDS41800.1																																																																																			.	.		0.632	DTX3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407848.1	NM_178502		T	58001168	C	T	58001168	2	4	64	1	0	0	0	0	0	0	0	1	4797	581	21	3		3	DTX3	12	58001168	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	4090055	58001168	75850727	192	7909										
USP15	9958	hgsc.bcm.edu	37	chr12	62790141	62790141	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgccgctataatctgattgcTgtttccaaccactatggagg	9	10	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:62790141T>C	ENST00000280377.5	+	20	2695	c.2637T>C	c.(2635-2637)gcT>gcC	p.A879A	USP15_ENST00000353364.3_Silent_p.A850A|USP15_ENST00000393654.3_Silent_p.A854A	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	879	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		ATCTGATTGCTGTTTCCAACC	0.378																																					p.A879A	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.T2637C						.						127	117	120					12																	62790141		2203	4300	6503	SO:0001819	synonymous_variant	9958	exon20			GATTGCTGTTTCC	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2637T>C	chr12.hg19:g.62790141T>C		124.0	0.0		75.0	6.0	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	hg19	CCDS58251.1																																																																																			.	.		0.378	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		C	62790141	T	C	62790141	2	2	64	1	0	0	0	0	0	0	0	1	17061	1567	55	2		2	USP15	12	62790141	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	4788973	62790141	71061754	193	7910										
PPP1R12A	4659	hgsc.bcm.edu	37	chr12	80266678	80266678	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	taatatttgctccattttctAccagaaacttcaccatatca	2	11	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:80266678A>G	ENST00000450142.2	-	2	544	c.278T>C	c.(277-279)gTa>gCa	p.V93A	PPP1R12A_ENST00000437004.2_Missense_Mutation_p.V93A|PPP1R12A_ENST00000546369.1_Missense_Mutation_p.V6A|PPP1R12A_ENST00000550107.1_Missense_Mutation_p.V93A|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.V93A	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	93					centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						TCCATTTTCTACCAGAAACTT	0.358																																					p.V93A		Atlas-SNP	.											.	PPP1R12A	76	.	0			c.T278C						.						102	95	97					12																	80266678		1883	4160	6043	SO:0001583	missense	4659	exon2			TTTTCTACCAGAA	D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7618	protein-coding gene	gene with protein product	"myosin phosphatase-targeting subunit 1", "myosin binding subunit"	602021	"protein phosphatase 1, regulatory (inhibitor) subunit 12A"	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.278T>C	chr12.hg19:g.80266678A>G	ENSP00000389168:p.Val93Ala	122.0	0.0		74.0	4.0	NM_002480	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	hg19	CCDS44947.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.632309	0.87660	.	.	ENSG00000058272	ENST00000261207;ENST00000546189;ENST00000360825;ENST00000341878;ENST00000312727;ENST00000450142;ENST00000437004;ENST00000546369;ENST00000550107;ENST00000547330;ENST00000550510	T;T;T;D;T;T;T	0.83163	-0.24;-0.24;-0.24;-1.69;-0.24;-0.1;-0.17	5.02	5.02	0.67125	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	D	0.87398	0.6167	L	0.41573	1.285	0.80722	D	1	D;P;D;D	0.64830	0.993;0.878;0.982;0.994	D;D;D;D	0.83275	0.993;0.972;0.989;0.996	D	0.88754	0.3252	10	0.72032	D	0.01	.	15.0448	0.71819	1.0:0.0:0.0:0.0	.	93;93;93;93	F8W8Q6;O14974-2;O14974-3;O14974	.;.;.;MYPT1_HUMAN	A	93;93;93;93;93;93;93;6;93;93;21	ENSP00000261207:V93A;ENSP00000389168:V93A;ENSP00000416769:V93A;ENSP00000449514:V6A;ENSP00000446855:V93A;ENSP00000446816:V93A;ENSP00000447338:V21A	ENSP00000261207:V93A	V	-	2	0	PPP1R12A	78790809	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.087000	0.94110	2.006000	0.58801	0.477000	0.44152	GTA	.	.		0.358	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		G	80266678	A	G	80266678	3	3	64	1	0	0	0	0	1	0	0	0	12366	391	14	2	2910	2	PPP1R12A	12	80266678	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	17476537	80266678	53585217	194	7911										
CEP290	80184	hgsc.bcm.edu	37	chr12	88523495	88523495	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agttgataatgatcgttttcTttttttaactgatctattac	5	5	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:88523495T>C	ENST00000552810.1	-	10	1171	c.828A>G	c.(826-828)aaA>aaG	p.K276K	CEP290_ENST00000397838.3_5'Flank|CEP290_ENST00000309041.7_Silent_p.K276K	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	276					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						GATCGTTTTCTTTTTTTAACT	0.274																																					p.K276K		Atlas-SNP	.											.,1	CEP290	195	.	0			c.A828G						.						45	40	41					12																	88523495		1734	3858	5592	SO:0001819	synonymous_variant	80184	exon10			GTTTTCTTTTTTT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.828A>G	chr12.hg19:g.88523495T>C		154.0	0.0		62.0	3.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Silent	SNP	ENST00000552810.1	hg19	CCDS55858.1																																																																																			.	.		0.274	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88523495	T	C	88523495	2	2	64	1	0	0	0	0	0	0	0	1	3255	1606	56	2		2	CEP290	12	88523495	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	8256817	88523495	45328400	195	7912										
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94631455	94631455	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aataggtcttctacattaagTccattgagccacagaaagta	7	8	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:94631455T>C	ENST00000258526.4	+	10	2245	c.1996T>C	c.(1996-1998)Tcc>Ccc	p.S666P		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	666					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CTACATTAAGTCCATTGAGCC	0.408																																					p.S666P		Atlas-SNP	.											.	PLXNC1	135	.	0			c.T1996C						.						77	69	71					12																	94631455		2203	4300	6503	SO:0001583	missense	10154	exon10			ATTAAGTCCATTG	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.1996T>C	chr12.hg19:g.94631455T>C	ENSP00000258526:p.Ser666Pro	71.0	0.0		55.0	4.0	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.694898	0.48202	.	.	ENSG00000136040	ENST00000258526	T	0.80994	-1.44	5.75	2.08	0.27032	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.446825	0.25848	N	0.027909	T	0.73908	0.3647	L	0.29908	0.895	0.80722	D	1	P	0.42518	0.782	P	0.48598	0.583	T	0.70963	-0.4729	10	0.59425	D	0.04	.	7.2307	0.26040	0.1253:0.0:0.3471:0.5276	.	666	O60486	PLXC1_HUMAN	P	666	ENSP00000258526:S666P	ENSP00000258526:S666P	S	+	1	0	PLXNC1	93155586	0.999000	0.42202	0.999000	0.59377	0.991000	0.79684	2.268000	0.43338	0.509000	0.28195	0.533000	0.62120	TCC	.	.		0.408	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			C	94631455	T	C	94631455	3	2	64	1	0	0	0	0	1	0	0	0	12135	1667	58	2	2034	2	PLXNC1	12	94631455	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	6107960	94631455	39220440	196	7913										
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99447084	99447084	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gccatcatgcccaatgggtcTcatctgtaataaagaaaatt	7	9	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:99447084T>C	ENST00000547776.2	-	17	2628	c.2629A>G	c.(2629-2631)Aga>Gga	p.R877G	ANKS1B_ENST00000549558.2_Missense_Mutation_p.R103G|ANKS1B_ENST00000549025.2_Missense_Mutation_p.R46G|ANKS1B_ENST00000546960.1_Missense_Mutation_p.R103G|ANKS1B_ENST00000550693.2_Missense_Mutation_p.R103G|ANKS1B_ENST00000332712.7_Missense_Mutation_p.R103G|ANKS1B_ENST00000549493.2_Missense_Mutation_p.R103G|ANKS1B_ENST00000547010.1_Missense_Mutation_p.R453G|ANKS1B_ENST00000329257.7_Missense_Mutation_p.R877G|ANKS1B_ENST00000547446.1_Missense_Mutation_p.R72G|ANKS1B_ENST00000546568.1_Missense_Mutation_p.R103G	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	877						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		CCAATGGGTCTCATCTGTAAT	0.398																																					p.R877G		Atlas-SNP	.											.	ANKS1B	180	.	0			c.A2629G						.						46	44	44					12																	99447084		1898	4121	6019	SO:0001583	missense	56899	exon17			TGGGTCTCATCTG	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.2629A>G	chr12.hg19:g.99447084T>C	ENSP00000449629:p.Arg877Gly	93.0	0.0		71.0	4.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.21|13.21	2.168333|2.168333	0.38315|0.38315	.|.	.|.	ENSG00000185046|ENSG00000185046	ENST00000549558;ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000550693;ENST00000549025;ENST00000549493;ENST00000547446;ENST00000546568;ENST00000332712;ENST00000407362;ENST00000546960;ENST00000552245|ENST00000550778	D;D;D;D;D;D;D;D;D;D;D|.	0.81821|.	-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54|.	6.16|6.16	5.0|5.0	0.66597|0.66597	Sterile alpha motif/pointed domain (2);|.	0.057170|.	0.64402|.	D|.	0.000003|.	T|.	0.51890|.	0.1701|.	L|L	0.29908|0.29908	0.895|0.895	0.39116|0.39116	D|D	0.961567|0.961567	B;B;B;B;B;B;P;B;B;B;B|.	0.35456|.	0.006;0.0;0.02;0.159;0.024;0.0;0.502;0.001;0.032;0.064;0.024|.	B;B;B;B;B;B;B;B;B;B;B|.	0.37451|.	0.026;0.001;0.028;0.153;0.072;0.004;0.25;0.004;0.069;0.063;0.072|.	T|.	0.50457|.	-0.8826|.	10|.	0.72032|.	D|.	0.01|.	-13.3012|-13.3012	12.2552|12.2552	0.54619|0.54619	0.0:0.0:0.1417:0.8583|0.0:0.0:0.1417:0.8583	.|.	72;103;103;103;91;103;103;46;453;877;103|.	F8VPM3;Q7Z6G8-4;Q7Z6G8-5;F8VZ47;F8VQW6;Q7Z6G8-2;Q7Z6G8-3;F8VZR9;Q7Z6G8-6;Q7Z6G8;Q7Z6G8-7|.	.;.;.;.;.;.;.;.;.;ANS1B_HUMAN;.|.	G|W	103;877;453;877;452;103;46;103;72;103;103;39;103;103|148	ENSP00000448993:R103G;ENSP00000449629:R877G;ENSP00000448512:R453G;ENSP00000331381:R877G;ENSP00000447999:R103G;ENSP00000447312:R46G;ENSP00000448203:R103G;ENSP00000450015:R72G;ENSP00000448205:R103G;ENSP00000332683:R103G;ENSP00000447839:R103G|.	ENSP00000331381:R877G|.	R|X	-|-	1|3	2|0	ANKS1B|ANKS1B	97971215|97971215	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	1.738000|1.738000	0.38207|0.38207	1.116000|1.116000	0.41820|0.41820	0.528000|0.528000	0.53228|0.53228	AGA|TGA	.	.		0.398	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		C	99447084	T	C	99447084	3	2	64	1	0	0	0	0	1	0	0	0	689	1559	54	2	1348	2	ANKS1B	12	99447084	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	4815629	99447084	34404811	197	7914										
ANO4	121601	hgsc.bcm.edu	37	chr12	101333217	101333217	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gatgatgccagcagattggaAgccgggggagaggtaagagt	18	5	0	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:101333217A>G	ENST00000392977.3	+	4	495	c.285A>G	c.(283-285)gaA>gaG	p.E95E	ANO4_ENST00000538618.1_Silent_p.E261E|ANO4_ENST00000299222.9_5'UTR|ANO4_ENST00000392979.3_Silent_p.E60E			Q32M45	ANO4_HUMAN	anoctamin 4	95					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						GCAGATTGGAAGCCGGGGGAG	0.428										HNSCC(74;0.22)																											p.E60E		Atlas-SNP	.											.	ANO4	183	.	0			c.A180G						.						91	93	92					12																	101333217		2203	4300	6503	SO:0001819	synonymous_variant	121601	exon3			ATTGGAAGCCGGG	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.285A>G	chr12.hg19:g.101333217A>G		110.0	0.0		63.0	4.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Silent	SNP	ENST00000392977.3	hg19																																																																																				.	.		0.428	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		G	101333217	A	G	101333217	2	3	64	1	0	0	0	0	0	0	0	1	699	69	3	2		2	ANO4	12	101333217	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1886133	101333217	32518678	198	7915										
SYCP3	50511	hgsc.bcm.edu	37	chr12	102122736	102122736	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tggattgaagagacttccgaAcacttgctatctcttgctgc	9	10	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:102122736A>G	ENST00000392927.3	-	9	811	c.680T>C	c.(679-681)gTt>gCt	p.V227A	SYCP3_ENST00000392924.1_Missense_Mutation_p.V227A|SYCP3_ENST00000266743.2_Missense_Mutation_p.V227A|CHPT1_ENST00000229266.3_3'UTR	NM_001177948.1|NM_001177949.1|NM_153694.4	NP_001171419.1|NP_001171420.1|NP_710161.1	Q8IZU3	SYCP3_HUMAN	synaptonemal complex protein 3	227	Gln-rich.				male meiosis I (GO:0007141)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	11						AGACTTCCGAACACTTGCTAT	0.299																																					p.V227A		Atlas-SNP	.											.	SYCP3	19	.	0			c.T680C						.						115	112	113					12																	102122736		2203	4297	6500	SO:0001583	missense	50511	exon9			TTCCGAACACTTG	AF492003, AI075991	CCDS9087.1	12q23.2	2007-02-05			ENSG00000139351	ENSG00000139351			18130	protein-coding gene	gene with protein product		604759				12213195, 10854409	Standard	NM_153694		Approved		uc001tis.3	Q8IZU3	OTTHUMG00000150132	ENST00000392927.3:c.680T>C	chr12.hg19:g.102122736A>G	ENSP00000376658:p.Val227Ala	118.0	0.0		71.0	4.0	NM_001177949		Missense_Mutation	SNP	ENST00000392927.3	hg19	CCDS9087.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.463282	0.84425	.	.	ENSG00000139351	ENST00000266743;ENST00000392927;ENST00000392924	.	.	.	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000002	T	0.79695	0.4490	M	0.81682	2.555	0.58432	D	0.999997	D	0.89917	1.0	D	0.71184	0.972	T	0.82975	-0.0190	9	0.87932	D	0	-2.195	15.5193	0.75854	1.0:0.0:0.0:0.0	.	227	Q8IZU3	SYCP3_HUMAN	A	227	.	ENSP00000266743:V227A	V	-	2	0	SYCP3	100646867	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	6.341000	0.72977	2.067000	0.61834	0.374000	0.22700	GTT	.	.		0.299	SYCP3-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316478.2	NM_153694		G	102122736	A	G	102122736	3	3	64	1	0	0	0	0	1	0	0	0	15449	43	2	2	34	2	SYCP3	12	102122736	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	789519	102122736	31729159	199	7916										
STAB2	55576	hgsc.bcm.edu	37	chr12	104157304	104157304	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	taatgttgcagctcttggcaAgcagcagcctgagaatatct	10	9	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:104157304A>G	ENST00000388887.2	+	68	7727	c.7523A>G	c.(7522-7524)aAg>aGg	p.K2508R	RP11-341G23.4_ENST00000551299.1_RNA|RP11-341G23.4_ENST00000550029.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GCTCTTGGCAAGCAGCAGCCT	0.512																																					p.K2508R		Atlas-SNP	.											.	STAB2	370	.	0			c.A7523G						.						282	270	274					12																	104157304		2203	4300	6503	SO:0001583	missense	55576	exon68			TTGGCAAGCAGCA	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.7523A>G	chr12.hg19:g.104157304A>G	ENSP00000373539:p.Lys2508Arg	156.0	0.0		92.0	4.0	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	A	12.30	1.896213	0.33442	.	.	ENSG00000136011	ENST00000388887;ENST00000552777	T;T	0.64260	-0.09;0.21	4.52	2.15	0.27550	.	0.637583	0.13848	N	0.358543	T	0.46678	0.1405	L	0.49350	1.555	0.27930	N	0.937906	P	0.43094	0.799	B	0.37943	0.261	T	0.37174	-0.9717	10	0.07325	T	0.83	.	6.9649	0.24617	0.8163:0.0:0.1837:0.0	.	2508	Q8WWQ8	STAB2_HUMAN	R	2508;10	ENSP00000373539:K2508R;ENSP00000446629:K10R	ENSP00000373539:K2508R	K	+	2	0	STAB2	102681434	0.997000	0.39634	0.999000	0.59377	0.747000	0.42532	3.766000	0.55280	0.270000	0.21984	0.379000	0.24179	AAG	.	.		0.512	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			G	104157304	A	G	104157304	3	3	64	1	0	0	0	0	1	0	0	0	15253	72	3	2	7793	2	STAB2	12	104157304	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	2034568	104157304	29694591	200	7917										
NT5DC3	51559	hgsc.bcm.edu	37	chr12	104208807	104208807	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	caaggtgtaatcataatcgaAgccatagatttcaatgtctg	8	7	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:104208807A>G	ENST00000392876.3	-	2	341	c.301T>C	c.(301-303)Ttc>Ctc	p.F101L		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	101						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						TCATAATCGAAGCCATAGATT	0.403																																					p.F101L		Atlas-SNP	.											.	NT5DC3	113	.	0			c.T301C						.						124	114	118					12																	104208807		2203	4300	6503	SO:0001583	missense	51559	exon2			AATCGAAGCCATA	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.301T>C	chr12.hg19:g.104208807A>G	ENSP00000376615:p.Phe101Leu	183.0	0.0		98.0	5.0	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Missense_Mutation	SNP	ENST00000392876.3	hg19	CCDS41824.1	.	.	.	.	.	.	.	.	.	.	A	35	5.459670	0.96240	.	.	ENSG00000111696	ENST00000392876	T	0.50548	0.74	5.87	5.87	0.94306	HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.77343	0.4116	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83617	0.0137	10	0.87932	D	0	-27.9503	16.5764	0.84681	1.0:0.0:0.0:0.0	.	101	Q86UY8	NT5D3_HUMAN	L	101	ENSP00000376615:F101L	ENSP00000376615:F101L	F	-	1	0	NT5DC3	102732937	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.877000	0.92386	2.371000	0.80710	0.533000	0.62120	TTC	.	.		0.403	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575		G	104208807	A	G	104208807	3	3	64	1	0	0	0	0	1	0	0	0	10701	72	3	2	1397	2	NT5DC3	12	104208807	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	51503	104208807	29643088	201	7918										
DAO	1610	hgsc.bcm.edu	37	chr12	109288138	109288138	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agccaggccgggggcagatcAtgaaggtgagtgtgagggtg	20	6	1	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:109288138A>G	ENST00000228476.3	+	7	811	c.607A>G	c.(607-609)Atg>Gtg	p.M203V	DAO_ENST00000551281.1_Missense_Mutation_p.M137V	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	203					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	GGGGCAGATCATGAAGGTGAG	0.532																																					p.M203V		Atlas-SNP	.											.	DAO	58	.	0			c.A607G						.						48	39	42					12																	109288138		2203	4300	6503	SO:0001583	missense	1610	exon7			CAGATCATGAAGG	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.607A>G	chr12.hg19:g.109288138A>G	ENSP00000228476:p.Met203Val	83.0	0.0		44.0	4.0	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	hg19	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	A	12.85	2.062280	0.36373	.	.	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547768	T;T;T	0.79454	-1.27;-1.27;-1.27	5.51	4.3	0.51218	FAD dependent oxidoreductase (1);	0.088548	0.85682	D	0.000000	T	0.44623	0.1302	N	0.01015	-1.05	0.23435	N	0.997689	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.26155	-1.0111	10	0.02654	T	1	-18.9327	12.0939	0.53744	0.7717:0.2283:0.0:0.0	.	203;186	P14920;Q7Z312	OXDA_HUMAN;.	V	137;203;80	ENSP00000446853:M137V;ENSP00000228476:M203V;ENSP00000449967:M80V	ENSP00000228476:M203V	M	+	1	0	DAO	107812267	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.955000	0.49121	2.108000	0.64289	0.409000	0.27619	ATG	.	.		0.532	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			G	109288138	A	G	109288138	3	3	64	1	0	0	0	0	1	0	0	0	4233	217	8	2	629	2	DAO	12	109288138	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5079331	109288138	24563757	202	7919										
CIT	11113	hgsc.bcm.edu	37	chr12	120241020	120241020	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttcacttactcagatctacCaagaatccccagtgccttgc	5	14	3	2	rs145965687	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:120241020C>G	ENST00000261833.7	-	10	1337	c.1285G>C	c.(1285-1287)Ggt>Cgt	p.G429R	CIT_ENST00000392521.2_Missense_Mutation_p.G429R	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	429	AGC-kinase C-terminal.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		TCAGATCTACCAAGAATCCCC	0.532																																					p.G429R		Atlas-SNP	.											.	CIT	535	.	0			c.G1285C						.						82	84	83					12																	120241020		2203	4300	6503	SO:0001583	missense	11113	exon10			ATCTACCAAGAAT	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.1285G>C	chr12.hg19:g.120241020C>G	ENSP00000261833:p.Gly429Arg	112.0	0.0		77.0	53.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.41|14.41	2.527671|2.527671	0.44969|0.44969	.|.	.|.	ENSG00000122966|ENSG00000122966	ENST00000392521;ENST00000261833|ENST00000392520	T;T|T	0.64438|0.13307	-0.1;-0.09|2.6	5.43|5.43	5.43|5.43	0.79202|0.79202	AGC-kinase, C-terminal (1);|.	0.340590|.	0.27861|.	N|.	0.017557|.	T|T	0.09642|0.09642	0.0237|0.0237	N|N	0.08118|0.08118	0|0	0.34036|0.34036	D|D	0.654392|0.654392	B;B|.	0.22683|.	0.008;0.073|.	B;B|.	0.23716|.	0.003;0.048|.	T|T	0.26052|0.26052	-1.0114|-1.0114	10|7	0.28530|0.37606	T|T	0.3|0.19	.|.	10.2233|10.2233	0.43209|0.43209	0.0:0.9107:0.0:0.0893|0.0:0.9107:0.0:0.0893	.|.	429;429|.	Q2M5E1;O14578|.	.;CTRO_HUMAN|.	R|F	429|56	ENSP00000376306:G429R;ENSP00000261833:G429R|ENSP00000376305:L56F	ENSP00000261833:G429R|ENSP00000376305:L56F	G|L	-|-	1|3	0|2	CIT|CIT	118725403|118725403	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.429000|2.429000	0.44758|0.44758	2.546000|2.546000	0.85860|0.85860	0.655000|0.655000	0.94253|0.94253	GGT|TTG	.	C|1.000;T|0.000		0.532	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		G	120241020	C	G	120241020	3	3	64	1	0	0	0	0	1	0	0	0	3440	594	21	4	4950	4	CIT	12	120241020	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	10952882	120241020	13610875	203	7920										
CCDC62	84660	hgsc.bcm.edu	37	chr12	123285708	123285708	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cagaccttgaaaataaccacCcaaaagtcgatattaagagg	7	9	0	3	rs373036488		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:123285708C>T	ENST00000253079.6	+	9	1359	c.1015C>T	c.(1015-1017)Cca>Tca	p.P339S	CCDC62_ENST00000392441.4_Missense_Mutation_p.P339S|CCDC62_ENST00000537566.1_Missense_Mutation_p.P100S|CCDC62_ENST00000392440.2_Missense_Mutation_p.P100S	NM_201435.4	NP_958843.2	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62	339					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		AAATAACCACCCAAAAGTCGA	0.358																																					p.P339S		Atlas-SNP	.											.	CCDC62	119	.	0			c.C1015T						.						64	67	66					12																	123285708		2203	4300	6503	SO:0001583	missense	84660	exon9			AACCACCCAAAAG		CCDS9238.1	12q24.31	2009-08-18			ENSG00000130783	ENSG00000130783			30723	protein-coding gene	gene with protein product	"cancer/testis antigen 109"	613481				18563714, 19126643	Standard	NM_201435		Approved	TSP-NY, FLJ40344, CT109, ERAP75	uc001udc.3	Q6P9F0	OTTHUMG00000168764	ENST00000253079.6:c.1015C>T	chr12.hg19:g.123285708C>T	ENSP00000253079:p.Pro339Ser	124.0	0.0		81.0	4.0	NM_201435	A8K8V1|B3KUP3|Q6ZVF2|Q86VJ0|Q9BYZ5	Missense_Mutation	SNP	ENST00000253079.6	hg19	CCDS9238.1	.	.	.	.	.	.	.	.	.	.	C	6.804	0.517475	0.13005	.	.	ENSG00000130783	ENST00000253079;ENST00000392441;ENST00000537566;ENST00000392440	T;T;T;T	0.47177	1.47;1.47;0.85;0.85	5.41	0.358	0.16084	.	0.628588	0.14138	N	0.338882	T	0.29817	0.0745	L	0.29908	0.895	0.09310	N	1	B;B;B	0.20671	0.047;0.018;0.009	B;B;B	0.18561	0.019;0.022;0.007	T	0.22626	-1.0211	10	0.16896	T	0.51	0.043	7.9296	0.29895	0.0:0.5458:0.0:0.4542	.	339;100;339	Q6P9F0-2;Q6P9F0-3;Q6P9F0	.;.;CCD62_HUMAN	S	339;339;100;100	ENSP00000253079:P339S;ENSP00000376236:P339S;ENSP00000445045:P100S;ENSP00000376235:P100S	ENSP00000253079:P339S	P	+	1	0	CCDC62	121851661	0.138000	0.22547	0.043000	0.18650	0.432000	0.31715	0.298000	0.19120	-0.210000	0.10140	-0.150000	0.13652	CCA	.	.		0.358	CCDC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400930.1	NM_032573		T	123285708	C	T	123285708	3	4	64	1	0	0	0	0	1	0	0	0	2835	623	22	3	1049	3	CCDC62	12	123285708	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	3044688	123285708	10566187	204	7921										
DDX55	57696	hgsc.bcm.edu	37	chr12	124104625	124104625	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttgagaagggcttgttgacaActggcaaaagaacaatcaag	11	6	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:124104625A>G	ENST00000238146.4	+	14	1791	c.1741A>G	c.(1741-1743)Act>Gct	p.T581A	DDX55_ENST00000538744.1_Missense_Mutation_p.T550A|DDX55_ENST00000421670.3_Missense_Mutation_p.T188A	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	581						membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		CTTGTTGACAACTGGCAAAAG	0.398																																					p.T581A		Atlas-SNP	.											.	DDX55	51	.	0			c.A1741G						.						104	103	104					12																	124104625		2203	4300	6503	SO:0001583	missense	57696	exon14			TTGACAACTGGCA	AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"DEAD-boxes"	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.1741A>G	chr12.hg19:g.124104625A>G	ENSP00000238146:p.Thr581Ala	149.0	0.0		88.0	4.0	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Missense_Mutation	SNP	ENST00000238146.4	hg19	CCDS9251.1	.	.	.	.	.	.	.	.	.	.	A	9.954	1.220976	0.22457	.	.	ENSG00000111364	ENST00000238146;ENST00000538744;ENST00000421670	T;T;T	0.40756	4.11;3.83;1.02	5.85	2.08	0.27032	.	2.145490	0.01173	N	0.006909	T	0.24353	0.0590	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20739	-1.0266	10	0.08837	T	0.75	-18.306	1.0416	0.01560	0.4427:0.1518:0.2584:0.147	.	581	Q8NHQ9	DDX55_HUMAN	A	581;550;188	ENSP00000238146:T581A;ENSP00000443114:T550A;ENSP00000442332:T188A	ENSP00000238146:T581A	T	+	1	0	DDX55	122670578	0.006000	0.16342	0.766000	0.31476	0.917000	0.54804	0.200000	0.17257	1.038000	0.40049	0.533000	0.62120	ACT	.	.		0.398	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2			G	124104625	A	G	124104625	3	3	64	1	0	0	0	0	1	0	0	0	4375	43	2	2	1795	2	DDX55	12	124104625	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	818917	124104625	9747270	205	7922										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124824953	124824953	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctcgctcccgctcggacgagGacgtggtggttggttttgtc	15	11	0	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr12:124824953G>A	ENST00000405201.1	-	36	5375	c.5375C>T	c.(5374-5376)tCc>tTc	p.S1792F	NCOR2_ENST00000404621.1_Missense_Mutation_p.S1782F|NCOR2_ENST00000429285.2_Missense_Mutation_p.S1782F|NCOR2_ENST00000356219.3_Missense_Mutation_p.S1799F|NCOR2_ENST00000404121.2_Missense_Mutation_p.S1353F|NCOR2_ENST00000397355.1_Missense_Mutation_p.S1783F			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1800					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		CTCGGACGAGGACGTGGTGGT	0.622																																					p.S1792F		Atlas-SNP	.											.	NCOR2	475	.	0			c.C5375T						.						71	81	77					12																	124824953		2080	4215	6295	SO:0001583	missense	9612	exon38			GACGAGGACGTGG	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5375C>T	chr12.hg19:g.124824953G>A	ENSP00000384018:p.Ser1792Phe	90.0	0.0		51.0	4.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	G	11.24	1.580150	0.28180	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285	T;T;T;T;T;T	0.20881	2.05;2.3;2.04;2.3;2.04;2.3	3.89	3.89	0.44902	.	0.424514	0.24029	N	0.042206	T	0.38532	0.1044	L	0.43152	1.355	0.44432	D	0.997353	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.78314	0.915;0.991;0.961	T	0.30794	-0.9966	10	0.72032	D	0.01	-11.8694	15.4561	0.75314	0.0:0.0:1.0:0.0	.	1782;1783;1792	C9J0Q5;C9J239;C9JFD3	.;.;.	F	1792;1782;1799;1783;1791;1353;1782	ENSP00000384018:S1792F;ENSP00000384202:S1782F;ENSP00000348551:S1799F;ENSP00000380513:S1783F;ENSP00000385618:S1353F;ENSP00000400281:S1782F	ENSP00000348551:S1799F	S	-	2	0	NCOR2	123390906	0.963000	0.33076	0.356000	0.25785	0.152000	0.21847	6.150000	0.71801	1.701000	0.51217	0.491000	0.48974	TCC	.	.		0.622	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124824953	G	A	124824953	3	1	64	1	0	0	0	0	1	0	0	0	10245	1174	41	3	2217	3	NCOR2	12	124824953	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	720328	124824953	9026942	206	7923										
SACS	26278	hgsc.bcm.edu	37	chr13	23909856	23909856	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aaagattctggaccattctgTctgatgctggaacagacgaa	10	8	3	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr13:23909856T>C	ENST00000382292.3	-	9	8432	c.8159A>G	c.(8158-8160)gAc>gGc	p.D2720G	SACS_ENST00000382298.3_Missense_Mutation_p.D2720G|SACS_ENST00000402364.1_Missense_Mutation_p.D1970G			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2720					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GACCATTCTGTCTGATGCTGG	0.373																																					p.D2720G		Atlas-SNP	.											.	SACS	871	.	0			c.A8159G						.						69	70	70					13																	23909856		2203	4299	6502	SO:0001583	missense	26278	exon10			ATTCTGTCTGATG	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.8159A>G	chr13.hg19:g.23909856T>C	ENSP00000371729:p.Asp2720Gly	106.0	0.0		72.0	4.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	25.4	4.635701	0.87760	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.93811	-3.29;-3.29;-3.29	5.56	5.56	0.83823	ATPase-like, ATP-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95089	0.8409	L	0.44542	1.39	0.53688	D	0.999978	D	0.89917	1.0	D	0.87578	0.998	D	0.95378	0.8470	10	0.56958	D	0.05	.	15.7067	0.77588	0.0:0.0:0.0:1.0	.	2720	Q9NZJ4	SACS_HUMAN	G	2720;1970;2720	ENSP00000371729:D2720G;ENSP00000385844:D1970G;ENSP00000371735:D2720G	ENSP00000371729:D2720G	D	-	2	0	SACS	22807856	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.698000	0.84413	2.116000	0.64780	0.379000	0.24179	GAC	.	.		0.373	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23909856	T	C	23909856	3	2	64	1	0	0	0	0	1	0	0	0	13819	1667	58	2	5584	2	SACS	13	23909856	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		23909856	91260022	207	7924										
FLT3	2322	hgsc.bcm.edu	37	chr13	28608538	28608538	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgttgtcttggatgaaagggAaggggcctgcaacaaaagag	15	5	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr13:28608538A>G	ENST00000241453.7	-	13	1685	c.1604T>C	c.(1603-1605)tTc>tCc	p.F535S	FLT3_ENST00000537084.1_Missense_Mutation_p.F535S|FLT3_ENST00000380982.4_Missense_Mutation_p.F535S	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	535					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	GATGAAAGGGAAGGGGCCTGC	0.388			"Mis, O"		"AML, ALL"																																p.F535S		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.T1604C						.						84	78	80					13																	28608538		2203	4300	6503	SO:0001583	missense	2322	exon13			AAAGGGAAGGGGC	U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1604T>C	chr13.hg19:g.28608538A>G	ENSP00000241453:p.Phe535Ser	144.0	0.0		90.0	4.0	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	hg19	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.451128	0.43531	.	.	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	T;T;T	0.77098	-1.0;-1.07;-0.79	5.62	4.39	0.52855	.	0.370601	0.26324	N	0.025031	T	0.59582	0.2204	N	0.22421	0.69	0.28042	N	0.933702	B;B	0.30664	0.014;0.289	B;B	0.23275	0.014;0.045	T	0.50608	-0.8808	10	0.19590	T	0.45	.	10.0892	0.42436	0.8513:0.0:0.0:0.1487	.	535;535	P36888-2;P36888	.;FLT3_HUMAN	S	535	ENSP00000241453:F535S;ENSP00000370369:F535S;ENSP00000438139:F535S	ENSP00000241453:F535S	F	-	2	0	FLT3	27506538	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	4.966000	0.63715	2.139000	0.66308	0.533000	0.62120	TTC	.	.		0.388	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			G	28608538	A	G	28608538	3	3	64	1	0	0	0	0	1	0	0	0	5950	246	9	2	1425	2	FLT3	13	28608538	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	4698682	28608538	86561340	208	7925										
RB1	5925	hgsc.bcm.edu	37	chr13	49027248	49027248	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aatcacactgcagcagatatGtaagcaaaatatatgttatg	7	6	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr13:49027248G>A	ENST00000267163.4	+	18	1952		c.e18+1			NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(12)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CAGCAGATATGTAAGCAAAAT	0.338		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											.		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	RB1_ENST00000267163,bladder,carcinoma,0,1	RB1	1068	.	27	Whole gene deletion(15)|Unknown(12)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|urinary_tract(3)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|lung(1)|liver(1)	c.1814+1G>A	GRCh37	CS961682	RB1	S		.						85	81	82					13																	49027248		2203	4300	6503	SO:0001630	splice_region_variant	5925	exon18	Familial Cancer Database		AGATATGTAAGCA	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1814+1G>A	chr13.hg19:g.49027248G>A		40.0	0.0		24.0	2.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Splice_Site	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.362184	0.82353	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5489	0.95310	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RB1	47925249	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	7.717000	0.84732	2.717000	0.92951	0.655000	0.94253	.	.	.		0.338	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		Intron	A	49027248	G	A	49027248	5	1	64	1	0	0	0	0	0	0	1	0	13113	1391	48	3	1885	3	RB1	13	49027248	Splice_Site	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	20418710	49027248	66142630	209	7926										
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60240729	60240729	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cagtttaacttataaagctcGtaatcttgccagcagggctt	8	9	1	0	rs546723182		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr13:60240729G>A	ENST00000400324.4	-	28	3791	c.3571C>T	c.(3571-3573)Cga>Tga	p.R1191*	DIAPH3_ENST00000400320.1_Nonsense_Mutation_p.R1145*|DIAPH3_ENST00000377908.2_Nonsense_Mutation_p.R1180*|DIAPH3_ENST00000400319.1_Nonsense_Mutation_p.R1121*|DIAPH3_ENST00000400330.1_Nonsense_Mutation_p.R1191*	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	1191					actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		TATAAAGCTCGTAATCTTGCC	0.323																																					p.R1191X		Atlas-SNP	.											DIAPH3,colon,carcinoma,0,1	DIAPH3	139	.	0			c.C3571T						.						66	62	63					13																	60240729		1802	4064	5866	SO:0001587	stop_gained	81624	exon28			AAGCTCGTAATCT	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.3571C>T	chr13.hg19:g.60240729G>A	ENSP00000383178:p.Arg1191*	80.0	0.0		50.0	2.0	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Nonsense_Mutation	SNP	ENST00000400324.4	hg19	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	G	41	8.741087	0.98935	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320	.	.	.	5.55	3.72	0.42706	.	1.783920	0.04654	U	0.407671	.	.	.	.	.	.	0.21064	N	0.999792	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.3327	0.49485	0.0696:0.0:0.8023:0.1281	.	.	.	.	X	1191;1191;1180;1145;1121;1180;1121;1145	.	ENSP00000367141:R1180X	R	-	1	2	DIAPH3	59138730	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.694000	0.47035	2.602000	0.87976	0.655000	0.94253	CGA	.	.		0.323	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		A	60240729	G	A	60240729	4	1	64	1	0	0	0	0	0	1	0	0	4522	1153	40	1	14	1	DIAPH3	13	60240729	Nonsense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	11213481	60240729	54929149	210	7927										
SLITRK6	84189	hgsc.bcm.edu	37	chr13	86370190	86370190	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cttgctaaaggcacttggttCaatcactgtgataaaattgt	8	7	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr13:86370190C>T	ENST00000400286.2	-	2	1052	c.454G>A	c.(454-456)Gaa>Aaa	p.E152K		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	152					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		GCACTTGGTTCAATCACTGTG	0.353																																					p.E152K		Atlas-SNP	.											.	SLITRK6	150	.	0			c.G454A						.						126	119	121					13																	86370190		1853	4084	5937	SO:0001583	missense	84189	exon2			TTGGTTCAATCAC	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.454G>A	chr13.hg19:g.86370190C>T	ENSP00000383143:p.Glu152Lys	124.0	0.0		72.0	4.0	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	hg19	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.479653	0.84747	.	.	ENSG00000184564	ENST00000400286	T	0.53206	0.63	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.57460	0.2055	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.51810	-0.8658	10	0.33940	T	0.23	-20.3885	19.4432	0.94831	0.0:1.0:0.0:0.0	.	152	Q9H5Y7	SLIK6_HUMAN	K	152	ENSP00000383143:E152K	ENSP00000383143:E152K	E	-	1	0	SLITRK6	85268191	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GAA	.	.		0.353	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		T	86370190	C	T	86370190	3	4	64	1	0	0	0	0	1	0	0	0	14762	835	29	3	2075	3	SLITRK6	13	86370190	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	26129461	86370190	28799688	211	7928										
FARP1	10160	hgsc.bcm.edu	37	chr13	99038053	99038053	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctggccgttgccaacacgggAattctagtgtttcaggtgag	13	9	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr13:99038053A>T	ENST00000319562.6	+	8	1009	c.744A>T	c.(742-744)ggA>ggT	p.G248G	FARP1_ENST00000595437.1_Silent_p.G248G|FARP1_ENST00000376586.2_Silent_p.G248G	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	248	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CCAACACGGGAATTCTAGTGT	0.537																																					p.G248G		Atlas-SNP	.											.	FARP1	207	.	0			c.A744T						.						99	85	90					13																	99038053		2203	4300	6503	SO:0001819	synonymous_variant	10160	exon8			CACGGGAATTCTA	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.744A>T	chr13.hg19:g.99038053A>T		25.0	0.0		39.0	20.0	NM_005766	Q5JVI9|Q6IQ29	Silent	SNP	ENST00000319562.6	hg19	CCDS9487.1																																																																																			.	.		0.537	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		T	99038053	A	T	99038053	2	4	64	1	0	0	0	0	0	0	0	1	5684	233	9	4		4	FARP1	13	99038053	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	12667863	99038053	16131825	212	7929										
TM9SF2	9375	hgsc.bcm.edu	37	chr13	100172292	100172292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	taaatattcttctcccaggtTtgatttttgccaagcatcag	6	9	3	1	rs376468098		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr13:100172292T>C	ENST00000376387.4	+	3	432	c.242T>C	c.(241-243)tTt>tCt	p.F81S	TM9SF2_ENST00000463709.1_3'UTR	NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	81					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					TCTCCCAGGTTTGATTTTTGC	0.368																																					p.F81S		Atlas-SNP	.											.	TM9SF2	52	.	0			c.T242C						.						67	67	67					13																	100172292		2203	4300	6503	SO:0001583	missense	9375	exon3			CCAGGTTTGATTT	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.242T>C	chr13.hg19:g.100172292T>C	ENSP00000365567:p.Phe81Ser	75.0	0.0		86.0	4.0	NM_004800	A8K399|Q2TAY5	Missense_Mutation	SNP	ENST00000376387.4	hg19	CCDS9493.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.046988	0.75846	.	.	ENSG00000125304	ENST00000376387	T	0.50277	0.75	5.75	5.75	0.90469	.	0.045387	0.85682	D	0.000000	T	0.71929	0.3398	H	0.95611	3.695	0.80722	D	1	D;P	0.52996	0.957;0.721	P;P	0.52267	0.694;0.694	T	0.81961	-0.0693	10	0.87932	D	0	-19.6936	16.0933	0.81104	0.0:0.0:0.0:1.0	.	81;81	E9PHW5;Q99805	.;TM9S2_HUMAN	S	81	ENSP00000365567:F81S	ENSP00000365567:F81S	F	+	2	0	TM9SF2	98970293	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	6.592000	0.74095	2.207000	0.71202	0.477000	0.44152	TTT	.	.		0.368	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3			C	100172292	T	C	100172292	3	2	64	1	0	0	0	0	1	0	0	0	15993	1841	64	2	252	2	TM9SF2	13	100172292	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1134239	100172292	14997586	213	7930										
F10	2159	hgsc.bcm.edu	37	chr13	113803258	113803258	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aacacggagcaggaggagggCggtgaggcggtgcacgaggt	21	7	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr13:113803258C>T	ENST00000375559.3	+	8	932	c.894C>T	c.(892-894)ggC>ggT	p.G298G	F10_ENST00000375551.3_Missense_Mutation_p.A295V|F10_ENST00000409306.1_Missense_Mutation_p.A297V	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	298	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(4)|lung(10)|pancreas(1)|stomach(1)	18	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Antihemophilic Factor(DB00025)|Apixaban(DB06605)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Menadione(DB00170)|Rivaroxaban(DB06228)	AGGAGGAGGGCGGTGAGGCGG	0.607																																					p.G298G		Atlas-SNP	.											.	F10	53	.	0			c.C894T						.						161	136	144					13																	113803258		2203	4300	6503	SO:0001819	synonymous_variant	2159	exon8			GGAGGGCGGTGAG		CCDS9530.1	13q34	2012-10-02			ENSG00000126218	ENSG00000126218	3.4.21.6		3528	protein-coding gene	gene with protein product		613872					Standard	XM_005268298		Approved		uc001vsx.3	P00742	OTTHUMG00000017374	ENST00000375559.3:c.894C>T	chr13.hg19:g.113803258C>T		361.0	0.0		420.0	26.0	NM_000504	Q14340	Silent	SNP	ENST00000375559.3	hg19	CCDS9530.1	.	.	.	.	.	.	.	.	.	.	C	0.094	-1.162845	0.01673	.	.	ENSG00000126218	ENST00000409306;ENST00000375551	D;D	0.95656	-3.71;-3.77	4.99	-0.441	0.12257	.	.	.	.	.	D	0.90710	0.7085	.	.	.	0.09310	N	1	P;P	0.44006	0.824;0.824	B;B	0.41135	0.24;0.348	T	0.82995	-0.0180	8	0.38643	T	0.18	.	5.7129	0.17945	0.2181:0.3549:0.359:0.0681	.	297;295	B7ZBK1;Q5JVE8	.;.	V	297;295	ENSP00000387092:A297V;ENSP00000364701:A295V	ENSP00000364701:A295V	A	+	2	0	F10	112851259	0.244000	0.23889	0.153000	0.22517	0.139000	0.21198	0.516000	0.22817	0.101000	0.17610	0.313000	0.20887	GCG	.	.		0.607	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3			T	113803258	C	T	113803258	2	4	64	1	0	0	0	0	0	0	0	1	5338	755	27	1		1	F10	13	113803258	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	13630966	113803258	1366620	214	7931										
DCUN1D2	55208	hgsc.bcm.edu	37	chr13	114112422	114112422	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tctataagaacgggccaagcTcctaaaggaaagcaagcaaa	9	9	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr13:114112422T>C	ENST00000478244.1	-	7	984	c.702A>G	c.(700-702)ggA>ggG	p.G234G	DCUN1D2_ENST00000332592.3_Splice_Site_p.G101G	NM_001014283.1	NP_001014305.1	Q6PH85	DCNL2_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 2	234	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.									breast(1)|endometrium(1)|large_intestine(1)|lung(3)|stomach(1)	7	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.029)|GBM - Glioblastoma multiforme(44;0.234)			CGGGCCAAGCTCCTAAAGGAA	0.438											OREG0022535	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G234G		Atlas-SNP	.											.	DCUN1D2	17	.	0			c.A702G						.						152	157	155					13																	114112422		2203	4300	6503	SO:0001630	splice_region_variant	55208	exon7			CCAAGCTCCTAAA	AK001566	CCDS32013.1	13q34	2013-06-10	2013-06-10	2005-10-04	ENSG00000150401	ENSG00000150401			20328	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 17", "DCN1, defective in cullin neddylation 1, domain containing 2 (S. cerevisiae)"	C13orf17		15988528	Standard	XM_005268320		Approved	FLJ10704, FLJ20092	uc001vtr.1	Q6PH85	OTTHUMG00000017390	ENST00000478244.1:c.701-1A>G	chr13.hg19:g.114112422T>C		79.0	0.0	1455	89.0	5.0	NM_001014283	Q5JSA5|Q5JSA6|Q5JSA7|Q9NVJ1|Q9NXR6	Silent	SNP	ENST00000478244.1	hg19	CCDS32013.1																																																																																			.	.		0.438	DCUN1D2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045938.4	NM_018185	Silent	C	114112422	T	C	114112422	5	2	64	1	0	0	0	0	0	0	1	0	4316	1565	54	2	81	2	DCUN1D2	13	114112422	Splice_Site	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	309164	114112422	1057456	215	7932										
OR11H6	122748	hgsc.bcm.edu	37	chr14	20692756	20692756	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aagatcatcactctggtataCacagcaatgactccattctt	5	11	4	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:20692756C>T	ENST00000315519.2	+	1	966	c.888C>T	c.(886-888)taC>taT	p.Y296Y		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	296						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		CTCTGGTATACACAGCAATGA	0.423																																					p.Y296Y		Atlas-SNP	.											.	OR11H6	60	.	0			c.C888T						.						116	112	113					14																	20692756		2203	4300	6503	SO:0001819	synonymous_variant	122748	exon1			GGTATACACAGCA		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"GPCR / Class A : Olfactory receptors"	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.888C>T	chr14.hg19:g.20692756C>T		117.0	0.0		97.0	4.0	NM_001004480	Q6IF08	Silent	SNP	ENST00000315519.2	hg19	CCDS32033.1																																																																																			.	.		0.423	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1			T	20692756	C	T	20692756	2	4	64	1	0	0	0	0	0	0	0	1	10938	489	17	3		3	OR11H6	14	20692756	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10		20692756	86656784	216	7933										
TEP1	7011	hgsc.bcm.edu	37	chr14	20859791	20859791	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctctttggacagagcctgtcTgcattagcatctgtcagata	9	10	4	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:20859791T>C	ENST00000262715.5	-	13	2104	c.2064A>G	c.(2062-2064)gcA>gcG	p.A688A	TEP1_ENST00000556935.1_Silent_p.A580A	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	688					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AGAGCCTGTCTGCATTAGCAT	0.542																																					p.A688A		Atlas-SNP	.											.	TEP1	224	.	0			c.A2064G						.						150	131	137					14																	20859791		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon13			CCTGTCTGCATTA		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.2064A>G	chr14.hg19:g.20859791T>C		149.0	0.0		72.0	4.0	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	.		0.542	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		C	20859791	T	C	20859791	2	2	64	1	0	0	0	0	0	0	0	1	15774	1567	55	2		2	TEP1	14	20859791	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	167035	20859791	86489749	217	7934										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23530644	23530644	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atcgagtccgctcccgccgcTccatttcccgttcccgttct	7	19	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:23530644T>C	ENST00000262710.1	-	17	3788	c.3461A>G	c.(3460-3462)gAg>gGg	p.E1154G	ACIN1_ENST00000357481.2_Missense_Mutation_p.E396G|ACIN1_ENST00000557515.1_Missense_Mutation_p.E395G|ACIN1_ENST00000397341.3_Missense_Mutation_p.E396G|ACIN1_ENST00000457657.1_Missense_Mutation_p.E1114G|ACIN1_ENST00000605057.1_Missense_Mutation_p.E1096G|ACIN1_ENST00000555053.1_Missense_Mutation_p.E1141G|ACIN1_ENST00000338631.6_Missense_Mutation_p.E427G	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	1154	Arg/Asp/Glu/Lys-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		CTCCCGCCGCTCCATTTCCCG	0.677																																					p.E1154G		Atlas-SNP	.											.	ACIN1	147	.	0			c.A3461G						.						62	65	64					14																	23530644		2203	4300	6503	SO:0001583	missense	22985	exon17			CGCCGCTCCATTT	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.3461A>G	chr14.hg19:g.23530644T>C	ENSP00000262710:p.Glu1154Gly	136.0	0.0		89.0	4.0	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.306310	0.81247	.	.	ENSG00000100813	ENST00000557515;ENST00000338631;ENST00000357481;ENST00000262710;ENST00000457657;ENST00000397341;ENST00000555053	T;T;T;T;T;T;T	0.08008	3.14;3.14;3.14;3.14;3.14;3.14;3.14	4.79	3.63	0.41609	.	0.000000	0.40064	N	0.001186	T	0.16257	0.0391	L	0.52573	1.65	0.54753	D	0.999981	D;D;P;P;P	0.59767	0.986;0.976;0.935;0.844;0.844	P;P;P;B;B	0.58721	0.844;0.703;0.575;0.347;0.347	T	0.01252	-1.1405	10	0.36615	T	0.2	-13.8898	9.8837	0.41249	0.0:0.0831:0.0:0.9169	.	1141;1154;1114;427;396	G3V3M7;Q9UKV3;E7EQT4;Q9UKV3-2;Q9UKV3-3	.;ACINU_HUMAN;.;.;.	G	395;427;396;1154;1114;396;1141	ENSP00000451138:E395G;ENSP00000345541:E427G;ENSP00000350073:E396G;ENSP00000262710:E1154G;ENSP00000405677:E1114G;ENSP00000380502:E396G;ENSP00000451328:E1141G	ENSP00000262710:E1154G	E	-	2	0	ACIN1	22600484	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.439000	0.73430	0.940000	0.37473	0.460000	0.39030	GAG	.	.		0.677	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23530644	T	C	23530644	3	2	64	1	0	0	0	0	1	0	0	0	142	1551	54	2	576	2	ACIN1	14	23530644	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2670853	23530644	83818896	218	7935										
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24884365	24884365	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggaccaggagcatgaggaggCcttcctggccctgaagcgag	16	11	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:24884365C>T	ENST00000382554.3	+	9	3728	c.3410C>T	c.(3409-3411)gCc>gTc	p.A1137V		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1137					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						CATGAGGAGGCCTTCCTGGCC	0.657																																					p.A1137V		Atlas-SNP	.											.	NYNRIN	120	.	0			c.C3410T						.						37	43	41					14																	24884365		2089	4196	6285	SO:0001583	missense	57523	exon9			AGGAGGCCTTCCT	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.3410C>T	chr14.hg19:g.24884365C>T	ENSP00000371994:p.Ala1137Val	36.0	0.0		15.0	12.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.725702	0.69074	.	.	ENSG00000205978	ENST00000382554	T	0.54279	0.58	4.61	4.61	0.57282	.	.	.	.	.	T	0.60945	0.2308	M	0.72353	2.195	0.26064	N	0.981317	D	0.54047	0.964	P	0.49561	0.615	T	0.58702	-0.7590	9	0.87932	D	0	.	12.8162	0.57667	0.0:1.0:0.0:0.0	.	1137	Q9P2P1	NYNRI_HUMAN	V	1137	ENSP00000371994:A1137V	ENSP00000371994:A1137V	A	+	2	0	NYNRIN	23954205	0.997000	0.39634	1.000000	0.80357	0.987000	0.75469	3.304000	0.51866	2.379000	0.81126	0.561000	0.74099	GCC	.	.		0.657	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			T	24884365	C	T	24884365	3	4	64	1	0	0	0	0	1	0	0	0	10805	739	26	3	3440	3	NYNRIN	14	24884365	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	1353721	24884365	82465175	219	7936										
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24885708	24885708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atgtgaaagattactgcaggAgctgcttgttctgcatcccc	10	10	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:24885708A>G	ENST00000382554.3	+	9	5071	c.4753A>G	c.(4753-4755)Agc>Ggc	p.S1585G		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1585					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						TTACTGCAGGAGCTGCTTGTT	0.587																																					p.S1585G		Atlas-SNP	.											.	NYNRIN	120	.	0			c.A4753G						.						49	52	51					14																	24885708		2015	4170	6185	SO:0001583	missense	57523	exon9			TGCAGGAGCTGCT	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.4753A>G	chr14.hg19:g.24885708A>G	ENSP00000371994:p.Ser1585Gly	83.0	0.0		55.0	4.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	A	11.00	1.511102	0.27036	.	.	ENSG00000205978	ENST00000382554;ENST00000206466	T	0.10573	2.86	5.25	4.05	0.47172	.	0.195318	0.31660	N	0.007269	T	0.05090	0.0136	N	0.12887	0.27	0.24807	N	0.992663	P	0.42409	0.779	B	0.37989	0.262	T	0.26643	-1.0097	10	0.48119	T	0.1	.	4.6423	0.12555	0.743:0.0:0.0889:0.1681	.	1585	Q9P2P1	NYNRI_HUMAN	G	1585;114	ENSP00000371994:S1585G	ENSP00000206466:S114G	S	+	1	0	NYNRIN	23955548	1.000000	0.71417	1.000000	0.80357	0.195000	0.23768	2.786000	0.47790	2.194000	0.70268	0.533000	0.62120	AGC	.	.		0.587	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			G	24885708	A	G	24885708	3	3	64	1	0	0	0	0	1	0	0	0	10805	304	11	2	4783	2	NYNRIN	14	24885708	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1343	24885708	82463832	220	7937										
STRN3	29966	hgsc.bcm.edu	37	chr14	31425396	31425396	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttattcttcttactaagtccTtcttcaggttctcttgacct	4	11	5	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:31425396T>C	ENST00000357479.5	-	2	531	c.335A>G	c.(334-336)aAg>aGg	p.K112R	STRN3_ENST00000355683.5_Missense_Mutation_p.K112R	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	112					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		TACTAAGTCCTTCTTCAGGTT	0.323																																					p.K112R		Atlas-SNP	.											.	STRN3	117	.	0			c.A335G						.						173	148	157					14																	31425396		2203	4298	6501	SO:0001583	missense	29966	exon2			AAGTCCTTCTTCA		CCDS9641.1, CCDS41938.1	14q13-q21	2013-01-10			ENSG00000196792	ENSG00000196792		"WD repeat domain containing"	15720	protein-coding gene	gene with protein product	"cell cycle S/G2 nuclear autoantigen"	614766				7864889, 10681496	Standard	NM_014574		Approved	SG2NA	uc001wqu.2	Q13033	OTTHUMG00000140201	ENST00000357479.5:c.335A>G	chr14.hg19:g.31425396T>C	ENSP00000350071:p.Lys112Arg	148.0	0.0		93.0	4.0	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Missense_Mutation	SNP	ENST00000357479.5	hg19	CCDS41938.1	.	.	.	.	.	.	.	.	.	.	t	15.92	2.976434	0.53720	.	.	ENSG00000196792	ENST00000355683;ENST00000357479	D;D	0.85258	-1.96;-1.96	5.26	5.26	0.73747	Striatin, N-terminal (1);	0.086613	0.85682	D	0.000000	T	0.80639	0.4661	L	0.48174	1.505	0.41730	D	0.989555	B;P	0.37914	0.372;0.611	B;B	0.36959	0.114;0.237	T	0.78420	-0.2211	10	0.19147	T	0.46	-6.4889	15.4709	0.75439	0.0:0.0:0.0:1.0	.	112;112	Q13033-2;Q13033	.;STRN3_HUMAN	R	112	ENSP00000347909:K112R;ENSP00000350071:K112R	ENSP00000347909:K112R	K	-	2	0	STRN3	30495147	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	6.102000	0.71486	2.111000	0.64477	0.454000	0.30748	AAG	.	.		0.323	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574		C	31425396	T	C	31425396	3	2	64	1	0	0	0	0	1	0	0	0	15345	1609	56	2	2126	2	STRN3	14	31425396	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	6539688	31425396	75924144	221	7938										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31583498	31583498	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctaaaataacttaccattttTccattttccttttctttatc	0	10	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:31583498T>C	ENST00000399332.1	-	31	6155	c.5667A>G	c.(5665-5667)ggA>ggG	p.G1889G	HECTD1_ENST00000553700.1_Silent_p.G1889G	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1889					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTACCATTTTTCCATTTTCCT	0.274																																					p.G1889G		Atlas-SNP	.											.	HECTD1	159	.	0			c.A5667G						.						78	68	71					14																	31583498		1803	4059	5862	SO:0001819	synonymous_variant	25831	exon31			CATTTTTCCATTT	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.5667A>G	chr14.hg19:g.31583498T>C		204.0	0.0		98.0	4.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	T	5.688	0.311445	0.10789	.	.	ENSG00000092148	ENST00000554882	.	.	.	5.72	1.68	0.24146	.	.	.	.	.	T	0.51295	0.1666	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34428	-0.9829	4	.	.	.	-12.7179	4.976	0.14140	0.0:0.2838:0.1454:0.5707	.	.	.	.	G	255	.	.	E	-	2	0	HECTD1	30653249	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	0.770000	0.26618	0.036000	0.15547	0.482000	0.46254	GAA	.	.		0.274	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			C	31583498	T	C	31583498	2	2	64	1	0	0	0	0	0	0	0	1	7048	1770	62	2		2	HECTD1	14	31583498	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	158102	31583498	75766042	222	7939										
C14orf126	112487	hgsc.bcm.edu	37	chr14	31917645	31917645	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctgtctcacttaatttcacaTttaacagtgtattaactggg	6	8	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:31917645T>C	ENST00000310850.4	-	3	313	c.197A>G	c.(196-198)aAt>aGt	p.N66S	CTD-2213F21.2_ENST00000502430.2_RNA|RP11-176H8.1_ENST00000547378.1_Intron|DTD2_ENST00000356180.4_Missense_Mutation_p.N66S	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	66					D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)										TAATTTCACATTTAACAGTGT	0.358																																					p.N66S		Atlas-SNP	.											.	.	.	.	0			c.A197G						.						74	78	77					14																	31917645		2203	4300	6503	SO:0001583	missense	112487	exon3			TTCACATTTAACA	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 126"	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.197A>G	chr14.hg19:g.31917645T>C	ENSP00000312224:p.Asn66Ser	123.0	0.0		74.0	4.0	NM_080664	D3DS87	Missense_Mutation	SNP	ENST00000310850.4	hg19	CCDS9643.1	.	.	.	.	.	.	.	.	.	.	T	15.34	2.803867	0.50315	.	.	ENSG00000129480	ENST00000310850;ENST00000356180	T;T	0.49432	0.78;0.78	5.96	5.96	0.96718	D-Tyr tRNAtyr deacylase-like domain (2);	0.041873	0.85682	D	0.000000	T	0.46870	0.1415	L	0.55213	1.73	0.53688	D	0.999975	P	0.40909	0.732	B	0.42495	0.389	T	0.49597	-0.8923	10	0.54805	T	0.06	-1.1029	10.7267	0.46072	0.0:0.0707:0.0:0.9293	.	66	Q96FN9	DTD2_HUMAN	S	66	ENSP00000312224:N66S;ENSP00000348503:N66S	ENSP00000312224:N66S	N	-	2	0	C14orf126	30987396	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.606000	0.61126	2.270000	0.75569	0.533000	0.62120	AAT	.	.		0.358	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664		C	31917645	T	C	31917645	3	2	64	1	0	0	0	0	1	0	0	0	1745	1493	52	2	313	2	C14orf126	14	31917645	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	334147	31917645	75431895	223	7940										
FANCM	57697	hgsc.bcm.edu	37	chr14	45644656	45644656	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cctaccaaatgataaaaggaCatcagatacagatgaaattg	7	7	1	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:45644656C>T	ENST00000267430.5	+	14	2784	c.2699C>T	c.(2698-2700)aCa>aTa	p.T900I	FANCM_ENST00000542564.2_Missense_Mutation_p.T874I	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	900					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						GATAAAAGGACATCAGATACA	0.294								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.T900I		Atlas-SNP	.											.,1	FANCM	225	.	0			c.C2699T						.						78	86	84					14																	45644656		2203	4293	6496	SO:0001583	missense	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAAGGACATCAGA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.2699C>T	chr14.hg19:g.45644656C>T	ENSP00000267430:p.Thr900Ile	76.0	0.0		30.0	2.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	C	9.134	1.012218	0.19277	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.18502	2.82;2.82;2.21	5.24	-2.59	0.06209	.	3.122250	0.00921	N	0.002597	T	0.08268	0.0206	N	0.08118	0	0.09310	N	1	B;B	0.30763	0.294;0.146	B;B	0.14023	0.01;0.01	T	0.28138	-1.0053	10	0.62326	D	0.03	.	6.2592	0.20891	0.0:0.3897:0.1274:0.4828	.	874;900	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	I	900;874;416	ENSP00000267430:T900I;ENSP00000442493:T874I;ENSP00000452033:T416I	ENSP00000267430:T900I	T	+	2	0	FANCM	44714406	0.004000	0.15560	0.000000	0.03702	0.697000	0.40408	-0.116000	0.10724	-0.368000	0.08040	0.591000	0.81541	ACA	.	.		0.294	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45644656	C	T	45644656	3	4	64	1	0	0	0	0	1	0	0	0	5679	478	17	3	2753	3	FANCM	14	45644656	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	13727011	45644656	61704884	224	7941										
POLE2	5427	hgsc.bcm.edu	37	chr14	50118040	50118040	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	acggacgcagtttctgcacaTtttatttactaagtcttcac	6	10	3	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:50118040T>C	ENST00000216367.5	-	16	1366	c.1267A>G	c.(1267-1269)Atg>Gtg	p.M423V	POLE2_ENST00000554396.1_Missense_Mutation_p.M423V|POLE2_ENST00000539565.2_Missense_Mutation_p.M397V|POLE2_ENST00000556584.1_5'UTR	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	423					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	TTTCTGCACATTTTATTTACT	0.338																																					p.M423V		Atlas-SNP	.											.	POLE2	36	.	0			c.A1267G						.						74	75	75					14																	50118040		2203	4300	6503	SO:0001583	missense	5427	exon16			TGCACATTTTATT	AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479		"DNA polymerases"	9178	protein-coding gene	gene with protein product	"DNA polymerase epsilon subunit B"	602670	"polymerase (DNA directed), epsilon 2 (p59 subunit)"			9405441, 9443964	Standard	NM_002692		Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.1267A>G	chr14.hg19:g.50118040T>C	ENSP00000216367:p.Met423Val	159.0	0.0		83.0	4.0	NM_001197331	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	Missense_Mutation	SNP	ENST00000216367.5	hg19	CCDS32073.1	.	.	.	.	.	.	.	.	.	.	T	15.95	2.984872	0.53934	.	.	ENSG00000100479	ENST00000216367;ENST00000539565;ENST00000554396	T;T;T	0.27557	1.66;1.66;1.66	5.52	5.52	0.82312	DNA polymerase alpha/epsilon, subunit B (1);	0.000000	0.85682	D	0.000000	T	0.43831	0.1265	M	0.79614	2.46	0.58432	D	0.999999	B;B;B	0.18863	0.031;0.01;0.006	B;B;B	0.33846	0.171;0.06;0.032	T	0.41413	-0.9510	10	0.54805	T	0.06	-17.3453	15.938	0.79729	0.0:0.0:0.0:1.0	.	423;397;423	A4FU92;B4DDE6;P56282	.;.;DPOE2_HUMAN	V	423;397;423	ENSP00000216367:M423V;ENSP00000446313:M397V;ENSP00000451621:M423V	ENSP00000216367:M423V	M	-	1	0	POLE2	49187790	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.836000	0.86788	2.222000	0.72286	0.533000	0.62120	ATG	.	.		0.338	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410512.1	NM_002692		C	50118040	T	C	50118040	3	2	64	1	0	0	0	0	1	0	0	0	12206	1493	52	2	332	2	POLE2	14	50118040	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	4473384	50118040	57231500	225	7942										
OTX2	5015	hgsc.bcm.edu	37	chr14	57268484	57268484	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggaatttccacgaggatgtcTgatctttataatccaagcag	9	8	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:57268484T>A	ENST00000555006.1	-	4	1247	c.839A>T	c.(838-840)cAg>cTg	p.Q280L	OTX2_ENST00000408990.3_Missense_Mutation_p.Q280L|RP11-1085N6.6_ENST00000602485.1_lincRNA|OTX2_ENST00000339475.5_Missense_Mutation_p.Q288L			P32243	OTX2_HUMAN	orthodenticle homeobox 2	280					axon guidance (GO:0007411)|cell fate specification (GO:0001708)|diencephalon morphogenesis (GO:0048852)|dorsal/ventral pattern formation (GO:0009953)|endoderm development (GO:0007492)|eye photoreceptor cell fate commitment (GO:0042706)|forebrain development (GO:0030900)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|neuron fate determination (GO:0048664)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|protein complex assembly (GO:0006461)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of smoothened signaling pathway (GO:0008589)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|nucleus (GO:0005634)|protein complex (GO:0043234)	eukaryotic initiation factor 4E binding (GO:0008190)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	19	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					CGAGGATGTCTGATCTTTATA	0.413																																					p.Q288L		Atlas-SNP	.											.	OTX2	47	.	0			c.A863T						.						66	70	69					14																	57268484		2203	4300	6503	SO:0001583	missense	5015	exon3			GATGTCTGATCTT	AF298117	CCDS9728.1, CCDS41960.1	14q22.3	2014-09-17	2007-02-15		ENSG00000165588	ENSG00000165588		"Homeoboxes / PRD class"	8522	protein-coding gene	gene with protein product		600037	"orthodenticle homolog 2 (Drosophila)"			7959790	Standard	NM_021728		Approved		uc031qor.1	P32243	OTTHUMG00000152338	ENST00000555006.1:c.839A>T	chr14.hg19:g.57268484T>A	ENSP00000452336:p.Gln280Leu	149.0	0.0		78.0	4.0	NM_001270525	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	Missense_Mutation	SNP	ENST00000555006.1	hg19	CCDS41960.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.358934	0.41801	.	.	ENSG00000165588	ENST00000339475;ENST00000408990;ENST00000555006	D;D;D	0.95980	-3.87;-3.83;-3.83	5.65	5.65	0.86999	.	0.378689	0.19745	N	0.107022	D	0.96528	0.8867	M	0.88377	2.95	0.80722	D	1	P;P	0.45902	0.868;0.716	B;P	0.45794	0.358;0.493	D	0.97198	0.9862	10	0.87932	D	0	.	15.2098	0.73214	0.0:0.0:0.0:1.0	.	288;280	F1T0D1;P32243	.;OTX2_HUMAN	L	288;280;280	ENSP00000343819:Q288L;ENSP00000386185:Q280L;ENSP00000452336:Q280L	ENSP00000343819:Q288L	Q	-	2	0	OTX2	56338237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.857000	0.86963	2.371000	0.80710	0.533000	0.62120	CAG	.	.		0.413	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411522.1	NM_021728.		A	57268484	T	A	57268484	3	1	64	1	0	0	0	0	1	0	0	0	11330	1580	55	4	34	4	OTX2	14	57268484	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	7150444	57268484	50081056	226	7943										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64641759	64641759	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aactgacctgaaaactaaagAgtctgtgggtaggagaatca	11	6	2	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:64641759A>G	ENST00000344113.4	+	95	17545	c.17333A>G	c.(17332-17334)gAg>gGg	p.E5778G	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Missense_Mutation_p.E5643G|SYNE2_ENST00000555002.1_Missense_Mutation_p.E2412G|SYNE2_ENST00000358025.3_Missense_Mutation_p.E5778G|SYNE2_ENST00000357395.3_Missense_Mutation_p.E2163G|SYNE2_ENST00000394768.2_Missense_Mutation_p.E2163G	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5778					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAAACTAAAGAGTCTGTGGGT	0.453																																					p.E5778G		Atlas-SNP	.											.	SYNE2	577	.	0			c.A17333G						.						110	111	111					14																	64641759		2203	4300	6503	SO:0001583	missense	23224	exon95			CTAAAGAGTCTGT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.17333A>G	chr14.hg19:g.64641759A>G	ENSP00000341781:p.Glu5778Gly	96.0	0.0		59.0	4.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	11.81	1.749142	0.30955	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.58060	1.22;1.22;1.22;0.36;1.22;1.22	5.58	4.41	0.53225	.	0.407306	0.21011	N	0.081689	T	0.50086	0.1595	M	0.62723	1.935	0.24361	N	0.994872	B;B;B;B;B	0.31077	0.009;0.001;0.073;0.012;0.307	B;B;B;B;B	0.30572	0.025;0.003;0.037;0.018;0.117	T	0.45775	-0.9238	10	0.46703	T	0.11	.	12.3724	0.55261	0.6757:0.3243:0.0:0.0	.	2163;166;5643;5778;5778	Q8WXH0-7;Q7Z362;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;.;SYNE2_HUMAN;.	G	5778;2163;5778;5643;5649;2412;2163	ENSP00000350719:E5778G;ENSP00000349969:E2163G;ENSP00000341781:E5778G;ENSP00000452570:E5643G;ENSP00000450831:E2412G;ENSP00000378249:E2163G	ENSP00000261678:E5649G	E	+	2	0	SYNE2	63711512	0.925000	0.31364	0.494000	0.27515	0.024000	0.10985	2.650000	0.46665	1.011000	0.39340	0.482000	0.46254	GAG	.	.		0.453	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64641759	A	G	64641759	3	3	64	1	0	0	0	0	1	0	0	0	15461	304	11	2	17707	2	SYNE2	14	64641759	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	7373275	64641759	42707781	227	7944										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68215323	68215323	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cacagcaatcaagtaggcagAacgcagtttgcaacatatca	8	10	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:68215323A>G	ENST00000347230.4	-	42	7588	c.7450T>C	c.(7450-7452)Tct>Cct	p.S2484P	RN7SL213P_ENST00000463482.2_RNA	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	2484					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		AAGTAGGCAGAACGCAGTTTG	0.542																																					p.S2484P		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.T7450C						.						69	57	61					14																	68215323		2203	4300	6503	SO:0001583	missense	23503	exon42			AGGCAGAACGCAG	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.7450T>C	chr14.hg19:g.68215323A>G	ENSP00000251119:p.Ser2484Pro	117.0	0.0		68.0	4.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	A	15.96	2.988091	0.53934	.	.	ENSG00000072121	ENST00000347230;ENST00000411699	T	0.30182	1.54	5.54	5.54	0.83059	.	0.126103	0.53938	D	0.000043	T	0.32526	0.0832	L	0.49126	1.545	0.80722	D	1	B	0.22276	0.067	B	0.22152	0.038	T	0.09530	-1.0670	10	0.72032	D	0.01	-15.0401	15.9657	0.79968	1.0:0.0:0.0:0.0	.	2484	Q68DK2	ZFY26_HUMAN	P	2484;2463	ENSP00000251119:S2484P	ENSP00000251119:S2484P	S	-	1	0	ZFYVE26	67285076	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.538000	0.67193	2.236000	0.73375	0.533000	0.62120	TCT	.	.		0.542	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		G	68215323	A	G	68215323	3	3	64	1	0	0	0	0	1	0	0	0	17683	246	9	2	173	2	ZFYVE26	14	68215323	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	3573564	68215323	39134217	228	7945										
DLST	1743	hgsc.bcm.edu	37	chr14	75365074	75365074	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttgtaatattttcacagtaAcatccaggagatgagggctc	9	7	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:75365074A>G	ENST00000334220.4	+	11	834	c.773A>G	c.(772-774)aAc>aGc	p.N258S	DLST_ENST00000334212.6_Missense_Mutation_p.N172S|DLST_ENST00000555190.1_3'UTR	NM_001933.4	NP_001924.2	P36957	ODO2_HUMAN	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	258					cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|generation of precursor metabolites and energy (GO:0006091)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|oxoglutarate dehydrogenase complex (GO:0045252)	dihydrolipoyllysine-residue succinyltransferase activity (GO:0004149)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00698)		TTTCACAGTAACATCCAGGAG	0.423																																					p.N258S		Atlas-SNP	.											.	DLST	42	.	0			c.A773G						.						93	90	91					14																	75365074		2203	4300	6503	SO:0001583	missense	1743	exon11			ACAGTAACATCCA		CCDS9833.1	14q23.1	2008-08-11			ENSG00000119689	ENSG00000119689	2.3.1.61		2911	protein-coding gene	gene with protein product		126063		DLTS		8009371	Standard	NM_001933		Approved		uc001xqv.2	P36957		ENST00000334220.4:c.773A>G	chr14.hg19:g.75365074A>G	ENSP00000335304:p.Asn258Ser	140.0	0.0		92.0	4.0	NM_001933	B7Z5W8|E7ESY5|Q7LDY7|Q9BQ32	Missense_Mutation	SNP	ENST00000334220.4	hg19	CCDS9833.1	.	.	.	.	.	.	.	.	.	.	A	12.13	1.845180	0.32606	.	.	ENSG00000119689	ENST00000334220;ENST00000334212;ENST00000554806	T;T;T	0.42131	0.98;0.98;0.98	5.84	5.84	0.93424	2-oxoacid dehydrogenase acyltransferase, catalytic domain (1);Chloramphenicol acetyltransferase-like domain (1);	0.037870	0.85682	D	0.000000	T	0.39279	0.1072	L	0.43554	1.36	0.80722	D	1	B;B;B;B;B	0.28470	0.067;0.213;0.213;0.137;0.135	B;B;B;B;B	0.34346	0.065;0.18;0.18;0.115;0.089	T	0.17319	-1.0373	10	0.14656	T	0.56	-18.3689	16.21	0.82150	1.0:0.0:0.0:0.0	.	172;258;258;170;174	B7Z5W8;Q6IBS5;P36957;Q86TQ8;Q86TW7	.;.;ODO2_HUMAN;.;.	S	258;172;241	ENSP00000335304:N258S;ENSP00000335465:N172S;ENSP00000451957:N241S	ENSP00000238671:N241S	N	+	2	0	DLST	74434827	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	8.938000	0.92943	2.236000	0.73375	0.528000	0.53228	AAC	.	.		0.423	DLST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413637.1			G	75365074	A	G	75365074	3	3	64	1	0	0	0	0	1	0	0	0	4571	43	2	2	815	2	DLST	14	75365074	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	7149751	75365074	31984466	229	7946										
CATSPERB	79820	hgsc.bcm.edu	37	chr14	92102785	92102785	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctacccagagtgtatcacttTtccatagtgtatattgccga	7	10	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:92102785T>C	ENST00000256343.3	-	17	1882	c.1726A>G	c.(1726-1728)Aaa>Gaa	p.K576E		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	576					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				TGTATCACTTTTCCATAGTGT	0.368																																					p.K576E		Atlas-SNP	.											.	CATSPERB	114	.	0			c.A1726G						.						162	149	153					14																	92102785		2203	4300	6503	SO:0001583	missense	79820	exon17			TCACTTTTCCATA	AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.1726A>G	chr14.hg19:g.92102785T>C	ENSP00000256343:p.Lys576Glu	195.0	0.0		123.0	5.0	NM_024764	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	hg19	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	T	15.89	2.965873	0.53507	.	.	ENSG00000133962	ENST00000256343	T	0.52526	0.66	4.26	4.26	0.50523	.	0.000000	0.64402	D	0.000019	T	0.60392	0.2265	M	0.62723	1.935	0.09310	N	0.999998	D	0.64830	0.994	D	0.63597	0.916	T	0.53287	-0.8460	10	0.72032	D	0.01	-31.2804	9.9607	0.41695	0.0:0.0:0.0:1.0	.	576	Q9H7T0	CTSRB_HUMAN	E	576	ENSP00000256343:K576E	ENSP00000256343:K576E	K	-	1	0	CATSPERB	91172538	0.975000	0.34042	0.298000	0.25002	0.163000	0.22366	3.217000	0.51184	1.923000	0.55706	0.260000	0.18958	AAA	.	.		0.368	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		C	92102785	T	C	92102785	3	2	64	1	0	0	0	0	1	0	0	0	2693	1850	64	2	1668	2	CATSPERB	14	92102785	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	16737711	92102785	15246755	230	7947										
CCNK	8812	hgsc.bcm.edu	37	chr14	99968582	99968582	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	actgcagtgggaaccagagaTcatagcagtagcagtgatgt	13	7	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:99968582T>C	ENST00000389879.5	+	7	737	c.614T>C	c.(613-615)aTc>aCc	p.I205T	CCNK_ENST00000557165.1_3'UTR|CCNK_ENST00000555049.1_Missense_Mutation_p.I205T	NM_001099402.1	NP_001092872.1	O75909	CCNK_HUMAN	cyclin K	205					cellular response to DNA damage stimulus (GO:0006974)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of cell cycle arrest (GO:0071157)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cyclin K-CDK12 complex (GO:0002944)|cyclin K-CDK13 complex (GO:0002945)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase binding (GO:0019901)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|endometrium(2)|lung(3)	6		all_cancers(154;0.224)|all_epithelial(191;0.0643)|Melanoma(154;0.0866)				GAACCAGAGATCATAGCAGTA	0.398																																					p.I205T		Atlas-SNP	.											.	CCNK	32	.	0			c.T614C						.						95	88	90					14																	99968582		1931	4131	6062	SO:0001583	missense	8812	exon7			CAGAGATCATAGC	AF060515	CCDS45160.1	14q32.2	2014-07-03			ENSG00000090061	ENSG00000090061			1596	protein-coding gene	gene with protein product		603544				9632813, 10574912	Standard	NM_001099402		Approved	CPR4	uc001ygi.4	O75909	OTTHUMG00000171495	ENST00000389879.5:c.614T>C	chr14.hg19:g.99968582T>C	ENSP00000374529:p.Ile205Thr	152.0	0.0		93.0	4.0	NM_001099402	Q59FT6|Q86U16|Q96B63|Q9NNY9	Missense_Mutation	SNP	ENST00000389879.5	hg19	CCDS45160.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.365861	0.82463	.	.	ENSG00000090061	ENST00000437596;ENST00000216279;ENST00000380246;ENST00000389879;ENST00000557441;ENST00000555049	T;T;T	0.40476	1.03;1.03;1.03	5.95	5.95	0.96441	Cyclin-like (2);	0.049118	0.85682	D	0.000000	T	0.51244	0.1663	N	0.26042	0.785	0.80722	D	1	D;D	0.71674	0.998;0.996	D;D	0.71414	0.973;0.965	T	0.47071	-0.9145	10	0.33940	T	0.23	-15.5048	16.4237	0.83790	0.0:0.0:0.0:1.0	.	205;205	O75909;O75909-2	CCNK_HUMAN;.	T	205;207;207;205;205;205	ENSP00000374529:I205T;ENSP00000450792:I205T;ENSP00000452307:I205T	ENSP00000216279:I207T	I	+	2	0	CCNK	99038335	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.013000	0.88655	2.279000	0.76181	0.533000	0.62120	ATC	.	.		0.398	CCNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413721.1			C	99968582	T	C	99968582	3	2	64	1	0	0	0	0	1	0	0	0	2932	1435	50	2	636	2	CCNK	14	99968582	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	7865797	99968582	7380958	231	7948										
CDC42BPB	9578	hgsc.bcm.edu	37	chr14	103466024	103466024	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agcagggtcagtaaatcaccAcccacatagtaatccatgac	7	12	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:103466024A>G	ENST00000361246.2	-	5	762	c.474T>C	c.(472-474)ggT>ggC	p.G158G		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		GTAAATCACCACCCACATAGT	0.448																																					p.G158G		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.T474C						.						113	97	102					14																	103466024		2203	4300	6503	SO:0001819	synonymous_variant	9578	exon5			ATCACCACCCACA	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"CDC42-binding protein kinase beta (DMPK-like)"			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.474T>C	chr14.hg19:g.103466024A>G		175.0	0.0		98.0	5.0	NM_006035		Silent	SNP	ENST00000361246.2	hg19	CCDS9978.1																																																																																			.	.		0.448	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		G	103466024	A	G	103466024	2	3	64	1	0	0	0	0	0	0	0	1	3075	146	6	2		2	CDC42BPB	14	103466024	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	3497442	103466024	3883516	232	7949										
EIF5	1983	hgsc.bcm.edu	37	chr14	103803078	103803078	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttgatgttaagaatgaccgTtacattgtcaatggatctca	8	6	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:103803078T>C	ENST00000216554.3	+	5	895	c.219T>C	c.(217-219)cgT>cgC	p.R73R	EIF5_ENST00000558506.1_Silent_p.R73R|EIF5_ENST00000392715.2_Silent_p.R73R|EIF5_ENST00000560200.1_3'UTR|SNORA28_ENST00000606769.1_RNA	NM_001969.4	NP_001960.2	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	73					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(3)|kidney(2)|large_intestine(3)|lung(5)|pancreas(2)|skin(2)|upper_aerodigestive_tract(1)	18		Melanoma(154;0.155)	Epithelial(46;0.182)			AGAATGACCGTTACATTGTCA	0.388																																					p.R73R		Atlas-SNP	.											.	EIF5	40	.	0			c.T219C						.						132	121	125					14																	103803078		2203	4300	6503	SO:0001819	synonymous_variant	1983	exon5			TGACCGTTACATT	U49436	CCDS9980.1	14q32.32	2006-05-11				ENSG00000100664			3299	protein-coding gene	gene with protein product		601710				8663286	Standard	NM_001969		Approved		uc001ymq.4	P55010		ENST00000216554.3:c.219T>C	chr14.hg19:g.103803078T>C		97.0	0.0		80.0	4.0	NM_001969	Q53XB3|Q9H5N2|Q9UG48	Silent	SNP	ENST00000216554.3	hg19	CCDS9980.1																																																																																			.	.		0.388	EIF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415329.2	NM_001969		C	103803078	T	C	103803078	2	2	64	1	0	0	0	0	0	0	0	1	5042	1712	60	2		2	EIF5	14	103803078	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	337054	103803078	3546462	233	7950										
PPP1R13B	23368	hgsc.bcm.edu	37	chr14	104206859	104206859	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aggctgtggtgtgcccgtggAcagtgacccgtgaagaaacg	16	9	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr14:104206859A>G	ENST00000202556.9	-	12	2176	c.1894T>C	c.(1894-1896)Tcc>Ccc	p.S632P	PPP1R13B_ENST00000423488.2_Missense_Mutation_p.S51P|PPP1R13B_ENST00000555391.1_5'UTR	NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	632	Pro-rich.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				GTGCCCGTGGACAGTGACCCG	0.587																																					p.S632P		Atlas-SNP	.											.	PPP1R13B	72	.	0			c.T1894C						.						33	42	39					14																	104206859		2085	4208	6293	SO:0001583	missense	23368	exon12			CCGTGGACAGTGA	AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14950	protein-coding gene	gene with protein product		606455	"protein phosphatase 1, regulatory (inhibitor) subunit 13B"			9872452	Standard	NM_015316		Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.1894T>C	chr14.hg19:g.104206859A>G	ENSP00000202556:p.Ser632Pro	114.0	0.0		75.0	5.0	NM_015316	B2RMX5|O94870	Missense_Mutation	SNP	ENST00000202556.9	hg19	CCDS41997.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.698031	0.30142	.	.	ENSG00000088808	ENST00000202556;ENST00000423488;ENST00000380023	T;T	0.55413	0.7;0.52	5.48	0.92	0.19397	.	0.471590	0.24876	N	0.034887	T	0.28366	0.0701	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13255	-1.0516	10	0.22109	T	0.4	.	6.5986	0.22687	0.3434:0.3871:0.2695:0.0	.	632	Q96KQ4	ASPP1_HUMAN	P	632;51;499	ENSP00000202556:S632P;ENSP00000395213:S51P	ENSP00000202556:S632P	S	-	1	0	PPP1R13B	103276612	0.988000	0.35896	0.005000	0.12908	0.046000	0.14306	1.435000	0.34969	0.125000	0.18397	0.533000	0.62120	TCC	.	.		0.587	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316		G	104206859	A	G	104206859	3	3	64	1	0	0	0	0	1	0	0	0	12369	275	10	2	1402	2	PPP1R13B	14	104206859	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	403781	104206859	3142681	234	7951										
ATP10A	57194	hgsc.bcm.edu	37	chr15	26026243	26026243	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gttggcggtctcgatgtggcAtagcccgtcggggtcactgg	17	10	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:26026243A>G	ENST00000356865.6	-	2	688	c.577T>C	c.(577-579)Tgc>Cgc	p.C193R		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	193					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TCGATGTGGCATAGCCCGTCG	0.592																																					p.C193R		Atlas-SNP	.											.	ATP10A	270	.	0			c.T577C						.						97	95	96					15																	26026243		2203	4300	6503	SO:0001583	missense	57194	exon2			TGTGGCATAGCCC	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.577T>C	chr15.hg19:g.26026243A>G	ENSP00000349325:p.Cys193Arg	167.0	0.0		114.0	5.0	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.289408	0.80914	.	.	ENSG00000206190	ENST00000356865	T	0.76968	-1.06	4.67	4.67	0.58626	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.93096	0.7802	H	0.99379	4.54	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.95508	0.8583	10	0.87932	D	0	-28.2241	13.4539	0.61187	1.0:0.0:0.0:0.0	.	193	O60312	AT10A_HUMAN	R	193	ENSP00000349325:C193R	ENSP00000349325:C193R	C	-	1	0	ATP10A	23577336	1.000000	0.71417	0.998000	0.56505	0.893000	0.52053	8.778000	0.91785	1.967000	0.57214	0.459000	0.35465	TGC	.	.		0.592	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		G	26026243	A	G	26026243	3	3	64	1	0	0	0	0	1	0	0	0	1116	217	8	2	4002	2	ATP10A	15	26026243	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10		26026243	76505149	235	7952										
FMN1	342184	hgsc.bcm.edu	37	chr15	33091107	33091107	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agctgggtgtgatctccttcTcaccagactttggcttcatc	9	12	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:33091107T>C	ENST00000559047.1	-	16	4027	c.4028A>G	c.(4027-4029)gAg>gGg	p.E1343G	FMN1_ENST00000334528.9_Missense_Mutation_p.E1120G|FMN1_ENST00000561249.1_Missense_Mutation_p.E1245G			Q68DA7	FMN1_HUMAN	formin 1	1343	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GATCTCCTTCTCACCAGACTT	0.423																																					p.E1120G		Atlas-SNP	.											.	FMN1	174	.	0			c.A3359G						.						97	86	90					15																	33091107		1883	4123	6006	SO:0001583	missense	342184	exon15			TCCTTCTCACCAG	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.4028A>G	chr15.hg19:g.33091107T>C	ENSP00000454047:p.Glu1343Gly	103.0	0.0		78.0	4.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.94	3.919629	0.73098	.	.	ENSG00000248905	ENST00000334528	T	0.42513	0.97	5.86	5.86	0.93980	.	0.095507	0.64402	D	0.000001	T	0.65678	0.2714	M	0.76328	2.33	.	.	.	D	0.89917	1.0	D	0.80764	0.994	T	0.71083	-0.4695	9	0.87932	D	0	.	16.2444	0.82434	0.0:0.0:0.0:1.0	.	1120	Q68DA7-5	.	G	1120	ENSP00000333950:E1120G	ENSP00000333950:E1120G	E	-	2	0	FMN1	30878399	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.673000	0.83973	2.237000	0.73441	0.533000	0.62120	GAG	.	.		0.423	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		C	33091107	T	C	33091107	3	2	64	1	0	0	0	0	1	0	0	0	5957	1551	54	2	243	2	FMN1	15	33091107	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	7064864	33091107	69440285	236	7953										
C15orf55	256646	hgsc.bcm.edu	37	chr15	34646648	34646648	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgtccatctcttcccttagtGtacattccgaagaaggcagc	8	12	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:34646648G>A	ENST00000333756.4	+	5	1148	c.993G>A	c.(991-993)gtG>gtA	p.V331V	NUTM1_ENST00000537011.1_Splice_Site_p.V359V|NUTM1_ENST00000438749.3_Splice_Site_p.V349V	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	331						cytoplasm (GO:0005737)|nucleus (GO:0005634)											TTCCCTTAGTGTACATTCCGA	0.552																																					p.V331V		Atlas-SNP	.											.	C15orf55	110	.	0			c.G993A						.						78	81	80					15																	34646648		2201	4298	6499	SO:0001630	splice_region_variant	256646	exon5			CTTAGTGTACATT	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"nuclear protein in testis"	608963	"chromosome 15 open reading frame 55"	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.992-1G>A	chr15.hg19:g.34646648G>A		160.0	0.0		68.0	4.0	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Silent	SNP	ENST00000333756.4	hg19	CCDS32190.1																																																																																			.	.		0.552	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741	Silent	A	34646648	G	A	34646648	5	1	64	1	0	0	0	0	0	0	1	0	1805	1391	48	3	1011	3	C15orf55	15	34646648	Splice_Site	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	1555541	34646648	67884744	237	7954										
BUB1B	701	hgsc.bcm.edu	37	chr15	40504778	40504778	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	taaatgaagattttgatcatTtttgcagctgttatcaatat	6	4	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:40504778T>C	ENST00000287598.6	+	19	2659	c.2464T>C	c.(2464-2466)Ttt>Ctt	p.F822L	BUB1B_ENST00000412359.3_Missense_Mutation_p.F836L	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	822	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		TTTTGATCATTTTTGCAGCTG	0.323			"Mis, N, F, S"			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome																												p.F822L		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.T2464C						.						118	112	114					15																	40504778		2203	4300	6503	SO:0001583	missense	701	exon19	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GATCATTTTTGCA	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"budding uninhibited by benzimidazoles 1 (yeast homolog), beta", "budding uninhibited by benzimidazoles 1 homolog beta (yeast)"			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.2464T>C	chr15.hg19:g.40504778T>C	ENSP00000287598:p.Phe822Leu	109.0	0.0		73.0	4.0	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Missense_Mutation	SNP	ENST00000287598.6	hg19	CCDS10053.1	.	.	.	.	.	.	.	.	.	.	T	1.869	-0.460686	0.04508	.	.	ENSG00000156970	ENST00000287598;ENST00000412359;ENST00000442874	T;T	0.17528	2.27;2.27	5.1	3.98	0.46160	Protein kinase-like domain (1);	1.512990	0.04034	N	0.301971	T	0.09818	0.0241	N	0.04959	-0.14	0.23089	N	0.998311	B	0.02656	0.0	B	0.01281	0.0	T	0.31613	-0.9937	10	0.09843	T	0.71	-0.0257	9.9917	0.41874	0.0:0.0807:0.0:0.9193	.	822	O60566	BUB1B_HUMAN	L	822;836;705	ENSP00000287598:F822L;ENSP00000398470:F836L	ENSP00000287598:F822L	F	+	1	0	BUB1B	38292070	0.001000	0.12720	0.910000	0.35882	0.483000	0.33249	0.106000	0.15354	0.801000	0.34066	0.533000	0.62120	TTT	.	.		0.323	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4			C	40504778	T	C	40504778	3	2	64	1	0	0	0	0	1	0	0	0	1573	1841	64	2	2538	2	BUB1B	15	40504778	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	5858130	40504778	62026614	238	7955										
CASC4	113201	hgsc.bcm.edu	37	chr15	44695118	44695118	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgaaaatgaatcccctgttgAtccgcagcatggctctaaac	8	11	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:44695118A>G	ENST00000299957.6	+	9	1405	c.1106A>G	c.(1105-1107)gAt>gGt	p.D369G	CASC4_ENST00000345795.2_Intron|RP11-516C1.1_ENST00000558047.1_RNA|CASC4_ENST00000360824.3_Intron	NM_138423.3	NP_612432.2	Q6P4E1	CASC4_HUMAN	cancer susceptibility candidate 4	369						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(2)	17		all_cancers(109;1.69e-13)|all_epithelial(112;3.94e-11)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.027)		all cancers(107;2.91e-20)|GBM - Glioblastoma multiforme(94;1.57e-06)|COAD - Colon adenocarcinoma(120;0.217)|Colorectal(105;0.237)		TCCCCTGTTGATCCGCAGCAT	0.443																																					p.D369G		Atlas-SNP	.											.	CASC4	34	.	0			c.A1106G						.						97	86	89					15																	44695118		2198	4298	6496	SO:0001583	missense	113201	exon9			CTGTTGATCCGCA	AF103804	CCDS10108.1, CCDS10109.1	15q15.1	2010-11-24			ENSG00000166734	ENSG00000166734			24892	protein-coding gene	gene with protein product						10497265	Standard	NM_138423		Approved	H63, DKFZp459F1927	uc001ztp.3	Q6P4E1	OTTHUMG00000131133	ENST00000299957.6:c.1106A>G	chr15.hg19:g.44695118A>G	ENSP00000299957:p.Asp369Gly	158.0	0.0		77.0	4.0	NM_138423	B4DPZ6|G5E934|Q6UY45|Q96EM1	Missense_Mutation	SNP	ENST00000299957.6	hg19	CCDS10108.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.719327	0.89205	.	.	ENSG00000166734	ENST00000299957;ENST00000416522	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.76463	0.3991	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.74219	-0.3736	9	0.33141	T	0.24	.	16.3948	0.83586	1.0:0.0:0.0:0.0	.	369;369	G5E934;Q6P4E1	.;CASC4_HUMAN	G	369;348	.	ENSP00000299957:D369G	D	+	2	0	CASC4	42482410	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.283000	0.95860	2.326000	0.78906	0.533000	0.62120	GAT	.	.		0.443	CASC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253815.1	NM_138423		G	44695118	A	G	44695118	3	3	64	1	0	0	0	0	1	0	0	0	2664	333	12	2	1140	2	CASC4	15	44695118	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	4190340	44695118	57836274	239	7956										
USP8	9101	hgsc.bcm.edu	37	chr15	50791193	50791193	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agtttgatgatcatgaagttTctgatatctccgtttcttct	7	7	5	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:50791193T>C	ENST00000396444.3	+	20	3603	c.3265T>C	c.(3265-3267)Tct>Cct	p.S1089P	RP11-562A8.5_ENST00000560159.1_lincRNA|RP11-562A8.4_ENST00000560380.1_RNA|USP8_ENST00000307179.4_Missense_Mutation_p.S1089P|USP8_ENST00000433963.1_Missense_Mutation_p.S1089P|USP50_ENST00000530218.1_5'Flank|USP8_ENST00000425032.3_Missense_Mutation_p.S983P	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	1089	USP.				cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		TCATGAAGTTTCTGATATCTC	0.428																																					p.S1089P		Atlas-SNP	.											.	USP8	90	.	0			c.T3265C						.						89	82	85					15																	50791193		2196	4294	6490	SO:0001583	missense	9101	exon20			GAAGTTTCTGATA	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"Ubiquitin-specific peptidases"	12631	protein-coding gene	gene with protein product		603158	"ubiquitin specific protease 8"			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.3265T>C	chr15.hg19:g.50791193T>C	ENSP00000379721:p.Ser1089Pro	167.0	0.0		77.0	4.0	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	hg19	CCDS10137.1	.	.	.	.	.	.	.	.	.	.	T	17.64	3.438900	0.63067	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032;ENST00000419830;ENST00000396440	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	5.64	3.31	0.37934	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.049041	0.85682	D	0.000000	T	0.57475	0.2056	M	0.88105	2.93	0.80722	D	1	D;D	0.65815	0.984;0.995	P;P	0.60068	0.799;0.868	T	0.59053	-0.7526	10	0.62326	D	0.03	-14.7262	7.9124	0.29798	0.1229:0.0667:0.0:0.8103	.	983;1089	B4DKA8;P40818	.;UBP8_HUMAN	P	1089;1089;1089;983;307;302	ENSP00000379721:S1089P;ENSP00000405537:S1089P;ENSP00000302239:S1089P;ENSP00000412682:S983P	ENSP00000302239:S1089P	S	+	1	0	USP8	48578485	1.000000	0.71417	0.809000	0.32408	0.917000	0.54804	4.536000	0.60636	0.489000	0.27749	0.482000	0.46254	TCT	.	.		0.428	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		C	50791193	T	C	50791193	3	2	64	1	0	0	0	0	1	0	0	0	17104	1783	62	2	3339	2	USP8	15	50791193	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	6096075	50791193	51740199	240	7957										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51748508	51748508	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	taggtcataaatacttacagTattgatggactgggtgtgaa	11	4	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:51748508T>C	ENST00000251076.5	-	37	8617	c.8330A>G	c.(8329-8331)tAc>tGc	p.Y2777C	RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000449909.3_Missense_Mutation_p.Y2141C|RP11-707P17.2_ENST00000560727.1_RNA|DMXL2_ENST00000543779.2_Missense_Mutation_p.Y2778C|RP11-707P17.2_ENST00000559173.1_RNA|RP11-707P17.2_ENST00000559977.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2777						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		ATACTTACAGTATTGATGGAC	0.274																																					p.Y2778C		Atlas-SNP	.											.	DMXL2	262	.	0			c.A8333G						.						66	72	70					15																	51748508		2196	4292	6488	SO:0001583	missense	23312	exon37			TTACAGTATTGAT	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.8330A>G	chr15.hg19:g.51748508T>C	ENSP00000251076:p.Tyr2777Cys	197.0	0.0		99.0	4.0	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	T	19.83	3.900687	0.72754	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909;ENST00000436119	T;T;T	0.01446	4.88;4.88;4.88	5.26	4.14	0.48551	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.09024	0.0223	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.974	D;D;D;P	0.91635	0.999;0.993;0.997;0.727	T	0.00664	-1.1620	10	0.87932	D	0	.	11.0239	0.47734	0.0:0.0727:0.0:0.9273	.	2778;2141;2777;2778	F5GWF1;B2RTR3;Q8TDJ6;B7ZMH3	.;.;DMXL2_HUMAN;.	C	2777;2778;2141;343	ENSP00000251076:Y2777C;ENSP00000441858:Y2778C;ENSP00000400855:Y2141C	ENSP00000251076:Y2777C	Y	-	2	0	DMXL2	49535800	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	7.501000	0.81600	1.012000	0.39366	0.533000	0.62120	TAC	.	.		0.274	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		C	51748508	T	C	51748508	3	2	64	1	0	0	0	0	1	0	0	0	4597	1638	57	2	808	2	DMXL2	15	51748508	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	957315	51748508	50782884	241	7958										
NEDD4	4734	hgsc.bcm.edu	37	chr15	56207944	56207944	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gacttttcacagacagtctgTctgggagtattattcgaaag	10	7	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:56207944T>C	ENST00000508342.1	-	1	1385	c.1086A>G	c.(1084-1086)agA>agG	p.R362R	NEDD4_ENST00000435532.3_Intron|NEDD4_ENST00000506154.1_Silent_p.R362R|NEDD4_ENST00000338963.2_Silent_p.R362R	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	362					adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		AGACAGTCTGTCTGGGAGTAT	0.418																																					p.R362R		Atlas-SNP	.											.	NEDD4	167	.	0			c.A1086G						.						49	49	49					15																	56207944		2191	4290	6481	SO:0001819	synonymous_variant	4734	exon1			AGTCTGTCTGGGA	D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"receptor-potentiating factor 1"	602278	"neural precursor cell expressed, developmentally down-regulated 4"			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.1086A>G	chr15.hg19:g.56207944T>C		67.0	0.0		59.0	4.0	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Silent	SNP	ENST00000508342.1	hg19																																																																																				.	.		0.418	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		C	56207944	T	C	56207944	2	2	64	1	0	0	0	0	0	0	0	1	10319	1664	58	2		2	NEDD4	15	56207944	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	4459436	56207944	46323448	242	7959										
NARG2	79664	hgsc.bcm.edu	37	chr15	60741135	60741135	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gacaattgctcagaaacagaAggctgtttagaattttctaa	8	6	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:60741135A>G	ENST00000261520.4	-	10	2265	c.2031T>C	c.(2029-2031)ccT>ccC	p.P677P	NARG2_ENST00000439632.1_Silent_p.P540P	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						CAGAAACAGAAGGCTGTTTAG	0.393																																					p.P677P		Atlas-SNP	.											NARG2,NS,carcinoma,0,1	NARG2	82	.	0			c.T2031C						.						62	66	65					15																	60741135		2201	4299	6500	SO:0001819	synonymous_variant	79664	exon10			AACAGAAGGCTGT																												ENST00000261520.4:c.2031T>C	chr15.hg19:g.60741135A>G		163.0	0.0		70.0	3.0	NM_024611		Silent	SNP	ENST00000261520.4	hg19	CCDS10176.1																																																																																			.	.		0.393	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			G	60741135	A	G	60741135	2	3	64	1	0	0	0	0	0	0	0	1	10178	59	3	2		2	NARG2	15	60741135	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	4533191	60741135	41790257	243	7960										
IQCH	64799	hgsc.bcm.edu	37	chr15	67553702	67553702	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gacattcagagtcttgaaacAgcaatcaaaaggactgaagt	9	7	3	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:67553702A>G	ENST00000335894.4	+	2	210	c.144A>G	c.(142-144)acA>acG	p.T48T	IQCH_ENST00000512104.1_Silent_p.T48T|IQCH_ENST00000546225.1_5'UTR|IQCH_ENST00000358767.3_5'UTR	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	48										NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		GTCTTGAAACAGCAATCAAAA	0.368																																					p.T48T		Atlas-SNP	.											.	IQCH	81	.	0			c.A144G						.						96	109	105					15																	67553702		2201	4298	6499	SO:0001819	synonymous_variant	64799	exon2			TGAAACAGCAATC	AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.144A>G	chr15.hg19:g.67553702A>G		81.0	0.0		57.0	4.0	NM_022784	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Silent	SNP	ENST00000335894.4	hg19	CCDS32273.1																																																																																			.	.		0.368	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784		G	67553702	A	G	67553702	2	3	64	1	0	0	0	0	0	0	0	1	7820	175	7	2		2	IQCH	15	67553702	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	6812567	67553702	34977690	244	7961										
SCAPER	49855	hgsc.bcm.edu	37	chr15	77059425	77059425	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttttagcaaggacttctgccAtggactataaagttaaaaac	7	7	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:77059425A>G	ENST00000563290.1	-	11	1348	c.1253T>C	c.(1252-1254)aTg>aCg	p.M418T	SCAPER_ENST00000538941.2_Missense_Mutation_p.M172T|SCAPER_ENST00000324767.7_Missense_Mutation_p.M418T			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	418	Glu-rich.					endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						GACTTCTGCCATGGACTATAA	0.338																																					p.M418T		Atlas-SNP	.											.	SCAPER	160	.	0			c.T1253C						.						68	54	58					15																	77059425		1815	4062	5877	SO:0001583	missense	49855	exon10			TCTGCCATGGACT	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.1253T>C	chr15.hg19:g.77059425A>G	ENSP00000454973:p.Met418Thr	155.0	0.0		76.0	4.0	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	hg19	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	A	16.95	3.264612	0.59431	.	.	ENSG00000140386	ENST00000324767;ENST00000538941;ENST00000303521	T;T	0.24151	1.9;1.87	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.32615	0.0835	N	0.14661	0.345	0.53005	D	0.999964	D;D;D	0.69078	0.994;0.997;0.997	D;D;D	0.76575	0.983;0.988;0.988	T	0.14755	-1.0461	10	0.19147	T	0.46	.	15.9905	0.80202	1.0:0.0:0.0:0.0	.	418;439;172	Q6NSF1;Q9BY12-2;F5H7X8	.;.;.	T	418;172;440	ENSP00000326924:M418T;ENSP00000442190:M172T	ENSP00000303560:M440T	M	-	2	0	SCAPER	74846480	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.759000	0.91667	2.183000	0.69458	0.397000	0.26171	ATG	.	.		0.338	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		G	77059425	A	G	77059425	3	3	64	1	0	0	0	0	1	0	0	0	13893	217	8	2	3037	2	SCAPER	15	77059425	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	9505723	77059425	25471967	245	7962										
DNAJA4	55466	hgsc.bcm.edu	37	chr15	78572631	78572631	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctttctctggaaaagcttccTcagctggaagctttactccc	7	13	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:78572631T>C	ENST00000394852.3	+	7	1213	c.1023T>C	c.(1021-1023)ccT>ccC	p.P341P	DNAJA4_ENST00000343789.3_Silent_p.P341P|WDR61_ENST00000559332.1_5'Flank|DNAJA4_ENST00000394855.3_Silent_p.P370P|DNAJA4_ENST00000446172.2_Silent_p.P314P|RP11-762H8.4_ENST00000558192.1_RNA	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	341					negative regulation of inclusion body assembly (GO:0090084)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	8						AAAAGCTTCCTCAGCTGGAAG	0.468																																					p.P370P		Atlas-SNP	.											.	DNAJA4	63	.	0			c.T1110C						.						62	63	63					15																	78572631		2196	4293	6489	SO:0001819	synonymous_variant	55466	exon8			GCTTCCTCAGCTG	AF116663	CCDS10299.2, CCDS45316.1, CCDS45317.1	15q24.1	2011-09-02			ENSG00000140403	ENSG00000140403		"Heat shock proteins / DNAJ (HSP40)"	14885	protein-coding gene	gene with protein product						11147971	Standard	NM_018602		Approved	PRO1472	uc002bdi.3	Q8WW22	OTTHUMG00000143733	ENST00000394852.3:c.1023T>C	chr15.hg19:g.78572631T>C		76.0	0.0		60.0	4.0	NM_018602	E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Silent	SNP	ENST00000394852.3	hg19	CCDS45316.1																																																																																			.	.		0.468	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	NM_018602		C	78572631	T	C	78572631	2	2	64	1	0	0	0	0	0	0	0	1	4616	1538	54	2		2	DNAJA4	15	78572631	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1513206	78572631	23958761	246	7963										
IL16	3603	hgsc.bcm.edu	37	chr15	81517943	81517943	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcagctggcagacacatcggAggctgggcccagcagtgttc	15	12	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:81517943A>G	ENST00000302987.4	+	1	203	c.203A>G	c.(202-204)gAg>gGg	p.E68G	IL16_ENST00000394660.2_Missense_Mutation_p.E68G			Q14005	IL16_HUMAN	interleukin 16	68					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GACACATCGGAGGCTGGGCCC	0.542																																					p.E68G		Atlas-SNP	.											.	IL16	254	.	0			c.A203G						.						59	59	59					15																	81517943		2016	4184	6200	SO:0001583	missense	3603	exon2			CATCGGAGGCTGG	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.203A>G	chr15.hg19:g.81517943A>G	ENSP00000302935:p.Glu68Gly	114.0	0.0		69.0	4.0	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813497	0.50527	.	.	ENSG00000172349	ENST00000394655;ENST00000360547;ENST00000394660;ENST00000302987	T;T	0.17213	2.29;2.29	4.18	4.18	0.49190	.	0.000000	0.38778	N	0.001572	T	0.28665	0.0710	M	0.70595	2.14	0.58432	D	0.999999	P;P	0.51057	0.941;0.939	P;P	0.51895	0.683;0.634	T	0.02603	-1.1135	10	0.45353	T	0.12	.	10.2922	0.43603	0.8345:0.1655:0.0:0.0	.	68;68	Q14005;Q14005-2	IL16_HUMAN;.	G	68;110;68;68	ENSP00000378155:E68G;ENSP00000302935:E68G	ENSP00000302935:E68G	E	+	2	0	IL16	79304998	0.999000	0.42202	0.991000	0.47740	0.586000	0.36452	3.924000	0.56476	1.751000	0.51876	0.460000	0.39030	GAG	.	.		0.542	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		G	81517943	A	G	81517943	3	3	64	1	0	0	0	0	1	0	0	0	7642	304	11	2	205	2	IL16	15	81517943	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	2945312	81517943	21013449	247	7964										
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85438313	85438313	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccaaagctgaggaggtttctCaagcctcagggccatccccg	11	14	2	1	rs371921369|rs2277576		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:85438313C>T	ENST00000286749.3	+	5	510	c.420C>T	c.(418-420)ctC>ctT	p.L140L	SLC28A1_ENST00000537703.1_Silent_p.L62L|SLC28A1_ENST00000394573.1_Silent_p.L140L|SLC28A1_ENST00000538177.1_Silent_p.L140L|SLC28A1_ENST00000537216.1_Silent_p.L140L|SLC28A1_ENST00000338602.2_Silent_p.L140L|SLC28A1_ENST00000537624.1_Silent_p.L140L			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	140			L -> LV (in A). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.L140L(2)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GGAGGTTTCTCAAGCCTCAGG	0.637																																					p.L140L		Atlas-SNP	.											SLC28A1_ENST00000338602,NS,carcinoma,0,1	SLC28A1	118	.	2	Substitution - coding silent(2)	lung(2)	c.C420T						.						45	47	47					15																	85438313		2203	4298	6501	SO:0001819	synonymous_variant	9154	exon6			GTTTCTCAAGCCT	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"Solute carriers"	11001	protein-coding gene	gene with protein product		606207	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.420C>T	chr15.hg19:g.85438313C>T		102.0	2.0		63.0	6.0	NM_201651	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	hg19	CCDS10334.1																																																																																			.	.		0.637	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			T	85438313	C	T	85438313	2	4	64	1	0	0	0	0	0	0	0	1	14546	813	29	3		3	SLC28A1	15	85438313	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	3920370	85438313	17093079	248	7965										
FANCI	55215	hgsc.bcm.edu	37	chr15	89804010	89804010	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atacacttgttgtatccagtTggtggaatcgggggatttgc	13	6	0	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:89804010T>C	ENST00000310775.7	+	4	310	c.224T>C	c.(223-225)tTg>tCg	p.L75S	FANCI_ENST00000567996.1_Missense_Mutation_p.L75S|FANCI_ENST00000451393.2_5'UTR|FANCI_ENST00000300027.8_Missense_Mutation_p.L75S	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	75					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					TGTATCCAGTTGGTGGAATCG	0.428								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.L75S		Atlas-SNP	.											.	FANCI	129	.	0			c.T224C						.						123	116	119					15																	89804010		2200	4299	6499	SO:0001583	missense	55215	exon4	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TCCAGTTGGTGGA	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.224T>C	chr15.hg19:g.89804010T>C	ENSP00000310842:p.Leu75Ser	153.0	0.0		93.0	4.0	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	hg19	CCDS45346.1	.	.	.	.	.	.	.	.	.	.	T	31	5.102816	0.94245	.	.	ENSG00000140525	ENST00000300027;ENST00000310775;ENST00000447611	T;T;T	0.43688	0.94;0.94;0.94	5.43	5.43	0.79202	.	0.000000	0.56097	D	0.000035	T	0.63873	0.2548	M	0.70595	2.14	0.80722	D	1	D;D	0.89917	0.979;1.0	P;D	0.91635	0.85;0.999	T	0.65372	-0.6184	10	0.48119	T	0.1	-8.843	15.469	0.75426	0.0:0.0:0.0:1.0	.	75;75	Q9NVI1;Q9NVI1-1	FANCI_HUMAN;.	S	75	ENSP00000300027:L75S;ENSP00000310842:L75S;ENSP00000413249:L75S	ENSP00000300027:L75S	L	+	2	0	FANCI	87605014	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.076000	0.76806	2.050000	0.60909	0.533000	0.62120	TTG	.	.		0.428	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		C	89804010	T	C	89804010	3	2	64	1	0	0	0	0	1	0	0	0	5677	1821	63	2	234	2	FANCI	15	89804010	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	4365697	89804010	12727382	249	7966										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99460002	99460002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtggggagaaagggccttgcTgcgcctgccccaaaactgaa	14	11	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr15:99460002T>C	ENST00000268035.6	+	10	2709	c.2098T>C	c.(2098-2100)Tgc>Cgc	p.C700R	IGF1R_ENST00000558762.1_Missense_Mutation_p.C700R	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	700	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	AGGGCCTTGCTGCGCCTGCCC	0.552																																					p.C700R		Atlas-SNP	.											.	IGF1R	147	.	0			c.T2098C						.						71	70	70					15																	99460002		2197	4297	6494	SO:0001583	missense	3480	exon10			CCTTGCTGCGCCT	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2098T>C	chr15.hg19:g.99460002T>C	ENSP00000268035:p.Cys700Arg	150.0	0.0		95.0	4.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.499277	0.85069	.	.	ENSG00000140443	ENST00000268035	T	0.81247	-1.47	5.07	5.07	0.68467	Fibronectin, type III (2);	0.000000	0.64402	D	0.000004	D	0.89361	0.6693	M	0.78916	2.43	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.988	D	0.90827	0.4713	10	0.87932	D	0	.	14.9905	0.71384	0.0:0.0:0.0:1.0	.	700;700	C9J5X1;P08069	.;IGF1R_HUMAN	R	700	ENSP00000268035:C700R	ENSP00000268035:C700R	C	+	1	0	IGF1R	97277525	1.000000	0.71417	0.990000	0.47175	0.969000	0.65631	7.868000	0.87116	2.125000	0.65367	0.533000	0.62120	TGC	.	.		0.552	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		C	99460002	T	C	99460002	3	2	64	1	0	0	0	0	1	0	0	0	7580	1580	55	2	2136	2	IGF1R	15	99460002	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	9655992	99460002	3071390	250	7967										
C1QTNF8	390664	hgsc.bcm.edu	37	chr16	1143730	1143730	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcatgatgtgcaggtaggtcTccttgtagttccaggtgtgc	14	8	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:1143730T>C	ENST00000328449.5	-	4	803	c.530A>G	c.(529-531)gAg>gGg	p.E177G		NM_207419.3	NP_997302.2	P60827	C1QT8_HUMAN	C1q and tumor necrosis factor related protein 8	177	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				lung(2)|prostate(1)|skin(1)	4		Hepatocellular(780;0.00369)				CAGGTAGGTCTCCTTGTAGTT	0.672																																					p.E177G		Atlas-SNP	.											.	C1QTNF8	15	.	0			c.A530G						.						52	55	54					16																	1143730		2198	4293	6491	SO:0001583	missense	390664	exon4			TAGGTCTCCTTGT	AY358832	CCDS32358.1	16p13.3	2014-08-12			ENSG00000184471	ENSG00000184471			31374	protein-coding gene	gene with protein product		614147				12975309	Standard	NM_207419		Approved	UNQ5829, CTRP8	uc010uuw.1	P60827	OTTHUMG00000167756	ENST00000328449.5:c.530A>G	chr16.hg19:g.1143730T>C	ENSP00000330426:p.Glu177Gly	66.0	0.0		70.0	4.0	NM_207419	B7U178	Missense_Mutation	SNP	ENST00000328449.5	hg19	CCDS32358.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307720	0.40795	.	.	ENSG00000184471	ENST00000328449	T	0.75704	-0.96	3.43	2.33	0.28932	Tumour necrosis factor-like (2);Complement C1q protein (2);	0.000000	0.53938	D	0.000055	D	0.83069	0.5174	M	0.87381	2.88	0.39218	D	0.963453	D	0.89917	1.0	D	0.73380	0.98	T	0.79560	-0.1753	10	0.40728	T	0.16	.	3.5733	0.07925	0.1943:0.1084:0.0:0.6973	.	177	P60827	C1QT8_HUMAN	G	177	ENSP00000330426:E177G	ENSP00000330426:E177G	E	-	2	0	C1QTNF8	1083731	1.000000	0.71417	0.939000	0.37840	0.055000	0.15305	4.027000	0.57239	0.423000	0.26033	0.528000	0.53228	GAG	.	.		0.672	C1QTNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396120.1	XM_372606		C	1143730	T	C	1143730	3	2	64	1	0	0	0	0	1	0	0	0	1971	1551	54	2	232	2	C1QTNF8	16	1143730	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		1143730	89211023	251	7968										
ZNF263	10127	hgsc.bcm.edu	37	chr16	3340153	3340153	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gagagactttaccccttctcTgagtgtggggaagctgtgag	14	8	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:3340153T>C	ENST00000219069.5	+	6	2523	c.1647T>C	c.(1645-1647)tcT>tcC	p.S549S	ZNF263_ENST00000538765.1_Silent_p.S197S	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	549					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						ACCCCTTCTCTGAGTGTGGGG	0.473																																					p.S549S		Atlas-SNP	.											.	ZNF263	58	.	0			c.T1647C						.						43	40	41					16																	3340153		2197	4300	6497	SO:0001819	synonymous_variant	10127	exon6			CTTCTCTGAGTGT	AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"Zinc fingers, C2H2-type", "-", "-", "-"	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.1647T>C	chr16.hg19:g.3340153T>C		119.0	0.0		118.0	5.0	NM_005741	B2R634|O43387|Q96H95	Silent	SNP	ENST00000219069.5	hg19	CCDS10499.1																																																																																			.	.		0.473	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2			C	3340153	T	C	3340153	2	2	64	1	0	0	0	0	0	0	0	1	17818	1567	55	2		2	ZNF263	16	3340153	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2196423	3340153	87014600	252	7969										
USP7	7874	hgsc.bcm.edu	37	chr16	9009382	9009382	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	attttccacattatcgagcaActgaaaaagaatgttttggc	7	7	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:9009382A>G	ENST00000344836.4	-	9	1105	c.907T>C	c.(907-909)Ttg>Ctg	p.L303L	USP7_ENST00000535863.1_Splice_Site_p.L204L|USP7_ENST00000381886.4_Splice_Site_p.L287L	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	303	USP.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						TTATCGAGCAACTGAAAAAGA	0.333																																					p.L303L		Atlas-SNP	.											.	USP7	116	.	0			c.T907C						.						78	73	75					16																	9009382		2197	4300	6497	SO:0001630	splice_region_variant	7874	exon9			CGAGCAACTGAAA	Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"Ubiquitin-specific peptidases"	12630	protein-coding gene	gene with protein product		602519	"ubiquitin specific protease 7 (herpes virus-associated)"	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.907-1T>C	chr16.hg19:g.9009382A>G		132.0	0.0		104.0	5.0	NM_003470	A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	hg19	CCDS32385.1																																																																																			.	.		0.333	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2		Silent	G	9009382	A	G	9009382	5	3	64	1	0	0	0	0	0	0	1	0	17103	57	2	2	2493	2	USP7	16	9009382	Splice_Site	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5669229	9009382	81345371	253	7970										
C16orf88	400506	hgsc.bcm.edu	37	chr16	19725915	19725915	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttccttcttgtgttttttgAgcttcttgccaactctggtt	7	9	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:19725915A>G	ENST00000219837.7	-	2	521	c.443T>C	c.(442-444)cTc>cCc	p.L148P	IQCK_ENST00000320394.6_5'Flank|KNOP1_ENST00000568230.1_5'Flank|AC002550.5_ENST00000565916.1_RNA	NM_001012991.2	NP_001013009.2	Q1ED39	KNOP1_HUMAN	lysine-rich nucleolar protein 1	148	Lys-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										GTGTTTTTTGAGCTTCTTGCC	0.547																																					p.L148P		Atlas-SNP	.											.	C16orf88	41	.	0			c.T443C						.						48	53	52					16																	19725915		2167	4287	6454	SO:0001583	missense	400506	exon2			TTTTTGAGCTTCT	BC047010	CCDS42127.1	16p12.3	2013-03-12	2013-03-12	2013-03-12	ENSG00000103550	ENSG00000103550			34404	protein-coding gene	gene with protein product	"family with sequence similarity 191, member A", "testis-specific gene 118"		"chromosome 16 open reading frame 88"	C16orf88			Standard	NM_001012991		Approved	101F10.1, FAM191A, TSG118	uc002dgq.3	Q1ED39		ENST00000219837.7:c.443T>C	chr16.hg19:g.19725915A>G	ENSP00000219837:p.Leu148Pro	95.0	0.0		68.0	4.0	NM_001012991	O43328|Q5FWF3	Missense_Mutation	SNP	ENST00000219837.7	hg19	CCDS42127.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.549815	0.27652	.	.	ENSG00000103550	ENST00000219837	T	0.23950	1.88	4.61	-2.03	0.07365	.	6.817630	0.00397	N	0.000046	T	0.12902	0.0313	N	0.11560	0.145	0.58432	D	0.999999	B	0.11235	0.004	B	0.13407	0.009	T	0.28744	-1.0034	9	.	.	.	-0.066	4.6376	0.12531	0.3509:0.0:0.4689:0.1801	.	148	Q1ED39	CP088_HUMAN	P	148	ENSP00000219837:L148P	.	L	-	2	0	C16orf88	19633416	0.984000	0.35163	0.985000	0.45067	0.901000	0.52897	0.261000	0.18442	-0.158000	0.11040	0.459000	0.35465	CTC	.	.		0.547	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2	NM_001012991		G	19725915	A	G	19725915	3	3	64	1	0	0	0	0	1	0	0	0	1843	304	11	2	949	2	C16orf88	16	19725915	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	10716533	19725915	70628838	254	7971										
HS3ST2	9956	hgsc.bcm.edu	37	chr16	22826066	22826066	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgctgctgcgacgacctgggTcggagccgcctcctcggcgc	15	16	0	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:22826066T>C	ENST00000261374.3	+	1	569	c.135T>C	c.(133-135)ggT>ggC	p.G45G		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	45					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)			breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		ACGACCTGGGTCGGAGCCGCC	0.701																																					p.G45G		Atlas-SNP	.											.	HS3ST2	59	.	0			c.T135C						.						8	10	10					16																	22826066		2127	4170	6297	SO:0001819	synonymous_variant	9956	exon1			CCTGGGTCGGAGC	AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"Sulfotransferases, membrane-bound"	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.135T>C	chr16.hg19:g.22826066T>C		54.0	0.0		73.0	4.0	NM_006043	Q52LZ1	Silent	SNP	ENST00000261374.3	hg19	CCDS10606.1																																																																																			.	.		0.701	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043		C	22826066	T	C	22826066	2	2	64	1	0	0	0	0	0	0	0	1	7373	1654	58	2		2	HS3ST2	16	22826066	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	3100151	22826066	67528687	255	7972										
ARHGAP17	55114	hgsc.bcm.edu	37	chr16	24958829	24958829	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttctggcccataacaagttAgggcctaacacaatcgcaat	7	11	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:24958829A>G	ENST00000289968.6	-	14	1284	c.1215T>C	c.(1213-1215)ccT>ccC	p.P405P	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000303665.5_Silent_p.P405P	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	405	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		ATAACAAGTTAGGGCCTAACA	0.413																																					p.P405P		Atlas-SNP	.											.	ARHGAP17	138	.	0			c.T1215C						.						120	104	110					16																	24958829		2197	4300	6497	SO:0001819	synonymous_variant	55114	exon14			CAAGTTAGGGCCT	AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"Rho GTPase activating proteins"	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.1215T>C	chr16.hg19:g.24958829A>G		64.0	0.0		68.0	4.0	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Silent	SNP	ENST00000289968.6	hg19	CCDS32409.1																																																																																			.	.		0.413	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054		G	24958829	A	G	24958829	2	3	64	1	0	0	0	0	0	0	0	1	867	407	15	2		2	ARHGAP17	16	24958829	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	2132763	24958829	65395924	256	7973										
XPO6	23214	hgsc.bcm.edu	37	chr16	28124248	28124248	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atcgacaagtcgcagggcagAggcatcagtgattctgttga	13	8	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:28124248A>G	ENST00000304658.5	-	16	2628	c.2128T>C	c.(2128-2130)Tct>Cct	p.S710P	XPO6_ENST00000565698.1_Missense_Mutation_p.S696P	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	710					protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						CGCAGGGCAGAGGCATCAGTG	0.587																																					p.S710P		Atlas-SNP	.											.	XPO6	177	.	0			c.T2128C						.						60	64	63					16																	28124248		1962	4151	6113	SO:0001583	missense	23214	exon16			GGGCAGAGGCATC	AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"Exportins"	19733	protein-coding gene	gene with protein product		608411	"RAN binding protein 20"	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.2128T>C	chr16.hg19:g.28124248A>G	ENSP00000302790:p.Ser710Pro	66.0	0.0		88.0	4.0	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	hg19	CCDS42135.1	.	.	.	.	.	.	.	.	.	.	A	14.53	2.562942	0.45694	.	.	ENSG00000169180	ENST00000304658	T	0.70282	-0.47	5.64	5.64	0.86602	Armadillo-like helical (1);Armadillo-type fold (1);	0.171220	0.53938	D	0.000053	T	0.59865	0.2225	L	0.40543	1.245	0.46564	D	0.999107	P;P	0.38335	0.497;0.627	B;B	0.34489	0.091;0.184	T	0.59166	-0.7505	10	0.25106	T	0.35	-14.0359	13.816	0.63292	1.0:0.0:0.0:0.0	.	710;710	B7ZM10;Q96QU8	.;XPO6_HUMAN	P	710	ENSP00000302790:S710P	ENSP00000302790:S710P	S	-	1	0	XPO6	28031749	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.939000	0.70179	2.162000	0.67917	0.455000	0.32223	TCT	.	.		0.587	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		G	28124248	A	G	28124248	3	3	64	1	0	0	0	0	1	0	0	0	17463	304	11	2	1285	2	XPO6	16	28124248	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	3165419	28124248	62230505	257	7974										
SETD1A	9739	hgsc.bcm.edu	37	chr16	30978231	30978231	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cagaacgcggccaagcagcaAgccaaggaggaggataaaga	14	9	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:30978231A>G	ENST00000262519.8	+	9	3218	c.2532A>G	c.(2530-2532)caA>caG	p.Q844Q		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	844					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CCAAGCAGCAAGCCAAGGAGG	0.642																																					p.Q844Q		Atlas-SNP	.											.	SETD1A	143	.	0			c.A2532G						.						29	26	27					16																	30978231		2185	4285	6470	SO:0001819	synonymous_variant	9739	exon9			GCAGCAAGCCAAG	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.2532A>G	chr16.hg19:g.30978231A>G		82.0	0.0		80.0	4.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Silent	SNP	ENST00000262519.8	hg19	CCDS32435.1																																																																																			.	.		0.642	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		G	30978231	A	G	30978231	2	3	64	1	0	0	0	0	0	0	0	1	14145	69	3	2		2	SETD1A	16	30978231	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	2853983	30978231	59376522	258	7975										
SLC12A3	6559	hgsc.bcm.edu	37	chr16	56913123	56913123	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcacagctgccactacggccTcatcaactattaccaggtac	7	15	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:56913123T>C	ENST00000563236.1	+	10	1344	c.1319T>C	c.(1318-1320)cTc>cCc	p.L440P	SLC12A3_ENST00000566786.1_Missense_Mutation_p.L439P|SLC12A3_ENST00000262502.5_Missense_Mutation_p.L439P|SLC12A3_ENST00000438926.2_Missense_Mutation_p.L440P			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	440					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CACTACGGCCTCATCAACTAT	0.632																																					p.L440P		Atlas-SNP	.											.	SLC12A3	99	.	0			c.T1319C						.						31	33	33					16																	56913123		2197	4300	6497	SO:0001583	missense	6559	exon10			ACGGCCTCATCAA		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"Solute carriers"	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.1319T>C	chr16.hg19:g.56913123T>C	ENSP00000456149:p.Leu440Pro	109.0	0.0		79.0	4.0	NM_001126108	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	hg19	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	T	19.25	3.791560	0.70452	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	4.91	4.91	0.64330	Amino acid permease domain (1);	0.061080	0.64402	D	0.000003	D	0.86698	0.5995	H	0.95470	3.675	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.997	D	0.90750	0.4656	9	0.87932	D	0	.	14.5276	0.67900	0.0:0.0:0.0:1.0	.	439;440;440	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	P	439;440	.	ENSP00000262502:L440P	L	+	2	0	SLC12A3	55470624	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	7.906000	0.87423	1.825000	0.53177	0.379000	0.24179	CTC	.	.		0.632	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			C	56913123	T	C	56913123	3	2	64	1	0	0	0	0	1	0	0	0	14399	1551	54	2	1357	2	SLC12A3	16	56913123	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	25934892	56913123	33441630	259	7976										
CDH16	1014	hgsc.bcm.edu	37	chr16	66946026	66946026	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	accacctcatgacttggagcTgcctcataactgaggttctg	9	12	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:66946026T>C	ENST00000299752.4	-	13	1759	c.1566A>G	c.(1564-1566)gcA>gcG	p.A522A	CDH16_ENST00000568632.1_Silent_p.A425A|CDH16_ENST00000394055.3_Silent_p.A522A|CDH16_ENST00000570262.1_Silent_p.A442A|CDH16_ENST00000565796.1_Silent_p.A522A	NM_001204744.1|NM_001204745.1|NM_004062.3	NP_001191673.1|NP_001191674.1|NP_004053.1	O75309	CAD16_HUMAN	cadherin 16, KSP-cadherin	522	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(3)|large_intestine(10)|lung(15)|ovary(2)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		GACTTGGAGCTGCCTCATAAC	0.642																																					p.A522A		Atlas-SNP	.											.	CDH16	91	.	0			c.A1566G						.						42	41	42					16																	66946026		2200	4300	6500	SO:0001819	synonymous_variant	1014	exon13			TGGAGCTGCCTCA	AF016272	CCDS10823.1, CCDS56002.1, CCDS58471.1, CCDS58472.1	16q22.1	2010-01-26			ENSG00000166589	ENSG00000166589		"Cadherins / Major cadherins"	1755	protein-coding gene	gene with protein product		603118				9721215, 7615566	Standard	NM_004062		Approved		uc002eql.3	O75309	OTTHUMG00000137518	ENST00000299752.4:c.1566A>G	chr16.hg19:g.66946026T>C		96.0	0.0		75.0	4.0	NM_004062	B4DPA8|H3BPD3|Q6UW93	Silent	SNP	ENST00000299752.4	hg19	CCDS10823.1																																																																																			.	.		0.642	CDH16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268839.2	NM_004062		C	66946026	T	C	66946026	2	2	64	1	0	0	0	0	0	0	0	1	3103	1567	55	2		2	CDH16	16	66946026	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	10032903	66946026	23408727	260	7977										
ATP6V0D1	9114	hgsc.bcm.edu	37	chr16	67477048	67477048	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cgatgttcatctcgtcaaggTcctgctctgaaatgcagtcc	9	12	4	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:67477048T>C	ENST00000290949.3	-	4	665	c.515A>G	c.(514-516)gAc>gGc	p.D172G	ATP6V0D1_ENST00000602876.1_Missense_Mutation_p.D95G|ATP6V0D1_ENST00000540149.1_Missense_Mutation_p.D213G|ATP6V0D1_ENST00000567694.1_5'Flank	NM_004691.4	NP_004682.2	P61421	VA0D1_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1	172					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP hydrolysis coupled proton transport (GO:0015991)|brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|cellular protein metabolic process (GO:0044267)|cilium assembly (GO:0042384)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|synaptic vesicle (GO:0008021)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)			large_intestine(3)|lung(3)|urinary_tract(2)	8		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)		CTCGTCAAGGTCCTGCTCTGA	0.562																																					p.D172G		Atlas-SNP	.											.	ATP6V0D1	25	.	0			c.A515G						.						158	144	149					16																	67477048		2198	4300	6498	SO:0001583	missense	9114	exon4			TCAAGGTCCTGCT	X71490	CCDS10838.1	16q22	2010-04-21	2006-01-20	2002-05-10	ENSG00000159720	ENSG00000159720		"ATPases / V-type"	13724	protein-coding gene	gene with protein product		607028	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), member D", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 1", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D1"	ATP6D		8250920	Standard	NM_004691		Approved	ATP6DV, VATX, VPATPD, P39, Vma6	uc002ete.1	P61421	OTTHUMG00000137515	ENST00000290949.3:c.515A>G	chr16.hg19:g.67477048T>C	ENSP00000290949:p.Asp172Gly	187.0	0.0		145.0	6.0	NM_004691	P12953|Q02547	Missense_Mutation	SNP	ENST00000290949.3	hg19	CCDS10838.1	.	.	.	.	.	.	.	.	.	.	T	16.57	3.161553	0.57368	.	.	ENSG00000159720	ENST00000290949;ENST00000426604;ENST00000540149	T;T	0.34275	1.37;1.37	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.70745	0.3259	H	0.95504	3.68	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.78314	0.991;0.989	T	0.80151	-0.1502	10	0.66056	D	0.02	-34.6226	14.546	0.68030	0.0:0.0:0.0:1.0	.	213;172	F5GYQ1;P61421	.;VA0D1_HUMAN	G	172;95;213	ENSP00000290949:D172G;ENSP00000441282:D213G	ENSP00000290949:D172G	D	-	2	0	ATP6V0D1	66034549	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.307000	0.72815	2.133000	0.65898	0.533000	0.62120	GAC	.	.		0.562	ATP6V0D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268835.1	NM_004691		C	67477048	T	C	67477048	3	2	64	1	0	0	0	0	1	0	0	0	1173	1667	58	2	560	2	ATP6V0D1	16	67477048	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	531022	67477048	22877705	261	7978										
CENPT	80152	hgsc.bcm.edu	37	chr16	67864301	67864301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccacacactcactattcttcTgcagcccaggcccactgctc	5	19	3	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:67864301T>C	ENST00000562787.1	-	11	1402	c.854A>G	c.(853-855)cAg>cGg	p.Q285R	CENPT_ENST00000564817.1_Missense_Mutation_p.Q285R|CENPT_ENST00000440851.2_Missense_Mutation_p.Q285R|CENPT_ENST00000562947.1_5'UTR|CENPT_ENST00000219172.3_Missense_Mutation_p.Q285R	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T	285	Flexible stalk domain. {ECO:0000250}.				chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		ACTATTCTTCTGCAGCCCAGG	0.587																																					p.Q285R		Atlas-SNP	.											.	CENPT	26	.	0			c.A854G						.						66	73	71					16																	67864301		2130	4257	6387	SO:0001583	missense	80152	exon11			TTCTTCTGCAGCC	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3		ENST00000562787.1:c.854A>G	chr16.hg19:g.67864301T>C	ENSP00000457810:p.Gln285Arg	119.0	0.0		94.0	6.0	NM_025082	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	hg19	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.832296	0.50845	.	.	ENSG00000102901	ENST00000440851;ENST00000219172	T;T	0.50548	0.74;0.74	4.98	2.74	0.32292	.	0.572147	0.16294	N	0.220785	T	0.44350	0.1289	M	0.74881	2.28	0.09310	N	0.999999	B;B	0.11235	0.004;0.004	B;B	0.11329	0.006;0.006	T	0.37572	-0.9700	10	0.34782	T	0.22	-5.75	6.7835	0.23659	0.0:0.1917:0.0:0.8083	.	285;285	Q96BT3;B3KPB2	CENPT_HUMAN;.	R	285	ENSP00000400140:Q285R;ENSP00000219172:Q285R	ENSP00000219172:Q285R	Q	-	2	0	CENPT	66421802	0.832000	0.29368	0.021000	0.16686	0.009000	0.06853	1.969000	0.40510	0.456000	0.26937	-0.376000	0.06991	CAG	.	.		0.587	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		C	67864301	T	C	67864301	3	2	64	1	0	0	0	0	1	0	0	0	3244	1580	55	2	855	2	CENPT	16	67864301	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	387253	67864301	22490452	262	7979										
EDC4	23644	hgsc.bcm.edu	37	chr16	67916724	67916724	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcagccaccgtggccggcagTgttcgtgctgaggtgcagca	16	12	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:67916724T>C	ENST00000358933.5	+	26	3824	c.3585T>C	c.(3583-3585)agT>agC	p.S1195S	CTC-479C5.10_ENST00000572067.1_lincRNA|NRN1L_ENST00000576147.1_5'Flank|NRN1L_ENST00000339176.3_5'Flank	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	1195					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		TGGCCGGCAGTGTTCGTGCTG	0.647											OREG0023890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1195S		Atlas-SNP	.											.	EDC4	101	.	0			c.T3585C						.						56	52	53					16																	67916724		2198	4300	6498	SO:0001819	synonymous_variant	23644	exon26			CGGCAGTGTTCGT	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.3585T>C	chr16.hg19:g.67916724T>C		89.0	0.0	1103	76.0	4.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Silent	SNP	ENST00000358933.5	hg19	CCDS10849.1																																																																																			.	.		0.647	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		C	67916724	T	C	67916724	2	2	64	1	0	0	0	0	0	0	0	1	4910	1693	59	2		2	EDC4	16	67916724	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	52423	67916724	22438029	263	7980										
PHLPP2	23035	hgsc.bcm.edu	37	chr16	71683278	71683278	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tacttccacctctaccttgcTgccattggttatgaccccct	5	16	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:71683278T>C	ENST00000568954.1	-	19	3865	c.3487A>G	c.(3487-3489)Agc>Ggc	p.S1163G	PHLPP2_ENST00000540628.1_Intron|PHLPP2_ENST00000356272.3_Missense_Mutation_p.S1163G|PHLPP2_ENST00000567016.1_Missense_Mutation_p.S1198G|PHLPP2_ENST00000360429.3_Intron|PHLPP2_ENST00000393524.2_Missense_Mutation_p.S1096G			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	1163					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						TCTACCTTGCTGCCATTGGTT	0.552																																					p.S1163G		Atlas-SNP	.											.	PHLPP2	96	.	0			c.A3487G						.						69	69	69					16																	71683278		2198	4300	6498	SO:0001583	missense	23035	exon18			CCTTGCTGCCATT	BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	29149	protein-coding gene	gene with protein product		611066	"PH domain and leucine rich repeat protein phosphatase-like"	PHLPPL		17386267	Standard	NM_001289003		Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000568954.1:c.3487A>G	chr16.hg19:g.71683278T>C	ENSP00000457991:p.Ser1163Gly	72.0	0.0		69.0	4.0	NM_015020	A1L374|Q9NV17|Q9Y2E3	Missense_Mutation	SNP	ENST00000568954.1	hg19	CCDS32479.1	.	.	.	.	.	.	.	.	.	.	T	18.48	3.632192	0.67015	.	.	ENSG00000040199	ENST00000356272;ENST00000393524	T;T	0.62639	0.67;0.01	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.79137	0.4395	M	0.75264	2.295	0.54753	D	0.99998	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.98	T	0.81446	-0.0929	10	0.87932	D	0	-21.3651	15.7393	0.77876	0.0:0.0:0.0:1.0	.	1096;1163	Q6ZVD8-3;Q6ZVD8	.;PHLP2_HUMAN	G	1163;1096	ENSP00000348611:S1163G;ENSP00000377159:S1096G	ENSP00000348611:S1163G	S	-	1	0	PHLPP2	70240779	1.000000	0.71417	1.000000	0.80357	0.532000	0.34746	6.103000	0.71492	2.308000	0.77769	0.533000	0.62120	AGC	.	.		0.552	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434139.1	NM_015020		C	71683278	T	C	71683278	3	2	64	1	0	0	0	0	1	0	0	0	11864	1580	55	2	488	2	PHLPP2	16	71683278	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	3766554	71683278	18671475	264	7981										
CHST6	4166	hgsc.bcm.edu	37	chr16	75513087	75513087	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	acgcgccagagccttggctgTctgctcccgggagcgcagca	14	15	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:75513087T>C	ENST00000332272.4	-	3	819	c.640A>G	c.(640-642)Aca>Gca	p.T214A	RP11-77K12.4_ENST00000530512.3_RNA|CHST6_ENST00000390664.2_Missense_Mutation_p.T214A	NM_021615.4	NP_067628.1	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6	214					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GCCTTGGCTGTCTGCTCCCGG	0.726																																					p.T214A		Atlas-SNP	.											.	CHST6	57	.	0			c.A640G						.						21	22	22					16																	75513087		2195	4287	6482	SO:0001583	missense	4166	exon3			TGGCTGTCTGCTC	AF280086	CCDS10918.1	16q22	2008-02-05			ENSG00000183196	ENSG00000183196		"Sulfotransferases, membrane-bound"	6938	protein-coding gene	gene with protein product		605294		MCDC1		8644739, 11017086	Standard	NM_021615		Approved		uc002fef.3	Q9GZX3	OTTHUMG00000137612	ENST00000332272.4:c.640A>G	chr16.hg19:g.75513087T>C	ENSP00000328983:p.Thr214Ala	8.0	0.0		75.0	4.0	NM_021615	D3DUK3	Missense_Mutation	SNP	ENST00000332272.4	hg19	CCDS10918.1	.	.	.	.	.	.	.	.	.	.	T	5.691	0.312125	0.10789	.	.	ENSG00000183196	ENST00000332272;ENST00000390664	D;D	0.99716	-6.51;-6.51	4.68	0.867	0.19085	Sulfotransferase domain (1);	0.364119	0.28977	N	0.013535	D	0.95931	0.8675	N	0.04387	-0.21	0.27160	N	0.96118	B	0.10296	0.003	B	0.17979	0.02	D	0.93532	0.6870	10	0.02654	T	1	.	3.3358	0.07101	0.2253:0.329:0.0:0.4457	.	214	Q9GZX3	CHST6_HUMAN	A	214	ENSP00000328983:T214A;ENSP00000375079:T214A	ENSP00000328983:T214A	T	-	1	0	CHST6	74070588	0.754000	0.28360	0.978000	0.43139	0.175000	0.22909	0.095000	0.15127	0.176000	0.19873	-0.376000	0.06991	ACA	.	.		0.726	CHST6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435478.1	NM_021615		C	75513087	T	C	75513087	3	2	64	1	0	0	0	0	1	0	0	0	3410	1667	58	2	551	2	CHST6	16	75513087	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	3829809	75513087	14841666	265	7982										
CHST5	23563	hgsc.bcm.edu	37	chr16	75563627	75563627	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggtcgcgcaccaggtgcacgAtgcgcaggttgagcgcgggg	19	11	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:75563627A>G	ENST00000336257.3	-	3	2050	c.656T>C	c.(655-657)aTc>aCc	p.I219T	RP11-77K12.7_ENST00000460606.1_3'UTR|CHST5_ENST00000541075.1_Missense_Mutation_p.I225T	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	219					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)	24						CAGGTGCACGATGCGCAGGTT	0.706																																					p.I219T		Atlas-SNP	.											CHST5,right_upper_lobe,carcinoma,0,1	CHST5	47	.	0			c.T656C						.						45	49	48					16																	75563627		2197	4299	6496	SO:0001583	missense	23563	exon3			TGCACGATGCGCA	AF176839	CCDS10919.1	16q23.1	2008-02-05			ENSG00000135702	ENSG00000135702		"Sulfotransferases, membrane-bound"	1973	protein-coding gene	gene with protein product		604817				10491328, 11017086	Standard	NM_024533		Approved	I-GLCNAC-6-ST, FLJ22167	uc002fei.3	Q9GZS9	OTTHUMG00000137610	ENST00000336257.3:c.656T>C	chr16.hg19:g.75563627A>G	ENSP00000338783:p.Ile219Thr	23.0	0.0		27.0	2.0	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Missense_Mutation	SNP	ENST00000336257.3	hg19	CCDS10919.1	.	.	.	.	.	.	.	.	.	.	A	13.35	2.210082	0.39003	.	.	ENSG00000135702	ENST00000336257;ENST00000541075	D;D	0.85556	-2.0;-2.0	2.84	2.84	0.33178	Sulfotransferase domain (1);	0.054428	0.64402	D	0.000001	D	0.91509	0.7319	M	0.85462	2.755	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.76071	0.978;0.987	D	0.91667	0.5347	10	0.72032	D	0.01	.	10.0936	0.42462	1.0:0.0:0.0:0.0	.	225;219	Q9GZS9-2;Q9GZS9	.;CHST5_HUMAN	T	219;225	ENSP00000338783:I219T;ENSP00000441220:I225T	ENSP00000338783:I219T	I	-	2	0	CHST5	74121128	1.000000	0.71417	0.999000	0.59377	0.038000	0.13279	8.717000	0.91425	1.296000	0.44742	0.260000	0.18958	ATC	.	.		0.706	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126		G	75563627	A	G	75563627	3	3	64	1	0	0	0	0	1	0	0	0	3409	333	12	2	583	2	CHST5	16	75563627	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	50540	75563627	14791126	266	7983										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89341222	89341227	+	Splice_Site	DEL	CTGGCT	CTGGCT	-													0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggcatgcagacgggccctacCtggctctccaggggcatgtt							TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	CTGGCT	CTGGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr16:89341222_89341227delCTGGCT	ENST00000301030.4	-	11	8168_8173	c.7708_7713delAGCCAG	c.(7708-7713)agccagdel	p.SQ2570del	ANKRD11_ENST00000378330.2_Splice_Site_p.SQ2570del	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2570					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CGGGCCCTACCTGGCTCTCCAGGGGC	0.641																																					p.2570_2571del		Atlas-Indel,Pindel	.											.	ANKRD11	195	.	0			c.7709_7713del						.																																			SO:0001630	splice_region_variant	29123	exon11			.	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.7713+1AGCCAG>-	chr16.hg19:g.89341222_89341227delCTGGCT		90.0	0.0		69.0	18.0	NM_013275	Q6NTG1|Q6QMF8	Frame_Shift_Del	DEL	ENST00000301030.4	hg19	CCDS32513.1																																																																																			.	.		0.641	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	In_Frame_Del	-	89341227	CTGGCT	-	89341222	8	5	64	1	0	1	0	1	0	0	1	0	639	695	24	0	290	0	ANKRD11	16	89341222	Splice_Site	DEL	CTGGCT	TCGA-CC-A3MA-01A-11D-A20W-10	13777595	89341222	1013531	267	7984										
SMG6	23293	hgsc.bcm.edu	37	chr17	2203182	2203182	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttgcttcttcagtcgtggccTctccttggtcctatcctgtc	8	14	3	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:2203182T>C	ENST00000263073.6	-	2	915	c.865A>G	c.(865-867)Agg>Ggg	p.R289G	SMG6_ENST00000544865.1_Missense_Mutation_p.R258G	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	289	Interaction with telomeric DNA.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						AGTCGTGGCCTCTCCTTGGTC	0.567																																					p.R289G	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A865G						.						82	72	75					17																	2203182		2203	4300	6503	SO:0001583	missense	23293	exon2			GTGGCCTCTCCTT	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"EST1 telomerase component homolog A (S. cerevisiae)"	610963	"chromosome 17 open reading frame 31", "smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.865A>G	chr17.hg19:g.2203182T>C	ENSP00000263073:p.Arg289Gly	135.0	0.0		90.0	4.0	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	hg19	CCDS11016.1	.	.	.	.	.	.	.	.	.	.	T	16.10	3.028541	0.54790	.	.	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.11712	2.75;2.75	5.35	4.2	0.49525	.	0.542190	0.21297	N	0.076880	T	0.07728	0.0194	L	0.27053	0.805	0.41774	D	0.989784	B	0.29936	0.262	B	0.21360	0.034	T	0.27571	-1.0070	10	0.39692	T	0.17	-8.2077	11.6871	0.51492	0.0:0.0:0.148:0.852	.	289	Q86US8	EST1A_HUMAN	G	289;258	ENSP00000263073:R289G;ENSP00000443920:R258G	ENSP00000263073:R289G	R	-	1	2	SMG6	2149932	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.087000	0.41653	2.015000	0.59207	0.533000	0.62120	AGG	.	.		0.567	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			C	2203182	T	C	2203182	3	2	64	1	0	0	0	0	1	0	0	0	14812	1550	54	2	3466	2	SMG6	17	2203182	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		2203182	78992028	268	7985										
PELP1	27043	hgsc.bcm.edu	37	chr17	4575334	4575334	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gactcagggggaggcagagcTggaggcagggttgggggtgg	24	5	1	1	rs139398595	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:4575334T>G	ENST00000574876.1	-	16	2969	c.2952A>C	c.(2950-2952)ccA>ccC	p.P984P	PELP1_ENST00000269230.7_Silent_p.P894P|PELP1_ENST00000301396.4_Silent_p.P1128P|PELP1_ENST00000572293.1_Silent_p.P1034P|PELP1_ENST00000436683.2_Intron			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	984	Glu-rich.|Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GAGGCAGAGCTGGAGGCAGGG	0.617																																					p.P984P		Atlas-SNP	.											.	PELP1	102	.	0			c.A2952C						.						36	40	38					17																	4575334		2011	4156	6167	SO:0001819	synonymous_variant	27043	exon16			CAGAGCTGGAGGC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"proline, glutamic acid and leucine rich protein 1"			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2952A>C	chr17.hg19:g.4575334T>G		48.0	0.0		19.0	5.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	hg19	CCDS58503.1																																																																																			.	.		0.617	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		G	4575334	T	G	4575334	2	3	64	1	0	0	0	0	0	0	0	1	11734	1567	55	5		5	PELP1	17	4575334	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2372152	4575334	76619876	269	7986										
TP53	7157	hgsc.bcm.edu	37	chr17	7579349	7579349	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tggctgtcccagaatgcaagAagcccagacggaaaccgtag	12	11	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:7579349A>C	ENST00000269305.4	-	4	527	c.338T>G	c.(337-339)tTc>tGc	p.F113C	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.F113C|TP53_ENST00000455263.2_Missense_Mutation_p.F113C|TP53_ENST00000413465.2_Missense_Mutation_p.F113C|TP53_ENST00000359597.4_Missense_Mutation_p.F113C|TP53_ENST00000445888.2_Missense_Mutation_p.F113C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	113	Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		F -> C (in sporadic cancers; somatic mutation).|F -> G (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|F -> I (in a sporadic cancer; somatic mutation).|F -> L (in sporadic cancers; somatic mutation).|F -> S (in sporadic cancers; somatic mutation).|F -> V (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.F113C(11)|p.0?(8)|p.F113S(4)|p.G59fs*23(3)|p.V73fs*9(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.G112fs*9(1)|p.F113del(1)|p.Y107fs*44(1)|p.G112_S116delGFLHS(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGAATGCAAGAAGCCCAGACG	0.607		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.F113C	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000413465,NS,carcinoma,0,16	TP53	33396	.	35	Substitution - Missense(15)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(4)	upper_aerodigestive_tract(6)|lung(5)|large_intestine(4)|bone(4)|central_nervous_system(3)|ovary(3)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|breast(2)|stomach(1)|liver(1)|oesophagus(1)|autonomic_ganglia(1)	c.T338G						.						65	61	62					17																	7579349		2203	4300	6503	SO:0001583	missense	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TGCAAGAAGCCCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.338T>G	chr17.hg19:g.7579349A>C	ENSP00000269305:p.Phe113Cys	200.0	0.0		137.0	84.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	18.70	3.680367	0.68042	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99867	-7.31;-7.31;-7.31;-7.31;-7.31;-7.31;-7.31;-7.31	4.75	4.75	0.60458	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99854	0.9932	M	0.89414	3.03	0.52099	D	0.999945	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.995;1.0;1.0;1.0	D	0.96472	0.9349	10	0.87932	D	0	-31.6488	12.5363	0.56144	1.0:0.0:0.0:0.0	.	74;113;113;113;113;113;113	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	113	ENSP00000410739:F113C;ENSP00000352610:F113C;ENSP00000269305:F113C;ENSP00000398846:F113C;ENSP00000391127:F113C;ENSP00000391478:F113C;ENSP00000424104:F113C;ENSP00000426252:F113C	ENSP00000269305:F113C	F	-	2	0	TP53	7520074	1.000000	0.71417	0.986000	0.45419	0.960000	0.62799	5.450000	0.66626	2.125000	0.65367	0.533000	0.62120	TTC	.	.		0.607	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7579349	A	C	7579349	3	2	64	1	0	0	0	0	1	0	0	0	16396	246	9	5	964	5	TP53	17	7579349	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	3004015	7579349	73615861	270	7987										
C17orf68	80169	hgsc.bcm.edu	37	chr17	8131865	8131865	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcctttccagctcaaaagaaAgcacaataggacggaggaca	9	10	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:8131865A>G	ENST00000315684.8	-	22	3477	c.3470T>C	c.(3469-3471)cTt>cCt	p.L1157P		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	1157					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						CTCAAAAGAAAGCACAATAGG	0.498																																					p.L1157P		Atlas-SNP	.											.	CTC1	75	.	0			c.T3470C						.						233	237	235					17																	8131865		1955	4141	6096	SO:0001583	missense	80169	exon22			AAAGAAAGCACAA	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"conserved telomere maintenance component 1", "alpha accessory factor 132", "conserved telomere capping protein 1"	613129	"tmp494178", "chromosome 17 open reading frame 68"	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.3470T>C	chr17.hg19:g.8131865A>G	ENSP00000313759:p.Leu1157Pro	122.0	0.0		95.0	4.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Missense_Mutation	SNP	ENST00000315684.8	hg19	CCDS42259.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.267293	0.59540	.	.	ENSG00000178971	ENST00000315684	D	0.88896	-2.44	5.56	5.56	0.83823	.	0.151994	0.42294	D	0.000721	D	0.93213	0.7838	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	D	0.93736	0.7046	10	0.87932	D	0	-16.3838	12.1138	0.53854	1.0:0.0:0.0:0.0	.	1157	Q2NKJ3	CTC1_HUMAN	P	1157	ENSP00000313759:L1157P	ENSP00000313759:L1157P	L	-	2	0	CTC1	8072590	0.998000	0.40836	1.000000	0.80357	0.973000	0.67179	4.985000	0.63845	2.133000	0.65898	0.533000	0.62120	CTT	.	.		0.498	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		G	8131865	A	G	8131865	3	3	64	1	0	0	0	0	1	0	0	0	1878	72	3	2	191	2	C17orf68	17	8131865	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	552516	8131865	73063345	271	7988										
GAS7	8522	hgsc.bcm.edu	37	chr17	9843452	9843452	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tacccactcacccttcctccTgtgaagccaaggagttctga	7	15	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:9843452T>C	ENST00000432992.2	-	8	957	c.797A>G	c.(796-798)cAg>cGg	p.Q266R	GAS7_ENST00000437099.2_Missense_Mutation_p.Q202R|GAS7_ENST00000580865.1_Missense_Mutation_p.Q126R|GAS7_ENST00000585266.1_Missense_Mutation_p.Q206R|GAS7_ENST00000542249.1_Missense_Mutation_p.Q202R|GAS7_ENST00000323816.4_Missense_Mutation_p.Q206R|GAS7_ENST00000540214.1_Intron|GAS7_ENST00000583882.1_Intron|GAS7_ENST00000396115.2_Intron|GAS7_ENST00000579158.1_Missense_Mutation_p.Q202R	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7	266	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						CCCTTCCTCCTGTGAAGCCAA	0.512			T	MLL	AML*																																p.Q266R		Atlas-SNP	.		Dom	yes		17	17p	8522	growth arrest-specific 7		L	.	GAS7	113	.	0			c.A797G						.						188	164	172					17																	9843452		2203	4300	6503	SO:0001583	missense	8522	exon8			TCCTCCTGTGAAG	AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18							4169	protein-coding gene	gene with protein product		603127				9736752	Standard	NM_001130831		Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.797A>G	chr17.hg19:g.9843452T>C	ENSP00000407552:p.Gln266Arg	130.0	0.0		85.0	4.0	NM_201433	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	Missense_Mutation	SNP	ENST00000432992.2	hg19	CCDS11152.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.477493	0.63849	.	.	ENSG00000007237	ENST00000323816;ENST00000396115;ENST00000437099;ENST00000432992;ENST00000537970;ENST00000541114	T	0.16897	2.31	4.99	4.99	0.66335	Fps/Fes/Fer/CIP4 homology (3);	0.000000	0.64402	D	0.000001	T	0.17323	0.0416	M	0.64997	1.995	0.58432	D	0.999999	P;P;B;P	0.39535	0.483;0.677;0.076;0.483	B;B;B;B	0.33121	0.11;0.158;0.035;0.158	T	0.02821	-1.1106	9	.	.	.	4.219	12.5728	0.56347	0.0:0.0:0.0:1.0	.	218;206;126;266	B7Z2L1;A8KAC2;O60861-2;O60861	.;.;.;GAS7_HUMAN	R	266;206;205;126;206;80	ENSP00000379421:Q206R	.	Q	-	2	0	GAS7	9784177	1.000000	0.71417	0.998000	0.56505	0.965000	0.64279	7.122000	0.77169	2.223000	0.72356	0.533000	0.62120	CAG	.	.		0.512	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439883.1	NM_003644, NM_201432, NM_201433		C	9843452	T	C	9843452	3	2	64	1	0	0	0	0	1	0	0	0	6258	1580	55	2	661	2	GAS7	17	9843452	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1711587	9843452	71351758	272	7989										
MYH3	4621	hgsc.bcm.edu	37	chr17	10532990	10532990	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cgatatccgcacgttcctcgGcctcctccagctcatgctga	8	17	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:10532990G>A	ENST00000583535.1	-	40	5807	c.5720C>T	c.(5719-5721)gCc>gTc	p.A1907V	MYH3_ENST00000226209.7_Missense_Mutation_p.A1907V	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1907					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						ACGTTCCTCGGCCTCCTCCAG	0.547																																					p.A1907V		Atlas-SNP	.											.	MYH3	227	.	0			c.C5720T						.						84	75	78					17																	10532990		2203	4300	6503	SO:0001583	missense	4621	exon40			TCCTCGGCCTCCT		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.5720C>T	chr17.hg19:g.10532990G>A	ENSP00000464317:p.Ala1907Val	114.0	0.0		79.0	4.0	NM_002470	Q15492	Missense_Mutation	SNP	ENST00000583535.1	hg19	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	G	34	5.336525	0.95758	.	.	ENSG00000109063	ENST00000226209	D	0.82984	-1.67	5.0	5.0	0.66597	Myosin tail (1);	.	.	.	.	D	0.93232	0.7844	M	0.94021	3.485	0.53688	D	0.999971	D	0.58970	0.984	D	0.67548	0.952	D	0.94010	0.7283	9	0.54805	T	0.06	.	18.8532	0.92241	0.0:0.0:1.0:0.0	.	1907	P11055	MYH3_HUMAN	V	1907	ENSP00000226209:A1907V	ENSP00000226209:A1907V	A	-	2	0	MYH3	10473715	1.000000	0.71417	0.978000	0.43139	0.916000	0.54674	9.657000	0.98554	2.769000	0.95229	0.655000	0.94253	GCC	.	.		0.547	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		A	10532990	G	A	10532990	3	1	64	1	0	0	0	0	1	0	0	0	10045	1203	42	3	110	3	MYH3	17	10532990	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	689538	10532990	70662220	273	7990										
ZNF287	57336	hgsc.bcm.edu	37	chr17	16456389	16456389	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gaagtattttcctatgtacaAtaccatatgagacatgattg	7	6	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:16456389A>G	ENST00000395824.1	-	6	1684	c.1067T>C	c.(1066-1068)aTt>aCt	p.I356T	ZNF287_ENST00000395825.3_Missense_Mutation_p.I356T			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	349					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		CCTATGTACAATACCATATGA	0.368																																					p.I356T		Atlas-SNP	.											.	ZNF287	60	.	0			c.T1067C						.						87	84	85					17																	16456389		2203	4300	6503	SO:0001583	missense	57336	exon6			TGTACAATACCAT	AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"Zinc fingers, C2H2-type", "-", "-", "-"	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.1067T>C	chr17.hg19:g.16456389A>G	ENSP00000379168:p.Ile356Thr	102.0	0.0		86.0	4.0	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	hg19	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.213909	0.00289	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	T;T	0.14893	2.47;2.47	5.31	0.626	0.17670	.	0.936048	0.08977	N	0.866350	T	0.08626	0.0214	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42949	-0.9421	10	0.11485	T	0.65	.	4.23	0.10599	0.5157:0.0:0.3338:0.1505	.	349	Q9HBT7	ZN287_HUMAN	T	356	ENSP00000379169:I356T;ENSP00000379168:I356T	ENSP00000379168:I356T	I	-	2	0	ZNF287	16397114	0.000000	0.05858	0.054000	0.19295	0.004000	0.04260	0.902000	0.28459	0.177000	0.19895	-0.297000	0.09499	ATT	.	.		0.368	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1			G	16456389	A	G	16456389	3	3	64	1	0	0	0	0	1	0	0	0	17840	101	4	2	1222	2	ZNF287	17	16456389	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5923399	16456389	64738821	274	7991										
TRIM16L	147166	hgsc.bcm.edu	37	chr17	18638692	18638692	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gctgccttctggctttccaaGaaggaaaacgccatccggat	10	12	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:18638692G>T	ENST00000449552.2	+	7	2450	c.966G>T	c.(964-966)aaG>aaT	p.K322N	TRIM16L_ENST00000395671.4_Missense_Mutation_p.K322N|TRIM16L_ENST00000572555.1_Missense_Mutation_p.K322N|TRIM16L_ENST00000395672.2_Missense_Mutation_p.K322N|TRIM16L_ENST00000395902.3_Missense_Mutation_p.K376N|TRIM16L_ENST00000571708.1_Missense_Mutation_p.K322N|TRIM16L_ENST00000414850.2_3'UTR			Q309B1	TR16L_HUMAN	tripartite motif containing 16-like	322	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)	9						GGCTTTCCAAGAAGGAAAACG	0.517																																					p.K322N		Atlas-SNP	.											.	TRIM16L	15	.	0			c.G966T						.						50	50	50					17																	18638692		2203	4300	6503	SO:0001583	missense	147166	exon5			TTCCAAGAAGGAA	DQ232882	CCDS32588.1	17p11.2	2011-02-10	2011-01-25		ENSG00000108448	ENSG00000108448			32670	protein-coding gene	gene with protein product			"tripartite motif-containing 16-like"				Standard	XM_005256479		Approved	TRIM70	uc002gui.1	Q309B1	OTTHUMG00000059050	ENST00000449552.2:c.966G>T	chr17.hg19:g.18638692G>T	ENSP00000461386:p.Lys322Asn	161.0	0.0		182.0	74.0	NM_001037330	A0PK10|B2RUW6|B4DQK2|B4DWQ8	Missense_Mutation	SNP	ENST00000449552.2	hg19	CCDS32588.1	.	.	.	.	.	.	.	.	.	.	g	12.62	1.991570	0.35131	.	.	ENSG00000108448	ENST00000395902;ENST00000395672;ENST00000395671	T;T;T	0.69175	-0.38;-0.38;-0.38	3.35	2.37	0.29283	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.135643	0.49305	U	0.000141	T	0.70842	0.3270	L	0.43554	1.36	0.40720	D	0.982651	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.66945	-0.5795	10	0.34782	T	0.22	-22.435	8.3174	0.32108	0.1242:0.0:0.8758:0.0	.	376;538;322	B4DE22;B3KMJ2;Q309B1	.;.;TR16L_HUMAN	N	376;322;322	ENSP00000379239:K376N;ENSP00000379031:K322N;ENSP00000379030:K322N	ENSP00000379030:K322N	K	+	3	2	TRIM16L	18579417	1.000000	0.71417	1.000000	0.80357	0.435000	0.31806	5.627000	0.67784	0.607000	0.29982	0.194000	0.17425	AAG	.	.		0.517	TRIM16L-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130670.3	NM_001037330		T	18638692	G	T	18638692	3	4	64	1	0	0	0	0	1	0	0	0	16507	933	33	3	980	3	TRIM16L	17	18638692	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	2182303	18638692	62556518	275	7992										
WSB1	26118	hgsc.bcm.edu	37	chr17	25630657	25630657	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atcaaaatatgggatgtataTacaggtatggattcatagtt	9	3	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:25630657T>A	ENST00000262394.2	+	3	790	c.474T>A	c.(472-474)taT>taA	p.Y158*	WSB1_ENST00000579733.1_Intron|WSB1_ENST00000348811.2_Intron|WSB1_ENST00000427287.2_Nonsense_Mutation_p.Y127*|WSB1_ENST00000583193.1_Intron|WSB1_ENST00000581185.1_Nonsense_Mutation_p.Y158*	NM_015626.8	NP_056441.6	Q9Y6I7	WSB1_HUMAN	WD repeat and SOCS box containing 1	158					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)				lung(3)	3	all_cancers(1;2e-13)|all_epithelial(1;4.8e-15)|Lung NSC(42;0.00152)		BRCA - Breast invasive adenocarcinoma(3;0.0152)	UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		GGGATGTATATACAGGTATGG	0.378																																					p.Y158X		Atlas-SNP	.											.	WSB1	29	.	0			c.T474A						.						126	133	130					17																	25630657		2203	4300	6503	SO:0001587	stop_gained	26118	exon3			TGTATATACAGGT	AF069313	CCDS11220.1, CCDS11221.1	17q11.2	2013-01-09	2011-01-25		ENSG00000109046	ENSG00000109046		"WD repeat domain containing"	19221	protein-coding gene	gene with protein product		610091	"WD repeat and SOCS box-containing 1"			10354473, 12076535	Standard	XR_243778		Approved	DKFZp564A122, DKFZp564B0482, SWIP1	uc002gzd.1	Q9Y6I7	OTTHUMG00000132293	ENST00000262394.2:c.474T>A	chr17.hg19:g.25630657T>A	ENSP00000262394:p.Tyr158*	115.0	0.0		90.0	34.0	NM_015626	Q9NRB1|Q9UBH9|Q9UG25|Q9UNN6|Q9Y656	Nonsense_Mutation	SNP	ENST00000262394.2	hg19	CCDS11220.1	.	.	.	.	.	.	.	.	.	.	T	38	6.910434	0.97928	.	.	ENSG00000109046	ENST00000262394;ENST00000427287	.	.	.	6.04	1.53	0.23141	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-6.4536	9.3047	0.37867	0.0:0.4004:0.0:0.5996	.	.	.	.	X	158;127	.	ENSP00000262394:Y158X	Y	+	3	2	WSB1	22654784	0.999000	0.42202	1.000000	0.80357	0.968000	0.65278	0.611000	0.24268	0.547000	0.28938	-0.376000	0.06991	TAT	.	.		0.378	WSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255391.4	NM_015626		A	25630657	T	A	25630657	4	1	64	1	0	0	0	0	0	1	0	0	17419	1413	49	4	484	4	WSB1	17	25630657	Nonsense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	6991965	25630657	55564553	276	7993										
MYO1D	4642	hgsc.bcm.edu	37	chr17	31087321	31087321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cactcacatgtttccaggggAtcccttcccgctggtattcc	8	15	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:31087321A>G	ENST00000318217.5	-	10	1587	c.1283T>C	c.(1282-1284)aTc>aCc	p.I428T	MYO1D_ENST00000583621.1_Missense_Mutation_p.I428T|MYO1D_ENST00000579584.1_Missense_Mutation_p.I428T|MYO1D_ENST00000394649.4_Missense_Mutation_p.I340T|MYO1D_ENST00000584232.1_5'UTR	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	428	Myosin motor.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			TTTCCAGGGGATCCCTTCCCG	0.363																																					p.I428T		Atlas-SNP	.											.	MYO1D	93	.	0			c.T1283C						.						189	184	185					17																	31087321		2203	4300	6503	SO:0001583	missense	4642	exon10			CAGGGGATCCCTT	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"Myosins / Myosin superfamily : Class I"	7598	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 108"	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.1283T>C	chr17.hg19:g.31087321A>G	ENSP00000324527:p.Ile428Thr	95.0	0.0		116.0	5.0	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	hg19	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.963843	0.74131	.	.	ENSG00000176658	ENST00000318217	T	0.80393	-1.37	5.46	5.46	0.80206	Myosin head, motor domain (2);	0.000000	0.40064	U	0.001200	D	0.93752	0.8003	H	0.99042	4.41	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.75484	0.986;0.981	D	0.95834	0.8860	10	0.87932	D	0	.	13.7799	0.63077	1.0:0.0:0.0:0.0	.	339;428	Q7Z3N6;O94832	.;MYO1D_HUMAN	T	428	ENSP00000324527:I428T	ENSP00000324527:I428T	I	-	2	0	MYO1D	28111434	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	9.339000	0.96797	2.206000	0.71126	0.533000	0.62120	ATC	.	.		0.363	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			G	31087321	A	G	31087321	3	3	64	1	0	0	0	0	1	0	0	0	10080	333	12	2	1789	2	MYO1D	17	31087321	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5456664	31087321	50107889	277	7994										
KRT24	192666	hgsc.bcm.edu	37	chr17	38858135	38858135	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcatcagcagccaatctggcAttgtcaatgtgcaaaatgat	8	9	4	1	rs11309872	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:38858135A>C	ENST00000264651.2	-	2	722	c.666T>G	c.(664-666)aaT>aaG	p.N222K		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	222	Coil 1B.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				CCAATCTGGCATTGTCAATGT	0.333																																					p.N222K	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.,1	KRT24	60	.	0			c.T666G						.						70	54	60					17																	38858135		2078	3619	5697	SO:0001583	missense	192666	exon2			TCTGGCATTGTCA		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"-", "Intermediate filaments type I, keratins (acidic)"	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.666T>G	chr17.hg19:g.38858135A>C	ENSP00000264651:p.Asn222Lys	291.0	0.0		341.0	14.0	NM_019016	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	hg19	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	A	19.92	3.917086	0.73098	.	.	ENSG00000167916	ENST00000264651	D	0.89050	-2.46	6.04	2.68	0.31781	Filament (1);	.	.	.	.	D	0.95472	0.8529	H	0.96048	3.76	0.43874	D	0.996486	D	0.89917	1.0	D	0.91635	0.999	D	0.94407	0.7628	9	0.87932	D	0	.	9.1141	0.36746	0.7194:0.0:0.2806:0.0	.	222	Q2M2I5	K1C24_HUMAN	K	222	ENSP00000264651:N222K	ENSP00000264651:N222K	N	-	3	2	KRT24	36111661	0.974000	0.33945	1.000000	0.80357	0.995000	0.86356	0.275000	0.18698	0.540000	0.28808	0.459000	0.35465	AAT	.	.		0.333	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		C	38858135	A	C	38858135	3	2	64	1	0	0	0	0	1	0	0	0	8470	214	8	5	939	5	KRT24	17	38858135	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	7770814	38858135	42337075	278	7995										
GHDC	84514	hgsc.bcm.edu	37	chr17	40343211	40343211	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atggggctgctctggctgtaGgtttaggcccagcacccctg	14	12	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:40343211G>C	ENST00000301671.8	-	5	1348	c.907C>G	c.(907-909)Cta>Gta	p.L303V	GHDC_ENST00000590520.1_5'Flank|GHDC_ENST00000428494.2_Missense_Mutation_p.L264V|GHDC_ENST00000587427.1_Missense_Mutation_p.L303V|GHDC_ENST00000414034.3_Missense_Mutation_p.L303V|GHDC_ENST00000436923.2_Missense_Mutation_p.L303V|GHDC_ENST00000593209.1_Missense_Mutation_p.L303V			Q8N2G8	GHDC_HUMAN	GH3 domain containing	303						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		TCTGGCTGTAGGTTTAGGCCC	0.627																																					p.L303V		Atlas-SNP	.											.	GHDC	63	.	0			c.C907G						.						33	38	36					17																	40343211		2203	4300	6503	SO:0001583	missense	84514	exon6			GCTGTAGGTTTAG	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.907C>G	chr17.hg19:g.40343211G>C	ENSP00000301671:p.Leu303Val	71.0	0.0		72.0	34.0	NM_001142623	B4DQS4|E9PDB5|Q9BXM6	Missense_Mutation	SNP	ENST00000301671.8	hg19	CCDS11422.1	.	.	.	.	.	.	.	.	.	.	G	10.96	1.500047	0.26861	.	.	ENSG00000167925	ENST00000393854;ENST00000428494;ENST00000414034;ENST00000301671;ENST00000436923	.	.	.	4.03	2.04	0.26737	.	0.000000	0.64402	D	0.000017	T	0.66167	0.2762	M	0.69185	2.1	0.38752	D	0.954132	D;P;D	0.76494	0.994;0.754;0.999	D;P;D	0.87578	0.94;0.65;0.998	T	0.63328	-0.6662	9	0.30078	T	0.28	-8.7373	4.661	0.12643	0.1912:0.0:0.6372:0.1716	.	264;303;303	E9PDB5;Q8N2G8-2;Q8N2G8	.;.;GHDC_HUMAN	V	247;264;303;303;303	.	ENSP00000301671:L303V	L	-	1	2	GHDC	37596737	1.000000	0.71417	0.979000	0.43373	0.257000	0.26127	1.724000	0.38064	0.383000	0.24910	-0.219000	0.12488	CTA	.	.		0.627	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		C	40343211	G	C	40343211	3	2	64	1	0	0	0	0	1	0	0	0	6377	991	35	4	794	4	GHDC	17	40343211	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	1485076	40343211	40851999	279	7996										
HOXB6	3216	hgsc.bcm.edu	37	chr17	46673963	46673963	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcgattgtagtgaaactcctTctccagctccagcgtctggt	10	12	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:46673963T>C	ENST00000484302.2	-	3	1109	c.487A>G	c.(487-489)Aag>Gag	p.K163E	HOXB-AS3_ENST00000474040.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB6_ENST00000225648.3_Missense_Mutation_p.K163E|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB5_ENST00000239151.5_5'Flank|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB6_ENST00000490419.1_5'Flank|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000492897.3_RNA			P17509	HXB6_HUMAN	homeobox B6	163					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte homeostasis (GO:0034101)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K163E(1)		breast(1)|kidney(1)|large_intestine(1)|lung(4)	7						TGAAACTCCTTCTCCAGCTCC	0.612																																					p.K163E		Atlas-SNP	.											HOXB6,NS,carcinoma,0,1	HOXB6	13	.	1	Substitution - Missense(1)	breast(1)	c.A487G						.						121	110	114					17																	46673963		2203	4299	6502	SO:0001583	missense	3216	exon4			ACTCCTTCTCCAG		CCDS11531.1	17q21.32	2011-06-20	2005-12-22		ENSG00000108511	ENSG00000108511		"Homeoboxes / ANTP class : HOXL subclass"	5117	protein-coding gene	gene with protein product		142961	"homeo box B6"	HOX2, HOX2B		1973146, 1358459	Standard	XM_005257284		Approved		uc002ins.1	P17509	OTTHUMG00000159912	ENST00000484302.2:c.487A>G	chr17.hg19:g.46673963T>C	ENSP00000420009:p.Lys163Glu	73.0	0.0		85.0	4.0	NM_018952	A8K835|D3DTV5|P09068|Q9HB11|Q9UGH2	Missense_Mutation	SNP	ENST00000484302.2	hg19	CCDS11531.1	.	.	.	.	.	.	.	.	.	.	T	33	5.273866	0.95459	.	.	ENSG00000108511	ENST00000484302;ENST00000225648	D;D	0.96041	-3.89;-3.89	4.84	4.84	0.62591	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.97074	0.9044	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97693	1.0180	10	0.87932	D	0	.	14.248	0.66001	0.0:0.0:0.0:1.0	.	163	P17509	HXB6_HUMAN	E	163	ENSP00000420009:K163E;ENSP00000225648:K163E	ENSP00000225648:K163E	K	-	1	0	HOXB6	44028962	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.785000	0.85724	2.037000	0.60232	0.460000	0.39030	AAG	.	.		0.612	HOXB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358146.2			C	46673963	T	C	46673963	3	2	64	1	0	0	0	0	1	0	0	0	7314	1792	62	2	191	2	HOXB6	17	46673963	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	6330752	46673963	34521247	280	7997										
SEPT4	5414	hgsc.bcm.edu	37	chr17	56603141	56603141	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gatttgcccaggccagactcTcctgagaggagagaggacag	14	10	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:56603141T>C	ENST00000317268.3	-	4	629	c.453A>G	c.(451-453)ggA>ggG	p.G151G	SEPT4_ENST00000579371.1_Splice_Site_p.G52G|SEPT4_ENST00000580844.1_Splice_Site_p.G52G|RP11-112H10.4_ENST00000580769.1_RNA|SEPT4_ENST00000393086.1_Splice_Site_p.G132G|SEPT4_ENST00000580809.1_Splice_Site_p.G33G|SEPT4_ENST00000317256.6_Splice_Site_p.G132G|SEPT4_ENST00000580791.1_5'Flank|RP11-112H10.4_ENST00000578022.1_RNA|SEPT4_ENST00000426861.1_Splice_Site_p.G132G|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000412945.3_Splice_Site_p.G143G|SEPT4_ENST00000583114.1_Splice_Site_p.G4G|SEPT4_ENST00000457347.2_Splice_Site_p.G166G	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	151	Septin-type G.				apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGCCAGACTCTCCTGAGAGGA	0.493																																					p.G166G		Atlas-SNP	.											.	SEPT4	48	.	0			c.A498G						.						72	64	67					17																	56603141		2203	4300	6503	SO:0001630	splice_region_variant	5414	exon5			AGACTCTCCTGAG	AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"Septins"	9165	protein-coding gene	gene with protein product	"bradeoin", "septin-M"	603696	"peanut-like 2 (Drosophila)"	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.452-1A>G	chr17.hg19:g.56603141T>C		80.0	0.0		58.0	4.0	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Silent	SNP	ENST00000317268.3	hg19	CCDS11610.1																																																																																			.	.		0.493	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417	Silent	C	56603141	T	C	56603141	5	2	64	1	0	0	0	0	0	0	1	0	14081	1565	54	2	1104	2	SEPT4	17	56603141	Splice_Site	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	9929178	56603141	24592069	281	7998										
TEX14	56155	hgsc.bcm.edu	37	chr17	56638968	56638968	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggtcctcatccagagtagagTgagctctgtttaaggacaag	12	8	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:56638968T>C	ENST00000240361.8	-	30	4293	c.4208A>G	c.(4207-4209)cAc>cGc	p.H1403R	TEX14_ENST00000349033.5_Missense_Mutation_p.H1357R|TEX14_ENST00000389934.3_Missense_Mutation_p.H1397R|TEX14_ENST00000584699.1_5'UTR			Q8IWB6	TEX14_HUMAN	testis expressed 14	1403					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CAGAGTAGAGTGAGCTCTGTT	0.483																																					p.H1403R		Atlas-SNP	.											.	TEX14	343	.	0			c.A4208G						.						116	111	113					17																	56638968		2203	4300	6503	SO:0001583	missense	56155	exon30			GTAGAGTGAGCTC	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.4208A>G	chr17.hg19:g.56638968T>C	ENSP00000240361:p.His1403Arg	114.0	0.0		109.0	5.0	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	T	18.39	3.612708	0.66672	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.25085	1.82;1.82;1.82	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000012	T	0.46405	0.1391	M	0.63843	1.955	0.34185	D	0.671351	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.998	T	0.61917	-0.6964	10	0.87932	D	0	-6.7257	11.1812	0.48629	0.0:0.0:0.0:1.0	.	1403;1357;1397	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	R	1403;1397;1357	ENSP00000240361:H1403R;ENSP00000374584:H1397R;ENSP00000268910:H1357R	ENSP00000240361:H1403R	H	-	2	0	TEX14	53993967	1.000000	0.71417	0.994000	0.49952	0.979000	0.70002	3.662000	0.54510	2.143000	0.66587	0.533000	0.62120	CAC	.	.		0.483	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			C	56638968	T	C	56638968	3	2	64	1	0	0	0	0	1	0	0	0	15793	1696	59	2	301	2	TEX14	17	56638968	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	35827	56638968	24556242	282	7999										
PSMD12	5718	hgsc.bcm.edu	37	chr17	65337110	65337110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgataattcctgctaatctgTctactttagcaaagatggtc	7	8	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:65337110T>C	ENST00000356126.3	-	11	1327	c.1220A>G	c.(1219-1221)gAc>gGc	p.D407G	PSMD12_ENST00000357146.4_Missense_Mutation_p.D387G	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	407	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					TGCTAATCTGTCTACTTTAGC	0.358																																					p.D407G		Atlas-SNP	.											.	PSMD12	32	.	0			c.A1220G						.						84	85	85					17																	65337110		2203	4300	6503	SO:0001583	missense	5718	exon11			AATCTGTCTACTT	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.1220A>G	chr17.hg19:g.65337110T>C	ENSP00000348442:p.Asp407Gly	89.0	0.0		94.0	4.0	NM_002816	A6NP15|Q53HA2|Q6P053	Missense_Mutation	SNP	ENST00000356126.3	hg19	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.406055	0.83230	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	T;T	0.70164	-0.46;-0.46	4.81	4.81	0.61882	Winged helix-turn-helix transcription repressor DNA-binding (1);Proteasome component (PCI) domain (2);	0.047814	0.85682	N	0.000000	D	0.85639	0.5743	M	0.93763	3.455	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.81914	0.995;0.995	D	0.89589	0.3826	10	0.87932	D	0	-7.5001	14.3834	0.66926	0.0:0.0:0.0:1.0	.	387;407	A6NP15;O00232	.;PSD12_HUMAN	G	407;387	ENSP00000348442:D407G;ENSP00000349667:D387G	ENSP00000348442:D407G	D	-	2	0	PSMD12	62767572	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.644000	0.83416	1.808000	0.52836	0.397000	0.26171	GAC	.	.		0.358	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		C	65337110	T	C	65337110	3	2	64	1	0	0	0	0	1	0	0	0	12707	1667	58	2	154	2	PSMD12	17	65337110	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	8698142	65337110	15858100	283	8000										
NUP85	79902	hgsc.bcm.edu	37	chr17	73214301	73214301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tggccctctcctcctccatcTccttgactgggtccggctcc	8	19	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:73214301T>C	ENST00000245544.4	+	7	568	c.497T>C	c.(496-498)cTc>cCc	p.L166P	NUP85_ENST00000447371.2_Intron|NUP85_ENST00000541827.1_Missense_Mutation_p.L120P|NUP85_ENST00000449421.2_3'UTR|NUP85_ENST00000579298.1_Missense_Mutation_p.L166P|NUP85_ENST00000579324.1_Missense_Mutation_p.L54P	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	166					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			CTCCTCCATCTCCTTGACTGG	0.527																																					p.L166P		Atlas-SNP	.											.	NUP85	44	.	0			c.T497C						.						138	117	124					17																	73214301		2203	4300	6503	SO:0001583	missense	79902	exon7			TCCATCTCCTTGA	AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450			8734	protein-coding gene	gene with protein product		170285				8124707	Standard	XM_005257690		Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000245544.4:c.497T>C	chr17.hg19:g.73214301T>C	ENSP00000245544:p.Leu166Pro	115.0	0.0		110.0	6.0	NM_024844	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Missense_Mutation	SNP	ENST00000245544.4	hg19	CCDS32730.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.668512	0.47677	.	.	ENSG00000125450	ENST00000245544;ENST00000541827;ENST00000449421	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.84297	0.5441	M	0.86420	2.815	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.87120	0.2190	9	0.87932	D	0	-20.273	16.2343	0.82363	0.0:0.0:0.0:1.0	.	120;166	B4DMQ3;Q9BW27	.;NUP85_HUMAN	P	166;120;120	.	ENSP00000245544:L166P	L	+	2	0	NUP85	70725896	1.000000	0.71417	0.992000	0.48379	0.983000	0.72400	7.588000	0.82629	2.234000	0.73211	0.533000	0.62120	CTC	.	.		0.527	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844		C	73214301	T	C	73214301	3	2	64	1	0	0	0	0	1	0	0	0	10779	1551	54	2	523	2	NUP85	17	73214301	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	7877191	73214301	7980909	284	8001										
RNF157	114804	hgsc.bcm.edu	37	chr17	74169787	74169787	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcctctgggaacttacttgaCgagcctcagtgtgtcctttc	10	12	2	1	rs144334591		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:74169787C>T	ENST00000269391.6	-	3	424	c.292G>A	c.(292-294)Gtc>Atc	p.V98I	RNF157_ENST00000319945.6_Missense_Mutation_p.V98I	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	98							zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			ACTTACTTGACGAGCCTCAGT	0.567																																					p.V98I	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.G292A						.	C	ILE/VAL	2,4404	6.2+/-15.9	0,2,2201	46	40	42		292	5.3	0.9	17	dbSNP_134	42	0,8600		0,0,4300	no	missense	RNF157	NM_052916.2	29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	98/680	74169787	2,13004	2203	4300	6503	SO:0001583	missense	114804	exon3			ACTTGACGAGCCT	AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"RING-type (C3HC4) zinc fingers"	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.292G>A	chr17.hg19:g.74169787C>T	ENSP00000269391:p.Val98Ile	152.0	0.0		131.0	62.0	NM_052916	Q8NB72|Q96N56	Missense_Mutation	SNP	ENST00000269391.6	hg19	CCDS32740.1	.	.	.	.	.	.	.	.	.	.	C	32	5.129204	0.94473	4.54E-4	0.0	ENSG00000141576	ENST00000269391;ENST00000319945;ENST00000301610	T;T	0.33438	1.41;1.41	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.49915	0.1585	M	0.63169	1.94	0.80722	D	1	D;P	0.59767	0.986;0.873	P;P	0.58577	0.841;0.459	T	0.45702	-0.9243	10	0.45353	T	0.12	.	18.5089	0.90909	0.0:1.0:0.0:0.0	.	98;98	Q96PX1-2;Q96PX1	.;RN157_HUMAN	I	98;98;60	ENSP00000269391:V98I;ENSP00000321837:V98I	ENSP00000269391:V98I	V	-	1	0	RNF157	71681382	1.000000	0.71417	0.948000	0.38648	0.879000	0.50718	7.689000	0.84165	2.437000	0.82529	0.655000	0.94253	GTC	.	C|1.000;T|0.000		0.567	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732		T	74169787	C	T	74169787	3	4	64	1	0	0	0	0	1	0	0	0	13469	536	19	1	1815	1	RNF157	17	74169787	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	955486	74169787	7025423	285	8002										
ST6GALNAC2	10610	hgsc.bcm.edu	37	chr17	74562230	74562230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gccggccttgtgcaggtcccTccacagggcagcttccaggg	14	15	0	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr17:74562230T>C	ENST00000225276.5	-	9	1400	c.1081A>G	c.(1081-1083)Agg>Ggg	p.R361G		NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	361					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						TGCAGGTCCCTCCACAGGGCA	0.507																																					p.R361G		Atlas-SNP	.											.	ST6GALNAC2	29	.	0			c.A1081G						.						121	106	111					17																	74562230		2203	4300	6503	SO:0001583	missense	10610	exon9			GGTCCCTCCACAG	U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"Sialyltransferases"	10867	protein-coding gene	gene with protein product		610137	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)", "sialyltransferase-like 1"	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.1081A>G	chr17.hg19:g.74562230T>C	ENSP00000225276:p.Arg361Gly	94.0	0.0		86.0	4.0	NM_006456	Q12971	Missense_Mutation	SNP	ENST00000225276.5	hg19	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	T	5.185	0.219605	0.09863	.	.	ENSG00000070731	ENST00000225276	T	0.30448	1.53	5.35	-4.58	0.03410	.	0.657770	0.15273	N	0.271114	T	0.18718	0.0449	L	0.45744	1.44	0.20638	N	0.999873	B	0.09022	0.002	B	0.14023	0.01	T	0.17868	-1.0355	10	0.27785	T	0.31	-0.4421	4.7423	0.13020	0.1036:0.1375:0.5154:0.2435	.	361	Q9UJ37	SIA7B_HUMAN	G	361	ENSP00000225276:R361G	ENSP00000225276:R361G	R	-	1	2	ST6GALNAC2	72073825	0.002000	0.14202	0.016000	0.15963	0.124000	0.20399	-0.154000	0.10130	-0.756000	0.04703	-0.313000	0.08912	AGG	.	.		0.507	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456		C	74562230	T	C	74562230	3	2	64	1	0	0	0	0	1	0	0	0	15239	1550	54	2	47	2	ST6GALNAC2	17	74562230	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	392443	74562230	6632980	286	8003										
PTPRM	5797	hgsc.bcm.edu	37	chr18	8376068	8376068	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtgtgcatgaaatccgagagAtcagacagtttcacttcact	9	9	3	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr18:8376068A>G	ENST00000332175.8	+	23	4194	c.3157A>G	c.(3157-3159)Atc>Gtc	p.I1053V	PTPRM_ENST00000580170.1_Missense_Mutation_p.I1066V|PTPRM_ENST00000400053.4_Missense_Mutation_p.I991V|PTPRM_ENST00000444013.1_Missense_Mutation_p.I840V|PTPRM_ENST00000400060.4_Missense_Mutation_p.I1067V	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1053	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				AATCCGAGAGATCAGACAGTT	0.547																																					p.I1066V		Atlas-SNP	.											.	PTPRM	185	.	0			c.A3196G						.						92	91	91					18																	8376068		2203	4300	6503	SO:0001583	missense	5797	exon25			CGAGAGATCAGAC	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3157A>G	chr18.hg19:g.8376068A>G	ENSP00000331418:p.Ile1053Val	68.0	0.0		67.0	4.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.720594	0.30503	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	6.04	6.04	0.98038	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.096128	0.64402	D	0.000001	T	0.09113	0.0225	N	0.00894	-1.105	0.58432	D	0.999999	B;B;B	0.18166	0.026;0.004;0.004	B;B;B	0.20577	0.03;0.011;0.011	T	0.25012	-1.0144	10	0.02654	T	1	.	16.6349	0.85050	1.0:0.0:0.0:0.0	.	840;1066;1053	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	V	1053;1067;991;840	ENSP00000331418:I1053V;ENSP00000382933:I1067V;ENSP00000382927:I991V;ENSP00000387608:I840V	ENSP00000331418:I1053V	I	+	1	0	PTPRM	8366068	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.369000	0.73109	2.330000	0.79161	0.477000	0.44152	ATC	.	.		0.547	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			G	8376068	A	G	8376068	3	3	64	1	0	0	0	0	1	0	0	0	12821	333	12	2	3294	2	PTPRM	18	8376068	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10		8376068	69701180	287	8004										
DSG4	147409	hgsc.bcm.edu	37	chr18	28972131	28972131	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	attttagtactcagccagtaTtgaagagaattgtttaagtt	8	4	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr18:28972131T>C	ENST00000308128.4	+	8	968	c.833T>C	c.(832-834)aTt>aCt	p.I278T	RP11-534N16.1_ENST00000581856.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.I278T|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	278	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Missing (in HYPT6). {ECO:0000269|PubMed:12705872, ECO:0000269|PubMed:15191570}.		anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TCAGCCAGTATTGAAGAGAAT	0.299																																					p.I278T		Atlas-SNP	.											.	DSG4	343	.	0			c.T833C						.						105	105	105					18																	28972131		2203	4300	6503	SO:0001583	missense	147409	exon8			CCAGTATTGAAGA	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.833T>C	chr18.hg19:g.28972131T>C	ENSP00000311859:p.Ile278Thr	91.0	0.0		91.0	4.0	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	hg19	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.218936	0.79464	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.56776	0.44;0.44	5.66	5.66	0.87406	Cadherin (4);Cadherin-like (1);	0.000000	0.35207	N	0.003361	T	0.77916	0.4202	M	0.90082	3.085	0.44309	D	0.997188	D;D	0.76494	0.999;0.999	D;D	0.97110	1.0;0.995	T	0.82281	-0.0535	10	0.59425	D	0.04	.	16.1787	0.81885	0.0:0.0:0.0:1.0	.	278;278	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	T	278	ENSP00000311859:I278T;ENSP00000352785:I278T	ENSP00000311859:I278T	I	+	2	0	DSG4	27226129	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.253000	0.78320	2.283000	0.76528	0.533000	0.62120	ATT	.	.		0.299	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		C	28972131	T	C	28972131	3	2	64	1	0	0	0	0	1	0	0	0	4781	1493	52	2	863	2	DSG4	18	28972131	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	20596063	28972131	49105117	288	8005										
BCL2	596	hgsc.bcm.edu	37	chr18	60795978	60795978	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cgcatgctggggccgtacagTtccacaaaggcatcctgcag	12	13	0	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr18:60795978T>C	ENST00000398117.1	-	2	2061	c.600A>G	c.(598-600)gaA>gaG	p.E200E	BCL2_ENST00000590515.1_5'UTR|BCL2_ENST00000333681.4_Silent_p.E200E	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	200					actin filament organization (GO:0007015)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|axonogenesis (GO:0007409)|B cell homeostasis (GO:0001782)|B cell lineage commitment (GO:0002326)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|behavioral fear response (GO:0001662)|branching involved in ureteric bud morphogenesis (GO:0001658)|CD8-positive, alpha-beta T cell lineage commitment (GO:0043375)|cell aging (GO:0007569)|cell growth (GO:0016049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to organic substance (GO:0071310)|cochlear nucleus development (GO:0021747)|defense response to virus (GO:0051607)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|ear development (GO:0043583)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|female pregnancy (GO:0007565)|focal adhesion assembly (GO:0048041)|gland morphogenesis (GO:0022612)|glomerulus development (GO:0032835)|hair follicle morphogenesis (GO:0031069)|homeostasis of number of cells within a tissue (GO:0048873)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|melanin metabolic process (GO:0006582)|melanocyte differentiation (GO:0030318)|mesenchymal cell development (GO:0014031)|metanephros development (GO:0001656)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of autophagy (GO:0010507)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cellular pH reduction (GO:0032848)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of retinal cell programmed cell death (GO:0046671)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|oocyte development (GO:0048599)|organ growth (GO:0035265)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pigment granule organization (GO:0048753)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell growth (GO:0030307)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron maturation (GO:0014042)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smooth muscle cell migration (GO:0014911)|post-embryonic development (GO:0009791)|protein dephosphorylation (GO:0006470)|protein polyubiquitination (GO:0000209)|reactive oxygen species metabolic process (GO:0072593)|regulation of calcium ion transport (GO:0051924)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glycoprotein biosynthetic process (GO:0010559)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|regulation of protein stability (GO:0031647)|regulation of transmembrane transporter activity (GO:0022898)|regulation of viral genome replication (GO:0045069)|release of cytochrome c from mitochondria (GO:0001836)|renal system process (GO:0003014)|response to acid chemical (GO:0001101)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to iron ion (GO:0010039)|response to ischemia (GO:0002931)|response to nicotine (GO:0035094)|response to radiation (GO:0009314)|response to toxic substance (GO:0009636)|response to UV-B (GO:0010224)|single organismal cell-cell adhesion (GO:0016337)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|channel inhibitor activity (GO:0016248)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(106)|kidney(1)|large_intestine(1)|lung(3)	113		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Ibuprofen(DB01050)|Paclitaxel(DB01229)|Rasagiline(DB01367)	GGCCGTACAGTTCCACAAAGG	0.542			T	IGH@	"NHL, CLL"																																p.E200E		Atlas-SNP	.		Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	.	BCL2	272	.	0			c.A600G						.						39	35	36					18																	60795978		2203	4300	6503	SO:0001819	synonymous_variant	596	exon3			GTACAGTTCCACA	M14745	CCDS11981.1, CCDS45882.1	18q21.3	2014-03-07			ENSG00000171791	ENSG00000171791		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	990	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 50"	151430					Standard	XM_006722523		Approved	Bcl-2, PPP1R50	uc002lit.1	P10415	OTTHUMG00000132791	ENST00000398117.1:c.600A>G	chr18.hg19:g.60795978T>C		132.0	0.0		119.0	42.0	NM_000633	C9JHD5|P10416|Q13842|Q16197	Silent	SNP	ENST00000398117.1	hg19	CCDS11981.1																																																																																			.	.		0.542	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657		C	60795978	T	C	60795978	2	2	64	1	0	0	0	0	0	0	0	1	1365	1722	60	2		2	BCL2	18	60795978	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	31823847	60795978	17281270	289	8006										
WDR18	57418	hgsc.bcm.edu	37	chr19	985884	985884	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggaccagctccagcagaagaTcatgtgccccgggcctgtca	12	14	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:985884T>C	ENST00000251289.5	+	2	253	c.230T>C	c.(229-231)aTc>aCc	p.I77T	WDR18_ENST00000591997.1_3'UTR|WDR18_ENST00000587001.2_Missense_Mutation_p.I77T	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	77					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCAGAAGATCATGTGCCCC	0.602																																					p.I77T		Atlas-SNP	.											.	WDR18	20	.	0			c.T230C						.						128	102	111					19																	985884		2203	4300	6503	SO:0001583	missense	57418	exon2			AGAAGATCATGTG		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"WD repeat domain containing"	17956	protein-coding gene	gene with protein product	"Involved in Processing ITS2 3 homolog (S. cerevisiae)"					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.230T>C	chr19.hg19:g.985884T>C	ENSP00000251289:p.Ile77Thr	98.0	0.0		96.0	4.0	NM_024100	O60390|Q9BWR2	Missense_Mutation	SNP	ENST00000251289.5	hg19	CCDS12051.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.576465	0.45902	.	.	ENSG00000065268	ENST00000251289	T	0.16897	2.31	4.09	4.09	0.47781	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.166320	0.51477	D	0.000089	T	0.20210	0.0486	M	0.66939	2.045	0.47341	D	0.999393	P	0.39576	0.679	B	0.39840	0.311	T	0.03695	-1.1012	10	0.22706	T	0.39	.	12.4664	0.55762	0.0:0.0:0.0:1.0	.	77	Q9BV38	WDR18_HUMAN	T	77	ENSP00000251289:I77T	ENSP00000251289:I77T	I	+	2	0	WDR18	936884	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	7.008000	0.76341	1.732000	0.51606	0.529000	0.55759	ATC	.	.		0.602	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2			C	985884	T	C	985884	3	2	64	1	0	0	0	0	1	0	0	0	17293	1435	50	2	236	2	WDR18	19	985884	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		985884	58143099	290	8007										
DAPK3	1613	hgsc.bcm.edu	37	chr19	3959236	3959236	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	caggcggctgaagcggcgctTgaggccgctggtccccagca	16	14	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:3959236T>C	ENST00000545797.2	-	9	1471	c.1228A>G	c.(1228-1230)Aag>Gag	p.K410E	MIR637_ENST00000385000.1_RNA|DAPK3_ENST00000301264.3_Missense_Mutation_p.K410E			O43293	DAPK3_HUMAN	death-associated protein kinase 3	410					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|chromatin modification (GO:0016568)|cytokinesis (GO:0000910)|intracellular signal transduction (GO:0035556)|negative regulation of translation (GO:0017148)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of cell motility (GO:2000145)|regulation of focal adhesion assembly (GO:0051893)|regulation of mitosis (GO:0007088)|regulation of mitotic cell cycle (GO:0007346)|regulation of smooth muscle contraction (GO:0006940)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|leucine zipper domain binding (GO:0043522)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGCGGCGCTTGAGGCCGCTG	0.701																																					p.K410E		Atlas-SNP	.											.	DAPK3	56	.	0			c.A1228G						.						11	12	12					19																	3959236		2191	4274	6465	SO:0001583	missense	1613	exon8			GGCGCTTGAGGCC	AB007144	CCDS12116.1	19p13.3	2008-02-05				ENSG00000167657			2676	protein-coding gene	gene with protein product		603289				9488481	Standard	XM_005259508		Approved	ZIP, ZIPK	uc002lzc.1	O43293		ENST00000545797.2:c.1228A>G	chr19.hg19:g.3959236T>C	ENSP00000442973:p.Lys410Glu	13.0	0.0		64.0	4.0	NM_001348	A0AVN4|B3KQE2|Q05JY4	Missense_Mutation	SNP	ENST00000545797.2	hg19	CCDS12116.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.332791	0.41297	.	.	ENSG00000167657	ENST00000301264;ENST00000545797	T;T	0.68624	-0.34;-0.34	4.91	2.72	0.32119	.	0.059737	0.64402	D	0.000004	T	0.48786	0.1519	L	0.27053	0.805	0.35240	D	0.777718	B	0.32160	0.358	B	0.24006	0.05	T	0.51942	-0.8641	10	0.36615	T	0.2	.	11.9147	0.52759	0.0:0.0:0.4192:0.5808	.	410	O43293	DAPK3_HUMAN	E	410	ENSP00000301264:K410E;ENSP00000442973:K410E	ENSP00000301264:K410E	K	-	1	0	DAPK3	3910236	1.000000	0.71417	0.986000	0.45419	0.735000	0.41995	3.590000	0.53979	0.198000	0.20407	0.459000	0.35465	AAG	.	.		0.701	DAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457817.2	NM_001348		C	3959236	T	C	3959236	3	2	64	1	0	0	0	0	1	0	0	0	4239	1821	63	2	140	2	DAPK3	19	3959236	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2973352	3959236	55169747	291	8008										
GPR108	56927	hgsc.bcm.edu	37	chr19	6731272	6731272	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	caggatggcgatgatgcgggTgaagtagacgtagcagatga	17	5	0	5			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:6731272T>C	ENST00000264080.7	-	16	1398	c.1372A>G	c.(1372-1374)Acc>Gcc	p.T458A	GPR108_ENST00000598626.1_5'UTR|GPR108_ENST00000430424.4_Missense_Mutation_p.T216A	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	458						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						ATGATGCGGGTGAAGTAGACG	0.682																																					p.T458A		Atlas-SNP	.											.	GPR108	35	.	0			c.A1372G						.						41	47	45					19																	6731272		2173	4260	6433	SO:0001583	missense	56927	exon16			TGCGGGTGAAGTA		CCDS42479.1	19p13.3	2014-01-30				ENSG00000125734		"GPCR / Unclassified : 7TM orphan receptors"	17829	protein-coding gene	gene with protein product							Standard	NM_001080452		Approved	LUSTR2	uc002mfp.3	Q9NPR9	OTTHUMG00000170129	ENST00000264080.7:c.1372A>G	chr19.hg19:g.6731272T>C	ENSP00000264080:p.Thr458Ala	95.0	0.0		134.0	6.0	NM_001080452	B9EJD7	Missense_Mutation	SNP	ENST00000264080.7	hg19	CCDS42479.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.741077	0.49151	.	.	ENSG00000125734	ENST00000548402;ENST00000264080;ENST00000430424	T	0.28666	1.6	3.9	3.9	0.45041	.	0.078892	0.48767	U	0.000180	T	0.54727	0.1876	M	0.89353	3.025	0.48040	D	0.999573	D	0.58620	0.983	P	0.59357	0.856	T	0.63028	-0.6728	10	0.72032	D	0.01	-19.1803	10.7038	0.45944	0.0:0.0:0.0:1.0	.	458	Q9NPR9	GP108_HUMAN	A	50;458;216	ENSP00000264080:T458A	ENSP00000264080:T458A	T	-	1	0	GPR108	6682272	1.000000	0.71417	0.831000	0.32960	0.005000	0.04900	4.395000	0.59678	1.429000	0.47314	0.254000	0.18369	ACC	.	.		0.682	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2			C	6731272	T	C	6731272	3	2	64	1	0	0	0	0	1	0	0	0	6632	1696	59	2	271	2	GPR108	19	6731272	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2772036	6731272	52397711	292	8009										
MUC16	94025	hgsc.bcm.edu	37	chr19	9020072	9020072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gctcagctcccagtacagccGctctctgttgagtccagggc	11	15	2	1	rs566860711		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:9020072G>A	ENST00000397910.4	-	21	37626	c.37423C>T	c.(37423-37425)Cgg>Tgg	p.R12475W		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12477	SEA 3. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGTACAGCCGCTCTCTGTTG	0.557																																					p.R12475W		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,1	MUC16	4315	.	0			c.C37423T						.						179	157	164					19																	9020072		1949	4155	6104	SO:0001583	missense	94025	exon21			ACAGCCGCTCTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.37423C>T	chr19.hg19:g.9020072G>A	ENSP00000381008:p.Arg12475Trp	220.0	0.0		247.0	90.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	11.31	1.602258	0.28534	.	.	ENSG00000181143	ENST00000397910	T	0.38240	1.15	3.32	-3.03	0.05429	.	.	.	.	.	T	0.33673	0.0871	L	0.43923	1.385	.	.	.	D	0.64830	0.994	P	0.51016	0.656	T	0.45600	-0.9250	8	0.87932	D	0	.	5.9414	0.19196	0.0:0.1762:0.2883:0.5355	.	12475	B5ME49	.	W	12475	ENSP00000381008:R12475W	ENSP00000381008:R12475W	R	-	1	2	MUC16	8881072	0.000000	0.05858	0.049000	0.19019	0.498000	0.33706	-1.965000	0.01511	-0.169000	0.10834	0.555000	0.69702	CGG	.	.		0.557	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9020072	G	A	9020072	3	1	64	1	0	0	0	0	1	0	0	0	9982	1086	38	1	6356	1	MUC16	19	9020072	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	2288800	9020072	50108911	293	8010										
ZNF823	55552	hgsc.bcm.edu	37	chr19	11832694	11832694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtagacattcatagggtttcTctccagtgtgaattctttca	8	8	4	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:11832694T>C	ENST00000341191.6	-	4	1808	c.1655A>G	c.(1654-1656)gAg>gGg	p.E552G	ZNF823_ENST00000545749.1_Missense_Mutation_p.E370G	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	552					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						ATAGGGTTTCTCTCCAGTGTG	0.428										HNSCC(68;0.2)																											p.E552G		Atlas-SNP	.											.	ZNF823	104	.	0			c.A1655G						.						78	80	79					19																	11832694		2203	4300	6503	SO:0001583	missense	55552	exon4			GGTTTCTCTCCAG	X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"Zinc fingers, C2H2-type", "-"	30936	protein-coding gene	gene with protein product	"ZFP 36 for a zinc finger protein"						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.1655A>G	chr19.hg19:g.11832694T>C	ENSP00000340683:p.Glu552Gly	98.0	0.0		95.0	4.0	NM_001080493	A0PJL4|B7Z8D4|Q6P4A9	Missense_Mutation	SNP	ENST00000341191.6	hg19	CCDS45981.1	.	.	.	.	.	.	.	.	.	.	-	14.24	2.476478	0.44044	.	.	ENSG00000197933	ENST00000545749;ENST00000341191	T;T	0.27557	1.66;1.66	0.856	0.856	0.19019	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30854	0.0778	M	0.70903	2.155	0.27682	N	0.946391	B	0.14438	0.01	B	0.11329	0.006	T	0.35076	-0.9803	9	0.72032	D	0.01	.	7.2396	0.26090	0.0:0.0:0.0:1.0	.	552	P16415	ZN823_HUMAN	G	370;552	ENSP00000440162:E370G;ENSP00000340683:E552G	ENSP00000340683:E552G	E	-	2	0	ZNF823	11693694	0.627000	0.27129	0.050000	0.19076	0.472000	0.32918	2.551000	0.45820	0.630000	0.30394	0.254000	0.18369	GAG	.	.		0.428	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493		C	11832694	T	C	11832694	3	2	64	1	0	0	0	0	1	0	0	0	18194	1551	54	2	181	2	ZNF823	19	11832694	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2812622	11832694	47296289	294	8011										
ZNF700	90592	hgsc.bcm.edu	37	chr19	12059745	12059745	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	catgaaagaagtcacatgggAgagaagccttatcaatgcaa	10	7	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:12059745A>G	ENST00000254321.5	+	4	1049	c.906A>G	c.(904-906)ggA>ggG	p.G302G	CTD-2006C1.12_ENST00000586394.1_RNA|ZNF700_ENST00000482090.1_Silent_p.G284G|ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000590798.1_Intron|ZNF763_ENST00000538752.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	302					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						GTCACATGGGAGAGAAGCCTT	0.393																																					p.G305G		Atlas-SNP	.											.	ZNF700	81	.	0			c.A915G						.						55	54	55					19																	12059745		2203	4300	6503	SO:0001819	synonymous_variant	90592	exon4			CATGGGAGAGAAG	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"Zinc fingers, C2H2-type", "-"	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.906A>G	chr19.hg19:g.12059745A>G		63.0	0.0		94.0	4.0	NM_001271848	B9EGU4	Silent	SNP	ENST00000254321.5	hg19	CCDS32915.1																																																																																			.	.		0.393	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		G	12059745	A	G	12059745	2	3	64	1	0	0	0	0	0	0	0	1	18119	291	11	2		2	ZNF700	19	12059745	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	227051	12059745	47069238	295	8012										
RAD23A	5886	hgsc.bcm.edu	37	chr19	13059162	13059162	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cccccacgacgtccccagagTctgtgtcagggtaaggcggg	14	14	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:13059162T>C	ENST00000586534.1	+	3	467	c.406T>C	c.(406-408)Tct>Cct	p.S136P	RAD23A_ENST00000316856.3_Missense_Mutation_p.S136P|RAD23A_ENST00000541222.1_5'UTR|RAD23A_ENST00000592268.1_Missense_Mutation_p.S136P|RAD23A_ENST00000588826.2_3'UTR			P54725	RD23A_HUMAN	RAD23 homolog A (S. cerevisiae)	136					nucleotide-excision repair (GO:0006289)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)|ubiquitin-specific protease binding (GO:1990381)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12						GTCCCCAGAGTCTGTGTCAGG	0.652								Nucleotide excision repair (NER)																													p.S136P		Atlas-SNP	.											.	RAD23A	29	.	0			c.T406C						.						37	43	40					19																	13059162		2203	4300	6503	SO:0001583	missense	5886	exon3			CCAGAGTCTGTGT		CCDS12289.1, CCDS59357.1, CCDS59358.1	19p13.2	2008-07-17	2001-11-28			ENSG00000179262			9812	protein-coding gene	gene with protein product	"RAD23, yeast homolog, A"	600061	"RAD23 (S. cerevisiae) homolog A"			7851894	Standard	NM_005053		Approved	HHR23A, MGC111083	uc002mvw.2	P54725		ENST00000586534.1:c.406T>C	chr19.hg19:g.13059162T>C	ENSP00000467024:p.Ser136Pro	79.0	0.0		76.0	4.0	NM_005053	K7ESE3|Q59EU8|Q5M7Z1	Missense_Mutation	SNP	ENST00000586534.1	hg19	CCDS12289.1	.	.	.	.	.	.	.	.	.	.	T	10.72	1.430046	0.25726	.	.	ENSG00000179262	ENST00000316856	T	0.18174	2.23	4.68	2.46	0.29980	.	0.692989	0.14559	N	0.312194	T	0.06325	0.0163	N	0.08118	0	0.80722	D	1	B;B;B	0.27765	0.062;0.001;0.188	B;B;B	0.22152	0.023;0.002;0.038	T	0.29731	-1.0002	10	0.14656	T	0.56	-29.7701	4.2873	0.10862	0.1877:0.0:0.2256:0.5867	.	136;153;136	A8K1J3;Q59EU8;P54725	.;.;RD23A_HUMAN	P	136	ENSP00000321365:S136P	ENSP00000321365:S136P	S	+	1	0	RAD23A	12920162	0.999000	0.42202	0.980000	0.43619	0.969000	0.65631	1.174000	0.31932	1.753000	0.51906	0.528000	0.53228	TCT	.	.		0.652	RAD23A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452752.1	NM_005053		C	13059162	T	C	13059162	3	2	64	1	0	0	0	0	1	0	0	0	12997	1667	58	2	416	2	RAD23A	19	13059162	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	999417	13059162	46069821	296	8013										
DCAF15	90379	hgsc.bcm.edu	37	chr19	14070706	14070706	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctatgacatcgtcattctggAggtgggcccagggcgggcag	16	10	2	1	rs3217681|rs141180609|rs373011773	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:14070706A>G	ENST00000254337.6	+	9	1460	c.1439A>G	c.(1438-1440)gAg>gGg	p.E480G		NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15	480					protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						GTCATTCTGGAGGTGGGCCCA	0.592											OREG0025301	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E480G		Atlas-SNP	.											.	DCAF15	30	.	0			c.A1439G						.						63	60	61					19																	14070706		2203	4300	6503	SO:0001630	splice_region_variant	90379	exon9			TTCTGGAGGTGGG	BC002926	CCDS32926.1	19p13.12	2009-07-17	2009-07-17	2009-07-17	ENSG00000132017	ENSG00000132017		"DDB1 and CUL4 associated factors"	25095	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 72"	C19orf72			Standard	NM_138353		Approved	MGC99481	uc002mxt.3	Q66K64		ENST00000254337.6:c.1440+1A>G	chr19.hg19:g.14070706A>G		113.0	0.0	692	104.0	6.0	NM_138353	B3KS86|Q96DW0|Q9BU31	Missense_Mutation	SNP	ENST00000254337.6	hg19	CCDS32926.1	.	.	.	.	.	.	.	.	.	.	a	18.18	3.566035	0.65651	.	.	ENSG00000132017	ENST00000254337	.	.	.	4.49	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.47967	0.1474	L	0.32530	0.975	0.58432	D	0.999999	P	0.49783	0.928	P	0.46758	0.526	T	0.53732	-0.8397	9	0.87932	D	0	-22.7842	12.778	0.57459	1.0:0.0:0.0:0.0	.	480	Q66K64	DCA15_HUMAN	G	480	.	ENSP00000254337:E480G	E	+	2	0	DCAF15	13931706	1.000000	0.71417	0.999000	0.59377	0.435000	0.31806	8.035000	0.88872	1.677000	0.50941	0.448000	0.29417	GAG	.	.		0.592	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353	Missense_Mutation	G	14070706	A	G	14070706	5	3	64	1	0	0	0	0	0	0	1	0	4269	318	11	2	1473	2	DCAF15	19	14070706	Splice_Site	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1011544	14070706	45058277	297	8014										
AKAP8	10270	hgsc.bcm.edu	37	chr19	15484733	15484733	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcatggctctgggccgtaagAggccatgtgcatggcagggg	18	9	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:15484733A>G	ENST00000269701.2	-	4	295	c.235T>C	c.(235-237)Tct>Cct	p.S79P		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	79					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						GGGCCGTAAGAGGCCATGTGC	0.647																																					p.S79P	GBM(190;1671 2163 3274 27186 30476)	Atlas-SNP	.											.	AKAP8	68	.	0			c.T235C						.						46	45	46					19																	15484733		2203	4300	6503	SO:0001583	missense	10270	exon4			CGTAAGAGGCCAT	Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"A-kinase anchor proteins"	378	protein-coding gene	gene with protein product	"A-kinase anchor protein, 95kDa"	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.235T>C	chr19.hg19:g.15484733A>G	ENSP00000269701:p.Ser79Pro	104.0	0.0		97.0	5.0	NM_005858		Missense_Mutation	SNP	ENST00000269701.2	hg19	CCDS12329.1	.	.	.	.	.	.	.	.	.	.	A	12.18	1.860126	0.32884	.	.	ENSG00000105127	ENST00000269701	T	0.51071	0.72	5.07	1.29	0.21616	.	0.255751	0.28371	N	0.015591	T	0.47021	0.1423	L	0.56769	1.78	0.20703	N	0.999866	D	0.60575	0.988	P	0.53313	0.723	T	0.30387	-0.9980	10	0.35671	T	0.21	-20.7731	4.1839	0.10388	0.4484:0.0:0.0968:0.4548	.	79	O43823	AKAP8_HUMAN	P	79	ENSP00000269701:S79P	ENSP00000269701:S79P	S	-	1	0	AKAP8	15345733	0.938000	0.31826	0.169000	0.22859	0.045000	0.14185	1.071000	0.30666	0.340000	0.23745	-1.182000	0.01712	TCT	.	.		0.647	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858		G	15484733	A	G	15484733	3	3	64	1	0	0	0	0	1	0	0	0	457	304	11	2	1887	2	AKAP8	19	15484733	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1414027	15484733	43644250	298	8015										
EPS15L1	58513	hgsc.bcm.edu	37	chr19	16513229	16513229	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gggctccatcgagcacctggTcatactgctccaggctcctg	11	15	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:16513229T>C	ENST00000248070.6	-	16	1833	c.1694A>G	c.(1693-1695)gAc>gGc	p.D565G	EPS15L1_ENST00000597937.1_Missense_Mutation_p.D565G|EPS15L1_ENST00000594975.1_Missense_Mutation_p.D565G|EPS15L1_ENST00000455140.2_Missense_Mutation_p.D565G|EPS15L1_ENST00000602009.1_Missense_Mutation_p.D411G|EPS15L1_ENST00000535753.2_Missense_Mutation_p.D565G	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	565					endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						GAGCACCTGGTCATACTGCTC	0.587																																					p.D565G		Atlas-SNP	.											.	EPS15L1	81	.	0			c.A1694G						.						73	70	71					19																	16513229		2203	4300	6503	SO:0001583	missense	58513	exon16			ACCTGGTCATACT	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.1694A>G	chr19.hg19:g.16513229T>C	ENSP00000248070:p.Asp565Gly	84.0	0.0		100.0	4.0	NM_021235	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	SNP	ENST00000248070.6	hg19	CCDS32944.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.814992	0.32053	.	.	ENSG00000127527	ENST00000455140;ENST00000248070;ENST00000535753	T;T;T	0.32753	1.98;1.9;1.44	5.5	4.46	0.54185	.	0.332800	0.34200	N	0.004179	T	0.17365	0.0417	N	0.14661	0.345	0.34217	D	0.675011	B;B;B;B;B;B	0.25441	0.031;0.008;0.126;0.036;0.017;0.071	B;B;B;B;B;B	0.26969	0.05;0.011;0.034;0.009;0.034;0.075	T	0.18272	-1.0342	10	0.33940	T	0.23	.	7.9339	0.29918	0.0:0.1007:0.0:0.8993	.	565;565;564;565;565;565	A8K5P4;A5PL29;A5PKY0;A2RRF3;Q9UBC2;G3V0H2	.;.;.;.;EP15R_HUMAN;.	G	565	ENSP00000393313:D565G;ENSP00000248070:D565G;ENSP00000440103:D565G	ENSP00000248070:D565G	D	-	2	0	EPS15L1	16374229	0.999000	0.42202	0.061000	0.19648	0.485000	0.33311	2.584000	0.46102	0.917000	0.36895	0.533000	0.62120	GAC	.	.		0.587	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		C	16513229	T	C	16513229	3	2	64	1	0	0	0	0	1	0	0	0	5195	1667	58	2	932	2	EPS15L1	19	16513229	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1028496	16513229	42615754	299	8016										
KCNN1	3780	hgsc.bcm.edu	37	chr19	18108964	18108964	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctctctgtctcccgcagaccCagaccgtcatgtacgacctt	7	17	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:18108964C>T	ENST00000222249.9	+	11	1700	c.1381C>T	c.(1381-1383)Cag>Tag	p.Q461*	ARRDC2_ENST00000379656.3_5'Flank	NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	461	Calmodulin-binding. {ECO:0000250}.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	CCCGCAGACCCAGACCGTCAT	0.637																																					p.Q461X		Atlas-SNP	.											.	KCNN1	74	.	0			c.C1381T						.						14	17	16					19																	18108964		2170	4269	6439	SO:0001587	stop_gained	3780	exon11			CAGACCCAGACCG	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.1381C>T	chr19.hg19:g.18108964C>T	ENSP00000476519:p.Gln461*	73.0	0.0		59.0	4.0	NM_002248	Q5KR10|Q6DJU4	Nonsense_Mutation	SNP	ENST00000222249.9	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.662760	0.96734	.	.	ENSG00000105642	ENST00000222249	.	.	.	4.18	4.18	0.49190	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-22.2419	14.0513	0.64739	0.0:1.0:0.0:0.0	.	.	.	.	X	478	.	ENSP00000222249:Q478X	Q	+	1	0	KCNN1	17969964	1.000000	0.71417	0.988000	0.46212	0.036000	0.12997	6.975000	0.76128	1.890000	0.54733	0.306000	0.20318	CAG	.	.		0.637	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		T	18108964	C	T	18108964	4	4	64	1	0	0	0	0	0	1	0	0	8087	595	21	3	1415	3	KCNN1	19	18108964	Nonsense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	1595735	18108964	41020019	300	8017										
ZNF714	148206	hgsc.bcm.edu	37	chr19	21299779	21299779	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtgtacaaaaaaggttatgaActaaaccagtgtttgacaac	8	6	0	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:21299779A>T	ENST00000596143.1	+	5	634	c.309A>T	c.(307-309)gaA>gaT	p.E103D	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AAGGTTATGAACTAAACCAGT	0.323																																					p.E103D		Atlas-SNP	.											.	ZNF714	121	.	0			c.A309T						.																																			SO:0001583	missense	148206	exon5			TTATGAACTAAAC	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.309A>T	chr19.hg19:g.21299779A>T	ENSP00000472368:p.Glu103Asp	112.0	0.0		106.0	7.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	7.284	0.609628	0.14066	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.394	-0.788	0.10939	.	.	.	.	.	T	0.22898	0.0553	L	0.46157	1.445	0.09310	N	1	P;B	0.41848	0.763;0.39	B;B	0.32805	0.153;0.142	T	0.11108	-1.0601	7	0.72032	D	0.01	.	.	.	.	.	104;103	Q96N38-2;A6NEM4	.;.	D	103	.	ENSP00000291770:E103D	E	+	3	2	ZNF714	21091619	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.660000	0.25009	-0.649000	0.05430	-0.714000	0.03626	GAA	.	.		0.323	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		T	21299779	A	T	21299779	3	4	64	1	0	0	0	0	1	0	0	0	18133	40	2	4	319	4	ZNF714	19	21299779	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	3190815	21299779	37829204	301	8018										
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35504479	35504479	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgggagatgtgatcgccctgAgcgacatcacctcctcgggg	14	12	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:35504479A>G	ENST00000317991.5	+	9	946	c.754A>G	c.(754-756)Agc>Ggc	p.S252G	GRAMD1A_ENST00000599564.1_Missense_Mutation_p.S339G|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.S245G|CTD-2527I21.14_ENST00000605640.1_RNA|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.S18G	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	252						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GATCGCCCTGAGCGACATCAC	0.642																																					p.S252G		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.A754G						.						25	28	27					19																	35504479		2090	4214	6304	SO:0001583	missense	57655	exon9			GCCCTGAGCGACA	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"KIAA1533"	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.754A>G	chr19.hg19:g.35504479A>G	ENSP00000441032:p.Ser252Gly	91.0	0.0		90.0	4.0	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	hg19	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.039533	0.55003	.	.	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.48522	0.81;1.84;1.85	4.71	4.71	0.59529	.	1.745710	0.02419	N	0.082418	T	0.44664	0.1304	L	0.29908	0.895	0.29679	N	0.841835	B;B;B;B;B	0.21905	0.001;0.018;0.062;0.002;0.007	B;B;B;B;B	0.25759	0.003;0.023;0.063;0.005;0.007	T	0.32534	-0.9903	10	0.45353	T	0.12	.	12.2142	0.54396	1.0:0.0:0.0:0.0	.	252;252;18;245;339	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2;F5GZ02	.;GRM1A_HUMAN;.;.;.	G	339;18;252;245	ENSP00000423728:S18G;ENSP00000441032:S252G;ENSP00000439267:S245G	ENSP00000441032:S252G	S	+	1	0	GRAMD1A	40196319	1.000000	0.71417	0.996000	0.52242	0.916000	0.54674	2.361000	0.44160	1.988000	0.58038	0.397000	0.26171	AGC	.	.		0.642	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		G	35504479	A	G	35504479	3	3	64	1	0	0	0	0	1	0	0	0	6756	304	11	2	788	2	GRAMD1A	19	35504479	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	14204700	35504479	23624504	302	8019										
C19orf55	148137	hgsc.bcm.edu	37	chr19	36258938	36258938	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcggaggccctgcttgcccaGggccgccctgctgctgcagg	15	16	0	0	rs398034467|rs5827939		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:36258938G>A	ENST00000396908.4	+	9	1264	c.1191G>A	c.(1189-1191)caG>caA	p.Q397Q	AC002398.13_ENST00000589397.1_RNA|C19orf55_ENST00000544099.1_Silent_p.Q397Q	NM_001039887.2	NP_001034976.2	Q2NL68	PRSR3_HUMAN		398										cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGCTTGCCCAGGGCCGCCCTG	0.731																																					.		Atlas-SNP	.											.,11	C19orf55	39	.	0			c.1190+1G>A						.						1	1	1					19																	36258938		567	1236	1803	SO:0001630	splice_region_variant	148137	exon9			TGCCCAGGGCCGC																												ENST00000396908.4:c.1191+1G>A	chr19.hg19:g.36258938G>A		10.0	0.0		19.0	4.0	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Splice_Site	SNP	ENST00000396908.4	hg19																																																																																				.	.		0.731	C19orf55-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			Silent	A	36258938	G	A	36258938	5	1	64	1	0	0	0	0	0	0	1	0	1939	991	35	3	1225	3	C19orf55	19	36258938	Splice_Site	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	754459	36258938	22870045	303	8020										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36351240	36351240	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctgcttcgccacacactgtgCaggagggagagaaggtcatt	13	10	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:36351240C>T	ENST00000360202.5	+	6	913	c.715C>T	c.(715-717)Cag>Tag	p.Q239*	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Nonsense_Mutation_p.Q239*|KIRREL2_ENST00000262625.7_Nonsense_Mutation_p.Q239*|KIRREL2_ENST00000347900.6_Nonsense_Mutation_p.Q189*	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	239	Ig-like C2-type 3.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ACACACTGTGCAGGAGGGAGA	0.612																																					p.Q239X		Atlas-SNP	.											.	KIRREL2	170	.	0			c.C715T						.						77	63	67					19																	36351240		2203	4300	6503	SO:0001587	stop_gained	84063	exon6			ACTGTGCAGGAGG	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.715C>T	chr19.hg19:g.36351240C>T	ENSP00000353331:p.Gln239*	47.0	0.0		63.0	4.0	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Nonsense_Mutation	SNP	ENST00000360202.5	hg19	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	C	36	5.681926	0.96774	.	.	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	.	.	.	3.86	3.86	0.44501	.	0.478185	0.15997	N	0.234521	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-5.7555	11.5369	0.50643	0.0:1.0:0.0:0.0	.	.	.	.	X	239;189;239;219	.	ENSP00000262625:Q239X	Q	+	1	0	KIRREL2	41043080	0.992000	0.36948	1.000000	0.80357	0.689000	0.40095	2.252000	0.43196	2.182000	0.69389	0.449000	0.29647	CAG	.	.		0.612	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		T	36351240	C	T	36351240	4	4	64	1	0	0	0	0	0	1	0	0	8334	711	25	3	737	3	KIRREL2	19	36351240	Nonsense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	92302	36351240	22777743	304	8021										
ZNF567	163081	hgsc.bcm.edu	37	chr19	37211090	37211090	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgtgggaaggcctttagaatGaagtcatacctcattgatca	10	7	3	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:37211090G>T	ENST00000536254.2	+	6	1686	c.1464G>T	c.(1462-1464)atG>atT	p.M488I	ZNF567_ENST00000360729.4_Missense_Mutation_p.M457I|ZNF567_ENST00000585696.1_Missense_Mutation_p.M457I|ZNF567_ENST00000392163.2_Missense_Mutation_p.M457I|ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000588311.1_Missense_Mutation_p.M457I			Q8N184	ZN567_HUMAN	zinc finger protein 567	488					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CCTTTAGAATGAAGTCATACC	0.413																																					p.M457I		Atlas-SNP	.											.	ZNF567	61	.	0			c.G1371T						.						85	83	83					19																	37211090		2203	4300	6503	SO:0001583	missense	163081	exon4			TAGAATGAAGTCA	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"Zinc fingers, C2H2-type", "-"	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.1464G>T	chr19.hg19:g.37211090G>T	ENSP00000441838:p.Met488Ile	92.0	0.0		108.0	32.0	NM_152603	B3KX49|Q6N044	Missense_Mutation	SNP	ENST00000536254.2	hg19		.	.	.	.	.	.	.	.	.	.	G	12.68	2.011518	0.35511	.	.	ENSG00000189042	ENST00000536254;ENST00000378686;ENST00000360729;ENST00000423498;ENST00000392163	T;T;T	0.35236	1.32;1.32;1.32	4.88	1.58	0.23477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.128065	0.36101	N	0.002795	T	0.26376	0.0644	N	0.04746	-0.17	0.09310	N	0.999998	B;P	0.44281	0.003;0.831	B;P	0.54664	0.002;0.758	T	0.05241	-1.0897	10	0.42905	T	0.14	.	6.7195	0.23323	0.1726:0.1509:0.6765:0.0	.	488;457	Q8N184;F8WEL6	ZN567_HUMAN;.	I	488;432;457;487;457	ENSP00000441838:M488I;ENSP00000353957:M457I;ENSP00000376003:M457I	ENSP00000353957:M457I	M	+	3	0	ZNF567	41902930	0.000000	0.05858	0.984000	0.44739	0.997000	0.91878	-0.239000	0.08965	0.754000	0.32968	0.561000	0.74099	ATG	.	.		0.413	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603		T	37211090	G	T	37211090	3	4	64	1	0	0	0	0	1	0	0	0	18013	1290	45	3	1381	3	ZNF567	19	37211090	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	859850	37211090	21917893	305	8022										
ZNF793	390927	hgsc.bcm.edu	37	chr19	38023265	38023265	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tttgtttcaacagatacctgTgtcattcaaagatgtggttg	9	6	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:38023265T>C	ENST00000587143.1	+	4	258	c.23T>C	c.(22-24)gTg>gCg	p.V8A	ZNF793_ENST00000542455.1_Missense_Mutation_p.V8A|ZNF793_ENST00000587986.1_Missense_Mutation_p.V8A|ZNF793_ENST00000588578.1_Missense_Mutation_p.V8A|ZNF793_ENST00000445217.1_Missense_Mutation_p.V8A|ZNF793_ENST00000589319.1_Missense_Mutation_p.V8A			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	8	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAGATACCTGTGTCATTCAAA	0.493																																					p.V8A	Melanoma(44;400 1431 1499 19093)	Atlas-SNP	.											.	ZNF793	50	.	0			c.T23C						.						53	54	54					19																	38023265		2157	4287	6444	SO:0001583	missense	390927	exon6			TACCTGTGTCATT	AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.23T>C	chr19.hg19:g.38023265T>C	ENSP00000468605:p.Val8Ala	82.0	0.0		88.0	4.0	NM_001013659	E9PGN4|Q7Z3Q9	Missense_Mutation	SNP	ENST00000587143.1	hg19	CCDS46062.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.976537	0.53720	.	.	ENSG00000188227	ENST00000542455;ENST00000418827;ENST00000445217;ENST00000322299	T;T	0.05717	3.4;3.4	3.53	3.53	0.40419	Krueppel-associated box (4);	.	.	.	.	T	0.34019	0.0883	H	0.96301	3.8	0.24906	N	0.992077	D;D	0.71674	0.998;0.995	D;P	0.71870	0.975;0.901	T	0.28332	-1.0047	9	0.87932	D	0	.	10.3278	0.43805	0.0:0.0:0.0:1.0	.	8;8	Q6ZN11;E9PGN4	ZN793_HUMAN;.	A	8;8;8;7	ENSP00000444355:V8A;ENSP00000396402:V8A	ENSP00000318811:V7A	V	+	2	0	ZNF793	42715105	1.000000	0.71417	1.000000	0.80357	0.501000	0.33797	4.696000	0.61774	1.590000	0.49995	0.460000	0.39030	GTG	.	.		0.493	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		C	38023265	T	C	38023265	3	2	64	1	0	0	0	0	1	0	0	0	18180	1696	59	2	29	2	ZNF793	19	38023265	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	812175	38023265	21105718	306	8023										
PSG4	5672	hgsc.bcm.edu	37	chr19	43699239	43699239	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctgtttcatttctcgtgacaTtgggtagaatgaggatcctg	11	7	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:43699239T>C	ENST00000405312.3	-	4	1133	c.896A>G	c.(895-897)aAt>aGt	p.N299S	PSG4_ENST00000244295.9_Intron|PSG4_ENST00000433626.2_Missense_Mutation_p.N206S	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	299	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				TCTCGTGACATTGGGTAGAAT	0.478																																					p.T299S		Atlas-SNP	.											PSG4_ENST00000405312,NS,carcinoma,0,1	PSG4	129	.	0			c.C896G						.						238	218	225					19																	43699239		2202	4295	6497	SO:0001583	missense	5672	exon4			GTGACATTGGGTA		CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9521	protein-coding gene	gene with protein product	"pregnancy-specific beta-1-glycoprotein 4"	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.896A>G	chr19.hg19:g.43699239T>C	ENSP00000384770:p.Asn299Ser	69.0	1.0		67.0	6.0	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Missense_Mutation	SNP	ENST00000405312.3	hg19	CCDS46093.1	.	.	.	.	.	.	.	.	.	.	c	1.820	-0.472562	0.04445	.	.	ENSG00000243137	ENST00000405312;ENST00000433626	T;T	0.10288	2.89;2.89	1.45	-2.17	0.07059	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.04227	0.0117	N	0.05230	-0.09	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.40979	-0.9534	9	0.22706	T	0.39	.	5.8772	0.18836	0.0:0.3561:0.0:0.6439	.	206;299	E7EX79;Q00888	.;PSG4_HUMAN	S	299;206	ENSP00000384770:N299S;ENSP00000387864:N206S	ENSP00000384770:N299S	N	-	2	0	PSG4	48391079	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-3.469000	0.00460	-1.969000	0.01005	-2.870000	0.00099	AAT	.	.		0.478	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633		C	43699239	T	C	43699239	3	2	64	1	0	0	0	0	1	0	0	0	12669	1493	52	2	375	2	PSG4	19	43699239	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	5675974	43699239	15429744	307	8024										
ZNF576	79177	hgsc.bcm.edu	37	chr19	44103100	44103100	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cgtggcccagaagctgcaggGggtcctcttcatctgcttca	12	13	4	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:44103100G>A	ENST00000336564.4	+	3	357	c.203G>A	c.(202-204)gGg>gAg	p.G68E	IRGQ_ENST00000422989.1_5'Flank|ZNF576_ENST00000528387.1_Missense_Mutation_p.G68E|ZNF576_ENST00000529930.1_Missense_Mutation_p.G68E|SRRM5_ENST00000526798.1_Intron|SRRM5_ENST00000607544.1_Intron|ZNF576_ENST00000391965.2_Missense_Mutation_p.G68E|ZNF576_ENST00000533118.1_Missense_Mutation_p.G68E|ZNF576_ENST00000525771.1_Missense_Mutation_p.G68E	NM_001145347.1	NP_001138819.1	Q9H609	ZN576_HUMAN	zinc finger protein 576	68					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(1)|prostate(1)	2		Prostate(69;0.0199)				AAGCTGCAGGGGGTCCTCTTC	0.637																																					p.G68E		Atlas-SNP	.											.	ZNF576	11	.	0			c.G203A						.						91	106	101					19																	44103100		2203	4300	6503	SO:0001583	missense	79177	exon3			TGCAGGGGGTCCT	AK026353	CCDS12625.1	19q13.31	2013-09-20			ENSG00000124444	ENSG00000124444		"Zinc fingers, C2H2-type"	28357	protein-coding gene	gene with protein product						12477932	Standard	NM_024327		Approved	MGC2508	uc002owz.2	Q9H609	OTTHUMG00000165479	ENST00000336564.4:c.203G>A	chr19.hg19:g.44103100G>A	ENSP00000337852:p.Gly68Glu	133.0	0.0		173.0	80.0	NM_001145347	Q9BU03	Missense_Mutation	SNP	ENST00000336564.4	hg19	CCDS12625.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766090	0.69878	.	.	ENSG00000124444	ENST00000391965;ENST00000525771;ENST00000533118;ENST00000528387;ENST00000529930;ENST00000336564	T;T;T;T;T;T	0.01252	5.1;5.1;5.1;5.1;5.1;5.1	3.93	3.93	0.45458	.	0.164033	0.36972	N	0.002318	T	0.02119	0.0066	N	0.11064	0.09	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.70103	-0.4964	10	0.08381	T	0.77	-15.9544	11.7501	0.51843	0.0:0.0:1.0:0.0	.	68	Q9H609	ZN576_HUMAN	E	68	ENSP00000375827:G68E;ENSP00000436182:G68E;ENSP00000435899:G68E;ENSP00000435934:G68E;ENSP00000435463:G68E;ENSP00000337852:G68E	ENSP00000337852:G68E	G	+	2	0	ZNF576	48794940	0.995000	0.38212	0.999000	0.59377	0.922000	0.55478	1.051000	0.30417	2.500000	0.84329	0.591000	0.81541	GGG	.	.		0.637	ZNF576-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384397.1	NM_024327		A	44103100	G	A	44103100	3	1	64	1	0	0	0	0	1	0	0	0	18023	1232	43	3	209	3	ZNF576	19	44103100	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	403861	44103100	15025883	308	8025										
ZNF226	7769	hgsc.bcm.edu	37	chr19	44679880	44679880	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atagtaaataaagcagatggTcccaataatactgggaatcc	8	7	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:44679880T>C	ENST00000590089.1	+	7	832	c.465T>C	c.(463-465)ggT>ggC	p.G155G	ZNF226_ENST00000588883.1_3'UTR|ZNF226_ENST00000454662.2_Silent_p.G155G|ZNF226_ENST00000337433.5_Silent_p.G155G			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	155					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)						Prostate(69;0.0352)|all_neural(266;0.202)				AAGCAGATGGTCCCAATAATA	0.408																																					p.G155G	Pancreas(115;581 1665 13228 19278 50070)	Atlas-SNP	.											.	.	.	.	0			c.T465C						.						36	33	34					19																	44679880		1828	4079	5907	SO:0001819	synonymous_variant	7769	exon6			AGATGGTCCCAAT	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"Zinc fingers, C2H2-type", "-"	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.465T>C	chr19.hg19:g.44679880T>C		104.0	0.0		81.0	4.0	NM_001032372	Q8WWE6|Q96TE6|Q9NS44	Silent	SNP	ENST00000590089.1	hg19	CCDS46102.1																																																																																			.	.		0.408	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1			C	44679880	T	C	44679880	2	2	64	1	0	0	0	0	0	0	0	1	17795	1654	58	2		2	ZNF226	19	44679880	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	576780	44679880	14449103	309	8026										
PLEKHA4	57664	hgsc.bcm.edu	37	chr19	49357343	49357343	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cgcacaacttggtcagcagcGtctggagaaaggagagcggg	16	9	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:49357343G>A	ENST00000263265.6	-	11	1652	c.1097C>T	c.(1096-1098)aCg>aTg	p.T366M	PLEKHA4_ENST00000355496.5_Splice_Site_p.T341M	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	366						cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		GGTCAGCAGCGTCTGGAGAAA	0.612																																					p.T366M		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.C1097T						.						43	43	43					19																	49357343		2203	4300	6503	SO:0001630	splice_region_variant	57664	exon11			AGCAGCGTCTGGA	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"Pleckstrin homology (PH) domain containing"	14339	protein-coding gene	gene with protein product		607769	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.1096-1C>T	chr19.hg19:g.49357343G>A		106.0	0.0		121.0	59.0	NM_020904	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	hg19	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.070509	0.55539	.	.	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.36340	1.26;1.26	4.91	3.85	0.44370	.	0.165964	0.39544	N	0.001332	T	0.41282	0.1152	L	0.40543	1.245	0.23862	N	0.996632	D;D	0.67145	0.995;0.996	P;P	0.54706	0.759;0.72	T	0.22836	-1.0205	10	0.72032	D	0.01	.	11.2063	0.48771	0.0:0.1854:0.8146:0.0	.	341;366	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	M	366;341	ENSP00000263265:T366M;ENSP00000347683:T341M	ENSP00000263265:T366M	T	-	2	0	PLEKHA4	54049155	0.977000	0.34250	0.783000	0.31826	0.631000	0.37964	2.023000	0.41040	1.393000	0.46605	0.563000	0.77884	ACG	.	.		0.612	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		Missense_Mutation	A	49357343	G	A	49357343	5	1	64	1	0	0	0	0	0	0	1	0	12067	1159	40	1	1282	1	PLEKHA4	19	49357343	Splice_Site	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	4677463	49357343	9771640	310	8027										
DHDH	27294	hgsc.bcm.edu	37	chr19	49442857	49442857	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ccgggcccaggctgggggggCcctgctggacatcggcatct	17	14	1	0	rs543413361		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:49442857C>G	ENST00000221403.2	+	4	558	c.518C>G	c.(517-519)gCc>gGc	p.A173G	DHDH_ENST00000523250.1_Intron|DHDH_ENST00000522614.1_Missense_Mutation_p.A173G	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	173					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		GCTGGGGGGGCCCTGCTGGAC	0.602													C|||	1	0.000199681	8e-04	0	5008	,	,		17572	0		0	False		,,,				2504	0				p.A173G		Atlas-SNP	.											DHDH,colon,carcinoma,0,1	DHDH	35	.	0			c.C518G						.						53	56	55					19																	49442857		2203	4300	6503	SO:0001583	missense	27294	exon4			GGGGGGCCCTGCT	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.518C>G	chr19.hg19:g.49442857C>G	ENSP00000221403:p.Ala173Gly	62.0	0.0		63.0	3.0	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	hg19	CCDS12741.1	.	.	.	.	.	.	.	.	.	.	C	1.710	-0.499278	0.04291	.	.	ENSG00000104808	ENST00000221403;ENST00000522614	T;T	0.38560	1.13;1.13	5.12	0.225	0.15325	.	0.219759	0.45606	N	0.000342	T	0.35653	0.0939	L	0.45228	1.405	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.36138	-0.9760	10	0.42905	T	0.14	-7.1401	17.2381	0.87005	0.0:0.6748:0.3252:0.0	rs58913518	173	Q9UQ10	DHDH_HUMAN	G	173	ENSP00000221403:A173G;ENSP00000428672:A173G	ENSP00000221403:A173G	A	+	2	0	DHDH	54134669	0.094000	0.21725	0.003000	0.11579	0.006000	0.05464	0.971000	0.29396	0.096000	0.17463	-0.270000	0.10280	GCC	.	.		0.602	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475		G	49442857	C	G	49442857	3	3	64	1	0	0	0	0	1	0	0	0	4481	739	26	4	532	4	DHDH	19	49442857	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	85514	49442857	9686126	311	8028										
ZNF611	81856	hgsc.bcm.edu	37	chr19	53208850	53208850	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgaccaaaggtcttcccacaTtcattacacttgtaaggttt	6	10	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:53208850T>C	ENST00000319783.1	-	7	1774	c.1458A>G	c.(1456-1458)gaA>gaG	p.E486E	ZNF611_ENST00000602162.1_Silent_p.E417E|ZNF611_ENST00000453741.2_Silent_p.E417E|ZNF611_ENST00000595798.1_Silent_p.E417E|ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000540744.1_Silent_p.E486E|ZNF611_ENST00000543227.1_Silent_p.E486E	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	486					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TCTTCCCACATTCATTACACT	0.358																																					p.E486E		Atlas-SNP	.											.	ZNF611	72	.	0			c.A1458G						.						92	94	93					19																	53208850		2203	4300	6503	SO:0001819	synonymous_variant	81856	exon7			CCCACATTCATTA	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"Zinc fingers, C2H2-type", "-"	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.1458A>G	chr19.hg19:g.53208850T>C		103.0	0.0		103.0	5.0	NM_030972	B3KRD5|Q69YG9	Silent	SNP	ENST00000319783.1	hg19	CCDS12855.1																																																																																			.	.		0.358	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972		C	53208850	T	C	53208850	2	2	64	1	0	0	0	0	0	0	0	1	18052	1490	52	2		2	ZNF611	19	53208850	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	3765993	53208850	5920133	312	8029										
ZNF816A	125893	hgsc.bcm.edu	37	chr19	53454471	53454471	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gggattctgaagctgaggaaGcaccgatagacttgtccaat	12	8	1	3	rs200901929|rs79566976		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:53454471G>C	ENST00000357666.4	-	5	857	c.557C>G	c.(556-558)gCt>gGt	p.A186G	ZNF816_ENST00000434371.2_Intron|ZNF321P_ENST00000391777.3_Intron|ZNF816_ENST00000444460.2_Missense_Mutation_p.A186G	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	186					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						AGCTGAGGAAGCACCGATAGA	0.373																																					p.A186G		Atlas-SNP	.											.	ZNF816	73	.	0			c.C557G						.						89	112	104					19																	53454471		2202	4300	6502	SO:0001583	missense	125893	exon4			GAGGAAGCACCGA	BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"Zinc fingers, C2H2-type", "-"	26995	protein-coding gene	gene with protein product			"zinc finger protein 816A"	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.557C>G	chr19.hg19:g.53454471G>C	ENSP00000350295:p.Ala186Gly	91.0	0.0		81.0	6.0	NM_001202457	A8K7H5|Q3KR39|Q659B3	Missense_Mutation	SNP	ENST00000357666.4	hg19	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	-	1.630	-0.519183	0.04171	.	.	ENSG00000180257	ENST00000357666;ENST00000444460	T;T	0.05649	3.41;3.41	1.58	0.318	0.15867	.	.	.	.	.	T	0.08758	0.0217	N	0.19112	0.55	0.09310	N	1	D	0.69078	0.997	D	0.75020	0.985	T	0.35624	-0.9781	9	0.15952	T	0.53	.	5.7046	0.17901	0.0:0.4142:0.5858:0.0	.	186	Q0VGE8	ZN816_HUMAN	G	186	ENSP00000350295:A186G;ENSP00000403266:A186G	ENSP00000350295:A186G	A	-	2	0	ZNF816	58146283	0.000000	0.05858	0.002000	0.10522	0.176000	0.22953	-0.783000	0.04638	-0.053000	0.13289	0.185000	0.17295	GCT	.	.		0.373	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		C	53454471	G	C	53454471	3	2	64	1	0	0	0	0	1	0	0	0	18192	971	34	4	1402	4	ZNF816A	19	53454471	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	245621	53454471	5674512	313	8030										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53643997	53643997	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctctctgatgccttgcaagcTttgatgtttgactaaaggct	9	9	1	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:53643997T>C	ENST00000334197.7	-	5	2152	c.2084A>G	c.(2083-2085)aAg>aGg	p.K695R	ZNF347_ENST00000452676.2_Missense_Mutation_p.K696R|ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_Missense_Mutation_p.K696R	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	695					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		CCTTGCAAGCTTTGATGTTTG	0.433																																					p.K696R	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.A2087G						.						141	134	136					19																	53643997		2203	4300	6503	SO:0001583	missense	84671	exon5			GCAAGCTTTGATG	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2084A>G	chr19.hg19:g.53643997T>C	ENSP00000334146:p.Lys695Arg	88.0	0.0		122.0	6.0	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	hg19	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	T	1.642	-0.516307	0.04200	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.07688	3.17;3.17	2.87	-0.786	0.10946	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03564	0.0102	N	0.12887	0.27	0.09310	N	1	B;B	0.28055	0.199;0.029	B;B	0.30572	0.117;0.051	T	0.45498	-0.9257	9	0.15499	T	0.54	.	1.6483	0.02766	0.1603:0.1023:0.3294:0.4081	.	696;695	G5E9N4;Q96SE7	.;ZN347_HUMAN	R	695;696	ENSP00000334146:K695R;ENSP00000405218:K696R	ENSP00000334146:K695R	K	-	2	0	ZNF347	58335809	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.448000	0.02394	-0.409000	0.07553	-1.281000	0.01382	AAG	.	.		0.433	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		C	53643997	T	C	53643997	3	2	64	1	0	0	0	0	1	0	0	0	17876	1609	56	2	439	2	ZNF347	19	53643997	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	189526	53643997	5484986	314	8031										
ZNF805	390980	hgsc.bcm.edu	37	chr19	57765823	57765823	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atgagtgcagtgaatgtggaAaggccttcagtcgcagctcg	14	8	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr19:57765823A>G	ENST00000414468.2	+	4	1636	c.1636A>G	c.(1636-1638)Aag>Gag	p.K546E	ZNF805_ENST00000535550.1_Missense_Mutation_p.K413E|ZNF805_ENST00000354309.4_Missense_Mutation_p.K413E	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	546					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(3)|lung(1)|stomach(1)	9						TGAATGTGGAAAGGCCTTCAG	0.478																																					p.K546E		Atlas-SNP	.											.	ZNF805	30	.	0			c.A1636G						.						106	99	101					19																	57765823		692	1591	2283	SO:0001583	missense	390980	exon4			TGTGGAAAGGCCT	AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"Zinc fingers, C2H2-type", "-"	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.1636A>G	chr19.hg19:g.57765823A>G	ENSP00000412999:p.Lys546Glu	91.0	0.0		85.0	4.0	NM_001023563	B4DNM5	Missense_Mutation	SNP	ENST00000414468.2	hg19	CCDS46207.1	.	.	.	.	.	.	.	.	.	.	A	19.89	3.911528	0.72983	.	.	ENSG00000204524	ENST00000535550;ENST00000414468;ENST00000354309	T;T;T	0.27104	1.69;1.69;1.69	4.62	4.62	0.57501	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.51477	D	0.000086	T	0.46483	0.1395	M	0.64170	1.965	0.27692	N	0.946071	D	0.76494	0.999	D	0.71870	0.975	T	0.38802	-0.9644	10	0.87932	D	0	.	13.4151	0.60963	1.0:0.0:0.0:0.0	.	546	Q5CZA5	ZN805_HUMAN	E	413;546;413	ENSP00000440067:K413E;ENSP00000412999:K546E;ENSP00000365414:K413E	ENSP00000365414:K413E	K	+	1	0	ZNF805	62457635	0.996000	0.38824	0.996000	0.52242	0.998000	0.95712	6.541000	0.73865	2.063000	0.61619	0.460000	0.39030	AAG	.	.		0.478	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1	NM_001023563		G	57765823	A	G	57765823	3	3	64	1	0	0	0	0	1	0	0	0	18187	15	1	2	1650	2	ZNF805	19	57765823	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	4121826	57765823	1363160	315	8032										
SMOX	54498	hgsc.bcm.edu	37	chr20	4162577	4162577	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gaatgaccctgacgacccagAggctaccaagcgcctgaagc	11	14	0	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr20:4162577A>G	ENST00000305958.4	+	4	788	c.563A>G	c.(562-564)gAg>gGg	p.E188G	SMOX_ENST00000346595.2_Intron|SMOX_ENST00000379460.2_Missense_Mutation_p.E188G|SMOX_ENST00000484515.1_3'UTR|SMOX_ENST00000278795.3_Missense_Mutation_p.E188G|SMOX_ENST00000339123.6_Missense_Mutation_p.E188G	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	188					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	GACGACCCAGAGGCTACCAAG	0.567																																					p.E188G		Atlas-SNP	.											.	SMOX	119	.	0			c.A563G						.						76	78	77					20																	4162577		2203	4300	6503	SO:0001583	missense	54498	exon4			ACCCAGAGGCTAC	AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"chromosome 20 open reading frame 16"	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.563A>G	chr20.hg19:g.4162577A>G	ENSP00000307252:p.Glu188Gly	104.0	0.0		92.0	6.0	NM_175839	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Missense_Mutation	SNP	ENST00000305958.4	hg19	CCDS13075.1	.	.	.	.	.	.	.	.	.	.	A	20.0	3.931186	0.73327	.	.	ENSG00000088826	ENST00000339123;ENST00000305958;ENST00000278795;ENST00000379460;ENST00000457205	T;T;T;T;T	0.09911	2.93;2.93;2.93;2.93;2.93	5.44	5.44	0.79542	Amine oxidase (1);	0.105379	0.64402	D	0.000005	T	0.33702	0.0872	M	0.79614	2.46	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;0.999;1.0;0.978;0.994	D;D;D;P;P	0.83275	0.996;0.99;0.996;0.844;0.896	T	0.05835	-1.0861	10	0.54805	T	0.06	-19.3387	13.4909	0.61395	1.0:0.0:0.0:0.0	.	165;188;188;188;188	B4DE63;Q9NWM0-6;Q9NWM0;Q9NWM0-2;Q9NWM0-4	.;.;SMOX_HUMAN;.;.	G	188;188;188;188;45	ENSP00000344595:E188G;ENSP00000307252:E188G;ENSP00000278795:E188G;ENSP00000368773:E188G;ENSP00000407269:E45G	ENSP00000278795:E188G	E	+	2	0	SMOX	4110577	1.000000	0.71417	0.996000	0.52242	0.960000	0.62799	5.100000	0.64560	2.082000	0.62665	0.456000	0.33151	GAG	.	.		0.567	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842		G	4162577	A	G	4162577	3	3	64	1	0	0	0	0	1	0	0	0	14818	304	11	2	573	2	SMOX	20	4162577	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10		4162577	58862943	316	8033										
KIF16B	55614	hgsc.bcm.edu	37	chr20	16360047	16360047	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	atctagattctttgtcatgtTcacattttaaacactctagg	5	8	5	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr20:16360047T>C	ENST00000354981.2	-	19	2757	c.2600A>G	c.(2599-2601)gAa>gGa	p.E867G	KIF16B_ENST00000378003.2_Missense_Mutation_p.E93G|KIF16B_ENST00000408042.1_Missense_Mutation_p.E867G|KIF16B_ENST00000355755.3_Missense_Mutation_p.E867G	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	867	Glu-rich.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						TTTGTCATGTTCACATTTTAA	0.408																																					p.E867G		Atlas-SNP	.											.	KIF16B	305	.	0			c.A2600G						.						150	148	149					20																	16360047		2203	4300	6503	SO:0001583	missense	55614	exon19			TCATGTTCACATT	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.2600A>G	chr20.hg19:g.16360047T>C	ENSP00000347076:p.Glu867Gly	74.0	0.0		82.0	4.0	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	hg19	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	T	3.052	-0.195247	0.06259	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000378003;ENST00000408042	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.6	-5.84	0.02318	.	1.633290	0.02854	N	0.129421	T	0.06371	0.0164	N	0.03608	-0.345	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.31724	-0.9933	10	0.21540	T	0.41	.	5.6248	0.17477	0.086:0.2973:0.4689:0.1478	.	867;867;867;867	Q96L93-4;Q96L93-2;Q96L93-6;Q96L93	.;.;.;KI16B_HUMAN	G	867;867;711;93;867	ENSP00000347076:E867G;ENSP00000347995:E867G;ENSP00000367242:E93G;ENSP00000384164:E867G	ENSP00000347076:E867G	E	-	2	0	KIF16B	16308047	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.022000	0.13511	-0.428000	0.07339	-0.263000	0.10527	GAA	.	.		0.408	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		C	16360047	T	C	16360047	3	2	64	1	0	0	0	0	1	0	0	0	8287	1783	62	2	1385	2	KIF16B	20	16360047	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	12197470	16360047	46665473	317	8034										
OVOL2	58495	hgsc.bcm.edu	37	chr20	18022238	18022238	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gttgaagcccttgccgcagaAggtgcacaggtgtcttttca	12	10	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr20:18022238A>G	ENST00000278780.6	-	3	693	c.451T>C	c.(451-453)Ttc>Ctc	p.F151L	OVOL2_ENST00000483661.1_5'UTR	NM_021220.2	NP_067043.2	Q9BRP0	OVOL2_HUMAN	ovo-like zinc finger 2	151					angiogenesis (GO:0001525)|dorsal/ventral pattern formation (GO:0009953)|embryonic digestive tract morphogenesis (GO:0048557)|endocardium formation (GO:0060214)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of keratinocyte proliferation (GO:0010837)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)	6						TTGCCGCAGAAGGTGCACAGG	0.562																																					p.F151L		Atlas-SNP	.											.	OVOL2	18	.	0			c.T451C						.						155	97	117					20																	18022238		2203	4300	6503	SO:0001583	missense	58495	exon3			CGCAGAAGGTGCA	AK022284	CCDS13132.1	20p11.23	2013-10-17	2013-10-17	2005-05-31	ENSG00000125850	ENSG00000125850		"Zinc fingers, C2H2-type"	15804	protein-coding gene	gene with protein product			"zinc finger protein 339", "ovo-like 2 (Drosophila)"	ZNF339			Standard	NM_021220		Approved	bA504H3.3, HOVO2	uc002wqi.1	Q9BRP0	OTTHUMG00000031960	ENST00000278780.6:c.451T>C	chr20.hg19:g.18022238A>G	ENSP00000278780:p.Phe151Leu	114.0	0.0		123.0	5.0	NM_021220	Q5T8B4|Q9BX22|Q9HA54|Q9Y4M0	Missense_Mutation	SNP	ENST00000278780.6	hg19	CCDS13132.1	.	.	.	.	.	.	.	.	.	.	A	36	5.679291	0.96774	.	.	ENSG00000125850	ENST00000278780	T	0.05996	3.36	5.73	5.73	0.89815	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.10637	0.0260	N	0.04805	-0.155	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.52609	-0.8553	10	0.33141	T	0.24	-33.5679	16.0048	0.80354	1.0:0.0:0.0:0.0	.	151	Q9BRP0	OVOL2_HUMAN	L	151	ENSP00000278780:F151L	ENSP00000278780:F151L	F	-	1	0	OVOL2	17970238	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.418000	0.80167	2.180000	0.69256	0.533000	0.62120	TTC	.	.		0.562	OVOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078148.5	NM_021220		G	18022238	A	G	18022238	3	3	64	1	0	0	0	0	1	0	0	0	11336	72	3	2	384	2	OVOL2	20	18022238	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	1662191	18022238	45003282	318	8035										
SLC24A3	57419	hgsc.bcm.edu	37	chr20	19698204	19698204	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agcagggggctgatctactcCgtaggcttgctcctggcctc	13	13	1	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr20:19698204C>T	ENST00000328041.6	+	16	1949	c.1752C>T	c.(1750-1752)tcC>tcT	p.S584S		NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	584					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TGATCTACTCCGTAGGCTTGC	0.507																																					p.S584S		Atlas-SNP	.											.	SLC24A3	92	.	0			c.C1752T						.						293	289	290					20																	19698204		2203	4300	6503	SO:0001819	synonymous_variant	57419	exon16			CTACTCCGTAGGC	AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"Solute carriers"	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.1752C>T	chr20.hg19:g.19698204C>T		235.0	0.0		241.0	103.0	NM_020689	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Silent	SNP	ENST00000328041.6	hg19	CCDS13140.1																																																																																			.	.		0.507	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689		T	19698204	C	T	19698204	2	4	64	1	0	0	0	0	0	0	0	1	14482	639	23	1		1	SLC24A3	20	19698204	Silent	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	1675966	19698204	43327316	319	8036										
NECAB3	63941	hgsc.bcm.edu	37	chr20	32246573	32246573	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgaagtccacatagcagcgcAgggctcggtggaagtcctgc	14	11	0	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr20:32246573A>G	ENST00000246190.6	-	9	1002	c.947T>C	c.(946-948)cTg>cCg	p.L316P	NECAB3_ENST00000375238.4_Missense_Mutation_p.L282P|NECAB3_ENST00000606525.1_5'UTR|RP1-63M2.6_ENST00000607224.1_RNA	NM_031232.3	NP_112509.3	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	316	ABM.				protein metabolic process (GO:0019538)|protein secretion (GO:0009306)|regulation of amyloid precursor protein biosynthetic process (GO:0042984)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|Golgi cis cisterna (GO:0000137)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			large_intestine(3)|lung(5)|skin(2)	10						ATAGCAGCGCAGGGCTCGGTG	0.662																																					p.L316P		Atlas-SNP	.											.	NECAB3	27	.	0			c.T947C						.						36	40	38					20																	32246573		1982	4152	6134	SO:0001583	missense	63941	exon9			CAGCGCAGGGCTC	AB039947	CCDS42866.1, CCDS42867.1	20q11.21	2013-01-10	2007-12-06	2007-12-06	ENSG00000125967	ENSG00000125967		"N-terminal EF-hand calcium binding proteins", "EF-hand domain containing"	15851	protein-coding gene	gene with protein product	"EF-hand calcium binding protein 3"	612478	"amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein"	SYTIP2, APBA2BP		10833507	Standard	NM_031232		Approved	XB51, dJ63M2.4, NIP1, dJ63M2.5, EFCBP3	uc002wzn.4	Q96P71	OTTHUMG00000032264	ENST00000246190.6:c.947T>C	chr20.hg19:g.32246573A>G	ENSP00000246190:p.Leu316Pro	158.0	0.0		149.0	6.0	NM_031232	A8K780|E1P5N2|Q5JWF5|Q5JWF6|Q5JWF7|Q86VV1|Q9H433|Q9H8G8|Q9HBW7|Q9HCQ9	Missense_Mutation	SNP	ENST00000246190.6	hg19	CCDS42866.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.954416	0.73902	.	.	ENSG00000125967	ENST00000375238;ENST00000246190;ENST00000439478	T;T;T	0.38560	1.25;1.25;1.13	4.89	4.89	0.63831	Dimeric alpha-beta barrel (1);Antibiotic biosynthesis monooxygenase (1);	0.000000	0.64402	D	0.000004	T	0.65678	0.2714	M	0.81112	2.525	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.71307	-0.4632	10	0.87932	D	0	-8.487	13.4869	0.61371	1.0:0.0:0.0:0.0	.	193;316;282	E1P5N3;Q96P71;Q96P71-2	.;NECA3_HUMAN;.	P	282;316;264	ENSP00000364386:L282P;ENSP00000246190:L316P;ENSP00000392064:L264P	ENSP00000246190:L316P	L	-	2	0	NECAB3	31710234	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.808000	0.86044	1.841000	0.53522	0.379000	0.24179	CTG	.	.		0.662	NECAB3-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078724.2			G	32246573	A	G	32246573	3	3	64	1	0	0	0	0	1	0	0	0	10315	188	7	2	259	2	NECAB3	20	32246573	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	12548369	32246573	30778947	320	8037										
RPN2	6185	hgsc.bcm.edu	37	chr20	35865012	35865012	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gactcatgtatgtctactggActcagctcaacatgttccag	8	11	4	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr20:35865012A>G	ENST00000237530.6	+	16	2094	c.1783A>G	c.(1783-1785)Act>Gct	p.T595A	RPN2_ENST00000470352.1_3'UTR|RPN2_ENST00000373622.5_Missense_Mutation_p.T563A	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II	595					aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				TGTCTACTGGACTCAGCTCAA	0.498																																					p.T595A		Atlas-SNP	.											.	RPN2	45	.	0			c.A1783G						.						137	107	117					20																	35865012		2203	4300	6503	SO:0001583	missense	6185	exon16			TACTGGACTCAGC	Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"oligosaccharyltransferase complex subunit (non-catalytic)"	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.1783A>G	chr20.hg19:g.35865012A>G	ENSP00000237530:p.Thr595Ala	126.0	0.0		111.0	5.0	NM_002951	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Missense_Mutation	SNP	ENST00000237530.6	hg19	CCDS13291.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.753956	0.69648	.	.	ENSG00000118705	ENST00000237530;ENST00000373622;ENST00000397161;ENST00000437329	T;T;T	0.45668	0.89;0.89;0.89	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.53498	0.1800	L	0.54323	1.7	0.58432	D	0.999994	D;P	0.58620	0.983;0.938	P;P	0.60286	0.872;0.831	T	0.48990	-0.8985	10	0.31617	T	0.26	-13.7218	12.941	0.58345	1.0:0.0:0.0:0.0	.	563;595	Q5JYR6;P04844	.;RPN2_HUMAN	A	595;563;102;102	ENSP00000237530:T595A;ENSP00000362724:T563A;ENSP00000409580:T102A	ENSP00000237530:T595A	T	+	1	0	RPN2	35298426	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.761000	0.91691	2.153000	0.67306	0.459000	0.35465	ACT	.	.		0.498	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079076.2	NM_002951		G	35865012	A	G	35865012	3	3	64	1	0	0	0	0	1	0	0	0	13623	275	10	2	1845	2	RPN2	20	35865012	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	3618439	35865012	27160508	321	8038										
FAM83D	81610	hgsc.bcm.edu	37	chr20	37576564	37576564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gaaatatctactatgcaaggTcaggaactaagattattggg	10	5	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr20:37576564T>C	ENST00000217429.4	+	3	828	c.787T>C	c.(787-789)Tca>Cca	p.S263P		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	233					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				CTATGCAAGGTCAGGAACTAA	0.438																																					p.S263P		Atlas-SNP	.											.	FAM83D	60	.	0			c.T787C						.						131	126	128					20																	37576564		1953	4138	6091	SO:0001583	missense	81610	exon3			GCAAGGTCAGGAA	AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 129"	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.787T>C	chr20.hg19:g.37576564T>C	ENSP00000217429:p.Ser263Pro	77.0	0.0		88.0	4.0	NM_030919	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Missense_Mutation	SNP	ENST00000217429.4	hg19	CCDS42872.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.896460	0.91962	.	.	ENSG00000101447	ENST00000217429;ENST00000424027	T	0.13089	2.62	6.16	5.01	0.66863	.	0.065751	0.64402	D	0.000005	T	0.41143	0.1146	M	0.86864	2.845	0.54753	D	0.999989	D	0.89917	1.0	D	0.81914	0.995	T	0.42447	-0.9451	10	0.72032	D	0.01	.	12.1733	0.54172	0.128:0.0:0.0:0.872	.	233	Q9H4H8	FA83D_HUMAN	P	263;217	ENSP00000217429:S263P	ENSP00000217429:S263P	S	+	1	0	FAM83D	37009978	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.868000	0.69605	2.367000	0.80283	0.528000	0.53228	TCA	.	.		0.438	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1			C	37576564	T	C	37576564	3	2	64	1	0	0	0	0	1	0	0	0	5644	1667	58	2	797	2	FAM83D	20	37576564	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1711552	37576564	25448956	322	8039										
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51872639	51872639	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtctgatctgggcccacaagAgcgtatgcaaatctctaagt	10	10	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr20:51872639A>G	ENST00000371497.5	+	2	3529	c.2642A>G	c.(2641-2643)gAg>gGg	p.E881G	TSHZ2_ENST00000329613.6_Missense_Mutation_p.E878G|TSHZ2_ENST00000603338.2_Missense_Mutation_p.E878G|RP4-678D15.1_ENST00000606932.1_RNA	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	881					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			GGCCCACAAGAGCGTATGCAA	0.502																																					p.E881G		Atlas-SNP	.											.	TSHZ2	209	.	0			c.A2642G						.						86	83	84					20																	51872639		2203	4300	6503	SO:0001583	missense	128553	exon2			CACAAGAGCGTAT	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2642A>G	chr20.hg19:g.51872639A>G	ENSP00000360552:p.Glu881Gly	104.0	0.0		86.0	4.0	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.218555	0.79464	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.27890	1.64;1.64	5.8	5.8	0.92144	Homeobox (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.50069	0.1594	L	0.47190	1.495	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.50541	-0.8816	10	0.87932	D	0	-1.386	16.1354	0.81481	1.0:0.0:0.0:0.0	.	881	Q9NRE2	TSH2_HUMAN	G	881;878;407	ENSP00000360552:E881G;ENSP00000333114:E878G	ENSP00000333114:E878G	E	+	2	0	TSHZ2	51306046	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.956000	0.93066	2.206000	0.71126	0.523000	0.50628	GAG	.	.		0.502	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		G	51872639	A	G	51872639	3	3	64	1	0	0	0	0	1	0	0	0	16639	304	11	2	2648	2	TSHZ2	20	51872639	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	14296075	51872639	11152881	323	8040										
LSM14B	149986	hgsc.bcm.edu	37	chr20	60706422	60706422	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctttttgtagatgacaaggcTgagaagggggaagagaagga	16	3	0	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr20:60706422T>C	ENST00000279068.6	+	7	1006	c.846T>C	c.(844-846)gcT>gcC	p.A282A	LSM14B_ENST00000253001.4_Silent_p.A282A	NM_144703.2	NP_653304.2	Q9BX40	LS14B_HUMAN	LSM14B, SCD6 homolog B (S. cerevisiae)	282					multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)	ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|lung(4)	8	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			ATGACAAGGCTGAGAAGGGGG	0.582																																					p.A282A		Atlas-SNP	.											.	LSM14B	62	.	0			c.T846C						.						44	49	48					20																	60706422		2013	4170	6183	SO:0001819	synonymous_variant	149986	exon7			CAAGGCTGAGAAG	AF172328	CCDS46626.1	20q13.33	2010-01-27	2006-12-21	2006-01-24	ENSG00000149657	ENSG00000149657			15887	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 40", "family with sequence similarity 61, member B", "LSM14 homolog B (SCD6, S. cerevisiae)"	C20orf40, FAM61B			Standard	NM_144703		Approved	FT005, bA11M20.3, FLJ25473, LSM13, RAP55B	uc010gjy.1	Q9BX40	OTTHUMG00000032901	ENST00000279068.6:c.846T>C	chr20.hg19:g.60706422T>C		99.0	0.0		85.0	4.0	NM_144703	Q6PFW8|Q96LH8	Silent	SNP	ENST00000279068.6	hg19	CCDS46626.1																																																																																			.	.		0.582	LSM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079996.4	NM_144703		C	60706422	T	C	60706422	2	2	64	1	0	0	0	0	0	0	0	1	9064	1567	55	2		2	LSM14B	20	60706422	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	8833783	60706422	2319098	324	8041										
GART	2618	hgsc.bcm.edu	37	chr21	34882122	34882122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ttaagacagccactctggccTtttttttttcaaaagagaaa	6	8	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr21:34882122T>C	ENST00000381831.3	-	18	2683	c.2420A>G	c.(2419-2421)aAg>aGg	p.K807R	GART_ENST00000543717.1_Missense_Mutation_p.K359R|GART_ENST00000381839.3_Missense_Mutation_p.K807R|GART_ENST00000381815.4_Missense_Mutation_p.K807R	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	807	AIRS.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)	p.K807fs*7(2)		NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	CACTCTGGCCTTTTTTTTTTC	0.448																																					p.K807R		Atlas-SNP	.											.,5	GART	81	.	2	Deletion - Frameshift(2)	ovary(2)	c.A2420G						.						66	70	68					21																	34882122		2203	4300	6503	SO:0001583	missense	2618	exon18			CTGGCCTTTTTTT	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2420A>G	chr21.hg19:g.34882122T>C	ENSP00000371253:p.Lys807Arg	58.0	0.0		78.0	4.0	NM_001136005	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	hg19	CCDS13627.1	.	.	.	.	.	.	.	.	.	.	T	8.259	0.810646	0.16537	.	.	ENSG00000159131	ENST00000414353;ENST00000381815;ENST00000381831;ENST00000381839;ENST00000543717	T;T;T;T	0.46063	1.46;1.46;1.46;0.88	5.52	1.39	0.22231	.	0.269064	0.42420	N	0.000720	T	0.19927	0.0479	N	0.08118	0	0.42171	D	0.991646	B	0.09022	0.002	B	0.12156	0.007	T	0.05699	-1.0869	10	0.20046	T	0.44	-12.4071	9.947	0.41616	0.0:0.2362:0.0:0.7638	.	807	P22102	PUR2_HUMAN	R	71;807;807;807;359	ENSP00000371236:K807R;ENSP00000371253:K807R;ENSP00000371261:K807R;ENSP00000443579:K359R	ENSP00000371236:K807R	K	-	2	0	GART	33803992	1.000000	0.71417	0.803000	0.32268	0.561000	0.35649	1.563000	0.36364	0.393000	0.25203	0.482000	0.46254	AAG	.	.		0.448	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819		C	34882122	T	C	34882122	3	2	64	1	0	0	0	0	1	0	0	0	6251	1609	56	2	632	2	GART	21	34882122	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		34882122	13247773	325	8042										
FAM3B	54097	hgsc.bcm.edu	37	chr21	42720630	42720630	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcaaaaggcttggaactcccTtccgaaattcagagagaaaa	9	9	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr21:42720630T>C	ENST00000357985.2	+	7	743	c.597T>C	c.(595-597)ccT>ccC	p.P199P	FAM3B_ENST00000398647.3_Silent_p.P151P|FAM3B_ENST00000479810.2_3'UTR|FAM3B_ENST00000398652.3_Silent_p.P238P|FAM3B_ENST00000398646.3_Silent_p.P222P	NM_058186.3	NP_478066.3	P58499	FAM3B_HUMAN	family with sequence similarity 3, member B	199					apoptotic process (GO:0006915)|insulin secretion (GO:0030073)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			central_nervous_system(2)|endometrium(1)|lung(2)	5		Prostate(19;1.57e-07)|all_epithelial(19;0.0404)				TGGAACTCCCTTCCGAAATTC	0.423																																					p.P199P		Atlas-SNP	.											.	FAM3B	22	.	0			c.T597C						.						81	77	79					21																	42720630		2203	4300	6503	SO:0001819	synonymous_variant	54097	exon7			ACTCCCTTCCGAA	AF494379	CCDS13671.1, CCDS42930.1	21q22.3	2014-08-14	2002-05-23	2002-06-20	ENSG00000183844	ENSG00000183844			1253	protein-coding gene	gene with protein product	"pancreatic-derived factor"	608617	"chromosome 21 open reading frame 11"	C21orf11			Standard	NM_058186		Approved	D21M16SJHU19e, PRED44, 2-21, ORF9, C21orf76, PANDER	uc002yzb.1	P58499	OTTHUMG00000086752	ENST00000357985.2:c.597T>C	chr21.hg19:g.42720630T>C		150.0	0.0		96.0	4.0	NM_058186		Silent	SNP	ENST00000357985.2	hg19	CCDS13671.1																																																																																			.	.		0.423	FAM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195142.1	NM_058186		C	42720630	T	C	42720630	2	2	64	1	0	0	0	0	0	0	0	1	5565	1596	56	2		2	FAM3B	21	42720630	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	7838508	42720630	5409265	326	8043										
PKNOX1	5316	hgsc.bcm.edu	37	chr21	44441414	44441414	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tatttttcaactttaaaagcTtcagttacagttaaaccaag	4	7	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr21:44441414T>C	ENST00000291547.5	+	8	933	c.722T>C	c.(721-723)cTt>cCt	p.L241P	PKNOX1_ENST00000432907.2_Splice_Site_p.L124P	NM_004571.3	NP_004562.2	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	241					angiogenesis (GO:0001525)|camera-type eye development (GO:0043010)|erythrocyte differentiation (GO:0030218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|prostate(1)	22						CTTTAAAAGCTTCAGTTACAG	0.418																																					p.L241P		Atlas-SNP	.											.	PKNOX1	40	.	0			c.T722C						.						50	48	49					21																	44441414		2203	4300	6503	SO:0001630	splice_region_variant	5316	exon8			AAAAGCTTCAGTT		CCDS13692.1, CCDS68211.1	21q22.3	2011-06-20			ENSG00000160199	ENSG00000160199		"Homeoboxes / TALE class"	9022	protein-coding gene	gene with protein product		602100				9479508	Standard	NM_001286258		Approved	PREP1	uc002zcq.1	P55347	OTTHUMG00000086833	ENST00000291547.5:c.721-1T>C	chr21.hg19:g.44441414T>C		100.0	0.0		100.0	4.0	NM_004571	O00528|Q8IWT7	Missense_Mutation	SNP	ENST00000291547.5	hg19	CCDS13692.1	.	.	.	.	.	.	.	.	.	.	T	18.15	3.560728	0.65538	.	.	ENSG00000160199	ENST00000291547;ENST00000432907	D;D	0.87729	-2.01;-2.29	5.59	5.59	0.84812	.	0.236840	0.33813	N	0.004528	D	0.90618	0.7058	L	0.48362	1.52	0.80722	D	1	D;D	0.71674	0.998;0.996	P;D	0.65874	0.897;0.939	D	0.90970	0.4819	10	0.52906	T	0.07	-12.3065	15.7594	0.78067	0.0:0.0:0.0:1.0	.	241;241	P55347;P55347-2	PKNX1_HUMAN;.	P	241;124	ENSP00000291547:L241P;ENSP00000402243:L124P	ENSP00000291547:L241P	L	+	2	0	PKNOX1	43314483	1.000000	0.71417	0.954000	0.39281	0.759000	0.43091	7.280000	0.78610	2.114000	0.64651	0.533000	0.62120	CTT	.	.		0.418	PKNOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195520.3		Missense_Mutation	C	44441414	T	C	44441414	5	2	64	1	0	0	0	0	0	0	1	0	11991	1623	56	2	748	2	PKNOX1	21	44441414	Splice_Site	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1720784	44441414	3688481	327	8044										
CARD10	29775	hgsc.bcm.edu	37	chr22	37902375	37902375	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtactgcaactggatccggtCacggctctggatggcctagg	14	11	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr22:37902375C>A	ENST00000403299.1	-	8	1423	c.1207G>T	c.(1207-1209)Gac>Tac	p.D403Y	CARD10_ENST00000406271.3_Missense_Mutation_p.D117Y|CARD10_ENST00000251973.5_Missense_Mutation_p.D403Y|CARD10_ENST00000494166.1_5'Flank			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	403					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					TGGATCCGGTCACGGCTCTGG	0.622																																					p.D403Y		Atlas-SNP	.											.	CARD10	55	.	0			c.G1207T						.						54	50	52					22																	37902375		2203	4300	6503	SO:0001583	missense	29775	exon7			TCCGGTCACGGCT	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1207G>T	chr22.hg19:g.37902375C>A	ENSP00000384570:p.Asp403Tyr	207.0	0.0		230.0	68.0	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	hg19	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.095456	0.76870	.	.	ENSG00000100065	ENST00000403299;ENST00000406271;ENST00000251973;ENST00000437756	T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.16	5.31	4.29	0.51040	.	0.169713	0.50627	D	0.000119	D	0.86514	0.5951	M	0.73962	2.25	0.44092	D	0.996855	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.87541	0.2459	10	0.87932	D	0	-35.6918	12.0009	0.53230	0.0:0.9202:0.0:0.0798	.	403;117	Q9BWT7;Q8NC81	CAR10_HUMAN;.	Y	403;117;403;44	ENSP00000384570:D403Y;ENSP00000385799:D117Y;ENSP00000251973:D403Y;ENSP00000416239:D44Y	ENSP00000251973:D403Y	D	-	1	0	CARD10	36232321	0.999000	0.42202	0.862000	0.33874	0.993000	0.82548	4.295000	0.59049	1.235000	0.43724	0.561000	0.74099	GAC	.	.		0.622	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		A	37902375	C	A	37902375	3	1	64	1	0	0	0	0	1	0	0	0	2646	826	29	3	1947	3	CARD10	22	37902375	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10		37902375	13402191	328	8045										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38119756	38119756	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ctctcccaacagaaccactcAacgagagaattccagaacat	5	14	2	3	rs71322688|rs67890459|rs201160789|rs77530465|rs55745992	byFrequency	TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr22:38119756A>G	ENST00000406386.3	+	7	1448	c.1193A>G	c.(1192-1194)cAa>cGa	p.Q398R		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	398					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.Q398R(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					AGAACCACTCAACGAGAGAAT	0.552																																					p.Q398R		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	.	1	Substitution - Missense(1)	lung(1)	c.A1193G						.						117	100	106					22																	38119756		1849	3515	5364	SO:0001583	missense	11078	exon7			CCACTCAACGAGA	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1193A>G	chr22.hg19:g.38119756A>G	ENSP00000384312:p.Gln398Arg	1.0	0.0		13.0	8.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	7.038	0.561918	0.13498	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.33216	1.42	2.53	2.53	0.30540	.	.	.	.	.	T	0.27629	0.0679	L	0.44542	1.39	0.09310	N	0.99999	P	0.47604	0.898	P	0.47402	0.546	T	0.07578	-1.0765	9	0.21540	T	0.41	.	5.6825	0.17784	0.7186:0.2814:0.0:0.0	.	398	Q9H2D6	TARA_HUMAN	R	398	ENSP00000384312:Q398R	ENSP00000384312:Q398R	Q	+	2	0	TRIOBP	36449702	0.002000	0.14202	0.064000	0.19789	0.071000	0.16799	0.831000	0.27476	1.186000	0.42985	0.165000	0.16767	CAA	.	.		0.552	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			G	38119756	A	G	38119756	3	3	64	1	0	0	0	0	1	0	0	0	16568	130	5	2	1211	2	TRIOBP	22	38119756	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	217381	38119756	13184810	329	8046										
PRR5	55615	hgsc.bcm.edu	37	chr22	45110469	45110469	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gttttcttccctctgcccccAgcatccacaacggggtgatc	8	16	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr22:45110469A>G	ENST00000336985.6	+	2	411		c.e2-1		ARHGAP8_ENST00000389773.5_Splice_Site|PRR5-ARHGAP8_ENST00000352766.7_Splice_Site|PRR5_ENST00000403581.1_Splice_Site|PRR5-ARHGAP8_ENST00000361473.5_Splice_Site|ARHGAP8_ENST00000517296.3_Splice_Site|PRR5_ENST00000477331.1_Splice_Site|PRR5_ENST00000006251.7_Splice_Site	NM_181333.3	NP_851850.1	P85299	PRR5_HUMAN	proline rich 5 (renal)						cell cycle (GO:0007049)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)	TORC2 complex (GO:0031932)				central_nervous_system(1)|endometrium(2)|lung(6)|prostate(1)|skin(1)	11		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		CTCTGCCCCCAGCATCCACAA	0.632																																					.		Atlas-SNP	.											.	PRR5	75	.	0			c.108-2A>G						.						89	86	87					22																	45110469		2203	4300	6503	SO:0001630	splice_region_variant	55615	exon3			GCCCCCAGCATCC	AF177331	CCDS14058.1, CCDS14059.1, CCDS56232.1, CCDS74875.1	22q13.3	2011-02-10			ENSG00000186654	ENSG00000186654			31682	protein-coding gene	gene with protein product	"protein observed with Rictor-1"	609406				15718101, 17599906	Standard	NM_001017528		Approved	PP610, FLJ20185k, Protor-1		P85299	OTTHUMG00000150460	ENST00000336985.6:c.135-1A>G	chr22.hg19:g.45110469A>G		82.0	0.0		107.0	5.0	NM_001017528	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Splice_Site	SNP	ENST00000336985.6	hg19	CCDS14058.1	.	.	.	.	.	.	.	.	.	.	a	13.43	2.234276	0.39498	.	.	ENSG00000186654;ENSG00000186654;ENSG00000186654;ENSG00000186654;ENSG00000186654;ENSG00000186654;ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484	ENST00000432186;ENST00000006251;ENST00000403581;ENST00000336985;ENST00000403696;ENST00000457960;ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773	.	.	.	4.06	4.06	0.47325	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3195	0.54977	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRR5;PRR5-ARHGAP8;ARHGAP8	43489133	1.000000	0.71417	0.982000	0.44146	0.498000	0.33706	3.862000	0.56009	1.857000	0.53885	0.524000	0.50904	.	.	.		0.632	PRR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318200.2	NM_001017528	Intron	G	45110469	A	G	45110469	5	3	64	1	0	0	0	0	0	0	1	0	12612	202	7	2	139	2	PRR5	22	45110469	Splice_Site	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	6990713	45110469	6194097	330	8047										
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50720335	50720335	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tgacgccacctgtgaagttcTcaaaggtggggtcaggcacg	14	10	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chr22:50720335T>C	ENST00000449103.1	-	20	3433	c.3293A>G	c.(3292-3294)gAg>gGg	p.E1098G	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Missense_Mutation_p.E1098G			O15031	PLXB2_HUMAN	plexin B2	1098					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TGTGAAGTTCTCAAAGGTGGG	0.642																																					p.E1098G		Atlas-SNP	.											.	PLXNB2	172	.	0			c.A3293G						.						51	59	56					22																	50720335		2052	4178	6230	SO:0001583	missense	23654	exon20			AAGTTCTCAAAGG		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.3293A>G	chr22.hg19:g.50720335T>C	ENSP00000409171:p.Glu1098Gly	38.0	0.0		39.0	4.0	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	hg19	CCDS43035.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.86|17.86	3.491591|3.491591	0.64074|0.64074	.|.	.|.	ENSG00000196576|ENSG00000196576	ENST00000449103;ENST00000359337|ENST00000427829	T;T|.	0.04119|.	3.7;3.7|.	4.63|4.63	4.63|4.63	0.57726|0.57726	.|.	0.644761|.	0.14308|.	N|.	0.327867|.	T|T	0.58337|0.58337	0.2115|0.2115	L|L	0.40543|0.40543	1.245|1.245	0.46096|0.46096	D|D	0.998869|0.998869	B|.	0.28439|.	0.212|.	B|.	0.27380|.	0.079|.	T|T	0.55866|0.55866	-0.8073|-0.8073	10|5	0.37606|.	T|.	0.19|.	.|.	14.1854|14.1854	0.65603|0.65603	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1098|.	O15031|.	PLXB2_HUMAN|.	G|G	1098|116	ENSP00000409171:E1098G;ENSP00000352288:E1098G|.	ENSP00000352288:E1098G|.	E|R	-|-	2|1	0|2	PLXNB2|PLXNB2	49062462|49062462	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.819000|0.819000	0.46315|0.46315	5.101000|5.101000	0.64566|0.64566	1.950000|1.950000	0.56595|0.56595	0.260000|0.260000	0.18958|0.18958	GAG|AGA	.	.		0.642	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		C	50720335	T	C	50720335	3	2	64	1	0	0	0	0	1	0	0	0	12133	1551	54	2	2295	2	PLXNB2	22	50720335	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	5609866	50720335	584231	331	8048										
ACOT9	23597	hgsc.bcm.edu	37	chrX	23726023	23726023	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtctaaagagctcctcttccTctgggctttcagggatgagt	11	10	4	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:23726023T>C	ENST00000336430.7	-	9	805	c.674A>G	c.(673-675)gAg>gGg	p.E225G	ACOT9_ENST00000492081.1_3'UTR|ACOT9_ENST00000379303.5_Missense_Mutation_p.E234G|ACOT9_ENST00000379295.1_Missense_Mutation_p.E165G	NM_001033583.2	NP_001028755.2	Q9Y305	ACOT9_HUMAN	acyl-CoA thioesterase 9	225					acyl-CoA metabolic process (GO:0006637)	mitochondrion (GO:0005739)	acetyl-CoA hydrolase activity (GO:0003986)|carboxylic ester hydrolase activity (GO:0052689)			breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(4)|pancreas(1)|skin(1)	15						CTCCTCTTCCTCTGGGCTTTC	0.303																																					p.E234G		Atlas-SNP	.											.	ACOT9	33	.	0			c.A701G						.						31	29	29					X																	23726023		2203	4299	6502	SO:0001583	missense	23597	exon10			TCTTCCTCTGGGC	AF132950	CCDS35216.1, CCDS43924.1	Xp22.11	2008-02-05			ENSG00000123130	ENSG00000123130		"Acyl CoA thioesterases"	17152	protein-coding gene	gene with protein product		300862				10383425, 10810093, 16103133, 16940157	Standard	XM_005274471		Approved	CGI-16, MT-ACT48, ACATE2	uc004dao.3	Q9Y305	OTTHUMG00000021257	ENST00000336430.7:c.674A>G	chrX.hg19:g.23726023T>C	ENSP00000336580:p.Glu225Gly	80.0	0.0		79.0	4.0	NM_001037171	B3KNC9|B7ZM94	Missense_Mutation	SNP	ENST00000336430.7	hg19	CCDS35216.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.220404	0.79464	.	.	ENSG00000123130	ENST00000379303;ENST00000336430;ENST00000379295;ENST00000473710	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.4	5.4	0.78164	.	0.044427	0.85682	D	0.000000	T	0.64327	0.2588	M	0.90705	3.14	0.80722	D	1	P;P;D	0.54772	0.954;0.947;0.968	P;P;P	0.61800	0.691;0.611;0.894	T	0.72697	-0.4215	10	0.66056	D	0.02	-19.281	14.4943	0.67674	0.0:0.0:0.0:1.0	.	192;225;234	Q9Y305-2;Q9Y305;Q9Y305-4	.;ACOT9_HUMAN;.	G	234;225;165;151	ENSP00000368605:E234G;ENSP00000336580:E225G;ENSP00000368597:E165G;ENSP00000420490:E151G	ENSP00000336580:E225G	E	-	2	0	ACOT9	23635944	1.000000	0.71417	0.871000	0.34182	0.782000	0.44232	5.477000	0.66799	1.803000	0.52742	0.381000	0.24937	GAG	.	.		0.303	ACOT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056065.1	NM_012332		C	23726023	T	C	23726023	3	2	64	1	0	0	0	0	1	0	0	0	157	1551	54	2	673	2	ACOT9	23	23726023	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10		23726023	131544537	332	8049										
MAGEB10	139422	hgsc.bcm.edu	37	chrX	27839847	27839847	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cagatatgctgagaaatgtaAcccaaatgtccaagagccag	9	9	0	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:27839847A>G	ENST00000356790.2	+	3	669	c.424A>G	c.(424-426)Acc>Gcc	p.T142A		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	142	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						GAGAAATGTAACCCAAATGTC	0.438																																					p.T142A		Atlas-SNP	.											.	MAGEB10	107	.	0			c.A424G						.						63	60	61					X																	27839847		2202	4300	6502	SO:0001583	missense	139422	exon3			AATGTAACCCAAA		CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.424A>G	chrX.hg19:g.27839847A>G	ENSP00000368304:p.Thr142Ala	113.0	0.0		84.0	4.0	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Missense_Mutation	SNP	ENST00000356790.2	hg19	CCDS35221.1	.	.	.	.	.	.	.	.	.	.	A	0.033	-1.324496	0.01309	.	.	ENSG00000177689	ENST00000356790	T	0.04551	3.6	2.62	0.0418	0.14214	.	0.757856	0.11792	U	0.529088	T	0.03739	0.0106	L	0.43923	1.385	0.09310	N	1	B	0.30973	0.302	B	0.33568	0.166	T	0.44128	-0.9348	10	0.08599	T	0.76	.	2.5435	0.04731	0.5407:0.2854:0.1739:0.0	.	142	Q96LZ2	MAGBA_HUMAN	A	142	ENSP00000368304:T142A	ENSP00000368304:T142A	T	+	1	0	MAGEB10	27749768	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.270000	0.08584	-0.080000	0.12685	0.345000	0.21793	ACC	.	.		0.438	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506		G	27839847	A	G	27839847	3	3	64	1	0	0	0	0	1	0	0	0	9182	43	2	2	426	2	MAGEB10	23	27839847	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	4113824	27839847	127430713	333	8050										
USP9X	8239	hgsc.bcm.edu	37	chrX	41088999	41088999	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcacatagtgctaggatgacActtgcaaaagcttgtgaact	9	8	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:41088999A>G	ENST00000324545.8	+	43	8031	c.7398A>G	c.(7396-7398)acA>acG	p.T2466T	USP9X_ENST00000378308.2_Silent_p.T2466T	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	2466					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CTAGGATGACACTTGCAAAAG	0.413																																					p.T2466T	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.A7398G						.						89	86	87					X																	41088999		2203	4300	6503	SO:0001819	synonymous_variant	8239	exon43			GATGACACTTGCA	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.7398A>G	chrX.hg19:g.41088999A>G		79.0	0.0		108.0	5.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Silent	SNP	ENST00000324545.8	hg19	CCDS43930.1																																																																																			.	.		0.413	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		G	41088999	A	G	41088999	2	3	64	1	0	0	0	0	0	0	0	1	17105	146	6	2		2	USP9X	23	41088999	Silent	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	13249152	41088999	114181561	334	8051										
ZNF41	7592	hgsc.bcm.edu	37	chrX	47307022	47307022	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tactacattcatagtgtcttTctccagtatgagacttctga	6	9	4	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:47307022T>C	ENST00000377065.4	-	5	2786	c.2147A>G	c.(2146-2148)gAa>gGa	p.E716G	ZNF41_ENST00000397050.2_Missense_Mutation_p.E726G|ZNF41_ENST00000313116.7_Missense_Mutation_p.E716G|ZNF41_ENST00000465311.1_5'Flank	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	758					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				ATAGTGTCTTTCTCCAGTATG	0.408																																					p.E716G		Atlas-SNP	.											.	ZNF41	71	.	0			c.A2147G						.						131	115	120					X																	47307022		2203	4300	6503	SO:0001583	missense	7592	exon5			TGTCTTTCTCCAG	X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"Zinc fingers, C2H2-type", "-"	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.2147A>G	chrX.hg19:g.47307022T>C	ENSP00000366265:p.Glu716Gly	94.0	0.0		78.0	4.0	NM_007130	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	hg19	CCDS14279.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.184257	0.57800	.	.	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050	T;T;T	0.27557	1.66;1.66;1.66	3.69	3.69	0.42338	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35615	N	0.003096	T	0.54663	0.1872	M	0.82323	2.585	0.29809	N	0.831831	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.81914	0.946;0.946;0.995;0.963;0.978	T	0.57039	-0.7879	10	0.87932	D	0	.	9.9233	0.41476	0.0:0.0:0.0:1.0	.	716;718;726;750;758	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	G	716;716;726	ENSP00000315173:E716G;ENSP00000366265:E716G;ENSP00000380243:E726G	ENSP00000315173:E716G	E	-	2	0	ZNF41	47191966	0.554000	0.26522	0.999000	0.59377	0.955000	0.61496	3.389000	0.52516	1.700000	0.51204	0.486000	0.48141	GAA	.	.		0.408	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380		C	47307022	T	C	47307022	3	2	64	1	0	0	0	0	1	0	0	0	17904	1783	62	2	196	2	ZNF41	23	47307022	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	6218023	47307022	107963538	335	8052										
ZNF630	57232	hgsc.bcm.edu	37	chrX	47919903	47919903	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gttccaacttaaagattacaTctggttttatacctgaacac	5	9	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:47919903T>C	ENST00000409324.3	-	4	390	c.164A>G	c.(163-165)gAt>gGt	p.D55G	ZNF630_ENST00000442455.3_Missense_Mutation_p.D41G|ZNF630_ENST00000276054.4_5'UTR|ZNF630-AS1_ENST00000436124.1_RNA	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	55	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						AAAGATTACATCTGGTTTTAT	0.448																																					p.D55G		Atlas-SNP	.											.	ZNF630	71	.	0			c.A164G						.						176	134	147					X																	47919903		1559	3573	5132	SO:0001583	missense	57232	exon4			ATTACATCTGGTT	AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"Zinc fingers, C2H2-type", "-"	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.164A>G	chrX.hg19:g.47919903T>C	ENSP00000386393:p.Asp55Gly	22.0	0.0		27.0	21.0	NM_001037735	F8WAG4|Q5H8Z5	Missense_Mutation	SNP	ENST00000409324.3	hg19	CCDS35237.2	.	.	.	.	.	.	.	.	.	.	.	9.927	1.213667	0.22289	.	.	ENSG00000221994	ENST00000442455;ENST00000409324;ENST00000428686	T;T;T	0.00892	5.57;5.57;5.57	2.13	-4.27	0.03744	Krueppel-associated box (3);	.	.	.	.	T	0.01029	0.0034	L	0.54323	1.7	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41448	-0.9508	9	0.45353	T	0.12	.	3.7256	0.08473	0.1795:0.3978:0.0:0.4227	.	55	Q2M218	ZN630_HUMAN	G	41;55;55	ENSP00000393163:D41G;ENSP00000386393:D55G;ENSP00000407278:D55G	ENSP00000386393:D55G	D	-	2	0	ZNF630	47804847	0.000000	0.05858	0.006000	0.13384	0.514000	0.34195	-0.324000	0.07986	-1.222000	0.02587	-0.451000	0.05528	GAT	.	.		0.448	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735		C	47919903	T	C	47919903	3	2	64	1	0	0	0	0	1	0	0	0	18069	1435	50	2	1817	2	ZNF630	23	47919903	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	612881	47919903	107350657	336	8053										
AKAP4	8852	hgsc.bcm.edu	37	chrX	49958534	49958534	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cagctgtcagttccacagctTcataggccatttcagaagca	8	12	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:49958534T>C	ENST00000376056.2	-	5	953	c.803A>G	c.(802-804)gAa>gGa	p.E268G	AKAP4_ENST00000376058.2_Intron|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000358526.2_Missense_Mutation_p.E277G|AKAP4_ENST00000376064.3_Missense_Mutation_p.E268G					A kinase (PRKA) anchor protein 4											NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					TTCCACAGCTTCATAGGCCAT	0.488																																					p.E277G		Atlas-SNP	.											.	AKAP4	131	.	0			c.A830G						.						78	70	73					X																	49958534		2203	4300	6503	SO:0001583	missense	8852	exon5			ACAGCTTCATAGG	AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"A-kinase anchor proteins"	374	protein-coding gene	gene with protein product	"A-kinase anchor protein 82 kDa", "testis-specific gene HI", "protein kinase A anchoring protein 4", "cancer/testis antigen 99"	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.803A>G	chrX.hg19:g.49958534T>C	ENSP00000365224:p.Glu268Gly	46.0	0.0		65.0	4.0	NM_003886		Missense_Mutation	SNP	ENST00000376056.2	hg19	CCDS14330.1	.	.	.	.	.	.	.	.	.	.	T	3.704	-0.060975	0.07317	.	.	ENSG00000147081	ENST00000376056;ENST00000358526;ENST00000376064	T;T;T	0.14391	2.51;2.51;2.51	4.9	3.68	0.42216	A-kinase anchor 110kDa, C-terminal (1);	0.137867	0.32120	N	0.006554	T	0.11707	0.0285	L	0.55990	1.75	0.21064	N	0.999794	B	0.31413	0.322	B	0.26202	0.067	T	0.22312	-1.0220	9	.	.	.	-10.1688	6.8947	0.24249	0.2086:0.0:0.0:0.7914	.	277	Q5JQC9	AKAP4_HUMAN	G	268;277;268	ENSP00000365224:E268G;ENSP00000351327:E277G;ENSP00000365232:E268G	.	E	-	2	0	AKAP4	49845274	0.861000	0.29849	0.091000	0.20842	0.078000	0.17371	2.080000	0.41586	0.496000	0.27904	0.242000	0.17961	GAA	.	.		0.488	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		C	49958534	T	C	49958534	3	2	64	1	0	0	0	0	1	0	0	0	453	1783	62	2	1742	2	AKAP4	23	49958534	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2038631	49958534	105312026	337	8054										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53565344	53565344	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	acgaatgtagtctaccaggaCagcaaaaggcccatcagcaa	9	11	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:53565344C>T	ENST00000342160.3	-	76	12407	c.11950G>A	c.(11950-11952)Gtc>Atc	p.V3984I	HUWE1_ENST00000262854.6_Missense_Mutation_p.V3984I			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	3984					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TCTACCAGGACAGCAAAAGGC	0.522																																					p.V3984I		Atlas-SNP	.											.	HUWE1	724	.	0			c.G11950A						.						174	105	128					X																	53565344		2203	4300	6503	SO:0001583	missense	10075	exon77			CCAGGACAGCAAA	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.11950G>A	chrX.hg19:g.53565344C>T	ENSP00000340648:p.Val3984Ile	92.0	0.0		85.0	4.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.57|17.57	3.422409|3.422409	0.62622|0.62622	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000427052;ENST00000426907|ENST00000342160;ENST00000262854	.|T;T	.|0.38240	.|1.15;1.15	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	.|0.244896	.|0.33075	.|N	.|0.005303	T|T	0.44350|0.44350	0.1289|0.1289	N|N	0.20807|0.20807	0.61|0.61	0.80722|0.80722	D|D	1|1	.|P;P;D	.|0.61697	.|0.859;0.841;0.99	.|B;P;D	.|0.70935	.|0.259;0.785;0.971	T|T	0.30504|0.30504	-0.9976|-0.9976	5|10	.|0.25751	.|T	.|0.34	.|.	16.9563|16.9563	0.86260|0.86260	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|806;3984;3968	.|Q5H935;Q7Z6Z7;Q7Z6Z7-2	.|.;HUWE1_HUMAN;.	Y|I	3017;806|3984	.|ENSP00000340648:V3984I;ENSP00000262854:V3984I	.|ENSP00000262854:V3984I	C|V	-|-	2|1	0|0	HUWE1|HUWE1	53582069|53582069	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	7.044000|7.044000	0.76578|0.76578	2.267000|2.267000	0.75376|0.75376	0.529000|0.529000	0.55759|0.55759	TGT|GTC	.	.		0.522	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53565344	C	T	53565344	3	4	64	1	0	0	0	0	1	0	0	0	7470	478	17	3	1206	3	HUWE1	23	53565344	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	3606810	53565344	101705216	338	8055										
FAM120C	54954	hgsc.bcm.edu	37	chrX	54162988	54162988	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	actgaataatactcaactgcTttcttgaatcgctctatttt	4	9	3	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:54162988T>C	ENST00000375180.2	-	5	1250	c.1194A>G	c.(1192-1194)aaA>aaG	p.K398K	FAM120C_ENST00000328235.4_Silent_p.K398K	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	398							poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						ACTCAACTGCTTTCTTGAATC	0.408																																					p.K398K		Atlas-SNP	.											.	FAM120C	89	.	0			c.A1194G						.						306	255	272					X																	54162988		2203	4300	6503	SO:0001819	synonymous_variant	54954	exon5			AACTGCTTTCTTG	AY150025	CCDS14356.1, CCDS55421.1, CCDS75987.1	Xp11.22	2011-04-13	2006-07-04	2006-07-04	ENSG00000184083	ENSG00000184083			16949	protein-coding gene	gene with protein product		300741	"chromosome X open reading frame 17"	CXorf17		14585507	Standard	XM_006724589		Approved	ORF34, FLJ20506	uc004dsz.4	Q9NX05	OTTHUMG00000021625	ENST00000375180.2:c.1194A>G	chrX.hg19:g.54162988T>C		76.0	0.0		75.0	4.0	NM_017848	B2RMT7	Silent	SNP	ENST00000375180.2	hg19	CCDS14356.1																																																																																			.	.		0.408	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056795.2	NM_017848		C	54162988	T	C	54162988	2	2	64	1	0	0	0	0	0	0	0	1	5423	1606	56	2		2	FAM120C	23	54162988	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	597644	54162988	101107572	339	8056										
LAS1L	81887	hgsc.bcm.edu	37	chrX	64754435	64754435	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cacagaacagataaaccgtcAcctggtcccactcggccctg	8	16	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:64754435A>G	ENST00000374811.3	-	1	201	c.161T>C	c.(160-162)gTg>gCg	p.V54A	LAS1L_ENST00000374804.5_Missense_Mutation_p.V54A|LAS1L_ENST00000374807.5_Missense_Mutation_p.V54A|LAS1L_ENST00000312391.8_Missense_Mutation_p.V54A	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	54					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						ATAAACCGTCACCTGGTCCCA	0.597																																					p.V54A		Atlas-SNP	.											.	LAS1L	72	.	0			c.T161C						.						112	72	86					X																	64754435		2203	4300	6503	SO:0001583	missense	81887	exon1			ACCGTCACCTGGT	BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.161T>C	chrX.hg19:g.64754435A>G	ENSP00000363944:p.Val54Ala	73.0	0.0		74.0	4.0	NM_031206	A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Missense_Mutation	SNP	ENST00000374811.3	hg19	CCDS14381.1	.	.	.	.	.	.	.	.	.	.	a	19.91	3.914181	0.72983	.	.	ENSG00000001497	ENST00000374807;ENST00000374811;ENST00000374804;ENST00000312391	.	.	.	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.77691	0.4168	M	0.78285	2.405	0.45777	D	0.998665	D;D;P	0.76494	0.999;0.957;0.939	D;P;D	0.80764	0.994;0.895;0.958	T	0.80115	-0.1517	9	0.62326	D	0.03	.	11.7215	0.51685	1.0:0.0:0.0:0.0	.	54;54;54	Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2	.;.;LAS1L_HUMAN	A	54	.	ENSP00000308649:V54A	V	-	2	0	LAS1L	64671160	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.451000	0.60047	1.896000	0.54893	0.486000	0.48141	GTG	.	.		0.597	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206		G	64754435	A	G	64754435	3	3	64	1	0	0	0	0	1	0	0	0	8645	159	6	2	2099	2	LAS1L	23	64754435	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	10591447	64754435	90516125	340	8057										
YIPF6	286451	hgsc.bcm.edu	37	chrX	67731743	67731743	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agacatccccgtagaaggagAaatcaccattcctatgagat	8	10	1	4			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:67731743A>G	ENST00000462683.1	+	2	854	c.110A>G	c.(109-111)gAa>gGa	p.E37G	YIPF6_ENST00000374622.2_Intron|YIPF6_ENST00000470730.1_3'UTR	NM_173834.3	NP_776195.2	Q96EC8	YIPF6_HUMAN	Yip1 domain family, member 6	37					intestinal epithelial cell development (GO:0060576)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(1)	7						GTAGAAGGAGAAATCACCATT	0.423																																					p.E37G		Atlas-SNP	.											.	YIPF6	27	.	0			c.A110G						.						170	149	156					X																	67731743		2203	4300	6503	SO:0001583	missense	286451	exon2			AAGGAGAAATCAC	BC012469	CCDS14389.1, CCDS56604.1	Xq13.1	2008-02-05			ENSG00000181704	ENSG00000181704		"Yip1 domain family"	28304	protein-coding gene	gene with protein product						12477932	Standard	NM_173834		Approved	MGC21416, FinGER6	uc004dwz.3	Q96EC8	OTTHUMG00000021745	ENST00000462683.1:c.110A>G	chrX.hg19:g.67731743A>G	ENSP00000417573:p.Glu37Gly	47.0	0.0		50.0	4.0	NM_173834	B4E1U7|G5E997|Q5JP08	Missense_Mutation	SNP	ENST00000462683.1	hg19	CCDS14389.1	.	.	.	.	.	.	.	.	.	.	A	17.64	3.440731	0.63067	.	.	ENSG00000181704	ENST00000462683	T	0.47528	0.84	5.66	5.66	0.87406	.	0.048265	0.85682	D	0.000000	T	0.41166	0.1147	L	0.54323	1.7	0.80722	D	1	P	0.36683	0.565	B	0.32980	0.156	T	0.27773	-1.0064	10	0.23891	T	0.37	-18.4373	12.7643	0.57383	1.0:0.0:0.0:0.0	.	37	Q96EC8	YIPF6_HUMAN	G	37	ENSP00000417573:E37G	ENSP00000417573:E37G	E	+	2	0	YIPF6	67648468	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	7.102000	0.77005	1.921000	0.55644	0.427000	0.28365	GAA	.	.		0.423	YIPF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057016.1	NM_173834		G	67731743	A	G	67731743	3	3	64	1	0	0	0	0	1	0	0	0	17497	246	9	2	116	2	YIPF6	23	67731743	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	2977308	67731743	87538817	341	8058										
STARD8	9754	hgsc.bcm.edu	37	chrX	67937131	67937131	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	caggaaagtaagtgctggtcTcctatggggtcctctgatct	12	9	3	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:67937131T>C	ENST00000252336.6	+	5	507	c.135T>C	c.(133-135)tcT>tcC	p.S45S	STARD8_ENST00000374599.3_Silent_p.S125S|STARD8_ENST00000374597.3_Silent_p.S45S	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	45					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	50						AGTGCTGGTCTCCTATGGGGT	0.577																																					p.S125S		Atlas-SNP	.											.	STARD8	282	.	0			c.T375C						.						72	42	52					X																	67937131		2203	4300	6503	SO:0001819	synonymous_variant	9754	exon6			CTGGTCTCCTATG	D80011	CCDS14390.1, CCDS48134.1	Xq13.1	2011-09-13	2007-08-16		ENSG00000130052	ENSG00000130052		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19161	protein-coding gene	gene with protein product		300689	"START domain containing 8"			8724849	Standard	NM_001142504		Approved	KIAA0189, ARHGAP38	uc004dxb.3	Q92502	OTTHUMG00000021748	ENST00000252336.6:c.135T>C	chrX.hg19:g.67937131T>C		96.0	0.0		78.0	4.0	NM_001142503	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Silent	SNP	ENST00000252336.6	hg19	CCDS14390.1																																																																																			.	.		0.577	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725		C	67937131	T	C	67937131	2	2	64	1	0	0	0	0	0	0	0	1	15278	1538	54	2		2	STARD8	23	67937131	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	205388	67937131	87333429	342	8059										
MED12	9968	hgsc.bcm.edu	37	chrX	70357194	70357194	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtgtaccggcagcagcaaccTgcggtgccccaaggacagcg	14	14	0	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:70357194T>C	ENST00000374080.3	+	39	5741	c.5709T>C	c.(5707-5709)ccT>ccC	p.P1903P	MED12_ENST00000333646.6_Silent_p.P1903P|MED12_ENST00000374102.1_Silent_p.P1903P			Q93074	MED12_HUMAN	mediator complex subunit 12	1903	Gln-rich.|Interaction with CTNNB1 and GLI3.				androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					AGCAGCAACCTGCGGTGCCCC	0.592			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.P1903P		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.T5709C						.						38	36	37					X																	70357194		1947	4117	6064	SO:0001819	synonymous_variant	9968	exon39			GCAACCTGCGGTG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.5709T>C	chrX.hg19:g.70357194T>C		83.0	0.0		86.0	4.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	hg19	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	-	5.226	0.227107	0.09916	.	.	ENSG00000184634	ENST00000444034	.	.	.	4.85	0.931	0.19460	.	.	.	.	.	T	0.41511	0.1162	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21314	-1.0249	4	.	.	.	-12.3723	0.8819	0.01236	0.1563:0.1912:0.1584:0.4941	.	.	.	.	P	124	.	.	L	+	2	0	MED12	70273919	0.148000	0.22702	0.624000	0.29186	0.827000	0.46813	-0.193000	0.09573	-0.107000	0.12088	0.427000	0.28365	CTG	.	.		0.592	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		C	70357194	T	C	70357194	2	2	64	1	0	0	0	0	0	0	0	1	9437	1567	55	2		2	MED12	23	70357194	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2420063	70357194	84913366	343	8060										
FLJ44635	0	hgsc.bcm.edu	37	chrX	71379912	71379912	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	aatcactggtgtcgatagtgTcatgaatcatcacctgcaag	9	9	4	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:71379912T>C								BX119917.1 (7648 upstream) : PIN4 (21613 downstream)														p.V78A(1)									GTCGATAGTGTCATGAATCAT	0.433																																					p.V78A		Atlas-SNP	.											.	FLJ44635	13	.	1	Substitution - Missense(1)	large_intestine(1)	c.T233C						.						96	80	86					X																	71379912		2203	4300	6503	SO:0001628	intergenic_variant	0	exon2			ATAGTGTCATGAA																													chrX.hg19:g.71379912T>C		88.0	0.0		99.0	4.0	NM_207422		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.433									C	71379912	T	C	71379912	1	2	64	0	1	0	0	0	0	0	0	0	5939	1667	58	2		2	FLJ44635	23	71379912	IGR	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1022718	71379912	83890648	344	8061										
GPRASP1	9737	hgsc.bcm.edu	37	chrX	101909698	101909698	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	caatagcaggtccaggtttaGgtctaagaaagaagtctatg	11	6	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:101909698G>T	ENST00000361600.5	+	5	1658	c.857G>T	c.(856-858)aGg>aTg	p.R286M	RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000415986.1_Missense_Mutation_p.R286M|GPRASP1_ENST00000537097.1_Missense_Mutation_p.R286M|GPRASP1_ENST00000444152.1_Missense_Mutation_p.R286M	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	286					endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						TCCAGGTTTAGGTCTAAGAAA	0.488																																					p.R286M		Atlas-SNP	.											.	GPRASP1	140	.	0			c.G857T						.						111	110	111					X																	101909698		2203	4300	6503	SO:0001583	missense	9737	exon3			GGTTTAGGTCTAA	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"Armadillo repeat containing"	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.857G>T	chrX.hg19:g.101909698G>T	ENSP00000355146:p.Arg286Met	76.0	0.0		80.0	66.0	NM_001099411	O43168|Q96LA1	Missense_Mutation	SNP	ENST00000361600.5	hg19	CCDS35352.1	.	.	.	.	.	.	.	.	.	.	G	9.348	1.064649	0.20067	.	.	ENSG00000198932	ENST00000415986;ENST00000444152;ENST00000361600;ENST00000537097	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	1.95	-0.111	0.13576	.	.	.	.	.	T	0.28532	0.0706	L	0.59436	1.845	0.09310	N	1	P	0.49090	0.919	P	0.49561	0.615	T	0.13575	-1.0504	9	0.48119	T	0.1	-2.244	4.3479	0.11141	0.166:0.2325:0.6015:0.0	.	286	Q5JY77	GASP1_HUMAN	M	286	ENSP00000393691:R286M;ENSP00000409420:R286M;ENSP00000355146:R286M;ENSP00000445683:R286M	ENSP00000355146:R286M	R	+	2	0	GPRASP1	101796354	0.104000	0.21937	0.002000	0.10522	0.241000	0.25554	1.971000	0.40530	-0.116000	0.11893	0.279000	0.19357	AGG	.	.		0.488	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		T	101909698	G	T	101909698	3	4	64	1	0	0	0	0	1	0	0	0	6731	1000	35	3	859	3	GPRASP1	23	101909698	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	30529786	101909698	53360862	345	8062										
GPRASP1	9737	hgsc.bcm.edu	37	chrX	101912553	101912553	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	acataattcagacatacataTgtaaagtgtgtgaggaaacc	8	6	1	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:101912553T>C	ENST00000361600.5	+	5	4513	c.3712T>C	c.(3712-3714)Tgt>Cgt	p.C1238R	RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000415986.1_Missense_Mutation_p.C1238R|GPRASP1_ENST00000537097.1_Missense_Mutation_p.C1238R|GPRASP1_ENST00000444152.1_Missense_Mutation_p.C1238R	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	1238	OPRD1-binding.				endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						GACATACATATGTAAAGTGTG	0.408																																					p.C1238R		Atlas-SNP	.											.	GPRASP1	140	.	0			c.T3712C						.						93	85	88					X																	101912553		2203	4300	6503	SO:0001583	missense	9737	exon3			TACATATGTAAAG	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"Armadillo repeat containing"	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.3712T>C	chrX.hg19:g.101912553T>C	ENSP00000355146:p.Cys1238Arg	57.0	0.0		76.0	4.0	NM_001099411	O43168|Q96LA1	Missense_Mutation	SNP	ENST00000361600.5	hg19	CCDS35352.1	.	.	.	.	.	.	.	.	.	.	T	8.852	0.944939	0.18356	.	.	ENSG00000198932	ENST00000415986;ENST00000444152;ENST00000361600;ENST00000537097	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	2.58	2.58	0.30949	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.45657	0.1353	M	0.63428	1.95	0.42123	D	0.991436	D	0.89917	1.0	D	0.91635	0.999	T	0.35649	-0.9780	9	0.40728	T	0.16	-4.7672	6.2679	0.20939	0.0:0.0:0.0:1.0	.	1238	Q5JY77	GASP1_HUMAN	R	1238	ENSP00000393691:C1238R;ENSP00000409420:C1238R;ENSP00000355146:C1238R;ENSP00000445683:C1238R	ENSP00000355146:C1238R	C	+	1	0	GPRASP1	101799209	0.988000	0.35896	0.823000	0.32752	0.747000	0.42532	2.952000	0.49097	1.274000	0.44362	0.376000	0.23039	TGT	.	.		0.408	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		C	101912553	T	C	101912553	3	2	64	1	0	0	0	0	1	0	0	0	6731	1464	51	2	3714	2	GPRASP1	23	101912553	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2855	101912553	53358007	346	8063										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	104478544	104478544	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gtgtcaatgtccttgactgtTgcagagaatgaatcaggcct	11	8	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:104478544T>C	ENST00000372582.1	+	4	1155	c.399T>C	c.(397-399)gtT>gtC	p.V133V	IL1RAPL2_ENST00000344799.4_Silent_p.V133V	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	133					central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CCTTGACTGTTGCAGAGAATG	0.398																																					p.V133V		Atlas-SNP	.											.	IL1RAPL2	105	.	0			c.T399C						.						134	127	129					X																	104478544		2203	4299	6502	SO:0001819	synonymous_variant	26280	exon4			GACTGTTGCAGAG	AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.399T>C	chrX.hg19:g.104478544T>C		64.0	0.0		66.0	4.0	NM_017416	Q2M3U3|Q9NZN0	Silent	SNP	ENST00000372582.1	hg19	CCDS14517.1																																																																																			.	.		0.398	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		C	104478544	T	C	104478544	2	2	64	1	0	0	0	0	0	0	0	1	7671	1799	63	2		2	IL1RAPL2	23	104478544	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	2565991	104478544	50792016	347	8064										
ANKRD58	347454	hgsc.bcm.edu	37	chrX	118893082	118893082	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cccgatcaccggctactcggTtctgcactggctggccaagc	11	16	2	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:118893082T>C	ENST00000343905.3	+	1	507	c.452T>C	c.(451-453)gTt>gCt	p.V151A		NM_001105576.2	NP_001099046.1	A6NJG2	SWAHD_HUMAN	sosondowah ankyrin repeat domain family member D	151																	GGCTACTCGGTTCTGCACTGG	0.692																																					p.V151A		Atlas-SNP	.											.	.	.	.	0			c.T452C						.						5	7	6					X																	118893082		1993	4028	6021	SO:0001583	missense	347454	exon1			ACTCGGTTCTGCA		CCDS43984.1	Xq24	2013-01-10	2012-01-12	2012-01-12	ENSG00000187808	ENSG00000187808		"Ankyrin repeat domain containing"	32960	protein-coding gene	gene with protein product			"ankyrin repeat domain 58"	ANKRD58		22234889	Standard	NM_001105576		Approved		uc010nql.3	A6NJG2	OTTHUMG00000159606	ENST00000343905.3:c.452T>C	chrX.hg19:g.118893082T>C	ENSP00000340975:p.Val151Ala	26.0	0.0		54.0	4.0	NM_001105576		Missense_Mutation	SNP	ENST00000343905.3	hg19	CCDS43984.1	.	.	.	.	.	.	.	.	.	.	T	7.913	0.736951	0.15574	.	.	ENSG00000187808	ENST00000343905	T	0.60040	0.22	3.96	2.78	0.32641	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.24890	0.0604	N	0.02842	-0.48	0.24460	N	0.99445	B	0.21071	0.051	B	0.21917	0.037	T	0.34950	-0.9808	9	0.02654	T	1	-11.1899	5.0882	0.14694	0.0:0.2252:0.0:0.7748	.	151	A6NJG2	ANR58_HUMAN	A	151	ENSP00000340975:V151A	ENSP00000340975:V151A	V	+	2	0	ANKRD58	118777110	0.023000	0.18921	0.982000	0.44146	0.884000	0.51177	0.475000	0.22164	1.466000	0.48025	0.153000	0.16174	GTT	.	.		0.692	SOWAHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356469.1	NM_001105576		C	118893082	T	C	118893082	3	2	64	1	0	0	0	0	1	0	0	0	684	1725	60	2	454	2	ANKRD58	23	118893082	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	14414538	118893082	36377478	348	8065										
NKAP	79576	hgsc.bcm.edu	37	chrX	119068493	119068493	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcttttcctttttcttggctTtctttgctctccttttgtta	4	10	4	0	rs199876887		TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:119068493T>C	ENST00000371410.3	-	5	867	c.701A>G	c.(700-702)aAa>aGa	p.K234R	NKAP_ENST00000477789.1_5'UTR	NM_024528.3	NP_078804.2	Q8N5F7	NKAP_HUMAN	NFKB activating protein	234	Lys-rich.|Necessary for interaction with CIR1.				granulocyte differentiation (GO:0030851)|hematopoietic stem cell proliferation (GO:0071425)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|stem cell maintenance (GO:0019827)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)	20						TTTCTTGGCTTTCTTTGCTCT	0.249																																					p.K234R		Atlas-SNP	.											.	NKAP	53	.	0			c.A701G						.						78	78	78					X																	119068493		2203	4297	6500	SO:0001583	missense	79576	exon5			TTGGCTTTCTTTG	BC012770	CCDS14592.1	Xq24	2010-07-20			ENSG00000101882	ENSG00000101882			29873	protein-coding gene	gene with protein product	"NF kappaB activating protein"	300766				14550261	Standard	NM_024528		Approved	FLJ22626	uc004esh.3	Q8N5F7	OTTHUMG00000022284	ENST00000371410.3:c.701A>G	chrX.hg19:g.119068493T>C	ENSP00000360464:p.Lys234Arg	96.0	0.0		97.0	4.0	NM_024528	Q6IPW6|Q96BQ2|Q9H638	Missense_Mutation	SNP	ENST00000371410.3	hg19	CCDS14592.1	.	.	.	.	.	.	.	.	.	.	T	9.027	0.986423	0.18889	.	.	ENSG00000101882	ENST00000371410	T	0.17854	2.25	3.98	3.98	0.46160	.	0.282570	0.38548	N	0.001660	T	0.37046	0.0989	M	0.69823	2.125	0.38612	D	0.950922	D;D	0.67145	0.993;0.996	D;D	0.73708	0.956;0.981	T	0.24512	-1.0158	10	0.35671	T	0.21	-13.9031	11.5561	0.50748	0.0:0.0:0.0:1.0	.	234;234	Q8N5F7;A0PJ73	NKAP_HUMAN;.	R	234	ENSP00000360464:K234R	ENSP00000360464:K234R	K	-	2	0	NKAP	118952521	1.000000	0.71417	0.899000	0.35326	0.018000	0.09664	3.996000	0.57009	1.556000	0.49512	0.441000	0.28932	AAA	.	.		0.249	NKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058072.1	NM_024528		C	119068493	T	C	119068493	3	2	64	1	0	0	0	0	1	0	0	0	10448	1841	64	2	566	2	NKAP	23	119068493	Missense_Mutation	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	175411	119068493	36202067	349	8066										
XIAP	331	hgsc.bcm.edu	37	chrX	123020184	123020184	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	tcagaacacaggcgacacttTcctaattgcttctttgtttt	6	10	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:123020184T>C	ENST00000371199.3	+	2	971	c.672T>C	c.(670-672)ttT>ttC	p.F224F	XIAP_ENST00000355640.3_Silent_p.F224F|XIAP_ENST00000468691.1_Intron|XIAP_ENST00000434753.3_Silent_p.F224F	NM_001167.3	NP_001158.2	P98170	XIAP_HUMAN	X-linked inhibitor of apoptosis	224					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|copper ion homeostasis (GO:0055070)|inhibition of cysteine-type endopeptidase activity involved in apoptotic process (GO:1990001)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of protein ubiquitination (GO:0031398)|protein ubiquitination (GO:0016567)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)	25						GGCGACACTTTCCTAATTGCT	0.418									X-linked Lymphoproliferative syndrome																												p.F224F		Atlas-SNP	.											.	XIAP	56	.	0			c.T672C						.						119	107	111					X																	123020184		2203	4300	6503	SO:0001819	synonymous_variant	331	exon2	Familial Cancer Database	XLP, Duncan syndrome, Familial Fatal Epstein-Barr Infection, incl. XLP2	ACACTTTCCTAAT	U45880	CCDS14606.1	Xq25	2014-09-17	2008-03-04	2008-03-04	ENSG00000101966	ENSG00000101966		"Baculoviral IAP repeat containing"	592	protein-coding gene	gene with protein product		300079	"baculoviral IAP repeat-containing 4"	API3, BIRC4		8552191, 8654366	Standard	NM_001167		Approved	hILP	uc010nqu.3	P98170	OTTHUMG00000022336	ENST00000371199.3:c.672T>C	chrX.hg19:g.123020184T>C		60.0	0.0		90.0	4.0	NM_001204401	D3DTF2|Q9NQ14	Silent	SNP	ENST00000371199.3	hg19	CCDS14606.1																																																																																			.	.		0.418	XIAP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058165.5	NM_001167		C	123020184	T	C	123020184	2	2	64	1	0	0	0	0	0	0	0	1	17443	1780	62	2		2	XIAP	23	123020184	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	3951691	123020184	32250376	350	8067										
OCRL	4952	hgsc.bcm.edu	37	chrX	128695175	128695175	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gattccaagaactggacttgAgcacagaagccttcttctac	8	11	2	3			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:128695175A>G	ENST00000371113.4	+	10	1009	c.844A>G	c.(844-846)Agc>Ggc	p.S282G	OCRL_ENST00000357121.5_Missense_Mutation_p.S282G	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	282	5-phosphatase.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						ACTGGACTTGAGCACAGAAGC	0.398																																					p.S282G		Atlas-SNP	.											.	OCRL	117	.	0			c.A844G						.						161	155	157					X																	128695175		2203	4300	6503	SO:0001583	missense	4952	exon10			GACTTGAGCACAG	U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.844A>G	chrX.hg19:g.128695175A>G	ENSP00000360154:p.Ser282Gly	111.0	0.0		112.0	5.0	NM_000276	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	hg19	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.358713	0.82243	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	T;T	0.79940	-1.32;-1.32	5.44	5.44	0.79542	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.89128	0.6627	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.976;0.994	D	0.90467	0.4450	10	0.87932	D	0	.	13.7631	0.62979	1.0:0.0:0.0:0.0	.	282;282	Q01968-2;Q01968	.;OCRL_HUMAN	G	282	ENSP00000360154:S282G;ENSP00000349635:S282G	ENSP00000349635:S282G	S	+	1	0	OCRL	128522856	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	8.962000	0.93254	1.915000	0.55452	0.486000	0.48141	AGC	.	.		0.398	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		G	128695175	A	G	128695175	3	3	64	1	0	0	0	0	1	0	0	0	10832	304	11	2	882	2	OCRL	23	128695175	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5674991	128695175	26575385	351	8068										
ARHGAP36	158763	hgsc.bcm.edu	37	chrX	130220617	130220617	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gcccgggctgctgtccttgcTcaaagcaagccttctgatga	11	13	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:130220617T>C	ENST00000276211.5	+	11	1809	c.1464T>C	c.(1462-1464)gcT>gcC	p.A488A	ARHGAP36_ENST00000370921.1_Silent_p.A352A|ARHGAP36_ENST00000370922.1_Silent_p.A476A	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	488					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						CTGTCCTTGCTCAAAGCAAGC	0.532																																					p.A488A		Atlas-SNP	.											.	ARHGAP36	171	.	0			c.T1464C						.						84	75	78					X																	130220617		2203	4300	6503	SO:0001819	synonymous_variant	158763	exon11			CCTTGCTCAAAGC		CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"Rho GTPase activating proteins"	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.1464T>C	chrX.hg19:g.130220617T>C		61.0	0.0		78.0	4.0	NM_144967	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Silent	SNP	ENST00000276211.5	hg19	CCDS14628.1																																																																																			.	.		0.532	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967		C	130220617	T	C	130220617	2	2	64	1	0	0	0	0	0	0	0	1	883	1538	54	2		2	ARHGAP36	23	130220617	Silent	SNP	T	TCGA-CC-A3MA-01A-11D-A20W-10	1525442	130220617	25049943	352	8069										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144905987	144905987	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	agactcacgataaaacagacGgccatgtctacaactatatc	6	11	2	2			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:144905987G>A	ENST00000370490.1	+	1	6299	c.2044G>A	c.(2044-2046)Ggc>Agc	p.G682S	SLITRK2_ENST00000447897.2_Missense_Mutation_p.G682S|SLITRK2_ENST00000434188.2_Missense_Mutation_p.G682S|TMEM257_ENST00000408967.2_5'Flank|SLITRK2_ENST00000428560.2_Missense_Mutation_p.G682S|SLITRK2_ENST00000413937.2_Missense_Mutation_p.G682S			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	682					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TAAAACAGACGGCCATGTCTA	0.488																																					p.G682S		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G2044A						.						76	68	71					X																	144905987		2203	4300	6503	SO:0001583	missense	84631	exon5			ACAGACGGCCATG	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.2044G>A	chrX.hg19:g.144905987G>A	ENSP00000359521:p.Gly682Ser	57.0	0.0		51.0	43.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	hg19	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.073220	0.36566	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.55413	0.62;0.52;0.52;0.52;0.52;0.52	5.67	5.67	0.87782	.	0.294597	0.36815	N	0.002391	T	0.45034	0.1322	L	0.55990	1.75	0.30799	N	0.74006	B	0.32396	0.369	B	0.26202	0.067	T	0.48340	-0.9044	10	0.10636	T	0.68	-9.5346	16.0092	0.80385	0.0:0.0:1.0:0.0	.	682	Q9H156	SLIK2_HUMAN	S	682	ENSP00000334374:G682S;ENSP00000411681:G682S;ENSP00000359521:G682S;ENSP00000397015:G682S;ENSP00000407347:G682S;ENSP00000412010:G682S	ENSP00000334374:G682S	G	+	1	0	SLITRK2	144713679	1.000000	0.71417	0.952000	0.39060	0.919000	0.55068	3.575000	0.53870	2.380000	0.81148	0.600000	0.82982	GGC	.	.		0.488	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144905987	G	A	144905987	3	1	64	1	0	0	0	0	1	0	0	0	14758	1116	39	1	2046	1	SLITRK2	23	144905987	Missense_Mutation	SNP	G	TCGA-CC-A3MA-01A-11D-A20W-10	14685370	144905987	10364573	353	8070										
PASD1	139135	hgsc.bcm.edu	37	chrX	150832684	150832684	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	gttctcggtggatcaggtggActcagtggaccaggagggcc	17	9	3	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:150832684A>G	ENST00000370357.4	+	11	1180	c.935A>G	c.(934-936)gAc>gGc	p.D312G		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	312						nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					GATCAGGTGGACTCAGTGGAC	0.587																																					p.D312G		Atlas-SNP	.											.	PASD1	286	.	0			c.A935G						.						110	93	99					X																	150832684		2203	4300	6503	SO:0001583	missense	139135	exon11			AGGTGGACTCAGT	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"cancer/testis antigen 63"					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.935A>G	chrX.hg19:g.150832684A>G	ENSP00000359382:p.Asp312Gly	131.0	0.0		100.0	4.0	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	hg19	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	A	10.90	1.481685	0.26598	.	.	ENSG00000166049	ENST00000370357	T	0.69040	-0.37	3.17	0.718	0.18202	.	.	.	.	.	T	0.45175	0.1329	N	0.19112	0.55	0.09310	N	1	B	0.23650	0.089	B	0.16289	0.015	T	0.26849	-1.0091	9	0.42905	T	0.14	.	4.5669	0.12191	0.6948:0.0:0.3052:0.0	.	312	Q8IV76	PASD1_HUMAN	G	312	ENSP00000359382:D312G	ENSP00000359382:D312G	D	+	2	0	PASD1	150583340	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.264000	0.18497	0.048000	0.15891	0.486000	0.48141	GAC	.	.		0.587	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		G	150832684	A	G	150832684	3	3	64	1	0	0	0	0	1	0	0	0	11480	275	10	2	973	2	PASD1	23	150832684	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	5926697	150832684	4437876	354	8071										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153040831	153040831	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	cctggcggcccattacgtgcAcaggaaccccaagctcatgc	10	16	1	0			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:153040831A>G	ENST00000361971.5	+	25	4421	c.4307A>G	c.(4306-4308)cAc>cGc	p.H1436R	PLXNB3_ENST00000538966.1_Missense_Mutation_p.H1459R|SRPK3_ENST00000489426.1_5'Flank|PLXNB3_ENST00000538776.1_Missense_Mutation_p.H1089R	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1436					axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CATTACGTGCACAGGAACCCC	0.652																																					p.H1459R		Atlas-SNP	.											.	PLXNB3	208	.	0			c.A4376G						.						53	33	40					X																	153040831		2190	4293	6483	SO:0001583	missense	5365	exon26			ACGTGCACAGGAA	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.4307A>G	chrX.hg19:g.153040831A>G	ENSP00000355378:p.His1436Arg	43.0	0.0		88.0	4.0	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.645|8.645	0.896801|0.896801	0.17686|0.17686	.|.	.|.	ENSG00000198753|ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776|ENST00000411613	T;T;T|.	0.10860|.	2.83;2.83;2.83|.	5.01|5.01	-0.442|-0.442	0.12253|0.12253	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);|.	0.836106|.	0.10902|.	N|.	0.621467|.	T|T	0.08980|0.08980	0.0222|0.0222	N|N	0.02011|0.02011	-0.69|-0.69	0.27729|0.27729	N|N	0.944889|0.944889	B;B;B|.	0.06786|.	0.0;0.001;0.0|.	B;B;B|.	0.12837|.	0.008;0.005;0.008|.	T|T	0.34576|0.34576	-0.9823|-0.9823	10|5	0.27785|.	T|.	0.31|.	.|.	5.2162|5.2162	0.15344|0.15344	0.3838:0.3211:0.2951:0.0|0.3838:0.3211:0.2951:0.0	.|.	1089;1459;1436|.	B7Z3H9;F5H773;Q9ULL4|.	.;.;PLXB3_HUMAN|.	R|A	1459;1436;1089|142	ENSP00000442736:H1459R;ENSP00000355378:H1436R;ENSP00000445569:H1089R|.	ENSP00000355378:H1436R|.	H|T	+|+	2|1	0|0	PLXNB3|PLXNB3	152694025|152694025	1.000000|1.000000	0.71417|0.71417	0.131000|0.131000	0.22000|0.22000	0.222000|0.222000	0.24845|0.24845	1.915000|1.915000	0.39976|0.39976	-0.047000|-0.047000	0.13423|0.13423	0.430000|0.430000	0.28490|0.28490	CAC|ACA	.	.		0.652	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			G	153040831	A	G	153040831	3	3	64	1	0	0	0	0	1	0	0	0	12134	159	6	2	4519	2	PLXNB3	23	153040831	Missense_Mutation	SNP	A	TCGA-CC-A3MA-01A-11D-A20W-10	2208147	153040831	2229729	355	8072										
F8	2157	hgsc.bcm.edu	37	chrX	154194405	154194405	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0198300283286119	7	1	0.663418954827281	0.505462060820785	0.699870545751857	0.068649885583524	0.521678321678322	0	ggccattgttcaaatattgaCttttataacttctgtataag	6	6	2	1			TCGA-CC-A3MA-01A-11D-A20W-10	TCGA-CC-A3MA-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f89d0a39-0177-499b-bb65-3cb17b108023	60141338-5497-4228-a24f-74b33d3d49af	g.chrX:154194405C>T	ENST00000360256.4	-	9	1483	c.1283G>A	c.(1282-1284)aGt>aAt	p.S428N	F8_ENST00000483822.1_5'UTR	NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	428	F5/8 type A 2.|Plastocyanin-like 3.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CAAATATTGACTTTTATAACT	0.353																																					p.S428N		Atlas-SNP	.											.	F8	646	.	0			c.G1283A						.						72	67	69					X																	154194405		2203	4300	6503	SO:0001583	missense	2157	exon9			TATTGACTTTTAT	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.1283G>A	chrX.hg19:g.154194405C>T	ENSP00000353393:p.Ser428Asn	50.0	0.0		91.0	4.0	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	hg19	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	C	9.803	1.181175	0.21787	.	.	ENSG00000185010	ENST00000360256	D	0.98747	-5.11	5.33	3.13	0.36017	Cupredoxin (2);	0.367118	0.34676	N	0.003775	D	0.94706	0.8292	N	0.20328	0.56	0.09310	N	1	B	0.17465	0.022	B	0.14578	0.011	D	0.87998	0.2754	10	0.25751	T	0.34	-5.5738	8.8433	0.35155	0.0:0.7626:0.0:0.2374	.	428	P00451	FA8_HUMAN	N	428	ENSP00000353393:S428N	ENSP00000353393:S428N	S	-	2	0	F8	153847599	0.250000	0.23951	0.933000	0.37362	0.983000	0.72400	0.214000	0.17541	0.966000	0.38159	0.529000	0.55759	AGT	.	.		0.353	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			T	154194405	C	T	154194405	3	4	64	1	0	0	0	0	1	0	0	0	5352	565	20	3	5872	3	F8	23	154194405	Missense_Mutation	SNP	C	TCGA-CC-A3MA-01A-11D-A20W-10	1153574	154194405	1076155	356	8073										
SLC2A7	155184	hgsc.bcm.edu	37	chr1	9074919	9074919	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtccgtgtggcctctcagccTcctcagagctgcggaaagca	12	14	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:9074919T>C	ENST00000400906.1	-	7	723	c.724A>G	c.(724-726)Agg>Ggg	p.R242G		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	242					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			NS(1)|breast(1)|endometrium(4)|large_intestine(10)|lung(4)|prostate(2)|skin(2)	24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		CCTCTCAGCCTCCTCAGAGCT	0.692																																					p.R242G		Atlas-SNP	.											.	SLC2A7	56	.	0			c.A724G						.						13	15	14					1																	9074919		2197	4296	6493	SO:0001583	missense	155184	exon7			TCAGCCTCCTCAG	AL356306	CCDS98.2	1p36.2	2013-05-22			ENSG00000197241	ENSG00000197241		"Solute carriers"	13445	protein-coding gene	gene with protein product	"intestinal facilitative glucose transporter 7"	610371				11780753	Standard	NM_207420		Approved	GLUT7	uc009vmo.1	Q6PXP3	OTTHUMG00000057499	ENST00000400906.1:c.724A>G	chr1.hg19:g.9074919T>C	ENSP00000383698:p.Arg242Gly	17.0	0.0		37.0	4.0	NM_207420	A2A333	Missense_Mutation	SNP	ENST00000400906.1	hg19	CCDS98.2	.	.	.	.	.	.	.	.	.	.	T	11.26	1.585937	0.28268	.	.	ENSG00000197241	ENST00000400906	T	0.76186	-1.0	4.12	-1.16	0.09678	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.284899	0.31123	N	0.008214	T	0.77903	0.4200	M	0.93375	3.41	0.09310	N	1	B	0.30727	0.292	B	0.37731	0.257	T	0.71066	-0.4700	10	0.49607	T	0.09	.	5.9998	0.19515	0.0:0.2097:0.3487:0.4416	.	242	Q6PXP3	GTR7_HUMAN	G	242	ENSP00000383698:R242G	ENSP00000383698:R242G	R	-	1	2	SLC2A7	8997506	0.018000	0.18449	0.001000	0.08648	0.091000	0.18340	0.549000	0.23329	-0.108000	0.12066	0.402000	0.26972	AGG	.	.		0.692	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420		C	9074919	T	C	9074919	3	2	65	1	0	0	0	0	1	0	0	0	14565	1550	54	2	838	2	SLC2A7	1	9074919	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		9074919	240175702	1	8074										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12403094	12403094	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tttgaatttgaagcaagaggAaagttaagacacaggtaaag	11	3	0	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:12403094A>G	ENST00000358136.3	+	42	9001	c.8871A>G	c.(8869-8871)ggA>ggG	p.G2957G	VPS13D_ENST00000356315.4_Silent_p.G2932G	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		AAGCAAGAGGAAAGTTAAGAC	0.368																																					p.G2957G		Atlas-SNP	.											.	VPS13D	316	.	0			c.A8871G						.						83	78	80					1																	12403094		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon42			AAGAGGAAAGTTA	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.8871A>G	chr1.hg19:g.12403094A>G		61.0	0.0		62.0	4.0	NM_015378		Silent	SNP	ENST00000358136.3	hg19	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	A	9.197	1.027583	0.19512	.	.	ENSG00000048707	ENST00000011700	.	.	.	5.52	4.4	0.53042	.	.	.	.	.	T	0.58061	0.2096	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54289	-0.8316	4	.	.	.	.	7.6015	0.28079	0.7891:0.0:0.2109:0.0	.	.	.	.	G	1779	.	.	E	+	2	0	VPS13D	12325681	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.909000	0.48758	0.947000	0.37659	0.528000	0.53228	GAA	.	.		0.368	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		G	12403094	A	G	12403094	2	3	65	1	0	0	0	0	0	0	0	1	17207	233	9	2		2	VPS13D	1	12403094	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3328175	12403094	236847527	2	8075										
SPEN	23013	hgsc.bcm.edu	37	chr1	16254901	16254901	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaccatgagaggaggccgatTgaacgaagtcaaagtcctgt	13	8	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:16254901T>C	ENST00000375759.3	+	11	2370	c.2166T>C	c.(2164-2166)atT>atC	p.I722I		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	722	Arg-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GGAGGCCGATTGAACGAAGTC	0.498																																					p.I722I		Atlas-SNP	.											.	SPEN	374	.	0			c.T2166C						.						94	94	94					1																	16254901		2203	4300	6503	SO:0001819	synonymous_variant	23013	exon11			GCCGATTGAACGA		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.2166T>C	chr1.hg19:g.16254901T>C		144.0	0.0		95.0	4.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	hg19	CCDS164.1																																																																																			.	.		0.498	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		C	16254901	T	C	16254901	2	2	65	1	0	0	0	0	0	0	0	1	15053	1800	63	2		2	SPEN	1	16254901	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3851807	16254901	232995720	3	8076										
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21176020	21176020	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acattgctgaaatttctggtTttgctattagtgaggccccc	9	9	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:21176020T>C	ENST00000264211.8	-	23	3802	c.3608A>G	c.(3607-3609)aAa>aGa	p.K1203R	EIF4G3_ENST00000536266.1_Missense_Mutation_p.K807R|EIF4G3_ENST00000602326.1_Missense_Mutation_p.K1209R|EIF4G3_ENST00000374937.3_Missense_Mutation_p.K1209R|EIF4G3_ENST00000374935.3_Missense_Mutation_p.K923R|EIF4G3_ENST00000537738.1_Missense_Mutation_p.K693R|EIF4G3_ENST00000400422.1_Missense_Mutation_p.K1203R	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1203					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		AATTTCTGGTTTTGCTATTAG	0.318																																					p.K1239R		Atlas-SNP	.											.	EIF4G3	300	.	0			c.A3716G						.						77	71	73					1																	21176020		2203	4300	6503	SO:0001583	missense	8672	exon27			TCTGGTTTTGCTA	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.3608A>G	chr1.hg19:g.21176020T>C	ENSP00000264211:p.Lys1203Arg	151.0	0.0		84.0	4.0	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	hg19	CCDS214.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.615994	0.46631	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266	T;T;T;T;T;T	0.08282	3.6;3.6;3.47;3.11;3.61;3.3	6.08	6.08	0.98989	.	0.318396	0.36519	N	0.002547	T	0.15003	0.0362	N	0.12182	0.205	0.80722	D	1	D;B;B;D;D	0.76494	0.999;0.33;0.165;0.997;0.985	D;B;B;D;P	0.79784	0.993;0.222;0.051;0.985;0.767	T	0.16394	-1.0404	10	0.62326	D	0.03	-19.0926	15.2149	0.73258	0.0:0.0:0.0:1.0	.	1398;923;807;1209;1203	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	R	1203;1399;1203;923;693;1209;807	ENSP00000264211:K1203R;ENSP00000383274:K1203R;ENSP00000364071:K923R;ENSP00000442010:K693R;ENSP00000364073:K1209R;ENSP00000444693:K807R	ENSP00000264211:K1203R	K	-	2	0	EIF4G3	21048607	1.000000	0.71417	0.575000	0.28536	0.047000	0.14425	5.384000	0.66225	2.333000	0.79357	0.533000	0.62120	AAA	.	.		0.318	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		C	21176020	T	C	21176020	3	2	65	1	0	0	0	0	1	0	0	0	5040	1841	64	2	1185	2	EIF4G3	1	21176020	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4921119	21176020	228074601	4	8077										
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21221985	21221985	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	taccttcagtatcagtaggcTtccaggattctagaaagagg	10	8	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:21221985T>C	ENST00000264211.8	-	11	2035	c.1841A>G	c.(1840-1842)aAg>aGg	p.K614R	EIF4G3_ENST00000544689.1_Missense_Mutation_p.K157R|EIF4G3_ENST00000536266.1_Missense_Mutation_p.K218R|EIF4G3_ENST00000374933.3_5'UTR|EIF4G3_ENST00000602326.1_Missense_Mutation_p.K620R|EIF4G3_ENST00000374937.3_Missense_Mutation_p.K620R|EIF4G3_ENST00000374935.3_Missense_Mutation_p.K334R|EIF4G3_ENST00000537738.1_Missense_Mutation_p.K67R|EIF4G3_ENST00000400422.1_Missense_Mutation_p.K614R	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	614					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		ATCAGTAGGCTTCCAGGATTC	0.438																																					p.K620R		Atlas-SNP	.											.	EIF4G3	300	.	0			c.A1859G						.						94	96	95					1																	21221985		2203	4300	6503	SO:0001583	missense	8672	exon15			GTAGGCTTCCAGG	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.1841A>G	chr1.hg19:g.21221985T>C	ENSP00000264211:p.Lys614Arg	86.0	0.0		67.0	4.0	NM_001198802	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	hg19	CCDS214.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.716201	0.68844	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266;ENST00000374933;ENST00000544689	T;T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77;0.77	4.72	4.72	0.59763	.	0.232507	0.44902	D	0.000416	T	0.55768	0.1941	L	0.39147	1.195	0.80722	D	1	P;B;B;D;B	0.58268	0.93;0.209;0.268;0.982;0.369	P;B;B;D;B	0.67548	0.554;0.055;0.209;0.952;0.064	T	0.55685	-0.8102	10	0.48119	T	0.1	-17.0836	10.6392	0.45584	0.0:0.0:0.1608:0.8392	.	809;334;218;620;614	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	R	614;810;614;334;67;620;218;157;157	ENSP00000264211:K614R;ENSP00000383274:K614R;ENSP00000364071:K334R;ENSP00000442010:K67R;ENSP00000364073:K620R;ENSP00000444693:K218R;ENSP00000444401:K157R	ENSP00000264211:K614R	K	-	2	0	EIF4G3	21094572	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.913000	0.48790	1.887000	0.54652	0.377000	0.23210	AAG	.	.		0.438	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		C	21221985	T	C	21221985	3	2	65	1	0	0	0	0	1	0	0	0	5040	1609	56	2	3000	2	EIF4G3	1	21221985	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	45965	21221985	228028636	5	8078										
MACF1	23499	hgsc.bcm.edu	37	chr1	39751339	39751339	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cagatgtcattatgtacattCaggagtgtgaaggtctcatc	10	7	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:39751339C>A	ENST00000372915.3	+	13	1519	c.1432C>A	c.(1432-1434)Cag>Aag	p.Q478K	MACF1_ENST00000564288.1_Missense_Mutation_p.Q473K|MACF1_ENST00000567887.1_Missense_Mutation_p.Q510K|MACF1_ENST00000361689.2_Missense_Mutation_p.Q478K|MACF1_ENST00000545844.1_Missense_Mutation_p.Q478K|MACF1_ENST00000317713.7_Missense_Mutation_p.Q478K|MACF1_ENST00000539005.1_Missense_Mutation_p.Q478K			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	478					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TATGTACATTCAGGAGTGTGA	0.483																																					p.Q478K		Atlas-SNP	.											.	MACF1	909	.	0			c.C1432A						.						110	98	102					1																	39751339		2203	4300	6503	SO:0001583	missense	23499	exon15			TACATTCAGGAGT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.1432C>A	chr1.hg19:g.39751339C>A	ENSP00000362006:p.Gln478Lys	257.0	0.0		194.0	153.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	C	19.68	3.872429	0.72180	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262;ENST00000372900	D;D;D;D;D;D;D	0.93189	-3.18;-3.18;-3.18;-3.18;-3.18;-3.18;-3.18	5.93	5.93	0.95920	.	.	.	.	.	D	0.92718	0.7685	M	0.65975	2.015	0.80722	D	1	B;P	0.44734	0.011;0.842	B;P	0.45276	0.022;0.475	D	0.89732	0.3927	9	0.02654	T	1	.	20.3539	0.98825	0.0:1.0:0.0:0.0	.	478;443	F8W8Q1;Q9UPN3-3	.;.	K	478;478;478;478;478;436;627;638	ENSP00000439537:Q478K;ENSP00000362006:Q478K;ENSP00000354573:Q478K;ENSP00000313438:Q478K;ENSP00000444364:Q478K;ENSP00000435070:Q436K;ENSP00000437059:Q627K	ENSP00000313438:Q478K	Q	+	1	0	MACF1	39523926	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.741000	0.68638	2.826000	0.97356	0.655000	0.94253	CAG	.	.		0.483	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39751339	C	A	39751339	3	1	65	1	0	0	0	0	1	0	0	0	9153	827	29	3	1482	3	MACF1	1	39751339	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	18529354	39751339	209499282	6	8079										
TMCO2	127391	hgsc.bcm.edu	37	chr1	40713792	40713792	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctcagcaaacaagtttgggaCtattagataatcttgctcca	7	9	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:40713792C>T	ENST00000372766.3	+	1	220	c.127C>T	c.(127-129)Cta>Tta	p.L43L	TMCO2_ENST00000468258.1_Intron	NM_001008740.3	NP_001008740.1	Q7Z6W1	TMCO2_HUMAN	transmembrane and coiled-coil domains 2	43						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(1)|ovary(1)	6	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			AAGTTTGGGACTATTAGATAA	0.393																																					p.L43L		Atlas-SNP	.											.	TMCO2	23	.	0			c.C127T						.						188	190	189					1																	40713792		2203	4300	6503	SO:0001819	synonymous_variant	127391	exon1			TTGGGACTATTAG	AL050341	CCDS30684.1	1p34.2	2014-02-12			ENSG00000188800	ENSG00000188800			23312	protein-coding gene	gene with protein product							Standard	NM_001008740		Approved	dJ39G22.2	uc001cfe.2	Q7Z6W1	OTTHUMG00000005764	ENST00000372766.3:c.127C>T	chr1.hg19:g.40713792C>T		104.0	0.0		77.0	4.0	NM_001008740		Silent	SNP	ENST00000372766.3	hg19	CCDS30684.1																																																																																			.	.		0.393	TMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015769.1	NM_001008740		T	40713792	C	T	40713792	2	4	65	1	0	0	0	0	0	0	0	1	16011	564	20	3		3	TMCO2	1	40713792	Silent	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	962453	40713792	208536829	7	8080										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43890875	43890875	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acactctacctccaccaaagAcaggtgagacaggccatctg	8	14	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:43890875A>G	ENST00000562955.1	+	18	2642	c.2642A>G	c.(2641-2643)gAc>gGc	p.D881G	SZT2_ENST00000372442.1_Missense_Mutation_p.D39G	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	881					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						TCCACCAAAGACAGGTGAGAC	0.567																																					p.D881G		Atlas-SNP	.											.	SZT2	383	.	0			c.A2642G						.						92	70	77					1																	43890875		2203	4300	6503	SO:0001583	missense	23334	exon18			CCAAAGACAGGTG	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.2642A>G	chr1.hg19:g.43890875A>G	ENSP00000457168:p.Asp881Gly	125.0	0.0		77.0	5.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	hg19	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	A	33	5.228427	0.95173	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.68595	0.3018	L	0.42245	1.32	0.37764	D	0.926442	P;D	0.76494	0.844;0.999	B;D	0.65443	0.42;0.935	T	0.74337	-0.3698	9	0.72032	D	0.01	.	15.9527	0.79855	1.0:0.0:0.0:0.0	.	881;881	Q5T011-4;Q5T011-5	.;.	G	39	.	ENSP00000361519:D39G	D	+	2	0	SZT2	43663462	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.151000	0.94674	2.173000	0.68751	0.533000	0.62120	GAC	.	.		0.567	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		G	43890875	A	G	43890875	3	3	65	1	0	0	0	0	1	0	0	0	8187	275	10	2	122	2	KIAA0467	1	43890875	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3177083	43890875	205359746	8	8081										
DOCK7	85440	hgsc.bcm.edu	37	chr1	62941000	62941000	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tctgcatgtcctcaatagcaActtcaattggtgttaagatg	8	8	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:62941000A>G	ENST00000340370.5	-	46	5908	c.5891T>C	c.(5890-5892)gTt>gCt	p.V1964A	DOCK7_ENST00000489185.1_5'UTR|DOCK7_ENST00000251157.5_Missense_Mutation_p.V1984A	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1995	DHR-2.				activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						CTCAATAGCAACTTCAATTGG	0.383																																					p.V1984A		Atlas-SNP	.											.	DOCK7	184	.	0			c.T5951C						.						155	146	149					1																	62941000		2203	4300	6503	SO:0001583	missense	85440	exon46			ATAGCAACTTCAA		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.5891T>C	chr1.hg19:g.62941000A>G	ENSP00000340742:p.Val1964Ala	199.0	0.0		134.0	6.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	hg19	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.543161	0.86022	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441	T;T	0.20200	2.09;2.09	5.74	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.48295	0.1492	M	0.82517	2.595	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.998;0.998;0.997;0.999;0.987	D;D;D;D;D;D	0.87578	0.998;0.973;0.995;0.99;0.998;0.96	T	0.52094	-0.8621	10	0.72032	D	0.01	.	11.7864	0.52045	0.9313:0.0:0.0687:0.0	.	1995;1984;1964;1953;1955;1986	Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6	DOCK7_HUMAN;.;.;.;.;.	A	1995;1984;1964;725	ENSP00000251157:V1984A;ENSP00000340742:V1964A	ENSP00000251157:V1984A	V	-	2	0	DOCK7	62713588	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.296000	0.96104	0.999000	0.39023	0.533000	0.62120	GTT	.	.		0.383	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		G	62941000	A	G	62941000	3	3	65	1	0	0	0	0	1	0	0	0	4694	43	2	2	454	2	DOCK7	1	62941000	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	19050125	62941000	186309621	9	8082										
ROR1	4919	hgsc.bcm.edu	37	chr1	64605903	64605903	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgcgatgaaacttcatccgTcccaaagccccgtgacttgt	8	14	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:64605903T>C	ENST00000371079.1	+	6	1097	c.722T>C	c.(721-723)gTc>gCc	p.V241A	RP11-24J23.2_ENST00000424995.1_RNA|ROR1_ENST00000482426.1_3'UTR|ROR1_ENST00000371080.1_Missense_Mutation_p.V241A|ROR1_ENST00000545203.1_5'UTR	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	241	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						ACTTCATCCGTCCCAAAGCCC	0.463																																					p.V241A		Atlas-SNP	.											.	ROR1	113	.	0			c.T722C						.						132	114	120					1																	64605903		2203	4300	6503	SO:0001583	missense	4919	exon6			CATCCGTCCCAAA	M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"Immunoglobulin superfamily / I-set domain containing"	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.722T>C	chr1.hg19:g.64605903T>C	ENSP00000360120:p.Val241Ala	162.0	0.0		116.0	5.0	NM_001083592	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	hg19	CCDS626.1	.	.	.	.	.	.	.	.	.	.	T	0.026	-1.371417	0.01225	.	.	ENSG00000185483	ENST00000371080;ENST00000371079;ENST00000544776	T;T	0.74737	-0.87;-0.87	5.92	1.09	0.20402	Frizzled domain (2);Kringle (1);	0.607504	0.13432	N	0.388367	T	0.19525	0.0469	N	0.02315	-0.6	0.21220	N	0.99975	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.38499	-0.9658	10	0.06625	T	0.88	.	10.2088	0.43128	0.0:0.349:0.0:0.651	.	241;241	Q01973;Q66K77	ROR1_HUMAN;.	A	241;241;244	ENSP00000360121:V241A;ENSP00000360120:V241A	ENSP00000360120:V241A	V	+	2	0	ROR1	64378491	0.000000	0.05858	0.159000	0.22649	0.484000	0.33280	0.379000	0.20585	-0.050000	0.13356	-0.263000	0.10527	GTC	.	.		0.463	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		C	64605903	T	C	64605903	3	2	65	1	0	0	0	0	1	0	0	0	13541	1667	58	2	744	2	ROR1	1	64605903	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1664903	64605903	184644718	10	8083										
C1orf173	127254	hgsc.bcm.edu	37	chr1	75078418	75078418	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aacaggagcttaacctgttcAcctgcatcccattcaggaaa	7	12	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:75078418A>G	ENST00000326665.5	-	9	1294	c.1076T>C	c.(1075-1077)gTg>gCg	p.V359A	RP4-612J11.1_ENST00000416017.1_RNA|C1orf173_ENST00000420661.2_Missense_Mutation_p.V162A	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		359										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TAACCTGTTCACCTGCATCCC	0.423																																					p.V359A		Atlas-SNP	.											.	C1orf173	380	.	0			c.T1076C						.						99	96	97					1																	75078418		2203	4300	6503	SO:0001583	missense	127254	exon9			CTGTTCACCTGCA																												ENST00000326665.5:c.1076T>C	chr1.hg19:g.75078418A>G	ENSP00000322609:p.Val359Ala	68.0	0.0		61.0	5.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	hg19	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.872260	0.91587	.	.	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.21031	2.47;2.03	5.63	5.63	0.86233	.	.	.	.	.	T	0.29126	0.0724	L	0.52364	1.645	0.51233	D	0.999916	D;D	0.89917	0.997;1.0	D;D	0.74674	0.941;0.984	T	0.01496	-1.1340	9	0.29301	T	0.29	-21.4021	15.8025	0.78463	1.0:0.0:0.0:0.0	.	162;359	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	A	359;162	ENSP00000322609:V359A;ENSP00000398581:V162A	ENSP00000322609:V359A	V	-	2	0	C1orf173	74851006	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.877000	0.92386	2.265000	0.75225	0.533000	0.62120	GTG	.	.		0.423	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			G	75078418	A	G	75078418	3	3	65	1	0	0	0	0	1	0	0	0	2016	159	6	2	3540	2	C1orf173	1	75078418	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	10472515	75078418	174172203	11	8084										
TYW3	127253	hgsc.bcm.edu	37	chr1	75199081	75199081	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	accaccagctcctgcgctggCcgcatcctactccttgaccg	8	19	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:75199081C>T	ENST00000370867.3	+	1	242	c.153C>T	c.(151-153)ggC>ggT	p.G51G	CRYZ_ENST00000370872.3_5'Flank|TYW3_ENST00000457880.2_Silent_p.G51G|CRYZ_ENST00000340866.5_5'Flank|CRYZ_ENST00000417775.1_5'UTR|CRYZ_ENST00000370871.3_5'Flank|TYW3_ENST00000421739.2_Silent_p.G51G|TYW3_ENST00000479111.1_5'UTR	NM_138467.2	NP_612476.1	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	51					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|ovary(2)|prostate(1)|skin(1)	15						CCTGCGCTGGCCGCATCCTAC	0.587																																					p.G51G		Atlas-SNP	.											.	TYW3	36	.	0			c.C153T						.						89	77	81					1																	75199081		2203	4300	6503	SO:0001819	synonymous_variant	127253	exon1			CGCTGGCCGCATC	BX647591	CCDS666.1, CCDS53334.1	1p31.1	2008-02-05	2006-05-25	2006-05-25	ENSG00000162623	ENSG00000162623			24757	protein-coding gene	gene with protein product		611245	"chromosome 1 open reading frame 171"	C1orf171		17150819	Standard	NM_138467		Approved	FLJ40918	uc001dgn.3	Q6IPR3	OTTHUMG00000009641	ENST00000370867.3:c.153C>T	chr1.hg19:g.75199081C>T		62.0	0.0		43.0	5.0	NM_001162916	B4DSP9|E9PGR7|Q5HYJ0|Q8N7L1	Silent	SNP	ENST00000370867.3	hg19	CCDS666.1																																																																																			.	.		0.587	TYW3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026573.1	NM_138467		T	75199081	C	T	75199081	2	4	65	1	0	0	0	0	0	0	0	1	16835	726	26	3		3	TYW3	1	75199081	Silent	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	120663	75199081	174051540	12	8085										
CDC7	8317	hgsc.bcm.edu	37	chr1	91978625	91978625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgtctcttaggtatgccttgGtagactttggtttggcccaa	11	8	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:91978625G>A	ENST00000428239.1	+	7	842	c.583G>A	c.(583-585)Gta>Ata	p.V195I	CDC7_ENST00000430031.2_Missense_Mutation_p.V167I|CDC7_ENST00000234626.6_Missense_Mutation_p.V195I	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	195	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		GTATGCCTTGGTAGACTTTGG	0.363																																					p.V195I		Atlas-SNP	.											.	CDC7	74	.	0			c.G583A						.						54	57	56					1																	91978625		2203	4300	6503	SO:0001583	missense	8317	exon7			GCCTTGGTAGACT	AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1", "CDC7 cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 homolog (S. cerevisiae)"	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.583G>A	chr1.hg19:g.91978625G>A	ENSP00000393139:p.Val195Ile	166.0	0.0		73.0	4.0	NM_001134419	D3DT31|O00558|Q5T5U5	Missense_Mutation	SNP	ENST00000428239.1	hg19	CCDS734.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.826243	0.90955	.	.	ENSG00000097046	ENST00000430031;ENST00000234626;ENST00000428239	T;T;T	0.05513	3.43;3.43;3.43	5.54	5.54	0.83059	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.06600	0.0169	N	0.10916	0.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.58634	-0.7602	10	0.20519	T	0.43	-14.5766	19.4811	0.95009	0.0:0.0:1.0:0.0	.	167;195	B7Z5H7;O00311	.;CDC7_HUMAN	I	167;195;195	ENSP00000407477:V167I;ENSP00000234626:V195I;ENSP00000393139:V195I	ENSP00000234626:V195I	V	+	1	0	CDC7	91751213	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.439000	0.97543	2.580000	0.87095	0.563000	0.77884	GTA	.	.		0.363	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027928.1	NM_003503		A	91978625	G	A	91978625	3	1	65	1	0	0	0	0	1	0	0	0	3086	1261	44	3	605	3	CDC7	1	91978625	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	16779544	91978625	157271996	13	8086										
CDC7	8317	hgsc.bcm.edu	37	chr1	91978829	91978829	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttaaaagaccctacacaaatGcacaaattcagattaaacaa	3	9	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:91978829G>T	ENST00000428239.1	+	7	1046	c.787G>T	c.(787-789)Gca>Tca	p.A263S	CDC7_ENST00000430031.2_Missense_Mutation_p.A235S|CDC7_ENST00000234626.6_Missense_Mutation_p.A263S	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	263	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		CTACACAAATGCACAAATTCA	0.393																																					p.A263S		Atlas-SNP	.											.	CDC7	74	.	0			c.G787T						.						83	87	85					1																	91978829		2203	4300	6503	SO:0001583	missense	8317	exon7			ACAAATGCACAAA	AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1", "CDC7 cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 homolog (S. cerevisiae)"	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.787G>T	chr1.hg19:g.91978829G>T	ENSP00000393139:p.Ala263Ser	192.0	0.0		125.0	20.0	NM_001134419	D3DT31|O00558|Q5T5U5	Missense_Mutation	SNP	ENST00000428239.1	hg19	CCDS734.1	.	.	.	.	.	.	.	.	.	.	G	6.557	0.471144	0.12461	.	.	ENSG00000097046	ENST00000430031;ENST00000234626;ENST00000428239	T;T;T	0.46063	0.88;1.04;1.04	5.89	0.572	0.17357	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.528279	0.20582	N	0.089503	T	0.03739	0.0106	N	0.03608	-0.345	0.25224	N	0.989889	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.003	T	0.41270	-0.9518	10	0.06494	T	0.89	-5.082	4.5672	0.12193	0.308:0.0:0.4429:0.2491	.	235;263	B7Z5H7;O00311	.;CDC7_HUMAN	S	235;263;263	ENSP00000407477:A235S;ENSP00000234626:A263S;ENSP00000393139:A263S	ENSP00000234626:A263S	A	+	1	0	CDC7	91751417	0.051000	0.20477	0.987000	0.45799	0.997000	0.91878	0.184000	0.16939	0.111000	0.17947	0.557000	0.71058	GCA	.	.		0.393	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027928.1	NM_003503		T	91978829	G	T	91978829	3	4	65	1	0	0	0	0	1	0	0	0	3086	1319	46	3	809	3	CDC7	1	91978829	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	204	91978829	157271792	14	8087										
LPPR4	9890	hgsc.bcm.edu	37	chr1	99771896	99771896	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcacatccctgaggagactcAggaaaacataagcacctccc	8	14	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:99771896A>G	ENST00000370185.3	+	7	2119	c.1622A>G	c.(1621-1623)cAg>cGg	p.Q541R	LPPR4_ENST00000370184.1_Missense_Mutation_p.Q383R|LPPR4_ENST00000457765.1_Missense_Mutation_p.Q483R	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		541					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		GAGGAGACTCAGGAAAACATA	0.557																																					p.Q541R		Atlas-SNP	.											LPPR4,NS,carcinoma,0,1	LPPR4	143	.	0			c.A1622G						.						100	105	103					1																	99771896		2203	4300	6503	SO:0001583	missense	0	exon7			AGACTCAGGAAAA																												ENST00000370185.3:c.1622A>G	chr1.hg19:g.99771896A>G	ENSP00000359204:p.Gln541Arg	56.0	0.0		36.0	2.0	NM_014839	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Missense_Mutation	SNP	ENST00000370185.3	hg19	CCDS757.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.800675	0.50315	.	.	ENSG00000117600	ENST00000370185;ENST00000457765;ENST00000263178;ENST00000370184	T;T;T	0.24538	2.41;2.39;1.85	5.62	5.62	0.85841	.	0.060559	0.64402	D	0.000001	T	0.10035	0.0246	L	0.29908	0.895	0.49798	D	0.999823	B;B	0.33512	0.372;0.415	B;B	0.31495	0.116;0.131	T	0.09751	-1.0660	9	.	.	.	-11.4707	15.8077	0.78527	1.0:0.0:0.0:0.0	.	483;541	E7EPS1;Q7Z2D5	.;LPPR4_HUMAN	R	541;483;541;383	ENSP00000359204:Q541R;ENSP00000394913:Q483R;ENSP00000359203:Q383R	.	Q	+	2	0	RP4-788L13.1	99544484	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.853000	0.92222	2.131000	0.65755	0.482000	0.46254	CAG	.	.		0.557	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2			G	99771896	A	G	99771896	3	3	65	1	0	0	0	0	1	0	0	0	8936	188	7	2	1648	2	LPPR4	1	99771896	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	7793067	99771896	149478725	15	8088										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103481281	103481281	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccatcagcccctggtaagccAggacgtcctggggggcccta	13	15	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:103481281A>G	ENST00000370096.3	-	12	1743	c.1431T>C	c.(1429-1431)ccT>ccC	p.P477P	COL11A1_ENST00000353414.4_Silent_p.P438P|COL11A1_ENST00000358392.2_Silent_p.P489P|COL11A1_ENST00000512756.1_Silent_p.P361P	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	477	Collagen-like 1.|Triple-helical region (interrupted).				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CTGGTAAGCCAGGACGTCCTG	0.358																																					p.P489P		Atlas-SNP	.											.	COL11A1	972	.	0			c.T1467C						.						33	32	33					1																	103481281		2203	4298	6501	SO:0001819	synonymous_variant	1301	exon12			TAAGCCAGGACGT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1431T>C	chr1.hg19:g.103481281A>G		163.0	0.0		97.0	4.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.358	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		G	103481281	A	G	103481281	2	3	65	1	0	0	0	0	0	0	0	1	3669	175	7	2		2	COL11A1	1	103481281	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3709385	103481281	145769340	16	8089										
VAV3	10451	hgsc.bcm.edu	37	chr1	108292166	108292166	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tttccttcatttcatagttaTcaccttttctcttacatacg	2	11	4	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:108292166T>A	ENST00000370056.4	-	14	1584	c.1310A>T	c.(1309-1311)gAt>gTt	p.D437V	VAV3_ENST00000527011.1_Missense_Mutation_p.D437V|VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000371846.4_Missense_Mutation_p.D372V	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	437	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TTCATAGTTATCACCTTTTCT	0.323																																					p.D437V		Atlas-SNP	.											.	VAV3	176	.	0			c.A1310T						.						151	135	141					1																	108292166		2202	4297	6499	SO:0001583	missense	10451	exon14			TAGTTATCACCTT	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1310A>T	chr1.hg19:g.108292166T>A	ENSP00000359073:p.Asp437Val	108.0	0.0		57.0	4.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.10|17.10	3.302722|3.302722	0.60195|0.60195	.|.	.|.	ENSG00000134215|ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000371846|ENST00000490388	D;D;D|.	0.88818|.	-2.43;-2.43;-2.43|.	5.83|5.83	5.83|5.83	0.93111|0.93111	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67627|0.67627	0.2913|0.2913	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	B;P;B;B|.	0.35456|.	0.001;0.502;0.01;0.263|.	B;P;B;P|.	0.49922|.	0.037;0.626;0.056;0.521|.	T|T	0.68318|0.68318	-0.5440|-0.5440	10|5	0.87932|.	D|.	0|.	.|.	16.2141|16.2141	0.82191|0.82191	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	437;437;372;437|.	B7ZLR1;E9PQ97;B4DHL6;Q9UKW4|.	.;.;.;VAV3_HUMAN|.	V|L	437;437;372|432	ENSP00000359073:D437V;ENSP00000432540:D437V;ENSP00000360912:D372V|.	ENSP00000359073:D437V|.	D|I	-|-	2|1	0|0	VAV3|VAV3	108093689|108093689	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.698000|7.698000	0.84413|0.84413	2.224000|2.224000	0.72417|0.72417	0.528000|0.528000	0.53228|0.53228	GAT|ATA	.	.		0.323	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		A	108292166	T	A	108292166	3	1	65	1	0	0	0	0	1	0	0	0	17148	1435	50	4	1314	4	VAV3	1	108292166	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4810885	108292166	140958455	17	8090										
C1orf59	113802	hgsc.bcm.edu	37	chr1	109191529	109191529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caggtggctcactcttaagcTttccacttgttgggacacct	9	12	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:109191529T>C	ENST00000370032.5	-	8	1261	c.841A>G	c.(841-843)Agc>Ggc	p.S281G	HENMT1_ENST00000402983.1_Missense_Mutation_p.S281G|HENMT1_ENST00000370031.1_Missense_Mutation_p.S312G|HENMT1_ENST00000493676.1_5'UTR	NM_144584.2	NP_653185.2	Q5T8I9	HENMT_HUMAN	HEN1 methyltransferase homolog 1 (Arabidopsis)	281					gene silencing by RNA (GO:0031047)|piRNA metabolic process (GO:0034587)|RNA methylation (GO:0001510)	P granule (GO:0043186)	metal ion binding (GO:0046872)|O-methyltransferase activity (GO:0008171)|RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	16						ACTCTTAAGCTTTCCACTTGT	0.488																																					p.S281G		Atlas-SNP	.											.	HENMT1	38	.	0			c.A841G						.						75	69	71					1																	109191529		2203	4300	6503	SO:0001583	missense	113802	exon8			TTAAGCTTTCCAC		CCDS787.1	1p13.3	2011-01-28	2011-01-28	2011-01-28	ENSG00000162639	ENSG00000162639			26400	protein-coding gene	gene with protein product	"HEN1 methyltransferase homolog (Arabidopsis)"	612178	"chromosome 1 open reading frame 59"	C1orf59			Standard	NM_144584		Approved	FLJ30525, HEN1	uc001dvt.4	Q5T8I9	OTTHUMG00000011123	ENST00000370032.5:c.841A>G	chr1.hg19:g.109191529T>C	ENSP00000359049:p.Ser281Gly	97.0	0.0		63.0	4.0	NM_144584	A8MRR6|B1AM16|B1AM17|Q96EJ7|Q96NN0	Missense_Mutation	SNP	ENST00000370032.5	hg19	CCDS787.1	.	.	.	.	.	.	.	.	.	.	T	9.608	1.130631	0.21041	.	.	ENSG00000162639	ENST00000402983;ENST00000370031;ENST00000370032;ENST00000420055	T;T;T;T	0.31247	1.92;1.9;1.92;1.5	5.6	2.09	0.27110	.	1.373870	0.03974	N	0.292129	T	0.04770	0.0129	N	0.08118	0	0.09310	N	1	B	0.27068	0.167	B	0.23275	0.045	T	0.29971	-0.9994	10	0.21540	T	0.41	-5.0206	5.885	0.18876	0.0:0.1572:0.3207:0.5221	.	281	Q5T8I9	HENMT_HUMAN	G	281;312;281;281	ENSP00000385655:S281G;ENSP00000359048:S312G;ENSP00000359049:S281G;ENSP00000403953:S281G	ENSP00000359048:S312G	S	-	1	0	HENMT1	108993052	0.000000	0.05858	0.001000	0.08648	0.065000	0.16274	-0.021000	0.12504	0.119000	0.18210	0.533000	0.62120	AGC	.	.		0.488	HENMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030592.1	NM_144584		C	109191529	T	C	109191529	3	2	65	1	0	0	0	0	1	0	0	0	2053	1609	56	2	344	2	C1orf59	1	109191529	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	899363	109191529	140059092	18	8091										
AMPD2	271	hgsc.bcm.edu	37	chr1	110173318	110173318	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgtgcaggagccgctgatggAggagtacagcatcgccaccc	14	13	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:110173318A>G	ENST00000256578.3	+	17	2693	c.2333A>G	c.(2332-2334)gAg>gGg	p.E778G	AMPD2_ENST00000393688.3_Missense_Mutation_p.E659G|AMPD2_ENST00000528667.1_Missense_Mutation_p.E778G|AMPD2_ENST00000342115.4_Missense_Mutation_p.E697G|RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000528454.1_Missense_Mutation_p.E660G|AMPD2_ENST00000358729.4_Missense_Mutation_p.E703G	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2	778			E -> D (in PCH9). {ECO:0000269|PubMed:23911318}.		cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		CCGCTGATGGAGGAGTACAGC	0.647																																					p.E778G		Atlas-SNP	.											.	AMPD2	75	.	0			c.A2333G						.						39	35	37					1																	110173318		2203	4299	6502	SO:0001583	missense	271	exon17			TGATGGAGGAGTA	S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"AMPD isoform L"	102771	"adenosine monophosphate deaminase 2 (isoform L)"			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	ENST00000256578.3:c.2333A>G	chr1.hg19:g.110173318A>G	ENSP00000256578:p.Glu778Gly	94.0	0.0		68.0	4.0	NM_004037	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Missense_Mutation	SNP	ENST00000256578.3	hg19	CCDS805.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.938647	0.92526	.	.	ENSG00000116337	ENST00000342115;ENST00000528667;ENST00000256578;ENST00000358729;ENST00000528454;ENST00000393688	D;D;D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94;-1.94;-1.94	4.9	4.9	0.64082	Adenosine/AMP deaminase (1);	0.000000	0.85682	D	0.000000	D	0.92384	0.7583	M	0.90198	3.095	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.926;0.974;1.0;0.999	D	0.93847	0.7142	10	0.72032	D	0.01	-31.8313	14.3437	0.66646	1.0:0.0:0.0:0.0	.	703;659;778;697	Q01433-4;Q01433-3;Q01433;Q01433-2	.;.;AMPD2_HUMAN;.	G	697;778;778;703;660;659	ENSP00000345498:E697G;ENSP00000436541:E778G;ENSP00000256578:E778G;ENSP00000351573:E703G;ENSP00000437164:E660G;ENSP00000377292:E659G	ENSP00000256578:E778G	E	+	2	0	AMPD2	109974841	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.081000	0.94049	2.071000	0.62044	0.402000	0.26972	GAG	.	.		0.647	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1			G	110173318	A	G	110173318	3	3	65	1	0	0	0	0	1	0	0	0	586	304	11	2	2440	2	AMPD2	1	110173318	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	981789	110173318	139077303	19	8092										
PTPN22	26191	hgsc.bcm.edu	37	chr1	114367766	114367766	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acataagtaccaacttactcTttttcatgtttcgcaaaatt	3	9	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:114367766T>C	ENST00000359785.5	-	19	2414	c.2279A>G	c.(2278-2280)aAg>aGg	p.K760R	PTPN22_ENST00000528414.1_Missense_Mutation_p.K705R|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000525799.1_Missense_Mutation_p.K633R|RP5-1073O3.2_ENST00000429398.1_RNA|PTPN22_ENST00000420377.2_Missense_Mutation_p.K760R|PTPN22_ENST00000538253.1_Missense_Mutation_p.K516R|RP5-1073O3.2_ENST00000448199.1_RNA	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	760					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAACTTACTCTTTTTCATGTT	0.219																																					p.K760R		Atlas-SNP	.											PTPN22,NS,carcinoma,0,1	PTPN22	90	.	0			c.A2279G						.						15	16	16					1																	114367766		2155	4228	6383	SO:0001583	missense	26191	exon19			TTACTCTTTTTCA	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.2279A>G	chr1.hg19:g.114367766T>C	ENSP00000352833:p.Lys760Arg	132.0	0.0		53.0	3.0	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	hg19	CCDS863.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.139383	0.77775	.	.	ENSG00000134242	ENST00000359785;ENST00000528414;ENST00000538253;ENST00000420377;ENST00000525799	T;T;T;T;T	0.61980	0.06;0.06;0.06;0.06;0.06	5.23	5.23	0.72850	.	0.000000	0.64402	D	0.000014	T	0.69940	0.3167	M	0.76328	2.33	0.42906	D	0.994248	D;D;D;D;D	0.89917	0.99;0.997;0.995;1.0;0.995	P;D;P;D;P	0.80764	0.864;0.921;0.849;0.994;0.804	T	0.70934	-0.4737	10	0.35671	T	0.21	.	11.804	0.52143	0.0:0.0:0.0:1.0	.	516;633;760;705;760	F5H2S8;E9PPI1;E9PMT0;E9PLD8;Q9Y2R2	.;.;.;.;PTN22_HUMAN	R	760;705;516;760;633	ENSP00000352833:K760R;ENSP00000435176:K705R;ENSP00000439372:K516R;ENSP00000388229:K760R;ENSP00000432674:K633R	ENSP00000352833:K760R	K	-	2	0	PTPN22	114169289	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.098000	0.57748	2.100000	0.63781	0.477000	0.44152	AAG	.	.		0.219	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		C	114367766	T	C	114367766	3	2	65	1	0	0	0	0	1	0	0	0	12802	1609	56	2	156	2	PTPN22	1	114367766	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4194448	114367766	134882855	20	8093										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120458101	120458101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gagactctggggatggtgtcAggtagggatgctcaccctgg	17	8	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:120458101A>G	ENST00000256646.2	-	34	7463	c.7244T>C	c.(7243-7245)cTg>cCg	p.L2415P		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2415					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGATGGTGTCAGGTAGGGATG	0.572			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.L2415P		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.T7244C						.						115	105	108					1																	120458101		2203	4300	6503	SO:0001583	missense	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GGTGTCAGGTAGG	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.7244T>C	chr1.hg19:g.120458101A>G	ENSP00000256646:p.Leu2415Pro	150.0	0.0		108.0	5.0	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	hg19	CCDS908.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.590592	0.66219	.	.	ENSG00000134250	ENST00000256646	T	0.79141	-1.24	5.35	5.35	0.76521	Domain of unknown function DUF3454, notch (1);	0.000000	0.29722	U	0.011371	T	0.80048	0.4552	L	0.45581	1.43	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80125	-0.1513	10	0.39692	T	0.17	.	14.5066	0.67758	1.0:0.0:0.0:0.0	.	2415	Q04721	NOTC2_HUMAN	P	2415	ENSP00000256646:L2415P	ENSP00000256646:L2415P	L	-	2	0	NOTCH2	120259624	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.262000	0.95591	2.027000	0.59764	0.482000	0.46254	CTG	.	.		0.572	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		G	120458101	A	G	120458101	3	3	65	1	0	0	0	0	1	0	0	0	10557	188	7	2	175	2	NOTCH2	1	120458101	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	6090335	120458101	128792520	21	8094										
SETDB1	9869	hgsc.bcm.edu	37	chr1	150933423	150933423	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acatattcctgttcctccctCaatccctgtaggtggctgca	7	14	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:150933423C>G	ENST00000271640.5	+	16	3075	c.2885C>G	c.(2884-2886)tCa>tGa	p.S962*	SETDB1_ENST00000368969.4_Nonsense_Mutation_p.S962*	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	962	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			GTTCCTCCCTCAATCCCTGTA	0.547																																					p.S962X		Atlas-SNP	.											.	SETDB1	204	.	0			c.C2885G						.						117	120	119					1																	150933423		2203	4300	6503	SO:0001587	stop_gained	9869	exon16			CTCCCTCAATCCC	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.2885C>G	chr1.hg19:g.150933423C>G	ENSP00000271640:p.Ser962*	140.0	0.0		203.0	14.0	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Nonsense_Mutation	SNP	ENST00000271640.5	hg19	CCDS44217.1	.	.	.	.	.	.	.	.	.	.	C	34	5.297677	0.95574	.	.	ENSG00000143379	ENST00000271640;ENST00000368969;ENST00000498193	.	.	.	5.47	3.6	0.41247	.	1.371790	0.04323	N	0.351050	.	.	.	.	.	.	0.22975	N	0.998482	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	10.4496	0.44513	0.0:0.848:0.0:0.152	.	.	.	.	X	962	.	ENSP00000271640:S962X	S	+	2	0	SETDB1	149200047	0.000000	0.05858	0.002000	0.10522	0.483000	0.33249	0.430000	0.21428	0.670000	0.31165	0.462000	0.41574	TCA	.	.		0.547	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			G	150933423	C	G	150933423	4	3	65	1	0	0	0	0	0	1	0	0	14153	838	29	4	2943	4	SETDB1	1	150933423	Nonsense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	30475322	150933423	98317198	22	8095										
LMNA	4000	hgsc.bcm.edu	37	chr1	156108485	156108485	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtggggggcagtgggggtggCagcttcggggacaatctggt	22	6	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:156108485C>T	ENST00000368300.4	+	11	2117	c.1905C>T	c.(1903-1905)ggC>ggT	p.G635G	LMNA_ENST00000473598.2_Silent_p.G536G|LMNA_ENST00000347559.2_Silent_p.G605G|LMNA_ENST00000448611.2_Silent_p.G523G|LMNA_ENST00000368299.3_Intron|LMNA_ENST00000496738.1_3'UTR	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	635	Tail.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					GTGGGGGTGGCAGCTTCGGGG	0.642									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												p.G635G		Atlas-SNP	.											.	LMNA	31	.	0			c.C1905T						.						23	24	23					1																	156108485		2203	4298	6501	SO:0001819	synonymous_variant	4000	exon11	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	GGGTGGCAGCTTC	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1905C>T	chr1.hg19:g.156108485C>T		192.0	0.0		242.0	50.0	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	hg19	CCDS1129.1																																																																																			.	.		0.642	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707		T	156108485	C	T	156108485	2	4	65	1	0	0	0	0	0	0	0	1	8857	697	25	3		3	LMNA	1	156108485	Silent	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	5175062	156108485	93142136	23	8096										
CD1D	912	hgsc.bcm.edu	37	chr1	158151417	158151417	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcccagggcacgttcagcgaCcagcagtgggagacgctgca	14	13	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:158151417C>G	ENST00000368171.3	+	3	733	c.234C>G	c.(232-234)gaC>gaG	p.D78E		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	78					antigen processing and presentation, endogenous lipid antigen via MHC class Ib (GO:0048006)|detection of bacterium (GO:0016045)|heterotypic cell-cell adhesion (GO:0034113)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of T cell proliferation (GO:0042102)|T cell selection (GO:0045058)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	beta-2-microglobulin binding (GO:0030881)|cell adhesion molecule binding (GO:0050839)|exogenous lipid antigen binding (GO:0030884)|histone binding (GO:0042393)|lipid antigen binding (GO:0030882)|receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(1)|prostate(3)|urinary_tract(2)	30	all_hematologic(112;0.0378)					CGTTCAGCGACCAGCAGTGGG	0.587																																					p.D78E		Atlas-SNP	.											.	CD1D	60	.	0			c.C234G						.						69	75	73					1																	158151417		2203	4300	6503	SO:0001583	missense	912	exon3			CAGCGACCAGCAG	BC027926	CCDS1173.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158473	ENSG00000158473		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1637	protein-coding gene	gene with protein product		188410	"CD1D antigen, d polypeptide", "CD1d antigen"			2463622	Standard	NM_001766		Approved		uc001frr.3	P15813	OTTHUMG00000022436	ENST00000368171.3:c.234C>G	chr1.hg19:g.158151417C>G	ENSP00000357153:p.Asp78Glu	50.0	0.0		54.0	5.0	NM_001766	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Missense_Mutation	SNP	ENST00000368171.3	hg19	CCDS1173.1	.	.	.	.	.	.	.	.	.	.	C	12.16	1.853548	0.32791	.	.	ENSG00000158473	ENST00000368171	T	0.06371	3.31	4.33	-2.76	0.05896	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	2.111690	0.01888	N	0.038335	T	0.01765	0.0056	L	0.54323	1.7	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.45425	-0.9262	10	0.33141	T	0.24	-2.2381	0.7721	0.01026	0.2681:0.2197:0.3184:0.1939	.	78	P15813	CD1D_HUMAN	E	78	ENSP00000357153:D78E	ENSP00000357153:D78E	D	+	3	2	CD1D	156418041	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-1.955000	0.01523	-0.383000	0.07858	0.655000	0.94253	GAC	.	.		0.587	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766		G	158151417	C	G	158151417	3	3	65	1	0	0	0	0	1	0	0	0	2979	506	18	4	240	4	CD1D	1	158151417	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	2042932	158151417	91099204	24	8097										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158646052	158646052	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atctgaaggatgggaaagtgTcagcttctctgctttagcac	11	8	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:158646052T>C	ENST00000368147.4	-	8	1171	c.991A>G	c.(991-993)Aca>Gca	p.T331A		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	331					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGGGAAAGTGTCAGCTTCTCT	0.483																																					p.T331A		Atlas-SNP	.											.	SPTA1	720	.	0			c.A991G						.						211	199	203					1																	158646052		1928	4144	6072	SO:0001583	missense	6708	exon8			AAAGTGTCAGCTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.991A>G	chr1.hg19:g.158646052T>C	ENSP00000357129:p.Thr331Ala	128.0	0.0		148.0	6.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.546629	0.00926	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.32515	1.45;1.45	5.24	-2.44	0.06502	.	1.172060	0.06713	N	0.773574	T	0.02727	0.0082	N	0.03209	-0.39	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.40572	-0.9556	10	0.05721	T	0.95	.	7.9173	0.29825	0.0:0.1795:0.534:0.2865	.	331	P02549	SPTA1_HUMAN	A	331	ENSP00000357130:T331A;ENSP00000357129:T331A	ENSP00000357129:T331A	T	-	1	0	SPTA1	156912676	0.995000	0.38212	0.007000	0.13788	0.161000	0.22273	0.814000	0.27239	-0.211000	0.10124	-0.256000	0.11100	ACA	.	.		0.483	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158646052	T	C	158646052	3	2	65	1	0	0	0	0	1	0	0	0	15131	1667	58	2	6448	2	SPTA1	1	158646052	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	494635	158646052	90604569	25	8098										
OR6K2	81448	hgsc.bcm.edu	37	chr1	158669522	158669522	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaaaaaaatatcttagcttgAcctatgtgcttttttatagc	6	6	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:158669522A>G	ENST00000359610.2	-	1	964	c.921T>C	c.(919-921)ggT>ggC	p.G307G		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	307						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					TCTTAGCTTGACCTATGTGCT	0.388																																					p.G307G		Atlas-SNP	.											.	OR6K2	104	.	0			c.T921C						.						76	74	75					1																	158669522		2203	4300	6503	SO:0001819	synonymous_variant	81448	exon1			AGCTTGACCTATG	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.921T>C	chr1.hg19:g.158669522A>G		104.0	0.0		94.0	4.0	NM_001005279	B9EH33|Q6IFR6	Silent	SNP	ENST00000359610.2	hg19	CCDS30902.1																																																																																			.	.		0.388	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		G	158669522	A	G	158669522	2	3	65	1	0	0	0	0	0	0	0	1	11211	262	10	2		2	OR6K2	1	158669522	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	23470	158669522	90581099	26	8099										
ITLN2	142683	hgsc.bcm.edu	37	chr1	160922449	160922449	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttccttgatttctttgcagcTtctaggcagggaagaaaagg	11	7	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:160922449T>C	ENST00000368029.3	-	3	211	c.154A>G	c.(154-156)Agc>Ggc	p.S52G	ITLN2_ENST00000494442.1_5'Flank|RP11-544M22.1_ENST00000356006.3_RNA	NM_080878.2	NP_543154.1	Q8WWU7	ITLN2_HUMAN	intelectin 2	52	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	19	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			TCTTTGCAGCTTCTAGGCAGG	0.468																																					p.S52G		Atlas-SNP	.											.	ITLN2	35	.	0			c.A154G						.						115	110	112					1																	160922449		2203	4300	6503	SO:0001583	missense	142683	exon3			TGCAGCTTCTAGG	AY065973	CCDS1212.1	1q22-q23.5	2013-02-06			ENSG00000158764	ENSG00000158764		"Fibrinogen C domain containing"	20599	protein-coding gene	gene with protein product		609874				11181563	Standard	NM_080878		Approved	HL-2	uc001fxd.3	Q8WWU7	OTTHUMG00000028605	ENST00000368029.3:c.154A>G	chr1.hg19:g.160922449T>C	ENSP00000357008:p.Ser52Gly	80.0	0.0		92.0	4.0	NM_080878	Q17RR2|Q5VYI0	Missense_Mutation	SNP	ENST00000368029.3	hg19	CCDS1212.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.565549	0.45694	.	.	ENSG00000158764	ENST00000368029	T	0.76709	-1.04	3.95	3.95	0.45737	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.082933	0.44483	U	0.000449	D	0.84009	0.5378	M	0.91561	3.22	0.30639	N	0.7567	D;P	0.55800	0.973;0.846	P;P	0.59643	0.861;0.79	T	0.82190	-0.0580	10	0.87932	D	0	-13.7152	10.7917	0.46436	0.0:0.0:0.0:1.0	.	51;52	A6NI51;Q8WWU7	.;ITLN2_HUMAN	G	52	ENSP00000357008:S52G	ENSP00000357008:S52G	S	-	1	0	ITLN2	159189073	0.997000	0.39634	0.990000	0.47175	0.049000	0.14656	1.990000	0.40717	1.627000	0.50400	0.459000	0.35465	AGC	.	.		0.468	ITLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071465.1	NM_080878		C	160922449	T	C	160922449	3	2	65	1	0	0	0	0	1	0	0	0	7920	1609	56	2	847	2	ITLN2	1	160922449	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2252927	160922449	88328172	27	8100										
FMO1	2326	hgsc.bcm.edu	37	chr1	171236701	171236701	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggaacatgttgaagaaggcaGagccagtctctacaagtctg	12	8	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:171236701G>A	ENST00000354841.4	+	2	283	c.152G>A	c.(151-153)aGa>aAa	p.R51K	FMO1_ENST00000469112.1_3'UTR|FMO1_ENST00000402921.2_Intron|FMO1_ENST00000367750.3_Missense_Mutation_p.R51K	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	51					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	GAAGAAGGCAGAGCCAGTCTC	0.443																																					p.R51K		Atlas-SNP	.											.	FMO1	79	.	0			c.G152A						.						167	145	152					1																	171236701		2203	4300	6503	SO:0001583	missense	2326	exon3			AAGGCAGAGCCAG	M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.152G>A	chr1.hg19:g.171236701G>A	ENSP00000346901:p.Arg51Lys	124.0	0.0		191.0	46.0	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Missense_Mutation	SNP	ENST00000354841.4	hg19	CCDS1294.1	.	.	.	.	.	.	.	.	.	.	G	16.46	3.130494	0.56828	.	.	ENSG00000010932	ENST00000367750;ENST00000433267;ENST00000354841	T;T;T	0.58358	0.34;0.34;0.34	5.38	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.52693	0.1750	L	0.55990	1.75	0.80722	D	1	B;D	0.69078	0.179;0.997	B;D	0.63381	0.348;0.914	T	0.52786	-0.8529	10	0.34782	T	0.22	1.9125	12.9846	0.58583	0.0795:0.0:0.9205:0.0	.	51;51	B2RCG5;Q01740	.;FMO1_HUMAN	K	51	ENSP00000356724:R51K;ENSP00000406982:R51K;ENSP00000346901:R51K	ENSP00000346901:R51K	R	+	2	0	FMO1	169503325	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.609000	0.61148	1.252000	0.44001	-0.136000	0.14681	AGA	.	.		0.443	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021		A	171236701	G	A	171236701	3	1	65	1	0	0	0	0	1	0	0	0	5962	942	33	3	158	3	FMO1	1	171236701	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	10314252	171236701	78013920	28	8101										
TNN	63923	hgsc.bcm.edu	37	chr1	175067580	175067580	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tacgtggtgcgctacacctcTgctggtggagagaccaggga	15	10	1	1	rs61747978	byFrequency	TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:175067580T>G	ENST00000239462.4	+	9	2081	c.1968T>G	c.(1966-1968)tcT>tcG	p.S656S		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	656	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GCTACACCTCTGCTGGTGGAG	0.612																																					p.S656S		Atlas-SNP	.											.	TNN	297	.	0			c.T1968G						.						96	92	93					1																	175067580		2203	4300	6503	SO:0001819	synonymous_variant	63923	exon9			CACCTCTGCTGGT	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1968T>G	chr1.hg19:g.175067580T>G		277.0	0.0		656.0	58.0	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	hg19	CCDS30943.1																																																																																			.	T|0.981;C|0.019		0.612	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		G	175067580	T	G	175067580	2	3	65	1	0	0	0	0	0	0	0	1	16338	1567	55	5		5	TNN	1	175067580	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3830879	175067580	74183041	29	8102										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177247856	177247856	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aaaaagacccatcggatcctAcgccggctcttcaacctctg	7	15	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:177247856A>T	ENST00000361539.4	+	7	1482	c.1170A>T	c.(1168-1170)ctA>ctT	p.L390L	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	390			L -> V (in dbSNP:rs3176443).		cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											ATCGGATCCTACGCCGGCTCT	0.612																																					p.L390L		Atlas-SNP	.											.	FAM5B	191	.	0			c.A1170T						.						82	86	85					1																	177247856		2203	4300	6503	SO:0001819	synonymous_variant	57795	exon7			GATCCTACGCCGG		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1170A>T	chr1.hg19:g.177247856A>T		117.0	0.0		116.0	49.0	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Silent	SNP	ENST00000361539.4	hg19	CCDS1320.1																																																																																			.	.		0.612	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		T	177247856	A	T	177247856	2	4	65	1	0	0	0	0	0	0	0	1	5601	378	14	4		4	FAM5B	1	177247856	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2180276	177247856	72002765	30	8103										
SEC16B	89866	hgsc.bcm.edu	37	chr1	177901667	177901667	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	accccagcgcccgcagctgcTcccccgctggatgcggatcc	11	20	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:177901667T>C	ENST00000308284.6	-	24	3059	c.2970A>G	c.(2968-2970)ggA>ggG	p.G990G	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	990					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CCGCAGCTGCTCCCCCGCTGG	0.657																																					p.G990G		Atlas-SNP	.											.	SEC16B	92	.	0			c.A2970G						.						11	15	14					1																	177901667		2022	4111	6133	SO:0001819	synonymous_variant	89866	exon24			AGCTGCTCCCCCG	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"regucalcin gene promotor region related protein"	612855	"leucine zipper transcription regulator 2"	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2970A>G	chr1.hg19:g.177901667T>C		130.0	0.0		143.0	6.0	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	hg19	CCDS44281.1																																																																																			.	.		0.657	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		C	177901667	T	C	177901667	2	2	65	1	0	0	0	0	0	0	0	1	14002	1538	54	2		2	SEC16B	1	177901667	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	653811	177901667	71348954	31	8104										
QSOX1	5768	hgsc.bcm.edu	37	chr1	180163522	180163522	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caacagggtcaatgctcgccTtgcaggtaaggaaggaccat	12	10	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:180163522T>C	ENST00000367602.3	+	11	1537	c.1463T>C	c.(1462-1464)cTt>cCt	p.L488P	QSOX1_ENST00000367600.5_Missense_Mutation_p.L488P			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	488	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						AATGCTCGCCTTGCAGGTAAG	0.597																																					p.L488P		Atlas-SNP	.											.	QSOX1	79	.	0			c.T1463C						.						63	52	56					1																	180163522		2203	4300	6503	SO:0001583	missense	5768	exon11			CTCGCCTTGCAGG	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"quiescin Q6"	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.1463T>C	chr1.hg19:g.180163522T>C	ENSP00000356574:p.Leu488Pro	130.0	0.0		98.0	5.0	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Missense_Mutation	SNP	ENST00000367602.3	hg19	CCDS1337.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.994310	0.54041	.	.	ENSG00000116260	ENST00000367602;ENST00000367600	T;T	0.71103	-0.54;-0.54	4.75	4.75	0.60458	Erv1/Alr (3);ERV/ALR sulphydryl oxidase (1);	0.073163	0.56097	D	0.000022	D	0.86932	0.6052	M	0.93106	3.38	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.986;1.0	D	0.89955	0.4082	10	0.87932	D	0	-25.514	13.2551	0.60074	0.0:0.0:0.0:1.0	.	488;488;488;488	A8K4C2;A8K477;O00391;O00391-2	.;.;QSOX1_HUMAN;.	P	488	ENSP00000356574:L488P;ENSP00000356572:L488P	ENSP00000356572:L488P	L	+	2	0	QSOX1	178430145	1.000000	0.71417	1.000000	0.80357	0.135000	0.20990	7.322000	0.79097	1.786000	0.52430	0.379000	0.24179	CTT	.	.		0.597	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826		C	180163522	T	C	180163522	3	2	65	1	0	0	0	0	1	0	0	0	12898	1609	56	2	1505	2	QSOX1	1	180163522	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2261855	180163522	69087099	32	8105										
TPR	7175	hgsc.bcm.edu	37	chr1	186340129	186340129	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcaatattgcgatcctgagcAatttcaagttctttgttttt	7	7	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:186340129A>G	ENST00000367478.4	-	3	599	c.303T>C	c.(301-303)atT>atC	p.I101I	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	101	Necessary for interaction with HSF1.				carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		GATCCTGAGCAATTTCAAGTT	0.318			T	NTRK1	papillary thyroid																																p.I101I		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.T303C						.						192	176	181					1																	186340129		1828	4087	5915	SO:0001819	synonymous_variant	7175	exon3			CTGAGCAATTTCA	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.303T>C	chr1.hg19:g.186340129A>G		102.0	0.0		84.0	4.0	NM_003292	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	hg19	CCDS41446.1																																																																																			.	.		0.318	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		G	186340129	A	G	186340129	2	3	65	1	0	0	0	0	0	0	0	1	16431	126	5	2		2	TPR	1	186340129	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	6176607	186340129	62910492	33	8106										
C1orf27	54953	hgsc.bcm.edu	37	chr1	186375351	186375351	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cattttatggagatgttggaTcacacaattcaaatagaaga	8	5	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:186375351T>C	ENST00000287859.6	+	12	1262	c.1137T>C	c.(1135-1137)gaT>gaC	p.D379D	C1orf27_ENST00000367470.3_Silent_p.D356D|C1orf27_ENST00000419367.3_Silent_p.D347D|C1orf27_ENST00000432021.3_Silent_p.D356D	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	379						integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						AGATGTTGGATCACACAATTC	0.358																																					p.D379D		Atlas-SNP	.											.	C1orf27	41	.	0			c.T1137C						.						137	130	132					1																	186375351		1854	4103	5957	SO:0001819	synonymous_variant	54953	exon12			GTTGGATCACACA	BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"transactivated by recombinant transforming growth factor beta"	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.1137T>C	chr1.hg19:g.186375351T>C		79.0	0.0		73.0	4.0	NM_017847	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Silent	SNP	ENST00000287859.6	hg19	CCDS53448.1																																																																																			.	.		0.358	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847		C	186375351	T	C	186375351	2	2	65	1	0	0	0	0	0	0	0	1	2038	1432	50	2		2	C1orf27	1	186375351	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	35222	186375351	62875270	34	8107										
NR5A2	2494	hgsc.bcm.edu	37	chr1	199997033	199997033	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctttaaagcacggacttacaCctattggtaagtaggagttt	9	7	0	0	rs142187332		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:199997033C>T	ENST00000367362.3	+	1	304	c.58C>T	c.(58-60)Cct>Tct	p.P20S	NR5A2_ENST00000236914.3_Missense_Mutation_p.P20S	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	20					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					CGGACTTACACCTATTGGTAA	0.323																																					p.M20L	Melanoma(179;1138 2773 15678 26136)	Atlas-SNP	.											.	NR5A2	83	.	0			c.A58T						.	C	SER/PRO,SER/PRO	1,4405	2.1+/-5.4	0,1,2202	119	121	120		58,58	2.7	0.9	1	dbSNP_134	120	0,8600		0,0,4300	no	missense,missense	NR5A2	NM_003822.3,NM_205860.1	74,74	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	20/496,20/542	199997033	1,13005	2203	4300	6503	SO:0001583	missense	2494	exon1			CTTACACCTATTG	U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"Nuclear hormone receptors"	7984	protein-coding gene	gene with protein product	"liver receptor homolog-1"	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.58C>T	chr1.hg19:g.199997033C>T	ENSP00000356331:p.Pro20Ser	56.0	0.0		71.0	4.0	NM_003822	B4E2P3|O95642|Q147U3	Missense_Mutation	SNP	ENST00000367362.3	hg19	CCDS1401.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.870|4.870	0.161693|0.161693	0.09287|0.09287	2.27E-4|2.27E-4	0.0|0.0	ENSG00000116833|ENSG00000116833	ENST00000367362;ENST00000236914;ENST00000537715;ENST00000542116|ENST00000447034	D;D|.	0.94138|.	-3.33;-3.36|.	5.77|5.77	2.68|2.68	0.31781|0.31781	.|.	0.124523|.	0.37095|.	N|.	0.002260|.	T|T	0.23492|0.23492	0.0568|0.0568	N|N	0.08118|0.08118	0|0	0.53005|0.53005	D|D	0.999965|0.999965	B;B|.	0.06786|.	0.0;0.001|.	B;B|.	0.06405|.	0.002;0.002|.	T|T	0.03784|0.03784	-1.1004|-1.1004	9|5	.|.	.|.	.|.	.|.	3.04|3.04	0.06135|0.06135	0.1289:0.4521:0.2655:0.1534|0.1289:0.4521:0.2655:0.1534	.|.	20;20|.	F1D8R9;O00482|.	.;NR5A2_HUMAN|.	S|I	20|8	ENSP00000356331:P20S;ENSP00000236914:P20S|.	.|.	P|T	+|+	1|2	0|0	NR5A2|NR5A2	198263656|198263656	0.760000|0.760000	0.28428|0.28428	0.855000|0.855000	0.33649|0.33649	0.536000|0.536000	0.34869|0.34869	0.659000|0.659000	0.24994|0.24994	0.757000|0.757000	0.33036|0.33036	0.655000|0.655000	0.94253|0.94253	CCT|ACC	.	C|1.000;T|0.000		0.323	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2			T	199997033	C	T	199997033	3	4	65	1	0	0	0	0	1	0	0	0	10645	507	18	3	60	3	NR5A2	1	199997033	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	13621682	199997033	49253588	35	8108										
CR1	1378	hgsc.bcm.edu	37	chr1	207679429	207679429	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgctaaggacaggtgcagacGtaagtaactctggagtggga	15	6	1	1	rs199647026		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:207679429G>A	ENST00000367049.4	+	2	301		c.e2+1		CR1_ENST00000400960.2_Splice_Site|CR1_ENST00000367052.1_Splice_Site|CR1_ENST00000367053.1_Splice_Site|CR1_ENST00000367050.4_Splice_Site|CR1_ENST00000367051.1_Splice_Site	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)						complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						AGGTGCAGACGTAAGTAACTC	0.418																																					.		Atlas-SNP	.											.	CR1	354	.	0			c.301+1G>A						.						129	118	121					1																	207679429		1847	4088	5935	SO:0001630	splice_region_variant	1378	exon2			GCAGACGTAAGTA	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.301+1G>A	chr1.hg19:g.207679429G>A		139.0	0.0		117.0	30.0	NM_000573	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Splice_Site	SNP	ENST00000367049.4	hg19	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.217183	0.39201	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049;ENST00000529814	.	.	.	4.13	4.13	0.48395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.0894	0.53717	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CR1	205746052	0.999000	0.42202	0.990000	0.47175	0.546000	0.35178	2.336000	0.43938	2.303000	0.77524	0.591000	0.81541	.	.	.		0.418	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	Intron	A	207679429	G	A	207679429	5	1	65	1	0	0	0	0	0	0	1	0	3842	1159	40	1	308	1	CR1	1	207679429	Splice_Site	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	7682396	207679429	41571192	36	8109										
RCOR3	55758	hgsc.bcm.edu	37	chr1	211486825	211486825	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cctcctgccccatcatccacTccaacaccaacagcccctat	2	22	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:211486825T>C	ENST00000367005.4	+	11	1344	c.1203T>C	c.(1201-1203)acT>acC	p.T401T	RCOR3_ENST00000367006.4_Missense_Mutation_p.S379P|RCOR3_ENST00000419091.2_Silent_p.T459T|RCOR3_ENST00000526255.1_3'UTR	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	401	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		CATCATCCACTCCAACACCAA	0.572																																					p.S379P		Atlas-SNP	.											.	RCOR3	51	.	0			c.T1135C						.						144	108	120					1																	211486825		2203	4300	6503	SO:0001819	synonymous_variant	55758	exon11			ATCCACTCCAACA	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.1203T>C	chr1.hg19:g.211486825T>C		122.0	0.0		127.0	6.0	NM_001136224	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	hg19	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	T	11.22	1.575110	0.28092	.	.	ENSG00000117625	ENST00000367006	T	0.51071	0.72	5.07	3.95	0.45737	.	.	.	.	.	T	0.35828	0.0945	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.32903	-0.9889	8	0.59425	D	0.04	-13.3938	6.4228	0.21754	0.0:0.0806:0.1589:0.7605	.	379	Q9P2K3-2	.	P	379	ENSP00000355973:S379P	ENSP00000355973:S379P	S	+	1	0	RCOR3	209553448	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.812000	0.38952	1.910000	0.55303	0.528000	0.53228	TCC	.	.		0.572	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		C	211486825	T	C	211486825	2	2	65	1	0	0	0	0	0	0	0	1	13199	1551	54	2		2	RCOR3	1	211486825	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3807396	211486825	37763796	37	8110										
USH2A	7399	hgsc.bcm.edu	37	chr1	216373462	216373462	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtgtctaagaagtattgaatAcctgaaatgaaaagaaaaaa	8	3	1	5			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:216373462A>G	ENST00000307340.3	-	17	3704	c.3318T>C	c.(3316-3318)agT>agC	p.S1106S	RP5-1099E6.3_ENST00000420867.1_RNA|USH2A_ENST00000366942.3_Splice_Site_p.S1106S|USH2A_ENST00000366943.2_Splice_Site_p.S1106S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1106	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AGTATTGAATACCTGAAATGA	0.318										HNSCC(13;0.011)																											p.S1106S		Atlas-SNP	.											.	USH2A	1168	.	0			c.T3318C						.						37	37	37					1																	216373462		2199	4300	6499	SO:0001630	splice_region_variant	7399	exon17			TTGAATACCTGAA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.3317-1T>C	chr1.hg19:g.216373462A>G		41.0	0.0		17.0	10.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.318	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	Silent	G	216373462	A	G	216373462	5	3	65	1	0	0	0	0	0	0	1	0	17051	405	14	2	12528	2	USH2A	1	216373462	Splice_Site	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	4886637	216373462	32877159	38	8111										
EPHX1	2052	hgsc.bcm.edu	37	chr1	226030103	226030103	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctctcctgtgggtctggctgCctatattctagagaagtttt	10	9	3	1	rs373882933		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:226030103C>A	ENST00000366837.4	+	7	1164	c.968C>A	c.(967-969)gCc>gAc	p.A323D	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Missense_Mutation_p.A323D	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	323					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					GGTCTGGCTGCCTATATTCTA	0.587																																					p.A323D		Atlas-SNP	.											.	EPHX1	57	.	0			c.C968A						.						121	129	126					1																	226030103		2203	4300	6503	SO:0001583	missense	2052	exon7			TGGCTGCCTATAT	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.968C>A	chr1.hg19:g.226030103C>A	ENSP00000355802:p.Ala323Asp	85.0	0.0		111.0	53.0	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Missense_Mutation	SNP	ENST00000366837.4	hg19	CCDS1547.1	.	.	.	.	.	.	.	.	.	.	C	33	5.238492	0.95240	.	.	ENSG00000143819	ENST00000272167;ENST00000366837	T;T	0.15017	2.46;2.46	5.33	5.33	0.75918	Alpha/beta hydrolase fold-1 (1);	0.000000	0.85682	D	0.000000	T	0.62380	0.2423	H	0.98351	4.21	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78698	-0.2103	10	0.87932	D	0	-4.0191	19.3842	0.94550	0.0:1.0:0.0:0.0	.	323	P07099	HYEP_HUMAN	D	323	ENSP00000272167:A323D;ENSP00000355802:A323D	ENSP00000272167:A323D	A	+	2	0	EPHX1	224096726	1.000000	0.71417	0.996000	0.52242	0.976000	0.68499	7.695000	0.84257	2.644000	0.89710	0.655000	0.94253	GCC	.	.		0.587	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120		A	226030103	C	A	226030103	3	1	65	1	0	0	0	0	1	0	0	0	5181	739	26	3	990	3	EPHX1	1	226030103	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	9656641	226030103	23220518	39	8112										
LYST	1130	hgsc.bcm.edu	37	chr1	235945311	235945311	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgataaacaatggccaatcaTgcaaaatgttttattgctat	6	6	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:235945311T>C	ENST00000389794.3	-	15	5113	c.4939A>G	c.(4939-4941)Atg>Gtg	p.M1647V	LYST_ENST00000536965.1_3'UTR|LYST_ENST00000389793.2_Missense_Mutation_p.M1647V			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1647					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.M1647V(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TGGCCAATCATGCAAAATGTT	0.363																																					p.M1647V		Atlas-SNP	.											LYST,NS,carcinoma,0,1	LYST	370	.	1	Substitution - Missense(1)	lung(1)	c.A4939G						.						103	101	102					1																	235945311		2203	4300	6503	SO:0001583	missense	1130	exon15			CAATCATGCAAAA	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.4939A>G	chr1.hg19:g.235945311T>C	ENSP00000374444:p.Met1647Val	90.0	0.0		100.0	4.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.884273	0.51908	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.61980	0.06;0.06	5.57	4.43	0.53597	.	0.036259	0.85682	D	0.000000	T	0.56441	0.1985	M	0.62723	1.935	0.80722	D	1	P	0.40282	0.711	B	0.32980	0.156	T	0.61004	-0.7150	10	0.66056	D	0.02	.	13.0983	0.59206	0.0:0.0:0.134:0.866	.	1647	Q99698	LYST_HUMAN	V	1647	ENSP00000374444:M1647V;ENSP00000374443:M1647V	ENSP00000374443:M1647V	M	-	1	0	LYST	234011934	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.477000	0.81069	1.028000	0.39785	0.528000	0.53228	ATG	.	.		0.363	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			C	235945311	T	C	235945311	3	2	65	1	0	0	0	0	1	0	0	0	9137	1464	51	2	6622	2	LYST	1	235945311	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	9915208	235945311	13305310	40	8113										
GPR137B	7107	hgsc.bcm.edu	37	chr1	236306000	236306000	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccgtgggacccagcccgcaaCgactcgctgccgcccacgct	11	20	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:236306000C>T	ENST00000366592.3	+	1	169	c.78C>T	c.(76-78)aaC>aaT	p.N26N	GPR137B_ENST00000366591.4_Silent_p.N26N	NM_003272.3	NP_003263.1	O60478	G137B_HUMAN	G protein-coupled receptor 137B	26						integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)		p.N26N(2)		endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			CAGCCCGCAACGACTCGCTGC	0.746																																					p.N26N		Atlas-SNP	.											GPR137B_ENST00000366591,NS,carcinoma,0,2	GPR137B	57	.	2	Substitution - coding silent(2)	endometrium(2)	c.C78T						.						31	23	26					1																	236306000		2200	4298	6498	SO:0001819	synonymous_variant	7107	exon1			CCGCAACGACTCG	AF027826	CCDS1609.1	1q42-q43	2012-08-10	2006-01-26	2006-01-26	ENSG00000077585	ENSG00000077585			11862	protein-coding gene	gene with protein product		604658	"transmembrane 7 superfamily member 1 (upregulated in kidney)"	TM7SF1		9521871	Standard	NM_003272		Approved		uc001hxq.3	O60478	OTTHUMG00000037994	ENST00000366592.3:c.78C>T	chr1.hg19:g.236306000C>T		36.0	0.0		27.0	2.0	NM_003272	Q53EK7|Q5TAE6|Q6FHI3	Silent	SNP	ENST00000366592.3	hg19	CCDS1609.1																																																																																			.	.		0.746	GPR137B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092761.1	NM_003272		T	236306000	C	T	236306000	2	4	65	1	0	0	0	0	0	0	0	1	6654	535	19	1		1	GPR137B	1	236306000	Silent	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	360689	236306000	12944621	41	8114										
RYR2	6262	hgsc.bcm.edu	37	chr1	237540721	237540721	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcatcttagttagcgtgtccTctgaaaggtacttggtaagt	10	7	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:237540721T>C	ENST00000366574.2	+	8	879	c.562T>C	c.(562-564)Tct>Cct	p.S188P	RYR2_ENST00000542537.1_Missense_Mutation_p.S172P|RYR2_ENST00000360064.6_Missense_Mutation_p.S186P	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	188	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TAGCGTGTCCTCTGAAAGGTA	0.413																																					p.S188P		Atlas-SNP	.											.	RYR2	1273	.	0			c.T562C						.						115	114	114					1																	237540721		1976	4146	6122	SO:0001583	missense	6262	exon8			GTGTCCTCTGAAA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.562T>C	chr1.hg19:g.237540721T>C	ENSP00000355533:p.Ser188Pro	89.0	0.0		73.0	4.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.586663	0.86851	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.92149	-2.98;-2.98;-2.98	5.17	5.17	0.71159	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);MIR motif (2);	0.000000	0.64402	D	0.000009	D	0.95239	0.8456	M	0.81239	2.535	0.80722	D	1	D	0.63880	0.993	P	0.60012	0.867	D	0.95784	0.8819	10	0.87932	D	0	.	14.2946	0.66302	0.0:0.0:0.0:1.0	.	188	Q92736	RYR2_HUMAN	P	188;186;172	ENSP00000355533:S188P;ENSP00000353174:S186P;ENSP00000443798:S172P	ENSP00000353174:S186P	S	+	1	0	RYR2	235607344	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.701000	0.84566	2.083000	0.62718	0.455000	0.32223	TCT	.	.		0.413	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237540721	T	C	237540721	3	2	65	1	0	0	0	0	1	0	0	0	13784	1551	54	2	592	2	RYR2	1	237540721	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1234721	237540721	11709900	42	8115										
CHRM3	1131	hgsc.bcm.edu	37	chr1	240072218	240072218	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctggtcaaggagaagaaagcGgcccagaccctcagtgcgat	13	11	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr1:240072218G>A	ENST00000255380.4	+	5	2246	c.1467G>A	c.(1465-1467)gcG>gcA	p.A489A		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	489					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	AGAAGAAAGCGGCCCAGACCC	0.507																																					p.A489A		Atlas-SNP	.											.	CHRM3	118	.	0			c.G1467A						.						139	131	134					1																	240072218		2203	4300	6503	SO:0001819	synonymous_variant	1131	exon5			GAAAGCGGCCCAG	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.1467G>A	chr1.hg19:g.240072218G>A		148.0	0.0		147.0	36.0	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Silent	SNP	ENST00000255380.4	hg19	CCDS1616.1																																																																																			.	.		0.507	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		A	240072218	G	A	240072218	2	1	65	1	0	0	0	0	0	0	0	1	3380	1103	39	1		1	CHRM3	1	240072218	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	2531497	240072218	9178403	43	8116										
COLEC11	78989	hgsc.bcm.edu	37	chr2	3691494	3691494	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcaagccggcctggcccgtgTcttcatcggcatcaacgacc	11	16	3	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:3691494T>C	ENST00000349077.4	+	7	705	c.602T>C	c.(601-603)gTc>gCc	p.V201A	COLEC11_ENST00000418971.2_Missense_Mutation_p.V215A|COLEC11_ENST00000404205.1_Missense_Mutation_p.V127A|COLEC11_ENST00000382062.2_Missense_Mutation_p.V177A|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000236693.7_Missense_Mutation_p.V198A|COLEC11_ENST00000402794.1_Missense_Mutation_p.V151A|COLEC11_ENST00000402922.1_Missense_Mutation_p.V151A|COLEC11_ENST00000403096.3_Missense_Mutation_p.V175A	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	201	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		CTGGCCCGTGTCTTCATCGGC	0.662																																					p.V215A		Atlas-SNP	.											.	COLEC11	93	.	0			c.T644C						.						46	52	50					2																	3691494		2203	4300	6503	SO:0001583	missense	78989	exon8			CCCGTGTCTTCAT	BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"Collectins"	17213	protein-coding gene	gene with protein product	"Collectin K1"	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.602T>C	chr2.hg19:g.3691494T>C	ENSP00000339168:p.Val201Ala	76.0	0.0		79.0	4.0	NM_001255985	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Missense_Mutation	SNP	ENST00000349077.4	hg19	CCDS1649.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.361178	0.41801	.	.	ENSG00000118004	ENST00000382062;ENST00000236693;ENST00000349077;ENST00000418971;ENST00000403096;ENST00000402794;ENST00000404205;ENST00000402922	T;T;T;T;T;T;T;T	0.19105	2.17;2.17;2.17;2.17;2.17;2.17;2.17;2.17	5.3	5.3	0.74995	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.055315	0.64402	D	0.000001	T	0.29817	0.0745	L	0.33189	0.99	0.80722	D	1	D;D;D;D;D;D;P;P;P	0.76494	0.997;0.999;0.999;0.982;0.999;0.999;0.885;0.906;0.812	D;D;D;D;D;D;P;P;P	0.81914	0.99;0.995;0.995;0.968;0.995;0.994;0.58;0.705;0.699	T	0.04216	-1.0968	10	0.02654	T	1	-28.5708	14.4159	0.67151	0.0:0.0:0.0:1.0	.	127;151;151;175;153;177;177;201;198	Q9BWP8-8;Q9BWP8-7;Q9BWP8-6;Q9BWP8-4;Q9BWP8-5;Q9BWP8-3;Q9BWP8-2;Q9BWP8;Q9BWP8-9	.;.;.;.;.;.;.;COL11_HUMAN;.	A	177;198;201;215;175;151;127;151	ENSP00000371494:V177A;ENSP00000236693:V198A;ENSP00000339168:V201A;ENSP00000411770:V215A;ENSP00000385130:V175A;ENSP00000384882:V151A;ENSP00000385827:V127A;ENSP00000385653:V151A	ENSP00000236693:V198A	V	+	2	0	COLEC11	3669369	1.000000	0.71417	0.997000	0.53966	0.018000	0.09664	6.140000	0.71738	1.996000	0.58369	0.383000	0.25322	GTC	.	.		0.662	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027		C	3691494	T	C	3691494	3	2	65	1	0	0	0	0	1	0	0	0	3713	1667	58	2	707	2	COLEC11	2	3691494	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		3691494	239507879	44	8117										
ASAP2	8853	hgsc.bcm.edu	37	chr2	9533657	9533657	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cccgttgccaagacgcccagCgtaatggaagccttgagcca	11	14	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:9533657C>A	ENST00000281419.3	+	24	2905	c.2565C>A	c.(2563-2565)agC>agA	p.S855R	ASAP2_ENST00000315273.4_Missense_Mutation_p.S810R|ASAP2_ENST00000491413.1_3'UTR	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	855	Pro-rich.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						AGACGCCCAGCGTAATGGAAG	0.701																																					p.S855R		Atlas-SNP	.											.	ASAP2	91	.	0			c.C2565A						.						14	15	15					2																	9533657		2201	4298	6499	SO:0001583	missense	8853	exon24			GCCCAGCGTAATG	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2565C>A	chr2.hg19:g.9533657C>A	ENSP00000281419:p.Ser855Arg	71.0	0.0		80.0	12.0	NM_003887	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	hg19	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	C	5.440	0.266321	0.10294	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.59083	0.43;0.29	5.36	-6.75	0.01738	.	6.995770	0.00550	N	0.000258	T	0.42944	0.1225	L	0.34521	1.04	0.24168	N	0.995632	P;B	0.40794	0.729;0.123	B;B	0.42959	0.403;0.135	T	0.43261	-0.9402	10	0.28530	T	0.3	.	2.9644	0.05903	0.0926:0.3469:0.2278:0.3327	.	810;855	O43150-2;O43150	.;ASAP2_HUMAN	R	855;810	ENSP00000281419:S855R;ENSP00000316404:S810R	ENSP00000281419:S855R	S	+	3	2	ASAP2	9451108	0.041000	0.20044	0.000000	0.03702	0.011000	0.07611	-1.141000	0.03207	-1.110000	0.02992	0.462000	0.41574	AGC	.	.		0.701	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		A	9533657	C	A	9533657	3	1	65	1	0	0	0	0	1	0	0	0	1011	767	27	1	2659	1	ASAP2	2	9533657	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	5842163	9533657	233665716	45	8118										
PSME4	23198	hgsc.bcm.edu	37	chr2	54163250	54163250	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tacatatggatcccaatctaTgtaccctatattatctgtag	5	9	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:54163250T>C	ENST00000404125.1	-	7	863	c.808A>G	c.(808-810)Ata>Gta	p.I270V	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	270					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			TCCCAATCTATGTACCCTATA	0.378																																					p.I270V		Atlas-SNP	.											.	PSME4	247	.	0			c.A808G						.						115	121	119					2																	54163250		2203	4300	6503	SO:0001583	missense	23198	exon7			AATCTATGTACCC	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.808A>G	chr2.hg19:g.54163250T>C	ENSP00000384211:p.Ile270Val	67.0	0.0		59.0	4.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	18.07	3.542602	0.65198	.	.	ENSG00000068878	ENST00000404125	T	0.24723	1.84	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.19805	0.0476	L	0.28344	0.845	0.80722	D	1	B	0.30542	0.284	B	0.31290	0.127	T	0.06391	-1.0829	10	0.16896	T	0.51	.	15.804	0.78477	0.0:0.0:0.0:1.0	.	270	Q14997	PSME4_HUMAN	V	270	ENSP00000384211:I270V	ENSP00000374643:I270V	I	-	1	0	PSME4	54016754	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.923000	0.63412	2.135000	0.66039	0.455000	0.32223	ATA	.	.		0.378	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		C	54163250	T	C	54163250	3	2	65	1	0	0	0	0	1	0	0	0	12721	1464	51	2	4883	2	PSME4	2	54163250	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	44629593	54163250	189036123	46	8119										
BCL11A	53335	hgsc.bcm.edu	37	chr2	60687558	60687558	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tctattcagtttttatatcaTtattcaacactcgatcactg	3	9	5	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:60687558T>G	ENST00000335712.6	-	4	2716	c.2489A>C	c.(2488-2490)aAt>aCt	p.N830T	BCL11A_ENST00000537768.1_Intron|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000356842.4_Intron|BCL11A_ENST00000358510.4_Missense_Mutation_p.N796T|BCL11A_ENST00000538214.1_Intron	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	830					B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			TTTTATATCATTATTCAACAC	0.443			T	IGH@	B-CLL																																p.N830T		Atlas-SNP	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.A2489C						.						97	101	100					2																	60687558		2203	4300	6503	SO:0001583	missense	53335	exon4			ATATCATTATTCA	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"Zinc fingers, C2H2-type"	13221	protein-coding gene	gene with protein product		606557	"ecotropic viral integration site 9"	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.2489A>C	chr2.hg19:g.60687558T>G	ENSP00000338774:p.Asn830Thr	84.0	0.0		50.0	31.0	NM_022893	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	hg19	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	T	6.371	0.436556	0.12104	.	.	ENSG00000119866	ENST00000335712;ENST00000358510	T;T	0.06142	3.39;3.34	6.17	6.17	0.99709	.	0.191271	0.44688	D	0.000439	T	0.06600	0.0169	N	0.22421	0.69	0.80722	D	1	B;B	0.16166	0.002;0.016	B;B	0.16289	0.007;0.015	T	0.36696	-0.9737	10	0.41790	T	0.15	-2.1995	16.8222	0.85835	0.0:0.0:0.0:1.0	.	796;830	Q9H165-6;Q9H165	.;BC11A_HUMAN	T	830;796	ENSP00000338774:N830T;ENSP00000351307:N796T	ENSP00000338774:N830T	N	-	2	0	BCL11A	60541062	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.772000	0.55325	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.443	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		G	60687558	T	G	60687558	3	3	65	1	0	0	0	0	1	0	0	0	1363	1493	52	5	128	5	BCL11A	2	60687558	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6524308	60687558	182511815	47	8120										
USP34	9736	hgsc.bcm.edu	37	chr2	61571021	61571021	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggaggtgagatgtcagttccGcatgtgaattaatctgaact	12	6	2	3	rs373411362	byFrequency	TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:61571021G>T	ENST00000398571.2	-	16	2505	c.2429C>A	c.(2428-2430)gCg>gAg	p.A810E		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	810					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TGTCAGTTCCGCATGTGAATT	0.373																																					p.A810E		Atlas-SNP	.											.	USP34	334	.	0			c.C2429A						.						156	144	148					2																	61571021		1915	4129	6044	SO:0001583	missense	9736	exon16			AGTTCCGCATGTG	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.2429C>A	chr2.hg19:g.61571021G>T	ENSP00000381577:p.Ala810Glu	196.0	0.0		173.0	112.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.479739	0.84747	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	T	0.04194	3.68	5.67	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.07863	0.0197	L	0.40543	1.245	0.58432	D	0.999997	D	0.54397	0.966	P	0.46940	0.532	T	0.21177	-1.0253	10	0.46703	T	0.11	.	14.779	0.69751	0.0694:0.0:0.9306:0.0	.	810	Q70CQ2	UBP34_HUMAN	E	658;658;810	ENSP00000381577:A810E	ENSP00000263989:A658E	A	-	2	0	USP34	61424525	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.046000	0.89438	1.399000	0.46721	0.603000	0.83216	GCG	.	.		0.373	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			T	61571021	G	T	61571021	3	4	65	1	0	0	0	0	1	0	0	0	17080	1087	38	1	8471	1	USP34	2	61571021	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	883463	61571021	181628352	48	8121										
ACTR2	10097	hgsc.bcm.edu	37	chr2	65466992	65466992	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgtttcattccagtttgtgAagtgtggatatgcaggctct	11	7	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:65466992A>G	ENST00000260641.5	+	2	212	c.55A>G	c.(55-57)Aag>Gag	p.K19E	ACTR2_ENST00000476840.1_3'UTR|ACTR2_ENST00000377982.4_Missense_Mutation_p.K19E|ACTR2_ENST00000542850.1_5'UTR	NM_005722.3	NP_005713.1	P61160	ARP2_HUMAN	ARP2 actin-related protein 2 homolog (yeast)	19					Arp2/3 complex-mediated actin nucleation (GO:0034314)|asymmetric cell division (GO:0008356)|cellular component movement (GO:0006928)|cilium assembly (GO:0042384)|cytoplasmic transport (GO:0016482)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|meiotic chromosome movement towards spindle pole (GO:0016344)|meiotic cytokinesis (GO:0033206)|spindle localization (GO:0051653)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	12						CCAGTTTGTGAAGTGTGGATA	0.348																																					p.K19E		Atlas-SNP	.											.	ACTR2	30	.	0			c.A55G						.						105	100	102					2																	65466992		2203	4300	6503	SO:0001583	missense	10097	exon2			TTTGTGAAGTGTG	AF006082	CCDS1881.1, CCDS46307.1	2p14	2008-05-20	2001-11-28		ENSG00000138071	ENSG00000138071			169	protein-coding gene	gene with protein product		604221	"ARP2 (actin-related protein 2, yeast) homolog"			9230079	Standard	NM_001005386		Approved	ARP2	uc002sdp.3	P61160	OTTHUMG00000129540	ENST00000260641.5:c.55A>G	chr2.hg19:g.65466992A>G	ENSP00000260641:p.Lys19Glu	104.0	0.0		93.0	4.0	NM_001005386	B2RCP5|D6W5F4|E9PF41|O15142|Q96C82	Missense_Mutation	SNP	ENST00000260641.5	hg19	CCDS1881.1	.	.	.	.	.	.	.	.	.	.	A	32	5.174135	0.94807	.	.	ENSG00000138071	ENST00000260641;ENST00000377982	D;D	0.96522	-4.04;-4.04	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.99184	0.9717	H	0.99859	4.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98609	1.0662	10	0.87932	D	0	-15.4274	16.5764	0.84681	1.0:0.0:0.0:0.0	.	19;19	P61160;E9PF41	ARP2_HUMAN;.	E	19	ENSP00000260641:K19E;ENSP00000367220:K19E	ENSP00000260641:K19E	K	+	1	0	ACTR2	65320496	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.287000	0.95975	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.348	ACTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251730.1	NM_001005386		G	65466992	A	G	65466992	3	3	65	1	0	0	0	0	1	0	0	0	211	247	9	2	61	2	ACTR2	2	65466992	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3895971	65466992	177732381	49	8122										
ETAA1	54465	hgsc.bcm.edu	37	chr2	67632242	67632242	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgtaacagatgaagctcagAgcaaccttaacacaacagtt	7	10	1	3	rs375345566		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:67632242A>G	ENST00000272342.5	+	5	2558	c.2428A>G	c.(2428-2430)Agc>Ggc	p.S810G	ETAA1_ENST00000462772.1_3'UTR	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	810						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						TGAAGCTCAGAGCAACCTTAA	0.313																																					p.S810G		Atlas-SNP	.											.	ETAA1	88	.	0			c.A2428G						.						56	57	56					2																	67632242		2202	4300	6502	SO:0001583	missense	54465	exon5			GCTCAGAGCAACC	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"Ewing's tumor-associated antigen 1"			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.2428A>G	chr2.hg19:g.67632242A>G	ENSP00000272342:p.Ser810Gly	77.0	0.0		73.0	5.0	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	hg19	CCDS1882.1	.	.	.	.	.	.	.	.	.	.	A	10.32	1.318020	0.23994	.	.	ENSG00000143971	ENST00000272342	T	0.19532	2.14	5.39	0.0662	0.14360	.	0.825195	0.11209	N	0.587906	T	0.16811	0.0404	L	0.54323	1.7	0.09310	N	1	B	0.14438	0.01	B	0.12156	0.007	T	0.29640	-1.0005	10	0.48119	T	0.1	-11.9774	2.8321	0.05503	0.5576:0.1269:0.0708:0.2447	.	810	Q9NY74	ETAA1_HUMAN	G	810	ENSP00000272342:S810G	ENSP00000272342:S810G	S	+	1	0	ETAA1	67485746	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.940000	0.28992	0.397000	0.25310	-0.313000	0.08912	AGC	.	.		0.313	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		G	67632242	A	G	67632242	3	3	65	1	0	0	0	0	1	0	0	0	5269	304	11	2	2446	2	ETAA1	2	67632242	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2165250	67632242	175567131	50	8123										
EXOC6B	23233	hgsc.bcm.edu	37	chr2	72707813	72707813	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aagcacattagtgatgttggTgataaattcttccaagtact	8	6	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:72707813T>C	ENST00000272427.6	-	17	1862	c.1732A>G	c.(1732-1734)Acc>Gcc	p.T578A	EXOC6B_ENST00000410104.1_Missense_Mutation_p.T578A	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	578					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)				breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						GTGATGTTGGTGATAAATTCT	0.383																																					p.T578A		Atlas-SNP	.											.	EXOC6B	93	.	0			c.A1732G						.						86	88	87					2																	72707813		1887	4114	6001	SO:0001583	missense	23233	exon17			TGTTGGTGATAAA	AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036			17085	protein-coding gene	gene with protein product		607880	"SEC15-like 2 (S. cerevisiae)", "SEC15 homolog B (S. cerevisiae)"	SEC15L2, SEC15B		10231032, 11406615	Standard	NM_015189		Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.1732A>G	chr2.hg19:g.72707813T>C	ENSP00000272427:p.Thr578Ala	111.0	0.0		76.0	4.0	NM_015189	B8ZZY3	Missense_Mutation	SNP	ENST00000272427.6	hg19	CCDS46333.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.505127	0.44558	.	.	ENSG00000144036	ENST00000272427;ENST00000410104;ENST00000290144	T;T	0.28069	1.63;1.63	5.07	5.07	0.68467	.	0.069207	0.64402	D	0.000015	T	0.29817	0.0745	L	0.56769	1.78	0.49798	D	0.999821	B;B	0.33345	0.409;0.321	B;B	0.38755	0.172;0.281	T	0.06954	-1.0798	10	0.02654	T	1	.	12.7493	0.57300	0.0:0.0:0.0:1.0	.	578;578	Q9Y2D4;Q9Y2D4-2	EXC6B_HUMAN;.	A	578	ENSP00000272427:T578A;ENSP00000386698:T578A	ENSP00000272427:T578A	T	-	1	0	EXOC6B	72561321	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.197000	0.42696	1.906000	0.55180	0.496000	0.49642	ACC	.	.		0.383	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327558.1	XM_039570		C	72707813	T	C	72707813	3	2	65	1	0	0	0	0	1	0	0	0	5311	1696	59	2	727	2	EXOC6B	2	72707813	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	5075571	72707813	170491560	51	8124										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84924794	84924794	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gatgaactggagcaggttttAgcggccaccagaccaagagc	13	10	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:84924794A>G	ENST00000237449.6	+	46	7628	c.7620A>G	c.(7618-7620)ttA>ttG	p.L2540L	DNAH6_ENST00000602588.1_Silent_p.L512L|DNAH6_ENST00000398278.2_Silent_p.L2491L|DNAH6_ENST00000389394.3_Silent_p.L2540L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2540	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						AGCAGGTTTTAGCGGCCACCA	0.423																																					p.L2540L		Atlas-SNP	.											.	DNAH6	194	.	0			c.A7620G						.						127	119	121					2																	84924794		692	1591	2283	SO:0001819	synonymous_variant	1768	exon47			GGTTTTAGCGGCC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7620A>G	chr2.hg19:g.84924794A>G		83.0	0.0		64.0	4.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.423	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84924794	A	G	84924794	2	3	65	1	0	0	0	0	0	0	0	1	4607	417	15	2		2	DNAH6	2	84924794	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	12216981	84924794	158274579	52	8125										
PTCD3	55037	hgsc.bcm.edu	37	chr2	86348628	86348628	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgtgtctcttgaaacaacaAatagtctcttggatttattg	7	7	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:86348628A>G	ENST00000254630.7	+	8	631	c.565A>G	c.(565-567)Aat>Gat	p.N189D	PTCD3_ENST00000409277.3_Silent_p.Q147Q|PTCD3_ENST00000465560.1_3'UTR	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	189					mitochondrial translation (GO:0032543)|regulation of translation (GO:0006417)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						TGAAACAACAAATAGTCTCTT	0.378																																					p.N189D		Atlas-SNP	.											.	PTCD3	51	.	0			c.A565G						.						118	112	114					2																	86348628		2203	4300	6503	SO:0001583	missense	55037	exon8			ACAACAAATAGTC		CCDS33235.1	2p11.2	2014-02-12	2012-02-24		ENSG00000132300	ENSG00000132300			24717	protein-coding gene	gene with protein product		614918				8889548	Standard	NM_017952		Approved	FLJ20758, DKFZp666K071	uc002sqw.2	Q96EY7	OTTHUMG00000153168	ENST00000254630.7:c.565A>G	chr2.hg19:g.86348628A>G	ENSP00000254630:p.Asn189Asp	116.0	0.0		98.0	4.0	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Missense_Mutation	SNP	ENST00000254630.7	hg19	CCDS33235.1	.	.	.	.	.	.	.	.	.	.	A	16.91	3.253542	0.59212	.	.	ENSG00000132300	ENST00000254630	T	0.31769	1.48	5.14	5.14	0.70334	.	0.228496	0.50627	D	0.000108	T	0.30978	0.0782	M	0.64567	1.98	0.80722	D	1	P	0.38617	0.64	B	0.32980	0.156	T	0.17018	-1.0383	10	0.52906	T	0.07	-12.0355	14.2408	0.65956	1.0:0.0:0.0:0.0	.	189	Q96EY7	PTCD3_HUMAN	D	189	ENSP00000254630:N189D	ENSP00000254630:N189D	N	+	1	0	PTCD3	86202139	1.000000	0.71417	0.976000	0.42696	0.961000	0.63080	4.593000	0.61034	2.054000	0.61138	0.533000	0.62120	AAT	.	.		0.378	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952		G	86348628	A	G	86348628	3	3	65	1	0	0	0	0	1	0	0	0	12741	14	1	2	595	2	PTCD3	2	86348628	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1423834	86348628	156850745	53	8126										
FER1L5	90342	hgsc.bcm.edu	37	chr2	97365352	97365352	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gatccagctctatgacttcgAcctattttcacctgatgata	6	11	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:97365352A>G	ENST00000457909.1	+	0	4179							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						TATGACTTCGACCTATTTTCA	0.488																																					p.D1586G		Atlas-SNP	.											.	FER1L5	113	.	0			c.A4757G						.						239	237	238					2																	97365352		1969	4146	6115			90342	exon42			ACTTCGACCTATT	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		chr2.hg19:g.97365352A>G		105.0	0.0		106.0	5.0	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.38	2.517859	0.44763	.	.	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	5.29	5.29	0.74685	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.47455	U	0.000237	D	0.87912	0.6297	H	0.97390	3.995	.	.	.	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.92700	0.6174	8	0.87932	D	0	-24.998	14.2097	0.65756	1.0:0.0:0.0:0.0	.	303;1586;304	B7ZLI3;A0AVI2;A0AVI2-2	.;FR1L5_HUMAN;.	G	1586;1599;304	.	ENSP00000442027:D304G	D	+	2	0	FER1L5	96729079	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	9.097000	0.94193	2.006000	0.58801	0.528000	0.53228	GAC	.	.		0.488	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		G	97365352	A	G	97365352	1	3	65	0	1	0	0	0	0	0	0	0	5822	275	10	2		2	FER1L5	2	97365352	RNA	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	11016724	97365352	145834021	54	8127										
DPP10	57628	hgsc.bcm.edu	37	chr2	116593811	116593811	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtggatccgtggttgcacctAtcacagacttgaaattgtat	10	8	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:116593811A>C	ENST00000410059.1	+	22	2509	c.2029A>C	c.(2029-2031)Atc>Ctc	p.I677L	DPP10_ENST00000310323.8_Missense_Mutation_p.I670L|DPP10_ENST00000393147.2_Missense_Mutation_p.I681L|DPP10_ENST00000409163.1_Missense_Mutation_p.I627L	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	677						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						GGTTGCACCTATCACAGACTT	0.348																																					p.I681L		Atlas-SNP	.											.	DPP10	415	.	0			c.A2041C						.						88	85	86					2																	116593811		2203	4300	6503	SO:0001583	missense	57628	exon22			GCACCTATCACAG	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.2029A>C	chr2.hg19:g.116593811A>C	ENSP00000386565:p.Ile677Leu	142.0	0.0		118.0	17.0	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	A	19.89	3.911273	0.72983	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.81	4.65	0.58169	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.117279	0.64402	D	0.000016	T	0.53786	0.1818	L	0.56396	1.775	0.42488	D	0.992886	B;B;B;B	0.25486	0.069;0.127;0.085;0.085	P;P;P;P	0.56751	0.705;0.522;0.751;0.805	T	0.57189	-0.7854	10	0.56958	D	0.05	-9.7773	11.201	0.48741	0.9283:0.0:0.0717:0.0	.	670;681;673;677	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	L	677;627;681;670	ENSP00000386565:I677L;ENSP00000387038:I627L;ENSP00000376855:I681L;ENSP00000309066:I670L	ENSP00000309066:I670L	I	+	1	0	DPP10	116310281	0.999000	0.42202	0.995000	0.50966	0.992000	0.81027	3.883000	0.56168	1.011000	0.39340	0.533000	0.62120	ATC	.	.		0.348	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		C	116593811	A	C	116593811	3	2	65	1	0	0	0	0	1	0	0	0	4729	449	16	5	2286	5	DPP10	2	116593811	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	19228459	116593811	126605562	55	8128										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125192079	125192079	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agaatcagatgttgctgactTtgatggccgaagctcacttc	10	9	2	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:125192079T>G	ENST00000431078.1	+	5	912	c.548T>G	c.(547-549)tTt>tGt	p.F183C		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	183	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GTTGCTGACTTTGATGGCCGA	0.423																																					p.F183C		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.T548G						.						124	113	117					2																	125192079		1921	4125	6046	SO:0001583	missense	129684	exon5			CTGACTTTGATGG	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.548T>G	chr2.hg19:g.125192079T>G	ENSP00000399013:p.Phe183Cys	232.0	0.0		185.0	86.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.956074	0.73902	.	.	ENSG00000155052	ENST00000431078	D	0.90732	-2.72	5.48	5.48	0.80851	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.48767	D	0.000162	D	0.95573	0.8561	M	0.91510	3.215	0.80722	D	1	D	0.71674	0.998	P	0.60173	0.87	D	0.96444	0.9329	10	0.87932	D	0	.	14.7735	0.69699	0.0:0.0:0.0:1.0	.	183	Q8WYK1	CNTP5_HUMAN	C	183	ENSP00000399013:F183C	ENSP00000399013:F183C	F	+	2	0	CNTNAP5	124908549	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.896000	0.87350	2.084000	0.62774	0.533000	0.62120	TTT	.	.		0.423	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			G	125192079	T	G	125192079	3	3	65	1	0	0	0	0	1	0	0	0	3652	1841	64	5	566	5	CNTNAP5	2	125192079	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	8598268	125192079	118007294	56	8129										
CCDC148	130940	hgsc.bcm.edu	37	chr2	159035423	159035423	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggcttctagccgccgtgctcTctctttgtcttcatgagctt	9	13	5	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:159035423T>C	ENST00000283233.5	-	12	1769	c.1456A>G	c.(1456-1458)Aga>Gga	p.R486G	CCDC148-AS1_ENST00000412781.2_RNA|CCDC148_ENST00000409187.1_Missense_Mutation_p.R495G	NM_138803.3	NP_620158.3	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148	486										endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						CGCCGTGCTCTCTCTTTGTCT	0.363																																					p.R486G		Atlas-SNP	.											.	CCDC148	64	.	0			c.A1456G						.						94	94	94					2																	159035423		2203	4300	6503	SO:0001583	missense	130940	exon12			GTGCTCTCTCTTT		CCDS33304.1	2q24.1	2007-12-07			ENSG00000153237	ENSG00000153237			25191	protein-coding gene	gene with protein product							Standard	NM_138803		Approved	MGC125588	uc002tzq.3	Q8NFR7	OTTHUMG00000153973	ENST00000283233.5:c.1456A>G	chr2.hg19:g.159035423T>C	ENSP00000283233:p.Arg486Gly	91.0	0.0		89.0	4.0	NM_138803	F5H839|Q3B7I3|Q3B7I4|Q3KR41|Q4ZG12|Q4ZG23|Q53TM6|Q96BN5|Q96LM2	Missense_Mutation	SNP	ENST00000283233.5	hg19	CCDS33304.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.526812	0.44969	.	.	ENSG00000153237	ENST00000283233;ENST00000409187	T;T	0.33216	1.43;1.42	5.71	5.71	0.89125	.	.	.	.	.	T	0.36690	0.0976	L	0.27053	0.805	0.80722	D	1	D;D	0.63046	0.992;0.992	P;P	0.59357	0.856;0.813	T	0.18335	-1.0340	9	0.62326	D	0.03	-11.812	10.8974	0.47031	0.0:0.0:0.1573:0.8427	.	495;486	B8ZZV3;Q8NFR7	.;CC148_HUMAN	G	486;495	ENSP00000283233:R486G;ENSP00000386674:R495G	ENSP00000283233:R486G	R	-	1	2	CCDC148	158743669	0.985000	0.35326	1.000000	0.80357	0.282000	0.26991	2.011000	0.40922	2.178000	0.69098	0.533000	0.62120	AGA	.	.		0.363	CCDC148-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333270.1	NM_138803		C	159035423	T	C	159035423	3	2	65	1	0	0	0	0	1	0	0	0	2784	1559	54	2	331	2	CCDC148	2	159035423	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	33843344	159035423	84163950	57	8130										
GALNT3	2591	hgsc.bcm.edu	37	chr2	166613715	166613715	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcgaaaaacatgtccaacaaCagagcaaggcataatctcca	7	11	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:166613715C>T	ENST00000392701.3	-	7	2009	c.1234G>A	c.(1234-1236)Gtt>Att	p.V412I	GALNT3_ENST00000409882.1_Missense_Mutation_p.V150I	NM_004482.3	NP_004473.2	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	412	Catalytic subdomain B.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(1)	20						TGTCCAACAACAGAGCAAGGC	0.398																																					p.V412I		Atlas-SNP	.											.	GALNT3	65	.	0			c.G1234A						.						110	104	106					2																	166613715		2203	4300	6503	SO:0001583	missense	2591	exon7			CAACAACAGAGCA		CCDS2226.1	2q24-q31	2014-03-13	2014-03-13		ENSG00000115339	ENSG00000115339	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4125	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 3"	601756	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)"			9592121, 15133511	Standard	NM_004482		Approved	GalNAc-T3, HHS, HFTC	uc010fph.1	Q14435	OTTHUMG00000132157	ENST00000392701.3:c.1234G>A	chr2.hg19:g.166613715C>T	ENSP00000376465:p.Val412Ile	86.0	0.0		89.0	4.0	NM_004482	Q53TG9|Q7Z476	Missense_Mutation	SNP	ENST00000392701.3	hg19	CCDS2226.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754872	0.49362	.	.	ENSG00000115339	ENST00000392701;ENST00000409882;ENST00000412248	T;T;T	0.62941	-0.01;-0.01;-0.01	5.9	5.9	0.94986	.	0.122271	0.56097	D	0.000033	T	0.59252	0.2180	L	0.45581	1.43	0.53005	D	0.999962	B	0.14012	0.009	B	0.18561	0.022	T	0.51340	-0.8718	10	0.25751	T	0.34	.	20.2626	0.98452	0.0:1.0:0.0:0.0	.	412	Q14435	GALT3_HUMAN	I	412;150;412	ENSP00000376465:V412I;ENSP00000386955:V150I;ENSP00000412643:V412I	ENSP00000376465:V412I	V	-	1	0	GALNT3	166321961	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.372000	0.44257	2.802000	0.96397	0.650000	0.86243	GTT	.	.		0.398	GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255205.2	NM_004482		T	166613715	C	T	166613715	3	4	65	1	0	0	0	0	1	0	0	0	6222	478	17	3	687	3	GALNT3	2	166613715	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	7578292	166613715	76585658	58	8131										
BBS5	129880	hgsc.bcm.edu	37	chr2	170343593	170343593	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttttaggtagactcttggtaAcaaatttaagaattctctgg	8	5	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:170343593A>G	ENST00000295240.3	+	3	533	c.157A>G	c.(157-159)Aca>Gca	p.T53A	BBS5_ENST00000392663.2_Missense_Mutation_p.T53A|RP11-724O16.1_ENST00000513963.1_Missense_Mutation_p.T53A|BBS5_ENST00000554017.1_Missense_Mutation_p.T53A	NM_152384.2	NP_689597.1	Q8N3I7	BBS5_HUMAN	Bardet-Biedl syndrome 5	53					cilium assembly (GO:0042384)|heart looping (GO:0001947)|melanosome transport (GO:0032402)|motile cilium assembly (GO:0044458)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphate binding (GO:0032266)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						ACTCTTGGTAACAAATTTAAG	0.343									Bardet-Biedl syndrome																												p.T53A		Atlas-SNP	.											.	BBS5	27	.	0			c.A157G						.						175	182	180					2																	170343593		2203	4300	6503	SO:0001583	missense	129880	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TTGGTAACAAATT	AY604003	CCDS2233.1	2q31	2011-08-02			ENSG00000163093	ENSG00000163093			970	protein-coding gene	gene with protein product		603650				9888993, 10053027	Standard	NM_152384		Approved	DKFZp762I194		Q8N3I7	OTTHUMG00000132207	ENST00000295240.3:c.157A>G	chr2.hg19:g.170343593A>G	ENSP00000295240:p.Thr53Ala	87.0	0.0		83.0	4.0	NM_152384	D3DPC3|Q6PKN0	Missense_Mutation	SNP	ENST00000295240.3	hg19	CCDS2233.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.734544	0.89482	.	.	ENSG00000163093;ENSG00000163093;ENSG00000163093;ENSG00000251569	ENST00000295240;ENST00000554017;ENST00000392663;ENST00000513963	T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.91147	0.7212	M	0.88570	2.965	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.985;0.996;0.998	D	0.92831	0.6280	10	0.87932	D	0	-16.5329	15.6945	0.77484	1.0:0.0:0.0:0.0	.	53;53;53	E9PBE3;Q8N3I7-2;Q8N3I7	.;.;BBS5_HUMAN	A	53	ENSP00000295240:T53A;ENSP00000452313:T53A;ENSP00000376431:T53A;ENSP00000424363:T53A	ENSP00000295240:T53A	T	+	1	0	BBS5;RP11-724O16.1	170051839	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.012000	0.93624	2.094000	0.63399	0.533000	0.62120	ACA	.	.		0.343	BBS5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255265.2	NM_152384		G	170343593	A	G	170343593	3	3	65	1	0	0	0	0	1	0	0	0	1340	43	2	2	167	2	BBS5	2	170343593	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3729878	170343593	72855780	59	8132										
TTN	7273	hgsc.bcm.edu	37	chr2	179401122	179401122	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	taaggtttttcactgaaaagAcagtttctcgaatttcttct	6	7	4	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:179401122A>G	ENST00000591111.1	-	307	95653	c.95429T>C	c.(95428-95430)gTc>gCc	p.V31810A	TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V24578A|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V33451A|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V30883A|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V24386A|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V24511A|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000450692.2_RNA			Q8WZ42	TITIN_HUMAN	titin	31810	Fibronectin type-III 131. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACTGAAAAGACAGTTTCTCG	0.378																																					p.V33451A		Atlas-SNP	.											.	TTN	18412	.	0			c.T100352C						.						80	77	78					2																	179401122		1855	4102	5957	SO:0001583	missense	7273	exon357			GAAAAGACAGTTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.95429T>C	chr2.hg19:g.179401122A>G	ENSP00000465570:p.Val31810Ala	119.0	0.0		99.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.65	2.599264	0.46318	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	5.76	5.76	0.90799	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.48750	0.1517	N	0.16708	0.43	0.42993	D	0.994499	P;P;P;P	0.48503	0.835;0.835;0.835;0.911	P;P;P;P	0.49752	0.468;0.468;0.468;0.621	T	0.56420	-0.7982	9	0.87932	D	0	.	16.0677	0.80897	1.0:0.0:0.0:0.0	.	24386;24511;24578;31810	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	30883;24386;24578;24511;24383	ENSP00000343764:V30883A;ENSP00000434586:V24386A;ENSP00000340554:V24578A;ENSP00000352154:V24511A	ENSP00000340554:V24578A	V	-	2	0	TTN	179109368	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.088000	0.50175	2.185000	0.69588	0.460000	0.39030	GTC	.	.		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179401122	A	G	179401122	3	3	65	1	0	0	0	0	1	0	0	0	16750	275	10	2	7651	2	TTN	2	179401122	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	9057529	179401122	63798251	60	8133										
TTN	7273	hgsc.bcm.edu	37	chr2	179648880	179648880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cacccctacttcctttttcaCctcaacgccagcttcactct	2	19	4	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:179648880C>T	ENST00000591111.1	-	16	2916	c.2692G>A	c.(2692-2694)Gtg>Atg	p.V898M	TTN_ENST00000342175.6_Missense_Mutation_p.V852M|TTN_ENST00000589042.1_Missense_Mutation_p.V898M|TTN_ENST00000342992.6_Missense_Mutation_p.V898M|TTN_ENST00000460472.2_Missense_Mutation_p.V852M|TTN_ENST00000359218.5_Missense_Mutation_p.V852M|TTN_ENST00000360870.5_Missense_Mutation_p.V898M			Q8WZ42	TITIN_HUMAN	titin	33935					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCTTTTTCACCTCAACGCCA	0.552																																					p.V898M		Atlas-SNP	.											.	TTN	18412	.	0			c.G2692A						.						159	126	137					2																	179648880		2203	4300	6503	SO:0001583	missense	7273	exon16			TTTTCACCTCAAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2692G>A	chr2.hg19:g.179648880C>T	ENSP00000465570:p.Val898Met	256.0	0.0		259.0	12.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.79	2.042797	0.36085	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.63580	-0.05;0.21;0.2;0.18;0.32	5.52	5.52	0.82312	Ribonuclease H-like (1);	.	.	.	.	T	0.62841	0.2461	L	0.29908	0.895	0.22468	N	0.999075	P;P;P;P;D	0.59357	0.868;0.868;0.868;0.868;0.985	B;B;B;B;P	0.58391	0.38;0.38;0.38;0.38;0.838	T	0.56721	-0.7932	9	0.87932	D	0	.	7.5186	0.27614	0.0:0.802:0.0:0.198	.	852;852;852;898;898	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	M	898;852;852;852;852;898	ENSP00000343764:V898M;ENSP00000434586:V852M;ENSP00000340554:V852M;ENSP00000352154:V852M;ENSP00000354117:V898M	ENSP00000340554:V852M	V	-	1	0	TTN	179357125	0.999000	0.42202	1.000000	0.80357	0.752000	0.42762	1.504000	0.35726	2.767000	0.95098	0.655000	0.94253	GTG	.	.		0.552	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179648880	C	T	179648880	3	4	65	1	0	0	0	0	1	0	0	0	16750	507	18	3	108684	3	TTN	2	179648880	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	247758	179648880	63550493	61	8134										
NDUFS1	4719	hgsc.bcm.edu	37	chr2	207008850	207008850	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgacgttttagcccatcataGgcaaatctagaaaacagaaa	7	8	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:207008850G>A	ENST00000233190.6	-	10	1145	c.879C>T	c.(877-879)gcC>gcT	p.A293A	NDUFS1_ENST00000440274.1_Silent_p.A257A|NDUFS1_ENST00000455934.2_Silent_p.A307A|NDUFS1_ENST00000457011.1_Silent_p.A177A|NDUFS1_ENST00000432169.1_Silent_p.A182A|NDUFS1_ENST00000449699.1_Silent_p.A293A|NDUFS1_ENST00000423725.1_Silent_p.A236A	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	293	4Fe-4S Mo/W bis-MGD-type. {ECO:0000255|PROSITE-ProRule:PRU01004}.				apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCCCATCATAGGCAAATCTAG	0.358																																					p.A307A		Atlas-SNP	.											.	NDUFS1	82	.	0			c.C921T						.						90	88	88					2																	207008850		2203	4300	6503	SO:0001819	synonymous_variant	4719	exon10			ATCATAGGCAAAT		CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7707	protein-coding gene	gene with protein product	"complex I 75kDa subunit", "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"	157655	"NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.879C>T	chr2.hg19:g.207008850G>A		84.0	0.0		67.0	4.0	NM_001199984	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Silent	SNP	ENST00000233190.6	hg19	CCDS2366.1																																																																																			.	.		0.358	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006		A	207008850	G	A	207008850	2	1	65	1	0	0	0	0	0	0	0	1	10300	987	35	3		3	NDUFS1	2	207008850	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	27359970	207008850	36190523	62	8135										
MREG	55686	hgsc.bcm.edu	37	chr2	216861060	216861060	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tggcctgctgattacgaatgActatcaaattgtacagggtt	10	7	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:216861060A>G	ENST00000263268.6	-	2	519	c.224T>C	c.(223-225)gTc>gCc	p.V75A		NM_018000.2	NP_060470.2	Q8N565	MREG_HUMAN	melanoregulin	75						plasma membrane (GO:0005886)				large_intestine(1)|lung(2)	3		Renal(323;0.0328)		Epithelial(149;4.64e-07)|all cancers(144;5.56e-05)|LUSC - Lung squamous cell carcinoma(224;0.00832)|Lung(261;0.0111)		ATTACGAATGACTATCAAATT	0.448																																					p.V75A		Atlas-SNP	.											.	MREG	10	.	0			c.T224C						.						106	107	107					2																	216861060		1933	4139	6072	SO:0001583	missense	55686	exon2			CGAATGACTATCA	AK000978	CCDS46513.1	2q35	2013-09-27			ENSG00000118242	ENSG00000118242			25478	protein-coding gene	gene with protein product		609207				19240024, 22275436	Standard	NM_018000		Approved	FLJ10116, DSU, WDT2	uc002vfo.3	Q8N565	OTTHUMG00000154828	ENST00000263268.6:c.224T>C	chr2.hg19:g.216861060A>G	ENSP00000263268:p.Val75Ala	93.0	0.0		85.0	5.0	NM_018000	Q53R89|Q53TC1|Q5XKB6|Q9NWC9|Q9P1S1	Missense_Mutation	SNP	ENST00000263268.6	hg19	CCDS46513.1	.	.	.	.	.	.	.	.	.	.	A	12.18	1.860193	0.32884	.	.	ENSG00000118242	ENST00000236976;ENST00000263268;ENST00000439791;ENST00000424992;ENST00000420348	T	0.43688	0.94	5.33	5.33	0.75918	.	0.380247	0.31484	N	0.007577	T	0.31482	0.0798	L	0.44542	1.39	0.39279	D	0.964533	B	0.29590	0.25	B	0.26969	0.075	T	0.17992	-1.0351	10	0.24483	T	0.36	-11.4091	8.6043	0.33764	0.8293:0.0:0.0:0.1707	.	75	Q8N565	MREG_HUMAN	A	75;75;21;21;21	ENSP00000263268:V75A	ENSP00000236976:V75A	V	-	2	0	MREG	216569305	0.513000	0.26194	0.848000	0.33437	0.986000	0.74619	3.225000	0.51246	2.244000	0.73946	0.528000	0.53228	GTC	.	.		0.448	MREG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337297.1	NM_018000		G	216861060	A	G	216861060	3	3	65	1	0	0	0	0	1	0	0	0	9769	275	10	2	436	2	MREG	2	216861060	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	9852210	216861060	26338313	63	8136										
PSMD1	5707	hgsc.bcm.edu	37	chr2	232028362	232028362	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcttcagatgccgaaagttcAgtataaatcgaactgtaaac	7	8	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:232028362A>G	ENST00000308696.6	+	21	2564	c.2402A>G	c.(2401-2403)cAg>cGg	p.Q801R	PSMD1_ENST00000409643.1_Intron|PSMD1_ENST00000373635.4_Intron	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	801					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	CCGAAAGTTCAGTATAAATCG	0.373																																					p.Q801R		Atlas-SNP	.											.	PSMD1	77	.	0			c.A2402G						.						110	108	109					2																	232028362		2203	4300	6503	SO:0001583	missense	5707	exon21			AAGTTCAGTATAA	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.2402A>G	chr2.hg19:g.232028362A>G	ENSP00000309474:p.Gln801Arg	80.0	0.0		75.0	4.0	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	hg19	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	A	17.08	3.297464	0.60086	.	.	ENSG00000173692	ENST00000308696	.	.	.	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.55305	0.1912	L	0.42686	1.345	0.80722	D	1	B	0.22211	0.066	B	0.22753	0.041	T	0.54589	-0.8271	9	0.44086	T	0.13	-12.0276	14.5377	0.67973	1.0:0.0:0.0:0.0	.	801	Q99460	PSMD1_HUMAN	R	801	.	ENSP00000309474:Q801R	Q	+	2	0	PSMD1	231736606	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.139000	0.94554	2.002000	0.58637	0.454000	0.30748	CAG	.	.		0.373	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			G	232028362	A	G	232028362	3	3	65	1	0	0	0	0	1	0	0	0	12704	188	7	2	2484	2	PSMD1	2	232028362	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	15167302	232028362	11171011	64	8137										
AGXT	189	hgsc.bcm.edu	37	chr2	241813472	241813472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgctcatctccttcagtgacAaggccaagtgagtgacccac	9	14	3	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr2:241813472A>G	ENST00000307503.3	+	6	1060	c.673A>G	c.(673-675)Aag>Gag	p.K225E		NM_000030.2	NP_000021.1	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase	225					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process (GO:0042853)|L-cysteine catabolic process (GO:0019448)|oxalic acid secretion (GO:0046724)|pyruvate biosynthetic process (GO:0042866)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alanine-glyoxylate transaminase activity (GO:0008453)|amino acid binding (GO:0016597)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|receptor binding (GO:0005102)|serine-pyruvate transaminase activity (GO:0004760)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)	18		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)	Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)	CTTCAGTGACAAGGCCAAGTG	0.647																																					p.K225E		Atlas-SNP	.											AGXT,NS,adenoma,0,1	AGXT	50	.	0			c.A673G						.						79	71	74					2																	241813472		2203	4300	6503	SO:0001583	missense	189	exon6			AGTGACAAGGCCA	D13368	CCDS2543.1	2q37.3	2008-02-05	2007-04-13		ENSG00000172482	ENSG00000172482	2.6.1.44, 2.6.1.51		341	protein-coding gene	gene with protein product	"oxalosis I", "primary hyperoxaluria type 1", "L-alanine: glyoxylate aminotransferase 1", "serine:pyruvate aminotransferase", "glycolicaciduria"	604285		SPAT		2039493, 2045108	Standard	NM_000030		Approved	AGXT1, PH1, AGT, SPT, AGT1	uc002waa.4	P21549	OTTHUMG00000133354	ENST00000307503.3:c.673A>G	chr2.hg19:g.241813472A>G	ENSP00000302620:p.Lys225Glu	69.0	1.0		79.0	4.0	NM_000030	Q53QU6	Missense_Mutation	SNP	ENST00000307503.3	hg19	CCDS2543.1	.	.	.	.	.	.	.	.	.	.	A	13.80	2.343753	0.41498	.	.	ENSG00000172482	ENST00000307503	D	0.93076	-3.16	4.1	4.1	0.47936	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.271874	0.41294	D	0.000904	D	0.91355	0.7273	L	0.58925	1.835	0.39174	D	0.96264	B	0.26195	0.144	B	0.32289	0.143	D	0.90652	0.4583	10	0.62326	D	0.03	-25.1712	10.5155	0.44887	0.8247:0.1752:0.0:0.0	.	225	P21549	SPYA_HUMAN	E	225	ENSP00000302620:K225E	ENSP00000302620:K225E	K	+	1	0	AGXT	241462145	0.272000	0.24172	0.998000	0.56505	0.507000	0.33981	1.577000	0.36515	1.634000	0.50500	0.472000	0.43445	AAG	.	.		0.647	AGXT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257186.1	NM_000030		G	241813472	A	G	241813472	3	3	65	1	0	0	0	0	1	0	0	0	404	131	5	2	695	2	AGXT	2	241813472	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	9785110	241813472	1385901	65	8138										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1337367	1337367	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tttgtatctcaagagacgggAaacttgtacattgccaaagt	9	7	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:1337367A>G	ENST00000446702.2	+	6	1164	c.537A>G	c.(535-537)ggA>ggG	p.G179G	CNTN6_ENST00000539053.1_Silent_p.G107G|CNTN6_ENST00000350110.2_Silent_p.G179G			Q9UQ52	CNTN6_HUMAN	contactin 6	179	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AAGAGACGGGAAACTTGTACA	0.418																																					p.G179G		Atlas-SNP	.											.	CNTN6	245	.	0			c.A537G						.						105	96	99					3																	1337367		2203	4300	6503	SO:0001819	synonymous_variant	27255	exon6			GACGGGAAACTTG	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.537A>G	chr3.hg19:g.1337367A>G		123.0	0.0		78.0	4.0	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	hg19	CCDS2557.1																																																																																			.	.		0.418	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		G	1337367	A	G	1337367	2	3	65	1	0	0	0	0	0	0	0	1	3647	233	9	2		2	CNTN6	3	1337367	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10		1337367	196685063	66	8139										
CNTN4	152330	hgsc.bcm.edu	37	chr3	3097904	3097904	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acagctaggtccagtttatgAcaaaagttatctgaaggact	9	7	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:3097904A>G	ENST00000397461.1	+	24	3465	c.3081A>G	c.(3079-3081)tgA>tgG	p.*1027W	CNTN4_ENST00000427331.1_Nonstop_Mutation_p.*1027W|CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000448906.2_Nonstop_Mutation_p.*699W|CNTN4_ENST00000358480.3_Nonstop_Mutation_p.*808W|CNTN4_ENST00000397459.2_Nonstop_Mutation_p.*699W|CNTN4_ENST00000418658.1_Nonstop_Mutation_p.*1027W	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	0					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)		p.*699W(1)|p.*1027W(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		CCAGTTTATGACAAAAGTTAT	0.398																																					p.X1027W		Atlas-SNP	.											CNTN4_ENST00000418658,rectum,carcinoma,0,2	CNTN4	335	.	2	Nonstop extension(2)	large_intestine(2)	c.A3081G						.						103	92	95					3																	3097904		2203	4300	6503	SO:0001578	stop_lost	152330	exon25			TTTATGACAAAAG	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.3081A>G	chr3.hg19:g.3097904A>G	ENSP00000380602:p.*1027Trpext*16	74.0	0.0		48.0	2.0	NM_175607	B2RAX3|Q8IX14|Q8TC35	Missense_Mutation	SNP	ENST00000397461.1	hg19	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813180	0.50527	.	.	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6012	0.76626	1.0:0.0:0.0:0.0	.	.	.	.	W	1027;1027;1027;808;699;699	.	.	X	+	3	0	CNTN4	3072904	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	8.167000	0.89668	2.094000	0.63399	0.482000	0.46254	TGA	.	.		0.398	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			G	3097904	A	G	3097904	4	3	65	1	0	0	0	0	0	0	0	0	3645	288	10	2	3167	2	CNTN4	3	3097904	Nonstop_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1760537	3097904	194924526	67	8140										
CAND2	23066	hgsc.bcm.edu	37	chr3	12858556	12858556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tggtcaacgagagcgacatgCatgtggcccagctggctgtg	15	10	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:12858556C>T	ENST00000456430.2	+	10	2166	c.2125C>T	c.(2125-2127)Cat>Tat	p.H709Y	CAND2_ENST00000295989.5_Missense_Mutation_p.H616Y	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	709					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GAGCGACATGCATGTGGCCCA	0.677																																					p.H709Y	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.C2125T						.						27	28	28					3																	12858556		2162	4266	6428	SO:0001583	missense	23066	exon10			GACATGCATGTGG		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.2125C>T	chr3.hg19:g.12858556C>T	ENSP00000387641:p.His709Tyr	81.0	0.0		88.0	4.0	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.112438	0.77210	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.52057	0.68;0.68	4.98	4.98	0.66077	Armadillo-like helical (1);Armadillo-type fold (1);	0.057587	0.64402	D	0.000002	T	0.71871	0.3391	M	0.87758	2.905	0.80722	D	1	D;D	0.76494	0.999;0.962	D;D	0.72982	0.979;0.946	T	0.75269	-0.3377	10	0.45353	T	0.12	-41.4719	16.104	0.81205	0.0:1.0:0.0:0.0	.	709;616	O75155;O75155-2	CAND2_HUMAN;.	Y	616;709	ENSP00000295989:H616Y;ENSP00000387641:H709Y	ENSP00000295989:H616Y	H	+	1	0	CAND2	12833556	1.000000	0.71417	0.990000	0.47175	0.953000	0.61014	5.875000	0.69660	2.451000	0.82905	0.561000	0.74099	CAT	.	.		0.677	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		T	12858556	C	T	12858556	3	4	65	1	0	0	0	0	1	0	0	0	2618	710	25	3	2163	3	CAND2	3	12858556	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	9760652	12858556	185163874	68	8141										
ZNF860	344787	hgsc.bcm.edu	37	chr3	32030646	32030646	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cttcctcagggacacttgacTtttagggatgtggctataga	11	8	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:32030646T>C	ENST00000360311.4	+	2	624	c.75T>C	c.(73-75)acT>acC	p.T25T		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	25	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						GACACTTGACTTTTAGGGATG	0.478																																					p.T25T		Atlas-SNP	.											.	ZNF860	96	.	0			c.T75C						.						48	44	45					3																	32030646		692	1591	2283	SO:0001819	synonymous_variant	344787	exon2			CTTGACTTTTAGG	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"Zinc fingers, C2H2-type", "-"	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.75T>C	chr3.hg19:g.32030646T>C		135.0	0.0		72.0	4.0	NM_001137674	B4DFA4	Silent	SNP	ENST00000360311.4	hg19	CCDS46784.1																																																																																			.	.		0.478	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1			C	32030646	T	C	32030646	2	2	65	1	0	0	0	0	0	0	0	1	18209	1596	56	2		2	ZNF860	3	32030646	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	19172090	32030646	165991784	69	8142										
GLB1	2720	hgsc.bcm.edu	37	chr3	33110429	33110429	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcagaaaactggtactgtccTggccagggctcatgaaagtt	11	9	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:33110429T>C	ENST00000399402.3	-	3	320	c.189A>G	c.(187-189)ccA>ccG	p.P63P	GLB1_ENST00000445488.2_Silent_p.P141P|GLB1_ENST00000307377.8_Intron|GLB1_ENST00000307363.5_Silent_p.P93P	NM_001079811.1	NP_001073279	P16278	BGAL_HUMAN	galactosidase, beta 1	93					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)	beta-galactosidase activity (GO:0004565)|galactoside binding (GO:0016936)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	21		Melanoma(143;0.104)				GGTACTGTCCTGGCCAGGGCT	0.532																																					p.P93P		Atlas-SNP	.											.	GLB1	51	.	0			c.A279G						.						102	101	101					3																	33110429		1950	4142	6092	SO:0001819	synonymous_variant	2720	exon3			CTGTCCTGGCCAG	M22590	CCDS43061.1, CCDS43062.1, CCDS46785.1	3p22.3	2012-10-02			ENSG00000170266	ENSG00000170266	3.2.1.23		4298	protein-coding gene	gene with protein product		611458	"elastin receptor 1, 67kDa", "elastin receptor 1 (67kD)"	ELNR1		110522, 3143362	Standard	NM_000404		Approved	EBP	uc003cfi.1	P16278	OTTHUMG00000155781	ENST00000399402.3:c.189A>G	chr3.hg19:g.33110429T>C		136.0	0.0		95.0	4.0	NM_000404	B2R7H8|B7Z6B0|P16279	Silent	SNP	ENST00000399402.3	hg19	CCDS43062.1																																																																																			.	.		0.532	GLB1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341570.2	NM_000404		C	33110429	T	C	33110429	2	2	65	1	0	0	0	0	0	0	0	1	6435	1567	55	2		2	GLB1	3	33110429	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1079783	33110429	164912001	70	8143										
XIRP1	165904	hgsc.bcm.edu	37	chr3	39226588	39226588	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccccttggtgggaaccttccAtgggctgctctcctgagggg	14	13	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:39226588A>G	ENST00000340369.3	-	2	4577	c.4349T>C	c.(4348-4350)aTg>aCg	p.M1450T	XIRP1_ENST00000421646.1_Missense_Mutation_p.M133T|XIRP1_ENST00000396251.1_3'UTR	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1450					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GGAACCTTCCATGGGCTGCTC	0.627																																					p.M1450T		Atlas-SNP	.											.	XIRP1	173	.	0			c.T4349C						.						53	65	61					3																	39226588		2203	4300	6503	SO:0001583	missense	165904	exon2			CCTTCCATGGGCT	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.4349T>C	chr3.hg19:g.39226588A>G	ENSP00000343140:p.Met1450Thr	64.0	0.0		49.0	14.0	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	A	10.26	1.300437	0.23650	.	.	ENSG00000168334	ENST00000340369;ENST00000421646	T;T	0.20069	3.77;2.1	4.33	-8.67	0.00863	.	1.219840	0.05617	U	0.579108	T	0.08447	0.0210	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30794	-0.9966	10	0.13853	T	0.58	.	0.8619	0.01195	0.1928:0.2363:0.338:0.2329	.	1450	Q702N8	XIRP1_HUMAN	T	1450;133	ENSP00000343140:M1450T;ENSP00000391645:M133T	ENSP00000343140:M1450T	M	-	2	0	XIRP1	39201592	0.000000	0.05858	0.000000	0.03702	0.493000	0.33554	-0.032000	0.12266	-1.801000	0.01245	0.533000	0.62120	ATG	.	.		0.627	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		G	39226588	A	G	39226588	3	3	65	1	0	0	0	0	1	0	0	0	17444	217	8	2	1186	2	XIRP1	3	39226588	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	6116159	39226588	158795842	71	8144										
ULK4	54986	hgsc.bcm.edu	37	chr3	41439687	41439687	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgtccgggttttcccctccAtacagctgaaccagtataga	8	13	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:41439687A>G	ENST00000301831.4	-	35	4023	c.3561T>C	c.(3559-3561)taT>taC	p.Y1187Y		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	1187					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TTTCCCCTCCATACAGCTGAA	0.393																																					p.Y1187Y		Atlas-SNP	.											.	ULK4	150	.	0			c.T3561C						.						90	86	88					3																	41439687		1840	4081	5921	SO:0001819	synonymous_variant	54986	exon35			CCCTCCATACAGC	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.3561T>C	chr3.hg19:g.41439687A>G		115.0	0.0		73.0	4.0	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Silent	SNP	ENST00000301831.4	hg19	CCDS43071.1																																																																																			.	.		0.393	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		G	41439687	A	G	41439687	2	3	65	1	0	0	0	0	0	0	0	1	16993	224	8	2		2	ULK4	3	41439687	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2213099	41439687	156582743	72	8145										
TRAK1	22906	hgsc.bcm.edu	37	chr3	42234621	42234660	+	Frame_Shift_Del	DEL	AAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCT	AAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCT	-													0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggaactggccaagaagacggAagatgctgcccgccagcaag					rs201576814	byFrequency	TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	AAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCT	AAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:42234621_42234660delAAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCT	ENST00000327628.5	+	8	1224_1263	c.824_863delAAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCT	c.(823-864)gaagatgctgcccgccagcaagaggagatcacacacctgctafs	p.EDAARQQEEITHLL275fs	TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000449246.1_Frame_Shift_Del_p.EDAARQQEEITHLL201fs|TRAK1_ENST00000396175.1_Frame_Shift_Del_p.EDAARQQEEITHLL217fs|TRAK1_ENST00000341421.3_Frame_Shift_Del_p.EDAARQQEEITHLL217fs	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	275	HAP1 N-terminal.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						AAGAAGACGGAAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCTATCGCAAATA	0.475																																					p.275_288del	GBM(44;195 884 22595 31865 41850)	Pindel	.											.	TRAK1	188	.	0			c.823_862del						.																																			SO:0001589	frameshift_variant	22906	exon8			.		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.824_863delAAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCT	chr3.hg19:g.42234621_42234660delAAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCT	ENSP00000328998:p.Glu275fs	162.0	0.0		84.0	12.0	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Frame_Shift_Del	DEL	ENST00000327628.5	hg19	CCDS43072.1																																																																																			.	.		0.475	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		-	42234660	AAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCT	-	42234621	7	5	65	1	0	1	0	1	0	0	0	0	16464	246	9	0	970	0	TRAK1	3	42234621	Frame_Shift_Del	DEL	AAGATGCTGCCCGCCAGCAAGAGGAGATCACACACCTGCT	TCGA-CC-A3MB-01A-11D-A20W-10	794934	42234621	155787809	73	8146										
CCK	885	hgsc.bcm.edu	37	chr3	42305118	42305118	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgcacaggcacacgccgctgTtcatggctgtagcgagcaaa	12	13	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:42305118T>C	ENST00000396169.2	-	4	910	c.5A>G	c.(4-6)aAc>aGc	p.N2S	CCK_ENST00000434608.1_Missense_Mutation_p.N2S|CCK_ENST00000334681.5_Missense_Mutation_p.N2S	NM_000729.4	NP_000720.1	P06307	CCKN_HUMAN	cholecystokinin	2					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axonogenesis (GO:0007409)|behavioral fear response (GO:0001662)|eating behavior (GO:0042755)|negative regulation of appetite (GO:0032099)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein oligomerization (GO:0032461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|release of cytochrome c from mitochondria (GO:0001836)|signal transduction (GO:0007165)	axon (GO:0030424)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|terminal bouton (GO:0043195)	hormone activity (GO:0005179)|neuropeptide hormone activity (GO:0005184)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6		Ovarian(412;0.0728)		KIRC - Kidney renal clear cell carcinoma(284;0.219)		CACGCCGCTGTTCATGGCTGT	0.692																																					p.N2S		Atlas-SNP	.											.	CCK	15	.	0			c.A5G						.						7	8	8					3																	42305118		2133	4141	6274	SO:0001583	missense	885	exon4			CCGCTGTTCATGG		CCDS2696.1	3p22.1	2013-02-25			ENSG00000187094	ENSG00000187094		"Endogenous ligands"	1569	protein-coding gene	gene with protein product	"prepro-cholecystokinin", "cholecystokinin triacontatriapeptide"	118440				3856870	Standard	NM_001174138		Approved		uc021wwk.1	P06307	OTTHUMG00000131796	ENST00000396169.2:c.5A>G	chr3.hg19:g.42305118T>C	ENSP00000379472:p.Asn2Ser	52.0	0.0		51.0	4.0	NM_000729		Missense_Mutation	SNP	ENST00000396169.2	hg19	CCDS2696.1	.	.	.	.	.	.	.	.	.	.	T	5.712	0.315814	0.10789	.	.	ENSG00000187094	ENST00000396169;ENST00000334681;ENST00000434608	T;T;T	0.21543	2.0;2.0;2.0	5.26	5.26	0.73747	Gastrin/cholecystokinin peptide hormone (1);	0.313869	0.38720	N	0.001593	T	0.34337	0.0894	M	0.69185	2.1	0.27807	N	0.942295	D;P	0.56968	0.978;0.684	P;B	0.58077	0.832;0.272	T	0.30995	-0.9959	10	0.05833	T	0.94	-28.8149	14.6476	0.68772	0.0:0.0:0.0:1.0	.	2;2	B7Z6Q9;P06307	.;CCKN_HUMAN	S	2	ENSP00000379472:N2S;ENSP00000335657:N2S;ENSP00000409124:N2S	ENSP00000335657:N2S	N	-	2	0	CCK	42280122	1.000000	0.71417	0.944000	0.38274	0.152000	0.21847	4.459000	0.60102	2.116000	0.64780	0.533000	0.62120	AAC	.	.		0.692	CCK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343380.1	NM_000729		C	42305118	T	C	42305118	3	2	65	1	0	0	0	0	1	0	0	0	2881	1725	60	2	350	2	CCK	3	42305118	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	70497	42305118	155717312	74	8147										
CDCP1	64866	hgsc.bcm.edu	37	chr3	45153758	45153758	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gctgatggagtgagtgactcCgtctgggcagctctcacccg	14	12	2	3	rs149422328	byFrequency	TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:45153758C>G	ENST00000296129.1	-	3	606	c.472G>C	c.(472-474)Gga>Cga	p.G158R	CDCP1_ENST00000490471.1_5'Flank|CDCP1_ENST00000425231.2_Missense_Mutation_p.G158R	NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	158						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		TGAGTGACTCCGTCTGGGCAG	0.557																																					p.G158R		Atlas-SNP	.											.	CDCP1	61	.	0			c.G472C						.						149	147	148					3																	45153758		2203	4300	6503	SO:0001583	missense	64866	exon3			TGACTCCGTCTGG	AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"CD molecules"	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.472G>C	chr3.hg19:g.45153758C>G	ENSP00000296129:p.Gly158Arg	94.0	0.0		60.0	28.0	NM_178181	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Missense_Mutation	SNP	ENST00000296129.1	hg19	CCDS2727.1	.	.	.	.	.	.	.	.	.	.	C	10.79	1.448476	0.26074	.	.	ENSG00000163814	ENST00000296129;ENST00000425231	T;T	0.42900	1.98;0.96	5.42	4.46	0.54185	.	0.725192	0.14128	N	0.339564	T	0.46190	0.1380	L	0.57536	1.79	0.09310	N	1	D;D	0.60575	0.988;0.966	P;P	0.53450	0.659;0.726	T	0.29882	-0.9997	10	0.18276	T	0.48	.	7.5699	0.27900	0.3663:0.5146:0.1191:0.0	.	158;158	Q9H5V8-3;Q9H5V8	.;CDCP1_HUMAN	R	158	ENSP00000296129:G158R;ENSP00000399342:G158R	ENSP00000296129:G158R	G	-	1	0	CDCP1	45128762	0.001000	0.12720	0.117000	0.21633	0.206000	0.24218	1.015000	0.29963	2.537000	0.85549	0.563000	0.77884	GGA	.	C|1.000;T|0.000		0.557	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842		G	45153758	C	G	45153758	3	3	65	1	0	0	0	0	1	0	0	0	3095	661	23	4	2074	4	CDCP1	3	45153758	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	2848640	45153758	152868672	75	8148										
SHISA5	51246	hgsc.bcm.edu	37	chr3	48510952	48510952	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggcatgcaccacagtggtggAtgtggtggtggtgacaaccg	17	8	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:48510952A>G	ENST00000296444.2	-	5	787	c.451T>C	c.(451-453)Tcc>Ccc	p.S151P	SHISA5_ENST00000465449.1_5'UTR|SHISA5_ENST00000426002.1_Missense_Mutation_p.S48P|SHISA5_ENST00000444115.1_Missense_Mutation_p.S120P|SHISA5_ENST00000442747.1_Missense_Mutation_p.S120P|SHISA5_ENST00000443308.2_Missense_Mutation_p.S144P	NM_001272065.1|NM_016479.3	NP_001258994.1|NP_057563.3	Q8N114	SHSA5_HUMAN	shisa family member 5	151	Poly-Thr.				intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			large_intestine(1)|lung(1)	2						ACAGTGGTGGATGTGGTGGTG	0.612																																					p.S151P		Atlas-SNP	.											.	SHISA5	10	.	0			c.T451C						.						99	94	96					3																	48510952		2203	4300	6503	SO:0001583	missense	51246	exon5			TGGTGGATGTGGT	AF520698	CCDS2770.1, CCDS63621.1, CCDS63622.1, CCDS63623.1	3p21.31	2013-07-31	2013-07-31		ENSG00000164054	ENSG00000164054		"Shisa homologs"	30376	protein-coding gene	gene with protein product		607290	"shisa homolog 5 (Xenopus laevis)"			11042152, 12135983	Standard	NM_016479		Approved	SCOTIN, hShisa5	uc011bbk.1	Q8N114	OTTHUMG00000133529	ENST00000296444.2:c.451T>C	chr3.hg19:g.48510952A>G	ENSP00000296444:p.Ser151Pro	114.0	0.0		91.0	5.0	NM_016479	B3KW99|F8W9N8|Q69YY9|Q7Z433|Q8NHL9|Q96MW8|Q9BV58	Missense_Mutation	SNP	ENST00000296444.2	hg19	CCDS2770.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.240734	0.39598	.	.	ENSG00000164054	ENST00000296444;ENST00000444115;ENST00000426002;ENST00000442747;ENST00000443308	T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75	5.05	-7.29	0.01451	.	0.591742	0.16951	N	0.192888	T	0.31765	0.0807	L	0.29908	0.895	0.09310	N	0.999997	B;P;P;B	0.42123	0.13;0.729;0.771;0.039	B;B;B;B	0.43052	0.059;0.284;0.406;0.059	T	0.38045	-0.9679	10	0.52906	T	0.07	-15.2617	11.0558	0.47918	0.7015:0.223:0.0:0.0755	.	48;144;151;48	Q8N114-4;F8W9N8;Q8N114;Q8N114-3	.;.;SHSA5_HUMAN;.	P	151;120;48;120;144	ENSP00000296444:S151P;ENSP00000407957:S120P;ENSP00000390388:S48P;ENSP00000408223:S120P;ENSP00000395373:S144P	ENSP00000296444:S151P	S	-	1	0	SHISA5	48485956	0.000000	0.05858	0.012000	0.15200	0.933000	0.57130	-1.311000	0.02723	-1.218000	0.02601	-0.445000	0.05633	TCC	.	.		0.612	SHISA5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257504.3	NM_016479		G	48510952	A	G	48510952	3	3	65	1	0	0	0	0	1	0	0	0	14298	333	12	2	279	2	SHISA5	3	48510952	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3357194	48510952	149511478	76	8149										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51378810	51378810	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atcattcactacttcaacaaAggcaaggtatgcatcattag	6	9	4	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:51378810A>G	ENST00000266037.9	+	38	3932	c.3909A>G	c.(3907-3909)aaA>aaG	p.K1303K		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1303	DHR-2.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ACTTCAACAAAGGCAAGGTAT	0.542																																					p.K1303K		Atlas-SNP	.											.	DOCK3	397	.	0			c.A3909G						.						69	70	69					3																	51378810		2082	4227	6309	SO:0001819	synonymous_variant	1795	exon38			CAACAAAGGCAAG	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.3909A>G	chr3.hg19:g.51378810A>G		153.0	0.0		99.0	4.0	NM_004947	O15017	Silent	SNP	ENST00000266037.9	hg19	CCDS46835.1																																																																																			.	.		0.542	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		G	51378810	A	G	51378810	2	3	65	1	0	0	0	0	0	0	0	1	4690	69	3	2		2	DOCK3	3	51378810	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2867858	51378810	146643620	77	8150										
SFMBT1	51460	hgsc.bcm.edu	37	chr3	52962211	52962211	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gacagcgaatgtgcacctggAggggggctgatgtgtaggcc	18	8	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:52962211A>C	ENST00000394752.3	-	9	1426	c.1044T>G	c.(1042-1044)ccT>ccG	p.P348P	SFMBT1_ENST00000394750.1_Silent_p.P348P|SFMBT1_ENST00000358080.2_Silent_p.P348P|SFMBT1_ENST00000296295.6_Silent_p.P348P	NM_016329.3	NP_057413.2	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	348					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|negative regulation of muscle organ development (GO:0048635)|negative regulation of transcription, DNA-templated (GO:0045892)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	24				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		GTGCACCTGGAGGGGGGCTGA	0.527																																					p.P348P		Atlas-SNP	.											.	SFMBT1	53	.	0			c.T1044G						.						122	118	120					3																	52962211		2203	4300	6503	SO:0001819	synonymous_variant	51460	exon9			ACCTGGAGGGGGG	AF168132	CCDS2867.1	3p21.31	2013-01-10			ENSG00000163935	ENSG00000163935		"Sterile alpha motif (SAM) domain containing"	20255	protein-coding gene	gene with protein product		607319				10661410	Standard	NM_016329		Approved	RU1, DKFZp434L243, SFMBT	uc003dgh.3	Q9UHJ3	OTTHUMG00000159052	ENST00000394752.3:c.1044T>G	chr3.hg19:g.52962211A>C		48.0	0.0		28.0	12.0	NM_016329	Q402F7|Q96C73|Q9Y4Q9	Silent	SNP	ENST00000394752.3	hg19	CCDS2867.1																																																																																			.	.		0.527	SFMBT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353040.3	NM_016329		C	52962211	A	C	52962211	2	2	65	1	0	0	0	0	0	0	0	1	14172	291	11	5		5	SFMBT1	3	52962211	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1583401	52962211	145060219	78	8151										
PTPRG	5793	hgsc.bcm.edu	37	chr3	62180755	62180755	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaaagccaccattagccatgTctcacccgatagcctttacc	6	15	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:62180755T>C	ENST00000474889.1	+	10	1615	c.1238T>C	c.(1237-1239)gTc>gCc	p.V413A	PTPRG_ENST00000295874.10_Missense_Mutation_p.V413A	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	413	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		ATTAGCCATGTCTCACCCGAT	0.502																																					p.V413A		Atlas-SNP	.											.	PTPRG	153	.	0			c.T1238C						.						149	135	139					3																	62180755		2203	4300	6503	SO:0001583	missense	5793	exon10			GCCATGTCTCACC	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.1238T>C	chr3.hg19:g.62180755T>C	ENSP00000418112:p.Val413Ala	131.0	0.0		80.0	6.0	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	hg19	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.850405	0.71719	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.57436	0.4;0.4	5.81	5.81	0.92471	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.120930	0.56097	D	0.000031	T	0.51381	0.1671	L	0.32530	0.975	0.58432	D	0.999999	P;P	0.38597	0.604;0.639	B;B	0.44085	0.183;0.44	T	0.55860	-0.8074	10	0.87932	D	0	.	16.155	0.81657	0.0:0.0:0.0:1.0	.	413;413	P23470-2;P23470	.;PTPRG_HUMAN	A	413	ENSP00000418112:V413A;ENSP00000295874:V413A	ENSP00000295874:V413A	V	+	2	0	PTPRG	62155795	1.000000	0.71417	0.982000	0.44146	0.996000	0.88848	7.541000	0.82084	2.221000	0.72209	0.533000	0.62120	GTC	.	.		0.502	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		C	62180755	T	C	62180755	3	2	65	1	0	0	0	0	1	0	0	0	12817	1667	58	2	1276	2	PTPRG	3	62180755	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	9218544	62180755	135841675	79	8152										
KBTBD8	84541	hgsc.bcm.edu	37	chr3	67049555	67049555	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agacattgtagtggaagtggAtcacgggaaaacattttcct	11	6	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:67049555A>G	ENST00000417314.2	+	2	216	c.167A>G	c.(166-168)gAt>gGt	p.D56G	KBTBD8_ENST00000469661.1_3'UTR|KBTBD8_ENST00000460576.1_Intron|KBTBD8_ENST00000295568.4_Missense_Mutation_p.D30G			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	56	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		GTGGAAGTGGATCACGGGAAA	0.448																																					p.D56G		Atlas-SNP	.											.	KBTBD8	101	.	0			c.A167G						.						190	170	177					3																	67049555		2203	4300	6503	SO:0001583	missense	84541	exon2			AAGTGGATCACGG	AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"BTB/POZ domain containing"	30691	protein-coding gene	gene with protein product	"T-cell activation kelch repeat protein"					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.167A>G	chr3.hg19:g.67049555A>G	ENSP00000401878:p.Asp56Gly	139.0	0.0		94.0	4.0	NM_032505	B4DTW6|Q96JI5	Missense_Mutation	SNP	ENST00000417314.2	hg19	CCDS2906.2	.	.	.	.	.	.	.	.	.	.	A	15.71	2.912815	0.52439	.	.	ENSG00000163376	ENST00000295568;ENST00000417314;ENST00000460784	T;T;T	0.64618	-0.11;-0.11;-0.11	5.62	5.62	0.85841	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.152533	0.64402	D	0.000019	T	0.43634	0.1256	N	0.03268	-0.37	0.53688	D	0.999977	P	0.43231	0.801	P	0.48952	0.596	T	0.44544	-0.9321	10	0.08381	T	0.77	.	11.232	0.48918	0.8634:0.0:0.0:0.1366	.	56	Q8NFY9	KBTB8_HUMAN	G	30;56;30	ENSP00000295568:D30G;ENSP00000401878:D56G;ENSP00000418075:D30G	ENSP00000295568:D30G	D	+	2	0	KBTBD8	67132245	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.425000	0.80255	2.267000	0.75376	0.383000	0.25322	GAT	.	.		0.448	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505		G	67049555	A	G	67049555	3	3	65	1	0	0	0	0	1	0	0	0	8008	333	12	2	173	2	KBTBD8	3	67049555	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	4868800	67049555	130972875	80	8153										
EPHA6	285220	hgsc.bcm.edu	37	chr3	96533714	96533714	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcctgcgctgccgccacttcTctttaagggagaggaaaaga	12	11	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:96533714T>C	ENST00000389672.5	+	1	285	c.247T>C	c.(247-249)Tct>Cct	p.S83P	EPHA6_ENST00000470610.2_Missense_Mutation_p.S83P|EPHA6_ENST00000542517.1_5'UTR	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	0	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						CCGCCACTTCTCTTTAAGGGA	0.577																																					p.S83P		Atlas-SNP	.											.	EPHA6	439	.	0			c.T247C						.						13	18	16					3																	96533714		1910	4074	5984	SO:0001583	missense	285220	exon1			CACTTCTCTTTAA	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.247T>C	chr3.hg19:g.96533714T>C	ENSP00000374323:p.Ser83Pro	128.0	0.0		109.0	5.0	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	hg19	CCDS46876.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.809|8.809	0.934807|0.934807	0.18206|0.18206	.|.	.|.	ENSG00000080224|ENSG00000080224	ENST00000506569|ENST00000470610;ENST00000389672	.|T;T	.|0.75477	.|4.96;-0.94	5.35|5.35	1.46|1.46	0.22682|0.22682	.|.	.|.	.|.	.|.	.|.	T|T	0.48370|0.48370	0.1496|0.1496	N|N	0.08118|0.08118	0|0	0.18873|0.18873	N|N	0.999988|0.999988	.|B;B	.|0.21821	.|0.026;0.061	.|B;B	.|0.21546	.|0.029;0.035	T|T	0.33033|0.33033	-0.9884|-0.9884	5|9	.|0.34782	.|T	.|0.22	.|.	1.4965|1.4965	0.02467|0.02467	0.1773:0.0957:0.1847:0.5423|0.1773:0.0957:0.1847:0.5423	.|.	.|83;83	.|B3KS12;E7EU71	.|.;.	P|P	27|83	.|ENSP00000420598:S83P;ENSP00000374323:S83P	.|ENSP00000374323:S83P	L|S	+|+	2|1	0|0	EPHA6|EPHA6	98016404|98016404	0.857000|0.857000	0.29778|0.29778	0.387000|0.387000	0.26183|0.26183	0.258000|0.258000	0.26162|0.26162	1.437000|1.437000	0.34991|0.34991	0.271000|0.271000	0.22005|0.22005	0.477000|0.477000	0.44152|0.44152	CTC|TCT	.	.		0.577	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		C	96533714	T	C	96533714	3	2	65	1	0	0	0	0	1	0	0	0	5173	1551	54	2	249	2	EPHA6	3	96533714	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	29484159	96533714	101488716	81	8154										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113379962	113379962	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acaggagtcacaagattgcaAgtcctctgtactggcaccac	9	12	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:113379962A>G	ENST00000478658.1	-	5	584	c.567T>C	c.(565-567)acT>acC	p.T189T	KIAA2018_ENST00000316407.4_Silent_p.T189T|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	189						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						CAAGATTGCAAGTCCTCTGTA	0.463																																					p.T189T		Atlas-SNP	.											KIAA2018,NS,carcinoma,0,1	KIAA2018	180	.	0			c.T567C						.						128	130	129					3																	113379962		1934	4132	6066	SO:0001819	synonymous_variant	205717	exon7			ATTGCAAGTCCTC	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.567T>C	chr3.hg19:g.113379962A>G		98.0	0.0		97.0	4.0	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.		0.463	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		G	113379962	A	G	113379962	2	3	65	1	0	0	0	0	0	0	0	1	8277	59	3	2		2	KIAA2018	3	113379962	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	16846248	113379962	84642468	82	8155										
GRAMD1C	54762	hgsc.bcm.edu	37	chr3	113601609	113601609	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttctttgcagtttttcttcaCatcttttggtgccagggata	8	8	4	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:113601609C>T	ENST00000358160.4	+	6	962	c.470C>T	c.(469-471)aCa>aTa	p.T157I	GRAMD1C_ENST00000479212.1_3'UTR|GRAMD1C_ENST00000452134.2_5'UTR	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	157						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						TTTTTCTTCACATCTTTTGGT	0.358																																					p.T157I		Atlas-SNP	.											.	GRAMD1C	71	.	0			c.C470T						.						169	172	171					3																	113601609		2203	4300	6503	SO:0001583	missense	54762	exon6			TCTTCACATCTTT		CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.470C>T	chr3.hg19:g.113601609C>T	ENSP00000350881:p.Thr157Ile	137.0	0.0		123.0	5.0	NM_017577	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Missense_Mutation	SNP	ENST00000358160.4	hg19	CCDS33826.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.025097	0.75390	.	.	ENSG00000178075	ENST00000358160	T	0.36878	1.23	5.52	5.52	0.82312	.	0.481200	0.22915	N	0.054096	T	0.56046	0.1959	M	0.81802	2.56	0.80722	D	1	D	0.59767	0.986	P	0.53954	0.738	T	0.60068	-0.7335	10	0.52906	T	0.07	.	16.9402	0.86216	0.0:1.0:0.0:0.0	.	157	Q8IYS0	GRM1C_HUMAN	I	157	ENSP00000350881:T157I	ENSP00000350881:T157I	T	+	2	0	GRAMD1C	115084299	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.427000	0.59888	2.587000	0.87381	0.643000	0.83706	ACA	.	.		0.358	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577		T	113601609	C	T	113601609	3	4	65	1	0	0	0	0	1	0	0	0	6758	478	17	3	492	3	GRAMD1C	3	113601609	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	221647	113601609	84420821	83	8156										
ARHGAP31	57514	hgsc.bcm.edu	37	chr3	119133131	119133131	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cctccactcccacctgctccTccccctccaactcctctgga	3	24	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:119133131T>C	ENST00000264245.4	+	12	2887	c.2355T>C	c.(2353-2355)ccT>ccC	p.P785P		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	785	Pro-rich.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						CACCTGCTCCTCCCCCTCCAA	0.537																																					p.P785P	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.T2355C						.						52	55	54					3																	119133131		1924	4126	6050	SO:0001819	synonymous_variant	57514	exon12			TGCTCCTCCCCCT		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.2355T>C	chr3.hg19:g.119133131T>C		56.0	0.0		40.0	4.0	NM_020754	Q9ULL6	Silent	SNP	ENST00000264245.4	hg19	CCDS43135.1																																																																																			.	.		0.537	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			C	119133131	T	C	119133131	2	2	65	1	0	0	0	0	0	0	0	1	880	1538	54	2		2	ARHGAP31	3	119133131	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	5531522	119133131	78889299	84	8157										
LRRC58	116064	hgsc.bcm.edu	37	chr3	120053943	120053943	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gatctctcgaggcagatatgTcagcaagttattgtgaagac	11	7	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:120053943T>C	ENST00000295628.3	-	3	768	c.673A>G	c.(673-675)Aca>Gca	p.T225A		NM_001099678.1	NP_001093148.1	Q96CX6	LRC58_HUMAN	leucine rich repeat containing 58	225										large_intestine(2)|lung(5)	7				GBM - Glioblastoma multiforme(114;0.147)		GGCAGATATGTCAGCAAGTTA	0.348																																					p.T225A		Atlas-SNP	.											.	LRRC58	18	.	0			c.A673G						.						101	92	95					3																	120053943		1871	4106	5977	SO:0001583	missense	116064	exon3			GATATGTCAGCAA	BC013757	CCDS46892.1	3q13.33	2006-01-06			ENSG00000163428	ENSG00000163428			26968	protein-coding gene	gene with protein product							Standard	NM_001099678		Approved		uc003edr.2	Q96CX6	OTTHUMG00000159407	ENST00000295628.3:c.673A>G	chr3.hg19:g.120053943T>C	ENSP00000295628:p.Thr225Ala	53.0	0.0		73.0	4.0	NM_001099678		Missense_Mutation	SNP	ENST00000295628.3	hg19	CCDS46892.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.566493	0.45694	.	.	ENSG00000163428	ENST00000295628	T	0.27104	1.69	5.37	4.14	0.48551	.	0.045963	0.85682	D	0.000000	T	0.23727	0.0574	M	0.72894	2.215	0.51233	D	0.999914	P	0.38827	0.649	B	0.36186	0.219	T	0.03231	-1.1058	10	0.12766	T	0.61	-6.669	9.2641	0.37630	0.1605:0.0:0.0:0.8395	.	225	Q96CX6	LRC58_HUMAN	A	225	ENSP00000295628:T225A	ENSP00000295628:T225A	T	-	1	0	LRRC58	121536633	1.000000	0.71417	0.998000	0.56505	0.921000	0.55340	5.840000	0.69402	2.036000	0.60181	0.533000	0.62120	ACA	.	.		0.348	LRRC58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355142.1	XM_057296		C	120053943	T	C	120053943	3	2	65	1	0	0	0	0	1	0	0	0	9023	1667	58	2	450	2	LRRC58	3	120053943	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	920812	120053943	77968487	85	8158										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	120941989	120941989	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aatttctaactttatgtgaaAcgccctatccaaatggtaag	6	8	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:120941989A>G	ENST00000273666.6	+	11	1367	c.1096A>G	c.(1096-1098)Acg>Gcg	p.T366A	STXBP5L_ENST00000492541.1_Missense_Mutation_p.T366A|STXBP5L_ENST00000471454.1_Missense_Mutation_p.T366A|STXBP5L_ENST00000472879.1_Missense_Mutation_p.T366A|STXBP5L_ENST00000497029.1_Missense_Mutation_p.T366A	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	366					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		TTTATGTGAAACGCCCTATCC	0.294																																					p.T366A		Atlas-SNP	.											.	STXBP5L	159	.	0			c.A1096G						.						113	106	108					3																	120941989		1842	4091	5933	SO:0001583	missense	9515	exon11			TGTGAAACGCCCT	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.1096A>G	chr3.hg19:g.120941989A>G	ENSP00000273666:p.Thr366Ala	72.0	0.0		60.0	4.0	NM_014980	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	hg19	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	A	18.11	3.550852	0.65311	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.37752	1.87;1.87;1.67;1.18;1.67;1.88	4.5	4.5	0.54988	WD40 repeat-like-containing domain (1);Lethal giant larvae homologue 2 (1);	0.000000	0.85682	D	0.000000	T	0.48370	0.1496	L	0.37800	1.135	0.80722	D	1	P;D	0.71674	0.693;0.998	B;D	0.80764	0.41;0.994	T	0.42050	-0.9474	10	0.39692	T	0.17	-19.3352	13.9784	0.64287	1.0:0.0:0.0:0.0	.	366;366	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	A	366	ENSP00000273666:T366A;ENSP00000420019:T366A;ENSP00000419627:T366A;ENSP00000420287:T366A;ENSP00000420666:T366A;ENSP00000420167:T366A	ENSP00000273666:T366A	T	+	1	0	STXBP5L	122424679	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.139000	0.94554	1.878000	0.54408	0.379000	0.24179	ACG	.	.		0.294	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			G	120941989	A	G	120941989	3	3	65	1	0	0	0	0	1	0	0	0	15372	43	2	2	1134	2	STXBP5L	3	120941989	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	888046	120941989	77080441	86	8159										
UROC1	131669	hgsc.bcm.edu	37	chr3	126229602	126229602	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gccagcagctcctggacatcCggggggaagtagcgcagggc	17	12	0	0	rs557996880		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:126229602C>T	ENST00000290868.2	-	2	215	c.162G>A	c.(160-162)ccG>ccA	p.P54P	UROC1_ENST00000383579.3_Silent_p.P54P	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	54					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		CCTGGACATCCGGGGGGAAGT	0.637													C|||	1	0.000199681	0	0	5008	,	,		17990	0		0	False		,,,				2504	0.001				p.P54P		Atlas-SNP	.											.	UROC1	150	.	0			c.G162A						.						52	49	50					3																	126229602		2203	4300	6503	SO:0001819	synonymous_variant	131669	exon2			GACATCCGGGGGG	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"urocanase 1"	613012	"urocanase domain containing 1"			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.162G>A	chr3.hg19:g.126229602C>T		39.0	0.0		45.0	9.0	NM_001165974	E9PE13|Q14C64|Q68CJ7	Silent	SNP	ENST00000290868.2	hg19	CCDS3038.1																																																																																			.	.		0.637	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639		T	126229602	C	T	126229602	2	4	65	1	0	0	0	0	0	0	0	1	17043	639	23	1		1	UROC1	3	126229602	Silent	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	5287613	126229602	71792828	87	8160										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129291728	129291728	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acttgccctccttagaggcgTtcacggtcaccacacctgag	9	15	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:129291728T>C	ENST00000324093.4	-	14	3072	c.2894A>G	c.(2893-2895)aAc>aGc	p.N965S	PLXND1_ENST00000393239.1_Missense_Mutation_p.N965S	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	965	IPT/TIG 1.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						CTTAGAGGCGTTCACGGTCAC	0.687																																					p.N965S	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.A2894G						.						67	57	61					3																	129291728		2203	4300	6503	SO:0001583	missense	23129	exon14			GAGGCGTTCACGG	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.2894A>G	chr3.hg19:g.129291728T>C	ENSP00000317128:p.Asn965Ser	66.0	0.0		94.0	4.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.687798	0.29962	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.77098	-1.07;-1.07	5.1	5.1	0.69264	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.339429	0.30210	N	0.010145	T	0.70237	0.3201	L	0.28458	0.855	0.40700	D	0.982472	P	0.45428	0.858	P	0.47705	0.555	T	0.66999	-0.5781	10	0.08381	T	0.77	.	13.4772	0.61316	0.0:0.0:0.0:1.0	.	965	Q9Y4D7	PLXD1_HUMAN	S	965	ENSP00000317128:N965S;ENSP00000376931:N965S	ENSP00000317128:N965S	N	-	2	0	PLXND1	130774418	0.998000	0.40836	0.997000	0.53966	0.330000	0.28571	3.838000	0.55828	1.916000	0.55485	0.533000	0.62120	AAC	.	.		0.687	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		C	129291728	T	C	129291728	3	2	65	1	0	0	0	0	1	0	0	0	12136	1725	60	2	2975	2	PLXND1	3	129291728	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3062126	129291728	68730702	88	8161										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130098302	130098302	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agaaagattcactcgctgacCtcgtgttcctggtggatgag	12	9	1	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:130098302C>A	ENST00000432398.2	+	4	1203	c.709C>A	c.(709-711)Ctc>Atc	p.L237I	COL6A5_ENST00000265379.6_Missense_Mutation_p.L237I	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	237	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						ACTCGCTGACCTCGTGTTCCT	0.463																																					p.L237I		Atlas-SNP	.											.	COL6A5	205	.	0			c.C709A						.						65	55	58					3																	130098302		692	1591	2283	SO:0001583	missense	256076	exon4			GCTGACCTCGTGT	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.709C>A	chr3.hg19:g.130098302C>A	ENSP00000390895:p.Leu237Ile	163.0	0.0		201.0	90.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.	.	.	.	.	.	.	.	.	.	C	4.968	0.179746	0.09443	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.81247	-1.47;-1.47	5.31	-2.66	0.06077	.	.	.	.	.	T	0.53012	0.1770	N	0.04373	-0.215	0.23050	N	0.998372	B	0.15719	0.014	B	0.16722	0.016	T	0.48364	-0.9042	9	0.02654	T	1	.	9.4981	0.38999	0.4544:0.1671:0.3785:0.0	.	237	A8TX70-2	.	I	237	ENSP00000390895:L237I;ENSP00000265379:L237I	ENSP00000265379:L237I	L	+	1	0	COL6A5	131580992	0.046000	0.20272	0.030000	0.17652	0.147000	0.21601	0.094000	0.15107	-0.321000	0.08627	-0.302000	0.09304	CTC	.	.		0.463	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		A	130098302	C	A	130098302	3	1	65	1	0	0	0	0	1	0	0	0	3704	681	24	3	719	3	COL6A5	3	130098302	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	806574	130098302	67924128	89	8162										
ASTE1	28990	hgsc.bcm.edu	37	chr3	130735014	130735014	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aggtctggctctgggagaggAgtggacagcagctggttgag	19	6	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:130735014A>G	ENST00000264992.3	-	5	2124	c.1683T>C	c.(1681-1683)acT>acC	p.T561T	ATP2C1_ENST00000504381.1_Missense_Mutation_p.S870G|ASTE1_ENST00000514044.1_Silent_p.T561T|ATP2C1_ENST00000533801.2_Missense_Mutation_p.S920G|ATP2C1_ENST00000328560.8_Missense_Mutation_p.E883G|ATP2C1_ENST00000359644.3_Missense_Mutation_p.S925G|ATP2C1_ENST00000422190.2_Missense_Mutation_p.S915G|ATP2C1_ENST00000507488.2_Missense_Mutation_p.S899G|ATP2C1_ENST00000513801.1_Missense_Mutation_p.S899G|ATP2C1_ENST00000393221.4_Missense_Mutation_p.S949G	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	561					DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						CTGGGAGAGGAGTGGACAGCA	0.468																																					p.S949G		Atlas-SNP	.											.	ATP2C1	94	.	0			c.A2845G						.						115	106	109					3																	130735014		2203	4300	6503	SO:0001819	synonymous_variant	27032	exon28			GAGAGGAGTGGAC	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.1683T>C	chr3.hg19:g.130735014A>G		74.0	0.0		105.0	5.0	NM_001199180	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Missense_Mutation	SNP	ENST00000264992.3	hg19	CCDS3068.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.343|9.343	1.063646|1.063646	0.20067|0.20067	.|.	.|.	ENSG00000017260|ENSG00000017260	ENST00000328560|ENST00000504381;ENST00000507488;ENST00000393221;ENST00000533801;ENST00000513801;ENST00000359644;ENST00000422190;ENST00000347421	D|D;D;D;D;D;D;D	0.92699|0.92495	-3.09|-3.04;-3.0;-3.0;-3.05;-3.0;-2.99;-3.0	5.71|5.71	-11.4|-11.4	0.00090|0.00090	.|.	.|.	.|.	.|.	.|.	T|T	0.80259|0.80259	0.4590|0.4590	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B|B;B;B;B	0.02656|0.02656	0.0|0.0;0.0;0.0;0.0	B|B;B;B;B	0.01281|0.01281	0.0|0.0;0.0;0.0;0.0	T|T	0.47649|0.47649	-0.9101|-0.9101	8|7	0.06365|.	T|.	0.9|.	-4.0654|-4.0654	6.6922|6.6922	0.23179|0.23179	0.135:0.5575:0.1563:0.1512|0.135:0.5575:0.1563:0.1512	.|.	883|949;920;915;949	P98194-2|G3XAH8;B4DSW3;P98194-5;B7Z3X9	.|.;.;.;.	G|G	883|870;899;949;920;899;925;915;934	ENSP00000329664:E883G|ENSP00000425320:S870G;ENSP00000421326:S899G;ENSP00000376914:S949G;ENSP00000432956:S920G;ENSP00000422872:S899G;ENSP00000352665:S925G;ENSP00000402677:S915G	ENSP00000329664:E883G|.	E|S	+|+	2|1	0|0	ATP2C1|ATP2C1	132217704|132217704	0.000000|0.000000	0.05858|0.05858	0.021000|0.021000	0.16686|0.16686	0.328000|0.328000	0.28507|0.28507	-1.785000|-1.785000	0.01767|0.01767	-3.068000|-3.068000	0.00254|0.00254	-0.250000|-0.250000	0.11733|0.11733	GAG|AGT	.	.		0.468	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		G	130735014	A	G	130735014	2	3	65	1	0	0	0	0	0	0	0	1	1062	304	11	2		2	ASTE1	3	130735014	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	636712	130735014	67287416	90	8163										
SR140	23350	hgsc.bcm.edu	37	chr3	142740318	142740318	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttttctttctgccctagttcTtgatgattacgcacctggct	7	11	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:142740318T>C	ENST00000473835.2	+	10	863	c.773T>C	c.(772-774)cTt>cCt	p.L258P	U2SURP_ENST00000397933.2_5'UTR|U2SURP_ENST00000493598.2_Missense_Mutation_p.L257P	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	258					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						GCCCTAGTTCTTGATGATTAC	0.328																																					p.L258P		Atlas-SNP	.											.	U2SURP	66	.	0			c.T773C						.						81	72	75					3																	142740318		1822	4085	5907	SO:0001583	missense	23350	exon10			TAGTTCTTGATGA	BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"RNA binding motif (RRM) containing"	30855	protein-coding gene	gene with protein product	"functional spliceosome-associated protein a", "Ser/Arg-rich domain protein, 140 kDa", "U2 associated SR140 protein"					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.773T>C	chr3.hg19:g.142740318T>C	ENSP00000418563:p.Leu258Pro	152.0	0.0		98.0	4.0	NM_001080415	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Missense_Mutation	SNP	ENST00000473835.2	hg19	CCDS46928.1	.	.	.	.	.	.	.	.	.	.	T	13.97	2.394831	0.42512	.	.	ENSG00000163714	ENST00000473835;ENST00000319822;ENST00000493598	T;T	0.11277	2.79;2.79	5.55	5.55	0.83447	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.11367	0.0277	L	0.41236	1.265	0.80722	D	1	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.0;0.004;0.001	T	0.08371	-1.0725	10	0.29301	T	0.29	-15.9505	15.7038	0.77563	0.0:0.0:0.0:1.0	.	258;257;258	B4DK81;O15042-2;O15042	.;.;SR140_HUMAN	P	258;258;257	ENSP00000418563:L258P;ENSP00000422011:L257P	ENSP00000322376:L258P	L	+	2	0	U2SURP	144223008	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	7.698000	0.84413	2.105000	0.64084	0.383000	0.25322	CTT	.	.		0.328	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415		C	142740318	T	C	142740318	3	2	65	1	0	0	0	0	1	0	0	0	15146	1609	56	2	811	2	SR140	3	142740318	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	12005304	142740318	55282112	91	8164										
LRRIQ4	344657	hgsc.bcm.edu	37	chr3	169548290	169548290	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gttatttcagagtctcaaagAgctatatatagagaacaatc	7	6	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:169548290A>G	ENST00000340806.6	+	3	1205	c.1205A>G	c.(1204-1206)gAg>gGg	p.E402G		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	402										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						AGTCTCAAAGAGCTATATATA	0.368																																					p.E402G		Atlas-SNP	.											.	LRRIQ4	68	.	0			c.A1205G						.						46	44	45					3																	169548290		1831	4088	5919	SO:0001583	missense	344657	exon3			TCAAAGAGCTATA		CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"leucine rich repeat containing 64"						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.1205A>G	chr3.hg19:g.169548290A>G	ENSP00000342188:p.Glu402Gly	62.0	0.0		66.0	4.0	NM_001080460		Missense_Mutation	SNP	ENST00000340806.6	hg19	CCDS46951.1	.	.	.	.	.	.	.	.	.	.	A	15.60	2.881762	0.51908	.	.	ENSG00000188306	ENST00000340806	T	0.59772	0.24	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000001	T	0.70133	0.3189	L	0.49699	1.58	0.45183	D	0.99819	D	0.89917	1.0	D	0.91635	0.999	T	0.66131	-0.6000	10	0.25751	T	0.34	.	15.8917	0.79303	1.0:0.0:0.0:0.0	.	402	A6NIV6	LRIQ4_HUMAN	G	402	ENSP00000342188:E402G	ENSP00000342188:E402G	E	+	2	0	LRRIQ4	171030984	1.000000	0.71417	0.999000	0.59377	0.080000	0.17528	6.302000	0.72788	2.228000	0.72767	0.533000	0.62120	GAG	.	.		0.368	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460		G	169548290	A	G	169548290	3	3	65	1	0	0	0	0	1	0	0	0	9040	304	11	2	1215	2	LRRIQ4	3	169548290	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	26807972	169548290	28474140	92	8165										
MFN1	55669	hgsc.bcm.edu	37	chr3	179095207	179095207	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tttgttcagagtttcatcctAatccagatgtattaaaaata	5	6	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:179095207A>G	ENST00000471841.1	+	12	1426	c.1300A>G	c.(1300-1302)Aat>Gat	p.N434D	MFN1_ENST00000280653.7_Missense_Mutation_p.N434D|MFN1_ENST00000263969.5_Missense_Mutation_p.N434D	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	434					mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			GTTTCATCCTAATCCAGATGT	0.279																																					p.N434D		Atlas-SNP	.											.	MFN1	72	.	0			c.A1300G						.						68	71	70					3																	179095207		2198	4294	6492	SO:0001583	missense	55669	exon12			CATCCTAATCCAG	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.1300A>G	chr3.hg19:g.179095207A>G	ENSP00000420617:p.Asn434Asp	107.0	0.0		96.0	4.0	NM_033540	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Missense_Mutation	SNP	ENST00000471841.1	hg19	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	A	12.59	1.983662	0.35036	.	.	ENSG00000171109	ENST00000471841;ENST00000280653;ENST00000539169;ENST00000263969;ENST00000474903	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	5.49	2.92	0.33932	.	0.198932	0.56097	D	0.000036	T	0.65217	0.2670	N	0.04203	-0.255	0.28201	N	0.927348	B;B;B	0.19817	0.039;0.028;0.028	B;B;B	0.15484	0.008;0.013;0.008	T	0.53725	-0.8398	10	0.19147	T	0.46	-7.8035	9.1892	0.37189	0.4081:0.0:0.0:0.5919	.	434;462;434	Q8IWA4-3;Q4AEJ4;Q8IWA4	.;.;MFN1_HUMAN	D	434;434;434;434;297	ENSP00000420617:N434D;ENSP00000280653:N434D;ENSP00000263969:N434D;ENSP00000419926:N297D	ENSP00000263969:N434D	N	+	1	0	MFN1	180577901	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.258000	0.58822	0.880000	0.35969	0.482000	0.46254	AAT	.	.		0.279	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		G	179095207	A	G	179095207	3	3	65	1	0	0	0	0	1	0	0	0	9532	362	13	2	1342	2	MFN1	3	179095207	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	9546917	179095207	18927223	93	8166										
CCDC39	339829	hgsc.bcm.edu	37	chr3	180361933	180361933	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	taaaacctttggctttatcaAgttctttctctgatctgtcg	6	9	4	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:180361933A>G	ENST00000442201.2	-	12	1759	c.1640T>C	c.(1639-1641)cTt>cCt	p.L547P	CCDC39_ENST00000273654.4_Missense_Mutation_p.L631P	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	547					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)		p.L631R(1)|p.L547R(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			GGCTTTATCAAGTTCTTTCTC	0.308																																					p.L547P		Atlas-SNP	.											CCDC39_ENST00000442201,caecum,carcinoma,0,2	CCDC39	242	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1640C						.						160	145	150					3																	180361933		1488	3303	4791	SO:0001583	missense	339829	exon12			TTATCAAGTTCTT	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.1640T>C	chr3.hg19:g.180361933A>G	ENSP00000405708:p.Leu547Pro	97.0	0.0		81.0	5.0	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	hg19	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	A	14.59	2.581707	0.46006	.	.	ENSG00000145075	ENST00000273654;ENST00000442201	T;T	0.23552	1.9;1.9	5.56	5.56	0.83823	.	0.162313	0.41396	D	0.000899	T	0.53899	0.1825	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.59295	-0.7481	10	0.72032	D	0.01	-5.8948	15.0019	0.71479	1.0:0.0:0.0:0.0	.	547	Q9UFE4	CCD39_HUMAN	P	631;547	ENSP00000273654:L631P;ENSP00000405708:L547P	ENSP00000273654:L631P	L	-	2	0	CCDC39	181844627	0.999000	0.42202	0.926000	0.36857	0.128000	0.20619	5.752000	0.68728	2.240000	0.73641	0.533000	0.62120	CTT	.	.		0.308	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		G	180361933	A	G	180361933	3	3	65	1	0	0	0	0	1	0	0	0	2813	72	3	2	1221	2	CCDC39	3	180361933	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1266726	180361933	17660497	94	8167										
ABCC5	10057	hgsc.bcm.edu	37	chr3	183655819	183655819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tccagataactccaccagacGgaagagggccatccccagcg	10	15	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr3:183655819G>A	ENST00000334444.6	-	26	3964	c.3724C>T	c.(3724-3726)Cgt>Tgt	p.R1242C	ABCC5_ENST00000265586.6_Missense_Mutation_p.R1199C	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	1242	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	TCCACCAGACGGAAGAGGGCC	0.507																																					p.R1242C		Atlas-SNP	.											.	ABCC5	142	.	0			c.C3724T						.						90	89	89					3																	183655819		2022	4196	6218	SO:0001583	missense	10057	exon26			CCAGACGGAAGAG	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.3724C>T	chr3.hg19:g.183655819G>A	ENSP00000333926:p.Arg1242Cys	126.0	0.0		124.0	27.0	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Missense_Mutation	SNP	ENST00000334444.6	hg19	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516365	0.85495	.	.	ENSG00000114770	ENST00000334444;ENST00000265586	D;D	0.92397	-3.03;-3.03	5.73	5.73	0.89815	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.054165	0.85682	D	0.000000	D	0.97021	0.9027	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97312	0.9938	10	0.87932	D	0	-12.7027	19.8948	0.96954	0.0:0.0:1.0:0.0	.	1199;1242	Q86UX3;O15440	.;MRP5_HUMAN	C	1242;1199	ENSP00000333926:R1242C;ENSP00000265586:R1199C	ENSP00000265586:R1199C	R	-	1	0	ABCC5	185138513	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	4.345000	0.59360	2.699000	0.92147	0.655000	0.94253	CGT	.	.		0.507	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		A	183655819	G	A	183655819	3	1	65	1	0	0	0	0	1	0	0	0	56	1116	39	1	609	1	ABCC5	3	183655819	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	3293886	183655819	14366611	95	8168										
PPP2R2C	5522	hgsc.bcm.edu	37	chr4	6377634	6377634	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gccttttatctcgttcggtaAtcttccataatttgatagtt	6	8	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:6377634A>T	ENST00000382599.4	-	4	575	c.359T>A	c.(358-360)aTt>aAt	p.I120N	PPP2R2C_ENST00000507294.1_Missense_Mutation_p.I113N|PPP2R2C_ENST00000314348.8_5'UTR|PPP2R2C_ENST00000506140.1_Missense_Mutation_p.I113N|PPP2R2C_ENST00000335585.5_Missense_Mutation_p.I120N|PPP2R2C_ENST00000515571.1_Missense_Mutation_p.I103N			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	120					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						TCGTTCGGTAATCTTCCATAA	0.428																																					p.I120N		Atlas-SNP	.											.	PPP2R2C	63	.	0			c.T359A						.						118	119	119					4																	6377634		2203	4300	6503	SO:0001583	missense	5522	exon4			TCGGTAATCTTCC	AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9306	protein-coding gene	gene with protein product	"PP2A subunit B isoform gamma"	605997	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform"			10574460, 10945473	Standard	NM_020416		Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.359T>A	chr4.hg19:g.6377634A>T	ENSP00000372042:p.Ile120Asn	208.0	0.0		190.0	92.0	NM_181876	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Missense_Mutation	SNP	ENST00000382599.4	hg19		.	.	.	.	.	.	.	.	.	.	A	22.9	4.343812	0.82022	.	.	ENSG00000074211	ENST00000335585;ENST00000506140;ENST00000515571;ENST00000382599;ENST00000507294	T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42	4.32	4.32	0.51571	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.182769	0.48767	D	0.000167	T	0.54415	0.1857	M	0.75447	2.3	0.58432	D	0.999998	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;1.0	D;D;D;D;D	0.87578	0.996;0.998;0.993;0.993;0.993	T	0.60239	-0.7302	10	0.87932	D	0	-24.9874	13.1313	0.59385	1.0:0.0:0.0:0.0	.	113;216;120;103;120	B7Z3Y1;Q59GC6;Q9Y2T4;Q9Y2T4-3;Q9Y2T4-2	.;.;2ABG_HUMAN;.;.	N	120;113;103;120;113	ENSP00000335083:I120N;ENSP00000423649:I113N;ENSP00000422374:I103N;ENSP00000372042:I120N;ENSP00000425247:I113N	ENSP00000335083:I120N	I	-	2	0	PPP2R2C	6428535	1.000000	0.71417	0.911000	0.35937	0.984000	0.73092	8.404000	0.90210	1.937000	0.56155	0.459000	0.35465	ATT	.	.		0.428	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876		T	6377634	A	T	6377634	3	4	65	1	0	0	0	0	1	0	0	0	12398	101	4	4	1008	4	PPP2R2C	4	6377634	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10		6377634	184776642	96	8169										
WDR1	9948	hgsc.bcm.edu	37	chr4	10090367	10090367	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgacaaagcggctgtggtccTgcaggaaaacaattacctgc	11	10	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:10090367T>C	ENST00000499869.2	-	6	752		c.e6-2		WDR1_ENST00000382451.2_Splice_Site|WDR1_ENST00000515743.1_Splice_Site|WDR1_ENST00000382452.2_Splice_Site|WDR1_ENST00000502702.1_Splice_Site			O75083	WDR1_HUMAN	WD repeat domain 1						blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		GCTGTGGTCCTGCAGGAAAAC	0.522																																					.		Atlas-SNP	.											.	WDR1	93	.	0			c.139-2A>G						.						37	39	38					4																	10090367		1969	4158	6127	SO:0001630	splice_region_variant	9948	exon4			TGGTCCTGCAGGA	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"WD repeat domain containing"	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.559-2A>G	chr4.hg19:g.10090367T>C		66.0	0.0		70.0	5.0	NM_005112	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Splice_Site	SNP	ENST00000499869.2	hg19	CCDS54740.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384800	0.82792	.	.	ENSG00000071127	ENST00000499869;ENST00000382452;ENST00000382451;ENST00000443592;ENST00000502702;ENST00000439733;ENST00000508079	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6845	0.69040	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR1	9699465	1.000000	0.71417	0.987000	0.45799	0.952000	0.60782	7.389000	0.79806	2.065000	0.61736	0.383000	0.25322	.	.	.		0.522	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1		Intron	C	10090367	T	C	10090367	5	2	65	1	0	0	0	0	0	0	1	0	17287	1594	55	2	1303	2	WDR1	4	10090367	Splice_Site	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3712733	10090367	181063909	97	8170										
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15539668	15539668	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gagcaggaggtgagggagagAgcagcccagagcaggaggag	21	6	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:15539668A>G	ENST00000503292.1	+	17	2091	c.1911A>G	c.(1909-1911)agA>agG	p.R637R	CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000389652.5_Silent_p.R588R|CC2D2A_ENST00000424120.1_Silent_p.R637R|CC2D2A_ENST00000413206.1_Silent_p.R637R	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	637					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						TGAGGGAGAGAGCAGCCCAGA	0.627																																					p.R637R		Atlas-SNP	.											.	CC2D2A	158	.	0			c.A1911G						.						42	52	48					4																	15539668		2173	4278	6451	SO:0001819	synonymous_variant	57545	exon17			GGAGAGAGCAGCC	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.1911A>G	chr4.hg19:g.15539668A>G		84.0	0.0		117.0	5.0	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	hg19	CCDS47026.1																																																																																			.	.		0.627	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		G	15539668	A	G	15539668	2	3	65	1	0	0	0	0	0	0	0	1	2730	301	11	2		2	CC2D2A	4	15539668	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	5449301	15539668	175614608	98	8171										
PPARGC1A	10891	hgsc.bcm.edu	37	chr4	23816124	23816124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	actgtacctgggcttctttgAtggtggtggcaccacagtct	12	10	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:23816124A>G	ENST00000264867.2	-	8	1101	c.982T>C	c.(982-984)Tca>Cca	p.S328P	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	328	Interaction with PPARG.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				GGCTTCTTTGATGGTGGTGGC	0.502																																					p.S328P	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.T982C						.						129	132	131					4																	23816124		2203	4300	6503	SO:0001583	missense	10891	exon8			TCTTTGATGGTGG	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"RNA binding motif (RRM) containing"	9237	protein-coding gene	gene with protein product		604517	"peroxisome proliferative activated receptor, gamma, coactivator 1", "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.982T>C	chr4.hg19:g.23816124A>G	ENSP00000264867:p.Ser328Pro	100.0	0.0		79.0	4.0	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	hg19	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	A	10.58	1.388839	0.25118	.	.	ENSG00000109819	ENST00000264867	T	0.26957	1.7	6.06	2.11	0.27256	.	0.444709	0.24156	N	0.041025	T	0.11707	0.0285	N	0.13003	0.285	0.80722	D	1	P	0.48764	0.915	B	0.37650	0.255	T	0.10613	-1.0622	10	0.36615	T	0.2	-0.055	7.3728	0.26810	0.5074:0.1224:0.0:0.3702	.	328	Q9UBK2	PRGC1_HUMAN	P	328	ENSP00000264867:S328P	ENSP00000264867:S328P	S	-	1	0	PPARGC1A	23425222	0.972000	0.33761	0.581000	0.28614	0.915000	0.54546	1.094000	0.30951	0.126000	0.18424	-0.336000	0.08194	TCA	.	.		0.502	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261		G	23816124	A	G	23816124	3	3	65	1	0	0	0	0	1	0	0	0	12309	333	12	2	1438	2	PPARGC1A	4	23816124	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	8276456	23816124	167338152	99	8172										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30724545	30724545	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	actatgaggccacccgggagTtcaacgtggtcatcgtggcg	14	11	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:30724545T>C	ENST00000361762.2	+	1	2509	c.1501T>C	c.(1501-1503)Ttc>Ctc	p.F501L	PCDH7_ENST00000543491.1_Missense_Mutation_p.F501L	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	501	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						CACCCGGGAGTTCAACGTGGT	0.592																																					p.F501L		Atlas-SNP	.											.	PCDH7	215	.	0			c.T1501C						.						73	60	65					4																	30724545		2203	4300	6503	SO:0001583	missense	5099	exon1			CGGGAGTTCAACG	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1501T>C	chr4.hg19:g.30724545T>C	ENSP00000355243:p.Phe501Leu	62.0	0.0		73.0	4.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.45|16.45	3.125807|3.125807	0.56721|0.56721	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000361762;ENST00000543491;ENST00000333135|ENST00000511884	T;T|.	0.52983|.	0.64;0.64|.	5.26|5.26	5.26|5.26	0.73747|0.73747	Cadherin (4);Cadherin-like (1);|.	.|.	.|.	.|.	.|.	T|T	0.53818|0.53818	0.1820|0.1820	L|L	0.27053|0.27053	0.805|0.805	0.58432|0.58432	D|D	0.999993|0.999993	B;B;B|.	0.22604|.	0.059;0.059;0.072|.	B;B;B|.	0.32980|.	0.097;0.097;0.156|.	T|T	0.50668|0.50668	-0.8801|-0.8801	9|5	0.87932|.	D|.	0|.	.|.	15.3401|15.3401	0.74290|0.74290	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	501;454;501|.	F5GWJ1;O60245-3;O60245|.	.;.;PCDH7_HUMAN|.	L|A	501;501;454|190	ENSP00000355243:F501L;ENSP00000441802:F501L|.	ENSP00000330302:F454L|.	F|V	+|+	1|2	0|0	PCDH7|PCDH7	30333643|30333643	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.868000|7.868000	0.87116|0.87116	2.208000|2.208000	0.71279|0.71279	0.533000|0.533000	0.62120|0.62120	TTC|GTT	.	.		0.592	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		C	30724545	T	C	30724545	3	2	65	1	0	0	0	0	1	0	0	0	11525	1725	60	2	1503	2	PCDH7	4	30724545	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6908421	30724545	160429731	100	8173										
ARAP2	116984	hgsc.bcm.edu	37	chr4	36069848	36069848	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttaagctagagtccacggacTctttatcacacttttcactg	6	11	3	1	rs202134005		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:36069848T>C	ENST00000303965.4	-	33	5285	c.4796A>G	c.(4795-4797)gAg>gGg	p.E1599G		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1599					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						GTCCACGGACTCTTTATCACA	0.458																																					p.E1599G		Atlas-SNP	.											.	ARAP2	210	.	0			c.A4796G						.						78	82	81					4																	36069848		2203	4300	6503	SO:0001583	missense	116984	exon33			ACGGACTCTTTAT	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.4796A>G	chr4.hg19:g.36069848T>C	ENSP00000302895:p.Glu1599Gly	59.0	0.0		57.0	4.0	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	hg19	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	T	5.928	0.355203	0.11239	.	.	ENSG00000047365	ENST00000303965	T	0.10099	2.91	6.08	-0.583	0.11706	.	0.707951	0.14215	N	0.333783	T	0.05502	0.0145	L	0.29908	0.895	0.09310	N	1	P	0.36282	0.546	B	0.30401	0.115	T	0.30534	-0.9975	10	0.62326	D	0.03	.	1.3284	0.02130	0.133:0.2237:0.1386:0.5047	.	1599	Q8WZ64	ARAP2_HUMAN	G	1599	ENSP00000302895:E1599G	ENSP00000302895:E1599G	E	-	2	0	ARAP2	35746243	0.309000	0.24518	0.000000	0.03702	0.001000	0.01503	1.463000	0.35277	-0.270000	0.09285	-1.137000	0.01932	GAG	.	T|0.999;A|0.001		0.458	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		C	36069848	T	C	36069848	3	2	65	1	0	0	0	0	1	0	0	0	839	1551	54	2	322	2	ARAP2	4	36069848	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	5345303	36069848	155084428	101	8174										
AFP	174	hgsc.bcm.edu	37	chr4	74308085	74308085	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cttctttgggctgctcgctaTgacaaaataattccatcttg	7	10	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:74308085T>C	ENST00000395792.2	+	5	655	c.555T>C	c.(553-555)taT>taC	p.Y185Y	AFP_ENST00000226359.2_Silent_p.Y185Y	NM_001134.1	NP_001125.1	P02771	FETA_HUMAN	alpha-fetoprotein	185	Albumin 1. {ECO:0000255|PROSITE- ProRule:PRU00769}.				ovulation from ovarian follicle (GO:0001542)|progesterone metabolic process (GO:0042448)|SMAD protein signal transduction (GO:0060395)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(3)|lung(13)|ovary(1)|skin(1)|urinary_tract(1)	22	Breast(15;0.00102)		Epithelial(6;2.42e-05)|all cancers(17;0.000268)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTGCTCGCTATGACAAAATAA	0.383									Alpha-Fetoprotein, Hereditary Persistence of																												p.Y185Y		Atlas-SNP	.											.	AFP	60	.	0			c.T555C						.						97	92	94					4																	74308085		2203	4300	6503	SO:0001819	synonymous_variant	174	exon5	Familial Cancer Database	HPAFP	TCGCTATGACAAA	V01514	CCDS3556.1	4q13.3	2012-05-16			ENSG00000081051	ENSG00000081051			317	protein-coding gene	gene with protein product		104150		HPAFP			Standard	NM_001134		Approved	FETA	uc003hgz.1	P02771	OTTHUMG00000130011	ENST00000395792.2:c.555T>C	chr4.hg19:g.74308085T>C		114.0	0.0		63.0	4.0	NM_001134	B2RBU3	Silent	SNP	ENST00000395792.2	hg19	CCDS3556.1																																																																																			.	.		0.383	AFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252284.3			C	74308085	T	C	74308085	2	2	65	1	0	0	0	0	0	0	0	1	363	1471	51	2		2	AFP	4	74308085	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	38238237	74308085	116846191	102	8175										
SDAD1	55153	hgsc.bcm.edu	37	chr4	76882410	76882410	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gccaggtcttggagaagttcTtcagtcatggccagaggaca	13	9	4	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:76882410T>C	ENST00000356260.5	-	15	1351	c.1233A>G	c.(1231-1233)gaA>gaG	p.E411E	SDAD1_ENST00000513089.1_5'UTR|SDAD1_ENST00000395711.4_Silent_p.E374E	NM_018115.2	NP_060585.2	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	411					actin cytoskeleton organization (GO:0030036)|protein transport (GO:0015031)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal large subunit export from nucleus (GO:0000055)	nucleolus (GO:0005730)				breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	19			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GGAGAAGTTCTTCAGTCATGG	0.383																																					p.E411E		Atlas-SNP	.											.	SDAD1	47	.	0			c.A1233G						.						147	133	138					4																	76882410		2203	4300	6503	SO:0001819	synonymous_variant	55153	exon15			AAGTTCTTCAGTC	AF132198	CCDS3573.2, CCDS75147.1	4q21.21	2010-11-24			ENSG00000198301	ENSG00000198301			25537	protein-coding gene	gene with protein product						11483580	Standard	NM_001288984		Approved	FLJ10498	uc003hje.4	Q9NVU7	OTTHUMG00000130111	ENST00000356260.5:c.1233A>G	chr4.hg19:g.76882410T>C		142.0	0.0		87.0	4.0	NM_018115	Q32Q11|Q68D52|Q7Z5U4|Q9H831|Q9H9P6	Silent	SNP	ENST00000356260.5	hg19	CCDS3573.2																																																																																			.	.		0.383	SDAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252418.3	NM_018115		C	76882410	T	C	76882410	2	2	65	1	0	0	0	0	0	0	0	1	13965	1606	56	2		2	SDAD1	4	76882410	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2574325	76882410	114271866	103	8176										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79204044	79204044	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggctcaggtaacttgctacgAgccctcttgcccaccatgtc	9	15	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:79204044A>G	ENST00000325942.6	+	12	1618	c.1178A>G	c.(1177-1179)gAg>gGg	p.E393G	FRAS1_ENST00000264899.6_Missense_Mutation_p.E393G|FRAS1_ENST00000264895.6_Missense_Mutation_p.E393G	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	393	VWFC 6. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ACTTGCTACGAGCCCTCTTGC	0.552																																					p.E393G		Atlas-SNP	.											.	FRAS1	779	.	0			c.A1178G						.						82	88	86					4																	79204044		2017	4169	6186	SO:0001583	missense	80144	exon12			GCTACGAGCCCTC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1178A>G	chr4.hg19:g.79204044A>G	ENSP00000326330:p.Glu393Gly	131.0	0.0		97.0	6.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.83|10.83	1.461386|1.461386	0.26248|0.26248	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000264899;ENST00000534913|ENST00000502446	T;T;T|.	0.55588|.	0.51;0.51;0.51|.	5.6|5.6	4.43|4.43	0.53597|0.53597	von Willebrand factor, type C (3);|.	0.378731|.	0.26944|.	N|.	0.021701|.	T|T	0.41465|0.41465	0.1160|0.1160	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	0.999999|0.999999	B;B;P;P|.	0.37914|.	0.088;0.228;0.611;0.61|.	B;B;B;B|.	0.36186|.	0.045;0.071;0.159;0.219|.	T|T	0.30387|0.30387	-0.9980|-0.9980	10|5	0.25751|.	T|.	0.34|.	.|.	6.7757|6.7757	0.23619|0.23619	0.6439:0.281:0.0751:0.0|0.6439:0.281:0.0751:0.0	.|.	393;393;393;393|.	E9PHH6;Q86XX4;E7EWM9;A2RRR8|.	.;FRAS1_HUMAN;.;.|.	G|G	393;393;393;133|322	ENSP00000326330:E393G;ENSP00000264895:E393G;ENSP00000264899:E393G|.	ENSP00000264895:E393G|.	E|S	+|+	2|1	0|0	FRAS1|FRAS1	79423068|79423068	0.986000|0.986000	0.35501|0.35501	0.938000|0.938000	0.37757|0.37757	0.180000|0.180000	0.23129|0.23129	1.302000|1.302000	0.33459|0.33459	2.127000|2.127000	0.65507|0.65507	0.460000|0.460000	0.39030|0.39030	GAG|AGC	.	.		0.552	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			G	79204044	A	G	79204044	3	3	65	1	0	0	0	0	1	0	0	0	6050	304	11	2	1224	2	FRAS1	4	79204044	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2321634	79204044	111950232	104	8177										
PRKG2	5593	hgsc.bcm.edu	37	chr4	82027009	82027009	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cctcaggtcgtcgtgttatcTtcctgggaaaatccattttt	8	10	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:82027009T>C	ENST00000395578.1	-	16	2137	c.2021A>G	c.(2020-2022)aAg>aGg	p.K674R	PRKG2_ENST00000264399.1_Missense_Mutation_p.K674R|PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000545647.1_Missense_Mutation_p.K254R|PRKG2_ENST00000418486.2_Missense_Mutation_p.K645R			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	674	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						TCGTGTTATCTTCCTGGGAAA	0.423																																					p.K674R		Atlas-SNP	.											.	PRKG2	195	.	0			c.A2021G						.						132	126	128					4																	82027009		2203	4300	6503	SO:0001583	missense	5593	exon15			GTTATCTTCCTGG	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.2021A>G	chr4.hg19:g.82027009T>C	ENSP00000378945:p.Lys674Arg	142.0	0.0		92.0	4.0	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Missense_Mutation	SNP	ENST00000395578.1	hg19	CCDS3589.1	.	.	.	.	.	.	.	.	.	.	t	9.445	1.089091	0.20390	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486;ENST00000545647	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	5.41	5.41	0.78517	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.175610	0.64402	D	0.000011	T	0.43590	0.1254	N	0.21617	0.685	0.46203	D	0.998929	B;B	0.06786	0.0;0.001	B;B	0.12837	0.005;0.008	T	0.34700	-0.9818	10	0.19147	T	0.46	-25.3915	7.7601	0.28946	0.1355:0.0:0.1409:0.7236	.	645;674	E7EPE6;Q13237	.;KGP2_HUMAN	R	674;674;645;254	ENSP00000378945:K674R;ENSP00000264399:K674R;ENSP00000389038:K645R;ENSP00000439967:K254R	ENSP00000264399:K674R	K	-	2	0	PRKG2	82246033	0.948000	0.32251	1.000000	0.80357	0.933000	0.57130	1.311000	0.33562	2.064000	0.61679	0.402000	0.26972	AAG	.	.		0.423	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		C	82027009	T	C	82027009	3	2	65	1	0	0	0	0	1	0	0	0	12535	1609	56	2	283	2	PRKG2	4	82027009	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2822965	82027009	109127267	105	8178										
SEC31A	22872	hgsc.bcm.edu	37	chr4	83778913	83778913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	attcttctttttcctctttaAtgtgctaaagagatgaaaaa	5	6	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:83778913A>G	ENST00000395310.2	-	15	1813	c.1631T>C	c.(1630-1632)aTt>aCt	p.I544T	SEC31A_ENST00000432794.1_Missense_Mutation_p.I544T|SEC31A_ENST00000505984.1_Missense_Mutation_p.I505T|SEC31A_ENST00000264405.5_Missense_Mutation_p.I277T|SEC31A_ENST00000500777.2_Missense_Mutation_p.I505T|SEC31A_ENST00000509142.1_Missense_Mutation_p.I544T|SEC31A_ENST00000448323.1_Missense_Mutation_p.I544T|SEC31A_ENST00000508479.1_Missense_Mutation_p.I544T|SEC31A_ENST00000326950.5_Missense_Mutation_p.I505T|SEC31A_ENST00000443462.2_Missense_Mutation_p.I539T|SEC31A_ENST00000348405.4_Missense_Mutation_p.I505T|SEC31A_ENST00000508502.1_Missense_Mutation_p.I544T|SEC31A_ENST00000355196.2_Missense_Mutation_p.I544T|SEC31A_ENST00000311785.7_Missense_Mutation_p.I544T|SEC31A_ENST00000505472.1_Missense_Mutation_p.I544T|SEC31A_ENST00000513858.1_Missense_Mutation_p.I505T	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	544					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)	p.I544T(1)	SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				TTCCTCTTTAATGTGCTAAAG	0.323																																					p.I544T		Atlas-SNP	.											SEC31A_ENST00000395310,NS,malignant_melanoma,0,1	SEC31A	227	.	1	Substitution - Missense(1)	NS(1)	c.T1631C						.						92	97	96					4																	83778913		2203	4300	6503	SO:0001583	missense	22872	exon15			TCTTTAATGTGCT	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.1631T>C	chr4.hg19:g.83778913A>G	ENSP00000378721:p.Ile544Thr	50.0	0.0		21.0	2.0	NM_001077206	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Missense_Mutation	SNP	ENST00000395310.2	hg19	CCDS3596.1	.	.	.	.	.	.	.	.	.	.	A	0.943	-0.709004	0.03230	.	.	ENSG00000138674	ENST00000348405;ENST00000513858;ENST00000395310;ENST00000443462;ENST00000509142;ENST00000432794;ENST00000448323;ENST00000326950;ENST00000311785;ENST00000505472;ENST00000500777;ENST00000508502;ENST00000355196;ENST00000264405;ENST00000505984;ENST00000508479;ENST00000510167	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.37058	1.43;1.27;2.46;2.47;1.31;2.35;2.46;1.43;1.31;1.22;1.27;2.46;2.46;3.31;2.42;2.34;2.29	5.85	0.223	0.15292	.	0.923261	0.09376	N	0.810635	T	0.15696	0.0378	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B;B;B;B	0.15473	0.0;0.0;0.0;0.013;0.0;0.012;0.001;0.0;0.001	B;B;B;B;B;B;B;B;B	0.13407	0.001;0.0;0.001;0.009;0.001;0.009;0.002;0.001;0.004	T	0.31861	-0.9928	10	0.02654	T	1	-0.7542	1.8387	0.03145	0.5093:0.1293:0.2359:0.1255	.	539;505;544;505;505;544;544;544;277	B4DIW6;B7ZL00;D6RHZ5;O94979-6;O94979-4;O94979-3;O94979-2;O94979;O94979-7	.;.;.;.;.;.;.;SC31A_HUMAN;.	T	505;505;544;539;544;544;544;505;544;544;505;544;544;277;505;544;132	ENSP00000337602:I505T;ENSP00000426886:I505T;ENSP00000378721:I544T;ENSP00000408027:I539T;ENSP00000426569:I544T;ENSP00000407944:I544T;ENSP00000400926:I544T;ENSP00000325087:I505T;ENSP00000309070:I544T;ENSP00000421633:I544T;ENSP00000421464:I505T;ENSP00000424635:I544T;ENSP00000347329:I544T;ENSP00000264405:I277T;ENSP00000424451:I505T;ENSP00000425999:I544T;ENSP00000422267:I132T	ENSP00000264405:I277T	I	-	2	0	SEC31A	83997937	0.000000	0.05858	0.402000	0.26371	0.850000	0.48378	0.107000	0.15375	0.444000	0.26612	0.533000	0.62120	ATT	.	.		0.323	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		G	83778913	A	G	83778913	3	3	65	1	0	0	0	0	1	0	0	0	14013	101	4	2	2083	2	SEC31A	4	83778913	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1751904	83778913	107375363	106	8179										
AFF1	4299	hgsc.bcm.edu	37	chr4	88052964	88052964	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gattcataatgtcattaaaaTccttctcagatgccacagcg	6	10	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:88052964T>A	ENST00000307808.6	+	17	3520	c.3100T>A	c.(3100-3102)Tcc>Acc	p.S1034T	AFF1_ENST00000395146.4_Missense_Mutation_p.S1041T|AFF1_ENST00000544085.1_Missense_Mutation_p.S672T	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	1034					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		GTCATTAAAATCCTTCTCAGA	0.308																																					p.S1041T		Atlas-SNP	.											.	AFF1	102	.	0			c.T3121A						.						110	106	107					4																	88052964		2203	4300	6503	SO:0001583	missense	4299	exon18			TTAAAATCCTTCT	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.3100T>A	chr4.hg19:g.88052964T>A	ENSP00000305689:p.Ser1034Thr	181.0	0.0		104.0	19.0	NM_001166693	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	hg19	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	T	0.509	-0.867598	0.02590	.	.	ENSG00000172493	ENST00000395146;ENST00000307808;ENST00000544085	T;T;T	0.63913	-0.07;-0.07;-0.07	5.42	1.47	0.22746	.	0.646159	0.15139	N	0.278410	T	0.43523	0.1251	L	0.37850	1.14	0.24807	N	0.992668	B;B;B	0.21071	0.051;0.051;0.051	B;B;B	0.21151	0.033;0.033;0.033	T	0.19160	-1.0314	10	0.19147	T	0.46	-6.1251	3.4385	0.07454	0.2542:0.2297:0.0:0.5161	.	1041;1034;1034	E9PBM3;Q14C88;P51825	.;.;AFF1_HUMAN	T	1041;1034;672	ENSP00000378578:S1041T;ENSP00000305689:S1034T;ENSP00000440843:S672T	ENSP00000305689:S1034T	S	+	1	0	AFF1	88271988	0.997000	0.39634	0.997000	0.53966	0.046000	0.14306	0.140000	0.16056	0.374000	0.24650	-0.290000	0.09829	TCC	.	.		0.308	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		A	88052964	T	A	88052964	3	1	65	1	0	0	0	0	1	0	0	0	356	1435	50	4	3208	4	AFF1	4	88052964	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4274051	88052964	103101312	107	8180										
MEPE	56955	hgsc.bcm.edu	37	chr4	88766777	88766777	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agagaggggacaatgatataTctcctttcagtggggacggc	14	7	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:88766777T>C	ENST00000424957.3	+	4	830	c.757T>C	c.(757-759)Tct>Cct	p.S253P	MEPE_ENST00000361056.3_Missense_Mutation_p.S253P|MEPE_ENST00000540395.1_Missense_Mutation_p.S140P|MEPE_ENST00000497649.2_Missense_Mutation_p.S229P|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000395102.4_Missense_Mutation_p.S284P|MEPE_ENST00000560249.1_Missense_Mutation_p.S140P	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	253					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		CAATGATATATCTCCTTTCAG	0.428																																					p.S253P		Atlas-SNP	.											.	MEPE	86	.	0			c.T757C						.						67	68	68					4																	88766777		2203	4300	6503	SO:0001583	missense	56955	exon4			GATATATCTCCTT	AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.757T>C	chr4.hg19:g.88766777T>C	ENSP00000416984:p.Ser253Pro	118.0	0.0		78.0	4.0	NM_020203	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	hg19	CCDS3625.1	.	.	.	.	.	.	.	.	.	.	T	9.418	1.082280	0.20309	.	.	ENSG00000152595	ENST00000535138;ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.54866	0.56;0.57;0.55;0.57;0.56	4.7	-2.57	0.06248	.	1.040440	0.07586	N	0.921176	T	0.39279	0.1072	L	0.47716	1.5	0.09310	N	1	B	0.31931	0.347	B	0.35353	0.201	T	0.33214	-0.9877	10	0.35671	T	0.21	0.7078	0.6275	0.00788	0.1777:0.2003:0.3115:0.3105	.	253	Q9NQ76	MEPE_HUMAN	P	253;253;284;229;140;253	ENSP00000416984:S253P;ENSP00000378534:S284P;ENSP00000422747:S229P;ENSP00000443491:S140P;ENSP00000354341:S253P	ENSP00000354341:S253P	S	+	1	0	MEPE	88985801	0.000000	0.05858	0.000000	0.03702	0.596000	0.36781	0.060000	0.14342	-0.600000	0.05790	0.459000	0.35465	TCT	.	.		0.428	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1			C	88766777	T	C	88766777	3	2	65	1	0	0	0	0	1	0	0	0	9487	1435	50	2	767	2	MEPE	4	88766777	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	713813	88766777	102387499	108	8181										
SPRY1	10252	hgsc.bcm.edu	37	chr4	124323669	124323669	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cactgtctattgtaagctggAgagctgcccctcccggggtc	12	13	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:124323669A>G	ENST00000394339.2	+	2	1263	c.923A>G	c.(922-924)gAg>gGg	p.E308G	SPRY1_ENST00000339241.1_Missense_Mutation_p.E308G	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)	308	Cys-rich.				epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				NS(1)|large_intestine(4)|lung(2)|ovary(1)|skin(3)	11						TGTAAGCTGGAGAGCTGCCCC	0.488																																					p.E308G		Atlas-SNP	.											.	SPRY1	28	.	0			c.A923G						.						90	93	92					4																	124323669		2203	4300	6503	SO:0001583	missense	10252	exon2			AGCTGGAGAGCTG	AF041037	CCDS3731.1	4q	2009-04-17	2001-11-28		ENSG00000164056	ENSG00000164056			11269	protein-coding gene	gene with protein product		602465	"sprouty (Drosophila) homolog 1 (antagonist of FGF signaling)"			9458049, 15962011	Standard	NM_001258038		Approved	hSPRY1	uc003ifa.4	O43609	OTTHUMG00000133071	ENST00000394339.2:c.923A>G	chr4.hg19:g.124323669A>G	ENSP00000377871:p.Glu308Gly	132.0	0.0		92.0	4.0	NM_001258039	D3DNX6|Q6PNE0	Missense_Mutation	SNP	ENST00000394339.2	hg19	CCDS3731.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.260928	0.39995	.	.	ENSG00000164056	ENST00000339241;ENST00000394339	T;T	0.56611	0.45;0.45	5.06	2.6	0.31112	.	0.151388	0.42172	D	0.000748	T	0.35038	0.0918	L	0.36672	1.1	0.39071	D	0.960712	P	0.37781	0.608	B	0.32980	0.156	T	0.10520	-1.0626	9	.	.	.	-7.9472	7.2843	0.26328	0.7778:0.1462:0.0759:0.0	.	308	O43609	SPY1_HUMAN	G	308	ENSP00000343785:E308G;ENSP00000377871:E308G	.	E	+	2	0	SPRY1	124543119	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.897000	0.63231	0.393000	0.25203	0.459000	0.35465	GAG	.	.		0.488	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1			G	124323669	A	G	124323669	3	3	65	1	0	0	0	0	1	0	0	0	15120	304	11	2	925	2	SPRY1	4	124323669	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	35556892	124323669	66830607	109	8182										
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125592939	125592939	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccccagctttaaccaacagcTgtagcacttcttgttccttg	6	14	1	0	rs200716397		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:125592939T>C	ENST00000504087.1	-	4	2530	c.1493A>G	c.(1492-1494)cAg>cGg	p.Q498R	ANKRD50_ENST00000515641.1_Missense_Mutation_p.Q319R	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	498										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						AACCAACAGCTGTAGCACTTC	0.448																																					p.Q498R		Atlas-SNP	.											.	ANKRD50	136	.	0			c.A1493G						.						96	92	93					4																	125592939		2203	4300	6503	SO:0001583	missense	57182	exon4			AACAGCTGTAGCA	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1493A>G	chr4.hg19:g.125592939T>C	ENSP00000425658:p.Gln498Arg	116.0	0.0		76.0	4.0	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	hg19	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.117095	0.37339	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.62639	0.01;2.4	4.93	4.93	0.64822	Ankyrin repeat-containing domain (3);	0.140256	0.49305	D	0.000151	T	0.47284	0.1437	N	0.20357	0.565	0.58432	D	0.999997	B	0.22414	0.069	B	0.28709	0.093	T	0.38845	-0.9642	10	0.13108	T	0.6	.	14.7385	0.69434	0.0:0.0:0.0:1.0	.	498	Q9ULJ7	ANR50_HUMAN	R	498;319	ENSP00000425658:Q498R;ENSP00000425355:Q319R	ENSP00000425658:Q498R	Q	-	2	0	ANKRD50	125812389	1.000000	0.71417	0.997000	0.53966	0.711000	0.40976	7.365000	0.79537	2.083000	0.62718	0.454000	0.30748	CAG	.	T|0.999;C|0.001		0.448	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		C	125592939	T	C	125592939	3	2	65	1	0	0	0	0	1	0	0	0	677	1580	55	2	2800	2	ANKRD50	4	125592939	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1269270	125592939	65561337	110	8183										
UCP1	7350	hgsc.bcm.edu	37	chr4	141484605	141484605	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttcacgacctctgtgggttgCccaatgaatactgccactcc	8	14	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:141484605C>T	ENST00000262999.3	-	3	468	c.393G>A	c.(391-393)ggG>ggA	p.G131G		NM_021833.4	NP_068605.1	P25874	UCP1_HUMAN	uncoupling protein 1 (mitochondrial, proton carrier)	131					brown fat cell differentiation (GO:0050873)|cellular metabolic process (GO:0044237)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|stomach(1)	16	all_hematologic(180;0.162)					CTGTGGGTTGCCCAATGAATA	0.433																																					p.G131G		Atlas-SNP	.											.	UCP1	33	.	0			c.G393A						.						119	104	109					4																	141484605		2203	4300	6503	SO:0001819	synonymous_variant	7350	exon3			GGGTTGCCCAATG	X51955	CCDS3753.1	4q28-q31	2013-05-22			ENSG00000109424	ENSG00000109424		"Solute carriers"	12517	protein-coding gene	gene with protein product		113730		UCP		2380264	Standard	NM_021833		Approved	SLC25A7	uc011chj.2	P25874	OTTHUMG00000133415	ENST00000262999.3:c.393G>A	chr4.hg19:g.141484605C>T		110.0	0.0		72.0	32.0	NM_021833	Q13218|Q4KMZ3|Q68G66	Silent	SNP	ENST00000262999.3	hg19	CCDS3753.1																																																																																			.	.		0.433	UCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257273.1			T	141484605	C	T	141484605	2	4	65	1	0	0	0	0	0	0	0	1	16945	726	26	3		3	UCP1	4	141484605	Silent	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	15891666	141484605	49669671	111	8184										
RNF150	57484	hgsc.bcm.edu	37	chr4	141888829	141888829	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acctctggatgtaataaaagAcgagccatgcgagggaaatg	12	7	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:141888829A>G	ENST00000515673.2	-	2	716	c.683T>C	c.(682-684)gTc>gCc	p.V228A	RNF150_ENST00000379512.2_Missense_Mutation_p.V87A|RNF150_ENST00000507500.1_Missense_Mutation_p.V228A|RNF150_ENST00000420921.2_Missense_Mutation_p.V87A|RNF150_ENST00000515057.1_5'UTR|RNF150_ENST00000306799.3_Intron			Q9ULK6	RN150_HUMAN	ring finger protein 150	228						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					GTAATAAAAGACGAGCCATGC	0.408																																					p.V228A		Atlas-SNP	.											.	RNF150	94	.	0			c.T683C						.						110	105	107					4																	141888829		2203	4300	6503	SO:0001583	missense	57484	exon2			TAAAAGACGAGCC	AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"RING-type (C3HC4) zinc fingers"	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.683T>C	chr4.hg19:g.141888829A>G	ENSP00000425840:p.Val228Ala	124.0	0.0		97.0	5.0	NM_020724	Q3T1D0|Q6ZNW6	Missense_Mutation	SNP	ENST00000515673.2	hg19	CCDS34065.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.909328	0.92107	.	.	ENSG00000170153	ENST00000379512;ENST00000420921;ENST00000515673;ENST00000507500;ENST00000506101	T;T;T;T;T	0.16073	2.37;2.37;3.35;3.38;2.4	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.31888	0.0811	L	0.39245	1.2	0.80722	D	1	P;D	0.63880	0.729;0.993	B;P	0.62298	0.444;0.9	T	0.00896	-1.1523	10	0.48119	T	0.1	.	16.6277	0.84984	1.0:0.0:0.0:0.0	.	228;228	Q9ULK6-3;Q9ULK6	.;RN150_HUMAN	A	87;87;228;228;59	ENSP00000368827:V87A;ENSP00000394581:V87A;ENSP00000425840:V228A;ENSP00000425568:V228A;ENSP00000425947:V59A	ENSP00000368827:V87A	V	-	2	0	RNF150	142108279	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.330000	0.79161	0.528000	0.53228	GTC	.	.		0.408	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090		G	141888829	A	G	141888829	3	3	65	1	0	0	0	0	1	0	0	0	13466	275	10	2	657	2	RNF150	4	141888829	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	404224	141888829	49265447	112	8185										
POU4F2	5458	hgsc.bcm.edu	37	chr4	147561644	147561644	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	catctgcaggttcgagtcccTcacactgtcccacaataata	6	14	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:147561644T>C	ENST00000281321.3	+	2	1162	c.914T>C	c.(913-915)cTc>cCc	p.L305P	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	305	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					TTCGAGTCCCTCACACTGTCC	0.617																																					p.L305P		Atlas-SNP	.											.	POU4F2	83	.	0			c.T914C						.						76	77	76					4																	147561644		2203	4300	6503	SO:0001583	missense	5458	exon2			AGTCCCTCACACT	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9219	protein-coding gene	gene with protein product		113725	"POU domain, class 4, transcription factor 2", "POU domain class 4, transcription factor 2"	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.914T>C	chr4.hg19:g.147561644T>C	ENSP00000281321:p.Leu305Pro	76.0	0.0		51.0	4.0	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Missense_Mutation	SNP	ENST00000281321.3	hg19	CCDS34074.1	.	.	.	.	.	.	.	.	.	.	T	17.78	3.472386	0.63737	.	.	ENSG00000151615	ENST00000281321	D	0.86865	-2.18	5.37	5.37	0.77165	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.85682	D	0.000000	D	0.94925	0.8359	M	0.92169	3.28	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96064	0.9041	10	0.87932	D	0	.	15.3779	0.74625	0.0:0.0:0.0:1.0	.	305	Q12837	PO4F2_HUMAN	P	305	ENSP00000281321:L305P	ENSP00000281321:L305P	L	+	2	0	POU4F2	147781094	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.018000	0.88722	2.045000	0.60652	0.459000	0.35465	CTC	.	.		0.617	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		C	147561644	T	C	147561644	3	2	65	1	0	0	0	0	1	0	0	0	12288	1551	54	2	920	2	POU4F2	4	147561644	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	5672815	147561644	43592632	113	8186										
TTC29	83894	hgsc.bcm.edu	37	chr4	147860979	147860979	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggaatttttctggaggagcaAggcagcttctgtctggctaa	13	7	3	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:147860979A>G	ENST00000325106.4	-	3	295	c.69T>C	c.(67-69)ccT>ccC	p.P23P	TTC29_ENST00000398886.4_Silent_p.P49P|RP11-292D4.2_ENST00000515530.1_RNA|TTC29_ENST00000513335.1_Silent_p.P49P	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	23										breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					TGGAGGAGCAAGGCAGCTTCT	0.433																																					p.P23P		Atlas-SNP	.											.	TTC29	63	.	0			c.T69C						.						79	84	83					4																	147860979		1871	4097	5968	SO:0001819	synonymous_variant	83894	exon3			GGAGCAAGGCAGC	AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"Tetratricopeptide (TTC) repeat domain containing"	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.69T>C	chr4.hg19:g.147860979A>G		175.0	0.0		74.0	4.0	NM_031956	A4GU95|Q9BXB6	Silent	SNP	ENST00000325106.4	hg19	CCDS47141.1																																																																																			.	.		0.433	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956		G	147860979	A	G	147860979	2	3	65	1	0	0	0	0	0	0	0	1	16711	59	3	2		2	TTC29	4	147860979	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	299335	147860979	43293297	114	8187										
LRBA	987	hgsc.bcm.edu	37	chr4	151773418	151773418	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	attaatttgtcatcattaccAaacatgtccagtttttcacc	3	10	3	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:151773418A>G	ENST00000357115.3	-	23	3687	c.3444T>C	c.(3442-3444)ttT>ttC	p.F1148F	LRBA_ENST00000510413.1_Silent_p.F1148F|LRBA_ENST00000535741.1_Silent_p.F1148F|LRBA_ENST00000507224.1_Silent_p.F1148F	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1148						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					CATCATTACCAAACATGTCCA	0.388																																					p.F1148F		Atlas-SNP	.											.	LRBA	253	.	0			c.T3444C						.						85	85	85					4																	151773418		2203	4300	6503	SO:0001819	synonymous_variant	987	exon23			ATTACCAAACATG	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.3444T>C	chr4.hg19:g.151773418A>G		118.0	0.0		52.0	4.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Silent	SNP	ENST00000357115.3	hg19	CCDS3773.1																																																																																			.	.		0.388	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			G	151773418	A	G	151773418	2	3	65	1	0	0	0	0	0	0	0	1	8940	127	5	2		2	LRBA	4	151773418	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3912439	151773418	39380858	115	8188										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155156115	155156115	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gataattccagtgatagttgTcttttccatcatgatcagag	8	7	3	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:155156115T>C	ENST00000357232.4	-	25	8323	c.8324A>G	c.(8323-8325)gAc>gGc	p.D2775G		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2775					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GTGATAGTTGTCTTTTCCATC	0.398																																					p.D2775G		Atlas-SNP	.											.	DCHS2	594	.	0			c.A8324G						.						109	106	107					4																	155156115		2203	4300	6503	SO:0001583	missense	54798	exon25			TAGTTGTCTTTTC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.8324A>G	chr4.hg19:g.155156115T>C	ENSP00000349768:p.Asp2775Gly	171.0	0.0		89.0	4.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.283224	0.23392	.	.	ENSG00000197410	ENST00000357232	T	0.29397	1.57	5.94	3.23	0.37069	.	0.755250	0.12439	N	0.468821	T	0.07188	0.0182	N	0.00446	-1.495	0.48452	D	0.999652	B	0.02656	0.0	B	0.01281	0.0	T	0.32693	-0.9897	10	0.02654	T	1	.	7.7008	0.28621	0.2363:0.6398:0.0:0.1239	.	2775	Q6V1P9	PCD23_HUMAN	G	2775	ENSP00000349768:D2775G	ENSP00000349768:D2775G	D	-	2	0	DCHS2	155375565	0.000000	0.05858	0.001000	0.08648	0.921000	0.55340	0.489000	0.22387	0.113000	0.18004	-0.226000	0.12346	GAC	.	.		0.398	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		C	155156115	T	C	155156115	3	2	65	1	0	0	0	0	1	0	0	0	4290	1667	58	2	430	2	DCHS2	4	155156115	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3382697	155156115	35998161	116	8189										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155278418	155278418	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atctctaaactgttcattacTtccttgtctgctgaaaagtt	5	9	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:155278418T>C	ENST00000357232.4	-	6	752	c.753A>G	c.(751-753)gaA>gaG	p.E251E	DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	251	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		tgttcattacttccttgtctg	0.433																																					p.E251E		Atlas-SNP	.											.	DCHS2	594	.	0			c.A753G						.						138	144	142					4																	155278418		2203	4300	6503	SO:0001819	synonymous_variant	54798	exon6			CATTACTTCCTTG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.753A>G	chr4.hg19:g.155278418T>C		42.0	0.0		33.0	4.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	hg19	CCDS3785.1																																																																																			.	.		0.433	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		C	155278418	T	C	155278418	2	2	65	1	0	0	0	0	0	0	0	1	4290	1606	56	2		2	DCHS2	4	155278418	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	122303	155278418	35875858	117	8190										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169282339	169282339	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atgcaaaatctttcaaacacTttaaaagctgtcccatacgc	4	11	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:169282339T>C	ENST00000511577.1	-	37	5199	c.4952A>G	c.(4951-4953)aAg>aGg	p.K1651R	DDX60L_ENST00000260184.7_Missense_Mutation_p.K1651R			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1651							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TTTCAAACACTTTAAAAGCTG	0.279																																					p.K1651R		Atlas-SNP	.											DDX60L,colon,carcinoma,0,1	DDX60L	116	.	0			c.A4952G						.						85	78	80					4																	169282339		1817	4084	5901	SO:0001583	missense	91351	exon37			AAACACTTTAAAA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.4952A>G	chr4.hg19:g.169282339T>C	ENSP00000422423:p.Lys1651Arg	113.0	0.0		94.0	4.0	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.165	-1.077056	0.01903	.	.	ENSG00000181381	ENST00000260184;ENST00000511577	T;T	0.17054	2.3;2.3	2.06	-4.12	0.03916	.	.	.	.	.	T	0.05868	0.0153	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.24440	-1.0160	9	0.27785	T	0.31	.	0.815	0.01100	0.4195:0.2578:0.1442:0.1785	.	1651	Q5H9U9	DDX6L_HUMAN	R	1651	ENSP00000260184:K1651R;ENSP00000422423:K1651R	ENSP00000260184:K1651R	K	-	2	0	DDX60L	169518914	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-3.425000	0.00475	-2.886000	0.00317	-0.756000	0.03474	AAG	.	.		0.279	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		C	169282339	T	C	169282339	3	2	65	1	0	0	0	0	1	0	0	0	4381	1609	56	2	176	2	DDX60L	4	169282339	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	14003921	169282339	21871937	118	8191										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169317190	169317190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctcagaaatttccagaatctTcagattctccaggaaattaa	5	9	4	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:169317190T>C	ENST00000511577.1	-	27	3824	c.3577A>G	c.(3577-3579)Aag>Gag	p.K1193E	DDX60L_ENST00000260184.7_Missense_Mutation_p.K1193E|DDX60L_ENST00000505890.1_Missense_Mutation_p.K1194E			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1193							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TCCAGAATCTTCAGATTCTCC	0.338																																					p.K1193E		Atlas-SNP	.											.	DDX60L	116	.	0			c.A3577G						.						77	70	72					4																	169317190		1799	4067	5866	SO:0001583	missense	91351	exon27			GAATCTTCAGATT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.3577A>G	chr4.hg19:g.169317190T>C	ENSP00000422423:p.Lys1193Glu	207.0	0.0		146.0	6.0	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.222|3.222	-0.159294|-0.159294	0.06544|0.06544	.|.	.|.	ENSG00000181381|ENSG00000181381	ENST00000514580|ENST00000260184;ENST00000511577;ENST00000505890	.|T;T;T	.|0.41065	.|1.01;1.01;2.21	1.91|1.91	-0.84|-0.84	0.10755|0.10755	.|.	.|0.177811	.|0.25906	.|N	.|0.027530	T|T	0.15739|0.15739	0.0379|0.0379	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.10296	.|0.003;0.001;0.003	.|B;B;B	.|0.09377	.|0.004;0.003;0.004	T|T	0.22626|0.22626	-1.0211|-1.0211	5|10	.|0.11485	.|T	.|0.65	.|.	5.5504|5.5504	0.17087|0.17087	0.0:0.3043:0.0:0.6957|0.0:0.3043:0.0:0.6957	.|.	.|1193;1194;1193	.|E9PAP8;D6R906;Q5H9U9	.|.;.;DDX6L_HUMAN	G|E	80|1193;1193;1194	.|ENSP00000260184:K1193E;ENSP00000422423:K1193E;ENSP00000422202:K1194E	.|ENSP00000260184:K1193E	E|K	-|-	2|1	0|0	DDX60L|DDX60L	169553765|169553765	0.965000|0.965000	0.33210|0.33210	0.001000|0.001000	0.08648|0.08648	0.024000|0.024000	0.10985|0.10985	1.677000|1.677000	0.37576|0.37576	-0.190000|-0.190000	0.10465|0.10465	0.260000|0.260000	0.18958|0.18958	GAA|AAG	.	.		0.338	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		C	169317190	T	C	169317190	3	2	65	1	0	0	0	0	1	0	0	0	4381	1792	62	2	1591	2	DDX60L	4	169317190	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	34851	169317190	21837086	119	8192										
ASB5	140458	hgsc.bcm.edu	37	chr4	177190150	177190150	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctatgtagaaatgactgaggAtggcaaggctgattttcaca	11	6	1	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:177190150A>G	ENST00000296525.3	-	1	223	c.110T>C	c.(109-111)aTc>aCc	p.I37T		NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	37					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		ATGACTGAGGATGGCAAGGCT	0.393																																					p.I37T		Atlas-SNP	.											.	ASB5	88	.	0			c.T110C						.						111	102	105					4																	177190150		2203	4300	6503	SO:0001583	missense	140458	exon1			CTGAGGATGGCAA	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"Ankyrin repeat domain containing"	17180	protein-coding gene	gene with protein product		615050	"ankyrin repeat and SOCS box-containing 5"				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.110T>C	chr4.hg19:g.177190150A>G	ENSP00000296525:p.Ile37Thr	101.0	0.0		77.0	4.0	NM_080874	Q8N7B5	Missense_Mutation	SNP	ENST00000296525.3	hg19	CCDS3827.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.807455	0.90623	.	.	ENSG00000164122	ENST00000296525	T	0.39406	1.08	5.84	5.84	0.93424	.	0.052352	0.64402	D	0.000001	T	0.45155	0.1328	L	0.36672	1.1	0.80722	D	1	D	0.53151	0.958	P	0.49502	0.613	T	0.45527	-0.9255	10	0.87932	D	0	-24.5455	16.2233	0.82274	1.0:0.0:0.0:0.0	.	37	Q8WWX0	ASB5_HUMAN	T	37	ENSP00000296525:I37T	ENSP00000296525:I37T	I	-	2	0	ASB5	177427144	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.328000	0.96403	2.243000	0.73865	0.482000	0.46254	ATC	.	.		0.393	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1			G	177190150	A	G	177190150	3	3	65	1	0	0	0	0	1	0	0	0	1026	333	12	2	907	2	ASB5	4	177190150	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	7872960	177190150	13964126	120	8193										
FAM149A	25854	hgsc.bcm.edu	37	chr4	187077241	187077241	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cctgtttccccgcgtgactgTgtcaaagatgccgtggcagc	12	13	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:187077241T>C	ENST00000356371.5	+	7	1344	c.1344T>C	c.(1342-1344)tgT>tgC	p.C448C	FAM149A_ENST00000514153.1_Silent_p.C157C|FAM149A_ENST00000227065.4_Silent_p.C157C|FAM149A_ENST00000389354.5_Silent_p.C157C|FAM149A_ENST00000514829.1_3'UTR|FAM149A_ENST00000502970.1_Silent_p.C157C|FAM149A_ENST00000503432.1_Silent_p.C157C			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	448										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		CGCGTGACTGTGTCAAAGATG	0.448																																					p.C157C		Atlas-SNP	.											.	FAM149A	52	.	0			c.T471C						.						128	116	120					4																	187077241		2203	4300	6503	SO:0001819	synonymous_variant	25854	exon6			TGACTGTGTCAAA	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.1344T>C	chr4.hg19:g.187077241T>C		108.0	0.0		71.0	4.0	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Silent	SNP	ENST00000356371.5	hg19																																																																																				.	.		0.448	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		C	187077241	T	C	187077241	2	2	65	1	0	0	0	0	0	0	0	1	5460	1702	59	2		2	FAM149A	4	187077241	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	9887091	187077241	4077035	121	8194										
KLKB1	3818	hgsc.bcm.edu	37	chr4	187175807	187175807	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tctgtcagacattacaaaagAtacacctttctcacaaataa	3	10	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr4:187175807A>G	ENST00000264690.6	+	12	1566	c.1379A>G	c.(1378-1380)gAt>gGt	p.D460G	KLKB1_ENST00000513864.1_Missense_Mutation_p.D460G	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	460	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		ATTACAAAAGATACACCTTTC	0.373																																					p.D460G		Atlas-SNP	.											.	KLKB1	155	.	0			c.A1379G						.						110	110	110					4																	187175807		2203	4300	6503	SO:0001583	missense	3818	exon12			CAAAAGATACACC	M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"Kallikreins"	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.1379A>G	chr4.hg19:g.187175807A>G	ENSP00000264690:p.Asp460Gly	136.0	0.0		79.0	4.0	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Missense_Mutation	SNP	ENST00000264690.6	hg19	CCDS34120.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.100|6.100	0.386632|0.386632	0.11524|0.11524	.|.	.|.	ENSG00000164344|ENSG00000164344	ENST00000264690;ENST00000513864;ENST00000418715|ENST00000511608	D;D|.	0.88201|.	-2.35;-2.35|.	5.8|5.8	4.58|4.58	0.56647|0.56647	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);|.	0.588693|.	0.18084|.	N|.	0.152207|.	T|T	0.16257|0.16257	0.0391|0.0391	N|N	0.02213|0.02213	-0.635|-0.635	0.09310|0.09310	N|N	1|1	B;B;B|.	0.15473|.	0.013;0.0;0.013|.	B;B;B|.	0.24006|.	0.05;0.007;0.05|.	T|T	0.13308|0.13308	-1.0514|-1.0514	10|5	0.24483|.	T|.	0.36|.	.|.	11.9666|11.9666	0.53038|0.53038	0.7285:0.2715:0.0:0.0|0.7285:0.2715:0.0:0.0	.|.	422;460;460|.	E7EQA8;A8K9A9;P03952|.	.;.;KLKB1_HUMAN|.	G|V	460;460;422|508	ENSP00000264690:D460G;ENSP00000424469:D460G|.	ENSP00000264690:D460G|.	D|I	+|+	2|1	0|0	KLKB1|KLKB1	187412801|187412801	0.813000|0.813000	0.29090|0.29090	0.970000|0.970000	0.41538|0.41538	0.050000|0.050000	0.14768|0.14768	3.885000|3.885000	0.56182|0.56182	2.220000|2.220000	0.72140|0.72140	0.533000|0.533000	0.62120|0.62120	GAT|ATA	.	.		0.373	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892		G	187175807	A	G	187175807	3	3	65	1	0	0	0	0	1	0	0	0	8421	333	12	2	1421	2	KLKB1	4	187175807	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	98566	187175807	3978469	122	8195										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5454689	5454689	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agtgaaactgcttctgaaggAactctggctctgtgtaaaca	10	8	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:5454689A>G	ENST00000296564.7	+	11	851	c.629A>G	c.(628-630)gAa>gGa	p.E210G	KIAA0947_ENST00000512608.1_3'UTR	NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		210					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						CTTCTGAAGGAACTCTGGCTC	0.453																																					p.E210G		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A629G						.						59	63	61					5																	5454689		1943	4145	6088	SO:0001583	missense	23379	exon11			TGAAGGAACTCTG																												ENST00000296564.7:c.629A>G	chr5.hg19:g.5454689A>G	ENSP00000296564:p.Glu210Gly	64.0	0.0		83.0	4.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.886501	0.91814	.	.	ENSG00000164151	ENST00000296564	T	0.16597	2.33	5.25	5.25	0.73442	.	0.237224	0.33040	N	0.005353	T	0.30854	0.0778	L	0.32530	0.975	0.33444	D	0.582714	D	0.89917	1.0	D	0.87578	0.998	T	0.41822	-0.9487	10	0.87932	D	0	-29.1098	13.3984	0.60868	1.0:0.0:0.0:0.0	.	210	Q9Y2F5	K0947_HUMAN	G	210	ENSP00000296564:E210G	ENSP00000296564:E210G	E	+	2	0	KIAA0947	5507689	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	5.027000	0.64109	2.109000	0.64355	0.528000	0.53228	GAA	.	.		0.453	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			G	5454689	A	G	5454689	3	3	65	1	0	0	0	0	1	0	0	0	8211	246	9	2	671	2	KIAA0947	5	5454689	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10		5454689	175460571	123	8196										
CDH9	1007	hgsc.bcm.edu	37	chr5	26906841	26906841	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gttgtacctgattctgggtcCactgaaaaatatggctgtcc	10	9	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:26906841C>A	ENST00000231021.4	-	4	802	c.630G>T	c.(628-630)gtG>gtT	p.V210V		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	210	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						ATTCTGGGTCCACTGAAAAAT	0.328																																					p.V210V	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.G630T						.						106	96	99					5																	26906841		2203	4300	6503	SO:0001819	synonymous_variant	1007	exon4			TGGGTCCACTGAA	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.630G>T	chr5.hg19:g.26906841C>A		87.0	0.0		73.0	20.0	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	hg19	CCDS3893.1																																																																																			.	.		0.328	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26906841	C	A	26906841	2	1	65	1	0	0	0	0	0	0	0	1	3119	581	21	3		3	CDH9	5	26906841	Silent	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	21452152	26906841	154008419	124	8197										
RICTOR	253260	hgsc.bcm.edu	37	chr5	38958582	38958582	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acccttgtctccaaggtgggAtaacgctggtttcatctgaa	10	10	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:38958582A>T	ENST00000357387.3	-	24	2413	c.2383T>A	c.(2383-2385)Tcc>Acc	p.S795T	RICTOR_ENST00000296782.5_Missense_Mutation_p.S795T|RICTOR_ENST00000503698.1_5'UTR	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					CCAAGGTGGGATAACGCTGGT	0.318																																					p.S795T		Atlas-SNP	.											.	RICTOR	182	.	0			c.T2383A						.						89	96	94					5																	38958582		2203	4300	6503	SO:0001583	missense	253260	exon24			GGTGGGATAACGC		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.2383T>A	chr5.hg19:g.38958582A>T	ENSP00000349959:p.Ser795Thr	220.0	0.0		217.0	93.0	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	A	9.671	1.146620	0.21288	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.43294	0.95;0.95	5.11	5.11	0.69529	Armadillo-type fold (1);	0.051792	0.85682	D	0.000000	T	0.29389	0.0732	N	0.19112	0.55	0.49915	D	0.999835	B;B	0.11235	0.004;0.002	B;B	0.15052	0.012;0.005	T	0.10567	-1.0624	10	0.87932	D	0	-7.6383	11.249	0.49015	0.9254:0.0:0.0746:0.0	.	795;795	Q6R327;Q6R327-3	RICTR_HUMAN;.	T	795	ENSP00000349959:S795T;ENSP00000296782:S795T	ENSP00000296782:S795T	S	-	1	0	RICTOR	38994339	1.000000	0.71417	0.994000	0.49952	0.974000	0.67602	5.423000	0.66458	2.059000	0.61396	0.460000	0.39030	TCC	.	.		0.318	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		T	38958582	A	T	38958582	3	4	65	1	0	0	0	0	1	0	0	0	13373	333	12	4	2803	4	RICTOR	5	38958582	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	12051741	38958582	141956678	125	8198										
OXCT1	5019	hgsc.bcm.edu	37	chr5	41794835	41794835	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aaagaggctcctggaagaatAgtaactgtttccttgcctaa	9	8	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:41794835A>G	ENST00000196371.5	-	12	1276	c.1116T>C	c.(1114-1116)acT>acC	p.T372T	OXCT1_ENST00000513081.1_5'Flank|OXCT1_ENST00000512084.1_5'Flank|OXCT1_ENST00000510634.1_5'Flank|OXCT1_ENST00000509987.1_Silent_p.T186T	NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	372					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	CTGGAAGAATAGTAACTGTTT	0.398																																					p.T372T		Atlas-SNP	.											.	OXCT1	54	.	0			c.T1116C						.						65	63	64					5																	41794835		2203	4300	6503	SO:0001819	synonymous_variant	5019	exon12			AAGAATAGTAACT	U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"3-oxoacid CoA transferase"	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.1116T>C	chr5.hg19:g.41794835A>G		46.0	0.0		66.0	4.0	NM_000436	B2R5V2|B7Z528	Silent	SNP	ENST00000196371.5	hg19	CCDS3937.1																																																																																			.	.		0.398	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436		G	41794835	A	G	41794835	2	3	65	1	0	0	0	0	0	0	0	1	11338	407	15	2		2	OXCT1	5	41794835	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2836253	41794835	139120425	126	8199										
FAM169A	26049	hgsc.bcm.edu	37	chr5	74130327	74130327	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcataatcagtactgctatgAcacaggaatgggatctcatt	9	8	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:74130327A>G	ENST00000389156.4	-	5	504	c.414T>C	c.(412-414)tgT>tgC	p.C138C	FAM169A_ENST00000380515.3_Intron|FAM169A_ENST00000510496.1_Silent_p.C138C	NM_015566.2	NP_056381.1	Q9Y6X4	F169A_HUMAN	family with sequence similarity 169, member A	138						membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	27						TACTGCTATGACACAGGAATG	0.383																																					p.C138C		Atlas-SNP	.											.	FAM169A	61	.	0			c.T414C						.						138	125	129					5																	74130327		1850	4094	5944	SO:0001819	synonymous_variant	26049	exon5			GCTATGACACAGG		CCDS43330.1	5q13.3	2008-08-08			ENSG00000198780	ENSG00000198780			29138	protein-coding gene	gene with protein product		615769				10048485	Standard	NM_015566		Approved	KIAA0888	uc003kdm.4	Q9Y6X4	OTTHUMG00000162930	ENST00000389156.4:c.414T>C	chr5.hg19:g.74130327A>G		119.0	0.0		99.0	4.0	NM_015566	A8K1T9|Q6MZT0|Q9H989	Silent	SNP	ENST00000389156.4	hg19	CCDS43330.1																																																																																			.	.		0.383	FAM169A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371092.2			G	74130327	A	G	74130327	2	3	65	1	0	0	0	0	0	0	0	1	5492	273	10	2		2	FAM169A	5	74130327	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	32335492	74130327	106784933	127	8200										
ACOT12	134526	hgsc.bcm.edu	37	chr5	80655835	80655835	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	catgatcttgttcagttagaAgtgtgactggttttaaatga	10	4	2	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:80655835A>G	ENST00000307624.3	-	5	411	c.383T>C	c.(382-384)cTt>cCt	p.L128P	ACOT12_ENST00000513751.1_Missense_Mutation_p.L128P	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	128					acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		TTCAGTTAGAAGTGTGACTGG	0.313																																					p.L128P		Atlas-SNP	.											.	ACOT12	57	.	0			c.T383C						.						102	103	103					5																	80655835		2203	4298	6501	SO:0001583	missense	134526	exon5			GTTAGAAGTGTGA	AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	24436	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 15"	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.383T>C	chr5.hg19:g.80655835A>G	ENSP00000303246:p.Leu128Pro	73.0	0.0		83.0	4.0	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	hg19	CCDS4055.1	.	.	.	.	.	.	.	.	.	.	A	5.472	0.272129	0.10349	.	.	ENSG00000172497	ENST00000307624;ENST00000513751	T;T	0.25749	1.78;1.78	5.04	3.88	0.44766	.	0.158933	0.43579	N	0.000556	T	0.17023	0.0409	N	0.26130	0.795	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.04900	-1.0919	10	0.30854	T	0.27	-4.5878	10.0132	0.41999	0.9184:0.0:0.0816:0.0	.	128;128	Q5FWE9;Q8WYK0	.;ACO12_HUMAN	P	128	ENSP00000303246:L128P;ENSP00000421628:L128P	ENSP00000303246:L128P	L	-	2	0	ACOT12	80691591	1.000000	0.71417	0.500000	0.27589	0.085000	0.17905	4.204000	0.58460	0.876000	0.35872	0.533000	0.62120	CTT	.	.		0.313	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767		G	80655835	A	G	80655835	3	3	65	1	0	0	0	0	1	0	0	0	150	72	3	2	1328	2	ACOT12	5	80655835	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	6525508	80655835	100259425	128	8201										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101755554	101755554	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cataatcttcattgatcccaGcaaattgcactggattacag	6	10	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:101755554G>A	ENST00000506729.1	-	8	1619	c.1448C>T	c.(1447-1449)gCt>gTt	p.A483V	SLCO6A1_ENST00000389019.3_Missense_Mutation_p.A421V|SLCO6A1_ENST00000513675.1_Intron|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.A483V|SLCO6A1_ENST00000514551.1_5'Flank|SLCO6A1_ENST00000379810.1_Intron			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	483						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		ATTGATCCCAGCAAATTGCAC	0.313																																					p.A483V		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.C1448T						.						105	111	109					5																	101755554		2203	4300	6503	SO:0001583	missense	133482	exon8			ATCCCAGCAAATT	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1448C>T	chr5.hg19:g.101755554G>A	ENSP00000421339:p.Ala483Val	243.0	0.0		195.0	13.0	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	hg19	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.670638	0.47781	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019	T;T;T	0.40225	1.04;1.04;1.04	4.99	4.13	0.48395	Major facilitator superfamily domain, general substrate transporter (1);	0.182863	0.36591	N	0.002520	T	0.66187	0.2764	M	0.87097	2.86	0.80722	D	1	D;D	0.89917	1.0;0.985	D;P	0.76575	0.988;0.873	T	0.71817	-0.4478	10	0.87932	D	0	.	10.8295	0.46652	0.0895:0.0:0.9105:0.0	.	421;483	Q86UG4-2;Q86UG4	.;SO6A1_HUMAN	V	483;483;421	ENSP00000421339:A483V;ENSP00000369135:A483V;ENSP00000373671:A421V	ENSP00000369135:A483V	A	-	2	0	SLCO6A1	101783453	1.000000	0.71417	0.997000	0.53966	0.041000	0.13682	3.794000	0.55492	1.473000	0.48159	0.655000	0.94253	GCT	.	.		0.313	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		A	101755554	G	A	101755554	3	1	65	1	0	0	0	0	1	0	0	0	14747	971	34	3	735	3	SLCO6A1	5	101755554	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	21099719	101755554	79159706	129	8202										
PPIP5K2	23262	hgsc.bcm.edu	37	chr5	102490644	102490644	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acaacttaagactgtattagAgatgtgagtatctttttgaa	8	4	1	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:102490644A>G	ENST00000358359.3	+	13	1909	c.1400A>G	c.(1399-1401)gAg>gGg	p.E467G	PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000414217.1_Missense_Mutation_p.E467G|PPIP5K2_ENST00000321521.9_Missense_Mutation_p.E467G	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	467					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						ACTGTATTAGAGATGTGAGTA	0.323																																					p.E467G		Atlas-SNP	.											.	PPIP5K2	98	.	0			c.A1400G						.						72	72	72					5																	102490644		2203	4298	6501	SO:0001583	missense	23262	exon12			TATTAGAGATGTG	AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"histidine acid phosphatase domain containing 1"	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.1400A>G	chr5.hg19:g.102490644A>G	ENSP00000351126:p.Glu467Gly	68.0	0.0		55.0	4.0	NM_015216	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	hg19		.	.	.	.	.	.	.	.	.	.	A	25.6	4.657462	0.88154	.	.	ENSG00000145725	ENST00000321521;ENST00000507921;ENST00000358359;ENST00000451606;ENST00000414217	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	5.11	5.11	0.69529	.	0.000000	0.64402	D	0.000003	T	0.63616	0.2526	M	0.82823	2.61	0.80722	D	1	D;P;D	0.89917	1.0;0.684;1.0	D;P;D	0.91635	0.995;0.703;0.999	T	0.70193	-0.4939	10	0.87932	D	0	-15.3301	15.1899	0.73035	1.0:0.0:0.0:0.0	.	389;467;467	D6RBU4;O43314-2;O43314	.;.;VIP2_HUMAN	G	467;389;467;467;467	ENSP00000313070:E467G;ENSP00000422525:E389G;ENSP00000351126:E467G;ENSP00000416016:E467G	ENSP00000313070:E467G	E	+	2	0	PPIP5K2	102518543	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.243000	0.95416	2.040000	0.60383	0.533000	0.62120	GAG	.	.		0.323	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		G	102490644	A	G	102490644	3	3	65	1	0	0	0	0	1	0	0	0	12345	304	11	2	1446	2	PPIP5K2	5	102490644	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	735090	102490644	78424616	130	8203										
EFNA5	1946	hgsc.bcm.edu	37	chr5	106763128	106763128	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcgctcagtcttatcttctgGgacggagtcctcatagtgag	12	10	5	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:106763128G>T	ENST00000333274.6	-	2	489	c.208C>A	c.(208-210)Cca>Aca	p.P70T	EFNA5_ENST00000509503.1_Missense_Mutation_p.P70T	NM_001962.2	NP_001953.1	P52803	EFNA5_HUMAN	ephrin-A5	70	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|ephrin receptor signaling pathway (GO:0048013)|nervous system development (GO:0007399)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell-cell adhesion (GO:0022407)|regulation of focal adhesion assembly (GO:0051893)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rho GTPase activity (GO:0032319)|retinal ganglion cell axon guidance (GO:0031290)	anchored component of external side of plasma membrane (GO:0031362)|plasma membrane (GO:0005886)	chemorepellent activity (GO:0045499)|ephrin receptor binding (GO:0046875)			large_intestine(6)	6		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		TTATCTTCTGGGACGGAGTCC	0.448																																					p.P70T		Atlas-SNP	.											.	EFNA5	16	.	0			c.C208A						.						133	133	133					5																	106763128		2202	4300	6502	SO:0001583	missense	1946	exon2			CTTCTGGGACGGA	U26403	CCDS4097.1	5q21	2011-03-09			ENSG00000184349	ENSG00000184349		"Ephrins"	3225	protein-coding gene	gene with protein product		601535		EPLG7		8661153, 9245480	Standard	NM_001962		Approved	AF1, LERK7	uc003kol.3	P52803	OTTHUMG00000128741	ENST00000333274.6:c.208C>A	chr5.hg19:g.106763128G>T	ENSP00000328777:p.Pro70Thr	123.0	0.0		97.0	4.0	NM_001962		Missense_Mutation	SNP	ENST00000333274.6	hg19	CCDS4097.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245779	0.80024	.	.	ENSG00000184349	ENST00000333274;ENST00000509503	D;D	0.92647	-3.08;-3.08	6.06	6.06	0.98353	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.92838	0.7722	M	0.69185	2.1	0.80722	D	1	P;B	0.35011	0.48;0.13	B;B	0.41332	0.354;0.136	D	0.90068	0.4161	10	0.28530	T	0.3	-5.8591	20.6208	0.99490	0.0:0.0:1.0:0.0	.	70;70	D6RDV5;P52803	.;EFNA5_HUMAN	T	70	ENSP00000328777:P70T;ENSP00000426989:P70T	ENSP00000328777:P70T	P	-	1	0	EFNA5	106791027	1.000000	0.71417	0.965000	0.40720	0.993000	0.82548	9.476000	0.97823	2.882000	0.98803	0.655000	0.94253	CCA	.	.		0.448	EFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250652.1	NM_001962		T	106763128	G	T	106763128	3	4	65	1	0	0	0	0	1	0	0	0	4956	1232	43	3	494	3	EFNA5	5	106763128	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	4272484	106763128	74152132	131	8204										
FER	2241	hgsc.bcm.edu	37	chr5	108380491	108380491	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aaaataaaatttttacaagaAgccaagtgagttatttaaag	6	3	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:108380491A>G	ENST00000281092.4	+	15	2208	c.1824A>G	c.(1822-1824)gaA>gaG	p.E608E	FER_ENST00000438717.2_Silent_p.E433E	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	608	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		TTTTACAAGAAGCCAAGTGAG	0.244																																					p.E608E	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.A1824G						.						45	50	48					5																	108380491		2187	4288	6475	SO:0001819	synonymous_variant	2241	exon15			ACAAGAAGCCAAG	J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	3655	protein-coding gene	gene with protein product	"phosphoprotein NCP94", "protein phosphatase 1, regulatory subunit 74"	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.1824A>G	chr5.hg19:g.108380491A>G		108.0	0.0		95.0	4.0	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	hg19	CCDS4098.1																																																																																			.	.		0.244	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246		G	108380491	A	G	108380491	2	3	65	1	0	0	0	0	0	0	0	1	5821	69	3	2		2	FER	5	108380491	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1617363	108380491	72534769	132	8205										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112903376	112903376	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tccagccaatggtcaagctgCagcaattaaggcactgccca	9	13	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:112903376C>T	ENST00000161863.4	+	23	3287	c.3074C>T	c.(3073-3075)gCa>gTa	p.A1025V		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1025					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GGTCAAGCTGCAGCAATTAAG	0.343																																					p.A1025V		Atlas-SNP	.											.	YTHDC2	118	.	0			c.C3074T						.						61	58	59					5																	112903376		2202	4300	6502	SO:0001583	missense	64848	exon23			AAGCTGCAGCAAT	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.3074C>T	chr5.hg19:g.112903376C>T	ENSP00000161863:p.Ala1025Val	96.0	0.0		90.0	4.0	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.947965	0.53186	.	.	ENSG00000047188	ENST00000161863;ENST00000511372	T	0.02525	4.26	5.47	4.55	0.56014	Domain of unknown function DUF1605 (1);	0.247198	0.39210	N	0.001422	T	0.03959	0.0111	L	0.40543	1.245	0.80722	D	1	B	0.25007	0.116	B	0.30401	0.115	T	0.49688	-0.8913	10	0.37606	T	0.19	.	12.9506	0.58399	0.2839:0.7161:0.0:0.0	.	1025	Q9H6S0	YTDC2_HUMAN	V	1025;935	ENSP00000161863:A1025V	ENSP00000161863:A1025V	A	+	2	0	YTHDC2	112931275	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.662000	0.54510	2.561000	0.86390	0.655000	0.94253	GCA	.	.		0.343	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		T	112903376	C	T	112903376	3	4	65	1	0	0	0	0	1	0	0	0	17512	710	25	3	3164	3	YTHDC2	5	112903376	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	4522885	112903376	68011884	133	8206										
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125813469	125813469	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgccctgatcatagcaacagTcacagacagggtgagtatgc	11	11	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:125813469T>C	ENST00000285689.3	+	6	1033	c.572T>C	c.(571-573)gTc>gCc	p.V191A	GRAMD3_ENST00000515200.1_Missense_Mutation_p.V168A|RP11-517I3.1_ENST00000512500.1_RNA|GRAMD3_ENST00000511134.1_Missense_Mutation_p.V175A|GRAMD3_ENST00000544396.1_Missense_Mutation_p.V87A|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000543198.1_Missense_Mutation_p.V168A|GRAMD3_ENST00000502348.1_Missense_Mutation_p.V82A|GRAMD3_ENST00000513040.1_Missense_Mutation_p.V206A|GRAMD3_ENST00000542322.1_Missense_Mutation_p.V199A	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	191						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		ATAGCAACAGTCACAGACAGG	0.498																																					p.V206A		Atlas-SNP	.											.	GRAMD3	30	.	0			c.T617C						.						93	95	94					5																	125813469		2203	4300	6503	SO:0001583	missense	65983	exon6			CAACAGTCACAGA	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"HCV NS3 transactivated protein 2"					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.572T>C	chr5.hg19:g.125813469T>C	ENSP00000285689:p.Val191Ala	87.0	0.0		91.0	4.0	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	hg19	CCDS4136.1	.	.	.	.	.	.	.	.	.	.	T	4.550	0.102200	0.08731	.	.	ENSG00000155324	ENST00000513040;ENST00000506445;ENST00000543367;ENST00000285689;ENST00000515200;ENST00000542322;ENST00000544396;ENST00000543198;ENST00000502348;ENST00000511134	T;T;T;T;T;T;T;T;T	0.28666	1.6;1.6;1.61;1.62;1.6;1.65;1.62;1.64;1.61	5.55	4.35	0.52113	.	0.474819	0.24945	N	0.034352	T	0.40546	0.1121	M	0.65975	2.015	0.36053	D	0.840867	D;B;B;D;D	0.63046	0.992;0.007;0.039;0.991;0.992	P;B;B;P;P	0.54759	0.749;0.01;0.018;0.76;0.749	T	0.47898	-0.9081	10	0.08837	T	0.75	.	11.676	0.51430	0.133:0.0:0.0:0.867	.	175;87;199;206;191	B7Z8T2;B7Z1F2;B7Z3R1;B7Z6D8;Q96HH9	.;.;.;.;GRAM3_HUMAN	A	206;205;175;191;168;199;87;168;82;175	ENSP00000426120:V206A;ENSP00000424985:V205A;ENSP00000285689:V191A;ENSP00000426143:V168A;ENSP00000441876:V199A;ENSP00000444049:V87A;ENSP00000442902:V168A;ENSP00000427596:V82A;ENSP00000426088:V175A	ENSP00000285689:V191A	V	+	2	0	GRAMD3	125841368	0.003000	0.15002	0.961000	0.40146	0.683000	0.39861	0.754000	0.26390	0.986000	0.38683	0.533000	0.62120	GTC	.	.		0.498	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927		C	125813469	T	C	125813469	3	2	65	1	0	0	0	0	1	0	0	0	6760	1667	58	2	808	2	GRAMD3	5	125813469	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	12910093	125813469	55101791	134	8207										
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188502	140188502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gggtggcactggtggcgcagTgagcgagctggtgccatggt	20	8	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:140188502T>C	ENST00000530339.1	+	1	1730	c.1730T>C	c.(1729-1731)gTg>gCg	p.V577A	PCDHA4_ENST00000512229.2_Missense_Mutation_p.V577A|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.V577A|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	577					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGCGCAGTGAGCGAGCTG	0.662																																					p.V577A		Atlas-SNP	.											.	PCDHA4	419	.	0			c.T1730C						.						93	87	89					5																	140188502		2202	4299	6501	SO:0001583	missense	56144	exon1			GCGCAGTGAGCGA	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"Cadherins / Protocadherins : Clustered"	8670	other	complex locus constituent	"ortholog of mouse CNR1, KIAA0345-like 10"	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1730T>C	chr5.hg19:g.140188502T>C	ENSP00000435300:p.Val577Ala	60.0	0.0		94.0	4.0	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	hg19	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	t	0.011	-1.736368	0.00681	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.38240	1.15;1.15;1.15	4.08	2.86	0.33363	Cadherin-like (1);	1.047260	0.07710	U	0.941924	T	0.23094	0.0558	N	0.21583	0.68	0.09310	N	1	B;B;B	0.18610	0.005;0.029;0.019	B;B;B	0.21151	0.012;0.033;0.02	T	0.31752	-0.9932	10	0.21540	T	0.41	.	4.7115	0.12875	0.0:0.1405:0.1829:0.6766	.	577;577;577	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	A	577	ENSP00000423470:V577A;ENSP00000349344:V577A;ENSP00000435300:V577A	ENSP00000349344:V577A	V	+	2	0	PCDHA4	140168686	0.013000	0.17824	0.165000	0.22776	0.045000	0.14185	0.521000	0.22893	0.529000	0.28599	0.397000	0.26171	GTG	.	.		0.662	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		C	140188502	T	C	140188502	3	2	65	1	0	0	0	0	1	0	0	0	11535	1696	59	2	1732	2	PCDHA4	5	140188502	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	14375033	140188502	40726758	135	8208										
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140605206	140605206	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctcggtgctcctgttcgtggCggtgcggctgtgcaggagga	18	10	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:140605206C>T	ENST00000239449.4	+	1	2129	c.2129C>T	c.(2128-2130)gCg>gTg	p.A710V	PCDHB14_ENST00000515856.2_Missense_Mutation_p.A557V	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	710					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A710V(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGTTCGTGGCGGTGCGGCTG	0.706																																					p.A710V	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											PCDHB14,NS,carcinoma,0,1	PCDHB14	132	.	1	Substitution - Missense(1)	prostate(1)	c.C2129T						.						69	84	79					5																	140605206		2180	4234	6414	SO:0001583	missense	56122	exon1			TCGTGGCGGTGCG	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"Cadherins / Protocadherins : Clustered"	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.2129C>T	chr5.hg19:g.140605206C>T	ENSP00000239449:p.Ala710Val	34.0	0.0		57.0	4.0	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	hg19	CCDS4256.1	.	.	.	.	.	.	.	.	.	.	-	15.77	2.930353	0.52866	.	.	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.15603	2.41;2.41	4.36	0.0913	0.14467	.	.	.	.	.	T	0.25344	0.0616	M	0.91561	3.22	0.09310	N	1	B	0.22541	0.071	B	0.17722	0.019	T	0.26189	-1.0110	9	0.45353	T	0.12	.	6.8613	0.24067	0.0:0.5331:0.2524:0.2145	.	710	Q9Y5E9	PCDBE_HUMAN	V	557;710	ENSP00000444518:A557V;ENSP00000239449:A710V	ENSP00000239449:A710V	A	+	2	0	PCDHB14	140585390	0.000000	0.05858	0.066000	0.19879	0.362000	0.29581	-0.294000	0.08309	0.027000	0.15297	-0.181000	0.13052	GCG	.	.		0.706	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		T	140605206	C	T	140605206	3	4	65	1	0	0	0	0	1	0	0	0	11548	768	27	1	2131	1	PCDHB14	5	140605206	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	416704	140605206	40310054	136	8209										
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140744024	140744024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cggaggagctggacaaaggcTccttcgtcggcaacatagcc	13	12	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:140744024T>C	ENST00000518069.1	+	1	127	c.127T>C	c.(127-129)Tcc>Ccc	p.S43P	PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	43	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACAAAGGCTCCTTCGTCGG	0.647																																					p.S43P		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.T127C						.						36	46	43					5																	140744024		2194	4299	6493	SO:0001583	missense	56110	exon1			AAAGGCTCCTTCG	AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.127T>C	chr5.hg19:g.140744024T>C	ENSP00000429834:p.Ser43Pro	108.0	0.0		90.0	4.0	NM_032054	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	hg19	CCDS54925.1	.	.	.	.	.	.	.	.	.	.	.	17.77	3.472337	0.63737	.	.	ENSG00000253485	ENST00000518069	T	0.39997	1.05	5.38	2.84	0.33178	Cadherin, N-terminal (1);Cadherin (1);Cadherin-like (1);	.	.	.	.	T	0.77478	0.4136	H	0.99156	4.45	0.29025	N	0.886035	D;D	0.64830	0.976;0.994	D;D	0.71656	0.935;0.974	T	0.75628	-0.3252	9	0.87932	D	0	.	12.0617	0.53566	0.0:0.0:0.2729:0.7271	.	43;43	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	P	43	ENSP00000429834:S43P	ENSP00000429834:S43P	S	+	1	0	PCDHGA5	140724208	0.047000	0.20315	0.997000	0.53966	0.970000	0.65996	0.300000	0.19156	0.385000	0.24970	0.456000	0.33151	TCC	.	.		0.647	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		C	140744024	T	C	140744024	3	2	65	1	0	0	0	0	1	0	0	0	11566	1551	54	2	129	2	PCDHGA5	5	140744024	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	138818	140744024	40171236	137	8210										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141059772	141059772	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acggtcctgggcttcggcacGggcttagggggctgggcttg	19	10	0	0	rs146312944		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:141059772G>A	ENST00000239440.4	-	2	347	c.282C>T	c.(280-282)ccC>ccT	p.P94P	ARAP3_ENST00000508305.1_Silent_p.P16P	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	94	Pro-rich.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GCTTCGGCACGGGCTTAGGGG	0.652																																					p.P94P		Atlas-SNP	.											.	ARAP3	139	.	0			c.C282T						.	G		0,4406		0,0,2203	48	58	54		282	-7.8	1	5	dbSNP_134	54	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ARAP3	NM_022481.5		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		94/1545	141059772	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	64411	exon2			CGGCACGGGCTTA	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.282C>T	chr5.hg19:g.141059772G>A		150.0	0.0		134.0	66.0	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	hg19	CCDS4266.1																																																																																			.	G|1.000;A|0.000		0.652	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		A	141059772	G	A	141059772	2	1	65	1	0	0	0	0	0	0	0	1	840	1103	39	1		1	ARAP3	5	141059772	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	315748	141059772	39855488	138	8211										
FAT2	2196	hgsc.bcm.edu	37	chr5	150945475	150945475	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agagtcctgcgggctaggggCctcccaccatcactggccca	12	16	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:150945475C>A	ENST00000261800.5	-	1	3030	c.3018G>T	c.(3016-3018)agG>agT	p.R1006S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1006	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGGCTAGGGGCCTCCCACCAT	0.607																																					p.R1006S		Atlas-SNP	.											.	FAT2	465	.	0			c.G3018T						.						47	39	41					5																	150945475		2203	4300	6503	SO:0001583	missense	2196	exon1			TAGGGGCCTCCCA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3018G>T	chr5.hg19:g.150945475C>A	ENSP00000261800:p.Arg1006Ser	128.0	0.0		154.0	9.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	11.12	1.546049	0.27652	.	.	ENSG00000086570	ENST00000261800	T	0.52295	0.67	5.29	2.37	0.29283	Cadherin (4);Cadherin-like (1);	0.469806	0.21212	N	0.078281	T	0.22666	0.0547	N	0.03029	-0.43	0.39950	D	0.974527	B	0.23540	0.087	B	0.34590	0.186	T	0.06534	-1.0821	10	0.10636	T	0.68	.	8.4861	0.33071	0.0:0.6866:0.0:0.3134	.	1006	Q9NYQ8	FAT2_HUMAN	S	1006	ENSP00000261800:R1006S	ENSP00000261800:R1006S	R	-	3	2	FAT2	150925668	0.042000	0.20092	0.998000	0.56505	0.986000	0.74619	-0.122000	0.10627	1.141000	0.42275	-0.345000	0.07892	AGG	.	.		0.607	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150945475	C	A	150945475	3	1	65	1	0	0	0	0	1	0	0	0	5698	738	26	3	10123	3	FAT2	5	150945475	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	9885703	150945475	29969785	139	8212										
SGCD	6444	hgsc.bcm.edu	37	chr5	155935693	155935693	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cttacaacctctctacgccaAagaaatccagtcccgaccag	5	16	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:155935693A>T	ENST00000435422.3	+	3	759	c.272A>T	c.(271-273)aAa>aTa	p.K91I	SGCD_ENST00000517913.1_Missense_Mutation_p.K92I|SGCD_ENST00000337851.4_Missense_Mutation_p.K92I|SGCD_ENST00000447401.1_Missense_Mutation_p.K92I	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	91					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTCTACGCCAAAGAAATCCAG	0.428																																					p.K92I		Atlas-SNP	.											.	SGCD	52	.	0			c.A275T						.						91	82	85					5																	155935693		1852	4105	5957	SO:0001583	missense	6444	exon4			ACGCCAAAGAAAT	BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29						10807	protein-coding gene	gene with protein product		601411	"sarcoglycan, delta (35kD dystrophin-associated glycoprotein)"			8776597, 8841194, 10974018	Standard	NM_000337		Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000435422.3:c.272A>T	chr5.hg19:g.155935693A>T	ENSP00000403003:p.Lys91Ile	70.0	0.0		63.0	32.0	NM_000337	A8K9S9|Q53XA5|Q99644	Missense_Mutation	SNP	ENST00000435422.3	hg19	CCDS47327.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.683865	0.88639	.	.	ENSG00000170624	ENST00000517913;ENST00000435422;ENST00000337851;ENST00000447401	D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63	5.49	5.49	0.81192	.	0.046978	0.85682	D	0.000000	D	0.96772	0.8946	M	0.75085	2.285	0.58432	D	0.999999	D;D;D	0.89917	0.997;0.997;1.0	D;D;D	0.85130	0.995;0.991;0.997	D	0.96600	0.9444	10	0.46703	T	0.11	-7.3453	14.4502	0.67379	1.0:0.0:0.0:0.0	.	91;92;92	Q92629;Q92629-2;Q92629-3	SGCD_HUMAN;.;.	I	92;91;92;92	ENSP00000429378:K92I;ENSP00000403003:K91I;ENSP00000338343:K92I;ENSP00000408324:K92I	ENSP00000338343:K92I	K	+	2	0	SGCD	155868271	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.832000	0.92079	2.205000	0.71048	0.477000	0.44152	AAA	.	.		0.428	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3			T	155935693	A	T	155935693	3	4	65	1	0	0	0	0	1	0	0	0	14216	14	1	4	285	4	SGCD	5	155935693	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	4990218	155935693	24979567	140	8213										
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156755023	156755023	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttgtctacaagctggcagacCagatctttgcttactacaaa	7	10	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:156755023C>G	ENST00000521420.1	+	18	2135	c.2044C>G	c.(2044-2046)Cag>Gag	p.Q682E	CYFIP2_ENST00000347377.6_Missense_Mutation_p.Q708E|CYFIP2_ENST00000318218.6_Missense_Mutation_p.Q733E|CYFIP2_ENST00000377576.3_Missense_Mutation_p.Q708E|CYFIP2_ENST00000435847.2_Missense_Mutation_p.Q407E|CYFIP2_ENST00000522463.1_Missense_Mutation_p.Q512E|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000541131.1_Missense_Mutation_p.Q633E					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GCTGGCAGACCAGATCTTTGC	0.473																																					p.Q708E		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C2122G						.						80	78	79					5																	156755023		1930	4147	6077	SO:0001583	missense	26999	exon19			GCAGACCAGATCT	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.2044C>G	chr5.hg19:g.156755023C>G	ENSP00000430904:p.Gln682Glu	115.0	0.0		108.0	21.0	NM_001037332		Missense_Mutation	SNP	ENST00000521420.1	hg19		.	.	.	.	.	.	.	.	.	.	C	23.8	4.464423	0.84425	.	.	ENSG00000055163	ENST00000318218;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576;ENST00000541131;ENST00000435847	T;T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84;1.84	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.48223	0.1488	M	0.75085	2.285	0.80722	D	1	P;P;D;P;P;B	0.54772	0.792;0.952;0.968;0.951;0.705;0.303	P;P;P;P;B;P	0.56960	0.519;0.81;0.764;0.6;0.343;0.471	T	0.28490	-1.0042	10	0.33141	T	0.24	-31.9868	19.8968	0.96969	0.0:1.0:0.0:0.0	.	572;512;682;708;708;733	A8MUM2;E7EW33;E7EVJ5;E7EVF4;Q96F07-2;Q96F07	.;.;.;.;.;CYFP2_HUMAN	E	733;512;682;708;708;633;407	ENSP00000325817:Q733E;ENSP00000428009:Q512E;ENSP00000430904:Q682E;ENSP00000313567:Q708E;ENSP00000366799:Q708E;ENSP00000444645:Q633E;ENSP00000403793:Q407E	ENSP00000325817:Q733E	Q	+	1	0	CYFIP2	156687601	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.691000	0.91804	0.655000	0.94253	CAG	.	.		0.473	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		G	156755023	C	G	156755023	3	3	65	1	0	0	0	0	1	0	0	0	4140	595	21	4	2192	4	CYFIP2	5	156755023	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	819330	156755023	24160237	141	8214										
HMMR	3161	hgsc.bcm.edu	37	chr5	162911119	162911119	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaaaaacaggcattgttgaaTgaacatggtgcagctcagga	12	6	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr5:162911119T>G	ENST00000358715.3	+	16	1863	c.1827T>G	c.(1825-1827)aaT>aaG	p.N609K	RP11-80G7.1_ENST00000521666.1_RNA|HMMR_ENST00000353866.3_Missense_Mutation_p.N594K|RP11-80G7.1_ENST00000514724.2_RNA|HMMR_ENST00000432118.2_Missense_Mutation_p.N523K|HMMR_ENST00000393915.4_Missense_Mutation_p.N610K			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	609					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	CATTGTTGAATGAACATGGTG	0.299																																					p.N610K		Atlas-SNP	.											.	HMMR	64	.	0			c.T1830G						.						46	50	48					5																	162911119		2203	4298	6501	SO:0001583	missense	3161	exon16			GTTGAATGAACAT	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"CD molecules"	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.1827T>G	chr5.hg19:g.162911119T>G	ENSP00000351554:p.Asn609Lys	127.0	0.0		133.0	9.0	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	hg19	CCDS4362.1	.	.	.	.	.	.	.	.	.	.	T	18.93	3.726716	0.69074	.	.	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.09817	2.94;2.94;2.94;2.94;2.94	5.45	5.45	0.79879	.	0.126941	0.64402	D	0.000001	T	0.18467	0.0443	M	0.75264	2.295	0.43399	D	0.99552	P;P;P;P	0.51791	0.825;0.948;0.911;0.911	B;B;P;P	0.46885	0.444;0.439;0.53;0.53	T	0.04635	-1.0937	10	0.22109	T	0.4	-12.7716	12.8745	0.57982	0.0:0.0:0.1355:0.8645	.	523;610;594;609	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	K	495;594;610;586;523;609	ENSP00000400527:N495K;ENSP00000185942:N594K;ENSP00000377492:N610K;ENSP00000402673:N523K;ENSP00000351554:N609K	ENSP00000185942:N594K	N	+	3	2	HMMR	162843697	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.327000	0.52045	2.189000	0.69895	0.528000	0.53228	AAT	.	.		0.299	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484		G	162911119	T	G	162911119	3	3	65	1	0	0	0	0	1	0	0	0	7251	1461	51	5	1892	5	HMMR	5	162911119	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6156096	162911119	18004141	142	8215										
KIF13A	63971	hgsc.bcm.edu	37	chr6	17834225	17834225	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tctgtttttctcagcttctcTtcccaagtcactgttagttc	5	12	4	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:17834225T>C	ENST00000259711.6	-	12	1338	c.1233A>G	c.(1231-1233)gaA>gaG	p.E411E	KIF13A_ENST00000378816.5_Silent_p.E411E|KIF13A_ENST00000378843.2_Silent_p.E411E|KIF13A_ENST00000378826.2_Silent_p.E411E|KIF13A_ENST00000378814.5_Silent_p.E411E	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	411					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TCAGCTTCTCTTCCCAAGTCA	0.373																																					p.E411E		Atlas-SNP	.											.	KIF13A	276	.	0			c.A1233G						.						161	147	151					6																	17834225		1844	4086	5930	SO:0001819	synonymous_variant	63971	exon12			CTTCTCTTCCCAA	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.1233A>G	chr6.hg19:g.17834225T>C		115.0	0.0		125.0	5.0	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	hg19	CCDS47381.1																																																																																			.	.		0.373	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			C	17834225	T	C	17834225	2	2	65	1	0	0	0	0	0	0	0	1	8283	1606	56	2		2	KIF13A	6	17834225	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		17834225	153280842	143	8216										
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156843	26156843	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gctggctatgacgtggagaaGaacaacagccgcatcaagct	12	10	1	3	rs150948103	byFrequency	TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:26156843G>T	ENST00000304218.3	+	1	285	c.225G>T	c.(223-225)aaG>aaT	p.K75N	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	75	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						ACGTGGAGAAGAACAACAGCC	0.592																																					p.K75N		Atlas-SNP	.											HIST1H1E,NS,carcinoma,0,1	HIST1H1E	69	.	0			c.G225T						.						43	47	45					6																	26156843		2203	4300	6503	SO:0001583	missense	3008	exon1			GGAGAAGAACAAC	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"Histones / Replication-dependent"	4718	protein-coding gene	gene with protein product		142220	"H1 histone family, member 4", "histone 1, H1e"	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.225G>T	chr6.hg19:g.26156843G>T	ENSP00000307705:p.Lys75Asn	129.0	0.0		118.0	28.0	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	hg19	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	20.4	3.984303	0.74474	.	.	ENSG00000168298	ENST00000304218	T	0.12672	2.66	5.35	3.56	0.40772	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.099310	0.64402	D	0.000002	T	0.15782	0.0380	L	0.55990	1.75	0.58432	D	0.999993	P	0.38048	0.616	P	0.54460	0.753	T	0.00904	-1.1520	10	0.87932	D	0	-1.8185	10.4346	0.44428	0.2217:0.0:0.7783:0.0	.	75	P10412	H14_HUMAN	N	75	ENSP00000307705:K75N	ENSP00000307705:K75N	K	+	3	2	HIST1H1E	26264822	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.912000	0.39946	0.738000	0.32606	0.561000	0.74099	AAG	.	G|0.994;A|0.006		0.592	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		T	26156843	G	T	26156843	3	4	65	1	0	0	0	0	1	0	0	0	7135	933	33	3	227	3	HIST1H1E	6	26156843	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	8322618	26156843	144958224	144	8217										
BAT2	7916	hgsc.bcm.edu	37	chr6	31599888	31599888	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccaccaccaggagccccaccTtcaccagccccagcccgctt	6	23	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:31599888T>C	ENST00000376033.2	+	16	3672	c.3438T>C	c.(3436-3438)ccT>ccC	p.P1146P	PRRC2A_ENST00000376007.4_Silent_p.P1146P	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1146	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GAGCCCCACCTTCACCAGCCC	0.677																																					p.P1146P		Atlas-SNP	.											.	PRRC2A	152	.	0			c.T3438C						.						31	41	38					6																	31599888		1509	2707	4216	SO:0001819	synonymous_variant	7916	exon16			CCCACCTTCACCA	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3438T>C	chr6.hg19:g.31599888T>C		90.0	0.0		87.0	4.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	hg19	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	T	5.099	0.203843	0.09704	.	.	ENSG00000204469	ENST00000424184;ENST00000435052	.	.	.	5.29	-9.35	0.00633	.	.	.	.	.	T	0.27063	0.0663	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55341	-0.8156	5	0.87932	D	0	-0.929	0.8815	0.01235	0.198:0.2525:0.2908:0.2587	.	.	.	.	L	1144;1133	.	ENSP00000407986:F1144L	F	+	1	0	PRRC2A	31707867	0.000000	0.05858	0.192000	0.23308	0.930000	0.56654	-0.456000	0.06754	-1.260000	0.02465	-0.912000	0.02778	TTC	.	.		0.677	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		C	31599888	T	C	31599888	2	2	65	1	0	0	0	0	0	0	0	1	1319	1596	56	2		2	BAT2	6	31599888	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	5443045	31599888	139515179	145	8218										
BAT3	7917	hgsc.bcm.edu	37	chr6	31610072	31610072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctcaagacccaggcctccagGactccctgcgccaccagaag	9	18	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:31610072G>A	ENST00000375964.6	-	15	2375	c.2062C>T	c.(2062-2064)Cct>Tct	p.P688S	BAG6_ENST00000404765.2_Missense_Mutation_p.P718S|BAG6_ENST00000470875.1_5'UTR|BAG6_ENST00000362049.6_Missense_Mutation_p.P682S|BAG6_ENST00000439687.2_Missense_Mutation_p.P556S|BAG6_ENST00000375976.4_Missense_Mutation_p.P682S|BAG6_ENST00000211379.5_Missense_Mutation_p.P682S	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	688					brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						AGGCCTCCAGGACTCCCTGCG	0.682																																					p.P688S		Atlas-SNP	.											.	BAG6	73	.	0			c.C2062T						.						9	9	9					6																	31610072		1497	2694	4191	SO:0001583	missense	7917	exon15			CTCCAGGACTCCC	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"HLA-B associated transcript 3"	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.2062C>T	chr6.hg19:g.31610072G>A	ENSP00000365131:p.Pro688Ser	66.0	0.0		102.0	7.0	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Missense_Mutation	SNP	ENST00000375964.6	hg19	CCDS47403.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.626236	0.28978	.	.	ENSG00000204463	ENST00000375976;ENST00000375964;ENST00000211379;ENST00000404765;ENST00000439687;ENST00000362049;ENST00000437771	T;T;T;T;T;T;T	0.53206	1.52;1.51;1.52;1.51;0.63;1.49;0.82	5.75	4.83	0.62350	.	0.067860	0.56097	D	0.000030	T	0.19927	0.0479	N	0.19112	0.55	0.32818	D	0.502398	B;B;B;B	0.23185	0.043;0.073;0.081;0.056	B;B;B;B	0.25405	0.027;0.06;0.014;0.022	T	0.08249	-1.0731	10	0.42905	T	0.14	.	13.5612	0.61790	0.0:0.1562:0.8438:0.0	.	556;682;688;682	E7EMZ4;F8VXY4;P46379;P46379-2	.;.;BAG6_HUMAN;.	S	682;688;682;718;556;682;718	ENSP00000365143:P682S;ENSP00000365131:P688S;ENSP00000211379:P682S;ENSP00000384494:P718S;ENSP00000402856:P556S;ENSP00000354875:P682S;ENSP00000397978:P718S	ENSP00000211379:P682S	P	-	1	0	BAG6	31718051	0.965000	0.33210	0.998000	0.56505	0.984000	0.73092	1.762000	0.38451	2.731000	0.93534	0.650000	0.86243	CCT	.	.		0.682	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703		A	31610072	G	A	31610072	3	1	65	1	0	0	0	0	1	0	0	0	1322	1174	41	3	1380	3	BAT3	6	31610072	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	10184	31610072	139504995	146	8219										
FAM83B	222584	hgsc.bcm.edu	37	chr6	54805894	54805894	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atttgctgaaaagttctaaaAgcatgcacaatgtgactcat	7	7	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:54805894A>G	ENST00000306858.7	+	5	2241	c.2125A>G	c.(2125-2127)Agc>Ggc	p.S709G	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	709										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					AAGTTCTAAAAGCATGCACAA	0.403																																					p.S709G		Atlas-SNP	.											.	FAM83B	186	.	0			c.A2125G						.						91	93	92					6																	54805894		2203	4300	6503	SO:0001583	missense	222584	exon5			TCTAAAAGCATGC	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 143"	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.2125A>G	chr6.hg19:g.54805894A>G	ENSP00000304078:p.Ser709Gly	72.0	0.0		78.0	4.0	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	hg19	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.005123	0.54254	.	.	ENSG00000168143	ENST00000306858	T	0.34859	1.34	5.55	5.55	0.83447	.	3.202220	0.00924	N	0.002632	T	0.56202	0.1969	M	0.69823	2.125	0.45962	D	0.998789	D	0.69078	0.997	D	0.75020	0.985	T	0.21999	-1.0229	10	0.45353	T	0.12	-21.4701	15.9896	0.80193	1.0:0.0:0.0:0.0	.	709	Q5T0W9	FA83B_HUMAN	G	709	ENSP00000304078:S709G	ENSP00000304078:S709G	S	+	1	0	FAM83B	54913853	1.000000	0.71417	0.995000	0.50966	0.583000	0.36354	6.540000	0.73861	2.238000	0.73509	0.533000	0.62120	AGC	.	.		0.403	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		G	54805894	A	G	54805894	3	3	65	1	0	0	0	0	1	0	0	0	5642	72	3	2	2139	2	FAM83B	6	54805894	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	23195822	54805894	116309173	147	8220										
FAM46A	55603	hgsc.bcm.edu	37	chr6	82461742	82461742	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccgccaccgccgaagtcgccGccgccgaagtcgccgccgcc	12	22	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:82461742G>A	ENST00000320172.6	-	2	431	c.117C>T	c.(115-117)ggC>ggT	p.G39G	FAM46A_ENST00000369756.3_Silent_p.G120G|FAM46A_ENST00000369754.3_Silent_p.G58G	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	39			Missing. {ECO:0000269|PubMed:12054608, ECO:0000269|PubMed:16545789}.		regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		cgaagtcgccgccgccgaagt	0.667																																					p.G39G		Atlas-SNP	.											.	FAM46A	37	.	0			c.C117T						.						7	8	8					6																	82461742		1601	3424	5025	SO:0001819	synonymous_variant	55603	exon2			GTCGCCGCCGCCG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.117C>T	chr6.hg19:g.82461742G>A		14.0	0.0		34.0	4.0	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	hg19	CCDS34489.1																																																																																			.	.		0.667	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			A	82461742	G	A	82461742	2	1	65	1	0	0	0	0	0	0	0	1	5573	1074	38	1		1	FAM46A	6	82461742	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	27655848	82461742	88653325	148	8221										
PGM3	5238	hgsc.bcm.edu	37	chr6	83889643	83889643	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	taaacaattctgtctgcatcTccatcaaaagaacagcatct	4	11	5	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:83889643T>C	ENST00000283977.4	-	6	714	c.588A>G	c.(586-588)ggA>ggG	p.G196G	PGM3_ENST00000512866.1_Silent_p.G277G|PGM3_ENST00000513973.1_Silent_p.G277G|PGM3_ENST00000506587.1_Silent_p.G305G					phosphoglucomutase 3											NS(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	18		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)		TGTCTGCATCTCCATCAAAAG	0.343																																					p.G305G		Atlas-SNP	.											.	PGM3	39	.	0			c.A915G						.						147	124	132					6																	83889643		2203	4300	6503	SO:0001819	synonymous_variant	5238	exon8			TGCATCTCCATCA	BC001258	CCDS4997.1, CCDS56435.1, CCDS56436.1, CCDS75487.1	6q14.1-q15	2012-10-02			ENSG00000013375	ENSG00000013375	5.4.2.3		8907	protein-coding gene	gene with protein product	"acetylglucosamine phosphomutase"	172100				12174217, 10721701	Standard	NM_001199917		Approved	AGM1, DKFZP434B187, PAGM	uc011dyz.2	O95394	OTTHUMG00000015110	ENST00000283977.4:c.588A>G	chr6.hg19:g.83889643T>C		116.0	0.0		108.0	5.0	NM_001199917		Silent	SNP	ENST00000283977.4	hg19																																																																																				.	.		0.343	PGM3-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000366385.2	NM_015599		C	83889643	T	C	83889643	2	2	65	1	0	0	0	0	0	0	0	1	11809	1538	54	2		2	PGM3	6	83889643	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1427901	83889643	87225424	149	8222										
MDN1	23195	hgsc.bcm.edu	37	chr6	90428856	90428856	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	attatcctagtctccttaccTgaacatcatagggagtgata	7	9	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:90428856T>C	ENST00000369393.3	-	41	6171	c.6056A>G	c.(6055-6057)cAg>cGg	p.Q2019R	MDN1_ENST00000428876.1_Splice_Site_p.Q2019R			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2019					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCTCCTTACCTGAACATCATA	0.413																																					p.Q2019R		Atlas-SNP	.											.	MDN1	478	.	0			c.A6056G						.						102	93	96					6																	90428856		2203	4300	6503	SO:0001630	splice_region_variant	23195	exon41			CTTACCTGAACAT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.6057+1A>G	chr6.hg19:g.90428856T>C		60.0	0.0		57.0	4.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.499108	0.44455	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03553	3.89;3.89	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.02807	0.0084	M	0.70275	2.135	0.58432	D	0.99999	B	0.16166	0.016	B	0.27076	0.076	T	0.32508	-0.9904	10	0.18276	T	0.48	.	14.3369	0.66598	0.0:0.0:0.0:1.0	.	2019	Q9NU22	MDN1_HUMAN	R	2019	ENSP00000358400:Q2019R;ENSP00000413970:Q2019R	ENSP00000358400:Q2019R	Q	-	2	0	MDN1	90485577	1.000000	0.71417	0.998000	0.56505	0.784000	0.44337	5.493000	0.66899	1.954000	0.56735	0.455000	0.32223	CAG	.	.		0.413	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		Missense_Mutation	C	90428856	T	C	90428856	5	2	65	1	0	0	0	0	0	0	1	0	9424	1594	55	2	10982	2	MDN1	6	90428856	Splice_Site	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6539213	90428856	80686211	150	8223										
MANEA	79694	hgsc.bcm.edu	37	chr6	96053973	96053973	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caagtgtgggcccaggatacAtagataccagcatccgtcca	10	12	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:96053973A>G	ENST00000358812.4	+	5	1215	c.1081A>G	c.(1081-1083)Ata>Gta	p.I361V		NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	361	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		CCCAGGATACATAGATACCAG	0.428																																					p.I361V		Atlas-SNP	.											.	MANEA	58	.	0			c.A1081G						.						94	102	100					6																	96053973		2203	4300	6503	SO:0001583	missense	79694	exon5			GGATACATAGATA	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.1081A>G	chr6.hg19:g.96053973A>G	ENSP00000351669:p.Ile361Val	59.0	0.0		46.0	4.0	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Missense_Mutation	SNP	ENST00000358812.4	hg19	CCDS5032.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.759533	0.49468	.	.	ENSG00000172469	ENST00000358812	.	.	.	6.17	4.95	0.65309	.	0.042725	0.85682	D	0.000000	T	0.41236	0.1150	L	0.54965	1.715	0.51767	D	0.999931	P	0.46277	0.875	P	0.45037	0.467	T	0.28744	-1.0034	9	0.16896	T	0.51	-22.0161	12.5523	0.56233	0.8614:0.1386:0.0:0.0	.	361	Q5SRI9	MANEA_HUMAN	V	361	.	ENSP00000351669:I361V	I	+	1	0	MANEA	96160694	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.638000	0.46562	2.371000	0.80710	0.533000	0.62120	ATA	.	.		0.428	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641		G	96053973	A	G	96053973	3	3	65	1	0	0	0	0	1	0	0	0	9230	217	8	2	1095	2	MANEA	6	96053973	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	5625117	96053973	75061094	151	8224										
NDUFAF4	29078	hgsc.bcm.edu	37	chr6	97339243	97339243	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caatctgaattccttcggctCttgacatgtttcagcagctt	7	11	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:97339243C>T	ENST00000316149.7	-	3	344	c.265G>A	c.(265-267)Gag>Aag	p.E89K	NDUFAF4_ENST00000489477.1_5'UTR	NM_014165.3	NP_054884.1	Q9P032	NDUF4_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 4	89					mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)				large_intestine(5)|lung(3)|ovary(1)|skin(1)	10						TCCTTCGGCTCTTGACATGTT	0.338																																					p.E89K		Atlas-SNP	.											NDUFAF4,colon,carcinoma,0,1	NDUFAF4	16	.	0			c.G265A						.						73	76	75					6																	97339243		2202	4300	6502	SO:0001583	missense	29078	exon3			TCGGCTCTTGACA	AF161474	CCDS5037.1	6q16.3	2012-10-12	2012-05-08	2009-03-18	ENSG00000123545	ENSG00000123545		"Mitochondrial respiratory chain complex assembly factors"	21034	protein-coding gene	gene with protein product		611776	"chromosome 6 open reading frame 66", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4"	C6orf66		11042152, 18179882	Standard	NM_014165		Approved	HSPC125, bA22L21.1, My013, HRPAP20	uc003pow.3	Q9P032	OTTHUMG00000015246	ENST00000316149.7:c.265G>A	chr6.hg19:g.97339243C>T	ENSP00000358272:p.Glu89Lys	48.0	0.0		38.0	2.0	NM_014165	B2R4J5	Missense_Mutation	SNP	ENST00000316149.7	hg19	CCDS5037.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.095262	0.00364	.	.	ENSG00000123545	ENST00000316149	D	0.82526	-1.62	3.88	-0.359	0.12571	.	0.376069	0.27084	N	0.021007	T	0.41858	0.1177	L	0.36672	1.1	0.09310	N	1	B	0.15141	0.012	B	0.12156	0.007	T	0.42816	-0.9429	10	0.02654	T	1	-7.467	4.2716	0.10789	0.0:0.3023:0.3191:0.3785	.	89	Q9P032	NDUF4_HUMAN	K	89	ENSP00000358272:E89K	ENSP00000358272:E89K	E	-	1	0	NDUFAF4	97445964	0.000000	0.05858	0.028000	0.17463	0.052000	0.14988	-0.796000	0.04575	-0.086000	0.12550	0.655000	0.94253	GAG	.	.		0.338	NDUFAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041567.1	NM_014165		T	97339243	C	T	97339243	3	4	65	1	0	0	0	0	1	0	0	0	10286	922	32	3	266	3	NDUFAF4	6	97339243	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	1285270	97339243	73775824	152	8225										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101109765	101109765	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gagcaaagtgaggtaatggcTgagtttatcatgcgttgtta	13	4	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:101109765T>C	ENST00000369162.2	-	16	2964	c.2620A>G	c.(2620-2622)Agc>Ggc	p.S874G		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	874	Helicase C-terminal 1. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		AGGTAATGGCTGAGTTTATCA	0.398																																					p.S874G		Atlas-SNP	.											.	ASCC3	205	.	0			c.A2620G						.						194	187	190					6																	101109765		2203	4300	6503	SO:0001583	missense	10973	exon16			AATGGCTGAGTTT	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.2620A>G	chr6.hg19:g.101109765T>C	ENSP00000358159:p.Ser874Gly	108.0	0.0		110.0	5.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	T	18.80	3.701149	0.68501	.	.	ENSG00000112249	ENST00000369162	D	0.91351	-2.83	5.76	5.76	0.90799	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83797	0.5332	L	0.42008	1.315	0.80722	D	1	P	0.51449	0.945	B	0.41466	0.358	D	0.85473	0.1174	10	0.45353	T	0.12	.	16.3786	0.83431	0.0:0.0:0.0:1.0	.	874	Q8N3C0	HELC1_HUMAN	G	874	ENSP00000358159:S874G	ENSP00000358159:S874G	S	-	1	0	ASCC3	101216486	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.043000	0.71004	2.323000	0.78572	0.528000	0.53228	AGC	.	.		0.398	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		C	101109765	T	C	101109765	3	2	65	1	0	0	0	0	1	0	0	0	1033	1580	55	2	4096	2	ASCC3	6	101109765	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3770522	101109765	70005302	153	8226										
FRK	2444	hgsc.bcm.edu	37	chr6	116263618	116263618	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atctgaatatgaagagtctgTttcaaaatagtcttcaagtt	7	5	5	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:116263618T>C	ENST00000606080.1	-	8	1923	c.1477A>G	c.(1477-1479)Aca>Gca	p.T493A	FRK_ENST00000538210.1_Missense_Mutation_p.T351A	NM_002031.2	NP_002022.1	P42685	FRK_HUMAN	fyn-related Src family tyrosine kinase	493					cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|skin(1)|urinary_tract(1)	27		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	Regorafenib(DB08896)	GAAGAGTCTGTTTCAAAATAG	0.348																																					p.T493A		Atlas-SNP	.											.	FRK	78	.	0			c.A1477G						.						121	119	120					6																	116263618		2203	4300	6503	SO:0001583	missense	2444	exon8			AGTCTGTTTCAAA	U00803	CCDS5103.1	6q21-q22.3	2014-06-25	2014-06-25		ENSG00000111816	ENSG00000111816	2.7.10.1	"SH2 domain containing"	3955	protein-coding gene	gene with protein product		606573	"PTK5 protein tyrosine kinase 5", "fyn-related kinase"	PTK5		7510261	Standard	NM_002031		Approved	RAK, GTK	uc003pwi.1	P42685	OTTHUMG00000015424	ENST00000606080.1:c.1477A>G	chr6.hg19:g.116263618T>C	ENSP00000476145:p.Thr493Ala	143.0	0.0		102.0	5.0	NM_002031	B4DY49|Q13128|Q9NTR5	Missense_Mutation	SNP	ENST00000606080.1	hg19	CCDS5103.1	.	.	.	.	.	.	.	.	.	.	T	9.235	1.036780	0.19669	.	.	ENSG00000111816	ENST00000368626;ENST00000538210	T;T	0.73258	-0.73;-0.7	5.07	-2.3	0.06785	.	1.288910	0.05491	N	0.556561	T	0.22205	0.0535	N	0.04148	-0.265	0.23215	N	0.998102	B	0.02656	0.0	B	0.01281	0.0	T	0.15178	-1.0446	10	0.56958	D	0.05	.	3.1631	0.06527	0.1057:0.2662:0.0989:0.5292	.	493	P42685	FRK_HUMAN	A	493;351	ENSP00000357615:T493A;ENSP00000443075:T351A	ENSP00000357615:T493A	T	-	1	0	FRK	116370311	0.000000	0.05858	0.946000	0.38457	0.776000	0.43924	0.034000	0.13776	-0.144000	0.11314	0.482000	0.46254	ACA	.	.		0.348	FRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041924.2	NM_002031		C	116263618	T	C	116263618	3	2	65	1	0	0	0	0	1	0	0	0	6056	1725	60	2	44	2	FRK	6	116263618	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	15153853	116263618	54851449	154	8227										
ZUFSP	221302	hgsc.bcm.edu	37	chr6	116987986	116987986	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caggaattttctagattcagTtaagttctctgaatagaagc	8	6	3	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:116987986T>C	ENST00000368576.3	-	2	613	c.370A>G	c.(370-372)Act>Gct	p.T124A	ZUFSP_ENST00000368573.1_Missense_Mutation_p.T124A|ZUFSP_ENST00000471919.1_5'UTR	NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	124							metal ion binding (GO:0046872)	p.T124A(1)		NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		CTAGATTCAGTTAAGTTCTCT	0.353																																					p.T124A		Atlas-SNP	.											ZUFSP,NS,carcinoma,0,1	ZUFSP	46	.	1	Substitution - Missense(1)	kidney(1)	c.A370G						.						109	103	105					6																	116987986		2203	4298	6501	SO:0001583	missense	221302	exon2			ATTCAGTTAAGTT	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"Zinc fingers, C2H2-type"	21224	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 113"	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.370A>G	chr6.hg19:g.116987986T>C	ENSP00000357565:p.Thr124Ala	171.0	1.0		134.0	6.0	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Missense_Mutation	SNP	ENST00000368576.3	hg19	CCDS5110.1	.	.	.	.	.	.	.	.	.	.	T	10.69	1.420125	0.25552	.	.	ENSG00000153975	ENST00000368576;ENST00000368573	T	0.42900	0.96	5.75	0.136	0.14780	.	0.916720	0.09557	N	0.786063	T	0.07954	0.0199	L	0.27053	0.805	0.28771	N	0.900391	B	0.06786	0.001	B	0.04013	0.001	T	0.36163	-0.9759	10	0.08179	T	0.78	-9.1578	5.5646	0.17163	0.0:0.152:0.2707:0.5773	.	124	Q96AP4	ZUFSP_HUMAN	A	124	ENSP00000357565:T124A	ENSP00000357562:T124A	T	-	1	0	ZUFSP	117094679	0.510000	0.26171	0.950000	0.38849	0.954000	0.61252	0.185000	0.16958	0.075000	0.16796	-0.316000	0.08728	ACT	.	.		0.353	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062		C	116987986	T	C	116987986	3	2	65	1	0	0	0	0	1	0	0	0	18261	1725	60	2	1402	2	ZUFSP	6	116987986	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	724368	116987986	54127081	155	8228										
GJA1	2697	hgsc.bcm.edu	37	chr6	121768871	121768871	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caagctggttactggcgacaGaaacaattcttcttgccgca	9	11	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:121768871G>A	ENST00000282561.3	+	2	1035	c.878G>A	c.(877-879)aGa>aAa	p.R293K		NM_000165.3	NP_000156.1	P17302	CXA1_HUMAN	gap junction protein, alpha 1, 43kDa	293					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|atrial cardiac muscle cell action potential (GO:0086014)|atrial ventricular junction remodeling (GO:0003294)|blood vessel morphogenesis (GO:0048514)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|cell-cell signaling (GO:0007267)|cellular response to mechanical stimulus (GO:0071260)|chronic inflammatory response (GO:0002544)|embryonic digit morphogenesis (GO:0042733)|endothelium development (GO:0003158)|epithelial cell maturation (GO:0002070)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lens development in camera-type eye (GO:0002088)|membrane organization (GO:0061024)|milk ejection (GO:0060156)|muscle contraction (GO:0006936)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of gene expression (GO:0010629)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|osteoblast differentiation (GO:0001649)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of cell communication by chemical coupling (GO:0010652)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein oligomerization (GO:0051259)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of bone mineralization (GO:0030500)|regulation of bone remodeling (GO:0046850)|regulation of calcium ion transport (GO:0051924)|regulation of tight junction assembly (GO:2000810)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to fluid shear stress (GO:0034405)|response to peptide hormone (GO:0043434)|response to pH (GO:0009268)|signal transduction (GO:0007165)|skeletal muscle tissue regeneration (GO:0043403)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vascular transport (GO:0010232)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|contractile fiber (GO:0043292)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gap junction (GO:0005921)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial outer membrane (GO:0005741)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion transmembrane transporter activity (GO:0015075)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(2)|large_intestine(10)|liver(2)|lung(13)|ovary(2)	33				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	ACTGGCGACAGAAACAATTCT	0.493																																					p.R293K		Atlas-SNP	.											.	GJA1	61	.	0			c.G878A						.						70	71	71					6																	121768871		2203	4300	6503	SO:0001583	missense	2697	exon2			GCGACAGAAACAA	BC026329	CCDS5123.1	6q22.31	2013-05-10	2007-01-16		ENSG00000152661	ENSG00000152661		"Ion channels / Gap junction proteins (connexins)"	4274	protein-coding gene	gene with protein product	"oculodentodigital dysplasia (syndactyly type III)", "connexin 43"	121014	"gap junction protein, alpha-like", "gap junction protein, alpha 1, 43kDa (connexin 43)"	ODDD, GJAL		10331943, 1646158	Standard	NM_000165		Approved	CX43, ODD, ODOD, SDTY3	uc003pyr.3	P17302	OTTHUMG00000015479	ENST00000282561.3:c.878G>A	chr6.hg19:g.121768871G>A	ENSP00000282561:p.Arg293Lys	85.0	0.0		50.0	6.0	NM_000165	B2R5U9|Q6FHU1|Q9Y5I8	Missense_Mutation	SNP	ENST00000282561.3	hg19	CCDS5123.1	.	.	.	.	.	.	.	.	.	.	G	3.809	-0.040069	0.07497	.	.	ENSG00000152661	ENST00000440608;ENST00000282561	T	0.81415	-1.49	5.18	5.18	0.71444	Gap junction alpha-1 protein (Cx43), C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.51924	0.1703	N	0.14661	0.345	0.45403	D	0.998381	B	0.09022	0.002	B	0.19148	0.024	T	0.55630	-0.8111	10	0.07644	T	0.81	.	18.8905	0.92399	0.0:0.0:1.0:0.0	.	293	P17302	CXA1_HUMAN	K	277;293	ENSP00000282561:R293K	ENSP00000282561:R293K	R	+	2	0	GJA1	121810570	1.000000	0.71417	1.000000	0.80357	0.201000	0.24016	6.511000	0.73733	2.694000	0.91930	0.585000	0.79938	AGA	.	.		0.493	GJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042023.1	NM_000165		A	121768871	G	A	121768871	3	1	65	1	0	0	0	0	1	0	0	0	6408	942	33	3	880	3	GJA1	6	121768871	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	4780885	121768871	49346196	156	8229										
CENPW	387103	hgsc.bcm.edu	37	chr6	126661441	126661441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tggcgctgtcgaccatagtcTcccagaggaagcagataaag	12	10	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:126661441T>C	ENST00000368328.4	+	1	122	c.22T>C	c.(22-24)Tcc>Ccc	p.S8P	CENPW_ENST00000368326.1_Missense_Mutation_p.S8P|CENPW_ENST00000368325.1_Missense_Mutation_p.S8P			Q5EE01	CENPW_HUMAN	centromere protein W	8					CENP-A containing nucleosome assembly (GO:0034080)|chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|kinetochore (GO:0000776)|nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(2)|large_intestine(1)|lung(3)	6						GACCATAGTCTCCCAGAGGAA	0.552																																					p.S8P		Atlas-SNP	.											.	CENPW	7	.	0			c.T22C						.						92	82	86					6																	126661441		2203	4300	6503	SO:0001583	missense	387103	exon1			ATAGTCTCCCAGA	BC039556	CCDS34529.1, CCDS69196.1, CCDS75516.1	6q22.32	2013-11-05	2010-04-16	2010-04-16	ENSG00000203760	ENSG00000203760			21488	protein-coding gene	gene with protein product	"cancer-upregulated gene 2"	611264	"chromosome 6 open reading frame 173"	C6orf173		17610844, 19070575	Standard	NM_001286524		Approved	CUG2	uc003qao.3	Q5EE01	OTTHUMG00000015518	ENST00000368328.4:c.22T>C	chr6.hg19:g.126661441T>C	ENSP00000357311:p.Ser8Pro	66.0	0.0		68.0	4.0	NM_001012507	A6NIR0|A6NJC2	Missense_Mutation	SNP	ENST00000368328.4	hg19	CCDS34529.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.457897	0.43634	.	.	ENSG00000203760	ENST00000368326;ENST00000368325;ENST00000368328	.	.	.	5.52	-3.96	0.04106	.	0.613491	0.14700	N	0.303603	T	0.08891	0.0220	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.21586	-1.0241	8	0.59425	D	0.04	-2.9097	2.1334	0.03755	0.1209:0.2813:0.1235:0.4743	.	8	Q5EE01	CENPW_HUMAN	P	8	.	ENSP00000357308:S8P	S	+	1	0	CENPW	126703134	0.001000	0.12720	0.000000	0.03702	0.199000	0.23934	0.550000	0.23345	-0.302000	0.08869	-0.371000	0.07208	TCC	.	.		0.552	CENPW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042104.1			C	126661441	T	C	126661441	3	2	65	1	0	0	0	0	1	0	0	0	3246	1551	54	2	24	2	CENPW	6	126661441	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4892570	126661441	44453626	157	8230										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128388889	128388889	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cattccatggctccggcttcTctcttggttcggtgtgggtg	13	11	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:128388889T>C	ENST00000368215.3	-	12	1931	c.1932A>G	c.(1930-1932)agA>agG	p.R644R	PTPRK_ENST00000368227.3_Silent_p.R644R|PTPRK_ENST00000368226.4_Silent_p.R644R|PTPRK_ENST00000368207.3_Silent_p.R644R|PTPRK_ENST00000368210.3_Silent_p.R644R|PTPRK_ENST00000368213.5_Silent_p.R644R|PTPRK_ENST00000532331.1_Silent_p.R644R|RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000524481.1_5'UTR			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	644	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.	Cleavage. {ECO:0000305}.			cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		CTCCGGCTTCTCTCTTGGTTC	0.463																																					p.R644R		Atlas-SNP	.											.	PTPRK	330	.	0			c.A1932G						.						74	79	78					6																	128388889		2203	4300	6503	SO:0001819	synonymous_variant	5796	exon12			GGCTTCTCTCTTG	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.1932A>G	chr6.hg19:g.128388889T>C		97.0	0.0		83.0	4.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Silent	SNP	ENST00000368215.3	hg19																																																																																				.	.		0.463	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			C	128388889	T	C	128388889	2	2	65	1	0	0	0	0	0	0	0	1	12820	1548	54	2		2	PTPRK	6	128388889	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1727448	128388889	42726178	158	8231										
MOXD1	26002	hgsc.bcm.edu	37	chr6	132649228	132649228	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aatggagtgccaagggataaTccaacatgaggtggataaga	13	5	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:132649228T>C	ENST00000367963.3	-	6	988	c.870A>G	c.(868-870)ggA>ggG	p.G290G	MOXD1_ENST00000336749.3_Silent_p.G222G|MOXD1_ENST00000489128.1_5'Flank	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	290						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		CAAGGGATAATCCAACATGAG	0.398																																					p.G290G		Atlas-SNP	.											.	MOXD1	136	.	0			c.A870G						.						100	96	98					6																	132649228		2203	4300	6503	SO:0001819	synonymous_variant	26002	exon6			GGATAATCCAACA	AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.870A>G	chr6.hg19:g.132649228T>C		118.0	0.0		102.0	5.0	NM_015529	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Silent	SNP	ENST00000367963.3	hg19	CCDS5152.2																																																																																			.	.		0.398	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529		C	132649228	T	C	132649228	2	2	65	1	0	0	0	0	0	0	0	1	9729	1422	50	2		2	MOXD1	6	132649228	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4260339	132649228	38465839	159	8232										
HBS1L	10767	hgsc.bcm.edu	37	chr6	135323935	135323935	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcattttagcaacttttggcAcaatttcagattcacttcgc	5	10	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:135323935A>G	ENST00000367837.5	-	5	682	c.476T>C	c.(475-477)gTg>gCg	p.V159A	HBS1L_ENST00000527578.1_5'UTR|HBS1L_ENST00000367826.2_Missense_Mutation_p.V117A|HBS1L_ENST00000367824.4_5'UTR|HBS1L_ENST00000415177.2_Missense_Mutation_p.V94A|HBS1L_ENST00000314674.3_3'UTR|HBS1L_ENST00000445176.2_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	159					signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		AACTTTTGGCACAATTTCAGA	0.388																																					p.V159A		Atlas-SNP	.											.	HBS1L	75	.	0			c.T476C						.						115	106	109					6																	135323935		2203	4300	6503	SO:0001583	missense	10767	exon5			TTTGGCACAATTT	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"eRF3 family member"	612450	"HBS1 (S. cerevisiae)-like", "HBS1-like (S. cerevisiae)"			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.476T>C	chr6.hg19:g.135323935A>G	ENSP00000356811:p.Val159Ala	152.0	0.0		125.0	5.0	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	hg19	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.086398	0.55861	.	.	ENSG00000112339	ENST00000367837;ENST00000415177;ENST00000367826;ENST00000533274;ENST00000524715	T;T;T;T	0.65732	-0.04;-0.02;-0.03;-0.17	6.13	4.91	0.64330	.	0.053770	0.64402	D	0.000001	T	0.46756	0.1409	M	0.61703	1.905	0.80722	D	1	B;B	0.17038	0.02;0.012	B;B	0.18871	0.023;0.019	T	0.52200	-0.8607	10	0.46703	T	0.11	-15.1372	13.2493	0.60041	0.8678:0.1322:0.0:0.0	.	117;159	Q9Y450-4;Q9Y450	.;HBS1L_HUMAN	A	159;94;117;29;137	ENSP00000356811:V159A;ENSP00000389826:V94A;ENSP00000356800:V117A;ENSP00000434533:V29A	ENSP00000356800:V117A	V	-	2	0	HBS1L	135365628	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.768000	0.74980	2.367000	0.80283	0.529000	0.55759	GTG	.	.		0.388	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			G	135323935	A	G	135323935	3	3	65	1	0	0	0	0	1	0	0	0	6996	159	6	2	1634	2	HBS1L	6	135323935	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2674707	135323935	35791132	160	8233										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138576727	138576727	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gccgaggatcaggctgctccTgcactgcgccggccctgagc	14	16	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:138576727T>C	ENST00000251691.4	+	10	1091	c.925T>C	c.(925-927)Tgc>Cgc	p.C309R		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		AGGCTGCTCCTGCACTGCGCC	0.637																																					p.C309R		Atlas-SNP	.											.	KIAA1244	236	.	0			c.T925C						.						68	63	64					6																	138576727		2203	4300	6503	SO:0001583	missense	57221	exon10			TGCTCCTGCACTG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.925T>C	chr6.hg19:g.138576727T>C	ENSP00000251691:p.Cys309Arg	86.0	0.0		85.0	4.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	T	13.89	2.371438	0.42003	.	.	ENSG00000112379	ENST00000251691	T	0.16597	2.33	5.68	4.5	0.54988	.	0.275771	0.43260	D	0.000595	T	0.03871	0.0109	N	0.08118	0	0.58432	D	0.999995	B	0.18166	0.026	B	0.15484	0.013	T	0.20773	-1.0265	10	0.52906	T	0.07	-3.334	12.8709	0.57965	0.0:0.0:0.1361:0.8638	.	309	Q5TH69	BIG3_HUMAN	R	309	ENSP00000251691:C309R	ENSP00000251691:C309R	C	+	1	0	KIAA1244	138618420	1.000000	0.71417	0.987000	0.45799	0.628000	0.37860	6.248000	0.72418	0.972000	0.38314	0.533000	0.62120	TGC	.	.		0.637	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		C	138576727	T	C	138576727	3	2	65	1	0	0	0	0	1	0	0	0	8226	1580	55	2	963	2	KIAA1244	6	138576727	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3252792	138576727	32538340	161	8234										
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143092668	143092668	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cttcctctccctggacggtgAtaccgtggaggctgctgctc	12	14	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:143092668A>G	ENST00000367604.1	-	4	3847	c.3208T>C	c.(3208-3210)Tca>Cca	p.S1070P	HIVEP2_ENST00000012134.2_Missense_Mutation_p.S1070P|HIVEP2_ENST00000367603.2_Missense_Mutation_p.S1070P			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1070					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		CTGGACGGTGATACCGTGGAG	0.557																																					p.S1070P	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.T3208C						.						35	37	37					6																	143092668		2021	4170	6191	SO:0001583	missense	3097	exon5			ACGGTGATACCGT	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.3208T>C	chr6.hg19:g.143092668A>G	ENSP00000356576:p.Ser1070Pro	78.0	0.0		95.0	4.0	NM_006734	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	hg19	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.332044	0.81801	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.57752	0.38;0.38;0.38	5.67	5.67	0.87782	.	0.049534	0.85682	D	0.000000	T	0.63698	0.2533	M	0.71581	2.175	0.58432	D	0.999995	D	0.89917	1.0	D	0.71870	0.975	T	0.64007	-0.6508	10	0.38643	T	0.18	-23.8527	15.9165	0.79524	1.0:0.0:0.0:0.0	.	1070	P31629	ZEP2_HUMAN	P	1070	ENSP00000356576:S1070P;ENSP00000356575:S1070P;ENSP00000012134:S1070P	ENSP00000012134:S1070P	S	-	1	0	HIVEP2	143134361	1.000000	0.71417	0.025000	0.17156	0.228000	0.25075	4.072000	0.57563	2.169000	0.68431	0.460000	0.39030	TCA	.	.		0.557	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			G	143092668	A	G	143092668	3	3	65	1	0	0	0	0	1	0	0	0	7196	333	12	2	4156	2	HIVEP2	6	143092668	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	4515941	143092668	28022399	162	8235										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146243946	146243946	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccatttgtgttgtaagtaagAactgaagacctctgcaatca	8	8	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:146243946A>G	ENST00000367505.2	-	19	3836	c.3572T>C	c.(3571-3573)tTc>tCc	p.F1191S	SHPRH_ENST00000438092.2_Missense_Mutation_p.F1195S|SHPRH_ENST00000367503.3_Missense_Mutation_p.F1195S|SHPRH_ENST00000275233.7_Missense_Mutation_p.F1191S			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1191					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TGTAAGTAAGAACTGAAGACC	0.403																																					p.F1195S		Atlas-SNP	.											.	SHPRH	169	.	0			c.T3584C						.						93	87	89					6																	146243946		1888	4099	5987	SO:0001583	missense	257218	exon19			AGTAAGAACTGAA	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.3572T>C	chr6.hg19:g.146243946A>G	ENSP00000356475:p.Phe1191Ser	91.0	0.0		78.0	4.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	hg19	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	A	21.0	4.084493	0.76642	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85	5.44	4.13	0.48395	.	0.142264	0.48767	D	0.000162	T	0.64962	0.2646	L	0.43152	1.355	0.46336	D	0.998993	P;D;D	0.63880	0.664;0.987;0.993	B;P;P	0.56916	0.143;0.649;0.809	T	0.63033	-0.6727	10	0.23891	T	0.37	-16.797	8.4383	0.32799	0.6169:0.0:0.0:0.3831	.	390;1191;1195	B3KX98;Q149N8;Q149N8-4	.;SHPRH_HUMAN;.	S	1191;1195;1195;1191	ENSP00000356475:F1191S;ENSP00000356473:F1195S;ENSP00000412797:F1195S;ENSP00000275233:F1191S	ENSP00000275233:F1191S	F	-	2	0	SHPRH	146285639	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.328000	0.65887	2.187000	0.69744	0.528000	0.53228	TTC	.	.		0.403	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		G	146243946	A	G	146243946	3	3	65	1	0	0	0	0	1	0	0	0	14306	246	9	2	1544	2	SHPRH	6	146243946	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3151278	146243946	24871121	163	8236										
LATS1	9113	hgsc.bcm.edu	37	chr6	150001056	150001058	+	In_Frame_Del	DEL	AGA	AGA	-													0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgtccatctgaagccagtgcAgaggccaaagtcagtcaatt					rs56382749	byFrequency	TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:150001056_150001058delAGA	ENST00000543571.1	-	5	3093_3095	c.2546_2548delTCT	c.(2545-2550)ctctgc>cgc	p.849_850LC>R	LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_In_Frame_Del_p.849_850LC>R	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		AAGCCAGTGCAGAGGCCAAAGTC	0.3																																					p.849_850del		Atlas-Indel,Pindel	.											.	LATS1	241	.	0			c.2547_2549del						.																																			SO:0001651	inframe_deletion	9113	exon5			.	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2546_2548delTCT	chr6.hg19:g.150001056_150001058delAGA	ENSP00000437550:p.Leu849_Cys850delinsArg	208.0	0.0		150.0	116.0	NM_004690		In_Frame_Del	DEL	ENST00000543571.1	hg19	CCDS34551.1																																																																																			.	.		0.3	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		-	150001058	AGA	-	150001056	7	5	65	1	0	1	0	1	0	0	0	0	8655	188	7	0	860	0	LATS1	6	150001056	In_Frame_Del	DEL	AGA	TCGA-CC-A3MB-01A-11D-A20W-10	3757110	150001056	21114011	164	8237										
ESR1	2099	hgsc.bcm.edu	37	chr6	152265434	152265434	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caacctttggccaagcccgcTcatgatcaaacgctctaaga	7	14	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:152265434T>C	ENST00000206249.3	+	4	1249	c.887T>C	c.(886-888)cTc>cCc	p.L296P	ESR1_ENST00000443427.1_Missense_Mutation_p.L296P|ESR1_ENST00000440973.1_Missense_Mutation_p.L296P|ESR1_ENST00000338799.5_Missense_Mutation_p.L296P|ESR1_ENST00000406599.1_Intron|ESR1_ENST00000427531.2_Missense_Mutation_p.L123P|ESR1_ENST00000482101.1_3'UTR|ESR1_ENST00000456483.2_Intron	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	296	Hinge.|Interaction with AKAP13.|Mediates interaction with DNTTIP2.|Self-association.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	CCAAGCCCGCTCATGATCAAA	0.562																																					p.L296P		Atlas-SNP	.											.	ESR1	94	.	0			c.T887C						.						114	112	113					6																	152265434		2203	4300	6503	SO:0001583	missense	2099	exon4			GCCCGCTCATGAT	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"Nuclear hormone receptors"	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.887T>C	chr6.hg19:g.152265434T>C	ENSP00000206249:p.Leu296Pro	99.0	0.0		109.0	5.0	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Missense_Mutation	SNP	ENST00000206249.3	hg19	CCDS5234.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.310|8.310	0.821943|0.821943	0.16678|0.16678	.|.	.|.	ENSG00000091831|ENSG00000091831	ENST00000440973;ENST00000338799;ENST00000431219;ENST00000443427;ENST00000206249;ENST00000431590;ENST00000544394|ENST00000427531	D;D;D;D;D|.	0.93547|.	-3.14;-3.14;-3.14;-3.14;-3.24|.	5.66|5.66	5.66|5.66	0.87406|0.87406	Nuclear hormone receptor, ligand-binding (1);|.	0.430373|.	0.24752|.	N|.	0.035893|.	T|T	0.55705|0.55705	0.1937|0.1937	M|M	0.68952|0.68952	2.095|2.095	0.43598|0.43598	D|D	0.995954|0.995954	P;B;D;B;P;P|.	0.59767|.	0.955;0.001;0.986;0.006;0.699;0.574|.	P;B;D;B;P;B|.	0.66351|.	0.616;0.011;0.943;0.006;0.474;0.282|.	T|T	0.59989|0.59989	-0.7350|-0.7350	10|5	0.34782|.	T|.	0.22|.	.|.	10.2659|10.2659	0.43455|0.43455	0.0:0.0738:0.0:0.9262|0.0:0.0738:0.0:0.9262	.|.	200;77;38;295;296;296|.	B0QYW6;E7EVR3;Q9Y2W8;A8KAF4;G4XH65;P03372|.	.;.;.;.;.;ESR1_HUMAN|.	P|P	296;296;77;296;296;224;123|201	ENSP00000405330:L296P;ENSP00000342630:L296P;ENSP00000387500:L296P;ENSP00000206249:L296P;ENSP00000445454:L123P|.	ENSP00000206249:L296P|.	L|S	+|+	2|1	0|0	ESR1|ESR1	152307127|152307127	0.761000|0.761000	0.28439|0.28439	0.078000|0.078000	0.20375|0.20375	0.458000|0.458000	0.32498|0.32498	2.704000|2.704000	0.47118|0.47118	2.164000|2.164000	0.68074|0.68074	0.533000|0.533000	0.62120|0.62120	CTC|TCA	.	.		0.562	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1			C	152265434	T	C	152265434	3	2	65	1	0	0	0	0	1	0	0	0	5258	1551	54	2	901	2	ESR1	6	152265434	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2264378	152265434	18849633	165	8238										
MTRF1L	54516	hgsc.bcm.edu	37	chr6	153313995	153313995	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aaggaataagtacacacctgTtggaagatgaactatccgga	10	7	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:153313995T>C	ENST00000367233.5	-	5	801	c.802A>G	c.(802-804)Aca>Gca	p.T268A	MTRF1L_ENST00000367230.1_Missense_Mutation_p.T232A|MTRF1L_ENST00000367231.5_Missense_Mutation_p.T268A|MTRF1L_ENST00000464135.1_5'UTR	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	268						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		TACACACCTGTTGGAAGATGA	0.408																																					p.T268A		Atlas-SNP	.											.	MTRF1L	21	.	0			c.A802G						.						90	89	89					6																	153313995		2203	4300	6503	SO:0001583	missense	54516	exon5			CACCTGTTGGAAG	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.802A>G	chr6.hg19:g.153313995T>C	ENSP00000356202:p.Thr268Ala	42.0	0.0		63.0	4.0	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Missense_Mutation	SNP	ENST00000367233.5	hg19	CCDS5243.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.610409	0.87258	.	.	ENSG00000112031	ENST00000367233;ENST00000367231;ENST00000367230;ENST00000414771;ENST00000448966	T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81	5.02	5.02	0.67125	Peptide chain release factor class I/class II (1);	0.000000	0.85682	D	0.000000	T	0.55449	0.1921	H	0.95079	3.62	0.80722	D	1	P;P;D;P	0.60575	0.754;0.831;0.988;0.87	P;P;D;P	0.70935	0.518;0.459;0.971;0.484	T	0.71474	-0.4582	10	0.87932	D	0	.	14.7403	0.69448	0.0:0.0:0.0:1.0	.	232;268;232;268	B4DMX1;Q9UGC7-2;Q9UGC7-4;Q9UGC7	.;.;.;RF1ML_HUMAN	A	268;268;232;119;132	ENSP00000356202:T268A;ENSP00000356200:T268A;ENSP00000356199:T232A;ENSP00000414383:T119A;ENSP00000415113:T132A	ENSP00000356199:T232A	T	-	1	0	MTRF1L	153355688	1.000000	0.71417	0.980000	0.43619	0.871000	0.50021	8.008000	0.88588	1.901000	0.55032	0.528000	0.53228	ACA	.	.		0.408	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041		C	153313995	T	C	153313995	3	2	65	1	0	0	0	0	1	0	0	0	9969	1725	60	2	352	2	MTRF1L	6	153313995	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1048561	153313995	17801072	166	8239										
NOX3	50508	hgsc.bcm.edu	37	chr6	155775983	155775983	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaatgaaataaggtttcgacTgacaggtattagaattagca	10	4	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:155775983T>C	ENST00000159060.2	-	3	319	c.217A>G	c.(217-219)Agt>Ggt	p.S73G		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	73	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		AGGTTTCGACTGACAGGTATT	0.373																																					p.S73G		Atlas-SNP	.											.	NOX3	93	.	0			c.A217G						.						68	67	67					6																	155775983		2203	4300	6503	SO:0001583	missense	50508	exon3			TTCGACTGACAGG	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.217A>G	chr6.hg19:g.155775983T>C	ENSP00000159060:p.Ser73Gly	60.0	0.0		80.0	4.0	NM_015718	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	hg19	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	T	14.00	2.404765	0.42613	.	.	ENSG00000074771	ENST00000159060	D	0.95342	-3.68	5.91	4.73	0.59995	Flavoprotein transmembrane component (1);	0.072971	0.64402	D	0.000016	D	0.90947	0.7154	L	0.54323	1.7	0.34075	D	0.658918	P	0.40578	0.722	P	0.45998	0.5	D	0.90484	0.4462	10	0.87932	D	0	-10.2081	10.4134	0.44307	0.3703:0.0:0.0:0.6297	.	73	Q9HBY0	NOX3_HUMAN	G	73	ENSP00000159060:S73G	ENSP00000159060:S73G	S	-	1	0	NOX3	155817675	1.000000	0.71417	0.932000	0.37286	0.987000	0.75469	1.650000	0.37292	1.025000	0.39708	0.528000	0.53228	AGT	.	.		0.373	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			C	155775983	T	C	155775983	3	2	65	1	0	0	0	0	1	0	0	0	10566	1580	55	2	1533	2	NOX3	6	155775983	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2461988	155775983	15339084	167	8240										
AGPAT4	56895	hgsc.bcm.edu	37	chr6	161567572	161567572	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgaccttctcctggtagagcTtgtgcagccaggccgagcac	12	13	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:161567572T>C	ENST00000320285.4	-	7	1039	c.827A>G	c.(826-828)aAg>aGg	p.K276R	AGPAT4_ENST00000366911.5_3'UTR|AGPAT4_ENST00000366908.5_3'UTR|AGPAT4_ENST00000457520.2_Missense_Mutation_p.K114R	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	276					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(10)|lung(10)|ovary(2)|skin(2)	25		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		CTGGTAGAGCTTGTGCAGCCA	0.602																																					p.K276R		Atlas-SNP	.											.	AGPAT4	50	.	0			c.A827G						.						128	98	108					6																	161567572		2203	4300	6503	SO:0001583	missense	56895	exon7			TAGAGCTTGTGCA	AF156776	CCDS5280.1	6q25.3	2013-02-05	2013-02-05		ENSG00000026652	ENSG00000026652	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20885	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, delta"	614795	"1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"				Standard	XM_005267052		Approved	LPAAT-delta, dJ473J16.2	uc003qtr.1	Q9NRZ5	OTTHUMG00000015966	ENST00000320285.4:c.827A>G	chr6.hg19:g.161567572T>C	ENSP00000314036:p.Lys276Arg	68.0	0.0		64.0	4.0	NM_020133	B4DSF9|Q5TEF0	Missense_Mutation	SNP	ENST00000320285.4	hg19	CCDS5280.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.89|15.89	2.966761|2.966761	0.53507|0.53507	.|.	.|.	ENSG00000026652|ENSG00000026652	ENST00000320285;ENST00000457520|ENST00000437165	D|.	0.93547|.	-3.24|.	4.95|4.95	2.55|2.55	0.30701|0.30701	.|.	0.049400|.	0.85682|.	D|.	0.000000|.	T|T	0.59742|0.59742	0.2216|0.2216	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	B;B|.	0.21606|.	0.058;0.032|.	B;B|.	0.20184|.	0.028;0.012|.	T|T	0.60063|0.60063	-0.7336|-0.7336	10|5	0.51188|.	T|.	0.08|.	-32.4046|-32.4046	7.8161|7.8161	0.29260|0.29260	0.0:0.1759:0.0:0.8241|0.0:0.1759:0.0:0.8241	.|.	114;276|.	B4DSF9;Q9NRZ5|.	.;PLCD_HUMAN|.	R|G	276;114|55	ENSP00000314036:K276R|.	ENSP00000314036:K276R|.	K|S	-|-	2|1	0|0	AGPAT4|AGPAT4	161487562|161487562	0.998000|0.998000	0.40836|0.40836	0.997000|0.997000	0.53966|0.53966	0.907000|0.907000	0.53573|0.53573	2.512000|2.512000	0.45485|0.45485	0.331000|0.331000	0.23511|0.23511	0.459000|0.459000	0.35465|0.35465	AAG|AGC	.	.		0.602	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133		C	161567572	T	C	161567572	3	2	65	1	0	0	0	0	1	0	0	0	389	1609	56	2	321	2	AGPAT4	6	161567572	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	5791589	161567572	9547495	168	8241										
PDE10A	10846	hgsc.bcm.edu	37	chr6	165863852	165863852	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcatattcgtatcttggtacTttggattaaaaataacaaaa	6	5	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:165863852T>C	ENST00000366882.1	-	5	350		c.e5-2		PDE10A_ENST00000354448.4_Splice_Site|PDE10A_ENST00000539869.2_Splice_Site			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A						blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	ATCTTGGTACTTTGGATTAAA	0.299																																					.	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											.	PDE10A	154	.	0			c.226-2A>G						.						92	85	88					6																	165863852		2203	4300	6503	SO:0001630	splice_region_variant	10846	exon5			TGGTACTTTGGAT	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.196-2A>G	chr6.hg19:g.165863852T>C		100.0	0.0		84.0	5.0	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Splice_Site	SNP	ENST00000366882.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.44	3.391248	0.62066	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3089	0.66403	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDE10A	165783842	1.000000	0.71417	0.711000	0.30485	0.532000	0.34746	7.708000	0.84633	1.843000	0.53566	0.460000	0.39030	.	.	.		0.299	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1		Intron	C	165863852	T	C	165863852	5	2	65	1	0	0	0	0	0	0	1	0	11639	1623	56	2	2221	2	PDE10A	6	165863852	Splice_Site	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4296280	165863852	5251215	169	8242										
PDCD2	5134	hgsc.bcm.edu	37	chr6	170886665	170886665	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctttacggtgtatctgttacAtcctgcttccacacaaattc	5	12	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr6:170886665A>G	ENST00000541970.1	-	6	1095	c.1017T>C	c.(1015-1017)gaT>gaC	p.D339D	PDCD2_ENST00000392090.2_Silent_p.D306D	NM_001199462.1|NM_002598.3	NP_001186391.1|NP_002589.2	Q16342	PDCD2_HUMAN	programmed cell death 2	339					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(5)	9		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)		TATCTGTTACATCCTGCTTCC	0.423																																					p.D339D	Colon(60;1476 1726 39478)	Atlas-SNP	.											.	PDCD2	13	.	0			c.T1017C						.						91	85	87					6																	170886665		2203	4300	6503	SO:0001819	synonymous_variant	5134	exon6			TGTTACATCCTGC	AJ420535	CCDS5316.1, CCDS47521.1, CCDS56460.1, CCDS56461.1, CCDS56462.1, CCDS75557.1	6q27	2008-02-05			ENSG00000071994	ENSG00000071994		"Zinc fingers, MYND-type"	8762	protein-coding gene	gene with protein product		600866				7606924	Standard	NM_002598		Approved	ZMYND7, RP8	uc003qxw.3	Q16342	OTTHUMG00000016083	ENST00000541970.1:c.1017T>C	chr6.hg19:g.170886665A>G		107.0	0.0		99.0	4.0	NM_002598	E9PCU7|F5GYS7|Q58HM9|Q58HN0|Q9UH12	Silent	SNP	ENST00000541970.1	hg19	CCDS5316.1																																																																																			.	.		0.423	PDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043269.2	NM_002598		G	170886665	A	G	170886665	2	3	65	1	0	0	0	0	0	0	0	1	11628	214	8	2		2	PDCD2	6	170886665	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	5022813	170886665	228402	170	8243										
CARD11	84433	hgsc.bcm.edu	37	chr7	2963882	2963882	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggtacctttccagagagaacTtcctgaacatgaggttgacc	10	10	0	5			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:2963882T>C	ENST00000396946.4	-	15	2328	c.1925A>G	c.(1924-1926)aAg>aGg	p.K642R		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	642					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CAGAGAGAACTTCCTGAACAT	0.592			Mis		DLBCL																																p.K642R		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.A1925G						.						79	63	69					7																	2963882		2203	4300	6503	SO:0001583	missense	84433	exon15			GAGAACTTCCTGA	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1925A>G	chr7.hg19:g.2963882T>C	ENSP00000380150:p.Lys642Arg	82.0	0.0		91.0	4.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	12.17	1.858781	0.32884	.	.	ENSG00000198286	ENST00000396946;ENST00000355508	T;T	0.50813	0.73;0.73	5.15	5.15	0.70609	PDZ/DHR/GLGF (1);	0.054299	0.64402	D	0.000001	T	0.39911	0.1096	N	0.14661	0.345	0.58432	D	0.999998	D	0.54601	0.967	P	0.53266	0.722	T	0.15235	-1.0444	10	0.12103	T	0.63	-52.0719	13.5571	0.61765	0.0:0.0:0.0:1.0	.	642	Q9BXL7	CAR11_HUMAN	R	642;113	ENSP00000380150:K642R;ENSP00000347695:K113R	ENSP00000347695:K113R	K	-	2	0	CARD11	2930408	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.135000	0.77276	1.957000	0.56846	0.454000	0.30748	AAG	.	.		0.592	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		C	2963882	T	C	2963882	3	2	65	1	0	0	0	0	1	0	0	0	2647	1609	56	2	1583	2	CARD11	7	2963882	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		2963882	156174781	171	8244										
ICA1	3382	hgsc.bcm.edu	37	chr7	8198174	8198175	+	Missense_Mutation	DNP	TG	TG	CT													0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tacctggtatgttgctagcaTgtgagacaagagattgcatc							TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:8198174_8198175TG>CT	ENST00000402384.3	-	7	953_954	c.687_688CA>AG	c.(685-690)caCAtg>caAGtg	p.229_230HM>QV	ICA1_ENST00000422063.2_Missense_Mutation_p.229_230HM>QV|ICA1_ENST00000406470.2_Missense_Mutation_p.229_230HM>QV|ICA1_ENST00000265577.7_Missense_Mutation_p.228_229HM>QV|ICA1_ENST00000407906.1_Missense_Mutation_p.229_230HM>QV|ICA1_ENST00000401396.1_Missense_Mutation_p.217_218HM>QV|ICA1_ENST00000396675.3_Missense_Mutation_p.229_230HM>QV			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa	229	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		GTTGCTAGCATGTGAGACAAGA	0.371																																					p.M230V|p.H229Q		Atlas-SNP	.											.	ICA1	65	.	0			c.A688G|c.C687A						.																																			SO:0001583	missense	3382	exon7			CTAGCATGTGAGA|TAGCATGTGAGAC		CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"islet cell autoantigen 1 (69kD)"			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.687_688delinsCT	chr7.hg19:g.8198174_8198175delinsCT	ENSP00000385570:p.H229_M230delinsQV	134.0	0.0		108.0|111.0	46.0|47.0	NM_022307	A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Missense_Mutation	SNP	ENST00000402384.3	hg19	CCDS34602.1																																																																																			.	.		0.371	ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324793.1	NM_004968		CT	8198175	TG	CT	8198174	3	2	65	1	0	0	0	0	1	0	0	0	7486	1464	51	2	795	2	ICA1	7	8198174	Missense_Mutation	DNP	TG	TCGA-CC-A3MB-01A-11D-A20W-10	5234292	8198174	150940489	172	8245										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47849144	47849144	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tacggtagagttgaacacagAggtggatcaggctgagtgcc	15	7	1	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:47849144A>G	ENST00000289672.2	-	51	7663	c.7613T>C	c.(7612-7614)cTc>cCc	p.L2538P	C7orf69_ENST00000258776.4_Intron|C7orf69_ENST00000418326.2_Intron|PKD1L1_ENST00000462350.1_5'UTR	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2538					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TTGAACACAGAGGTGGATCAG	0.458																																					p.L2538P		Atlas-SNP	.											.	PKD1L1	328	.	0			c.T7613C						.						56	50	52					7																	47849144		2203	4300	6503	SO:0001583	missense	168507	exon51			ACACAGAGGTGGA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.7613T>C	chr7.hg19:g.47849144A>G	ENSP00000289672:p.Leu2538Pro	45.0	0.0		45.0	5.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	A	10.82	1.459366	0.26248	.	.	ENSG00000158683	ENST00000289672	T	0.71461	-0.57	5.19	4.03	0.46877	Polycystin cation channel, PKD1/PKD2 (1);	0.232977	0.26840	N	0.022235	T	0.76695	0.4023	L	0.50333	1.59	0.50632	D	0.999881	D	0.76494	0.999	D	0.77004	0.989	T	0.75575	-0.3270	10	0.66056	D	0.02	-12.1737	6.8389	0.23951	0.8166:0.0:0.1834:0.0	.	2538	Q8TDX9	PK1L1_HUMAN	P	2538	ENSP00000289672:L2538P	ENSP00000289672:L2538P	L	-	2	0	PKD1L1	47815669	0.102000	0.21896	0.011000	0.14972	0.021000	0.10359	2.223000	0.42936	0.812000	0.34326	0.460000	0.39030	CTC	.	.		0.458	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		G	47849144	A	G	47849144	3	3	65	1	0	0	0	0	1	0	0	0	11973	304	11	2	964	2	PKD1L1	7	47849144	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	39650970	47849144	111289519	173	8246										
GNAI1	2770	hgsc.bcm.edu	37	chr7	79764532	79764532	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggtggagcggagtaagatgaTcgaccgcaacctccgtgagg	16	9	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:79764532T>C	ENST00000351004.3	+	1	429	c.56T>C	c.(55-57)aTc>aCc	p.I19T	GNAI1_ENST00000457358.2_5'Flank|GNAI1_ENST00000490206.1_3'UTR	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	19					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						AGTAAGATGATCGACCGCAAC	0.731																																					p.I19T		Atlas-SNP	.											.	GNAI1	44	.	0			c.T56C						.						14	15	15					7																	79764532		2186	4284	6470	SO:0001583	missense	2770	exon1			AGATGATCGACCG	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"Gi1 protein alpha subunit"	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.56T>C	chr7.hg19:g.79764532T>C	ENSP00000343027:p.Ile19Thr	82.0	0.0		98.0	4.0	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Missense_Mutation	SNP	ENST00000351004.3	hg19	CCDS5595.1	.	.	.	.	.	.	.	.	.	.	T	33	5.204931	0.95033	.	.	ENSG00000127955	ENST00000442586;ENST00000351004	D	0.89270	-2.49	3.91	3.91	0.45181	.	0.054690	0.64402	N	0.000001	D	0.94981	0.8376	H	0.94385	3.53	0.80722	D	1	P	0.48640	0.913	P	0.60012	0.867	D	0.95709	0.8756	9	.	.	.	.	11.6898	0.51508	0.0:0.0:0.0:1.0	.	19	P63096	GNAI1_HUMAN	T	19	ENSP00000343027:I19T	.	I	+	2	0	GNAI1	79602468	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.302000	0.78861	1.631000	0.50456	0.372000	0.22366	ATC	.	.		0.731	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		C	79764532	T	C	79764532	3	2	65	1	0	0	0	0	1	0	0	0	6512	1435	50	2	58	2	GNAI1	7	79764532	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	31915388	79764532	79374131	174	8247										
PCLO	27445	hgsc.bcm.edu	37	chr7	82581498	82581498	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caacgggtttttcatcttctAttattttggtcatcacactt	5	9	5	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:82581498A>T	ENST00000333891.9	-	5	9108	c.8771T>A	c.(8770-8772)aTa>aAa	p.I2924K	PCLO_ENST00000423517.2_Missense_Mutation_p.I2924K|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTCATCTTCTATTATTTTGGT	0.433																																					p.I2924K		Atlas-SNP	.											Q9Y6V0-3,colon,carcinoma,-1,3	PCLO	1506	.	0			c.T8771A						.						145	142	143					7																	82581498		1909	4123	6032	SO:0001583	missense	27445	exon5			TCTTCTATTATTT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.8771T>A	chr7.hg19:g.82581498A>T	ENSP00000334319:p.Ile2924Lys	41.0	2.0		48.0	5.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.018568	0.35606	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19394	2.15;2.16	5.68	5.68	0.88126	.	.	.	.	.	T	0.30696	0.0773	L	0.50333	1.59	0.80722	D	1	P;P	0.46220	0.874;0.874	P;P	0.48227	0.447;0.571	T	0.02758	-1.1114	9	0.87932	D	0	.	15.9242	0.79603	1.0:0.0:0.0:0.0	.	2924;2924	Q9Y6V0-5;Q9Y6V0-6	.;.	K	2855;2924;2924	ENSP00000334319:I2924K;ENSP00000388393:I2924K	ENSP00000334319:I2924K	I	-	2	0	PCLO	82419434	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.606000	0.74159	2.152000	0.67230	0.460000	0.39030	ATA	.	.		0.433	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82581498	A	T	82581498	3	4	65	1	0	0	0	0	1	0	0	0	11592	449	16	4	6758	4	PCLO	7	82581498	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2816966	82581498	76557165	175	8248										
FZD1	8321	hgsc.bcm.edu	37	chr7	90894459	90894459	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gggcccgggccggggcagcaAccgccgccgccgcctcagca	16	19	1	0	rs71292991|rs139480179	byFrequency	TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:90894459A>G	ENST00000287934.2	+	1	677	c.264A>G	c.(262-264)caA>caG	p.Q88Q		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	88					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.Q88_P89insP(2)|p.Q88_P89insA(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			cggggcAGCAACCGCCGCCGC	0.741																																					p.Q88Q		Atlas-SNP	.											.,4	FZD1	64	.	3	Insertion - In frame(3)	breast(2)|liver(1)	c.A264G						.						10	11	11					7																	90894459		2176	4257	6433	SO:0001819	synonymous_variant	8321	exon1			GCAGCAACCGCCG	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"GPCR / Class F : Frizzled receptors"	4038	protein-coding gene	gene with protein product	"Wnt receptor", "frizzled, Drosophila, homolog of, 1"	603408	"frizzled (Drosophila) homolog 1", "frizzled homolog 1 (Drosophila)", "frizzled 1, seven transmembrane spanning receptor", "frizzled family receptor 1"			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.264A>G	chr7.hg19:g.90894459A>G		6.0	1.0		19.0	2.0	NM_003505	A4D1E8|O94815|Q549T8	Silent	SNP	ENST00000287934.2	hg19	CCDS5620.1																																																																																			.	.		0.741	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		G	90894459	A	G	90894459	2	3	65	1	0	0	0	0	0	0	0	1	6136	40	2	2		2	FZD1	7	90894459	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	8312961	90894459	68244204	176	8249										
KRIT1	889	hgsc.bcm.edu	37	chr7	91851228	91851228	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aagcaaacctgtttttcaacTtccaagggaagtctcacatc	6	11	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:91851228T>C	ENST00000340022.2	-	14	2569	c.1551A>G	c.(1549-1551)gaA>gaG	p.E517E	KRIT1_ENST00000394503.2_Silent_p.E469E|KRIT1_ENST00000412043.2_Silent_p.E517E|KRIT1_ENST00000394505.2_Silent_p.E517E|KRIT1_ENST00000394507.1_Silent_p.E517E	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	517	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				angiogenesis (GO:0001525)|cell redox homeostasis (GO:0045454)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|positive regulation of protein binding (GO:0032092)|regulation of catalytic activity (GO:0050790)|regulation of establishment of cell polarity (GO:2000114)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(2)|stomach(1)	22	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GTTTTTCAACTTCCAAGGGAA	0.373																																					p.E517E		Atlas-SNP	.											.	KRIT1	66	.	0			c.A1551G						.						64	63	63					7																	91851228		2203	4300	6503	SO:0001819	synonymous_variant	889	exon15			TTCAACTTCCAAG	AJ294850	CCDS5624.1, CCDS34679.1	7q21.2	2014-09-17	2005-03-15	2005-03-17	ENSG00000001631	ENSG00000001631		"Ankyrin repeat domain containing"	1573	protein-coding gene	gene with protein product		604214	"cerebral cavernous malformations 1"	CCM1		7604043, 11342228	Standard	NM_194455		Approved	CAM	uc003ulu.1	O00522	OTTHUMG00000131187	ENST00000340022.2:c.1551A>G	chr7.hg19:g.91851228T>C		50.0	0.0		73.0	4.0	NM_194456	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Silent	SNP	ENST00000340022.2	hg19	CCDS5624.1																																																																																			.	.		0.373	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1			C	91851228	T	C	91851228	2	2	65	1	0	0	0	0	0	0	0	1	8454	1606	56	2		2	KRIT1	7	91851228	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	956769	91851228	67287435	177	8250										
ANKIB1	54467	hgsc.bcm.edu	37	chr7	92028083	92028083	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tttgaagatgccagtgtcagTgaaggtagaggaacccagat	13	6	1	5			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:92028083T>C	ENST00000265742.3	+	20	3466	c.3090T>C	c.(3088-3090)agT>agC	p.S1030S		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	1030							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CCAGTGTCAGTGAAGGTAGAG	0.488																																					p.S1030S		Atlas-SNP	.											.	ANKIB1	92	.	0			c.T3090C						.						54	54	54					7																	92028083		1916	4130	6046	SO:0001819	synonymous_variant	54467	exon20			TGTCAGTGAAGGT	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"Ankyrin repeat domain containing"	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.3090T>C	chr7.hg19:g.92028083T>C		103.0	0.0		129.0	51.0	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Silent	SNP	ENST00000265742.3	hg19	CCDS47639.1																																																																																			.	.		0.488	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			C	92028083	T	C	92028083	2	2	65	1	0	0	0	0	0	0	0	1	630	1693	59	2		2	ANKIB1	7	92028083	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	176855	92028083	67110580	178	8251										
AP4M1	9179	hgsc.bcm.edu	37	chr7	99704091	99704091	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agagggagcccttcgctgggAcctgcctcgggtgcaaggag	17	11	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:99704091A>G	ENST00000359593.4	+	14	1249	c.1091A>G	c.(1090-1092)gAc>gGc	p.D364G	AP4M1_ENST00000421755.1_Missense_Mutation_p.D364G|AP4M1_ENST00000429084.1_Missense_Mutation_p.D371G|AP4M1_ENST00000422582.1_Missense_Mutation_p.D236G	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	364	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTTCGCTGGGACCTGCCTCGG	0.622																																					p.D364G	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											.	AP4M1	39	.	0			c.A1091G						.						44	48	46					7																	99704091		2203	4299	6502	SO:0001583	missense	9179	exon14			GCTGGGACCTGCC	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"mu-adaptin-related protein-2", "mu subunit of AP-4", "AP-4 adapter complex mu subunit", "adaptor-related protein complex AP-4 mu4 subunit"	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.1091A>G	chr7.hg19:g.99704091A>G	ENSP00000352603:p.Asp364Gly	77.0	0.0		77.0	4.0	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Missense_Mutation	SNP	ENST00000359593.4	hg19	CCDS5685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.83|10.83	1.460580|1.460580	0.26248|0.26248	.|.	.|.	ENSG00000221838|ENSG00000221838	ENST00000438383;ENST00000429084;ENST00000359593;ENST00000421755;ENST00000422582;ENST00000450807|ENST00000445295	T;T;T;T;T;T|.	0.19806|.	2.12;2.12;2.12;2.12;2.12;2.12|.	4.81|4.81	4.81|4.81	0.61882|0.61882	Clathrin adaptor, mu subunit, C-terminal (3);|.	0.376195|.	0.31415|.	N|.	0.007691|.	T|T	0.34978|0.34978	0.0916|0.0916	N|N	0.05078|0.05078	-0.115|-0.115	0.40804|0.40804	D|D	0.983369|0.983369	B;B;B|.	0.13594|.	0.008;0.007;0.002|.	B;B;B|.	0.25291|.	0.059;0.025;0.025|.	T|T	0.27706|0.27706	-1.0066|-1.0066	10|5	0.72032|.	D|.	0.01|.	-11.5438|-11.5438	12.3578|12.3578	0.55186|0.55186	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	316;371;364|.	B4DKN7;C9JC87;O00189|.	.;.;AP4M1_HUMAN|.	G|A	296;371;364;364;236;116|90	ENSP00000401613:D296G;ENSP00000403663:D371G;ENSP00000352603:D364G;ENSP00000412185:D364G;ENSP00000406676:D236G;ENSP00000391585:D116G|.	ENSP00000352603:D364G|.	D|T	+|+	2|1	0|0	AP4M1|AP4M1	99542027|99542027	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	2.834000|2.834000	0.48167|0.48167	2.023000|2.023000	0.59567|0.59567	0.459000|0.459000	0.35465|0.35465	GAC|ACC	.	.		0.622	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722		G	99704091	A	G	99704091	3	3	65	1	0	0	0	0	1	0	0	0	753	275	10	2	1145	2	AP4M1	7	99704091	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	7676008	99704091	59434572	179	8252										
FBXO24	26261	hgsc.bcm.edu	37	chr7	100187324	100187324	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctaggagacaggagggcaggAgcagggagggggcaatcagg	21	6	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:100187324A>G	ENST00000241071.6	+	2	361				FBXO24_ENST00000465843.1_Intron|PCOLCE-AS1_ENST00000442166.2_RNA|FBXO24_ENST00000360609.2_Intron|FBXO24_ENST00000498195.1_Intron|FBXO24_ENST00000427939.2_Missense_Mutation_p.S21G|FBXO24_ENST00000468962.1_Intron	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24						protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					GGAGGGCAGGAGCAGGGAGGG	0.657																																					p.S21G		Atlas-SNP	.											.	FBXO24	125	.	0			c.A61G						.						44	48	47					7																	100187324		692	1591	2283	SO:0001627	intron_variant	26261	exon1			GGCAGGAGCAGGG	AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"F-boxes /  "other""	13595	protein-coding gene	gene with protein product		609097	"F-box only protein 24"			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.40-276A>G	chr7.hg19:g.100187324A>G		118.0	0.0		130.0	6.0	NM_012172	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	hg19	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	A	11.49	1.655255	0.29425	.	.	ENSG00000106336	ENST00000427939	T	0.15372	2.43	3.59	3.59	0.41128	.	.	.	.	.	T	0.14270	0.0345	.	.	.	0.80722	D	1	B	0.20261	0.043	B	0.14578	0.011	T	0.05632	-1.0873	8	0.87932	D	0	.	8.8159	0.34996	1.0:0.0:0.0:0.0	.	21	B4DX91	.	G	21	ENSP00000416558:S21G	ENSP00000416558:S21G	S	+	1	0	FBXO24	100025260	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	1.084000	0.30828	1.668000	0.50843	0.392000	0.25879	AGC	.	.		0.657	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1			G	100187324	A	G	100187324	1	3	65	0	1	0	0	0	0	0	0	0	5743	304	11	2		2	FBXO24	7	100187324	Intron	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	483233	100187324	58951339	180	8253										
MLL5	55904	hgsc.bcm.edu	37	chr7	104746372	104746372	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atagatttaattcaccctgtCaagaaagatccagaagtcct	6	9	2	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:104746372C>T	ENST00000311117.3	+	19	3063	c.2518C>T	c.(2518-2520)Caa>Taa	p.Q840*	KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000257745.4_Nonsense_Mutation_p.Q840*|KMT2E_ENST00000334877.4_Nonsense_Mutation_p.Q840*|CTB-152G17.6_ENST00000607968.1_RNA	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	840					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										TTCACCCTGTCAAGAAAGATC	0.348																																					p.Q840X		Atlas-SNP	.											.	MLL5	173	.	0			c.C2518T						.						89	96	93					7																	104746372		2203	4300	6503	SO:0001587	stop_gained	55904	exon18			CCCTGTCAAGAAA	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2518C>T	chr7.hg19:g.104746372C>T	ENSP00000312379:p.Gln840*	154.0	0.0		152.0	24.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Nonsense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	C	42	9.739784	0.99252	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745	.	.	.	5.81	5.81	0.92471	.	0.319059	0.29846	N	0.011058	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	20.0804	0.97772	0.0:1.0:0.0:0.0	.	.	.	.	X	840;840;840;760;840	.	ENSP00000257745:Q840X	Q	+	1	0	MLL5	104533608	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.335000	0.65929	2.738000	0.93877	0.655000	0.94253	CAA	.	.		0.348	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104746372	C	T	104746372	4	4	65	1	0	0	0	0	0	1	0	0	9633	827	29	3	2584	3	MLL5	7	104746372	Nonsense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	4559048	104746372	54392291	181	8254										
DUS4L	11062	hgsc.bcm.edu	37	chr7	107216859	107216859	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gatctttgtcaaaaggctgaAgcaacaggagtttcatggat	11	6	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:107216859A>G	ENST00000265720.3	+	7	890	c.528A>G	c.(526-528)gaA>gaG	p.E176E	DUS4L_ENST00000402620.1_Silent_p.E55E	NM_001270419.1|NM_181581.2	NP_001257348.1|NP_853559.1	O95620	DUS4L_HUMAN	dihydrouridine synthase 4-like (S. cerevisiae)	176							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	8						AAAAGGCTGAAGCAACAGGAG	0.348																																					p.E176E		Atlas-SNP	.											.	DUS4L	27	.	0			c.A528G						.						82	76	78					7																	107216859		2203	4300	6503	SO:0001819	synonymous_variant	11062	exon7			GGCTGAAGCAACA	U62767	CCDS5745.1	7q22-q31	2007-12-04			ENSG00000105865	ENSG00000105865			21517	protein-coding gene	gene with protein product	"protein similar to E.coli yhdg and R. capsulatus nifR3"						Standard	NM_181581		Approved	PP35, DUS4	uc031syv.1	O95620	OTTHUMG00000154763	ENST00000265720.3:c.528A>G	chr7.hg19:g.107216859A>G		69.0	0.0		98.0	4.0	NM_001270419	B4DLX0|Q2NKK1	Silent	SNP	ENST00000265720.3	hg19	CCDS5745.1																																																																																			.	.		0.348	DUS4L-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336967.2	NM_181581		G	107216859	A	G	107216859	2	3	65	1	0	0	0	0	0	0	0	1	4810	69	3	2		2	DUS4L	7	107216859	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2470487	107216859	51921804	182	8255										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107807498	107807498	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccgagaaccatttacaatttCttttctccattcttctttgc	3	12	4	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:107807498C>T	ENST00000425651.2	-	27	3333	c.3334G>A	c.(3334-3336)Gaa>Aaa	p.E1112K	NRCAM_ENST00000379022.4_Missense_Mutation_p.E1112K|NRCAM_ENST00000413765.2_Intron|NRCAM_ENST00000379028.3_Missense_Mutation_p.E1112K|NRCAM_ENST00000379024.4_Intron|NRCAM_ENST00000351718.4_Intron	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1112	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						TTTACAATTTCTTTTCTCCAT	0.383																																					p.E1112K		Atlas-SNP	.											.	NRCAM	267	.	0			c.G3334A						.						77	77	77					7																	107807498		1871	4099	5970	SO:0001583	missense	4897	exon27			CAATTTCTTTTCT		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3334G>A	chr7.hg19:g.107807498C>T	ENSP00000401244:p.Glu1112Lys	95.0	0.0		77.0	4.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.091947	0.55968	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000425651;ENST00000379022	T;T;T	0.56776	0.44;0.44;0.44	5.67	4.79	0.61399	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.149927	0.64402	N	0.000014	T	0.44201	0.1282	L	0.34521	1.04	0.80722	D	1	B	0.06786	0.001	B	0.13407	0.009	T	0.32508	-0.9904	10	0.48119	T	0.1	.	15.2425	0.73482	0.0:0.9322:0.0:0.0678	.	1112	Q92823	NRCAM_HUMAN	K	1112	ENSP00000368314:E1112K;ENSP00000401244:E1112K;ENSP00000368308:E1112K	ENSP00000368308:E1112K	E	-	1	0	NRCAM	107594734	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.249000	0.65427	1.532000	0.49169	0.643000	0.83706	GAA	.	.		0.383	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		T	107807498	C	T	107807498	3	4	65	1	0	0	0	0	1	0	0	0	10653	922	32	3	626	3	NRCAM	7	107807498	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	590639	107807498	51331165	183	8256										
KLHDC10	23008	hgsc.bcm.edu	37	chr7	129762020	129762020	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aactgaaaccaaacaacctaTcctgtgatctaccagaagag	6	11	1	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:129762020T>C	ENST00000335420.5	+	5	891	c.757T>C	c.(757-759)Tcc>Ccc	p.S253P		NM_014997.3	NP_055812.1	Q6PID8	KLD10_HUMAN	kelch domain containing 10	253						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|liver(2)|lung(10)|prostate(1)	17						AAACAACCTATCCTGTGATCT	0.408																																					p.S253P		Atlas-SNP	.											.	KLHDC10	36	.	0			c.T757C						.						150	119	130					7																	129762020		2203	4300	6503	SO:0001583	missense	23008	exon5			AACCTATCCTGTG		CCDS5815.1	7q32.2	2008-08-20			ENSG00000128607	ENSG00000128607			22194	protein-coding gene	gene with protein product	"scruin like at the midline homolog (Drosophila)"	615152					Standard	NM_014997		Approved	KIAA0265, slim	uc003vpj.2	Q6PID8	OTTHUMG00000157654	ENST00000335420.5:c.757T>C	chr7.hg19:g.129762020T>C	ENSP00000334140:p.Ser253Pro	87.0	0.0		80.0	4.0	NM_014997	Q86Y99|Q92554	Missense_Mutation	SNP	ENST00000335420.5	hg19	CCDS5815.1	.	.	.	.	.	.	.	.	.	.	T	9.802	1.180775	0.21787	.	.	ENSG00000128607	ENST00000335420;ENST00000468226	T;T	0.11277	2.79;2.79	5.47	4.33	0.51752	Galactose oxidase, beta-propeller (1);	0.161589	0.56097	D	0.000025	T	0.03348	0.0097	N	0.01209	-0.955	0.41995	D	0.990864	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.42865	-0.9426	10	0.26408	T	0.33	-9.9164	7.5016	0.27522	0.0:0.1601:0.0:0.8399	.	102;110;253	Q96G43;Q6PID8-2;Q6PID8	.;.;KLD10_HUMAN	P	253;110	ENSP00000334140:S253P;ENSP00000420034:S110P	ENSP00000334140:S253P	S	+	1	0	KLHDC10	129549256	0.998000	0.40836	0.986000	0.45419	0.333000	0.28666	3.650000	0.54424	2.064000	0.61679	0.533000	0.62120	TCC	.	.		0.408	KLHDC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349347.2			C	129762020	T	C	129762020	3	2	65	1	0	0	0	0	1	0	0	0	8364	1435	50	2	775	2	KLHDC10	7	129762020	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	21954522	129762020	29376643	184	8257										
TMEM209	84928	hgsc.bcm.edu	37	chr7	129818251	129818251	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcaataattacctttgatccTttcaaacaagtattcctgat	3	9	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:129818251T>C	ENST00000397622.2	-	10	1359	c.1237A>G	c.(1237-1239)Agg>Ggg	p.R413G	TMEM209_ENST00000462753.1_Missense_Mutation_p.R412G|RP11-775D22.3_ENST00000483283.1_RNA|TMEM209_ENST00000473456.1_Intron|TMEM209_ENST00000336804.8_Intron	NM_032842.3	NP_116231.2	Q96SK2	TM209_HUMAN	transmembrane protein 209	413						integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	12	Melanoma(18;0.0435)					CCTTTGATCCTTTCAAACAAG	0.333																																					p.R413G		Atlas-SNP	.											.	TMEM209	31	.	0			c.A1237G						.						48	44	45					7																	129818251		1806	4068	5874	SO:0001583	missense	84928	exon10			TGATCCTTTCAAA		CCDS47712.1, CCDS75661.1	7q32.2	2008-02-26			ENSG00000146842	ENSG00000146842			21898	protein-coding gene	gene with protein product						12958361	Standard	NM_032842		Approved	FLJ14803, NET31	uc003vpn.2	Q96SK2	OTTHUMG00000157653	ENST00000397622.2:c.1237A>G	chr7.hg19:g.129818251T>C	ENSP00000380747:p.Arg413Gly	60.0	0.0		54.0	4.0	NM_032842	A4D1L1|Q49A50|Q6PF00|Q8NCH3|Q96SL6	Missense_Mutation	SNP	ENST00000397622.2	hg19	CCDS47712.1	.	.	.	.	.	.	.	.	.	.	T	19.71	3.878794	0.72294	.	.	ENSG00000146842	ENST00000397622;ENST00000462753	T;T	0.68765	-0.35;-0.35	5.78	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.82056	0.4954	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.83686	0.0174	10	0.87932	D	0	-22.8922	11.1495	0.48451	0.0:0.0:0.2951:0.7049	.	413	Q96SK2	TM209_HUMAN	G	413;412	ENSP00000380747:R413G;ENSP00000419697:R412G	ENSP00000380747:R413G	R	-	1	2	TMEM209	129605487	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.923000	0.48868	0.976000	0.38417	0.477000	0.44152	AGG	.	.		0.333	TMEM209-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349339.1	NM_032842		C	129818251	T	C	129818251	3	2	65	1	0	0	0	0	1	0	0	0	16149	1608	56	2	472	2	TMEM209	7	129818251	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	56231	129818251	29320412	185	8258										
AGAP3	116988	hgsc.bcm.edu	37	chr7	150825737	150825737	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaagtatgtgacgctctgtgAcaacgggctgctcacctatc	11	11	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr7:150825737A>G	ENST00000463381.1	+	10	1104	c.608A>G	c.(607-609)gAc>gGc	p.D203G	AGAP3_ENST00000397238.2_Missense_Mutation_p.D431G	NM_001281300.1	NP_001268229.1	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	395	Small GTPase-like.				cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						ACGCTCTGTGACAACGGGCTG	0.572																																					p.D431G		Atlas-SNP	.											.	AGAP3	121	.	0			c.A1292G						.						66	72	70					7																	150825737		2030	4174	6204	SO:0001583	missense	116988	exon10			TCTGTGACAACGG	AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16923	protein-coding gene	gene with protein product			"centaurin, gamma 3"	CENTG3			Standard	NM_001042535		Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000463381.1:c.608A>G	chr7.hg19:g.150825737A>G	ENSP00000418016:p.Asp203Gly	61.0	0.0		75.0	4.0	NM_031946	B3KNZ8|E9PAL8|Q59EN0|Q96RK3	Missense_Mutation	SNP	ENST00000463381.1	hg19		.	.	.	.	.	.	.	.	.	.	A	23.3	4.405484	0.83230	.	.	ENSG00000133612	ENST00000463381;ENST00000397238;ENST00000335355	T;T	0.79141	-1.24;-1.24	5.26	5.26	0.73747	.	0.138177	0.47852	D	0.000210	D	0.86756	0.6009	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.79784	0.946;0.993	D	0.88217	0.2894	10	0.72032	D	0.01	.	14.3791	0.66900	1.0:0.0:0.0:0.0	.	431;203	Q96P47-4;B3KNZ8	.;.	G	203;431;395	ENSP00000418016:D203G;ENSP00000380413:D431G	ENSP00000334157:D395G	D	+	2	0	AGAP3	150456670	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	4.490000	0.60319	1.996000	0.58369	0.533000	0.62120	GAC	.	.		0.572	AGAP3-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000351909.2	NM_031946		G	150825737	A	G	150825737	3	3	65	1	0	0	0	0	1	0	0	0	369	275	10	2	1397	2	AGAP3	7	150825737	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	21007486	150825737	8312926	186	8259										
PPP3CC	5533	hgsc.bcm.edu	37	chr8	22333119	22333119	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgggtgactatgtggacagAggctatttcagtatagaggt	14	5	1	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:22333119A>G	ENST00000240139.5	+	3	681	c.354A>G	c.(352-354)agA>agG	p.R118R	PPP3CC_ENST00000518852.1_Silent_p.R118R|PPP3CC_ENST00000289963.8_Silent_p.R118R|PPP3CC_ENST00000397775.3_Silent_p.R118R	NM_005605.4	NP_005596.2	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma isozyme	118					apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		ATGTGGACAGAGGCTATTTCA	0.343																																					p.R118R		Atlas-SNP	.											.	PPP3CC	39	.	0			c.A354G						.						99	94	95					8																	22333119		2202	4300	6502	SO:0001819	synonymous_variant	5533	exon3			GGACAGAGGCTAT		CCDS34859.1, CCDS59094.1, CCDS59093.1	8p21.3	2010-03-17	2010-03-05		ENSG00000120910	ENSG00000120910	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9316	protein-coding gene	gene with protein product	"calcineurin A gamma", "protein phosphatase 2B, catalytic subunit, gamma isoform"	114107	"protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform (calcineurin A gamma)", "protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform"			1339277	Standard	NM_005605		Approved	CALNA3, PP2Bgamma	uc011kzi.2	P48454	OTTHUMG00000163802	ENST00000240139.5:c.354A>G	chr8.hg19:g.22333119A>G		90.0	0.0		85.0	4.0	NM_001243974	B4DRT5|Q9BSS6|Q9H4M5	Silent	SNP	ENST00000240139.5	hg19	CCDS34859.1																																																																																			.	.		0.343	PPP3CC-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375652.1	NM_005605		G	22333119	A	G	22333119	2	3	65	1	0	0	0	0	0	0	0	1	12411	301	11	2		2	PPP3CC	8	22333119	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10		22333119	124030903	187	8260										
GPR124	25960	hgsc.bcm.edu	37	chr8	37672476	37672476	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cttcctgggactgtcactgcTggagaagctgtaagtgctgg	14	9	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:37672476T>C	ENST00000412232.2	+	2	342	c.329T>C	c.(328-330)cTg>cCg	p.L110P	GPR124_ENST00000315215.7_Missense_Mutation_p.L110P	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	110					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			CTGTCACTGCTGGAGAAGCTG	0.597																																					p.L110P		Atlas-SNP	.											.	GPR124	85	.	0			c.T329C						.						107	100	102					8																	37672476		2203	4300	6503	SO:0001583	missense	25960	exon2			CACTGCTGGAGAA	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.329T>C	chr8.hg19:g.37672476T>C	ENSP00000406367:p.Leu110Pro	117.0	0.0		98.0	4.0	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	T	18.75	3.691058	0.68271	.	.	ENSG00000020181	ENST00000428068;ENST00000416514;ENST00000315215;ENST00000412232	T;T;T	0.81330	-1.48;-1.48;-1.48	5.68	5.68	0.88126	.	0.000000	0.64402	D	0.000015	D	0.94032	0.8088	H	0.99600	4.65	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.71870	0.975;0.966	D	0.96070	0.9045	10	0.87932	D	0	-10.7013	13.2865	0.60245	0.0:0.0:0.0:1.0	.	110;110	Q96PE1-2;Q96PE1	.;GP124_HUMAN	P	68;103;110;110	ENSP00000400860:L68P;ENSP00000323508:L110P;ENSP00000406367:L110P	ENSP00000323508:L110P	L	+	2	0	GPR124	37791634	1.000000	0.71417	1.000000	0.80357	0.771000	0.43674	4.207000	0.58480	2.156000	0.67533	0.459000	0.35465	CTG	.	.		0.597	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			C	37672476	T	C	37672476	3	2	65	1	0	0	0	0	1	0	0	0	6646	1580	55	2	314	2	GPR124	8	37672476	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	15339357	37672476	108691546	188	8261										
AGPAT6	137964	hgsc.bcm.edu	37	chr8	41472557	41472557	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tggagccacagtttaccctgTtgctatcaaggtataagacc	9	10	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:41472557T>C	ENST00000396987.3	+	10	1970	c.1043T>C	c.(1042-1044)gTt>gCt	p.V348A	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	348					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			GTTTACCCTGTTGCTATCAAG	0.458																																					p.V348A		Atlas-SNP	.											.	AGPAT6	32	.	0			c.T1043C						.						85	79	81					8																	41472557		2203	4300	6503	SO:0001583	missense	137964	exon10			ACCCTGTTGCTAT	AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	20880	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, zeta"	608143	"1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.1043T>C	chr8.hg19:g.41472557T>C	ENSP00000380184:p.Val348Ala	124.0	0.0		90.0	5.0	NM_178819	Q86V89	Missense_Mutation	SNP	ENST00000396987.3	hg19	CCDS6117.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.947797	0.92593	.	.	ENSG00000158669	ENST00000396987	D	0.96011	-3.88	5.03	5.03	0.67393	Phospholipid/glycerol acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.97158	0.9071	M	0.84082	2.675	0.80722	D	1	P	0.45902	0.868	P	0.57283	0.817	D	0.97454	1.0030	10	0.56958	D	0.05	.	14.0909	0.64990	0.0:0.0:0.0:1.0	.	348	Q86UL3	GPAT4_HUMAN	A	348	ENSP00000380184:V348A	ENSP00000380184:V348A	V	+	2	0	AGPAT6	41591714	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.868000	0.87116	2.120000	0.65058	0.533000	0.62120	GTT	.	.		0.458	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819		C	41472557	T	C	41472557	3	2	65	1	0	0	0	0	1	0	0	0	391	1725	60	2	1077	2	AGPAT6	8	41472557	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3800081	41472557	104891465	189	8262										
MYST3	7994	hgsc.bcm.edu	37	chr8	41791551	41791551	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tagtgtgggagtcttcttcgTggtcgtcctcagacccagcc	12	12	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:41791551T>C	ENST00000396930.3	-	18	4730	c.4187A>G	c.(4186-4188)cAc>cGc	p.H1396R	KAT6A_ENST00000265713.2_Missense_Mutation_p.H1396R|KAT6A_ENST00000406337.1_Missense_Mutation_p.H1396R	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1396					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GTCTTCTTCGTGGTCGTCCTC	0.498																																					p.H1396R		Atlas-SNP	.											.	.	.	.	0			c.A4187G						.						122	110	114					8																	41791551		2203	4300	6503	SO:0001583	missense	7994	exon18			TCTTCGTGGTCGT	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.4187A>G	chr8.hg19:g.41791551T>C	ENSP00000380136:p.His1396Arg	125.0	0.0		98.0	4.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	T	9.002	0.980344	0.18812	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.59224	0.28;0.28;0.28	5.97	2.44	0.29823	.	0.426282	0.25267	N	0.031920	T	0.33381	0.0861	N	0.19112	0.55	0.38446	D	0.946846	B	0.12630	0.006	B	0.16289	0.015	T	0.11299	-1.0593	10	0.07644	T	0.81	-11.7636	6.6275	0.22839	0.0:0.1964:0.1343:0.6693	.	1396	Q92794	KAT6A_HUMAN	R	1396	ENSP00000265713:H1396R;ENSP00000385888:H1396R;ENSP00000380136:H1396R	ENSP00000265713:H1396R	H	-	2	0	KAT6A	41910708	0.960000	0.32886	0.997000	0.53966	0.799000	0.45148	1.378000	0.34328	0.527000	0.28560	0.533000	0.62120	CAC	.	.		0.498	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		C	41791551	T	C	41791551	3	2	65	1	0	0	0	0	1	0	0	0	10113	1696	59	2	1831	2	MYST3	8	41791551	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	318994	41791551	104572471	190	8263										
PLAT	5327	hgsc.bcm.edu	37	chr8	42045063	42045063	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgcccctgtagctgatgcccTggtcctcgtagcacgtggcc	12	15	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:42045063T>C	ENST00000220809.4	-	6	648	c.392A>G	c.(391-393)cAg>cGg	p.Q131R	PLAT_ENST00000519510.1_Intron|PLAT_ENST00000429089.2_Missense_Mutation_p.Q131R|PLAT_ENST00000270189.6_Missense_Mutation_p.Q131R|PLAT_ENST00000429710.2_Intron|PLAT_ENST00000352041.3_Missense_Mutation_p.Q85R|PLAT_ENST00000524009.1_Intron	NM_000930.3	NP_000921.1	P00750	TPA_HUMAN	plasminogen activator, tissue	131	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|fibrinolysis (GO:0042730)|negative regulation of proteolysis (GO:0045861)|plasminogen activation (GO:0031639)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of ovulation (GO:0060279)|proteolysis (GO:0006508)|regulation of synaptic plasticity (GO:0048167)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|smooth muscle cell migration (GO:0014909)|synaptic transmission, glutamatergic (GO:0035249)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|synapse (GO:0045202)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|skin(1)|soft_tissue(1)|urinary_tract(1)	27	all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)		Aminocaproic Acid(DB00513)|Ibuprofen(DB01050)|Iloprost(DB01088)|Urokinase(DB00013)	GCTGATGCCCTGGTCCTCGTA	0.642																																					p.Q131R		Atlas-SNP	.											.	PLAT	62	.	0			c.A392G						.						44	37	40					8																	42045063		2203	4300	6503	SO:0001583	missense	5327	exon6			ATGCCCTGGTCCT		CCDS6126.1, CCDS6127.1	8p11.21	2012-10-02			ENSG00000104368	ENSG00000104368			9051	protein-coding gene	gene with protein product		173370					Standard	NM_033011		Approved		uc003xos.2	P00750	OTTHUMG00000164072	ENST00000220809.4:c.392A>G	chr8.hg19:g.42045063T>C	ENSP00000220809:p.Gln131Arg	69.0	0.0		73.0	4.0	NM_000930	A8K022|B2R8E8|Q15103|Q503B0|Q6PJA5|Q7Z7N2|Q86YK8|Q9BU99|Q9BZW1	Missense_Mutation	SNP	ENST00000220809.4	hg19	CCDS6126.1	.	.	.	.	.	.	.	.	.	.	T	7.377	0.627944	0.14257	.	.	ENSG00000104368	ENST00000270189;ENST00000429089;ENST00000220809;ENST00000352041;ENST00000520523;ENST00000521694	T;T;T;T;T;T	0.61274	0.12;0.12;0.12;0.12;0.12;0.12	5.95	-1.74	0.08056	Kringle (4);Kringle-like fold (1);	1.089850	0.06732	N	0.776814	T	0.28962	0.0719	N	0.11255	0.115	0.09310	N	0.999995	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.003	T	0.16335	-1.0406	10	0.11794	T	0.64	.	1.9809	0.03426	0.3448:0.0706:0.1863:0.3984	.	131;85;131	B8ZX62;P00750-3;P00750	.;.;TPA_HUMAN	R	131;131;131;85;131;131	ENSP00000270189:Q131R;ENSP00000392045:Q131R;ENSP00000220809:Q131R;ENSP00000270188:Q85R;ENSP00000428797:Q131R;ENSP00000429801:Q131R	ENSP00000220809:Q131R	Q	-	2	0	PLAT	42164220	0.000000	0.05858	0.543000	0.28128	0.249000	0.25844	-0.092000	0.11129	0.099000	0.17552	0.533000	0.62120	CAG	.	.		0.642	PLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377100.1	NM_000930		C	42045063	T	C	42045063	3	2	65	1	0	0	0	0	1	0	0	0	12030	1580	55	2	1332	2	PLAT	8	42045063	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	253512	42045063	104318959	191	8264										
HGSNAT	138050	hgsc.bcm.edu	37	chr8	43047567	43047567	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cacctttaccagcacccatcTtctgctgtgagtgagactcg	8	14	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:43047567T>C	ENST00000458501.2	+	13	1455	c.1455T>C	c.(1453-1455)tcT>tcC	p.S485S	HGSNAT_ENST00000379644.4_Silent_p.S457S|HGSNAT_ENST00000297798.7_Silent_p.S189S|HGSNAT_ENST00000521576.1_Silent_p.S174S			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	485					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			AGCACCCATCTTCTGCTGTGA	0.498																																					p.S457S		Atlas-SNP	.											.	HGSNAT	85	.	0			c.T1371C						.						62	59	60					8																	43047567		1983	4158	6141	SO:0001819	synonymous_variant	138050	exon13			CCCATCTTCTGCT		CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"transmembrane protein 76"	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.1455T>C	chr8.hg19:g.43047567T>C		70.0	0.0		88.0	4.0	NM_152419	B4E2V0	Silent	SNP	ENST00000458501.2	hg19		.	.	.	.	.	.	.	.	.	.	T	5.170	0.217015	0.09810	.	.	ENSG00000165102	ENST00000524016	.	.	.	5.23	-6.48	0.01896	.	.	.	.	.	T	0.46833	0.1413	.	.	.	0.40583	D	0.981413	.	.	.	.	.	.	T	0.48222	-0.9054	4	.	.	.	-10.3472	6.8837	0.24187	0.2236:0.4955:0.0:0.2809	.	.	.	.	L	159	.	.	F	+	1	0	HGSNAT	43166724	0.850000	0.29656	0.010000	0.14722	0.001000	0.01503	-0.163000	0.09997	-1.636000	0.01533	-1.303000	0.01326	TTC	.	.		0.498	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038		C	43047567	T	C	43047567	2	2	65	1	0	0	0	0	0	0	0	1	7097	1596	56	2		2	HGSNAT	8	43047567	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1002504	43047567	103316455	192	8265										
RP1	6101	hgsc.bcm.edu	37	chr8	55542178	55542178	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tctttggataaactgtatgcTctttgtggtcaacattgccc	8	9	3	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:55542178T>C	ENST00000220676.1	+	4	5884	c.5736T>C	c.(5734-5736)gcT>gcC	p.A1912A		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1912					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AACTGTATGCTCTTTGTGGTC	0.388																																					p.A1912A	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.T5736C						.						93	92	93					8																	55542178		2203	4300	6503	SO:0001819	synonymous_variant	6101	exon4			GTATGCTCTTTGT	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.5736T>C	chr8.hg19:g.55542178T>C		77.0	0.0		58.0	4.0	NM_006269		Silent	SNP	ENST00000220676.1	hg19	CCDS6160.1																																																																																			.	.		0.388	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		C	55542178	T	C	55542178	2	2	65	1	0	0	0	0	0	0	0	1	13547	1538	54	2		2	RP1	8	55542178	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	12494611	55542178	90821844	193	8266										
CHD7	55636	hgsc.bcm.edu	37	chr8	61757511	61757511	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aaaccatctgcagaaccatcCtggtgtactgtcttaatcat	6	11	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:61757511C>G	ENST00000423902.2	+	22	5418	c.4939C>G	c.(4939-4941)Ctg>Gtg	p.L1647V	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1647					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CAGAACCATCCTGGTGTACTG	0.483																																					p.L1647V		Atlas-SNP	.											.	CHD7	534	.	0			c.C4939G						.						114	113	113					8																	61757511		1965	4162	6127	SO:0001583	missense	55636	exon22			ACCATCCTGGTGT	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.4939C>G	chr8.hg19:g.61757511C>G	ENSP00000392028:p.Leu1647Val	78.0	0.0		99.0	5.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.293511	0.60086	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.87334	-2.24	5.63	4.75	0.60458	.	0.000000	0.64402	D	0.000004	D	0.93530	0.7935	M	0.88906	2.99	0.80722	D	1	D	0.54964	0.969	P	0.60541	0.876	D	0.94686	0.7870	10	0.87932	D	0	-14.2895	15.1709	0.72872	0.0:0.9312:0.0:0.0688	.	1647	Q9P2D1	CHD7_HUMAN	V	1647	ENSP00000392028:L1647V	ENSP00000307304:L1647V	L	+	1	2	CHD7	61920065	1.000000	0.71417	0.996000	0.52242	0.535000	0.34838	2.073000	0.41519	1.487000	0.48415	0.655000	0.94253	CTG	.	.		0.483	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		G	61757511	C	G	61757511	3	3	65	1	0	0	0	0	1	0	0	0	3332	680	24	4	5021	4	CHD7	8	61757511	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	6215333	61757511	84606511	194	8267										
PDE7A	5150	hgsc.bcm.edu	37	chr8	66636575	66636575	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gggttacaaatatcagcacaTttcaaagccatctagcaaac	6	10	3	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:66636575T>C	ENST00000401827.3	-	11	1520	c.1077A>G	c.(1075-1077)aaA>aaG	p.K359K	PDE7A_ENST00000396642.3_Silent_p.K359K|PDE7A_ENST00000379419.4_Silent_p.K333K|PDE7A_ENST00000518667.1_5'Flank	NM_001242318.2	NP_001229247.1	Q13946	PDE7A_HUMAN	phosphodiesterase 7A	359	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			large_intestine(5)|lung(3)|stomach(1)|urinary_tract(1)	10			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	TATCAGCACATTTCAAAGCCA	0.363																																					p.K359K		Atlas-SNP	.											.	PDE7A	78	.	0			c.A1077G						.						118	108	112					8																	66636575		2203	4300	6503	SO:0001819	synonymous_variant	5150	exon11			AGCACATTTCAAA	L12052	CCDS34901.1, CCDS56538.1	8q13	2008-03-18				ENSG00000205268	3.1.4.17	"Phosphodiesterases"	8791	protein-coding gene	gene with protein product		171885				8389765, 9521885	Standard	NM_001242318		Approved	HCP1	uc003xvq.3	Q13946		ENST00000401827.3:c.1077A>G	chr8.hg19:g.66636575T>C		73.0	0.0		58.0	4.0	NM_001242318	A0AVH6|A8K436|A8K9G5|O15380|Q96T72	Silent	SNP	ENST00000401827.3	hg19	CCDS56538.1																																																																																			.	.		0.363	PDE7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378905.1			C	66636575	T	C	66636575	2	2	65	1	0	0	0	0	0	0	0	1	11660	1490	52	2		2	PDE7A	8	66636575	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4879064	66636575	79727447	195	8268										
PREX2	80243	hgsc.bcm.edu	37	chr8	69002857	69002857	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cttcaccctggacagtgcatTatcaaggtgaatggaatcaa	9	9	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:69002857T>C	ENST00000288368.4	+	20	2434	c.2157T>C	c.(2155-2157)atT>atC	p.I719I	RP11-403D15.2_ENST00000526901.1_RNA|PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	719	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						GACAGTGCATTATCAAGGTGA	0.433																																					p.I719I		Atlas-SNP	.											.	PREX2	614	.	0			c.T2157C						.						114	102	106					8																	69002857		2203	4300	6503	SO:0001819	synonymous_variant	80243	exon20			GTGCATTATCAAG	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2157T>C	chr8.hg19:g.69002857T>C		116.0	0.0		94.0	4.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	hg19	CCDS6201.1																																																																																			.	.		0.433	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		C	69002857	T	C	69002857	2	2	65	1	0	0	0	0	0	0	0	1	12489	1742	61	2		2	PREX2	8	69002857	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2366282	69002857	77361165	196	8269										
PI15	51050	hgsc.bcm.edu	37	chr8	75737542	75737542	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tctcccttctctgtgaagcaAgtaccgtcgtcctactcaat	6	14	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:75737542A>G	ENST00000260113.2	+	2	237	c.58A>G	c.(58-60)Agt>Ggt	p.S20G	RP11-758M4.4_ENST00000523860.1_RNA|RP11-758M4.4_ENST00000518128.1_RNA|PI15_ENST00000523773.1_Missense_Mutation_p.S20G	NM_015886.3	NP_056970.1	O43692	PI15_HUMAN	peptidase inhibitor 15	20						extracellular vesicular exosome (GO:0070062)	peptidase inhibitor activity (GO:0030414)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|skin(1)	30	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)			CTGTGAAGCAAGTACCGTCGT	0.468																																					p.S20G		Atlas-SNP	.											.	PI15	73	.	0			c.A58G						.						219	213	215					8																	75737542		2203	4300	6503	SO:0001583	missense	51050	exon2			GAAGCAAGTACCG	D45027	CCDS6218.1	8q13.3	2005-08-17	2005-08-17		ENSG00000137558	ENSG00000137558			8946	protein-coding gene	gene with protein product		607076	"protease inhibitor 15"			8882727, 9473672	Standard	XM_005251255		Approved	P25TI	uc003yal.3	O43692	OTTHUMG00000164528	ENST00000260113.2:c.58A>G	chr8.hg19:g.75737542A>G	ENSP00000260113:p.Ser20Gly	131.0	0.0		120.0	5.0	NM_015886	Q68CY1	Missense_Mutation	SNP	ENST00000260113.2	hg19	CCDS6218.1	.	.	.	.	.	.	.	.	.	.	A	9.589	1.125683	0.20959	.	.	ENSG00000137558	ENST00000260113;ENST00000523773	T;T	0.09630	2.96;2.96	4.77	3.59	0.41128	.	0.238443	0.41938	D	0.000786	T	0.08935	0.0221	L	0.52573	1.65	0.34216	D	0.67487	B	0.19817	0.039	B	0.16289	0.015	T	0.18241	-1.0343	10	0.13108	T	0.6	.	7.0667	0.25156	0.6969:0.1598:0.0:0.1432	.	20	O43692	PI15_HUMAN	G	20	ENSP00000260113:S20G;ENSP00000428567:S20G	ENSP00000260113:S20G	S	+	1	0	PI15	75900097	1.000000	0.71417	0.578000	0.28575	0.974000	0.67602	4.447000	0.60020	0.946000	0.37632	0.459000	0.35465	AGT	.	.		0.468	PI15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379115.1	NM_015886		G	75737542	A	G	75737542	3	3	65	1	0	0	0	0	1	0	0	0	11877	72	3	2	60	2	PI15	8	75737542	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	6734685	75737542	70626480	197	8270										
KLF10	7071	hgsc.bcm.edu	37	chr8	103664250	103664250	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	catcagatttgacacttgagAgggttcaaagtcagaaggac	11	7	3	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:103664250A>G	ENST00000285407.6	-	3	610	c.310T>C	c.(310-312)Tct>Cct	p.S104P	KLF10_ENST00000395884.3_Missense_Mutation_p.S93P	NM_005655.2	NP_005646.1	Q13118	KLF10_HUMAN	Kruppel-like factor 10	104					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular response to peptide (GO:1901653)|cellular response to starvation (GO:0009267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of circadian rhythm (GO:0042752)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(3)	18	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			GACACTTGAGAGGGTTCAAAG	0.398											OREG0018913	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S104P	Esophageal Squamous(16;495 519 2144 16528 44005)	Atlas-SNP	.											.	KLF10	44	.	0			c.T310C						.						58	63	61					8																	103664250		2202	4300	6502	SO:0001583	missense	7071	exon3			CTTGAGAGGGTTC	U21847	CCDS6294.1, CCDS47905.1	8q22.3	2014-09-17	2004-11-29	2004-12-01	ENSG00000155090	ENSG00000155090		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11810	protein-coding gene	gene with protein product		601878	"TGFB inducible early growth response"	TIEG		8584037, 9721211	Standard	NM_001032282		Approved	EGRA, TIEG1	uc011lhk.1	Q13118	OTTHUMG00000164735	ENST00000285407.6:c.310T>C	chr8.hg19:g.103664250A>G	ENSP00000285407:p.Ser104Pro	80.0	0.0	1375	87.0	4.0	NM_005655	A8MVH0|B2R794|L0R4P6|L0R679|O75411|Q503B2	Missense_Mutation	SNP	ENST00000285407.6	hg19	CCDS6294.1	.	.	.	.	.	.	.	.	.	.	A	16.90	3.250118	0.59212	.	.	ENSG00000155090	ENST00000285407;ENST00000395884	T;T	0.19250	2.16;2.23	6.02	4.87	0.63330	.	0.073459	0.64402	D	0.000017	T	0.30603	0.0770	M	0.64997	1.995	0.39380	D	0.966241	P;P	0.51791	0.948;0.948	P;P	0.51487	0.671;0.671	T	0.11372	-1.0590	10	0.87932	D	0	.	7.9059	0.29761	0.7938:0.1377:0.0685:0.0	.	104;93	Q13118;O75411	KLF10_HUMAN;.	P	104;93	ENSP00000285407:S104P;ENSP00000379222:S93P	ENSP00000285407:S104P	S	-	1	0	KLF10	103733426	1.000000	0.71417	0.989000	0.46669	0.992000	0.81027	3.741000	0.55090	1.116000	0.41820	0.533000	0.62120	TCT	.	.		0.398	KLF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379967.1			G	103664250	A	G	103664250	3	3	65	1	0	0	0	0	1	0	0	0	8347	304	11	2	1140	2	KLF10	8	103664250	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	27926708	103664250	42699772	198	8271										
RAD21	5885	hgsc.bcm.edu	37	chr8	117870613	117870613	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aaatcattttcttgtaaaatActgatgttcccaacttcttc	3	9	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:117870613A>G	ENST00000297338.2	-	5	746	c.459T>C	c.(457-459)agT>agC	p.S153S	RAD21_ENST00000523547.1_5'UTR	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	153					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					CTTGTAAAATACTGATGTTCC	0.333																																					p.S153S		Atlas-SNP	.											.	RAD21	95	.	0			c.T459C						.						115	115	115					8																	117870613		2203	4300	6503	SO:0001819	synonymous_variant	5885	exon5			TAAAATACTGATG	BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"sister chromatid cohesion 1"	606462	"RAD21 (S. pombe) homolog"			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.459T>C	chr8.hg19:g.117870613A>G		67.0	0.0		77.0	4.0	NM_006265	A8K0E0|Q15001|Q99568	Silent	SNP	ENST00000297338.2	hg19	CCDS6321.1																																																																																			.	.		0.333	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		G	117870613	A	G	117870613	2	3	65	1	0	0	0	0	0	0	0	1	12996	388	14	2		2	RAD21	8	117870613	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	14206363	117870613	28493409	199	8272			1	9		3	3	78	N	T_C_A	5.154165e-07
RAD21	5885	hgsc.bcm.edu	37	chr8	117870655	117870655	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctcatggttatctcttccacTctactctgattcaagctgaa	5	12	5	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:117870655T>C	ENST00000297338.2	-	5	704	c.417A>G	c.(415-417)agA>agG	p.R139R	RAD21_ENST00000523547.1_5'UTR	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	139					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TCTCTTCCACTCTACTCTGAT	0.318																																					p.R139R		Atlas-SNP	.											.	RAD21	95	.	0			c.A417G						.						133	131	132					8																	117870655		2203	4300	6503	SO:0001819	synonymous_variant	5885	exon5			TTCCACTCTACTC	BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"sister chromatid cohesion 1"	606462	"RAD21 (S. pombe) homolog"			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.417A>G	chr8.hg19:g.117870655T>C		76.0	0.0		96.0	4.0	NM_006265	A8K0E0|Q15001|Q99568	Silent	SNP	ENST00000297338.2	hg19	CCDS6321.1																																																																																			.	.		0.318	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		C	117870655	T	C	117870655	2	2	65	1	0	0	0	0	0	0	0	1	12996	1548	54	2		2	RAD21	8	117870655	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	42	117870655	28493367	200	8273			1	9		3	3	78	N	T_C_A	5.154165e-07
RAD21	5885	hgsc.bcm.edu	37	chr8	117870690	117870690	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gctgaactgctgggccacatCgatgtcactttaaaagaagg	11	9	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:117870690C>A	ENST00000297338.2	-	5	669	c.382G>T	c.(382-384)Gat>Tat	p.D128Y	RAD21_ENST00000523547.1_5'UTR	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	128					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TGGGCCACATCGATGTCACTT	0.318																																					p.D128Y		Atlas-SNP	.											.	RAD21	95	.	0			c.G382T						.						120	116	117					8																	117870690		2203	4300	6503	SO:0001583	missense	5885	exon5			CCACATCGATGTC	BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"sister chromatid cohesion 1"	606462	"RAD21 (S. pombe) homolog"			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.382G>T	chr8.hg19:g.117870690C>A	ENSP00000297338:p.Asp128Tyr	56.0	0.0		82.0	4.0	NM_006265	A8K0E0|Q15001|Q99568	Missense_Mutation	SNP	ENST00000297338.2	hg19	CCDS6321.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.844976	0.91197	.	.	ENSG00000164754	ENST00000297338;ENST00000520992;ENST00000517485	T;T;T	0.59772	0.24;1.32;1.32	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.79197	0.4405	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.75830	-0.3179	10	0.26408	T	0.33	-0.1517	19.9542	0.97213	0.0:1.0:0.0:0.0	.	128	O60216	RAD21_HUMAN	Y	128	ENSP00000297338:D128Y;ENSP00000429342:D128Y;ENSP00000427923:D128Y	ENSP00000297338:D128Y	D	-	1	0	RAD21	117939871	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.728000	0.93425	0.650000	0.86243	GAT	.	.		0.318	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		A	117870690	C	A	117870690	3	1	65	1	0	0	0	0	1	0	0	0	12996	884	31	1	1553	1	RAD21	8	117870690	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	35	117870690	28493332	201	8274			1	9		3	3	78	N	T_C_A	5.154165e-07
TAF2	6873	hgsc.bcm.edu	37	chr8	120810035	120810035	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aaagacttcatgaaggtatgAtgtggtatgtttcagcaatg	11	4	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:120810035A>G	ENST00000378164.2	-	7	1142	c.844T>C	c.(844-846)Tca>Cca	p.S282P		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	282					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TGAAGGTATGATGTGGTATGT	0.338																																					p.S282P		Atlas-SNP	.											.	TAF2	204	.	0			c.T844C						.						89	87	87					8																	120810035		2203	4299	6502	SO:0001583	missense	6873	exon7			GGTATGATGTGGT	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.844T>C	chr8.hg19:g.120810035A>G	ENSP00000367406:p.Ser282Pro	91.0	0.0		95.0	4.0	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	hg19	CCDS34937.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.212616	0.79240	.	.	ENSG00000064313	ENST00000378164	T	0.02837	4.14	6.07	6.07	0.98685	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.065598	0.64402	D	0.000006	T	0.06508	0.0167	L	0.49126	1.545	0.58432	D	0.999996	P	0.45428	0.858	P	0.49387	0.609	T	0.47222	-0.9134	10	0.30854	T	0.27	-25.6241	12.4822	0.55850	0.8607:0.1393:0.0:0.0	.	282	Q6P1X5	TAF2_HUMAN	P	282	ENSP00000367406:S282P	ENSP00000367406:S282P	S	-	1	0	TAF2	120879216	1.000000	0.71417	0.897000	0.35233	0.989000	0.77384	7.269000	0.78482	2.326000	0.78906	0.533000	0.62120	TCA	.	.		0.338	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		G	120810035	A	G	120810035	3	3	65	1	0	0	0	0	1	0	0	0	15539	333	12	2	2835	2	TAF2	8	120810035	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2939345	120810035	25553987	202	8275										
DSCC1	79075	hgsc.bcm.edu	37	chr8	120850618	120850618	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agcaaaaatatgatttctggTctcgagtgtctatccaccag	8	9	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:120850618T>C	ENST00000313655.4	-	8	1168	c.954A>G	c.(952-954)agA>agG	p.R318R		NM_024094.2	NP_076999.2	Q9BVC3	DCC1_HUMAN	DNA replication and sister chromatid cohesion 1	318					DNA replication (GO:0006260)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			NS(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|pancreas(1)	9	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TGATTTCTGGTCTCGAGTGTC	0.368																																					p.R318R		Atlas-SNP	.											.	DSCC1	40	.	0			c.A954G						.						108	109	109					8																	120850618		2203	4300	6503	SO:0001819	synonymous_variant	79075	exon8			TTCTGGTCTCGAG		CCDS6330.1	8q24.12	2013-05-24	2013-05-24		ENSG00000136982	ENSG00000136982			24453	protein-coding gene	gene with protein product	"defective in sister chromatid cohesion homolog 1 (S. cerevisiae)"	613203	"defective in sister chromatid cohesion 1 homolog (S. cerevisiae)"			12766176, 20826785	Standard	NM_024094		Approved	DCC1, hDCC1, MGC5528	uc003yov.3	Q9BVC3	OTTHUMG00000165010	ENST00000313655.4:c.954A>G	chr8.hg19:g.120850618T>C		118.0	0.0		137.0	6.0	NM_024094	Q969N5	Silent	SNP	ENST00000313655.4	hg19	CCDS6330.1																																																																																			.	.		0.368	DSCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381443.1	NM_024094		C	120850618	T	C	120850618	2	2	65	1	0	0	0	0	0	0	0	1	4772	1664	58	2		2	DSCC1	8	120850618	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	40583	120850618	25513404	203	8276										
PPP1R16A	84988	hgsc.bcm.edu	37	chr8	145726669	145726669	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcgcagagctcaggccgccgCccccggaggtgagcgccccg	16	18	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr8:145726669C>T	ENST00000292539.4	+	10	2112	c.1195C>T	c.(1195-1197)Ccc>Tcc	p.P399S	PPP1R16A_ENST00000435887.1_Missense_Mutation_p.P399S|CTD-2517M22.14_ENST00000532766.1_RNA|CTD-2517M14.5_ENST00000569326.1_RNA|GPT_ENST00000394955.2_5'Flank|GPT_ENST00000528431.1_5'Flank			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	399						plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CAGGCCGCCGCCCCCGGAGGT	0.736																																					p.P399S		Atlas-SNP	.											.	PPP1R16A	25	.	0			c.C1195T						.						9	12	11					8																	145726669		2134	4173	6307	SO:0001583	missense	84988	exon9			CCGCCGCCCCCGG		CCDS6429.1	8q24.3	2013-01-10	2011-10-04		ENSG00000160972	ENSG00000160972		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14941	protein-coding gene	gene with protein product		609172	"protein phosphatase 1, regulatory (inhibitor) subunit 16A"			11948623	Standard	NM_032902		Approved	MGC14333, MYPT3	uc003zdf.3	Q96I34	OTTHUMG00000165173	ENST00000292539.4:c.1195C>T	chr8.hg19:g.145726669C>T	ENSP00000292539:p.Pro399Ser	1.0	0.0		7.0	7.0	NM_032902	D3DWM5	Missense_Mutation	SNP	ENST00000292539.4	hg19	CCDS6429.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872668	0.51695	.	.	ENSG00000160972	ENST00000292539;ENST00000435887	T;T	0.70282	-0.47;-0.47	4.72	0.134	0.14771	.	0.480552	0.19810	N	0.105544	T	0.51449	0.1675	L	0.56769	1.78	0.09310	N	1	B	0.31435	0.323	B	0.24006	0.05	T	0.33701	-0.9858	10	0.07644	T	0.81	.	2.4722	0.04566	0.1267:0.4131:0.2754:0.1848	.	399	Q96I34	PP16A_HUMAN	S	399	ENSP00000292539:P399S;ENSP00000391126:P399S	ENSP00000292539:P399S	P	+	1	0	PPP1R16A	145697477	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-0.049000	0.11924	0.053000	0.16036	0.462000	0.41574	CCC	.	.		0.736	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382459.1	NM_032902		T	145726669	C	T	145726669	3	4	65	1	0	0	0	0	1	0	0	0	12377	739	26	3	1229	3	PPP1R16A	8	145726669	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	24876051	145726669	637353	204	8277										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2029231	2029231	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agacttcccacaggaaggcaTgcatcaaatgcataaggtaa	9	9	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:2029231T>C	ENST00000382203.1	+	2	418	c.209T>C	c.(208-210)aTg>aCg	p.M70T	SMARCA2_ENST00000382194.1_Missense_Mutation_p.M70T|SMARCA2_ENST00000349721.2_Missense_Mutation_p.M70T|SMARCA2_ENST00000357248.2_Missense_Mutation_p.M70T			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	70					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		CAGGAAGGCATGCATCAAATG	0.498																																					p.M70T		Atlas-SNP	.											.	SMARCA2	313	.	0			c.T209C						.						40	33	35					9																	2029231		2203	4300	6503	SO:0001583	missense	6595	exon2			AAGGCATGCATCA	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.209T>C	chr9.hg19:g.2029231T>C	ENSP00000371638:p.Met70Thr	103.0	0.0		73.0	4.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.755525	0.49362	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000450198;ENST00000439732;ENST00000382203;ENST00000382194	D;D;T;D;D	0.88046	-2.33;-2.31;0.58;-2.33;-2.31	5.61	5.61	0.85477	.	0.151372	0.56097	D	0.000024	D	0.83562	0.5281	L	0.43923	1.385	0.80722	D	1	B;B	0.20988	0.05;0.004	B;B	0.17979	0.02;0.006	T	0.79948	-0.1588	10	0.48119	T	0.1	-10.7341	15.7983	0.78428	0.0:0.0:0.0:1.0	.	70;70	P51531-2;P51531	.;SMCA2_HUMAN	T	70	ENSP00000265773:M70T;ENSP00000349788:M70T;ENSP00000392081:M70T;ENSP00000371638:M70T;ENSP00000371629:M70T	ENSP00000265773:M70T	M	+	2	0	SMARCA2	2019231	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.302000	0.72788	2.125000	0.65367	0.455000	0.32223	ATG	.	.		0.498	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		C	2029231	T	C	2029231	3	2	65	1	0	0	0	0	1	0	0	0	14784	1464	51	2	211	2	SMARCA2	9	2029231	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		2029231	139184200	205	8278										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18636002	18636002	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	attcgccttgtcttaaaaggTcctgatcacttatgtaagta	7	8	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:18636002T>C	ENST00000380548.4	+	6	1002	c.663T>C	c.(661-663)ggT>ggC	p.G221G	ADAMTSL1_ENST00000327883.7_Silent_p.G221G|ADAMTSL1_ENST00000276935.6_Silent_p.G221G|ADAMTSL1_ENST00000380566.4_Silent_p.G221G	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	221						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		TCTTAAAAGGTCCTGATCACT	0.348																																					p.G221G		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.T663C						.						213	200	204					9																	18636002		2203	4300	6503	SO:0001819	synonymous_variant	92949	exon6			AAAAGGTCCTGAT	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.663T>C	chr9.hg19:g.18636002T>C		163.0	0.0		98.0	4.0	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	hg19	CCDS47954.1																																																																																			.	.		0.348	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			C	18636002	T	C	18636002	2	2	65	1	0	0	0	0	0	0	0	1	274	1654	58	2		2	ADAMTSL1	9	18636002	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	16606771	18636002	122577429	206	8279										
NFX1	4799	hgsc.bcm.edu	37	chr9	33351736	33351736	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgactgtggtcacccgtgtaTggcaccctgccataccagct	10	14	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:33351736T>C	ENST00000379540.3	+	16	2665	c.2603T>C	c.(2602-2604)aTg>aCg	p.M868T	NFX1_ENST00000379521.4_Missense_Mutation_p.M868T|Y_RNA_ENST00000363674.1_RNA	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	868					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		CACCCGTGTATGGCACCCTGC	0.552																																					p.M868T		Atlas-SNP	.											.	NFX1	85	.	0			c.T2603C						.						74	71	72					9																	33351736		2203	4300	6503	SO:0001583	missense	4799	exon16			CGTGTATGGCACC	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.2603T>C	chr9.hg19:g.33351736T>C	ENSP00000368856:p.Met868Thr	54.0	0.0		54.0	4.0	NM_147133	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	hg19	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	T	12.59	1.983493	0.35036	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000263220	T;T	0.38240	1.15;1.15	5.88	4.68	0.58851	Zinc finger, NF-X1-type (1);	0.337134	0.39146	N	0.001448	T	0.19087	0.0458	N	0.12831	0.26	0.80722	D	1	B;P	0.40476	0.003;0.718	B;B	0.38880	0.01;0.284	T	0.05305	-1.0893	10	0.12766	T	0.61	.	10.9663	0.47414	0.0:0.0:0.1564:0.8436	.	868;868	Q12986;Q12986-2	NFX1_HUMAN;.	T	868;868;65	ENSP00000368856:M868T;ENSP00000368836:M868T	ENSP00000263220:M65T	M	+	2	0	NFX1	33341736	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.795000	0.38784	2.246000	0.74042	0.533000	0.62120	ATG	.	.		0.552	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			C	33351736	T	C	33351736	3	2	65	1	0	0	0	0	1	0	0	0	10396	1464	51	2	2747	2	NFX1	9	33351736	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	14715734	33351736	107861695	207	8280										
CREB3	7094	hgsc.bcm.edu	37	chr9	35733445	35733445	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaagagtctattggagaaggAggggcttattctgcctgaga	15	5	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:35733445A>G	ENST00000314888.9	-	0	0				CREB3_ENST00000353704.2_Missense_Mutation_p.E133G|CREB3_ENST00000486056.1_3'UTR|TLN1_ENST00000540444.1_5'Flank	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTGGAGAAGGAGGGGCTTATT	0.463																																					p.E133G		Atlas-SNP	.											.	CREB3	24	.	0			c.A398G						.						101	91	95					9																	35733445		2203	4300	6503	SO:0001631	upstream_gene_variant	10488	exon4			AGAAGGAGGGGCT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874		chr9.hg19:g.35733445A>G	Exception_encountered	125.0	0.0		84.0	4.0	NM_006368	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	A	31	5.083431	0.94050	.	.	ENSG00000107175	ENST00000353704	D	0.83075	-1.68	4.88	4.88	0.63580	Eukaryotic transcription factor, Skn-1-like, DNA-binding (1);	0.054574	0.64402	D	0.000001	D	0.90157	0.6924	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.995	D	0.91360	0.5111	10	0.87932	D	0	.	13.6285	0.62181	1.0:0.0:0.0:0.0	.	157;133	O43889;O43889-2	CREB3_HUMAN;.	G	133	ENSP00000342136:E133G	ENSP00000342136:E133G	E	+	2	0	CREB3	35723445	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.928000	0.63447	1.970000	0.57323	0.528000	0.53228	GAG	.	.		0.463	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		G	35733445	A	G	35733445	1	3	65	0	1	0	0	0	0	0	0	0	3857	304	11	2		2	CREB3	9	35733445	5'Flank	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2381709	35733445	105479986	208	8281										
SMC5	23137	hgsc.bcm.edu	37	chr9	72967130	72967130	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgcaaaatcttccttattcTgaaaagatgacagttttgtt	6	7	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:72967130T>C	ENST00000361138.5	+	25	3247	c.3189T>C	c.(3187-3189)tcT>tcC	p.S1063S	SMC5_ENST00000471372.1_3'UTR	NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	1063					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						TTCCTTATTCTGAAAAGATGA	0.378																																					p.S1063S		Atlas-SNP	.											.	SMC5	96	.	0			c.T3189C						.						84	87	86					9																	72967130		2203	4300	6503	SO:0001819	synonymous_variant	23137	exon25			TTATTCTGAAAAG	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"Structural maintenance of chromosomes proteins"	20465	protein-coding gene	gene with protein product		609386	"SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.3189T>C	chr9.hg19:g.72967130T>C		102.0	0.0		80.0	4.0	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Silent	SNP	ENST00000361138.5	hg19	CCDS6632.1																																																																																			.	.		0.378	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		C	72967130	T	C	72967130	2	2	65	1	0	0	0	0	0	0	0	1	14801	1567	55	2		2	SMC5	9	72967130	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	37233685	72967130	68246301	209	8282										
C9orf41	138199	hgsc.bcm.edu	37	chr9	77614715	77614715	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttccttgacaagcataacctAgcatagctatttcccaggcc	6	13	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:77614715A>G	ENST00000376834.3	-	4	814	c.662T>C	c.(661-663)cTa>cCa	p.L221P	C9orf41_ENST00000376837.3_Intron	NM_152420.1	NP_689633.1	Q8N4J0	CI041_HUMAN	chromosome 9 open reading frame 41	221										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|urinary_tract(2)	17						AGCATAACCTAGCATAGCTAT	0.358																																					p.L221P		Atlas-SNP	.											.	C9orf41	57	.	0			c.T662C						.						99	98	98					9																	77614715		2203	4300	6503	SO:0001583	missense	138199	exon4			TAACCTAGCATAG	AK098661	CCDS6649.1	9q21.31	2012-03-15			ENSG00000156017	ENSG00000156017			23435	protein-coding gene	gene with protein product						12477932	Standard	NM_152420		Approved	FLJ25795	uc004ajq.3	Q8N4J0	OTTHUMG00000020032	ENST00000376834.3:c.662T>C	chr9.hg19:g.77614715A>G	ENSP00000366030:p.Leu221Pro	43.0	0.0		24.0	4.0	NM_152420	Q7Z383|Q8N7C5	Missense_Mutation	SNP	ENST00000376834.3	hg19	CCDS6649.1	.	.	.	.	.	.	.	.	.	.	A	18.14	3.557523	0.65425	.	.	ENSG00000156017	ENST00000376834;ENST00000451153	T;T	0.04502	3.61;3.61	6.07	6.07	0.98685	N2227-like (1);	0.067331	0.64402	D	0.000009	T	0.23926	0.0579	M	0.88241	2.94	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.01725	-1.1287	10	0.38643	T	0.18	-8.7332	11.6865	0.51490	0.868:0.0:0.0:0.132	.	221	Q8N4J0	CI041_HUMAN	P	221;160	ENSP00000366030:L221P;ENSP00000396353:L160P	ENSP00000366030:L221P	L	-	2	0	C9orf41	76804535	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.840000	0.75369	2.326000	0.78906	0.533000	0.62120	CTA	.	.		0.358	C9orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052703.1	NM_152420		G	77614715	A	G	77614715	3	3	65	1	0	0	0	0	1	0	0	0	2484	420	15	2	587	2	C9orf41	9	77614715	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	4647585	77614715	63598716	210	8283										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79986002	79986002	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgggaaaggtttagtaggagCggtagcaaggccaactggag	17	5	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:79986002C>T	ENST00000360280.3	+	67	9274	c.9014C>T	c.(9013-9015)gCg>gTg	p.A3005V	VPS13A_ENST00000376634.4_Missense_Mutation_p.A3005V|VPS13A_ENST00000357409.5_Missense_Mutation_p.A3005V|VPS13A_ENST00000376636.3_Missense_Mutation_p.A2966V	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	3005					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TTAGTAGGAGCGGTAGCAAGG	0.408																																					p.A3005V		Atlas-SNP	.											VPS13A_ENST00000376634,NS,carcinoma,0,3	VPS13A	735	.	0			c.C9014T						.						103	97	99					9																	79986002		2203	4300	6503	SO:0001583	missense	23230	exon67			TAGGAGCGGTAGC	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.9014C>T	chr9.hg19:g.79986002C>T	ENSP00000353422:p.Ala3005Val	105.0	0.0		92.0	4.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	C	16.28	3.077693	0.55753	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.41758	1.16;0.99;1.08;1.12	5.77	5.77	0.91146	Autophagy-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	N	0.10809	0.05	0.80722	D	1	P;D;D;D	0.69078	0.568;0.997;0.985;0.994	B;D;P;P	0.69824	0.23;0.966;0.614;0.765	T	0.43925	-0.9361	9	.	.	.	.	19.9576	0.97228	0.0:1.0:0.0:0.0	.	2966;3005;3005;3005	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	V	3005;2966;3005;3005	ENSP00000365821:A3005V;ENSP00000365823:A2966V;ENSP00000353422:A3005V;ENSP00000349985:A3005V	.	A	+	2	0	VPS13A	79175822	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	4.088000	0.57678	2.885000	0.99019	0.655000	0.94253	GCG	.	.		0.408	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		T	79986002	C	T	79986002	3	4	65	1	0	0	0	0	1	0	0	0	17204	768	27	1	9280	1	VPS13A	9	79986002	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	2371287	79986002	61227429	211	8284										
IARS	3376	hgsc.bcm.edu	37	chr9	95051645	95051645	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttaaattcagtccaaaactcCaagattttctcttcttcagc	3	11	4	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:95051645C>T	ENST00000375643.3	-	2	323	c.57G>A	c.(55-57)ttG>ttA	p.L19L	IARS_ENST00000443024.2_Silent_p.L19L|IARS_ENST00000375629.3_5'UTR|IARS_ENST00000447699.2_5'UTR	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	19					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	TCCAAAACTCCAAGATTTTCT	0.299																																					p.L19L		Atlas-SNP	.											.	IARS	74	.	0			c.G57A						.						46	46	46					9																	95051645		2199	4294	6493	SO:0001819	synonymous_variant	3376	exon2			AAACTCCAAGATT	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	5330	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 1, cytoplasmic"	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.57G>A	chr9.hg19:g.95051645C>T		115.0	0.0		58.0	4.0	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Silent	SNP	ENST00000375643.3	hg19	CCDS6694.1																																																																																			.	.		0.299	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161		T	95051645	C	T	95051645	2	4	65	1	0	0	0	0	0	0	0	1	7482	593	21	3		3	IARS	9	95051645	Silent	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	15065643	95051645	46161786	212	8285										
IPPK	64768	hgsc.bcm.edu	37	chr9	95411768	95411768	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cacagaatcggccggtgctcTgcaaagcggtaggtttggag	15	9	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:95411768T>C	ENST00000287996.3	-	5	657	c.381A>G	c.(379-381)gcA>gcG	p.A127A		NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	127					inositol phosphate metabolic process (GO:0043647)|inositol phosphorylation (GO:0052746)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|inositol pentakisphosphate 2-kinase activity (GO:0035299)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(2)|urinary_tract(1)	15						GCCGGTGCTCTGCAAAGCGGT	0.502																																					p.A127A		Atlas-SNP	.											.	IPPK	34	.	0			c.A381G						.						154	119	131					9																	95411768		2203	4300	6503	SO:0001819	synonymous_variant	64768	exon5			GTGCTCTGCAAAG	AK023225	CCDS6699.1	9q22.31	2010-12-02	2005-10-20	2005-10-20	ENSG00000127080	ENSG00000127080			14645	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 12"	C9orf12		12084730	Standard	NM_022755		Approved	INSP5K2, FLJ13163, IP5K, IPK1	uc004asl.1	Q9H8X2	OTTHUMG00000020231	ENST00000287996.3:c.381A>G	chr9.hg19:g.95411768T>C		118.0	0.0		92.0	4.0	NM_022755	Q5T9F7|Q9H7V8	Silent	SNP	ENST00000287996.3	hg19	CCDS6699.1																																																																																			.	.		0.502	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755		C	95411768	T	C	95411768	2	2	65	1	0	0	0	0	0	0	0	1	7810	1567	55	2		2	IPPK	9	95411768	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	360123	95411768	45801663	213	8286										
C9orf3	84909	hgsc.bcm.edu	37	chr9	97535345	97535345	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccctttttccatgccaggagCcacccgttgccatgtcaaca	7	16	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:97535345C>T	ENST00000375315.2	+	2	859	c.859C>T	c.(859-861)Cca>Tca	p.P287S	C9orf3_ENST00000277198.2_Missense_Mutation_p.P287S|C9orf3_ENST00000297979.5_Missense_Mutation_p.P287S	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	287					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		ATGCCAGGAGCCACCCGTTGC	0.478																																					p.P287S		Atlas-SNP	.											.	C9orf3	100	.	0			c.C859T						.						136	128	130					9																	97535345		2203	4300	6503	SO:0001583	missense	84909	exon3			CAGGAGCCACCCG	AF043896	CCDS6713.1, CCDS55327.1, CCDS55328.1	9q22	2013-06-27			ENSG00000148120	ENSG00000148120			1361	protein-coding gene	gene with protein product	aminopeptidase O					15687497	Standard	NM_001193329		Approved	C90RF3, FLJ14675, APO, AOPEP, AP-O	uc004ava.3	Q8N6M6	OTTHUMG00000020276	ENST00000375315.2:c.859C>T	chr9.hg19:g.97535345C>T	ENSP00000364464:p.Pro287Ser	188.0	0.0		97.0	4.0	NM_001193331	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	hg19	CCDS55328.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.311883	0.81358	.	.	ENSG00000148120	ENST00000277198;ENST00000297979;ENST00000375315;ENST00000424143;ENST00000428313	T;T;T;T;T	0.03920	3.76;3.76;3.76;3.76;3.76	5.09	5.09	0.68999	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.12902	0.0313	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.89917	1.0;0.992;1.0;1.0	D;D;D;D	0.97110	0.997;0.956;1.0;0.988	T	0.35919	-0.9769	10	0.14252	T	0.57	-7.173	18.6869	0.91568	0.0:1.0:0.0:0.0	.	287;287;287;287	Q8N6M6;Q8N6M6-4;Q8N6M6-2;Q8N6M6-3	AMPO_HUMAN;.;.;.	S	287;287;287;110;69	ENSP00000277198:P287S;ENSP00000297979:P287S;ENSP00000364464:P287S;ENSP00000402171:P110S;ENSP00000401854:P69S	ENSP00000277198:P287S	P	+	1	0	C9orf3	96575166	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.204000	0.77872	2.644000	0.89710	0.585000	0.79938	CCA	.	.		0.478	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823		T	97535345	C	T	97535345	3	4	65	1	0	0	0	0	1	0	0	0	2479	739	26	3	865	3	C9orf3	9	97535345	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	2123577	97535345	43678086	214	8287										
HSD17B3	3293	hgsc.bcm.edu	37	chr9	99006632	99006632	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tggatgatgacttcttttgcTttatattcctcttgcagggc	9	8	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:99006632T>C	ENST00000375263.3	-	9	698	c.651A>G	c.(649-651)aaA>aaG	p.K217K	HSD17B3_ENST00000464104.1_5'UTR|HSD17B3_ENST00000375262.2_Silent_p.K217K|RP11-240L7.4_ENST00000448857.1_RNA	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	217					androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				CTTCTTTTGCTTTATATTCCT	0.552																																					p.K217K		Atlas-SNP	.											.	HSD17B3	32	.	0			c.A651G						.						232	196	208					9																	99006632		2203	4300	6503	SO:0001819	synonymous_variant	3293	exon9			TTTTGCTTTATAT		CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5212	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 12C, member 2"	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.651A>G	chr9.hg19:g.99006632T>C		104.0	0.0		75.0	4.0	NM_000197	Q5U0Q6	Silent	SNP	ENST00000375263.3	hg19	CCDS6716.1																																																																																			.	.		0.552	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197		C	99006632	T	C	99006632	2	2	65	1	0	0	0	0	0	0	0	1	7394	1606	56	2		2	HSD17B3	9	99006632	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1471287	99006632	42206799	215	8288										
OR2K2	26248	hgsc.bcm.edu	37	chr9	114089950	114089950	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aaggctttaggtacatagagAgggcagccccataatacaaa	10	8	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:114089950A>G	ENST00000374428.1	-	1	850	c.851T>C	c.(850-852)cTc>cCc	p.L284P	OR2K2_ENST00000302681.1_Missense_Mutation_p.L255P			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	284						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						GTACATAGAGAGGGCAGCCCC	0.423																																					p.L255P		Atlas-SNP	.											.	OR2K2	77	.	0			c.T764C						.						116	115	115					9																	114089950		2203	4300	6503	SO:0001583	missense	26248	exon1			ATAGAGAGGGCAG	X64977	CCDS6778.1	9q31.3	2012-08-09			ENSG00000171133	ENSG00000171133		"GPCR / Class A : Olfactory receptors"	8264	protein-coding gene	gene with protein product				OR2AR1P		1370859, 17010214	Standard	NM_205859		Approved	HTPCRH06, HSHTPCRH06	uc011lwp.2	Q8NGT1	OTTHUMG00000020488	ENST00000374428.1:c.851T>C	chr9.hg19:g.114089950A>G	ENSP00000363550:p.Leu284Pro	101.0	0.0		61.0	4.0	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Missense_Mutation	SNP	ENST00000374428.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.97	1.502956	0.26949	.	.	ENSG00000171133	ENST00000302681;ENST00000374428	T;T	0.47528	0.84;0.84	4.55	4.55	0.56014	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35936	U	0.002900	T	0.72145	0.3424	M	0.93462	3.42	0.22531	N	0.999015	D	0.89917	1.0	D	0.97110	1.0	T	0.67106	-0.5754	10	0.87932	D	0	.	6.9177	0.24369	0.8983:0.0:0.1017:0.0	.	284	Q8NGT1	OR2K2_HUMAN	P	255;284	ENSP00000305055:L255P;ENSP00000363550:L284P	ENSP00000305055:L255P	L	-	2	0	OR2K2	113129771	0.000000	0.05858	0.188000	0.23233	0.440000	0.31957	0.816000	0.27267	2.047000	0.60756	0.482000	0.46254	CTC	.	.		0.423	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859		G	114089950	A	G	114089950	3	3	65	1	0	0	0	0	1	0	0	0	11014	304	11	2	189	2	OR2K2	9	114089950	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	15083318	114089950	27123481	216	8289										
DNAJC25	548645	hgsc.bcm.edu	37	chr9	114411855	114411855	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctcaaaaaagccaaagaaaaAggcaaaaacaaaaagtccaa	5	8	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:114411855A>G	ENST00000313525.3	+	3	668	c.612A>G	c.(610-612)aaA>aaG	p.K204K	DNAJC25-GNG10_ENST00000374294.3_Intron|DNAJC25_ENST00000556107.1_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	204						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						CCAAAGAAAAAGGCAAAAACA	0.403																																					p.K204K		Atlas-SNP	.											.	DNAJC25	20	.	0			c.A612G						.						42	41	41					9																	114411855		1840	4090	5930	SO:0001819	synonymous_variant	548645	exon3			AGAAAAAGGCAAA		CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"Heat shock proteins / DNAJ (HSP40)"	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.612A>G	chr9.hg19:g.114411855A>G		118.0	0.0		81.0	4.0	NM_001015882	Q5QTD8|Q96BN9	Silent	SNP	ENST00000313525.3	hg19	CCDS43862.1																																																																																			.	.		0.403	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882		G	114411855	A	G	114411855	2	3	65	1	0	0	0	0	0	0	0	1	4645	69	3	2		2	DNAJC25	9	114411855	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	321905	114411855	26801576	217	8290										
SLC46A2	57864	hgsc.bcm.edu	37	chr9	115652239	115652239	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccagacacggtatccacggcGgggagctcctggctgggttt	15	12	0	1	rs577863419		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:115652239G>A	ENST00000374228.4	-	1	954	c.723C>T	c.(721-723)ccC>ccT	p.P241P		NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	241					negative regulation of T cell apoptotic process (GO:0070233)|regulation of T cell differentiation (GO:0045580)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(1)	18						TATCCACGGCGGGGAGCTCCT	0.602													G|||	1	0.000199681	0	0.0014	5008	,	,		18617	0		0	False		,,,				2504	0				p.P241P		Atlas-SNP	.											.	SLC46A2	30	.	0			c.C723T						.						70	63	65					9																	115652239		2203	4300	6503	SO:0001819	synonymous_variant	57864	exon1			CACGGCGGGGAGC	AF242557	CCDS6786.1	9q32	2013-05-22	2007-03-29	2007-03-29	ENSG00000119457	ENSG00000119457		"Solute carriers"	16055	protein-coding gene	gene with protein product		608956	"thymic stromal co-transporter"	TSCOT		10978518, 12826694	Standard	NM_033051		Approved	Ly110	uc004bgk.3	Q9BY10	OTTHUMG00000020513	ENST00000374228.4:c.723C>T	chr9.hg19:g.115652239G>A		92.0	0.0		70.0	51.0	NM_033051	B1ALK1|Q86VT0|Q96NE2	Silent	SNP	ENST00000374228.4	hg19	CCDS6786.1																																																																																			.	.		0.602	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051		A	115652239	G	A	115652239	2	1	65	1	0	0	0	0	0	0	0	1	14660	1103	39	1		1	SLC46A2	9	115652239	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	1240384	115652239	25561192	218	8291										
RGS3	5998	hgsc.bcm.edu	37	chr9	116358041	116358041	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	catcgcgatccaggcatgcaAggaggtaggacctcagggca	14	11	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:116358041A>G	ENST00000374140.2	+	25	3616	c.3407A>G	c.(3406-3408)aAg>aGg	p.K1136R	RGS3_ENST00000342620.5_Missense_Mutation_p.K106R|RGS3_ENST00000462403.1_Missense_Mutation_p.K249R|RGS3_ENST00000394646.3_Missense_Mutation_p.K529R|RGS3_ENST00000374134.3_Missense_Mutation_p.K457R|RGS3_ENST00000350696.5_Missense_Mutation_p.K1136R|RGS3_ENST00000462143.1_Missense_Mutation_p.K457R|RGS3_ENST00000343817.5_Missense_Mutation_p.K855R	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	1136	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						CAGGCATGCAAGGAGGTAGGA	0.577																																					p.K1136R		Atlas-SNP	.											.	RGS3	251	.	0			c.A3407G						.						147	119	129					9																	116358041		2203	4300	6503	SO:0001583	missense	5998	exon25			CATGCAAGGAGGT	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"Regulators of G-protein signaling"	9999	protein-coding gene	gene with protein product		602189	"regulator of G-protein signalling 3"			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3407A>G	chr9.hg19:g.116358041A>G	ENSP00000363255:p.Lys1136Arg	93.0	0.0		77.0	4.0	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	hg19	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.022065	0.54576	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000343817;ENST00000394646;ENST00000474719;ENST00000462143;ENST00000342620;ENST00000374134;ENST00000462403	T;T;T;T;T;T;T;T	0.01963	4.53;4.53;4.53;4.53;4.53;4.53;4.53;4.53	5.46	5.46	0.80206	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.64402	D	0.000001	T	0.05777	0.0151	N	0.20530	0.585	0.58432	D	0.999999	B;B;P;D;D;P	0.89917	0.029;0.132;0.93;1.0;1.0;0.943	B;B;P;D;D;P	0.85130	0.064;0.222;0.753;0.995;0.997;0.84	T	0.61715	-0.7006	10	0.28530	T	0.3	.	14.7768	0.69736	1.0:0.0:0.0:0.0	.	529;249;1032;855;1026;1136	B3KUB2;Q5VZ06;P49796-6;P49796-4;B3KWG8;P49796	.;.;.;.;.;RGS3_HUMAN	R	1136;1136;855;529;304;457;106;457;249	ENSP00000363255:K1136R;ENSP00000259406:K1136R;ENSP00000340284:K855R;ENSP00000378141:K529R;ENSP00000420356:K457R;ENSP00000343359:K106R;ENSP00000363249:K457R;ENSP00000436168:K249R	ENSP00000343359:K106R	K	+	2	0	RGS3	115397862	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	9.142000	0.94618	2.073000	0.62155	0.374000	0.22700	AAG	.	.		0.577	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		G	116358041	A	G	116358041	3	3	65	1	0	0	0	0	1	0	0	0	13321	72	3	2	4177	2	RGS3	9	116358041	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	705802	116358041	24855390	219	8292										
CEP110	11064	hgsc.bcm.edu	37	chr9	123937427	123937427	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttggtcaccagcacctctgcAgattcagcgtcatcacccag	8	15	5	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:123937427A>G	ENST00000373855.1	+	43	7139	c.6879A>G	c.(6877-6879)gcA>gcG	p.A2293A	CNTRL_ENST00000238341.5_Silent_p.A2293A|CNTRL_ENST00000373850.1_Silent_p.A1741A|CNTRL_ENST00000373845.2_3'UTR			Q7Z7A1	CNTRL_HUMAN	centriolin	2293	Sufficient for interaction with HOOK2.				cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						GCACCTCTGCAGATTCAGCGT	0.463																																					p.A2293A		Atlas-SNP	.											.	CNTRL	161	.	0			c.A6879G						.						117	108	111					9																	123937427		2203	4300	6503	SO:0001819	synonymous_variant	11064	exon41			CTCTGCAGATTCA	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.6879A>G	chr9.hg19:g.123937427A>G		109.0	0.0		79.0	4.0	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Silent	SNP	ENST00000373855.1	hg19	CCDS35118.1																																																																																			.	.		0.463	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123937427	A	G	123937427	2	3	65	1	0	0	0	0	0	0	0	1	3247	175	7	2		2	CEP110	9	123937427	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	7579386	123937427	17276004	220	8293										
RC3H2	54542	hgsc.bcm.edu	37	chr9	125613389	125613389	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tggtcttcacctaaactctgTttcttctgctttggtggctc	8	11	5	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:125613389T>C	ENST00000373670.1	-	19	3951	c.3351A>G	c.(3349-3351)aaA>aaG	p.K1117K	RC3H2_ENST00000357244.2_Silent_p.K1117K			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	1117					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						CTAAACTCTGTTTCTTCTGCT	0.388																																					p.K1117K		Atlas-SNP	.											.	RC3H2	150	.	0			c.A3351G						.						215	207	210					9																	125613389		1952	4149	6101	SO:0001819	synonymous_variant	54542	exon20			ACTCTGTTTCTTC	AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"RING-type (C3HC4) zinc fingers", "Zinc fingers, CCCH-type domain containing"	21461	protein-coding gene	gene with protein product		615231	"membrane associated DNA binding protein", "ring finger and CCCH-type zinc finger domains 2"	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.3351A>G	chr9.hg19:g.125613389T>C		147.0	0.0		77.0	5.0	NM_001100588	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Silent	SNP	ENST00000373670.1	hg19	CCDS43874.1	.	.	.	.	.	.	.	.	.	.	T	9.320	1.057854	0.19987	.	.	ENSG00000056586	ENST00000454740	.	.	.	5.89	3.58	0.41010	.	.	.	.	.	T	0.58308	0.2113	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51741	-0.8667	4	.	.	.	-27.7648	8.4184	0.32685	0.0:0.1514:0.0:0.8486	.	.	.	.	S	176	.	.	N	-	2	0	RC3H2	124653210	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.517000	0.45529	0.502000	0.28037	0.533000	0.62120	AAC	.	.		0.388	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835		C	125613389	T	C	125613389	2	2	65	1	0	0	0	0	0	0	0	1	13182	1722	60	2		2	RC3H2	9	125613389	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1675962	125613389	15600042	221	8294										
ENG	2022	hgsc.bcm.edu	37	chr9	130588025	130588025	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgtgcgcctccttgtggccgGccacgccttccaagtggcag	13	15	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:130588025G>A	ENST00000373203.4	-	5	1038	c.638C>T	c.(637-639)gCc>gTc	p.A213V	ENG_ENST00000480266.1_5'Flank|ENG_ENST00000344849.3_Missense_Mutation_p.A213V	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	213	Required for interaction with EGL.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						CTTGTGGCCGGCCACGCCTTC	0.697									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia																												p.A213V		Atlas-SNP	.											.	ENG	44	.	0			c.C638T						.						10	12	11					9																	130588025		2172	4246	6418	SO:0001583	missense	2022	exon5	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	TGGCCGGCCACGC	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"CD molecules"	3349	protein-coding gene	gene with protein product		131195	"Osler-Rendu-Weber syndrome 1"	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.638C>T	chr9.hg19:g.130588025G>A	ENSP00000362299:p.Ala213Val	26.0	0.0		24.0	4.0	NM_001114753	Q14248|Q14926|Q5T9C0	Missense_Mutation	SNP	ENST00000373203.4	hg19	CCDS48029.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.824379	0.32237	.	.	ENSG00000106991	ENST00000373203;ENST00000344849;ENST00000545345;ENST00000546301	T;T	0.43688	0.94;1.53	3.87	3.87	0.44632	.	1.021630	0.07794	N	0.955460	T	0.36524	0.0970	L	0.47716	1.5	0.09310	N	1	P;P	0.35077	0.483;0.483	B;B	0.30943	0.122;0.122	T	0.13602	-1.0503	10	0.31617	T	0.26	-1.9289	11.6549	0.51313	0.0:0.0:1.0:0.0	.	213;213	Q5T9B9;P17813	.;EGLN_HUMAN	V	213;213;213;31	ENSP00000362299:A213V;ENSP00000341917:A213V	ENSP00000341917:A213V	A	-	2	0	ENG	129627846	0.272000	0.24172	0.433000	0.26760	0.479000	0.33129	2.844000	0.48246	2.468000	0.83385	0.549000	0.68633	GCC	.	.		0.697	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1			A	130588025	G	A	130588025	3	1	65	1	0	0	0	0	1	0	0	0	5119	1203	42	3	1408	3	ENG	9	130588025	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	4974636	130588025	10625406	222	8295										
PKN3	29941	hgsc.bcm.edu	37	chr9	131469012	131469012	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gagaggaagctcctggcagcTgcccagcagatgctgcggga	16	11	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:131469012T>C	ENST00000291906.4	+	4	825	c.432T>C	c.(430-432)gcT>gcC	p.A144A		NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	144					epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						TCCTGGCAGCTGCCCAGCAGA	0.657																																					p.A144A		Atlas-SNP	.											.	PKN3	62	.	0			c.T432C						.						10	12	11					9																	131469012		2191	4280	6471	SO:0001819	synonymous_variant	29941	exon4			GGCAGCTGCCCAG	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.432T>C	chr9.hg19:g.131469012T>C		57.0	0.0		54.0	5.0	NM_013355	Q9UM03	Silent	SNP	ENST00000291906.4	hg19	CCDS6908.1																																																																																			.	.		0.657	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		C	131469012	T	C	131469012	2	2	65	1	0	0	0	0	0	0	0	1	11990	1567	55	2		2	PKN3	9	131469012	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	880987	131469012	9744419	223	8296										
ADAMTS13	11093	hgsc.bcm.edu	37	chr9	136304502	136304502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tctagaatatgtcacatttcTgacagttacccccaacctga	5	12	3	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr9:136304502T>C	ENST00000371929.3	+	15	2165	c.1721T>C	c.(1720-1722)cTg>cCg	p.L574P	ADAMTS13_ENST00000356589.2_Missense_Mutation_p.L543P|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.L574P|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000536611.1_Missense_Mutation_p.L246P	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	574	Spacer.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GTCACATTTCTGACAGTTACC	0.507																																					p.L574P		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.T1721C						.						159	135	143					9																	136304502		2203	4300	6503	SO:0001583	missense	11093	exon15			CATTTCTGACAGT	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"ADAM metallopeptidases with thrombospondin type 1 motif"	1366	protein-coding gene	gene with protein product		604134	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.1721T>C	chr9.hg19:g.136304502T>C	ENSP00000360997:p.Leu574Pro	123.0	0.0		78.0	4.0	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	hg19	CCDS6970.1	.	.	.	.	.	.	.	.	.	.	T	14.35	2.510677	0.44660	.	.	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589;ENST00000536611	T;T;T;T	0.70749	-0.5;-0.51;-0.48;-0.05	5.13	5.13	0.70059	.	.	.	.	.	D	0.84915	0.5578	M	0.85777	2.775	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.998	D	0.87145	0.2205	9	0.62326	D	0.03	.	13.7749	0.63048	0.0:0.0:0.0:1.0	.	574;543;574;246	Q76LX8;Q76LX8-3;Q76LX8-2;Q9UGQ1	ATS13_HUMAN;.;.;.	P	574;574;543;246	ENSP00000360997:L574P;ENSP00000347927:L574P;ENSP00000348997:L543P;ENSP00000444504:L246P	ENSP00000347927:L574P	L	+	2	0	ADAMTS13	135294323	1.000000	0.71417	0.948000	0.38648	0.130000	0.20726	6.680000	0.74518	1.928000	0.55862	0.379000	0.24179	CTG	.	.		0.507	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025		C	136304502	T	C	136304502	3	2	65	1	0	0	0	0	1	0	0	0	258	1580	55	2	1779	2	ADAMTS13	9	136304502	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4835490	136304502	4908929	224	8297										
GATA3	2625	hgsc.bcm.edu	37	chr10	8115947	8115947	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccatccagcctgtcctttggAccacaccacccctccagcat	5	20	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:8115947A>G	ENST00000346208.3	+	6	1748	c.1293A>G	c.(1291-1293)ggA>ggG	p.G431G	GATA3_ENST00000461472.1_3'UTR|GATA3_ENST00000379328.3_Silent_p.G432G			P23771	GATA3_HUMAN	GATA binding protein 3	431					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.P433fs*>13(1)		NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						TGTCCTTTGGACCACACCACC	0.637			"F, N, S"		breast		"HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"																														p.G432G		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	1	Insertion - Frameshift(1)	breast(1)	c.A1296G						.						91	76	81					10																	8115947		2203	4300	6503	SO:0001819	synonymous_variant	2625	exon6			CTTTGGACCACAC	X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"GATA zinc finger domain containing"	4172	protein-coding gene	gene with protein product		131320	"GATA-binding protein 3"			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.1293A>G	chr10.hg19:g.8115947A>G		69.0	0.0		104.0	6.0	NM_001002295	Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	hg19	CCDS7083.1																																																																																			.	.		0.637	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		G	8115947	A	G	8115947	2	3	65	1	0	0	0	0	0	0	0	1	6263	262	10	2		2	GATA3	10	8115947	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10		8115947	127418800	225	8298										
PHYH	5264	hgsc.bcm.edu	37	chr10	13333891	13333891	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cataatattaggtccagtgaAgcactccacatatttcagaa	6	9	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:13333891A>G	ENST00000263038.4	-	5	494	c.436T>C	c.(436-438)Ttc>Ctc	p.F146L	PHYH_ENST00000396920.3_Missense_Mutation_p.F127L|PHYH_ENST00000396913.2_Missense_Mutation_p.F46L	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	146					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|isoprenoid metabolic process (GO:0006720)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|electron carrier activity (GO:0009055)|L-ascorbic acid binding (GO:0031418)|metal ion binding (GO:0046872)|phytanoyl-CoA dioxygenase activity (GO:0048244)			NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	GGTCCAGTGAAGCACTCCACA	0.338																																					p.F146L		Atlas-SNP	.											.	PHYH	50	.	0			c.T436C						.						95	91	93					10																	13333891		2203	4300	6503	SO:0001583	missense	5264	exon5			CAGTGAAGCACTC		CCDS7097.1, CCDS41489.1	10p13	2010-04-27	2006-01-09		ENSG00000107537	ENSG00000107537	1.14.11.18		8940	protein-coding gene	gene with protein product	"Refsum disease", "phytanoyl-CoA dioxygenase"	602026	"phytanoyl-CoA hydroxylase (Refsum disease)", "phytanoyl-CoA hydroxylase"			9326939	Standard	XM_005252469		Approved	PAHX, RD, PHYH1	uc001imf.3	O14832	OTTHUMG00000017693	ENST00000263038.4:c.436T>C	chr10.hg19:g.13333891A>G	ENSP00000263038:p.Phe146Leu	44.0	0.0		63.0	4.0	NM_006214	A8MTS8|B1ALH5	Missense_Mutation	SNP	ENST00000263038.4	hg19	CCDS7097.1	.	.	.	.	.	.	.	.	.	.	A	17.16	3.319038	0.60524	.	.	ENSG00000107537	ENST00000396913;ENST00000263038;ENST00000396920;ENST00000453759;ENST00000479604	D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05;-2.05	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.88097	0.6345	L	0.53561	1.675	0.80722	D	1	B;B	0.31581	0.175;0.329	B;P	0.51297	0.162;0.665	D	0.84332	0.0522	10	0.23891	T	0.37	-27.393	11.3912	0.49815	0.8647:0.0:0.0:0.1353	.	127;146	B1ALH6;O14832	.;PAHX_HUMAN	L	46;146;127;46;146	ENSP00000380121:F46L;ENSP00000263038:F146L;ENSP00000380126:F127L;ENSP00000412525:F46L;ENSP00000420117:F146L	ENSP00000263038:F146L	F	-	1	0	PHYH	13373897	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.182000	0.77689	2.145000	0.66743	0.533000	0.62120	TTC	.	.		0.338	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2			G	13333891	A	G	13333891	3	3	65	1	0	0	0	0	1	0	0	0	11873	72	3	2	600	2	PHYH	10	13333891	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	5217944	13333891	122200856	226	8299										
C10orf140	387640	hgsc.bcm.edu	37	chr10	21806681	21806681	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gggagagggcaaacatttgcTtccctttaatgatgaggtag	13	6	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:21806681T>C	ENST00000449193.2	-	4	2323	c.71A>G	c.(70-72)aAg>aGg	p.K24R	SKIDA1_ENST00000444772.3_Missense_Mutation_p.K24R|SKIDA1_ENST00000487107.1_5'Flank	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	24						nucleus (GO:0005634)											AAACATTTGCTTCCCTTTAAT	0.507																																					p.K24R		Atlas-SNP	.											.	.	.	.	0			c.A71G						.						51	52	52					10																	21806681		2001	4162	6163	SO:0001583	missense	387640	exon4			ATTTGCTTCCCTT	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 140"	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.71A>G	chr10.hg19:g.21806681T>C	ENSP00000410041:p.Lys24Arg	90.0	0.0		148.0	6.0	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Missense_Mutation	SNP	ENST00000449193.2	hg19	CCDS44363.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.346497	0.41599	.	.	ENSG00000180592	ENST00000449193;ENST00000444772	D;D	0.82344	-1.6;-1.6	4.9	4.9	0.64082	DNA binding domain, putative (1);Transforming protein Ski (2);	0.135854	0.49916	D	0.000139	D	0.84270	0.5435	N	0.19112	0.55	0.39975	D	0.974847	D;D	0.76494	0.995;0.999	D;D	0.74674	0.926;0.984	D	0.87308	0.2310	10	0.66056	D	0.02	.	14.5119	0.67794	0.0:0.0:0.0:1.0	.	24;24	Q1XH10;E9PAX1	DLN1_HUMAN;.	R	24	ENSP00000410041:K24R;ENSP00000442432:K24R	ENSP00000442432:K24R	K	-	2	0	C10orf140	21846687	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.929000	0.63455	1.834000	0.53371	0.254000	0.18369	AAG	.	.		0.507	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		C	21806681	T	C	21806681	3	2	65	1	0	0	0	0	1	0	0	0	1597	1609	56	2	2659	2	C10orf140	10	21806681	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	8472790	21806681	113728066	227	8300										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55945028	55945028	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtgaagctctgggtcttttgTctttgaaaaaaaatgacatc	9	6	3	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:55945028T>C	ENST00000320301.6	-	12	1700	c.1306A>G	c.(1306-1308)Aca>Gca	p.T436A	PCDH15_ENST00000437009.1_Splice_Site_p.T436A|PCDH15_ENST00000395438.1_Splice_Site_p.T436A|PCDH15_ENST00000395446.1_Splice_Site_p.T436A|PCDH15_ENST00000395430.1_Splice_Site_p.T436A|PCDH15_ENST00000373965.2_Splice_Site_p.T443A|PCDH15_ENST00000395432.2_Splice_Site_p.T399A|PCDH15_ENST00000373955.1_Splice_Site_p.T436A|PCDH15_ENST00000395445.1_Splice_Site_p.T443A|PCDH15_ENST00000409834.1_Splice_Site_p.T47A|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395433.1_Splice_Site_p.T414A|PCDH15_ENST00000361849.3_Splice_Site_p.T436A|PCDH15_ENST00000414778.1_Splice_Site_p.T441A|PCDH15_ENST00000373957.3_Splice_Site_p.T414A|PCDH15_ENST00000395442.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	436	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GGGTCTTTTGTCTTTGAAAAA	0.358										HNSCC(58;0.16)																											p.T441A		Atlas-SNP	.											PCDH15_ENST00000417177,colon,carcinoma,0,4	PCDH15	1715	.	0			c.A1321G						.						101	99	100					10																	55945028		2203	4300	6503	SO:0001630	splice_region_variant	65217	exon13			CTTTTGTCTTTGA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1306-1A>G	chr10.hg19:g.55945028T>C		130.0	0.0		72.0	3.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	T	15.80	2.940979	0.52972	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.60424	0.19;0.75;0.75;0.78;0.19;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75	5.29	5.29	0.74685	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.72661	0.3488	M	0.63843	1.955	0.45648	D	0.998579	D;D;D;P;D;D;D;D;D;D;D;D;P;D;D	0.76494	0.997;0.999;0.985;0.592;0.996;0.999;0.997;0.992;0.982;0.993;0.999;0.992;0.815;0.994;0.999	D;D;D;P;D;D;D;D;P;P;D;D;P;P;D	0.76575	0.981;0.988;0.959;0.672;0.973;0.988;0.981;0.962;0.898;0.898;0.988;0.962;0.674;0.897;0.988	T	0.74748	-0.3560	9	0.56958	D	0.05	.	14.4908	0.67649	0.0:0.0:0.0:1.0	.	414;436;436;441;436;399;436;436;443;443;436;441;436;414;436	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	A	443;441;436;436;47;443;436;399;436;414;414;436;436;441;436;436	ENSP00000363076:T443A;ENSP00000410304:T441A;ENSP00000378826:T436A;ENSP00000386693:T47A;ENSP00000378832:T443A;ENSP00000378833:T436A;ENSP00000378820:T399A;ENSP00000354950:T436A;ENSP00000378821:T414A;ENSP00000363068:T414A;ENSP00000322604:T436A;ENSP00000378818:T436A;ENSP00000412628:T436A;ENSP00000363066:T436A	ENSP00000322604:T436A	T	-	1	0	PCDH15	55615034	1.000000	0.71417	0.998000	0.56505	0.828000	0.46876	5.664000	0.68045	2.131000	0.65755	0.482000	0.46254	ACA	.	.		0.358	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	Missense_Mutation	C	55945028	T	C	55945028	5	2	65	1	0	0	0	0	0	0	1	0	11520	1681	58	2	6268	2	PCDH15	10	55945028	Splice_Site	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	34138347	55945028	79589719	228	8301										
PCDH15	65217	hgsc.bcm.edu	37	chr10	56288150	56288150	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttatttttgtcatcttacccTcatattgccagtctggagtc	6	10	4	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:56288150T>C	ENST00000320301.6	-	3	486				PCDH15_ENST00000437009.1_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395430.1_Intron|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395432.2_Intron|PCDH15_ENST00000373955.1_Intron|RP11-257I14.1_ENST00000422842.1_RNA|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395433.1_Intron|PCDH15_ENST00000361849.3_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395442.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15						equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CATCTTACCCTCATATTGCCA	0.318										HNSCC(58;0.16)																											p.E35G		Atlas-SNP	.											.	PCDH15	1715	.	0			c.A104G						.						142	133	136					10																	56288150		1567	3580	5147	SO:0001627	intron_variant	65217	exon3			TTACCCTCATATT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.92-513A>G	chr10.hg19:g.56288150T>C		91.0	0.0		73.0	4.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.		0.318	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		C	56288150	T	C	56288150	1	2	65	0	1	0	0	0	0	0	0	0	11520	1551	54	2		2	PCDH15	10	56288150	Intron	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	343122	56288150	79246597	229	8302										
CCDC6	8030	hgsc.bcm.edu	37	chr10	61612353	61612353	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcattagtgaggaattcttcTtctttctcataatttacagc	5	8	5	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:61612353T>C	ENST00000263102.6	-	2	642	c.411A>G	c.(409-411)gaA>gaG	p.E137E		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	137	5 X 29 AA tandem repeats.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		GGAATTCTTCTTCTTTCTCAT	0.373			T	RET	NSCLC																																p.E137E		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	CCDC6	44	.	0			c.A411G						.						118	122	120					10																	61612353		2203	4300	6503	SO:0001819	synonymous_variant	8030	exon2			TTCTTCTTCTTTC	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"	601985	"DNA segment on chromosome 10 (unique) 170"	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.411A>G	chr10.hg19:g.61612353T>C		128.0	0.0		84.0	4.0	NM_005436	Q15250|Q6GSG7	Silent	SNP	ENST00000263102.6	hg19	CCDS7257.1																																																																																			.	.		0.373	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436		C	61612353	T	C	61612353	2	2	65	1	0	0	0	0	0	0	0	1	2832	1606	56	2		2	CCDC6	10	61612353	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	5324203	61612353	73922394	230	8303										
ANK3	288	hgsc.bcm.edu	37	chr10	61843261	61843261	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atgatttaccttgatggaaaAtggcagtctattttctttga	8	5	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:61843261A>G	ENST00000280772.2	-	33	4380	c.4189T>C	c.(4189-4191)Ttt>Ctt	p.F1397L	ANK3_ENST00000373827.2_Missense_Mutation_p.F1391L|Y_RNA_ENST00000365320.1_RNA|ANK3_ENST00000503366.1_Missense_Mutation_p.F1398L|ANK3_ENST00000355288.2_Missense_Mutation_p.F531L	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1397	UPA domain. {ECO:0000250}.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTGATGGAAAATGGCAGTCTA	0.289																																					p.F1398L		Atlas-SNP	.											.	ANK3	703	.	0			c.T4192C						.						44	47	46					10																	61843261		2202	4294	6496	SO:0001583	missense	288	exon34			TGGAAAATGGCAG	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.4189T>C	chr10.hg19:g.61843261A>G	ENSP00000280772:p.Phe1397Leu	88.0	0.0		59.0	4.0	NM_001204404	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.924684	0.52653	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000355288;ENST00000423532;ENST00000503366;ENST00000395299;ENST00000373817;ENST00000395293;ENST00000395304;ENST00000544789	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	5.9	5.9	0.94986	.	0.000000	0.40222	N	0.001149	T	0.41604	0.1166	L	0.55103	1.725	0.80722	D	1	B;D;B;D;B;P	0.69078	0.001;0.989;0.007;0.997;0.024;0.956	B;D;B;D;B;D	0.72338	0.004;0.977;0.011;0.97;0.029;0.931	T	0.26849	-1.0091	10	0.02654	T	1	.	16.3322	0.83039	1.0:0.0:0.0:0.0	.	1398;531;1391;1397;632;531	E9PE32;A8KA62;Q5CZH9;Q12955;F5GXK0;B1AQT2	.;.;.;ANK3_HUMAN;.;.	L	1397;1391;531;531;1398;1377;632;1032;1032;530	ENSP00000280772:F1397L;ENSP00000362933:F1391L;ENSP00000347436:F531L;ENSP00000425236:F1398L	ENSP00000280772:F1397L	F	-	1	0	ANK3	61513267	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.511000	0.81718	2.251000	0.74343	0.528000	0.53228	TTT	.	.		0.289	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		G	61843261	A	G	61843261	3	3	65	1	0	0	0	0	1	0	0	0	622	101	4	2	9301	2	ANK3	10	61843261	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	230908	61843261	73691486	231	8304										
CCAR1	55749	hgsc.bcm.edu	37	chr10	70515291	70515291	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gatctaagtgtgtgcacacaAtggtaagtactaattcattt	8	6	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:70515291A>G	ENST00000265872.6	+	13	1742	c.1623A>G	c.(1621-1623)caA>caG	p.Q541Q	SNORD98_ENST00000408255.1_RNA|CCAR1_ENST00000483264.1_3'UTR|CCAR1_ENST00000543719.1_Silent_p.Q526Q|CCAR1_ENST00000535016.1_Silent_p.Q526Q	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	541					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						TGTGCACACAATGGTAAGTAC	0.398																																					p.Q541Q		Atlas-SNP	.											.	CCAR1	118	.	0			c.A1623G						.						191	184	187					10																	70515291		2203	4300	6503	SO:0001819	synonymous_variant	55749	exon13			CACACAATGGTAA	AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.1623A>G	chr10.hg19:g.70515291A>G		160.0	0.0		95.0	4.0	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Silent	SNP	ENST00000265872.6	hg19	CCDS7282.1																																																																																			.	.		0.398	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		G	70515291	A	G	70515291	2	3	65	1	0	0	0	0	0	0	0	1	2732	98	4	2		2	CCAR1	10	70515291	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	8672030	70515291	65019456	232	8305										
STOX1	219736	hgsc.bcm.edu	37	chr10	70641820	70641820	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atgaatacagctcagattgtAgtaacgcaggaatcactttt	8	7	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:70641820A>G	ENST00000298596.6	+	2	500	c.417A>G	c.(415-417)gtA>gtG	p.V139V	STOX1_ENST00000421961.2_Silent_p.V29V|STOX1_ENST00000399169.4_Silent_p.V139V|STOX1_ENST00000399162.2_Silent_p.V139V|STOX1_ENST00000399165.4_Silent_p.V139V	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	139						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						CTCAGATTGTAGTAACGCAGG	0.363																																					p.V139V		Atlas-SNP	.											.	STOX1	75	.	0			c.A417G						.						161	144	149					10																	70641820		1850	4093	5943	SO:0001819	synonymous_variant	219736	exon2			GATTGTAGTAACG	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"chromosome 10 open reading frame 24"	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.417A>G	chr10.hg19:g.70641820A>G		161.0	0.0		85.0	4.0	NM_001130160	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Silent	SNP	ENST00000298596.6	hg19	CCDS41535.1																																																																																			.	.		0.363	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		G	70641820	A	G	70641820	2	3	65	1	0	0	0	0	0	0	0	1	15334	407	15	2		2	STOX1	10	70641820	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	126529	70641820	64892927	233	8306										
HKDC1	80201	hgsc.bcm.edu	37	chr10	71025391	71025391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gattctgcagcagctgggccTggacagcacgtgtgaggaca	15	10	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:71025391T>C	ENST00000354624.5	+	17	2556	c.2423T>C	c.(2422-2424)cTg>cCg	p.L808P	RP11-227H15.5_ENST00000413220.1_RNA	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	808	Hexokinase type-2 2.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						CAGCTGGGCCTGGACAGCACG	0.667																																					p.L808P		Atlas-SNP	.											.	HKDC1	98	.	0			c.T2423C						.						66	63	64					10																	71025391		2203	4299	6502	SO:0001583	missense	80201	exon17			TGGGCCTGGACAG		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.2423T>C	chr10.hg19:g.71025391T>C	ENSP00000346643:p.Leu808Pro	76.0	0.0		88.0	27.0	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	hg19	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.438870	0.83885	.	.	ENSG00000156510	ENST00000354624	D	0.97455	-4.39	4.76	4.76	0.60689	Hexokinase, C-terminal (1);	0.000000	0.64402	D	0.000001	D	0.98960	0.9646	H	0.96633	3.855	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99395	1.0926	10	0.87932	D	0	-13.8423	14.7247	0.69336	0.0:0.0:0.0:1.0	.	808	Q2TB90	HKDC1_HUMAN	P	808	ENSP00000346643:L808P	ENSP00000346643:L808P	L	+	2	0	HKDC1	70695397	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.868000	0.87116	2.121000	0.65114	0.460000	0.39030	CTG	.	.		0.667	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		C	71025391	T	C	71025391	3	2	65	1	0	0	0	0	1	0	0	0	7202	1580	55	2	2489	2	HKDC1	10	71025391	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	383571	71025391	64509356	234	8307										
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72292498	72292498	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgacttgcatgtgacggaggAggtgtacaagcggcccctct	14	11	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:72292498A>G	ENST00000263563.6	+	6	1023	c.755A>G	c.(754-756)gAg>gGg	p.E252G		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	252						cytosol (GO:0005829)											GTGACGGAGGAGGTGTACAAG	0.622																																					p.E252G		Atlas-SNP	.											.	.	.	.	0			c.A755G						.						182	155	164					10																	72292498		2203	4300	6503	SO:0001583	missense	27143	exon6			CGGAGGAGGTGTA	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"paladin", "KIAA1274"	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.755A>G	chr10.hg19:g.72292498A>G	ENSP00000263563:p.Glu252Gly	94.0	0.0		79.0	4.0	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	hg19	CCDS31215.1	.	.	.	.	.	.	.	.	.	.	A	15.59	2.877638	0.51801	.	.	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.35789	1.29	5.34	4.21	0.49690	.	0.048651	0.85682	N	0.000000	T	0.47673	0.1458	M	0.86178	2.8	0.80722	D	1	P	0.36633	0.562	B	0.41412	0.356	T	0.53005	-0.8499	10	0.87932	D	0	-23.5125	11.0369	0.47806	0.9261:0.0:0.0739:0.0	.	252	Q9ULE6	PALD_HUMAN	G	252	ENSP00000263563:E252G	ENSP00000263563:E252G	E	+	2	0	KIAA1274	71962504	1.000000	0.71417	1.000000	0.80357	0.423000	0.31445	7.291000	0.78721	0.977000	0.38444	0.459000	0.35465	GAG	.	.		0.622	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		G	72292498	A	G	72292498	3	3	65	1	0	0	0	0	1	0	0	0	8229	304	11	2	773	2	KIAA1274	10	72292498	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1267107	72292498	63242249	235	8308										
MYST4	23522	hgsc.bcm.edu	37	chr10	76735857	76735857	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caaaatctaaagcccacttcTttggcaaaagagatattaga	6	8	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:76735857T>C	ENST00000287239.4	+	8	2251	c.1762T>C	c.(1762-1764)Ttt>Ctt	p.F588L	KAT6B_ENST00000372711.1_Intron|KAT6B_ENST00000372714.1_Intron|KAT6B_ENST00000372725.1_Intron|KAT6B_ENST00000372724.1_Intron	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	588	Negatively regulates HAT activity.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										AGCCCACTTCTTTGGCAAAAG	0.443																																					p.F588L		Atlas-SNP	.											.	.	.	.	0			c.T1762C						.						88	86	86					10																	76735857		2203	4300	6503	SO:0001583	missense	23522	exon8			CACTTCTTTGGCA	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.1762T>C	chr10.hg19:g.76735857T>C	ENSP00000287239:p.Phe588Leu	86.0	0.0		64.0	4.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	hg19	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	T	8.894	0.954625	0.18431	.	.	ENSG00000156650	ENST00000287239	T	0.75367	-0.93	6.08	6.08	0.98989	.	0.305290	0.23682	N	0.045608	T	0.55433	0.1920	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.53287	-0.8460	9	.	.	.	-9.6649	15.214	0.73250	0.0:0.0:0.0:1.0	.	588	Q8WYB5	KAT6B_HUMAN	L	588	ENSP00000287239:F588L	.	F	+	1	0	KAT6B	76405863	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.426000	0.52778	2.330000	0.79161	0.533000	0.62120	TTT	.	.		0.443	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		C	76735857	T	C	76735857	3	2	65	1	0	0	0	0	1	0	0	0	10114	1609	56	2	1784	2	MYST4	10	76735857	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4443359	76735857	58798890	236	8309										
KCNMA1	3778	hgsc.bcm.edu	37	chr10	78669796	78669796	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aagggctgcgtgaggtacagTtctgtatcagggtcatcatc	13	8	4	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:78669796T>C	ENST00000286628.8	-	25	3074	c.3075A>G	c.(3073-3075)gaA>gaG	p.E1025E	RP11-443A13.5_ENST00000458661.2_RNA|KCNMA1_ENST00000372443.1_Silent_p.E994E|KCNMA1_ENST00000406533.3_Silent_p.E1029E|KCNMA1_ENST00000404771.3_Silent_p.E1025E|RP11-443A13.5_ENST00000426234.1_RNA|KCNMA1_ENST00000354353.5_Silent_p.E1028E|RP11-443A13.5_ENST00000600782.1_RNA|KCNMA1_ENST00000286627.5_Silent_p.E967E|KCNMA1_ENST00000372440.1_Silent_p.E967E|KCNMA1_ENST00000404857.1_Silent_p.E1008E	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	1025					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)	p.E967E(1)		breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	TGAGGTACAGTTCTGTATCAG	0.473																																					p.E1025E		Atlas-SNP	.											KCNMA1_ENST00000406533,bladder,carcinoma,-2,1	KCNMA1	370	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.A3075G						.						169	124	139					10																	78669796		2203	4300	6503	SO:0001819	synonymous_variant	3778	exon25			GTACAGTTCTGTA	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.3075A>G	chr10.hg19:g.78669796T>C		61.0	0.0		39.0	4.0	NM_001161352	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Silent	SNP	ENST00000286628.8	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.367|9.367	1.069505|1.069505	0.20147|0.20147	.|.	.|.	ENSG00000156113|ENSG00000156113	ENST00000372403|ENST00000372421;ENST00000434208	.|.	.|.	.|.	5.97|5.97	3.63|3.63	0.41609|0.41609	.|.	.|.	.|.	.|.	.|.	T|T	0.58366|0.58366	0.2117|0.2117	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.51841|0.51841	-0.8654|-0.8654	4|4	.|.	.|.	.|.	-13.6099|-13.6099	8.4362|8.4362	0.32789|0.32789	0.0:0.2154:0.0:0.7846|0.0:0.2154:0.0:0.7846	.|.	.|.	.|.	.|.	S|A	918|956;675	.|.	.|.	N|T	-|-	2|1	0|0	KCNMA1|KCNMA1	78339802|78339802	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.918000|0.918000	0.54935|0.54935	1.620000|1.620000	0.36976|0.36976	0.505000|0.505000	0.28104|0.28104	0.533000|0.533000	0.62120|0.62120	AAC|ACT	.	.		0.473	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247		C	78669796	T	C	78669796	2	2	65	1	0	0	0	0	0	0	0	1	8082	1722	60	2		2	KCNMA1	10	78669796	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1933939	78669796	56864951	237	8310										
OPN4	94233	hgsc.bcm.edu	37	chr10	88421086	88421086	+	Frame_Shift_Del	DEL	C	C	-													0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agctcggtgccagccgtcatCgccaaggcctctgcaatcca					rs192913605	byFrequency	TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:88421086delC	ENST00000241891.5	+	7	1181	c.1014delC	c.(1012-1014)atcfs	p.I338fs	OPN4_ENST00000372071.2_Frame_Shift_Del_p.I349fs	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	338					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						CAGCCGTCATCGCCAAGGCCT	0.587																																					p.I349fs		Atlas-INDEL	.											.	OPN4	61	.	0			c.1046delT						.						256	178	205					10																	88421086		2203	4300	6503	SO:0001589	frameshift_variant	94233	exon8			.	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"GPCR / Class A : Opsin receptors"	14449	protein-coding gene	gene with protein product	"melanopsin"	606665	"opsin 4 (melanopsin)"			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.1014delC	chr10.hg19:g.88421086delC	ENSP00000241891:p.Ile338fs	111.0	0.0		93.0	34.0	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Frame_Shift_Del	DEL	ENST00000241891.5	hg19	CCDS7376.1																																																																																			.	.		0.587	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282		-	88421086	C	-	88421086	7	5	65	1	0	1	0	1	0	0	0	0	10891	874	31	0	1077	0	OPN4	10	88421086	Frame_Shift_Del	DEL	C	TCGA-CC-A3MB-01A-11D-A20W-10	9751290	88421086	47113661	238	8311										
KIF20B	9585	hgsc.bcm.edu	37	chr10	91484863	91484863	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggatttggttggtaaatgtgAcactcgagaagaagcagcga	14	5	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:91484863A>G	ENST00000371728.3	+	15	2014	c.1949A>G	c.(1948-1950)gAc>gGc	p.D650G	KIF20B_ENST00000416354.1_Missense_Mutation_p.D650G|KIF20B_ENST00000260753.4_Missense_Mutation_p.D650G|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000394289.2_Missense_Mutation_p.D650G	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	650					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						GGTAAATGTGACACTCGAGAA	0.368																																					p.D650G		Atlas-SNP	.											.	KIF20B	191	.	0			c.A1949G						.						133	130	131					10																	91484863		2203	4300	6503	SO:0001583	missense	9585	exon15			AATGTGACACTCG	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.1949A>G	chr10.hg19:g.91484863A>G	ENSP00000360793:p.Asp650Gly	104.0	0.0		74.0	4.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	hg19		.	.	.	.	.	.	.	.	.	.	A	9.689	1.151343	0.21371	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.18174	2.23;2.23;2.23;2.23	5.49	3.2	0.36748	.	0.251074	0.28166	N	0.016359	T	0.11750	0.0286	L	0.60455	1.87	0.09310	N	1	P;B	0.39665	0.682;0.004	B;B	0.30401	0.115;0.006	T	0.18681	-1.0329	10	0.22706	T	0.39	-2.1015	4.6081	0.12387	0.5526:0.276:0.1714:0.0	.	650;650	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	G	650	ENSP00000260753:D650G;ENSP00000411545:D650G;ENSP00000377830:D650G;ENSP00000360793:D650G	ENSP00000260753:D650G	D	+	2	0	KIF20B	91474843	0.894000	0.30519	0.636000	0.29352	0.711000	0.40976	1.835000	0.39181	0.906000	0.36621	-0.250000	0.11733	GAC	.	.		0.368	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		G	91484863	A	G	91484863	3	3	65	1	0	0	0	0	1	0	0	0	8296	275	10	2	2003	2	KIF20B	10	91484863	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3063777	91484863	44049884	239	8312										
IDE	3416	hgsc.bcm.edu	37	chr10	94268589	94268589	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agtatttctgaaggtcaggtAtgggaaatgtcacatagaga	12	4	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:94268589A>G	ENST00000265986.6	-	7	1012	c.956T>C	c.(955-957)aTa>aCa	p.I319T		NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	319					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	AAGGTCAGGTATGGGAAATGT	0.368																																					p.I319T		Atlas-SNP	.											.	IDE	77	.	0			c.T956C						.						152	153	153					10																	94268589		2203	4300	6503	SO:0001583	missense	3416	exon7			TCAGGTATGGGAA	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.956T>C	chr10.hg19:g.94268589A>G	ENSP00000265986:p.Ile319Thr	105.0	0.0		85.0	4.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.396905	0.62177	.	.	ENSG00000119912	ENST00000265986	T	0.06933	3.24	5.28	5.28	0.74379	Peptidase M16, C-terminal (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.23766	0.0575	L	0.46885	1.475	0.80722	D	1	P	0.37233	0.588	P	0.62089	0.898	T	0.01192	-1.1423	10	0.34782	T	0.22	-16.0308	15.5041	0.75725	1.0:0.0:0.0:0.0	.	319	P14735	IDE_HUMAN	T	319	ENSP00000265986:I319T	ENSP00000265986:I319T	I	-	2	0	IDE	94258569	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.287000	0.95975	2.131000	0.65755	0.455000	0.32223	ATA	.	.		0.368	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		G	94268589	A	G	94268589	3	3	65	1	0	0	0	0	1	0	0	0	7502	449	16	2	2179	2	IDE	10	94268589	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2783726	94268589	41266158	240	8313										
MYOF	26509	hgsc.bcm.edu	37	chr10	95109578	95109578	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	actgtaccactttcatgaagAgaacagaacttggaaagttg	9	7	1	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:95109578A>G	ENST00000359263.4	-	36	4069	c.4070T>C	c.(4069-4071)cTc>cCc	p.L1357P	MYOF_ENST00000371501.4_Missense_Mutation_p.L1357P|MYOF_ENST00000371502.4_Missense_Mutation_p.L1357P|MYOF_ENST00000358334.5_Missense_Mutation_p.L1344P	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1357					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TTTCATGAAGAGAACAGAACT	0.443																																					p.L1357P		Atlas-SNP	.											.	MYOF	177	.	0			c.T4070C						.						103	102	102					10																	95109578		1910	4127	6037	SO:0001583	missense	26509	exon36			ATGAAGAGAACAG	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.4070T>C	chr10.hg19:g.95109578A>G	ENSP00000352208:p.Leu1357Pro	147.0	0.0		83.0	4.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.268520	0.80469	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	5.53	5.53	0.82687	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.85435	0.5696	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88899	0.3351	10	0.87932	D	0	-16.8222	15.6595	0.77174	1.0:0.0:0.0:0.0	.	1344;1357	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	P	1344;1357;1357;1357	ENSP00000351094:L1344P;ENSP00000352208:L1357P;ENSP00000360556:L1357P;ENSP00000360557:L1357P	ENSP00000351094:L1344P	L	-	2	0	MYOF	95099568	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.273000	0.95719	2.102000	0.63906	0.459000	0.35465	CTC	.	.		0.443	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		G	95109578	A	G	95109578	3	3	65	1	0	0	0	0	1	0	0	0	10098	304	11	2	2191	2	MYOF	10	95109578	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	840989	95109578	40425169	241	8314										
C10orf28	27291	hgsc.bcm.edu	37	chr10	99991351	99991351	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgaagttcctgatattgaccTcagtgattgtgaattcccac	8	9	1	5			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:99991351T>C	ENST00000298999.3	+	6	2171	c.1868T>C	c.(1867-1869)cTc>cCc	p.L623P	R3HCC1L_ENST00000370584.3_Missense_Mutation_p.L623P|R3HCC1L_ENST00000370586.2_Missense_Mutation_p.L29P|R3HCC1L_ENST00000314594.5_Missense_Mutation_p.L39P	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	637							nucleotide binding (GO:0000166)										GATATTGACCTCAGTGATTGT	0.398																																					p.L637P		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.T1910C						.						127	119	122					10																	99991351		2203	4300	6503	SO:0001583	missense	27291	exon7			TTGACCTCAGTGA	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 28"	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1868T>C	chr10.hg19:g.99991351T>C	ENSP00000298999:p.Leu623Pro	124.0	0.0		75.0	5.0	NM_001256619	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	hg19	CCDS31267.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.341703	0.81911	.	.	ENSG00000166024	ENST00000370584;ENST00000298999;ENST00000370586;ENST00000314594;ENST00000544834	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	5.83	5.83	0.93111	.	0.065933	0.64402	D	0.000014	T	0.61375	0.2342	M	0.77820	2.39	0.80722	D	1	P;D;P	0.89917	0.937;1.0;0.708	P;D;B	0.80764	0.735;0.994;0.383	T	0.63625	-0.6595	9	.	.	.	-5.5482	15.1559	0.72743	0.0:0.0:0.0:1.0	.	29;637;623	Q7Z5L2-3;Q7Z5L2;Q7Z5L2-2	.;GIDRP_HUMAN;.	P	623;623;29;39;30	ENSP00000359616:L623P;ENSP00000298999:L623P;ENSP00000359618:L29P;ENSP00000314018:L39P	.	L	+	2	0	C10orf28	99981341	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.328000	0.72915	2.214000	0.71695	0.533000	0.62120	CTC	.	.		0.398	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472		C	99991351	T	C	99991351	3	2	65	1	0	0	0	0	1	0	0	0	1603	1551	54	2	1874	2	C10orf28	10	99991351	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4881773	99991351	35543396	242	8315										
CCDC147	159686	hgsc.bcm.edu	37	chr10	106128250	106128250	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atgctaaacttcagcaagagAatgaacagcacagtttggtc	9	8	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:106128250A>G	ENST00000369704.3	+	6	996	c.862A>G	c.(862-864)Aat>Gat	p.N288D	CCDC147_ENST00000312902.5_5'UTR	NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		288						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		TCAGCAAGAGAATGAACAGCA	0.438																																					p.N288D		Atlas-SNP	.											.	CCDC147	137	.	0			c.A862G						.						118	106	110					10																	106128250		2203	4300	6503	SO:0001583	missense	159686	exon6			CAAGAGAATGAAC																												ENST00000369704.3:c.862A>G	chr10.hg19:g.106128250A>G	ENSP00000358718:p.Asn288Asp	80.0	0.0		73.0	4.0	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	hg19	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.710926	0.30322	.	.	ENSG00000120051	ENST00000369704	T	0.33438	1.41	6.17	6.17	0.99709	.	0.284681	0.44285	D	0.000468	T	0.34077	0.0885	L	0.51422	1.61	0.80722	D	1	B	0.33583	0.418	B	0.35655	0.207	T	0.06698	-1.0812	10	0.49607	T	0.09	-28.6057	16.8222	0.85835	1.0:0.0:0.0:0.0	.	288	Q5T655	CC147_HUMAN	D	288	ENSP00000358718:N288D	ENSP00000358718:N288D	N	+	1	0	CCDC147	106118240	1.000000	0.71417	0.998000	0.56505	0.468000	0.32798	4.953000	0.63624	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.438	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			G	106128250	A	G	106128250	3	3	65	1	0	0	0	0	1	0	0	0	2783	246	9	2	884	2	CCDC147	10	106128250	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	6136899	106128250	29406497	243	8316										
CCDC147	159686	hgsc.bcm.edu	37	chr10	106160619	106160619	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caagaagcttcgccgggaaaAggggattcttgccaggagta	14	8	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:106160619A>G	ENST00000369704.3	+	13	2131	c.1997A>G	c.(1996-1998)aAg>aGg	p.K666R	snoU13_ENST00000458914.1_RNA	NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		666						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		CGCCGGGAAAAGGGGATTCTT	0.478																																					p.K666R		Atlas-SNP	.											.	CCDC147	137	.	0			c.A1997G						.						73	79	77					10																	106160619		2203	4300	6503	SO:0001583	missense	159686	exon13			GGGAAAAGGGGAT																												ENST00000369704.3:c.1997A>G	chr10.hg19:g.106160619A>G	ENSP00000358718:p.Lys666Arg	80.0	0.0		87.0	4.0	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	hg19	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	A	14.13	2.444759	0.43429	.	.	ENSG00000120051	ENST00000369704	T	0.52754	0.65	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.37732	0.1014	L	0.38175	1.15	0.80722	D	1	B	0.30709	0.291	B	0.29267	0.1	T	0.19095	-1.0316	10	0.10902	T	0.67	-33.0534	16.2813	0.82687	1.0:0.0:0.0:0.0	.	666	Q5T655	CC147_HUMAN	R	666	ENSP00000358718:K666R	ENSP00000358718:K666R	K	+	2	0	CCDC147	106150609	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.244000	0.73946	0.533000	0.62120	AAG	.	.		0.478	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			G	106160619	A	G	106160619	3	3	65	1	0	0	0	0	1	0	0	0	2783	72	3	2	2047	2	CCDC147	10	106160619	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	32369	106160619	29374128	244	8317										
SHOC2	8036	hgsc.bcm.edu	37	chr10	112771425	112771425	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caaccccaacctgcatagccTtccctttgagctggcactct	6	17	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:112771425T>C	ENST00000369452.4	+	9	1943	c.1598T>C	c.(1597-1599)cTt>cCt	p.L533P	SHOC2_ENST00000265277.5_Missense_Mutation_p.L487P|SHOC2_ENST00000489390.1_3'UTR	NM_007373.3	NP_031399.2	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog (C. elegans)	533					fibroblast growth factor receptor signaling pathway (GO:0008543)|positive regulation of Ras protein signal transduction (GO:0046579)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase binding (GO:0019903)|protein phosphatase regulator activity (GO:0019888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(2)	17				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		CTGCATAGCCTTCCCTTTGAG	0.413																																					p.L533P		Atlas-SNP	.											.	SHOC2	49	.	0			c.T1598C						.						124	121	122					10																	112771425		2203	4300	6503	SO:0001583	missense	8036	exon9			ATAGCCTTCCCTT	AB020669	CCDS7568.1, CCDS58095.1	10q25	2014-09-17	2001-11-28		ENSG00000108061	ENSG00000108061			15454	protein-coding gene	gene with protein product		602775	"soc-2 (suppressor of clear, C.elegans) homolog"			9618511, 9674433, 10783161	Standard	NM_007373		Approved	KIAA0862, SOC2, SUR-8, SOC-2, SUR8	uc001kzl.4	Q9UQ13	OTTHUMG00000019047	ENST00000369452.4:c.1598T>C	chr10.hg19:g.112771425T>C	ENSP00000358464:p.Leu533Pro	99.0	0.0		82.0	4.0	NM_007373	A8K9W8|B3KR23|O76063|Q5VZS8|Q5VZS9	Missense_Mutation	SNP	ENST00000369452.4	hg19	CCDS7568.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.686051	0.88639	.	.	ENSG00000108061	ENST00000265277;ENST00000369452;ENST00000451838	T;T;D	0.86432	1.34;1.34;-2.12	5.42	5.42	0.78866	.	0.056560	0.64402	N	0.000001	D	0.96380	0.8819	H	0.98738	4.315	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.97110	0.991;1.0	D	0.98152	1.0442	10	0.87932	D	0	.	15.4447	0.75220	0.0:0.0:0.0:1.0	.	487;533	Q9UQ13-2;Q9UQ13	.;SHOC2_HUMAN	P	487;533;323	ENSP00000265277:L487P;ENSP00000358464:L533P;ENSP00000408275:L323P	ENSP00000265277:L487P	L	+	2	0	SHOC2	112761415	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.988000	0.88194	2.040000	0.60383	0.533000	0.62120	CTT	.	.		0.413	SHOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050355.1	NM_007373		C	112771425	T	C	112771425	3	2	65	1	0	0	0	0	1	0	0	0	14302	1609	56	2	1628	2	SHOC2	10	112771425	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6610806	112771425	22763322	245	8318										
C10orf137	26098	hgsc.bcm.edu	37	chr10	127431772	127431772	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tatgtacaagtattaaagagAatgggtaacattagaaatga	9	2	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr10:127431772A>G	ENST00000356792.4	+	18	2749	c.2517A>G	c.(2515-2517)agA>agG	p.R839R	RP11-383C5.7_ENST00000449436.1_RNA|C10orf137_ENST00000337623.3_Silent_p.R805R|RP11-383C5.7_ENST00000600784.1_RNA|RP11-383C5.7_ENST00000593871.1_RNA|RP11-383C5.7_ENST00000602030.1_RNA|RP11-383C5.7_ENST00000594025.1_RNA	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		839					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TATTAAAGAGAATGGGTAACA	0.358																																					p.R839R		Atlas-SNP	.											.	C10orf137	153	.	0			c.A2517G						.						120	120	120					10																	127431772		2203	4300	6503	SO:0001819	synonymous_variant	26098	exon18			AAAGAGAATGGGT																												ENST00000356792.4:c.2517A>G	chr10.hg19:g.127431772A>G		99.0	0.0		84.0	4.0	NM_001202438	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Silent	SNP	ENST00000356792.4	hg19	CCDS55733.1																																																																																			.	.		0.358	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			G	127431772	A	G	127431772	2	3	65	1	0	0	0	0	0	0	0	1	1596	243	9	2		2	C10orf137	10	127431772	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	14660347	127431772	8102975	246	8319										
OR52B4	143496	hgsc.bcm.edu	37	chr11	4389188	4389188	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcaccagcaagatccctgacTcagagatgaaggtggaatgg	12	9	2	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:4389188T>C	ENST00000408920.2	-	1	428	c.338A>G	c.(337-339)gAg>gGg	p.E113G		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	113					cognition (GO:0050890)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATCCCTGACTCAGAGATGAA	0.473																																					p.E113G		Atlas-SNP	.											.	OR52B4	56	.	0			c.A338G						.						96	98	97					11																	4389188		2114	4244	6358	SO:0001583	missense	143496	exon1			CCTGACTCAGAGA	AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"GPCR / Class A : Olfactory receptors"	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.338A>G	chr11.hg19:g.4389188T>C	ENSP00000386160:p.Glu113Gly	101.0	0.0		83.0	4.0	NM_001005161	A6NP68|Q6IFK6	Missense_Mutation	SNP	ENST00000408920.2	hg19	CCDS41609.1	.	.	.	.	.	.	.	.	.	.	T	16.99	3.273614	0.59649	.	.	ENSG00000221996	ENST00000408920	T	0.00388	7.59	5.28	5.28	0.74379	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000016	T	0.01558	0.0050	H	0.95679	3.705	0.38208	D	0.940391	D	0.76494	0.999	D	0.69307	0.963	T	0.30707	-0.9969	10	0.87932	D	0	.	14.1695	0.65500	0.0:0.0:0.0:1.0	.	113	Q8NGK2	O52B4_HUMAN	G	113	ENSP00000386160:E113G	ENSP00000386160:E113G	E	-	2	0	OR52B4	4345764	0.998000	0.40836	1.000000	0.80357	0.363000	0.29612	2.257000	0.43240	2.220000	0.72140	0.528000	0.53228	GAG	.	.		0.473	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3	NM_001005161		C	4389188	T	C	4389188	3	2	65	1	0	0	0	0	1	0	0	0	11121	1551	54	2	610	2	OR52B4	11	4389188	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		4389188	130617328	247	8320										
USH1C	10083	hgsc.bcm.edu	37	chr11	17522671	17522671	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atgggggagtccacaccgccTtccagggccaggtctaagga	14	12	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:17522671T>C	ENST00000318024.4	-	18	1515	c.1407A>G	c.(1405-1407)gaA>gaG	p.E469E	USH1C_ENST00000527720.1_Silent_p.E438E|USH1C_ENST00000005226.7_Silent_p.E769E|USH1C_ENST00000527020.1_Silent_p.E450E|USH1C_ENST00000529563.1_5'UTR	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	469	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						CCACACCGCCTTCCAGGGCCA	0.602																																					p.E769E		Atlas-SNP	.											.	USH1C	157	.	0			c.A2307G						.						65	55	58					11																	17522671		2200	4293	6493	SO:0001819	synonymous_variant	10083	exon23			ACCGCCTTCCAGG	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1407A>G	chr11.hg19:g.17522671T>C		86.0	0.0		79.0	4.0	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	hg19	CCDS31438.1																																																																																			.	.		0.602	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		C	17522671	T	C	17522671	2	2	65	1	0	0	0	0	0	0	0	1	17049	1606	56	2		2	USH1C	11	17522671	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	13133483	17522671	117483845	248	8321										
NELL1	4745	hgsc.bcm.edu	37	chr11	20940817	20940817	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcttgcccaacctgcagtgaTttcttaagcctggtgcaagg	11	11	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:20940817T>C	ENST00000357134.5	+	7	848	c.696T>C	c.(694-696)gaT>gaC	p.D232D	NELL1_ENST00000325319.5_Silent_p.D175D|NELL1_ENST00000298925.5_Silent_p.D260D|NELL1_ENST00000532434.1_Silent_p.D232D	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	232					cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						CCTGCAGTGATTTCTTAAGCC	0.303																																					p.D232D		Atlas-SNP	.											.	NELL1	179	.	0			c.T696C						.						109	106	107					11																	20940817		2203	4299	6502	SO:0001819	synonymous_variant	4745	exon7			CAGTGATTTCTTA	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.696T>C	chr11.hg19:g.20940817T>C		117.0	0.0		97.0	5.0	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	hg19	CCDS7855.1																																																																																			.	.		0.303	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		C	20940817	T	C	20940817	2	2	65	1	0	0	0	0	0	0	0	1	10342	1490	52	2		2	NELL1	11	20940817	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3418146	20940817	114065699	249	8322										
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26708028	26708028	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttccttctttcgttacctgcAcaacacctcccatgacagat	4	15	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:26708028A>G	ENST00000396005.3	-	10	1526	c.1217T>C	c.(1216-1218)gTg>gCg	p.V406A		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	406					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						CGTTACCTGCACAACACCTCC	0.433																																					p.V406A		Atlas-SNP	.											.	SLC5A12	134	.	0			c.T1217C						.						104	106	106					11																	26708028		2009	4175	6184	SO:0001583	missense	159963	exon10			ACCTGCACAACAC	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1217T>C	chr11.hg19:g.26708028A>G	ENSP00000379326:p.Val406Ala	82.0	0.0		76.0	4.0	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	hg19	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	A	12.11	1.838775	0.32513	.	.	ENSG00000148942	ENST00000396005	D	0.87334	-2.24	5.55	5.55	0.83447	.	0.331495	0.22064	U	0.065127	D	0.87083	0.6089	L	0.58302	1.8	0.80722	D	1	B	0.29270	0.24	B	0.36092	0.217	D	0.86308	0.1684	10	0.66056	D	0.02	.	14.6556	0.68831	1.0:0.0:0.0:0.0	.	406	Q1EHB4	SC5AC_HUMAN	A	406	ENSP00000379326:V406A	ENSP00000379326:V406A	V	-	2	0	SLC5A12	26664604	0.392000	0.25229	0.003000	0.11579	0.088000	0.18126	5.230000	0.65321	2.099000	0.63709	0.482000	0.46254	GTG	.	.		0.433	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		G	26708028	A	G	26708028	3	3	65	1	0	0	0	0	1	0	0	0	14679	159	6	2	663	2	SLC5A12	11	26708028	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	5767211	26708028	108298488	250	8323										
PRDM11	56981	hgsc.bcm.edu	37	chr11	45203337	45203337	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aatgaccgagaacatgaaggAgtgcttggcccagaccaatg	12	9	0	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:45203337A>G	ENST00000530656.1	+	2	122	c.122A>G	c.(121-123)gAg>gGg	p.E41G	PRDM11_ENST00000424263.2_Missense_Mutation_p.E7G|PRDM11_ENST00000263765.4_Missense_Mutation_p.E41G			Q9NQV5	PRD11_HUMAN	PR domain containing 11	41							methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						AACATGAAGGAGTGCTTGGCC	0.602																																					p.E7G	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											.	PRDM11	53	.	0			c.A20G						.						109	96	101					11																	45203337		2203	4299	6502	SO:0001583	missense	56981	exon2			TGAAGGAGTGCTT	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"PR-domain containing protein 11"						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.122A>G	chr11.hg19:g.45203337A>G	ENSP00000435976:p.Glu41Gly	27.0	0.0		33.0	4.0	NM_001256695	Q8N9F1	Missense_Mutation	SNP	ENST00000530656.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.40	2.821512	0.50633	.	.	ENSG00000019485	ENST00000263765;ENST00000530656;ENST00000526442;ENST00000424263	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.28	4.09	0.47781	.	0.179711	0.38605	N	0.001627	T	0.30634	0.0771	N	0.14661	0.345	0.32351	N	0.558416	B	0.33171	0.4	B	0.30855	0.121	T	0.50355	-0.8838	10	0.87932	D	0	-23.3036	12.7893	0.57523	0.8541:0.1458:0.0:0.0	.	41	Q9NQV5	PRD11_HUMAN	G	41;41;7;7	ENSP00000263765:E41G;ENSP00000435976:E41G;ENSP00000431898:E7G;ENSP00000394314:E7G	ENSP00000263765:E41G	E	+	2	0	PRDM11	45159913	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.024000	0.57218	2.001000	0.58596	0.402000	0.26972	GAG	.	.		0.602	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229		G	45203337	A	G	45203337	3	3	65	1	0	0	0	0	1	0	0	0	12464	304	11	2	128	2	PRDM11	11	45203337	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	18495309	45203337	89803179	251	8324										
CELF1	10658	hgsc.bcm.edu	37	chr11	47510436	47510436	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tatcccttaggacgttgattTcatacacagcaccatactgt	6	11	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:47510436T>C	ENST00000358597.3	-	1	130	c.131A>G	c.(130-132)gAa>gGa	p.E44G	CELF1_ENST00000532048.1_Missense_Mutation_p.E71G|AC090559.1_ENST00000578625.1_RNA|CELF1_ENST00000310513.5_Missense_Mutation_p.E44G|CELF1_ENST00000361904.3_Missense_Mutation_p.E44G|CELF1_ENST00000531165.1_Missense_Mutation_p.E71G|CELF1_ENST00000395292.2_Missense_Mutation_p.E44G|CELF1_ENST00000395290.2_Missense_Mutation_p.E44G			Q92879	CELF1_HUMAN	CUGBP, Elav-like family member 1	44	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of translation (GO:0017148)|positive regulation of multicellular organism growth (GO:0040018)|regulation of RNA splicing (GO:0043484)|RNA interference (GO:0016246)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation repressor activity, nucleic acid binding (GO:0000900)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(2)	18						GACGTTGATTTCATACACAGC	0.468																																					p.E71G	Pancreas(163;1949 1966 9906 43218 43785)	Atlas-SNP	.											.	CELF1	43	.	0			c.A212G						.						164	166	165					11																	47510436		2201	4298	6499	SO:0001583	missense	10658	exon4			TTGATTTCATACA	U63289	CCDS7938.1, CCDS7939.1, CCDS31482.1, CCDS53622.1, CCDS53623.1	11p11	2013-02-12	2010-02-19	2010-02-19				"RNA binding motif (RRM) containing"	2549	protein-coding gene	gene with protein product	"CUG RNA-binding protein", "nuclear polyadenylated RNA-binding protein, 50-kD", "bruno-like 2", "embryo deadenylation element binding protein"	601074	"CUG triplet repeat, RNA-binding protein 1", "CUG triplet repeat, RNA binding protein 1"	CUGBP1		8948631, 9371827	Standard	NM_006560		Approved	CUG-BP, hNab50, BRUNOL2, NAB50, CUGBP, NAPOR, EDEN-BP	uc001nfl.3	Q92879		ENST00000358597.3:c.131A>G	chr11.hg19:g.47510436T>C	ENSP00000351409:p.Glu44Gly	87.0	0.0		85.0	4.0	NM_001172639	B4E2U5|D3DQS0|F8W940|Q4LE52|Q9NP83|Q9NR06	Missense_Mutation	SNP	ENST00000358597.3	hg19	CCDS31482.1	.	.	.	.	.	.	.	.	.	.	T	31	5.091145	0.94149	.	.	ENSG00000149187	ENST00000395290;ENST00000358597;ENST00000395292;ENST00000310513;ENST00000361904;ENST00000531165;ENST00000532048;ENST00000530151;ENST00000528434;ENST00000525841;ENST00000543178;ENST00000535982;ENST00000526419	T;T;T;T;T;T;T;T;T;T;T;T;T	0.75154	-0.91;1.22;1.22;1.22;1.22;1.22;1.22;-0.91;1.22;-0.91;-0.91;1.22;1.22	5.69	5.69	0.88448	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.83589	0.5287	L	0.61387	1.9	0.80722	D	1	D;D;P;P;D;P	0.71674	0.998;0.958;0.921;0.921;0.958;0.936	D;P;B;B;P;B	0.64687	0.928;0.726;0.31;0.182;0.726;0.345	D	0.85463	0.1168	10	0.87932	D	0	-12.2654	15.9416	0.79758	0.0:0.0:0.0:1.0	.	44;71;71;44;44;44	F8W940;G5EA30;Q92879-4;Q92879-2;Q92879-3;Q92879	.;.;.;.;.;CELF1_HUMAN	G	44;44;44;44;44;71;71;44;71;44;44;71;44	ENSP00000378705:E44G;ENSP00000351409:E44G;ENSP00000378706:E44G;ENSP00000308386:E44G;ENSP00000354639:E44G;ENSP00000436864:E71G;ENSP00000435926:E71G;ENSP00000433986:E44G;ENSP00000435320:E71G;ENSP00000436191:E44G;ENSP00000444825:E44G;ENSP00000438044:E71G;ENSP00000435423:E44G	ENSP00000308386:E44G	E	-	2	0	CELF1	47467012	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.036000	0.88901	2.170000	0.68504	0.459000	0.35465	GAA	.	.		0.468	CELF1-024	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398352.1	NM_006560		C	47510436	T	C	47510436	3	2	65	1	0	0	0	0	1	0	0	0	3217	1783	62	2	1380	2	CELF1	11	47510436	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2307099	47510436	87496080	252	8325										
OSBP	5007	hgsc.bcm.edu	37	chr11	59347665	59347665	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acctttcttgctacatcccgAgagaagtagctataaggaac	8	10	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:59347665A>G	ENST00000263847.1	-	11	2339	c.1860T>C	c.(1858-1860)tcT>tcC	p.S620S		NM_002556.2	NP_002547.1	P22059	OSBP1_HUMAN	oxysterol binding protein	620					lipid transport (GO:0006869)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	oxysterol binding (GO:0008142)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CTACATCCCGAGAGAAGTAGC	0.338																																					p.S620S		Atlas-SNP	.											.	OSBP	57	.	0			c.T1860C						.						84	84	84					11																	59347665		2201	4295	6496	SO:0001819	synonymous_variant	5007	exon11			ATCCCGAGAGAAG	AF185696	CCDS7974.1	11q12-q13	2013-01-10			ENSG00000110048	ENSG00000110048		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	8503	protein-coding gene	gene with protein product		167040					Standard	NM_002556		Approved	OSBP1	uc001noc.1	P22059	OTTHUMG00000167422	ENST00000263847.1:c.1860T>C	chr11.hg19:g.59347665A>G		57.0	0.0		44.0	4.0	NM_002556	Q6P524	Silent	SNP	ENST00000263847.1	hg19	CCDS7974.1																																																																																			.	.		0.338	OSBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394555.1			G	59347665	A	G	59347665	2	3	65	1	0	0	0	0	0	0	0	1	11282	291	11	2		2	OSBP	11	59347665	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	11837229	59347665	75658851	253	8326										
MS4A14	84689	hgsc.bcm.edu	37	chr11	60184403	60184403	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atacagcaataccaattctgGcaattccacaaaggcaatct	5	11	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:60184403G>A	ENST00000300187.6	+	5	2239	c.1962G>A	c.(1960-1962)tgG>tgA	p.W654*	MS4A14_ENST00000531783.1_Nonsense_Mutation_p.W687*|MS4A14_ENST00000531787.1_Nonsense_Mutation_p.W542*|MS4A14_ENST00000395005.2_Nonsense_Mutation_p.W637*	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	654	Gln-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						ACCAATTCTGGCAATTCCACA	0.463																																					p.W687X		Atlas-SNP	.											.	MS4A14	120	.	0			c.G2061A						.						83	86	85					11																	60184403		2203	4300	6503	SO:0001587	stop_gained	84689	exon6			ATTCTGGCAATTC	AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"membrane-spanning 4-domains, subfamily A, member 16"	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.1962G>A	chr11.hg19:g.60184403G>A	ENSP00000300187:p.Trp654*	102.0	0.0		90.0	17.0	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Nonsense_Mutation	SNP	ENST00000300187.6	hg19	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.116769	0.77323	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	.	.	.	3.78	0.219	0.15274	.	7.817370	0.00166	N	0.000002	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	6.0394	0.19726	0.1041:0.0:0.5168:0.3791	.	.	.	.	X	542;654;637;687	.	ENSP00000300187:W654X	W	+	3	0	MS4A14	59940979	0.015000	0.18098	0.000000	0.03702	0.018000	0.09664	-0.108000	0.10857	-0.093000	0.12396	0.650000	0.86243	TGG	.	.		0.463	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			A	60184403	G	A	60184403	4	1	65	1	0	0	0	0	0	1	0	0	9867	1212	42	3	1980	3	MS4A14	11	60184403	Nonsense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	836738	60184403	74822113	254	8327										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62286551	62286551	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtgcctggagttcaccctccAgtttggggctagggagaggg	17	9	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:62286551A>G	ENST00000378024.4	-	5	15612	c.15338T>C	c.(15337-15339)cTg>cCg	p.L5113P	AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5113					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TTCACCCTCCAGTTTGGGGCT	0.473																																					p.L5113P		Atlas-SNP	.											.	AHNAK	532	.	0			c.T15338C						.						69	73	72					11																	62286551		2202	4299	6501	SO:0001583	missense	79026	exon5			CCCTCCAGTTTGG	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.15338T>C	chr11.hg19:g.62286551A>G	ENSP00000367263:p.Leu5113Pro	127.0	0.0		96.0	4.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	A	12.56	1.973824	0.34848	.	.	ENSG00000124942	ENST00000378024	T	0.00922	5.54	4.88	4.88	0.63580	.	0.859367	0.09745	N	0.761381	T	0.04998	0.0134	M	0.70903	2.155	0.39622	D	0.970046	D	0.58970	0.984	D	0.64506	0.926	T	0.51188	-0.8737	10	0.34782	T	0.22	-0.5009	14.4566	0.67420	1.0:0.0:0.0:0.0	.	5113	Q09666	AHNK_HUMAN	P	5113	ENSP00000367263:L5113P	ENSP00000367263:L5113P	L	-	2	0	AHNAK	62043127	0.421000	0.25465	0.615000	0.29064	0.571000	0.35966	4.269000	0.58890	1.958000	0.56883	0.443000	0.29094	CTG	.	.		0.473	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		G	62286551	A	G	62286551	3	3	65	1	0	0	0	0	1	0	0	0	414	188	7	2	2454	2	AHNAK	11	62286551	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2102148	62286551	72719965	255	8328										
INTS5	80789	hgsc.bcm.edu	37	chr11	62417403	62417403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gagcatgttcccgggctgagAgttggtggcccagaatgggg	18	8	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:62417403A>G	ENST00000330574.2	-	2	201	c.149T>C	c.(148-150)cTc>cCc	p.L50P	RP11-831H9.11_ENST00000528405.1_3'UTR	NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	50					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(6)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	36						CCGGGCTGAGAGTTGGTGGCC	0.537																																					p.L50P		Atlas-SNP	.											.	INTS5	81	.	0			c.T149C						.						76	84	81					11																	62417403		2202	4299	6501	SO:0001583	missense	80789	exon2			GCTGAGAGTTGGT	AK123587	CCDS8027.1	11q12.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000185085	ENSG00000185085			29352	protein-coding gene	gene with protein product		611349	"KIAA1698"	KIAA1698		16239144	Standard	NM_030628		Approved	INT5	uc001nud.3	Q6P9B9	OTTHUMG00000167605	ENST00000330574.2:c.149T>C	chr11.hg19:g.62417403A>G	ENSP00000327889:p.Leu50Pro	95.0	0.0		93.0	4.0	NM_030628	Q8N6W5|Q9C0G5	Missense_Mutation	SNP	ENST00000330574.2	hg19	CCDS8027.1	.	.	.	.	.	.	.	.	.	.	A	19.39	3.818182	0.71028	.	.	ENSG00000185085	ENST00000330574	.	.	.	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000001	T	0.74898	0.3777	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77202	-0.2674	9	0.66056	D	0.02	.	12.9592	0.58447	1.0:0.0:0.0:0.0	.	50	Q6P9B9	INT5_HUMAN	P	50	.	ENSP00000327889:L50P	L	-	2	0	INTS5	62173979	1.000000	0.71417	0.998000	0.56505	0.815000	0.46073	8.723000	0.91458	1.946000	0.56461	0.459000	0.35465	CTC	.	.		0.537	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628		G	62417403	A	G	62417403	3	3	65	1	0	0	0	0	1	0	0	0	7790	304	11	2	2914	2	INTS5	11	62417403	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	130852	62417403	72589113	256	8329										
SF1	7536	hgsc.bcm.edu	37	chr11	64534515	64534515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cactgggaggcggcggcggcGgcggcatcatgcccataggt	18	12	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:64534515G>A	ENST00000377390.3	-	12	1776	c.1439C>T	c.(1438-1440)cCg>cTg	p.P480L	SF1_ENST00000377394.3_Silent_p.A481A|SF1_ENST00000334944.5_Missense_Mutation_p.P480L|SF1_ENST00000377387.1_Missense_Mutation_p.P605L|SF1_ENST00000422298.2_Missense_Mutation_p.P365L|SF1_ENST00000227503.9_Missense_Mutation_p.P480L|SF1_ENST00000489544.1_5'Flank|SF1_ENST00000433274.2_Missense_Mutation_p.P454L	NM_004630.3	NP_004621.2	Q15637	SF01_HUMAN	splicing factor 1	480	Pro-rich.				Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of steroid biosynthetic process (GO:0050810)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribosome (GO:0005840)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	31						CGGCGGCGGCGGCGGCATCAT	0.692																																					p.P605L		Atlas-SNP	.											.	SF1	124	.	0			c.C1814T						.						18	23	22					11																	64534515		2197	4285	6482	SO:0001583	missense	7536	exon12			GGCGGCGGCGGCA	D26120	CCDS8080.1, CCDS8081.1, CCDS31599.1, CCDS44642.1, CCDS44642.2, CCDS53660.1, CCDS53661.1	11q13	2014-09-17	2001-12-19	2002-01-11	ENSG00000168066	ENSG00000168066		"Zinc fingers, CCHC domain containing"	12950	protein-coding gene	gene with protein product		601516	"zinc finger protein 162"	ZNF162		7912130, 9573336	Standard	NM_201997		Approved	ZFM1, ZCCHC25	uc001oaz.2	Q15637	OTTHUMG00000066833	ENST00000377390.3:c.1439C>T	chr11.hg19:g.64534515G>A	ENSP00000366607:p.Pro480Leu	61.0	0.0		74.0	14.0	NM_001178030	B7Z1Q1|C9JJE2|Q14818|Q14819|Q15913|Q8IY00|Q92744|Q92745|Q969H7|Q9BW01|Q9UEI0	Missense_Mutation	SNP	ENST00000377390.3	hg19	CCDS31599.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.54|13.54	2.266620|2.266620	0.40095|0.40095	.|.	.|.	ENSG00000168066|ENSG00000168066	ENST00000377387;ENST00000377390;ENST00000227503;ENST00000334944;ENST00000422298;ENST00000443908;ENST00000433274|ENST00000413725	T;T;T;T;T;T;T|.	0.51817|.	0.75;0.76;0.76;0.74;0.69;0.85;0.77|.	4.54|4.54	4.54|4.54	0.55810|0.55810	.|.	0.311799|.	0.33895|.	N|.	0.004451|.	T|T	0.70954|0.70954	0.3283|0.3283	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	0.999;0.999;0.999;0.999;1.0|.	D;D;D;D;D|.	0.79108|.	0.913;0.96;0.982;0.992;0.992|.	T|T	0.70263|0.70263	-0.4920|-0.4920	9|4	0.66056|.	D|.	0.02|.	.|.	15.5846|15.5846	0.76473|0.76473	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	365;480;480;480;605|.	B4DX42;Q15637-4;Q15637;Q15637-2;Q15637-5|.	.;.;SF01_HUMAN;.;.|.	L|C	605;480;480;480;365;132;454|50	ENSP00000366604:P605L;ENSP00000366607:P480L;ENSP00000227503:P480L;ENSP00000334414:P480L;ENSP00000413084:P365L;ENSP00000391198:P132L;ENSP00000396793:P454L|.	ENSP00000227503:P480L|.	P|R	-|-	2|1	0|0	SF1|SF1	64291091|64291091	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.898000|0.898000	0.52572|0.52572	6.317000|6.317000	0.72862|0.72862	2.466000|2.466000	0.83321|0.83321	0.561000|0.561000	0.74099|0.74099	CCG|CGC	.	.		0.692	SF1-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143242.1	NM_004630		A	64534515	G	A	64534515	3	1	65	1	0	0	0	0	1	0	0	0	14160	1116	39	1	622	1	SF1	11	64534515	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	2117112	64534515	70472001	257	8330										
PACS1	55690	hgsc.bcm.edu	37	chr11	66006669	66006669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgccctccacatcaccacccTccagctcgggcctgagccga	8	20	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:66006669T>C	ENST00000320580.4	+	21	2383	c.2350T>C	c.(2350-2352)Tcc>Ccc	p.S784P	PACS1_ENST00000529757.1_Missense_Mutation_p.S320P|PACS1_ENST00000524815.1_5'Flank	NM_018026.3	NP_060496.2	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	784					protein targeting to Golgi (GO:0000042)|protein targeting to plasma membrane (GO:0072661)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	COPI-coated vesicle (GO:0030137)|cytosol (GO:0005829)	ion channel binding (GO:0044325)		RBM14/PACS1(2)	breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(8)|ovary(6)|skin(2)|urinary_tract(1)	37						ATCACCACCCTCCAGCTCGGG	0.632																																					p.S784P		Atlas-SNP	.											.	PACS1	71	.	0			c.T2350C						.						122	105	110					11																	66006669		2200	4295	6495	SO:0001583	missense	55690	exon21			CCACCCTCCAGCT	AB033001	CCDS8129.1	11q13.1-q13.2	2008-02-05			ENSG00000175115	ENSG00000175115			30032	protein-coding gene	gene with protein product		607492				12855553, 14608369	Standard	NM_018026		Approved	FLJ10209, KIAA1175	uc001oha.2	Q6VY07	OTTHUMG00000166889	ENST00000320580.4:c.2350T>C	chr11.hg19:g.66006669T>C	ENSP00000316454:p.Ser784Pro	88.0	0.0		95.0	5.0	NM_018026	Q6PJY6|Q6PKB6|Q7Z590|Q7Z5W4|Q8N8K6|Q96MW0|Q9NW92|Q9ULP5	Missense_Mutation	SNP	ENST00000320580.4	hg19	CCDS8129.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.018890	0.75275	.	.	ENSG00000175115	ENST00000320580;ENST00000529757	T;T	0.47528	0.84;0.84	4.94	4.94	0.65067	.	0.127785	0.52532	D	0.000070	T	0.57359	0.2048	L	0.49350	1.555	0.80722	D	1	D	0.65815	0.995	P	0.58820	0.846	T	0.56432	-0.7980	10	0.39692	T	0.17	-23.7671	13.9082	0.63850	0.0:0.0:0.0:1.0	.	784	Q6VY07	PACS1_HUMAN	P	784;320	ENSP00000316454:S784P;ENSP00000432858:S320P	ENSP00000316454:S784P	S	+	1	0	PACS1	65763245	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	3.683000	0.54663	1.993000	0.58246	0.454000	0.30748	TCC	.	.		0.632	PACS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391690.2	NM_018026		C	66006669	T	C	66006669	3	2	65	1	0	0	0	0	1	0	0	0	11381	1551	54	2	2432	2	PACS1	11	66006669	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1472154	66006669	68999847	258	8331										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66472881	66472881	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aactcgcacagtgcctcataGctctgctctagcttggccac	8	15	3	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:66472881G>C	ENST00000533211.1	-	15	2197	c.1866C>G	c.(1864-1866)agC>agG	p.S622R	SPTBN2_ENST00000529997.1_Missense_Mutation_p.S622R|SPTBN2_ENST00000309996.2_Missense_Mutation_p.S622R			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	622					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GTGCCTCATAGCTCTGCTCTA	0.642																																					p.S622R		Atlas-SNP	.											.	SPTBN2	188	.	0			c.C1866G						.						30	34	33					11																	66472881		2194	4279	6473	SO:0001583	missense	6712	exon14			CTCATAGCTCTGC	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.1866C>G	chr11.hg19:g.66472881G>C	ENSP00000432568:p.Ser622Arg	96.0	0.0		118.0	73.0	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	G	7.848	0.723341	0.15439	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.43294	0.95;0.95;0.95	4.45	4.45	0.53987	.	0.119815	0.64402	D	0.000019	T	0.17874	0.0429	N	0.01473	-0.845	0.40405	D	0.979692	B	0.18013	0.025	B	0.15052	0.012	T	0.11567	-1.0582	10	0.14252	T	0.57	.	16.002	0.80301	0.0:0.0:1.0:0.0	.	622	O15020	SPTN2_HUMAN	R	622	ENSP00000432568:S622R;ENSP00000311489:S622R;ENSP00000433593:S622R	ENSP00000311489:S622R	S	-	3	2	SPTBN2	66229457	1.000000	0.71417	1.000000	0.80357	0.105000	0.19272	3.886000	0.56190	2.294000	0.77228	0.491000	0.48974	AGC	.	.		0.642	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		C	66472881	G	C	66472881	3	2	65	1	0	0	0	0	1	0	0	0	15135	962	34	4	5402	4	SPTBN2	11	66472881	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	466212	66472881	68533635	259	8332										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78467981	78467981	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtctcctggatgatgtccagAgggttaggggagccaaggca	16	8	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:78467981A>G	ENST00000278550.7	-	19	3087	c.2625T>C	c.(2623-2625)ccT>ccC	p.P875P	RP11-673F18.1_ENST00000526741.1_RNA	NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	875					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										TGATGTCCAGAGGGTTAGGGG	0.592																																					p.P875P		Atlas-SNP	.											.	.	.	.	0			c.T2625C						.						70	76	74					11																	78467981		2165	4264	6429	SO:0001819	synonymous_variant	26011	exon19			GTCCAGAGGGTTA	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.2625T>C	chr11.hg19:g.78467981A>G		100.0	0.0		98.0	4.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	hg19	CCDS44688.1																																																																																			.	.		0.592	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			G	78467981	A	G	78467981	2	3	65	1	0	0	0	0	0	0	0	1	10846	291	11	2		2	ODZ4	11	78467981	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	11995100	78467981	56538535	260	8333										
CCDC90B	60492	hgsc.bcm.edu	37	chr11	82984887	82984887	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atatccagtttattatctgcTctgattcgactggtttcatg	7	8	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:82984887T>C	ENST00000529689.1	-	6	923	c.489A>G	c.(487-489)agA>agG	p.R163R	CCDC90B_ENST00000455220.2_Silent_p.R154R|CCDC90B_ENST00000529611.1_Silent_p.R62R|CCDC90B_ENST00000525503.1_Silent_p.R62R|CCDC90B_ENST00000529073.1_Intron			Q9GZT6	CC90B_HUMAN	coiled-coil domain containing 90B	163						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Acute lymphoblastic leukemia(157;0.103)				TATTATCTGCTCTGATTCGAC	0.284																																					p.R163R		Atlas-SNP	.											.	CCDC90B	20	.	0			c.A489G						.						77	73	75					11																	82984887		2198	4296	6494	SO:0001819	synonymous_variant	60492	exon6			ATCTGCTCTGATT	BC048795	CCDS8266.1, CCDS66190.1, CCDS66191.1	11q14.1	2006-10-23			ENSG00000137500	ENSG00000137500			28108	protein-coding gene	gene with protein product						11230166	Standard	XM_005274154		Approved	MDS025, MDS011	uc001pae.3	Q9GZT6	OTTHUMG00000167078	ENST00000529689.1:c.489A>G	chr11.hg19:g.82984887T>C		137.0	0.0		93.0	4.0	NM_021825	A8K8I4|B3KP87|B4E3L2|Q3B781|Q9GZU6	Silent	SNP	ENST00000529689.1	hg19	CCDS8266.1																																																																																			.	.		0.284	CCDC90B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392940.2	NM_021825		C	82984887	T	C	82984887	2	2	65	1	0	0	0	0	0	0	0	1	2871	1548	54	2		2	CCDC90B	11	82984887	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4516906	82984887	52021629	261	8334										
SYTL2	54843	hgsc.bcm.edu	37	chr11	85420461	85420461	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	actccttcagtgactccacaTattcaattgcaaactgaata	4	11	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:85420461T>C	ENST00000528231.1	-	12	2190	c.1913A>G	c.(1912-1914)tAt>tGt	p.Y638C	SYTL2_ENST00000525702.1_Missense_Mutation_p.Y80C|SYTL2_ENST00000529581.1_Missense_Mutation_p.Y80C|SYTL2_ENST00000389960.4_Missense_Mutation_p.Y614C|SYTL2_ENST00000527523.1_Missense_Mutation_p.Y606C|SYTL2_ENST00000533892.1_Missense_Mutation_p.Y40C|SYTL2_ENST00000525423.1_Missense_Mutation_p.Y960C|SYTL2_ENST00000354566.3_Missense_Mutation_p.Y976C|SYTL2_ENST00000524452.1_Missense_Mutation_p.Y614C|SYTL2_ENST00000316356.4_Missense_Mutation_p.Y639C|SYTL2_ENST00000359152.5_Missense_Mutation_p.Y1484C|SYTL2_ENST00000389958.3_Missense_Mutation_p.Y69C	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	638	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TGACTCCACATATTCAATTGC	0.408																																					p.Y976C		Atlas-SNP	.											.	SYTL2	231	.	0			c.A2927G						.						126	120	122					11																	85420461		2203	4299	6502	SO:0001583	missense	54843	exon7			TCCACATATTCAA	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1913A>G	chr11.hg19:g.85420461T>C	ENSP00000431701:p.Tyr638Cys	97.0	0.0		92.0	4.0	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	hg19	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.508725	0.85282	.	.	ENSG00000137501	ENST00000389960;ENST00000359152;ENST00000354566;ENST00000316356;ENST00000525702;ENST00000525423;ENST00000529581;ENST00000389958;ENST00000530351;ENST00000528231;ENST00000533892;ENST00000527523;ENST00000524452;ENST00000527794;ENST00000529534;ENST00000534414;ENST00000526999	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71	5.99	5.99	0.97316	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.50820	0.1638	H	0.94698	3.57	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	T	0.65175	-0.6232	9	.	.	.	-15.6856	16.4943	0.84223	0.0:0.0:0.0:1.0	.	606;614;638;639;456;936;960;976;69;40	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15;Q9HCH5-11;Q9HCH5-7;Q9HCH5-8;Q9HCH5-9;Q9HCH5-4	.;.;SYTL2_HUMAN;.;.;.;.;.;.;.	C	614;1484;976;639;80;960;80;69;355;638;40;606;614;40;80;133;80	ENSP00000374610:Y614C;ENSP00000352065:Y1484C;ENSP00000346576:Y976C;ENSP00000318803:Y639C;ENSP00000432996:Y80C;ENSP00000432694:Y960C;ENSP00000435855:Y80C;ENSP00000374608:Y69C;ENSP00000435009:Y355C;ENSP00000431701:Y638C;ENSP00000432144:Y40C;ENSP00000434010:Y606C;ENSP00000435238:Y614C;ENSP00000437005:Y40C;ENSP00000432137:Y80C;ENSP00000434111:Y80C	.	Y	-	2	0	SYTL2	85098109	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.040000	0.89188	2.291000	0.77112	0.533000	0.62120	TAT	.	.		0.408	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		C	85420461	T	C	85420461	3	2	65	1	0	0	0	0	1	0	0	0	15498	1406	49	2	919	2	SYTL2	11	85420461	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2435574	85420461	49586055	262	8335										
KDM4D	55693	hgsc.bcm.edu	37	chr11	94731384	94731384	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctatggctaccatgctggctTcaaccatggtttcaactgcg	9	12	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:94731384T>C	ENST00000335080.5	+	3	1680	c.848T>C	c.(847-849)tTc>tCc	p.F283S	KDM4D_ENST00000536741.1_Missense_Mutation_p.F283S	NM_018039.2	NP_060509.2	Q6B0I6	KDM4D_HUMAN	lysine (K)-specific demethylase 4D	283	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(16)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CATGCTGGCTTCAACCATGGT	0.512																																					p.F283S		Atlas-SNP	.											.	KDM4D	58	.	0			c.T848C						.						67	71	70					11																	94731384		2201	4298	6499	SO:0001583	missense	55693	exon3			CTGGCTTCAACCA	AK001113	CCDS8302.1	11q21	2012-03-28	2009-04-06	2009-04-06	ENSG00000186280	ENSG00000186280		"Chromatin-modifying enzymes / K-demethylases"	25498	protein-coding gene	gene with protein product		609766	"jumonji domain containing 2D"	JMJD2D		15138608	Standard	NM_018039		Approved	FLJ10251	uc001pfe.3	Q6B0I6	OTTHUMG00000167838	ENST00000335080.5:c.848T>C	chr11.hg19:g.94731384T>C	ENSP00000334181:p.Phe283Ser	107.0	0.0		85.0	5.0	NM_018039	B3KPC4|Q0VF39|Q9NT41|Q9NW76	Missense_Mutation	SNP	ENST00000335080.5	hg19	CCDS8302.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.945705	0.53079	.	.	ENSG00000186280	ENST00000335080	T	0.74632	-0.86	3.73	3.73	0.42828	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.64402	U	0.000001	D	0.89248	0.6661	H	0.96365	3.81	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.91411	0.5151	10	0.87932	D	0	-19.0431	11.0593	0.47938	0.0:0.0:0.0:1.0	.	283	Q6B0I6	KDM4D_HUMAN	S	283	ENSP00000334181:F283S	ENSP00000334181:F283S	F	+	2	0	KDM4D	94371032	1.000000	0.71417	1.000000	0.80357	0.209000	0.24338	7.564000	0.82326	1.937000	0.56155	0.379000	0.24179	TTC	.	.		0.512	KDM4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396558.2	NM_018039		C	94731384	T	C	94731384	3	2	65	1	0	0	0	0	1	0	0	0	8140	1783	62	2	850	2	KDM4D	11	94731384	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	9310923	94731384	40275132	263	8336										
MMP10	4319	hgsc.bcm.edu	37	chr11	102641564	102641564	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tactctttaatatgtgtgtcAccatcctggcattggggtca	9	9	3	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:102641564A>G	ENST00000279441.4	-	10	1427	c.1391T>C	c.(1390-1392)gTg>gCg	p.V464A		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	464					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	TATGTGTGTCACCATCCTGGC	0.353																																					p.V464A		Atlas-SNP	.											.	MMP10	44	.	0			c.T1391C						.						129	112	118					11																	102641564		2203	4299	6502	SO:0001583	missense	4319	exon10			TGTGTCACCATCC	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"matrix metalloproteinase 10 (stromelysin 2)"	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.1391T>C	chr11.hg19:g.102641564A>G	ENSP00000279441:p.Val464Ala	88.0	0.0		96.0	4.0	NM_002425	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	hg19	CCDS8321.1	.	.	.	.	.	.	.	.	.	.	A	13.28	2.188904	0.38707	.	.	ENSG00000166670	ENST00000279441	T	0.02579	4.24	3.96	3.96	0.45880	Hemopexin/matrixin (2);	0.000000	0.33401	U	0.004956	T	0.17323	0.0416	M	0.88377	2.95	0.20196	N	0.999925	D	0.89917	1.0	D	0.87578	0.998	T	0.02417	-1.1162	10	0.87932	D	0	.	12.4759	0.55814	1.0:0.0:0.0:0.0	.	464	P09238	MMP10_HUMAN	A	464	ENSP00000279441:V464A	ENSP00000279441:V464A	V	-	2	0	MMP10	102146774	0.418000	0.25440	0.637000	0.29366	0.006000	0.05464	5.560000	0.67332	1.766000	0.52107	0.533000	0.62120	GTG	.	.		0.353	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1			G	102641564	A	G	102641564	3	3	65	1	0	0	0	0	1	0	0	0	9658	159	6	2	43	2	MMP10	11	102641564	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	7910180	102641564	32364952	264	8337										
DDI1	414301	hgsc.bcm.edu	37	chr11	103908147	103908147	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agagagcaagagaggcttcgTctctacacagccgacccact	10	13	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:103908147T>C	ENST00000302259.3	+	1	840	c.597T>C	c.(595-597)cgT>cgC	p.R199R	PDGFD_ENST00000302251.5_Intron|PDGFD_ENST00000393158.2_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	199							aspartic-type endopeptidase activity (GO:0004190)			central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		AGAGGCTTCGTCTCTACACAG	0.512																																					p.R199R		Atlas-SNP	.											DDI1_ENST00000302259,colon,carcinoma,+2,2	DDI1	222	.	0			c.T597C						.						63	70	67					11																	103908147		2202	4299	6501	SO:0001819	synonymous_variant	414301	exon1			GCTTCGTCTCTAC		CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.597T>C	chr11.hg19:g.103908147T>C		68.0	0.0		64.0	3.0	NM_001001711	Q7Z4U6|Q8WTS3	Silent	SNP	ENST00000302259.3	hg19	CCDS31660.1																																																																																			.	.		0.512	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711		C	103908147	T	C	103908147	2	2	65	1	0	0	0	0	0	0	0	1	4330	1654	58	2		2	DDI1	11	103908147	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1266583	103908147	31098369	265	8338										
ATM	472	hgsc.bcm.edu	37	chr11	108138031	108138031	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttaccctgatagtagtgttaGtgatgcaaacgaacctggag	11	7	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:108138031G>C	ENST00000452508.2	+	18	2789	c.2600G>C	c.(2599-2601)aGt>aCt	p.S867T	AP001925.1_ENST00000596081.1_5'Flank|ATM_ENST00000278616.4_Missense_Mutation_p.S867T			Q13315	ATM_HUMAN	ATM serine/threonine kinase	867					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	AGTAGTGTTAGTGATGCAAAC	0.353			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.S867T		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.G2600C						.						109	102	104					11																	108138031		2201	4298	6499	SO:0001583	missense	472	exon17	Familial Cancer Database	AT, Louis-Bar syndrome	GTGTTAGTGATGC	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2600G>C	chr11.hg19:g.108138031G>C	ENSP00000388058:p.Ser867Thr	124.0	0.0		68.0	31.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	3.064	-0.192659	0.06259	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.71934	-0.61;-0.61;-0.61	4.89	-2.89	0.05665	Armadillo-type fold (1);	0.765648	0.13145	N	0.410333	T	0.46405	0.1391	N	0.21448	0.665	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20739	-1.0266	10	0.38643	T	0.18	.	2.0851	0.03644	0.3268:0.2348:0.3338:0.1046	.	867	Q13315	ATM_HUMAN	T	867	ENSP00000435747:S867T;ENSP00000278616:S867T;ENSP00000388058:S867T	ENSP00000278616:S867T	S	+	2	0	ATM	107643241	0.005000	0.15991	0.007000	0.13788	0.003000	0.03518	-0.306000	0.08178	-0.400000	0.07656	-0.469000	0.05056	AGT	.	.		0.353	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108138031	G	C	108138031	3	2	65	1	0	0	0	0	1	0	0	0	1109	1029	36	4	2662	4	ATM	11	108138031	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	4229884	108138031	26868485	266	8339										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117376187	117376187	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	accacgcacgatgagctggcGctcccggctcacggtggcgg	15	15	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:117376187G>A	ENST00000321322.6	-	9	2225	c.2224C>T	c.(2224-2226)Cgc>Tgc	p.R742C	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R472C	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	682	Ig-like C2-type 8.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		ATGAGCTGGCGCTCCCGGCTC	0.602																																					p.R742C		Atlas-SNP	.											DSCAML1,NS,carcinoma,0,1	DSCAML1	286	.	0			c.C2224T						.						81	79	80					11																	117376187		2201	4296	6497	SO:0001583	missense	57453	exon9			GCTGGCGCTCCCG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2224C>T	chr11.hg19:g.117376187G>A	ENSP00000315465:p.Arg742Cys	74.0	0.0		98.0	4.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	G	16.05	3.013066	0.54468	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.66460	-0.21;-0.21	4.91	3.96	0.45880	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.58524	0.2128	N	0.02539	-0.55	0.80722	D	1	D	0.76494	0.999	D	0.67725	0.953	T	0.68432	-0.5410	9	0.56958	D	0.05	.	12.2131	0.54391	0.0:0.0:0.69:0.31	.	682	Q8TD84	DSCL1_HUMAN	C	472;742;449	ENSP00000434335:R472C;ENSP00000315465:R742C	ENSP00000315465:R742C	R	-	1	0	DSCAML1	116881397	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.256000	0.51492	1.213000	0.43380	0.491000	0.48974	CGC	.	.		0.602	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		A	117376187	G	A	117376187	3	1	65	1	0	0	0	0	1	0	0	0	4771	1087	38	1	4217	1	DSCAML1	11	117376187	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	9238156	117376187	17630329	267	8340										
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134072727	134072727	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atacctccagatccaactgtTtcaccactgctgtctatgtt	5	13	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr11:134072727T>C	ENST00000534548.2	-	13	1663	c.1599A>G	c.(1597-1599)gaA>gaG	p.E533E		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	533					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		ATCCAACTGTTTCACCACTGC	0.388																																					p.E533E		Atlas-SNP	.											.	NCAPD3	141	.	0			c.A1599G						.						162	151	155					11																	134072727		2201	4297	6498	SO:0001819	synonymous_variant	23310	exon13			AACTGTTTCACCA	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.1599A>G	chr11.hg19:g.134072727T>C		142.0	0.0		97.0	4.0	NM_015261	A6NFS2|Q4KMQ9	Silent	SNP	ENST00000534548.2	hg19	CCDS31723.1																																																																																			.	.		0.388	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		C	134072727	T	C	134072727	2	2	65	1	0	0	0	0	0	0	0	1	10215	1838	64	2		2	NCAPD3	11	134072727	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	16696540	134072727	933789	268	8341										
TEAD4	7004	hgsc.bcm.edu	37	chr12	3128294	3128294	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cccgcagtgtgaagcctttcTctcagcaaacctatgctgtc	8	14	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:3128294T>C	ENST00000397122.2	+	6	439	c.154T>C	c.(154-156)Tct>Cct	p.S52P	TEAD4_ENST00000359864.2_Missense_Mutation_p.S181P|TEAD4_ENST00000358409.2_Missense_Mutation_p.S138P	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4	181					gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			GAAGCCTTTCTCTCAGCAAAC	0.657																																					p.S181P		Atlas-SNP	.											.	TEAD4	45	.	0			c.T541C						.						105	87	93					12																	3128294		2203	4300	6503	SO:0001583	missense	7004	exon8			CCTTTCTCTCAGC	X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561		ENST00000397122.2:c.154T>C	chr12.hg19:g.3128294T>C	ENSP00000380311:p.Ser52Pro	120.0	0.0		93.0	4.0	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Missense_Mutation	SNP	ENST00000397122.2	hg19	CCDS41737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.89|12.89	2.072748|2.072748	0.36566|0.36566	.|.	.|.	ENSG00000197905|ENSG00000197905	ENST00000544666|ENST00000358409;ENST00000359864;ENST00000397122	.|T;T;T	.|0.31247	.|1.5;1.5;1.5	5.0|5.0	5.0|5.0	0.66597|0.66597	.|.	.|0.065251	.|0.64402	.|D	.|0.000006	T|T	0.33818|0.33818	0.0876|0.0876	L|L	0.51422|0.51422	1.61|1.61	0.49798|0.49798	D|D	0.999824|0.999824	.|P	.|0.35242	.|0.492	.|P	.|0.44732	.|0.459	T|T	0.18335|0.18335	-1.0340|-1.0340	5|10	.|0.46703	.|T	.|0.11	-14.8685|-14.8685	6.854|6.854	0.24030|0.24030	0.1481:0.0:0.1539:0.698|0.1481:0.0:0.1539:0.698	.|.	.|181	.|Q15561	.|TEAD4_HUMAN	P|P	103|138;181;52	.|ENSP00000351184:S138P;ENSP00000352926:S181P;ENSP00000380311:S52P	.|ENSP00000351184:S138P	L|S	+|+	2|1	0|0	TEAD4|TEAD4	2998555|2998555	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	2.763000|2.763000	0.47605|0.47605	1.876000|1.876000	0.54355|0.54355	0.459000|0.459000	0.35465|0.35465	CTC|TCT	.	.		0.657	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213		C	3128294	T	C	3128294	3	2	65	1	0	0	0	0	1	0	0	0	15756	1551	54	2	563	2	TEAD4	12	3128294	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		3128294	130723601	269	8342										
PZP	5858	hgsc.bcm.edu	37	chr12	9334596	9334596	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tggctagacagttttcaatcTcaaatttttcagagtctcca	6	9	4	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:9334596T>C	ENST00000261336.2	-	14	1692	c.1664A>G	c.(1663-1665)gAg>gGg	p.E555G	PZP_ENST00000381997.2_Missense_Mutation_p.E424G	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	555					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.S420_E426delSEKFEIE(1)|p.S551_E557delSEKFEIE(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GTTTTCAATCTCAAATTTTTC	0.388																																					p.E555G	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	2	Deletion - In frame(2)	prostate(2)	c.A1664G						.						55	57	57					12																	9334596		2203	4300	6503	SO:0001583	missense	5858	exon14			TCAATCTCAAATT	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.1664A>G	chr12.hg19:g.9334596T>C	ENSP00000261336:p.Glu555Gly	132.0	0.0		123.0	6.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	11.04	1.522000	0.27211	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.64438	-0.1;-0.1	3.94	2.68	0.31781	Alpha-2-macroglobulin, N-terminal 2 (1);	0.302961	0.26207	U	0.025715	T	0.68979	0.3060	M	0.86805	2.84	0.09310	N	1	P;P	0.45768	0.866;0.866	P;P	0.48598	0.583;0.507	T	0.62859	-0.6765	10	0.54805	T	0.06	.	7.6612	0.28404	0.0:0.0:0.2127:0.7873	.	424;555	P20742-2;P20742	.;PZP_HUMAN	G	555;424	ENSP00000261336:E555G;ENSP00000371427:E424G	ENSP00000261336:E555G	E	-	2	0	PZP	9225863	0.302000	0.24454	0.109000	0.21407	0.020000	0.10135	3.846000	0.55888	1.580000	0.49851	0.383000	0.25322	GAG	.	.		0.388	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		C	9334596	T	C	9334596	3	2	65	1	0	0	0	0	1	0	0	0	12884	1551	54	2	2876	2	PZP	12	9334596	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6206302	9334596	124517299	270	8343										
EPS8	2059	hgsc.bcm.edu	37	chr12	15774278	15774278	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgcttccttcatcaaaagaTtccactcctgaatcactagc	4	14	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:15774278T>C	ENST00000281172.5	-	21	2878	c.2442A>G	c.(2440-2442)gaA>gaG	p.E814E	EPS8_ENST00000543612.1_Silent_p.E814E|EPS8_ENST00000543523.1_Silent_p.E814E|EPS8_ENST00000542903.1_Silent_p.E554E|EPS8_ENST00000540613.1_Silent_p.E554E	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	814	Effector region. {ECO:0000250}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		CATCAAAAGATTCCACTCCTG	0.378																																					p.E814E		Atlas-SNP	.											.	EPS8	70	.	0			c.A2442G						.						91	84	87					12																	15774278		2202	4300	6502	SO:0001819	synonymous_variant	2059	exon21			AAAAGATTCCACT	U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.2442A>G	chr12.hg19:g.15774278T>C		64.0	0.0		67.0	6.0	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Silent	SNP	ENST00000281172.5	hg19	CCDS31753.1																																																																																			.	.		0.378	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			C	15774278	T	C	15774278	2	2	65	1	0	0	0	0	0	0	0	1	5196	1490	52	2		2	EPS8	12	15774278	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6439682	15774278	118077617	271	8344										
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21392086	21392086	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aaataaaaataaacattttgTcccttctgctggggcagata	7	7	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:21392086T>C	ENST00000256958.2	+	15	2135	c.2039T>C	c.(2038-2040)gTc>gCc	p.V680A		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	680					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	AAACATTTTGTCCCTTCTGCT	0.348																																					p.V680A		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.T2039C						.						64	71	69					12																	21392086		2203	4300	6503	SO:0001583	missense	10599	exon15			ATTTTGTCCCTTC		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.2039T>C	chr12.hg19:g.21392086T>C	ENSP00000256958:p.Val680Ala	67.0	0.0		70.0	4.0	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	hg19	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	T	4.563	0.104523	0.08731	.	.	ENSG00000134538	ENST00000256958	T	0.37584	1.19	2.81	1.65	0.23941	.	15.110800	0.00397	N	0.000042	T	0.32102	0.0818	L	0.58101	1.795	0.09310	N	1	B	0.20780	0.048	B	0.16289	0.015	T	0.13098	-1.0522	10	0.08837	T	0.75	.	4.577	0.12238	0.0:0.1577:0.0:0.8423	.	680	Q9Y6L6	SO1B1_HUMAN	A	680	ENSP00000256958:V680A	ENSP00000256958:V680A	V	+	2	0	SLCO1B1	21283353	0.000000	0.05858	0.001000	0.08648	0.096000	0.18686	0.006000	0.13152	0.482000	0.27582	0.260000	0.18958	GTC	.	.		0.348	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		C	21392086	T	C	21392086	3	2	65	1	0	0	0	0	1	0	0	0	14738	1667	58	2	2093	2	SLCO1B1	12	21392086	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	5617808	21392086	112459809	272	8345										
SLCO1A2	6579	hgsc.bcm.edu	37	chr12	21453353	21453353	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cattttcatttttaatgatgTcagcattagtctctagtcct	5	8	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:21453353T>C	ENST00000307378.6	-	9	1559	c.839A>G	c.(838-840)gAc>gGc	p.D280G	SLCO1A2_ENST00000390670.3_Missense_Mutation_p.D278G|SLCO1A2_ENST00000452078.1_Missense_Mutation_p.D280G|SLCO1A2_ENST00000537524.1_Missense_Mutation_p.D148G|SLCO1A2_ENST00000458504.1_Missense_Mutation_p.D148G	NM_134431.3	NP_602307.1	P46721	SO1A2_HUMAN	solute carrier organic anion transporter family, member 1A2	280					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(6)|upper_aerodigestive_tract(1)	48					Aminohippurate(DB00345)|Atorvastatin(DB01076)|Bumetanide(DB00887)|Chlorambucil(DB00291)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Enalapril(DB00584)|Erythromycin(DB00199)|Estradiol(DB00783)|Estriol(DB04573)|Estrone(DB00655)|Fexofenadine(DB00950)|Glyburide(DB01016)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Indinavir(DB00224)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Mirabegron(DB08893)|Naloxone(DB01183)|Naproxen(DB00788)|Nelfinavir(DB00220)|Ouabain(DB01092)|Pravastatin(DB00175)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rocuronium(DB00728)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Simvastatin(DB00641)|Spironolactone(DB00421)|Sumatriptan(DB00669)|Tauroursodeoxycholic acid(DB08834)|Testosterone(DB00624)|Tolbutamide(DB01124)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)	TTTAATGATGTCAGCATTAGT	0.343																																					p.D280G		Atlas-SNP	.											.	SLCO1A2	107	.	0			c.A839G						.						102	100	101					12																	21453353		2203	4300	6503	SO:0001583	missense	6579	exon9			ATGATGTCAGCAT		CCDS8686.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000084453	ENSG00000084453		"Solute carriers"	10956	protein-coding gene	gene with protein product		602883	"solute carrier family 21 (organic anion transporter), member 3"	SLC21A3		9007731	Standard	NM_134431		Approved	OATP, OATP1A2, OATP-A	uc001rer.3	P46721	OTTHUMG00000156259	ENST00000307378.6:c.839A>G	chr12.hg19:g.21453353T>C	ENSP00000305974:p.Asp280Gly	64.0	0.0		44.0	4.0	NM_134431	Q9UGP7|Q9UL38	Missense_Mutation	SNP	ENST00000307378.6	hg19	CCDS8686.1	.	.	.	.	.	.	.	.	.	.	T	13.41	2.229734	0.39399	.	.	ENSG00000084453	ENST00000307378;ENST00000452078;ENST00000458504;ENST00000537524;ENST00000390670	T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.2	5.55	3.14	0.36123	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.575101	0.19124	N	0.122094	T	0.48390	0.1497	L	0.52573	1.65	0.09310	N	0.999999	B;B;B	0.13594	0.003;0.008;0.001	B;B;B	0.13407	0.009;0.009;0.008	T	0.34254	-0.9836	10	0.26408	T	0.33	.	10.3709	0.44053	0.0:0.1365:0.0:0.8635	.	260;278;280	Q8IV69;P46721-2;P46721	.;.;SO1A2_HUMAN	G	280;280;148;148;278	ENSP00000305974:D280G;ENSP00000393973:D280G;ENSP00000394854:D148G;ENSP00000439401:D148G;ENSP00000375088:D278G	ENSP00000305974:D280G	D	-	2	0	SLCO1A2	21344620	0.951000	0.32395	0.023000	0.16930	0.385000	0.30292	2.318000	0.43779	0.924000	0.37069	0.460000	0.39030	GAC	.	.		0.343	SLCO1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343648.3	NM_021094		C	21453353	T	C	21453353	3	2	65	1	0	0	0	0	1	0	0	0	14737	1667	58	2	1205	2	SLCO1A2	12	21453353	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	61267	21453353	112398542	273	8346										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26568256	26568256	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgtaacaggagttcggtttTtcagcctatcaacttccata	7	10	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:26568256T>C	ENST00000381340.3	-	51	7702	c.7286A>G	c.(7285-7287)aAa>aGa	p.K2429R	RP11-513G19.1_ENST00000535324.1_RNA	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	2429					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	AGTTCGGTTTTTCAGCCTATC	0.398																																					p.K2429R		Atlas-SNP	.											.	ITPR2	270	.	0			c.A7286G						.						105	100	102					12																	26568256		1853	4091	5944	SO:0001583	missense	3709	exon51			CGGTTTTTCAGCC	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.7286A>G	chr12.hg19:g.26568256T>C	ENSP00000370744:p.Lys2429Arg	87.0	0.0		100.0	4.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	T	14.14	2.447444	0.43429	.	.	ENSG00000123104	ENST00000381340	D	0.91686	-2.89	5.08	2.6	0.31112	Ion transport (1);	0.128225	0.53938	D	0.000046	D	0.85008	0.5599	N	0.08118	0	0.80722	D	1	P	0.41624	0.757	P	0.50617	0.646	T	0.78663	-0.2116	10	0.16896	T	0.51	.	7.8866	0.29653	0.0:0.0721:0.1374:0.7905	.	2429	Q14571	ITPR2_HUMAN	R	2429	ENSP00000370744:K2429R	ENSP00000370744:K2429R	K	-	2	0	ITPR2	26459523	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.813000	0.48002	0.961000	0.38030	0.482000	0.46254	AAA	.	.		0.398	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		C	26568256	T	C	26568256	3	2	65	1	0	0	0	0	1	0	0	0	7930	1841	64	2	847	2	ITPR2	12	26568256	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	5114903	26568256	107283639	274	8347										
BICD1	636	hgsc.bcm.edu	37	chr12	32369322	32369322	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgcagaacgagctgaaacagAgccgggctgtggtcactaat	13	9	1	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:32369322A>G	ENST00000281474.5	+	2	458	c.355A>G	c.(355-357)Agc>Ggc	p.S119G	BICD1_ENST00000548411.1_Missense_Mutation_p.S119G	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	119					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GCTGAAACAGAGCCGGGCTGT	0.502																																					p.S119G		Atlas-SNP	.											.	BICD1	89	.	0			c.A355G						.						102	94	97					12																	32369322		2203	4300	6503	SO:0001583	missense	636	exon2			AAACAGAGCCGGG	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.355A>G	chr12.hg19:g.32369322A>G	ENSP00000281474:p.Ser119Gly	127.0	0.0		116.0	5.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.347499	0.82022	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	T;T	0.30714	1.52;1.52	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.36413	0.0966	M	0.65975	2.015	0.80722	D	1	B;B	0.31655	0.058;0.334	B;B	0.34038	0.055;0.174	T	0.12142	-1.0559	10	0.35671	T	0.21	.	15.9745	0.80049	1.0:0.0:0.0:0.0	.	119;119	F8W113;Q96G01	.;BICD1_HUMAN	G	119	ENSP00000446793:S119G;ENSP00000281474:S119G	ENSP00000281474:S119G	S	+	1	0	BICD1	32260589	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.310000	0.78947	2.168000	0.68352	0.533000	0.62120	AGC	.	.		0.502	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		G	32369322	A	G	32369322	3	3	65	1	0	0	0	0	1	0	0	0	1428	304	11	2	361	2	BICD1	12	32369322	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	5801066	32369322	101482573	275	8348										
BICD1	636	hgsc.bcm.edu	37	chr12	32520657	32520657	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agtgctcacaactagccgggAggcaagactgcccaactgtc	11	13	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:32520657A>G	ENST00000281474.5	+	9	2921	c.2818A>G	c.(2818-2820)Agg>Ggg	p.R940G	BICD1_ENST00000548411.1_3'UTR	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	940					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			ACTAGCCGGGAGGCAAGACTG	0.512																																					p.R940G		Atlas-SNP	.											.	BICD1	89	.	0			c.A2818G						.						122	105	111					12																	32520657		2203	4300	6503	SO:0001583	missense	636	exon9			GCCGGGAGGCAAG	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.2818A>G	chr12.hg19:g.32520657A>G	ENSP00000281474:p.Arg940Gly	60.0	0.0		73.0	4.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	A	12.17	1.857288	0.32791	.	.	ENSG00000151746	ENST00000281474	T	0.46063	0.88	5.25	4.1	0.47936	.	0.132974	0.34676	N	0.003777	T	0.18045	0.0433	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06250	-1.0837	10	0.11794	T	0.64	.	5.2631	0.15584	0.6824:0.1511:0.1665:0.0	.	940	Q96G01	BICD1_HUMAN	G	940	ENSP00000281474:R940G	ENSP00000281474:R940G	R	+	1	2	BICD1	32411924	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.404000	0.52623	0.830000	0.34757	0.482000	0.46254	AGG	.	.		0.512	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		G	32520657	A	G	32520657	3	3	65	1	0	0	0	0	1	0	0	0	1428	295	11	2	2852	2	BICD1	12	32520657	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	151335	32520657	101331238	276	8349										
RACGAP1	29127	hgsc.bcm.edu	37	chr12	50384062	50384062	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gatgtgacttcacttgagcaTtggagaagcaaaaaagttgc	11	6	1	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:50384062T>C	ENST00000427314.2	-	19	2111	c.1888A>G	c.(1888-1890)Atg>Gtg	p.M630V	RACGAP1_ENST00000551016.1_Missense_Mutation_p.M630V|RACGAP1_ENST00000434422.1_Missense_Mutation_p.M630V|RACGAP1_ENST00000454520.2_Missense_Mutation_p.M630V|RACGAP1_ENST00000548961.1_Intron|RACGAP1_ENST00000312377.5_Missense_Mutation_p.M630V|RACGAP1_ENST00000547905.1_Missense_Mutation_p.M630V	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						CACTTGAGCATTGGAGAAGCA	0.418																																					p.M630V		Atlas-SNP	.											.	RACGAP1	36	.	0			c.A1888G						.						131	116	121					12																	50384062		2203	4300	6503	SO:0001583	missense	29127	exon19			TGAGCATTGGAGA		CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000427314.2:c.1888A>G	chr12.hg19:g.50384062T>C	ENSP00000404190:p.Met630Val	83.0	0.0		75.0	5.0	NM_013277		Missense_Mutation	SNP	ENST00000427314.2	hg19	CCDS8795.1	.	.	.	.	.	.	.	.	.	.	t	9.144	1.014630	0.19355	.	.	ENSG00000161800	ENST00000427314;ENST00000312377;ENST00000434422;ENST00000454520;ENST00000551016;ENST00000547905	T;T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87;1.87	4.69	0.658	0.17855	.	0.798245	0.12112	N	0.498426	T	0.17195	0.0413	L	0.44542	1.39	0.18873	N	0.999988	B	0.02656	0.0	B	0.01281	0.0	T	0.27536	-1.0071	10	0.34782	T	0.22	-0.931	2.2851	0.04124	0.3809:0.0725:0.1246:0.422	.	630	Q9H0H5	RGAP1_HUMAN	V	630	ENSP00000404190:M630V;ENSP00000309871:M630V;ENSP00000413241:M630V;ENSP00000404808:M630V;ENSP00000449374:M630V;ENSP00000449370:M630V	ENSP00000309871:M630V	M	-	1	0	RACGAP1	48670329	0.254000	0.23992	0.983000	0.44433	0.912000	0.54170	0.312000	0.19397	-0.073000	0.12842	-0.364000	0.07487	ATG	.	.		0.418	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277		C	50384062	T	C	50384062	3	2	65	1	0	0	0	0	1	0	0	0	12992	1493	52	2	14	2	RACGAP1	12	50384062	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	17863405	50384062	83467833	277	8350										
OR10A7	121364	hgsc.bcm.edu	37	chr12	55614885	55614885	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caaccccgagatgcaagtttCcctctttatttttttcctgg	6	12	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:55614885C>A	ENST00000326258.1	+	1	77	c.77C>A	c.(76-78)tCc>tAc	p.S26Y		NM_001005280.1	NP_001005280.1	Q8NGE5	O10A7_HUMAN	olfactory receptor, family 10, subfamily A, member 7	26						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|lung(11)|ovary(4)|prostate(2)|skin(3)	24						ATGCAAGTTTCCCTCTTTATT	0.383																																					p.S26Y		Atlas-SNP	.											.	OR10A7	53	.	0			c.C77A						.						221	227	225					12																	55614885		2203	4300	6503	SO:0001583	missense	121364	exon1			AAGTTTCCCTCTT	BK004327	CCDS31815.1	12q13.13	2012-08-09				ENSG00000179919		"GPCR / Class A : Olfactory receptors"	15329	protein-coding gene	gene with protein product							Standard	NM_001005280		Approved		uc010spf.2	Q8NGE5	OTTHUMG00000169860	ENST00000326258.1:c.77C>A	chr12.hg19:g.55614885C>A	ENSP00000326718:p.Ser26Tyr	263.0	1.0		176.0	82.0	NM_001005280	Q6IFD5|Q96R19	Missense_Mutation	SNP	ENST00000326258.1	hg19	CCDS31815.1	.	.	.	.	.	.	.	.	.	.	c	7.565	0.665485	0.14710	.	.	ENSG00000179919	ENST00000326258	T	0.00433	7.43	2.91	2.01	0.26516	.	0.396182	0.18651	N	0.134993	T	0.00241	0.0007	N	0.22421	0.69	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.38520	-0.9657	10	0.38643	T	0.18	.	6.4416	0.21853	0.0:0.6947:0.0:0.3053	.	26	Q8NGE5	O10A7_HUMAN	Y	26	ENSP00000326718:S26Y	ENSP00000326718:S26Y	S	+	2	0	OR10A7	53901152	0.000000	0.05858	0.079000	0.20413	0.961000	0.63080	-0.565000	0.05929	0.797000	0.33971	0.637000	0.83480	TCC	.	.		0.383	OR10A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406308.1			A	55614885	C	A	55614885	3	1	65	1	0	0	0	0	1	0	0	0	10904	855	30	3	79	3	OR10A7	12	55614885	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	5230823	55614885	78237010	278	8351										
MARS	4141	hgsc.bcm.edu	37	chr12	57905511	57905511	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gactggaggagtggttggggAggacattgcctggcagtgac	19	6	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:57905511A>G	ENST00000262027.5	+	12	1533	c.1399A>G	c.(1399-1401)Agg>Ggg	p.R467G	RN7SL312P_ENST00000582079.1_RNA|MARS_ENST00000447721.2_3'UTR|RNU6-594P_ENST00000517056.1_RNA|MARS_ENST00000315473.5_Missense_Mutation_p.R233G	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	467					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	GTGGTTGGGGAGGACATTGCC	0.507																																					p.R467G		Atlas-SNP	.											.	MARS	84	.	0			c.A1399G						.						133	113	119					12																	57905511		2203	4300	6503	SO:0001583	missense	4141	exon12			TTGGGGAGGACAT	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.1399A>G	chr12.hg19:g.57905511A>G	ENSP00000262027:p.Arg467Gly	101.0	0.0		124.0	5.0	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	hg19	CCDS8942.1	.	.	.	.	.	.	.	.	.	.	A	14.46	2.540758	0.45280	.	.	ENSG00000166986	ENST00000262027;ENST00000315473	T;T	0.44482	1.5;0.92	5.1	5.1	0.69264	Aminoacyl-tRNA synthetase, class I (M) (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.145183	0.64402	D	0.000011	T	0.20047	0.0482	N	0.02973	-0.45	0.29710	N	0.839494	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.09058	-1.0692	10	0.42905	T	0.14	-10.2481	10.7769	0.46354	0.8411:0.1589:0.0:0.0	.	233;340;467	A6NC17;B4E0E9;P56192	.;.;SYMC_HUMAN	G	467;233	ENSP00000262027:R467G;ENSP00000314653:R233G	ENSP00000262027:R467G	R	+	1	2	MARS	56191778	0.997000	0.39634	0.933000	0.37362	0.970000	0.65996	2.242000	0.43106	2.053000	0.61076	0.402000	0.26972	AGG	.	.		0.507	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		G	57905511	A	G	57905511	3	3	65	1	0	0	0	0	1	0	0	0	9325	295	11	2	1445	2	MARS	12	57905511	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2290626	57905511	75946384	279	8352										
LRIG3	121227	hgsc.bcm.edu	37	chr12	59274407	59274407	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cagagtaggatgaaccaaagTgattggagatgacacactga	12	6	0	6			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:59274407T>C	ENST00000320743.3	-	13	2043	c.1757A>G	c.(1756-1758)cAc>cGc	p.H586R	LRIG3_ENST00000379141.4_Missense_Mutation_p.H526R	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	586	Ig-like C2-type 1.				otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			TGAACCAAAGTGATTGGAGAT	0.448			T	ROS1	NSCLC																																p.H586R		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.A1757G						.						72	67	69					12																	59274407		2203	4300	6503	SO:0001583	missense	121227	exon13			CCAAAGTGATTGG	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.1757A>G	chr12.hg19:g.59274407T>C	ENSP00000326759:p.His586Arg	135.0	0.0		119.0	5.0	NM_153377	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	hg19	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.073961	0.76415	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.65549	-0.16;-0.16	6.04	6.04	0.98038	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.39083	N	0.001467	T	0.70649	0.3248	L	0.37507	1.11	0.58432	D	0.999998	P;D	0.64830	0.881;0.994	P;D	0.68353	0.874;0.957	T	0.68454	-0.5404	9	.	.	.	.	16.5763	0.84648	0.0:0.0:0.0:1.0	.	526;586	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	R	526;586	ENSP00000368436:H526R;ENSP00000326759:H586R	.	H	-	2	0	LRIG3	57560674	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.075000	0.71261	2.317000	0.78254	0.459000	0.35465	CAC	.	.		0.448	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		C	59274407	T	C	59274407	3	2	65	1	0	0	0	0	1	0	0	0	8955	1696	59	2	1630	2	LRIG3	12	59274407	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1368896	59274407	74577488	280	8353										
LRIG3	121227	hgsc.bcm.edu	37	chr12	59276667	59276667	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcaccacacacaaagccatcTgggctaacagcaaaaatgct	6	13	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:59276667T>C	ENST00000320743.3	-	12	1750	c.1464A>G	c.(1462-1464)ccA>ccG	p.P488P	LRIG3_ENST00000379141.4_Silent_p.P428P	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	488	LRRCT.				otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P488P(1)	LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			CAAAGCCATCTGGGCTAACAG	0.413			T	ROS1	NSCLC																																p.P488P		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	LRIG3,NS,carcinoma,0,1	LRIG3	120	.	1	Substitution - coding silent(1)	kidney(1)	c.A1464G						.						90	84	86					12																	59276667		2203	4300	6503	SO:0001819	synonymous_variant	121227	exon12			GCCATCTGGGCTA	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.1464A>G	chr12.hg19:g.59276667T>C		69.0	0.0		72.0	3.0	NM_153377	Q6UXL7|Q8NC72	Silent	SNP	ENST00000320743.3	hg19	CCDS8960.1																																																																																			.	.		0.413	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		C	59276667	T	C	59276667	2	2	65	1	0	0	0	0	0	0	0	1	8955	1567	55	2		2	LRIG3	12	59276667	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2260	59276667	74575228	281	8354										
TMBIM4	51643	hgsc.bcm.edu	37	chr12	66531841	66531841	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	taatacgtactcttcaggtgAcagtttatgcatcagtgagt	9	7	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:66531841A>G	ENST00000358230.3	-	7	736	c.616T>C	c.(616-618)Tca>Cca	p.S206P	TMBIM4_ENST00000542724.1_Missense_Mutation_p.S175P|TMBIM4_ENST00000398033.4_3'UTR|TMBIM4_ENST00000539652.1_3'UTR|TMBIM4_ENST00000556010.1_3'UTR|TMBIM4_ENST00000286424.7_Missense_Mutation_p.S253P|TMBIM4_ENST00000544599.1_Missense_Mutation_p.S29P	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	206					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|regulation of calcium-mediated signaling (GO:0050848)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		TCTTCAGGTGACAGTTTATGC	0.413																																					p.S206P		Atlas-SNP	.											.	TMBIM4	47	.	0			c.T616C						.						123	120	121					12																	66531841		1946	4151	6097	SO:0001583	missense	51643	exon7			CAGGTGACAGTTT	AF113127	CCDS41805.1, CCDS61187.1, CCDS73493.1	12q14.3	2014-05-09			ENSG00000155957	ENSG00000155957			24257	protein-coding gene	gene with protein product						11042152, 10810093	Standard	NM_001282609		Approved	CGI-119, S1R, ZPRO, LFG4, GAAP	uc001stc.3	Q9HC24	OTTHUMG00000168973	ENST00000358230.3:c.616T>C	chr12.hg19:g.66531841A>G	ENSP00000350965:p.Ser206Pro	114.0	0.0		81.0	4.0	NM_016056	Q542Z6|Q9UHY5|Q9Y3C2	Missense_Mutation	SNP	ENST00000358230.3	hg19	CCDS41805.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.928131	0.92389	.	.	ENSG00000155957	ENST00000358230;ENST00000544599;ENST00000286424;ENST00000539043;ENST00000539427;ENST00000542724	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.70245	0.3202	M	0.87097	2.86	0.80722	D	1	P;D;D	0.89917	0.746;1.0;1.0	P;D;D	0.97110	0.561;1.0;1.0	T	0.74515	-0.3640	9	.	.	.	-11.1003	16.8222	0.85835	1.0:0.0:0.0:0.0	.	253;175;206	G3XAA5;G3V1M2;Q9HC24	.;.;TMBI4_HUMAN	P	206;29;253;206;251;175	ENSP00000350965:S206P;ENSP00000444639:S29P;ENSP00000286424:S253P;ENSP00000441291:S175P	.	S	-	1	0	TMBIM4	64818108	1.000000	0.71417	0.943000	0.38184	0.988000	0.76386	8.222000	0.89777	2.371000	0.80710	0.533000	0.62120	TCA	.	.		0.413	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056		G	66531841	A	G	66531841	3	3	65	1	0	0	0	0	1	0	0	0	15997	275	10	2	104	2	TMBIM4	12	66531841	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	7255174	66531841	67320054	282	8355										
CPSF6	11052	hgsc.bcm.edu	37	chr12	69644987	69644987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgcaaataatggagatgccCcagaagaccgagattacatg	10	9	0	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:69644987C>T	ENST00000435070.2	+	2	249	c.139C>T	c.(139-141)Cca>Tca	p.P47S	CPSF6_ENST00000456847.3_Missense_Mutation_p.P47S|CPSF6_ENST00000266679.8_Missense_Mutation_p.P47S|CPSF6_ENST00000551516.1_Intron|CPSF6_ENST00000550987.1_3'UTR	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa	47					mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(7)|lung(8)	16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			TGGAGATGCCCCAGAAGACCG	0.423																																					p.P47S		Atlas-SNP	.											.	CPSF6	96	.	0			c.C139T						.						87	76	80					12																	69644987		2203	4300	6503	SO:0001583	missense	11052	exon2			GATGCCCCAGAAG	X67336	CCDS8988.1, CCDS73494.1	12q15	2013-06-18	2002-08-29			ENSG00000111605		"RNA binding motif (RRM) containing"	13871	protein-coding gene	gene with protein product	"cleavage factor Im complex 68 kDa subunit"	604979	"cleavage and polyadenylation specific factor 6, 68kD subunit"			9659921, 17267687	Standard	NM_007007		Approved	CFIM, HPBRII-4, HPBRII-7, CFIM68	uc001sut.4	Q16630		ENST00000435070.2:c.139C>T	chr12.hg19:g.69644987C>T	ENSP00000391774:p.Pro47Ser	89.0	0.0		69.0	4.0	NM_007007	A8K7K9|Q53ES1|Q9BSJ7|Q9BW18	Missense_Mutation	SNP	ENST00000435070.2	hg19	CCDS8988.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.334606	0.81801	.	.	ENSG00000111605	ENST00000435070;ENST00000456847;ENST00000266679	.	.	.	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.49440	0.1557	L	0.38531	1.155	0.80722	D	1	P;B	0.38167	0.621;0.244	B;B	0.36845	0.234;0.18	T	0.47018	-0.9149	8	.	.	.	-5.016	18.5948	0.91226	0.0:1.0:0.0:0.0	.	47;47	Q16630-2;Q16630	.;CPSF6_HUMAN	S	47	.	.	P	+	1	0	CPSF6	67931254	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.440000	0.80464	2.558000	0.86282	0.563000	0.77884	CCA	.	.		0.423	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	NM_007007		T	69644987	C	T	69644987	3	4	65	1	0	0	0	0	1	0	0	0	3831	623	22	3	145	3	CPSF6	12	69644987	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	3113146	69644987	64206908	283	8356										
CNOT2	4848	hgsc.bcm.edu	37	chr12	70724192	70724192	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tagccccaacagaagctcgcCaagcataatatgtatgccaa	7	12	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:70724192C>A	ENST00000418359.3	+	7	963	c.512C>A	c.(511-513)cCa>cAa	p.P171Q	CNOT2_ENST00000548230.1_3'UTR|CNOT2_ENST00000229195.3_Missense_Mutation_p.P171Q	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	171					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription corepressor binding (GO:0001226)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(2)|urinary_tract(1)	20	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			AGAAGCTCGCCAAGCATAATA	0.443																																					p.P171Q		Atlas-SNP	.											.	CNOT2	53	.	0			c.C512A						.						147	138	141					12																	70724192		2203	4300	6503	SO:0001583	missense	4848	exon7			GCTCGCCAAGCAT	AF180473	CCDS31857.1	12q15	2008-05-14				ENSG00000111596			7878	protein-coding gene	gene with protein product		604909		NOT2		10637334	Standard	NM_014515		Approved	CDC36, NOT2H	uc001svv.3	Q9NZN8		ENST00000418359.3:c.512C>A	chr12.hg19:g.70724192C>A	ENSP00000412091:p.Pro171Gln	199.0	0.0		126.0	70.0	NM_001199302	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Missense_Mutation	SNP	ENST00000418359.3	hg19	CCDS31857.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630056	0.67015	.	.	ENSG00000111596	ENST00000552231;ENST00000229195;ENST00000418359;ENST00000550641;ENST00000548159;ENST00000549750;ENST00000551043;ENST00000551873;ENST00000550194	T;T;T;T	0.44083	0.93;0.93;0.94;0.93	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.54679	0.1873	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.39418	-0.9615	10	0.21014	T	0.42	-5.4664	19.8769	0.96880	0.0:1.0:0.0:0.0	.	171	Q9NZN8	CNOT2_HUMAN	Q	171;171;171;151;162;171;171;86;171	ENSP00000229195:P171Q;ENSP00000412091:P171Q;ENSP00000449659:P162Q;ENSP00000449260:P171Q	ENSP00000229195:P171Q	P	+	2	0	CNOT2	69010459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.767000	0.95098	0.557000	0.71058	CCA	.	.		0.443	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404260.1			A	70724192	C	A	70724192	3	1	65	1	0	0	0	0	1	0	0	0	3621	594	21	3	530	3	CNOT2	12	70724192	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	1079205	70724192	63127703	284	8357										
NAV3	89795	hgsc.bcm.edu	37	chr12	78388596	78388596	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	catacagtctggcagccagaTatgcaactcagtctaatcac	7	12	4	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:78388596T>C	ENST00000397909.2	+	6	858	c.685T>C	c.(685-687)Tat>Cat	p.Y229H	NAV3_ENST00000228327.6_Missense_Mutation_p.Y229H|NAV3_ENST00000536525.2_Missense_Mutation_p.Y229H|NAV3_ENST00000266692.7_Missense_Mutation_p.Y229H			Q8IVL0	NAV3_HUMAN	neuron navigator 3	229						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GGCAGCCAGATATGCAACTCA	0.338										HNSCC(70;0.22)																											p.Y229H		Atlas-SNP	.											.	NAV3	506	.	0			c.T685C						.						134	126	128					12																	78388596		1829	4106	5935	SO:0001583	missense	89795	exon6			GCCAGATATGCAA	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.685T>C	chr12.hg19:g.78388596T>C	ENSP00000381007:p.Tyr229His	89.0	0.0		56.0	4.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	T	15.81	2.943815	0.53079	.	.	ENSG00000067798	ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.95	5.95	0.96441	.	0.465406	0.15758	U	0.246047	T	0.49338	0.1551	N	0.19112	0.55	0.80722	D	1	P;D	0.89917	0.664;1.0	B;D	0.85130	0.347;0.997	T	0.33523	-0.9865	10	0.15952	T	0.53	-16.1262	16.4237	0.83790	0.0:0.0:0.0:1.0	.	229;229	Q8IVL0;Q8IVL0-2	NAV3_HUMAN;.	H	229	ENSP00000446628:Y229H;ENSP00000446132:Y229H;ENSP00000381007:Y229H;ENSP00000228327:Y229H;ENSP00000266692:Y229H	ENSP00000228327:Y229H	Y	+	1	0	NAV3	76912727	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.347000	0.65998	2.279000	0.76181	0.533000	0.62120	TAT	.	.		0.338	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		C	78388596	T	C	78388596	3	2	65	1	0	0	0	0	1	0	0	0	10194	1406	49	2	707	2	NAV3	12	78388596	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	7664404	78388596	55463299	285	8358										
PPP1R12A	4659	hgsc.bcm.edu	37	chr12	80191131	80191131	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gttcgggtagaacgacttctTcctattgttttctcagcttc	8	10	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:80191131T>C	ENST00000450142.2	-	16	2402	c.2136A>G	c.(2134-2136)ggA>ggG	p.G712G	PPP1R12A_ENST00000261207.5_Silent_p.G712G|PPP1R12A_ENST00000437004.2_Silent_p.G712G|PPP1R12A_ENST00000546369.1_Silent_p.G625G|PPP1R12A_ENST00000550107.1_Silent_p.G656G	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	712	Interaction with ROCK2.				centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						AACGACTTCTTCCTATTGTTT	0.343																																					p.G712G		Atlas-SNP	.											.	PPP1R12A	76	.	0			c.A2136G						.						82	68	72					12																	80191131		1826	4083	5909	SO:0001819	synonymous_variant	4659	exon16			ACTTCTTCCTATT	D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7618	protein-coding gene	gene with protein product	"myosin phosphatase-targeting subunit 1", "myosin binding subunit"	602021	"protein phosphatase 1, regulatory (inhibitor) subunit 12A"	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.2136A>G	chr12.hg19:g.80191131T>C		97.0	0.0		69.0	4.0	NM_002480	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Silent	SNP	ENST00000450142.2	hg19	CCDS44947.1	.	.	.	.	.	.	.	.	.	.	T	9.648	1.140698	0.21205	.	.	ENSG00000058272	ENST00000553081	.	.	.	5.31	4.16	0.48862	.	.	.	.	.	T	0.47021	0.1423	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40664	-0.9551	4	.	.	.	.	3.2024	0.06653	0.1379:0.0752:0.1435:0.6435	.	.	.	.	G	304	.	.	E	-	2	0	PPP1R12A	78715262	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.393000	0.44442	0.850000	0.35239	0.482000	0.46254	GAA	.	.		0.343	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		C	80191131	T	C	80191131	2	2	65	1	0	0	0	0	0	0	0	1	12366	1770	62	2		2	PPP1R12A	12	80191131	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1802535	80191131	53660764	286	8359										
VEZT	55591	hgsc.bcm.edu	37	chr12	95650962	95650962	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aagtggctgaaaccatcaaaAgttggatttttttttctcag	8	6	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:95650962A>G	ENST00000436874.1	+	3	310	c.205A>G	c.(205-207)Agt>Ggt	p.S69G	VEZT_ENST00000356859.4_3'UTR|VEZT_ENST00000261219.6_Missense_Mutation_p.S21G	NM_017599.3	NP_060069.3	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane protein	69					chordate embryonic development (GO:0043009)|single organismal cell-cell adhesion (GO:0016337)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stereocilia ankle link complex (GO:0002142)				endometrium(2)|kidney(3)|large_intestine(1)|lung(14)|ovary(2)|upper_aerodigestive_tract(1)	23						AACCATCAAAAGTTGGATTTT	0.348																																					p.S69G		Atlas-SNP	.											.	VEZT	106	.	0			c.A205G						.						97	92	94					12																	95650962		1825	4073	5898	SO:0001583	missense	55591	exon3			ATCAAAAGTTGGA	AF216644	CCDS44954.1	12q22	2011-02-15			ENSG00000028203	ENSG00000028203			18258	protein-coding gene	gene with protein product						11080149, 16199027, 21156161	Standard	NM_017599		Approved	DKFZP761C241	uc001tdz.2	Q9HBM0	OTTHUMG00000170182	ENST00000436874.1:c.205A>G	chr12.hg19:g.95650962A>G	ENSP00000410083:p.Ser69Gly	75.0	0.0		42.0	4.0	NM_017599	Q6P1Q3|Q9H2F4|Q9H2U5|Q9NT70|Q9NVW0|Q9UF91	Missense_Mutation	SNP	ENST00000436874.1	hg19	CCDS44954.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.181072	0.57800	.	.	ENSG00000028203	ENST00000436874;ENST00000261219;ENST00000551472;ENST00000552821;ENST00000551311;ENST00000397792;ENST00000397796	T;T;T;T	0.46819	2.41;2.44;0.86;2.44	5.58	5.58	0.84498	.	0.322723	0.41294	D	0.000917	T	0.41328	0.1154	L	0.38175	1.15	0.36491	D	0.868436	B;B;B;B	0.30686	0.24;0.191;0.29;0.191	B;B;B;B	0.29785	0.067;0.049;0.107;0.03	T	0.51036	-0.8756	10	0.54805	T	0.06	-23.309	15.7537	0.78009	1.0:0.0:0.0:0.0	.	69;69;21;21	C9J154;Q9HBM0;F8W8C2;F2Z3A6	.;VEZA_HUMAN;.;.	G	69;21;88;60;21;21;69	ENSP00000410083:S69G;ENSP00000261219:S21G;ENSP00000449701:S88G;ENSP00000380894:S21G	ENSP00000261219:S21G	S	+	1	0	VEZT	94175093	1.000000	0.71417	0.997000	0.53966	0.836000	0.47400	6.326000	0.72905	2.126000	0.65437	0.383000	0.25322	AGT	.	.		0.348	VEZT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407804.2	NM_017599		G	95650962	A	G	95650962	3	3	65	1	0	0	0	0	1	0	0	0	17171	72	3	2	215	2	VEZT	12	95650962	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	15459831	95650962	38200933	287	8360										
IKBIP	121457	hgsc.bcm.edu	37	chr12	99007913	99007913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cacttgtaatcttgagaccaAcatcttttgccatggaagtt	7	9	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:99007913A>G	ENST00000342502.2	-	3	914	c.503T>C	c.(502-504)gTt>gCt	p.V168A	IKBIP_ENST00000420861.1_Missense_Mutation_p.V62A|IKBIP_ENST00000393042.3_3'UTR	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein	168					response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						CTTGAGACCAACATCTTTTGC	0.353																																					p.V168A		Atlas-SNP	.											.	IKBIP	46	.	0			c.T503C						.						100	91	94					12																	99007913		2203	4300	6503	SO:0001583	missense	121457	exon3			AGACCAACATCTT	AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"I kappa B kinase interacting protein"	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.503T>C	chr12.hg19:g.99007913A>G	ENSP00000343471:p.Val168Ala	101.0	0.0		79.0	4.0	NM_201612	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Missense_Mutation	SNP	ENST00000342502.2	hg19	CCDS9067.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.708374	0.48517	.	.	ENSG00000166130	ENST00000342502;ENST00000420861	T;T	0.55588	0.66;0.51	5.48	5.48	0.80851	.	.	.	.	.	T	0.50103	0.1596	L	0.61218	1.895	0.09310	N	1	P	0.42692	0.787	B	0.34536	0.185	T	0.54364	-0.8305	9	0.66056	D	0.02	.	15.5806	0.76432	1.0:0.0:0.0:0.0	.	168	Q70UQ0	IKIP_HUMAN	A	168;62	ENSP00000343471:V168A;ENSP00000398023:V62A	ENSP00000343471:V168A	V	-	2	0	IKBIP	97532044	0.540000	0.26410	0.819000	0.32651	0.992000	0.81027	6.709000	0.74665	2.084000	0.62774	0.533000	0.62120	GTT	.	.		0.353	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687		G	99007913	A	G	99007913	3	3	65	1	0	0	0	0	1	0	0	0	7618	43	2	2	553	2	IKBIP	12	99007913	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3356951	99007913	34843982	288	8361										
BCL7A	605	hgsc.bcm.edu	37	chr12	122492735	122492735	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttctgatgagcagaattcacAgtcctcgatggaacattcga	9	9	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:122492735A>G	ENST00000261822.4	+	5	670	c.464A>G	c.(463-465)cAg>cGg	p.Q155R	BCL7A_ENST00000538010.1_Missense_Mutation_p.Q155R	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	155					negative regulation of transcription, DNA-templated (GO:0045892)					haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		CAGAATTCACAGTCCTCGATG	0.537			T	MYC	BNHL						OREG0022214	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q155R	GBM(17;197 467 16477 23242 44349)	Atlas-SNP	.		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	.	BCL7A	31	.	0			c.A464G						.						129	136	134					12																	122492735		2203	4300	6503	SO:0001583	missense	605	exon5			ATTCACAGTCCTC	X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.464A>G	chr12.hg19:g.122492735A>G	ENSP00000261822:p.Gln155Arg	68.0	0.0	1519	75.0	4.0	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Missense_Mutation	SNP	ENST00000261822.4	hg19	CCDS53841.1	.	.	.	.	.	.	.	.	.	.	A	12.23	1.875805	0.33162	.	.	ENSG00000110987	ENST00000538010;ENST00000261822	T;T	0.46451	0.87;0.9	6.07	4.91	0.64330	.	0.171731	0.52532	D	0.000080	T	0.30039	0.0752	N	0.19112	0.55	0.43342	D	0.995396	P;P	0.41848	0.651;0.763	B;B	0.42282	0.115;0.382	T	0.03095	-1.1073	10	0.18276	T	0.48	.	12.6969	0.57010	0.8763:0.0:0.0:0.1236	.	155;155	Q4VC05;Q4VC05-2	BCL7A_HUMAN;.	R	155	ENSP00000445868:Q155R;ENSP00000261822:Q155R	ENSP00000261822:Q155R	Q	+	2	0	BCL7A	120977118	1.000000	0.71417	0.976000	0.42696	0.819000	0.46315	4.651000	0.61447	1.093000	0.41377	-0.333000	0.08304	CAG	.	.		0.537	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1			G	122492735	A	G	122492735	3	3	65	1	0	0	0	0	1	0	0	0	1378	188	7	2	482	2	BCL7A	12	122492735	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	23484822	122492735	11359160	289	8362										
RAN	5901	hgsc.bcm.edu	37	chr12	131359255	131359255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgaaggcgaaatccattgtcTtccaccgaaagaagaatctt	8	9	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr12:131359255T>C	ENST00000543796.1	+	5	670	c.412T>C	c.(412-414)Ttc>Ctc	p.F138L	RAN_ENST00000392369.2_Missense_Mutation_p.F138L|RAN_ENST00000254675.3_Missense_Mutation_p.F50L|RAN_ENST00000392367.3_Missense_Mutation_p.F155L|RAN_ENST00000541630.1_Missense_Mutation_p.F50L			P62826	RAN_HUMAN	RAN, member RAS oncogene family	138					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|cellular protein complex localization (GO:0034629)|DNA metabolic process (GO:0006259)|gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(2)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		ATCCATTGTCTTCCACCGAAA	0.393																																					p.F138L		Atlas-SNP	.											.	RAN	18	.	0			c.T412C						.						88	79	82					12																	131359255		2203	4300	6503	SO:0001583	missense	5901	exon5			ATTGTCTTCCACC	M31469	CCDS9271.1, CCDS73546.1	12q24.33	2014-05-09			ENSG00000132341	ENSG00000132341			9846	protein-coding gene	gene with protein product		601179				8421051	Standard	XM_005253592		Approved	ARA24, TC4, Gsp1	uc001uir.3	P62826	OTTHUMG00000134328	ENST00000543796.1:c.412T>C	chr12.hg19:g.131359255T>C	ENSP00000446215:p.Phe138Leu	114.0	0.0		95.0	4.0	NM_006325	A8K3Z8|P17080|P28746|P28747|Q6IPB2|Q86V08|Q8NI90|Q9CSP3|Q9CWI7|Q9CZA2|Q9UDJ5|Q9UEU9	Missense_Mutation	SNP	ENST00000543796.1	hg19	CCDS9271.1	.	.	.	.	.	.	.	.	.	.	T	19.34	3.809451	0.70797	.	.	ENSG00000132341	ENST00000543796;ENST00000448750;ENST00000541630;ENST00000392369;ENST00000254675;ENST00000535090;ENST00000392367	T;T;T;T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84	3.94	3.94	0.45596	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.68118	0.2966	L	0.52266	1.64	0.80722	D	1	P;P	0.46277	0.875;0.875	B;B	0.40565	0.333;0.333	T	0.73341	-0.4013	10	0.87932	D	0	-11.6413	12.2939	0.54833	0.0:0.0:0.0:1.0	.	138;138	A8K3Z8;P62826	.;RAN_HUMAN	L	138;156;50;138;50;134;155	ENSP00000446215:F138L;ENSP00000396127:F156L;ENSP00000441210:F50L;ENSP00000376176:F138L;ENSP00000254675:F50L;ENSP00000444042:F134L;ENSP00000376174:F155L	ENSP00000254675:F50L	F	+	1	0	RAN	129925208	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.590000	0.82653	1.554000	0.49487	0.460000	0.39030	TTC	.	.		0.393	RAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259441.2	NM_006325		C	131359255	T	C	131359255	3	2	65	1	0	0	0	0	1	0	0	0	13039	1609	56	2	426	2	RAN	12	131359255	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	8866520	131359255	2492640	290	8363										
SACS	26278	hgsc.bcm.edu	37	chr13	23915617	23915617	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agttctggggataagtggcaTctcatcaaataaagtcaaat	9	6	4	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr13:23915617T>C	ENST00000382292.3	-	9	2671	c.2398A>G	c.(2398-2400)Atg>Gtg	p.M800V	SACS_ENST00000382298.3_Missense_Mutation_p.M800V|SACS_ENST00000402364.1_Missense_Mutation_p.M50V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	800					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.M653L(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ATAAGTGGCATCTCATCAAAT	0.358																																					p.M800V		Atlas-SNP	.											SACS,colon,carcinoma,0,1	SACS	871	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2398G						.						79	79	79					13																	23915617		2203	4300	6503	SO:0001583	missense	26278	exon10			GTGGCATCTCATC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.2398A>G	chr13.hg19:g.23915617T>C	ENSP00000371729:p.Met800Val	50.0	0.0		35.0	2.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.65|12.65	2.002593|2.002593	0.35320|0.35320	.|.	.|.	ENSG00000151835|ENSG00000151835	ENST00000455470|ENST00000382292;ENST00000402364;ENST00000382298	.|D;D;D	.|0.86627	.|-2.04;-2.15;-2.04	6.05|6.05	4.85|4.85	0.62838|0.62838	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.83317|0.83317	0.5228|0.5228	L|L	0.46741|0.46741	1.465|1.465	0.36329|0.36329	D|D	0.858766|0.858766	.|P;B	.|0.49783	.|0.928;0.053	.|B;B	.|0.44108	.|0.441;0.02	D|D	0.84155|0.84155	0.0425|0.0425	5|10	.|0.35671	.|T	.|0.21	.|.	10.5988|10.5988	0.45354|0.45354	0.2571:0.0:0.0:0.7429|0.2571:0.0:0.0:0.7429	.|.	.|699;800	.|B2REB1;Q9NZJ4	.|.;SACS_HUMAN	G|V	699|800;50;800	.|ENSP00000371729:M800V;ENSP00000385844:M50V;ENSP00000371735:M800V	.|ENSP00000371729:M800V	D|M	-|-	2|1	0|0	SACS|SACS	22813617|22813617	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	4.618000|4.618000	0.61211|0.61211	1.089000|1.089000	0.41292|0.41292	-0.341000|-0.341000	0.08007|0.08007	GAT|ATG	.	.		0.358	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23915617	T	C	23915617	3	2	65	1	0	0	0	0	1	0	0	0	13819	1435	50	2	11345	2	SACS	13	23915617	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		23915617	91254261	291	8364										
RNF17	56163	hgsc.bcm.edu	37	chr13	25399863	25399863	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tccagttcaagatcaagcctGtgtagctaaatttgaagatg	9	7	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr13:25399863G>A	ENST00000255324.5	+	16	2250	c.2198G>A	c.(2197-2199)tGt>tAt	p.C733Y	RNF17_ENST00000381921.1_Missense_Mutation_p.C733Y	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	733	Tudor 1. {ECO:0000255|PROSITE- ProRule:PRU00211}.				multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		GATCAAGCCTGTGTAGCTAAA	0.368																																					p.C733Y		Atlas-SNP	.											.	RNF17	259	.	0			c.G2198A						.						105	101	103					13																	25399863		2203	4300	6503	SO:0001583	missense	56163	exon16			AAGCCTGTGTAGC	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.2198G>A	chr13.hg19:g.25399863G>A	ENSP00000255324:p.Cys733Tyr	87.0	0.0		45.0	4.0	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	hg19	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	G	16.34	3.095649	0.56075	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000418120	T;T;T	0.16743	2.32;2.32;2.32	4.69	4.69	0.59074	Tudor subgroup (1);Maternal tudor protein (1);Tudor domain (1);	0.269718	0.36703	N	0.002453	T	0.42720	0.1215	M	0.77820	2.39	0.80722	D	1	D;P	0.76494	0.999;0.843	D;P	0.87578	0.998;0.682	T	0.32640	-0.9899	10	0.45353	T	0.12	.	14.9002	0.70672	0.0:0.0:1.0:0.0	.	733;733	B7Z7S1;Q9BXT8	.;RNF17_HUMAN	Y	733;733;592;57	ENSP00000255324:C733Y;ENSP00000371346:C733Y;ENSP00000388892:C57Y	ENSP00000255324:C733Y	C	+	2	0	RNF17	24297863	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	5.781000	0.68964	2.312000	0.78011	0.491000	0.48974	TGT	.	.		0.368	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		A	25399863	G	A	25399863	3	1	65	1	0	0	0	0	1	0	0	0	13476	1377	48	3	2260	3	RNF17	13	25399863	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	1484246	25399863	89770015	292	8365										
FRY	10129	hgsc.bcm.edu	37	chr13	32698997	32698997	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtatgcagaagtcattggagTgttggcacaagccaagtaag	13	6	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr13:32698997T>C	ENST00000380250.3	+	7	1197	c.701T>C	c.(700-702)gTg>gCg	p.V234A		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	234						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GTCATTGGAGTGTTGGCACAA	0.468																																					p.V234A		Atlas-SNP	.											.	FRY	312	.	0			c.T701C						.						134	132	133					13																	32698997		1969	4160	6129	SO:0001583	missense	10129	exon7			TTGGAGTGTTGGC	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.701T>C	chr13.hg19:g.32698997T>C	ENSP00000369600:p.Val234Ala	92.0	0.0		87.0	4.0	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.9|25.9	4.684629|4.684629	0.88639|0.88639	.|.	.|.	ENSG00000073910|ENSG00000073910	ENST00000267067|ENST00000380250	.|T	.|0.25414	.|1.8	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.46776|0.46776	0.1410|0.1410	M|M	0.74546|0.74546	2.27|2.27	0.80722|0.80722	D|D	1|1	.|P	.|0.45283	.|0.855	.|P	.|0.56916	.|0.809	T|T	0.34030|0.34030	-0.9845|-0.9845	6|10	0.87932|0.30854	D|T	0|0.27	.|.	15.5243|15.5243	0.75890|0.75890	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|234	.|Q5TBA9	.|FRY_HUMAN	R|A	161|234	.|ENSP00000369600:V234A	ENSP00000267067:C161R|ENSP00000369600:V234A	C|V	+|+	1|2	0|0	FRY|FRY	31596997|31596997	1.000000|1.000000	0.71417|0.71417	0.924000|0.924000	0.36721|0.36721	0.991000|0.991000	0.79684|0.79684	8.040000|8.040000	0.89188|0.89188	2.081000|2.081000	0.62600|0.62600	0.459000|0.459000	0.35465|0.35465	TGT|GTG	.	.		0.468	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		C	32698997	T	C	32698997	3	2	65	1	0	0	0	0	1	0	0	0	6071	1696	59	2	727	2	FRY	13	32698997	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	7299134	32698997	82470881	293	8366										
NBEA	26960	hgsc.bcm.edu	37	chr13	35758164	35758164	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tttgaaccatggattccttgCcaagttaattcctgagcaga	8	9	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr13:35758164C>A	ENST00000400445.3	+	30	5417	c.4883C>A	c.(4882-4884)gCc>gAc	p.A1628D	NBEA_ENST00000379939.2_Missense_Mutation_p.A1625D|NBEA_ENST00000310336.4_Missense_Mutation_p.A1628D|NBEA_ENST00000540320.1_Missense_Mutation_p.A1628D	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1628					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GGATTCCTTGCCAAGTTAATT	0.403																																					p.A1628D		Atlas-SNP	.											.	NBEA	340	.	0			c.C4883A						.						115	104	107					13																	35758164		1881	4118	5999	SO:0001583	missense	26960	exon30			TCCTTGCCAAGTT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.4883C>A	chr13.hg19:g.35758164C>A	ENSP00000383295:p.Ala1628Asp	149.0	0.0		126.0	73.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.966615	0.53507	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.82	5.82	0.92795	.	0.153376	0.46442	D	0.000282	T	0.48021	0.1477	N	0.08118	0	0.80722	D	1	D	0.71674	0.998	D	0.73708	0.981	T	0.44314	-0.9336	10	0.14656	T	0.56	.	18.2756	0.90081	0.0:1.0:0.0:0.0	.	1625	Q5T321	.	D	1628;1628;1625;1628	ENSP00000440951:A1628D;ENSP00000383295:A1628D;ENSP00000369271:A1625D;ENSP00000308534:A1628D	ENSP00000308534:A1628D	A	+	2	0	NBEA	34656164	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.770000	0.62309	2.753000	0.94483	0.467000	0.42956	GCC	.	.		0.403	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35758164	C	A	35758164	3	1	65	1	0	0	0	0	1	0	0	0	10196	739	26	3	5001	3	NBEA	13	35758164	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	3059167	35758164	79411714	294	8367										
NAA16	79612	hgsc.bcm.edu	37	chr13	41891035	41891035	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctcaagttttgcaagatgatTctgtcgaacccaaaatttgc	7	9	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr13:41891035T>C	ENST00000379406.3	+	2	432	c.108T>C	c.(106-108)atT>atC	p.I36I	NAA16_ENST00000403412.3_Silent_p.I36I|NAA16_ENST00000379367.3_Silent_p.I36I	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	36					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						GCAAGATGATTCTGTCGAACC	0.323																																					p.I36I		Atlas-SNP	.											.	NAA16	74	.	0			c.T108C						.						110	114	113					13																	41891035		2203	4300	6503	SO:0001819	synonymous_variant	79612	exon2			GATGATTCTGTCG	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.108T>C	chr13.hg19:g.41891035T>C		86.0	0.0		81.0	4.0	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Silent	SNP	ENST00000379406.3	hg19	CCDS9379.1																																																																																			.	.		0.323	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		C	41891035	T	C	41891035	2	2	65	1	0	0	0	0	0	0	0	1	10128	1771	62	2		2	NAA16	13	41891035	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6132871	41891035	73278843	295	8368										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42875524	42875524	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cttttctgcagcagtggtgcAtacgatagtaaatgaaactt	9	7	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr13:42875524A>G	ENST00000025301.2	+	8	2817	c.2642A>G	c.(2641-2643)cAt>cGt	p.H881R		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	881					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		GCAGTGGTGCATACGATAGTA	0.313																																					p.H881R		Atlas-SNP	.											.	AKAP11	146	.	0			c.A2642G						.						30	29	30					13																	42875524		2199	4299	6498	SO:0001583	missense	11215	exon8			TGGTGCATACGAT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.2642A>G	chr13.hg19:g.42875524A>G	ENSP00000025301:p.His881Arg	93.0	0.0		116.0	5.0	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	8.513	0.867015	0.17250	.	.	ENSG00000023516	ENST00000025301	T	0.14266	2.52	6.03	3.61	0.41365	.	0.266662	0.33290	N	0.005078	T	0.14313	0.0346	L	0.57536	1.79	0.34657	D	0.722294	B	0.11235	0.004	B	0.12156	0.007	T	0.10291	-1.0636	10	0.28530	T	0.3	.	10.3825	0.44121	0.8684:0.0:0.1316:0.0	.	881	Q9UKA4	AKA11_HUMAN	R	881	ENSP00000025301:H881R	ENSP00000025301:H881R	H	+	2	0	AKAP11	41773524	1.000000	0.71417	0.668000	0.29813	0.242000	0.25591	5.557000	0.67313	0.528000	0.28580	0.533000	0.62120	CAT	.	.		0.313	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		G	42875524	A	G	42875524	3	3	65	1	0	0	0	0	1	0	0	0	447	217	8	2	2664	2	AKAP11	13	42875524	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	984489	42875524	72294354	296	8369										
NALCN	259232	hgsc.bcm.edu	37	chr13	101890168	101890168	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atgaagagtagttccaattaCgagtagtagttcgaatttgt	10	4	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr13:101890168C>T	ENST00000251127.6	-	12	1453	c.1372G>A	c.(1372-1374)Gta>Ata	p.V458I	NALCN_ENST00000470333.1_5'UTR|NALCN_ENST00000376196.3_Missense_Mutation_p.V458I	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	458					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTTCCAATTACGAGTAGTAGT	0.318																																					p.V458I		Atlas-SNP	.											NALCN,NS,carcinoma,0,1	NALCN	431	.	0			c.G1372A						.						167	179	175					13																	101890168		2203	4300	6503	SO:0001583	missense	259232	exon12			CAATTACGAGTAG	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1372G>A	chr13.hg19:g.101890168C>T	ENSP00000251127:p.Val458Ile	75.0	0.0		41.0	2.0	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.408356	0.42715	.	.	ENSG00000102452	ENST00000251127;ENST00000376196	D;D	0.98762	-5.12;-5.12	5.24	5.24	0.73138	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.95711	0.8605	L	0.31526	0.94	0.80722	D	1	P;P;P	0.45827	0.78;0.867;0.78	B;B;B	0.32393	0.145;0.142;0.145	D	0.95607	0.8668	10	0.39692	T	0.17	.	19.1638	0.93546	0.0:1.0:0.0:0.0	.	458;458;458	F2Z323;B3KSZ6;Q8IZF0	.;.;NALCN_HUMAN	I	458	ENSP00000251127:V458I;ENSP00000365367:V458I	ENSP00000251127:V458I	V	-	1	0	NALCN	100688169	1.000000	0.71417	0.090000	0.20809	0.358000	0.29455	7.441000	0.80485	2.593000	0.87608	0.491000	0.48974	GTA	.	.		0.318	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		T	101890168	C	T	101890168	3	4	65	1	0	0	0	0	1	0	0	0	10157	536	19	1	3976	1	NALCN	13	101890168	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	59014644	101890168	13279710	297	8370										
TPPP2	122664	hgsc.bcm.edu	37	chr14	21500171	21500171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttgcgggacgggaagagatgActgacaacacaggctatgtg	15	7	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:21500171A>G	ENST00000321760.6	+	4	596	c.448A>G	c.(448-450)Act>Gct	p.T150A	AL161668.5_ENST00000533984.1_lincRNA|RP11-998D10.1_ENST00000531638.1_5'Flank|TPPP2_ENST00000530140.2_Missense_Mutation_p.T150A|NDRG2_ENST00000403829.3_Intron	NM_173846.4	NP_776245.2	P59282	TPPP2_HUMAN	tubulin polymerization-promoting protein family member 2	150						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		GGAAGAGATGACTGACAACAC	0.547																																					p.T150A		Atlas-SNP	.											TPPP2,NS,carcinoma,0,1	TPPP2	22	.	0			c.A448G						.						212	159	177					14																	21500171		2203	4300	6503	SO:0001583	missense	122664	exon4			GAGATGACTGACA	AY072034	CCDS9566.1	14q11.2	2014-01-21	2007-05-02	2007-05-02	ENSG00000179636	ENSG00000179636			19293	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 8"	C14orf8		15590652, 17105200	Standard	NM_173846		Approved	p25beta, p18, CT152	uc001vzh.3	P59282	OTTHUMG00000029642	ENST00000321760.6:c.448A>G	chr14.hg19:g.21500171A>G	ENSP00000317595:p.Thr150Ala	96.0	0.0		63.0	3.0	NM_173846	Q2VYF3	Missense_Mutation	SNP	ENST00000321760.6	hg19	CCDS9566.1	.	.	.	.	.	.	.	.	.	.	A	0.059	-1.227811	0.01518	.	.	ENSG00000179636	ENST00000321760;ENST00000530140	T;T	0.41400	1.0;1.0	4.71	3.48	0.39840	.	0.250070	0.40222	N	0.001148	T	0.19287	0.0463	N	0.11789	0.175	0.09310	N	1	B	0.33777	0.425	B	0.34931	0.192	T	0.11891	-1.0569	10	0.13108	T	0.6	-3.9563	4.5232	0.11969	0.701:0.1986:0.1004:0.0	.	150	P59282	TPPP2_HUMAN	A	150	ENSP00000317595:T150A;ENSP00000435356:T150A	ENSP00000317595:T150A	T	+	1	0	TPPP2	20570011	0.000000	0.05858	0.137000	0.22149	0.014000	0.08584	0.173000	0.16724	2.098000	0.63641	0.533000	0.62120	ACT	.	.		0.547	TPPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073914.3	NM_173846		G	21500171	A	G	21500171	3	3	65	1	0	0	0	0	1	0	0	0	16429	275	10	2	458	2	TPPP2	14	21500171	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10		21500171	85849369	298	8371										
PSME1	5720	hgsc.bcm.edu	37	chr14	24607958	24607958	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cctgtaggctgtgttatatgAcatcatcctgaagaacttcg	9	9	1	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:24607958A>G	ENST00000206451.6	+	11	788	c.683A>G	c.(682-684)gAc>gGc	p.D228G	PSME1_ENST00000382708.3_3'UTR|RP11-468E2.5_ENST00000558478.1_lincRNA|PSME1_ENST00000561435.1_Missense_Mutation_p.T231A|EMC9_ENST00000558200.1_5'Flank|PSME1_ENST00000559123.1_Missense_Mutation_p.D69G	NM_001281528.1|NM_006263.2	NP_001268457.1|NP_006254.1	Q06323	PSME1_HUMAN	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)	228					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(265;0.00831)		GTGTTATATGACATCATCCTG	0.512																																					p.D228G		Atlas-SNP	.											.	PSME1	18	.	0			c.A683G						.						76	76	76					14																	24607958		2203	4300	6503	SO:0001583	missense	5720	exon11			TATATGACATCAT		CCDS9612.1, CCDS41930.1, CCDS61415.1	14q11.2	2008-08-29			ENSG00000092010	ENSG00000092010		"Proteasome (prosome, macropain) subunits"	9568	protein-coding gene	gene with protein product		600654				8269930	Standard	NM_006263		Approved	IFI5111, PA28alpha	uc001wmh.3	Q06323	OTTHUMG00000028795	ENST00000206451.6:c.683A>G	chr14.hg19:g.24607958A>G	ENSP00000206451:p.Asp228Gly	83.0	0.0		69.0	4.0	NM_006263	A6NJG9|H0YNE3|Q6IBM2|Q9UEF4	Missense_Mutation	SNP	ENST00000206451.6	hg19	CCDS9612.1	.	.	.	.	.	.	.	.	.	.	a	17.60	3.429557	0.62844	.	.	ENSG00000092010	ENST00000206451	T	0.58652	0.32	5.18	4.04	0.47022	Proteasome activator pa28, REG beta subunit (2);	.	.	.	.	T	0.73055	0.3538	M	0.77313	2.365	0.26512	N	0.974589	D	0.89917	1.0	D	0.97110	1.0	T	0.62950	-0.6745	9	0.66056	D	0.02	.	7.3739	0.26817	0.9035:0.0:0.0965:0.0	.	228	Q06323	PSME1_HUMAN	G	228	ENSP00000206451:D228G	ENSP00000206451:D228G	D	+	2	0	PSME1	23677798	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.063000	0.76714	0.994000	0.38892	0.533000	0.62120	GAC	.	.		0.512	PSME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071910.2	NM_006263		G	24607958	A	G	24607958	3	3	65	1	0	0	0	0	1	0	0	0	12718	275	10	2	809	2	PSME1	14	24607958	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3107787	24607958	82741582	299	8372										
RNF31	55072	hgsc.bcm.edu	37	chr14	24618770	24618770	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agaccctgcctggggtcctgCagggtacccacctgagcccc	12	17	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:24618770C>T	ENST00000324103.6	+	6	1107	c.787C>T	c.(787-789)Cag>Tag	p.Q263*	RNF31_ENST00000382687.3_Nonsense_Mutation_p.Q112*|PSME2_ENST00000560410.1_5'Flank|RP11-468E2.4_ENST00000558468.1_5'Flank|PSME2_ENST00000471700.2_5'Flank|RNF31_ENST00000559275.1_Nonsense_Mutation_p.Q112*|PSME2_ENST00000216802.5_5'Flank	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	263	Polyubiquitin-binding.				CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		TGGGGTCCTGCAGGGTACCCA	0.562																																					p.Q263X		Atlas-SNP	.											RNF31,NS,carcinoma,-2,1	RNF31	95	.	0			c.C787T						.						66	67	66					14																	24618770		1953	4137	6090	SO:0001587	stop_gained	55072	exon6			GTCCTGCAGGGTA	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"RING-type (C3HC4) zinc fingers"	16031	protein-coding gene	gene with protein product	"HOIL-1-interacting protein"	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.787C>T	chr14.hg19:g.24618770C>T	ENSP00000315112:p.Gln263*	66.0	0.0		43.0	2.0	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Nonsense_Mutation	SNP	ENST00000324103.6	hg19	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.846219	0.91277	.	.	ENSG00000092098	ENST00000324103;ENST00000382687	.	.	.	5.53	4.64	0.57946	.	1.201630	0.05956	N	0.639731	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	-6.8187	11.8256	0.52265	0.1752:0.8248:0.0:0.0	.	.	.	.	X	263;112	.	ENSP00000315112:Q263X	Q	+	1	0	RNF31	23688610	0.288000	0.24324	0.003000	0.11579	0.009000	0.06853	4.360000	0.59455	1.318000	0.45170	-0.169000	0.13324	CAG	.	.		0.562	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		T	24618770	C	T	24618770	4	4	65	1	0	0	0	0	0	1	0	0	13502	711	25	3	809	3	RNF31	14	24618770	Nonsense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	10812	24618770	82730770	300	8373										
KIAA0391	9692	hgsc.bcm.edu	37	chr14	35593210	35593210	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tataatgactgtatccagggAgctctccttcatcaagatgt	8	9	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:35593210A>G	ENST00000557565.1	+	2	1140	c.759A>G	c.(757-759)ggA>ggG	p.G253G	KIAA0391_ENST00000603544.1_Silent_p.G253G|KIAA0391_ENST00000604948.1_Silent_p.G158G|KIAA0391_ENST00000534898.4_Silent_p.G253G|KIAA0391_ENST00000250377.7_Silent_p.G158G|KIAA0391_ENST00000321130.10_Silent_p.G253G|PPP2R3C_ENST00000261475.5_5'Flank|PPP2R3C_ENST00000555644.1_5'Flank|KIAA0391_ENST00000605870.1_Intron|KIAA0391_ENST00000603588.1_Intron	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	253					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		GTATCCAGGGAGCTCTCCTTC	0.358																																					p.G253G		Atlas-SNP	.											.	KIAA0391	35	.	0			c.A759G						.						49	48	48					14																	35593210		2203	4300	6503	SO:0001819	synonymous_variant	9692	exon2			CCAGGGAGCTCTC	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 3", "proteinaceous RNase P"	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.759A>G	chr14.hg19:g.35593210A>G		95.0	0.0		68.0	4.0	NM_014672	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Silent	SNP	ENST00000557565.1	hg19	CCDS32063.1																																																																																			.	.		0.358	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		G	35593210	A	G	35593210	2	3	65	1	0	0	0	0	0	0	0	1	8181	291	11	2		2	KIAA0391	14	35593210	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	10974440	35593210	71756330	301	8374										
KIAA0831	22863	hgsc.bcm.edu	37	chr14	55836380	55836380	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	taaaccaggaggtcaccgagGctgctgcagaggagatcatc	13	10	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:55836380G>T	ENST00000247178.5	-	10	1471	c.1436C>A	c.(1435-1437)gCc>gAc	p.A479D		NM_014924.4	NP_055739.2	Q6ZNE5	BAKOR_HUMAN	autophagy related 14	479	BATS. {ECO:0000250}.				autophagic vacuole assembly (GO:0000045)|endosome to lysosome transport (GO:0008333)|positive regulation of autophagy (GO:0010508)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|pre-autophagosomal structure membrane (GO:0034045)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(2)	13						GGTCACCGAGGCTGCTGCAGA	0.542																																					p.A479D		Atlas-SNP	.											.	ATG14	36	.	0			c.C1436A						.						135	130	132					14																	55836380		2203	4300	6503	SO:0001583	missense	22863	exon10			ACCGAGGCTGCTG	AB020638	CCDS32087.1	14q22.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000126775	ENSG00000126775			19962	protein-coding gene	gene with protein product	"Barkor", "beclin 1-associated autophagy-related key regulator"	613515	"KIAA0831", "ATG14 autophagy related 14 homolog (S. cerevisiae)"	KIAA0831		18843052	Standard	NM_014924		Approved	ATG14L	uc001xbx.2	Q6ZNE5	OTTHUMG00000172129	ENST00000247178.5:c.1436C>A	chr14.hg19:g.55836380G>T	ENSP00000247178:p.Ala479Asp	115.0	0.0		93.0	4.0	NM_014924	A6NJE4|A8K9U5|B7ZWP5|O94920|Q32MK7|Q32MK8	Missense_Mutation	SNP	ENST00000247178.5	hg19	CCDS32087.1	.	.	.	.	.	.	.	.	.	.	G	33	5.270069	0.95429	.	.	ENSG00000126775	ENST00000247178	T	0.39592	1.07	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.50309	0.1608	L	0.46157	1.445	0.80722	D	1	D	0.54047	0.964	P	0.51101	0.659	T	0.53143	-0.8480	10	0.72032	D	0.01	-16.8052	18.7624	0.91858	0.0:0.0:1.0:0.0	.	479	Q6ZNE5	BAKOR_HUMAN	D	479	ENSP00000247178:A479D	ENSP00000247178:A479D	A	-	2	0	ATG14	54906133	1.000000	0.71417	0.992000	0.48379	0.984000	0.73092	7.334000	0.79224	2.649000	0.89929	0.555000	0.69702	GCC	.	.		0.542	ATG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416992.1	NM_014924		T	55836380	G	T	55836380	3	4	65	1	0	0	0	0	1	0	0	0	8204	1203	42	3	46	3	KIAA0831	14	55836380	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	20243170	55836380	51513160	302	8375										
RTN1	6252	hgsc.bcm.edu	37	chr14	60070638	60070638	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggagccacatcaggactgcaAactgaagaacgaaagcatta	10	9	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:60070638A>G	ENST00000267484.5	-	6	2449	c.2114T>C	c.(2113-2115)tTt>tCt	p.F705S	RTN1_ENST00000342503.4_Splice_Site_p.F137S|RTN1_ENST00000557422.1_5'UTR|RTN1_ENST00000395090.1_Splice_Site_p.F122S	NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	705	Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		CAGGACTGCAAACTGAAGAAC	0.438																																					p.F705S		Atlas-SNP	.											.	RTN1	139	.	0			c.T2114C						.						155	135	142					14																	60070638		2203	4300	6503	SO:0001630	splice_region_variant	6252	exon6			ACTGCAAACTGAA	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.2113-1T>C	chr14.hg19:g.60070638A>G		41.0	0.0		43.0	4.0	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	hg19	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.809775	0.90707	.	.	ENSG00000139970	ENST00000432103;ENST00000267484;ENST00000395090;ENST00000342503;ENST00000433623	T;T;T	0.48201	0.82;0.82;0.82	5.32	5.32	0.75619	.	0.044542	0.85682	D	0.000000	T	0.75287	0.3829	M	0.92459	3.31	0.80722	D	1	D;D;D	0.67145	0.996;0.968;0.985	D;D;D	0.71656	0.974;0.95;0.956	T	0.82426	-0.0463	10	0.87932	D	0	.	15.6363	0.76958	1.0:0.0:0.0:0.0	.	122;705;137	A8MT72;Q16799;Q16799-3	.;RTN1_HUMAN;.	S	285;705;122;137;631	ENSP00000267484:F705S;ENSP00000378525:F122S;ENSP00000340716:F137S	ENSP00000267484:F705S	F	-	2	0	RTN1	59140391	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	9.287000	0.95975	2.165000	0.68154	0.369000	0.22263	TTT	.	.		0.438	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2		Missense_Mutation	G	60070638	A	G	60070638	5	3	65	1	0	0	0	0	0	0	1	0	13740	28	1	2	232	2	RTN1	14	60070638	Splice_Site	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	4234258	60070638	47278902	303	8376										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64519805	64519805	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttaagtaaaatgagagctatTgatttgcaaattaagaaaat	7	2	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:64519805T>C	ENST00000344113.4	+	48	9386	c.9174T>C	c.(9172-9174)atT>atC	p.I3058I	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.I3091I|SYNE2_ENST00000358025.3_Silent_p.I3058I	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3058					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGAGAGCTATTGATTTGCAAA	0.348																																					p.I3058I		Atlas-SNP	.											.	SYNE2	577	.	0			c.T9174C						.						54	54	54					14																	64519805		1824	4074	5898	SO:0001819	synonymous_variant	23224	exon48			AGCTATTGATTTG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.9174T>C	chr14.hg19:g.64519805T>C		146.0	0.0		84.0	4.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.348	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		C	64519805	T	C	64519805	2	2	65	1	0	0	0	0	0	0	0	1	15461	1800	63	2		2	SYNE2	14	64519805	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4449167	64519805	42829735	304	8377										
ZBTB1	22890	hgsc.bcm.edu	37	chr14	64989571	64989571	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cattgaaaatatctgtgcatGtggtaaatgtggacaaatac	9	5	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:64989571G>T	ENST00000554015.1	+	4	1780	c.1349G>T	c.(1348-1350)tGt>tTt	p.C450F	RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000394712.2_Missense_Mutation_p.C450F|ZBTB1_ENST00000358738.3_Missense_Mutation_p.C450F			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	450					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		ATCTGTGCATGTGGTAAATGT	0.438																																					p.C450F		Atlas-SNP	.											.	ZBTB1	93	.	0			c.G1349T						.						107	105	106					14																	64989571		2203	4300	6503	SO:0001583	missense	22890	exon2			GTGCATGTGGTAA	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.1349G>T	chr14.hg19:g.64989571G>T	ENSP00000451000:p.Cys450Phe	88.0	0.0		62.0	44.0	NM_014950	A8K6S8|Q86SW8	Missense_Mutation	SNP	ENST00000554015.1	hg19	CCDS45126.1	.	.	.	.	.	.	.	.	.	.	G	17.72	3.458707	0.63401	.	.	ENSG00000126804	ENST00000554015;ENST00000358738;ENST00000394712	T;T;T	0.18016	2.24;2.43;2.24	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000001	T	0.31231	0.0790	L	0.29908	0.895	0.80722	D	1	D;P	0.58268	0.982;0.948	P;P	0.60473	0.875;0.603	T	0.00961	-1.1499	10	0.87932	D	0	-18.564	20.5568	0.99304	0.0:0.0:1.0:0.0	.	450;450	Q9Y2K1-2;Q9Y2K1	.;ZBTB1_HUMAN	F	450	ENSP00000451000:C450F;ENSP00000351587:C450F;ENSP00000378201:C450F	ENSP00000351587:C450F	C	+	2	0	ZBTB1	64059324	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.476000	0.97823	2.861000	0.98227	0.655000	0.94253	TGT	.	.		0.438	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1			T	64989571	G	T	64989571	3	4	65	1	0	0	0	0	1	0	0	0	17537	1377	48	3	1351	3	ZBTB1	14	64989571	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	469766	64989571	42359969	305	8378										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68248209	68248209	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agccgacttctcagagatgcAtccttcacgggaaacaggta	10	11	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:68248209A>G	ENST00000347230.4	-	22	4548	c.4410T>C	c.(4408-4410)gaT>gaC	p.D1470D	ZFYVE26_ENST00000555452.1_Silent_p.D1470D	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1470					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		TCAGAGATGCATCCTTCACGG	0.522																																					p.D1470D		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.T4410C						.						111	107	108					14																	68248209		2203	4300	6503	SO:0001819	synonymous_variant	23503	exon22			AGATGCATCCTTC	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.4410T>C	chr14.hg19:g.68248209A>G		68.0	0.0		49.0	4.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	hg19	CCDS9788.1																																																																																			.	.		0.522	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		G	68248209	A	G	68248209	2	3	65	1	0	0	0	0	0	0	0	1	17683	214	8	2		2	ZFYVE26	14	68248209	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3258638	68248209	39101331	306	8379										
RGS6	9628	hgsc.bcm.edu	37	chr14	72945005	72945005	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttgaacgcacagatcgacagAcattgtttgaaaatgtccaa	8	8	0	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:72945005A>G	ENST00000553530.1	+	12	1029	c.822A>G	c.(820-822)agA>agG	p.R274R	RGS6_ENST00000556437.1_Silent_p.R274R|RGS6_ENST00000343854.6_Silent_p.R274R|RGS6_ENST00000406236.4_Silent_p.R274R|RGS6_ENST00000402788.2_Silent_p.R274R|RGS6_ENST00000407322.4_Silent_p.R274R|RGS6_ENST00000555571.1_Silent_p.R274R|RGS6_ENST00000554782.1_Silent_p.R135R|RGS6_ENST00000404301.2_Silent_p.R274R|RGS6_ENST00000434263.2_Silent_p.R205R|RGS6_ENST00000355512.6_Silent_p.R274R|RGS6_ENST00000553525.1_Silent_p.R274R	NM_001204417.1|NM_001204418.1|NM_001204420.1|NM_001204421.1|NM_001204422.1|NM_004296.5	NP_001191346.1|NP_001191347.1|NP_001191349.1|NP_001191350.1|NP_001191351.1|NP_004287.3	P49758	RGS6_HUMAN	regulator of G-protein signaling 6	274	G protein gamma.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neuron differentiation (GO:0045666)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		AGATCGACAGACATTGTTTGA	0.338																																					p.R274R	Ovarian(143;1926 2468 21071 48641)	Atlas-SNP	.											.	RGS6	92	.	0			c.A822G						.						128	125	126					14																	72945005		2203	4299	6502	SO:0001819	synonymous_variant	9628	exon12			CGACAGACATTGT	AF073920	CCDS9808.1, CCDS55924.1, CCDS73655.1	14q24.3	2008-07-28	2007-08-14			ENSG00000182732		"Regulators of G-protein signaling"	10002	protein-coding gene	gene with protein product		603894	"regulator of G-protein signalling 6"			10083744, 14734556	Standard	NM_004296		Approved		uc010ttn.2	P49758		ENST00000553530.1:c.822A>G	chr14.hg19:g.72945005A>G		95.0	0.0		61.0	4.0	NM_001204424	C9JE95|F8W7W5|O75576|O75577|Q7Z4K3|Q7Z4K4|Q7Z4K5|Q7Z4K6|Q8TE13|Q8TE14|Q8TE15|Q8TE16|Q8TE17|Q8TE18|Q8TE19|Q8TE20|Q8TE21|Q8TE22|Q9UDS8|Q9UDT0|Q9Y245|Q9Y647	Silent	SNP	ENST00000553530.1	hg19	CCDS9808.1																																																																																			.	.		0.338	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2			G	72945005	A	G	72945005	2	3	65	1	0	0	0	0	0	0	0	1	13324	272	10	2		2	RGS6	14	72945005	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	4696796	72945005	34404535	307	8380										
ZC3H14	79882	hgsc.bcm.edu	37	chr14	89039002	89039002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gccagcaccctctgaagatgTgattgatattaagccagaac	9	10	1	5			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:89039002T>C	ENST00000251038.5	+	6	737	c.512T>C	c.(511-513)gTg>gCg	p.V171A	ZC3H14_ENST00000555755.1_Missense_Mutation_p.V171A|ZC3H14_ENST00000336693.4_Missense_Mutation_p.V137A|ZC3H14_ENST00000359301.3_Missense_Mutation_p.V137A|ZC3H14_ENST00000556945.1_Missense_Mutation_p.V171A|ZC3H14_ENST00000393514.5_Missense_Mutation_p.V171A|ZC3H14_ENST00000302216.8_Missense_Mutation_p.V171A|ZC3H14_ENST00000557607.1_Missense_Mutation_p.V16A	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	171						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						TCTGAAGATGTGATTGATATT	0.418																																					p.V171A		Atlas-SNP	.											.	ZC3H14	71	.	0			c.T512C						.						129	128	128					14																	89039002		2203	4300	6503	SO:0001583	missense	79882	exon6			AAGATGTGATTGA	AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"Zinc fingers, CCCH-type domain containing"	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.512T>C	chr14.hg19:g.89039002T>C	ENSP00000251038:p.Val171Ala	131.0	0.0		90.0	4.0	NM_001160104	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Missense_Mutation	SNP	ENST00000251038.5	hg19	CCDS32133.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.4|22.4	4.286972|4.286972	0.80803|0.80803	.|.	.|.	ENSG00000100722|ENSG00000100722	ENST00000251038;ENST00000393530;ENST00000353091;ENST00000359301;ENST00000302216;ENST00000380684;ENST00000556945;ENST00000556158;ENST00000557607;ENST00000555799;ENST00000555755;ENST00000393514;ENST00000336693|ENST00000556000	.|.	.|.	.|.	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	0.057386|.	0.64402|.	N|.	0.000001|.	T|.	0.73265|.	0.3565|.	M|M	0.66939|0.66939	2.045|2.045	0.49915|0.49915	D|D	0.999839|0.999839	P;D;B;P;D;P|.	0.71674|.	0.577;0.998;0.3;0.493;0.998;0.493|.	B;D;B;B;D;B|.	0.77557|.	0.269;0.99;0.197;0.338;0.99;0.232|.	T|.	0.72606|.	-0.4242|.	9|.	0.39692|.	T|.	0.17|.	-3.8199|-3.8199	16.1838|16.1838	0.81934|0.81934	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	171;152;171;171;171;171|.	G3V256;F8W848;G3V5R4;Q6PJT7-2;Q6PJT7-3;Q6PJT7|.	.;.;.;.;.;ZC3HE_HUMAN|.	A|R	171;171;171;137;171;152;171;158;16;137;171;171;137|87	.|.	ENSP00000251038:V171A|.	V|X	+|+	2|1	0|0	ZC3H14|ZC3H14	88108755|88108755	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.575000|6.575000	0.74018|0.74018	2.225000|2.225000	0.72522|0.72522	0.533000|0.533000	0.62120|0.62120	GTG|TGA	.	.		0.418	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824		C	89039002	T	C	89039002	3	2	65	1	0	0	0	0	1	0	0	0	17581	1696	59	2	534	2	ZC3H14	14	89039002	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	16093997	89039002	18310538	308	8381										
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91770230	91770230	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgctgcctctgcaggctttcGttctccgtctccttggccgt	10	15	3	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:91770230G>A	ENST00000389857.6	-	20	3536	c.3450C>T	c.(3448-3450)aaC>aaT	p.N1150N		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1150					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GCAGGCTTTCGTTCTCCGTCT	0.657																																					p.N1150N		Atlas-SNP	.											.	CCDC88C	192	.	0			c.C3450T						.						72	80	78					14																	91770230		2159	4255	6414	SO:0001819	synonymous_variant	440193	exon20			GCTTTCGTTCTCC		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"Dvl-associating protein with a high frequency of leucine residues", "spinocerebellar ataxia 40"	611204	"KIAA1509"	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.3450C>T	chr14.hg19:g.91770230G>A		104.0	0.0		76.0	5.0	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	hg19	CCDS45151.1																																																																																			.	.		0.657	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		A	91770230	G	A	91770230	2	1	65	1	0	0	0	0	0	0	0	1	2867	1136	40	1		1	CCDC88C	14	91770230	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	2731228	91770230	15579310	309	8382										
SLC24A4	123041	hgsc.bcm.edu	37	chr14	92790275	92790275	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgcggtgctggccctggtgtGctgtgcgtccggcctcttcg	16	14	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:92790275G>A	ENST00000532405.1	+	1	327	c.101G>A	c.(100-102)tGc>tAc	p.C34Y	SLC24A4_ENST00000531433.1_Missense_Mutation_p.C34Y|SLC24A4_ENST00000351924.5_Missense_Mutation_p.C17Y|SLC24A4_ENST00000393265.2_Intron|SLC24A4_ENST00000298877.1_Missense_Mutation_p.C17Y			Q8NFF2	NCKX4_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	34					amelogenesis (GO:0097186)|cellular calcium ion homeostasis (GO:0006874)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|sensory perception of smell (GO:0007608)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(20)|ovary(2)|skin(1)	36		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		GCCCTGGTGTGCTGTGCGTCC	0.697																																					p.C34Y	NSCLC(10;315 435 10383 28450 38798)	Atlas-SNP	.											.	SLC24A4	112	.	0			c.G101A						.						49	49	49					14																	92790275		2203	4300	6503	SO:0001583	missense	123041	exon2			TGGTGTGCTGTGC	AF520704	CCDS9903.1, CCDS45155.1, CCDS45156.1, CCDS9903.2, CCDS45155.2	14q32.12	2013-05-22			ENSG00000140090	ENSG00000140090		"Solute carriers"	10978	protein-coding gene	gene with protein product		609840					Standard	NM_153646		Approved	NCKX4	uc001yak.3	Q8NFF2	OTTHUMG00000167589	ENST00000532405.1:c.101G>A	chr14.hg19:g.92790275G>A	ENSP00000431840:p.Cys34Tyr	79.0	0.0		90.0	15.0	NM_153647	B4DHE7|B9ZVY2|Q8N8U6|Q8NCX1|Q8NFF0|Q8NFF1	Missense_Mutation	SNP	ENST00000532405.1	hg19	CCDS9903.2	.	.	.	.	.	.	.	.	.	.	G	8.678	0.904495	0.17760	.	.	ENSG00000140090	ENST00000531433;ENST00000532405;ENST00000298877;ENST00000351924	T;T;T;T	0.66815	0.18;0.18;-0.22;-0.23	4.61	4.61	0.57282	.	0.203246	0.46145	D	0.000309	T	0.46249	0.1383	N	0.08118	0	0.39520	D	0.968499	B;B	0.20988	0.05;0.022	B;B	0.23275	0.037;0.045	T	0.43180	-0.9407	10	0.22706	T	0.39	.	14.379	0.66900	0.0:0.0:1.0:0.0	.	34;34	Q8NFF2-3;Q8NFF2	.;NCKX4_HUMAN	Y	34;34;17;17	ENSP00000433302:C34Y;ENSP00000431840:C34Y;ENSP00000298877:C17Y;ENSP00000337789:C17Y	ENSP00000298877:C17Y	C	+	2	0	SLC24A4	91860028	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.422000	0.52749	2.120000	0.65058	0.462000	0.41574	TGC	.	.		0.697	SLC24A4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395240.1	NM_153646		A	92790275	G	A	92790275	3	1	65	1	0	0	0	0	1	0	0	0	14483	1319	46	3	52	3	SLC24A4	14	92790275	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	1020045	92790275	14559265	310	8383										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94007149	94007149	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgataaacacgatcagaggcTgctcagtcaattcggaatat	9	8	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr14:94007149T>C	ENST00000393151.2	+	13	1496	c.1496T>C	c.(1495-1497)cTg>cCg	p.L499P	UNC79_ENST00000555664.1_Missense_Mutation_p.L499P|UNC79_ENST00000553484.1_Missense_Mutation_p.L499P|UNC79_ENST00000256339.4_Missense_Mutation_p.L322P			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	499					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						GATCAGAGGCTGCTCAGTCAA	0.428																																					p.L322P		Atlas-SNP	.											.	UNC79	366	.	0			c.T965C						.						88	91	90					14																	94007149		2203	4300	6503	SO:0001583	missense	57578	exon13			AGAGGCTGCTCAG	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.1496T>C	chr14.hg19:g.94007149T>C	ENSP00000376858:p.Leu499Pro	91.0	0.0		75.0	4.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	T	23.3	4.403283	0.83230	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	5.61	5.61	0.85477	.	0.000000	0.64402	D	0.000003	T	0.47619	0.1455	L	0.54323	1.7	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.83275	0.996;0.994	T	0.45891	-0.9230	10	0.72032	D	0.01	-11.1342	15.7948	0.78401	0.0:0.0:0.0:1.0	.	499;499	C9JQL1;Q9P2D8	.;UNC79_HUMAN	P	322;499;499;499;499	ENSP00000256339:L322P;ENSP00000450868:L499P;ENSP00000451360:L499P;ENSP00000376858:L499P	ENSP00000256339:L322P	L	+	2	0	KIAA1409	93076902	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.040000	0.89188	2.128000	0.65567	0.528000	0.53228	CTG	.	.		0.428	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		C	94007149	T	C	94007149	3	2	65	1	0	0	0	0	1	0	0	0	8239	1580	55	2	1003	2	KIAA1409	14	94007149	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1216874	94007149	13342391	311	8384										
EHD4	30844	hgsc.bcm.edu	37	chr15	42245961	42245961	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tggcagcttgctggtccttaCcgattcaggaaagcgtttcc	11	11	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr15:42245961C>A	ENST00000220325.4	-	2	497		c.e2+1			NM_139265.3	NP_644670.1	Q9H223	EHD4_HUMAN	EH-domain containing 4						cellular response to growth factor stimulus (GO:0071363)|endocytic recycling (GO:0032456)|pinocytosis (GO:0006907)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein homooligomerization (GO:0051260)|regulation of endocytosis (GO:0030100)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(7)|ovary(2)|stomach(1)|urinary_tract(1)	20		all_cancers(109;2.54e-12)|all_epithelial(112;6.59e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		OV - Ovarian serous cystadenocarcinoma(18;1.6e-19)|GBM - Glioblastoma multiforme(94;3.77e-06)|COAD - Colon adenocarcinoma(120;0.0474)|Colorectal(105;0.0538)		CTGGTCCTTACCGATTCAGGA	0.453																																					.		Atlas-SNP	.											.	EHD4	46	.	0			c.413+1G>T						.						95	98	97					15																	42245961		2203	4299	6502	SO:0001630	splice_region_variant	30844	exon3			TCCTTACCGATTC	AF181265	CCDS10081.1	15q11.1	2013-01-10			ENSG00000103966	ENSG00000103966		"EF-hand domain containing"	3245	protein-coding gene	gene with protein product		605892		PAST4		10673336, 11533061	Standard	NM_139265		Approved		uc001zot.3	Q9H223	OTTHUMG00000130370	ENST00000220325.4:c.413+1G>T	chr15.hg19:g.42245961C>A		77.0	0.0		66.0	36.0	NM_139265	Q9HAR1|Q9NZN2	Splice_Site	SNP	ENST00000220325.4	hg19	CCDS10081.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.964340	0.92791	.	.	ENSG00000103966	ENST00000220325	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3539	0.98825	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	EHD4	40033253	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.487000	0.81328	2.826000	0.97356	0.655000	0.94253	.	.	.		0.453	EHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252737.2	NM_139265	Intron	A	42245961	C	A	42245961	5	1	65	1	0	0	0	0	0	0	1	0	4982	521	18	3	1231	3	EHD4	15	42245961	Splice_Site	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10		42245961	60285431	312	8385										
CEP152	22995	hgsc.bcm.edu	37	chr15	49060502	49060502	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcttgatttgtatttctcagTtttccttcagtttctttaag	5	7	4	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr15:49060502T>C	ENST00000380950.2	-	15	2119	c.1932A>G	c.(1930-1932)aaA>aaG	p.K644K	CEP152_ENST00000399334.3_Silent_p.K644K|CEP152_ENST00000325747.5_Silent_p.K551K|CEP152_ENST00000559398.1_5'Flank	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	644					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TATTTCTCAGTTTTCCTTCAG	0.289																																					p.K644K		Atlas-SNP	.											.	CEP152	145	.	0			c.A1932G						.						169	153	158					15																	49060502		1826	4075	5901	SO:0001819	synonymous_variant	22995	exon15			TCTCAGTTTTCCT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.1932A>G	chr15.hg19:g.49060502T>C		100.0	0.0		83.0	4.0	NM_014985	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.		0.289	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		C	49060502	T	C	49060502	2	2	65	1	0	0	0	0	0	0	0	1	3250	1722	60	2		2	CEP152	15	49060502	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6814541	49060502	53470890	313	8386										
FAM81A	145773	hgsc.bcm.edu	37	chr15	59801108	59801108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cttgtcaatatcagagcagaGcaccaaactgaagatgtctc	8	10	3	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr15:59801108G>A	ENST00000288228.5	+	6	777	c.590G>A	c.(589-591)aGc>aAc	p.S197N		NM_152450.2	NP_689663.2	Q8TBF8	FA81A_HUMAN	family with sequence similarity 81, member A	197										endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10						TCAGAGCAGAGCACCAAACTG	0.353																																					p.S197N		Atlas-SNP	.											.	FAM81A	31	.	0			c.G590A						.						79	73	75					15																	59801108		1824	4081	5905	SO:0001583	missense	145773	exon6			AGCAGAGCACCAA		CCDS45269.1	15q22.2	2012-10-02			ENSG00000157470	ENSG00000157470			28379	protein-coding gene	gene with protein product							Standard	NM_152450		Approved	MGC26690	uc002agc.2	Q8TBF8	OTTHUMG00000171915	ENST00000288228.5:c.590G>A	chr15.hg19:g.59801108G>A	ENSP00000288228:p.Ser197Asn	583.0	0.0		567.0	149.0	NM_152450		Missense_Mutation	SNP	ENST00000288228.5	hg19	CCDS45269.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.208478	0.39003	.	.	ENSG00000157470	ENST00000288228	T	0.30182	1.54	5.73	5.73	0.89815	.	0.160367	0.49916	D	0.000121	T	0.28001	0.0690	L	0.33485	1.01	0.30256	N	0.793619	P	0.50528	0.936	P	0.47673	0.554	T	0.13818	-1.0495	10	0.30854	T	0.27	-11.2995	10.196	0.43054	0.0939:0.0:0.9061:0.0	.	197	Q8TBF8	FA81A_HUMAN	N	197	ENSP00000288228:S197N	ENSP00000288228:S197N	S	+	2	0	FAM81A	57588400	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.383000	0.59600	2.714000	0.92807	0.561000	0.74099	AGC	.	.		0.353	FAM81A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415876.1	NM_152450		A	59801108	G	A	59801108	3	1	65	1	0	0	0	0	1	0	0	0	5636	971	34	3	608	3	FAM81A	15	59801108	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	10740606	59801108	42730284	314	8387										
CLN6	54982	hgsc.bcm.edu	37	chr15	68500609	68500609	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gagcgccacaagcaagagggTcagtgcgaaggaggagaaga	17	7	1	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr15:68500609T>C	ENST00000249806.5	-	7	962	c.805A>G	c.(805-807)Acc>Gcc	p.T269A	RP11-315D16.2_ENST00000562767.1_Intron|CALML4_ENST00000395465.3_5'Flank|CALML4_ENST00000540479.1_5'Flank|CLN6_ENST00000418702.2_Missense_Mutation_p.T140A|CLN6_ENST00000565471.1_Missense_Mutation_p.T116A|CALML4_ENST00000448060.2_5'Flank|CALML4_ENST00000467889.1_5'Flank|CLN6_ENST00000538696.1_Missense_Mutation_p.T301A|CLN6_ENST00000566347.1_Missense_Mutation_p.T206A	NM_017882.2	NP_060352.1	Q9NWW5	CLN6_HUMAN	ceroid-lipofuscinosis, neuronal 6, late infantile, variant	269					cell death (GO:0008219)|cellular macromolecule catabolic process (GO:0044265)|cholesterol metabolic process (GO:0008203)|ganglioside metabolic process (GO:0001573)|glycosaminoglycan metabolic process (GO:0030203)|locomotion involved in locomotory behavior (GO:0031987)|lysosomal lumen acidification (GO:0007042)|positive regulation of proteolysis (GO:0045862)|protein catabolic process (GO:0030163)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						AGCAAGAGGGTCAGTGCGAAG	0.602																																					p.T269A		Atlas-SNP	.											.	CLN6	16	.	0			c.A805G						.						124	117	119					15																	68500609		2200	4298	6498	SO:0001583	missense	54982	exon7			AGAGGGTCAGTGC	AK000568	CCDS10227.1	15q23	2014-09-17			ENSG00000128973	ENSG00000128973			2077	protein-coding gene	gene with protein product		606725				9097964, 11727201	Standard	NM_017882		Approved	FLJ20561, HsT18960, nclf	uc002arf.3	Q9NWW5	OTTHUMG00000133286	ENST00000249806.5:c.805A>G	chr15.hg19:g.68500609T>C	ENSP00000249806:p.Thr269Ala	121.0	0.0		113.0	6.0	NM_017882	A8K560|B4DDH6|Q6IAB1|Q96SR0	Missense_Mutation	SNP	ENST00000249806.5	hg19	CCDS10227.1	.	.	.	.	.	.	.	.	.	.	T	11.64	1.699536	0.30142	.	.	ENSG00000128973	ENST00000249806;ENST00000418702;ENST00000538696	D;D;D	0.94793	-3.52;-3.52;-3.52	5.34	1.76	0.24704	.	0.171254	0.51477	N	0.000095	D	0.89368	0.6695	L	0.43152	1.355	0.47374	D	0.999405	B;B;B	0.19583	0.037;0.003;0.012	B;B;B	0.19148	0.024;0.007;0.017	T	0.80690	-0.1270	10	0.22109	T	0.4	-33.318	8.9728	0.35917	0.0:0.2163:0.0:0.7837	.	301;140;269	B4DDH6;E7ESV1;Q9NWW5	.;.;CLN6_HUMAN	A	269;140;301	ENSP00000249806:T269A;ENSP00000393826:T140A;ENSP00000445770:T301A	ENSP00000249806:T269A	T	-	1	0	CLN6	66287663	0.745000	0.28261	0.974000	0.42286	0.353000	0.29299	0.896000	0.28377	0.371000	0.24564	0.379000	0.24179	ACC	.	.		0.602	CLN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257066.1	NM_017882		C	68500609	T	C	68500609	3	2	65	1	0	0	0	0	1	0	0	0	3547	1667	58	2	134	2	CLN6	15	68500609	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	8699501	68500609	34030783	315	8388										
PAQR5	54852	hgsc.bcm.edu	37	chr15	69672244	69672244	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gttccatgagcaaggcatccTgttcggctaccgccatccac	9	15	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr15:69672244T>C	ENST00000340965.3	+	4	742	c.74T>C	c.(73-75)cTg>cCg	p.L25P	PAQR5_ENST00000561153.1_Missense_Mutation_p.L25P|PAQR5_ENST00000395407.2_Missense_Mutation_p.L25P|PAQR5_ENST00000561027.1_3'UTR	NM_001104554.1	NP_001098024.1	Q9NXK6	MPRG_HUMAN	progestin and adipoQ receptor family member V	25					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)|steroid binding (GO:0005496)			endometrium(3)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|skin(1)	11						CAAGGCATCCTGTTCGGCTAC	0.537																																					p.L25P		Atlas-SNP	.											.	PAQR5	35	.	0			c.T74C						.						266	240	249					15																	69672244		2200	4298	6498	SO:0001583	missense	54852	exon4			GCATCCTGTTCGG		CCDS10232.1	15q22.31	2012-08-10			ENSG00000137819	ENSG00000137819			29645	protein-coding gene	gene with protein product	"membrane progestin receptor gamma"	607781				12574519	Standard	NM_001104554		Approved	FLJ20190, MPRG	uc002arz.2	Q9NXK6	OTTHUMG00000133322	ENST00000340965.3:c.74T>C	chr15.hg19:g.69672244T>C	ENSP00000343877:p.Leu25Pro	80.0	0.0		90.0	4.0	NM_001104554	Q8IXU2	Missense_Mutation	SNP	ENST00000340965.3	hg19	CCDS10232.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.723899	0.89298	.	.	ENSG00000137819	ENST00000395407;ENST00000340965	T;T	0.29917	1.55;1.55	5.68	5.68	0.88126	.	0.052632	0.64402	D	0.000001	T	0.49029	0.1533	M	0.66939	2.045	0.80722	D	1	D	0.60160	0.987	P	0.58266	0.836	T	0.50906	-0.8772	10	0.62326	D	0.03	0.0445	13.865	0.63583	0.0:0.0:0.0:1.0	.	25	Q9NXK6	MPRG_HUMAN	P	25	ENSP00000378803:L25P;ENSP00000343877:L25P	ENSP00000343877:L25P	L	+	2	0	PAQR5	67459298	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	7.625000	0.83145	2.152000	0.67230	0.533000	0.62120	CTG	.	.		0.537	PAQR5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416671.1	NM_017705		C	69672244	T	C	69672244	3	2	65	1	0	0	0	0	1	0	0	0	11447	1580	55	2	80	2	PAQR5	15	69672244	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1171635	69672244	32859148	316	8389										
RCCD1	91433	hgsc.bcm.edu	37	chr15	91500890	91500890	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gctggagccacggctgttggAggcgttgcagggcctagtca	17	10	1	0	rs75741610		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr15:91500890A>G	ENST00000394258.2	+	4	816	c.614A>G	c.(613-615)gAg>gGg	p.E205G	RCCD1_ENST00000556618.1_Missense_Mutation_p.E205G|RCCD1_ENST00000555155.1_Missense_Mutation_p.E205G|RCCD1_ENST00000556774.1_Intron|AC068831.6_ENST00000553321.1_RNA	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	205						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			CGGCTGTTGGAGGCGTTGCAG	0.617																																					p.E205G		Atlas-SNP	.											.	RCCD1	9	.	0			c.A614G						.						86	83	84					15																	91500890		2198	4298	6496	SO:0001583	missense	91433	exon4			TGTTGGAGGCGTT		CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.614A>G	chr15.hg19:g.91500890A>G	ENSP00000377801:p.Glu205Gly	99.0	0.0		121.0	10.0	NM_001017919	B2RTP9|Q29RX6	Missense_Mutation	SNP	ENST00000394258.2	hg19	CCDS32333.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.334691	0.81801	.	.	ENSG00000166965	ENST00000394258;ENST00000555155;ENST00000556618	T;T;T	0.80214	-1.35;-1.35;-1.35	3.59	3.59	0.41128	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.84866	0.5567	L	0.49455	1.56	0.80722	D	1	D;D	0.67145	0.995;0.996	D;D	0.67382	0.919;0.951	D	0.85723	0.1326	10	0.62326	D	0.03	.	12.1904	0.54268	1.0:0.0:0.0:0.0	.	205;205	G3V2I3;A6NED2	.;RCCD1_HUMAN	G	205	ENSP00000377801:E205G;ENSP00000450678:E205G;ENSP00000451963:E205G	ENSP00000377801:E205G	E	+	2	0	RCCD1	89301894	1.000000	0.71417	0.996000	0.52242	0.741000	0.42261	6.470000	0.73558	1.426000	0.47256	0.397000	0.26171	GAG	.	.		0.617	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544		G	91500890	A	G	91500890	3	3	65	1	0	0	0	0	1	0	0	0	13190	304	11	2	624	2	RCCD1	15	91500890	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	21828646	91500890	11030502	317	8390										
CHD2	1106	hgsc.bcm.edu	37	chr15	93489406	93489406	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttgcattgacagcttccacaGtaggaacaactcaaaaacca	6	11	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr15:93489406G>C	ENST00000394196.4	+	12	2405	c.1337G>C	c.(1336-1338)aGt>aCt	p.S446T	CHD2_ENST00000557381.1_Missense_Mutation_p.S446T|CHD2_ENST00000536619.1_Missense_Mutation_p.S459T|CHD2_ENST00000420239.2_Missense_Mutation_p.S446T	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	446	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			AGCTTCCACAGTAGGAACAAC	0.413																																					p.S446T		Atlas-SNP	.											.	CHD2	280	.	0			c.G1337C						.						81	82	82					15																	93489406		2197	4298	6495	SO:0001583	missense	1106	exon12			TCCACAGTAGGAA	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.1337G>C	chr15.hg19:g.93489406G>C	ENSP00000377747:p.Ser446Thr	276.0	1.0		186.0	68.0	NM_001042572	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	12.29	1.893022	0.33442	.	.	ENSG00000173575	ENST00000394196;ENST00000557381;ENST00000420239;ENST00000536619	T;T;T;T	0.73681	-0.77;-0.77;-0.77;-0.77	5.57	3.33	0.38152	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (2);	0.467569	0.15445	U	0.261968	T	0.58119	0.2100	N	0.14661	0.345	0.28055	N	0.933226	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.11329	0.006;0.001;0.001	T	0.55995	-0.8052	10	0.54805	T	0.06	-7.073	11.5016	0.50441	0.2318:0.0:0.7682:0.0	.	459;446;446	B7Z3I4;O14647;O14647-2	.;CHD2_HUMAN;.	T	446;446;446;459	ENSP00000377747:S446T;ENSP00000451366:S446T;ENSP00000406581:S446T;ENSP00000443618:S459T	ENSP00000377747:S446T	S	+	2	0	CHD2	91290410	0.967000	0.33354	0.998000	0.56505	0.983000	0.72400	0.759000	0.26461	1.498000	0.48600	0.655000	0.94253	AGT	.	.		0.413	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		C	93489406	G	C	93489406	3	2	65	1	0	0	0	0	1	0	0	0	3327	1029	36	4	1379	4	CHD2	15	93489406	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	1988516	93489406	9041986	318	8391										
CHD2	1106	hgsc.bcm.edu	37	chr15	93489423	93489423	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acagtaggaacaactcaaaaAccatcccaacaagagaatgc	6	11	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr15:93489423A>G	ENST00000394196.4	+	12	2422	c.1354A>G	c.(1354-1356)Acc>Gcc	p.T452A	CHD2_ENST00000557381.1_Missense_Mutation_p.T452A|CHD2_ENST00000536619.1_Missense_Mutation_p.T465A|CHD2_ENST00000420239.2_Missense_Mutation_p.T452A	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	452	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			CAACTCAAAAACCATCCCAAC	0.428																																					p.T452A		Atlas-SNP	.											.	CHD2	280	.	0			c.A1354G						.						74	76	75					15																	93489423		2197	4298	6495	SO:0001583	missense	1106	exon12			TCAAAAACCATCC	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.1354A>G	chr15.hg19:g.93489423A>G	ENSP00000377747:p.Thr452Ala	288.0	0.0		199.0	76.0	NM_001042572	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	A	17.84	3.487357	0.63962	.	.	ENSG00000173575	ENST00000394196;ENST00000557381;ENST00000420239;ENST00000536619	D;D;T;T	0.93133	-3.17;-3.17;0.86;0.85	5.57	5.57	0.84162	Chromo domain/shadow (1);	0.000000	0.35096	U	0.003459	D	0.91399	0.7286	L	0.53729	1.69	0.53688	D	0.999978	B;B;P	0.35139	0.047;0.002;0.486	B;B;B	0.35550	0.065;0.035;0.205	D	0.90425	0.4420	10	0.37606	T	0.19	-30.4941	16.0216	0.80499	1.0:0.0:0.0:0.0	.	465;452;452	B7Z3I4;O14647;O14647-2	.;CHD2_HUMAN;.	A	452;452;452;465	ENSP00000377747:T452A;ENSP00000451366:T452A;ENSP00000406581:T452A;ENSP00000443618:T465A	ENSP00000377747:T452A	T	+	1	0	CHD2	91290427	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.088000	0.76901	2.242000	0.73789	0.533000	0.62120	ACC	.	.		0.428	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		G	93489423	A	G	93489423	3	3	65	1	0	0	0	0	1	0	0	0	3327	43	2	2	1396	2	CHD2	15	93489423	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	17	93489423	9041969	319	8392										
MRPS34	65993	hgsc.bcm.edu	37	chr16	1822511	1822511	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cccgcgcctcgctctcagtcTtccctgatgaagaaaaagag	9	14	2	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr16:1822511T>C	ENST00000397375.2	-	3	403	c.368A>G	c.(367-369)aAg>aGg	p.K123R	EME2_ENST00000307394.7_5'Flank|NME3_ENST00000219302.3_5'Flank|MRPS34_ENST00000177742.3_Missense_Mutation_p.K130R|EME2_ENST00000568449.1_5'Flank|NME3_ENST00000563498.1_5'Flank	NM_023936.1	NP_076425.1	P82930	RT34_HUMAN	mitochondrial ribosomal protein S34	123						mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|skin(2)	3						GCTCTCAGTCTTCCCTGATGA	0.627																																					p.K123R		Atlas-SNP	.											MRPS34,bladder,carcinoma,0,1	MRPS34	7	.	0			c.A368G						.						68	73	71					16																	1822511		2197	4300	6497	SO:0001583	missense	65993	exon3			TCAGTCTTCCCTG	BC001182	CCDS10444.1, CCDS73805.1	16p13.3	2012-09-13			ENSG00000074071	ENSG00000074071		"Mitochondrial ribosomal proteins / small subunits"	16618	protein-coding gene	gene with protein product		611994					Standard	NM_023936		Approved	MRP-S12, MGC2616	uc002cmo.3	P82930	OTTHUMG00000128636	ENST00000397375.2:c.368A>G	chr16.hg19:g.1822511T>C	ENSP00000380531:p.Lys123Arg	89.0	0.0		65.0	3.0	NM_023936	Q9BVI7	Missense_Mutation	SNP	ENST00000397375.2	hg19	CCDS10444.1	.	.	.	.	.	.	.	.	.	.	T	13.78	2.339933	0.41398	.	.	ENSG00000074071	ENST00000397375;ENST00000177742	T;T	0.53640	0.61;0.61	4.02	0.499	0.16914	.	0.231983	0.40908	N	0.000986	T	0.26521	0.0648	N	0.17872	0.535	0.41738	D	0.98959	B;B	0.11235	0.004;0.003	B;B	0.12156	0.007;0.007	T	0.05599	-1.0875	10	0.21014	T	0.42	-5.5931	7.5514	0.27800	0.0:0.265:0.0:0.735	.	130;123	C9JJ19;P82930	.;RT34_HUMAN	R	123;130	ENSP00000380531:K123R;ENSP00000177742:K130R	ENSP00000177742:K130R	K	-	2	0	MRPS34	1762512	1.000000	0.71417	0.003000	0.11579	0.056000	0.15407	3.873000	0.56093	-0.104000	0.12154	0.459000	0.35465	AAG	.	.		0.627	MRPS34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250506.1	NM_023936		C	1822511	T	C	1822511	3	2	65	1	0	0	0	0	1	0	0	0	9852	1609	56	2	292	2	MRPS34	16	1822511	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		1822511	88532242	320	8393										
SPN	6693	hgsc.bcm.edu	37	chr16	29675097	29675097	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtgctggtggtaagcccagaCgctctggggagcacaacagc	15	11	1	1	rs556201400		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr16:29675097C>T	ENST00000360121.3	+	2	140	c.48C>T	c.(46-48)gaC>gaT	p.D16D	SPN_ENST00000395389.2_Silent_p.D16D	NM_001030288.2|NM_003123.4	NP_001025459.1|NP_003114.1	O75398	DEAF1_HUMAN	sialophorin	0	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|stomach(1)	15						TAAGCCCAGACGCTCTGGGGA	0.587													t|||	1	0.000199681	0	0.0014	5008	,	,		17775	0		0	False		,,,				2504	0				p.D16D		Atlas-SNP	.											.	SPN	44	.	0			c.C48T						.						117	127	124					16																	29675097		2197	4300	6497	SO:0001819	synonymous_variant	6693	exon2			CCCAGACGCTCTG	J04536	CCDS10650.1	16p11.2	2008-07-31	2008-07-31		ENSG00000197471	ENSG00000197471		"CD molecules"	11249	protein-coding gene	gene with protein product	"leukosialin"	182160	"sialophorin (gpL115, leukosialin, CD43)"			2784859, 2521952	Standard	NM_001030288		Approved	LSN, CD43, GPL115	uc002dtm.4	P16150	OTTHUMG00000097765	ENST00000360121.3:c.48C>T	chr16.hg19:g.29675097C>T		105.0	0.0		100.0	4.0	NM_001030288	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Silent	SNP	ENST00000360121.3	hg19	CCDS10650.1																																																																																			.	.		0.587	SPN-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215001.2			T	29675097	C	T	29675097	2	4	65	1	0	0	0	0	0	0	0	1	15088	535	19	1		1	SPN	16	29675097	Silent	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	27852586	29675097	60679656	321	8394										
VPS35	55737	hgsc.bcm.edu	37	chr16	46708512	46708512	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acctgctgtgaaaatatatcAaaaagtttaatatccgctgg	7	7	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr16:46708512A>G	ENST00000299138.7	-	9	1033	c.975T>C	c.(973-975)ttT>ttC	p.F325F	VPS35_ENST00000568642.1_5'UTR	NM_018206.4	NP_060676.2	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35 homolog (S. cerevisiae)	325					cell death (GO:0008219)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|retromer complex (GO:0030904)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|pancreas(1)|prostate(1)|urinary_tract(1)	23		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				AAAATATATCAAAAAGTTTAA	0.343																																					p.F325F		Atlas-SNP	.											.	VPS35	49	.	0			c.T975C						.						38	38	38					16																	46708512		2203	4300	6503	SO:0001819	synonymous_variant	55737	exon9			TATATCAAAAAGT	AF175265	CCDS10721.1	16q12	2012-06-27	2006-12-19		ENSG00000069329	ENSG00000069329		"Parkinson disease"	13487	protein-coding gene	gene with protein product		601501	"vacuolar protein sorting 35 (yeast homolog)", "vacuolar protein sorting 35 (yeast)"			11112353, 21763482	Standard	NM_018206		Approved	FLJ10752, MEM3, PARK17	uc002eef.4	Q96QK1	OTTHUMG00000132542	ENST00000299138.7:c.975T>C	chr16.hg19:g.46708512A>G		100.0	0.0		77.0	4.0	NM_018206	Q561W2|Q9H016|Q9H096|Q9H4P3|Q9H8J0|Q9NRS7|Q9NVG2|Q9NX80|Q9NZK2	Silent	SNP	ENST00000299138.7	hg19	CCDS10721.1																																																																																			.	.		0.343	VPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255742.3			G	46708512	A	G	46708512	2	3	65	1	0	0	0	0	0	0	0	1	17218	127	5	2		2	VPS35	16	46708512	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	17033415	46708512	43646241	322	8395										
HEATR3	55027	hgsc.bcm.edu	37	chr16	50136189	50136189	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaacattgggtgctttctgcTtgaagttaccaccaaagatc	9	9	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr16:50136189T>C	ENST00000299192.7	+	14	1954	c.1763T>C	c.(1762-1764)cTt>cCt	p.L588P	RP11-429P3.5_ENST00000566770.1_RNA|HEATR3_ENST00000285767.4_Missense_Mutation_p.L502P	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	588										cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TGCTTTCTGCTTGAAGTTACC	0.423																																					p.L588P		Atlas-SNP	.											.	HEATR3	59	.	0			c.T1763C						.						200	172	182					16																	50136189		2198	4300	6498	SO:0001583	missense	55027	exon14			TTCTGCTTGAAGT	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.1763T>C	chr16.hg19:g.50136189T>C	ENSP00000299192:p.Leu588Pro	100.0	0.0		79.0	4.0	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Missense_Mutation	SNP	ENST00000299192.7	hg19	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	T	18.89	3.719032	0.68844	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	T;T	0.69926	-0.44;-0.44	5.49	5.49	0.81192	Armadillo-type fold (1);	0.057544	0.64402	D	0.000001	T	0.80226	0.4584	M	0.67953	2.075	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.73380	0.98;0.909	T	0.82299	-0.0526	10	0.72032	D	0.01	.	15.8841	0.79226	0.0:0.0:0.0:1.0	.	502;588	B7WNW7;Q7Z4Q2	.;HEAT3_HUMAN	P	502;588	ENSP00000285767:L502P;ENSP00000299192:L588P	ENSP00000285767:L502P	L	+	2	0	HEATR3	48693690	1.000000	0.71417	0.967000	0.41034	0.734000	0.41952	5.319000	0.65835	2.215000	0.71742	0.528000	0.53228	CTT	.	.		0.423	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		C	50136189	T	C	50136189	3	2	65	1	0	0	0	0	1	0	0	0	7038	1609	56	2	1817	2	HEATR3	16	50136189	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3427677	50136189	40218564	323	8396										
RBL2	5934	hgsc.bcm.edu	37	chr16	53513864	53513864	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctggcagcagtgatagcagaAgccatcagaattctccaaca	9	11	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr16:53513864A>G	ENST00000262133.6	+	19	2979	c.2842A>G	c.(2842-2844)Agc>Ggc	p.S948G	RBL2_ENST00000544545.1_Intron|RBL2_ENST00000379935.4_3'UTR	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	948	Domain B.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TGATAGCAGAAGCCATCAGAA	0.353																																					p.S948G		Atlas-SNP	.											.	RBL2	115	.	0			c.A2842G						.						69	72	71					16																	53513864		2198	4300	6498	SO:0001583	missense	5934	exon19			AGCAGAAGCCATC	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2842A>G	chr16.hg19:g.53513864A>G	ENSP00000262133:p.Ser948Gly	141.0	0.0		98.0	4.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	hg19	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.048109	0.36085	.	.	ENSG00000103479	ENST00000262133;ENST00000379935	D	0.90197	-2.63	5.59	5.59	0.84812	Retinoblastoma-associated protein, B-box (1);Cyclin-like (1);	0.148202	0.64402	D	0.000012	D	0.84800	0.5552	L	0.34521	1.04	0.80722	D	1	P;B	0.39424	0.673;0.126	B;B	0.37550	0.253;0.096	D	0.84786	0.0776	10	0.46703	T	0.11	-15.5902	10.8547	0.46792	0.8421:0.1579:0.0:0.0	.	658;948	E9PG04;Q08999	.;RBL2_HUMAN	G	948;658	ENSP00000262133:S948G	ENSP00000262133:S948G	S	+	1	0	RBL2	52071365	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.954000	0.56708	2.126000	0.65437	0.528000	0.53228	AGC	.	.		0.353	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		G	53513864	A	G	53513864	3	3	65	1	0	0	0	0	1	0	0	0	13125	72	3	2	2916	2	RBL2	16	53513864	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3377675	53513864	36840889	324	8397										
TSNAXIP1	80152	hgsc.bcm.edu	37	chr16	67859617	67859617	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	taaccctggctcttaagatgAcccggcaagacctgacccgc	9	15	1	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr16:67859617A>G	ENST00000562787.1	-	0	2345				TSNAXIP1_ENST00000388833.3_Missense_Mutation_p.T234A|TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.T288A|TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.T219A	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T						chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		TCTTAAGATGACCCGGCAAGA	0.582																																					p.T234A		Atlas-SNP	.											.	TSNAXIP1	66	.	0			c.A700G						.						109	115	113					16																	67859617		2065	4218	6283	SO:0001628	intergenic_variant	55815	exon8			AAGATGACCCGGC	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3			chr16.hg19:g.67859617A>G		74.0	0.0		80.0	4.0	NM_018430	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	hg19	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	A	1.325	-0.598275	0.03744	.	.	ENSG00000102904	ENST00000415766;ENST00000388833;ENST00000431934	.	.	.	5.8	-5.82	0.02333	.	0.903009	0.09563	N	0.785321	T	0.16428	0.0395	N	0.02213	-0.635	0.26558	N	0.973781	B;B;B;B	0.06786	0.001;0.001;0.0;0.0	B;B;B;B	0.08055	0.003;0.002;0.001;0.002	T	0.44467	-0.9326	9	0.02654	T	1	-0.017	19.6123	0.95613	0.1619:0.0:0.8381:0.0	.	219;288;24;234	E7ENJ7;B4DXD0;B4DY78;Q2TAA8	.;.;.;TXIP1_HUMAN	A	219;234;24	.	ENSP00000373485:T234A	T	+	1	0	TSNAXIP1	66417118	0.269000	0.24143	0.298000	0.25002	0.761000	0.43186	-0.162000	0.10012	-1.067000	0.03160	-0.912000	0.02778	ACC	.	.		0.582	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		G	67859617	A	G	67859617	1	3	65	0	1	0	0	0	0	0	0	0	16647	275	10	2		2	TSNAXIP1	16	67859617	IGR	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	14345753	67859617	22495136	325	8398										
ABR	29	hgsc.bcm.edu	37	chr17	975915	975915	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgtcctcgttgatgctggacAggaagttctgggagatgcgg	16	7	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:975915A>G	ENST00000302538.5	-	8	979	c.833T>C	c.(832-834)cTg>cCg	p.L278P	ABR_ENST00000544583.2_Missense_Mutation_p.L232P|ABR_ENST00000291107.2_Missense_Mutation_p.L241P|ABR_ENST00000574437.1_Missense_Mutation_p.L232P|ABR_ENST00000536794.2_Missense_Mutation_p.L60P	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	278	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		GATGCTGGACAGGAAGTTCTG	0.657																																					p.L278P	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.T833C						.						111	87	95					17																	975915		2203	4300	6503	SO:0001583	missense	29	exon8			CTGGACAGGAAGT	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	81	protein-coding gene	gene with protein product		600365	"active BCR-related gene"			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.833T>C	chr17.hg19:g.975915A>G	ENSP00000303909:p.Leu278Pro	153.0	0.0		121.0	5.0	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Missense_Mutation	SNP	ENST00000302538.5	hg19	CCDS10999.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.984029	0.93044	.	.	ENSG00000159842	ENST00000302538;ENST00000544583;ENST00000291107;ENST00000536794;ENST00000382259	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.88	5.88	0.94601	Dbl homology (DH) domain (5);	0.060841	0.64402	D	0.000002	T	0.80909	0.4714	M	0.83012	2.62	0.80722	D	1	D;D;D;D	0.89917	0.995;0.995;0.999;1.0	D;D;D;D	0.91635	0.934;0.976;0.992;0.999	D	0.83833	0.0253	10	0.87932	D	0	.	15.4693	0.75429	1.0:0.0:0.0:0.0	.	60;162;241;278	B7Z683;Q6ZT60;Q12979-2;Q12979	.;.;.;ABR_HUMAN	P	278;232;241;60;162	ENSP00000303909:L278P;ENSP00000442048:L232P;ENSP00000291107:L241P;ENSP00000437429:L60P	ENSP00000291107:L241P	L	-	2	0	ABR	922665	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.257000	0.95545	2.227000	0.72691	0.528000	0.53228	CTG	.	.		0.657	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			G	975915	A	G	975915	3	3	65	1	0	0	0	0	1	0	0	0	99	188	7	2	1810	2	ABR	17	975915	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10		975915	80219295	326	8399										
PRPF8	10594	hgsc.bcm.edu	37	chr17	1585147	1585147	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcaacggctggtggtcatagAaccagtccaacacaggggcg	13	11	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:1585147A>G	ENST00000572621.1	-	4	885	c.620T>C	c.(619-621)tTc>tCc	p.F207S	PRPF8_ENST00000304992.6_Missense_Mutation_p.F207S			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	207					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GTGGTCATAGAACCAGTCCAA	0.547																																					p.F207S		Atlas-SNP	.											.	PRPF8	169	.	0			c.T620C						.						92	99	96					17																	1585147		2203	4300	6503	SO:0001583	missense	10594	exon5			TCATAGAACCAGT	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.620T>C	chr17.hg19:g.1585147A>G	ENSP00000460348:p.Phe207Ser	127.0	0.0		89.0	4.0	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	A	19.51	3.840408	0.71488	.	.	ENSG00000174231	ENST00000304992	T	0.51325	0.71	5.7	5.7	0.88788	Pre-mRNA-processing-splicing factor 8 (2);	0.052615	0.85682	D	0.000000	T	0.71854	0.3389	M	0.89095	3.005	0.80722	D	1	P	0.45569	0.861	P	0.58820	0.846	T	0.77509	-0.2561	10	0.87932	D	0	.	15.9682	0.79991	1.0:0.0:0.0:0.0	.	207	Q6P2Q9	PRP8_HUMAN	S	207	ENSP00000304350:F207S	ENSP00000304350:F207S	F	-	2	0	PRPF8	1531897	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.307000	0.96226	2.176000	0.68965	0.454000	0.30748	TTC	.	.		0.547	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			G	1585147	A	G	1585147	3	3	65	1	0	0	0	0	1	0	0	0	12587	246	9	2	6543	2	PRPF8	17	1585147	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	609232	1585147	79610063	327	8400										
ZNF232	7775	hgsc.bcm.edu	37	chr17	5009459	5009459	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttttcccacagtcactacacTtatagggtttctctccagaa	5	12	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:5009459T>C	ENST00000250076.3	-	5	1649	c.995A>G	c.(994-996)aAg>aGg	p.K332R	ZNF232_ENST00000575898.1_Missense_Mutation_p.K323R|ZNF232_ENST00000575538.1_5'Flank|ZNF232_ENST00000416429.2_3'UTR	NM_014519.2	NP_055334.2	Q9UNY5	ZN232_HUMAN	zinc finger protein 232	305					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|prostate(2)	11						GTCACTACACTTATAGGGTTT	0.413																																					p.K332R		Atlas-SNP	.											ZNF232,NS,carcinoma,0,1	ZNF232	42	.	0			c.A995G						.						108	111	110					17																	5009459		2203	4300	6503	SO:0001583	missense	7775	exon5			CTACACTTATAGG	AF080169	CCDS11068.1	17p13.2	2013-01-09			ENSG00000167840	ENSG00000167840		"-", "Zinc fingers, C2H2-type"	13026	protein-coding gene	gene with protein product						11311944	Standard	NM_014519		Approved	ZSCAN11	uc002gat.3	Q9UNY5	OTTHUMG00000099450	ENST00000250076.3:c.995A>G	chr17.hg19:g.5009459T>C	ENSP00000250076:p.Lys332Arg	44.0	0.0		24.0	2.0	NM_014519		Missense_Mutation	SNP	ENST00000250076.3	hg19	CCDS11068.1	.	.	.	.	.	.	.	.	.	.	T	10.06	1.245936	0.22796	.	.	ENSG00000167840	ENST00000250076	T	0.35973	1.28	2.99	0.766	0.18476	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.494253	0.15116	N	0.279675	T	0.20618	0.0496	L	0.31371	0.925	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.15093	-1.0449	10	0.34782	T	0.22	.	3.0462	0.06154	0.0:0.2573:0.2274:0.5153	.	305;296	Q9UNY5;Q9UNY5-2	ZN232_HUMAN;.	R	332	ENSP00000250076:K332R	ENSP00000250076:K332R	K	-	2	0	ZNF232	4950183	0.000000	0.05858	0.041000	0.18516	0.997000	0.91878	-0.645000	0.05409	0.111000	0.17947	0.533000	0.62120	AAG	.	.		0.413	ZNF232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216915.1	NM_014519		C	5009459	T	C	5009459	3	2	65	1	0	0	0	0	1	0	0	0	17800	1609	56	2	343	2	ZNF232	17	5009459	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3424312	5009459	76185751	328	8401										
C17orf87	388325	hgsc.bcm.edu	37	chr17	5124625	5124625	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttgcttgtgtttcaggggctTggcaatttcccatttcttgc	10	9	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:5124625T>C	ENST00000574081.1	-	3	270	c.166A>G	c.(166-168)Aag>Gag	p.K56E	SCIMP_ENST00000574297.1_Missense_Mutation_p.K56E|SCIMP_ENST00000571800.1_Missense_Mutation_p.K49E|RP11-333E1.1_ENST00000573772.1_RNA|RP11-333E1.1_ENST00000575601.1_RNA|SCIMP_ENST00000399600.4_Missense_Mutation_p.K49E|RP11-333E1.1_ENST00000571689.1_RNA	NM_001271842.1|NM_207103.3	NP_001258771.1|NP_996986.1	Q6UWF3	SCIMP_HUMAN	SLP adaptor and CSK interacting membrane protein	56					positive regulation of ERK1 and ERK2 cascade (GO:0070374)	immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|tetraspanin-enriched microdomain (GO:0097197)|uropod membrane (GO:0031259)											TTCAGGGGCTTGGCAATTTCC	0.398																																					p.K56E		Atlas-SNP	.											.	.	.	.	0			c.A166G						.						210	192	198					17																	5124625		1854	4095	5949	SO:0001583	missense	388325	exon3			GGGGCTTGGCAAT	AY358809	CCDS42242.1, CCDS62044.1	17p13.2	2011-11-24	2011-11-23	2011-11-23	ENSG00000161929	ENSG00000161929			33504	protein-coding gene	gene with protein product	"SLP65/SLP76, Csk-interacting membrane protein"	614406	"chromosome 17 open reading frame 87"	C17orf87		21930792	Standard	NM_207103		Approved	DTFT5783, UNQ5783, FLJ32580, MGC163426, MGC163428	uc002gbh.3	Q6UWF3	OTTHUMG00000132914	ENST00000574081.1:c.166A>G	chr17.hg19:g.5124625T>C	ENSP00000461269:p.Lys56Glu	116.0	0.0		99.0	4.0	NM_207103	A6XGL4|B4DLK1|Q96MD0	Missense_Mutation	SNP	ENST00000574081.1	hg19	CCDS42242.1	.	.	.	.	.	.	.	.	.	.	t	17.81	3.479880	0.63849	.	.	ENSG00000161929	ENST00000399600;ENST00000399592	.	.	.	4.58	4.58	0.56647	.	0.548812	0.17726	N	0.164061	T	0.47358	0.1441	M	0.61703	1.905	0.09310	N	1	P;P;P	0.50528	0.728;0.936;0.728	B;P;B	0.48425	0.297;0.577;0.297	T	0.46205	-0.9208	9	0.66056	D	0.02	-5.4106	10.6338	0.45551	0.0:0.0:0.0:1.0	.	49;49;56	A6XGL4;Q6UWF3-2;Q6UWF3	.;.;CQ087_HUMAN	E	56;45	.	ENSP00000382501:K45E	K	-	1	0	C17orf87	5065349	0.238000	0.23825	0.008000	0.14137	0.330000	0.28571	3.289000	0.51747	2.285000	0.76669	0.529000	0.55759	AAG	.	.		0.398	SCIMP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256425.2	NM_207103		C	5124625	T	C	5124625	3	2	65	1	0	0	0	0	1	0	0	0	1891	1821	63	2	283	2	C17orf87	17	5124625	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	115166	5124625	76070585	329	8402										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000420246.2_Missense_Mutation_p.R249S|TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	191.0	0.0		123.0	91.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	65	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	2452909	7577534	73617676	330	8403										
NCOR1	9611	hgsc.bcm.edu	37	chr17	15973762	15973762	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	attccacgggatagtttgctAggccccgtgattaaggattt	11	8	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:15973762A>G	ENST00000268712.3	-	31	4487	c.4230T>C	c.(4228-4230)ccT>ccC	p.P1410P	NCOR1_ENST00000395857.3_5'UTR|NCOR1_ENST00000395851.1_Silent_p.P1426P	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1410	Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ATAGTTTGCTAGGCCCCGTGA	0.448																																					p.P1426P		Atlas-SNP	.											.	NCOR1	240	.	0			c.T4278C						.						174	167	169					17																	15973762		2203	4300	6503	SO:0001819	synonymous_variant	9611	exon30			TTTGCTAGGCCCC	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.4230T>C	chr17.hg19:g.15973762A>G		143.0	0.0		85.0	4.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.		0.448	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		G	15973762	A	G	15973762	2	3	65	1	0	0	0	0	0	0	0	1	10244	407	15	2		2	NCOR1	17	15973762	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	8396228	15973762	65221448	331	8404										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26946934	26946934	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tatttgggccacatgctgccGcacagcctcctgcaaatgca	9	14	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:26946934G>A	ENST00000528896.2	-	30	5538	c.5464C>T	c.(5464-5466)Cgg>Tgg	p.R1822W	SPAG5-AS1_ENST00000424210.1_RNA|KIAA0100_ENST00000544884.1_Missense_Mutation_p.R1679W|KIAA0100_ENST00000579924.2_5'Flank|KIAA0100_ENST00000389003.3_Missense_Mutation_p.R1679W|SPAG5-AS1_ENST00000414744.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	1822						extracellular region (GO:0005576)		p.R1822W(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					ACATGCTGCCGCACAGCCTCC	0.493																																					p.R1822W		Atlas-SNP	.											KIAA0100,colon,carcinoma,0,1	KIAA0100	175	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5464T						.						99	91	94					17																	26946934		2203	4300	6503	SO:0001583	missense	9703	exon30			GCTGCCGCACAGC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.5464C>T	chr17.hg19:g.26946934G>A	ENSP00000436773:p.Arg1822Trp	69.0	0.0		82.0	4.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.522641	0.64747	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.55413	0.52;0.52	5.53	3.24	0.37175	FMP27,  C-terminal (1);	0.051185	0.64402	D	0.000001	T	0.71929	0.3398	M	0.80332	2.49	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77117	-0.2706	10	0.72032	D	0.01	.	13.3585	0.60642	0.0:0.0:0.5836:0.4164	.	1822	Q14667	K0100_HUMAN	W	1822;1792;1822;1679	ENSP00000436773:R1822W;ENSP00000446443:R1679W	ENSP00000005905:R1822W	R	-	1	2	KIAA0100	23971061	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.408000	0.34668	1.435000	0.47434	0.655000	0.94253	CGG	.	.		0.493	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		A	26946934	G	A	26946934	3	1	65	1	0	0	0	0	1	0	0	0	8163	1086	38	1	1283	1	KIAA0100	17	26946934	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	10973172	26946934	54248276	332	8405										
RFFL	117584	hgsc.bcm.edu	37	chr17	33339090	33339090	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aggttaccatgtggccacacTccagaagaacacagtcaatg	9	11	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:33339090T>C	ENST00000315249.7	-	7	1211	c.989A>G	c.(988-990)gAg>gGg	p.E330G	RFFL_ENST00000584655.1_Missense_Mutation_p.E294G|RFFL_ENST00000413582.2_Missense_Mutation_p.E322G|RFFL_ENST00000394597.2_Missense_Mutation_p.E330G|RFFL_ENST00000378516.2_Missense_Mutation_p.E322G|RFFL_ENST00000447669.2_Missense_Mutation_p.E330G|RFFL_ENST00000415395.2_Missense_Mutation_p.E330G|RP5-837J1.2_ENST00000578488.1_RNA|RFFL_ENST00000268850.7_Missense_Mutation_p.E294G|RAD51L3-RFFL_ENST00000593039.1_Missense_Mutation_p.E239G					ring finger and FYVE-like domain containing E3 ubiquitin protein ligase											kidney(1)|large_intestine(2)|lung(3)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		GTGGCCACACTCCAGAAGAAC	0.527																																					p.E330G		Atlas-SNP	.											.	RFFL	27	.	0			c.A989G						.						145	109	121					17																	33339090		2203	4300	6503	SO:0001583	missense	117584	exon7			CCACACTCCAGAA	AF434816	CCDS11286.1	17q12	2012-02-23	2012-02-23		ENSG00000092871	ENSG00000092871		"RING-type (C3HC4) zinc fingers"	24821	protein-coding gene	gene with protein product		609735	"ring finger and FYVE-like domain containing"			15229288	Standard	NR_037713		Approved	rififylin, fring, RNF189, RNF34L	uc002hin.1	Q8WZ73	OTTHUMG00000132933	ENST00000315249.7:c.989A>G	chr17.hg19:g.33339090T>C	ENSP00000326170:p.Glu330Gly	114.0	0.0		119.0	5.0	NM_001017368		Missense_Mutation	SNP	ENST00000315249.7	hg19	CCDS11286.1	.	.	.	.	.	.	.	.	.	.	T	32	5.157861	0.94686	.	.	ENSG00000092871	ENST00000315249;ENST00000394597;ENST00000378516;ENST00000268850	T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23	5.65	5.65	0.86999	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.000000	0.85682	D	0.000000	T	0.82144	0.4973	L	0.28649	0.875	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.994;1.0;0.994	D	0.84323	0.0517	10	0.87932	D	0	-25.117	15.2098	0.73214	0.0:0.0:0.0:1.0	.	294;330;322	Q8WZ73-3;Q8WZ73;Q8WZ73-2	.;RFFL_HUMAN;.	G	330;330;322;294	ENSP00000326170:E330G;ENSP00000378096:E330G;ENSP00000367777:E322G;ENSP00000268850:E294G	ENSP00000268850:E294G	E	-	2	0	RFFL	30363203	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.868000	0.87116	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.527	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256460.2	NM_057178		C	33339090	T	C	33339090	3	2	65	1	0	0	0	0	1	0	0	0	13265	1551	54	2	106	2	RFFL	17	33339090	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6392156	33339090	47856120	333	8406										
NLE1	54475	hgsc.bcm.edu	37	chr17	33460235	33460235	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cacttgccactctctggccaTctggactccagtcaacagca	7	16	3	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:33460235T>C	ENST00000442241.4	-	12	1439	c.1400A>G	c.(1399-1401)gAt>gGt	p.D467G	NLE1_ENST00000586869.1_Missense_Mutation_p.D175G|NLE1_ENST00000360831.5_Missense_Mutation_p.D425G	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	467					hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				TCTCTGGCCATCTGGACTCCA	0.592																																					p.D467G		Atlas-SNP	.											.	NLE1	42	.	0			c.A1400G						.						200	145	163					17																	33460235		2203	4300	6503	SO:0001583	missense	54475	exon12			TGGCCATCTGGAC		CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"WD repeat domain containing"	19889	protein-coding gene	gene with protein product	"Notchless gene homolog, (Drosophila)"						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.1400A>G	chr17.hg19:g.33460235T>C	ENSP00000413572:p.Asp467Gly	106.0	0.0		97.0	4.0	NM_018096	O60868|Q59GJ8|Q9BU54	Missense_Mutation	SNP	ENST00000442241.4	hg19	CCDS11291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.6|25.6	4.652398|4.652398	0.88056|0.88056	.|.	.|.	ENSG00000073536|ENSG00000073536	ENST00000442241;ENST00000360831;ENST00000537697|ENST00000436188	T|.	0.63255|.	-0.03|.	5.41|5.41	5.41|5.41	0.78517|0.78517	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);G-protein, beta subunit (1);|.	0.092597|.	0.64402|.	D|.	0.000001|.	T|T	0.59542|0.59542	0.2201|0.2201	L|L	0.42632|0.42632	1.34|1.34	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.56697|0.56697	-0.7936|-0.7936	10|5	0.87932|.	D|.	0|.	-13.9533|-13.9533	13.4332|13.4332	0.61068|0.61068	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	467|.	Q9NVX2|.	NLE1_HUMAN|.	G|V	467;175;443|286	ENSP00000413572:D467G|.	ENSP00000354075:D175G|.	D|M	-|-	2|1	0|0	NLE1|NLE1	30484348|30484348	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	7.087000|7.087000	0.76893|0.76893	2.261000|2.261000	0.74972|0.74972	0.460000|0.460000	0.39030|0.39030	GAT|ATG	.	.		0.592	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096		C	33460235	T	C	33460235	3	2	65	1	0	0	0	0	1	0	0	0	10469	1435	50	2	65	2	NLE1	17	33460235	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	121145	33460235	47734975	334	8407										
ACACA	31	hgsc.bcm.edu	37	chr17	35598870	35598870	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tggagttacaagttactaccTctgtaccagctgaacaatgc	8	10	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:35598870T>C	ENST00000394406.2	-	23	3110	c.2920A>G	c.(2920-2922)Agg>Ggg	p.R974G	ACACA_ENST00000360679.3_Splice_Site_p.R916G|ACACA_ENST00000335166.5_Splice_Site_p.R896G|ACACA_ENST00000353139.5_Splice_Site_p.R1011G	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	974					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGTTACTACCTCTGTACCAGC	0.408																																					p.R1011G	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.A3031G						.						115	101	106					17																	35598870		2203	4300	6503	SO:0001630	splice_region_variant	31	exon23			ACTACCTCTGTAC	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.2921+1A>G	chr17.hg19:g.35598870T>C		135.0	0.0		87.0	4.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	hg19	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.877936	0.51801	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	4.89	4.89	0.63831	Acetyl-CoA carboxylase, central domain (1);	0.141252	0.64402	D	0.000005	T	0.67627	0.2913	M	0.88640	2.97	0.80722	D	1	P;B;B	0.34815	0.47;0.014;0.011	P;B;B	0.49012	0.598;0.033;0.019	T	0.72551	-0.4259	10	0.59425	D	0.04	-6.8596	13.8335	0.63395	0.0:0.0:0.0:1.0	.	1011;974;916	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	G	1011;916;974;998;896	ENSP00000344789:R1011G;ENSP00000353898:R916G;ENSP00000377928:R974G;ENSP00000335323:R896G	ENSP00000335323:R896G	R	-	1	2	ACACA	32672983	1.000000	0.71417	1.000000	0.80357	0.574000	0.36063	6.161000	0.71868	2.049000	0.60858	0.482000	0.46254	AGG	.	.		0.408	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	Missense_Mutation	C	35598870	T	C	35598870	5	2	65	1	0	0	0	0	0	0	1	0	106	1565	54	2	4256	2	ACACA	17	35598870	Splice_Site	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2138635	35598870	45596340	335	8408										
MED1	5469	hgsc.bcm.edu	37	chr17	37566928	37566928	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ggtgtcggcttgaatggtttCagctttcctccgaatagccc	11	11	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:37566928C>T	ENST00000394287.3	-	17	1751	c.1546G>A	c.(1546-1548)Gaa>Aaa	p.E516K	MED1_ENST00000300651.6_Missense_Mutation_p.E516K			O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		TGAATGGTTTCAGCTTTCCTC	0.483										HNSCC(31;0.082)																											p.E516K	Pancreas(21;279 768 2492 4877 24026)	Atlas-SNP	.											.	MED1	123	.	0			c.G1546A						.						88	81	83					17																	37566928		2203	4300	6503	SO:0001583	missense	5469	exon17			TGGTTTCAGCTTT	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"PPAR binding protein"	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000394287.3:c.1546G>A	chr17.hg19:g.37566928C>T	ENSP00000377828:p.Glu516Lys	181.0	0.0		130.0	6.0	NM_004774	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000394287.3	hg19		.	.	.	.	.	.	.	.	.	.	C	16.47	3.131115	0.56828	.	.	ENSG00000125686	ENST00000394287;ENST00000300651	T;T	0.56103	0.48;0.48	5.8	5.8	0.92144	.	.	.	.	.	T	0.46112	0.1376	N	0.22421	0.69	0.80722	D	1	P;B	0.34546	0.456;0.42	B;B	0.36808	0.233;0.09	T	0.45056	-0.9287	9	0.54805	T	0.06	-14.153	20.0505	0.97625	0.0:1.0:0.0:0.0	.	516;516	Q15648;Q15648-3	MED1_HUMAN;.	K	516	ENSP00000377828:E516K;ENSP00000300651:E516K	ENSP00000300651:E516K	E	-	1	0	MED1	34820454	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.456000	0.80751	2.739000	0.93911	0.561000	0.74099	GAA	.	.		0.483	MED1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000256944.1	NM_004774		T	37566928	C	T	37566928	3	4	65	1	0	0	0	0	1	0	0	0	9434	835	29	3	3203	3	MED1	17	37566928	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	1968058	37566928	43628282	336	8409										
PSMD3	5709	hgsc.bcm.edu	37	chr17	38140566	38140566	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gacatcaaggagcacgtgaaAcagctagagaaagcggtttc	12	8	1	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:38140566A>G	ENST00000264639.4	+	2	414	c.240A>G	c.(238-240)aaA>aaG	p.K80K	PSMD3_ENST00000541736.1_Intron	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	80					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Colorectal(19;0.000442)					AGCACGTGAAACAGCTAGAGA	0.512																																					p.K80K	Ovarian(186;531 2051 6385 19668 48409)	Atlas-SNP	.											.	PSMD3	56	.	0			c.A240G						.						59	56	57					17																	38140566		2203	4300	6503	SO:0001819	synonymous_variant	5709	exon2			CGTGAAACAGCTA	D67025	CCDS11356.1	17q21.2	2010-07-23			ENSG00000108344	ENSG00000108344		"Proteasome (prosome, macropain) subunits"	9560	protein-coding gene	gene with protein product			"tissue specific transplantation antigen 2"	TSTA2		9017604	Standard	NM_002809		Approved	S3, P58, Rpn3	uc002htn.2	O43242	OTTHUMG00000133251	ENST00000264639.4:c.240A>G	chr17.hg19:g.38140566A>G		99.0	0.0		99.0	4.0	NM_002809	B3KMW9|B4DT72|Q96EI2|Q9BQA4	Silent	SNP	ENST00000264639.4	hg19	CCDS11356.1																																																																																			.	.		0.512	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1	NM_002809		G	38140566	A	G	38140566	2	3	65	1	0	0	0	0	0	0	0	1	12711	40	2	2		2	PSMD3	17	38140566	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	573638	38140566	43054644	337	8410										
KLHL11	55175	hgsc.bcm.edu	37	chr17	40010298	40010298	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ataatgaagacatcatctttGtaatagcaaatggctgctcc	7	8	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:40010298G>A	ENST00000319121.3	-	2	1881	c.1821C>T	c.(1819-1821)taC>taT	p.Y607Y	RP11-156E6.1_ENST00000560400.1_RNA	NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	607										NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				CATCATCTTTGTAATAGCAAA	0.428																																					p.Y607Y		Atlas-SNP	.											.	KLHL11	44	.	0			c.C1821T						.						93	93	93					17																	40010298		2203	4300	6503	SO:0001819	synonymous_variant	55175	exon2			ATCTTTGTAATAG		CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"Kelch-like", "BTB/POZ domain containing"	19008	protein-coding gene	gene with protein product			"kelch-like 11 (Drosophila)"				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.1821C>T	chr17.hg19:g.40010298G>A		119.0	0.0		81.0	4.0	NM_018143		Silent	SNP	ENST00000319121.3	hg19	CCDS11411.1																																																																																			.	.		0.428	KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143		A	40010298	G	A	40010298	2	1	65	1	0	0	0	0	0	0	0	1	8376	1372	48	3		3	KLHL11	17	40010298	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	1869732	40010298	41184912	338	8411										
HDAC5	10014	hgsc.bcm.edu	37	chr17	42168677	42168677	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgccgggcctgctccagcaAcagcacatgctgcagcaggg	13	15	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:42168677A>G	ENST00000393622.2	-	11	1679	c.1348T>C	c.(1348-1350)Ttg>Ctg	p.L450L	HDAC5_ENST00000225983.6_Silent_p.L451L|HDAC5_ENST00000336057.5_Silent_p.L450L|HDAC5_ENST00000586802.1_Silent_p.L450L	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	450					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		TGCTCCAGCAACAGCACATGC	0.632																																					p.L451L		Atlas-SNP	.											.	HDAC5	67	.	0			c.T1351C						.						25	24	24					17																	42168677		2203	4298	6501	SO:0001819	synonymous_variant	10014	exon11			CCAGCAACAGCAC	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.1348T>C	chr17.hg19:g.42168677A>G		75.0	0.0		109.0	5.0	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Silent	SNP	ENST00000393622.2	hg19	CCDS45696.1																																																																																			.	.		0.632	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		G	42168677	A	G	42168677	2	3	65	1	0	0	0	0	0	0	0	1	7019	40	2	2		2	HDAC5	17	42168677	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2158379	42168677	39026533	339	8412										
UBTF	7343	hgsc.bcm.edu	37	chr17	42284734	42284734	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgtcctcgtcatcctcttcaTtctggggggtgagaaaggat	12	10	4	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:42284734T>C	ENST00000302904.4	-	21	2663	c.2171A>G	c.(2170-2172)aAt>aGt	p.N724S	CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000529383.1_Splice_Site_p.N724S|UBTF_ENST00000436088.1_Splice_Site_p.N724S|UBTF_ENST00000343638.5_Splice_Site_p.N687S|UBTF_ENST00000527034.1_Splice_Site_p.M686V|UBTF_ENST00000533177.1_Splice_Site_p.N687S|UBTF_ENST00000393606.3_Splice_Site_p.N687S|UBTF_ENST00000526094.1_Splice_Site_p.N687S			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	724	Asp/Glu/Ser-rich (acidic).				chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		atcCTCTTCATTCTGGGGGGT	0.612																																					p.N724S		Atlas-SNP	.											.	UBTF	65	.	0			c.A2171G						.						123	80	94					17																	42284734		2203	4300	6503	SO:0001630	splice_region_variant	7343	exon21			TCTTCATTCTGGG	BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.2170-1A>G	chr17.hg19:g.42284734T>C		121.0	0.0		104.0	5.0	NM_014233	A8K6R8	Missense_Mutation	SNP	ENST00000302904.4	hg19	CCDS11480.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.343|9.343	1.063501|1.063501	0.20067|0.20067	.|.	.|.	ENSG00000108312|ENSG00000108312	ENST00000527034|ENST00000343638;ENST00000302904;ENST00000533177;ENST00000436088;ENST00000393606;ENST00000526094;ENST00000529383	D|D;D;D;D;D;D;D	0.98192|0.97924	-4.78|-4.61;-3.86;-4.61;-3.86;-4.61;-4.61;-3.86	4.95|4.95	3.87|3.87	0.44632|0.44632	.|.	.|0.653608	.|0.14315	.|N	.|0.327400	D|D	0.92854|0.92854	0.7727|0.7727	N|N	0.19112|0.19112	0.55|0.55	0.29230|0.29230	N|N	0.873351|0.873351	.|B;B	.|0.06786	.|0.001;0.0	.|B;B	.|0.04013	.|0.001;0.0	D|D	0.85436|0.85436	0.1152|0.1152	7|10	0.87932|0.14252	D|T	0|0.57	-13.223|-13.223	9.0709|9.0709	0.36491|0.36491	0.0:0.0844:0.0:0.9156|0.0:0.0844:0.0:0.9156	.|.	.|687;724	.|P17480-2;P17480	.|.;UBF1_HUMAN	V|S	686|687;724;687;724;687;687;724	ENSP00000431539:M686V|ENSP00000345297:N687S;ENSP00000302640:N724S;ENSP00000437180:N687S;ENSP00000390669:N724S;ENSP00000377231:N687S;ENSP00000432925:N687S;ENSP00000435708:N724S	ENSP00000431539:M686V|ENSP00000302640:N724S	M|N	-|-	1|2	0|0	UBTF|UBTF	39640260|39640260	0.999000|0.999000	0.42202|0.42202	0.983000|0.983000	0.44433|0.44433	0.925000|0.925000	0.55904|0.55904	3.444000|3.444000	0.52914|0.52914	1.035000|1.035000	0.39972|0.39972	0.459000|0.459000	0.35465|0.35465	ATG|AAT	.	.		0.612	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233	Missense_Mutation	C	42284734	T	C	42284734	5	2	65	1	0	0	0	0	0	0	1	0	16924	1507	52	2	127	2	UBTF	17	42284734	Splice_Site	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	116057	42284734	38910476	340	8413										
WNT9B	7484	hgsc.bcm.edu	37	chr17	44953863	44953863	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctggggacctggtgtacatgGaggactcacccagcttctgc	13	12	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:44953863G>T	ENST00000290015.2	+	4	906	c.853G>T	c.(853-855)Gag>Tag	p.E285*	WNT9B_ENST00000393461.2_Nonsense_Mutation_p.E285*	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	285					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to starvation (GO:0009267)|collecting duct development (GO:0072044)|cornea development in camera-type eye (GO:0061303)|embryonic cranial skeleton morphogenesis (GO:0048701)|establishment of planar polarity involved in nephron morphogenesis (GO:0072046)|in utero embryonic development (GO:0001701)|kidney rudiment formation (GO:0072003)|male genitalia development (GO:0030539)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesonephric duct formation (GO:0072181)|metanephric tubule formation (GO:0072174)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|positive regulation of catalytic activity (GO:0043085)|regulation of asymmetric cell division (GO:0009786)|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003339)|regulation of protein phosphorylation (GO:0001932)|regulation of tube size (GO:0035150)|response to retinoic acid (GO:0032526)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			large_intestine(2)|lung(8)	10			BRCA - Breast invasive adenocarcinoma(9;0.0257)			GGTGTACATGGAGGACTCACC	0.677																																					p.E285X		Atlas-SNP	.											.	WNT9B	37	.	0			c.G853T						.						46	50	48					17																	44953863		2201	4293	6494	SO:0001587	stop_gained	7484	exon4			TACATGGAGGACT	AF028703	CCDS11506.1	17q21	2008-01-07	2003-03-11	2003-03-14		ENSG00000158955		"Wingless-type MMTV integration sites"	12779	protein-coding gene	gene with protein product		602864	"wingless-type MMTV integration site family, member 15"	WNT15		9441749, 11713592	Standard	NM_003396		Approved	WNT14B	uc002ikw.1	O14905		ENST00000290015.2:c.853G>T	chr17.hg19:g.44953863G>T	ENSP00000290015:p.Glu285*	145.0	0.0		137.0	76.0	NM_003396	Q6UXT4|Q96Q09	Nonsense_Mutation	SNP	ENST00000290015.2	hg19	CCDS11506.1	.	.	.	.	.	.	.	.	.	.	G	32	5.162681	0.94727	.	.	ENSG00000158955	ENST00000376843;ENST00000393461;ENST00000290015	.	.	.	4.69	4.69	0.59074	.	0.051938	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.8129	0.88622	0.0:0.0:1.0:0.0	.	.	.	.	X	279;285;285	.	ENSP00000290015:E285X	E	+	1	0	WNT9B	42308862	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.653000	0.98506	2.434000	0.82447	0.561000	0.74099	GAG	.	.		0.677	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396		T	44953863	G	T	44953863	4	4	65	1	0	0	0	0	0	1	0	0	17414	1175	41	3	867	3	WNT9B	17	44953863	Nonsense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	2669129	44953863	36241347	341	8414										
IGF2BP1	10642	hgsc.bcm.edu	37	chr17	47103022	47103022	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aatattccaccccagctccgAtgggaagtaagtgtttgggg	12	9	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:47103022A>G	ENST00000290341.3	+	3	613	c.279A>G	c.(277-279)cgA>cgG	p.R93R	IGF2BP1_ENST00000431824.2_Silent_p.R93R|IGF2BP1_ENST00000515586.1_3'UTR	NM_006546.3	NP_006537.3	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding protein 1	93	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of mRNA stability involved in response to stress (GO:0010610)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CCCAGCTCCGATGGGAAGTAA	0.478																																					p.R93R	Esophageal Squamous(198;1041 2123 8248 37119 38268)	Atlas-SNP	.											.	IGF2BP1	80	.	0			c.A279G						.						35	34	35					17																	47103022		2203	4300	6503	SO:0001819	synonymous_variant	10642	exon3			GCTCCGATGGGAA	AF198254	CCDS11543.1, CCDS54138.1	17q21.32	2013-02-12			ENSG00000159217	ENSG00000159217		"RNA binding motif (RRM) containing"	28866	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 1"	608288				9891060, 11992722	Standard	NM_001160423		Approved	IMP-1	uc002iom.3	Q9NZI8	OTTHUMG00000161173	ENST00000290341.3:c.279A>G	chr17.hg19:g.47103022A>G		100.0	0.0		99.0	4.0	NM_001160423	C9JT33	Silent	SNP	ENST00000290341.3	hg19	CCDS11543.1																																																																																			.	.		0.478	IGF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364046.1	NM_006546		G	47103022	A	G	47103022	2	3	65	1	0	0	0	0	0	0	0	1	7582	320	12	2		2	IGF2BP1	17	47103022	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2149159	47103022	34092188	342	8415										
MYST2	11143	hgsc.bcm.edu	37	chr17	47874270	47874270	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gttcagaaactgagcaagtgGttgatttttcagatagaggt	12	4	2	5			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:47874270G>T	ENST00000259021.4	+	3	602	c.322G>T	c.(322-324)Gtt>Ttt	p.V108F	KAT7_ENST00000503935.2_5'UTR|KAT7_ENST00000509773.1_Missense_Mutation_p.V108F|KAT7_ENST00000424009.2_Missense_Mutation_p.V108F|KAT7_ENST00000510819.1_Intron|KAT7_ENST00000435742.2_5'UTR|KAT7_ENST00000454930.2_Intron	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	108					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TGAGCAAGTGGTTGATTTTTC	0.483																																					p.V108F		Atlas-SNP	.											.	.	.	.	0			c.G322T						.						132	134	133					17																	47874270		2203	4300	6503	SO:0001583	missense	11143	exon3			CAAGTGGTTGATT	AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17016	protein-coding gene	gene with protein product	"histone acetyltransferase binding to ORC1"	609880	"MYST histone acetyltransferase 2"	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.322G>T	chr17.hg19:g.47874270G>T	ENSP00000259021:p.Val108Phe	146.0	0.0		121.0	99.0	NM_007067	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	hg19	CCDS11554.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741140	0.69304	.	.	ENSG00000136504	ENST00000259021;ENST00000509773;ENST00000424009	.	.	.	5.93	5.93	0.95920	.	0.136549	0.49305	D	0.000152	T	0.73202	0.3557	L	0.36672	1.1	0.80722	D	1	D;B;D	0.64830	0.99;0.054;0.994	D;B;D	0.73380	0.954;0.022;0.98	T	0.72037	-0.4411	9	0.51188	T	0.08	-12.3404	19.9388	0.97151	0.0:0.0:1.0:0.0	.	108;108;108	B4DFB4;O95251;G5E9K7	.;KAT7_HUMAN;.	F	108	.	ENSP00000259021:V108F	V	+	1	0	KAT7	45229269	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.836000	0.86788	2.815000	0.96918	0.561000	0.74099	GTT	.	.		0.483	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067		T	47874270	G	T	47874270	3	4	65	1	0	0	0	0	1	0	0	0	10112	1261	44	3	332	3	MYST2	17	47874270	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	771248	47874270	33320940	343	8416										
TEX2	55852	hgsc.bcm.edu	37	chr17	62290595	62290595	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcaagctggacagattggagAgttctgaagcacttgaagat	12	6	2	5			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:62290595A>G	ENST00000583097.1	-	2	1155	c.983T>C	c.(982-984)cTc>cCc	p.L328P	TEX2_ENST00000258991.3_Missense_Mutation_p.L328P|TEX2_ENST00000584379.1_Missense_Mutation_p.L328P			Q8IWB9	TEX2_HUMAN	testis expressed 2	328					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		CAGATTGGAGAGTTCTGAAGC	0.458																																					p.L328P		Atlas-SNP	.											.	TEX2	89	.	0			c.T983C						.						72	68	70					17																	62290595		2203	4300	6503	SO:0001583	missense	55852	exon2			TTGGAGAGTTCTG	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"transmembrane protein 96"		"testis expressed sequence 2"			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.983T>C	chr17.hg19:g.62290595A>G	ENSP00000462665:p.Leu328Pro	88.0	0.0		100.0	4.0	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	hg19		.	.	.	.	.	.	.	.	.	.	A	11.18	1.564080	0.27915	.	.	ENSG00000136478	ENST00000258991	T	0.62639	0.01	6.03	6.03	0.97812	.	0.058903	0.64402	D	0.000001	T	0.76962	0.4061	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	T	0.78597	-0.2142	10	0.72032	D	0.01	-16.796	16.5582	0.84512	1.0:0.0:0.0:0.0	.	328;328	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	P	328	ENSP00000258991:L328P	ENSP00000258991:L328P	L	-	2	0	TEX2	59644327	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.050000	0.76620	2.308000	0.77769	0.533000	0.62120	CTC	.	.		0.458	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		G	62290595	A	G	62290595	3	3	65	1	0	0	0	0	1	0	0	0	15796	304	11	2	2465	2	TEX2	17	62290595	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	14416325	62290595	18904615	344	8417										
ABCA9	10350	hgsc.bcm.edu	37	chr17	67041411	67041411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	taaagatgactctcactgcgTctattgaatagttcaaatcc	6	9	3	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:67041411T>C	ENST00000340001.4	-	4	582	c.371A>G	c.(370-372)gAc>gGc	p.D124G	ABCA9_ENST00000453985.2_Missense_Mutation_p.D124G|ABCA9_ENST00000370732.2_Missense_Mutation_p.D124G|ABCA9_ENST00000495634.1_Missense_Mutation_p.D124G	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	124					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					TCTCACTGCGTCTATTGAATA	0.398																																					p.D124G		Atlas-SNP	.											.	ABCA9	192	.	0			c.A371G						.						145	138	141					17																	67041411		2203	4300	6503	SO:0001583	missense	10350	exon4			ACTGCGTCTATTG	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.371A>G	chr17.hg19:g.67041411T>C	ENSP00000342216:p.Asp124Gly	103.0	0.0		87.0	4.0	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	hg19	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	T	3.031	-0.199645	0.06219	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749	D;D	0.88741	-2.42;-2.42	3.83	3.83	0.44106	.	0.158806	0.28683	U	0.014491	D	0.84032	0.5383	L	0.53249	1.67	0.25963	N	0.982592	B;B	0.13145	0.007;0.001	B;B	0.17098	0.017;0.012	T	0.70439	-0.4871	10	0.24483	T	0.36	.	9.2771	0.37705	0.0:0.0:0.0:1.0	.	124;124	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	G	124;107;124;119	ENSP00000342216:D124G;ENSP00000359767:D124G	ENSP00000342216:D124G	D	-	2	0	ABCA9	64553006	0.083000	0.21467	0.813000	0.32504	0.002000	0.02628	2.223000	0.42936	1.964000	0.57103	0.482000	0.46254	GAC	.	.		0.398	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		C	67041411	T	C	67041411	3	2	65	1	0	0	0	0	1	0	0	0	39	1667	58	2	4647	2	ABCA9	17	67041411	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4750816	67041411	14153799	345	8418										
GPR142	350383	hgsc.bcm.edu	37	chr17	72368628	72368628	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	actttccgggccactgtccgAcaggtcatccacgatgccta	9	15	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:72368628A>G	ENST00000335666.4	+	4	1326	c.1278A>G	c.(1276-1278)cgA>cgG	p.R426R		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	426						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						CCACTGTCCGACAGGTCATCC	0.617																																					p.R426R		Atlas-SNP	.											.	GPR142	74	.	0			c.A1278G						.						72	63	66					17																	72368628		2203	4300	6503	SO:0001819	synonymous_variant	350383	exon4			TGTCCGACAGGTC	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"GPCR / Class A : Orphans"	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.1278A>G	chr17.hg19:g.72368628A>G		91.0	0.0		99.0	5.0	NM_181790	A4CYJ8|Q86SL3	Silent	SNP	ENST00000335666.4	hg19	CCDS11698.1																																																																																			.	.		0.617	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790		G	72368628	A	G	72368628	2	3	65	1	0	0	0	0	0	0	0	1	6658	262	10	2		2	GPR142	17	72368628	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	5327217	72368628	8826582	346	8419										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73751906	73751906	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cggccgctgcagggctacagTgtggagtaccagctgctgaa	15	11	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:73751906T>C	ENST00000200181.3	+	35	4870	c.4683T>C	c.(4681-4683)agT>agC	p.S1561S	ITGB4_ENST00000579662.1_Silent_p.S1491S|ITGB4_ENST00000449880.2_Silent_p.S1544S|ITGB4_ENST00000450894.3_Silent_p.S1491S|ITGB4_ENST00000339591.3_Silent_p.S1544S|GALK1_ENST00000225614.2_Intron	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1561	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGGGCTACAGTGTGGAGTACC	0.682																																					p.S1561S		Atlas-SNP	.											.	ITGB4	165	.	0			c.T4683C						.						23	25	24					17																	73751906		2203	4298	6501	SO:0001819	synonymous_variant	3691	exon35			CTACAGTGTGGAG		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.4683T>C	chr17.hg19:g.73751906T>C		63.0	0.0		112.0	5.0	NM_000213	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	hg19	CCDS11727.1																																																																																			.	.		0.682	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			C	73751906	T	C	73751906	2	2	65	1	0	0	0	0	0	0	0	1	7906	1693	59	2		2	ITGB4	17	73751906	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1383278	73751906	7443304	347	8420										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76503588	76503588	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgctgggagtcccccgggagCtgggtgcggatgtcttcgga	18	11	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:76503588C>G	ENST00000585328.1	-	28	4651	c.4527G>C	c.(4525-4527)caG>caC	p.Q1509H	DNAH17_ENST00000389840.5_Missense_Mutation_p.Q1508H	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1508	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CCCCCGGGAGCTGGGTGCGGA	0.597																																					p.Q1512H		Atlas-SNP	.											.	DNAH17	347	.	0			c.G4536C						.						45	51	49					17																	76503588		2078	4244	6322	SO:0001583	missense	8632	exon28			CGGGAGCTGGGTG	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.4527G>C	chr17.hg19:g.76503588C>G	ENSP00000465516:p.Gln1509His	129.0	0.0		151.0	30.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	C	19.19	3.779539	0.70107	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.64260	-0.09	4.97	3.78	0.43462	Dynein heavy chain, domain-2 (1);	.	.	.	.	D	0.86556	0.5961	H	0.98918	4.37	0.40204	D	0.977548	D	0.89917	1.0	D	0.91635	0.999	D	0.91547	0.5254	9	0.87932	D	0	.	13.2232	0.59901	0.0:0.859:0.0:0.141	.	1508	Q9UFH2	DYH17_HUMAN	H	1509;1508	ENSP00000374490:Q1508H	ENSP00000300671:Q1509H	Q	-	3	2	DNAH17	74015183	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.195000	0.51013	2.276000	0.75962	0.563000	0.77884	CAG	.	.		0.597	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		G	76503588	C	G	76503588	3	3	65	1	0	0	0	0	1	0	0	0	4603	796	28	4	9068	4	DNAH17	17	76503588	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	2751682	76503588	4691622	348	8421										
C17orf70	80233	hgsc.bcm.edu	37	chr17	79517603	79517603	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccaggcagtcacagtgcacaTcctcgtcaggcagaaaattc	9	13	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr17:79517603T>C	ENST00000327787.8	-	3	963	c.917A>G	c.(916-918)gAt>gGt	p.D306G	C17orf70_ENST00000425898.2_5'Flank|C17orf70_ENST00000537152.1_Missense_Mutation_p.D155G			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	306					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			ACAGTGCACATCCTCGTCAGG	0.602																																					p.D306G		Atlas-SNP	.											.	C17orf70	79	.	0			c.A917G						.						52	53	52					17																	79517603		2202	4300	6502	SO:0001583	missense	80233	exon3			TGCACATCCTCGT	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"Fanconi anemia-associated protein, 100kDa"	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.917A>G	chr17.hg19:g.79517603T>C	ENSP00000333283:p.Asp306Gly	116.0	0.0		118.0	5.0	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Missense_Mutation	SNP	ENST00000327787.8	hg19	CCDS32765.2	.	.	.	.	.	.	.	.	.	.	T	13.61	2.289544	0.40494	.	.	ENSG00000185504	ENST00000327787;ENST00000537152;ENST00000541246;ENST00000544302	T;T	0.33865	1.4;1.39	3.91	2.82	0.32997	.	0.475716	0.22063	N	0.065154	T	0.37625	0.1010	L	0.57536	1.79	0.09310	N	1	P	0.45957	0.869	P	0.47827	0.558	T	0.12889	-1.0530	10	0.28530	T	0.3	.	8.1149	0.30937	0.0:0.1009:0.0:0.8991	.	306	Q0VG06	FP100_HUMAN	G	306;155;155;155	ENSP00000333283:D306G;ENSP00000440151:D155G	ENSP00000333283:D306G	D	-	2	0	C17orf70	77128045	0.005000	0.15991	0.001000	0.08648	0.904000	0.53231	1.298000	0.33412	0.553000	0.29044	0.460000	0.39030	GAT	.	.		0.602	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161		C	79517603	T	C	79517603	3	2	65	1	0	0	0	0	1	0	0	0	1879	1435	50	2	1756	2	C17orf70	17	79517603	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3014015	79517603	1677607	349	8422										
NDC80	10403	hgsc.bcm.edu	37	chr18	2578079	2578079	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tttatggcttcctgtgccccTcatacgaacttcctgacaca	6	14	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr18:2578079T>C	ENST00000261597.4	+	5	597	c.415T>C	c.(415-417)Tca>Cca	p.S139P		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	139	Interaction with RB1.|Interaction with the N-terminus of CDCA1.|Nuclear localization.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						CCTGTGCCCCTCATACGAACT	0.383																																					p.S139P		Atlas-SNP	.											NDC80,colon,carcinoma,0,1	NDC80	62	.	0			c.T415C						.						140	131	134					18																	2578079		2203	4300	6503	SO:0001583	missense	10403	exon5			TGCCCCTCATACG	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.415T>C	chr18.hg19:g.2578079T>C	ENSP00000261597:p.Ser139Pro	148.0	0.0		102.0	7.0	NM_006101	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	hg19	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.769882	0.49680	.	.	ENSG00000080986	ENST00000261597;ENST00000543946	T	0.47528	0.84	5.8	5.8	0.92144	.	0.169262	0.52532	D	0.000062	T	0.57315	0.2045	M	0.73962	2.25	0.33405	D	0.577903	D	0.61697	0.99	P	0.52881	0.712	T	0.70506	-0.4853	10	0.36615	T	0.2	-7.8095	10.4429	0.44477	0.2522:0.0:0.0:0.7478	.	139	O14777	NDC80_HUMAN	P	139	ENSP00000261597:S139P	ENSP00000261597:S139P	S	+	1	0	NDC80	2568079	0.999000	0.42202	0.862000	0.33874	0.532000	0.34746	2.820000	0.48057	2.216000	0.71823	0.533000	0.62120	TCA	.	.		0.383	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101		C	2578079	T	C	2578079	3	2	65	1	0	0	0	0	1	0	0	0	10251	1551	54	2	429	2	NDC80	18	2578079	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		2578079	75499169	350	8423										
SPIRE1	56907	hgsc.bcm.edu	37	chr18	12453092	12453092	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acagaactgacaggtataagAccaagtgaagaaggaaaacc	10	7	0	5			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr18:12453092A>G	ENST00000409402.4	-	14	2089	c.1822T>C	c.(1822-1824)Tct>Cct	p.S608P	SPIRE1_ENST00000453447.2_Missense_Mutation_p.S474P|SPIRE1_ENST00000464481.1_5'UTR|SPIRE1_ENST00000383356.2_Missense_Mutation_p.S435P|SPIRE1_ENST00000410092.3_Missense_Mutation_p.S594P|SPIRE1_ENST00000309836.5_Missense_Mutation_p.S397P	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1											breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						CAGGTATAAGACCAAGTGAAG	0.323																																					p.S608P		Atlas-SNP	.											.	SPIRE1	120	.	0			c.T1822C						.						61	63	62					18																	12453092		2203	4300	6503	SO:0001583	missense	56907	exon14			TATAAGACCAAGT	AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"spire homolog 1 (Drosophila)", "spire family actin nucleation factor 1"			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.1822T>C	chr18.hg19:g.12453092A>G	ENSP00000387266:p.Ser608Pro	111.0	0.0		59.0	4.0	NM_001128626		Missense_Mutation	SNP	ENST00000409402.4	hg19	CCDS45829.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.532550	0.45073	.	.	ENSG00000134278	ENST00000453447;ENST00000409402;ENST00000410092;ENST00000309836;ENST00000383356	T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06	5.95	4.8	0.61643	Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.69744	0.3145	N	0.19112	0.55	0.58432	D	0.999999	B;B;B	0.32717	0.144;0.381;0.298	B;B;B	0.43155	0.156;0.23;0.41	T	0.64188	-0.6466	10	0.23302	T	0.38	-11.4703	11.9386	0.52888	0.9324:0.0:0.0676:0.0	.	594;397;608	Q08AE8-2;B4DWX0;Q08AE8	.;.;SPIR1_HUMAN	P	474;608;594;397;435	ENSP00000407050:S474P;ENSP00000387266:S608P;ENSP00000387226:S594P;ENSP00000309661:S397P;ENSP00000372847:S435P	ENSP00000309661:S397P	S	-	1	0	SPIRE1	12443092	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.654000	0.91092	1.076000	0.40961	0.528000	0.53228	TCT	.	.		0.323	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818		G	12453092	A	G	12453092	3	3	65	1	0	0	0	0	1	0	0	0	15086	275	10	2	464	2	SPIRE1	18	12453092	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	9875013	12453092	65624156	351	8424										
CEP192	55125	hgsc.bcm.edu	37	chr18	13103589	13103589	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agcgccaccttatgtcaaggTcagtcatgactgcctcagat	9	12	4	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr18:13103589T>C	ENST00000325971.8	+	37	6756		c.e37+2		CEP192_ENST00000430049.2_Splice_Site|CEP192_ENST00000506447.1_Splice_Site|CEP192_ENST00000540847.2_Splice_Site			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa						centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TATGTCAAGGTCAGTCATGAC	0.383																																					.		Atlas-SNP	.											CEP192_ENST00000506447,NS,neuroblastoma,0,2	CEP192	340	.	0			c.6951+2T>C						.						156	131	139					18																	13103589		2203	4300	6503	SO:0001630	splice_region_variant	55125	exon39			TCAAGGTCAGTCA	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.5163+2T>C	chr18.hg19:g.13103589T>C		89.0	0.0		69.0	4.0	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Splice_Site	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	T	16.56	3.156149	0.57259	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049;ENST00000540847	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.261	0.73621	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CEP192	13093589	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	5.760000	0.68793	2.244000	0.73946	0.528000	0.53228	.	.	.		0.383	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	Intron	C	13103589	T	C	13103589	5	2	65	1	0	0	0	0	0	0	1	0	3253	1681	58	2	7103	2	CEP192	18	13103589	Splice_Site	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	650497	13103589	64973659	352	8425										
ELP2	55250	hgsc.bcm.edu	37	chr18	33709907	33709907	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	agttggcgacatggtggcacCcgtgctggagacttctcacg	14	11	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr18:33709907C>T	ENST00000358232.6	+	1	74	c.11C>T	c.(10-12)cCc>cTc	p.P4L	ELP2_ENST00000542824.1_Missense_Mutation_p.P4L|SLC39A6_ENST00000440549.2_5'Flank|ELP2_ENST00000423854.2_Missense_Mutation_p.P4L|ELP2_ENST00000442325.2_Missense_Mutation_p.P4L|ELP2_ENST00000350494.6_Missense_Mutation_p.P4L|SLC39A6_ENST00000590986.1_5'Flank|SLC39A6_ENST00000269187.5_5'Flank|ELP2_ENST00000351393.6_Missense_Mutation_p.P4L	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	4					chromatin organization (GO:0006325)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)				NS(1)|breast(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|urinary_tract(2)	30						ATGGTGGCACCCGTGCTGGAG	0.617																																					p.P4L		Atlas-SNP	.											ELP2_ENST00000350494,NS,carcinoma,0,2	ELP2	70	.	0			c.C11T						.						75	69	71					18																	33709907		2203	4300	6503	SO:0001583	missense	55250	exon1			TGGCACCCGTGCT	AK001741	CCDS11918.1, CCDS56065.1, CCDS56066.1, CCDS56067.1, CCDS56068.1, CCDS56069.1	18q12.1	2013-01-10	2012-08-08	2007-04-20	ENSG00000134759	ENSG00000134759		"Elongator acetyltransferase complex subunits", "WD repeat domain containing"	18248	protein-coding gene	gene with protein product			"signal transducer and activator of transcription 3 interacting protein 1", "elongation protein 2 homolog (S. cerevisiae)"	STATIP1		11714725, 10954736	Standard	NM_001242875		Approved	FLJ10879, StIP	uc002kzk.2	Q6IA86	OTTHUMG00000132589	ENST00000358232.6:c.11C>T	chr18.hg19:g.33709907C>T	ENSP00000350967:p.Pro4Leu	112.0	0.0		97.0	4.0	NM_001242879	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Missense_Mutation	SNP	ENST00000358232.6	hg19	CCDS11918.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.527182	0.85706	.	.	ENSG00000134759	ENST00000358232;ENST00000351393;ENST00000442325;ENST00000423854;ENST00000350494;ENST00000542824	T;T;T;T;T;T	0.59638	0.25;0.41;0.72;0.88;0.48;0.4	5.61	5.61	0.85477	.	0.279476	0.41097	D	0.000943	T	0.57388	0.2050	L	0.36672	1.1	0.21473	N	0.999674	P;P;P;P;P;P	0.45283	0.763;0.855;0.565;0.8;0.532;0.698	P;P;B;P;P;B	0.49999	0.548;0.548;0.33;0.628;0.506;0.424	T	0.51911	-0.8645	10	0.28530	T	0.3	-1.0655	15.1309	0.72523	0.0:1.0:0.0:0.0	.	4;4;4;4;4;4	B4DTG0;E7EP23;E9PCX0;Q6IA86-2;Q6IA86-3;Q6IA86	.;.;.;.;.;ELP2_HUMAN	L	4	ENSP00000350967:P4L;ENSP00000257191:P4L;ENSP00000414851:P4L;ENSP00000391202:P4L;ENSP00000316051:P4L;ENSP00000443800:P4L	ENSP00000316051:P4L	P	+	2	0	ELP2	31963905	0.001000	0.12720	0.006000	0.13384	0.631000	0.37964	1.318000	0.33643	2.645000	0.89757	0.585000	0.79938	CCC	.	.		0.617	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255		T	33709907	C	T	33709907	3	4	65	1	0	0	0	0	1	0	0	0	5082	623	22	3	13	3	ELP2	18	33709907	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	20606318	33709907	44367341	353	8426										
MOCOS	55034	hgsc.bcm.edu	37	chr18	33775247	33775247	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctatcttgaccatgcaggtgCcaccttgttctcccagagcc	8	15	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr18:33775247C>A	ENST00000261326.5	+	2	191	c.170C>A	c.(169-171)gCc>gAc	p.A57D		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CATGCAGGTGCCACCTTGTTC	0.393																																					p.A57D		Atlas-SNP	.											MOCOS,NS,carcinoma,0,1	MOCOS	84	.	0			c.C170A						.						150	152	151					18																	33775247		2203	4300	6503	SO:0001583	missense	55034	exon2			CAGGTGCCACCTT	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.170C>A	chr18.hg19:g.33775247C>A	ENSP00000261326:p.Ala57Asp	76.0	0.0		34.0	2.0	NM_017947		Missense_Mutation	SNP	ENST00000261326.5	hg19	CCDS11919.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.935348	0.92458	.	.	ENSG00000075643	ENST00000261326	D	0.87029	-2.2	5.41	5.41	0.78517	Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.127935	0.51477	D	0.000099	D	0.93429	0.7904	M	0.87827	2.91	0.40700	D	0.982472	D	0.57571	0.98	P	0.62885	0.908	D	0.94542	0.7746	10	0.72032	D	0.01	-16.3106	14.718	0.69284	0.0:1.0:0.0:0.0	.	57	Q96EN8	MOCOS_HUMAN	D	57	ENSP00000261326:A57D	ENSP00000261326:A57D	A	+	2	0	MOCOS	32029245	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.645000	0.67909	2.538000	0.85594	0.563000	0.77884	GCC	.	.		0.393	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			A	33775247	C	A	33775247	3	1	65	1	0	0	0	0	1	0	0	0	9698	739	26	3	176	3	MOCOS	18	33775247	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	65340	33775247	44302001	354	8427										
SETBP1	26040	hgsc.bcm.edu	37	chr18	42533197	42533197	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gggacagtgacgtgagtgggAgtaaaaggaggagctatgaa	18	3	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr18:42533197A>G	ENST00000282030.5	+	4	4188	c.3892A>G	c.(3892-3894)Agt>Ggt	p.S1298G		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1298						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		CGTGAGTGGGAGTAAAAGGAG	0.507									Schinzel-Giedion syndrome																												p.S1298G		Atlas-SNP	.											.	SETBP1	577	.	0			c.A3892G						.						143	131	135					18																	42533197		2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AGTGGGAGTAAAA	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.3892A>G	chr18.hg19:g.42533197A>G	ENSP00000282030:p.Ser1298Gly	82.0	0.0		54.0	4.0	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	hg19	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	A	15.26	2.779574	0.49891	.	.	ENSG00000152217	ENST00000282030	T	0.69685	-0.42	6.17	5.02	0.67125	.	0.161329	0.56097	D	0.000036	T	0.49762	0.1576	N	0.24115	0.695	0.29490	N	0.855677	B	0.10296	0.003	B	0.11329	0.006	T	0.40459	-0.9562	10	0.17832	T	0.49	.	11.0663	0.47976	0.9305:0.0:0.0695:0.0	.	1298	Q9Y6X0	SETBP_HUMAN	G	1298	ENSP00000282030:S1298G	ENSP00000282030:S1298G	S	+	1	0	SETBP1	40787195	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.748000	0.55142	1.159000	0.42565	0.533000	0.62120	AGT	.	.		0.507	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		G	42533197	A	G	42533197	3	3	65	1	0	0	0	0	1	0	0	0	14144	304	11	2	4095	2	SETBP1	18	42533197	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	8757950	42533197	35544051	355	8428										
TCEB3B	51224	hgsc.bcm.edu	37	chr18	44560140	44560140	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtccagggaaagcagcttccTcccggaactttggtgaagag	13	10	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr18:44560140T>C	ENST00000332567.4	-	1	1848	c.1496A>G	c.(1495-1497)gAg>gGg	p.E499G	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	499					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						AGCAGCTTCCTCCCGGAACTT	0.602																																					p.E499G		Atlas-SNP	.											.	TCEB3B	141	.	0			c.A1496G						.						67	77	73					18																	44560140		2203	4300	6503	SO:0001583	missense	51224	exon1			GCTTCCTCCCGGA	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1496A>G	chr18.hg19:g.44560140T>C	ENSP00000331302:p.Glu499Gly	169.0	0.0		113.0	5.0	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	hg19	CCDS11932.1	.	.	.	.	.	.	.	.	.	.	T	11.63	1.695036	0.30052	.	.	ENSG00000206181	ENST00000332567	T	0.11821	2.74	1.87	1.87	0.25490	.	0.710197	0.12250	N	0.485692	T	0.19805	0.0476	M	0.65975	2.015	0.22940	N	0.998531	P	0.45715	0.865	P	0.48524	0.58	T	0.08680	-1.0710	10	0.46703	T	0.11	-21.5747	5.7908	0.18359	0.0:0.0:0.0:1.0	.	499	Q8IYF1	ELOA2_HUMAN	G	499	ENSP00000331302:E499G	ENSP00000331302:E499G	E	-	2	0	TCEB3B	42814138	0.068000	0.21057	0.041000	0.18516	0.004000	0.04260	0.918000	0.28678	1.133000	0.42147	0.496000	0.49642	GAG	.	.		0.602	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		C	44560140	T	C	44560140	3	2	65	1	0	0	0	0	1	0	0	0	15697	1551	54	2	769	2	TCEB3B	18	44560140	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2026943	44560140	33517108	356	8429										
ALPK2	115701	hgsc.bcm.edu	37	chr18	56246468	56246468	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cactctcttgtcagctgccgTctcccaacactggctcatcc	6	18	4	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr18:56246468T>C	ENST00000361673.3	-	4	1753	c.1540A>G	c.(1540-1542)Acg>Gcg	p.T514A	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	514						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TCAGCTGCCGTCTCCCAACAC	0.512											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T514A		Atlas-SNP	.											ALPK2_ENST00000361673,colon,carcinoma,0,2	ALPK2	487	.	0			c.A1540G						.						202	202	202					18																	56246468		2203	4300	6503	SO:0001583	missense	115701	exon4			CTGCCGTCTCCCA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.1540A>G	chr18.hg19:g.56246468T>C	ENSP00000354991:p.Thr514Ala	115.0	0.0	1014	66.0	3.0	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	hg19	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	T	9.814	1.184031	0.21870	.	.	ENSG00000198796	ENST00000361673	T	0.41758	0.99	5.58	1.82	0.25136	.	1.941730	0.02824	N	0.125923	T	0.29458	0.0734	N	0.22421	0.69	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.13045	-1.0524	10	0.27082	T	0.32	-0.2389	5.0466	0.14487	0.0:0.1566:0.295:0.5485	.	514	Q86TB3	ALPK2_HUMAN	A	514	ENSP00000354991:T514A	ENSP00000354991:T514A	T	-	1	0	ALPK2	54397448	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.796000	0.26986	0.364000	0.24374	-0.290000	0.09829	ACG	.	.		0.512	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		C	56246468	T	C	56246468	3	2	65	1	0	0	0	0	1	0	0	0	545	1667	58	2	5012	2	ALPK2	18	56246468	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	11686328	56246468	21830780	357	8430										
HMHA1	23526	hgsc.bcm.edu	37	chr19	1074826	1074826	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cctgcggcggcttgaacacgAgaagcgcaggaaggagatca	15	10	1	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:1074826A>G	ENST00000313093.2	+	10	1364	c.1133A>G	c.(1132-1134)gAg>gGg	p.E378G	HMHA1_ENST00000536472.1_Missense_Mutation_p.E218G|HMHA1_ENST00000590577.1_5'Flank|HMHA1_ENST00000586866.1_Missense_Mutation_p.E382G|HMHA1_ENST00000590214.1_Missense_Mutation_p.E405G|HMHA1_ENST00000539243.2_Missense_Mutation_p.E394G|HMHA1_ENST00000543365.1_Missense_Mutation_p.E261G	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	378					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTGAACACGAGAAGCGCAGG	0.766																																					p.E394G		Atlas-SNP	.											.	HMHA1	78	.	0			c.A1181G						.						7	9	8					19																	1074826		2106	4169	6275	SO:0001583	missense	23526	exon10			AACACGAGAAGCG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"Rho GTPase activating proteins"	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.1133A>G	chr19.hg19:g.1074826A>G	ENSP00000316772:p.Glu378Gly	38.0	0.0		73.0	4.0	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	hg19	CCDS32863.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.996526	0.93167	.	.	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000544746;ENST00000536472;ENST00000412039;ENST00000543365	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	4.45	4.45	0.53987	.	0.000000	0.85682	D	0.000000	T	0.69033	0.3066	M	0.84326	2.69	0.58432	D	0.999996	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.998	T	0.74203	-0.3741	10	0.87932	D	0	-37.3036	11.7632	0.51916	1.0:0.0:0.0:0.0	.	218;394;261;378	F5H4A3;F6QP70;F5H1R4;Q92619	.;.;.;HMHA1_HUMAN	G	394;378;378;218;372;261	ENSP00000439601:E394G;ENSP00000316772:E378G;ENSP00000445109:E218G;ENSP00000438979:E261G	ENSP00000316772:E378G	E	+	2	0	HMHA1	1025826	1.000000	0.71417	0.999000	0.59377	0.912000	0.54170	5.468000	0.66743	1.778000	0.52293	0.459000	0.35465	GAG	.	.		0.766	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1			G	1074826	A	G	1074826	3	3	65	1	0	0	0	0	1	0	0	0	7249	304	11	2	1171	2	HMHA1	19	1074826	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10		1074826	58054157	358	8431										
MUM1	84939	hgsc.bcm.edu	37	chr19	1360617	1360617	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcttgtgcctgaatggatctTccctttcagaggacgacacg	11	11	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:1360617T>C	ENST00000415183.3	+	4	726	c.700T>C	c.(700-702)Tcc>Ccc	p.S234P	MUM1_ENST00000591806.1_Missense_Mutation_p.S234P|MUM1_ENST00000311401.5_Missense_Mutation_p.S165P|MUM1_ENST00000344663.3_Missense_Mutation_p.S234P			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	233					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAATGGATCTTCCCTTTCAGA	0.572																																					p.S234P		Atlas-SNP	.											.	MUM1	54	.	0			c.T700C						.						70	68	69					19																	1360617		2203	4300	6503	SO:0001583	missense	84939	exon5			GGATCTTCCCTTT	AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.700T>C	chr19.hg19:g.1360617T>C	ENSP00000394925:p.Ser234Pro	80.0	0.0		88.0	4.0	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	hg19		.	.	.	.	.	.	.	.	.	.	T	10.59	1.391501	0.25118	.	.	ENSG00000160953	ENST00000344663;ENST00000311401;ENST00000415183;ENST00000542512	T;T;T	0.25085	1.85;1.85;1.82	4.36	-1.95	0.07548	.	0.552015	0.16587	N	0.207953	T	0.11750	0.0286	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.15473	0.001;0.003;0.01;0.013	B;B;B;B	0.16722	0.003;0.003;0.016;0.014	T	0.15150	-1.0447	10	0.59425	D	0.04	.	1.4347	0.02341	0.1343:0.2134:0.3723:0.28	.	234;234;165;233	B7ZLY8;D6W5Y8;Q2TAK8-2;Q2TAK8	.;.;.;MUM1_HUMAN	P	234;165;234;163	ENSP00000345789:S234P;ENSP00000309135:S165P;ENSP00000394925:S234P	ENSP00000309135:S165P	S	+	1	0	MUM1	1311617	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.168000	0.03123	-0.513000	0.06496	-0.440000	0.05779	TCC	.	.		0.572	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853		C	1360617	T	C	1360617	3	2	65	1	0	0	0	0	1	0	0	0	9994	1783	62	2	714	2	MUM1	19	1360617	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	285791	1360617	57768366	359	8432										
ARHGEF18	23370	hgsc.bcm.edu	37	chr19	7533871	7533871	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccggctggccaagagcgatgTgcccatccagctgctcagcg	13	15	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:7533871T>C	ENST00000359920.6	+	17	3330	c.3077T>C	c.(3076-3078)gTg>gCg	p.V1026A	CTD-2207O23.3_ENST00000593531.1_Missense_Mutation_p.C984R|ARHGEF18_ENST00000319670.9_Missense_Mutation_p.V868A	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	1026					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				AAGAGCGATGTGCCCATCCAG	0.697																																					p.V1026A		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.T3077C						.						20	19	19					19																	7533871		2180	4285	6465	SO:0001583	missense	23370	exon17			GCGATGTGCCCAT	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	17090	protein-coding gene	gene with protein product	"Rho-specific guanine nucleotide exchange factor p114"		"rho/rac guanine nucleotide exchange factor (GEF) 18"			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.3077T>C	chr19.hg19:g.7533871T>C	ENSP00000352995:p.Val1026Ala	46.0	0.0		69.0	4.0	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	hg19	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.294159	0.81025	.	.	ENSG00000104880	ENST00000319670;ENST00000359920	T;T	0.61392	0.11;0.11	5.11	5.11	0.69529	.	0.000000	0.45361	D	0.000368	T	0.71239	0.3316	M	0.66939	2.045	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.996	T	0.68519	-0.5387	10	0.22706	T	0.39	-36.1186	12.8551	0.57880	0.0:0.0:0.0:1.0	.	868;1026	Q6ZSZ5-2;Q6ZSZ5	.;ARHGI_HUMAN	A	868;1026	ENSP00000319200:V868A;ENSP00000352995:V1026A	ENSP00000319200:V868A	V	+	2	0	ARHGEF18	7439871	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	7.423000	0.80229	1.934000	0.56057	0.460000	0.39030	GTG	.	.		0.697	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		C	7533871	T	C	7533871	3	2	65	1	0	0	0	0	1	0	0	0	901	1696	59	2	3143	2	ARHGEF18	19	7533871	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6173254	7533871	51595112	360	8433										
KRI1	65095	hgsc.bcm.edu	37	chr19	10671691	10671691	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaactcaccagttccttcagGgaatctgggttccgaatctc	9	12	4	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:10671691G>C	ENST00000312962.6	-	8	688	c.669C>G	c.(667-669)tcC>tcG	p.S223S	KRI1_ENST00000537964.1_5'UTR|KRI1_ENST00000361821.5_Silent_p.S219S	NM_023008.3	NP_075384.3	Q8N9T8	KRI1_HUMAN	KRI1 homolog (S. cerevisiae)	217	Glu-rich.					nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			GTTCCTTCAGGGAATCTGGGT	0.547																																					p.S223S		Atlas-SNP	.											.	KRI1	65	.	0			c.C669G						.						113	85	95					19																	10671691		2203	4300	6503	SO:0001819	synonymous_variant	65095	exon8			CTTCAGGGAATCT		CCDS12242.1	19p13.2	2008-02-05			ENSG00000129347	ENSG00000129347			25769	protein-coding gene	gene with protein product						12878157	Standard	NM_023008		Approved	FLJ12949	uc002moy.1	Q8N9T8	OTTHUMG00000150343	ENST00000312962.6:c.669C>G	chr19.hg19:g.10671691G>C		93.0	0.0		110.0	26.0	NM_023008	Q2M1R5|Q2M1R7|Q7L5J7|Q96G92|Q9BU50|Q9H6I1|Q9H978	Silent	SNP	ENST00000312962.6	hg19	CCDS12242.1	.	.	.	.	.	.	.	.	.	.	G	6.238	0.412061	0.11812	.	.	ENSG00000129347	ENST00000543682	.	.	.	4.56	-0.338	0.12651	.	.	.	.	.	T	0.21307	0.0513	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24657	-1.0154	4	.	.	.	-4.1918	2.6004	0.04865	0.1608:0.2642:0.4397:0.1353	.	.	.	.	R	161	.	.	P	-	2	0	KRI1	10532691	0.000000	0.05858	0.038000	0.18304	0.203000	0.24098	-0.275000	0.08525	0.156000	0.19299	-0.360000	0.07572	CCC	.	.		0.547	KRI1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317705.1	NM_023008		C	10671691	G	C	10671691	2	2	65	1	0	0	0	0	0	0	0	1	8453	1219	43	4		4	KRI1	19	10671691	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	3137820	10671691	48457292	361	8434										
C19orf57	79173	hgsc.bcm.edu	37	chr19	14000257	14000257	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcggggacacacggaaccccTcgaggtctcgttcgaggttc	14	13	1	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:14000257T>C	ENST00000586783.1	-	5	1411	c.1412A>G	c.(1411-1413)gAg>gGg	p.E471G	C19orf57_ENST00000346736.2_Missense_Mutation_p.E471G|C19orf57_ENST00000454313.1_Missense_Mutation_p.E471G|C19orf57_ENST00000591586.1_Intron			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	471					multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			ACGGAACCCCTCGAGGTCTCG	0.602																																					p.E471G		Atlas-SNP	.											.	C19orf57	34	.	0			c.A1412G						.						64	67	66					19																	14000257		2203	4300	6503	SO:0001583	missense	79173	exon6			AACCCCTCGAGGT	BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.1412A>G	chr19.hg19:g.14000257T>C	ENSP00000465822:p.Glu471Gly	78.0	0.0		91.0	4.0	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.16	2.750544	0.49257	.	.	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.47177	0.85;0.85	4.69	-2.65	0.06095	.	2.277220	0.01710	N	0.027661	T	0.34366	0.0895	L	0.29908	0.895	0.09310	N	1	B;B	0.17465	0.022;0.022	B;B	0.17979	0.02;0.02	T	0.11060	-1.0603	10	0.33141	T	0.24	0.9965	5.5723	0.17204	0.1543:0.4594:0.0:0.3863	.	471;471	Q0VDD7-2;Q0VDD7	.;CS057_HUMAN	G	471	ENSP00000404382:E471G;ENSP00000254336:E471G	ENSP00000254336:E471G	E	-	2	0	C19orf57	13861257	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.568000	0.05909	-0.779000	0.04560	0.519000	0.50382	GAG	.	.		0.602	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323		C	14000257	T	C	14000257	3	2	65	1	0	0	0	0	1	0	0	0	1941	1551	54	2	513	2	C19orf57	19	14000257	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3328566	14000257	45128726	362	8435										
ZNF253	56242	hgsc.bcm.edu	37	chr19	20003478	20003478	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aataaacataagaaaattcaTattgaacgaaaaccctacat	3	7	1	2	rs377662376		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:20003478T>C	ENST00000589717.1	+	4	1514	c.1422T>C	c.(1420-1422)caT>caC	p.H474H	ZNF253_ENST00000355650.4_Silent_p.H398H|AC011477.1_ENST00000578823.1_RNA|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	474					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGAAAATTCATATTGAACGAA	0.333																																					p.H474H		Atlas-SNP	.											.	ZNF253	99	.	0			c.T1422C						.						64	73	70					19																	20003478		2071	4236	6307	SO:0001819	synonymous_variant	56242	exon4			AATTCATATTGAA	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"Zinc fingers, C2H2-type", "-"	13497	protein-coding gene	gene with protein product		606954	"zinc finger protein 411"	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.1422T>C	chr19.hg19:g.20003478T>C		59.0	0.0		57.0	4.0	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Silent	SNP	ENST00000589717.1	hg19	CCDS42532.1																																																																																			.	.		0.333	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047		C	20003478	T	C	20003478	2	2	65	1	0	0	0	0	0	0	0	1	17812	1403	49	2		2	ZNF253	19	20003478	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	6003221	20003478	39125505	363	8436										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22155053	22155053	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtttactaaagactgacaacCagctgaaggctttgccacat	8	10	0	3	rs373937489		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:22155053C>A	ENST00000397126.4	-	4	2931	c.2783G>T	c.(2782-2784)tGg>tTg	p.W928L	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	928					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				GACTGACAACCAGCTGAAGGC	0.393																																					p.W928L		Atlas-SNP	.											.	ZNF208	817	.	0			c.G2783T						.						52	54	53					19																	22155053		2053	4210	6263	SO:0001583	missense	7757	exon4			GACAACCAGCTGA	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2783G>T	chr19.hg19:g.22155053C>A	ENSP00000380315:p.Trp928Leu	101.0	0.0		68.0	13.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	1.440	-0.567797	0.03910	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.06142	3.34	3.07	-6.14	0.02111	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04679	0.0127	.	.	.	0.09310	N	1	P	0.50066	0.931	P	0.51833	0.681	T	0.15407	-1.0438	8	0.11182	T	0.66	.	1.2557	0.01991	0.1471:0.2899:0.1456:0.4173	.	828	O43345	ZN208_HUMAN	L	928;828	ENSP00000380315:W928L	ENSP00000380315:W928L	W	-	2	0	ZNF208	21946893	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.300000	0.02751	-1.180000	0.02734	-0.385000	0.06624	TGG	.	.		0.393	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		A	22155053	C	A	22155053	3	1	65	1	0	0	0	0	1	0	0	0	17781	595	21	3	1063	3	ZNF208	19	22155053	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	2151575	22155053	36973930	364	8437										
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35514222	35514222	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cagcccacacctttgagtccTggcacagcctggccctggcc	10	18	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:35514222T>C	ENST00000317991.5	+	18	2128	c.1936T>C	c.(1936-1938)Tgg>Cgg	p.W646R	GRAMD1A_ENST00000599564.1_Missense_Mutation_p.W729R|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.W408R|CTD-2527I21.14_ENST00000605640.1_RNA|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.W635R	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	646						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CTTTGAGTCCTGGCACAGCCT	0.642																																					p.W646R		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.T1936C						.						203	207	206					19																	35514222		1981	4156	6137	SO:0001583	missense	57655	exon18			GAGTCCTGGCACA	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"KIAA1533"	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.1936T>C	chr19.hg19:g.35514222T>C	ENSP00000441032:p.Trp646Arg	119.0	0.0		96.0	4.0	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	hg19	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.041309	0.75732	.	.	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.49432	0.78;1.82;1.8	4.76	4.76	0.60689	.	0.078084	0.56097	D	0.000029	T	0.60818	0.2298	L	0.49778	1.585	0.49687	D	0.999816	D;D;D;D	0.89917	0.998;0.995;1.0;0.998	D;P;D;D	0.91635	0.974;0.897;0.999;0.974	T	0.60105	-0.7328	10	0.42905	T	0.14	.	12.3323	0.55046	0.0:0.0:0.0:1.0	.	642;646;408;635	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2	.;GRM1A_HUMAN;.;.	R	728;408;646;635	ENSP00000423728:W408R;ENSP00000441032:W646R;ENSP00000439267:W635R	ENSP00000441032:W646R	W	+	1	0	GRAMD1A	40206062	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.511000	0.73733	2.013000	0.59113	0.473000	0.43528	TGG	.	.		0.642	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		C	35514222	T	C	35514222	3	2	65	1	0	0	0	0	1	0	0	0	6756	1580	55	2	2006	2	GRAMD1A	19	35514222	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	13359169	35514222	23614761	365	8438										
C19orf55	148137	hgsc.bcm.edu	37	chr19	36258938	36258938	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcggaggccctgcttgcccaGggccgccctgctgctgcagg	15	16	0	0	rs398034467|rs5827939		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:36258938G>A	ENST00000396908.4	+	9	1264	c.1191G>A	c.(1189-1191)caG>caA	p.Q397Q	C19orf55_ENST00000544099.1_Silent_p.Q397Q|AC002398.13_ENST00000589397.1_RNA	NM_001039887.2	NP_001034976.2	Q2NL68	PRSR3_HUMAN		398										cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGCTTGCCCAGGGCCGCCCTG	0.731																																					.		Atlas-SNP	.											.,11	C19orf55	39	.	0			c.1190+1G>A						.						1	1	1					19																	36258938		567	1236	1803	SO:0001630	splice_region_variant	148137	exon9			TGCCCAGGGCCGC																												ENST00000396908.4:c.1191+1G>A	chr19.hg19:g.36258938G>A		6.0	0.0		9.0	2.0	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Splice_Site	SNP	ENST00000396908.4	hg19																																																																																				.	.		0.731	C19orf55-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			Silent	A	36258938	G	A	36258938	5	1	65	1	0	0	0	0	0	0	1	0	1939	991	35	3	1225	3	C19orf55	19	36258938	Splice_Site	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	744716	36258938	22870045	366	8439										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36353409	36353409	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgcagacttgctgcccactGtgcggatagtggccggagtg	15	11	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:36353409G>A	ENST00000360202.5	+	12	1723	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	KIRREL2_ENST00000262625.7_Missense_Mutation_p.V509M|KIRREL2_ENST00000592409.1_Intron|KIRREL2_ENST00000347900.6_Missense_Mutation_p.V459M|NPHS1_ENST00000591817.1_Intron	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	509					cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCTGCCCACTGTGCGGATAGT	0.622																																					p.V509M		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G1525A						.						116	118	117					19																	36353409		2203	4300	6503	SO:0001583	missense	84063	exon12			CCCACTGTGCGGA	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.1525G>A	chr19.hg19:g.36353409G>A	ENSP00000353331:p.Val509Met	50.0	0.0		74.0	4.0	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	hg19	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.447449	0.25987	.	.	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.68331	-0.32;-0.08;-0.3	4.37	0.797	0.18654	.	0.213928	0.23351	N	0.049124	T	0.58694	0.2140	M	0.61703	1.905	0.31070	N	0.713108	B;B;B;B	0.27765	0.061;0.062;0.188;0.17	B;B;B;B	0.30572	0.066;0.055;0.083;0.117	T	0.57888	-0.7733	10	0.52906	T	0.07	-5.2741	6.1253	0.20176	0.105:0.3683:0.5267:0.0	.	489;509;459;509	Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;KIRR2_HUMAN;.;.	M	509;459;509;489	ENSP00000262625:V509M;ENSP00000345067:V459M;ENSP00000353331:V509M	ENSP00000262625:V509M	V	+	1	0	KIRREL2	41045249	0.719000	0.27986	0.988000	0.46212	0.686000	0.39977	0.484000	0.22308	0.087000	0.17167	0.491000	0.48974	GTG	.	.		0.622	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		A	36353409	G	A	36353409	3	1	65	1	0	0	0	0	1	0	0	0	8334	1377	48	3	1571	3	KIRREL2	19	36353409	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	94471	36353409	22775574	367	8440										
ZNF345	25850	hgsc.bcm.edu	37	chr19	37368330	37368330	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acagaattcacacaggtgagAaaccttatgaatgtatagat	8	6	1	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:37368330A>G	ENST00000529555.1	+	2	1386	c.598A>G	c.(598-600)Aaa>Gaa	p.K200E	ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.K200E|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000420450.1_Missense_Mutation_p.K200E			Q14585	ZN345_HUMAN	zinc finger protein 345	200					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CACAGGTGAGAAACCTTATGA	0.418																																					p.K200E		Atlas-SNP	.											.	ZNF345	68	.	0			c.A598G						.						67	65	66					19																	37368330		2203	4300	6503	SO:0001583	missense	25850	exon4			GGTGAGAAACCTT	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"Zinc fingers, C2H2-type"	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.598A>G	chr19.hg19:g.37368330A>G	ENSP00000431202:p.Lys200Glu	61.0	0.0		76.0	4.0	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	hg19	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.898255	0.72639	.	.	ENSG00000251247	ENST00000420450;ENST00000529555	T;T	0.27104	1.69;1.69	3.86	3.86	0.44501	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.48390	0.1497	M	0.75085	2.285	0.30349	N	0.784943	D	0.89917	1.0	D	0.72075	0.976	T	0.49351	-0.8949	8	.	.	.	.	10.9193	0.47154	1.0:0.0:0.0:0.0	.	200	Q14585	ZN345_HUMAN	E	200	ENSP00000431216:K200E;ENSP00000431202:K200E	.	K	+	1	0	ZNF345	42060170	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.095000	0.64529	1.731000	0.51592	0.459000	0.35465	AAA	.	.		0.418	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1			G	37368330	A	G	37368330	3	3	65	1	0	0	0	0	1	0	0	0	17874	247	9	2	600	2	ZNF345	19	37368330	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1014921	37368330	21760653	368	8441										
AXL	558	hgsc.bcm.edu	37	chr19	41762508	41762508	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	accgtgtctacaccagcaagAgcgatgtggtaggtgcactc	12	11	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:41762508A>G	ENST00000301178.4	+	18	2378	c.2188A>G	c.(2188-2190)Agc>Ggc	p.S730G	AXL_ENST00000359092.3_Missense_Mutation_p.S721G|AXL_ENST00000593513.1_Missense_Mutation_p.S462G	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	730	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						CACCAGCAAGAGCGATGTGGT	0.567																																					p.S730G		Atlas-SNP	.											.	AXL	126	.	0			c.A2188G						.						168	118	135					19																	41762508		2203	4300	6503	SO:0001583	missense	558	exon18			AGCAAGAGCGATG	M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	2.7.10.1	"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	905	protein-coding gene	gene with protein product		109135				1656220	Standard	NM_021913		Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.2188A>G	chr19.hg19:g.41762508A>G	ENSP00000301178:p.Ser730Gly	112.0	0.0		122.0	5.0	NM_021913	Q8N5L2|Q9UD27	Missense_Mutation	SNP	ENST00000301178.4	hg19	CCDS12575.1	.	.	.	.	.	.	.	.	.	.	A	19.16	3.773466	0.69992	.	.	ENSG00000167601	ENST00000301178;ENST00000359092	D;D	0.89196	-2.48;-2.48	4.49	4.49	0.54785	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94640	0.8272	M	0.88842	2.985	0.52501	D	0.999953	D;D	0.89917	1.0;1.0	D;D	0.71184	0.966;0.972	D	0.95436	0.8521	10	0.87932	D	0	-10.0188	13.1778	0.59637	1.0:0.0:0.0:0.0	.	721;730	P30530-2;P30530	.;UFO_HUMAN	G	730;721	ENSP00000301178:S730G;ENSP00000351995:S721G	ENSP00000301178:S730G	S	+	1	0	AXL	46454348	1.000000	0.71417	0.993000	0.49108	0.447000	0.32167	8.989000	0.93506	2.004000	0.58718	0.482000	0.46254	AGC	.	.		0.567	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2			G	41762508	A	G	41762508	3	3	65	1	0	0	0	0	1	0	0	0	1238	304	11	2	2258	2	AXL	19	41762508	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	4394178	41762508	17366475	369	8442										
CCDC8	83987	hgsc.bcm.edu	37	chr19	46915065	46915065	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	atctgcagcctcttccctctGattatctgcagcctctgccc	6	17	5	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:46915065G>C	ENST00000307522.3	-	1	1776	c.1003C>G	c.(1003-1005)Cag>Gag	p.Q335E		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	335					microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;4.66e-05)|all cancers(93;0.000582)|Epithelial(262;0.00428)|GBM - Glioblastoma multiforme(486;0.0421)		TCTTCCCTCTGATTATCTGCA	0.602																																					p.Q335E		Atlas-SNP	.											.	CCDC8	56	.	0			c.C1003G						.						94	100	98					19																	46915065		2203	4300	6503	SO:0001583	missense	83987	exon1			CCCTCTGATTATC	BC025243	CCDS12685.1	19q13.33	2012-04-17			ENSG00000169515	ENSG00000169515		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25367	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 20"	614145				11230166	Standard	NM_032040		Approved	DKFZp564K0322, 3M3, PPP1R20	uc002pep.3	Q9H0W5	OTTHUMG00000162348	ENST00000307522.3:c.1003C>G	chr19.hg19:g.46915065G>C	ENSP00000303158:p.Gln335Glu	205.0	0.0		160.0	20.0	NM_032040	Q8TB26	Missense_Mutation	SNP	ENST00000307522.3	hg19	CCDS12685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.69|12.69	2.013964|2.013964	0.35511|0.35511	.|.	.|.	ENSG00000169515|ENSG00000169515	ENST00000540252|ENST00000307522	.|T	.|0.13196	.|2.61	4.3|4.3	4.3|4.3	0.51218|0.51218	.|.	.|0.495473	.|0.15037	.|N	.|0.284089	T|T	0.18800|0.18800	0.0451|0.0451	M|M	0.65498|0.65498	2.005|2.005	0.09310|0.09310	N|N	1|1	.|P	.|0.50819	.|0.939	.|B	.|0.42851	.|0.4	T|T	0.15521|0.15521	-1.0434|-1.0434	6|10	0.35671|0.25751	T|T	0.21|0.34	-2.9829|-2.9829	15.0527|15.0527	0.71888|0.71888	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|335	.|Q9H0W5	.|CCDC8_HUMAN	M|E	181|335	.|ENSP00000303158:Q335E	ENSP00000441180:I181M|ENSP00000303158:Q335E	I|Q	-|-	3|1	3|0	CCDC8|CCDC8	51606905|51606905	0.004000|0.004000	0.15560|0.15560	0.140000|0.140000	0.22221|0.22221	0.039000|0.039000	0.13416|0.13416	1.446000|1.446000	0.35090|0.35090	2.317000|2.317000	0.78254|0.78254	0.561000|0.561000	0.74099|0.74099	ATC|CAG	.	.		0.602	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	NM_032040		C	46915065	G	C	46915065	3	2	65	1	0	0	0	0	1	0	0	0	2855	1299	45	4	617	4	CCDC8	19	46915065	Missense_Mutation	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	5152557	46915065	12213918	370	8443										
PRKD2	25865	hgsc.bcm.edu	37	chr19	47207810	47207810	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgaggcgcaccgagtggccaCtggccagagacgtggatgac	16	12	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:47207810C>G	ENST00000291281.4	-	4	833	c.608G>C	c.(607-609)aGt>aCt	p.S203T	PRKD2_ENST00000601806.1_Missense_Mutation_p.S46T|PRKD2_ENST00000595515.1_Missense_Mutation_p.S203T|PRKD2_ENST00000600194.1_Missense_Mutation_p.S46T|PRKD2_ENST00000433867.1_Missense_Mutation_p.S203T			Q9BZL6	KPCD2_HUMAN	protein kinase D2	203					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		CGAGTGGCCACTGGCCAGAGA	0.662											OREG0025578	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S203T		Atlas-SNP	.											.	PRKD2	94	.	0			c.G608C						.						36	40	39					19																	47207810		2203	4300	6503	SO:0001583	missense	25865	exon4			TGGCCACTGGCCA	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"Pleckstrin homology (PH) domain containing"	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.608G>C	chr19.hg19:g.47207810C>G	ENSP00000291281:p.Ser203Thr	106.0	0.0	945	100.0	26.0	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000291281.4	hg19	CCDS12689.1	.	.	.	.	.	.	.	.	.	.	C	9.805	1.181466	0.21787	.	.	ENSG00000105287	ENST00000291281;ENST00000433867	T;T	0.66280	-0.2;-0.2	5.26	5.26	0.73747	.	0.122405	0.51477	D	0.000092	T	0.48077	0.1480	L	0.36672	1.1	0.42933	D	0.994321	B;B	0.31931	0.024;0.347	B;B	0.30716	0.027;0.119	T	0.41963	-0.9479	10	0.12103	T	0.63	-21.2032	11.8621	0.52471	0.0:0.9147:0.0:0.0853	.	203;203	E7ER94;Q9BZL6	.;KPCD2_HUMAN	T	203	ENSP00000291281:S203T;ENSP00000393978:S203T	ENSP00000291281:S203T	S	-	2	0	PRKD2	51899650	0.999000	0.42202	1.000000	0.80357	0.302000	0.27658	2.251000	0.43187	2.447000	0.82792	0.313000	0.20887	AGT	.	.		0.662	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		G	47207810	C	G	47207810	3	3	65	1	0	0	0	0	1	0	0	0	12531	565	20	4	2088	4	PRKD2	19	47207810	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	292745	47207810	11921173	371	8444										
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47424967	47424967	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gtccaaagaccattctaagcTctctatggaactggagggaa	10	9	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:47424967T>C	ENST00000404338.3	+	1	3035	c.3035T>C	c.(3034-3036)cTc>cCc	p.L1012P		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	1012					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										CATTCTAAGCTCTCTATGGAA	0.438																																					p.L1012P		Atlas-SNP	.											.	.	.	.	0			c.T3035C						.						73	69	71					19																	47424967		1893	4132	6025	SO:0001583	missense	2909	exon1			CTAAGCTCTCTAT	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.3035T>C	chr19.hg19:g.47424967T>C	ENSP00000385720:p.Leu1012Pro	113.0	0.0		123.0	5.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	T	15.02	2.709991	0.48517	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	T	0.08546	3.08	5.76	5.76	0.90799	.	0.233903	0.44097	D	0.000491	T	0.11879	0.0289	N	0.22421	0.69	0.58432	D	0.999996	D	0.54047	0.964	P	0.52066	0.689	T	0.07481	-1.0770	10	0.44086	T	0.13	-16.5649	15.0486	0.71846	0.0:0.0:0.0:1.0	.	1012	Q9NRY4-2	.	P	1012	ENSP00000385720:L1012P	ENSP00000324820:L1012P	L	+	2	0	ARHGAP35	52116807	0.949000	0.32298	0.982000	0.44146	0.919000	0.55068	2.300000	0.43620	2.200000	0.70718	0.533000	0.62120	CTC	.	.		0.438	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		C	47424967	T	C	47424967	3	2	65	1	0	0	0	0	1	0	0	0	6804	1551	54	2	3037	2	ARHGAP35	19	47424967	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	217157	47424967	11704016	372	8445										
GPR77	27202	hgsc.bcm.edu	37	chr19	47844736	47844736	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cagtgccctcctgtgctgggCagcccgacgctgccggccgc	14	18	0	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:47844736C>A	ENST00000595464.1	+	2	898	c.680C>A	c.(679-681)gCa>gAa	p.A227E	C5AR2_ENST00000600626.1_Missense_Mutation_p.A227E|C5AR2_ENST00000257267.2_Missense_Mutation_p.A227E	NM_001271749.1	NP_001258678.1	Q9P296	C5AR2_HUMAN	complement component 5a receptor 2	227					chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of interleukin-8 secretion (GO:2000482)	apical part of cell (GO:0045177)|basal plasma membrane (GO:0009925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C5a anaphylatoxin receptor activity (GO:0004944)										CTGTGCTGGGCAGCCCGACGC	0.667																																					p.A227E		Atlas-SNP	.											.	.	.	.	0			c.C680A						.						28	36	34					19																	47844736		2179	4260	6439	SO:0001583	missense	27202	exon2			GCTGGGCAGCCCG	AB038237	CCDS12699.1	19q13.33	2013-01-28	2013-01-28	2013-01-28		ENSG00000134830		"GPCR / Class A : Complement component receptors"	4527	protein-coding gene	gene with protein product		609949	"G protein-coupled receptor 77"	GPR77		11165367	Standard	NM_018485		Approved	C5L2	uc010ela.1	Q9P296		ENST00000595464.1:c.680C>A	chr19.hg19:g.47844736C>A	ENSP00000472620:p.Ala227Glu	27.0	0.0		38.0	16.0	NM_001271750	B2RA09	Missense_Mutation	SNP	ENST00000595464.1	hg19	CCDS12699.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.909012	0.52439	.	.	ENSG00000134830	ENST00000257267	T	0.38560	1.13	4.11	-6.76	0.01732	GPCR, rhodopsin-like superfamily (1);	0.952150	0.08746	U	0.899814	T	0.40347	0.1113	M	0.62723	1.935	0.09310	N	1	D	0.54601	0.967	P	0.58266	0.836	T	0.41556	-0.9502	10	0.12430	T	0.62	.	0.5786	0.00708	0.2218:0.1518:0.245:0.3814	.	227	Q9P296	C5ARL_HUMAN	E	227	ENSP00000257267:A227E	ENSP00000257267:A227E	A	+	2	0	GPR77	52536576	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-1.026000	0.03596	-0.867000	0.04063	0.313000	0.20887	GCA	.	.		0.667	C5AR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466926.1	NM_018485		A	47844736	C	A	47844736	3	1	65	1	0	0	0	0	1	0	0	0	6717	710	25	3	682	3	GPR77	19	47844736	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	419769	47844736	11284247	373	8446										
TBC1D17	79735	hgsc.bcm.edu	37	chr19	50381446	50381446	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cctgcacaccagcgctaagaAgtatcaggaccgagactctc	9	14	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:50381446A>G	ENST00000221543.5	+	2	367	c.68A>G	c.(67-69)aAg>aGg	p.K23R	AKT1S1_ENST00000391832.3_5'Flank|AKT1S1_ENST00000482622.1_5'UTR|TBC1D17_ENST00000598789.1_3'UTR|AKT1S1_ENST00000391833.1_5'Flank|AKT1S1_ENST00000391834.2_5'Flank|AKT1S1_ENST00000391831.1_5'Flank|TBC1D17_ENST00000535102.2_Intron|AKT1S1_ENST00000344175.5_5'Flank|AKT1S1_ENST00000391835.1_5'Flank	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	23					autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		AGCGCTAAGAAGTATCAGGAC	0.642																																					p.K23R		Atlas-SNP	.											.	TBC1D17	39	.	0			c.A68G						.						45	38	41					19																	50381446		2195	4288	6483	SO:0001583	missense	79735	exon2			CTAAGAAGTATCA	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.68A>G	chr19.hg19:g.50381446A>G	ENSP00000221543:p.Lys23Arg	77.0	0.0		89.0	4.0	NM_024682	B4DT12|B9A6L8|F5H1W7	Missense_Mutation	SNP	ENST00000221543.5	hg19	CCDS12785.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610046	0.46527	.	.	ENSG00000104946	ENST00000221543	T	0.34859	1.34	5.72	2.16	0.27623	Domain of unknown function DUF3548 (1);	0.060857	0.64402	D	0.000004	T	0.14442	0.0349	N	0.05383	-0.06	0.80722	D	1	B	0.10296	0.003	B	0.17979	0.02	T	0.06625	-1.0816	10	0.19590	T	0.45	-37.0567	3.5835	0.07962	0.5379:0.1918:0.2703:0.0	.	23	Q9HA65	TBC17_HUMAN	R	23	ENSP00000221543:K23R	ENSP00000221543:K23R	K	+	2	0	TBC1D17	55073258	0.999000	0.42202	1.000000	0.80357	0.975000	0.68041	1.270000	0.33086	0.985000	0.38656	0.459000	0.35465	AAG	.	.		0.642	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682		G	50381446	A	G	50381446	3	3	65	1	0	0	0	0	1	0	0	0	15621	72	3	2	74	2	TBC1D17	19	50381446	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	2536710	50381446	8747537	374	8447										
SIGLEC7	27036	hgsc.bcm.edu	37	chr19	51649119	51649119	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tttttctctacagcatccacAgctctggggaacagctcatc	7	13	3	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:51649119A>G	ENST00000317643.6	+	4	837	c.768A>G	c.(766-768)acA>acG	p.T256T	SIGLEC7_ENST00000305628.7_Silent_p.T163T|SIGLEC7_ENST00000600577.1_Intron	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	256	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		CAGCATCCACAGCTCTGGGGA	0.512																																					p.T256T		Atlas-SNP	.											.	SIGLEC7	74	.	0			c.A768G						.						154	153	153					19																	51649119		2203	4300	6503	SO:0001819	synonymous_variant	27036	exon4			ATCCACAGCTCTG	AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10876	protein-coding gene	gene with protein product		604410	"sialic acid binding Ig-like lectin 19, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 2"	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.768A>G	chr19.hg19:g.51649119A>G		72.0	0.0		61.0	4.0	NM_014385	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Silent	SNP	ENST00000317643.6	hg19	CCDS12826.1																																																																																			.	.		0.512	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543		G	51649119	A	G	51649119	2	3	65	1	0	0	0	0	0	0	0	1	14328	175	7	2		2	SIGLEC7	19	51649119	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1267673	51649119	7479864	375	8448										
ZNF836	162962	hgsc.bcm.edu	37	chr19	52658668	52658668	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaagtggaattaaagacctgGccacattcaatacatttgta	8	7	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:52658668G>A	ENST00000322146.8	-	5	2789	c.2268C>T	c.(2266-2268)ggC>ggT	p.G756G	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Silent_p.G756G	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	756					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						TAAAGACCTGGCCACATTCAA	0.423																																					p.G756G		Atlas-SNP	.											.	ZNF836	158	.	0			c.C2268T						.						86	91	90					19																	52658668		2182	4286	6468	SO:0001819	synonymous_variant	162962	exon5			GACCTGGCCACAT	BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"Zinc fingers, C2H2-type", "-"	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.2268C>T	chr19.hg19:g.52658668G>A		96.0	0.0		64.0	4.0	NM_001102657		Silent	SNP	ENST00000322146.8	hg19	CCDS46162.1																																																																																			.	.		0.423	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		A	52658668	G	A	52658668	2	1	65	1	0	0	0	0	0	0	0	1	18202	1190	42	3		3	ZNF836	19	52658668	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	1009549	52658668	6470315	376	8449										
ZNF534	147658	hgsc.bcm.edu	37	chr19	52938454	52938454	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cagggagtgcatcaaaggtgTgaacacaggtgagagctcag	15	7	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:52938454T>C	ENST00000332323.6	+	3	363	c.302T>C	c.(301-303)gTg>gCg	p.V101A	ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000301085.4_Missense_Mutation_p.V88A|ZNF534_ENST00000433050.1_Missense_Mutation_p.V88A	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	101					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						ATCAAAGGTGTGAACACAGGT	0.478																																					p.V101A		Atlas-SNP	.											.	ZNF534	105	.	0			c.T302C						.						77	66	69					19																	52938454		1568	3582	5150	SO:0001583	missense	147658	exon3			AAGGTGTGAACAC	AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"Zinc fingers, C2H2-type", "-"	26337	protein-coding gene	gene with protein product			"KRAB domain only 3"	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.302T>C	chr19.hg19:g.52938454T>C	ENSP00000327538:p.Val101Ala	108.0	0.0		92.0	4.0	NM_001143939	Q76KX9	Missense_Mutation	SNP	ENST00000332323.6	hg19	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	T	5.044	0.193778	0.09599	.	.	ENSG00000198633	ENST00000301085;ENST00000332323;ENST00000433050;ENST00000391790	T;T;T	0.07567	5.62;3.18;3.2	1.67	-1.98	0.07480	.	.	.	.	.	T	0.06462	0.0166	L	0.42744	1.35	0.09310	N	1	P;P;B	0.38767	0.504;0.646;0.138	B;B;B	0.35770	0.057;0.21;0.082	T	0.31110	-0.9955	9	0.45353	T	0.12	.	5.4986	0.16817	0.0:0.0:0.602:0.398	.	88;101;88	Q76KX8-2;Q76KX8;Q1T7F5	.;ZN534_HUMAN;.	A	88;101;88;100	ENSP00000301085:V88A;ENSP00000327538:V101A;ENSP00000391358:V88A	ENSP00000301085:V88A	V	+	2	0	ZNF534	57630266	0.003000	0.15002	0.001000	0.08648	0.002000	0.02628	-0.251000	0.08818	-0.145000	0.11294	0.338000	0.21704	GTG	.	.		0.478	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512		C	52938454	T	C	52938454	3	2	65	1	0	0	0	0	1	0	0	0	17988	1696	59	2	312	2	ZNF534	19	52938454	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	279786	52938454	6190529	377	8450										
CACNG8	59283	hgsc.bcm.edu	37	chr19	54485412	54485412	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cccgaagcgggacgaggagaAgaaaaaccactactcgtacg	12	11	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:54485412A>G	ENST00000270458.2	+	4	690	c.587A>G	c.(586-588)aAg>aGg	p.K196R	MIR935_ENST00000401179.1_RNA	NM_031895.5	NP_114101	Q8WXS5	CCG8_HUMAN	calcium channel, voltage-dependent, gamma subunit 8	196					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			kidney(1)|large_intestine(3)|lung(8)|urinary_tract(1)	13	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		GACGAGGAGAAGAAAAACCAC	0.627																																					p.K196R		Atlas-SNP	.											.	CACNG8	29	.	0			c.A587G						.						53	43	46					19																	54485412		2202	4299	6501	SO:0001583	missense	59283	exon4			AGGAGAAGAAAAA	AF288388	CCDS33104.1	19q13.4	2008-05-02			ENSG00000142408	ENSG00000142408		"Calcium channel subunits"	13628	protein-coding gene	gene with protein product		606900				11170751	Standard	NM_031895		Approved		uc002qcs.2	Q8WXS5	OTTHUMG00000064908	ENST00000270458.2:c.587A>G	chr19.hg19:g.54485412A>G	ENSP00000270458:p.Lys196Arg	82.0	0.0		106.0	5.0	NM_031895	Q9BXT0|Q9BY23	Missense_Mutation	SNP	ENST00000270458.2	hg19	CCDS33104.1	.	.	.	.	.	.	.	.	.	.	.	21.1	4.104143	0.76983	.	.	ENSG00000142408	ENST00000270458	T	0.50001	0.76	2.28	2.28	0.28536	.	0.000000	0.64402	U	0.000005	T	0.52629	0.1746	M	0.83953	2.67	0.31060	N	0.714201	P	0.44816	0.844	P	0.45610	0.487	T	0.67597	-0.5630	9	0.62326	D	0.03	-27.083	8.1583	0.31183	1.0:0.0:0.0:0.0	.	196	Q8WXS5	CCG8_HUMAN	R	196	ENSP00000270458:K196R	ENSP00000270458:K196R	K	+	2	0	CACNG8	59177224	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.417000	0.73337	1.066000	0.40716	0.241000	0.17934	AAG	.	.		0.627	CACNG8-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139361.3			G	54485412	A	G	54485412	3	3	65	1	0	0	0	0	1	0	0	0	2565	72	3	2	601	2	CACNG8	19	54485412	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1546958	54485412	4643571	378	8451										
ZNF17	7565	hgsc.bcm.edu	37	chr19	57932584	57932584	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cctcattcggcaccaaaaagTtcacactagggaaagaactt	7	11	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:57932584T>C	ENST00000601808.1	+	3	1937	c.1724T>C	c.(1723-1725)gTt>gCt	p.V575A	ZNF17_ENST00000307658.7_Missense_Mutation_p.V577A|AC004076.7_ENST00000597410.1_Intron	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	575					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		CACCAAAAAGTTCACACTAGG	0.408																																					p.V575A	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.T1724C						.						51	51	51					19																	57932584		2020	4211	6231	SO:0001583	missense	7565	exon3			AAAAAGTTCACAC	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"Zinc fingers, C2H2-type", "-"	12958	protein-coding gene	gene with protein product			"zinc finger protein 17 (HPF3, KOX 10)"			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.1724T>C	chr19.hg19:g.57932584T>C	ENSP00000471905:p.Val575Ala	100.0	0.0		79.0	4.0	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Missense_Mutation	SNP	ENST00000601808.1	hg19	CCDS42636.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.685649	0.47991	.	.	ENSG00000186272	ENST00000307658	.	.	.	2.45	1.37	0.22104	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47377	0.1442	L	0.38531	1.155	0.09310	N	1	D;B	0.71674	0.998;0.129	D;B	0.67103	0.949;0.048	T	0.28138	-1.0053	8	0.87932	D	0	.	5.7423	0.18100	0.0:0.2658:0.0:0.7342	.	577;575	P17021-2;P17021	.;ZNF17_HUMAN	A	575	.	ENSP00000302455:V575A	V	+	2	0	ZNF17	62624396	0.001000	0.12720	0.011000	0.14972	0.697000	0.40408	1.101000	0.31037	0.166000	0.19597	0.383000	0.25322	GTT	.	.		0.408	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959		C	57932584	T	C	57932584	3	2	65	1	0	0	0	0	1	0	0	0	17758	1725	60	2	1734	2	ZNF17	19	57932584	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3447172	57932584	1196399	379	8452										
ZNF549	256051	hgsc.bcm.edu	37	chr19	58048846	58048846	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aaccaggacagtggagagaaAcacatcagaaaggaggagag	14	6	1	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr19:58048846A>G	ENST00000376233.3	+	4	655	c.474A>G	c.(472-474)aaA>aaG	p.K158K	ZNF550_ENST00000601415.1_Intron|ZNF549_ENST00000602149.1_Intron|ZNF549_ENST00000240719.3_Silent_p.K145K|ZNF549_ENST00000594943.1_Intron	NM_001199295.1	NP_001186224	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GTGGAGAGAAACACATCAGAA	0.458																																					p.K158K		Atlas-SNP	.											.	ZNF549	118	.	0			c.A474G						.						79	72	74					19																	58048846		2203	4300	6503	SO:0001819	synonymous_variant	256051	exon4			AGAGAAACACATC	AK092236	CCDS12952.1, CCDS56106.1	19q13.43	2013-01-08				ENSG00000121406		"Zinc fingers, C2H2-type", "-"	26632	protein-coding gene	gene with protein product						12477932	Standard	NM_153263		Approved	FLJ34917	uc002qpb.2	Q6P9A3		ENST00000376233.3:c.474A>G	chr19.hg19:g.58048846A>G		117.0	0.0		100.0	5.0	NM_001199295	B3KV91|O43336|Q8NAR4	Silent	SNP	ENST00000376233.3	hg19	CCDS56106.1																																																																																			.	.		0.458	ZNF549-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466780.1	NM_153263		G	58048846	A	G	58048846	2	3	65	1	0	0	0	0	0	0	0	1	17996	40	2	2		2	ZNF549	19	58048846	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	116262	58048846	1080137	380	8453										
UBOX5	22888	hgsc.bcm.edu	37	chr20	3102976	3102976	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gggacagatggctcagctggGcccagggtccggcactgggg	19	11	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr20:3102976G>A	ENST00000217173.2	-	3	780	c.309C>T	c.(307-309)ggC>ggT	p.G103G	UBOX5_ENST00000348031.2_Silent_p.G103G|UBOX5-AS1_ENST00000446537.1_RNA	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5											endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						GCTCAGCTGGGCCCAGGGTCC	0.557																																					p.G103G		Atlas-SNP	.											.	UBOX5	47	.	0			c.C309T						.						59	59	59					20																	3102976		2203	4300	6503	SO:0001819	synonymous_variant	22888	exon3			AGCTGGGCCCAGG	AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"RING-type (C3HC4) zinc fingers", "U-box domain containing"	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.309C>T	chr20.hg19:g.3102976G>A		114.0	0.0		102.0	47.0	NM_014948		Silent	SNP	ENST00000217173.2	hg19	CCDS13046.1																																																																																			.	.		0.557	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		A	3102976	G	A	3102976	2	1	65	1	0	0	0	0	0	0	0	1	16909	1190	42	3		3	UBOX5	20	3102976	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10		3102976	59922544	381	8454										
OVOL2	58495	hgsc.bcm.edu	37	chr20	18022310	18022310	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	catgcgctgcagacggaagcCcttgccacacaggtcacagc	11	15	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr20:18022310C>G	ENST00000278780.6	-	3	621	c.379G>C	c.(379-381)Ggc>Cgc	p.G127R	OVOL2_ENST00000483661.1_5'UTR	NM_021220.2	NP_067043.2	Q9BRP0	OVOL2_HUMAN	ovo-like zinc finger 2	127					angiogenesis (GO:0001525)|dorsal/ventral pattern formation (GO:0009953)|embryonic digestive tract morphogenesis (GO:0048557)|endocardium formation (GO:0060214)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of keratinocyte proliferation (GO:0010837)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)	6						AGACGGAAGCCCTTGCCACAC	0.617																																					p.G127R		Atlas-SNP	.											.	OVOL2	18	.	0			c.G379C						.						120	80	93					20																	18022310		2203	4300	6503	SO:0001583	missense	58495	exon3			GGAAGCCCTTGCC	AK022284	CCDS13132.1	20p11.23	2013-10-17	2013-10-17	2005-05-31	ENSG00000125850	ENSG00000125850		"Zinc fingers, C2H2-type"	15804	protein-coding gene	gene with protein product			"zinc finger protein 339", "ovo-like 2 (Drosophila)"	ZNF339			Standard	NM_021220		Approved	bA504H3.3, HOVO2	uc002wqi.1	Q9BRP0	OTTHUMG00000031960	ENST00000278780.6:c.379G>C	chr20.hg19:g.18022310C>G	ENSP00000278780:p.Gly127Arg	157.0	0.0		142.0	6.0	NM_021220	Q5T8B4|Q9BX22|Q9HA54|Q9Y4M0	Missense_Mutation	SNP	ENST00000278780.6	hg19	CCDS13132.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.142366	0.57044	.	.	ENSG00000125850	ENST00000278780	T	0.75938	-0.98	5.57	0.66	0.17868	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.706306	0.14785	N	0.298588	T	0.61627	0.2362	L	0.27053	0.805	0.30601	N	0.760484	P	0.41366	0.747	B	0.43508	0.422	T	0.60712	-0.7209	10	0.72032	D	0.01	-13.263	6.295	0.21081	0.2774:0.6108:0.0:0.1117	.	127	Q9BRP0	OVOL2_HUMAN	R	127	ENSP00000278780:G127R	ENSP00000278780:G127R	G	-	1	0	OVOL2	17970310	0.292000	0.24362	0.990000	0.47175	0.998000	0.95712	0.629000	0.24538	-0.132000	0.11557	0.655000	0.94253	GGC	.	.		0.617	OVOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078148.5	NM_021220		G	18022310	C	G	18022310	3	3	65	1	0	0	0	0	1	0	0	0	11336	623	22	4	456	4	OVOL2	20	18022310	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	14919334	18022310	45003210	382	8455										
NINL	22981	hgsc.bcm.edu	37	chr20	25442240	25442240	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gttcctgattcaggcattcaAgttcaactctaagtttttgg	8	8	4	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr20:25442240A>G	ENST00000278886.6	-	21	3687	c.3614T>C	c.(3613-3615)cTt>cCt	p.L1205P	NINL_ENST00000422516.1_Missense_Mutation_p.L856P|NINL_ENST00000464285.1_5'Flank	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1205					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CAGGCATTCAAGTTCAACTCT	0.443																																					p.L1205P		Atlas-SNP	.											.	NINL	148	.	0			c.T3614C						.						174	148	157					20																	25442240		2203	4300	6503	SO:0001583	missense	22981	exon21			CATTCAAGTTCAA		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.3614T>C	chr20.hg19:g.25442240A>G	ENSP00000278886:p.Leu1205Pro	98.0	0.0		94.0	4.0	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	hg19	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	A	14.45	2.538279	0.45176	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.38722	3.29;1.12	4.81	3.71	0.42584	.	0.092912	0.43919	D	0.000502	T	0.55970	0.1954	L	0.58101	1.795	0.41456	D	0.988018	B;D	0.89917	0.087;1.0	B;D	0.80764	0.063;0.994	T	0.56739	-0.7929	10	0.72032	D	0.01	-3.3487	8.2593	0.31775	0.9077:0.0:0.0923:0.0	.	856;1205	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	P	1205;856	ENSP00000278886:L1205P;ENSP00000410431:L856P	ENSP00000278886:L1205P	L	-	2	0	NINL	25390240	0.993000	0.37304	0.939000	0.37840	0.509000	0.34042	2.534000	0.45676	0.865000	0.35603	0.454000	0.30748	CTT	.	.		0.443	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		G	25442240	A	G	25442240	3	3	65	1	0	0	0	0	1	0	0	0	10429	72	3	2	550	2	NINL	20	25442240	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	7419930	25442240	37583280	383	8456										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31021502	31021502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cagacaacttggcacgtgccTctgcatctccagacagaatt	8	13	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr20:31021502T>C	ENST00000375687.4	+	12	1925	c.1501T>C	c.(1501-1503)Tct>Cct	p.S501P	ASXL1_ENST00000306058.5_Missense_Mutation_p.S496P	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	501	Interaction with NCOA1. {ECO:0000250}.				bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						GGCACGTGCCTCTGCATCTCC	0.567			"F, N, Mis"		"MDS, CMML"																																p.S501P		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.T1501C						.						121	125	124					20																	31021502		2203	4300	6503	SO:0001583	missense	171023	exon11			CGTGCCTCTGCAT	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.1501T>C	chr20.hg19:g.31021502T>C	ENSP00000364839:p.Ser501Pro	97.0	0.0		138.0	6.0	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	hg19	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	T	11.77	1.739158	0.30774	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.15603	2.41;2.41	4.38	4.38	0.52667	.	0.120886	0.64402	D	0.000020	T	0.13628	0.0330	L	0.45137	1.4	0.35903	D	0.830526	B;P	0.35714	0.068;0.517	B;B	0.40636	0.01;0.335	T	0.19289	-1.0310	10	0.24483	T	0.36	-8.7631	1.9683	0.03400	0.1476:0.0888:0.2485:0.5151	.	496;501	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	P	501;501;501;440;496	ENSP00000364839:S501P;ENSP00000305119:S496P	ENSP00000305119:S496P	S	+	1	0	ASXL1	30485163	1.000000	0.71417	0.953000	0.39169	0.097000	0.18754	1.587000	0.36622	2.198000	0.70561	0.533000	0.62120	TCT	.	.		0.567	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		C	31021502	T	C	31021502	3	2	65	1	0	0	0	0	1	0	0	0	1066	1551	54	2	1553	2	ASXL1	20	31021502	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	5579262	31021502	32004018	384	8457										
ZNF335	63925	hgsc.bcm.edu	37	chr20	44586259	44586259	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cccccagttcccgctgagcaCtcatgttcagcagaagatcc	8	16	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr20:44586259C>G	ENST00000322927.2	-	17	2508	c.2408G>C	c.(2407-2409)aGt>aCt	p.S803T	ZNF335_ENST00000426788.1_Missense_Mutation_p.S648T	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	803					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				CCGCTGAGCACTCATGTTCAG	0.617																																					p.S803T		Atlas-SNP	.											.	ZNF335	115	.	0			c.G2408C						.						62	55	58					20																	44586259		2203	4300	6503	SO:0001583	missense	63925	exon17			TGAGCACTCATGT	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.2408G>C	chr20.hg19:g.44586259C>G	ENSP00000325326:p.Ser803Thr	89.0	0.0		93.0	4.0	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	hg19	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.738862	0.89573	.	.	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	T;T	0.21191	2.2;2.02	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.34571	0.0902	L	0.34521	1.04	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.78314	0.991;0.98	T	0.01238	-1.1409	10	0.27785	T	0.31	-13.011	16.1908	0.81987	0.0:1.0:0.0:0.0	.	648;803	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	T	803;580;648	ENSP00000325326:S803T;ENSP00000397098:S648T	ENSP00000243961:S580T	S	-	2	0	ZNF335	44019666	1.000000	0.71417	0.964000	0.40570	0.972000	0.66771	6.548000	0.73896	2.735000	0.93741	0.563000	0.77884	AGT	.	.		0.617	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		G	44586259	C	G	44586259	3	3	65	1	0	0	0	0	1	0	0	0	17867	565	20	4	1668	4	ZNF335	20	44586259	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	13564757	44586259	18439261	385	8458										
SPATA2	9825	hgsc.bcm.edu	37	chr20	48524814	48524814	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gctgagcgagcgcaaggagcTctccaccacctcatagaact	10	14	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr20:48524814T>C	ENST00000422556.1	-	2	563	c.214A>G	c.(214-216)Agc>Ggc	p.S72G	SPATA2_ENST00000289431.5_Missense_Mutation_p.S72G|SPATA2_ENST00000543716.1_Intron	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	72					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	20	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			CGCAAGGAGCTCTCCACCACC	0.607																																					p.S72G		Atlas-SNP	.											.	SPATA2	36	.	0			c.A214G						.						82	70	74					20																	48524814		2203	4300	6503	SO:0001583	missense	9825	exon2			AGGAGCTCTCCAC	AB018300	CCDS13422.1	20q13.13	2014-06-13			ENSG00000158480	ENSG00000158480			14681	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 145"	607662					Standard	NM_001135773		Approved	KIAA0757, PD1, tamo, PPP1R145	uc002xuw.3	Q9UM82	OTTHUMG00000032704	ENST00000422556.1:c.214A>G	chr20.hg19:g.48524814T>C	ENSP00000416799:p.Ser72Gly	73.0	0.0		116.0	5.0	NM_006038	E1P626|O94857	Missense_Mutation	SNP	ENST00000422556.1	hg19	CCDS13422.1	.	.	.	.	.	.	.	.	.	.	T	15.11	2.736872	0.49045	.	.	ENSG00000158480	ENST00000289431;ENST00000422556	T;T	0.72051	-0.62;-0.62	4.38	2.04	0.26737	.	0.050219	0.85682	D	0.000000	T	0.57755	0.2075	L	0.44542	1.39	0.80722	D	1	B	0.30605	0.287	B	0.24394	0.053	T	0.50259	-0.8849	10	0.31617	T	0.26	-4.8772	11.3129	0.49375	0.0:0.0:0.3102:0.6898	.	72	Q9UM82	SPAT2_HUMAN	G	72	ENSP00000289431:S72G;ENSP00000416799:S72G	ENSP00000289431:S72G	S	-	1	0	SPATA2	47958221	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.068000	0.50018	0.292000	0.22492	0.533000	0.62120	AGC	.	.		0.607	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038		C	48524814	T	C	48524814	3	2	65	1	0	0	0	0	1	0	0	0	15020	1551	54	2	1356	2	SPATA2	20	48524814	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	3938555	48524814	14500706	386	8459										
FAM65C	140876	hgsc.bcm.edu	37	chr20	49214133	49214133	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcaccggagaccctgggagcCcccaaacagggacagctcat	11	15	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr20:49214133C>A	ENST00000327979.2	-	14	2173	c.1762G>T	c.(1762-1764)Ggc>Tgc	p.G588C	FAM65C_ENST00000535356.1_Missense_Mutation_p.G592C|FAM65C_ENST00000045083.2_Missense_Mutation_p.G588C			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	588										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCCTGGGAGCCCCCAAACAGG	0.652																																					p.G588C		Atlas-SNP	.											.	FAM65C	87	.	0			c.G1762T						.						53	47	49					20																	49214133		2201	4300	6501	SO:0001583	missense	140876	exon14			GGGAGCCCCCAAA	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.1762G>T	chr20.hg19:g.49214133C>A	ENSP00000332663:p.Gly588Cys	109.0	0.0		140.0	18.0	NM_080829	Q5QPB6|Q9NQQ2	Missense_Mutation	SNP	ENST00000327979.2	hg19	CCDS13431.2	.	.	.	.	.	.	.	.	.	.	C	13.78	2.339966	0.41398	.	.	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	T;T;T	0.15372	2.43;2.43;2.43	4.6	3.39	0.38822	.	0.087335	0.85682	D	0.000000	T	0.30696	0.0773	M	0.68317	2.08	0.47737	D	0.999507	D;D	0.76494	0.998;0.999	D;D	0.65443	0.927;0.935	T	0.05954	-1.0854	10	0.72032	D	0.01	-35.1959	4.0709	0.09882	0.0:0.6553:0.0:0.3447	.	592;588	F5H0X2;Q96MK2	.;FA65C_HUMAN	C	588;588;592	ENSP00000332663:G588C;ENSP00000045083:G588C;ENSP00000439802:G592C	ENSP00000045083:G588C	G	-	1	0	FAM65C	48647540	1.000000	0.71417	1.000000	0.80357	0.165000	0.22458	1.676000	0.37565	2.256000	0.74724	0.561000	0.74099	GGC	.	.		0.652	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			A	49214133	C	A	49214133	3	1	65	1	0	0	0	0	1	0	0	0	5609	623	22	3	1114	3	FAM65C	20	49214133	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	689319	49214133	13811387	387	8460										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58442784	58442784	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acattattccttctcttaaaTtctgaattgagcctctcgta	4	10	3	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr20:58442784T>C	ENST00000357552.3	-	39	4332	c.4107A>G	c.(4105-4107)gaA>gaG	p.E1369E	SYCP2_ENST00000371001.2_Silent_p.E1369E			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	1369					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			TTCTCTTAAATTCTGAATTGA	0.328																																					p.E1369E		Atlas-SNP	.											.	SYCP2	204	.	0			c.A4107G						.						52	55	54					20																	58442784		2203	4295	6498	SO:0001819	synonymous_variant	10388	exon38			CTTAAATTCTGAA	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.4107A>G	chr20.hg19:g.58442784T>C		111.0	0.0		100.0	4.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Silent	SNP	ENST00000357552.3	hg19	CCDS13482.1																																																																																			.	.		0.328	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		C	58442784	T	C	58442784	2	2	65	1	0	0	0	0	0	0	0	1	15447	1490	52	2		2	SYCP2	20	58442784	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	9228651	58442784	4582736	388	8461										
CDH4	1002	hgsc.bcm.edu	37	chr20	60318825	60318825	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgctggtggcccagacctcgTccccgcactctggacacaag	11	16	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr20:60318825T>C	ENST00000360469.5	+	3	464	c.376T>C	c.(376-378)Tcc>Ccc	p.S126P	RP11-429E11.2_ENST00000447909.1_RNA|CDH4_ENST00000543233.1_Missense_Mutation_p.S52P|RP11-429E11.2_ENST00000442888.1_RNA	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	126					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			CCAGACCTCGTCCCCGCACTC	0.642																																					p.S126P		Atlas-SNP	.											.	CDH4	172	.	0			c.T376C						.						51	41	45					20																	60318825		2198	4300	6498	SO:0001583	missense	1002	exon3			ACCTCGTCCCCGC	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.376T>C	chr20.hg19:g.60318825T>C	ENSP00000353656:p.Ser126Pro	77.0	0.0		97.0	4.0	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	hg19	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	T	3.595	-0.082855	0.07141	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.56776	0.44;0.45	5.0	1.22	0.21188	Cadherin-like (1);	1.747780	0.03392	N	0.202093	T	0.31263	0.0791	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13926	-1.0491	9	.	.	.	.	5.3668	0.16117	0.0:0.2406:0.2983:0.4611	.	126	P55283	CADH4_HUMAN	P	126;34;52	ENSP00000353656:S126P;ENSP00000443301:S52P	.	S	+	1	0	CDH4	59752220	0.000000	0.05858	0.001000	0.08648	0.150000	0.21749	0.133000	0.15912	-0.035000	0.13691	0.402000	0.26972	TCC	.	.		0.642	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		C	60318825	T	C	60318825	3	2	65	1	0	0	0	0	1	0	0	0	3114	1667	58	2	386	2	CDH4	20	60318825	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	1876041	60318825	2706695	389	8462										
KCNJ6	3763	hgsc.bcm.edu	37	chr21	38997717	38997717	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acccgtcctccagggtcaggAcaggtgtgaaccggtaaccc	12	14	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr21:38997717A>G	ENST00000609713.1	-	4	1605	c.1016T>C	c.(1015-1017)gTc>gCc	p.V339A	KCNJ6_ENST00000288309.6_Missense_Mutation_p.V339A	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	339					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	CAGGGTCAGGACAGGTGTGAA	0.537																																					p.V339A	Pancreas(48;379 1118 2936 19024 28214)	Atlas-SNP	.											.	KCNJ6	58	.	0			c.T1016C						.						91	98	95					21																	38997717		2048	4216	6264	SO:0001583	missense	3763	exon4			GTCAGGACAGGTG	U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.1016T>C	chr21.hg19:g.38997717A>G	ENSP00000477437:p.Val339Ala	114.0	0.0		80.0	4.0	NM_002240	Q3MJ74|Q53WW6	Missense_Mutation	SNP	ENST00000609713.1	hg19	CCDS42927.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.761425	0.89932	.	.	ENSG00000157542	ENST00000400482;ENST00000288309	D;D	0.95412	-3.7;-3.7	5.88	5.88	0.94601	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.052029	0.85682	D	0.000000	D	0.97611	0.9217	M	0.80847	2.515	0.80722	D	1	D	0.64830	0.994	D	0.70227	0.968	D	0.98314	1.0525	10	0.87932	D	0	.	16.3009	0.82811	1.0:0.0:0.0:0.0	.	339	P48051	IRK6_HUMAN	A	339	ENSP00000383330:V339A;ENSP00000288309:V339A	ENSP00000288309:V339A	V	-	2	0	KCNJ6	37919587	1.000000	0.71417	0.993000	0.49108	0.918000	0.54935	8.962000	0.93254	2.246000	0.74042	0.533000	0.62120	GTC	.	.		0.537	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194828.2	NM_002240		G	38997717	A	G	38997717	3	3	65	1	0	0	0	0	1	0	0	0	8064	275	10	2	259	2	KCNJ6	21	38997717	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10		38997717	9132178	390	8463										
BRWD1	54014	hgsc.bcm.edu	37	chr21	40590495	40590495	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tcttcatctcttgatttctgAccccattcaccagcttgtgg	6	13	5	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr21:40590495A>G	ENST00000333229.2	-	30	3801	c.3474T>C	c.(3472-3474)ggT>ggC	p.G1158G	BRWD1_ENST00000342449.3_Silent_p.G1158G|BRWD1-IT1_ENST00000435608.1_RNA|BRWD1_ENST00000380800.3_Silent_p.G1158G	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1158					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TTGATTTCTGACCCCATTCAC	0.328																																					p.G1158G	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.T3474C						.						136	121	126					21																	40590495		2203	4300	6503	SO:0001819	synonymous_variant	54014	exon30			TTTCTGACCCCAT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.3474T>C	chr21.hg19:g.40590495A>G		92.0	0.0		86.0	5.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	hg19	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	A	9.000	0.979959	0.18812	.	.	ENSG00000185658	ENST00000424441	.	.	.	5.36	-3.9	0.04181	.	.	.	.	.	T	0.37732	0.1014	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.36768	-0.9734	4	.	.	.	-8.878	1.3199	0.02114	0.2806:0.1085:0.3337:0.2773	.	.	.	.	P	144	.	.	S	-	1	0	BRWD1	39512365	0.000000	0.05858	0.989000	0.46669	0.996000	0.88848	-1.778000	0.01778	-0.539000	0.06273	0.460000	0.39030	TCA	.	.		0.328	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		G	40590495	A	G	40590495	2	3	65	1	0	0	0	0	0	0	0	1	1527	262	10	2		2	BRWD1	21	40590495	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1592778	40590495	7539400	391	8464										
LCA5L	150082	hgsc.bcm.edu	37	chr21	40782216	40782216	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgtcaaaggtggaacatctgAtttttgggttccctggtgtc	12	7	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr21:40782216A>G	ENST00000358268.2	-	8	1666	c.1138T>C	c.(1138-1140)Tca>Cca	p.S380P	LCA5L_ENST00000288350.3_Missense_Mutation_p.S380P|LCA5L_ENST00000380671.2_Missense_Mutation_p.S380P|LCA5L_ENST00000495240.1_5'UTR|WRB_ENST00000541890.1_Intron			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	380										breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				GGAACATCTGATTTTTGGGTT	0.368																																					p.S380P		Atlas-SNP	.											.	LCA5L	57	.	0			c.T1138C						.						232	223	226					21																	40782216		2203	4300	6503	SO:0001583	missense	150082	exon8			CATCTGATTTTTG	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 13"	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.1138T>C	chr21.hg19:g.40782216A>G	ENSP00000351008:p.Ser380Pro	135.0	0.0		100.0	4.0	NM_152505	D3DSI0|Q3ZCT0	Missense_Mutation	SNP	ENST00000358268.2	hg19	CCDS13665.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.624322	0.66901	.	.	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268	T;T;T	0.57436	0.4;0.4;0.4	4.97	3.66	0.41972	.	0.156285	0.40302	N	0.001139	T	0.62368	0.2422	M	0.63843	1.955	0.34886	D	0.745045	D	0.76494	0.999	D	0.64776	0.929	T	0.71328	-0.4626	10	0.56958	D	0.05	-12.843	6.9073	0.24315	0.7421:0.0:0.0:0.2579	.	380	O95447	LCA5L_HUMAN	P	380	ENSP00000288350:S380P;ENSP00000370046:S380P;ENSP00000351008:S380P	ENSP00000288350:S380P	S	-	1	0	LCA5L	39704086	0.995000	0.38212	0.998000	0.56505	0.958000	0.62258	2.318000	0.43779	1.997000	0.58415	0.533000	0.62120	TCA	.	.		0.368	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		G	40782216	A	G	40782216	3	3	65	1	0	0	0	0	1	0	0	0	8666	333	12	2	886	2	LCA5L	21	40782216	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	191721	40782216	7347679	392	8465										
UBASH3A	53347	hgsc.bcm.edu	37	chr21	43829672	43829672	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgccagtgtgcaaagaacagAgctcatgaggtcttcccaca	10	12	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr21:43829672A>G	ENST00000319294.6	+	3	340	c.309A>G	c.(307-309)agA>agG	p.R103R	UBASH3A_ENST00000450356.1_Silent_p.R103R|UBASH3A_ENST00000291535.6_Silent_p.R103R|UBASH3A_ENST00000398367.1_Silent_p.R103R	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	103					negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.R103R(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						CAAAGAACAGAGCTCATGAGG	0.537																																					p.R103R		Atlas-SNP	.											UBASH3A,NS,carcinoma,0,1	UBASH3A	72	.	1	Substitution - coding silent(1)	lung(1)	c.A309G						.						136	119	125					21																	43829672		2203	4300	6503	SO:0001819	synonymous_variant	53347	exon3			GAACAGAGCTCAT	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.309A>G	chr21.hg19:g.43829672A>G		77.0	0.0		41.0	2.0	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	hg19	CCDS13687.1																																																																																			.	.		0.537	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895		G	43829672	A	G	43829672	2	3	65	1	0	0	0	0	0	0	0	1	16854	301	11	2		2	UBASH3A	21	43829672	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3047456	43829672	4300223	393	8466										
MRPL40	64976	hgsc.bcm.edu	37	chr22	19422404	19422404	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ttattacccctctaaagttcTtggataaagcaaggtaagga	8	7	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr22:19422404T>C	ENST00000333130.3	+	3	936	c.283T>C	c.(283-285)Ttg>Ctg	p.L95L	HIRA_ENST00000541063.1_Intron|HIRA_ENST00000546308.1_Intron|MRPL40_ENST00000443660.1_3'UTR	NM_003776.2	NP_003767.2	Q9NQ50	RM40_HUMAN	mitochondrial ribosomal protein L40	95					anatomical structure morphogenesis (GO:0009653)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|upper_aerodigestive_tract(1)	2	Colorectal(54;0.0993)					TCTAAAGTTCTTGGATAAAGC	0.413																																					p.L95L		Atlas-SNP	.											.	MRPL40	13	.	0			c.T283C						.						74	79	78					22																	19422404		2203	4300	6503	SO:0001819	synonymous_variant	64976	exon3			AAGTTCTTGGATA	AB051624	CCDS13760.1	22q11.2	2012-09-13	2002-11-13		ENSG00000185608	ENSG00000185608		"Mitochondrial ribosomal proteins / large subunits"	14491	protein-coding gene	gene with protein product		605089	"nuclear localization signal deleted in velocardiofacial syndrome"	NLVCF		9790763, 11543634	Standard	NM_003776		Approved	MRP-L22	uc002zpg.3	Q9NQ50	OTTHUMG00000150136	ENST00000333130.3:c.283T>C	chr22.hg19:g.19422404T>C		62.0	0.0		54.0	4.0	NM_003776	B3KVZ7|O95134	Silent	SNP	ENST00000333130.3	hg19	CCDS13760.1																																																																																			.	.		0.413	MRPL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316491.2	NM_003776		C	19422404	T	C	19422404	2	2	65	1	0	0	0	0	0	0	0	1	9813	1606	56	2		2	MRPL40	22	19422404	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10		19422404	31882162	394	8467										
SGSM1	129049	hgsc.bcm.edu	37	chr22	25263061	25263061	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	accctccgtccgcttccagcGtctactgggactatgccatg	9	16	1	0	rs375323027		TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr22:25263061G>A	ENST00000400359.4	+	10	935	c.928G>A	c.(928-930)Gtc>Atc	p.V310I	SGSM1_ENST00000400358.4_Splice_Site_p.V310I	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	310	Required for interaction with RAP family members.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						CGCTTCCAGCGTCTACTGGGA	0.617																																					p.V310I		Atlas-SNP	.											.	SGSM1	150	.	0			c.G928A						.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4152		0,0,2076	39	43	42		928,928,928,928	3.2	1	22		42	1,8449		0,1,4224	no	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	29,29,29,29	0,1,6300	AA,AG,GG		0.0118,0.0,0.0079	probably-damaging,probably-damaging,probably-damaging,probably-damaging	310/1149,310/1094,310/1033,310/1088	25263061	1,12601	2076	4225	6301	SO:0001630	splice_region_variant	129049	exon10			TCCAGCGTCTACT	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"Small G protein signaling modulators"	29410	protein-coding gene	gene with protein product		611417	"RUN and TBC1 domain containing 2"	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.927-1G>A	chr22.hg19:g.25263061G>A		86.0	0.0		116.0	8.0	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	hg19	CCDS46674.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.999133	0.54147	0.0	1.18E-4	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.31769	1.48;1.48	4.19	3.17	0.36434	.	0.301547	0.35772	N	0.002981	T	0.31295	0.0792	N	0.25485	0.75	0.80722	D	1	D;D;P;D	0.67145	0.996;0.963;0.865;0.984	P;B;P;P	0.56514	0.8;0.435;0.488;0.557	T	0.01998	-1.1232	10	0.21540	T	0.41	-5.2056	11.3382	0.49516	0.0896:0.0:0.9104:0.0	.	310;426;443;310	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	I	426;310;310	ENSP00000383211:V310I;ENSP00000383212:V310I	ENSP00000383211:V310I	V	+	1	0	SGSM1	23593061	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.453000	0.80700	0.913000	0.36797	0.555000	0.69702	GTC	.	.		0.617	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	Missense_Mutation	A	25263061	G	A	25263061	5	1	65	1	0	0	0	0	0	0	1	0	14237	1159	40	1	966	1	SGSM1	22	25263061	Splice_Site	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	5840657	25263061	26041505	395	8468										
MYH9	4627	hgsc.bcm.edu	37	chr22	36696312	36696312	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccagctgctcctcaagctccTgccgggggccagagacacgg	13	16	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr22:36696312T>C	ENST00000216181.5	-	23	3069		c.e23-2			NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle						actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						CTCAAGCTCCTGCCGGGGGCC	0.617			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												.		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.2839-2A>G						.						47	48	47					22																	36696312		2203	4300	6503	SO:0001630	splice_region_variant	4627	exon24	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	AGCTCCTGCCGGG		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.2839-2A>G	chr22.hg19:g.36696312T>C		52.0	0.0		60.0	4.0	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Splice_Site	SNP	ENST00000216181.5	hg19	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.911790	0.72983	.	.	ENSG00000100345	ENST00000337818;ENST00000216181	.	.	.	5.16	5.16	0.70880	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2996	0.73936	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYH9	35026258	1.000000	0.71417	0.883000	0.34634	0.822000	0.46500	8.002000	0.88514	2.073000	0.62155	0.533000	0.62120	.	.	.		0.617	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	Intron	C	36696312	T	C	36696312	5	2	65	1	0	0	0	0	0	0	1	0	10051	1594	55	2	3121	2	MYH9	22	36696312	Splice_Site	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	11433251	36696312	14608254	396	8469										
SMC1B	27127	hgsc.bcm.edu	37	chr22	45802675	45802675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgctttgactattatgcctaTcttttccaactctgcaatgt	5	10	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chr22:45802675T>C	ENST00000357450.4	-	3	369	c.370A>G	c.(370-372)Ata>Gta	p.I124V	SMC1B_ENST00000404354.3_Missense_Mutation_p.I124V	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	124					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		ATTATGCCTATCTTTTCCAAC	0.299																																					p.I124V		Atlas-SNP	.											.	SMC1B	215	.	0			c.A370G						.						82	78	79					22																	45802675		1816	4068	5884	SO:0001583	missense	27127	exon3			TGCCTATCTTTTC	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.370A>G	chr22.hg19:g.45802675T>C	ENSP00000350036:p.Ile124Val	83.0	0.0		95.0	4.0	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	hg19	CCDS43027.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.183854	0.57800	.	.	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.10099	2.91;3.27	5.89	5.89	0.94794	.	0.000000	0.64402	D	0.000003	T	0.17619	0.0423	L	0.49126	1.545	0.53688	D	0.999973	P;P	0.36183	0.542;0.485	B;P	0.45794	0.279;0.493	T	0.06162	-1.0842	10	0.17369	T	0.5	.	15.4934	0.75629	0.0:0.0:0.0:1.0	.	124;124	Q8NDV3-2;Q8NDV3-3	.;.	V	124	ENSP00000350036:I124V;ENSP00000385902:I124V	ENSP00000350036:I124V	I	-	1	0	SMC1B	44181339	0.877000	0.30153	1.000000	0.80357	0.973000	0.67179	0.618000	0.24373	2.254000	0.74563	0.459000	0.35465	ATA	.	.		0.299	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		C	45802675	T	C	45802675	3	2	65	1	0	0	0	0	1	0	0	0	14797	1435	50	2	3429	2	SMC1B	22	45802675	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	9106363	45802675	5501891	397	8470										
STS	412	hgsc.bcm.edu	37	chrX	7177588	7177588	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cgtcggggtcaccctccttaCccttgctgcactcaattgtc	8	16	2	0			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:7177588C>T	ENST00000217961.4	+	5	816	c.596C>T	c.(595-597)aCc>aTc	p.T199I		NM_000351.4	NP_000342.2	P08842	STS_HUMAN	steroid sulfatase (microsomal), isozyme S	199					cellular protein metabolic process (GO:0044267)|epidermis development (GO:0008544)|female pregnancy (GO:0007565)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|steroid catabolic process (GO:0006706)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|steryl-sulfatase activity (GO:0004773)|sulfuric ester hydrolase activity (GO:0008484)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(1)	27		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Norelgestromin(DB06713)	ACCCTCCTTACCCTTGCTGCA	0.567									Ichthyosis																												p.T199I		Atlas-SNP	.											.	STS	64	.	0			c.C596T						.						104	71	82					X																	7177588		2203	4299	6502	SO:0001583	missense	412	exon5	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCCTTACCCTTGC	M16505	CCDS14127.1	Xp22.32	2013-06-10	2007-07-19		ENSG00000101846	ENSG00000101846	3.1.6.2	"Arylsulfatase family"	11425	protein-coding gene	gene with protein product	"arylsulfatase C"	300747	"steroid sulfatase (microsomal), arylsulfatase C, isozyme S"	ARSC1			Standard	NM_000351		Approved	ARSC	uc004cry.4	P08842	OTTHUMG00000021102	ENST00000217961.4:c.596C>T	chrX.hg19:g.7177588C>T	ENSP00000217961:p.Thr199Ile	101.0	0.0		99.0	4.0	NM_000351	B2RA47	Missense_Mutation	SNP	ENST00000217961.4	hg19	CCDS14127.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.933832	0.52866	.	.	ENSG00000101846	ENST00000217961	D	0.93859	-3.3	3.96	3.09	0.35607	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.357664	0.27846	N	0.017615	D	0.96349	0.8809	M	0.88775	2.98	0.09310	N	1	D	0.63880	0.993	D	0.67548	0.952	D	0.90790	0.4686	10	0.72032	D	0.01	.	9.99	0.41865	0.0:0.8947:0.0:0.1053	.	199	P08842	STS_HUMAN	I	199	ENSP00000217961:T199I	ENSP00000217961:T199I	T	+	2	0	STS	7187588	0.915000	0.31059	0.002000	0.10522	0.004000	0.04260	6.507000	0.73717	0.528000	0.28580	0.544000	0.68410	ACC	.	.		0.567	STS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055686.1	NM_000351		T	7177588	C	T	7177588	3	4	65	1	0	0	0	0	1	0	0	0	15347	507	18	3	614	3	STS	23	7177588	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10		7177588	148092972	398	8471										
FANCB	2187	hgsc.bcm.edu	37	chrX	14868753	14868753	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	acttttcatctaagatatggAcagaattttcttcttcacca	4	9	5	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:14868753A>G	ENST00000324138.3	-	6	1523	c.1370T>C	c.(1369-1371)gTc>gCc	p.V457A	FANCB_ENST00000398334.1_Missense_Mutation_p.V457A	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	457					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					TAAGATATGGACAGAATTTTC	0.318								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.V457A		Atlas-SNP	.											.	FANCB	78	.	0			c.T1370C						.						93	75	81					X																	14868753		2203	4300	6503	SO:0001583	missense	2187	exon6	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ATATGGACAGAAT	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"Fanconi anemia, complementation groups"	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.1370T>C	chrX.hg19:g.14868753A>G	ENSP00000326819:p.Val457Ala	70.0	0.0		81.0	4.0	NM_152633	B2RMZ4|Q7Z2U2|Q86XG1	Missense_Mutation	SNP	ENST00000324138.3	hg19	CCDS14161.1	.	.	.	.	.	.	.	.	.	.	a	8.024	0.760374	0.15914	.	.	ENSG00000181544	ENST00000324138;ENST00000398334;ENST00000452869	.	.	.	5.85	-1.27	0.09347	.	0.780233	0.12465	N	0.466481	T	0.37019	0.0988	L	0.56769	1.78	0.09310	N	1	B	0.14438	0.01	B	0.14578	0.011	T	0.27971	-1.0058	9	0.25751	T	0.34	0.0345	6.1971	0.20555	0.4505:0.0:0.4208:0.1286	.	457	Q8NB91	FANCB_HUMAN	A	457	.	ENSP00000326819:V457A	V	-	2	0	FANCB	14778674	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.235000	0.17948	-0.218000	0.10018	0.433000	0.28618	GTC	.	.		0.318	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633		G	14868753	A	G	14868753	3	3	65	1	0	0	0	0	1	0	0	0	5671	275	10	2	1225	2	FANCB	23	14868753	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	7691165	14868753	140401807	399	8472										
CA5B	11238	hgsc.bcm.edu	37	chrX	15768152	15768152	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gatttcaagctaaagatggtGgtgatgaacagcctgagggt	14	5	1	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:15768152G>A	ENST00000318636.3	+	2	142	c.6G>A	c.(4-6)gtG>gtA	p.V2V	CA5B_ENST00000380313.1_3'UTR|CA5B_ENST00000454127.2_Silent_p.V2V	NM_007220.3	NP_009151.1	Q8WTZ4	CA5BL_HUMAN	carbonic anhydrase VB, mitochondrial	0						mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)|prostate(1)|stomach(2)	9	Hepatocellular(33;0.183)					TAAAGATGGTGGTGATGAACA	0.483																																					p.V2V		Atlas-SNP	.											.	CA5B	23	.	0			c.G6A						.						118	111	113					X																	15768152		2203	4300	6503	SO:0001819	synonymous_variant	11238	exon2			GATGGTGGTGATG	AB021660	CCDS14171.1	Xp22.1	2008-08-13			ENSG00000169239	ENSG00000169239		"Carbonic anhydrases"	1378	protein-coding gene	gene with protein product		300230				10409679	Standard	XM_005274442		Approved		uc004cxe.3	Q9Y2D0	OTTHUMG00000021183	ENST00000318636.3:c.6G>A	chrX.hg19:g.15768152G>A		65.0	0.0		85.0	4.0	NM_007220	A6NEZ4	Silent	SNP	ENST00000318636.3	hg19	CCDS14171.1																																																																																			.	.		0.483	CA5B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354933.1	NM_007220		A	15768152	G	A	15768152	2	1	65	1	0	0	0	0	0	0	0	1	2522	1335	47	3		3	CA5B	23	15768152	Silent	SNP	G	TCGA-CC-A3MB-01A-11D-A20W-10	899399	15768152	139502408	400	8473										
PDHA1	5160	hgsc.bcm.edu	37	chrX	19368150	19368150	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tacaggatgatgcagactgtAcgccgaatggagttgaaagc	13	7	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:19368150A>G	ENST00000422285.2	+	3	318	c.213A>G	c.(211-213)gtA>gtG	p.V71V	PDHA1_ENST00000545074.1_Silent_p.V71V|PDHA1_ENST00000540249.1_Silent_p.V71V|PDHA1_ENST00000379805.3_Silent_p.V71V|PDHA1_ENST00000379806.5_Silent_p.V109V			P08559	ODPA_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 1	71					acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)	18	Hepatocellular(33;0.183)					TGCAGACTGTACGCCGAATGG	0.483																																					p.V109V		Atlas-SNP	.											.	PDHA1	85	.	0			c.A327G						.						245	192	210					X																	19368150		2203	4300	6503	SO:0001819	synonymous_variant	5160	exon4			GACTGTACGCCGA		CCDS14192.1, CCDS55380.1, CCDS55381.1, CCDS55382.1	Xp22.1	2008-02-05			ENSG00000131828	ENSG00000131828	1.2.4.1		8806	protein-coding gene	gene with protein product		300502		PDHA			Standard	NM_001173454		Approved		uc004czh.4	P08559	OTTHUMG00000021224	ENST00000422285.2:c.213A>G	chrX.hg19:g.19368150A>G		114.0	0.0		114.0	5.0	NM_001173454	A5YVE9|B2R5P7|B7Z3T7|B7Z3X5|Q53H41|Q5JPT8|Q9NP12|Q9UBJ8|Q9UBU0|Q9UNG4|Q9UNG5	Silent	SNP	ENST00000422285.2	hg19	CCDS14192.1																																																																																			.	.		0.483	PDHA1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055977.1			G	19368150	A	G	19368150	2	3	65	1	0	0	0	0	0	0	0	1	11673	378	14	2		2	PDHA1	23	19368150	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	3599998	19368150	135902410	401	8474										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23411680	23411680	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	caaggtgaagttcatcgtctTcaatccgtcctttgtataca	7	10	3	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:23411680T>C	ENST00000379361.4	+	3	2905	c.2045T>C	c.(2044-2046)tTc>tCc	p.F682S		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	682					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						TTCATCGTCTTCAATCCGTCC	0.493																																					p.F682S		Atlas-SNP	.											.	PTCHD1	213	.	0			c.T2045C						.						91	82	85					X																	23411680		2203	4300	6503	SO:0001583	missense	139411	exon3			TCGTCTTCAATCC	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.2045T>C	chrX.hg19:g.23411680T>C	ENSP00000368666:p.Phe682Ser	90.0	0.0		80.0	4.0	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	hg19	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	T	17.03	3.283986	0.59867	.	.	ENSG00000165186	ENST00000379361	D	0.91011	-2.77	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.93667	0.7977	L	0.57536	1.79	0.58432	D	0.999998	D	0.60160	0.987	D	0.67725	0.953	D	0.94194	0.7444	10	0.72032	D	0.01	.	14.3778	0.66889	0.0:0.0:0.0:1.0	.	682	Q96NR3	PTHD1_HUMAN	S	682	ENSP00000368666:F682S	ENSP00000368666:F682S	F	+	2	0	PTCHD1	23321601	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	7.694000	0.84235	1.775000	0.52247	0.430000	0.28490	TTC	.	.		0.493	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		C	23411680	T	C	23411680	3	2	65	1	0	0	0	0	1	0	0	0	12744	1783	62	2	2055	2	PTCHD1	23	23411680	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	4043530	23411680	131858880	402	8475										
SYTL5	94122	hgsc.bcm.edu	37	chrX	37913595	37913595	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	cggggagacccttgtcaggcTtgctcactgagggtatgcag	15	10	2	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:37913595T>C	ENST00000357972.5	+	3	795	c.249T>C	c.(247-249)gcT>gcC	p.A83A	SYTL5_ENST00000297875.2_Silent_p.A83A|SYTL5_ENST00000456733.2_Silent_p.A83A|TM4SF2_ENST00000465127.1_Intron			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	83	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						CTTGTCAGGCTTGCTCACTGA	0.507																																					p.A83A		Atlas-SNP	.											.	SYTL5	72	.	0			c.T249C						.						94	81	85					X																	37913595		2202	4300	6502	SO:0001819	synonymous_variant	94122	exon2			TCAGGCTTGCTCA		CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"exophilin 9"						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.249T>C	chrX.hg19:g.37913595T>C		45.0	0.0		67.0	4.0	NM_001163334	A2RRF2	Silent	SNP	ENST00000357972.5	hg19	CCDS14244.1																																																																																			.	.		0.507	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780		C	37913595	T	C	37913595	2	2	65	1	0	0	0	0	0	0	0	1	15501	1596	56	2		2	SYTL5	23	37913595	Silent	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	14501915	37913595	117356965	403	8476										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50351123	50351123	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	tgacaagtccagtgctgggtTctcaaggcaaggatggaaag	14	7	1	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:50351123T>C	ENST00000289292.7	-	6	3302	c.3019A>G	c.(3019-3021)Aac>Gac	p.N1007D	SHROOM4_ENST00000460112.3_Missense_Mutation_p.N891D|SHROOM4_ENST00000376020.2_Missense_Mutation_p.N1007D			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1007					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					AGTGCTGGGTTCTCAAGGCAA	0.433																																					p.N1007D		Atlas-SNP	.											.	SHROOM4	171	.	0			c.A3019G						.						51	48	49					X																	50351123		2203	4300	6503	SO:0001583	missense	57477	exon6			CTGGGTTCTCAAG	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3019A>G	chrX.hg19:g.50351123T>C	ENSP00000289292:p.Asn1007Asp	102.0	0.0		99.0	5.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.991725	0.54041	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.19250	2.58;2.58;2.16	5.51	5.51	0.81932	.	0.217639	0.36815	N	0.002395	T	0.34629	0.0904	L	0.34521	1.04	0.39593	D	0.969615	D	0.76494	0.999	D	0.78314	0.991	T	0.19877	-1.0292	10	0.87932	D	0	.	12.4646	0.55751	0.0:0.0:0.0:1.0	.	1007	Q9ULL8	SHRM4_HUMAN	D	1007;1007;891	ENSP00000289292:N1007D;ENSP00000365188:N1007D;ENSP00000421450:N891D	ENSP00000289292:N1007D	N	-	1	0	SHROOM4	50367863	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	4.916000	0.63362	1.849000	0.53698	0.486000	0.48141	AAC	.	.		0.433	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		C	50351123	T	C	50351123	3	2	65	1	0	0	0	0	1	0	0	0	14311	1783	62	2	1478	2	SHROOM4	23	50351123	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	12437528	50351123	104919437	404	8477										
TSPYL2	64061	hgsc.bcm.edu	37	chrX	53115034	53115034	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gaatcctgaccacaatgaggTccccaacaacgagaccactg	8	14	0	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:53115034T>C	ENST00000375442.4	+	6	1592	c.1460T>C	c.(1459-1461)gTc>gCc	p.V487A		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	487	Asn-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						CACAATGAGGTCCCcaacaac	0.478																																					p.V487A		Atlas-SNP	.											.	TSPYL2	53	.	0			c.T1460C						.						229	170	190					X																	53115034		2203	4300	6503	SO:0001583	missense	64061	exon6			ATGAGGTCCCCAA	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.1460T>C	chrX.hg19:g.53115034T>C	ENSP00000364591:p.Val487Ala	87.0	0.0		101.0	5.0	NM_022117	O94799|Q96DG7|Q9BZW6	Missense_Mutation	SNP	ENST00000375442.4	hg19	CCDS14350.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.160611	0.00321	.	.	ENSG00000184205	ENST00000375442	T	0.19669	2.13	2.63	-5.25	0.02781	.	1.286020	0.05786	U	0.609421	T	0.07908	0.0198	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28267	-1.0049	10	0.13470	T	0.59	-3.1879	3.6647	0.08252	0.2125:0.5025:0.1553:0.1297	.	127;487	Q59GC7;Q9H2G4	.;TSYL2_HUMAN	A	487	ENSP00000364591:V487A	ENSP00000364591:V487A	V	+	2	0	TSPYL2	53131759	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.511000	0.02260	-2.595000	0.00454	-0.832000	0.03076	GTC	.	.		0.478	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		C	53115034	T	C	53115034	3	2	65	1	0	0	0	0	1	0	0	0	16675	1667	58	2	1482	2	TSPYL2	23	53115034	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	2763911	53115034	102155526	405	8478										
RPS6KA6	27330	hgsc.bcm.edu	37	chrX	83389804	83389804	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	gcatacctgttaatttgataTgtcctatttcatcaagcaaa	5	8	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:83389804T>C	ENST00000262752.2	-	8	639	c.632A>G	c.(631-633)cAt>cGt	p.H211R	RPS6KA6_ENST00000543399.1_Missense_Mutation_p.H211R	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	211	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						TAATTTGATATGTCCTATTTC	0.229																																					p.H211R		Atlas-SNP	.											.	RPS6KA6	116	.	0			c.A632G						.						33	33	33					X																	83389804		2177	4237	6414	SO:0001583	missense	27330	exon8			TTGATATGTCCTA	AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.632A>G	chrX.hg19:g.83389804T>C	ENSP00000262752:p.His211Arg	58.0	0.0		52.0	4.0	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	hg19	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.507262	0.64410	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.64618	-0.11;-0.11	4.4	4.4	0.53042	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.052055	0.85682	D	0.000000	T	0.62672	0.2447	L	0.52011	1.625	0.80722	D	1	P;P	0.38827	0.649;0.649	P;P	0.44422	0.449;0.449	T	0.67043	-0.5770	10	0.87932	D	0	.	13.0112	0.58731	0.0:0.0:0.0:1.0	.	211;211	B7ZL90;Q9UK32	.;KS6A6_HUMAN	R	211	ENSP00000262752:H211R;ENSP00000440830:H211R	ENSP00000262752:H211R	H	-	2	0	RPS6KA6	83276460	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.331000	0.79192	1.437000	0.47472	0.425000	0.28330	CAT	.	.		0.229	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		C	83389804	T	C	83389804	3	2	65	1	0	0	0	0	1	0	0	0	13670	1464	51	2	1665	2	RPS6KA6	23	83389804	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	30274770	83389804	71880756	406	8479										
GPRASP2	114928	hgsc.bcm.edu	37	chrX	101970641	101970641	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	aagcctatgttgattcctggTctggatctgaggatgaggcc	13	8	2	3			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:101970641T>C	ENST00000535209.1	+	4	1675	c.844T>C	c.(844-846)Tct>Cct	p.S282P	GPRASP2_ENST00000332262.5_Missense_Mutation_p.S282P|GPRASP2_ENST00000543253.1_Missense_Mutation_p.S282P			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	282						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						TGATTCCTGGTCTGGATCTGA	0.512																																					p.S282P		Atlas-SNP	.											.	GPRASP2	89	.	0			c.T844C						.						111	110	110					X																	101970641		2203	4300	6503	SO:0001583	missense	114928	exon4			TCCTGGTCTGGAT	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"Armadillo repeat containing"	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.844T>C	chrX.hg19:g.101970641T>C	ENSP00000437394:p.Ser282Pro	95.0	0.0		100.0	4.0	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	hg19	CCDS14501.1	.	.	.	.	.	.	.	.	.	.	T	7.665	0.685835	0.14973	.	.	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.19105	2.17;2.17;2.17	4.1	4.1	0.47936	.	0.000000	0.45867	D	0.000323	T	0.20981	0.0505	L	0.52126	1.63	0.35730	D	0.817837	P	0.43094	0.799	P	0.46172	0.506	T	0.16247	-1.0409	10	0.25106	T	0.35	-15.3059	5.3771	0.16172	0.0:0.1241:0.0:0.8759	.	282	Q96D09	GASP2_HUMAN	P	282	ENSP00000437872:S282P;ENSP00000437394:S282P;ENSP00000339057:S282P	ENSP00000339057:S282P	S	+	1	0	GPRASP2	101857297	0.998000	0.40836	0.983000	0.44433	0.024000	0.10985	0.290000	0.18975	1.830000	0.53286	0.486000	0.48141	TCT	.	.		0.512	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		C	101970641	T	C	101970641	3	2	65	1	0	0	0	0	1	0	0	0	6732	1667	58	2	846	2	GPRASP2	23	101970641	Missense_Mutation	SNP	T	TCGA-CC-A3MB-01A-11D-A20W-10	18580837	101970641	53299919	407	8480										
TMEM164	84187	hgsc.bcm.edu	37	chrX	109247199	109247199	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	catcctgaggcagacgaaggAggacggtaggggtagccctg	17	9	0	2			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:109247199A>G	ENST00000372073.1	+	2	533	c.197A>G	c.(196-198)gAg>gGg	p.E66G	TMEM164_ENST00000288381.4_Missense_Mutation_p.E66G|TMEM164_ENST00000372068.2_Missense_Mutation_p.E66G|TMEM164_ENST00000372072.3_Intron			Q5U3C3	TM164_HUMAN	transmembrane protein 164	66						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|skin(1)	14						CAGACGAAGGAGGACGGTAGG	0.627																																					p.E66G		Atlas-SNP	.											.	TMEM164	59	.	0			c.A197G						.						64	60	61					X																	109247199		2203	4300	6503	SO:0001583	missense	84187	exon2			CGAAGGAGGACGG	AK094127	CCDS14550.2, CCDS55475.1	Xq22.3	2008-02-05			ENSG00000157600	ENSG00000157600			26217	protein-coding gene	gene with protein product						12477932	Standard	NM_032227		Approved	FLJ22679, RP13-360B22.2	uc004eom.3	Q5U3C3	OTTHUMG00000022192	ENST00000372073.1:c.197A>G	chrX.hg19:g.109247199A>G	ENSP00000361143:p.Glu66Gly	114.0	0.0		120.0	5.0	NM_032227	B3KSQ8|F5H2P2	Missense_Mutation	SNP	ENST00000372073.1	hg19	CCDS14550.2	.	.	.	.	.	.	.	.	.	.	a	8.567	0.879169	0.17395	.	.	ENSG00000157600	ENST00000372073;ENST00000372068;ENST00000288381;ENST00000501872	T;T;T	0.48201	0.85;0.85;0.82	4.32	4.32	0.51571	.	0.617074	0.16464	N	0.213279	T	0.30572	0.0769	L	0.29908	0.895	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.14727	-1.0462	10	0.26408	T	0.33	-6.4129	4.3317	0.11066	0.5128:0.16:0.0:0.3272	.	66;66	Q9H617;Q5U3C3	.;TM164_HUMAN	G	66	ENSP00000361143:E66G;ENSP00000361138:E66G;ENSP00000288381:E66G	ENSP00000288381:E66G	E	+	2	0	TMEM164	109133855	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.061000	0.64319	1.591000	0.50007	0.414000	0.27820	GAG	.	.		0.627	TMEM164-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057898.1	NM_032227		G	109247199	A	G	109247199	3	3	65	1	0	0	0	0	1	0	0	0	16094	304	11	2	199	2	TMEM164	23	109247199	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	7276558	109247199	46023361	408	8481										
PAK3	5063	hgsc.bcm.edu	37	chrX	110439078	110439078	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ctgatttaatagtgcctgcaAgctttggatttcctgcactc	8	10	0	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:110439078A>T	ENST00000372010.1	+	16	1606	c.1164A>T	c.(1162-1164)caA>caT	p.Q388H	PAK3_ENST00000262836.4_Missense_Mutation_p.Q388H|PAK3_ENST00000417227.1_Missense_Mutation_p.Q394H|PAK3_ENST00000425146.1_Missense_Mutation_p.Q373H|PAK3_ENST00000360648.4_Missense_Mutation_p.Q409H|PAK3_ENST00000372007.5_Missense_Mutation_p.Q373H|PAK3_ENST00000446737.1_Missense_Mutation_p.Q373H|PAK3_ENST00000519681.1_Missense_Mutation_p.Q394H|PAK3_ENST00000518291.1_Missense_Mutation_p.Q409H			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	388	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						AGTGCCTGCAAGCTTTGGATT	0.318										TSP Lung(19;0.15)																											p.Q409H		Atlas-SNP	.											.	PAK3	179	.	0			c.A1227T						.						106	103	104					X																	110439078		2203	4300	6503	SO:0001583	missense	5063	exon13			CCTGCAAGCTTTG	AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.1164A>T	chrX.hg19:g.110439078A>T	ENSP00000361080:p.Gln388His	46.0	0.0		58.0	49.0	NM_001128168	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Missense_Mutation	SNP	ENST00000372010.1	hg19	CCDS48153.1	.	.	.	.	.	.	.	.	.	.	A	17.78	3.472376	0.63737	.	.	ENSG00000077264	ENST00000446737;ENST00000425146;ENST00000372010;ENST00000519681;ENST00000372007;ENST00000518291;ENST00000360648;ENST00000417227;ENST00000262836	T;T;T;T;T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22	5.15	3.96	0.45880	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.69433	0.3110	L	0.35723	1.085	0.80722	D	1	D;P;D;P;D	0.58268	0.978;0.901;0.982;0.901;0.982	P;P;P;P;P	0.62491	0.843;0.56;0.903;0.69;0.903	T	0.70332	-0.4901	10	0.51188	T	0.08	.	10.6458	0.45619	0.9195:0.0:0.0805:0.0	.	394;409;388;373;388	O75914-4;O75914-3;O75914;O75914-2;B1GX77	.;.;PAK3_HUMAN;.;.	H	373;373;388;394;373;409;409;394;388	ENSP00000410853:Q373H;ENSP00000401982:Q373H;ENSP00000361080:Q388H;ENSP00000429113:Q394H;ENSP00000361077:Q373H;ENSP00000428921:Q409H;ENSP00000353864:Q409H;ENSP00000389172:Q394H;ENSP00000262836:Q388H	ENSP00000262836:Q388H	Q	+	3	2	PAK3	110325734	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.052000	0.57420	1.823000	0.53134	0.486000	0.48141	CAA	.	.		0.318	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		T	110439078	A	T	110439078	3	4	65	1	0	0	0	0	1	0	0	0	11411	69	3	4	1277	4	PAK3	23	110439078	Missense_Mutation	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	1191879	110439078	44831482	409	8482										
GRIA3	2892	hgsc.bcm.edu	37	chrX	122551504	122551504	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccttatgaatggcacttggaAgacaacaatgaagaacctcg	9	9	0	4			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:122551504A>G	ENST00000371251.1	+	11	1804	c.1752A>G	c.(1750-1752)gaA>gaG	p.E584E	GRIA3_ENST00000541091.1_Silent_p.E568E|GRIA3_ENST00000264357.5_Silent_p.E584E|GRIA3_ENST00000542149.1_Silent_p.E584E|GRIA3_ENST00000371256.5_Silent_p.E584E			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	584					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	GGCACTTGGAAGACAACAATG	0.423																																					p.E584E		Atlas-SNP	.											.	GRIA3	386	.	0			c.A1752G						.						256	230	239					X																	122551504		2203	4300	6503	SO:0001819	synonymous_variant	2892	exon11			CTTGGAAGACAAC	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.1752A>G	chrX.hg19:g.122551504A>G		103.0	0.0		97.0	4.0	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Silent	SNP	ENST00000371251.1	hg19	CCDS14604.1																																																																																			.	.		0.423	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		G	122551504	A	G	122551504	2	3	65	1	0	0	0	0	0	0	0	1	6778	69	3	2		2	GRIA3	23	122551504	Silent	SNP	A	TCGA-CC-A3MB-01A-11D-A20W-10	12112426	122551504	32719056	410	8483										
ARHGAP36	158763	hgsc.bcm.edu	37	chrX	130222734	130222734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0194647201946472	8	1	0.718342151675485	0.897927689594356	0.673445767195767	0.169802333889021	0.751940625889747	0	ccgggagaaggaggccaaaaCtggcgtcagctacttctttc	12	11	2	1			TCGA-CC-A3MB-01A-11D-A20W-10	TCGA-CC-A3MB-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b81ffdd9-b1d2-409e-abbb-27eb123acb69	73e746f4-36ea-4aec-8af3-a825b5917e67	g.chrX:130222734C>T	ENST00000276211.5	+	12	1964	c.1619C>T	c.(1618-1620)aCt>aTt	p.T540I	ARHGAP36_ENST00000370921.1_Missense_Mutation_p.T404I|ARHGAP36_ENST00000370922.1_Missense_Mutation_p.T528I	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	540					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						GAGGCCAAAACTGGCGTCAGC	0.542																																					p.T540I		Atlas-SNP	.											.	ARHGAP36	171	.	0			c.C1619T						.						85	79	81					X																	130222734		2203	4300	6503	SO:0001583	missense	158763	exon12			CCAAAACTGGCGT		CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"Rho GTPase activating proteins"	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.1619C>T	chrX.hg19:g.130222734C>T	ENSP00000276211:p.Thr540Ile	79.0	0.0		88.0	4.0	NM_144967	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Missense_Mutation	SNP	ENST00000276211.5	hg19	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	C	10.16	1.273071	0.23221	.	.	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000412432;ENST00000370921	T;T;T;T	0.11604	2.76;2.78;2.78;2.77	4.31	3.43	0.39272	.	0.489143	0.17402	N	0.175495	T	0.05823	0.0152	N	0.08118	0	0.26772	N	0.969788	P;P;P	0.40431	0.717;0.717;0.594	B;B;B	0.40066	0.318;0.318;0.169	T	0.24225	-1.0166	10	0.40728	T	0.16	.	7.499	0.27507	0.0:0.8806:0.0:0.1194	.	509;528;540	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	I	540;528;509;404	ENSP00000276211:T540I;ENSP00000359960:T528I;ENSP00000408515:T509I;ENSP00000359959:T404I	ENSP00000276211:T540I	T	+	2	0	ARHGAP36	130050415	1.000000	0.71417	0.994000	0.49952	0.611000	0.37282	1.699000	0.37804	1.133000	0.42147	0.600000	0.82982	ACT	.	.		0.542	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967		T	130222734	C	T	130222734	3	4	65	1	0	0	0	0	1	0	0	0	883	565	20	3	1661	3	ARHGAP36	23	130222734	Missense_Mutation	SNP	C	TCGA-CC-A3MB-01A-11D-A20W-10	7671230	130222734	25047826	411	8484										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7797423	7797423	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gaaggctgcctttgggaattGccaggtcacggggtcatgtg	16	8	2	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:7797423G>A	ENST00000303635.7	+	15	3658	c.3451G>A	c.(3451-3453)Gcc>Acc	p.A1151T	CAMTA1_ENST00000439411.2_Missense_Mutation_p.A1151T	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TTTGGGAATTGCCAGGTCACG	0.582			T	WWTR1	epitheliod hemangioendothelioma																																p.A1151T		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.G3451A						.						97	99	98					1																	7797423		2203	4300	6503	SO:0001583	missense	23261	exon15			GGAATTGCCAGGT	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3451G>A	chr1.hg19:g.7797423G>A	ENSP00000306522:p.Ala1151Thr	61.0	0.0		60.0	25.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	hg19	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	G	33	5.236368	0.95240	.	.	ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646	T;T	0.56103	0.48;0.48	5.91	5.91	0.95273	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.79713	0.4493	M	0.90425	3.115	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;D	0.91635	0.999;0.996;0.998;0.992	T	0.82680	-0.0337	10	0.87932	D	0	-24.0447	20.2985	0.98592	0.0:0.0:1.0:0.0	.	1151;238;107;1151	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1	.;.;.;CMTA1_HUMAN	T	1151;1151;238;107	ENSP00000306522:A1151T;ENSP00000402561:A1151T	ENSP00000306522:A1151T	A	+	1	0	CAMTA1	7720010	1.000000	0.71417	0.989000	0.46669	0.990000	0.78478	9.807000	0.99171	2.793000	0.96121	0.655000	0.94253	GCC	.	.		0.582	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		A	7797423	G	A	7797423	3	1	66	1	0	0	0	0	1	0	0	0	2615	1319	46	3	3509	3	CAMTA1	1	7797423	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10		7797423	241453198	1	8485										
SPEN	23013	hgsc.bcm.edu	37	chr1	16259330	16259330	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	cagatgcaccagagggccttGccccagaggacagggacaag	14	12	0	3	rs550359408		TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:16259330G>T	ENST00000375759.3	+	11	6799	c.6595G>T	c.(6595-6597)Gcc>Tcc	p.A2199S		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2199	Interaction with MSX2. {ECO:0000250}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		AGAGGGCCTTGCCCCAGAGGA	0.582													G|||	1	0.000199681	0	0	5008	,	,		18040	0.001		0	False		,,,				2504	0				p.A2199S		Atlas-SNP	.											.	SPEN	374	.	0			c.G6595T						.						54	54	54					1																	16259330		2203	4300	6503	SO:0001583	missense	23013	exon11			GGCCTTGCCCCAG		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.6595G>T	chr1.hg19:g.16259330G>T	ENSP00000364912:p.Ala2199Ser	96.0	0.0		86.0	28.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	2.623	-0.288185	0.05605	.	.	ENSG00000065526	ENST00000375759	T	0.08807	3.05	5.05	-0.175	0.13315	.	.	.	.	.	T	0.02342	0.0072	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47156	-0.9139	9	0.07325	T	0.83	-1.2267	5.6873	0.17811	0.0834:0.1089:0.5737:0.234	.	2199	Q96T58	MINT_HUMAN	S	2199	ENSP00000364912:A2199S	ENSP00000364912:A2199S	A	+	1	0	SPEN	16131917	0.000000	0.05858	0.002000	0.10522	0.257000	0.26127	-0.343000	0.07791	0.047000	0.15862	0.462000	0.41574	GCC	.	.		0.582	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16259330	G	T	16259330	3	4	66	1	0	0	0	0	1	0	0	0	15053	1319	46	3	6637	3	SPEN	1	16259330	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	8461907	16259330	232991291	2	8486										
ALG6	29929	hgsc.bcm.edu	37	chr1	63876884	63876884	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tatcttgtgactgcgacctcCtagggtcactggcattttgc	10	11	2	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:63876884C>A	ENST00000371108.4	+	8	867	c.562C>A	c.(562-564)Cta>Ata	p.L188I	ALG6_ENST00000263440.4_Missense_Mutation_p.L190I	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	188					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosyltransferase activity (GO:0046527)			endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CTGCGACCTCCTAGGGTCACT	0.368																																					p.L188I		Atlas-SNP	.											.	ALG6	33	.	0			c.C562A						.						205	203	204					1																	63876884		2203	4300	6503	SO:0001583	missense	29929	exon8			GACCTCCTAGGGT	AF063604	CCDS30735.1	1p31.3	2013-03-01	2013-03-01		ENSG00000088035	ENSG00000088035	2.4.1.267		23157	protein-coding gene	gene with protein product	"dolichyl-P-Glc:Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"	604566	"asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase)", "asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"			10359825, 11875054	Standard	NM_013339		Approved		uc021oof.1	Q9Y672	OTTHUMG00000009140	ENST00000371108.4:c.562C>A	chr1.hg19:g.63876884C>A	ENSP00000360149:p.Leu188Ile	191.0	0.0		173.0	10.0	NM_013339	B3KMU2|Q5SXR9|Q9H3I0	Missense_Mutation	SNP	ENST00000371108.4	hg19	CCDS30735.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.166270	0.38217	.	.	ENSG00000088035	ENST00000371108;ENST00000263440	D;D	0.83992	-1.79;-1.79	5.46	4.54	0.55810	.	0.066389	0.64402	D	0.000008	T	0.71500	0.3347	L	0.46819	1.47	0.46586	D	0.999112	B	0.19935	0.04	B	0.35278	0.199	T	0.70400	-0.4882	10	0.37606	T	0.19	-4.4893	11.573	0.50845	0.0:0.8556:0.0:0.1444	.	190	A2A2G4	.	I	188;190	ENSP00000360149:L188I;ENSP00000263440:L190I	ENSP00000263440:L190I	L	+	1	2	ALG6	63649472	0.258000	0.24033	0.998000	0.56505	0.772000	0.43724	0.444000	0.21661	1.446000	0.47643	0.591000	0.81541	CTA	.	.		0.368	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339		A	63876884	C	A	63876884	3	1	66	1	0	0	0	0	1	0	0	0	522	680	24	3	588	3	ALG6	1	63876884	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	47617554	63876884	185373737	3	8487										
LRRIQ3	127255	hgsc.bcm.edu	37	chr1	74649130	74649130	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tattgcttacctgatttccaTggagatcaagtttgattaat	7	6	1	3	rs552021191		TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:74649130T>G	ENST00000395089.1	-	1	238	c.239A>C	c.(238-240)cAt>cCt	p.H80P	LRRIQ3_ENST00000370909.2_Missense_Mutation_p.H80P|LRRIQ3_ENST00000354431.4_Missense_Mutation_p.H80P|LRRIQ3_ENST00000370911.3_Missense_Mutation_p.H80P			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	80										NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						CTGATTTCCATGGAGATCAAG	0.303																																					p.H80P		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.A239C						.						62	67	66					1																	74649130		2199	4294	6493	SO:0001583	missense	127255	exon2			TTTCCATGGAGAT	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.239A>C	chr1.hg19:g.74649130T>G	ENSP00000378524:p.His80Pro	168.0	0.0		144.0	36.0	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	hg19	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	T	18.47	3.630914	0.67015	.	.	ENSG00000162620	ENST00000395089;ENST00000354431;ENST00000370909;ENST00000388972;ENST00000370911	T;T;T;T	0.33216	1.9;1.9;1.42;1.9	5.27	5.27	0.74061	.	0.190840	0.35013	N	0.003510	T	0.44498	0.1296	M	0.73598	2.24	0.38529	D	0.948936	D	0.60575	0.988	P	0.62813	0.907	T	0.51537	-0.8693	10	0.72032	D	0.01	.	14.4564	0.67418	0.0:0.0:0.0:1.0	.	80	A6PVS8	LRIQ3_HUMAN	P	80	ENSP00000378524:H80P;ENSP00000346414:H80P;ENSP00000359946:H80P;ENSP00000359948:H80P	ENSP00000346414:H80P	H	-	2	0	LRRIQ3	74421718	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.224000	0.65288	2.102000	0.63906	0.533000	0.62120	CAT	.	.		0.303	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		G	74649130	T	G	74649130	3	3	66	1	0	0	0	0	1	0	0	0	9039	1464	51	5	1663	5	LRRIQ3	1	74649130	Missense_Mutation	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	10772246	74649130	174601491	4	8488										
OLFM3	118427	hgsc.bcm.edu	37	chr1	102302451	102302451	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctaccttttccagtagttggCgaagttgcctgcttttggca	10	10	0	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:102302451C>A	ENST00000338858.5	-	2	259	c.260G>T	c.(259-261)cGc>cTc	p.R87L	OLFM3_ENST00000359814.3_Missense_Mutation_p.R87L|OLFM3_ENST00000370103.4_Missense_Mutation_p.R67L|OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000536598.1_5'UTR			Q96PB7	NOE3_HUMAN	olfactomedin 3	87					eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)		p.R67L(1)|p.R87L(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		CAGTAGTTGGCGAAGTTGCCT	0.458																																					p.R67L		Atlas-SNP	.											OLFM3_ENST00000338858,NS,carcinoma,0,2	OLFM3	178	.	2	Substitution - Missense(2)	lung(2)	c.G200T						.						125	117	120					1																	102302451		2203	4300	6503	SO:0001583	missense	118427	exon2			AGTTGGCGAAGTT	AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"optimedin"	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.260G>T	chr1.hg19:g.102302451C>A	ENSP00000345192:p.Arg87Leu	97.0	0.0		83.0	23.0	NM_058170	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Missense_Mutation	SNP	ENST00000338858.5	hg19		.	.	.	.	.	.	.	.	.	.	C	31	5.060999	0.93846	.	.	ENSG00000118733	ENST00000370103;ENST00000338858;ENST00000359814	T;T;T	0.53206	0.63;0.63;0.63	5.62	5.62	0.85841	.	0.055319	0.64402	D	0.000001	T	0.62672	0.2447	M	0.66939	2.045	0.80722	D	1	D;D	0.69078	0.979;0.997	D;D	0.79784	0.91;0.993	T	0.61242	-0.7102	10	0.48119	T	0.1	.	19.2804	0.94051	0.0:1.0:0.0:0.0	.	67;87	Q5T3V6;Q96PB7	.;NOE3_HUMAN	L	67;87;87	ENSP00000359121:R67L;ENSP00000345192:R87L;ENSP00000352867:R87L	ENSP00000345192:R87L	R	-	2	0	OLFM3	102075039	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.047000	0.71038	2.639000	0.89480	0.585000	0.79938	CGC	.	.		0.458	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1			A	102302451	C	A	102302451	3	1	66	1	0	0	0	0	1	0	0	0	10863	768	27	1	1196	1	OLFM3	1	102302451	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	27653321	102302451	146948170	5	8489										
PRMT6	55170	hgsc.bcm.edu	37	chr1	107600118	107600118	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctcagctagagctctcccgcGccggcttggagcaggagctg	14	14	2	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:107600118G>T	ENST00000370078.1	+	1	818	c.781G>T	c.(781-783)Gcc>Tcc	p.A261S	PRMT6_ENST00000361318.5_Missense_Mutation_p.A202S			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	261	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)			biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		GCTCTCCCGCGCCGGCTTGGA	0.677																																					p.A261S		Atlas-SNP	.											.	PRMT6	55	.	0			c.G781T						.						18	21	20					1																	107600118		1915	4124	6039	SO:0001583	missense	55170	exon1			TCCCGCGCCGGCT	AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"Protein arginine methyltransferases"	18241	protein-coding gene	gene with protein product		608274	"HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.781G>T	chr1.hg19:g.107600118G>T	ENSP00000359095:p.Ala261Ser	22.0	0.0		27.0	15.0	NM_018137	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Missense_Mutation	SNP	ENST00000370078.1	hg19	CCDS41360.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.95|11.95	1.792575|1.792575	0.31685|0.31685	.|.	.|.	ENSG00000198890|ENSG00000198890	ENST00000361318;ENST00000370078|ENST00000540389	T;T|.	0.22945|.	1.93;1.93|.	4.98|4.98	1.9|1.9	0.25705|0.25705	.|.	0.849552|.	0.10338|.	N|.	0.686655|.	T|T	0.18425|0.18425	0.0442|0.0442	L|L	0.43152|0.43152	1.355|1.355	0.20703|0.20703	N|N	0.999862|0.999862	B|.	0.02656|.	0.0|.	B|.	0.09377|.	0.004|.	T|T	0.31392|0.31392	-0.9945|-0.9945	10|6	0.66056|0.87932	D|D	0.02|0	-21.247|-21.247	2.9449|2.9449	0.05842|0.05842	0.1022:0.1761:0.5397:0.182|0.1022:0.1761:0.5397:0.182	.|.	261|.	Q96LA8|.	ANM6_HUMAN|.	S|L	202;261|154	ENSP00000355145:A202S;ENSP00000359095:A261S|.	ENSP00000355145:A202S|ENSP00000440829:R154L	A|R	+|+	1|2	0|0	PRMT6|PRMT6	107401641|107401641	0.592000|0.592000	0.26832|0.26832	0.591000|0.591000	0.28745|0.28745	0.630000|0.630000	0.37929|0.37929	2.512000|2.512000	0.45485|0.45485	0.221000|0.221000	0.20879|0.20879	0.442000|0.442000	0.29010|0.29010	GCC|CGC	.	.		0.677	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137		T	107600118	G	T	107600118	3	4	66	1	0	0	0	0	1	0	0	0	12552	1087	38	1	783	1	PRMT6	1	107600118	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	5297667	107600118	141650503	6	8490										
CAPZA1	829	hgsc.bcm.edu	37	chr1	113192075	113192075	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ttaataatgacaatctcctcAgggaaggggcagcacagtaa	10	8	2	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:113192075A>T	ENST00000263168.3	+	3	811	c.139A>T	c.(139-141)Agg>Tgg	p.R47W	CAPZA1_ENST00000476936.1_3'UTR	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	47					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAATCTCCTCAGGGAAGGGGC	0.368																																					p.R47W		Atlas-SNP	.											.	CAPZA1	16	.	0			c.A139T						.						107	103	104					1																	113192075		2203	4300	6503	SO:0001583	missense	829	exon3			CTCCTCAGGGAAG	U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.139A>T	chr1.hg19:g.113192075A>T	ENSP00000263168:p.Arg47Trp	104.0	0.0		93.0	25.0	NM_006135	Q53FQ6|Q6FHD5	Missense_Mutation	SNP	ENST00000263168.3	hg19	CCDS30805.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.668677	0.88348	.	.	ENSG00000116489	ENST00000263168	.	.	.	5.39	5.39	0.77823	.	0.101850	0.64402	D	0.000003	T	0.71702	0.3371	M	0.66939	2.045	0.51767	D	0.99993	D	0.69078	0.997	D	0.74674	0.984	T	0.76242	-0.3031	9	0.72032	D	0.01	-26.4961	15.0963	0.72238	1.0:0.0:0.0:0.0	.	47	P52907	CAZA1_HUMAN	W	47	.	ENSP00000263168:R47W	R	+	1	2	CAPZA1	112993598	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.939000	0.70179	2.043000	0.60533	0.482000	0.46254	AGG	.	.		0.368	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135		T	113192075	A	T	113192075	3	4	66	1	0	0	0	0	1	0	0	0	2642	179	7	4	149	4	CAPZA1	1	113192075	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	5591957	113192075	136058546	7	8491										
LCE5A	254910	hgsc.bcm.edu	37	chr1	152484032	152484032	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tgtcctgccagcagagccagCagcagtgccagcctcctccc	10	18	0	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:152484032C>A	ENST00000334269.2	+	2	198	c.22C>A	c.(22-24)Cag>Aag	p.Q8K	CRCT1_ENST00000368790.3_5'Flank	NM_178438.4	NP_848525.1	Q5TCM9	LCE5A_HUMAN	late cornified envelope 5A	8	Cys-rich.				keratinization (GO:0031424)			p.Q8E(1)		lung(3)|ovary(1)|prostate(3)	7	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCAGAGCCAGCAGCAGTGCCA	0.493																																					p.Q8K		Atlas-SNP	.											LCE5A,NS,carcinoma,0,1	LCE5A	15	.	1	Substitution - Missense(1)	prostate(1)	c.C22A						.						78	75	76					1																	152484032		2203	4300	6503	SO:0001583	missense	254910	exon2			AGCCAGCAGCAGT	BI670518	CCDS1011.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000186207	ENSG00000186207		"Late cornified envelopes"	16614	protein-coding gene	gene with protein product		612619	"small proline rich-like (epidermal differentiation complex) 5A"	SPRL5A		11698679	Standard	NM_178438		Approved	LEP18	uc001ezy.3	Q5TCM9	OTTHUMG00000014401	ENST00000334269.2:c.22C>A	chr1.hg19:g.152484032C>A	ENSP00000333952:p.Gln8Lys	52.0	0.0		114.0	14.0	NM_178438		Missense_Mutation	SNP	ENST00000334269.2	hg19	CCDS1011.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687947	0.29962	.	.	ENSG00000186207	ENST00000334269	T	0.03982	3.74	5.13	2.98	0.34508	.	.	.	.	.	T	0.02012	0.0063	M	0.75447	2.3	0.22457	N	0.999089	B	0.20052	0.041	B	0.19666	0.026	T	0.50101	-0.8867	9	0.07175	T	0.84	-0.2166	11.301	0.49306	0.257:0.743:0.0:0.0	.	8	Q5TCM9	LCE5A_HUMAN	K	8	ENSP00000333952:Q8K	ENSP00000333952:Q8K	Q	+	1	0	LCE5A	150750656	0.992000	0.36948	1.000000	0.80357	0.998000	0.95712	-0.093000	0.11111	0.476000	0.27440	0.603000	0.83216	CAG	.	.		0.493	LCE5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040059.1	NM_178438		A	152484032	C	A	152484032	3	1	66	1	0	0	0	0	1	0	0	0	8684	711	25	3	24	3	LCE5A	1	152484032	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	39291957	152484032	96766589	8	8492										
RAB25	57111	hgsc.bcm.edu	37	chr1	156035802	156035802	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	cgcaccaccatcggggttgaGttctccacccgcactgtgat	10	15	1	2			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:156035802G>A	ENST00000361084.5	+	2	385	c.144G>A	c.(142-144)gaG>gaA	p.E48E	RAB25_ENST00000487325.1_Intron	NM_020387.2	NP_065120.2	P57735	RAB25_HUMAN	RAB25, member RAS oncogene family	48					positive regulation of cell proliferation (GO:0008284)|protein transport (GO:0015031)|pseudopodium organization (GO:0031268)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	Hepatocellular(266;0.158)|all_neural(408;0.195)					TCGGGGTTGAGTTCTCCACCC	0.607																																					p.E48E		Atlas-SNP	.											.	RAB25	18	.	0			c.G144A						.						62	68	66					1																	156035802		2158	4272	6430	SO:0001819	synonymous_variant	57111	exon2			GGTTGAGTTCTCC	AF083124	CCDS41413.1	1q22	2008-07-03			ENSG00000132698	ENSG00000132698		"RAB, member RAS oncogene"	18238	protein-coding gene	gene with protein product		612942				11697911	Standard	NM_020387		Approved	CATX-8	uc001fnc.3	P57735	OTTHUMG00000017457	ENST00000361084.5:c.144G>A	chr1.hg19:g.156035802G>A		44.0	0.0		94.0	4.0	NM_020387	Q5VYA2|Q8NG24|Q96GB1|Q9BT12	Silent	SNP	ENST00000361084.5	hg19	CCDS41413.1																																																																																			.	.		0.607	RAB25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046185.1			A	156035802	G	A	156035802	2	1	66	1	0	0	0	0	0	0	0	1	12927	1020	36	3		3	RAB25	1	156035802	Silent	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	3551770	156035802	93214819	9	8493										
ETV3	2117	hgsc.bcm.edu	37	chr1	157095349	157095349	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gcctggtgatgggctataggAgaagatggtgggagtcaggg	20	4	1	3			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:157095349A>G	ENST00000368192.4	-	5	887	c.823T>C	c.(823-825)Tcc>Ccc	p.S275P		NM_001145312.1	NP_001138784.1	P41162	ETV3_HUMAN	ets variant 3	275					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	9	Hepatocellular(266;0.158)	Prostate(1639;0.174)				GGGCTATAGGAGAAGATGGTG	0.552																																					p.S275P		Atlas-SNP	.											.	ETV3	50	.	0			c.T823C						.						147	146	146					1																	157095349		692	1591	2283	SO:0001583	missense	2117	exon5			TATAGGAGAAGAT	BC022868	CCDS1164.1, CCDS44250.1	1q21-q23	2008-09-12	2008-09-12		ENSG00000117036	ENSG00000117036			3492	protein-coding gene	gene with protein product		164873	"ets variant gene 3, ETS family transcriptional repressor", "ets variant gene 3"			8020980	Standard	NM_005240		Approved	PE-1	uc001fqr.2	P41162	OTTHUMG00000034298	ENST00000368192.4:c.823T>C	chr1.hg19:g.157095349A>G	ENSP00000357175:p.Ser275Pro	102.0	0.0		219.0	85.0	NM_001145312	B4E3M7|Q8TAC8|Q9BX30	Missense_Mutation	SNP	ENST00000368192.4	hg19	CCDS44250.1	.	.	.	.	.	.	.	.	.	.	A	14.20	2.463361	0.43736	.	.	ENSG00000117036	ENST00000368192	T	0.36699	1.24	4.9	3.76	0.43208	.	0.274126	0.31648	N	0.007288	T	0.11239	0.0274	L	0.28274	0.84	0.80722	D	1	B	0.20988	0.05	B	0.17722	0.019	T	0.05468	-1.0883	10	0.30854	T	0.27	.	9.966	0.41725	0.918:0.0:0.082:0.0	.	275	P41162	ETV3_HUMAN	P	275	ENSP00000357175:S275P	ENSP00000357175:S275P	S	-	1	0	ETV3	155361973	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.309000	0.43699	0.995000	0.38917	0.459000	0.35465	TCC	.	.		0.552	ETV3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082843.2	NM_005240		G	157095349	A	G	157095349	3	3	66	1	0	0	0	0	1	0	0	0	5281	304	11	2	719	2	ETV3	1	157095349	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	1059547	157095349	92155272	10	8494										
CD55	1604	hgsc.bcm.edu	37	chr1	207510136	207510136	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	caacttctcagaaaaccaccAcaaaaaccaccacaccaaat	1	16	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr1:207510136A>C	ENST00000367064.3	+	7	1210	c.952A>C	c.(952-954)Aca>Cca	p.T318P	CD55_ENST00000314754.8_Missense_Mutation_p.T318P|CD55_ENST00000465534.1_3'UTR|CD55_ENST00000391920.4_Missense_Mutation_p.T318P|CD55_ENST00000367067.4_3'UTR|CD55_ENST00000367062.4_Missense_Mutation_p.T318P|CD55_ENST00000391921.4_Missense_Mutation_p.T254P|CD55_ENST00000367065.5_Missense_Mutation_p.T318P|CD55_ENST00000367063.2_Missense_Mutation_p.T318P	NM_000574.3	NP_000565.1	P08174	DAF_HUMAN	CD55 molecule, decay accelerating factor for complement (Cromer blood group)	318	Ser/Thr-rich.				CD4-positive, alpha-beta T cell cytokine production (GO:0035743)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|maternal process involved in parturition (GO:0060137)|negative regulation of complement activation (GO:0045916)|positive regulation of CD4-positive, alpha-beta T cell activation (GO:2000516)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of complement activation (GO:0030449)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|respiratory burst (GO:0045730)|response to peptide hormone (GO:0043434)|response to virus (GO:0009615)|spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	enzyme inhibitor activity (GO:0004857)|lipid binding (GO:0008289)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16					Chloramphenicol(DB00446)	GAAAACCACCACAAAAACCAC	0.433																																					p.T318P		Atlas-SNP	.											.	CD55	55	.	0			c.A952C						.						203	187	192					1																	207510136		2203	4300	6503	SO:0001583	missense	1604	exon7			ACCACCACAAAAA	BC001288	CCDS31006.1, CCDS44307.1, CCDS73022.1	1q32	2014-09-17	2006-03-28	2006-02-23	ENSG00000196352	ENSG00000196352		"CD molecules", "Blood group antigens"	2665	protein-coding gene	gene with protein product		125240	"decay accelerating factor for complement (CD55, Cromer blood group system)"	DAF			Standard	XM_005273077		Approved	CR, TC, CROM	uc001hfr.4	P08174	OTTHUMG00000036255	ENST00000367064.3:c.952A>C	chr1.hg19:g.207510136A>C	ENSP00000356031:p.Thr318Pro	104.0	0.0		158.0	81.0	NM_001114752	B1AP14|D3DT83|D3DT84|E7ER69|P09679|P78361|Q14UF2|Q14UF3|Q14UF4|Q14UF5|Q14UF6	Missense_Mutation	SNP	ENST00000367064.3	hg19	CCDS31006.1	.	.	.	.	.	.	.	.	.	.	A	15.18	2.755763	0.49362	.	.	ENSG00000196352	ENST00000367064;ENST00000367063;ENST00000391921;ENST00000536840;ENST00000314754;ENST00000367065;ENST00000391920;ENST00000367062	T;T;T;T;T;T;T	0.36878	1.26;1.46;1.63;1.38;1.36;1.23;1.24	3.43	-0.682	0.11339	.	.	.	.	.	T	0.37598	0.1009	L	0.29908	0.895	0.09310	N	0.999994	D;P;B;D;B;P	0.65815	0.995;0.932;0.116;0.962;0.116;0.627	D;P;B;P;B;B	0.70487	0.969;0.84;0.033;0.573;0.033;0.139	T	0.27157	-1.0082	9	0.24483	T	0.36	.	4.6885	0.12769	0.4232:0.3884:0.0:0.1885	.	318;254;318;318;318;318	Q14UF6;B1AP15;Q14UF4;P08174-2;P08174;B1AP13	.;.;.;.;DAF_HUMAN;.	P	318;318;254;254;318;318;318;318	ENSP00000356031:T318P;ENSP00000356030:T318P;ENSP00000375788:T254P;ENSP00000316333:T318P;ENSP00000356032:T318P;ENSP00000375787:T318P;ENSP00000356029:T318P	ENSP00000316333:T318P	T	+	1	0	CD55	205576759	0.027000	0.19231	0.005000	0.12908	0.110000	0.19582	0.223000	0.17719	-0.097000	0.12307	0.246000	0.17985	ACA	.	.		0.433	CD55-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088208.2	NM_000574		C	207510136	A	C	207510136	3	2	66	1	0	0	0	0	1	0	0	0	3026	159	6	5	978	5	CD55	1	207510136	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	50414787	207510136	41740485	11	8495										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29296015	29296015	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tcgggctctggtgcaaggtcCcagctggtttgcttgcccag	14	12	1	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr2:29296015C>A	ENST00000331664.5	-	1	1112	c.1113G>T	c.(1111-1113)tgG>tgT	p.W371C		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	371					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GTGCAAGGTCCCAGCTGGTTT	0.582																																					p.W371C		Atlas-SNP	.											.	C2orf71	146	.	0			c.G1113T						.						60	61	61					2																	29296015		2124	4249	6373	SO:0001583	missense	388939	exon1			AAGGTCCCAGCTG		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.1113G>T	chr2.hg19:g.29296015C>A	ENSP00000332809:p.Trp371Cys	99.0	0.0		103.0	42.0	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	hg19	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	C	12.09	1.833224	0.32421	.	.	ENSG00000179270	ENST00000331664	T	0.21734	1.99	5.51	3.57	0.40892	.	0.646123	0.15732	N	0.247398	T	0.17152	0.0412	L	0.39633	1.23	0.49798	D	0.999821	B	0.14438	0.01	B	0.13407	0.009	T	0.03945	-1.0990	10	0.41790	T	0.15	-3.002	8.6972	0.34303	0.458:0.4217:0.1203:0.0	.	371	A6NGG8	CB071_HUMAN	C	371	ENSP00000332809:W371C	ENSP00000332809:W371C	W	-	3	0	C2orf71	29149519	0.993000	0.37304	1.000000	0.80357	0.637000	0.38172	0.257000	0.18369	1.291000	0.44653	0.561000	0.74099	TGG	.	.		0.582	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29296015	C	A	29296015	3	1	66	1	0	0	0	0	1	0	0	0	2193	624	22	3	2761	3	C2orf71	2	29296015	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10		29296015	213903358	12	8496										
NLRC4	58484	hgsc.bcm.edu	37	chr2	32463205	32463205	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tggaagcaacagttacctagGattttcactgcatttgcaga	9	8	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr2:32463205G>A	ENST00000404025.2	-	7	3005	c.2517C>T	c.(2515-2517)atC>atT	p.I839I	NLRC4_ENST00000360906.5_Silent_p.I839I|NLRC4_ENST00000342905.6_Silent_p.I174I|NLRC4_ENST00000402280.1_Silent_p.I839I			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	839					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					AGTTACCTAGGATTTTCACTG	0.363																																					p.I839I		Atlas-SNP	.											.	NLRC4	165	.	0			c.C2517T						.						150	143	145					2																	32463205		2203	4300	6503	SO:0001819	synonymous_variant	58484	exon6			ACCTAGGATTTTC	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.2517C>T	chr2.hg19:g.32463205G>A		88.0	0.0		87.0	20.0	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Silent	SNP	ENST00000404025.2	hg19	CCDS33174.1																																																																																			.	.		0.363	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		A	32463205	G	A	32463205	2	1	66	1	0	0	0	0	0	0	0	1	10478	1164	41	3		3	NLRC4	2	32463205	Silent	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	3167190	32463205	210736168	13	8497										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32640007	32640007	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gtttaacaaactctaagagtGaaaagacaaaggaaaagcac	8	6	1	3			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr2:32640007G>T	ENST00000421745.2	+	10	1782	c.1648G>T	c.(1648-1650)Gaa>Taa	p.E550*		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	550					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CTCTAAGAGTGAAAAGACAAA	0.378																																					p.E550X	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.G1648T						.						59	61	61					2																	32640007		2203	4300	6503	SO:0001587	stop_gained	57448	exon10			AAGAGTGAAAAGA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.1648G>T	chr2.hg19:g.32640007G>T	ENSP00000393596:p.Glu550*	101.0	0.0		98.0	5.0	NM_016252	Q9ULD1	Nonsense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	38	7.113143	0.98070	.	.	ENSG00000115760	ENST00000421745	.	.	.	5.07	5.07	0.68467	.	0.123114	0.53938	D	0.000052	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	18.8213	0.92099	0.0:0.0:1.0:0.0	.	.	.	.	X	550	.	ENSP00000393596:E550X	E	+	1	0	BIRC6	32493511	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.751000	0.98889	2.528000	0.85240	0.650000	0.86243	GAA	.	.		0.378	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32640007	G	T	32640007	4	4	66	1	0	0	0	0	0	1	0	0	1438	1291	45	3	1686	3	BIRC6	2	32640007	Nonsense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	176802	32640007	210559366	14	8498										
C2orf55	343990	hgsc.bcm.edu	37	chr2	99449388	99449388	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	acccgcacaggccgagtagcGtcctgtccggactcaggaat	12	14	1	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr2:99449388G>A	ENST00000397899.2	-	4	643	c.312C>T	c.(310-312)gaC>gaT	p.D104D	KIAA1211L_ENST00000462314.1_Intron	NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	104																	GCCGAGTAGCGTCCTGTCCGG	0.537																																					p.D104D		Atlas-SNP	.											C2orf55,NS,carcinoma,0,1	.	.	.	0			c.C312T						.						142	153	150					2																	99449388		1930	4131	6061	SO:0001819	synonymous_variant	343990	exon4			AGTAGCGTCCTGT	BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 55"	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.312C>T	chr2.hg19:g.99449388G>A		56.0	0.0		53.0	9.0	NM_207362		Silent	SNP	ENST00000397899.2	hg19	CCDS42720.1																																																																																			.	.		0.537	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362		A	99449388	G	A	99449388	2	1	66	1	0	0	0	0	0	0	0	1	2178	1136	40	1		1	C2orf55	2	99449388	Silent	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	66809381	99449388	143749985	15	8499										
UBXN4	23190	hgsc.bcm.edu	37	chr2	136513213	136513213	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctcagtccagaaatgcagagCtttgtgagataccacccact	8	12	1	3			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr2:136513213C>T	ENST00000272638.9	+	5	771	c.460C>T	c.(460-462)Ctt>Ttt	p.L154F	UBXN4_ENST00000490163.1_3'UTR	NM_014607.3	NP_055422.1	Q92575	UBXN4_HUMAN	UBX domain protein 4	154					response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	24						AAATGCAGAGCTTTGTGAGAT	0.403																																					p.L154F		Atlas-SNP	.											UBXN4,NS,carcinoma,0,1	UBXN4	54	.	0			c.C460T						.						110	105	106					2																	136513213		1854	4108	5962	SO:0001583	missense	23190	exon5			GCAGAGCTTTGTG	D87684	CCDS42761.1	2q21.3-q22.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000144224	ENSG00000144224		"UBX domain containing"	14860	protein-coding gene	gene with protein product	"erasin"	611216	"UBX domain-containing 2", "UBX domain containing 2"	UBXDC1, UBXD2		16968747	Standard	NM_014607		Approved	KIAA0242	uc002tur.3	Q92575	OTTHUMG00000153577	ENST00000272638.9:c.460C>T	chr2.hg19:g.136513213C>T	ENSP00000272638:p.Leu154Phe	32.0	0.0		31.0	12.0	NM_014607	A8K9W4|Q4ZG56|Q8IYM5	Missense_Mutation	SNP	ENST00000272638.9	hg19	CCDS42761.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.801463	0.31869	.	.	ENSG00000144224	ENST00000272638;ENST00000430594	T	0.47177	0.85	5.3	4.42	0.53409	.	0.719824	0.13327	N	0.396207	T	0.42743	0.1216	L	0.54323	1.7	0.24617	N	0.993691	P	0.49961	0.93	B	0.39068	0.289	T	0.33828	-0.9853	10	0.56958	D	0.05	.	11.4784	0.50312	0.0:0.9124:0.0:0.0876	.	154	Q92575	UBXN4_HUMAN	F	154;136	ENSP00000272638:L154F	ENSP00000272638:L154F	L	+	1	0	UBXN4	136229683	0.442000	0.25633	0.368000	0.25939	0.764000	0.43329	0.991000	0.29654	1.232000	0.43678	0.557000	0.71058	CTT	.	.		0.403	UBXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331696.1	NM_014607		T	136513213	C	T	136513213	3	4	66	1	0	0	0	0	1	0	0	0	16931	797	28	3	478	3	UBXN4	2	136513213	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	37063825	136513213	106686160	16	8500										
PSMD14	10213	hgsc.bcm.edu	37	chr2	162227718	162227718	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tggttggtatcacagtcaccCtggctttggttgttggcttt	12	8	2	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr2:162227718C>G	ENST00000409682.3	+	7	1051	c.347C>G	c.(346-348)cCt>cGt	p.P116R		NM_005805.5	NP_005796.1	O00487	PSDE_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	116	MPN.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K63-linked deubiquitination (GO:0070536)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle, lid subcomplex (GO:0008541)	endopeptidase activator activity (GO:0061133)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|proteasome binding (GO:0070628)|ubiquitin thiolesterase activity (GO:0004221)			breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	12						CACAGTCACCCTGGCTTTGGT	0.463																																					p.P116R		Atlas-SNP	.											.	PSMD14	22	.	0			c.C347G						.						151	151	151					2																	162227718		2013	4179	6192	SO:0001583	missense	10213	exon7			GTCACCCTGGCTT	U86782	CCDS46437.1	2q14.3	2008-05-22			ENSG00000115233	ENSG00000115233		"Proteasome (prosome, macropain) subunits"	16889	protein-coding gene	gene with protein product		607173				9374539	Standard	NM_005805		Approved	POH1, pad1, Rpn11	uc002ubu.3	O00487	OTTHUMG00000153882	ENST00000409682.3:c.347C>G	chr2.hg19:g.162227718C>G	ENSP00000386541:p.Pro116Arg	261.0	0.0		263.0	55.0	NM_005805	B3KNW2|O00176	Missense_Mutation	SNP	ENST00000409682.3	hg19	CCDS46437.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.851033	0.71719	.	.	ENSG00000115233	ENST00000409682	D	0.87412	-2.25	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.96765	0.8944	H	0.98754	4.32	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97907	1.0306	10	0.87932	D	0	-1.1902	20.1392	0.98050	0.0:1.0:0.0:0.0	.	116	O00487	PSDE_HUMAN	R	116	ENSP00000386541:P116R	ENSP00000386541:P116R	P	+	2	0	PSMD14	161935964	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.052000	0.71080	2.751000	0.94390	0.591000	0.81541	CCT	.	.		0.463	PSMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332833.1	NM_005805		G	162227718	C	G	162227718	3	3	66	1	0	0	0	0	1	0	0	0	12709	681	24	4	365	4	PSMD14	2	162227718	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	25714505	162227718	80971655	17	8501										
CPS1	1373	hgsc.bcm.edu	37	chr2	211471635	211471635	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	agtgaatgccagactgtcccGaagctctgctctggcctcaa	10	13	3	2			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr2:211471635G>T	ENST00000233072.5	+	18	2358	c.2162G>T	c.(2161-2163)cGa>cTa	p.R721L	CPS1_ENST00000451903.2_Missense_Mutation_p.R270L|CPS1_ENST00000430249.2_Missense_Mutation_p.R727L	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	721	ATP-grasp 1.		R -> Q (in CPS1D). {ECO:0000269|PubMed:21120950}.	RLSRS -> KMSPN (in Ref. 1; BAA14328). {ECO:0000305}.	anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	AGACTGTCCCGAAGCTCTGCT	0.443																																					p.R727L		Atlas-SNP	.											CPS1_ENST00000430249,colon,carcinoma,0,2	CPS1	485	.	0			c.G2180T						.						83	74	77					2																	211471635		2203	4300	6503	SO:0001583	missense	1373	exon19			TGTCCCGAAGCTC	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2162G>T	chr2.hg19:g.211471635G>T	ENSP00000233072:p.Arg721Leu	118.0	0.0		107.0	45.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	33	5.198622	0.94997	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.98777	-5.13;-5.13;-5.13	5.73	5.73	0.89815	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Carbamoyl-phosphate synthase, large subunit, CPS-domain (1);	0.000000	0.85682	D	0.000000	D	0.99664	0.9875	H	0.99859	4.855	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97157	0.9835	10	0.87932	D	0	-28.6625	19.9597	0.97242	0.0:0.0:1.0:0.0	.	731;721	Q59HF8;P31327	.;CPSM_HUMAN	L	727;729;721;270	ENSP00000402608:R727L;ENSP00000233072:R721L;ENSP00000406136:R270L	ENSP00000233072:R721L	R	+	2	0	CPS1	211179880	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	9.472000	0.97709	2.723000	0.93209	0.586000	0.80456	CGA	.	.		0.443	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211471635	G	T	211471635	3	4	66	1	0	0	0	0	1	0	0	0	3825	1058	37	1	2254	1	CPS1	2	211471635	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	49243917	211471635	31727738	18	8502										
C2orf57	165100	hgsc.bcm.edu	37	chr2	232458647	232458647	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	acagctcggggcccagcttgCgctcggtccccagcctggtg	14	16	0	0	rs375509340		TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr2:232458647C>A	ENST00000313965.2	+	1	1073	c.985C>A	c.(985-987)Cgc>Agc	p.R329S		NM_152614.2	NP_689827.2	Q53QW1	CB057_HUMAN	chromosome 2 open reading frame 57	329										endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	19		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)		GCCCAGCTTGCGCTCGGTCCC	0.667																																					p.R329S		Atlas-SNP	.											.	C2orf57	35	.	0			c.C985A						.						44	47	46					2																	232458647		2203	4300	6503	SO:0001583	missense	165100	exon1			AGCTTGCGCTCGG	BC034405	CCDS2487.1	2q37.1	2008-02-05			ENSG00000177673	ENSG00000177673			28563	protein-coding gene	gene with protein product						12477932	Standard	NM_152614		Approved	MGC35154	uc002vrz.3	Q53QW1	OTTHUMG00000133226	ENST00000313965.2:c.985C>A	chr2.hg19:g.232458647C>A	ENSP00000315557:p.Arg329Ser	39.0	0.0		42.0	11.0	NM_152614	Q8N4F2	Missense_Mutation	SNP	ENST00000313965.2	hg19	CCDS2487.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.762614	0.31228	.	.	ENSG00000177673	ENST00000313965	T	0.25912	1.77	5.15	5.15	0.70609	.	0.000000	0.34507	N	0.003919	T	0.35068	0.0919	L	0.29908	0.895	0.32051	N	0.596887	D	0.58970	0.984	P	0.61132	0.884	T	0.32955	-0.9887	10	0.59425	D	0.04	-6.4431	13.9928	0.64378	0.0:1.0:0.0:0.0	.	329	Q53QW1	CB057_HUMAN	S	329	ENSP00000315557:R329S	ENSP00000315557:R329S	R	+	1	0	C2orf57	232166891	0.703000	0.27826	0.939000	0.37840	0.033000	0.12548	1.954000	0.40362	2.683000	0.91414	0.557000	0.71058	CGC	.	.		0.667	C2orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256962.1	NM_152614		A	232458647	C	A	232458647	3	1	66	1	0	0	0	0	1	0	0	0	2180	768	27	1	987	1	C2orf57	2	232458647	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	20987012	232458647	10740726	19	8503										
NEU2	4759	hgsc.bcm.edu	37	chr2	233899496	233899496	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ggggcctggctccccagcccAgtggctgctctacactcacc	11	18	2	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr2:233899496A>T	ENST00000233840.3	+	2	872	c.872A>T	c.(871-873)cAg>cTg	p.Q291L		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	291					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	TCCCCAGCCCAGTGGCTGCTC	0.701																																					p.Q291L		Atlas-SNP	.											.	NEU2	42	.	0			c.A872T						.						25	31	29					2																	233899496		2193	4280	6473	SO:0001583	missense	4759	exon2			CAGCCCAGTGGCT	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"N-acetyl-alpha-neuraminidase 2"	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.872A>T	chr2.hg19:g.233899496A>T	ENSP00000233840:p.Gln291Leu	67.0	0.0		36.0	12.0	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	hg19	CCDS2501.1	.	.	.	.	.	.	.	.	.	.	A	2.438	-0.329182	0.05314	.	.	ENSG00000115488	ENST00000233840	D	0.85339	-1.97	5.05	-10.1	0.00402	Neuraminidase (2);	3.993760	0.00954	N	0.003010	T	0.73999	0.3659	N	0.22421	0.69	0.09310	N	1	B	0.20368	0.044	B	0.24394	0.053	T	0.65240	-0.6216	10	0.33141	T	0.24	2.1376	10.0018	0.41933	0.0968:0.4552:0.383:0.065	.	291	Q9Y3R4	NEUR2_HUMAN	L	291	ENSP00000233840:Q291L	ENSP00000233840:Q291L	Q	+	2	0	NEU2	233607740	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-3.244000	0.00542	-4.887000	0.00028	-0.316000	0.08728	CAG	.	.		0.701	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383		T	233899496	A	T	233899496	3	4	66	1	0	0	0	0	1	0	0	0	10351	188	7	4	878	4	NEU2	2	233899496	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	1440849	233899496	9299877	20	8504										
LMCD1	29995	hgsc.bcm.edu	37	chr3	8574486	8574524	+	Splice_Site	DEL	TCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTG	TCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTG	-													0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tgggatgcaaggggacgtgtTcgggcttcgagccacattca					rs553073357|rs199520704|rs201761622		TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	TCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTG	TCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr3:8574486_8574524delTCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTG	ENST00000157600.3	+	2	338_363	c.106_131delTCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTG	c.(106-132)tcgggcttcgagccacattcatggagg>g	p.SGFEPHSWR36del	LMCD1_ENST00000454244.1_Intron|LMCD1_ENST00000535732.1_Splice_Site_p.SGFEPHSWR36del|LMCD1_ENST00000397386.3_Splice_Site_p.FGLRATFME9del|LMCD1-AS1_ENST00000439407.1_RNA	NM_014583.2	NP_055398.1	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1	36	Cys-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|regulation of cardiac muscle hypertrophy (GO:0010611)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.H41P(1)		breast(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)	16				OV - Ovarian serous cystadenocarcinoma(96;0.124)		GGGGACGTGTTCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTGTCAGGAGGGT	0.531																																					p.35_44del		Atlas-Indel,Pindel	.											.	LMCD1	38	.	1	Substitution - Missense(1)	large_intestine(1)	c.105_131del						.																																			SO:0001630	splice_region_variant	29995	exon2			.	AF169284	CCDS33688.1, CCDS63533.1, CCDS63534.1	3p26-p24	2008-07-18			ENSG00000071282	ENSG00000071282			6633	protein-coding gene	gene with protein product	"dyxin"	604859				10662546	Standard	NM_001278233		Approved		uc003bqq.4	Q9NZU5	OTTHUMG00000154971	ENST00000157600.3:c.131+1TCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTG>-	chr3.hg19:g.8574486_8574524delTCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTG		153.0	0.0		82.0	14.0	NM_014583	B4DG80	In_Frame_Del	DEL	ENST00000157600.3	hg19	CCDS33688.1																																																																																			.	.		0.531	LMCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337854.1	NM_014583	In_Frame_Del	-	8574524	TCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTG	-	8574486	8	5	66	1	0	1	0	1	0	0	1	0	8853	1783	62	0	112	0	LMCD1	3	8574486	Splice_Site	DEL	TCGGGCTTCGAGCCACATTCATGGAGGTAACAGATTTTG	TCGA-CC-A3MC-01A-11D-A22F-10		8574486	189447944	21	8505										
FANCD2	2177	hgsc.bcm.edu	37	chr3	10128833	10128833	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tacagccagagcgtccattaCttgcagaatttccatcaaag	7	11	1	2	rs566518051		TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr3:10128833C>T	ENST00000419585.1	+	34	3512	c.3351C>T	c.(3349-3351)taC>taT	p.Y1117Y	FANCD2_ENST00000383807.1_Silent_p.Y1117Y|FANCD2_ENST00000383806.1_Silent_p.Y1117Y|FANCD2OS_ENST00000436517.1_5'UTR|FANCD2_ENST00000287647.3_Silent_p.Y1117Y|FANCD2OS_ENST00000524279.1_Intron			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	1117					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GCGTCCATTACTTGCAGAATT	0.393			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	1	0.000199681	0	0	5008	,	,		19392	0		0	False		,,,				2504	0.001				p.Y1117Y		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.C3351T						.						230	227	228					3																	10128833		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon34	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CCATTACTTGCAG	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.3351C>T	chr3.hg19:g.10128833C>T		134.0	0.0		152.0	44.0	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	hg19	CCDS33696.1																																																																																			.	.		0.393	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			T	10128833	C	T	10128833	2	4	66	1	0	0	0	0	0	0	0	1	5673	576	20	3		3	FANCD2	3	10128833	Silent	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	1554347	10128833	187893597	22	8506										
TMF1	7110	hgsc.bcm.edu	37	chr3	69097137	69097137	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	taacaggaggagaaggtgtaTtgctctgcctgtcttcatgt	12	7	3	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr3:69097137T>C	ENST00000398559.2	-	2	935	c.719A>G	c.(718-720)aAt>aGt	p.N240S	CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|MIR3136_ENST00000583498.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.N240S|CTD-2013N24.2_ENST00000596274.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	240					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		AGAAGGTGTATTGCTCTGCCT	0.403																																					p.N240S		Atlas-SNP	.											.	TMF1	77	.	0			c.A719G						.						101	102	102					3																	69097137		1949	4150	6099	SO:0001583	missense	7110	exon2			GGTGTATTGCTCT		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.719A>G	chr3.hg19:g.69097137T>C	ENSP00000381567:p.Asn240Ser	121.0	0.0		135.0	44.0	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	hg19	CCDS43105.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.333595	0.41297	.	.	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248;ENST00000438636	T;T	0.76709	-1.04;-1.04	5.72	5.72	0.89469	.	0.082561	0.85682	D	0.000000	D	0.84061	0.5389	M	0.64997	1.995	0.58432	D	0.999994	D;D	0.61697	0.99;0.983	P;P	0.57244	0.816;0.659	D	0.85116	0.0966	10	0.54805	T	0.06	-18.5448	16.0634	0.80856	0.0:0.0:0.0:1.0	.	240;240	P82094-2;P82094	.;TMF1_HUMAN	S	240;240;153;240	ENSP00000381567:N240S;ENSP00000438706:N240S	ENSP00000348582:N153S	N	-	2	0	TMF1	69179827	1.000000	0.71417	0.991000	0.47740	0.068000	0.16541	8.037000	0.88933	2.192000	0.70111	0.524000	0.50904	AAT	.	.		0.403	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		C	69097137	T	C	69097137	3	2	66	1	0	0	0	0	1	0	0	0	16243	1493	52	2	2626	2	TMF1	3	69097137	Missense_Mutation	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	58968304	69097137	128925293	23	8507										
ROBO1	6091	hgsc.bcm.edu	37	chr3	79639035	79639036	+	Frame_Shift_Ins	INS	-	-	A													0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tgaggagtgatatcatgaccINSaaaaaaggaacatgtttcca					rs200846416		TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr3:79639035_79639036insA	ENST00000464233.1	-	2	139_140	c.26_27insT	c.(25-27)ttgfs	p.L9fs		NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	9					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		ATATCATGACCAAAAAAGGAAC	0.391																																					p.L9fs		Atlas-INDEL	.											.	ROBO1	833	.	0			c.27_28insT						.																																			SO:0001589	frameshift_variant	6091	exon2			.	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.27dupT	chr3.hg19:g.79639041_79639041dupA	ENSP00000420321:p.Leu9fs	84.0	0.0		97.0	12.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Frame_Shift_Ins	INS	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.		0.391	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	79639036	-	A	79639035	7	5	66	1	0	1	1	0	0	0	0	0	13528	593	21	0	5120	0	ROBO1	3	79639035	Frame_Shift_Ins	INS	-	TCGA-CC-A3MC-01A-11D-A22F-10	10541898	79639035	118383395	24	8508										
MYH15	22989	hgsc.bcm.edu	37	chr3	108156479	108156479	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gattcagctttaaattgcccTccagtttgtgcagttccctt	7	11	1	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr3:108156479T>G	ENST00000273353.3	-	26	3259	c.3203A>C	c.(3202-3204)gAg>gCg	p.E1068A		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1068						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TAAATTGCCCTCCAGTTTGTG	0.458																																					p.E1068A		Atlas-SNP	.											.	MYH15	223	.	0			c.A3203C						.						235	228	230					3																	108156479		1905	4127	6032	SO:0001583	missense	22989	exon26			TTGCCCTCCAGTT	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3203A>C	chr3.hg19:g.108156479T>G	ENSP00000273353:p.Glu1068Ala	125.0	0.0		123.0	38.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618381	0.66787	.	.	ENSG00000144821	ENST00000273353	D	0.93659	-3.26	5.56	5.56	0.83823	.	.	.	.	.	D	0.95611	0.8573	M	0.82517	2.595	0.54753	D	0.999985	P	0.51351	0.944	P	0.52424	0.698	D	0.96157	0.9112	9	0.87932	D	0	.	16.002	0.80301	0.0:0.0:0.0:1.0	.	1068	Q9Y2K3	MYH15_HUMAN	A	1068	ENSP00000273353:E1068A	ENSP00000273353:E1068A	E	-	2	0	MYH15	109639169	1.000000	0.71417	0.395000	0.26283	0.157000	0.22087	4.925000	0.63425	2.241000	0.73720	0.533000	0.62120	GAG	.	.		0.458	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		G	108156479	T	G	108156479	3	3	66	1	0	0	0	0	1	0	0	0	10043	1551	54	5	2705	5	MYH15	3	108156479	Missense_Mutation	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	28517444	108156479	89865951	25	8509										
ACPP	55	hgsc.bcm.edu	37	chr3	132061394	132061394	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tctttctctgtttgtgtttcAggattttatagctaccttgg	8	7	3	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr3:132061394A>C	ENST00000336375.5	+	6	645		c.e6-1		ACPP_ENST00000475741.1_Splice_Site|ACPP_ENST00000351273.7_Splice_Site	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate						adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						TTTGTGTTTCAGGATTTTATA	0.383																																					.		Atlas-SNP	.											.	ACPP	118	.	0			c.556-2A>C						.						122	128	126					3																	132061394		2203	4300	6503	SO:0001630	splice_region_variant	55	exon6			TGTTTCAGGATTT		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.556-1A>C	chr3.hg19:g.132061394A>C		84.0	0.0		76.0	18.0	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Splice_Site	SNP	ENST00000336375.5	hg19	CCDS3073.1	.	.	.	.	.	.	.	.	.	.	A	19.70	3.875668	0.72180	.	.	ENSG00000014257	ENST00000336375;ENST00000495911;ENST00000475741;ENST00000351273	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.043	0.58910	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACPP	133544084	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.412000	0.59787	2.333000	0.79357	0.482000	0.46254	.	.	.		0.383	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099	Intron	C	132061394	A	C	132061394	5	2	66	1	0	0	0	0	0	0	1	0	167	202	7	5	576	5	ACPP	3	132061394	Splice_Site	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	23904915	132061394	65961036	26	8510										
CLCN2	1181	hgsc.bcm.edu	37	chr3	184070097	184070097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ttacctcttcagggctcatcTcgccttccaggtccgcgtca	8	16	5	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr3:184070097T>C	ENST00000265593.4	-	21	2465	c.2294A>G	c.(2293-2295)gAg>gGg	p.E765G	CLCN2_ENST00000344937.7_Missense_Mutation_p.E748G|CLCN2_ENST00000434054.2_Missense_Mutation_p.E721G|CLCN2_ENST00000457512.1_Missense_Mutation_p.E765G|CLCN2_ENST00000423355.2_3'UTR|EIF2B5_ENST00000444495.1_Intron	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	765					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	AGGGCTCATCTCGCCTTCCAG	0.597																																					p.E765G		Atlas-SNP	.											.	CLCN2	74	.	0			c.A2294G						.						92	82	86					3																	184070097		2203	4300	6503	SO:0001583	missense	1181	exon21			CTCATCTCGCCTT	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"Ion channels / Chloride channels : Voltage-sensitive"	2020	protein-coding gene	gene with protein product		600570	"chloride channel 2"			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.2294A>G	chr3.hg19:g.184070097T>C	ENSP00000265593:p.Glu765Gly	77.0	0.0		82.0	23.0	NM_004366	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	ENST00000265593.4	hg19	CCDS3263.1	.	.	.	.	.	.	.	.	.	.	t	11.76	1.736179	0.30774	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42	5.07	5.07	0.68467	.	0.440518	0.27424	N	0.019431	T	0.77791	0.4183	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.72587	-0.4248	10	0.44086	T	0.13	-13.3713	7.1422	0.25562	0.0:0.0766:0.1475:0.7759	.	721;765;748;765;721	E9PBD9;E9PCD2;P51788-3;P51788;B4DZ58	.;.;.;CLCN2_HUMAN;.	G	765;748;721;765	ENSP00000265593:E765G;ENSP00000345056:E748G;ENSP00000400425:E721G;ENSP00000391928:E765G	ENSP00000265593:E765G	E	-	2	0	CLCN2	185552791	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	1.984000	0.40658	2.133000	0.65898	0.379000	0.24179	GAG	.	.		0.597	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			C	184070097	T	C	184070097	3	2	66	1	0	0	0	0	1	0	0	0	3465	1551	54	2	418	2	CLCN2	3	184070097	Missense_Mutation	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	52008703	184070097	13952333	27	8511										
NAAA	27163	hgsc.bcm.edu	37	chr4	76857288	76857288	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	attctttaagaattgcacatCcactgtcagcttgcgtaaga	7	9	2	2			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr4:76857288C>A	ENST00000286733.4	-	3	573	c.472G>T	c.(472-474)Gat>Tat	p.D158Y	NAAA_ENST00000505594.1_Missense_Mutation_p.D57Y|NAAA_ENST00000399497.3_Missense_Mutation_p.D158Y|NAAA_ENST00000507956.1_Missense_Mutation_p.D158Y|NAAA_ENST00000507187.2_Missense_Mutation_p.D158Y	NM_014435.3	NP_055250.2	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase	158					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	11						AATTGCACATCCACTGTCAGC	0.413																																					p.D158Y		Atlas-SNP	.											.	NAAA	26	.	0			c.G472T						.						149	137	141					4																	76857288		1863	4114	5977	SO:0001583	missense	27163	exon3			GCACATCCACTGT	M92449	CCDS43239.1	4q21.1	2011-09-23	2008-04-24	2008-04-24	ENSG00000138744	ENSG00000138744	3.5.1.-		736	protein-coding gene	gene with protein product		607469	"N-acylsphingosine amidohydrolase (acid ceramidase)-like"	ASAHL		10610717, 1446826	Standard	NM_001042402		Approved		uc003hjb.3	Q02083	OTTHUMG00000160855	ENST00000286733.4:c.472G>T	chr4.hg19:g.76857288C>A	ENSP00000286733:p.Asp158Tyr	63.0	0.0		66.0	10.0	NM_014435	Q5KTF2|Q96EY2|Q9BRA8	Missense_Mutation	SNP	ENST00000286733.4	hg19	CCDS43239.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.352310	0.24512	.	.	ENSG00000138744	ENST00000399497;ENST00000286733;ENST00000507956;ENST00000505594;ENST00000399490;ENST00000507187	T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;0.87	5.9	4.17	0.49024	.	0.202861	0.51477	D	0.000093	D	0.82462	0.5042	L	0.59436	1.845	0.36839	D	0.887306	D;P;D	0.63880	0.984;0.798;0.993	D;B;D	0.63381	0.914;0.341;0.914	T	0.82301	-0.0525	10	0.30078	T	0.28	-14.7971	11.1999	0.48734	0.0:0.8517:0.0:0.1483	.	57;158;158	B4DVL2;D6R9S9;Q02083	.;.;NAAA_HUMAN	Y	158;158;158;57;158;158	ENSP00000382420:D158Y;ENSP00000286733:D158Y;ENSP00000427641:D158Y;ENSP00000426977:D57Y;ENSP00000423142:D158Y	ENSP00000286733:D158Y	D	-	1	0	NAAA	77076312	0.998000	0.40836	0.971000	0.41717	0.070000	0.16714	2.597000	0.46214	0.825000	0.34637	0.650000	0.86243	GAT	.	.		0.413	NAAA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362843.4			A	76857288	C	A	76857288	3	1	66	1	0	0	0	0	1	0	0	0	10136	855	30	3	646	3	NAAA	4	76857288	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10		76857288	114296988	28	8512										
TSLP	85480	hgsc.bcm.edu	37	chr5	110409217	110409217	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gcctatgagcagccacattgCcttactgaaatccagagcct	8	13	0	3			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr5:110409217C>T	ENST00000344895.3	+	3	424	c.225C>T	c.(223-225)tgC>tgT	p.C75C	TSLP_ENST00000379706.4_5'UTR|TSLP_ENST00000420978.2_Silent_p.C75C	NM_033035.4	NP_149024.1	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin	75						extracellular space (GO:0005615)				breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)		AGCCACATTGCCTTACTGAAA	0.502																																					p.C75C		Atlas-SNP	.											.	TSLP	22	.	0			c.C225T						.						147	153	151					5																	110409217		2202	4300	6502	SO:0001819	synonymous_variant	85480	exon3			ACATTGCCTTACT	BC040592	CCDS4101.1	5q22.1	2007-08-24			ENSG00000145777	ENSG00000145777			30743	protein-coding gene	gene with protein product		607003				11418668, 11480573	Standard	NM_033035		Approved		uc003kpb.2	Q969D9	OTTHUMG00000128791	ENST00000344895.3:c.225C>T	chr5.hg19:g.110409217C>T		98.0	0.0		136.0	18.0	NM_033035	Q8IW99	Silent	SNP	ENST00000344895.3	hg19	CCDS4101.1																																																																																			.	.		0.502	TSLP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250717.1	NM_033035		T	110409217	C	T	110409217	2	4	66	1	0	0	0	0	0	0	0	1	16643	747	26	3		3	TSLP	5	110409217	Silent	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10		110409217	70506043	29	8513										
TSSK1B	83942	hgsc.bcm.edu	37	chr5	112769739	112769739	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tgcatccagcagtggctgagGatctcgtcgatgtggagccg	15	10	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr5:112769739G>T	ENST00000390666.3	-	1	989	c.798C>A	c.(796-798)atC>atA	p.I266I	CTD-2201G3.1_ENST00000510381.2_RNA|MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000383058.4_RNA|CTD-2201G3.1_ENST00000416046.2_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	266	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		AGTGGCTGAGGATCTCGTCGA	0.617																																					p.I266I		Atlas-SNP	.											.	TSSK1B	89	.	0			c.C798A						.						43	42	43					5																	112769739		2202	4300	6502	SO:0001819	synonymous_variant	83942	exon1			GCTGAGGATCTCG	AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"serine/threonine kinase 22D (spermiogenesis associated)", "testis-specific serine kinase 1"	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.798C>A	chr5.hg19:g.112769739G>T		44.0	0.0		62.0	14.0	NM_032028	B2R8D9	Silent	SNP	ENST00000390666.3	hg19	CCDS4112.1																																																																																			.	.		0.617	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028		T	112769739	G	T	112769739	2	4	66	1	0	0	0	0	0	0	0	1	16683	1164	41	3		3	TSSK1B	5	112769739	Silent	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	2360522	112769739	68145521	30	8514										
PCDHGB5	56102	hgsc.bcm.edu	37	chr5	140778538	140778538	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	cagaaattacttattccttcTacagaaccgggcaaatcttt	5	10	2	2			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr5:140778538T>C	ENST00000576222.1	+	1	2546				PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTATTCCTTCTACAGAACCGG	0.443																																					p.Y282H		Atlas-SNP	.											.	.	.	.	0			c.T844C						.						94	100	98					5																	140778538		1935	4140	6075	SO:0001627	intron_variant	56101	exon1			TCCTTCTACAGAA	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+26162T>C	chr5.hg19:g.140778538T>C		59.0	0.0		89.0	23.0	NM_018925	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.		0.443	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		C	140778538	T	C	140778538	1	2	66	0	1	0	0	0	0	0	0	0	11575	1522	53	2		2	PCDHGB5	5	140778538	Intron	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	28008799	140778538	40136722	31	8515										
GPRIN1	114787	hgsc.bcm.edu	37	chr5	176026296	176026296	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ggctctgcctttcctgtaaaCatgggatctgccttccgtga	10	12	2	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr5:176026296C>T	ENST00000303991.4	-	2	717	c.540G>A	c.(538-540)atG>atA	p.M180I		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	180					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTCCTGTAAACATGGGATCTG	0.502																																					p.M180I		Atlas-SNP	.											.	GPRIN1	77	.	0			c.G540A						.						63	66	65					5																	176026296		2203	4300	6503	SO:0001583	missense	114787	exon2			TGTAAACATGGGA	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.540G>A	chr5.hg19:g.176026296C>T	ENSP00000305839:p.Met180Ile	103.0	0.0		134.0	12.0	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	hg19	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	C	6.933	0.541925	0.13250	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.08008	3.14	5.25	3.34	0.38264	.	1.212230	0.06084	N	0.662396	T	0.07908	0.0198	L	0.40543	1.245	0.09310	N	1	B	0.13145	0.007	B	0.15484	0.013	T	0.39440	-0.9614	10	0.28530	T	0.3	4.7924	3.5392	0.07804	0.1777:0.5606:0.1714:0.0904	.	180	Q7Z2K8	GRIN1_HUMAN	I	180	ENSP00000305839:M180I	ENSP00000305839:M180I	M	-	3	0	GPRIN1	175958902	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.748000	0.04818	1.205000	0.43262	0.655000	0.94253	ATG	.	.		0.502	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899		T	176026296	C	T	176026296	3	4	66	1	0	0	0	0	1	0	0	0	6738	478	17	3	2490	3	GPRIN1	5	176026296	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	35247758	176026296	4888964	32	8516										
FAM65B	9750	hgsc.bcm.edu	37	chr6	24847845	24847845	+	Frame_Shift_Del	DEL	G	G	-													0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gagcggctgcggtgcagcttGgcaaagaaagtgtcttgcaa							TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr6:24847845delG	ENST00000259698.4	-	13	1327	c.1152delC	c.(1150-1152)gccfs	p.A384fs	FAM65B_ENST00000538035.1_Intron|FAM65B_ENST00000510784.2_Intron|FAM65B_ENST00000378023.4_Intron|FAM65B_ENST00000540914.1_Intron	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	384					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						GGTGCAGCTTGGCAAAGAAAG	0.602																																					p.K385fs		Atlas-INDEL	.											.	FAM65B	134	.	0			c.1153delA						.						42	47	46					6																	24847845		692	1591	2283	SO:0001589	frameshift_variant	9750	exon13			.	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.1152delC	chr6.hg19:g.24847845delG	ENSP00000259698:p.Ala384fs	38.0	0.0		36.0	14.0	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Frame_Shift_Del	DEL	ENST00000259698.4	hg19	CCDS47383.1																																																																																			.	.		0.602	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			-	24847845	G	-	24847845	7	5	66	1	0	1	0	1	0	0	0	0	5608	1335	47	0	2108	0	FAM65B	6	24847845	Frame_Shift_Del	DEL	G	TCGA-CC-A3MC-01A-11D-A22F-10		24847845	146267222	33	8517										
TTBK1	84630	hgsc.bcm.edu	37	chr6	43250675	43250675	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	agcctcaggctaatgggaagGaggaagaggaggaggaggag	20	4	1	1	rs543120452		TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr6:43250675G>T	ENST00000259750.4	+	14	2280	c.2197G>T	c.(2197-2199)Gag>Tag	p.E733*		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	733	Glu-rich.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			TAATGGGAaggaggaagagga	0.582																																					p.E733X		Atlas-SNP	.											.	TTBK1	124	.	0			c.G2197T						.						27	27	27					6																	43250675		2203	4300	6503	SO:0001587	stop_gained	84630	exon14			GGGAAGGAGGAAG	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.2197G>T	chr6.hg19:g.43250675G>T	ENSP00000259750:p.Glu733*	56.0	0.0		66.0	25.0	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Nonsense_Mutation	SNP	ENST00000259750.4	hg19	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	G	36	5.922496	0.97105	.	.	ENSG00000146216	ENST00000259750	.	.	.	4.12	4.12	0.48240	.	0.573824	0.14998	N	0.286270	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	9.3516	0.38142	0.0:0.0:0.7862:0.2138	.	.	.	.	X	733	.	ENSP00000259750:E733X	E	+	1	0	TTBK1	43358653	0.371000	0.25056	0.998000	0.56505	0.949000	0.60115	0.574000	0.23714	1.835000	0.53391	0.555000	0.69702	GAG	.	.		0.582	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			T	43250675	G	T	43250675	4	4	66	1	0	0	0	0	0	1	0	0	16691	1175	41	3	2247	3	TTBK1	6	43250675	Nonsense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	18402830	43250675	127864392	34	8518										
SLC16A10	117247	hgsc.bcm.edu	37	chr6	111540208	111540208	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	attggatttctgctcggattCatgtctatacccatgactgt	8	9	3	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr6:111540208C>T	ENST00000368851.5	+	5	1453	c.1278C>T	c.(1276-1278)ttC>ttT	p.F426F	SLC16A10_ENST00000368850.3_Silent_p.F112F	NM_018593.4	NP_061063.2	Q8TF71	MOT10_HUMAN	solute carrier family 16 (aromatic amino acid transporter), member 10	426					amino acid transport (GO:0006865)|aromatic amino acid transport (GO:0015801)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)	12		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)	Droxidopa(DB06262)|Glycine(DB00145)|L-Alanine(DB00160)|L-Arginine(DB00125)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Cystine(DB00138)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Histidine(DB00117)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Lysine(DB00123)|L-Methionine(DB00134)|L-Phenylalanine(DB00120)|L-Proline(DB00172)|L-Serine(DB00133)|L-Threonine(DB00156)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|L-Valine(DB00161)|Liothyronine(DB00279)|Liotrix(DB01583)|Pyruvic acid(DB00119)	TGCTCGGATTCATGTCTATAC	0.408																																					p.F426F		Atlas-SNP	.											.	SLC16A10	33	.	0			c.C1278T						.						143	126	132					6																	111540208		2203	4300	6503	SO:0001819	synonymous_variant	117247	exon5			CGGATTCATGTCT	AF116652	CCDS5089.1	6q21-q22	2014-01-28	2013-07-18		ENSG00000112394	ENSG00000112394		"Solute carriers"	17027	protein-coding gene	gene with protein product		607550	"solute carrier family 16 (monocarboxylic acid transporters), member 10"			11278508, 11827462	Standard	NM_018593		Approved	TAT1, MCT10	uc003pus.3	Q8TF71	OTTHUMG00000015371	ENST00000368851.5:c.1278C>T	chr6.hg19:g.111540208C>T		195.0	0.0		195.0	82.0	NM_018593	B3KWY0|Q6ZMG0|Q8WVI5	Silent	SNP	ENST00000368851.5	hg19	CCDS5089.1																																																																																			.	.		0.408	SLC16A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041822.2			T	111540208	C	T	111540208	2	4	66	1	0	0	0	0	0	0	0	1	14418	825	29	3		3	SLC16A10	6	111540208	Silent	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	68289533	111540208	59574859	35	8519										
IL20RA	53832	hgsc.bcm.edu	37	chr6	137323486	137323486	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gtcaaattcatttccataaaTcaaaatctataaagagaaaa	3	6	4	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr6:137323486T>C	ENST00000316649.5	-	7	1106	c.871A>G	c.(871-873)Att>Gtt	p.I291V	RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000367748.1_Missense_Mutation_p.I180V|IL20RA_ENST00000541547.1_Missense_Mutation_p.I242V|IL20RA_ENST00000468393.1_5'Flank	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha	291					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		TTTCCATAAATCAAAATCTAT	0.308																																					p.I291V		Atlas-SNP	.											.	IL20RA	54	.	0			c.A871G						.						22	26	24					6																	137323486		2147	4196	6343	SO:0001583	missense	53832	exon7			CATAAATCAAAAT	AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"Interleukins and interleukin receptors"	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.871A>G	chr6.hg19:g.137323486T>C	ENSP00000314976:p.Ile291Val	71.0	0.0		73.0	20.0	NM_014432	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Missense_Mutation	SNP	ENST00000316649.5	hg19	CCDS5181.1	.	.	.	.	.	.	.	.	.	.	T	9.284	1.048943	0.19827	.	.	ENSG00000016402	ENST00000316649;ENST00000367748;ENST00000541547	T;T;T	0.61274	0.37;1.84;0.12	5.81	4.62	0.57501	.	0.684874	0.14796	N	0.297930	T	0.34048	0.0884	M	0.61703	1.905	0.30836	N	0.73616	P;P	0.39181	0.663;0.473	B;B	0.35278	0.199;0.091	T	0.11690	-1.0577	10	0.32370	T	0.25	-6.8675	10.2775	0.43519	0.0:0.0:0.3189:0.6811	.	180;291	Q9UHF4-2;Q9UHF4	.;I20RA_HUMAN	V	291;180;242	ENSP00000314976:I291V;ENSP00000356722:I180V;ENSP00000437843:I242V	ENSP00000314976:I291V	I	-	1	0	IL20RA	137365179	1.000000	0.71417	1.000000	0.80357	0.068000	0.16541	1.044000	0.30329	0.989000	0.38761	0.533000	0.62120	ATT	.	.		0.308	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432		C	137323486	T	C	137323486	3	2	66	1	0	0	0	0	1	0	0	0	7677	1435	50	2	794	2	IL20RA	6	137323486	Missense_Mutation	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	25783278	137323486	33791581	36	8520										
EIF4H	7458	hgsc.bcm.edu	37	chr7	73609125	73609125	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tagtcgcccaggcgaccggcGaacaggcccccccatgggca	13	17	0	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr7:73609125G>T	ENST00000265753.8	+	6	663	c.524G>T	c.(523-525)cGa>cTa	p.R175L	EIF4H_ENST00000495187.1_3'UTR|EIF4H_ENST00000353999.6_Missense_Mutation_p.R155L	NM_022170.1	NP_071496.1	Q15056	IF4H_HUMAN	eukaryotic translation initiation factor 4H	175					cellular protein metabolic process (GO:0044267)|developmental growth (GO:0048589)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|sexual reproduction (GO:0019953)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|lung(2)|prostate(1)	4						GGCGACCGGCGAACAGGCCCC	0.572																																					p.R175L		Atlas-SNP	.											.	EIF4H	19	.	0			c.G524T						.						49	59	56					7																	73609125		2202	4299	6501	SO:0001583	missense	7458	exon6			ACCGGCGAACAGG		CCDS5564.1, CCDS5565.1	7q11.23	2013-02-12	2006-11-27	2006-11-27	ENSG00000106682	ENSG00000106682		"RNA binding motif (RRM) containing"	12741	protein-coding gene	gene with protein product		603431	"Williams-Beuren syndrome chromosome region 1"	WBSCR1		9516461, 15078951	Standard	NM_022170		Approved	WSCR1, KIAA0038	uc003uad.1	Q15056	OTTHUMG00000023025	ENST00000265753.8:c.524G>T	chr7.hg19:g.73609125G>T	ENSP00000265753:p.Arg175Leu	72.0	0.0		63.0	16.0	NM_022170	A8K3R1|D3DXF6|D3DXF8	Missense_Mutation	SNP	ENST00000265753.8	hg19	CCDS5564.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.490058	0.84962	.	.	ENSG00000106682	ENST00000265753;ENST00000353999	T;T	0.37411	1.32;1.2	4.61	4.61	0.57282	.	0.000000	0.64402	D	0.000001	T	0.50360	0.1611	L	0.56769	1.78	0.80722	D	1	P;P	0.42785	0.79;0.686	P;P	0.56343	0.796;0.63	T	0.37056	-0.9722	10	0.30078	T	0.28	-5.9129	14.3085	0.66400	0.0:0.0:1.0:0.0	.	155;175	Q15056-2;Q15056	.;IF4H_HUMAN	L	175;155	ENSP00000265753:R175L;ENSP00000265754:R155L	ENSP00000265753:R175L	R	+	2	0	EIF4H	73247061	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.946000	0.56644	2.397000	0.81536	0.563000	0.77884	CGA	.	.		0.572	EIF4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252375.2	NM_022170		T	73609125	G	T	73609125	3	4	66	1	0	0	0	0	1	0	0	0	5041	1058	37	1	546	1	EIF4H	7	73609125	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10		73609125	85529538	37	8521										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77551943	77551943	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gtgtactcccaacttaggatAcccaaaggacaataacaaat	6	10	0	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr7:77551943A>G	ENST00000248550.7	+	10	1043	c.967A>G	c.(967-969)Acc>Gcc	p.T323A	PHTF2_ENST00000424760.1_Missense_Mutation_p.T285A|PHTF2_ENST00000307305.8_Missense_Mutation_p.T285A|PHTF2_ENST00000422959.2_Missense_Mutation_p.T289A|PHTF2_ENST00000450574.1_Missense_Mutation_p.T289A|PHTF2_ENST00000415251.2_Missense_Mutation_p.T285A|PHTF2_ENST00000454592.1_3'UTR|PHTF2_ENST00000275575.7_Missense_Mutation_p.T285A|PHTF2_ENST00000416283.2_Missense_Mutation_p.T289A			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	323					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						AACTTAGGATACCCAAAGGAC	0.373																																					p.T289A		Atlas-SNP	.											.	PHTF2	104	.	0			c.A865G						.						56	52	54					7																	77551943		1835	4086	5921	SO:0001583	missense	57157	exon9			TAGGATACCCAAA	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.967A>G	chr7.hg19:g.77551943A>G	ENSP00000248550:p.Thr323Ala	86.0	0.0		60.0	17.0	NM_001127359	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	hg19		.	.	.	.	.	.	.	.	.	.	A	0.017	-1.492519	0.01009	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000415251;ENST00000275575;ENST00000450574;ENST00000416283;ENST00000248550	.	.	.	5.33	-0.00888	0.14003	.	0.904024	0.09556	N	0.786323	T	0.16854	0.0405	N	0.14661	0.345	0.23386	N	0.997783	B;B;B;B;B;B;B;B;B	0.19073	0.033;0.0;0.0;0.0;0.0;0.004;0.0;0.0;0.001	B;B;B;B;B;B;B;B;B	0.17979	0.02;0.0;0.001;0.0;0.0;0.005;0.0;0.0;0.001	T	0.32481	-0.9905	9	0.07325	T	0.83	0.2545	6.1327	0.20215	0.6723:0.1247:0.203:0.0	.	127;285;148;289;323;289;285;285;285	Q8WVD6;Q8N3S3-4;Q8N5I6;Q8N3S3-2;Q8N3S3;G5E9H7;Q8N3S3-3;B3KQZ2;E9PEE3	.;.;.;.;PHTF2_HUMAN;.;.;.;.	A	289;289;285;285;285;285;289;289;323	.	ENSP00000248550:T323A	T	+	1	0	PHTF2	77389879	0.027000	0.19231	0.695000	0.30226	0.088000	0.18126	0.078000	0.14761	-0.240000	0.09696	0.383000	0.25322	ACC	.	.		0.373	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		G	77551943	A	G	77551943	3	3	66	1	0	0	0	0	1	0	0	0	11872	391	14	2	899	2	PHTF2	7	77551943	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	3942818	77551943	81586720	38	8522										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88963648	88963648	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ccacgttcaaagcaaggatgGccacaccactcttcaatggc	8	14	3	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr7:88963648G>T	ENST00000333190.4	+	4	1961	c.1352G>T	c.(1351-1353)gGc>gTc	p.G451V		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	451							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AGCAAGGATGGCCACACCACT	0.403										HNSCC(36;0.09)																											p.G451V		Atlas-SNP	.											.	ZNF804B	322	.	0			c.G1352T						.						74	71	72					7																	88963648		2200	4297	6497	SO:0001583	missense	219578	exon4			AGGATGGCCACAC	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1352G>T	chr7.hg19:g.88963648G>T	ENSP00000329638:p.Gly451Val	98.0	0.0		98.0	28.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124073	0.56613	.	.	ENSG00000182348	ENST00000333190	T	0.10763	2.84	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000003	T	0.37348	0.1000	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.06752	-1.0809	10	0.87932	D	0	-14.3725	19.5755	0.95441	0.0:0.0:1.0:0.0	.	451	A4D1E1	Z804B_HUMAN	V	451	ENSP00000329638:G451V	ENSP00000329638:G451V	G	+	2	0	ZNF804B	88801584	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	7.024000	0.76443	2.865000	0.98341	0.655000	0.94253	GGC	.	.		0.403	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88963648	G	T	88963648	3	4	66	1	0	0	0	0	1	0	0	0	18186	1203	42	3	1366	3	ZNF804B	7	88963648	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	11411705	88963648	70175015	39	8523										
GNB2	2783	hgsc.bcm.edu	37	chr7	100275413	100275413	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gcttcctggatgacaaccaaAtcatcaccagctctggggat	9	12	3	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr7:100275413A>G	ENST00000303210.4	+	7	951	c.469A>G	c.(469-471)Atc>Gtc	p.I157V	GNB2_ENST00000393924.1_Missense_Mutation_p.I157V|GNB2_ENST00000424361.1_Missense_Mutation_p.I113V|GNB2_ENST00000393926.1_Missense_Mutation_p.I157V|GNB2_ENST00000419828.1_Missense_Mutation_p.I57V|GNB2_ENST00000427895.1_Missense_Mutation_p.I57V|GNB2_ENST00000436220.1_Missense_Mutation_p.I113V	NM_005273.3	NP_005264.2	P62879	GBB2_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2	157					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|lung(3)|ovary(2)|prostate(1)	7	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)	Ovarian(593;0.238)				TGACAACCAAATCATCACCAG	0.632																																					p.I157V		Atlas-SNP	.											.	GNB2	29	.	0			c.A469G						.						64	53	56					7																	100275413		2203	4300	6503	SO:0001583	missense	2783	exon7			AACCAAATCATCA	M16514	CCDS5703.1	7q21.3-q22.1	2013-01-10			ENSG00000172354	ENSG00000172354		"WD repeat domain containing"	4398	protein-coding gene	gene with protein product	"G protein, beta-2 subunit", "guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 2", "signal-transducing guanine nucleotide-binding regulatory protein beta subunit", "transducin beta chain 2"	139390				9799793	Standard	NM_005273		Approved		uc003uwb.3	P62879	OTTHUMG00000137419	ENST00000303210.4:c.469A>G	chr7.hg19:g.100275413A>G	ENSP00000305260:p.Ile157Val	46.0	0.0		56.0	16.0	NM_005273	B3KPU1|P11016|P54312	Missense_Mutation	SNP	ENST00000303210.4	hg19	CCDS5703.1	.	.	.	.	.	.	.	.	.	.	.	26.1	4.701133	0.88924	.	.	ENSG00000172354	ENST00000303210;ENST00000451587;ENST00000436220;ENST00000424361;ENST00000419828;ENST00000427895;ENST00000393926;ENST00000431068;ENST00000393924	T;T;T;T;T;T;T;T;T	0.61392	0.11;0.11;0.11;0.11;0.11;0.11;0.11;0.11;0.11	4.79	4.79	0.61399	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.54175	0.1842	N	0.16307	0.4	0.58432	D	0.999997	P	0.38617	0.64	P	0.51193	0.662	T	0.59778	-0.7390	10	0.59425	D	0.04	-2.8288	12.3252	0.55007	1.0:0.0:0.0:0.0	.	157	P62879	GBB2_HUMAN	V	157;157;113;113;57;57;157;157;157	ENSP00000305260:I157V;ENSP00000399904:I157V;ENSP00000401873:I113V;ENSP00000389391:I113V;ENSP00000390543:I57V;ENSP00000400286:I57V;ENSP00000377503:I157V;ENSP00000390077:I157V;ENSP00000377501:I157V	ENSP00000305260:I157V	I	+	1	0	GNB2	100113349	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.220000	0.78008	2.014000	0.59158	0.379000	0.24179	ATC	.	.		0.632	GNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268391.2	NM_005273		G	100275413	A	G	100275413	3	3	66	1	0	0	0	0	1	0	0	0	6525	101	4	2	491	2	GNB2	7	100275413	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	11311765	100275413	58863250	40	8524										
NDUFA5	4698	hgsc.bcm.edu	37	chr7	123197496	123197496	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	cacagccaatcccacaaggcCagtggtctgttcaaaaacaa	7	13	2	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr7:123197496C>A	ENST00000355749.2	-	2	487	c.28G>T	c.(28-30)Ggc>Tgc	p.G10C	NDUFA5_ENST00000471770.1_Missense_Mutation_p.G10C|NDUFA5_ENST00000467117.1_5'UTR	NM_001282419.1|NM_005000.2	NP_001269348.1|NP_004991.1	Q16718	NDUA5_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5	10					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.G10S(1)		large_intestine(1)|urinary_tract(1)	2						CCCACAAGGCCAGTGGTCTGT	0.438																																					p.G10C		Atlas-SNP	.											NDUFA5,bladder,carcinoma,0,1	NDUFA5	6	.	1	Substitution - Missense(1)	urinary_tract(1)	c.G28T						.						117	88	98					7																	123197496		2203	4300	6503	SO:0001583	missense	4698	exon2			CAAGGCCAGTGGT		CCDS5788.1, CCDS64760.1, CCDS75655.1, CCDS75656.1	7q31.33	2013-06-19	2013-06-19		ENSG00000128609	ENSG00000128609		"Mitochondrial respiratory chain complex / Complex I"	7688	protein-coding gene	gene with protein product	"complex I 13kDa subunit B", "ubiquinone reductase", "type I dehydrogenase", "NADH-ubiquinone oxidoreductase 13 kDa-B subunit"	601677	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5 (13kD, B13)", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDa"			9763677, 9021153	Standard	XM_005250371		Approved	B13, NUFM, CI-13KD-B, UQOR13, CI-13kB	uc003vks.3	Q16718	OTTHUMG00000157348	ENST00000355749.2:c.28G>T	chr7.hg19:g.123197496C>A	ENSP00000347988:p.Gly10Cys	96.0	0.0		103.0	38.0	NM_005000	B2RD98|Q5H9R2|Q6IRX7	Missense_Mutation	SNP	ENST00000355749.2	hg19	CCDS5788.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.2|26.2	4.713270|4.713270	0.89112|0.89112	.|.	.|.	ENSG00000128609|ENSG00000128609	ENST00000471770;ENST00000355749;ENST00000470123;ENST00000340034|ENST00000378795	.|.	.|.	.|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|.	.|.	.|.	.|.	D|D	0.87374|0.87374	0.6161|0.6161	H|H	0.94847|0.94847	3.59|3.59	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.993|.	D|D	0.90497|0.90497	0.4471|0.4471	8|5	0.87932|.	D|.	0|.	.|.	18.4182|18.4182	0.90577|0.90577	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	10;10|.	E7ENS4;Q16718|.	.;NDUA5_HUMAN|.	C|L	10;10;20;10|5	.|.	ENSP00000341719:G10C|.	G|W	-|-	1|2	0|0	NDUFA5|NDUFA5	122984732|122984732	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	4.896000|4.896000	0.63222|0.63222	2.640000|2.640000	0.89533|0.89533	0.655000|0.655000	0.94253|0.94253	GGC|TGG	.	.		0.438	NDUFA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348533.1	NM_005000		A	123197496	C	A	123197496	3	1	66	1	0	0	0	0	1	0	0	0	10277	594	21	3	338	3	NDUFA5	7	123197496	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	22922083	123197496	35941167	41	8525										
POT1	25913	hgsc.bcm.edu	37	chr7	124475442	124475442	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	actattaaacttgttcgagaGtttgcaaatttcactgagtg	8	6	1	2			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr7:124475442G>A	ENST00000357628.3	-	15	1994	c.1396C>T	c.(1396-1398)Ctc>Ttc	p.L466F	POT1_ENST00000393329.1_Missense_Mutation_p.L335F	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	466					DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47						TTGTTCGAGAGTTTGCAAATT	0.358																																					p.L466F	Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)	Atlas-SNP	.											.	POT1	186	.	0			c.C1396T						.						136	137	137					7																	124475442		2203	4300	6503	SO:0001583	missense	25913	exon15			TCGAGAGTTTGCA	AK022580	CCDS5793.1	7q31.33	2013-01-21	2013-01-21		ENSG00000128513	ENSG00000128513			17284	protein-coding gene	gene with protein product		606478	"protection of telomeres 1 homolog (S. pombe)"			11349150, 12391173	Standard	NR_003102		Approved	hPot1, DKFZp586D211	uc003vlm.3	Q9NUX5	OTTHUMG00000157194	ENST00000357628.3:c.1396C>T	chr7.hg19:g.124475442G>A	ENSP00000350249:p.Leu466Phe	84.0	0.0		85.0	15.0	NM_015450	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Missense_Mutation	SNP	ENST00000357628.3	hg19	CCDS5793.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.603755	0.87157	.	.	ENSG00000128513	ENST00000357628;ENST00000393329;ENST00000451720;ENST00000265391	T;T	0.62364	0.03;0.03	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.80336	0.4604	M	0.78049	2.395	0.54753	D	0.999989	D	0.89917	1.0	D	0.87578	0.998	T	0.82464	-0.0444	10	0.87932	D	0	-10.4882	17.938	0.89018	0.0:0.0:1.0:0.0	.	466	Q9NUX5	POTE1_HUMAN	F	466;335;466;465	ENSP00000350249:L466F;ENSP00000377002:L335F	ENSP00000265391:L465F	L	-	1	0	POT1	124262678	1.000000	0.71417	0.623000	0.29173	0.990000	0.78478	4.205000	0.58466	2.648000	0.89879	0.591000	0.81541	CTC	.	.		0.358	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1			A	124475442	G	A	124475442	3	1	66	1	0	0	0	0	1	0	0	0	12269	1029	36	3	528	3	POT1	7	124475442	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	1277946	124475442	34663221	42	8526										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131925877	131925877	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gtcgcctgagccaaggcactCgccgcagctctgatactgac	11	15	1	3			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr7:131925877C>A	ENST00000359827.3	-	5	2514	c.1552G>T	c.(1552-1554)Gag>Tag	p.E518*	PLXNA4_ENST00000321063.4_Nonsense_Mutation_p.E518*			Q9HCM2	PLXA4_HUMAN	plexin A4	518	PSI 1.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CCAAGGCACTCGCCGCAGCTC	0.597																																					p.E518X		Atlas-SNP	.											.	PLXNA4	873	.	0			c.G1552T						.						42	49	46					7																	131925877		2139	4276	6415	SO:0001587	stop_gained	91584	exon5			GGCACTCGCCGCA	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.1552G>T	chr7.hg19:g.131925877C>A	ENSP00000352882:p.Glu518*	77.0	0.0		75.0	31.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Nonsense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	42	9.366496	0.99150	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	.	.	.	5.23	5.23	0.72850	.	0.053552	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	17.5561	0.87890	0.0:1.0:0.0:0.0	.	.	.	.	X	518	.	ENSP00000323194:E518X	E	-	1	0	PLXNA4	131576417	1.000000	0.71417	0.978000	0.43139	0.995000	0.86356	4.521000	0.60532	2.425000	0.82216	0.561000	0.74099	GAG	.	.		0.597	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	131925877	C	A	131925877	4	1	66	1	0	0	0	0	0	1	0	0	12131	893	31	1	4244	1	PLXNA4	7	131925877	Nonsense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	7450435	131925877	27212786	43	8527										
TAS2R38	5726	hgsc.bcm.edu	37	chr7	141673256	141673256	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctcaacttctggaagtgggtAagctggatagcactcaggaa	12	8	3	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr7:141673256A>G	ENST00000547270.1	-	1	317	c.234T>C	c.(232-234)ctT>ctC	p.L78L		NM_176817.4	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	78					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			NS(2)|breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)|stomach(1)	21	Melanoma(164;0.0171)					GGAAGTGGGTAAGCTGGATAG	0.517																																					p.L78L		Atlas-SNP	.											.	TAS2R38	51	.	0			c.T234C						.						147	140	143					7																	141673256		2203	4300	6503	SO:0001819	synonymous_variant	5726	exon1			GTGGGTAAGCTGG	AF494231	CCDS34765.1	7q34	2012-10-03	2003-05-29	2003-05-30	ENSG00000257138	ENSG00000257138		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	9584	protein-coding gene	gene with protein product		607751	"phenylthiocarbamide tasting"	PTC		12624758, 12584440	Standard	NM_176817		Approved	T2R61	uc003vwx.1	P59533	OTTHUMG00000158374	ENST00000547270.1:c.234T>C	chr7.hg19:g.141673256A>G		73.0	0.0		69.0	28.0	NM_176817	A4D1U6|P59552|Q2M3E8|Q645W3|Q86UK3	Silent	SNP	ENST00000547270.1	hg19	CCDS34765.1																																																																																			.	.		0.517	TAS2R38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350810.2	NM_176817		G	141673256	A	G	141673256	2	3	66	1	0	0	0	0	0	0	0	1	15590	349	13	2		2	TAS2R38	7	141673256	Silent	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	9747379	141673256	17465407	44	8528										
NOBOX	135935	hgsc.bcm.edu	37	chr7	144096113	144096113	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	agcaacatccatcagcagtgGcatcagttggggggtgtgga	15	8	2	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr7:144096113G>T	ENST00000467773.1	-	8	1398	c.1399C>A	c.(1399-1401)Cca>Aca	p.P467T	NOBOX_ENST00000483238.1_Missense_Mutation_p.P435T|NOBOX_ENST00000223140.5_Missense_Mutation_p.P350T	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	467	Pro-rich.				oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					ATCAGCAGTGGCATCAGTTGG	0.627																																					p.P467T		Atlas-SNP	.											.	NOBOX	130	.	0			c.C1399A						.						9	10	10					7																	144096113		1915	4132	6047	SO:0001583	missense	135935	exon8			GCAGTGGCATCAG			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"Homeoboxes / PRD class"	22448	protein-coding gene	gene with protein product	"newborn ovary homeobox-encoding gene"	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1399C>A	chr7.hg19:g.144096113G>T	ENSP00000419457:p.Pro467Thr	130.0	0.0		92.0	26.0	NM_001080413	A6NCD3|A8MZN5	Missense_Mutation	SNP	ENST00000467773.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.42	1.931841	0.34096	.	.	ENSG00000106410	ENST00000483238;ENST00000467773;ENST00000223140	D;D;D	0.96685	-3.5;-4.09;-3.61	4.78	3.89	0.44902	.	0.309371	0.32301	N	0.006296	D	0.97266	0.9106	M	0.69823	2.125	0.44500	D	0.997447	D	0.89917	1.0	D	0.91635	0.999	D	0.95953	0.8956	10	0.33141	T	0.24	-6.5832	11.1343	0.48365	0.0921:0.0:0.9079:0.0	.	467	O60393	NOBOX_HUMAN	T	435;467;350	ENSP00000419565:P435T;ENSP00000419457:P467T;ENSP00000223140:P350T	ENSP00000223140:P350T	P	-	1	0	NOBOX	143727046	1.000000	0.71417	0.723000	0.30687	0.045000	0.14185	1.974000	0.40559	0.995000	0.38917	0.655000	0.94253	CCA	.	.		0.627	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420		T	144096113	G	T	144096113	3	4	66	1	0	0	0	0	1	0	0	0	10521	1203	42	3	688	3	NOBOX	7	144096113	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	2422857	144096113	15042550	45	8529										
INSIG1	3638	hgsc.bcm.edu	37	chr7	155093275	155093275	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ttgtcaacttttttaaaacaGctgttgttggcctactgtac	7	8	1	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr7:155093275G>C	ENST00000340368.4	+	3	623		c.e3-1		INSIG1_ENST00000342407.5_Intron|INSIG1_ENST00000344756.4_Intron	NM_005542.4	NP_005533.2	O15503	INSI1_HUMAN	insulin induced gene 1						cell proliferation (GO:0008283)|cholesterol biosynthetic process (GO:0006695)|cranial suture morphogenesis (GO:0060363)|inner ear morphogenesis (GO:0042472)|metabolic process (GO:0008152)|middle ear morphogenesis (GO:0042474)|negative regulation of cargo loading into COPII-coated vesicle (GO:1901303)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of steroid biosynthetic process (GO:0010894)|palate development (GO:0060021)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|SREBP-SCAP-Insig complex (GO:0032937)				endometrium(2)|kidney(2)|large_intestine(1)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	19	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTTTAAAACAGCTGTTGTTGG	0.418																																					.		Atlas-SNP	.											.	INSIG1	20	.	0			c.413-1G>C						.						160	151	154					7																	155093275		2203	4300	6503	SO:0001630	splice_region_variant	3638	exon3			AAAACAGCTGTTG		CCDS5938.1, CCDS5939.1	7q36	2008-07-18			ENSG00000186480	ENSG00000186480			6083	protein-coding gene	gene with protein product	"INSIG-1 membrane protein"	602055				9268630	Standard	NM_005542		Approved	CL-6, MGC1405	uc003wly.3	O15503	OTTHUMG00000151330	ENST00000340368.4:c.413-1G>C	chr7.hg19:g.155093275G>C		99.0	0.0		66.0	21.0	NM_005542	A4D2N1|A8K6L0|Q53XW8|Q9BUV5	Splice_Site	SNP	ENST00000340368.4	hg19	CCDS5938.1	.	.	.	.	.	.	.	.	.	.	G	12.21	1.868648	0.32977	.	.	ENSG00000186480	ENST00000340368;ENST00000476756	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8026	0.92023	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	INSIG1	154724208	1.000000	0.71417	0.994000	0.49952	0.097000	0.18754	9.451000	0.97610	2.602000	0.87976	0.655000	0.94253	.	.	.		0.418	INSIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322244.3	NM_198336	Intron	C	155093275	G	C	155093275	5	2	66	1	0	0	0	0	0	0	1	0	7774	985	34	4	418	4	INSIG1	7	155093275	Splice_Site	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	10997162	155093275	4045388	46	8530										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77766040	77766041	+	Frame_Shift_Ins	INS	-	-	A													0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	agcagaaacaaaagataatgINSaaaaaagagaactcactaat							TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr8:77766040_77766041insA	ENST00000521891.2	+	10	7331_7332	c.6883_6884insA	c.(6883-6885)gaafs	p.E2295fs	ZFHX4_ENST00000518282.1_Frame_Shift_Ins_p.E2269fs|ZFHX4_ENST00000455469.2_Frame_Shift_Ins_p.E2250fs|ZFHX4_ENST00000050961.6_Frame_Shift_Ins_p.E2250fs	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2250					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAAAGATAATGAAAAAAGAGAA	0.396										HNSCC(33;0.089)																											p.E2295fs		Atlas-INDEL	.											.	ZFHX4	878	.	0			c.6883_6884insA						.																																			SO:0001589	frameshift_variant	79776	exon10			.		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6889dupA	chr8.hg19:g.77766046_77766046dupA	ENSP00000430497:p.Glu2295fs	94.0	0.0		139.0	67.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Frame_Shift_Ins	INS	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.396	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77766041	-	A	77766040	7	5	66	1	0	1	1	0	0	0	0	0	17650	1291	45	0	6917	0	ZFHX4	8	77766040	Frame_Shift_Ins	INS	-	TCGA-CC-A3MC-01A-11D-A22F-10		77766040	68597982	47	8531										
TM7SF4	81501	hgsc.bcm.edu	37	chr8	105361460	105361460	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ttcgctcgtcctgcttggcaCtggcctcttcatgaagcgat	10	13	2	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr8:105361460C>A	ENST00000297581.2	+	2	729	c.680C>A	c.(679-681)aCt>aAt	p.T227N	DCSTAMP_ENST00000517991.1_Missense_Mutation_p.T227N|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	227					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											CTGCTTGGCACTGGCCTCTTC	0.493																																					p.T227N		Atlas-SNP	.											.	.	.	.	0			c.C680A						.						101	93	96					8																	105361460		2203	4300	6503	SO:0001583	missense	81501	exon2			TTGGCACTGGCCT	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"Dendritic cells (DC)-specific transmembrane protein", "IL-Four INDuced"	605933	"transmembrane 7 superfamily member 4"	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.680C>A	chr8.hg19:g.105361460C>A	ENSP00000297581:p.Thr227Asn	47.0	0.0		97.0	14.0	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	hg19	CCDS6301.1	.	.	.	.	.	.	.	.	.	.	C	19.86	3.906201	0.72868	.	.	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.33654	1.4	5.52	5.52	0.82312	.	0.047727	0.85682	D	0.000000	T	0.58278	0.2111	M	0.64997	1.995	0.53005	D	0.99996	D	0.89917	1.0	D	0.78314	0.991	T	0.54840	-0.8233	9	.	.	.	-17.6184	17.6314	0.88109	0.0:1.0:0.0:0.0	.	227	Q9H295	TM7S4_HUMAN	N	227	ENSP00000297581:T227N	.	T	+	2	0	TM7SF4	105430636	1.000000	0.71417	0.997000	0.53966	0.919000	0.55068	4.683000	0.61679	2.624000	0.88883	0.555000	0.69702	ACT	.	.		0.493	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		A	105361460	C	A	105361460	3	1	66	1	0	0	0	0	1	0	0	0	15991	565	20	3	682	3	TM7SF4	8	105361460	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	27595420	105361460	41002562	48	8532										
EIF3E	3646	hgsc.bcm.edu	37	chr8	109229677	109229726	+	Splice_Site	DEL	TGCATTAAGATATCTAAGAAAAAATATAAAAGTTATTTAATAACTTACCC	TGCATTAAGATATCTAAGAAAAAATATAAAAGTTATTTAATAACTTACCC	-													0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tgtggacacattgtctgaatTgcattaagatatctaagaaa							TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	TGCATTAAGATATCTAAGAAAAAATATAAAAGTTATTTAATAACTTACCC	TGCATTAAGATATCTAAGAAAAAATATAAAAGTTATTTAATAACTTACCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr8:109229677_109229726delTGCATTAAGATATCTAAGAAAAAATATAAAAGTTATTTAATAACTTACCC	ENST00000220849.5	-	8	785_797	c.723_735delGGGTAAGTTATTAAATAACTTTTATATTTTTTCTTAGATATCTTAATGCA	c.(721-735)cagggtaagttatta>ca	p.QGKLL241fs	EIF3E_ENST00000519030.1_Splice_Site_p.QGKLL148fs|EIF3E_ENST00000519517.1_5'UTR	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E										EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			TTGTCTGAATTGCATTAAGATATCTAAGAAAAAATATAAAAGTTATTTAATAACTTACCCAGGGTGAGAT	0.336																																					p.241_246del	GBM(15;360 410 8460 34179 52246)	Pindel	.											.	EIF3E	73	.	0			c.723_736del						.																																			SO:0001630	splice_region_variant	3646	exon8			.	U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"eukaryotic translation initiation factor 3, subunit 6 48kDa"	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.723-1GGGTAAGTTATTAAATAACTTTTATATTTTTTCTTAGATATCTTAATGCA>-	chr8.hg19:g.109229677_109229726delTGCATTAAGATATCTAAGAAAAAATATAAAAGTTATTTAATAACTTACCC		12.0	0.0		19.0	15.0	NM_001568		Frame_Shift_Del	DEL	ENST00000220849.5	hg19	CCDS6308.1																																																																																			.	.		0.336	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568	Frame_Shift_Del	-	109229726	TGCATTAAGATATCTAAGAAAAAATATAAAAGTTATTTAATAACTTACCC	-	109229677	8	5	66	1	0	1	0	1	0	0	1	0	5017	1799	63	0	626	0	EIF3E	8	109229677	Splice_Site	DEL	TGCATTAAGATATCTAAGAAAAAATATAAAAGTTATTTAATAACTTACCC	TCGA-CC-A3MC-01A-11D-A22F-10	3868217	109229677	37134345	49	8533										
SUSD3	203328	hgsc.bcm.edu	37	chr9	95846880	95846880	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gcagcgtggacaaggaccctGggatccccagagctctaagc	13	13	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr9:95846880G>A	ENST00000375472.3	+	5	655	c.619G>A	c.(619-621)Ggg>Agg	p.G207R	SUSD3_ENST00000375469.1_Missense_Mutation_p.G194R	NM_145006.2	NP_659443.1	Q96L08	SUSD3_HUMAN	sushi domain containing 3	207						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	13						CAAGGACCCTGGGATCCCCAG	0.617																																					p.G207R		Atlas-SNP	.											.	SUSD3	32	.	0			c.G619A						.						108	99	102					9																	95846880		2203	4300	6503	SO:0001583	missense	203328	exon5			GACCCTGGGATCC	AK128289	CCDS6701.1, CCDS69620.1, CCDS75857.1	9q22.32	2004-01-29			ENSG00000157303	ENSG00000157303			28391	protein-coding gene	gene with protein product						12975309	Standard	NM_001287007		Approved	MGC26847	uc004atb.3	Q96L08	OTTHUMG00000020241	ENST00000375472.3:c.619G>A	chr9.hg19:g.95846880G>A	ENSP00000364621:p.Gly207Arg	43.0	0.0		36.0	9.0	NM_145006	Q49AA6|Q6UXV7	Missense_Mutation	SNP	ENST00000375472.3	hg19	CCDS6701.1	.	.	.	.	.	.	.	.	.	.	G	2.695	-0.272242	0.05716	.	.	ENSG00000157303	ENST00000375472;ENST00000375469	T;T	0.60040	0.22;0.63	4.33	-6.6	0.01824	.	1.212030	0.06033	N	0.653491	T	0.31451	0.0797	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.13656	-1.0501	10	0.21540	T	0.41	-2.2038	0.3483	0.00345	0.3556:0.251:0.1658:0.2275	.	194;207	Q96L08-2;Q96L08	.;SUSD3_HUMAN	R	207;194	ENSP00000364621:G207R;ENSP00000364618:G194R	ENSP00000364618:G194R	G	+	1	0	SUSD3	94886701	0.025000	0.19082	0.000000	0.03702	0.006000	0.05464	-0.532000	0.06164	-1.418000	0.02014	-1.785000	0.00643	GGG	.	.		0.617	SUSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053120.1	NM_145006		A	95846880	G	A	95846880	3	1	66	1	0	0	0	0	1	0	0	0	15424	1348	47	3	637	3	SUSD3	9	95846880	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10		95846880	45366551	50	8534										
SURF4	6836	hgsc.bcm.edu	37	chr9	136234218	136234218	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	tggtgtcgatgtagtcgcgcTgctcgctccactggaaccac	12	13	0	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr9:136234218T>A	ENST00000371989.3	-	2	281	c.152A>T	c.(151-153)cAg>cTg	p.Q51L	SURF4_ENST00000485435.2_Missense_Mutation_p.Q51L|SURF4_ENST00000371991.3_Missense_Mutation_p.Q51L|SURF4_ENST00000467910.1_5'UTR|SURF4_ENST00000545297.1_Missense_Mutation_p.Q51L	NM_001280788.1|NM_001280790.1|NM_001280791.1|NM_033161.2	NP_001267717.1|NP_001267719.1|NP_001267720.1|NP_149351.1	O15260	SURF4_HUMAN	surfeit 4	51					Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(5)	8				OV - Ovarian serous cystadenocarcinoma(145;5.32e-07)|Epithelial(140;4.56e-06)|all cancers(34;4.25e-05)		GTAGTCGCGCTGCTCGCTCCA	0.612																																					p.Q51L		Atlas-SNP	.											.	SURF4	20	.	0			c.A152T						.						123	98	106					9																	136234218		2203	4300	6503	SO:0001583	missense	6836	exon2			TCGCGCTGCTCGC		CCDS6968.1, CCDS65177.1, CCDS65178.1, CCDS75929.1	9q33-q34	2008-07-21			ENSG00000148248	ENSG00000148248			11476	protein-coding gene	gene with protein product	"surfeit locus protein 4", "surface 4 integral membrane protein"	185660				8499913, 7540914	Standard	NM_033161		Approved	ERV29, FLJ22993, MGC102753	uc004cdj.3	O15260	OTTHUMG00000020868	ENST00000371989.3:c.152A>T	chr9.hg19:g.136234218T>A	ENSP00000361057:p.Gln51Leu	38.0	0.0		38.0	8.0	NM_033161	B7Z6A4|O60923|Q5T8U6|Q9UNZ0|Q9UNZ1	Missense_Mutation	SNP	ENST00000371989.3	hg19	CCDS6968.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.989404	0.93106	.	.	ENSG00000148248	ENST00000371989;ENST00000485435;ENST00000545297;ENST00000541390;ENST00000371991	.	.	.	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	D	0.85539	0.5720	M	0.93594	3.435	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;1.0	D;D;D;D	0.81914	0.978;0.992;0.973;0.995	D	0.89348	0.3659	9	0.87932	D	0	-5.6625	13.8621	0.63566	0.0:0.0:0.0:1.0	.	51;42;51;51	B7Z6A4;B7Z7A8;O15260-2;O15260	.;.;.;SURF4_HUMAN	L	51;51;51;42;51	.	ENSP00000361057:Q51L	Q	-	2	0	SURF4	135224039	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.912000	0.87465	1.858000	0.53909	0.533000	0.62120	CAG	.	.		0.612	SURF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054886.1	NM_033161		A	136234218	T	A	136234218	3	1	66	1	0	0	0	0	1	0	0	0	15420	1580	55	4	677	4	SURF4	9	136234218	Missense_Mutation	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	40387338	136234218	4979213	51	8535										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137630606	137630606	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ttctagggtcttcccggaccTccaggaaccatgggtcccac	10	15	2	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr9:137630606T>C	ENST00000371817.3	+	11	1860	c.1446T>C	c.(1444-1446)ccT>ccC	p.P482P		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	482	Interrupted collagenous region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TTCCCGGACCTCCAGGAACCA	0.557																																					p.P482P		Atlas-SNP	.											.	COL5A1	323	.	0			c.T1446C						.						68	80	76					9																	137630606		2203	4300	6503	SO:0001819	synonymous_variant	1289	exon11			CGGACCTCCAGGA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1446T>C	chr9.hg19:g.137630606T>C		76.0	0.0		62.0	18.0	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	hg19	CCDS6982.1																																																																																			.	.		0.557	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		C	137630606	T	C	137630606	2	2	66	1	0	0	0	0	0	0	0	1	3698	1538	54	2		2	COL5A1	9	137630606	Silent	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	1396388	137630606	3582825	52	8536										
STAM	8027	hgsc.bcm.edu	37	chr10	17730065	17730065	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	aaaaattaaaggctcttatgGttgaatggacagatgaattt	9	3	1	3			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr10:17730065G>A	ENST00000377524.3	+	5	552	c.337G>A	c.(337-339)Gtt>Att	p.V113I	STAM_ENST00000540523.1_Missense_Mutation_p.V2I	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	113	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						GGCTCTTATGGTTGAATGGAC	0.343																																					p.V113I		Atlas-SNP	.											.	STAM	60	.	0			c.G337A						.						116	121	119					10																	17730065		2203	4300	6503	SO:0001583	missense	8027	exon5			CTTATGGTTGAAT	U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"HSE1 homolog (S. cerevisiae)"	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.337G>A	chr10.hg19:g.17730065G>A	ENSP00000366746:p.Val113Ile	104.0	0.0		81.0	33.0	NM_003473	B0YJ99|D3DRU5|Q8N6D9	Missense_Mutation	SNP	ENST00000377524.3	hg19	CCDS7122.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.020537	0.93462	.	.	ENSG00000136738	ENST00000377524;ENST00000445846;ENST00000377500;ENST00000540523	T;T	0.22336	1.96;2.01	5.83	5.83	0.93111	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.000000	0.85682	D	0.000000	T	0.45296	0.1335	L	0.60455	1.87	0.80722	D	1	D	0.59357	0.985	D	0.68483	0.958	T	0.09443	-1.0674	10	0.48119	T	0.1	-29.0262	20.1133	0.97917	0.0:0.0:1.0:0.0	.	113	Q92783	STAM1_HUMAN	I	113;63;16;2	ENSP00000366746:V113I;ENSP00000438073:V2I	ENSP00000366721:V16I	V	+	1	0	STAM	17770071	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.796000	0.99103	2.762000	0.94881	0.591000	0.81541	GTT	.	.		0.343	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473		A	17730065	G	A	17730065	3	1	66	1	0	0	0	0	1	0	0	0	15263	1261	44	3	355	3	STAM	10	17730065	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10		17730065	117804682	53	8537										
SVIL	6840	hgsc.bcm.edu	37	chr10	29818698	29818698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ggacctgtcctgcagacggcGtagcctctgctccacagctg	12	15	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr10:29818698G>A	ENST00000355867.4	-	12	2934	c.2182C>T	c.(2182-2184)Cgc>Tgc	p.R728C	SVIL_ENST00000375398.2_Missense_Mutation_p.R728C|SVIL_ENST00000375400.3_Missense_Mutation_p.R334C	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	728					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				TGCAGACGGCGTAGCCTCTGC	0.502																																					p.R728C		Atlas-SNP	.											.	SVIL	226	.	0			c.C2182T						.						122	107	112					10																	29818698		2203	4300	6503	SO:0001583	missense	6840	exon12			GACGGCGTAGCCT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.2182C>T	chr10.hg19:g.29818698G>A	ENSP00000348128:p.Arg728Cys	58.0	0.0		59.0	11.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.363477	0.61513	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.66995	-0.24;-0.24;-0.24	5.21	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.80330	0.4603	M	0.76328	2.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.81217	-0.1033	9	.	.	.	-18.1198	13.7812	0.63084	0.0:0.0:0.7213:0.2787	.	334;728	O95425-2;O95425	.;SVIL_HUMAN	C	334;728;728	ENSP00000364549:R334C;ENSP00000364547:R728C;ENSP00000348128:R728C	.	R	-	1	0	SVIL	29858704	0.996000	0.38824	0.205000	0.23548	0.629000	0.37895	2.510000	0.45468	1.284000	0.44531	0.591000	0.81541	CGC	.	.		0.502	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			A	29818698	G	A	29818698	3	1	66	1	0	0	0	0	1	0	0	0	15436	1145	40	1	4570	1	SVIL	10	29818698	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	12088633	29818698	105716049	54	8538										
CPN1	1369	hgsc.bcm.edu	37	chr10	101825001	101825001	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ggcggtgcggcggacccctcGgacccggtgctcaaaggact	16	14	1	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr10:101825001G>A	ENST00000370418.3	-	4	954	c.703C>T	c.(703-705)Cga>Tga	p.R235*		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	235	Catalytic.				response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		CGGACCCCTCGGACCCGGTGC	0.612																																					p.R235X		Atlas-SNP	.											CPN1,neck,malignant_melanoma,0,1	CPN1	62	.	0			c.C703T						.						63	65	64					10																	101825001		2203	4300	6503	SO:0001587	stop_gained	1369	exon4			CCCCTCGGACCCG	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"anaphylatoxin inactivator", "arginine carboxypeptidase", "carboxypeptidase K", "kininase I", "lysine carboxypeptidase"	603103	"carboxypeptidase N, polypeptide 1, 50kD"			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.703C>T	chr10.hg19:g.101825001G>A	ENSP00000359446:p.Arg235*	47.0	0.0		33.0	8.0	NM_001308	B1AP59	Nonsense_Mutation	SNP	ENST00000370418.3	hg19	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.911836	0.92178	.	.	ENSG00000120054	ENST00000370418;ENST00000441382	.	.	.	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.432	12.2185	0.54420	0.0:0.0:0.7045:0.2955	.	.	.	.	X	235;32	.	ENSP00000359446:R235X	R	-	1	2	CPN1	101814991	1.000000	0.71417	0.429000	0.26710	0.462000	0.32619	3.075000	0.50073	2.382000	0.81193	0.561000	0.74099	CGA	.	.		0.612	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		A	101825001	G	A	101825001	4	1	66	1	0	0	0	0	0	1	0	0	3811	1124	39	1	697	1	CPN1	10	101825001	Nonsense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	72006303	101825001	33709746	55	8539										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114910795	114910795	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	cccaccacatcatacgctacAcacgacgggcattccgcatc	6	18	1	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr10:114910795A>T	ENST00000355995.4	+	9	1421	c.914A>T	c.(913-915)cAc>cTc	p.H305L	TCF7L2_ENST00000534894.1_Missense_Mutation_p.H305L|TCF7L2_ENST00000538897.1_Missense_Mutation_p.H305L|TCF7L2_ENST00000545257.1_Missense_Mutation_p.H305L|TCF7L2_ENST00000369386.1_5'Flank|TCF7L2_ENST00000542695.1_Missense_Mutation_p.H21L|TCF7L2_ENST00000355717.4_Missense_Mutation_p.H329L|TCF7L2_ENST00000543371.1_Missense_Mutation_p.H305L|TCF7L2_ENST00000369397.4_Missense_Mutation_p.H282L|TCF7L2_ENST00000369389.1_Missense_Mutation_p.H16L|TCF7L2_ENST00000352065.5_Missense_Mutation_p.H282L|TCF7L2_ENST00000536810.1_Missense_Mutation_p.H305L			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	305	Mediates interaction with MAD2L2.|Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CATACGCTACACACGACGGGC	0.493			T	VTI1A	colorectal																																p.H329L		Atlas-SNP	.		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	.	TCF7L2	298	.	0			c.A986T						.						222	174	190					10																	114910795		2203	4300	6503	SO:0001583	missense	6934	exon9			CGCTACACACGAC	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.914A>T	chr10.hg19:g.114910795A>T	ENSP00000348274:p.His305Leu	104.0	0.0		84.0	19.0	NM_001146283	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	hg19		.	.	.	.	.	.	.	.	.	.	a	23.7	4.446928	0.84101	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000355717;ENST00000538897;ENST00000534894;ENST00000369397;ENST00000352065;ENST00000542695;ENST00000369389;ENST00000277945	D;D;D;D;D;D;D;D;D;D;D;D	0.99319	-5.18;-5.18;-5.19;-5.21;-5.7;-5.74;-5.71;-5.18;-5.7;-5.15;-5.71;-5.68	5.17	5.17	0.71159	.	0.146153	0.64402	D	0.000010	D	0.99363	0.9776	M	0.84326	2.69	0.80722	D	1	P;P;P;P;P;D;D;P;D;P;P;D;D;P;D;P;D;D;D	0.67145	0.803;0.895;0.892;0.944;0.945;0.996;0.972;0.937;0.992;0.803;0.773;0.984;0.968;0.902;0.99;0.945;0.974;0.981;0.996	P;P;P;D;P;D;P;P;D;P;B;P;P;P;D;P;D;D;D	0.76071	0.579;0.579;0.621;0.909;0.621;0.917;0.835;0.561;0.909;0.474;0.358;0.889;0.843;0.476;0.987;0.621;0.969;0.925;0.933	D	0.98988	1.0807	10	0.52906	T	0.07	-19.1255	15.0145	0.71573	1.0:0.0:0.0:0.0	.	162;122;204;305;176;220;278;282;282;248;305;282;282;287;329;282;305;278;282	B4DJZ2;B7Z9Z6;B4DWD5;Q9NQB0;C6ZRK4;C6ZRJ6;C6ZRJ9;F8W742;B4DRJ8;C6ZRK2;B9X074;C6ZRJ8;C6ZRK1;C6ZRJ7;F8W7T5;C6ZRK5;Q9NQB0-7;Q9NQB0-10;Q6FHW4	.;.;.;TF7L2_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	L	305;305;305;305;329;305;305;282;282;21;16;22	ENSP00000348274:H305L;ENSP00000440547:H305L;ENSP00000444972:H305L;ENSP00000446238:H305L;ENSP00000347949:H329L;ENSP00000446172:H305L;ENSP00000443626:H305L;ENSP00000358404:H282L;ENSP00000344823:H282L;ENSP00000443883:H21L;ENSP00000358396:H16L;ENSP00000277945:H22L	ENSP00000277945:H22L	H	+	2	0	TCF7L2	114900785	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.302000	0.78861	1.955000	0.56771	0.533000	0.62120	CAC	.	.		0.493	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		T	114910795	A	T	114910795	3	4	66	1	0	0	0	0	1	0	0	0	15713	159	6	4	1093	4	TCF7L2	10	114910795	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	13085794	114910795	20623952	56	8540										
ACCS	84680	hgsc.bcm.edu	37	chr11	44096174	44096174	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	atcttcagcctccgggaggaAgtggccaagttcctgtcttt	11	11	3	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr11:44096174A>C	ENST00000263776.8	+	5	866	c.432A>C	c.(430-432)gaA>gaC	p.E144D	ACCS_ENST00000432284.2_Missense_Mutation_p.S121R|ACCS_ENST00000533208.1_3'UTR|CTD-2609K8.3_ENST00000531268.1_RNA	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	144					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						TCCGGGAGGAAGTGGCCAAGT	0.567																																					p.E144D	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											.	ACCS	64	.	0			c.A432C						.						180	161	167					11																	44096174		2203	4300	6503	SO:0001583	missense	84680	exon5			GGAGGAAGTGGCC	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.432A>C	chr11.hg19:g.44096174A>C	ENSP00000263776:p.Glu144Asp	54.0	0.0		45.0	13.0	NM_032592	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	hg19	CCDS7907.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.64|16.64	3.178139|3.178139	0.57692|0.57692	.|.	.|.	ENSG00000110455|ENSG00000110455	ENST00000263776|ENST00000432284	T|T	0.22743|0.42131	1.94|0.98	5.78|5.78	5.78|5.78	0.91487|0.91487	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.62405|0.62405	0.2425|0.2425	M|M	0.78456|0.78456	2.415|2.415	0.26504|0.26504	N|N	0.974715|0.974715	D;D|D	0.76494|0.61080	0.999;0.999|0.989	D;D|P	0.79108|0.58873	0.966;0.992|0.847	T|T	0.60915|0.60915	-0.7168|-0.7168	10|9	0.44086|0.87932	T|D	0.13|0	-13.5312|-13.5312	14.3393|14.3393	0.66614|0.66614	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	71;144|121	B4DYM9;Q96QU6|B4E219	.;1A1L1_HUMAN|.	D|R	144|121	ENSP00000263776:E144D|ENSP00000391775:S121R	ENSP00000263776:E144D|ENSP00000391775:S121R	E|S	+|+	3|1	2|0	ACCS|ACCS	44052750|44052750	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	1.719000|1.719000	0.38011|0.38011	2.205000|2.205000	0.71048|0.71048	0.533000|0.533000	0.62120|0.62120	GAA|AGT	.	.		0.567	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		C	44096174	A	C	44096174	3	2	66	1	0	0	0	0	1	0	0	0	133	69	3	5	446	5	ACCS	11	44096174	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10		44096174	90910342	57	8541										
C11orf80	79703	hgsc.bcm.edu	37	chr11	66568539	66568539	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctttgaaccttgggaatggaAttgctcttttggtcgactcc	10	9	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr11:66568539A>G	ENST00000360962.4	+	8	818	c.811A>G	c.(811-813)Att>Gtt	p.I271V	C11orf80_ENST00000525449.2_Missense_Mutation_p.I116V|C11orf80_ENST00000540737.1_Missense_Mutation_p.I105V|C11orf80_ENST00000346672.4_Missense_Mutation_p.I116V|C11orf80_ENST00000527634.1_Missense_Mutation_p.I52V|C11orf80_ENST00000532565.2_Missense_Mutation_p.I52V	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	271										autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						TGGGAATGGAATTGCTCTTTT	0.443																																					p.I271V		Atlas-SNP	.											.	C11orf80	31	.	0			c.A811G						.						125	118	120					11																	66568539		1957	4159	6116	SO:0001583	missense	79703	exon8			AATGGAATTGCTC			11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.811A>G	chr11.hg19:g.66568539A>G	ENSP00000354227:p.Ile271Val	86.0	0.0		91.0	16.0	NM_024650	Q9H677	Missense_Mutation	SNP	ENST00000360962.4	hg19	CCDS53664.1	.	.	.	.	.	.	.	.	.	.	A	14.48	2.549148	0.45383	.	.	ENSG00000173715	ENST00000524551;ENST00000525908;ENST00000360962;ENST00000346672;ENST00000527634;ENST00000528340;ENST00000540737;ENST00000525449	T;T	0.36878	1.37;1.23	4.98	1.29	0.21616	.	0.532611	0.17254	N	0.181021	T	0.22166	0.0534	L	0.27053	0.805	0.22389	N	0.999142	B;B;B	0.20052	0.015;0.015;0.041	B;B;B	0.19666	0.015;0.015;0.026	T	0.16512	-1.0400	10	0.35671	T	0.21	-1.6408	6.7445	0.23454	0.7164:0.0:0.2836:0.0	.	52;116;105	E9PKM2;Q8N6T0;E9PKZ8	.;CK080_HUMAN;.	V	52;222;271;116;52;105;105;116	ENSP00000432039:I222V;ENSP00000354227:I271V	ENSP00000317408:I116V	I	+	1	0	C11orf80	66325115	1.000000	0.71417	0.927000	0.36925	0.779000	0.44077	1.723000	0.38053	0.062000	0.16340	0.456000	0.33151	ATT	.	.		0.443	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024650		G	66568539	A	G	66568539	3	3	66	1	0	0	0	0	1	0	0	0	1666	101	4	2	841	2	C11orf80	11	66568539	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	22472365	66568539	68437977	58	8542										
FOLR2	2350	hgsc.bcm.edu	37	chr11	71932083	71932083	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctatgagtgctcacccaaccTggggccctggatccagcagg	12	14	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr11:71932083T>A	ENST00000298223.6	+	3	507	c.320T>A	c.(319-321)cTg>cAg	p.L107Q	FOLR2_ENST00000454954.2_Missense_Mutation_p.L66Q|FOLR2_ENST00000449475.2_Missense_Mutation_p.L124Q	NM_000803.4|NM_001113534.1|NM_001113535.1|NM_001113536.1	NP_000794.3|NP_001107006.1|NP_001107007.1|NP_001107008.1	P14207	FOLR2_HUMAN	folate receptor 2 (fetal)	107					folic acid transport (GO:0015884)	anchored component of external side of plasma membrane (GO:0031362)|extracellular region (GO:0005576)|membrane (GO:0016020)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)			breast(3)|large_intestine(3)|ovary(1)|skin(1)	8					Folic Acid(DB00158)	TCACCCAACCTGGGGCCCTGG	0.622																																					p.L107Q		Atlas-SNP	.											.	FOLR2	29	.	0			c.T320A						.						25	25	25					11																	71932083		2200	4293	6493	SO:0001583	missense	2350	exon3			CCAACCTGGGGCC	AK222539	CCDS8212.1	11q13.3-q14.1	2010-04-08			ENSG00000165457	ENSG00000165457			3793	protein-coding gene	gene with protein product		136425				1133088, 7698003	Standard	NM_000803		Approved		uc009ytf.3	P14207	OTTHUMG00000150394	ENST00000298223.6:c.320T>A	chr11.hg19:g.71932083T>A	ENSP00000298223:p.Leu107Gln	64.0	0.0		60.0	24.0	NM_001113535	Q05CA5|Q6GTE8	Missense_Mutation	SNP	ENST00000298223.6	hg19	CCDS8212.1	.	.	.	.	.	.	.	.	.	.	t	18.88	3.717531	0.68844	.	.	ENSG00000165457	ENST00000449475;ENST00000298223;ENST00000454954;ENST00000539412;ENST00000536778;ENST00000535625;ENST00000321324;ENST00000538353	T;T;T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	4.37	3.25	0.37280	Folate receptor-like (1);	0.000000	0.64402	D	0.000013	D	0.88923	0.6569	M	0.93106	3.38	0.45464	D	0.998439	D	0.89917	1.0	D	0.97110	1.0	D	0.88508	0.3087	10	0.87932	D	0	.	8.5883	0.33670	0.0:0.0931:0.0:0.9069	.	107	P14207	FOLR2_HUMAN	Q	124;107;66;118;122;107;120;107	ENSP00000405638:L124Q;ENSP00000298223:L107Q;ENSP00000414094:L66Q;ENSP00000441547:L118Q;ENSP00000438568:L122Q;ENSP00000444794:L107Q;ENSP00000321957:L120Q;ENSP00000440337:L107Q	ENSP00000298223:L107Q	L	+	2	0	FOLR2	71609731	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.917000	0.63369	0.729000	0.32403	0.374000	0.22700	CTG	.	.		0.622	FOLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317923.2	NM_000803		A	71932083	T	A	71932083	3	1	66	1	0	0	0	0	1	0	0	0	5990	1580	55	4	326	4	FOLR2	11	71932083	Missense_Mutation	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	5363544	71932083	63074433	59	8543										
TECTA	7007	hgsc.bcm.edu	37	chr11	121036027	121036027	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gggggcggactgtcccaaccGaacttgcgagctgggcaatg	16	11	0	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr11:121036027G>T	ENST00000392793.1	+	17	5589	c.5318G>T	c.(5317-5319)cGa>cTa	p.R1773L	TECTA_ENST00000264037.2_Missense_Mutation_p.R1773L			O75443	TECTA_HUMAN	tectorin alpha	1773					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGTCCCAACCGAACTTGCGAG	0.542																																					p.R1773L		Atlas-SNP	.											TECTA,NS,carcinoma,0,1	TECTA	329	.	0			c.G5318T						.						196	161	173					11																	121036027		2203	4299	6502	SO:0001583	missense	7007	exon16			CCAACCGAACTTG	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.5318G>T	chr11.hg19:g.121036027G>T	ENSP00000376543:p.Arg1773Leu	208.0	0.0		203.0	40.0	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.597665	0.46318	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.36340	1.26;1.26	5.74	5.74	0.90152	.	0.372397	0.28766	N	0.014209	T	0.24736	0.0600	N	0.19112	0.55	0.34327	D	0.687201	P	0.40660	0.726	B	0.33690	0.168	T	0.18681	-1.0329	10	0.19590	T	0.45	.	19.9403	0.97159	0.0:0.0:1.0:0.0	.	1773	O75443	TECTA_HUMAN	L	1773	ENSP00000376543:R1773L;ENSP00000264037:R1773L	ENSP00000264037:R1773L	R	+	2	0	TECTA	120541237	1.000000	0.71417	0.945000	0.38365	0.909000	0.53808	5.735000	0.68587	2.712000	0.92718	0.650000	0.86243	CGA	.	.		0.542	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		T	121036027	G	T	121036027	3	4	66	1	0	0	0	0	1	0	0	0	15762	1058	37	1	5380	1	TECTA	11	121036027	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	49103944	121036027	13970489	60	8544										
OR10G7	390265	hgsc.bcm.edu	37	chr11	123909699	123909699	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gaacgctgtcagtagggtggCgttggacatttcttctcata	12	8	3	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr11:123909699C>T	ENST00000330487.5	-	1	18	c.10G>A	c.(10-12)Gcc>Acc	p.A4T		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AGTAGGGTGGCGTTGGACATT	0.488																																					p.A4T		Atlas-SNP	.											.	OR10G7	103	.	0			c.G10A						.						87	76	80					11																	123909699		2200	4299	6499	SO:0001583	missense	390265	exon1			GGGTGGCGTTGGA	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"GPCR / Class A : Olfactory receptors"	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.10G>A	chr11.hg19:g.123909699C>T	ENSP00000329689:p.Ala4Thr	178.0	0.0		133.0	49.0	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	hg19	CCDS31705.1	.	.	.	.	.	.	.	.	.	.	C	0.165	-1.077648	0.01903	.	.	ENSG00000182634	ENST00000330487	T	0.00507	6.92	3.38	-6.76	0.01732	.	3.429150	0.00851	N	0.001833	T	0.00241	0.0007	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46020	-0.9221	10	0.07325	T	0.83	.	7.9091	0.29780	0.0815:0.0994:0.1147:0.7044	.	4	Q8NGN6	O10G7_HUMAN	T	4	ENSP00000329689:A4T	ENSP00000329689:A4T	A	-	1	0	OR10G7	123414909	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.737000	0.00055	-3.306000	0.00191	-2.177000	0.00319	GCC	.	.		0.488	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463		T	123909699	C	T	123909699	3	4	66	1	0	0	0	0	1	0	0	0	10911	768	27	1	929	1	OR10G7	11	123909699	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	2873672	123909699	11096817	61	8545										
IPO8	10526	hgsc.bcm.edu	37	chr12	30789975	30789975	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	cttcccggtttaccagttgtCtagtagcacagacctgcttt	8	12	1	1	rs61751231	byFrequency	TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr12:30789975C>A	ENST00000256079.4	-	22	2974	c.2636G>T	c.(2635-2637)aGa>aTa	p.R879I	IPO8_ENST00000544829.1_Missense_Mutation_p.R674I	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	879					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TACCAGTTGTCTAGTAGCACA	0.398																																					p.R879I		Atlas-SNP	.											.	IPO8	105	.	0			c.G2636T						.						118	109	112					12																	30789975		2203	4300	6503	SO:0001583	missense	10526	exon22			AGTTGTCTAGTAG	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.2636G>T	chr12.hg19:g.30789975C>A	ENSP00000256079:p.Arg879Ile	97.0	0.0		71.0	7.0	NM_006390	B7Z7M3	Missense_Mutation	SNP	ENST00000256079.4	hg19	CCDS8719.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.86|14.86	2.660895|2.660895	0.47572|0.47572	.|.	.|.	ENSG00000133704|ENSG00000133704	ENST00000535598|ENST00000256079;ENST00000545286;ENST00000544829	.|T;T	.|0.53857	.|1.6;0.6	5.06|5.06	3.23|3.23	0.37069|0.37069	.|Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.70081|0.70081	0.3183|0.3183	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	.|D;D;P	.|0.89917	.|0.993;1.0;0.638	.|D;D;B	.|0.91635	.|0.93;0.999;0.313	T|T	0.69764|0.69764	-0.5057|-0.5057	5|10	.|0.44086	.|T	.|0.13	-10.2807|-10.2807	11.9359|11.9359	0.52874|0.52874	0.0:0.8563:0.0:0.1437|0.0:0.8563:0.0:0.1437	.|.	.|674;355;879	.|B7Z7M3;Q59F59;O15397	.|.;.;IPO8_HUMAN	Y|I	37|879;355;674	.|ENSP00000256079:R879I;ENSP00000444520:R674I	.|ENSP00000256079:R879I	D|R	-|-	1|2	0|0	IPO8|IPO8	30681242|30681242	0.066000|0.066000	0.20996|0.20996	0.089000|0.089000	0.20774|0.20774	0.130000|0.130000	0.20726|0.20726	2.773000|2.773000	0.47686|0.47686	0.645000|0.645000	0.30675|0.30675	-0.157000|-0.157000	0.13467|0.13467	GAC|AGA	.	C|0.992;T|0.008		0.398	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		A	30789975	C	A	30789975	3	1	66	1	0	0	0	0	1	0	0	0	7807	913	32	3	493	3	IPO8	12	30789975	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10		30789975	103061920	62	8546										
NACA	4666	hgsc.bcm.edu	37	chr12	57113603	57113603	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ggatgtactttggaaagaagGggaatttttaggggctgcct	15	4	0	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr12:57113603G>T	ENST00000454682.1	-	3	1992	c.1711C>A	c.(1711-1713)Cct>Act	p.P571T	NACA_ENST00000548563.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.P571T|NACA_ENST00000393891.4_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000552540.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	571	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						TGGAAAGAAGGGGAATTTTTA	0.507			T	BCL6	NHL																																p.P571T		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.C1711A						.						66	66	66					12																	57113603		1568	3582	5150	SO:0001583	missense	4666	exon3			AAGAAGGGGAATT	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.1711C>A	chr12.hg19:g.57113603G>T	ENSP00000403817:p.Pro571Thr	128.0	0.0		117.0	11.0	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	hg19		.	.	.	.	.	.	.	.	.	.	G	8.757	0.922697	0.18056	.	.	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.53640	0.66;0.61	3.55	-2.58	0.06228	.	.	.	.	.	T	0.23926	0.0579	N	0.08118	0	0.09310	N	1	B;B	0.25351	0.124;0.051	B;B	0.26969	0.055;0.075	T	0.26950	-1.0088	9	0.87932	D	0	.	5.5362	0.17013	0.2233:0.502:0.2748:0.0	.	571;571	E9PAV3;F8VU71	.;.	T	571	ENSP00000403817:P571T;ENSP00000448035:P571T	ENSP00000403817:P571T	P	-	1	0	NACA	55399870	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.569000	0.05902	-0.129000	0.11620	-1.944000	0.00493	CCT	.	.		0.507	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		T	57113603	G	T	57113603	3	4	66	1	0	0	0	0	1	0	0	0	10142	1232	43	3	4553	3	NACA	12	57113603	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	26323628	57113603	76738292	63	8547										
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105519876	105519876	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	atttgcacatagtattcggtCaatttttgcaaatgtagaag	8	5	1	1	rs190039477		TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr12:105519876C>G	ENST00000332180.5	+	11	968	c.881C>G	c.(880-882)tCa>tGa	p.S294*		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						AGTATTCGGTCAATTTTTGCA	0.313																																					p.S294X		Atlas-SNP	.											.	KIAA1033	83	.	0			c.C881G						.						112	100	103					12																	105519876		1819	4077	5896	SO:0001587	stop_gained	23325	exon11			TTCGGTCAATTTT	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.881C>G	chr12.hg19:g.105519876C>G	ENSP00000328062:p.Ser294*	159.0	0.0		113.0	38.0	NM_015275		Nonsense_Mutation	SNP	ENST00000332180.5	hg19	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	C	30	5.056560	0.93793	.	.	ENSG00000136051	ENST00000332180	.	.	.	5.56	5.56	0.83823	.	0.103125	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	.	19.5177	0.95171	0.0:1.0:0.0:0.0	.	.	.	.	X	294	.	ENSP00000328062:S294X	S	+	2	0	KIAA1033	104044006	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.920000	0.70017	2.605000	0.88082	0.557000	0.71058	TCA	.	C|1.000;T|0.000		0.313	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		G	105519876	C	G	105519876	4	3	66	1	0	0	0	0	0	1	0	0	8215	838	29	4	923	4	KIAA1033	12	105519876	Nonsense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	48406273	105519876	28332019	64	8548										
LAMP1	3916	hgsc.bcm.edu	37	chr13	113960890	113960890	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	caacttctctgctgccttctCagtgaactacgacaccaaga	6	14	2	2			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr13:113960890C>T	ENST00000332556.4	+	2	346	c.152C>T	c.(151-153)tCa>tTa	p.S51L	LAMP1_ENST00000397181.3_Missense_Mutation_p.S51L	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	51	First lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			GCTGCCTTCTCAGTGAACTAC	0.478																																					p.S51L		Atlas-SNP	.											.	LAMP1	41	.	0			c.C152T						.						128	125	126					13																	113960890		2054	4220	6274	SO:0001583	missense	3916	exon2			CCTTCTCAGTGAA	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.152C>T	chr13.hg19:g.113960890C>T	ENSP00000333298:p.Ser51Leu	78.0	0.0		83.0	48.0	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Missense_Mutation	SNP	ENST00000332556.4	hg19	CCDS41909.1	.	.	.	.	.	.	.	.	.	.	C	1.527	-0.545454	0.04024	.	.	ENSG00000185896	ENST00000332556;ENST00000397181	T;T	0.34072	1.51;1.38	5.24	-4.04	0.04010	Lysosome-associated membrane glycoprotein, conserved site (1);	0.508978	0.20061	N	0.100086	T	0.12092	0.0294	N	0.04686	-0.185	0.09310	N	1	B;B	0.12013	0.0;0.005	B;B	0.09377	0.002;0.004	T	0.26087	-1.0113	10	0.16420	T	0.52	-0.9467	6.6254	0.22826	0.0:0.4712:0.3116:0.2171	.	51;51	B4DWL3;P11279	.;LAMP1_HUMAN	L	51	ENSP00000333298:S51L;ENSP00000415354:S51L	ENSP00000333298:S51L	S	+	2	0	LAMP1	113008891	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.598000	0.00419	-0.496000	0.06650	-0.302000	0.09304	TCA	.	.		0.478	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			T	113960890	C	T	113960890	3	4	66	1	0	0	0	0	1	0	0	0	8626	838	29	3	158	3	LAMP1	13	113960890	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10		113960890	1208988	65	8549										
C14orf145	145508	hgsc.bcm.edu	37	chr14	81251620	81251620	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gcaatttcttcctccaagtgAgctttctcaactttcatctg	5	12	4	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr14:81251620A>C	ENST00000555265.1	-	15	2205	c.1830T>G	c.(1828-1830)gcT>gcG	p.A610A	CEP128_ENST00000281129.3_Silent_p.A610A			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	610						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						CCTCCAAGTGAGCTTTCTCAA	0.448																																					p.A610A		Atlas-SNP	.											.	CEP128	146	.	0			c.T1830G						.						186	178	181					14																	81251620		2203	4300	6503	SO:0001819	synonymous_variant	145508	exon14			CAAGTGAGCTTTC	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.1830T>G	chr14.hg19:g.81251620A>C		193.0	0.0		143.0	16.0	NM_152446	B9EK52|Q86X97|Q96ML4	Silent	SNP	ENST00000555265.1	hg19	CCDS32130.1																																																																																			.	.		0.448	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		C	81251620	A	C	81251620	2	2	66	1	0	0	0	0	0	0	0	1	1751	291	11	5		5	C14orf145	14	81251620	Silent	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10		81251620	26097920	66	8550										
RYR3	6263	hgsc.bcm.edu	37	chr15	33936690	33936690	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	aagcgcctcccgacgtttgtCaacgtgccaaaggatcatcc	9	14	2	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr15:33936690C>A	ENST00000389232.4	+	28	3805	c.3735C>A	c.(3733-3735)gtC>gtA	p.V1245V	RYR3_ENST00000415757.3_Silent_p.V1245V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1245	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CGACGTTTGTCAACGTGCCAA	0.512																																					p.V1245V		Atlas-SNP	.											.	RYR3	760	.	0			c.C3735A						.						73	72	73					15																	33936690		1996	4161	6157	SO:0001819	synonymous_variant	6263	exon28			GTTTGTCAACGTG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.3735C>A	chr15.hg19:g.33936690C>A		77.0	0.0		105.0	44.0	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.512	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	33936690	C	A	33936690	2	1	66	1	0	0	0	0	0	0	0	1	13785	813	29	3		3	RYR3	15	33936690	Silent	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10		33936690	68594702	67	8551										
DISP2	85455	hgsc.bcm.edu	37	chr15	40660976	40660976	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gcaaggccccgatggcacccAggacctgggactccgctttg	13	15	0	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr15:40660976A>T	ENST00000267889.3	+	8	2750	c.2663A>T	c.(2662-2664)cAg>cTg	p.Q888L	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	888					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		GATGGCACCCAGGACCTGGGA	0.622																																					p.Q888L		Atlas-SNP	.											.	DISP2	86	.	0			c.A2663T						.						32	34	34					15																	40660976		2203	4300	6503	SO:0001583	missense	85455	exon8			GCACCCAGGACCT	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2663A>T	chr15.hg19:g.40660976A>T	ENSP00000267889:p.Gln888Leu	45.0	0.0		40.0	12.0	NM_033510	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	hg19	CCDS10056.1	.	.	.	.	.	.	.	.	.	.	A	0.088	-1.172339	0.01646	.	.	ENSG00000140323	ENST00000267889	T	0.11712	2.75	4.99	0.938	0.19500	.	0.856524	0.10507	N	0.666624	T	0.02649	0.0080	N	0.00926	-1.1	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.46400	-0.9194	10	0.10636	T	0.68	-4.1397	3.9036	0.09172	0.4827:0.0:0.3371:0.1802	.	888	A7MBM2	DISP2_HUMAN	L	888	ENSP00000267889:Q888L	ENSP00000267889:Q888L	Q	+	2	0	DISP2	38448268	0.000000	0.05858	0.083000	0.20561	0.630000	0.37929	0.212000	0.17497	0.017000	0.15025	-0.542000	0.04241	CAG	.	.		0.622	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		T	40660976	A	T	40660976	3	4	66	1	0	0	0	0	1	0	0	0	4542	188	7	4	2693	4	DISP2	15	40660976	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	6724286	40660976	61870416	68	8552										
MAP1A	4130	hgsc.bcm.edu	37	chr15	43815176	43815176	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gaaggagctgtcttctgagcCccagacacccccagcccaga	10	16	2	3			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr15:43815176C>T	ENST00000300231.5	+	4	1955	c.1505C>T	c.(1504-1506)cCc>cTc	p.P502L	MAP1A_ENST00000399453.1_Missense_Mutation_p.P502L|MAP1A_ENST00000382031.1_Missense_Mutation_p.P740L			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	502	9 X 3 AA repeats of K-K-[DE].				microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TCTTCTGAGCCCCAGACACCC	0.562																																					p.P502L		Atlas-SNP	.											.	MAP1A	189	.	0			c.C1505T						.						47	48	48					15																	43815176		1967	4134	6101	SO:0001583	missense	4130	exon4			CTGAGCCCCAGAC	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.1505C>T	chr15.hg19:g.43815176C>T	ENSP00000300231:p.Pro502Leu	116.0	0.0		118.0	40.0	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.349227	0.24426	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231;ENST00000442025	T;T;T	0.46063	0.88;0.88;0.88	5.07	5.07	0.68467	.	0.275737	0.19642	N	0.109428	T	0.35828	0.0945	M	0.63428	1.95	0.41925	D	0.990538	B	0.16802	0.019	B	0.17433	0.018	T	0.19289	-1.0310	10	0.20519	T	0.43	-7.6473	6.5579	0.22469	0.2978:0.6187:0.0:0.0835	.	502	P78559	MAP1A_HUMAN	L	740;502;502;502	ENSP00000371462:P740L;ENSP00000382380:P502L;ENSP00000300231:P502L	ENSP00000300231:P502L	P	+	2	0	MAP1A	41602468	0.651000	0.27340	1.000000	0.80357	0.873000	0.50193	1.389000	0.34453	2.804000	0.96469	0.655000	0.94253	CCC	.	.		0.562	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		T	43815176	C	T	43815176	3	4	66	1	0	0	0	0	1	0	0	0	9236	623	22	3	1507	3	MAP1A	15	43815176	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	3154200	43815176	58716216	69	8553										
GCOM1	100820829	hgsc.bcm.edu	37	chr15	57953696	57953696	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	agaaacagctcttaatactgCagcttttagaaaagatatct	6	7	2	3			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr15:57953696C>G	ENST00000267853.5	+	11	1262	c.1168C>G	c.(1168-1170)Cag>Gag	p.Q390E	GCOM1_ENST00000380561.2_Intron|GCOM1_ENST00000572390.1_Intron|MYZAP_ENST00000380565.4_Intron|GCOM1_ENST00000380568.3_Missense_Mutation_p.Q390E|GCOM1_ENST00000380560.2_Missense_Mutation_p.Q321E|GCOM1_ENST00000396180.1_Missense_Mutation_p.Q359E|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000587652.1_Missense_Mutation_p.Q390E|GCOM1_ENST00000574161.1_Missense_Mutation_p.Q390E|GCOM1_ENST00000380569.2_Missense_Mutation_p.Q390E			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	390					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											CTTAATACTGCAGCTTTTAGA	0.318																																					p.Q390E		Atlas-SNP	.											.	GCOM1	66	.	0			c.C1168G						.						64	61	62					15																	57953696		2191	4291	6482	SO:0001583	missense	145781	exon11			ATACTGCAGCTTT	FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"myocardium-enriched zonula adherens protein"	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.1168C>G	chr15.hg19:g.57953696C>G	ENSP00000267853:p.Gln390Glu	135.0	0.0		157.0	38.0	NM_001018090	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	hg19	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.162678	0.38217	.	.	ENSG00000137878	ENST00000380569;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380568;ENST00000461709	T;T;T;T;T;T	0.25250	2.1;2.12;2.14;2.08;2.09;1.81	5.88	5.88	0.94601	.	0.104213	0.64402	D	0.000002	T	0.29223	0.0727	N	0.11724	0.165	0.80722	D	1	D;B;P	0.63046	0.992;0.245;0.459	D;B;B	0.74674	0.984;0.367;0.086	T	0.04216	-1.0968	10	0.07644	T	0.81	-25.8335	15.7229	0.77728	0.0:1.0:0.0:0.0	.	390;390;390	P0CAP1-2;P0CAP1-11;P0CAP1	.;.;GCOM1_HUMAN	E	390;359;321;390;390;105	ENSP00000369943:Q390E;ENSP00000379483:Q359E;ENSP00000369933:Q321E;ENSP00000267853:Q390E;ENSP00000369942:Q390E;ENSP00000431396:Q105E	ENSP00000267853:Q390E	Q	+	1	0	GCOM1	55740988	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.007000	0.57093	2.789000	0.95967	0.655000	0.94253	CAG	.	.		0.318	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100		G	57953696	C	G	57953696	3	3	66	1	0	0	0	0	1	0	0	0	6312	711	25	4	1210	4	GCOM1	15	57953696	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	14138520	57953696	44577696	70	8554										
MYO1E	4643	hgsc.bcm.edu	37	chr15	59502718	59502718	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	taaatgaacacttaccacttTgttctctatgaggtcacata	5	9	2	2			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr15:59502718T>G	ENST00000288235.4	-	13	1756	c.1357A>C	c.(1357-1359)Aaa>Caa	p.K453Q	RNU4-80P_ENST00000363200.1_RNA	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	453	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		CTTACCACTTTGTTCTCTATG	0.353																																					p.K453Q		Atlas-SNP	.											.	MYO1E	99	.	0			c.A1357C						.						185	176	179					15																	59502718		2191	4290	6481	SO:0001583	missense	4643	exon13			CCACTTTGTTCTC	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.1357A>C	chr15.hg19:g.59502718T>G	ENSP00000288235:p.Lys453Gln	119.0	0.0		97.0	32.0	NM_004998	Q14778	Missense_Mutation	SNP	ENST00000288235.4	hg19	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	T	17.34	3.365824	0.61513	.	.	ENSG00000157483	ENST00000288235	D	0.96104	-3.91	5.36	5.36	0.76844	Myosin head, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.97337	0.9129	M	0.88570	2.965	0.80722	D	1	D	0.61697	0.99	P	0.55508	0.777	D	0.97933	1.0321	10	0.66056	D	0.02	.	15.5164	0.75828	0.0:0.0:0.0:1.0	.	453	Q12965	MYO1E_HUMAN	Q	453	ENSP00000288235:K453Q	ENSP00000288235:K453Q	K	-	1	0	MYO1E	57290010	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.841000	0.86834	2.257000	0.74773	0.459000	0.35465	AAA	.	.		0.353	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		G	59502718	T	G	59502718	3	3	66	1	0	0	0	0	1	0	0	0	10081	1821	63	5	2033	5	MYO1E	15	59502718	Missense_Mutation	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	1549022	59502718	43028674	71	8555										
CLPX	10845	hgsc.bcm.edu	37	chr15	65443162	65443162	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	aagacagcaatatgacagttTagctgtttgcagcatctgct	9	8	1	2			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr15:65443162T>C	ENST00000300107.3	-	14	2089	c.1901A>G	c.(1900-1902)tAa>tGa	p.*634*		NM_006660.3	NP_006651.2	O76031	CLPX_HUMAN	caseinolytic mitochondrial matrix peptidase chaperone subunit	0					ATP catabolic process (GO:0006200)|positive regulation of peptidase activity (GO:0010952)|protein folding (GO:0006457)|proteolysis involved in cellular protein catabolic process (GO:0051603)	endopeptidase Clp complex (GO:0009368)|mitochondrial endopeptidase Clp complex (GO:0009841)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|metal ion binding (GO:0046872)|peptidase activator activity (GO:0016504)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)|skin(2)	16						TATGACAGTTTAGCTGTTTGC	0.403																																					p.X634X		Atlas-SNP	.											.	CLPX	49	.	0			c.A1901G						.						167	163	165					15																	65443162		2202	4299	6501	SO:0001819	synonymous_variant	10845	exon14			ACAGTTTAGCTGT	AJ006267	CCDS10202.1	15q22.31	2013-09-12	2013-09-12		ENSG00000166855	ENSG00000166855		"ATPases / AAA-type"	2088	protein-coding gene	gene with protein product		615611	"ClpX (caseinolytic protease X, E. coli) homolog", "ClpX caseinolytic protease X homolog (E. coli)", "ClpX caseinolytic peptidase X homolog (E. coli)"			22841477	Standard	NM_006660		Approved		uc002aom.3	O76031	OTTHUMG00000133139	ENST00000300107.3:c.1901A>G	chr15.hg19:g.65443162T>C		57.0	0.0		33.0	11.0	NM_006660	A1L428|A8K8F1|B9EGI8|Q9H4D9	Silent	SNP	ENST00000300107.3	hg19	CCDS10202.1																																																																																			.	.		0.403	CLPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256828.2	NM_006660		C	65443162	T	C	65443162	2	2	66	1	0	0	0	0	0	0	0	1	3558	1761	61	2		2	CLPX	15	65443162	Silent	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	5940444	65443162	37088230	72	8556										
NEIL1	79661	hgsc.bcm.edu	37	chr15	75641492	75641492	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gtcttccgcttcggcatgtcCggctcttttcagctggtgcc	11	14	3	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr15:75641492C>T	ENST00000564784.1	+	3	875	c.246C>T	c.(244-246)tcC>tcT	p.S82S	NEIL1_ENST00000569035.1_Silent_p.S82S|NEIL1_ENST00000355059.4_Silent_p.S82S|NEIL1_ENST00000567959.1_Intron			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	82			S -> C (in dbSNP:rs5745905). {ECO:0000269|Ref.3}.		base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						TCGGCATGTCCGGCTCTTTTC	0.687								Base excision repair (BER), DNA glycosylases																													p.S168S		Atlas-SNP	.											.	NEIL1	36	.	0			c.C504T						.						37	34	35					15																	75641492		2197	4294	6491	SO:0001819	synonymous_variant	79661	exon2			CATGTCCGGCTCT	AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.246C>T	chr15.hg19:g.75641492C>T		17.0	0.0		15.0	5.0	NM_001256552	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Silent	SNP	ENST00000564784.1	hg19	CCDS10278.1																																																																																			.	.		0.687	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608		T	75641492	C	T	75641492	2	4	66	1	0	0	0	0	0	0	0	1	10327	639	23	1		1	NEIL1	15	75641492	Silent	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	10198330	75641492	26889900	73	8557										
LINS1	55180	hgsc.bcm.edu	37	chr15	101112222	101112222	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	attgcagagagggctgaagaTgaggctttaagaaggtcagt	15	4	1	5			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr15:101112222T>A	ENST00000314742.8	-	6	1493	c.1271A>T	c.(1270-1272)cAt>cTt	p.H424L	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	424										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						GGGCTGAAGATGAGGCTTTAA	0.413																																					p.H424L		Atlas-SNP	.											.	LINS	62	.	0			c.A1271T						.						92	88	89					15																	101112222		2203	4300	6503	SO:0001583	missense	55180	exon6			TGAAGATGAGGCT	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"lines homolog 1 (Drosophila)"	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1271A>T	chr15.hg19:g.101112222T>A	ENSP00000318423:p.His424Leu	43.0	0.0		38.0	9.0	NM_001040616	Q96FW2|Q9NVQ3	Missense_Mutation	SNP	ENST00000314742.8	hg19	CCDS10385.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.572337	0.86542	.	.	ENSG00000140471	ENST00000314742	T	0.17528	2.27	6.07	4.93	0.64822	.	0.333575	0.35262	N	0.003333	T	0.34832	0.0911	M	0.69823	2.125	0.80722	D	1	D	0.56746	0.977	P	0.55923	0.787	T	0.12656	-1.0539	10	0.87932	D	0	-5.0496	13.4669	0.61260	0.0:0.0:0.1306:0.8694	.	424	Q8NG48	LINES_HUMAN	L	424	ENSP00000318423:H424L	ENSP00000318423:H424L	H	-	2	0	LINS	98929745	1.000000	0.71417	0.965000	0.40720	0.968000	0.65278	3.127000	0.50484	1.078000	0.41014	0.533000	0.62120	CAT	.	.		0.413	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148		A	101112222	T	A	101112222	3	1	66	1	0	0	0	0	1	0	0	0	8827	1464	51	4	1010	4	LINS1	15	101112222	Missense_Mutation	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10	25470730	101112222	1419170	74	8558										
PKD1	5310	hgsc.bcm.edu	37	chr16	2158258	2158258	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctgccacgcactgacctgtgTcgaagccacacaggcccagt	10	16	0	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr16:2158258T>C	ENST00000262304.4	-	15	7118	c.6910A>G	c.(6910-6912)Aca>Gca	p.T2304A	PKD1_ENST00000423118.1_Missense_Mutation_p.T2304A|PKD1_ENST00000561991.1_5'Flank	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2304	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTGACCTGTGTCGAAGCCACA	0.667																																					p.T2304A		Atlas-SNP	.											.	PKD1	184	.	0			c.A6910G						.						23	26	25					16																	2158258		2183	4281	6464	SO:0001583	missense	5310	exon15			CCTGTGTCGAAGC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.6910A>G	chr16.hg19:g.2158258T>C	ENSP00000262304:p.Thr2304Ala	28.0	0.0		21.0	8.0	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	hg19	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	t	12.50	1.958122	0.34565	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101;ENST00000382481	T;T	0.69561	-0.41;-0.41	5.05	2.71	0.32032	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);Polycystin cation channel (1);	0.311612	0.31233	N	0.008020	T	0.60792	0.2296	L	0.56769	1.78	0.23198	N	0.998135	P;P	0.43024	0.798;0.566	B;B	0.44044	0.439;0.438	T	0.52223	-0.8604	10	0.39692	T	0.17	.	5.8446	0.18659	0.3393:0.0:0.1039:0.5568	.	2304;2304	P98161-3;P98161	.;PKD1_HUMAN	A	2304;2304;1655;583	ENSP00000262304:T2304A;ENSP00000399501:T2304A	ENSP00000262304:T2304A	T	-	1	0	PKD1	2098259	0.986000	0.35501	0.021000	0.16686	0.885000	0.51271	1.987000	0.40687	0.225000	0.20959	0.445000	0.29226	ACA	.	.		0.667	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			C	2158258	T	C	2158258	3	2	66	1	0	0	0	0	1	0	0	0	11972	1667	58	2	6129	2	PKD1	16	2158258	Missense_Mutation	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10		2158258	88196495	75	8559										
BCKDK	10295	hgsc.bcm.edu	37	chr16	31121012	31121012	+	Frame_Shift_Del	DEL	C	C	-													0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	agaaaagtgctcggtacctgCagcaagaacttccagtgagg							TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr16:31121012delC	ENST00000394951.1	+	5	906	c.283delC	c.(283-285)cagfs	p.Q96fs	BCKDK_ENST00000219794.6_Frame_Shift_Del_p.Q96fs|BCKDK_ENST00000394950.3_Frame_Shift_Del_p.Q96fs|BCKDK_ENST00000287507.3_Frame_Shift_Del_p.Q96fs|AC135050.1_ENST00000517000.2_RNA			O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase	96					branched-chain amino acid catabolic process (GO:0009083)|cellular amino acid catabolic process (GO:0009063)|phosphorylation (GO:0016310)|protein phosphorylation (GO:0006468)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrion (GO:0005739)	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity (GO:0047323)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|stomach(1)	2						TCGGTACCTGCAGCAAGAACT	0.552																																					p.L94fs		Atlas-Indel,Pindel	.											.	BCKDK	52	.	0			c.282delG						.						76	72	73					16																	31121012		2197	4300	6497	SO:0001589	frameshift_variant	10295	exon4			.	AF026548	CCDS10705.1, CCDS45467.1, CCDS61917.1	16p11.2	2008-05-14			ENSG00000103507	ENSG00000103507			16902	protein-coding gene	gene with protein product		614901				1889817	Standard	NM_005881		Approved		uc002eaw.5	O14874	OTTHUMG00000047356	ENST00000394951.1:c.283delC	chr16.hg19:g.31121012delC	ENSP00000378405:p.Gln96fs	80.0	0.0		77.0	24.0	NM_005881	A8MY43|Q6FGL4|Q96G95|Q96IN5	Frame_Shift_Del	DEL	ENST00000394951.1	hg19	CCDS10705.1																																																																																			.	.		0.552	BCKDK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108514.1	NM_005881		-	31121012	C	-	31121012	7	5	66	1	0	1	0	1	0	0	0	0	1361	711	25	0	293	0	BCKDK	16	31121012	Frame_Shift_Del	DEL	C	TCGA-CC-A3MC-01A-11D-A22F-10	28962754	31121012	59233741	76	8560										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89352532	89352532	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gagttggccactttcagcggCgtctcgcctttcctgttgct	11	13	2	0	rs149525788		TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr16:89352532C>T	ENST00000301030.4	-	8	1267	c.807G>A	c.(805-807)acG>acA	p.T269T	ANKRD11_ENST00000378330.2_Silent_p.T269T	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	269					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CTTTCAGCGGCGTCTCGCCTT	0.602																																					p.T269T		Atlas-SNP	.											.	ANKRD11	195	.	0			c.G807A						.						161	152	155					16																	89352532		2198	4300	6498	SO:0001819	synonymous_variant	29123	exon8			CAGCGGCGTCTCG	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.807G>A	chr16.hg19:g.89352532C>T		32.0	0.0		22.0	10.0	NM_001256183	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	hg19	CCDS32513.1																																																																																			.	C|1.000;G|0.000		0.602	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		T	89352532	C	T	89352532	2	4	66	1	0	0	0	0	0	0	0	1	639	755	27	1		1	ANKRD11	16	89352532	Silent	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	58231520	89352532	1002221	77	8561										
PSMB6	5694	hgsc.bcm.edu	37	chr17	4701710	4701710	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	cgccgttgccactttaccacCcgcctgaatcctgggattct	8	16	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr17:4701710C>A	ENST00000270586.3	+	6	764	c.713C>A	c.(712-714)cCc>cAc	p.P238H	RP11-81A22.5_ENST00000571067.1_lincRNA	NM_001270481.1|NM_002798.2	NP_001257410.1|NP_002789.1	P28072	PSB6_HUMAN	proteasome (prosome, macropain) subunit, beta type, 6	238					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	endopeptidase activity (GO:0004175)|threonine-type endopeptidase activity (GO:0004298)			endometrium(3)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11						ACTTTACCACCCGCCTGAATC	0.478																																					p.P238H		Atlas-SNP	.											.	PSMB6	20	.	0			c.C713A						.						101	94	97					17																	4701710		2203	4300	6503	SO:0001583	missense	5694	exon6			TACCACCCGCCTG	BC000835	CCDS11056.1, CCDS73944.1	17p13	2004-02-18			ENSG00000142507	ENSG00000142507		"Proteasome (prosome, macropain) subunits"	9543	protein-coding gene	gene with protein product		600307				8066462, 1888762	Standard	NM_002798		Approved	Y, DELTA	uc002fzb.4	P28072	OTTHUMG00000090777	ENST00000270586.3:c.713C>A	chr17.hg19:g.4701710C>A	ENSP00000270586:p.Pro238His	57.0	0.0		37.0	14.0	NM_002798	Q96J55	Missense_Mutation	SNP	ENST00000270586.3	hg19	CCDS11056.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.655578	0.29425	.	.	ENSG00000142507	ENST00000270586	T	0.30714	1.52	5.43	2.27	0.28462	.	0.087960	0.44483	D	0.000441	T	0.14270	0.0345	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18524	-1.0334	10	0.87932	D	0	-11.7244	6.4178	0.21725	0.3216:0.593:0.0:0.0855	.	238	P28072	PSB6_HUMAN	H	238	ENSP00000270586:P238H	ENSP00000270586:P238H	P	+	2	0	PSMB6	4648668	0.063000	0.20901	0.001000	0.08648	0.028000	0.11728	0.862000	0.27899	0.230000	0.21059	-0.136000	0.14681	CCC	.	.		0.478	PSMB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207559.2	NM_002798		A	4701710	C	A	4701710	3	1	66	1	0	0	0	0	1	0	0	0	12693	623	22	3	735	3	PSMB6	17	4701710	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10		4701710	76493500	78	8562										
EIF5A	1984	hgsc.bcm.edu	37	chr17	7213030	7213030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	caatgcagtgctcagcattaCgtaagaatggctttgtggtg	12	7	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr17:7213030C>T	ENST00000336458.8	+	2	477	c.76C>T	c.(76-78)Cgt>Tgt	p.R26C	EIF5A_ENST00000336452.7_Missense_Mutation_p.R56C|EIF5A_ENST00000419711.2_Missense_Mutation_p.R26C|EIF5A_ENST00000416016.2_Missense_Mutation_p.R26C|EIF5A_ENST00000576930.1_Missense_Mutation_p.R26C|EIF5A_ENST00000572815.1_Missense_Mutation_p.R26C|EIF5A_ENST00000573542.1_Missense_Mutation_p.R26C|EIF5A_ENST00000571955.1_Missense_Mutation_p.R26C	NM_001970.4	NP_001961.1	P63241	IF5A1_HUMAN	eukaryotic translation initiation factor 5A	26	DOHH-binding.				apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|mRNA export from nucleus (GO:0006406)|nucleocytoplasmic transport (GO:0006913)|peptidyl-lysine modification to peptidyl-hypusine (GO:0008612)|positive regulation of cell proliferation (GO:0008284)|positive regulation of translational elongation (GO:0045901)|positive regulation of translational termination (GO:0045905)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|translational frameshifting (GO:0006452)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation elongation factor activity (GO:0003746)|U6 snRNA binding (GO:0017070)			endometrium(2)|kidney(1)|large_intestine(2)|urinary_tract(1)	6						CTCAGCATTACGTAAGAATGG	0.512																																					p.R56C		Atlas-SNP	.											EIF5A_ENST00000336452,NS,carcinoma,0,3	EIF5A	28	.	0			c.C166T						.						189	174	179					17																	7213030		2203	4300	6503	SO:0001583	missense	1984	exon2			GCATTACGTAAGA		CCDS11099.1, CCDS45601.1	17p13-p12	2009-05-01			ENSG00000132507	ENSG00000132507			3300	protein-coding gene	gene with protein product		600187				7759117	Standard	NM_001143760		Approved	EIF5A1, EIF-5A, MGC99547, MGC104255	uc002gfr.3	P63241	OTTHUMG00000102197	ENST00000336458.8:c.76C>T	chr17.hg19:g.7213030C>T	ENSP00000336776:p.Arg26Cys	52.0	0.0		26.0	17.0	NM_001143760	A8K9A0|D3DTP2|P10159|Q16182|Q7L7L3|Q7Z4L1|Q9D0G2	Missense_Mutation	SNP	ENST00000336458.8	hg19	CCDS11099.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.242343	0.58995	.	.	ENSG00000132507	ENST00000336452;ENST00000336458;ENST00000419711;ENST00000416016	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	4.15	4.15	0.48705	Translation protein SH3-like (1);Translation protein SH3-like, subgroup (1);	0.171029	0.37530	N	0.002052	T	0.65995	0.2745	H	0.97659	4.05	0.80722	D	1	B;P	0.39376	0.418;0.67	B;B	0.32762	0.097;0.152	T	0.80065	-0.1538	10	0.72032	D	0.01	-19.2679	15.3693	0.74551	0.0:1.0:0.0:0.0	.	26;56	P63241;P63241-2	IF5A1_HUMAN;.	C	56;26;26;26	ENSP00000336702:R56C;ENSP00000336776:R26C;ENSP00000390677:R26C;ENSP00000396073:R26C	ENSP00000336702:R56C	R	+	1	0	EIF5A	7153754	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.295000	0.59049	2.158000	0.67659	0.400000	0.26472	CGT	.	.		0.512	EIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220047.3	NM_001970		T	7213030	C	T	7213030	3	4	66	1	0	0	0	0	1	0	0	0	5043	536	19	1	172	1	EIF5A	17	7213030	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	2511320	7213030	73982180	79	8563										
COX10	1352	hgsc.bcm.edu	37	chr17	13980195	13980195	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	cctctctcaccgcccagcctAtctttgtccagaaagccaaa	5	17	3	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr17:13980195A>G	ENST00000261643.3	+	3	398	c.321A>G	c.(319-321)ctA>ctG	p.L107L	COX10_ENST00000429152.2_Silent_p.L107L|COX10_ENST00000537334.1_Intron|COX10_ENST00000536205.1_5'UTR	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	107					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		CGCCCAGCCTATCTTTGTCCA	0.418																																					p.L107L		Atlas-SNP	.											.	COX10	36	.	0			c.A321G						.						86	81	83					17																	13980195		2203	4300	6503	SO:0001819	synonymous_variant	1352	exon3			CAGCCTATCTTTG	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.321A>G	chr17.hg19:g.13980195A>G		147.0	0.0		102.0	44.0	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Silent	SNP	ENST00000261643.3	hg19	CCDS11166.1	.	.	.	.	.	.	.	.	.	.	A	4.413	0.076389	0.08485	.	.	ENSG00000006695	ENST00000429152	.	.	.	5.35	-4.16	0.03869	.	.	.	.	.	T	0.17959	0.0431	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24584	-1.0156	4	.	.	.	.	1.9448	0.03354	0.4282:0.0959:0.2815:0.1944	.	.	.	.	V	68	.	.	I	+	1	0	COX10	13920920	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-1.818000	0.01717	-1.031000	0.03308	-1.229000	0.01577	ATC	.	.		0.418	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		G	13980195	A	G	13980195	2	3	66	1	0	0	0	0	0	0	0	1	3764	436	16	2		2	COX10	17	13980195	Silent	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	6767165	13980195	67215015	80	8564										
DGKE	8526	hgsc.bcm.edu	37	chr17	54925299	54925299	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctaggtttttgatgtaactaAaactcctcctatcaaagccc	5	11	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr17:54925299A>G	ENST00000284061.3	+	5	941	c.761A>G	c.(760-762)aAa>aGa	p.K254R		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	254	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					GATGTAACTAAAACTCCTCCT	0.388																																					p.K254R		Atlas-SNP	.											.	DGKE	47	.	0			c.A761G						.						85	87	86					17																	54925299		2203	4300	6503	SO:0001583	missense	8526	exon5			TAACTAAAACTCC	U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"diacylglycerol kinase, epsilon (64kD)"			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.761A>G	chr17.hg19:g.54925299A>G	ENSP00000284061:p.Lys254Arg	52.0	0.0		52.0	12.0	NM_003647	Q8TBM4|Q9UKQ3	Missense_Mutation	SNP	ENST00000284061.3	hg19	CCDS11590.1	.	.	.	.	.	.	.	.	.	.	A	14.21	2.468249	0.43839	.	.	ENSG00000153933	ENST00000284061	T	0.22134	1.97	5.57	5.57	0.84162	Diacylglycerol kinase, catalytic domain (3);	0.189132	0.56097	D	0.000034	T	0.18299	0.0439	N	0.26162	0.8	0.80722	D	1	B;B	0.14438	0.01;0.01	B;B	0.23716	0.048;0.048	T	0.03354	-1.1045	10	0.36615	T	0.2	.	15.7272	0.77770	1.0:0.0:0.0:0.0	.	254;254	A1L4Q0;P52429	.;DGKE_HUMAN	R	254	ENSP00000284061:K254R	ENSP00000284061:K254R	K	+	2	0	DGKE	52280298	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.538000	0.60650	2.102000	0.63906	0.482000	0.46254	AAA	.	.		0.388	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647		G	54925299	A	G	54925299	3	3	66	1	0	0	0	0	1	0	0	0	4470	14	1	2	775	2	DGKE	17	54925299	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	40945104	54925299	26269911	81	8565										
CLTC	1213	hgsc.bcm.edu	37	chr17	57758348	57758348	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	taaaggctttcatgactgcaGaccttcctaatgaactcatt	6	10	2	3			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr17:57758348G>C	ENST00000269122.3	+	19	3269	c.2995G>C	c.(2995-2997)Gac>Cac	p.D999H	CLTC_ENST00000393043.1_Missense_Mutation_p.D999H|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	999	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CATGACTGCAGACCTTCCTAA	0.418			T	"ALK, TFE3"	"ALCL, renal "																																p.D999H		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.G2995C						.						147	141	143					17																	57758348		2203	4300	6503	SO:0001583	missense	1213	exon19			ACTGCAGACCTTC	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2995G>C	chr17.hg19:g.57758348G>C	ENSP00000269122:p.Asp999His	134.0	0.0		136.0	43.0	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.811597	0.90707	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.23147	1.92;1.92	5.09	5.09	0.68999	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.045427	0.85682	D	0.000000	T	0.60274	0.2256	M	0.91920	3.255	0.80722	D	1	P;P	0.48834	0.725;0.916	P;D	0.63877	0.791;0.919	T	0.70396	-0.4883	10	0.87932	D	0	.	18.4981	0.90872	0.0:0.0:1.0:0.0	.	999;999	Q00610;Q00610-2	CLH1_HUMAN;.	H	999	ENSP00000269122:D999H;ENSP00000376763:D999H	ENSP00000269122:D999H	D	+	1	0	CLTC	55113130	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.374000	0.81015	0.650000	0.86243	GAC	.	.		0.418	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		C	57758348	G	C	57758348	3	2	66	1	0	0	0	0	1	0	0	0	3568	942	33	4	3069	4	CLTC	17	57758348	Missense_Mutation	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	2833049	57758348	23436862	82	8566										
TANC2	26115	hgsc.bcm.edu	37	chr17	61476233	61476233	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	aagatgaagaggaagtagagCgagcacagatcaacagcttt	12	6	1	5			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr17:61476233C>T	ENST00000424789.2	+	17	3071	c.3067C>T	c.(3067-3069)Cga>Tga	p.R1023*	RP11-269G24.3_ENST00000583552.1_RNA|TANC2_ENST00000389520.4_Nonsense_Mutation_p.R1023*|AC015923.1_ENST00000431604.1_RNA	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	1023					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						GGAAGTAGAGCGAGCACAGAT	0.453																																					p.R1023X		Atlas-SNP	.											.	TANC2	266	.	0			c.C3067T						.						114	116	115					17																	61476233		1975	4157	6132	SO:0001587	stop_gained	26115	exon17			GTAGAGCGAGCAC	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.3067C>T	chr17.hg19:g.61476233C>T	ENSP00000387593:p.Arg1023*	126.0	0.0		136.0	43.0	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Nonsense_Mutation	SNP	ENST00000424789.2	hg19	CCDS45754.1	.	.	.	.	.	.	.	.	.	.	C	40	8.250445	0.98727	.	.	ENSG00000170921	ENST00000389520;ENST00000424789	.	.	.	5.92	4.95	0.65309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.2632	0.66099	0.3834:0.6166:0.0:0.0	.	.	.	.	X	1023	.	ENSP00000374171:R1023X	R	+	1	2	TANC2	58829965	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.200000	0.51051	1.504000	0.48704	0.561000	0.74099	CGA	.	.		0.453	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			T	61476233	C	T	61476233	4	4	66	1	0	0	0	0	0	1	0	0	15560	760	27	1	3133	1	TANC2	17	61476233	Nonsense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	3717885	61476233	19718977	83	8567										
AFMID	7083	hgsc.bcm.edu	37	chr17	76183502	76183502	+	5'Flank	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	agcaaggttccttggaagaaGatgtctgcagaggtaggtgg	16	5	1	3			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr17:76183502G>A	ENST00000301634.7	-	0	0				TK1_ENST00000588734.1_5'Flank|AFMID_ENST00000586731.1_De_novo_Start_InFrame|AFMID_ENST00000409257.5_Silent_p.K17K|TK1_ENST00000590862.1_5'Flank|AFMID_ENST00000588800.1_Silent_p.K17K|TK1_ENST00000405273.1_5'Flank|TK1_ENST00000590430.1_5'Flank|AFMID_ENST00000589256.1_Silent_p.K17K|AFMID_ENST00000327898.5_Silent_p.K17K|AFMID_ENST00000591952.1_Silent_p.K17K	NM_003258.4	NP_003249.3	P04183	KITH_HUMAN	thymidine kinase 1, soluble						deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|digestive tract development (GO:0048565)|DNA replication (GO:0006260)|fetal process involved in parturition (GO:0060138)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to copper ion (GO:0046688)|response to cortisol (GO:0051414)|response to nutrient levels (GO:0031667)|response to toxic substance (GO:0009636)|skeletal muscle cell proliferation (GO:0014856)|small molecule metabolic process (GO:0044281)|thymidine metabolic process (GO:0046104)	cytosol (GO:0005829)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|nucleoside kinase activity (GO:0019206)|thymidine kinase activity (GO:0004797)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|urinary_tract(2)	4			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.0804)|Lung(188;0.23)		Trifluridine(DB00432)|Zidovudine(DB00495)	CTTGGAAGAAGATGTCTGCAG	0.527																																					p.K17K		Atlas-SNP	.											.	AFMID	38	.	0			c.G51A						.						149	130	137					17																	76183502		2203	4300	6503	SO:0001631	upstream_gene_variant	125061	exon1			GAAGAAGATGTCT		CCDS11754.1	17q23.2-q25.3	2012-10-02			ENSG00000167900	ENSG00000167900	2.7.1.21		11830	protein-coding gene	gene with protein product		188300					Standard	NM_003258		Approved		uc002juw.2	P04183	OTTHUMG00000150674		chr17.hg19:g.76183502G>A	Exception_encountered	49.0	0.0		47.0	20.0	NM_001145526	B2RC58|Q969V0|Q9UMG9	Silent	SNP	ENST00000301634.7	hg19	CCDS11754.1																																																																																			.	.		0.527	TK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319577.1	NM_003258		A	76183502	G	A	76183502	1	1	66	0	1	0	0	0	0	0	0	0	362	933	33	3		3	AFMID	17	76183502	5'Flank	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10	14707269	76183502	5011708	84	8568										
EMILIN2	84034	hgsc.bcm.edu	37	chr18	2891529	2891529	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	aagaacgctgaagaacattgCttttacattgaggaaaccct	8	8	0	4			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr18:2891529C>T	ENST00000254528.3	+	4	1563	c.1404C>T	c.(1402-1404)tgC>tgT	p.C468C		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	468					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		AAGAACATTGCTTTTACATTG	0.463																																					p.C468C		Atlas-SNP	.											.	EMILIN2	97	.	0			c.C1404T						.						98	106	103					18																	2891529		2203	4300	6503	SO:0001819	synonymous_variant	84034	exon4			ACATTGCTTTTAC	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.1404C>T	chr18.hg19:g.2891529C>T		89.0	0.0		99.0	42.0	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Silent	SNP	ENST00000254528.3	hg19	CCDS11828.1																																																																																			.	.		0.463	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2891529	C	T	2891529	2	4	66	1	0	0	0	0	0	0	0	1	5096	805	28	3		3	EMILIN2	18	2891529	Silent	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10		2891529	75185719	85	8569										
CYB5A	1528	hgsc.bcm.edu	37	chr18	71959015	71959027	+	Frame_Shift_Del	DEL	GTGGTGCAGGATC	GTGGTGCAGGATC	-													0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ttggtcaaatcgtacaccttGtggtgcaggatcagccaggt							TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	GTGGTGCAGGATC	GTGGTGCAGGATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr18:71959015_71959027delGTGGTGCAGGATC	ENST00000340533.4	-	1	224_236	c.84_96delGATCCTGCACCAC	c.(82-96)ctgatcctgcaccacfs	p.LILHH28fs	CYB5A_ENST00000299438.9_5'Flank|CYB5A_ENST00000397914.4_Frame_Shift_Del_p.LILHH28fs|CYB5A_ENST00000494131.2_Frame_Shift_Del_p.LILHH28fs	NM_148923.3	NP_683725.1	P00167	CYB5_HUMAN	cytochrome b5 type A (microsomal)	28	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				hydrogen ion transmembrane transport (GO:1902600)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	aldo-keto reductase (NADP) activity (GO:0004033)|cytochrome-c oxidase activity (GO:0004129)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(1)|lung(1)|skin(1)	4		Esophageal squamous(42;0.0749)|Prostate(75;0.157)|Melanoma(33;0.211)				CGTACACCTTGTGGTGCAGGATCAGCCAGGTGC	0.587											OREG0025052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.29_33del	NSCLC(176;1530 2076 2606 27426 50572)|Ovarian(151;328 1870 2837 37860 52175)	Atlas-Indel,Pindel	.											.	CYB5A	9	.	0			c.85_97del						.																																			SO:0001589	frameshift_variant	1528	exon1			.	M22865	CCDS12004.1, CCDS12005.1, CCDS54188.1	18q23	2006-01-30	2006-01-30	2006-01-30	ENSG00000166347	ENSG00000166347		"Cytochrome b genes"	2570	protein-coding gene	gene with protein product		613218	"cytochrome b-5", "cytochrome b5 (microsomal)"	CYB5		1840560	Standard	NM_148923		Approved		uc002lli.3	P00167	OTTHUMG00000132843	ENST00000340533.4:c.84_96delGATCCTGCACCAC	chr18.hg19:g.71959015_71959027delGTGGTGCAGGATC	ENSP00000341625:p.Leu28fs	52.0	0.0	1134	61.0	13.0	NM_001914	A8MV91|F8WEU4|Q6IB14	Frame_Shift_Del	DEL	ENST00000340533.4	hg19	CCDS12004.1																																																																																			.	.		0.587	CYB5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256316.1	NM_001914, NM_148923		-	71959027	GTGGTGCAGGATC	-	71959015	7	5	66	1	0	1	0	1	0	0	0	0	4124	1368	48	0	341	0	CYB5A	18	71959015	Frame_Shift_Del	DEL	GTGGTGCAGGATC	TCGA-CC-A3MC-01A-11D-A22F-10	69067486	71959015	6118233	86	8570										
RANBP3	8498	hgsc.bcm.edu	37	chr19	5931460	5931460	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gcttcggaaggacttctccaTgcagcagtgtcaggggatgc	14	10	2	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr19:5931460T>C	ENST00000340578.6	-	8	705	c.648A>G	c.(646-648)gcA>gcG	p.A216A	RANBP3_ENST00000034275.8_Silent_p.A148A|RANBP3_ENST00000591092.1_Silent_p.A148A|RANBP3_ENST00000439268.2_Silent_p.A216A|RANBP3_ENST00000541471.1_Silent_p.A88A|RANBP3_ENST00000591124.1_5'Flank	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3	216					intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						GACTTCTCCATGCAGCAGTGT	0.647																																					p.A216A		Atlas-SNP	.											.	RANBP3	36	.	0			c.A648G						.						42	48	46					19																	5931460		2134	4246	6380	SO:0001819	synonymous_variant	8498	exon8			TCTCCATGCAGCA	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4		ENST00000340578.6:c.648A>G	chr19.hg19:g.5931460T>C		66.0	0.0		39.0	19.0	NM_007322	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Silent	SNP	ENST00000340578.6	hg19	CCDS42478.1																																																																																			.	.		0.647	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322		C	5931460	T	C	5931460	2	2	66	1	0	0	0	0	0	0	0	1	13044	1451	51	2		2	RANBP3	19	5931460	Silent	SNP	T	TCGA-CC-A3MC-01A-11D-A22F-10		5931460	53197523	87	8571										
PKN1	5585	hgsc.bcm.edu	37	chr19	14574553	14574553	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	aaaattttctccaagcagcaAggtgagagggtgctccaggc	12	9	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr19:14574553A>C	ENST00000242783.6	+	10	1659	c.1494A>C	c.(1492-1494)caA>caC	p.Q498H	PKN1_ENST00000342216.4_Splice_Site_p.Q504H	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	498					activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						CCAAGCAGCAAGGTGAGAGGG	0.617																																					p.Q504H	NSCLC(185;2539 2965 10733 52867)	Atlas-SNP	.											.	PKN1	99	.	0			c.A1512C						.						66	72	70					19																	14574553		2053	4191	6244	SO:0001630	splice_region_variant	5585	exon10			GCAGCAAGGTGAG	S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"protein kinase C-like 1"	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.1495+1A>C	chr19.hg19:g.14574553A>C		94.0	0.0		97.0	32.0	NM_213560	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Missense_Mutation	SNP	ENST00000242783.6	hg19	CCDS42513.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.441295	0.43326	.	.	ENSG00000123143	ENST00000242783;ENST00000342216	T;T	0.37058	1.22;1.22	4.72	2.47	0.30058	.	0.000000	0.64402	U	0.000003	T	0.53270	0.1786	M	0.76170	2.325	0.38450	D	0.946931	D;D	0.69078	0.997;0.995	D;D	0.81914	0.995;0.99	T	0.53746	-0.8395	10	0.72032	D	0.01	-13.5973	5.9547	0.19267	0.5415:0.0:0.4585:0.0	.	504;498	Q16512-2;Q16512	.;PKN1_HUMAN	H	498;504	ENSP00000242783:Q498H;ENSP00000343325:Q504H	ENSP00000242783:Q498H	Q	+	3	2	PKN1	14435553	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	1.426000	0.34870	0.227000	0.20999	0.454000	0.30748	CAA	.	.		0.617	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560	Missense_Mutation	C	14574553	A	C	14574553	5	2	66	1	0	0	0	0	0	0	1	0	11988	86	3	5	1575	5	PKN1	19	14574553	Splice_Site	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	8643093	14574553	44554430	88	8572										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15300099	15300099	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctcaccgatagagcactcgtCcacatcctggtcacatgccc	7	17	2	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr19:15300099C>G	ENST00000263388.2	-	7	1252	c.1177G>C	c.(1177-1179)Gac>Cac	p.D393H		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	393	EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			GAGCACTCGTCCACATCCTGG	0.632																																					p.D393H		Atlas-SNP	.											.	NOTCH3	340	.	0			c.G1177C						.						84	82	83					19																	15300099		2203	4300	6503	SO:0001583	missense	4854	exon7			ACTCGTCCACATC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1177G>C	chr19.hg19:g.15300099C>G	ENSP00000263388:p.Asp393His	39.0	0.0		33.0	12.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.680284	0.68042	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.95622	-3.76	4.68	4.68	0.58851	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.98043	0.9355	M	0.89840	3.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.99316	1.0905	9	0.87932	D	0	.	16.3746	0.83381	0.0:1.0:0.0:0.0	.	396;393	Q59FL3;Q9UM47	.;NOTC3_HUMAN	H	393;395	ENSP00000263388:D393H	ENSP00000263388:D393H	D	-	1	0	NOTCH3	15161099	1.000000	0.71417	0.998000	0.56505	0.539000	0.34962	5.645000	0.67909	2.154000	0.67381	0.491000	0.48974	GAC	.	.		0.632	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		G	15300099	C	G	15300099	3	3	66	1	0	0	0	0	1	0	0	0	10559	855	30	4	5896	4	NOTCH3	19	15300099	Missense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	725546	15300099	43828884	89	8573										
ZNF98	148198	hgsc.bcm.edu	37	chr19	22575694	22575694	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctgtaaattttcacgtccacAttttttatatgttctcagta	4	8	2	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr19:22575694A>T	ENST00000357774.5	-	4	464	c.343T>A	c.(343-345)Tgt>Agt	p.C115S		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	115					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				TCACGTCCACATTTTTTATAT	0.328																																					p.C115S		Atlas-SNP	.											.	ZNF98	230	.	0			c.T343A						.						62	50	54					19																	22575694		1949	4162	6111	SO:0001583	missense	148198	exon4			GTCCACATTTTTT		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"Zinc fingers, C2H2-type", "-"	13174	protein-coding gene	gene with protein product	"zinc finger protein 739"	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.343T>A	chr19.hg19:g.22575694A>T	ENSP00000350418:p.Cys115Ser	323.0	1.0		284.0	105.0	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	hg19	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	6.372	0.436684	0.12104	.	.	ENSG00000197360	ENST00000357774	T	0.06218	3.33	0.916	-1.36	0.09085	.	.	.	.	.	T	0.06962	0.0177	M	0.66297	2.02	0.09310	N	1	B	0.18863	0.031	B	0.21917	0.037	T	0.40683	-0.9550	9	0.38643	T	0.18	.	2.3219	0.04213	0.5256:0.0:0.0:0.4744	.	115	A6NK75	ZNF98_HUMAN	S	115	ENSP00000350418:C115S	ENSP00000350418:C115S	C	-	1	0	ZNF98	22367534	0.000000	0.05858	0.174000	0.22961	0.170000	0.22686	-0.037000	0.12164	0.257000	0.21650	0.254000	0.18369	TGT	.	.		0.328	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		T	22575694	A	T	22575694	3	4	66	1	0	0	0	0	1	0	0	0	18218	217	8	4	1379	4	ZNF98	19	22575694	Missense_Mutation	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	7275595	22575694	36553289	90	8574										
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38633246	38633246	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ccagaaaccccttacacagtAtcaccagcaggggccgacag	9	15	1	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr19:38633246A>G	ENST00000222345.6	+	12	3938	c.3429A>G	c.(3427-3429)gtA>gtG	p.V1143V		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1143					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CTTACACAGTATCACCAGCAG	0.617											OREG0025445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V1143V		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.A3429G						.						226	218	221					19																	38633246		2203	4300	6503	SO:0001819	synonymous_variant	23094	exon12			CACAGTATCACCA	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3429A>G	chr19.hg19:g.38633246A>G		32.0	0.0	879	27.0	7.0	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	hg19	CCDS33007.1																																																																																			.	.		0.617	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		G	38633246	A	G	38633246	2	3	66	1	0	0	0	0	0	0	0	1	14346	436	16	2		2	SIPA1L3	19	38633246	Silent	SNP	A	TCGA-CC-A3MC-01A-11D-A22F-10	16057552	38633246	20495737	91	8575										
PRMT1	3276	hgsc.bcm.edu	37	chr19	50187272	50187272	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	agcgagtggatgggctactgCctcttctacgagtccatgct	12	11	2	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr19:50187272C>A	ENST00000391851.4	+	5	576	c.447C>A	c.(445-447)tgC>tgA	p.C149*	PRMT1_ENST00000532489.1_Nonsense_Mutation_p.C121*|MIR5088_ENST00000581740.1_RNA|PRMT1_ENST00000454376.2_Nonsense_Mutation_p.C167*	NM_198318.4	NP_938074.2	Q99873	ANM1_HUMAN	protein arginine methyltransferase 1	157	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.			DIIISEWMGYCLFYESMLNTVLYARDKWL -> ASSSASGW ATASSTSPCSTPCSMPGTSV (in Ref. 2; BAA11029). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of megakaryocyte differentiation (GO:0045653)|neuron projection development (GO:0031175)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|protein methylation (GO:0006479)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|identical protein binding (GO:0042802)|methyltransferase activity (GO:0008168)|N-methyltransferase activity (GO:0008170)|poly(A) RNA binding (GO:0044822)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2)	12		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)		TGGGCTACTGCCTCTTCTACG	0.632																																					p.C167X		Atlas-SNP	.											.	PRMT1	31	.	0			c.C501A						.						207	136	160					19																	50187272		2203	4300	6503	SO:0001587	stop_gained	3276	exon6			CTACTGCCTCTTC	D66904	CCDS42592.1, CCDS46145.1, CCDS74425.1	19q13	2014-06-12	2006-02-16	2006-02-16	ENSG00000126457	ENSG00000126457	2.1.1.125	"Protein arginine methyltransferases"	5187	protein-coding gene	gene with protein product		602950	"HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 2", "HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)"	HRMT1L2		9545638	Standard	NM_001207042		Approved	HCP1, ANM1	uc010enf.2	Q99873	OTTHUMG00000167568	ENST00000391851.4:c.447C>A	chr19.hg19:g.50187272C>A	ENSP00000375724:p.Cys149*	90.0	0.0		87.0	22.0	NM_001536	B4E3C3|G5E9B6|Q15529|Q2VP93|Q6LEU5|Q8WUW5|Q99872|Q99874|Q9NZ04|Q9NZ05|Q9NZ06	Nonsense_Mutation	SNP	ENST00000391851.4	hg19	CCDS42592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.5|22.5	4.302155|4.302155	0.81136|0.81136	.|.	.|.	ENSG00000126457|ENSG00000126457	ENST00000524771|ENST00000529284;ENST00000532489;ENST00000527382;ENST00000534465;ENST00000391851;ENST00000449059;ENST00000454376;ENST00000526224	.|.	.|.	.|.	4.15|4.15	3.11|3.11	0.35812|0.35812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.27697|.	0.0681|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.29119|.	-1.0022|.	3|.	.|0.10111	.|T	.|0.7	-4.5292|-4.5292	6.2474|6.2474	0.20827|0.20827	0.0:0.7754:0.0:0.2246|0.0:0.7754:0.0:0.2246	.|.	.|.	.|.	.|.	D|X	177|121;121;121;121;149;143;167;121	.|.	.|ENSP00000375724:C149X	A|C	+|+	2|3	0|2	PRMT1|PRMT1	54879084|54879084	0.369000|0.369000	0.25039|0.25039	1.000000|1.000000	0.80357|0.80357	0.930000|0.930000	0.56654|0.56654	-0.264000|-0.264000	0.08658|0.08658	0.933000|0.933000	0.37291|0.37291	0.591000|0.591000	0.81541|0.81541	GCC|TGC	.	.		0.632	PRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395065.1	NM_001536		A	50187272	C	A	50187272	4	1	66	1	0	0	0	0	0	1	0	0	12547	747	26	3	523	3	PRMT1	19	50187272	Nonsense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	11554026	50187272	8941711	92	8576										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18374289	18374289	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ctatggataattgcacaaagGgccaagccacttttccagga	9	10	0	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr22:18374289G>C	ENST00000441493.2	-	12	2008	c.1656C>G	c.(1654-1656)gcC>gcG	p.A552A	MICAL3_ENST00000207726.7_Silent_p.A552A|MICAL3_ENST00000444520.1_Silent_p.A552A|MICAL3_ENST00000414725.2_Silent_p.A552A|MICAL3_ENST00000429452.1_Silent_p.A552A|MICAL3_ENST00000400561.2_Silent_p.A552A|MICAL3_ENST00000585038.1_Silent_p.A552A|MICAL3_ENST00000383094.3_Silent_p.A552A	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	552	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		TTGCACAAAGGGCCAAGCCAC	0.473																																					p.A552A		Atlas-SNP	.											.	MICAL3	53	.	0			c.C1656G						.						101	85	90					22																	18374289		1568	3582	5150	SO:0001819	synonymous_variant	57553	exon12			ACAAAGGGCCAAG	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.1656C>G	chr22.hg19:g.18374289G>C		169.0	0.0		170.0	56.0	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.		0.473	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			C	18374289	G	C	18374289	2	2	66	1	0	0	0	0	0	0	0	1	9580	1219	43	4		4	MICAL3	22	18374289	Silent	SNP	G	TCGA-CC-A3MC-01A-11D-A22F-10		18374289	32930277	93	8577										
TNRC6B	23112	hgsc.bcm.edu	37	chr22	40662452	40662452	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	gaggtggacgccagcccaatCaaggatggtcttctggaaag	14	9	3	0			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chr22:40662452C>T	ENST00000454349.2	+	5	2429	c.2218C>T	c.(2218-2220)Caa>Taa	p.Q740*	TNRC6B_ENST00000402203.1_Intron|TNRC6B_ENST00000301923.9_Intron|TNRC6B_ENST00000335727.9_Nonsense_Mutation_p.Q740*	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	740	Interaction with argonaute proteins.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						CCAGCCCAATCAAGGATGGTC	0.522																																					p.Q740X		Atlas-SNP	.											TNRC6B_ENST00000454349,NS,carcinoma,0,1	TNRC6B	195	.	0			c.C2218T						.						36	36	36					22																	40662452		1887	4115	6002	SO:0001587	stop_gained	23112	exon5			CCCAATCAAGGAT	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.2218C>T	chr22.hg19:g.40662452C>T	ENSP00000401946:p.Gln740*	49.0	0.0		112.0	54.0	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Nonsense_Mutation	SNP	ENST00000454349.2	hg19	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	C	37	6.126756	0.97305	.	.	ENSG00000100354	ENST00000454349;ENST00000400140;ENST00000335727	.	.	.	5.46	5.46	0.80206	.	0.591582	0.18879	N	0.128612	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	0.0239	19.3029	0.94150	0.0:1.0:0.0:0.0	.	.	.	.	X	740	.	ENSP00000338371:Q740X	Q	+	1	0	TNRC6B	38992398	1.000000	0.71417	0.995000	0.50966	0.422000	0.31414	3.532000	0.53553	2.575000	0.86900	0.561000	0.74099	CAA	.	.		0.522	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				T	40662452	C	T	40662452	4	4	66	1	0	0	0	0	0	1	0	0	16356	827	29	3	2357	3	TNRC6B	22	40662452	Nonsense_Mutation	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10	22288163	40662452	10642114	94	8578										
HCFC1	3054	hgsc.bcm.edu	37	chrX	153224782	153224782	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0631578947368421	6	1	1.5492213570634	2.28694581280788	1.33405172413793	0.619909502262444	1	0	ccccagtgaccactcctcacCgttccctgggcactctgtgt	8	18	2	1			TCGA-CC-A3MC-01A-11D-A22F-10	TCGA-CC-A3MC-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	53285fbd-271b-4966-99a6-be108d4ca51c	b6adfc43-1baa-4942-bf7d-41745f3c0f90	g.chrX:153224782C>A	ENST00000310441.7	-	9	2571	c.1605G>T	c.(1603-1605)acG>acT	p.T535T	HCFC1_ENST00000369984.4_Splice_Site_p.T535T|HCFC1_ENST00000354233.3_Splice_Site_p.T466T|HCFC1_ENST00000461098.1_5'Flank	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	535	Required for interaction with OGT.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CACTCCTCACCGTTCCCTGGG	0.612																																					p.T535T		Atlas-SNP	.											.	HCFC1	284	.	0			c.G1605T						.						135	142	139					X																	153224782		2087	4173	6260	SO:0001630	splice_region_variant	3054	exon9			CCTCACCGTTCCC		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"VP16-accessory protein", "protein phosphatase 1, regulatory subunit 89"	300019	"mental retardation, X-linked 3", "host cell factor C1 (VP16-accessory protein)"	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.1605+1G>T	chrX.hg19:g.153224782C>A		45.0	0.0		43.0	26.0	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	hg19	CCDS44020.1																																																																																			.	.		0.612	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334	Silent	A	153224782	C	A	153224782	5	1	66	1	0	0	0	0	0	0	1	0	7000	666	23	1	4574	1	HCFC1	23	153224782	Splice_Site	SNP	C	TCGA-CC-A3MC-01A-11D-A22F-10		153224782	2045778	95	8579										
MTOR	2475	hgsc.bcm.edu	37	chr1	11298100	11298100	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	caagacacagtagcgaatgtCagggtctgcaagagcaatgg	13	8	2	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr1:11298100C>G	ENST00000361445.4	-	13	2084	c.2008G>C	c.(2008-2010)Gac>Cac	p.D670H		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	670					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TAGCGAATGTCAGGGTCTGCA	0.552																																					p.D670H		Atlas-SNP	.											.	MTOR	327	.	0			c.G2008C						.						55	49	51					1																	11298100		2203	4300	6503	SO:0001583	missense	2475	exon13			GAATGTCAGGGTC	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.2008G>C	chr1.hg19:g.11298100C>G	ENSP00000354558:p.Asp670His	161.0	0.0		160.0	50.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.842137	0.91197	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.32988	1.43	5.83	5.83	0.93111	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.45074	0.1324	M	0.62209	1.925	0.80722	D	1	P	0.50617	0.937	P	0.49276	0.605	T	0.33727	-0.9857	10	0.56958	D	0.05	-4.7663	20.115	0.97926	0.0:1.0:0.0:0.0	.	670	P42345	MTOR_HUMAN	H	670	ENSP00000354558:D670H	ENSP00000354558:D670H	D	-	1	0	MTOR	11220687	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	7.456000	0.80751	2.761000	0.94854	0.650000	0.86243	GAC	.	.		0.552	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		G	11298100	C	G	11298100	3	3	67	1	0	0	0	0	1	0	0	0	9963	826	29	4	5825	4	MTOR	1	11298100	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10		11298100	237952521	1	8580										
PLEKHM2	23207	hgsc.bcm.edu	37	chr1	16060357	16060357	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	aaattcgaggatgccttgagCctcatccacagcgcctggca	10	13	1	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr1:16060357C>T	ENST00000375799.3	+	20	3215	c.2988C>T	c.(2986-2988)agC>agT	p.S996S	RP11-288I21.1_ENST00000453804.1_RNA|PLEKHM2_ENST00000375793.2_Silent_p.S976S|PLEKHM2_ENST00000477849.1_3'UTR|SLC25A34_ENST00000294454.5_5'Flank	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	996					Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		ATGCCTTGAGCCTCATCCACA	0.647																																					p.S996S		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.C2988T						.						60	70	67					1																	16060357		2082	4203	6285	SO:0001819	synonymous_variant	23207	exon20			CTTGAGCCTCATC	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"Pleckstrin homology (PH) domain containing"	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.2988C>T	chr1.hg19:g.16060357C>T		265.0	0.0		182.0	50.0	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Silent	SNP	ENST00000375799.3	hg19	CCDS44063.1																																																																																			.	.		0.647	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164		T	16060357	C	T	16060357	2	4	67	1	0	0	0	0	0	0	0	1	12090	738	26	3		3	PLEKHM2	1	16060357	Silent	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	4762257	16060357	233190264	2	8581										
KIRREL	55243	hgsc.bcm.edu	37	chr1	158059547	158059547	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tgaggcagtgcagtatgctgTgaggggtgacggtggcaagg	20	5	0	3			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr1:158059547T>C	ENST00000359209.6	+	10	1278	c.1211T>C	c.(1210-1212)gTg>gCg	p.V404A	KIRREL_ENST00000360089.4_Missense_Mutation_p.V240A|KIRREL_ENST00000368173.3_Missense_Mutation_p.V420A|KIRREL_ENST00000392272.2_Missense_Mutation_p.V301A|KIRREL_ENST00000368172.1_Missense_Mutation_p.V218A|KIRREL_ENST00000416935.2_Missense_Mutation_p.V304A			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	404	Ig-like C2-type 5.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					CAGTATGCTGTGAGGGGTGAC	0.602																																					p.V404A		Atlas-SNP	.											.	KIRREL	346	.	0			c.T1211C						.						148	132	137					1																	158059547		2203	4300	6503	SO:0001583	missense	55243	exon10			ATGCTGTGAGGGG	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15734	protein-coding gene	gene with protein product	"nephrin-like protein 1"	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.1211T>C	chr1.hg19:g.158059547T>C	ENSP00000352138:p.Val404Ala	187.0	0.0		228.0	43.0	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Missense_Mutation	SNP	ENST00000359209.6	hg19	CCDS1172.2	.	.	.	.	.	.	.	.	.	.	T	12.66	2.003914	0.35320	.	.	ENSG00000183853	ENST00000360089;ENST00000368173;ENST00000392272;ENST00000359209;ENST00000416935;ENST00000368172	T;T;T;T;T;T	0.03004	4.08;4.08;4.08;4.08;4.08;4.08	5.28	5.28	0.74379	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.775469	0.10417	N	0.677174	T	0.00998	0.0033	N	0.16368	0.405	0.50171	D	0.999853	B;B;B;B	0.11235	0.0;0.004;0.0;0.003	B;B;B;B	0.13407	0.005;0.009;0.002;0.007	T	0.49418	-0.8942	10	0.16420	T	0.52	-8.7755	7.8514	0.29457	0.0:0.0934:0.0:0.9066	.	304;240;218;404	B4DN67;Q5W0F9;Q5W0G0;Q96J84	.;.;.;KIRR1_HUMAN	A	240;420;301;404;304;218	ENSP00000353202:V240A;ENSP00000357155:V420A;ENSP00000376098:V301A;ENSP00000352138:V404A;ENSP00000389674:V304A;ENSP00000357154:V218A	ENSP00000352138:V404A	V	+	2	0	KIRREL	156326171	0.884000	0.30299	0.645000	0.29479	0.521000	0.34408	2.182000	0.42556	1.992000	0.58205	0.377000	0.23210	GTG	.	.		0.602	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240		C	158059547	T	C	158059547	3	2	67	1	0	0	0	0	1	0	0	0	8333	1696	59	2	1249	2	KIRREL	1	158059547	Missense_Mutation	SNP	T	TCGA-CC-A5UC-01A-11D-A28X-10	141999190	158059547	91191074	3	8582										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181767459	181767459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	cctaagtgagagctccatccCctctgtctctgacaccagca	7	16	2	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr1:181767459C>T	ENST00000367573.2	+	48	6431	c.6431C>T	c.(6430-6432)cCc>cTc	p.P2144L	CACNA1E_ENST00000367567.4_Missense_Mutation_p.P1708L|CACNA1E_ENST00000360108.3_Missense_Mutation_p.P2125L|CACNA1E_ENST00000367570.1_Missense_Mutation_p.P2101L|CACNA1E_ENST00000357570.5_Missense_Mutation_p.P2095L|CACNA1E_ENST00000358338.5_Missense_Mutation_p.P2033L|CACNA1E_ENST00000526775.1_Missense_Mutation_p.P2082L	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2144					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AGCTCCATCCCCTCTGTCTCT	0.567																																					p.P2144L		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C6431T						.						125	135	131					1																	181767459		2024	4178	6202	SO:0001583	missense	777	exon48			CCATCCCCTCTGT	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6431C>T	chr1.hg19:g.181767459C>T	ENSP00000356545:p.Pro2144Leu	24.0	0.0		34.0	6.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.932592	0.34096	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96136	-3.85;-3.84;-3.8;-3.84;-3.92;-3.8;-3.8	5.59	4.68	0.58851	.	0.421997	0.27659	N	0.018397	D	0.92838	0.7722	N	0.19112	0.55	0.58432	D	0.999997	D;B	0.56035	0.974;0.002	P;B	0.56343	0.796;0.003	D	0.89826	0.3992	10	0.05525	T	0.97	.	14.2396	0.65948	0.0:0.9277:0.0:0.0723	.	2082;2101	Q15878-2;Q15878-3	.;.	L	2101;2082;2095;2033;1708;2125;2144	ENSP00000356542:P2101L;ENSP00000434814:P2082L;ENSP00000350183:P2095L;ENSP00000351101:P2033L;ENSP00000356539:P1708L;ENSP00000353222:P2125L;ENSP00000356545:P2144L	ENSP00000350183:P2095L	P	+	2	0	CACNA1E	180034082	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.560000	0.53763	1.358000	0.45922	0.563000	0.77884	CCC	.	.		0.567	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181767459	C	T	181767459	3	4	67	1	0	0	0	0	1	0	0	0	2544	623	22	3	6488	3	CACNA1E	1	181767459	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	23707912	181767459	67483162	4	8583										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185992215	185992215	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	aaaaccctgttggaagatgcTggcagatacacatgtgtggc	12	8	0	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr1:185992215T>C	ENST00000271588.4	+	36	5908	c.5679T>C	c.(5677-5679)gcT>gcC	p.A1893A	HMCN1_ENST00000367492.2_Silent_p.A1893A	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1893	Ig-like C2-type 16.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGGAAGATGCTGGCAGATACA	0.413																																					p.A1893A		Atlas-SNP	.											.	HMCN1	797	.	0			c.T5679C						.						127	124	125					1																	185992215		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon36			AGATGCTGGCAGA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.5679T>C	chr1.hg19:g.185992215T>C		142.0	0.0		150.0	28.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.413	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	185992215	T	C	185992215	2	2	67	1	0	0	0	0	0	0	0	1	7229	1567	55	2		2	HMCN1	1	185992215	Silent	SNP	T	TCGA-CC-A5UC-01A-11D-A28X-10	4224756	185992215	63258406	5	8584										
SERTAD4	56256	hgsc.bcm.edu	37	chr1	210412936	210412936	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	aggattttcacccaccactcAgcagctgtagccataaagta	7	12	2	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr1:210412936A>T	ENST00000367012.3	+	3	504	c.274A>T	c.(274-276)Agc>Tgc	p.S92C	SERTAD4_ENST00000490620.1_3'UTR	NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	92						nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		CCCACCACTCAGCAGCTGTAG	0.338																																					p.S92C		Atlas-SNP	.											.	SERTAD4	53	.	0			c.A274T						.						77	85	82					1																	210412936		2203	4300	6503	SO:0001583	missense	56256	exon3			CCACTCAGCAGCT	BC012083	CCDS1494.1	1q32.1-q41	2008-02-05			ENSG00000082497	ENSG00000082497			25236	protein-coding gene	gene with protein product						12477932	Standard	NM_019605		Approved	DJ667H12.2	uc001hhy.3	Q9NUC0	OTTHUMG00000036391	ENST00000367012.3:c.274A>T	chr1.hg19:g.210412936A>T	ENSP00000355979:p.Ser92Cys	140.0	0.0		186.0	65.0	NM_019605	B2RD32	Missense_Mutation	SNP	ENST00000367012.3	hg19	CCDS1494.1	.	.	.	.	.	.	.	.	.	.	a	14.43	2.534486	0.45073	.	.	ENSG00000082497	ENST00000367012	.	.	.	6.16	5.04	0.67666	.	0.193616	0.51477	D	0.000099	T	0.40094	0.1103	N	0.17082	0.46	0.31297	N	0.688734	D	0.63046	0.992	P	0.54401	0.751	T	0.50118	-0.8865	9	0.72032	D	0.01	-24.4619	12.0816	0.53673	0.9336:0.0:0.0664:0.0	.	92	Q9NUC0	SRTD4_HUMAN	C	92	.	ENSP00000355979:S92C	S	+	1	0	SERTAD4	208479559	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.314000	0.43743	1.158000	0.42547	0.529000	0.55759	AGC	.	.		0.338	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1	NM_019605		T	210412936	A	T	210412936	3	4	67	1	0	0	0	0	1	0	0	0	14138	188	7	4	280	4	SERTAD4	1	210412936	Missense_Mutation	SNP	A	TCGA-CC-A5UC-01A-11D-A28X-10	24420721	210412936	38837685	6	8585										
DISP1	84976	hgsc.bcm.edu	37	chr1	223176572	223176572	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	gccctctccatgttcgtcacCagttttaccactgctgctgc	7	16	2	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr1:223176572C>A	ENST00000284476.6	+	8	1997	c.1833C>A	c.(1831-1833)acC>acA	p.T611T		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	611	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		TGTTCGTCACCAGTTTTACCA	0.448																																					p.T611T		Atlas-SNP	.											.	DISP1	145	.	0			c.C1833A						.						144	133	137					1																	223176572		2203	4300	6503	SO:0001819	synonymous_variant	84976	exon10			CGTCACCAGTTTT	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.1833C>A	chr1.hg19:g.223176572C>A		150.0	0.0		177.0	14.0	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Silent	SNP	ENST00000284476.6	hg19	CCDS1536.1																																																																																			.	.		0.448	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		A	223176572	C	A	223176572	2	1	67	1	0	0	0	0	0	0	0	1	4541	581	21	3		3	DISP1	1	223176572	Silent	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	12763636	223176572	26074049	7	8586										
PLB1	151056	hgsc.bcm.edu	37	chr2	28761221	28761221	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	ggcggcgtggatgagctgatGggggtgctggactacctgca	19	8	0	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr2:28761221G>A	ENST00000327757.5	+	10	635	c.591G>A	c.(589-591)atG>atA	p.M197I	PLB1_ENST00000422425.2_Missense_Mutation_p.M208I	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	197	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					ATGAGCTGATGGGGGTGCTGG	0.662																																					p.M208I		Atlas-SNP	.											.	PLB1	255	.	0			c.G624A						.						43	41	42					2																	28761221		2203	4300	6503	SO:0001583	missense	151056	exon10			GCTGATGGGGGTG		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.591G>A	chr2.hg19:g.28761221G>A	ENSP00000330442:p.Met197Ile	42.0	0.0		33.0	13.0	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	hg19	CCDS33168.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.589|8.589	0.884032|0.884032	0.17467|0.17467	.|.	.|.	ENSG00000163803|ENSG00000163803	ENST00000416713;ENST00000327757;ENST00000422425|ENST00000404858	T;T;T|.	0.21932|.	1.98;2.82;2.83|.	5.0|5.0	-9.99|-9.99	0.00435|0.00435	.|.	1.745490|.	0.03019|.	N|.	0.150533|.	T|.	0.11110|.	0.0271|.	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	N|N	1|1	B;B|.	0.09022|.	0.002;0.0|.	B;B|.	0.08055|.	0.003;0.0|.	T|.	0.10132|.	-1.0643|.	10|.	0.19147|.	T|.	0.46|.	-0.5139|-0.5139	4.4555|4.4555	0.11642|0.11642	0.2273:0.2661:0.4257:0.0809|0.2273:0.2661:0.4257:0.0809	.|.	208;197|.	Q6P1J6-3;Q6P1J6|.	.;PLB1_HUMAN|.	I|X	152;197;208|207	ENSP00000407076:M152I;ENSP00000330442:M197I;ENSP00000416440:M208I|.	ENSP00000330442:M197I|.	M|W	+|+	3|2	0|0	PLB1|PLB1	28614725|28614725	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.191000|0.191000	0.23601|0.23601	-6.157000|-6.157000	0.00078|0.00078	-4.322000|-4.322000	0.00056|0.00056	0.491000|0.491000	0.48974|0.48974	ATG|TGG	.	.		0.662	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			A	28761221	G	A	28761221	3	1	67	1	0	0	0	0	1	0	0	0	12033	1348	47	3	662	3	PLB1	2	28761221	Missense_Mutation	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10		28761221	214438152	8	8587										
MBD5	55777	hgsc.bcm.edu	37	chr2	149226010	149226010	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	gtaatgcctgaatgtaagaaTcctttcaagttaatgattgg	9	5	1	3			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr2:149226010T>C	ENST00000407073.1	+	9	1495	c.498T>C	c.(496-498)aaT>aaC	p.N166N	MBD5_ENST00000404807.1_Silent_p.N166N	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	166					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		AATGTAAGAATCCTTTCAAGT	0.423																																					p.N166N		Atlas-SNP	.											.	MBD5	164	.	0			c.T498C						.						62	60	60					2																	149226010		2203	4300	6503	SO:0001819	synonymous_variant	55777	exon9			TAAGAATCCTTTC	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.498T>C	chr2.hg19:g.149226010T>C		105.0	0.0		131.0	9.0	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Silent	SNP	ENST00000407073.1	hg19	CCDS33302.1																																																																																			.	.		0.423	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			C	149226010	T	C	149226010	2	2	67	1	0	0	0	0	0	0	0	1	9356	1432	50	2		2	MBD5	2	149226010	Silent	SNP	T	TCGA-CC-A5UC-01A-11D-A28X-10	120464789	149226010	93973363	9	8588										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196759699	196759699	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	atgcattaataatatacttgCcttttcacatatatcattta	2	7	2	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr2:196759699C>A	ENST00000312428.6	-	30	4997		c.e30+1			NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7						cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AATATACTTGCCTTTTCACAT	0.313																																					.		Atlas-SNP	.											.	DNAH7	512	.	0			c.4896+1G>T						.						57	53	54					2																	196759699		1836	4072	5908	SO:0001630	splice_region_variant	56171	exon31			TACTTGCCTTTTC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.4896+1G>T	chr2.hg19:g.196759699C>A		195.0	0.0		205.0	46.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Splice_Site	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	19.16	3.773716	0.69992	.	.	ENSG00000118997	ENST00000312428	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9814	0.92756	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNAH7	196467944	1.000000	0.71417	0.978000	0.43139	0.875000	0.50365	3.111000	0.50360	2.826000	0.97356	0.655000	0.94253	.	.	.		0.313	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	Intron	A	196759699	C	A	196759699	5	1	67	1	0	0	0	0	0	0	1	0	4608	753	26	3	7321	3	DNAH7	2	196759699	Splice_Site	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	47533689	196759699	46439674	10	8589										
SLC25A38	54977	hgsc.bcm.edu	37	chr3	39433444	39433444	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tggcctgacagcaactctccTtcgagatgcgcccttctcag	9	15	2	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr3:39433444T>G	ENST00000273158.4	+	5	934	c.557T>G	c.(556-558)cTt>cGt	p.L186R		NM_017875.2	NP_060345.2			solute carrier family 25, member 38											breast(1)|endometrium(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		GCAACTCTCCTTCGAGATGCG	0.502																																					p.L186R		Atlas-SNP	.											.	SLC25A38	25	.	0			c.T557G						.						89	91	90					3																	39433444		2203	4300	6503	SO:0001583	missense	54977	exon5			CTCTCCTTCGAGA	BC013194	CCDS2685.1	3p22.1	2013-05-22			ENSG00000144659	ENSG00000144659		"Solute carriers"	26054	protein-coding gene	gene with protein product		610819				16949250	Standard	NM_017875		Approved	FLJ20551	uc003cjo.2	Q96DW6	OTTHUMG00000131289	ENST00000273158.4:c.557T>G	chr3.hg19:g.39433444T>G	ENSP00000273158:p.Leu186Arg	156.0	0.0		184.0	31.0	NM_017875		Missense_Mutation	SNP	ENST00000273158.4	hg19	CCDS2685.1	.	.	.	.	.	.	.	.	.	.	t	21.6	4.171309	0.78452	.	.	ENSG00000144659	ENST00000273158	D	0.81821	-1.54	4.89	4.89	0.63831	Mitochondrial carrier domain (2);	0.062472	0.64402	D	0.000003	D	0.93028	0.7781	H	0.98111	4.15	0.58432	D	0.999998	D	0.89917	1.0	D	0.77004	0.989	D	0.94775	0.7948	10	0.62326	D	0.03	-17.5579	12.7386	0.57239	0.0:0.0:0.0:1.0	.	186	Q96DW6	S2538_HUMAN	R	186	ENSP00000273158:L186R	ENSP00000273158:L186R	L	+	2	0	SLC25A38	39408448	1.000000	0.71417	0.814000	0.32528	0.993000	0.82548	5.929000	0.70096	1.950000	0.56595	0.455000	0.32223	CTT	.	.		0.502	SLC25A38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254057.3	NM_017875		G	39433444	T	G	39433444	3	3	67	1	0	0	0	0	1	0	0	0	14517	1609	56	5	575	5	SLC25A38	3	39433444	Missense_Mutation	SNP	T	TCGA-CC-A5UC-01A-11D-A28X-10		39433444	158588986	11	8590										
WDR52	55779	hgsc.bcm.edu	37	chr3	113092280	113092280	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	gaaagtgatagtttggatggGattgtcctctgtatccgcaa	12	6	1	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr3:113092280G>A	ENST00000295868.2	-	18	2584	c.2422C>T	c.(2422-2424)Ccc>Tcc	p.P808S	WDR52_ENST00000393845.2_Missense_Mutation_p.P808S	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						GTTTGGATGGGATTGTCCTCT	0.368																																					p.P808S		Atlas-SNP	.											.	WDR52	151	.	0			c.C2422T						.						149	140	143					3																	113092280		2203	4300	6503	SO:0001583	missense	55779	exon18			GGATGGGATTGTC																												ENST00000295868.2:c.2422C>T	chr3.hg19:g.113092280G>A	ENSP00000295868:p.Pro808Ser	99.0	0.0		89.0	9.0	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	hg19	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	G	16.04	3.010923	0.54361	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.17528	2.27;2.27	5.39	4.51	0.55191	WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.26557	0.0649	L	0.34521	1.04	0.80722	D	1	D	0.71674	0.998	P	0.58820	0.846	T	0.02075	-1.1218	9	0.66056	D	0.02	.	13.865	0.63583	0.0:0.0:0.8471:0.1529	.	808	Q96MT7	WDR52_HUMAN	S	808	ENSP00000377428:P808S;ENSP00000295868:P808S	ENSP00000295868:P808S	P	-	1	0	WDR52	114574970	1.000000	0.71417	0.987000	0.45799	0.329000	0.28539	5.696000	0.68287	1.403000	0.46800	0.655000	0.94253	CCC	.	.		0.368	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			A	113092280	G	A	113092280	3	1	67	1	0	0	0	0	1	0	0	0	17319	1174	41	3	3229	3	WDR52	3	113092280	Missense_Mutation	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10	73658836	113092280	84930150	12	8591										
MRPL3	11222	hgsc.bcm.edu	37	chr3	131208896	131208896	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tcggcggcaatccaagttccCggtaaaattccaatatggat	9	10	0	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr3:131208896C>T	ENST00000264995.3	-	5	644	c.497G>A	c.(496-498)cGg>cAg	p.R166Q	MRPL3_ENST00000506946.1_5'UTR|MRPL3_ENST00000425847.2_Missense_Mutation_p.R193Q	NM_007208.3	NP_009139.1	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	166					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						TCCAAGTTCCCGGTAAAATTC	0.363																																					p.R166Q		Atlas-SNP	.											MRPL3,right_upper_lobe,carcinoma,0,1	MRPL3	32	.	0			c.G497A						.						65	64	64					3																	131208896		2203	4300	6503	SO:0001583	missense	11222	exon5			AGTTCCCGGTAAA	X06323	CCDS3071.1	3q21-q23	2012-09-13			ENSG00000114686	ENSG00000114686		"Mitochondrial ribosomal proteins / large subunits"	10379	protein-coding gene	gene with protein product		607118		RPML3		2891103	Standard	NM_007208		Approved	MRL3	uc003eoh.3	P09001	OTTHUMG00000159607	ENST00000264995.3:c.497G>A	chr3.hg19:g.131208896C>T	ENSP00000264995:p.Arg166Gln	42.0	0.0		64.0	12.0	NM_007208	Q6IBT2	Missense_Mutation	SNP	ENST00000264995.3	hg19	CCDS3071.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.167846	0.38315	.	.	ENSG00000114686	ENST00000264995;ENST00000425847;ENST00000507669;ENST00000512877	T;T;T;T	0.42513	2.13;2.13;2.13;0.97	5.31	-0.531	0.11894	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.446138	0.24691	N	0.036387	T	0.28732	0.0712	L	0.31845	0.965	0.40319	D	0.978802	B;B	0.17667	0.012;0.023	B;B	0.17979	0.02;0.012	T	0.09796	-1.0658	10	0.23302	T	0.38	-0.0849	12.5056	0.55979	0.0:0.7842:0.0:0.2158	.	193;166	E7ETU7;P09001	.;RM03_HUMAN	Q	166;193;61;133	ENSP00000264995:R166Q;ENSP00000398536:R193Q;ENSP00000422419:R61Q;ENSP00000422035:R133Q	ENSP00000264995:R166Q	R	-	2	0	MRPL3	132691586	0.823000	0.29233	0.987000	0.45799	0.926000	0.56050	-0.104000	0.10923	-0.405000	0.07599	0.462000	0.41574	CGG	.	.		0.363	MRPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356471.3	NM_007208		T	131208896	C	T	131208896	3	4	67	1	0	0	0	0	1	0	0	0	9802	652	23	1	573	1	MRPL3	3	131208896	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	18116616	131208896	66813534	13	8592										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66467871	66467871	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	ggctgttgcagtcccgcaggGtaaatttgagttctatgaag	13	7	1	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr4:66467871G>A	ENST00000273854.3	-	3	998	c.398C>T	c.(397-399)aCc>aTc	p.T133I	EPHA5_ENST00000432638.2_Missense_Mutation_p.T133I|EPHA5_ENST00000354839.4_Missense_Mutation_p.T133I|EPHA5_ENST00000511294.1_Missense_Mutation_p.T133I	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	133	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						GTCCCGCAGGGTAAATTTGAG	0.428										TSP Lung(17;0.13)																											p.T133I		Atlas-SNP	.											.	EPHA5	315	.	0			c.C398T						.						82	86	85					4																	66467871		2203	4300	6503	SO:0001583	missense	2044	exon3			CGCAGGGTAAATT	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.398C>T	chr4.hg19:g.66467871G>A	ENSP00000273854:p.Thr133Ile	43.0	0.0		41.0	7.0	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	hg19	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117328	0.77323	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	5.67	5.67	0.87782	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.64402	D	0.000005	T	0.45637	0.1352	M	0.86097	2.795	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;1.0	D;D;D;D	0.97110	1.0;0.992;0.999;0.996	T	0.48410	-0.9038	10	0.87932	D	0	.	19.7625	0.96325	0.0:0.0:1.0:0.0	.	133;133;133;133	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	I	133	ENSP00000273854:T133I;ENSP00000389208:T133I;ENSP00000346899:T133I;ENSP00000427638:T133I	ENSP00000273854:T133I	T	-	2	0	EPHA5	66150466	1.000000	0.71417	0.996000	0.52242	0.791000	0.44710	9.869000	0.99810	2.677000	0.91161	0.650000	0.86243	ACC	.	.		0.428	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		A	66467871	G	A	66467871	3	1	67	1	0	0	0	0	1	0	0	0	5172	1261	44	3	2779	3	EPHA5	4	66467871	Missense_Mutation	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10		66467871	124686405	14	8593										
ATOH1	474	hgsc.bcm.edu	37	chr4	94750441	94750441	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	gcagcaagagccccgggccgGtgaaagtgcgggaacagctg	17	11	0	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr4:94750441G>T	ENST00000306011.3	+	1	400	c.364G>T	c.(364-366)Gtg>Ttg	p.V122L		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	122					auditory receptor cell fate determination (GO:0042668)|auditory receptor cell fate specification (GO:0042667)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|cerebral cortex development (GO:0021987)|inner ear morphogenesis (GO:0042472)|negative regulation of apoptotic process (GO:0043066)|neuron migration (GO:0001764)|positive regulation of auditory receptor cell differentiation (GO:0045609)|positive regulation of neuron differentiation (GO:0045666)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)		CCCCGGGCCGGTGAAAGTGCG	0.692																																					p.V122L		Atlas-SNP	.											.	ATOH1	40	.	0			c.G364T						.						21	31	27					4																	94750441		2202	4299	6501	SO:0001583	missense	474	exon1			GGGCCGGTGAAAG	U61148	CCDS3638.1	4q22	2013-05-21			ENSG00000172238	ENSG00000172238		"Basic helix-loop-helix proteins"	797	protein-coding gene	gene with protein product		601461				8872459	Standard	NM_005172		Approved	HATH1, MATH-1, Math1, bHLHa14	uc003hta.1	Q92858	OTTHUMG00000130972	ENST00000306011.3:c.364G>T	chr4.hg19:g.94750441G>T	ENSP00000302216:p.Val122Leu	132.0	0.0		110.0	12.0	NM_005172	Q14CT9	Missense_Mutation	SNP	ENST00000306011.3	hg19	CCDS3638.1	.	.	.	.	.	.	.	.	.	.	G	3.285	-0.146188	0.06627	.	.	ENSG00000172238	ENST00000306011	D	0.97328	-4.34	4.2	3.33	0.38152	.	0.281352	0.30473	N	0.009548	D	0.89808	0.6822	N	0.14661	0.345	0.26559	N	0.973771	B	0.09022	0.002	B	0.04013	0.001	T	0.77135	-0.2699	10	0.09843	T	0.71	-16.6657	6.6623	0.23020	0.2122:0.0:0.7878:0.0	.	122	Q92858	ATOH1_HUMAN	L	122	ENSP00000302216:V122L	ENSP00000302216:V122L	V	+	1	0	ATOH1	94969464	0.976000	0.34144	0.770000	0.31555	0.111000	0.19643	2.238000	0.43070	2.161000	0.67846	0.549000	0.68633	GTG	.	.		0.692	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172		T	94750441	G	T	94750441	3	4	67	1	0	0	0	0	1	0	0	0	1112	1261	44	3	366	3	ATOH1	4	94750441	Missense_Mutation	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10	28282570	94750441	96403835	15	8594										
ANKRD34B	340120	hgsc.bcm.edu	37	chr5	79855469	79855469	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	atcttctgaatttatagcatAaacaagagctgagtaactag	7	6	2	3			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr5:79855469A>G	ENST00000338682.3	-	5	1042	c.370T>C	c.(370-372)Tat>Cat	p.Y124H		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	124						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	28		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		TTTATAGCATAAACAAGAGCT	0.443																																					p.Y124H		Atlas-SNP	.											.	ANKRD34B	61	.	0			c.T370C						.						125	127	126					5																	79855469		2203	4300	6503	SO:0001583	missense	340120	exon5			TAGCATAAACAAG		CCDS34194.1	5q14.1	2014-08-12			ENSG00000189127	ENSG00000189127		"Ankyrin repeat domain containing"	33736	protein-coding gene	gene with protein product							Standard	NM_001004441		Approved	DP58	uc003kgw.3	A5PLL1	OTTHUMG00000162541	ENST00000338682.3:c.370T>C	chr5.hg19:g.79855469A>G	ENSP00000339802:p.Tyr124His	145.0	0.0		128.0	33.0	NM_001004441	B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	hg19	CCDS34194.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.159369	0.38119	.	.	ENSG00000189127	ENST00000338682	T	0.35605	1.3	6.03	4.88	0.63580	Ankyrin repeat-containing domain (3);	0.000000	0.64402	U	0.000002	T	0.35913	0.0948	L	0.48877	1.53	0.58432	D	0.999992	P	0.48350	0.909	P	0.47015	0.534	T	0.05716	-1.0868	10	0.25106	T	0.35	-8.9732	10.9227	0.47174	0.9268:0.0:0.0732:0.0	.	124	A5PLL1	AN34B_HUMAN	H	124	ENSP00000339802:Y124H	ENSP00000339802:Y124H	Y	-	1	0	ANKRD34B	79891225	1.000000	0.71417	0.844000	0.33320	0.856000	0.48823	6.231000	0.72307	1.109000	0.41680	0.533000	0.62120	TAT	.	.		0.443	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441		G	79855469	A	G	79855469	3	3	67	1	0	0	0	0	1	0	0	0	663	362	13	2	1178	2	ANKRD34B	5	79855469	Missense_Mutation	SNP	A	TCGA-CC-A5UC-01A-11D-A28X-10		79855469	101059791	16	8595										
TRIM36	55521	hgsc.bcm.edu	37	chr5	114462308	114462308	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tacagtgtatgtgaacagtcCacttggcgttcataaaggca	10	8	1	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr5:114462308C>T	ENST00000282369.3	-	10	2200	c.2079G>A	c.(2077-2079)gtG>gtA	p.V693V	TRIM36_ENST00000513154.1_Silent_p.V681V|TRIM36_ENST00000514154.1_Silent_p.V538V	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	693	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		GTGAACAGTCCACTTGGCGTT	0.408																																					p.V693V		Atlas-SNP	.											.	TRIM36	126	.	0			c.G2079A						.						112	100	104					5																	114462308		2202	4300	6502	SO:0001819	synonymous_variant	55521	exon10			ACAGTCCACTTGG	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16280	protein-coding gene	gene with protein product	"zinc-binding protein Rbcc728", "tripartite motif protein 36", "RING finger protein 98"	609317	"tripartite motif-containing 36"			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.2079G>A	chr5.hg19:g.114462308C>T		120.0	0.0		129.0	31.0	NM_018700	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Silent	SNP	ENST00000282369.3	hg19	CCDS4115.1																																																																																			.	.		0.408	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		T	114462308	C	T	114462308	2	4	67	1	0	0	0	0	0	0	0	1	16525	581	21	3		3	TRIM36	5	114462308	Silent	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	34606839	114462308	66452952	17	8596										
REEP2	51308	hgsc.bcm.edu	37	chr5	137780443	137780443	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	cttcccctccaatcccatagGagatcgacgagtacatcacg	7	15	1	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr5:137780443G>C	ENST00000254901.5	+	5	426	c.304G>C	c.(304-306)Gag>Cag	p.E102Q	REEP2_ENST00000378339.2_Splice_Site_p.E102Q|REEP2_ENST00000506158.1_Splice_Site_p.E64Q	NM_016606.2	NP_057690.2	Q9BRK0	REEP2_HUMAN	receptor accessory protein 2	102					cell death (GO:0008219)|endoplasmic reticulum tubular network organization (GO:0071786)|protein transport into membrane raft (GO:0032596)|regulation of intracellular transport (GO:0032386)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			AATCCCATAGGAGATCGACGA	0.622																																					p.E102Q		Atlas-SNP	.											.	REEP2	21	.	0			c.G304C						.						72	59	64					5																	137780443		2203	4300	6503	SO:0001630	splice_region_variant	51308	exon5			CCATAGGAGATCG	AK056193	CCDS4205.1, CCDS64259.1	5q31	2014-03-12	2006-02-07	2006-02-07	ENSG00000132563	ENSG00000132563		"Receptor accessory proteins"	17975	protein-coding gene	gene with protein product		609347	"chromosome 5 open reading frame 19"	C5orf19		16271481, 15550249, 24388663	Standard	NM_016606		Approved	SGC32445, SPG72	uc003lda.4	Q9BRK0	OTTHUMG00000129205	ENST00000254901.5:c.304-1G>C	chr5.hg19:g.137780443G>C		121.0	0.0		109.0	24.0	NM_016606	Q53EM8|Q9NYF2	Missense_Mutation	SNP	ENST00000254901.5	hg19	CCDS4205.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.38|18.38	3.612242|3.612242	0.66672|0.66672	.|.	.|.	ENSG00000132563|ENSG00000132563	ENST00000378339;ENST00000254901;ENST00000506158|ENST00000512126	D;D;D|.	0.89415|.	-2.51;-2.49;-1.68|.	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78097|0.78097	0.4230|0.4230	M|M	0.81614|0.81614	2.55|2.55	0.80722|0.80722	D|D	1|1	P;D|.	0.56968|.	0.94;0.978|.	P;P|.	0.60949|.	0.77;0.881|.	T|T	0.79045|0.79045	-0.1964|-0.1964	9|5	.|.	.|.	.|.	-4.6113|-4.6113	17.4888|17.4888	0.87696|0.87696	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	102;102|.	A8K3D2;Q9BRK0|.	.;REEP2_HUMAN|.	Q|S	102;102;64|139	ENSP00000367590:E102Q;ENSP00000254901:E102Q;ENSP00000422530:E64Q|.	.|.	E|R	+|+	1|3	0|2	REEP2|REEP2	137808342|137808342	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.047000|0.047000	0.14425|0.14425	9.527000|9.527000	0.98044|0.98044	2.674000|2.674000	0.91012|0.91012	0.655000|0.655000	0.94253|0.94253	GAG|AGG	.	.		0.622	REEP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251284.1	NM_016606	Missense_Mutation	C	137780443	G	C	137780443	5	2	67	1	0	0	0	0	0	0	1	0	13220	1188	41	4	322	4	REEP2	5	137780443	Splice_Site	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10	23318135	137780443	43134817	18	8597										
EDN1	1906	hgsc.bcm.edu	37	chr6	12294540	12294540	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	ggaataatcataagaaaggaAaagactgttccaagcttggg	11	5	1	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr6:12294540A>G	ENST00000379375.5	+	4	703	c.436A>G	c.(436-438)Aaa>Gaa	p.K146E		NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	146					artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				TAAGAAAGGAAAAGACTGTTC	0.363																																					p.K146E		Atlas-SNP	.											.	EDN1	23	.	0			c.A436G						.						98	98	98					6																	12294540		2203	4300	6503	SO:0001583	missense	1906	exon4			AAAGGAAAAGACT	S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401		"Endogenous ligands"	3176	protein-coding gene	gene with protein product		131240					Standard	NM_001168319		Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.436A>G	chr6.hg19:g.12294540A>G	ENSP00000368683:p.Lys146Glu	419.0	0.0		396.0	117.0	NM_001955	Q96DA1	Missense_Mutation	SNP	ENST00000379375.5	hg19	CCDS4522.1	.	.	.	.	.	.	.	.	.	.	A	10.93	1.488697	0.26686	.	.	ENSG00000078401	ENST00000379375	D	0.84660	-1.88	5.85	4.7	0.59300	.	0.487586	0.24354	N	0.039247	T	0.71550	0.3353	M	0.66506	2.035	0.23036	N	0.998396	B;B	0.21381	0.055;0.055	B;B	0.15052	0.012;0.012	T	0.63216	-0.6687	10	0.37606	T	0.19	-4.084	9.4862	0.38931	0.8688:0.0:0.1312:0.0	.	146;146	Q6FH53;P05305	.;EDN1_HUMAN	E	146	ENSP00000368683:K146E	ENSP00000368683:K146E	K	+	1	0	EDN1	12402526	0.873000	0.30073	0.997000	0.53966	0.108000	0.19459	2.343000	0.44001	2.238000	0.73509	0.533000	0.62120	AAA	.	.		0.363	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039872.1	NM_001955		G	12294540	A	G	12294540	3	3	67	1	0	0	0	0	1	0	0	0	4918	15	1	2	450	2	EDN1	6	12294540	Missense_Mutation	SNP	A	TCGA-CC-A5UC-01A-11D-A28X-10		12294540	158820527	19	8598										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38891940	38891940	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	gttggtggatcctccaactgTaagttttactttcccaatgt	8	9	0	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr6:38891940T>C	ENST00000359357.3	+	71	10565		c.e71+2		DNAH8_ENST00000449981.2_Splice_Site|RP1-207H1.3_ENST00000416948.1_RNA|DNAH8_ENST00000441566.1_Splice_Site|RP1-207H1.3_ENST00000418399.1_RNA			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8						cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CCTCCAACTGTAAGTTTTACT	0.383																																					.		Atlas-SNP	.											.	DNAH8	1239	.	0			c.10962+2T>C						.						74	83	80					6																	38891940		2202	4300	6502	SO:0001630	splice_region_variant	1769	exon73			CAACTGTAAGTTT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.10311+2T>C	chr6.hg19:g.38891940T>C		44.0	0.0		44.0	17.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Splice_Site	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	T	20.7	4.027496	0.75390	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8524	0.70306	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAH8	38999918	1.000000	0.71417	0.986000	0.45419	0.870000	0.49936	6.896000	0.75665	2.244000	0.73946	0.533000	0.62120	.	.	.		0.383	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	Intron	C	38891940	T	C	38891940	5	2	67	1	0	0	0	0	0	0	1	0	4609	1652	57	2	10587	2	DNAH8	6	38891940	Splice_Site	SNP	T	TCGA-CC-A5UC-01A-11D-A28X-10	26597400	38891940	132223127	20	8599										
DST	667	hgsc.bcm.edu	37	chr6	56391319	56391319	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	aagcactgctcacttcattaAgggagtccagtaaggctttg	10	9	2	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr6:56391319A>C	ENST00000361203.3	-	64	17016	c.17009T>G	c.(17008-17010)cTt>cGt	p.L5670R	DST_ENST00000370754.5_Missense_Mutation_p.L5959R|DST_ENST00000340834.4_5'UTR|DST_ENST00000446842.2_Missense_Mutation_p.L5455R|DST_ENST00000244364.6_Missense_Mutation_p.L3367R|DST_ENST00000312431.6_3'UTR|DST_ENST00000421834.2_Missense_Mutation_p.L3693R|DST_ENST00000370769.4_Missense_Mutation_p.L5781R|DST_ENST00000370788.2_Missense_Mutation_p.L3584R			Q03001	DYST_HUMAN	dystonin	5674					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CACTTCATTAAGGGAGTCCAG	0.423																																					p.L3367R		Atlas-SNP	.											.	DST	1427	.	0			c.T10100G						.						252	232	238					6																	56391319		1940	4160	6100	SO:0001583	missense	667	exon50			TCATTAAGGGAGT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.17009T>G	chr6.hg19:g.56391319A>C	ENSP00000354508:p.Leu5670Arg	110.0	0.0		108.0	33.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.06	3.539840	0.65085	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.73	5.73	0.89815	.	0.000000	0.47455	D	0.000235	T	0.64638	0.2616	M	0.79123	2.44	0.37156	D	0.902364	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.998;0.997	D;D;D;P;D	0.91635	0.998;0.995;0.999;0.844;0.947	T	0.70425	-0.4875	9	0.87932	D	0	.	16.3197	0.82945	1.0:0.0:0.0:0.0	.	3693;5781;5959;5779;3367	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	R	3367;5959;5781;3693;5455;3584;5670	ENSP00000244364:L3367R;ENSP00000359790:L5959R;ENSP00000359805:L5781R;ENSP00000400883:L3693R;ENSP00000393645:L5455R;ENSP00000359824:L3584R;ENSP00000354508:L5670R	ENSP00000244364:L3367R	L	-	2	0	DST	56499278	1.000000	0.71417	0.953000	0.39169	0.869000	0.49853	9.287000	0.95975	2.302000	0.77476	0.533000	0.62120	CTT	.	.		0.423	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56391319	A	C	56391319	3	2	67	1	0	0	0	0	1	0	0	0	4785	72	3	5	5555	5	DST	6	56391319	Missense_Mutation	SNP	A	TCGA-CC-A5UC-01A-11D-A28X-10	17499379	56391319	114723748	21	8600										
GLCCI1	113263	hgsc.bcm.edu	37	chr7	8125841	8125841	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	aggtctcgtcagcctatctcGgcccctctcttttcatgtcc	7	16	5	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr7:8125841G>A	ENST00000223145.5	+	8	1874	c.1317G>A	c.(1315-1317)tcG>tcA	p.S439S		NM_138426.3	NP_612435.1	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	439						cytoplasm (GO:0005737)		p.S439S(1)		endometrium(4)|large_intestine(4)|lung(13)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	25		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)		AGCCTATCTCGGCCCCTCTCT	0.388																																					p.S439S		Atlas-SNP	.											GLCCI1,right_upper_lobe,carcinoma,0,1	GLCCI1	50	.	1	Substitution - coding silent(1)	lung(1)	c.G1317A						.						105	118	114					7																	8125841		2203	4300	6503	SO:0001819	synonymous_variant	113263	exon8			TATCTCGGCCCCT	BC050291	CCDS34601.1	7p22.2	2008-08-18			ENSG00000106415	ENSG00000106415			18713	protein-coding gene	gene with protein product		614283					Standard	NM_138426		Approved	GIG18, FAM117C, TSSN1	uc003srk.4	Q86VQ1	OTTHUMG00000151984	ENST00000223145.5:c.1317G>A	chr7.hg19:g.8125841G>A		27.0	0.0		35.0	3.0	NM_138426	A4D103|Q96FD0	Silent	SNP	ENST00000223145.5	hg19	CCDS34601.1																																																																																			.	.		0.388	GLCCI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324672.1	NM_138426		A	8125841	G	A	8125841	2	1	67	1	0	0	0	0	0	0	0	1	6439	1103	39	1		1	GLCCI1	7	8125841	Silent	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10		8125841	151012822	22	8601										
POU6F2	11281	hgsc.bcm.edu	37	chr7	39379463	39379463	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tacatctcagctgcaacaggCgcctcagccccagcagcacc	8	18	2	0	rs150071017	byFrequency	TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr7:39379463C>A	ENST00000403058.1	+	6	888	c.734C>A	c.(733-735)gCg>gAg	p.A245E	POU6F2_ENST00000559001.1_Missense_Mutation_p.A237E|POU6F2_ENST00000518318.2_Missense_Mutation_p.A245E|POU6F2_ENST00000517348.1_3'UTR	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	245	Gln-rich.|Pro-rich.				central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						ctgcaacaggcgcctcagccc	0.667																																					p.A245E		Atlas-SNP	.											.	POU6F2	117	.	0			c.C734A						.						88	95	93					7																	39379463		2203	4295	6498	SO:0001583	missense	11281	exon6			AACAGGCGCCTCA	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.734C>A	chr7.hg19:g.39379463C>A	ENSP00000384004:p.Ala245Glu	59.0	0.0		75.0	14.0	NM_007252	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Missense_Mutation	SNP	ENST00000403058.1	hg19	CCDS34620.2	.	.	.	.	.	.	.	.	.	.	C	6.081	0.383302	0.11524	.	.	ENSG00000106536	ENST00000403058;ENST00000518318	T;D	0.84873	1.07;-1.91	2.03	2.03	0.26663	.	.	.	.	.	T	0.67739	0.2925	N	0.14661	0.345	0.09310	N	1	B;B	0.28880	0.226;0.015	B;B	0.18871	0.023;0.002	T	0.55101	-0.8193	9	0.26408	T	0.33	.	5.8656	0.18773	0.3125:0.6874:0.0:0.0	.	245;245	P78424-2;P78424	.;PO6F2_HUMAN	E	245	ENSP00000384004:A245E;ENSP00000430514:A245E	ENSP00000384004:A245E	A	+	2	0	POU6F2	39345988	0.009000	0.17119	0.054000	0.19295	0.510000	0.34073	0.122000	0.15687	1.426000	0.47256	0.557000	0.71058	GCG	.	C|0.994;T|0.006		0.667	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252		A	39379463	C	A	39379463	3	1	67	1	0	0	0	0	1	0	0	0	12294	768	27	1	752	1	POU6F2	7	39379463	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	31253622	39379463	119759200	23	8602										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47886599	47886599	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	actgtatagttcactgccttAgctaaatatctgtttggagg	9	7	2	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr7:47886599A>C	ENST00000289672.2	-	32	5081	c.5031T>G	c.(5029-5031)gcT>gcG	p.A1677A		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1677					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TCACTGCCTTAGCTAAATATC	0.393																																					p.A1677A		Atlas-SNP	.											.	PKD1L1	328	.	0			c.T5031G						.						103	98	100					7																	47886599		2203	4300	6503	SO:0001819	synonymous_variant	168507	exon32			TGCCTTAGCTAAA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5031T>G	chr7.hg19:g.47886599A>C		193.0	0.0		181.0	52.0	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	hg19	CCDS34633.1																																																																																			.	.		0.393	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		C	47886599	A	C	47886599	2	2	67	1	0	0	0	0	0	0	0	1	11973	407	15	5		5	PKD1L1	7	47886599	Silent	SNP	A	TCGA-CC-A5UC-01A-11D-A28X-10	8507136	47886599	111252064	24	8603										
WRN	7486	hgsc.bcm.edu	37	chr8	30941291	30941351	+	Splice_Site	DEL	TTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATT	TTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATT	-													0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	agatttagaaatggagatgcTtaaggtatgtttacaattat					rs182813211|rs2737325	byFrequency	TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	TTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATT	TTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr8:30941291_30941351delTTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATT	ENST00000298139.5	+	10	1595_1599	c.1346_1350delTTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATT	c.(1345-1350)cttaag>c	p.LK449fs		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	449	2 X 27 AA tandem repeats of H-L-S-P-N-D- N-E-N-D-T-S-Y-V-I-E-S-D-E-D-L-E-M-E-M-L- K.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		ATGGAGATGCTTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATTAAGTAAAATA	0.261			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.449_450del	Ovarian(18;161 598 2706 14834 27543)	Pindel	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"L, E, M, O"	.	WRN	116	.	0			c.1345_1350del						.																																			SO:0001630	splice_region_variant	7486	exon10	Familial Cancer Database	WS, Adult Progeria	.		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"Werner syndrome"			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1350+1TTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATT>-	chr8.hg19:g.30941291_30941351delTTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATT		160.0	0.0		188.0	18.0	NM_000553	A1KYY9	In_Frame_Del	DEL	ENST00000298139.5	hg19	CCDS6082.1																																																																																			.	.		0.261	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		Frame_Shift_Del	-	30941351	TTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATT	-	30941291	8	5	67	1	0	1	0	1	0	0	1	0	17417	1609	56	0	1380	0	WRN	8	30941291	Splice_Site	DEL	TTAAGGTATGTTTACAATTATAAAAATATTACTTCAAGTTCTTTCCAAAGGACATTTAATT	TCGA-CC-A5UC-01A-11D-A28X-10		30941291	115422731	25	8604										
ALDH1B1	219	hgsc.bcm.edu	37	chr9	38396047	38396047	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	ccggatggatgcctctgagcGgggccggctgctgaaccgcc	16	14	1	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr9:38396047G>T	ENST00000377698.3	+	2	455	c.302G>T	c.(301-303)cGg>cTg	p.R101L		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	101					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)			NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		GCCTCTGAGCGGGGCCGGCTG	0.642																																					p.R101L		Atlas-SNP	.											.	ALDH1B1	50	.	0			c.G302T						.						70	79	76					9																	38396047		2203	4300	6503	SO:0001583	missense	219	exon2			CTGAGCGGGGCCG	M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"Aldehyde dehydrogenases"	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.302G>T	chr9.hg19:g.38396047G>T	ENSP00000366927:p.Arg101Leu	79.0	0.0		90.0	28.0	NM_000692	B2R8F0|Q8WX76|Q9BV45	Missense_Mutation	SNP	ENST00000377698.3	hg19	CCDS6615.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.929275	0.73327	.	.	ENSG00000137124	ENST00000377698	D	0.88277	-2.36	5.28	2.46	0.29980	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.56097	D	0.000033	D	0.96021	0.8704	H	0.99368	4.535	0.46078	D	0.998859	D	0.54397	0.966	P	0.60789	0.879	D	0.94294	0.7531	10	0.87932	D	0	.	8.8734	0.35330	0.248:0.0:0.7519:0.0	.	101	P30837	AL1B1_HUMAN	L	101	ENSP00000366927:R101L	ENSP00000366927:R101L	R	+	2	0	ALDH1B1	38386047	0.990000	0.36364	0.996000	0.52242	0.998000	0.95712	5.978000	0.70501	0.242000	0.21303	0.655000	0.94253	CGG	.	.		0.642	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1			T	38396047	G	T	38396047	3	4	67	1	0	0	0	0	1	0	0	0	493	1116	39	1	304	1	ALDH1B1	9	38396047	Missense_Mutation	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10		38396047	102817384	26	8605										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73426150	73426150	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	cgggagtcaagagagaaaaaCggcaggcatcctgtcaaaaa	12	8	2	2	rs200079844	byFrequency	TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr9:73426150C>A	ENST00000396292.4	-	5	524	c.525G>T	c.(523-525)ccG>ccT	p.P175P	TRPM3_ENST00000408909.2_Intron|TRPM3_ENST00000396283.1_Silent_p.P175P|TRPM3_ENST00000357533.2_Intron|MIR204_ENST00000385200.1_RNA|TRPM3_ENST00000361823.5_Intron|TRPM3_ENST00000377110.3_Intron|TRPM3_ENST00000377101.1_Intron|TRPM3_ENST00000377105.1_Intron|TRPM3_ENST00000396285.1_Intron|TRPM3_ENST00000423814.3_Silent_p.P330P|TRPM3_ENST00000360823.2_Silent_p.P175P|TRPM3_ENST00000377106.1_Silent_p.P175P|TRPM3_ENST00000358082.3_Silent_p.P175P|TRPM3_ENST00000396280.5_Intron|TRPM3_ENST00000377111.2_Intron			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	328					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						GAGAGAAAAACGGCAGGCATC	0.338																																					p.P175P		Atlas-SNP	.											TRPM3,colon,carcinoma,0,2	TRPM3	700	.	0			c.G525T						.						60	64	63					9																	73426150		2203	4300	6503	SO:0001819	synonymous_variant	80036	exon7			GAAAAACGGCAGG	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000396292.4:c.525G>T	chr9.hg19:g.73426150C>A		122.0	0.0		144.0	30.0	NM_001007470	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000396292.4	hg19	CCDS6635.1																																																																																			.	C|1.000;T|0.000		0.338	TRPM3-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214161.2	NM_206945		A	73426150	C	A	73426150	2	1	67	1	0	0	0	0	0	0	0	1	16602	523	19	1		1	TRPM3	9	73426150	Silent	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	35030103	73426150	67787281	27	8606										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113137703	113137703	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	cagtcacactggtaaggggcCacacagcgacctccgttcag	11	14	2	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr9:113137703C>T	ENST00000401783.2	-	46	10881	c.10545G>A	c.(10543-10545)gtG>gtA	p.V3515V	SVEP1_ENST00000374469.1_Silent_p.V3492V|SVEP1_ENST00000297826.5_Silent_p.V1441V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3515	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GGTAAGGGGCCACACAGCGAC	0.498																																					p.V3515V		Atlas-SNP	.											.	SVEP1	326	.	0			c.G10545A						.						32	32	32					9																	113137703		1861	4050	5911	SO:0001819	synonymous_variant	79987	exon46			AGGGGCCACACAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.10545G>A	chr9.hg19:g.113137703C>T		180.0	0.0		173.0	28.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.		0.498	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113137703	C	T	113137703	2	4	67	1	0	0	0	0	0	0	0	1	15435	581	21	3		3	SVEP1	9	113137703	Silent	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	39711553	113137703	28075728	28	8607										
COL13A1	1305	hgsc.bcm.edu	37	chr10	71700763	71700763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	gggagcttcaggtttggacgGcaggcctgggccaccggtga	18	10	1	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr10:71700763G>A	ENST00000398978.3	+	34	2357	c.1865G>A	c.(1864-1866)gGc>gAc	p.G622D	COL13A1_ENST00000398972.3_Missense_Mutation_p.G608D|COL13A1_ENST00000354547.3_Missense_Mutation_p.G600D|COL13A1_ENST00000356340.3_Missense_Mutation_p.G622D|COL13A1_ENST00000398968.3_Missense_Mutation_p.G603D|COL13A1_ENST00000398971.3_Missense_Mutation_p.G607D|COL13A1_ENST00000398966.3_Missense_Mutation_p.G600D|COL13A1_ENST00000398973.3_Intron|COL13A1_ENST00000520133.1_Intron|COL13A1_ENST00000520267.1_Missense_Mutation_p.G550D|COL13A1_ENST00000357811.3_Intron|COL13A1_ENST00000522165.1_Intron|COL13A1_ENST00000398969.3_Missense_Mutation_p.G550D|COL13A1_ENST00000398964.3_Missense_Mutation_p.G593D|COL13A1_ENST00000398974.3_Missense_Mutation_p.G610D|COL13A1_ENST00000517713.1_Intron	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						GGTTTGGACGGCAGGCCTGGG	0.577																																					p.G622D		Atlas-SNP	.											.	COL13A1	133	.	0			c.G1865A						.						202	224	216					10																	71700763		2036	4176	6212	SO:0001583	missense	1305	exon34			TGGACGGCAGGCC	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"Collagens"	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.1865G>A	chr10.hg19:g.71700763G>A	ENSP00000381949:p.Gly622Asp	86.0	0.0		73.0	21.0	NM_001130103		Missense_Mutation	SNP	ENST00000398978.3	hg19	CCDS44419.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.16|17.16	3.319267|3.319267	0.60524|0.60524	.|.	.|.	ENSG00000197467|ENSG00000197467	ENST00000398975|ENST00000398974;ENST00000398971;ENST00000398968;ENST00000398966;ENST00000398964;ENST00000398969;ENST00000356340;ENST00000398972;ENST00000398978;ENST00000354547;ENST00000520267	.|D;D;D;D;D;D;D;D;D;D;D	.|0.99619	.|-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28	4.9|4.9	4.9|4.9	0.64082|0.64082	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.99825|0.99825	0.9922|0.9922	H|H	0.98351|0.98351	4.21|4.21	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D;D;D;D;D	.|0.97110	.|0.998;1.0;1.0;1.0;1.0;0.972;1.0;0.999;1.0;1.0;1.0	D|D	0.96515|0.96515	0.9381|0.9381	5|10	.|0.87932	.|D	.|0	-4.8829|-4.8829	18.095|18.095	0.89487|0.89487	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|550;622;608;600;603;608;610;607;600;593;622	.|B9EGD2;Q5TAT6;Q5TAT6-6;E7ES55;E7ES51;E7ES47;E7ES46;E7ES49;Q5TAT6-2;E7ES56;G5E987	.|.;CODA1_HUMAN;.;.;.;.;.;.;.;.;.	T|D	152|610;607;603;600;593;550;622;608;622;600;550	.|ENSP00000381946:G610D;ENSP00000381943:G607D;ENSP00000381940:G603D;ENSP00000381938:G600D;ENSP00000381936:G593D;ENSP00000381941:G550D;ENSP00000348695:G622D;ENSP00000381944:G608D;ENSP00000381949:G622D;ENSP00000346553:G600D;ENSP00000428057:G550D	.|ENSP00000346553:G600D	A|G	+|+	1|2	0|0	COL13A1|COL13A1	71370769|71370769	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	1.000000|1.000000	0.99986|0.99986	7.662000|7.662000	0.83803|0.83803	2.259000|2.259000	0.74868|0.74868	0.655000|0.655000	0.94253|0.94253	GCA|GGC	.	.		0.577	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203		A	71700763	G	A	71700763	3	1	67	1	0	0	0	0	1	0	0	0	3672	1203	42	3	1999	3	COL13A1	10	71700763	Missense_Mutation	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10		71700763	63833984	29	8608										
TDRD1	56165	hgsc.bcm.edu	37	chr10	115987675	115987675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tcttgtgcttttagaaaagaTgtataggatgaattgctgct	10	4	1	3			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr10:115987675T>C	ENST00000369280.1	+	23	3642	c.3182T>C	c.(3181-3183)aTg>aCg	p.M1061T	TDRD1_ENST00000369282.1_Missense_Mutation_p.M1061T|TDRD1_ENST00000251864.2_Missense_Mutation_p.M1137T|TDRD1_ENST00000369281.2_Missense_Mutation_p.M1023T|TDRD1_ENST00000422662.1_Missense_Mutation_p.M665T			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	1061					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TTAGAAAAGATGTATAGGATG	0.313																																					p.M1137T		Atlas-SNP	.											.	TDRD1	126	.	0			c.T3410C						.						118	111	113					10																	115987675		2202	4300	6502	SO:0001583	missense	56165	exon24			AAAAGATGTATAG	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.3182T>C	chr10.hg19:g.115987675T>C	ENSP00000358286:p.Met1061Thr	51.0	0.0		42.0	10.0	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	hg19		.	.	.	.	.	.	.	.	.	.	T	8.712	0.912326	0.17907	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000422662;ENST00000369280	T;T;T;T;T	0.16196	3.12;3.2;2.36;2.58;3.13	6.02	-7.26	0.01466	.	1.226810	0.05785	N	0.609334	T	0.05364	0.0142	N	0.01705	-0.755	0.09310	N	1	P;B;B;B;B	0.35033	0.481;0.0;0.0;0.0;0.0	B;B;B;B;B	0.36092	0.217;0.0;0.0;0.0;0.0	T	0.31138	-0.9954	10	0.13853	T	0.58	6.1833	8.5995	0.33736	0.0871:0.1746:0.0858:0.6524	.	665;1137;1023;1137;1023	Q9BXT4-4;Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2	.;TDRD1_HUMAN;.;.;.	T	1061;1137;1023;665;1061	ENSP00000358288:M1061T;ENSP00000251864:M1137T;ENSP00000358287:M1023T;ENSP00000402794:M665T;ENSP00000358286:M1061T	ENSP00000251864:M1137T	M	+	2	0	TDRD1	115977665	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.115000	0.00292	-1.773000	0.01290	-0.924000	0.02725	ATG	.	.		0.313	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			C	115987675	T	C	115987675	3	2	67	1	0	0	0	0	1	0	0	0	15745	1464	51	2	3500	2	TDRD1	10	115987675	Missense_Mutation	SNP	T	TCGA-CC-A5UC-01A-11D-A28X-10	44286912	115987675	19547072	30	8609										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1262923	1262923	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	gcagtgacgaccactgcaggGgacgtgccacaaccccgcca	12	16	0	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr11:1262923G>A	ENST00000529681.1	+	31	4871	c.4813G>A	c.(4813-4815)Gga>Aga	p.G1605R	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.G1608R	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1605	7 X Cys-rich subdomain repeats.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCACTGCAGGGGACGTGCCAC	0.647																																					p.G1605R		Atlas-SNP	.											.	MUC5B	473	.	0			c.G4813A						.						20	27	24					11																	1262923		2113	4210	6323	SO:0001583	missense	727897	exon31			TGCAGGGGACGTG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.4813G>A	chr11.hg19:g.1262923G>A	ENSP00000436812:p.Gly1605Arg	132.0	0.0		102.0	24.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	10.66	1.412011	0.25465	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21734	1.99;2.13	3.82	-6.16	0.02098	.	.	.	.	.	T	0.09512	0.0234	N	0.19112	0.55	0.09310	N	1	B;B	0.28233	0.204;0.204	B;B	0.27076	0.076;0.071	T	0.31081	-0.9956	9	0.87932	D	0	.	1.1342	0.01752	0.3639:0.2632:0.2396:0.1332	.	2298;1608	A7Y9J9;E9PBJ0	.;.	R	1605;1608;1606;1675	ENSP00000436812:G1605R;ENSP00000415793:G1608R	ENSP00000343037:G1606R	G	+	1	0	MUC5B	1219499	0.000000	0.05858	0.000000	0.03702	0.145000	0.21501	-1.050000	0.03510	-1.390000	0.02087	0.306000	0.20318	GGA	.	.		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1262923	G	A	1262923	3	1	67	1	0	0	0	0	1	0	0	0	9988	1233	43	3	4944	3	MUC5B	11	1262923	Missense_Mutation	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10		1262923	133743593	31	8610										
PPP1CA	5499	hgsc.bcm.edu	37	chr11	67166225	67166225	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	catgagggtctcgtccacacTcatcatggcgccagcattgt	10	13	3	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr11:67166225T>C	ENST00000376745.4	-	6	998	c.850A>G	c.(850-852)Agt>Ggt	p.S284G	PPP1CA_ENST00000358239.4_Missense_Mutation_p.S240G|PPP1CA_ENST00000312989.7_Missense_Mutation_p.S295G|PPP1CA_ENST00000532446.1_5'UTR	NM_001008709.1|NM_002708.3	NP_001008709.1|NP_002699.1	P62136	PP1A_HUMAN	protein phosphatase 1, catalytic subunit, alpha isozyme	284					branching morphogenesis of an epithelial tube (GO:0048754)|cell cycle (GO:0007049)|cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|lung development (GO:0030324)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|MLL5-L complex (GO:0070688)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein phosphatase type 1 complex (GO:0000164)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)|ribonucleoprotein complex binding (GO:0043021)			breast(1)|lung(2)|pancreas(1)|urinary_tract(3)	7			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			TCGTCCACACTCATCATGGCG	0.567																																					p.S295G		Atlas-SNP	.											.	PPP1CA	83	.	0			c.A883G						.						101	92	95					11																	67166225		2200	4295	6495	SO:0001583	missense	5499	exon6			CCACACTCATCAT		CCDS8160.1, CCDS8161.1, CCDS31618.1	11q13	2013-01-18	2010-03-05			ENSG00000172531	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9281	protein-coding gene	gene with protein product		176875	"protein phosphatase 1, catalytic subunit, alpha isoform"	PPP1A			Standard	NM_002708		Approved	PP1A, PP-1A, PP1alpha	uc001oku.1	P62136		ENST00000376745.4:c.850A>G	chr11.hg19:g.67166225T>C	ENSP00000365936:p.Ser284Gly	104.0	0.0		76.0	5.0	NM_001008709	A6NNR3|B2R908|P08129|P20653|P22802|Q07161	Missense_Mutation	SNP	ENST00000376745.4	hg19	CCDS8160.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.995146	0.54147	.	.	ENSG00000172531	ENST00000312989;ENST00000451458;ENST00000376745;ENST00000358239;ENST00000527663	T;T;T;T	0.05649	3.41;3.41;3.41;3.41	5.62	5.62	0.85841	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);	0.000000	0.85682	D	0.000000	T	0.14013	0.0339	M	0.78637	2.42	0.80722	D	1	B;B;B;B;B;B	0.26483	0.092;0.092;0.15;0.032;0.003;0.011	B;B;B;B;B;B	0.32533	0.032;0.032;0.147;0.023;0.008;0.018	T	0.00970	-1.1496	10	0.66056	D	0.02	-15.1124	14.8196	0.70062	0.0:0.0:0.0:1.0	.	381;381;284;240;295;293	B3KXM2;E9PDP1;P62136;A6NNR3;Q07161;F8W0W8	.;.;PP1A_HUMAN;.;.;.	G	295;381;284;240;249	ENSP00000326031:S295G;ENSP00000365936:S284G;ENSP00000350974:S240G;ENSP00000431146:S249G	ENSP00000326031:S295G	S	-	1	0	PPP1CA	66922801	1.000000	0.71417	0.998000	0.56505	0.590000	0.36582	8.020000	0.88740	2.140000	0.66376	0.460000	0.39030	AGT	.	.		0.567	PPP1CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395487.1	NM_002708		C	67166225	T	C	67166225	3	2	67	1	0	0	0	0	1	0	0	0	12361	1551	54	2	150	2	PPP1CA	11	67166225	Missense_Mutation	SNP	T	TCGA-CC-A5UC-01A-11D-A28X-10	65903302	67166225	67840291	32	8611										
UBASH3B	84959	hgsc.bcm.edu	37	chr11	122647740	122647740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tctgtcttacaggttattctCccatgtcggtgaccccttcc	7	14	3	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr11:122647740C>T	ENST00000284273.5	+	3	599	c.224C>T	c.(223-225)tCc>tTc	p.S75F		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	75	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		AGGTTATTCTCCCATGTCGGT	0.547																																					p.S75F		Atlas-SNP	.											.	UBASH3B	73	.	0			c.C224T						.						81	70	74					11																	122647740		2202	4299	6501	SO:0001583	missense	84959	exon3			TATTCTCCCATGT	AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.224C>T	chr11.hg19:g.122647740C>T	ENSP00000284273:p.Ser75Phe	125.0	0.0		96.0	4.0	NM_032873	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Missense_Mutation	SNP	ENST00000284273.5	hg19	CCDS31694.1	.	.	.	.	.	.	.	.	.	.	C	18.03	3.533188	0.64972	.	.	ENSG00000154127	ENST00000284273	T	0.25749	1.78	5.54	5.54	0.83059	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);UBA-like (1);	0.048805	0.85682	D	0.000000	T	0.32852	0.0843	L	0.60904	1.88	0.80722	D	1	B	0.28801	0.223	B	0.32289	0.143	T	0.06734	-1.0810	10	0.48119	T	0.1	-18.496	19.4812	0.95011	0.0:1.0:0.0:0.0	.	75	Q8TF42	UBS3B_HUMAN	F	75	ENSP00000284273:S75F	ENSP00000284273:S75F	S	+	2	0	UBASH3B	122152950	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.711000	0.84669	2.600000	0.87896	0.655000	0.94253	TCC	.	.		0.547	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873		T	122647740	C	T	122647740	3	4	67	1	0	0	0	0	1	0	0	0	16855	855	30	3	234	3	UBASH3B	11	122647740	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	55481515	122647740	12358776	33	8612										
GRAMD1B	57476	hgsc.bcm.edu	37	chr11	123483491	123483491	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tctccacagagctgcgctatCgaaaacagccctgggggtta	11	12	1	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr11:123483491C>A	ENST00000529750.1	+	14	1840	c.1513C>A	c.(1513-1515)Cga>Aga	p.R505R	GRAMD1B_ENST00000456860.2_Silent_p.R512R|GRAMD1B_ENST00000450171.2_Silent_p.R196R|GRAMD1B_ENST00000322282.7_Silent_p.R505R	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	505						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		GCTGCGCTATCGAAAACAGCC	0.532																																					p.R505R		Atlas-SNP	.											.	GRAMD1B	122	.	0			c.C1513A						.						44	46	45					11																	123483491		1938	4135	6073	SO:0001819	synonymous_variant	57476	exon14			CGCTATCGAAAAC	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.1513C>A	chr11.hg19:g.123483491C>A		107.0	0.0		122.0	31.0	NM_020716	Q6UW85|Q9ULL9	Silent	SNP	ENST00000529750.1	hg19	CCDS53720.1																																																																																			.	.		0.532	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		A	123483491	C	A	123483491	2	1	67	1	0	0	0	0	0	0	0	1	6757	876	31	1		1	GRAMD1B	11	123483491	Silent	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	835751	123483491	11523025	34	8613										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41966919	41966919	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	gaagcacaatggcagccaccCagtcctcttccggacagagc	10	15	1	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr12:41966919C>G	ENST00000402685.2	+	10	2346	c.2338C>G	c.(2338-2340)Cag>Gag	p.Q780E	PDZRN4_ENST00000539469.2_Missense_Mutation_p.Q522E|PDZRN4_ENST00000298919.7_Missense_Mutation_p.Q520E	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	780							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				GGCAGCCACCCAGTCCTCTTC	0.507																																					p.Q780E		Atlas-SNP	.											.	PDZRN4	346	.	0			c.C2338G						.						105	104	104					12																	41966919		2203	4300	6503	SO:0001583	missense	29951	exon10			GCCACCCAGTCCT	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2338C>G	chr12.hg19:g.41966919C>G	ENSP00000384197:p.Gln780Glu	114.0	0.0		136.0	21.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.251865	0.00268	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.47177	0.85;0.85;0.85	4.72	4.72	0.59763	.	1.575960	0.03275	N	0.185383	T	0.45276	0.1334	L	0.45137	1.4	0.23464	N	0.997621	B;B;B	0.23185	0.081;0.001;0.0	B;B;B	0.18263	0.021;0.004;0.003	T	0.49744	-0.8907	10	0.02654	T	1	-10.3849	18.5778	0.91161	0.0:1.0:0.0:0.0	.	780;520;522	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	E	780;522;520	ENSP00000384197:Q780E;ENSP00000439990:Q522E;ENSP00000298919:Q520E	ENSP00000298919:Q520E	Q	+	1	0	PDZRN4	40253186	0.984000	0.35163	0.035000	0.18076	0.133000	0.20885	4.177000	0.58276	2.565000	0.86533	0.650000	0.86243	CAG	.	.		0.507	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		G	41966919	C	G	41966919	3	3	67	1	0	0	0	0	1	0	0	0	11719	595	21	4	2449	4	PDZRN4	12	41966919	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10		41966919	91884976	35	8614										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56478884	56478884	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	ggacccaggtctacgatgggAagtttgccatcttcgtcatg	12	10	3	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr12:56478884A>T	ENST00000267101.3	+	3	780	c.340A>T	c.(340-342)Aag>Tag	p.K114*	ERBB3_ENST00000411731.2_Nonsense_Mutation_p.K114*|ERBB3_ENST00000415288.2_Nonsense_Mutation_p.K55*|ERBB3_ENST00000450146.2_Intron	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	114					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CTACGATGGGAAGTTTGCCAT	0.552																																					p.K114X		Atlas-SNP	.											.	ERBB3	350	.	0			c.A340T						.						208	177	187					12																	56478884		2203	4300	6503	SO:0001587	stop_gained	2065	exon3			GATGGGAAGTTTG	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.340A>T	chr12.hg19:g.56478884A>T	ENSP00000267101:p.Lys114*	128.0	0.0		141.0	16.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Nonsense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.166814	0.78339	.	.	ENSG00000065361	ENST00000549282;ENST00000549061;ENST00000267101;ENST00000394099;ENST00000411731;ENST00000549672;ENST00000415288	.	.	.	5.82	4.65	0.58169	.	0.076168	0.53938	D	0.000055	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.1525	0.54057	0.8567:0.1433:0.0:0.0	.	.	.	.	X	114;55;114;114;114;55;55	.	ENSP00000267101:K114X	K	+	1	0	ERBB3	54765151	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	5.099000	0.64554	0.983000	0.38602	0.533000	0.62120	AAG	.	.		0.552	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			T	56478884	A	T	56478884	4	4	67	1	0	0	0	0	0	1	0	0	5210	247	9	4	350	4	ERBB3	12	56478884	Nonsense_Mutation	SNP	A	TCGA-CC-A5UC-01A-11D-A28X-10	14511965	56478884	77373011	36	8615										
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72021636	72021636	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tagcgatgtcatcagtctcaTttgtaaagtatctgacatca	7	8	5	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr12:72021636T>A	ENST00000378743.3	-	21	4383	c.4025A>T	c.(4024-4026)aAt>aTt	p.N1342I		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1342					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ATCAGTCTCATTTGTAAAGTA	0.358																																					p.N1342I		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.A4025T						.						107	97	100					12																	72021636		1874	4115	5989	SO:0001583	missense	196441	exon21			GTCTCATTTGTAA	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.4025A>T	chr12.hg19:g.72021636T>A	ENSP00000368017:p.Asn1342Ile	91.0	0.0		76.0	11.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	hg19	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	T	18.19	3.569065	0.65765	.	.	ENSG00000133858	ENST00000378743	T	0.33654	1.4	5.38	3.04	0.35103	.	0.108239	0.64402	D	0.000006	T	0.23649	0.0572	N	0.24115	0.695	0.80722	D	1	B	0.29085	0.232	B	0.29440	0.102	T	0.05500	-1.0881	10	0.66056	D	0.02	.	8.415	0.32666	0.0:0.2522:0.0:0.7478	.	1342	O60293	ZC3H1_HUMAN	I	1342	ENSP00000368017:N1342I	ENSP00000368017:N1342I	N	-	2	0	ZFC3H1	70307903	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.954000	0.40362	0.366000	0.24427	-0.274000	0.10170	AAT	.	.		0.358	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		A	72021636	T	A	72021636	3	1	67	1	0	0	0	0	1	0	0	0	17648	1493	52	4	2004	4	ZFC3H1	12	72021636	Missense_Mutation	SNP	T	TCGA-CC-A5UC-01A-11D-A28X-10	15542752	72021636	61830259	37	8616										
TRPM1	4308	hgsc.bcm.edu	37	chr15	31318460	31318460	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	cagcctctttagctcctcgtCgctaaggaagagctctgtgt	10	12	2	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr15:31318460C>T	ENST00000256552.6	-	27	3658	c.3511G>A	c.(3511-3513)Gac>Aac	p.D1171N	TRPM1_ENST00000397795.2_Missense_Mutation_p.D1149N|TRPM1_ENST00000542188.1_Missense_Mutation_p.D1188N|RP11-348B17.1_ENST00000561299.1_RNA|RP11-348B17.1_ENST00000558755.1_RNA	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		AGCTCCTCGTCGCTAAGGAAG	0.537																																					p.D1188N		Atlas-SNP	.											.	TRPM1	183	.	0			c.G3562A						.						55	55	55					15																	31318460		2064	4207	6271	SO:0001583	missense	4308	exon26			CCTCGTCGCTAAG	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.3511G>A	chr15.hg19:g.31318460C>T	ENSP00000256552:p.Asp1171Asn	43.0	0.0		38.0	5.0	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	hg19	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.206180	0.58343	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.31510	1.49;1.49;1.49	5.5	5.5	0.81552	.	0.751346	0.13163	N	0.408935	T	0.33059	0.0850	L	0.41573	1.285	0.45541	D	0.998497	B;B	0.22003	0.055;0.063	B;B	0.20184	0.028;0.017	T	0.11641	-1.0579	10	0.87932	D	0	-6.1344	19.7537	0.96281	0.0:1.0:0.0:0.0	.	1143;1149	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	N	1149;1188;1171;1149	ENSP00000380897:D1149N;ENSP00000437849:D1188N;ENSP00000256552:D1171N	ENSP00000256552:D1171N	D	-	1	0	TRPM1	29105752	1.000000	0.71417	0.984000	0.44739	0.766000	0.43426	4.737000	0.62066	2.736000	0.93811	0.591000	0.81541	GAC	.	.		0.537	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		T	31318460	C	T	31318460	3	4	67	1	0	0	0	0	1	0	0	0	16600	884	31	1	1374	1	TRPM1	15	31318460	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10		31318460	71212932	38	8617										
FSIP1	161835	hgsc.bcm.edu	37	chr15	40062634	40062634	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	agtgattatcctacctgaacActcagagattatctgatgtt	7	8	2	4			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr15:40062634A>G	ENST00000350221.3	-	3	513	c.304T>C	c.(304-306)Tgt>Cgt	p.C102R	RP11-37C7.1_ENST00000558616.1_RNA	NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	102										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		CTACCTGAACACTCAGAGATT	0.328																																					p.C102R		Atlas-SNP	.											.	FSIP1	53	.	0			c.T304C						.						165	151	156					15																	40062634		2203	4300	6503	SO:0001583	missense	161835	exon3			CTGAACACTCAGA	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.304T>C	chr15.hg19:g.40062634A>G	ENSP00000280236:p.Cys102Arg	45.0	0.0		42.0	7.0	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	hg19	CCDS10050.1	.	.	.	.	.	.	.	.	.	.	a	4.147	0.025712	0.08054	.	.	ENSG00000150667	ENST00000350221	T	0.21734	1.99	4.38	0.0837	0.14434	.	0.671284	0.14279	N	0.329646	T	0.12390	0.0301	L	0.31294	0.92	0.18873	N	0.999981	B	0.06786	0.001	B	0.09377	0.004	T	0.31194	-0.9952	9	.	.	.	1.6157	6.8569	0.24046	0.5378:0.0:0.4622:0.0	.	102	Q8NA03	FSIP1_HUMAN	R	102	ENSP00000280236:C102R	.	C	-	1	0	FSIP1	37849926	0.004000	0.15560	0.081000	0.20488	0.887000	0.51463	0.314000	0.19432	-0.066000	0.12998	-0.266000	0.10368	TGT	.	.		0.328	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		G	40062634	A	G	40062634	3	3	67	1	0	0	0	0	1	0	0	0	6082	159	6	2	1481	2	FSIP1	15	40062634	Missense_Mutation	SNP	A	TCGA-CC-A5UC-01A-11D-A28X-10	8744174	40062634	62468758	39	8618										
PLA2G4E	123745	hgsc.bcm.edu	37	chr15	42285005	42285005	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tgaccctgtagccttcctggCtgcgctgccggagctcctcc	11	17	0	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr15:42285005C>T	ENST00000399518.3	-	13	1886	c.1400G>A	c.(1399-1401)aGc>aAc	p.S467N	CTD-2382E5.1_ENST00000499478.2_RNA|PLA2G4E_ENST00000413860.2_Missense_Mutation_p.S438N	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	455	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		GCCTTCCTGGCTGCGCTGCCG	0.607																																					p.S467N		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.G1400A						.						48	51	50					15																	42285005		1921	4134	6055	SO:0001583	missense	123745	exon13			TCCTGGCTGCGCT		CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.1400G>A	chr15.hg19:g.42285005C>T	ENSP00000382434:p.Ser467Asn	114.0	0.0		74.0	7.0	NM_001206670	Q6ZSC0	Missense_Mutation	SNP	ENST00000399518.3	hg19	CCDS55962.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.240352	0.39598	.	.	ENSG00000188089	ENST00000399518;ENST00000413860	T;T	0.11495	2.77;2.77	5.52	4.55	0.56014	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.546854	0.21451	N	0.074337	T	0.09247	0.0228	L	0.40543	1.245	0.26021	N	0.981864	B;B	0.10296	0.003;0.003	B;B	0.15052	0.012;0.012	T	0.13442	-1.0509	10	0.28530	T	0.3	4.8632	8.9083	0.35537	0.0:0.765:0.153:0.0819	.	438;455	C9JK77;Q3MJ16	.;PA24E_HUMAN	N	467;438	ENSP00000382434:S467N;ENSP00000413897:S438N	ENSP00000382434:S467N	S	-	2	0	PLA2G4E	40072297	0.005000	0.15991	0.993000	0.49108	0.615000	0.37417	0.043000	0.13971	2.586000	0.87340	0.655000	0.94253	AGC	.	.		0.607	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442		T	42285005	C	T	42285005	3	4	67	1	0	0	0	0	1	0	0	0	12014	797	28	3	1238	3	PLA2G4E	15	42285005	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	2222371	42285005	60246387	40	8619										
AXIN1	8312	hgsc.bcm.edu	37	chr16	396352	396352	+	Frame_Shift_Del	DEL	C	C	-													0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tccctgtccctgacccagagCtctggtcactacagactttg							TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr16:396352delC	ENST00000262320.3	-	2	1045	c.674delG	c.(673-675)agcfs	p.S226fs	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Frame_Shift_Del_p.S226fs	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	226	Interaction with TP53. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				TGACCCAGAGCTCTGGTCACT	0.493																																					p.S225fs		Atlas-INDEL	.											.	AXIN1	290	.	0			c.675delC						.						92	90	91					16																	396352		2203	4300	6503	SO:0001589	frameshift_variant	8312	exon2			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.674delG	chr16.hg19:g.396352delC	ENSP00000262320:p.Ser226fs	59.0	0.0		56.0	10.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Del	DEL	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.493	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			-	396352	C	-	396352	7	5	67	1	0	1	0	1	0	0	0	0	1236	797	28	0	1954	0	AXIN1	16	396352	Frame_Shift_Del	DEL	C	TCGA-CC-A5UC-01A-11D-A28X-10		396352	89958401	41	8620										
ADCY9	115	hgsc.bcm.edu	37	chr16	4033250	4033250	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tacctgatggacaccgcgagGgacagcacctccagcagcag	12	14	0	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr16:4033250G>A	ENST00000294016.3	-	7	3040	c.2502C>T	c.(2500-2502)tcC>tcT	p.S834S		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	834					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						ACACCGCGAGGGACAGCACCT	0.662											OREG0023573	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S834S		Atlas-SNP	.											.	ADCY9	151	.	0			c.C2502T						.						17	14	15					16																	4033250		2120	4136	6256	SO:0001819	synonymous_variant	115	exon7			CGCGAGGGACAGC	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2502C>T	chr16.hg19:g.4033250G>A		67.0	0.0	615	40.0	13.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	hg19	CCDS32382.1																																																																																			.	.		0.662	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			A	4033250	G	A	4033250	2	1	67	1	0	0	0	0	0	0	0	1	301	1219	43	3		3	ADCY9	16	4033250	Silent	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10	3636898	4033250	86321503	42	8621										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31926823	31926823	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	agaatgtggcaaagcctttcGctgtagttcataccttacta	8	9	1	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr16:31926823G>A	ENST00000300870.10	+	4	1462	c.1253G>A	c.(1252-1254)cGc>cAc	p.R418H		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	418					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R418H(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						AAAGCCTTTCGCTGTAGTTCA	0.363																																					p.R418H		Atlas-SNP	.											ZNF267,rectum,carcinoma,0,1	ZNF267	94	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1253A						.						43	48	46					16																	31926823		2197	4297	6494	SO:0001583	missense	10308	exon4			CCTTTCGCTGTAG	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.1253G>A	chr16.hg19:g.31926823G>A	ENSP00000300870:p.Arg418His	35.0	0.0		34.0	11.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Missense_Mutation	SNP	ENST00000300870.10	hg19	CCDS32440.1	.	.	.	.	.	.	.	.	.	.	.	4.243	0.044049	0.08196	.	.	ENSG00000185947	ENST00000300870	T	0.01005	5.45	0.458	-0.616	0.11583	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00666	0.0022	L	0.35723	1.085	0.09310	N	1	P	0.43542	0.81	B	0.29862	0.108	T	0.50101	-0.8867	9	0.35671	T	0.21	.	3.7552	0.08582	0.6257:0.0:0.3743:0.0	.	418	Q14586	ZN267_HUMAN	H	418	ENSP00000300870:R418H	ENSP00000300870:R418H	R	+	2	0	ZNF267	31834324	0.000000	0.05858	0.026000	0.17262	0.025000	0.11179	-2.107000	0.01337	-0.354000	0.08212	-0.350000	0.07774	CGC	.	.		0.363	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		A	31926823	G	A	31926823	3	1	67	1	0	0	0	0	1	0	0	0	17821	1087	38	1	1267	1	ZNF267	16	31926823	Missense_Mutation	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10	27893573	31926823	58427930	43	8622										
ACSF3	197322	hgsc.bcm.edu	37	chr16	89180877	89180877	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	ctctgtccgggcccctgaccActgccgtgcgcctgccaggt	12	18	1	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr16:89180877A>G	ENST00000317447.4	+	6	1485	c.1108A>G	c.(1108-1110)Act>Gct	p.T370A	ACSF3_ENST00000378345.4_Missense_Mutation_p.T105A|ACSF3_ENST00000406948.3_Missense_Mutation_p.T370A|CTD-2555A7.3_ENST00000562782.1_RNA	NM_001127214.2|NM_001243279.1|NM_001284316.1|NM_174917.3	NP_001120686.1|NP_001230208.1|NP_001271245.1|NP_777577.2	Q4G176	ACSF3_HUMAN	acyl-CoA synthetase family member 3	370					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|malonate catabolic process (GO:0090410)	mitochondrion (GO:0005739)	acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)|malonyl-CoA synthetase activity (GO:0090409)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(9)|prostate(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(80;0.0281)		GCCCCTGACCACTGCCGTGCG	0.637																																					p.T370A		Atlas-SNP	.											.	ACSF3	40	.	0			c.A1108G						.						86	85	86					16																	89180877		2198	4300	6498	SO:0001583	missense	197322	exon6			CTGACCACTGCCG	AK075499	CCDS10974.1, CCDS73926.1	16q24.3	2013-01-15			ENSG00000176715	ENSG00000176715		"Acyl-CoA synthetase family"	27288	protein-coding gene	gene with protein product	"malonyl-CoA synthetase"	614245				17762044, 21846720	Standard	XM_005256293		Approved		uc010cig.2	Q4G176	OTTHUMG00000138044	ENST00000317447.4:c.1108A>G	chr16.hg19:g.89180877A>G	ENSP00000320646:p.Thr370Ala	87.0	0.0		53.0	17.0	NM_174917	A8K4J8|C9JQL6|Q6INA0|Q8N2F7	Missense_Mutation	SNP	ENST00000317447.4	hg19	CCDS10974.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.223|1.223	-0.626392|-0.626392	0.03610|0.03610	.|.	.|.	ENSG00000176715|ENSG00000176715	ENST00000543676|ENST00000537895;ENST00000317447;ENST00000540697;ENST00000406948;ENST00000378345;ENST00000544543	.|D;T;T;T;T;T	.|0.81996	.|-1.56;1.05;1.05;1.05;1.05;1.05	0.727|0.727	-1.45|-1.45	0.08828|0.08828	.|AMP-dependent synthetase/ligase (1);	.|1.542160	.|0.03558	.|N	.|0.226552	T|T	0.60235|0.60235	0.2253|0.2253	N|N	0.05306|0.05306	-0.075|-0.075	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	T|T	0.44436|0.44436	-0.9328|-0.9328	4|9	.|0.12430	.|T	.|0.62	.|.	.|.	.|.	.|.	.|.	.|370	.|Q4G176	.|ACSF3_HUMAN	R|A	117|105;370;105;370;105;105	.|ENSP00000439201:T105A;ENSP00000320646:T370A;ENSP00000445397:T105A;ENSP00000384627:T370A;ENSP00000367596:T105A;ENSP00000442781:T105A	.|ENSP00000320646:T370A	H|T	+|+	2|1	0|0	ACSF3|ACSF3	87708378|87708378	0.057000|0.057000	0.20700|0.20700	0.002000|0.002000	0.10522|0.10522	0.001000|0.001000	0.01503|0.01503	0.209000|0.209000	0.17435|0.17435	-2.115000|-2.115000	0.00831|0.00831	-1.899000|-1.899000	0.00529|0.00529	CAC|ACT	.	.		0.637	ACSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269919.1	NM_174917		G	89180877	A	G	89180877	3	3	67	1	0	0	0	0	1	0	0	0	176	159	6	2	1122	2	ACSF3	16	89180877	Missense_Mutation	SNP	A	TCGA-CC-A5UC-01A-11D-A28X-10	57254054	89180877	1173876	44	8623										
AATK	9625	hgsc.bcm.edu	37	chr17	79094590	79094590	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	gcacctccccggggccagagCcttgtgcctccccggaaacc	11	19	0	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr17:79094590C>T	ENST00000326724.4	-	11	3170	c.3146G>A	c.(3145-3147)gGc>gAc	p.G1049D	AATK_ENST00000417379.1_Missense_Mutation_p.G946D	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1049					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GGGGCCAGAGCCTTGTGCCTC	0.731																																					p.G1049D		Atlas-SNP	.											.	AATK	102	.	0			c.G3146A						.						5	6	5					17																	79094590		1817	4017	5834	SO:0001583	missense	9625	exon11			CCAGAGCCTTGTG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.3146G>A	chr17.hg19:g.79094590C>T	ENSP00000324196:p.Gly1049Asp	47.0	0.0		33.0	5.0	NM_001080395	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	hg19	CCDS45807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.994|5.994	0.367328|0.367328	0.11352|0.11352	.|.	.|.	ENSG00000181409|ENSG00000181409	ENST00000417379|ENST00000326724	.|T	.|0.76448	.|-1.02	4.28|4.28	0.663|0.663	0.17885|0.17885	.|.	.|1.515330	.|0.04128	.|N	.|0.317559	T|T	0.63733|0.63733	0.2536|0.2536	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	.|B	.|0.09022	.|0.002	.|B	.|0.06405	.|0.002	T|T	0.49360|0.49360	-0.8948|-0.8948	5|10	.|0.34782	.|T	.|0.22	.|.	3.3419|3.3419	0.07122|0.07122	0.1864:0.48:0.0:0.3335|0.1864:0.48:0.0:0.3335	.|.	.|1049	.|Q6ZMQ8	.|LMTK1_HUMAN	T|D	1002|1049	.|ENSP00000324196:G1049D	.|ENSP00000324196:G1049D	A|G	-|-	1|2	0|0	AATK|AATK	76709185|76709185	0.000000|0.000000	0.05858|0.05858	0.027000|0.027000	0.17364|0.17364	0.445000|0.445000	0.32107|0.32107	-1.541000|-1.541000	0.02198|0.02198	0.756000|0.756000	0.33013|0.33013	0.462000|0.462000	0.41574|0.41574	GCT|GGC	.	.		0.731	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		T	79094590	C	T	79094590	3	4	67	1	0	0	0	0	1	0	0	0	26	739	26	3	994	3	AATK	17	79094590	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10		79094590	2100620	45	8624										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22156012	22156012	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	ccacattcttcacatttgtaGggtttctcaccagtatgaat	6	10	3	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr19:22156012G>T	ENST00000397126.4	-	4	1972	c.1824C>A	c.(1822-1824)ccC>ccA	p.P608P	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	608					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				CACATTTGTAGGGTTTCTCAC	0.363																																					p.P608P		Atlas-SNP	.											.	ZNF208	817	.	0			c.C1824A						.						56	59	58					19																	22156012		2088	4240	6328	SO:0001819	synonymous_variant	7757	exon4			TTTGTAGGGTTTC	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1824C>A	chr19.hg19:g.22156012G>T		30.0	0.0		28.0	5.0	NM_007153		Silent	SNP	ENST00000397126.4	hg19	CCDS54240.1																																																																																			.	.		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22156012	G	T	22156012	2	4	67	1	0	0	0	0	0	0	0	1	17781	987	35	3		3	ZNF208	19	22156012	Silent	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10		22156012	36972971	46	8625										
RHPN2	85415	hgsc.bcm.edu	37	chr19	33493213	33493213	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	cagggccgcgtagtggtgggCcttcacgcaggctaagctgg	17	11	1	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr19:33493213C>T	ENST00000254260.3	-	9	1080	c.1045G>A	c.(1045-1047)Gcc>Acc	p.A349T	RHPN2_ENST00000400226.4_Missense_Mutation_p.A198T	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	349	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TAGTGGTGGGCCTTCACGCAG	0.632																																					p.A349T		Atlas-SNP	.											.	RHPN2	107	.	0			c.G1045A						.						53	51	52					19																	33493213		2203	4300	6503	SO:0001583	missense	85415	exon9			GGTGGGCCTTCAC	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1045G>A	chr19.hg19:g.33493213C>T	ENSP00000254260:p.Ala349Thr	194.0	0.0		192.0	22.0	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	hg19	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	11.59	1.683979	0.29872	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.18960	2.18;2.18	4.61	2.03	0.26663	BRO1 domain (3);	0.401087	0.29853	N	0.011024	T	0.21881	0.0527	L	0.56199	1.76	0.41435	D	0.987886	B	0.22800	0.075	B	0.23574	0.047	T	0.15723	-1.0427	10	0.49607	T	0.09	-5.0597	13.7833	0.63094	0.3704:0.6296:0.0:0.0	.	349	Q8IUC4	RHPN2_HUMAN	T	349;79;198	ENSP00000254260:A349T;ENSP00000402244:A198T	ENSP00000254260:A349T	A	-	1	0	RHPN2	38185053	1.000000	0.71417	1.000000	0.80357	0.261000	0.26267	1.888000	0.39708	0.992000	0.38840	0.455000	0.32223	GCC	.	.		0.632	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		T	33493213	C	T	33493213	3	4	67	1	0	0	0	0	1	0	0	0	13366	739	26	3	1043	3	RHPN2	19	33493213	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10	11337201	33493213	25635770	47	8626										
LILRB5	10990	hgsc.bcm.edu	37	chr19	54756260	54756260	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tcctggatgtcagcaactggGctggccctgggggaggacac	16	11	1	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr19:54756260G>T	ENST00000316219.5	-	11	1649	c.1542C>A	c.(1540-1542)agC>agA	p.S514R	LILRB5_ENST00000345866.6_Missense_Mutation_p.S415R|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000450632.1_Missense_Mutation_p.S506R|LILRB5_ENST00000449561.2_Missense_Mutation_p.S515R	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	514					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CAGCAACTGGGCTGGCCCTGG	0.592																																					p.S515R		Atlas-SNP	.											.	LILRB5	176	.	0			c.C1545A						.						93	91	92					19																	54756260		2203	4300	6503	SO:0001583	missense	10990	exon11			AACTGGGCTGGCC	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1542C>A	chr19.hg19:g.54756260G>T	ENSP00000320390:p.Ser514Arg	77.0	0.0		55.0	10.0	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	hg19	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.330413	0.24167	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00507	7.0;6.92;7.03;7.02	2.08	-4.16	0.03869	.	.	.	.	.	T	0.00815	0.0027	L	0.57536	1.79	0.09310	N	1	B;D;B;D	0.76494	0.068;0.991;0.007;0.999	B;P;B;D	0.68943	0.022;0.906;0.018;0.961	T	0.36138	-0.9760	9	0.52906	T	0.07	.	0.8149	0.01100	0.2692:0.3422:0.2163:0.1723	.	506;415;515;514	C9JMK7;O75023-2;O75023-3;O75023	.;.;.;LIRB5_HUMAN	R	514;506;515;415	ENSP00000320390:S514R;ENSP00000414225:S506R;ENSP00000406478:S515R;ENSP00000263430:S415R	ENSP00000320390:S514R	S	-	3	2	LILRB5	59448072	0.151000	0.22747	0.000000	0.03702	0.013000	0.08279	-0.133000	0.10451	-1.492000	0.01838	-0.225000	0.12378	AGC	.	.		0.592	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			T	54756260	G	T	54756260	3	4	67	1	0	0	0	0	1	0	0	0	8803	1194	42	3	242	3	LILRB5	19	54756260	Missense_Mutation	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10	21263047	54756260	4372723	48	8627										
ZNF551	90233	hgsc.bcm.edu	37	chr19	58198623	58198623	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	tgaattcattcaccaccagaGacgtcacactggaggagtgc	10	11	3	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr19:58198623G>C	ENST00000282296.5	+	3	1165	c.980G>C	c.(979-981)aGa>aCa	p.R327T	ZNF551_ENST00000356715.4_Missense_Mutation_p.R311T|AC003006.7_ENST00000594684.1_Intron|AC003006.7_ENST00000599221.1_Intron|ZNF551_ENST00000596085.1_Intron			Q7Z340	ZN551_HUMAN	zinc finger protein 551	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CACCACCAGAGACGTCACACT	0.418																																					p.R327T		Atlas-SNP	.											.	ZNF551	65	.	0			c.G980C						.						89	86	87					19																	58198623		2203	4300	6503	SO:0001583	missense	90233	exon3			ACCAGAGACGTCA	BX538151	CCDS12959.1, CCDS12959.2	19q13.43	2013-09-20			ENSG00000204519	ENSG00000204519		"Zinc fingers, C2H2-type", "-"	25108	protein-coding gene	gene with protein product							Standard	NM_138347		Approved	DKFZp686H1038	uc002qpw.5	Q7Z340	OTTHUMG00000183470	ENST00000282296.5:c.980G>C	chr19.hg19:g.58198623G>C	ENSP00000282296:p.Arg327Thr	77.0	0.0		75.0	23.0	NM_138347	B4DU22|P17034|Q8N246|Q9BRY1	Missense_Mutation	SNP	ENST00000282296.5	hg19	CCDS12959.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.77|13.77	2.335484|2.335484	0.41398|0.41398	.|.	.|.	ENSG00000204519|ENSG00000228006	ENST00000356715;ENST00000282296|ENST00000541705	.|.	.|.	.|.	2.57|2.57	0.227|0.227	0.15359|0.15359	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	.|0.202887	.|0.23021	.|U	.|0.052853	T|T	0.41627|0.41627	0.1167|0.1167	M|M	0.63169|0.63169	1.94|1.94	0.09310|0.09310	N|N	1|1	D|.	0.55385|.	0.971|.	B|.	0.42916|.	0.402|.	T|T	0.29027|0.29027	-1.0025|-1.0025	8|7	0.54805|0.40728	T|T	0.06|0.16	.|.	6.3397|6.3397	0.21316|0.21316	0.116:0.1864:0.6976:0.0|0.116:0.1864:0.6976:0.0	.|.	327|.	Q7Z340|.	ZN551_HUMAN|.	T|C	327;311|261	.|.	ENSP00000282296:R311T|ENSP00000437781:S261C	R|S	+|-	2|2	0|0	ZNF551|AC004017.1	62890435|62890435	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.025000|-0.025000	0.12413|0.12413	0.016000|0.016000	0.14998|0.14998	-0.258000|-0.258000	0.10820|0.10820	AGA|TCT	.	.		0.418	ZNF551-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466803.2	NM_138347		C	58198623	G	C	58198623	3	2	67	1	0	0	0	0	1	0	0	0	17998	942	33	4	942	4	ZNF551	19	58198623	Missense_Mutation	SNP	G	TCGA-CC-A5UC-01A-11D-A28X-10	3442363	58198623	930360	49	8628										
PCK1	5105	hgsc.bcm.edu	37	chr20	56137828	56137828	+	Frame_Shift_Del	DEL	G	G	-													0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	aagatcggcatcgagctgacGgattcaccctacgtggtggc					rs530695277		TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr20:56137828delG	ENST00000319441.4	+	4	647	c.483delG	c.(481-483)acgfs	p.T161fs	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Frame_Shift_Del_p.T29fs	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	161					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			TCGAGCTGACGGATTCACCCT	0.612																																					p.T161fs		Atlas-Indel,Pindel	.											PCK1,colon,carcinoma,0,1	PCK1	95	.	0			c.482delC						.						73	61	65					20																	56137828		2203	4300	6503	SO:0001589	frameshift_variant	5105	exon4			.		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.483delG	chr20.hg19:g.56137828delG	ENSP00000319814:p.Thr161fs	136.0	0.0		140.0	29.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Frame_Shift_Del	DEL	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	.		0.612	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			-	56137828	G	-	56137828	7	5	67	1	0	1	0	1	0	0	0	0	11590	1103	39	0	493	0	PCK1	20	56137828	Frame_Shift_Del	DEL	G	TCGA-CC-A5UC-01A-11D-A28X-10		56137828	6887692	50	8629										
PNPLA3	80339	hgsc.bcm.edu	37	chr22	44328955	44328955	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	ctctcgagagcttttgtcccCccggatctcaaggtgagttg	11	12	2	2			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chr22:44328955C>T	ENST00000216180.3	+	4	857	c.684C>T	c.(682-684)ccC>ccT	p.P228P	PNPLA3_ENST00000423180.2_Silent_p.P224P|PNPLA3_ENST00000478713.1_3'UTR	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	228					acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				CTTTTGTCCCCCCGGATCTCA	0.542																																					p.P228P		Atlas-SNP	.											.	PNPLA3	53	.	0			c.C684T						.						111	103	106					22																	44328955		2203	4300	6503	SO:0001819	synonymous_variant	80339	exon4			TGTCCCCCCGGAT		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"Patatin-like phospholipase domain containing"	18590	protein-coding gene	gene with protein product		609567	"chromosome 22 open reading frame 20", "adiponutrin"	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.684C>T	chr22.hg19:g.44328955C>T		80.0	0.0		121.0	22.0	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Silent	SNP	ENST00000216180.3	hg19	CCDS14054.1																																																																																			.	.		0.542	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225		T	44328955	C	T	44328955	2	4	67	1	0	0	0	0	0	0	0	1	12175	610	22	3		3	PNPLA3	22	44328955	Silent	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10		44328955	6975611	51	8630										
UBQLN2	29978	hgsc.bcm.edu	37	chrX	56590709	56590709	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	ctcccaggagtaactccacaCctatttccacaaatagcaac	4	15	0	0			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chrX:56590709C>G	ENST00000338222.5	+	1	684	c.403C>G	c.(403-405)Cct>Gct	p.P135A		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	135					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)	21						TAACTCCACACCTATTTCCAC	0.577																																					p.P135A	Esophageal Squamous(104;218 1492 6022 10838 28884)	Atlas-SNP	.											.	UBQLN2	55	.	0			c.C403G						.						38	35	36					X																	56590709		2203	4300	6503	SO:0001583	missense	29978	exon1			TCCACACCTATTT	AF189009	CCDS14374.1	Xp11.21	2014-09-17			ENSG00000188021	ENSG00000188021		"Ubiquilin family"	12509	protein-coding gene	gene with protein product	"NEDD4 binding protein 4"	300264				10675567	Standard	NM_013444		Approved	Chap1, Dsk2, RIHFB2157, LIC-2, CHAP1/DSK2, PLIC-2, N4BP4, PLIC2	uc004dus.3	Q9UHD9	OTTHUMG00000021669	ENST00000338222.5:c.403C>G	chrX.hg19:g.56590709C>G	ENSP00000345195:p.Pro135Ala	138.0	0.0		127.0	19.0	NM_013444	O94798|Q5D027|Q9H3W6|Q9HAZ4	Missense_Mutation	SNP	ENST00000338222.5	hg19	CCDS14374.1	.	.	.	.	.	.	.	.	.	.	C	0.042	-1.282245	0.01398	.	.	ENSG00000188021	ENST00000338222;ENST00000535171	D	0.82803	-1.65	4.94	2.1	0.27182	.	0.450163	0.22458	N	0.059784	T	0.56396	0.1982	N	0.03608	-0.345	0.31421	N	0.674324	B;B	0.29481	0.245;0.032	B;B	0.27500	0.08;0.008	T	0.51841	-0.8654	10	0.18276	T	0.48	-0.1927	3.859	0.08988	0.0:0.5046:0.1767:0.3187	.	135;135	B4DZF1;Q9UHD9	.;UBQL2_HUMAN	A	135	ENSP00000345195:P135A	ENSP00000345195:P135A	P	+	1	0	UBQLN2	56607434	0.935000	0.31712	0.734000	0.30879	0.177000	0.22998	0.470000	0.22084	0.192000	0.20272	-0.217000	0.12591	CCT	.	.		0.577	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444		G	56590709	C	G	56590709	3	3	67	1	0	0	0	0	1	0	0	0	16912	507	18	4	405	4	UBQLN2	23	56590709	Missense_Mutation	SNP	C	TCGA-CC-A5UC-01A-11D-A28X-10		56590709	98679851	52	8631										
LONRF3	79836	hgsc.bcm.edu	37	chrX	118145797	118145797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.68974358974359	3.31076923076923	0	0.333333333333333	1	0	gccttaataagaatgtgcctAttttcgtgtgtactatggcc	9	8	0	1			TCGA-CC-A5UC-01A-11D-A28X-10	TCGA-CC-A5UC-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	14c093b0-daba-46f0-9fee-73efbe76cc2b	0e3769b2-9456-4937-bd2b-27960a8ab40c	g.chrX:118145797A>G	ENST00000371628.3	+	8	1703	c.1672A>G	c.(1672-1674)Att>Gtt	p.I558V	LONRF3_ENST00000422289.2_Missense_Mutation_p.I302V|LONRF3_ENST00000472173.1_3'UTR|LONRF3_ENST00000304778.7_Missense_Mutation_p.I517V	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	558	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						GAATGTGCCTATTTTCGTGTG	0.433																																					p.I558V		Atlas-SNP	.											.	LONRF3	138	.	0			c.A1672G						.						339	255	283					X																	118145797		2203	4300	6503	SO:0001583	missense	79836	exon8			GTGCCTATTTTCG	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"RING-type (C3HC4) zinc fingers"	21152	protein-coding gene	gene with protein product			"ring finger protein 127"	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.1672A>G	chrX.hg19:g.118145797A>G	ENSP00000360690:p.Ile558Val	147.0	0.0		103.0	28.0	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	hg19	CCDS35374.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.1|26.1	4.708470|4.708470	0.89018|0.89018	.|.	.|.	ENSG00000175556|ENSG00000175556	ENST00000365713;ENST00000304778;ENST00000371628;ENST00000422289|ENST00000439603	T;T;T;T|.	0.39592|.	1.07;1.07;1.07;1.07|.	6.07|6.07	6.07|6.07	0.98685|0.98685	Peptidase S16, lon N-terminal (1);PUA-like domain (1);|.	0.102234|.	0.64402|.	D|.	0.000017|.	T|T	0.64886|0.64886	0.2639|0.2639	L|L	0.53561|0.53561	1.675|1.675	0.48452|0.48452	D|D	0.999654|0.999654	D;P;D|.	0.71674|.	0.998;0.854;0.988|.	D;P;D|.	0.67725|.	0.951;0.747;0.953|.	T|T	0.62868|0.62868	-0.6763|-0.6763	10|5	0.27785|.	T|.	0.31|.	-16.9782|-16.9782	14.5728|14.5728	0.68224|0.68224	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	302;517;558|.	B3KUN7;Q496Y0-2;Q496Y0|.	.;.;LONF3_HUMAN|.	V|C	517;517;558;302|323	ENSP00000360691:I517V;ENSP00000307732:I517V;ENSP00000360690:I558V;ENSP00000408894:I302V|.	ENSP00000307732:I517V|.	I|Y	+|+	1|2	0|0	LONRF3|LONRF3	118029825|118029825	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	9.339000|9.339000	0.96797|0.96797	2.041000|2.041000	0.60428|0.60428	0.481000|0.481000	0.45027|0.45027	ATT|TAT	.	.		0.433	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778		G	118145797	A	G	118145797	3	3	67	1	0	0	0	0	1	0	0	0	8905	449	16	2	1702	2	LONRF3	23	118145797	Missense_Mutation	SNP	A	TCGA-CC-A5UC-01A-11D-A28X-10	61555088	118145797	37124763	53	8632										
SCNN1D	6339	hgsc.bcm.edu	37	chr1	1223365	1223365	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctacggccactgcaccgccgGcggggaaggcgtggaggtgg	19	12	0	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:1223365G>T	ENST00000338555.2	+	9	2262	c.1118G>T	c.(1117-1119)gGc>gTc	p.G373V	SCNN1D_ENST00000379116.5_Missense_Mutation_p.G537V|SCNN1D_ENST00000400928.3_Missense_Mutation_p.G373V|SCNN1D_ENST00000325425.8_Missense_Mutation_p.G439V			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	373					ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	TGCACCGCCGGCGGGGAAGGC	0.711																																					p.G537V		Atlas-SNP	.											.	SCNN1D	60	.	0			c.G1610T						.						6	8	7					1																	1223365		1996	4043	6039	SO:0001583	missense	6339	exon12			CCGCCGGCGGGGA	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10601	protein-coding gene	gene with protein product		601328	"sodium channel, nonvoltage-gated 1, delta", "sodium channel, non-voltage-gated 1, delta"			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.1118G>T	chr1.hg19:g.1223365G>T	ENSP00000339504:p.Gly373Val	150.0	0.0		105.0	52.0	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Missense_Mutation	SNP	ENST00000338555.2	hg19		.	.	.	.	.	.	.	.	.	.	G	13.85	2.359030	0.41801	.	.	ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928	T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03	3.48	1.5	0.22942	.	0.449819	0.18883	U	0.128527	T	0.68650	0.3024	M	0.64997	1.995	0.09310	N	0.999997	D;D;D	0.60160	0.971;0.971;0.987	P;P;P	0.61722	0.856;0.893;0.737	T	0.56786	-0.7921	10	0.44086	T	0.13	.	7.8758	0.29592	0.3149:0.0:0.6851:0.0	.	195;373;537	B1AMF2;P51172;A6NNF7	.;SCNND_HUMAN;.	V	404;537;373;439;373	ENSP00000368411:G537V;ENSP00000339504:G373V;ENSP00000321594:G439V;ENSP00000383717:G373V	ENSP00000321594:G439V	G	+	2	0	SCNN1D	1213228	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	1.731000	0.38135	0.597000	0.29811	-0.671000	0.03813	GGC	.	.		0.711	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978		T	1223365	G	T	1223365	3	4	68	1	0	0	0	0	1	0	0	0	13944	1203	42	3	1350	3	SCNN1D	1	1223365	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10		1223365	248027256	1	8633										
PRDM16	63976	hgsc.bcm.edu	37	chr1	3328344	3328344	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cttgtacccccggccgcctcTgctacctcccacatcgctgc	7	21	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:3328344T>A	ENST00000270722.5	+	9	1632	c.1583T>A	c.(1582-1584)cTg>cAg	p.L528Q	PRDM16_ENST00000442529.2_Missense_Mutation_p.L528Q|PRDM16_ENST00000511072.1_Missense_Mutation_p.L529Q|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000441472.2_Missense_Mutation_p.L528Q|PRDM16_ENST00000378391.2_Missense_Mutation_p.L528Q|PRDM16_ENST00000514189.1_Missense_Mutation_p.L529Q|PRDM16_ENST00000378398.3_Missense_Mutation_p.L529Q			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	528	Pro-rich.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		CGGCCGCCTCTGCTACCTCCC	0.706			T	EVI1	"MDS, AML"																																p.L528Q		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.T1583A						.						63	81	75					1																	3328344		1932	4125	6057	SO:0001583	missense	63976	exon9			CGCCTCTGCTACC	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.1583T>A	chr1.hg19:g.3328344T>A	ENSP00000270722:p.Leu528Gln	50.0	0.0		27.0	10.0	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	hg19	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	T	19.77	3.889585	0.72524	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.09538	2.99;3.03;3.04;3.03;3.03;3.02;3.04;2.97;2.99	5.33	5.33	0.75918	.	0.000000	0.40064	U	0.001198	T	0.34135	0.0887	M	0.75264	2.295	0.48185	D	0.999608	D;D;D;D	0.89917	0.993;1.0;1.0;1.0	P;D;D;D	0.97110	0.77;0.999;1.0;0.999	T	0.09684	-1.0663	10	0.87932	D	0	.	15.3332	0.74231	0.0:0.0:0.0:1.0	.	528;528;528;528	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	Q	529;529;528;528;528;529;528;344;344;337	ENSP00000426975:L529Q;ENSP00000367651:L529Q;ENSP00000407968:L528Q;ENSP00000405253:L528Q;ENSP00000367643:L528Q;ENSP00000421400:L529Q;ENSP00000270722:L528Q;ENSP00000422504:L344Q;ENSP00000425796:L337Q	ENSP00000270722:L528Q	L	+	2	0	PRDM16	3318204	1.000000	0.71417	0.920000	0.36463	0.995000	0.86356	6.179000	0.71974	2.042000	0.60477	0.491000	0.48974	CTG	.	.		0.706	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		A	3328344	T	A	3328344	3	1	68	1	0	0	0	0	1	0	0	0	12469	1580	55	4	1617	4	PRDM16	1	3328344	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	2104979	3328344	245922277	2	8634										
KIF1B	23095	hgsc.bcm.edu	37	chr1	10384901	10384901	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	acgaaagcgaaaccactgtgActggcagcgatcccttctat	9	12	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:10384901A>C	ENST00000377086.1	+	26	2825	c.2623A>C	c.(2623-2625)Act>Cct	p.T875P	KIF1B_ENST00000377081.1_Missense_Mutation_p.T875P|KIF1B_ENST00000263934.6_Missense_Mutation_p.T829P			O60333	KIF1B_HUMAN	kinesin family member 1B	875					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		AACCACTGTGACTGGCAGCGA	0.448																																					p.T829P		Atlas-SNP	.											.	KIF1B	242	.	0			c.A2485C						.						180	169	173					1																	10384901		2203	4300	6503	SO:0001583	missense	23095	exon24			ACTGTGACTGGCA	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.2623A>C	chr1.hg19:g.10384901A>C	ENSP00000366290:p.Thr875Pro	78.0	0.0		83.0	35.0	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	A	18.81	3.703957	0.68501	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.75938	-0.98;-0.98;-0.98	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.80276	0.4593	L	0.35723	1.085	0.80722	D	1	D;D;D;D;D;D	0.76494	0.99;0.979;0.993;0.992;0.999;0.997	D;P;D;D;D;D	0.78314	0.944;0.906;0.944;0.93;0.958;0.991	T	0.77968	-0.2388	10	0.30078	T	0.28	.	16.2194	0.82247	1.0:0.0:0.0:0.0	.	861;835;875;849;875;829	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	P	875;829;875;875	ENSP00000263934:T829P;ENSP00000366290:T875P;ENSP00000366284:T875P	ENSP00000263934:T829P	T	+	1	0	KIF1B	10307488	1.000000	0.71417	0.997000	0.53966	0.961000	0.63080	9.339000	0.96797	2.234000	0.73211	0.528000	0.53228	ACT	.	.		0.448	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			C	10384901	A	C	10384901	3	2	68	1	0	0	0	0	1	0	0	0	8293	275	10	5	4064	5	KIF1B	1	10384901	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	7056557	10384901	238865720	3	8635										
PLA2G2F	64600	hgsc.bcm.edu	37	chr1	20474788	20474788	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	agaggagtaccgtggcttccTcaatgtctactgccagggcc	12	12	2	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:20474788T>A	ENST00000375102.3	+	5	632	c.530T>A	c.(529-531)cTc>cAc	p.L177H		NM_022819.3	NP_073730.3	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	134					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CGTGGCTTCCTCAATGTCTAC	0.582																																					p.L177H		Atlas-SNP	.											.	PLA2G2F	28	.	0			c.T530A						.						173	143	153					1																	20474788		2203	4300	6503	SO:0001583	missense	64600	exon5			GCTTCCTCAATGT	AL158172	CCDS204.2	1p35	2008-09-19			ENSG00000158786	ENSG00000158786	3.1.1.4		30040	protein-coding gene	gene with protein product						11112443	Standard	NM_022819		Approved		uc009vpp.1	Q9BZM2	OTTHUMG00000002704	ENST00000375102.3:c.530T>A	chr1.hg19:g.20474788T>A	ENSP00000364243:p.Leu177His	310.0	1.0		193.0	81.0	NM_022819	Q5R385|Q8N217|Q9H506	Missense_Mutation	SNP	ENST00000375102.3	hg19	CCDS204.2	.	.	.	.	.	.	.	.	.	.	T	8.916	0.959937	0.18507	.	.	ENSG00000158786	ENST00000375102	D	0.83506	-1.73	5.19	5.19	0.71726	.	0.292816	0.24750	N	0.035913	D	0.87581	0.6213	M	0.69358	2.11	0.29667	N	0.842809	D	0.89917	1.0	D	0.69479	0.964	T	0.81621	-0.0850	10	0.15499	T	0.54	-24.8592	11.431	0.50041	0.0:0.0:0.0:1.0	.	177	Q9BZM2-2	.	H	177	ENSP00000364243:L177H	ENSP00000364243:L177H	L	+	2	0	PLA2G2F	20347375	1.000000	0.71417	0.997000	0.53966	0.019000	0.09904	2.345000	0.44018	1.967000	0.57214	0.460000	0.39030	CTC	.	.		0.582	PLA2G2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007687.1	NM_022819		A	20474788	T	A	20474788	3	1	68	1	0	0	0	0	1	0	0	0	12008	1551	54	4	548	4	PLA2G2F	1	20474788	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	10089887	20474788	228775833	4	8636										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27107029	27107029	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	agttccagcagagccaggccAgcctcctccacatgcagaac	9	16	0	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:27107029A>T	ENST00000324856.7	+	20	7011	c.6640A>T	c.(6640-6642)Agc>Tgc	p.S2214C	ARID1A_ENST00000540690.1_Missense_Mutation_p.S542C|ARID1A_ENST00000374152.2_Missense_Mutation_p.S1831C|ARID1A_ENST00000457599.2_Missense_Mutation_p.S1997C	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2214					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GAGCCAGGCCAGCCTCCTCCA	0.627			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.S2214C		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.A6640T						.						69	68	69					1																	27107029		2203	4300	6503	SO:0001583	missense	8289	exon20			CAGGCCAGCCTCC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.6640A>T	chr1.hg19:g.27107029A>T	ENSP00000320485:p.Ser2214Cys	124.0	0.0		90.0	38.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.74|12.74	2.027754|2.027754	0.35797|0.35797	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000430799|ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	.|T;T;T;T	.|0.36699	.|1.24;1.24;1.24;1.24	4.6|4.6	4.6|4.6	0.57074|0.57074	.|Armadillo-like helical (1);	.|0.183447	.|0.50627	.|D	.|0.000103	T|T	0.50531|0.50531	0.1621|0.1621	M|M	0.63428|0.63428	1.95|1.95	0.34106|0.34106	D|D	0.662488|0.662488	.|D;D;D	.|0.76494	.|0.999;0.999;0.998	.|P;D;P	.|0.68192	.|0.871;0.956;0.891	T|T	0.63620|0.63620	-0.6596|-0.6596	5|10	.|0.52906	.|T	.|0.07	-10.5505|-10.5505	6.9016|6.9016	0.24285|0.24285	0.8215:0.0:0.1785:0.0|0.8215:0.0:0.1785:0.0	.|.	.|1831;2214;1997	.|O14497-3;O14497;O14497-2	.|.;ARI1A_HUMAN;.	L|C	1110|2214;1997;1831;542	.|ENSP00000320485:S2214C;ENSP00000387636:S1997C;ENSP00000363267:S1831C;ENSP00000442437:S542C	.|ENSP00000320485:S2214C	Q|S	+|+	2|1	0|0	ARID1A|ARID1A	26979616|26979616	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	2.502000|2.502000	0.45398|0.45398	2.063000|2.063000	0.61619|0.61619	0.482000|0.482000	0.46254|0.46254	CAG|AGC	.	.		0.627	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27107029	A	T	27107029	3	4	68	1	0	0	0	0	1	0	0	0	913	188	7	4	6718	4	ARID1A	1	27107029	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	6632241	27107029	222143592	5	8637										
MAP3K6	9064	hgsc.bcm.edu	37	chr1	27684710	27684710	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ccataactgaggcagcgcttCggggggctgggtgggtgctg	19	9	0	1	rs376956203		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:27684710C>T	ENST00000493901.1	-	22	3116	c.2877G>A	c.(2875-2877)ccG>ccA	p.P959P	MAP3K6_ENST00000374040.3_Silent_p.P951P|MAP3K6_ENST00000357582.2_Silent_p.P959P	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	959					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GGCAGCGCTTCGGGGGGCTGG	0.607											OREG0013282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P959P		Atlas-SNP	.											.	MAP3K6	134	.	0			c.G2877A						.	C		1,4405	2.1+/-5.4	0,1,2202	58	68	64		2877	-9.6	0.5	1		64	0,8600		0,0,4300	no	coding-synonymous	MAP3K6	NM_004672.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		959/1289	27684710	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9064	exon21			GCGCTTCGGGGGG	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6858	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 2"	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.2877G>A	chr1.hg19:g.27684710C>T		128.0	0.0	796	96.0	43.0	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Silent	SNP	ENST00000493901.1	hg19	CCDS299.1	.	.	.	.	.	.	.	.	.	.	C	9.550	1.115587	0.20795	2.27E-4	0.0	ENSG00000142733	ENST00000472410	.	.	.	4.82	-9.64	0.00541	.	.	.	.	.	T	0.46560	0.1399	.	.	.	0.50039	D	0.999841	.	.	.	.	.	.	T	0.55768	-0.8089	4	.	.	.	.	8.4087	0.32629	0.0:0.2498:0.4034:0.3468	.	.	.	.	Q	683	.	.	R	-	2	0	MAP3K6	27557297	0.000000	0.05858	0.530000	0.27963	0.964000	0.63967	-4.514000	0.00222	-2.160000	0.00786	-0.143000	0.13931	CGA	.	.		0.607	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672		T	27684710	C	T	27684710	2	4	68	1	0	0	0	0	0	0	0	1	9263	871	31	1		1	MAP3K6	1	27684710	Silent	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	577681	27684710	221565911	6	8638										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34038176	34038176	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cactctgcagtggcctcagcGcctgcctggaggtggtagcc	14	14	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:34038176G>A	ENST00000373381.4	-	50	7868	c.7692C>T	c.(7690-7692)ggC>ggT	p.G2564G		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2566	Sushi 15. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TGGCCTCAGCGCCTGCCTGGA	0.587																																					p.G2566G		Atlas-SNP	.											CSMD2_ENST00000373381,colon,carcinoma,0,2	CSMD2	946	.	0			c.C7698T						.						140	118	125					1																	34038176		2203	4300	6503	SO:0001819	synonymous_variant	114784	exon51			CTCAGCGCCTGCC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.7692C>T	chr1.hg19:g.34038176G>A		107.0	0.0		87.0	35.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	hg19																																																																																				.	.		0.587	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	34038176	G	A	34038176	2	1	68	1	0	0	0	0	0	0	0	1	3947	1074	38	1		1	CSMD2	1	34038176	Silent	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	6353466	34038176	215212445	7	8639										
MTF1	4520	hgsc.bcm.edu	37	chr1	38287832	38287832	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ggagaactggtggcaccattTaatatccattgtaagttctg	10	7	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:38287832T>G	ENST00000373036.4	-	9	1868	c.1728A>C	c.(1726-1728)ttA>ttC	p.L576F		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	576					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TGGCACCATTTAATATCCATT	0.408																																					p.L576F		Atlas-SNP	.											.	MTF1	67	.	0			c.A1728C						.						151	145	147					1																	38287832		2203	4300	6503	SO:0001583	missense	4520	exon9			ACCATTTAATATC	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1728A>C	chr1.hg19:g.38287832T>G	ENSP00000362127:p.Leu576Phe	233.0	0.0		163.0	78.0	NM_005955	B2RAK6|Q96CB1	Missense_Mutation	SNP	ENST00000373036.4	hg19	CCDS30676.1	.	.	.	.	.	.	.	.	.	.	T	16.99	3.273522	0.59649	.	.	ENSG00000188786	ENST00000373036	T	0.56611	0.45	5.85	-3.48	0.04739	.	0.000000	0.64402	D	0.000001	T	0.60843	0.2300	L	0.58810	1.83	0.39847	D	0.97318	D	0.76494	0.999	D	0.85130	0.997	T	0.62978	-0.6739	10	0.87932	D	0	.	9.4143	0.38512	0.0:0.3386:0.0987:0.5627	.	576	Q14872	MTF1_HUMAN	F	576	ENSP00000362127:L576F	ENSP00000362127:L576F	L	-	3	2	MTF1	38060419	0.975000	0.34042	0.991000	0.47740	0.997000	0.91878	0.006000	0.13152	-0.377000	0.07930	0.459000	0.35465	TTA	.	.		0.408	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955		G	38287832	T	G	38287832	3	3	68	1	0	0	0	0	1	0	0	0	9931	1751	61	5	545	5	MTF1	1	38287832	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	4249656	38287832	210962789	8	8640										
CCDC30	728621	hgsc.bcm.edu	37	chr1	43055011	43055011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ggaaacttctatatcagaacGtagatgagttacacaggcaa	9	7	2	3	rs145632548		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:43055011G>A	ENST00000340612.4	+	8	1240	c.1240G>A	c.(1240-1242)Gta>Ata	p.V414I	CCDC30_ENST00000342022.4_Missense_Mutation_p.V414I|CCDC30_ENST00000507855.1_Missense_Mutation_p.V203I|CCDC30_ENST00000390640.4_Missense_Mutation_p.V203I|CCDC30_ENST00000428554.2_Missense_Mutation_p.V414I			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	414						extracellular vesicular exosome (GO:0070062)		p.V414I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						ATATCAGAACGTAGATGAGTT	0.368																																					p.V414I		Atlas-SNP	.											CCDC30,NS,carcinoma,0,1	CCDC30	78	.	1	Substitution - Missense(1)	endometrium(1)	c.G1240A						.	G	ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	81	81	81		1240	-3.7	0	1	dbSNP_134	81	0,8600		0,0,4300	no	missense	CCDC30	NM_001080850.2	29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	414/784	43055011	2,13004	2203	4300	6503	SO:0001583	missense	728621	exon9			CAGAACGTAGATG	AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"prefoldin 6-like"					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1240G>A	chr1.hg19:g.43055011G>A	ENSP00000340378:p.Val414Ile	67.0	0.0		46.0	18.0	NM_001080850	Q14F06|Q5VVM5	Missense_Mutation	SNP	ENST00000340612.4	hg19	CCDS30690.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.746155	0.00669	4.54E-4	0.0	ENSG00000186409	ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640	T;T;T;T;T	0.46819	0.86;0.9;0.86;0.86;0.9	5.08	-3.69	0.04450	.	1.492440	0.03555	N	0.226154	T	0.21186	0.0510	N	0.02916	-0.46	0.09310	N	1	B;B;B	0.18741	0.003;0.002;0.03	B;B;B	0.08055	0.003;0.002;0.002	T	0.11792	-1.0573	10	0.21540	T	0.41	.	6.8615	0.24069	0.4497:0.0:0.4358:0.1145	.	414;198;203	Q5VVM6;Q6N081;Q5VVM6-2	CCD30_HUMAN;.;.	I	414;203;414;414;203	ENSP00000397035:V414I;ENSP00000426711:V203I;ENSP00000340378:V414I;ENSP00000339280:V414I;ENSP00000375051:V203I	ENSP00000340378:V414I	V	+	1	0	CCDC30	42827598	0.000000	0.05858	0.005000	0.12908	0.014000	0.08584	-0.827000	0.04424	-1.298000	0.02348	-1.579000	0.00862	GTA	.	G|1.000;A|0.000		0.368	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030		A	43055011	G	A	43055011	3	1	68	1	0	0	0	0	1	0	0	0	2807	1145	40	1	1270	1	CCDC30	1	43055011	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	4767179	43055011	206195610	9	8641										
LRIG2	9860	hgsc.bcm.edu	37	chr1	113655151	113655151	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	atctgactattcgcactggtGccatggccagattagaatgt	10	9	1	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:113655151G>T	ENST00000361127.5	+	14	2047	c.1849G>T	c.(1849-1851)Gcc>Tcc	p.A617S	LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	617	Ig-like C2-type 2.				innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		TCGCACTGGTGCCATGGCCAG	0.488																																					p.A617S		Atlas-SNP	.											.	LRIG2	67	.	0			c.G1849T						.						148	140	142					1																	113655151		2203	4300	6503	SO:0001583	missense	9860	exon14			ACTGGTGCCATGG	AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"Immunoglobulin superfamily / I-set domain containing"	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.1849G>T	chr1.hg19:g.113655151G>T	ENSP00000355396:p.Ala617Ser	123.0	0.0		79.0	17.0	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	hg19	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.696152	0.48202	.	.	ENSG00000198799	ENST00000361127	T	0.75477	-0.94	5.45	5.45	0.79879	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.052902	0.85682	D	0.000000	T	0.37100	0.0991	N	0.01624	-0.795	0.41346	D	0.987332	B	0.21753	0.06	B	0.29353	0.101	T	0.42882	-0.9425	10	0.17832	T	0.49	.	19.2881	0.94087	0.0:0.0:1.0:0.0	.	617	O94898	LRIG2_HUMAN	S	617	ENSP00000355396:A617S	ENSP00000355396:A617S	A	+	1	0	LRIG2	113456674	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.091000	0.64505	2.560000	0.86352	0.591000	0.81541	GCC	.	.		0.488	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		T	113655151	G	T	113655151	3	4	68	1	0	0	0	0	1	0	0	0	8954	1319	46	3	1903	3	LRIG2	1	113655151	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	70600140	113655151	135595470	10	8642										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144854658	144854658	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ccctttctgttgattctcccTggataagaggaacagactct	8	11	3	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:144854658T>A	ENST00000369354.3	-	42	7003		c.e42-2		PDE4DIP_ENST00000524974.1_Splice_Site|PDE4DIP_ENST00000369356.4_Splice_Site|PDE4DIP_ENST00000313382.9_Splice_Site|PDE4DIP_ENST00000530740.1_Splice_Site|PDE4DIP_ENST00000369359.4_Splice_Site			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein						cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGATTCTCCCTGGATAAGAGG	0.468			T	PDGFRB	MPD																																.		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.6814-2A>T						.						206	184	191					1																	144854658		2203	4300	6503	SO:0001630	splice_region_variant	9659	exon43			TCTCCCTGGATAA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6814-2A>T	chr1.hg19:g.144854658T>A		126.0	0.0		145.0	9.0	NM_001198834	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Splice_Site	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	.	12.59	1.985123	0.35036	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	.	.	.	3.82	3.82	0.43975	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.8488	0.24003	0.2071:0.0:0.0:0.7929	.	.	.	.	.	-1	.	.	.	-	.	.	PDE4DIP	143566015	1.000000	0.71417	0.951000	0.38953	0.219000	0.24729	5.810000	0.69179	1.542000	0.49330	0.363000	0.22086	.	.	.		0.468	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	Intron	A	144854658	T	A	144854658	5	1	68	1	0	0	0	0	0	0	1	0	11652	1594	55	4	240	4	PDE4DIP	1	144854658	Splice_Site	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	31199507	144854658	104395963	11	8643										
RNF115	27246	hgsc.bcm.edu	37	chr1	145688137	145688137	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gcttaaatggtgaggactctActcggcaaagccagagcact	11	10	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:145688137A>T	ENST00000369291.5	+	9	1036	c.832A>T	c.(832-834)Act>Tct	p.T278S		NM_014455.2	NP_055270.1			ring finger protein 115											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13						TGAGGACTCTACTCGGCAAAG	0.463																																					p.T278S		Atlas-SNP	.											.	RNF115	27	.	0			c.A832T						.						126	115	119					1																	145688137		2203	4300	6503	SO:0001583	missense	27246	exon9			GACTCTACTCGGC	AF419857	CCDS72863.1	1q12	2013-01-09	2008-06-16	2008-06-16	ENSG00000121848	ENSG00000265491		"RING-type (C3HC4) zinc fingers"	18154	protein-coding gene	gene with protein product			"zinc finger protein 364"	ZNF364			Standard	NM_014455		Approved	CL469780	uc001eoj.3	Q9Y4L5	OTTHUMG00000013758	ENST00000369291.5:c.832A>T	chr1.hg19:g.145688137A>T	ENSP00000358297:p.Thr278Ser	166.0	0.0		242.0	61.0	NM_014455		Missense_Mutation	SNP	ENST00000369291.5	hg19	CCDS922.1	.	.	.	.	.	.	.	.	.	.	A	11.35	1.611452	0.28712	.	.	ENSG00000121848	ENST00000369291	T	0.11063	2.81	5.65	5.65	0.86999	Zinc finger, RING/FYVE/PHD-type (1);	0.095666	0.64402	D	0.000001	T	0.02380	0.0073	L	0.27053	0.805	0.34595	D	0.715882	P	0.34864	0.473	B	0.24848	0.056	T	0.33317	-0.9873	10	0.09338	T	0.73	-15.6679	13.8738	0.63638	1.0:0.0:0.0:0.0	.	278	Q9Y4L5	RN115_HUMAN	S	278	ENSP00000358297:T278S	ENSP00000358297:T278S	T	+	1	0	RNF115	144399494	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.984000	0.63838	2.371000	0.80710	0.533000	0.62120	ACT	.	.		0.463	RNF115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038554.2	NM_014455		T	145688137	A	T	145688137	3	4	68	1	0	0	0	0	1	0	0	0	13445	391	14	4	866	4	RNF115	1	145688137	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	833479	145688137	103562484	12	8644										
KPRP	448834	hgsc.bcm.edu	37	chr1	152732782	152732782	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	agtgccagacccagggctccTatgggagcttcactgaacag	12	12	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:152732782T>A	ENST00000606109.1	+	1	746	c.718T>A	c.(718-720)Tat>Aat	p.Y240N	KPRP_ENST00000368773.1_Missense_Mutation_p.Y240N			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	240						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCAGGGCTCCTATGGGAGCTT	0.607																																					p.Y240N		Atlas-SNP	.											.	KPRP	152	.	0			c.T718A						.						66	72	70					1																	152732782		2203	4300	6503	SO:0001583	missense	448834	exon2			GGCTCCTATGGGA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.718T>A	chr1.hg19:g.152732782T>A	ENSP00000475216:p.Tyr240Asn	80.0	0.0		146.0	35.0	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	hg19	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	T	13.16	2.153197	0.38021	.	.	ENSG00000203786	ENST00000368773	T	0.17213	2.29	5.52	3.04	0.35103	.	0.352416	0.20931	N	0.083090	T	0.09069	0.0224	L	0.32530	0.975	0.09310	N	1	P	0.51351	0.944	P	0.53722	0.733	T	0.07673	-1.0760	10	0.72032	D	0.01	-6.5442	5.4458	0.16535	0.0:0.0895:0.1749:0.7356	.	240	Q5T749	KPRP_HUMAN	N	240	ENSP00000357762:Y240N	ENSP00000357762:Y240N	Y	+	1	0	KPRP	150999406	0.003000	0.15002	0.003000	0.11579	0.300000	0.27592	1.321000	0.33678	1.028000	0.39785	-0.290000	0.09829	TAT	.	.		0.607	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		A	152732782	T	A	152732782	3	1	68	1	0	0	0	0	1	0	0	0	8445	1522	53	4	720	4	KPRP	1	152732782	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	7044645	152732782	96517839	13	8645										
LCE1B	353132	hgsc.bcm.edu	37	chr1	152785001	152785001	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gccctcccaagtgcctcaccCctagatgccccccaaagtgt	7	19	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:152785001C>G	ENST00000360090.3	+	1	555	c.79C>G	c.(79-81)Cct>Gct	p.P27A		NM_178349.1	NP_848126.1	Q5T7P3	LCE1B_HUMAN	late cornified envelope 1B	27	Pro-rich.				keratinization (GO:0031424)					breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|skin(2)	18	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gtgccTCACCCCTAGATGCCC	0.632																																					p.P27A		Atlas-SNP	.											.	LCE1B	45	.	0			c.C79G						.						98	99	99					1																	152785001		2203	4300	6503	SO:0001583	missense	353132	exon1			CTCACCCCTAGAT	BI670515	CCDS1027.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000196734	ENSG00000196734		"Late cornified envelopes"	16611	protein-coding gene	gene with protein product		612604	"small proline rich-like (epidermal differentiation complex) 2A"	SPRL2A		11698679	Standard	NM_178349		Approved	LEP2	uc001faq.3	Q5T7P3	OTTHUMG00000014402	ENST00000360090.3:c.79C>G	chr1.hg19:g.152785001C>G	ENSP00000353203:p.Pro27Ala	245.0	1.0		367.0	174.0	NM_178349	A4IF40	Missense_Mutation	SNP	ENST00000360090.3	hg19	CCDS1027.1	.	.	.	.	.	.	.	.	.	.	C	1.808	-0.475384	0.04414	.	.	ENSG00000196734	ENST00000360090;ENST00000439693	T	0.04194	3.68	4.34	4.34	0.51931	.	0.000000	0.36740	N	0.002422	T	0.04679	0.0127	M	0.87180	2.865	0.09310	N	1	P	0.39282	0.666	B	0.35240	0.198	T	0.04840	-1.0923	10	0.87932	D	0	.	12.5252	0.56083	0.0:1.0:0.0:0.0	.	27	Q5T7P3	LCE1B_HUMAN	A	27	ENSP00000353203:P27A	ENSP00000353203:P27A	P	+	1	0	LCE1B	151051625	0.063000	0.20901	0.022000	0.16811	0.003000	0.03518	1.966000	0.40481	2.398000	0.81561	0.650000	0.86243	CCT	.	.		0.632	LCE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040060.1	NM_178349		G	152785001	C	G	152785001	3	3	68	1	0	0	0	0	1	0	0	0	8669	623	22	4	81	4	LCE1B	1	152785001	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	52219	152785001	96465620	14	8646										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155449286	155449286	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gaactgggttcaacaaaaccTgcatcactacttacagggct	8	11	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:155449286T>A	ENST00000368346.3	-	3	4014	c.3375A>T	c.(3373-3375)gcA>gcT	p.A1125A	ASH1L_ENST00000392403.3_Silent_p.A1125A			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1125					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CAACAAAACCTGCATCACTAC	0.463																																					p.A1125A		Atlas-SNP	.											.	ASH1L	279	.	0			c.A3375T						.						97	88	91					1																	155449286		2203	4300	6503	SO:0001819	synonymous_variant	55870	exon3			AAAACCTGCATCA	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.3375A>T	chr1.hg19:g.155449286T>A		142.0	0.0		186.0	52.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.		0.463	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155449286	T	A	155449286	2	1	68	1	0	0	0	0	0	0	0	1	1041	1567	55	4		4	ASH1L	1	155449286	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	2664285	155449286	93801335	15	8647										
HAPLN2	60484	hgsc.bcm.edu	37	chr1	156594457	156594457	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gagggctccgtgcgctacccTgtgctcaccgcacgcgcccc	12	19	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:156594457T>A	ENST00000255039.1	+	6	1028	c.621T>A	c.(619-621)ccT>ccA	p.P207P	HAPLN2_ENST00000494218.1_3'UTR	NM_021817.2	NP_068589.1	Q9GZV7	HPLN2_HUMAN	hyaluronan and proteoglycan link protein 2	207	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|establishment of blood-nerve barrier (GO:0008065)|extracellular matrix assembly (GO:0085029)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	7	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGCGCTACCCTGTGCTCACCG	0.731																																					p.P207P		Atlas-SNP	.											.	HAPLN2	20	.	0			c.T621A						.						11	13	13					1																	156594457		2186	4290	6476	SO:0001819	synonymous_variant	60484	exon6			CTACCCTGTGCTC	AB049054	CCDS1148.1	1q23.1	2013-01-11			ENSG00000132702	ENSG00000132702		"Immunoglobulin superfamily / V-set domain containing"	17410	protein-coding gene	gene with protein product	"brain link protein 1"					11027579, 11873941	Standard	NM_021817		Approved	BRAL1	uc001fpn.1	Q9GZV7	OTTHUMG00000033205	ENST00000255039.1:c.621T>A	chr1.hg19:g.156594457T>A		31.0	0.0		30.0	7.0	NM_021817	Q5T3J0	Silent	SNP	ENST00000255039.1	hg19	CCDS1148.1																																																																																			.	.		0.731	HAPLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081039.1	NM_021817		A	156594457	T	A	156594457	2	1	68	1	0	0	0	0	0	0	0	1	6964	1567	55	4		4	HAPLN2	1	156594457	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	1145171	156594457	92656164	16	8648										
CRABP2	1382	hgsc.bcm.edu	37	chr1	156670823	156670823	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	acgctgcagccacagcaatcTtcctcagcatcacattcacc	5	17	4	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:156670823T>A	ENST00000368222.3	-	2	246	c.92A>T	c.(91-93)aAg>aTg	p.K31M	CRABP2_ENST00000368221.1_Missense_Mutation_p.K31M	NM_001199723.1|NM_001878.3	NP_001186652.1|NP_001869.1	P29373	RABP2_HUMAN	cellular retinoic acid binding protein 2	31					epidermis development (GO:0008544)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(2)|lung(3)|upper_aerodigestive_tract(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)				Alitretinoin(DB00523)|Tretinoin(DB00755)	CACAGCAATCTTCCTCAGCAT	0.552																																					p.K31M		Atlas-SNP	.											.	CRABP2	13	.	0			c.A92T						.						87	75	79					1																	156670823		2203	4300	6503	SO:0001583	missense	1382	exon3			GCAATCTTCCTCA	BC001109	CCDS1152.1	1q21.3	2013-03-01	2001-11-28		ENSG00000143320	ENSG00000143320		"Fatty acid binding protein family"	2339	protein-coding gene	gene with protein product		180231	"cellular retinoic acid-binding protein 2"			1654334	Standard	NM_001878		Approved	CRABP-II	uc001fpr.3	P29373	OTTHUMG00000041300	ENST00000368222.3:c.92A>T	chr1.hg19:g.156670823T>A	ENSP00000357205:p.Lys31Met	77.0	0.0		116.0	31.0	NM_001199723	B2R4Z8|D3DVC5|F1T098|Q6ICN6	Missense_Mutation	SNP	ENST00000368222.3	hg19	CCDS1152.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.720299	0.48728	.	.	ENSG00000143320	ENST00000368222;ENST00000368221;ENST00000368220	T;T;T	0.10573	2.86;2.86;2.86	4.44	4.44	0.53790	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.176056	0.49305	D	0.000160	T	0.10294	0.0252	M	0.68728	2.09	0.53688	D	0.999973	B	0.31893	0.345	B	0.40825	0.341	T	0.01553	-1.1326	10	0.87932	D	0	.	11.7023	0.51577	0.0:0.0:0.0:1.0	.	31	P29373	RABP2_HUMAN	M	31	ENSP00000357205:K31M;ENSP00000357204:K31M;ENSP00000357203:K31M	ENSP00000357203:K31M	K	-	2	0	CRABP2	154937447	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.536000	0.53582	1.873000	0.54277	0.533000	0.62120	AAG	.	.		0.552	CRABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098966.1	NM_001878		A	156670823	T	A	156670823	3	1	68	1	0	0	0	0	1	0	0	0	3846	1609	56	4	336	4	CRABP2	1	156670823	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	76366	156670823	92579798	17	8649										
FCRL1	115350	hgsc.bcm.edu	37	chr1	157767574	157767574	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tctgctctgaggaatgctgtTgtctgccatgcacagccact	10	12	3	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:157767574T>A	ENST00000368176.3	-	9	1254				FCRL1_ENST00000489998.1_Intron|FCRL1_ENST00000358292.3_Missense_Mutation_p.Q345L|FCRL1_ENST00000491942.1_Intron	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GGAATGCTGTTGTCTGCCATG	0.493																																					p.Q345L	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.A1034T						.						187	165	172					1																	157767574		692	1591	2283	SO:0001627	intron_variant	115350	exon8			TGCTGTTGTCTGC	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.1186+83A>T	chr1.hg19:g.157767574T>A		125.0	0.0		202.0	33.0	NM_001159397	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Missense_Mutation	SNP	ENST00000368176.3	hg19	CCDS1170.1	.	.	.	.	.	.	.	.	.	.	T	6.493	0.459209	0.12342	.	.	ENSG00000163534	ENST00000358292	T	0.39997	1.05	3.34	0.348	0.16026	.	.	.	.	.	T	0.09291	0.0229	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.34576	-0.9823	8	0.28530	T	0.3	.	5.5908	0.17299	0.0:0.6105:0.0:0.3895	.	345	Q96LA6-3	.	L	345	ENSP00000351039:Q345L	ENSP00000351039:Q345L	Q	-	2	0	FCRL1	156034198	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.197000	0.03038	0.071000	0.16664	-0.899000	0.02877	CAA	.	.		0.493	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938		A	157767574	T	A	157767574	1	1	68	0	1	0	0	0	0	0	0	0	5802	1812	63	4		4	FCRL1	1	157767574	Intron	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	1096751	157767574	91483047	18	8650										
NUF2	83540	hgsc.bcm.edu	37	chr1	163295880	163295880	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cccagatataatgtagctgaGattgtgattcatattcgcaa	8	7	1	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:163295880G>C	ENST00000271452.3	+	2	318	c.39G>C	c.(37-39)gaG>gaC	p.E13D	NUF2_ENST00000367900.3_Missense_Mutation_p.E13D|NUF2_ENST00000524800.1_Missense_Mutation_p.E13D|NUF2_ENST00000490881.1_3'UTR	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	13	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					ATGTAGCTGAGATTGTGATTC	0.358																																					p.E13D		Atlas-SNP	.											.	NUF2	138	.	0			c.G39C						.						123	125	124					1																	163295880		2203	4300	6503	SO:0001583	missense	83540	exon2			AGCTGAGATTGTG	BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"cancer/testis antigen 106"	611772	"cell division cycle associated 1", "NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.39G>C	chr1.hg19:g.163295880G>C	ENSP00000271452:p.Glu13Asp	58.0	0.0		93.0	18.0	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	hg19	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	G	11.04	1.522069	0.27211	.	.	ENSG00000143228	ENST00000534289;ENST00000450453;ENST00000524800;ENST00000442820;ENST00000367900;ENST00000271452	T;T;T	0.34472	1.36;1.39;1.39	5.84	2.79	0.32731	.	0.272209	0.42548	N	0.000693	T	0.07683	0.0193	N	0.22421	0.69	0.32964	D	0.521419	B;B;B	0.20780	0.026;0.026;0.048	B;B;B	0.20184	0.022;0.022;0.028	T	0.27157	-1.0082	9	0.22109	T	0.4	-14.3809	5.403	0.16306	0.2522:0.1547:0.5931:0.0	.	13;13;13	E9PQC4;Q9BZD4;B1AQT4	.;NUF2_HUMAN;.	D	13	ENSP00000436888:E13D;ENSP00000356875:E13D;ENSP00000271452:E13D	ENSP00000271452:E13D	E	+	3	2	NUF2	161562504	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	0.473000	0.22132	0.402000	0.25451	0.650000	0.86243	GAG	.	.		0.358	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697		C	163295880	G	C	163295880	3	2	68	1	0	0	0	0	1	0	0	0	10756	933	33	4	41	4	NUF2	1	163295880	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	5528306	163295880	85954741	19	8651										
C1orf49	84066	hgsc.bcm.edu	37	chr1	178490806	178490806	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gaatatgtgtttccaacctaGcgcagctgcagaacctacca	8	12	0	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:178490806G>T	ENST00000367643.3	+	9	663		c.e9-1		TEX35_ENST00000258298.2_Intron|TEX35_ENST00000367641.3_3'UTR|TEX35_ENST00000367639.1_Intron|TEX35_ENST00000367642.3_3'UTR|TEX35_ENST00000319416.2_Intron	NM_001170723.1	NP_001164194.1			testis expressed 35																		TTCCAACCTAGCGCAGCTGCA	0.522																																					.		Atlas-SNP	.											.	TEX35	15	.	0			c.587-1G>T						.						147	130	135					1																	178490806		692	1591	2283	SO:0001630	splice_region_variant	84066	exon9			AACCTAGCGCAGC	AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"Testis-Specific Conserved gene 24kDa"		"chromosome 1 open reading frame 49"	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000367643.3:c.587-1G>T	chr1.hg19:g.178490806G>T		149.0	0.0		189.0	38.0	NM_001170723		Splice_Site	SNP	ENST00000367643.3	hg19	CCDS53433.1	.	.	.	.	.	.	.	.	.	.	G	4.852	0.158294	0.09236	.	.	ENSG00000240021	ENST00000367643	.	.	.	4.46	1.29	0.21616	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.4709	0.11712	0.2088:0.1842:0.607:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C1orf49	176757429	0.002000	0.14202	0.001000	0.08648	0.009000	0.06853	0.417000	0.21214	0.443000	0.26582	-0.247000	0.11927	.	.	.		0.522	TEX35-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098171.1	NM_032126	Intron	T	178490806	G	T	178490806	5	4	68	1	0	0	0	0	0	0	1	0	2043	985	34	3	644	3	C1orf49	1	178490806	Splice_Site	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	15194926	178490806	70759815	20	8652										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196197434	196197434	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	actgggctcactgtttggaaGgtaggccagtggatctggtc	15	8	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:196197434G>C	ENST00000294725.9	-	28	4243	c.3328C>G	c.(3328-3330)Ctt>Gtt	p.L1110V	KCNT2_ENST00000451324.2_3'UTR|KCNT2_ENST00000609185.1_Missense_Mutation_p.L1043V|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000367433.5_Missense_Mutation_p.L1086V|KCNT2_ENST00000367431.4_Missense_Mutation_p.L1044V			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	1110					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						CTGTTTGGAAGGTAGGCCAGT	0.363																																					p.L1110V		Atlas-SNP	.											.	KCNT2	243	.	0			c.C3328G						.						70	68	69					1																	196197434		2203	4300	6503	SO:0001583	missense	343450	exon28			TTGGAAGGTAGGC	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.3328C>G	chr1.hg19:g.196197434G>C	ENSP00000294725:p.Leu1110Val	60.0	0.0		87.0	17.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	hg19	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	G	2.967	-0.213363	0.06140	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.13901	2.56;2.55;2.84	5.71	5.71	0.89125	.	0.118608	0.38663	N	0.001617	T	0.02533	0.0077	N	0.00075	-2.25	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.44329	-0.9335	10	0.02654	T	1	-17.3912	14.1206	0.65184	0.0:0.2652:0.7348:0.0	.	1086;1043;1110	Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;KCNT2_HUMAN	V	1086;1044;1110	ENSP00000356403:L1086V;ENSP00000356401:L1044V;ENSP00000294725:L1110V	ENSP00000294725:L1110V	L	-	1	0	KCNT2	194464057	1.000000	0.71417	0.999000	0.59377	0.968000	0.65278	4.398000	0.59697	2.699000	0.92147	0.650000	0.86243	CTT	.	.		0.363	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		C	196197434	G	C	196197434	3	2	68	1	0	0	0	0	1	0	0	0	8101	1000	35	4	83	4	KCNT2	1	196197434	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	17706628	196197434	53053187	21	8653										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201060850	201060850	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gcatagatgatgaccataaaGaggaccagcagggcgatgtg	14	7	0	4			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:201060850G>A	ENST00000362061.3	-	5	838	c.612C>T	c.(610-612)ctC>ctT	p.L204L	CACNA1S_ENST00000367338.3_Silent_p.L204L	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	204					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGACCATAAAGAGGACCAGCA	0.552																																					p.L204L		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C612T						.						97	80	86					1																	201060850		2203	4300	6503	SO:0001819	synonymous_variant	779	exon5			CATAAAGAGGACC	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.612C>T	chr1.hg19:g.201060850G>A		211.0	0.0		220.0	32.0	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	hg19	CCDS1407.1																																																																																			.	.		0.552	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201060850	G	A	201060850	2	1	68	1	0	0	0	0	0	0	0	1	2549	929	33	3		3	CACNA1S	1	201060850	Silent	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	4863416	201060850	48189771	22	8654										
MFSD4	148808	hgsc.bcm.edu	37	chr1	205553249	205553249	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cccaaagtttcagtcacaccTaggtaggggctctaatgaat	9	10	3	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:205553249T>A	ENST00000367147.4	+	4	950	c.857T>A	c.(856-858)cTa>cAa	p.L286Q	MFSD4_ENST00000539267.1_Missense_Mutation_p.L286Q|MFSD4_ENST00000536357.1_Missense_Mutation_p.L199Q	NM_181644.4	NP_857595.3	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing 4	286					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			CAGTCACACCTAGGTAGGGGC	0.532																																					p.L286Q		Atlas-SNP	.											.	MFSD4	46	.	0			c.T857A						.						52	53	53					1																	205553249		2203	4300	6503	SO:0001583	missense	148808	exon4			CACACCTAGGTAG	BC036549	CCDS1455.1	1q32.1	2008-02-05			ENSG00000174514	ENSG00000174514			25433	protein-coding gene	gene with protein product							Standard	NM_181644		Approved	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004	uc001hcv.4	Q8N468	OTTHUMG00000037197	ENST00000367147.4:c.857T>A	chr1.hg19:g.205553249T>A	ENSP00000356115:p.Leu286Gln	54.0	0.0		46.0	12.0	NM_181644	B7Z8X3|Q6UY25|Q8NAY0|Q8TCP4	Missense_Mutation	SNP	ENST00000367147.4	hg19	CCDS1455.1	.	.	.	.	.	.	.	.	.	.	T	1.021	-0.684999	0.03328	.	.	ENSG00000174514	ENST00000367147;ENST00000539267;ENST00000536357	T;T;T	0.57273	0.41;0.41;2.02	5.84	1.41	0.22369	Major facilitator superfamily domain, general substrate transporter (1);	0.956968	0.08882	N	0.879917	T	0.19046	0.0457	N	0.01352	-0.895	0.09310	N	0.999998	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.08055	0.003;0.003;0.002	T	0.28554	-1.0040	10	0.11794	T	0.64	-4.415	3.9693	0.09446	0.2826:0.5003:0.1374:0.0797	.	231;199;286	B7Z8X0;B7Z8X3;Q8N468	.;.;MFSD4_HUMAN	Q	286;286;199	ENSP00000356115:L286Q;ENSP00000445329:L286Q;ENSP00000440183:L199Q	ENSP00000356115:L286Q	L	+	2	0	MFSD4	203819872	0.027000	0.19231	0.939000	0.37840	0.240000	0.25518	-0.260000	0.08708	0.810000	0.34279	-0.252000	0.11476	CTA	.	.		0.532	MFSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090391.1	NM_181644		A	205553249	T	A	205553249	3	1	68	1	0	0	0	0	1	0	0	0	9542	1522	53	4	871	4	MFSD4	1	205553249	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	4492399	205553249	43697372	23	8655										
PRSS38	339501	hgsc.bcm.edu	37	chr1	228003457	228003457	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tcatgggcccactcgggcccTctgccctgggccttctgctg	12	17	3	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:228003457T>A	ENST00000366757.3	+	1	64	c.40T>A	c.(40-42)Tct>Act	p.S14T		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	14						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						ACTCGGGCCCTCTGCCCTGGG	0.667																																					p.S14T		Atlas-SNP	.											.	PRSS38	55	.	0			c.T40A						.						24	26	26					1																	228003457		2203	4299	6502	SO:0001583	missense	339501	exon1			GGGCCCTCTGCCC		CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"Serine peptidases / Serine peptidases"	29625	protein-coding gene	gene with protein product	"marapsin 2"					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.40T>A	chr1.hg19:g.228003457T>A	ENSP00000355719:p.Ser14Thr	131.0	0.0		129.0	43.0	NM_183062	Q7RTY6	Missense_Mutation	SNP	ENST00000366757.3	hg19	CCDS1563.1	.	.	.	.	.	.	.	.	.	.	T	2.527	-0.309307	0.05458	.	.	ENSG00000185888	ENST00000366757	D	0.88124	-2.34	1.78	-3.55	0.04639	.	.	.	.	.	T	0.64713	0.2623	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48103	-0.9064	9	0.33940	T	0.23	.	1.8858	0.03237	0.207:0.1495:0.4553:0.1882	.	14	A1L453	PRS38_HUMAN	T	14	ENSP00000355719:S14T	ENSP00000355719:S14T	S	+	1	0	PRSS38	226070080	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.165000	0.09968	-1.825000	0.01207	0.334000	0.21626	TCT	.	.		0.667	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062		A	228003457	T	A	228003457	3	1	68	1	0	0	0	0	1	0	0	0	12639	1551	54	4	42	4	PRSS38	1	228003457	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	22450208	228003457	21247164	24	8656										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228563447	228563447	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cggatatcggggaggtgtacGcggatggggtgctgctggtc	20	7	0	0	rs370427130		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr1:228563447G>A	ENST00000422127.1	+	98	22752	c.22708G>A	c.(22708-22710)Gcg>Acg	p.A7570T	OBSCN_ENST00000570156.2_Missense_Mutation_p.A8527T|OBSCN_ENST00000366707.4_Missense_Mutation_p.A5204T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7570	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGAGGTGTACGCGGATGGGGT	0.632																																					p.A8527T		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,2	OBSCN	2142	.	0			c.G25579A						.		THR/ALA	0,4246		0,0,2123	68	83	78		22708	2.5	0	1		78	1,8481		0,1,4240	no	missense	OBSCN	NM_001098623.1	58	0,1,6363	AA,AG,GG		0.0118,0.0,0.0079	possibly-damaging	7570/7969	228563447	1,12727	2123	4241	6364	SO:0001583	missense	84033	exon109			GTGTACGCGGATG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.22708G>A	chr1.hg19:g.228563447G>A	ENSP00000409493:p.Ala7570Thr	184.0	0.0		171.0	41.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.07|15.07	2.723815|2.723815	0.48728|0.48728	0.0|0.0	1.18E-4|1.18E-4	ENSG00000154358|ENSG00000154358	ENST00000422127;ENST00000366707|ENST00000441106	T;T|.	0.22539|.	1.95;1.95|.	5.33|5.33	2.45|2.45	0.29901|0.29901	Fibronectin, type III (3);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.35595|0.35595	0.0937|0.0937	L|L	0.38175|0.38175	1.15|1.15	0.09310|0.09310	N|N	1|1	B|.	0.13594|.	0.008|.	B|.	0.08055|.	0.003|.	T|T	0.21655|0.21655	-1.0239|-1.0239	9|5	0.16896|.	T|.	0.51|.	.|.	8.8253|8.8253	0.35052|0.35052	0.368:0.0:0.632:0.0|0.368:0.0:0.632:0.0	.|.	7570|.	Q5VST9|.	OBSCN_HUMAN|.	T|H	7570;5204|2186	ENSP00000409493:A7570T;ENSP00000355668:A5204T|.	ENSP00000355668:A5204T|.	A|R	+|+	1|2	0|0	OBSCN|OBSCN	226630070|226630070	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.030000|0.030000	0.12068|0.12068	1.042000|1.042000	0.30303|0.30303	0.382000|0.382000	0.24878|0.24878	0.506000|0.506000	0.49869|0.49869	GCG|CGC	.	.		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228563447	G	A	228563447	3	1	68	1	0	0	0	0	1	0	0	0	10821	1087	38	1	24304	1	OBSCN	1	228563447	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	559990	228563447	20687174	25	8657										
ITSN2	50618	hgsc.bcm.edu	37	chr2	24438936	24438936	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	acctttaaaaattctttgaaAtctgtgtcttcatctgtctt	4	8	6	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr2:24438936A>G	ENST00000355123.4	-	32	4415	c.3972T>C	c.(3970-3972)gaT>gaC	p.D1324D	ITSN2_ENST00000361999.3_Silent_p.D1297D|AC009228.1_ENST00000413989.1_RNA|AC009228.1_ENST00000413254.1_RNA|AC009228.1_ENST00000430105.1_RNA	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1324	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATTCTTTGAAATCTGTGTCTT	0.512																																					p.D1324D		Atlas-SNP	.											.	ITSN2	224	.	0			c.T3972C						.						75	76	75					2																	24438936		2203	4300	6503	SO:0001819	synonymous_variant	50618	exon32			TTTGAAATCTGTG	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.3972T>C	chr2.hg19:g.24438936A>G		60.0	0.0		87.0	16.0	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	hg19	CCDS1710.2																																																																																			.	.		0.512	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		G	24438936	A	G	24438936	2	3	68	1	0	0	0	0	0	0	0	1	7936	98	4	2		2	ITSN2	2	24438936	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10		24438936	218760437	26	8658										
DTNB	1838	hgsc.bcm.edu	37	chr2	25705696	25705696	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	agtgggcactccagaggacaTgtggctaaccatggtgtcat	13	9	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr2:25705696T>C	ENST00000406818.3	-	10	1297	c.1048A>G	c.(1048-1050)Atg>Gtg	p.M350V	DTNB_ENST00000545439.1_Missense_Mutation_p.M146V|DTNB_ENST00000288642.8_Missense_Mutation_p.M350V|DTNB_ENST00000407186.1_Missense_Mutation_p.M350V|DTNB_ENST00000405222.1_Missense_Mutation_p.M350V|DTNB_ENST00000407038.3_Missense_Mutation_p.M350V|DTNB_ENST00000404103.3_Missense_Mutation_p.M350V|DTNB_ENST00000496972.2_Missense_Mutation_p.M293V|DTNB_ENST00000407661.3_Missense_Mutation_p.M350V	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	350						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCAGAGGACATGTGGCTAACC	0.478																																					p.M350V		Atlas-SNP	.											.	DTNB	43	.	0			c.A1048G						.						95	98	97					2																	25705696		2032	4173	6205	SO:0001583	missense	1838	exon10			AGGACATGTGGCT	AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.1048A>G	chr2.hg19:g.25705696T>C	ENSP00000384084:p.Met350Val	96.0	0.0		111.0	76.0	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Missense_Mutation	SNP	ENST00000406818.3	hg19	CCDS46237.1	.	.	.	.	.	.	.	.	.	.	T	8.269	0.812967	0.16537	.	.	ENSG00000138101	ENST00000496972;ENST00000406818;ENST00000404103;ENST00000407661;ENST00000407038;ENST00000405222;ENST00000407186;ENST00000288642;ENST00000545439;ENST00000535791	T;T;T;T;T;T;T;T;T	0.39056	2.42;2.41;2.41;2.41;2.38;2.38;2.38;2.42;1.1	5.13	-1.79	0.07932	.	0.497633	0.23902	N	0.043438	T	0.18002	0.0432	N	0.14661	0.345	0.22745	N	0.998784	B;B;B;B;B;B;B;B;B;B;B;B	0.15141	0.003;0.001;0.004;0.001;0.001;0.001;0.001;0.0;0.0;0.012;0.005;0.007	B;B;B;B;B;B;B;B;B;B;B;B	0.16289	0.002;0.004;0.015;0.006;0.003;0.007;0.0;0.001;0.002;0.004;0.004;0.01	T	0.13656	-1.0501	10	0.19590	T	0.45	-2.4242	4.6247	0.12472	0.0:0.2509:0.2991:0.45	.	350;146;293;350;350;293;350;350;350;350;350;350	E7EVB6;B7Z202;F5GZG4;O60941-3;B7Z6A9;B7Z733;E9PEY4;Q96AW0;O60941-2;O60941-4;G5E9F6;O60941	.;.;.;.;.;.;.;.;.;.;.;DTNB_HUMAN	V	293;350;350;350;350;350;350;350;146;203	ENSP00000444463:M293V;ENSP00000384084:M350V;ENSP00000385482:M350V;ENSP00000385193:M350V;ENSP00000384767:M350V;ENSP00000384787:M350V;ENSP00000385784:M350V;ENSP00000288642:M350V;ENSP00000444961:M146V	ENSP00000288642:M350V	M	-	1	0	DTNB	25559200	0.934000	0.31675	0.980000	0.43619	0.999000	0.98932	-0.265000	0.08644	-0.479000	0.06813	0.528000	0.53228	ATG	.	.		0.478	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147		C	25705696	T	C	25705696	3	2	68	1	0	0	0	0	1	0	0	0	4791	1464	51	2	879	2	DTNB	2	25705696	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	1266760	25705696	217493677	27	8659										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73678026	73678026	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aggctttggaagtttcagttGctcctggaccagttgaccag	12	9	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr2:73678026G>T	ENST00000264448.6	+	8	4480	c.4369G>T	c.(4369-4371)Gct>Tct	p.A1457S	ALMS1_ENST00000409009.1_Missense_Mutation_p.A1415S|ALMS1_ENST00000377715.1_Missense_Mutation_p.A1457S	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1457	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AGTTTCAGTTGCTCCTGGACC	0.483																																					p.A1457S		Atlas-SNP	.											.	ALMS1	384	.	0			c.G4369T						.						113	113	113					2																	73678026		1897	4116	6013	SO:0001583	missense	7840	exon8			TCAGTTGCTCCTG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.4369G>T	chr2.hg19:g.73678026G>T	ENSP00000264448:p.Ala1457Ser	91.0	0.0		124.0	75.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	2.651	-0.281998	0.05642	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.16897	3.21;3.21;2.31	4.18	-2.39	0.06602	.	3.675970	0.00757	N	0.001105	T	0.14399	0.0348	L	0.42245	1.32	0.09310	N	1	B;B;B	0.26708	0.157;0.123;0.047	B;B;B	0.26416	0.069;0.022;0.022	T	0.22626	-1.0211	10	0.11485	T	0.65	.	7.8188	0.29276	0.1755:0.5539:0.2706:0.0	.	1457;1415;1457	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	S	1415;1457;1457	ENSP00000386627:A1415S;ENSP00000264448:A1457S;ENSP00000366944:A1457S	ENSP00000264448:A1457S	A	+	1	0	ALMS1	73531534	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-1.247000	0.02893	-0.504000	0.06577	-0.274000	0.10170	GCT	.	.		0.483	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73678026	G	T	73678026	3	4	68	1	0	0	0	0	1	0	0	0	535	1319	46	3	4399	3	ALMS1	2	73678026	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	47972330	73678026	169521347	28	8660										
SULT1C4	27233	hgsc.bcm.edu	37	chr2	108999919	108999919	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgaaaggatggtgggaagccAaagacaaacaccgtattctc	11	8	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr2:108999919A>T	ENST00000272452.2	+	5	894	c.568A>T	c.(568-570)Aaa>Taa	p.K190*	SULT1C4_ENST00000409309.3_Nonsense_Mutation_p.K115*	NM_006588.2	NP_006579.2	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 4	190					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						GTGGGAAGCCAAAGACAAACA	0.468																																					p.K190X		Atlas-SNP	.											.	SULT1C4	41	.	0			c.A568T						.						139	117	125					2																	108999919		2203	4300	6503	SO:0001587	stop_gained	27233	exon5			GAAGCCAAAGACA	AF055584	CCDS2077.1	2q12.3	2008-09-04	2007-03-16	2007-03-16	ENSG00000198075	ENSG00000198075		"Sulfotransferases, cytosolic"	11457	protein-coding gene	gene with protein product		608357	"sulfotransferase family, cytosolic, 1C, member 2"	SULT1C2		10783263, 9852044	Standard	NM_006588		Approved	SULT1C	uc002tea.1	O75897	OTTHUMG00000130958	ENST00000272452.2:c.568A>T	chr2.hg19:g.108999919A>T	ENSP00000272452:p.Lys190*	82.0	0.0		93.0	55.0	NM_006588	Q069I8|Q08AS5|Q53S63	Nonsense_Mutation	SNP	ENST00000272452.2	hg19	CCDS2077.1	.	.	.	.	.	.	.	.	.	.	A	37	6.179726	0.97352	.	.	ENSG00000198075	ENST00000272452;ENST00000409309	.	.	.	4.76	4.76	0.60689	.	0.109265	0.41294	D	0.000919	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9031	0.63817	1.0:0.0:0.0:0.0	.	.	.	.	X	190;115	.	ENSP00000272452:K190X	K	+	1	0	SULT1C4	108366351	0.693000	0.27728	0.005000	0.12908	0.853000	0.48598	4.695000	0.61767	2.125000	0.65367	0.496000	0.49642	AAA	.	.		0.468	SULT1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253561.1	NM_006588		T	108999919	A	T	108999919	4	4	68	1	0	0	0	0	0	1	0	0	15394	131	5	4	586	4	SULT1C4	2	108999919	Nonsense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	35321893	108999919	134199454	29	8661										
NEB	4703	hgsc.bcm.edu	37	chr2	152539201	152539201	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgaggatgtctgaagctcgcTttgccttttccatttctaag	9	9	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr2:152539201T>A	ENST00000172853.10	-	29	3065	c.2918A>T	c.(2917-2919)aAg>aTg	p.K973M	NEB_ENST00000603639.1_Missense_Mutation_p.K973M|NEB_ENST00000604864.1_Missense_Mutation_p.K973M|NEB_ENST00000427231.2_Missense_Mutation_p.K973M|NEB_ENST00000397345.3_Missense_Mutation_p.K973M|NEB_ENST00000409198.1_Missense_Mutation_p.K973M			P20929	NEBU_HUMAN	nebulin	973					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGAAGCTCGCTTTGCCTTTTC	0.463																																					p.K973M		Atlas-SNP	.											.	NEB	1697	.	0			c.A2918T						.						108	108	108					2																	152539201		2046	4188	6234	SO:0001583	missense	4703	exon29			GCTCGCTTTGCCT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.2918A>T	chr2.hg19:g.152539201T>A	ENSP00000172853:p.Lys973Met	77.0	0.0		109.0	31.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	T	21.3	4.127982	0.77549	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.10573	2.86;2.93;2.92;2.86	5.89	5.89	0.94794	.	0.107337	0.64402	D	0.000006	T	0.41096	0.1144	M	0.90650	3.135	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.49624	-0.8920	10	0.87932	D	0	.	15.2948	0.73894	0.0:0.0:0.0:1.0	.	973	P20929	NEBU_HUMAN	M	973	ENSP00000386259:K973M;ENSP00000380505:K973M;ENSP00000416578:K973M;ENSP00000172853:K973M	ENSP00000172853:K973M	K	-	2	0	NEB	152247447	1.000000	0.71417	1.000000	0.80357	0.626000	0.37791	5.018000	0.64054	2.254000	0.74563	0.459000	0.35465	AAG	.	.		0.463	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152539201	T	A	152539201	3	1	68	1	0	0	0	0	1	0	0	0	10311	1609	56	4	23384	4	NEB	2	152539201	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	43539282	152539201	90660172	30	8662										
IFIH1	64135	hgsc.bcm.edu	37	chr2	163124064	163124064	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgcagtgctttgttttctctTacaatgtaaagttccctata	6	8	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr2:163124064T>C	ENST00000263642.2	-	15	3218	c.2823A>G	c.(2821-2823)gtA>gtG	p.V941V		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	941					cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						TGTTTTCTCTTACAATGTAAA	0.403																																					p.V941V		Atlas-SNP	.											.	IFIH1	102	.	0			c.A2823G						.						160	134	143					2																	163124064		2203	4300	6503	SO:0001819	synonymous_variant	64135	exon15			TTCTCTTACAATG	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"helicard"	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.2823A>G	chr2.hg19:g.163124064T>C		43.0	0.0		34.0	15.0	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Silent	SNP	ENST00000263642.2	hg19	CCDS2217.1																																																																																			.	.		0.403	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		C	163124064	T	C	163124064	2	2	68	1	0	0	0	0	0	0	0	1	7529	1741	61	2		2	IFIH1	2	163124064	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	10584863	163124064	80075309	31	8663										
MFSD6	54842	hgsc.bcm.edu	37	chr2	191301292	191301292	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	agtcaccagttaactatcctGccaacaaattcttcctttac	3	13	2	0	rs115585862	byFrequency	TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr2:191301292G>A	ENST00000392328.1	+	3	861	c.537G>A	c.(535-537)ctG>ctA	p.L179L	MFSD6_ENST00000281416.7_Silent_p.L179L	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	179					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						TAACTATCCTGCCAACAAATT	0.438																																					p.L179L		Atlas-SNP	.											.	MFSD6	58	.	0			c.G537A						.						92	102	99					2																	191301292		2202	4300	6502	SO:0001819	synonymous_variant	54842	exon3			TATCCTGCCAACA		CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.537G>A	chr2.hg19:g.191301292G>A		86.0	0.0		93.0	32.0	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Silent	SNP	ENST00000392328.1	hg19	CCDS2306.1																																																																																			.	G|0.996;T|0.004		0.438	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1			A	191301292	G	A	191301292	2	1	68	1	0	0	0	0	0	0	0	1	9544	1306	46	3		3	MFSD6	2	191301292	Silent	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	28177228	191301292	51898081	32	8664										
RFTN2	130132	hgsc.bcm.edu	37	chr2	198508920	198508920	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgctgcgtcatttgtttgtgCctcagaagttaggggacatt	12	7	2	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr2:198508920C>T	ENST00000295049.4	-	3	936	c.400G>A	c.(400-402)Gca>Aca	p.A134T		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	134					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						TTTGTTTGTGCCTCAGAAGTT	0.408																																					p.A134T		Atlas-SNP	.											.	RFTN2	68	.	0			c.G400A						.						186	175	179					2																	198508920		2203	4300	6503	SO:0001583	missense	130132	exon3			TTTGTGCCTCAGA	AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 11"	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.400G>A	chr2.hg19:g.198508920C>T	ENSP00000295049:p.Ala134Thr	104.0	0.0		130.0	73.0	NM_144629	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Missense_Mutation	SNP	ENST00000295049.4	hg19	CCDS2323.1	.	.	.	.	.	.	.	.	.	.	C	7.265	0.605945	0.14002	.	.	ENSG00000162944	ENST00000295049	T	0.28666	1.6	5.39	1.67	0.24075	.	0.647125	0.16704	N	0.202992	T	0.09069	0.0224	N	0.01800	-0.715	0.25336	N	0.98899	B	0.02656	0.0	B	0.04013	0.001	T	0.37526	-0.9702	10	0.05436	T	0.98	-0.7503	8.1483	0.31126	0.0:0.229:0.0:0.771	.	134	Q52LD8	RFTN2_HUMAN	T	134	ENSP00000295049:A134T	ENSP00000295049:A134T	A	-	1	0	RFTN2	198217165	0.055000	0.20627	0.867000	0.34043	0.991000	0.79684	1.735000	0.38176	0.130000	0.18549	-0.312000	0.09012	GCA	.	.		0.408	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629		T	198508920	C	T	198508920	3	4	68	1	0	0	0	0	1	0	0	0	13274	739	26	3	1133	3	RFTN2	2	198508920	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	7207628	198508920	44690453	33	8665										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212812232	212812232	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttaaaaatattgccaaggcaTatcgatcctcataaagtttt	5	7	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr2:212812232T>A	ENST00000342788.4	-	3	654	c.344A>T	c.(343-345)tAt>tTt	p.Y115F	ERBB4_ENST00000484474.1_5'UTR|ERBB4_ENST00000402597.1_Missense_Mutation_p.Y115F|ERBB4_ENST00000436443.1_Missense_Mutation_p.Y115F	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	115					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	TGCCAAGGCATATCGATCCTC	0.383										TSP Lung(8;0.080)																											p.Y115F		Atlas-SNP	.											.	ERBB4	480	.	0			c.A344T						.						117	111	113					2																	212812232		2203	4300	6503	SO:0001583	missense	2066	exon3			AAGGCATATCGAT	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.344A>T	chr2.hg19:g.212812232T>A	ENSP00000342235:p.Tyr115Phe	97.0	0.0		94.0	58.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.72|12.72	2.021945|2.021945	0.35701|0.35701	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000260943|ENST00000342788;ENST00000436443;ENST00000402597;ENST00000435846	.|D;D;D;D	.|0.84442	.|-1.85;-1.85;-1.85;-1.85	5.54|5.54	5.54|5.54	0.83059|0.83059	.|EGF receptor, L domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.80691|0.80691	0.4671|0.4671	N|N	0.20445|0.20445	0.575|0.575	0.50632|0.50632	D|D	0.999887|0.999887	.|P;B;P;P	.|0.47545	.|0.874;0.078;0.874;0.897	.|P;B;P;P	.|0.51355	.|0.537;0.091;0.537;0.667	T|T	0.77742|0.77742	-0.2474|-0.2474	5|10	.|0.20519	.|T	.|0.43	.|.	12.2419|12.2419	0.54546|0.54546	0.0:0.0:0.1419:0.8581|0.0:0.0:0.1419:0.8581	.|.	.|115;115;115;115	.|Q15303-4;Q15303-2;Q15303-3;Q15303	.|.;.;.;ERBB4_HUMAN	L|F	115|115;115;115;56	.|ENSP00000342235:Y115F;ENSP00000403204:Y115F;ENSP00000385565:Y115F;ENSP00000405564:Y56F	.|ENSP00000342235:Y115F	M|Y	-|-	1|2	0|0	ERBB4|ERBB4	212520477|212520477	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.991000|4.991000	0.63883|0.63883	2.102000|2.102000	0.63906|0.63906	0.455000|0.455000	0.32223|0.32223	ATG|TAT	.	.		0.383	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	212812232	T	A	212812232	3	1	68	1	0	0	0	0	1	0	0	0	5211	1406	49	4	3686	4	ERBB4	2	212812232	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	14303312	212812232	30387141	34	8666										
SEPT2	4735	hgsc.bcm.edu	37	chr2	242283230	242283230	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aagccaaaggaaagaaggtcAgaggccgcctctacccctgg	12	12	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr2:242283230A>T	ENST00000391973.2	+	9	1288	c.760A>T	c.(760-762)Aga>Tga	p.R254*	SEPT2_ENST00000407971.1_Nonsense_Mutation_p.R214*|SEPT2_ENST00000360051.3_Nonsense_Mutation_p.R254*|SEPT2_ENST00000402092.2_Nonsense_Mutation_p.R254*|SEPT2_ENST00000391971.2_Nonsense_Mutation_p.R254*|SEPT2_ENST00000401990.1_Nonsense_Mutation_p.R264*	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	254	Septin-type G.				cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		AAAGAAGGTCAGAGGCCGCCT	0.493																																					p.R254X		Atlas-SNP	.											.	SEPT2	33	.	0			c.A760T						.						249	254	252					2																	242283230		2203	4300	6503	SO:0001587	stop_gained	4735	exon10			AAGGTCAGAGGCC	D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"Septins"	7729	protein-coding gene	gene with protein product		601506	"neural precursor cell expressed, developmentally down-regulated 5"	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.760A>T	chr2.hg19:g.242283230A>T	ENSP00000375834:p.Arg254*	123.0	0.0		162.0	44.0	NM_001008491	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Nonsense_Mutation	SNP	ENST00000391973.2	hg19	CCDS2548.1	.	.	.	.	.	.	.	.	.	.	A	38	7.165442	0.98107	.	.	ENSG00000168385	ENST00000391973;ENST00000360051;ENST00000391971;ENST00000401990;ENST00000407971;ENST00000402092;ENST00000391972;ENST00000421717	.	.	.	6.08	-12.0	0.00017	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	28.9819	0.99999	0.1681:0.8319:0.0:0.0	.	.	.	.	X	254;254;254;264;214;254;289;109	.	ENSP00000353157:R254X	R	+	1	2	SEPT2	241931903	0.971000	0.33674	0.814000	0.32528	0.999000	0.98932	0.341000	0.19909	-1.205000	0.02645	0.533000	0.62120	AGA	.	.		0.493	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155		T	242283230	A	T	242283230	4	4	68	1	0	0	0	0	0	1	0	0	14079	180	7	4	790	4	SEPT2	2	242283230	Nonsense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	29470998	242283230	916143	35	8667										
CHL1	10752	hgsc.bcm.edu	37	chr3	383657	383657	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aaaagggagatctatacttcGcaaacgtggaagaaaaggac	11	6	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:383657G>T	ENST00000256509.2	+	7	1213	c.571G>T	c.(571-573)Gca>Tca	p.A191S	CHL1_ENST00000397491.2_Missense_Mutation_p.A191S	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0	Glu-rich.|Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		TCTATACTTCGCAAACGTGGA	0.378																																					p.A191S		Atlas-SNP	.											.	CHL1	242	.	0			c.G571T						.						91	85	87					3																	383657		2203	4300	6503	SO:0001583	missense	10752	exon5			TACTTCGCAAACG	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.571G>T	chr3.hg19:g.383657G>T	ENSP00000256509:p.Ala191Ser	229.0	0.0		340.0	174.0	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	G	9.659	1.143662	0.21205	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.37411	1.2;1.2	5.43	5.43	0.79202	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.060122	0.64402	D	0.000002	T	0.25717	0.0626	N	0.03891	-0.335	0.47778	D	0.999517	P;P;P	0.46277	0.581;0.581;0.875	B;B;P	0.51974	0.218;0.218;0.686	T	0.05886	-1.0858	10	0.02654	T	1	.	17.7511	0.88434	0.0:0.0:1.0:0.0	.	191;191;191	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	S	191	ENSP00000256509:A191S;ENSP00000380628:A191S	ENSP00000256509:A191S	A	+	1	0	CHL1	358657	1.000000	0.71417	0.968000	0.41197	0.986000	0.74619	6.372000	0.73123	2.696000	0.92011	0.591000	0.81541	GCA	.	.		0.378	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		T	383657	G	T	383657	3	4	68	1	0	0	0	0	1	0	0	0	3351	1087	38	1	589	1	CHL1	3	383657	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10		383657	197638773	36	8668										
FBLN2	2199	hgsc.bcm.edu	37	chr3	13670761	13670761	+	Silent	SNP	T	T	C													0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgtgactgcaaagccggcttTcagcgggatgcctttggccg							TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:13670761T>C	ENST00000295760.7	+	12	2739	c.2670T>C	c.(2668-2670)ttT>ttC	p.F890F	FBLN2_ENST00000404922.3_Silent_p.F937F|FBLN2_ENST00000492059.1_Silent_p.F937F|FBLN2_ENST00000535798.1_Silent_p.F916F	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	890	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			AAGCCGGCTTTCAGCGGGATG	0.647																																					p.F937F		Atlas-SNP	.											.	FBLN2	137	.	0			c.T2811C						.						30	35	33					3																	13670761		2086	4209	6295	SO:0001819	synonymous_variant	2199	exon13			CGGCTTTCAGCGG	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"Fibulins"	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.2670T>C	chr3.hg19:g.13670761T>C		112.0	0.0		107.0	60.0	NM_001004019	B7Z9C5|Q8IUI0|Q8IUI1	Silent	SNP	ENST00000295760.7	hg19	CCDS46762.1																																																																																			.	.		0.647	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019		C	13670761	T	C	13670761	2	2	68	1	0	0	0	0	0	0	0	1	5707	1780	62	2		2	FBLN2	3	13670761	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	13287104	13670761	184351669	37	8669	38	3								
FBLN2	2199	hgsc.bcm.edu	37	chr3	13670764	13670765	+	Frame_Shift_Del	DEL	GC	GC	-													0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gactgcaaagccggctttcaGcgggatgcctttggccgggg							TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:13670764_13670765delGC	ENST00000295760.7	+	12	2742_2743	c.2673_2674delGC	c.(2671-2676)cagcggfs	p.R892fs	FBLN2_ENST00000404922.3_Frame_Shift_Del_p.R939fs|FBLN2_ENST00000492059.1_Frame_Shift_Del_p.R939fs|FBLN2_ENST00000535798.1_Frame_Shift_Del_p.R918fs	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	892	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			CCGGCTTTCAGCGGGATGCCTT	0.649																																					p.938_938del		Atlas-INDEL	.											.	FBLN2	137	.	0			c.2813_2814del						.																																			SO:0001589	frameshift_variant	2199	exon13			.	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"Fibulins"	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.2673_2674delGC	chr3.hg19:g.13670764_13670765delGC	ENSP00000295760:p.Arg892fs	108.0	0.0		106.0	54.0	NM_001165035	B7Z9C5|Q8IUI0|Q8IUI1	Frame_Shift_Del	DEL	ENST00000295760.7	hg19	CCDS46762.1																																																																																			.	.		0.649	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019		-	13670765	GC	-	13670764	7	5	68	1	0	1	0	1	0	0	0	0	5707	962	34	0	1550	0	FBLN2	3	13670764	Frame_Shift_Del	DEL	GC	TCGA-CC-A5UD-01A-11D-A28X-10	3	13670764	184351666	38	8670	38	3								
FBLN2	2199	hgsc.bcm.edu	37	chr3	13670765	13670766	+	Frame_Shift_Del	DEL	CG	CG	-													0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	actgcaaagccggctttcagCgggatgcctttggccggggc							TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:13670765_13670766delCG	ENST00000295760.7	+	12	2743_2744	c.2674_2675delCG	c.(2674-2676)cggfs	p.R892fs	FBLN2_ENST00000404922.3_Frame_Shift_Del_p.R939fs|FBLN2_ENST00000492059.1_Frame_Shift_Del_p.R939fs|FBLN2_ENST00000535798.1_Frame_Shift_Del_p.R918fs	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	892	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			CGGCTTTCAGCGGGATGCCTTT	0.653																																					p.938_939del		Pindel	.											.	FBLN2	137	.	0			c.2814_2815del						.																																			SO:0001589	frameshift_variant	2199	exon13			.	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"Fibulins"	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.2674_2675delCG	chr3.hg19:g.13670765_13670766delCG	ENSP00000295760:p.Arg892fs	109.0	0.0		105.0	31.0	NM_001165035	B7Z9C5|Q8IUI0|Q8IUI1	Frame_Shift_Del	DEL	ENST00000295760.7	hg19	CCDS46762.1																																																																																			.	.		0.653	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019		-	13670766	CG	-	13670765	7	5	68	1	0	1	0	1	0	0	0	0	5707	759	27	0	1551	0	FBLN2	3	13670765	Frame_Shift_Del	DEL	CG	TCGA-CC-A5UD-01A-11D-A28X-10	1	13670765	184351665	39	8671	38	3								
SCN11A	11280	hgsc.bcm.edu	37	chr3	38951586	38951586	+	Frame_Shift_Del	DEL	G	G	-													0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aagcttctcccaggaatcttGggtcatcagccggaacatgg							TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:38951586delG	ENST00000302328.3	-	8	1270	c.1072delC	c.(1072-1074)caafs	p.Q358fs	SCN11A_ENST00000456224.3_Frame_Shift_Del_p.Q358fs|SCN11A_ENST00000450244.1_Frame_Shift_Del_p.Q358fs|AC116038.1_ENST00000401122.1_RNA|SCN11A_ENST00000444237.2_Frame_Shift_Del_p.Q358fs	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	358					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAGGAATCTTGGGTCATCAGC	0.398																																					p.Q358fs		Atlas-Indel,Pindel	.											.	SCN11A	296	.	0			c.1073delA						.						80	74	76					3																	38951586		2203	4300	6503	SO:0001589	frameshift_variant	11280	exon8			.	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.1072delC	chr3.hg19:g.38951586delG	ENSP00000307599:p.Gln358fs	59.0	0.0		94.0	23.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Frame_Shift_Del	DEL	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.		0.398	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		-	38951586	G	-	38951586	7	5	68	1	0	1	0	1	0	0	0	0	13928	1357	47	0	4379	0	SCN11A	3	38951586	Frame_Shift_Del	DEL	G	TCGA-CC-A5UD-01A-11D-A28X-10	25280821	38951586	159070844	40	8672										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266101	41266101	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gcaacagtcttacctggactCtggaatccattctggtgcca	9	12	3	0	rs121913416|rs121913400		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:41266101C>A	ENST00000349496.5	+	3	378	c.98C>A	c.(97-99)tCt>tAt	p.S33Y	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33Y|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26Y|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33Y|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33Y	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33Y	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,359	CTNNB1	4904	.	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98A						.						92	77	82					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>A	chr3.hg19:g.41266101C>A	ENSP00000344456:p.Ser33Tyr	139.0	0.0		145.0	44.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.449496	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	Y	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26Y;ENSP00000385604:S33Y;ENSP00000412219:S33Y;ENSP00000379486:S33Y;ENSP00000344456:S33Y;ENSP00000411226:S26Y;ENSP00000379488:S33Y;ENSP00000409302:S33Y;ENSP00000401599:S33Y	ENSP00000344456:S33Y	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266101	C	A	41266101	3	1	68	1	0	0	0	0	1	0	0	0	4018	913	32	3	104	3	CTNNB1	3	41266101	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	2314515	41266101	156756329	41	8673										
KIF15	56992	hgsc.bcm.edu	37	chr3	44879894	44879894	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gaccaagaaggaagccctgaTtcaggaacttcagcacaagg	11	10	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:44879894T>A	ENST00000326047.4	+	27	3448	c.3299T>A	c.(3298-3300)aTt>aAt	p.I1100N	KIF15_ENST00000425755.1_Missense_Mutation_p.I735N	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1100					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		GAAGCCCTGATTCAGGAACTT	0.517																																					p.I1100N		Atlas-SNP	.											.	KIF15	103	.	0			c.T3299A						.						55	58	57					3																	44879894		2203	4300	6503	SO:0001583	missense	56992	exon27			CCCTGATTCAGGA	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.3299T>A	chr3.hg19:g.44879894T>A	ENSP00000324020:p.Ile1100Asn	155.0	0.0		150.0	86.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	hg19	CCDS33744.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.15|19.15	3.771885|3.771885	0.69992|0.69992	.|.	.|.	ENSG00000163808|ENSG00000163808	ENST00000396031|ENST00000326047;ENST00000425755	.|T;T	.|0.57595	.|0.39;0.39	5.26|5.26	5.26|5.26	0.73747|0.73747	.|.	.|0.000000	.|0.52532	.|D	.|0.000074	T|T	0.60599|0.60599	0.2281|0.2281	L|L	0.29908|0.29908	0.895|0.895	0.54753|0.54753	D|D	0.999987|0.999987	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	T|T	0.62034|0.62034	-0.6939|-0.6939	6|10	0.20519|0.48119	T|T	0.43|0.1	.|.	13.4068|13.4068	0.60917|0.60917	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1100	.|Q9NS87	.|KIF15_HUMAN	E|N	1098|1100;735	.|ENSP00000324020:I1100N;ENSP00000389982:I735N	ENSP00000379348:D1098E|ENSP00000324020:I1100N	D|I	+|+	3|2	2|0	KIF15|KIF15	44854898|44854898	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	5.254000|5.254000	0.65457|0.65457	1.983000|1.983000	0.57843|0.57843	0.528000|0.528000	0.53228|0.53228	GAT|ATT	.	.		0.517	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			A	44879894	T	A	44879894	3	1	68	1	0	0	0	0	1	0	0	0	8286	1493	52	4	3405	4	KIF15	3	44879894	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	3613793	44879894	153142536	42	8674										
CCR1	1230	hgsc.bcm.edu	37	chr3	46244963	46244963	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cctccgtcacttgcacagccAggtccaaatgtctgctctgc	8	16	3	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:46244963A>T	ENST00000296140.3	-	2	967	c.842T>A	c.(841-843)cTg>cAg	p.L281Q	CCR3_ENST00000357422.2_Intron	NM_001295.2	NP_001286.1	P32246	CCR1_HUMAN	chemokine (C-C motif) receptor 1	281					calcium ion transport (GO:0006816)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|exocytosis (GO:0006887)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of bone mineralization (GO:0030502)|negative regulation of gene expression (GO:0010629)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of osteoclast differentiation (GO:0045672)|response to wounding (GO:0009611)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine (C-C motif) ligand 7 binding (GO:0035717)|chemokine receptor activity (GO:0004950)|phosphatidylinositol phospholipase C activity (GO:0004435)			autonomic_ganglia(1)|large_intestine(6)|lung(6)|pancreas(1)|skin(3)	17				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		TTGCACAGCCAGGTCCAAATG	0.498																																					p.L281Q		Atlas-SNP	.											.	CCR1	36	.	0			c.T842A						.						64	58	60					3																	46244963		2203	4300	6503	SO:0001583	missense	1230	exon2			ACAGCCAGGTCCA		CCDS2737.1	3p21	2012-08-08			ENSG00000163823	ENSG00000163823		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1602	protein-coding gene	gene with protein product		601159		SCYAR1, CMKBR1		7679328	Standard	NM_001295		Approved	CKR-1, MIP1aR, CD191	uc003cph.1	P32246	OTTHUMG00000133451	ENST00000296140.3:c.842T>A	chr3.hg19:g.46244963A>T	ENSP00000296140:p.Leu281Gln	114.0	0.0		131.0	77.0	NM_001295	Q86VA9	Missense_Mutation	SNP	ENST00000296140.3	hg19	CCDS2737.1	.	.	.	.	.	.	.	.	.	.	A	10.74	1.434353	0.25813	.	.	ENSG00000163823	ENST00000296140	T	0.38887	1.11	5.33	5.33	0.75918	GPCR, rhodopsin-like superfamily (1);	1.332120	0.04950	N	0.460228	T	0.41949	0.1181	N	0.05330	-0.07	0.32229	N	0.574219	D	0.61080	0.989	D	0.73708	0.981	T	0.38112	-0.9676	10	0.15066	T	0.55	.	6.1068	0.20077	0.7682:0.0:0.078:0.1538	.	281	P32246	CCR1_HUMAN	Q	281	ENSP00000296140:L281Q	ENSP00000296140:L281Q	L	-	2	0	CCR1	46219967	0.995000	0.38212	0.997000	0.53966	0.029000	0.11900	4.004000	0.57068	2.145000	0.66743	0.533000	0.62120	CTG	.	.		0.498	CCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257325.2	NM_001295		T	46244963	A	T	46244963	3	4	68	1	0	0	0	0	1	0	0	0	2941	188	7	4	229	4	CCR1	3	46244963	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	1365069	46244963	151777467	43	8675										
NME6	10201	hgsc.bcm.edu	37	chr3	48339972	48339972	+	Frame_Shift_Del	DEL	T	T	-													0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgatcagggctagagtgagcTggagagcctgagggcttcgc							TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:48339972delT	ENST00000452211.1	-	3	272	c.35delA	c.(34-36)cagfs	p.Q12fs	NME6_ENST00000444069.1_Intron|NME6_ENST00000450160.1_Frame_Shift_Del_p.Q12fs|NME6_ENST00000415644.1_Frame_Shift_Del_p.Q12fs|NME6_ENST00000415053.1_Frame_Shift_Del_p.Q12fs|NME6_ENST00000451657.1_Frame_Shift_Del_p.Q12fs|NME6_ENST00000426723.1_Frame_Shift_Del_p.Q12fs|NME6_ENST00000442597.1_Frame_Shift_Del_p.Q12fs|NME6_ENST00000426689.2_Frame_Shift_Del_p.Q12fs|ZNF589_ENST00000412564.1_Intron|NME6_ENST00000435684.1_Frame_Shift_Del_p.Q12fs|NME6_ENST00000421967.1_Frame_Shift_Del_p.Q20fs|NME6_ENST00000447314.1_Intron			O75414	NDK6_HUMAN	NME/NM23 nucleoside diphosphate kinase 6	12					apoptotic process (GO:0006915)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|negative regulation of cell growth (GO:0030308)|negative regulation of mitosis (GO:0045839)|UTP biosynthetic process (GO:0006228)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			breast(1)|large_intestine(5)	6				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		TAGAGTGAGCTGGAGAGCCTG	0.542																																					p.Q20fs		Atlas-Indel,Pindel	.											.	NME6	14	.	0			c.60delG						.						106	87	93					3																	48339972		2203	4300	6503	SO:0001589	frameshift_variant	10201	exon2			.	AF051941	CCDS2763.1	3p21.31	2012-05-18	2012-05-18		ENSG00000172113	ENSG00000172113			20567	protein-coding gene	gene with protein product		608294	"non-metastatic cells 6, protein expressed in (nucleoside-diphosphate kinase)"			10453732, 19852809	Standard	NM_005793		Approved	NM23-H6, IPIA-ALPHA	uc003cso.3	O75414	OTTHUMG00000133531	ENST00000452211.1:c.35delA	chr3.hg19:g.48339972delT	ENSP00000392352:p.Gln12fs	109.0	0.0		97.0	27.0	NM_005793	B4DGW7|B4DM99|Q53HM5|Q96E73|Q9BQ63	Frame_Shift_Del	DEL	ENST00000452211.1	hg19																																																																																				.	.		0.542	NME6-005	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000346107.1	NM_005793		-	48339972	T	-	48339972	7	5	68	1	0	1	0	1	0	0	0	0	10504	1580	55	0	545	0	NME6	3	48339972	Frame_Shift_Del	DEL	T	TCGA-CC-A5UD-01A-11D-A28X-10	2095009	48339972	149682458	44	8676										
P4HTM	54681	hgsc.bcm.edu	37	chr3	49042389	49042389	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ggggggccactaccatgcccAcgtggacagtgggcctgtgt	16	12	0	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:49042389A>T	ENST00000383729.4	+	6	1354	c.983A>T	c.(982-984)cAc>cTc	p.H328L	WDR6_ENST00000608424.1_5'Flank|WDR6_ENST00000448293.1_5'Flank|WDR6_ENST00000395474.3_5'Flank|WDR6_ENST00000415265.2_5'Flank|P4HTM_ENST00000343546.4_Missense_Mutation_p.H328L	NM_177939.2	NP_808808.1	Q9NXG6	P4HTM_HUMAN	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	328	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21					Vitamin C(DB00126)	TACCATGCCCACGTGGACAGT	0.612																																					p.H328L		Atlas-SNP	.											.	P4HTM	71	.	0			c.A983T						.						119	94	103					3																	49042389		2203	4300	6503	SO:0001583	missense	54681	exon6			ATGCCCACGTGGA		CCDS2781.2, CCDS43089.1	3p21.31	2009-01-14			ENSG00000178467	ENSG00000178467			28858	protein-coding gene	gene with protein product	"Prolyl hydroxlase domain-containing 4", "hypoxia inducible factor prolyl 4 hydroxylase"	614584				12163023, 17726031	Standard	XR_245139		Approved	P4H-TM, PHD4, PH4, HIFPH4, FLJ20262, EGLN4, PH-4	uc003cvh.3	Q9NXG6	OTTHUMG00000074057	ENST00000383729.4:c.983A>T	chr3.hg19:g.49042389A>T	ENSP00000373235:p.His328Leu	110.0	0.0		102.0	58.0	NM_177938	Q6PAG6|Q8TCJ9|Q8WV55|Q96F22|Q9BW77	Missense_Mutation	SNP	ENST00000383729.4	hg19	CCDS43089.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.932321	0.92389	.	.	ENSG00000178467	ENST00000383729;ENST00000343546	D	0.95342	-3.68	5.29	5.29	0.74685	Oxoglutarate/iron-dependent oxygenase (2);Prolyl 4-hydroxylase, alpha subunit (1);	0.107966	0.64402	D	0.000002	D	0.97087	0.9048	H	0.96547	3.84	0.58432	D	0.999999	B;P	0.45672	0.277;0.864	B;P	0.48368	0.202;0.575	D	0.98121	1.0425	10	0.87932	D	0	-17.3852	15.3015	0.73955	1.0:0.0:0.0:0.0	.	328;328	Q9NXG6-3;Q9NXG6	.;P4HTM_HUMAN	L	328	ENSP00000373235:H328L	ENSP00000341422:H328L	H	+	2	0	P4HTM	49017393	1.000000	0.71417	0.982000	0.44146	0.975000	0.68041	8.919000	0.92770	2.017000	0.59298	0.529000	0.55759	CAC	.	.		0.612	P4HTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157211.1	NM_177938		T	49042389	A	T	49042389	3	4	68	1	0	0	0	0	1	0	0	0	11369	159	6	4	1005	4	P4HTM	3	49042389	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	702417	49042389	148980041	45	8677										
ITIH4	3700	hgsc.bcm.edu	37	chr3	52848087	52848087	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gcacctcctggtaaaactggCctgagatacaaagggtggat	12	9	0	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:52848087C>A	ENST00000266041.4	-	23	2723	c.2627G>T	c.(2626-2628)gGc>gTc	p.G876V	RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000406595.1_Splice_Site_p.G846V|ITIH4_ENST00000485816.1_Splice_Site_p.G881V|ITIH4_ENST00000346281.5_Splice_Site_p.G860V	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	876					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GTAAAACTGGCCTGAGATACA	0.587																																					p.G876V		Atlas-SNP	.											.	ITIH4	74	.	0			c.G2627T						.						43	37	39					3																	52848087		2203	4300	6503	SO:0001630	splice_region_variant	3700	exon23			AACTGGCCTGAGA	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"plasma Kallikrein-sensitive glycoprotein"	600564	"inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.2627-1G>T	chr3.hg19:g.52848087C>A		111.0	0.0		99.0	27.0	NM_002218	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Missense_Mutation	SNP	ENST00000266041.4	hg19	CCDS2865.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.76|17.76	3.467946|3.467946	0.63625|0.63625	.|.	.|.	ENSG00000055955|ENSG00000055955	ENST00000266041;ENST00000346281;ENST00000485816;ENST00000406595;ENST00000538421|ENST00000441637	T;T;T;T|.	0.32988|.	1.43;1.43;1.43;1.43|.	5.04|5.04	4.1|4.1	0.47936|0.47936	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);|.	0.000000|.	0.56097|.	D|.	0.000022|.	T|T	0.66147|0.66147	0.2760|0.2760	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;1.0;1.0;0.999|.	T|T	0.64504|0.64504	-0.6392|-0.6392	10|5	0.87932|.	D|.	0|.	.|.	10.2271|10.2271	0.43231|0.43231	0.1975:0.8025:0.0:0.0|0.1975:0.8025:0.0:0.0	.|.	846;881;876;860|.	E9PGN5;B7ZKJ8;Q14624;Q14624-2|.	.;.;ITIH4_HUMAN;.|.	V|C	876;860;881;846;834|664	ENSP00000266041:G876V;ENSP00000340520:G860V;ENSP00000417824:G881V;ENSP00000384425:G846V|.	ENSP00000266041:G876V|.	G|W	-|-	2|3	0|0	ITIH4|ITIH4	52823127|52823127	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.761000|0.761000	0.43186|0.43186	3.763000|3.763000	0.55257|0.55257	2.785000|2.785000	0.95823|0.95823	0.655000|0.655000	0.94253|0.94253	GGC|TGG	.	.		0.587	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	Missense_Mutation	A	52848087	C	A	52848087	5	1	68	1	0	0	0	0	0	0	1	0	7915	753	26	3	173	3	ITIH4	3	52848087	Splice_Site	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	3805698	52848087	145174343	46	8678										
B3GALNT1	8706	hgsc.bcm.edu	37	chr3	160803895	160803895	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgggttttttggtaaaatccTctataggaataattatcaat	7	4	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:160803895T>A	ENST00000392781.2	-	8	1395	c.648A>T	c.(646-648)agA>agT	p.R216S	B3GALNT1_ENST00000473285.1_Missense_Mutation_p.R216S|B3GALNT1_ENST00000417187.1_Intron|B3GALNT1_ENST00000392780.1_Missense_Mutation_p.R216S|B3GALNT1_ENST00000488170.1_Missense_Mutation_p.R216S|B3GALNT1_ENST00000392779.2_Missense_Mutation_p.R216S|B3GALNT1_ENST00000320474.4_Missense_Mutation_p.R216S	NM_001038628.1	NP_001033717.1	O75752	B3GL1_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	216					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity (GO:0047273)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)			GGTAAAATCCTCTATAGGAAT	0.353																																					p.R216S		Atlas-SNP	.											.	B3GALNT1	34	.	0			c.A648T						.						31	32	32					3																	160803895		2201	4295	6496	SO:0001583	missense	8706	exon8			AAATCCTCTATAG	Y15062	CCDS3193.1	3q25	2014-07-18	2006-06-14	2006-05-09	ENSG00000169255	ENSG00000169255	2.4.1.79	"Blood group antigens", "Beta 3-glycosyltransferases"	918	protein-coding gene	gene with protein product	"globoside synthase", "P antigen synthase"	603094	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 (Globoside blood group)", "UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1 (Globoside blood group)"	B3GALT3		9582303, 10993897	Standard	XM_005247861		Approved	beta3Gal-T3, galT3, P1, GLOB	uc003fdv.3	O75752	OTTHUMG00000159064	ENST00000392781.2:c.648A>T	chr3.hg19:g.160803895T>A	ENSP00000376532:p.Arg216Ser	28.0	0.0		26.0	5.0	NM_001038628	D3DNM4|Q3Y531|Q6IAI5|Q8NFM8|Q8NFM9|Q9HA06	Missense_Mutation	SNP	ENST00000392781.2	hg19	CCDS3193.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.459023	0.63401	.	.	ENSG00000169255	ENST00000320474;ENST00000392779;ENST00000392780;ENST00000392781;ENST00000473285;ENST00000488170	D;D;D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81;-1.81;-1.81	5.94	3.59	0.41128	.	0.000000	0.85682	D	0.000000	D	0.90566	0.7043	M	0.85099	2.735	0.40752	D	0.982924	D	0.61697	0.99	P	0.61800	0.894	D	0.89720	0.3918	10	0.87932	D	0	.	8.0452	0.30545	0.0:0.2125:0.0:0.7875	.	216	O75752	B3GL1_HUMAN	S	216	ENSP00000323479:R216S;ENSP00000376530:R216S;ENSP00000376531:R216S;ENSP00000376532:R216S;ENSP00000418226:R216S;ENSP00000420163:R216S	ENSP00000323479:R216S	R	-	3	2	B3GALNT1	162286589	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.192000	0.32150	0.514000	0.28300	0.459000	0.35465	AGA	.	.		0.353	B3GALNT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353125.1	NM_033167		A	160803895	T	A	160803895	3	1	68	1	0	0	0	0	1	0	0	0	1245	1548	54	4	351	4	B3GALNT1	3	160803895	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	107955808	160803895	37218535	47	8679										
ZBBX	79740	hgsc.bcm.edu	37	chr3	166960387	166960387	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cagtgattggctgctgaaatCtgggaactcttctgaggtta	12	7	3	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:166960387C>T	ENST00000392766.2	-	20	2522	c.2182G>A	c.(2182-2184)Gat>Aat	p.D728N	ZBBX_ENST00000392767.2_Missense_Mutation_p.D728N|ZBBX_ENST00000307529.5_Missense_Mutation_p.D767N|ZBBX_ENST00000455345.2_Missense_Mutation_p.D767N|ZBBX_ENST00000392764.1_Missense_Mutation_p.D699N	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	728						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						CTGCTGAAATCTGGGAACTCT	0.363																																					p.D767N		Atlas-SNP	.											ZBBX_ENST00000455345,colon,carcinoma,0,2	ZBBX	299	.	0			c.G2299A						.						95	93	93					3																	166960387		1824	4077	5901	SO:0001583	missense	79740	exon21			TGAAATCTGGGAA	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.2182G>A	chr3.hg19:g.166960387C>T	ENSP00000376519:p.Asp728Asn	29.0	0.0		48.0	16.0	NM_001199201	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	hg19	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	C	7.397	0.632051	0.14322	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	5.62	4.73	0.59995	.	0.374827	0.21088	N	0.080369	T	0.30070	0.0753	N	0.08118	0	0.09310	N	1	B;B	0.27316	0.175;0.109	B;B	0.26416	0.069;0.019	T	0.11641	-1.0579	10	0.21540	T	0.41	-0.446	10.8196	0.46597	0.0:0.9109:0.0:0.0891	.	767;728	A8MT70-2;A8MT70	.;ZBBX_HUMAN	N	728;728;767;767;699	ENSP00000376519:D728N;ENSP00000376520:D728N;ENSP00000390232:D767N;ENSP00000305065:D767N;ENSP00000376517:D699N	ENSP00000305065:D767N	D	-	1	0	ZBBX	168443081	0.017000	0.18338	0.015000	0.15790	0.005000	0.04900	0.367000	0.20382	2.640000	0.89533	0.591000	0.81541	GAT	.	.		0.363	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		T	166960387	C	T	166960387	3	4	68	1	0	0	0	0	1	0	0	0	17531	913	32	3	228	3	ZBBX	3	166960387	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	6156492	166960387	31062043	48	8680										
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184039550	184039550	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cccctccgaatcccctgtgcCcattgctccaactgcccaac	5	21	0	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr3:184039550C>G	ENST00000346169.2	+	10	1449	c.1178C>G	c.(1177-1179)cCc>cGc	p.P393R	EIF4G1_ENST00000319274.6_Missense_Mutation_p.P393R|EIF4G1_ENST00000414031.1_Missense_Mutation_p.P353R|EIF4G1_ENST00000441154.1_Missense_Mutation_p.P229R|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000392537.2_Missense_Mutation_p.P306R|EIF4G1_ENST00000382330.3_Missense_Mutation_p.P400R|EIF4G1_ENST00000342981.4_Missense_Mutation_p.P393R|EIF4G1_ENST00000352767.3_Missense_Mutation_p.P400R|EIF4G1_ENST00000435046.2_Missense_Mutation_p.P197R|EIF4G1_ENST00000434061.2_Missense_Mutation_p.P197R|EIF4G1_ENST00000427845.1_Missense_Mutation_p.P306R|EIF4G1_ENST00000424196.1_Missense_Mutation_p.P400R|EIF4G1_ENST00000411531.1_Missense_Mutation_p.P353R|EIF4G1_ENST00000350481.5_Missense_Mutation_p.P229R	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	393					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCCCCTGTGCCCATTGCTCCA	0.607																																					p.P400R		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C1199G						.						177	192	187					3																	184039550		2203	4300	6503	SO:0001583	missense	1981	exon11			CTGTGCCCATTGC	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1178C>G	chr3.hg19:g.184039550C>G	ENSP00000316879:p.Pro393Arg	195.0	0.0		155.0	96.0	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	hg19	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.512773	0.44660	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000434061;ENST00000457456;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.32753	4.05;4.04;3.96;2.93;2.93;4.04;3.1;3.87;4.04;3.94;4.03;4.05;4.04;4.03;2.53;3.87;3.86;1.44;3.87	5.07	4.2	0.49525	.	0.511843	0.20969	N	0.082430	T	0.37376	0.1001	N	0.24115	0.695	0.41262	D	0.986781	D;P;D;D	0.71674	0.995;0.769;0.998;0.995	P;B;D;P	0.78314	0.854;0.372;0.991;0.854	T	0.08953	-1.0697	10	0.30078	T	0.28	-6.3191	10.8383	0.46700	0.0:0.9119:0.0:0.0881	.	400;393;393;400	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	R	393;353;306;393;400;400;334;229;400;306;393;393;400;353;229;229;197;197;197	ENSP00000316879:P393R;ENSP00000391935:P353R;ENSP00000376320:P306R;ENSP00000391412:P393R;ENSP00000413159:P400R;ENSP00000371767:P400R;ENSP00000403269:P334R;ENSP00000317600:P229R;ENSP00000338020:P400R;ENSP00000407682:P306R;ENSP00000343450:P393R;ENSP00000323737:P393R;ENSP00000416255:P400R;ENSP00000395974:P353R;ENSP00000398145:P229R;ENSP00000399858:P229R;ENSP00000411826:P197R;ENSP00000399969:P197R;ENSP00000404754:P197R	ENSP00000323737:P393R	P	+	2	0	EIF4G1	185522244	.	.	0.746000	0.31095	0.938000	0.57974	.	.	1.499000	0.48617	0.563000	0.77884	CCC	.	.		0.607	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		G	184039550	C	G	184039550	3	3	68	1	0	0	0	0	1	0	0	0	5038	623	22	4	1208	4	EIF4G1	3	184039550	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	17079163	184039550	13982880	49	8681										
LDB2	9079	hgsc.bcm.edu	37	chr4	16510279	16510279	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tggaatttttcctttttctcCgtttggttgttggttgcctt	9	7	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr4:16510279C>T	ENST00000304523.5	-	7	1093	c.770G>A	c.(769-771)cGg>cAg	p.R257Q	LDB2_ENST00000503178.2_Missense_Mutation_p.R133Q|LDB2_ENST00000441778.2_Missense_Mutation_p.R257Q|LDB2_ENST00000502640.1_Missense_Mutation_p.R257Q|LDB2_ENST00000515064.1_Missense_Mutation_p.R257Q|RP11-446J8.1_ENST00000512370.1_RNA	NM_001290.3	NP_001281.1	O43679	LDB2_HUMAN	LIM domain binding 2	257					epithelial structure maintenance (GO:0010669)|hair follicle development (GO:0001942)|positive regulation of cellular component biogenesis (GO:0044089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell maintenance (GO:0035019)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	LIM domain binding (GO:0030274)|transcription cofactor activity (GO:0003712)	p.R257Q(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(23)|urinary_tract(1)	33						CCTTTTTCTCCGTTTGGTTGT	0.478																																					p.R257Q		Atlas-SNP	.											LDB2_ENST00000441778,NS,carcinoma,0,1	LDB2	129	.	2	Substitution - Missense(2)	lung(2)	c.G770A						.						251	205	221					4																	16510279		2203	4300	6503	SO:0001583	missense	9079	exon7			TTTCTCCGTTTGG	AF068651	CCDS3420.1, CCDS47031.1	4p16	2008-08-01			ENSG00000169744	ENSG00000169744			6533	protein-coding gene	gene with protein product		603450				9853615, 9880598, 10861853	Standard	NM_001290		Approved	CLIM1, LDB1	uc003goz.3	O43679	OTTHUMG00000048212	ENST00000304523.5:c.770G>A	chr4.hg19:g.16510279C>T	ENSP00000306772:p.Arg257Gln	97.0	0.0		108.0	52.0	NM_001290	O60619|O75480	Missense_Mutation	SNP	ENST00000304523.5	hg19	CCDS3420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.691075|5.691075	0.96793|0.96793	.|.	.|.	ENSG00000169744|ENSG00000169744	ENST00000507464|ENST00000515064;ENST00000441778;ENST00000304523;ENST00000502640;ENST00000503178	.|T;T;T;T;T	.|0.25250	.|1.81;1.81;1.81;1.81;1.81	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	.|0.000000	.|0.64402	.|D	.|0.000010	T|T	0.55497|0.55497	0.1924|0.1924	M|M	0.81497|0.81497	2.545|2.545	0.80722|0.80722	D|D	1|1	.|D;D;D;P;D;D;D	.|0.89917	.|0.999;0.994;0.968;0.716;1.0;0.998;1.0	.|D;P;B;B;D;D;D	.|0.83275	.|0.974;0.885;0.269;0.169;0.996;0.99;0.996	T|T	0.51276|0.51276	-0.8726|-0.8726	5|10	.|0.38643	.|T	.|0.18	-17.6274|-17.6274	19.1044|19.1044	0.93287|0.93287	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|133;223;257;257;257;257;233	.|B7Z2D3;B7Z6D0;E9PFI4;G5E9Y7;O43679-2;O43679;O43679-3	.|.;.;.;.;.;LDB2_HUMAN;.	R|Q	178|257;257;257;257;133	.|ENSP00000422552:R257Q;ENSP00000392089:R257Q;ENSP00000306772:R257Q;ENSP00000423963:R257Q;ENSP00000440940:R133Q	.|ENSP00000306772:R257Q	G|R	-|-	1|2	0|0	LDB2|LDB2	16119377|16119377	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	7.818000|7.818000	0.86416|0.86416	2.756000|2.756000	0.94617|0.94617	0.655000|0.655000	0.94253|0.94253	GGA|CGG	.	.		0.478	LDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250321.2			T	16510279	C	T	16510279	3	4	68	1	0	0	0	0	1	0	0	0	8705	652	23	1	468	1	LDB2	4	16510279	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10		16510279	174643997	50	8682										
FRYL	285527	hgsc.bcm.edu	37	chr4	48529665	48529665	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aaatcctcattagaagaaaaTacaacctgatgcccgattaa	5	9	1	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr4:48529665T>C	ENST00000503238.1	-	50	7145	c.7146A>G	c.(7144-7146)gtA>gtG	p.V2382V	FRYL_ENST00000507873.2_5'UTR|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Silent_p.V2382V|FRYL_ENST00000537810.1_Silent_p.V2382V			O94915	FRYL_HUMAN	FRY-like	2382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						TAGAAGAAAATACAACCTGAT	0.408																																					p.V2382V		Atlas-SNP	.											.	FRYL	242	.	0			c.A7146G						.						138	129	132					4																	48529665		1814	4071	5885	SO:0001819	synonymous_variant	285527	exon53			AGAAAATACAACC	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.7146A>G	chr4.hg19:g.48529665T>C		41.0	0.0		50.0	27.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	T	0.351	-0.944630	0.02304	.	.	ENSG00000075539	ENST00000514617	.	.	.	5.53	-2.73	0.05950	.	.	.	.	.	T	0.48040	0.1478	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42749	-0.9433	4	.	.	.	.	5.0552	0.14529	0.2558:0.4279:0.0:0.3163	.	.	.	.	V	1252	.	.	I	-	1	0	FRYL	48224422	0.943000	0.32029	0.988000	0.46212	0.045000	0.14185	0.051000	0.14141	-0.186000	0.10533	-0.441000	0.05720	ATT	.	.		0.408	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			C	48529665	T	C	48529665	2	2	68	1	0	0	0	0	0	0	0	1	6072	1393	49	2		2	FRYL	4	48529665	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	32019386	48529665	142624611	51	8683										
KIT	3815	hgsc.bcm.edu	37	chr4	55593652	55593652	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	caattatgtttacatagaccCaacacaacttccttatgatc	3	11	0	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr4:55593652C>A	ENST00000288135.5	+	11	1815	c.1718C>A	c.(1717-1719)cCa>cAa	p.P573Q		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	573					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.Y570_L576del(9)|p.P573L(4)|p.V560_L576del(4)|p.Y553_T574>S(3)|p.V555_P573del(3)|p.I563_L576del(2)|p.Q556_L576del(2)|p.N564_Y578del(2)|p.W557_Q575del(2)|p.N564_L576del(2)|p.I571_L576del(2)|p.Y568_T574del(2)|p.Y568_L576>CV(1)|p.N564_T574del(1)|p.K558_Q575del(1)|p.M552_T574>TESA(1)|p.N567_L576>E(1)|p.E561_P577del(1)|p.I571_N587del(1)|p.V569_L576>G(1)|p.V569_L576del(1)|p.K558_L576>NV(1)|p.V569_Q575del(1)|p.N564_P577del(1)|p.V559_L576del(1)|p.Q556_T574del(1)|p.E562_P573del(1)|p.Q556_P573del(1)|p.N567_P573del(1)|p.Y570_L576delYIDPTQL(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TACATAGACCCAACACAACTT	0.413		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.P573Q		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	KIT,colon,carcinoma,0,5	KIT	7396	.	55	Deletion - In frame(43)|Complex - deletion inframe(8)|Substitution - Missense(4)	soft_tissue(48)|skin(4)|eye(2)|testis(1)	c.C1718A						.						77	76	77					4																	55593652		2203	4300	6503	SO:0001583	missense	3815	exon11	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	TAGACCCAACACA	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1718C>A	chr4.hg19:g.55593652C>A	ENSP00000288135:p.Pro573Gln	91.0	0.0		138.0	77.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.875954	0.91664	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.97924	-4.61;-4.61	6.06	6.06	0.98353	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000007	D	0.98792	0.9593	M	0.81341	2.54	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.991	D;D;D	0.77557	0.954;0.99;0.91	D	0.99429	1.0935	10	0.87932	D	0	.	20.613	0.99472	0.0:1.0:0.0:0.0	.	80;569;573	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	Q	573;569	ENSP00000288135:P573Q;ENSP00000390987:P569Q	ENSP00000288135:P573Q	P	+	2	0	KIT	55288409	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.663000	0.83820	2.876000	0.98609	0.655000	0.94253	CCA	.	.		0.413	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			A	55593652	C	A	55593652	3	1	68	1	0	0	0	0	1	0	0	0	8338	594	21	3	1760	3	KIT	4	55593652	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	7063987	55593652	135560624	52	8684										
MAPK10	5602	hgsc.bcm.edu	37	chr4	86989078	86989078	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctggacatggtgttcctagtTgttcaattaccttattccac	7	10	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr4:86989078T>A	ENST00000359221.3	-	10	1359	c.833A>T	c.(832-834)cAa>cTa	p.Q278L	MAPK10_ENST00000395161.2_Missense_Mutation_p.Q278L|MAPK10_ENST00000395157.3_Missense_Mutation_p.Q133L|MAPK10_ENST00000449047.2_Missense_Mutation_p.Q133L|MAPK10_ENST00000395169.3_Missense_Mutation_p.Q240L|MAPK10_ENST00000361569.2_Missense_Mutation_p.Q278L|MAPK10_ENST00000395166.1_Missense_Mutation_p.Q240L|MAPK10_ENST00000395160.3_Missense_Mutation_p.Q133L			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	278	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)			breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		TGTTCCTAGTTGTTCAATTAC	0.418																																					p.Q278L		Atlas-SNP	.											.	MAPK10	106	.	0			c.A833T						.						122	112	115					4																	86989078		2203	4300	6503	SO:0001583	missense	5602	exon10			CCTAGTTGTTCAA	U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.833A>T	chr4.hg19:g.86989078T>A	ENSP00000352157:p.Gln278Leu	100.0	0.0		92.0	67.0	NM_002753	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Missense_Mutation	SNP	ENST00000359221.3	hg19	CCDS34026.1	.	.	.	.	.	.	.	.	.	.	T	12.89	2.073778	0.36566	.	.	ENSG00000109339	ENST00000395169;ENST00000359221;ENST00000395157;ENST00000361569;ENST00000395166;ENST00000395160;ENST00000449047;ENST00000395161	T;T;T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.28	5.28	0.74379	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.32224	0.0822	N	0.01679	-0.765	0.80722	D	1	B;B;B;B;B	0.16603	0.003;0.018;0.006;0.006;0.003	B;B;B;B;B	0.21360	0.015;0.034;0.01;0.01;0.011	T	0.40384	-0.9566	10	0.02654	T	1	-13.6375	15.5104	0.75776	0.0:0.0:0.0:1.0	.	164;133;240;278;278	B7Z1Z1;Q499Y8;P53779-3;P53779-2;P53779	.;.;.;.;MK10_HUMAN	L	240;278;133;278;240;133;133;278	ENSP00000378598:Q240L;ENSP00000352157:Q278L;ENSP00000378586:Q133L;ENSP00000355297:Q278L;ENSP00000378595:Q240L;ENSP00000378589:Q133L;ENSP00000414469:Q133L;ENSP00000378590:Q278L	ENSP00000352157:Q278L	Q	-	2	0	MAPK10	87208102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.111000	0.64477	0.533000	0.62120	CAA	.	.		0.418	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			A	86989078	T	A	86989078	3	1	68	1	0	0	0	0	1	0	0	0	9281	1812	63	4	586	4	MAPK10	4	86989078	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	31395426	86989078	104165198	53	8685										
NEIL3	55247	hgsc.bcm.edu	37	chr4	178256896	178256896	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aatccacttgagtataaataTaaaaatggagcttctcctgt	6	7	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr4:178256896T>C	ENST00000264596.3	+	3	451	c.333T>C	c.(331-333)taT>taC	p.Y111Y		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	111					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		AGTATAAATATAAAAATGGAG	0.313								Base excision repair (BER), DNA glycosylases																													p.Y111Y		Atlas-SNP	.											.	NEIL3	89	.	0			c.T333C						.						57	63	61					4																	178256896		2200	4298	6498	SO:0001819	synonymous_variant	55247	exon3			TAAATATAAAAAT	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 3"	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.333T>C	chr4.hg19:g.178256896T>C		108.0	0.0		91.0	79.0	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Silent	SNP	ENST00000264596.3	hg19	CCDS3828.1																																																																																			.	.		0.313	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		C	178256896	T	C	178256896	2	2	68	1	0	0	0	0	0	0	0	1	10329	1413	49	2		2	NEIL3	4	178256896	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	91267818	178256896	12897380	54	8686										
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1053526	1053526	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgagcaggaccagctgcgcaTcctgggacttgttgaggacg	15	10	0	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:1053526T>C	ENST00000264930.5	-	23	3141	c.3098A>G	c.(3097-3099)gAt>gGt	p.D1033G		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	1033					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CAGCTGCGCATCCTGGGACTT	0.622																																					p.D1033G		Atlas-SNP	.											.	SLC12A7	97	.	0			c.A3098G						.						176	138	151					5																	1053526		2203	4300	6503	SO:0001583	missense	10723	exon23			TGCGCATCCTGGG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.3098A>G	chr5.hg19:g.1053526T>C	ENSP00000264930:p.Asp1033Gly	164.0	0.0		211.0	36.0	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	hg19	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	T	7.233	0.599660	0.13939	.	.	ENSG00000113504	ENST00000264930	T	0.50813	0.73	3.88	2.67	0.31697	.	0.393288	0.24717	N	0.036172	T	0.34308	0.0893	L	0.39020	1.185	0.41687	D	0.989329	B	0.12630	0.006	B	0.12837	0.008	T	0.12811	-1.0533	10	0.52906	T	0.07	.	6.9588	0.24585	0.0:0.1257:0.0:0.8743	.	1033	Q9Y666	S12A7_HUMAN	G	1033	ENSP00000264930:D1033G	ENSP00000264930:D1033G	D	-	2	0	SLC12A7	1106526	0.696000	0.27757	0.628000	0.29241	0.201000	0.24016	1.715000	0.37971	0.468000	0.27243	0.402000	0.26972	GAT	.	.		0.622	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		C	1053526	T	C	1053526	3	2	68	1	0	0	0	0	1	0	0	0	14403	1435	50	2	161	2	SLC12A7	5	1053526	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		1053526	179861734	55	8687										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13830159	13830159	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gttaagaaaagcccaaattcAgggttcatagtcacattatc	7	8	3	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:13830159A>T	ENST00000265104.4	-	37	6329	c.6225T>A	c.(6223-6225)ccT>ccA	p.P2075P		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2075	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GCCCAAATTCAGGGTTCATAG	0.388									Kartagener syndrome																												p.P2075P		Atlas-SNP	.											.	DNAH5	868	.	0			c.T6225A						.						81	79	80					5																	13830159		2203	4300	6503	SO:0001819	synonymous_variant	1767	exon37	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AAATTCAGGGTTC	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.6225T>A	chr5.hg19:g.13830159A>T		163.0	0.0		233.0	44.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	hg19	CCDS3882.1																																																																																			.	.		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13830159	A	T	13830159	2	4	68	1	0	0	0	0	0	0	0	1	4606	175	7	4		4	DNAH5	5	13830159	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	12776633	13830159	167085101	56	8688										
FBXL7	23194	hgsc.bcm.edu	37	chr5	15928539	15928539	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	actggaagtctcaggctgttAcaatatctccaacgaggccg	10	11	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:15928539A>T	ENST00000504595.1	+	3	1149	c.668A>T	c.(667-669)tAc>tTc	p.Y223F	FBXL7_ENST00000510662.1_Missense_Mutation_p.Y176F|FBXL7_ENST00000329673.7_Missense_Mutation_p.Y211F	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	223					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						TCAGGCTGTTACAATATCTCC	0.567																																					p.Y223F		Atlas-SNP	.											.	FBXL7	138	.	0			c.A668T						.						97	94	95					5																	15928539		2049	4193	6242	SO:0001583	missense	23194	exon3			GCTGTTACAATAT	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.668A>T	chr5.hg19:g.15928539A>T	ENSP00000423630:p.Tyr223Phe	153.0	0.0		246.0	53.0	NM_012304	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	hg19	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	A	11.08	1.532215	0.27387	.	.	ENSG00000183580	ENST00000504595;ENST00000510662;ENST00000329673	T;T;T	0.02369	4.32;4.32;4.32	5.14	5.14	0.70334	.	0.056384	0.64402	D	0.000001	T	0.02807	0.0084	L	0.38953	1.18	0.53688	D	0.999974	P	0.36086	0.536	B	0.31614	0.133	T	0.56475	-0.7973	10	0.10377	T	0.69	.	14.9504	0.71067	1.0:0.0:0.0:0.0	.	223	Q9UJT9	FBXL7_HUMAN	F	223;176;211	ENSP00000423630:Y223F;ENSP00000425184:Y176F;ENSP00000329632:Y211F	ENSP00000329632:Y211F	Y	+	2	0	FBXL7	15981539	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.348000	0.73009	1.944000	0.56390	0.459000	0.35465	TAC	.	.		0.567	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		T	15928539	A	T	15928539	3	4	68	1	0	0	0	0	1	0	0	0	5732	391	14	4	678	4	FBXL7	5	15928539	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	2098380	15928539	164986721	57	8689										
MYO10	4651	hgsc.bcm.edu	37	chr5	16704767	16704767	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttccctccgcttctccagttTctgttccaaggattctcgaa	6	14	3	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:16704767T>A	ENST00000513610.1	-	22	2651	c.2197A>T	c.(2197-2199)Aaa>Taa	p.K733*	MYO10_ENST00000427430.2_Nonsense_Mutation_p.K90*|MYO10_ENST00000515803.1_Nonsense_Mutation_p.K72*|MYO10_ENST00000274203.9_Nonsense_Mutation_p.K90*|MYO10_ENST00000512061.1_5'UTR|MYO10_ENST00000505695.1_Nonsense_Mutation_p.K72*	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	733	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						TTCTCCAGTTTCTGTTCCAAG	0.537																																					p.K733X		Atlas-SNP	.											.	MYO10	198	.	0			c.A2197T						.						69	72	71					5																	16704767		2022	4182	6204	SO:0001587	stop_gained	4651	exon22			CCAGTTTCTGTTC	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2197A>T	chr5.hg19:g.16704767T>A	ENSP00000421280:p.Lys733*	58.0	0.0		64.0	16.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Nonsense_Mutation	SNP	ENST00000513610.1	hg19	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	T	42	9.260413	0.99117	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430;ENST00000513882	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.5602	0.50772	0.0:0.0:0.1493:0.8507	.	.	.	.	X	733;72;90;72;90;744	.	ENSP00000274203:K90X	K	-	1	0	MYO10	16757767	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.363000	0.52321	1.919000	0.55581	0.460000	0.39030	AAA	.	.		0.537	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16704767	T	A	16704767	4	1	68	1	0	0	0	0	0	1	0	0	10071	1792	62	4	4059	4	MYO10	5	16704767	Nonsense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	776228	16704767	164210493	58	8690										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71494849	71494849	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gatgaagaagattatgactaTgagtcttatgagaagaccac	10	5	1	7			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:71494849T>C	ENST00000296755.7	+	5	5965	c.5667T>C	c.(5665-5667)taT>taC	p.Y1889Y		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1889					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ATTATGACTATGAGTCTTATG	0.468																																					p.Y1889Y	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T5667C						.						73	77	75					5																	71494849		2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			TGACTATGAGTCT	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.5667T>C	chr5.hg19:g.71494849T>C		54.0	0.0		48.0	27.0	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	hg19	CCDS4012.1																																																																																			.	.		0.468	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		C	71494849	T	C	71494849	2	2	68	1	0	0	0	0	0	0	0	1	9237	1471	51	2		2	MAP1B	5	71494849	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	54790082	71494849	109420411	59	8691										
VCAN	1462	hgsc.bcm.edu	37	chr5	82834673	82834673	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgtctcatcccatagcaaaaGaagaaacggtaatgatggaa	9	7	1	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:82834673G>A	ENST00000265077.3	+	8	6416	c.5851G>A	c.(5851-5853)Gaa>Aaa	p.E1951K	VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000343200.5_Missense_Mutation_p.E964K|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1951	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CATAGCAAAAGAAGAAACGGT	0.443																																					p.E1951K		Atlas-SNP	.											.	VCAN	498	.	0			c.G5851A						.						84	81	82					5																	82834673		2203	4300	6503	SO:0001583	missense	1462	exon8			GCAAAAGAAGAAA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.5851G>A	chr5.hg19:g.82834673G>A	ENSP00000265077:p.Glu1951Lys	66.0	0.0		56.0	14.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.672703	0.29693	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.87103	-2.18;-2.21;2.83	5.81	4.02	0.46733	.	0.507528	0.19438	N	0.114261	T	0.81997	0.4941	M	0.61703	1.905	0.19575	N	0.999964	P;D	0.54397	0.775;0.966	B;B	0.39660	0.306;0.265	T	0.75800	-0.3190	10	0.62326	D	0.03	.	5.3563	0.16063	0.2051:0.161:0.6339:0.0	.	964;1951	P13611-2;P13611	.;CSPG2_HUMAN	K	1951;964;964	ENSP00000265077:E1951K;ENSP00000340062:E964K;ENSP00000426251:E964K	ENSP00000265077:E1951K	E	+	1	0	VCAN	82870429	0.936000	0.31750	0.034000	0.17996	0.036000	0.12997	1.535000	0.36061	0.792000	0.33850	-0.218000	0.12543	GAA	.	.		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82834673	G	A	82834673	3	1	68	1	0	0	0	0	1	0	0	0	17153	943	33	3	5877	3	VCAN	5	82834673	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	11339824	82834673	98080587	60	8692										
GPR98	84059	hgsc.bcm.edu	37	chr5	89971058	89971058	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctggcccctttgtctccactAggcttgctgcagttctccac	8	16	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:89971058A>T	ENST00000405460.2	+	24	5206		c.e24-1		GPR98_ENST00000450321.2_Splice_Site	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98						detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TGTCTCCACTAGGCTTGCTGC	0.493																																					.		Atlas-SNP	.											.	GPR98	605	.	0			c.5111-2A>T						.						42	42	42					5																	89971058		2045	4208	6253	SO:0001630	splice_region_variant	84059	exon24			TCCACTAGGCTTG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.5111-1A>T	chr5.hg19:g.89971058A>T		82.0	0.0		59.0	23.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Splice_Site	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	13.93	2.382524	0.42207	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4972	0.75662	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPR98	90006814	1.000000	0.71417	0.944000	0.38274	0.162000	0.22319	8.712000	0.91403	2.120000	0.65058	0.533000	0.62120	.	.	.		0.493	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	Intron	T	89971058	A	T	89971058	5	4	68	1	0	0	0	0	0	0	1	0	6730	434	15	4	5203	4	GPR98	5	89971058	Splice_Site	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	7136385	89971058	90944202	61	8693										
TCF7	6932	hgsc.bcm.edu	37	chr5	133480499	133480499	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgtgagcagaccctggctcgCctaagaaatgccgtgctcgc	12	13	0	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:133480499C>T	ENST00000321584.4	+	10	1271				TCF7_ENST00000378560.4_Missense_Mutation_p.P248S|TCF7_ENST00000321603.6_Intron|TCF7_ENST00000395023.1_Intron|TCF7_ENST00000395029.1_Missense_Mutation_p.P363S|TCF7_ENST00000378564.1_Intron|TCF7_ENST00000518915.1_Intron|TCF7_ENST00000432532.2_Missense_Mutation_p.P248S|TCF7_ENST00000342854.5_Intron|TCF7_ENST00000520958.1_Intron			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)						alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCCTGGCTCGCCTAAGAAATG	0.602																																					p.P248S		Atlas-SNP	.											.	TCF7	81	.	0			c.C742T						.						104	105	104					5																	133480499		2110	4216	6326	SO:0001627	intron_variant	6932	exon9			GGCTCGCCTAAGA	Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.1076-933C>T	chr5.hg19:g.133480499C>T		218.0	0.0		107.0	38.0	NM_201634	B3KSH3|Q86WR9|Q9UKI4	Missense_Mutation	SNP	ENST00000321584.4	hg19		.	.	.	.	.	.	.	.	.	.	C	19.00	3.742881	0.69418	.	.	ENSG00000081059	ENST00000361590;ENST00000395029;ENST00000378560;ENST00000432532	D;D;D	0.99264	-5.63;-5.59;-5.65	5.97	5.97	0.96955	.	0.150059	0.43260	D	0.000588	D	0.99007	0.9661	L	0.39397	1.21	0.58432	D	0.999996	D	0.89917	1.0	D	0.83275	0.996	D	0.99222	1.0879	10	0.21540	T	0.41	.	20.428	0.99075	0.0:1.0:0.0:0.0	.	363	B7WNT5	.	S	363;363;248;248	ENSP00000378472:P363S;ENSP00000367822:P248S;ENSP00000397946:P248S	ENSP00000354863:P363S	P	+	1	0	TCF7	133508398	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.981000	0.70524	2.837000	0.97791	0.655000	0.94253	CCT	.	.		0.602	TCF7-201	KNOWN	basic	protein_coding	protein_coding		NM_201634		T	133480499	C	T	133480499	1	4	68	0	1	0	0	0	0	0	0	0	15711	739	26	3		3	TCF7	5	133480499	Intron	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	43509441	133480499	47434761	62	8694										
PITX1	5307	hgsc.bcm.edu	37	chr5	134364795	134364795	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	catggactgcgacgacagcgGgctcatggagttgaagaagg	16	8	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:134364795G>C	ENST00000265340.7	-	3	1035	c.619C>G	c.(619-621)Ccg>Gcg	p.P207A	PITX1_ENST00000506438.1_Missense_Mutation_p.P207A	NM_002653.4	NP_002644.4	P78337	PITX1_HUMAN	paired-like homeodomain 1	207	Interacts with PIT-1. {ECO:0000250}.				anatomical structure morphogenesis (GO:0009653)|branchiomeric skeletal muscle development (GO:0014707)|cartilage development (GO:0051216)|embryonic hindlimb morphogenesis (GO:0035116)|myoblast fate commitment (GO:0048625)|pituitary gland development (GO:0021983)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)			central_nervous_system(1)|cervix(3)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	READ - Rectum adenocarcinoma(2;0.0607)		GACGACAGCGGGCTCATGGAG	0.642																																					p.P207A		Atlas-SNP	.											.	PITX1	31	.	0			c.C619G						.						81	81	81					5																	134364795		2203	4300	6503	SO:0001583	missense	5307	exon3			ACAGCGGGCTCAT	AF009648	CCDS4182.1	5q31.1	2011-06-20	2007-07-12		ENSG00000069011	ENSG00000069011		"Homeoboxes / PRD class"	9004	protein-coding gene	gene with protein product		602149	"paired-like homeodomain transcription factor 1"	BFT		9337397, 9070926	Standard	NM_002653		Approved	PTX1, POTX	uc010jea.3	P78337	OTTHUMG00000149983	ENST00000265340.7:c.619C>G	chr5.hg19:g.134364795G>C	ENSP00000265340:p.Pro207Ala	193.0	0.0		122.0	46.0	NM_002653	A8K3M0|D3DQB0|O14677|O60425|Q9BTI5	Missense_Mutation	SNP	ENST00000265340.7	hg19	CCDS4182.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.182016	0.57800	.	.	ENSG00000069011	ENST00000265340;ENST00000506438	D;D	0.92805	-3.11;-3.11	4.39	4.39	0.52855	.	0.000000	0.85682	D	0.000000	D	0.95661	0.8589	M	0.77103	2.36	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	D	0.96144	0.9102	10	0.62326	D	0.03	.	15.9519	0.79846	0.0:0.0:1.0:0.0	.	207	P78337	PITX1_HUMAN	A	207	ENSP00000265340:P207A;ENSP00000427542:P207A	ENSP00000265340:P207A	P	-	1	0	PITX1	134392694	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.715000	0.84713	1.991000	0.58162	0.462000	0.41574	CCG	.	.		0.642	PITX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251195.3			C	134364795	G	C	134364795	3	2	68	1	0	0	0	0	1	0	0	0	11963	1232	43	4	329	4	PITX1	5	134364795	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	884296	134364795	46550465	63	8695										
PSD2	84249	hgsc.bcm.edu	37	chr5	139189340	139189340	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tggagggctggcgtgctggcAgagggggacaatgcttccag	19	8	0	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:139189340A>T	ENST00000274710.3	+	2	520	c.315A>T	c.(313-315)gcA>gcT	p.A105A		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	105					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGTGCTGGCAGAGGGGGACA	0.602																																					p.A105A		Atlas-SNP	.											.	PSD2	88	.	0			c.A315T						.						81	90	87					5																	139189340		2203	4300	6503	SO:0001819	synonymous_variant	84249	exon2			GCTGGCAGAGGGG	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.315A>T	chr5.hg19:g.139189340A>T		90.0	0.0		59.0	32.0	NM_032289	D3DQD3|Q8N3J8	Silent	SNP	ENST00000274710.3	hg19	CCDS4216.1																																																																																			.	.		0.602	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139189340	A	T	139189340	2	4	68	1	0	0	0	0	0	0	0	1	12659	175	7	4		4	PSD2	5	139189340	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	4824545	139189340	41725920	64	8696										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139909162	139909162	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttggcccagccacacttttcAatcacttcagcagtcttttt	5	13	4	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:139909162A>T	ENST00000360839.2	+	29	6785	c.6631A>T	c.(6631-6633)Aat>Tat	p.N2211Y	ANKHD1_ENST00000297183.6_Missense_Mutation_p.N2211Y|ANKHD1_ENST00000544120.1_Missense_Mutation_p.N594Y|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.N2211Y|SNORD45_ENST00000363181.1_RNA	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	2211						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACACTTTTCAATCACTTCAG	0.473																																					p.N2211Y		Atlas-SNP	.											.	ANKHD1	233	.	0			c.A6631T						.						155	150	152					5																	139909162		2203	4300	6503	SO:0001583	missense	54882	exon29			CTTTTCAATCACT	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.6631A>T	chr5.hg19:g.139909162A>T	ENSP00000354085:p.Asn2211Tyr	123.0	0.0		93.0	41.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.24|16.24	3.068127|3.068127	0.55539|0.55539	.|.	.|.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996;ENSG00000254996|ENSG00000131503	ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000433049;ENST00000544120;ENST00000532219;ENST00000437495|ENST00000435794;ENST00000432301	T;T;T;T;T;T;T|.	0.69306|.	-0.33;-0.39;1.74;1.74;1.32;-0.39;0.71|.	4.76|4.76	4.76|4.76	0.60689|0.60689	.|.	0.049886|.	0.85682|.	D|.	0.000000|.	T|T	0.68128|0.68128	0.2967|0.2967	L|L	0.53249|0.53249	1.67|1.67	0.58432|0.58432	D|D	0.99999|0.99999	D;D;D;D;D;D|.	0.76494|.	0.999;0.998;0.999;0.998;0.998;0.995|.	D;D;D;D;D;D|.	0.80764|.	0.993;0.988;0.987;0.99;0.994;0.991|.	T|T	0.66889|0.66889	-0.5809|-0.5809	10|5	0.54805|.	T|.	0.06|.	.|.	14.8011|14.8011	0.69916|0.69916	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	594;641;594;2211;2211;2211|.	Q8IWG5;Q9H059;F6WFL0;E9PF56;Q8IWZ2;Q8IWZ3|.	.;.;.;.;.;ANKH1_HUMAN|.	Y|L	2211;2211;2211;867;733;594;2211;222|701;661	ENSP00000354085:N2211Y;ENSP00000297183:N2211Y;ENSP00000393204:N867Y;ENSP00000390034:N733Y;ENSP00000437687:N594Y;ENSP00000432016:N2211Y;ENSP00000396882:N222Y|.	ENSP00000396882:N222Y|.	N|Q	+|+	1|2	0|0	ANKHD1-EIF4EBP3;ANKHD1|ANKHD1	139889346|139889346	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	5.543000|5.543000	0.67225|0.67225	2.154000|2.154000	0.67381|0.67381	0.477000|0.477000	0.44152|0.44152	AAT|CAA	.	.		0.473	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		T	139909162	A	T	139909162	3	4	68	1	0	0	0	0	1	0	0	0	628	130	5	4	6851	4	ANKHD1	5	139909162	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	719822	139909162	41006098	65	8697										
PCDHAC1	56135	hgsc.bcm.edu	37	chr5	140308516	140308516	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aggagggcagctttctgcccAgaacttgtatttagtaattg	11	7	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:140308516A>T	ENST00000253807.2	+	1	2039	c.2039A>T	c.(2038-2040)cAg>cTg	p.Q680L	PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.Q680L|PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA11_ENST00000398640.2_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	680					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTTCTGCCCAGAACTTGTAT	0.478																																					p.Q680L		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.A2039T						.						133	129	130					5																	140308516		2203	4300	6503	SO:0001583	missense	56135	exon1			CTGCCCAGAACTT	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"Cadherins / Protocadherins : Clustered"	8676	other	complex locus constituent	"PCDH-ALPHA-C1"	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.2039A>T	chr5.hg19:g.140308516A>T	ENSP00000253807:p.Gln680Leu	79.0	0.0		52.0	24.0	NM_031882	Q9Y5F5|Q9Y5I5	Missense_Mutation	SNP	ENST00000253807.2	hg19	CCDS4241.1	.	.	.	.	.	.	.	.	.	.	A	0.160	-1.081800	0.01888	.	.	ENSG00000248383	ENST00000409700;ENST00000253807	T;T	0.43294	0.95;0.98	5.95	-0.666	0.11399	.	.	.	.	.	T	0.12178	0.0296	N	0.03983	-0.305	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26883	-1.0090	9	0.02654	T	1	.	0.1142	0.00059	0.27:0.1856:0.2463:0.2982	.	680;680	Q9H158;Q9H158-2	PCDC1_HUMAN;.	L	680	ENSP00000386356:Q680L;ENSP00000253807:Q680L	ENSP00000253807:Q680L	Q	+	2	0	PCDHAC1	140288700	0.459000	0.25768	0.997000	0.53966	0.997000	0.91878	1.145000	0.31577	-0.080000	0.12685	0.460000	0.39030	CAG	.	.		0.478	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		T	140308516	A	T	140308516	3	4	68	1	0	0	0	0	1	0	0	0	11541	188	7	4	2041	4	PCDHAC1	5	140308516	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	399354	140308516	40606744	66	8698										
SLC36A3	285641	hgsc.bcm.edu	37	chr5	150663626	150663626	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	agcaattgggcaagttgaggGtgatgctggcctgggtgtct	17	6	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:150663626G>T	ENST00000335230.3	-	8	1364	c.953C>A	c.(952-954)aCc>aAc	p.T318N	SLC36A3_ENST00000377713.3_Missense_Mutation_p.T359N	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	318						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAAGTTGAGGGTGATGCTGGC	0.502																																					p.T359N		Atlas-SNP	.											.	SLC36A3	54	.	0			c.C1076A						.						176	149	158					5																	150663626		2203	4300	6503	SO:0001583	missense	285641	exon9			TTGAGGGTGATGC	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"Solute carriers"	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.953C>A	chr5.hg19:g.150663626G>T	ENSP00000334750:p.Thr318Asn	145.0	0.0		111.0	49.0	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Missense_Mutation	SNP	ENST00000335230.3	hg19	CCDS4314.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.083773	0.76642	.	.	ENSG00000186334	ENST00000335230;ENST00000377713	T;T	0.02682	4.2;4.2	4.2	3.32	0.38043	.	0.160048	0.52532	D	0.000061	T	0.21962	0.0529	H	0.95884	3.735	0.58432	D	0.999994	D;D;D	0.69078	0.996;0.997;0.993	D;D;D	0.73380	0.945;0.98;0.966	T	0.21008	-1.0258	10	0.87932	D	0	.	12.8121	0.57645	0.084:0.0:0.916:0.0	.	359;318;303	Q495N2-3;Q495N2;Q495N2-2	.;S36A3_HUMAN;.	N	318;359	ENSP00000334750:T318N;ENSP00000366942:T359N	ENSP00000334750:T318N	T	-	2	0	SLC36A3	150643819	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.780000	0.62382	2.348000	0.79779	0.655000	0.94253	ACC	.	.		0.502	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774		T	150663626	G	T	150663626	3	4	68	1	0	0	0	0	1	0	0	0	14610	1261	44	3	471	3	SLC36A3	5	150663626	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	10355110	150663626	30251634	67	8699										
MGAT1	4245	hgsc.bcm.edu	37	chr5	180218676	180218676	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ccctcccacgtcagtgggggCgccaggtggacacggcggcc	16	16	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr5:180218676C>T	ENST00000446023.2	-	3	2046	c.1296G>A	c.(1294-1296)gcG>gcA	p.A432A	MGAT1_ENST00000427865.2_Silent_p.A432A|MGAT1_ENST00000307826.4_Silent_p.A432A|MGAT1_ENST00000393340.3_Silent_p.A432A|MGAT1_ENST00000333055.3_Silent_p.A432A	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	432					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCAGTGGGGGCGCCAGGTGGA	0.622																																					p.A432A		Atlas-SNP	.											.	MGAT1	48	.	0			c.G1296A						.						39	41	40					5																	180218676		2203	4300	6503	SO:0001819	synonymous_variant	4245	exon3			TGGGGGCGCCAGG	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.1296G>A	chr5.hg19:g.180218676C>T		282.0	0.0		213.0	96.0	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Silent	SNP	ENST00000446023.2	hg19	CCDS4458.1																																																																																			.	.		0.622	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618		T	180218676	C	T	180218676	2	4	68	1	0	0	0	0	0	0	0	1	9551	755	27	1		1	MGAT1	5	180218676	Silent	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	29555050	180218676	696584	68	8700										
BAT5	7920	hgsc.bcm.edu	37	chr6	31660873	31660873	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctgtcccccggtgcaggggcTctgggcgaagcagggccaca	16	14	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr6:31660873T>A	ENST00000395952.3	-	7	719	c.557A>T	c.(556-558)gAg>gTg	p.E186V	ABHD16A_ENST00000538874.1_Missense_Mutation_p.S88C|ABHD16A_ENST00000375842.4_5'UTR|ABHD16A_ENST00000440843.2_Missense_Mutation_p.E153V|ABHD16A_ENST00000471644.1_5'Flank|XXbac-BPG32J3.20_ENST00000461287.1_3'UTR	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	186						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						GTGCAGGGGCTCTGGGCGAAG	0.637																																					p.E186V		Atlas-SNP	.											.	ABHD16A	34	.	0			c.A557T						.						44	44	44					6																	31660873		2203	4300	6503	SO:0001583	missense	7920	exon7			AGGGGCTCTGGGC	AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"Abhydrolase domain containing"	13921	protein-coding gene	gene with protein product		142620	"HLA-B associated transcript 5"	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.557A>T	chr6.hg19:g.31660873T>A	ENSP00000379282:p.Glu186Val	80.0	0.0		69.0	53.0	NM_021160	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Missense_Mutation	SNP	ENST00000395952.3	hg19	CCDS4713.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.3|26.3	4.723270|4.723270	0.89298|0.89298	.|.	.|.	ENSG00000204427|ENSG00000204427	ENST00000395952;ENST00000440843|ENST00000538874	.|.	.|.	.|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.053058|.	0.64402|.	D|.	0.000001|.	T|T	0.56171|0.56171	0.1967|0.1967	L|L	0.49350|0.49350	1.555|1.555	0.32386|0.32386	N|N	0.553967|0.553967	B;P|D	0.48911|0.76494	0.346;0.917|0.999	B;B|D	0.44315|0.65874	0.077;0.446|0.939	T|T	0.62751|0.62751	-0.6788|-0.6788	9|8	0.56958|0.87932	D|D	0.05|0	-22.2172|-22.2172	13.8019|13.8019	0.63206|0.63206	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	153;186|88	B7Z4R6;O95870|B7Z8I9	.;ABHGA_HUMAN|.	V|C	186;153|88	.|.	ENSP00000379282:E186V|ENSP00000442151:S88C	E|S	-|-	2|1	0|0	ABHD16A|ABHD16A	31768852|31768852	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.017000|5.017000	0.64047|0.64047	2.144000|2.144000	0.66660|0.66660	0.459000|0.459000	0.35465|0.35465	GAG|AGC	.	.		0.637	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4			A	31660873	T	A	31660873	3	1	68	1	0	0	0	0	1	0	0	0	1324	1551	54	4	1175	4	BAT5	6	31660873	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		31660873	139454194	69	8701										
PSMB9	5698	hgsc.bcm.edu	37	chr6	32826201	32826201	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttgccattggtggctccggcAgcacctttatctatggttat	10	10	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr6:32826201A>T	ENST00000374859.2	+	5	520	c.451A>T	c.(451-453)Agc>Tgc	p.S151C	PSMB9_ENST00000453265.2_Missense_Mutation_p.S107C|PSMB9_ENST00000395330.1_Missense_Mutation_p.S128C	NM_002800.4	NP_002791.1	P28065	PSB9_HUMAN	proteasome (prosome, macropain) subunit, beta type, 9	151					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			large_intestine(4)|lung(4)|skin(1)	9					Carfilzomib(DB08889)	TGGCTCCGGCAGCACCTTTAT	0.527																																					p.S151C		Atlas-SNP	.											.	PSMB9	16	.	0			c.A451T						.						89	100	96					6																	32826201		1508	2708	4216	SO:0001583	missense	5698	exon5			TCCGGCAGCACCT		CCDS4759.1	6p21.3	2013-03-27	2013-03-27		ENSG00000240065	ENSG00000240065		"Proteasome (prosome, macropain) subunits"	9546	protein-coding gene	gene with protein product		177045	"proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional protease 2)", "large multifunctional peptidase 2"	LMP2		1922385, 1529427	Standard	NM_002800		Approved	RING12, beta1i, PSMB6i	uc003sga.3	P28065	OTTHUMG00000031287	ENST00000374859.2:c.451A>T	chr6.hg19:g.32826201A>T	ENSP00000363993:p.Ser151Cys	94.0	0.0		75.0	31.0	NM_002800	B0V0T1|Q16523|Q5JNW4	Missense_Mutation	SNP	ENST00000374859.2	hg19	CCDS4759.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443498	0.83993	.	.	ENSG00000240065	ENST00000395330;ENST00000414474;ENST00000374859;ENST00000453265;ENST00000395333	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.63390	0.2507	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.72191	-0.4365	10	0.87932	D	0	-0.7704	12.7006	0.57029	1.0:0.0:0.0:0.0	.	107;151	B4DZW2;P28065	.;PSB9_HUMAN	C	128;128;151;107;107	ENSP00000378739:S128C;ENSP00000394363:S128C;ENSP00000363993:S151C;ENSP00000394773:S107C	ENSP00000363993:S151C	S	+	1	0	PSMB9	32934179	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	8.158000	0.89649	2.155000	0.67459	0.523000	0.50628	AGC	.	.		0.527	PSMB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076624.5	NM_002800		T	32826201	A	T	32826201	3	4	68	1	0	0	0	0	1	0	0	0	12696	188	7	4	469	4	PSMB9	6	32826201	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	1165328	32826201	138288866	70	8702										
DEF6	50619	hgsc.bcm.edu	37	chr6	35280290	35280290	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	catccacgaggtctaccaggAgctcatccaagatgtcctga	9	13	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr6:35280290A>T	ENST00000316637.5	+	4	640	c.635A>T	c.(634-636)gAg>gTg	p.E212V	DEF6_ENST00000542066.1_Intron	NM_022047.3	NP_071330.3	Q9H4E7	DEFI6_HUMAN	differentially expressed in FDCP 6 homolog (mouse)	212						cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	15						GTCTACCAGGAGCTCATCCAA	0.632																																					p.E212V		Atlas-SNP	.											.	DEF6	36	.	0			c.A635T						.						35	39	37					6																	35280290		2203	4300	6503	SO:0001583	missense	50619	exon4			ACCAGGAGCTCAT	AJ276095	CCDS4802.1	6p21.33-p21.1	2013-01-10	2001-11-28		ENSG00000023892	ENSG00000023892		"Pleckstrin homology (PH) domain containing"	2760	protein-coding gene	gene with protein product	"SWAP-70-like adaptor protein of T cells"	610094	"differentially expressed in FDCP (mouse homolog) 6"			19251698	Standard	NM_022047		Approved	IBP, SLAT, SWAP70L	uc003okk.3	Q9H4E7	OTTHUMG00000014563	ENST00000316637.5:c.635A>T	chr6.hg19:g.35280290A>T	ENSP00000319831:p.Glu212Val	167.0	0.0		93.0	76.0	NM_022047	Q86VF4	Missense_Mutation	SNP	ENST00000316637.5	hg19	CCDS4802.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.566612	0.86439	.	.	ENSG00000023892	ENST00000394658;ENST00000316637	T	0.23754	1.89	5.52	4.32	0.51571	.	0.046069	0.85682	D	0.000000	T	0.44138	0.1279	M	0.85945	2.785	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.991	T	0.54330	-0.8310	10	0.87932	D	0	-34.0732	12.7379	0.57236	0.8627:0.1373:0.0:0.0	.	212;212	B2RBP7;Q9H4E7	.;DEFI6_HUMAN	V	175;212	ENSP00000319831:E212V	ENSP00000319831:E212V	E	+	2	0	DEF6	35388268	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.213000	0.95133	0.991000	0.38814	0.533000	0.62120	GAG	.	.		0.632	DEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040276.1	NM_022047		T	35280290	A	T	35280290	3	4	68	1	0	0	0	0	1	0	0	0	4388	304	11	4	649	4	DEF6	6	35280290	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	2454089	35280290	135834777	71	8703										
NCR2	9436	hgsc.bcm.edu	37	chr6	41309647	41309647	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	caagcccctgagtctccatcTaccatccctgtcccttcaca	4	19	3	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr6:41309647T>C	ENST00000373089.5	+	3	598	c.510T>C	c.(508-510)tcT>tcC	p.S170S	NCR2_ENST00000373083.4_Silent_p.S170S|NCR2_ENST00000373086.3_Silent_p.S170S	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	170					cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	14	Ovarian(28;0.0327)|Colorectal(47;0.196)					AGTCTCCATCTACCATCCCTG	0.642																																					p.S170S		Atlas-SNP	.											.	NCR2	44	.	0			c.T510C						.						103	95	98					6																	41309647		2203	4300	6503	SO:0001819	synonymous_variant	9436	exon3			TCCATCTACCATC	AJ225109	CCDS4855.1, CCDS56428.1, CCDS56429.1	6p21.1	2013-01-11	2002-11-13	2002-11-15	ENSG00000096264	ENSG00000096264		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	6732	protein-coding gene	gene with protein product		604531	"lymphocyte antigen 95 (activating NK-receptor; NK-p44)"	LY95		10049942	Standard	NM_004828		Approved	NK-p44, CD336	uc003oqh.2	O95944	OTTHUMG00000014678	ENST00000373089.5:c.510T>C	chr6.hg19:g.41309647T>C		106.0	0.0		63.0	50.0	NM_004828	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Silent	SNP	ENST00000373089.5	hg19	CCDS4855.1																																																																																			.	.		0.642	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3			C	41309647	T	C	41309647	2	2	68	1	0	0	0	0	0	0	0	1	10247	1509	53	2		2	NCR2	6	41309647	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	6029357	41309647	129805420	72	8704										
FRK	2444	hgsc.bcm.edu	37	chr6	116277657	116277657	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tccatgtctcatcaactctgTaataatataaattggatctt	4	8	4	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr6:116277657T>A	ENST00000606080.1	-	5	1362	c.916A>T	c.(916-918)Aca>Tca	p.T306S	FRK_ENST00000538210.1_Missense_Mutation_p.T164S	NM_002031.2	NP_002022.1	P42685	FRK_HUMAN	fyn-related Src family tyrosine kinase	306	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|skin(1)|urinary_tract(1)	27		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	Regorafenib(DB08896)	ATCAACTCTGTAATAATATAA	0.353																																					p.T306S		Atlas-SNP	.											.	FRK	78	.	0			c.A916T						.						95	102	100					6																	116277657		2203	4300	6503	SO:0001583	missense	2444	exon5			ACTCTGTAATAAT	U00803	CCDS5103.1	6q21-q22.3	2014-06-25	2014-06-25		ENSG00000111816	ENSG00000111816	2.7.10.1	"SH2 domain containing"	3955	protein-coding gene	gene with protein product		606573	"PTK5 protein tyrosine kinase 5", "fyn-related kinase"	PTK5		7510261	Standard	NM_002031		Approved	RAK, GTK	uc003pwi.1	P42685	OTTHUMG00000015424	ENST00000606080.1:c.916A>T	chr6.hg19:g.116277657T>A	ENSP00000476145:p.Thr306Ser	63.0	0.0		31.0	12.0	NM_002031	B4DY49|Q13128|Q9NTR5	Missense_Mutation	SNP	ENST00000606080.1	hg19	CCDS5103.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.743712	0.89663	.	.	ENSG00000111816	ENST00000368626;ENST00000538210	T;T	0.35789	1.29;1.29	5.74	5.74	0.90152	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.48333	0.1494	L	0.55481	1.735	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.51919	-0.8644	10	0.72032	D	0.01	.	16.0351	0.80621	0.0:0.0:0.0:1.0	.	306	P42685	FRK_HUMAN	S	306;164	ENSP00000357615:T306S;ENSP00000443075:T164S	ENSP00000357615:T306S	T	-	1	0	FRK	116384350	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.186000	0.69663	0.533000	0.62120	ACA	.	.		0.353	FRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041924.2	NM_002031		A	116277657	T	A	116277657	3	1	68	1	0	0	0	0	1	0	0	0	6056	1638	57	4	617	4	FRK	6	116277657	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	74968010	116277657	54837410	73	8705										
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143092423	143092423	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	atctgtggctgggccaggtgCagtggccccgagctcagcgg	17	12	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr6:143092423C>A	ENST00000367604.1	-	4	4092	c.3453G>T	c.(3451-3453)ctG>ctT	p.L1151L	HIVEP2_ENST00000012134.2_Silent_p.L1151L|HIVEP2_ENST00000367603.2_Silent_p.L1151L			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GGGCCAGGTGCAGTGGCCCCG	0.587																																					p.L1151L	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.G3453T						.						60	66	64					6																	143092423		2014	4195	6209	SO:0001819	synonymous_variant	3097	exon5			CAGGTGCAGTGGC	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.3453G>T	chr6.hg19:g.143092423C>A		88.0	0.0		91.0	35.0	NM_006734	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	hg19	CCDS43510.1																																																																																			.	.		0.587	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			A	143092423	C	A	143092423	2	1	68	1	0	0	0	0	0	0	0	1	7196	697	25	3		3	HIVEP2	6	143092423	Silent	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	26814766	143092423	28022644	74	8706										
TIAM2	26230	hgsc.bcm.edu	37	chr6	155569180	155569180	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tttctggacgcccggaacccCaccaagcagcattcctccac	7	18	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr6:155569180C>T	ENST00000461783.3	+	22	4972	c.3699C>T	c.(3697-3699)ccC>ccT	p.P1233P	TIAM2_ENST00000456877.2_Silent_p.P545P|TIAM2_ENST00000529824.2_Silent_p.P1233P|TIAM2_ENST00000456144.1_Silent_p.P1233P|TIAM2_ENST00000528391.2_Silent_p.P569P|TIAM2_ENST00000367174.2_Silent_p.P609P|TIAM2_ENST00000360366.4_Silent_p.P1257P|TIAM2_ENST00000318981.5_Silent_p.P1233P|TIAM2_ENST00000275246.7_Silent_p.P158P			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1233	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		CCCGGAACCCCACCAAGCAGC	0.527											OREG0017745	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P1233P		Atlas-SNP	.											.	TIAM2	161	.	0			c.C3699T						.						75	74	75					6																	155569180		2203	4300	6503	SO:0001819	synonymous_variant	26230	exon19			GAACCCCACCAAG		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.3699C>T	chr6.hg19:g.155569180C>T		125.0	0.0	1771	83.0	69.0	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	hg19	CCDS34558.1																																																																																			.	.		0.527	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155569180	C	T	155569180	2	4	68	1	0	0	0	0	0	0	0	1	15906	581	21	3		3	TIAM2	6	155569180	Silent	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	12476757	155569180	15545887	75	8707										
CARD11	84433	hgsc.bcm.edu	37	chr7	2984108	2984108	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gcaggtccttggccttcatcTgctgctgcagcttgatgacc	11	13	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:2984108T>A	ENST00000396946.4	-	5	825	c.422A>T	c.(421-423)cAg>cTg	p.Q141L	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	141					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GGCCTTCATCTGCTGCTGCAG	0.622			Mis		DLBCL																																p.Q141L		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.A422T						.						91	83	86					7																	2984108		2203	4300	6503	SO:0001583	missense	84433	exon5			TTCATCTGCTGCT	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.422A>T	chr7.hg19:g.2984108T>A	ENSP00000380150:p.Gln141Leu	102.0	0.0		79.0	33.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	15.23	2.772177	0.49680	.	.	ENSG00000198286	ENST00000396946	T	0.35973	1.28	4.38	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.44117	0.1278	L	0.47716	1.5	0.58432	D	0.99999	P	0.45634	0.863	P	0.51582	0.674	T	0.43653	-0.9378	10	0.62326	D	0.03	-32.9619	13.9133	0.63881	0.0:0.0:0.0:1.0	.	141	Q9BXL7	CAR11_HUMAN	L	141	ENSP00000380150:Q141L	ENSP00000380150:Q141L	Q	-	2	0	CARD11	2950634	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.477000	0.81069	1.750000	0.51863	0.533000	0.62120	CAG	.	.		0.622	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2984108	T	A	2984108	3	1	68	1	0	0	0	0	1	0	0	0	2647	1580	55	4	3126	4	CARD11	7	2984108	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		2984108	156154555	76	8708										
SDK1	221935	hgsc.bcm.edu	37	chr7	4188918	4188918	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gccggcaccccccagagagcTcctggtgccccaggcagaag	13	17	0	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:4188918T>A	ENST00000404826.2	+	30	4587	c.4448T>A	c.(4447-4449)cTc>cAc	p.L1483H	SDK1_ENST00000389531.3_Missense_Mutation_p.L1483H	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1483	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CCCAGAGAGCTCCTGGTGCCC	0.667																																					p.L1483H		Atlas-SNP	.											.	SDK1	361	.	0			c.T4448A						.						22	25	24					7																	4188918		2203	4300	6503	SO:0001583	missense	221935	exon30			GAGAGCTCCTGGT	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4448T>A	chr7.hg19:g.4188918T>A	ENSP00000385899:p.Leu1483His	75.0	0.0		54.0	16.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.126943	0.56721	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.59364	0.27;0.27	5.06	5.06	0.68205	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000043	T	0.73079	0.3541	M	0.78456	2.415	0.09310	N	0.999994	D;D	0.89917	0.998;1.0	D;D	0.74674	0.919;0.984	T	0.66642	-0.5872	10	0.72032	D	0.01	.	9.3635	0.38210	0.0:0.0805:0.0:0.9195	.	1483;1483	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	H	1483	ENSP00000385899:L1483H;ENSP00000374182:L1483H	ENSP00000374182:L1483H	L	+	2	0	SDK1	4155444	0.732000	0.28121	0.998000	0.56505	0.935000	0.57460	2.273000	0.43381	1.907000	0.55213	0.460000	0.39030	CTC	.	.		0.667	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		A	4188918	T	A	4188918	3	1	68	1	0	0	0	0	1	0	0	0	13983	1551	54	4	4566	4	SDK1	7	4188918	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	1204810	4188918	154949745	77	8709										
SDK1	221935	hgsc.bcm.edu	37	chr7	4201422	4201422	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctcctgtgtgtttcagttccAggagagcccccgggatctgt	12	12	2	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:4201422A>T	ENST00000404826.2	+	32	4873	c.4734A>T	c.(4732-4734)ccA>ccT	p.P1578P	SDK1_ENST00000389531.3_Silent_p.P1578P	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1578					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TTTCAGTTCCAGGAGAGCCCC	0.602																																					p.P1578P		Atlas-SNP	.											.	SDK1	361	.	0			c.A4734T						.						112	101	105					7																	4201422		2203	4300	6503	SO:0001819	synonymous_variant	221935	exon32			AGTTCCAGGAGAG	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4734A>T	chr7.hg19:g.4201422A>T		134.0	0.0		90.0	39.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	hg19	CCDS34590.1																																																																																			.	.		0.602	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4201422	A	T	4201422	2	4	68	1	0	0	0	0	0	0	0	1	13983	175	7	4		4	SDK1	7	4201422	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	12504	4201422	154937241	78	8710										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20698148	20698148	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gaaatttaatacattggtagGggaaaaaggagctcaaatga	11	3	1	1	rs199505251		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:20698148G>T	ENST00000404938.2	+	14	2208	c.1556G>T	c.(1555-1557)gGg>gTg	p.G519V	ABCB5_ENST00000443026.2_Missense_Mutation_p.G74V|ABCB5_ENST00000406935.1_Missense_Mutation_p.G74V|ABCB5_ENST00000258738.6_Missense_Mutation_p.G74V	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	519	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						ACATTGGTAGGGGAAAAAGGA	0.418																																					p.G519V		Atlas-SNP	.											.	ABCB5	357	.	0			c.G1556T						.						89	83	85					7																	20698148		2203	4300	6503	SO:0001583	missense	340273	exon14			TGGTAGGGGAAAA	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.1556G>T	chr7.hg19:g.20698148G>T	ENSP00000384881:p.Gly519Val	55.0	0.0		25.0	11.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.882530	0.91740	.	.	ENSG00000004846	ENST00000404938;ENST00000443026;ENST00000406935;ENST00000258738	D;D;D;D	0.92249	-2.31;-3.0;-3.0;-2.31	5.86	5.86	0.93980	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.64402	D	0.000016	D	0.96883	0.8982	M	0.88979	2.995	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;0.998	D	0.96886	0.9649	10	0.87932	D	0	.	19.5509	0.95319	0.0:0.0:1.0:0.0	.	74;519;74;74	B5MD19;A7BKA4;Q2M3G0;Q2M3G0-2	.;.;ABCB5_HUMAN;.	V	519;74;74;74	ENSP00000384881:G519V;ENSP00000406730:G74V;ENSP00000383899:G74V;ENSP00000258738:G74V	ENSP00000258738:G74V	G	+	2	0	ABCB5	20664673	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	9.618000	0.98365	2.937000	0.99478	0.650000	0.86243	GGG	.	G|0.999;A|0.001		0.418	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		T	20698148	G	T	20698148	3	4	68	1	0	0	0	0	1	0	0	0	44	1232	43	3	1606	3	ABCB5	7	20698148	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	16496726	20698148	138440515	79	8711										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20762841	20762841	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	agaacttaagcatgctggaaAggtaaaatgaagactgttat	10	4	0	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:20762841A>T	ENST00000404938.2	+	21	3276	c.2624A>T	c.(2623-2625)aAg>aTg	p.K875M	ABCB5_ENST00000258738.6_Splice_Site_p.K430M	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	875	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						CATGCTGGAAAGGTAAAATGA	0.363																																					p.K875M		Atlas-SNP	.											.	ABCB5	357	.	0			c.A2624T						.						82	77	78					7																	20762841		2203	4300	6503	SO:0001630	splice_region_variant	340273	exon21			CTGGAAAGGTAAA	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.2625+1A>T	chr7.hg19:g.20762841A>T		77.0	0.0		44.0	6.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	A	18.42	3.619024	0.66787	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.90620	-2.7;-2.7	4.85	4.85	0.62838	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.64402	D	0.000007	D	0.95430	0.8516	M	0.86805	2.84	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.995;0.999	D	0.95924	0.8933	10	0.87932	D	0	.	12.724	0.57159	1.0:0.0:0.0:0.0	.	875;53;430	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	M	875;430	ENSP00000384881:K875M;ENSP00000258738:K430M	ENSP00000258738:K430M	K	+	2	0	ABCB5	20729366	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.714000	0.68422	2.175000	0.68902	0.533000	0.62120	AAG	.	.		0.363	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	Missense_Mutation	T	20762841	A	T	20762841	5	4	68	1	0	0	0	0	0	0	1	0	44	86	3	4	2743	4	ABCB5	7	20762841	Splice_Site	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	64693	20762841	138375822	80	8712										
TBX20	57057	hgsc.bcm.edu	37	chr7	35293206	35293206	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tggcccgagaggagagttggGgcttgggggacgccgtgaac	20	8	0	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:35293206G>T	ENST00000408931.3	-	1	552	c.26C>A	c.(25-27)cCc>cAc	p.P9H		NM_001077653.2|NM_001166220.1	NP_001071121.1|NP_001159692.1	Q9UMR3	TBX20_HUMAN	T-box 20	9					aortic valve morphogenesis (GO:0003180)|atrial septum morphogenesis (GO:0060413)|blood circulation (GO:0008015)|cardiac chamber formation (GO:0003207)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|dorsal/ventral pattern formation (GO:0009953)|embryonic heart tube elongation (GO:0036306)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion formation (GO:0003272)|endocardial cushion morphogenesis (GO:0003203)|endoderm formation (GO:0001706)|foramen ovale closure (GO:0035922)|heart looping (GO:0001947)|lateral mesoderm formation (GO:0048370)|muscle contraction (GO:0006936)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|outflow tract septum morphogenesis (GO:0003148)|patterning of blood vessels (GO:0001569)|pericardium morphogenesis (GO:0003344)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve formation (GO:0003193)|pulmonary vein morphogenesis (GO:0060577)|tricuspid valve development (GO:0003175)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(9)|prostate(1)|skin(1)|stomach(1)	18						GGAGAGTTGGGGCTTGGGGGA	0.637																																					p.P9H		Atlas-SNP	.											.	TBX20	96	.	0			c.C26A						.						48	50	50					7																	35293206		2203	4300	6503	SO:0001583	missense	57057	exon1			AGTTGGGGCTTGG	AJ237589	CCDS43568.1	7p14.3	2014-09-17			ENSG00000164532	ENSG00000164532		"T-boxes"	11598	protein-coding gene	gene with protein product		606061				10936053	Standard	NM_001077653		Approved		uc011kas.2	Q9UMR3	OTTHUMG00000099411	ENST00000408931.3:c.26C>A	chr7.hg19:g.35293206G>T	ENSP00000386170:p.Pro9His	46.0	0.0		29.0	12.0	NM_001077653	A4D1Y6|Q000T4|Q0IJ70|Q0VAS1|Q9Y2N5	Missense_Mutation	SNP	ENST00000408931.3	hg19	CCDS43568.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.174865	0.78564	.	.	ENSG00000164532	ENST00000408931	D	0.88354	-2.37	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.91307	0.7259	L	0.29908	0.895	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.92734	0.6202	10	0.87932	D	0	.	18.0684	0.89398	0.0:0.0:1.0:0.0	.	9	Q9UMR3	TBX20_HUMAN	H	9	ENSP00000386170:P9H	ENSP00000386170:P9H	P	-	2	0	TBX20	35259731	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	9.414000	0.97362	2.349000	0.79799	0.462000	0.41574	CCC	.	.		0.637	TBX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216870.2	NM_020417		T	35293206	G	T	35293206	3	4	68	1	0	0	0	0	1	0	0	0	15671	1232	43	3	1350	3	TBX20	7	35293206	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	14530365	35293206	123845457	81	8713										
GLI3	2737	hgsc.bcm.edu	37	chr7	42088201	42088201	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gtagggatgtggagggctgaAgggagactcggaagcagcag	20	5	0	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:42088201A>T	ENST00000395925.3	-	5	652	c.568T>A	c.(568-570)Ttc>Atc	p.F190I	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	190					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GGAGGGCTGAAGGGAGACTCG	0.567									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.F190I		Atlas-SNP	.											.	GLI3	312	.	0			c.T568A						.						152	155	154					7																	42088201		2203	4300	6503	SO:0001583	missense	2737	exon5	Familial Cancer Database	;	GGCTGAAGGGAGA		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.568T>A	chr7.hg19:g.42088201A>T	ENSP00000379258:p.Phe190Ile	240.0	0.0		167.0	55.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	A	36	5.633993	0.96682	.	.	ENSG00000106571	ENST00000395925	T	0.46063	0.88	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.43100	0.1232	M	0.67397	2.05	0.80722	D	1	P	0.39862	0.692	B	0.34590	0.186	T	0.50734	-0.8793	10	0.72032	D	0.01	.	16.003	0.80308	1.0:0.0:0.0:0.0	.	190	P10071	GLI3_HUMAN	I	190	ENSP00000379258:F190I	ENSP00000379258:F190I	F	-	1	0	GLI3	42054726	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.328000	0.96403	2.247000	0.74100	0.482000	0.46254	TTC	.	.		0.567	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42088201	A	T	42088201	3	4	68	1	0	0	0	0	1	0	0	0	6447	72	3	4	4218	4	GLI3	7	42088201	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	6794995	42088201	117050462	82	8714										
POM121L12	285877	hgsc.bcm.edu	37	chr7	53103631	53103631	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	acccaggaccccgccaagccGcagcgggtggtctccgaggg	15	16	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:53103631G>A	ENST00000408890.4	+	1	283	c.267G>A	c.(265-267)ccG>ccA	p.P89P		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	89								p.P89P(1)		endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CCGCCAAGCCGCAGCGGGTGG	0.697																																					p.P89P		Atlas-SNP	.											POM121L12,NS,carcinoma,0,1	POM121L12	146	.	1	Substitution - coding silent(1)	lung(1)	c.G267A						.						14	17	16					7																	53103631		1855	4063	5918	SO:0001819	synonymous_variant	285877	exon1			CAAGCCGCAGCGG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.267G>A	chr7.hg19:g.53103631G>A		22.0	1.0		29.0	15.0	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	hg19	CCDS43584.1																																																																																			.	.		0.697	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		A	53103631	G	A	53103631	2	1	68	1	0	0	0	0	0	0	0	1	12250	1074	38	1		1	POM121L12	7	53103631	Silent	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	11015430	53103631	106035032	83	8715										
ASNS	440	hgsc.bcm.edu	37	chr7	97484710	97484710	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gtaagttcatctgatccttcTccagagaagatcaccacgct	7	12	4	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:97484710T>A	ENST00000394309.3	-	9	1563	c.1092A>T	c.(1090-1092)ggA>ggT	p.G364G	ASNS_ENST00000175506.4_Silent_p.G364G|ASNS_ENST00000394308.3_Silent_p.G364G|ASNS_ENST00000437628.1_Silent_p.G281G|ASNS_ENST00000444334.1_Silent_p.G343G|ASNS_ENST00000455086.1_Silent_p.G281G|ASNS_ENST00000422745.1_Silent_p.G343G	NM_133436.3	NP_597680.2	P08243	ASNS_HUMAN	asparagine synthetase (glutamine-hydrolyzing)	364	Asparagine synthetase.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|asparagine biosynthetic process (GO:0006529)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular protein metabolic process (GO:0044267)|cellular response to glucose starvation (GO:0042149)|cellular response to hormone stimulus (GO:0032870)|endoplasmic reticulum unfolded protein response (GO:0030968)|glutamine metabolic process (GO:0006541)|L-asparagine biosynthetic process (GO:0070981)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|positive regulation of mitotic cell cycle (GO:0045931)|response to amino acid (GO:0043200)|response to follicle-stimulating hormone (GO:0032354)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)|ATP binding (GO:0005524)|cofactor binding (GO:0048037)			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	CTGATCCTTCTCCAGAGAAGA	0.343																																					p.G364G	Melanoma(70;6 1280 3108 3799 51123)|GBM(6;275 291 425 9929 27738)	Atlas-SNP	.											.	ASNS	97	.	0			c.A1092T						.						107	100	103					7																	97484710		2203	4300	6503	SO:0001819	synonymous_variant	440	exon9			TCCTTCTCCAGAG	M27396	CCDS5652.1, CCDS55131.1, CCDS55132.1	7q21.3	2012-10-02	2010-05-07		ENSG00000070669	ENSG00000070669	6.3.5.4		753	protein-coding gene	gene with protein product		108370	"asparagine synthetase"				Standard	NM_001673		Approved		uc003uov.4	P08243	OTTHUMG00000022892	ENST00000394309.3:c.1092A>T	chr7.hg19:g.97484710T>A		32.0	0.0		45.0	13.0	NM_133436	A4D1I8|B4DXZ1|B7ZAA9|D6W5R3|E9PCI3|E9PCX6|P08184|Q15666|Q549T9|Q96HD0	Silent	SNP	ENST00000394309.3	hg19	CCDS5652.1																																																																																			.	.		0.343	ASNS-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333645.1	NM_001673, NM_183356		A	97484710	T	A	97484710	2	1	68	1	0	0	0	0	0	0	0	1	1048	1538	54	4		4	ASNS	7	97484710	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	44381079	97484710	61653953	84	8716										
LMOD2	442721	hgsc.bcm.edu	37	chr7	123302237	123302237	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgtggaaatcctacagtgatTgaggacgctttggacaagat	12	6	0	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:123302237T>A	ENST00000458573.2	+	2	754	c.597T>A	c.(595-597)atT>atA	p.I199I	LMOD2_ENST00000456238.2_Intron	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	199						cytoskeleton (GO:0005856)											CTACAGTGATTGAGGACGCTT	0.433																																					p.I199I		Atlas-SNP	.											.	LMOD2	62	.	0			c.T597A						.						61	60	60					7																	123302237		2016	4176	6192	SO:0001819	synonymous_variant	442721	exon2			AGTGATTGAGGAC	AC006333	CCDS47693.1	7q31.32	2008-08-08			ENSG00000170807	ENSG00000170807			6648	protein-coding gene	gene with protein product		608006					Standard	NM_207163		Approved		uc003vky.2	Q6P5Q4	OTTHUMG00000157149	ENST00000458573.2:c.597T>A	chr7.hg19:g.123302237T>A		97.0	0.0		85.0	38.0	NM_207163	A4D0W9|A4D0Y2|Q8WVJ8	Silent	SNP	ENST00000458573.2	hg19	CCDS47693.1																																																																																			.	.		0.433	LMOD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348525.1			A	123302237	T	A	123302237	2	1	68	1	0	0	0	0	0	0	0	1	8866	1800	63	4		4	LMOD2	7	123302237	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	25817527	123302237	35836426	85	8717										
LEP	3952	hgsc.bcm.edu	37	chr7	127894794	127894794	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gcaggacatgctgtggcagcTggacctcagccctgggtgct	15	12	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:127894794T>A	ENST00000308868.4	+	3	533	c.482T>A	c.(481-483)cTg>cAg	p.L161Q		NM_000230.2	NP_000221.1	P41159	LEP_HUMAN	leptin	161					adipose tissue development (GO:0060612)|adult feeding behavior (GO:0008343)|bile acid metabolic process (GO:0008206)|bone mineralization involved in bone maturation (GO:0035630)|cellular response to L-ascorbic acid (GO:0071298)|cellular response to retinoic acid (GO:0071300)|central nervous system neuron development (GO:0021954)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|eating behavior (GO:0042755)|energy reserve metabolic process (GO:0006112)|fatty acid beta-oxidation (GO:0006635)|female pregnancy (GO:0007565)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process (GO:0006114)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|leptin-mediated signaling pathway (GO:0033210)|leukocyte tethering or rolling (GO:0050901)|negative regulation of apoptotic process (GO:0043066)|negative regulation of appetite (GO:0032099)|negative regulation of cartilage development (GO:0061037)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of glutamine transport (GO:2000486)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vasoconstriction (GO:0045906)|ovulation from ovarian follicle (GO:0001542)|placenta development (GO:0001890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of developmental growth (GO:0048639)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of ion transport (GO:0043270)|positive regulation of luteinizing hormone secretion (GO:0033686)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of blood pressure (GO:0008217)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis (GO:0006111)|regulation of insulin secretion (GO:0050796)|regulation of intestinal cholesterol absorption (GO:0030300)|regulation of lipoprotein lipid oxidation (GO:0060587)|regulation of steroid biosynthetic process (GO:0050810)|response to dietary excess (GO:0002021)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to vitamin E (GO:0033197)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)				endometrium(1)|large_intestine(2)|lung(5)	8						CTGTGGCAGCTGGACCTCAGC	0.592																																					p.L161Q		Atlas-SNP	.											.	LEP	17	.	0			c.T482A						.						21	22	21					7																	127894794		2202	4297	6499	SO:0001583	missense	3952	exon3			GGCAGCTGGACCT		CCDS5800.1	7q31	2008-03-06	2008-03-06		ENSG00000174697	ENSG00000174697			6553	protein-coding gene	gene with protein product		164160	"leptin (murine obesity homolog)", "leptin (obesity homolog, mouse)"	OBS, OB		1686014, 16932309	Standard	NM_000230		Approved		uc003vml.2	P41159	OTTHUMG00000157564	ENST00000308868.4:c.482T>A	chr7.hg19:g.127894794T>A	ENSP00000312652:p.Leu161Gln	40.0	0.0		25.0	13.0	NM_000230	O15158|Q56A88	Missense_Mutation	SNP	ENST00000308868.4	hg19	CCDS5800.1	.	.	.	.	.	.	.	.	.	.	T	18.48	3.632859	0.67015	.	.	ENSG00000174697	ENST00000308868	T	0.71222	-0.55	5.54	5.54	0.83059	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.000000	0.45606	D	0.000353	D	0.82692	0.5092	M	0.74881	2.28	0.42842	D	0.994059	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85018	0.0910	10	0.87932	D	0	-12.7464	12.0609	0.53562	0.0:0.0:0.0:1.0	.	161;161	A4D0Y8;P41159	.;LEP_HUMAN	Q	161	ENSP00000312652:L161Q	ENSP00000312652:L161Q	L	+	2	0	LEP	127682030	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	4.140000	0.58031	2.108000	0.64289	0.533000	0.62120	CTG	.	.		0.592	LEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349174.1			A	127894794	T	A	127894794	3	1	68	1	0	0	0	0	1	0	0	0	8736	1580	55	4	488	4	LEP	7	127894794	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	4592557	127894794	31243869	86	8718										
CNOT4	4850	hgsc.bcm.edu	37	chr7	135095305	135095305	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgtcactttgttcttattttTatcaactgaacccgtagata	5	8	3	2	rs548144515		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:135095305T>A	ENST00000315544.5	-	7	1060	c.781A>T	c.(781-783)Aaa>Taa	p.K261*	CNOT4_ENST00000428680.2_Nonsense_Mutation_p.K261*|CNOT4_ENST00000423368.2_Nonsense_Mutation_p.K261*|CNOT4_ENST00000541284.1_Nonsense_Mutation_p.K261*|CNOT4_ENST00000451834.1_Nonsense_Mutation_p.K261*|CNOT4_ENST00000414802.1_Nonsense_Mutation_p.K261*|CNOT4_ENST00000361528.4_Nonsense_Mutation_p.K261*|CNOT4_ENST00000356162.4_Nonsense_Mutation_p.K261*	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	261					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						TTCTTATTTTTATCAACTGAA	0.343																																					p.K261X	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.A781T						.						132	128	129					7																	135095305		1838	4083	5921	SO:0001587	stop_gained	4850	exon7			TATTTTTATCAAC	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"RNA binding motif (RRM) containing"	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.781A>T	chr7.hg19:g.135095305T>A	ENSP00000326731:p.Lys261*	78.0	0.0		63.0	30.0	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Nonsense_Mutation	SNP	ENST00000315544.5	hg19	CCDS55166.1	.	.	.	.	.	.	.	.	.	.	T	40	8.069415	0.98638	.	.	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.0371	15.644	0.77033	0.0:0.0:0.0:1.0	.	.	.	.	X	261	.	ENSP00000262563:K261X	K	-	1	0	CNOT4	134745845	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.101000	0.63845	0.533000	0.62120	AAA	.	.		0.343	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		A	135095305	T	A	135095305	4	1	68	1	0	0	0	0	0	1	0	0	3623	1763	61	4	1263	4	CNOT4	7	135095305	Nonsense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	7200511	135095305	24043358	87	8719										
MGAM	8972	hgsc.bcm.edu	37	chr7	141765270	141765270	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctgaagaagtctatcattggTgcgtgggtccttccccaggg	13	10	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:141765270T>A	ENST00000549489.2	+	38	4713		c.e38+2		MGAM_ENST00000475668.2_Splice_Site	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)						carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CTATCATTGGTGCGTGGGTCC	0.592																																					.		Atlas-SNP	.											.	MGAM	767	.	0			c.4618+2T>A						.						73	79	77					7																	141765270		2033	4185	6218	SO:0001630	splice_region_variant	8972	exon38			CATTGGTGCGTGG	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4618+2T>A	chr7.hg19:g.141765270T>A		90.0	0.0		64.0	37.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Splice_Site	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.881642	0.51908	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	.	.	.	3.97	3.97	0.46021	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8945	0.52650	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	MGAM	141411739	1.000000	0.71417	0.957000	0.39632	0.492000	0.33523	7.896000	0.87350	1.436000	0.47453	0.254000	0.18369	.	.	.		0.592	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		Intron	A	141765270	T	A	141765270	5	1	68	1	0	0	0	0	0	0	1	0	9550	1710	59	4	4766	4	MGAM	7	141765270	Splice_Site	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	6669965	141765270	17373393	88	8720										
SSPO	23145	hgsc.bcm.edu	37	chr7	149529876	149529876	+	RNA	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ggagccatacctgcagagccAgtgtgactgctgcagctacc	12	13	0	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:149529876A>T	ENST00000378016.2	+	0	15293							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTGCAGAGCCAGTGTGACTGC	0.637																																					p.Q5097L		Atlas-SNP	.											.	.	.	.	0			c.A15290T						.						43	50	48					7																	149529876		2057	4206	6263			23145	exon109			AGAGCCAGTGTGA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149529876A>T		86.0	0.0		40.0	17.0	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.637	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149529876	A	T	149529876	1	4	68	0	1	0	0	0	0	0	0	0	15204	188	7	4		4	SSPO	7	149529876	RNA	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	7764606	149529876	9608787	89	8721										
WDR60	55112	hgsc.bcm.edu	37	chr7	158672638	158672638	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	caaagcaacgtggatagaaaAgagaaatcggcaaaagatga	11	5	0	4			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr7:158672638A>G	ENST00000407559.3	+	5	995	c.837A>G	c.(835-837)aaA>aaG	p.K279K		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	279					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		TGGATAGAAAAGAGAAATCGG	0.478																																					p.K279K		Atlas-SNP	.											.	WDR60	94	.	0			c.A837G						.						69	73	72					7																	158672638		1882	4096	5978	SO:0001819	synonymous_variant	55112	exon5			TAGAAAAGAGAAA		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"WD repeat domain containing"	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.837A>G	chr7.hg19:g.158672638A>G		213.0	0.0		189.0	72.0	NM_018051	Q9NW58	Silent	SNP	ENST00000407559.3	hg19	CCDS47757.1																																																																																			.	.		0.478	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051		G	158672638	A	G	158672638	2	3	68	1	0	0	0	0	0	0	0	1	17326	69	3	2		2	WDR60	7	158672638	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	9142762	158672638	466025	90	8722										
LZTS1	11178	hgsc.bcm.edu	37	chr8	20112615	20112615	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttcttgaggtgggaggacttGcgcagcttgtactgcgaagc	15	8	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr8:20112615G>A	ENST00000381569.1	-	2	435	c.78C>T	c.(76-78)cgC>cgT	p.R26R	LZTS1_ENST00000265801.6_Silent_p.R26R|LZTS1_ENST00000522290.1_Silent_p.R26R			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	26					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		GGGAGGACTTGCGCAGCTTGT	0.612																																					p.R26R		Atlas-SNP	.											.	LZTS1	72	.	0			c.C78T						.						68	70	69					8																	20112615		2203	4300	6503	SO:0001819	synonymous_variant	11178	exon1			GGACTTGCGCAGC	AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"F37/Esophageal cancer-related gene-coding leucine-zipper motif"			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.78C>T	chr8.hg19:g.20112615G>A		99.0	0.0		105.0	27.0	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Silent	SNP	ENST00000381569.1	hg19	CCDS6015.1																																																																																			.	.		0.612	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		A	20112615	G	A	20112615	2	1	68	1	0	0	0	0	0	0	0	1	9147	1306	46	3		3	LZTS1	8	20112615	Silent	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10		20112615	126251407	91	8723										
C8orf58	541565	hgsc.bcm.edu	37	chr8	22458397	22458397	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cgctgactctccatgcagatGgggctggcgagggcctggca	16	12	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr8:22458397G>T	ENST00000289989.5	+	2	117	c.43G>T	c.(43-45)Ggg>Tgg	p.G15W	AC037459.4_ENST00000430850.2_Missense_Mutation_p.M122I|C8orf58_ENST00000409586.3_Missense_Mutation_p.G15W|C8orf58_ENST00000453427.2_3'UTR			Q8NAV2	CH058_HUMAN	chromosome 8 open reading frame 58	15										endometrium(1)|lung(1)|ovary(1)|skin(1)	4		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00563)|Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		CCATGCAGATGGGGCTGGCGA	0.672																																					p.G15W		Atlas-SNP	.											.	C8orf58	17	.	0			c.G43T						.						18	18	18					8																	22458397		2188	4290	6478	SO:0001583	missense	541565	exon2			GCAGATGGGGCTG	BC012750	CCDS34862.1, CCDS56527.1, CCDS75708.1	8p21.3	2010-08-17			ENSG00000241852	ENSG00000241852			32233	protein-coding gene	gene with protein product							Standard	NM_001013842		Approved	FLJ34715	uc003xce.3	Q8NAV2	OTTHUMG00000154160	ENST00000289989.5:c.43G>T	chr8.hg19:g.22458397G>T	ENSP00000289989:p.Gly15Trp	76.0	0.0		64.0	42.0	NM_001013842	B4DI44	Missense_Mutation	SNP	ENST00000289989.5	hg19	CCDS34862.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	14.33|14.33	2.502875|2.502875	0.44558|0.44558	.|.	.|.	ENSG00000248235;ENSG00000241852;ENSG00000241852|ENSG00000248235	ENST00000450780;ENST00000409586;ENST00000289989|ENST00000430850;ENST00000447849	.|D	.|0.86694	.|-2.16	4.63|4.63	0.416|0.416	0.16416|0.16416	.|.	0.277746|.	0.25768|.	N|.	0.028436|.	D|D	0.84942|0.84942	0.5584|0.5584	M|M	0.70595|0.70595	2.14|2.14	0.30818|0.30818	N|N	0.738143|0.738143	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	T|T	0.76790|0.76790	-0.2829|-0.2829	9|7	0.87932|0.28530	D|T	0|0.3	-8.0847|-8.0847	3.0475|3.0475	0.06158|0.06158	0.0979:0.3382:0.3903:0.1736|0.0979:0.3382:0.3903:0.1736	.|.	15;15|.	Q8NAV2-2;Q8NAV2|.	.;CH058_HUMAN|.	W|I	84;15;15|122;106	.|ENSP00000428700:M122I	ENSP00000399696:G84W|ENSP00000428700:M122I	G|M	+|+	1|3	0|0	AC037459.4;C8orf58|AC037459.4	22514342|22514342	0.017000|0.017000	0.18338|0.18338	0.342000|0.342000	0.25602|0.25602	0.247000|0.247000	0.25773|0.25773	0.056000|0.056000	0.14256|0.14256	0.077000|0.077000	0.16863|0.16863	0.448000|0.448000	0.29417|0.29417	GGG|ATG	.	.		0.672	C8orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334183.1	NM_001013842		T	22458397	G	T	22458397	3	4	68	1	0	0	0	0	1	0	0	0	2435	1348	47	3	49	3	C8orf58	8	22458397	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	2345782	22458397	123905625	92	8724										
UNC5D	137970	hgsc.bcm.edu	37	chr8	35542098	35542098	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cctccccatttttctctctcAgtgaatggaggctggtcttc	8	13	3	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr8:35542098A>T	ENST00000404895.2	+	6	1079		c.e6-1		UNC5D_ENST00000416672.1_Splice_Site|UNC5D_ENST00000287272.2_Intron|UNC5D_ENST00000420357.1_Intron|UNC5D_ENST00000453357.2_Splice_Site	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)						apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		TTTCTCTCTCAGTGAATGGAG	0.532																																					.		Atlas-SNP	.											.	UNC5D	393	.	0			c.752-2A>T						.						88	86	86					8																	35542098		2203	4300	6503	SO:0001630	splice_region_variant	137970	exon6			TCTCTCAGTGAAT	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.752-1A>T	chr8.hg19:g.35542098A>T		109.0	0.0		85.0	16.0	NM_080872	Q8WYP7	Splice_Site	SNP	ENST00000404895.2	hg19	CCDS6093.2	.	.	.	.	.	.	.	.	.	.	A	21.2	4.110921	0.77210	.	.	ENSG00000156687	ENST00000404895;ENST00000416672;ENST00000453357	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1367	0.72572	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UNC5D	35661640	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.039000	0.60335	0.533000	0.62120	.	.	.		0.532	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2		Intron	T	35542098	A	T	35542098	5	4	68	1	0	0	0	0	0	0	1	0	17010	202	7	4	772	4	UNC5D	8	35542098	Splice_Site	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	13083701	35542098	110821924	93	8725										
CHD7	55636	hgsc.bcm.edu	37	chr8	61765635	61765635	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cggacggattatcacatcctCaatgaccctgagttatcctt	7	12	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr8:61765635C>T	ENST00000423902.2	+	31	6830	c.6351C>T	c.(6349-6351)ctC>ctT	p.L2117L	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2117					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			ATCACATCCTCAATGACCCTG	0.502																																					p.L2117L		Atlas-SNP	.											.	CHD7	534	.	0			c.C6351T						.						87	95	92					8																	61765635		2044	4183	6227	SO:0001819	synonymous_variant	55636	exon31			CATCCTCAATGAC	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.6351C>T	chr8.hg19:g.61765635C>T		176.0	0.0		182.0	50.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	hg19	CCDS47865.1																																																																																			.	.		0.502	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		T	61765635	C	T	61765635	2	4	68	1	0	0	0	0	0	0	0	1	3332	813	29	3		3	CHD7	8	61765635	Silent	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	26223537	61765635	84598387	94	8726										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116599393	116599393	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gccagatgggcggcctccacAttgggactatcccttagagt	12	12	0	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr8:116599393A>C	ENST00000220888.5	-	4	2655	c.2496T>G	c.(2494-2496)aaT>aaG	p.N832K	TRPS1_ENST00000519076.1_Missense_Mutation_p.N586K|TRPS1_ENST00000395715.3_Missense_Mutation_p.N845K|TRPS1_ENST00000519674.1_Missense_Mutation_p.N832K|TRPS1_ENST00000520276.1_Missense_Mutation_p.N836K			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	832					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CGGCCTCCACATTGGGACTAT	0.617									Langer-Giedion syndrome																												p.N845K		Atlas-SNP	.											.	TRPS1	516	.	0			c.T2535G						.						60	62	62					8																	116599393		1879	4108	5987	SO:0001583	missense	7227	exon5	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	CTCCACATTGGGA	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2496T>G	chr8.hg19:g.116599393A>C	ENSP00000220888:p.Asn832Lys	51.0	0.0		117.0	20.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	A	12.33	1.905969	0.33628	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276;ENST00000519674	D;D;D;D;T	0.98362	-4.89;-4.86;-4.84;-4.87;0.89	5.76	-0.777	0.10981	.	0.373808	0.30879	N	0.008691	D	0.95633	0.8580	L	0.27053	0.805	0.39207	D	0.963248	B;P;P	0.46220	0.01;0.801;0.874	B;B;P	0.47402	0.017;0.344;0.546	D	0.92846	0.6293	10	0.56958	D	0.05	.	11.8384	0.52340	0.5558:0.0:0.4442:0.0	.	836;832;845	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	K	845;832;586;836;832	ENSP00000379065:N845K;ENSP00000220888:N832K;ENSP00000428910:N586K;ENSP00000428680:N836K;ENSP00000429174:N832K	ENSP00000220888:N832K	N	-	3	2	TRPS1	116668568	0.003000	0.15002	0.901000	0.35422	0.697000	0.40408	-1.834000	0.01693	-0.082000	0.12640	-0.256000	0.11100	AAT	.	.		0.617	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		C	116599393	A	C	116599393	3	2	68	1	0	0	0	0	1	0	0	0	16608	214	8	5	1361	5	TRPS1	8	116599393	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	54833758	116599393	29764629	95	8727										
LRRC6	23639	hgsc.bcm.edu	37	chr8	133595953	133595953	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ggtggtaccttgtatttgttTgttctctgctcctgtccgag	11	9	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr8:133595953T>A	ENST00000519595.1	-	11	1312	c.1214A>T	c.(1213-1215)cAa>cTa	p.Q405L	LRRC6_ENST00000518642.1_Missense_Mutation_p.Q402L|LRRC6_ENST00000250173.1_Missense_Mutation_p.Q405L			Q86X45	TILB_HUMAN	leucine rich repeat containing 6	405					cilium movement (GO:0003341)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|inner dynein arm assembly (GO:0036159)|male gonad development (GO:0008584)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|reproductive system development (GO:0061458)|sperm motility (GO:0030317)	cilium (GO:0005929)|cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|urinary_tract(2)	34	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			TGTATTTGTTTGTTCTCTGCT	0.398																																					p.Q405L		Atlas-SNP	.											.	LRRC6	58	.	0			c.A1214T						.						234	198	210					8																	133595953		2203	4300	6503	SO:0001583	missense	23639	exon11			TTTGTTTGTTCTC	U60666	CCDS6365.1	8q24	2013-02-22			ENSG00000129295	ENSG00000129295			16725	protein-coding gene	gene with protein product	"leucine rich testes protein"	614930				10775177, 23122586	Standard	NM_012472		Approved	TSLRP, LRTP, CILD19	uc003ytk.4	Q86X45	OTTHUMG00000164646	ENST00000519595.1:c.1214A>T	chr8.hg19:g.133595953T>A	ENSP00000429791:p.Gln405Leu	95.0	0.0		289.0	44.0	NM_012472	Q13648|Q4G183	Missense_Mutation	SNP	ENST00000519595.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.719	-0.784234	0.02907	.	.	ENSG00000129295	ENST00000519595;ENST00000522789;ENST00000518642;ENST00000250173;ENST00000395414	T;T;T;T	0.54071	0.74;0.89;0.59;0.74	4.57	2.14	0.27477	.	0.982780	0.08353	N	0.959001	T	0.43942	0.1270	L	0.50333	1.59	0.09310	N	1	B	0.22983	0.078	B	0.21546	0.035	T	0.34576	-0.9823	10	0.33940	T	0.23	-1.7026	4.7981	0.13282	0.0:0.0991:0.1902:0.7107	.	405	Q86X45	LRRC6_HUMAN	L	405;145;402;405;405	ENSP00000429791:Q405L;ENSP00000428015:Q145L;ENSP00000428610:Q402L;ENSP00000250173:Q405L	ENSP00000250173:Q405L	Q	-	2	0	LRRC6	133665135	0.014000	0.17966	0.012000	0.15200	0.014000	0.08584	0.106000	0.15354	0.355000	0.24131	0.477000	0.44152	CAA	.	.		0.398	LRRC6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379578.1	NM_012472		A	133595953	T	A	133595953	3	1	68	1	0	0	0	0	1	0	0	0	9025	1812	63	4	194	4	LRRC6	8	133595953	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	16996560	133595953	12768069	96	8728										
PUF60	22827	hgsc.bcm.edu	37	chr8	144899155	144899155	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	atgctcatgtgctcctgctcGctcagcatctctggccgctc	9	16	3	0	rs372944670		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr8:144899155G>A	ENST00000526683.1	-	11	1860	c.1305C>T	c.(1303-1305)agC>agT	p.S435S	SCRIB_ENST00000356994.2_5'Flank|PUF60_ENST00000524570.1_5'Flank|SCRIB_ENST00000377533.3_5'Flank|PUF60_ENST00000349157.6_Silent_p.S418S|SCRIB_ENST00000320476.3_5'Flank|PUF60_ENST00000313352.7_Silent_p.S375S|PUF60_ENST00000527197.1_Silent_p.S389S|PUF60_ENST00000456095.2_Silent_p.S406S|PUF60_ENST00000453551.2_Silent_p.S392S	NM_001271098.1|NM_078480.2	NP_001258027.1|NP_510965.1	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa	435	Inhibits homodimerization.|Inhibits transcriptional repression, interaction with ERCC3 and apoptosis induction.				apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(3)|lung(7)|prostate(2)	14	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GCTCCTGCTCGCTCAGCATCT	0.627																																					p.S435S		Atlas-SNP	.											.	PUF60	26	.	0			c.C1305T						.	G	,,	1,4341		0,1,2170	43	40	41		1176,1254,1305	-8.5	0.9	8		41	0,8538		0,0,4269	no	coding-synonymous,coding-synonymous,coding-synonymous	PUF60	NM_001136033.1,NM_014281.3,NM_078480.1	,,	0,1,6439	AA,AG,GG		0.0,0.023,0.0078	,,	392/517,418/543,435/560	144899155	1,12879	2171	4269	6440	SO:0001819	synonymous_variant	22827	exon11			CTGCTCGCTCAGC	AF114818	CCDS47933.1, CCDS47934.1, CCDS47935.1, CCDS59514.1, CCDS59515.1, CCDS59516.1	8q24.3	2013-02-12	2007-07-27		ENSG00000179950	ENSG00000179950		"RNA binding motif (RRM) containing"	17042	protein-coding gene	gene with protein product	"siah binding protein 1", "FBP interacting repressor", "pyrimidine tract binding splicing factor", "Ro ribonucleoprotein binding protein 1"	604819				10668799, 10882074, 17579712	Standard	NM_078480		Approved	FIR, SIAHBP1, RoBPI	uc003yzs.4	Q9UHX1	OTTHUMG00000165155	ENST00000526683.1:c.1305C>T	chr8.hg19:g.144899155G>A		111.0	0.0		128.0	10.0	NM_078480	A8K8K8|Q969E7|Q96D94|Q96H63|Q99628|Q9NZA0|Q9UJY7	Silent	SNP	ENST00000526683.1	hg19	CCDS47934.1																																																																																			.	.		0.627	PUF60-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382222.1	NM_014281		A	144899155	G	A	144899155	2	1	68	1	0	0	0	0	0	0	0	1	12839	1078	38	1		1	PUF60	8	144899155	Silent	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	11303202	144899155	1464867	97	8729										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144943295	144943295	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cgagtctgcaggctgccgccTggggcaggtgcaccccgtgg	17	14	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr8:144943295T>A	ENST00000525985.1	-	2	4198	c.4127A>T	c.(4126-4128)cAg>cTg	p.Q1376L				P58107	EPIPL_HUMAN	epiplakin 1	1376						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGCTGCCGCCTGGGGCAGGTG	0.647																																					p.Q1376L		Atlas-SNP	.											.	EPPK1	199	.	0			c.A4127T						.						15	18	17					8																	144943295		2098	4213	6311	SO:0001583	missense	83481	exon1			GCCGCCTGGGGCA	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4127A>T	chr8.hg19:g.144943295T>A	ENSP00000436337:p.Gln1376Leu	51.0	0.0		100.0	41.0	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.99	1.507695	0.27036	.	.	ENSG00000227184	ENST00000525985	T	0.66815	-0.23	4.66	-1.21	0.09524	.	.	.	.	.	T	0.32315	0.0825	N	0.04090	-0.28	0.20196	N	0.999923	B	0.02656	0.0	B	0.06405	0.002	T	0.19418	-1.0306	9	0.08179	T	0.78	.	2.0822	0.03637	0.5618:0.101:0.1171:0.2201	.	1376	E9PPU0	.	L	1376	ENSP00000436337:Q1376L	ENSP00000436337:Q1376L	Q	-	2	0	EPPK1	145015283	0.014000	0.17966	0.490000	0.27465	0.692000	0.40212	2.568000	0.45965	-0.311000	0.08754	0.533000	0.62120	CAG	.	.		0.647	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144943295	T	A	144943295	3	1	68	1	0	0	0	0	1	0	0	0	5192	1580	55	4	3139	4	EPPK1	8	144943295	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	44140	144943295	1420727	98	8730										
SLC39A4	55630	hgsc.bcm.edu	37	chr8	145640635	145640635	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cagcgtcatagggacctcgcTgctgtgctgctggaacacaa	12	12	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr8:145640635T>A	ENST00000301305.3	-	3	748	c.643A>T	c.(643-645)Agc>Tgc	p.S215C	SLC39A4_ENST00000531013.1_5'Flank|SLC39A4_ENST00000276833.5_Missense_Mutation_p.S190C	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	215					cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			GGGACCTCGCTGCTGTGCTGC	0.687																																					p.S215C		Atlas-SNP	.											.	SLC39A4	54	.	0			c.A643T						.						48	49	49					8																	145640635		2202	4299	6501	SO:0001583	missense	55630	exon3			CCTCGCTGCTGTG	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"Solute carriers"	17129	protein-coding gene	gene with protein product		607059	"acrodermatitis enteropathica, zinc-deficiency type"	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.643A>T	chr8.hg19:g.145640635T>A	ENSP00000301305:p.Ser215Cys	161.0	0.0		273.0	34.0	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	hg19	CCDS6424.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.840512	0.51057	.	.	ENSG00000147804	ENST00000276833;ENST00000301305;ENST00000526658	T;T;T	0.57107	0.42;0.42;0.42	5.3	0.336	0.15958	.	1.006370	0.07985	N	0.986169	T	0.41166	0.1147	L	0.36672	1.1	0.09310	N	1	B;B	0.22480	0.011;0.07	B;B	0.15870	0.008;0.014	T	0.35151	-0.9800	10	0.66056	D	0.02	-4.4124	7.6192	0.28175	0.0:0.4401:0.0:0.5599	.	215;190	Q6P5W5;A6NDY5	S39A4_HUMAN;.	C	190;215;121	ENSP00000276833:S190C;ENSP00000301305:S215C;ENSP00000434512:S121C	ENSP00000276833:S190C	S	-	1	0	SLC39A4	145611443	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.077000	0.11394	-0.151000	0.11176	-0.394000	0.06481	AGC	.	.		0.687	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1			A	145640635	T	A	145640635	3	1	68	1	0	0	0	0	1	0	0	0	14635	1580	55	4	1340	4	SLC39A4	8	145640635	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	697340	145640635	723387	99	8731										
SLC24A2	25769	hgsc.bcm.edu	37	chr9	19786418	19786418	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aactcatcacagacaatggcTaaggctatgaacatgtagat	8	8	2	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr9:19786418T>A	ENST00000341998.2	-	1	508	c.447A>T	c.(445-447)ttA>ttT	p.L149F	SLC24A2_ENST00000286344.3_Missense_Mutation_p.L149F	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	149					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		AGACAATGGCTAAGGCTATGA	0.458																																					p.L149F		Atlas-SNP	.											.	SLC24A2	93	.	0			c.A447T						.						89	84	86					9																	19786418		2203	4300	6503	SO:0001583	missense	25769	exon1			AATGGCTAAGGCT	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"Solute carriers"	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.447A>T	chr9.hg19:g.19786418T>A	ENSP00000344801:p.Leu149Phe	31.0	0.0		33.0	27.0	NM_001193288	B7ZLL8|Q9NTN5|Q9NZQ4	Missense_Mutation	SNP	ENST00000341998.2	hg19	CCDS6493.1	.	.	.	.	.	.	.	.	.	.	T	17.51	3.407084	0.62399	.	.	ENSG00000155886	ENST00000341998;ENST00000286344	T;T	0.67345	-0.26;-0.26	5.76	5.76	0.90799	Sodium/calcium exchanger membrane region (1);	0.000000	0.85682	D	0.000000	D	0.85588	0.5731	M	0.91717	3.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.88768	0.3262	9	.	.	.	.	16.0738	0.80955	0.0:0.0:0.0:1.0	.	149;149	Q9UI40-2;Q9UI40	.;NCKX2_HUMAN	F	149	ENSP00000344801:L149F;ENSP00000286344:L149F	.	L	-	3	2	SLC24A2	19776418	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.692000	0.47018	2.192000	0.70111	0.533000	0.62120	TTA	.	.		0.458	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344		A	19786418	T	A	19786418	3	1	68	1	0	0	0	0	1	0	0	0	14481	1519	53	4	1578	4	SLC24A2	9	19786418	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		19786418	121427013	100	8732										
TLE4	7091	hgsc.bcm.edu	37	chr9	82333727	82333727	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ggacctggaatcccccggcaTgctcgccagatcaacaccct	9	17	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr9:82333727T>A	ENST00000376552.2	+	15	2449	c.1431T>A	c.(1429-1431)caT>caA	p.H477Q	TLE4_ENST00000376537.4_Missense_Mutation_p.H509Q|TLE4_ENST00000376534.4_Missense_Mutation_p.H114Q|TLE4_ENST00000265284.6_Missense_Mutation_p.H452Q|TLE4_ENST00000376520.4_Missense_Mutation_p.H509Q|TLE4_ENST00000376544.3_Missense_Mutation_p.H408Q	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	477					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						TCCCCCGGCATGCTCGCCAGA	0.602																																					p.H477Q		Atlas-SNP	.											.	TLE4	187	.	0			c.T1431A						.						119	110	113					9																	82333727		2203	4300	6503	SO:0001583	missense	7091	exon15			CCGGCATGCTCGC	M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"WD repeat domain containing"	11840	protein-coding gene	gene with protein product		605132	"transducin-like enhancer of split 4, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.1431T>A	chr9.hg19:g.82333727T>A	ENSP00000365735:p.His477Gln	168.0	0.0		156.0	36.0	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	hg19	CCDS43837.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.34|12.34	1.908985|1.908985	0.33721|0.33721	.|.	.|.	ENSG00000106829|ENSG00000106829	ENST00000496114|ENST00000376552;ENST00000376544;ENST00000376520;ENST00000376537;ENST00000376534;ENST00000265284	.|T;T;T;T;T;T	.|0.10573	.|2.86;2.86;2.86;2.86;2.86;2.86	5.83|5.83	-1.61|-1.61	0.08399|0.08399	.|WD40 repeat-like-containing domain (1);	.|0.093065	.|0.64402	.|D	.|0.000001	T|T	0.26846|0.26846	0.0657|0.0657	M|M	0.77616|0.77616	2.38|2.38	0.58432|0.58432	D|D	0.999994|0.999994	.|B;D;B;P	.|0.60575	.|0.418;0.988;0.026;0.536	.|B;D;B;B	.|0.71184	.|0.181;0.972;0.113;0.264	T|T	0.02358|0.02358	-1.1171|-1.1171	5|10	.|0.46703	.|T	.|0.11	-22.0444|-22.0444	10.9983|10.9983	0.47589|0.47589	0.0:0.3854:0.0:0.6146|0.0:0.3854:0.0:0.6146	.|.	.|452;408;509;477	.|F8W6T6;Q04727-2;Q04727-3;Q04727	.|.;.;.;TLE4_HUMAN	S|Q	293|477;408;509;509;114;452	.|ENSP00000365735:H477Q;ENSP00000365727:H408Q;ENSP00000365703:H509Q;ENSP00000365720:H509Q;ENSP00000365717:H114Q;ENSP00000265284:H452Q	.|ENSP00000265284:H452Q	C|H	+|+	1|3	0|2	TLE4|TLE4	81523547|81523547	0.006000|0.006000	0.16342|0.16342	0.955000|0.955000	0.39395|0.39395	0.414000|0.414000	0.31173|0.31173	-1.001000|-1.001000	0.03690|0.03690	-0.108000|-0.108000	0.12066|0.12066	-0.959000|-0.959000	0.02639|0.02639	TGC|CAT	.	.		0.602	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237		A	82333727	T	A	82333727	3	1	68	1	0	0	0	0	1	0	0	0	15956	1461	51	4	1489	4	TLE4	9	82333727	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	62547309	82333727	58879704	101	8733										
FAM75C1	441452	hgsc.bcm.edu	37	chr9	90535600	90535600	+	RNA	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	actcagtggcacttccactgGacaccgtccctcaaagcttg	8	15	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr9:90535600G>C	ENST00000602681.1	+	0	1504							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											ACTTCCACTGGACACCGTCCC	0.582																																					p.D260H		Atlas-SNP	.											.	.	.	.	0			c.G778C						.						41	38	39					9																	90535600		692	1590	2282			441452	exon4			CCACTGGACACCG	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"family with sequence similarity 75, member C1"	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		chr9.hg19:g.90535600G>C		167.0	0.0		191.0	50.0	NM_001145124		Missense_Mutation	SNP	ENST00000602681.1	hg19																																																																																				.	.		0.582	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124		C	90535600	G	C	90535600	1	2	68	0	1	0	0	0	0	0	0	0	5631	1174	41	4		4	FAM75C1	9	90535600	RNA	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	8201873	90535600	50677831	102	8734										
C9orf5	23731	hgsc.bcm.edu	37	chr9	111853343	111853343	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tcctatttcaggccttcgtcTgcccagagtaggtgaagggg	13	10	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr9:111853343T>A	ENST00000374586.3	-	5	1040	c.1009A>T	c.(1009-1011)Aga>Tga	p.R337*		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	337						integral component of membrane (GO:0016021)											GGCCTTCGTCTGCCCAGAGTA	0.502																																					p.R337X		Atlas-SNP	.											.	.	.	.	0			c.A1009T						.						100	103	102					9																	111853343		1917	4120	6037	SO:0001587	stop_gained	23731	exon5			TTCGTCTGCCCAG	AF153415	CCDS43858.1	9q31	2012-03-06	2012-03-06	2012-03-06	ENSG00000106771	ENSG00000106771			1363	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 5"	C9orf5		10564813	Standard	NM_032012		Approved	CG-2	uc004bdt.4	Q9H330	OTTHUMG00000020469	ENST00000374586.3:c.1009A>T	chr9.hg19:g.111853343T>A	ENSP00000363714:p.Arg337*	66.0	0.0		90.0	57.0	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Nonsense_Mutation	SNP	ENST00000374586.3	hg19	CCDS43858.1	.	.	.	.	.	.	.	.	.	.	T	37	6.125630	0.97305	.	.	ENSG00000106771	ENST00000374587;ENST00000374586;ENST00000223608	.	.	.	5.68	4.52	0.55395	.	0.367463	0.29466	N	0.012068	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.1413	13.0146	0.58749	0.0:0.0:0.1347:0.8653	.	.	.	.	X	337	.	ENSP00000223608:R337X	R	-	1	2	C9orf5	110893164	1.000000	0.71417	0.992000	0.48379	0.974000	0.67602	5.505000	0.66981	0.962000	0.38057	0.460000	0.39030	AGA	.	.		0.502	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012		A	111853343	T	A	111853343	4	1	68	1	0	0	0	0	0	1	0	0	2488	1588	55	4	1686	4	C9orf5	9	111853343	Nonsense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	21317743	111853343	29360088	103	8735										
C9orf84	158401	hgsc.bcm.edu	37	chr9	114500592	114500592	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gcactttcgtaggcaaaaatAtctcaattttagtgtcatta	6	7	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr9:114500592A>T	ENST00000318737.4	-	10	1321	c.1193T>A	c.(1192-1194)aTa>aAa	p.I398K	C9orf84_ENST00000374283.5_Missense_Mutation_p.I462K|C9orf84_ENST00000374287.3_Missense_Mutation_p.I398K|C9orf84_ENST00000394777.4_Missense_Mutation_p.I359K|C9orf84_ENST00000394779.3_Missense_Mutation_p.I359K	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	398										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						AGGCAAAAATATCTCAATTTT	0.284																																					p.I398K		Atlas-SNP	.											.	C9orf84	207	.	0			c.T1193A						.						102	99	100					9																	114500592		2202	4296	6498	SO:0001583	missense	158401	exon10			AAAAATATCTCAA	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.1193T>A	chr9.hg19:g.114500592A>T	ENSP00000322108:p.Ile398Lys	43.0	0.0		63.0	29.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	hg19	CCDS6781.3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.708|5.708	0.315176|0.315176	0.10789|0.10789	.|.	.|.	ENSG00000165181|ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000374287;ENST00000318737;ENST00000374283|ENST00000394778	T;T;T;T;T|.	0.57436|.	0.67;0.67;0.67;0.67;0.4|.	4.84|4.84	3.63|3.63	0.41609|0.41609	.|.	0.748880|.	0.12282|.	N|.	0.482799|.	T|T	0.29652|0.29652	0.0740|0.0740	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	0.999998|0.999998	B;P;P;B|.	0.36909|.	0.343;0.571;0.573;0.145|.	B;B;B;B|.	0.40228|.	0.225;0.323;0.219;0.063|.	T|T	0.21655|0.21655	-1.0239|-1.0239	10|6	0.35671|0.87932	T|D	0.21|0	0.3369|0.3369	7.0555|7.0555	0.25097|0.25097	0.8899:0.0:0.1101:0.0|0.8899:0.0:0.1101:0.0	.|.	359;462;398;359|.	A6PVK7;Q5VXU9-2;Q5VXU9;A2A2V3|.	.;.;CI084_HUMAN;.|.	K|N	359;359;398;398;462|13	ENSP00000378259:I359K;ENSP00000378257:I359K;ENSP00000363405:I398K;ENSP00000322108:I398K;ENSP00000363401:I462K|.	ENSP00000322108:I398K|ENSP00000378258:Y13N	I|Y	-|-	2|1	0|0	C9orf84|C9orf84	113540413|113540413	0.045000|0.045000	0.20229|0.20229	0.017000|0.017000	0.16124|0.16124	0.048000|0.048000	0.14542|0.14542	1.371000|1.371000	0.34250|0.34250	0.904000|0.904000	0.36572|0.36572	0.477000|0.477000	0.44152|0.44152	ATA|TAT	.	.		0.284	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		T	114500592	A	T	114500592	3	4	68	1	0	0	0	0	1	0	0	0	2502	449	16	4	3209	4	C9orf84	9	114500592	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	2647249	114500592	26712839	104	8736										
HDHD3	81932	hgsc.bcm.edu	37	chr9	116135994	116135994	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ccacggggtccagtgcctgtGggccaaccaccaggaagctg	14	14	0	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr9:116135994G>A	ENST00000238379.5	-	2	1538	c.641C>T	c.(640-642)cCa>cTa	p.P214L	HDHD3_ENST00000374180.3_Missense_Mutation_p.P214L|HDHD3_ENST00000485934.1_5'Flank	NM_031219.2	NP_112496.1	Q9BSH5	HDHD3_HUMAN	haloacid dehalogenase-like hydrolase domain containing 3	214						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			large_intestine(2)|liver(1)	3						CAGTGCCTGTGGGCCAACCAC	0.587																																					p.P214L		Atlas-SNP	.											.	HDHD3	10	.	0			c.C641T						.						76	77	77					9																	116135994		2203	4300	6503	SO:0001583	missense	81932	exon2			GCCTGTGGGCCAA	AK097067	CCDS6793.1	9q33.1	2006-04-12	2004-08-09	2004-08-12	ENSG00000119431	ENSG00000119431			28171	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 158"	C9orf158		12477932	Standard	NM_031219		Approved	MGC12904	uc004bhi.1	Q9BSH5	OTTHUMG00000020524	ENST00000238379.5:c.641C>T	chr9.hg19:g.116135994G>A	ENSP00000238379:p.Pro214Leu	90.0	0.0		105.0	64.0	NM_031219	B2RD47	Missense_Mutation	SNP	ENST00000238379.5	hg19	CCDS6793.1	.	.	.	.	.	.	.	.	.	.	G	3.841	-0.033745	0.07543	.	.	ENSG00000119431	ENST00000238379;ENST00000374180	T;T	0.42900	0.96;0.96	5.74	4.85	0.62838	HAD-like domain (2);	0.629853	0.15851	N	0.241518	T	0.24509	0.0594	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.12400	-1.0549	10	0.21540	T	0.41	-4.1136	13.8332	0.63393	0.0733:0.0:0.9267:0.0	.	214	Q9BSH5	HDHD3_HUMAN	L	214	ENSP00000238379:P214L;ENSP00000363295:P214L	ENSP00000238379:P214L	P	-	2	0	HDHD3	115175815	0.599000	0.26891	0.004000	0.12327	0.058000	0.15608	4.784000	0.62411	1.438000	0.47492	0.650000	0.86243	CCA	.	.		0.587	HDHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053731.1	NM_031219		A	116135994	G	A	116135994	3	1	68	1	0	0	0	0	1	0	0	0	7033	1348	47	3	118	3	HDHD3	9	116135994	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	1635402	116135994	25077437	105	8737										
NCS1	23413	hgsc.bcm.edu	37	chr9	132980139	132980139	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gcttcatcaaggactgccccAgtgggcagctggatgcggca	14	12	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr9:132980139A>T	ENST00000372398.3	+	3	204	c.118A>T	c.(118-120)Agt>Tgt	p.S40C	NCS1_ENST00000458469.1_Missense_Mutation_p.S22C|NCS1_ENST00000493042.1_3'UTR	NM_014286.3	NP_055101.2	P62166	NCS1_HUMAN	neuronal calcium sensor 1	40	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion transmembrane transport (GO:0070588)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of exocytosis (GO:0045921)|regulation of neuron projection development (GO:0010975)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|voltage-gated calcium channel activity (GO:0005245)			large_intestine(1)|lung(4)|stomach(1)	6						GGACTGCCCCAGTGGGCAGCT	0.552																																					p.S40C	Melanoma(30;182 1162 22581 33240)	Atlas-SNP	.											.	NCS1	18	.	0			c.A118T						.						91	94	93					9																	132980139		2203	4300	6503	SO:0001583	missense	23413	exon3			TGCCCCAGTGGGC	AF186409	CCDS6932.1	9q34.11	2013-01-10	2010-01-27	2010-01-27	ENSG00000107130	ENSG00000107130		"EF-hand domain containing"	3953	protein-coding gene	gene with protein product		603315	"frequenin (Drosophila) homolog", "frequenin homolog (Drosophila)"	FREQ		11092894	Standard	NM_014286		Approved	NCS-1	uc004bzi.2	P62166	OTTHUMG00000020801	ENST00000372398.3:c.118A>T	chr9.hg19:g.132980139A>T	ENSP00000361475:p.Ser40Cys	123.0	0.0		139.0	39.0	NM_014286	E9PAY3|P36610|Q9UK26	Missense_Mutation	SNP	ENST00000372398.3	hg19	CCDS6932.1	.	.	.	.	.	.	.	.	.	.	A	15.21	2.765467	0.49574	.	.	ENSG00000107130	ENST00000372398;ENST00000458469	T;T	0.70282	-0.47;-0.47	4.55	3.41	0.39046	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.76751	0.4031	M	0.83012	2.62	0.58432	D	0.999998	D;D	0.71674	0.998;0.995	P;P	0.51016	0.656;0.574	T	0.77869	-0.2427	10	0.87932	D	0	.	9.1584	0.37007	0.9131:0.0:0.0869:0.0	.	22;40	E9PAY3;P62166	.;NCS1_HUMAN	C	40;22	ENSP00000361475:S40C;ENSP00000404103:S22C	ENSP00000361475:S40C	S	+	1	0	NCS1	132019960	1.000000	0.71417	0.987000	0.45799	0.015000	0.08874	9.107000	0.94261	0.621000	0.30232	-0.379000	0.06801	AGT	.	.		0.552	NCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054637.1	NM_014286		T	132980139	A	T	132980139	3	4	68	1	0	0	0	0	1	0	0	0	10249	188	7	4	142	4	NCS1	9	132980139	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	16844145	132980139	8233292	106	8738										
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134525525	134525525	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gttacactgaccttctgcctTtgagacctggaagccacagc	9	13	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr9:134525525T>G	ENST00000372189.3	-	3	378	c.255A>C	c.(253-255)caA>caC	p.Q85H	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.Q103H|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.Q102H	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	85					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		CCTTCTGCCTTTGAGACCTGG	0.483																																					p.Q103H		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.A309C						.						41	41	41					9																	134525525		1956	4166	6122	SO:0001583	missense	2889	exon3			CTGCCTTTGAGAC	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.255A>C	chr9.hg19:g.134525525T>G	ENSP00000361263:p.Gln85His	95.0	0.0		89.0	67.0	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	hg19	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	T	17.76	3.469334	0.63625	.	.	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000372189;ENST00000372190;ENST00000337036;ENST00000357686;ENST00000427994	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.91	-0.299	0.12808	.	0.277274	0.33591	N	0.004760	T	0.43722	0.1260	L	0.36672	1.1	0.25666	N	0.98595	D;D;D	0.67145	0.996;0.992;0.995	D;D;D	0.77004	0.986;0.976;0.989	T	0.33343	-0.9872	10	0.54805	T	0.06	.	10.2702	0.43479	0.0:0.5406:0.0:0.4594	.	102;85;103	Q68DL3;Q13905;Q13905-3	.;RPGF1_HUMAN;.	H	85;102;85;103;11;102;103	ENSP00000361269:Q102H;ENSP00000361263:Q85H;ENSP00000361264:Q103H;ENSP00000402174:Q103H	ENSP00000266110:Q85H	Q	-	3	2	RAPGEF1	133515346	0.990000	0.36364	0.998000	0.56505	0.996000	0.88848	-0.007000	0.12810	-0.026000	0.13895	-0.250000	0.11733	CAA	.	.		0.483	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		G	134525525	T	G	134525525	3	3	68	1	0	0	0	0	1	0	0	0	13058	1838	64	5	3066	5	RAPGEF1	9	134525525	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	1545386	134525525	6687906	107	8739										
CUBN	8029	hgsc.bcm.edu	37	chr10	16877186	16877186	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aaatgccttgtgatagtctcTgttgcaatcttagaggaaaa	9	6	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr10:16877186T>A	ENST00000377833.4	-	64	10254	c.10189A>T	c.(10189-10191)Aga>Tga	p.R3397*		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3397	CUB 26. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGATAGTCTCTGTTGCAATCT	0.413																																					p.R3397X		Atlas-SNP	.											.	CUBN	515	.	0			c.A10189T						.						116	106	110					10																	16877186		2203	4300	6503	SO:0001587	stop_gained	8029	exon64			AGTCTCTGTTGCA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.10189A>T	chr10.hg19:g.16877186T>A	ENSP00000367064:p.Arg3397*	80.0	0.0		242.0	68.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Nonsense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	51	17.343323	0.99884	.	.	ENSG00000107611	ENST00000377833;ENST00000545090	.	.	.	4.84	2.39	0.29439	.	0.000000	0.45606	D	0.000358	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.6817	0.51461	0.0:0.0:0.301:0.6989	.	.	.	.	X	3397;238	.	ENSP00000367064:R3397X	R	-	1	2	CUBN	16917192	1.000000	0.71417	1.000000	0.80357	0.407000	0.30961	1.127000	0.31357	0.896000	0.36366	0.459000	0.35465	AGA	.	.		0.413	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16877186	T	A	16877186	4	1	68	1	0	0	0	0	0	1	0	0	4053	1588	55	4	698	4	CUBN	10	16877186	Nonsense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		16877186	118657561	108	8740										
GPR158	57512	hgsc.bcm.edu	37	chr10	25701321	25701321	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gaagataagtatttacgactTgccatcatctccttccaagc	6	11	2	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr10:25701321T>G	ENST00000376351.3	+	4	1613	c.1254T>G	c.(1252-1254)ctT>ctG	p.L418L		NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	418					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						ATTTACGACTTGCCATCATCT	0.522																																					p.L418L		Atlas-SNP	.											.	GPR158	255	.	0			c.T1254G						.						257	222	234					10																	25701321		2203	4300	6503	SO:0001819	synonymous_variant	57512	exon4			ACGACTTGCCATC	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.1254T>G	chr10.hg19:g.25701321T>G		115.0	0.0		296.0	82.0	NM_020752	Q6QR81|Q9ULT3	Silent	SNP	ENST00000376351.3	hg19	CCDS31166.1																																																																																			.	.		0.522	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		G	25701321	T	G	25701321	2	3	68	1	0	0	0	0	0	0	0	1	6671	1799	63	5		5	GPR158	10	25701321	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	8824135	25701321	109833426	109	8741										
P4HA1	5033	hgsc.bcm.edu	37	chr10	74803644	74803660	+	Intron	DEL	CCTCTTAGATACTCTGT	CCTCTTAGATACTCTGT	-													0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttctctccattactcccttaCctcttagatactctgtactg					rs200350484|rs1130892		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	CCTCTTAGATACTCTGT	CCTCTTAGATACTCTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr10:74803644_74803660delCCTCTTAGATACTCTGT	ENST00000307116.2	-	9	1265				P4HA1_ENST00000412021.2_Intron|P4HA1_ENST00000373008.2_Splice_Site_p.YRVSKR378fs|P4HA1_ENST00000263556.3_Splice_Site_p.YRVSKR378fs|P4HA1_ENST00000440381.1_Splice_Site_p.YRVSKR378fs|P4HA1_ENST00000394890.2_Intron			P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha polypeptide I						collagen fibril organization (GO:0030199)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|procollagen-proline 4-dioxygenase complex (GO:0016222)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TACTCCCTTACCTCTTAGATACTCTGTACTGTGCTGT	0.406																																					p.378_383del	Colon(147;367 2405 2662 52127)	Atlas-Indel,Pindel	.											.	P4HA1	86	.	0			c.1134_1148del						.																																			SO:0001627	intron_variant	5033	exon9			.		CCDS7320.1, CCDS41537.1, CCDS44432.1	10q21.3-q23.1	2008-12-09	2008-12-09		ENSG00000122884	ENSG00000122884	1.14.11.2		8546	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(I)"	176710	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I"	P4HA		2556027	Standard	NM_001017962		Approved	C-P4Halpha(I)	uc001jtg.3	P13674	OTTHUMG00000018449	ENST00000307116.2:c.1148+1078ACAGAGTATCTAAGAGG>-	chr10.hg19:g.74803644_74803660delCCTCTTAGATACTCTGT		76.0	0.0		24.0	13.0	NM_001142596	C9JL12|Q15082|Q15083|Q5VSQ5	In_Frame_Del	DEL	ENST00000307116.2	hg19																																																																																				.	.		0.406	P4HA1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000048601.1	NM_000917		-	74803660	CCTCTTAGATACTCTGT	-	74803644	6	5	68	0	1	1	0	1	0	0	0	0	11365	521	18	0		0	P4HA1	10	74803644	Intron	DEL	CCTCTTAGATACTCTGT	TCGA-CC-A5UD-01A-11D-A28X-10	49102323	74803644	60731103	110	8742										
PTEN	5728	hgsc.bcm.edu	37	chr10	89712017	89712017	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gttcagtggcggaacttgcaGtaagtgcttgaaattctcat	11	7	2	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr10:89712017G>T	ENST00000371953.3	+	6	1991		c.e6+1		PTEN_ENST00000472832.1_Splice_Site	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(5)|p.Y27fs*1(2)|p.G165_*404del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GGAACTTGCAGTAAGTGCTTG	0.343		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											.		Atlas-SNP	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,NS,carcinoma,0,4	PTEN	3652	.	50	Whole gene deletion(37)|Deletion - Frameshift(7)|Unknown(5)|Deletion - In frame(1)	prostate(16)|central_nervous_system(11)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|endometrium(2)|breast(2)|soft_tissue(1)|urinary_tract(1)|kidney(1)	c.634+1G>T						.						139	138	138					10																	89712017		2203	4300	6503	SO:0001630	splice_region_variant	5728	exon6	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	CTTGCAGTAAGTG	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.634+1G>T	chr10.hg19:g.89712017G>T		39.0	0.0		16.0	12.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Splice_Site	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.161219	0.78226	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1698	0.98157	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTEN	89701997	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.365000	0.97139	2.777000	0.95525	0.585000	0.79938	.	.	.		0.343	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	Intron	T	89712017	G	T	89712017	5	4	68	1	0	0	0	0	0	0	1	0	12750	1043	36	3	657	3	PTEN	10	89712017	Splice_Site	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	14908373	89712017	45822730	111	8743										
OR51D1	390038	hgsc.bcm.edu	37	chr11	4661967	4661967	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	agagatctgttcaagggtccTctgtatgttctcacaaggtg	11	8	4	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr11:4661967T>A	ENST00000357605.2	+	1	1023	c.947T>A	c.(946-948)cTc>cAc	p.L316H	OR51E1_ENST00000396952.5_5'Flank	NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	316						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCAAGGGTCCTCTGTATGTTC	0.463																																					p.L316H		Atlas-SNP	.											.	OR51D1	49	.	0			c.T947A						.						70	70	70					11																	4661967		2201	4298	6499	SO:0001583	missense	390038	exon1			GGGTCCTCTGTAT	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"GPCR / Class A : Olfactory receptors"	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.947T>A	chr11.hg19:g.4661967T>A	ENSP00000350222:p.Leu316His	67.0	0.0		100.0	25.0	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	hg19	CCDS31357.1	.	.	.	.	.	.	.	.	.	.	T	9.552	1.116072	0.20795	.	.	ENSG00000197428	ENST00000357605	T	0.39592	1.07	4.56	2.23	0.28157	.	0.889887	0.09306	N	0.820190	T	0.61060	0.2317	M	0.87038	2.855	0.09310	N	1	D	0.55385	0.971	P	0.56788	0.806	T	0.46789	-0.9166	10	0.62326	D	0.03	.	7.0583	0.25111	0.0:0.1847:0.0:0.8153	.	316	Q8NGF3	O51D1_HUMAN	H	316	ENSP00000350222:L316H	ENSP00000350222:L316H	L	+	2	0	OR51D1	4618543	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.672000	0.25187	0.361000	0.24292	-0.521000	0.04368	CTC	.	.		0.463	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751		A	4661967	T	A	4661967	3	1	68	1	0	0	0	0	1	0	0	0	11102	1551	54	4	949	4	OR51D1	11	4661967	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		4661967	130344549	112	8744										
EIF3F	8665	hgsc.bcm.edu	37	chr11	8017529	8017529	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctacctggccaacctcacacAgtcacagattgcactcaatg	6	15	3	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr11:8017529A>T	ENST00000533626.1	+	10	1660	c.1034A>T	c.(1033-1035)cAg>cTg	p.Q345L	EIF3F_ENST00000449102.2_Missense_Mutation_p.Q196L|EIF3F_ENST00000537635.1_Missense_Mutation_p.Q360L|EIF3F_ENST00000309828.4_Missense_Mutation_p.Q345L					eukaryotic translation initiation factor 3, subunit F											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)	13				Epithelial(150;1.44e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AACCTCACACAGTCACAGATT	0.483																																					p.Q345L		Atlas-SNP	.											.	EIF3F	23	.	0			c.A1034T						.						185	182	183					11																	8017529		2201	4296	6497	SO:0001583	missense	8665	exon8			TCACACAGTCACA	U94855, AK093511	CCDS7785.1	11p15.4	2010-03-10	2007-07-27	2007-07-27	ENSG00000175390	ENSG00000175390			3275	protein-coding gene	gene with protein product		603914	"eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa"	EIF3S5		9341143	Standard	NM_003754		Approved	eIF3-epsilon, eIF3-p47, eIF3f	uc001mfw.3	O00303		ENST00000533626.1:c.1034A>T	chr11.hg19:g.8017529A>T	ENSP00000431800:p.Gln345Leu	57.0	0.0		62.0	16.0	NM_003754		Missense_Mutation	SNP	ENST00000533626.1	hg19	CCDS7785.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.779383	0.90195	.	.	ENSG00000175390	ENST00000533626;ENST00000537635;ENST00000309828;ENST00000538607;ENST00000449102	T;T;T;T	0.44881	1.47;1.47;1.47;0.91	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.54351	0.1853	L	0.53249	1.67	0.80722	D	1	P	0.51653	0.947	P	0.57324	0.818	T	0.57648	-0.7775	10	0.87932	D	0	-11.5192	13.646	0.62281	1.0:0.0:0.0:0.0	.	345	O00303	EIF3F_HUMAN	L	345;360;345;295;196	ENSP00000431800:Q345L;ENSP00000442283:Q360L;ENSP00000310040:Q345L;ENSP00000396929:Q196L	ENSP00000310040:Q345L	Q	+	2	0	EIF3F	7974105	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.139000	0.94554	2.270000	0.75569	0.459000	0.35465	CAG	.	.		0.483	EIF3F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385713.2	NM_003754		T	8017529	A	T	8017529	3	4	68	1	0	0	0	0	1	0	0	0	5018	188	7	4	1064	4	EIF3F	11	8017529	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	3355562	8017529	126988987	113	8745										
IPO7	10527	hgsc.bcm.edu	37	chr11	9462080	9462080	+	Frame_Shift_Del	DEL	A	A	-													0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tctggctaagcaggctggtgAagatggagatgatgaagatt							TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr11:9462080delA	ENST00000379719.3	+	23	2916	c.2774delA	c.(2773-2775)gaafs	p.E925fs		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	925	Asp-rich.				innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		CAGGCTGGTGAAGATGGAGAT	0.418																																					p.E925fs		Atlas-Indel,Pindel	.											.	IPO7	72	.	0			c.2773delG						.						120	111	114					11																	9462080		2201	4294	6495	SO:0001589	frameshift_variant	10527	exon23			.	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.2774delA	chr11.hg19:g.9462080delA	ENSP00000369042:p.Glu925fs	137.0	0.0		152.0	48.0	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Frame_Shift_Del	DEL	ENST00000379719.3	hg19	CCDS31425.1																																																																																			.	.		0.418	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		-	9462080	A	-	9462080	7	5	68	1	0	1	0	1	0	0	0	0	7806	246	9	0	2864	0	IPO7	11	9462080	Frame_Shift_Del	DEL	A	TCGA-CC-A5UD-01A-11D-A28X-10	1444551	9462080	125544436	114	8746										
LRRC4C	57689	hgsc.bcm.edu	37	chr11	40137322	40137322	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cccctaagtctagtcggcgcAaagaaggaattctgttaaaa	9	9	2	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr11:40137322A>G	ENST00000278198.2	-	2	2484	c.521T>C	c.(520-522)tTg>tCg	p.L174S	LRRC4C_ENST00000527150.1_Missense_Mutation_p.L174S|LRRC4C_ENST00000528697.1_Missense_Mutation_p.L174S|LRRC4C_ENST00000530763.1_Missense_Mutation_p.L174S			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	174					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TAGTCGGCGCAAAGAAGGAAT	0.423																																					p.L174S		Atlas-SNP	.											.	LRRC4C	190	.	0			c.T521C						.						91	91	91					11																	40137322		2203	4300	6503	SO:0001583	missense	57689	exon7			CGGCGCAAAGAAG	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.521T>C	chr11.hg19:g.40137322A>G	ENSP00000278198:p.Leu174Ser	52.0	0.0		76.0	18.0	NM_001258419	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	hg19	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.053096	0.55218	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	5.82	5.82	0.92795	.	0.000000	0.64402	D	0.000001	T	0.77572	0.4150	H	0.99379	4.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87606	0.2500	10	0.87932	D	0	.	15.3632	0.74499	1.0:0.0:0.0:0.0	.	174	Q9HCJ2	LRC4C_HUMAN	S	174	ENSP00000278198:L174S;ENSP00000436976:L174S;ENSP00000437132:L174S;ENSP00000434761:L174S	ENSP00000278198:L174S	L	-	2	0	LRRC4C	40093898	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.287000	0.95975	2.222000	0.72286	0.528000	0.53228	TTG	.	.		0.423	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		G	40137322	A	G	40137322	3	3	68	1	0	0	0	0	1	0	0	0	9017	131	5	2	1405	2	LRRC4C	11	40137322	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	30675242	40137322	94869194	115	8747										
OR8K5	219453	hgsc.bcm.edu	37	chr11	55926911	55926911	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gaaggcatttttcacctcttCgtttcttaagctgtaaatca	6	9	4	0	rs376114385		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr11:55926911C>A	ENST00000313447.1	-	1	882	c.883G>T	c.(883-885)Gaa>Taa	p.E295*		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				TTCACCTCTTCGTTTCTTAAG	0.303																																					p.E295X		Atlas-SNP	.											.	OR8K5	82	.	0			c.G883T						.						70	67	68					11																	55926911		2201	4296	6497	SO:0001587	stop_gained	219453	exon1			CCTCTTCGTTTCT	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"GPCR / Class A : Olfactory receptors"	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.883G>T	chr11.hg19:g.55926911C>A	ENSP00000323853:p.Glu295*	81.0	0.0		39.0	13.0	NM_001004058	Q6IFB5	Nonsense_Mutation	SNP	ENST00000313447.1	hg19	CCDS31521.1	.	.	.	.	.	.	.	.	.	.	T	12.07	1.827281	0.32329	.	.	ENSG00000181752	ENST00000313447	.	.	.	3.88	3.88	0.44766	.	0.228496	0.30999	N	0.008446	.	.	.	.	.	.	0.32023	N	0.600555	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.1093	0.30905	0.0:0.104:0.0:0.896	.	.	.	.	X	295	.	ENSP00000323853:E295X	E	-	1	0	OR8K5	55683487	0.581000	0.26741	1.000000	0.80357	0.598000	0.36846	1.221000	0.32503	0.651000	0.30788	-0.929000	0.02709	GAA	.	.		0.303	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058		A	55926911	C	A	55926911	4	1	68	1	0	0	0	0	0	1	0	0	11254	893	31	1	43	1	OR8K5	11	55926911	Nonsense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	15789589	55926911	79079605	116	8748										
OR4D9	390199	hgsc.bcm.edu	37	chr11	59283045	59283045	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctcctcatatcttacacggtCatcttgatgatgctgaggtc	8	11	4	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr11:59283045C>A	ENST00000329328.3	+	1	660	c.660C>A	c.(658-660)gtC>gtA	p.V220V		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						CTTACACGGTCATCTTGATGA	0.498																																					p.V220V		Atlas-SNP	.											.	OR4D9	47	.	0			c.C660A						.						229	199	209					11																	59283045		2201	4295	6496	SO:0001819	synonymous_variant	390199	exon1			CACGGTCATCTTG	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"GPCR / Class A : Olfactory receptors"	15178	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily D, member 9 pseudogene"				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.660C>A	chr11.hg19:g.59283045C>A		94.0	0.0		78.0	36.0	NM_001004711	Q6IFF3	Silent	SNP	ENST00000329328.3	hg19	CCDS31564.1																																																																																			.	.		0.498	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711		A	59283045	C	A	59283045	2	1	68	1	0	0	0	0	0	0	0	1	11068	813	29	3		3	OR4D9	11	59283045	Silent	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	3356134	59283045	75723471	117	8749										
IL18BP	10068	hgsc.bcm.edu	37	chr11	71712350	71712350	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	attgagcacctcccaggccgActgtgggaggggagcaccag	15	12	0	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr11:71712350A>G	ENST00000393703.4	+	4	876	c.339A>G	c.(337-339)cgA>cgG	p.R113R	IL18BP_ENST00000531053.1_Silent_p.R113R|IL18BP_ENST00000393705.4_Silent_p.R113R|IL18BP_ENST00000337131.5_Silent_p.R113R|IL18BP_ENST00000393707.4_Intron|IL18BP_ENST00000260049.5_Silent_p.R113R|IL18BP_ENST00000497194.2_Silent_p.R113R|IL18BP_ENST00000404792.1_Silent_p.R113R	NM_001039660.1	NP_001034749.1	O95998	I18BP_HUMAN	interleukin 18 binding protein	113	Ig-like C2-type.				cellular response to hydrogen peroxide (GO:0070301)|cellular response to tumor necrosis factor (GO:0071356)|extracellular negative regulation of signal transduction (GO:1900116)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	interleukin-18 binding (GO:0042007)|receptor antagonist activity (GO:0048019)			endometrium(2)|kidney(1)|large_intestine(3)|lung(1)	7						TCCCAGGCCGACTGTGGGAGG	0.617																																					p.R113R		Atlas-SNP	.											.	IL18BP	15	.	0			c.A339G						.						42	44	43					11																	71712350		2061	4179	6240	SO:0001819	synonymous_variant	10068	exon4			AGGCCGACTGTGG	AF110798	CCDS8206.2, CCDS44666.1	11q13	2013-01-11			ENSG00000137496	ENSG00000137496		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5987	protein-coding gene	gene with protein product	"MC51L-53L-54L homolog gene product"	604113				10023777	Standard	NM_001145055		Approved	IL18BPa	uc001orf.1	O95998	OTTHUMG00000133713	ENST00000393703.4:c.339A>G	chr11.hg19:g.71712350A>G		108.0	0.0		85.0	36.0	NM_001145057	B3KUZ0|B7WPK4|O95993|O96027|Q9NZA9|Q9UBR7	Silent	SNP	ENST00000393703.4	hg19	CCDS8206.2																																																																																			.	.		0.617	IL18BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258012.2	NM_173042		G	71712350	A	G	71712350	2	3	68	1	0	0	0	0	0	0	0	1	7655	262	10	2		2	IL18BP	11	71712350	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	12429305	71712350	63294166	118	8750										
ATM	472	hgsc.bcm.edu	37	chr11	108114838	108114838	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttttttccaaggctattcagTgtgcgaggtaatctaatctc	8	8	3	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr11:108114838T>A	ENST00000452508.2	+	7	844	c.655T>A	c.(655-657)Tgt>Agt	p.C219S	ATM_ENST00000278616.4_Missense_Mutation_p.C219S			Q13315	ATM_HUMAN	ATM serine/threonine kinase	219					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GGCTATTCAGTGTGCGAGGTA	0.328			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.C219S		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.T655A						.						86	84	85					11																	108114838		2201	4298	6499	SO:0001583	missense	472	exon6	Familial Cancer Database	AT, Louis-Bar syndrome	ATTCAGTGTGCGA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.655T>A	chr11.hg19:g.108114838T>A	ENSP00000388058:p.Cys219Ser	54.0	0.0		39.0	14.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	4.297	0.054359	0.08291	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.01613	4.73;5.0;5.0	5.42	1.97	0.26223	.	1.397370	0.03926	N	0.284447	T	0.01695	0.0054	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.50215	-0.8854	10	0.22109	T	0.4	.	1.0028	0.01481	0.3223:0.0961:0.1672:0.4144	.	219	Q13315	ATM_HUMAN	S	219	ENSP00000435747:C219S;ENSP00000278616:C219S;ENSP00000388058:C219S	ENSP00000278616:C219S	C	+	1	0	ATM	107620048	0.997000	0.39634	0.012000	0.15200	0.505000	0.33919	1.916000	0.39986	0.105000	0.17753	0.533000	0.62120	TGT	.	.		0.328	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108114838	T	A	108114838	3	1	68	1	0	0	0	0	1	0	0	0	1109	1696	59	4	673	4	ATM	11	108114838	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	36402488	108114838	26891678	119	8751										
MLL	4297	hgsc.bcm.edu	37	chr11	118347664	118347664	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gtgccttaccatgggaagaaCgagaaaagattttgtcttcc	10	8	1	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr11:118347664C>T	ENST00000389506.5	+	4	3301	c.3301C>T	c.(3301-3303)Cga>Tga	p.R1101*	KMT2A_ENST00000354520.4_Nonsense_Mutation_p.R1101*|KMT2A_ENST00000534358.1_Nonsense_Mutation_p.R1101*			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1101					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										ATGGGAAGAACGAGAAAAGAT	0.458																																					p.R1101X		Atlas-SNP	.											.	MLL	548	.	0			c.C3301T						.						120	111	114					11																	118347664		2200	4296	6496	SO:0001587	stop_gained	4297	exon4			GAAGAACGAGAAA	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.3301C>T	chr11.hg19:g.118347664C>T	ENSP00000374157:p.Arg1101*	151.0	0.0		121.0	44.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Nonsense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	41	8.645073	0.98899	.	.	ENSG00000118058	ENST00000534358;ENST00000531904;ENST00000389506;ENST00000354520;ENST00000359313;ENST00000533790	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.9396	0.70983	0.1429:0.8571:0.0:0.0	.	.	.	.	X	1101;1134;1101;1101;11;179	.	ENSP00000346516:R1101X	R	+	1	2	MLL	117852874	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.577000	0.53885	2.771000	0.95319	0.655000	0.94253	CGA	.	.		0.458	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118347664	C	T	118347664	4	4	68	1	0	0	0	0	0	1	0	0	9629	528	19	1	3315	1	MLL	11	118347664	Nonsense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	10232826	118347664	16658852	120	8752										
CHEK1	1111	hgsc.bcm.edu	37	chr11	125514071	125514071	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ccagcccctcatacattgatAaattggtacaagggatcagc	8	11	2	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr11:125514071A>T	ENST00000534070.1	+	10	1264	c.1009A>T	c.(1009-1011)Aaa>Taa	p.K337*	CHEK1_ENST00000428830.2_Nonsense_Mutation_p.K337*|CHEK1_ENST00000544373.1_Nonsense_Mutation_p.K337*|CHEK1_ENST00000524737.1_Nonsense_Mutation_p.K337*|CHEK1_ENST00000438015.1_Nonsense_Mutation_p.K337*|CHEK1_ENST00000278916.3_Nonsense_Mutation_p.K337*|CHEK1_ENST00000427383.2_Nonsense_Mutation_p.K353*|CHEK1_ENST00000532449.1_3'UTR	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	337					cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		ATACATTGATAAATTGGTACA	0.473								Other conserved DNA damage response genes																													p.K337X		Atlas-SNP	.											.	CHEK1	44	.	0			c.A1009T						.						139	132	135					11																	125514071		2201	4299	6500	SO:0001587	stop_gained	1111	exon10			ATTGATAAATTGG	AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"CHK1 (checkpoint, S.pombe) homolog", "CHK1 checkpoint homolog (S. pombe)"			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.1009A>T	chr11.hg19:g.125514071A>T	ENSP00000435371:p.Lys337*	66.0	0.0		77.0	39.0	NM_001244846	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Nonsense_Mutation	SNP	ENST00000534070.1	hg19	CCDS8459.1	.	.	.	.	.	.	.	.	.	.	A	45	11.692524	0.99592	.	.	ENSG00000149554	ENST00000438015;ENST00000427383;ENST00000428830;ENST00000544373;ENST00000534070;ENST00000524737;ENST00000278916	.	.	.	5.72	5.72	0.89469	.	0.226724	0.45867	D	0.000334	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-21.1455	15.0031	0.71489	1.0:0.0:0.0:0.0	.	.	.	.	X	337;353;337;337;337;337;337	.	ENSP00000278916:K337X	K	+	1	0	CHEK1	125019281	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	1.494000	0.35616	2.194000	0.70268	0.533000	0.62120	AAA	.	.		0.473	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274		T	125514071	A	T	125514071	4	4	68	1	0	0	0	0	0	1	0	0	3336	363	13	4	1043	4	CHEK1	11	125514071	Nonsense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	7166407	125514071	9492445	121	8753										
KLRC4	8302	hgsc.bcm.edu	37	chr12	10561527	10561527	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttacaaggaataagaactatTgtttttaacacagtggccat	7	6	0	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr12:10561527T>A	ENST00000309384.1	-	2	451	c.270A>T	c.(268-270)acA>acT	p.T90T	KLRC4-KLRK1_ENST00000539300.1_Missense_Mutation_p.N82Y	NM_013431.2	NP_038459.1	O43908	NKG2F_HUMAN	killer cell lectin-like receptor subfamily C, member 4	90					cellular defense response (GO:0006968)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						TAAGAACTATTGTTTTTAACA	0.393																																					p.T90T		Atlas-SNP	.											.	KLRC4	23	.	0			c.A270T						.						136	139	138					12																	10561527		2203	4300	6503	SO:0001819	synonymous_variant	8302	exon2			AACTATTGTTTTT	U96846	CCDS8624.1	12p13.2-p12.3	2008-08-05			ENSG00000183542	ENSG00000183542		"Killer cell lectin-like receptors"	6377	protein-coding gene	gene with protein product		602893				9598306	Standard	NM_013431		Approved	NKG2-F	uc001qye.3	O43908	OTTHUMG00000168575	ENST00000309384.1:c.270A>T	chr12.hg19:g.10561527T>A		344.0	0.0		317.0	180.0	NM_013431	O60851	Silent	SNP	ENST00000309384.1	hg19	CCDS8624.1																																																																																			.	.		0.393	KLRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400108.1	NM_013431		A	10561527	T	A	10561527	2	1	68	1	0	0	0	0	0	0	0	1	8427	1799	63	4		4	KLRC4	12	10561527	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		10561527	123290368	122	8754										
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50190491	50190491	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ggcctgtgggcctctggggtAcccccaccccaagctgactt	12	16	1	1	rs34210566		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr12:50190491A>G	ENST00000335999.6	-	8	1353	c.1152T>C	c.(1150-1152)ggT>ggC	p.G384G		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	380	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CCTCTGGGGTACCCCCACCCC	0.662																																					p.G384G		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.T1152C						.						21	24	23					12																	50190491		1866	4078	5944	SO:0001819	synonymous_variant	57701	exon8			TGGGGTACCCCCA	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.1152T>C	chr12.hg19:g.50190491A>G		43.0	0.0		37.0	8.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	hg19	CCDS41781.2	.	.	.	.	.	.	.	.	.	.	A	3.399	-0.122675	0.06795	.	.	ENSG00000167566	ENST00000433948	.	.	.	4.12	-1.43	0.08884	.	.	.	.	.	T	0.18718	0.0449	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24977	-1.0145	4	.	.	.	-0.1118	1.0098	0.01495	0.258:0.3226:0.2622:0.1572	.	.	.	.	H	99	.	.	Y	-	1	0	NCKAP5L	48476758	0.000000	0.05858	0.863000	0.33907	0.890000	0.51754	-0.199000	0.09491	0.107000	0.17824	-0.543000	0.04237	TAC	.	.		0.662	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		G	50190491	A	G	50190491	2	3	68	1	0	0	0	0	0	0	0	1	10233	378	14	2		2	NCKAP5L	12	50190491	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	39628964	50190491	83661404	123	8755										
SP7	121340	hgsc.bcm.edu	37	chr12	53723037	53723037	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cttgtaaagggggctggataAgcatcccccatggttttgga	13	8	0	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr12:53723037A>T	ENST00000536324.2	-	3	472	c.189T>A	c.(187-189)gcT>gcA	p.A63A	SP7_ENST00000303846.3_Silent_p.A63A|SP7_ENST00000537210.2_Silent_p.A45A	NM_001173467.1	NP_001166938.1	Q8TDD2	SP7_HUMAN	Sp7 transcription factor	63					hematopoietic stem cell differentiation (GO:0060218)|osteoblast differentiation (GO:0001649)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(2)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	14						GGGCTGGATAAGCATCCCCCA	0.552																																					p.A63A		Atlas-SNP	.											.	SP7	30	.	0			c.T189A						.						185	188	187					12																	53723037		2046	4182	6228	SO:0001819	synonymous_variant	121340	exon2			TGGATAAGCATCC	AF477981	CCDS44897.1, CCDS73475.1	12q13.13	2013-01-08				ENSG00000170374		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	17321	protein-coding gene	gene with protein product		606633				11792318	Standard	NM_152860		Approved	osterix, OSX	uc001sct.3	Q8TDD2		ENST00000536324.2:c.189T>A	chr12.hg19:g.53723037A>T		67.0	0.0		63.0	24.0	NM_152860	B3KY26|Q3MJ72|Q7Z718	Silent	SNP	ENST00000536324.2	hg19	CCDS44897.1																																																																																			.	.		0.552	SP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406917.1			T	53723037	A	T	53723037	2	4	68	1	0	0	0	0	0	0	0	1	14984	59	3	4		4	SP7	12	53723037	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	3532546	53723037	80128858	124	8756										
CALCOCO1	57658	hgsc.bcm.edu	37	chr12	54118967	54118967	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttggggatgtaggtccgggcTacattgagaaagttgactcc	14	7	0	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr12:54118967T>A	ENST00000550804.1	-	2	120	c.60A>T	c.(58-60)gtA>gtT	p.V20V	CALCOCO1_ENST00000547885.1_5'UTR|CALCOCO1_ENST00000548263.1_Silent_p.V20V|CALCOCO1_ENST00000430117.2_Silent_p.V20V|CALCOCO1_ENST00000262059.4_Silent_p.V20V			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	20	N-terminal AD (CTNNB1 binding site). {ECO:0000250}.|p300 KIX-binding. {ECO:0000250}.				intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						AGGTCCGGGCTACATTGAGAA	0.527																																					p.V20V		Atlas-SNP	.											.	CALCOCO1	50	.	0			c.A60T						.						190	147	162					12																	54118967		2203	4300	6503	SO:0001819	synonymous_variant	57658	exon2			CCGGGCTACATTG	AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"coiled-coil leucine zipper coactivator 1", "inorganic pyrophosphatase activator"					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.60A>T	chr12.hg19:g.54118967T>A		230.0	0.0		246.0	146.0	NM_020898	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Silent	SNP	ENST00000550804.1	hg19	CCDS8864.1																																																																																			.	.		0.527	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898		A	54118967	T	A	54118967	2	1	68	1	0	0	0	0	0	0	0	1	2579	1509	53	4		4	CALCOCO1	12	54118967	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	395930	54118967	79732928	125	8757										
METTL1	25895	hgsc.bcm.edu	37	chr12	58163625	58163625	+	5'Flank	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gacaggcgatgttctggaagCcacctgcaggagctgcgcgt	15	11	1	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr12:58163625C>A	ENST00000300209.8	+	0	0				METTL1_ENST00000548681.1_5'Flank|METTL21B_ENST00000548256.1_5'Flank|METTL21B_ENST00000333012.5_5'Flank|METTL21B_ENST00000551420.1_5'Flank|METTL1_ENST00000257848.7_Intron|CYP27B1_ENST00000228606.4_5'Flank|METTL1_ENST00000324871.7_Missense_Mutation_p.G130V	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B							cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						GTTCTGGAAGCCACCTGCAGG	0.577																																					p.G130V		Atlas-SNP	.											.	METTL1	14	.	0			c.G389T						.						67	60	63					12																	58163625		2203	4300	6503	SO:0001631	upstream_gene_variant	4234	exon3			TGGAAGCCACCTG	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"family with sequence similarity 119, member B"	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459		chr12.hg19:g.58163625C>A	Exception_encountered	157.0	0.0		135.0	77.0	NM_005371	Q9H749|Q9Y3W2	Missense_Mutation	SNP	ENST00000300209.8	hg19	CCDS8957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.887|9.887	1.203272|1.203272	0.22121|0.22121	.|.	.|.	ENSG00000037897|ENSG00000037897	ENST00000324871|ENST00000548504	T|.	0.57595|.	0.39|.	5.12|5.12	4.21|4.21	0.49690|0.49690	.|.	0.529823|.	0.20871|.	N|.	0.084175|.	T|T	0.38878|0.38878	0.1057|0.1057	L|L	0.49126|0.49126	1.545|1.545	0.09310|0.09310	N|N	0.999997|0.999997	B|.	0.28760|.	0.221|.	B|.	0.32090|.	0.14|.	T|T	0.30822|0.30822	-0.9965|-0.9965	10|5	0.49607|.	T|.	0.09|.	-11.493|-11.493	4.7347|4.7347	0.12982|0.12982	0.1825:0.6479:0.0:0.1695|0.1825:0.6479:0.0:0.1695	.|.	130|.	Q9UBP6|.	TRMB_HUMAN|.	V|C	130|8	ENSP00000314441:G130V|.	ENSP00000314441:G130V|.	G|W	-|-	2|3	0|0	METTL1|METTL1	56449892|56449892	0.994000|0.994000	0.37717|0.37717	0.999000|0.999000	0.59377|0.59377	0.998000|0.998000	0.95712|0.95712	1.290000|1.290000	0.33319|0.33319	1.107000|1.107000	0.41642|0.41642	0.655000|0.655000	0.94253|0.94253	GGC|TGG	.	.		0.577	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433		A	58163625	C	A	58163625	1	1	68	0	1	0	0	0	0	0	0	0	9502	739	26	3		3	METTL1	12	58163625	5'Flank	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	4044658	58163625	75688270	126	8758										
LGR5	8549	hgsc.bcm.edu	37	chr12	71960645	71960645	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttaactggagcacagatctcAtctcttcctcaaaccgtctg	6	13	4	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr12:71960645A>T	ENST00000266674.5	+	11	1334	c.1023A>T	c.(1021-1023)tcA>tcT	p.S341S	LGR5_ENST00000540815.2_Silent_p.S317S|LGR5_ENST00000536515.1_Silent_p.S269S			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	341					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						CACAGATCTCATCTCTTCCTC	0.398																																					p.S341S		Atlas-SNP	.											.	LGR5	103	.	0			c.A1023T						.						217	198	205					12																	71960645		2203	4300	6503	SO:0001819	synonymous_variant	8549	exon11			GATCTCATCTCTT	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"GPCR / Class A : Orphans"	4504	protein-coding gene	gene with protein product		606667	"G protein-coupled receptor 49", "leucine-rich repeat-containing G protein-coupled receptor 5"	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.1023A>T	chr12.hg19:g.71960645A>T		125.0	0.0		176.0	91.0	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Silent	SNP	ENST00000266674.5	hg19	CCDS9000.1																																																																																			.	.		0.398	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667		T	71960645	A	T	71960645	2	4	68	1	0	0	0	0	0	0	0	1	8766	204	8	4		4	LGR5	12	71960645	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	13797020	71960645	61891250	127	8759										
USP44	84101	hgsc.bcm.edu	37	chr12	95927304	95927304	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tctgaggtagagagtactttAtcttttgctggtgatgctgg	13	5	2	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr12:95927304A>T	ENST00000258499.3	-	2	1017	c.729T>A	c.(727-729)gaT>gaA	p.D243E	USP44_ENST00000393091.2_Missense_Mutation_p.D243E|USP44_ENST00000537435.2_Missense_Mutation_p.D243E|USP44_ENST00000552440.1_Missense_Mutation_p.D243E	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	243					mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						AGAGTACTTTATCTTTTGCTG	0.413																																					p.D243E		Atlas-SNP	.											.	USP44	83	.	0			c.T729A						.						128	121	123					12																	95927304		2203	4300	6503	SO:0001583	missense	84101	exon2			TACTTTATCTTTT	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"Ubiquitin-specific peptidases"	20064	protein-coding gene	gene with protein product		610993	"ubiquitin specific protease 44"			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.729T>A	chr12.hg19:g.95927304A>T	ENSP00000258499:p.Asp243Glu	63.0	0.0		72.0	19.0	NM_032147	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	hg19	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	A	0.003	-2.485665	0.00163	.	.	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435	T;T;T;T	0.13778	3.8;3.8;2.56;3.8	4.96	-7.15	0.01521	.	1.368430	0.04103	N	0.313222	T	0.06826	0.0174	L	0.33485	1.01	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37619	-0.9698	10	0.06099	T	0.92	.	3.4391	0.07457	0.142:0.412:0.2847:0.1613	.	243	Q9H0E7	UBP44_HUMAN	E	243	ENSP00000258499:D243E;ENSP00000376806:D243E;ENSP00000448670:D243E;ENSP00000442629:D243E	ENSP00000258499:D243E	D	-	3	2	USP44	94451435	0.000000	0.05858	0.007000	0.13788	0.023000	0.10783	-1.056000	0.03489	-0.838000	0.04218	-1.765000	0.00666	GAT	.	.		0.413	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		T	95927304	A	T	95927304	3	4	68	1	0	0	0	0	1	0	0	0	17090	446	16	4	1429	4	USP44	12	95927304	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	23966659	95927304	37924591	128	8760										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112685903	112685903	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gtaatcataaaagaaaggcaTgttgttctccagtttcccct	7	9	2	1	rs374617773		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr12:112685903T>A	ENST00000430131.2	-	26	4095	c.2950A>T	c.(2950-2952)Atg>Ttg	p.M984L	HECTD4_ENST00000550722.1_Missense_Mutation_p.M1260L|HECTD4_ENST00000377560.5_Missense_Mutation_p.M1234L			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	984					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										AAGAAAGGCATGTTGTTCTCC	0.363																																					p.M1272L		Atlas-SNP	.											.	.	.	.	0			c.A3814T						.						96	92	93					12																	112685903		1920	4143	6063	SO:0001583	missense	283450	exon27			AAGGCATGTTGTT	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.2950A>T	chr12.hg19:g.112685903T>A	ENSP00000404379:p.Met984Leu	67.0	0.0		80.0	16.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	T	12.11	1.840430	0.32513	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.41065	1.02;1.02;1.01	5.79	4.66	0.58398	.	.	.	.	.	T	0.24044	0.0582	N	0.14661	0.345	0.19775	N	0.999958	B	0.06786	0.001	B	0.04013	0.001	T	0.07790	-1.0754	9	0.27082	T	0.32	.	6.9182	0.24371	0.0:0.2102:0.0:0.7898	.	984	Q9Y4D8	K0614_HUMAN	L	1234;984;1260	ENSP00000366783:M1234L;ENSP00000404379:M984L;ENSP00000449784:M1260L	ENSP00000366783:M1234L	M	-	1	0	C12orf51	111170286	0.998000	0.40836	1.000000	0.80357	0.897000	0.52465	0.848000	0.27710	2.223000	0.72356	0.454000	0.30748	ATG	.	.		0.363	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		A	112685903	T	A	112685903	3	1	68	1	0	0	0	0	1	0	0	0	1698	1464	51	4	9240	4	C12orf51	12	112685903	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	16758599	112685903	21165992	129	8761										
NOS1	4842	hgsc.bcm.edu	37	chr12	117669901	117669901	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctggaagatggtgcagggcgGgaggcggagctcgtctgtcc	19	9	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr12:117669901G>C	ENST00000338101.4	-	22	3377	c.3373C>G	c.(3373-3375)Ccg>Gcg	p.P1125A	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.P1091A			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GTGCAGGGCGGGAGGCGGAGC	0.602																																					p.P1125A	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C3373G						.						68	75	73					12																	117669901		2152	4265	6417	SO:0001583	missense	4842	exon23			AGGGCGGGAGGCG		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.3373C>G	chr12.hg19:g.117669901G>C	ENSP00000337459:p.Pro1125Ala	190.0	0.0		158.0	54.0	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	18.26	3.584315	0.65992	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.65916	-0.18;-0.18	4.55	4.55	0.56014	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.82006	0.4943	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85985	0.1485	10	0.87932	D	0	-28.2414	17.4925	0.87708	0.0:0.0:1.0:0.0	.	1091	P29475	NOS1_HUMAN	A	986;1091;1091;1125	ENSP00000320758:P1091A;ENSP00000337459:P1125A	ENSP00000320758:P1091A	P	-	1	0	NOS1	116154284	1.000000	0.71417	0.930000	0.37139	0.337000	0.28794	9.657000	0.98554	2.371000	0.80710	0.305000	0.20034	CCG	.	.		0.602	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			C	117669901	G	C	117669901	3	2	68	1	0	0	0	0	1	0	0	0	10550	1232	43	4	1065	4	NOS1	12	117669901	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	4983998	117669901	16181994	130	8762										
PAN3	255967	hgsc.bcm.edu	37	chr13	28748529	28748529	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aacaaaatatcccctgatgcAggtatccttagtataaattc	5	9	0	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr13:28748529A>T	ENST00000380958.3	+	2	703	c.551A>T	c.(550-552)cAg>cTg	p.Q184L	PAN3_ENST00000399613.1_Splice_Site_p.Q38L	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit											endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		CCCCTGATGCAGGTATCCTTA	0.378																																					p.Q184L		Atlas-SNP	.											.	PAN3	123	.	0			c.A551T						.						76	75	75					13																	28748529		2203	4300	6503	SO:0001630	splice_region_variant	255967	exon2			TGATGCAGGTATC	AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.552+1A>T	chr13.hg19:g.28748529A>T		33.0	0.0		29.0	20.0	NM_175854		Missense_Mutation	SNP	ENST00000380958.3	hg19	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	A	27.8	4.862722	0.91511	.	.	ENSG00000152520	ENST00000380958;ENST00000399613	T;T	0.61040	0.14;0.43	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.65933	0.2739	L	0.29908	0.895	0.80722	D	1	D;P;P	0.63046	0.992;0.908;0.908	D;D;P	0.72982	0.979;0.922;0.888	T	0.70178	-0.4943	10	0.87932	D	0	-7.4408	15.2951	0.73898	1.0:0.0:0.0:0.0	.	184;184;184	Q58A45-4;Q58A45;Q58A45-3	.;PAN3_HUMAN;.	L	184;38	ENSP00000370345:Q184L;ENSP00000382522:Q38L	ENSP00000370345:Q184L	Q	+	2	0	PAN3	27646529	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.842000	0.92136	2.013000	0.59113	0.482000	0.46254	CAG	.	.		0.378	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854	Missense_Mutation	T	28748529	A	T	28748529	5	4	68	1	0	0	0	0	0	0	1	0	11424	202	7	4	557	4	PAN3	13	28748529	Splice_Site	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10		28748529	86421349	131	8763										
USPL1	10208	hgsc.bcm.edu	37	chr13	31232186	31232186	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	acataagttttccatcccaaGttgtaaatacaaacatgcag	5	9	0	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr13:31232186G>T	ENST00000255304.4	+	9	2314	c.1972G>T	c.(1972-1974)Gtt>Ttt	p.V658F		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	658					Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		TCCATCCCAAGTTGTAAATAC	0.353																																					p.V658F	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.G1972T						.						77	76	76					13																	31232186		2203	4300	6503	SO:0001583	missense	10208	exon9			TCCCAAGTTGTAA	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 22"	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.1972G>T	chr13.hg19:g.31232186G>T	ENSP00000255304:p.Val658Phe	45.0	0.0		72.0	4.0	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	hg19	CCDS9336.1	.	.	.	.	.	.	.	.	.	.	G	3.048	-0.196008	0.06259	.	.	ENSG00000132952	ENST00000255304	T	0.15372	2.43	4.81	-2.03	0.07365	.	1.172930	0.06112	N	0.667347	T	0.07007	0.0178	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.14023	0.01	T	0.36817	-0.9732	10	0.22109	T	0.4	-0.3871	2.3207	0.04209	0.3403:0.3922:0.1484:0.1191	.	658	Q5W0Q7	USPL1_HUMAN	F	658	ENSP00000255304:V658F	ENSP00000255304:V658F	V	+	1	0	USPL1	30130186	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.010000	0.03656	-0.280000	0.09154	0.655000	0.94253	GTT	.	.		0.353	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		T	31232186	G	T	31232186	3	4	68	1	0	0	0	0	1	0	0	0	17107	1029	36	3	2002	3	USPL1	13	31232186	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	2483657	31232186	83937692	132	8764										
N4BP2L2	10443	hgsc.bcm.edu	37	chr13	33092036	33092036	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gaggtctttgtgtgcttttgTgtgatggttccactgaattc	12	6	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr13:33092036T>C	ENST00000267068.3	-	6	1819	c.1655A>G	c.(1654-1656)cAc>cGc	p.H552R	N4BP2L2_ENST00000504114.1_Missense_Mutation_p.H108R|N4BP2L2_ENST00000399396.3_Missense_Mutation_p.H123R|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.H552R|N4BP2L2_ENST00000357505.6_Missense_Mutation_p.H108R	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	552					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TGTGCTTTTGTGTGATGGTTC	0.408																																					p.H552R		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.A1655G						.						159	149	153					13																	33092036		2203	4300	6503	SO:0001583	missense	10443	exon6			CTTTTGTGTGATG	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"phosphonoformate immuno-associated protein 5"	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.1655A>G	chr13.hg19:g.33092036T>C	ENSP00000267068:p.His552Arg	74.0	0.0		77.0	43.0	NM_014887	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	hg19	CCDS9346.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.320244	0.60634	.	.	ENSG00000244754	ENST00000504114;ENST00000357505;ENST00000399396;ENST00000446957;ENST00000505213;ENST00000267068	T;T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2;1.2	5.59	5.59	0.84812	.	1.200800	0.06311	N	0.702734	T	0.51975	0.1706	L	0.47190	1.495	0.34385	D	0.693499	B;D;B;P	0.58620	0.355;0.983;0.07;0.51	B;P;B;B	0.54544	0.203;0.755;0.024;0.202	T	0.48559	-0.9025	10	0.52906	T	0.07	-0.3805	15.7685	0.78146	0.0:0.0:0.0:1.0	.	108;123;552;552	B4DPY1;Q92802-3;Q92802;Q92802-2	.;.;N42L2_HUMAN;.	R	108;108;123;552;552;552	ENSP00000427477:H108R;ENSP00000350104:H108R;ENSP00000382328:H123R;ENSP00000394239:H552R;ENSP00000423362:H552R;ENSP00000267068:H552R	ENSP00000267068:H552R	H	-	2	0	N4BP2L2	31990036	1.000000	0.71417	0.975000	0.42487	0.963000	0.63663	6.765000	0.74965	2.132000	0.65825	0.528000	0.53228	CAC	.	.		0.408	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887		C	33092036	T	C	33092036	3	2	68	1	0	0	0	0	1	0	0	0	10121	1696	59	2	1961	2	N4BP2L2	13	33092036	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	1859850	33092036	82077842	133	8765										
NBEA	26960	hgsc.bcm.edu	37	chr13	35923307	35923307	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aaatgaagctgagtttatttTgaacagacaaagagccgagg	11	5	0	5			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr13:35923307T>A	ENST00000400445.3	+	37	6500	c.5966T>A	c.(5965-5967)tTg>tAg	p.L1989*	NBEA_ENST00000540320.1_Nonsense_Mutation_p.L1989*|NBEA_ENST00000379939.2_Nonsense_Mutation_p.L1986*|NBEA_ENST00000310336.4_Nonsense_Mutation_p.L1989*	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1989					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GAGTTTATTTTGAACAGACAA	0.338																																					p.L1989X		Atlas-SNP	.											.	NBEA	340	.	0			c.T5966A						.						97	94	95					13																	35923307		1848	4099	5947	SO:0001587	stop_gained	26960	exon37			TTATTTTGAACAG	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5966T>A	chr13.hg19:g.35923307T>A	ENSP00000383295:p.Leu1989*	130.0	0.0		102.0	30.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Nonsense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	T	51	17.382056	0.99885	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	.	.	.	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6691	0.77258	0.0:0.0:0.0:1.0	.	.	.	.	X	1989;1989;1986;1989;616	.	ENSP00000308534:L1989X	L	+	2	0	NBEA	34821307	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.503000	0.81632	2.108000	0.64289	0.533000	0.62120	TTG	.	.		0.338	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35923307	T	A	35923307	4	1	68	1	0	0	0	0	0	1	0	0	10196	1821	63	4	6112	4	NBEA	13	35923307	Nonsense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	2831271	35923307	79246571	134	8766										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77763108	77763108	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctgagacagttcttgcaaaaGacctctttaaaatgtgtaca	7	8	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr13:77763108G>T	ENST00000544440.2	-	30	4132	c.4115C>A	c.(4114-4116)tCt>tAt	p.S1372Y	MYCBP2_ENST00000407578.2_Missense_Mutation_p.S1410Y|MYCBP2_ENST00000357337.6_Missense_Mutation_p.S1372Y|MYCBP2_ENST00000360084.5_5'UTR					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TCTTGCAAAAGACCTCTTTAA	0.378																																					p.S1410Y		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.C4229A						.						120	119	119					13																	77763108		2203	4300	6503	SO:0001583	missense	23077	exon30			GCAAAAGACCTCT	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.4115C>A	chr13.hg19:g.77763108G>T	ENSP00000444596:p.Ser1372Tyr	57.0	0.0		54.0	4.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	G	27.8	4.862122	0.91511	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.29917	1.55;1.55;1.55	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.27866	0.0686	N	0.08118	0	0.58432	D	0.999999	P	0.44090	0.826	P	0.47470	0.548	T	0.19418	-1.0306	10	0.66056	D	0.02	.	19.8965	0.96963	0.0:0.0:1.0:0.0	.	1372	O75592	MYCB2_HUMAN	Y	1372;1410;1372	ENSP00000349892:S1372Y;ENSP00000384288:S1410Y;ENSP00000444596:S1372Y	ENSP00000349892:S1372Y	S	-	2	0	MYCBP2	76661109	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.717000	0.92951	0.655000	0.94253	TCT	.	.		0.378	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		T	77763108	G	T	77763108	3	4	68	1	0	0	0	0	1	0	0	0	10027	942	33	3	10023	3	MYCBP2	13	77763108	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	41839801	77763108	37406770	135	8767										
ABCC4	10257	hgsc.bcm.edu	37	chr13	95822825	95822825	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgacttgcagctttgaggtaCtgcaactgatgagtcactaa	10	8	1	4			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr13:95822825C>G	ENST00000376887.4	-	14	1899	c.1785G>C	c.(1783-1785)caG>caC	p.Q595H	ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000412704.1_Missense_Mutation_p.Q595H|ABCC4_ENST00000536256.1_Missense_Mutation_p.Q520H|ABCC4_ENST00000431522.1_Missense_Mutation_p.Q595H	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	595	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	CTTTGAGGTACTGCAACTGAT	0.388																																					p.Q595H		Atlas-SNP	.											.	ABCC4	248	.	0			c.G1785C						.						103	95	98					13																	95822825		2203	4300	6503	SO:0001583	missense	10257	exon14			GAGGTACTGCAAC	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"ATP binding cassette transporters / subfamily C"	55	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter (ABC superfamily)", "bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)", "multidrug resistance-associated protein 4", "multispecific organic anion transporter B"	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.1785G>C	chr13.hg19:g.95822825C>G	ENSP00000366084:p.Gln595His	47.0	0.0		44.0	19.0	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	hg19	CCDS9474.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.491407	0.44249	.	.	ENSG00000125257	ENST00000412704;ENST00000376887;ENST00000536256;ENST00000431522	D;D;D;D	0.88741	-2.42;-2.42;-1.81;-2.42	5.61	3.75	0.43078	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.87164	0.6109	L	0.31371	0.925	0.80722	D	1	B;B;P;B;P	0.47841	0.246;0.386;0.648;0.386;0.901	B;B;P;B;P	0.54544	0.083;0.175;0.596;0.175;0.755	D	0.85787	0.1365	10	0.87932	D	0	.	8.0651	0.30657	0.0:0.6654:0.0:0.3346	.	520;595;595;595;595	B7Z3Q7;A8K2Q2;O15439-2;Q8IVZ4;O15439	.;.;.;.;MRP4_HUMAN	H	595;595;520;595	ENSP00000388657:Q595H;ENSP00000366084:Q595H;ENSP00000442024:Q520H;ENSP00000398562:Q595H	ENSP00000366084:Q595H	Q	-	3	2	ABCC4	94620826	0.999000	0.42202	1.000000	0.80357	0.967000	0.64934	0.626000	0.24492	0.624000	0.30286	0.555000	0.69702	CAG	.	.		0.388	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845		G	95822825	C	G	95822825	3	3	68	1	0	0	0	0	1	0	0	0	55	564	20	4	2313	4	ABCC4	13	95822825	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	18059717	95822825	19347053	136	8768										
FSCB	84075	hgsc.bcm.edu	37	chr14	44975744	44975744	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgttgttccttgtccactttTtctacaggggggatgttcat	10	8	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr14:44975744T>C	ENST00000340446.4	-	1	738	c.447A>G	c.(445-447)gaA>gaG	p.E149E	RP11-163M18.1_ENST00000556228.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	149						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		TGTCCACTTTTTCTACAGGGG	0.418																																					p.E149E		Atlas-SNP	.											.	FSCB	173	.	0			c.A447G						.						195	195	195					14																	44975744		2203	4300	6503	SO:0001819	synonymous_variant	84075	exon1			CACTTTTTCTACA	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"chromosome 14 open reading frame 155"	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.447A>G	chr14.hg19:g.44975744T>C		146.0	0.0		167.0	107.0	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Silent	SNP	ENST00000340446.4	hg19	CCDS9679.1																																																																																			.	.		0.418	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		C	44975744	T	C	44975744	2	2	68	1	0	0	0	0	0	0	0	1	6074	1838	64	2		2	FSCB	14	44975744	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		44975744	62373796	137	8769										
PLEKHG3	26030	hgsc.bcm.edu	37	chr14	65209799	65209799	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ggctggggagatgtcaccacAgcgtttcttcttcaacccgt	11	12	4	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr14:65209799A>T	ENST00000394691.1	+	17	3185	c.3038A>T	c.(3037-3039)cAg>cTg	p.Q1013L	PLEKHG3_ENST00000247226.7_Missense_Mutation_p.Q957L|PLEKHG3_ENST00000484731.2_Missense_Mutation_p.Q518L|PLEKHG3_ENST00000471182.2_Missense_Mutation_p.Q546L|PLEKHG3_ENST00000492928.1_Intron			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	1013							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		ATGTCACCACAGCGTTTCTTC	0.642																																					p.Q957L		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.A2870T						.						84	89	88					14																	65209799		2203	4300	6503	SO:0001583	missense	26030	exon15			CACCACAGCGTTT	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20364	protein-coding gene	gene with protein product			"KIAA0599"	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.3038A>T	chr14.hg19:g.65209799A>T	ENSP00000378183:p.Gln1013Leu	92.0	0.0		73.0	22.0	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Missense_Mutation	SNP	ENST00000394691.1	hg19		.	.	.	.	.	.	.	.	.	.	A	7.975	0.749874	0.15778	.	.	ENSG00000126822	ENST00000247226;ENST00000394691;ENST00000471182;ENST00000484731	T;T;T;T	0.60672	0.62;0.17;1.52;1.52	5.55	-2.69	0.06022	.	0.515912	0.18076	N	0.152448	T	0.36936	0.0985	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.26547	0.152;0.066;0.014;0.024	B;B;B;B	0.24394	0.053;0.053;0.013;0.03	T	0.16335	-1.0406	10	0.46703	T	0.11	.	6.4868	0.22093	0.5123:0.2439:0.2438:0.0	.	546;518;1013;957	A1L390-2;G3V311;A1L390;A1L390-3	.;.;PKHG3_HUMAN;.	L	957;1013;546;518	ENSP00000247226:Q957L;ENSP00000378183:Q1013L;ENSP00000450945:Q546L;ENSP00000450973:Q518L	ENSP00000247226:Q957L	Q	+	2	0	PLEKHG3	64279552	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.084000	0.14891	-0.442000	0.07190	-1.101000	0.02118	CAG	.	.		0.642	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549		T	65209799	A	T	65209799	3	4	68	1	0	0	0	0	1	0	0	0	12079	188	7	4	2924	4	PLEKHG3	14	65209799	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	20234055	65209799	42139741	138	8770										
C14orf145	145508	hgsc.bcm.edu	37	chr14	80997175	80997175	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgaagtctttgaaatcttctAgtaggctcagtttctcaggc	9	8	5	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr14:80997175A>C	ENST00000555265.1	-	22	3311	c.2936T>G	c.(2935-2937)cTa>cGa	p.L979R	CEP128_ENST00000281129.3_Missense_Mutation_p.L979R|CEP128_ENST00000553717.1_5'UTR			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	979						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						GAAATCTTCTAGTAGGCTCAG	0.383																																					p.L979R		Atlas-SNP	.											.	CEP128	146	.	0			c.T2936G						.						93	87	89					14																	80997175		2203	4300	6503	SO:0001583	missense	145508	exon21			TCTTCTAGTAGGC	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2936T>G	chr14.hg19:g.80997175A>C	ENSP00000451162:p.Leu979Arg	71.0	0.0		68.0	38.0	NM_152446	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	hg19	CCDS32130.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.062342	0.76187	.	.	ENSG00000100629	ENST00000281129;ENST00000555265;ENST00000393619	T;T	0.58060	0.36;0.36	5.62	5.62	0.85841	.	0.104996	0.43110	D	0.000601	T	0.68742	0.3034	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66674	-0.5864	10	0.35671	T	0.21	.	16.1219	0.81365	1.0:0.0:0.0:0.0	.	979	Q6ZU80	CE128_HUMAN	R	979	ENSP00000281129:L979R;ENSP00000451162:L979R	ENSP00000281129:L979R	L	-	2	0	CEP128	80066928	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	7.135000	0.77276	2.254000	0.74563	0.528000	0.53228	CTA	.	.		0.383	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		C	80997175	A	C	80997175	3	2	68	1	0	0	0	0	1	0	0	0	1751	420	15	5	364	5	C14orf145	14	80997175	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	15787376	80997175	26352365	139	8771										
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91787522	91787522	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cgcacttgaggccgctctccTccaacaccagggacgcgtcc	10	18	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr14:91787522T>A	ENST00000389857.6	-	13	1555	c.1469A>T	c.(1468-1470)gAg>gTg	p.E490V		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	490					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GCCGCTCTCCTCCAACACCAG	0.622																																					p.E490V		Atlas-SNP	.											.	CCDC88C	192	.	0			c.A1469T						.						45	46	46					14																	91787522		2019	4169	6188	SO:0001583	missense	440193	exon13			CTCTCCTCCAACA		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"Dvl-associating protein with a high frequency of leucine residues", "spinocerebellar ataxia 40"	611204	"KIAA1509"	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.1469A>T	chr14.hg19:g.91787522T>A	ENSP00000374507:p.Glu490Val	110.0	0.0		97.0	22.0	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	hg19	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	T	16.57	3.158978	0.57368	.	.	ENSG00000015133	ENST00000389857	T	0.23754	1.89	4.98	4.98	0.66077	.	0.298098	0.23396	U	0.048640	T	0.41143	0.1146	M	0.70595	2.14	0.80722	D	1	D	0.53151	0.958	P	0.55161	0.77	T	0.35847	-0.9772	10	0.72032	D	0.01	-27.8784	9.85	0.41051	0.0:0.088:0.0:0.912	.	490	Q9P219	DAPLE_HUMAN	V	490	ENSP00000374507:E490V	ENSP00000374507:E490V	E	-	2	0	CCDC88C	90857275	1.000000	0.71417	0.999000	0.59377	0.247000	0.25773	4.525000	0.60559	2.011000	0.59026	0.459000	0.35465	GAG	.	.		0.622	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		A	91787522	T	A	91787522	3	1	68	1	0	0	0	0	1	0	0	0	2867	1551	54	4	4689	4	CCDC88C	14	91787522	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	10790347	91787522	15562018	140	8772										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54306838	54306838	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctaatggaagctctctcctgTcatcttcggaccgggagcta	10	12	3	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr15:54306838T>A	ENST00000260323.11	+	1	1738	c.1738T>A	c.(1738-1740)Tca>Aca	p.S580T	UNC13C_ENST00000545554.1_Missense_Mutation_p.S580T|UNC13C_ENST00000537900.1_Missense_Mutation_p.S580T	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	580					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CTCTCTCCTGTCATCTTCGGA	0.438																																					p.S580T		Atlas-SNP	.											.	UNC13C	674	.	0			c.T1738A						.						66	64	64					15																	54306838		1892	4113	6005	SO:0001583	missense	440279	exon1			CTCCTGTCATCTT	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.1738T>A	chr15.hg19:g.54306838T>A	ENSP00000260323:p.Ser580Thr	44.0	0.0		35.0	28.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	T	17.91	3.503774	0.64298	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.83914	-1.78;-1.78;-1.78	5.17	5.17	0.71159	.	.	.	.	.	D	0.84906	0.5576	L	0.27053	0.805	0.47547	D	0.999452	D	0.58268	0.982	D	0.67548	0.952	D	0.86873	0.2037	9	0.72032	D	0.01	.	14.3313	0.66559	0.0:0.0:0.0:1.0	.	580	Q8NB66	UN13C_HUMAN	T	580	ENSP00000260323:S580T;ENSP00000438156:S580T;ENSP00000442569:S580T	ENSP00000260323:S580T	S	+	1	0	UNC13C	52094130	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.522000	0.81844	2.168000	0.68352	0.533000	0.62120	TCA	.	.		0.438	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54306838	T	A	54306838	3	1	68	1	0	0	0	0	1	0	0	0	17001	1667	58	4	1740	4	UNC13C	15	54306838	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		54306838	48224554	141	8773										
MESDC1	59274	hgsc.bcm.edu	37	chr15	81295203	81295203	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctcaagttcctgacggacgcGtgcgccctggccagtgacaa	12	14	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr15:81295203G>T	ENST00000267984.2	+	1	1909	c.591G>T	c.(589-591)gcG>gcT	p.A197A		NM_022566.2	NP_072088.1	Q9H1K6	MESD1_HUMAN	mesoderm development candidate 1	197										endometrium(1)|lung(2)	3						TGACGGACGCGTGCGCCCTGG	0.692																																					p.A197A		Atlas-SNP	.											.	MESDC1	7	.	0			c.G591T						.						29	30	30					15																	81295203		2198	4293	6491	SO:0001819	synonymous_variant	59274	exon1			GGACGCGTGCGCC	AY007810	CCDS10316.1	15q13	2008-07-18			ENSG00000140406	ENSG00000140406			13519	protein-coding gene	gene with protein product		615466				11247670	Standard	NM_022566		Approved	MGC99595	uc002bfz.3	Q9H1K6	OTTHUMG00000144185	ENST00000267984.2:c.591G>T	chr15.hg19:g.81295203G>T		2.0	0.0		9.0	7.0	NM_022566		Silent	SNP	ENST00000267984.2	hg19	CCDS10316.1																																																																																			.	.		0.692	MESDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291390.1	NM_022566		T	81295203	G	T	81295203	2	4	68	1	0	0	0	0	0	0	0	1	9489	1132	40	1		1	MESDC1	15	81295203	Silent	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	26988365	81295203	21236189	142	8774										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101606245	101606246	+	Frame_Shift_Del	DEL	GT	GT	-													0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ctccccagcaagttcttccaGtgtgcctttctccaccgact							TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr15:101606245_101606246delGT	ENST00000388948.3	+	32	5962_5963	c.5603_5604delGT	c.(5602-5604)agtfs	p.S1868fs	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Frame_Shift_Del_p.S1865fs|LRRK1_ENST00000532145.1_3'UTR	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AGTTCTTCCAGTGTGCCTTTCT	0.624																																					p.1868_1868del		Atlas-Indel,Pindel	.											.	LRRK1	310	.	0			c.5602_5603del						.																																			SO:0001589	frameshift_variant	79705	exon32			.	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.5603_5604delGT	chr15.hg19:g.101606247_101606248delGT	ENSP00000373600:p.Ser1868fs	104.0	0.0		70.0	57.0	NM_024652		Frame_Shift_Del	DEL	ENST00000388948.3	hg19	CCDS42086.1																																																																																			.	.		0.624	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		-	101606246	GT	-	101606245	7	5	68	1	0	1	0	1	0	0	0	0	9041	1029	36	0	5725	0	LRRK1	15	101606245	Frame_Shift_Del	DEL	GT	TCGA-CC-A5UD-01A-11D-A28X-10	20311042	101606245	925147	143	8775										
CLCN7	1186	hgsc.bcm.edu	37	chr16	1511413	1511413	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gcgtccagctcaccgtgtgaTtgatccgccgctcctcctcc	9	18	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr16:1511413T>A	ENST00000382745.4	-	4	949	c.344A>T	c.(343-345)aAt>aTt	p.N115I	CLCN7_ENST00000448525.1_Missense_Mutation_p.N91I|CLCN7_ENST00000262318.8_Missense_Mutation_p.N91I	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	115					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				CACCGTGTGATTGATCCGCCG	0.682																																					p.N115I		Atlas-SNP	.											.	CLCN7	53	.	0			c.A344T						.						23	18	20					16																	1511413		2105	4141	6246	SO:0001583	missense	1186	exon4			GTGTGATTGATCC	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ion channels / Chloride channels : Voltage-sensitive"	2025	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 63"	602727	"chloride channel 7"			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.344A>T	chr16.hg19:g.1511413T>A	ENSP00000372193:p.Asn115Ile	68.0	0.0		59.0	26.0	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Missense_Mutation	SNP	ENST00000382745.4	hg19	CCDS32361.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.578206	0.45902	.	.	ENSG00000103249	ENST00000448525;ENST00000262318;ENST00000382745;ENST00000428756	D;D	0.91894	-2.93;-2.93	5.0	5.0	0.66597	Chloride channel, core (2);	0.132635	0.64402	D	0.000002	D	0.84674	0.5524	N	0.20986	0.625	0.50467	D	0.999871	B;P	0.49961	0.395;0.93	B;B	0.39068	0.197;0.289	D	0.83988	0.0336	10	0.27082	T	0.32	-40.6302	13.5235	0.61582	0.0:0.0:0.0:1.0	.	91;115	E9PDB9;P51798	.;CLCN7_HUMAN	I	91;68;115;57	ENSP00000410907:N91I;ENSP00000372193:N115I	ENSP00000262318:N68I	N	-	2	0	CLCN7	1451414	1.000000	0.71417	0.998000	0.56505	0.050000	0.14768	4.363000	0.59473	1.869000	0.54173	0.383000	0.25322	AAT	.	.		0.682	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		A	1511413	T	A	1511413	3	1	68	1	0	0	0	0	1	0	0	0	3470	1493	52	4	2161	4	CLCN7	16	1511413	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		1511413	88843340	144	8776										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	10032379	10032379	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gcttgctgctggatggacgcTccaaactggaagaaggtaga	14	8	0	2	rs35898789		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr16:10032379T>A	ENST00000396573.2	-	4	753	c.444A>T	c.(442-444)ggA>ggT	p.G148G	GRIN2A_ENST00000562109.1_Silent_p.G148G|GRIN2A_ENST00000566670.1_5'UTR|GRIN2A_ENST00000396575.2_Silent_p.G148G|GRIN2A_ENST00000330684.3_Silent_p.G148G|GRIN2A_ENST00000535259.1_5'UTR|GRIN2A_ENST00000404927.2_Silent_p.G148G	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	148					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GGATGGACGCTCCAAACTGGA	0.507																																					p.G148G		Atlas-SNP	.											.	GRIN2A	366	.	0			c.A444T						.						55	50	52					16																	10032379		2193	4288	6481	SO:0001819	synonymous_variant	2903	exon4			GGACGCTCCAAAC		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.444A>T	chr16.hg19:g.10032379T>A		26.0	0.0		29.0	18.0	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	hg19	CCDS10539.1																																																																																			.	.		0.507	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	10032379	T	A	10032379	2	1	68	1	0	0	0	0	0	0	0	1	6788	1538	54	4		4	GRIN2A	16	10032379	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	8520966	10032379	80322374	145	8777										
ERN2	10595	hgsc.bcm.edu	37	chr16	23711862	23711862	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttgttcacacaggctcacctTcagggtcgtcgagtggctgg	13	11	3	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr16:23711862T>A	ENST00000457008.2	-	12	1405	c.1367A>T	c.(1366-1368)gAa>gTa	p.E456V	ERN2_ENST00000256797.4_Missense_Mutation_p.E556V					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		AGGCTCACCTTCAGGGTCGTC	0.567																																					p.E556V		Atlas-SNP	.											.	ERN2	131	.	0			c.A1667T						.						99	99	99					16																	23711862		2197	4300	6497	SO:0001583	missense	10595	exon13			TCACCTTCAGGGT	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"ER to nucleus signalling 2"			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.1367A>T	chr16.hg19:g.23711862T>A	ENSP00000413812:p.Glu456Val	58.0	0.0		59.0	34.0	NM_033266		Missense_Mutation	SNP	ENST00000457008.2	hg19		.	.	.	.	.	.	.	.	.	.	T	10.35	1.325269	0.24080	.	.	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.61627	0.09;0.16	4.1	4.1	0.47936	.	0.463784	0.22028	N	0.065637	T	0.43299	0.1241	L	0.27053	0.805	0.48185	D	0.999602	P;B	0.48694	0.914;0.183	B;B	0.42995	0.404;0.058	T	0.29761	-1.0001	10	0.33940	T	0.23	.	9.7718	0.40593	0.0:0.0:0.0:1.0	.	456;508	E7ETG2;A5YM65	.;.	V	556;456	ENSP00000256797:E556V;ENSP00000413812:E456V	ENSP00000256797:E556V	E	-	2	0	ERN2	23619363	1.000000	0.71417	0.994000	0.49952	0.045000	0.14185	1.870000	0.39529	2.083000	0.62718	0.459000	0.35465	GAA	.	.		0.567	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1			A	23711862	T	A	23711862	3	1	68	1	0	0	0	0	1	0	0	0	5240	1783	62	4	1297	4	ERN2	16	23711862	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	13679483	23711862	66642891	146	8778										
GPR172B	55065	hgsc.bcm.edu	37	chr17	4936947	4936947	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	atcaggcccagcaggaaggcAccatgggctgagaacagctg	14	11	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr17:4936947A>T	ENST00000424747.1	-	3	1549	c.837T>A	c.(835-837)ggT>ggA	p.G279G	SLC52A1_ENST00000254853.5_Silent_p.G279G|SLC52A1_ENST00000512825.2_Silent_p.G279G	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	279					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										GCAGGAAGGCACCATGGGCTG	0.622																																					p.G279G		Atlas-SNP	.											.	.	.	.	0			c.T837A						.						68	50	56					17																	4936947		2203	4300	6503	SO:0001819	synonymous_variant	55065	exon3			GAAGGCACCATGG	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"Solute carriers"	30225	protein-coding gene	gene with protein product	"riboflavin transporter 1"	607883	"G protein-coupled receptor 172B"	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.837T>A	chr17.hg19:g.4936947A>T		108.0	0.0		84.0	72.0	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Silent	SNP	ENST00000424747.1	hg19	CCDS11066.1																																																																																			.	.		0.622	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986		T	4936947	A	T	4936947	2	4	68	1	0	0	0	0	0	0	0	1	6678	146	6	4		4	GPR172B	17	4936947	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10		4936947	76258263	147	8779										
TP53	7157	hgsc.bcm.edu	37	chr17	7578461	7578461	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gtagatggccatggcgcggaCgcgggtgccgggcgggggtg	23	9	0	1	rs121912654		TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr17:7578461C>A	ENST00000269305.4	-	5	658	c.469G>T	c.(469-471)Gtc>Ttc	p.V157F	TP53_ENST00000445888.2_Missense_Mutation_p.V157F|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.V157F|TP53_ENST00000413465.2_Missense_Mutation_p.V157F|TP53_ENST00000420246.2_Missense_Mutation_p.V157F|TP53_ENST00000359597.4_Missense_Mutation_p.V157F	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	157	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> A (in sporadic cancers; somatic mutation).|V -> D (in sporadic cancers; somatic mutation).|V -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|V -> G (in sporadic cancers; somatic mutation).|V -> I (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9419979}.|V -> L (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V157F(161)|p.V157I(10)|p.0?(8)|p.V157L(6)|p.V64F(6)|p.V25F(6)|p.R156_I162delRVRAMAI(2)|p.T155fs*23(2)|p.V157del(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.V157fs*22(2)|p.V157fs*24(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156_V157del(1)|p.R156_V157insV(1)|p.R156_R158delRVR(1)|p.R156fs*12(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.V157_M160delVRAM(1)|p.D148fs*23(1)|p.V157_R158delVR(1)|p.S149fs*72(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*20(1)|p.V157_I162delVRAMAI(1)|p.V157fs*23(1)|p.V157fs*21(1)|p.V157fs*25(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGCGCGGACGCGGGTGCCG	0.617		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.V157F	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,+1,5	TP53	33396	.	231	Substitution - Missense(189)|Deletion - Frameshift(15)|Deletion - In frame(14)|Whole gene deletion(8)|Insertion - Frameshift(3)|Insertion - In frame(1)|Complex - frameshift(1)	lung(69)|liver(30)|upper_aerodigestive_tract(26)|breast(19)|oesophagus(14)|ovary(13)|stomach(9)|large_intestine(7)|haematopoietic_and_lymphoid_tissue(7)|central_nervous_system(6)|bone(5)|vulva(4)|urinary_tract(4)|skin(3)|pancreas(3)|endometrium(2)|kidney(2)|biliary_tract(2)|soft_tissue(2)|prostate(1)|adrenal_gland(1)|salivary_gland(1)|thymus(1)	c.G469T						.						50	52	51					17																	7578461		2202	4300	6502	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CGCGGACGCGGGT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.469G>T	chr17.hg19:g.7578461C>A	ENSP00000269305:p.Val157Phe	199.0	2.0		82.0	61.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.865109	0.32977	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99822	-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94	5.47	2.42	0.29668	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.216722	0.39210	N	0.001429	D	0.99718	0.9891	M	0.86420	2.815	0.33606	D	0.603	D;D;D;D;D;D;D	0.89917	1.0;0.998;0.999;0.999;0.999;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.997;0.994;0.984;0.981;0.996;0.998;0.996	D	0.97998	1.0358	10	0.72032	D	0.01	-16.7152	5.3541	0.16051	0.0:0.6119:0.146:0.2421	.	118;157;157;64;157;157;157	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	F	157;157;157;157;157;157;146;64;25;64;25;157	ENSP00000410739:V157F;ENSP00000352610:V157F;ENSP00000269305:V157F;ENSP00000398846:V157F;ENSP00000391127:V157F;ENSP00000391478:V157F;ENSP00000425104:V25F;ENSP00000423862:V64F;ENSP00000424104:V157F	ENSP00000269305:V157F	V	-	1	0	TP53	7519186	0.137000	0.22531	0.013000	0.15412	0.150000	0.21749	0.548000	0.23314	0.386000	0.24997	-0.253000	0.11424	GTC	.	.		0.617	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578461	C	A	7578461	3	1	68	1	0	0	0	0	1	0	0	0	16396	536	19	1	829	1	TP53	17	7578461	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	2641514	7578461	73616749	148	8780										
ZNF286A	57335	hgsc.bcm.edu	37	chr17	15619693	15619693	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aaggatcttatgccttccatAcacttgaaaaaagcttgaaa	6	8	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr17:15619693A>T	ENST00000464847.2	+	5	1208	c.655A>T	c.(655-657)Aca>Tca	p.T219S	ZNF286A_ENST00000593105.1_Missense_Mutation_p.T209S|ZNF286A_ENST00000395894.2_3'UTR|ZNF286A_ENST00000421016.1_Missense_Mutation_p.T219S|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000581529.1_3'UTR|ZNF286A_ENST00000413242.2_Missense_Mutation_p.T219S|ZNF286A_ENST00000583566.1_Missense_Mutation_p.T219S|ZNF286A_ENST00000472486.1_3'UTR			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	219					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		TGCCTTCCATACACTTGAAAA	0.338																																					p.T219S		Atlas-SNP	.											.	ZNF286A	58	.	0			c.A655T						.						36	35	35					17																	15619693		2183	4272	6455	SO:0001583	missense	57335	exon6			TTCCATACACTTG	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"Zinc fingers, C2H2-type", "-"	13501	protein-coding gene	gene with protein product			"zinc finger protein 286"	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.655A>T	chr17.hg19:g.15619693A>T	ENSP00000464218:p.Thr219Ser	86.0	0.0		96.0	49.0	NM_020652	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	hg19	CCDS11172.1	.	.	.	.	.	.	.	.	.	.	a	2.925	-0.222388	0.06061	.	.	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894	T;T	0.28255	1.62;1.62	4.06	2.98	0.34508	.	0.812016	0.10443	N	0.674020	T	0.23370	0.0565	L	0.42744	1.35	0.09310	N	1	B	0.17038	0.02	B	0.16722	0.016	T	0.29610	-1.0006	10	0.21540	T	0.41	-0.9894	5.4125	0.16356	0.774:0.0:0.226:0.0	.	219	Q9HBT8	Z286A_HUMAN	S	219;209;219	ENSP00000397163:T219S;ENSP00000408168:T209S	ENSP00000435872:T219S	T	+	1	0	ZNF286A	15560418	0.004000	0.15560	0.509000	0.27700	0.825000	0.46686	1.156000	0.31712	0.729000	0.32403	0.528000	0.53228	ACA	.	.		0.338	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		T	15619693	A	T	15619693	3	4	68	1	0	0	0	0	1	0	0	0	17838	391	14	4	673	4	ZNF286A	17	15619693	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	8041232	15619693	65575517	149	8781										
RHBDL3	162494	hgsc.bcm.edu	37	chr17	30616020	30616020	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ccaccctggttcatgatcacAgtcacgctgctggaggcaag	11	13	3	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr17:30616020A>T	ENST00000269051.4	+	4	518	c.504A>T	c.(502-504)acA>acT	p.T168T	RHBDL3_ENST00000536287.1_Silent_p.T70T|RHBDL3_ENST00000538145.1_Silent_p.T160T	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	168						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				TCATGATCACAGTCACGCTGC	0.597																																					p.T168T		Atlas-SNP	.											.	RHBDL3	49	.	0			c.A504T						.						50	49	49					17																	30616020		2203	4300	6503	SO:0001819	synonymous_variant	162494	exon4			GATCACAGTCACG	AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"EF-hand domain containing"	16502	protein-coding gene	gene with protein product			"rhomboid, veinlet-like 4 (Drosophila)"	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.504A>T	chr17.hg19:g.30616020A>T		246.0	0.0		180.0	106.0	NM_138328	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Silent	SNP	ENST00000269051.4	hg19	CCDS32613.1																																																																																			.	.		0.597	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328		T	30616020	A	T	30616020	2	4	68	1	0	0	0	0	0	0	0	1	13338	175	7	4		4	RHBDL3	17	30616020	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	14996327	30616020	50579190	150	8782										
MRPL45	84311	hgsc.bcm.edu	37	chr17	36478426	36478426	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tggccctcagctgaaaccagAagaagaatatgaagaggcac	11	9	1	6			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr17:36478426A>T	ENST00000312513.5	+	8	1030	c.869A>T	c.(868-870)gAa>gTa	p.E290V	GPR179_ENST00000584976.1_5'Flank	NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	290						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CTGAAACCAGAAGAAGAATAT	0.542											OREG0024353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E290V		Atlas-SNP	.											.	MRPL45	27	.	0			c.A869T						.						70	70	70					17																	36478426		2203	4300	6503	SO:0001583	missense	84311	exon8			AACCAGAAGAAGA	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"Mitochondrial ribosomal proteins / large subunits"	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.869A>T	chr17.hg19:g.36478426A>T	ENSP00000308901:p.Glu290Val	86.0	0.0	863	50.0	11.0	NM_032351	A1L436|Q6ZMJ5	Missense_Mutation	SNP	ENST00000312513.5	hg19	CCDS11326.1	.	.	.	.	.	.	.	.	.	.	A	4.085	0.013785	0.07959	.	.	ENSG00000174100	ENST00000312513	T	0.43294	0.95	5.23	1.83	0.25207	.	0.806405	0.11676	N	0.540263	T	0.19485	0.0468	N	0.08118	0	0.09310	N	0.999999	B	0.12013	0.005	B	0.04013	0.001	T	0.24225	-1.0166	10	0.21014	T	0.42	1.5056	5.7292	0.18030	0.1697:0.3013:0.529:0.0	.	290	Q9BRJ2	RM45_HUMAN	V	290	ENSP00000308901:E290V	ENSP00000308901:E290V	E	+	2	0	MRPL45	33731953	0.737000	0.28175	0.083000	0.20561	0.002000	0.02628	1.100000	0.31025	0.321000	0.23259	-0.202000	0.12741	GAA	.	.		0.542	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351		T	36478426	A	T	36478426	3	4	68	1	0	0	0	0	1	0	0	0	9818	246	9	4	829	4	MRPL45	17	36478426	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	5862406	36478426	44716784	151	8783										
KIF19	124602	hgsc.bcm.edu	37	chr17	72351437	72351437	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cccatggcaaagatggatgcTcccggcataactgaggggcc	13	12	0	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr17:72351437T>C	ENST00000389916.4	+	20	3121	c.2983T>C	c.(2983-2985)Tcc>Ccc	p.S995P		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	995					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						AGATGGATGCTCCCGGCATAA	0.652																																					p.S995P		Atlas-SNP	.											.	KIF19	102	.	0			c.T2983C						.						29	31	30					17																	72351437		1941	4139	6080	SO:0001583	missense	124602	exon20			GGATGCTCCCGGC	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2983T>C	chr17.hg19:g.72351437T>C	ENSP00000374566:p.Ser995Pro	52.0	0.0		53.0	10.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	T	9.744	1.165620	0.21538	.	.	ENSG00000196169	ENST00000389916	T	0.70399	-0.48	4.69	1.19	0.21007	.	.	.	.	.	T	0.38214	0.1032	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21484	-1.0244	9	0.33940	T	0.23	.	3.2687	0.06874	0.2264:0.3311:0.0:0.4424	.	995	Q2TAC6	KIF19_HUMAN	P	995	ENSP00000374566:S995P	ENSP00000374566:S995P	S	+	1	0	KIF19	69863032	0.000000	0.05858	0.015000	0.15790	0.580000	0.36256	0.378000	0.20569	0.033000	0.15463	0.454000	0.30748	TCC	.	.		0.652	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		C	72351437	T	C	72351437	3	2	68	1	0	0	0	0	1	0	0	0	8291	1551	54	2	3061	2	KIF19	17	72351437	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	35873011	72351437	8843773	152	8784										
GALK1	2584	hgsc.bcm.edu	37	chr17	73760089	73760089	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cagccgctggggctcatcggCaccctcagaggtggtgagga	16	12	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr17:73760089C>A	ENST00000588479.1	-	2	818	c.244G>T	c.(244-246)Gcc>Tcc	p.A82S	GALK1_ENST00000437911.1_Missense_Mutation_p.A112S|GALK1_ENST00000225614.2_Missense_Mutation_p.A82S			P51570	GALK1_HUMAN	galactokinase 1	82					carbohydrate metabolic process (GO:0005975)|galactitol metabolic process (GO:0019402)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|galactose binding (GO:0005534)			endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	5	all_cancers(13;1.5e-07)		all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGCTCATCGGCACCCTCAGAG	0.637																																					p.A82S		Atlas-SNP	.											.	GALK1	17	.	0			c.G244T						.						26	25	25					17																	73760089		2201	4299	6500	SO:0001583	missense	2584	exon2			CATCGGCACCCTC		CCDS11728.1	17q25.1	2013-09-19			ENSG00000108479	ENSG00000108479	2.7.1.6		4118	protein-coding gene	gene with protein product		604313		GALK		7670469	Standard	NM_000154		Approved		uc002jpk.3	P51570	OTTHUMG00000179832	ENST00000588479.1:c.244G>T	chr17.hg19:g.73760089C>A	ENSP00000465930:p.Ala82Ser	69.0	0.0		57.0	17.0	NM_000154	B2RC07|B4E1G6	Missense_Mutation	SNP	ENST00000588479.1	hg19	CCDS11728.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.233864	0.58886	.	.	ENSG00000108479	ENST00000225614;ENST00000437911;ENST00000375188	D;D	0.83837	-1.77;-1.77	5.1	5.1	0.69264	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.104471	0.64402	N	0.000004	D	0.85583	0.5730	M	0.78637	2.42	0.80722	D	1	P;B	0.36647	0.563;0.012	B;B	0.40741	0.339;0.039	D	0.84903	0.0843	10	0.33940	T	0.23	-20.2379	18.5096	0.90911	0.0:1.0:0.0:0.0	.	82;82	B4E1A8;P51570	.;GALK1_HUMAN	S	82;112;185	ENSP00000225614:A82S;ENSP00000406305:A112S	ENSP00000225614:A82S	A	-	1	0	GALK1	71271684	1.000000	0.71417	0.262000	0.24481	0.787000	0.44495	7.164000	0.77533	2.369000	0.80426	0.655000	0.94253	GCC	.	.		0.637	GALK1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448430.1			A	73760089	C	A	73760089	3	1	68	1	0	0	0	0	1	0	0	0	6211	710	25	3	962	3	GALK1	17	73760089	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	1408652	73760089	7435121	153	8785										
FASN	2194	hgsc.bcm.edu	37	chr17	80049390	80049390	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttgggcctcaggatgatgtgCacgttggagcccccgaagcc	14	12	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr17:80049390C>T	ENST00000306749.2	-	9	1418	c.1200G>A	c.(1198-1200)gtG>gtA	p.V400V		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	400	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GGATGATGTGCACGTTGGAGC	0.716																																					p.V400V	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G1200A						.						31	32	32					17																	80049390		2175	4289	6464	SO:0001819	synonymous_variant	2194	exon9			GATGTGCACGTTG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.1200G>A	chr17.hg19:g.80049390C>T		157.0	0.0		128.0	36.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.716	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80049390	C	T	80049390	2	4	68	1	0	0	0	0	0	0	0	1	5691	697	25	3		3	FASN	17	80049390	Silent	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10	6289301	80049390	1145820	154	8786										
MC2R	4158	hgsc.bcm.edu	37	chr18	13885429	13885429	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	caatggaaattgtgaaaaatAtctcctccggcaaaaccaca	6	10	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr18:13885429A>G	ENST00000327606.3	-	2	269	c.89T>C	c.(88-90)aTa>aCa	p.I30T		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	30					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)			breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	TGTGAAAAATATCTCCTCCGG	0.413																																					p.I30T	Colon(141;1584 1782 35999 48227 48692)	Atlas-SNP	.											.	MC2R	78	.	0			c.T89C						.						150	130	137					18																	13885429		2203	4300	6503	SO:0001583	missense	4158	exon2			AAAAATATCTCCT		CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"GPCR / Class A : Melanocortin receptors"	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.89T>C	chr18.hg19:g.13885429A>G	ENSP00000333821:p.Ile30Thr	62.0	0.0		65.0	23.0	NM_000529	A8K016|Q3MI45|Q504X6	Missense_Mutation	SNP	ENST00000327606.3	hg19	CCDS11869.1	.	.	.	.	.	.	.	.	.	.	A	15.40	2.822711	0.50739	.	.	ENSG00000185231	ENST00000327606;ENST00000399821	T;T	0.39406	1.08;1.08	4.13	4.13	0.48395	.	0.190266	0.44097	D	0.000491	T	0.35537	0.0935	L	0.47716	1.5	0.36431	D	0.864923	B	0.33583	0.418	B	0.28139	0.086	T	0.52343	-0.8588	10	0.87932	D	0	.	13.4468	0.61146	1.0:0.0:0.0:0.0	.	30	Q01718	ACTHR_HUMAN	T	30	ENSP00000333821:I30T;ENSP00000382718:I30T	ENSP00000333821:I30T	I	-	2	0	MC2R	13875429	0.993000	0.37304	0.572000	0.28498	0.761000	0.43186	8.280000	0.89903	1.643000	0.50594	0.528000	0.53228	ATA	.	.		0.413	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2			G	13885429	A	G	13885429	3	3	68	1	0	0	0	0	1	0	0	0	9373	449	16	2	808	2	MC2R	18	13885429	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10		13885429	64191819	155	8787										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31320038	31320038	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tctgtcttttctgaagggacAgataataagggaaatgagct	11	5	3	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr18:31320038A>T	ENST00000269197.5	+	11	2670	c.2670A>T	c.(2668-2670)acA>acT	p.T890T		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	890					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						CTGAAGGGACAGATAATAAGG	0.348																																					p.T890T		Atlas-SNP	.											.	ASXL3	405	.	0			c.A2670T						.						95	95	95					18																	31320038		1862	4093	5955	SO:0001819	synonymous_variant	80816	exon11			AGGGACAGATAAT	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.2670A>T	chr18.hg19:g.31320038A>T		53.0	0.0		50.0	21.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Silent	SNP	ENST00000269197.5	hg19	CCDS45847.1																																																																																			.	.		0.348	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			T	31320038	A	T	31320038	2	4	68	1	0	0	0	0	0	0	0	1	1068	175	7	4		4	ASXL3	18	31320038	Silent	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	17434609	31320038	46757210	156	8788										
MAP2K2	5605	hgsc.bcm.edu	37	chr19	4110509	4110509	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgccccggacgcactcaccaTgtgttccatgcaaatgctga	9	14	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr19:4110509T>A	ENST00000262948.5	-	3	701	c.448A>T	c.(448-450)Atg>Ttg	p.M150L	MAP2K2_ENST00000394867.4_Missense_Mutation_p.M53L|MAP2K2_ENST00000599345.1_5'UTR	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	150	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)						Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	GCACTCACCATGTGTTCCATG	0.627																																					p.M150L		Atlas-SNP	.											MAP2K2_ENST00000262948,right_upper_lobe,carcinoma,0,2	MAP2K2	72	.	0			c.A448T						.						76	66	69					19																	4110509		2203	4300	6503	SO:0001583	missense	5605	exon3			TCACCATGTGTTC	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.448A>T	chr19.hg19:g.4110509T>A	ENSP00000262948:p.Met150Leu	59.0	0.0		17.0	8.0	NM_030662		Missense_Mutation	SNP	ENST00000262948.5	hg19	CCDS12120.1	.	.	.	.	.	.	.	.	.	.	t	29.9	5.046015	0.93685	.	.	ENSG00000126934	ENST00000262948;ENST00000394867	D;D	0.92249	-3.0;-3.0	5.3	5.3	0.74995	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94235	0.8149	L	0.46741	1.465	0.80722	D	1	D	0.67145	0.996	D	0.85130	0.997	D	0.94821	0.7987	10	0.87932	D	0	-55.061	14.0565	0.64772	0.0:0.0:0.0:1.0	.	150	P36507	MP2K2_HUMAN	L	150;53	ENSP00000262948:M150L;ENSP00000378336:M53L	ENSP00000262948:M150L	M	-	1	0	MAP2K2	4061509	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.849000	0.86908	1.999000	0.58509	0.459000	0.35465	ATG	.	.		0.627	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2			A	4110509	T	A	4110509	3	1	68	1	0	0	0	0	1	0	0	0	9246	1464	51	4	790	4	MAP2K2	19	4110509	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10		4110509	55018474	157	8789										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23543010	23543010	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tcctcttatgtgtagtaaggTgtgaaggctggctaaatgct	12	6	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr19:23543010T>A	ENST00000300619.7	-	4	2976	c.2771A>T	c.(2770-2772)cAc>cTc	p.H924L	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Missense_Mutation_p.H892L|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	924					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TGTAGTAAGGTGTGAAGGCTG	0.408																																					p.H924L		Atlas-SNP	.											.	ZNF91	349	.	0			c.A2771T						.						62	66	65					19																	23543010		2185	4291	6476	SO:0001583	missense	7644	exon4			GTAAGGTGTGAAG	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.2771A>T	chr19.hg19:g.23543010T>A	ENSP00000300619:p.His924Leu	22.0	0.0		28.0	9.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	T	2.959	-0.215012	0.06101	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.13089	2.62;2.62	1.31	1.31	0.21738	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06554	0.0168	N	0.11673	0.155	0.09310	N	1	B;P	0.43477	0.036;0.808	B;B	0.41332	0.017;0.354	T	0.29640	-1.0005	9	0.12766	T	0.61	.	7.5137	0.27587	0.0:0.0:0.0:1.0	.	892;924	Q05481-2;Q05481	.;ZNF91_HUMAN	L	924;892	ENSP00000300619:H924L;ENSP00000380272:H892L	ENSP00000300619:H924L	H	-	2	0	ZNF91	23334850	0.000000	0.05858	0.006000	0.13384	0.013000	0.08279	-0.369000	0.07533	0.565000	0.29255	0.165000	0.16767	CAC	.	.		0.408	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		A	23543010	T	A	23543010	3	1	68	1	0	0	0	0	1	0	0	0	18215	1696	59	4	808	4	ZNF91	19	23543010	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	19432501	23543010	35585973	158	8790										
NUP62	23636	hgsc.bcm.edu	37	chr19	50412454	50412454	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgggtgtgggagcagctggcTgtgtggcacctgctgtggtg	20	7	0	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr19:50412454T>C	ENST00000596217.1	-	2	2498	c.611A>G	c.(610-612)cAg>cGg	p.Q204R	NUP62_ENST00000413454.1_Missense_Mutation_p.Q204R|NUP62_ENST00000422090.2_Missense_Mutation_p.Q204R|NUP62_ENST00000352066.3_Missense_Mutation_p.Q204R|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000597723.1_Missense_Mutation_p.Q204R|IL4I1_ENST00000341114.3_Intron|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000597029.1_Missense_Mutation_p.Q204R			P37198	NUP62_HUMAN	nucleoporin 62kDa	204	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.				carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		AGCAGCTGGCTGTGTGGCACC	0.622																																					p.Q204R		Atlas-SNP	.											.	NUP62	50	.	0			c.A611G						.						77	74	75					19																	50412454		2203	4300	6503	SO:0001583	missense	23636	exon3			GCTGGCTGTGTGG	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"nuclear pore glycoprotein p62"	605815	"nucleoporin 62kD"			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.611A>G	chr19.hg19:g.50412454T>C	ENSP00000471191:p.Gln204Arg	106.0	0.0		86.0	38.0	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Missense_Mutation	SNP	ENST00000596217.1	hg19	CCDS12788.1	.	.	.	.	.	.	.	.	.	.	T	5.727	0.318587	0.10845	.	.	ENSG00000213024	ENST00000352066;ENST00000422090;ENST00000413454	T;T;T	0.37411	1.2;1.2;1.2	4.92	3.88	0.44766	Nucleoporin, NSP1-like, C-terminal (1);	0.460715	0.14835	U	0.295642	T	0.32823	0.0842	M	0.62723	1.935	0.27556	N	0.950354	B	0.33073	0.396	B	0.29785	0.107	T	0.17048	-1.0382	9	.	.	.	-7.928	8.7263	0.34471	0.0:0.0:0.1919:0.8081	.	204	P37198	NUP62_HUMAN	R	204	ENSP00000305503:Q204R;ENSP00000407331:Q204R;ENSP00000387991:Q204R	.	Q	-	2	0	NUP62	55104266	0.770000	0.28543	0.990000	0.47175	0.035000	0.12851	0.557000	0.23454	0.977000	0.38444	0.459000	0.35465	CAG	.	.		0.622	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		C	50412454	T	C	50412454	3	2	68	1	0	0	0	0	1	0	0	0	10777	1580	55	2	961	2	NUP62	19	50412454	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	26869444	50412454	8716529	159	8791										
ZNF581	51545	hgsc.bcm.edu	37	chr19	56156253	56156253	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgtcctaccttcagcgacacAgcatcacccactcggaggta	8	15	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr19:56156253A>T	ENST00000587252.1	+	2	589	c.316A>T	c.(316-318)Agc>Tgc	p.S106C	ZNF581_ENST00000270451.5_Missense_Mutation_p.S106C|ZNF581_ENST00000588537.1_Missense_Mutation_p.S106C			Q9P0T4	ZN581_HUMAN	zinc finger protein 581	106					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)|ovary(1)	3		Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		TCAGCGACACAGCATCACCCA	0.597																																					p.S106C		Atlas-SNP	.											.	ZNF581	13	.	0			c.A316T						.						75	69	71					19																	56156253		2203	4300	6503	SO:0001583	missense	51545	exon2			CGACACAGCATCA	AK026203	CCDS12932.1	19q13.42	2013-09-20			ENSG00000171425	ENSG00000171425		"Zinc fingers, C2H2-type"	25017	protein-coding gene	gene with protein product						11042152	Standard	NM_016535		Approved	HSPC189, FLJ22550	uc002qlq.3	Q9P0T4	OTTHUMG00000180869	ENST00000587252.1:c.316A>T	chr19.hg19:g.56156253A>T	ENSP00000466047:p.Ser106Cys	229.0	0.0		170.0	85.0	NM_016535	B2RDM6	Missense_Mutation	SNP	ENST00000587252.1	hg19	CCDS12932.1	.	.	.	.	.	.	.	.	.	.	A	18.66	3.671045	0.67814	.	.	ENSG00000171425	ENST00000270451	T	0.07800	3.16	3.9	0.285	0.15705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13970	0.0338	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.07195	-1.0785	9	0.87932	D	0	.	5.9637	0.19313	0.5968:0.3132:0.09:0.0	.	106	Q9P0T4	ZN581_HUMAN	C	106	ENSP00000270451:S106C	ENSP00000270451:S106C	S	+	1	0	ZNF581	60848065	0.083000	0.21467	0.504000	0.27639	0.987000	0.75469	0.487000	0.22356	-0.121000	0.11787	0.334000	0.21626	AGC	.	.		0.597	ZNF581-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453430.1	NM_016535		T	56156253	A	T	56156253	3	4	68	1	0	0	0	0	1	0	0	0	18028	188	7	4	318	4	ZNF581	19	56156253	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	5743799	56156253	2972730	160	8792										
ZNF835	90485	hgsc.bcm.edu	37	chr19	57175003	57175003	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gccagggcacccctgttgacAggtttctcctccctgtgaga	11	14	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr19:57175003A>T	ENST00000537055.2	-	2	1795	c.1564T>A	c.(1564-1566)Tgt>Agt	p.C522S		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	522					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CCCTGTTGACAGGTTTCTCCT	0.587																																					p.C522S		Atlas-SNP	.											.	ZNF835	106	.	0			c.T1564A						.						64	69	67					19																	57175003		2132	4255	6387	SO:0001583	missense	90485	exon2			GTTGACAGGTTTC	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.1564T>A	chr19.hg19:g.57175003A>T	ENSP00000444747:p.Cys522Ser	188.0	0.0		143.0	56.0	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	hg19	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	A	1.071	-0.670007	0.03403	.	.	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.05786	3.39	2.39	-1.51	0.08664	.	.	.	.	.	T	0.02767	0.0083	N	0.14661	0.345	0.09310	N	1	B	0.27229	0.172	B	0.21708	0.036	T	0.44421	-0.9329	9	0.28530	T	0.3	.	0.5427	0.00648	0.2752:0.202:0.3232:0.1996	.	544	Q9Y2P0	ZN835_HUMAN	S	544;522	ENSP00000444747:C522S	ENSP00000341756:C544S	C	-	1	0	ZNF835	61866815	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.920000	0.00334	-0.412000	0.07519	-0.441000	0.05720	TGT	.	.		0.587	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		T	57175003	A	T	57175003	3	4	68	1	0	0	0	0	1	0	0	0	18201	188	7	4	51	4	ZNF835	19	57175003	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	1018750	57175003	1953980	161	8793										
HSPA12B	116835	hgsc.bcm.edu	37	chr20	3732438	3732438	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	cacccgcccgaaaagctgctGgttcgcgacggccgccgctg	13	17	0	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr20:3732438G>A	ENST00000254963.2	+	13	1831	c.1686G>A	c.(1684-1686)ctG>ctA	p.L562L	HSPA12B_ENST00000542646.1_Silent_p.L396L	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	562							ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						AAAAGCTGCTGGTTCGCGACG	0.736																																					p.L562L		Atlas-SNP	.											.	HSPA12B	43	.	0			c.G1686A						.						3	3	3					20																	3732438		1699	3441	5140	SO:0001819	synonymous_variant	116835	exon13			GCTGCTGGTTCGC	AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"Heat shock proteins / HSP70"	16193	protein-coding gene	gene with protein product		610702	"chromosome 20 open reading frame 60"	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.1686G>A	chr20.hg19:g.3732438G>A		2.0	0.0		5.0	5.0	NM_052970	D3DVX7|Q2TAK3|Q9BR52	Silent	SNP	ENST00000254963.2	hg19	CCDS13061.1																																																																																			.	.		0.736	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970		A	3732438	G	A	3732438	2	1	68	1	0	0	0	0	0	0	0	1	7414	1335	47	3		3	HSPA12B	20	3732438	Silent	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10		3732438	59293082	162	8794										
RALGAPA2	57186	hgsc.bcm.edu	37	chr20	20585826	20585826	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	agagtggaaatacctttgccTcgttgcttcttttccttttg	8	9	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr20:20585826T>A	ENST00000202677.7	-	15	2038	c.2031A>T	c.(2029-2031)cgA>cgT	p.R677R	RALGAPA2_ENST00000495793.1_5'UTR	NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	677					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						TACCTTTGCCTCGTTGCTTCT	0.413																																					p.R677R		Atlas-SNP	.											.	RALGAPA2	274	.	0			c.A2031T						.						83	78	80					20																	20585826		1886	4114	6000	SO:0001819	synonymous_variant	57186	exon15			TTTGCCTCGTTGC	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.2031A>T	chr20.hg19:g.20585826T>A		99.0	0.0		97.0	23.0	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Silent	SNP	ENST00000202677.7	hg19	CCDS46584.1	.	.	.	.	.	.	.	.	.	.	T	10.75	1.437964	0.25900	.	.	ENSG00000188559	ENST00000430436	.	.	.	5.28	2.98	0.34508	.	.	.	.	.	T	0.55305	0.1912	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49011	-0.8983	4	.	.	.	.	7.0116	0.24865	0.133:0.0731:0.0:0.7939	.	.	.	.	V	494	.	.	E	-	2	0	RALGAPA2	20533826	0.997000	0.39634	1.000000	0.80357	0.981000	0.71138	0.348000	0.20031	0.809000	0.34255	0.377000	0.23210	GAG	.	.		0.413	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		A	20585826	T	A	20585826	2	1	68	1	0	0	0	0	0	0	0	1	13029	1538	54	4		4	RALGAPA2	20	20585826	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	16853388	20585826	42439694	163	8795										
PMEPA1	56937	hgsc.bcm.edu	37	chr20	56227157	56227157	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	ttctctttgctccagatggcTgcgctctctaggggcgcgat	12	12	2	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr20:56227157T>A	ENST00000341744.3	-	4	1135	c.816A>T	c.(814-816)gcA>gcT	p.A272A	PMEPA1_ENST00000395816.3_Silent_p.A222A|PMEPA1_ENST00000395814.1_Silent_p.A222A|PMEPA1_ENST00000347215.4_Silent_p.A237A|PMEPA1_ENST00000265626.4_Silent_p.A222A	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	272					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						TCCAGATGGCTGCGCTCTCTA	0.642																																					p.A272A		Atlas-SNP	.											.	PMEPA1	29	.	0			c.A816T						.						26	29	28					20																	56227157		2199	4295	6494	SO:0001819	synonymous_variant	56937	exon4			GATGGCTGCGCTC	AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"solid tumor-associated 1"	606564	"transmembrane, prostate androgen induced RNA"	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.816A>T	chr20.hg19:g.56227157T>A		27.0	0.0		37.0	12.0	NM_020182	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Silent	SNP	ENST00000341744.3	hg19	CCDS13463.1																																																																																			.	.		0.642	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182		A	56227157	T	A	56227157	2	1	68	1	0	0	0	0	0	0	0	1	12141	1567	55	4		4	PMEPA1	20	56227157	Silent	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	35641331	56227157	6798363	164	8796										
TRMT2A	27037	hgsc.bcm.edu	37	chr22	20102931	20102931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gttatcctccccatccacccCgacgccaaccagaaactcac	4	20	1	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr22:20102931C>T	ENST00000252136.7	-	4	1136	c.748G>A	c.(748-750)Ggg>Agg	p.G250R	TRMT2A_ENST00000403707.3_Missense_Mutation_p.G250R|TRMT2A_ENST00000404751.3_Missense_Mutation_p.G250R|RANBP1_ENST00000331821.3_5'Flank|TRMT2A_ENST00000439169.2_Missense_Mutation_p.G250R|RANBP1_ENST00000402752.1_5'Flank|TRMT2A_ENST00000492988.1_5'UTR|RANBP1_ENST00000430524.1_5'Flank	NM_001257994.1|NM_022727.5|NM_182984.4	NP_001244923.1|NP_073564.3|NP_892029.2	Q8IZ69	TRM2A_HUMAN	tRNA methyltransferase 2 homolog A (S. cerevisiae)	250					RNA processing (GO:0006396)		nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)			breast(2)|endometrium(2)|lung(5)	9						CCATCCACCCCGACGCCAACC	0.612																																					p.G250R		Atlas-SNP	.											.	TRMT2A	34	.	0			c.G748A						.						75	66	69					22																	20102931		2203	4300	6503	SO:0001583	missense	27037	exon4			CCACCCCGACGCC	BC017184	CCDS13774.1, CCDS58793.1	22q11.21	2014-02-12	2012-06-12		ENSG00000099899	ENSG00000099899			24974	protein-coding gene	gene with protein product	"HpaII tiny fragments locus 9C"	611151				9417108, 18075473	Standard	NM_022727		Approved	HTF9C	uc002zrl.2	Q8IZ69	OTTHUMG00000150454	ENST00000252136.7:c.748G>A	chr22.hg19:g.20102931C>T	ENSP00000252136:p.Gly250Arg	75.0	0.0		58.0	21.0	NM_001257994	D3DX25|Q32P57|Q96ME6|Q9H732	Missense_Mutation	SNP	ENST00000252136.7	hg19	CCDS13774.1	.	.	.	.	.	.	.	.	.	.	C	36	5.646134	0.96704	.	.	ENSG00000099899	ENST00000252136;ENST00000403707;ENST00000404751;ENST00000439169	T;T;T	0.46063	0.89;0.89;0.88	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.64114	0.2569	M	0.73598	2.24	0.80722	D	1	D;P;D	0.69078	0.997;0.625;0.997	P;B;P	0.61722	0.893;0.186;0.893	T	0.67401	-0.5680	10	0.72032	D	0.01	-48.5105	19.0103	0.92870	0.0:1.0:0.0:0.0	.	250;250;250	F2Z2W7;Q8IZ69-2;Q8IZ69	.;.;TRM2A_HUMAN	R	250	ENSP00000252136:G250R;ENSP00000385807:G250R;ENSP00000395738:G250R	ENSP00000252136:G250R	G	-	1	0	TRMT2A	18482931	1.000000	0.71417	0.445000	0.26908	0.990000	0.78478	5.614000	0.67695	2.595000	0.87683	0.561000	0.74099	GGG	.	.		0.612	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727		T	20102931	C	T	20102931	3	4	68	1	0	0	0	0	1	0	0	0	16580	652	23	1	1165	1	TRMT2A	22	20102931	Missense_Mutation	SNP	C	TCGA-CC-A5UD-01A-11D-A28X-10		20102931	31201635	165	8797										
ELFN2	114794	hgsc.bcm.edu	37	chr22	37771020	37771020	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tcgcactcacagttgaagggGttgccggccagctcacacac	11	14	2	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr22:37771020G>T	ENST00000402918.2	-	3	1340	c.555C>A	c.(553-555)aaC>aaA	p.N185K	RP1-63G5.5_ENST00000430883.1_RNA|RP1-63G5.8_ENST00000609322.1_RNA|ELFN2_ENST00000435824.1_5'Flank	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	185	LRRCT.				negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					AGTTGAAGGGGTTGCCGGCCA	0.632																																					p.N185K		Atlas-SNP	.											.	ELFN2	89	.	0			c.C555A						.						39	42	41					22																	37771020		2203	4299	6502	SO:0001583	missense	114794	exon3			GAAGGGGTTGCCG	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing"	29396	protein-coding gene	gene with protein product			"leucine rich repeat containing 62", "extracellular leucine-rich repeat and fibronectin type III containing 2", "extracellular leucine-rich repeat and fibronectin type III domain containing 2", "protein phosphatase 1, regulatory subunit 29"	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.555C>A	chr22.hg19:g.37771020G>T	ENSP00000385277:p.Asn185Lys	181.0	0.0		118.0	43.0	NM_052906	Q96PY3	Missense_Mutation	SNP	ENST00000402918.2	hg19	CCDS33642.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.770414	0.49680	.	.	ENSG00000166897	ENST00000349653;ENST00000402918	T;T	0.66099	-0.19;-0.19	4.84	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.75729	0.3889	M	0.71206	2.165	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.78288	-0.2262	10	0.87932	D	0	-36.2791	11.7337	0.51752	0.1436:0.0:0.8564:0.0	.	185	Q5R3F8	PPR29_HUMAN	K	185	ENSP00000300147:N185K;ENSP00000385277:N185K	ENSP00000300147:N185K	N	-	3	2	ELFN2	36100966	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.181000	0.50903	2.399000	0.81585	0.514000	0.50259	AAC	.	.		0.632	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906		T	37771020	G	T	37771020	3	4	68	1	0	0	0	0	1	0	0	0	5060	1252	44	3	1911	3	ELFN2	22	37771020	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	17668089	37771020	13533546	166	8798										
SMCR7L	54471	hgsc.bcm.edu	37	chr22	39909580	39909580	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tgtgctggagcagaacctgtGgtcatgtattcctggtgaag	14	7	1	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chr22:39909580G>T	ENST00000325301.2	+	6	1068	c.644G>T	c.(643-645)tGg>tTg	p.W215L	MIEF1_ENST00000404569.1_Missense_Mutation_p.W215L|MIEF1_ENST00000402881.1_Missense_Mutation_p.W215L	NM_019008.4	NP_061881.2	Q9NQG6	MID51_HUMAN	mitochondrial elongation factor 1	215					mitochondrial fission (GO:0000266)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|GDP binding (GO:0019003)|identical protein binding (GO:0042802)										CAGAACCTGTGGTCATGTATT	0.507																																					p.W215L		Atlas-SNP	.											.	SMCR7L	33	.	0			c.G644T						.						130	112	118					22																	39909580		2203	4300	6503	SO:0001583	missense	54471	exon6			ACCTGTGGTCATG	AL365515	CCDS13995.1	22q13.1	2013-09-23	2013-09-23	2013-09-23	ENSG00000100335	ENSG00000100335			25979	protein-coding gene	gene with protein product		615497	"Smith-Magenis syndrome chromosome region, candidate 7-like"	SMCR7L		21508961, 21701560	Standard	NM_019008		Approved	FLJ20232, MiD51	uc003axx.3	Q9NQG6	OTTHUMG00000151105	ENST00000325301.2:c.644G>T	chr22.hg19:g.39909580G>T	ENSP00000327124:p.Trp215Leu	112.0	0.0		72.0	29.0	NM_019008	Q7L890|Q9BUI3	Missense_Mutation	SNP	ENST00000325301.2	hg19	CCDS13995.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327002	0.81690	.	.	ENSG00000100335	ENST00000402881;ENST00000325301;ENST00000404569	T;T;T	0.07216	3.21;3.21;3.21	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.31734	0.0806	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.87578	0.992;0.998	T	0.00148	-1.1989	10	0.31617	T	0.26	-18.1649	20.6439	0.99570	0.0:0.0:1.0:0.0	.	215;215	Q9NQG6;B0QY95	MID51_HUMAN;.	L	215	ENSP00000385110:W215L;ENSP00000327124:W215L;ENSP00000385191:W215L	ENSP00000327124:W215L	W	+	2	0	SMCR7L	38239526	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	9.858000	0.99539	2.884000	0.98904	0.655000	0.94253	TGG	.	.		0.507	MIEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321325.1	NM_019008		T	39909580	G	T	39909580	3	4	68	1	0	0	0	0	1	0	0	0	14806	1357	47	3	658	3	SMCR7L	22	39909580	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	2138560	39909580	11394986	167	8799										
SFRS17A	8227	hgsc.bcm.edu	37	chrX	1718233	1718233	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aggagcagaagcagctgcagGagaagatcaagctggaggag	17	6	1	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chrX:1718233G>T	ENST00000313871.3	+	4	1256	c.1060G>T	c.(1060-1062)Gag>Tag	p.E354*	AKAP17A_ENST00000381261.3_Nonsense_Mutation_p.E354*	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	354					B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						GCAGCTGCAGGAGAAGATCAA	0.622																																					p.E354X		Atlas-SNP	.											.	AKAP17A	46	.	0			c.G1060T						.						79	83	82					X																	1718233		2203	4293	6496	SO:0001587	stop_gained	8227	exon4			CTGCAGGAGAAGA	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"Pseudoautosomal regions / PAR1", "A-kinase anchor proteins"	18783	protein-coding gene	gene with protein product		312095, 465000	"chromosome X and Y open reading frame 3", "splicing factor, arginine/serine-rich 17A"	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.1060G>T	chrX.hg19:g.1718233G>T	ENSP00000324827:p.Glu354*	178.0	0.0		65.0	40.0	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Nonsense_Mutation	SNP	ENST00000313871.3	hg19	CCDS14116.1	.	.	.	.	.	.	.	.	.	.	g	18.51	3.639024	0.67130	.	.	ENSG00000197976	ENST00000313871;ENST00000381261	.	.	.	1.74	1.74	0.24563	.	0.238718	0.34580	U	0.003859	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	11.9908	0.53173	0.0:0.0:1.0:0.0	.	.	.	.	X	354	.	ENSP00000324827:E354X	E	+	1	0	AKAP17A	1678233	1.000000	0.71417	0.002000	0.10522	0.459000	0.32528	1.708000	0.37899	0.657000	0.30906	0.100000	0.15512	GAG	.	.		0.622	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		T	1718233	G	T	1718233	4	4	68	1	0	0	0	0	0	1	0	0	14188	1175	41	3	1070	3	SFRS17A	23	1718233	Nonsense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10		1718233	153552327	168	8800										
ARX	170302	hgsc.bcm.edu	37	chrX	25033712	25033712	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	tcagcggagcaggcaagctcTgcgcggctcccagcaaccgc	13	16	2	0			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chrX:25033712T>A	ENST00000379044.4	-	1	353	c.143A>T	c.(142-144)cAg>cTg	p.Q48L		NM_139058.2	NP_620689.1	Q96QS3	ARX_HUMAN	aristaless related homeobox	48					axon guidance (GO:0007411)|cell proliferation in forebrain (GO:0021846)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex tangential migration (GO:0021800)|embryonic olfactory bulb interneuron precursor migration (GO:0021831)|epithelial cell fate commitment (GO:0072148)|globus pallidus development (GO:0021759)|lipid digestion (GO:0044241)|positive regulation of organ growth (GO:0046622)|regulation of cell proliferation (GO:0042127)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			kidney(1)|large_intestine(2)|lung(1)	4						AGGCAAGCTCTGCGCGGCTCC	0.602																																					p.Q48L		Atlas-SNP	.											.	ARX	19	.	0			c.A143T						.						32	28	30					X																	25033712		2201	4299	6500	SO:0001583	missense	170302	exon1			AAGCTCTGCGCGG	AY038071	CCDS14215.1	Xp21.3	2011-06-20			ENSG00000004848	ENSG00000004848		"Homeoboxes / PRD class"	18060	protein-coding gene	gene with protein product	"cancer/testis antigen 121"	300382	"mental retardation, X-linked 54", "mental retardation, X-linked 43", "mental retardation, X-linked 36", "mental retardation, X-linked 29", "mental retardation, X-linked 32", "mental retardation, X-linked 33", "mental retardation, X-linked 38", "mental retardation, X-linked 87", "mental retardation, X-linked 76"	MRXS1, PRTS, MRX76, MRX54, MRX43, MRX36, MRX29, MRX32, MRX33, MRX38, MRX87		11889467, 15850492, 17480217	Standard	NM_139058		Approved	ISSX, CT121, EIEE1	uc004dbp.4	Q96QS3	OTTHUMG00000021275	ENST00000379044.4:c.143A>T	chrX.hg19:g.25033712T>A	ENSP00000368332:p.Gln48Leu	132.0	0.0		48.0	40.0	NM_139058		Missense_Mutation	SNP	ENST00000379044.4	hg19	CCDS14215.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.317523	0.60524	.	.	ENSG00000004848	ENST00000379044	D	0.89552	-2.53	4.9	3.7	0.42460	.	0.000000	0.64402	U	0.000001	D	0.84995	0.5596	L	0.58101	1.795	0.42529	D	0.99303	P	0.38922	0.651	B	0.35859	0.212	T	0.83127	-0.0115	10	0.72032	D	0.01	.	9.4992	0.39006	0.0:0.0:0.335:0.6649	.	48	Q96QS3	ARX_HUMAN	L	48	ENSP00000368332:Q48L	ENSP00000368332:Q48L	Q	-	2	0	ARX	24943633	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.555000	0.45854	0.668000	0.31126	0.486000	0.48141	CAG	.	.		0.602	ARX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056109.1			A	25033712	T	A	25033712	3	1	68	1	0	0	0	0	1	0	0	0	1004	1580	55	4	1565	4	ARX	23	25033712	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	23315479	25033712	130236848	169	8801										
ERCC6L	54821	hgsc.bcm.edu	37	chrX	71425152	71425152	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	gtcattaaccagctggacttGttttctgaagacagtgtttc	9	8	2	2			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chrX:71425152G>T	ENST00000334463.3	-	2	3600	c.3465C>A	c.(3463-3465)aaC>aaA	p.N1155K	ERCC6L_ENST00000373657.1_Missense_Mutation_p.N1032K|PIN4_ENST00000423432.2_Intron	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	1155					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					AGCTGGACTTGTTTTCTGAAG	0.498																																					p.N1155K		Atlas-SNP	.											.	ERCC6L	98	.	0			c.C3465A						.						97	88	91					X																	71425152		2203	4300	6503	SO:0001583	missense	54821	exon2			GGACTTGTTTTCT	AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871			20794	protein-coding gene	gene with protein product	"PLK1-interacting checkpoint helicase"	300687	"excision repair cross-complementing rodent repair deficiency, complementation group 6-like"			17218258	Standard	NM_017669		Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000334463.3:c.3465C>A	chrX.hg19:g.71425152G>T	ENSP00000334675:p.Asn1155Lys	59.0	0.0		49.0	39.0	NM_017669	Q8NCI1|Q96H93|Q9NXQ8	Missense_Mutation	SNP	ENST00000334463.3	hg19	CCDS35329.1	.	.	.	.	.	.	.	.	.	.	G	10.40	1.340716	0.24339	.	.	ENSG00000186871	ENST00000373657;ENST00000334463	D;D	0.90676	-2.68;-2.71	5.58	-1.91	0.07641	.	.	.	.	.	T	0.80232	0.4585	L	0.31294	0.92	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.64588	-0.6372	9	0.39692	T	0.17	-1.8011	1.5871	0.02646	0.292:0.2532:0.3272:0.1277	.	1155	Q2NKX8	ERC6L_HUMAN	K	1032;1155	ENSP00000362761:N1032K;ENSP00000334675:N1155K	ENSP00000334675:N1155K	N	-	3	2	ERCC6L	71341877	0.000000	0.05858	0.001000	0.08648	0.058000	0.15608	-0.286000	0.08399	-0.170000	0.10816	0.600000	0.82982	AAC	.	.		0.498	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		T	71425152	G	T	71425152	3	4	68	1	0	0	0	0	1	0	0	0	5220	1368	48	3	291	3	ERCC6L	23	71425152	Missense_Mutation	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	46391440	71425152	83845408	170	8802										
BRWD3	254065	hgsc.bcm.edu	37	chrX	79989645	79989645	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	actctaattcagcaattttcTcaggaacctcagaacccaaa	4	12	4	1			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chrX:79989645T>A	ENST00000373275.4	-	11	1274	c.1058A>T	c.(1057-1059)gAg>gTg	p.E353V		NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	353					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						AGCAATTTTCTCAGGAACCTC	0.323																																					p.E353V		Atlas-SNP	.											.	BRWD3	251	.	0			c.A1058T						.						116	109	112					X																	79989645		2203	4298	6501	SO:0001583	missense	254065	exon11			ATTTTCTCAGGAA		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.1058A>T	chrX.hg19:g.79989645T>A	ENSP00000362372:p.Glu353Val	81.0	0.0		63.0	6.0	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	hg19	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.210659	0.79240	.	.	ENSG00000165288	ENST00000373275	T	0.18960	2.18	5.34	5.34	0.76211	WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);WD40-repeat-containing domain (1);	0.167651	0.53938	D	0.000058	T	0.28830	0.0715	L	0.41710	1.295	0.36637	D	0.876605	P	0.40282	0.711	P	0.49953	0.627	T	0.16958	-1.0385	9	.	.	.	-8.1349	14.3934	0.66996	0.0:0.0:0.0:1.0	.	353	Q6RI45	BRWD3_HUMAN	V	353	ENSP00000362372:E353V	.	E	-	2	0	BRWD3	79876301	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.610000	0.61155	1.976000	0.57569	0.441000	0.28932	GAG	.	.		0.323	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		A	79989645	T	A	79989645	3	1	68	1	0	0	0	0	1	0	0	0	1528	1551	54	4	4474	4	BRWD3	23	79989645	Missense_Mutation	SNP	T	TCGA-CC-A5UD-01A-11D-A28X-10	8564493	79989645	75280915	171	8803										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83126557	83126557	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aatgataaatcaagacctttGaaatcacaaataacagttac	4	7	2	3			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chrX:83126557G>A	ENST00000329312.4	+	3	193	c.156G>A	c.(154-156)ttG>ttA	p.L52L		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	52					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						CAAGACCTTTGAAATCACAAA	0.299																																					p.L52L		Atlas-SNP	.											.	CYLC1	272	.	0			c.G156A						.						61	56	58					X																	83126557		2203	4297	6500	SO:0001819	synonymous_variant	1538	exon3			ACCTTTGAAATCA	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.156G>A	chrX.hg19:g.83126557G>A		99.0	0.0		58.0	35.0	NM_021118	A0AVQ8|Q5JQQ9	Silent	SNP	ENST00000329312.4	hg19	CCDS35341.1																																																																																			.	.		0.299	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		A	83126557	G	A	83126557	2	1	68	1	0	0	0	0	0	0	0	1	4143	1281	45	3		3	CYLC1	23	83126557	Silent	SNP	G	TCGA-CC-A5UD-01A-11D-A28X-10	3136912	83126557	72144003	172	8804										
SAGE1	55511	hgsc.bcm.edu	37	chrX	134994077	134994077	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	6	1	1.45723204994797	0.941129032258065	1.6367461430575	0.131221719457014	0.709357990687916	0	aattaatgatgatataaaatAtcaattaatgaaagaagttc	5	2	1	4			TCGA-CC-A5UD-01A-11D-A28X-10	TCGA-CC-A5UD-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b1d8861-8326-40ac-b595-5862822407d8	c0bd90d9-4ca2-40af-af50-d23f00558550	g.chrX:134994077A>T	ENST00000370709.3	+	17	2486	c.2486A>T	c.(2485-2487)tAt>tTt	p.Y829F	SAGE1_ENST00000537770.1_Missense_Mutation_p.Y453F|SAGE1_ENST00000535938.1_Missense_Mutation_p.Y829F|SAGE1_ENST00000324447.3_Missense_Mutation_p.Y829F			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	829						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					GATATAAAATATCAATTAATG	0.358																																					p.Y829F		Atlas-SNP	.											.	SAGE1	160	.	0			c.A2486T						.						42	43	43					X																	134994077		2203	4297	6500	SO:0001583	missense	55511	exon18			TAAAATATCAATT	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.2486A>T	chrX.hg19:g.134994077A>T	ENSP00000359743:p.Tyr829Phe	55.0	0.0		37.0	31.0	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	hg19	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	A	10.73	1.433633	0.25813	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000537770;ENST00000370709	T;T;T;T	0.30448	1.53;1.53;1.56;1.53	2.43	0.972	0.19704	.	0.641883	0.15518	N	0.258210	T	0.18341	0.0440	L	0.46157	1.445	0.09310	N	1	P;B	0.35982	0.531;0.005	B;B	0.32289	0.143;0.002	T	0.12293	-1.0553	10	0.10902	T	0.67	.	5.1531	0.15021	0.414:0.0:0.0:0.586	.	453;829	F5H2Z8;Q9NXZ1	.;SAGE1_HUMAN	F	829;829;453;829	ENSP00000323191:Y829F;ENSP00000445959:Y829F;ENSP00000438276:Y453F;ENSP00000359743:Y829F	ENSP00000323191:Y829F	Y	+	2	0	SAGE1	134821743	0.000000	0.05858	0.006000	0.13384	0.797000	0.45037	0.352000	0.20113	0.934000	0.37316	0.150000	0.16122	TAT	.	.		0.358	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		T	134994077	A	T	134994077	3	4	68	1	0	0	0	0	1	0	0	0	13824	449	16	4	2552	4	SAGE1	23	134994077	Missense_Mutation	SNP	A	TCGA-CC-A5UD-01A-11D-A28X-10	51867520	134994077	20276483	173	8805										
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17331929	17331929	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gccaggttgcagggccggagCcgcagccgcaccccccacag	14	18	0	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:17331929C>A	ENST00000326735.8	-	3	261	c.228G>T	c.(226-228)cgG>cgT	p.R76R	ATP13A2_ENST00000452699.1_Silent_p.R76R|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Silent_p.R76R			Q9NQ11	AT132_HUMAN	ATPase type 13A2	76					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGGGCCGGAGCCGCAGCCGCA	0.607																																					p.R76R		Atlas-SNP	.											.	ATP13A2	85	.	0			c.G228T						.						21	27	25					1																	17331929		2202	4299	6501	SO:0001819	synonymous_variant	23400	exon3			CCGGAGCCGCAGC	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.228G>T	chr1.hg19:g.17331929C>A		236.0	0.0		199.0	35.0	NM_001141973	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	hg19	CCDS175.1	.	.	.	.	.	.	.	.	.	.	c	10.56	1.384756	0.25031	.	.	ENSG00000159363	ENST00000510069;ENST00000509619	.	.	.	4.36	2.14	0.27477	.	.	.	.	.	T	0.67107	0.2858	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	T	0.66040	-0.6022	4	.	.	.	-29.9618	13.4176	0.60979	0.0:0.5158:0.4842:0.0	.	.	.	.	S	52;69	.	.	A	-	1	0	ATP13A2	17204516	0.787000	0.28750	0.990000	0.47175	0.987000	0.75469	-0.035000	0.12205	0.913000	0.36797	0.486000	0.48141	GCT	.	.		0.607	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		A	17331929	C	A	17331929	2	1	69	1	0	0	0	0	0	0	0	1	1124	726	26	3		3	ATP13A2	1	17331929	Silent	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10		17331929	231918692	1	8806										
LAPTM5	7805	hgsc.bcm.edu	37	chr1	31208055	31208055	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggagtttctcttctcctccaCcgagttcatgcacttgatca	7	13	4	1	rs370275111		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:31208055C>A	ENST00000294507.3	-	7	738	c.664G>T	c.(664-666)Gtg>Ttg	p.V222L		NM_006762.2	NP_006753.1	Q13571	LAPM5_HUMAN	lysosomal protein transmembrane 5	222					transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)				large_intestine(2)|lung(7)|skin(1)	10		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)		TTCTCCTCCACCGAGTTCATG	0.537																																					p.V222L		Atlas-SNP	.											.	LAPTM5	30	.	0			c.G664T						.						318	276	290					1																	31208055		2203	4300	6503	SO:0001583	missense	7805	exon7			CCTCCACCGAGTT	U51240	CCDS337.1	1p34	2009-07-20	2009-07-20		ENSG00000162511	ENSG00000162511			29612	protein-coding gene	gene with protein product		601476	"lysosomal multispanning membrane protein 5"			8661146, 12527926	Standard	NM_006762		Approved		uc001bsc.2	Q13571	OTTHUMG00000003707	ENST00000294507.3:c.664G>T	chr1.hg19:g.31208055C>A	ENSP00000294507:p.Val222Leu	94.0	0.0		91.0	12.0	NM_006762	Q13240|Q14698|Q3KP54	Missense_Mutation	SNP	ENST00000294507.3	hg19	CCDS337.1	.	.	.	.	.	.	.	.	.	.	C	5.819	0.335391	0.11013	.	.	ENSG00000162511	ENST00000294507;ENST00000424259	T	0.45668	0.89	5.7	2.82	0.32997	.	0.565140	0.17768	N	0.162685	T	0.21387	0.0515	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.19745	-1.0296	10	0.22706	T	0.39	-6.5039	9.7721	0.40595	0.0:0.7581:0.0:0.2419	.	222	Q13571	LAPM5_HUMAN	L	222	ENSP00000294507:V222L	ENSP00000294507:V222L	V	-	1	0	LAPTM5	30980642	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	0.677000	0.25262	0.357000	0.24183	-0.797000	0.03246	GTG	.	.		0.537	LAPTM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010463.1	NM_006762		A	31208055	C	A	31208055	3	1	69	1	0	0	0	0	1	0	0	0	8635	507	18	3	132	3	LAPTM5	1	31208055	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	13876126	31208055	218042566	2	8807										
LCK	3932	hgsc.bcm.edu	37	chr1	32741654	32741655	+	Missense_Mutation	DNP	CC	CC	AA													0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggcctgcatgaactggtccgCcattacaccagtgagcccga							TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:32741654_32741655CC>AA	ENST00000336890.5	+	7	759_760	c.621_622CC>AA	c.(619-624)cgCCat>cgAAat	p.H208N	LCK_ENST00000333070.4_Missense_Mutation_p.H208N|LCK_ENST00000373564.3_Missense_Mutation_p.H266N	NM_005356.3	NP_005347.3	P06239	LCK_HUMAN	LCK proto-oncogene, Src family tyrosine kinase	208	Interaction with PTPRH.|SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.			VRHYTN -> ASAITPI (in Ref. 1; CAA28691). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aging (GO:0007568)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular zinc ion homeostasis (GO:0006882)|dephosphorylation (GO:0016311)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hemopoiesis (GO:0030097)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|positive regulation of uterine smooth muscle contraction (GO:0070474)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of defense response to virus by virus (GO:0050690)|regulation of lymphocyte activation (GO:0051249)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to zinc ion (GO:0010043)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|pericentriolar material (GO:0000242)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|ATP binding (GO:0005524)|ATPase binding (GO:0051117)|CD4 receptor binding (GO:0042609)|CD8 receptor binding (GO:0042610)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine kinase activity (GO:0004713)|SH2 domain binding (GO:0042169)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)|Ponatinib(DB08901)	AACTGGTCCGCCATTACACCAG	0.569			T	TRB@	T-ALL																																p.R207R|p.H208N		Atlas-SNP	.		Dom	yes		1	1p35-p34.3	3932	lymphocyte-specific protein tyrosine kinase		L	.	LCK	124	.	0			c.C621A|c.C622A						.																																			SO:0001583	missense	3932	exon7			GGTCCGCCATTAC|GTCCGCCATTACA	M36881	CCDS359.1	1p34.3	2014-09-17	2014-06-25		ENSG00000182866	ENSG00000182866	2.7.10.1	"SH2 domain containing"	6524	protein-coding gene	gene with protein product		153390	"lymphocyte-specific protein tyrosine kinase"			2787474	Standard	XM_005270862		Approved		uc001buy.3	P06239	OTTHUMG00000007463	Exception_encountered	chr1.hg19:g.32741654_32741655delinsAA	ENSP00000337825:p.His208Asn	126.0|124.0	0.0		158.0	116.0	NM_005356	D3DPP8|P07100|Q12850|Q13152|Q5TDH8|Q5TDH9|Q7RTZ3|Q96DW4|Q9NYT8	Silent|Missense_Mutation	SNP	ENST00000336890.5	hg19	CCDS359.1																																																																																			.	.		0.569	LCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019616.4	NM_005356		AA	32741655	CC	AA	32741654	3	1	69	1	0	0	0	0	1	0	0	0	8685	726	26	3	643	3	LCK	1	32741654	Missense_Mutation	DNP	CC	TCGA-CC-A5UE-01A-11D-A28X-10	1533599	32741654	216508967	3	8808										
HECTD3	79654	hgsc.bcm.edu	37	chr1	45469577	45469577	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gctggcaggcgactgcggccCgtgacaaagcgcaggaagcg	17	12	0	1	rs373641285		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:45469577C>T	ENST00000372172.4	-	19	2450	c.2379G>A	c.(2377-2379)acG>acA	p.T793T	HECTD3_ENST00000486132.1_5'UTR|HECTD3_ENST00000372168.3_Silent_p.T403T	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	793	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					GACTGCGGCCCGTGACAAAGC	0.617																																					p.T793T		Atlas-SNP	.											.	HECTD3	158	.	0			c.G2379A						.	C		0,4124		0,0,2062	41	49	46		2379	-11.9	0	1		46	1,8345		0,1,4172	no	coding-synonymous	HECTD3	NM_024602.5		0,1,6234	TT,TC,CC		0.012,0.0,0.0080		793/862	45469577	1,12469	2062	4173	6235	SO:0001819	synonymous_variant	79654	exon19			GCGGCCCGTGACA	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.2379G>A	chr1.hg19:g.45469577C>T		170.0	0.0		182.0	53.0	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Silent	SNP	ENST00000372172.4	hg19	CCDS41318.1																																																																																			.	.		0.617	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		T	45469577	C	T	45469577	2	4	69	1	0	0	0	0	0	0	0	1	7050	639	23	1		1	HECTD3	1	45469577	Silent	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	12727923	45469577	203781044	4	8809										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103478004	103478004	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tccagttagacccattgggcCaggtgggcctctcagagcaa	12	12	1	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:103478004C>G	ENST00000370096.3	-	14	1906	c.1594G>C	c.(1594-1596)Ggc>Cgc	p.G532R	COL11A1_ENST00000512756.1_Missense_Mutation_p.G416R|COL11A1_ENST00000353414.4_Missense_Mutation_p.G493R|COL11A1_ENST00000358392.2_Missense_Mutation_p.G544R	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	532	Collagen-like 2.|Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCCATTGGGCCAGGTGGGCCT	0.388																																					p.G544R		Atlas-SNP	.											COL11A1_ENST00000370096,bladder,carcinoma,0,2	COL11A1	972	.	0			c.G1630C						.						40	42	41					1																	103478004		2203	4300	6503	SO:0001583	missense	1301	exon14			TTGGGCCAGGTGG	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1594G>C	chr1.hg19:g.103478004C>G	ENSP00000359114:p.Gly532Arg	139.0	0.0		204.0	148.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364436	0.82463	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239	D;D;D;D;D	0.99353	-5.77;-5.77;-5.77;-5.77;-3.98	5.94	5.94	0.96194	.	0.054058	0.85682	D	0.000000	D	0.99813	0.9918	H	0.99391	4.545	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96880	0.9645	10	0.87932	D	0	.	19.9503	0.97197	0.0:1.0:0.0:0.0	.	416;493;544;532	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	R	532;544;493;416;544	ENSP00000359114:G532R;ENSP00000351163:G544R;ENSP00000302551:G493R;ENSP00000426533:G416R;ENSP00000408640:G544R	ENSP00000302551:G493R	G	-	1	0	COL11A1	103250592	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.192000	0.77771	2.812000	0.96745	0.557000	0.71058	GGC	.	.		0.388	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		G	103478004	C	G	103478004	3	3	69	1	0	0	0	0	1	0	0	0	3669	594	21	4	4042	4	COL11A1	1	103478004	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	58008427	103478004	145772617	5	8810										
TCHH	7062	hgsc.bcm.edu	37	chr1	152080252	152080253	+	Missense_Mutation	DNP	GG	GG	CT													0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	actttccgtcacgctgttggGggcgcagctgctgttcttcc							TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:152080252_152080253GG>CT	ENST00000368804.1	-	2	5439_5440	c.5440_5441CC>AG	c.(5440-5442)CCc>AGc	p.P1814S		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1814	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACGCTGTTGGGGGCGCAGCTGC	0.609																																					p.P1814R|p.P1814T		Atlas-SNP	.											.	TCHH	275	.	0			c.C5441G|c.C5440A						.																																			SO:0001583	missense	7062	exon3			TGTTGGGGGCGCA|GTTGGGGGCGCAG	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.5440_5441delinsCT	chr1.hg19:g.152080252_152080253delinsCT	ENSP00000357794:p.Pro1814Ser	89.0|88.0	0.0		86.0|85.0	10.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1																																																																																			.	.		0.609	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		CT	152080253	GG	CT	152080252	3	2	69	1	0	0	0	0	1	0	0	0	15715	1232	43	4	394	4	TCHH	1	152080252	Missense_Mutation	DNP	GG	TCGA-CC-A5UE-01A-11D-A28X-10	48602248	152080252	97170369	6	8811			1	10		3	3	33	N	T_GG	8.216295e-09
TCHH	7062	hgsc.bcm.edu	37	chr1	152080269	152080269	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tgggggcgcagctgctgttcTtccctctcctggcgtagctg	14	13	2	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:152080269T>C	ENST00000368804.1	-	2	5423	c.5424A>G	c.(5422-5424)gaA>gaG	p.E1808E		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1808	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTGCTGTTCTTCCCTCTCCT	0.597																																					p.E1808E		Atlas-SNP	.											TCHH,bladder,carcinoma,0,3	TCHH	275	.	0			c.A5424G						.						78	79	78					1																	152080269		2010	4183	6193	SO:0001819	synonymous_variant	7062	exon3			CTGTTCTTCCCTC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.5424A>G	chr1.hg19:g.152080269T>C		96.0	0.0		80.0	8.0	NM_007113	Q5VUI3	Silent	SNP	ENST00000368804.1	hg19	CCDS41396.1																																																																																			.	.		0.597	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152080269	T	C	152080269	2	2	69	1	0	0	0	0	0	0	0	1	15715	1606	56	2		2	TCHH	1	152080269	Silent	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10	17	152080269	97170352	7	8812			1	10		3	3	33	N	T_GG	8.216295e-09
TCHH	7062	hgsc.bcm.edu	37	chr1	152080284	152080284	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tgttcttccctctcctggcgTagctgttcctcctcgcggaa	9	15	2	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:152080284T>G	ENST00000368804.1	-	2	5408	c.5409A>C	c.(5407-5409)ctA>ctC	p.L1803L		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1803	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTCCTGGCGTAGCTGTTCCT	0.577																																					p.L1803L		Atlas-SNP	.											TCHH,bladder,carcinoma,0,1	TCHH	275	.	0			c.A5409C						.						80	80	80					1																	152080284		1984	4176	6160	SO:0001819	synonymous_variant	7062	exon3			CTGGCGTAGCTGT	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.5409A>C	chr1.hg19:g.152080284T>G		93.0	0.0		79.0	6.0	NM_007113	Q5VUI3	Silent	SNP	ENST00000368804.1	hg19	CCDS41396.1																																																																																			.	.		0.577	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		G	152080284	T	G	152080284	2	3	69	1	0	0	0	0	0	0	0	1	15715	1625	57	5		5	TCHH	1	152080284	Silent	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10	15	152080284	97170337	8	8813			1	10		3	3	33	N	T_GG	8.216295e-09
SEC16B	89866	hgsc.bcm.edu	37	chr1	177934193	177934193	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cacacttactggaagtgggtCtcactatttgttccaaatgg	9	9	1	0	rs564535526	byFrequency	TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:177934193C>T	ENST00000308284.6	-	4	611	c.522G>A	c.(520-522)gaG>gaA	p.E174E	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000464631.2_Silent_p.E174E	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	174	Required for endoplasmic reticulum localization.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						GGAAGTGGGTCTCACTATTTG	0.443																																					p.E174E		Atlas-SNP	.											.	SEC16B	92	.	0			c.G522A						.						111	107	109					1																	177934193		1938	4141	6079	SO:0001819	synonymous_variant	89866	exon4			GTGGGTCTCACTA	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"regucalcin gene promotor region related protein"	612855	"leucine zipper transcription regulator 2"	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.522G>A	chr1.hg19:g.177934193C>T		109.0	0.0		114.0	85.0	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	hg19	CCDS44281.1																																																																																			.	.		0.443	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		T	177934193	C	T	177934193	2	4	69	1	0	0	0	0	0	0	0	1	14002	912	32	3		3	SEC16B	1	177934193	Silent	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	25853909	177934193	71316428	9	8814										
RYR2	6262	hgsc.bcm.edu	37	chr1	237850763	237850763	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ttttgtcttcagcctattctGcaaacttggagttcttgtca	7	9	5	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:237850763G>T	ENST00000366574.2	+	63	9343	c.9026G>T	c.(9025-9027)tGc>tTc	p.C3009F	RYR2_ENST00000609119.1_Intron|RYR2_ENST00000360064.6_Missense_Mutation_p.C3007F|RYR2_ENST00000542537.1_Missense_Mutation_p.C2993F	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3009					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGCCTATTCTGCAAACTTGGA	0.368																																					p.C3009F		Atlas-SNP	.											.	RYR2	1273	.	0			c.G9026T						.						49	45	46					1																	237850763		1822	4083	5905	SO:0001583	missense	6262	exon63			TATTCTGCAAACT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.9026G>T	chr1.hg19:g.237850763G>T	ENSP00000355533:p.Cys3009Phe	111.0	0.0		93.0	12.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112579	0.77210	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000540213	T;D;T	0.97279	-0.2;-4.32;-0.2	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000002	D	0.98454	0.9485	M	0.82823	2.61	0.80722	D	1	D	0.71674	0.998	D	0.65987	0.94	D	0.99282	1.0896	10	0.87932	D	0	-14.3809	19.6091	0.95594	0.0:0.0:1.0:0.0	.	3009	Q92736	RYR2_HUMAN	F	3009;3007;2993;4	ENSP00000355533:C3009F;ENSP00000353174:C3007F;ENSP00000443798:C2993F	ENSP00000353174:C3007F	C	+	2	0	RYR2	235917386	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.420000	0.97426	2.650000	0.89964	0.655000	0.94253	TGC	.	.		0.368	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237850763	G	T	237850763	3	4	69	1	0	0	0	0	1	0	0	0	13784	1319	46	3	9276	3	RYR2	1	237850763	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	59916570	237850763	11399858	10	8815										
SDCCAG8	10806	hgsc.bcm.edu	37	chr1	243437866	243437866	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggtcattagaacatgaggaaAccaatatgcctactatgcac	8	9	1	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:243437866A>G	ENST00000366541.3	+	4	446	c.328A>G	c.(328-330)Acc>Gcc	p.T110A	SDCCAG8_ENST00000391846.1_Missense_Mutation_p.T110A|SDCCAG8_ENST00000343783.6_Intron|SDCCAG8_ENST00000355875.4_Missense_Mutation_p.T110A	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	110					establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		ACATGAGGAAACCAATATGCC	0.294																																					p.T110A		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.A328G						.						86	84	84					1																	243437866		2203	4297	6500	SO:0001583	missense	10806	exon4			GAGGAAACCAATA	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.328A>G	chr1.hg19:g.243437866A>G	ENSP00000355499:p.Thr110Ala	160.0	0.0		146.0	22.0	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	hg19	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	A	2.670	-0.277739	0.05679	.	.	ENSG00000054282	ENST00000355875;ENST00000391846;ENST00000366541	T;T	0.41065	1.01;1.01	4.94	2.07	0.26955	.	1.369320	0.04167	N	0.324135	T	0.27489	0.0675	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.16364	-1.0405	10	0.14252	T	0.57	1.8244	4.641	0.12548	0.4711:0.1692:0.3597:0.0	.	110	Q86SQ7	SDCG8_HUMAN	A	110	ENSP00000348137:T110A;ENSP00000355499:T110A	ENSP00000348137:T110A	T	+	1	0	SDCCAG8	241504489	0.005000	0.15991	0.036000	0.18154	0.015000	0.08874	0.387000	0.20718	0.170000	0.19704	0.460000	0.39030	ACC	.	.		0.294	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		G	243437866	A	G	243437866	3	3	69	1	0	0	0	0	1	0	0	0	13974	43	2	2	342	2	SDCCAG8	1	243437866	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	5587103	243437866	5812755	11	8816										
OR2T27	403239	hgsc.bcm.edu	37	chr1	248813752	248813752	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ctcccagccaggctgccgccAcaatcaaccagcagatcttg	8	17	2	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:248813752A>G	ENST00000344889.3	-	1	433	c.434T>C	c.(433-435)gTg>gCg	p.V145A		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGCTGCCGCCACAATCAACCA	0.552																																					p.V145A		Atlas-SNP	.											.	OR2T27	52	.	0			c.T434C						.						56	42	47					1																	248813752		2196	4246	6442	SO:0001583	missense	403239	exon1			GCCGCCACAATCA		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"GPCR / Class A : Olfactory receptors"	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.434T>C	chr1.hg19:g.248813752A>G	ENSP00000342008:p.Val145Ala	427.0	0.0		268.0	101.0	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	hg19	CCDS31124.1	.	.	.	.	.	.	.	.	.	.	.	1.572	-0.533764	0.04082	.	.	ENSG00000187701	ENST00000344889	T	0.39056	1.1	3.3	2.18	0.27775	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35838	N	0.002957	T	0.22166	0.0534	L	0.28192	0.835	0.09310	N	1	B	0.19200	0.034	B	0.18871	0.023	T	0.22661	-1.0210	10	0.05833	T	0.94	.	7.8352	0.29365	0.8862:0.0:0.1138:0.0	.	145	Q8NH04	O2T27_HUMAN	A	145	ENSP00000342008:V145A	ENSP00000342008:V145A	V	-	2	0	OR2T27	246880375	0.000000	0.05858	0.089000	0.20774	0.057000	0.15508	0.541000	0.23207	1.511000	0.48818	0.163000	0.16589	GTG	.	.		0.552	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824		G	248813752	A	G	248813752	3	3	69	1	0	0	0	0	1	0	0	0	11030	159	6	2	522	2	OR2T27	1	248813752	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	5375886	248813752	436869	12	8817										
GCKR	2646	hgsc.bcm.edu	37	chr2	27741789	27741789	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tccaagctcttctggcgggcGctggccatgctgcaggtagg	15	12	2	0	rs367961156		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:27741789G>T	ENST00000264717.2	+	17	1620	c.1557G>T	c.(1555-1557)gcG>gcT	p.A519A	GCKR_ENST00000424318.2_Silent_p.A329A	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	519					carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|negative regulation of glucokinase activity (GO:0033132)|positive regulation of glucokinase activity (GO:0033133)|protein import into nucleus, translocation (GO:0000060)|regulation of glucose transport (GO:0010827)|response to fructose (GO:0009750)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	carbohydrate binding (GO:0030246)|enzyme inhibitor activity (GO:0004857)|fructose-6-phosphate binding (GO:0070095)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					TCTGGCGGGCGCTGGCCATGC	0.522																																					p.A519A		Atlas-SNP	.											.	GCKR	73	.	0			c.G1557T						.						76	81	79					2																	27741789		2203	4300	6503	SO:0001819	synonymous_variant	2646	exon17			GCGGGCGCTGGCC	Z48475	CCDS1757.1	2p23	2008-05-21	2004-05-20		ENSG00000084734	ENSG00000084734			4196	protein-coding gene	gene with protein product		600842	"glucokinase (hexokinase 4) regulatory protein"			9570959, 8662230	Standard	NM_001486		Approved		uc002rky.3	Q14397	OTTHUMG00000128426	ENST00000264717.2:c.1557G>T	chr2.hg19:g.27741789G>T		85.0	0.0		62.0	21.0	NM_001486	A1L4C2|B4DPQ2|Q53RY6|Q99522	Silent	SNP	ENST00000264717.2	hg19	CCDS1757.1																																																																																			.	.		0.522	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250214.1	NM_001486		T	27741789	G	T	27741789	2	4	69	1	0	0	0	0	0	0	0	1	6302	1074	38	1		1	GCKR	2	27741789	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		27741789	215457584	13	8818										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33585803	33585803	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tgtacatcaggcgtgggatgGggagataactgcgaaatctt	14	6	2	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:33585803G>T	ENST00000404816.2	+	27	4493	c.4140G>T	c.(4138-4140)tgG>tgT	p.W1380C	LTBP1_ENST00000418533.2_Missense_Mutation_p.W1012C|LTBP1_ENST00000272273.5_Missense_Mutation_p.W278C|LTBP1_ENST00000402934.1_Missense_Mutation_p.W999C|LTBP1_ENST00000390003.4_Missense_Mutation_p.W1055C|LTBP1_ENST00000404525.1_Missense_Mutation_p.W1001C|LTBP1_ENST00000354476.3_Missense_Mutation_p.W1381C|LTBP1_ENST00000407925.1_Missense_Mutation_p.W1054C			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1380	TB 3.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GCGTGGGATGGGGAGATAACT	0.493																																					p.W1380C		Atlas-SNP	.											.	LTBP1	317	.	0			c.G4140T						.						112	102	105					2																	33585803		2203	4300	6503	SO:0001583	missense	4052	exon27			GGGATGGGGAGAT		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.4140G>T	chr2.hg19:g.33585803G>T	ENSP00000386043:p.Trp1380Cys	134.0	0.0		136.0	43.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	G	17.12	3.308822	0.60305	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273;ENST00000422669	D;D;D;D;D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97	5.07	5.07	0.68467	Matrix fibril-associated (3);TGF-beta binding (1);	.	.	.	.	D	0.99223	0.9730	M	0.92555	3.32	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.999;1.0;0.999;1.0;0.999;0.999;1.0	D	0.99198	1.0872	9	0.87932	D	0	.	18.8234	0.92106	0.0:0.0:1.0:0.0	.	278;1380;1012;1001;1054;1055;1381	E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.;LTBP1_HUMAN;.;.;.;.;.	C	1380;1381;1055;1012;999;1001;1054;278;216	ENSP00000386043:W1380C;ENSP00000346467:W1381C;ENSP00000374653:W1055C;ENSP00000393057:W1012C;ENSP00000384373:W999C;ENSP00000385359:W1001C;ENSP00000384091:W1054C;ENSP00000272273:W278C;ENSP00000395211:W216C	ENSP00000272273:W278C	W	+	3	0	LTBP1	33439307	1.000000	0.71417	1.000000	0.80357	0.248000	0.25809	9.743000	0.98849	2.497000	0.84241	0.563000	0.77884	TGG	.	.		0.493	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		T	33585803	G	T	33585803	3	4	69	1	0	0	0	0	1	0	0	0	9082	1241	43	3	4301	3	LTBP1	2	33585803	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	5844014	33585803	209613570	14	8819										
SOS1	6654	hgsc.bcm.edu	37	chr2	39222434	39222434	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tataactaattttccttggcTcctgctgcagaggtgtggga	11	8	0	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:39222434T>C	ENST00000426016.1	-	21	3262	c.3176A>G	c.(3175-3177)gAg>gGg	p.E1059G	SOS1_ENST00000402219.2_Missense_Mutation_p.E1059G|SOS1-IT1_ENST00000594472.1_RNA|SOS1_ENST00000395038.2_Missense_Mutation_p.E1059G			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	1059					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				TTTCCTTGGCTCCTGCTGCAG	0.463									Noonan syndrome																												p.E1059G		Atlas-SNP	.											.	SOS1	134	.	0			c.A3176G						.						137	130	132					2																	39222434		2203	4300	6503	SO:0001583	missense	6654	exon20	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CTTGGCTCCTGCT	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.3176A>G	chr2.hg19:g.39222434T>C	ENSP00000387784:p.Glu1059Gly	144.0	0.0		138.0	70.0	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	hg19	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.021765	0.93462	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	T;T;T	0.78816	-1.07;-1.07;-1.21	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.85969	0.5821	M	0.62723	1.935	0.80722	D	1	D	0.64830	0.994	D	0.64687	0.928	D	0.86854	0.2025	10	0.66056	D	0.02	.	16.6438	0.85155	0.0:0.0:0.0:1.0	.	1059	Q07889	SOS1_HUMAN	G	1059;1059;791;1059;1059	ENSP00000387784:E1059G;ENSP00000384675:E1059G;ENSP00000378479:E1059G	ENSP00000263879:E1059G	E	-	2	0	SOS1	39075938	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.331000	0.79192	2.333000	0.79357	0.533000	0.62120	GAG	.	.		0.463	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		C	39222434	T	C	39222434	3	2	69	1	0	0	0	0	1	0	0	0	14951	1551	54	2	841	2	SOS1	2	39222434	Missense_Mutation	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10	5636631	39222434	203976939	15	8820										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50463974	50463974	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gcctgaagaactgtccactcGcaccaatacggcttctttct	7	14	2	2	rs199546979		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:50463974G>T	ENST00000406316.2	-	18	4975	c.3499C>A	c.(3499-3501)Cga>Aga	p.R1167R	NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000405472.3_Silent_p.R1159R|NRXN1_ENST00000342183.5_Silent_p.R132R|NRXN1_ENST00000404971.1_Silent_p.R1207R|NRXN1_ENST00000406859.3_Silent_p.R1167R|NRXN1_ENST00000402717.3_Silent_p.R1159R|NRXN1_ENST00000401669.2_Silent_p.R1167R|NRXN1_ENST00000401710.1_Silent_p.R185R	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1167	Laminin G-like 6. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.R1207*(1)|p.R1208*(1)|p.R132*(1)|p.R1167*(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CTGTCCACTCGCACCAATACG	0.423																																					p.R1207R		Atlas-SNP	.											NRXN1_ENST00000536085,NS,carcinoma,0,3	NRXN1	1118	.	4	Substitution - Nonsense(4)	endometrium(4)	c.C3619A						.						120	107	111					2																	50463974		2203	4300	6503	SO:0001819	synonymous_variant	9378	exon19			CCACTCGCACCAA	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3499C>A	chr2.hg19:g.50463974G>T		147.0	0.0		153.0	66.0	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	hg19	CCDS54360.1																																																																																			.	.		0.423	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50463974	G	T	50463974	2	4	69	1	0	0	0	0	0	0	0	1	10674	1095	38	1		1	NRXN1	2	50463974	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	11241540	50463974	192735399	16	8821										
EFEMP1	2202	hgsc.bcm.edu	37	chr2	56144961	56144961	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cgactgcagcagcactggccAcaaaaccacccccgggcaac	9	18	0	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:56144961A>G	ENST00000394555.2	-	4	791	c.356T>C	c.(355-357)gTg>gCg	p.V119A	EFEMP1_ENST00000424836.2_Missense_Mutation_p.V61A|EFEMP1_ENST00000355426.3_Missense_Mutation_p.V119A|EFEMP1_ENST00000394554.1_Missense_Mutation_p.V119A	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	119					epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGCACTGGCCACAAAACCACC	0.597																																					p.V119A	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.T356C						.						56	55	55					2																	56144961		2203	4300	6503	SO:0001583	missense	2202	exon4			CTGGCCACAAAAC	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"Fibulins"	3218	protein-coding gene	gene with protein product	"fibulin 3"	601548	"fibrillin-like", "EGF-containing fibulin-like extracellular matrix protein 1"	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.356T>C	chr2.hg19:g.56144961A>G	ENSP00000378058:p.Val119Ala	75.0	0.0		76.0	35.0	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Missense_Mutation	SNP	ENST00000394555.2	hg19	CCDS1857.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.912922	0.52439	.	.	ENSG00000115380	ENST00000394555;ENST00000394554;ENST00000424836;ENST00000355426;ENST00000438672;ENST00000439193	D;D;T;D;T;T	0.83591	-1.74;-1.74;-1.26;-1.74;-1.21;-1.32	4.58	4.58	0.56647	.	0.490245	0.17300	N	0.179299	T	0.64583	0.2611	N	0.08118	0	0.18873	N	0.999982	B;B	0.22541	0.005;0.071	B;B	0.18263	0.015;0.021	T	0.44143	-0.9347	10	0.08837	T	0.75	.	12.5594	0.56273	1.0:0.0:0.0:0.0	.	61;119	B4DW75;Q12805	.;FBLN3_HUMAN	A	119;119;61;119;119;119	ENSP00000378058:V119A;ENSP00000378057:V119A;ENSP00000399145:V61A;ENSP00000347596:V119A;ENSP00000392055:V119A;ENSP00000408195:V119A	ENSP00000347596:V119A	V	-	2	0	EFEMP1	55998465	0.429000	0.25530	0.929000	0.37066	0.995000	0.86356	2.748000	0.47483	2.285000	0.76669	0.528000	0.53228	GTG	.	.		0.597	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2			G	56144961	A	G	56144961	3	3	69	1	0	0	0	0	1	0	0	0	4943	159	6	2	1157	2	EFEMP1	2	56144961	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	5680987	56144961	187054412	17	8822										
ASTL	431705	hgsc.bcm.edu	37	chr2	96798324	96798324	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	acggatatagcggtcccggtCggcccgcgtgtgctcgtgcc	15	14	0	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:96798324C>A	ENST00000342380.2	-	6	591	c.592G>T	c.(592-594)Gac>Tac	p.D198Y		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						CGGTCCCGGTCGGCCCGCGTG	0.657																																					p.D198Y		Atlas-SNP	.											.	ASTL	59	.	0			c.G592T						.						67	64	65					2																	96798324		2203	4300	6503	SO:0001583	missense	431705	exon6			CCCGGTCGGCCCG	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"sperm acrosomal SLLP1 binding"	608860	"astacin-like metalloendopeptidase (M12 family)"			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.592G>T	chr2.hg19:g.96798324C>A	ENSP00000343674:p.Asp198Tyr	267.0	0.0		211.0	101.0	NM_001002036		Missense_Mutation	SNP	ENST00000342380.2	hg19	CCDS33249.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.598821	0.66332	.	.	ENSG00000188886	ENST00000342380	T	0.76186	-1.0	4.41	4.41	0.53225	Peptidase, metallopeptidase (1);Peptidase M12A, astacin (2);Metallopeptidase, catalytic domain (1);	0.000000	0.48286	D	0.000185	D	0.92113	0.7500	H	0.99555	4.625	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.95296	0.8399	10	0.87932	D	0	-18.085	14.5671	0.68185	0.0:1.0:0.0:0.0	.	198	Q6HA08	ASTL_HUMAN	Y	198	ENSP00000343674:D198Y	ENSP00000343674:D198Y	D	-	1	0	ASTL	96162051	1.000000	0.71417	0.870000	0.34147	0.434000	0.31775	7.050000	0.76620	2.008000	0.58898	0.551000	0.68910	GAC	.	.		0.657	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			A	96798324	C	A	96798324	3	1	69	1	0	0	0	0	1	0	0	0	1063	884	31	1	718	1	ASTL	2	96798324	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	40653363	96798324	146401049	18	8823										
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105886085	105886085	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cagctcgtgcaccaggatatGcagcgccttctcatgctcgc	10	15	1	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:105886085G>A	ENST00000393359.2	-	11	2476	c.2050C>T	c.(2050-2052)Cat>Tat	p.H684Y	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.H684Y			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	684					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						ACCAGGATATGCAGCGCCTTC	0.642																																					p.H684Y	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C2050T						.						27	27	27					2																	105886085		2203	4300	6503	SO:0001583	missense	9392	exon11			GGATATGCAGCGC	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.2050C>T	chr2.hg19:g.105886085G>A	ENSP00000377027:p.His684Tyr	98.0	0.0		84.0	31.0	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	hg19	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.892431	0.52121	.	.	ENSG00000135966	ENST00000393359;ENST00000258449;ENST00000543724	T;T	0.19394	2.15;2.15	5.54	4.64	0.57946	.	0.388763	0.31031	N	0.008390	T	0.34542	0.0901	M	0.74881	2.28	0.44843	D	0.997859	D;B	0.58620	0.983;0.178	P;B	0.51229	0.663;0.393	T	0.19321	-1.0309	10	0.66056	D	0.02	-8.0679	11.254	0.49043	0.0:0.138:0.7185:0.1435	.	139;684	B3KMM9;Q8WUH2	.;TGFA1_HUMAN	Y	684;684;139	ENSP00000377027:H684Y;ENSP00000258449:H684Y	ENSP00000258449:H684Y	H	-	1	0	TGFBRAP1	105252517	1.000000	0.71417	0.948000	0.38648	0.616000	0.37450	3.594000	0.54008	1.308000	0.44962	0.462000	0.41574	CAT	.	.		0.642	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		A	105886085	G	A	105886085	3	1	69	1	0	0	0	0	1	0	0	0	15839	1319	46	3	540	3	TGFBRAP1	2	105886085	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	9087761	105886085	137313288	19	8824										
RGPD3	653489	hgsc.bcm.edu	37	chr2	107051593	107051593	+	Frame_Shift_Del	DEL	C	C	-													0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ttcaacaatggcaaaactttCttccaataatgaacacttct							TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:107051593delC	ENST00000409886.3	-	13	1911	c.1824delG	c.(1822-1824)aagfs	p.K609fs	RGPD3_ENST00000304514.7_Frame_Shift_Del_p.K609fs	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	609					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						GCAAAACTTTCTTCCAATAAT	0.323																																					p.K609fs		Atlas-INDEL	.											.	RGPD3	316	.	0			c.1825delA						.																																			SO:0001589	frameshift_variant	653489	exon13			.		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"Tetratricopeptide (TTC) repeat domain containing"	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.1824delG	chr2.hg19:g.107051593delC	ENSP00000386588:p.Lys609fs	602.0	0.0		479.0	82.0	NM_001144013	B8ZZM4	Frame_Shift_Del	DEL	ENST00000409886.3	hg19	CCDS46379.1																																																																																			.	.		0.323	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931		-	107051593	C	-	107051593	7	5	69	1	0	1	0	1	0	0	0	0	13302	912	32	0	3496	0	RGPD3	2	107051593	Frame_Shift_Del	DEL	C	TCGA-CC-A5UE-01A-11D-A28X-10	1165508	107051593	136147780	20	8825										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109369517	109369517	+	Frame_Shift_Del	DEL	A	A	-													0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggagaagtgttcattattggAagaaagttttgccattgttg							TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:109369517delA	ENST00000283195.6	+	13	1945	c.1819delA	c.(1819-1821)aagfs	p.K608fs		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	608					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TCATTATTGGAAGAAAGTTTT	0.323																																					p.W606X		Atlas-INDEL	.											.	RANBP2	488	.	0			c.1818delG						.						18	19	19					2																	109369517		1806	3961	5767	SO:0001589	frameshift_variant	5903	exon13			.	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.1819delA	chr2.hg19:g.109369517delA	ENSP00000283195:p.Lys608fs	641.0	0.0		511.0	114.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Frame_Shift_Del	DEL	ENST00000283195.6	hg19	CCDS2079.1																																																																																			.	.		0.323	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		-	109369517	A	-	109369517	7	5	69	1	0	1	0	1	0	0	0	0	13043	247	9	0	1869	0	RANBP2	2	109369517	Frame_Shift_Del	DEL	A	TCGA-CC-A5UE-01A-11D-A28X-10	2317924	109369517	133829856	21	8826										
POTEF	728378	hgsc.bcm.edu	37	chr2	130832599	130832599	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gatctgggtcatcttctcgcGgttggccttagggttcaggg	15	9	5	0	rs532998196		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:130832599G>A	ENST00000409914.2	-	17	2845	c.2446C>T	c.(2446-2448)Cgc>Tgc	p.R816C	POTEF_ENST00000357462.5_Missense_Mutation_p.R816C	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	816	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						ATCTTCTCGCGGTTGGCCTTA	0.597													.|||	1	0.000199681	0	0	5008	,	,		20953	0.001		0	False		,,,				2504	0				p.R816C		Atlas-SNP	.											POTEF,trunk,malignant_melanoma,+1,1	POTEF	140	.	0			c.C2446T						.						120	131	127					2																	130832599		2203	4300	6503	SO:0001583	missense	728378	exon17			TCTCGCGGTTGGC	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33905	protein-coding gene	gene with protein product			"ANKRD26-like family C, member 1B"	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2446C>T	chr2.hg19:g.130832599G>A	ENSP00000386786:p.Arg816Cys	526.0	2.0		446.0	225.0	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	hg19	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	13.07	2.126044	0.37533	.	.	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.97114	-4.25;-4.25	.	.	.	Actin/actin-like conserved site (1);	.	.	.	.	D	0.98988	0.9655	H	0.99958	5.055	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.95089	0.8220	8	0.87932	D	0	.	2.8768	0.05634	3.0E-4:2.0E-4:0.5045:0.4949	.	816	A5A3E0	POTEF_HUMAN	C	816	ENSP00000350052:R816C;ENSP00000386786:R816C	ENSP00000350052:R816C	R	-	1	0	POTEF	130549069	1.000000	0.71417	0.235000	0.24058	0.237000	0.25408	2.711000	0.47177	0.119000	0.18210	0.121000	0.15741	CGC	.	.		0.597	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		A	130832599	G	A	130832599	3	1	69	1	0	0	0	0	1	0	0	0	12274	1116	39	1	785	1	POTEF	2	130832599	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	21463082	130832599	112366774	22	8827										
LCT	3938	hgsc.bcm.edu	37	chr2	136579639	136579639	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	aaactcattaatatcaaaccCaatggtgagcacttggtctt	6	9	3	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:136579639C>T	ENST00000264162.2	-	5	947	c.937G>A	c.(937-939)Ggg>Agg	p.G313R	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	313	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	ATATCAAACCCAATGGTGAGC	0.333																																					p.G313R		Atlas-SNP	.											.	LCT	309	.	0			c.G937A						.						130	134	132					2																	136579639		2203	4300	6503	SO:0001583	missense	3938	exon5			CAAACCCAATGGT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.937G>A	chr2.hg19:g.136579639C>T	ENSP00000264162:p.Gly313Arg	77.0	0.0		76.0	16.0	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	hg19	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.630371	0.87660	.	.	ENSG00000115850	ENST00000264162	T	0.35236	1.32	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.59514	0.2199	M	0.63843	1.955	0.54753	D	0.99998	D	0.89917	1.0	D	0.83275	0.996	T	0.60188	-0.7312	10	0.87932	D	0	-32.4761	17.9984	0.89191	0.0:1.0:0.0:0.0	.	313	P09848	LPH_HUMAN	R	313	ENSP00000264162:G313R	ENSP00000264162:G313R	G	-	1	0	LCT	136296109	1.000000	0.71417	0.916000	0.36221	0.996000	0.88848	4.791000	0.62460	2.832000	0.97577	0.655000	0.94253	GGG	.	.		0.333	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		T	136579639	C	T	136579639	3	4	69	1	0	0	0	0	1	0	0	0	8702	594	21	3	4898	3	LCT	2	136579639	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	5747040	136579639	106619734	23	8828										
TTN	7273	hgsc.bcm.edu	37	chr2	179463972	179463972	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tacatattcatggccttctaGcaatttgggaatcgtgtacg	9	8	2	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:179463972G>A	ENST00000591111.1	-	240	51849	c.51625C>T	c.(51625-51627)Cta>Tta	p.L17209L	TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Silent_p.L9785L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.L9977L|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Silent_p.L18850L|TTN_ENST00000342992.6_Silent_p.L16282L|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Silent_p.L9910L			Q8WZ42	TITIN_HUMAN	titin	17209	Fibronectin type-III 24. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGGCCTTCTAGCAATTTGGGA	0.423																																					p.L18850L		Atlas-SNP	.											.	TTN	18412	.	0			c.C56548T						.						195	185	188					2																	179463972		1899	4114	6013	SO:0001819	synonymous_variant	7273	exon290			CTTCTAGCAATTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.51625C>T	chr2.hg19:g.179463972G>A		123.0	0.0		112.0	51.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179463972	G	A	179463972	2	1	69	1	0	0	0	0	0	0	0	1	16750	962	34	3		3	TTN	2	179463972	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	42884333	179463972	63735401	24	8829										
TTN	7273	hgsc.bcm.edu	37	chr2	179665290	179665290	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ctggatttcggctccatcccGgtagaacttcaccacaggtg	10	13	1	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:179665290G>T	ENST00000591111.1	-	4	639	c.415C>A	c.(415-417)Cgg>Agg	p.R139R	TTN_ENST00000360870.5_Silent_p.R139R|TTN_ENST00000460472.2_Silent_p.R139R|TTN_ENST00000342175.6_Silent_p.R139R|TTN_ENST00000589042.1_Silent_p.R139R|TTN_ENST00000342992.6_Silent_p.R139R|TTN_ENST00000359218.5_Silent_p.R139R			Q8WZ42	TITIN_HUMAN	titin	32757	Ig-like 2.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTCCATCCCGGTAGAACTTC	0.507																																					p.R139R		Atlas-SNP	.											TTN_ENST00000360870,NS,lymphoid_neoplasm,0,18	TTN	18412	.	0			c.C415A						.						141	125	130					2																	179665290		2203	4300	6503	SO:0001819	synonymous_variant	7273	exon4			CATCCCGGTAGAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.415C>A	chr2.hg19:g.179665290G>T		108.0	0.0		132.0	51.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.507	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179665290	G	T	179665290	2	4	69	1	0	0	0	0	0	0	0	1	16750	1115	39	1		1	TTN	2	179665290	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	201318	179665290	63534083	25	8830										
MYO1B	4430	hgsc.bcm.edu	37	chr2	192273885	192273885	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tactcacaaggagctaaaaaGgattttccacttgtggaggg	11	7	1	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:192273885G>C	ENST00000392318.3	+	26	2994	c.2747G>C	c.(2746-2748)aGg>aCg	p.R916T	MYO1B_ENST00000304164.4_Missense_Mutation_p.R916T|MYO1B_ENST00000339514.4_Missense_Mutation_p.R858T|MYO1B_ENST00000439065.2_Missense_Mutation_p.R161T|MYO1B_ENST00000392316.1_Missense_Mutation_p.R887T	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	916					actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			GAGCTAAAAAGGATTTTCCAC	0.323																																					p.R916T		Atlas-SNP	.											.	MYO1B	160	.	0			c.G2747C						.						82	87	86					2																	192273885		2203	4300	6503	SO:0001583	missense	4430	exon26			TAAAAAGGATTTT	L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.2747G>C	chr2.hg19:g.192273885G>C	ENSP00000376132:p.Arg916Thr	85.0	0.0		100.0	49.0	NM_001161819	O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	hg19	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.137546	0.37728	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316;ENST00000439065	D;D;D;D;T	0.87334	-2.23;-2.24;-2.24;-2.24;0.26	5.79	5.79	0.91817	.	0.236043	0.50627	D	0.000106	T	0.81612	0.4859	L	0.37630	1.12	0.54753	D	0.999982	P;B;B	0.38922	0.651;0.136;0.12	B;B;B	0.32677	0.15;0.071;0.076	T	0.81433	-0.0935	10	0.39692	T	0.17	.	18.201	0.89838	0.0:0.0:1.0:0.0	.	161;916;858	E7EPB4;O43795;O43795-2	.;MYO1B_HUMAN;.	T	858;916;916;887;161	ENSP00000341903:R858T;ENSP00000376132:R916T;ENSP00000306382:R916T;ENSP00000376130:R887T;ENSP00000391442:R161T	ENSP00000306382:R916T	R	+	2	0	MYO1B	191982130	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.511000	0.67024	2.740000	0.93945	0.561000	0.74099	AGG	.	.		0.323	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		C	192273885	G	C	192273885	3	2	69	1	0	0	0	0	1	0	0	0	10078	1000	35	4	2845	4	MYO1B	2	192273885	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	12608595	192273885	50925488	26	8831										
CTLA4	1493	hgsc.bcm.edu	37	chr2	204732726	204732726	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	acctggctaccaggacctggCcctgcactctcctgtttttt	8	15	1	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:204732726C>A	ENST00000302823.3	+	1	218	c.61C>A	c.(61-63)Ccc>Acc	p.P21T	CTLA4_ENST00000427473.2_5'Flank|CTLA4_ENST00000487393.1_3'UTR|CTLA4_ENST00000472206.1_Missense_Mutation_p.P21T|CTLA4_ENST00000295854.6_Missense_Mutation_p.P21T	NM_005214.4	NP_005205.2	P16410	CTLA4_HUMAN	cytotoxic T-lymphocyte-associated protein 4	21					B cell receptor signaling pathway (GO:0050853)|cellular response to DNA damage stimulus (GO:0006974)|immune response (GO:0006955)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of immune response (GO:0050777)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of apoptotic process (GO:0043065)|T cell costimulation (GO:0031295)	clathrin-coated endocytic vesicle (GO:0045334)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				large_intestine(4)|lung(4)|skin(1)	9					Ipilimumab(DB06186)	CAGGACCTGGCCCTGCACTCT	0.522																																					p.P21T		Atlas-SNP	.											.	CTLA4	24	.	0			c.C61A						.						157	136	143					2																	204732726		2203	4300	6503	SO:0001583	missense	1493	exon1			ACCTGGCCCTGCA		CCDS2362.1, CCDS42803.1	2q33	2014-02-03			ENSG00000163599	ENSG00000163599		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	2505	protein-coding gene	gene with protein product		123890	"celiac disease 3", "insulin-dependent diabetes mellitus 12"	CELIAC3, IDDM12		3220103, 8817351	Standard	NM_005214		Approved	CD152, CD, GSE, CD28, ICOS	uc002vak.2	P16410	OTTHUMG00000132877	ENST00000302823.3:c.61C>A	chr2.hg19:g.204732726C>A	ENSP00000303939:p.Pro21Thr	113.0	0.0		91.0	38.0	NM_005214	A0N1S0|E9PDH0|O95653|Q0PP65|Q52MC1|Q53TD5|Q5S005|Q8WXJ1|Q96P43|Q9UKN9	Missense_Mutation	SNP	ENST00000302823.3	hg19	CCDS2362.1	.	.	.	.	.	.	.	.	.	.	C	7.253	0.603599	0.14002	.	.	ENSG00000163599	ENST00000302823;ENST00000541886;ENST00000295854;ENST00000472206	T;T;T	0.38560	1.13;1.13;1.13	6.02	-0.369	0.12534	.	0.517115	0.19439	N	0.114222	T	0.41627	0.1167	L	0.50333	1.59	0.80722	D	1	P;D;B	0.53312	0.775;0.959;0.44	B;P;B	0.50192	0.344;0.634;0.146	T	0.31806	-0.9930	10	0.56958	D	0.05	-4.4291	9.1707	0.37078	0.0:0.4989:0.0:0.5011	.	21;21;21	P16410-4;Q8TDA6;P16410	.;.;CTLA4_HUMAN	T	21	ENSP00000303939:P21T;ENSP00000295854:P21T;ENSP00000417779:P21T	ENSP00000295854:P21T	P	+	1	0	CTLA4	204440971	0.614000	0.27017	0.157000	0.22605	0.005000	0.04900	-0.103000	0.10940	-0.126000	0.11682	-0.345000	0.07892	CCC	.	.		0.522	CTLA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256365.1	NM_005214		A	204732726	C	A	204732726	3	1	69	1	0	0	0	0	1	0	0	0	4013	739	26	3	63	3	CTLA4	2	204732726	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	12458841	204732726	38466647	27	8832										
PARD3B	117583	hgsc.bcm.edu	37	chr2	205829899	205829899	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ttgctgtgtttgaagaacaaGaaccactccacaagattgag	9	8	0	5			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:205829899G>A	ENST00000406610.2	+	3	454	c.247G>A	c.(247-249)Gaa>Aaa	p.E83K	PARD3B_ENST00000349953.3_Missense_Mutation_p.E83K|PARD3B_ENST00000351153.1_Missense_Mutation_p.E83K|PARD3B_ENST00000358768.2_Missense_Mutation_p.E83K|PARD3B_ENST00000462231.1_Missense_Mutation_p.E83K	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	83					cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		TGAAGAACAAGAACCACTCCA	0.473																																					p.E83K		Atlas-SNP	.											.	PARD3B	314	.	0			c.G247A						.						115	110	111					2																	205829899		1907	4118	6025	SO:0001583	missense	117583	exon3			GAACAAGAACCAC	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19", "par-3 partitioning defective 3 homolog B (C. elegans)"	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.247G>A	chr2.hg19:g.205829899G>A	ENSP00000385848:p.Glu83Lys	67.0	0.0		72.0	16.0	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Missense_Mutation	SNP	ENST00000406610.2	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.344670	0.95807	.	.	ENSG00000116117	ENST00000406610;ENST00000358768;ENST00000351153;ENST00000349953	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.66479	0.2793	M	0.64997	1.995	0.45502	D	0.998462	D;D;P;D;D	0.65815	0.995;0.977;0.931;0.99;0.995	D;P;P;P;D	0.63877	0.917;0.856;0.647;0.816;0.919	T	0.66586	-0.5886	10	0.56958	D	0.05	.	19.6505	0.95798	0.0:0.0:1.0:0.0	.	83;83;83;83;83	Q8TEW8-3;Q8TEW8;E9PE87;Q8TEW8-2;Q8TEW8-5	.;PAR3L_HUMAN;.;.;.	K	83	ENSP00000385848:E83K;ENSP00000351618:E83K;ENSP00000317261:E83K;ENSP00000340280:E83K	ENSP00000340280:E83K	E	+	1	0	PARD3B	205538144	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.957000	0.63652	2.635000	0.89317	0.563000	0.77884	GAA	.	.		0.473	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177		A	205829899	G	A	205829899	3	1	69	1	0	0	0	0	1	0	0	0	11453	943	33	3	257	3	PARD3B	2	205829899	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	1097173	205829899	37369474	28	8833										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209141531	209141531	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cagtattaaaacgcctcaagGaaatcatggaggggaaaagc	11	7	2	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:209141531G>C	ENST00000264380.4	+	4	576	c.418G>C	c.(418-420)Gaa>Caa	p.E140Q	PIKFYVE_ENST00000392202.3_Intron|PIKFYVE_ENST00000308862.6_Intron|PIKFYVE_ENST00000407449.1_Missense_Mutation_p.E140Q	NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	140					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						ACGCCTCAAGGAAATCATGGA	0.453																																					p.E140Q		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.G418C						.						62	62	62					2																	209141531		2203	4300	6503	SO:0001583	missense	200576	exon4			CTCAAGGAAATCA	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.418G>C	chr2.hg19:g.209141531G>C	ENSP00000264380:p.Glu140Gln	109.0	0.0		125.0	65.0	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	hg19	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	G	31	5.088991	0.94100	.	.	ENSG00000115020	ENST00000264380;ENST00000407449;ENST00000422495;ENST00000452564	T;T;T;T	0.66099	1.55;-0.19;-0.15;1.7	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.68016	0.2955	N	0.19112	0.55	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.993	D;D;D	0.80764	0.986;0.994;0.968	T	0.63681	-0.6582	10	0.23891	T	0.37	-25.0021	20.1047	0.97888	0.0:0.0:1.0:0.0	.	140;140;140	Q9Y2I7;E9PDH4;Q08AR7	FYV1_HUMAN;.;.	Q	140;140;152;140	ENSP00000264380:E140Q;ENSP00000384356:E140Q;ENSP00000414477:E152Q;ENSP00000405736:E140Q	ENSP00000264380:E140Q	E	+	1	0	PIKFYVE	208849776	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.553000	0.98118	2.762000	0.94881	0.655000	0.94253	GAA	.	.		0.453	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		C	209141531	G	C	209141531	3	2	69	1	0	0	0	0	1	0	0	0	11933	1175	41	4	428	4	PIKFYVE	2	209141531	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	3311632	209141531	34057842	29	8834										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220500114	220500114	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggagggccgtgacctgctgcGctccgtggctgctttccagc	15	14	0	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:220500114G>T	ENST00000358055.3	+	13	2380	c.1868G>T	c.(1867-1869)cGc>cTc	p.R623L	SLC4A3_ENST00000273063.6_Missense_Mutation_p.R650L|SLC4A3_ENST00000373762.3_Missense_Mutation_p.R650L|SLC4A3_ENST00000373760.2_Missense_Mutation_p.R623L|SLC4A3_ENST00000317151.3_Missense_Mutation_p.R623L			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	623					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GACCTGCTGCGCTCCGTGGCT	0.632																																					p.R650L		Atlas-SNP	.											.	SLC4A3	144	.	0			c.G1949T						.						73	67	69					2																	220500114		2203	4300	6503	SO:0001583	missense	6508	exon13			TGCTGCGCTCCGT		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1868G>T	chr2.hg19:g.220500114G>T	ENSP00000350756:p.Arg623Leu	345.0	0.0		239.0	114.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	hg19	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629752	0.46944	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151	T;T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29;-1.29	4.91	4.91	0.64330	Bicarbonate transporter, cytoplasmic (1);Phosphotransferase/anion transporter (1);	0.128381	0.48286	D	0.000199	T	0.72236	0.3435	L	0.45137	1.4	0.53688	D	0.999978	B;B;B	0.20261	0.002;0.009;0.043	B;B;B	0.21708	0.006;0.004;0.036	T	0.67534	-0.5646	10	0.33141	T	0.24	.	9.5122	0.39085	0.1323:0.0:0.8677:0.0	.	327;623;650	P48751-2;P48751;P48751-3	.;B3A3_HUMAN;.	L	623;623;650;650;623	ENSP00000350756:R623L;ENSP00000362865:R623L;ENSP00000273063:R650L;ENSP00000362867:R650L;ENSP00000314006:R623L	ENSP00000273063:R650L	R	+	2	0	SLC4A3	220208358	0.949000	0.32298	1.000000	0.80357	0.986000	0.74619	2.191000	0.42640	2.260000	0.74910	0.637000	0.83480	CGC	.	.		0.632	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		T	220500114	G	T	220500114	3	4	69	1	0	0	0	0	1	0	0	0	14670	1087	38	1	1995	1	SLC4A3	2	220500114	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	11358583	220500114	22699259	30	8835										
PRSS45	29122	hgsc.bcm.edu	37	chr3	46784019	46784019	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cttttcccaggacaacacccCagccagaatccatctgccct	5	18	1	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:46784019C>T	ENST00000460241.1	-	4	1129				PRSS45_ENST00000442359.2_Missense_Mutation_p.G170R			Q9UI38	TSP50_HUMAN	protease, serine, 50						proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						GACAACACCCCAGCCAGAATC	0.537																																					p.G170R	Pancreas(41;915 1239 11561 17469)	Atlas-SNP	.											.	PRSS45	12	.	0			c.G508A						.						130	150	143					3																	46784019		1969	4162	6131	SO:0001627	intron_variant	377047	exon4			ACACCCCAGCCAG	AF100707	CCDS2745.1	3p21.31	2011-05-24			ENSG00000206549	ENSG00000206549		"Serine peptidases / Serine peptidases"	17910	protein-coding gene	gene with protein product	"cancer/testis antigen 20", "testes specific protease 50"	607950				10397268	Standard	NM_013270		Approved	TSP50, CT20	uc003cqe.1	Q9UI38	OTTHUMG00000164067	ENST00000460241.1:c.541+6095G>A	chr3.hg19:g.46784019C>T		159.0	0.0		137.0	59.0	NM_199183		Missense_Mutation	SNP	ENST00000460241.1	hg19	CCDS2745.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872096	0.91587	.	.	ENSG00000188086	ENST00000331814;ENST00000442359	D	0.99545	-6.13	5.65	5.65	0.86999	.	0.000000	0.56097	D	0.000021	D	0.99585	0.9850	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98018	1.0369	9	0.87932	D	0	.	15.093	0.72211	0.0:1.0:0.0:0.0	.	170	Q7RTY3-2	.	R	202;170	ENSP00000401932:G170R	ENSP00000330940:G202R	G	-	1	0	PRSS45	46759023	1.000000	0.71417	0.986000	0.45419	0.966000	0.64601	6.208000	0.72165	2.941000	0.99782	0.655000	0.94253	GGG	.	.		0.537	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1			T	46784019	C	T	46784019	1	4	69	0	1	0	0	0	0	0	0	0	12641	594	21	3		3	PRSS45	3	46784019	Intron	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10		46784019	151238411	31	8836										
ERC2	26059	hgsc.bcm.edu	37	chr3	55717878	55717878	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cggctatgcccatatgccctCctcgtcatcctgcggccggc	10	18	1	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:55717878C>G	ENST00000288221.6	-	17	3112	c.2857G>C	c.(2857-2859)Gag>Cag	p.E953Q		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	953						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		CATATGCCCTCCTCGTCATCC	0.483																																					p.E951Q		Atlas-SNP	.											.	ERC2	221	.	0			c.G2851C						.						48	53	51					3																	55717878		1864	4109	5973	SO:0001583	missense	26059	exon16			TGCCCTCCTCGTC	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2857G>C	chr3.hg19:g.55717878C>G	ENSP00000288221:p.Glu953Gln	153.0	0.0		87.0	27.0	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	hg19	CCDS46851.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070877	0.76301	.	.	ENSG00000187672	ENST00000288221	T	0.35605	1.3	5.22	5.22	0.72569	.	0.123643	0.53938	D	0.000053	T	0.32556	0.0833	N	0.19112	0.55	0.38483	D	0.947761	P	0.39094	0.659	B	0.42959	0.403	T	0.33445	-0.9868	10	0.72032	D	0.01	-0.1583	17.3208	0.87235	0.0:1.0:0.0:0.0	.	953	O15083	ERC2_HUMAN	Q	953	ENSP00000288221:E953Q	ENSP00000288221:E953Q	E	-	1	0	ERC2	55692918	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.287000	0.65645	2.611000	0.88343	0.561000	0.74099	GAG	.	.		0.483	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		G	55717878	C	G	55717878	3	3	69	1	0	0	0	0	1	0	0	0	5213	864	30	4	20	4	ERC2	3	55717878	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	8933859	55717878	142304552	32	8837										
LMOD3	56203	hgsc.bcm.edu	37	chr3	69167886	69167886	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	acactgctgtgacgaatgtcGtttagcagctgatctctggg	12	9	1	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:69167886G>T	ENST00000420581.2	-	2	1799	c.1620C>A	c.(1618-1620)aaC>aaA	p.N540K	LMOD3_ENST00000489031.1_Missense_Mutation_p.N540K|LMOD3_ENST00000475434.1_Missense_Mutation_p.N540K	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	540	WH2.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		GACGAATGTCGTTTAGCAGCT	0.473																																					p.N540K		Atlas-SNP	.											.	LMOD3	92	.	0			c.C1620A						.						98	98	98					3																	69167886		1974	4175	6149	SO:0001583	missense	56203	exon2			AATGTCGTTTAGC	AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.1620C>A	chr3.hg19:g.69167886G>T	ENSP00000414670:p.Asn540Lys	197.0	0.0		137.0	46.0	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Missense_Mutation	SNP	ENST00000420581.2	hg19	CCDS46862.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318800	0.41096	.	.	ENSG00000163380	ENST00000420581;ENST00000489031;ENST00000475434	T;T;T	0.12147	2.71;2.71;2.71	5.84	-5.3	0.02738	.	0.198063	0.56097	D	0.000039	T	0.09862	0.0242	L	0.53249	1.67	0.44485	D	0.997428	P	0.44690	0.841	B	0.37780	0.258	T	0.12863	-1.0531	10	0.25751	T	0.34	-36.7382	11.8227	0.52247	0.7624:0.0:0.1554:0.0822	.	540	Q0VAK6	LMOD3_HUMAN	K	540	ENSP00000414670:N540K;ENSP00000417210:N540K;ENSP00000418645:N540K	ENSP00000414670:N540K	N	-	3	2	LMOD3	69250576	0.176000	0.23096	0.948000	0.38648	0.934000	0.57294	-0.239000	0.08965	-0.929000	0.03757	-0.216000	0.12614	AAC	.	.		0.473	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529		T	69167886	G	T	69167886	3	4	69	1	0	0	0	0	1	0	0	0	8867	1136	40	1	70	1	LMOD3	3	69167886	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	13450008	69167886	128854544	33	8838										
ACAD11	84129	hgsc.bcm.edu	37	chr3	132378583	132378583	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	caaatcggactcgccagtagCacctggcttcatgatcaccc	8	15	2	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:132378583C>A	ENST00000264990.6	-	1	984	c.13G>T	c.(13-15)Gct>Tct	p.A5S	ACAD11_ENST00000355458.3_Missense_Mutation_p.A5S|UBA5_ENST00000493720.2_5'Flank|UBA5_ENST00000494238.2_5'Flank|UBA5_ENST00000473651.1_5'Flank|ACAD11_ENST00000489991.1_5'UTR|UBA5_ENST00000356232.4_5'UTR|UBA5_ENST00000264991.4_Intron|ACAD11_ENST00000481970.2_Missense_Mutation_p.A5S|ACAD11_ENST00000545291.1_5'UTR	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	5					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)	p.A5S(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						TCGCCAGTAGCACCTGGCTTC	0.607											OREG0015804	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A5S		Atlas-SNP	.											ACAD11,NS,carcinoma,0,1	ACAD11	78	.	1	Substitution - Missense(1)	ovary(1)	c.G13T						.						67	69	69					3																	132378583		2203	4300	6503	SO:0001583	missense	84129	exon1			CAGTAGCACCTGG	BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"acyl-Coenzyme A dehydrogenase family, member 11"				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.13G>T	chr3.hg19:g.132378583C>A	ENSP00000264990:p.Ala5Ser	125.0	0.0	1594	72.0	34.0	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Missense_Mutation	SNP	ENST00000264990.6	hg19	CCDS3074.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.503451	0.44558	.	.	ENSG00000240303	ENST00000355458;ENST00000264990;ENST00000481970	D;D;T	0.96619	-4.03;-4.07;1.91	5.86	2.12	0.27331	.	.	.	.	.	D	0.93324	0.7872	L	0.60455	1.87	0.09310	N	0.999994	B;B	0.28713	0.22;0.043	B;B	0.25140	0.058;0.027	D	0.84386	0.0552	8	.	.	.	.	7.8768	0.29599	0.0:0.6718:0.0:0.3282	.	5;5	D6RDI8;Q709F0	.;ACD11_HUMAN	S	5	ENSP00000347636:A5S;ENSP00000264990:A5S;ENSP00000420907:A5S	.	A	-	1	0	ACAD11	133861273	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.390000	0.20768	0.112000	0.17975	-0.157000	0.13467	GCT	.	.		0.607	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169		A	132378583	C	A	132378583	3	1	69	1	0	0	0	0	1	0	0	0	109	710	25	3	2409	3	ACAD11	3	132378583	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	63210697	132378583	65643847	34	8839										
GPR149	344758	hgsc.bcm.edu	37	chr3	154146874	154146874	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	accaggcagccccagggcgtGcgcacgaaggcgccccagcc	14	18	0	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:154146874G>A	ENST00000389740.2	-	1	630	c.531C>T	c.(529-531)cgC>cgT	p.R177R		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	177					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CCCAGGGCGTGCGCACGAAGG	0.667																																					p.R177R		Atlas-SNP	.											.	GPR149	134	.	0			c.C531T						.						24	30	28					3																	154146874		2053	4183	6236	SO:0001819	synonymous_variant	344758	exon1			GGGCGTGCGCACG	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.531C>T	chr3.hg19:g.154146874G>A		54.0	0.0		33.0	19.0	NM_001038705		Silent	SNP	ENST00000389740.2	hg19	CCDS43162.1																																																																																			.	.		0.667	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		A	154146874	G	A	154146874	2	1	69	1	0	0	0	0	0	0	0	1	6662	1306	46	3		3	GPR149	3	154146874	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	21768291	154146874	43875556	35	8840										
LRCH3	84859	hgsc.bcm.edu	37	chr3	197562626	197562626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cgaggtgagacagcccaaggGaccagacccagacagcctta	12	13	0	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:197562626G>A	ENST00000425562.2	+	9	1184	c.1184G>A	c.(1183-1185)gGa>gAa	p.G395E	LRCH3_ENST00000414675.2_Intron|LRCH3_ENST00000441090.2_Intron|LRCH3_ENST00000438796.2_Missense_Mutation_p.G395E|LRCH3_ENST00000536618.1_5'UTR|LRCH3_ENST00000334859.4_Missense_Mutation_p.G395E			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	395						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		CAGCCCAAGGGACCAGACCCA	0.488																																					p.G395E		Atlas-SNP	.											.	LRCH3	96	.	0			c.G1184A						.						173	155	161					3																	197562626		2203	4300	6503	SO:0001583	missense	84859	exon9			CCAAGGGACCAGA	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1184G>A	chr3.hg19:g.197562626G>A	ENSP00000393579:p.Gly395Glu	119.0	0.0		88.0	33.0	NM_032773	B4E0T7|Q96FP9|Q9NT52	Missense_Mutation	SNP	ENST00000425562.2	hg19		.	.	.	.	.	.	.	.	.	.	G	13.60	2.286497	0.40494	.	.	ENSG00000186001	ENST00000438796;ENST00000334859;ENST00000425562	T;T;T	0.19669	2.13;2.38;2.15	5.27	1.05	0.20165	.	0.443402	0.23504	N	0.047478	T	0.12732	0.0309	L	0.29908	0.895	0.58432	D	0.999995	B;P	0.36282	0.196;0.546	B;B	0.33690	0.158;0.168	T	0.13845	-1.0494	10	0.21540	T	0.41	0.1108	10.4819	0.44698	0.0:0.2413:0.5089:0.2498	.	395;395	Q96II8-2;Q96II8-3	.;.	E	395	ENSP00000399751:G395E;ENSP00000334375:G395E;ENSP00000393579:G395E	ENSP00000334375:G395E	G	+	2	0	LRCH3	199047023	1.000000	0.71417	0.055000	0.19348	0.791000	0.44710	1.512000	0.35812	-0.018000	0.14079	0.644000	0.83932	GGA	.	.		0.488	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773		A	197562626	G	A	197562626	3	1	69	1	0	0	0	0	1	0	0	0	8943	1174	41	3	1218	3	LRCH3	3	197562626	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	43415752	197562626	459804	36	8841										
TLR1	7096	hgsc.bcm.edu	37	chr4	38798659	38798659	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tccaagtagctgcagagggaGgtcacagtcacagccaacac	11	12	2	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr4:38798659G>A	ENST00000502213.2	-	3	2023	c.1794C>T	c.(1792-1794)acC>acT	p.T598T	TLR1_ENST00000510552.1_5'Flank|TLR1_ENST00000308979.2_Silent_p.T598T			Q15399	TLR1_HUMAN	toll-like receptor 1	598					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						TGCAGAGGGAGGTCACAGTCA	0.537																																					p.T598T	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.C1794T						.						69	89	82					4																	38798659		2203	4300	6503	SO:0001819	synonymous_variant	7096	exon4			GAGGGAGGTCACA	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1794C>T	chr4.hg19:g.38798659G>A		205.0	1.0		128.0	75.0	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.		0.537	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			A	38798659	G	A	38798659	2	1	69	1	0	0	0	0	0	0	0	1	15964	987	35	3		3	TLR1	4	38798659	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		38798659	152355617	37	8842										
ALB	213	hgsc.bcm.edu	37	chr4	74272392	74272393	+	Frame_Shift_Ins	INS	-	-	ATCA													0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tcagcagtgtccatttgaagINSatcatgtaaaattagtgaat					rs560085213		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr4:74272392_74272393insATCA	ENST00000295897.4	+	3	273_274	c.184_185insATCA	c.(184-186)gatfs	p.-62fs	ALB_ENST00000415165.2_Intron|ALB_ENST00000503124.1_5'UTR|ALB_ENST00000509063.1_Frame_Shift_Ins_p.-62fs|ALB_ENST00000401494.3_Intron	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin						apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCCATTTGAAGATCATGTAAAA	0.322																																					p.D62fs		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.184_185insATCA						.																																			SO:0001589	frameshift_variant	213	exon3			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.185_188dupATCA	chr4.hg19:g.74272393_74272396dupATCA	ENSP00000295897:p.Asp62fs	71.0	0.0		45.0	29.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Ins	INS	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.322	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477		ATCA	74272393	-	ATCA	74272392	7	5	69	1	0	1	1	0	0	0	0	0	486	942	33	0	194	0	ALB	4	74272392	Frame_Shift_Ins	INS	-	TCGA-CC-A5UE-01A-11D-A28X-10	35473733	74272392	116881884	38	8843										
C4orf49	84709	hgsc.bcm.edu	37	chr4	140187811	140187811	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cttcctcctgtaaatcatctCcagcagaggactctgactca	6	14	4	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr4:140187811C>A	ENST00000398955.1	-	4	844	c.665G>T	c.(664-666)gGa>gTa	p.G222V		NM_032623.3	NP_116012.2	Q8TDB4	HUMMR_HUMAN	mitochondria-localized glutamic acid-rich protein	222					anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cellular response to gonadotropin-releasing hormone (GO:0097211)|cellular response to hypoxia (GO:0071456)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of mitochondrion organization (GO:0010822)|protein targeting to mitochondrion (GO:0006626)|retrograde axon cargo transport (GO:0008090)	integral component of mitochondrial outer membrane (GO:0031307)|mitochondrion (GO:0005739)											TAAATCATCTCCAGCAGAGGA	0.453																																					p.G222V		Atlas-SNP	.											.	.	.	.	0			c.G665T						.						72	67	69					4																	140187811		1920	4137	6057	SO:0001583	missense	84709	exon4			TCATCTCCAGCAG	AF484960	CCDS43269.1	4q31.1	2014-02-19	2014-02-19	2012-04-17	ENSG00000137463	ENSG00000137463			29969	protein-coding gene	gene with protein product	"ovary-specific acidic protein", "corneal endothelium-specific protein 1", "hypoxia up-regulated mitochondrial movement regulator"		"chromosome 4 open reading frame 49"	C4orf49			Standard	NM_032623		Approved	OSAP, CESP-1, HUMMR	uc003ihr.1	Q8TDB4	OTTHUMG00000161325	ENST00000398955.1:c.665G>T	chr4.hg19:g.140187811C>A	ENSP00000381928:p.Gly222Val	25.0	0.0		26.0	18.0	NM_032623	Q9BZC3	Missense_Mutation	SNP	ENST00000398955.1	hg19	CCDS43269.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.757452	0.49468	.	.	ENSG00000137463	ENST00000398955	T	0.49139	0.79	5.59	-0.419	0.12340	.	0.596958	0.16975	N	0.191951	T	0.47002	0.1422	L	0.29908	0.895	0.20638	N	0.99987	D	0.61080	0.989	P	0.59487	0.858	T	0.41052	-0.9530	10	0.66056	D	0.02	-24.2898	9.1165	0.36762	0.0:0.4509:0.0:0.5491	.	222	Q8TDB4	CD049_HUMAN	V	222	ENSP00000381928:G222V	ENSP00000381928:G222V	G	-	2	0	C4orf49	140407261	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.489000	0.06490	-0.045000	0.13468	-0.218000	0.12543	GGA	.	.		0.453	MGARP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364536.1	NM_032623		A	140187811	C	A	140187811	3	1	69	1	0	0	0	0	1	0	0	0	2277	855	30	3	61	3	C4orf49	4	140187811	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	65915419	140187811	50966465	39	8844										
FGA	2243	hgsc.bcm.edu	37	chr4	155505651	155505651	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tcagcctcagagcctacccgGaagtgatattctgcataagc	9	12	3	2	rs376434823		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr4:155505651G>C	ENST00000302053.3	-	6	2304	c.2226C>G	c.(2224-2226)ttC>ttG	p.F742L		NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	742	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	AGCCTACCCGGAAGTGATATT	0.522																																					p.F742L	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.C2226G						.						134	132	133					4																	155505651		2203	4300	6503	SO:0001583	missense	2243	exon6			TACCCGGAAGTGA		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.2226C>G	chr4.hg19:g.155505651G>C	ENSP00000306361:p.Phe742Leu	162.0	0.0		112.0	82.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	0.172	-1.070654	0.01918	.	.	ENSG00000171560	ENST00000302053	D	0.99454	-5.92	5.7	-1.7	0.08159	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.841848	0.11129	N	0.596578	D	0.98232	0.9415	M	0.79011	2.435	0.09310	N	0.99999	P	0.41080	0.737	B	0.41135	0.348	D	0.96069	0.9044	10	0.40728	T	0.16	.	3.5098	0.07704	0.2379:0.4336:0.2006:0.1279	.	742	P02671	FIBA_HUMAN	L	742	ENSP00000306361:F742L	ENSP00000306361:F742L	F	-	3	2	FGA	155725101	0.000000	0.05858	0.000000	0.03702	0.387000	0.30353	-1.885000	0.01620	-0.821000	0.04312	-0.145000	0.13849	TTC	.	.		0.522	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		C	155505651	G	C	155505651	3	2	69	1	0	0	0	0	1	0	0	0	5838	1165	41	4	378	4	FGA	4	155505651	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	15317840	155505651	35648625	40	8845										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169305825	169305825	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cagcatgagtcgcaggaccaGggttatgctgagagggaact	15	8	0	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr4:169305825G>C	ENST00000511577.1	-	30	4301	c.4054C>G	c.(4054-4056)Ctg>Gtg	p.L1352V	DDX60L_ENST00000260184.7_Missense_Mutation_p.L1352V			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1352	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CGCAGGACCAGGGTTATGCTG	0.502																																					p.L1352V		Atlas-SNP	.											.	DDX60L	116	.	0			c.C4054G						.						75	74	74					4																	169305825		2203	4300	6503	SO:0001583	missense	91351	exon30			GGACCAGGGTTAT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.4054C>G	chr4.hg19:g.169305825G>C	ENSP00000422423:p.Leu1352Val	328.0	0.0		354.0	173.0	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	hg19		.	.	.	.	.	.	.	.	.	.	G	6.687	0.495373	0.12762	.	.	ENSG00000181381	ENST00000260184;ENST00000511577	T;T	0.22743	1.94;1.94	3.55	1.78	0.24846	Helicase, C-terminal (1);	.	.	.	.	T	0.24198	0.0586	M	0.63428	1.95	0.09310	N	1	D	0.60160	0.987	P	0.46110	0.504	T	0.11792	-1.0573	9	0.59425	D	0.04	.	6.8818	0.24177	0.4152:0.0:0.5848:0.0	.	1352	Q5H9U9	DDX6L_HUMAN	V	1352	ENSP00000260184:L1352V;ENSP00000422423:L1352V	ENSP00000260184:L1352V	L	-	1	2	DDX60L	169542400	0.420000	0.25457	0.004000	0.12327	0.087000	0.18053	0.732000	0.26072	0.047000	0.15862	0.563000	0.77884	CTG	.	.		0.502	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		C	169305825	G	C	169305825	3	2	69	1	0	0	0	0	1	0	0	0	4381	991	35	4	1102	4	DDX60L	4	169305825	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	13800174	169305825	21848451	41	8846										
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9066573	9066573	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gtgccgtcgctagaacagtaCcgcatttcgattctctgtct	9	12	2	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr5:9066573C>T	ENST00000382496.5	-	17	2924	c.2259G>A	c.(2257-2259)cgG>cgA	p.R753R		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	753	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						TAGAACAGTACCGCATTTCGA	0.537																																					p.R753R		Atlas-SNP	.											.	SEMA5A	236	.	0			c.G2259A						.						179	171	174					5																	9066573		2203	4300	6503	SO:0001819	synonymous_variant	9037	exon17			ACAGTACCGCATT	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.2259G>A	chr5.hg19:g.9066573C>T		181.0	0.0		157.0	50.0	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	hg19	CCDS3875.1																																																																																			.	.		0.537	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			T	9066573	C	T	9066573	2	4	69	1	0	0	0	0	0	0	0	1	14052	494	18	3		3	SEMA5A	5	9066573	Silent	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10		9066573	171848687	42	8847										
FAM105A	54491	hgsc.bcm.edu	37	chr5	14601219	14601219	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	aggctacatttatattcaggGcacaagctgaaatggtaggt	11	6	1	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr5:14601219G>T	ENST00000274217.3	+	2	330	c.210G>T	c.(208-210)ggG>ggT	p.G70G		NM_019018.2	NP_061891.1	Q9NUU6	F105A_HUMAN	family with sequence similarity 105, member A	70										large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Lung NSC(4;0.00592)					TATATTCAGGGCACAAGCTGA	0.388																																					p.G70G		Atlas-SNP	.											.	FAM105A	32	.	0			c.G210T						.						180	170	174					5																	14601219		2203	4300	6503	SO:0001819	synonymous_variant	54491	exon2			TTCAGGGCACAAG		CCDS3884.1	5p15.2	2014-02-24			ENSG00000145569	ENSG00000145569		"OTU domain containing"	25629	protein-coding gene	gene with protein product						12477932	Standard	NM_019018		Approved	FLJ11127, NET20	uc003jfj.3	Q9NUU6	OTTHUMG00000131056	ENST00000274217.3:c.210G>T	chr5.hg19:g.14601219G>T		63.0	0.0		56.0	24.0	NM_019018	Q53H50|Q9H037	Silent	SNP	ENST00000274217.3	hg19	CCDS3884.1																																																																																			.	.		0.388	FAM105A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253710.1	NM_019018		T	14601219	G	T	14601219	2	4	69	1	0	0	0	0	0	0	0	1	5392	1190	42	3		3	FAM105A	5	14601219	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	5534646	14601219	166314041	43	8848										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38412649	38412649	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ccatcatcgtaagtgagaccAaaatcaaactagggggttgg	11	8	2	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr5:38412649A>T	ENST00000354891.3	+	11	1739	c.1393A>T	c.(1393-1395)Aaa>Taa	p.K465*	EGFLAM_ENST00000397202.2_5'UTR|EGFLAM_ENST00000322350.5_Nonsense_Mutation_p.K465*|EGFLAM_ENST00000336740.6_Nonsense_Mutation_p.K231*	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	465	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					AAGTGAGACCAAAATCAAACT	0.493																																					p.K465X	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.A1393T						.						107	104	105					5																	38412649		2203	4300	6503	SO:0001587	stop_gained	133584	exon11			GAGACCAAAATCA	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.1393A>T	chr5.hg19:g.38412649A>T	ENSP00000346964:p.Lys465*	85.0	0.0		55.0	4.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Nonsense_Mutation	SNP	ENST00000354891.3	hg19	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	A	41	8.922489	0.99004	.	.	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000339580	.	.	.	6.07	4.88	0.63580	.	0.533583	0.22745	N	0.056154	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.4788	13.4556	0.61197	0.8693:0.1307:0.0:0.0	.	.	.	.	X	465;465;231;231	.	ENSP00000313084:K465X	K	+	1	0	EGFLAM	38448406	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.801000	0.47908	1.081000	0.41110	0.528000	0.53228	AAA	.	.		0.493	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		T	38412649	A	T	38412649	4	4	69	1	0	0	0	0	0	1	0	0	4968	131	5	4	1449	4	EGFLAM	5	38412649	Nonsense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	23811430	38412649	142502611	44	8849										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141337154	141337154	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ctcgatccagccgcctgcctGtgctgagcaagccttcctca	9	17	1	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr5:141337154G>C	ENST00000231484.3	-	1	1473	c.263C>G	c.(262-264)aCa>aGa	p.T88R	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	88	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCCTGCCTGTGCTGAGCAA	0.622																																					p.T88R		Atlas-SNP	.											.	PCDH12	133	.	0			c.C263G						.						53	55	54					5																	141337154		2203	4300	6503	SO:0001583	missense	51294	exon1			CTGCCTGTGCTGA	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.263C>G	chr5.hg19:g.141337154G>C	ENSP00000231484:p.Thr88Arg	236.0	0.0		194.0	102.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.248274	0.59103	.	.	ENSG00000113555	ENST00000231484	T	0.28666	1.6	4.81	4.81	0.61882	Cadherin, N-terminal (1);Cadherin (4);	0.000000	0.85682	D	0.000000	T	0.58963	0.2159	M	0.90369	3.11	0.50313	D	0.999867	D	0.89917	1.0	D	0.91635	0.999	T	0.65121	-0.6245	10	0.72032	D	0.01	.	8.8967	0.35470	0.0987:0.0:0.9013:0.0	.	88	Q9NPG4	PCD12_HUMAN	R	88	ENSP00000231484:T88R	ENSP00000231484:T88R	T	-	2	0	PCDH12	141317338	1.000000	0.71417	0.945000	0.38365	0.348000	0.29142	7.796000	0.85898	2.504000	0.84457	0.563000	0.77884	ACA	.	.		0.622	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		C	141337154	G	C	141337154	3	2	69	1	0	0	0	0	1	0	0	0	11519	1377	48	4	3307	4	PCDH12	5	141337154	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	102924505	141337154	39578106	45	8850										
HNRNPH1	3187	hgsc.bcm.edu	37	chr5	179043937	179043937	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gctcctgctgtagaattcaaGaagagttctacatatctgtg	9	8	3	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr5:179043937G>T	ENST00000356731.5	-	10	2675	c.1140C>A	c.(1138-1140)ttC>ttA	p.F380L	HNRNPH1_ENST00000442819.2_Missense_Mutation_p.F380L|HNRNPH1_ENST00000511300.2_Intron|HNRNPH1_ENST00000510411.1_Intron|HNRNPH1_ENST00000524180.1_5'Flank|HNRNPH1_ENST00000329433.6_Missense_Mutation_p.F380L|HNRNPH1_ENST00000393432.4_Missense_Mutation_p.F380L			P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1 (H)	380	2 X 16 AA Gly-rich approximate repeats.|2 X 19 AA perfect repeats.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1)	14						TAGAATTCAAGAAGAGTTCTA	0.383																																					p.F380L		Atlas-SNP	.											.	HNRNPH1	62	.	0			c.C1140A						.						102	100	100					5																	179043937		2203	4300	6503	SO:0001583	missense	3187	exon11			ATTCAAGAAGAGT	BC001348	CCDS4446.1	5q35.3	2013-02-12		2008-04-18	ENSG00000169045	ENSG00000169045		"RNA binding motif (RRM) containing"	5041	protein-coding gene	gene with protein product		601035		HNRPH1		7499401	Standard	NM_005520		Approved	hnRNPH	uc003mkf.5	P31943	OTTHUMG00000130908	ENST00000356731.5:c.1140C>A	chr5.hg19:g.179043937G>T	ENSP00000349168:p.Phe380Leu	269.0	0.0		173.0	64.0	NM_001257293	B3KW86|D3DWQ2|Q6IBM4	Missense_Mutation	SNP	ENST00000356731.5	hg19	CCDS4446.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	g|g|g	24.5|24.5|24.5	4.537888|4.537888|4.537888	0.85917|0.85917|0.85917	.|.|.	.|.|.	ENSG00000169045|ENSG00000169045|ENSG00000169045	ENST00000393432;ENST00000442819;ENST00000356731;ENST00000329433;ENST00000523921|ENST00000523449|ENST00000521173	T;T;T;T;T|.|.	0.11604|.|.	2.76;2.76;2.76;2.76;2.76|.|.	5.81|5.81|5.81	5.81|5.81|5.81	0.92471|0.92471|0.92471	.|.|.	0.000000|.|.	0.64402|.|.	D|.|.	0.000016|.|.	T|T|T	0.66587|0.66587|0.66587	0.2804|0.2804|0.2804	L|L|L	0.61036|0.61036|0.61036	1.89|1.89|1.89	0.80722|0.80722|0.80722	D|D|D	1|1|1	D|.|.	0.54964|.|.	0.969|.|.	P|.|.	0.54856|.|.	0.762|.|.	T|T|T	0.64089|0.64089|0.64089	-0.6489|-0.6489|-0.6489	10|5|5	0.05351|.|.	T|.|.	0.99|.|.	-3.7755|-3.7755|-3.7755	13.294|13.294|13.294	0.60286|0.60286|0.60286	0.0723:0.0:0.9277:0.0|0.0723:0.0:0.9277:0.0|0.0723:0.0:0.9277:0.0	.|.|.	380|.|.	P31943|.|.	HNRH1_HUMAN|.|.	L|I|Y	380;380;380;380;174|48|255	ENSP00000377082:F380L;ENSP00000397797:F380L;ENSP00000349168:F380L;ENSP00000327539:F380L;ENSP00000429270:F174L|.|.	ENSP00000327539:F380L|.|.	F|L|S	-|-|-	3|1|2	2|0|0	HNRNPH1|HNRNPH1|HNRNPH1	178976543|178976543|178976543	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	3.427000|3.427000|3.427000	0.52785|0.52785|0.52785	2.734000|2.734000|2.734000	0.93682|0.93682|0.93682	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	TTC|CTT|TCT	.	.		0.383	HNRNPH1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253497.3	NM_005520		T	179043937	G	T	179043937	3	4	69	1	0	0	0	0	1	0	0	0	7275	933	33	3	221	3	HNRNPH1	5	179043937	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	37706783	179043937	1871323	46	8851										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327490	16327490	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	actcgtacgggtgaggaaccGacttgccgcctgccttgccc	12	15	0	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr6:16327490G>A	ENST00000244769.4	-	8	1988	c.1052C>T	c.(1051-1053)tCg>tTg	p.S351L	ATXN1_ENST00000436367.1_Missense_Mutation_p.S351L	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	351					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				GTGAGGAACCGACTTGCCGCC	0.667																																					p.S351L		Atlas-SNP	.											.	ATXN1	117	.	0			c.C1052T						.						58	66	63					6																	16327490		2203	4300	6503	SO:0001583	missense	6310	exon7			GGAACCGACTTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1052C>T	chr6.hg19:g.16327490G>A	ENSP00000244769:p.Ser351Leu	97.0	0.0		92.0	8.0	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902268	0.33628	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.78364	-1.17;-1.17	4.86	3.99	0.46301	.	0.948079	0.08837	N	0.886373	T	0.47377	0.1442	N	0.22421	0.69	0.20196	N	0.999923	B	0.28880	0.226	B	0.17098	0.017	T	0.42464	-0.9450	10	0.38643	T	0.18	-5.3967	13.0006	0.58672	0.0788:0.0:0.9212:0.0	.	351	P54253	ATX1_HUMAN	L	351	ENSP00000244769:S351L;ENSP00000416360:S351L	ENSP00000244769:S351L	S	-	2	0	ATXN1	16435469	1.000000	0.71417	0.513000	0.27749	0.526000	0.34562	6.107000	0.71517	1.031000	0.39867	0.561000	0.74099	TCG	.	.		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		A	16327490	G	A	16327490	3	1	69	1	0	0	0	0	1	0	0	0	1209	1059	37	1	1403	1	ATXN1	6	16327490	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		16327490	154787577	47	8852										
ZDHHC4	55146	hgsc.bcm.edu	37	chr7	6620253	6620253	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tgctgatgggtcttgttcttAtctgcgtctgctcgaaaacc	10	10	4	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:6620253A>G	ENST00000396706.2	+	3	504	c.61A>G	c.(61-63)Atc>Gtc	p.I21V	ZDHHC4_ENST00000396707.2_Missense_Mutation_p.I21V|ZDHHC4_ENST00000335965.6_Missense_Mutation_p.I21V|ZDHHC4_ENST00000396709.1_Missense_Mutation_p.I21V|ZDHHC4_ENST00000396713.2_Missense_Mutation_p.I21V|ZDHHC4_ENST00000496017.1_3'UTR|AC079742.4_ENST00000434951.1_RNA|ZDHHC4_ENST00000405731.3_Missense_Mutation_p.I21V			Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	21						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)		TCTTGTTCTTATCTGCGTCTG	0.493																																					p.I21V		Atlas-SNP	.											.	ZDHHC4	36	.	0			c.A61G						.						359	313	328					7																	6620253		2203	4300	6503	SO:0001583	missense	55146	exon3			GTTCTTATCTGCG	AF201931	CCDS5352.1	7p22.1	2011-01-11			ENSG00000136247	ENSG00000136247		"Zinc fingers, DHHC-type"	18471	protein-coding gene	gene with protein product							Standard	NM_018106		Approved	FLJ10479, ZNF374	uc003sqj.3	Q9NPG8	OTTHUMG00000023579	ENST00000396706.2:c.61A>G	chr7.hg19:g.6620253A>G	ENSP00000379934:p.Ile21Val	237.0	1.0		168.0	88.0	NM_018106	A4D2N9|Q53EV7|Q6FIB5|Q9H0R9	Missense_Mutation	SNP	ENST00000396706.2	hg19	CCDS5352.1	.	.	.	.	.	.	.	.	.	.	a	1.652	-0.513707	0.04200	.	.	ENSG00000136247	ENST00000405731;ENST00000396713;ENST00000396707;ENST00000335965;ENST00000396709;ENST00000483589;ENST00000396706	T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.64;1.49	4.9	-3.41	0.04839	.	0.947078	0.08924	N	0.873990	T	0.10981	0.0268	N	0.14661	0.345	0.09310	N	0.999994	B;B	0.13145	0.0;0.007	B;B	0.14578	0.001;0.011	T	0.33701	-0.9858	10	0.07482	T	0.82	-16.4868	0.4997	0.00578	0.2144:0.2867:0.2499:0.2489	.	21;21	Q9NPG8;C9J5I9	ZDHC4_HUMAN;.	V	21	ENSP00000385027:I21V;ENSP00000379941:I21V;ENSP00000379935:I21V;ENSP00000337475:I21V;ENSP00000379937:I21V;ENSP00000418496:I21V;ENSP00000379934:I21V	ENSP00000337475:I21V	I	+	1	0	ZDHHC4	6586778	0.015000	0.18098	0.011000	0.14972	0.168000	0.22595	0.072000	0.14617	-0.467000	0.06932	0.533000	0.62120	ATC	.	.		0.493	ZDHHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207477.3	NM_018106		G	6620253	A	G	6620253	3	3	69	1	0	0	0	0	1	0	0	0	17632	449	16	2	63	2	ZDHHC4	7	6620253	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10		6620253	152518410	48	8853										
CRHR2	1395	hgsc.bcm.edu	37	chr7	30721587	30721587	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggcacggcctctccacgaggGctccggcagcgctgcggggc	17	16	1	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:30721587G>T	ENST00000471646.1	-	2	590	c.173C>A	c.(172-174)gCc>gAc	p.A58D	CRHR2_ENST00000348438.4_Missense_Mutation_p.A85D|CRHR2_ENST00000506074.2_Missense_Mutation_p.A58D|CRHR2_ENST00000341843.4_Missense_Mutation_p.A44D	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	58					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CTCCACGAGGGCTCCGGCAGC	0.672																																					p.A85D		Atlas-SNP	.											.	CRHR2	104	.	0			c.C254A						.						30	28	29					7																	30721587		2202	4298	6500	SO:0001583	missense	1395	exon3			ACGAGGGCTCCGG		CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"GPCR / Class B : Corticotropin-releasing factor receptors"	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.173C>A	chr7.hg19:g.30721587G>T	ENSP00000418722:p.Ala58Asp	102.0	0.0		56.0	10.0	NM_001202475	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Missense_Mutation	SNP	ENST00000471646.1	hg19	CCDS5429.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.177198	0.38413	.	.	ENSG00000106113	ENST00000471646;ENST00000348438;ENST00000341843;ENST00000506074	T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03	4.27	3.39	0.38822	GPCR, family 2, secretin-like, conserved site (1);GPCR, family 2, extracellular hormone receptor domain (3);	0.472371	0.21192	N	0.078631	T	0.46927	0.1418	L	0.41573	1.285	0.30685	N	0.751898	B;B;P;B;B	0.36048	0.173;0.185;0.534;0.257;0.173	B;B;B;B;B	0.35550	0.046;0.066;0.205;0.149;0.046	T	0.46034	-0.9220	10	0.24483	T	0.36	.	6.294	0.21075	0.1011:0.1865:0.7124:0.0	.	58;58;85;44;58	B3SXT0;B3SXS6;Q13324-2;Q13324-3;Q13324	.;.;.;.;CRFR2_HUMAN	D	58;85;44;58	ENSP00000418722:A58D;ENSP00000340943:A85D;ENSP00000344304:A44D;ENSP00000426498:A58D	ENSP00000344304:A44D	A	-	2	0	CRHR2	30688112	0.858000	0.29795	0.998000	0.56505	0.991000	0.79684	2.020000	0.41010	1.151000	0.42436	0.655000	0.94253	GCC	.	.		0.672	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3			T	30721587	G	T	30721587	3	4	69	1	0	0	0	0	1	0	0	0	3874	1203	42	3	1106	3	CRHR2	7	30721587	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	24101334	30721587	128417076	49	8854										
NEUROD6	63974	hgsc.bcm.edu	37	chr7	31378831	31378831	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ttctctagaaaactttctgcAcatctgggattctggcatta	7	9	4	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:31378831A>T	ENST00000297142.3	-	2	374	c.52T>A	c.(52-54)Tgc>Agc	p.C18S		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	18					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						AACTTTCTGCACATCTGGGAT	0.388																																					p.C18S		Atlas-SNP	.											.	NEUROD6	84	.	0			c.T52A						.						132	147	142					7																	31378831		2203	4300	6503	SO:0001583	missense	63974	exon2			TTCTGCACATCTG	AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"Basic helix-loop-helix proteins"	13804	protein-coding gene	gene with protein product		611513	"neurogenic differentiation 6"			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.52T>A	chr7.hg19:g.31378831A>T	ENSP00000297142:p.Cys18Ser	26.0	0.0		28.0	18.0	NM_022728	Q548T9|Q9H3H6	Missense_Mutation	SNP	ENST00000297142.3	hg19	CCDS5434.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.397903	0.25205	.	.	ENSG00000164600	ENST00000297142	D	0.94723	-3.5	5.28	5.28	0.74379	.	0.050512	0.85682	D	0.000000	D	0.90065	0.6897	L	0.36672	1.1	0.52099	D	0.999943	B	0.30326	0.276	B	0.25759	0.063	D	0.87798	0.2623	10	0.20046	T	0.44	-21.8478	15.2475	0.73517	1.0:0.0:0.0:0.0	.	18	Q96NK8	NDF6_HUMAN	S	18	ENSP00000297142:C18S	ENSP00000297142:C18S	C	-	1	0	NEUROD6	31345356	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.522000	0.73783	2.012000	0.59069	0.528000	0.53228	TGC	.	.		0.388	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728		T	31378831	A	T	31378831	3	4	69	1	0	0	0	0	1	0	0	0	10360	159	6	4	965	4	NEUROD6	7	31378831	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	657244	31378831	127759832	50	8855										
C7orf25	79020	hgsc.bcm.edu	37	chr7	42949411	42949411	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gcttttagggtgtctcccgtCccaaaaattgttaatgagcg	10	9	1	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:42949411C>T	ENST00000350427.4	-	2	1364	c.1089G>A	c.(1087-1089)ggG>ggA	p.G363G	PSMA2_ENST00000442788.1_3'UTR|C7orf25_ENST00000431882.2_Silent_p.G421G|C7orf25_ENST00000438029.1_Silent_p.G363G|C7orf25_ENST00000447342.1_Silent_p.G363G			Q9BPX7	CG025_HUMAN	chromosome 7 open reading frame 25	363										endometrium(6)|kidney(1)|large_intestine(7)|lung(2)|skin(1)	17						TGTCTCCCGTCCCAAAAATTG	0.423																																					p.G421G		Atlas-SNP	.											.	C7orf25	36	.	0			c.G1263A						.						83	80	81					7																	42949411		2203	4300	6503	SO:0001819	synonymous_variant	79020	exon2			TCCCGTCCCAAAA	BC001845	CCDS5466.1, CCDS47576.1	7p14.1	2011-11-24			ENSG00000136197	ENSG00000136197			21703	protein-coding gene	gene with protein product							Standard	NM_024054		Approved	MGC2821	uc003thx.4	Q9BPX7	OTTHUMG00000128869	ENST00000350427.4:c.1089G>A	chr7.hg19:g.42949411C>T		126.0	0.0		134.0	81.0	NM_001099858	A4D1V2|J3KR36|Q9H779	Silent	SNP	ENST00000350427.4	hg19	CCDS5466.1																																																																																			.	.		0.423	C7orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250814.2	NM_024054		T	42949411	C	T	42949411	2	4	69	1	0	0	0	0	0	0	0	1	2382	842	30	3		3	C7orf25	7	42949411	Silent	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	11570580	42949411	116189252	51	8856										
LRCH4	4034	hgsc.bcm.edu	37	chr7	100174773	100174773	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	agccctgagccctggcttcaAgaggctggaacaaggagagg	15	10	1	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:100174773A>G	ENST00000310300.6	-	12	1352	c.1300T>C	c.(1300-1302)Ttg>Ctg	p.L434L	LRCH4_ENST00000497245.1_5'UTR	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	434					nervous system development (GO:0007399)	PML body (GO:0016605)				NS(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	23	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CCTGGCTTCAAGAGGCTGGAA	0.642																																					p.L434L		Atlas-SNP	.											.	LRCH4	53	.	0			c.T1300C						.						51	56	55					7																	100174773		2203	4300	6503	SO:0001819	synonymous_variant	4034	exon12			GCTTCAAGAGGCT	AF053356	CCDS34706.1	7q22	2008-05-20	2004-05-27	2004-05-28	ENSG00000077454	ENSG00000077454			6691	protein-coding gene	gene with protein product				LRN, LRRN1		9799793	Standard	XM_005250346		Approved		uc003uvj.3	O75427	OTTHUMG00000159544	ENST00000310300.6:c.1300T>C	chr7.hg19:g.100174773A>G		133.0	0.0		67.0	21.0	NM_002319	A4D2D5|Q8WV85|Q96ID0	Silent	SNP	ENST00000310300.6	hg19	CCDS34706.1																																																																																			.	.		0.642	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319		G	100174773	A	G	100174773	2	3	69	1	0	0	0	0	0	0	0	1	8944	69	3	2		2	LRCH4	7	100174773	Silent	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	57225362	100174773	58963890	52	8857										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117351762	117351762	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggaagaaaagatttaactctTgaaacacccaactcagtctt	6	9	3	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:117351762T>A	ENST00000160373.3	-	23	4912	c.4821A>T	c.(4819-4821)tcA>tcT	p.S1607S	CFTR_ENST00000608965.1_Intron	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1607					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		ATTTAACTCTTGAAACACCCA	0.423																																					p.S1607S		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.A4821T						.						135	119	125					7																	117351762		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon23			AACTCTTGAAACA		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.4821A>T	chr7.hg19:g.117351762T>A		40.0	0.0		42.0	23.0	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	T	8.629	0.893191	0.17613	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.87	-2.48	0.06423	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.9221	1.527	0.02527	0.1147:0.2524:0.2381:0.3948	.	.	.	.	X	1095	.	.	K	-	1	0	CTTNBP2	117138998	0.998000	0.40836	0.990000	0.47175	0.996000	0.88848	0.244000	0.18124	-0.406000	0.07588	0.528000	0.53228	AAG	.	.		0.423	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		A	117351762	T	A	117351762	2	1	69	1	0	0	0	0	0	0	0	1	4047	1799	63	4		4	CTTNBP2	7	117351762	Silent	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10	17176989	117351762	41786901	53	8858										
CADPS2	93664	hgsc.bcm.edu	37	chr7	122303420	122303420	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	agggccattctatttggctgTttgcacaagtcctcttcacc	8	12	3	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:122303420T>C	ENST00000449022.2	-	3	676	c.657A>G	c.(655-657)aaA>aaG	p.K219K	CADPS2_ENST00000412584.2_Silent_p.K219K|CADPS2_ENST00000313070.7_Silent_p.K219K|CADPS2_ENST00000334010.7_Silent_p.K219K	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	219					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						TATTTGGCTGTTTGCACAAGT	0.418																																					p.K219K		Atlas-SNP	.											.	CADPS2	116	.	0			c.A657G						.						156	145	149					7																	122303420		1915	4144	6059	SO:0001819	synonymous_variant	93664	exon3			TGGCTGTTTGCAC		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.657A>G	chr7.hg19:g.122303420T>C		90.0	0.0		98.0	61.0	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Silent	SNP	ENST00000449022.2	hg19	CCDS55158.1																																																																																			.	.		0.418	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		C	122303420	T	C	122303420	2	2	69	1	0	0	0	0	0	0	0	1	2573	1722	60	2		2	CADPS2	7	122303420	Silent	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10	4951658	122303420	36835243	54	8859										
SND1	27044	hgsc.bcm.edu	37	chr7	127721412	127721412	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tctgccgactgaacatgcagGtctgggcccactatgaggag	13	11	2	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:127721412G>C	ENST00000354725.3	+	18	2163	c.1969G>C	c.(1969-1971)Gtc>Ctc	p.V657L	MIR593_ENST00000384856.1_RNA	NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	657	TNase-like 4. {ECO:0000255|PROSITE- ProRule:PRU00272}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)			central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						GAACATGCAGGTCTGGGCCCA	0.572																																					p.V657L		Atlas-SNP	.											.	SND1	104	.	0			c.G1969C						.						104	79	87					7																	127721412		2203	4300	6503	SO:0001630	splice_region_variant	27044	exon18			ATGCAGGTCTGGG		CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"Tudor domain containing"	30646	protein-coding gene	gene with protein product	"p100 EBNA2 co-activator", "Tudor-SN"	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.1969-1G>C	chr7.hg19:g.127721412G>C		125.0	0.0		92.0	53.0	NM_014390	Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	hg19	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.726980	0.30593	.	.	ENSG00000197157	ENST00000354725;ENST00000438400;ENST00000486037	T;T	0.38077	1.85;1.16	4.85	3.8	0.43715	Staphylococcal nuclease (SNase-like) (4);Staphylococcal nuclease (SNase-like), OB-fold (1);	0.543995	0.20281	N	0.095459	T	0.20414	0.0491	N	0.17594	0.5	0.51233	D	0.999915	B	0.02656	0.0	B	0.09377	0.004	T	0.04991	-1.0913	9	.	.	.	-16.5034	9.1195	0.36778	0.139:0.0:0.861:0.0	.	657	Q7KZF4	SND1_HUMAN	L	657;647;143	ENSP00000346762:V657L;ENSP00000419327:V143L	.	V	+	1	0	SND1	127508648	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.398000	0.34554	0.923000	0.37045	0.561000	0.74099	GTC	.	.		0.572	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390	Missense_Mutation	C	127721412	G	C	127721412	5	2	69	1	0	0	0	0	0	0	1	0	14859	1275	44	4	2039	4	SND1	7	127721412	Splice_Site	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	5417992	127721412	31417251	55	8860										
METTL2B	55798	hgsc.bcm.edu	37	chr7	128133954	128133954	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tgcccaagggcagtcttgatAttatcattctcatatttgtt	7	8	3	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:128133954A>G	ENST00000262432.8	+	6	803	c.766A>G	c.(766-768)Att>Gtt	p.I256V	METTL2B_ENST00000480046.1_Missense_Mutation_p.I191V|RP11-212P7.3_ENST00000462662.1_RNA	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	256					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						CAGTCTTGATATTATCATTCT	0.433																																					p.I256V		Atlas-SNP	.											.	METTL2B	34	.	0			c.A766G						.						123	115	118					7																	128133954		2202	4283	6485	SO:0001583	missense	55798	exon6			CTTGATATTATCA	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"methyltransferase like 2"	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.766A>G	chr7.hg19:g.128133954A>G	ENSP00000262432:p.Ile256Val	174.0	0.0		160.0	103.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	hg19	CCDS5803.2	.	.	.	.	.	.	.	.	.	.	A	0.184	-1.059334	0.01950	.	.	ENSG00000165055	ENST00000262432;ENST00000480046;ENST00000481392	T;T;T	0.11277	2.79;2.79;2.79	3.16	-1.29	0.09288	Methyltransferase type 12 (1);	0.330183	0.33217	N	0.005152	T	0.03220	0.0094	N	0.03294	-0.36	0.33538	D	0.594458	B;B	0.06786	0.0;0.001	B;B	0.13407	0.007;0.009	T	0.49312	-0.8953	10	0.02654	T	1	-4.4082	9.8744	0.41194	0.2271:0.0:0.7729:0.0	.	191;256	Q6P1Q9-2;Q6P1Q9	.;MTL2B_HUMAN	V	256;191;20	ENSP00000262432:I256V;ENSP00000418402:I191V;ENSP00000418989:I20V	ENSP00000262432:I256V	I	+	1	0	METTL2B	127921190	0.879000	0.30193	0.944000	0.38274	0.780000	0.44128	0.187000	0.16998	-0.171000	0.10797	0.164000	0.16699	ATT	.	.		0.433	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396		G	128133954	A	G	128133954	3	3	69	1	0	0	0	0	1	0	0	0	9509	449	16	2	788	2	METTL2B	7	128133954	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	412542	128133954	31004709	56	8861										
HIPK2	28996	hgsc.bcm.edu	37	chr7	139285298	139285298	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gaccggtcaatagtgcaggcTgctgcatgatgggattataa	13	7	1	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:139285298T>A	ENST00000406875.3	-	11	2394	c.2300A>T	c.(2299-2301)cAg>cTg	p.Q767L	HIPK2_ENST00000342645.6_Missense_Mutation_p.Q767L|HIPK2_ENST00000428878.2_Missense_Mutation_p.Q740L	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	767	Interaction with POU4F1. {ECO:0000250}.|Interaction with SKI and SMAD1.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					TAGTGCAGGCTGCTGCATGAT	0.542																																					p.Q767L		Atlas-SNP	.											.	HIPK2	192	.	0			c.A2300T						.						110	115	113					7																	139285298		2125	4239	6364	SO:0001583	missense	28996	exon11			GCAGGCTGCTGCA	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.2300A>T	chr7.hg19:g.139285298T>A	ENSP00000385571:p.Gln767Leu	213.0	0.0		166.0	86.0	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	hg19		.	.	.	.	.	.	.	.	.	.	T	27.0	4.787393	0.90367	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.28454	1.61;1.61;1.61	4.57	4.57	0.56435	.	.	.	.	.	T	0.53626	0.1808	.	.	.	0.58432	D	0.999994	P;P	0.50528	0.936;0.908	P;D	0.64144	0.885;0.922	T	0.59429	-0.7456	8	0.87932	D	0	.	14.4024	0.67056	0.0:0.0:0.0:1.0	.	767;740	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	L	767;740;767	ENSP00000385571:Q767L;ENSP00000413724:Q740L;ENSP00000343108:Q767L	ENSP00000343108:Q767L	Q	-	2	0	HIPK2	138935838	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.482000	0.81143	2.044000	0.60594	0.528000	0.53228	CAG	.	.		0.542	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		A	139285298	T	A	139285298	3	1	69	1	0	0	0	0	1	0	0	0	7126	1580	55	4	1316	4	HIPK2	7	139285298	Missense_Mutation	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10	11151344	139285298	19853365	57	8862										
TBXAS1	6916	hgsc.bcm.edu	37	chr7	139655333	139655333	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gtggactcctggcaggccccTgaggatccctttgtgaaaca	12	12	0	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:139655333T>A	ENST00000336425.5	+	11	1004	c.615T>A	c.(613-615)ccT>ccA	p.P205P	TBXAS1_ENST00000411653.1_Silent_p.P205P|TBXAS1_ENST00000425687.1_Silent_p.P138P|TBXAS1_ENST00000448866.1_Silent_p.P205P|TBXAS1_ENST00000436047.2_Silent_p.P206P|TBXAS1_ENST00000414508.2_Silent_p.P206P|TBXAS1_ENST00000458722.1_Silent_p.P251P|TBXAS1_ENST00000263552.6_Silent_p.P206P|TBXAS1_ENST00000462275.1_3'UTR|TBXAS1_ENST00000416849.2_Silent_p.P252P			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	205					arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	GGCAGGCCCCTGAGGATCCCT	0.572																																					p.P252P		Atlas-SNP	.											.	TBXAS1	121	.	0			c.T756A						.						78	82	81					7																	139655333		2203	4300	6503	SO:0001819	synonymous_variant	6916	exon8			GGCCCCTGAGGAT	L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"Cytochrome P450s"	11609	protein-coding gene	gene with protein product	"cytochrome P450, family 5, subfamily A, polypeptide 1"	274180	"thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000336425.5:c.615T>A	chr7.hg19:g.139655333T>A		61.0	0.0		45.0	9.0	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Silent	SNP	ENST00000336425.5	hg19																																																																																				.	.		0.572	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1			A	139655333	T	A	139655333	2	1	69	1	0	0	0	0	0	0	0	1	15679	1567	55	4		4	TBXAS1	7	139655333	Silent	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10	370035	139655333	19483330	58	8863										
TUSC3	7991	hgsc.bcm.edu	37	chr8	15397946	15397946	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	actgccctgccgcgatggggGcccggggcgctccttcacgc	15	17	1	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr8:15397946G>T	ENST00000503731.1	+	1	155	c.7G>T	c.(7-9)Gcc>Tcc	p.A3S	TUSC3_ENST00000382020.4_Missense_Mutation_p.A3S|TUSC3_ENST00000503191.1_Intron|TUSC3_ENST00000506802.1_Missense_Mutation_p.A3S|TUSC3_ENST00000509380.1_Missense_Mutation_p.A3S	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	3					cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		CGCGATGGGGGCCCGGGGCGC	0.741																																					p.A3S		Atlas-SNP	.											.	TUSC3	98	.	0			c.G7T						.						10	11	10					8																	15397946		2131	4236	6367	SO:0001583	missense	7991	exon1			ATGGGGGCCCGGG	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.7G>T	chr8.hg19:g.15397946G>T	ENSP00000424544:p.Ala3Ser	40.0	0.0		17.0	8.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534879	0.64972	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.48201	0.84;0.82;0.83;0.84	4.3	3.42	0.39159	.	0.157787	0.30051	N	0.010532	T	0.25644	0.0624	N	0.08118	0	0.23351	N	0.997859	B;B;B;B;B;B	0.15930	0.015;0.006;0.01;0.006;0.006;0.001	B;B;B;B;B;B	0.10450	0.002;0.002;0.005;0.001;0.002;0.003	T	0.16660	-1.0395	10	0.54805	T	0.06	0.0533	8.073	0.30699	0.1079:0.0:0.8921:0.0	.	3;3;3;3;3;3	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	S	3	ENSP00000371450:A3S;ENSP00000425777:A3S;ENSP00000423426:A3S;ENSP00000424544:A3S	ENSP00000221167:A3S	A	+	1	0	TUSC3	15442317	1.000000	0.71417	0.988000	0.46212	0.762000	0.43233	0.923000	0.28757	1.412000	0.46977	0.563000	0.77884	GCC	.	.		0.741	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		T	15397946	G	T	15397946	3	4	69	1	0	0	0	0	1	0	0	0	16793	1203	42	3	9	3	TUSC3	8	15397946	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		15397946	130966076	59	8864										
AZIN1	51582	hgsc.bcm.edu	37	chr8	103842142	103842142	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	atataatacatgaaggctggTtcatcacttccggttttttc	7	8	2	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr8:103842142T>A	ENST00000337198.5	-	10	2090	c.927A>T	c.(925-927)gaA>gaT	p.E309D	AZIN1_ENST00000347770.4_Missense_Mutation_p.E309D	NM_148174.2	NP_680479.1	O14977	AZIN1_HUMAN	antizyme inhibitor 1	309					cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|negative regulation of protein catabolic process (GO:0042177)|polyamine biosynthetic process (GO:0006596)|positive regulation of polyamine transmembrane transport (GO:1902269)|regulation of cellular amino acid metabolic process (GO:0006521)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|enzyme inhibitor activity (GO:0004857)|ornithine decarboxylase activator activity (GO:0042978)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	9	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)			TGAAGGCTGGTTCATCACTTC	0.328																																					p.E309D		Atlas-SNP	.											.	AZIN1	26	.	0			c.A927T						.						96	99	98					8																	103842142		2203	4300	6503	SO:0001583	missense	51582	exon11			GGCTGGTTCATCA	AAC25391	CCDS6295.1	8p22-q21.3	2005-03-21	2005-03-21	2005-03-21		ENSG00000155096			16432	protein-coding gene	gene with protein product	"ornithine decarboxylase 1-like"	607909	"ornithine decarboxylase antizyme inhibitor"	OAZIN		9349715, 9110174	Standard	XM_005250969		Approved	OAZI, ODC1L	uc003yky.3	O14977		ENST00000337198.5:c.927A>T	chr8.hg19:g.103842142T>A	ENSP00000337180:p.Glu309Asp	94.0	0.0		129.0	88.0	NM_015878	A6NCD5|Q6IBQ7|Q96D20	Missense_Mutation	SNP	ENST00000337198.5	hg19	CCDS6295.1	.	.	.	.	.	.	.	.	.	.	T	12.58	1.981586	0.34942	.	.	ENSG00000155096	ENST00000337198;ENST00000347770	T;T	0.40476	1.03;1.03	6.03	2.45	0.29901	Orn/DAP/Arg decarboxylase 2, C-terminal (1);Alanine racemase/group IV decarboxylase, C-terminal (2);	0.133093	0.64402	N	0.000002	T	0.28101	0.0693	L	0.39326	1.205	0.40459	D	0.980222	B	0.02656	0.0	B	0.04013	0.001	T	0.07731	-1.0757	10	0.21540	T	0.41	-16.894	6.002	0.19525	0.0:0.1974:0.1276:0.675	.	309	O14977	AZIN1_HUMAN	D	309	ENSP00000337180:E309D;ENSP00000321507:E309D	ENSP00000337180:E309D	E	-	3	2	AZIN1	103911318	0.946000	0.32159	1.000000	0.80357	0.998000	0.95712	-0.052000	0.11865	0.196000	0.20367	0.455000	0.32223	GAA	.	.		0.328	AZIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380133.1			A	103842142	T	A	103842142	3	1	69	1	0	0	0	0	1	0	0	0	1242	1722	60	4	431	4	AZIN1	8	103842142	Missense_Mutation	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10	88444196	103842142	42521880	60	8865										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73736204	73736204	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gaccccttccaaattccaccAggaaaacaagaaactgaaaa	5	12	0	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:73736204A>T	ENST00000377111.2	-	1	310	c.67T>A	c.(67-69)Tgg>Agg	p.W23R	TRPM3_ENST00000423814.3_Intron|TRPM3_ENST00000377110.3_Missense_Mutation_p.W23R|TRPM3_ENST00000357533.2_Intron	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	23					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						AAATTCCACCAGGAAAACAAG	0.507																																					p.W23R		Atlas-SNP	.											.	TRPM3	700	.	0			c.T67A						.						82	83	83					9																	73736204		1911	4119	6030	SO:0001583	missense	80036	exon1			TCCACCAGGAAAA	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.67T>A	chr9.hg19:g.73736204A>T	ENSP00000366315:p.Trp23Arg	88.0	0.0		68.0	36.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.026	-1.374688	0.01214	.	.	ENSG00000083067	ENST00000377111;ENST00000377110	T;T	0.57595	0.39;0.56	5.68	-0.796	0.10912	.	.	.	.	.	T	0.26048	0.0635	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.15838	-1.0423	9	0.09590	T	0.72	.	10.7478	0.46191	0.5318:0.0:0.4682:0.0	.	23;23;23	Q9HCF6;Q9HCF6-2;Q9HCF6-10	TRPM3_HUMAN;.;.	R	23	ENSP00000366315:W23R;ENSP00000366314:W23R	ENSP00000366314:W23R	W	-	1	0	TRPM3	72926024	0.769000	0.28531	0.651000	0.29564	0.763000	0.43281	-0.053000	0.11846	-0.051000	0.13334	-0.479000	0.04858	TGG	.	.		0.507	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		T	73736204	A	T	73736204	3	4	69	1	0	0	0	0	1	0	0	0	16602	188	7	4	5279	4	TRPM3	9	73736204	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10		73736204	67477227	61	8866										
COL15A1	1306	hgsc.bcm.edu	37	chr9	101798606	101798607	+	Frame_Shift_Ins	INS	-	-	T													0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ttgaccagggagaaagggggINSatggatggagccagtattgt							TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:101798606_101798607insT	ENST00000375001.3	+	21	2760_2761	c.2337_2338insT	c.(2338-2340)atgfs	p.M780fs		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	780	Triple-helical region 3 (COL3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				GAGAAAGGGGGATGGATGGAGC	0.54																																					p.G779fs		Atlas-INDEL	.											.	COL15A1	211	.	0			c.2337_2338insT						.																																			SO:0001589	frameshift_variant	1306	exon21			.	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	Exception_encountered	chr9.hg19:g.101798606_101798607insT	ENSP00000364140:p.Met780fs	96.0	0.0		49.0	11.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Frame_Shift_Ins	INS	ENST00000375001.3	hg19	CCDS35081.1																																																																																			.	.		0.54	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		T	101798607	-	T	101798606	7	5	69	1	0	1	1	0	0	0	0	0	3674	1161	41	0	2419	0	COL15A1	9	101798606	Frame_Shift_Ins	INS	-	TCGA-CC-A5UE-01A-11D-A28X-10	28062402	101798606	39414825	62	8867										
ZFP37	7539	hgsc.bcm.edu	37	chr9	115812084	115812084	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ttcttacccattgaggcttgGttgcagtagttctccagcat	9	10	2	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:115812084G>T	ENST00000374227.3	-	2	228	c.201C>A	c.(199-201)aaC>aaA	p.N67K	ZFP37_ENST00000555206.1_Missense_Mutation_p.N68K|ZFP37_ENST00000553380.1_Missense_Mutation_p.N82K	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	67	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						TTGAGGCTTGGTTGCAGTAGT	0.423																																					p.N67K		Atlas-SNP	.											.	ZFP37	93	.	0			c.C201A						.						214	174	188					9																	115812084		2203	4300	6503	SO:0001583	missense	7539	exon2			GGCTTGGTTGCAG	AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"Zinc fingers, C2H2-type", "-"	12863	protein-coding gene	gene with protein product		602951	"zinc finger protein homologous to Zfp37 in mouse", "zinc finger protein 37 homolog (mouse)"				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.201C>A	chr9.hg19:g.115812084G>T	ENSP00000363344:p.Asn67Lys	156.0	0.0		121.0	70.0	NM_003408	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Missense_Mutation	SNP	ENST00000374227.3	hg19	CCDS6787.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.163398	0.38217	.	.	ENSG00000136866	ENST00000374227;ENST00000555206;ENST00000553380	T;T;T	0.02579	4.24;4.24;4.24	4.18	-0.204	0.13200	Krueppel-associated box (4);	0.149871	0.30969	N	0.008504	T	0.10680	0.0261	H	0.97214	3.96	0.09310	N	1	B;B;B	0.27882	0.16;0.16;0.192	B;B;B	0.35413	0.128;0.128;0.202	T	0.11108	-1.0601	10	0.87932	D	0	-7.4885	7.7301	0.28781	0.4509:0.0:0.5491:0.0	.	68;82;67	G3V3L7;Q9Y6Q3-2;Q9Y6Q3	.;.;ZFP37_HUMAN	K	67;68;82	ENSP00000363344:N67K;ENSP00000451310:N68K;ENSP00000452552:N82K	ENSP00000363344:N67K	N	-	3	2	ZFP37	114851905	0.000000	0.05858	0.057000	0.19452	0.754000	0.42855	-0.077000	0.11394	-0.037000	0.13646	0.555000	0.69702	AAC	.	.		0.423	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		T	115812084	G	T	115812084	3	4	69	1	0	0	0	0	1	0	0	0	17663	1252	44	3	1703	3	ZFP37	9	115812084	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	14013478	115812084	25401347	63	8868										
OR1B1	347169	hgsc.bcm.edu	37	chr9	125391806	125391806	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tgtgaagcattaggggcaaaGctcatcatgagtgacagtca	12	7	3	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:125391806G>A	ENST00000304833.3	-	1	46	c.9C>T	c.(7-9)agC>agT	p.S3S	RP11-64P14.7_ENST00000431442.1_RNA|RP11-64P14.7_ENST00000419604.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	3						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						TAGGGGCAAAGCTCATCATGA	0.428																																					p.S3S		Atlas-SNP	.											.	OR1B1	48	.	0			c.C9T						.						72	74	73					9																	125391806		2195	4279	6474	SO:0001819	synonymous_variant	347169	exon1			GGCAAAGCTCATC	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"GPCR / Class A : Olfactory receptors"	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.9C>T	chr9.hg19:g.125391806G>A		94.0	0.0		94.0	40.0	NM_001004450	Q6IFN3	Silent	SNP	ENST00000304833.3	hg19	CCDS35126.1																																																																																			.	.		0.428	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450		A	125391806	G	A	125391806	2	1	69	1	0	0	0	0	0	0	0	1	10960	962	34	3		3	OR1B1	9	125391806	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	9579722	125391806	15821625	64	8869										
NTNG2	84628	hgsc.bcm.edu	37	chr9	135117276	135117276	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cctgcagccaacgtgtgcgaCgacgaccagctgctgtgcca	12	15	0	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:135117276C>A	ENST00000393229.3	+	8	2147	c.1371C>A	c.(1369-1371)gaC>gaA	p.D457E	NTNG2_ENST00000393228.4_Missense_Mutation_p.D449E|NTNG2_ENST00000490694.1_3'UTR|NTNG2_ENST00000360670.3_Missense_Mutation_p.D463E	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	457					axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)				central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		ACGTGTGCGACGACGACCAGC	0.731																																					p.D457E		Atlas-SNP	.											.	NTNG2	66	.	0			c.C1371A						.						7	8	7					9																	135117276		2047	4050	6097	SO:0001583	missense	84628	exon8			GTGCGACGACGAC	AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"Netrins"	14288	protein-coding gene	gene with protein product	"Netrin-G2"		"netrin G1"	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.1371C>A	chr9.hg19:g.135117276C>A	ENSP00000376921:p.Asp457Glu	36.0	0.0		14.0	5.0	NM_032536	Q5JUJ2|Q6UXY0|Q96JH0	Missense_Mutation	SNP	ENST00000393229.3	hg19	CCDS6946.1	.	.	.	.	.	.	.	.	.	.	c	11.49	1.653576	0.29425	.	.	ENSG00000196358	ENST00000393229;ENST00000393228;ENST00000360670	D;D;D	0.91631	-2.88;-2.88;-2.88	3.39	1.22	0.21188	EGF, extracellular (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.071801	0.52532	U	0.000075	D	0.94558	0.8247	M	0.78637	2.42	0.31534	N	0.660762	D	0.76494	0.999	D	0.85130	0.997	D	0.91931	0.5555	10	0.54805	T	0.06	.	8.3416	0.32247	0.0:0.6839:0.0:0.3161	.	457	Q96CW9	NTNG2_HUMAN	E	457;449;463	ENSP00000376921:D457E;ENSP00000376920:D449E;ENSP00000353888:D463E	ENSP00000353888:D463E	D	+	3	2	NTNG2	134107097	0.961000	0.32948	0.998000	0.56505	0.025000	0.11179	0.182000	0.16900	0.162000	0.19483	-1.676000	0.00740	GAC	.	.		0.731	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536		A	135117276	C	A	135117276	3	1	69	1	0	0	0	0	1	0	0	0	10714	535	19	1	1397	1	NTNG2	9	135117276	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	9725470	135117276	6096155	65	8870										
TPRN	286262	hgsc.bcm.edu	37	chr9	140093451	140093451	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ccactgaccttctttcttgaGgagccagccttggtgaggca	11	12	2	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:140093451G>A	ENST00000409012.4	-	1	1799	c.1713C>T	c.(1711-1713)tcC>tcT	p.S571S	TPRN_ENST00000321773.2_Silent_p.S510S|TPRN_ENST00000541945.1_Intron	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	571					sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						TCTTTCTTGAGGAGCCAGCCT	0.627																																					p.S571S		Atlas-SNP	.											.	TPRN	28	.	0			c.C1713T						.						60	57	58					9																	140093451		2203	4299	6502	SO:0001819	synonymous_variant	286262	exon1			TCTTGAGGAGCCA	AK074735	CCDS56594.1	9q34.3	2011-01-06	2010-03-24	2010-03-24	ENSG00000176058	ENSG00000176058			26894	protein-coding gene	gene with protein product		613354	"chromosome 9 open reading frame 75", "deafness, autosomal recessive 79"	C9orf75, DFNB79		20170898, 20170899	Standard	NM_001128228		Approved	FLJ90254	uc004clu.3	Q4KMQ1	OTTHUMG00000020984	ENST00000409012.4:c.1713C>T	chr9.hg19:g.140093451G>A		115.0	0.0		56.0	12.0	NM_001128228	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Silent	SNP	ENST00000409012.4	hg19	CCDS56594.1																																																																																			.	.		0.627	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691		A	140093451	G	A	140093451	2	1	69	1	0	0	0	0	0	0	0	1	16436	987	35	3		3	TPRN	9	140093451	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	4976175	140093451	1119980	66	8871										
SYT15	83849	hgsc.bcm.edu	37	chr10	46965864	46965864	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggagaacttcagcaccctctGggtgatggtcttgctggaca	13	10	3	2	rs202146218	byFrequency	TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:46965864G>T	ENST00000374321.4	-	5	739	c.673C>A	c.(673-675)Cag>Aag	p.Q225K	RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Missense_Mutation_p.Q278K|SYT15_ENST00000503753.1_Missense_Mutation_p.Q225K|SYT15_ENST00000374325.3_Missense_Mutation_p.Q225K	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	225	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						AGCACCCTCTGGGTGATGGTC	0.592																																					p.Q225K	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											.	SYT15	165	.	0			c.C673A						.						39	42	41					10																	46965864		2117	4239	6356	SO:0001583	missense	83849	exon5			CCCTCTGGGTGAT	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"Synaptotagmins"	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.673C>A	chr10.hg19:g.46965864G>T	ENSP00000363441:p.Gln225Lys	142.0	0.0		90.0	31.0	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	hg19	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	14.75	2.629328	0.46944	.	.	ENSG00000204176	ENST00000416127;ENST00000374328;ENST00000374325;ENST00000503753;ENST00000374330;ENST00000374323;ENST00000374321;ENST00000512997	D;T;T;T;T;T	0.95377	-3.69;3.21;3.21;3.21;3.21;3.21	5.13	5.13	0.70059	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.349077	0.31031	N	0.008394	D	0.92665	0.7669	N	0.26042	0.785	0.54753	D	0.999982	B;B	0.25206	0.056;0.12	B;B	0.36186	0.076;0.219	D	0.89516	0.3775	10	0.27082	T	0.32	.	16.4476	0.83942	0.0:0.0:1.0:0.0	.	225;225	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	K	225;15;225;225;64;278;225;109	ENSP00000363448:Q15K;ENSP00000363445:Q225K;ENSP00000427607:Q225K;ENSP00000363443:Q278K;ENSP00000363441:Q225K;ENSP00000424803:Q109K	ENSP00000363441:Q225K	Q	-	1	0	SYT15	46385870	1.000000	0.71417	0.955000	0.39395	0.401000	0.30781	5.731000	0.68554	2.550000	0.86006	0.561000	0.74099	CAG	.	.		0.592	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912		T	46965864	G	T	46965864	3	4	69	1	0	0	0	0	1	0	0	0	15486	1357	47	3	662	3	SYT15	10	46965864	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		46965864	88568883	67	8872										
CHST3	9469	hgsc.bcm.edu	37	chr10	73765630	73765630	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggactcactttgccccaggaCtgccgggactttgtgcacag	12	13	1	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:73765630C>A	ENST00000373115.4	+	2	467	c.30C>A	c.(28-30)gaC>gaA	p.D10E		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	10					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						TGCCCCAGGACTGCCGGGACT	0.522																																					p.D10E		Atlas-SNP	.											.	CHST3	36	.	0			c.C30A						.						147	133	138					10																	73765630		2203	4300	6503	SO:0001583	missense	9469	exon2			CCAGGACTGCCGG	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"Sulfotransferases, membrane-bound"	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.30C>A	chr10.hg19:g.73765630C>A	ENSP00000362207:p.Asp10Glu	95.0	0.0		62.0	47.0	NM_004273	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	hg19	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.660319	0.67586	.	.	ENSG00000122863	ENST00000373115	D	0.96802	-4.13	5.82	-0.827	0.10802	.	0.188213	0.37053	N	0.002280	D	0.91509	0.7319	L	0.44542	1.39	0.28254	N	0.925154	B	0.06786	0.001	B	0.06405	0.002	D	0.84614	0.0680	10	0.87932	D	0	-28.5081	5.5251	0.16953	0.0:0.2793:0.4232:0.2976	.	10	Q7LGC8	CHST3_HUMAN	E	10	ENSP00000362207:D10E	ENSP00000362207:D10E	D	+	3	2	CHST3	73435636	0.014000	0.17966	0.993000	0.49108	0.686000	0.39977	-0.010000	0.12743	0.035000	0.15519	0.655000	0.94253	GAC	.	.		0.522	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273		A	73765630	C	A	73765630	3	1	69	1	0	0	0	0	1	0	0	0	3407	564	20	3	32	3	CHST3	10	73765630	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	26799766	73765630	61769117	68	8873										
LOXL4	84171	hgsc.bcm.edu	37	chr10	100021841	100021841	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cagaaaggtagccacgatggCgccgggggtggcatatcacc	15	11	1	1	rs377758453		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:100021841C>T	ENST00000260702.3	-	3	557	c.407G>A	c.(406-408)cGc>cAc	p.R136H		NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	136						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		GCCACGATGGCGCCGGGGGTG	0.602																																					p.R136H		Atlas-SNP	.											.	LOXL4	60	.	0			c.G407A						.	C	HIS/ARG	0,4406		0,0,2203	47	43	44		407	3.8	1	10		44	1,8599	1.2+/-3.3	0,1,4299	no	missense	LOXL4	NM_032211.6	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	136/757	100021841	1,13005	2203	4300	6503	SO:0001583	missense	84171	exon3			CGATGGCGCCGGG	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.407G>A	chr10.hg19:g.100021841C>T	ENSP00000260702:p.Arg136His	75.0	0.0		51.0	11.0	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Missense_Mutation	SNP	ENST00000260702.3	hg19	CCDS7473.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.402475	0.62288	0.0	1.16E-4	ENSG00000138131	ENST00000260702	T	0.49139	0.79	4.69	3.78	0.43462	Speract/scavenger receptor-related (1);	0.103756	0.64402	D	0.000004	T	0.65417	0.2689	M	0.74881	2.28	0.36182	D	0.849478	D	0.89917	1.0	D	0.70935	0.971	T	0.75354	-0.3347	10	0.72032	D	0.01	.	12.1953	0.54294	0.0:0.9173:0.0:0.0827	.	136	Q96JB6	LOXL4_HUMAN	H	136	ENSP00000260702:R136H	ENSP00000260702:R136H	R	-	2	0	LOXL4	100011831	0.875000	0.30112	0.998000	0.56505	0.329000	0.28539	1.151000	0.31651	2.157000	0.67596	0.561000	0.74099	CGC	.	.		0.602	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211		T	100021841	C	T	100021841	3	4	69	1	0	0	0	0	1	0	0	0	8911	768	27	1	1915	1	LOXL4	10	100021841	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	26256211	100021841	35512906	69	8874										
NOLC1	9221	hgsc.bcm.edu	37	chr10	103921354	103921354	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	agaatgaggctgccaaggagGcagagactcctcaggccaag	14	10	1	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:103921354G>T	ENST00000605788.1	+	11	2018	c.1783G>T	c.(1783-1785)Gca>Tca	p.A595S	NOLC1_ENST00000488254.2_Missense_Mutation_p.A596S|NOLC1_ENST00000603742.1_Missense_Mutation_p.A314S|NOLC1_ENST00000477977.1_3'UTR|NOLC1_ENST00000405356.1_Missense_Mutation_p.A605S	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	595					cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		TGCCAAGGAGGCAGAGACTCC	0.478																																					p.A595S		Atlas-SNP	.											.	NOLC1	61	.	0			c.G1783T						.						45	41	42					10																	103921354		2203	4300	6503	SO:0001583	missense	9221	exon11			AAGGAGGCAGAGA	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.1783G>T	chr10.hg19:g.103921354G>T	ENSP00000474710:p.Ala595Ser	99.0	0.0		45.0	33.0	NM_004741	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	hg19	CCDS7530.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.217457	0.39201	.	.	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.47177	0.85	6.07	0.394	0.16299	.	0.528716	0.18826	N	0.130117	T	0.31231	0.0790	L	0.45581	1.43	0.34553	D	0.711586	B;B;B	0.34372	0.451;0.451;0.272	B;B;B	0.31442	0.13;0.13;0.045	T	0.23726	-1.0180	10	0.25106	T	0.35	0.3724	4.0351	0.09725	0.3199:0.0:0.2444:0.4357	.	596;605;595	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	S	605;595	ENSP00000385410:A605S	ENSP00000359024:A595S	A	+	1	0	NOLC1	103911344	0.006000	0.16342	0.967000	0.41034	0.881000	0.50899	-0.537000	0.06128	0.022000	0.15160	0.650000	0.86243	GCA	.	.		0.478	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		T	103921354	G	T	103921354	3	4	69	1	0	0	0	0	1	0	0	0	10538	1203	42	3	1825	3	NOLC1	10	103921354	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	3899513	103921354	31613393	70	8875										
SFXN2	118980	hgsc.bcm.edu	37	chr10	104489489	104489489	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tcccccaacagaaagcgccgCccttggtgggccgctgggtg	14	15	0	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:104489489C>T	ENST00000369893.5	+	6	684	c.517C>T	c.(517-519)Ccc>Tcc	p.P173S		NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	173				QMALSYFTATTTAVATAVGMNMLTKKAPPLVGRWVPFAAVA AANCVNIPMMRQQELIKGI -> KRRPWWAAGCPLPLWLRL TVSISP (in Ref. 4). {ECO:0000305}.	iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		GAAAGCGCCGCCCTTGGTGGG	0.552											OREG0020485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P173S		Atlas-SNP	.											.	SFXN2	40	.	0			c.C517T						.						74	83	80					10																	104489489		2203	4300	6503	SO:0001583	missense	118980	exon6			GCGCCGCCCTTGG	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"Sideroflexins"	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.517C>T	chr10.hg19:g.104489489C>T	ENSP00000358909:p.Pro173Ser	33.0	0.0	1382	25.0	21.0	NM_178858	Q5JSM6	Missense_Mutation	SNP	ENST00000369893.5	hg19	CCDS7539.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.612353	0.66672	.	.	ENSG00000156398	ENST00000369893	T	0.33216	1.42	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.46386	0.1390	M	0.69358	2.11	0.80722	D	1	P	0.46656	0.882	P	0.53102	0.718	T	0.21211	-1.0252	10	0.34782	T	0.22	-14.0701	15.4376	0.75157	0.1394:0.8605:0.0:0.0	.	173	Q96NB2	SFXN2_HUMAN	S	173	ENSP00000358909:P173S	ENSP00000358909:P173S	P	+	1	0	SFXN2	104479479	0.998000	0.40836	0.900000	0.35374	0.245000	0.25701	3.938000	0.56583	2.675000	0.91044	0.655000	0.94253	CCC	.	.		0.552	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359		T	104489489	C	T	104489489	3	4	69	1	0	0	0	0	1	0	0	0	14210	739	26	3	535	3	SFXN2	10	104489489	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	568135	104489489	31045258	71	8876										
AFAP1L2	84632	hgsc.bcm.edu	37	chr10	116061116	116061116	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cctggccgggtccttaccgcAgctgtgagctctgacaggtc	13	14	1	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:116061116A>C	ENST00000304129.4	-	13	1568	c.1539T>G	c.(1537-1539)gcT>gcG	p.A513A	AFAP1L2_ENST00000491814.1_5'UTR|AFAP1L2_ENST00000369271.3_Silent_p.A513A|AFAP1L2_ENST00000545353.1_Silent_p.A566A			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	513					inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		TCCTTACCGCAGCTGTGAGCT	0.587																																					p.A513A		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.T1539G						.						89	77	81					10																	116061116		2203	4300	6503	SO:0001819	synonymous_variant	84632	exon13			TACCGCAGCTGTG	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"Pleckstrin homology (PH) domain containing"	25901	protein-coding gene	gene with protein product		612420	"KIAA1914"	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.1539T>G	chr10.hg19:g.116061116A>C		74.0	0.0		34.0	27.0	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	hg19	CCDS31286.1																																																																																			.	.		0.587	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550		C	116061116	A	C	116061116	2	2	69	1	0	0	0	0	0	0	0	1	355	175	7	5		5	AFAP1L2	10	116061116	Silent	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	11571627	116061116	19473631	72	8877										
MMP21	118856	hgsc.bcm.edu	37	chr10	127455372	127455372	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	actaccttccagtatgcattGcctttgaaaaagaaaatgga	7	8	0	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:127455372G>A	ENST00000368808.3	-	7	1568	c.1569C>T	c.(1567-1569)ggC>ggT	p.G523G		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	523					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	AGTATGCATTGCCTTTGAAAA	0.358																																					p.G523G		Atlas-SNP	.											.	MMP21	46	.	0			c.C1569T						.						127	127	127					10																	127455372		2203	4300	6503	SO:0001819	synonymous_variant	118856	exon7			TGCATTGCCTTTG	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1569C>T	chr10.hg19:g.127455372G>A		97.0	0.0		57.0	42.0	NM_147191	Q5VZP9|Q8NG02	Silent	SNP	ENST00000368808.3	hg19	CCDS7647.1																																																																																			.	.		0.358	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			A	127455372	G	A	127455372	2	1	69	1	0	0	0	0	0	0	0	1	9669	1306	46	3		3	MMP21	10	127455372	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	11394256	127455372	8079375	73	8878										
TH	7054	hgsc.bcm.edu	37	chr11	2189846	2189846	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggtgggggcccccagctcgcGgcctctgggcgggccgggtc	20	15	1	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:2189846G>A	ENST00000381178.1	-	4	473	c.455C>T	c.(454-456)cCg>cTg	p.P152L	TH_ENST00000381175.1_Missense_Mutation_p.P148L|TH_ENST00000333684.5_Missense_Mutation_p.P125L|TH_ENST00000352909.3_Missense_Mutation_p.P121L	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	152					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CCCAGCTCGCGGCCTCTGGGC	0.627																																					p.P152L		Atlas-SNP	.											.	TH	43	.	0			c.C455T						.						11	15	14					11																	2189846		2170	4289	6459	SO:0001583	missense	7054	exon4			GCTCGCGGCCTCT	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"tyrosine 3-monooxygenase"	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.455C>T	chr11.hg19:g.2189846G>A	ENSP00000370571:p.Pro152Leu	33.0	0.0		18.0	12.0	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Missense_Mutation	SNP	ENST00000381178.1	hg19	CCDS7731.1	.	.	.	.	.	.	.	.	.	.	G	0.099	-1.155156	0.01700	.	.	ENSG00000180176	ENST00000381178;ENST00000381175;ENST00000352909;ENST00000333684	D;D;D;D	0.99418	-5.87;-5.87;-5.87;-5.56	3.14	-0.0864	0.13681	.	0.671891	0.14769	N	0.299505	D	0.97046	0.9035	N	0.20986	0.625	0.19575	N	0.999968	B;B;B;B;B;B	0.09022	0.0;0.002;0.002;0.002;0.001;0.001	B;B;B;B;B;B	0.06405	0.001;0.001;0.001;0.001;0.001;0.002	D	0.93140	0.6540	10	0.36615	T	0.2	.	10.848	0.46754	0.1924:0.0:0.8076:0.0	.	125;125;121;121;152;148	B7ZL73;Q0PWM2;Q0PWM3;P07101-3;P07101;P07101-2	.;.;.;.;TY3H_HUMAN;.	L	152;148;121;125	ENSP00000370571:P152L;ENSP00000370567:P148L;ENSP00000325951:P121L;ENSP00000328814:P125L	ENSP00000328814:P125L	P	-	2	0	TH	2146422	0.251000	0.23961	0.000000	0.03702	0.000000	0.00434	1.341000	0.33907	-0.317000	0.08677	-2.087000	0.00375	CCG	.	.		0.627	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360		A	2189846	G	A	2189846	3	1	69	1	0	0	0	0	1	0	0	0	15853	1116	39	1	1175	1	TH	11	2189846	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		2189846	132816670	74	8879										
OR2D3	120775	hgsc.bcm.edu	37	chr11	6943217	6943217	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggagaaagtgcttctctcatAggcagtgacctctgagtctg	12	9	4	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:6943217A>T	ENST00000317834.3	+	1	1013	c.985A>T	c.(985-987)Agg>Tgg	p.R329W		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	329						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTTCTCTCATAGGCAGTGACC	0.403																																					p.R329W		Atlas-SNP	.											OR2D3,NS,carcinoma,0,1	OR2D3	51	.	0			c.A985T						.						53	55	54					11																	6943217		2200	4294	6494	SO:0001583	missense	120775	exon1			TCTCATAGGCAGT	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"GPCR / Class A : Olfactory receptors"	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.985A>T	chr11.hg19:g.6943217A>T	ENSP00000320560:p.Arg329Trp	54.0	0.0		48.0	20.0	NM_001004684	B2RP06|Q6IFG8|Q96R51	Missense_Mutation	SNP	ENST00000317834.3	hg19	CCDS31417.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.428322	0.43122	.	.	ENSG00000178358	ENST00000317834	T	0.01584	4.75	4.38	0.74	0.18330	.	1.633600	0.03837	N	0.269968	T	0.02727	0.0082	N	0.14661	0.345	0.09310	N	1	D	0.63880	0.993	P	0.55923	0.787	T	0.37220	-0.9715	10	0.87932	D	0	12.9762	2.8365	0.05516	0.5936:0.0:0.2031:0.2033	.	329	Q8NGH3	OR2D3_HUMAN	W	329	ENSP00000320560:R329W	ENSP00000320560:R329W	R	+	1	2	OR2D3	6899793	0.300000	0.24435	0.000000	0.03702	0.000000	0.00434	1.143000	0.31553	0.106000	0.17784	-0.438000	0.05819	AGG	.	.		0.403	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684		T	6943217	A	T	6943217	3	4	69	1	0	0	0	0	1	0	0	0	11004	411	15	4	987	4	OR2D3	11	6943217	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	4753371	6943217	128063299	75	8880										
ST5	6764	hgsc.bcm.edu	37	chr11	8752447	8752447	+	Frame_Shift_Del	DEL	G	G	-													0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ctctgggcaagggggaggcaGgcagcgacccctgctacatc							TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:8752447delG	ENST00000534127.1	-	6	775	c.390delC	c.(388-390)gccfs	p.A130fs	ST5_ENST00000526757.1_Intron|ST5_ENST00000530438.1_Intron|ST5_ENST00000357665.1_Frame_Shift_Del_p.A130fs|ST5_ENST00000313726.6_Frame_Shift_Del_p.A130fs	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	130					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		GGGGGAGGCAGGCAGCGACCC	0.667																																					p.C131fs		Atlas-INDEL	.											.	ST5	85	.	0			c.391delT						.						46	54	51					11																	8752447		2201	4296	6497	SO:0001589	frameshift_variant	6764	exon3			.	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"DENN/MADD domain containing"	11350	protein-coding gene	gene with protein product	"DENN/MADD domain containing 2B"	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.390delC	chr11.hg19:g.8752447delG	ENSP00000433528:p.Ala130fs	47.0	0.0		22.0	12.0	NM_213618	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Frame_Shift_Del	DEL	ENST00000534127.1	hg19	CCDS7791.1																																																																																			.	.		0.667	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		-	8752447	G	-	8752447	7	5	69	1	0	1	0	1	0	0	0	0	15235	987	35	0	3095	0	ST5	11	8752447	Frame_Shift_Del	DEL	G	TCGA-CC-A5UE-01A-11D-A28X-10	1809230	8752447	126254069	76	8881										
RAG1	5896	hgsc.bcm.edu	37	chr11	36595488	36595488	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	acccccacacaccatcctgtGacatctgcaacactgcccgt	5	19	1	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:36595488G>T	ENST00000299440.5	+	2	746	c.634G>T	c.(634-636)Gac>Tac	p.D212Y		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	212	Interaction with importin alpha-1.				adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				ACCATCCTGTGACATCTGCAA	0.527									Familial Hemophagocytic Lymphohistiocytosis																												p.D212Y	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.G634T						.						78	71	74					11																	36595488		2202	4298	6500	SO:0001583	missense	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TCCTGTGACATCT	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.634G>T	chr11.hg19:g.36595488G>T	ENSP00000299440:p.Asp212Tyr	81.0	0.0		74.0	17.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	hg19	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.111924	0.56398	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	T;T	0.38401	1.14;1.14	5.9	5.9	0.94986	.	0.357073	0.31199	N	0.008065	T	0.62221	0.2410	M	0.92317	3.295	0.44469	D	0.997404	D	0.55385	0.971	P	0.53102	0.718	T	0.71800	-0.4483	10	0.87932	D	0	.	15.7737	0.78193	0.0:0.1354:0.8646:0.0	.	212	P15918	RAG1_HUMAN	Y	212	ENSP00000434610:D212Y;ENSP00000299440:D212Y	ENSP00000299440:D212Y	D	+	1	0	RAG1	36552064	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.169000	0.31871	2.822000	0.97130	0.650000	0.86243	GAC	.	.		0.527	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		T	36595488	G	T	36595488	3	4	69	1	0	0	0	0	1	0	0	0	13018	1290	45	3	636	3	RAG1	11	36595488	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	27843041	36595488	98411028	77	8882										
TMEM132A	54972	hgsc.bcm.edu	37	chr11	60698051	60698051	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cccacactctggactgccaaGctggaccgcttcaagggctc	10	16	2	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:60698051G>T	ENST00000453848.2	+	5	1094	c.936G>T	c.(934-936)aaG>aaT	p.K312N	TMEM132A_ENST00000005286.4_Missense_Mutation_p.K312N			Q24JP5	T132A_HUMAN	transmembrane protein 132A	312						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						GGACTGCCAAGCTGGACCGCT	0.622																																					p.K312N		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G936T						.						81	86	84					11																	60698051		2203	4299	6502	SO:0001583	missense	54972	exon5			TGCCAAGCTGGAC	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.936G>T	chr11.hg19:g.60698051G>T	ENSP00000405823:p.Lys312Asn	80.0	0.0		42.0	11.0	NM_178031	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	hg19	CCDS44618.1	.	.	.	.	.	.	.	.	.	.	G	13.76	2.334728	0.41297	.	.	ENSG00000006118	ENST00000544065;ENST00000444690;ENST00000453848;ENST00000005286	T;T;T	0.13778	2.78;2.56;2.56	5.4	3.49	0.39957	.	0.082213	0.49305	D	0.000141	T	0.12817	0.0311	L	0.50333	1.59	0.32122	N	0.587816	B;B;B;B	0.21225	0.053;0.021;0.029;0.029	B;B;B;B	0.18561	0.022;0.022;0.022;0.022	T	0.05666	-1.0871	10	0.87932	D	0	.	7.7328	0.28796	0.1576:0.1383:0.7041:0.0	.	301;62;312;312	Q24JP5-3;Q24JP5-4;Q24JP5;Q24JP5-2	.;.;T132A_HUMAN;.	N	50;62;312;312	ENSP00000442754:K50N;ENSP00000405823:K312N;ENSP00000005286:K312N	ENSP00000005286:K312N	K	+	3	2	TMEM132A	60454627	0.995000	0.38212	0.999000	0.59377	0.914000	0.54420	0.631000	0.24568	1.421000	0.47157	0.655000	0.94253	AAG	.	.		0.622	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		T	60698051	G	T	60698051	3	4	69	1	0	0	0	0	1	0	0	0	16060	962	34	3	954	3	TMEM132A	11	60698051	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	24102563	60698051	74308465	78	8883										
DDB1	1642	hgsc.bcm.edu	37	chr11	61096943	61096943	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gccttgagttctttattatcGcgatctagtggaataacctt	8	8	2	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:61096943G>A	ENST00000301764.7	-	4	838	c.441C>T	c.(439-441)cgC>cgT	p.R147R	DDB1_ENST00000450997.2_Intron|DDB1_ENST00000545930.1_5'Flank	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	147	Interaction with CDT1.|WD repeat beta-propeller A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						CTTTATTATCGCGATCTAGTG	0.483								Nucleotide excision repair (NER)																													p.R147R		Atlas-SNP	.											.	DDB1	100	.	0			c.C441T						.						94	92	93					11																	61096943		2203	4299	6502	SO:0001819	synonymous_variant	1642	exon4			ATTATCGCGATCT	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.441C>T	chr11.hg19:g.61096943G>A		120.0	0.0		82.0	5.0	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Silent	SNP	ENST00000301764.7	hg19	CCDS31576.1																																																																																			.	.		0.483	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		A	61096943	G	A	61096943	2	1	69	1	0	0	0	0	0	0	0	1	4325	1074	38	1		1	DDB1	11	61096943	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	398892	61096943	73909573	79	8884										
FAT3	120114	hgsc.bcm.edu	37	chr11	92577730	92577730	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gaagacacctggagaatatcAtgcgcatctcagccatcttg	9	11	3	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:92577730A>G	ENST00000298047.6	+	18	11214	c.11197A>G	c.(11197-11199)Atg>Gtg	p.M3733V	FAT3_ENST00000533797.1_Missense_Mutation_p.M68V|FAT3_ENST00000409404.2_Missense_Mutation_p.M3733V|FAT3_ENST00000525166.1_Missense_Mutation_p.M3583V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3733					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGAGAATATCATGCGCATCTC	0.532										TCGA Ovarian(4;0.039)																											p.M3733V		Atlas-SNP	.											.	FAT3	1822	.	0			c.A11197G						.						89	88	88					11																	92577730		2111	4239	6350	SO:0001583	missense	120114	exon18			AATATCATGCGCA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.11197A>G	chr11.hg19:g.92577730A>G	ENSP00000298047:p.Met3733Val	234.0	0.0		157.0	71.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	A	2.265	-0.368362	0.05069	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	5.97	0.735	0.18300	.	.	.	.	.	T	0.05640	0.0148	N	0.00377	-1.585	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40534	-0.9558	9	0.02654	T	1	.	5.7419	0.18098	0.6342:0.1295:0.2362:0.0	.	3733;3733	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	V	3733;3733;3583;68	ENSP00000298047:M3733V;ENSP00000387040:M3733V;ENSP00000432586:M3583V;ENSP00000436399:M68V	ENSP00000298047:M3733V	M	+	1	0	FAT3	92217378	1.000000	0.71417	0.579000	0.28588	0.699000	0.40488	1.802000	0.38853	0.082000	0.17018	-0.256000	0.11100	ATG	.	.		0.532	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		G	92577730	A	G	92577730	3	3	69	1	0	0	0	0	1	0	0	0	5699	217	8	2	11267	2	FAT3	11	92577730	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	31480787	92577730	42428786	80	8885										
DDI1	414301	hgsc.bcm.edu	37	chr11	103908038	103908038	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tctgtccctgctcaaggaacGcaaccctcccttggcggaag	10	15	2	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:103908038G>A	ENST00000302259.3	+	1	731	c.488G>A	c.(487-489)cGc>cAc	p.R163H	PDGFD_ENST00000302251.5_Intron|PDGFD_ENST00000393158.2_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	163							aspartic-type endopeptidase activity (GO:0004190)	p.R163L(2)		central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		CTCAAGGAACGCAACCCTCCC	0.612																																					p.R163H		Atlas-SNP	.											DDI1_ENST00000302259,caecum,carcinoma,0,2	DDI1	222	.	2	Substitution - Missense(2)	lung(2)	c.G488A						.						64	62	62					11																	103908038		2202	4299	6501	SO:0001583	missense	414301	exon1			AGGAACGCAACCC		CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.488G>A	chr11.hg19:g.103908038G>A	ENSP00000302805:p.Arg163His	78.0	0.0		47.0	11.0	NM_001001711	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	hg19	CCDS31660.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.179662	0.78564	.	.	ENSG00000170967	ENST00000302259	T	0.24908	1.83	5.02	4.1	0.47936	.	0.000000	0.85682	D	0.000000	T	0.48187	0.1486	M	0.75615	2.305	0.42064	D	0.991176	D	0.89917	1.0	D	0.91635	0.999	T	0.46816	-0.9164	10	0.37606	T	0.19	-25.855	11.9064	0.52715	0.0857:0.0:0.9143:0.0	.	163	Q8WTU0	DDI1_HUMAN	H	163	ENSP00000302805:R163H	ENSP00000302805:R163H	R	+	2	0	DDI1	103413248	1.000000	0.71417	1.000000	0.80357	0.758000	0.43043	7.217000	0.77982	1.480000	0.48289	0.655000	0.94253	CGC	.	.		0.612	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711		A	103908038	G	A	103908038	3	1	69	1	0	0	0	0	1	0	0	0	4330	1087	38	1	490	1	DDI1	11	103908038	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	11330308	103908038	31098478	81	8886										
MLL	4297	hgsc.bcm.edu	37	chr11	118376454	118376454	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cacttaatacttcatctcacCgaactgtccccaacatcata	2	15	3	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:118376454C>T	ENST00000389506.5	+	27	9838	c.9838C>T	c.(9838-9840)Cga>Tga	p.R3280*	KMT2A_ENST00000354520.4_Nonsense_Mutation_p.R3242*|KMT2A_ENST00000534358.1_Nonsense_Mutation_p.R3283*			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3280					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.R3283*(1)|p.R3280*(1)									TTCATCTCACCGAACTGTCCC	0.433																																					p.R3283X		Atlas-SNP	.											MLL_ENST00000534358,bladder,carcinoma,0,2	MLL	548	.	2	Substitution - Nonsense(2)	urinary_tract(2)	c.C9847T						.						109	109	109					11																	118376454		2200	4295	6495	SO:0001587	stop_gained	4297	exon27			TCTCACCGAACTG	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.9838C>T	chr11.hg19:g.118376454C>T	ENSP00000374157:p.Arg3280*	71.0	0.0		65.0	29.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Nonsense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	50	16.745021	0.99871	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	.	.	.	5.98	4.04	0.47022	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5277	0.39173	0.2425:0.6837:0.0:0.0739	.	.	.	.	X	3283;3280;3242;2190	.	ENSP00000346516:R3242X	R	+	1	2	MLL	117881664	0.995000	0.38212	1.000000	0.80357	0.982000	0.71751	2.957000	0.49137	2.847000	0.97988	0.591000	0.81541	CGA	.	.		0.433	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118376454	C	T	118376454	4	4	69	1	0	0	0	0	0	1	0	0	9629	644	23	1	9944	1	MLL	11	118376454	Nonsense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	14468416	118376454	16630062	82	8887										
ROBO4	54538	hgsc.bcm.edu	37	chr11	124765401	124765401	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gttgctgtcagggcctcgagCccggccagaggatggtctca	15	12	2	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:124765401C>A	ENST00000306534.3	-	6	1473	c.988G>T	c.(988-990)Gct>Tct	p.A330S	ROBO4_ENST00000533054.1_Missense_Mutation_p.A185S|ROBO4_ENST00000526899.1_5'Flank	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	330	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GGGCCTCGAGCCCGGCCAGAG	0.617																																					p.A330S		Atlas-SNP	.											.	ROBO4	130	.	0			c.G988T						.						49	57	54					11																	124765401		2198	4290	6488	SO:0001583	missense	54538	exon6			CTCGAGCCCGGCC	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.988G>T	chr11.hg19:g.124765401C>A	ENSP00000304945:p.Ala330Ser	34.0	0.0		43.0	21.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	hg19	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.474876	0.63737	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.52983	0.64;0.64	4.72	3.81	0.43845	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.38959	N	0.001520	T	0.49423	0.1556	L	0.57536	1.79	0.18873	N	0.999981	D;D	0.53619	0.961;0.958	P;P	0.52066	0.689;0.531	T	0.39961	-0.9588	10	0.10902	T	0.67	.	11.065	0.47970	0.0:0.9129:0.0:0.087	.	220;330	Q8WZ75-3;Q8WZ75	.;ROBO4_HUMAN	S	330;220;185	ENSP00000304945:A330S;ENSP00000437129:A185S	ENSP00000304945:A330S	A	-	1	0	ROBO4	124270611	0.518000	0.26234	0.956000	0.39512	0.997000	0.91878	0.572000	0.23684	1.216000	0.43427	0.561000	0.74099	GCT	.	.		0.617	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		A	124765401	C	A	124765401	3	1	69	1	0	0	0	0	1	0	0	0	13531	739	26	3	2087	3	ROBO4	11	124765401	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	6388947	124765401	10241115	83	8888										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40657644	40657644	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ttcatcataagctaaatatgGttaaaaaacagtgtttcaag	6	5	3	0	rs267603454		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr12:40657644G>T	ENST00000298910.7	+	14	1655	c.1597G>T	c.(1597-1599)Gtt>Ttt	p.V533F	LRRK2_ENST00000343742.2_Missense_Mutation_p.V533F	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	533					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GCTAAATATGGTTAAAAAACA	0.299																																					p.V533F		Atlas-SNP	.											.	LRRK2	763	.	0			c.G1597T						.						83	88	86					12																	40657644		2203	4297	6500	SO:0001583	missense	120892	exon14			AATATGGTTAAAA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.1597G>T	chr12.hg19:g.40657644G>T	ENSP00000298910:p.Val533Phe	140.0	0.0		101.0	21.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	8.364	0.833807	0.16820	.	.	ENSG00000188906	ENST00000416796;ENST00000343742;ENST00000298910	T;T;T	0.64991	-0.13;1.35;1.35	5.66	-1.91	0.07641	Armadillo-like helical (1);Armadillo-type fold (1);	0.485960	0.21586	N	0.072179	T	0.31796	0.0808	N	0.08118	0	0.09310	N	1	B;B	0.29188	0.002;0.236	B;B	0.29353	0.003;0.101	T	0.16928	-1.0386	10	0.72032	D	0.01	.	1.846	0.03159	0.4417:0.1376:0.2887:0.1319	.	533;533	E9PC85;Q5S007	.;LRRK2_HUMAN	F	281;533;533	ENSP00000398726:V281F;ENSP00000341930:V533F;ENSP00000298910:V533F	ENSP00000298910:V533F	V	+	1	0	LRRK2	38943911	0.982000	0.34865	0.006000	0.13384	0.125000	0.20455	0.056000	0.14256	-0.158000	0.11040	-0.142000	0.14014	GTT	.	.		0.299	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40657644	G	T	40657644	3	4	69	1	0	0	0	0	1	0	0	0	9042	1261	44	3	1651	3	LRRK2	12	40657644	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		40657644	93194251	84	8889										
CCNT1	904	hgsc.bcm.edu	37	chr12	49089809	49089809	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	aagttccaaggtcacagtggCgtcaacatactcccaccagt	8	13	2	0	rs35965578	byFrequency	TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr12:49089809C>A	ENST00000261900.3	-	7	901	c.679G>T	c.(679-681)Gcc>Tcc	p.A227S		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	227					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						GTCACAGTGGCGTCAACATAC	0.498																																					p.A227S		Atlas-SNP	.											.	CCNT1	55	.	0			c.G679T						.						105	81	89					12																	49089809		2203	4300	6503	SO:0001583	missense	904	exon7			CAGTGGCGTCAAC	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.679G>T	chr12.hg19:g.49089809C>A	ENSP00000261900:p.Ala227Ser	125.0	0.0		94.0	24.0	NM_001240	A9XU13|E7EX76|O60581	Missense_Mutation	SNP	ENST00000261900.3	hg19	CCDS8766.1	.	.	.	.	.	.	.	.	.	.	c	14.13	2.443468	0.43429	.	.	ENSG00000129315	ENST00000261900	T	0.38887	1.11	5.79	5.79	0.91817	.	0.169435	0.53938	D	0.000051	T	0.29126	0.0724	N	0.12182	0.205	0.30771	N	0.743014	B	0.02656	0.0	B	0.10450	0.005	T	0.08764	-1.0706	10	0.24483	T	0.36	-8.8347	18.7919	0.91976	0.0:1.0:0.0:0.0	.	227	O60563	CCNT1_HUMAN	S	227	ENSP00000261900:A227S	ENSP00000261900:A227S	A	-	1	0	CCNT1	47376076	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.645000	0.46621	2.740000	0.93945	0.561000	0.74099	GCC	.	C|0.500;G|0.500		0.498	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		A	49089809	C	A	49089809	3	1	69	1	0	0	0	0	1	0	0	0	2936	768	27	1	1513	1	CCNT1	12	49089809	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	8432165	49089809	84762086	85	8890										
PDX1	3651	hgsc.bcm.edu	37	chr13	28498513	28498513	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gtacatctcacggccgcgccGggtggagctggctgtcatgt	15	12	2	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr13:28498513G>T	ENST00000381033.4	+	2	646	c.527G>T	c.(526-528)cGg>cTg	p.R176L	PDX1-AS1_ENST00000499662.2_RNA	NM_000209.3	NP_000200.1	O00330	ODPX_HUMAN	pancreatic and duodenal homeobox 1	0					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)					all_cancers(110;0.175)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155)	Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0402)|all cancers(112;0.0404)|OV - Ovarian serous cystadenocarcinoma(117;0.197)		CGGCCGCGCCGGGTGGAGCTG	0.572																																					p.R176L		Atlas-SNP	.											.	PDX1	7	.	0			c.G527T						.						54	57	56					13																	28498513		2203	4300	6503	SO:0001583	missense	3651	exon2			CGCGCCGGGTGGA	AF035260	CCDS9327.1	13q12.1	2012-03-09	2006-12-01	2006-12-01	ENSG00000139515	ENSG00000139515		"Homeoboxes / ANTP class : HOXL subclass"	6107	protein-coding gene	gene with protein product	"somatostatin transcription factor 1"	600733	"insulin promoter factor 1, homeodomain transcription factor"	IPF1		7590740	Standard	NM_000209		Approved	IDX-1, STF-1, PDX-1, MODY4	uc001urt.2	P52945	OTTHUMG00000016638	ENST00000381033.4:c.527G>T	chr13.hg19:g.28498513G>T	ENSP00000370421:p.Arg176Leu	161.0	1.0		45.0	38.0	NM_000209	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000381033.4	hg19	CCDS9327.1	.	.	.	.	.	.	.	.	.	.	G	34	5.293103	0.95546	.	.	ENSG00000139515	ENST00000381033	D	0.97232	-4.3	4.86	4.86	0.63082	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99099	0.9690	H	0.97291	3.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99167	1.0863	10	0.87932	D	0	.	18.338	0.90295	0.0:0.0:1.0:0.0	.	176	P52945	PDX1_HUMAN	L	176	ENSP00000370421:R176L	ENSP00000370421:R176L	R	+	2	0	PDX1	27396513	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.770000	0.98971	2.382000	0.81193	0.555000	0.69702	CGG	.	.		0.572	PDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044310.2	NM_000209		T	28498513	G	T	28498513	3	4	69	1	0	0	0	0	1	0	0	0	11704	1116	39	1	533	1	PDX1	13	28498513	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		28498513	86671365	86	8891										
HNRNPC	3183	hgsc.bcm.edu	37	chr14	21679444	21679444	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tccttcctcagcctctttttCatcatccttgatcaactcca	2	16	5	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr14:21679444C>A	ENST00000320084.7	-	8	1098	c.859G>T	c.(859-861)Gaa>Taa	p.E287*	HNRNPC_ENST00000449098.1_Nonsense_Mutation_p.E274*|HNRNPC_ENST00000555309.1_Nonsense_Mutation_p.E286*|HNRNPC_ENST00000554455.1_Nonsense_Mutation_p.E287*|HNRNPC_ENST00000336053.6_3'UTR|HNRNPC_ENST00000556628.1_Nonsense_Mutation_p.E207*|HNRNPC_ENST00000557201.1_Nonsense_Mutation_p.E287*|HNRNPC_ENST00000553753.1_3'UTR|HNRNPC_ENST00000555883.1_Nonsense_Mutation_p.E231*|HNRNPC_ENST00000430246.2_Nonsense_Mutation_p.E274*|HNRNPC_ENST00000556142.1_3'UTR|HNRNPC_ENST00000556897.1_Nonsense_Mutation_p.E274*|HNRNPC_ENST00000420743.2_Nonsense_Mutation_p.E287*|HNRNPC_ENST00000556513.1_3'UTR|HNRNPC_ENST00000554969.1_Nonsense_Mutation_p.E274*|HNRNPC_ENST00000553300.1_Nonsense_Mutation_p.E274*|HNRNPC_ENST00000555914.1_Nonsense_Mutation_p.E273*	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	287	Asp/Glu-rich (acidic).				3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		GCCTCTTTTTCATCATCCTTG	0.478																																					p.E287X	NSCLC(108;607 2244 12726 38757)	Atlas-SNP	.											.	HNRNPC	31	.	0			c.G859T						.						129	139	136					14																	21679444		2153	4265	6418	SO:0001587	stop_gained	3183	exon9			CTTTTTCATCATC		CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"RNA binding motif (RRM) containing"	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.859G>T	chr14.hg19:g.21679444C>A	ENSP00000319690:p.Glu287*	129.0	0.0		75.0	30.0	NM_031314	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Nonsense_Mutation	SNP	ENST00000320084.7	hg19	CCDS41915.1	.	.	.	.	.	.	.	.	.	.	C	37	6.573695	0.97676	.	.	ENSG00000092199	ENST00000320084;ENST00000449098;ENST00000554969;ENST00000554455;ENST00000430246;ENST00000400042;ENST00000555914;ENST00000555309;ENST00000556628;ENST00000555883;ENST00000557201;ENST00000553300;ENST00000556897;ENST00000420743;ENST00000557157;ENST00000445284;ENST00000554539	.	.	.	5.85	5.85	0.93711	.	0.264293	0.28549	U	0.014958	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	18.9211	0.92525	0.0:1.0:0.0:0.0	.	.	.	.	X	287;274;274;287;274;83;273;286;207;231;287;274;274;287;195;287;171	.	ENSP00000319690:E287X	E	-	1	0	HNRNPC	20749284	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.962000	0.63687	2.755000	0.94549	0.655000	0.94253	GAA	.	.		0.478	HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1			A	21679444	C	A	21679444	4	1	69	1	0	0	0	0	0	1	0	0	7271	835	29	3	65	3	HNRNPC	14	21679444	Nonsense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10		21679444	85670096	87	8892										
LTBP2	4053	hgsc.bcm.edu	37	chr14	75016623	75016623	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ccagaaggctcccacactgcCacagcagtcctcctgggtag	10	16	0	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr14:75016623C>A	ENST00000261978.4	-	8	2118	c.1732G>T	c.(1732-1734)Ggc>Tgc	p.G578C	LTBP2_ENST00000556690.1_Missense_Mutation_p.G578C|LTBP2_ENST00000557425.1_5'UTR|CTD-2207P18.1_ENST00000554552.1_lincRNA	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	578	TB 1.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CCCACACTGCCACAGCAGTCC	0.622																																					p.G578C		Atlas-SNP	.											.	LTBP2	158	.	0			c.G1732T						.						111	96	101					14																	75016623		2203	4300	6503	SO:0001583	missense	4053	exon8			CACTGCCACAGCA		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.1732G>T	chr14.hg19:g.75016623C>A	ENSP00000261978:p.Gly578Cys	154.0	0.0		79.0	31.0	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	hg19	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.340642	0.81911	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	D;D	0.84298	-1.83;-1.83	5.61	4.72	0.59763	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.42964	D	0.000640	D	0.90345	0.6979	M	0.69823	2.125	0.48696	D	0.999692	D	0.76494	0.999	D	0.70016	0.967	D	0.89024	0.3437	10	0.31617	T	0.26	.	12.9331	0.58299	0.0:0.9251:0.0:0.0749	.	578	Q14767	LTBP2_HUMAN	C	578	ENSP00000261978:G578C;ENSP00000451477:G578C	ENSP00000261978:G578C	G	-	1	0	LTBP2	74086376	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	5.559000	0.67326	1.521000	0.48983	0.655000	0.94253	GGC	.	.		0.622	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		A	75016623	C	A	75016623	3	1	69	1	0	0	0	0	1	0	0	0	9083	594	21	3	3849	3	LTBP2	14	75016623	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	53337179	75016623	32332917	88	8893										
MLH3	27030	hgsc.bcm.edu	37	chr14	75515470	75515470	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	atagagttctggggtagaccGgtgccgaagacttgaattca	13	7	2	4			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr14:75515470G>A	ENST00000556740.1	-	1	924	c.889C>T	c.(889-891)Cgg>Tgg	p.R297W	MLH3_ENST00000355774.2_Missense_Mutation_p.R297W|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000238662.7_Missense_Mutation_p.R297W|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000556257.1_Missense_Mutation_p.R297W			Q9UHC1	MLH3_HUMAN	mutL homolog 3	297					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GGGGTAGACCGGTGCCGAAGA	0.398								Mismatch excision repair (MMR)																													p.R297W		Atlas-SNP	.											.	MLH3	200	.	0			c.C889T						.						105	113	110					14																	75515470		2203	4299	6502	SO:0001583	missense	27030	exon2			TAGACCGGTGCCG	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.889C>T	chr14.hg19:g.75515470G>A	ENSP00000452316:p.Arg297Trp	109.0	0.0		58.0	16.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	hg19	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.953462	0.53293	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740	D;D;D;D	0.84442	-1.85;-1.85;-1.85;-1.85	5.8	2.85	0.33270	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, C-terminal (1);	0.123449	0.53938	D	0.000053	D	0.91710	0.7379	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.92559	0.6056	10	0.87932	D	0	-6.8703	15.1529	0.72717	0.0:0.0:0.6313:0.3687	.	297;297	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	W	297	ENSP00000348020:R297W;ENSP00000238662:R297W;ENSP00000451540:R297W;ENSP00000452316:R297W	ENSP00000238662:R297W	R	-	1	2	MLH3	74585223	0.858000	0.29795	0.952000	0.39060	0.684000	0.39900	1.816000	0.38992	0.774000	0.33427	0.655000	0.94253	CGG	.	.		0.398	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		A	75515470	G	A	75515470	3	1	69	1	0	0	0	0	1	0	0	0	9627	1115	39	1	3520	1	MLH3	14	75515470	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	498847	75515470	31834070	89	8894										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24921322	24921322	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gacacccatgctgcctgctcGgaaccccccgaggtttggac	11	16	0	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:24921322G>A	ENST00000329468.2	+	1	782	c.308G>A	c.(307-309)cGg>cAg	p.R103Q		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	103					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CTGCCTGCTCGGAACCCCCCG	0.677																																					p.R103Q		Atlas-SNP	.											C15orf2,colon,carcinoma,0,1	.	.	.	0			c.G308A						.						38	31	33					15																	24921322		2199	4291	6490	SO:0001583	missense	23742	exon1			CTGCTCGGAACCC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.308G>A	chr15.hg19:g.24921322G>A	ENSP00000333735:p.Arg103Gln	39.0	0.0		24.0	11.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	12.22	1.871769	0.33069	.	.	ENSG00000185823	ENST00000329468	T	0.08008	3.14	2.15	-4.3	0.03710	.	.	.	.	.	T	0.13670	0.0331	L	0.38175	1.15	0.09310	N	1	D	0.69078	0.997	D	0.67103	0.949	T	0.05989	-1.0852	9	0.52906	T	0.07	.	7.3249	0.26549	0.2365:0.5849:0.1787:0.0	.	103	Q9NZP6	CO002_HUMAN	Q	103	ENSP00000333735:R103Q	ENSP00000333735:R103Q	R	+	2	0	C15orf2	22472415	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.051000	0.03507	-2.205000	0.00742	-1.483000	0.00984	CGG	.	.		0.677	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24921322	G	A	24921322	3	1	69	1	0	0	0	0	1	0	0	0	1786	1116	39	1	310	1	C15orf2	15	24921322	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		24921322	77610070	90	8895										
HERC2	8924	hgsc.bcm.edu	37	chr15	28518063	28518063	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	agcgtgcctctctgcacagcCagctccagcaggatggccag	12	15	1	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:28518063C>A	ENST00000261609.7	-	8	996	c.888G>T	c.(886-888)ctG>ctT	p.L296L		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TCTGCACAGCCAGCTCCAGCA	0.592																																					p.L296L		Atlas-SNP	.											.	HERC2	501	.	0			c.G888T						.						43	41	42					15																	28518063		2203	4300	6503	SO:0001819	synonymous_variant	8924	exon8			CACAGCCAGCTCC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.888G>T	chr15.hg19:g.28518063C>A		40.0	0.0		24.0	11.0	NM_004667		Silent	SNP	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.592	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28518063	C	A	28518063	2	1	69	1	0	0	0	0	0	0	0	1	7067	581	21	3		3	HERC2	15	28518063	Silent	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	3596741	28518063	74013329	91	8896										
RTF1	23168	hgsc.bcm.edu	37	chr15	41763423	41763423	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ttccttacctgaagaattgaAtcgggttcgattatcacggc	9	9	1	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:41763423A>G	ENST00000389629.4	+	8	1091	c.1079A>G	c.(1078-1080)aAt>aGt	p.N360S		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	360	Plus3. {ECO:0000255|PROSITE- ProRule:PRU00693}.				DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		GAAGAATTGAATCGGGTTCGA	0.438																																					p.N360S		Atlas-SNP	.											.	RTF1	76	.	0			c.A1079G						.						151	147	149					15																	41763423		2203	4300	6503	SO:0001583	missense	23168	exon8			AATTGAATCGGGT	D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"KIAA0252"	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.1079A>G	chr15.hg19:g.41763423A>G	ENSP00000374280:p.Asn360Ser	110.0	0.0		72.0	16.0	NM_015138	Q96BX6	Missense_Mutation	SNP	ENST00000389629.4	hg19	CCDS32200.2	.	.	.	.	.	.	.	.	.	.	A	17.91	3.504255	0.64410	.	.	ENSG00000137815	ENST00000389629	.	.	.	5.87	5.87	0.94306	Plus-3 domain, subgroup (1);Plus-3 (2);	0.000000	0.85682	D	0.000000	T	0.60753	0.2293	N	0.17082	0.46	0.80722	D	1	P	0.49253	0.921	D	0.68353	0.957	T	0.57476	-0.7805	9	0.19147	T	0.46	-25.3025	16.2806	0.82678	1.0:0.0:0.0:0.0	.	360	Q92541	RTF1_HUMAN	S	360	.	ENSP00000374280:N360S	N	+	2	0	RTF1	39550715	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.248000	0.74166	0.533000	0.62120	AAT	.	.		0.438	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138		G	41763423	A	G	41763423	3	3	69	1	0	0	0	0	1	0	0	0	13736	101	4	2	1109	2	RTF1	15	41763423	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	13245360	41763423	60767969	92	8897										
FBN1	2200	hgsc.bcm.edu	37	chr15	48829964	48829964	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gctgagttgtccctggcacaTctggttgctgatcacagtaa	11	10	2	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:48829964T>A	ENST00000316623.5	-	7	1035	c.580A>T	c.(580-582)Atg>Ttg	p.M194L		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	194	TB 1.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CCCTGGCACATCTGGTTGCTG	0.498																																					p.M194L		Atlas-SNP	.											.	FBN1	310	.	0			c.A580T						.						76	77	77					15																	48829964		2197	4296	6493	SO:0001583	missense	2200	exon7			GGCACATCTGGTT	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.580A>T	chr15.hg19:g.48829964T>A	ENSP00000325527:p.Met194Leu	71.0	0.0		72.0	20.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.358987	0.41801	.	.	ENSG00000166147	ENST00000316623;ENST00000544030;ENST00000537463	D;T	0.92446	-3.04;-0.07	5.44	5.44	0.79542	Matrix fibril-associated (3);TGF-beta binding (1);	0.037975	0.85682	D	0.000000	D	0.85940	0.5814	N	0.22421	0.69	0.80722	D	1	B	0.18166	0.026	B	0.25614	0.062	T	0.81123	-0.1076	10	0.10902	T	0.67	.	15.6649	0.77221	0.0:0.0:0.0:1.0	.	194	P35555	FBN1_HUMAN	L	194	ENSP00000325527:M194L;ENSP00000440294:M194L	ENSP00000325527:M194L	M	-	1	0	FBN1	46617256	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.097000	0.71452	2.281000	0.76405	0.533000	0.62120	ATG	.	.		0.498	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48829964	T	A	48829964	3	1	69	1	0	0	0	0	1	0	0	0	5710	1435	50	4	8275	4	FBN1	15	48829964	Missense_Mutation	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10	7066541	48829964	53701428	93	8898										
LYSMD4	145748	hgsc.bcm.edu	37	chr15	100269392	100269392	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	aagtgacggctggcactgcaActgctagtctgggggcttgc	15	10	1	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:100269392A>T	ENST00000409796.1	-	3	889	c.827T>A	c.(826-828)gTt>gAt	p.V276D	LYSMD4_ENST00000604213.1_Intron|LYSMD4_ENST00000545021.1_Missense_Mutation_p.V150D|LYSMD4_ENST00000344791.2_Missense_Mutation_p.V277D|LYSMD4_ENST00000332728.4_Missense_Mutation_p.V276D	NM_001284417.1|NM_001284418.1|NM_001284420.1	NP_001271346.1|NP_001271347.1|NP_001271349.1	Q5XG99	LYSM4_HUMAN	LysM, putative peptidoglycan-binding, domain containing 4	276						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)	10	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)			TGGCACTGCAACTGCTAGTCT	0.527																																					p.V277D		Atlas-SNP	.											.	LYSMD4	21	.	0			c.T830A						.						82	83	83					15																	100269392		2203	4300	6503	SO:0001583	missense	145748	exon6			ACTGCAACTGCTA	BC041097	CCDS10381.1, CCDS66876.1, CCDS66877.1, CCDS73788.1	15q26.3	2005-10-24			ENSG00000183060	ENSG00000183060			26571	protein-coding gene	gene with protein product						12477932	Standard	NM_001284418		Approved	FLJ33008	uc002bvl.3	Q5XG99	OTTHUMG00000149853	ENST00000409796.1:c.827T>A	chr15.hg19:g.100269392A>T	ENSP00000386283:p.Val276Asp	181.0	0.0		138.0	56.0	NM_152449	A6NII6|A8K2N1|Q96LY7	Missense_Mutation	SNP	ENST00000409796.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.29	1.894802	0.33442	.	.	ENSG00000183060	ENST00000409796;ENST00000344791;ENST00000332728;ENST00000545021	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	4.96	0.872	0.19113	.	0.695791	0.13061	N	0.416876	T	0.14485	0.0350	L	0.36672	1.1	0.09310	N	1	P;P	0.35982	0.531;0.531	B;B	0.31686	0.134;0.071	T	0.25641	-1.0126	10	0.87932	D	0	-5.0315	0.7236	0.00944	0.4796:0.1703:0.1858:0.1642	.	277;276	Q5XG99-2;Q5XG99	.;LYSM4_HUMAN	D	276;277;276;150	ENSP00000386283:V276D;ENSP00000342840:V277D;ENSP00000333008:V276D;ENSP00000445357:V150D	ENSP00000333008:V276D	V	-	2	0	LYSMD4	98086915	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.071000	0.11505	0.192000	0.20272	0.528000	0.53228	GTT	.	.		0.527	LYSMD4-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335634.1	NM_152449		T	100269392	A	T	100269392	3	4	69	1	0	0	0	0	1	0	0	0	9136	43	2	4	67	4	LYSMD4	15	100269392	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	51439428	100269392	2262000	94	8899										
AXIN1	8312	hgsc.bcm.edu	37	chr16	348096	348097	+	Frame_Shift_Ins	INS	-	-	A													0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gctgtacgtgctcgtccaggINSatgctctcagggttctcctc							TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr16:348096_348097insA	ENST00000262320.3	-	6	1780_1781	c.1409_1410insT	c.(1408-1410)atcfs	p.I470fs	AXIN1_ENST00000354866.3_Frame_Shift_Ins_p.I470fs|AXIN1_ENST00000481769.1_5'UTR	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	470	Interaction with CTNNB1. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GCTCGTCCAGGATGCTCTCAGG	0.688											OREG0003699	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.I470fs		Atlas-Indel,Pindel	.											.	AXIN1	290	.	0			c.1410_1411insT						.																																			SO:0001589	frameshift_variant	8312	exon6			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1410dupT	chr16.hg19:g.348097_348097dupA	ENSP00000262320:p.Ile470fs	67.0	0.0	587	21.0	14.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Ins	INS	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.688	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	348097	-	A	348096	7	5	69	1	0	1	1	0	0	0	0	0	1236	1164	41	0	1202	0	AXIN1	16	348096	Frame_Shift_Ins	INS	-	TCGA-CC-A5UE-01A-11D-A28X-10		348096	90006657	95	8900										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000420246.2_Missense_Mutation_p.R249S|TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	249.0	2.0		89.0	69.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	69	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10		7577534	73617676	96	8901										
MYH10	4628	hgsc.bcm.edu	37	chr17	8390877	8390877	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	acagcaagcgcccgctgtttCctctcatcctccagctccgc	7	19	1	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:8390877C>T	ENST00000269243.4	-	34	4965	c.4827G>A	c.(4825-4827)agG>agA	p.R1609R	MYH10_ENST00000379980.4_Silent_p.R1625R|MYH10_ENST00000396239.1_Silent_p.R1630R|MYH10_ENST00000360416.3_Silent_p.R1640R	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1609					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CCCGCTGTTTCCTCTCATCCT	0.542																																					p.R1640R		Atlas-SNP	.											.	MYH10	148	.	0			c.G4920A						.						211	214	213					17																	8390877		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon36			CTGTTTCCTCTCA	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.4827G>A	chr17.hg19:g.8390877C>T		58.0	0.0		41.0	29.0	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	hg19	CCDS11144.1																																																																																			.	.		0.542	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			T	8390877	C	T	8390877	2	4	69	1	0	0	0	0	0	0	0	1	10039	854	30	3		3	MYH10	17	8390877	Silent	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	813343	8390877	72804333	97	8902										
RHBDL3	162494	hgsc.bcm.edu	37	chr17	30616004	30616004	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ctacacctgctgccccccacCctggttcatgatcacagtca	6	18	3	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:30616004C>T	ENST00000269051.4	+	4	502	c.488C>T	c.(487-489)cCc>cTc	p.P163L	RHBDL3_ENST00000538145.1_Missense_Mutation_p.P155L|RHBDL3_ENST00000536287.1_Missense_Mutation_p.P65L	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	163						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				TGCCCCCCACCCTGGTTCATG	0.612																																					p.P163L		Atlas-SNP	.											.	RHBDL3	49	.	0			c.C488T						.						58	55	56					17																	30616004		2203	4300	6503	SO:0001583	missense	162494	exon4			CCCCACCCTGGTT	AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"EF-hand domain containing"	16502	protein-coding gene	gene with protein product			"rhomboid, veinlet-like 4 (Drosophila)"	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.488C>T	chr17.hg19:g.30616004C>T	ENSP00000269051:p.Pro163Leu	359.0	0.0		194.0	83.0	NM_138328	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Missense_Mutation	SNP	ENST00000269051.4	hg19	CCDS32613.1	.	.	.	.	.	.	.	.	.	.	C	32	5.187494	0.94923	.	.	ENSG00000141314	ENST00000431505;ENST00000269051;ENST00000538145;ENST00000536287	T;T;T;T	0.14640	2.49;2.49;2.49;2.49	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.42200	0.1192	M	0.76170	2.325	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	T	0.13980	-1.0489	10	0.87932	D	0	-12.0137	20.4239	0.99064	0.0:1.0:0.0:0.0	.	163;155;163	E9PD28;Q495Y5;P58872	.;.;RHBL3_HUMAN	L	163;163;155;65	ENSP00000394849:P163L;ENSP00000269051:P163L;ENSP00000442092:P155L;ENSP00000466508:P65L	ENSP00000269051:P163L	P	+	2	0	RHBDL3	27640117	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.453000	0.80700	2.828000	0.97474	0.655000	0.94253	CCC	.	.		0.612	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328		T	30616004	C	T	30616004	3	4	69	1	0	0	0	0	1	0	0	0	13338	623	22	3	502	3	RHBDL3	17	30616004	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	22225127	30616004	50579206	98	8903										
NKIRAS2	28511	hgsc.bcm.edu	37	chr17	40174597	40174597	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ctatagcacagatagcagagAgtcttttcagcgtgtggagc	12	8	2	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:40174597A>G	ENST00000307641.5	+	3	896	c.275A>G	c.(274-276)gAg>gGg	p.E92G	ZNF385C_ENST00000461831.1_5'Flank|NKIRAS2_ENST00000479407.1_Missense_Mutation_p.S60G|NKIRAS2_ENST00000393884.2_Missense_Mutation_p.E90G|NKIRAS2_ENST00000393885.4_Missense_Mutation_p.E92G|NKIRAS2_ENST00000462043.2_Intron|NKIRAS2_ENST00000449471.4_Intron|NKIRAS2_ENST00000316082.4_Missense_Mutation_p.E92G|NKIRAS2_ENST00000393881.3_Missense_Mutation_p.E92G|NKIRAS2_ENST00000393880.1_Missense_Mutation_p.E92G	NM_001001349.2	NP_001001349.1	Q9NYR9	KBRS2_HUMAN	NFKB inhibitor interacting Ras-like 2	92	Small GTPase-like.				I-kappaB kinase/NF-kappaB signaling (GO:0007249)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	9		all_cancers(22;1.1e-05)|Breast(137;0.000143)|all_epithelial(22;0.000319)				GATAGCAGAGAGTCTTTTCAG	0.547																																					p.E92G		Atlas-SNP	.											.	NKIRAS2	15	.	0			c.A275G						.						81	73	76					17																	40174597		2203	4300	6503	SO:0001583	missense	28511	exon3			GCAGAGAGTCTTT	AF229840	CCDS11415.1, CCDS45679.1, CCDS45680.1	17q21.31	2014-05-09	2004-05-20		ENSG00000168256	ENSG00000168256			17898	protein-coding gene	gene with protein product		604497	"NFKB inhibitor interacting Ras-like protein 2"			10657303	Standard	NM_001001349		Approved	KBRAS2, DKFZP434N1526, kappaB-Ras2	uc002hys.3	Q9NYR9	OTTHUMG00000133503	ENST00000307641.5:c.275A>G	chr17.hg19:g.40174597A>G	ENSP00000303580:p.Glu92Gly	91.0	0.0		45.0	23.0	NM_001144927	A6NCZ5|B3KNN0|B4DNM3|Q6PK52|Q96KC7|Q9NSX1	Missense_Mutation	SNP	ENST00000307641.5	hg19	CCDS11415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.4|22.4	4.280799|4.280799	0.80692|0.80692	.|.	.|.	ENSG00000168256|ENSG00000168256	ENST00000307641;ENST00000393884;ENST00000393880;ENST00000393881;ENST00000393885;ENST00000316082|ENST00000449471	T;T;T;T;T;T|.	0.80994|.	-1.44;-1.44;-1.44;-1.44;-1.44;-0.4|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Small GTP-binding protein domain (1);|.	0.045277|.	0.85682|.	D|.	0.000000|.	T|T	0.53981|0.53981	0.1830|0.1830	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D|B	0.53885|0.21381	0.963|0.055	P|B	0.55260|0.29942	0.772|0.109	T|T	0.48980|0.48980	-0.8986|-0.8986	9|6	0.54805|.	T|.	0.06|.	-12.6837|-12.6837	15.7679|15.7679	0.78141|0.78141	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	92|60	Q9NYR9|E9PAZ8	KBRS2_HUMAN|.	G|G	92;90;92;92;92;92|60	ENSP00000303580:E92G;ENSP00000377462:E90G;ENSP00000377458:E92G;ENSP00000377459:E92G;ENSP00000377463:E92G;ENSP00000312773:E92G|.	ENSP00000303580:E92G|.	E|S	+|+	2|1	0|0	NKIRAS2|NKIRAS2	37428123|37428123	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.339000|0.339000	0.28857|0.28857	9.339000|9.339000	0.96797|0.96797	2.194000|2.194000	0.70268|0.70268	0.477000|0.477000	0.44152|0.44152	GAG|AGT	.	.		0.547	NKIRAS2-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257457.1	NM_017595		G	40174597	A	G	40174597	3	3	69	1	0	0	0	0	1	0	0	0	10454	304	11	2	281	2	NKIRAS2	17	40174597	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	9558593	40174597	41020613	99	8904										
CRHR1	1394	hgsc.bcm.edu	37	chr17	43861914	43861914	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gccgagcgagcccgaggatgGgagggcacccgcagctccgt	17	14	0	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:43861914G>T	ENST00000398285.3	+	1	4	c.4G>T	c.(4-6)Gga>Tga	p.G2*	CRHR1_ENST00000339069.5_Intron|CRHR1_ENST00000293493.7_Intron|RP11-105N13.4_ENST00000587305.1_RNA|CRHR1_ENST00000314537.5_Nonsense_Mutation_p.G2*|CRHR1_ENST00000577353.1_Nonsense_Mutation_p.G2*|CRHR1_ENST00000352855.5_Nonsense_Mutation_p.G2*	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	2					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CCCGAGGATGGGAGGGCACCC	0.766																																					p.G2X	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.G4T						.						7	12	10					17																	43861914		1850	4016	5866	SO:0001587	stop_gained	1394	exon1			AGGATGGGAGGGC	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"GPCR / Class B : Corticotropin-releasing factor receptors"	2357	protein-coding gene	gene with protein product	"corticotropin-releasing factor receptor"	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.4G>T	chr17.hg19:g.43861914G>T	ENSP00000381333:p.Gly2*	74.0	0.0		31.0	15.0	NM_001145148	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Nonsense_Mutation	SNP	ENST00000398285.3	hg19	CCDS45712.1	.	.	.	.	.	.	.	.	.	.	G	38	7.270165	0.98179	.	.	ENSG00000120088	ENST00000398285;ENST00000314537;ENST00000347197;ENST00000352855	.	.	.	3.01	3.01	0.34805	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	9.657	0.39932	0.0:0.0:1.0:0.0	.	.	.	.	X	2	.	ENSP00000326060:G2X	G	+	1	0	CRHR1	41217677	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	1.690000	0.37711	1.714000	0.51371	0.442000	0.29010	GGA	.	.		0.766	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3			T	43861914	G	T	43861914	4	4	69	1	0	0	0	0	0	1	0	0	3873	1233	43	3	6	3	CRHR1	17	43861914	Nonsense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	3687317	43861914	37333296	100	8905										
ITGA3	3675	hgsc.bcm.edu	37	chr17	48149396	48149396	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	cctactacttcgagaggaaaGaggaagtagggggtgccatc	14	8	0	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:48149396G>T	ENST00000320031.8	+	7	1336	c.1006G>T	c.(1006-1008)Gag>Tag	p.E336*	ITGA3_ENST00000007722.7_Nonsense_Mutation_p.E336*|ITGA3_ENST00000544892.1_Nonsense_Mutation_p.E111*	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	336					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						CGAGAGGAAAGAGGAAGTAGG	0.582																																					p.E336X		Atlas-SNP	.											.	ITGA3	128	.	0			c.G1006T						.						79	65	70					17																	48149396		2203	4300	6503	SO:0001587	stop_gained	3675	exon7			AGGAAAGAGGAAG	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"CD molecules", "Integrins"	6139	protein-coding gene	gene with protein product		605025	"antigen identified by monoclonal antibody J143"	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.1006G>T	chr17.hg19:g.48149396G>T	ENSP00000315190:p.Glu336*	213.0	0.0		155.0	68.0	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Nonsense_Mutation	SNP	ENST00000320031.8	hg19	CCDS11558.1	.	.	.	.	.	.	.	.	.	.	G	39	7.379660	0.98248	.	.	ENSG00000005884	ENST00000544892;ENST00000007722;ENST00000538917;ENST00000320031	.	.	.	5.55	3.57	0.40892	.	0.196127	0.53938	D	0.000055	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	10.7526	0.46217	0.1567:0.0:0.8433:0.0	.	.	.	.	X	111;336;322;336	.	ENSP00000007722:E336X	E	+	1	0	ITGA3	45504395	0.897000	0.30589	0.874000	0.34290	0.389000	0.30415	1.705000	0.37867	1.351000	0.45789	0.563000	0.77884	GAG	.	.		0.582	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		T	48149396	G	T	48149396	4	4	69	1	0	0	0	0	0	1	0	0	7886	943	33	3	1032	3	ITGA3	17	48149396	Nonsense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	4287482	48149396	33045814	101	8906										
MED13	9969	hgsc.bcm.edu	37	chr17	60024306	60024306	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	atctgaagtctgatttgagtCaagtgggtgggagtgtttac	14	4	3	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:60024306C>G	ENST00000397786.2	-	29	6440	c.6364G>C	c.(6364-6366)Gac>Cac	p.D2122H		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	2122					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TGATTTGAGTCAAGTGGGTGG	0.398																																					p.D2122H		Atlas-SNP	.											.	MED13	181	.	0			c.G6364C						.						175	179	178					17																	60024306		1968	4164	6132	SO:0001583	missense	9969	exon29			TTGAGTCAAGTGG	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.6364G>C	chr17.hg19:g.60024306C>G	ENSP00000380888:p.Asp2122His	125.0	0.0		168.0	27.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.896684	0.91962	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	D	0.83506	-1.73	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	D	0.92525	0.7626	M	0.86651	2.83	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93627	0.6953	10	0.87932	D	0	-9.3552	18.9301	0.92561	0.0:1.0:0.0:0.0	.	2122	Q9UHV7	MED13_HUMAN	H	2122;2121	ENSP00000380888:D2122H	ENSP00000262436:D2121H	D	-	1	0	MED13	57379088	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.429000	0.80309	2.464000	0.83262	0.467000	0.42956	GAC	.	.		0.398	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		G	60024306	C	G	60024306	3	3	69	1	0	0	0	0	1	0	0	0	9439	826	29	4	168	4	MED13	17	60024306	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	11874910	60024306	21170904	102	8907										
USH1G	124590	hgsc.bcm.edu	37	chr17	72916210	72916210	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	caggcccgagagcgagcgggCgctcttgcgcccatcctcgg	15	16	1	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:72916210C>A	ENST00000319642.1	-	2	903	c.721G>T	c.(721-723)Gcc>Tcc	p.A241S		NM_001282489.1|NM_173477.2	NP_001269418.1|NP_775748.2	Q495M9	USH1G_HUMAN	Usher syndrome 1G (autosomal recessive)	241					equilibrioception (GO:0050957)|inner ear morphogenesis (GO:0042472)|inner ear receptor cell differentiation (GO:0060113)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	spectrin binding (GO:0030507)		HN1/USH1G(2)	endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14	all_lung(278;0.172)|Lung NSC(278;0.207)					AGCGAGCGGGCGCTCTTGCGC	0.692																																					p.A241S		Atlas-SNP	.											.	USH1G	40	.	0			c.G721T						.						36	41	39					17																	72916210		2201	4279	6480	SO:0001583	missense	124590	exon2			AGCGGGCGCTCTT	AK091243	CCDS32725.1	17q25.1	2013-01-10			ENSG00000182040	ENSG00000182040		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	16356	protein-coding gene	gene with protein product		607696				12588794	Standard	NM_001282489		Approved	Sans, FLJ33924, ANKS4A	uc002jme.1	Q495M9	OTTHUMG00000178864	ENST00000319642.1:c.721G>T	chr17.hg19:g.72916210C>A	ENSP00000320076:p.Ala241Ser	32.0	0.0		39.0	28.0	NM_173477	Q8N251	Missense_Mutation	SNP	ENST00000319642.1	hg19	CCDS32725.1	.	.	.	.	.	.	.	.	.	.	C	10.27	1.302940	0.23736	.	.	ENSG00000182040	ENST00000319642	T	0.70045	-0.45	3.68	2.7	0.31948	.	0.154968	0.42172	D	0.000741	T	0.42765	0.1217	N	0.08118	0	0.25320	N	0.98913	B	0.09022	0.002	B	0.12156	0.007	T	0.22661	-1.0210	10	0.22109	T	0.4	-23.5737	11.8892	0.52620	0.0:0.9078:0.0:0.0922	.	241	Q495M9	USH1G_HUMAN	S	241	ENSP00000320076:A241S	ENSP00000320076:A241S	A	-	1	0	USH1G	70427805	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	4.718000	0.61930	2.075000	0.62263	0.485000	0.47835	GCC	.	.		0.692	USH1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443676.1	NM_173477		A	72916210	C	A	72916210	3	1	69	1	0	0	0	0	1	0	0	0	17050	768	27	1	672	1	USH1G	17	72916210	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	12891904	72916210	8279000	103	8908										
LRRC45	201255	hgsc.bcm.edu	37	chr17	79988573	79988573	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ctgcggctccgggaggcggaGatcgcccgcatccgggacga	17	14	0	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:79988573G>C	ENST00000306688.3	+	17	2247	c.1905G>C	c.(1903-1905)gaG>gaC	p.E635D	RAC3_ENST00000306897.4_5'Flank	NM_144999.2	NP_659436.1	Q96CN5	LRC45_HUMAN	leucine rich repeat containing 45	635						centrosome (GO:0005813)				lung(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	5	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GGGAGGCGGAGATCGCCCGCA	0.701																																					p.E635D		Atlas-SNP	.											.	LRRC45	22	.	0			c.G1905C						.						8	11	10					17																	79988573		2130	4212	6342	SO:0001583	missense	201255	exon17			GGCGGAGATCGCC	BC014109	CCDS11797.1	17q25.3	2005-08-09				ENSG00000169683			28302	protein-coding gene	gene with protein product						12477932	Standard	NM_144999		Approved	MGC20806	uc002kde.3	Q96CN5		ENST00000306688.3:c.1905G>C	chr17.hg19:g.79988573G>C	ENSP00000306760:p.Glu635Asp	72.0	0.0		74.0	49.0	NM_144999		Missense_Mutation	SNP	ENST00000306688.3	hg19	CCDS11797.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.092972	0.56075	.	.	ENSG00000169683	ENST00000306688	T	0.45276	0.9	4.5	2.49	0.30216	.	0.070853	0.56097	D	0.000036	T	0.24160	0.0585	N	0.24115	0.695	0.38100	D	0.93724	B	0.17465	0.022	B	0.14578	0.011	T	0.08146	-1.0736	9	.	.	.	-20.4498	7.3647	0.26766	0.1596:0.1385:0.7019:0.0	.	635	Q96CN5	LRC45_HUMAN	D	635	ENSP00000306760:E635D	.	E	+	3	2	LRRC45	77581862	1.000000	0.71417	0.134000	0.22075	0.989000	0.77384	2.128000	0.42045	0.514000	0.28300	0.491000	0.48974	GAG	.	.		0.701	LRRC45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442058.1	NM_144999		C	79988573	G	C	79988573	3	2	69	1	0	0	0	0	1	0	0	0	9011	933	33	4	1971	4	LRRC45	17	79988573	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	7072363	79988573	1206637	104	8909										
DCC	1630	hgsc.bcm.edu	37	chr18	50923774	50923774	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	taacaaaaaacagaaggtccAgtacttggagcatgactgca	9	8	0	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr18:50923774A>T	ENST00000442544.2	+	18	3401	c.2785A>T	c.(2785-2787)Agt>Tgt	p.S929C	DCC_ENST00000581580.1_Missense_Mutation_p.S564C|DCC_ENST00000412726.1_Missense_Mutation_p.S757C	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	929	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CAGAAGGTCCAGTACTTGGAG	0.438																																					p.S929C		Atlas-SNP	.											.	DCC	360	.	0			c.A2785T						.						123	105	111					18																	50923774		2203	4300	6503	SO:0001583	missense	1630	exon18			AGGTCCAGTACTT	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.2785A>T	chr18.hg19:g.50923774A>T	ENSP00000389140:p.Ser929Cys	87.0	0.0		73.0	20.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	A	15.21	2.766314	0.49574	.	.	ENSG00000187323	ENST00000442544;ENST00000412726	T;T	0.60672	0.17;0.17	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.80449	0.4625	M	0.89785	3.06	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.84390	0.0554	10	0.66056	D	0.02	.	15.1301	0.72517	1.0:0.0:0.0:0.0	.	757;757;929	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	C	929;757	ENSP00000389140:S929C;ENSP00000397322:S757C	ENSP00000397322:S757C	S	+	1	0	DCC	49177772	1.000000	0.71417	0.958000	0.39756	0.971000	0.66376	9.220000	0.95180	2.213000	0.71641	0.528000	0.53228	AGT	.	.		0.438	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	50923774	A	T	50923774	3	4	69	1	0	0	0	0	1	0	0	0	4284	188	7	4	2855	4	DCC	18	50923774	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10		50923774	27153474	105	8910										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11096863	11096863	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gtgggctgacctttctctgcAggttacccctcgcccctggg	12	15	1	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:11096863A>T	ENST00000429416.3	+	5	636		c.e5-1		SMARCA4_ENST00000541122.2_Splice_Site|SMARCA4_ENST00000413806.3_Splice_Site|SMARCA4_ENST00000344626.4_Splice_Site|SMARCA4_ENST00000358026.2_Splice_Site|SMARCA4_ENST00000590574.1_Splice_Site|SMARCA4_ENST00000450717.3_Splice_Site|SMARCA4_ENST00000589677.1_Splice_Site|SMARCA4_ENST00000444061.3_Splice_Site	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4						aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CTTTCTCTGCAGGTTACCCCT	0.607			"F, N, Mis"		NSCLC																																.		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.356-2A>T						.						42	42	42					19																	11096863		2203	4299	6502	SO:0001630	splice_region_variant	6597	exon4			CTCTGCAGGTTAC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.356-1A>T	chr19.hg19:g.11096863A>T		87.0	0.0		34.0	25.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Splice_Site	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	17.06	3.292810	0.60086	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	.	.	.	4.43	4.43	0.53597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8185	0.57679	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMARCA4	10957863	1.000000	0.71417	0.992000	0.48379	0.711000	0.40976	4.620000	0.61226	1.868000	0.54150	0.379000	0.24179	.	.	.		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	Intron	T	11096863	A	T	11096863	5	4	69	1	0	0	0	0	0	0	1	0	14785	202	7	4	364	4	SMARCA4	19	11096863	Splice_Site	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10		11096863	48032120	106	8911										
PLD3	23646	hgsc.bcm.edu	37	chr19	40872522	40872522	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tgtccccatccccagctgaaGgtgcctgcagaggagcccgc	12	16	0	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:40872522G>T	ENST00000409587.1	+	4	430	c.33G>T	c.(31-33)aaG>aaT	p.K11N	PLD3_ENST00000409419.1_Missense_Mutation_p.K11N|PLD3_ENST00000356508.5_Missense_Mutation_p.K11N|PLD3_ENST00000409281.1_Missense_Mutation_p.K11N|PLD3_ENST00000409735.4_Missense_Mutation_p.K11N			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	11					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			CCCAGCTGAAGGTGCCTGCAG	0.632																																					p.K11N		Atlas-SNP	.											.	PLD3	71	.	0			c.G33T						.						53	60	57					19																	40872522		2203	4300	6503	SO:0001583	missense	23646	exon4			GCTGAAGGTGCCT	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"phospholipase D3"			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.33G>T	chr19.hg19:g.40872522G>T	ENSP00000387050:p.Lys11Asn	69.0	0.0		44.0	25.0	NM_012268	Q92853|Q9BW87	Missense_Mutation	SNP	ENST00000409587.1	hg19	CCDS33027.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.300667	0.60195	.	.	ENSG00000105223	ENST00000392032;ENST00000409419;ENST00000409587;ENST00000356508;ENST00000536031;ENST00000409735;ENST00000409281;ENST00000359274	T;T;T;T;T;T;T	0.53206	0.63;0.78;0.78;0.78;0.78;0.78;0.67	4.39	3.36	0.38483	.	0.415050	0.25484	N	0.030344	T	0.49881	0.1583	N	0.22421	0.69	0.44711	D	0.997706	D;D	0.89917	1.0;0.981	D;D	0.83275	0.996;0.95	T	0.48175	-0.9058	10	0.48119	T	0.1	-12.0868	8.3596	0.32351	0.1049:0.0:0.8951:0.0	.	11;11	B4DEL6;Q8IV08	.;PLD3_HUMAN	N	11	ENSP00000375886:K11N;ENSP00000386293:K11N;ENSP00000387050:K11N;ENSP00000348901:K11N;ENSP00000386938:K11N;ENSP00000387022:K11N;ENSP00000352220:K11N	ENSP00000348901:K11N	K	+	3	2	PLD3	45564362	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	2.007000	0.40883	1.441000	0.47550	0.655000	0.94253	AAG	.	.		0.632	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268		T	40872522	G	T	40872522	3	4	69	1	0	0	0	0	1	0	0	0	12056	991	35	3	39	3	PLD3	19	40872522	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	29775659	40872522	18256461	107	8912										
HNRNPUL1	11100	hgsc.bcm.edu	37	chr19	41807519	41807519	+	Frame_Shift_Del	DEL	C	C	-													0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gcaaagctattgtaatttgtCccactgacgaggacctaaaa							TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:41807519delC	ENST00000392006.3	+	11	1770	c.1597delC	c.(1597-1599)cccfs	p.P533fs	HNRNPUL1_ENST00000602130.1_Frame_Shift_Del_p.P533fs|HNRNPUL1_ENST00000595018.1_Frame_Shift_Del_p.P433fs|HNRNPUL1_ENST00000352456.3_Frame_Shift_Del_p.P433fs|HNRNPUL1_ENST00000378215.4_Frame_Shift_Del_p.P419fs|HNRNPUL1_ENST00000593587.1_Frame_Shift_Del_p.P433fs|HNRNPUL1_ENST00000263367.3_Frame_Shift_Del_p.P444fs	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	533	Necessary for interaction with BRD7 and transcriptional activation.|Necessary for interaction with TP53.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						TGTAATTTGTCCCACTGACGA	0.448																																					p.C532fs		Pindel	.											.	HNRNPUL1	73	.	0			c.1596delT						.						149	132	138					19																	41807519		2203	4300	6503	SO:0001589	frameshift_variant	11100	exon11			.	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"E1B 55kDa associated protein 5"	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.1597delC	chr19.hg19:g.41807519delC	ENSP00000375863:p.Pro533fs	103.0	0.0		67.0	28.0	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Frame_Shift_Del	DEL	ENST00000392006.3	hg19	CCDS12576.1																																																																																			.	.		0.448	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040		-	41807519	C	-	41807519	7	5	69	1	0	1	0	1	0	0	0	0	7283	855	30	0	1639	0	HNRNPUL1	19	41807519	Frame_Shift_Del	DEL	C	TCGA-CC-A5UE-01A-11D-A28X-10	934997	41807519	17321464	108	8913										
ZNF223	7766	hgsc.bcm.edu	37	chr19	44571032	44571032	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ataattgtaaagaatgtgggAagagcttcagacggtcctcc	11	7	1	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:44571032A>G	ENST00000434772.3	+	5	1306	c.1051A>G	c.(1051-1053)Aag>Gag	p.K351E	ZNF223_ENST00000591793.1_Missense_Mutation_p.K461E	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				AGAATGTGGGAAGAGCTTCAG	0.438																																					p.K351E		Atlas-SNP	.											.	ZNF223	61	.	0			c.A1051G						.						101	104	103					19																	44571032		2203	4300	6503	SO:0001583	missense	7766	exon5			TGTGGGAAGAGCT	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"Zinc fingers, C2H2-type", "-"	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.1051A>G	chr19.hg19:g.44571032A>G	ENSP00000401947:p.Lys351Glu	124.0	0.0		96.0	36.0	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Missense_Mutation	SNP	ENST00000434772.3	hg19	CCDS12635.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.945120	0.92593	.	.	ENSG00000178386	ENST00000434772	T	0.27104	1.69	2.46	2.46	0.29980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49474	0.1559	M	0.82517	2.595	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	T	0.53107	-0.8485	9	0.66056	D	0.02	.	9.5423	0.39260	1.0:0.0:0.0:0.0	.	351	Q9UK11	ZN223_HUMAN	E	351	ENSP00000401947:K351E	ENSP00000401947:K351E	K	+	1	0	ZNF223	49262872	0.951000	0.32395	0.041000	0.18516	0.972000	0.66771	2.519000	0.45546	1.118000	0.41863	0.260000	0.18958	AAG	.	.		0.438	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2			G	44571032	A	G	44571032	3	3	69	1	0	0	0	0	1	0	0	0	17792	247	9	2	1065	2	ZNF223	19	44571032	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10	2763513	44571032	14557951	109	8914										
VASP	7408	hgsc.bcm.edu	37	chr19	46021343	46021343	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gcatggccagtgccctagagGcgttggaaggtcagaaatgg	16	8	1	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:46021343G>T	ENST00000245932.6	+	3	690	c.334G>T	c.(334-336)Gcg>Tcg	p.A112S	VASP_ENST00000586619.1_3'UTR	NM_003370.3	NP_003361.1	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein	112	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|neural tube closure (GO:0001843)|positive regulation of actin filament polymerization (GO:0030838)|protein homotetramerization (GO:0051289)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	profilin binding (GO:0005522)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)	18		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		TGCCCTAGAGGCGTTGGAAGG	0.642																																					p.A112S		Atlas-SNP	.											.	VASP	26	.	0			c.G334T						.						24	26	25					19																	46021343		2203	4299	6502	SO:0001583	missense	7408	exon3			CTAGAGGCGTTGG		CCDS33051.1	19q13.32	2012-02-22			ENSG00000125753	ENSG00000125753			12652	protein-coding gene	gene with protein product		601703				8812448	Standard	XM_005259199		Approved		uc002pcg.3	P50552		ENST00000245932.6:c.334G>T	chr19.hg19:g.46021343G>T	ENSP00000245932:p.Ala112Ser	148.0	0.0		68.0	26.0	NM_003370	B2RBT9|Q6PIZ1|Q93035	Missense_Mutation	SNP	ENST00000245932.6	hg19	CCDS33051.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.537725	0.65085	.	.	ENSG00000125753	ENST00000245932	T	0.42513	0.97	4.89	3.84	0.44239	EVH1 (1);Pleckstrin homology-type (1);	0.064889	0.64402	D	0.000011	T	0.21387	0.0515	N	0.08118	0	0.45284	D	0.998281	B	0.10296	0.003	B	0.19946	0.027	T	0.05566	-1.0877	10	0.08179	T	0.78	-12.0642	12.5819	0.56394	0.0:0.0:0.8323:0.1677	.	112	P50552	VASP_HUMAN	S	112	ENSP00000245932:A112S	ENSP00000245932:A112S	A	+	1	0	VASP	50713183	0.985000	0.35326	0.984000	0.44739	0.900000	0.52787	2.737000	0.47393	1.173000	0.42796	-0.181000	0.13052	GCG	.	.		0.642	VASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459589.1			T	46021343	G	T	46021343	3	4	69	1	0	0	0	0	1	0	0	0	17143	1203	42	3	344	3	VASP	19	46021343	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	1450311	46021343	13107640	110	8915										
PPP2R1A	5518	hgsc.bcm.edu	37	chr19	52714742	52714742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tgctgtgaaggcggaacttcGacagtgagtctctgcctcct	12	11	1	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:52714742G>A	ENST00000322088.6	+	4	558	c.500G>A	c.(499-501)cGa>cAa	p.R167Q	PPP2R1A_ENST00000462990.1_5'UTR|PPP2R1A_ENST00000444322.2_Missense_Mutation_p.R112Q|PPP2R1A_ENST00000473455.2_3'UTR	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha	167	PP2A subunit B binding.|Polyoma small and medium T antigens Binding.|SV40 small T antigen binding.				apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		GCGGAACTTCGACAGTGAGTC	0.617			Mis		clear cell ovarian carcinoma																																p.R167Q		Atlas-SNP	.		Dom?	yes		19	19q13.41	5518	"protein phosphatase 2, regulatory subunit A, alpha"		E	.	PPP2R1A	187	.	0			c.G500A						.						52	49	50					19																	52714742		2203	4300	6503	SO:0001583	missense	5518	exon4			AACTTCGACAGTG		CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9302	protein-coding gene	gene with protein product	"protein phosphatase 2A, regulatory subunit A, alpha isoform", "protein phosphatase 2, 65kDa regulatory subunit A"	605983	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform"				Standard	NR_033500		Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.500G>A	chr19.hg19:g.52714742G>A	ENSP00000324804:p.Arg167Gln	36.0	0.0		43.0	16.0	NM_014225	Q13773|Q6ICQ3|Q96DH3	Missense_Mutation	SNP	ENST00000322088.6	hg19	CCDS12849.1	.	.	.	.	.	.	.	.	.	.	G	34	5.307079	0.95629	.	.	ENSG00000105568	ENST00000423369;ENST00000391791;ENST00000322088;ENST00000444322	T;T	0.06687	3.27;3.27	4.58	4.58	0.56647	Armadillo-like helical (1);Armadillo-type fold (1);	0.123358	0.33553	N	0.004795	T	0.39759	0.1090	H	0.94620	3.56	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.916;0.991;0.991	T	0.55016	-0.8206	10	0.87932	D	0	-1.3519	15.2851	0.73822	0.0:0.0:1.0:0.0	.	112;167;167	F5H3X9;A8K7B7;P30153	.;.;2AAA_HUMAN	Q	157;87;167;112	ENSP00000324804:R167Q;ENSP00000415067:R112Q	ENSP00000324804:R167Q	R	+	2	0	PPP2R1A	57406554	1.000000	0.71417	0.979000	0.43373	0.989000	0.77384	8.532000	0.90613	2.547000	0.85894	0.655000	0.94253	CGA	.	.		0.617	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267967.2	NM_014225		A	52714742	G	A	52714742	3	1	69	1	0	0	0	0	1	0	0	0	12394	1058	37	1	514	1	PPP2R1A	19	52714742	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	6693399	52714742	6414241	111	8916										
ZNF534	147658	hgsc.bcm.edu	37	chr19	52941617	52941617	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	agaagccttacaaatgtagtGaatgtggcaaagcatttagt	10	5	0	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:52941617G>T	ENST00000332323.6	+	4	1004	c.943G>T	c.(943-945)Gaa>Taa	p.E315*	ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000433050.1_Nonsense_Mutation_p.E302*	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						CAAATGTAGTGAATGTGGCAA	0.398																																					p.E315X		Atlas-SNP	.											.	ZNF534	105	.	0			c.G943T						.						70	61	64					19																	52941617		1568	3582	5150	SO:0001587	stop_gained	147658	exon4			TGTAGTGAATGTG	AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"Zinc fingers, C2H2-type", "-"	26337	protein-coding gene	gene with protein product			"KRAB domain only 3"	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.943G>T	chr19.hg19:g.52941617G>T	ENSP00000327538:p.Glu315*	122.0	0.0		87.0	28.0	NM_001143939	Q76KX9	Nonsense_Mutation	SNP	ENST00000332323.6	hg19	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.384284	0.42308	.	.	ENSG00000198633	ENST00000332323;ENST00000433050;ENST00000391790	.	.	.	1.82	0.468	0.16732	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	9.1116	0.36732	0.0:0.2272:0.7728:0.0	.	.	.	.	X	315;302;314	.	ENSP00000327538:E315X	E	+	1	0	ZNF534	57633429	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-0.781000	0.04648	0.983000	0.38602	0.467000	0.42956	GAA	.	.		0.398	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512		T	52941617	G	T	52941617	4	4	69	1	0	0	0	0	0	1	0	0	17988	1291	45	3	957	3	ZNF534	19	52941617	Nonsense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	226875	52941617	6187366	112	8917										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35437004	35437004	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gcttcatgaagagcagcaggAagttgtgcttgaattgctgg	14	6	1	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr20:35437004A>G	ENST00000357779.3	-	8	2338	c.2012T>C	c.(2011-2013)tTc>tCc	p.F671S	SOGA1_ENST00000456801.2_Missense_Mutation_p.F512S|SOGA1_ENST00000279034.6_Missense_Mutation_p.F671S|SOGA1_ENST00000237536.4_Missense_Mutation_p.F909S			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	671					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						GAGCAGCAGGAAGTTGTGCTT	0.572											OREG0025909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F909S		Atlas-SNP	.											.	SOGA1	136	.	0			c.T2726C						.						49	54	52					20																	35437004		2009	4168	6177	SO:0001583	missense	140710	exon8			AGCAGGAAGTTGT	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.2012T>C	chr20.hg19:g.35437004A>G	ENSP00000350424:p.Phe671Ser	69.0	0.0	855	51.0	20.0	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	hg19		.	.	.	.	.	.	.	.	.	.	A	24.6	4.546492	0.86022	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.28	5.28	0.74379	.	0.054564	0.85682	D	0.000000	T	0.33323	0.0859	L	0.40543	1.245	0.37256	D	0.906773	P	0.44734	0.842	B	0.37650	0.255	T	0.32428	-0.9907	10	0.29301	T	0.29	-34.8934	14.3227	0.66496	1.0:0.0:0.0:0.0	.	671	O94964-4	.	S	909;671;512;671	ENSP00000237536:F909S;ENSP00000279034:F671S;ENSP00000413886:F512S;ENSP00000350424:F671S	ENSP00000237536:F909S	F	-	2	0	KIAA0889	34870418	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.064000	0.64338	2.216000	0.71823	0.533000	0.62120	TTC	.	.		0.572	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		G	35437004	A	G	35437004	3	3	69	1	0	0	0	0	1	0	0	0	2085	246	9	2	2353	2	C20orf117	20	35437004	Missense_Mutation	SNP	A	TCGA-CC-A5UE-01A-11D-A28X-10		35437004	27588516	113	8918										
WFDC3	140686	hgsc.bcm.edu	37	chr20	44403077	44403077	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	atcagcacagctagggcaccGggatctctgcaagtagaaga	12	10	2	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr20:44403077G>A	ENST00000243938.4	-	7	769	c.686C>T	c.(685-687)cCg>cTg	p.P229L	WFDC3_ENST00000372632.2_Missense_Mutation_p.P135L|WFDC3_ENST00000372630.2_Missense_Mutation_p.P92L|WFDC3_ENST00000481847.1_5'UTR	NM_080614.1	NP_542181.1	Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3	229						extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P229L(1)		endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				CTAGGGCACCGGGATCTctgc	0.498																																					p.P229L		Atlas-SNP	.											WFDC3,NS,carcinoma,0,1	WFDC3	18	.	1	Substitution - Missense(1)	endometrium(1)	c.C686T						.						118	108	111					20																	44403077		2203	4300	6503	SO:0001583	missense	140686	exon7			GGCACCGGGATCT	AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116		"WAP four-disulfide core domain containing"	15957	protein-coding gene	gene with protein product						12206714, 10680116	Standard	NM_080614		Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000243938.4:c.686C>T	chr20.hg19:g.44403077G>A	ENSP00000243938:p.Pro229Leu	70.0	0.0		53.0	12.0	NM_080614	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	Missense_Mutation	SNP	ENST00000243938.4	hg19	CCDS33478.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.45|16.45	3.127840|3.127840	0.56721|0.56721	.|.	.|.	ENSG00000124116|ENSG00000124116	ENST00000243938;ENST00000372630;ENST00000372632|ENST00000337205	T;T;T|.	0.21734|.	1.99;1.99;2.0|.	3.39|3.39	-2.53|-2.53	0.06326|0.06326	.|.	1.482020|.	0.04855|.	N|.	0.443060|.	T|T	0.19644|0.19644	0.0472|0.0472	N|N	0.22421|0.22421	0.69|0.69	0.18873|0.18873	N|N	0.999988|0.999988	B|.	0.12013|.	0.005|.	B|.	0.08055|.	0.003|.	T|T	0.26849|0.26849	-1.0091|-1.0091	10|5	0.59425|.	D|.	0.04|.	0.1205|0.1205	3.6363|3.6363	0.08150|0.08150	0.504:0.0:0.3045:0.1915|0.504:0.0:0.3045:0.1915	.|.	229|.	Q8IUB2|.	WFDC3_HUMAN|.	L|W	229;92;135|223	ENSP00000243938:P229L;ENSP00000361713:P92L;ENSP00000361715:P135L|.	ENSP00000243938:P229L|.	P|R	-|-	2|1	0|2	WFDC3|WFDC3	43836484|43836484	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.767000|0.767000	0.43475|0.43475	-1.356000|-1.356000	0.02609|0.02609	-0.521000|-0.521000	0.06426|0.06426	0.650000|0.650000	0.86243|0.86243	CCG|CGG	.	.		0.498	WFDC3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316858.1			A	44403077	G	A	44403077	3	1	69	1	0	0	0	0	1	0	0	0	17368	1116	39	1	13	1	WFDC3	20	44403077	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	8966073	44403077	18622443	114	8919										
PREX1	57580	hgsc.bcm.edu	37	chr20	47342858	47342858	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gcgggtacttgcagatcctcTggatcggagacaacaggtag	14	9	1	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr20:47342858T>A	ENST00000371941.3	-	5	612	c.590A>T	c.(589-591)cAg>cTg	p.Q197L	PREX1_ENST00000396220.1_Missense_Mutation_p.Q197L	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	197	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GCAGATCCTCTGGATCGGAGA	0.483																																					p.Q197L		Atlas-SNP	.											.	PREX1	441	.	0			c.A590T						.						95	80	85					20																	47342858		2203	4300	6503	SO:0001583	missense	57580	exon5			ATCCTCTGGATCG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.590A>T	chr20.hg19:g.47342858T>A	ENSP00000361009:p.Gln197Leu	187.0	0.0		128.0	57.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	t	31	5.078331	0.94000	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.77358	-1.09;-1.09	5.51	5.51	0.81932	Guanine-nucleotide dissociation stimulator, CDC24, conserved site (1);Dbl homology (DH) domain (5);	0.000000	0.52532	U	0.000077	D	0.91700	0.7376	H	0.95982	3.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94123	0.7381	10	0.87932	D	0	.	14.906	0.70718	0.0:0.0:0.0:1.0	.	197	Q8TCU6	PREX1_HUMAN	L	197	ENSP00000361009:Q197L;ENSP00000379522:Q197L	ENSP00000361009:Q197L	Q	-	2	0	PREX1	46776265	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.292000	0.78731	2.215000	0.71742	0.529000	0.55759	CAG	.	.		0.483	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47342858	T	A	47342858	3	1	69	1	0	0	0	0	1	0	0	0	12488	1580	55	4	4533	4	PREX1	20	47342858	Missense_Mutation	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10	2939781	47342858	15682662	115	8920										
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51872915	51872915	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggtggagcaagagatctcccGggtatcgtcggctcagaggt	16	9	2	2	rs201353411		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr20:51872915G>T	ENST00000371497.5	+	2	3805	c.2918G>T	c.(2917-2919)cGg>cTg	p.R973L	TSHZ2_ENST00000603338.2_Missense_Mutation_p.R970L|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R970L	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	973					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			GAGATCTCCCGGGTATCGTCG	0.488																																					p.R973L		Atlas-SNP	.											TSHZ2,NS,carcinoma,0,1	TSHZ2	209	.	0			c.G2918T						.						75	69	71					20																	51872915		2203	4300	6503	SO:0001583	missense	128553	exon2			TCTCCCGGGTATC	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2918G>T	chr20.hg19:g.51872915G>T	ENSP00000360552:p.Arg973Leu	130.0	1.0		126.0	43.0	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.857789	0.71834	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.15718	2.4;2.4	5.7	5.7	0.88788	.	0.098653	0.64402	D	0.000002	T	0.25419	0.0618	N	0.16478	0.41	0.53005	D	0.999962	D	0.63046	0.992	P	0.57846	0.828	T	0.03829	-1.1000	10	0.87932	D	0	0.2578	19.8272	0.96622	0.0:0.0:1.0:0.0	.	973	Q9NRE2	TSH2_HUMAN	L	973;970;499	ENSP00000360552:R973L;ENSP00000333114:R970L	ENSP00000333114:R970L	R	+	2	0	TSHZ2	51306322	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.860000	0.55995	2.685000	0.91497	0.643000	0.83706	CGG	.	.		0.488	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		T	51872915	G	T	51872915	3	4	69	1	0	0	0	0	1	0	0	0	16639	1116	39	1	2924	1	TSHZ2	20	51872915	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	4530057	51872915	11152605	116	8921										
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57288476	57288476	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ggatctctaccatgccccagGacggtggaaatcaacaacac	9	13	2	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr20:57288476G>A	ENST00000356091.6	+	9	1290	c.1002G>A	c.(1000-1002)aaG>aaA	p.K334K	RP11-261P9.4_ENST00000530479.1_RNA|NPEPL1_ENST00000525967.1_Splice_Site_p.K306K|NPEPL1_ENST00000525817.1_Splice_Site_p.K286K|STX16-NPEPL1_ENST00000530122.1_3'UTR	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	334						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			CATGCCCCAGGACGGTGGAAA	0.607																																					p.K334K		Atlas-SNP	.											.	NPEPL1	36	.	0			c.G1002A						.						34	39	37					20																	57288476		2061	4181	6242	SO:0001630	splice_region_variant	79716	exon9			CCCCAGGACGGTG	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.1002-1G>A	chr20.hg19:g.57288476G>A		159.0	0.0		125.0	53.0	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	hg19	CCDS46621.1																																																																																			.	.		0.607	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	Silent	A	57288476	G	A	57288476	5	1	69	1	0	0	0	0	0	0	1	0	10583	1188	41	3	882	3	NPEPL1	20	57288476	Splice_Site	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	5415561	57288476	5737044	117	8922										
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28217002	28217002	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gcgccaaaaagctgctgtcgGgccgcagctccagatccagc	12	15	0	1			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr21:28217002G>T	ENST00000284984.3	-	1	726	c.272C>A	c.(271-273)cCc>cAc	p.P91H		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	91					heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		GCTGCTGTCGGGCCGCAGCTC	0.692											OREG0026151	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P91H		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.C272A						.						10	12	11					21																	28217002		2190	4278	6468	SO:0001583	missense	9510	exon1			CTGTCGGGCCGCA	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.272C>A	chr21.hg19:g.28217002G>T	ENSP00000284984:p.Pro91His	82.0	0.0	800	56.0	15.0	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	hg19	CCDS33524.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.658283	0.47467	.	.	ENSG00000154734	ENST00000284984	T	0.07800	3.16	4.06	3.18	0.36537	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.11793	0.0287	L	0.56769	1.78	0.58432	D	0.999999	B	0.18166	0.026	B	0.29176	0.099	T	0.04320	-1.0960	9	0.49607	T	0.09	.	11.7641	0.51920	0.0862:0.0:0.9138:0.0	.	91	Q9UHI8	ATS1_HUMAN	H	91	ENSP00000284984:P91H	ENSP00000284984:P91H	P	-	2	0	ADAMTS1	27138873	1.000000	0.71417	0.912000	0.35992	0.236000	0.25371	5.919000	0.70005	0.925000	0.37094	0.555000	0.69702	CCC	.	.		0.692	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			T	28217002	G	T	28217002	3	4	69	1	0	0	0	0	1	0	0	0	255	1232	43	3	2667	3	ADAMTS1	21	28217002	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		28217002	19912893	118	8923										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34100328	34100328	+	5'Flank	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ccgggagcgtcacttccgctCcagcaggcccatctcttccg	10	18	2	0			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr21:34100328C>A	ENST00000322229.7	-	0	0				SYNJ1_ENST00000382499.2_Missense_Mutation_p.W8C|PAXBP1-AS1_ENST00000455170.1_RNA|SYNJ1_ENST00000382491.3_5'Flank|SYNJ1_ENST00000433931.2_Missense_Mutation_p.W8C|PAXBP1-AS1_ENST00000458479.1_RNA|SYNJ1_ENST00000357345.3_5'Flank|PAXBP1-AS1_ENST00000440052.1_RNA			O43426	SYNJ1_HUMAN	synaptojanin 1						cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						CACTTCCGCTCCAGCAGGCCC	0.741											OREG0003584|OREG0003585	type=REGULATORY REGION|Gene=AK056384|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=SYNJ1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.W8C		Atlas-SNP	.											.	SYNJ1	253	.	0			c.G24T						.						3	6	5					21																	34100328		616	1499	2115	SO:0001631	upstream_gene_variant	8867	exon1			TCCGCTCCAGCAG	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926		chr21.hg19:g.34100328C>A	Exception_encountered	12.0	0.0	845	11.0	10.0	NM_203446	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	hg19	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332360	0.81801	.	.	ENSG00000159082	ENST00000382499;ENST00000433931	D;D	0.93488	-3.23;-2.39	4.7	3.74	0.42951	.	.	.	.	.	D	0.85022	0.5602	N	0.08118	0	0.80722	D	1	B	0.27732	0.187	B	0.27170	0.077	D	0.83919	0.0300	9	0.56958	D	0.05	.	11.9699	0.53058	0.173:0.827:0.0:0.0	.	8	C9JFZ1	.	C	8	ENSP00000371939:W8C;ENSP00000409667:W8C	ENSP00000371939:W8C	W	-	3	0	SYNJ1	33022199	0.950000	0.32346	0.997000	0.53966	0.886000	0.51366	1.664000	0.37439	2.322000	0.78497	0.650000	0.86243	TGG	.	.		0.741	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	34100328	C	A	34100328	1	1	69	0	1	0	0	0	0	0	0	0	15467	856	30	3		3	SYNJ1	21	34100328	5'Flank	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	5883326	34100328	14029567	119	8924										
DIP2A	23181	hgsc.bcm.edu	37	chr21	47952072	47952072	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tttccgaatagtgaccctgtGatgttcatggttgcatttta	9	7	1	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr21:47952072G>T	ENST00000417564.2	+	10	1248	c.1227G>T	c.(1225-1227)gtG>gtT	p.V409V	DIP2A_ENST00000435722.3_Silent_p.V409V|DIP2A_ENST00000457905.3_Silent_p.V409V|DIP2A_ENST00000400274.1_Silent_p.V405V|DIP2A_ENST00000318711.7_Silent_p.V410V|DIP2A_ENST00000427143.2_Silent_p.V345V|DIP2A_ENST00000466639.1_Silent_p.V366V			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	409					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GTGACCCTGTGATGTTCATGG	0.418																																					p.V409V		Atlas-SNP	.											.	DIP2A	332	.	0			c.G1227T						.						178	172	174					21																	47952072		1954	4146	6100	SO:0001819	synonymous_variant	23181	exon10			CCCTGTGATGTTC	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.1227G>T	chr21.hg19:g.47952072G>T		153.0	0.0		124.0	76.0	NM_206891	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	hg19	CCDS46655.1																																																																																			.	.		0.418	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		T	47952072	G	T	47952072	2	4	69	1	0	0	0	0	0	0	0	1	4529	1277	45	3		3	DIP2A	21	47952072	Silent	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	13851744	47952072	177823	120	8925										
NEFH	4744	hgsc.bcm.edu	37	chr22	29886676	29886676	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gaaggccacagaagacaaggCcgccaaggggaagtaaggca	15	9	0	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr22:29886676C>A	ENST00000310624.6	+	4	3080	c.3047C>A	c.(3046-3048)gCc>gAc	p.A1016D		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	1022	Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GAAGACAAGGCCGCCAAGGGG	0.498																																					p.A1016D		Atlas-SNP	.											.	NEFH	178	.	0			c.C3047A						.						26	27	27					22																	29886676		2201	4297	6498	SO:0001583	missense	4744	exon4			ACAAGGCCGCCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.3047C>A	chr22.hg19:g.29886676C>A	ENSP00000311997:p.Ala1016Asp	80.0	0.0		65.0	39.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	hg19	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.327626	0.24080	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.89810	-2.57	5.94	4.91	0.64330	.	0.123818	0.37095	N	0.002242	D	0.87525	0.6199	L	0.57536	1.79	0.36312	D	0.857701	D	0.54397	0.966	P	0.44860	0.462	D	0.90671	0.4598	10	0.87932	D	0	.	11.6908	0.51514	0.1396:0.7262:0.1342:0.0	.	1022	P12036	NFH_HUMAN	D	967;1016	ENSP00000311997:A1016D	ENSP00000311997:A1016D	A	+	2	0	NEFH	28216676	0.098000	0.21812	0.939000	0.37840	0.185000	0.23345	1.202000	0.32271	1.504000	0.48704	0.561000	0.74099	GCC	.	.		0.498	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29886676	C	A	29886676	3	1	69	1	0	0	0	0	1	0	0	0	10323	739	26	3	3061	3	NEFH	22	29886676	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10		29886676	21417890	121	8926										
CDC42EP1	11135	hgsc.bcm.edu	37	chr22	37964608	37964608	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gctggccctgccctcggcagGcactggggagcaggctggga	18	13	0	0	rs568152455		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr22:37964608G>T	ENST00000249014.4	+	3	1377	c.957G>T	c.(955-957)agG>agT	p.R319S		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	319					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					CCCTCGGCAGGCACTGGGGAG	0.701																																					p.R319S		Atlas-SNP	.											.	CDC42EP1	53	.	0			c.G957T						.						11	13	12					22																	37964608		2192	4285	6477	SO:0001583	missense	11135	exon3			CGGCAGGCACTGG	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"55 kDa bone marrow stromal/endothelial cell protein", "serum constituent protein"	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.957G>T	chr22.hg19:g.37964608G>T	ENSP00000249014:p.Arg319Ser	132.0	0.0		71.0	27.0	NM_152243	A8K825|Q96GN1	Missense_Mutation	SNP	ENST00000249014.4	hg19	CCDS13949.1	.	.	.	.	.	.	.	.	.	.	G	32	5.151370	0.94645	.	.	ENSG00000128283	ENST00000249014	T	0.34072	1.38	4.81	4.81	0.61882	.	2.233790	0.01933	N	0.041365	T	0.32585	0.0834	L	0.27053	0.805	0.36720	D	0.881119	P	0.38922	0.651	B	0.30943	0.122	T	0.36696	-0.9737	10	0.40728	T	0.16	-25.9918	17.2474	0.87032	0.0:0.0:1.0:0.0	.	319	Q00587	BORG5_HUMAN	S	319	ENSP00000249014:R319S	ENSP00000249014:R319S	R	+	3	2	CDC42EP1	36294554	1.000000	0.71417	0.989000	0.46669	0.335000	0.28730	3.665000	0.54532	2.375000	0.81037	0.561000	0.74099	AGG	.	.		0.701	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243		T	37964608	G	T	37964608	3	4	69	1	0	0	0	0	1	0	0	0	3077	1194	42	3	963	3	CDC42EP1	22	37964608	Missense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10	8077932	37964608	13339958	122	8927										
KCNJ4	3761	hgsc.bcm.edu	37	chr22	38823369	38823377	+	In_Frame_Del	DEL	ACACCAGGA	ACACCAGGA	-													0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	gtggacaatgatgatgggcgAcaccaggaagatgcggtcca							TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	ACACCAGGA	ACACCAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr22:38823369_38823377delACACCAGGA	ENST00000303592.3	-	2	1019_1027	c.761_769delTCCTGGTGT	c.(760-771)ttcctggtgtcg>tcg	p.FLV254del	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	254					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					ATGATGGGCGACACCAGGAAGATGCGGTC	0.603																																					p.254_257del		Atlas-Indel,Pindel	.											.	KCNJ4	74	.	0			c.762_770del						.																																			SO:0001651	inframe_deletion	3761	exon2			.	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.761_769delTCCTGGTGT	chr22.hg19:g.38823369_38823377delACACCAGGA	ENSP00000306497:p.Phe254_Val256del	182.0	0.0		145.0	28.0	NM_004981	Q14D44	In_Frame_Del	DEL	ENST00000303592.3	hg19	CCDS13971.1																																																																																			.	.		0.603	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981		-	38823377	ACACCAGGA	-	38823369	7	5	69	1	0	1	0	1	0	0	0	0	8062	275	10	0	572	0	KCNJ4	22	38823369	In_Frame_Del	DEL	ACACCAGGA	TCGA-CC-A5UE-01A-11D-A28X-10	858761	38823369	12481197	123	8928										
TAF1	6872	hgsc.bcm.edu	37	chrX	70674056	70674056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tactaagactgcccaggagaTtgtgaacgtctgttaccaga	10	9	1	4			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chrX:70674056T>C	ENST00000373790.4	+	33	4838	c.4787T>C	c.(4786-4788)aTt>aCt	p.I1596T	TAF1_ENST00000423759.1_Missense_Mutation_p.I1617T|TAF1_ENST00000449580.1_Missense_Mutation_p.I1596T|TAF1_ENST00000276072.3_Missense_Mutation_p.I1617T|TAF1_ENST00000461764.1_3'UTR	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1596	Interaction with ASF1A and ASF1B.|Protein kinase 2.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GCCCAGGAGATTGTGAACGTC	0.403																																					p.I1617T		Atlas-SNP	.											.	TAF1	439	.	0			c.T4850C						.						85	73	77					X																	70674056		2203	4300	6503	SO:0001583	missense	6872	exon33			AGGAGATTGTGAA		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.4787T>C	chrX.hg19:g.70674056T>C	ENSP00000362895:p.Ile1596Thr	104.0	0.0		78.0	66.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	T	19.71	3.877669	0.72294	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000395779;ENST00000276072	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	4.84	4.84	0.62591	Bromodomain (3);	0.000000	0.85682	D	0.000000	T	0.63224	0.2493	M	0.77712	2.385	0.80722	D	1	D;D;D;D	0.67145	0.988;0.994;0.978;0.996	P;D;P;P	0.69307	0.882;0.963;0.818;0.871	T	0.68522	-0.5386	10	0.87932	D	0	.	12.6958	0.57003	0.0:0.0:0.0:1.0	.	250;1596;1596;1617	A5CVC9;P21675-4;P21675;P21675-2	.;.;TAF1_HUMAN;.	T	1596;1596;1617;302;1617	ENSP00000362895:I1596T;ENSP00000389000:I1596T;ENSP00000406549:I1617T;ENSP00000276072:I1617T	ENSP00000276072:I1617T	I	+	2	0	TAF1	70590781	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.636000	0.74299	1.789000	0.52484	0.345000	0.21793	ATT	.	.		0.403	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		C	70674056	T	C	70674056	3	2	69	1	0	0	0	0	1	0	0	0	15528	1493	52	2	4980	2	TAF1	23	70674056	Missense_Mutation	SNP	T	TCGA-CC-A5UE-01A-11D-A28X-10		70674056	84596504	124	8929										
USP26	83844	hgsc.bcm.edu	37	chrX	132159790	132159790	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	tgagccggtaggtatgatctCccttatcatcatttcttttt	7	9	4	2			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chrX:132159790C>A	ENST00000511190.1	-	6	2928	c.2459G>T	c.(2458-2460)gGa>gTa	p.G820V	USP26_ENST00000370832.1_Missense_Mutation_p.G820V|USP26_ENST00000406273.1_Missense_Mutation_p.G820V	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	820	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					GGTATGATCTCCCTTATCATC	0.383																																					p.G820V	NSCLC(104;342 1621 36940 47097 52632)	Atlas-SNP	.											.	USP26	135	.	0			c.G2459T						.						179	161	167					X																	132159790		2203	4300	6503	SO:0001583	missense	83844	exon1			TGATCTCCCTTAT	AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"Ubiquitin-specific peptidases"	13485	protein-coding gene	gene with protein product		300309	"ubiquitin specific protease 26"			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.2459G>T	chrX.hg19:g.132159790C>A	ENSP00000423390:p.Gly820Val	16.0	0.0		52.0	11.0	NM_031907	B9WRT6|Q5H9H4	Missense_Mutation	SNP	ENST00000511190.1	hg19	CCDS14635.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.623327	0.28889	.	.	ENSG00000134588	ENST00000370832;ENST00000511190;ENST00000406273	T;T;T	0.30182	1.54;1.54;1.54	3.75	-5.55	0.02536	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	3.009010	0.01261	N	0.009165	T	0.42630	0.1211	L	0.46157	1.445	0.09310	N	1	D	0.59767	0.986	P	0.62089	0.898	T	0.55173	-0.8182	10	0.62326	D	0.03	2.8848	7.9187	0.29833	0.0:0.1744:0.1333:0.6923	.	820	Q9BXU7	UBP26_HUMAN	V	820	ENSP00000359869:G820V;ENSP00000423390:G820V;ENSP00000384360:G820V	ENSP00000359869:G820V	G	-	2	0	USP26	131987456	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.215000	0.01222	-1.639000	0.01527	-0.503000	0.04515	GGA	.	.		0.383	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907		A	132159790	C	A	132159790	3	1	69	1	0	0	0	0	1	0	0	0	17072	855	30	3	285	3	USP26	23	132159790	Missense_Mutation	SNP	C	TCGA-CC-A5UE-01A-11D-A28X-10	61485734	132159790	23110770	125	8930										
USP9Y	8287	hgsc.bcm.edu	37	chrY	14951877	14951877	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0317460317460317	4	1	0.81619937694704	1.63239875389408	0.544132917964694	1	1	0	ttgactatgactgggaaagaGaatgtgcaattaaattcaat	9	4	1	3			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chrY:14951877G>T	ENST00000338981.3	+	36	6370	c.5425G>T	c.(5425-5427)Gaa>Taa	p.E1809*	USP9Y_ENST00000426564.2_3'UTR	NM_004654.3	NP_004645.2	O00507	USP9Y_HUMAN	ubiquitin specific peptidase 9, Y-linked	1809	USP.				BMP signaling pathway (GO:0030509)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)	co-SMAD binding (GO:0070410)|cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(8)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CTGGGAAAGAGAATGTGCAAT	0.388																																					p.E1809X		Atlas-SNP	.											.	USP9Y	49	.	0			c.G5425T						.						54	50	51					Y																	14951877		599	1932	2531	SO:0001587	stop_gained	8287	exon36			GAAAGAGAATGTG	Y13618	CCDS14781.1	Yq11.2	2010-04-09	2009-03-17		ENSG00000114374	ENSG00000114374		"Ubiquitin-specific peptidases"	12633	protein-coding gene	gene with protein product	"fat facets-like homolog (Drosophila)"	400005	"ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)"			8922996, 9384609, 19246359	Standard	NM_004654		Approved	DFFRY	uc004fst.1	O00507	OTTHUMG00000036469	ENST00000338981.3:c.5425G>T	chrY.hg19:g.14951877G>T	ENSP00000342812:p.Glu1809*	82.0	0.0		35.0	28.0	NM_004654	O14601	Nonsense_Mutation	SNP	ENST00000338981.3	hg19	CCDS14781.1																																																																																			.	.		0.388	USP9Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088703.2	NM_004654		T	14951877	G	T	14951877	4	4	69	1	0	0	0	0	0	1	0	0	17106	943	33	3	5559	3	USP9Y	24	14951877	Nonsense_Mutation	SNP	G	TCGA-CC-A5UE-01A-11D-A28X-10		14951877	44421689	126	8931										
CROCC	9696	hgsc.bcm.edu	37	chr1	17273389	17273389	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ggcgcggcagggcctggaggGctccctacgagtggcggagc	20	12	0	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:17273389G>T	ENST00000375541.5	+	17	2486	c.2417G>T	c.(2416-2418)gGc>gTc	p.G806V	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GGCCTGGAGGGCTCCCTACGA	0.697																																					p.G806V		Atlas-SNP	.											.	CROCC	185	.	0			c.G2417T						.						15	14	14					1																	17273389		2159	4240	6399	SO:0001583	missense	9696	exon17			TGGAGGGCTCCCT	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2417G>T	chr1.hg19:g.17273389G>T	ENSP00000364691:p.Gly806Val	226.0	0.0		203.0	40.0	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.165929	0.38217	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.09630	2.96	3.35	3.35	0.38373	.	.	.	.	.	T	0.17662	0.0424	L	0.44542	1.39	0.52501	D	0.999953	D;D;D	0.71674	0.998;0.997;0.997	P;P;P	0.62184	0.862;0.899;0.899	T	0.00936	-1.1508	9	0.38643	T	0.18	.	6.674	0.23083	0.1271:0.0:0.8729:0.0	.	669;109;806	A1L0S8;Q5TZA2-2;Q5TZA2	.;.;CROCC_HUMAN	V	806;687	ENSP00000364691:G806V	ENSP00000364691:G806V	G	+	2	0	CROCC	17145976	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	3.046000	0.49846	2.167000	0.68274	0.462000	0.41574	GGC	.	.		0.697	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		T	17273389	G	T	17273389	3	4	70	1	0	0	0	0	1	0	0	0	3895	1203	42	3	2483	3	CROCC	1	17273389	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10		17273389	231977232	1	8932										
TMEM59	9528	hgsc.bcm.edu	37	chr1	54506502	54506502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gtgcgcttgtgaatttctcaTttgcagatctgctgaaatag	10	7	2	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:54506502T>C	ENST00000234831.5	-	6	883	c.634A>G	c.(634-636)Atg>Gtg	p.M212V	TMEM59_ENST00000371348.1_Missense_Mutation_p.M81V|TMEM59_ENST00000371341.1_Missense_Mutation_p.M81V|TMEM59_ENST00000371344.1_Missense_Mutation_p.M81V	NM_004872.3	NP_004863.2	Q9BXS4	TMM59_HUMAN	transmembrane protein 59	212					autophagy (GO:0006914)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of protein glycosylation in Golgi (GO:0090285)|negative regulation of protein processing (GO:0010955)|positive regulation of autophagy (GO:0010508)	extracellular vesicular exosome (GO:0070062)|Golgi cis cisterna (GO:0000137)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			kidney(3)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7						GAATTTCTCATTTGCAGATCT	0.328																																					p.M212V		Atlas-SNP	.											.	TMEM59	28	.	0			c.A634G						.						91	91	91					1																	54506502		2203	4298	6501	SO:0001583	missense	9528	exon6			TTCTCATTTGCAG	AF047439	CCDS586.1	1p32.3	2008-05-14	2005-07-22	2005-07-22	ENSG00000116209	ENSG00000116209			1239	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 8"	C1orf8		9653160	Standard	NM_004872		Approved	HSPC001	uc001cwp.3	Q9BXS4	OTTHUMG00000008437	ENST00000234831.5:c.634A>G	chr1.hg19:g.54506502T>C	ENSP00000234831:p.Met212Val	210.0	0.0		210.0	35.0	NM_004872	B3KQL7|O75393|Q4VBP9|Q5T705|Q96KX7	Missense_Mutation	SNP	ENST00000234831.5	hg19	CCDS586.1	.	.	.	.	.	.	.	.	.	.	T	11.22	1.574744	0.28092	.	.	ENSG00000116209	ENST00000371348;ENST00000371344;ENST00000234831;ENST00000371341;ENST00000371338;ENST00000420738;ENST00000440019;ENST00000452421	T;T	0.39592	1.1;1.07	5.23	2.81	0.32909	.	0.146289	0.64402	D	0.000007	T	0.25158	0.0611	N	0.19112	0.55	0.80722	D	1	B;B;B;B	0.33073	0.396;0.396;0.002;0.007	B;B;B;B	0.35550	0.205;0.205;0.007;0.016	T	0.04621	-1.0938	10	0.39692	T	0.17	-4.9108	5.8473	0.18673	0.1319:0.0:0.2803:0.5878	.	223;223;213;212	E9PGZ9;Q5T704;D3DQ48;Q9BXS4	.;.;.;TMM59_HUMAN	V	81;81;212;81;223;81;81;223	ENSP00000234831:M212V;ENSP00000397772:M223V	ENSP00000234831:M212V	M	-	1	0	TMEM59	54279090	0.987000	0.35691	0.997000	0.53966	0.985000	0.73830	2.054000	0.41335	0.958000	0.37956	0.528000	0.53228	ATG	.	.		0.328	TMEM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023254.2	NM_004872		C	54506502	T	C	54506502	3	2	70	1	0	0	0	0	1	0	0	0	16200	1493	52	2	349	2	TMEM59	1	54506502	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	37233113	54506502	194744119	2	8933										
LRRIQ3	127255	hgsc.bcm.edu	37	chr1	74507591	74507591	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	actggtatccaatttttcatCcacaatttcatcttcagact	3	11	4	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:74507591C>G	ENST00000395089.1	-	6	1023	c.1024G>C	c.(1024-1026)Gat>Cat	p.D342H	LRRIQ3_ENST00000354431.4_Missense_Mutation_p.D342H			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	342										NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						AATTTTTCATCCACAATTTCA	0.308																																					p.D342H		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.G1024C						.						35	35	35					1																	74507591		1815	4038	5853	SO:0001583	missense	127255	exon7			TTTCATCCACAAT	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.1024G>C	chr1.hg19:g.74507591C>G	ENSP00000378524:p.Asp342His	48.0	0.0		60.0	8.0	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	hg19	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.387115	0.42308	.	.	ENSG00000162620	ENST00000395089;ENST00000354431	T;T	0.12984	2.63;2.63	5.21	2.14	0.27477	.	0.533626	0.15733	N	0.247334	T	0.04952	0.0133	L	0.29908	0.895	0.09310	N	1	P	0.44578	0.838	P	0.47206	0.541	T	0.24657	-1.0154	10	0.52906	T	0.07	.	5.5334	0.16997	0.1583:0.6752:0.0:0.1666	.	342	A6PVS8	LRIQ3_HUMAN	H	342	ENSP00000378524:D342H;ENSP00000346414:D342H	ENSP00000346414:D342H	D	-	1	0	LRRIQ3	74280179	0.072000	0.21174	0.001000	0.08648	0.002000	0.02628	0.920000	0.28705	0.710000	0.31997	0.650000	0.86243	GAT	.	.		0.308	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		G	74507591	C	G	74507591	3	3	70	1	0	0	0	0	1	0	0	0	9039	855	30	4	858	4	LRRIQ3	1	74507591	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	20001089	74507591	174743030	3	8934										
TNNI3K	100526835	hgsc.bcm.edu	37	chr1	74737339	74737339	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gagctgatatacagcaggttGgatacggtggcctcactgcc	13	10	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:74737339G>T	ENST00000370899.3	+	7	731	c.694G>T	c.(694-696)Gga>Tga	p.G232*	FPGT-TNNI3K_ENST00000370895.1_Nonsense_Mutation_p.G232*|TNNI3K_ENST00000370891.2_Nonsense_Mutation_p.G232*|TNNI3K_ENST00000326637.3_Nonsense_Mutation_p.G131*|FPGT-TNNI3K_ENST00000557284.2_Nonsense_Mutation_p.G245*	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		ACAGCAGGTTGGATACGGTGG	0.423																																					p.G232X		Atlas-SNP	.											TNNI3K,caecum,carcinoma,0,1	.	.	.	0			c.G694T						.						187	178	181					1																	74737339		2203	4299	6502	SO:0001587	stop_gained	100526835	exon7			CAGGTTGGATACG			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.694G>T	chr1.hg19:g.74737339G>T	ENSP00000359936:p.Gly232*	95.0	0.0		113.0	13.0	NM_001112808		Nonsense_Mutation	SNP	ENST00000370899.3	hg19		.	.	.	.	.	.	.	.	.	.	G	38	6.713695	0.97784	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000557284;ENST00000370891;ENST00000326637	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	18.6094	0.91279	0.0:0.0:1.0:0.0	.	.	.	.	X	232;232;232;232;131	.	ENSP00000322251:G131X	G	+	1	0	RP11-653A5.2;AC093158.1	74509927	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	8.212000	0.89756	2.696000	0.92011	0.655000	0.94253	GGA	.	.		0.423	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			T	74737339	G	T	74737339	4	4	70	1	0	0	0	0	0	1	0	0	16344	1349	47	3	764	3	TNNI3K	1	74737339	Nonsense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	229748	74737339	174513282	4	8935										
CHIA	27159	hgsc.bcm.edu	37	chr1	111861237	111861237	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	aacactggaattggtgccccCacctctggtgctggtcctgc	11	14	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:111861237C>T	ENST00000369740.1	+	9	955	c.852C>T	c.(850-852)ccC>ccT	p.P284P	CHIA_ENST00000343320.6_Silent_p.P284P|CHIA_ENST00000451398.2_Silent_p.P123P|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000483391.1_Silent_p.P123P|CHIA_ENST00000430615.1_Silent_p.P176P|CHIA_ENST00000353665.6_Silent_p.P123P	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	284					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TTGGTGCCCCCACCTCTGGTG	0.532																																					p.P284P		Atlas-SNP	.											.	CHIA	115	.	0			c.C852T						.						147	143	144					1																	111861237		2203	4300	6503	SO:0001819	synonymous_variant	27159	exon9			TGCCCCCACCTCT	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.852C>T	chr1.hg19:g.111861237C>T		157.0	0.0		149.0	27.0	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	hg19	CCDS41368.1																																																																																			.	.		0.532	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			T	111861237	C	T	111861237	2	4	70	1	0	0	0	0	0	0	0	1	3344	581	21	3		3	CHIA	1	111861237	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	37123898	111861237	137389384	5	8936										
LOR	4014	hgsc.bcm.edu	37	chr1	153233779	153233779	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ggctgcttctcctccggtggCggcggctcctccgggggcgg	18	15	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:153233779C>G	ENST00000368742.3	+	2	411	c.354C>G	c.(352-354)ggC>ggG	p.G118G		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	118					keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			lung(2)	2	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			cctccggtggcggcggctcct	0.766																																					p.G118G		Atlas-SNP	.											.	LOR	19	.	0			c.C354G						.																																			SO:0001819	synonymous_variant	4014	exon2			CGGTGGCGGCGGC	M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.354C>G	chr1.hg19:g.153233779C>G		31.0	0.0		29.0	6.0	NM_000427	Q5T869|Q5XKF8	Silent	SNP	ENST00000368742.3	hg19	CCDS30870.1																																																																																			.	.		0.766	LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039107.1	NM_000427		G	153233779	C	G	153233779	2	3	70	1	0	0	0	0	0	0	0	1	8906	755	27	4		4	LOR	1	153233779	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	41372542	153233779	96016842	6	8937										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158583532	158583532	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tccctggatccacagcatccAggaacttctcaaacttgggc	8	14	1	0	rs536323126		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:158583532A>T	ENST00000368147.4	-	50	7148	c.6968T>A	c.(6967-6969)cTg>cAg	p.L2323Q	SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2323	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CACAGCATCCAGGAACTTCTC	0.522																																					p.L2323Q		Atlas-SNP	.											.	SPTA1	720	.	0			c.T6968A						.						74	72	73					1																	158583532		1945	4143	6088	SO:0001583	missense	6708	exon50			GCATCCAGGAACT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6968T>A	chr1.hg19:g.158583532A>T	ENSP00000357129:p.Leu2323Gln	144.0	0.0		187.0	25.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.301405	0.81136	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.25414	1.8;1.8	5.1	5.1	0.69264	EF-hand-like domain (1);	0.000000	0.26800	N	0.022435	T	0.42698	0.1214	M	0.74647	2.275	0.52501	D	0.999952	D	0.89917	1.0	D	0.83275	0.996	T	0.45702	-0.9243	10	0.87932	D	0	.	13.8682	0.63600	1.0:0.0:0.0:0.0	.	2323	P02549	SPTA1_HUMAN	Q	2323;2320	ENSP00000357130:L2323Q;ENSP00000357129:L2320Q	ENSP00000357129:L2320Q	L	-	2	0	SPTA1	156850156	1.000000	0.71417	0.974000	0.42286	0.883000	0.51084	8.258000	0.89853	2.150000	0.67090	0.528000	0.53228	CTG	.	.		0.522	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158583532	A	T	158583532	3	4	70	1	0	0	0	0	1	0	0	0	15131	188	7	4	303	4	SPTA1	1	158583532	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	5349753	158583532	90667089	7	8938										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158609400	158609400	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ccaacatctctctctccaatAgctgatgcttcttgagtagg	7	12	3	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:158609400A>T	ENST00000368147.4	-	35	5132	c.4952T>A	c.(4951-4953)cTa>cAa	p.L1651Q		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1651					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TCTCTCCAATAGCTGATGCTT	0.473																																					p.L1651Q		Atlas-SNP	.											.	SPTA1	720	.	0			c.T4952A						.						174	166	168					1																	158609400		1911	4138	6049	SO:0001583	missense	6708	exon35			TCCAATAGCTGAT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.4952T>A	chr1.hg19:g.158609400A>T	ENSP00000357129:p.Leu1651Gln	63.0	0.0		93.0	8.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.707908	0.89018	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48201	0.82;0.82	5.35	5.35	0.76521	.	0.000000	0.26939	N	0.021725	T	0.60117	0.2244	M	0.83483	2.645	0.58432	D	0.999993	D	0.89917	1.0	D	0.81914	0.995	T	0.60167	-0.7316	10	0.17832	T	0.49	.	14.5989	0.68427	1.0:0.0:0.0:0.0	.	1651	P02549	SPTA1_HUMAN	Q	1651	ENSP00000357130:L1651Q;ENSP00000357129:L1651Q	ENSP00000357129:L1651Q	L	-	2	0	SPTA1	156876024	1.000000	0.71417	0.937000	0.37676	0.988000	0.76386	8.385000	0.90163	2.371000	0.80710	0.533000	0.62120	CTA	.	.		0.473	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158609400	A	T	158609400	3	4	70	1	0	0	0	0	1	0	0	0	15131	420	15	4	2379	4	SPTA1	1	158609400	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	25868	158609400	90641221	8	8939										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158650442	158650442	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttagctaccagctccacttgGaagtcttcaaatttcttatg	6	10	3	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:158650442G>A	ENST00000368147.4	-	5	789	c.609C>T	c.(607-609)ttC>ttT	p.F203F		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	203					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.Q204fs*5(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					GCTCCACTTGGAAGTCTTCAA	0.478																																					p.F203F		Atlas-SNP	.											SPTA1,NS,carcinoma,-2,1	SPTA1	720	.	1	Deletion - Frameshift(1)	endometrium(1)	c.C609T						.						134	134	134					1																	158650442		1902	4120	6022	SO:0001819	synonymous_variant	6708	exon5			CACTTGGAAGTCT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.609C>T	chr1.hg19:g.158650442G>A		77.0	0.0		135.0	33.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.		0.478	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158650442	G	A	158650442	2	1	70	1	0	0	0	0	0	0	0	1	15131	1165	41	3		3	SPTA1	1	158650442	Silent	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	41042	158650442	90600179	9	8940										
NOS1AP	9722	hgsc.bcm.edu	37	chr1	162336963	162336963	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ccgctgggcgcgggcttggcTgactttgcccaccctgcggg	16	15	0	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:162336963T>C	ENST00000361897.5	+	10	1629	c.1227T>C	c.(1225-1227)gcT>gcC	p.A409A	RP11-565P22.6_ENST00000431696.1_Silent_p.A95A|NOS1AP_ENST00000530878.1_Silent_p.A404A|NOS1AP_ENST00000454693.1_3'UTR|NOS1AP_ENST00000493151.1_Silent_p.A114A	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	409					regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			CGGGCTTGGCTGACTTTGCCC	0.677																																					p.A409A		Atlas-SNP	.											.	NOS1AP	139	.	0			c.T1227C						.						61	69	66					1																	162336963		2203	4300	6503	SO:0001819	synonymous_variant	9722	exon10			CTTGGCTGACTTT	AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"C-terminal PDZ domain ligand of neuronal nitric oxide synthase"	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.1227T>C	chr1.hg19:g.162336963T>C		86.0	0.0		92.0	9.0	NM_014697	B7ZLF5|O43564|Q3T551|Q5VU95	Silent	SNP	ENST00000361897.5	hg19	CCDS1237.1																																																																																			.	.		0.677	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697		C	162336963	T	C	162336963	2	2	70	1	0	0	0	0	0	0	0	1	10551	1567	55	2		2	NOS1AP	1	162336963	Silent	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	3686521	162336963	86913658	10	8941										
IER5	51278	hgsc.bcm.edu	37	chr1	181058762	181058762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gctcgaccccgctcaagaagCcccgccggaacttagagcag	11	16	1	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:181058762C>T	ENST00000367577.4	+	1	1125	c.724C>T	c.(724-726)Ccc>Tcc	p.P242S	RP11-309G3.3_ENST00000606938.1_lincRNA	NM_016545.4	NP_057629.2	Q5VY09	IER5_HUMAN	immediate early response 5	242										lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	4						GCTCAAGAAGCCCCGCCGGAA	0.736																																					p.P242S		Atlas-SNP	.											.	IER5	15	.	0			c.C724T						.						16	16	16					1																	181058762		2068	4075	6143	SO:0001583	missense	51278	exon1			AAGAAGCCCCGCC	BC000128	CCDS1343.1	1q25.3	2008-02-05			ENSG00000162783	ENSG00000162783			5393	protein-coding gene	gene with protein product		607177				10049588, 11102586	Standard	NM_016545		Approved		uc001got.4	Q5VY09	OTTHUMG00000035178	ENST00000367577.4:c.724C>T	chr1.hg19:g.181058762C>T	ENSP00000356549:p.Pro242Ser	86.0	0.0		116.0	22.0	NM_016545	B2RBV3|Q8WY68|Q9NY49|Q9NZP9	Missense_Mutation	SNP	ENST00000367577.4	hg19	CCDS1343.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530484	0.45073	.	.	ENSG00000162783	ENST00000367577	T	0.10099	2.91	3.82	1.86	0.25419	.	0.193681	0.33110	U	0.005280	T	0.09598	0.0236	L	0.50333	1.59	0.32883	D	0.510825	B	0.29085	0.232	B	0.30855	0.121	T	0.16867	-1.0388	10	0.27785	T	0.31	.	6.6991	0.23215	0.0:0.7184:0.18:0.1016	.	242	Q5VY09	IER5_HUMAN	S	242	ENSP00000356549:P242S	ENSP00000356549:P242S	P	+	1	0	IER5	179325385	0.995000	0.38212	0.989000	0.46669	0.969000	0.65631	2.267000	0.43329	0.113000	0.18004	0.456000	0.33151	CCC	.	.		0.736	IER5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085142.1	NM_016545		T	181058762	C	T	181058762	3	4	70	1	0	0	0	0	1	0	0	0	7517	739	26	3	726	3	IER5	1	181058762	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	18721799	181058762	68191859	11	8942										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181479649	181479649	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	atcctggccaccatcattgcCaactgcatcgtcctggccct	7	17	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:181479649C>A	ENST00000367573.2	+	2	303	c.303C>A	c.(301-303)gcC>gcA	p.A101A	CACNA1E_ENST00000526775.1_Silent_p.A101A|CACNA1E_ENST00000358338.5_Silent_p.A52A|CACNA1E_ENST00000367570.1_Silent_p.A101A|CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000360108.3_Silent_p.A101A|CACNA1E_ENST00000357570.5_Silent_p.A52A	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	101					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CCATCATTGCCAACTGCATCG	0.552																																					p.A101A		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C303A						.						125	125	125					1																	181479649		2124	4228	6352	SO:0001819	synonymous_variant	777	exon2			CATTGCCAACTGC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.303C>A	chr1.hg19:g.181479649C>A		124.0	0.0		134.0	25.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.552	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181479649	C	A	181479649	2	1	70	1	0	0	0	0	0	0	0	1	2544	581	21	3		3	CACNA1E	1	181479649	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	420887	181479649	67770972	12	8943										
CR2	1380	hgsc.bcm.edu	37	chr1	207647159	207647159	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tctccagaaacatgccagcaTgtgagacagagtcttcaaga	9	10	3	4	rs566892752		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr1:207647159T>A	ENST00000367058.3	+	11	2181	c.1992T>A	c.(1990-1992)caT>caA	p.H664Q	CR2_ENST00000367059.3_Missense_Mutation_p.H664Q|CR2_ENST00000458541.2_Missense_Mutation_p.H637Q|CR2_ENST00000367057.3_Missense_Mutation_p.H723Q	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	664	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CATGCCAGCATGTGAGACAGA	0.423																																					p.H723Q		Atlas-SNP	.											.	CR2	164	.	0			c.T2169A						.						129	130	129					1																	207647159		2203	4300	6503	SO:0001583	missense	1380	exon12			CCAGCATGTGAGA	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1992T>A	chr1.hg19:g.207647159T>A	ENSP00000356025:p.His664Gln	90.0	0.0		149.0	19.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	T	12.56	1.973641	0.34848	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.47528	1.9;0.84;1.9;1.9	5.47	0.472	0.16758	Complement control module (1);Sushi/SCR/CCP (2);	.	.	.	.	T	0.22820	0.0551	N	0.08118	0	0.09310	N	1	B;B;B	0.21225	0.011;0.053;0.016	B;B;B	0.23574	0.034;0.043;0.047	T	0.23904	-1.0175	9	0.21540	T	0.41	.	4.5686	0.12198	0.0:0.2594:0.1579:0.5827	.	664;664;723	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	Q	664;723;664;637	ENSP00000356025:H664Q;ENSP00000356024:H723Q;ENSP00000356026:H664Q;ENSP00000404222:H637Q	ENSP00000356024:H723Q	H	+	3	2	CR2	205713782	0.000000	0.05858	0.019000	0.16419	0.379000	0.30106	-0.058000	0.11750	0.067000	0.16545	0.533000	0.62120	CAT	.	.		0.423	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		A	207647159	T	A	207647159	3	1	70	1	0	0	0	0	1	0	0	0	3844	1461	51	4	2215	4	CR2	1	207647159	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	26167510	207647159	41603462	13	8944										
KIF3C	3797	hgsc.bcm.edu	37	chr2	26203290	26203290	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcctgctgttcccgccgcagGtcctccagcatcttctcctt	8	18	2	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:26203290G>C	ENST00000264712.3	-	1	2076	c.1497C>G	c.(1495-1497)gaC>gaG	p.D499E	KIF3C_ENST00000405914.1_Missense_Mutation_p.D499E	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	499					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCGCCGCAGGTCCTCCAGCA	0.642																																					p.D499E		Atlas-SNP	.											.	KIF3C	79	.	0			c.C1497G						.						61	59	60					2																	26203290		2203	4300	6503	SO:0001583	missense	3797	exon1			CCGCAGGTCCTCC		CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731		"Kinesins"	6321	protein-coding gene	gene with protein product		602845				9480755	Standard	NM_002254		Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000264712.3:c.1497C>G	chr2.hg19:g.26203290G>C	ENSP00000264712:p.Asp499Glu	69.0	0.0		81.0	25.0	NM_002254	O43544|Q4ZG18|Q53SX5|Q562F7	Missense_Mutation	SNP	ENST00000264712.3	hg19	CCDS1719.1	.	.	.	.	.	.	.	.	.	.	G	4.176	0.031237	0.08101	.	.	ENSG00000084731	ENST00000264712;ENST00000542511;ENST00000405914	T;T	0.70869	-0.52;-0.52	5.62	1.17	0.20885	.	0.237978	0.47852	N	0.000220	T	0.37544	0.1007	N	0.04820	-0.15	0.34777	D	0.734384	B;B	0.26258	0.014;0.145	B;B	0.20955	0.01;0.032	T	0.29088	-1.0023	10	0.07644	T	0.81	.	4.2636	0.10752	0.3725:0.0:0.4803:0.1472	.	499;499	B7ZM25;O14782	.;KIF3C_HUMAN	E	499;305;499	ENSP00000264712:D499E;ENSP00000385030:D499E	ENSP00000264712:D499E	D	-	3	2	KIF3C	26056794	0.996000	0.38824	0.995000	0.50966	0.988000	0.76386	0.357000	0.20199	-0.070000	0.12908	-0.136000	0.14681	GAC	.	.		0.642	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1			C	26203290	G	C	26203290	3	2	70	1	0	0	0	0	1	0	0	0	8311	1252	44	4	916	4	KIF3C	2	26203290	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10		26203290	216996083	14	8945										
FAM98A	25940	hgsc.bcm.edu	37	chr2	33810623	33810623	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gatggcacaggcagtcttttCtcttatagagccgctgcttg	11	10	2	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:33810623C>A	ENST00000238823.8	-	7	1002	c.862G>T	c.(862-864)Gaa>Taa	p.E288*	FAM98A_ENST00000403368.1_Nonsense_Mutation_p.E288*|FAM98A_ENST00000498340.1_5'Flank|FAM98A_ENST00000441530.2_Nonsense_Mutation_p.E93*			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	289							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					GCAGTCTTTTCTCTTATAGAG	0.348																																					p.E288X		Atlas-SNP	.											.	FAM98A	42	.	0			c.G862T						.						55	57	56					2																	33810623		2203	4300	6503	SO:0001587	stop_gained	25940	exon7			TCTTTTCTCTTAT		CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.862G>T	chr2.hg19:g.33810623C>A	ENSP00000238823:p.Glu288*	222.0	0.0		232.0	62.0	NM_015475	B2RNA2|Q9Y3Y6	Nonsense_Mutation	SNP	ENST00000238823.8	hg19	CCDS33179.1	.	.	.	.	.	.	.	.	.	.	C	18.26	3.585137	0.66105	.	.	ENSG00000119812	ENST00000238823;ENST00000395190;ENST00000403368;ENST00000441530	.	.	.	5.37	5.37	0.77165	.	0.052327	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-17.6522	19.4591	0.94908	0.0:1.0:0.0:0.0	.	.	.	.	X	288;289;288;93	.	ENSP00000238823:E288X	E	-	1	0	FAM98A	33664127	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	5.866000	0.69590	2.681000	0.91329	0.313000	0.20887	GAA	.	.		0.348	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475		A	33810623	C	A	33810623	4	1	70	1	0	0	0	0	0	1	0	0	5664	922	32	3	702	3	FAM98A	2	33810623	Nonsense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	7607333	33810623	209388750	15	8946										
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40656977	40656977	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tcaattactgaaaggagaatCtcaggagcagaagatcccag	10	8	2	4			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:40656977C>A	ENST00000403092.1	-	2	477	c.444G>T	c.(442-444)gaG>gaT	p.E148D	SLC8A1_ENST00000332839.4_Missense_Mutation_p.E148D|SLC8A1_ENST00000542756.1_Missense_Mutation_p.E148D|SLC8A1_ENST00000405269.1_Missense_Mutation_p.E148D|SLC8A1_ENST00000406391.2_Missense_Mutation_p.E148D|SLC8A1_ENST00000402441.1_Missense_Mutation_p.E148D|SLC8A1_ENST00000542024.1_Missense_Mutation_p.E148D|SLC8A1_ENST00000406785.2_Missense_Mutation_p.E148D|SLC8A1_ENST00000408028.2_Missense_Mutation_p.E148D|SLC8A1_ENST00000405901.3_Missense_Mutation_p.E148D			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	148					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	AAAGGAGAATCTCAGGAGCAG	0.468																																					p.E148D		Atlas-SNP	.											SLC8A1,NS,carcinoma,0,1	SLC8A1	221	.	0			c.G444T						.						127	117	120					2																	40656977		2203	4300	6503	SO:0001583	missense	6546	exon1			GAGAATCTCAGGA		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.444G>T	chr2.hg19:g.40656977C>A	ENSP00000384763:p.Glu148Asp	62.0	0.0		91.0	34.0	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	hg19	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.756586	0.49362	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49;-0.49;-0.49;-0.49;-0.49;-0.49	5.59	3.8	0.43715	Sodium/calcium exchanger membrane region (1);	0.048392	0.85682	D	0.000000	D	0.84795	0.5551	M	0.91510	3.215	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.988;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.992;1.0;1.0;1.0	D	0.84502	0.0617	10	0.87932	D	0	.	7.5544	0.27817	0.0:0.7416:0.0:0.2584	.	148;148;148;148;148	P32418-4;P32418-2;P32418-3;F6VPY9;P32418	.;.;.;.;NAC1_HUMAN	D	148	ENSP00000383886:E148D;ENSP00000440727:E148D;ENSP00000384763:E148D;ENSP00000385678:E148D;ENSP00000385188:E148D;ENSP00000385535:E148D;ENSP00000332931:E148D;ENSP00000384908:E148D;ENSP00000385811:E148D;ENSP00000443515:E148D	ENSP00000332931:E148D	E	-	3	2	SLC8A1	40510481	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	0.814000	0.27239	0.734000	0.32515	0.563000	0.77884	GAG	.	.		0.468	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		A	40656977	C	A	40656977	3	1	70	1	0	0	0	0	1	0	0	0	14721	912	32	3	2625	3	SLC8A1	2	40656977	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	6846354	40656977	202542396	16	8947										
KIAA1841	84542	hgsc.bcm.edu	37	chr2	61298747	61298747	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttatattatgacagtgtgcaAaaaggtttgatgaattaaag	9	2	0	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:61298747A>T	ENST00000402291.1	+	4	398	c.157A>T	c.(157-159)Aaa>Taa	p.K53*	KIAA1841_ENST00000482513.1_3'UTR|KIAA1841_ENST00000356719.2_Nonsense_Mutation_p.K53*|KIAA1841_ENST00000453873.1_Nonsense_Mutation_p.K53*|KIAA1841_ENST00000295031.5_Nonsense_Mutation_p.K53*	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	53										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			ACAGTGTGCAAAAAGGTTTGA	0.408																																					p.K53X		Atlas-SNP	.											.	KIAA1841	95	.	0			c.A157T						.						59	61	61					2																	61298747		2203	4300	6503	SO:0001587	stop_gained	84542	exon4			TGTGCAAAAAGGT	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.157A>T	chr2.hg19:g.61298747A>T	ENSP00000385579:p.Lys53*	99.0	0.0		148.0	44.0	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Nonsense_Mutation	SNP	ENST00000402291.1	hg19	CCDS46296.1	.	.	.	.	.	.	.	.	.	.	A	36	5.819980	0.96989	.	.	ENSG00000162929	ENST00000402291;ENST00000295031;ENST00000356719;ENST00000453873	.	.	.	5.71	5.71	0.89125	.	0.126684	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.4043	15.9958	0.80243	1.0:0.0:0.0:0.0	.	.	.	.	X	53	.	ENSP00000295031:K53X	K	+	1	0	KIAA1841	61152251	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.478000	0.60230	2.188000	0.69820	0.533000	0.62120	AAA	.	.		0.408	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506		T	61298747	A	T	61298747	4	4	70	1	0	0	0	0	0	1	0	0	8270	15	1	4	163	4	KIAA1841	2	61298747	Nonsense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	20641770	61298747	181900626	17	8948										
TTC31	64427	hgsc.bcm.edu	37	chr2	74718274	74718274	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcgtcaaaaggaacggaagcGacaggagcgtttggagcagt	16	7	1	0	rs368112249		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:74718274G>T	ENST00000233623.5	+	6	573	c.566G>T	c.(565-567)cGa>cTa	p.R189L	TTC31_ENST00000463189.1_3'UTR|TTC31_ENST00000410003.1_Missense_Mutation_p.R189L|TTC31_ENST00000442235.2_Missense_Mutation_p.R45L	NM_022492.4	NP_071937.4	Q49AM3	TTC31_HUMAN	tetratricopeptide repeat domain 31	189										breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						GAACGGAAGCGACAGGAGCGT	0.488																																					p.R189L		Atlas-SNP	.											.	TTC31	23	.	0			c.G566T						.						121	123	122					2																	74718274		2065	4199	6264	SO:0001583	missense	64427	exon6			GGAAGCGACAGGA	AK026819	CCDS42701.1	2p13.1	2013-01-11			ENSG00000115282	ENSG00000115282		"Tetratricopeptide (TTC) repeat domain containing"	25759	protein-coding gene	gene with protein product						12477932	Standard	NM_022492		Approved	FLJ12788	uc002slt.2	Q49AM3	OTTHUMG00000152887	ENST00000233623.5:c.566G>T	chr2.hg19:g.74718274G>T	ENSP00000233623:p.Arg189Leu	111.0	0.0		152.0	52.0	NM_022492	Q4KN40|Q53FD4|Q9H9F7	Missense_Mutation	SNP	ENST00000233623.5	hg19	CCDS42701.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.892047	0.52014	.	.	ENSG00000115282	ENST00000545977;ENST00000410003;ENST00000441635;ENST00000442235;ENST00000233623	T;T;T	0.68479	1.0;0.4;-0.33	3.85	1.96	0.26148	.	0.351137	0.24975	N	0.034108	T	0.54208	0.1844	L	0.49350	1.555	0.09310	N	1	B;B;B;B	0.15141	0.004;0.012;0.002;0.004	B;B;B;B	0.15052	0.012;0.005;0.003;0.008	T	0.51450	-0.8704	10	0.72032	D	0.01	-7.975	4.1987	0.10455	0.123:0.0:0.6108:0.2663	.	45;159;189;118	B4DZV1;Q86XF2;Q49AM3;F5H175	.;.;TTC31_HUMAN;.	L	118;189;189;45;189	ENSP00000387213:R189L;ENSP00000416823:R45L;ENSP00000233623:R189L	ENSP00000233623:R189L	R	+	2	0	TTC31	74571782	0.784000	0.28713	0.102000	0.21198	0.989000	0.77384	-0.061000	0.11693	0.547000	0.28938	0.561000	0.74099	CGA	.	.		0.488	TTC31-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328422.1	NM_022492		T	74718274	G	T	74718274	3	4	70	1	0	0	0	0	1	0	0	0	16715	1058	37	1	588	1	TTC31	2	74718274	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	13419527	74718274	168481099	18	8949										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141083347	141083347	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	aaaccttgtttgctgctgacAgagactactgaattagagcc	9	9	0	4			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:141083347A>C	ENST00000389484.3	-	80	13295	c.12324T>G	c.(12322-12324)tcT>tcG	p.S4108S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4108					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGCTGCTGACAGAGACTACTG	0.358										TSP Lung(27;0.18)																											p.S4108S	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T12324G						.						107	97	100					2																	141083347		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon80			GCTGACAGAGACT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12324T>G	chr2.hg19:g.141083347A>C		95.0	0.0		120.0	43.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	1.845	-0.466487	0.04476	.	.	ENSG00000168702	ENST00000437977	.	.	.	5.22	-2.71	0.05986	.	.	.	.	.	T	0.50394	0.1613	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44003	-0.9356	4	.	.	.	.	6.904	0.24299	0.4589:0.0:0.4211:0.12	.	.	.	.	R	340	.	.	L	-	2	0	LRP1B	140799817	0.057000	0.20700	0.811000	0.32455	0.204000	0.24138	-0.417000	0.07088	-0.523000	0.06409	-1.150000	0.01838	CTG	.	.		0.358	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141083347	A	C	141083347	2	2	70	1	0	0	0	0	0	0	0	1	8964	175	7	5		5	LRP1B	2	141083347	Silent	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	66365073	141083347	102116026	19	8950										
ZEB2	9839	hgsc.bcm.edu	37	chr2	145182398	145182399	+	Missense_Mutation	DNP	TC	TC	AA													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttgcggtctggatcgtggctTctggccccatagtgtcatag							TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:145182398_145182399TC>AA	ENST00000558170.2	-	4	1551_1552	c.367_368GA>TT	c.(367-369)GAa>TTa	p.E123L	ZEB2_ENST00000539609.3_Intron|ZEB2_ENST00000409487.3_Missense_Mutation_p.E123L|ZEB2_ENST00000303660.4_Missense_Mutation_p.E123L	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	123					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		GATCGTGGCTTCTGGCCCCATA	0.446																																					p.E123V|p.E123X	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											.	ZEB2	218	.	0			c.A368T|c.G367T						.																																			SO:0001583	missense	9839	exon4			GTGGCTTCTGGCC|TGGCTTCTGGCCC	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.367_368delinsAA	chr2.hg19:g.145182398_145182399delinsAA	ENSP00000454157:p.Glu123Leu	101.0|100.0	0.0		118.0|116.0	34.0|33.0	NM_014795	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000558170.2	hg19	CCDS2186.1																																																																																			.	.		0.446	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		AA	145182399	TC	AA	145182398	3	1	70	1	0	0	0	0	1	0	0	0	17639	1783	62	4	3304	4	ZEB2	2	145182398	Missense_Mutation	DNP	TC	TCGA-CC-A7IE-01A-21D-A382-10	4099051	145182398	98016975	20	8951										
CRYGA	1418	hgsc.bcm.edu	37	chr2	209028038	209028038	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gtggccctggtaattgggacGctcatagagcatccagcagc	13	11	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:209028038G>T	ENST00000304502.4	-	2	161	c.142C>A	c.(142-144)Cgt>Agt	p.R48S		NM_014617.3	NP_055432.2	P11844	CRGA_HUMAN	crystallin, gamma A	48	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			endometrium(1)|kidney(3)|large_intestine(1)|lung(7)	12				Epithelial(149;0.067)|LUSC - Lung squamous cell carcinoma(261;0.0708)|Lung(261;0.135)		TAATTGGGACGCTCATAGAGC	0.587																																					p.R48S		Atlas-SNP	.											.	CRYGA	31	.	0			c.C142A						.						52	57	55					2																	209028038		2203	4300	6503	SO:0001583	missense	1418	exon2			TGGGACGCTCATA		CCDS33367.1	2q34	2013-02-14			ENSG00000168582	ENSG00000168582			2408	protein-coding gene	gene with protein product	"gamma crystallin 5"	123660		CRYG1			Standard	NM_014617		Approved	CRYG5, CRY-g-A		P11844	OTTHUMG00000154796	ENST00000304502.4:c.142C>A	chr2.hg19:g.209028038G>T	ENSP00000302105:p.Arg48Ser	123.0	0.0		212.0	73.0	NM_014617	Q53ST5	Missense_Mutation	SNP	ENST00000304502.4	hg19	CCDS33367.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.732041	0.48939	.	.	ENSG00000168582	ENST00000304502	T	0.74947	-0.89	4.64	3.76	0.43208	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.188078	0.46145	D	0.000305	T	0.73442	0.3587	M	0.89353	3.025	0.47659	D	0.999486	P	0.44309	0.832	B	0.36989	0.238	T	0.76599	-0.2900	10	0.66056	D	0.02	.	7.4831	0.27417	0.1939:0.0:0.8061:0.0	.	48	P11844	CRGA_HUMAN	S	48	ENSP00000302105:R48S	ENSP00000302105:R48S	R	-	1	0	CRYGA	208736283	0.380000	0.25131	1.000000	0.80357	0.990000	0.78478	0.842000	0.27627	1.287000	0.44583	0.655000	0.94253	CGT	.	.		0.587	CRYGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337096.1	NM_014617		T	209028038	G	T	209028038	3	4	70	1	0	0	0	0	1	0	0	0	3916	1087	38	1	390	1	CRYGA	2	209028038	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	63845640	209028038	34171335	21	8952										
CPS1	1373	hgsc.bcm.edu	37	chr2	211459263	211459263	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttcctttttctcactgataaAgaaaggaaaagctaccacca	5	10	1	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:211459263A>G	ENST00000233072.5	+	12	1392	c.1196A>G	c.(1195-1197)aAg>aGg	p.K399R	CPS1_ENST00000451903.2_5'UTR|CPS1_ENST00000430249.2_Missense_Mutation_p.K405R	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	399	Glutamine amidotransferase type-1.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TCACTGATAAAGAAAGGAAAA	0.363																																					p.K405R		Atlas-SNP	.											.	CPS1	485	.	0			c.A1214G						.						128	117	121					2																	211459263		2203	4300	6503	SO:0001583	missense	1373	exon13			TGATAAAGAAAGG	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.1196A>G	chr2.hg19:g.211459263A>G	ENSP00000233072:p.Lys399Arg	83.0	0.0		95.0	24.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	A	12.41	1.928851	0.34002	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000536125	D;D	0.89810	-2.57;-2.57	5.88	5.88	0.94601	Pre-ATP-grasp fold (1);Glutamine amidotransferase type 1 (1);	0.092296	0.64402	D	0.000001	D	0.83691	0.5309	L	0.33245	0.995	0.80722	D	1	B;B	0.13145	0.007;0.007	B;B	0.13407	0.009;0.009	T	0.78468	-0.2192	10	0.22109	T	0.4	5.7195	16.275	0.82640	1.0:0.0:0.0:0.0	.	409;399	Q59HF8;P31327	.;CPSM_HUMAN	R	405;407;399;399	ENSP00000402608:K405R;ENSP00000233072:K399R	ENSP00000233072:K399R	K	+	2	0	CPS1	211167508	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	6.295000	0.72744	2.248000	0.74166	0.477000	0.44152	AAG	.	.		0.363	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			G	211459263	A	G	211459263	3	3	70	1	0	0	0	0	1	0	0	0	3825	72	3	2	1264	2	CPS1	2	211459263	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	2431225	211459263	31740110	22	8953										
MARCH4	57574	hgsc.bcm.edu	37	chr2	217124066	217124066	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgactctcatgaccagctctCggctgctgcctgggggactt	12	13	2	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:217124066C>A	ENST00000273067.4	-	4	2968	c.1202G>T	c.(1201-1203)cGa>cTa	p.R401L	AC012513.6_ENST00000417481.1_RNA	NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	401						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R401Q(1)		breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		GACCAGCTCTCGGCTGCTGCC	0.612																																					p.R401L		Atlas-SNP	.											MARCH4,right_upper_lobe,carcinoma,-1,1	MARCH4	50	.	1	Substitution - Missense(1)	lung(1)	c.G1202T						.						79	79	79					2																	217124066		2203	4300	6503	SO:0001583	missense	57574	exon4			AGCTCTCGGCTGC	AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	29269	protein-coding gene	gene with protein product		608208	"membrane-associated ring finger (C3HC4) 4"			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.1202G>T	chr2.hg19:g.217124066C>A	ENSP00000273067:p.Arg401Leu	106.0	0.0		95.0	28.0	NM_020814	Q4KMN7|Q86WR8	Missense_Mutation	SNP	ENST00000273067.4	hg19	CCDS33376.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708330	0.89018	.	.	ENSG00000144583	ENST00000273067	T	0.21031	2.03	5.47	5.47	0.80525	.	0.200639	0.41500	D	0.000876	T	0.45357	0.1338	M	0.64997	1.995	0.58432	D	0.999999	D	0.71674	0.998	D	0.70016	0.967	T	0.30268	-0.9984	10	0.56958	D	0.05	-15.6821	18.3253	0.90251	0.0:1.0:0.0:0.0	.	401	Q9P2E8	MARH4_HUMAN	L	401	ENSP00000273067:R401L	ENSP00000273067:R401L	R	-	2	0	MARCH4	216832311	1.000000	0.71417	0.997000	0.53966	0.902000	0.53008	5.999000	0.70665	2.567000	0.86603	0.561000	0.74099	CGA	.	.		0.612	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814		A	217124066	C	A	217124066	3	1	70	1	0	0	0	0	1	0	0	0	9312	884	31	1	34	1	MARCH4	2	217124066	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	5664803	217124066	26075307	23	8954										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222301824	222301824	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cattctccatgtactctgttAtgatcattactggtttacct	5	10	3	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:222301824A>G	ENST00000281821.2	-	12	2134	c.2093T>C	c.(2092-2094)aTa>aCa	p.I698T	EPHA4_ENST00000392071.4_Missense_Mutation_p.I647T|EPHA4_ENST00000409938.1_Missense_Mutation_p.I698T|EPHA4_ENST00000409854.1_Missense_Mutation_p.I698T	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	698	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GTACTCTGTTATGATCATTAC	0.373																																					p.I698T		Atlas-SNP	.											.	EPHA4	263	.	0			c.T2093C						.						105	107	107					2																	222301824		2203	4300	6503	SO:0001583	missense	2043	exon12			TCTGTTATGATCA	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.2093T>C	chr2.hg19:g.222301824A>G	ENSP00000281821:p.Ile698Thr	92.0	0.0		79.0	20.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	A	19.52	3.842526	0.71488	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071	D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11	6.03	6.03	0.97812	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93471	0.7917	M	0.79926	2.475	0.80722	D	1	D	0.64830	0.994	D	0.69142	0.962	D	0.94130	0.7387	10	0.87932	D	0	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	698	P54764	EPHA4_HUMAN	T	698;698;698;647	ENSP00000281821:I698T;ENSP00000386276:I698T;ENSP00000386829:I698T;ENSP00000375923:I647T	ENSP00000281821:I698T	I	-	2	0	EPHA4	222010068	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.339000	0.96797	2.302000	0.77476	0.533000	0.62120	ATA	.	.		0.373	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			G	222301824	A	G	222301824	3	3	70	1	0	0	0	0	1	0	0	0	5171	449	16	2	891	2	EPHA4	2	222301824	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	5177758	222301824	20897549	24	8955										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225659771	225659771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ccatcaaaacagtccttataCgcttagtcaggtccttcacc	5	14	3	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:225659771C>T	ENST00000258390.7	-	45	5046	c.4979G>A	c.(4978-4980)cGt>cAt	p.R1660H	DOCK10_ENST00000409592.3_Missense_Mutation_p.R1654H	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1660					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1658H(1)|p.R198H(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		AGTCCTTATACGCTTAGTCAG	0.478																																					p.R1660H		Atlas-SNP	.											DOCK10_ENST00000373702,colon,carcinoma,0,2	DOCK10	308	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4979A						.						142	143	143					2																	225659771		2005	4185	6190	SO:0001583	missense	55619	exon45			CTTATACGCTTAG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.4979G>A	chr2.hg19:g.225659771C>T	ENSP00000258390:p.Arg1660His	103.0	0.0		137.0	32.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	35	5.577896	0.96565	.	.	ENSG00000135905	ENST00000409592;ENST00000258390;ENST00000373702	T;T	0.65178	4.66;-0.14	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.83603	0.5290	M	0.91090	3.175	0.58432	D	0.999999	D;P;D;D	0.76494	0.972;0.95;0.984;0.999	B;B;P;D	0.64410	0.444;0.439;0.74;0.925	D	0.86564	0.1843	10	0.87932	D	0	.	20.0637	0.97700	0.0:1.0:0.0:0.0	.	1660;514;1654;322	Q96BY6;B4DF07;B3FL70;B4DEY4	DOC10_HUMAN;.;.;.	H	1654;1660;198	ENSP00000386694:R1654H;ENSP00000258390:R1660H	ENSP00000258390:R1660H	R	-	2	0	DOCK10	225368015	1.000000	0.71417	0.985000	0.45067	0.992000	0.81027	7.487000	0.81328	2.751000	0.94390	0.650000	0.86243	CGT	.	.		0.478	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			T	225659771	C	T	225659771	3	4	70	1	0	0	0	0	1	0	0	0	4687	536	19	1	1629	1	DOCK10	2	225659771	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	3357947	225659771	17539602	25	8956										
C2orf54	79919	hgsc.bcm.edu	37	chr2	241834941	241834941	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgcttgcagtgtacgatggcTgctaccagcaggtccttgag	13	10	0	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr2:241834941T>C	ENST00000388934.4	-	1	632	c.474A>G	c.(472-474)gcA>gcG	p.A158A		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	158										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		GTACGATGGCTGCTACCAGCA	0.607																																					p.A158A		Atlas-SNP	.											.	C2orf54	14	.	0			c.A474G						.						20	24	23					2																	241834941		2198	4292	6490	SO:0001819	synonymous_variant	79919	exon1			GATGGCTGCTACC	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.474A>G	chr2.hg19:g.241834941T>C		83.0	0.0		78.0	17.0	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	hg19	CCDS42839.1																																																																																			.	.		0.607	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437		C	241834941	T	C	241834941	2	2	70	1	0	0	0	0	0	0	0	1	2177	1567	55	2		2	C2orf54	2	241834941	Silent	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	16175170	241834941	1364432	26	8957										
CHL1	10752	hgsc.bcm.edu	37	chr3	407776	407776	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	aagatggagaagcctttgaaAttaatggcacagaagatggc	12	5	0	5			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr3:407776A>G	ENST00000256509.2	+	15	2371	c.1729A>G	c.(1729-1731)Att>Gtt	p.I577V	CHL1-AS1_ENST00000608098.1_RNA|CHL1_ENST00000397491.2_Missense_Mutation_p.I561V|CHL1-AS1_ENST00000417612.1_RNA	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		AGCCTTTGAAATTAATGGCAC	0.348																																					p.I577V		Atlas-SNP	.											.	CHL1	242	.	0			c.A1729G						.						118	114	115					3																	407776		2203	4300	6503	SO:0001583	missense	10752	exon13			TTTGAAATTAATG	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.1729A>G	chr3.hg19:g.407776A>G	ENSP00000256509:p.Ile577Val	136.0	0.0		204.0	18.0	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	A	5.461	0.270192	0.10349	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.79141	-1.24;-1.24	5.18	1.2	0.21068	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.545750	0.03247	N	0.181280	T	0.64843	0.2635	L	0.27975	0.815	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.12837	0.008;0.008;0.002	T	0.43621	-0.9380	10	0.31617	T	0.26	.	3.1981	0.06640	0.5311:0.0:0.1763:0.2926	.	561;561;577	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	V	577;561	ENSP00000256509:I577V;ENSP00000380628:I561V	ENSP00000256509:I577V	I	+	1	0	CHL1	382776	0.010000	0.17322	0.000000	0.03702	0.948000	0.59901	0.478000	0.22212	0.017000	0.15025	0.460000	0.39030	ATT	.	.		0.348	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		G	407776	A	G	407776	3	3	70	1	0	0	0	0	1	0	0	0	3351	101	4	2	1779	2	CHL1	3	407776	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10		407776	197614654	27	8958										
SETD2	29072	hgsc.bcm.edu	37	chr3	47088108	47088108	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ctgaagacttggctgggcatAactctaaaagataaaatgaa	9	6	1	4			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr3:47088108A>C	ENST00000409792.3	-	16	7009	c.6967T>G	c.(6967-6969)Tat>Gat	p.Y2323D		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2323	Gln-rich.|Low charge region.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GGCTGGGCATAACTCTAAAAG	0.393			"N, F, S, Mis"		clear cell renal carcinoma																																p.Y2323D		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.T6967G						.						50	51	51					3																	47088108		2203	4300	6503	SO:0001583	missense	29072	exon16			GGGCATAACTCTA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6967T>G	chr3.hg19:g.47088108A>C	ENSP00000386759:p.Tyr2323Asp	86.0	0.0		92.0	26.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	A	23.6	4.436419	0.83885	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	T	0.47869	0.83	5.87	5.87	0.94306	.	0.000000	0.49916	D	0.000134	T	0.65249	0.2673	L	0.53249	1.67	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.66168	-0.5991	10	0.56958	D	0.05	.	16.2718	0.82624	1.0:0.0:0.0:0.0	.	2323;2323	F2Z317;Q9BYW2	.;SETD2_HUMAN	D	2323	ENSP00000386759:Y2323D	ENSP00000386759:Y2323D	Y	-	1	0	SETD2	47063112	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.993000	0.88291	2.239000	0.73571	0.528000	0.53228	TAT	.	.		0.393	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		C	47088108	A	C	47088108	3	2	70	1	0	0	0	0	1	0	0	0	14146	362	13	5	751	5	SETD2	3	47088108	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	46680332	47088108	150934322	28	8959										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48699314	48699314	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgatgcaggagctgtcctcgCcgtgcgtggtgctgaatcca	14	11	0	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr3:48699314C>A	ENST00000164024.4	-	1	1034	c.754G>T	c.(754-756)Gcg>Tcg	p.A252S	RP11-148G20.1_ENST00000421275.1_RNA|CELSR3_ENST00000544264.1_Missense_Mutation_p.A252S	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	252					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GCTGTCCTCGCCGTGCGTGGT	0.692											OREG0004260	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=CELSR3|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.A252S		Atlas-SNP	.											.	CELSR3	237	.	0			c.G754T						.						30	37	35					3																	48699314		2198	4292	6490	SO:0001583	missense	1951	exon1			TCCTCGCCGTGCG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.754G>T	chr3.hg19:g.48699314C>A	ENSP00000164024:p.Ala252Ser	66.0	0.0	956	77.0	11.0	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.817406	0.32145	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.70399	-0.48;-0.47	5.2	5.2	0.72013	.	.	.	.	.	T	0.52306	0.1726	N	0.08118	0	0.09310	N	1	B;B	0.14012	0.002;0.009	B;B	0.11329	0.004;0.006	T	0.11324	-1.0592	9	0.12430	T	0.62	.	17.6776	0.88235	0.0:1.0:0.0:0.0	.	252;322	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	S	252	ENSP00000164024:A252S;ENSP00000445694:A252S	ENSP00000164024:A252S	A	-	1	0	CELSR3	48674318	0.000000	0.05858	0.253000	0.24343	0.683000	0.39861	0.447000	0.21710	2.722000	0.93159	0.655000	0.94253	GCG	.	.		0.692	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48699314	C	A	48699314	3	1	70	1	0	0	0	0	1	0	0	0	3225	739	26	3	9324	3	CELSR3	3	48699314	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	1611206	48699314	149323116	29	8960										
NISCH	11188	hgsc.bcm.edu	37	chr3	52525454	52525454	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	agcacctcatggtcgtgctgTcctctctggaacgcacgccc	10	16	2	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr3:52525454T>G	ENST00000479054.1	+	21	3901	c.3829T>G	c.(3829-3831)Tcc>Gcc	p.S1277A	NISCH_ENST00000345716.4_Missense_Mutation_p.S1277A			Q9Y2I1	NISCH_HUMAN	nischarin	1277					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	GGTCGTGCTGTCCTCTCTGGA	0.607																																					p.S1277A		Atlas-SNP	.											.	NISCH	97	.	0			c.T3829G						.						85	64	71					3																	52525454		2203	4300	6503	SO:0001583	missense	11188	exon20			GTGCTGTCCTCTC	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"imidazoline receptor candidate", "I-1 receptor candidate protein", "imidazoline receptor antisera selected"	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.3829T>G	chr3.hg19:g.52525454T>G	ENSP00000418232:p.Ser1277Ala	63.0	0.0		77.0	26.0	NM_007184	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	hg19	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.079608	0.76528	.	.	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000433196;ENST00000414197	T;T	0.17691	2.26;2.26	5.8	4.64	0.57946	.	0.180012	0.50627	D	0.000105	T	0.14614	0.0353	L	0.34521	1.04	0.39107	D	0.961404	B	0.23650	0.089	B	0.23852	0.049	T	0.04467	-1.0949	10	0.51188	T	0.08	-32.8662	11.8542	0.52427	0.0:0.0681:0.0:0.9318	.	1277	Q9Y2I1	NISCH_HUMAN	A	1277;1277;201;621	ENSP00000418232:S1277A;ENSP00000339958:S1277A	ENSP00000339958:S1277A	S	+	1	0	NISCH	52500494	0.998000	0.40836	0.944000	0.38274	0.804000	0.45430	3.187000	0.50950	1.029000	0.39812	0.459000	0.35465	TCC	.	.		0.607	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		G	52525454	T	G	52525454	3	3	70	1	0	0	0	0	1	0	0	0	10441	1667	58	5	3907	5	NISCH	3	52525454	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	3826140	52525454	145496976	30	8961										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151162741	151162741	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gtccaatgaatggtgggcagGggatttccaacagcttcaca	12	9	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr3:151162741G>A	ENST00000282466.3	-	4	5027	c.5028C>T	c.(5026-5028)ccC>ccT	p.P1676P		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1676	Ig-like C2-type 3.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGGTGGGCAGGGGATTTCCAA	0.388																																					p.P1676P		Atlas-SNP	.											.	IGSF10	279	.	0			c.C5028T						.						78	82	80					3																	151162741		2203	4300	6503	SO:0001819	synonymous_variant	285313	exon4			GGGCAGGGGATTT	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5028C>T	chr3.hg19:g.151162741G>A		81.0	0.0		95.0	9.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	hg19	CCDS3160.1																																																																																			.	.		0.388	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151162741	G	A	151162741	2	1	70	1	0	0	0	0	0	0	0	1	7606	1219	43	3		3	IGSF10	3	151162741	Silent	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	98637287	151162741	46859689	31	8962										
GMPS	8833	hgsc.bcm.edu	37	chr3	155655379	155655379	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ctctataattttttttaataGgtggtattaaagatggtcac	7	4	2	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr3:155655379G>A	ENST00000496455.2	+	16	2315		c.e16-1		GMPS_ENST00000295920.7_Splice_Site	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase						glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|GMP synthase (glutamine-hydrolyzing) activity (GO:0003922)|GMP synthase activity (GO:0003921)|pyrophosphatase activity (GO:0016462)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamine(DB00130)	TTTTTTAATAGGTGGTATTAA	0.353			T	MLL	AML																																.	Ovarian(153;896 1876 4149 15499 28134)	Atlas-SNP	.		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	.	GMPS	70	.	0			c.1981-1G>A						.						58	58	58					3																	155655379		1808	4074	5882	SO:0001630	splice_region_variant	8833	exon16			TTAATAGGTGGTA	U10860	CCDS46941.1	3q25.31	2013-06-18	2013-06-18		ENSG00000163655	ENSG00000163655	6.3.5.2		4378	protein-coding gene	gene with protein product	"GMP synthase"	600358	"guanine monphosphate synthetase"			8089153, 9195163	Standard	NM_003875		Approved		uc003faq.3	P49915	OTTHUMG00000158551	ENST00000496455.2:c.1981-1G>A	chr3.hg19:g.155655379G>A		165.0	0.0		221.0	112.0	NM_003875	A8K639|B4DXV7|F8W720	Splice_Site	SNP	ENST00000496455.2	hg19	CCDS46941.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.283208	0.80803	.	.	ENSG00000163655	ENST00000496455;ENST00000295920;ENST00000537975;ENST00000541628	.	.	.	4.97	4.97	0.65823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2479	0.89993	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GMPS	157138073	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	9.185000	0.94900	2.322000	0.78497	0.655000	0.94253	.	.	.		0.353	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351260.2		Intron	A	155655379	G	A	155655379	5	1	70	1	0	0	0	0	0	0	1	0	6506	1014	35	3	2042	3	GMPS	3	155655379	Splice_Site	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	4492638	155655379	42367051	32	8963										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164907422	164907422	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cttggaagaagttcagaaatGttattaaatcctcgctcttt	7	7	2	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr3:164907422G>A	ENST00000475390.1	-	2	1640	c.1197C>T	c.(1195-1197)aaC>aaT	p.N399N	SLITRK3_ENST00000241274.3_Silent_p.N399N			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	399	LRRNT.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						GTTCAGAAATGTTATTAAATC	0.403										HNSCC(40;0.11)																											p.N399N		Atlas-SNP	.											.	SLITRK3	263	.	0			c.C1197T						.						109	109	109					3																	164907422		2203	4300	6503	SO:0001819	synonymous_variant	22865	exon2			AGAAATGTTATTA	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1197C>T	chr3.hg19:g.164907422G>A		111.0	0.0		145.0	13.0	NM_014926	Q1RMY6	Silent	SNP	ENST00000475390.1	hg19	CCDS3197.1																																																																																			.	.		0.403	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		A	164907422	G	A	164907422	2	1	70	1	0	0	0	0	0	0	0	1	14759	1368	48	3		3	SLITRK3	3	164907422	Silent	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	9252043	164907422	33115008	33	8964										
TFRC	7037	hgsc.bcm.edu	37	chr3	195792415	195792415	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cattcttgctttctgaggttAccatcctacatgtagagtct	7	10	3	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr3:195792415A>G	ENST00000360110.4	-	10	1266	c.1097T>C	c.(1096-1098)gTa>gCa	p.V366A	TFRC_ENST00000535031.1_Missense_Mutation_p.V84A|TFRC_ENST00000392396.3_Missense_Mutation_p.V366A|TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000420415.1_Missense_Mutation_p.V285A|TFRC_ENST00000465288.1_5'Flank	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	366					cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|osteoclast differentiation (GO:0030316)|positive regulation of bone resorption (GO:0045780)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transferrin receptor activity (GO:0004998)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)	Gallium nitrate(DB05260)	TTCTGAGGTTACCATCCTACA	0.398			T	BCL6	NHL																																p.V366A		Atlas-SNP	.		Dom	yes		3	3q29	7037	"transferrin receptor (p90, CD71)"		L	.	TFRC	54	.	0			c.T1097C						.						148	147	148					3																	195792415		2203	4300	6503	SO:0001583	missense	7037	exon10			GAGGTTACCATCC	X01060	CCDS3312.1	3q29	2013-09-19	2013-09-19		ENSG00000072274	ENSG00000072274		"CD molecules"	11763	protein-coding gene	gene with protein product		190010	"transferrin receptor (p90, CD71)"				Standard	NM_003234		Approved	CD71, TFR1, p90	uc003fwa.4	P02786	OTTHUMG00000155714	ENST00000360110.4:c.1097T>C	chr3.hg19:g.195792415A>G	ENSP00000353224:p.Val366Ala	33.0	0.0		60.0	4.0	NM_001128148	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Missense_Mutation	SNP	ENST00000360110.4	hg19	CCDS3312.1	.	.	.	.	.	.	.	.	.	.	A	7.515	0.655395	0.14580	.	.	ENSG00000072274	ENST00000360110;ENST00000420415;ENST00000392396;ENST00000535031	T;T;T;T	0.73258	3.11;3.11;3.11;-0.73	4.98	-7.22	0.01485	.	2.290060	0.01034	N	0.004191	T	0.57021	0.2025	L	0.60455	1.87	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.36138	-0.9760	10	0.13470	T	0.59	2.6608	2.5417	0.04727	0.486:0.2724:0.0999:0.1417	.	366	P02786	TFR1_HUMAN	A	366;285;366;84	ENSP00000353224:V366A;ENSP00000390133:V285A;ENSP00000376197:V366A;ENSP00000437753:V84A	ENSP00000353224:V366A	V	-	2	0	TFRC	197276812	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.984000	0.01487	-1.103000	0.03019	-0.619000	0.04042	GTA	.	.		0.398	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1			G	195792415	A	G	195792415	3	3	70	1	0	0	0	0	1	0	0	0	15827	391	14	2	1225	2	TFRC	3	195792415	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	30884993	195792415	2230015	34	8965										
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6863293	6863293	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ggagaatagaaaggacacagAgtataaagaggagcccttgt	13	5	0	4			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr4:6863293A>T	ENST00000307659.5	+	7	1639	c.1184A>T	c.(1183-1185)gAg>gTg	p.E395V	KIAA0232_ENST00000425103.1_Missense_Mutation_p.E395V	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	395							ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						AAGGACACAGAGTATAAAGAG	0.438																																					p.E395V		Atlas-SNP	.											.	KIAA0232	102	.	0			c.A1184T						.						60	63	62					4																	6863293		1867	4102	5969	SO:0001583	missense	9778	exon7			ACACAGAGTATAA	D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.1184A>T	chr4.hg19:g.6863293A>T	ENSP00000303928:p.Glu395Val	108.0	0.0		78.0	11.0	NM_014743	A7E2D2	Missense_Mutation	SNP	ENST00000307659.5	hg19	CCDS43209.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.703767	0.48412	.	.	ENSG00000170871	ENST00000425103;ENST00000307659	.	.	.	5.9	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.64427	0.2597	M	0.66939	2.045	0.54753	D	0.999989	P	0.45715	0.865	P	0.49665	0.618	T	0.67333	-0.5697	9	0.87932	D	0	-24.7468	11.7686	0.51945	0.9313:0.0:0.0687:0.0	.	395	Q92628	K0232_HUMAN	V	395	.	ENSP00000303928:E395V	E	+	2	0	KIAA0232	6914194	1.000000	0.71417	0.159000	0.22649	0.076000	0.17211	6.893000	0.75649	1.049000	0.40321	0.533000	0.62120	GAG	.	.		0.438	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		T	6863293	A	T	6863293	3	4	70	1	0	0	0	0	1	0	0	0	8172	304	11	4	1202	4	KIAA0232	4	6863293	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10		6863293	184290983	35	8966										
CPZ	8532	hgsc.bcm.edu	37	chr4	8605757	8605757	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gctgccgcccaccttcatccGcttcagccaccactcctacg	6	21	2	0	rs376798665		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr4:8605757G>A	ENST00000360986.4	+	4	725	c.551G>A	c.(550-552)cGc>cAc	p.R184H	CPZ_ENST00000382480.2_Missense_Mutation_p.R47H|CPZ_ENST00000429646.2_5'UTR|CPZ_ENST00000315782.6_Missense_Mutation_p.R173H	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	184					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						ACCTTCATCCGCTTCAGCCAC	0.701																																					p.R184H		Atlas-SNP	.											.	CPZ	95	.	0			c.G551A						.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4348		0,0,2174	30	25	26		551,140,518	-2.9	0.2	4		26	2,8516		0,2,4257	no	missense,missense,missense	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	29,29,29	0,2,6431	AA,AG,GG		0.0235,0.0,0.0155	benign,benign,benign	184/653,47/516,173/642	8605757	2,12864	2174	4259	6433	SO:0001583	missense	8532	exon4			TCATCCGCTTCAG	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.551G>A	chr4.hg19:g.8605757G>A	ENSP00000354255:p.Arg184His	90.0	0.0		69.0	13.0	NM_001014447	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	hg19	CCDS33953.1	.	.	.	.	.	.	.	.	.	.	G	7.156	0.584727	0.13749	0.0	2.35E-4	ENSG00000109625	ENST00000360986;ENST00000382480;ENST00000315782	T;T;T	0.03301	3.98;3.98;3.98	3.86	-2.92	0.05615	.	0.595436	0.18160	N	0.149807	T	0.01870	0.0059	N	0.12182	0.205	0.80722	D	1	B;B	0.20671	0.047;0.028	B;B	0.14578	0.011;0.005	T	0.49021	-0.8982	10	0.54805	T	0.06	-15.3796	5.3119	0.15835	0.6471:0.0:0.2035:0.1494	.	173;184	Q66K79-2;Q66K79	.;CBPZ_HUMAN	H	184;47;173	ENSP00000354255:R184H;ENSP00000371920:R47H;ENSP00000315074:R173H	ENSP00000315074:R173H	R	+	2	0	CPZ	8656657	0.061000	0.20836	0.155000	0.22561	0.108000	0.19459	-0.006000	0.12833	-0.543000	0.06240	-0.228000	0.12330	CGC	.	.		0.701	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		A	8605757	G	A	8605757	3	1	70	1	0	0	0	0	1	0	0	0	3841	1087	38	1	565	1	CPZ	4	8605757	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	1742464	8605757	182548519	36	8967										
GC	2638	hgsc.bcm.edu	37	chr4	72634108	72634108	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	acaagttggctgacctgttcAaacgtgccactgggaaattt	10	9	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr4:72634108A>G	ENST00000273951.8	-	3	514	c.171T>C	c.(169-171)ttT>ttC	p.F57F	GC_ENST00000503472.1_5'UTR|GC_ENST00000513476.1_Silent_p.F57F|GC_ENST00000504199.1_Silent_p.F76F	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	57	Albumin 1. {ECO:0000255|PROSITE- ProRule:PRU00769}.				small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	actin binding (GO:0003779)|calcidiol binding (GO:1902118)|vitamin D binding (GO:0005499)|vitamin transporter activity (GO:0051183)			endometrium(5)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	45		all_hematologic(202;0.107)	Lung(101;0.148)		Alfacalcidol(DB01436)|Cholecalciferol(DB00169)	TGACCTGTTCAAACGTGCCAC	0.453																																					p.F76F		Atlas-SNP	.											.	GC	132	.	0			c.T228C						.						66	59	61					4																	72634108		2203	4300	6503	SO:0001819	synonymous_variant	2638	exon4			CTGTTCAAACGTG	L10641	CCDS3550.1, CCDS56332.1	4q12-q13	2008-08-29			ENSG00000145321	ENSG00000145321			4187	protein-coding gene	gene with protein product		139200				558959	Standard	NM_000583		Approved	DBP, VDBP, hDBP	uc010iif.3	P02774	OTTHUMG00000129915	ENST00000273951.8:c.171T>C	chr4.hg19:g.72634108A>G		291.0	0.0		230.0	14.0	NM_001204307	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Silent	SNP	ENST00000273951.8	hg19	CCDS3550.1																																																																																			.	.		0.453	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2			G	72634108	A	G	72634108	2	3	70	1	0	0	0	0	0	0	0	1	6290	127	5	2		2	GC	4	72634108	Silent	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	64028351	72634108	118520168	37	8968										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	73956454	73956454	+	Frame_Shift_Del	DEL	T	T	-													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttggaagtatcagactgatgTaaaggatctgaatttggcaa							TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr4:73956454delT	ENST00000358602.4	-	29	7007	c.6891delA	c.(6889-6891)ttafs	p.L2297fs	ANKRD17_ENST00000330838.6_Frame_Shift_Del_p.L2046fs|ANKRD17_ENST00000509867.2_Frame_Shift_Del_p.L2184fs	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2297					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CAGACTGATGTAAAGGATCTG	0.433																																					p.H2298fs		Atlas-Indel,Pindel	.											.	ANKRD17	214	.	0			c.6892delC						.						132	139	137					4																	73956454		2203	4300	6503	SO:0001589	frameshift_variant	26057	exon29			.	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.6891delA	chr4.hg19:g.73956454delT	ENSP00000351416:p.Leu2297fs	158.0	0.0		146.0	31.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Frame_Shift_Del	DEL	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.433	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		-	73956454	T	-	73956454	7	5	70	1	0	1	0	1	0	0	0	0	646	1635	57	0	944	0	ANKRD17	4	73956454	Frame_Shift_Del	DEL	T	TCGA-CC-A7IE-01A-21D-A382-10	1322346	73956454	117197822	38	8969										
MAPK10	5602	hgsc.bcm.edu	37	chr4	87022310	87022310	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcctgctgtcctggccagtcCaaagtccaggattttcaatg	10	12	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr4:87022310C>T	ENST00000359221.3	-	8	1151	c.625G>A	c.(625-627)Gga>Aga	p.G209R	MAPK10_ENST00000395161.2_Missense_Mutation_p.G209R|MAPK10_ENST00000513839.1_5'Flank|MAPK10_ENST00000395157.3_Missense_Mutation_p.G64R|MAPK10_ENST00000449047.2_Missense_Mutation_p.G64R|MAPK10_ENST00000395169.3_Missense_Mutation_p.G171R|MAPK10_ENST00000395166.1_Missense_Mutation_p.G171R|MAPK10_ENST00000395160.3_Missense_Mutation_p.G64R|MAPK10_ENST00000361569.2_Missense_Mutation_p.G209R			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	209	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)			breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		CTGGCCAGTCCAAAGTCCAGG	0.438																																					p.G209R		Atlas-SNP	.											.	MAPK10	106	.	0			c.G625A						.						109	93	99					4																	87022310		2203	4300	6503	SO:0001583	missense	5602	exon8			CCAGTCCAAAGTC	U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.625G>A	chr4.hg19:g.87022310C>T	ENSP00000352157:p.Gly209Arg	128.0	0.0		107.0	25.0	NM_002753	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Missense_Mutation	SNP	ENST00000359221.3	hg19	CCDS34026.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.3|29.3	4.991094|4.991094	0.93106|0.93106	.|.	.|.	ENSG00000109339|ENSG00000109339	ENST00000395169;ENST00000359221;ENST00000395157;ENST00000361569;ENST00000395166;ENST00000395160;ENST00000449047;ENST00000395161|ENST00000515400	D;D;D;D;D;D;D;D|.	0.98192|.	-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78|.	6.03|6.03	5.19|5.19	0.71726|0.71726	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.095507|.	0.64402|.	D|.	0.000001|.	D|.	0.88187|.	0.6369|.	H|H	0.97659|0.97659	4.05|4.05	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	1.0;1.0;0.995;0.997;0.998|.	D|.	0.92335|.	0.5877|.	10|.	0.87932|.	D|.	0|.	-6.5185|-6.5185	15.2436|15.2436	0.73490|0.73490	0.0:0.9329:0.0:0.0671|0.0:0.9329:0.0:0.0671	.|.	95;64;171;209;209|.	B7Z1Z1;Q499Y8;P53779-3;P53779-2;P53779|.	.;.;.;.;MK10_HUMAN|.	R|X	171;209;64;209;171;64;64;209|121	ENSP00000378598:G171R;ENSP00000352157:G209R;ENSP00000378586:G64R;ENSP00000355297:G209R;ENSP00000378595:G171R;ENSP00000378589:G64R;ENSP00000414469:G64R;ENSP00000378590:G209R|.	ENSP00000352157:G209R|.	G|W	-|-	1|2	0|0	MAPK10|MAPK10	87241334|87241334	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.818000|7.818000	0.86416|0.86416	1.558000|1.558000	0.49541|0.49541	0.557000|0.557000	0.71058|0.71058	GGA|TGG	.	.		0.438	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			T	87022310	C	T	87022310	3	4	70	1	0	0	0	0	1	0	0	0	9281	603	21	3	802	3	MAPK10	4	87022310	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	13065856	87022310	104131966	39	8970										
CXXC4	80319	hgsc.bcm.edu	37	chr4	105393500	105393500	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	taaaagaaccatcggaatgcTtcagcgctgggaacaggtgt	12	8	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr4:105393500T>A	ENST00000426831.1	-	2	590	c.576A>T	c.(574-576)gaA>gaT	p.E192D	CXXC4_ENST00000394767.2_Missense_Mutation_p.E361D|CXXC4_ENST00000466963.1_5'UTR			Q9H2H0	CXXC4_HUMAN	CXXC finger protein 4	192					negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)|zygotic specification of dorsal/ventral axis (GO:0007352)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)	DNA binding (GO:0003677)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(123;3.05e-08)		ATCGGAATGCTTCAGCGCTGG	0.338																																					p.E361D		Atlas-SNP	.											.	CXXC4	20	.	0			c.A1083T						.						104	109	107					4																	105393500		2202	4299	6501	SO:0001583	missense	80319	exon3			GAATGCTTCAGCG		CCDS3665.1, CCDS3665.2	4q22-q24	2014-02-18	2011-12-01		ENSG00000168772	ENSG00000168772			24593	protein-coding gene	gene with protein product	"Dvl-binding protein IDAX (inhibition of the Dvl and Axin complex)"	611645				11113207	Standard	NM_025212		Approved	IDAX	uc003hxf.2	Q9H2H0	OTTHUMG00000131121	ENST00000426831.1:c.576A>T	chr4.hg19:g.105393500T>A	ENSP00000412267:p.Glu192Asp	671.0	1.0		522.0	109.0	NM_025212		Missense_Mutation	SNP	ENST00000426831.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.92	2.081517	0.36758	.	.	ENSG00000168772	ENST00000394767;ENST00000426831	.	.	.	5.36	5.36	0.76844	.	0.930043	0.09045	N	0.856610	T	0.64800	0.2631	N	0.22421	0.69	0.42198	D	0.991753	P	0.52842	0.956	P	0.62184	0.899	T	0.58869	-0.7560	9	0.48119	T	0.1	-0.5135	15.3495	0.74370	0.0:0.0:0.0:1.0	.	192	Q9H2H0	CXXC4_HUMAN	D	192	.	ENSP00000378248:E192D	E	-	3	2	CXXC4	105612949	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.927000	0.56499	2.028000	0.59812	0.533000	0.62120	GAA	.	.		0.338	CXXC4-201	KNOWN	basic	protein_coding	protein_coding		NM_025212		A	105393500	T	A	105393500	3	1	70	1	0	0	0	0	1	0	0	0	4100	1606	56	4	24	4	CXXC4	4	105393500	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	18371190	105393500	85760776	40	8971										
ANK2	287	hgsc.bcm.edu	37	chr4	114244937	114244937	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcgcctctccatgtcttgaaCgtgacaacagcaggtgaact	10	12	2	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr4:114244937C>T	ENST00000357077.4	+	26	2953				ANK2_ENST00000506722.1_Missense_Mutation_p.R954C|ANK2_ENST00000264366.6_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000509550.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal						atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ATGTCTTGAACGTGACAACAG	0.448																																					p.R954C		Atlas-SNP	.											.	ANK2	576	.	0			c.C2860T						.						98	86	90					4																	114244937		1568	3582	5150	SO:0001627	intron_variant	287	exon28			CTTGAACGTGACA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.2900+5161C>T	chr4.hg19:g.114244937C>T		101.0	0.0		94.0	20.0	NM_001127493	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.168322	0.57584	.	.	ENSG00000145362	ENST00000506722;ENST00000343056	T	0.66815	-0.23	5.53	5.53	0.82687	.	.	.	.	.	T	0.52597	0.1744	N	0.08118	0	0.80722	D	1	P	0.47350	0.894	B	0.43052	0.406	T	0.58053	-0.7704	9	0.38643	T	0.18	.	19.4713	0.94963	0.0:1.0:0.0:0.0	.	954	Q01484-5	.	C	954	ENSP00000421067:R954C	ENSP00000340561:R954C	R	+	1	0	ANK2	114464386	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.380000	0.66202	2.587000	0.87381	0.563000	0.77884	CGT	.	.		0.448	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114244937	C	T	114244937	1	4	70	0	1	0	0	0	0	0	0	0	621	536	19	1		1	ANK2	4	114244937	Intron	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	8851437	114244937	76909339	41	8972										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155252859	155252859	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gttatgacatagatggtgccTgctggacctgcacaaaaagg	12	8	0	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr4:155252859T>A	ENST00000357232.4	-	10	2240	c.2241A>T	c.(2239-2241)gcA>gcT	p.A747A	DCHS2_ENST00000507542.1_5'Flank|DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	747	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AGATGGTGCCTGCTGGACCTG	0.473																																					p.A747A		Atlas-SNP	.											.	DCHS2	594	.	0			c.A2241T						.						49	43	45					4																	155252859		2203	4300	6503	SO:0001819	synonymous_variant	54798	exon10			GGTGCCTGCTGGA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.2241A>T	chr4.hg19:g.155252859T>A		192.0	0.0		170.0	42.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	hg19	CCDS3785.1																																																																																			.	.		0.473	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155252859	T	A	155252859	2	1	70	1	0	0	0	0	0	0	0	1	4290	1567	55	4		4	DCHS2	4	155252859	Silent	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	41007922	155252859	35901417	42	8973										
FAM151B	167555	hgsc.bcm.edu	37	chr5	79817830	79817830	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttttcttttaagggtacagtTggacaatggtgaaagagatg	12	3	1	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr5:79817830T>C	ENST00000282226.4	+	5	699	c.544T>C	c.(544-546)Tgg>Cgg	p.W182R	FAM151B_ENST00000511718.1_3'UTR	NM_205548.2	NP_991111.2	Q6UXP7	F151B_HUMAN	family with sequence similarity 151, member B	182										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	7		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		AGGGTACAGTTGGACAATGGT	0.318																																					p.W182R		Atlas-SNP	.											.	FAM151B	25	.	0			c.T544C						.						90	85	87					5																	79817830		2203	4300	6503	SO:0001583	missense	167555	exon5			TACAGTTGGACAA		CCDS4051.1	5q14.1	2007-12-18	2007-12-18		ENSG00000152380	ENSG00000152380			33716	protein-coding gene	gene with protein product							Standard	NM_205548		Approved	UNQ9217	uc003kgv.2	Q6UXP7	OTTHUMG00000131303	ENST00000282226.4:c.544T>C	chr5.hg19:g.79817830T>C	ENSP00000282226:p.Trp182Arg	61.0	0.0		54.0	20.0	NM_205548	A2RRE4	Missense_Mutation	SNP	ENST00000282226.4	hg19	CCDS4051.1	.	.	.	.	.	.	.	.	.	.	T	10.87	1.472617	0.26423	.	.	ENSG00000152380	ENST00000282226	T	0.10288	2.89	5.77	5.77	0.91146	.	0.108809	0.64402	D	0.000002	T	0.21307	0.0513	L	0.42686	1.345	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.03453	-1.1035	10	0.06236	T	0.91	-13.1571	15.0752	0.72071	0.0:0.0:0.0:1.0	.	182	Q6UXP7	F151B_HUMAN	R	182	ENSP00000282226:W182R	ENSP00000282226:W182R	W	+	1	0	FAM151B	79853586	1.000000	0.71417	0.990000	0.47175	0.993000	0.82548	6.945000	0.75947	2.208000	0.71279	0.533000	0.62120	TGG	.	.		0.318	FAM151B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254072.1	NM_205548		C	79817830	T	C	79817830	3	2	70	1	0	0	0	0	1	0	0	0	5464	1812	63	2	562	2	FAM151B	5	79817830	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10		79817830	101097430	43	8974										
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109178131	109178131	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttctgatataaaaagccaaaAtagattttatactgacctaa	4	6	1	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr5:109178131A>G	ENST00000261483.4	+	17	3721	c.2669A>G	c.(2668-2670)aAt>aGt	p.N890S		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	890					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		AAAAGCCAAAATAGATTTTAT	0.313																																					p.N890S		Atlas-SNP	.											.	MAN2A1	136	.	0			c.A2669G						.						51	57	55					5																	109178131		2201	4287	6488	SO:0001583	missense	4124	exon17			GCCAAAATAGATT		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.2669A>G	chr5.hg19:g.109178131A>G	ENSP00000261483:p.Asn890Ser	449.0	0.0		473.0	178.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	A	13.91	2.378208	0.42105	.	.	ENSG00000112893	ENST00000261483	D	0.83075	-1.68	5.49	4.32	0.51571	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.202673	0.51477	N	0.000091	T	0.75788	0.3897	L	0.43152	1.355	0.44834	D	0.997846	B	0.21071	0.051	B	0.25405	0.06	T	0.67177	-0.5736	10	0.18276	T	0.48	-21.9466	11.4115	0.49929	0.9288:0.0:0.0712:0.0	.	890	Q16706	MA2A1_HUMAN	S	890	ENSP00000261483:N890S	ENSP00000261483:N890S	N	+	2	0	MAN2A1	109206030	1.000000	0.71417	0.992000	0.48379	0.992000	0.81027	8.239000	0.89811	1.012000	0.39366	0.477000	0.44152	AAT	.	.		0.313	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			G	109178131	A	G	109178131	3	3	70	1	0	0	0	0	1	0	0	0	9223	101	4	2	2735	2	MAN2A1	5	109178131	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	29360301	109178131	71737129	44	8975										
SLC12A2	6558	hgsc.bcm.edu	37	chr5	127520082	127520082	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	atagcttttgaggaaatcatTgagccatacagacttcatga	8	7	2	4			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr5:127520082T>A	ENST00000262461.2	+	25	3513	c.3324T>A	c.(3322-3324)atT>atA	p.I1108I	SLC12A2_ENST00000343225.4_Silent_p.I1092I|SLC12A2_ENST00000507791.1_3'UTR	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	1108					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	AGGAAATCATTGAGCCATACA	0.284																																					p.I1108I		Atlas-SNP	.											.	SLC12A2	119	.	0			c.T3324A						.						97	99	98					5																	127520082		2202	4300	6502	SO:0001819	synonymous_variant	6558	exon25			AATCATTGAGCCA		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.3324T>A	chr5.hg19:g.127520082T>A		323.0	0.0		345.0	61.0	NM_001046	Q8N713|Q8WWH7	Silent	SNP	ENST00000262461.2	hg19	CCDS4144.1																																																																																			.	.		0.284	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		A	127520082	T	A	127520082	2	1	70	1	0	0	0	0	0	0	0	1	14398	1800	63	4		4	SLC12A2	5	127520082	Silent	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	18341951	127520082	53395178	45	8976										
PCDHB2	56133	hgsc.bcm.edu	37	chr5	140476346	140476346	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	agcctccgcgctcggccaccGccacgctgcacgtgctcctg	11	20	0	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr5:140476346G>A	ENST00000194155.4	+	1	2120	c.1972G>A	c.(1972-1974)Gcc>Acc	p.A658T		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	658	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A658T(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCGGCCACCGCCACGCTGCA	0.711																																					p.A658T		Atlas-SNP	.											PCDHB2,NS,carcinoma,0,1	PCDHB2	163	.	1	Substitution - Missense(1)	prostate(1)	c.G1972A						.						35	35	35					5																	140476346		1915	3814	5729	SO:0001583	missense	56133	exon1			GCCACCGCCACGC	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"Cadherins / Protocadherins : Clustered"	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1972G>A	chr5.hg19:g.140476346G>A	ENSP00000194155:p.Ala658Thr	107.0	0.0		74.0	28.0	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	hg19	CCDS4244.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.104468	0.37145	.	.	ENSG00000112852	ENST00000194155	T	0.50548	0.74	3.99	3.99	0.46301	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.44871	0.1314	L	0.49571	1.57	0.28971	N	0.889222	B	0.29590	0.25	B	0.24848	0.056	T	0.50406	-0.8832	9	0.66056	D	0.02	.	16.1298	0.81418	0.0:0.0:1.0:0.0	.	658	Q9Y5E7	PCDB2_HUMAN	T	658	ENSP00000194155:A658T	ENSP00000194155:A658T	A	+	1	0	PCDHB2	140456530	0.260000	0.24053	1.000000	0.80357	0.344000	0.29017	3.030000	0.49720	1.921000	0.55644	0.456000	0.33151	GCC	.	.		0.711	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		A	140476346	G	A	140476346	3	1	70	1	0	0	0	0	1	0	0	0	11551	1087	38	1	1974	1	PCDHB2	5	140476346	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	12956264	140476346	40438914	46	8977										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140562936	140562936	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttgccaccgtctccgccaggGatttagacggcggagccaat	12	13	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr5:140562936G>T	ENST00000361016.2	+	1	1957	c.802G>T	c.(802-804)Gat>Tat	p.D268Y		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	268	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCCGCCAGGGATTTAGACGG	0.478																																					p.D268Y		Atlas-SNP	.											.	PCDHB16	159	.	0			c.G802T						.						62	64	64					5																	140562936		2203	4300	6503	SO:0001583	missense	57717	exon1			GCCAGGGATTTAG	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.802G>T	chr5.hg19:g.140562936G>T	ENSP00000354293:p.Asp268Tyr	68.0	0.0		72.0	20.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.377667	0.82682	.	.	ENSG00000196963	ENST00000361016	T	0.75260	-0.92	4.75	4.75	0.60458	Cadherin (5);Cadherin-like (1);	0.000000	0.35585	N	0.003116	D	0.93141	0.7816	H	0.99820	4.81	0.54753	D	0.999984	D	0.89917	1.0	D	0.97110	1.0	D	0.96830	0.9610	10	0.87932	D	0	.	17.7391	0.88403	0.0:0.0:1.0:0.0	.	268	Q9NRJ7	PCDBG_HUMAN	Y	268	ENSP00000354293:D268Y	ENSP00000354293:D268Y	D	+	1	0	PCDHB16	140543120	1.000000	0.71417	0.142000	0.22268	0.891000	0.51852	9.792000	0.99085	2.169000	0.68431	0.591000	0.81541	GAT	.	.		0.478	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		T	140562936	G	T	140562936	3	4	70	1	0	0	0	0	1	0	0	0	11550	1174	41	3	804	3	PCDHB16	5	140562936	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	86590	140562936	40352324	47	8978										
SOX30	11063	hgsc.bcm.edu	37	chr5	157053481	157053481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	caatgtccagctgaggcacaGggtttaagttttcttcccca	9	11	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr5:157053481G>A	ENST00000265007.6	-	5	2470	c.2129C>T	c.(2128-2130)cCt>cTt	p.P710L	SOX30_ENST00000311371.5_3'UTR|SOX30_ENST00000519442.1_Missense_Mutation_p.P405L	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	710					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTGAGGCACAGGGTTTAAGTT	0.458																																					p.P710L	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.C2129T						.						135	113	120					5																	157053481		2203	4300	6503	SO:0001583	missense	11063	exon5			GGCACAGGGTTTA	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"SRY (sex determining region Y)-boxes"	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.2129C>T	chr5.hg19:g.157053481G>A	ENSP00000265007:p.Pro710Leu	82.0	0.0		78.0	49.0	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	hg19	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	G	8.431	0.848514	0.17034	.	.	ENSG00000039600	ENST00000265007;ENST00000519442	D;D	0.98234	-4.54;-4.81	5.56	3.79	0.43588	.	0.101159	0.44285	D	0.000466	D	0.94231	0.8148	N	0.24115	0.695	0.46874	D	0.999231	B;B	0.32653	0.027;0.379	B;B	0.23716	0.012;0.048	D	0.92207	0.5773	10	0.87932	D	0	.	11.0271	0.47751	0.145:0.0:0.855:0.0	.	405;710	B4DXW7;O94993	.;SOX30_HUMAN	L	710;405	ENSP00000265007:P710L;ENSP00000427984:P405L	ENSP00000265007:P710L	P	-	2	0	SOX30	156986059	1.000000	0.71417	0.162000	0.22713	0.027000	0.11550	4.668000	0.61568	0.833000	0.34828	-0.142000	0.14014	CCT	.	.		0.458	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		A	157053481	G	A	157053481	3	1	70	1	0	0	0	0	1	0	0	0	14967	1000	35	3	136	3	SOX30	5	157053481	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	16490545	157053481	23861779	48	8979										
TLX3	30012	hgsc.bcm.edu	37	chr5	170736625	170736626	+	Missense_Mutation	DNP	GG	GG	AT													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	acctgagcctagcgcccgcaGgcgtgatccgggtgccggcg					rs368190023		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr5:170736625_170736626GG>AT	ENST00000296921.5	+	1	338_339	c.256_257GG>AT	c.(256-258)GGc>ATc	p.G86I		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	86					central nervous system development (GO:0007417)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|respiratory gaseous exchange (GO:0007585)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AGCGCCCGCAGGCGTGATCCGG	0.733			T	BCL11B	T-ALL																																p.G86S|p.G86V	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"T-cell leukemia, homeobox 3 (HOX11L2)"		L	.	TLX3	23	.	0			c.G256A|c.G257T						.																																			SO:0001583	missense	30012	exon1			CCCGCAGGCGTGA|CCGCAGGCGTGAT	AJ223798	CCDS34288.1	5q35.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000164438	ENSG00000164438		"Homeoboxes / ANTP class : NKL subclass"	13532	protein-coding gene	gene with protein product		604640	"homeo box 11-like 2", "T-cell leukemia, homeobox 3"	HOX11L2		11435718, 11435716	Standard	NM_021025		Approved	RNX	uc003mbf.3	O43711	OTTHUMG00000163207	Exception_encountered	chr5.hg19:g.170736625_170736626delinsAT	ENSP00000296921:p.Gly86Ile	118.0|117.0	0.0		129.0|130.0	64.0|65.0	NM_021025	Q96AD3	Missense_Mutation	SNP	ENST00000296921.5	hg19	CCDS34288.1																																																																																			.	.		0.733	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3			AT	170736626	GG	AT	170736625	3	1	70	1	0	0	0	0	1	0	0	0	15977	1000	35	3	258	3	TLX3	5	170736625	Missense_Mutation	DNP	GG	TCGA-CC-A7IE-01A-21D-A382-10	13683144	170736625	10178635	49	8980										
CNOT6	57472	hgsc.bcm.edu	37	chr5	180001165	180001165	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tcttactgcctttcctgcccCaagtcaacggcatccacctt	5	17	2	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr5:180001165C>G	ENST00000393356.1	+	14	2063	c.1639C>G	c.(1639-1641)Caa>Gaa	p.Q547E	CNOT6_ENST00000261951.4_Missense_Mutation_p.Q547E			Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	547	Nuclease domain. {ECO:0000250}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	exoribonuclease activity (GO:0004532)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|skin(1)	23	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		TTTCCTGCCCCAAGTCAACGG	0.517																																					p.Q547E		Atlas-SNP	.											.	CNOT6	47	.	0			c.C1639G						.						115	120	118					5																	180001165		2203	4300	6503	SO:0001583	missense	57472	exon12			CTGCCCCAAGTCA	AB033020	CCDS4455.1	5q35.3	2014-06-17			ENSG00000113300	ENSG00000113300			14099	protein-coding gene	gene with protein product		608951				11889047	Standard	XM_005265953		Approved	CCR4, KIAA1194, Ccr4a	uc003mlx.3	Q9ULM6	OTTHUMG00000130935	ENST00000393356.1:c.1639C>G	chr5.hg19:g.180001165C>G	ENSP00000377024:p.Gln547Glu	129.0	0.0		132.0	37.0	NM_015455	A7MD46|D3DWR0	Missense_Mutation	SNP	ENST00000393356.1	hg19	CCDS4455.1	.	.	.	.	.	.	.	.	.	.	C	2.020	-0.424892	0.04701	.	.	ENSG00000113300	ENST00000261951;ENST00000393356	T;T	0.28666	1.6;1.6	5.62	4.75	0.60458	.	0.354425	0.29473	N	0.012058	T	0.22399	0.0540	L	0.38175	1.15	0.34626	D	0.71911	B	0.09022	0.002	B	0.12156	0.007	T	0.16719	-1.0393	9	.	.	.	-0.0497	9.6219	0.39727	0.0:0.7834:0.1427:0.0739	.	547	Q9ULM6	CNOT6_HUMAN	E	547	ENSP00000261951:Q547E;ENSP00000377024:Q547E	.	Q	+	1	0	CNOT6	179933771	1.000000	0.71417	0.980000	0.43619	0.779000	0.44077	1.192000	0.32150	2.639000	0.89480	0.585000	0.79938	CAA	.	.		0.517	CNOT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253532.1	NM_015455		G	180001165	C	G	180001165	3	3	70	1	0	0	0	0	1	0	0	0	3624	595	21	4	1681	4	CNOT6	5	180001165	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	9264540	180001165	914095	50	8981										
HIST1H4D	8360	hgsc.bcm.edu	37	chr6	26189297	26189297	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cctttccgcccttaccgcggCcagacatcttgaaaccacag	7	17	1	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr6:26189297C>G	ENST00000340756.2	-	1	7	c.8G>C	c.(7-9)gGc>gCc	p.G3A		NM_003539.3	NP_003530.1	P62805	H4_HUMAN	histone cluster 1, H4d	3					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|large_intestine(2)|lung(1)|prostate(1)	8		all_hematologic(11;0.196)				CTTACCGCGGCCAGACATCTT	0.512																																					p.G3A		Atlas-SNP	.											.	HIST1H4D	28	.	0			c.G8C						.						49	53	51					6																	26189297		2203	4300	6503	SO:0001583	missense	8360	exon1			CCGCGGCCAGACA	X60482	CCDS4589.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000188987	ENSG00000277157		"Histones / Replication-dependent"	4782	protein-coding gene	gene with protein product		602823	"H4 histone family, member B", "histone 1, H4d"	H4FB		9119399, 12408966	Standard	NM_003539		Approved	H4/b	uc003ngu.3	P62805	OTTHUMG00000014423	ENST00000340756.2:c.8G>C	chr6.hg19:g.26189297C>G	ENSP00000343282:p.Gly3Ala	38.0	0.0		60.0	17.0	NM_003539	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000340756.2	hg19	CCDS4589.1	.	.	.	.	.	.	.	.	.	.	.	13.03	2.116706	0.37339	.	.	ENSG00000188987	ENST00000340756	.	.	.	5.32	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	.	.	.	0.40658	D	0.982103	.	.	.	.	.	.	T	0.71279	-0.4640	6	0.87932	D	0	.	13.0254	0.58812	0.0:0.9221:0.0:0.0779	.	.	.	.	A	3	.	ENSP00000343282:G3A	G	-	2	0	HIST1H4D	26297276	1.000000	0.71417	0.842000	0.33263	0.030000	0.12068	7.434000	0.80377	1.254000	0.44035	-0.142000	0.14014	GGC	.	.		0.512	HIST1H4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040085.1	NM_003539		G	26189297	C	G	26189297	3	3	70	1	0	0	0	0	1	0	0	0	7177	739	26	4	307	4	HIST1H4D	6	26189297	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10		26189297	144925770	51	8982										
MEP1A	4224	hgsc.bcm.edu	37	chr6	46803136	46803136	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cctacctgtcagcctgagccAggggcagcccagccgacaga	12	16	1	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr6:46803136A>T	ENST00000230588.4	+	13	1943	c.1934A>T	c.(1933-1935)cAg>cTg	p.Q645L		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	645					digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			AGCCTGAGCCAGGGGCAGCCC	0.607																																					p.Q645L		Atlas-SNP	.											.	MEP1A	93	.	0			c.A1934T						.						22	21	21					6																	46803136		2203	4300	6503	SO:0001583	missense	4224	exon13			TGAGCCAGGGGCA		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.1934A>T	chr6.hg19:g.46803136A>T	ENSP00000230588:p.Gln645Leu	88.0	0.0		108.0	35.0	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	hg19	CCDS4918.1	.	.	.	.	.	.	.	.	.	.	A	7.561	0.664682	0.14710	.	.	ENSG00000112818	ENST00000230588	T	0.24908	1.83	5.35	2.88	0.33553	.	0.784026	0.12295	N	0.481627	T	0.08582	0.0213	L	0.56769	1.78	0.18873	N	0.999981	B;B	0.30482	0.118;0.281	B;B	0.22601	0.025;0.04	T	0.27191	-1.0081	10	0.33940	T	0.23	-3.3402	6.602	0.22705	0.7619:0.1552:0.0828:0.0	.	673;645	B7ZL91;Q16819	.;MEP1A_HUMAN	L	645	ENSP00000230588:Q645L	ENSP00000230588:Q645L	Q	+	2	0	MEP1A	46911095	0.973000	0.33851	0.102000	0.21198	0.027000	0.11550	1.558000	0.36309	0.330000	0.23485	0.528000	0.53228	CAG	.	.		0.607	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		T	46803136	A	T	46803136	3	4	70	1	0	0	0	0	1	0	0	0	9484	188	7	4	1984	4	MEP1A	6	46803136	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	20613839	46803136	124311931	52	8983										
CRISP1	167	hgsc.bcm.edu	37	chr6	49825047	49825047	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	aaacatccaaccctcacataCtttcatggacaacataggca	4	13	2	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr6:49825047C>A	ENST00000335847.4	-	2	168		c.e2+1		CRISP1_ENST00000329411.5_Splice_Site|CRISP1_ENST00000507853.1_Splice_Site|CRISP1_ENST00000355791.2_Splice_Site|CRISP1_ENST00000505118.1_Splice_Site|CRISP1_ENST00000536021.1_Splice_Site	NM_001131.2	NP_001122.2	P54107	CRIS1_HUMAN	cysteine-rich secretory protein 1						binding of sperm to zona pellucida (GO:0007339)|fusion of sperm to egg plasma membrane (GO:0007342)|regulation of acrosome reaction (GO:0060046)	extracellular space (GO:0005615)|nucleus (GO:0005634)	calcium channel regulator activity (GO:0005246)			endometrium(1)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0358)					CCCTCACATACTTTCATGGAC	0.348																																					.		Atlas-SNP	.											.	CRISP1	45	.	0			c.66+1G>T						.						84	77	79					6																	49825047		2203	4300	6503	SO:0001630	splice_region_variant	167	exon3			CACATACTTTCAT	D38451	CCDS4931.1, CCDS4932.1	6p21.2-p21.1	2008-02-05	2003-09-03	2003-09-05	ENSG00000124812	ENSG00000124812			304	protein-coding gene	gene with protein product		601193	"acidic epididymal glycoprotein-like 1"	AEGL1		8838800	Standard	NM_001131		Approved	CRISP-1, ARP, HUMARP, HSCRISP1D, HSCRISP1G	uc003ozw.2	P54107	OTTHUMG00000014827	ENST00000335847.4:c.66+1G>T	chr6.hg19:g.49825047C>A		335.0	0.0		416.0	118.0	NM_170609	B5BU98|O00698|Q13248|Q14082|Q96SF6	Splice_Site	SNP	ENST00000335847.4	hg19	CCDS4931.1	.	.	.	.	.	.	.	.	.	.	C	7.857	0.725186	0.15439	.	.	ENSG00000124812	ENST00000507853;ENST00000335847;ENST00000355791;ENST00000329411;ENST00000505118;ENST00000536021	.	.	.	4.22	2.45	0.29901	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7782	0.23630	0.0:0.791:0.0:0.209	.	.	.	.	.	-1	.	.	.	-	.	.	CRISP1	49933006	0.797000	0.28877	0.530000	0.27963	0.018000	0.09664	1.357000	0.34090	0.743000	0.32719	0.655000	0.94253	.	.	.		0.348	CRISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040875.2	NM_001131	Intron	A	49825047	C	A	49825047	5	1	70	1	0	0	0	0	0	0	1	0	3881	579	20	3	710	3	CRISP1	6	49825047	Splice_Site	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	3021911	49825047	121290020	53	8984										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75853040	75853040	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tttccaggcacaggttcccaAaagacattcatagtgctgtg	9	10	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr6:75853040A>G	ENST00000322507.8	-	26	5064	c.4755T>C	c.(4753-4755)ttT>ttC	p.F1585F	COL12A1_ENST00000345356.6_Silent_p.F421F|COL12A1_ENST00000483888.2_Silent_p.F1585F|COL12A1_ENST00000416123.2_Silent_p.F1585F	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1585	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CAGGTTCCCAAAAGACATTCA	0.408																																					p.F1585F		Atlas-SNP	.											.	COL12A1	385	.	0			c.T4755C						.						143	130	134					6																	75853040		1870	4121	5991	SO:0001819	synonymous_variant	1303	exon26			TTCCCAAAAGACA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4755T>C	chr6.hg19:g.75853040A>G		109.0	0.0		122.0	23.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.408	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		G	75853040	A	G	75853040	2	3	70	1	0	0	0	0	0	0	0	1	3671	11	1	2		2	COL12A1	6	75853040	Silent	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	26027993	75853040	95262027	54	8985										
C6orf168	84553	hgsc.bcm.edu	37	chr6	99781226	99781227	+	Splice_Site	DNP	CC	CC	AG													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gacaccccagaggggactcaCcagtagaagtgctcctccac							TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr6:99781226_99781227CC>AG	ENST00000389677.5	-	3	881_882	c.599_600GG>CT	c.(598-600)tGG>tCT	p.W200S	FAXC_ENST00000538471.1_Intron	NM_032511.2	NP_115900.1	Q5TGI0	FAXC_HUMAN	failed axon connections homolog (Drosophila)	200						integral component of membrane (GO:0016021)											AGGGGACTCACCAGTAGAAGTG	0.495																																					.|p.W200S		Atlas-SNP	.											.	.	.	.	0			c.599+1G>T|c.G599C						.																																			SO:0001630	splice_region_variant	84553	exon4|exon3			GACTCACCAGTAG|ACTCACCAGTAGA	BC011583	CCDS34500.1	6q16.3	2012-02-07	2012-02-07	2012-02-07	ENSG00000146267	ENSG00000146267			20742	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 168"	C6orf168		12477932	Standard	NM_032511		Approved	MGC2817, dJ273F20	uc003ppj.4	Q5TGI0	OTTHUMG00000015261	ENST00000389677.5:c.599_600delinsAG	chr6.hg19:g.99781226_99781227delinsAG		81.0|83.0	0.0		79.0|81.0	22.0|23.0	NM_032511	B3KU39|Q96F61|Q96LU3|Q9BR58|Q9BSS2	Splice_Site|Missense_Mutation	SNP	ENST00000389677.5	hg19	CCDS34500.1																																																																																			.	.		0.495	FAXC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041589.4	NM_032511	Missense_Mutation	AG	99781227	CC	AG	99781226	5	1	70	1	0	0	0	0	0	0	1	0	2345	521	18	3	645	3	C6orf168	6	99781226	Splice_Site	DNP	CC	TCGA-CC-A7IE-01A-21D-A382-10	23928186	99781226	71333841	55	8986										
WASF1	8936	hgsc.bcm.edu	37	chr6	110448713	110448713	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttatatttgccaaggaaataTtggttacacattccagttca	6	7	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr6:110448713T>A	ENST00000392589.1	-	4	928	c.92A>T	c.(91-93)aAt>aTt	p.N31I	WASF1_ENST00000359451.2_Missense_Mutation_p.N31I|WASF1_ENST00000392587.2_Missense_Mutation_p.N31I|WASF1_ENST00000392588.1_Missense_Mutation_p.N31I|WASF1_ENST00000392586.1_Missense_Mutation_p.N31I	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	31					actin filament polymerization (GO:0030041)|cellular component movement (GO:0006928)|lamellipodium morphogenesis (GO:0072673)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|Rac protein signal transduction (GO:0016601)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|lamellipodium (GO:0030027)|mitochondrial outer membrane (GO:0005741)|SCAR complex (GO:0031209)|synapse (GO:0045202)	protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)		CAAGGAAATATTGGTTACACA	0.358																																					p.N31I		Atlas-SNP	.											.	WASF1	35	.	0			c.A92T						.						105	102	103					6																	110448713		2203	4300	6503	SO:0001583	missense	8936	exon3			GAAATATTGGTTA	D87459	CCDS5080.1	6q21	2010-08-20			ENSG00000112290	ENSG00000112290		"A-kinase anchor proteins"	12732	protein-coding gene	gene with protein product		605035				9843499, 9889097	Standard	XM_005267204		Approved	WAVE1, SCAR1, KIAA0269, WAVE	uc003pty.1	Q92558	OTTHUMG00000015357	ENST00000392589.1:c.92A>T	chr6.hg19:g.110448713T>A	ENSP00000376368:p.Asn31Ile	125.0	0.0		135.0	28.0	NM_001024935	E1P5F2|Q5SZK7	Missense_Mutation	SNP	ENST00000392589.1	hg19	CCDS5080.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.017181	0.75161	.	.	ENSG00000112290	ENST00000392586;ENST00000392587;ENST00000392589;ENST00000392588;ENST00000359451;ENST00000444391;ENST00000265601;ENST00000368938;ENST00000419252;ENST00000447287	T;T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.68970	0.3059	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72890	-0.4155	10	0.39692	T	0.17	.	16.4534	0.84003	0.0:0.0:0.0:1.0	.	31	Q92558	WASF1_HUMAN	I	31	ENSP00000376365:N31I;ENSP00000376366:N31I;ENSP00000376368:N31I;ENSP00000376367:N31I;ENSP00000352425:N31I;ENSP00000407041:N31I;ENSP00000265601:N31I;ENSP00000357934:N31I;ENSP00000404142:N31I;ENSP00000402663:N31I	ENSP00000265601:N31I	N	-	2	0	WASF1	110555406	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.285000	0.76669	0.477000	0.44152	AAT	.	.		0.358	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931		A	110448713	T	A	110448713	3	1	70	1	0	0	0	0	1	0	0	0	17267	1493	52	4	1619	4	WASF1	6	110448713	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	10667487	110448713	60666354	56	8987										
DSE	29940	hgsc.bcm.edu	37	chr6	116756880	116756880	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tcaatagatctttcctttccTtcaagtctggaaaactgggg	8	9	4	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr6:116756880T>C	ENST00000331677.3	+	7	1693	c.1249T>C	c.(1249-1251)Ttc>Ctc	p.F417L	DSE_ENST00000359564.2_Missense_Mutation_p.F417L|DSE_ENST00000452085.3_Missense_Mutation_p.F417L|DSE_ENST00000537543.1_Missense_Mutation_p.F436L			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	417					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		TTTCCTTTCCTTCAAGTCTGG	0.423																																					p.F417L		Atlas-SNP	.											.	DSE	98	.	0			c.T1249C						.						77	73	75					6																	116756880		2203	4300	6503	SO:0001583	missense	29940	exon6			CTTTCCTTCAAGT	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"squamous cell carcinoma antigen recognized by T cells 2"	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.1249T>C	chr6.hg19:g.116756880T>C	ENSP00000332151:p.Phe417Leu	149.0	0.0		199.0	52.0	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	hg19	CCDS5107.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.354546	0.82243	.	.	ENSG00000111817	ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T	0.26518	1.73;1.73;1.73;1.73	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.44286	0.1286	M	0.75777	2.31	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.73380	0.98;0.98	T	0.44877	-0.9299	10	0.62326	D	0.03	-21.5989	16.4943	0.84223	0.0:0.0:0.0:1.0	.	436;417	B7Z765;Q9UL01	.;DSE_HUMAN	L	417;436;417;417	ENSP00000404049:F417L;ENSP00000441152:F436L;ENSP00000332151:F417L;ENSP00000352567:F417L	ENSP00000332151:F417L	F	+	1	0	DSE	116863573	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.985000	0.88162	2.291000	0.77112	0.533000	0.62120	TTC	.	.		0.423	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352		C	116756880	T	C	116756880	3	2	70	1	0	0	0	0	1	0	0	0	4776	1609	56	2	1267	2	DSE	6	116756880	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	6308167	116756880	54358187	57	8988										
TRDN	10345	hgsc.bcm.edu	37	chr6	123673710	123673710	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ccactgtcttggttgttttcTcttccttctttccaggtaca	6	12	3	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr6:123673710T>A	ENST00000398178.3	-	21	1364	c.1343A>T	c.(1342-1344)gAg>gTg	p.E448V	TRDN_ENST00000334268.4_Missense_Mutation_p.E448V	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	448					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		GGTTGTTTTCTCTTCCTTCTT	0.383																																					p.E449V		Atlas-SNP	.											.	TRDN	88	.	0			c.A1346T						.						162	148	152					6																	123673710		1835	4090	5925	SO:0001583	missense	10345	exon21			GTTTTCTCTTCCT	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1343A>T	chr6.hg19:g.123673710T>A	ENSP00000381240:p.Glu448Val	103.0	0.0		99.0	26.0	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	hg19	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.008482	0.75046	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.30182	1.54;1.55	5.66	5.66	0.87406	.	0.109888	0.40554	N	0.001071	T	0.31104	0.0786	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.996;0.996;0.997	T	0.09997	-1.0649	10	0.41790	T	0.15	-12.9629	13.5732	0.61858	0.0:0.0:0.0:1.0	.	448;449;448	Q5SWK9;Q8IVK2;Q13061	.;.;TRDN_HUMAN	V	448;450;448	ENSP00000381240:E448V;ENSP00000333984:E448V	ENSP00000333984:E448V	E	-	2	0	TRDN	123715409	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.933000	0.48948	2.285000	0.76669	0.533000	0.62120	GAG	.	.		0.383	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	123673710	T	A	123673710	3	1	70	1	0	0	0	0	1	0	0	0	16483	1551	54	4	930	4	TRDN	6	123673710	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	6916830	123673710	47441357	58	8989										
TAB2	23118	hgsc.bcm.edu	37	chr6	149700569	149700569	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	accgagaatattcagcacctCacggaccctacattagcaca	6	14	2	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr6:149700569C>A	ENST00000367456.1	+	4	2095	c.1518C>A	c.(1516-1518)ctC>ctA	p.L506L	TAB2_ENST00000286332.5_Silent_p.L506L|TAB2_ENST00000536230.1_Silent_p.L474L|TAB2_ENST00000392282.1_Silent_p.L506L|TAB2_ENST00000538427.1_Silent_p.L506L			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	506					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase activity (GO:0045860)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						TTCAGCACCTCACGGACCCTA	0.428																																					p.L506L		Atlas-SNP	.											.	TAB2	55	.	0			c.C1518A						.						92	86	88					6																	149700569		2203	4300	6503	SO:0001819	synonymous_variant	23118	exon5			GCACCTCACGGAC	AF241230	CCDS5214.1	6q25.1	2010-08-05	2010-02-05	2010-02-05	ENSG00000055208	ENSG00000055208			17075	protein-coding gene	gene with protein product		605101	"mitogen-activated protein kinase kinase kinase 7 interacting protein 2"	MAP3K7IP2		9872452, 10882101	Standard	XR_250046		Approved	KIAA0733	uc010kib.2	Q9NYJ8	OTTHUMG00000015783	ENST00000367456.1:c.1518C>A	chr6.hg19:g.149700569C>A		152.0	0.0		190.0	57.0	NM_015093	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Silent	SNP	ENST00000367456.1	hg19	CCDS5214.1																																																																																			.	.		0.428	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3			A	149700569	C	A	149700569	2	1	70	1	0	0	0	0	0	0	0	1	15511	813	29	3		3	TAB2	6	149700569	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	26026859	149700569	21414498	59	8990										
CYP2W1	54905	hgsc.bcm.edu	37	chr7	1026832	1026832	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gggacggagacgacctcggcCacgctgcagtgggccgcact	16	14	0	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr7:1026832C>T	ENST00000308919.7	+	6	922	c.909C>T	c.(907-909)gcC>gcT	p.A303A	CYP2W1_ENST00000340150.6_Silent_p.A247A	NM_017781.2	NP_060251.2	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W, polypeptide 1	303					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		CGACCTCGGCCACGCTGCAGT	0.726																																					p.A303A		Atlas-SNP	.											.	CYP2W1	28	.	0			c.C909T						.						12	14	13					7																	1026832		2155	4233	6388	SO:0001819	synonymous_variant	54905	exon6			CTCGGCCACGCTG	AK000366	CCDS5319.2	7p22.3	2004-07-05			ENSG00000073067	ENSG00000073067		"Cytochrome P450s"	20243	protein-coding gene	gene with protein product		615967					Standard	XM_005249792		Approved	FLJ20359, MGC34287	uc003sjq.1	Q8TAV3	OTTHUMG00000074071	ENST00000308919.7:c.909C>T	chr7.hg19:g.1026832C>T		100.0	0.0		151.0	68.0	NM_017781		Silent	SNP	ENST00000308919.7	hg19	CCDS5319.2																																																																																			.	.		0.726	CYP2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157249.1	NM_017781		T	1026832	C	T	1026832	2	4	70	1	0	0	0	0	0	0	0	1	4178	581	21	3		3	CYP2W1	7	1026832	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10		1026832	158111831	60	8991										
CBX3	11335	hgsc.bcm.edu	37	chr7	26246056	26246056	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcagagcctgaagaatttgtCgtggaaaaagtactagatcg	12	6	0	4	rs575959807		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr7:26246056C>T	ENST00000337620.4	+	3	521	c.93C>T	c.(91-93)gtC>gtT	p.V31V	CBX3_ENST00000396386.2_Silent_p.V31V|CBX3_ENST00000409747.1_Silent_p.V31V|CBX3_ENST00000497498.1_3'UTR	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3	31	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						AAGAATTTGTCGTGGAAAAAG	0.333													c|||	1	0.000199681	0	0	5008	,	,		22801	0		0	False		,,,				2504	0.001				p.V31V		Atlas-SNP	.											CBX3,NS,carcinoma,0,1	CBX3	25	.	0			c.C93T						.						127	131	129					7																	26246056		2203	4300	6503	SO:0001819	synonymous_variant	11335	exon3			ATTTGTCGTGGAA	U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"HP1 gamma homolog (Drosophila)"	604477	"chromobox homolog 3 (Drosophila HP1 gamma)"			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.93C>T	chr7.hg19:g.26246056C>T		135.0	0.0		158.0	22.0	NM_016587	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Silent	SNP	ENST00000337620.4	hg19	CCDS5398.1																																																																																			.	.		0.333	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276		T	26246056	C	T	26246056	2	4	70	1	0	0	0	0	0	0	0	1	2721	871	31	1		1	CBX3	7	26246056	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	25219224	26246056	132892607	61	8992										
GNAT3	346562	hgsc.bcm.edu	37	chr7	80088145	80088145	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gtctagaaactggttcttgaTgtagtttcctgcatcttcaa	8	8	4	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr7:80088145T>C	ENST00000398291.3	-	8	1000	c.907A>G	c.(907-909)Atc>Gtc	p.I303V	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	303					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						TGGTTCTTGATGTAGTTTCCT	0.308																																					p.I303V		Atlas-SNP	.											.	GNAT3	65	.	0			c.A907G						.						59	56	57					7																	80088145		1811	4081	5892	SO:0001583	missense	346562	exon8			TCTTGATGTAGTT		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.907A>G	chr7.hg19:g.80088145T>C	ENSP00000381339:p.Ile303Val	70.0	0.0		64.0	11.0	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Missense_Mutation	SNP	ENST00000398291.3	hg19	CCDS47625.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.968736	0.74131	.	.	ENSG00000214415	ENST00000398291	D	0.89415	-2.51	5.47	5.47	0.80525	.	0.000000	0.85682	U	0.000000	D	0.95191	0.8441	M	0.88031	2.925	0.80722	D	1	D	0.58268	0.982	D	0.81914	0.995	D	0.95681	0.8732	9	.	.	.	.	15.8518	0.78937	0.0:0.0:0.0:1.0	.	303	A8MTJ3	GNAT3_HUMAN	V	303	ENSP00000381339:I303V	.	I	-	1	0	GNAT3	79926081	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.281000	0.72632	2.216000	0.71823	0.528000	0.53228	ATC	.	.		0.308	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370		C	80088145	T	C	80088145	3	2	70	1	0	0	0	0	1	0	0	0	6521	1464	51	2	159	2	GNAT3	7	80088145	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	53842089	80088145	79050518	62	8993										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107689935	107689935	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	attaattttcttttcagcagAtgatgatatgtgataatatt	6	3	2	4			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr7:107689935A>G	ENST00000388781.3	-	27	4041	c.3958T>C	c.(3958-3960)Tct>Cct	p.S1320P	LAMB4_ENST00000388780.3_Missense_Mutation_p.S1320P|LAMB4_ENST00000205386.4_Missense_Mutation_p.S1320P	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1320	Domain II.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						TTTTCAGCAGATGATGATATG	0.299																																					p.S1320P		Atlas-SNP	.											.	LAMB4	253	.	0			c.T3958C						.						164	143	150					7																	107689935		2202	4299	6501	SO:0001583	missense	22798	exon27			CAGCAGATGATGA	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.3958T>C	chr7.hg19:g.107689935A>G	ENSP00000373433:p.Ser1320Pro	79.0	0.0		77.0	19.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	hg19	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	A	12.68	2.011560	0.35511	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000422975;ENST00000388780	T;T;T;T	0.32988	1.43;1.43;1.86;1.45	4.97	3.8	0.43715	.	0.364446	0.21981	N	0.066320	T	0.26774	0.0655	N	0.19112	0.55	0.58432	D	0.999992	P;D	0.54047	0.731;0.964	B;P	0.52267	0.395;0.694	T	0.03296	-1.1051	10	0.54805	T	0.06	.	6.8523	0.24022	0.7614:0.1538:0.0848:0.0	.	1320;1320	A4D0S4-3;A4D0S4	.;LAMB4_HUMAN	P	1320;1320;346;1320	ENSP00000205386:S1320P;ENSP00000373433:S1320P;ENSP00000416562:S346P;ENSP00000373432:S1320P	ENSP00000205386:S1320P	S	-	1	0	LAMB4	107477171	0.966000	0.33281	0.831000	0.32960	0.992000	0.81027	2.172000	0.42463	0.890000	0.36211	0.533000	0.62120	TCT	.	.		0.299	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		G	107689935	A	G	107689935	3	3	70	1	0	0	0	0	1	0	0	0	8622	333	12	2	1359	2	LAMB4	7	107689935	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	27601790	107689935	51448728	63	8994										
PRSS37	136242	hgsc.bcm.edu	37	chr7	141537856	141537856	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	atctgaatggggttaattgtCtgttcagtaccgtctctgac	10	8	4	2	rs201423018		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr7:141537856C>T	ENST00000350549.3	-	3	605	c.234G>A	c.(232-234)caG>caA	p.Q78Q	PRSS37_ENST00000438520.1_Silent_p.Q78Q	NM_001008270.2|NM_001171951.1	NP_001008271.2|NP_001165422.1	A4D1T9	PRS37_HUMAN	protease, serine, 37	78	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				binding of sperm to zona pellucida (GO:0007339)|cell migration (GO:0016477)|protein maturation (GO:0051604)	extracellular region (GO:0005576)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(3)	15						GGTTAATTGTCTGTTCAGTAC	0.483																																					p.Q78Q		Atlas-SNP	.											.	PRSS37	42	.	0			c.G234A						.						248	211	224					7																	141537856		2203	4300	6503	SO:0001819	synonymous_variant	136242	exon3			AATTGTCTGTTCA		CCDS34764.1	7q34	2010-05-07			ENSG00000165076	ENSG00000165076		"Serine peptidases / Serine peptidases"	29211	protein-coding gene	gene with protein product							Standard	NM_001008270		Approved		uc003vws.2	A4D1T9	OTTHUMG00000157174	ENST00000350549.3:c.234G>A	chr7.hg19:g.141537856C>T		114.0	0.0		127.0	46.0	NM_001171951	B2RPB5	Silent	SNP	ENST00000350549.3	hg19	CCDS34764.1																																																																																			.	C|1.000;G|0.000		0.483	PRSS37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347763.1	NM_001008270		T	141537856	C	T	141537856	2	4	70	1	0	0	0	0	0	0	0	1	12638	912	32	3		3	PRSS37	7	141537856	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	33847921	141537856	17600807	64	8995										
NCOA2	10499	hgsc.bcm.edu	37	chr8	71082595	71082597	+	In_Frame_Del	DEL	AAG	AAG	-													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgccttccaggttcactacaAagaagaacccatcaagggcc							TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr8:71082595_71082597delAAG	ENST00000452400.2	-	6	562_564	c.381_383delCTT	c.(379-384)ttcttt>ttt	p.127_128FF>F		NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	127	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			GTTCACTACAAAGAAGAACCCAT	0.394			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.128_128del		Atlas-Indel,Pindel	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.382_384del						.																																			SO:0001651	inframe_deletion	10499	exon6			.	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.381_383delCTT	chr8.hg19:g.71082598_71082600delAAG	ENSP00000399968:p.Phe128del	120.0	0.0		162.0	29.0	NM_006540	Q14CD2	In_Frame_Del	DEL	ENST00000452400.2	hg19	CCDS47872.1																																																																																			.	.		0.394	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			-	71082597	AAG	-	71082595	7	5	70	1	0	1	0	1	0	0	0	0	10238	14	1	0	4083	0	NCOA2	8	71082595	In_Frame_Del	DEL	AAG	TCGA-CC-A7IE-01A-21D-A382-10		71082595	75281427	65	8996										
KCNS2	3788	hgsc.bcm.edu	37	chr8	99440321	99440321	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tcgcacacgctgctgcgcttCcccgagacgcgcctgggccg	13	18	0	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr8:99440321C>T	ENST00000287042.4	+	2	464	c.114C>T	c.(112-114)ttC>ttT	p.F38F	KCNS2_ENST00000521839.1_Silent_p.F38F	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	38					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			TGCTGCGCTTCCCCGAGACGC	0.657																																					p.F38F	Pancreas(138;844 2489 9202 24627)	Atlas-SNP	.											.	KCNS2	93	.	0			c.C114T						.						46	42	44					8																	99440321		2203	4300	6503	SO:0001819	synonymous_variant	3788	exon2			GCGCTTCCCCGAG	AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.114C>T	chr8.hg19:g.99440321C>T		82.0	0.0		154.0	17.0	NM_020697	A8KAN1	Silent	SNP	ENST00000287042.4	hg19	CCDS6279.1																																																																																			.	.		0.657	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		T	99440321	C	T	99440321	2	4	70	1	0	0	0	0	0	0	0	1	8098	854	30	3		3	KCNS2	8	99440321	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	28357726	99440321	46923701	66	8997										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113326738	113326738	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgatattataacccttttccActgaaatgctccatgcacac	4	12	0	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr8:113326738A>T	ENST00000297405.5	-	48	7713	c.7469T>A	c.(7468-7470)gTg>gAg	p.V2490E	CSMD3_ENST00000352409.3_Missense_Mutation_p.V2420E|CSMD3_ENST00000343508.3_Missense_Mutation_p.V2450E|CSMD3_ENST00000455883.2_Missense_Mutation_p.V2386E	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2490	CUB 14. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ACCCTTTTCCACTGAAATGCT	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.V2490E		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T7469A						.						122	116	118					8																	113326738		2203	4300	6503	SO:0001583	missense	114788	exon48			TTTTCCACTGAAA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7469T>A	chr8.hg19:g.113326738A>T	ENSP00000297405:p.Val2490Glu	169.0	0.0		252.0	47.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.679435	0.88542	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08	4.98	4.98	0.66077	CUB (5);	0.000000	0.64402	D	0.000008	T	0.76176	0.3951	H	0.97758	4.07	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.84232	0.0467	10	0.51188	T	0.08	.	14.8078	0.69971	1.0:0.0:0.0:0.0	.	2386;2490;2450	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	E	2450;2490;1760;2386;2420	ENSP00000345799:V2450E;ENSP00000297405:V2490E;ENSP00000341558:V1760E;ENSP00000412263:V2386E;ENSP00000343124:V2420E	ENSP00000297405:V2490E	V	-	2	0	CSMD3	113395914	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.135000	0.94478	2.081000	0.62600	0.472000	0.43445	GTG	.	.		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113326738	A	T	113326738	3	4	70	1	0	0	0	0	1	0	0	0	3948	159	6	4	3750	4	CSMD3	8	113326738	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	13886417	113326738	33037284	67	8998										
GPAA1	8733	hgsc.bcm.edu	37	chr8	145140854	145140854	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cttggcagcctgttcctgtgGcgggagctgcaggaggcgcc	17	12	0	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr8:145140854G>T	ENST00000355091.4	+	12	1813	c.1692G>T	c.(1690-1692)tgG>tgT	p.W564C	GPAA1_ENST00000361036.6_Missense_Mutation_p.W504C	NM_003801.3	NP_003792.1	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment 1	564					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein complex assembly (GO:0006461)|protein retention in ER lumen (GO:0006621)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	tubulin binding (GO:0015631)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(2)	19	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGTTCCTGTGGCGGGAGCTGC	0.672																																					p.W564C		Atlas-SNP	.											.	GPAA1	40	.	0			c.G1692T						.						31	35	33					8																	145140854		1956	4114	6070	SO:0001583	missense	8733	exon12			CCTGTGGCGGGAG	AB006969	CCDS43776.1	8q24.3	2012-12-10	2012-12-10		ENSG00000197858	ENSG00000197858			4446	protein-coding gene	gene with protein product	"GPI transamidase subunit"	603048	"anchor attachment protein 1 (Gaa1p, yeast) homolog", "GPAA1P anchor attachment protein 1 homolog (yeast)", "glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast)"			9828142	Standard	NM_003801		Approved	GAA1, hGAA1	uc003zax.3	O43292	OTTHUMG00000165438	ENST00000355091.4:c.1692G>T	chr8.hg19:g.145140854G>T	ENSP00000347206:p.Trp564Cys	19.0	0.0		44.0	11.0	NM_003801	Q9NSS0|Q9UQ31	Missense_Mutation	SNP	ENST00000355091.4	hg19	CCDS43776.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.745914	0.49151	.	.	ENSG00000197858	ENST00000355091;ENST00000361036	.	.	.	5.53	5.53	0.82687	.	0.195419	0.46758	D	0.000261	T	0.65322	0.2680	L	0.55990	1.75	0.58432	D	0.999991	D	0.62365	0.991	P	0.57204	0.815	T	0.64390	-0.6419	9	0.42905	T	0.14	-14.3805	12.6505	0.56757	0.0:0.1663:0.8337:0.0	.	564	O43292	GPAA1_HUMAN	C	564;504	.	ENSP00000347206:W564C	W	+	3	0	GPAA1	145212842	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.246000	0.43142	2.602000	0.87976	0.655000	0.94253	TGG	.	.		0.672	GPAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384070.1	NM_003801		T	145140854	G	T	145140854	3	4	70	1	0	0	0	0	1	0	0	0	6595	1212	42	3	1738	3	GPAA1	8	145140854	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	31814116	145140854	1223168	68	8999										
RECQL4	113655	hgsc.bcm.edu	37	chr8	145737119	145737119	+	IGR	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gagaacttctcctctggcctCagggacaggaactggcggat	13	11	3	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr8:145737119C>T	ENST00000301327.4	+	0	1548				RECQL4_ENST00000428558.2_Silent_p.L1149L|RECQL4_ENST00000532237.1_5'UTR|CTD-2517M22.17_ENST00000580385.1_RNA	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CCTCTGGCCTCAGGGACAGGA	0.672																																					p.L1149L		Atlas-SNP	.											.	RECQL4	75	.	0			c.G3447A						.						66	79	75					8																	145737119		2162	4256	6418	SO:0001628	intergenic_variant	9401	exon21			TGGCCTCAGGGAC		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		chr8.hg19:g.145737119C>T		71.0	0.0		118.0	7.0	NM_004260		Silent	SNP	ENST00000301327.4	hg19	CCDS6431.1																																																																																			.	.		0.672	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		T	145737119	C	T	145737119	1	4	70	0	1	0	0	0	0	0	0	0	13217	813	29	3		3	RECQL4	8	145737119	IGR	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	596265	145737119	626903	69	9000										
ZNF7	7553	hgsc.bcm.edu	37	chr8	146067302	146067302	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cagcttaatcagcatcagagAatccacacgggagagaaacc	9	11	2	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr8:146067302A>G	ENST00000528372.1	+	5	1050	c.810A>G	c.(808-810)agA>agG	p.R270R	ZNF7_ENST00000325241.6_Silent_p.R270R|ZNF7_ENST00000544249.1_Silent_p.R174R|ZNF7_ENST00000529819.1_3'UTR|ZNF7_ENST00000446747.2_Silent_p.R281R|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000525266.1_Intron			P17097	ZNF7_HUMAN	zinc finger protein 7	270					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		AGCATCAGAGAATCCACACGG	0.478																																					p.R270R		Atlas-SNP	.											.	ZNF7	62	.	0			c.A810G						.						78	81	80					8																	146067302		2203	4300	6503	SO:0001819	synonymous_variant	7553	exon5			TCAGAGAATCCAC	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.810A>G	chr8.hg19:g.146067302A>G		63.0	0.0		140.0	60.0	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Silent	SNP	ENST00000528372.1	hg19	CCDS6435.1																																																																																			.	.		0.478	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		G	146067302	A	G	146067302	2	3	70	1	0	0	0	0	0	0	0	1	18117	243	9	2		2	ZNF7	8	146067302	Silent	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	330183	146067302	296720	70	9001										
RPS6	6194	hgsc.bcm.edu	37	chr9	19376359	19376380	+	Frame_Shift_Del	DEL	TTTGTTCCTGGCGCTTCTCCTT	TTTGTTCCTGGCGCTTCTCCTT	-													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	aagtctgcgtctcttcgcaaTttgttcctggcgcttctcct					rs3206714|rs3209385|rs17852447		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	TTTGTTCCTGGCGCTTCTCCTT	TTTGTTCCTGGCGCTTCTCCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr9:19376359_19376380delTTTGTTCCTGGCGCTTCTCCTT	ENST00000380394.4	-	6	719_740	c.661_682delAAGGAGAAGCGCCAGGAACAAA	c.(661-684)aaggagaagcgccaggaacaaattfs	p.KEKRQEQI221fs	RPS6_ENST00000380384.1_Frame_Shift_Del_p.KEKRQEQI190fs|RPS6_ENST00000498815.1_5'UTR|RPS6_ENST00000315377.4_Frame_Shift_Del_p.KEKRQEQI190fs|RP11-513M16.8_ENST00000609982.1_RNA	NM_001010.2	NP_001001.2	P62753	RS6_HUMAN	ribosomal protein S6	221			K -> R (in dbSNP:rs17852447). {ECO:0000269|PubMed:15489334}.		activation-induced cell death of T cells (GO:0006924)|cellular protein metabolic process (GO:0044267)|erythrocyte development (GO:0048821)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|oogenesis stage (GO:0022605)|placenta development (GO:0001890)|positive regulation of apoptotic process (GO:0043065)|ribosomal small subunit assembly (GO:0000028)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell differentiation in thymus (GO:0033077)|T cell proliferation involved in immune response (GO:0002309)|TOR signaling (GO:0031929)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|dendrite (GO:0030425)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|urinary_tract(1)	7		Colorectal(97;3.46e-05)|Myeloproliferative disorder(762;0.0255)		Lung(42;0.161)|LUSC - Lung squamous cell carcinoma(42;0.234)		CTCTTCGCAATTTGTTCCTGGCGCTTCTCCTTAGCCTCCTAA	0.423																																					p.221_228del		Pindel	.											.	RPS6	25	.	0			c.662_683del						.																																			SO:0001589	frameshift_variant	6194	exon6			.		CCDS6492.1	9p21	2011-04-05			ENSG00000137154	ENSG00000137154		"S ribosomal proteins"	10429	protein-coding gene	gene with protein product	"40S ribosomal protein S6", "phosphoprotein NP33"	180460				1577483	Standard	NM_001010		Approved	S6	uc003znv.1	P62753	OTTHUMG00000019642	ENST00000380394.4:c.661_682delAAGGAGAAGCGCCAGGAACAAA	chr9.hg19:g.19376359_19376380delTTTGTTCCTGGCGCTTCTCCTT	ENSP00000369757:p.Lys221fs	126.0	0.0		97.0	10.0	NM_001010	P08227|P10660|Q4VBY7|Q8N6Z7	Frame_Shift_Del	DEL	ENST00000380394.4	hg19	CCDS6492.1																																																																																			.	.		0.423	RPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051858.1	NM_001010		-	19376380	TTTGTTCCTGGCGCTTCTCCTT	-	19376359	7	5	70	1	0	1	0	1	0	0	0	0	13664	1493	52	0	71	0	RPS6	9	19376359	Frame_Shift_Del	DEL	TTTGTTCCTGGCGCTTCTCCTT	TCGA-CC-A7IE-01A-21D-A382-10		19376359	121837072	71	9002										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87342704	87342704	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	attgaatgagtccaaatacaTctgtactaaaatacatgtta	5	6	1	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr9:87342704T>C	ENST00000323115.4	+	8	1342	c.989T>C	c.(988-990)aTc>aCc	p.I330T	NTRK2_ENST00000304053.6_Missense_Mutation_p.I330T|NTRK2_ENST00000376213.1_Missense_Mutation_p.I330T|NTRK2_ENST00000359847.3_Missense_Mutation_p.I330T|NTRK2_ENST00000277120.3_Missense_Mutation_p.I330T|NTRK2_ENST00000376214.1_Missense_Mutation_p.I330T|NTRK2_ENST00000376208.1_Missense_Mutation_p.I330T|NTRK2_ENST00000395882.1_Missense_Mutation_p.I330T|NTRK2_ENST00000395866.2_Missense_Mutation_p.I174T			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	330	Ig-like C2-type 2.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	TCCAAATACATCTGTACTAAA	0.468										TSP Lung(25;0.17)																											p.I330T		Atlas-SNP	.											.	NTRK2	331	.	0			c.T989C						.						118	115	116					9																	87342704		2203	4300	6503	SO:0001583	missense	4915	exon9			AATACATCTGTAC	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.989T>C	chr9.hg19:g.87342704T>C	ENSP00000314586:p.Ile330Thr	132.0	0.0		140.0	45.0	NM_001018065	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Missense_Mutation	SNP	ENST00000323115.4	hg19	CCDS35050.1	.	.	.	.	.	.	.	.	.	.	T	19.60	3.858801	0.71834	.	.	ENSG00000148053	ENST00000376214;ENST00000376213;ENST00000395882;ENST00000376208;ENST00000304053;ENST00000277120;ENST00000323115;ENST00000359847;ENST00000395866	T;T;T;T;T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5	5.91	5.91	0.95273	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.73598	0.3607	M	0.78801	2.425	0.54753	D	0.999988	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999;0.998;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;0.996;0.996;0.999;0.969;0.948;1.0;0.998	T	0.75405	-0.3329	10	0.51188	T	0.08	.	16.3333	0.83050	0.0:0.0:0.0:1.0	.	174;330;330;330;330;330;376;330	B4DFV9;Q16620-3;Q16620-5;Q5VWE5;Q16620;Q16620-4;Q59GJ1;Q16620-2	.;.;.;.;NTRK2_HUMAN;.;.;.	T	330;330;330;330;330;330;330;330;174	ENSP00000365387:I330T;ENSP00000365386:I330T;ENSP00000379221:I330T;ENSP00000365381:I330T;ENSP00000306167:I330T;ENSP00000277120:I330T;ENSP00000314586:I330T;ENSP00000352906:I330T;ENSP00000379207:I174T	ENSP00000277120:I330T	I	+	2	0	NTRK2	86532524	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.961000	0.70356	2.258000	0.74832	0.477000	0.44152	ATC	.	.		0.468	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			C	87342704	T	C	87342704	3	2	70	1	0	0	0	0	1	0	0	0	10716	1435	50	2	1019	2	NTRK2	9	87342704	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	67966345	87342704	53870727	72	9003										
PDCL	5082	hgsc.bcm.edu	37	chr9	125585315	125585315	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cttcccactgatcttctcctGgaggtctttctgtttctgtt	7	12	5	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr9:125585315G>T	ENST00000259467.4	-	3	499	c.334C>A	c.(334-336)Cag>Aag	p.Q112K		NM_005388.4	NP_005379.3	Q13371	PHLP_HUMAN	phosducin-like	112					heterotrimeric G-protein complex assembly (GO:1902605)|intracellular signal transduction (GO:0035556)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)	p.Q112*(2)		endometrium(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10						ATCTTCTCCTGGAGGTCTTTC	0.507																																					p.Q112K		Atlas-SNP	.											PDCL,NS,carcinoma,0,1	PDCL	24	.	2	Substitution - Nonsense(2)	lung(2)	c.C334A						.						255	212	227					9																	125585315		2203	4300	6503	SO:0001583	missense	5082	exon3			TCTCCTGGAGGTC	AF083325	CCDS6845.1	9q12-q13	2008-07-21			ENSG00000136940	ENSG00000136940			8770	protein-coding gene	gene with protein product		604421				10095058	Standard	NM_005388		Approved	PhLP, DKFZp564M1863	uc004bmz.2	Q13371	OTTHUMG00000020624	ENST00000259467.4:c.334C>A	chr9.hg19:g.125585315G>T	ENSP00000259467:p.Gln112Lys	91.0	0.0		74.0	4.0	NM_005388	Q4VXB6|Q96AF1|Q9UEW7|Q9UFL0|Q9UNX1|Q9UNX2	Missense_Mutation	SNP	ENST00000259467.4	hg19	CCDS6845.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.39|18.39	3.613184|3.613184	0.66672|0.66672	.|.	.|.	ENSG00000136940|ENSG00000136940	ENST00000436632;ENST00000394285|ENST00000259467	.|T	.|0.39056	.|1.1	5.98|5.98	5.07|5.07	0.68467|0.68467	.|Thioredoxin-like fold (1);Phosducin, thioredoxin-like domain (1);Phosducin, domain 2 (1);	.|0.153488	.|0.64402	.|D	.|0.000013	T|T	0.32224|0.32224	0.0822|0.0822	L|L	0.29908|0.29908	0.895|0.895	0.48341|0.48341	D|D	0.99963|0.99963	.|B;B	.|0.14012	.|0.009;0.009	.|B;B	.|0.17098	.|0.017;0.017	T|T	0.07102|0.07102	-1.0790|-1.0790	5|10	.|0.21014	.|T	.|0.42	-19.7386|-19.7386	14.6783|14.6783	0.68998|0.68998	0.0:0.2755:0.7245:0.0|0.0:0.2755:0.7245:0.0	.|.	.|112;112	.|Q4VXB6;Q13371	.|.;PHLP_HUMAN	Q|K	78;100|112	.|ENSP00000259467:Q112K	.|ENSP00000259467:Q112K	P|Q	-|-	2|1	0|0	PDCL|PDCL	124625136|124625136	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	3.644000|3.644000	0.54381|0.54381	1.497000|1.497000	0.48584|0.48584	0.563000|0.563000	0.77884|0.77884	CCA|CAG	.	.		0.507	PDCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053956.1	NM_005388		T	125585315	G	T	125585315	3	4	70	1	0	0	0	0	1	0	0	0	11635	1357	47	3	579	3	PDCL	9	125585315	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	38242611	125585315	15628116	73	9004										
GLE1	2733	hgsc.bcm.edu	37	chr9	131285594	131285601	+	Frame_Shift_Del	DEL	AAGCTGAG	AAGCTGAG	-													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gggacaccaagagaagctaaAagctgagcaccgtcacagag							TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	AAGCTGAG	AAGCTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr9:131285594_131285601delAAGCTGAG	ENST00000309971.4	+	5	723_730	c.617_624delAAGCTGAG	c.(616-624)aaagctgagfs	p.KAE206fs	GLE1_ENST00000372770.4_Frame_Shift_Del_p.KAE206fs|GLE1_ENST00000539582.1_5'UTR	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	206					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						GAGAAGCTAAAAGCTGAGCACCGTCACA	0.49																																					p.206_208del		Atlas-Indel,Pindel	.											.	GLE1	42	.	0			c.616_623del						.																																			SO:0001589	frameshift_variant	2733	exon5			.	AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"GLE1 (yeast homolog)-like, RNA export mediator", "GLE1 RNA export mediator-like (yeast)", "GLE1 RNA export mediator (yeast)", "lethal congenital contracture syndrome 1", "GLE1 RNA export mediator homolog (yeast)"	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.617_624delAAGCTGAG	chr9.hg19:g.131285594_131285601delAAGCTGAG	ENSP00000308622:p.Lys206fs	124.0	0.0		110.0	24.0	NM_001499	O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Frame_Shift_Del	DEL	ENST00000309971.4	hg19	CCDS35154.1																																																																																			.	.		0.49	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1	NM_001003722		-	131285601	AAGCTGAG	-	131285594	7	5	70	1	0	1	0	1	0	0	0	0	6443	14	1	0	635	0	GLE1	9	131285594	Frame_Shift_Del	DEL	AAGCTGAG	TCGA-CC-A7IE-01A-21D-A382-10	5700279	131285594	9927837	74	9005										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138647016	138647016	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgacactgtgggcgatccagGtgagtgccctaccctgcccc	12	15	0	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr9:138647016G>T	ENST00000263604.3	+	6	483		c.e6+1		KCNT1_ENST00000486577.2_Splice_Site|KCNT1_ENST00000371757.2_Splice_Site|KCNT1_ENST00000490355.2_Splice_Site|KCNT1_ENST00000491806.2_Splice_Site|KCNT1_ENST00000487664.1_Splice_Site|KCNT1_ENST00000298480.5_Splice_Site|KCNT1_ENST00000488444.2_Splice_Site			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1						potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		GGCGATCCAGGTGAGTGCCCT	0.592																																					.		Atlas-SNP	.											.	KCNT1	139	.	0			c.540+1G>T						.						102	80	88					9																	138647016		2203	4300	6503	SO:0001630	splice_region_variant	57582	exon6			ATCCAGGTGAGTG	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.483+1G>T	chr9.hg19:g.138647016G>T		43.0	0.0		57.0	25.0	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Splice_Site	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	G	9.364	1.068823	0.20147	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000473941;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	.	.	.	3.11	3.11	0.35812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1028	0.59231	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KCNT1	137786837	1.000000	0.71417	0.994000	0.49952	0.079000	0.17450	8.526000	0.90588	1.456000	0.47831	0.313000	0.20887	.	.	.		0.592	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822	Intron	T	138647016	G	T	138647016	5	4	70	1	0	0	0	0	0	0	1	0	8100	1275	44	3	563	3	KCNT1	9	138647016	Splice_Site	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	7361422	138647016	2566415	75	9006										
TAF3	83860	hgsc.bcm.edu	37	chr10	8051256	8051256	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ggccagtgccaaagcccccgTgcgcagcgtggtgactgaga	15	13	0	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:8051256T>A	ENST00000344293.5	+	5	2737	c.2531T>A	c.(2530-2532)gTg>gAg	p.V844E		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	844					maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						AAAGCCCCCGTGCGCAGCGTG	0.721																																					p.V844E		Atlas-SNP	.											.	TAF3	93	.	0			c.T2531A						.						11	11	11					10																	8051256		1724	3622	5346	SO:0001583	missense	83860	exon5			CCCCCGTGCGCAG	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"Zinc fingers, PHD-type"	17303	protein-coding gene	gene with protein product		606576	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.2531T>A	chr10.hg19:g.8051256T>A	ENSP00000340271:p.Val844Glu	78.0	0.0		85.0	14.0	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	hg19	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937558	0.52972	.	.	ENSG00000165632	ENST00000344293	D	0.84873	-1.91	6.07	6.07	0.98685	Zinc finger, FYVE/PHD-type (1);	0.000000	0.56097	D	0.000027	D	0.87597	0.6217	M	0.73962	2.25	0.58432	D	0.999999	D	0.57257	0.979	P	0.51487	0.671	D	0.85276	0.1059	10	0.07813	T	0.8	-21.776	16.6407	0.85098	0.0:0.0:0.0:1.0	.	844	Q5VWG9	TAF3_HUMAN	E	844	ENSP00000340271:V844E	ENSP00000340271:V844E	V	+	2	0	TAF3	8091262	1.000000	0.71417	0.066000	0.19879	0.042000	0.13812	5.716000	0.68437	2.326000	0.78906	0.533000	0.62120	GTG	.	.		0.721	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		A	8051256	T	A	8051256	3	1	70	1	0	0	0	0	1	0	0	0	15540	1696	59	4	2549	4	TAF3	10	8051256	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10		8051256	127483491	76	9007										
C1QL3	389941	hgsc.bcm.edu	37	chr10	16562897	16562897	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttggggccctggatgaaggtGggcagggactgcatgaggcc	19	8	0	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:16562897G>A	ENST00000298943.3	-	1	1107	c.168C>T	c.(166-168)ccC>ccT	p.P56P		NM_001010908.1	NP_001010908.1	Q5VWW1	C1QL3_HUMAN	complement component 1, q subcomponent-like 3	56					regulation of synapse organization (GO:0050807)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)				breast(1)|endometrium(3)|kidney(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	13						GGATGAAGGTGGGCAGGGACT	0.771																																					p.P56P		Atlas-SNP	.											.	C1QL3	27	.	0			c.C168T						.						4	8	7					10																	16562897		1843	3924	5767	SO:0001819	synonymous_variant	389941	exon1			GAAGGTGGGCAGG		CCDS31156.1	10p13	2012-03-26			ENSG00000165985	ENSG00000165985			19359	protein-coding gene	gene with protein product		615227				21378161	Standard	NM_001010908		Approved	K100, C1ql, C1QTNF13, CTRP13	uc001ioj.1	Q5VWW1	OTTHUMG00000017738	ENST00000298943.3:c.168C>T	chr10.hg19:g.16562897G>A		28.0	0.0		36.0	7.0	NM_001010908	A0PJY4|A0PJY5	Silent	SNP	ENST00000298943.3	hg19	CCDS31156.1																																																																																			.	.		0.771	C1QL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047003.1	XM_372305		A	16562897	G	A	16562897	2	1	70	1	0	0	0	0	0	0	0	1	1962	1335	47	3		3	C1QL3	10	16562897	Silent	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	8511641	16562897	118971850	77	9008										
GDF2	2658	hgsc.bcm.edu	37	chr10	48416588	48416588	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ccccagtgggctgtgggcgtTtcccccagcagaccctcgtc	12	17	0	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:48416588T>C	ENST00000249598.1	-	1	265	c.106A>G	c.(106-108)Aac>Gac	p.N36D		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	36					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						CTGTGGGCGTTTCCCCCAGCA	0.647																																					p.N36D		Atlas-SNP	.											.	GDF2	77	.	0			c.A106G						.						29	29	29					10																	48416588		2202	4300	6502	SO:0001583	missense	2658	exon1			GGGCGTTTCCCCC	AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"Endogenous ligands"	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.106A>G	chr10.hg19:g.48416588T>C	ENSP00000249598:p.Asn36Asp	76.0	0.0		79.0	21.0	NM_016204	Q5VSQ9|Q9Y571	Missense_Mutation	SNP	ENST00000249598.1	hg19	CCDS7219.1	.	.	.	.	.	.	.	.	.	.	T	0.422	-0.907819	0.02434	.	.	ENSG00000128802	ENST00000249598	T	0.76060	-0.99	5.19	1.67	0.24075	.	0.750927	0.13464	N	0.385950	T	0.41351	0.1155	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32107	-0.9919	10	0.05833	T	0.94	.	3.5212	0.07743	0.1759:0.3694:0.0:0.4547	.	36	Q9UK05	GDF2_HUMAN	D	36	ENSP00000249598:N36D	ENSP00000249598:N36D	N	-	1	0	GDF2	48036594	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	1.322000	0.33689	0.114000	0.18032	-0.290000	0.09829	AAC	.	.		0.647	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204		C	48416588	T	C	48416588	3	2	70	1	0	0	0	0	1	0	0	0	6322	1841	64	2	1191	2	GDF2	10	48416588	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	31853691	48416588	87118159	78	9009										
SUPV3L1	6832	hgsc.bcm.edu	37	chr10	70967559	70967559	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tctctctcagtttgccaggcAgtatagcaggaatgagcccc	10	12	2	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:70967559A>G	ENST00000359655.4	+	14	1847	c.1787A>G	c.(1786-1788)cAg>cGg	p.Q596R		NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	596					ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTTGCCAGGCAGTATAGCAGG	0.393																																					p.Q596R		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.A1787G						.						110	95	100					10																	70967559		2203	4300	6503	SO:0001583	missense	6832	exon14			CCAGGCAGTATAG	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"suppressor of var1 (S.cerevisiae) 3-like 1"			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.1787A>G	chr10.hg19:g.70967559A>G	ENSP00000352678:p.Gln596Arg	123.0	0.0		150.0	21.0	NM_003171	A8K301|O43630	Missense_Mutation	SNP	ENST00000359655.4	hg19	CCDS7287.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.392124	0.42410	.	.	ENSG00000156502	ENST00000359655	T	0.39056	1.1	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.34803	0.0910	L	0.41573	1.285	0.80722	D	1	B	0.24721	0.11	B	0.22880	0.042	T	0.11842	-1.0571	10	0.17832	T	0.49	-4.1582	15.4121	0.74933	1.0:0.0:0.0:0.0	.	596	Q8IYB8	SUV3_HUMAN	R	596	ENSP00000352678:Q596R	ENSP00000352678:Q596R	Q	+	2	0	SUPV3L1	70637565	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.976000	0.76135	2.113000	0.64589	0.528000	0.53228	CAG	.	.		0.393	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171		G	70967559	A	G	70967559	3	3	70	1	0	0	0	0	1	0	0	0	15417	188	7	2	1841	2	SUPV3L1	10	70967559	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	22550971	70967559	64567188	79	9010										
TYSND1	219743	hgsc.bcm.edu	37	chr10	71902607	71902607	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcccaccacactcacagcctCgcctgccagggaaggaagga	11	16	1	0	rs143461435		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:71902607C>T	ENST00000287078.6	-	3	1299	c.1300G>A	c.(1300-1302)Gag>Aag	p.E434K	TYSND1_ENST00000335494.5_Intron|TYSND1_ENST00000494143.1_5'UTR	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	434	Serine protease.				protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						CTCACAGCCTCGCCTGCCAGG	0.597																																					p.E434K		Atlas-SNP	.											.	TYSND1	20	.	0			c.G1300A						.	C	,LYS/GLU	0,4406		0,0,2203	53	39	44		,1300	3.4	0.6	10	dbSNP_134	44	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	TYSND1	NM_001040273.1,NM_173555.2	,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,benign	,434/567	71902607	1,13005	2203	4300	6503	SO:0001583	missense	219743	exon3			CAGCCTCGCCTGC	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.1300G>A	chr10.hg19:g.71902607C>T	ENSP00000287078:p.Glu434Lys	71.0	0.0		54.0	7.0	NM_173555	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	Missense_Mutation	SNP	ENST00000287078.6	hg19	CCDS31213.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.692646	0.48202	0.0	1.16E-4	ENSG00000156521	ENST00000287078	D	0.89552	-2.53	5.2	3.36	0.38483	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (2);	0.285900	0.33217	N	0.005145	D	0.86764	0.6011	M	0.85777	2.775	0.80722	D	1	P	0.35844	0.524	B	0.28991	0.097	D	0.84257	0.0481	10	0.59425	D	0.04	-12.7479	6.8769	0.24151	0.0:0.7261:0.0:0.2739	.	434	Q2T9J0	TYSD1_HUMAN	K	434	ENSP00000287078:E434K	ENSP00000287078:E434K	E	-	1	0	TYSND1	71572613	0.996000	0.38824	0.582000	0.28627	0.831000	0.47069	3.706000	0.54830	0.784000	0.33661	0.585000	0.79938	GAG	.	C|1.000;T|0.000		0.597	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555		T	71902607	C	T	71902607	3	4	70	1	0	0	0	0	1	0	0	0	16832	893	31	1	408	1	TYSND1	10	71902607	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	935048	71902607	63632140	80	9011										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72518013	72518013	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgggtgccacaatctgaaccCctacatcccattaacaagat	6	13	1	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:72518013C>G	ENST00000373207.1	+	21	3150	c.3150C>G	c.(3148-3150)ccC>ccG	p.P1050P	ADAMTS14_ENST00000373208.1_Silent_p.P1053P	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1050					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						AATCTGAACCCCTACATCCCA	0.552																																					p.P1053P		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.C3159G						.						116	102	107					10																	72518013		2203	4300	6503	SO:0001819	synonymous_variant	140766	exon21			TGAACCCCTACAT	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.3150C>G	chr10.hg19:g.72518013C>G		91.0	0.0		92.0	17.0	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	hg19	CCDS7306.1																																																																																			.	.		0.552	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		G	72518013	C	G	72518013	2	3	70	1	0	0	0	0	0	0	0	1	259	610	22	4		4	ADAMTS14	10	72518013	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	615406	72518013	63016734	81	9012										
DYDC1	143241	hgsc.bcm.edu	37	chr10	82098285	82098285	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gttaggtgctccataacgatCgctgatttcagctagtgttt	10	8	1	1	rs140462481	byFrequency	TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:82098285C>T	ENST00000372204.3	-	7	606	c.442G>A	c.(442-444)Gat>Aat	p.D148N	DYDC1_ENST00000421924.2_Missense_Mutation_p.D148N|DYDC1_ENST00000372202.1_Missense_Mutation_p.D148N	NM_138812.3	NP_620167.1	Q8WWB3	DYDC1_HUMAN	DPY30 domain containing 1	148										kidney(1)|large_intestine(3)|skin(1)	5			Colorectal(32;0.229)			CCATAACGATCGCTGATTTCA	0.333																																					p.D148N		Atlas-SNP	.											.	DYDC1	15	.	0			c.G442A						.						198	180	186					10																	82098285		2203	4300	6503	SO:0001583	missense	143241	exon6			AACGATCGCTGAT	BC019250	CCDS7366.1	10q22.3	2006-02-01			ENSG00000170788	ENSG00000170788			23460	protein-coding gene	gene with protein product		615154					Standard	NM_138812		Approved	bA36D19.5, DPY30D1	uc031pwj.1	Q8WWB3	OTTHUMG00000018609	ENST00000372204.3:c.442G>A	chr10.hg19:g.82098285C>T	ENSP00000361278:p.Asp148Asn	105.0	0.0		120.0	36.0	NM_001269053	A8K927|Q5QP03|Q5QP04|Q6WNP4|Q6ZU87	Missense_Mutation	SNP	ENST00000372204.3	hg19	CCDS7366.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.651479	0.47362	.	.	ENSG00000170788	ENST00000372204;ENST00000372202;ENST00000421924;ENST00000454362	.	.	.	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.53932	0.1827	M	0.68952	2.095	0.33019	D	0.528534	B;B	0.27951	0.195;0.087	B;B	0.20577	0.03;0.019	T	0.63673	-0.6584	9	0.33940	T	0.23	-28.3449	14.0068	0.64468	0.0:1.0:0.0:0.0	.	148;148	A8K927;Q8WWB3	.;DYDC1_HUMAN	N	148	.	ENSP00000361276:D148N	D	-	1	0	DYDC1	82088265	0.194000	0.23325	0.199000	0.23439	0.697000	0.40408	1.883000	0.39658	2.459000	0.83118	0.655000	0.94253	GAT	.	C|1.000;A|0.000		0.333	DYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049059.1	NM_138812		T	82098285	C	T	82098285	3	4	70	1	0	0	0	0	1	0	0	0	4840	884	31	1	99	1	DYDC1	10	82098285	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	9580272	82098285	53436462	82	9013										
PAPSS2	9060	hgsc.bcm.edu	37	chr10	89472858	89472858	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ctggtgctggaaaaacaacgAtaagttttgccctggaggag	13	7	0	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:89472858A>G	ENST00000361175.4	+	3	541	c.172A>G	c.(172-174)Ata>Gta	p.I58V	PAPSS2_ENST00000456849.1_Missense_Mutation_p.I58V|PAPSS2_ENST00000482258.1_3'UTR|PAPSS2_ENST00000427144.2_Missense_Mutation_p.I62V	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	58					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		AAAAACAACGATAAGTTTTGC	0.448																																					p.I58V		Atlas-SNP	.											.	PAPSS2	46	.	0			c.A172G						.						145	149	148					10																	89472858		2203	4300	6503	SO:0001583	missense	9060	exon3			ACAACGATAAGTT	AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.172A>G	chr10.hg19:g.89472858A>G	ENSP00000354436:p.Ile58Val	163.0	0.0		163.0	55.0	NM_001015880	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	Missense_Mutation	SNP	ENST00000361175.4	hg19	CCDS7385.1	.	.	.	.	.	.	.	.	.	.	A	2.035	-0.421352	0.04734	.	.	ENSG00000198682	ENST00000361175;ENST00000456849;ENST00000427144;ENST00000371981	T;T;T	0.78246	-1.16;-1.16;-1.16	5.87	0.992	0.19819	Adenylylsulphate kinase, C-terminal (3);	0.144289	0.64402	N	0.000009	T	0.58119	0.2100	N	0.25890	0.77	0.54753	D	0.999983	B;B	0.06786	0.001;0.001	B;B	0.18263	0.021;0.007	T	0.30679	-0.9970	10	0.13853	T	0.58	-13.112	5.8466	0.18669	0.607:0.1267:0.2662:0.0	.	58;58	O95340;O95340-2	PAPS2_HUMAN;.	V	58;58;62;57	ENSP00000354436:I58V;ENSP00000406157:I58V;ENSP00000397123:I62V	ENSP00000354436:I58V	I	+	1	0	PAPSS2	89462838	0.584000	0.26766	0.029000	0.17559	0.045000	0.14185	1.444000	0.35068	-0.074000	0.12820	-1.069000	0.02264	ATA	.	.		0.448	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049229.1			G	89472858	A	G	89472858	3	3	70	1	0	0	0	0	1	0	0	0	11444	333	12	2	182	2	PAPSS2	10	89472858	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	7374573	89472858	46061889	83	9014										
PLCE1	51196	hgsc.bcm.edu	37	chr10	96084326	96084326	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gctaaaggagcaggtgcaggTaaagtttaaagttattttgc	12	4	0	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:96084326T>C	ENST00000371380.3	+	30	6955		c.e30+2		PLCE1_ENST00000371375.1_Splice_Site|NOC3L_ENST00000543788.1_Intron|PLCE1_ENST00000371385.3_Splice_Site|PLCE1_ENST00000260766.3_Splice_Site			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1						activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				CAGGTGCAGGTAAAGTTTAAA	0.423																																					.		Atlas-SNP	.											.	PLCE1	543	.	0			c.6720+2T>C						.						81	80	80					10																	96084326		1875	4107	5982	SO:0001630	splice_region_variant	51196	exon31			TGCAGGTAAAGTT		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.6720+2T>C	chr10.hg19:g.96084326T>C		89.0	0.0		91.0	34.0	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Splice_Site	SNP	ENST00000371380.3	hg19	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.455335	0.63401	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2675	0.73672	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PLCE1	96074316	1.000000	0.71417	0.998000	0.56505	0.813000	0.45954	4.325000	0.59234	2.086000	0.62901	0.482000	0.46254	.	.	.		0.423	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	Intron	C	96084326	T	C	96084326	5	2	70	1	0	0	0	0	0	0	1	0	12043	1652	57	2	7126	2	PLCE1	10	96084326	Splice_Site	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	6611468	96084326	39450421	84	9015										
SEC31B	25956	hgsc.bcm.edu	37	chr10	102267799	102267799	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	agacagtgccttgatgtcctCtggaggctgctaaggcagga	14	9	1	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:102267799C>T	ENST00000370345.3	-	6	602	c.505G>A	c.(505-507)Gag>Aag	p.E169K	SEC31B_ENST00000535773.1_Missense_Mutation_p.E12K|SEC31B_ENST00000451524.1_Missense_Mutation_p.E169K|NDUFB8_ENST00000557395.1_3'UTR|SEC31B_ENST00000370329.5_Missense_Mutation_p.E172K|NDUFB8_ENST00000531258.1_3'UTR	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	169					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		TTGATGTCCTCTGGAGGCTGC	0.547																																					p.E169K		Atlas-SNP	.											.	SEC31B	84	.	0			c.G505A						.						148	129	135					10																	102267799		2203	4300	6503	SO:0001583	missense	25956	exon6			TGTCCTCTGGAGG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.505G>A	chr10.hg19:g.102267799C>T	ENSP00000359370:p.Glu169Lys	56.0	0.0		71.0	19.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	hg19	CCDS7495.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.925714	0.92319	.	.	ENSG00000075826	ENST00000370345;ENST00000451524;ENST00000535773;ENST00000370329	T;T;T;T	0.69926	0.62;0.3;-0.44;0.44	5.67	4.75	0.60458	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80297	0.4597	M	0.69358	2.11	0.80722	D	1	D;P;D;P;D	0.89917	0.982;0.803;1.0;0.803;0.999	P;P;D;B;D	0.83275	0.855;0.468;0.996;0.392;0.985	T	0.82307	-0.0522	10	0.62326	D	0.03	-16.0947	15.7133	0.77649	0.0:0.8631:0.1369:0.0	.	169;172;168;169;169	A8KAL6;B4DGE3;Q9NQW1-5;E9PKR7;Q9NQW1	.;.;.;.;SC31B_HUMAN	K	169;169;12;172	ENSP00000359370:E169K;ENSP00000391178:E169K;ENSP00000442621:E12K;ENSP00000359354:E172K	ENSP00000359354:E172K	E	-	1	0	SEC31B	102257789	1.000000	0.71417	0.909000	0.35828	0.839000	0.47603	7.731000	0.84895	1.387000	0.46486	0.462000	0.41574	GAG	.	.		0.547	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		T	102267799	C	T	102267799	3	4	70	1	0	0	0	0	1	0	0	0	14014	922	32	3	3118	3	SEC31B	10	102267799	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	6183473	102267799	33266948	85	9016										
CPXM2	119587	hgsc.bcm.edu	37	chr10	125557598	125557598	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gccaccatggggacgggtagCtcattgagaacagggatctc	14	10	2	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr10:125557598C>A	ENST00000241305.3	-	6	937	c.783G>T	c.(781-783)gaG>gaT	p.E261D	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	261	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		GGACGGGTAGCTCATTGAGAA	0.473																																					p.E261D		Atlas-SNP	.											.	CPXM2	120	.	0			c.G783T						.						130	111	118					10																	125557598		2203	4300	6503	SO:0001583	missense	119587	exon6			GGGTAGCTCATTG	AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase"					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.783G>T	chr10.hg19:g.125557598C>A	ENSP00000241305:p.Glu261Asp	102.0	0.0		120.0	21.0	NM_198148	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	hg19	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	C	5.200	0.222410	0.09863	.	.	ENSG00000121898	ENST00000241305;ENST00000540123;ENST00000418782	D	0.98178	-4.77	4.46	3.53	0.40419	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.626440	0.16833	N	0.197668	D	0.93716	0.7992	N	0.16037	0.36	0.80722	D	1	B	0.12630	0.006	B	0.22880	0.042	D	0.90036	0.4138	10	0.23302	T	0.38	-15.9855	9.3275	0.38001	0.0:0.8347:0.0:0.1653	.	261	Q8N436	CPXM2_HUMAN	D	261;94;261	ENSP00000241305:E261D	ENSP00000241305:E261D	E	-	3	2	CPXM2	125547588	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	1.801000	0.38843	2.292000	0.77174	0.557000	0.71058	GAG	.	.		0.473	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		A	125557598	C	A	125557598	3	1	70	1	0	0	0	0	1	0	0	0	3840	796	28	3	1523	3	CPXM2	10	125557598	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	23289799	125557598	9977149	86	9017										
SLC6A5	9152	hgsc.bcm.edu	37	chr11	20652251	20652251	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttccagggacactctaattgTcacctgcaccaacagtgcca	7	14	2	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr11:20652251T>C	ENST00000525748.1	+	10	1787	c.1514T>C	c.(1513-1515)gTc>gCc	p.V505A	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	505					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	ACTCTAATTGTCACCTGCACC	0.498																																					p.V505A		Atlas-SNP	.											.	SLC6A5	151	.	0			c.T1514C						.						214	186	195					11																	20652251		2203	4300	6503	SO:0001583	missense	9152	exon10			TAATTGTCACCTG	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"Solute carriers"	11051	protein-coding gene	gene with protein product	"glycine transporter 2"	604159	"solute carrier family 6 (neurotransmitter transporter, glycine), member 5"	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.1514T>C	chr11.hg19:g.20652251T>C	ENSP00000434364:p.Val505Ala	124.0	0.0		170.0	53.0	NM_004211	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	hg19	CCDS7854.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.767324	0.90020	.	.	ENSG00000165970	ENST00000525748	T	0.79033	-1.23	5.57	5.57	0.84162	.	0.167862	0.52532	D	0.000072	D	0.88355	0.6414	M	0.81614	2.55	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.89979	0.4099	10	0.87932	D	0	.	15.7239	0.77736	0.0:0.0:0.0:1.0	.	505	Q9Y345	SC6A5_HUMAN	A	505	ENSP00000434364:V505A	ENSP00000434364:V505A	V	+	2	0	SLC6A5	20608827	1.000000	0.71417	0.988000	0.46212	0.923000	0.55619	8.040000	0.89188	2.116000	0.64780	0.533000	0.62120	GTC	.	.		0.498	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211		C	20652251	T	C	20652251	3	2	70	1	0	0	0	0	1	0	0	0	14702	1667	58	2	1552	2	SLC6A5	11	20652251	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10		20652251	114354265	87	9018										
OR8H2	390151	hgsc.bcm.edu	37	chr11	55873358	55873358	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcttctgttttttatactatTgtgattcccgtgctgaatcc	7	9	1	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr11:55873358T>G	ENST00000313503.1	+	1	840	c.840T>G	c.(838-840)atT>atG	p.I280M		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	280						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					TTTATACTATTGTGATTCCCG	0.368										HNSCC(53;0.14)																											p.I280M		Atlas-SNP	.											.	OR8H2	117	.	0			c.T840G						.						78	86	83					11																	55873358		2201	4294	6495	SO:0001583	missense	390151	exon1			TACTATTGTGATT	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"GPCR / Class A : Olfactory receptors"	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.840T>G	chr11.hg19:g.55873358T>G	ENSP00000323982:p.Ile280Met	155.0	0.0		182.0	59.0	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	hg19	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	t	3.843	-0.033330	0.07543	.	.	ENSG00000181767	ENST00000313503	T	0.00164	8.64	3.35	0.69	0.18039	GPCR, rhodopsin-like superfamily (1);	0.116486	0.39475	N	0.001345	T	0.00178	0.0005	L	0.37750	1.13	0.09310	N	1	D	0.76494	0.999	D	0.76575	0.988	T	0.44772	-0.9306	10	0.07644	T	0.81	.	1.7012	0.02873	0.1367:0.1275:0.3041:0.4317	.	280	Q8N162	OR8H2_HUMAN	M	280	ENSP00000323982:I280M	ENSP00000323982:I280M	I	+	3	3	OR8H2	55629934	0.000000	0.05858	0.984000	0.44739	0.138000	0.21146	-2.914000	0.00697	0.022000	0.15160	0.362000	0.22060	ATT	.	.		0.368	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200		G	55873358	T	G	55873358	3	3	70	1	0	0	0	0	1	0	0	0	11247	1800	63	5	842	5	OR8H2	11	55873358	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	35221107	55873358	79133158	88	9019										
MRPL21	219927	hgsc.bcm.edu	37	chr11	68660463	68660463	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tactcgaacaagatcctttcTagaaggaagaaaaatcaaca	6	8	2	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr11:68660463T>C	ENST00000362034.2	-	6	459		c.e6-2		MRPL21_ENST00000567045.1_Splice_Site|MRPL21_ENST00000450904.2_Splice_Site	NM_181514.1|NM_181515.1	NP_852615.1|NP_852616.1	Q7Z2W9	RM21_HUMAN	mitochondrial ribosomal protein L21						translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(6)|prostate(1)	8			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			AGATCCTTTCTAGAAGGAAGA	0.318																																					.		Atlas-SNP	.											.	MRPL21	13	.	0			c.195-2A>G						.						73	67	69					11																	68660463		2200	4294	6494	SO:0001630	splice_region_variant	219927	exon7			CCTTTCTAGAAGG	AK096756	CCDS8186.1, CCDS44662.1	11q13.3	2012-09-13			ENSG00000197345	ENSG00000197345		"Mitochondrial ribosomal proteins / large subunits"	14479	protein-coding gene	gene with protein product		611834				11551941	Standard	NM_181514		Approved		uc001ooi.3	Q7Z2W9	OTTHUMG00000167893	ENST00000362034.2:c.450-2A>G	chr11.hg19:g.68660463T>C		104.0	0.0		74.0	20.0	NM_181515	A6NKU0|C9JPR2	Splice_Site	SNP	ENST00000362034.2	hg19	CCDS8186.1	.	.	.	.	.	.	.	.	.	.	T	14.77	2.636043	0.47049	.	.	ENSG00000197345	ENST00000450904;ENST00000362034;ENST00000447977	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9107	0.58179	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MRPL21	68417039	0.997000	0.39634	0.951000	0.38953	0.655000	0.38815	3.055000	0.49916	1.697000	0.51169	0.528000	0.53228	.	.	.		0.318	MRPL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396856.1	NM_181512	Intron	C	68660463	T	C	68660463	5	2	70	1	0	0	0	0	0	0	1	0	9796	1536	53	2	177	2	MRPL21	11	68660463	Splice_Site	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	12787105	68660463	66346053	89	9020										
GRM5	2915	hgsc.bcm.edu	37	chr11	88386445	88386445	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gggtttcggtggtttgtttcTggccggagcttcagataata	14	6	2	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr11:88386445T>C	ENST00000305447.4	-	3	1187	c.1038A>G	c.(1036-1038)ccA>ccG	p.P346P	GRM5_ENST00000305432.5_Silent_p.P346P|GRM5_ENST00000455756.2_Silent_p.P346P|GRM5_ENST00000418177.2_Silent_p.P346P|GRM5_ENST00000393297.1_Silent_p.P346P	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	346					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	GGTTTGTTTCTGGCCGGAGCT	0.458																																					p.P346P		Atlas-SNP	.											.	GRM5	414	.	0			c.A1038G						.						92	93	93					11																	88386445		2201	4299	6500	SO:0001819	synonymous_variant	2915	exon4			TGTTTCTGGCCGG	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1038A>G	chr11.hg19:g.88386445T>C		103.0	0.0		128.0	36.0	NM_000842	Q6J164	Silent	SNP	ENST00000305447.4	hg19	CCDS44694.1																																																																																			.	.		0.458	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		C	88386445	T	C	88386445	2	2	70	1	0	0	0	0	0	0	0	1	6809	1567	55	2		2	GRM5	11	88386445	Silent	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	19725982	88386445	46620071	90	9021										
FAT3	120114	hgsc.bcm.edu	37	chr11	92495256	92495256	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttgtggatgggaatgatgacGgaaagttctttattgaccct	12	5	1	3	rs568235366		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr11:92495256G>T	ENST00000298047.6	+	4	3921	c.3904G>T	c.(3904-3906)Gga>Tga	p.G1302*	FAT3_ENST00000409404.2_Nonsense_Mutation_p.G1302*|RP11-203F8.1_ENST00000529884.1_RNA|FAT3_ENST00000525166.1_Nonsense_Mutation_p.G1152*			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1302	Cadherin 12. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GAATGATGACGGAAAGTTCTT	0.428										TCGA Ovarian(4;0.039)																											p.G1302X		Atlas-SNP	.											.	FAT3	1822	.	0			c.G3904T						.						93	91	92					11																	92495256		1887	4117	6004	SO:0001587	stop_gained	120114	exon4			GATGACGGAAAGT	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.3904G>T	chr11.hg19:g.92495256G>T	ENSP00000298047:p.Gly1302*	126.0	0.0		156.0	41.0	NM_001008781	B5MDB0|Q96AU6	Nonsense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	42	9.451075	0.99175	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	19.5733	0.95430	0.0:0.0:1.0:0.0	.	.	.	.	X	1302;1302;1152	.	ENSP00000298047:G1302X	G	+	1	0	FAT3	92134904	1.000000	0.71417	0.981000	0.43875	0.379000	0.30106	6.557000	0.73937	2.618000	0.88619	0.563000	0.77884	GGA	.	.		0.428	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92495256	G	T	92495256	4	4	70	1	0	0	0	0	0	1	0	0	5699	1117	39	1	3918	1	FAT3	11	92495256	Nonsense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	4108811	92495256	42511260	91	9022										
ABCG4	64137	hgsc.bcm.edu	37	chr11	119031060	119031060	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ccttggtggcccaatctttgGggctgctgatcggagctgct	14	11	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr11:119031060G>C	ENST00000449422.2	+	13	1749	c.1561G>C	c.(1561-1563)Ggg>Cgg	p.G521R	ABCG4_ENST00000307417.3_Missense_Mutation_p.G521R|ABCG4_ENST00000531739.1_Missense_Mutation_p.G521R	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	521	ABC transmembrane type-2.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CCAATCTTTGGGGCTGCTGAT	0.632																																					p.G521R		Atlas-SNP	.											.	ABCG4	77	.	0			c.G1561C						.						49	49	49					11																	119031060		2200	4295	6495	SO:0001583	missense	64137	exon13			TCTTTGGGGCTGC	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"ATP binding cassette transporters / subfamily G"	13884	protein-coding gene	gene with protein product	"putative ABC transporter", "ATP-binding cassette, subfamily G, member 4"	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1561G>C	chr11.hg19:g.119031060G>C	ENSP00000406874:p.Gly521Arg	56.0	0.0		68.0	17.0	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	G	34	5.343088	0.95783	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739	T;T;T	0.79352	-1.26;-1.26;-1.26	5.2	5.2	0.72013	ABC-2 type transporter (1);	0.189632	0.56097	D	0.000027	D	0.92355	0.7574	H	0.96633	3.855	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	D	0.94556	0.7758	10	0.87932	D	0	-15.3271	18.9923	0.92798	0.0:0.0:1.0:0.0	.	521	Q9H172	ABCG4_HUMAN	R	521	ENSP00000304111:G521R;ENSP00000406874:G521R;ENSP00000434318:G521R	ENSP00000304111:G521R	G	+	1	0	ABCG4	118536270	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.648000	0.98483	2.720000	0.93068	0.558000	0.71614	GGG	.	.		0.632	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		C	119031060	G	C	119031060	3	2	70	1	0	0	0	0	1	0	0	0	70	1232	43	4	1607	4	ABCG4	11	119031060	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	26535804	119031060	15975456	92	9023										
USP2	9099	hgsc.bcm.edu	37	chr11	119228005	119228005	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tggacacagcgtacaggttgTaaacagcatggtctgaggag	14	7	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr11:119228005T>C	ENST00000260187.2	-	12	1916	c.1622A>G	c.(1621-1623)tAc>tGc	p.Y541C	USP2_ENST00000455332.2_Missense_Mutation_p.Y298C|USP2_ENST00000525735.1_Missense_Mutation_p.Y332C	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	541	USP.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		GTACAGGTTGTAAACAGCATG	0.597																																					p.Y541C		Atlas-SNP	.											.	USP2	71	.	0			c.A1622G						.						90	80	83					11																	119228005		2199	4295	6494	SO:0001583	missense	9099	exon12			AGGTTGTAAACAG	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"Ubiquitin-specific peptidases"	12618	protein-coding gene	gene with protein product		604725	"ubiquitin specific protease 2"			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.1622A>G	chr11.hg19:g.119228005T>C	ENSP00000260187:p.Tyr541Cys	106.0	0.0		141.0	44.0	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Missense_Mutation	SNP	ENST00000260187.2	hg19	CCDS8422.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.363808	0.82353	.	.	ENSG00000036672	ENST00000455332;ENST00000260187;ENST00000392808;ENST00000525735	T;T;T	0.22539	1.95;1.95;1.95	5.77	5.77	0.91146	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.65270	0.2675	H	0.99545	4.62	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.79359	-0.1836	10	0.87932	D	0	-5.887	11.6391	0.51222	0.1328:0.0:0.0:0.8672	.	298;541;332	E9PPM2;O75604;O75604-4	.;UBP2_HUMAN;.	C	298;541;288;332	ENSP00000407842:Y298C;ENSP00000260187:Y541C;ENSP00000436952:Y332C	ENSP00000260187:Y541C	Y	-	2	0	USP2	118733215	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.956000	0.87863	2.201000	0.70794	0.523000	0.50628	TAC	.	.		0.597	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997		C	119228005	T	C	119228005	3	2	70	1	0	0	0	0	1	0	0	0	17066	1638	57	2	203	2	USP2	11	119228005	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	196945	119228005	15778511	93	9024										
LRP6	4040	hgsc.bcm.edu	37	chr12	12356291	12356291	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgaaccatccattccagcacGttctatctttggcacttctc	5	14	3	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr12:12356291G>A	ENST00000261349.4	-	3	569	c.493C>T	c.(493-495)Cgt>Tgt	p.R165C	LRP6_ENST00000543091.1_Missense_Mutation_p.R165C	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	165	Beta-propeller 1.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				ATTCCAGCACGTTCTATCTTT	0.358																																					p.R165C		Atlas-SNP	.											.	LRP6	170	.	0			c.C493T						.						125	119	121					12																	12356291		2203	4300	6503	SO:0001583	missense	4040	exon3			CAGCACGTTCTAT	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.493C>T	chr12.hg19:g.12356291G>A	ENSP00000261349:p.Arg165Cys	113.0	0.0		127.0	30.0	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.763672	0.69878	.	.	ENSG00000070018	ENST00000261349;ENST00000543091;ENST00000535731	D;D;D	0.96200	-3.94;-3.94;-3.94	5.51	5.51	0.81932	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000009	D	0.97904	0.9311	M	0.83118	2.625	0.80722	D	1	D;P	0.89917	1.0;0.904	D;B	0.85130	0.997;0.227	D	0.98438	1.0585	10	0.72032	D	0.01	.	19.4043	0.94642	0.0:0.0:1.0:0.0	.	165;165	F5H7J9;O75581	.;LRP6_HUMAN	C	165;165;14	ENSP00000261349:R165C;ENSP00000442472:R165C;ENSP00000439765:R14C	ENSP00000261349:R165C	R	-	1	0	LRP6	12247558	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.265000	0.65519	2.574000	0.86865	0.655000	0.94253	CGT	.	.		0.358	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			A	12356291	G	A	12356291	3	1	70	1	0	0	0	0	1	0	0	0	8971	1145	40	1	4432	1	LRP6	12	12356291	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10		12356291	121495604	94	9025										
PKP2	5318	hgsc.bcm.edu	37	chr12	33031964	33031964	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	actgctggttcggtgaagatTtcctgcaatcaagcaaatat	9	8	1	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr12:33031964T>G	ENST00000070846.6	-	2	250	c.226A>C	c.(226-228)Aat>Cat	p.N76H	PKP2_ENST00000340811.4_Missense_Mutation_p.N76H	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	76			N -> S. {ECO:0000269|Ref.2}.		adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					CGGTGAAGATTTCCTGCAATC	0.338																																					p.N76H		Atlas-SNP	.											.	PKP2	110	.	0			c.A226C						.						70	67	68					12																	33031964		2203	4300	6503	SO:0001583	missense	5318	exon2			GAAGATTTCCTGC	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"Armadillo repeat containing"	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.226A>C	chr12.hg19:g.33031964T>G	ENSP00000070846:p.Asn76His	86.0	0.0		97.0	26.0	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	hg19	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.152253	0.78001	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	D;T	0.81821	-1.54;-1.47	5.7	5.7	0.88788	.	0.305323	0.28296	N	0.015862	D	0.84188	0.5417	L	0.53249	1.67	0.30627	N	0.757873	D;D;D	0.61080	0.986;0.976;0.989	P;P;P	0.55667	0.748;0.564;0.781	D	0.84520	0.0627	10	0.62326	D	0.03	-16.7933	14.1893	0.65628	0.0:0.0:0.0:1.0	.	76;76;76	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	H	76	ENSP00000342800:N76H;ENSP00000070846:N76H	ENSP00000070846:N76H	N	-	1	0	PKP2	32923231	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	3.129000	0.50500	2.164000	0.68074	0.528000	0.53228	AAT	.	.		0.338	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		G	33031964	T	G	33031964	3	3	70	1	0	0	0	0	1	0	0	0	11994	1841	64	5	2471	5	PKP2	12	33031964	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	20675673	33031964	100819931	95	9026										
ARID2	196528	hgsc.bcm.edu	37	chr12	46230676	46230676	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	atgttaagctcttggcagctAatcgtacctgtcttcgtttc	8	10	2	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr12:46230676A>T	ENST00000334344.6	+	8	1097	c.925A>T	c.(925-927)Aat>Tat	p.N309Y	ARID2_ENST00000422737.1_Missense_Mutation_p.N160Y|ARID2_ENST00000444670.1_5'Flank|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	309					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N309D(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CTTGGCAGCTAATCGTACCTG	0.408			"N, S, F"		hepatocellular carcinoma																																p.N309Y		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	ARID2,colon,carcinoma,0,1	ARID2	311	.	1	Substitution - Missense(1)	large_intestine(1)	c.A925T						.						188	176	180					12																	46230676		2203	4300	6503	SO:0001583	missense	196528	exon8			GCAGCTAATCGTA		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.925A>T	chr12.hg19:g.46230676A>T	ENSP00000335044:p.Asn309Tyr	160.0	0.0		166.0	62.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	19.95	3.921373	0.73213	.	.	ENSG00000189079	ENST00000334344;ENST00000422737	T;T	0.46451	0.87;0.87	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.64204	0.2577	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.67209	-0.5728	10	0.87932	D	0	-13.958	16.2628	0.82557	1.0:0.0:0.0:0.0	.	309	Q68CP9	ARID2_HUMAN	Y	309;160	ENSP00000335044:N309Y;ENSP00000415650:N160Y	ENSP00000335044:N309Y	N	+	1	0	ARID2	44516943	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.265000	0.78442	2.233000	0.73108	0.482000	0.46254	AAT	.	.		0.408	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46230676	A	T	46230676	3	4	70	1	0	0	0	0	1	0	0	0	915	362	13	4	955	4	ARID2	12	46230676	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	13198712	46230676	87621219	96	9027										
ARID2	196528	hgsc.bcm.edu	37	chr12	46254582	46254582	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ctgcatttgttctttttcacAgaacactcctatgccacctt	4	13	2	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr12:46254582A>G	ENST00000334344.6	+	16	4945		c.e16-1		ARID2_ENST00000422737.1_Splice_Site|ARID2_ENST00000444670.1_Splice_Site|ARID2_ENST00000479608.1_Splice_Site|ARID2_ENST00000457135.1_Splice_Site	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCTTTTTCACAGAACACTCCT	0.393			"N, S, F"		hepatocellular carcinoma																																.		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.4774-2A>G						.						60	56	57					12																	46254582		2203	4300	6503	SO:0001630	splice_region_variant	196528	exon16			TTTCACAGAACAC		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4774-1A>G	chr12.hg19:g.46254582A>G		43.0	0.0		67.0	24.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Splice_Site	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.199597	0.79015	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670;ENST00000457135	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2644	0.82568	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARID2	44540849	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.877000	0.87225	2.244000	0.73946	0.528000	0.53228	.	.	.		0.393	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	Intron	G	46254582	A	G	46254582	5	3	70	1	0	0	0	0	0	0	1	0	915	202	7	2	4834	2	ARID2	12	46254582	Splice_Site	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	23906	46254582	87597313	97	9028										
NEUROD4	58158	hgsc.bcm.edu	37	chr12	55420925	55420925	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gtattcaagagtttgggagaAtcgtcctttgggagccatct	12	7	2	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr12:55420925A>C	ENST00000242994.3	+	2	1080	c.702A>C	c.(700-702)gaA>gaC	p.E234D		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	234					amacrine cell differentiation (GO:0035881)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch signaling pathway (GO:0007219)|positive regulation of cell differentiation (GO:0045597)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	41						GTTTGGGAGAATCGTCCTTTG	0.517																																					p.E234D		Atlas-SNP	.											.	NEUROD4	87	.	0			c.A702C						.						100	100	100					12																	55420925		2203	4300	6503	SO:0001583	missense	58158	exon2			GGGAGAATCGTCC	AF203901	CCDS8886.1	12q13.13	2013-05-21	2012-02-22			ENSG00000123307		"Basic helix-loop-helix proteins"	13802	protein-coding gene	gene with protein product		611635	"neurogenic differentiation 4"				Standard	NM_021191		Approved	Atoh3, ATH-3, MATH-3, bHLHa4	uc001sgp.4	Q9HD90		ENST00000242994.3:c.702A>C	chr12.hg19:g.55420925A>C	ENSP00000242994:p.Glu234Asp	76.0	0.0		94.0	24.0	NM_021191	B2RAC9	Missense_Mutation	SNP	ENST00000242994.3	hg19	CCDS8886.1	.	.	.	.	.	.	.	.	.	.	A	12.97	2.096016	0.36952	.	.	ENSG00000123307	ENST00000242994	T	0.65549	-0.16	5.71	-3.01	0.05463	Neurogenic differentiation factor, domain of unknown function (1);	0.525209	0.21686	N	0.070655	T	0.38719	0.1051	N	0.16602	0.42	0.25139	N	0.990519	B	0.06786	0.001	B	0.19666	0.026	T	0.22382	-1.0218	10	0.29301	T	0.29	1.2164	9.4234	0.38565	0.1991:0.1942:0.6066:0.0	.	234	Q9HD90	NDF4_HUMAN	D	234	ENSP00000242994:E234D	ENSP00000242994:E234D	E	+	3	2	NEUROD4	53707192	0.001000	0.12720	0.954000	0.39281	0.975000	0.68041	-1.298000	0.02756	-0.341000	0.08376	0.533000	0.62120	GAA	.	.		0.517	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1			C	55420925	A	C	55420925	3	2	70	1	0	0	0	0	1	0	0	0	10359	98	4	5	704	5	NEUROD4	12	55420925	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	9166343	55420925	78430970	98	9029										
MGAT4C	25834	hgsc.bcm.edu	37	chr12	86373990	86373990	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	atactcctctggagcatgtaTaaccattaatcttcctgcaa	5	11	2	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr12:86373990T>C	ENST00000604798.1	-	8	1718	c.514A>G	c.(514-516)Ata>Gta	p.I172V	MGAT4C_ENST00000548651.1_Missense_Mutation_p.I172V|MGAT4C_ENST00000332156.1_Missense_Mutation_p.I172V|MGAT4C_ENST00000549405.2_Missense_Mutation_p.I172V|MGAT4C_ENST00000393205.2_Missense_Mutation_p.I201V|MGAT4C_ENST00000552808.2_Missense_Mutation_p.I172V|MGAT4C_ENST00000552435.2_Intron			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	172					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						GGAGCATGTATAACCATTAAT	0.393																																					p.I172V		Atlas-SNP	.											.	MGAT4C	110	.	0			c.A514G						.						106	105	105					12																	86373990		2203	4300	6503	SO:0001583	missense	25834	exon7			CATGTATAACCAT		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	30871	protein-coding gene	gene with protein product		607385	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.514A>G	chr12.hg19:g.86373990T>C	ENSP00000474896:p.Ile172Val	102.0	0.0		153.0	41.0	NM_013244	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	hg19	CCDS9030.1	.	.	.	.	.	.	.	.	.	.	T	11.02	1.515840	0.27123	.	.	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225	T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.48314	0.1493	L	0.41961	1.31	0.58432	D	0.999995	P;P	0.43701	0.815;0.815	P;P	0.46237	0.508;0.508	T	0.39354	-0.9618	10	0.32370	T	0.25	-0.1803	15.7677	0.78141	0.0:0.0:0.0:1.0	.	201;172	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	V	172;201;172;172;172;172;172	ENSP00000331664:I172V;ENSP00000376900:I201V;ENSP00000449022:I172V;ENSP00000446647:I172V;ENSP00000447253:I172V;ENSP00000449172:I172V	ENSP00000331664:I172V	I	-	1	0	MGAT4C	84898121	1.000000	0.71417	0.999000	0.59377	0.006000	0.05464	8.036000	0.88901	2.112000	0.64535	0.533000	0.62120	ATA	.	.		0.393	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		C	86373990	T	C	86373990	3	2	70	1	0	0	0	0	1	0	0	0	9556	1406	49	2	926	2	MGAT4C	12	86373990	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	30953065	86373990	47477905	99	9030										
TMCC3	57458	hgsc.bcm.edu	37	chr12	94976245	94976245	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	atccgggacatcaaagttgaGgttggtgtctgacccccctc	11	12	2	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr12:94976245G>C	ENST00000261226.4	-	2	279	c.148C>G	c.(148-150)Ctc>Gtc	p.L50V	TMCC3_ENST00000551457.1_Missense_Mutation_p.L19V	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	50						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						TCAAAGTTGAGGTTGGTGTCT	0.463																																					p.L50V		Atlas-SNP	.											.	TMCC3	63	.	0			c.C148G						.						112	110	111					12																	94976245		2203	4300	6503	SO:0001583	missense	57458	exon2			AGTTGAGGTTGGT	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"Transmembrane and coiled-coil domain containing"	29199	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 3"			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.148C>G	chr12.hg19:g.94976245G>C	ENSP00000261226:p.Leu50Val	80.0	0.0		84.0	19.0	NM_020698	Q8IWB2	Missense_Mutation	SNP	ENST00000261226.4	hg19	CCDS31877.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.126475	0.56721	.	.	ENSG00000057704	ENST00000261226;ENST00000551457;ENST00000548918	T;T	0.49720	1.3;0.77	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.56775	0.2008	L	0.27053	0.805	0.58432	D	0.999992	D	0.69078	0.997	D	0.72625	0.978	T	0.44892	-0.9298	10	0.18276	T	0.48	-32.3133	20.3522	0.98815	0.0:0.0:1.0:0.0	.	50	Q9ULS5	TMCC3_HUMAN	V	50;19;19	ENSP00000261226:L50V;ENSP00000449888:L19V	ENSP00000261226:L50V	L	-	1	0	TMCC3	93500376	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.036000	0.49767	2.821000	0.97095	0.485000	0.47835	CTC	.	.		0.463	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698		C	94976245	G	C	94976245	3	2	70	1	0	0	0	0	1	0	0	0	16009	1000	35	4	1297	4	TMCC3	12	94976245	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	8602255	94976245	38875650	100	9031										
SRRM4	84530	hgsc.bcm.edu	37	chr12	119594393	119594393	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tggtacagcagcagcagtagCcgctcggccagccgcagcta	13	14	0	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr12:119594393C>A	ENST00000267260.4	+	13	2014	c.1626C>A	c.(1624-1626)agC>agA	p.S542R		NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	542	Arg-rich.|Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						GCAGCAGTAGCCGCTCGGCCA	0.697																																					p.S542R		Atlas-SNP	.											.	SRRM4	131	.	0			c.C1626A						.						10	15	13					12																	119594393		1881	3901	5782	SO:0001583	missense	84530	exon13			CAGTAGCCGCTCG	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"neural-specific SR-related protein of 100 kDa"	613103	"KIAA1853"	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.1626C>A	chr12.hg19:g.119594393C>A	ENSP00000267260:p.Ser542Arg	140.0	0.0		167.0	54.0	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	hg19	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152019	0.57151	.	.	ENSG00000139767	ENST00000267260	T	0.39406	1.08	5.42	4.5	0.54988	.	0.152448	0.41097	D	0.000946	T	0.36717	0.0977	L	0.50333	1.59	0.38152	D	0.938772	B	0.11235	0.004	B	0.08055	0.003	T	0.22730	-1.0208	9	.	.	.	-7.1558	13.8905	0.63736	0.1517:0.8483:0.0:0.0	.	542	A7MD48	SRRM4_HUMAN	R	542	ENSP00000267260:S542R	.	S	+	3	2	SRRM4	118078776	0.804000	0.28969	1.000000	0.80357	0.992000	0.81027	0.000000	0.12993	2.555000	0.86185	0.650000	0.86243	AGC	.	.		0.697	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		A	119594393	C	A	119594393	3	1	70	1	0	0	0	0	1	0	0	0	15186	738	26	3	1676	3	SRRM4	12	119594393	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	24618148	119594393	14257502	101	9032										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124914165	124914166	+	Frame_Shift_Del	DEL	CT	CT	-													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gggcctggactcacctcctgCtctgagaggccatcgatgat					rs199934660		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr12:124914165_124914166delCT	ENST00000405201.1	-	10	1142_1143	c.1142_1143delAG	c.(1141-1143)gagfs	p.E381fs	NCOR2_ENST00000397355.1_Frame_Shift_Del_p.E381fs|NCOR2_ENST00000404621.1_Frame_Shift_Del_p.E380fs|NCOR2_ENST00000429285.2_Frame_Shift_Del_p.E380fs|NCOR2_ENST00000356219.3_Frame_Shift_Del_p.E381fs|NCOR2_ENST00000404121.2_5'UTR			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	381					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TCACCTCCTGCTCTGAGAGGCC	0.673																																					p.381_382del		Atlas-Indel,Pindel	.											.	NCOR2	475	.	0			c.1143_1144del						.																																			SO:0001589	frameshift_variant	9612	exon12			.	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1142_1143delAG	chr12.hg19:g.124914167_124914168delCT	ENSP00000384018:p.Glu381fs	116.0	0.0		115.0	26.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Frame_Shift_Del	DEL	ENST00000405201.1	hg19	CCDS41858.2																																																																																			.	.		0.673	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		-	124914166	CT	-	124914165	7	5	70	1	0	1	0	1	0	0	0	0	10245	796	28	0	6577	0	NCOR2	12	124914165	Frame_Shift_Del	DEL	CT	TCGA-CC-A7IE-01A-21D-A382-10	5319772	124914165	8937730	102	9033										
ZMYM5	9205	hgsc.bcm.edu	37	chr13	20399130	20399130	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tcttccagttgctcttgaaaTgtatcagctatggttgacgt	9	8	3	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr13:20399130T>C	ENST00000337963.4	-	8	1761	c.1497A>G	c.(1495-1497)acA>acG	p.T499T		NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	499						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		gctcttgaaatgtatcagcta	0.418																																					p.T499T		Atlas-SNP	.											.	ZMYM5	73	.	0			c.A1497G						.						70	63	65					13																	20399130		1568	3582	5150	SO:0001819	synonymous_variant	9205	exon8			TTGAAATGTATCA	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.1497A>G	chr13.hg19:g.20399130T>C		171.0	0.0		208.0	51.0	NM_001142684	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Silent	SNP	ENST00000337963.4	hg19																																																																																				.	.		0.418	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		C	20399130	T	C	20399130	2	2	70	1	0	0	0	0	0	0	0	1	17718	1451	51	2		2	ZMYM5	13	20399130	Silent	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10		20399130	94770748	103	9034										
FREM2	341640	hgsc.bcm.edu	37	chr13	39266309	39266309	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gctacaaacatgatggcactGagtcaagtgaagatagcttc	10	8	1	4			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr13:39266309G>C	ENST00000280481.7	+	1	5044	c.4828G>C	c.(4828-4830)Gag>Cag	p.E1610Q		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1610					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TGATGGCACTGAGTCAAGTGA	0.413																																					p.E1610Q		Atlas-SNP	.											.	FREM2	385	.	0			c.G4828C						.						124	116	119					13																	39266309		2203	4300	6503	SO:0001583	missense	341640	exon1			GGCACTGAGTCAA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.4828G>C	chr13.hg19:g.39266309G>C	ENSP00000280481:p.Glu1610Gln	162.0	0.0		166.0	48.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.819014	0.50633	.	.	ENSG00000150893	ENST00000280481	T	0.47177	0.85	6.08	5.24	0.73138	.	0.094077	0.64402	D	0.000001	T	0.63379	0.2506	M	0.92649	3.33	0.80722	D	1	P	0.40066	0.701	B	0.42959	0.403	T	0.69982	-0.4997	10	0.39692	T	0.17	.	15.6983	0.77517	0.0653:0.0:0.9347:0.0	.	1610	Q5SZK8	FREM2_HUMAN	Q	1610	ENSP00000280481:E1610Q	ENSP00000280481:E1610Q	E	+	1	0	FREM2	38164309	1.000000	0.71417	0.882000	0.34594	0.531000	0.34715	6.796000	0.75145	1.599000	0.50093	-0.126000	0.14955	GAG	.	.		0.413	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39266309	G	C	39266309	3	2	70	1	0	0	0	0	1	0	0	0	6053	1291	45	4	4830	4	FREM2	13	39266309	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	18867179	39266309	75903569	104	9035										
FNDC3A	22862	hgsc.bcm.edu	37	chr13	49742771	49742771	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tccaggcagaatataattctAtaaagggaactccttcagag	8	8	2	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr13:49742771A>G	ENST00000492622.2	+	10	1365	c.1060A>G	c.(1060-1062)Ata>Gta	p.I354V	FNDC3A_ENST00000541916.1_Missense_Mutation_p.I354V|FNDC3A_ENST00000398316.3_Missense_Mutation_p.I298V	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	354	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		ATATAATTCTATAAAGGGAAC	0.368																																					p.I354V		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A1060G						.						101	105	104					13																	49742771		2203	4300	6503	SO:0001583	missense	22862	exon10			AATTCTATAAAGG	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"Fibronectin type III domain containing"	20296	protein-coding gene	gene with protein product		615794	"fibronectin type III domain containing 3"	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.1060A>G	chr13.hg19:g.49742771A>G	ENSP00000417257:p.Ile354Val	144.0	0.0		195.0	63.0	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	hg19	CCDS41886.1	.	.	.	.	.	.	.	.	.	.	A	1.681	-0.506548	0.04231	.	.	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.56611	0.45;0.45;0.45	5.54	1.77	0.24775	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.314514	0.28360	N	0.015622	T	0.22166	0.0534	N	0.03967	-0.31	0.31818	N	0.626397	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.30031	-0.9992	10	0.07175	T	0.84	-2.1323	8.495	0.33123	0.5921:0.0:0.4079:0.0	.	298;354;354	Q9Y2H6-2;G5E9X3;Q9Y2H6	.;.;FND3A_HUMAN	V	354;290;354;298	ENSP00000417257:I354V;ENSP00000441831:I354V;ENSP00000381362:I298V	ENSP00000338579:I290V	I	+	1	0	FNDC3A	48640772	0.955000	0.32602	0.993000	0.49108	0.995000	0.86356	0.715000	0.25822	0.143000	0.18926	0.482000	0.46254	ATA	.	.		0.368	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		G	49742771	A	G	49742771	3	3	70	1	0	0	0	0	1	0	0	0	5977	449	16	2	1105	2	FNDC3A	13	49742771	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	10476462	49742771	65427107	105	9036										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77642923	77642923	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gttcccattcttcacggactCtggtagcttccatgcgaata	8	12	3	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr13:77642923C>G	ENST00000544440.2	-	70	11851	c.11834G>C	c.(11833-11835)aGa>aCa	p.R3945T	MYCBP2_ENST00000357337.6_Missense_Mutation_p.R3945T|MYCBP2_ENST00000407578.2_Missense_Mutation_p.R3983T					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TTCACGGACTCTGGTAGCTTC	0.398																																					p.R3983T		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.G11948C						.						203	169	180					13																	77642923		2203	4300	6503	SO:0001583	missense	23077	exon70			CGGACTCTGGTAG	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.11834G>C	chr13.hg19:g.77642923C>G	ENSP00000444596:p.Arg3945Thr	76.0	0.0		106.0	39.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.96|18.96	3.734610|3.734610	0.69189|0.69189	.|.	.|.	ENSG00000005810|ENSG00000005810	ENST00000429715|ENST00000357337;ENST00000407578;ENST00000544440	.|T;T;T	.|0.32023	.|1.48;1.47;1.48	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.38825|0.38825	0.1055|0.1055	M|M	0.65498|0.65498	2.005|2.005	0.58432|0.58432	D|D	0.999998|0.999998	.|P	.|0.47409	.|0.895	.|B	.|0.41236	.|0.351	T|T	0.41910|0.41910	-0.9482|-0.9482	5|10	.|0.87932	.|D	.|0	.|.	19.7962|19.7962	0.96484|0.96484	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|3945	.|O75592	.|MYCB2_HUMAN	H|T	365|3945;3983;3945	.|ENSP00000349892:R3945T;ENSP00000384288:R3983T;ENSP00000444596:R3945T	.|ENSP00000349892:R3945T	Q|R	-|-	3|2	2|0	MYCBP2|MYCBP2	76540924|76540924	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.969000|0.969000	0.65631|0.65631	7.442000|7.442000	0.80503|0.80503	2.675000|2.675000	0.91044|0.91044	0.650000|0.650000	0.86243|0.86243	CAG|AGA	.	.		0.398	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		G	77642923	C	G	77642923	3	3	70	1	0	0	0	0	1	0	0	0	10027	913	32	4	2144	4	MYCBP2	13	77642923	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	27900152	77642923	37526955	106	9037										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77743838	77743838	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ggaagaactcagcagttctgGaatgtcatcagctaaaaaaa	9	7	4	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr13:77743838G>C	ENST00000544440.2	-	39	5709	c.5692C>G	c.(5692-5694)Cca>Gca	p.P1898A	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Missense_Mutation_p.P1898A|MYCBP2_ENST00000407578.2_Missense_Mutation_p.P1936A					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		AGCAGTTCTGGAATGTCATCA	0.388																																					p.P1936A		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.C5806G						.						66	68	68					13																	77743838		2203	4300	6503	SO:0001583	missense	23077	exon39			GTTCTGGAATGTC	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.5692C>G	chr13.hg19:g.77743838G>C	ENSP00000444596:p.Pro1898Ala	656.0	0.0		724.0	230.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	G	15.31	2.794579	0.50102	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.27256	1.68;1.68;1.68	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.30070	0.0753	N	0.14661	0.345	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.02464	-1.1155	10	0.06099	T	0.92	.	18.5628	0.91107	0.0:0.0:1.0:0.0	.	1898	O75592	MYCB2_HUMAN	A	1898;1936;1898	ENSP00000349892:P1898A;ENSP00000384288:P1936A;ENSP00000444596:P1898A	ENSP00000349892:P1898A	P	-	1	0	MYCBP2	76641839	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.722000	0.98770	2.448000	0.82819	0.650000	0.86243	CCA	.	.		0.388	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77743838	G	C	77743838	3	2	70	1	0	0	0	0	1	0	0	0	10027	1174	41	4	8410	4	MYCBP2	13	77743838	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	100915	77743838	37426040	107	9038										
ABHD4	63874	hgsc.bcm.edu	37	chr14	23072409	23072410	+	Frame_Shift_Ins	INS	-	-	T													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cccttggtgatggtgcatggINSttttgggggcggcgtgggtc							TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr14:23072409_23072410insT	ENST00000428304.2	+	3	297_298	c.227_228insT	c.(226-231)ggttttfs	p.GF76fs	ABHD4_ENST00000544562.1_3'UTR	NM_022060.2	NP_071343.2	Q8TB40	ABHD4_HUMAN	abhydrolase domain containing 4	76					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(3)|prostate(1)	14	all_cancers(95;5.49e-05)			GBM - Glioblastoma multiforme(265;0.0153)		ATGGTGCATGGTTTTGGGGGCG	0.579																																					p.G76fs		Atlas-Indel,Pindel	.											.	ABHD4	30	.	0			c.227_228insT						.																																			SO:0001589	frameshift_variant	63874	exon3			.	AK022878	CCDS9572.1	14q11.1	2006-10-06			ENSG00000100439	ENSG00000100439		"Abhydrolase domain containing"	20154	protein-coding gene	gene with protein product							Standard	NM_022060		Approved	FLJ12816	uc001wgm.3	Q8TB40	OTTHUMG00000028686	ENST00000428304.2:c.231dupT	chr14.hg19:g.23072413_23072413dupT	ENSP00000414558:p.Gly76fs	114.0	0.0		103.0	29.0	NM_022060	B4DDH7|Q9H9E0	Frame_Shift_Ins	INS	ENST00000428304.2	hg19	CCDS9572.1																																																																																			.	.		0.579	ABHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071623.3			T	23072410	-	T	23072409	7	5	70	1	0	1	1	0	0	0	0	0	84	1261	44	0	237	0	ABHD4	14	23072409	Frame_Shift_Ins	INS	-	TCGA-CC-A7IE-01A-21D-A382-10		23072409	84277131	108	9039										
SLC22A17	51310	hgsc.bcm.edu	37	chr14	23815904	23815904	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cagcgggacgtggtcacagcGggtagggggtggctgccgca	20	10	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr14:23815904G>C	ENST00000206544.8	-	9	1906	c.1570C>G	c.(1570-1572)Cgc>Ggc	p.R524G	SLC22A17_ENST00000397260.3_Missense_Mutation_p.R395G|SLC22A17_ENST00000474057.1_5'UTR|SLC22A17_ENST00000354772.3_Missense_Mutation_p.R506G|SLC22A17_ENST00000397267.1_Missense_Mutation_p.R524G	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	524					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|vacuole (GO:0005773)	transmembrane signaling receptor activity (GO:0004888)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)		TGGTCACAGCGGGTAGGGGGT	0.692																																					p.R524G		Atlas-SNP	.											.	SLC22A17	32	.	0			c.C1570G						.						5	7	6					14																	23815904		2076	4104	6180	SO:0001583	missense	51310	exon9			CACAGCGGGTAGG	AJ243653	CCDS9593.1, CCDS9594.2	14q11.2	2013-05-22	2008-01-11		ENSG00000092096	ENSG00000092096		"Solute carriers"	23095	protein-coding gene	gene with protein product	"neutrophil gelatinase-associated lipocalin receptor"	611461				16377569	Standard	NM_016609		Approved	BOCT, BOIT, NGALR	uc001wjl.3	Q8WUG5	OTTHUMG00000028740	ENST00000206544.8:c.1570C>G	chr14.hg19:g.23815904G>C	ENSP00000206544:p.Arg524Gly	63.0	0.0		42.0	23.0	NM_020372	A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	Missense_Mutation	SNP	ENST00000206544.8	hg19	CCDS9593.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.516897	0.44763	.	.	ENSG00000092096	ENST00000354772;ENST00000397260;ENST00000206544;ENST00000397267	T;T;T;T	0.71817	-0.41;-0.6;-0.36;-0.36	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.65450	0.2692	N	0.08118	0	0.52501	D	0.999954	P;D	0.60575	0.946;0.988	P;P	0.56398	0.597;0.797	T	0.69510	-0.5126	10	0.44086	T	0.13	-17.4291	16.1662	0.81757	0.0:0.0:1.0:0.0	.	506;524	Q8WUG5-2;Q8WUG5	.;S22AH_HUMAN	G	506;395;524;524	ENSP00000346824:R506G;ENSP00000380430:R395G;ENSP00000206544:R524G;ENSP00000380437:R524G	ENSP00000206544:R524G	R	-	1	0	SLC22A17	22885744	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.934000	0.63491	2.804000	0.96469	0.462000	0.41574	CGC	.	.		0.692	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157223.3	NM_020372		C	23815904	G	C	23815904	3	2	70	1	0	0	0	0	1	0	0	0	14463	1116	39	4	50	4	SLC22A17	14	23815904	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	743495	23815904	83533636	109	9040										
MYH7	4625	hgsc.bcm.edu	37	chr14	23884288	23884288	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cgcttctgctcggcctccagCtcattctccagctcccgcac	7	20	3	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr14:23884288C>T	ENST00000355349.3	-	37	5637	c.5475G>A	c.(5473-5475)gaG>gaA	p.E1825E	CTD-2201G16.1_ENST00000557368.1_RNA|MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1825					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CGGCCTCCAGCTCATTCTCCA	0.652																																					p.E1825E		Atlas-SNP	.											.	MYH7	349	.	0			c.G5475A						.						104	101	102					14																	23884288		2203	4300	6503	SO:0001819	synonymous_variant	4625	exon37			CTCCAGCTCATTC	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.5475G>A	chr14.hg19:g.23884288C>T		38.0	0.0		39.0	14.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	hg19	CCDS9601.1																																																																																			.	.		0.652	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23884288	C	T	23884288	2	4	70	1	0	0	0	0	0	0	0	1	10048	796	28	3		3	MYH7	14	23884288	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	68384	23884288	83465252	110	9041										
PCK2	5106	hgsc.bcm.edu	37	chr14	24566238	24566238	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcacagtgcccgcctgtgccAaccagagggcatccacatct	10	16	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr14:24566238A>T	ENST00000216780.4	+	2	435	c.167A>T	c.(166-168)cAa>cTa	p.Q56L	NRL_ENST00000396997.1_5'Flank|PCK2_ENST00000560657.1_3'UTR|PCK2_ENST00000561286.1_Intron|PCK2_ENST00000396973.4_Missense_Mutation_p.Q56L|PCK2_ENST00000545054.2_5'UTR|PCK2_ENST00000558096.1_5'UTR|NRL_ENST00000561028.1_Intron|PCK2_ENST00000559250.1_Missense_Mutation_p.Q68L	NM_004563.2	NP_004554.2	Q16822	PCKGM_HUMAN	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	56					carbohydrate metabolic process (GO:0005975)|cellular response to glucose stimulus (GO:0071333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|NADH oxidation (GO:0006116)|oxaloacetate metabolic process (GO:0006107)|positive regulation of insulin secretion (GO:0032024)|pyruvate metabolic process (GO:0006090)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)|phosphoenolpyruvate carboxykinase activity (GO:0004611)			breast(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(265;0.0184)		CGCCTGTGCCAACCAGAGGGC	0.572																																					p.Q56L		Atlas-SNP	.											.	PCK2	66	.	0			c.A167T						.						90	82	85					14																	24566238		2203	4300	6503	SO:0001583	missense	5106	exon2			TGTGCCAACCAGA	AK129934	CCDS9609.1, CCDS41928.1	14q12	2006-06-09			ENSG00000100889	ENSG00000100889	4.1.1.32		8725	protein-coding gene	gene with protein product		614095				8645161, 9657976	Standard	XM_005267726		Approved	PEPCK, PEPCK2	uc001wlt.3	Q16822	OTTHUMG00000028791	ENST00000216780.4:c.167A>T	chr14.hg19:g.24566238A>T	ENSP00000216780:p.Gln56Leu	75.0	0.0		81.0	14.0	NM_001018073	O43253|Q86U01|Q9BV62	Missense_Mutation	SNP	ENST00000216780.4	hg19	CCDS9609.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.876787	0.91664	.	.	ENSG00000100889	ENST00000216780;ENST00000396973	T;T	0.04551	3.6;3.6	5.52	5.52	0.82312	Phosphoenolpyruvate carboxykinase, N-terminal (2);	0.150694	0.64402	D	0.000014	T	0.13030	0.0316	M	0.89478	3.035	0.80722	D	1	B;P;B	0.38767	0.038;0.646;0.013	B;B;B	0.39152	0.061;0.292;0.031	T	0.00715	-1.1597	10	0.62326	D	0.03	-15.7985	13.8779	0.63665	1.0:0.0:0.0:0.0	.	56;56;56	Q16822;Q16822-2;Q6IB91	PCKGM_HUMAN;.;.	L	56	ENSP00000216780:Q56L;ENSP00000380171:Q56L	ENSP00000216780:Q56L	Q	+	2	0	PCK2	23636078	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.909000	0.75735	2.216000	0.71823	0.528000	0.53228	CAA	.	.		0.572	PCK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071900.3	NM_001018073		T	24566238	A	T	24566238	3	4	70	1	0	0	0	0	1	0	0	0	11591	130	5	4	173	4	PCK2	14	24566238	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	681950	24566238	82783302	111	9042										
PRPF39	55015	hgsc.bcm.edu	37	chr14	45584061	45584061	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	acttactttttcctttcagtAcaattatcagaatccttgga	4	9	2	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr14:45584061A>G	ENST00000355765.6	+	14	2125	c.1955A>G	c.(1954-1956)tAc>tGc	p.Y652C		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	652					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						TCCTTTCAGTACAATTATCAG	0.328																																					p.Y652C		Atlas-SNP	.											.	PRPF39	46	.	0			c.A1955G						.						104	102	103					14																	45584061		2203	4297	6500	SO:0001630	splice_region_variant	55015	exon14			TTCAGTACAATTA	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"PRP39 pre-mRNA processing factor 39 homolog (yeast)", "PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.1954-1A>G	chr14.hg19:g.45584061A>G		233.0	0.0		226.0	44.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	A	14.41	2.526476	0.44969	.	.	ENSG00000185246	ENST00000355765	T	0.51325	0.71	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.64438	0.2598	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.63910	-0.6530	10	0.45353	T	0.12	-18.0984	15.6395	0.76984	1.0:0.0:0.0:0.0	.	652	Q86UA1	PRP39_HUMAN	C	652	ENSP00000348010:Y652C	ENSP00000348010:Y652C	Y	+	2	0	PRPF39	44653811	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.376000	0.79658	2.171000	0.68590	0.533000	0.62120	TAC	.	.		0.328	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2		Missense_Mutation	G	45584061	A	G	45584061	5	3	70	1	0	0	0	0	0	0	1	0	12581	405	14	2	2005	2	PRPF39	14	45584061	Splice_Site	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	21017823	45584061	61765479	112	9043			1	11		2	2	18	N	T_A	8.566439e-05
PRPF39	55015	hgsc.bcm.edu	37	chr14	45584078	45584078	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	agtacaattatcagaatcctTggaattatggacaatattat	6	5	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr14:45584078T>G	ENST00000355765.6	+	14	2142	c.1972T>G	c.(1972-1974)Tgg>Ggg	p.W658G		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	658					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						TCAGAATCCTTGGAATTATGG	0.303																																					p.W658G		Atlas-SNP	.											.	PRPF39	46	.	0			c.T1972G						.						107	105	106					14																	45584078		2203	4296	6499	SO:0001583	missense	55015	exon14			AATCCTTGGAATT	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"PRP39 pre-mRNA processing factor 39 homolog (yeast)", "PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.1972T>G	chr14.hg19:g.45584078T>G	ENSP00000348010:p.Trp658Gly	259.0	0.0		247.0	48.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	T	13.01	2.108004	0.37242	.	.	ENSG00000185246	ENST00000355765	T	0.46063	0.88	5.71	5.71	0.89125	.	0.311639	0.37530	N	0.002058	T	0.60379	0.2264	L	0.58101	1.795	0.58432	D	0.999993	D	0.67145	0.996	D	0.75484	0.986	T	0.57711	-0.7764	10	0.35671	T	0.21	-3.8418	15.6395	0.76984	0.0:0.0:0.0:1.0	.	658	Q86UA1	PRP39_HUMAN	G	658	ENSP00000348010:W658G	ENSP00000348010:W658G	W	+	1	0	PRPF39	44653828	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.356000	0.73046	2.171000	0.68590	0.533000	0.62120	TGG	.	.		0.303	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			G	45584078	T	G	45584078	3	3	70	1	0	0	0	0	1	0	0	0	12581	1812	63	5	2022	5	PRPF39	14	45584078	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	17	45584078	61765462	113	9044			1	11		2	2	18	N	T_A	8.566439e-05
MAP4K5	11183	hgsc.bcm.edu	37	chr14	50904667	50904668	+	Frame_Shift_Ins	INS	-	-	T													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	atatgggcagctaatcctggINSttttttggcatgttcaaaca					rs75938452		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr14:50904667_50904668insT	ENST00000013125.4	-	24	2085_2086	c.1767_1768insA	c.(1765-1770)aaaccafs	p.P590fs		NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	590	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					GCTAATCCTGGTTTTTTGGCAT	0.347																																					p.P590fs		Atlas-Indel,Pindel	.											.	MAP4K5	48	.	0			c.1768_1769insA						.																																			SO:0001589	frameshift_variant	11183	exon24			.	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6867	protein-coding gene	gene with protein product	"germinal center kinase-related"	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.1768dupA	chr14.hg19:g.50904673_50904673dupT	ENSP00000013125:p.Pro590fs	203.0	0.0		222.0	25.0	NM_006575	Q8IYF6	Frame_Shift_Ins	INS	ENST00000013125.4	hg19																																																																																				.	.		0.347	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575		T	50904668	-	T	50904667	7	5	70	1	0	1	1	0	0	0	0	0	9272	1261	44	0	808	0	MAP4K5	14	50904667	Frame_Shift_Ins	INS	-	TCGA-CC-A7IE-01A-21D-A382-10	5320589	50904667	56444873	114	9045										
KIAA0247	9766	hgsc.bcm.edu	37	chr14	70171412	70171412	+	Frame_Shift_Del	DEL	G	G	-													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ctcattctcctcctcgtggtGctgtttgtgctgctgcagcc							TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr14:70171412delG	ENST00000342745.4	+	4	724	c.411delG	c.(409-411)gtgfs	p.V137fs		NM_014734.3	NP_055549.1	Q92537	K0247_HUMAN	KIAA0247	137						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)	10				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)		TCCTCGTGGTGCTGTTTGTGC	0.522																																					p.V137fs		Atlas-INDEL	.											.	KIAA0247	30	.	0			c.410delT						.						87	69	75					14																	70171412		2203	4300	6503	SO:0001589	frameshift_variant	9766	exon4			.	D87434	CCDS9796.1	14q24.1	2012-11-29			ENSG00000100647	ENSG00000100647			19956	protein-coding gene	gene with protein product						9039502	Standard	NM_014734		Approved		uc001xlk.3	Q92537	OTTHUMG00000171234	ENST00000342745.4:c.411delG	chr14.hg19:g.70171412delG	ENSP00000344424:p.Val137fs	69.0	0.0		56.0	15.0	NM_014734		Frame_Shift_Del	DEL	ENST00000342745.4	hg19	CCDS9796.1																																																																																			.	.		0.522	KIAA0247-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412453.1	NM_014734		-	70171412	G	-	70171412	7	5	70	1	0	1	0	1	0	0	0	0	8174	1306	46	0	421	0	KIAA0247	14	70171412	Frame_Shift_Del	DEL	G	TCGA-CC-A7IE-01A-21D-A382-10	19266745	70171412	37178128	115	9046										
RYR3	6263	hgsc.bcm.edu	37	chr15	33926872	33926872	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gtcaaacagggacagcctgcGggaagctgtgcgcacttttg	14	10	1	0	rs369597197		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr15:33926872G>T	ENST00000389232.4	+	25	3183	c.3113G>T	c.(3112-3114)cGg>cTg	p.R1038L	RYR3_ENST00000415757.3_Missense_Mutation_p.R1038L	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1038	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GACAGCCTGCGGGAAGCTGTG	0.468																																					p.R1038L		Atlas-SNP	.											.	RYR3	760	.	0			c.G3113T						.						148	146	147					15																	33926872		1932	4139	6071	SO:0001583	missense	6263	exon25			GCCTGCGGGAAGC		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.3113G>T	chr15.hg19:g.33926872G>T	ENSP00000373884:p.Arg1038Leu	110.0	0.0		130.0	40.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.663120	0.67700	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.91521	-2.86;-2.86	5.2	5.2	0.72013	B30.2/SPRY domain (1);Ryanodine receptor Ryr (1);	0.000000	0.85682	D	0.000000	D	0.92338	0.7569	L	0.33245	0.995	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.79108	0.986;0.992	D	0.89594	0.3830	10	0.23302	T	0.38	.	19.2916	0.94102	0.0:0.0:1.0:0.0	.	1038;1038	Q15413-2;Q15413	.;RYR3_HUMAN	L	1038	ENSP00000373884:R1038L;ENSP00000399610:R1038L	ENSP00000354735:R1038L	R	+	2	0	RYR3	31714164	1.000000	0.71417	0.992000	0.48379	0.973000	0.67179	9.483000	0.97937	2.861000	0.98227	0.655000	0.94253	CGG	.	.		0.468	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33926872	G	T	33926872	3	4	70	1	0	0	0	0	1	0	0	0	13785	1116	39	1	3211	1	RYR3	15	33926872	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10		33926872	68604520	116	9047										
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40241361	40241361	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cacgtgcagtcatttctcagCgagcataacaagccccctcc	7	16	2	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr15:40241361C>A	ENST00000263791.5	+	4	448	c.405C>A	c.(403-405)agC>agA	p.S135R	snoU13_ENST00000459610.1_RNA|EIF2AK4_ENST00000382727.2_Missense_Mutation_p.S135R|EIF2AK4_ENST00000559624.1_Missense_Mutation_p.S135R	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	135	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		CATTTCTCAGCGAGCATAACA	0.473																																					p.S135R		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.C405A						.						206	186	192					15																	40241361		1931	4131	6062	SO:0001583	missense	440275	exon4			TCTCAGCGAGCAT	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.405C>A	chr15.hg19:g.40241361C>A	ENSP00000263791:p.Ser135Arg	79.0	0.0		83.0	18.0	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	hg19	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.820748	0.50633	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.48836	0.8;0.8	5.8	-4.04	0.04010	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (2);	0.126303	0.64402	D	0.000001	T	0.40886	0.1135	L	0.56124	1.755	0.26713	N	0.970938	B;B	0.33238	0.403;0.264	B;B	0.42030	0.15;0.373	T	0.46062	-0.9218	10	0.15952	T	0.53	-3.654	11.0609	0.47946	0.0824:0.3973:0.0:0.5203	.	135;135	Q9P2K8;Q9P2K8-3	E2AK4_HUMAN;.	R	135	ENSP00000263791:S135R;ENSP00000372174:S135R	ENSP00000263791:S135R	S	+	3	2	EIF2AK4	38028653	0.001000	0.12720	0.797000	0.32132	0.970000	0.65996	-1.617000	0.02051	-0.987000	0.03494	-1.164000	0.01763	AGC	.	.		0.473	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			A	40241361	C	A	40241361	3	1	70	1	0	0	0	0	1	0	0	0	5001	767	27	1	419	1	EIF2AK4	15	40241361	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	6314489	40241361	62290031	117	9048										
CGNL1	84952	hgsc.bcm.edu	37	chr15	57732594	57732594	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ggccacaccggatctcttaaAgggccagcaagagctcactc	10	14	2	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr15:57732594A>G	ENST00000281282.5	+	3	1700	c.1622A>G	c.(1621-1623)aAg>aGg	p.K541R		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	541	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		GATCTCTTAAAGGGCCAGCAA	0.473																																					p.K541R		Atlas-SNP	.											.	CGNL1	125	.	0			c.A1622G						.						74	65	68					15																	57732594		2192	4292	6484	SO:0001583	missense	84952	exon4			TCTTAAAGGGCCA	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.1622A>G	chr15.hg19:g.57732594A>G	ENSP00000281282:p.Lys541Arg	142.0	0.0		128.0	41.0	NM_001252335	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	hg19	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.148314	0.78001	.	.	ENSG00000128849	ENST00000281282	T	0.54675	0.56	4.81	4.81	0.61882	.	0.116735	0.37955	N	0.001863	T	0.55625	0.1932	L	0.39326	1.205	0.49389	D	0.999788	P	0.36990	0.577	P	0.48304	0.573	T	0.56884	-0.7905	10	0.45353	T	0.12	-36.2173	14.3915	0.66983	1.0:0.0:0.0:0.0	.	541	Q0VF96	CGNL1_HUMAN	R	541	ENSP00000281282:K541R	ENSP00000281282:K541R	K	+	2	0	CGNL1	55519886	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	8.946000	0.92992	1.791000	0.52520	0.460000	0.39030	AAG	.	.		0.473	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		G	57732594	A	G	57732594	3	3	70	1	0	0	0	0	1	0	0	0	3306	72	3	2	1628	2	CGNL1	15	57732594	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	17491233	57732594	44798798	118	9049										
THAP10	56906	hgsc.bcm.edu	37	chr15	71175114	71175114	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	acatacccacactacggtgaCggggccttttcaaagaaatt	8	11	1	2	rs544136510		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr15:71175114C>T	ENST00000249861.4	-	2	1075	c.563G>A	c.(562-564)cGt>cAt	p.R188H	LRRC49_ENST00000544974.2_Intron	NM_020147.3	NP_064532.1	Q9P2Z0	THA10_HUMAN	THAP domain containing 10	188							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						ACTACGGTGACGGGGCCTTTT	0.378													C|||	1	0.000199681	0	0	5008	,	,		20264	0		0	False		,,,				2504	0.001				p.R188H		Atlas-SNP	.											THAP10,NS,carcinoma,0,1	THAP10	19	.	0			c.G563A						.						115	113	114					15																	71175114		2199	4297	6496	SO:0001583	missense	56906	exon2			CGGTGACGGGGCC	AL360202	CCDS10237.1	15q22.32	2013-01-25			ENSG00000129028	ENSG00000129028		"THAP (C2CH-type zinc finger) domain containing"	23193	protein-coding gene	gene with protein product		612538				12575992	Standard	NM_020147		Approved		uc002asv.3	Q9P2Z0	OTTHUMG00000133388	ENST00000249861.4:c.563G>A	chr15.hg19:g.71175114C>T	ENSP00000249861:p.Arg188His	177.0	0.0		183.0	29.0	NM_020147	B2R8R0	Missense_Mutation	SNP	ENST00000249861.4	hg19	CCDS10237.1	.	.	.	.	.	.	.	.	.	.	C	0.256	-1.002823	0.02128	.	.	ENSG00000129028	ENST00000249861	.	.	.	3.09	-0.0811	0.13704	.	.	.	.	.	T	0.14960	0.0361	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.01281	0.0	T	0.19095	-1.0316	8	0.39692	T	0.17	.	1.6666	0.02803	0.1291:0.2141:0.4495:0.2073	.	188	Q9P2Z0	THA10_HUMAN	H	188	.	ENSP00000249861:R188H	R	-	2	0	THAP10	68962168	0.226000	0.23696	0.007000	0.13788	0.412000	0.31113	0.135000	0.15952	-0.222000	0.09958	-2.234000	0.00290	CGT	.	.		0.378	THAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257242.2	NM_020147		T	71175114	C	T	71175114	3	4	70	1	0	0	0	0	1	0	0	0	15857	536	19	1	218	1	THAP10	15	71175114	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	13442520	71175114	31356278	119	9050										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94945187	94945187	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tatggcaatatggaatacaaTgcagttccttaaaagctgct	8	7	0	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr15:94945187T>A	ENST00000357742.4	+	16	2024	c.2024T>A	c.(2023-2025)aTg>aAg	p.M675K	MCTP2_ENST00000451018.3_Missense_Mutation_p.M675K|MCTP2_ENST00000557742.1_Missense_Mutation_p.M263K|MCTP2_ENST00000331706.4_Missense_Mutation_p.M263K	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	675					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			TGGAATACAATGCAGTTCCTT	0.348																																					p.M675K		Atlas-SNP	.											.	MCTP2	122	.	0			c.T2024A						.						125	125	125					15																	94945187		2197	4298	6495	SO:0001583	missense	55784	exon16			ATACAATGCAGTT	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.2024T>A	chr15.hg19:g.94945187T>A	ENSP00000350377:p.Met675Lys	145.0	0.0		167.0	33.0	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	hg19	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	T	8.055	0.766831	0.15983	.	.	ENSG00000140563	ENST00000451018;ENST00000331706;ENST00000357742	T;T;T	0.64991	-0.13;0.01;-0.02	5.52	4.26	0.50523	.	1.009490	0.07921	N	0.975937	T	0.44456	0.1294	N	0.08118	0	0.09310	N	1	B;B;B	0.18968	0.0;0.032;0.002	B;B;B	0.22753	0.001;0.041;0.008	T	0.34079	-0.9843	10	0.26408	T	0.33	.	11.0723	0.48010	0.0:0.0785:0.0:0.9215	.	675;263;675	Q6DN12-2;Q6DN12-4;Q6DN12	.;.;MCTP2_HUMAN	K	675;263;675	ENSP00000395109:M675K;ENSP00000329646:M263K;ENSP00000350377:M675K	ENSP00000329646:M263K	M	+	2	0	MCTP2	92746191	0.135000	0.22499	0.001000	0.08648	0.844000	0.47949	3.343000	0.52167	0.802000	0.34089	0.529000	0.55759	ATG	.	.		0.348	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		A	94945187	T	A	94945187	3	1	70	1	0	0	0	0	1	0	0	0	9410	1464	51	4	2086	4	MCTP2	15	94945187	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	23770073	94945187	7586205	120	9051										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99467196	99467196	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ccggaacctgagaatcccaaTggattgattctaatgtatga	9	8	1	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr15:99467196T>A	ENST00000268035.6	+	12	3188	c.2577T>A	c.(2575-2577)aaT>aaA	p.N859K	IGF1R_ENST00000558762.1_Missense_Mutation_p.N859K	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	859	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	AGAATCCCAATGGATTGATTC	0.473																																					p.N859K		Atlas-SNP	.											.	IGF1R	147	.	0			c.T2577A						.						85	88	87					15																	99467196		2197	4297	6494	SO:0001583	missense	3480	exon12			TCCCAATGGATTG	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2577T>A	chr15.hg19:g.99467196T>A	ENSP00000268035:p.Asn859Lys	120.0	0.0		169.0	35.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.253717	0.80135	.	.	ENSG00000140443	ENST00000268035	T	0.61158	0.13	5.81	3.5	0.40072	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000011	T	0.79064	0.4383	M	0.93197	3.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79184	-0.1908	10	0.87932	D	0	.	8.1816	0.31313	0.0:0.2433:0.0:0.7567	.	859;859	C9J5X1;P08069	.;IGF1R_HUMAN	K	859	ENSP00000268035:N859K	ENSP00000268035:N859K	N	+	3	2	IGF1R	97284719	0.987000	0.35691	1.000000	0.80357	0.998000	0.95712	0.172000	0.16704	0.469000	0.27268	0.482000	0.46254	AAT	.	.		0.473	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99467196	T	A	99467196	3	1	70	1	0	0	0	0	1	0	0	0	7580	1461	51	4	2623	4	IGF1R	15	99467196	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	4522009	99467196	3064196	121	9052										
PKD1	5310	hgsc.bcm.edu	37	chr16	2149932	2149932	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gaagaggcagatgaggagaaCgcagcaggtggccctctgga	17	8	1	4	rs201780393		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr16:2149932C>T	ENST00000262304.4	-	29	10061	c.9853G>A	c.(9853-9855)Gtt>Att	p.V3285I	PKD1_ENST00000423118.1_Missense_Mutation_p.V3285I|RP11-304L19.3_ENST00000565937.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3285			V -> I (in PKD1). {ECO:0000269|PubMed:11316854}.		anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ATGAGGAGAACGCAGCAGGTG	0.637																																					p.V3285I		Atlas-SNP	.											.	PKD1	184	.	0			c.G9853A	GRCh37	CM014078	PKD1	M		.						14	11	12					16																	2149932		2135	4195	6330	SO:0001583	missense	5310	exon29			GGAGAACGCAGCA	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.9853G>A	chr16.hg19:g.2149932C>T	ENSP00000262304:p.Val3285Ile	158.0	0.0		152.0	63.0	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	hg19	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	C	4.104	0.017298	0.07959	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.36340	1.26;1.26	4.69	0.366	0.16136	.	0.797162	0.11329	N	0.575245	T	0.24967	0.0606	L	0.46157	1.445	0.09310	N	1	B;B	0.21905	0.062;0.01	B;B	0.15870	0.014;0.004	T	0.27088	-1.0084	10	0.16896	T	0.51	.	5.1969	0.15243	0.2889:0.4834:0.0:0.2277	.	3285;3285	P98161-3;P98161	.;PKD1_HUMAN	I	3285;3285;2620	ENSP00000262304:V3285I;ENSP00000399501:V3285I	ENSP00000262304:V3285I	V	-	1	0	PKD1	2089933	0.012000	0.17670	0.016000	0.15963	0.146000	0.21551	0.011000	0.13264	0.206000	0.20587	-0.324000	0.08512	GTT	.	C|0.999;T|0.001		0.637	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			T	2149932	C	T	2149932	3	4	70	1	0	0	0	0	1	0	0	0	11972	536	19	1	3130	1	PKD1	16	2149932	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10		2149932	88204821	122	9053										
ZNF75A	7627	hgsc.bcm.edu	37	chr16	3367850	3367850	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcggtcaagccttcttagacAccagaaactccacctgtgaa	8	13	2	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr16:3367850A>T	ENST00000574298.1	+	6	1345	c.872A>T	c.(871-873)cAc>cTc	p.H291L	ZNF75A_ENST00000498240.2_3'UTR	NM_153028.2	NP_694573.1	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|lung(7)|prostate(1)	12						CTTCTTAGACACCAGAAACTC	0.443																																					p.H291L		Atlas-SNP	.											.	ZNF75A	34	.	0			c.A872T						.						46	48	48					16																	3367850		2190	4296	6486	SO:0001583	missense	7627	exon6			TTAGACACCAGAA	X91826	CCDS10501.1	16p13.11	2013-01-08			ENSG00000162086	ENSG00000162086		"Zinc fingers, C2H2-type", "-"	13146	protein-coding gene	gene with protein product		601473				8661144	Standard	NM_153028		Approved	FLJ31529	uc002cut.4	Q96N20	OTTHUMG00000129356	ENST00000574298.1:c.872A>T	chr16.hg19:g.3367850A>T	ENSP00000459566:p.His291Leu	55.0	0.0		72.0	30.0	NM_153028	Q0VDI8|Q92669	Missense_Mutation	SNP	ENST00000574298.1	hg19	CCDS10501.1	.	.	.	.	.	.	.	.	.	.	A	15.70	2.910117	0.52439	.	.	ENSG00000162086	ENST00000293995	.	.	.	4.57	3.43	0.39272	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47093	D	0.000242	T	0.72342	0.3448	H	0.97516	4.02	0.34063	D	0.657549	B	0.21688	0.059	B	0.17433	0.018	T	0.77112	-0.2708	9	0.87932	D	0	.	8.6663	0.34123	0.829:0.0:0.0:0.171	.	291	Q96N20	ZN75A_HUMAN	L	291	.	ENSP00000293995:H291L	H	+	2	0	ZNF75A	3307851	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	6.964000	0.76061	0.832000	0.34804	0.455000	0.32223	CAC	.	.		0.443	ZNF75A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251506.2	NM_153028		T	3367850	A	T	3367850	3	4	70	1	0	0	0	0	1	0	0	0	18148	159	6	4	882	4	ZNF75A	16	3367850	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	1217918	3367850	86986903	123	9054										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21080830	21080830	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgatgtcctctgaactgaagAttggttccaggtacagccag	11	9	1	4			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr16:21080830A>G	ENST00000261383.3	-	23	3286	c.3287T>C	c.(3286-3288)aTc>aCc	p.I1096T	DNAH3_ENST00000415178.1_Missense_Mutation_p.I1096T	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1096	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TGAACTGAAGATTGGTTCCAG	0.438																																					p.I1096T		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T3287C						.						194	158	170					16																	21080830		2201	4300	6501	SO:0001583	missense	55567	exon23			CTGAAGATTGGTT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.3287T>C	chr16.hg19:g.21080830A>G	ENSP00000261383:p.Ile1096Thr	154.0	0.0		116.0	45.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.408536	0.83340	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.74315	-0.83;-0.83	5.15	5.15	0.70609	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	D	0.91573	0.7338	H	0.98426	4.23	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94762	0.7937	10	0.87932	D	0	.	15.2812	0.73787	1.0:0.0:0.0:0.0	.	1096	Q8TD57	DYH3_HUMAN	T	1096	ENSP00000261383:I1096T;ENSP00000394245:I1096T	ENSP00000261383:I1096T	I	-	2	0	DNAH3	20988331	1.000000	0.71417	0.991000	0.47740	0.994000	0.84299	9.276000	0.95745	2.086000	0.62901	0.533000	0.62120	ATC	.	.		0.438	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		G	21080830	A	G	21080830	3	3	70	1	0	0	0	0	1	0	0	0	4605	333	12	2	9222	2	DNAH3	16	21080830	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	17712980	21080830	69273923	124	9055										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30749946	30749947	+	Missense_Mutation	DNP	GG	GG	TT													0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgtgaaacgtcggagggggaGgccccccaagaagaacaggt							TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr16:30749946_30749947GG>TT	ENST00000262518.4	+	34	8970_8971	c.8585_8586GG>TT	c.(8584-8586)aGG>aTT	p.R2862I	SRCAP_ENST00000395059.2_Missense_Mutation_p.R2800I|SRCAP_ENST00000344771.4_Missense_Mutation_p.R2704I|RP11-2C24.4_ENST00000483578.1_lincRNA	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2862	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CGGAGGGGGAGGCCCCCCAAGA	0.614																																					p.R2862M|p.R2862S		Atlas-SNP	.											.	SRCAP	298	.	0			c.G8585T|c.G8586T						.																																			SO:0001583	missense	10847	exon34			GGGGGAGGCCCCC|GGGGAGGCCCCCC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	Exception_encountered	chr16.hg19:g.30749946_30749947delinsTT	ENSP00000262518:p.Arg2862Ile	57.0|56.0	0.0		100.0	20.0|19.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.		0.614	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		TT	30749947	GG	TT	30749946	3	4	70	1	0	0	0	0	1	0	0	0	15150	1000	35	3	8711	3	SRCAP	16	30749946	Missense_Mutation	DNP	GG	TCGA-CC-A7IE-01A-21D-A382-10	9669116	30749946	59604807	125	9056										
AARS	16	hgsc.bcm.edu	37	chr16	70301705	70301705	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ccttcttcagctcaggaaatGcatctccctgacaaagggga	9	12	4	1	rs561829699		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr16:70301705G>A	ENST00000261772.8	-	9	1222	c.1079C>T	c.(1078-1080)gCa>gTa	p.A360V	AARS_ENST00000564359.1_5'Flank	NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		CTCAGGAAATGCATCTCCCTG	0.522											OREG0023913	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A360V		Atlas-SNP	.											.	AARS	62	.	0			c.C1079T						.						106	96	99					16																	70301705		2198	4300	6498	SO:0001583	missense	16	exon9			GGAAATGCATCTC	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.1079C>T	chr16.hg19:g.70301705G>A	ENSP00000261772:p.Ala360Val	68.0	0.0	1121	61.0	11.0	NM_001605		Missense_Mutation	SNP	ENST00000261772.8	hg19	CCDS32474.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.448504	0.26074	.	.	ENSG00000090861	ENST00000261772	T	0.56611	0.45	5.81	5.81	0.92471	Alanyl-tRNA synthetase, class IIc, anti-codon-binding domain (1);Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.092298	0.85682	D	0.000000	T	0.44030	0.1274	L	0.33245	0.995	0.80722	D	1	B;B	0.31893	0.345;0.22	B;B	0.33392	0.163;0.163	T	0.25572	-1.0128	10	0.15952	T	0.53	-14.2566	17.5723	0.87937	0.0:0.0:1.0:0.0	.	368;360	E7ETK8;P49588	.;SYAC_HUMAN	V	360	ENSP00000261772:A360V	ENSP00000261772:A360V	A	-	2	0	AARS	68859206	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.735000	0.98825	2.736000	0.93811	0.655000	0.94253	GCA	.	.		0.522	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		A	70301705	G	A	70301705	3	1	70	1	0	0	0	0	1	0	0	0	19	1319	46	3	1879	3	AARS	16	70301705	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	39551759	70301705	20053048	126	9057										
ADAD2	161931	hgsc.bcm.edu	37	chr16	84229451	84229451	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	acctcggaaggtggcctcccGcacagcccacccatgcgcct	10	19	0	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr16:84229451G>A	ENST00000315906.5	+	7	1135	c.1083G>A	c.(1081-1083)ccG>ccA	p.P361P	RP11-486L19.2_ENST00000569834.1_RNA|ADAD2_ENST00000268624.3_Silent_p.P443P|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	361	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						GTGGCCTCCCGCACAGCCCAC	0.701																																					p.P443P		Atlas-SNP	.											.	ADAD2	46	.	0			c.G1329A						.						15	18	17					16																	84229451		2183	4278	6461	SO:0001819	synonymous_variant	161931	exon8			CCTCCCGCACAGC	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1083G>A	chr16.hg19:g.84229451G>A		87.0	0.0		70.0	23.0	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	hg19	CCDS45536.1																																																																																			.	.		0.701	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		A	84229451	G	A	84229451	2	1	70	1	0	0	0	0	0	0	0	1	232	1074	38	1		1	ADAD2	16	84229451	Silent	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	13927746	84229451	6125302	127	9058										
TCF25	22980	hgsc.bcm.edu	37	chr16	89965023	89965023	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tggagaagcgaggctgcccgCgcacggcgctggagtactgc	17	12	0	1	rs144328773	byFrequency	TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr16:89965023C>T	ENST00000263346.8	+	10	1137	c.1081C>T	c.(1081-1083)Cgc>Tgc	p.R361C	TCF25_ENST00000263347.7_Missense_Mutation_p.R126C	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	361					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		AGGCTGCCCGCGCACGGCGCT	0.582																																					p.R361C		Atlas-SNP	.											.	TCF25	61	.	0			c.C1081T						.						74	86	82					16																	89965023		2198	4300	6498	SO:0001583	missense	22980	exon10			TGCCCGCGCACGG	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.1081C>T	chr16.hg19:g.89965023C>T	ENSP00000263346:p.Arg361Cys	33.0	0.0		21.0	10.0	NM_014972	Q2MK75|Q9UPV3	Missense_Mutation	SNP	ENST00000263346.8	hg19	CCDS10987.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.734572	0.89482	.	.	ENSG00000141002	ENST00000263346;ENST00000263347	T;T	0.74315	-0.83;-0.83	5.63	5.63	0.86233	Tetratricopeptide-like helical (1);	0.053822	0.85682	D	0.000000	D	0.89870	0.6840	M	0.92691	3.335	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.91847	0.5488	10	0.87932	D	0	.	18.6717	0.91514	0.0:1.0:0.0:0.0	.	126;361	Q9H384;Q9BQ70	.;TCF25_HUMAN	C	361;126	ENSP00000263346:R361C;ENSP00000263347:R126C	ENSP00000263346:R361C	R	+	1	0	TCF25	88492524	1.000000	0.71417	0.986000	0.45419	0.699000	0.40488	5.407000	0.66363	2.654000	0.90174	0.561000	0.74099	CGC	.	C|0.999;A|0.001		0.582	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972		T	89965023	C	T	89965023	3	4	70	1	0	0	0	0	1	0	0	0	15708	768	27	1	1119	1	TCF25	16	89965023	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	5735572	89965023	389730	128	9059										
NCOR1	9611	hgsc.bcm.edu	37	chr17	15976836	15976836	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcttctctttaaactgatttCatgagctgttcttggactcc	7	10	3	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr17:15976836C>A	ENST00000268712.3	-	28	3975	c.3718G>T	c.(3718-3720)Gaa>Taa	p.E1240*	NCOR1_ENST00000395851.1_Nonsense_Mutation_p.E1256*|NCOR1_ENST00000395857.3_Intron	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1240	Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		AAACTGATTTCATGAGCTGTT	0.423																																					p.E1256X		Atlas-SNP	.											.	NCOR1	240	.	0			c.G3766T						.						146	126	133					17																	15976836		2203	4300	6503	SO:0001587	stop_gained	9611	exon27			TGATTTCATGAGC	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.3718G>T	chr17.hg19:g.15976836C>A	ENSP00000268712:p.Glu1240*	60.0	0.0		60.0	18.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Nonsense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	C	39	7.798834	0.98495	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849	.	.	.	5.91	5.91	0.95273	.	0.090566	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-14.1607	19.2934	0.94112	0.0:1.0:0.0:0.0	.	.	.	.	X	1240;1256;1147	.	ENSP00000268712:E1240X	E	-	1	0	NCOR1	15917561	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.348000	0.73009	2.808000	0.96608	0.655000	0.94253	GAA	.	.		0.423	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		A	15976836	C	A	15976836	4	1	70	1	0	0	0	0	0	1	0	0	10244	835	29	3	3680	3	NCOR1	17	15976836	Nonsense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10		15976836	65218374	129	9060										
CCDC144A	9720	hgsc.bcm.edu	37	chr17	16667283	16667283	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttttcaatcttcatagaactAatgagatgatagcagaggtc	8	6	3	4	rs558127337		TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr17:16667283A>G	ENST00000360524.8	+	15	3968	c.3892A>G	c.(3892-3894)Aat>Gat	p.N1298D	CCDC144A_ENST00000456009.1_Missense_Mutation_p.N1064D|CCDC144A_ENST00000443444.2_Missense_Mutation_p.N1298D|CCDC144A_ENST00000399273.1_Missense_Mutation_p.N1298D|RP11-219A15.1_ENST00000448331.3_Missense_Mutation_p.N1298D	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	1298																	TCATAGAACTAATGAGATGAT	0.368																																					p.N1298D		Atlas-SNP	.											.	CCDC144A	53	.	0			c.A3892G						.						118	129	125					17																	16667283		1866	4112	5978	SO:0001583	missense	9720	exon15			AGAACTAATGAGA	BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.3892A>G	chr17.hg19:g.16667283A>G	ENSP00000353717:p.Asn1298Asp	283.0	0.0		351.0	105.0	NM_014695	O60311|Q6ZU57	Missense_Mutation	SNP	ENST00000360524.8	hg19	CCDS45621.1	.	.	.	.	.	.	.	.	.	.	.	11.14	1.550975	0.27739	.	.	ENSG00000170160	ENST00000399273;ENST00000443444;ENST00000360524;ENST00000456009	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	2.1	-0.848	0.10727	.	.	.	.	.	T	0.26774	0.0655	L	0.33624	1.015	0.09310	N	1	D;P	0.56035	0.974;0.724	P;B	0.50440	0.641;0.258	T	0.16571	-1.0398	9	0.38643	T	0.18	.	6.2207	0.20679	0.4653:0.5347:0.0:0.0	.	1064;1298	A2RUR9-3;A2RUR9	.;C144A_HUMAN	D	1298;1298;1298;1064	ENSP00000382215:N1298D;ENSP00000439262:N1298D;ENSP00000353717:N1298D;ENSP00000394201:N1064D	ENSP00000353717:N1298D	N	+	1	0	CCDC144A	16608008	1.000000	0.71417	0.003000	0.11579	0.146000	0.21551	3.000000	0.49481	-0.402000	0.07633	0.155000	0.16302	AAT	.	.		0.368	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1			G	16667283	A	G	16667283	3	3	70	1	0	0	0	0	1	0	0	0	2779	362	13	2	3950	2	CCDC144A	17	16667283	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	690447	16667283	64527927	130	9061										
SLC5A10	125206	hgsc.bcm.edu	37	chr17	18872377	18872377	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ctccgcagctggacctgtacGcgggggctctgtttgtgcac	14	13	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr17:18872377G>A	ENST00000395645.3	+	6	484	c.466G>A	c.(466-468)Gcg>Acg	p.A156T	SLC5A10_ENST00000395642.1_Missense_Mutation_p.A100T|SLC5A10_ENST00000417251.2_Missense_Mutation_p.A156T|SLC5A10_ENST00000317977.6_Missense_Mutation_p.A100T|FAM83G_ENST00000388995.6_3'UTR|SLC5A10_ENST00000395647.2_Missense_Mutation_p.A156T|SLC5A10_ENST00000395643.2_Missense_Mutation_p.A156T	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	156					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.A156T(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						GGACCTGTACGCGGGGGCTCT	0.612																																					p.A156T		Atlas-SNP	.											SLC5A10,NS,carcinoma,0,1	SLC5A10	55	.	1	Substitution - Missense(1)	prostate(1)	c.G466A						.						123	97	106					17																	18872377		2203	4300	6503	SO:0001583	missense	125206	exon6			CTGTACGCGGGGG		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"Solute carriers"	23155	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 10"				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.466G>A	chr17.hg19:g.18872377G>A	ENSP00000379007:p.Ala156Thr	43.0	0.0		41.0	10.0	NM_001042450	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Missense_Mutation	SNP	ENST00000395645.3	hg19	CCDS42275.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.825416	0.50739	.	.	ENSG00000154025	ENST00000317977;ENST00000395647;ENST00000395642;ENST00000417251;ENST00000395645;ENST00000395643	D;D;D;D;D;D	0.92397	-3.03;-2.49;-3.03;-2.49;-2.49;-2.67	4.82	2.63	0.31362	.	0.057677	0.64402	D	0.000001	D	0.91576	0.7339	M	0.83774	2.66	0.80722	D	1	P;P;P;P;D	0.56521	0.882;0.857;0.882;0.857;0.976	B;B;B;B;B	0.43508	0.418;0.294;0.418;0.294;0.422	D	0.91139	0.4944	10	0.52906	T	0.07	.	11.5417	0.50669	0.0:0.0:0.4576:0.5424	.	156;156;156;156;100	B4DPI0;A0PJK1-2;A0PJK1;A0PJK1-4;A0PJK1-3	.;.;SC5AA_HUMAN;.;.	T	100;156;100;156;156;156	ENSP00000324346:A100T;ENSP00000379008:A156T;ENSP00000379004:A100T;ENSP00000401875:A156T;ENSP00000379007:A156T;ENSP00000379005:A156T	ENSP00000324346:A100T	A	+	1	0	SLC5A10	18813102	1.000000	0.71417	0.443000	0.26883	0.157000	0.22087	5.242000	0.65389	1.150000	0.42419	0.462000	0.41574	GCG	.	.		0.612	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351		A	18872377	G	A	18872377	3	1	70	1	0	0	0	0	1	0	0	0	14677	1087	38	1	488	1	SLC5A10	17	18872377	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	2205094	18872377	62322833	131	9062										
NOS2	4843	hgsc.bcm.edu	37	chr17	26096596	26096596	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	agctctttcagcatgaagagCgatttcttcagtttctagaa	8	8	5	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr17:26096596C>T	ENST00000313735.6	-	16	2057	c.1824G>A	c.(1822-1824)tcG>tcA	p.S608S		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	608	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.		S -> L (in dbSNP:rs2297518). {ECO:0000269|PubMed:7528017, ECO:0000269|PubMed:7531687, ECO:0000269|Ref.10}.		arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GCATGAAGAGCGATTTCTTCA	0.458																																					p.S608S		Atlas-SNP	.											NOS2,right_upper_lobe,carcinoma,0,1	NOS2	113	.	0			c.G1824A						.						111	101	105					17																	26096596		2203	4300	6503	SO:0001819	synonymous_variant	4843	exon16			GAAGAGCGATTTC	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"nitric oxide synthase 2A (inducible, hepatocytes)"	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.1824G>A	chr17.hg19:g.26096596C>T		177.0	0.0		234.0	69.0	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	hg19	CCDS11223.1																																																																																			.	.		0.458	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		T	26096596	C	T	26096596	2	4	70	1	0	0	0	0	0	0	0	1	10552	755	27	1		1	NOS2	17	26096596	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	7224219	26096596	55098614	132	9063										
SARM1	23098	hgsc.bcm.edu	37	chr17	26715488	26715488	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	catgggtgcccgcaactttgTgttggtgctatcacctggag	13	10	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr17:26715488T>G	ENST00000457710.3	+	7	2222	c.1751T>G	c.(1750-1752)gTg>gGg	p.V584G	SARM1_ENST00000379061.4_3'UTR	NM_015077.2	NP_055892.2	Q6SZW1	SARM1_HUMAN	sterile alpha and TIR motif containing 1	618	TIR.				innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of apoptotic process (GO:0042981)|regulation of dendrite morphogenesis (GO:0048814)|regulation of neuron death (GO:1901214)|response to glucose (GO:0009749)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of mitochondrial outer membrane (GO:0031315)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|synapse (GO:0045202)				cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	12	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		CGCAACTTTGTGTTGGTGCTA	0.532																																					p.V617G		Atlas-SNP	.											.	SARM1	40	.	0			c.T1850G						.						212	185	194					17																	26715488		2203	4300	6503	SO:0001583	missense	23098	exon8			ACTTTGTGTTGGT	AB011096		17q11	2013-01-10			ENSG00000004139	ENSG00000004139		"Sterile alpha motif (SAM) domain containing"	17074	protein-coding gene	gene with protein product		607732				9628581	Standard	NM_015077		Approved	SARM, SAMD2, KIAA0524	uc010crl.1	Q6SZW1	OTTHUMG00000132499	ENST00000457710.3:c.1751T>G	chr17.hg19:g.26715488T>G	ENSP00000406738:p.Val584Gly	64.0	0.0		87.0	27.0	NM_015077	O60277|Q7LGG3|Q9NXY5	Missense_Mutation	SNP	ENST00000457710.3	hg19		.	.	.	.	.	.	.	.	.	.	T	20.9	4.064155	0.76187	.	.	ENSG00000004139	ENST00000457710;ENST00000003834	.	.	.	5.39	5.39	0.77823	Toll/interleukin-1 receptor homology (TIR) domain (2);	0.063724	0.64402	D	0.000004	T	0.75700	0.3885	.	.	.	0.80722	D	1	D	0.65815	0.995	P	0.60415	0.874	T	0.79293	-0.1863	8	0.87932	D	0	-37.1449	14.1311	0.65255	0.0:0.0:0.0:1.0	.	618	Q6SZW1	SARM1_HUMAN	G	616;584	.	ENSP00000003834:V584G	V	+	2	0	SARM1	23739615	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.868000	0.87116	2.255000	0.74692	0.533000	0.62120	GTG	.	.		0.532	SARM1-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000255679.3	NM_015077		G	26715488	T	G	26715488	3	3	70	1	0	0	0	0	1	0	0	0	13857	1696	59	5	1877	5	SARM1	17	26715488	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	618892	26715488	54479722	133	9064										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76497896	76497896	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cagatggtcatgatcttcatCctgtcgccagcgttgaggtt	11	10	3	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr17:76497896C>T	ENST00000585328.1	-	34	5365	c.5241G>A	c.(5239-5241)agG>agA	p.R1747R	DNAH17-AS1_ENST00000598378.1_3'UTR|DNAH17_ENST00000389840.5_Silent_p.R1739R|RP11-559N14.5_ENST00000591373.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1739	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TGATCTTCATCCTGTCGCCAG	0.607																																					p.R1750R		Atlas-SNP	.											.	DNAH17	347	.	0			c.G5250A						.						157	159	158					17																	76497896		2182	4281	6463	SO:0001819	synonymous_variant	8632	exon34			CTTCATCCTGTCG	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.5241G>A	chr17.hg19:g.76497896C>T		38.0	0.0		49.0	12.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	hg19																																																																																				.	.		0.607	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		T	76497896	C	T	76497896	2	4	70	1	0	0	0	0	0	0	0	1	4603	854	30	3		3	DNAH17	17	76497896	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	49782408	76497896	4697314	134	9065										
RIT2	6014	hgsc.bcm.edu	37	chr18	40554066	40554066	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcagtgtccaagatgtccaaGtaagctggctcattgtcaat	10	9	2	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr18:40554066G>A	ENST00000326695.5	-	3	378	c.207C>T	c.(205-207)taC>taT	p.Y69Y	RIT2_ENST00000589109.1_Silent_p.Y69Y|RIT2_ENST00000282028.4_Silent_p.Y69Y|RIT2_ENST00000590910.1_Silent_p.Y69Y	NM_002930.2	NP_002921.1	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	69					neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGATGTCCAAGTAAGCTGGCT	0.368																																					p.Y69Y		Atlas-SNP	.											.	RIT2	56	.	0			c.C207T						.						76	66	70					18																	40554066		2203	4300	6503	SO:0001819	synonymous_variant	6014	exon3			GTCCAAGTAAGCT	BC018060	CCDS11921.1, CCDS62431.1	18q12.3	2014-05-09	2002-09-11	2002-09-13	ENSG00000152214	ENSG00000152214			10017	protein-coding gene	gene with protein product		609592	"Ric (Drosophila)-like, expressed in neurons"	RIN		8824319, 8918462	Standard	NM_002930		Approved	RIBA	uc002lav.4	Q99578	OTTHUMG00000132611	ENST00000326695.5:c.207C>T	chr18.hg19:g.40554066G>A		388.0	0.0		346.0	119.0	NM_001272077	B2R9L1|O15295|Q8TD69|Q8WVF6|Q92964	Silent	SNP	ENST00000326695.5	hg19	CCDS11921.1																																																																																			.	.		0.368	RIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255852.1	NM_002930		A	40554066	G	A	40554066	2	1	70	1	0	0	0	0	0	0	0	1	13402	1024	36	3		3	RIT2	18	40554066	Silent	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10		40554066	37523182	135	9066										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43532421	43532421	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	acagctgaactactgagcaaTgcatagatgtaagactccac	8	10	0	4			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr18:43532421T>C	ENST00000282041.5	-	3	1231	c.1197A>G	c.(1195-1197)gcA>gcG	p.A399A		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	399					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TACTGAGCAATGCATAGATGT	0.433																																					p.A399A		Atlas-SNP	.											.	EPG5	199	.	0			c.A1197G						.						105	101	102					18																	43532421		1936	4134	6070	SO:0001819	synonymous_variant	57724	exon3			GAGCAATGCATAG	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.1197A>G	chr18.hg19:g.43532421T>C		76.0	0.0		62.0	19.0	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	hg19	CCDS11926.2																																																																																			.	.		0.433	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43532421	T	C	43532421	2	2	70	1	0	0	0	0	0	0	0	1	8258	1451	51	2		2	KIAA1632	18	43532421	Silent	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	2978355	43532421	34544827	136	9067										
SH3GL1	6455	hgsc.bcm.edu	37	chr19	4366971	4366971	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	agcttggtcccctcggccccTccgaccttctcactgaccag	8	19	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr19:4366971T>A	ENST00000269886.3	-	2	244	c.66A>T	c.(64-66)ggA>ggT	p.G22G	SH3GL1_ENST00000417295.2_Silent_p.G22G|AC007292.6_ENST00000594444.1_RNA|SH3GL1_ENST00000598564.1_Silent_p.G22G	NM_003025.3	NP_003016.1	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	22	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|endosome (GO:0005768)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|endometrium(2)|kidney(16)|large_intestine(3)|lung(2)|ovary(2)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		CCTCGGCCCCTCCGACCTTCT	0.597			T	MLL	AL																																p.G22G	NSCLC(94;1152 2133 30346 33362)	Atlas-SNP	.		Dom	yes		19	19p13.3	6455	SH3-domain GRB2-like 1 (EEN)		L	.	SH3GL1	52	.	0			c.A66T						.						296	258	271					19																	4366971		2203	4300	6503	SO:0001819	synonymous_variant	6455	exon2			GGCCCCTCCGACC		CCDS32874.1, CCDS56076.1, CCDS59335.1	19p13.3	2008-07-22							10830	protein-coding gene	gene with protein product	"extra 11-19 leukemia fusion", "fusion partner of MLL", "SH3-containing Grb-2-like 1 protein", "SH3-containing protein EEN", "SH3 domain GRB2-like 1"	601768				9169142	Standard	NM_003025		Approved	SH3P8, SH3D2B, CNSA1, EEN, MGC111371	uc002maj.3	Q99961		ENST00000269886.3:c.66A>T	chr19.hg19:g.4366971T>A		51.0	0.0		51.0	6.0	NM_001199944	B4DRA1|E7EVZ4|M0QZV5|Q99668	Silent	SNP	ENST00000269886.3	hg19	CCDS32874.1																																																																																			.	.		0.597	SH3GL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458302.1	NM_003025		A	4366971	T	A	4366971	2	1	70	1	0	0	0	0	0	0	0	1	14265	1538	54	4		4	SH3GL1	19	4366971	Silent	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10		4366971	54762012	137	9068										
ANGPTL4	51129	hgsc.bcm.edu	37	chr19	8429440	8429440	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcctgagcgcgtgcgggtccGcctgtcagggaaccgagggg	19	12	1	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr19:8429440G>A	ENST00000301455.2	+	1	406	c.235G>A	c.(235-237)Gcc>Acc	p.A79T	ANGPTL4_ENST00000541807.1_Intron|ANGPTL4_ENST00000393962.2_Missense_Mutation_p.A79T	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	79					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular lipid metabolic process (GO:0044255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of lipoprotein lipase activity (GO:0051005)|positive regulation of angiogenesis (GO:0045766)|protein homooligomerization (GO:0051260)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	enzyme inhibitor activity (GO:0004857)			large_intestine(1)|lung(1)|ovary(2)|skin(2)	6						GTGCGGGTCCGCCTGTCAGGG	0.721																																					p.A79T		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.G235A						.						9	9	9					19																	8429440		2124	4147	6271	SO:0001583	missense	51129	exon1			GGGTCCGCCTGTC	AF202636	CCDS12200.1, CCDS42493.1	19p13.3	2013-10-07				ENSG00000167772		"Fibrinogen C domain containing"	16039	protein-coding gene	gene with protein product	"fasting-induced adipose factor", "hepatic angiopoietin-related protein", "PPARG angiopoietin related protein", "hepatic fibrinogen/angiopoietin-related protein", "peroxisome proliferator-activated receptor (PPAR) gamma induced angiopoietin-related protein", "angiopoietin-related protein 4"	605910				10698685, 10866690, 23960078	Standard	NM_139314		Approved	pp1158, PGAR, ARP4, HFARP, FIAF, NL2	uc002mjq.1	Q9BY76		ENST00000301455.2:c.235G>A	chr19.hg19:g.8429440G>A	ENSP00000301455:p.Ala79Thr	107.0	0.0		115.0	40.0	NM_001039667	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	hg19	CCDS12200.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.325607	0.41197	.	.	ENSG00000167772	ENST00000301455;ENST00000393962	T;T	0.45276	0.9;0.9	4.89	1.47	0.22746	.	1.117340	0.06816	N	0.791231	T	0.33614	0.0869	L	0.51422	1.61	0.39349	D	0.965725	B;B	0.16802	0.019;0.005	B;B	0.09377	0.004;0.001	T	0.14980	-1.0453	10	0.15066	T	0.55	.	5.955	0.19269	0.1709:0.0:0.6765:0.1526	.	79;79	A8MY84;Q9BY76	.;ANGL4_HUMAN	T	79	ENSP00000301455:A79T;ENSP00000377534:A79T	ENSP00000301455:A79T	A	+	1	0	ANGPTL4	8335440	0.181000	0.23161	0.300000	0.25030	0.061000	0.15899	0.663000	0.25053	0.116000	0.18110	0.486000	0.48141	GCC	.	.		0.721	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314		A	8429440	G	A	8429440	3	1	70	1	0	0	0	0	1	0	0	0	616	1087	38	1	237	1	ANGPTL4	19	8429440	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	4062469	8429440	50699543	138	9069										
LRP3	4037	hgsc.bcm.edu	37	chr19	33693781	33693781	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cagtgggaagctggagcagcAcacggagcggcgtggggtca	19	9	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr19:33693781A>G	ENST00000253193.7	+	3	351	c.149A>G	c.(148-150)cAc>cGc	p.H50R		NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	50	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)	15	Esophageal squamous(110;0.137)					CTGGAGCAGCACACGGAGCGG	0.672																																					p.H50R		Atlas-SNP	.											.	LRP3	46	.	0			c.A149G						.						34	28	30					19																	33693781		2202	4300	6502	SO:0001583	missense	4037	exon3			AGCAGCACACGGA	AB009462	CCDS12430.1	19q13.11	2013-05-30			ENSG00000130881	ENSG00000130881		"Low density lipoprotein receptors"	6695	protein-coding gene	gene with protein product		603159				9693042, 7959795	Standard	NM_002333		Approved	LRP-3, hLRp105	uc010edh.3	O75074	OTTHUMG00000180343	ENST00000253193.7:c.149A>G	chr19.hg19:g.33693781A>G	ENSP00000253193:p.His50Arg	82.0	0.0		91.0	32.0	NM_002333	B3KQD6|B4DKF2	Missense_Mutation	SNP	ENST00000253193.7	hg19	CCDS12430.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.098979	0.56183	.	.	ENSG00000130881	ENST00000253193	T	0.17370	2.28	5.12	5.12	0.69794	CUB (5);	0.000000	0.85682	D	0.000000	T	0.33118	0.0852	L	0.43923	1.385	0.80722	D	1	D	0.76494	0.999	D	0.69824	0.966	T	0.02966	-1.1088	10	0.56958	D	0.05	-53.6431	14.3813	0.66914	1.0:0.0:0.0:0.0	.	50	O75074	LRP3_HUMAN	R	50	ENSP00000253193:H50R	ENSP00000253193:H50R	H	+	2	0	LRP3	38385621	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.892000	0.63193	2.057000	0.61298	0.402000	0.26972	CAC	.	.		0.672	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4			G	33693781	A	G	33693781	3	3	70	1	0	0	0	0	1	0	0	0	8967	159	6	2	159	2	LRP3	19	33693781	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	25264341	33693781	25435202	139	9070										
BCAM	4059	hgsc.bcm.edu	37	chr19	45315505	45315505	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cacaatgcacgacacccgggGccgcagtcccccataccagc	9	19	0	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr19:45315505G>T	ENST00000270233.6	+	3	312	c.290G>T	c.(289-291)gGc>gTc	p.G97V	BCAM_ENST00000589651.1_Missense_Mutation_p.G97V	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	97	Ig-like V-type 1.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GACACCCGGGGCCGCAGTCCC	0.716																																					p.G97V		Atlas-SNP	.											.	BCAM	53	.	0			c.G290T						.						20	24	23					19																	45315505		2200	4296	6496	SO:0001583	missense	4059	exon3			CCCGGGGCCGCAG	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6722	protein-coding gene	gene with protein product		612773	"Lutheran blood group (Auberger b antigen included)", "basal cell adhesion molecule (Lu and Au blood groups)"	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.290G>T	chr19.hg19:g.45315505G>T	ENSP00000270233:p.Gly97Val	123.0	0.0		112.0	40.0	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	hg19	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	.	14.89	2.669301	0.47677	.	.	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.62364	0.03;0.09	3.43	2.38	0.29361	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55641	0.1933	L	0.29908	0.895	0.50813	D	0.999898	D	0.54047	0.964	P	0.53809	0.735	T	0.49661	-0.8916	9	0.34782	T	0.22	-9.1272	6.7393	0.23426	0.1352:0.0:0.8648:0.0	.	97	P50895	BCAM_HUMAN	V	97	ENSP00000270233:G97V;ENSP00000375817:G97V	ENSP00000270233:G97V	G	+	2	0	BCAM	50007345	0.959000	0.32827	0.866000	0.34008	0.614000	0.37383	0.446000	0.21694	0.771000	0.33359	0.313000	0.20887	GGC	.	.		0.716	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		T	45315505	G	T	45315505	3	4	70	1	0	0	0	0	1	0	0	0	1344	1203	42	3	300	3	BCAM	19	45315505	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	11621724	45315505	13813478	140	9071										
FCGRT	2217	hgsc.bcm.edu	37	chr19	50027980	50027980	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	aagtggcgatgagcaccactActgctgcattgtgcagcacg	12	11	0	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr19:50027980A>G	ENST00000221466.5	+	5	1304	c.818A>G	c.(817-819)tAc>tGc	p.Y273C	FCGRT_ENST00000599988.1_Intron|FCGRT_ENST00000596975.1_Missense_Mutation_p.Y181C|FCGRT_ENST00000426395.3_Missense_Mutation_p.Y273C|RCN3_ENST00000270645.3_5'Flank	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	273	Alpha-3.|Ig-like C1-type.				antigen processing and presentation (GO:0019882)|IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor (GO:0002416)|immune response (GO:0006955)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG binding (GO:0019864)			endometrium(3)|kidney(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	9		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		GAGCACCACTACTGCTGCATT	0.642																																					p.Y273C		Atlas-SNP	.											.	FCGRT	23	.	0			c.A818G						.						54	45	48					19																	50027980		2203	4300	6503	SO:0001583	missense	2217	exon5			ACCACTACTGCTG	U12255	CCDS12770.1	19q13.3	2013-01-11				ENSG00000104870		"Immunoglobulin superfamily / C1-set domain containing"	3621	protein-coding gene	gene with protein product		601437				7964511, 8646894	Standard	NM_001136019		Approved	FCRN, alpha-chain	uc002pog.2	P55899		ENST00000221466.5:c.818A>G	chr19.hg19:g.50027980A>G	ENSP00000221466:p.Tyr273Cys	14.0	0.0		19.0	6.0	NM_001136019	Q5HYM5|Q9HBV7|Q9NZ19	Missense_Mutation	SNP	ENST00000221466.5	hg19	CCDS12770.1	.	.	.	.	.	.	.	.	.	.	A	15.83	2.948209	0.53186	.	.	ENSG00000104870	ENST00000221466;ENST00000426395	T;T	0.05786	3.39;3.39	4.31	3.3	0.37823	Immunoglobulin/major histocompatibility complex, conserved site (1);Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.40640	N	0.001047	T	0.28001	0.0690	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.01874	-1.1256	10	0.87932	D	0	.	6.6251	0.22824	0.8912:0.0:0.1088:0.0	.	273	P55899	FCGRN_HUMAN	C	273	ENSP00000221466:Y273C;ENSP00000410798:Y273C	ENSP00000221466:Y273C	Y	+	2	0	FCGRT	54719792	0.991000	0.36638	1.000000	0.80357	0.747000	0.42532	3.973000	0.56845	0.817000	0.34445	0.379000	0.24179	TAC	.	.		0.642	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1			G	50027980	A	G	50027980	3	3	70	1	0	0	0	0	1	0	0	0	5794	391	14	2	832	2	FCGRT	19	50027980	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	4712475	50027980	9101003	141	9072										
MRPS26	64949	hgsc.bcm.edu	37	chr20	3027362	3027362	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcctgggcgcagcgcaaggaGcgggaagtgctgcagctgca	18	11	0	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr20:3027362G>C	ENST00000380325.3	+	3	586	c.462G>C	c.(460-462)gaG>gaC	p.E154D		NM_030811.3	NP_110438.1	Q9BYN8	RT26_HUMAN	mitochondrial ribosomal protein S26	154					DNA damage response, detection of DNA damage (GO:0042769)|peptide biosynthetic process (GO:0043043)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|lung(1)	2						AGCGCAAGGAGCGGGAAGTGC	0.716																																					p.E154D		Atlas-SNP	.											.	MRPS26	7	.	0			c.G462C						.						11	11	11					20																	3027362		2004	3917	5921	SO:0001583	missense	64949	exon3			CAAGGAGCGGGAA	AB051354	CCDS13043.1	20p13	2012-09-13	2004-09-22		ENSG00000125901	ENSG00000125901		"Mitochondrial ribosomal proteins / small subunits"	14045	protein-coding gene	gene with protein product		611988	"chromosome 20 open reading frame 193"	C20orf193		11543634	Standard	NM_030811		Approved	MRP-S13, MRP-S26, RPMS13, dJ534B8.3	uc002whs.3	Q9BYN8	OTTHUMG00000031721	ENST00000380325.3:c.462G>C	chr20.hg19:g.3027362G>C	ENSP00000369682:p.Glu154Asp	97.0	0.0		99.0	39.0	NM_030811	Q96Q58	Missense_Mutation	SNP	ENST00000380325.3	hg19	CCDS13043.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.932963	0.34096	.	.	ENSG00000125901	ENST00000380325	.	.	.	5.19	2.12	0.27331	.	0.000000	0.85682	D	0.000000	T	0.48995	0.1531	M	0.68317	2.08	0.27295	N	0.957731	D	0.56521	0.976	P	0.53266	0.722	T	0.43507	-0.9387	9	0.41790	T	0.15	-26.0267	9.5141	0.39095	0.1774:0.1085:0.7141:0.0	.	154	Q9BYN8	RT26_HUMAN	D	154	.	ENSP00000369682:E154D	E	+	3	2	MRPS26	2975362	0.985000	0.35326	0.624000	0.29186	0.084000	0.17831	2.041000	0.41213	-0.024000	0.13941	-1.587000	0.00848	GAG	.	.		0.716	MRPS26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077692.2	NM_030811		C	3027362	G	C	3027362	3	2	70	1	0	0	0	0	1	0	0	0	9846	962	34	4	472	4	MRPS26	20	3027362	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10		3027362	59998158	142	9073										
MACROD2	140733	hgsc.bcm.edu	37	chr20	16025252	16025252	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ggttgacaaggtaaatgaccCaacagagagtcaacaagaag	11	7	1	4			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr20:16025252C>A	ENST00000310348.4	+	17	1268	c.1268C>A	c.(1267-1269)cCa>cAa	p.P423Q	MACROD2_ENST00000407045.3_Missense_Mutation_p.P74Q|MACROD2_ENST00000402914.1_Missense_Mutation_p.P188Q|MACROD2_ENST00000217246.4_Intron|MACROD2_ENST00000378058.3_Missense_Mutation_p.P188Q			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	423					brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				GTAAATGACCCAACAGAGAGT	0.333																																					p.P188Q		Atlas-SNP	.											MACROD2,NS,adenocarcinoma,0,1	MACROD2	34	.	0			c.C563A						.						94	88	90					20																	16025252		2203	4300	6503	SO:0001583	missense	140733	exon13			ATGACCCAACAGA	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"chromosome 20 open reading frame 133"	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.1268C>A	chr20.hg19:g.16025252C>A	ENSP00000309809:p.Pro423Gln	162.0	1.0		151.0	38.0	NM_001033087	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	hg19	CCDS13120.2	.	.	.	.	.	.	.	.	.	.	C	18.33	3.600251	0.66332	.	.	ENSG00000172264	ENST00000310348;ENST00000402914;ENST00000378058;ENST00000407045	T;T;T	0.63255	1.34;-0.03;-0.03	5.81	4.86	0.63082	.	.	.	.	.	T	0.76263	0.3963	.	.	.	0.28303	N	0.923011	D;D	0.67145	0.996;0.981	D;P	0.68483	0.958;0.77	T	0.70110	-0.4962	8	0.48119	T	0.1	.	12.6792	0.56912	0.0:0.923:0.0:0.077	.	74;423	A1Z1Q3-6;A1Z1Q3	.;MACD2_HUMAN	Q	423;188;188;74	ENSP00000309809:P423Q;ENSP00000385290:P188Q;ENSP00000367297:P188Q	ENSP00000309809:P423Q	P	+	2	0	MACROD2	15973252	0.944000	0.32072	1.000000	0.80357	0.908000	0.53690	1.534000	0.36051	1.431000	0.47355	0.655000	0.94253	CCA	.	.		0.333	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676		A	16025252	C	A	16025252	3	1	70	1	0	0	0	0	1	0	0	0	9155	594	21	3	1334	3	MACROD2	20	16025252	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	12997890	16025252	47000268	143	9074										
RBM12	10137	hgsc.bcm.edu	37	chr20	34241608	34241608	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	atggaatatttgttatgtggGcacagactttggcagagttg	13	4	0	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr20:34241608G>T	ENST00000374114.3	-	3	1900	c.1637C>A	c.(1636-1638)gCc>gAc	p.A546D	CPNE1_ENST00000317677.5_5'Flank|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000397446.1_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.A546D|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000359646.1_Missense_Mutation_p.A546D|CPNE1_ENST00000317619.3_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	546						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			TGTTATGTGGGCACAGACTTT	0.398																																					p.A546D		Atlas-SNP	.											.	RBM12	93	.	0			c.C1637A						.						229	219	222					20																	34241608		2203	4300	6503	SO:0001583	missense	10137	exon2			ATGTGGGCACAGA	AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"RNA binding motif (RRM) containing"	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.1637C>A	chr20.hg19:g.34241608G>T	ENSP00000363228:p.Ala546Asp	84.0	0.0		111.0	24.0	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	hg19	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.449488	0.43531	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	T;T;T	0.15487	2.42;2.42;2.42	4.64	4.64	0.57946	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.073163	0.53938	D	0.000050	T	0.31670	0.0804	L	0.43152	1.355	0.80722	D	1	D	0.58620	0.983	D	0.66351	0.943	T	0.02026	-1.1227	10	0.72032	D	0.01	-4.7841	13.4776	0.61318	0.0:0.1566:0.8434:0.0	.	546	Q9NTZ6	RBM12_HUMAN	D	546;546;546;345	ENSP00000363228:A546D;ENSP00000352668:A546D;ENSP00000363217:A546D	ENSP00000339879:A345D	A	-	2	0	RBM12	33705022	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	3.521000	0.53472	2.400000	0.81607	0.563000	0.77884	GCC	.	.		0.398	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		T	34241608	G	T	34241608	3	4	70	1	0	0	0	0	1	0	0	0	13128	1203	42	3	1165	3	RBM12	20	34241608	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	18216356	34241608	28783912	144	9075										
NPBWR2	2832	hgsc.bcm.edu	37	chr20	62738102	62738102	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cattgtggccagtgccattgTcctgagagacgttggcaccc	12	12	0	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr20:62738102T>C	ENST00000369768.1	-	1	422	c.83A>G	c.(82-84)gAc>gGc	p.D28G		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	28					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					AGTGCCATTGTCCTGAGAGAC	0.632																																					p.D28G		Atlas-SNP	.											.	NPBWR2	36	.	0			c.A83G						.						83	80	81					20																	62738102		2203	4298	6501	SO:0001583	missense	2832	exon1			CCATTGTCCTGAG	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"GPCR / Class A : Neuropeptide receptors : W/B"	4530	protein-coding gene	gene with protein product		600731	"G protein-coupled receptor 8"	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.83A>G	chr20.hg19:g.62738102T>C	ENSP00000358783:p.Asp28Gly	58.0	0.0		70.0	31.0	NM_005286	Q6NWQ6|Q9H4K3	Missense_Mutation	SNP	ENST00000369768.1	hg19	CCDS13557.1	.	.	.	.	.	.	.	.	.	.	T	6.502	0.460805	0.12342	.	.	ENSG00000125522	ENST00000369768	T	0.73258	-0.73	2.75	1.55	0.23275	.	1.408510	0.06480	U	0.732638	T	0.51058	0.1652	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.28870	-1.0030	10	0.15952	T	0.53	.	4.4009	0.11386	0.0:0.1197:0.403:0.4773	.	28	P48146	NPBW2_HUMAN	G	28	ENSP00000358783:D28G	ENSP00000358783:D28G	D	-	2	0	NPBWR2	62208546	0.004000	0.15560	0.007000	0.13788	0.081000	0.17604	0.806000	0.27126	0.146000	0.19002	0.254000	0.18369	GAC	.	.		0.632	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286		C	62738102	T	C	62738102	3	2	70	1	0	0	0	0	1	0	0	0	10578	1667	58	2	921	2	NPBWR2	20	62738102	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	28496494	62738102	287418	145	9076										
UMODL1	89766	hgsc.bcm.edu	37	chr21	43531615	43531615	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ccactggccctccctggacaGctacagggaaactccatcat	8	16	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr21:43531615G>A	ENST00000408910.2	+	12	1899		c.e12-1		UMODL1_ENST00000400424.2_Splice_Site|UMODL1_ENST00000408989.2_Silent_p.Q761Q|C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400427.1_Silent_p.Q689Q	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1						adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						TCCCTGGACAGCTACAGGGAA	0.642																																					p.Q761Q	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.G2283A						.						50	55	53					21																	43531615		1972	4145	6117	SO:0001630	splice_region_variant	89766	exon11			TGGACAGCTACAG		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1900-1G>A	chr21.hg19:g.43531615G>A		99.0	0.0		107.0	35.0	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	hg19	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	G	9.056	0.993182	0.19043	.	.	ENSG00000177398	ENST00000400424;ENST00000408910	.	.	.	4.67	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1838	0.59670	0.0:0.1625:0.8375:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UMODL1	42404684	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.347000	0.20014	1.244000	0.43870	-0.175000	0.13238	.	.	.		0.642	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		Intron	A	43531615	G	A	43531615	5	1	70	1	0	0	0	0	0	0	1	0	16995	985	34	3	2325	3	UMODL1	21	43531615	Splice_Site	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10		43531615	4598280	146	9077										
PCBP3	54039	hgsc.bcm.edu	37	chr21	47350755	47350755	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	caaaatctgatgggccagtcAtcaggtaacacaaagccaca	8	11	3	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr21:47350755A>G	ENST00000400314.1	+	13	1190	c.852A>G	c.(850-852)tcA>tcG	p.S284S	PCBP3_ENST00000400310.1_Intron|PCBP3_ENST00000449640.1_Silent_p.S284S|PCBP3_ENST00000400308.1_Silent_p.S258S|PCBP3_ENST00000400309.1_Silent_p.S283S|PRED62_ENST00000593412.1_Intron|PCBP3_ENST00000400304.1_Silent_p.S274S			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	284					mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		tgggccagtcatcaggTAACA	0.547																																					p.S284S		Atlas-SNP	.											.	PCBP3	82	.	0			c.A852G						.						56	58	57					21																	47350755		2021	4192	6213	SO:0001819	synonymous_variant	54039	exon11			CCAGTCATCAGGT	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"poly(rC)-binding protein 3"			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.852A>G	chr21.hg19:g.47350755A>G		45.0	0.0		66.0	21.0	NM_020528	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Silent	SNP	ENST00000400314.1	hg19	CCDS42974.2																																																																																			.	.		0.547	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2			G	47350755	A	G	47350755	2	3	70	1	0	0	0	0	0	0	0	1	11511	204	8	2		2	PCBP3	21	47350755	Silent	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	3819140	47350755	779140	147	9078										
GGTLC2	91227	hgsc.bcm.edu	37	chr22	22989284	22989284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	ttcaatgatgaaatggatgaCttcagctctcccaacatcac	6	11	4	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr22:22989284C>A	ENST00000480559.1	+	2	237	c.237C>A	c.(235-237)gaC>gaA	p.D79E	GGTLC2_ENST00000448514.1_Missense_Mutation_p.D79E|POM121L1P_ENST00000402027.1_RNA	NM_199127.2	NP_954578.2	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase light chain 2	79					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)	gamma-glutamyltransferase activity (GO:0003840)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)		AAATGGATGACTTCAGCTCTC	0.592																																					p.D79E		Atlas-SNP	.											.	GGTLC2	20	.	0			c.C237A						.						116	116	116					22																	22989284		2203	4299	6502	SO:0001583	missense	91227	exon2			GGATGACTTCAGC	X98922	CCDS13802.2	22q11.21	2008-03-25	2008-03-10	2008-03-10	ENSG00000100121	ENSG00000100121		"Gamma-glutamyltransferases"	18596	protein-coding gene	gene with protein product		612339	"gamma-glutamyltransferase-like 4"	GGTL4		9074928, 18357469	Standard	NM_199127		Approved		uc010gtt.2	Q14390	OTTHUMG00000151177	ENST00000480559.1:c.237C>A	chr22.hg19:g.22989284C>A	ENSP00000419751:p.Asp79Glu	273.0	0.0		248.0	78.0	NM_199127	A1A516|A2VCM9|Q5NV76|Q6ISH0	Missense_Mutation	SNP	ENST00000480559.1	hg19	CCDS13802.2	.	.	.	.	.	.	.	.	.	.	c	10.97	1.500378	0.26861	.	.	ENSG00000100121	ENST00000480559;ENST00000448514	T;T	0.08634	3.07;3.07	.	.	.	.	0.000000	0.85682	D	0.000000	T	0.29588	0.0738	H	0.98089	4.145	0.28891	N	0.893841	P;P	0.45634	0.581;0.863	B;P	0.55161	0.414;0.77	T	0.22103	-1.0226	9	0.87932	D	0	-33.2948	2.6652	0.05046	0.0:0.5:0.0:0.5	.	79;79	Q14390;B7WND7	GGTL2_HUMAN;.	E	79	ENSP00000419751:D79E;ENSP00000415676:D79E	ENSP00000415676:D79E	D	+	3	2	GGTLC2	21319284	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	0.548000	0.23314	-0.000000	0.14550	0.000000	0.15137	GAC	.	.		0.592	GGTLC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321662.1	NM_199127		A	22989284	C	A	22989284	3	1	70	1	0	0	0	0	1	0	0	0	6374	564	20	3	243	3	GGTLC2	22	22989284	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10		22989284	28315282	148	9079										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26291221	26291221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	agaggctggactcggagctgAcagccaggaaagagctggag	17	8	0	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr22:26291221A>G	ENST00000407587.2	+	28	4814	c.4645A>G	c.(4645-4647)Aca>Gca	p.T1549A	CTA-125H2.2_ENST00000608507.1_RNA|CTA-125H2.2_ENST00000609889.1_RNA|CTA-125H2.2_ENST00000609570.1_RNA|CTA-125H2.2_ENST00000596813.1_RNA|CTA-125H2.2_ENST00000594856.1_RNA|CTA-125H2.2_ENST00000599792.1_RNA|CTA-125H2.2_ENST00000597548.1_RNA|CTA-125H2.2_ENST00000594585.1_RNA|CTA-125H2.2_ENST00000608115.1_RNA|CTA-125H2.2_ENST00000593715.1_RNA|CTA-125H2.2_ENST00000600269.1_RNA|CTA-125H2.2_ENST00000600211.1_RNA|CTA-125H2.2_ENST00000597284.1_RNA|CTA-125H2.2_ENST00000609823.1_RNA|CTA-125H2.2_ENST00000595102.1_RNA|CTA-125H2.2_ENST00000608257.1_RNA|CTA-125H2.2_ENST00000599080.1_RNA|CTA-125H2.2_ENST00000609809.1_RNA|CTA-125H2.2_ENST00000609157.1_RNA|CTA-125H2.2_ENST00000453457.3_RNA|CTA-125H2.2_ENST00000600903.1_RNA|CTA-125H2.2_ENST00000597614.2_RNA|CTA-125H2.2_ENST00000594542.1_RNA|CTA-125H2.2_ENST00000609820.1_RNA|CTA-125H2.2_ENST00000608921.1_RNA|CTA-125H2.2_ENST00000609275.1_RNA|CTA-125H2.2_ENST00000607895.1_RNA|MYO18B_ENST00000536101.1_Missense_Mutation_p.T1548A|MYO18B_ENST00000335473.7_Missense_Mutation_p.T1548A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1548	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CTCGGAGCTGACAGCCAGGAA	0.562																																					p.T1548A		Atlas-SNP	.											.	MYO18B	322	.	0			c.A4642G						.						31	37	35					22																	26291221		2103	4239	6342	SO:0001583	missense	84700	exon28			GAGCTGACAGCCA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.4645A>G	chr22.hg19:g.26291221A>G	ENSP00000386096:p.Thr1549Ala	91.0	0.0		82.0	27.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	A	5.135	0.210428	0.09757	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;T	0.86366	-2.11;-2.11;-1.11	5.26	-1.08	0.09936	.	1.188100	0.05910	N	0.631496	T	0.72309	0.3444	N	0.15975	0.35	0.09310	N	1	B;B;B;B	0.09022	0.001;0.001;0.002;0.001	B;B;B;B	0.09377	0.002;0.002;0.004;0.004	T	0.55835	-0.8078	10	0.20046	T	0.44	.	3.5095	0.07703	0.3633:0.0:0.2608:0.3759	.	1061;1548;1549;1548	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	A	1548;1548;1549	ENSP00000441229:T1548A;ENSP00000334563:T1548A;ENSP00000386096:T1549A	ENSP00000334563:T1548A	T	+	1	0	MYO18B	24621221	0.001000	0.12720	0.941000	0.38009	0.238000	0.25445	-0.191000	0.09601	0.028000	0.15324	-0.376000	0.06991	ACA	.	.		0.562	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26291221	A	G	26291221	3	3	70	1	0	0	0	0	1	0	0	0	10075	275	10	2	4748	2	MYO18B	22	26291221	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	3301937	26291221	25013345	149	9080										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26343703	26343703	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tgagcagctgtacaggctgcAgtttgagaaggcggacctcc	14	10	0	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr22:26343703A>T	ENST00000407587.2	+	36	5829	c.5660A>T	c.(5659-5661)cAg>cTg	p.Q1887L	MYO18B_ENST00000536101.1_Missense_Mutation_p.Q1886L|MYO18B_ENST00000335473.7_Missense_Mutation_p.Q1886L			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1886	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TACAGGCTGCAGTTTGAGAAG	0.557																																					p.Q1886L		Atlas-SNP	.											.	MYO18B	322	.	0			c.A5657T						.						53	56	55					22																	26343703		2100	4218	6318	SO:0001583	missense	84700	exon36			GGCTGCAGTTTGA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.5660A>T	chr22.hg19:g.26343703A>T	ENSP00000386096:p.Gln1887Leu	60.0	0.0		44.0	15.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	A	22.3	4.271870	0.80469	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.87491	-2.24;-2.24;-2.26	5.21	5.21	0.72293	.	0.167763	0.41097	D	0.000951	D	0.91456	0.7303	M	0.75264	2.295	0.43603	D	0.995969	P;D;D;D	0.59767	0.952;0.967;0.986;0.981	P;P;P;P	0.58660	0.575;0.684;0.843;0.833	D	0.92150	0.5727	10	0.59425	D	0.04	.	13.9144	0.63887	1.0:0.0:0.0:0.0	.	1399;1886;1887;1886	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	L	1886;1886;1887	ENSP00000441229:Q1886L;ENSP00000334563:Q1886L;ENSP00000386096:Q1887L	ENSP00000334563:Q1886L	Q	+	2	0	MYO18B	24673703	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	8.595000	0.90840	1.976000	0.57569	0.533000	0.62120	CAG	.	.		0.557	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26343703	A	T	26343703	3	4	70	1	0	0	0	0	1	0	0	0	10075	188	7	4	5795	4	MYO18B	22	26343703	Missense_Mutation	SNP	A	TCGA-CC-A7IE-01A-21D-A382-10	52482	26343703	24960863	150	9081										
EIF4ENIF1	56478	hgsc.bcm.edu	37	chr22	31850167	31850167	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	aaggcaaagtcccacttgccTtcattgtgctcactagcttg	8	12	2	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr22:31850167T>C	ENST00000397525.1	-	10	1698	c.1475A>G	c.(1474-1476)aAg>aGg	p.K492R	RP11-247I13.11_ENST00000464523.1_RNA|EIF4ENIF1_ENST00000397523.1_Missense_Mutation_p.K492R|EIF4ENIF1_ENST00000330125.5_Missense_Mutation_p.K492R|EIF4ENIF1_ENST00000344710.5_Splice_Site_p.K329R|EIF4ENIF1_ENST00000382180.2_Missense_Mutation_p.K171R	NM_001164501.1	NP_001157973.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	492						cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CCCACTTGCCTTCATTGTGCT	0.468																																					p.K492R		Atlas-SNP	.											.	EIF4ENIF1	80	.	0			c.A1475G						.						156	126	136					22																	31850167		2203	4300	6503	SO:0001583	missense	56478	exon10			CTTGCCTTCATTG	AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708			16687	protein-coding gene	gene with protein product		607445				10856257	Standard	NM_019843		Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000397525.1:c.1475A>G	chr22.hg19:g.31850167T>C	ENSP00000380659:p.Lys492Arg	100.0	0.0		110.0	38.0	NM_019843	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	Missense_Mutation	SNP	ENST00000397525.1	hg19	CCDS13898.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.189057	0.78789	.	.	ENSG00000184708	ENST00000344710;ENST00000397525;ENST00000330125;ENST00000397523;ENST00000382180;ENST00000418321	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.75221	0.3820	L	0.61218	1.895	0.58432	D	0.999994	D;D;D;D	0.76494	0.99;0.999;0.998;0.997	P;D;D;D	0.83275	0.814;0.996;0.934;0.994	T	0.71590	-0.4547	9	0.23302	T	0.38	-20.1134	14.547	0.68038	0.0:0.0:0.0:1.0	.	329;492;329;492	B1AKL3;Q9NRA8;Q9NRA8-2;B1AKL4	.;4ET_HUMAN;.;.	R	329;492;492;492;171;90	.	ENSP00000328103:K492R	K	-	2	0	EIF4ENIF1	30180167	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.429000	0.80309	2.367000	0.80283	0.528000	0.53228	AAG	.	.		0.468	EIF4ENIF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127926.1	NM_019843		C	31850167	T	C	31850167	3	2	70	1	0	0	0	0	1	0	0	0	5037	1623	56	2	1525	2	EIF4ENIF1	22	31850167	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	5506464	31850167	19454399	151	9082										
IL2RB	3560	hgsc.bcm.edu	37	chr22	37524527	37524527	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	gcagcaggtcatccctggagGggaaggtgcagtaggcgtcg	18	9	1	0			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr22:37524527G>A	ENST00000216223.5	-	10	1463	c.1265C>T	c.(1264-1266)cCc>cTc	p.P422L		NM_000878.3	NP_000869.1	P14784	IL2RB_HUMAN	interleukin 2 receptor, beta	422					cytokine-mediated signaling pathway (GO:0019221)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of apoptotic process (GO:0043066)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-2 binding (GO:0019976)|interleukin-2 receptor activity (GO:0004911)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(5)	23					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	ATCCCTGGAGGGGAAGGTGCA	0.682																																					p.P422L		Atlas-SNP	.											.	IL2RB	44	.	0			c.C1265T						.						24	25	24					22																	37524527		2203	4300	6503	SO:0001583	missense	3560	exon10			CTGGAGGGGAAGG	M26062	CCDS13942.1	22q13	2011-02-15			ENSG00000100385	ENSG00000100385		"Interleukins and interleukin receptors", "CD molecules"	6009	protein-coding gene	gene with protein product		146710	"interleukin 15 receptor, beta"	IL15RB			Standard	NM_000878		Approved	CD122	uc003aqv.1	P14784	OTTHUMG00000150534	ENST00000216223.5:c.1265C>T	chr22.hg19:g.37524527G>A	ENSP00000216223:p.Pro422Leu	73.0	0.0		83.0	31.0	NM_000878	B2R765	Missense_Mutation	SNP	ENST00000216223.5	hg19	CCDS13942.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.126183	0.56721	.	.	ENSG00000100385	ENST00000216223	T	0.28454	1.61	4.92	4.92	0.64577	.	0.610754	0.16759	N	0.200695	T	0.51805	0.1696	M	0.68952	2.095	0.45035	D	0.998055	D	0.89917	1.0	D	0.97110	1.0	T	0.47636	-0.9102	10	0.49607	T	0.09	-29.9354	11.2985	0.49292	0.0:0.0:0.805:0.195	.	422	P14784	IL2RB_HUMAN	L	422	ENSP00000216223:P422L	ENSP00000216223:P422L	P	-	2	0	IL2RB	35854473	0.994000	0.37717	0.956000	0.39512	0.349000	0.29174	2.688000	0.46984	2.404000	0.81709	0.655000	0.94253	CCC	.	.		0.682	IL2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318792.1			A	37524527	G	A	37524527	3	1	70	1	0	0	0	0	1	0	0	0	7696	1232	43	3	394	3	IL2RB	22	37524527	Missense_Mutation	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10	5674360	37524527	13780039	152	9083										
PPARA	5465	hgsc.bcm.edu	37	chr22	46594481	46594481	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cctggctcagatggctcggtCatcacgggtaagtgtgccgt	14	11	3	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chr22:46594481C>T	ENST00000396000.2	+	3	466	c.201C>T	c.(199-201)gtC>gtT	p.V67V	PPARA_ENST00000434345.2_Silent_p.V67V|PPARA_ENST00000262735.5_Silent_p.V67V|PPARA_ENST00000407236.1_Silent_p.V67V|PPARA_ENST00000402126.1_Silent_p.V67V			Q07869	PPARA_HUMAN	peroxisome proliferator-activated receptor alpha	67					behavioral response to nicotine (GO:0035095)|cellular lipid metabolic process (GO:0044255)|circadian regulation of gene expression (GO:0032922)|enamel mineralization (GO:0070166)|epidermis development (GO:0008544)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|negative regulation of appetite (GO:0032099)|negative regulation of blood pressure (GO:0045776)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of glycolytic process (GO:0045820)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter (GO:0072366)|regulation of circadian rhythm (GO:0042752)|regulation of glycolytic by positive regulation of transcription from RNA polymerase II promoter (GO:0072363)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|lipid binding (GO:0008289)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	15		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Indomethacin(DB00328)	ATGGCTCGGTCATCACGGGTA	0.408																																					p.V67V		Atlas-SNP	.											.	PPARA	36	.	0			c.C201T						.						63	66	65					22																	46594481		2203	4300	6503	SO:0001819	synonymous_variant	5465	exon3			CTCGGTCATCACG	L02932	CCDS33669.1	22q12-q13.1	2013-01-16	2006-10-17		ENSG00000186951	ENSG00000186951		"Nuclear hormone receptors"	9232	protein-coding gene	gene with protein product		170998	"peroxisome proliferative activated receptor, alpha"	PPAR		7684926, 10591208	Standard	XM_005261655		Approved	hPPAR, NR1C1	uc003bgx.1	Q07869	OTTHUMG00000150443	ENST00000396000.2:c.201C>T	chr22.hg19:g.46594481C>T		98.0	0.0		96.0	17.0	NM_001001928	B0G0X3|Q16241|Q6I9S0|Q92486|Q92689|Q9Y3N1	Silent	SNP	ENST00000396000.2	hg19	CCDS33669.1																																																																																			.	.		0.408	PPARA-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318129.3	NM_001001928		T	46594481	C	T	46594481	2	4	70	1	0	0	0	0	0	0	0	1	12306	813	29	3		3	PPARA	22	46594481	Silent	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	9069954	46594481	4710085	153	9084										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50341497	50341497	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	cctcgctgggcctcccgcaaGacagaaagttttctgctgat	10	13	1	3			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chrX:50341497G>T	ENST00000289292.7	-	8	4264	c.3981C>A	c.(3979-3981)gtC>gtA	p.V1327V	SHROOM4_ENST00000376020.2_Silent_p.V1327V|SHROOM4_ENST00000460112.3_Silent_p.V1211V|SHROOM4_ENST00000483955.1_5'Flank			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1327	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					CCTCCCGCAAGACAGAAAGTT	0.483																																					p.V1327V		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C3981A						.						28	23	25					X																	50341497		2203	4300	6503	SO:0001819	synonymous_variant	57477	exon8			CCGCAAGACAGAA	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3981C>A	chrX.hg19:g.50341497G>T		88.0	0.0		111.0	63.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	hg19	CCDS35277.1																																																																																			.	.		0.483	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		T	50341497	G	T	50341497	2	4	70	1	0	0	0	0	0	0	0	1	14311	929	33	3		3	SHROOM4	23	50341497	Silent	SNP	G	TCGA-CC-A7IE-01A-21D-A382-10		50341497	104929063	154	9085										
DGAT2L6	347516	hgsc.bcm.edu	37	chrX	69420190	69420190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	tctctcttttggtgtcttcaTcaactttgccactgaggcca	7	12	5	1			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chrX:69420190T>C	ENST00000333026.3	+	4	453	c.353T>C	c.(352-354)aTc>aCc	p.I118T		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	118					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(1)	12						GGTGTCTTCATCAACTTTGCC	0.458																																					p.I118T		Atlas-SNP	.											.	DGAT2L6	40	.	0			c.T353C						.						192	141	158					X																	69420190		2203	4300	6503	SO:0001583	missense	347516	exon4			TCTTCATCAACTT	AK129500	CCDS14397.1	Xq13.1	2008-02-05			ENSG00000184210	ENSG00000184210			23250	protein-coding gene	gene with protein product		300926				15671038	Standard	NM_198512		Approved	DC3, FLJ25989	uc004dxx.1	Q6ZPD8	OTTHUMG00000021774	ENST00000333026.3:c.353T>C	chrX.hg19:g.69420190T>C	ENSP00000328036:p.Ile118Thr	92.0	0.0		100.0	58.0	NM_198512	Q6IEE2	Missense_Mutation	SNP	ENST00000333026.3	hg19	CCDS14397.1	.	.	.	.	.	.	.	.	.	.	T	16.01	3.002015	0.54254	.	.	ENSG00000184210	ENST00000333026	D	0.94758	-3.51	5.35	4.18	0.49190	.	0.153864	0.44902	D	0.000415	D	0.89283	0.6671	L	0.33293	1	0.42425	D	0.992656	B	0.32862	0.387	B	0.36608	0.229	D	0.85012	0.0906	10	0.18276	T	0.48	-6.4929	8.3902	0.32524	0.0:0.0:0.3198:0.6802	.	118	Q6ZPD8	DG2L6_HUMAN	T	118	ENSP00000328036:I118T	ENSP00000328036:I118T	I	+	2	0	DGAT2L6	69336915	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	4.208000	0.58486	1.982000	0.57802	0.486000	0.48141	ATC	.	.		0.458	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057067.1	NM_198512		C	69420190	T	C	69420190	3	2	70	1	0	0	0	0	1	0	0	0	4461	1435	50	2	367	2	DGAT2L6	23	69420190	Missense_Mutation	SNP	T	TCGA-CC-A7IE-01A-21D-A382-10	19078693	69420190	85850370	155	9086										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118220842	118220842	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0448717948717949	7	1	0.997169811320755	1.09579100145138	0.962519122896481	0.37070938215103	1	0	atcaccactctcaagatcttCtttcttagagtaaatgcccc	4	13	5	2			TCGA-CC-A7IE-01A-21D-A382-10	TCGA-CC-A7IE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c1caf517-5052-48e3-ad80-8458b3d2ff5f	ab81329b-c119-4a5a-863c-5b50f48cee3f	g.chrX:118220842C>T	ENST00000402510.2	-	11	4350	c.4351G>A	c.(4351-4353)Gaa>Aaa	p.E1451K		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	1451										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TCAAGATCTTCTTTCTTAGAG	0.458																																					p.E1451K		Atlas-SNP	.											.	KIAA1210	171	.	0			c.G4351A						.						83	77	79					X																	118220842		1855	4092	5947	SO:0001583	missense	57481	exon11			GATCTTCTTTCTT	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.4351G>A	chrX.hg19:g.118220842C>T	ENSP00000384670:p.Glu1451Lys	78.0	0.0		115.0	68.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.75|17.75	3.466020|3.466020	0.63625|0.63625	.|.	.|.	ENSG00000250423|ENSG00000248857	ENST00000402510|ENST00000440399	T|.	0.16597|.	2.33|.	5.13|5.13	4.27|4.27	0.50696|0.50696	.|.	.|.	.|.	.|.	.|.	T|T	0.53400|0.53400	0.1794|0.1794	M|M	0.67953|0.67953	2.075|2.075	0.09310|0.09310	N|N	1|1	P|.	0.50943|.	0.94|.	P|.	0.49421|.	0.61|.	T|T	0.45862|0.45862	-0.9232|-0.9232	8|5	.|.	.|.	.|.	.|.	9.2317|9.2317	0.37441|0.37441	0.0:0.8952:0.0:0.1048|0.0:0.8952:0.0:0.1048	.|.	1451|.	Q9ULL0|.	K1210_HUMAN|.	K|K	1451|857	ENSP00000384670:E1451K|.	.|.	E|R	-|-	1|2	0|0	RP13-347D8.6|KIAA1210	118104870|118104870	0.021000|0.021000	0.18746|0.18746	0.005000|0.005000	0.12908|0.12908	0.007000|0.007000	0.05969|0.05969	1.299000|1.299000	0.33424|0.33424	1.233000|1.233000	0.43693|0.43693	0.513000|0.513000	0.50165|0.50165	GAA|AGA	.	.		0.458	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		T	118220842	C	T	118220842	3	4	70	1	0	0	0	0	1	0	0	0	8223	922	32	3	794	3	KIAA1210	23	118220842	Missense_Mutation	SNP	C	TCGA-CC-A7IE-01A-21D-A382-10	48800652	118220842	37049718	156	9087										
EFHD2	79180	hgsc.bcm.edu	37	chr1	15753664	15753664	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	agttcctcctgatcttccgcAaggcggcggccggggagctt	14	13	1	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr1:15753664A>G	ENST00000375980.4	+	3	552	c.475A>G	c.(475-477)Aag>Gag	p.K159E		NM_024329.5	NP_077305.2	Q96C19	EFHD2_HUMAN	EF-hand domain family, member D2	159	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					membrane (GO:0016020)	calcium ion binding (GO:0005509)			large_intestine(1)|skin(1)	2		Renal(390;0.00145)|Breast(348;0.00173)|Colorectal(325;0.00215)|all_lung(284;0.00366)|Lung NSC(340;0.00395)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)|Hepatocellular(190;0.152)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.59e-07)|COAD - Colon adenocarcinoma(227;3.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000119)|KIRC - Kidney renal clear cell carcinoma(229;0.00251)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		GATCTTCCGCAAGGCGGCGGC	0.701																																					p.K159E		Atlas-SNP	.											.	EFHD2	10	.	0			c.A475G						.						17	19	18					1																	15753664		2202	4299	6501	SO:0001583	missense	79180	exon3			TTCCGCAAGGCGG	BC014923	CCDS155.1	1p36	2014-07-01	2005-01-25		ENSG00000142634	ENSG00000142634		"EF-hand domain containing"	28670	protein-coding gene	gene with protein product	"swiprosin-1"		"EF hand domain containing 2"			21244694	Standard	NM_024329		Approved	MGC4342	uc001awh.2	Q96C19	OTTHUMG00000002254	ENST00000375980.4:c.475A>G	chr1.hg19:g.15753664A>G	ENSP00000365147:p.Lys159Glu	131.0	0.0		67.0	30.0	NM_024329	Q5JYW9	Missense_Mutation	SNP	ENST00000375980.4	hg19	CCDS155.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.20|18.20	3.571326|3.571326	0.65765|0.65765	.|.	.|.	ENSG00000142634|ENSG00000142634	ENST00000375980;ENST00000375975|ENST00000445566	T|.	0.46063|.	0.88|.	4.07|4.07	4.07|4.07	0.47477|0.47477	EF-hand-like domain (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.76456|0.76456	0.3990|0.3990	M|M	0.84948|0.84948	2.725|2.725	0.58432|0.58432	D|D	0.999991|0.999991	D|.	0.58620|.	0.983|.	P|.	0.58721|.	0.844|.	T|T	0.79562|0.79562	-0.1752|-0.1752	10|5	0.54805|.	T|.	0.06|.	-37.7629|-37.7629	12.5858|12.5858	0.56416|0.56416	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	159|.	Q96C19|.	EFHD2_HUMAN|.	E|R	159;60|61	ENSP00000365147:K159E|.	ENSP00000365142:K60E|.	K|Q	+|+	1|2	0|0	EFHD2|EFHD2	15626251|15626251	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.617000|0.617000	0.37484|0.37484	7.280000|7.280000	0.78610|0.78610	1.795000|1.795000	0.52594|0.52594	0.459000|0.459000	0.35465|0.35465	AAG|CAA	.	.		0.701	EFHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006433.1	NM_024329		G	15753664	A	G	15753664	3	3	71	1	0	0	0	0	1	0	0	0	4951	131	5	2	485	2	EFHD2	1	15753664	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10		15753664	233496957	1	9088										
ZMYM1	79830	hgsc.bcm.edu	37	chr1	35578710	35578710	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gtacagaagtacaaaaagacAatatgaaatctatgaaaata	6	4	1	4			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr1:35578710A>G	ENST00000373330.1	+	11	1453	c.1279A>G	c.(1279-1281)Aat>Gat	p.N427D	ZMYM1_ENST00000373329.1_3'UTR|ZMYM1_ENST00000359858.4_Missense_Mutation_p.N427D			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	427						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ACAAAAAGACAATATGAAATC	0.348																																					p.N427D		Atlas-SNP	.											.	ZMYM1	86	.	0			c.A1279G						.						66	62	63					1																	35578710		1873	4120	5993	SO:0001583	missense	79830	exon10			AAAGACAATATGA	AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"Zinc fingers, MYM type"	26253	protein-coding gene	gene with protein product			"zinc finger, MYM domain containing 1"			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.1279A>G	chr1.hg19:g.35578710A>G	ENSP00000362427:p.Asn427Asp	238.0	0.0		144.0	31.0	NM_024772	D3DPR7|Q7Z3Q4	Missense_Mutation	SNP	ENST00000373330.1	hg19	CCDS41302.1	.	.	.	.	.	.	.	.	.	.	A	9.135	1.012458	0.19277	.	.	ENSG00000197056	ENST00000417119;ENST00000359858;ENST00000373329;ENST00000373330	T;T;T;T	0.17528	2.27;2.55;2.29;2.55	4.52	3.39	0.38822	.	1.320380	0.04926	N	0.455904	T	0.14830	0.0358	L	0.44542	1.39	0.09310	N	1	B;B	0.26002	0.083;0.139	B;B	0.19946	0.027;0.027	T	0.35574	-0.9783	10	0.12103	T	0.63	-6.1605	6.8918	0.24234	0.8971:0.0:0.1029:0.0	.	408;427	B4DSJ9;Q5SVZ6	.;ZMYM1_HUMAN	D	427;427;352;427	ENSP00000394233:N427D;ENSP00000352920:N427D;ENSP00000362426:N352D;ENSP00000362427:N427D	ENSP00000352920:N427D	N	+	1	0	ZMYM1	35351297	0.000000	0.05858	0.002000	0.10522	0.340000	0.28889	-0.403000	0.07214	1.061000	0.40601	0.482000	0.46254	AAT	.	.		0.348	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772		G	35578710	A	G	35578710	3	3	71	1	0	0	0	0	1	0	0	0	17714	130	5	2	1313	2	ZMYM1	1	35578710	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	19825046	35578710	213671911	2	9089										
EBNA1BP2	149465	hgsc.bcm.edu	37	chr1	43637963	43637963	+	5'UTR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	caactcacagctactgctcaActtttgattgggacttccgc	7	13	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr1:43637963A>G	ENST00000372492.4	+	0	144				EBNA1BP2_ENST00000431635.2_Silent_p.L44L|WDR65_ENST00000528956.1_5'Flank|EBNA1BP2_ENST00000472982.1_5'Flank|EBNA1BP2_ENST00000236051.2_5'Flank	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN												NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTACTGCTCAACTTTTGATTG	0.602																																					p.L44L		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.T130C						.						63	61	61					1																	43637963		692	1591	2283	SO:0001623	5_prime_UTR_variant	10969	exon1			TGCTCAACTTTTG																												ENST00000372492.4:c.-181A>G	chr1.hg19:g.43637963A>G		93.0	0.0		49.0	13.0	NM_001159936	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	hg19																																																																																				.	.		0.602	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			G	43637963	A	G	43637963	1	3	71	0	1	0	0	0	0	0	0	0	4887	40	2	2		2	EBNA1BP2	1	43637963	5'UTR	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	8059253	43637963	205612658	3	9090										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67833704	67833704	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tacaatgtgtctgctctgatTtcaggtacctaattgttcac	7	9	4	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr1:67833704T>C	ENST00000262345.1	+	10	2095	c.1455T>C	c.(1453-1455)atT>atC	p.I485I	IL12RB2_ENST00000371000.1_Silent_p.I485I|IL12RB2_ENST00000544434.1_Silent_p.I485I|IL12RB2_ENST00000541374.1_Silent_p.I485I	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	485	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						CTGCTCTGATTTCAGGTACCT	0.498																																					p.I485I		Atlas-SNP	.											.	IL12RB2	94	.	0			c.T1455C						.						142	123	129					1																	67833704		2203	4300	6503	SO:0001819	synonymous_variant	3595	exon10			TCTGATTTCAGGT	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.1455T>C	chr1.hg19:g.67833704T>C		53.0	0.0		47.0	6.0	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Silent	SNP	ENST00000262345.1	hg19	CCDS638.1																																																																																			.	.		0.498	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		C	67833704	T	C	67833704	2	2	71	1	0	0	0	0	0	0	0	1	7636	1829	64	2		2	IL12RB2	1	67833704	Silent	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	24195741	67833704	181416917	4	9091										
MAN1A2	10905	hgsc.bcm.edu	37	chr1	117944848	117944848	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gaaataaaattcgagctgatCatgagaaggccttggaagaa	11	5	1	3			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr1:117944848C>T	ENST00000356554.3	+	2	1078	c.343C>T	c.(343-345)Cat>Tat	p.H115Y	MAN1A2_ENST00000482811.1_Intron	NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	115					cellular protein metabolic process (GO:0044267)|lung alveolus development (GO:0048286)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	27	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		TCGAGCTGATCATGAGAAGGC	0.363																																					p.H115Y	Ovarian(33;199 881 8228 13687 31538)	Atlas-SNP	.											.	MAN1A2	50	.	0			c.C343T						.						64	68	67					1																	117944848		2203	4300	6503	SO:0001583	missense	10905	exon2			GCTGATCATGAGA	AF027156	CCDS895.1	1p13	2008-02-05			ENSG00000198162	ENSG00000198162			6822	protein-coding gene	gene with protein product		604345				9592125	Standard	NM_006699		Approved	MAN1B	uc001ehd.1	O60476	OTTHUMG00000012149	ENST00000356554.3:c.343C>T	chr1.hg19:g.117944848C>T	ENSP00000348959:p.His115Tyr	186.0	0.0		122.0	27.0	NM_006699	Q9H510	Missense_Mutation	SNP	ENST00000356554.3	hg19	CCDS895.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.421808	0.25639	.	.	ENSG00000198162	ENST00000356554	D	0.83163	-1.69	5.67	5.67	0.87782	.	0.105494	0.64402	D	0.000004	T	0.68705	0.3030	M	0.65975	2.015	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.67730	-0.5595	10	0.02654	T	1	-9.1071	17.2449	0.87025	0.0:1.0:0.0:0.0	.	115	O60476	MA1A2_HUMAN	Y	115	ENSP00000348959:H115Y	ENSP00000348959:H115Y	H	+	1	0	MAN1A2	117746371	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.364000	0.79526	2.669000	0.90835	0.591000	0.81541	CAT	.	.		0.363	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033593.1	NM_006699		T	117944848	C	T	117944848	3	4	71	1	0	0	0	0	1	0	0	0	9220	826	29	3	349	3	MAN1A2	1	117944848	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	50111144	117944848	131305773	5	9092										
RCSD1	92241	hgsc.bcm.edu	37	chr1	167666394	167666394	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	caggcgattccgaaggtcacAgtcagactgtggagaacttg	13	9	2	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr1:167666394A>C	ENST00000367854.3	+	6	864	c.533A>C	c.(532-534)cAg>cCg	p.Q178P	RCSD1_ENST00000537350.1_Missense_Mutation_p.Q148P	NM_052862.3	NP_443094.3	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	178					cellular hyperosmotic response (GO:0071474)|skeletal muscle contraction (GO:0003009)	actin filament (GO:0005884)	actin filament binding (GO:0051015)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	24	all_hematologic(923;0.215)					CGAAGGTCACAGTCAGACTGT	0.502																																					p.Q178P		Atlas-SNP	.											.	RCSD1	64	.	0			c.A533C						.						77	75	75					1																	167666394		2203	4300	6503	SO:0001583	missense	92241	exon6			GGTCACAGTCAGA	BC072399	CCDS1263.1	1q24.2	2008-02-05			ENSG00000198771	ENSG00000198771			28310	protein-coding gene	gene with protein product		610579				12477932	Standard	NM_052862		Approved	MK2S4, MGC21854	uc001gem.3	Q6JBY9	OTTHUMG00000035318	ENST00000367854.3:c.533A>C	chr1.hg19:g.167666394A>C	ENSP00000356828:p.Gln178Pro	167.0	0.0		167.0	12.0	NM_052862	B1AK48|Q4G0E7|Q6IN93|Q8IZM2|Q96DX0|Q9NST4	Missense_Mutation	SNP	ENST00000367854.3	hg19	CCDS1263.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.265292	0.59431	.	.	ENSG00000198771	ENST00000367854;ENST00000361496;ENST00000537350	T;T	0.50548	0.75;0.74	5.44	5.44	0.79542	.	0.203521	0.39274	N	0.001401	T	0.49389	0.1554	L	0.54323	1.7	0.34477	D	0.703451	D;D	0.76494	0.998;0.999	D;D	0.80764	0.986;0.994	T	0.53954	-0.8365	9	0.33940	T	0.23	-28.3369	10.0869	0.42423	0.8407:0.0:0.0:0.1593	.	148;178	B7ZKW8;Q6JBY9	.;CPZIP_HUMAN	P	178;154;148	ENSP00000356828:Q178P;ENSP00000439409:Q148P	ENSP00000355291:Q154P	Q	+	2	0	RCSD1	165933018	1.000000	0.71417	0.993000	0.49108	0.662000	0.39071	3.667000	0.54547	2.051000	0.60960	0.477000	0.44152	CAG	.	.		0.502	RCSD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085451.1	NM_052862		C	167666394	A	C	167666394	3	2	71	1	0	0	0	0	1	0	0	0	13200	188	7	5	555	5	RCSD1	1	167666394	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	49721546	167666394	81584227	6	9093										
USH2A	7399	hgsc.bcm.edu	37	chr1	216040477	216040477	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tcggtgtaaaacccacactgTtgtgtacgaagagcatatat	9	8	0	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr1:216040477T>C	ENST00000307340.3	-	44	9103	c.8717A>G	c.(8716-8718)aAc>aGc	p.N2906S	USH2A_ENST00000366943.2_Missense_Mutation_p.N2906S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2906	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACCCACACTGTTGTGTACGAA	0.378										HNSCC(13;0.011)																											p.N2906S		Atlas-SNP	.											.	USH2A	1168	.	0			c.A8717G						.						102	91	95					1																	216040477		2203	4300	6503	SO:0001583	missense	7399	exon44			ACACTGTTGTGTA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.8717A>G	chr1.hg19:g.216040477T>C	ENSP00000305941:p.Asn2906Ser	129.0	0.0		134.0	57.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.944807	0.73672	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.61392	0.11;0.11	5.72	5.72	0.89469	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.47093	D	0.000257	T	0.77329	0.4114	M	0.80746	2.51	0.45087	D	0.998104	D	0.89917	1.0	D	0.87578	0.998	T	0.79085	-0.1948	10	0.49607	T	0.09	.	15.9962	0.80250	0.0:0.0:0.0:1.0	.	2906	O75445	USH2A_HUMAN	S	2906	ENSP00000305941:N2906S;ENSP00000355910:N2906S	ENSP00000305941:N2906S	N	-	2	0	USH2A	214107100	1.000000	0.71417	0.998000	0.56505	0.773000	0.43773	4.225000	0.58600	2.188000	0.69820	0.455000	0.32223	AAC	.	.		0.378	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	216040477	T	C	216040477	3	2	71	1	0	0	0	0	1	0	0	0	17051	1725	60	2	7007	2	USH2A	1	216040477	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	48374083	216040477	33210144	7	9094										
ZNF669	79862	hgsc.bcm.edu	37	chr1	247264138	247264138	+	Frame_Shift_Del	DEL	A	A	-													0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gaaaatctgaatgttttcccAcattccttacattcgtaggg							TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr1:247264138delA	ENST00000343381.6	-	4	1105	c.933delT	c.(931-933)tgtfs	p.C311fs	ZNF669_ENST00000358785.4_3'UTR|ZNF669_ENST00000448299.2_Frame_Shift_Del_p.C225fs	NM_024804.2	NP_079080.2	Q96BR6	ZN669_HUMAN	zinc finger protein 669	311					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(4)|large_intestine(2)|lung(6)	17	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)			ATGTTTTCCCACATTCCTTAC	0.378																																					p.G312fs		Atlas-Indel,Pindel	.											.	ZNF669	46	.	0			c.934delG						.						89	91	90					1																	247264138		2203	4300	6503	SO:0001589	frameshift_variant	79862	exon4			.		CCDS31088.1, CCDS44345.1	1q44	2013-01-08			ENSG00000188295	ENSG00000188295		"Zinc fingers, C2H2-type", "-"	25736	protein-coding gene	gene with protein product						12477932	Standard	NM_024804		Approved	FLJ12606	uc001ice.2	Q96BR6	OTTHUMG00000040869	ENST00000343381.6:c.933delT	chr1.hg19:g.247264138delA	ENSP00000342818:p.Cys311fs	84.0	0.0		92.0	22.0	NM_024804	B3KP94|Q5VT39|Q9H9Q6	Frame_Shift_Del	DEL	ENST00000343381.6	hg19	CCDS31088.1																																																																																			.	.		0.378	ZNF669-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000098394.4	NM_024804		-	247264138	A	-	247264138	7	5	71	1	0	1	0	1	0	0	0	0	18091	157	6	0	465	0	ZNF669	1	247264138	Frame_Shift_Del	DEL	A	TCGA-CC-A7IF-01A-11D-A33K-10	31223661	247264138	1986483	8	9095										
TRIM58	25893	hgsc.bcm.edu	37	chr1	248024000	248024000	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	aggccaacgtggggaaaaagActgtcatttggaaggtaaga	14	5	1	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr1:248024000A>G	ENST00000366481.3	+	2	550	c.502A>G	c.(502-504)Act>Gct	p.T168A		NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	168						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GGGGAAAAAGACTGTCATTTG	0.478																																					p.T168A		Atlas-SNP	.											.	TRIM58	143	.	0			c.A502G						.						106	106	106					1																	248024000		2203	4300	6503	SO:0001583	missense	25893	exon2			AAAAAGACTGTCA	AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	24150	protein-coding gene	gene with protein product			"tripartite motif-containing 58"				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.502A>G	chr1.hg19:g.248024000A>G	ENSP00000355437:p.Thr168Ala	163.0	0.0		140.0	67.0	NM_015431	Q6B0H9	Missense_Mutation	SNP	ENST00000366481.3	hg19	CCDS1636.1	.	.	.	.	.	.	.	.	.	.	A	0.802	-0.755082	0.03019	.	.	ENSG00000162722	ENST00000366481	T	0.04551	3.6	4.02	4.02	0.46733	.	0.250410	0.28109	N	0.016580	T	0.05135	0.0137	L	0.43757	1.38	0.09310	N	1	B	0.21688	0.059	B	0.20184	0.028	T	0.30563	-0.9974	10	0.30854	T	0.27	.	9.5646	0.39391	1.0:0.0:0.0:0.0	.	168	Q8NG06	TRI58_HUMAN	A	168	ENSP00000355437:T168A	ENSP00000355437:T168A	T	+	1	0	TRIM58	246090623	0.922000	0.31269	0.117000	0.21633	0.018000	0.09664	1.997000	0.40786	1.814000	0.52955	0.533000	0.62120	ACT	.	.		0.478	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431		G	248024000	A	G	248024000	3	3	71	1	0	0	0	0	1	0	0	0	16546	275	10	2	508	2	TRIM58	1	248024000	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	759862	248024000	1226621	9	9096										
OR14I1	401994	hgsc.bcm.edu	37	chr1	248844793	248844793	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	actgtgtatgtcagagcaatCactaaatcctgaatggacag	9	8	2	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr1:248844793C>A	ENST00000342623.3	-	1	836	c.813G>T	c.(811-813)gtG>gtT	p.V271V		NM_001004734.1	NP_001004734.1	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I, member 1	271						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(4)|large_intestine(2)|lung(24)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	35						TCAGAGCAATCACTAAATCCT	0.448																																					p.V271V		Atlas-SNP	.											.	OR14I1	64	.	0			c.G813T						.						117	108	111					1																	248844793		2203	4300	6503	SO:0001819	synonymous_variant	401994	exon1			AGCAATCACTAAA		CCDS31125.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000189181	ENSG00000189181		"GPCR / Class A : Olfactory receptors"	19575	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily BU, member 1"	OR5BU1P, OR5BU1			Standard	NM_001004734		Approved		uc001ieu.1	A6ND48	OTTHUMG00000040378	ENST00000342623.3:c.813G>T	chr1.hg19:g.248844793C>A		64.0	0.0		65.0	14.0	NM_001004734		Silent	SNP	ENST00000342623.3	hg19	CCDS31125.1																																																																																			.	.		0.448	OR14I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097128.1	NM_001004734		A	248844793	C	A	248844793	2	1	71	1	0	0	0	0	0	0	0	1	10956	813	29	3		3	OR14I1	1	248844793	Silent	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	820793	248844793	405828	10	9097										
FAM179A	165186	hgsc.bcm.edu	37	chr2	29259514	29259514	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ctcctcagagagagcttacaCcccatgctgctctccatcat	6	16	3	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr2:29259514C>A	ENST00000379558.4	+	18	2877	c.2526C>A	c.(2524-2526)caC>caA	p.H842Q	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Missense_Mutation_p.H787Q	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	842										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						AGAGCTTACACCCCATGCTGC	0.537																																					p.H842Q		Atlas-SNP	.											.	FAM179A	106	.	0			c.C2526A						.						132	104	113					2																	29259514		2203	4300	6503	SO:0001583	missense	165186	exon18			CTTACACCCCATG	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.2526C>A	chr2.hg19:g.29259514C>A	ENSP00000368876:p.His842Gln	98.0	0.0		90.0	36.0	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	hg19	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	C	8.920	0.960921	0.18583	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.12984	2.63;2.63	6.04	-3.33	0.04958	Armadillo-like helical (1);Armadillo-type fold (1);	0.649320	0.15513	N	0.258430	T	0.06234	0.0161	N	0.20401	0.57	0.24522	N	0.994158	B;B;B	0.27351	0.176;0.11;0.008	B;B;B	0.24541	0.054;0.024;0.007	T	0.42447	-0.9451	10	0.14252	T	0.57	.	8.6265	0.33892	0.0866:0.298:0.5113:0.1042	.	787;842;140	F8W8E4;Q6ZUX3;Q6ZUX3-3	.;F179A_HUMAN;.	Q	842;787	ENSP00000368876:H842Q;ENSP00000384699:H787Q	ENSP00000368876:H842Q	H	+	3	2	FAM179A	29113018	0.002000	0.14202	0.482000	0.27366	0.367000	0.29736	-0.785000	0.04628	-0.402000	0.07633	-0.311000	0.09066	CAC	.	.		0.537	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		A	29259514	C	A	29259514	3	1	71	1	0	0	0	0	1	0	0	0	5510	506	18	3	2592	3	FAM179A	2	29259514	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10		29259514	213939859	11	9098										
ASTL	431705	hgsc.bcm.edu	37	chr2	96799781	96799781	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	atttgttgctggttgctgacAgcagtcggaagggactctga	14	7	1	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr2:96799781A>C	ENST00000342380.2	-	4	259	c.260T>G	c.(259-261)cTg>cGg	p.L87R		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						GGTTGCTGACAGCAGTCGGAA	0.617																																					p.L87R		Atlas-SNP	.											.	ASTL	59	.	0			c.T260G						.						128	89	102					2																	96799781		2203	4300	6503	SO:0001583	missense	431705	exon4			GCTGACAGCAGTC	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"sperm acrosomal SLLP1 binding"	608860	"astacin-like metalloendopeptidase (M12 family)"			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.260T>G	chr2.hg19:g.96799781A>C	ENSP00000343674:p.Leu87Arg	67.0	0.0		36.0	13.0	NM_001002036		Missense_Mutation	SNP	ENST00000342380.2	hg19	CCDS33249.1	.	.	.	.	.	.	.	.	.	.	A	11.43	1.636919	0.29157	.	.	ENSG00000188886	ENST00000342380	T	0.68025	-0.3	4.95	3.7	0.42460	.	1.079380	0.07436	N	0.896553	T	0.54951	0.1890	L	0.27053	0.805	0.09310	N	1	P	0.44578	0.838	B	0.41691	0.364	T	0.47911	-0.9080	10	0.54805	T	0.06	-3.0998	7.5437	0.27753	0.8094:0.0:0.0:0.1906	.	87	Q6HA08	ASTL_HUMAN	R	87	ENSP00000343674:L87R	ENSP00000343674:L87R	L	-	2	0	ASTL	96163508	0.009000	0.17119	0.031000	0.17742	0.886000	0.51366	1.371000	0.34250	1.994000	0.58287	0.472000	0.43445	CTG	.	.		0.617	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			C	96799781	A	C	96799781	3	2	71	1	0	0	0	0	1	0	0	0	1063	188	7	5	1058	5	ASTL	2	96799781	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	67540267	96799781	146399592	12	9099										
ST6GAL2	84620	hgsc.bcm.edu	37	chr2	107423271	107423271	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	caggagcttctcatagagtaGtgggtggtacgccccgaggg	16	9	1	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr2:107423271G>A	ENST00000409382.3	-	6	2063	c.1453C>T	c.(1453-1455)Cta>Tta	p.L485L	ST6GAL2_ENST00000361686.4_Silent_p.L485L	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	485					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						TCATAGAGTAGTGGGTGGTAC	0.607																																					p.L485L		Atlas-SNP	.											.	ST6GAL2	159	.	0			c.C1453T						.						85	75	78					2																	107423271		2203	4300	6503	SO:0001819	synonymous_variant	84620	exon6			AGAGTAGTGGGTG	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"sialyltransferase 2 (monosialoganglioside sialyltransferase)"	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.1453C>T	chr2.hg19:g.107423271G>A		89.0	0.0		75.0	35.0	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	hg19	CCDS2073.1	.	.	.	.	.	.	.	.	.	.	G	9.624	1.134495	0.21123	.	.	ENSG00000144057	ENST00000361803	.	.	.	5.8	3.03	0.35002	.	.	.	.	.	T	0.58293	0.2112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50955	-0.8766	4	.	.	.	-30.1954	8.8633	0.35272	0.2863:0.0:0.7137:0.0	.	.	.	.	I	50	.	.	T	-	2	0	ST6GAL2	106789703	1.000000	0.71417	0.593000	0.28771	0.851000	0.48451	2.900000	0.48687	0.361000	0.24292	0.655000	0.94253	ACT	.	.		0.607	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		A	107423271	G	A	107423271	2	1	71	1	0	0	0	0	0	0	0	1	15237	1020	36	3		3	ST6GAL2	2	107423271	Silent	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	10623490	107423271	135776102	13	9100										
MAP2	4133	hgsc.bcm.edu	37	chr2	210588377	210588377	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tcagtccagatgtggttccaAggataacatcaaacattcgg	9	9	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr2:210588377A>T	ENST00000360351.4	+	13	5579				MAP2_ENST00000392194.1_Intron|MAP2_ENST00000447185.1_Intron|MAP2_ENST00000199940.6_Missense_Mutation_p.K412M|MAP2_ENST00000475600.1_3'UTR|RNA5SP118_ENST00000410385.1_RNA|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2						axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	TGTGGTTCCAAGGATAACATC	0.443																																					p.K412M	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.A1235T						.						100	98	98					2																	210588377		2203	4300	6503	SO:0001627	intron_variant	4133	exon12			GTTCCAAGGATAA		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.5074-2056A>T	chr2.hg19:g.210588377A>T		234.0	0.0		167.0	74.0	NM_001039538	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	hg19	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	A	15.60	2.882619	0.51908	.	.	ENSG00000078018	ENST00000199940	D	0.94862	-3.54	5.65	5.65	0.86999	.	.	.	.	.	D	0.92093	0.7494	L	0.44542	1.39	0.80722	D	1	B	0.28636	0.218	B	0.36186	0.219	D	0.90064	0.4158	9	0.49607	T	0.09	.	10.5518	0.45092	0.9188:0.0:0.0812:0.0	.	412	Q8IUX2	.	M	412	ENSP00000199940:K412M	ENSP00000199940:K412M	K	+	2	0	MAP2	210296622	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.682000	0.54656	2.144000	0.66660	0.533000	0.62120	AAG	.	.		0.443	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		T	210588377	A	T	210588377	1	4	71	0	1	0	0	0	0	0	0	0	9244	72	3	4		4	MAP2	2	210588377	Intron	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	103165106	210588377	32610996	14	9101										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225688292	225688292	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cttgtatttccaaatcacatGgtcggataggaccatgacaa	8	9	1	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr2:225688292G>T	ENST00000258390.7	-	28	3176	c.3109C>A	c.(3109-3111)Cat>Aat	p.H1037N	DOCK10_ENST00000409592.3_Missense_Mutation_p.H1031N	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1037					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		CAAATCACATGGTCGGATAGG	0.418																																					p.H1037N		Atlas-SNP	.											.	DOCK10	308	.	0			c.C3109A						.						158	147	151					2																	225688292		1895	4115	6010	SO:0001583	missense	55619	exon28			TCACATGGTCGGA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3109C>A	chr2.hg19:g.225688292G>T	ENSP00000258390:p.His1037Asn	91.0	0.0		89.0	44.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.386033	0.82902	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.64991	3.67;-0.13	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.82157	0.4976	M	0.84326	2.69	0.44309	D	0.997182	D;D	0.76494	0.999;0.996	D;D	0.78314	0.991;0.933	D	0.83482	0.0065	10	0.87932	D	0	.	20.2799	0.98512	0.0:0.0:1.0:0.0	.	1037;1031	Q96BY6;B3FL70	DOC10_HUMAN;.	N	1031;1037	ENSP00000386694:H1031N;ENSP00000258390:H1037N	ENSP00000258390:H1037N	H	-	1	0	DOCK10	225396536	1.000000	0.71417	0.333000	0.25482	0.914000	0.54420	8.192000	0.89718	2.800000	0.96347	0.643000	0.83706	CAT	.	.		0.418	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			T	225688292	G	T	225688292	3	4	71	1	0	0	0	0	1	0	0	0	4687	1348	47	3	3567	3	DOCK10	2	225688292	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	15099915	225688292	17511081	15	9102										
GPR149	344758	hgsc.bcm.edu	37	chr3	154146446	154146446	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tcatgggcagccaaaggacgActtttgtaagcgctaggatc	12	9	1	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr3:154146446A>T	ENST00000389740.2	-	1	1058	c.959T>A	c.(958-960)gTc>gAc	p.V320D		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	320					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CCAAAGGACGACTTTTGTAAG	0.572																																					p.V320D		Atlas-SNP	.											.	GPR149	134	.	0			c.T959A						.						115	114	114					3																	154146446		1984	4148	6132	SO:0001583	missense	344758	exon1			AGGACGACTTTTG	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.959T>A	chr3.hg19:g.154146446A>T	ENSP00000374390:p.Val320Asp	189.0	0.0		114.0	47.0	NM_001038705		Missense_Mutation	SNP	ENST00000389740.2	hg19	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	A	19.98	3.927782	0.73327	.	.	ENSG00000174948	ENST00000389740	T	0.74842	-0.88	4.87	2.46	0.29980	GPCR, rhodopsin-like superfamily (1);	0.128153	0.52532	D	0.000079	T	0.80226	0.4584	M	0.66939	2.045	0.80722	D	1	D	0.58620	0.983	P	0.60012	0.867	T	0.78671	-0.2113	10	0.87932	D	0	-10.5652	8.9808	0.35964	0.8476:0.0:0.1524:0.0	.	320	Q86SP6	GP149_HUMAN	D	320	ENSP00000374390:V320D	ENSP00000374390:V320D	V	-	2	0	GPR149	155629140	1.000000	0.71417	0.708000	0.30435	0.854000	0.48673	3.765000	0.55272	0.238000	0.21222	0.533000	0.62120	GTC	.	.		0.572	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		T	154146446	A	T	154146446	3	4	71	1	0	0	0	0	1	0	0	0	6662	275	10	4	1252	4	GPR149	3	154146446	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10		154146446	43875984	16	9103										
MFSD1	64747	hgsc.bcm.edu	37	chr3	158525238	158525238	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ttttggctgatggaatttggAagatttgtatttgggtaagt	13	1	0	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr3:158525238A>C	ENST00000264266.8	+	5	488	c.426A>C	c.(424-426)ggA>ggC	p.G142G	MFSD1_ENST00000415822.2_Silent_p.G191G|MFSD1_ENST00000392813.4_Silent_p.G152G			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	142					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TGGAATTTGGAAGATTTGTAT	0.279																																					p.G191G	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											.	MFSD1	88	.	0			c.A573C						.						176	178	177					3																	158525238		2203	4299	6502	SO:0001819	synonymous_variant	64747	exon5			ATTTGGAAGATTT	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.426A>C	chr3.hg19:g.158525238A>C		116.0	0.0		71.0	29.0	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Silent	SNP	ENST00000264266.8	hg19																																																																																				.	.		0.279	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		C	158525238	A	C	158525238	2	2	71	1	0	0	0	0	0	0	0	1	9536	233	9	5		5	MFSD1	3	158525238	Silent	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	4378792	158525238	39497192	17	9104										
VPS8	23355	hgsc.bcm.edu	37	chr3	184646286	184646286	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ggcatagttcaatttgaagaGagtcgactcatccggatggc	12	8	2	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr3:184646286G>C	ENST00000437079.3	+	32	2850	c.2679G>C	c.(2677-2679)gaG>gaC	p.E893D	VPS8_ENST00000446204.2_Missense_Mutation_p.E801D|VPS8_ENST00000436792.2_Missense_Mutation_p.E891D|VPS8_ENST00000287546.4_Missense_Mutation_p.E893D|VPS8_ENST00000463687.1_3'UTR	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	893							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			AATTTGAAGAGAGTCGACTCA	0.333																																					p.E893D		Atlas-SNP	.											.	VPS8	109	.	0			c.G2679C						.						124	118	120					3																	184646286		1836	4101	5937	SO:0001583	missense	23355	exon31			TGAAGAGAGTCGA	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"KIAA0804"	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.2679G>C	chr3.hg19:g.184646286G>C	ENSP00000397879:p.Glu893Asp	116.0	0.0		96.0	44.0	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	hg19	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.916965	0.33815	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.18960	2.18;2.18;2.18;2.18	5.79	4.92	0.64577	Quinonprotein alcohol dehydrogenase-like (1);	0.045746	0.85682	D	0.000000	T	0.16514	0.0397	N	0.16656	0.425	0.53005	D	0.999968	B;B;B	0.28783	0.142;0.207;0.222	B;B;B	0.37833	0.043;0.259;0.093	T	0.09079	-1.0691	10	0.13470	T	0.59	-11.5984	14.3333	0.66572	0.0717:0.0:0.9283:0.0	.	893;801;891	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	D	893;893;891;801	ENSP00000287546:E893D;ENSP00000397879:E893D;ENSP00000404704:E891D;ENSP00000405483:E801D	ENSP00000287546:E893D	E	+	3	2	VPS8	186128980	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.975000	0.49281	1.459000	0.47892	0.557000	0.71058	GAG	.	.		0.333	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		C	184646286	G	C	184646286	3	2	71	1	0	0	0	0	1	0	0	0	17233	933	33	4	2797	4	VPS8	3	184646286	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	26121048	184646286	13376144	18	9105										
LGI2	55203	hgsc.bcm.edu	37	chr4	25005095	25005095	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	acaaacttaagtcaacaattAtatgttcaaaaatctttgtt	3	6	3	0	rs150163590		TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr4:25005095A>G	ENST00000382114.4	-	8	1801	c.1616T>C	c.(1615-1617)aTa>aCa	p.I539T		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	539						extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				GTCAACAATTATATGTTCAAA	0.393																																					p.I539T		Atlas-SNP	.											.	LGI2	62	.	0			c.T1616C						.	A	THR/ILE	0,4402		0,0,2201	49	52	51		1616	5.6	0.9	4	dbSNP_134	51	1,8597	1.2+/-3.3	0,1,4298	no	missense	LGI2	NM_018176.3	89	0,1,6499	GG,GA,AA		0.0116,0.0,0.0077	benign	539/546	25005095	1,12999	2201	4299	6500	SO:0001583	missense	55203	exon8			ACAATTATATGTT	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.1616T>C	chr4.hg19:g.25005095A>G	ENSP00000371548:p.Ile539Thr	147.0	0.0		105.0	43.0	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	hg19	CCDS3431.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.267141	0.59540	0.0	1.16E-4	ENSG00000153012	ENST00000382114;ENST00000282970	T	0.62105	0.05	5.57	5.57	0.84162	.	0.175658	0.52532	D	0.000062	T	0.59514	0.2199	L	0.36672	1.1	0.28809	N	0.898337	P	0.39131	0.661	B	0.43155	0.41	T	0.62124	-0.6920	10	0.59425	D	0.04	-26.848	15.737	0.77853	1.0:0.0:0.0:0.0	.	539	Q8N0V4	LGI2_HUMAN	T	539;187	ENSP00000371548:I539T	ENSP00000282970:I187T	I	-	2	0	LGI2	24614193	0.998000	0.40836	0.914000	0.36105	0.982000	0.71751	4.859000	0.62954	2.113000	0.64589	0.455000	0.32223	ATA	.	A|1.000;G|0.000		0.393	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1			G	25005095	A	G	25005095	3	3	71	1	0	0	0	0	1	0	0	0	8761	449	16	2	25	2	LGI2	4	25005095	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10		25005095	166149181	19	9106										
GRXCR1	389207	hgsc.bcm.edu	37	chr4	42895442	42895442	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gccagtatctgtgggatagaTggactaggtgattccgatgg	15	6	1	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr4:42895442T>A	ENST00000399770.2	+	1	159	c.159T>A	c.(157-159)gaT>gaA	p.D53E	RN7SKP82_ENST00000516786.1_RNA	NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	53					auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						GTGGGATAGATGGACTAGGTG	0.507																																					p.D53E		Atlas-SNP	.											.	GRXCR1	78	.	0			c.T159A						.						184	186	186					4																	42895442		2005	4195	6200	SO:0001583	missense	389207	exon1			GATAGATGGACTA		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 88"	613283	"deafness, autosomal recessive 25"	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.159T>A	chr4.hg19:g.42895442T>A	ENSP00000382670:p.Asp53Glu	119.0	0.0		89.0	47.0	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	hg19	CCDS43225.1	.	.	.	.	.	.	.	.	.	.	T	10.16	1.273902	0.23221	.	.	ENSG00000215203	ENST00000399770	T	0.32988	1.43	5.16	2.68	0.31781	.	0.294115	0.31624	U	0.007326	T	0.11410	0.0278	N	0.16790	0.44	0.37838	D	0.928956	P	0.38535	0.635	B	0.30855	0.121	T	0.27806	-1.0063	10	0.02654	T	1	-15.4176	6.7281	0.23369	0.0:0.4067:0.0:0.5933	.	53	A8MXD5	GRCR1_HUMAN	E	53	ENSP00000382670:D53E	ENSP00000382670:D53E	D	+	3	2	GRXCR1	42590199	0.031000	0.19500	0.968000	0.41197	0.053000	0.15095	-0.665000	0.05286	0.410000	0.25675	-0.417000	0.06048	GAT	.	.		0.507	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476		A	42895442	T	A	42895442	3	1	71	1	0	0	0	0	1	0	0	0	6821	1461	51	4	161	4	GRXCR1	4	42895442	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	17890347	42895442	148258834	20	9107										
KDR	3791	hgsc.bcm.edu	37	chr4	55964415	55964415	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	catgacgatggacaagtagcCtgtcttcagttcccctccat	8	13	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr4:55964415C>G	ENST00000263923.4	-	17	2693	c.2398G>C	c.(2398-2400)Ggc>Cgc	p.G800R		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	800					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GACAAGTAGCCTGTCTTCAGT	0.463			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.G800R		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.G2398C						.						107	92	97					4																	55964415		2203	4300	6503	SO:0001583	missense	3791	exon17			AGTAGCCTGTCTT	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.2398G>C	chr4.hg19:g.55964415C>G	ENSP00000263923:p.Gly800Arg	139.0	0.0		83.0	21.0	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	hg19	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.802895	0.90623	.	.	ENSG00000128052	ENST00000263923	T	0.77877	-1.13	5.29	5.29	0.74685	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.86843	0.6030	L	0.60845	1.875	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87684	0.2549	10	0.87932	D	0	.	19.2932	0.94110	0.0:1.0:0.0:0.0	.	800	P35968	VGFR2_HUMAN	R	800	ENSP00000263923:G800R	ENSP00000263923:G800R	G	-	1	0	KDR	55659172	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	7.818000	0.86416	2.624000	0.88883	0.655000	0.94253	GGC	.	.		0.463	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			G	55964415	C	G	55964415	3	3	71	1	0	0	0	0	1	0	0	0	8148	681	24	4	1728	4	KDR	4	55964415	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	13068973	55964415	135189861	21	9108										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155412382	155412382	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cagagcagggagcgctgcgtCctggcgccgctgctgcctga	16	14	0	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr4:155412382C>T	ENST00000339452.1	-	1	486	c.126G>A	c.(124-126)agG>agA	p.R42R	DCHS2_ENST00000456341.2_Silent_p.R35R|DCHS2_ENST00000443500.1_Silent_p.R42R	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	545					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AGCGCTGCGTCCTGGCGCCGC	0.682																																					p.R42R		Atlas-SNP	.											.	DCHS2	594	.	0			c.G126A						.						20	34	30					4																	155412382		692	1591	2283	SO:0001819	synonymous_variant	54798	exon1			CTGCGTCCTGGCG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.126G>A	chr4.hg19:g.155412382C>T		86.0	0.0		63.0	14.0	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000339452.1	hg19	CCDS47150.1																																																																																			.	.		0.682	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552		T	155412382	C	T	155412382	2	4	71	1	0	0	0	0	0	0	0	1	4290	854	30	3		3	DCHS2	4	155412382	Silent	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	99447967	155412382	35741894	22	9109										
RAPGEF2	9693	hgsc.bcm.edu	37	chr4	160243510	160243510	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gcttttcagaacaactcttgGaatttatgcaccagttgcct	7	10	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr4:160243510G>T	ENST00000264431.4	+	4	801	c.382G>T	c.(382-384)Gaa>Taa	p.E128*	RAPGEF2_ENST00000504604.1_3'UTR	NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	128					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		ACAACTCTTGGAATTTATGCA	0.378																																					p.E128X		Atlas-SNP	.											.	RAPGEF2	171	.	0			c.G382T						.						99	90	93					4																	160243510		1887	4139	6026	SO:0001587	stop_gained	9693	exon4			CTCTTGGAATTTA	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.382G>T	chr4.hg19:g.160243510G>T	ENSP00000264431:p.Glu128*	152.0	0.0		71.0	53.0	NM_014247	D3DP27	Nonsense_Mutation	SNP	ENST00000264431.4	hg19	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.003154	0.74932	.	.	ENSG00000109756	ENST00000511336;ENST00000510510;ENST00000264431;ENST00000514565	.	.	.	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.6323	0.88112	0.0:0.0:1.0:0.0	.	.	.	.	X	56;126;128;109	.	ENSP00000264431:E128X	E	+	1	0	RAPGEF2	160462960	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.420000	0.97426	2.234000	0.73211	0.591000	0.81541	GAA	.	.		0.378	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		T	160243510	G	T	160243510	4	4	71	1	0	0	0	0	0	1	0	0	13059	1175	41	3	396	3	RAPGEF2	4	160243510	Nonsense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	4831128	160243510	30910766	23	9110										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175898867	175898867	+	Missense_Mutation	SNP	C	C	A													0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gacctcatgagttacctcccCagagtcaaccttgggtgatg							TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr4:175898867C>A	ENST00000359240.3	+	5	2861	c.2191C>A	c.(2191-2193)Cag>Aag	p.Q731K	ADAM29_ENST00000514159.1_Missense_Mutation_p.Q731K|ADAM29_ENST00000445694.1_Missense_Mutation_p.Q731K|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000404450.4_Missense_Mutation_p.Q731K	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	731					spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		GTTACCTCCCCAGAGTCAACC	0.468																																					p.Q731K	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.C2191A						.						109	101	104					4																	175898867		2203	4300	6503	SO:0001583	missense	11086	exon4			CCTCCCCAGAGTC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2191C>A	chr4.hg19:g.175898867C>A	ENSP00000352177:p.Gln731Lys	143.0	0.0		58.0	50.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	hg19	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.846237	0.00568	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01787	4.64;4.64;4.64;4.64	1.94	-0.328	0.12690	.	.	.	.	.	T	0.00998	0.0033	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48896	-0.8994	8	.	.	.	.	5.5148	0.16900	0.2255:0.5541:0.2204:0.0	.	731	Q9UKF5	ADA29_HUMAN	K	731	ENSP00000352177:Q731K;ENSP00000414544:Q731K;ENSP00000384229:Q731K;ENSP00000423517:Q731K	.	Q	+	1	0	ADAM29	176135442	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.324000	0.19610	-0.354000	0.08212	-0.195000	0.12781	CAG	.	.		0.468	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				A	175898867	C	A	175898867	3	1	71	1	0	0	0	0	1	0	0	0	247	595	21	3	2193	3	ADAM29	4	175898867	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	15655357	175898867	15255409	24	9111	39	2								
ADAM29	11086	hgsc.bcm.edu	37	chr4	175898869	175898869	+	Silent	SNP	G	G	A													0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cctcatgagttacctccccaGagtcaaccttgggtgatgcc							TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr4:175898869G>A	ENST00000359240.3	+	5	2863	c.2193G>A	c.(2191-2193)caG>caA	p.Q731Q	ADAM29_ENST00000514159.1_Silent_p.Q731Q|ADAM29_ENST00000445694.1_Silent_p.Q731Q|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000404450.4_Silent_p.Q731Q	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	731					spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TACCTCCCCAGAGTCAACCTT	0.473																																					p.Q731Q	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,colon,carcinoma,0,1	ADAM29	262	.	0			c.G2193A						.						112	103	106					4																	175898869		2203	4300	6503	SO:0001819	synonymous_variant	11086	exon4			TCCCCAGAGTCAA	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2193G>A	chr4.hg19:g.175898869G>A		142.0	1.0		58.0	50.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Silent	SNP	ENST00000359240.3	hg19	CCDS3823.1																																																																																			.	.		0.473	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				A	175898869	G	A	175898869	2	1	71	1	0	0	0	0	0	0	0	1	247	933	33	3		3	ADAM29	4	175898869	Silent	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	2	175898869	15255407	25	9112	39	2								
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5462512	5462512	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tgttgaagaaaccagctgtgGagacacagggagatctggtg	15	6	1	4			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr5:5462512G>C	ENST00000296564.7	+	13	3287	c.3065G>C	c.(3064-3066)gGa>gCa	p.G1022A		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1022					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						ACCAGCTGTGGAGACACAGGG	0.493																																					p.G1022A		Atlas-SNP	.											.	KIAA0947	301	.	0			c.G3065C						.						106	108	107					5																	5462512		1981	4164	6145	SO:0001583	missense	23379	exon13			GCTGTGGAGACAC																												ENST00000296564.7:c.3065G>C	chr5.hg19:g.5462512G>C	ENSP00000296564:p.Gly1022Ala	102.0	0.0		67.0	15.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	g	15.48	2.845800	0.51164	.	.	ENSG00000164151	ENST00000296564	T	0.14640	2.49	4.27	3.4	0.38934	.	0.867766	0.10011	N	0.727159	T	0.21761	0.0524	L	0.29908	0.895	0.09310	N	1	D	0.69078	0.997	D	0.64410	0.925	T	0.17018	-1.0383	10	0.39692	T	0.17	-21.1653	8.3389	0.32232	0.1126:0.0:0.8874:0.0	.	1022	Q9Y2F5	K0947_HUMAN	A	1022	ENSP00000296564:G1022A	ENSP00000296564:G1022A	G	+	2	0	KIAA0947	5515512	0.051000	0.20477	0.131000	0.22000	0.095000	0.18619	2.451000	0.44952	0.916000	0.36871	0.306000	0.20318	GGA	.	.		0.493	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			C	5462512	G	C	5462512	3	2	71	1	0	0	0	0	1	0	0	0	8211	1174	41	4	3115	4	KIAA0947	5	5462512	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10		5462512	175452748	26	9113										
ADCY2	108	hgsc.bcm.edu	37	chr5	7709399	7709399	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ccaaaatgagggcctcggtcCgcatgacccggtacttggag	13	12	0	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr5:7709399C>T	ENST00000338316.4	+	10	1566	c.1477C>T	c.(1477-1479)Cgc>Tgc	p.R493C	ADCY2_ENST00000537121.1_Missense_Mutation_p.R313C|RP11-711G10.1_ENST00000514105.2_RNA	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	493					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.R493S(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						GGCCTCGGTCCGCATGACCCG	0.587																																					p.R493C		Atlas-SNP	.											ADCY2_ENST00000537121,NS,carcinoma,-1,3	ADCY2	337	.	1	Substitution - Missense(1)	lung(1)	c.C1477T						.						75	63	67					5																	7709399		2203	4300	6503	SO:0001583	missense	108	exon10			TCGGTCCGCATGA	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1477C>T	chr5.hg19:g.7709399C>T	ENSP00000342952:p.Arg493Cys	94.0	0.0		85.0	29.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	c	21.7	4.183479	0.78677	.	.	ENSG00000078295	ENST00000338316;ENST00000537121	T;D	0.82619	-1.16;-1.63	5.62	4.73	0.59995	.	0.052729	0.64402	D	0.000001	D	0.90525	0.7031	M	0.78456	2.415	0.58432	D	0.999998	D;D	0.89917	0.999;1.0	P;D	0.68621	0.836;0.959	D	0.91702	0.5374	10	0.72032	D	0.01	.	15.7895	0.78343	0.1372:0.8628:0.0:0.0	.	313;493	B7Z2C1;Q08462	.;ADCY2_HUMAN	C	493;313	ENSP00000342952:R493C;ENSP00000444803:R313C	ENSP00000342952:R493C	R	+	1	0	ADCY2	7762399	0.990000	0.36364	0.934000	0.37439	0.985000	0.73830	2.958000	0.49145	1.330000	0.45394	0.558000	0.71614	CGC	.	.		0.587	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		T	7709399	C	T	7709399	3	4	71	1	0	0	0	0	1	0	0	0	294	652	23	1	1515	1	ADCY2	5	7709399	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	2246887	7709399	173205861	27	9114										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13917343	13917343	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cattagttgcatcagtgattCgaatatccatctcccgccaa	6	12	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr5:13917343C>T	ENST00000265104.4	-	8	1102	c.998G>A	c.(997-999)cGa>cAa	p.R333Q		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	333	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					ATCAGTGATTCGAATATCCAT	0.378									Kartagener syndrome																												p.R333Q		Atlas-SNP	.											.	DNAH5	868	.	0			c.G998A						.						143	120	127					5																	13917343		2203	4300	6503	SO:0001583	missense	1767	exon8	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GTGATTCGAATAT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.998G>A	chr5.hg19:g.13917343C>T	ENSP00000265104:p.Arg333Gln	64.0	0.0		63.0	26.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	13.41	2.230068	0.39399	.	.	ENSG00000039139	ENST00000265104	T	0.53857	0.6	5.54	3.44	0.39384	Dynein heavy chain, domain-1 (1);	0.194351	0.41823	N	0.000811	T	0.46347	0.1388	M	0.66939	2.045	0.32286	N	0.566894	B	0.06786	0.001	B	0.10450	0.005	T	0.50659	-0.8802	10	0.14656	T	0.56	.	10.3583	0.43977	0.0:0.74:0.1154:0.1446	.	333	Q8TE73	DYH5_HUMAN	Q	333	ENSP00000265104:R333Q	ENSP00000265104:R333Q	R	-	2	0	DNAH5	13970343	1.000000	0.71417	0.999000	0.59377	0.763000	0.43281	4.884000	0.63135	1.357000	0.45904	-0.219000	0.12488	CGA	.	.		0.378	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13917343	C	T	13917343	3	4	71	1	0	0	0	0	1	0	0	0	4606	884	31	1	13164	1	DNAH5	5	13917343	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	6207944	13917343	166997917	28	9115										
PJA2	9867	hgsc.bcm.edu	37	chr5	108714271	108714271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cctgttcaggagaacttccaTggttcttttccctatcattg	7	11	3	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr5:108714271T>C	ENST00000361189.2	-	4	1156	c.917A>G	c.(916-918)cAt>cGt	p.H306R	PJA2_ENST00000361557.3_Missense_Mutation_p.H306R|PJA2_ENST00000511624.1_5'Flank	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	306					long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		AGAACTTCCATGGTTCTTTTC	0.433																																					p.H306R		Atlas-SNP	.											.	PJA2	53	.	0			c.A917G						.						160	164	163					5																	108714271		2202	4300	6502	SO:0001583	missense	9867	exon4			CTTCCATGGTTCT	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"RING-type (C3HC4) zinc fingers"	17481	protein-coding gene	gene with protein product			"ring finger protein 131", "praja ring finger 2"	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.917A>G	chr5.hg19:g.108714271T>C	ENSP00000354775:p.His306Arg	90.0	0.0		86.0	18.0	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	hg19	CCDS4099.1	.	.	.	.	.	.	.	.	.	.	T	2.825	-0.243940	0.05906	.	.	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.05199	3.48;3.48	5.61	-2.87	0.05700	.	0.708561	0.13642	N	0.372925	T	0.03178	0.0093	N	0.14661	0.345	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.38585	-0.9654	10	0.41790	T	0.15	10.0301	6.0681	0.19873	0.1113:0.318:0.0:0.5708	.	306	O43164	PJA2_HUMAN	R	306	ENSP00000354775:H306R;ENSP00000355284:H306R	ENSP00000354775:H306R	H	-	2	0	PJA2	108742170	0.959000	0.32827	0.021000	0.16686	0.520000	0.34377	0.478000	0.22212	-0.291000	0.09012	-0.250000	0.11733	CAT	.	.		0.433	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819		C	108714271	T	C	108714271	3	2	71	1	0	0	0	0	1	0	0	0	11971	1464	51	2	1237	2	PJA2	5	108714271	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	94796928	108714271	72200989	29	9116										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140433011	140433011	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	caggatcacggccaaccagcTctttccactactgtctcact	6	16	3	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr5:140433011T>A	ENST00000306549.3	+	1	2033	c.1956T>A	c.(1954-1956)gcT>gcA	p.A652A		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	652	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCCAACCAGCTCTTTCCACTA	0.443																																					p.A652A		Atlas-SNP	.											.	PCDHB1	148	.	0			c.T1956A						.						142	138	139					5																	140433011		2203	4300	6503	SO:0001819	synonymous_variant	29930	exon1			ACCAGCTCTTTCC	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1956T>A	chr5.hg19:g.140433011T>A		108.0	0.0		81.0	33.0	NM_013340	Q2M257	Silent	SNP	ENST00000306549.3	hg19	CCDS4243.1																																																																																			.	.		0.443	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		A	140433011	T	A	140433011	2	1	71	1	0	0	0	0	0	0	0	1	11543	1538	54	4		4	PCDHB1	5	140433011	Silent	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	31718740	140433011	40482249	30	9117										
IRF4	3662	hgsc.bcm.edu	37	chr6	393203	393203	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gagttcggcatgagcgcggtGagctgcggcaacgggaagct	18	9	0	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr6:393203G>A	ENST00000380956.4	+	2	177	c.51G>A	c.(49-51)gtG>gtA	p.V17V	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	17					cytokine-mediated signaling pathway (GO:0019221)|defense response to protozoan (GO:0042832)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of DNA binding (GO:0043388)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of interleukin-13 biosynthetic process (GO:0045368)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of T-helper cell differentiation (GO:0045622)|T cell activation (GO:0042110)|T-helper 17 cell lineage commitment (GO:0072540)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear nucleosome (GO:0000788)|nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		TGAGCGCGGTGAGCTGCGGCA	0.706			T	IGH@	MM																																p.V17V		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.G51A						.						28	31	30					6																	393203		2179	4255	6434	SO:0001819	synonymous_variant	3662	exon2			CGCGGTGAGCTGC	U52682	CCDS4469.1	6p25-p23	2008-08-29			ENSG00000137265	ENSG00000137265			6119	protein-coding gene	gene with protein product		601900		MUM1		8921401, 18417578	Standard	NM_002460		Approved	LSIRF	uc003msz.4	Q15306	OTTHUMG00000016294	ENST00000380956.4:c.51G>A	chr6.hg19:g.393203G>A		134.0	0.0		123.0	51.0	NM_001195286	Q5VUI7|Q99660	Silent	SNP	ENST00000380956.4	hg19	CCDS4469.1																																																																																			.	.		0.706	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			A	393203	G	A	393203	2	1	71	1	0	0	0	0	0	0	0	1	7841	1277	45	3		3	IRF4	6	393203	Silent	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10		393203	170721864	31	9118										
AGER	177	hgsc.bcm.edu	37	chr6	32149151	32149151	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tcctctcctcggcgttgccgCctttgccacaagatgacccc	8	18	1	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr6:32149151C>T	ENST00000375076.4	-	10	1196	c.1095G>A	c.(1093-1095)agG>agA	p.R365R	AGER_ENST00000375069.3_Silent_p.R255R|AGER_ENST00000375067.3_Missense_Mutation_p.A314T|AGER_ENST00000375055.2_Intron|AGER_ENST00000438221.2_Intron|AGER_ENST00000375070.3_Silent_p.R396R|AGER_ENST00000375065.5_3'UTR|RNF5_ENST00000427134.2_Intron	NM_001136.4|NM_001206929.1|NM_001206932.1	NP_001127.1|NP_001193858.1|NP_001193861.1	Q15109	RAGE_HUMAN	advanced glycosylation end product-specific receptor	365					cell surface receptor signaling pathway (GO:0007166)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|neuron projection development (GO:0031175)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|response to wounding (GO:0009611)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|receptor activity (GO:0004872)|S100 protein binding (GO:0044548)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(1)|lung(5)|pancreas(2)	9						GGCGTTGCCGCCTTTGCCACA	0.652																																					p.A314T		Atlas-SNP	.											.	AGER	15	.	0			c.G940A						.						158	174	169					6																	32149151		1511	2709	4220	SO:0001819	synonymous_variant	177	exon9			TTGCCGCCTTTGC	M91211	CCDS4746.1, CCDS4747.1, CCDS56417.1, CCDS56418.1, CCDS75429.1	6p21.3	2013-01-29			ENSG00000204305	ENSG00000204305		"Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	320	protein-coding gene	gene with protein product		600214				7713518	Standard	NM_001136		Approved	RAGE	uc003oap.2	Q15109	OTTHUMG00000031120	ENST00000375076.4:c.1095G>A	chr6.hg19:g.32149151C>T		55.0	0.0		57.0	21.0	NM_172197	A2BFI7|A6NKF0|A7Y2U9|B0V176|Q15279|Q3L1R4|Q3L1R5|Q3L1R6|Q3L1R7|Q3L1R8|Q3L1S0|Q86SN1|Q9H2X7|Q9Y3R3|V5R6A3	Missense_Mutation	SNP	ENST00000375076.4	hg19	CCDS4746.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631693	0.46944	.	.	ENSG00000204305	ENST00000375067	D	0.85411	-1.98	5.29	1.23	0.21249	.	.	.	.	.	T	0.46927	0.1418	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39981	-0.9587	8	0.10377	T	0.69	-17.6448	7.408	0.27001	0.0:0.5571:0.0:0.4429	.	314	Q15109-2	.	T	314	ENSP00000364208:A314T	ENSP00000364208:A314T	A	-	1	0	AGER	32257129	0.348000	0.24861	0.010000	0.14722	0.317000	0.28152	0.476000	0.22180	0.330000	0.23485	0.551000	0.68910	GCG	.	.		0.652	AGER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076200.1	NM_001136		T	32149151	C	T	32149151	2	4	71	1	0	0	0	0	0	0	0	1	379	739	26	3		3	AGER	6	32149151	Silent	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	31755948	32149151	138965916	32	9119										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38858481	38858481	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gaagtttcaagcctcaaataTgtgagatgattgtgaattta	9	4	2	3			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr6:38858481T>C	ENST00000359357.3	+	56	8130	c.7876T>C	c.(7876-7878)Tgt>Cgt	p.C2626R	DNAH8_ENST00000449981.2_Missense_Mutation_p.C2843R|DNAH8_ENST00000441566.1_Missense_Mutation_p.C2590R			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2626	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GCCTCAAATATGTGAGATGAT	0.348																																					p.C2843R		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T8527C						.						192	185	187					6																	38858481		2203	4300	6503	SO:0001583	missense	1769	exon58			CAAATATGTGAGA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.7876T>C	chr6.hg19:g.38858481T>C	ENSP00000352312:p.Cys2626Arg	87.0	0.0		62.0	30.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	T	1.434	-0.569383	0.03910	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.33438	1.41;1.41;1.41	6.17	3.67	0.42095	.	0.252701	0.45126	N	0.000398	T	0.03739	0.0106	N	0.01779	-0.725	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.30179	-0.9987	10	0.12103	T	0.63	.	10.5834	0.45269	0.2561:0.0:0.0:0.7439	.	2626	Q96JB1	DYH8_HUMAN	R	2831;2831;2626;2590	ENSP00000333363:C2831R;ENSP00000352312:C2626R;ENSP00000402294:C2590R	ENSP00000333363:C2831R	C	+	1	0	DNAH8	38966459	1.000000	0.71417	0.999000	0.59377	0.657000	0.38888	3.236000	0.51336	1.126000	0.42016	0.533000	0.62120	TGT	.	.		0.348	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		C	38858481	T	C	38858481	3	2	71	1	0	0	0	0	1	0	0	0	4609	1464	51	2	8090	2	DNAH8	6	38858481	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	6709330	38858481	132256586	33	9120										
MAP7	9053	hgsc.bcm.edu	37	chr6	136704840	136704840	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gaatttagtaaagttgcagaTgaagaggagagccgcttgct	13	5	0	4			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr6:136704840T>A	ENST00000354570.3	-	6	1016	c.606A>T	c.(604-606)tcA>tcT	p.S202S	MAP7_ENST00000432797.2_Silent_p.S56S|MAP7_ENST00000454590.1_Silent_p.S224S|MAP7_ENST00000544465.1_Silent_p.S187S|MAP7_ENST00000438100.2_Intron	NM_001198616.1|NM_001198617.1|NM_001198619.1|NM_003980.4	NP_001185545.1|NP_001185546.1|NP_001185548.1|NP_003971.1	Q14244	MAP7_HUMAN	microtubule-associated protein 7	202					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|establishment or maintenance of cell polarity (GO:0007163)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells (GO:0048872)|Leydig cell differentiation (GO:0033327)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nucleus organization (GO:0006997)|organ growth (GO:0035265)|protein localization to plasma membrane (GO:0072659)|response to osmotic stress (GO:0006970)|response to retinoic acid (GO:0032526)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(11)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		AAGTTGCAGATGAAGAGGAGA	0.378																																					p.S224S		Atlas-SNP	.											.	MAP7	63	.	0			c.A672T						.						112	109	110					6																	136704840		2203	4300	6503	SO:0001819	synonymous_variant	9053	exon6			TGCAGATGAAGAG	X73882	CCDS5178.1, CCDS56452.1, CCDS56453.1, CCDS56454.1, CCDS56455.1, CCDS75527.1, CCDS75528.1, CCDS75529.1	6q23.2	2008-07-28			ENSG00000135525	ENSG00000135525			6869	protein-coding gene	gene with protein product		604108				8408219	Standard	NM_003980		Approved	E-MAP-115	uc011edg.2	Q14244	OTTHUMG00000015646	ENST00000354570.3:c.606A>T	chr6.hg19:g.136704840T>A		84.0	0.0		46.0	35.0	NM_001198609	B7Z290|B7Z400|B7Z5S7|B7Z9U7|C9JPS0|E9PCP3|F5H1E2|Q7Z6S0|Q8TAU5|Q9NY82|Q9NY83	Silent	SNP	ENST00000354570.3	hg19	CCDS5178.1																																																																																			.	.		0.378	MAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042382.2	NM_003980		A	136704840	T	A	136704840	2	1	71	1	0	0	0	0	0	0	0	1	9275	1451	51	4		4	MAP7	6	136704840	Silent	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	97846359	136704840	34410227	34	9121										
FBXL18	80028	hgsc.bcm.edu	37	chr7	5541166	5541166	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ccaggtagagccgcaccaccTcctggttgatgtagccgggg	14	13	0	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr7:5541166T>A	ENST00000382368.3	-	3	857	c.734A>T	c.(733-735)gAg>gTg	p.E245V	FBXL18_ENST00000453700.3_Missense_Mutation_p.E245V	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	245									FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		CCGCACCACCTCCTGGTTGAT	0.652																																					p.E245V		Atlas-SNP	.											.	FBXL18	99	.	0			c.A734T						.						31	38	36					7																	5541166		2085	4193	6278	SO:0001583	missense	80028	exon3			ACCACCTCCTGGT	AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"F-boxes / Leucine-rich repeats"	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.734A>T	chr7.hg19:g.5541166T>A	ENSP00000371805:p.Glu245Val	87.0	0.0		70.0	33.0	NM_024963	Q9BR90|Q9BTC7|Q9HAK7	Missense_Mutation	SNP	ENST00000382368.3	hg19	CCDS43546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.19|17.19	3.326978|3.326978	0.60743|0.60743	.|.	.|.	ENSG00000155034|ENSG00000155034	ENST00000382368;ENST00000312577;ENST00000453700|ENST00000458142	T;T|.	0.52057|.	0.71;0.68|.	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	0.103999|.	0.64402|.	D|.	0.000004|.	T|T	0.51873|0.51873	0.1700|0.1700	N|N	0.24115|0.24115	0.695|0.695	0.43777|0.43777	D|D	0.9963|0.9963	D;D|.	0.63880|.	0.993;0.985|.	P;P|.	0.56343|.	0.796;0.677|.	T|T	0.49113|0.49113	-0.8973|-0.8973	10|5	0.56958|.	D|.	0.05|.	.|.	14.6055|14.6055	0.68475|0.68475	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	245;245|.	F5H4Z4;Q96ME1-4|.	.;.|.	V|W	245|129	ENSP00000371805:E245V;ENSP00000444797:E245V|.	ENSP00000311990:E245V|.	E|R	-|-	2|1	0|2	FBXL18|FBXL18	5507692|5507692	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	6.240000|6.240000	0.72363|0.72363	2.044000|2.044000	0.60594|0.60594	0.533000|0.533000	0.62120|0.62120	GAG|AGG	.	.		0.652	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963		A	5541166	T	A	5541166	3	1	71	1	0	0	0	0	1	0	0	0	5722	1551	54	4	1434	4	FBXL18	7	5541166	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10		5541166	153597497	35	9122										
C7orf70	84792	hgsc.bcm.edu	37	chr7	6370320	6370355	+	In_Frame_Del	DEL	GCAGTCGTGACACCCGAGGCTCTCCTTTGGGGCACT	GCAGTCGTGACACCCGAGGCTCTCCTTTGGGGCACT	-													0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cggcactttttgatggcgtgGcagtcgtgacacccgaggct					rs138213138|rs368468737|rs75910050|rs374494633	byFrequency	TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	GCAGTCGTGACACCCGAGGCTCTCCTTTGGGGCACT	GCAGTCGTGACACCCGAGGCTCTCCTTTGGGGCACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr7:6370320_6370355delGCAGTCGTGACACCCGAGGCTCTCCTTTGGGGCACT	ENST00000313324.4	-	2	898_933	c.431_466delAGTGCCCCAAAGGAGAGCCTCGGGTGTCACGACTGC	c.(430-468)cagtgccccaaaggagagcctcgggtgtcacgactgcca>cca	p.QCPKGEPRVSRL144del	FAM220A_ENST00000533877.1_5'Flank	NM_001037163.1	NP_001032240.1	Q7Z4H9	F220A_HUMAN	family with sequence similarity 220, member A	144						nucleus (GO:0005634)		p.C145C(1)|p.P150H(1)									TGATGGCGTGGCAGTCGTGACACCCGAGGCTCTCCTTTGGGGCACTGTCCTCTGTG	0.602																																					p.144_156del		Pindel	.											.	.	.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	ovary(1)|lung(1)	c.432_467del						.																																			SO:0001651	inframe_deletion	84792	exon2			.	BC006110	CCDS34599.1	7p22.1	2012-03-19	2012-03-19	2012-03-19	ENSG00000178397	ENSG00000178397			22422	protein-coding gene	gene with protein product	"STAT3-interacting protein as a repressor"		"chromosome 7 open reading frame 70"	C7orf70			Standard	NM_001037163		Approved	SIPAR, MGC12966	uc003spu.3	Q7Z4H9	OTTHUMG00000122091	ENST00000313324.4:c.431_466delAGTGCCCCAAAGGAGAGCCTCGGGTGTCACGACTGC	chr7.hg19:g.6370320_6370355delGCAGTCGTGACACCCGAGGCTCTCCTTTGGGGCACT	ENSP00000317289:p.Gln144_Leu155del	98.0	0.0		42.0	12.0	NM_001037163	Q75ML2|Q8NA52|Q9BRR7	In_Frame_Del	DEL	ENST00000313324.4	hg19	CCDS34599.1																																																																																			.	.		0.602	FAM220A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000242853.2	NM_001037163		-	6370355	GCAGTCGTGACACCCGAGGCTCTCCTTTGGGGCACT	-	6370320	7	5	71	1	0	1	0	1	0	0	0	0	2417	1203	42	0	317	0	C7orf70	7	6370320	In_Frame_Del	DEL	GCAGTCGTGACACCCGAGGCTCTCCTTTGGGGCACT	TCGA-CC-A7IF-01A-11D-A33K-10	829154	6370320	152768343	36	9123										
ZNF680	340252	hgsc.bcm.edu	37	chr7	63982871	63982872	+	Frame_Shift_Del	DEL	AT	AT	-													0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	aggtcttcagtgaaatgagaAtatataactgaaagacataa							TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr7:63982871_63982872delAT	ENST00000309683.6	-	4	411_412	c.260_261delAT	c.(259-261)tatfs	p.Y87fs	ZNF680_ENST00000476563.1_5'UTR	NM_178558.4	NP_848653.2	Q8NEM1	ZN680_HUMAN	zinc finger protein 680	87					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	27		Lung NSC(55;0.118)|all_lung(88;0.243)				TGAAATGAGAATATATAACTGA	0.292																																					p.87_88del		Atlas-Indel,Pindel	.											.	ZNF680	58	.	0			c.261_262del						.																																			SO:0001589	frameshift_variant	340252	exon4			.	AK074911	CCDS34644.1, CCDS47594.1	7q11.21	2013-01-08			ENSG00000173041	ENSG00000173041		"Zinc fingers, C2H2-type", "-"	26897	protein-coding gene	gene with protein product	"hypothetical protein FLJ90430"					12477932	Standard	NM_178558		Approved	FLJ90430	uc003tta.2	Q8NEM1	OTTHUMG00000156542	ENST00000309683.6:c.260_261delAT	chr7.hg19:g.63982875_63982876delAT	ENSP00000309330:p.Tyr87fs	54.0	0.0		46.0	14.0	NM_178558	B3KVJ4|Q6ZNF3|Q8NC79	Frame_Shift_Del	DEL	ENST00000309683.6	hg19	CCDS34644.1																																																																																			.	.		0.292	ZNF680-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344568.1	NM_178558		-	63982872	AT	-	63982871	7	5	71	1	0	1	0	1	0	0	0	0	18102	108	4	0	1335	0	ZNF680	7	63982871	Frame_Shift_Del	DEL	AT	TCGA-CC-A7IF-01A-11D-A33K-10	57612551	63982871	95155792	37	9124										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98552830	98552830	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	caggatggaggacgggcaccAgatgctgacccactggaccc	14	13	0	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr7:98552830A>T	ENST00000359863.4	+	40	6028	c.5819A>T	c.(5818-5820)cAg>cTg	p.Q1940L	TRRAP_ENST00000446306.3_Missense_Mutation_p.Q1921L|TRRAP_ENST00000355540.3_Missense_Mutation_p.Q1922L	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1940					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GACGGGCACCAGATGCTGACC	0.612																																					p.Q1940L		Atlas-SNP	.											.	TRRAP	863	.	0			c.A5819T						.						52	45	48					7																	98552830		2203	4300	6503	SO:0001583	missense	8295	exon40			GGCACCAGATGCT	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.5819A>T	chr7.hg19:g.98552830A>T	ENSP00000352925:p.Gln1940Leu	83.0	0.0		69.0	35.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.43|18.43	3.622430|3.622430	0.66787|0.66787	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306|ENST00000456197	T;T|.	0.65916|.	-0.18;-0.18|.	5.56|5.56	4.41|4.41	0.53225|0.53225	.|.	0.060078|.	0.64402|.	D|.	0.000002|.	T|.	0.53948|.	0.1828|.	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	P;B;B|.	0.34743|.	0.466;0.242;0.392|.	B;B;B|.	0.31869|.	0.137;0.054;0.096|.	T|.	0.47381|.	-0.9122|.	10|.	0.27785|.	T|.	0.31|.	.|.	11.3043|11.3043	0.49325|0.49325	0.9289:0.0:0.0711:0.0|0.9289:0.0:0.0711:0.0	.|.	1922;1661;1940|.	Q9Y4A5-2;Q59FH1;Q9Y4A5|.	.;.;TRRAP_HUMAN|.	L|X	1940;1922;1920|1662	ENSP00000352925:Q1940L;ENSP00000347733:Q1922L|.	ENSP00000347733:Q1922L|.	Q|R	+|+	2|1	0|2	TRRAP|TRRAP	98390766|98390766	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	9.339000|9.339000	0.96797|0.96797	0.944000|0.944000	0.37579|0.37579	0.533000|0.533000	0.62120|0.62120	CAG|AGA	.	.		0.612	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		T	98552830	A	T	98552830	3	4	71	1	0	0	0	0	1	0	0	0	16616	188	7	4	5915	4	TRRAP	7	98552830	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	34569959	98552830	60585833	38	9125										
CYP3A5	1577	hgsc.bcm.edu	37	chr7	99270218	99270218	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cttacccttcgatttgtgaaGacagaataacattctttcac	5	10	2	3			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr7:99270218G>T	ENST00000222982.4	-	4	402	c.303C>A	c.(301-303)gtC>gtA	p.V101V	CYP3A5_ENST00000480723.1_5'UTR|CYP3A5_ENST00000343703.5_Silent_p.V91V|CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000439761.1_Silent_p.V101V	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	101					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GATTTGTGAAGACAGAATAAC	0.373																																					p.V101V		Atlas-SNP	.											.	CYP3A5	46	.	0			c.C303A						.						175	158	164					7																	99270218		2203	4300	6503	SO:0001819	synonymous_variant	1577	exon4			TGTGAAGACAGAA	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"Cytochrome P450s"	2638	protein-coding gene	gene with protein product		605325	"cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.303C>A	chr7.hg19:g.99270218G>T		149.0	0.0		131.0	48.0	NM_001190484	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Silent	SNP	ENST00000222982.4	hg19	CCDS5672.1																																																																																			.	.		0.373	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1			T	99270218	G	T	99270218	2	4	71	1	0	0	0	0	0	0	0	1	4182	929	33	3		3	CYP3A5	7	99270218	Silent	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	717388	99270218	59868445	39	9126										
ZNF777	27153	hgsc.bcm.edu	37	chr7	149152414	149152414	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cacgacccacttgctctccaGatggttcgcgaactccacgg	9	16	1	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr7:149152414G>T	ENST00000247930.4	-	2	1023	c.700C>A	c.(700-702)Ctg>Atg	p.L234M		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			TTGCTCTCCAGATGGTTCGCG	0.567																																					p.L234M		Atlas-SNP	.											.	ZNF777	63	.	0			c.C700A						.						78	89	85					7																	149152414		2203	4300	6503	SO:0001583	missense	27153	exon2			TCTCCAGATGGTT	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"Zinc fingers, C2H2-type", "-"	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.700C>A	chr7.hg19:g.149152414G>T	ENSP00000247930:p.Leu234Met	73.0	0.0		66.0	26.0	NM_015694	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	hg19	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.835354	0.50951	.	.	ENSG00000196453	ENST00000247930	T	0.28255	1.62	4.93	2.15	0.27550	.	0.000000	0.34932	N	0.003570	T	0.37972	0.1023	L	0.35542	1.07	0.26908	N	0.966969	D	0.76494	0.999	D	0.85130	0.997	T	0.08576	-1.0715	10	0.72032	D	0.01	-15.6501	6.3893	0.21577	0.3015:0.0:0.6985:0.0	.	234	Q9ULD5-2	.	M	234	ENSP00000247930:L234M	ENSP00000247930:L234M	L	-	1	2	ZNF777	148783347	0.986000	0.35501	0.950000	0.38849	0.966000	0.64601	1.844000	0.39269	0.503000	0.28060	-0.137000	0.14449	CTG	.	.		0.567	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694		T	149152414	G	T	149152414	3	4	71	1	0	0	0	0	1	0	0	0	18165	933	33	3	1815	3	ZNF777	7	149152414	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	49882196	149152414	9986249	40	9127										
GIMAP1	170575	hgsc.bcm.edu	37	chr7	150416151	150416151	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	taagcatgggaggaaggaagAtggcgacagatgaagaaaat	15	3	0	4			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr7:150416151A>C	ENST00000307194.5	+	2	156	c.16A>C	c.(16-18)Atg>Ctg	p.M6L		NM_130759.3	NP_570115.1	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	6					B cell differentiation (GO:0030183)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGGAAGGAAGATGGCGACAGA	0.413																																					p.M6L		Atlas-SNP	.											.	.	.	.	0			c.A16C						.						158	138	145					7																	150416151		2203	4300	6503	SO:0001583	missense	0	exon2			AGGAAGATGGCGA	AJ306287	CCDS5906.1	7q36.1	2014-04-04			ENSG00000213203	ENSG00000213203		"GTPases, IMAP"	23237	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 2"	608084				15474311, 18701445	Standard	NM_130759		Approved	HIMAP1, IMAP38, IMAP1, IAN2		Q8WWP7	OTTHUMG00000157489	ENST00000307194.5:c.16A>C	chr7.hg19:g.150416151A>C	ENSP00000302833:p.Met6Leu	73.0	0.0		50.0	23.0	NM_001199577	B2RCI3|Q8NAZ0	Missense_Mutation	SNP	ENST00000307194.5	hg19	CCDS5906.1	.	.	.	.	.	.	.	.	.	.	A	8.044	0.764579	0.15914	.	.	ENSG00000213203	ENST00000307194	T	0.04360	3.64	4.42	2.08	0.27032	.	105.238000	0.00741	U	0.001014	T	0.02455	0.0075	N	0.03608	-0.345	0.09310	N	0.999999	B	0.31485	0.325	B	0.21917	0.037	T	0.32903	-0.9889	10	0.23891	T	0.37	.	5.3634	0.16101	0.7725:0.0:0.2275:0.0	.	6	Q8WWP7	GIMA1_HUMAN	L	6	ENSP00000302833:M6L	ENSP00000302833:M6L	M	+	1	0	GIMAP1	150047084	0.014000	0.17966	0.516000	0.27786	0.112000	0.19704	0.054000	0.14205	0.846000	0.35142	0.533000	0.62120	ATG	.	.		0.413	GIMAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348951.2	NM_130759		C	150416151	A	C	150416151	3	2	71	1	0	0	0	0	1	0	0	0	6387	333	12	5	18	5	GIMAP1	7	150416151	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	1263737	150416151	8722512	41	9128										
HTR5A	3361	hgsc.bcm.edu	37	chr7	154862937	154862937	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ccgggcgccgctggcagctaGgtcggaggctgtgccagctt	17	13	0	0	rs141719500		TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr7:154862937G>T	ENST00000287907.2	+	1	904	c.328G>T	c.(328-330)Ggt>Tgt	p.G110C	HTR5A-AS1_ENST00000395731.2_Missense_Mutation_p.P26H|HTR5A-AS1_ENST00000493904.1_5'UTR|HTR5A-AS1_ENST00000543018.1_Missense_Mutation_p.P26H	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	110					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	CTGGCAGCTAGGTCGGAGGCT	0.662																																					p.G110C		Atlas-SNP	.											HTR5A,NS,carcinoma,0,1	HTR5A	114	.	0			c.G328T						.						50	42	45					7																	154862937		2203	4300	6503	SO:0001583	missense	3361	exon1			CAGCTAGGTCGGA		CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5300	protein-coding gene	gene with protein product		601305	"5-hydroxytryptamine (serotonin) receptor 5A"			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.328G>T	chr7.hg19:g.154862937G>T	ENSP00000287907:p.Gly110Cys	26.0	0.0		14.0	6.0	NM_024012	Q2M2D2	Missense_Mutation	SNP	ENST00000287907.2	hg19	CCDS5936.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.3|24.3	4.516282|4.516282	0.85495|0.85495	.|.	.|.	ENSG00000157219|ENSG00000220575	ENST00000287907|ENST00000395731;ENST00000543018	T|.	0.51325|.	0.71|.	4.52|4.52	4.52|4.52	0.55395|0.55395	GPCR, rhodopsin-like superfamily (1);|.	0.052450|.	0.85682|.	D|.	0.000000|.	D|D	0.90494|0.90494	0.7022|0.7022	H|H	0.98682|0.98682	4.3|4.3	0.80722|0.80722	D|D	1|1	D|D	0.89917|0.89917	1.0|1.0	D|D	0.97110|0.97110	1.0|1.0	D|D	0.94453|0.94453	0.7669|0.7669	10|8	0.87932|0.87932	D|D	0|0	.|.	17.4477|17.4477	0.87583|0.87583	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	110|26	P47898|B7Z8E6	5HT5A_HUMAN|.	C|H	110|26	ENSP00000287907:G110C|.	ENSP00000287907:G110C|ENSP00000379080:P26H	G|P	+|-	1|2	0|0	HTR5A|AC093726.4	154493870|154493870	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.824000|0.824000	0.46624|0.46624	9.228000|9.228000	0.95250|0.95250	2.338000|2.338000	0.79540|0.79540	0.563000|0.563000	0.77884|0.77884	GGT|CCT	.	G|1.000;C|0.000		0.662	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012		T	154862937	G	T	154862937	3	4	71	1	0	0	0	0	1	0	0	0	7459	1000	35	3	330	3	HTR5A	7	154862937	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	4446786	154862937	4275726	42	9129										
IMPAD1	54928	hgsc.bcm.edu	37	chr8	57892756	57892756	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cacgtgttcctcagtattaaTctgcattaaaaacaggtgac	7	9	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr8:57892756T>C	ENST00000262644.4	-	2	646	c.388A>G	c.(388-390)Att>Gtt	p.I130V		NM_017813.4	NP_060283.3	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	130					chondrocyte development (GO:0002063)|chondroitin sulfate metabolic process (GO:0030204)|embryonic digit morphogenesis (GO:0042733)|endochondral ossification (GO:0001958)|inositol biosynthetic process (GO:0006021)|phosphatidylinositol phosphorylation (GO:0046854)|post-embryonic development (GO:0009791)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|3'-nucleotidase activity (GO:0008254)|inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)				TCAGTATTAATCTGCATTAAA	0.343																																					p.I130V		Atlas-SNP	.											.	IMPAD1	27	.	0			c.A388G						.						72	63	66					8																	57892756		2203	4300	6503	SO:0001630	splice_region_variant	54928	exon2			TATTAATCTGCAT		CCDS6169.1	8q12.1	2013-05-16			ENSG00000104331	ENSG00000104331			26019	protein-coding gene	gene with protein product		614010				21549340	Standard	NM_017813		Approved	FLJ20421, IMPA3, gPAPP	uc003xte.4	Q9NX62	OTTHUMG00000164415	ENST00000262644.4:c.388-1A>G	chr8.hg19:g.57892756T>C		96.0	0.0		66.0	38.0	NM_017813	Q6NVY7	Missense_Mutation	SNP	ENST00000262644.4	hg19	CCDS6169.1	.	.	.	.	.	.	.	.	.	.	T	2.671	-0.277570	0.05679	.	.	ENSG00000104331	ENST00000262644;ENST00000517461	T;T	0.53206	0.63;0.91	5.66	5.66	0.87406	.	0.052331	0.85682	D	0.000000	T	0.22781	0.0550	N	0.05554	-0.025	0.53688	D	0.999977	B	0.11235	0.004	B	0.10450	0.005	T	0.15321	-1.0441	10	0.02654	T	1	0.0174	9.5556	0.39337	0.0:0.0779:0.0:0.9221	.	130	Q9NX62	IMPA3_HUMAN	V	130;55	ENSP00000262644:I130V;ENSP00000430185:I55V	ENSP00000262644:I130V	I	-	1	0	IMPAD1	58055310	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	4.712000	0.61888	2.152000	0.67230	0.528000	0.53228	ATT	.	.		0.343	IMPAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378665.1	NM_017813	Missense_Mutation	C	57892756	T	C	57892756	5	2	71	1	0	0	0	0	0	0	1	0	7734	1449	50	2	707	2	IMPAD1	8	57892756	Splice_Site	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10		57892756	88471266	43	9130										
TMEM74	157753	hgsc.bcm.edu	37	chr8	109796877	109796877	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	agatatcaaagatatggcagCctcttgggaccactcatttg	9	9	3	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr8:109796877C>A	ENST00000297459.3	-	2	629	c.451G>T	c.(451-453)Gct>Tct	p.A151S	TMEM74_ENST00000518838.1_Intron	NM_153015.1	NP_694560.1	Q96NL1	TMM74_HUMAN	transmembrane protein 74	151					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)			GATATGGCAGCCTCTTGGGAC	0.493																																					p.A151S		Atlas-SNP	.											.	TMEM74	70	.	0			c.G451T						.						83	87	86					8																	109796877		2203	4300	6503	SO:0001583	missense	157753	exon2			TGGCAGCCTCTTG	AK055230	CCDS6310.1	8q23.1	2009-11-06				ENSG00000164841			26409	protein-coding gene	gene with protein product		613935				12477932	Standard	NM_153015		Approved	FLJ30668, NET36	uc003ymy.1	Q96NL1		ENST00000297459.3:c.451G>T	chr8.hg19:g.109796877C>A	ENSP00000297459:p.Ala151Ser	143.0	0.0		240.0	114.0	NM_153015		Missense_Mutation	SNP	ENST00000297459.3	hg19	CCDS6310.1	.	.	.	.	.	.	.	.	.	.	C	6.360	0.434450	0.12045	.	.	ENSG00000164841	ENST00000297459	.	.	.	5.96	2.03	0.26663	.	0.457774	0.23573	N	0.046724	T	0.15392	0.0371	N	0.16478	0.41	0.19300	N	0.999978	B	0.18310	0.027	B	0.15052	0.012	T	0.20874	-1.0262	9	0.10902	T	0.67	-3.8437	2.2102	0.03945	0.3511:0.3112:0.2091:0.1285	.	151	Q96NL1	TMM74_HUMAN	S	151	.	ENSP00000297459:A151S	A	-	1	0	TMEM74	109866053	0.195000	0.23338	0.758000	0.31321	0.995000	0.86356	0.114000	0.15520	0.088000	0.17205	0.655000	0.94253	GCT	.	.		0.493	TMEM74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380755.1	NM_153015		A	109796877	C	A	109796877	3	1	71	1	0	0	0	0	1	0	0	0	16217	739	26	3	470	3	TMEM74	8	109796877	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	51904121	109796877	36567145	44	9131										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113418769	113418769	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tcaccaatacaagtaggtaaGgaatcattccactgggccaa	8	10	2	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr8:113418769G>T	ENST00000297405.5	-	35	6037	c.5793C>A	c.(5791-5793)tcC>tcA	p.S1931S	CSMD3_ENST00000352409.3_Silent_p.S1861S|CSMD3_ENST00000343508.3_Silent_p.S1891S|CSMD3_ENST00000455883.2_Silent_p.S1827S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1931	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S1931S(1)|p.S1891S(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAGTAGGTAAGGAATCATTCC	0.318										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S1931S		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,0,1	CSMD3	2325	.	2	Substitution - coding silent(2)	endometrium(2)	c.C5793A						.						81	82	81					8																	113418769		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon35			AGGTAAGGAATCA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.5793C>A	chr8.hg19:g.113418769G>T		170.0	0.0		222.0	85.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.318	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113418769	G	T	113418769	2	4	71	1	0	0	0	0	0	0	0	1	3948	987	35	3		3	CSMD3	8	113418769	Silent	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	3621892	113418769	32945253	45	9132										
MRPL13	28998	hgsc.bcm.edu	37	chr8	121444294	121444294	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tatgcgaagagtatacttttTgttcccatttgtttccagaa	7	7	0	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr8:121444294T>C	ENST00000306185.3	-	3	512	c.221A>G	c.(220-222)cAa>cGa	p.Q74R		NM_014078.5	NP_054797.2	Q9BYD1	RM13_HUMAN	mitochondrial ribosomal protein L13	74					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	6	Lung NSC(37;1.69e-07)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			GTATACTTTTTGTTCCCATTT	0.308																																					p.Q74R		Atlas-SNP	.											.	MRPL13	18	.	0			c.A221G						.						123	118	119					8																	121444294		2203	4295	6498	SO:0001583	missense	28998	exon3			ACTTTTTGTTCCC	AB049640	CCDS6332.1	8q22.1-q22.3	2012-09-13			ENSG00000172172	ENSG00000172172		"Mitochondrial ribosomal proteins / large subunits"	14278	protein-coding gene	gene with protein product		610200				11543634	Standard	NM_014078		Approved	L13, RPL13, L13mt, RPML13, L13A	uc003ypa.3	Q9BYD1	OTTHUMG00000165039	ENST00000306185.3:c.221A>G	chr8.hg19:g.121444294T>C	ENSP00000306548:p.Gln74Arg	138.0	0.0		207.0	21.0	NM_014078	B2R4R8|Q9UI04	Missense_Mutation	SNP	ENST00000306185.3	hg19	CCDS6332.1	.	.	.	.	.	.	.	.	.	.	T	13.33	2.204137	0.38905	.	.	ENSG00000172172	ENST00000306185;ENST00000518918	.	.	.	6.05	6.05	0.98169	Ribosomal protein L13 domain (2);	0.052647	0.85682	D	0.000000	T	0.67720	0.2923	M	0.67953	2.075	0.80722	D	1	P	0.38922	0.651	P	0.45428	0.48	T	0.65364	-0.6186	9	0.30078	T	0.28	-1.5778	15.5839	0.76468	0.0:0.0:0.0:1.0	.	74	Q9BYD1	RM13_HUMAN	R	74;50	.	ENSP00000306548:Q74R	Q	-	2	0	MRPL13	121513475	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.293000	0.78740	2.323000	0.78572	0.467000	0.42956	CAA	.	.		0.308	MRPL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381523.1	NM_014078		C	121444294	T	C	121444294	3	2	71	1	0	0	0	0	1	0	0	0	9787	1812	63	2	335	2	MRPL13	8	121444294	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	8025525	121444294	24919728	46	9133										
KDM4C	23081	hgsc.bcm.edu	37	chr9	6986628	6986628	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	aacctggggaaatcccagcgGtccccagtggagagagaaat	13	10	0	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr9:6986628G>C	ENST00000381309.3	+	11	2204	c.1639G>C	c.(1639-1641)Gtc>Ctc	p.V547L	KDM4C_ENST00000535193.1_Missense_Mutation_p.V569L|KDM4C_ENST00000543771.1_Missense_Mutation_p.V547L|KDM4C_ENST00000536108.1_Missense_Mutation_p.V366L|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.V547L|KDM4C_ENST00000428870.2_Missense_Mutation_p.V234L	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	547					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						AATCCCAGCGGTCCCCAGTGG	0.453																																					p.V569L		Atlas-SNP	.											.	KDM4C	186	.	0			c.G1705C						.						59	55	56					9																	6986628		2203	4300	6503	SO:0001583	missense	23081	exon11			CCAGCGGTCCCCA	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	17071	protein-coding gene	gene with protein product	"tudor domain containing 14C"	605469	"jumonji domain containing 2C"	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.1639G>C	chr9.hg19:g.6986628G>C	ENSP00000370710:p.Val547Leu	100.0	0.0		61.0	11.0	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	hg19	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	G	2.403	-0.337167	0.05278	.	.	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000536108;ENST00000428870	T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9	5.3	0.0488	0.14286	.	3.220070	0.00589	N	0.000340	T	0.34571	0.0902	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.22146	0.065;0.065;0.007;0.006	B;B;B;B	0.24269	0.032;0.052;0.003;0.007	T	0.10268	-1.0637	10	0.23891	T	0.37	4.0028	5.9871	0.19440	0.4136:0.0:0.4688:0.1176	.	547;569;547;547	F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;KDM4C_HUMAN;.	L	569;547;547;547;366;234	ENSP00000442382:V569L;ENSP00000445427:V547L;ENSP00000370710:V547L;ENSP00000370707:V547L;ENSP00000440656:V366L;ENSP00000405739:V234L	ENSP00000370707:V547L	V	+	1	0	KDM4C	6976628	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	0.001000	0.13038	0.065000	0.16485	-0.895000	0.02911	GTC	.	.		0.453	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		C	6986628	G	C	6986628	3	2	71	1	0	0	0	0	1	0	0	0	8139	1261	44	4	1747	4	KDM4C	9	6986628	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10		6986628	134226803	47	9134										
FREM1	158326	hgsc.bcm.edu	37	chr9	14816776	14816776	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ggaagaaactttctacccacCtcaacatgtagtacaaattc	5	11	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr9:14816776C>A	ENST00000380880.3	-	15	3423	c.2640G>T	c.(2638-2640)gaG>gaT	p.E880D	FREM1_ENST00000380881.4_Splice_Site_p.E881D|FREM1_ENST00000422223.2_Splice_Site_p.E880D			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	880					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TTCTACCCACCTCAACATGTA	0.398																																					p.E880D		Atlas-SNP	.											.	FREM1	261	.	0			c.G2640T						.						47	49	48					9																	14816776		1844	4090	5934	SO:0001630	splice_region_variant	158326	exon16			ACCCACCTCAACA	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.2640+1G>T	chr9.hg19:g.14816776C>A		63.0	0.0		40.0	25.0	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	hg19	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.907761	0.33721	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.29655	1.56;1.56;1.56	5.65	4.75	0.60458	.	0.293619	0.42053	D	0.000765	T	0.22475	0.0542	L	0.28694	0.88	0.31559	N	0.6578	B	0.32051	0.354	B	0.34301	0.179	T	0.20672	-1.0268	9	.	.	.	-11.5591	10.3539	0.43952	0.0:0.9128:0.0:0.0872	.	880	Q5H8C1	FREM1_HUMAN	D	881;880;880	ENSP00000370263:E881D;ENSP00000412940:E880D;ENSP00000370262:E880D	.	E	-	3	2	FREM1	14806776	1.000000	0.71417	0.996000	0.52242	0.177000	0.22998	4.992000	0.63889	1.636000	0.50526	-0.136000	0.14681	GAG	.	.		0.398	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	Missense_Mutation	A	14816776	C	A	14816776	5	1	71	1	0	0	0	0	0	0	1	0	6052	695	24	3	4041	3	FREM1	9	14816776	Splice_Site	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	7830148	14816776	126396655	48	9135										
GNE	10020	hgsc.bcm.edu	37	chr9	36246477	36246477	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gttcaatcattcgatatgtaTttctaaagccggggagaaat	9	6	3	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr9:36246477T>C	ENST00000539815.1	-	2	207	c.167A>G	c.(166-168)aAt>aGt	p.N56S	GNE_ENST00000543356.2_Missense_Mutation_p.N51S|GNE_ENST00000396594.3_Missense_Mutation_p.N87S|GNE_ENST00000539208.1_5'UTR|GNE_ENST00000447283.2_Missense_Mutation_p.N56S|GNE_ENST00000377902.5_Missense_Mutation_p.N56S			Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	56					carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)			endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			TCGATATGTATTTCTAAAGCC	0.408																																					p.N87S	GBM(184;106 2118 20004 35750 50727)	Atlas-SNP	.											.	GNE	141	.	0			c.A260G						.						40	42	42					9																	36246477		2182	4222	6404	SO:0001583	missense	10020	exon3			TATGTATTTCTAA	AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921			23657	protein-coding gene	gene with protein product		603824	"UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase"	IBM2		9305887, 9305888	Standard	NM_005476		Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539815.1:c.167A>G	chr9.hg19:g.36246477T>C	ENSP00000439155:p.Asn56Ser	47.0	0.0		33.0	22.0	NM_001128227	A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	Missense_Mutation	SNP	ENST00000539815.1	hg19	CCDS6602.1	.	.	.	.	.	.	.	.	.	.	T	5.379	0.255115	0.10185	.	.	ENSG00000159921	ENST00000377902;ENST00000396594;ENST00000339267;ENST00000539815;ENST00000543356;ENST00000447283	D;D;D;D	0.98926	-5.24;-5.24;-5.24;-5.24	5.02	5.02	0.67125	.	0.041538	0.85682	D	0.000000	D	0.94387	0.8195	N	0.11106	0.095	0.80722	D	1	B;B;B;B	0.25563	0.007;0.049;0.009;0.129	B;B;B;B	0.23716	0.007;0.019;0.012;0.048	D	0.93002	0.6424	10	0.15066	T	0.55	-17.5327	12.9937	0.58634	0.0:0.0:0.0:1.0	.	15;87;56;56	Q9Y223-3;Q9Y223-2;Q9Y223;A7UNU7	.;.;GLCNE_HUMAN;.	S	56;87;51;56;28;56	ENSP00000367134:N56S;ENSP00000379839:N87S;ENSP00000439155:N56S;ENSP00000414760:N56S	ENSP00000340770:N51S	N	-	2	0	GNE	36236477	1.000000	0.71417	1.000000	0.80357	0.031000	0.12232	7.301000	0.78850	2.006000	0.58801	0.383000	0.25322	AAT	.	.		0.408	GNE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052412.4	NM_005476		C	36246477	T	C	36246477	3	2	71	1	0	0	0	0	1	0	0	0	6530	1493	52	2	2041	2	GNE	9	36246477	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	21429701	36246477	104966954	49	9136										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73442764	73442764	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gggaacaaccgctacttactTgtgtttatcttctggagtga	10	8	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr9:73442764T>A	ENST00000377111.2	-	6	1215	c.972A>T	c.(970-972)acA>acT	p.T324T	TRPM3_ENST00000361823.5_Splice_Site_p.T171T|TRPM3_ENST00000396285.1_Splice_Site_p.T171T|TRPM3_ENST00000423814.3_Splice_Site_p.T326T|TRPM3_ENST00000360823.2_Splice_Site_p.T171T|TRPM3_ENST00000357533.2_Splice_Site_p.T326T|TRPM3_ENST00000358082.3_Splice_Site_p.T171T|TRPM3_ENST00000377105.1_Splice_Site_p.T171T|TRPM3_ENST00000396280.5_Splice_Site_p.T171T|TRPM3_ENST00000396283.1_Splice_Site_p.T171T|TRPM3_ENST00000377101.1_Splice_Site_p.T171T|TRPM3_ENST00000396292.4_Splice_Site_p.T171T|TRPM3_ENST00000377106.1_Splice_Site_p.T171T|TRPM3_ENST00000377110.3_Splice_Site_p.T324T|TRPM3_ENST00000408909.2_Splice_Site_p.T171T	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	324					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						GCTACTTACTTGTGTTTATCT	0.423																																					p.T324T		Atlas-SNP	.											.	TRPM3	700	.	0			c.A972T						.						185	168	174					9																	73442764		2203	4300	6503	SO:0001630	splice_region_variant	80036	exon6			CTTACTTGTGTTT	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.973+1A>T	chr9.hg19:g.73442764T>A		80.0	0.0		81.0	20.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377111.2	hg19		.	.	.	.	.	.	.	.	.	.	T	15.01	2.706398	0.48412	.	.	ENSG00000083067	ENST00000396280	.	.	.	5.53	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-21.6134	10.003	0.41940	0.0:0.1412:0.0:0.8588	.	.	.	.	X	171	.	.	K	-	1	0	TRPM3	72632584	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	0.469000	0.22067	0.931000	0.37242	0.528000	0.53228	AAG	.	.		0.423	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945	Silent	A	73442764	T	A	73442764	5	1	71	1	0	0	0	0	0	0	1	0	16602	1826	63	4	4354	4	TRPM3	9	73442764	Splice_Site	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	37196287	73442764	67770667	50	9137										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73479369	73479369	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tatgggggtctttggtgctgGgtatgatgtggacacattct	15	5	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr9:73479369G>C	ENST00000377111.2	-	2	479	c.236C>G	c.(235-237)cCc>cGc	p.P79R	TRPM3_ENST00000361823.5_5'UTR|TRPM3_ENST00000377097.3_5'Flank|TRPM3_ENST00000396285.1_5'Flank|TRPM3_ENST00000423814.3_Missense_Mutation_p.P81R|TRPM3_ENST00000360823.2_5'UTR|TRPM3_ENST00000357533.2_Missense_Mutation_p.P81R|TRPM3_ENST00000358082.3_5'Flank|TRPM3_ENST00000377105.1_5'UTR|TRPM3_ENST00000437699.3_5'UTR|TRPM3_ENST00000396280.5_5'Flank|TRPM3_ENST00000396283.1_5'UTR|TRPM3_ENST00000377101.1_5'UTR|TRPM3_ENST00000396292.4_5'Flank|TRPM3_ENST00000377106.1_5'UTR|TRPM3_ENST00000377110.3_Missense_Mutation_p.P79R|TRPM3_ENST00000408909.2_5'Flank	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	79					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TTTGGTGCTGGGTATGATGTG	0.328																																					p.P79R		Atlas-SNP	.											.	TRPM3	700	.	0			c.C236G						.						163	155	158					9																	73479369		1804	4075	5879	SO:0001583	missense	80036	exon2			GTGCTGGGTATGA	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.236C>G	chr9.hg19:g.73479369G>C	ENSP00000366315:p.Pro79Arg	51.0	0.0		38.0	12.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	hg19		.	.	.	.	.	.	.	.	.	.	G	23.5	4.425469	0.83667	.	.	ENSG00000083067	ENST00000377111;ENST00000377110;ENST00000357533;ENST00000423814	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	5.88	5.88	0.94601	.	0.132785	0.52532	D	0.000076	T	0.79405	0.4440	M	0.74546	2.27	0.80722	D	1	P;D;P;D	0.65815	0.835;0.973;0.946;0.995	B;P;P;D	0.65323	0.391;0.822;0.894;0.934	T	0.78961	-0.1997	10	0.54805	T	0.06	-0.864	20.2296	0.98347	0.0:0.0:1.0:0.0	.	79;81;79;79	Q9HCF6;Q4VXD2;Q9HCF6-2;Q9HCF6-10	TRPM3_HUMAN;.;.;.	R	79;79;81;81	ENSP00000366315:P79R;ENSP00000366314:P79R;ENSP00000350140:P81R;ENSP00000389542:P81R	ENSP00000350140:P81R	P	-	2	0	TRPM3	72669189	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.312000	0.78968	2.782000	0.95742	0.563000	0.77884	CCC	.	.		0.328	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		C	73479369	G	C	73479369	3	2	71	1	0	0	0	0	1	0	0	0	16602	1232	43	4	5106	4	TRPM3	9	73479369	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	36605	73479369	67734062	51	9138										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79322771	79322771	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cctccacccacgttctctggCtctagaaagttacattcttc	5	15	3	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr9:79322771C>T	ENST00000376718.3	-	8	4542	c.4419G>A	c.(4417-4419)gaG>gaA	p.E1473E	PRUNE2_ENST00000428286.1_Silent_p.E1114E	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1473					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CGTTCTCTGGCTCTAGAAAGT	0.448																																					p.E1473E		Atlas-SNP	.											.	PRUNE2	331	.	0			c.G4419A						.						47	48	48					9																	79322771		1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			CTCTGGCTCTAGA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.4419G>A	chr9.hg19:g.79322771C>T		65.0	0.0		37.0	19.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.488548	0.01018	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.49	-0.808	0.10868	.	.	.	.	.	T	0.21427	0.0516	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25572	-1.0128	4	.	.	.	-1.5801	3.323	0.07057	0.2949:0.2947:0.0:0.4104	.	.	.	.	T	795	.	.	A	-	1	0	PRUNE2	78512591	0.000000	0.05858	0.049000	0.19019	0.021000	0.10359	0.067000	0.14510	-0.106000	0.12110	-0.169000	0.13324	GCC	.	.		0.448	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		T	79322771	C	T	79322771	2	4	71	1	0	0	0	0	0	0	0	1	12653	796	28	3		3	PRUNE2	9	79322771	Silent	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	5843402	79322771	61890660	52	9139										
PSAT1	29968	hgsc.bcm.edu	37	chr9	80923477	80923477	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	aggctggaaacagctccttgTacaacacgcctccatgtttc	8	13	0	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr9:80923477T>C	ENST00000376588.3	+	6	786	c.718T>C	c.(718-720)Tac>Cac	p.Y240H	PSAT1_ENST00000347159.2_Missense_Mutation_p.Y240H	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1	240					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-serine biosynthetic process (GO:0006564)|pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	O-phospho-L-serine:2-oxoglutarate aminotransferase activity (GO:0004648)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						CAGCTCCTTGTACAACACGCC	0.527																																					p.Y240H	Colon(34;187 791 10662 18313 37609)	Atlas-SNP	.											.	PSAT1	33	.	0			c.T718C						.						92	75	81					9																	80923477		2203	4300	6503	SO:0001583	missense	29968	exon6			TCCTTGTACAACA	BC004863	CCDS6659.1, CCDS6660.1	9q21.2	2008-08-11			ENSG00000135069	ENSG00000135069			19129	protein-coding gene	gene with protein product		610936				12633500, 3651428	Standard	NM_058179		Approved	PSA	uc004ala.3	Q9Y617	OTTHUMG00000020066	ENST00000376588.3:c.718T>C	chr9.hg19:g.80923477T>C	ENSP00000365773:p.Tyr240His	40.0	0.0		31.0	18.0	NM_021154	Q5T7G5|Q5T7G6|Q96AW2|Q9BQ12	Missense_Mutation	SNP	ENST00000376588.3	hg19	CCDS6660.1	.	.	.	.	.	.	.	.	.	.	T	18.13	3.555298	0.65425	.	.	ENSG00000135069	ENST00000421149;ENST00000347159;ENST00000376588	D;D	0.87650	-2.28;-2.28	5.72	5.72	0.89469	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	D	0.93588	0.7953	M	0.82517	2.595	0.80722	D	1	D;B	0.89917	1.0;0.015	D;B	0.71414	0.973;0.025	D	0.94271	0.7511	10	0.66056	D	0.02	-7.6481	15.9995	0.80280	0.0:0.0:0.0:1.0	.	240;240	Q9Y617-2;Q9Y617	.;SERC_HUMAN	H	64;240;240	ENSP00000317606:Y240H;ENSP00000365773:Y240H	ENSP00000317606:Y240H	Y	+	1	0	PSAT1	80113297	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	7.645000	0.83430	2.186000	0.69663	0.528000	0.53228	TAC	.	.		0.527	PSAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052777.1	NM_021154		C	80923477	T	C	80923477	3	2	71	1	0	0	0	0	1	0	0	0	12656	1638	57	2	740	2	PSAT1	9	80923477	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	1600706	80923477	60289954	53	9140										
GFI1B	8328	hgsc.bcm.edu	37	chr9	135862139	135862139	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ccgtgtgcaggaagatgaacCgctctggcctcctgccctta	11	14	1	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr9:135862139C>T	ENST00000339463.3	+	6	893	c.74C>T	c.(73-75)cCg>cTg	p.P25L	GFI1B_ENST00000534944.1_Missense_Mutation_p.P25L|GFI1B_ENST00000372123.1_Missense_Mutation_p.P25L|GFI1B_ENST00000372122.1_Missense_Mutation_p.P25L|GFI1B_ENST00000372124.1_Missense_Mutation_p.P25L|GFI1B_ENST00000450530.1_Missense_Mutation_p.P25L			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	25					cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K9 methylation (GO:0051574)|regulation of erythrocyte differentiation (GO:0045646)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II transcription factor binding (GO:0001085)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		GAAGATGAACCGCTCTGGCCT	0.642																																					p.P25L		Atlas-SNP	.											.	GFI1B	37	.	0			c.C74T						.						59	53	55					9																	135862139		2203	4300	6503	SO:0001583	missense	8328	exon2			ATGAACCGCTCTG	AF081946	CCDS6957.1, CCDS48049.1	9q34.13	2014-09-17	2007-10-04		ENSG00000165702	ENSG00000165702		"Zinc fingers, C2H2-type"	4238	protein-coding gene	gene with protein product		604383	"growth factor independent 1B (potential regulator of CDKN1A, translocated in CML)"			9878267	Standard	NM_001135031		Approved		uc004ccg.3	Q5VTD9	OTTHUMG00000020848	ENST00000339463.3:c.74C>T	chr9.hg19:g.135862139C>T	ENSP00000344782:p.Pro25Leu	64.0	0.0		34.0	17.0	NM_001135031	O95270|Q5VTD8|Q6FHZ2|Q6T888	Missense_Mutation	SNP	ENST00000339463.3	hg19	CCDS6957.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.286287	0.23478	.	.	ENSG00000165702	ENST00000372124;ENST00000339463;ENST00000450530;ENST00000534944;ENST00000372123;ENST00000372122	T;T;T;T;T;T	0.08008	3.18;3.14;3.14;3.18;3.18;3.14	5.28	-2.43	0.06522	.	0.575690	0.17209	N	0.182786	T	0.03608	0.0103	N	0.04043	-0.29	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.37337	-0.9710	10	0.30078	T	0.28	-2.9696	12.6834	0.56934	0.0:0.229:0.0:0.771	.	25;25	Q5VTD9-2;Q5VTD9	.;GFI1B_HUMAN	L	25	ENSP00000361197:P25L;ENSP00000344782:P25L;ENSP00000409546:P25L;ENSP00000446134:P25L;ENSP00000361196:P25L;ENSP00000361195:P25L	ENSP00000344782:P25L	P	+	2	0	GFI1B	134851960	0.000000	0.05858	0.000000	0.03702	0.412000	0.31113	-0.037000	0.12164	-0.733000	0.04850	-0.266000	0.10368	CCG	.	.		0.642	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188		T	135862139	C	T	135862139	3	4	71	1	0	0	0	0	1	0	0	0	6348	652	23	1	76	1	GFI1B	9	135862139	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	54938662	135862139	5351292	54	9141										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138676396	138676396	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gccagtccttcgtgaaggacTacatgatcaccatcacccgg	9	14	2	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr9:138676396T>A	ENST00000263604.3	+	26	2902	c.2902T>A	c.(2902-2904)Tac>Aac	p.Y968N	KCNT1_ENST00000488444.2_Missense_Mutation_p.Y968N|KCNT1_ENST00000490355.2_Missense_Mutation_p.Y966N|KCNT1_ENST00000491806.2_Missense_Mutation_p.Y954N|KCNT1_ENST00000487664.1_Missense_Mutation_p.Y942N|KCNT1_ENST00000486577.2_Missense_Mutation_p.Y946N|KCNT1_ENST00000298480.5_Missense_Mutation_p.Y987N|KCNT1_ENST00000371757.2_Missense_Mutation_p.Y987N			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	968					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		CGTGAAGGACTACATGATCAC	0.706																																					p.Y987N		Atlas-SNP	.											.	KCNT1	139	.	0			c.T2959A						.						14	14	14					9																	138676396		2174	4286	6460	SO:0001583	missense	57582	exon26			AAGGACTACATGA	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.2902T>A	chr9.hg19:g.138676396T>A	ENSP00000263604:p.Tyr968Asn	114.0	0.0		62.0	24.0	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	T	23.9	4.472489	0.84640	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27	4.62	4.62	0.57501	.	0.075052	0.56097	U	0.000037	D	0.86360	0.5914	M	0.74647	2.275	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.99;0.99;0.997;0.987	D	0.85236	0.1035	10	0.30078	T	0.28	-22.1584	14.0134	0.64511	0.0:0.0:0.0:1.0	.	954;987;942;968	C9JYL2;B9EGP2;G5E9V0;Q5JUK3	.;.;.;KCNT1_HUMAN	N	942;987;987;946;954;968;966;968	ENSP00000417851:Y942N;ENSP00000298480:Y987N;ENSP00000360822:Y987N;ENSP00000263604:Y968N	ENSP00000263604:Y968N	Y	+	1	0	KCNT1	137816217	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.613000	0.61176	1.714000	0.51371	0.375000	0.23000	TAC	.	.		0.706	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		A	138676396	T	A	138676396	3	1	71	1	0	0	0	0	1	0	0	0	8100	1522	53	4	3061	4	KCNT1	9	138676396	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	2814257	138676396	2537035	55	9142										
FAM69B	138311	hgsc.bcm.edu	37	chr9	139612124	139612124	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tacgtgcactactcgtcctaCtcggagcgctgtcgcggcca	11	15	0	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr9:139612124C>A	ENST00000371692.4	+	2	255	c.159C>A	c.(157-159)taC>taA	p.Y53*		NM_152421.3	NP_689634.2	Q5VUD6	FA69B_HUMAN	family with sequence similarity 69, member B	53						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|large_intestine(2)|lung(1)|prostate(1)	8	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.03e-05)|Epithelial(140;0.00013)		ACTCGTCCTACTCGGAGCGCT	0.662																																					p.Y53X		Atlas-SNP	.											.	FAM69B	22	.	0			c.C159A						.						110	89	96					9																	139612124		2202	4300	6502	SO:0001587	stop_gained	138311	exon2			GTCCTACTCGGAG		CCDS7004.1	9q34.3	2012-08-03			ENSG00000165716	ENSG00000165716			28290	protein-coding gene	gene with protein product		614543				21334309	Standard	NM_152421		Approved	MGC20262, C9orf136	uc004cik.3	Q5VUD6	OTTHUMG00000020940	ENST00000371692.4:c.159C>A	chr9.hg19:g.139612124C>A	ENSP00000360757:p.Tyr53*	28.0	0.0		27.0	15.0	NM_152421	Q5VUD7|Q8N5N0|Q8WYU5	Nonsense_Mutation	SNP	ENST00000371692.4	hg19	CCDS7004.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.157802	0.78114	.	.	ENSG00000165716	ENST00000371692	.	.	.	4.67	1.75	0.24633	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.6156	8.2485	0.31704	0.0:0.7294:0.0:0.2706	.	.	.	.	X	53	.	ENSP00000360757:Y53X	Y	+	3	2	FAM69B	138731945	1.000000	0.71417	0.857000	0.33713	0.304000	0.27724	1.259000	0.32956	0.060000	0.16281	0.478000	0.44815	TAC	.	.		0.662	FAM69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055102.1	NM_152421		A	139612124	C	A	139612124	4	1	71	1	0	0	0	0	0	1	0	0	5611	576	20	3	165	3	FAM69B	9	139612124	Nonsense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	935728	139612124	1601307	56	9143										
PARD3	56288	hgsc.bcm.edu	37	chr10	34558586	34558586	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gattgcccctggcgcctaccTgtctacaggtgagggtttgg	14	11	1	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr10:34558586T>C	ENST00000374789.3	-	22	3752	c.3427A>G	c.(3427-3429)Agt>Ggt	p.S1143G	PARD3_ENST00000374790.3_Splice_Site_p.S1083G|PARD3_ENST00000545693.1_Splice_Site_p.S1127G|PARD3_ENST00000374788.3_Splice_Site_p.S1140G|PARD3_ENST00000350537.4_Splice_Site_p.S1097G|PARD3_ENST00000466092.1_5'Flank|PARD3_ENST00000374794.3_Splice_Site_p.S1031G|PARD3_ENST00000346874.4_Splice_Site_p.S1106G|PARD3_ENST00000545260.1_Splice_Site_p.S1053G	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	1143					apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				GGCGCCTACCTGTCTACAGGT	0.498																																					p.S1143G		Atlas-SNP	.											.	PARD3	131	.	0			c.A3427G						.						79	66	71					10																	34558586		2203	4300	6503	SO:0001630	splice_region_variant	56288	exon22			CCTACCTGTCTAC	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"atypical PKC isotype-specific interacting protein", "par-3 family cell polarity regulator alpha", "protein phosphatase 1, regulatory subunit 118"	606745	"par-3 (partitioning defective 3, C.elegans) homolog", "par-3 partitioning defective 3 homolog (C. elegans)"			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.3428+1A>G	chr10.hg19:g.34558586T>C		96.0	0.0		77.0	28.0	NM_019619	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Missense_Mutation	SNP	ENST00000374789.3	hg19	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	T	19.32	3.805839	0.70682	.	.	ENSG00000148498	ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790	T;T;T;T;T;T;T;T	0.20332	2.15;2.08;2.21;2.21;2.24;2.19;2.08;2.15	5.78	4.65	0.58169	.	0.252027	0.56097	N	0.000029	T	0.23965	0.0580	L	0.54323	1.7	0.80722	D	1	B;P;B;P;P;B;P;P	0.42296	0.004;0.729;0.001;0.775;0.675;0.002;0.675;0.547	B;B;B;B;B;B;B;B	0.41988	0.014;0.288;0.004;0.276;0.372;0.014;0.372;0.205	T	0.01626	-1.1309	10	0.52906	T	0.07	.	11.9932	0.53186	0.0:0.0676:0.0:0.9324	.	1031;1053;1060;1097;1127;1106;1140;1143	Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0	.;.;.;.;.;.;.;PARD3_HUMAN	G	1127;1053;1143;1140;1106;1031;1097;1083	ENSP00000443147:S1127G;ENSP00000440857:S1053G;ENSP00000363921:S1143G;ENSP00000363920:S1140G;ENSP00000340591:S1106G;ENSP00000363926:S1031G;ENSP00000311986:S1097G;ENSP00000363922:S1083G	ENSP00000340591:S1106G	S	-	1	0	PARD3	34598592	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	4.435000	0.59941	1.129000	0.42072	0.482000	0.46254	AGT	.	.		0.498	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619	Missense_Mutation	C	34558586	T	C	34558586	5	2	71	1	0	0	0	0	0	0	1	0	11452	1594	55	2	659	2	PARD3	10	34558586	Splice_Site	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10		34558586	100976161	57	9144										
CSTF2T	23283	hgsc.bcm.edu	37	chr10	53458521	53458521	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gctggtattggccctggagcTggaattccaccctggatagg	14	10	0	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr10:53458521T>A	ENST00000331173.4	-	1	834	c.789A>T	c.(787-789)ccA>ccT	p.P263P	PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000373985.1_Intron|PRKG1_ENST00000401604.2_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	263	Gly-rich.				mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		GCCCTGGAGCTGGAATTCCAC	0.567																																					p.P263P		Atlas-SNP	.											.	CSTF2T	64	.	0			c.A789T						.						44	48	47					10																	53458521		2203	4300	6503	SO:0001819	synonymous_variant	23283	exon1			TGGAGCTGGAATT	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"RNA binding motif (RRM) containing"	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.789A>T	chr10.hg19:g.53458521T>A		49.0	0.0		48.0	23.0	NM_015235	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Silent	SNP	ENST00000331173.4	hg19	CCDS7245.1																																																																																			.	.		0.567	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235		A	53458521	T	A	53458521	2	1	71	1	0	0	0	0	0	0	0	1	3987	1567	55	4		4	CSTF2T	10	53458521	Silent	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	18899935	53458521	82076226	58	9145										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55582876	55582876	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gtgaaatgtctgaatttgttGatacttgacttatgttttcc	8	5	1	4			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr10:55582876G>T	ENST00000320301.6	-	33	5004	c.4610C>A	c.(4609-4611)tCa>tAa	p.S1537*	PCDH15_ENST00000361849.3_Nonsense_Mutation_p.S1539*|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000437009.1_Nonsense_Mutation_p.S1468*|PCDH15_ENST00000395433.1_Nonsense_Mutation_p.S1514*|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000395432.2_Nonsense_Mutation_p.S1497*|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395430.1_Nonsense_Mutation_p.S1534*	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1537					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TGAATTTGTTGATACTTGACT	0.373										HNSCC(58;0.16)																											p.S1544X		Atlas-SNP	.											.	PCDH15	1715	.	0			c.C4631A						.						85	92	89					10																	55582876		2203	4299	6502	SO:0001587	stop_gained	65217	exon35			TTTGTTGATACTT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4610C>A	chr10.hg19:g.55582876G>T	ENSP00000322604:p.Ser1537*	65.0	0.0		53.0	22.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Nonsense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	41	9.141149	0.99078	.	.	ENSG00000150275	ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.4151	0.67145	0.0:0.0:0.8524:0.1476	.	.	.	.	X	1497;1539;1514;1537;1534;1544;1468	.	ENSP00000322604:S1537X	S	-	2	0	PCDH15	55252882	0.952000	0.32445	0.034000	0.17996	0.002000	0.02628	3.852000	0.55934	2.700000	0.92200	0.650000	0.86243	TCA	.	.		0.373	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	55582876	G	T	55582876	4	4	71	1	0	0	0	0	0	1	0	0	11520	1294	45	3	2867	3	PCDH15	10	55582876	Nonsense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	2124355	55582876	79951871	59	9146										
FAM190B	54462	hgsc.bcm.edu	37	chr10	86131217	86131217	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tgtttgtgtcatctacagagGagttaaaccaaaagtctttt	8	6	3	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr10:86131217G>T	ENST00000224756.8	+	2	594	c.409G>T	c.(409-411)Gag>Tag	p.E137*	CCSER2_ENST00000372088.2_Nonsense_Mutation_p.E137*|CCSER2_ENST00000359979.4_Nonsense_Mutation_p.E137*	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	137					microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)											ATCTACAGAGGAGTTAAACCA	0.343																																					p.E137X		Atlas-SNP	.											.	CCSER2	7	.	0			c.G409T						.						86	81	83					10																	86131217		2203	4299	6502	SO:0001587	stop_gained	54462	exon2			ACAGAGGAGTTAA		CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771			29197	protein-coding gene	gene with protein product			"KIAA1128", "family with sequence similarity 190, member B"	KIAA1128, FAM190B		10574461	Standard	XM_005269905		Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.409G>T	chr10.hg19:g.86131217G>T	ENSP00000224756:p.Glu137*	173.0	0.0		163.0	72.0	NM_018999	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Nonsense_Mutation	SNP	ENST00000224756.8	hg19	CCDS31235.1	.	.	.	.	.	.	.	.	.	.	G	36	5.764336	0.96906	.	.	ENSG00000107771	ENST00000359979;ENST00000224756;ENST00000372088	.	.	.	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-21.3851	17.8219	0.88653	0.0:0.0:1.0:0.0	.	.	.	.	X	137	.	ENSP00000224756:E137X	E	+	1	0	FAM190B	86121197	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.076000	0.64413	2.802000	0.96397	0.561000	0.74099	GAG	.	.		0.343	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999		T	86131217	G	T	86131217	4	4	71	1	0	0	0	0	0	1	0	0	5527	1175	41	3	411	3	FAM190B	10	86131217	Nonsense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	30548341	86131217	49403530	60	9147										
HPX	3263	hgsc.bcm.edu	37	chr11	6453022	6453022	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ccctttgtcaggaagacataTacctgggtgccctggaggac	12	11	1	1	rs377761910		TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr11:6453022T>C	ENST00000265983.3	-	9	1078	c.978A>G	c.(976-978)gtA>gtG	p.V326V		NM_000613.2	NP_000604.1	P02790	HEMO_HUMAN	hemopexin	326					cellular iron ion homeostasis (GO:0006879)|heme metabolic process (GO:0042168)|heme transport (GO:0015886)|hemoglobin metabolic process (GO:0020027)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|viral process (GO:0016032)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme transporter activity (GO:0015232)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(11)|prostate(1)	15		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)		GGAAGACATATACCTGGGTGC	0.517																																					p.V326V		Atlas-SNP	.											.	HPX	33	.	0			c.A978G						.	T		0,4402		0,0,2201	143	151	148		978	-11.4	0.1	11		148	2,8590	2.2+/-6.3	0,2,4294	no	coding-synonymous	HPX	NM_000613.2		0,2,6495	CC,CT,TT		0.0233,0.0,0.0154		326/463	6453022	2,12992	2201	4296	6497	SO:0001819	synonymous_variant	3263	exon9			GACATATACCTGG	J03048	CCDS7763.1	11p15.5-p15.4	2012-10-02			ENSG00000110169	ENSG00000110169			5171	protein-coding gene	gene with protein product		142290				2989777, 2842511	Standard	NM_000613		Approved		uc001mdg.2	P02790	OTTHUMG00000133399	ENST00000265983.3:c.978A>G	chr11.hg19:g.6453022T>C		45.0	0.0		42.0	20.0	NM_000613	B2R957	Silent	SNP	ENST00000265983.3	hg19	CCDS7763.1																																																																																			.	.		0.517	HPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257256.1	NM_000613		C	6453022	T	C	6453022	2	2	71	1	0	0	0	0	0	0	0	1	7355	1393	49	2		2	HPX	11	6453022	Silent	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10		6453022	128553494	61	9148										
OLFML1	283298	hgsc.bcm.edu	37	chr11	7530924	7530924	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	acttctaatgagataatcaaAtataacctgcagaagaggac	7	7	2	3			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr11:7530924A>C	ENST00000329293.3	+	3	1108	c.714A>C	c.(712-714)aaA>aaC	p.K238N	CTD-2516F10.2_ENST00000530201.1_RNA|OLFML1_ENST00000528758.1_3'UTR|OLFML1_ENST00000530135.1_Missense_Mutation_p.K238N	NM_198474.3	NP_940876.2	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1	238	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.					extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(3)|prostate(2)	24				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		AGATAATCAAATATAACCTGC	0.453																																					p.K238N		Atlas-SNP	.											.	OLFML1	54	.	0			c.A714C						.						49	51	50					11																	7530924		2201	4296	6497	SO:0001583	missense	283298	exon3			AATCAAATATAAC	AY358591	CCDS7779.1	11p15	2008-02-05			ENSG00000183801	ENSG00000183801			24473	protein-coding gene	gene with protein product							Standard	NM_198474		Approved	UNQ564	uc001mfi.3	Q6UWY5	OTTHUMG00000165527	ENST00000329293.3:c.714A>C	chr11.hg19:g.7530924A>C	ENSP00000332511:p.Lys238Asn	116.0	0.0		81.0	31.0	NM_198474	B4DP03|Q569G4	Missense_Mutation	SNP	ENST00000329293.3	hg19	CCDS7779.1	.	.	.	.	.	.	.	.	.	.	A	18.76	3.693527	0.68386	.	.	ENSG00000183801	ENST00000530135;ENST00000329293	D;D	0.92397	-3.03;-3.03	5.66	5.66	0.87406	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.95834	0.8644	M	0.81497	2.545	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.75484	0.971;0.986	D	0.96273	0.9200	10	0.87932	D	0	.	13.8537	0.63513	1.0:0.0:0.0:0.0	.	102;238	B4DN61;Q6UWY5	.;OLFL1_HUMAN	N	238	ENSP00000433455:K238N;ENSP00000332511:K238N	ENSP00000332511:K238N	K	+	3	2	OLFML1	7487500	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.898000	0.48672	2.153000	0.67306	0.460000	0.39030	AAA	.	.		0.453	OLFML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384656.1	NM_198474		C	7530924	A	C	7530924	3	2	71	1	0	0	0	0	1	0	0	0	10865	98	4	5	724	5	OLFML1	11	7530924	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	1077902	7530924	127475592	62	9149										
SLC17A6	57084	hgsc.bcm.edu	37	chr11	22380971	22380971	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tatttcagggttttcggagcTgccatacttcttacctctac	7	11	3	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr11:22380971T>G	ENST00000263160.3	+	4	908	c.471T>G	c.(469-471)gcT>gcG	p.A157A	CTD-2140G10.4_ENST00000534543.1_RNA	NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	157					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						TTTTCGGAGCTGCCATACTTC	0.368																																					p.A157A		Atlas-SNP	.											.	SLC17A6	135	.	0			c.T471G						.						116	106	110					11																	22380971		2203	4300	6503	SO:0001819	synonymous_variant	57084	exon4			CGGAGCTGCCATA	AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"Solute carriers"	16703	protein-coding gene	gene with protein product	"vesicular glutamate transporter 2", "differentiation-associated Na-dependent inorganic phosphate cotransporter"	607563	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.471T>G	chr11.hg19:g.22380971T>G		62.0	0.0		47.0	20.0	NM_020346	A6NKS2	Silent	SNP	ENST00000263160.3	hg19	CCDS7856.1																																																																																			.	.		0.368	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		G	22380971	T	G	22380971	2	3	71	1	0	0	0	0	0	0	0	1	14436	1567	55	5		5	SLC17A6	11	22380971	Silent	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	14850047	22380971	112625545	63	9150										
OR8J1	219477	hgsc.bcm.edu	37	chr11	56127868	56127868	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cctgggcatcatcaccctcaCcagtgttgactctcgacttc	7	16	4	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr11:56127868C>A	ENST00000303039.3	+	1	178	c.146C>A	c.(145-147)aCc>aAc	p.T49N		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	49						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T49N(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					ATCACCCTCACCAGTGTTGAC	0.507																																					p.T49N		Atlas-SNP	.											OR8J1,NS,carcinoma,0,1	OR8J1	87	.	1	Substitution - Missense(1)	lung(1)	c.C146A						.						162	147	152					11																	56127868		2201	4296	6497	SO:0001583	missense	219477	exon1			CCCTCACCAGTGT	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"GPCR / Class A : Olfactory receptors"	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.146C>A	chr11.hg19:g.56127868C>A	ENSP00000304060:p.Thr49Asn	168.0	0.0		145.0	71.0	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	hg19	CCDS31529.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.300860	0.60195	.	.	ENSG00000172487	ENST00000303039	T	0.03035	4.07	4.05	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.090101	0.48767	D	0.000167	T	0.17408	0.0418	M	0.90309	3.105	0.21933	N	0.999468	P	0.42973	0.796	P	0.59889	0.865	T	0.01566	-1.1323	10	0.87932	D	0	.	7.5856	0.27991	0.0:0.7983:0.0:0.2017	.	49	Q8NGP2	OR8J1_HUMAN	N	49	ENSP00000304060:T49N	ENSP00000304060:T49N	T	+	2	0	OR8J1	55884444	0.001000	0.12720	0.997000	0.53966	0.981000	0.71138	1.045000	0.30341	1.053000	0.40415	0.643000	0.83706	ACC	.	.		0.507	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205		A	56127868	C	A	56127868	3	1	71	1	0	0	0	0	1	0	0	0	11250	507	18	3	148	3	OR8J1	11	56127868	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	33746897	56127868	78878648	64	9151										
AQP11	282679	hgsc.bcm.edu	37	chr11	77301269	77301269	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	accccgcgcaccccacctggAcgctgacgctcgtctacttc	8	20	1	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr11:77301269A>T	ENST00000313578.3	+	1	590	c.232A>T	c.(232-234)Acg>Tcg	p.T78S	AQP11_ENST00000528638.1_Intron	NM_173039.2	NP_766627.1	Q8NBQ7	AQP11_HUMAN	aquaporin 11	78					endosomal lumen acidification (GO:0048388)|protein homooligomerization (GO:0051260)|proximal tubule development (GO:0072014)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			kidney(2)|large_intestine(1)|lung(5)	8	all_cancers(14;1.75e-17)|all_epithelial(13;4.7e-20)|Ovarian(111;0.249)		Epithelial(5;4.73e-49)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			CCCCACCTGGACGCTGACGCT	0.632																																					p.T78S		Atlas-SNP	.											.	AQP11	14	.	0			c.A232T						.						49	49	49					11																	77301269		2200	4292	6492	SO:0001583	missense	282679	exon1			ACCTGGACGCTGA	AB028147	CCDS8251.1	11q13.5	2008-02-05			ENSG00000178301	ENSG00000178301		"Ion channels / Aquaporins"	19940	protein-coding gene	gene with protein product		609914				16107722	Standard	NM_173039		Approved		uc001oyj.3	Q8NBQ7	OTTHUMG00000165194	ENST00000313578.3:c.232A>T	chr11.hg19:g.77301269A>T	ENSP00000318770:p.Thr78Ser	51.0	0.0		46.0	19.0	NM_173039		Missense_Mutation	SNP	ENST00000313578.3	hg19	CCDS8251.1	.	.	.	.	.	.	.	.	.	.	A	12.63	1.995996	0.35226	.	.	ENSG00000178301	ENST00000313578	D	0.84800	-1.9	5.53	-0.832	0.10785	Aquaporin-like (2);	0.500796	0.21099	N	0.080189	T	0.65260	0.2674	N	0.22421	0.69	0.26926	N	0.966578	B	0.13145	0.007	B	0.10450	0.005	T	0.46034	-0.9220	10	0.08837	T	0.75	-3.3863	2.4133	0.04430	0.279:0.2741:0.3467:0.1002	.	78	Q8NBQ7	AQP11_HUMAN	S	78	ENSP00000318770:T78S	ENSP00000318770:T78S	T	+	1	0	AQP11	76978917	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	1.142000	0.31540	0.181000	0.19994	0.397000	0.26171	ACG	.	.		0.632	AQP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382582.1	NM_173039		T	77301269	A	T	77301269	3	4	71	1	0	0	0	0	1	0	0	0	823	275	10	4	234	4	AQP11	11	77301269	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	21173401	77301269	57705247	65	9152										
MAML2	84441	hgsc.bcm.edu	37	chr11	95825257	95825257	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tgttgctgctgctgctgctgTtgttgctgctgctgctgctg	14	10	0	0	rs575986134	byFrequency	TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr11:95825257T>C	ENST00000524717.1	-	2	3222	c.1938A>G	c.(1936-1938)caA>caG	p.Q646Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	646					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgttgttgctgct	0.517			T	"MECT1, CRTC3"	salivary gland mucoepidermoid								T|||	5	0.000998403	0	0	5008	,	,		17451	0.005		0	False		,,,				2504	0				p.Q646Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,colon,carcinoma,0,1	MAML2	94	.	0			c.A1938G						.						37	42	40					11																	95825257		2095	4114	6209	SO:0001819	synonymous_variant	84441	exon2			CTGCTGTTGTTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1938A>G	chr11.hg19:g.95825257T>C		54.0	1.0		44.0	4.0	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.		0.517	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			C	95825257	T	C	95825257	2	2	71	1	0	0	0	0	0	0	0	1	9215	1722	60	2		2	MAML2	11	95825257	Silent	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	18523988	95825257	39181259	66	9153										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103018556	103018556	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	accctgtgaagactgtgattGatgatctcatccagaagtta	9	8	1	6			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr11:103018556G>A	ENST00000375735.2	+	19	2902	c.2758G>A	c.(2758-2760)Gat>Aat	p.D920N	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.D920N	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	920	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GACTGTGATTGATGATCTCAT	0.299																																					p.D920N		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.G2758A						.						118	116	117					11																	103018556		1843	4077	5920	SO:0001583	missense	79659	exon19			GTGATTGATGATC	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.2758G>A	chr11.hg19:g.103018556G>A	ENSP00000364887:p.Asp920Asn	61.0	0.0		46.0	14.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	35	5.552527	0.96501	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.28069	1.63;1.63	5.49	5.49	0.81192	.	0.499919	0.16053	U	0.231871	T	0.61438	0.2347	M	0.87547	2.89	0.80722	D	1	D;D	0.76494	0.97;0.999	P;D	0.72982	0.566;0.979	T	0.57365	-0.7824	10	0.17369	T	0.5	.	19.7446	0.96247	0.0:0.0:1.0:0.0	.	920;920	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	N	920	ENSP00000364887:D920N;ENSP00000381167:D920N	ENSP00000364887:D920N	D	+	1	0	DYNC2H1	102523766	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.374000	0.97172	2.751000	0.94390	0.650000	0.86243	GAT	.	.		0.299	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		A	103018556	G	A	103018556	3	1	71	1	0	0	0	0	1	0	0	0	4848	1290	45	3	2832	3	DYNC2H1	11	103018556	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	7193299	103018556	31987960	67	9154										
BUD13	84811	hgsc.bcm.edu	37	chr11	116628662	116628662	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ttgctgttgccggctctgggCaagcctgggcaaaaaggaac	14	10	1	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr11:116628662C>T	ENST00000260210.4	-	8	1527	c.1504G>A	c.(1504-1506)Gcc>Acc	p.A502T	BUD13_ENST00000375445.3_Missense_Mutation_p.A368T	NM_032725.3	NP_116114.1	Q9BRD0	BUD13_HUMAN	BUD13 homolog (S. cerevisiae)	502					mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)	nucleus (GO:0005634)|RES complex (GO:0070274)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|pancreas(2)|skin(1)|urinary_tract(1)	22	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)		CGGCTCTGGGCAAGCCTGGGC	0.468																																					p.A502T		Atlas-SNP	.											.	BUD13	41	.	0			c.G1504A						.						74	76	75					11																	116628662		2201	4296	6497	SO:0001583	missense	84811	exon8			TCTGGGCAAGCCT	BC006350	CCDS8374.1, CCDS53712.1	11q23.3	2012-06-07	2007-01-12		ENSG00000137656	ENSG00000137656			28199	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 71"		"BUD13 homolog (yeast)"			12477932	Standard	NM_032725		Approved	MGC13125, fSAP71, Cwc26	uc001ppn.3	Q9BRD0	OTTHUMG00000045136	ENST00000260210.4:c.1504G>A	chr11.hg19:g.116628662C>T	ENSP00000260210:p.Ala502Thr	42.0	0.0		35.0	13.0	NM_032725	A8K0S0|Q96LS7	Missense_Mutation	SNP	ENST00000260210.4	hg19	CCDS8374.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103346	0.76983	.	.	ENSG00000137656	ENST00000375445;ENST00000260210	T;T	0.19938	2.16;2.11	6.17	5.27	0.74061	.	0.091610	0.85682	D	0.000000	T	0.37571	0.1008	L	0.50919	1.6	0.80722	D	1	B;D	0.59767	0.441;0.986	B;P	0.61275	0.241;0.886	T	0.05683	-1.0870	9	.	.	.	-3.4742	15.5723	0.76349	0.0:0.9345:0.0:0.0655	.	368;502	Q9BRD0-2;Q9BRD0	.;BUD13_HUMAN	T	368;502	ENSP00000364594:A368T;ENSP00000260210:A502T	.	A	-	1	0	BUD13	116133872	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.300000	0.78841	1.632000	0.50472	0.655000	0.94253	GCC	.	.		0.468	BUD13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000104864.1	NM_032725		T	116628662	C	T	116628662	3	4	71	1	0	0	0	0	1	0	0	0	1575	710	25	3	367	3	BUD13	11	116628662	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	13610106	116628662	18377854	68	9155										
OR8G2	0	hgsc.bcm.edu	37	chr11	124095697	124095697	+	IGR	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	atgctggtgaactttgtgacAgagaagaacatcatctccta	9	8	2	4			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr11:124095697A>C								OR10D3 (38745 upstream) : OR8G1 (24725 downstream)																							ACTTTGTGACAGAGAAGAACA	0.438																																					p.T100T		Atlas-SNP	.											.	.	.	.	0			c.A300C						.						177	174	175					11																	124095697		2156	4293	6449	SO:0001628	intergenic_variant	26492	exon1			TGTGACAGAGAAG																													chr11.hg19:g.124095697A>C		103.0	0.0		68.0	21.0	NM_001007249		Silent	SNP		hg19																																																																																				.	.	0	0.438									C	124095697	A	C	124095697	1	2	71	0	1	0	0	0	0	0	0	0	11244	175	7	5		5	OR8G2	11	124095697	IGR	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	7467035	124095697	10910819	69	9156										
BCAT1	586	hgsc.bcm.edu	37	chr12	25002861	25002861	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	caaagagcagggctttggtaGgcttcttgactccaagagaa	12	8	1	3			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr12:25002861G>T	ENST00000261192.7	-	6	1059	c.533C>A	c.(532-534)cCt>cAt	p.P178H	BCAT1_ENST00000539282.1_Missense_Mutation_p.P190H|BCAT1_ENST00000538118.1_Missense_Mutation_p.P177H|BCAT1_ENST00000539780.1_Missense_Mutation_p.P141H|BCAT1_ENST00000342945.5_Missense_Mutation_p.P117H|BCAT1_ENST00000544418.1_5'UTR	NM_001178091.1|NM_005504.6	NP_001171562.1|NP_005495.2	P54687	BCAT1_HUMAN	branched chain amino-acid transaminase 1, cytosolic	178					branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cell proliferation (GO:0008283)|cellular nitrogen compound metabolic process (GO:0034641)|G1/S transition of mitotic cell cycle (GO:0000082)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)			breast(1)|large_intestine(1)|lung(3)|prostate(2)	7	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)	GGCTTTGGTAGGCTTCTTGAC	0.418																																					p.P190H		Atlas-SNP	.											.	BCAT1	44	.	0			c.C569A						.						63	63	63					12																	25002861		1847	4089	5936	SO:0001583	missense	586	exon6			TTGGTAGGCTTCT		CCDS44845.1, CCDS53760.1, CCDS53761.1, CCDS53762.1, CCDS53763.1	12p12.1	2012-10-02	2010-05-07		ENSG00000060982	ENSG00000060982	2.6.1.42		976	protein-coding gene	gene with protein product		113520	"branched chain aminotransferase 1, cytosolic"	BCT1		9165094	Standard	NM_005504		Approved		uc010six.2	P54687	OTTHUMG00000169053	ENST00000261192.7:c.533C>A	chr12.hg19:g.25002861G>T	ENSP00000261192:p.Pro178His	102.0	0.0		79.0	36.0	NM_001178093	B3KY27|B7Z2M5|B7Z5L0|F5H5E4|Q68DQ7|Q96MY9	Missense_Mutation	SNP	ENST00000261192.7	hg19	CCDS44845.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267356	0.80469	.	.	ENSG00000060982	ENST00000261192;ENST00000538118;ENST00000342945;ENST00000539282;ENST00000539780	T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85	5.33	5.33	0.75918	.	0.179879	0.49305	D	0.000149	T	0.64659	0.2618	H	0.95004	3.61	0.52501	D	0.999956	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.81914	0.986;0.992;0.976;0.995;0.991	T	0.76080	-0.3090	10	0.87932	D	0	-10.9616	19.0238	0.92925	0.0:0.0:1.0:0.0	.	141;190;117;178;177	B7Z5L0;F5H5E4;B3KY27;P54687;Q68DQ7	.;.;.;BCAT1_HUMAN;.	H	178;177;117;190;141	ENSP00000261192:P178H;ENSP00000440817:P177H;ENSP00000339805:P117H;ENSP00000443459:P190H;ENSP00000440827:P141H	ENSP00000261192:P178H	P	-	2	0	BCAT1	24894128	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	7.191000	0.77763	2.490000	0.84030	0.655000	0.94253	CCT	.	.		0.418	BCAT1-001	KNOWN	upstream_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402080.1	NM_005504		T	25002861	G	T	25002861	3	4	71	1	0	0	0	0	1	0	0	0	1354	1000	35	3	651	3	BCAT1	12	25002861	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10		25002861	108849034	70	9157										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43860553	43860553	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	attacatgatactttgtaacTttcatttctttacatctagg	4	7	3	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr12:43860553T>C	ENST00000389420.3	-	9	1268	c.1269A>G	c.(1267-1269)aaA>aaG	p.K423K	ADAMTS20_ENST00000553158.1_Silent_p.K423K	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	423	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ACTTTGTAACTTTCATTTCTT	0.328																																					p.K423K		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A1269G						.						117	118	118					12																	43860553		2203	4300	6503	SO:0001819	synonymous_variant	80070	exon9			TGTAACTTTCATT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1269A>G	chr12.hg19:g.43860553T>C		79.0	0.0		54.0	17.0	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.		0.328	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		C	43860553	T	C	43860553	2	2	71	1	0	0	0	0	0	0	0	1	266	1606	56	2		2	ADAMTS20	12	43860553	Silent	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	18857692	43860553	89991342	71	9158										
NFE2	4778	hgsc.bcm.edu	37	chr12	54686660	54686660	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cccgcacagggcctgaggagGgctctaaggccaagggggtc	17	12	1	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr12:54686660G>A	ENST00000540264.2	-	2	1129	c.620C>T	c.(619-621)cCc>cTc	p.P207L	RP11-968A15.8_ENST00000553061.1_RNA|NFE2_ENST00000435572.2_Missense_Mutation_p.P207L|NFE2_ENST00000312156.4_Missense_Mutation_p.P207L|NFE2_ENST00000553070.1_Missense_Mutation_p.P207L			Q16621	NFE2_HUMAN	nuclear factor, erythroid 2	207					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|hemostasis (GO:0007599)|labyrinthine layer blood vessel development (GO:0060716)|multicellular organismal development (GO:0007275)|negative regulation of bone mineralization (GO:0030502)|negative regulation of syncytium formation by plasma membrane fusion (GO:0034242)|nucleosome disassembly (GO:0006337)|positive regulation of peptidyl-lysine acetylation (GO:2000758)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(7)|upper_aerodigestive_tract(2)	16						GCCTGAGGAGGGCTCTAAGGC	0.607																																					p.P207L		Atlas-SNP	.											.	NFE2	28	.	0			c.C620T						.						45	43	43					12																	54686660		2203	4300	6503	SO:0001583	missense	4778	exon4			GAGGAGGGCTCTA	BC005044	CCDS8876.1	12q13	2013-08-23	2013-08-23			ENSG00000123405		"basic leucine zipper proteins"	7780	protein-coding gene	gene with protein product		601490	"nuclear factor (erythroid-derived 2), 45kD", "nuclear factor (erythroid-derived 2), 45kDa"			8355703	Standard	NM_001136023		Approved	NF-E2	uc001sfr.5	Q16621		ENST00000540264.2:c.620C>T	chr12.hg19:g.54686660G>A	ENSP00000439120:p.Pro207Leu	151.0	0.0		103.0	26.0	NM_001261461	Q07720|Q6ICV9	Missense_Mutation	SNP	ENST00000540264.2	hg19	CCDS8876.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.864415	0.32977	.	.	ENSG00000123405	ENST00000312156;ENST00000435572;ENST00000540264;ENST00000553070;ENST00000553198	.	.	.	4.99	4.99	0.66335	.	0.632696	0.16449	N	0.213949	T	0.21307	0.0513	N	0.08118	0	0.29767	N	0.835087	B	0.20052	0.041	B	0.19391	0.025	T	0.09773	-1.0659	9	0.09084	T	0.74	-1.7122	11.1153	0.48256	0.0:0.0:0.8158:0.1842	.	207	Q16621	NFE2_HUMAN	L	207	.	ENSP00000312436:P207L	P	-	2	0	NFE2	52972927	0.023000	0.18921	0.676000	0.29932	0.748000	0.42578	2.142000	0.42177	2.767000	0.95098	0.655000	0.94253	CCC	.	.		0.607	NFE2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405747.1	NM_006163		A	54686660	G	A	54686660	3	1	71	1	0	0	0	0	1	0	0	0	10375	1232	43	3	505	3	NFE2	12	54686660	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	10826107	54686660	79165235	72	9159										
DEPDC4	120863	hgsc.bcm.edu	37	chr12	100660786	100660786	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ggaagctcgttctgactgacAagtctacggaacctcggagt	12	10	2	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr12:100660786A>T	ENST00000416321.1	-	1	71	c.69T>A	c.(67-69)ctT>ctA	p.L23L	SCYL2_ENST00000360820.2_5'Flank	NM_152317.2	NP_689530.1	Q8N2C3	DEPD4_HUMAN	DEP domain containing 4	23					intracellular signal transduction (GO:0035556)					NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)|urinary_tract(1)	15						TCTGACTGACAAGTCTACGGA	0.622																																					p.L23L		Atlas-SNP	.											.	DEPDC4	34	.	0			c.T69A						.						81	88	85					12																	100660786		2203	4300	6503	SO:0001819	synonymous_variant	120863	exon1			ACTGACAAGTCTA	AK090824	CCDS9075.1	12q23	2006-03-30				ENSG00000166153			22952	protein-coding gene	gene with protein product						12477932	Standard	XM_005268628		Approved	DEP.4, FLJ33505	uc001thi.3	Q8N2C3		ENST00000416321.1:c.69T>A	chr12.hg19:g.100660786A>T		77.0	0.0		60.0	21.0	NM_152317	Q496C8|Q96BW0	Silent	SNP	ENST00000416321.1	hg19	CCDS9075.1																																																																																			.	.		0.622	DEPDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408482.1	NM_152317		T	100660786	A	T	100660786	2	4	71	1	0	0	0	0	0	0	0	1	4443	117	5	4		4	DEPDC4	12	100660786	Silent	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	45974126	100660786	33191109	73	9160										
CCDC53	51019	hgsc.bcm.edu	37	chr12	102433674	102433674	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ccattttgagatatctggcaTatcttggatccttggctaca	8	9	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr12:102433674T>C	ENST00000240079.6	-	5	568	c.407A>G	c.(406-408)tAt>tGt	p.Y136C	CCDC53_ENST00000539515.1_5'UTR|CCDC53_ENST00000545679.1_Missense_Mutation_p.Y135C	NM_016053.2	NP_057137.1	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53	136						actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|WASH complex (GO:0071203)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						ATATCTGGCATATCTTGGATC	0.403																																					p.Y136C		Atlas-SNP	.											.	CCDC53	14	.	0			c.A407G						.						220	207	211					12																	102433674		1867	4120	5987	SO:0001583	missense	51019	exon5			CTGGCATATCTTG	AF151874	CCDS44959.1, CCDS73512.1	12q23.3	2014-05-09			ENSG00000120860	ENSG00000120860			24256	protein-coding gene	gene with protein product						10810093, 20498093	Standard	XM_005268939		Approved	CGI-116	uc010svw.2	Q9Y3C0	OTTHUMG00000168187	ENST00000240079.6:c.407A>G	chr12.hg19:g.102433674T>C	ENSP00000240079:p.Tyr136Cys	67.0	0.0		64.0	36.0	NM_016053	B2RC74|Q53FF0|Q6IAI4|Q96QK0	Missense_Mutation	SNP	ENST00000240079.6	hg19	CCDS44959.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.910426	0.72983	.	.	ENSG00000120860	ENST00000240079;ENST00000545679	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.85873	0.5798	M	0.93507	3.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.89304	0.3628	9	0.87932	D	0	-12.213	13.7576	0.62946	0.0:0.0:0.0:1.0	.	135;136	F5GZ97;Q9Y3C0	.;CCD53_HUMAN	C	136;135	.	ENSP00000240079:Y136C	Y	-	2	0	CCDC53	100957804	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.025000	0.70864	2.233000	0.73108	0.524000	0.50904	TAT	.	.		0.403	CCDC53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398685.1	NM_016053		C	102433674	T	C	102433674	3	2	71	1	0	0	0	0	1	0	0	0	2825	1406	49	2	120	2	CCDC53	12	102433674	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	1772888	102433674	31418221	74	9161										
UBC	7316	hgsc.bcm.edu	37	chr12	125397123	125397123	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	attctcaatggtgtcactcgGctccacctcgagagtgatgg	11	11	2	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr12:125397123G>A	ENST00000536769.1	-	1	2771	c.1195C>T	c.(1195-1197)Ccg>Tcg	p.P399S	MIR5188_ENST00000583467.1_RNA|UBC_ENST00000546120.1_Missense_Mutation_p.P323S|UBC_ENST00000339647.5_Missense_Mutation_p.P399S|UBC_ENST00000538617.1_Intron|UBC_ENST00000536661.1_5'Flank			P0CG48	UBC_HUMAN	ubiquitin C	399	Ubiquitin-like 6. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		GTGTCACTCGGCTCCACCTCG	0.532																																					p.P399S		Atlas-SNP	.											.	UBC	79	.	0			c.C1195T						.						217	191	200					12																	125397123		2203	4297	6500	SO:0001583	missense	7316	exon2			CACTCGGCTCCAC		CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"polyubiquitin-C"	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000536769.1:c.1195C>T	chr12.hg19:g.125397123G>A	ENSP00000441543:p.Pro399Ser	310.0	0.0		238.0	87.0	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Missense_Mutation	SNP	ENST00000536769.1	hg19	CCDS9260.1	.	.	.	.	.	.	.	.	.	.	G	0.770	-0.766022	0.02974	.	.	ENSG00000150991	ENST00000536769;ENST00000541046;ENST00000339647;ENST00000546120	T;T;T	0.73575	-0.76;-0.76;-0.76	3.75	3.75	0.43078	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.46758	U	0.000261	T	0.51601	0.1684	N	0.05574	-0.02	0.80722	D	1	P	0.42456	0.78	B	0.41917	0.37	T	0.57934	-0.7725	10	0.02654	T	1	.	13.1544	0.59509	0.0:0.0:1.0:0.0	.	399	P0CG48	UBC_HUMAN	S	399;323;399;323	ENSP00000441543:P399S;ENSP00000344818:P399S;ENSP00000438394:P323S	ENSP00000344818:P399S	P	-	1	0	UBC	123963076	1.000000	0.71417	1.000000	0.80357	0.020000	0.10135	8.202000	0.89737	1.936000	0.56123	0.556000	0.70494	CCG	.	.		0.532	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009		A	125397123	G	A	125397123	3	1	71	1	0	0	0	0	1	0	0	0	16857	1203	42	3	866	3	UBC	12	125397123	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	22963449	125397123	8454772	75	9162										
COG3	83548	hgsc.bcm.edu	37	chr13	46083887	46083887	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ttctccagcagatcttcatgGaatgtggtatcctacggttc	9	10	3	1	rs551149553		TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr13:46083887G>T	ENST00000349995.5	+	15	1767	c.1655G>T	c.(1654-1656)gGa>gTa	p.G552V	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	552					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		GATCTTCATGGAATGTGGTAT	0.408																																					p.G552V	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.G1655T						.						210	201	204					13																	46083887		2203	4300	6503	SO:0001583	missense	83548	exon15			TTCATGGAATGTG	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1655G>T	chr13.hg19:g.46083887G>T	ENSP00000258654:p.Gly552Val	199.0	0.0		83.0	30.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.943981	0.92593	.	.	ENSG00000136152	ENST00000349995	T	0.42131	0.98	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.65616	0.2708	M	0.72479	2.2	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.91635	0.965;0.999	T	0.62642	-0.6811	10	0.42905	T	0.14	-15.3587	19.0006	0.92832	0.0:0.0:1.0:0.0	.	389;552	B4E2F3;Q96JB2	.;COG3_HUMAN	V	552	ENSP00000258654:G552V	ENSP00000258654:G552V	G	+	2	0	COG3	44981888	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.230000	0.95299	2.749000	0.94314	0.655000	0.94253	GGA	.	.		0.408	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			T	46083887	G	T	46083887	3	4	71	1	0	0	0	0	1	0	0	0	3661	1174	41	3	1713	3	COG3	13	46083887	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10		46083887	69085991	76	9163										
RB1	5925	hgsc.bcm.edu	37	chr13	48954325	48954326	+	Frame_Shift_Del	DEL	TC	TC	-													0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cttctgaatgacaacattttTcatatgtctttattggcgtg					rs34873197		TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr13:48954325_48954326delTC	ENST00000267163.4	+	16	1584_1585	c.1446_1447delTC	c.(1444-1449)tttcatfs	p.FH482fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	482	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.H483fs*9(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	ACAACATTTTTCATATGTCTTT	0.238		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.482_482del		Atlas-INDEL	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	24	Whole gene deletion(15)|Unknown(8)|Deletion - Frameshift(1)	bone(11)|breast(5)|eye(2)|central_nervous_system(2)|adrenal_gland(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.1445_1446del						.																																			SO:0001589	frameshift_variant	5925	exon16	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1446_1447delTC	chr13.hg19:g.48954325_48954326delTC	ENSP00000267163:p.Phe482fs	199.0	0.0		37.0	20.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Del	DEL	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.238	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			-	48954326	TC	-	48954325	7	5	71	1	0	1	0	1	0	0	0	0	13113	1780	62	0	1508	0	RB1	13	48954325	Frame_Shift_Del	DEL	TC	TCGA-CC-A7IF-01A-11D-A33K-10	2870438	48954325	66215553	77	9164	40	2								
RB1	5925	hgsc.bcm.edu	37	chr13	48954328	48954334	+	Frame_Shift_Del	DEL	TATGTCT	TATGTCT	-													0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ctgaatgacaacatttttcaTatgtctttattggcgtgcgc					rs367661403|rs587778832		TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	TATGTCT	TATGTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr13:48954328_48954334delTATGTCT	ENST00000267163.4	+	16	1587_1593	c.1449_1455delTATGTCT	c.(1447-1455)catatgtctfs	p.HMS483fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	483	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.M484fs*8(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	ACATTTTTCATATGTCTTTATTGGCGT	0.251		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.483_485del		Atlas-INDEL	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	24	Whole gene deletion(15)|Unknown(8)|Deletion - Frameshift(1)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|lung(1)	c.1448_1454del	GRCh37	CD962139|CI030637|CI071455|CM016043	RB1	D|I|M		.																																			SO:0001589	frameshift_variant	5925	exon16	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1449_1455delTATGTCT	chr13.hg19:g.48954328_48954334delTATGTCT	ENSP00000267163:p.His483fs	206.0	0.0		36.0	20.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Del	DEL	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.251	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			-	48954334	TATGTCT	-	48954328	7	5	71	1	0	1	0	1	0	0	0	0	13113	1403	49	0	1511	0	RB1	13	48954328	Frame_Shift_Del	DEL	TATGTCT	TCGA-CC-A7IF-01A-11D-A33K-10	3	48954328	66215550	78	9165	40	2								
UGGT2	55757	hgsc.bcm.edu	37	chr13	96555132	96555132	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ataaggaatgttttaattttAtctccagagtaaatagctgt	7	4	1	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr13:96555132A>G	ENST00000376747.3	-	21	2548	c.2478T>C	c.(2476-2478)gaT>gaC	p.D826D		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	826					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						TTTTAATTTTATCTCCAGAGT	0.313																																					p.D826D		Atlas-SNP	.											.	UGGT2	127	.	0			c.T2478C						.						81	88	86					13																	96555132		2201	4298	6499	SO:0001819	synonymous_variant	55757	exon21			AATTTTATCTCCA	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.2478T>C	chr13.hg19:g.96555132A>G		83.0	0.0		94.0	20.0	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Silent	SNP	ENST00000376747.3	hg19	CCDS9480.1																																																																																			.	.		0.313	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		G	96555132	A	G	96555132	2	3	71	1	0	0	0	0	0	0	0	1	16957	446	16	2		2	UGGT2	13	96555132	Silent	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	47600804	96555132	18614746	79	9166										
NPAS3	64067	hgsc.bcm.edu	37	chr14	34269611	34269611	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ccccgcagggcggcggcggtGggggtggcggtggcgggggg	27	10	0	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr14:34269611G>T	ENST00000356141.4	+	12	2098	c.2098G>T	c.(2098-2100)Ggg>Tgg	p.G700W	NPAS3_ENST00000346562.2_Missense_Mutation_p.G668W|NPAS3_ENST00000551492.1_Missense_Mutation_p.G705W|NPAS3_ENST00000548645.1_Missense_Mutation_p.G670W|NPAS3_ENST00000357798.5_Missense_Mutation_p.G687W			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	700	Gly-rich.				locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		CGGCGGCGGTGGGGGTGGCGG	0.741																																					p.G700W		Atlas-SNP	.											.	NPAS3	266	.	0			c.G2098T						.						13	17	16					14																	34269611		2110	4125	6235	SO:0001583	missense	64067	exon12			GGCGGTGGGGGTG	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.2098G>T	chr14.hg19:g.34269611G>T	ENSP00000348460:p.Gly700Trp	92.0	0.0		74.0	16.0	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	G	3.715	-0.058644	0.07317	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79	4.09	-0.934	0.10428	.	0.547135	0.16443	N	0.214209	T	0.28797	0.0714	N	0.08118	0	0.34107	D	0.662589	P;P;P;P	0.47604	0.898;0.836;0.898;0.898	P;B;P;P	0.46885	0.53;0.329;0.53;0.53	T	0.42732	-0.9434	10	0.72032	D	0.01	.	7.2409	0.26096	0.5271:0.0:0.4729:0.0	.	670;700;668;687	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	W	674;705;668;670;700;687	ENSP00000448373:G674W;ENSP00000450392:G705W;ENSP00000319610:G668W;ENSP00000448916:G670W;ENSP00000348460:G700W;ENSP00000350446:G687W	ENSP00000319610:G668W	G	+	1	0	NPAS3	33339362	.	.	0.153000	0.22517	0.064000	0.16182	.	.	-0.316000	0.08690	-0.350000	0.07774	GGG	.	.		0.741	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			T	34269611	G	T	34269611	3	4	71	1	0	0	0	0	1	0	0	0	10573	1348	47	3	2199	3	NPAS3	14	34269611	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10		34269611	73079929	80	9167										
KCNK10	54207	hgsc.bcm.edu	37	chr14	88707142	88707142	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ttcctattggactgactcccGcattgtcagcatcaagagca	8	12	2	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr14:88707142G>A	ENST00000340700.5	-	3	861	c.410C>T	c.(409-411)gCg>gTg	p.A137V	KCNK10_ENST00000319231.5_Missense_Mutation_p.A142V|KCNK10_ENST00000312350.5_Missense_Mutation_p.A142V	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	137					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	47						ACTGACTCCCGCATTGTCAGC	0.408																																					p.A142V		Atlas-SNP	.											.	KCNK10	273	.	0			c.C425T						.						92	83	86					14																	88707142		2203	4300	6503	SO:0001583	missense	54207	exon3			ACTCCCGCATTGT	AF279890	CCDS9880.1, CCDS9881.1, CCDS9882.1	14q31	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6273	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 97"	605873				10880510, 16382106	Standard	NM_021161		Approved	K2p10.1, TREK-2, TREK2, PPP1R97	uc001xwn.3	P57789		ENST00000340700.5:c.410C>T	chr14.hg19:g.88707142G>A	ENSP00000343104:p.Ala137Val	49.0	0.0		29.0	12.0	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Missense_Mutation	SNP	ENST00000340700.5	hg19	CCDS9880.1	.	.	.	.	.	.	.	.	.	.	G	34	5.300928	0.95601	.	.	ENSG00000100433	ENST00000340700;ENST00000312350;ENST00000319231;ENST00000556282	D;D;D;T	0.91894	-2.92;-2.93;-2.92;0.83	5.91	5.91	0.95273	.	0.045738	0.85682	D	0.000000	D	0.93936	0.8059	L	0.60455	1.87	0.80722	D	1	D;D;P	0.61697	0.99;0.99;0.642	P;P;B	0.54210	0.745;0.657;0.235	D	0.93446	0.6798	10	0.52906	T	0.07	.	19.9007	0.96985	0.0:0.0:1.0:0.0	.	137;142;142	P57789;B2R8T4;Q6B014	KCNKA_HUMAN;.;.	V	137;142;142;125	ENSP00000343104:A137V;ENSP00000310568:A142V;ENSP00000312811:A142V;ENSP00000452587:A125V	ENSP00000310568:A142V	A	-	2	0	KCNK10	87776895	1.000000	0.71417	0.838000	0.33150	0.992000	0.81027	7.511000	0.81718	2.791000	0.96007	0.655000	0.94253	GCG	.	.		0.408	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161		A	88707142	G	A	88707142	3	1	71	1	0	0	0	0	1	0	0	0	8068	1087	38	1	1226	1	KCNK10	14	88707142	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	54437531	88707142	18642398	81	9168										
BTBD7	55727	hgsc.bcm.edu	37	chr14	93720042	93720042	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gtcgaggacgaacatagatgCcagcatttttttgccgtaac	10	9	0	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr14:93720042C>T	ENST00000334746.5	-	7	2010	c.1703G>A	c.(1702-1704)gGc>gAc	p.G568D	BTBD7_ENST00000554565.1_Missense_Mutation_p.G217D|BTBD7_ENST00000393170.2_Missense_Mutation_p.G142D	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	568					multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		AACATAGATGCCAGCATTTTT	0.398																																					p.G568D		Atlas-SNP	.											.	BTBD7	112	.	0			c.G1703A						.						172	154	160					14																	93720042		2203	4300	6503	SO:0001583	missense	55727	exon7			TAGATGCCAGCAT	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"BTB/POZ domain containing"	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.1703G>A	chr14.hg19:g.93720042C>T	ENSP00000335615:p.Gly568Asp	61.0	0.0		62.0	20.0	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.994814	0.54041	.	.	ENSG00000011114	ENST00000334746;ENST00000554565;ENST00000553975;ENST00000393170	T;T	0.52295	0.97;0.67	5.75	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.66336	0.2779	L	0.61387	1.9	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.967	D;D;P	0.70016	0.964;0.967;0.71	T	0.70813	-0.4770	10	0.87932	D	0	.	16.8217	0.85748	0.0:0.8713:0.1287:0.0	.	142;217;568	E7ERI4;Q9P203-5;Q9P203	.;.;BTBD7_HUMAN	D	568;217;183;142	ENSP00000335615:G568D;ENSP00000451010:G217D	ENSP00000335615:G568D	G	-	2	0	BTBD7	92789795	1.000000	0.71417	0.923000	0.36655	0.018000	0.09664	7.487000	0.81328	1.409000	0.46915	-0.182000	0.12963	GGC	.	.		0.398	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		T	93720042	C	T	93720042	3	4	71	1	0	0	0	0	1	0	0	0	1548	739	26	3	1715	3	BTBD7	14	93720042	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	5012900	93720042	13629498	82	9169										
BAG5	9529	hgsc.bcm.edu	37	chr14	104026264	104026264	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	acttctcttctccctgcggaTcaacagcatccagggctagc	8	15	3	0	rs143892215		TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr14:104026264T>C	ENST00000445922.2	-	2	1484	c.1238A>G	c.(1237-1239)gAt>gGt	p.D413G	BAG5_ENST00000337322.4_Missense_Mutation_p.D454G|BAG5_ENST00000299204.4_Missense_Mutation_p.D413G|RP11-894P9.2_ENST00000556332.1_RNA	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	413	BAG 5. {ECO:0000255|PROSITE- ProRule:PRU00369}.				negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			TCCCTGCGGATCAACAGCATC	0.498																																					p.D454G	NSCLC(171;1832 2055 18950 31566 41632)	Atlas-SNP	.											.	BAG5	47	.	0			c.A1361G						.						87	84	85					14																	104026264		2203	4300	6503	SO:0001583	missense	9529	exon2			TGCGGATCAACAG	AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.1238A>G	chr14.hg19:g.104026264T>C	ENSP00000391713:p.Asp413Gly	121.0	0.0		98.0	44.0	NM_001015049	O94950|Q86W59	Missense_Mutation	SNP	ENST00000445922.2	hg19	CCDS9982.1	.	.	.	.	.	.	.	.	.	.	T	17.63	3.436991	0.62955	.	.	ENSG00000166170	ENST00000299204;ENST00000445922;ENST00000337322	D;D;D	0.90385	-2.66;-2.66;-2.66	5.74	5.74	0.90152	BAG domain (3);	0.106420	0.64402	D	0.000009	D	0.95227	0.8452	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.95592	0.8655	10	0.72032	D	0.01	-42.7673	16.3426	0.83092	0.0:0.0:0.0:1.0	.	413;454	Q9UL15;Q9UL15-2	BAG5_HUMAN;.	G	413;413;454	ENSP00000299204:D413G;ENSP00000391713:D413G;ENSP00000338814:D454G	ENSP00000299204:D413G	D	-	2	0	BAG5	103096017	1.000000	0.71417	0.997000	0.53966	0.256000	0.26092	7.446000	0.80609	2.317000	0.78254	0.460000	0.39030	GAT	.	T|1.000;A|0.000		0.498	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			C	104026264	T	C	104026264	3	2	71	1	0	0	0	0	1	0	0	0	1290	1435	50	2	109	2	BAG5	14	104026264	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	10306222	104026264	3323276	83	9170										
RASGRP1	10125	hgsc.bcm.edu	37	chr15	38794569	38794569	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ctcgcagcaatcttttcaaaTtcttcctgagaaatgtatcc	5	11	3	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr15:38794569T>G	ENST00000310803.5	-	12	1659	c.1482A>C	c.(1480-1482)gaA>gaC	p.E494D	RASGRP1_ENST00000559830.1_Missense_Mutation_p.E459D|RASGRP1_ENST00000450598.2_Missense_Mutation_p.E459D|RASGRP1_ENST00000539159.1_Missense_Mutation_p.E446D|RASGRP1_ENST00000558164.1_Missense_Mutation_p.E459D|RP11-102L12.2_ENST00000560231.1_RNA|RASGRP1_ENST00000561180.1_Missense_Mutation_p.E545D	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	494	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		TCTTTTCAAATTCTTCCTGAG	0.398																																					p.E494D		Atlas-SNP	.											.	RASGRP1	50	.	0			c.A1482C						.						91	82	85					15																	38794569		1836	4095	5931	SO:0001583	missense	10125	exon12			TTCAAATTCTTCC	AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"EF-hand domain containing"	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.1482A>C	chr15.hg19:g.38794569T>G	ENSP00000310244:p.Glu494Asp	88.0	0.0		78.0	43.0	NM_005739	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Missense_Mutation	SNP	ENST00000310803.5	hg19	CCDS45222.1	.	.	.	.	.	.	.	.	.	.	T	10.31	1.314558	0.23908	.	.	ENSG00000172575	ENST00000310803;ENST00000450598;ENST00000415523;ENST00000431814;ENST00000539159;ENST00000414708;ENST00000541438	T;T;T;T	0.79554	-1.28;-0.06;-1.28;-1.28	5.01	-2.22	0.06952	EF-hand-like domain (1);	0.051715	0.85682	D	0.000000	T	0.73737	0.3625	L	0.41079	1.255	0.48632	D	0.99968	B;B;B;B	0.26975	0.121;0.109;0.109;0.165	B;B;B;B	0.40602	0.069;0.317;0.317;0.334	T	0.57940	-0.7724	10	0.13108	T	0.6	-23.6629	13.1072	0.59253	0.0:0.2262:0.0:0.7738	.	459;459;494;459	C9JM27;C9JCE5;O95267;O95267-2	.;.;GRP1_HUMAN;.	D	494;459;459;459;446;459;459	ENSP00000310244:E494D;ENSP00000388540:E459D;ENSP00000444762:E446D;ENSP00000413105:E459D	ENSP00000310244:E494D	E	-	3	2	RASGRP1	36581861	0.478000	0.25917	0.970000	0.41538	0.989000	0.77384	-0.405000	0.07196	-0.648000	0.05437	-0.417000	0.06048	GAA	.	.		0.398	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739		G	38794569	T	G	38794569	3	3	71	1	0	0	0	0	1	0	0	0	13089	1490	52	5	935	5	RASGRP1	15	38794569	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10		38794569	63736823	84	9171										
ITGA11	22801	hgsc.bcm.edu	37	chr15	68657110	68657110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gcgcatgttgtctttccgctCggacacgttggacagggtga	14	10	1	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr15:68657110C>T	ENST00000315757.7	-	4	378	c.292G>A	c.(292-294)Gag>Aag	p.E98K	ITGA11_ENST00000423218.2_Missense_Mutation_p.E98K|ITGA11_ENST00000562826.1_5'UTR	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	98					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						TCTTTCCGCTCGGACACGTTG	0.632																																					p.E98K		Atlas-SNP	.											.	ITGA11	110	.	0			c.G292A						.						83	92	89					15																	68657110		2106	4220	6326	SO:0001583	missense	22801	exon4			TCCGCTCGGACAC	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.292G>A	chr15.hg19:g.68657110C>T	ENSP00000327290:p.Glu98Lys	118.0	0.0		123.0	28.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	hg19	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	c	32	5.173550	0.94807	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000537153	T;T	0.71934	-0.61;-0.61	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.82300	0.5007	M	0.80183	2.485	0.58432	D	0.999998	P;D	0.76494	0.791;0.999	B;D	0.65443	0.18;0.935	T	0.79591	-0.1740	10	0.12430	T	0.62	.	17.2813	0.87129	0.0:1.0:0.0:0.0	.	98;98	A8K8T0;Q9UKX5	.;ITA11_HUMAN	K	98	ENSP00000327290:E98K;ENSP00000403392:E98K	ENSP00000327290:E98K	E	-	1	0	ITGA11	66444164	1.000000	0.71417	0.975000	0.42487	0.988000	0.76386	7.230000	0.78097	2.342000	0.79632	0.556000	0.70494	GAG	.	.		0.632	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		T	68657110	C	T	68657110	3	4	71	1	0	0	0	0	1	0	0	0	7883	893	31	1	3382	1	ITGA11	15	68657110	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	29862541	68657110	33874282	85	9172										
CCNF	899	hgsc.bcm.edu	37	chr16	2499459	2499459	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ctggccagactgacgcacggGcagagtaaggagtggccctt	15	11	0	3			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr16:2499459G>T	ENST00000397066.4	+	12	1483	c.1395G>T	c.(1393-1395)ggG>ggT	p.G465G		NM_001761.2	NP_001752.2	P41002	CCNF_HUMAN	cyclin F	465					mitotic nuclear division (GO:0007067)|negative regulation of centrosome duplication (GO:0010826)|placenta development (GO:0001890)|protein ubiquitination (GO:0016567)|re-entry into mitotic cell cycle (GO:0000320)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	centriole (GO:0005814)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(2)|lung(5)|prostate(4)|skin(1)	20		Ovarian(90;0.17)				TGACGCACGGGCAGAGTAAGG	0.652																																					p.G465G		Atlas-SNP	.											.	CCNF	110	.	0			c.G1395T						.						27	29	28					16																	2499459		2197	4300	6497	SO:0001819	synonymous_variant	899	exon12			GCACGGGCAGAGT	Z36714	CCDS10467.1	16p13.3	2008-02-05			ENSG00000162063	ENSG00000162063		"F-boxes /  "other""	1591	protein-coding gene	gene with protein product		600227				7896286	Standard	NM_001761		Approved	FBX1, FBXO1	uc002cqd.1	P41002	OTTHUMG00000128858	ENST00000397066.4:c.1395G>T	chr16.hg19:g.2499459G>T		14.0	0.0		13.0	6.0	NM_001761	B2R8H3|Q96EG9	Silent	SNP	ENST00000397066.4	hg19	CCDS10467.1																																																																																			.	.		0.652	CCNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250801.1	NM_001761		T	2499459	G	T	2499459	2	4	71	1	0	0	0	0	0	0	0	1	2924	1190	42	3		3	CCNF	16	2499459	Silent	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10		2499459	87855294	86	9173										
RBBP6	5930	hgsc.bcm.edu	37	chr16	24579152	24579152	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ctagatgagtttacaaatgaTtttgctaaggaattgatgga	10	3	0	4			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr16:24579152T>G	ENST00000319715.4	+	16	2424	c.1992T>G	c.(1990-1992)gaT>gaG	p.D664E	RBBP6_ENST00000348022.2_Intron|RBBP6_ENST00000381039.3_Intron	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	664					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TTACAAATGATTTTGCTAAGG	0.328																																					p.D664E		Atlas-SNP	.											.	RBBP6	158	.	0			c.T1992G						.						70	75	74					16																	24579152		2197	4300	6497	SO:0001583	missense	5930	exon16			AAATGATTTTGCT		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.1992T>G	chr16.hg19:g.24579152T>G	ENSP00000317872:p.Asp664Glu	250.0	0.0		178.0	15.0	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	hg19	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.527439	0.44969	.	.	ENSG00000122257	ENST00000319715	T	0.34859	1.34	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000016	T	0.38983	0.1061	N	0.11201	0.11	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.29912	-0.9996	10	0.15066	T	0.55	-22.3832	15.8684	0.79084	0.0:0.0:0.0:1.0	.	664	Q7Z6E9	RBBP6_HUMAN	E	664	ENSP00000317872:D664E	ENSP00000317872:D664E	D	+	3	2	RBBP6	24486653	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.351000	0.59398	2.156000	0.67533	0.460000	0.39030	GAT	.	.		0.328	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		G	24579152	T	G	24579152	3	3	71	1	0	0	0	0	1	0	0	0	13118	1490	52	5	2108	5	RBBP6	16	24579152	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	22079693	24579152	65775601	87	9174										
DNAJA2	10294	hgsc.bcm.edu	37	chr16	47005262	47005262	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	aacaaaacaagatattcactTgagtggatgcatcatgtcct	7	8	2	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr16:47005262T>G	ENST00000317089.5	-	3	576	c.361A>C	c.(361-363)Aaa>Caa	p.K121Q	RP11-169E6.1_ENST00000562536.1_RNA	NM_005880.3	NP_005871.1	O60884	DNJA2_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 2	121					positive regulation of cell proliferation (GO:0008284)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	14		all_cancers(37;0.00125)|all_lung(18;0.00338)|all_epithelial(9;0.00358)|Lung NSC(13;0.0309)|Breast(268;0.116)				GATATTCACTTGAGTGGATGC	0.383																																					p.K121Q		Atlas-SNP	.											.	DNAJA2	28	.	0			c.A361C						.						92	88	89					16																	47005262		2203	4300	6503	SO:0001630	splice_region_variant	10294	exon3			TTCACTTGAGTGG	AF116720	CCDS10726.1	16q12.1	2011-09-02			ENSG00000069345	ENSG00000069345		"Heat shock proteins / DNAJ (HSP40)"	14884	protein-coding gene	gene with protein product		611322				9710638, 11147971	Standard	NM_005880		Approved	HIRIP4, DNAJ, CPR3, DNJ3	uc002eeo.2	O60884	OTTHUMG00000133104	ENST00000317089.5:c.362+1A>C	chr16.hg19:g.47005262T>G		99.0	0.0		225.0	158.0	NM_005880	B2R7L7|O14711	Missense_Mutation	SNP	ENST00000317089.5	hg19	CCDS10726.1	.	.	.	.	.	.	.	.	.	.	T	17.34	3.364029	0.61513	.	.	ENSG00000069345	ENST00000317089	T	0.43294	0.95	5.47	5.47	0.80525	HSP40/DnaJ peptide-binding (1);	0.000000	0.85682	D	0.000000	T	0.40448	0.1117	L	0.52011	1.625	0.80722	D	1	B	0.15141	0.012	B	0.12837	0.008	T	0.19224	-1.0312	10	0.44086	T	0.13	-20.3169	15.5365	0.76007	0.0:0.0:0.0:1.0	.	121	O60884	DNJA2_HUMAN	Q	121	ENSP00000314030:K121Q	ENSP00000314030:K121Q	K	-	1	0	DNAJA2	45562763	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	8.036000	0.88901	2.069000	0.61940	0.459000	0.35465	AAA	.	.		0.383	DNAJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256769.2		Missense_Mutation	G	47005262	T	G	47005262	5	3	71	1	0	0	0	0	0	0	1	0	4614	1826	63	5	905	5	DNAJA2	16	47005262	Splice_Site	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	22426110	47005262	43349491	88	9175										
CD68	968	hgsc.bcm.edu	37	chr17	7483022	7483022	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ctggctgtgcttttctcgggGgccctgctggggctactggc	16	12	1	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr17:7483022G>C	ENST00000250092.6	+	1	238	c.27G>C	c.(25-27)ggG>ggC	p.G9G	AC113189.5_ENST00000415124.1_RNA|AC113189.5_ENST00000417897.1_RNA|CD68_ENST00000380498.6_Silent_p.G9G|SNORA67_ENST00000384423.1_RNA|AC113189.5_ENST00000573187.1_RNA|SENP3-EIF4A1_ENST00000579777.1_RNA|SNORD10_ENST00000459579.1_RNA|AC113189.5_ENST00000572046.1_RNA	NM_001251.2	NP_001242.2	P34810	CD68_HUMAN	CD68 molecule	9					cellular response to organic substance (GO:0071310)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				endometrium(1)|lung(1)|skin(1)	3						TTTTCTCGGGGGCCCTGCTGG	0.647																																					p.G9G		Atlas-SNP	.											.	CD68	17	.	0			c.G27C						.						31	30	31					17																	7483022		2203	4299	6502	SO:0001819	synonymous_variant	968	exon1			CTCGGGGGCCCTG	S57235	CCDS11114.1, CCDS58512.1	17p13	2011-11-24	2006-03-28		ENSG00000129226	ENSG00000129226		"CD molecules"	1693	protein-coding gene	gene with protein product	"scavenger receptor class D, member 1", "CD68 antigen", "macrophage antigen CD68"	153634	"CD68 antigen"			9790779	Standard	NM_001251		Approved	SCARD1, macrosialin, GP110, DKFZp686M18236, LAMP4	uc002ghv.3	P34810	OTTHUMG00000108146	ENST00000250092.6:c.27G>C	chr17.hg19:g.7483022G>C		55.0	0.0		22.0	12.0	NM_001040059	B4DVT4|Q53HR6|Q53XI3|Q96BI7	Silent	SNP	ENST00000250092.6	hg19	CCDS11114.1																																																																																			.	.		0.647	CD68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226949.3	NM_001251		C	7483022	G	C	7483022	2	2	71	1	0	0	0	0	0	0	0	1	3032	1219	43	4		4	CD68	17	7483022	Silent	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10		7483022	73712188	89	9176										
CACNB1	782	hgsc.bcm.edu	37	chr17	37347830	37347830	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	agtctgatggacggctggtgTaggactccgctgagccctga	15	10	1	3			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr17:37347830T>C	ENST00000394303.3	-	3	395	c.188A>G	c.(187-189)tAc>tGc	p.Y63C	CACNB1_ENST00000344140.5_Missense_Mutation_p.Y63C|CACNB1_ENST00000394310.3_Missense_Mutation_p.Y63C|CACNB1_ENST00000582877.1_5'UTR	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit	63					axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	ACGGCTGGTGTAGGACTCCGC	0.602																																					p.Y63C	Esophageal Squamous(5;100 366 38393 41452 45827)	Atlas-SNP	.											.	CACNB1	89	.	0			c.A188G						.						69	58	62					17																	37347830		2203	4300	6503	SO:0001583	missense	782	exon3			CTGGTGTAGGACT		CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"Calcium channel subunits"	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.188A>G	chr17.hg19:g.37347830T>C	ENSP00000377840:p.Tyr63Cys	64.0	0.0		46.0	12.0	NM_199248	A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Missense_Mutation	SNP	ENST00000394303.3	hg19	CCDS42311.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.390062	0.82902	.	.	ENSG00000067191	ENST00000539338;ENST00000394303;ENST00000344140;ENST00000394310;ENST00000536613	T;T;T	0.78816	-1.16;-1.21;-1.17	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.87541	0.6203	M	0.77103	2.36	0.80722	D	1	D;D;B;D;D	0.89917	0.999;1.0;0.181;0.999;1.0	D;D;B;D;D	0.91635	0.995;0.999;0.276;0.993;0.999	D	0.88963	0.3395	10	0.66056	D	0.02	-12.9674	14.115	0.65146	0.0:0.0:0.0:1.0	.	16;63;63;63;63	F5H6X1;Q6TME4;Q02641-2;Q02641-3;Q02641	.;.;.;.;CACB1_HUMAN	C	13;63;63;63;16	ENSP00000377840:Y63C;ENSP00000345461:Y63C;ENSP00000377847:Y63C	ENSP00000345461:Y63C	Y	-	2	0	CACNB1	34601356	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.824000	0.86668	2.025000	0.59659	0.477000	0.44152	TAC	.	.		0.602	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3			C	37347830	T	C	37347830	3	2	71	1	0	0	0	0	1	0	0	0	2554	1638	57	2	1920	2	CACNB1	17	37347830	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	29864808	37347830	43847380	90	9177										
ZCCHC2	54877	hgsc.bcm.edu	37	chr18	60242216	60242216	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ttcctacccacaccccaggcCctgccccgagcccaagccct	6	23	0	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr18:60242216C>G	ENST00000269499.5	+	13	3320	c.2902C>G	c.(2902-2904)Cct>Gct	p.P968A	ZCCHC2_ENST00000586834.1_Missense_Mutation_p.P647A	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	968						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						CACCCCAGGCCCTGCCCCGAG	0.612																																					p.P968A		Atlas-SNP	.											.	ZCCHC2	64	.	0			c.C2902G						.						48	54	52					18																	60242216		2124	4235	6359	SO:0001583	missense	54877	exon13			CCAGGCCCTGCCC	AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"Zinc fingers, CCHC domain containing"	22916	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 49"	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.2902C>G	chr18.hg19:g.60242216C>G	ENSP00000269499:p.Pro968Ala	58.0	0.0		52.0	21.0	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Missense_Mutation	SNP	ENST00000269499.5	hg19	CCDS45880.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.645117	0.67358	.	.	ENSG00000141664	ENST00000269499	T	0.24350	1.86	4.77	4.77	0.60923	.	0.147675	0.45126	D	0.000397	T	0.41488	0.1161	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.18935	-1.0321	10	0.46703	T	0.11	-15.3702	18.3609	0.90374	0.0:1.0:0.0:0.0	.	968	Q9C0B9	ZCHC2_HUMAN	A	968	ENSP00000269499:P968A	ENSP00000269499:P968A	P	+	1	0	ZCCHC2	58393196	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.624000	0.74243	2.630000	0.89119	0.655000	0.94253	CCT	.	.		0.612	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742		G	60242216	C	G	60242216	3	3	71	1	0	0	0	0	1	0	0	0	17602	623	22	4	2952	4	ZCCHC2	18	60242216	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10		60242216	17835032	91	9178										
CDH7	1005	hgsc.bcm.edu	37	chr18	63511191	63511191	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gaagatgtagatgagcccccTgtgttctcttcacccttgta	9	11	2	3	rs139333396	byFrequency	TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr18:63511191T>A	ENST00000397968.2	+	7	1551	c.1125T>A	c.(1123-1125)ccT>ccA	p.P375P	CDH7_ENST00000536984.2_Silent_p.P375P|CDH7_ENST00000323011.3_Silent_p.P375P	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	375	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				ATGAGCCCCCTGTGTTCTCTT	0.488																																					p.P375P		Atlas-SNP	.											.	CDH7	362	.	0			c.T1125A						.						189	156	167					18																	63511191		2203	4300	6503	SO:0001819	synonymous_variant	1005	exon7			GCCCCCTGTGTTC	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1125T>A	chr18.hg19:g.63511191T>A		183.0	0.0		137.0	48.0	NM_004361	Q9H157	Silent	SNP	ENST00000397968.2	hg19	CCDS11993.1																																																																																			.	T|0.999;C|0.001		0.488	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		A	63511191	T	A	63511191	2	1	71	1	0	0	0	0	0	0	0	1	3117	1567	55	4		4	CDH7	18	63511191	Silent	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	3268975	63511191	14566057	92	9179										
MUC16	94025	hgsc.bcm.edu	37	chr19	9059979	9059979	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	atgtggaagaaacgggagaaGatgaggtcatgacaggtgaa	16	3	1	6			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr19:9059979G>T	ENST00000397910.4	-	3	27670	c.27467C>A	c.(27466-27468)tCt>tAt	p.S9156Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9158	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AACGGGAGAAGATGAGGTCAT	0.512																																					p.S9156Y		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	.	0			c.C27467A						.						81	78	79					19																	9059979		2045	4201	6246	SO:0001583	missense	94025	exon3			GGAGAAGATGAGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27467C>A	chr19.hg19:g.9059979G>T	ENSP00000381008:p.Ser9156Tyr	95.0	0.0		66.0	19.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	1.279	-0.610881	0.03690	.	.	ENSG00000181143	ENST00000397910	T	0.22336	1.96	2.26	-1.29	0.09288	.	.	.	.	.	T	0.10680	0.0261	N	0.08118	0	.	.	.	B	0.22080	0.064	B	0.28385	0.089	T	0.25676	-1.0125	8	0.87932	D	0	.	6.8976	0.24265	0.4413:0.0:0.5587:0.0	.	9156	B5ME49	.	Y	9156	ENSP00000381008:S9156Y	ENSP00000381008:S9156Y	S	-	2	0	MUC16	8920979	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.229000	0.17833	-0.589000	0.05874	-1.694000	0.00725	TCT	.	.		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9059979	G	T	9059979	3	4	71	1	0	0	0	0	1	0	0	0	9982	942	33	3	16384	3	MUC16	19	9059979	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10		9059979	50069004	93	9180										
MUC16	94025	hgsc.bcm.edu	37	chr19	9084032	9084032	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ctcagtgactaccaaaaggcTctcaggagtagctgaagttt	10	9	2	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr19:9084032T>A	ENST00000397910.4	-	1	7986	c.7783A>T	c.(7783-7785)Agc>Tgc	p.S2595C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2595	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ACCAAAAGGCTCTCAGGAGTA	0.458																																					p.S2595C		Atlas-SNP	.											.	MUC16	4315	.	0			c.A7783T						.						145	142	143					19																	9084032		1947	4140	6087	SO:0001583	missense	94025	exon1			AAAGGCTCTCAGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.7783A>T	chr19.hg19:g.9084032T>A	ENSP00000381008:p.Ser2595Cys	128.0	0.0		96.0	23.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	0.181	-1.061768	0.01950	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	0.225	-0.451	0.12214	.	.	.	.	.	T	0.01353	0.0044	N	0.08118	0	.	.	.	P	0.41041	0.736	B	0.34652	0.187	T	0.44345	-0.9334	7	0.87932	D	0	.	.	.	.	.	2595	B5ME49	.	C	2595	ENSP00000381008:S2595C	ENSP00000381008:S2595C	S	-	1	0	MUC16	8945032	0.014000	0.17966	0.087000	0.20705	0.089000	0.18198	-0.623000	0.05546	-0.946000	0.03677	-0.991000	0.02546	AGC	.	.		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9084032	T	A	9084032	3	1	71	1	0	0	0	0	1	0	0	0	9982	1551	54	4	36076	4	MUC16	19	9084032	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	24053	9084032	50044951	94	9181										
CALR	811	hgsc.bcm.edu	37	chr19	13054713	13054713	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	aagatgtccccggccaggccAaggacgagctgtagagaggc	15	11	0	2			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr19:13054713A>G	ENST00000316448.5	+	9	1313	c.1240A>G	c.(1240-1242)Aag>Gag	p.K414E	RAD23A_ENST00000592268.1_5'Flank|CTC-425F1.4_ENST00000589120.1_RNA|RAD23A_ENST00000316856.3_5'Flank|RAD23A_ENST00000586534.1_5'Flank|RAD23A_ENST00000541222.1_5'Flank	NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	414	C-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	CGGCCAGGCCAAGGACGAGCT	0.597																																					p.K414E		Atlas-SNP	.											.	CALR	31	.	0			c.A1240G						.						166	131	143					19																	13054713		2202	4299	6501	SO:0001583	missense	811	exon9			CAGGCCAAGGACG	M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"Sicca syndrome antigen A (autoantigen Ro; calreticulin)", "autoantigen Ro"	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.1240A>G	chr19.hg19:g.13054713A>G	ENSP00000320866:p.Lys414Glu	181.0	0.0		109.0	37.0	NM_004343	Q6IAT4|Q9UDG2	Missense_Mutation	SNP	ENST00000316448.5	hg19	CCDS12288.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744183	0.49151	.	.	ENSG00000179218	ENST00000316448;ENST00000539083	T	0.51817	0.69	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.39835	0.1093	N	0.19112	0.55	0.53688	D	0.99997	P	0.51449	0.945	P	0.45753	0.492	T	0.39461	-0.9613	10	0.59425	D	0.04	-39.2548	14.7288	0.69365	1.0:0.0:0.0:0.0	.	414	P27797	CALR_HUMAN	E	414;293	ENSP00000320866:K414E	ENSP00000320866:K414E	K	+	1	0	CALR	12915713	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	6.595000	0.74109	2.123000	0.65237	0.454000	0.30748	AAG	.	.		0.597	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343		G	13054713	A	G	13054713	3	3	71	1	0	0	0	0	1	0	0	0	2594	131	5	2	1274	2	CALR	19	13054713	Missense_Mutation	SNP	A	TCGA-CC-A7IF-01A-11D-A33K-10	3970681	13054713	46074270	95	9182										
STX10	8677	hgsc.bcm.edu	37	chr19	13259885	13259886	+	Frame_Shift_Ins	INS	-	-	A													0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	atgctacggctgttgggctgINSaccatatggtccttcatttc							TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr19:13259885_13259886insA	ENST00000587230.1	-	4	384_385	c.320_321insT	c.(319-321)gtcfs	p.V107fs	STX10_ENST00000343587.5_Intron|STX10_ENST00000242770.5_Frame_Shift_Ins_p.V107fs|IER2_ENST00000292433.3_5'Flank|IER2_ENST00000588173.1_5'Flank|IER2_ENST00000587885.1_5'Flank|STX10_ENST00000589083.1_Frame_Shift_Ins_p.V107fs	NM_001271609.1	NP_001258538.1	O60499	STX10_HUMAN	syntaxin 10	107					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion (GO:0006906)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|kidney(1)|lung(2)|prostate(1)	6			OV - Ovarian serous cystadenocarcinoma(19;3.41e-21)			CTGTTGGGCTGACCATATGGTC	0.554																																					p.V107fs		Atlas-Indel,Pindel	.											.	STX10	12	.	0			c.321_322insT						.																																			SO:0001589	frameshift_variant	8677	exon4			.	AF035531	CCDS32922.1, CCDS62569.1, CCDS62570.1, CCDS62571.1	19p13.13	2008-07-22				ENSG00000104915			11428	protein-coding gene	gene with protein product		603765				9446797	Standard	NM_003765		Approved	hsyn10, SYN10	uc021upq.2	O60499		ENST00000587230.1:c.321dupT	chr19.hg19:g.13259886_13259886dupA	ENSP00000466298:p.Val107fs	139.0	0.0		71.0	16.0	NM_003765	A6NC41|Q6IAP4|Q96AE8	Frame_Shift_Ins	INS	ENST00000587230.1	hg19	CCDS32922.1																																																																																			.	.		0.554	STX10-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452918.1	NM_003765		A	13259886	-	A	13259885	7	5	71	1	0	1	1	0	0	0	0	0	15351	1277	45	0	447	0	STX10	19	13259885	Frame_Shift_Ins	INS	-	TCGA-CC-A7IF-01A-11D-A33K-10	205172	13259885	45869098	96	9183										
NOVA2	4858	hgsc.bcm.edu	37	chr19	46457041	46457041	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	tctctgccccagctgacctgCttggctctgtcggggttcat	11	14	3	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr19:46457041C>A	ENST00000263257.5	-	3	587	c.393G>T	c.(391-393)aaG>aaT	p.K131N		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	131	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		AGCTGACCTGCTTGGCTCTGT	0.512																																					p.K131N		Atlas-SNP	.											.	NOVA2	38	.	0			c.G393T						.						237	212	220					19																	46457041		2203	4300	6503	SO:0001583	missense	4858	exon3			GACCTGCTTGGCT	U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"neuro-oncological ventral antigen 3"	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.393G>T	chr19.hg19:g.46457041C>A	ENSP00000263257:p.Lys131Asn	140.0	0.0		67.0	25.0	NM_002516	O43267|Q9UEA1	Missense_Mutation	SNP	ENST00000263257.5	hg19	CCDS12679.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.983346	0.35036	.	.	ENSG00000104967	ENST00000263257	T	0.63417	-0.04	4.86	1.6	0.23607	K Homology (1);K Homology, type 1 (1);	0.117466	0.56097	D	0.000028	T	0.66208	0.2766	L	0.47716	1.5	0.52099	D	0.99994	D	0.71674	0.998	D	0.76071	0.987	T	0.60005	-0.7347	10	0.29301	T	0.29	-11.151	6.6552	0.22984	0.0:0.6226:0.0:0.3774	.	131	Q9UNW9	NOVA2_HUMAN	N	131	ENSP00000263257:K131N	ENSP00000263257:K131N	K	-	3	2	NOVA2	51148881	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.371000	0.34250	0.266000	0.21894	0.563000	0.77884	AAG	.	.		0.512	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516		A	46457041	C	A	46457041	3	1	71	1	0	0	0	0	1	0	0	0	10564	796	28	3	1093	3	NOVA2	19	46457041	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	33197156	46457041	12671942	97	9184										
CARD8	22900	hgsc.bcm.edu	37	chr19	48734194	48734194	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	aacgcaatcgtcactgtgacCtcatcccttaccaggaagcc	7	15	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr19:48734194C>T	ENST00000359009.4	-	5	609	c.297G>A	c.(295-297)gaG>gaA	p.E99E	CARD8_ENST00000357778.5_5'UTR|CARD8_ENST00000447740.2_Silent_p.E154E|CARD8_ENST00000520153.1_Silent_p.E154E|CARD8_ENST00000519940.1_Silent_p.E204E|CARD8_ENST00000520015.1_Silent_p.E204E|CARD8_ENST00000391898.3_Silent_p.E204E|CARD8_ENST00000520753.1_Silent_p.E204E|CARD8_ENST00000521613.1_Silent_p.E154E|ZNF114_ENST00000597695.1_Intron			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	99			E -> A (in dbSNP:rs59878320). {ECO:0000269|PubMed:14702039}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		TCACTGTGACCTCATCCCTTA	0.587																																					p.E204E		Atlas-SNP	.											.	CARD8	53	.	0			c.G612A						.						61	47	52					19																	48734194		2203	4300	6503	SO:0001819	synonymous_variant	22900	exon6			TGTGACCTCATCC	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.297G>A	chr19.hg19:g.48734194C>T		135.0	0.0		98.0	68.0	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Silent	SNP	ENST00000359009.4	hg19																																																																																				.	.		0.587	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959		T	48734194	C	T	48734194	2	4	71	1	0	0	0	0	0	0	0	1	2653	680	24	3		3	CARD8	19	48734194	Silent	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	2277153	48734194	10394789	98	9185										
C20orf27	54976	hgsc.bcm.edu	37	chr20	3739248	3739248	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cgagtcatgcagcttctcatCaaagtggacgtggctgtggg	14	9	3	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr20:3739248C>A	ENST00000379772.3	-	3	907	c.97G>T	c.(97-99)Gat>Tat	p.D33Y	C20orf27_ENST00000217195.8_Missense_Mutation_p.D58Y	NM_001258429.1	NP_001245358.1	Q9GZN8	CT027_HUMAN	chromosome 20 open reading frame 27	33										central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)|urinary_tract(1)	7						AGCTTCTCATCAAAGTGGACG	0.572																																					p.D58Y		Atlas-SNP	.											.	C20orf27	17	.	0			c.G172T						.						140	117	125					20																	3739248		2203	4300	6503	SO:0001583	missense	54976	exon3			TCTCATCAAAGTG	AK000557	CCDS33436.1, CCDS58763.1	20p13	2011-01-25			ENSG00000101220	ENSG00000101220			15873	protein-coding gene	gene with protein product	"hypothetical protein LOC54976"					11780052	Standard	NM_001258429		Approved	FLJ20550	uc002wjh.2	Q9GZN8	OTTHUMG00000031753	ENST00000379772.3:c.97G>T	chr20.hg19:g.3739248C>A	ENSP00000369097:p.Asp33Tyr	46.0	0.0		23.0	18.0	NM_001039140	A8K4J0|D3DVX8|Q5JX81|Q9NWX3	Missense_Mutation	SNP	ENST00000379772.3	hg19	CCDS58763.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.7|24.7	4.559198|4.559198	0.86335|0.86335	.|.	.|.	ENSG00000101220|ENSG00000101220	ENST00000379772;ENST00000217195;ENST00000399672;ENST00000379765|ENST00000399683	.|.	.|.	.|.	4.69|4.69	4.69|4.69	0.59074|0.59074	.|.	0.063181|.	0.64402|.	U|.	0.000015|.	T|T	0.73345|0.73345	0.3575|0.3575	M|M	0.69823|0.69823	2.125|2.125	0.58432|0.58432	D|D	0.999998|0.999998	D;D;D|.	0.89917|.	0.958;0.997;1.0|.	P;D;D|.	0.81914|.	0.748;0.931;0.995|.	T|T	0.73186|0.73186	-0.4062|-0.4062	9|5	0.72032|.	D|.	0.01|.	-4.6801|-4.6801	15.5218|15.5218	0.75871|0.75871	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	33;58;33|.	Q9GZN8;Q9GZN8-2;E9PAL2|.	CT027_HUMAN;.;.|.	Y|F	33;58;33;33|26	.|.	ENSP00000217195:D58Y|.	D|L	-|-	1|3	0|2	C20orf27|C20orf27	3687248|3687248	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.845000|4.845000	0.62853|0.62853	2.613000|2.613000	0.88420|0.88420	0.650000|0.650000	0.86243|0.86243	GAT|TTG	.	.		0.572	C20orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077750.2	NM_001039140		A	3739248	C	A	3739248	3	1	71	1	0	0	0	0	1	0	0	0	2109	826	29	3	443	3	C20orf27	20	3739248	Missense_Mutation	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10		3739248	59286272	99	9186										
SSTR4	6754	hgsc.bcm.edu	37	chr20	23016896	23016896	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	ctcggagaagaaaatcaccaGgctggtgctgatggtcgtgg	15	8	1	3			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chr20:23016896G>A	ENST00000255008.3	+	1	840	c.776G>A	c.(775-777)aGg>aAg	p.R259K	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	259					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					AAAATCACCAGGCTGGTGCTG	0.622																																					p.R259K	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											.	SSTR4	83	.	0			c.G776A						.						165	175	172					20																	23016896		2198	4293	6491	SO:0001583	missense	6754	exon1			TCACCAGGCTGGT		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"GPCR / Class A : Somatostatin receptors"	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.776G>A	chr20.hg19:g.23016896G>A	ENSP00000255008:p.Arg259Lys	44.0	0.0		33.0	10.0	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	hg19	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.912077	0.52439	.	.	ENSG00000132671	ENST00000255008	T	0.34472	1.36	3.36	3.36	0.38483	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000008	T	0.34250	0.0891	L	0.38838	1.175	0.23056	N	0.998361	B	0.33379	0.41	B	0.40329	0.326	T	0.34179	-0.9839	10	0.51188	T	0.08	.	13.4152	0.60963	0.0:0.0:1.0:0.0	.	259	P31391	SSR4_HUMAN	K	259	ENSP00000255008:R259K	ENSP00000255008:R259K	R	+	2	0	SSTR4	22964896	0.816000	0.29132	0.358000	0.25811	0.922000	0.55478	2.982000	0.49337	1.694000	0.51137	0.655000	0.94253	AGG	.	.		0.622	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			A	23016896	G	A	23016896	3	1	71	1	0	0	0	0	1	0	0	0	15215	1000	35	3	778	3	SSTR4	20	23016896	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10	19277648	23016896	40008624	100	9187										
TBC1D25	4943	hgsc.bcm.edu	37	chrX	48418242	48418242	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cacatctacgggcgctgcacGacctgctcaccacctatgcc	8	18	2	0			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chrX:48418242G>T	ENST00000376771.4	+	6	1287	c.946G>T	c.(946-948)Gac>Tac	p.D316Y	snoU13_ENST00000459609.1_RNA|TBC1D25_ENST00000537536.1_Missense_Mutation_p.D62Y	NM_002536.2	NP_002527.1	Q3MII6	TBC25_HUMAN	TBC1 domain family, member 25	316	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of autophagic vacuole maturation (GO:1901096)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4						GGCGCTGCACGACCTGCTCAC	0.622																																					p.D316Y		Atlas-SNP	.											.	TBC1D25	70	.	0			c.G946T						.						40	34	36					X																	48418242		2203	4300	6503	SO:0001583	missense	4943	exon6			CTGCACGACCTGC	L08240	CCDS35242.1	Xp11.23	2014-01-28	2007-01-12	2007-01-12	ENSG00000068354	ENSG00000068354			8092	protein-coding gene	gene with protein product		311240	"ornithine aminotransferase-like 1"	OATL1		21383079	Standard	NM_002536		Approved		uc004dka.1	Q3MII6	OTTHUMG00000024123	ENST00000376771.4:c.946G>T	chrX.hg19:g.48418242G>T	ENSP00000365962:p.Asp316Tyr	77.0	0.0		63.0	53.0	NM_002536	Q08AN9|Q3MII4|Q8TAR9	Missense_Mutation	SNP	ENST00000376771.4	hg19	CCDS35242.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.757031	0.69648	.	.	ENSG00000068354	ENST00000376771;ENST00000537536	T;T	0.04809	3.55;3.55	5.79	5.79	0.91817	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.22205	0.0535	M	0.76574	2.34	0.58432	D	0.999993	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.76575	0.985;0.985;0.988	T	0.00100	-1.2065	10	0.87932	D	0	-19.2738	16.2999	0.82804	0.0:0.0:1.0:0.0	.	320;258;316	B4DF03;B4DGU3;Q3MII6	.;.;TBC25_HUMAN	Y	316;62	ENSP00000365962:D316Y;ENSP00000444091:D62Y	ENSP00000365962:D316Y	D	+	1	0	TBC1D25	48303186	1.000000	0.71417	0.950000	0.38849	0.814000	0.46013	9.078000	0.94023	2.454000	0.82982	0.529000	0.55759	GAC	.	.		0.622	TBC1D25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060764.2	NM_002536		T	48418242	G	T	48418242	3	4	71	1	0	0	0	0	1	0	0	0	15630	1058	37	1	968	1	TBC1D25	23	48418242	Missense_Mutation	SNP	G	TCGA-CC-A7IF-01A-11D-A33K-10		48418242	106852318	101	9188										
ARMCX1	51309	hgsc.bcm.edu	37	chrX	100808723	100808724	+	Missense_Mutation	DNP	CC	CC	AA													0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	agggaaaagacttacaatgcCcttaataacttgagtgtgaa							TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chrX:100808723_100808724CC>AA	ENST00000372829.3	+	4	1181_1182	c.810_811CC>AA	c.(808-813)gcCCtt>gcAAtt	p.L271I		NM_016608.1	NP_057692.1	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1	271						integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(2)|ovary(3)|pancreas(1)|urinary_tract(1)	19						CTTACAATGCCCTTAATAACTT	0.411																																					p.A270A|p.L271I		Atlas-SNP	.											.	ARMCX1	67	.	0			c.C810A|c.C811A						.																																			SO:0001583	missense	51309	exon4			CAATGCCCTTAAT|AATGCCCTTAATA	AB039670	CCDS14487.1	Xq21.33-q22.2	2014-03-21			ENSG00000126947	ENSG00000126947		"Armadillo repeat containing"	18073	protein-coding gene	gene with protein product		300362				11162520, 16221301, 22569362	Standard	NM_016608		Approved	ALEX1, GASP7	uc004ehv.3	Q9P291	OTTHUMG00000022033	Exception_encountered	chrX.hg19:g.100808723_100808724delinsAA	ENSP00000361917:p.Leu271Ile	34.0	0.0		33.0	27.0	NM_016608	Q53HK2|Q9H2Q0	Silent|Missense_Mutation	SNP	ENST00000372829.3	hg19	CCDS14487.1																																																																																			.	.		0.411	ARMCX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057561.1	NM_016608		AA	100808724	CC	AA	100808723	3	1	71	1	0	0	0	0	1	0	0	0	959	610	22	3	812	3	ARMCX1	23	100808723	Missense_Mutation	DNP	CC	TCGA-CC-A7IF-01A-11D-A33K-10	52390481	100808723	54461837	102	9189										
RHOXF1	158800	hgsc.bcm.edu	37	chrX	119243261	119243261	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	cttttattcttaaaccaaacCtacaatcagagggaaaaggg	7	8	2	1			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chrX:119243261C>G	ENST00000217999.2	-	3	519		c.e3-1		RP4-755D9.1_ENST00000553843.1_RNA	NM_139282.1	NP_644811.1	Q8NHV9	RHXF1_HUMAN	Rhox homeobox family, member 1						gamete generation (GO:0007276)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|sexual reproduction (GO:0019953)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	10						TAAACCAAACCTACAATCAGA	0.388																																					.		Atlas-SNP	.											.	RHOXF1	24	.	0			c.445-1G>C						.						69	58	62					X																	119243261		2203	4300	6503	SO:0001630	splice_region_variant	158800	exon4			CCAAACCTACAAT		CCDS14593.1	Xq24	2011-06-20			ENSG00000101883	ENSG00000101883		"Homeoboxes / PRD class"	29993	protein-coding gene	gene with protein product		300446				11980563, 12490318	Standard	NM_139282		Approved	OTEX, PEPP1	uc004esk.2	Q8NHV9	OTTHUMG00000022290	ENST00000217999.2:c.445-1G>C	chrX.hg19:g.119243261C>G		64.0	0.0		39.0	35.0	NM_139282	O95030|Q3SYE0	Splice_Site	SNP	ENST00000217999.2	hg19	CCDS14593.1	.	.	.	.	.	.	.	.	.	.	.	13.42	2.233303	0.39498	.	.	ENSG00000101883	ENST00000217999	.	.	.	3.23	3.23	0.37069	.	.	.	.	.	.	.	.	.	.	.	0.38797	D	0.955107	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.1652	0.37048	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RHOXF1	119127289	0.093000	0.21703	0.014000	0.15608	0.604000	0.37047	2.440000	0.44855	1.899000	0.54978	0.600000	0.82982	.	.	.		0.388	RHOXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058083.2	NM_139282	Intron	G	119243261	C	G	119243261	5	3	71	1	0	0	0	0	0	0	1	0	13362	695	24	4	114	4	RHOXF1	23	119243261	Splice_Site	SNP	C	TCGA-CC-A7IF-01A-11D-A33K-10	18434538	119243261	36027299	103	9190										
GPR119	139760	hgsc.bcm.edu	37	chrX	129518890	129518890	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	gaagaagacaaagaggagcaTggctgggaagaagccaacgc	15	7	0	4			TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chrX:129518890T>A	ENST00000276218.2	-	1	621	c.532A>T	c.(532-534)Atg>Ttg	p.M178L		NM_178471.2	NP_848566.1	Q8TDV5	GP119_HUMAN	G protein-coupled receptor 119	178					insulin secretion (GO:0030073)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(1)	11						AAGAGGAGCATGGCTGGGAAG	0.532																																					p.M178L		Atlas-SNP	.											.	GPR119	34	.	0			c.A532T						.						108	88	95					X																	129518890		2203	4300	6503	SO:0001583	missense	139760	exon1			GGAGCATGGCTGG	AY288416	CCDS14625.1	Xq26.1	2014-01-30			ENSG00000147262	ENSG00000147262		"GPCR / Class A : Orphans"	19060	protein-coding gene	gene with protein product		300513				12044878, 14623098	Standard	NM_178471		Approved	hGPCR2, GPCR2	uc011muv.2	Q8TDV5	OTTHUMG00000022397	ENST00000276218.2:c.532A>T	chrX.hg19:g.129518890T>A	ENSP00000276218:p.Met178Leu	54.0	0.0		38.0	32.0	NM_178471	Q495H7|Q4VBN3	Missense_Mutation	SNP	ENST00000276218.2	hg19	CCDS14625.1	.	.	.	.	.	.	.	.	.	.	T	0.167	-1.075821	0.01903	.	.	ENSG00000147262	ENST00000276218	T	0.28255	1.62	4.75	0.111	0.14619	GPCR, rhodopsin-like superfamily (1);	0.417657	0.24085	N	0.041691	T	0.05593	0.0147	N	0.00750	-1.22	0.22330	N	0.9992	B	0.02656	0.0	B	0.01281	0.0	T	0.27640	-1.0068	10	0.02654	T	1	0.0029	1.1145	0.01711	0.175:0.1613:0.3382:0.3254	.	178	Q8TDV5	GP119_HUMAN	L	178	ENSP00000276218:M178L	ENSP00000276218:M178L	M	-	1	0	GPR119	129346571	0.998000	0.40836	0.906000	0.35671	0.906000	0.53458	1.313000	0.33585	-0.332000	0.08489	-0.483000	0.04790	ATG	.	.		0.532	GPR119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058270.1	NM_178471		A	129518890	T	A	129518890	3	1	71	1	0	0	0	0	1	0	0	0	6642	1464	51	4	479	4	GPR119	23	129518890	Missense_Mutation	SNP	T	TCGA-CC-A7IF-01A-11D-A33K-10	10275629	129518890	25751670	104	9191										
RPS4Y1	6192	hgsc.bcm.edu	37	chrY	2722723	2722724	+	Frame_Shift_Ins	INS	-	-	CT													0.0388349514563107	4	1	1.0325138778747	0.838917525773196	1.11855670103093	0.582043343653251	1	0	catgatgctcgaaccatccgINSctacccagatcctgtcatca							TCGA-CC-A7IF-01A-11D-A33K-10	TCGA-CC-A7IF-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6bd5100-cf29-4f48-82d6-9f3a0c8891a2	37a06484-87a9-4ed4-b9bc-9f9a5ae7a317	g.chrY:2722723_2722724insCT	ENST00000250784.8	+	5	582_583	c.443_444insCT	c.(442-447)cgctacfs	p.Y149fs	RPS4Y1_ENST00000477725.1_3'UTR	NM_001008.3	NP_000999.1	P22090	RS4Y1_HUMAN	ribosomal protein S4, Y-linked 1	149					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)	RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			kidney(1)|lung(2)	3						CGAACCATCCGCTACCCAGATC	0.421																																					p.R148fs	Melanoma(193;1927 2965 17170 18413)	Atlas-Indel,Pindel	.											.	RPS4Y1	4	.	0			c.443_444insCT						.																																			SO:0001589	frameshift_variant	6192	exon5			.		CCDS14773.1	Yp11.3	2011-04-05	2004-05-21	2004-05-26	ENSG00000129824	ENSG00000129824		"S ribosomal proteins"	10425	protein-coding gene	gene with protein product	"ribosomal protein S4Y", "40S ribosomal protein S4, Y"	470000	"ribosomal protein S4, Y-linked"	RPS4Y			Standard	NM_001008		Approved	MGC5070, MGC119100, S4	uc004fqi.3	P22090	OTTHUMG00000036152	ENST00000250784.8:c.444_445dupCT	chrY.hg19:g.2722724_2722725dupCT	ENSP00000250784:p.Tyr149fs	141.0	0.0		122.0	99.0	NM_001008	A8K9V4	Frame_Shift_Ins	INS	ENST00000250784.8	hg19	CCDS14773.1																																																																																			.	.		0.421	RPS4Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088052.2	NM_001008		CT	2722724	-	CT	2722723	7	5	71	1	0	1	1	0	0	0	0	0	13661	1087	38	0	461	0	RPS4Y1	24	2722723	Frame_Shift_Ins	INS	-	TCGA-CC-A7IF-01A-11D-A33K-10		2722723	56650843	105	9192										
AURKAIP1	54998	hgsc.bcm.edu	37	chr1	1309214	1309214	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	aggtagatcttgggggtctgCcagccttcgggggcttcctt	15	10	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr1:1309214C>A	ENST00000338370.3	-	3	967	c.567G>T	c.(565-567)tgG>tgT	p.W189C	AURKAIP1_ENST00000378853.3_Missense_Mutation_p.W189C|AURKAIP1_ENST00000489799.1_5'Flank|AURKAIP1_ENST00000338338.5_Missense_Mutation_p.W189C|AURKAIP1_ENST00000321751.5_Missense_Mutation_p.W189C			Q9NWT8	AKIP_HUMAN	aurora kinase A interacting protein 1	189					negative regulation of mitosis (GO:0045839)|positive regulation of proteolysis (GO:0045862)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				kidney(1)|lung(2)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.82e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TGGGGGTCTGCCAGCCTTCGG	0.587																																					p.W189C		Atlas-SNP	.											.	AURKAIP1	12	.	0			c.G567T						.						43	50	48					1																	1309214		2203	4295	6498	SO:0001583	missense	54998	exon4			GGTCTGCCAGCCT		CCDS25.1	1p36.33	2014-02-12			ENSG00000175756	ENSG00000175756			24114	protein-coding gene	gene with protein product		609183				12244051	Standard	NM_017900		Approved	AKIP, AIP, FLJ20608	uc009vkb.1	Q9NWT8	OTTHUMG00000001413	ENST00000338370.3:c.567G>T	chr1.hg19:g.1309214C>A	ENSP00000342676:p.Trp189Cys	7.0	0.0		15.0	13.0	NM_001127230	Q5TA36|Q8TBD3	Missense_Mutation	SNP	ENST00000338370.3	hg19	CCDS25.1	.	.	.	.	.	.	.	.	.	.	c	15.96	2.988082	0.53934	.	.	ENSG00000175756	ENST00000338338;ENST00000338370;ENST00000321751;ENST00000378853	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	4.29	4.29	0.51040	.	0.000000	0.64402	D	0.000001	T	0.53012	0.1770	L	0.59436	1.845	0.80722	D	1	B	0.33748	0.423	B	0.38327	0.271	T	0.58651	-0.7599	10	0.52906	T	0.07	-19.491	14.27	0.66147	0.0:1.0:0.0:0.0	.	189	Q9NWT8	AKIP_HUMAN	C	189	ENSP00000340656:W189C;ENSP00000342676:W189C;ENSP00000319778:W189C;ENSP00000368130:W189C	ENSP00000319778:W189C	W	-	3	0	AURKAIP1	1299077	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	5.266000	0.65525	2.097000	0.63578	0.655000	0.94253	TGG	.	.		0.587	AURKAIP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008273.1	NM_017900		A	1309214	C	A	1309214	3	1	72	1	0	0	0	0	1	0	0	0	1222	740	26	3	36	3	AURKAIP1	1	1309214	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10		1309214	247941407	1	9193										
SPOCD1	90853	hgsc.bcm.edu	37	chr1	32256443	32256443	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	acaggagtccctgtggaagtGctggccacggccaaagccat	13	12	0	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr1:32256443G>A	ENST00000360482.2	-	16	3541	c.3412C>T	c.(3412-3414)Cac>Tac	p.H1138Y	SPOCD1_ENST00000373648.2_3'UTR|RP11-84A19.3_ENST00000527035.1_RNA|SPOCD1_ENST00000533231.1_Missense_Mutation_p.H1125Y|SPOCD1_ENST00000257100.3_Missense_Mutation_p.H618Y	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	1138					negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		CTGTGGAAGTGCTGGCCACGG	0.647																																					p.H1138Y		Atlas-SNP	.											.	SPOCD1	109	.	0			c.C3412T						.						20	20	20					1																	32256443		2190	4289	6479	SO:0001583	missense	90853	exon16			GGAAGTGCTGGCC	AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 146"					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.3412C>T	chr1.hg19:g.32256443G>A	ENSP00000353670:p.His1138Tyr	76.0	0.0		66.0	49.0	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	hg19	CCDS347.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.371525	0.42003	.	.	ENSG00000134668	ENST00000257100;ENST00000360482;ENST00000452755;ENST00000533231	T;T;T;T	0.52983	0.66;1.69;0.64;1.68	5.06	1.84	0.25277	.	.	.	.	.	T	0.28499	0.0705	L	0.29908	0.895	0.80722	D	1	B;B;B	0.32653	0.379;0.022;0.261	B;B;B	0.28553	0.091;0.008;0.042	T	0.17349	-1.0372	9	0.87932	D	0	-11.6897	2.7397	0.05250	0.0996:0.1711:0.5199:0.2093	.	1125;561;1138	Q6ZMY3-2;E9PPM7;Q6ZMY3	.;.;SPOC1_HUMAN	Y	618;1138;561;1125	ENSP00000257100:H618Y;ENSP00000353670:H1138Y;ENSP00000399778:H561Y;ENSP00000435851:H1125Y	ENSP00000257100:H618Y	H	-	1	0	SPOCD1	32029030	0.977000	0.34250	0.996000	0.52242	0.960000	0.62799	0.707000	0.25704	0.741000	0.32674	0.655000	0.94253	CAC	.	.		0.647	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		A	32256443	G	A	32256443	3	1	72	1	0	0	0	0	1	0	0	0	15093	1319	46	3	242	3	SPOCD1	1	32256443	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	30947229	32256443	216994178	2	9194										
HOOK1	51361	hgsc.bcm.edu	37	chr1	60324102	60324102	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	atcaacaattcttttcagagActaattgagcagcgtgatac	7	8	3	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr1:60324102A>G	ENST00000371208.3	+	13	1502	c.1245A>G	c.(1243-1245)agA>agG	p.R415R	HOOK1_ENST00000395561.2_Silent_p.R373R|HOOK1_ENST00000465876.1_3'UTR	NM_015888.4	NP_056972.1	Q9UJC3	HOOK1_HUMAN	hook microtubule-tethering protein 1	415	Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatid development (GO:0007286)	FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			biliary_tract(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|urinary_tract(1)	29	all_cancers(7;0.000129)					CTTTTCAGAGACTAATTGAGC	0.313																																					p.R415R		Atlas-SNP	.											.	HOOK1	54	.	0			c.A1245G						.						79	83	82					1																	60324102		2203	4300	6503	SO:0001819	synonymous_variant	51361	exon13			TCAGAGACTAATT	AF044923	CCDS612.1	1p32.1	2013-08-21	2013-08-21		ENSG00000134709	ENSG00000134709			19884	protein-coding gene	gene with protein product		607820	"hook homolog 1 (Drosophila)"			9927460	Standard	XM_005270922		Approved	HK1	uc001czo.3	Q9UJC3	OTTHUMG00000008990	ENST00000371208.3:c.1245A>G	chr1.hg19:g.60324102A>G		251.0	0.0		206.0	167.0	NM_015888	A8K8E9|A8MU44|B4DX15|O60561|Q5TG44	Silent	SNP	ENST00000371208.3	hg19	CCDS612.1																																																																																			.	.		0.313	HOOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024934.1	NM_015888		G	60324102	A	G	60324102	2	3	72	1	0	0	0	0	0	0	0	1	7291	272	10	2		2	HOOK1	1	60324102	Silent	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	28067659	60324102	188926519	3	9195										
KPRP	448834	hgsc.bcm.edu	37	chr1	152733416	152733416	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gcggccagttccccttcctcGcccagggcagtgtgagattc	12	15	0	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr1:152733416G>T	ENST00000606109.1	+	1	1380	c.1352G>T	c.(1351-1353)cGc>cTc	p.R451L	KPRP_ENST00000368773.1_Missense_Mutation_p.R451L			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	451	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCCTTCCTCGCCCAGGGCAG	0.617																																					p.R451L		Atlas-SNP	.											.	KPRP	152	.	0			c.G1352T						.						150	149	149					1																	152733416		2203	4300	6503	SO:0001583	missense	448834	exon2			TTCCTCGCCCAGG	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1352G>T	chr1.hg19:g.152733416G>T	ENSP00000475216:p.Arg451Leu	32.0	0.0		52.0	48.0	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	hg19	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.733361	0.48939	.	.	ENSG00000203786	ENST00000368773	T	0.15834	2.39	4.61	3.69	0.42338	.	0.189519	0.24323	N	0.039536	T	0.07773	0.0195	L	0.52573	1.65	0.09310	N	1	P	0.38020	0.615	B	0.41440	0.357	T	0.13656	-1.0501	10	0.56958	D	0.05	-1.0544	5.9247	0.19104	0.0963:0.0:0.7121:0.1916	.	451	Q5T749	KPRP_HUMAN	L	451	ENSP00000357762:R451L	ENSP00000357762:R451L	R	+	2	0	KPRP	151000040	0.000000	0.05858	0.002000	0.10522	0.214000	0.24535	0.351000	0.20096	1.280000	0.44463	0.462000	0.41574	CGC	.	.		0.617	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		T	152733416	G	T	152733416	3	4	72	1	0	0	0	0	1	0	0	0	8445	1087	38	1	1354	1	KPRP	1	152733416	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	92409314	152733416	96517205	4	9196										
ATP8B2	57198	hgsc.bcm.edu	37	chr1	154320946	154320946	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ccattgtgctcaccacagtcGtctgcatcatgcccgtggtt	9	14	3	0	rs368404389	byFrequency	TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr1:154320946G>A	ENST00000368489.3	+	27	3325	c.3325G>A	c.(3325-3327)Gtc>Atc	p.V1109I		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	1095					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CACCACAGTCGTCTGCATCAT	0.607													G|||	17	0.00339457	0	0	5008	,	,		10810	0		0	False		,,,				2504	0.0174				p.V1109I		Atlas-SNP	.											ATP8B2,bladder,carcinoma,0,1	ATP8B2	158	.	0			c.G3325A						.						92	76	81					1																	154320946		2203	4300	6503	SO:0001583	missense	57198	exon27			ACAGTCGTCTGCA	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.3325G>A	chr1.hg19:g.154320946G>A	ENSP00000357475:p.Val1109Ile	75.0	0.0		113.0	94.0	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	hg19	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	G	11.46	1.645918	0.29246	.	.	ENSG00000143515	ENST00000368489	T	0.42513	0.97	4.55	4.55	0.56014	.	0.222920	0.37577	N	0.002028	T	0.08980	0.0222	N	0.05177	-0.1	0.80722	D	1	B	0.14012	0.009	B	0.17433	0.018	T	0.14671	-1.0464	10	0.09843	T	0.71	.	11.984	0.53135	0.0:0.1753:0.8246:0.0	.	1109	P98198-3	.	I	1109	ENSP00000357475:V1109I	ENSP00000357475:V1109I	V	+	1	0	ATP8B2	152587570	0.995000	0.38212	0.981000	0.43875	0.778000	0.44026	2.371000	0.44248	2.349000	0.79799	0.491000	0.48974	GTC	.	.		0.607	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		A	154320946	G	A	154320946	3	1	72	1	0	0	0	0	1	0	0	0	1195	1145	40	1	3561	1	ATP8B2	1	154320946	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	1587530	154320946	94929675	5	9197										
RUSC1	23623	hgsc.bcm.edu	37	chr1	155292170	155292170	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ttggaggaagaggacgagagGgcggagcaggatctccctac	17	8	1	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr1:155292170G>A	ENST00000368352.5	+	2	757	c.606G>A	c.(604-606)agG>agA	p.R202R	RUSC1_ENST00000368349.4_5'Flank|RUSC1_ENST00000368354.3_Silent_p.R202R|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1_ENST00000292254.4_5'Flank|RUSC1_ENST00000368347.4_5'Flank|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1-AS1_ENST00000450199.1_RNA|RUSC1-AS1_ENST00000543656.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1	202					positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			AGGACGAGAGGGCGGAGCAGG	0.577																																					p.R202R		Atlas-SNP	.											.	RUSC1	85	.	0			c.G606A						.						50	52	51					1																	155292170		1924	4143	6067	SO:0001819	synonymous_variant	23623	exon2			CGAGAGGGCGGAG	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.606G>A	chr1.hg19:g.155292170G>A		228.0	0.0		363.0	310.0	NM_001105203	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Silent	SNP	ENST00000368352.5	hg19	CCDS41410.1																																																																																			.	.		0.577	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			A	155292170	G	A	155292170	2	1	72	1	0	0	0	0	0	0	0	1	13765	1223	43	3		3	RUSC1	1	155292170	Silent	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	971224	155292170	93958451	6	9198										
OR6Y1	391112	hgsc.bcm.edu	37	chr1	158517456	158517456	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	agcatcctccagccagtgtgCcacagagctggttggtcatg	12	12	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr1:158517456C>G	ENST00000302617.3	-	1	439	c.440G>C	c.(439-441)gGc>gCc	p.G147A		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	147						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G147A(1)		NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					AGCCAGTGTGCCACAGAGCTG	0.473																																					p.G147A		Atlas-SNP	.											OR6Y1,NS,carcinoma,0,1	OR6Y1	73	.	1	Substitution - Missense(1)	lung(1)	c.G440C						.						67	58	61					1																	158517456		2203	4300	6503	SO:0001583	missense	391112	exon1			AGTGTGCCACAGA	BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"GPCR / Class A : Olfactory receptors"	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.440G>C	chr1.hg19:g.158517456C>G	ENSP00000304807:p.Gly147Ala	72.0	0.0		91.0	83.0	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	hg19	CCDS30899.1	.	.	.	.	.	.	.	.	.	.	C	5.039	0.192940	0.09599	.	.	ENSG00000197532	ENST00000302617	T	0.35789	1.29	5.13	5.13	0.70059	GPCR, rhodopsin-like superfamily (1);	0.159452	0.29410	N	0.012223	T	0.05456	0.0144	N	0.03983	-0.305	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.23154	-1.0196	10	0.07482	T	0.82	.	12.2129	0.54389	0.0:0.7183:0.2817:0.0	.	147	Q8NGX8	OR6Y1_HUMAN	A	147	ENSP00000304807:G147A	ENSP00000304807:G147A	G	-	2	0	OR6Y1	156784080	0.000000	0.05858	0.692000	0.30179	0.875000	0.50365	0.305000	0.19254	2.653000	0.90120	0.563000	0.77884	GGC	.	.		0.473	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		G	158517456	C	G	158517456	3	3	72	1	0	0	0	0	1	0	0	0	11222	739	26	4	539	4	OR6Y1	1	158517456	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	3225286	158517456	90733165	7	9199										
C1orf111	284680	hgsc.bcm.edu	37	chr1	162344018	162344018	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ccctccctgaagcccctcttGatgtggctcttgaggaagtc	10	14	2	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr1:162344018G>T	ENST00000367935.5	-	3	685	c.606C>A	c.(604-606)atC>atA	p.I202I	RP11-565P22.6_ENST00000431696.1_Intron	NM_182581.3	NP_872387.2	Q5T0L3	CA111_HUMAN	chromosome 1 open reading frame 111	202										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			AGCCCCTCTTGATGTGGCTCT	0.602																																					p.I202I		Atlas-SNP	.											.	C1orf111	26	.	0			c.C606A						.						110	109	109					1																	162344018		2203	4300	6503	SO:0001819	synonymous_variant	284680	exon3			CCTCTTGATGTGG	BC032957	CCDS1238.1	1q23.3	2008-02-05			ENSG00000171722	ENSG00000171722			27648	protein-coding gene	gene with protein product						12477932	Standard	NM_182581		Approved		uc001gbx.2	Q5T0L3	OTTHUMG00000031375	ENST00000367935.5:c.606C>A	chr1.hg19:g.162344018G>T		89.0	0.0		122.0	42.0	NM_182581	Q6X961|Q8NEC3	Silent	SNP	ENST00000367935.5	hg19	CCDS1238.1																																																																																			.	.		0.602	C1orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076791.2	NM_182581		T	162344018	G	T	162344018	2	4	72	1	0	0	0	0	0	0	0	1	1986	1280	45	3		3	C1orf111	1	162344018	Silent	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	3826562	162344018	86906603	8	9200										
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220406172	220406172	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gttcattttcttcccatgctCcccaaccatcatcttcccag	3	17	4	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr1:220406172C>A	ENST00000358951.2	-	2	265	c.149G>T	c.(148-150)gGa>gTa	p.G50V		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	50					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		TTCCCATGCTCCCCAACCATC	0.328																																					p.G50V		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.G149T						.						215	194	201					1																	220406172		2203	4300	6503	SO:0001583	missense	25782	exon2			CATGCTCCCCAAC	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.149G>T	chr1.hg19:g.220406172C>A	ENSP00000351832:p.Gly50Val	111.0	0.0		213.0	178.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	hg19	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	C	17.30	3.355798	0.61293	.	.	ENSG00000118873	ENST00000358951	T	0.32988	1.43	5.51	5.51	0.81932	.	0.050568	0.85682	D	0.000000	T	0.36413	0.0966	L	0.36672	1.1	0.80722	D	1	P;B	0.52842	0.956;0.383	P;B	0.51016	0.656;0.203	T	0.07443	-1.0772	10	0.72032	D	0.01	.	15.27	0.73693	0.0:1.0:0.0:0.0	.	50;50	Q9H2M9-2;Q9H2M9	.;RBGPR_HUMAN	V	50	ENSP00000351832:G50V	ENSP00000351832:G50V	G	-	2	0	RAB3GAP2	218472795	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.187000	0.58344	2.756000	0.94617	0.655000	0.94253	GGA	.	.		0.328	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		A	220406172	C	A	220406172	3	1	72	1	0	0	0	0	1	0	0	0	12951	855	30	3	4168	3	RAB3GAP2	1	220406172	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	58062154	220406172	28844449	9	9201										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1241790	1241790	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gggagctgacacttcagaacGtgagcacacggtgtttctga	13	9	2	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr2:1241790G>A	ENST00000308624.5	+	10	978		c.e10+1		SNTG2_ENST00000407292.1_Splice_Site	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2						central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		ACTTCAGAACGTGAGCACACG	0.507																																					.		Atlas-SNP	.											.	SNTG2	125	.	0			c.849+1G>A						.						33	37	35					2																	1241790		2181	4273	6454	SO:0001630	splice_region_variant	54221	exon10			CAGAACGTGAGCA	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.849+1G>A	chr2.hg19:g.1241790G>A		44.0	0.0		51.0	15.0	NM_018968	Q05AH5	Splice_Site	SNP	ENST00000308624.5	hg19	CCDS46220.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.005186	0.35415	.	.	ENSG00000172554	ENST00000308624;ENST00000407292	.	.	.	4.51	4.51	0.55191	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0898	0.72185	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SNTG2	1224341	1.000000	0.71417	0.879000	0.34478	0.125000	0.20455	7.070000	0.76763	2.214000	0.71695	0.655000	0.94253	.	.	.		0.507	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968	Intron	A	1241790	G	A	1241790	5	1	72	1	0	0	0	0	0	0	1	0	14890	1159	40	1	888	1	SNTG2	2	1241790	Splice_Site	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10		1241790	241957583	10	9202										
APOB	338	hgsc.bcm.edu	37	chr2	21246408	21246408	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gaatcttacgttggctacttCcagttttactccagccttgg	8	11	1	0	rs150005693		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr2:21246408C>A	ENST00000233242.1	-	17	2720	c.2593G>T	c.(2593-2595)Gaa>Taa	p.E865*		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	865					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGGCTACTTCCAGTTTTACT	0.408																																					p.E865X		Atlas-SNP	.											.	APOB	761	.	0			c.G2593T						.						111	105	107					2																	21246408		2203	4300	6503	SO:0001587	stop_gained	338	exon17			CTACTTCCAGTTT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.2593G>T	chr2.hg19:g.21246408C>A	ENSP00000233242:p.Glu865*	76.0	0.0		101.0	64.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Nonsense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	37	6.358045	0.97502	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	.	.	.	5.35	4.42	0.53409	.	0.293217	0.29438	N	0.012158	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	.	10.5341	0.44994	0.1166:0.6808:0.2027:0.0	.	.	.	.	X	865	.	ENSP00000233242:E865X	E	-	1	0	APOB	21099913	0.016000	0.18221	0.415000	0.26534	0.324000	0.28378	1.481000	0.35476	2.675000	0.91044	0.655000	0.94253	GAA	.	C|1.000;T|0.000		0.408	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21246408	C	A	21246408	4	1	72	1	0	0	0	0	0	1	0	0	785	864	30	3	11150	3	APOB	2	21246408	Nonsense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	20004618	21246408	221952965	11	9203										
DPYSL5	56896	hgsc.bcm.edu	37	chr2	27156187	27156187	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ggctggtgacgttatcgcagCtgctaagatgcaaggtgagt	15	7	0	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr2:27156187C>G	ENST00000288699.6	+	7	934	c.776C>G	c.(775-777)gCt>gGt	p.A259G	DPYSL5_ENST00000401478.1_Missense_Mutation_p.A259G	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	259					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)|signal transduction (GO:0007165)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			breast(1)|endometrium(5)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTTATCGCAGCTGCTAAGATG	0.542																																					p.A259G		Atlas-SNP	.											.	DPYSL5	69	.	0			c.C776G						.						202	146	165					2																	27156187		2203	4300	6503	SO:0001583	missense	56896	exon7			TCGCAGCTGCTAA	AF264015	CCDS1730.1	2p23.3	2008-02-05			ENSG00000157851	ENSG00000157851			20637	protein-coding gene	gene with protein product		608383				10851247, 11034345	Standard	NM_020134		Approved	CRMP5, Ulip6, CRMP-5, CRAM	uc002rhu.4	Q9BPU6	OTTHUMG00000097071	ENST00000288699.6:c.776C>G	chr2.hg19:g.27156187C>G	ENSP00000288699:p.Ala259Gly	99.0	0.0		129.0	65.0	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Missense_Mutation	SNP	ENST00000288699.6	hg19	CCDS1730.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.260699	0.59431	.	.	ENSG00000157851	ENST00000288699;ENST00000401478	D;D	0.90261	-2.64;-2.64	6.04	5.16	0.70880	Amidohydrolase 1 (1);	0.257421	0.45606	D	0.000358	D	0.89952	0.6864	M	0.68317	2.08	0.37067	D	0.898366	B	0.12013	0.005	B	0.25759	0.063	D	0.88937	0.3377	10	0.54805	T	0.06	-3.3249	14.5526	0.68078	0.0:0.9288:0.0:0.0712	.	259	Q9BPU6	DPYL5_HUMAN	G	259	ENSP00000288699:A259G;ENSP00000385549:A259G	ENSP00000288699:A259G	A	+	2	0	DPYSL5	27009691	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	5.390000	0.66261	1.568000	0.49683	0.561000	0.74099	GCT	.	.		0.542	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134		G	27156187	C	G	27156187	3	3	72	1	0	0	0	0	1	0	0	0	4752	797	28	4	798	4	DPYSL5	2	27156187	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	5909779	27156187	216043186	12	9204										
FEZ2	9637	hgsc.bcm.edu	37	chr2	36808548	36808548	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tctgggtccggtgattcctgCatcatttcttcaatttcttc	7	11	5	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr2:36808548C>T	ENST00000405912.3	-	4	518	c.519G>A	c.(517-519)atG>atA	p.M173I	FEZ2_ENST00000305852.7_Missense_Mutation_p.M2I|FEZ2_ENST00000379245.4_Missense_Mutation_p.M173I	NM_005102.2	NP_005093.2	Q9UHY8	FEZ2_HUMAN	fasciculation and elongation protein zeta 2 (zygin II)	173					axon guidance (GO:0007411)|nervous system development (GO:0007399)|signal transduction (GO:0007165)					breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	7		all_hematologic(82;0.21)				GTGATTCCTGCATCATTTCTT	0.413																																					p.M173I		Atlas-SNP	.											.	FEZ2	13	.	0			c.G519A						.						177	170	172					2																	36808548		1859	4111	5970	SO:0001583	missense	9637	exon4			TTCCTGCATCATT	U60061	CCDS46257.1, CCDS46258.1	2p21	2008-05-15			ENSG00000171055	ENSG00000171055			3660	protein-coding gene	gene with protein product		604826				9096408	Standard	NM_005102		Approved		uc002rpg.2	Q9UHY8	OTTHUMG00000152148	ENST00000405912.3:c.519G>A	chr2.hg19:g.36808548C>T	ENSP00000385112:p.Met173Ile	146.0	0.0		175.0	16.0	NM_001042548	Q5EBN3|Q76LN0|Q99690	Missense_Mutation	SNP	ENST00000405912.3	hg19	CCDS46257.1	.	.	.	.	.	.	.	.	.	.	C	34	5.326875	0.95708	.	.	ENSG00000171055	ENST00000379245;ENST00000305852;ENST00000405912;ENST00000357996	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.60945	0.2308	M	0.67953	2.075	0.80722	D	1	D;D;D;D	0.76494	0.996;0.999;0.993;0.997	D;D;D;D	0.87578	0.986;0.998;0.981;0.992	T	0.55062	-0.8199	9	.	.	.	-14.3986	19.5705	0.95413	0.0:1.0:0.0:0.0	.	173;173;173;2	G3V0F5;Q9UHY8;Q9UHY8-2;Q7Z674	.;FEZ2_HUMAN;.;.	I	173;2;173;72	ENSP00000368547:M173I;ENSP00000305843:M2I;ENSP00000385112:M173I;ENSP00000350685:M72I	.	M	-	3	0	FEZ2	36662052	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.583000	0.82559	2.941000	0.99782	0.655000	0.94253	ATG	.	.		0.413	FEZ2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325432.1			T	36808548	C	T	36808548	3	4	72	1	0	0	0	0	1	0	0	0	5832	710	25	3	647	3	FEZ2	2	36808548	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	9652361	36808548	206390825	13	9205										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99013401	99013401	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	atctcatggaggccctcaccGagtaccccgaagccaagaag	10	14	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr2:99013401G>A	ENST00000272602.2	+	7	1807	c.1768G>A	c.(1768-1770)Gag>Aag	p.E590K	CNGA3_ENST00000409937.1_Missense_Mutation_p.E594K|CNGA3_ENST00000393504.1_Missense_Mutation_p.E590K|CNGA3_ENST00000436404.2_Missense_Mutation_p.E572K			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	590			E -> K (in ACHM2; also found in patients with cone-rod dystrophy; the dose- response relationship for cGMP-activation is shifted toward a lower cGMP concentration). {ECO:0000269|PubMed:15712225, ECO:0000269|PubMed:24903488}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						GGCCCTCACCGAGTACCCCGA	0.617																																					p.E590K		Atlas-SNP	.											.	CNGA3	118	.	0			c.G1768A	GRCh37	CM051026	CNGA3	M		.						54	54	54					2																	99013401		2203	4300	6503	SO:0001583	missense	1261	exon8			CTCACCGAGTACC	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.1768G>A	chr2.hg19:g.99013401G>A	ENSP00000272602:p.Glu590Lys	57.0	0.0		53.0	17.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333316	0.81801	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02	5.42	5.42	0.78866	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.94932	0.8361	L	0.60067	1.865	0.80722	D	1	D;D;D	0.71674	0.978;0.998;0.958	P;D;P	0.67900	0.861;0.954;0.741	D	0.94634	0.7824	10	0.56958	D	0.05	.	18.154	0.89686	0.0:0.0:1.0:0.0	.	594;572;590	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	K	590;572;590;594	ENSP00000377140:E590K;ENSP00000410070:E572K;ENSP00000272602:E590K;ENSP00000386761:E594K	ENSP00000272602:E590K	E	+	1	0	CNGA3	98379833	1.000000	0.71417	0.605000	0.28930	0.542000	0.35054	9.263000	0.95617	2.826000	0.97356	0.563000	0.77884	GAG	.	.		0.617	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		A	99013401	G	A	99013401	3	1	72	1	0	0	0	0	1	0	0	0	3600	1059	37	1	1794	1	CNGA3	2	99013401	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	62204853	99013401	144185972	14	9206										
SLC4A10	57282	hgsc.bcm.edu	37	chr2	162719562	162719562	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cagtcagaaccaaattccatGgacaaaaatggtaaatgttt	7	7	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr2:162719562G>T	ENST00000446997.1	+	6	849	c.756G>T	c.(754-756)atG>atT	p.M252I	SLC4A10_ENST00000535165.1_Missense_Mutation_p.M252I|SLC4A10_ENST00000375514.5_Missense_Mutation_p.M263I|SLC4A10_ENST00000272716.5_Missense_Mutation_p.M252I|SLC4A10_ENST00000421911.1_Missense_Mutation_p.M252I|SLC4A10_ENST00000493021.1_3'UTR|SLC4A10_ENST00000415876.2_Missense_Mutation_p.M252I	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	252					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	CAAATTCCATGGACAAAAATG	0.338																																					p.M263I		Atlas-SNP	.											.	SLC4A10	309	.	0			c.G789T						.						72	78	76					2																	162719562		1865	4123	5988	SO:0001583	missense	57282	exon7			TTCCATGGACAAA		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.756G>T	chr2.hg19:g.162719562G>T	ENSP00000393066:p.Met252Ile	136.0	0.0		110.0	92.0	NM_001178016	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	hg19	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.300954	0.60195	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000535165;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	5.81	5.81	0.92471	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.035707	0.85682	D	0.000000	T	0.60971	0.2310	L	0.54908	1.71	0.58432	D	0.999999	B;B;B;B	0.06786	0.0;0.001;0.0;0.001	B;B;B;B	0.15870	0.005;0.001;0.005;0.014	T	0.53788	-0.8389	10	0.30078	T	0.28	.	19.6853	0.95977	0.0:0.0:1.0:0.0	.	263;252;252;252	F8W675;E7EW28;Q6U841-2;Q6U841	.;.;.;S4A10_HUMAN	I	263;252;252;252;252;252;252;252	ENSP00000364664:M263I;ENSP00000395797:M252I;ENSP00000437527:M252I;ENSP00000272716:M252I;ENSP00000393066:M252I;ENSP00000404486:M252I	ENSP00000272716:M252I	M	+	3	0	SLC4A10	162427808	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.799000	0.85936	2.759000	0.94783	0.591000	0.81541	ATG	.	.		0.338	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		T	162719562	G	T	162719562	3	4	72	1	0	0	0	0	1	0	0	0	14666	1348	47	3	863	3	SLC4A10	2	162719562	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	63706161	162719562	80479811	15	9207										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171092541	171092541	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gtatgactcttcctatgacgCtcgctgtgacgtctggtcct	10	12	2	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr2:171092541C>A	ENST00000408978.4	+	7	787	c.644C>A	c.(643-645)gCt>gAt	p.A215D	MYO3B_ENST00000409044.3_Missense_Mutation_p.A215D|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Missense_Mutation_p.A224D	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	215	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TCCTATGACGCTCGCTGTGAC	0.483											OREG0014376	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A215D		Atlas-SNP	.											.	MYO3B	320	.	0			c.C644A						.						206	197	200					2																	171092541		2038	4199	6237	SO:0001583	missense	140469	exon7			ATGACGCTCGCTG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.644C>A	chr2.hg19:g.171092541C>A	ENSP00000386213:p.Ala215Asp	77.0	0.0	1890	78.0	17.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	hg19	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.956101	0.53293	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.048517	0.85682	D	0.000000	T	0.65964	0.2742	L	0.31926	0.97	0.46376	D	0.999018	P;D;P;D	0.53462	0.951;0.96;0.835;0.96	P;P;P;P	0.58130	0.743;0.833;0.576;0.833	T	0.66874	-0.5813	10	0.59425	D	0.04	.	13.4829	0.61348	0.0:0.9291:0.0:0.0708	.	215;215;215;215	Q8WXR4-5;B7ZM71;Q8WXR4-4;Q8WXR4	.;.;.;MYO3B_HUMAN	D	215;215;214;224;224	ENSP00000386497:A215D;ENSP00000386213:A215D;ENSP00000446237:A224D;ENSP00000335100:A224D	ENSP00000314213:A214D	A	+	2	0	MYO3B	170800787	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.025000	0.57225	2.793000	0.96121	0.655000	0.94253	GCT	.	.		0.483	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			A	171092541	C	A	171092541	3	1	72	1	0	0	0	0	1	0	0	0	10086	797	28	3	670	3	MYO3B	2	171092541	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	8372979	171092541	72106832	16	9208										
CDCP1	64866	hgsc.bcm.edu	37	chr3	45153829	45153829	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	actgcagctctaaaccgatgCtcttatgagctttgacatcc	7	12	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:45153829C>A	ENST00000296129.1	-	3	535	c.401G>T	c.(400-402)aGc>aTc	p.S134I	CDCP1_ENST00000490471.1_5'UTR|CDCP1_ENST00000425231.2_Missense_Mutation_p.S134I	NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	134						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		TAAACCGATGCTCTTATGAGC	0.552																																					p.S134I		Atlas-SNP	.											.	CDCP1	61	.	0			c.G401T						.						163	169	167					3																	45153829		2203	4300	6503	SO:0001583	missense	64866	exon3			CCGATGCTCTTAT	AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"CD molecules"	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.401G>T	chr3.hg19:g.45153829C>A	ENSP00000296129:p.Ser134Ile	140.0	0.0		163.0	96.0	NM_178181	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Missense_Mutation	SNP	ENST00000296129.1	hg19	CCDS2727.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.626685	0.28978	.	.	ENSG00000163814	ENST00000296129;ENST00000425231	T;T	0.47528	1.81;0.84	5.42	3.51	0.40186	.	0.927239	0.09386	N	0.809238	T	0.42899	0.1223	L	0.47716	1.5	0.09310	N	1	B;B	0.27416	0.178;0.178	B;B	0.30495	0.074;0.116	T	0.39800	-0.9596	10	0.54805	T	0.06	.	7.6706	0.28457	0.0:0.7193:0.0:0.2807	.	134;134	Q9H5V8-3;Q9H5V8	.;CDCP1_HUMAN	I	134	ENSP00000296129:S134I;ENSP00000399342:S134I	ENSP00000296129:S134I	S	-	2	0	CDCP1	45128833	0.003000	0.15002	0.484000	0.27391	0.376000	0.30014	0.158000	0.16422	0.551000	0.29008	0.563000	0.77884	AGC	.	.		0.552	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842		A	45153829	C	A	45153829	3	1	72	1	0	0	0	0	1	0	0	0	3095	797	28	3	2145	3	CDCP1	3	45153829	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10		45153829	152868601	17	9209										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47043973	47043973	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tatgagcagtgggcagcggcGccagtgggagcgcgcccaga	18	11	0	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:47043973G>T	ENST00000450053.3	+	32	5443	c.5264G>T	c.(5263-5265)cGc>cTc	p.R1755L	NBEAL2_ENST00000383740.2_Missense_Mutation_p.R34L|NBEAL2_ENST00000292309.5_Missense_Mutation_p.R1571L	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1755					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.R1755H(1)|p.R1132H(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		GGGCAGCGGCGCCAGTGGGAG	0.577																																					p.R1755L		Atlas-SNP	.											NBEAL2_ENST00000450053,NS,carcinoma,0,2	NBEAL2	267	.	2	Substitution - Missense(2)	lung(2)	c.G5264T						.						40	41	41					3																	47043973		2075	4186	6261	SO:0001583	missense	23218	exon32			AGCGGCGCCAGTG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.5264G>T	chr3.hg19:g.47043973G>T	ENSP00000415034:p.Arg1755Leu	56.0	0.0		46.0	27.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.09|13.09	2.134664|2.134664	0.37630|0.37630	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000292309;ENST00000383740;ENST00000450053	.|T;T;T	.|0.64618	.|-0.06;0.63;-0.11	5.03|5.03	1.62|1.62	0.23740|0.23740	.|.	.|0.507855	.|0.19286	.|N	.|0.118036	T|T	0.56337|0.56337	0.1978|0.1978	M|M	0.72353|0.72353	2.195|2.195	0.40524|0.40524	D|D	0.980869|0.980869	.|B;B	.|0.12630	.|0.006;0.003	.|B;B	.|0.18561	.|0.01;0.022	T|T	0.53158|0.53158	-0.8478|-0.8478	5|10	.|0.72032	.|D	.|0.01	.|.	5.6607|5.6607	0.17667|0.17667	0.2093:0.0:0.6476:0.1431|0.2093:0.0:0.6476:0.1431	.|.	.|1571;1755	.|Q6ZNJ1-2;Q6ZNJ1	.|.;NBEL2_HUMAN	S|L	1043|1571;34;1755	.|ENSP00000292309:R1571L;ENSP00000373246:R34L;ENSP00000415034:R1755L	.|ENSP00000292309:R1571L	A|R	+|+	1|2	0|0	NBEAL2|NBEAL2	47018977|47018977	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.381000|0.381000	0.30169|0.30169	2.278000|2.278000	0.43426|0.43426	0.118000|0.118000	0.18165|0.18165	-0.131000|-0.131000	0.14894|0.14894	GCC|CGC	.	.		0.577	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47043973	G	T	47043973	3	4	72	1	0	0	0	0	1	0	0	0	10198	1087	38	1	5390	1	NBEAL2	3	47043973	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	1890144	47043973	150978457	18	9210										
SETD2	29072	hgsc.bcm.edu	37	chr3	47155493	47155493	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cccatttggacaccgagaagAactgaaatgagaaaaggagg	12	7	0	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:47155493A>T	ENST00000409792.3	-	5	4630	c.4588T>A	c.(4588-4590)Tct>Act	p.S1530T		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1530	AWS. {ECO:0000255|PROSITE- ProRule:PRU00562}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CACCGAGAAGAACTGAAATGA	0.353			"N, F, S, Mis"		clear cell renal carcinoma																																p.S1530T		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.T4588A						.						98	99	99					3																	47155493		2203	4300	6503	SO:0001630	splice_region_variant	29072	exon5			GAGAAGAACTGAA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4587-1T>A	chr3.hg19:g.47155493A>T		116.0	0.0		166.0	12.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	A	18.45	3.625943	0.66901	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	D	0.81659	-1.52	5.44	5.44	0.79542	AWS (2);	0.000000	0.56097	D	0.000039	T	0.74191	0.3684	L	0.39566	1.225	0.80722	D	1	B;B	0.31009	0.303;0.303	B;B	0.27262	0.078;0.078	T	0.74244	-0.3728	10	0.52906	T	0.07	.	15.7674	0.78138	1.0:0.0:0.0:0.0	.	1530;1530	F2Z317;Q9BYW2	.;SETD2_HUMAN	T	1530	ENSP00000386759:S1530T	ENSP00000386759:S1530T	S	-	1	0	SETD2	47130497	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.883000	0.92426	2.188000	0.69820	0.477000	0.44152	TCT	.	.		0.353	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	Missense_Mutation	T	47155493	A	T	47155493	5	4	72	1	0	0	0	0	0	0	1	0	14146	260	9	4	3174	4	SETD2	3	47155493	Splice_Site	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	111520	47155493	150866937	19	9211										
ARL13B	200894	hgsc.bcm.edu	37	chr3	93755396	93755396	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	caaataaatttctgttttagGaaccatgttcagcaatctcg	6	8	3	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:93755396G>A	ENST00000394222.3	+	5	762	c.487G>A	c.(487-489)Gaa>Aaa	p.E163K	ARL13B_ENST00000535334.1_Splice_Site_p.E60K|ARL13B_ENST00000486562.1_3'UTR|ARL13B_ENST00000539730.1_5'UTR|ARL13B_ENST00000303097.7_Splice_Site_p.E56K|ARL13B_ENST00000471138.1_Splice_Site_p.E163K	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	163					cilium assembly (GO:0042384)|dorsal/ventral pattern formation (GO:0009953)|formation of radial glial scaffolds (GO:0021943)|heart looping (GO:0001947)|interneuron migration from the subpallium to the cortex (GO:0021830)|left/right axis specification (GO:0070986)|neural tube patterning (GO:0021532)|nonmotile primary cilium assembly (GO:0035058)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|intracellular (GO:0005622)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(2)	10						TCTGTTTTAGGAACCATGTTC	0.323																																					p.E163K		Atlas-SNP	.											.	ARL13B	52	.	0			c.G487A						.						50	53	52					3																	93755396		2203	4300	6503	SO:0001630	splice_region_variant	200894	exon5			TTTTAGGAACCAT	AL713789	CCDS2924.1, CCDS2925.1, CCDS54615.1	3q11	2014-05-09	2005-11-18	2005-11-18	ENSG00000169379	ENSG00000169379		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	25419	protein-coding gene	gene with protein product		608922	"ADP-ribosylation factor-like 2-like 1"	ARL2L1		15314642, 18674751	Standard	NR_033427		Approved	DKFZp761H079, JBTS8	uc003drf.3	Q3SXY8	OTTHUMG00000159012	ENST00000394222.3:c.487-1G>A	chr3.hg19:g.93755396G>A		282.0	0.0		361.0	37.0	NM_182896	D3DN29|G3V1S8|Q504W8|Q8TCL5	Missense_Mutation	SNP	ENST00000394222.3	hg19	CCDS2925.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.979751	0.92982	.	.	ENSG00000169379	ENST00000535334;ENST00000303097;ENST00000394222;ENST00000471138	T;T;T;T	0.76316	-1.01;-0.42;-1.01;-1.01	5.77	5.77	0.91146	.	0.051837	0.85682	D	0.000000	D	0.84334	0.5449	L	0.54965	1.715	0.80722	D	1	P;P;D;P	0.57571	0.909;0.771;0.98;0.877	P;P;P;P	0.58970	0.701;0.53;0.849;0.627	T	0.82238	-0.0556	9	.	.	.	-13.7506	19.9795	0.97321	0.0:0.0:1.0:0.0	.	60;163;56;163	G3V1S8;B4DLH1;Q3SXY8-2;Q3SXY8	.;.;.;AR13B_HUMAN	K	60;56;163;163	ENSP00000445145:E60K;ENSP00000306225:E56K;ENSP00000377769:E163K;ENSP00000420780:E163K	.	E	+	1	0	ARL13B	95238086	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.294000	0.78760	2.720000	0.93068	0.650000	0.86243	GAA	.	.		0.323	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896	Missense_Mutation	A	93755396	G	A	93755396	5	1	72	1	0	0	0	0	0	0	1	0	929	1188	41	3	505	3	ARL13B	3	93755396	Splice_Site	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	46599903	93755396	104267034	20	9212										
MYH15	22989	hgsc.bcm.edu	37	chr3	108203979	108203979	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gttgctcttctctaggtttcTgtttaaatttcatatttcca	5	8	4	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:108203979T>C	ENST00000273353.3	-	12	1189	c.1133A>G	c.(1132-1134)cAg>cGg	p.Q378R		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	378	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TCTAGGTTTCTGTTTAAATTT	0.418																																					p.Q378R		Atlas-SNP	.											.	MYH15	223	.	0			c.A1133G						.						134	124	127					3																	108203979		1872	4101	5973	SO:0001583	missense	22989	exon12			GGTTTCTGTTTAA	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1133A>G	chr3.hg19:g.108203979T>C	ENSP00000273353:p.Gln378Arg	65.0	0.0		70.0	29.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	19.55	3.849548	0.71603	.	.	ENSG00000144821	ENST00000273353	D	0.87809	-2.3	6.05	6.05	0.98169	Myosin head, motor domain (2);	.	.	.	.	D	0.89252	0.6662	M	0.79614	2.46	0.48395	D	0.999641	B	0.12013	0.005	B	0.30401	0.115	D	0.86424	0.1756	9	0.66056	D	0.02	.	16.5932	0.84781	0.0:0.0:0.0:1.0	.	378	Q9Y2K3	MYH15_HUMAN	R	378	ENSP00000273353:Q378R	ENSP00000273353:Q378R	Q	-	2	0	MYH15	109686669	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.089000	0.71384	2.320000	0.78422	0.528000	0.53228	CAG	.	.		0.418	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		C	108203979	T	C	108203979	3	2	72	1	0	0	0	0	1	0	0	0	10043	1580	55	2	4831	2	MYH15	3	108203979	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	14448583	108203979	89818451	21	9213										
SLC35A5	55032	hgsc.bcm.edu	37	chr3	112300032	112300032	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gtctttgacttcaggccctcCctggaatttttcttggaagc	9	11	3	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:112300032C>T	ENST00000492406.1	+	6	1351	c.1068C>T	c.(1066-1068)tcC>tcT	p.S356S	SLC35A5_ENST00000460713.1_3'UTR	NM_017945.2	NP_060415.1	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5	356					nucleotide-sugar transport (GO:0015780)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)|sugar:proton symporter activity (GO:0005351)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|skin(1)	11						TCAGGCCCTCCCTGGAATTTT	0.453																																					p.S356S		Atlas-SNP	.											.	SLC35A5	40	.	0			c.C1068T						.						65	66	65					3																	112300032		2203	4299	6502	SO:0001819	synonymous_variant	55032	exon6			GCCCTCCCTGGAA	AK000737	CCDS2967.1	3q13.13	2013-05-22			ENSG00000138459	ENSG00000138459		"Solute carriers"	20792	protein-coding gene	gene with protein product							Standard	NM_017945		Approved	FLJ20730	uc003dze.4	Q9BS91	OTTHUMG00000159263	ENST00000492406.1:c.1068C>T	chr3.hg19:g.112300032C>T		118.0	0.0		136.0	44.0	NM_017945	D3DN66|Q69YY6|Q6ZMD6|Q9NWM9	Silent	SNP	ENST00000492406.1	hg19	CCDS2967.1																																																																																			.	.		0.453	SLC35A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354184.1	NM_017945		T	112300032	C	T	112300032	2	4	72	1	0	0	0	0	0	0	0	1	14589	610	22	3		3	SLC35A5	3	112300032	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	4096053	112300032	85722398	22	9214										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112326103	112326103	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gaatggttatgtggcgcagaCctgagagaaaaaagaaaacc	12	6	0	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:112326103C>T	ENST00000206423.3	-	7	3379	c.2426G>A	c.(2425-2427)gGt>gAt	p.G809D	CCDC80_ENST00000439685.2_Splice_Site_p.G809D	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	809					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						GTGGCGCAGACCTGAGAGAAA	0.363																																					p.G809D		Atlas-SNP	.											.	CCDC80	100	.	0			c.G2426A						.						80	76	77					3																	112326103		2203	4300	6503	SO:0001630	splice_region_variant	151887	exon7			CGCAGACCTGAGA	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.2426-1G>A	chr3.hg19:g.112326103C>T		85.0	0.0		129.0	19.0	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	hg19	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.928462	0.52759	.	.	ENSG00000091986	ENST00000206423;ENST00000439685;ENST00000479368	T;T;T	0.38887	1.11;1.11;1.11	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.52980	0.1768	N	0.25286	0.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.47724	-0.9095	10	0.33141	T	0.24	.	19.976	0.97309	0.0:1.0:0.0:0.0	.	809;809	A3KC71;Q76M96	.;CCD80_HUMAN	D	809;809;87	ENSP00000206423:G809D;ENSP00000411814:G809D;ENSP00000418188:G87D	ENSP00000206423:G809D	G	-	2	0	CCDC80	113808793	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.152000	0.77419	2.713000	0.92767	0.655000	0.94253	GGT	.	.		0.363	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511	Missense_Mutation	T	112326103	C	T	112326103	5	4	72	1	0	0	0	0	0	0	1	0	2856	521	18	3	434	3	CCDC80	3	112326103	Splice_Site	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	26071	112326103	85696327	23	9215										
KLF15	28999	hgsc.bcm.edu	37	chr3	126062613	126062613	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ggctgctccgcgggaagcggTgcaccttgatgtgcttggag	17	10	0	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:126062613T>A	ENST00000296233.3	-	3	1438	c.1208A>T	c.(1207-1209)cAc>cTc	p.H403L		NM_014079.3	NP_054798.1	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	403					cardiac muscle hypertrophy in response to stress (GO:0014898)|cellular response to peptide (GO:1901653)|glial cell differentiation (GO:0010001)|glomerular visceral epithelial cell differentiation (GO:0072112)|glucose transport (GO:0015758)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(7)|ovary(2)|skin(2)	12				GBM - Glioblastoma multiforme(114;0.147)		CGGGAAGCGGTGCACCTTGAT	0.647																																					p.H403L		Atlas-SNP	.											.	KLF15	40	.	0			c.A1208T						.						52	50	50					3																	126062613		2203	4300	6503	SO:0001583	missense	28999	exon3			AAGCGGTGCACCT	AB029254	CCDS3036.1	3q21.3	2013-01-08			ENSG00000163884	ENSG00000163884		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	14536	protein-coding gene	gene with protein product	"kidney-enriched Kruppel-like factor"	606465				10982849	Standard	NM_014079		Approved	KKLF	uc011bkk.1	Q9UIH9	OTTHUMG00000162689	ENST00000296233.3:c.1208A>T	chr3.hg19:g.126062613T>A	ENSP00000296233:p.His403Leu	261.0	0.0		210.0	52.0	NM_014079		Missense_Mutation	SNP	ENST00000296233.3	hg19	CCDS3036.1	.	.	.	.	.	.	.	.	.	.	T	32	5.125359	0.94429	.	.	ENSG00000163884	ENST00000296233	T	0.78816	-1.21	5.13	5.13	0.70059	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.87708	0.6245	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89294	0.3621	10	0.87932	D	0	.	12.8907	0.58069	0.0:0.0:0.0:1.0	.	403	Q9UIH9	KLF15_HUMAN	L	403	ENSP00000296233:H403L	ENSP00000296233:H403L	H	-	2	0	KLF15	127545303	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.916000	0.87491	1.931000	0.55961	0.260000	0.18958	CAC	.	.		0.647	KLF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370096.1	NM_014079		A	126062613	T	A	126062613	3	1	72	1	0	0	0	0	1	0	0	0	8352	1696	59	4	46	4	KLF15	3	126062613	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	13736510	126062613	71959817	24	9216										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130103715	130103715	+	Missense_Mutation	SNP	C	C	A													0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	caagcagcatccaggagaaaCagtttgagcaaatcaagaga							TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:130103715C>A	ENST00000432398.2	+	5	1863	c.1369C>A	c.(1369-1371)Cag>Aag	p.Q457K	COL6A5_ENST00000265379.6_Missense_Mutation_p.Q457K	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	457	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						CCAGGAGAAACAGTTTGAGCA	0.418																																					p.Q457K		Atlas-SNP	.											.	COL6A5	205	.	0			c.C1369A						.						91	82	85					3																	130103715		692	1591	2283	SO:0001583	missense	256076	exon5			GAGAAACAGTTTG	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.1369C>A	chr3.hg19:g.130103715C>A	ENSP00000390895:p.Gln457Lys	100.0	0.0		131.0	69.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.	.	.	.	.	.	.	.	.	.	C	7.833	0.720224	0.15372	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.75821	-0.97;-0.97	5.82	-4.32	0.03688	.	.	.	.	.	T	0.67571	0.2907	L	0.46157	1.445	0.09310	N	1	B	0.09022	0.002	B	0.18871	0.023	T	0.57027	-0.7881	9	0.62326	D	0.03	.	16.2869	0.82725	0.0:0.2127:0.659:0.1284	.	457	A8TX70-2	.	K	457	ENSP00000390895:Q457K;ENSP00000265379:Q457K	ENSP00000265379:Q457K	Q	+	1	0	COL6A5	131586405	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.365000	0.07573	-0.758000	0.04690	-2.568000	0.00172	CAG	.	.		0.418	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		A	130103715	C	A	130103715	3	1	72	1	0	0	0	0	1	0	0	0	3704	479	17	3	1383	3	COL6A5	3	130103715	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	4041102	130103715	67918715	25	9217	41	2								
COL6A5	256076	hgsc.bcm.edu	37	chr3	130103724	130103724	+	Missense_Mutation	SNP	C	C	G													0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tccaggagaaacagtttgagCaaatcaagagatttatgttg							TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:130103724C>G	ENST00000432398.2	+	5	1872	c.1378C>G	c.(1378-1380)Caa>Gaa	p.Q460E	COL6A5_ENST00000265379.6_Missense_Mutation_p.Q460E	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	460	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						ACAGTTTGAGCAAATCAAGAG	0.433																																					p.Q460E		Atlas-SNP	.											.	COL6A5	205	.	0			c.C1378G						.						93	84	87					3																	130103724		692	1591	2283	SO:0001583	missense	256076	exon5			TTTGAGCAAATCA	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.1378C>G	chr3.hg19:g.130103724C>G	ENSP00000390895:p.Gln460Glu	103.0	0.0		134.0	67.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.	.	.	.	.	.	.	.	.	.	C	8.110	0.778660	0.16120	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.82255	-1.59;-1.59	5.82	-1.3	0.09259	.	.	.	.	.	T	0.73024	0.3534	L	0.28014	0.82	0.09310	N	0.999997	B	0.06786	0.001	B	0.10450	0.005	T	0.53690	-0.8403	9	0.02654	T	1	.	23.2065	0.99980	0.0:0.1713:0.8287:0.0	.	460	A8TX70-2	.	E	460	ENSP00000390895:Q460E;ENSP00000265379:Q460E	ENSP00000265379:Q460E	Q	+	1	0	COL6A5	131586414	0.863000	0.29885	0.012000	0.15200	0.002000	0.02628	1.329000	0.33770	-0.185000	0.10550	-0.312000	0.09012	CAA	.	.		0.433	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		G	130103724	C	G	130103724	3	3	72	1	0	0	0	0	1	0	0	0	3704	711	25	4	1392	4	COL6A5	3	130103724	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	9	130103724	67918706	26	9218	41	2								
TSC22D2	9819	hgsc.bcm.edu	37	chr3	150127752	150127752	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ggggattgcattagacacagCagtacttttgaccagactgc	11	9	0	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:150127752C>T	ENST00000361875.3	+	1	1631	c.615C>T	c.(613-615)agC>agT	p.S205S	TSC22D2_ENST00000361136.2_Silent_p.S205S	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	205					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TTAGACACAGCAGTACTTTTG	0.617																																					p.S205S		Atlas-SNP	.											.	TSC22D2	42	.	0			c.C615T						.						81	83	82					3																	150127752		2203	4300	6503	SO:0001819	synonymous_variant	9819	exon1			ACACAGCAGTACT	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.615C>T	chr3.hg19:g.150127752C>T		101.0	0.0		111.0	26.0	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Silent	SNP	ENST00000361875.3	hg19	CCDS3149.1																																																																																			.	.		0.617	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779		T	150127752	C	T	150127752	2	4	72	1	0	0	0	0	0	0	0	1	16623	709	25	3		3	TSC22D2	3	150127752	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	20024028	150127752	47894678	27	9219										
WDR49	151790	hgsc.bcm.edu	37	chr3	167277885	167277885	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tctgtgctgccagtcaaaagCcgagtctcatttgcatcaag	9	11	4	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:167277885C>T	ENST00000308378.3	-	5	923	c.618G>A	c.(616-618)cgG>cgA	p.R206R	WDR49_ENST00000476376.1_Silent_p.R31R|WDR49_ENST00000479765.1_Intron|WDR49_ENST00000453925.2_Silent_p.R259R	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	206										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						CAGTCAAAAGCCGAGTCTCAT	0.458																																					p.R206R		Atlas-SNP	.											.	WDR49	188	.	0			c.G618A						.						186	170	175					3																	167277885		2203	4300	6503	SO:0001819	synonymous_variant	151790	exon5			CAAAAGCCGAGTC	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.618G>A	chr3.hg19:g.167277885C>T		94.0	0.0		138.0	35.0	NM_178824	Q8N297	Silent	SNP	ENST00000308378.3	hg19	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	C	6.840	0.524142	0.13066	.	.	ENSG00000174776	ENST00000472600	.	.	.	4.94	4.06	0.47325	.	.	.	.	.	T	0.69223	0.3087	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68416	-0.5414	4	.	.	.	.	13.8469	0.63472	0.1545:0.8455:0.0:0.0	.	.	.	.	D	271	.	.	G	-	2	0	WDR49	168760579	0.999000	0.42202	0.986000	0.45419	0.665000	0.39181	1.393000	0.34497	1.196000	0.43129	0.591000	0.81541	GGC	.	.		0.458	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		T	167277885	C	T	167277885	2	4	72	1	0	0	0	0	0	0	0	1	17317	726	26	3		3	WDR49	3	167277885	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	17150133	167277885	30744545	28	9220										
EPHB3	2049	hgsc.bcm.edu	37	chr3	184295208	184295208	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tatcctgggcacccccagagCggcccaacggagtcatcctg	11	16	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:184295208C>A	ENST00000330394.2	+	6	1884	c.1432C>A	c.(1432-1434)Cgg>Agg	p.R478R	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	478	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			ACCCCCAGAGCGGCCCAACGG	0.612																																					p.R478R		Atlas-SNP	.											.	EPHB3	114	.	0			c.C1432A						.						50	54	53					3																	184295208		2203	4300	6503	SO:0001819	synonymous_variant	2049	exon6			CCAGAGCGGCCCA	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3394	protein-coding gene	gene with protein product		601839	"EphB3"	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.1432C>A	chr3.hg19:g.184295208C>A		380.0	1.0		377.0	201.0	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	hg19	CCDS3268.1																																																																																			.	.		0.612	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		A	184295208	C	A	184295208	2	1	72	1	0	0	0	0	0	0	0	1	5178	759	27	1		1	EPHB3	3	184295208	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	17017323	184295208	13727222	29	9221										
LMLN	89782	hgsc.bcm.edu	37	chr3	197687166	197687166	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ttactcgggctcaggcccggGccggagccggtggcgctgga	18	13	1	0	rs547037533		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr3:197687166G>T	ENST00000330198.4	+	1	96	c.74G>T	c.(73-75)gGc>gTc	p.G25V	LMLN_ENST00000420910.2_Missense_Mutation_p.G25V|IQCG_ENST00000480302.1_5'Flank|IQCG_ENST00000265239.6_5'Flank|LMLN_ENST00000332636.5_Silent_p.G13G|LMLN_ENST00000482695.1_Silent_p.G13G	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	25					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		TCAGGCCCGGGCCGGAGCCGG	0.697																																					p.G25V		Atlas-SNP	.											.	LMLN	53	.	0			c.G74T						.						23	29	27					3																	197687166		2200	4295	6495	SO:0001583	missense	89782	exon1			GCCCGGGCCGGAG	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.74G>T	chr3.hg19:g.197687166G>T	ENSP00000328829:p.Gly25Val	92.0	0.0		114.0	33.0	NM_001136049	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	hg19	CCDS3332.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.904640	0.33628	.	.	ENSG00000185621	ENST00000330198;ENST00000420910	T;T	0.49432	0.78;0.83	3.85	-0.54	0.11861	.	0.666329	0.13088	N	0.414790	T	0.28433	0.0703	N	0.19112	0.55	0.19300	N	0.999979	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.17137	-1.0379	10	0.56958	D	0.05	0.0861	6.5932	0.22658	0.0:0.3255:0.3414:0.3331	.	25;25	Q96KR4;F8WB28	LMLN_HUMAN;.	V	25	ENSP00000328829:G25V;ENSP00000410926:G25V	ENSP00000328829:G25V	G	+	2	0	LMLN	199171563	0.000000	0.05858	0.015000	0.15790	0.677000	0.39632	0.194000	0.17135	-0.220000	0.09988	0.456000	0.33151	GGC	.	.		0.697	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029		T	197687166	G	T	197687166	3	4	72	1	0	0	0	0	1	0	0	0	8856	1203	42	3	76	3	LMLN	3	197687166	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	13391958	197687166	335264	30	9222										
ZFYVE28	57732	hgsc.bcm.edu	37	chr4	2273119	2273119	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gtgcagaagccacaggcctcGtctggcacccactccggggg	14	15	1	1	rs146945400		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr4:2273119G>A	ENST00000290974.2	-	12	2790	c.2451C>T	c.(2449-2451)gaC>gaT	p.D817D	ZFYVE28_ENST00000508471.1_Silent_p.D122D|ZFYVE28_ENST00000511071.1_Silent_p.D787D|ZFYVE28_ENST00000515312.1_Silent_p.D747D	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	817					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						CACAGGCCTCGTCTGGCACCC	0.662																																					p.D817D		Atlas-SNP	.											ZFYVE28,NS,carcinoma,0,1	ZFYVE28	79	.	0			c.C2451T						.	G	,,	0,4402		0,0,2201	24	24	24		2361,2241,2451	-5.9	0.3	4	dbSNP_134	24	1,8591		0,1,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	ZFYVE28	NM_001172656.1,NM_001172659.1,NM_020972.2	,,	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	,,	787/858,747/818,817/888	2273119	1,12993	2201	4296	6497	SO:0001819	synonymous_variant	57732	exon12			GGCCTCGTCTGGC	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"Zinc fingers, FYVE domain containing"	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.2451C>T	chr4.hg19:g.2273119G>A		93.0	0.0		120.0	29.0	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Silent	SNP	ENST00000290974.2	hg19	CCDS33942.1																																																																																			.	G|1.000;A|0.000		0.662	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371		A	2273119	G	A	2273119	2	1	72	1	0	0	0	0	0	0	0	1	17685	1136	40	1		1	ZFYVE28	4	2273119	Silent	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10		2273119	188881157	31	9223										
SORCS2	57537	hgsc.bcm.edu	37	chr4	7705958	7705958	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cacaacttcaccagcacctcGgtgtttgtggacgggctgct	11	13	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr4:7705958G>T	ENST00000507866.2	+	14	1924	c.1815G>T	c.(1813-1815)tcG>tcT	p.S605S	SORCS2_ENST00000329016.9_Silent_p.S433S	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	605					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						CCAGCACCTCGGTGTTTGTGG	0.637																																					p.S605S		Atlas-SNP	.											.	SORCS2	98	.	0			c.G1815T						.						50	59	56					4																	7705958		2134	4233	6367	SO:0001819	synonymous_variant	57537	exon14			CACCTCGGTGTTT	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.1815G>T	chr4.hg19:g.7705958G>T		60.0	0.0		85.0	25.0	NM_020777	Q9P2L7	Silent	SNP	ENST00000507866.2	hg19	CCDS47008.1																																																																																			.	.		0.637	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		T	7705958	G	T	7705958	2	4	72	1	0	0	0	0	0	0	0	1	14946	1103	39	1		1	SORCS2	4	7705958	Silent	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	5432839	7705958	183448318	32	9224										
CHRNA9	55584	hgsc.bcm.edu	37	chr4	40351330	40351330	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ttatctcccagcagcctccgGagaaaaggtctccctgggag	11	13	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr4:40351330G>T	ENST00000310169.2	+	4	936	c.797G>T	c.(796-798)gGa>gTa	p.G266V		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	266					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|inner ear morphogenesis (GO:0042472)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine-activated cation-selective channel activity (GO:0004889)|calcium channel activity (GO:0005262)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(4)|stomach(1)	33					Galantamine(DB00674)|Nicotine(DB00184)	GCAGCCTCCGGAGAAAAGGTC	0.507																																					p.G266V	Esophageal Squamous(115;1297 1602 22235 25158 43327)	Atlas-SNP	.											.	CHRNA9	53	.	0			c.G797T						.						169	179	175					4																	40351330		2203	4300	6503	SO:0001583	missense	55584	exon4			CCTCCGGAGAAAA	AF227732	CCDS3459.1	4p14	2012-02-11	2012-02-07		ENSG00000174343	ENSG00000174343		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	14079	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 9 (neuronal)"	605116	"cholinergic receptor, nicotinic, alpha polypeptide 9"				Standard	NM_017581		Approved	NACHRA9	uc003gva.2	Q9UGM1	OTTHUMG00000099375	ENST00000310169.2:c.797G>T	chr4.hg19:g.40351330G>T	ENSP00000312663:p.Gly266Val	208.0	0.0		252.0	138.0	NM_017581	Q14CY7|Q4W5A2|Q9NYV2	Missense_Mutation	SNP	ENST00000310169.2	hg19	CCDS3459.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122748	0.77436	.	.	ENSG00000174343	ENST00000310169	D	0.88431	-2.38	5.55	4.71	0.59529	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.044547	0.85682	D	0.000000	D	0.95535	0.8549	M	0.92459	3.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96330	0.9243	10	0.87932	D	0	.	14.1466	0.65355	0.0719:0.0:0.9281:0.0	.	266	Q9UGM1	ACHA9_HUMAN	V	266	ENSP00000312663:G266V	ENSP00000312663:G266V	G	+	2	0	CHRNA9	40046087	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.869000	0.99810	1.360000	0.45960	0.561000	0.74099	GGA	.	.		0.507	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1			T	40351330	G	T	40351330	3	4	72	1	0	0	0	0	1	0	0	0	3391	1174	41	3	811	3	CHRNA9	4	40351330	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	32645372	40351330	150802946	33	9225										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55156636	55156636	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gtctggatgagcagagactgAgcgctgacagtggctacatc	14	9	1	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr4:55156636A>G	ENST00000257290.5	+	22	3368	c.3037A>G	c.(3037-3039)Agc>Ggc	p.S1013G	FIP1L1_ENST00000507166.1_Missense_Mutation_p.S773G	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	1013					adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	GCAGAGACTGAGCGCTGACAG	0.547			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.S1013G	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	.	PDGFRA	1583	.	0			c.A3037G						.						195	161	173					4																	55156636		2203	4300	6503	SO:0001583	missense	5156	exon22	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	AGACTGAGCGCTG	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.3037A>G	chr4.hg19:g.55156636A>G	ENSP00000257290:p.Ser1013Gly	126.0	0.0		186.0	24.0	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	hg19	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.596622	0.86953	.	.	ENSG00000145216;ENSG00000134853	ENST00000507166;ENST00000257290	T;T	0.78246	-1.16;-0.99	5.92	5.92	0.95590	.	0.000000	0.37483	U	0.002079	D	0.84188	0.5417	L	0.45581	1.43	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.83123	-0.0117	10	0.37606	T	0.19	.	16.3594	0.83251	1.0:0.0:0.0:0.0	.	1013	P16234	PGFRA_HUMAN	G	773;1013	ENSP00000423325:S773G;ENSP00000257290:S1013G	ENSP00000423325:S773G	S	+	1	0	FIP1L1;PDGFRA	54851393	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	8.803000	0.91915	2.266000	0.75297	0.455000	0.32223	AGC	.	.		0.547	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		G	55156636	A	G	55156636	3	3	72	1	0	0	0	0	1	0	0	0	11670	304	11	2	3119	2	PDGFRA	4	55156636	Missense_Mutation	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	14805306	55156636	135997640	34	9226										
SLC9A3	6550	hgsc.bcm.edu	37	chr5	475176	475176	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	caccgtctccccgggagacaGccagggcggcagcctggcca	14	17	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr5:475176G>T	ENST00000264938.3	-	16	2332	c.2323C>A	c.(2323-2325)Ctg>Atg	p.L775M	CTD-2228K2.5_ENST00000510604.1_5'Flank|CTD-2228K2.5_ENST00000342584.3_5'Flank|CTD-2228K2.5_ENST00000510714.1_5'Flank|CTD-2228K2.7_ENST00000606319.1_RNA|SLC9A3_ENST00000514375.1_Missense_Mutation_p.L766M|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	775					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CCGGGAGACAGCCAGGGCGGC	0.677																																					p.L775M		Atlas-SNP	.											.	SLC9A3	89	.	0			c.C2323A						.						27	34	32					5																	475176		2202	4298	6500	SO:0001583	missense	6550	exon16			GAGACAGCCAGGG		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.2323C>A	chr5.hg19:g.475176G>T	ENSP00000264938:p.Leu775Met	107.0	0.0		93.0	44.0	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	hg19	CCDS3855.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.851622	0.51270	.	.	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.74737	-0.87;-0.87	4.81	1.46	0.22682	.	7.006960	0.00357	N	0.000021	D	0.83640	0.5298	M	0.75264	2.295	0.29344	N	0.865825	D;D	0.71674	0.998;0.981	P;P	0.61658	0.892;0.77	T	0.62020	-0.6942	10	0.34782	T	0.22	.	7.2475	0.26129	0.2229:0.0:0.6406:0.1366	.	766;775	E9PF67;P48764	.;SL9A3_HUMAN	M	775;766	ENSP00000264938:L775M;ENSP00000422983:L766M	ENSP00000264938:L775M	L	-	1	2	SLC9A3	528176	0.999000	0.42202	0.988000	0.46212	0.957000	0.61999	1.019000	0.30014	0.436000	0.26393	0.462000	0.41574	CTG	.	.		0.677	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		T	475176	G	T	475176	3	4	72	1	0	0	0	0	1	0	0	0	14728	962	34	3	189	3	SLC9A3	5	475176	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10		475176	180440084	35	9227										
SLC6A3	6531	hgsc.bcm.edu	37	chr5	1406399	1406399	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	atgtcgtcgctgaactgcccAacacctgagggagaagaggt	13	10	0	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr5:1406399A>T	ENST00000270349.9	-	12	1630	c.1503T>A	c.(1501-1503)gtT>gtA	p.V501V	SLC6A3_ENST00000453492.2_Silent_p.V501V	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	501					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	TGAACTGCCCAACACCTGAGG	0.637																																					p.V501V		Atlas-SNP	.											.	SLC6A3	102	.	0			c.T1503A						.						74	68	70					5																	1406399		2203	4300	6503	SO:0001819	synonymous_variant	6531	exon12			CTGCCCAACACCT		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"Solute carriers"	11049	protein-coding gene	gene with protein product	"dopamine transporter"	126455	"solute carrier family 6 (neurotransmitter transporter, dopamine), member 3", "dopamine transporter 1"	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1503T>A	chr5.hg19:g.1406399A>T		87.0	0.0		86.0	27.0	NM_001044	A2RUN4|Q14996	Silent	SNP	ENST00000270349.9	hg19	CCDS3863.1																																																																																			.	.		0.637	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		T	1406399	A	T	1406399	2	4	72	1	0	0	0	0	0	0	0	1	14700	117	5	4		4	SLC6A3	5	1406399	Silent	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	931223	1406399	179508861	36	9228										
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65371047	65371047	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ctagacaaggccatgaactgGcaaaacaagaggtaagaata	10	7	0	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr5:65371047G>T	ENST00000284037.5	+	23	4341	c.3952G>T	c.(3952-3954)Gca>Tca	p.A1318S	ERBB2IP_ENST00000416865.2_Missense_Mutation_p.A516S|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.A1273S|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.A1266S|ERBB2IP_ENST00000380935.1_Intron|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.A1277S|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.A1277S|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.A1325S|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.A1277S|ERBB2IP_ENST00000503913.1_Intron|ERBB2IP_ENST00000508515.1_Intron	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1318					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		CCATGAACTGGCAAAACAAGA	0.363																																					p.A1325S		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.G3973T						.						81	83	82					5																	65371047		2203	4300	6503	SO:0001583	missense	55914	exon23			GAACTGGCAAAAC		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"densin-180-like protein", "ERBB2-interacting protein"	606944	"erbb2-interacting protein"			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.3952G>T	chr5.hg19:g.65371047G>T	ENSP00000284037:p.Ala1318Ser	294.0	0.0		323.0	155.0	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	hg19	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.582986	0.28268	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000416865;ENST00000380939;ENST00000380936;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000512354	T;T;T;T;T;T;T;T	0.38560	1.41;1.45;1.45;1.44;1.57;1.13;1.44;1.43	5.57	4.7	0.59300	PDZ/DHR/GLGF (1);	0.353110	0.28187	N	0.016277	T	0.27169	0.0666	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.08055	0.001;0.002;0.002;0.003;0.001;0.001;0.002	T	0.06250	-1.0837	10	0.09338	T	0.73	.	13.2407	0.59995	0.0:0.0:0.5899:0.4101	.	516;1277;1325;1325;1273;1318;1277	B4DIP2;Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-2	.;.;.;.;.;LAP2_HUMAN;.	S	1318;1277;516;1266;1277;1277;1273;1325;155	ENSP00000284037:A1318S;ENSP00000370330:A1277S;ENSP00000397833:A516S;ENSP00000370326:A1266S;ENSP00000370323:A1277S;ENSP00000370325:A1277S;ENSP00000422766:A1273S;ENSP00000426632:A1325S	ENSP00000284037:A1318S	A	+	1	0	ERBB2IP	65406803	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.134000	0.42102	1.335000	0.45486	0.650000	0.86243	GCA	.	.		0.363	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		T	65371047	G	T	65371047	3	4	72	1	0	0	0	0	1	0	0	0	5209	1203	42	3	3907	3	ERBB2IP	5	65371047	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	63964648	65371047	115544213	37	9229										
VCAN	1462	hgsc.bcm.edu	37	chr5	82816787	82816787	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ttagatttcagccaactacaTcaactggtattgcagaaaag	7	8	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr5:82816787T>A	ENST00000265077.3	+	7	3227	c.2662T>A	c.(2662-2664)Tca>Aca	p.S888T	VCAN_ENST00000512590.2_Missense_Mutation_p.S840T|VCAN_ENST00000342785.4_Missense_Mutation_p.S888T|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	888	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	GCCAACTACATCAACTGGTAT	0.388																																					p.S888T		Atlas-SNP	.											.	VCAN	498	.	0			c.T2662A						.						107	111	109					5																	82816787		2203	4300	6503	SO:0001583	missense	1462	exon7			ACTACATCAACTG	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2662T>A	chr5.hg19:g.82816787T>A	ENSP00000265077:p.Ser888Thr	84.0	0.0		114.0	52.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.448756	0.26074	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.27104	1.69;1.69;1.69	5.8	-0.797	0.10909	.	0.795307	0.10853	N	0.626997	T	0.17023	0.0409	L	0.60455	1.87	0.09310	N	1	B;P	0.47106	0.417;0.89	B;B	0.38378	0.153;0.272	T	0.19321	-1.0309	10	0.33940	T	0.23	.	0.3142	0.00292	0.2399:0.1797:0.154:0.4264	.	888;888	P13611-3;P13611	.;CSPG2_HUMAN	T	888;888;840	ENSP00000265077:S888T;ENSP00000342768:S888T;ENSP00000425959:S840T	ENSP00000265077:S888T	S	+	1	0	VCAN	82852543	0.001000	0.12720	0.495000	0.27527	0.738000	0.42128	0.426000	0.21363	0.442000	0.26555	0.533000	0.62120	TCA	.	.		0.388	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82816787	T	A	82816787	3	1	72	1	0	0	0	0	1	0	0	0	17153	1435	50	4	2684	4	VCAN	5	82816787	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	17445740	82816787	98098473	38	9230										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135561777	135561777	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cattttcacagcttttggccTtagatttgcagagttttatg	8	7	1	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr5:135561777T>A	ENST00000513104.1	-	9	2489	c.2207A>T	c.(2206-2208)aAg>aTg	p.K736M	TRPC7_ENST00000426057.2_Missense_Mutation_p.K620M|TRPC7_ENST00000355180.3_Missense_Mutation_p.K675M	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	736					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCTTTTGGCCTTAGATTTGCA	0.408																																					p.K736M		Atlas-SNP	.											.	TRPC7	126	.	0			c.A2207T						.						86	78	80					5																	135561777		1909	4119	6028	SO:0001583	missense	57113	exon9			TTGGCCTTAGATT	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.2207A>T	chr5.hg19:g.135561777T>A	ENSP00000426070:p.Lys736Met	122.0	0.0		148.0	50.0	NM_020389	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	hg19	CCDS47267.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.61|18.61	3.661672|3.661672	0.67700|0.67700	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000355180;ENST00000426057;ENST00000513104;ENST00000265193|ENST00000352189;ENST00000378459;ENST00000502753	D;D;D|.	0.81821|.	-1.54;-1.54;-1.54|.	4.99|4.99	4.99|4.99	0.66335|0.66335	.|.	0.120318|.	0.64402|.	D|.	0.000014|.	T|.	0.68467|.	0.3004|.	L|L	0.55213|0.55213	1.73|1.73	0.43076|0.43076	D|D	0.994728|0.994728	D;B;B;B|.	0.54397|.	0.966;0.104;0.444;0.444|.	P;B;B;B|.	0.52554|.	0.702;0.089;0.401;0.401|.	T|.	0.67741|.	-0.5592|.	10|.	0.66056|.	D|.	0.02|.	-24.4053|-24.4053	14.8563|14.8563	0.70341|0.70341	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	620;675;681;736|.	Q8IWP7;F5H5U9;Q70T25;Q9HCX4|.	.;.;.;TRPC7_HUMAN|.	M|Y	675;620;736;736|619;674;680	ENSP00000347312:K675M;ENSP00000441628:K620M;ENSP00000426070:K736M|.	ENSP00000265193:K736M|.	K|X	-|-	2|3	0|2	TRPC7|TRPC7	135589676|135589676	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	3.785000|3.785000	0.55424|0.55424	2.094000|2.094000	0.63399|0.63399	0.482000|0.482000	0.46254|0.46254	AAG|TAA	.	.		0.408	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135561777	T	A	135561777	3	1	72	1	0	0	0	0	1	0	0	0	16599	1609	56	4	397	4	TRPC7	5	135561777	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	52744990	135561777	45353483	39	9231										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140180920	140180920	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	aagcatggcaccttcgtgggCcgcatcgcgcaggacctggg	15	13	0	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr5:140180920C>A	ENST00000522353.2	+	1	138	c.138C>A	c.(136-138)ggC>ggA	p.G46G	PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA3_ENST00000532566.2_Silent_p.G46G|PCDHA2_ENST00000526136.1_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	46	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTTCGTGGGCCGCATCGCGC	0.662																																					p.G46G		Atlas-SNP	.											.	PCDHA3	396	.	0			c.C138A						.						53	62	59					5																	140180920		2203	4300	6503	SO:0001819	synonymous_variant	56145	exon1			CGTGGGCCGCATC	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.138C>A	chr5.hg19:g.140180920C>A		58.0	0.0		51.0	16.0	NM_031497	O75286	Silent	SNP	ENST00000522353.2	hg19	CCDS54915.1																																																																																			.	.		0.662	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		A	140180920	C	A	140180920	2	1	72	1	0	0	0	0	0	0	0	1	11534	726	26	3		3	PCDHA3	5	140180920	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	4619143	140180920	40734340	40	9232										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222940	140222940	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	agcggccaggctccaaaagcGtcatcgaggcagtcggctgg	15	12	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr5:140222940G>A	ENST00000531613.1	+	1	2034	c.2034G>A	c.(2032-2034)gcG>gcA	p.A678A	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA8_ENST00000378123.3_Silent_p.A678A|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	678	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCAAAAGCGTCATCGAGGC	0.632																																					p.A678A		Atlas-SNP	.											PCDHA8_ENST00000531613,NS,carcinoma,0,2	PCDHA8	366	.	0			c.G2034A						.						67	66	66					5																	140222940		2196	4266	6462	SO:0001819	synonymous_variant	56140	exon1			AAAAGCGTCATCG	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.2034G>A	chr5.hg19:g.140222940G>A		83.0	0.0		95.0	55.0	NM_031856	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	hg19	CCDS54919.1																																																																																			.	.		0.632	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		A	140222940	G	A	140222940	2	1	72	1	0	0	0	0	0	0	0	1	11539	1132	40	1		1	PCDHA8	5	140222940	Silent	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	42020	140222940	40692320	41	9233										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140562729	140562730	+	Frame_Shift_Ins	INS	-	-	A													0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tgagctagtgttggataaagINSagctggatcgggaggaggag							TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr5:140562729_140562730insA	ENST00000361016.2	+	1	1750_1751	c.595_596insA	c.(595-597)gagfs	p.E199fs		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	199	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTTGGATAAAGAGCTGGATCGG	0.48																																					p.E199fs		Atlas-Indel,Pindel	.											.	PCDHB16	159	.	0			c.595_596insA						.																																			SO:0001589	frameshift_variant	57717	exon1			.	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.596dupA	chr5.hg19:g.140562730_140562730dupA	ENSP00000354293:p.Glu199fs	69.0	0.0		77.0	28.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Frame_Shift_Ins	INS	ENST00000361016.2	hg19	CCDS4251.1																																																																																			.	.		0.48	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140562730	-	A	140562729	7	5	72	1	0	1	1	0	0	0	0	0	11550	943	33	0	597	0	PCDHB16	5	140562729	Frame_Shift_Ins	INS	-	TCGA-CC-A7IG-01A-11D-A33K-10	339789	140562729	40352531	42	9234										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140573693	140573693	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	caggtcgctggactacgaggCcctgcaggctttcgagttcc	13	13	0	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr5:140573693C>A	ENST00000239446.4	+	1	1752	c.1568C>A	c.(1567-1569)gCc>gAc	p.A523D		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	523	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GACTACGAGGCCCTGCAGGCT	0.706																																					p.A523D		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C1568A						.						91	110	103					5																	140573693		2203	4298	6501	SO:0001583	missense	56126	exon1			ACGAGGCCCTGCA	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1568C>A	chr5.hg19:g.140573693C>A	ENSP00000239446:p.Ala523Asp	53.0	0.0		62.0	21.0	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	hg19	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	c	15.99	2.995331	0.54147	.	.	ENSG00000120324	ENST00000239446	T	0.03301	3.98	3.53	3.53	0.40419	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.03827	0.0108	N	0.25201	0.72	0.36476	D	0.867571	B	0.26512	0.151	B	0.33690	0.168	T	0.40156	-0.9578	9	0.62326	D	0.03	.	9.1868	0.37176	0.3799:0.6201:0.0:0.0	.	523	Q9UN67	PCDBA_HUMAN	D	523	ENSP00000239446:A523D	ENSP00000239446:A523D	A	+	2	0	PCDHB10	140553877	0.009000	0.17119	0.993000	0.49108	0.971000	0.66376	1.474000	0.35398	1.994000	0.58287	0.549000	0.68633	GCC	.	.		0.706	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		A	140573693	C	A	140573693	3	1	72	1	0	0	0	0	1	0	0	0	11544	739	26	3	1570	3	PCDHB10	5	140573693	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	10964	140573693	40341567	43	9235										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169081429	169081429	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	atatacaacttccaaggcagCggagccccccagctctccct	7	17	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr5:169081429C>A	ENST00000256935.8	+	2	146	c.66C>A	c.(64-66)agC>agA	p.S22R		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	22	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCAAGGCAGCGGAGCCCCCC	0.562																																					p.S22R		Atlas-SNP	.											.	DOCK2	389	.	0			c.C66A						.						73	78	76					5																	169081429		2203	4300	6503	SO:0001583	missense	1794	exon2			AGGCAGCGGAGCC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.66C>A	chr5.hg19:g.169081429C>A	ENSP00000256935:p.Ser22Arg	51.0	0.0		50.0	16.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	0.900	-0.722739	0.03158	.	.	ENSG00000134516	ENST00000256935	T	0.08634	3.07	5.82	-11.6	0.00059	Src homology-3 domain (3);Variant SH3 (1);	0.736937	0.14140	N	0.338787	T	0.02807	0.0084	N	0.10707	0.03	0.09310	N	1	B	0.19445	0.036	B	0.20577	0.03	T	0.32903	-0.9889	10	0.26408	T	0.33	.	10.682	0.45819	0.0854:0.4963:0.0:0.4183	.	22	Q92608	DOCK2_HUMAN	R	22	ENSP00000256935:S22R	ENSP00000256935:S22R	S	+	3	2	DOCK2	169014007	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-2.616000	0.00881	-2.552000	0.00479	-2.412000	0.00220	AGC	.	.		0.562	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169081429	C	A	169081429	3	1	72	1	0	0	0	0	1	0	0	0	4689	767	27	1	72	1	DOCK2	5	169081429	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	28507736	169081429	11833831	44	9236										
F13A1	2162	hgsc.bcm.edu	37	chr6	6248626	6248626	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gctctgtccatcacatacagGcaagtgtccaggatgccatc	9	13	2	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr6:6248626G>T	ENST00000264870.3	-	6	982	c.717C>A	c.(715-717)tgC>tgA	p.C239*		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	239					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TCACATACAGGCAAGTGTCCA	0.423																																					p.C239X		Atlas-SNP	.											.	F13A1	135	.	0			c.C717A						.						83	74	77					6																	6248626		2203	4300	6503	SO:0001587	stop_gained	2162	exon6			ATACAGGCAAGTG	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"Transglutaminases"	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.717C>A	chr6.hg19:g.6248626G>T	ENSP00000264870:p.Cys239*	35.0	0.0		60.0	24.0	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Nonsense_Mutation	SNP	ENST00000264870.3	hg19	CCDS4496.1	.	.	.	.	.	.	.	.	.	.	G	39	7.555049	0.98355	.	.	ENSG00000124491	ENST00000264870;ENST00000441301	.	.	.	4.99	3.21	0.36854	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.054	0.42233	0.1625:0.0:0.8375:0.0	.	.	.	.	X	239;176	.	ENSP00000264870:C239X	C	-	3	2	F13A1	6193625	1.000000	0.71417	0.987000	0.45799	0.928000	0.56348	1.969000	0.40510	0.512000	0.28257	0.563000	0.77884	TGC	.	.		0.423	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129		T	6248626	G	T	6248626	4	4	72	1	0	0	0	0	0	1	0	0	5342	1195	42	3	1521	3	F13A1	6	6248626	Nonsense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10		6248626	164866441	45	9237										
MYLIP	29116	hgsc.bcm.edu	37	chr6	16145305	16145305	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gctctgtacaatgctggcgtTgtggacctcgtttcaagaaa	11	9	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr6:16145305T>A	ENST00000356840.3	+	6	1203	c.1005T>A	c.(1003-1005)gtT>gtA	p.V335V	MYLIP_ENST00000349606.4_Silent_p.V154V	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	335					cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			ATGCTGGCGTTGTGGACCTCG	0.483																																					p.V335V		Atlas-SNP	.											.	MYLIP	44	.	0			c.T1005A						.						114	117	116					6																	16145305		2203	4300	6503	SO:0001819	synonymous_variant	29116	exon6			TGGCGTTGTGGAC	AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.1005T>A	chr6.hg19:g.16145305T>A		141.0	0.0		213.0	97.0	NM_013262	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Silent	SNP	ENST00000356840.3	hg19	CCDS4536.1																																																																																			.	.		0.483	MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043864.1	NM_013262		A	16145305	T	A	16145305	2	1	72	1	0	0	0	0	0	0	0	1	10064	1799	63	4		4	MYLIP	6	16145305	Silent	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	9896679	16145305	154969762	46	9238										
SLC17A1	6568	hgsc.bcm.edu	37	chr6	25811666	25811666	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	atttataaacactccacccaAgcaaaagctgcctgttgcac	5	13	0	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr6:25811666A>G	ENST00000244527.4	-	10	1253	c.1138T>C	c.(1138-1140)Ttg>Ctg	p.L380L	SLC17A1_ENST00000476801.1_Silent_p.L380L|SLC17A1_ENST00000427328.1_Silent_p.L326L|SLC17A1_ENST00000468082.1_Silent_p.L326L	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	380					ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						ACTCCACCCAAGCAAAAGCTG	0.383																																					p.L380L		Atlas-SNP	.											.	SLC17A1	71	.	0			c.T1138C						.						144	149	147					6																	25811666		2203	4300	6503	SO:0001819	synonymous_variant	6568	exon10			CACCCAAGCAAAA		CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"Solute carriers"	10929	protein-coding gene	gene with protein product		182308	"solute carrier family 17 (sodium phosphate), member 1"	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.1138T>C	chr6.hg19:g.25811666A>G		250.0	0.0		395.0	26.0	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Silent	SNP	ENST00000244527.4	hg19	CCDS4565.1																																																																																			.	.		0.383	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2			G	25811666	A	G	25811666	2	3	72	1	0	0	0	0	0	0	0	1	14431	69	3	2		2	SLC17A1	6	25811666	Silent	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	9666361	25811666	145303401	47	9239										
SLC17A1	6568	hgsc.bcm.edu	37	chr6	25811734	25811734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tgtagaaggtggaactcaggTaaggcaggcagacaccaaag	14	7	1	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr6:25811734T>C	ENST00000244527.4	-	10	1185	c.1070A>G	c.(1069-1071)tAc>tGc	p.Y357C	SLC17A1_ENST00000476801.1_Missense_Mutation_p.Y357C|SLC17A1_ENST00000427328.1_Missense_Mutation_p.Y303C|SLC17A1_ENST00000468082.1_Missense_Mutation_p.Y303C	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	357					ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						GGAACTCAGGTAAGGCAGGCA	0.453																																					p.Y357C		Atlas-SNP	.											.	SLC17A1	71	.	0			c.A1070G						.						107	109	108					6																	25811734		2203	4300	6503	SO:0001583	missense	6568	exon10			CTCAGGTAAGGCA		CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"Solute carriers"	10929	protein-coding gene	gene with protein product		182308	"solute carrier family 17 (sodium phosphate), member 1"	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.1070A>G	chr6.hg19:g.25811734T>C	ENSP00000244527:p.Tyr357Cys	185.0	0.0		278.0	41.0	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Missense_Mutation	SNP	ENST00000244527.4	hg19	CCDS4565.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.603645	0.28534	.	.	ENSG00000124568	ENST00000244527;ENST00000427328;ENST00000476801;ENST00000468082	T;T;T;T	0.59772	0.24;0.24;0.24;0.24	3.49	2.3	0.28687	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.642833	0.12914	N	0.428672	T	0.63850	0.2546	M	0.84948	2.725	0.19300	N	0.999978	D;D	0.71674	0.996;0.998	D;D	0.70487	0.923;0.969	T	0.53158	-0.8478	10	0.87932	D	0	.	6.905	0.24303	0.0:0.0:0.2367:0.7633	.	303;357	Q14916-2;Q14916	.;NPT1_HUMAN	C	357;303;357;303	ENSP00000244527:Y357C;ENSP00000410549:Y303C;ENSP00000420614:Y357C;ENSP00000420546:Y303C	ENSP00000244527:Y357C	Y	-	2	0	SLC17A1	25919713	0.000000	0.05858	0.265000	0.24526	0.142000	0.21351	-0.060000	0.11712	0.689000	0.31550	0.533000	0.62120	TAC	.	.		0.453	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2			C	25811734	T	C	25811734	3	2	72	1	0	0	0	0	1	0	0	0	14431	1638	57	2	345	2	SLC17A1	6	25811734	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	68	25811734	145303333	48	9240										
DAAM2	23500	hgsc.bcm.edu	37	chr6	39864686	39864686	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	acttcatgaacaaagggcagCgtgggggcgcctacgggttc	15	10	1	1	rs146966805	byFrequency	TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr6:39864686C>A	ENST00000398904.2	+	20	2622	c.2440C>A	c.(2440-2442)Cgt>Agt	p.R814S	RP11-61I13.3_ENST00000430595.1_RNA|RP11-61I13.3_ENST00000437947.1_RNA|RP11-61I13.3_ENST00000420293.1_RNA|RP11-61I13.3_ENST00000606829.1_RNA|DAAM2_ENST00000274867.4_Missense_Mutation_p.R814S|DAAM2_ENST00000538976.1_Missense_Mutation_p.R814S			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	814	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					CAAAGGGCAGCGTGGGGGCGC	0.602																																					p.R814S		Atlas-SNP	.											DAAM2,caecum,carcinoma,0,1	DAAM2	101	.	0			c.C2440A						.						33	40	38					6																	39864686		2007	4165	6172	SO:0001583	missense	23500	exon20			GGGCAGCGTGGGG	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.2440C>A	chr6.hg19:g.39864686C>A	ENSP00000381876:p.Arg814Ser	63.0	0.0		89.0	42.0	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.827612	0.71143	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.19806	2.12;2.12;2.12	4.54	4.54	0.55810	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.49423	0.1556	H	0.96080	3.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.62774	-0.6783	10	0.87932	D	0	.	10.0014	0.41931	0.3183:0.6817:0.0:0.0	.	814;814	G5EA45;Q86T65	.;DAAM2_HUMAN	S	814	ENSP00000274867:R814S;ENSP00000381876:R814S;ENSP00000437808:R814S	ENSP00000274867:R814S	R	+	1	0	DAAM2	39972664	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.447000	0.44917	2.353000	0.79882	0.561000	0.74099	CGT	.	C|0.999;T|0.001		0.602	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			A	39864686	C	A	39864686	3	1	72	1	0	0	0	0	1	0	0	0	4218	768	27	1	2514	1	DAAM2	6	39864686	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	14052952	39864686	131250381	49	9241										
SLC29A1	2030	hgsc.bcm.edu	37	chr6	44198616	44198616	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	caggagaccaagttggacctCattagcaaaggtccgaagag	12	9	1	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr6:44198616C>T	ENST00000393841.1	+	9	1247	c.756C>T	c.(754-756)ctC>ctT	p.L252L	SLC29A1_ENST00000371740.5_Silent_p.L252L|SLC29A1_ENST00000472176.1_3'UTR|SLC29A1_ENST00000371755.3_Silent_p.L252L|SLC29A1_ENST00000371724.1_Silent_p.L252L|SLC29A1_ENST00000371731.1_Silent_p.L252L|SLC29A1_ENST00000371713.1_Silent_p.L252L|SLC29A1_ENST00000313248.7_Silent_p.L331L|SLC29A1_ENST00000371708.1_Silent_p.L252L|SLC29A1_ENST00000427851.2_Silent_p.L252L|SLC29A1_ENST00000393844.1_Silent_p.L252L	NM_001078177.1	NP_001071645.1	Q99808	S29A1_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 1	252					cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|lactation (GO:0007595)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sleep (GO:0030431)|transmembrane transport (GO:0055085)|uridine transport (GO:0015862)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	17	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Cytarabine(DB00987)|Didanosine(DB00900)|Fludarabine(DB01073)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Pemetrexed(DB00642)|Ribavirin(DB00811)|Zalcitabine(DB00943)	AGTTGGACCTCATTAGCAAAG	0.542																																					p.L252L		Atlas-SNP	.											.	SLC29A1	45	.	0			c.C756T						.						88	101	97					6																	44198616		2203	4300	6503	SO:0001819	synonymous_variant	2030	exon8			GGACCTCATTAGC	U81375	CCDS4908.1	6p21.1	2013-07-17	2013-07-17		ENSG00000112759	ENSG00000112759		"Solute carriers"	11003	protein-coding gene	gene with protein product		602193	"solute carrier family 29 (nucleoside transporters), member 1"	ENT1		8986748, 9344680	Standard	NM_004955		Approved		uc003owy.2	Q99808	OTTHUMG00000014759	ENST00000393841.1:c.756C>T	chr6.hg19:g.44198616C>T		75.0	0.0		94.0	53.0	NM_004955	B3KQV7|B3KQY5|Q5T9W9|Q9UJY2	Silent	SNP	ENST00000393841.1	hg19	CCDS4908.1																																																																																			.	.		0.542	SLC29A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040721.1			T	44198616	C	T	44198616	2	4	72	1	0	0	0	0	0	0	0	1	14549	813	29	3		3	SLC29A1	6	44198616	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	4333930	44198616	126916451	50	9242										
ORC3L	23595	hgsc.bcm.edu	37	chr6	88374575	88374575	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tcaacctcgtggactggtcaGaggtaggttgtagggaaaag	15	6	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr6:88374575G>C	ENST00000392844.3	+	18	1996	c.1948G>C	c.(1948-1950)Gag>Cag	p.E650Q	ORC3_ENST00000257789.4_Missense_Mutation_p.E651Q|ORC3_ENST00000546266.1_Missense_Mutation_p.E507Q	NM_012381.3|NM_181837.2	NP_036513.2|NP_862820.1	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3	650					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|neural precursor cell proliferation (GO:0061351)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|origin recognition complex (GO:0000808)	DNA replication origin binding (GO:0003688)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	28						GGACTGGTCAGAGGTAGGTTG	0.418																																					p.E651Q		Atlas-SNP	.											.	ORC3	51	.	0			c.G1951C						.						128	119	122					6																	88374575		2203	4300	6503	SO:0001583	missense	23595	exon18			TGGTCAGAGGTAG	AF093535	CCDS5012.1, CCDS43486.1, CCDS56440.1	6q	2010-10-12	2010-10-12	2010-10-12	ENSG00000135336	ENSG00000135336			8489	protein-coding gene	gene with protein product		604972	"origin recognition complex, subunit 3 (yeast homolog)-like", "origin recognition complex, subunit 3-like (yeast)", "origin recognition complex, subunit 3 honolog (yeast)"	ORC3L		9829972, 10402192	Standard	NM_181837		Approved	IMAGE50150, LATHEO	uc003pmg.3	Q9UBD5	OTTHUMG00000015179	ENST00000392844.3:c.1948G>C	chr6.hg19:g.88374575G>C	ENSP00000376586:p.Glu650Gln	97.0	0.0		119.0	94.0	NM_181837	A2A2T5|B4E025|Q13565|Q53GY6|Q5T159|Q6IUY7|Q86TN5|Q9UG44|Q9UNT6	Missense_Mutation	SNP	ENST00000392844.3	hg19	CCDS43486.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.348521	0.41599	.	.	ENSG00000135336	ENST00000392844;ENST00000257789;ENST00000546266	T;T;T	0.09538	3.36;3.36;2.97	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.03915	0.0110	N	0.04275	-0.24	0.80722	D	1	B;B;P	0.45044	0.063;0.371;0.849	B;B;P	0.47705	0.057;0.213;0.555	T	0.49370	-0.8947	10	0.09843	T	0.71	-18.6999	19.8718	0.96853	0.0:0.0:1.0:0.0	.	588;650;651	B4E014;Q9UBD5;Q9UBD5-2	.;ORC3_HUMAN;.	Q	650;651;507	ENSP00000376586:E650Q;ENSP00000257789:E651Q;ENSP00000444695:E507Q	ENSP00000257789:E651Q	E	+	1	0	ORC3	88431294	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.254000	0.72460	2.808000	0.96608	0.650000	0.86243	GAG	.	.		0.418	ORC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041452.2			C	88374575	G	C	88374575	3	2	72	1	0	0	0	0	1	0	0	0	11272	943	33	4	2021	4	ORC3L	6	88374575	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	44175959	88374575	82740492	51	9243										
LACE1	246269	hgsc.bcm.edu	37	chr6	108645051	108645051	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tatacggttcagacatccgaGagcatgaccccaactgccac	8	14	1	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr6:108645051G>T	ENST00000368977.4	+	2	348	c.162G>T	c.(160-162)gaG>gaT	p.E54D		NM_145315.3	NP_660358.2	Q8WV93	LACE1_HUMAN	lactation elevated 1	54						mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)		AGACATCCGAGAGCATGACCC	0.393																																					p.E54D		Atlas-SNP	.											.	LACE1	30	.	0			c.G162T						.						95	90	92					6																	108645051		2203	4300	6503	SO:0001583	missense	246269	exon2			ATCCGAGAGCATG	AF520418	CCDS5067.1	6q22.1	2006-11-10			ENSG00000135537	ENSG00000135537			16411	protein-coding gene	gene with protein product	"ATPase family gene 1 homolog (S. cerevisiae)"					12079282	Standard	XM_005266885		Approved	AFG1	uc003psj.3	Q8WV93	OTTHUMG00000015324	ENST00000368977.4:c.162G>T	chr6.hg19:g.108645051G>T	ENSP00000357973:p.Glu54Asp	70.0	0.0		83.0	71.0	NM_145315	Q8N6A3	Missense_Mutation	SNP	ENST00000368977.4	hg19	CCDS5067.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.419425	0.25552	.	.	ENSG00000135537	ENST00000368977;ENST00000437715	.	.	.	5.44	-0.536	0.11876	.	0.364212	0.26244	N	0.025490	T	0.11922	0.0290	L	0.36672	1.1	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.27191	-1.0081	9	0.49607	T	0.09	-1.0403	6.8782	0.24158	0.3331:0.2146:0.4523:0.0	.	54	Q8WV93	LACE1_HUMAN	D	54;21	.	ENSP00000357973:E54D	E	+	3	2	LACE1	108751744	0.185000	0.23213	0.003000	0.11579	0.031000	0.12232	0.264000	0.18497	-0.027000	0.13873	-0.326000	0.08463	GAG	.	.		0.393	LACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041719.4	NM_145315		T	108645051	G	T	108645051	3	4	72	1	0	0	0	0	1	0	0	0	8604	933	33	3	168	3	LACE1	6	108645051	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	20270476	108645051	62470016	52	9244										
CCR6	1235	hgsc.bcm.edu	37	chr6	167549831	167549831	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tgagatgttactgtgctcctTgcaggaggtcaggcagttct	13	8	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr6:167549831T>C	ENST00000341935.5	+	3	665	c.113T>C	c.(112-114)tTg>tCg	p.L38S	RP11-517H2.6_ENST00000609590.1_RNA|CCR6_ENST00000400926.2_Missense_Mutation_p.L38S|CCR6_ENST00000349984.4_Missense_Mutation_p.L38S	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	38					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|humoral immune response (GO:0006959)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	14		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		CTGTGCTCCTTGCAGGAGGTC	0.433																																					p.L38S		Atlas-SNP	.											.	CCR6	36	.	0			c.T113C						.						168	163	165					6																	167549831		2203	4300	6503	SO:0001583	missense	1235	exon3			GCTCCTTGCAGGA	U68030	CCDS5298.1	6q27	2012-08-08			ENSG00000112486	ENSG00000112486		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1607	protein-coding gene	gene with protein product		601835		STRL22		8886020	Standard	NM_031409		Approved	CKR-L3, GPR-CY4, CMKBR6, GPR29, DRY-6, DCR2, BN-1, CD196	uc010kkm.3	P51684	OTTHUMG00000016015	ENST00000341935.5:c.113T>C	chr6.hg19:g.167549831T>C	ENSP00000343952:p.Leu38Ser	87.0	0.0		66.0	48.0	NM_004367	E1P5C6|P78553|Q92846	Missense_Mutation	SNP	ENST00000341935.5	hg19	CCDS5298.1	.	.	.	.	.	.	.	.	.	.	T	9.710	1.156913	0.21454	.	.	ENSG00000112486	ENST00000400926;ENST00000341935;ENST00000349984	T;T;T	0.39997	1.05;1.05;1.05	4.72	3.5	0.40072	.	1.042900	0.07696	U	0.939472	T	0.16981	0.0408	L	0.35542	1.07	0.09310	N	1	B	0.25743	0.133	B	0.30716	0.119	T	0.40289	-0.9571	10	0.46703	T	0.11	.	8.5607	0.33509	0.3274:0.0:0.0:0.6726	.	38	P51684	CCR6_HUMAN	S	38	ENSP00000383715:L38S;ENSP00000343952:L38S;ENSP00000339393:L38S	ENSP00000343952:L38S	L	+	2	0	CCR6	167469821	0.998000	0.40836	0.001000	0.08648	0.045000	0.14185	3.655000	0.54460	0.601000	0.29879	0.459000	0.35465	TTG	.	.		0.433	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043118.1			C	167549831	T	C	167549831	3	2	72	1	0	0	0	0	1	0	0	0	2947	1821	63	2	119	2	CCR6	6	167549831	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	58904780	167549831	3565236	53	9245										
HECW1	23072	hgsc.bcm.edu	37	chr7	43484630	43484630	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ggaagaggacagagaagagcCcgagggggctactccaggca	17	9	0	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr7:43484630C>A	ENST00000395891.2	+	11	2464	c.1859C>A	c.(1858-1860)cCc>cAc	p.P620H	HECW1_ENST00000453890.1_Missense_Mutation_p.P620H	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	620					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						AGAGAAGAGCCCGAGGGGGCT	0.697																																					p.P620H		Atlas-SNP	.											.	HECW1	540	.	0			c.C1859A						.						9	14	12					7																	43484630		2015	4156	6171	SO:0001583	missense	23072	exon11			AAGAGCCCGAGGG	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.1859C>A	chr7.hg19:g.43484630C>A	ENSP00000379228:p.Pro620His	34.0	0.0		31.0	11.0	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	hg19	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	C	6.773	0.511580	0.12944	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.29917	1.55;1.55	3.94	-1.94	0.07571	.	4.721370	0.00357	N	0.000035	T	0.18635	0.0447	L	0.29908	0.895	0.09310	N	1	B;B	0.33448	0.168;0.412	B;B	0.27262	0.058;0.078	T	0.07462	-1.0771	10	0.48119	T	0.1	.	0.8368	0.01141	0.2687:0.3582:0.1195:0.2536	.	620;620	B4DH42;Q76N89	.;HECW1_HUMAN	H	620	ENSP00000379228:P620H;ENSP00000407774:P620H	ENSP00000265522:P620H	P	+	2	0	HECW1	43451155	0.000000	0.05858	0.000000	0.03702	0.498000	0.33706	-1.077000	0.03416	-0.570000	0.06022	0.563000	0.77884	CCC	.	.		0.697	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43484630	C	A	43484630	3	1	72	1	0	0	0	0	1	0	0	0	7051	623	22	3	1893	3	HECW1	7	43484630	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10		43484630	115654033	54	9246										
PCLO	27445	hgsc.bcm.edu	37	chr7	82583500	82583500	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	aacaatatgatcagcactagCtctaccatctggtggggcag	10	10	3	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr7:82583500C>A	ENST00000333891.9	-	5	7106	c.6769G>T	c.(6769-6771)Gct>Tct	p.A2257S	PCLO_ENST00000423517.2_Missense_Mutation_p.A2257S	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCAGCACTAGCTCTACCATCT	0.393																																					p.A2257S		Atlas-SNP	.											.	PCLO	1506	.	0			c.G6769T						.						77	74	75					7																	82583500		1874	4096	5970	SO:0001583	missense	27445	exon5			CACTAGCTCTACC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.6769G>T	chr7.hg19:g.82583500C>A	ENSP00000334319:p.Ala2257Ser	56.0	0.0		48.0	16.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	8.245	0.807719	0.16467	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.15718	2.4;2.4	5.7	-2.67	0.06059	.	.	.	.	.	T	0.10852	0.0265	N	0.22421	0.69	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.09377	0.004;0.003	T	0.28964	-1.0027	9	0.87932	D	0	.	9.3097	0.37895	0.0:0.4796:0.1134:0.407	.	2257;2257	Q9Y6V0-5;Q9Y6V0-6	.;.	S	2188;2257;2257	ENSP00000334319:A2257S;ENSP00000388393:A2257S	ENSP00000334319:A2257S	A	-	1	0	PCLO	82421436	0.000000	0.05858	0.015000	0.15790	0.587000	0.36485	-1.073000	0.03430	-0.757000	0.04697	-0.199000	0.12753	GCT	.	.		0.393	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82583500	C	A	82583500	3	1	72	1	0	0	0	0	1	0	0	0	11592	797	28	3	8760	3	PCLO	7	82583500	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	39098870	82583500	76555163	55	9247										
PCLO	27445	hgsc.bcm.edu	37	chr7	82764880	82764880	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gtagtggtaacaggtgcagtCttcagtttgggctggggtga	17	5	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr7:82764880C>A	ENST00000333891.9	-	3	2323	c.1986G>T	c.(1984-1986)aaG>aaT	p.K662N	PCLO_ENST00000423517.2_Missense_Mutation_p.K662N	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CAGGTGCAGTCTTCAGTTTGG	0.498																																					p.K662N		Atlas-SNP	.											.	PCLO	1506	.	0			c.G1986T						.						112	112	112					7																	82764880		2030	4177	6207	SO:0001583	missense	27445	exon3			TGCAGTCTTCAGT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.1986G>T	chr7.hg19:g.82764880C>A	ENSP00000334319:p.Lys662Asn	96.0	0.0		58.0	27.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	2.337	-0.352018	0.05173	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17370	2.28;2.28	5.46	4.58	0.56647	.	.	.	.	.	T	0.17023	0.0409	L	0.32530	0.975	0.80722	D	1	P;P	0.46512	0.879;0.879	B;B	0.43103	0.295;0.408	T	0.01553	-1.1326	9	0.87932	D	0	.	14.2118	0.65769	0.0:0.9279:0.0:0.0721	.	662;662	Q9Y6V0-5;Q9Y6V0-6	.;.	N	608;662;662	ENSP00000334319:K662N;ENSP00000388393:K662N	ENSP00000334319:K662N	K	-	3	2	PCLO	82602816	0.911000	0.30947	0.012000	0.15200	0.010000	0.07245	1.456000	0.35201	1.313000	0.45069	0.591000	0.81541	AAG	.	.		0.498	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82764880	C	A	82764880	3	1	72	1	0	0	0	0	1	0	0	0	11592	912	32	3	13551	3	PCLO	7	82764880	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	181380	82764880	76373783	56	9248										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121652602	121652602	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tatctccttcaactcagctcTtattttatgagacctcagct	4	12	5	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr7:121652602T>A	ENST00000393386.2	+	12	3913	c.3502T>A	c.(3502-3504)Tta>Ata	p.L1168I	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1168					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						AACTCAGCTCTTATTTTATGA	0.428																																					p.L1168I		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T3502A						.						206	201	203					7																	121652602		2203	4300	6503	SO:0001583	missense	5803	exon12			CAGCTCTTATTTT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.3502T>A	chr7.hg19:g.121652602T>A	ENSP00000377047:p.Leu1168Ile	102.0	0.0		45.0	18.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	T	11.82	1.752738	0.31046	.	.	ENSG00000106278	ENST00000393386	T	0.56611	0.45	5.51	0.193	0.15139	.	1.165150	0.06426	N	0.723254	T	0.48187	0.1486	M	0.67953	2.075	0.09310	N	1	B	0.32573	0.376	B	0.30401	0.115	T	0.42916	-0.9423	10	0.72032	D	0.01	.	4.9299	0.13912	0.0:0.2294:0.2542:0.5164	.	1168	P23471	PTPRZ_HUMAN	I	1168	ENSP00000377047:L1168I	ENSP00000377047:L1168I	L	+	1	2	PTPRZ1	121439838	0.002000	0.14202	0.037000	0.18230	0.995000	0.86356	0.620000	0.24403	-0.195000	0.10382	0.454000	0.30748	TTA	.	.		0.428	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121652602	T	A	121652602	3	1	72	1	0	0	0	0	1	0	0	0	12829	1606	56	4	3548	4	PTPRZ1	7	121652602	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	38887722	121652602	37486061	57	9249										
TRYX3	136541	hgsc.bcm.edu	37	chr7	141955440	141955440	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gtagtcagatttcaaatagaCcaagtaagggggagtggagc	14	5	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr7:141955440C>A	ENST00000552471.1	-	2	413	c.94G>T	c.(94-96)Gtc>Ttc	p.V32F	PRSS58_ENST00000547058.2_Missense_Mutation_p.V32F			Q8IYP2	PRS58_HUMAN	protease, serine, 58	32	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	19						TTCAAATAGACCAAGTAAGGG	0.468																																					p.V32F		Atlas-SNP	.											.	PRSS58	41	.	0			c.G94T						.						87	85	85					7																	141955440		2203	4300	6503	SO:0001583	missense	136541	exon3			AATAGACCAAGTA		CCDS5871.1	7q34	2012-10-03			ENSG00000258223	ENSG00000258223	3.4.21.4	"Serine peptidases / Serine peptidases"	39125	protein-coding gene	gene with protein product	"trypsin X3"						Standard	NM_001001317		Approved	TRYX3	uc003vxc.4	Q8IYP2	OTTHUMG00000158565	ENST00000552471.1:c.94G>T	chr7.hg19:g.141955440C>A	ENSP00000446916:p.Val32Phe	163.0	0.0		133.0	58.0	NM_001001317	B3KVJ6|D3DXD2	Missense_Mutation	SNP	ENST00000552471.1	hg19	CCDS5871.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.216875	0.58452	.	.	ENSG00000258223	ENST00000547058;ENST00000552471	D;D	0.87334	-2.24;-2.24	5.0	4.12	0.48240	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.91178	0.7221	M	0.92122	3.275	0.09310	N	1	D	0.58970	0.984	P	0.47346	0.544	D	0.85411	0.1137	9	0.87932	D	0	.	11.1741	0.48588	0.0:0.9106:0.0:0.0894	.	32	Q8IYP2	PRS58_HUMAN	F	32	ENSP00000447588:V32F;ENSP00000446916:V32F	ENSP00000307206:V32F	V	-	1	0	PRSS58	141601917	0.138000	0.22547	0.028000	0.17463	0.034000	0.12701	0.718000	0.25866	1.345000	0.45676	0.655000	0.94253	GTC	.	.		0.468	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317		A	141955440	C	A	141955440	3	1	72	1	0	0	0	0	1	0	0	0	16619	507	18	3	647	3	TRYX3	7	141955440	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	20302838	141955440	17183223	58	9250										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3141773	3141773	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cctccggaagggcggagccaCtccactccttcagcaggatg	12	15	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr8:3141773C>T	ENST00000520002.1	-	27	4604	c.4049G>A	c.(4048-4050)aGt>aAt	p.S1350N	CSMD1_ENST00000542608.1_Missense_Mutation_p.S1349N|CSMD1_ENST00000400186.3_Missense_Mutation_p.S1350N|CSMD1_ENST00000602723.1_Missense_Mutation_p.S1350N|CSMD1_ENST00000537824.1_Missense_Mutation_p.S1349N|CSMD1_ENST00000539096.1_Missense_Mutation_p.S1349N|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602557.1_Missense_Mutation_p.S1350N			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1350	CUB 8. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GGCGGAGCCACTCCACTCCTT	0.567											OREG0018505	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1349N		Atlas-SNP	.											.	CSMD1	1469	.	0			c.G4046A						.						101	112	109					8																	3141773		2130	4258	6388	SO:0001583	missense	64478	exon26			GAGCCACTCCACT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4049G>A	chr8.hg19:g.3141773C>T	ENSP00000430733:p.Ser1350Asn	140.0	0.0	608	38.0	23.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.0	4.235831	0.79800	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.60548	0.18;0.18;0.18;0.18;0.18	5.12	5.12	0.69794	CUB (5);	0.305751	0.32343	N	0.006233	T	0.79411	0.4441	M	0.85373	2.75	0.38795	D	0.955073	D;D;D	0.76494	0.998;0.999;0.994	D;D;D	0.77004	0.989;0.983;0.958	D	0.83966	0.0324	10	0.66056	D	0.02	.	18.573	0.91144	0.0:1.0:0.0:0.0	.	1350;1350;1350	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	N	1350;1350;1212;1349;1349;1349	ENSP00000383047:S1350N;ENSP00000430733:S1350N;ENSP00000441462:S1349N;ENSP00000446243:S1349N;ENSP00000441675:S1349N	ENSP00000320445:S1212N	S	-	2	0	CSMD1	3129180	0.999000	0.42202	1.000000	0.80357	0.974000	0.67602	3.879000	0.56138	2.375000	0.81037	0.563000	0.77884	AGT	.	.		0.567	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3141773	C	T	3141773	3	4	72	1	0	0	0	0	1	0	0	0	3946	565	20	3	6828	3	CSMD1	8	3141773	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10		3141773	143222249	59	9251										
MCPH1	79648	hgsc.bcm.edu	37	chr8	6302684	6302684	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ccaatttcacagcaaaaaccAtctccagtcctcggaaaact	4	14	2	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr8:6302684A>G	ENST00000344683.5	+	8	1517	c.1441A>G	c.(1441-1443)Atc>Gtc	p.I481V	MCPH1_ENST00000519480.1_Missense_Mutation_p.I481V|MCPH1_ENST00000522905.1_Missense_Mutation_p.I433V	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	481					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		AGCAAAAACCATCTCCAGTCC	0.448																																					p.I481V	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.A1441G						.						71	71	71					8																	6302684		1861	4108	5969	SO:0001583	missense	79648	exon8			AAAACCATCTCCA	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1441A>G	chr8.hg19:g.6302684A>G	ENSP00000342924:p.Ile481Val	111.0	0.0		49.0	22.0	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	hg19	CCDS43689.1	.	.	.	.	.	.	.	.	.	.	A	7.565	0.665610	0.14710	.	.	ENSG00000147316	ENST00000344683;ENST00000519480;ENST00000522905	T;T;T	0.09445	2.98;2.98;2.98	5.37	-3.5	0.04710	.	1.395730	0.03890	N	0.278519	T	0.09291	0.0229	L	0.51422	1.61	0.09310	N	1	B;B;B	0.14438	0.01;0.005;0.006	B;B;B	0.17098	0.01;0.017;0.006	T	0.35773	-0.9775	10	0.29301	T	0.29	-0.2221	1.834	0.03136	0.3818:0.1414:0.34:0.1369	.	433;481;481	E9PH63;Q8NEM0;E9PGU5	.;MCPH1_HUMAN;.	V	481;481;433	ENSP00000342924:I481V;ENSP00000430962:I481V;ENSP00000430768:I433V	ENSP00000342924:I481V	I	+	1	0	MCPH1	6290092	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.184000	0.09698	-0.505000	0.06568	-0.263000	0.10527	ATC	.	.		0.448	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		G	6302684	A	G	6302684	3	3	72	1	0	0	0	0	1	0	0	0	9407	217	8	2	1471	2	MCPH1	8	6302684	Missense_Mutation	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	3160911	6302684	140061338	60	9252										
CPA6	57094	hgsc.bcm.edu	37	chr8	68334896	68334896	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	aaggtattccatttttgtagGcccaatccattgagctacca	7	10	0	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr8:68334896G>T	ENST00000297770.4	-	11	1372	c.1157C>A	c.(1156-1158)gCc>gAc	p.A386D	CPA6_ENST00000297769.4_Missense_Mutation_p.A142D	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	386						proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			ATTTTTGTAGGCCCAATCCAT	0.353																																					p.A386D		Atlas-SNP	.											.	CPA6	69	.	0			c.C1157A						.						91	91	91					8																	68334896		2203	4300	6503	SO:0001583	missense	57094	exon11			TTGTAGGCCCAAT	AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.1157C>A	chr8.hg19:g.68334896G>T	ENSP00000297770:p.Ala386Asp	121.0	0.0		165.0	22.0	NM_020361	Q8NEX8|Q8TDE8|Q9NRI9	Missense_Mutation	SNP	ENST00000297770.4	hg19	CCDS6200.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110308	0.77210	.	.	ENSG00000165078	ENST00000297769;ENST00000297770	T;T	0.35236	1.32;2.61	5.86	5.86	0.93980	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.63462	0.2513	M	0.85777	2.775	0.45250	D	0.998256	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.992	T	0.60073	-0.7334	10	0.08599	T	0.76	.	20.1858	0.98214	0.0:0.0:1.0:0.0	.	142;386	Q8N4T0-3;Q8N4T0	.;CBPA6_HUMAN	D	142;386	ENSP00000297769:A142D;ENSP00000297770:A386D	ENSP00000297769:A142D	A	-	2	0	CPA6	68497450	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.445000	0.97587	2.777000	0.95525	0.591000	0.81541	GCC	.	.		0.353	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361		T	68334896	G	T	68334896	3	4	72	1	0	0	0	0	1	0	0	0	3796	1203	42	3	160	3	CPA6	8	68334896	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	62032212	68334896	78029126	61	9253										
NCOA2	10499	hgsc.bcm.edu	37	chr8	71087033	71087033	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gcatccttgtcgatgacaccCtgccctgtagaggatacatc	9	13	0	2	rs369349334		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr8:71087033C>A	ENST00000452400.2	-	5	502	c.321G>T	c.(319-321)caG>caT	p.Q107H		NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	107					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CGATGACACCCTGCCCTGTAG	0.413			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.Q107H		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.G321T						.						185	183	184					8																	71087033		2034	4186	6220	SO:0001583	missense	10499	exon5			GACACCCTGCCCT	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.321G>T	chr8.hg19:g.71087033C>A	ENSP00000399968:p.Gln107His	63.0	0.0		99.0	23.0	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	hg19	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499025	0.64298	.	.	ENSG00000140396	ENST00000452400	T	0.01854	4.6	5.55	2.61	0.31194	.	0.000000	0.85682	D	0.000000	T	0.08626	0.0214	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.02275	-1.1184	10	0.87932	D	0	.	9.5059	0.39046	0.0:0.6985:0.0:0.3015	.	107	Q15596	NCOA2_HUMAN	H	107	ENSP00000399968:Q107H	ENSP00000399968:Q107H	Q	-	3	2	NCOA2	71249587	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	0.849000	0.27723	0.900000	0.36469	0.655000	0.94253	CAG	.	.		0.413	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			A	71087033	C	A	71087033	3	1	72	1	0	0	0	0	1	0	0	0	10238	680	24	3	4149	3	NCOA2	8	71087033	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	2752137	71087033	75276989	62	9254										
CALB1	793	hgsc.bcm.edu	37	chr8	91094853	91094853	+	Frame_Shift_Del	DEL	C	C	-													0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gagaagataatcaccgtcagCgtcgaaatggagccagatct							TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr8:91094853delC	ENST00000265431.3	-	1	254	c.73delG	c.(73-75)gctfs	p.A25fs	CALB1_ENST00000518457.1_5'Flank	NM_004929.2	NP_004920.1	P05937	CALB1_HUMAN	calbindin 1, 28kDa	25	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to organic substance (GO:0071310)|cytosolic calcium ion homeostasis (GO:0051480)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|metanephric collecting duct development (GO:0072205)|metanephric connecting tubule development (GO:0072286)|metanephric distal convoluted tubule development (GO:0072221)|metanephric part of ureteric bud development (GO:0035502)|regulation of synaptic plasticity (GO:0048167)|retina layer formation (GO:0010842)|short-term memory (GO:0007614)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|vitamin D binding (GO:0005499)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(8)|pancreas(1)	11			BRCA - Breast invasive adenocarcinoma(11;0.00953)			TCACCGTCAGCGTCGAAATGG	0.502																																					p.A25fs	Melanoma(46;573 1182 27367 39727 48386)	Atlas-Indel,Pindel	.											.	CALB1	25	.	0			c.74delC						.						259	226	237					8																	91094853		2203	4300	6503	SO:0001589	frameshift_variant	793	exon1			.		CCDS6251.1	8q21.3	2013-01-10	2002-08-29		ENSG00000104327	ENSG00000104327		"EF-hand domain containing"	1434	protein-coding gene	gene with protein product		114050		CALB			Standard	NM_004929		Approved		uc003yel.1	P05937	OTTHUMG00000134314	ENST00000265431.3:c.73delG	chr8.hg19:g.91094853delC	ENSP00000265431:p.Ala25fs	84.0	0.0		156.0	62.0	NM_004929	B2R696|B7Z9J4	Frame_Shift_Del	DEL	ENST00000265431.3	hg19	CCDS6251.1																																																																																			.	.		0.502	CALB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259338.2	NM_004929		-	91094853	C	-	91094853	7	5	72	1	0	1	0	1	0	0	0	0	2575	768	27	0	756	0	CALB1	8	91094853	Frame_Shift_Del	DEL	C	TCGA-CC-A7IG-01A-11D-A33K-10	20007820	91094853	55269169	63	9255										
TG	7038	hgsc.bcm.edu	37	chr8	133899348	133899348	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ctcctggagcttccagaattCcttctcttcttgcaacatgc	6	14	2	1	rs369032480		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr8:133899348C>A	ENST00000220616.4	+	9	1771	c.1731C>A	c.(1729-1731)ttC>ttA	p.F577L	TG_ENST00000377869.1_Missense_Mutation_p.F577L	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	577					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TTCCAGAATTCCTTCTCTTCT	0.458																																					p.F577L		Atlas-SNP	.											.	TG	416	.	0			c.C1731A						.						105	102	103					8																	133899348		2203	4300	6503	SO:0001583	missense	7038	exon9			AGAATTCCTTCTC	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1731C>A	chr8.hg19:g.133899348C>A	ENSP00000220616:p.Phe577Leu	152.0	0.0		246.0	63.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	C	16.24	3.066703	0.55539	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.70282	-0.47;-0.43	5.02	1.99	0.26369	.	0.000000	0.64402	D	0.000002	T	0.72598	0.3480	L	0.34521	1.04	0.29138	N	0.879212	D	0.76494	0.999	D	0.77004	0.989	T	0.66228	-0.5976	10	0.87932	D	0	.	8.5533	0.33465	0.0:0.6621:0.0:0.3378	.	577	P01266	THYG_HUMAN	L	577	ENSP00000367100:F577L;ENSP00000220616:F577L	ENSP00000220616:F577L	F	+	3	2	TG	133968530	0.998000	0.40836	1.000000	0.80357	0.719000	0.41307	0.924000	0.28777	0.684000	0.31448	0.650000	0.86243	TTC	.	.		0.458	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133899348	C	A	133899348	3	1	72	1	0	0	0	0	1	0	0	0	15828	854	30	3	1765	3	TG	8	133899348	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	42804495	133899348	12464674	64	9256										
BAI1	575	hgsc.bcm.edu	37	chr8	143623348	143623348	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cgcactgccaccatcacgggCacactgaagcggccgtctct	10	17	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr8:143623348C>T	ENST00000517894.1	+	28	4647	c.3753C>T	c.(3751-3753)ggC>ggT	p.G1251G	BAI1_ENST00000323289.5_Silent_p.G1251G			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1251					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCATCACGGGCACACTGAAGC	0.672																																					p.G1251G		Atlas-SNP	.											.	BAI1	146	.	0			c.C3753T						.						7	9	9					8																	143623348		2059	4153	6212	SO:0001819	synonymous_variant	575	exon27			CACGGGCACACTG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.3753C>T	chr8.hg19:g.143623348C>T		37.0	0.0		49.0	14.0	NM_001702		Silent	SNP	ENST00000517894.1	hg19																																																																																				.	.		0.672	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		T	143623348	C	T	143623348	2	4	72	1	0	0	0	0	0	0	0	1	1298	697	25	3		3	BAI1	8	143623348	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	9724000	143623348	2740674	65	9257										
MAMDC2	256691	hgsc.bcm.edu	37	chr9	72723140	72723140	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tttccaggccattacatttaTgtggatacctcctttggcaa	7	10	0	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr9:72723140T>C	ENST00000377182.4	+	3	779	c.162T>C	c.(160-162)taT>taC	p.Y54Y	MAMDC2-AS1_ENST00000591368.1_RNA|MAMDC2-AS1_ENST00000414515.3_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	54	MAM 1. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						ATTACATTTATGTGGATACCT	0.443																																					p.Y54Y		Atlas-SNP	.											.	MAMDC2	55	.	0			c.T162C						.						115	114	114					9																	72723140		2203	4300	6503	SO:0001819	synonymous_variant	256691	exon3			CATTTATGTGGAT	BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.162T>C	chr9.hg19:g.72723140T>C		45.0	0.0		56.0	29.0	NM_153267	Q5VW47|Q8WX43|Q96BM4	Silent	SNP	ENST00000377182.4	hg19	CCDS6631.1																																																																																			.	.		0.443	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267		C	72723140	T	C	72723140	2	2	72	1	0	0	0	0	0	0	0	1	9212	1471	51	2		2	MAMDC2	9	72723140	Silent	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10		72723140	68490291	66	9258										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73151774	73151774	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	atcacagtggagctcatccaTagcagagacatagatgtcta	9	9	3	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr9:73151774T>C	ENST00000377110.3	-	25	4462	c.4219A>G	c.(4219-4221)Atg>Gtg	p.M1407V	TRPM3_ENST00000358082.3_Missense_Mutation_p.M1269V|TRPM3_ENST00000357533.2_Missense_Mutation_p.M1411V|TRPM3_ENST00000377106.1_Missense_Mutation_p.M1279V|TRPM3_ENST00000396285.1_Missense_Mutation_p.M1266V|TRPM3_ENST00000423814.3_Missense_Mutation_p.M1434V|TRPM3_ENST00000360823.2_Missense_Mutation_p.M1269V|TRPM3_ENST00000396280.5_Missense_Mutation_p.M1256V|TRPM3_ENST00000396292.4_Missense_Mutation_p.M1279V|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000377105.1_Missense_Mutation_p.M1266V|TRPM3_ENST00000408909.2_Missense_Mutation_p.M1266V			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1432					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						AGCTCATCCATAGCAGAGACA	0.512																																					p.M1407V		Atlas-SNP	.											.	TRPM3	700	.	0			c.A4219G						.						109	103	105					9																	73151774		2203	4300	6503	SO:0001583	missense	80036	exon25			CATCCATAGCAGA	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.4219A>G	chr9.hg19:g.73151774T>C	ENSP00000366314:p.Met1407Val	146.0	0.0		125.0	50.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377110.3	hg19	CCDS43835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.483|9.483	1.098784|1.098784	0.20552|0.20552	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814|ENST00000396280	T;T;T;T;T;T;T;T;T;T|.	0.54479|.	0.65;0.6;0.6;0.57;0.65;0.57;0.6;0.6;0.6;0.64|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.143086|.	0.64402|.	D|.	0.000004|.	T|T	0.48572|0.48572	0.1507|0.1507	N|N	0.24115|0.24115	0.695|0.695	0.32656|0.32656	N|N	0.518694|0.518694	B;B;B;B;B;B;B|.	0.33318|.	0.091;0.131;0.118;0.055;0.408;0.091;0.055|.	B;B;B;B;B;B;B|.	0.31337|.	0.051;0.046;0.049;0.023;0.128;0.035;0.016|.	T|T	0.56872|0.56872	-0.7907|-0.7907	10|5	0.27082|.	T|.	0.32|.	-31.395|-31.395	16.5446|16.5446	0.84426|0.84426	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1407;1397;1411;1269;1266;1379;1266|.	Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3|.	.;.;.;.;.;.;.|.	V|C	1407;1279;1269;1266;1411;1266;1266;1279;1269;1434|1255	ENSP00000366314:M1407V;ENSP00000366310:M1279V;ENSP00000354066:M1269V;ENSP00000366309:M1266V;ENSP00000350140:M1411V;ENSP00000386127:M1266V;ENSP00000379581:M1266V;ENSP00000379587:M1279V;ENSP00000350791:M1269V;ENSP00000389542:M1434V|.	ENSP00000350140:M1411V|.	M|Y	-|-	1|2	0|0	TRPM3|TRPM3	72341594|72341594	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.680000|5.680000	0.68168|0.68168	2.311000|2.311000	0.77944|0.77944	0.533000|0.533000	0.62120|0.62120	ATG|TAT	.	.		0.512	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945		C	73151774	T	C	73151774	3	2	72	1	0	0	0	0	1	0	0	0	16602	1406	49	2	908	2	TRPM3	9	73151774	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	428634	73151774	68061657	67	9259										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37455583	37455583	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gtgtgtttacccaaggctgcGcatcaaaaagaaatagataa	9	7	1	2	rs41276132		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr10:37455583G>T	ENST00000374660.1	+	19	2046	c.1947G>T	c.(1945-1947)gcG>gcT	p.A649A	ANKRD30A_ENST00000361713.1_Silent_p.A649A|ANKRD30A_ENST00000602533.1_Intron			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	586					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CCAAGGCTGCGCATCAAAAAG	0.299																																					p.A649A		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.G1947T						.						3	3	3					10																	37455583		1398	3151	4549	SO:0001819	synonymous_variant	91074	exon19			GGCTGCGCATCAA	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000374660.1:c.1947G>T	chr10.hg19:g.37455583G>T		702.0	1.0		789.0	155.0	NM_052997	Q5W025	Silent	SNP	ENST00000374660.1	hg19																																																																																				.	A|1.000;|0.000		0.299	ANKRD30A-002	PUTATIVE	NMD_exception|basic	protein_coding	protein_coding	OTTHUMT00000047589.2	NM_052997		T	37455583	G	T	37455583	2	4	72	1	0	0	0	0	0	0	0	1	658	1074	38	1		1	ANKRD30A	10	37455583	Silent	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10		37455583	98079164	68	9260										
HPS6	79803	hgsc.bcm.edu	37	chr10	103827340	103827340	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ccagaactggctccagctgaGctcctgcttctactgaggac	10	14	1	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr10:103827340G>T	ENST00000299238.5	+	1	2194	c.2109G>T	c.(2107-2109)gaG>gaT	p.E703D		NM_024747.5	NP_079023.2	Q86YV9	HPS6_HUMAN	Hermansky-Pudlak syndrome 6	703					blood coagulation (GO:0007596)|melanocyte differentiation (GO:0030318)|organelle organization (GO:0006996)|protein localization to membrane (GO:0072657)	BLOC-2 complex (GO:0031084)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|Rab GTPase binding (GO:0017137)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)	11		Colorectal(252;0.122)		Epithelial(162;5.93e-08)|all cancers(201;1.03e-06)		CTCCAGCTGAGCTCCTGCTTC	0.627									Hermansky-Pudlak syndrome																												p.E703D		Atlas-SNP	.											.	HPS6	38	.	0			c.G2109T						.						52	56	54					10																	103827340		2203	4300	6503	SO:0001583	missense	79803	exon1	Familial Cancer Database	HPS, HPS1-8	AGCTGAGCTCCTG	BC009258	CCDS7527.1	10q24.32	2014-06-18			ENSG00000166189	ENSG00000166189			18817	protein-coding gene	gene with protein product		607522				12548288	Standard	NM_024747		Approved	FLJ22501	uc001kuj.3	Q86YV9	OTTHUMG00000018945	ENST00000299238.5:c.2109G>T	chr10.hg19:g.103827340G>T	ENSP00000299238:p.Glu703Asp	33.0	0.0		44.0	22.0	NM_024747	Q5VV69|Q9H685	Missense_Mutation	SNP	ENST00000299238.5	hg19	CCDS7527.1	.	.	.	.	.	.	.	.	.	.	G	3.275	-0.148335	0.06627	.	.	ENSG00000166189	ENST00000299238	T	0.79352	-1.26	4.61	0.287	0.15714	.	0.243009	0.40728	N	0.001037	T	0.52273	0.1724	N	0.20401	0.57	0.26819	N	0.96882	B	0.06786	0.001	B	0.08055	0.003	T	0.17228	-1.0376	10	0.13470	T	0.59	-12.634	2.02	0.03506	0.1995:0.3177:0.3609:0.1219	.	703	Q86YV9	HPS6_HUMAN	D	703	ENSP00000299238:E703D	ENSP00000299238:E703D	E	+	3	2	HPS6	103817330	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	0.637000	0.24659	0.184000	0.20083	0.561000	0.74099	GAG	.	.		0.627	HPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050018.2	NM_024747		T	103827340	G	T	103827340	3	4	72	1	0	0	0	0	1	0	0	0	7352	962	34	3	2111	3	HPS6	10	103827340	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	66371757	103827340	31707407	69	9261										
LOC653486	147199	hgsc.bcm.edu	37	chr11	194445	194445	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tgctgggcagtcaggacggtGcctaagtggacctcagacat	14	10	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:194445G>A	ENST00000342878.2	+	3	303	c.283G>A	c.(283-285)Gcc>Acc	p.A95T	ODF3_ENST00000325113.4_5'Flank|ODF3_ENST00000525282.1_5'Flank|ODF3_ENST00000342593.5_5'Flank|BET1L_ENST00000410108.1_Intron	NM_145651.2	NP_663626.2	Q8TD33	SG1C1_HUMAN	secretoglobin, family 1C, member 1	95						extracellular region (GO:0005576)				endometrium(1)|liver(2)|lung(1)|skin(1)	5		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCAGGACGGTGCCTAAGTGGA	0.567																																					p.A95T		Atlas-SNP	.											.	.	.	.	0			c.G283A						.						144	152	150					11																	194445		2168	4262	6430	SO:0001583	missense	0	exon3			GACGGTGCCTAAG	AY026938	CCDS41581.1	11p15.5	2011-12-14			ENSG00000188076	ENSG00000188076		"Secretoglobins"	18394	protein-coding gene	gene with protein product		610176				22155607	Standard	NM_145651		Approved	RYD5	uc001loa.1	Q8TD33	OTTHUMG00000165539	ENST00000342878.2:c.283G>A	chr11.hg19:g.194445G>A	ENSP00000344545:p.Ala95Thr	73.0	0.0		58.0	21.0	NM_001097610	A8MSI9|Q14DW0	Missense_Mutation	SNP	ENST00000342878.2	hg19	CCDS41581.1	.	.	.	.	.	.	.	.	.	.	.	13.33	2.203518	0.38905	.	.	ENSG00000188076	ENST00000342878	T	0.26067	1.76	4.14	0.925	0.19424	.	0.674171	0.14117	N	0.340321	T	0.14356	0.0347	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.12837	0.008	T	0.22138	-1.0225	9	0.33141	T	0.24	.	4.2115	0.10514	0.1182:0.0:0.4313:0.4504	.	95	Q8TD33	SG1C1_HUMAN	T	95	ENSP00000344545:A95T	ENSP00000344545:A95T	A	+	1	0	SCGB1C1	184445	0.000000	0.05858	0.001000	0.08648	0.260000	0.26232	-0.203000	0.09438	0.199000	0.20427	0.491000	0.48974	GCC	.	.		0.567	SCGB1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384759.1	NM_145651		A	194445	G	A	194445	3	1	72	1	0	0	0	0	1	0	0	0	8895	1319	46	3	293	3	LOC653486	11	194445	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10		194445	134812071	70	9262										
PHRF1	57661	hgsc.bcm.edu	37	chr11	609135	609135	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tgccagccttgggggaagcaCatgtctcgccggaggtggct	16	11	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:609135C>G	ENST00000264555.5	+	14	3807	c.3679C>G	c.(3679-3681)Cat>Gat	p.H1227D	PHRF1_ENST00000416188.2_Missense_Mutation_p.H1226D|PHRF1_ENST00000533464.1_Missense_Mutation_p.H1223D|PHRF1_ENST00000413872.2_Missense_Mutation_p.H1225D	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1227					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GGGGGAAGCACATGTCTCGCC	0.697																																					p.H1226D		Atlas-SNP	.											.	PHRF1	188	.	0			c.C3676G						.						22	27	25					11																	609135		2116	4198	6314	SO:0001583	missense	57661	exon14			GAAGCACATGTCT	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.3679C>G	chr11.hg19:g.609135C>G	ENSP00000264555:p.His1227Asp	24.0	0.0		28.0	9.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	C	1.963	-0.438399	0.04636	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	4.45	-2.78	0.05859	.	1.710460	0.03392	N	0.202064	T	0.46425	0.1392	N	0.02539	-0.55	0.09310	N	1	B;B;B;B	0.10296	0.003;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.0;0.0;0.0	T	0.31194	-0.9952	10	0.13853	T	0.58	1.4132	0.3529	0.00352	0.3363:0.2591:0.1798:0.2249	.	1223;1225;1226;1227	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	D	1227;1225;1226;1223	ENSP00000264555:H1227D;ENSP00000388589:H1225D;ENSP00000410626:H1226D;ENSP00000431870:H1223D	ENSP00000264555:H1227D	H	+	1	0	PHRF1	599135	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.040000	0.12104	-0.816000	0.04340	-0.502000	0.04539	CAT	.	.		0.697	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		G	609135	C	G	609135	3	3	72	1	0	0	0	0	1	0	0	0	11870	478	17	4	3726	4	PHRF1	11	609135	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	414690	609135	134397381	71	9263										
MUC6	4588	hgsc.bcm.edu	37	chr11	1017131	1017131	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ggtgtcattggtggggctgtGtgggtggaccctgtggcctt	19	7	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:1017131G>T	ENST00000421673.2	-	31	5720	c.5670C>A	c.(5668-5670)caC>caA	p.H1890Q		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1890	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTGGGGCTGTGTGGGTGGACC	0.567																																					p.H1890Q		Atlas-SNP	.											.	MUC6	408	.	0			c.C5670A						.						561	572	569					11																	1017131		2201	4287	6488	SO:0001583	missense	4588	exon31			GGCTGTGTGGGTG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5670C>A	chr11.hg19:g.1017131G>T	ENSP00000406861:p.His1890Gln	139.0	0.0		126.0	21.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	6.765	0.510107	0.12883	.	.	ENSG00000184956	ENST00000421673	T	0.22336	1.96	3.21	-0.388	0.12459	.	.	.	.	.	T	0.22126	0.0533	L	0.49126	1.545	0.09310	N	1	P	0.42692	0.787	P	0.49502	0.613	T	0.17806	-1.0357	9	0.26408	T	0.33	.	3.4944	0.07649	0.2666:0.2124:0.5209:0.0	.	1890	Q6W4X9	MUC6_HUMAN	Q	1890	ENSP00000406861:H1890Q	ENSP00000406861:H1890Q	H	-	3	2	MUC6	1007131	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.453000	0.06778	0.158000	0.19367	-0.671000	0.03813	CAC	.	.		0.567	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		T	1017131	G	T	1017131	3	4	72	1	0	0	0	0	1	0	0	0	9989	1368	48	3	1661	3	MUC6	11	1017131	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	407996	1017131	133989385	72	9264										
ZNF215	7762	hgsc.bcm.edu	37	chr11	6964783	6964783	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ttctccatgaacagcacatcTactttccaaaccatttgaga	4	12	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:6964783T>A	ENST00000278319.5	+	6	1211	c.623T>A	c.(622-624)cTa>cAa	p.L208Q	ZNF215_ENST00000414517.2_Missense_Mutation_p.L208Q|ZNF215_ENST00000527171.1_3'UTR|ZNF215_ENST00000529903.1_Missense_Mutation_p.L208Q	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	208	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		ACAGCACATCTACTTTCCAAA	0.333																																					p.L208Q		Atlas-SNP	.											.	ZNF215	72	.	0			c.T623A						.						103	106	105					11																	6964783		2201	4296	6497	SO:0001583	missense	7762	exon6			CACATCTACTTTC	AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"Zinc fingers, C2H2-type", "-", "-", "-"	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.623T>A	chr11.hg19:g.6964783T>A	ENSP00000278319:p.Leu208Gln	145.0	0.0		104.0	46.0	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	hg19	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.241499	0.39598	.	.	ENSG00000149054	ENST00000278319;ENST00000414517;ENST00000529903	T;T;T	0.00832	5.64;5.64;5.64	3.94	-0.29	0.12847	Krueppel-associated box (3);	0.633514	0.12050	N	0.504221	T	0.00608	0.0020	N	0.12663	0.25	0.09310	N	1	B;B	0.26363	0.147;0.079	B;B	0.24701	0.035;0.055	T	0.46775	-0.9167	10	0.15066	T	0.55	-1.3258	6.9204	0.24385	0.5779:0.0:0.0:0.4221	.	208;208	Q96C84;Q9UL58	.;ZN215_HUMAN	Q	208	ENSP00000278319:L208Q;ENSP00000393202:L208Q;ENSP00000432306:L208Q	ENSP00000278319:L208Q	L	+	2	0	ZNF215	6921359	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.238000	0.08977	0.156000	0.19299	0.533000	0.62120	CTA	.	.		0.333	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1			A	6964783	T	A	6964783	3	1	72	1	0	0	0	0	1	0	0	0	17786	1522	53	4	637	4	ZNF215	11	6964783	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	5947652	6964783	128041733	73	9265										
FAR1	84188	hgsc.bcm.edu	37	chr11	13750208	13750208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ctatccttgtgatcctcatcTggcgcatttttattgcaaga	7	10	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:13750208T>C	ENST00000354817.3	+	12	1579	c.1435T>C	c.(1435-1437)Tgg>Cgg	p.W479R	FAR1_ENST00000532502.1_Missense_Mutation_p.W103R	NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	479					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)|wax biosynthetic process (GO:0010025)	integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13						GATCCTCATCTGGCGCATTTT	0.358																																					p.W479R		Atlas-SNP	.											.	FAR1	40	.	0			c.T1435C						.						226	210	216					11																	13750208		2200	4294	6494	SO:0001583	missense	84188	exon12			CTCATCTGGCGCA	AK026381	CCDS7813.1	11p15.2	2011-09-14	2008-06-06	2008-06-06	ENSG00000197601	ENSG00000197601	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	26222	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 1"		"male sterility domain containing 2"	MLSTD2		15220348, 15220349, 19027726	Standard	NM_032228		Approved	FLJ22728, SDR10E1	uc001mld.3	Q8WVX9	OTTHUMG00000165743	ENST00000354817.3:c.1435T>C	chr11.hg19:g.13750208T>C	ENSP00000346874:p.Trp479Arg	43.0	0.0		53.0	18.0	NM_032228	D3DQW8|Q5CZA3	Missense_Mutation	SNP	ENST00000354817.3	hg19	CCDS7813.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.913867	0.52439	.	.	ENSG00000197601	ENST00000354817;ENST00000532502	T	0.25579	1.79	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.26085	0.0636	L	0.34521	1.04	0.80722	D	1	P	0.37122	0.583	B	0.40165	0.321	T	0.03608	-1.1020	10	0.66056	D	0.02	-4.1202	15.7013	0.77544	0.0:0.0:0.0:1.0	.	479	Q8WVX9	FACR1_HUMAN	R	479;103	ENSP00000346874:W479R	ENSP00000346874:W479R	W	+	1	0	FAR1	13706784	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.174000	0.68829	0.528000	0.53228	TGG	.	.		0.358	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228		C	13750208	T	C	13750208	3	2	72	1	0	0	0	0	1	0	0	0	5682	1580	55	2	1477	2	FAR1	11	13750208	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	6785425	13750208	121256308	74	9266										
DPP3	10072	hgsc.bcm.edu	37	chr11	66259030	66259030	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	atagagagcttcacccagggCtccatcgaggcccacaagag	11	13	1	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:66259030C>A	ENST00000360510.2	+	8	929	c.864C>A	c.(862-864)ggC>ggA	p.G288G	DPP3_ENST00000541961.1_Silent_p.G288G|DPP3_ENST00000532677.1_Silent_p.G307G|DPP3_ENST00000530165.1_Silent_p.G258G|DPP3_ENST00000531863.1_Silent_p.G308G|DPP3_ENST00000453114.1_Silent_p.G288G			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	288					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						TCACCCAGGGCTCCATCGAGG	0.662											OREG0021109	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G288G		Atlas-SNP	.											.	DPP3	61	.	0			c.C864A						.						29	35	33					11																	66259030		2200	4295	6495	SO:0001819	synonymous_variant	10072	exon8			CCAGGGCTCCATC	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"dipeptidylpeptidase III", "dipeptidylpeptidase 3"			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.864C>A	chr11.hg19:g.66259030C>A		47.0	0.0	1090	53.0	22.0	NM_130443	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Silent	SNP	ENST00000360510.2	hg19	CCDS8141.1																																																																																			.	.		0.662	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2			A	66259030	C	A	66259030	2	1	72	1	0	0	0	0	0	0	0	1	4730	784	28	3		3	DPP3	11	66259030	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	52508822	66259030	68747486	75	9267										
ANO1	55107	hgsc.bcm.edu	37	chr11	69995875	69995875	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gactcaactaccgctgggacCtcacgggctttgaagaggaa	12	11	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:69995875C>T	ENST00000355303.5	+	12	1623	c.1318C>T	c.(1318-1320)Ctc>Ttc	p.L440F	ANO1_ENST00000530676.1_Missense_Mutation_p.L324F|ANO1_ENST00000398543.2_Missense_Mutation_p.L324F|ANO1_ENST00000316296.5_Missense_Mutation_p.L412F|ANO1_ENST00000531349.1_Missense_Mutation_p.L175F|ANO1_ENST00000538023.1_Missense_Mutation_p.L440F|RP11-805J14.3_ENST00000530525.1_RNA	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	440					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	CCGCTGGGACCTCACGGGCTT	0.582																																					p.L440F		Atlas-SNP	.											.	ANO1	156	.	0			c.C1318T						.						60	70	67					11																	69995875		2039	4191	6230	SO:0001583	missense	55107	exon12			TGGGACCTCACGG	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	21625	protein-coding gene	gene with protein product		610108	"oral cancer overexpressed 2", "transmembrane protein 16A"	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.1318C>T	chr11.hg19:g.69995875C>T	ENSP00000347454:p.Leu440Phe	136.0	0.0		108.0	50.0	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Missense_Mutation	SNP	ENST00000355303.5	hg19	CCDS44663.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.345718	0.82022	.	.	ENSG00000131620	ENST00000355303;ENST00000538023;ENST00000398543;ENST00000546327;ENST00000316296;ENST00000530676;ENST00000531349;ENST00000531300	T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.05	4.13	0.48395	.	0.000000	0.64402	D	0.000005	D	0.82779	0.5111	M	0.93720	3.45	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.86786	0.1982	9	.	.	.	.	12.5398	0.56163	0.0:0.9183:0.0:0.0817	.	175;412;440	E9PNA7;Q5XXA6-3;Q5XXA6	.;.;ANO1_HUMAN	F	440;440;324;224;412;324;175;17	ENSP00000347454:L440F;ENSP00000444689:L440F;ENSP00000381551:L324F;ENSP00000319477:L412F;ENSP00000435797:L324F;ENSP00000432843:L175F;ENSP00000435868:L17F	.	L	+	1	0	ANO1	69673523	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.221000	0.51215	2.367000	0.80283	0.555000	0.69702	CTC	.	.		0.582	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043		T	69995875	C	T	69995875	3	4	72	1	0	0	0	0	1	0	0	0	695	681	24	3	1364	3	ANO1	11	69995875	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	3736845	69995875	65010641	76	9268										
INTS4	92105	hgsc.bcm.edu	37	chr11	77692543	77692543	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tgatggcatcatccataatgCagtctggtgaaaatcctgct	9	9	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:77692543C>T	ENST00000534064.1	-	3	360	c.326G>A	c.(325-327)tGc>tAc	p.C109Y	INTS4_ENST00000529807.1_Missense_Mutation_p.C109Y	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	109					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			ATCCATAATGCAGTCTGGTGA	0.348																																					p.C109Y		Atlas-SNP	.											.	INTS4	89	.	0			c.G326A						.						114	101	105					11																	77692543		2200	4292	6492	SO:0001583	missense	92105	exon3			ATAATGCAGTCTG	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.326G>A	chr11.hg19:g.77692543C>T	ENSP00000434466:p.Cys109Tyr	56.0	0.0		58.0	24.0	NM_033547	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	hg19	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	C	8.223	0.803012	0.16397	.	.	ENSG00000149262	ENST00000534064;ENST00000529807	T;T	0.64438	-0.1;1.55	4.75	4.75	0.60458	Armadillo-like helical (1);Armadillo-type fold (1);	0.051425	0.85682	D	0.000000	T	0.52741	0.1753	L	0.36672	1.1	0.80722	D	1	P	0.47350	0.894	B	0.41723	0.365	T	0.56147	-0.8027	10	0.44086	T	0.13	-10.1431	13.6551	0.62333	0.0:0.8452:0.1548:0.0	.	109	Q96HW7	INT4_HUMAN	Y	109	ENSP00000434466:C109Y;ENSP00000433644:C109Y	ENSP00000407787:C109Y	C	-	2	0	INTS4	77370191	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.334000	0.65923	2.472000	0.83506	0.591000	0.81541	TGC	.	.		0.348	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		T	77692543	C	T	77692543	3	4	72	1	0	0	0	0	1	0	0	0	7789	710	25	3	2649	3	INTS4	11	77692543	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	7696668	77692543	57313973	77	9269										
C11orf82	220042	hgsc.bcm.edu	37	chr11	82644353	82644353	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	aatgccttggggacatatcaAtaacaacgtaacacagagct	8	9	1	1	rs369733646		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:82644353A>G	ENST00000533655.1	+	6	2185	c.1973A>G	c.(1972-1974)aAt>aGt	p.N658S	C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000329143.3_Missense_Mutation_p.N357S|C11orf82_ENST00000430323.2_Missense_Mutation_p.N658S|C11orf82_ENST00000528759.1_3'UTR	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		658					apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						GGACATATCAATAACAACGTA	0.343																																					p.N658S		Atlas-SNP	.											C11orf82,NS,carcinoma,0,1	C11orf82	71	.	0			c.A1973G						.	A	SER/ASN	0,4406		0,0,2203	164	154	157		1973	-8.4	0	11		157	1,8599	1.2+/-3.3	0,1,4299	no	missense	C11orf82	NM_145018.3	46	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	658/999	82644353	1,13005	2203	4300	6503	SO:0001583	missense	220042	exon6			ATATCAATAACAA																												ENST00000533655.1:c.1973A>G	chr11.hg19:g.82644353A>G	ENSP00000435421:p.Asn658Ser	78.0	0.0		82.0	18.0	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	hg19	CCDS8263.1	.	.	.	.	.	.	.	.	.	.	A	0.124	-1.121688	0.01785	0.0	1.16E-4	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	T;T;T	0.18960	2.45;2.45;2.18	5.93	-8.38	0.00973	.	1.184200	0.05810	N	0.613768	T	0.10680	0.0261	N	0.21448	0.665	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29792	-1.0000	9	.	.	.	.	7.8718	0.29571	0.5992:0.0757:0.2492:0.0758	.	658	Q8IXT1	NOXIN_HUMAN	S	658;658;357	ENSP00000414687:N658S;ENSP00000435421:N658S;ENSP00000329930:N357S	.	N	+	2	0	C11orf82	82322001	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.540000	0.06106	-1.470000	0.01888	-1.223000	0.01593	AAT	.	.		0.343	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1			G	82644353	A	G	82644353	3	3	72	1	0	0	0	0	1	0	0	0	1667	101	4	2	1987	2	C11orf82	11	82644353	Missense_Mutation	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	4951810	82644353	52362163	78	9270										
FAT3	120114	hgsc.bcm.edu	37	chr11	92577146	92577146	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	agtttctcacacttacatccGcgtgcgagtcattgaggaaa	9	10	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:92577146G>A	ENST00000298047.6	+	18	10630	c.10613G>A	c.(10612-10614)cGc>cAc	p.R3538H	FAT3_ENST00000533797.1_5'Flank|FAT3_ENST00000525166.1_Missense_Mutation_p.R3388H|FAT3_ENST00000409404.2_Missense_Mutation_p.R3538H			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3538	Cadherin 32. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ACTTACATCCGCGTGCGAGTC	0.468										TCGA Ovarian(4;0.039)																											p.R3538H		Atlas-SNP	.											.	FAT3	1822	.	0			c.G10613A						.						169	165	166					11																	92577146		1935	4142	6077	SO:0001583	missense	120114	exon18			ACATCCGCGTGCG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.10613G>A	chr11.hg19:g.92577146G>A	ENSP00000298047:p.Arg3538His	121.0	0.0		90.0	40.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	4.008	-0.001180	0.07819	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.07800	3.16;3.16;3.16	5.62	1.7	0.24286	.	.	.	.	.	T	0.04048	0.0113	N	0.05510	-0.035	0.33044	D	0.53182	B	0.09022	0.002	B	0.06405	0.002	T	0.28933	-1.0028	9	0.31617	T	0.26	.	7.2209	0.25985	0.5237:0.0:0.4763:0.0	.	3538	Q8TDW7-3	.	H	3538;3538;3388	ENSP00000298047:R3538H;ENSP00000387040:R3538H;ENSP00000432586:R3388H	ENSP00000298047:R3538H	R	+	2	0	FAT3	92216794	0.260000	0.24053	0.100000	0.21137	0.179000	0.23085	1.490000	0.35573	0.332000	0.23536	-0.254000	0.11334	CGC	.	.		0.468	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92577146	G	A	92577146	3	1	72	1	0	0	0	0	1	0	0	0	5699	1087	38	1	10683	1	FAT3	11	92577146	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	9932793	92577146	42429370	79	9271										
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94316706	94316706	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ccatcaagttctcccgtgtgCatccaggtcttcaatatcat	6	13	5	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:94316706C>A	ENST00000299001.6	+	5	817	c.606C>A	c.(604-606)tgC>tgA	p.C202*	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	202					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CTCCCGTGTGCATCCAGGTCT	0.418																																					p.C202X		Atlas-SNP	.											.	PIWIL4	70	.	0			c.C606A						.						160	160	160					11																	94316706		2201	4298	6499	SO:0001587	stop_gained	143689	exon5			CGTGTGCATCCAG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.606C>A	chr11.hg19:g.94316706C>A	ENSP00000299001:p.Cys202*	138.0	0.0		110.0	46.0	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Nonsense_Mutation	SNP	ENST00000299001.6	hg19	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280438	0.95489	.	.	ENSG00000134627	ENST00000299001	.	.	.	5.54	3.65	0.41850	.	0.069855	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.1243	11.7711	0.51960	0.0:0.8514:0.0:0.1486	.	.	.	.	X	202	.	ENSP00000299001:C202X	C	+	3	2	PIWIL4	93956354	1.000000	0.71417	0.998000	0.56505	0.835000	0.47333	0.953000	0.29162	1.593000	0.50029	0.650000	0.86243	TGC	.	.		0.418	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		A	94316706	C	A	94316706	4	1	72	1	0	0	0	0	0	1	0	0	11969	718	25	3	624	3	PIWIL4	11	94316706	Nonsense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	1739560	94316706	40689810	80	9272										
GUCY1A2	2977	hgsc.bcm.edu	37	chr11	106810405	106810405	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ctgggatcaaacatcaagtgGaaagggaaggctctacagaa	12	7	3	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:106810405G>C	ENST00000526355.2	-	4	1455	c.987C>G	c.(985-987)ttC>ttG	p.F329L	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.F329L|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.F329L	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	329					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	ACATCAAGTGGAAAGGGAAGG	0.468																																					p.F329L		Atlas-SNP	.											.	GUCY1A2	180	.	0			c.C987G						.						82	72	76					11																	106810405		2201	4298	6499	SO:0001583	missense	2977	exon4			CAAGTGGAAAGGG	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.987C>G	chr11.hg19:g.106810405G>C	ENSP00000431245:p.Phe329Leu	163.0	0.0		150.0	55.0	NM_000855	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	hg19	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.681297	0.47991	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.94758	-3.51;-3.51;-3.51	5.77	1.91	0.25777	Haem NO binding associated (1);	0.000000	0.47455	U	0.000240	D	0.97173	0.9076	M	0.91249	3.19	0.58432	D	0.999998	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.91635	0.992;0.999;0.992	D	0.95915	0.8926	10	0.87932	D	0	.	9.2424	0.37504	0.3777:0.0:0.6223:0.0	.	329;329;329	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	L	329	ENSP00000431245:F329L;ENSP00000282249:F329L;ENSP00000344874:F329L	ENSP00000282249:F329L	F	-	3	2	GUCY1A2	106315615	1.000000	0.71417	0.981000	0.43875	0.581000	0.36288	1.853000	0.39358	0.109000	0.17891	-0.952000	0.02654	TTC	.	.		0.468	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			C	106810405	G	C	106810405	3	2	72	1	0	0	0	0	1	0	0	0	6902	1165	41	4	1231	4	GUCY1A2	11	106810405	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	12493699	106810405	28196111	81	9273										
FAM55B	120406	hgsc.bcm.edu	37	chr11	114569227	114569227	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gctgctcatccaccccagtgAaggggtatcagctctctgga	11	13	3	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:114569227A>C	ENST00000389586.4	+	3	783	c.593A>C	c.(592-594)gAa>gCa	p.E198A	NXPE2_ENST00000375475.5_Missense_Mutation_p.E198A	NM_182495.5	NP_872301.2	Q96DL1	NXPE2_HUMAN	neurexophilin and PC-esterase domain family, member 2	198						integral component of membrane (GO:0016021)											CACCCCAGTGAAGGGGTATCA	0.527																																					p.E198A		Atlas-SNP	.											.	.	.	.	0			c.A593C						.						85	91	89					11																	114569227		692	1591	2283	SO:0001583	missense	120406	exon3			CCAGTGAAGGGGT	AK057953	CCDS44738.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000204361	ENSG00000204361			26331	protein-coding gene	gene with protein product			"family with sequence similarity 55, member B"	FAM55B			Standard	NM_182495		Approved	FLJ25224	uc009yyy.2	Q96DL1	OTTHUMG00000168293	ENST00000389586.4:c.593A>C	chr11.hg19:g.114569227A>C	ENSP00000374237:p.Glu198Ala	150.0	0.0		115.0	34.0	NM_182495	Q2NKI8	Missense_Mutation	SNP	ENST00000389586.4	hg19	CCDS44738.1	.	.	.	.	.	.	.	.	.	.	A	19.97	3.925452	0.73213	.	.	ENSG00000204361	ENST00000389586;ENST00000375475;ENST00000505358	T;T	0.37915	2.0;1.17	4.66	4.66	0.58398	.	0.000000	0.64402	D	0.000008	T	0.69405	0.3107	H	0.95611	3.695	0.47778	D	0.99951	D	0.89917	1.0	D	0.97110	1.0	T	0.78628	-0.2130	10	0.87932	D	0	.	12.076	0.53644	1.0:0.0:0.0:0.0	.	198	Q96DL1	FA55B_HUMAN	A	198	ENSP00000374237:E198A;ENSP00000364624:E198A	ENSP00000364624:E198A	E	+	2	0	FAM55B	114074437	1.000000	0.71417	0.996000	0.52242	0.779000	0.44077	7.402000	0.79972	1.740000	0.51718	0.482000	0.46254	GAA	.	.		0.527	NXPE2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399181.1	NM_182495		C	114569227	A	C	114569227	3	2	72	1	0	0	0	0	1	0	0	0	5593	246	9	5	603	5	FAM55B	11	114569227	Missense_Mutation	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	7758822	114569227	20437289	82	9274										
C2CD2L	1798	hgsc.bcm.edu	37	chr11	118980899	118980899	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gacctgcgtagaccaatctgAgcataccatggtaagggtct	11	10	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr11:118980899A>G	ENST00000409993.2	-	0	0				C2CD2L_ENST00000336702.3_Missense_Mutation_p.E147G|C2CD2L_ENST00000528586.1_5'Flank			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)						cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		GACCAATCTGAGCATACCATG	0.547																																					p.E147G		Atlas-SNP	.											.	C2CD2L	39	.	0			c.A440G						.						101	83	89					11																	118980899		2200	4295	6495	SO:0001631	upstream_gene_variant	9854	exon2			AATCTGAGCATAC	Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533		chr11.hg19:g.118980899A>G	Exception_encountered	103.0	0.0		75.0	35.0	NM_014807	O15216|Q86WV9|Q9BWE6	Missense_Mutation	SNP	ENST00000409993.2	hg19	CCDS8411.1	.	.	.	.	.	.	.	.	.	.	A	8.254	0.809598	0.16537	.	.	ENSG00000172375	ENST00000336702	T	0.23950	1.88	5.08	5.08	0.68730	.	0.363124	0.31612	N	0.007346	T	0.15955	0.0384	N	0.25647	0.755	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10154	-1.0642	10	0.23891	T	0.37	0.0021	7.6606	0.28400	0.9043:0.0:0.0957:0.0	.	147;147	O14523;O14523-2	C2C2L_HUMAN;.	G	147	ENSP00000338885:E147G	ENSP00000338885:E147G	E	+	2	0	C2CD2L	118486109	1.000000	0.71417	0.990000	0.47175	0.411000	0.31082	4.731000	0.62022	1.927000	0.55829	0.533000	0.62120	GAG	.	.		0.547	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382		G	118980899	A	G	118980899	1	3	72	0	1	0	0	0	0	0	0	0	2155	304	11	2		2	C2CD2L	11	118980899	5'Flank	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	4411672	118980899	16025617	83	9275										
PRB2	653247	hgsc.bcm.edu	37	chr12	11546698	11546698	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ggggacttcgggacttgtctCcttgtgggggtggtccttgt	17	8	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr12:11546698C>A	ENST00000389362.4	-	3	349	c.314G>T	c.(313-315)gGa>gTa	p.G105V	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	105	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GGACTTGTCTCCTTGTGGGGG	0.607																																					p.G105V		Atlas-SNP	.											.	PRB2	168	.	0			c.G314T						.						295	321	312					12																	11546698		2203	4300	6503	SO:0001583	missense	653247	exon3			TTGTCTCCTTGTG	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.314G>T	chr12.hg19:g.11546698C>A	ENSP00000374013:p.Gly105Val	129.0	0.0		122.0	56.0	NM_006248	O00599|P02811|P04281	Missense_Mutation	SNP	ENST00000389362.4	hg19	CCDS41757.2	.	.	.	.	.	.	.	.	.	.	.	5.747	0.322227	0.10900	.	.	ENSG00000121335	ENST00000389362	T	0.09445	2.98	1.0	-0.174	0.13319	.	.	.	.	.	T	0.09555	0.0235	M	0.82323	2.585	0.09310	N	1	P	0.39809	0.689	B	0.25987	0.065	T	0.28106	-1.0054	9	0.27082	T	0.32	.	2.2991	0.04158	0.0:0.3954:0.3405:0.264	.	105	P02812	PRB2_HUMAN	V	105	ENSP00000374013:G105V	ENSP00000374013:G105V	G	-	2	0	PRB2	11437965	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-1.529000	0.02223	0.542000	0.28846	0.000000	0.15137	GGA	.	.		0.607	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248		A	11546698	C	A	11546698	3	1	72	1	0	0	0	0	1	0	0	0	12455	855	30	3	940	3	PRB2	12	11546698	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10		11546698	122305197	84	9276										
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51890828	51890828	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tctgtttctctaagcgagagCtgagctggctagatgatctc	11	9	3	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr12:51890828C>G	ENST00000453097.2	+	22	3218	c.3001C>G	c.(3001-3003)Ctg>Gtg	p.L1001V	SLC4A8_ENST00000358657.3_Missense_Mutation_p.L1028V	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		TAAGCGAGAGCTGAGCTGGCT	0.408																																					p.L1001V		Atlas-SNP	.											.	SLC4A8	292	.	0			c.C3001G						.						101	101	101					12																	51890828		2203	4300	6503	SO:0001583	missense	9498	exon22			CGAGAGCTGAGCT	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"Solute carriers"	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.3001C>G	chr12.hg19:g.51890828C>G	ENSP00000405812:p.Leu1001Val	178.0	0.0		171.0	16.0	NM_001039960		Missense_Mutation	SNP	ENST00000453097.2	hg19	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188195	0.78789	.	.	ENSG00000050438	ENST00000358657;ENST00000453097;ENST00000319957;ENST00000551071	T;T	0.78364	-1.17;-1.17	5.63	4.74	0.60224	.	0.000000	0.85682	D	0.000000	D	0.86310	0.5902	M	0.84773	2.715	0.80722	D	1	D;D;B	0.58268	0.982;0.974;0.446	P;P;P	0.56278	0.775;0.795;0.552	D	0.88515	0.3092	10	0.66056	D	0.02	.	13.9884	0.64350	0.0:0.9257:0.0:0.0743	.	1028;1001;1001	Q2Y0W8-2;Q2Y0W8;Q2Y0W8-3	.;S4A8_HUMAN;.	V	1028;1001;1001;948	ENSP00000351483:L1028V;ENSP00000405812:L1001V	ENSP00000315789:L1001V	L	+	1	2	SLC4A8	50177095	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.968000	0.70413	1.528000	0.49103	-0.150000	0.13652	CTG	.	.		0.408	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		G	51890828	C	G	51890828	3	3	72	1	0	0	0	0	1	0	0	0	14674	796	28	4	3087	4	SLC4A8	12	51890828	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	40344130	51890828	81961067	85	9277										
CDK2	1017	hgsc.bcm.edu	37	chr12	56365394	56365394	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gatgtgaccaagccagtaccCcatcttcgactctgatagcc	8	14	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr12:56365394C>G	ENST00000266970.4	+	7	1122	c.882C>G	c.(880-882)ccC>ccG	p.P294P	RAB5B_ENST00000448789.2_5'Flank|CDK2_ENST00000440311.2_Silent_p.P234P|CDK2_ENST00000354056.4_Silent_p.P260P|RAB5B_ENST00000360299.5_5'Flank|CDK2_ENST00000553376.1_Silent_p.P342P|RAB5B_ENST00000553116.1_5'Flank|CDK2_ENST00000556656.1_3'UTR	NM_001798.3	NP_001789.2	P24941	CDK2_HUMAN	cyclin-dependent kinase 2	294					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|blood coagulation (GO:0007596)|cellular response to nitric oxide (GO:0071732)|centrosome duplication (GO:0051298)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone phosphorylation (GO:0016572)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|mitotic nuclear division (GO:0007067)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transport (GO:0006813)|Ras protein signal transduction (GO:0007265)|regulation of gene silencing (GO:0060968)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	Cajal body (GO:0015030)|centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|condensed chromosome (GO:0000793)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|X chromosome (GO:0000805)|Y chromosome (GO:0000806)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	18			UCEC - Uterine corpus endometrioid carcinoma (6;0.123)|OV - Ovarian serous cystadenocarcinoma(18;0.235)		Bosutinib(DB06616)	AGCCAGTACCCCATCTTCGAC	0.562																																					p.P294P		Atlas-SNP	.											.	CDK2	27	.	0			c.C882G						.						122	108	113					12																	56365394		2203	4300	6503	SO:0001819	synonymous_variant	1017	exon7			AGTACCCCATCTT	M68520	CCDS8898.1, CCDS8899.1	12q13	2011-11-08				ENSG00000123374		"Cyclin-dependent kinases"	1771	protein-coding gene	gene with protein product		116953				1717994, 8275715	Standard	NM_001798		Approved		uc001sit.4	P24941		ENST00000266970.4:c.882C>G	chr12.hg19:g.56365394C>G		116.0	0.0		91.0	31.0	NM_001798	A8K7C6|O75100	Silent	SNP	ENST00000266970.4	hg19	CCDS8898.1																																																																																			.	.		0.562	CDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409650.1			G	56365394	C	G	56365394	2	3	72	1	0	0	0	0	0	0	0	1	3138	610	22	4		4	CDK2	12	56365394	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	4474566	56365394	77486501	86	9278										
PPM1H	57460	hgsc.bcm.edu	37	chr12	63042384	63042384	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ccttcagcacaccccgggcaCgcatcaccaggtcctgagct	9	18	2	1	rs540042623		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr12:63042384C>A	ENST00000228705.6	-	10	1730	c.1430G>T	c.(1429-1431)cGt>cTt	p.R477L	PPM1H_ENST00000551214.1_5'UTR|snoU13_ENST00000459527.1_RNA	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	477	PP2C-like.						phosphoprotein phosphatase activity (GO:0004721)	p.R477H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		ACCCCGGGCACGCATCACCAG	0.522																																					p.R477L		Atlas-SNP	.											PPM1H,colon,carcinoma,0,1	PPM1H	42	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1430T						.						57	60	59					12																	63042384		2095	4238	6333	SO:0001583	missense	57460	exon10			CGGGCACGCATCA	AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	18583	protein-coding gene	gene with protein product	"neurite extension-related protein phosphatase related to PP2C"		"ras homolog gene family, member C like 1", "protein phosphatase 1H (PP2C domain containing)"	ARHCL1			Standard	NM_020700		Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.1430G>T	chr12.hg19:g.63042384C>A	ENSP00000228705:p.Arg477Leu	53.0	0.0		55.0	27.0	NM_020700	B1Q2A9|B2RXG4|Q6PI86	Missense_Mutation	SNP	ENST00000228705.6	hg19	CCDS44934.1	.	.	.	.	.	.	.	.	.	.	C	32	5.191308	0.94923	.	.	ENSG00000111110	ENST00000228705	T	0.08102	3.13	5.93	5.93	0.95920	Protein phosphatase 2C-like (4);	0.122569	0.56097	D	0.000035	T	0.18383	0.0441	L	0.35644	1.08	0.80722	D	1	P	0.46512	0.879	P	0.55923	0.787	T	0.00411	-1.1756	9	.	.	.	3.064	20.3507	0.98813	0.0:1.0:0.0:0.0	.	477	Q9ULR3	PPM1H_HUMAN	L	477	ENSP00000228705:R477L	.	R	-	2	0	PPM1H	61328651	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.207000	0.77899	2.808000	0.96608	0.655000	0.94253	CGT	.	.		0.522	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700		A	63042384	C	A	63042384	3	1	72	1	0	0	0	0	1	0	0	0	12353	536	19	1	118	1	PPM1H	12	63042384	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	6676990	63042384	70809511	87	9279										
TBX5	6910	hgsc.bcm.edu	37	chr12	114823367	114823367	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ttattctcaatctttaattgCgtgatctgaaggaaagagga	9	5	3	3	rs376519728		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr12:114823367C>A	ENST00000310346.4	-	7	1335	c.669G>T	c.(667-669)acG>acT	p.T223T	TBX5_ENST00000526441.1_Silent_p.T223T|TBX5_ENST00000349716.5_Silent_p.T173T|TBX5_ENST00000405440.2_Silent_p.T223T	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	223					apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.T223T(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		TCTTTAATTGCGTGATCTGAA	0.418																																					p.T223T	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											TBX5_ENST00000526441,caecum,carcinoma,0,4	TBX5	188	.	2	Substitution - coding silent(2)	lung(2)	c.G669T						.						106	94	98					12																	114823367		2203	4300	6503	SO:0001819	synonymous_variant	6910	exon7			TAATTGCGTGATC	U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"T-boxes"	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.669G>T	chr12.hg19:g.114823367C>A		88.0	0.0		70.0	17.0	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Silent	SNP	ENST00000310346.4	hg19	CCDS9173.1																																																																																			.	.		0.418	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		A	114823367	C	A	114823367	2	1	72	1	0	0	0	0	0	0	0	1	15676	755	27	1		1	TBX5	12	114823367	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	51780983	114823367	19028528	88	9280										
KNTC1	9735	hgsc.bcm.edu	37	chr12	123070262	123070262	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tgaagatggaattgttcttgAgtcacagatggtgcttccag	12	6	2	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr12:123070262A>T	ENST00000333479.7	+	37	3791	c.3614A>T	c.(3613-3615)gAg>gTg	p.E1205V	KNTC1_ENST00000450485.2_Intron	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	1205					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		ATTGTTCTTGAGTCACAGATG	0.378																																					p.E1205V		Atlas-SNP	.											.	KNTC1	182	.	0			c.A3614T						.						202	191	194					12																	123070262		1894	4119	6013	SO:0001583	missense	9735	exon37			TTCTTGAGTCACA		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.3614A>T	chr12.hg19:g.123070262A>T	ENSP00000328236:p.Glu1205Val	66.0	0.0		63.0	29.0	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	hg19	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.874452	0.91664	.	.	ENSG00000184445	ENST00000333479	T	0.15834	2.39	6.03	6.03	0.97812	.	0.048702	0.85682	D	0.000000	T	0.30916	0.0780	L	0.57536	1.79	0.80722	D	1	D	0.57571	0.98	P	0.51701	0.677	T	0.01786	-1.1274	10	0.87932	D	0	-25.9041	16.5724	0.84622	1.0:0.0:0.0:0.0	.	1205	P50748	KNTC1_HUMAN	V	1205	ENSP00000328236:E1205V	ENSP00000328236:E1205V	E	+	2	0	KNTC1	121636215	1.000000	0.71417	0.872000	0.34217	0.958000	0.62258	8.432000	0.90288	2.313000	0.78055	0.455000	0.32223	GAG	.	.		0.378	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			T	123070262	A	T	123070262	3	4	72	1	0	0	0	0	1	0	0	0	8437	304	11	4	3756	4	KNTC1	12	123070262	Missense_Mutation	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	8246895	123070262	10781633	89	9281										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124354994	124354994	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gagtaaattagttccagagtAtattcatgcccccgagagga	10	8	1	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr12:124354994A>T	ENST00000409039.3	+	43	7272	c.7247A>T	c.(7246-7248)tAt>tTt	p.Y2416F		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2416					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GTTCCAGAGTATATTCATGCC	0.433																																					p.Y2416F		Atlas-SNP	.											.	DNAH10	888	.	0			c.A7247T						.						87	82	83					12																	124354994		1851	4105	5956	SO:0001583	missense	196385	exon43			CAGAGTATATTCA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.7247A>T	chr12.hg19:g.124354994A>T	ENSP00000386770:p.Tyr2416Phe	65.0	0.0		64.0	15.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	26.3	4.728102	0.89390	.	.	ENSG00000197653	ENST00000409039	T	0.20332	2.08	5.06	5.06	0.68205	.	0.455836	0.19456	U	0.113803	T	0.32912	0.0845	L	0.49455	1.56	0.53688	D	0.999978	D	0.54207	0.965	P	0.59643	0.861	T	0.04551	-1.0943	10	0.07644	T	0.81	.	14.8535	0.70316	1.0:0.0:0.0:0.0	.	2416	Q8IVF4	DYH10_HUMAN	F	2416	ENSP00000386770:Y2416F	ENSP00000386770:Y2416F	Y	+	2	0	DNAH10	122920947	1.000000	0.71417	0.397000	0.26308	0.057000	0.15508	9.283000	0.95860	1.913000	0.55393	0.533000	0.62120	TAT	.	.		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124354994	A	T	124354994	3	4	72	1	0	0	0	0	1	0	0	0	4600	449	16	4	7417	4	DNAH10	12	124354994	Missense_Mutation	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	1284732	124354994	9496901	90	9282										
FREM2	341640	hgsc.bcm.edu	37	chr13	39262451	39262451	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cacccaagcccagtttcgtgGccatgatgatgatggaggtg	13	10	0	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr13:39262451G>A	ENST00000280481.7	+	1	1186	c.970G>A	c.(970-972)Gcc>Acc	p.A324T		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	324					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CAGTTTCGTGGCCATGATGAT	0.592																																					p.A324T		Atlas-SNP	.											.	FREM2	385	.	0			c.G970A						.						119	91	100					13																	39262451		2203	4300	6503	SO:0001583	missense	341640	exon1			TTCGTGGCCATGA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.970G>A	chr13.hg19:g.39262451G>A	ENSP00000280481:p.Ala324Thr	144.0	0.0		129.0	95.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087200	0.76642	.	.	ENSG00000150893	ENST00000280481	T	0.21543	2.0	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.46964	0.1420	M	0.70595	2.14	0.80722	D	1	D	0.60575	0.988	P	0.62184	0.899	T	0.36261	-0.9755	10	0.72032	D	0.01	.	20.218	0.98305	0.0:0.0:1.0:0.0	.	324	Q5SZK8	FREM2_HUMAN	T	324	ENSP00000280481:A324T	ENSP00000280481:A324T	A	+	1	0	FREM2	38160451	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.002000	0.57053	2.791000	0.96007	0.561000	0.74099	GCC	.	.		0.592	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39262451	G	A	39262451	3	1	72	1	0	0	0	0	1	0	0	0	6053	1203	42	3	972	3	FREM2	13	39262451	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10		39262451	75907427	91	9283										
EPSTI1	94240	hgsc.bcm.edu	37	chr13	43543304	43543304	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tctccaggttggccagctccTgctccgcaactaagccaggc	10	16	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr13:43543304T>A	ENST00000398762.3	-	3	256	c.257A>T	c.(256-258)cAg>cTg	p.Q86L	EPSTI1_ENST00000476830.2_5'UTR|EPSTI1_ENST00000313640.7_Missense_Mutation_p.Q86L|EPSTI1_ENST00000313624.7_Missense_Mutation_p.Q86L			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)	86										endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		GGCCAGCTCCTGCTCCGCAAC	0.488											OREG0022383	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q86L		Atlas-SNP	.											.	EPSTI1	47	.	0			c.A257T						.						84	68	74					13																	43543304		2203	4300	6503	SO:0001583	missense	94240	exon3			AGCTCCTGCTCCG	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"epithelial stromal interaction protein 1"	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814	ENST00000398762.3:c.257A>T	chr13.hg19:g.43543304T>A	ENSP00000381746:p.Gln86Leu	65.0	0.0	917	25.0	18.0	NM_001002264	Q8IVC7|Q8NDQ7	Missense_Mutation	SNP	ENST00000398762.3	hg19	CCDS9387.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.531280	0.27387	.	.	ENSG00000133106	ENST00000313640;ENST00000313624;ENST00000398762	T	0.23348	1.91	5.09	3.89	0.44902	.	0.280776	0.32624	N	0.005841	T	0.20659	0.0497	L	0.51422	1.61	0.26697	N	0.97123	B;P	0.36535	0.386;0.557	B;B	0.31101	0.124;0.085	T	0.14783	-1.0460	10	0.59425	D	0.04	-5.2976	8.9628	0.35858	0.0:0.0:0.1868:0.8132	.	86;86	Q96J88-2;Q96J88-3	.;.	L	86	ENSP00000318982:Q86L	ENSP00000318643:Q86L	Q	-	2	0	EPSTI1	42441304	0.968000	0.33430	0.914000	0.36105	0.182000	0.23217	1.875000	0.39578	0.939000	0.37446	0.528000	0.53228	CAG	.	.		0.488	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264		A	43543304	T	A	43543304	3	1	72	1	0	0	0	0	1	0	0	0	5200	1580	55	4	1019	4	EPSTI1	13	43543304	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	4280853	43543304	71626574	92	9284										
RB1	5925	hgsc.bcm.edu	37	chr13	49039196	49039228	+	In_Frame_Del	DEL	GGTCTTCATGCAGAGACTGAAAACAAATATTTT	GGTCTTCATGCAGAGACTGAAAACAAATATTTT	-													0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	attatagtattctataactcGgtcttcatgcagagactgaa					rs138637932|rs558114005		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	GGTCTTCATGCAGAGACTGAAAACAAATATTTT	GGTCTTCATGCAGAGACTGAAAACAAATATTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr13:49039196_49039228delGGTCTTCATGCAGAGACTGAAAACAAATATTTT	ENST00000267163.4	+	22	2412_2444	c.2274_2306delGGTCTTCATGCAGAGACTGAAAACAAATATTTT	c.(2272-2307)tcggtcttcatgcagagactgaaaacaaatattttg>tcg	p.VFMQRLKTNIL759del		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	759	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(12)|p.Q762*(2)|p.K765*(1)|p.M761fs*4(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TCTATAACTCGGTCTTCATGCAGAGACTGAAAACAAATATTTTGCAGTATGCT	0.3		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.758_769del		Atlas-Indel,Pindel	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	RB1_ENST00000267163,NS,carcinoma,0,2	RB1	1068	.	31	Whole gene deletion(15)|Unknown(12)|Substitution - Nonsense(3)|Deletion - Frameshift(1)	bone(11)|breast(5)|haematopoietic_and_lymphoid_tissue(4)|endometrium(3)|urinary_tract(2)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|liver(1)	c.2273_2305del	GRCh37	CD071386|CM030515|CM961237	RB1	D|M		.																																			SO:0001651	inframe_deletion	5925	exon22	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2274_2306delGGTCTTCATGCAGAGACTGAAAACAAATATTTT	chr13.hg19:g.49039196_49039228delGGTCTTCATGCAGAGACTGAAAACAAATATTTT	ENSP00000267163:p.Val759_Leu769del	163.0	0.0		51.0	17.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	In_Frame_Del	DEL	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.3	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			-	49039228	GGTCTTCATGCAGAGACTGAAAACAAATATTTT	-	49039196	7	5	72	1	0	1	0	1	0	0	0	0	13113	1103	39	0	2360	0	RB1	13	49039196	In_Frame_Del	DEL	GGTCTTCATGCAGAGACTGAAAACAAATATTTT	TCGA-CC-A7IG-01A-11D-A33K-10	5495892	49039196	66130682	93	9285										
ERCC5	2073	hgsc.bcm.edu	37	chr13	103518669	103518669	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	agcagaattcactgaaagctCaaaaacagcagcaagaacgg	9	9	2	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr13:103518669C>G	ENST00000355739.4	+	10	3680	c.2257C>G	c.(2257-2259)Caa>Gaa	p.Q753E	ERCC5_ENST00000375954.1_5'UTR|BIVM-ERCC5_ENST00000602836.1_Nonsense_Mutation_p.S1178*	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	753	I-domain.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					ACTGAAAGCTCAAAAACAGCA	0.433			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.Q1207E		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"		E	.	.	.	.	0			c.C3619G						.						59	63	62					13																	103518669		2203	4300	6503	SO:0001583	missense	0	exon18	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AAAGCTCAAAAAC	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"Cockayne syndrome"	133530	"xeroderma pigmentosum, complementation group G", "excision repair cross-complementing rodent repair deficiency, complementation group 5"	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.2257C>G	chr13.hg19:g.103518669C>G	ENSP00000347978:p.Gln753Glu	271.0	0.0		675.0	128.0	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	hg19	CCDS32004.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.610307	0.66558	.	.	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000375955	T	0.46063	0.88	5.77	4.93	0.64822	.	0.242319	0.43260	N	0.000594	T	0.55194	0.1905	M	0.70275	2.135	0.80722	D	1	P;P	0.48016	0.904;0.684	P;P	0.53809	0.735;0.525	T	0.55704	-0.8099	10	0.06757	T	0.87	-9.2917	19.8224	0.96603	0.0:0.8871:0.1129:0.0	.	753;1178	P28715;Q59FZ7	ERCC5_HUMAN;.	E	1178;753;585	ENSP00000347978:Q753E	ENSP00000347978:Q753E	Q	+	1	0	ERCC5	102316670	1.000000	0.71417	0.812000	0.32479	0.865000	0.49528	4.508000	0.60441	0.799000	0.34018	-0.795000	0.03280	CAA	.	.		0.433	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			G	103518669	C	G	103518669	3	3	72	1	0	0	0	0	1	0	0	0	5218	827	29	4	2295	4	ERCC5	13	103518669	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	54479473	103518669	11651209	94	9286										
HERC2	8924	hgsc.bcm.edu	37	chr15	28377352	28377352	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ctgtgaggcagagggtctggGcatctccactgccacaggcg	15	12	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr15:28377352G>A	ENST00000261609.7	-	81	12572	c.12464C>T	c.(12463-12465)gCc>gTc	p.A4155V		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GAGGGTCTGGGCATCTCCACT	0.617																																					p.A4155V		Atlas-SNP	.											.	HERC2	501	.	0			c.C12464T						.						70	57	61					15																	28377352		2203	4300	6503	SO:0001583	missense	8924	exon81			GTCTGGGCATCTC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.12464C>T	chr15.hg19:g.28377352G>A	ENSP00000261609:p.Ala4155Val	225.0	0.0		159.0	66.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	33	5.229150	0.95173	.	.	ENSG00000128731	ENST00000261609	T	0.80480	-1.38	4.87	4.87	0.63330	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.88713	0.6511	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	D	0.90164	0.4230	10	0.87932	D	0	.	18.0199	0.89252	0.0:0.0:1.0:0.0	.	4155	O95714	HERC2_HUMAN	V	4155	ENSP00000261609:A4155V	ENSP00000261609:A4155V	A	-	2	0	HERC2	26050947	1.000000	0.71417	0.987000	0.45799	0.739000	0.42172	9.860000	0.99555	2.241000	0.73720	0.555000	0.69702	GCC	.	.		0.617	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28377352	G	A	28377352	3	1	72	1	0	0	0	0	1	0	0	0	7067	1203	42	3	2092	3	HERC2	15	28377352	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10		28377352	74154040	95	9287										
WDR76	79968	hgsc.bcm.edu	37	chr15	44158353	44158353	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	actttcactgggcgatggctGaccaggttccaagccatgtg	12	11	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr15:44158353G>T	ENST00000263795.6	+	13	1714	c.1644G>T	c.(1642-1644)ctG>ctT	p.L548L	Y_RNA_ENST00000363521.1_RNA|WDR76_ENST00000381246.2_Silent_p.L484L|WDR76_ENST00000478130.1_3'UTR	NM_001167941.1|NM_024908.3	NP_001161413.1|NP_079184.2	Q9H967	WDR76_HUMAN	WD repeat domain 76	548										breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)	20		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)		GGCGATGGCTGACCAGGTTCC	0.448																																					p.L548L		Atlas-SNP	.											.	WDR76	34	.	0			c.G1644T						.						118	105	109					15																	44158353		2198	4298	6496	SO:0001819	synonymous_variant	79968	exon13			ATGGCTGACCAGG	AK023035	CCDS10106.1, CCDS53938.1	15q15.3	2013-01-09			ENSG00000092470	ENSG00000092470		"WD repeat domain containing"	25773	protein-coding gene	gene with protein product						12860291	Standard	NM_024908		Approved	FLJ12973	uc001zti.2	Q9H967	OTTHUMG00000060143	ENST00000263795.6:c.1644G>T	chr15.hg19:g.44158353G>T		87.0	0.0		94.0	39.0	NM_024908	A0MNP5|Q05CI4	Silent	SNP	ENST00000263795.6	hg19	CCDS10106.1																																																																																			.	.		0.448	WDR76-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133482.2	NM_024908		T	44158353	G	T	44158353	2	4	72	1	0	0	0	0	0	0	0	1	17341	1277	45	3		3	WDR76	15	44158353	Silent	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	15781001	44158353	58373039	96	9288										
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79058475	79058475	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cactgtgcctcctgtccacaGctccgccacgtcaggactag	9	17	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr15:79058475G>T	ENST00000388820.4	-	19	3988	c.3778C>A	c.(3778-3780)Ctg>Atg	p.L1260M	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1260					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CCTGTCCACAGCTCCGCCACG	0.672																																					p.L1260M		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C3778A						.						18	19	19					15																	79058475		2190	4289	6479	SO:0001583	missense	11173	exon19			TCCACAGCTCCGC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3778C>A	chr15.hg19:g.79058475G>T	ENSP00000373472:p.Leu1260Met	42.0	0.0		35.0	23.0	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	hg19	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	g	8.618	0.890829	0.17613	.	.	ENSG00000136378	ENST00000388820	T	0.59772	0.24	4.07	2.03	0.26663	.	1.454380	0.05546	U	0.566621	T	0.47985	0.1475	L	0.29908	0.895	0.09310	N	1	D	0.54397	0.966	P	0.45037	0.467	T	0.33497	-0.9866	10	0.33141	T	0.24	.	6.5866	0.22624	0.1059:0.3604:0.5337:0.0	.	1260	Q9UKP4	ATS7_HUMAN	M	1260	ENSP00000373472:L1260M	ENSP00000373472:L1260M	L	-	1	2	ADAMTS7	76845530	0.007000	0.16637	0.001000	0.08648	0.002000	0.02628	1.554000	0.36266	0.235000	0.21160	0.472000	0.43445	CTG	.	.		0.672	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		T	79058475	G	T	79058475	3	4	72	1	0	0	0	0	1	0	0	0	271	962	34	3	1306	3	ADAMTS7	15	79058475	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	34900122	79058475	23472917	97	9289										
KIF7	374654	hgsc.bcm.edu	37	chr15	90190176	90190176	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tatgaggtcgaggcacaaagGacccgggaggcaggccattc	15	10	0	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr15:90190176G>T	ENST00000394412.3	-	7	1749	c.1673C>A	c.(1672-1674)tCc>tAc	p.S558Y		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	558	Sufficient for interaction with NPHP1.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			AGGCACAAAGGACCCGGGAGG	0.687											OREG0023460	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S558Y		Atlas-SNP	.											.	KIF7	130	.	0			c.C1673A						.						24	27	26					15																	90190176		2198	4297	6495	SO:0001583	missense	374654	exon7			ACAAAGGACCCGG	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"Kinesins"	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.1673C>A	chr15.hg19:g.90190176G>T	ENSP00000377934:p.Ser558Tyr	81.0	0.0	1273	43.0	26.0	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	hg19	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	g	10.04	1.242794	0.22796	.	.	ENSG00000166813	ENST00000394412	T	0.70631	-0.5	5.17	3.04	0.35103	.	0.515669	0.21098	N	0.080209	T	0.64305	0.2586	L	0.44542	1.39	0.09310	N	1	P;P	0.42620	0.785;0.454	B;B	0.44224	0.444;0.133	T	0.57866	-0.7737	10	0.59425	D	0.04	.	9.2862	0.37758	0.0:0.1316:0.6735:0.195	.	45;558	B7ZKY4;Q2M1P5	.;KIF7_HUMAN	Y	558	ENSP00000377934:S558Y	ENSP00000377934:S558Y	S	-	2	0	KIF7	87991180	0.023000	0.18921	0.202000	0.23494	0.403000	0.30841	1.697000	0.37784	1.113000	0.41760	0.457000	0.33378	TCC	.	.		0.687	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		T	90190176	G	T	90190176	3	4	72	1	0	0	0	0	1	0	0	0	8318	1174	41	3	2410	3	KIF7	15	90190176	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	11131701	90190176	12341216	98	9290										
SERPINF2	5345	hgsc.bcm.edu	37	chr17	1657772	1657772	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	acaagcttttcggccctgacTtaaaacttgtgccccccatg	7	14	0	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:1657772T>C	ENST00000324015.3	+	10	1497	c.1420T>C	c.(1420-1422)Tta>Cta	p.L474L	SERPINF2_ENST00000450523.2_Silent_p.L410L|SERPINF2_ENST00000382061.4_Silent_p.L474L	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	474					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of proteolysis (GO:0030162)|response to organic substance (GO:0010033)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Ocriplasmin(DB08888)	CGGCCCTGACTTAAAACTTGT	0.617																																					p.L474L		Atlas-SNP	.											.	SERPINF2	33	.	0			c.T1420C						.						59	65	63					17																	1657772		2203	4300	6503	SO:0001819	synonymous_variant	5345	exon10			CCTGACTTAAAAC	D00174	CCDS11011.1, CCDS54064.1	17p13.3	2014-02-18	2005-08-18		ENSG00000167711	ENSG00000167711		"Serine (or cysteine) peptidase inhibitors"	9075	protein-coding gene	gene with protein product	"alpha-2-plasmin inhibitor", "alpha-2-antiplasmin"	613168	"serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2"	PLI		3416655, 24172014	Standard	NM_000934		Approved	API, ALPHA-2-PI, A2AP, AAP	uc002ftk.1	P08697	OTTHUMG00000090552	ENST00000324015.3:c.1420T>C	chr17.hg19:g.1657772T>C		37.0	0.0		46.0	35.0	NM_000934	B4E1B7|Q8N5U7|Q9UCG2|Q9UCG3	Silent	SNP	ENST00000324015.3	hg19	CCDS11011.1																																																																																			.	.		0.617	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207078.3	NM_000934		C	1657772	T	C	1657772	2	2	72	1	0	0	0	0	0	0	0	1	14130	1606	56	2		2	SERPINF2	17	1657772	Silent	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10		1657772	79537438	99	9291										
KIAA0753	9851	hgsc.bcm.edu	37	chr17	6511774	6511774	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ggggctagttttcacctttaGccatgcagcactgaaataaa	9	9	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:6511774G>C	ENST00000361413.3	-	10	2081	c.1723C>G	c.(1723-1725)Cta>Gta	p.L575V	KIAA0753_ENST00000572370.1_Missense_Mutation_p.L276V|KIAA0753_ENST00000589033.1_Missense_Mutation_p.L31V|KIAA0753_ENST00000542606.1_Missense_Mutation_p.L276V|KIAA0753_ENST00000575027.1_5'Flank	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	575						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TTCACCTTTAGCCATGCAGCA	0.468																																					p.L575V		Atlas-SNP	.											.	KIAA0753	63	.	0			c.C1723G						.						216	208	211					17																	6511774		1943	4140	6083	SO:0001583	missense	9851	exon10			CCTTTAGCCATGC		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1723C>G	chr17.hg19:g.6511774G>C	ENSP00000355250:p.Leu575Val	79.0	0.0		65.0	48.0	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	hg19	CCDS42247.1	.	.	.	.	.	.	.	.	.	.	G	2.493	-0.317071	0.05386	.	.	ENSG00000198920	ENST00000361413;ENST00000542606;ENST00000542826	D;D	0.85556	-2.0;-2.0	5.06	-1.62	0.08372	.	1.751100	0.03366	N	0.198230	T	0.80232	0.4585	M	0.65975	2.015	0.09310	N	0.999995	B	0.25272	0.122	B	0.25291	0.059	T	0.55335	-0.8157	10	0.28530	T	0.3	-0.1196	0.5849	0.00718	0.197:0.1786:0.3099:0.3146	.	575	Q2KHM9	K0753_HUMAN	V	575;276;31	ENSP00000355250:L575V;ENSP00000444634:L276V	ENSP00000355250:L575V	L	-	1	2	KIAA0753	6452498	0.980000	0.34600	0.400000	0.26346	0.231000	0.25187	0.801000	0.27055	-0.082000	0.12640	0.467000	0.42956	CTA	.	.		0.468	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804		C	6511774	G	C	6511774	3	2	72	1	0	0	0	0	1	0	0	0	8200	962	34	4	1220	4	KIAA0753	17	6511774	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	4854002	6511774	74683436	100	9292										
TP53	7157	hgsc.bcm.edu	37	chr17	7578188	7578188	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	aaaccagacctcaggcggctCatagggcaccaccacactat	8	15	2	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:7578188C>A	ENST00000269305.4	-	6	850	c.661G>T	c.(661-663)Gag>Tag	p.E221*	TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Nonsense_Mutation_p.E221*|TP53_ENST00000413465.2_Nonsense_Mutation_p.E221*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E221*|TP53_ENST00000455263.2_Nonsense_Mutation_p.E221*|TP53_ENST00000420246.2_Nonsense_Mutation_p.E221*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	221	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> Q (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E221*(14)|p.?(11)|p.0?(8)|p.E221fs*4(3)|p.E128*(3)|p.E221K(2)|p.Y220_P223delYEPP(1)|p.E221fs*2(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y220fs*25(1)|p.E221fs*26(1)|p.V218fs*26(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCAGGCGGCTCATAGGGCACC	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E221X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,colon,carcinoma,+1,1	TP53	33396	.	48	Substitution - Nonsense(17)|Unknown(11)|Whole gene deletion(8)|Deletion - Frameshift(4)|Deletion - In frame(3)|Insertion - Frameshift(3)|Substitution - Missense(2)	upper_aerodigestive_tract(9)|biliary_tract(5)|endometrium(5)|urinary_tract(5)|lung(5)|bone(4)|central_nervous_system(3)|oesophagus(2)|ovary(2)|vulva(1)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|salivary_gland(1)|breast(1)|skin(1)|large_intestine(1)|liver(1)	c.G661T						.						100	92	94					17																	7578188		2203	4300	6503	SO:0001587	stop_gained	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GCGGCTCATAGGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.661G>T	chr17.hg19:g.7578188C>A	ENSP00000269305:p.Glu221*	103.0	0.0		89.0	64.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	34	5.353387	0.95830	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	.	.	.	5.28	4.31	0.51392	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-8.6014	12.2235	0.54447	0.0:0.9162:0.0:0.0838	.	.	.	.	X	221;221;221;221;221;221;210;128;89;128	.	ENSP00000269305:E221X	E	-	1	0	TP53	7518913	1.000000	0.71417	0.299000	0.25016	0.996000	0.88848	6.045000	0.71020	1.364000	0.46038	0.563000	0.77884	GAG	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578188	C	A	7578188	4	1	72	1	0	0	0	0	0	1	0	0	16396	835	29	3	633	3	TP53	17	7578188	Nonsense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	1066414	7578188	73617022	101	9293										
RAI1	10743	hgsc.bcm.edu	37	chr17	17697493	17697493	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ccagctctgtggacacccagGctggcaactgcaagcccctt	10	16	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:17697493G>T	ENST00000353383.1	+	3	1700	c.1231G>T	c.(1231-1233)Gct>Tct	p.A411S	RAI1_ENST00000261641.6_Missense_Mutation_p.A411S	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	411					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GGACACCCAGGCTGGCAACTG	0.627																																					p.A411S		Atlas-SNP	.											.	RAI1	121	.	0			c.G1231T						.						99	99	99					17																	17697493		2203	4300	6503	SO:0001583	missense	10743	exon3			ACCCAGGCTGGCA	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"Smith-Magenis syndrome chromosome region"	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.1231G>T	chr17.hg19:g.17697493G>T	ENSP00000323074:p.Ala411Ser	105.0	0.0		58.0	36.0	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	G	3.092	-0.186592	0.06340	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641	T;T;T	0.25749	1.78;1.78;1.78	5.55	4.58	0.56647	.	0.421941	0.24433	N	0.038570	T	0.14399	0.0348	L	0.31664	0.95	0.09310	N	0.999998	B	0.16396	0.017	B	0.09377	0.004	T	0.18398	-1.0338	10	0.22109	T	0.4	.	2.867	0.05604	0.1566:0.1332:0.5545:0.1557	.	411	Q7Z5J4	RAI1_HUMAN	S	411	ENSP00000323074:A411S;ENSP00000379120:A411S;ENSP00000261641:A411S	ENSP00000261641:A411S	A	+	1	0	RAI1	17638218	0.966000	0.33281	0.893000	0.35052	0.316000	0.28119	1.139000	0.31504	1.342000	0.45619	0.561000	0.74099	GCT	.	.		0.627	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		T	17697493	G	T	17697493	3	4	72	1	0	0	0	0	1	0	0	0	13022	1203	42	3	1233	3	RAI1	17	17697493	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	10119305	17697493	63497717	102	9294										
RNF135	84282	hgsc.bcm.edu	37	chr17	29325932	29325932	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gagccgcgaccaggtcctggGaaggactatggactcttgtt	14	10	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:29325932G>T	ENST00000328381.5	+	5	1895	c.1022G>T	c.(1021-1023)gGa>gTa	p.G341V	RNF135_ENST00000443677.2_3'UTR|RNF135_ENST00000535306.2_3'UTR|RNF135_ENST00000324689.4_3'UTR	NM_032322.3	NP_115698.3	Q8IUD6	RN135_HUMAN	ring finger protein 135	341	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-beta production (GO:0032728)|protein ubiquitination (GO:0016567)|regulation of innate immune response (GO:0045088)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|ribonucleoprotein complex binding (GO:0043021)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|skin(2)|urinary_tract(1)	10		all_cancers(10;8.65e-08)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Myeloproliferative disorder(56;0.0255)				CAGGTCCTGGGAAGGACTATG	0.557																																					p.G341V		Atlas-SNP	.											.	RNF135	19	.	1	Unknown(1)	central_nervous_system(1)	c.G1022T						.						57	54	55					17																	29325932		2203	4300	6503	SO:0001583	missense	84282	exon5			TCCTGGGAAGGAC	AJ496729	CCDS11262.1, CCDS11263.1, CCDS54104.1	17q11.2	2013-01-09			ENSG00000181481	ENSG00000181481		"RING-type (C3HC4) zinc fingers"	21158	protein-coding gene	gene with protein product	"riplet"	611358				11468690, 19017631	Standard	NM_001184992		Approved	MGC13061	uc002hfz.3	Q8IUD6	OTTHUMG00000132867	ENST00000328381.5:c.1022G>T	chr17.hg19:g.29325932G>T	ENSP00000328340:p.Gly341Val	108.0	0.0		147.0	70.0	NM_032322	A0AVM5|B2R7G9|B6ZLM5|F5GX60|Q9BSE9	Missense_Mutation	SNP	ENST00000328381.5	hg19	CCDS11262.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.243868	0.79912	.	.	ENSG00000181481	ENST00000328381;ENST00000535605	T	0.73363	-0.74	5.21	5.21	0.72293	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.44097	D	0.000490	D	0.85630	0.5741	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82778	-0.0289	10	0.20046	T	0.44	-14.8505	16.6225	0.84934	0.0:0.0:1.0:0.0	.	341	Q8IUD6	RN135_HUMAN	V	341;160	ENSP00000328340:G341V	ENSP00000328340:G341V	G	+	2	0	RNF135	26350058	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	6.441000	0.73439	2.613000	0.88420	0.655000	0.94253	GGA	.	.		0.557	RNF135-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256342.3	NM_032322		T	29325932	G	T	29325932	3	4	72	1	0	0	0	0	1	0	0	0	13455	1174	41	3	1109	3	RNF135	17	29325932	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	11628439	29325932	51869278	103	9295										
MEOX1	4222	hgsc.bcm.edu	37	chr17	41738808	41738808	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ggtagtggggtagccctgagGccccattgccttccgagtgg	16	11	0	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:41738808G>A	ENST00000318579.4	-	1	514	c.95C>T	c.(94-96)gCc>gTc	p.A32V	MEOX1_ENST00000549132.1_Missense_Mutation_p.P3S|MEOX1_ENST00000393661.2_Intron|MEOX1_ENST00000329168.3_Missense_Mutation_p.A32V	NM_001040002.1|NM_004527.3	NP_001035091.1|NP_004518.1	P50221	MEOX1_HUMAN	mesenchyme homeobox 1	32					multicellular organismal development (GO:0007275)|somite specification (GO:0001757)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)		TAGCCCTGAGGCCCCATTGCC	0.662																																					p.A32V		Atlas-SNP	.											.	MEOX1	29	.	0			c.C95T						.						19	24	22					17																	41738808		2186	4281	6467	SO:0001583	missense	4222	exon1			CCTGAGGCCCCAT		CCDS11466.1, CCDS11467.1, CCDS42343.1	17q21.31	2014-07-15	2005-12-22					"Homeoboxes / ANTP class : HOXL subclass"	7013	protein-coding gene	gene with protein product		600147	"mesenchyme homeo box 1"			7987315	Standard	NM_013999		Approved	MOX1	uc002idz.3	P50221	OTTHUMG00000170513	ENST00000318579.4:c.95C>T	chr17.hg19:g.41738808G>A	ENSP00000321684:p.Ala32Val	96.0	0.0		144.0	59.0	NM_004527	A8K524|A8MWF9|Q15069	Missense_Mutation	SNP	ENST00000318579.4	hg19	CCDS11466.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.36|15.36	2.810657|2.810657	0.50421|0.50421	.|.	.|.	ENSG00000005102|ENSG00000005102	ENST00000318579;ENST00000329168|ENST00000549132	D;T|.	0.91295|.	-2.82;0.62|.	4.68|4.68	3.72|3.72	0.42706|0.42706	.|.	0.312282|.	0.33650|.	N|.	0.004689|.	T|T	0.63094|0.63094	0.2482|0.2482	L|L	0.53249|0.53249	1.67|1.67	0.50171|0.50171	D|D	0.99985|0.99985	B;B|.	0.12630|.	0.006;0.001|.	B;B|.	0.17433|.	0.018;0.002|.	T|T	0.65977|0.65977	-0.6037|-0.6037	10|6	0.59425|0.87932	D|D	0.04|0	-16.4|-16.4	11.2408|11.2408	0.48968|0.48968	0.0848:0.0:0.9152:0.0|0.0848:0.0:0.9152:0.0	.|.	32;32|.	Q15069;P50221|.	.;MEOX1_HUMAN|.	V|S	32|3	ENSP00000321684:A32V;ENSP00000328678:A32V|.	ENSP00000321684:A32V|ENSP00000449049:P3S	A|P	-|-	2|1	0|0	MEOX1|MEOX1	39094334|39094334	0.259000|0.259000	0.24043|0.24043	0.992000|0.992000	0.48379|0.48379	0.975000|0.975000	0.68041|0.68041	2.675000|2.675000	0.46875|0.46875	1.203000|1.203000	0.43233|0.43233	0.563000|0.563000	0.77884|0.77884	GCC|CCT	.	.		0.662	MEOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409452.1			A	41738808	G	A	41738808	3	1	72	1	0	0	0	0	1	0	0	0	9482	1203	42	3	681	3	MEOX1	17	41738808	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	12412876	41738808	39456402	104	9296										
ITGA2B	3674	hgsc.bcm.edu	37	chr17	42453683	42453683	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cctggcctctcaccctcgcaGctccacttgggcctctgccc	8	21	2	0	rs542591743		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:42453683G>C	ENST00000262407.5	-	23	2372	c.2341C>G	c.(2341-2343)Ctg>Gtg	p.L781V	ITGA2B_ENST00000353281.4_Missense_Mutation_p.L781V	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	781					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	CACCCTCGCAGCTCCACTTGG	0.602											OREG0024460	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0	0	5008	,	,		16982	0		0	False		,,,				2504	0.001				p.L781V		Atlas-SNP	.											.	ITGA2B	88	.	0			c.C2341G						.						98	112	107					17																	42453683		2203	4300	6503	SO:0001583	missense	3674	exon23			CTCGCAGCTCCAC		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"CD molecules", "Integrins"	6138	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 93"	607759	"integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.2341C>G	chr17.hg19:g.42453683G>C	ENSP00000262407:p.Leu781Val	77.0	0.0	908	91.0	42.0	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Missense_Mutation	SNP	ENST00000262407.5	hg19	CCDS32665.1	.	.	.	.	.	.	.	.	.	.	G	17.20	3.328672	0.60743	.	.	ENSG00000005961	ENST00000262407;ENST00000353281	T;T	0.47177	0.85;0.85	4.33	3.36	0.38483	Integrin alpha-2 (1);	0.000000	0.27936	U	0.017255	T	0.61776	0.2374	M	0.66939	2.045	0.80722	D	1	D;D	0.69078	0.974;0.997	P;D	0.68353	0.686;0.957	T	0.61671	-0.7015	10	0.49607	T	0.09	.	10.0083	0.41970	0.1008:0.0:0.8992:0.0	.	379;781	Q59FA8;P08514	.;ITA2B_HUMAN	V	781	ENSP00000262407:L781V;ENSP00000340536:L781V	ENSP00000262407:L781V	L	-	1	2	ITGA2B	39809209	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	3.885000	0.56182	1.040000	0.40099	0.462000	0.41574	CTG	.	.		0.602	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			C	42453683	G	C	42453683	3	2	72	1	0	0	0	0	1	0	0	0	7885	962	34	4	810	4	ITGA2B	17	42453683	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	714875	42453683	38741527	105	9297										
CRHR1	1394	hgsc.bcm.edu	37	chr17	43884410	43884410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ggggctgaaccccgtctctgCctccctccaggaccagcact	10	18	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:43884410C>T	ENST00000398285.3	+	2	68	c.68C>T	c.(67-69)gCc>gTc	p.A23V	CRHR1_ENST00000293493.7_5'UTR|CRHR1_ENST00000339069.5_5'UTR|RP11-105N13.4_ENST00000587305.1_RNA|CRHR1_ENST00000577353.1_Missense_Mutation_p.A23V|CRHR1_ENST00000352855.5_Missense_Mutation_p.A23V|CRHR1_ENST00000314537.5_Missense_Mutation_p.A23V	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	23					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CCCGTCTCTGCCTCCCTCCAG	0.607																																					p.A23V	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.C68T						.						64	71	69					17																	43884410		2095	4229	6324	SO:0001583	missense	1394	exon2			TCTCTGCCTCCCT	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"GPCR / Class B : Corticotropin-releasing factor receptors"	2357	protein-coding gene	gene with protein product	"corticotropin-releasing factor receptor"	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.68C>T	chr17.hg19:g.43884410C>T	ENSP00000381333:p.Ala23Val	40.0	0.0		58.0	27.0	NM_001145148	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Missense_Mutation	SNP	ENST00000398285.3	hg19	CCDS45712.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.751909	0.31046	.	.	ENSG00000120088	ENST00000398285;ENST00000314537;ENST00000347197;ENST00000352855	T;T;T;T	0.55052	0.54;0.54;0.54;0.9	4.14	3.13	0.36017	.	0.612843	0.14455	N	0.318549	T	0.31451	0.0797	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.29188	0.004;0.236;0.01;0.012	B;B;B;B	0.20767	0.005;0.031;0.005;0.017	T	0.07501	-1.0769	10	0.30078	T	0.28	.	9.6881	0.40111	0.0:0.7875:0.2125:0.0	.	23;23;23;23	P34998-4;P34998;P34998-3;P34998-2	.;CRFR1_HUMAN;.;.	V	23	ENSP00000381333:A23V;ENSP00000326060:A23V;ENSP00000239167:A23V;ENSP00000344068:A23V	ENSP00000326060:A23V	A	+	2	0	CRHR1	41240190	0.920000	0.31207	0.827000	0.32855	0.695000	0.40330	1.447000	0.35101	1.043000	0.40175	0.555000	0.69702	GCC	.	.		0.607	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3			T	43884410	C	T	43884410	3	4	72	1	0	0	0	0	1	0	0	0	3873	739	26	3	74	3	CRHR1	17	43884410	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	1430727	43884410	37310800	106	9298										
MAP3K3	4215	hgsc.bcm.edu	37	chr17	61768464	61768464	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cactgacccctcccctaggaGgtgagtgctctggagtgcga	13	13	1	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:61768464G>A	ENST00000361733.3	+	13	1535	c.1215G>A	c.(1213-1215)gaG>gaA	p.E405E	MAP3K3_ENST00000584573.1_Silent_p.E432E|MAP3K3_ENST00000361357.3_Silent_p.E436E|MAP3K3_ENST00000579585.1_Silent_p.E436E|MAP3K3_ENST00000577395.1_Silent_p.E401E	NM_002401.3	NP_002392.2	Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3	405	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)			breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	28						TCCCCTAGGAGGTGAGTGCTC	0.602																																					p.E436E		Atlas-SNP	.											.	MAP3K3	56	.	0			c.G1308A						.						77	66	69					17																	61768464		2203	4300	6503	SO:0001819	synonymous_variant	4215	exon14			CTAGGAGGTGAGT	U78876	CCDS32701.1, CCDS32702.1	17q	2011-06-09				ENSG00000198909		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6855	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 3", "MAPK/ERK kinase kinase 3"	602539		MEKK3		9006902	Standard	NM_002401		Approved	MAPKKK3	uc002jbf.3	Q99759		ENST00000361733.3:c.1215G>A	chr17.hg19:g.61768464G>A		50.0	0.0		33.0	14.0	NM_203351	B2RCW2|D3DU15|Q5BKZ6|Q8N3I9	Silent	SNP	ENST00000361733.3	hg19	CCDS32702.1																																																																																			.	.		0.602	MAP3K3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443867.1	NM_002401		A	61768464	G	A	61768464	2	1	72	1	0	0	0	0	0	0	0	1	9260	991	35	3		3	MAP3K3	17	61768464	Silent	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	17884054	61768464	19426746	107	9299										
C17orf28	283987	hgsc.bcm.edu	37	chr17	72959876	72959876	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cactgtggaccagaagaagcCcctccagtcggggtcctcaa	11	14	1	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:72959876C>A	ENST00000425042.2	-	3	423	c.346G>T	c.(346-348)Ggc>Tgc	p.G116C	HID1_ENST00000532900.1_5'UTR	NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	116					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)											CAGAAGAAGCCCCTCCAGTCG	0.672																																					p.G116C		Atlas-SNP	.											.	.	.	.	0			c.G346T						.						28	28	28					17																	72959876		2203	4300	6503	SO:0001583	missense	283987	exon3			AGAAGCCCCTCCA		CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"downregulated in multiple cancer 1"	605752	"chromosome 17 open reading frame 28"	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.346G>T	chr17.hg19:g.72959876C>A	ENSP00000413520:p.Gly116Cys	79.0	0.0		87.0	28.0	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Missense_Mutation	SNP	ENST00000425042.2	hg19	CCDS32726.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.049561	0.93740	.	.	ENSG00000167861	ENST00000425042;ENST00000534480	.	.	.	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.76126	0.3944	M	0.85197	2.74	0.80722	D	1	B;B	0.30824	0.296;0.122	B;B	0.39027	0.248;0.288	T	0.79300	-0.1860	9	0.62326	D	0.03	-29.8564	17.944	0.89034	0.0:1.0:0.0:0.0	.	116;116	Q8IV36-2;Q8IV36	.;CQ028_HUMAN	C	116	.	ENSP00000413520:G116C	G	-	1	0	C17orf28	70471471	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.614000	0.82996	2.240000	0.73641	0.650000	0.86243	GGC	.	.		0.672	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630		A	72959876	C	A	72959876	3	1	72	1	0	0	0	0	1	0	0	0	1855	623	22	3	2088	3	C17orf28	17	72959876	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	11191412	72959876	8235334	108	9300										
TBC1D16	125058	hgsc.bcm.edu	37	chr17	77922702	77922702	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cacattgggattgtcttcccCccggaagaactggttgttcc	10	12	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr17:77922702C>A	ENST00000310924.2	-	8	1625	c.1510G>T	c.(1510-1512)Ggg>Tgg	p.G504W	TBC1D16_ENST00000576768.1_Missense_Mutation_p.G129W|TBC1D16_ENST00000572862.1_Missense_Mutation_p.G142W|TBC1D16_ENST00000570373.1_Missense_Mutation_p.G143W|TBC1D16_ENST00000340848.7_Missense_Mutation_p.G142W	NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	504	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			TTGTCTTCCCCCCGGAAGAAC	0.572																																					p.G504W	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.G1510T						.						224	179	194					17																	77922702		2203	4300	6503	SO:0001583	missense	125058	exon8			CTTCCCCCCGGAA	AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.1510G>T	chr17.hg19:g.77922702C>A	ENSP00000309794:p.Gly504Trp	70.0	0.0		105.0	16.0	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Missense_Mutation	SNP	ENST00000310924.2	hg19	CCDS11766.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.255432	0.80135	.	.	ENSG00000167291	ENST00000340848;ENST00000310924	T;T	0.11604	2.76;2.76	5.18	4.21	0.49690	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.44644	0.1303	H	0.95504	3.68	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.999	T	0.60900	-0.7171	10	0.87932	D	0	-38.0032	13.3375	0.60526	0.0:0.9239:0.0:0.076	.	164;504;504;142	Q96DH7;Q8TBP0;B9A6L7;Q8N3Z4	.;TBC16_HUMAN;.;.	W	142;504	ENSP00000341517:G142W;ENSP00000309794:G504W	ENSP00000309794:G504W	G	-	1	0	TBC1D16	75537297	1.000000	0.71417	0.326000	0.25389	0.860000	0.49131	7.454000	0.80714	1.164000	0.42652	0.655000	0.94253	GGG	.	.		0.572	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020		A	77922702	C	A	77922702	3	1	72	1	0	0	0	0	1	0	0	0	15620	623	22	3	813	3	TBC1D16	17	77922702	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	4962826	77922702	3272508	109	9301										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21422647	21422647	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gattgccgaaggccagattgAgtttgacatctcagagcctg	12	9	1	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr18:21422647A>T	ENST00000313654.9	+	29	3777	c.3536A>T	c.(3535-3537)gAg>gTg	p.E1179V	LAMA3_ENST00000399516.3_Missense_Mutation_p.E1179V	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1179	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GGCCAGATTGAGTTTGACATC	0.527																																					p.E1179V		Atlas-SNP	.											.	LAMA3	397	.	0			c.A3536T						.						131	139	136					18																	21422647		2011	4185	6196	SO:0001583	missense	3909	exon29			AGATTGAGTTTGA	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3536A>T	chr18.hg19:g.21422647A>T	ENSP00000324532:p.Glu1179Val	132.0	0.0		183.0	75.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	A	9.776	1.173925	0.21704	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.17854	2.27;2.25	5.83	4.67	0.58626	.	.	.	.	.	T	0.16041	0.0386	L	0.41492	1.28	0.19575	N	0.999968	P;P	0.45986	0.577;0.87	B;B	0.41571	0.202;0.36	T	0.07328	-1.0778	9	0.29301	T	0.29	.	11.9307	0.52845	0.7053:0.2947:0.0:0.0	.	1179;1179	Q6VU67;Q16787	.;LAMA3_HUMAN	V	1179;1179;1177	ENSP00000324532:E1179V;ENSP00000382432:E1179V	ENSP00000324532:E1179V	E	+	2	0	LAMA3	19676645	1.000000	0.71417	0.978000	0.43139	0.855000	0.48748	2.354000	0.44098	1.040000	0.40099	0.533000	0.62120	GAG	.	.		0.527	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21422647	A	T	21422647	3	4	72	1	0	0	0	0	1	0	0	0	8616	304	11	4	3650	4	LAMA3	18	21422647	Missense_Mutation	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10		21422647	56654601	110	9302										
NOL4	8715	hgsc.bcm.edu	37	chr18	31523091	31523097	+	Frame_Shift_Del	DEL	CCAAGAT	CCAAGAT	-													0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ctcactctcacaagctgaagCcaagatactctctgcaactg							TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	CCAAGAT	CCAAGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr18:31523091_31523097delCCAAGAT	ENST00000261592.5	-	9	1771_1777	c.1474_1480delATCTTGG	c.(1474-1482)atcttggctfs	p.ILA492fs	NOL4_ENST00000535384.1_Frame_Shift_Del_p.ILA207fs|NOL4_ENST00000269185.4_Intron|NOL4_ENST00000538587.1_Frame_Shift_Del_p.ILA418fs|NOL4_ENST00000535475.1_Frame_Shift_Del_p.ILA273fs|NOL4_ENST00000589544.1_Intron	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	492						nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						CAAGCTGAAGCCAAGATACTCTCTGCA	0.42																																					p.492_494del		Atlas-Indel,Pindel	.											.	NOL4	139	.	0			c.1475_1481del						.																																			SO:0001589	frameshift_variant	8715	exon9			.	AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.1474_1480delATCTTGG	chr18.hg19:g.31523091_31523097delCCAAGAT	ENSP00000261592:p.Ile492fs	108.0	0.0		111.0	32.0	NM_003787	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Frame_Shift_Del	DEL	ENST00000261592.5	hg19	CCDS11907.2																																																																																			.	.		0.42	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		-	31523097	CCAAGAT	-	31523091	7	5	72	1	0	1	0	1	0	0	0	0	10533	739	26	0	448	0	NOL4	18	31523091	Frame_Shift_Del	DEL	CCAAGAT	TCGA-CC-A7IG-01A-11D-A33K-10	10100444	31523091	46554157	111	9303										
SIGLEC15	284266	hgsc.bcm.edu	37	chr18	43418741	43418741	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ccggctcacgccttccgcgcGctctgcactgccgaagggga	13	17	2	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr18:43418741G>T	ENST00000389474.3	+	4	772	c.555G>T	c.(553-555)gcG>gcT	p.A185A	SIGLEC15_ENST00000587418.1_5'UTR|SIGLEC15_ENST00000602118.2_3'UTR|SIGLEC15_ENST00000546268.1_Silent_p.A31A	NM_213602.2	NP_998767.1	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	185	Ig-like C2-type.				cellular response to lipoprotein particle stimulus (GO:0071402)|innate immune response (GO:0045087)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of bone resorption (GO:0045124)|regulation of osteoclast development (GO:2001204)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						CCTTCCGCGCGCTCTGCACTG	0.736																																					p.A185A		Atlas-SNP	.											.	SIGLEC15	10	.	0			c.G555T						.						6	7	7					18																	43418741		2114	4146	6260	SO:0001819	synonymous_variant	284266	exon4			CCGCGCGCTCTGC	AK095432	CCDS32819.1	18q21.1	2014-01-28	2007-05-31	2007-05-31	ENSG00000197046	ENSG00000197046		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	27596	protein-coding gene	gene with protein product			"CD33 antigen-like 3", "CD33 molecule-like 3"	CD33L3		17483134	Standard	NM_213602		Approved	HsT1361	uc002lbl.1	Q6ZMC9		ENST00000389474.3:c.555G>T	chr18.hg19:g.43418741G>T		13.0	0.0		14.0	7.0	NM_213602	A8K2Y5|B4DVQ9	Silent	SNP	ENST00000389474.3	hg19	CCDS32819.1																																																																																			.	.		0.736	SIGLEC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410768.2	NM_213602		T	43418741	G	T	43418741	2	4	72	1	0	0	0	0	0	0	0	1	14325	1074	38	1		1	SIGLEC15	18	43418741	Silent	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	11895650	43418741	34658507	112	9304										
C18orf25	147339	hgsc.bcm.edu	37	chr18	43796312	43796312	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cttccactatggctgccaagAaaaaccggcaatccagtgat	8	12	0	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr18:43796312A>T	ENST00000282059.6	+	2	840	c.466A>T	c.(466-468)Aaa>Taa	p.K156*	C18orf25_ENST00000321319.6_Nonsense_Mutation_p.K156*	NM_145055.3	NP_659492	Q96B23	CR025_HUMAN	chromosome 18 open reading frame 25	156										central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	11						GGCTGCCAAGAAAAACCGGCA	0.532																																					p.K156X		Atlas-SNP	.											.	C18orf25	27	.	0			c.A466T						.						49	52	51					18																	43796312		1958	4137	6095	SO:0001587	stop_gained	147339	exon2			GCCAAGAAAAACC	AL713661	CCDS42430.1, CCDS42431.1	18q21.1	2014-01-03			ENSG00000152242	ENSG00000152242			28172	protein-coding gene	gene with protein product	"ARKadia-like 1"					15722956	Standard	NM_001008239		Approved	MGC12909, ARKL1, RNF111L1	uc002lbw.3	Q96B23		ENST00000282059.6:c.466A>T	chr18.hg19:g.43796312A>T	ENSP00000282059:p.Lys156*	129.0	0.0		141.0	57.0	NM_145055	A8K123|A8KAB6|Q5XG78|Q6N058|Q86TB5|Q8TCQ5	Nonsense_Mutation	SNP	ENST00000282059.6	hg19	CCDS42430.1	.	.	.	.	.	.	.	.	.	.	A	39	7.487936	0.98316	.	.	ENSG00000152242	ENST00000282059;ENST00000321319	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.6571	15.5421	0.76062	1.0:0.0:0.0:0.0	.	.	.	.	X	156	.	ENSP00000282059:K156X	K	+	1	0	C18orf25	42050310	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.866000	0.92307	2.090000	0.63153	0.459000	0.35465	AAA	.	.		0.532	C18orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445242.1	NM_145055		T	43796312	A	T	43796312	4	4	72	1	0	0	0	0	0	1	0	0	1901	247	9	4	468	4	C18orf25	18	43796312	Nonsense_Mutation	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10	377571	43796312	34280936	113	9305										
ACSBG2	81616	hgsc.bcm.edu	37	chr19	6147641	6147641	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tgggaaattctgaatttcaaCcagtactatgaggcttgtcg	10	7	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr19:6147641C>G	ENST00000586696.1	+	3	528	c.252C>G	c.(250-252)aaC>aaG	p.N84K	ACSBG2_ENST00000252669.5_Missense_Mutation_p.N84K|ACSBG2_ENST00000588304.1_Missense_Mutation_p.N34K|ACSBG2_ENST00000591403.1_Missense_Mutation_p.N84K|ACSBG2_ENST00000588485.1_5'UTR			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	84					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGAATTTCAACCAGTACTATG	0.408																																					p.N84K		Atlas-SNP	.											.	ACSBG2	83	.	0			c.C252G						.						136	141	139					19																	6147641		2203	4300	6503	SO:0001583	missense	81616	exon3			TTTCAACCAGTAC		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.252C>G	chr19.hg19:g.6147641C>G	ENSP00000465589:p.Asn84Lys	99.0	0.0		111.0	24.0	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	hg19	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	C	0.672	-0.801612	0.02841	.	.	ENSG00000130377	ENST00000252669	T	0.39056	1.1	5.79	-0.698	0.11280	AMP-dependent synthetase/ligase (1);	1.056920	0.07401	N	0.890849	T	0.12092	0.0294	N	0.01779	-0.725	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.11329	0.002;0.006	T	0.33675	-0.9859	10	0.02654	T	1	-19.9618	1.5747	0.02622	0.248:0.3744:0.2233:0.1543	.	84;84	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	K	84	ENSP00000252669:N84K	ENSP00000252669:N84K	N	+	3	2	ACSBG2	6098641	0.395000	0.25254	0.400000	0.26346	0.108000	0.19459	0.106000	0.15354	0.370000	0.24538	-0.181000	0.13052	AAC	.	.		0.408	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		G	6147641	C	G	6147641	3	3	72	1	0	0	0	0	1	0	0	0	174	506	18	4	258	4	ACSBG2	19	6147641	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10		6147641	52981342	114	9306										
ZNF823	55552	hgsc.bcm.edu	37	chr19	11834023	11834023	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tgcaattaagagacgaatgaCccaagacgacttctccacac	7	12	1	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr19:11834023C>G	ENST00000341191.6	-	4	479	c.326G>C	c.(325-327)gGt>gCt	p.G109A	ZNF823_ENST00000545749.1_5'UTR|ZNF823_ENST00000440527.1_3'UTR|CTC-499B15.6_ENST00000586983.1_RNA	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	109					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						AGACGAATGACCCAAGACGAC	0.433										HNSCC(68;0.2)																											p.G109A		Atlas-SNP	.											.	ZNF823	104	.	0			c.G326C						.						155	147	149					19																	11834023		2202	4300	6502	SO:0001583	missense	55552	exon4			GAATGACCCAAGA	X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"Zinc fingers, C2H2-type", "-"	30936	protein-coding gene	gene with protein product	"ZFP 36 for a zinc finger protein"						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.326G>C	chr19.hg19:g.11834023C>G	ENSP00000340683:p.Gly109Ala	107.0	0.0		103.0	21.0	NM_001080493	A0PJL4|B7Z8D4|Q6P4A9	Missense_Mutation	SNP	ENST00000341191.6	hg19	CCDS45981.1	.	.	.	.	.	.	.	.	.	.	c	7.007	0.556105	0.13436	.	.	ENSG00000197933	ENST00000341191;ENST00000431998	T;T	0.06294	4.18;3.32	0.632	-0.616	0.11583	.	.	.	.	.	T	0.07954	0.0199	L	0.38649	1.16	0.23076	N	0.998334	D	0.58268	0.982	P	0.55112	0.769	T	0.32295	-0.9912	9	0.15499	T	0.54	.	4.8531	0.13547	0.0:0.7326:0.0:0.2674	.	109	P16415	ZN823_HUMAN	A	109;65	ENSP00000340683:G109A;ENSP00000410654:G65A	ENSP00000340683:G109A	G	-	2	0	ZNF823	11695023	0.000000	0.05858	0.005000	0.12908	0.040000	0.13550	-1.112000	0.03299	-0.206000	0.10203	0.298000	0.19748	GGT	.	.		0.433	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493		G	11834023	C	G	11834023	3	3	72	1	0	0	0	0	1	0	0	0	18194	507	18	4	1510	4	ZNF823	19	11834023	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	5686382	11834023	47294960	115	9307										
JAK3	3718	hgsc.bcm.edu	37	chr19	17942056	17942056	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ccagaaaatggggctctggcCtggctcgcggaccacgtagt	14	12	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr19:17942056C>T	ENST00000527670.1	-	20	2988	c.2959G>A	c.(2959-2961)Ggc>Agc	p.G987S	JAK3_ENST00000458235.1_Missense_Mutation_p.G987S|JAK3_ENST00000534444.1_Missense_Mutation_p.G987S			P52333	JAK3_HUMAN	Janus kinase 3	987	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GGGCTCTGGCCTGGCTCGCGG	0.657		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.G987S		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	JAK3	341	.	0			c.G2959A						.						75	76	76					19																	17942056		2203	4300	6503	SO:0001583	missense	3718	exon21			TCTGGCCTGGCTC	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.2959G>A	chr19.hg19:g.17942056C>T	ENSP00000432511:p.Gly987Ser	61.0	0.0		50.0	25.0	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	hg19	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.747543	0.89663	.	.	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	T;T;D	0.88975	0.07;0.07;-2.45	3.22	3.22	0.36961	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.136270	0.48286	D	0.000194	D	0.91774	0.7398	L	0.55743	1.74	0.80722	D	1	D;P	0.76494	0.999;0.837	D;P	0.70716	0.97;0.475	D	0.92121	0.5704	10	0.62326	D	0.03	-33.9145	12.7152	0.57111	0.0:1.0:0.0:0.0	.	987;987	P52333-2;P52333	.;JAK3_HUMAN	S	987	ENSP00000391676:G987S;ENSP00000432511:G987S;ENSP00000436421:G987S	ENSP00000391676:G987S	G	-	1	0	JAK3	17803056	1.000000	0.71417	0.946000	0.38457	0.877000	0.50540	7.623000	0.83113	1.763000	0.52060	0.407000	0.27541	GGC	.	.		0.657	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		T	17942056	C	T	17942056	3	4	72	1	0	0	0	0	1	0	0	0	7948	681	24	3	431	3	JAK3	19	17942056	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	6108033	17942056	41186927	116	9308										
ZNF85	7639	hgsc.bcm.edu	37	chr19	21132144	21132144	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ccgattctcaactcttactaCccataagataattcatactg	3	12	3	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr19:21132144C>A	ENST00000328178.8	+	4	937	c.824C>A	c.(823-825)aCc>aAc	p.T275N	ZNF85_ENST00000601023.1_Missense_Mutation_p.T216N|ZNF85_ENST00000345030.6_Missense_Mutation_p.T242N	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	275					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						ACTCTTACTACCCATAAGATA	0.338																																					p.T305N		Atlas-SNP	.											.	ZNF85	72	.	0			c.C914A						.						26	29	28					19																	21132144		2197	4288	6485	SO:0001583	missense	7639	exon5			TTACTACCCATAA	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"Zinc fingers, C2H2-type", "-"	13160	protein-coding gene	gene with protein product		603899	"zinc finger protein 85 (HPF4, HTF1)"			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.824C>A	chr19.hg19:g.21132144C>A	ENSP00000329793:p.Thr275Asn	73.0	0.0		49.0	10.0	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	hg19	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	0.046	-1.266920	0.01433	.	.	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.35789	1.29;1.29	1.35	-2.7	0.06004	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15132	0.0365	N	0.04203	-0.255	0.09310	N	1	P;P;B	0.42961	0.726;0.795;0.003	P;B;B	0.44696	0.458;0.268;0.026	T	0.10132	-1.0643	9	0.19590	T	0.45	.	2.64	0.04968	0.2163:0.2947:0.0:0.4889	.	242;216;275	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	N	275;242;150	ENSP00000329793:T275N;ENSP00000342340:T242N	ENSP00000329793:T275N	T	+	2	0	ZNF85	20923984	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-8.361000	0.00021	-0.973000	0.03555	-0.379000	0.06801	ACC	.	.		0.338	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		A	21132144	C	A	21132144	3	1	72	1	0	0	0	0	1	0	0	0	18208	507	18	3	838	3	ZNF85	19	21132144	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	3190088	21132144	37996839	117	9309										
ZNF98	148198	hgsc.bcm.edu	37	chr19	22575415	22575415	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ttctttacatttgtagggttTctctccactatgaattcttt	5	8	3	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr19:22575415T>C	ENST00000357774.5	-	4	743	c.622A>G	c.(622-624)Aaa>Gaa	p.K208E		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	208					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				TTGTAGGGTTTCTCTCCACTA	0.353																																					p.K208E		Atlas-SNP	.											.	ZNF98	230	.	0			c.A622G						.						9	9	9					19																	22575415		1826	4053	5879	SO:0001583	missense	148198	exon4			AGGGTTTCTCTCC		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"Zinc fingers, C2H2-type", "-"	13174	protein-coding gene	gene with protein product	"zinc finger protein 739"	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.622A>G	chr19.hg19:g.22575415T>C	ENSP00000350418:p.Lys208Glu	305.0	0.0		307.0	152.0	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	hg19	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	10.49	1.365928	0.24684	.	.	ENSG00000197360	ENST00000357774	T	0.27104	1.69	1.28	0.0438	0.14223	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31606	0.0802	M	0.86953	2.85	0.26586	N	0.973286	B	0.10296	0.003	B	0.15484	0.013	T	0.37478	-0.9704	9	0.87932	D	0	.	6.0583	0.19824	0.0:0.0:0.2636:0.7363	.	208	A6NK75	ZNF98_HUMAN	E	208	ENSP00000350418:K208E	ENSP00000350418:K208E	K	-	1	0	ZNF98	22367255	0.990000	0.36364	0.001000	0.08648	0.005000	0.04900	2.954000	0.49113	-0.285000	0.09089	-0.973000	0.02599	AAA	.	.		0.353	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		C	22575415	T	C	22575415	3	2	72	1	0	0	0	0	1	0	0	0	18218	1792	62	2	1100	2	ZNF98	19	22575415	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	1443271	22575415	36553568	118	9310										
LGI4	163175	hgsc.bcm.edu	37	chr19	35624619	35624619	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gtactgcaggtgggacaggcCcgcaaatgcatcgtcctcaa	12	12	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr19:35624619C>A	ENST00000310123.3	-	3	811	c.292G>T	c.(292-294)Ggc>Tgc	p.G98C	LGI4_ENST00000493050.1_5'UTR|LGI4_ENST00000591633.1_Missense_Mutation_p.G98C|LGI4_ENST00000392225.3_Missense_Mutation_p.G98C	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	98					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			TGGGACAGGCCCGCAAATGCA	0.582																																					p.G98C		Atlas-SNP	.											.	LGI4	32	.	0			c.G292T						.						40	35	37					19																	35624619		2203	4299	6502	SO:0001583	missense	163175	exon3			ACAGGCCCGCAAA	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.292G>T	chr19.hg19:g.35624619C>A	ENSP00000312273:p.Gly98Cys	39.0	0.0		58.0	28.0	NM_139284	B2RN53|B9EGS7|Q5M8T1	Missense_Mutation	SNP	ENST00000310123.3	hg19	CCDS12444.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.081095	0.55753	.	.	ENSG00000153902	ENST00000310123;ENST00000392225;ENST00000437421	D;D	0.91068	-2.78;-2.78	4.72	4.72	0.59763	.	0.000000	0.64402	D	0.000014	D	0.96204	0.8762	M	0.93197	3.39	0.47862	D	0.999539	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.96797	0.9586	10	0.87932	D	0	.	13.0321	0.58847	0.0:1.0:0.0:0.0	.	98;98	Q8N135-2;Q8N135	.;LGI4_HUMAN	C	98	ENSP00000312273:G98C;ENSP00000376059:G98C	ENSP00000312273:G98C	G	-	1	0	LGI4	40316459	1.000000	0.71417	0.953000	0.39169	0.444000	0.32077	5.245000	0.65405	2.452000	0.82932	0.563000	0.77884	GGC	.	.		0.582	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1			A	35624619	C	A	35624619	3	1	72	1	0	0	0	0	1	0	0	0	8763	623	22	3	1349	3	LGI4	19	35624619	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	13049204	35624619	23504364	119	9311										
PRODH2	58510	hgsc.bcm.edu	37	chr19	36297613	36297613	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	taggtgttccacacccagggCccgccttcacccgggctgtt	11	16	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr19:36297613C>A	ENST00000301175.3	-	7	1043	c.1026G>T	c.(1024-1026)ggG>ggT	p.G342G		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	342					proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ACACCCAGGGCCCGCCTTCAC	0.647																																					p.G342G		Atlas-SNP	.											.	PRODH2	68	.	0			c.G1026T						.						34	33	33					19																	36297613		2203	4300	6503	SO:0001819	synonymous_variant	58510	exon7			CCAGGGCCCGCCT	U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.1026G>T	chr19.hg19:g.36297613C>A		56.0	0.0		51.0	27.0	NM_021232		Silent	SNP	ENST00000301175.3	hg19	CCDS12478.1																																																																																			.	.		0.647	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232		A	36297613	C	A	36297613	2	1	72	1	0	0	0	0	0	0	0	1	12561	726	26	3		3	PRODH2	19	36297613	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	672994	36297613	22831370	120	9312										
RYR1	6261	hgsc.bcm.edu	37	chr19	39001379	39001379	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tccggctaaagtgctgggcaGcggtggccacgcctctaaca	13	13	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr19:39001379G>T	ENST00000359596.3	+	60	9080	c.9080G>T	c.(9079-9081)aGc>aTc	p.S3027I	RYR1_ENST00000355481.4_Missense_Mutation_p.S3027I|RYR1_ENST00000360985.3_Missense_Mutation_p.S3027I			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3027					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GTGCTGGGCAGCGGTGGCCAC	0.567																																					p.S3027I		Atlas-SNP	.											.	RYR1	708	.	0			c.G9080T						.						131	131	131					19																	39001379		2203	4300	6503	SO:0001583	missense	6261	exon60			TGGGCAGCGGTGG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.9080G>T	chr19.hg19:g.39001379G>T	ENSP00000352608:p.Ser3027Ile	94.0	0.0		91.0	41.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.652403	0.67472	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.66815	-0.23;-0.23;-0.23	4.85	4.85	0.62838	.	0.000000	0.85682	U	0.000000	T	0.80989	0.4730	M	0.72118	2.19	0.58432	D	0.999995	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.991	T	0.80725	-0.1254	10	0.42905	T	0.14	.	17.7783	0.88516	0.0:0.0:1.0:0.0	.	3027;3027	P21817-2;P21817	.;RYR1_HUMAN	I	3027	ENSP00000352608:S3027I;ENSP00000347667:S3027I;ENSP00000354254:S3027I	ENSP00000347667:S3027I	S	+	2	0	RYR1	43693219	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	9.381000	0.97205	2.524000	0.85096	0.561000	0.74099	AGC	.	.		0.567	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	39001379	G	T	39001379	3	4	72	1	0	0	0	0	1	0	0	0	13783	971	34	3	9318	3	RYR1	19	39001379	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	2703766	39001379	20127604	121	9313										
FCAR	2204	hgsc.bcm.edu	37	chr19	55396884	55396884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gcgctatcagtgccaatataGgatagggcactacagattcc	10	10	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr19:55396884G>A	ENST00000355524.3	+	3	318	c.308G>A	c.(307-309)aGg>aAg	p.R103K	FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000345937.4_Missense_Mutation_p.R103K|FCAR_ENST00000469767.1_Missense_Mutation_p.R103K|FCAR_ENST00000391725.3_Missense_Mutation_p.R103K|FCAR_ENST00000391724.3_Missense_Mutation_p.R91K|FCAR_ENST00000353758.4_Intron|FCAR_ENST00000359272.4_Missense_Mutation_p.R91K|FCAR_ENST00000391726.3_Missense_Mutation_p.R91K|FCAR_ENST00000391723.3_Missense_Mutation_p.R91K	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	103	Ig-like C2-type 1.				immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		TGCCAATATAGGATAGGGCAC	0.488																																					p.R103K		Atlas-SNP	.											.	FCAR	110	.	0			c.G308A						.						81	71	74					19																	55396884		2203	4300	6503	SO:0001583	missense	2204	exon3			AATATAGGATAGG	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.308G>A	chr19.hg19:g.55396884G>A	ENSP00000347714:p.Arg103Lys	83.0	0.0		86.0	31.0	NM_133279	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Missense_Mutation	SNP	ENST00000355524.3	hg19	CCDS12907.1	.	.	.	.	.	.	.	.	.	.	G	9.667	1.145791	0.21288	.	.	ENSG00000186431	ENST00000433231;ENST00000391726;ENST00000355524;ENST00000391725;ENST00000345937;ENST00000359272;ENST00000391723;ENST00000391724	T;T;T;T;T;T;T	0.12879	2.71;2.64;2.64;2.71;2.64;2.64;2.64	3.09	-2.25	0.06888	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.198147	0.24708	N	0.036246	T	0.10937	0.0267	M	0.62154	1.92	0.09310	N	1	B;B;B;B;B;B;B;B	0.30793	0.114;0.073;0.295;0.013;0.005;0.253;0.007;0.077	B;B;B;B;B;B;B;B	0.34824	0.093;0.079;0.19;0.022;0.016;0.082;0.013;0.031	T	0.35475	-0.9787	10	0.13470	T	0.59	.	4.639	0.12540	0.1179:0.0:0.3275:0.5546	.	91;91;91;91;103;103;103;103	Q92588;Q92593;Q92587;Q9UEK0;Q53X39;P24071-3;P24071;P24071-4	.;.;.;.;.;.;FCAR_HUMAN;.	K	103;91;103;103;103;91;91;91	ENSP00000375606:R91K;ENSP00000347714:R103K;ENSP00000375605:R103K;ENSP00000338257:R103K;ENSP00000352218:R91K;ENSP00000375603:R91K;ENSP00000375604:R91K	ENSP00000338257:R103K	R	+	2	0	FCAR	60088696	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.092000	0.03366	-0.319000	0.08652	-0.244000	0.11960	AGG	.	.		0.488	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000		A	55396884	G	A	55396884	3	1	72	1	0	0	0	0	1	0	0	0	5781	1000	35	3	318	3	FCAR	19	55396884	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	16395505	55396884	3732099	122	9314										
ZNF135	7694	hgsc.bcm.edu	37	chr19	58574854	58574854	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	aatgtcatctccctgctggaGcaagaggcagagctgtgggc	14	10	2	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr19:58574854G>T	ENST00000313434.5	+	4	302	c.201G>T	c.(199-201)gaG>gaT	p.E67D	ZNF135_ENST00000401053.4_Missense_Mutation_p.E79D|ZNF135_ENST00000511556.1_Missense_Mutation_p.E67D|ZNF135_ENST00000439855.2_Missense_Mutation_p.E67D|ZNF135_ENST00000506786.1_Missense_Mutation_p.E25D|ZNF135_ENST00000359978.6_Missense_Mutation_p.E79D	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	67	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		CCCTGCTGGAGCAAGAGGCAG	0.577																																					p.E79D		Atlas-SNP	.											.	ZNF135	159	.	0			c.G237T						.						112	97	102					19																	58574854		2203	4300	6503	SO:0001583	missense	7694	exon3			GCTGGAGCAAGAG	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"Zinc fingers, C2H2-type", "-"	12919	protein-coding gene	gene with protein product		604077	"zinc finger protein 61", "zinc finger protein 135 (clone pHZ-17)"	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.201G>T	chr19.hg19:g.58574854G>T	ENSP00000321406:p.Glu67Asp	100.0	0.0		112.0	51.0	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.77|11.77	1.738485|1.738485	0.30774|0.30774	.|.	.|.	ENSG00000176293|ENSG00000176293	ENST00000504540;ENST00000401053;ENST00000359978;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786|ENST00000391699	T;T;T;T;T;T|.	0.01113|.	5.32;5.32;5.32;5.32;5.32;5.32|.	2.51|2.51	0.346|0.346	0.16017|0.16017	Krueppel-associated box (3);|.	.|.	.|.	.|.	.|.	T|T	0.42449|0.42449	0.1203|0.1203	M|M	0.66297|0.66297	2.02|2.02	0.09310|0.09310	N|N	1|1	P;P;P|.	0.45212|.	0.853;0.853;0.853|.	B;B;B|.	0.39562|.	0.297;0.297;0.303|.	T|T	0.36962|0.36962	-0.9726|-0.9726	9|5	0.56958|.	D|.	0.05|.	.|.	4.4324|4.4324	0.11535|0.11535	0.3334:0.0:0.6666:0.0|0.3334:0.0:0.6666:0.0	.|.	67;67;79|.	E9PEV2;P52742;Q8N1I7|.	.;ZN135_HUMAN;.|.	D|I	79;79;79;67;67;67;25|73	ENSP00000441410:E79D;ENSP00000369437:E79D;ENSP00000444828:E67D;ENSP00000321406:E67D;ENSP00000422074:E67D;ENSP00000427691:E25D|.	ENSP00000321406:E67D|.	E|S	+|+	3|2	2|0	ZNF135|ZNF135	63266666|63266666	0.249000|0.249000	0.23941|0.23941	0.252000|0.252000	0.24328|0.24328	0.169000|0.169000	0.22640|0.22640	0.188000|0.188000	0.17018|0.17018	0.166000|0.166000	0.19597|0.19597	0.563000|0.563000	0.77884|0.77884	GAG|AGC	.	.		0.577	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		T	58574854	G	T	58574854	3	4	72	1	0	0	0	0	1	0	0	0	17740	962	34	3	284	3	ZNF135	19	58574854	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	3177970	58574854	554129	123	9315										
PCSK2	5126	hgsc.bcm.edu	37	chr20	17240976	17240976	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	acaccacaagcagcagctggAgagagaccccagggtgagtt	13	11	0	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr20:17240976A>G	ENST00000262545.2	+	2	584	c.269A>G	c.(268-270)gAg>gGg	p.E90G	PCSK2_ENST00000536609.1_Intron|PCSK2_ENST00000377899.1_Missense_Mutation_p.E71G	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	90					cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""Insulin(DB00071)|Insulin Regular(DB00030)"	CAGCAGCTGGAGAGAGACCCC	0.562																																					p.E90G		Atlas-SNP	.											.	PCSK2	112	.	0			c.A269G						.						87	84	85					20																	17240976		2203	4300	6503	SO:0001583	missense	5126	exon2			AGCTGGAGAGAGA	AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"neuroendocrine convertase 2", "KEX2-like endoprotease 2"	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.269A>G	chr20.hg19:g.17240976A>G	ENSP00000262545:p.Glu90Gly	121.0	0.0		107.0	59.0	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	hg19	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	A	13.47	2.247425	0.39697	.	.	ENSG00000125851	ENST00000377899;ENST00000262545	T;T	0.30182	1.54;1.54	5.45	5.45	0.79879	Proteinase inhibitor, propeptide (1);	0.123300	0.56097	D	0.000035	T	0.26738	0.0654	L	0.40543	1.245	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.04373	-1.0956	10	0.56958	D	0.05	-37.5868	11.8957	0.52656	1.0:0.0:0.0:0.0	.	90	P16519	NEC2_HUMAN	G	71;90	ENSP00000367131:E71G;ENSP00000262545:E90G	ENSP00000262545:E90G	E	+	2	0	PCSK2	17188976	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.112000	0.71547	2.065000	0.61736	0.460000	0.39030	GAG	.	.		0.562	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		G	17240976	A	G	17240976	3	3	72	1	0	0	0	0	1	0	0	0	11610	304	11	2	275	2	PCSK2	20	17240976	Missense_Mutation	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10		17240976	45784544	124	9316										
CST9L	128821	hgsc.bcm.edu	37	chr20	23546707	23546707	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	agcagtagctccattgagaaTacagtcttggactccaccta	8	11	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr20:23546707T>C	ENST00000376979.3	-	2	556	c.258A>G	c.(256-258)gtA>gtG	p.V86V		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	86						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					CCATTGAGAATACAGTCTTGG	0.453																																					p.V86V		Atlas-SNP	.											.	CST9L	25	.	0			c.A258G						.						184	161	169					20																	23546707		2203	4300	6503	SO:0001819	synonymous_variant	128821	exon2			TGAGAATACAGTC		CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"cystatin 9 (mouse)-like"			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.258A>G	chr20.hg19:g.23546707T>C		123.0	0.0		83.0	38.0	NM_080610	B2R5A1	Silent	SNP	ENST00000376979.3	hg19	CCDS13157.1																																																																																			.	.		0.453	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610		C	23546707	T	C	23546707	2	2	72	1	0	0	0	0	0	0	0	1	3982	1393	49	2		2	CST9L	20	23546707	Silent	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	6305731	23546707	39478813	125	9317										
TTLL9	164395	hgsc.bcm.edu	37	chr20	30522615	30522615	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tcaaaagcctgcagagtgtgCagaaggtgatcatcagtgac	12	8	3	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr20:30522615C>T	ENST00000375938.4	+	12	1181	c.928C>T	c.(928-930)Cag>Tag	p.Q310*	TTLL9_ENST00000375934.4_Silent_p.C277C|TTLL9_ENST00000310998.4_Nonsense_Mutation_p.Q275*|TTLL9_ENST00000375922.4_Nonsense_Mutation_p.Q252*|TTLL9_ENST00000535842.1_Nonsense_Mutation_p.Q310*|TTLL9_ENST00000375921.2_Intron			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	310	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GCAGAGTGTGCAGAAGGTGAT	0.567																																					p.Q310X		Atlas-SNP	.											.	TTLL9	95	.	0			c.C928T						.						118	118	118					20																	30522615		2085	4223	6308	SO:0001587	stop_gained	164395	exon12			AGTGTGCAGAAGG	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"Tubulin tyrosine ligase-like family"	16118	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 125"	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.928C>T	chr20.hg19:g.30522615C>T	ENSP00000365105:p.Gln310*	104.0	0.0		97.0	24.0	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Nonsense_Mutation	SNP	ENST00000375938.4	hg19	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	C	39	7.302232	0.98196	.	.	ENSG00000131044	ENST00000375938;ENST00000535842;ENST00000310998;ENST00000375935;ENST00000375922	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	17.4403	0.87563	0.0:1.0:0.0:0.0	.	.	.	.	X	310;310;275;299;252	.	ENSP00000308980:Q275X	Q	+	1	0	TTLL9	29986276	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.857000	0.75455	2.526000	0.85167	0.561000	0.74099	CAG	.	.		0.567	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409		T	30522615	C	T	30522615	4	4	72	1	0	0	0	0	0	1	0	0	16749	711	25	3	970	3	TTLL9	20	30522615	Nonsense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	6975908	30522615	32502905	126	9318										
C20orf70	140683	hgsc.bcm.edu	37	chr20	31768351	31768351	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cctcagcacaaaacccagctGcaaaccctcatctgaagagg	7	15	3	2			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr20:31768351G>T	ENST00000253362.2	+	8	881	c.735G>T	c.(733-735)ctG>ctT	p.L245L	BPIFA2_ENST00000354932.5_Silent_p.L245L			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	245						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										AAACCCAGCTGCAAACCCTCA	0.502																																					p.L245L		Atlas-SNP	.											.	.	.	.	0			c.G735T						.						86	82	83					20																	31768351		2203	4300	6503	SO:0001819	synonymous_variant	140683	exon8			CCAGCTGCAAACC	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"BPI fold containing"	16203	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 70"	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.735G>T	chr20.hg19:g.31768351G>T		116.0	0.0		119.0	30.0	NM_080574	Q9BQQ0	Silent	SNP	ENST00000253362.2	hg19	CCDS13214.1																																																																																			.	.		0.502	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574		T	31768351	G	T	31768351	2	4	72	1	0	0	0	0	0	0	0	1	2118	1306	46	3		3	C20orf70	20	31768351	Silent	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	1245736	31768351	31257169	127	9319										
PCK1	5105	hgsc.bcm.edu	37	chr20	56140768	56140769	+	Frame_Shift_Del	DEL	GA	GA	-													0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	agaaggaggtggaagacatcGagaagtatctggaggatcaa					rs201175342		TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr20:56140768_56140769delGA	ENST00000319441.4	+	10	1941_1942	c.1777_1778delGA	c.(1777-1779)gagfs	p.E593fs	PCK1_ENST00000543666.1_Frame_Shift_Del_p.E276fs	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	593					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			GGAAGACATCGAGAAGTATCTG	0.5																																					p.592_593del		Atlas-Indel,Pindel	.											.	PCK1	95	.	0			c.1776_1777del						.																																			SO:0001589	frameshift_variant	5105	exon10			.		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1777_1778delGA	chr20.hg19:g.56140770_56140771delGA	ENSP00000319814:p.Glu593fs	146.0	0.0		143.0	63.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Frame_Shift_Del	DEL	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	.		0.5	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			-	56140769	GA	-	56140768	7	5	72	1	0	1	0	1	0	0	0	0	11590	1059	37	0	1811	0	PCK1	20	56140768	Frame_Shift_Del	DEL	GA	TCGA-CC-A7IG-01A-11D-A33K-10	24372417	56140768	6884752	128	9320										
GNAS	2778	hgsc.bcm.edu	37	chr20	57428698	57428698	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cagcctggattccccagtggGgtccatgcaggccttgaggc	14	13	0	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr20:57428698G>T	ENST00000306120.3	+	1	188	c.188G>T	c.(187-189)gGg>gTg	p.G63V	GNAS-AS1_ENST00000424094.2_RNA|GNAS-AS1_ENST00000598163.1_RNA|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371102.4_Silent_p.G126G|GNAS_ENST00000371099.2_Silent_p.G126G|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000371100.4_Silent_p.G126G			P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			TCCCCAGTGGGGTCCATGCAG	0.637			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.G64V	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	.	GNAS	867	.	0			c.G191T						.						31	35	34					20																	57428698		1890	4108	5998	SO:0001583	missense	2778	exon1			CAGTGGGGTCCAT	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000306120.3:c.188G>T	chr20.hg19:g.57428698G>T	ENSP00000302237:p.Gly63Val	61.0	0.0		46.0	27.0	NM_001077490	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000306120.3	hg19		.	.	.	.	.	.	.	.	.	.	G	0.011	-1.732385	0.00687	.	.	ENSG00000087460	ENST00000306120	.	.	.	4.73	3.76	0.43208	.	.	.	.	.	T	0.31949	0.0813	.	.	.	0.09310	N	0.999991	.	.	.	.	.	.	T	0.18366	-1.0339	5	0.18276	T	0.48	.	10.736	0.46126	0.0:0.0:0.8089:0.1911	.	.	.	.	V	63	.	ENSP00000302237:G63V	G	+	2	0	GNAS	56862093	0.613000	0.27009	0.004000	0.12327	0.036000	0.12997	0.916000	0.28651	1.262000	0.44165	0.557000	0.71058	GGG	.	.		0.637	GNAS-050	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000267987.1	NM_000516		T	57428698	G	T	57428698	3	4	72	1	0	0	0	0	1	0	0	0	6518	1232	43	3	1122	3	GNAS	20	57428698	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10	1287930	57428698	5596822	129	9321										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19687499	19687499	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	tgagccatcctcacagtgcaGatgaccgtcacagagattca	9	12	3	4			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr21:19687499G>C	ENST00000284885.3	-	17	2029	c.1996C>G	c.(1996-1998)Ctg>Gtg	p.L666V		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	666	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TCACAGTGCAGATGACCGTCA	0.403																																					p.L666V		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.C1996G						.						171	140	150					21																	19687499		2203	4300	6503	SO:0001583	missense	5651	exon17			AGTGCAGATGACC		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1996C>G	chr21.hg19:g.19687499G>C	ENSP00000284885:p.Leu666Val	79.0	0.0		87.0	38.0	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	hg19	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	G	0.202	-1.043668	0.01997	.	.	ENSG00000154646	ENST00000284885	D	0.95307	-3.67	5.27	1.35	0.21983	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.815167	0.11580	N	0.549832	D	0.82536	0.5058	N	0.04148	-0.265	0.09310	N	1	B	0.09022	0.002	B	0.13407	0.009	T	0.69899	-0.5020	9	.	.	.	.	2.9886	0.05975	0.1604:0.1416:0.5517:0.1463	.	666	P98073	ENTK_HUMAN	V	666	ENSP00000284885:L666V	.	L	-	1	2	TMPRSS15	18609370	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.074000	0.14662	0.071000	0.16664	-0.181000	0.13052	CTG	.	.		0.403	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		C	19687499	G	C	19687499	3	2	72	1	0	0	0	0	1	0	0	0	16261	933	33	4	1099	4	TMPRSS15	21	19687499	Missense_Mutation	SNP	G	TCGA-CC-A7IG-01A-11D-A33K-10		19687499	28442396	130	9322										
TRAPPC10	7109	hgsc.bcm.edu	37	chr21	45504036	45504036	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	gaacgtatacactcaggcagCtgtgcgcctcggtgggctcc	13	13	1	0			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr21:45504036C>T	ENST00000291574.4	+	15	2447	c.2272C>T	c.(2272-2274)Ctg>Ttg	p.L758L		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	758					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						ACTCAGGCAGCTGTGCGCCTC	0.567																																					p.L758L		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.C2272T						.						93	69	77					21																	45504036		2203	4300	6503	SO:0001819	synonymous_variant	7109	exon15			AGGCAGCTGTGCG	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"Trafficking protein particle complex"	11868	protein-coding gene	gene with protein product	"trafficking protein particle complex subunit 130", "TRAPP 130 kDa subunit"	602103	"transmembrane protein 1"	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.2272C>T	chr21.hg19:g.45504036C>T		45.0	0.0		68.0	20.0	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	hg19	CCDS13704.1																																																																																			.	.		0.567	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		T	45504036	C	T	45504036	2	4	72	1	0	0	0	0	0	0	0	1	16472	796	28	3		3	TRAPPC10	21	45504036	Silent	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10	25816537	45504036	2625859	131	9323										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26164107	26164107	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	agaaatttccatcagccaacCcaacagcaagtccagcagtg	7	13	1	1			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr22:26164107C>G	ENST00000407587.2	+	4	393	c.224C>G	c.(223-225)cCc>cGc	p.P75R	MYO18B_ENST00000335473.7_Missense_Mutation_p.P75R|MYO18B_ENST00000536101.1_Missense_Mutation_p.P75R			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	75	Ser-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						ATCAGCCAACCCAACAGCAAG	0.522																																					p.P75R		Atlas-SNP	.											.	MYO18B	322	.	0			c.C224G						.						133	143	139					22																	26164107		2063	4205	6268	SO:0001583	missense	84700	exon4			GCCAACCCAACAG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.224C>G	chr22.hg19:g.26164107C>G	ENSP00000386096:p.Pro75Arg	266.0	0.0		266.0	71.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	16.86	3.238853	0.58995	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86865	-2.16;-2.16;-2.18	4.87	3.84	0.44239	.	0.000000	0.36234	N	0.002707	D	0.85492	0.5709	L	0.51422	1.61	0.09310	N	1	P	0.48016	0.904	P	0.48227	0.571	T	0.79408	-0.1816	10	0.87932	D	0	.	9.6041	0.39624	0.0:0.8983:0.0:0.1017	.	75	F5GYU7	.	R	75	ENSP00000441229:P75R;ENSP00000334563:P75R;ENSP00000386096:P75R	ENSP00000334563:P75R	P	+	2	0	MYO18B	24494107	0.005000	0.15991	0.014000	0.15608	0.317000	0.28152	2.097000	0.41748	2.271000	0.75665	0.484000	0.47621	CCC	.	.		0.522	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26164107	C	G	26164107	3	3	72	1	0	0	0	0	1	0	0	0	10075	623	22	4	234	4	MYO18B	22	26164107	Missense_Mutation	SNP	C	TCGA-CC-A7IG-01A-11D-A33K-10		26164107	25140459	132	9324										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46930838	46930838	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	cagaggtagcgccagggtgaTgaggccgccccctctctggc	15	14	1	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chr22:46930838T>C	ENST00000262738.3	-	1	2229	c.2230A>G	c.(2230-2232)Atc>Gtc	p.I744V	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Missense_Mutation_p.I744V	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	744	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GCCAGGGTGATGAGGCCGCCC	0.632																																					p.I744V		Atlas-SNP	.											.	CELSR1	242	.	0			c.A2230G						.						61	44	50					22																	46930838		2200	4300	6500	SO:0001583	missense	9620	exon1			GGGTGATGAGGCC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.2230A>G	chr22.hg19:g.46930838T>C	ENSP00000262738:p.Ile744Val	39.0	0.0		37.0	12.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	T	2.479	-0.320087	0.05386	.	.	ENSG00000075275	ENST00000262738;ENST00000395964	T;T	0.58060	0.36;0.36	4.6	3.57	0.40892	Cadherin (4);Cadherin-like (1);	0.078284	0.48767	U	0.000165	T	0.39860	0.1094	L	0.28694	0.88	0.31688	N	0.642239	B	0.30439	0.279	B	0.38225	0.268	T	0.41680	-0.9495	10	0.12430	T	0.62	.	9.2488	0.37543	0.0:0.0869:0.0:0.9131	.	744	Q9NYQ6	CELR1_HUMAN	V	744	ENSP00000262738:I744V;ENSP00000379293:I744V	ENSP00000262738:I744V	I	-	1	0	CELSR1	45309502	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	2.656000	0.46716	1.720000	0.51447	0.254000	0.18369	ATC	.	.		0.632	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		C	46930838	T	C	46930838	3	2	72	1	0	0	0	0	1	0	0	0	3223	1464	51	2	6954	2	CELSR1	22	46930838	Missense_Mutation	SNP	T	TCGA-CC-A7IG-01A-11D-A33K-10	20766731	46930838	4373728	133	9325										
UBA1	7317	hgsc.bcm.edu	37	chrX	47065468	47065468	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0300751879699248	4	1	0.700808625336927	1.61436272622256	0.259782507667999	0.576470588235294	1	0	ctatgatgacgattttttccAaaacctagatggcgtggcca	9	9	0	3			TCGA-CC-A7IG-01A-11D-A33K-10	TCGA-CC-A7IG-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b4be76e-ec2a-4157-a9ad-333f706662d5	b69cebd4-506b-4c1a-9724-dd4429b628b2	g.chrX:47065468A>G	ENST00000335972.6	+	15	1880	c.1697A>G	c.(1696-1698)cAa>cGa	p.Q566R	UBA1_ENST00000377269.3_5'Flank|UBA1_ENST00000377351.4_Missense_Mutation_p.Q566R|UBA1_ENST00000490869.1_Intron|INE1_ENST00000456273.1_RNA	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	566	2 approximate repeats.				cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GATTTTTTCCAAAACCTAGAT	0.557																																					p.Q566R		Atlas-SNP	.											.	UBA1	89	.	0			c.A1697G						.						60	41	47					X																	47065468		2203	4300	6503	SO:0001583	missense	7317	exon15			TTTTCCAAAACCT	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"Ubiquitin-like modifier activating enzymes"	12469	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog (yeast)", "POC20 centriolar protein homolog (Chlamydomonas)"	314370	"ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)", "ubiquitin-activating enzyme E1"	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.1697A>G	chrX.hg19:g.47065468A>G	ENSP00000338413:p.Gln566Arg	121.0	0.0		103.0	72.0	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	hg19	CCDS14275.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.715556	0.48622	.	.	ENSG00000130985	ENST00000377351;ENST00000335972	T;T	0.41400	1.0;1.0	4.61	4.61	0.57282	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.174906	0.49916	D	0.000137	T	0.30510	0.0767	N	0.16656	0.425	0.80722	D	1	B	0.27013	0.166	B	0.33121	0.158	T	0.13737	-1.0498	10	0.42905	T	0.14	-9.2467	12.3648	0.55222	1.0:0.0:0.0:0.0	.	566	P22314	UBA1_HUMAN	R	566	ENSP00000366568:Q566R;ENSP00000338413:Q566R	ENSP00000338413:Q566R	Q	+	2	0	UBA1	46950412	1.000000	0.71417	0.993000	0.49108	0.502000	0.33828	4.124000	0.57924	1.623000	0.50342	0.474000	0.43551	CAA	.	.		0.557	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334		G	47065468	A	G	47065468	3	3	72	1	0	0	0	0	1	0	0	0	16842	130	5	2	1751	2	UBA1	23	47065468	Missense_Mutation	SNP	A	TCGA-CC-A7IG-01A-11D-A33K-10		47065468	108205092	134	9326										
SCNN1D	6339	hgsc.bcm.edu	37	chr1	1222886	1222886	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgagcttggcttctcattccAgacagttccggaccttccac	8	14	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:1222886A>T	ENST00000338555.2	+	7	1962		c.e7-1		SCNN1D_ENST00000400928.3_Splice_Site|SCNN1D_ENST00000325425.8_Splice_Site|SCNN1D_ENST00000379116.5_Splice_Site			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit						ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	TTCTCATTCCAGACAGTTCCG	0.652																																					.		Atlas-SNP	.											.	SCNN1D	60	.	0			c.1311-2A>T						.						49	50	50					1																	1222886		2199	4295	6494	SO:0001630	splice_region_variant	6339	exon10			CATTCCAGACAGT	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10601	protein-coding gene	gene with protein product		601328	"sodium channel, nonvoltage-gated 1, delta", "sodium channel, non-voltage-gated 1, delta"			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.819-1A>T	chr1.hg19:g.1222886A>T		114.0	0.0		71.0	24.0	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Splice_Site	SNP	ENST00000338555.2	hg19		.	.	.	.	.	.	.	.	.	.	A	6.305	0.424337	0.11928	.	.	ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928;ENST00000379099	.	.	.	3.22	3.22	0.36961	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.6748	0.40034	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SCNN1D	1212749	0.025000	0.19082	0.876000	0.34364	0.165000	0.22458	0.354000	0.20146	1.464000	0.47987	0.260000	0.18958	.	.	.		0.652	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978	Intron	T	1222886	A	T	1222886	5	4	73	1	0	0	0	0	0	0	1	0	13944	202	7	4	1041	4	SCNN1D	1	1222886	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10		1222886	248027735	1	9327										
EXOSC10	5394	hgsc.bcm.edu	37	chr1	11141273	11141273	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtgtcatcccgggcgtagcTgagcatctcctcgggcagag	15	12	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:11141273T>A	ENST00000376936.4	-	11	1352	c.1303A>T	c.(1303-1305)Agc>Tgc	p.S435C	EXOSC10_ENST00000485606.1_5'UTR|EXOSC10_ENST00000304457.7_Missense_Mutation_p.S435C|EXOSC10_ENST00000544779.1_Missense_Mutation_p.S435C	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	435					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		CGGGCGTAGCTGAGCATCTCC	0.542																																					p.S435C	Colon(179;105 1987 14326 27364 29542)	Atlas-SNP	.											.	EXOSC10	59	.	0			c.A1303T						.						82	83	82					1																	11141273		2203	4300	6503	SO:0001583	missense	5394	exon11			CGTAGCTGAGCAT	BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 2 (100kD)"	605960	"polymyositis/scleroderma autoantigen 2, 100kDa"	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.1303A>T	chr1.hg19:g.11141273T>A	ENSP00000366135:p.Ser435Cys	161.0	0.0		128.0	55.0	NM_001001998	B1AKQ0|B1AKQ1|Q15158	Missense_Mutation	SNP	ENST00000376936.4	hg19	CCDS30584.1	.	.	.	.	.	.	.	.	.	.	T	12.45	1.941753	0.34283	.	.	ENSG00000171824	ENST00000376936;ENST00000304457;ENST00000544779	T;T;T	0.64618	-0.11;-0.11;-0.11	5.77	-2.5	0.06384	-5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2);	0.804998	0.12628	N	0.452412	T	0.60051	0.2239	L	0.46157	1.445	0.09310	N	1	P;P	0.43607	0.775;0.812	P;P	0.54856	0.649;0.762	T	0.54289	-0.8316	10	0.59425	D	0.04	-0.6509	3.0404	0.06137	0.1946:0.1299:0.46:0.2156	.	435;435	Q01780-2;Q01780	.;EXOSX_HUMAN	C	435	ENSP00000366135:S435C;ENSP00000307307:S435C;ENSP00000439473:S435C	ENSP00000307307:S435C	S	-	1	0	EXOSC10	11063860	0.008000	0.16893	0.004000	0.12327	0.029000	0.11900	0.306000	0.19279	-0.625000	0.05604	-1.137000	0.01932	AGC	.	.		0.542	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998		A	11141273	T	A	11141273	3	1	73	1	0	0	0	0	1	0	0	0	5316	1580	55	4	1414	4	EXOSC10	1	11141273	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	9918387	11141273	238109348	2	9328										
PRAMEF12	390999	hgsc.bcm.edu	37	chr1	12837669	12837669	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtcccctgccctcgctgtgGcatcagggcctcctatgacc	10	17	1	1	rs201008398	byFrequency	TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:12837669G>A	ENST00000357726.4	+	3	1406	c.1379G>A	c.(1378-1380)gGc>gAc	p.G460D		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	460					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CCTCGCTGTGGCATCAGGGCC	0.507																																					p.G460D		Atlas-SNP	.											.	PRAMEF12	69	.	0			c.G1379A						.						106	108	107					1																	12837669		2203	4300	6503	SO:0001583	missense	390999	exon3			GCTGTGGCATCAG		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"-"	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.1379G>A	chr1.hg19:g.12837669G>A	ENSP00000350358:p.Gly460Asp	291.0	0.0		275.0	125.0	NM_001080830		Missense_Mutation	SNP	ENST00000357726.4	hg19	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	14.06	2.421439	0.42918	.	.	ENSG00000116726	ENST00000357726	T	0.61859	0.07	2.24	-1.22	0.09494	.	1.264420	0.05864	N	0.623511	T	0.55625	0.1932	M	0.67953	2.075	0.09310	N	1	P	0.44877	0.845	P	0.45037	0.467	T	0.48210	-0.9055	10	0.51188	T	0.08	.	3.0303	0.06104	0.3141:0.2341:0.4519:0.0	.	460	O95522	PRA12_HUMAN	D	460	ENSP00000350358:G460D	ENSP00000350358:G460D	G	+	2	0	PRAMEF12	12760256	0.000000	0.05858	0.000000	0.03702	0.568000	0.35870	-0.711000	0.05019	-0.296000	0.08947	0.205000	0.17691	GGC	.	G|0.993;T|0.007		0.507	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760		A	12837669	G	A	12837669	3	1	73	1	0	0	0	0	1	0	0	0	12440	1203	42	3	1389	3	PRAMEF12	1	12837669	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1696396	12837669	236412952	3	9329										
PRAMEF4	400735	hgsc.bcm.edu	37	chr1	12942173	12942173	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcctcttggcattgaggaagCacccatgggccatagcttca	10	12	2	1	rs201789683		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:12942173C>G	ENST00000235349.5	-	3	447	c.377G>C	c.(376-378)tGc>tCc	p.C126S		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	126					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATTGAGGAAGCACCCATGGGC	0.493																																					p.C126S		Atlas-SNP	.											PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	.	0			c.G377C						.						44	56	52					1																	12942173		1381	2629	4010	SO:0001583	missense	400735	exon3			AGGAAGCACCCAT		CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"-"	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.377G>C	chr1.hg19:g.12942173C>G	ENSP00000235349:p.Cys126Ser	23.0	1.0		22.0	3.0	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	hg19	CCDS30592.1	.	.	.	.	.	.	.	.	.	.	c	8.575	0.881031	0.17467	.	.	ENSG00000243073	ENST00000235349	T	0.18016	2.24	1.35	0.315	0.15852	.	1.371720	0.04624	N	0.402516	T	0.19406	0.0466	L	0.53671	1.685	0.09310	N	1	P	0.50272	0.933	P	0.44811	0.461	T	0.23190	-1.0195	10	0.33940	T	0.23	.	5.2546	0.15540	0.0:0.6297:0.3703:0.0	.	126	O60810	PRAM4_HUMAN	S	126	ENSP00000235349:C126S	ENSP00000235349:C126S	C	-	2	0	PRAMEF4	12864760	0.002000	0.14202	0.003000	0.11579	0.008000	0.06430	0.188000	0.17018	0.112000	0.17975	0.194000	0.17425	TGC	.	C|0.500;G|0.500		0.493	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611		G	12942173	C	G	12942173	3	3	73	1	0	0	0	0	1	0	0	0	12449	710	25	4	1067	4	PRAMEF4	1	12942173	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	104504	12942173	236308448	4	9330										
EPHA2	1969	hgsc.bcm.edu	37	chr1	16459692	16459692	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cacatttggagatgacgcccTctaggcggatgatgttgtgg	14	8	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:16459692T>A	ENST00000358432.5	-	11	2190	c.2036A>T	c.(2035-2037)gAg>gTg	p.E679V		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	679	Mediates interaction with ARHGEF16 and ELMO2.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	GATGACGCCCTCTAGGCGGAT	0.612																																					p.E679V		Atlas-SNP	.											.	EPHA2	102	.	0			c.A2036T						.						71	70	70					1																	16459692		2203	4300	6503	SO:0001583	missense	1969	exon11			ACGCCCTCTAGGC	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3386	protein-coding gene	gene with protein product		176946	"EphA2"	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.2036A>T	chr1.hg19:g.16459692T>A	ENSP00000351209:p.Glu679Val	52.0	0.0		47.0	25.0	NM_004431	B5A968|Q8N3Z2	Missense_Mutation	SNP	ENST00000358432.5	hg19	CCDS169.1	.	.	.	.	.	.	.	.	.	.	t	27.9	4.873054	0.91664	.	.	ENSG00000142627	ENST00000358432	T	0.61040	0.14	5.5	5.5	0.81552	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000046	T	0.47563	0.1452	N	0.00611	-1.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71758	-0.4496	10	0.87932	D	0	.	14.4836	0.67599	0.0:0.0:0.0:1.0	.	679	P29317	EPHA2_HUMAN	V	679	ENSP00000351209:E679V	ENSP00000351209:E679V	E	-	2	0	EPHA2	16332279	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.030000	0.88816	2.119000	0.64992	0.515000	0.50301	GAG	.	.		0.612	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431		A	16459692	T	A	16459692	3	1	73	1	0	0	0	0	1	0	0	0	5169	1551	54	4	922	4	EPHA2	1	16459692	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3517519	16459692	232790929	5	9331										
UBR4	23352	hgsc.bcm.edu	37	chr1	19433356	19433356	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ataggaagacacttcttccaGgcatcataggatgccttggg	11	9	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:19433356G>A	ENST00000375254.3	-	82	12237	c.12210C>T	c.(12208-12210)gcC>gcT	p.A4070A	UBR4_ENST00000375226.2_Silent_p.A4046A|UBR4_ENST00000375267.2_Silent_p.A4070A|UBR4_ENST00000375224.1_5'Flank|UBR4_ENST00000375217.2_Silent_p.A4063A	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	4070					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		ACTTCTTCCAGGCATCATAGG	0.537																																					p.A4070A		Atlas-SNP	.											.	UBR4	415	.	0			c.C12210T						.						60	60	60					1																	19433356		2203	4300	6503	SO:0001819	synonymous_variant	23352	exon82			CTTCCAGGCATCA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.12210C>T	chr1.hg19:g.19433356G>A		255.0	0.0		184.0	83.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.		0.537	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19433356	G	A	19433356	2	1	73	1	0	0	0	0	0	0	0	1	16919	987	35	3		3	UBR4	1	19433356	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	2973664	19433356	229817265	6	9332										
CAMK2N1	55450	hgsc.bcm.edu	37	chr1	20811760	20811760	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcggccgcttgttctgcccgGcgccgaagaagttgttggtg	16	11	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:20811760G>C	ENST00000375078.3	-	1	953	c.113C>G	c.(112-114)gCc>gGc	p.A38G	CAMK2N1_ENST00000489020.1_5'Flank	NM_018584.5	NP_061054.2	Q7Z7J9	CK2N1_HUMAN	calcium/calmodulin-dependent protein kinase II inhibitor 1	38						cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	calcium-dependent protein kinase inhibitor activity (GO:0008427)			lung(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.0013)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000132)|Kidney(64;0.00016)|GBM - Glioblastoma multiforme(114;0.00116)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.195)		GTTCTGCCCGGCGCCGAAGAA	0.692																																					p.A38G		Atlas-SNP	.											.	CAMK2N1	7	.	0			c.C113G						.						13	17	15					1																	20811760		2195	4294	6489	SO:0001583	missense	55450	exon1			TGCCCGGCGCCGA	AY204901	CCDS207.1	1p36.12	2008-02-05			ENSG00000162545	ENSG00000162545			24190	protein-coding gene	gene with protein product		614986				12477932	Standard	NM_018584		Approved	CaMKIINalpha	uc001bdh.3	Q7Z7J9	OTTHUMG00000002837	ENST00000375078.3:c.113C>G	chr1.hg19:g.20811760G>C	ENSP00000364219:p.Ala38Gly	47.0	0.0		46.0	17.0	NM_018584		Missense_Mutation	SNP	ENST00000375078.3	hg19	CCDS207.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.433215	0.25813	.	.	ENSG00000162545	ENST00000375078	.	.	.	3.09	3.09	0.35607	.	0.528419	0.14185	N	0.335737	T	0.14270	0.0345	.	.	.	0.22728	N	0.998808	B	0.09022	0.002	B	0.04013	0.001	T	0.26121	-1.0112	8	0.02654	T	1	-11.6906	8.3155	0.32097	0.0:0.2454:0.7546:0.0	.	38	Q7Z7J9	CK2N1_HUMAN	G	38	.	ENSP00000364219:A38G	A	-	2	0	CAMK2N1	20684347	0.119000	0.22226	1.000000	0.80357	0.917000	0.54804	0.947000	0.29082	1.732000	0.51606	0.591000	0.81541	GCC	.	.		0.692	CAMK2N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007949.1	NM_018584		C	20811760	G	C	20811760	3	2	73	1	0	0	0	0	1	0	0	0	2605	1203	42	4	131	4	CAMK2N1	1	20811760	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1378404	20811760	228438861	7	9333										
RAP1GAP	5909	hgsc.bcm.edu	37	chr1	21940198	21940198	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atggtatgtccggcacttggTcctgagaagagaaagtcaca	12	8	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:21940198T>A	ENST00000374765.4	-	9	597	c.397A>T	c.(397-399)Acc>Tcc	p.T133S	RAP1GAP_ENST00000374763.2_Splice_Site_p.T133S|RAP1GAP_ENST00000290101.4_Splice_Site_p.T197S|RAP1GAP_ENST00000374757.3_5'UTR|RAP1GAP_ENST00000374761.2_Splice_Site_p.T164S|RAP1GAP_ENST00000542643.2_Splice_Site_p.T133S	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	133					GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		CGGCACTTGGTCCTGAGAAGA	0.572																																					p.T197S		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.A589T						.						141	121	128					1																	21940198		2203	4300	6503	SO:0001630	splice_region_variant	5909	exon9			ACTTGGTCCTGAG	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"RAP1, GTPase activating protein 1"	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.396-1A>T	chr1.hg19:g.21940198T>A		54.0	0.0		36.0	18.0	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Missense_Mutation	SNP	ENST00000374765.4	hg19	CCDS218.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.325947	0.24080	.	.	ENSG00000076864	ENST00000290101;ENST00000374761;ENST00000542643;ENST00000374765;ENST00000374763;ENST00000374758;ENST00000359708;ENST00000374757	D;D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4;-3.4	4.82	2.44	0.29823	.	0.000000	0.85682	D	0.000000	D	0.85375	0.5682	L	0.31476	0.935	0.80722	D	1	B;B;B;B	0.22604	0.072;0.061;0.002;0.035	B;B;B;B	0.24974	0.057;0.031;0.007;0.017	T	0.72174	-0.4370	10	0.09843	T	0.71	-7.3747	6.839	0.23953	0.0:0.1911:0.0:0.8089	.	133;133;164;133	P47736-2;P47736;P47736-3;Q7Z5S8	.;RPGP1_HUMAN;.;.	S	197;164;133;133;164;133;197;275	ENSP00000290101:T197S;ENSP00000363893:T164S;ENSP00000441661:T133S;ENSP00000363897:T133S;ENSP00000352739:T197S	ENSP00000290101:T197S	T	-	1	0	RAP1GAP	21812785	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.197000	0.51028	0.289000	0.22422	0.459000	0.35465	ACC	.	.		0.572	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	Missense_Mutation	A	21940198	T	A	21940198	5	1	73	1	0	0	0	0	0	0	1	0	13052	1681	58	4	1740	4	RAP1GAP	1	21940198	Splice_Site	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1128438	21940198	227310423	8	9334										
WNT4	54361	hgsc.bcm.edu	37	chr1	22446623	22446623	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccagtggaatttgcagctgcAgcgttcagccagctccacct	10	14	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:22446623A>G	ENST00000290167.6	-	5	1019	c.976T>C	c.(976-978)Tgc>Cgc	p.C326R	WNT4_ENST00000542383.1_Missense_Mutation_p.C271R	NM_030761.4	NP_110388.2	P56705	WNT4_HUMAN	wingless-type MMTV integration site family, member 4	326					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to starvation (GO:0009267)|cellular response to transforming growth factor beta stimulus (GO:0071560)|embryonic epithelial tube formation (GO:0001838)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization to plasma membrane (GO:0090002)|female gonad development (GO:0008585)|female sex determination (GO:0030237)|immature T cell proliferation in thymus (GO:0033080)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|mammary gland epithelium development (GO:0061180)|mesenchymal to epithelial transition (GO:0060231)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric nephron morphogenesis (GO:0072273)|metanephric tubule formation (GO:0072174)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell migration (GO:0030336)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of gene expression (GO:0010629)|negative regulation of male gonad development (GO:2000019)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of testicular blood vessel morphogenesis (GO:0061369)|negative regulation of testosterone biosynthetic process (GO:2000225)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of wound healing (GO:0061045)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via MAPK cascade (GO:0038030)|oocyte development (GO:0048599)|paramesonephric duct development (GO:0061205)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cortisol biosynthetic process (GO:2000066)|positive regulation of dermatome development (GO:0061184)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of meiosis (GO:0045836)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|protein palmitoylation (GO:0018345)|regulation of cell-cell adhesion (GO:0022407)|renal vesicle formation (GO:0072033)|renal vesicle induction (GO:0072034)|smooth muscle cell differentiation (GO:0051145)|somatotropin secreting cell differentiation (GO:0060126)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	8		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;9.02e-26)|Colorectal(126;1.71e-07)|COAD - Colon adenocarcinoma(152;1.17e-05)|GBM - Glioblastoma multiforme(114;2.01e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000568)|KIRC - Kidney renal clear cell carcinoma(1967;0.00277)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		TTGCAGCTGCAGCGTTCAGCC	0.657																																					p.C326R		Atlas-SNP	.											.	WNT4	33	.	0			c.T976C						.						38	34	36					1																	22446623		2203	4300	6503	SO:0001583	missense	54361	exon5			AGCTGCAGCGTTC	AL031281	CCDS223.1	1p36.23-p35.1	2013-02-28			ENSG00000162552	ENSG00000162552		"Wingless-type MMTV integration sites", "Endogenous ligands"	12783	protein-coding gene	gene with protein product		603490				8168088	Standard	NM_030761		Approved	WNT-4	uc001bfs.4	P56705	OTTHUMG00000002894	ENST00000290167.6:c.976T>C	chr1.hg19:g.22446623A>G	ENSP00000290167:p.Cys326Arg	57.0	0.0		33.0	15.0	NM_030761	B4DJF9|Q5TZQ0|Q96T81|Q9BXF5|Q9H1J8|Q9UJM2	Missense_Mutation	SNP	ENST00000290167.6	hg19	CCDS223.1	.	.	.	.	.	.	.	.	.	.	a	20.8	4.053594	0.75960	.	.	ENSG00000162552	ENST00000290167;ENST00000542383	D;D	0.91686	-2.89;-2.89	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	D	0.97586	0.9209	H	0.98487	4.245	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98616	1.0665	10	0.87932	D	0	.	13.2728	0.60170	1.0:0.0:0.0:0.0	.	326	P56705	WNT4_HUMAN	R	326;271	ENSP00000290167:C326R;ENSP00000441033:C271R	ENSP00000290167:C326R	C	-	1	0	WNT4	22319210	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.261000	0.95576	1.874000	0.54306	0.370000	0.22315	TGC	.	.		0.657	WNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008088.2			G	22446623	A	G	22446623	3	3	73	1	0	0	0	0	1	0	0	0	17405	188	7	2	83	2	WNT4	1	22446623	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	506425	22446623	226803998	9	9335										
ZNF436	80818	hgsc.bcm.edu	37	chr1	23689069	23689069	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctcacccgtgtgggtcctcTggtgctgagctaggtgagag	15	10	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:23689069T>C	ENST00000314011.4	-	4	942	c.806A>G	c.(805-807)cAg>cGg	p.Q269R	ZNF436_ENST00000374608.3_Missense_Mutation_p.Q269R	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	269					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		GTGGGTCCTCTGGTGCTGAGC	0.517																																					p.Q269R		Atlas-SNP	.											.	ZNF436	49	.	0			c.A806G						.						103	108	106					1																	23689069		2203	4300	6503	SO:0001583	missense	80818	exon4			GTCCTCTGGTGCT	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"Zinc fingers, C2H2-type", "-"	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.806A>G	chr1.hg19:g.23689069T>C	ENSP00000313582:p.Gln269Arg	140.0	0.0		114.0	5.0	NM_001077195	Q658I9	Missense_Mutation	SNP	ENST00000314011.4	hg19	CCDS233.1	.	.	.	.	.	.	.	.	.	.	T	15.89	2.967856	0.53507	.	.	ENSG00000125945	ENST00000314011;ENST00000374609;ENST00000374608	T;T;T	0.34667	1.35;3.2;1.35	5.79	5.79	0.91817	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000035	T	0.18551	0.0445	N	0.19112	0.55	0.29126	N	0.87995	P	0.42161	0.772	B	0.27262	0.078	T	0.19745	-1.0296	10	0.49607	T	0.09	-36.6231	9.3961	0.38404	0.1588:0.0:0.0:0.8412	.	269	Q9C0F3	ZN436_HUMAN	R	269	ENSP00000313582:Q269R;ENSP00000363737:Q269R;ENSP00000363736:Q269R	ENSP00000313582:Q269R	Q	-	2	0	ZNF436	23561656	0.082000	0.21442	1.000000	0.80357	0.975000	0.68041	0.427000	0.21379	2.212000	0.71576	0.533000	0.62120	CAG	.	.		0.517	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		C	23689069	T	C	23689069	3	2	73	1	0	0	0	0	1	0	0	0	17924	1580	55	2	610	2	ZNF436	1	23689069	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1242446	23689069	225561552	10	9336										
ZNF683	257101	hgsc.bcm.edu	37	chr1	26694278	26694278	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtctggaagtggtctgcagGctgagaagacctggagggca	17	7	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:26694278G>C	ENST00000436292.1	-	3	245	c.125C>G	c.(124-126)gCc>gGc	p.A42G	ZNF683_ENST00000403843.1_Missense_Mutation_p.A42G|ZNF683_ENST00000374204.1_Missense_Mutation_p.A42G|ZNF683_ENST00000349618.3_Missense_Mutation_p.A42G			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	42					natural killer cell differentiation (GO:0001779)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	15		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		TGGTCTGCAGGCTGAGAAGAC	0.622																																					p.A42G		Atlas-SNP	.											.	ZNF683	51	.	0			c.C125G						.						19	17	18					1																	26694278		2203	4299	6502	SO:0001583	missense	257101	exon3			CTGCAGGCTGAGA	BC029505	CCDS279.2	1p36.11	2013-01-08			ENSG00000176083	ENSG00000176083		"Zinc fingers, C2H2-type"	28495	protein-coding gene	gene with protein product	"hypothetical protein MGC33414"					12477932	Standard	NM_173574		Approved	MGC33414	uc009vsj.1	Q8IZ20	OTTHUMG00000003521	ENST00000436292.1:c.125C>G	chr1.hg19:g.26694278G>C	ENSP00000388792:p.Ala42Gly	107.0	0.0		75.0	36.0	NM_173574	Q5T141|Q5T146|Q5T147|Q5T149|Q8NEN4	Missense_Mutation	SNP	ENST00000436292.1	hg19		.	.	.	.	.	.	.	.	.	.	G	18.45	3.626722	0.66901	.	.	ENSG00000176083	ENST00000403843;ENST00000436292;ENST00000374204;ENST00000349618;ENST00000455900;ENST00000451801;ENST00000423508;ENST00000416125	T;T;T;T;T;T;T;T	0.31247	2.79;2.79;2.72;2.72;1.88;1.89;1.5;1.52	3.97	2.01	0.26516	.	0.373374	0.19610	N	0.110164	T	0.35189	0.0923	L	0.27053	0.805	0.09310	N	1	D;B	0.76494	0.999;0.024	D;B	0.79108	0.992;0.014	T	0.08186	-1.0734	10	0.37606	T	0.19	-2.1331	6.8965	0.24259	0.0:0.1936:0.6063:0.2002	.	42;42	Q8IZ20-2;Q8IZ20	.;ZN683_HUMAN	G	42;42;42;42;50;42;50;42	ENSP00000384782:A42G;ENSP00000388792:A42G;ENSP00000363320:A42G;ENSP00000344095:A42G;ENSP00000411289:A50G;ENSP00000411290:A42G;ENSP00000391584:A50G;ENSP00000401961:A42G	ENSP00000344095:A42G	A	-	2	0	ZNF683	26566865	0.008000	0.16893	0.058000	0.19502	0.948000	0.59901	0.626000	0.24492	0.424000	0.26061	0.462000	0.41574	GCC	.	.		0.622	ZNF683-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009794.2	NM_173574		C	26694278	G	C	26694278	3	2	73	1	0	0	0	0	1	0	0	0	18105	1203	42	4	1405	4	ZNF683	1	26694278	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3005209	26694278	222556343	11	9337										
NUDC	10726	hgsc.bcm.edu	37	chr1	27268120	27268120	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caaggagctaactgatgaagAggcagagaggctgcagctag	15	7	0	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:27268120A>G	ENST00000321265.5	+	3	455	c.332A>G	c.(331-333)gAg>gGg	p.E111G		NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	111				E -> K (in Ref. 4; BAA76628). {ECO:0000305}.	cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)				cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)		ACTGATGAAGAGGCAGAGAGG	0.637																																					p.E111G		Atlas-SNP	.											.	NUDC	15	.	0			c.A332G						.						38	39	38					1																	27268120		2203	4300	6503	SO:0001583	missense	10726	exon3			ATGAAGAGGCAGA		CCDS292.1	1p35-p34	2013-08-06	2013-08-06		ENSG00000090273	ENSG00000090273			8045	protein-coding gene	gene with protein product		610325	"nuclear distribution gene C homolog (A. nidulans)", "nuclear distribution C homolog (A. nidulans)"				Standard	NM_006600		Approved	NudC	uc001bng.2	Q9Y266	OTTHUMG00000004226	ENST00000321265.5:c.332A>G	chr1.hg19:g.27268120A>G	ENSP00000319664:p.Glu111Gly	200.0	0.0		175.0	15.0	NM_006600	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Missense_Mutation	SNP	ENST00000321265.5	hg19	CCDS292.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.572324	0.86542	.	.	ENSG00000090273	ENST00000435827;ENST00000321265;ENST00000452707	D	0.82081	-1.57	5.52	4.33	0.51752	.	0.141972	0.64402	D	0.000007	D	0.91209	0.7230	M	0.88906	2.99	0.58432	D	0.999999	D;D	0.76494	0.999;0.983	D;D	0.71184	0.972;0.917	D	0.92198	0.5765	10	0.59425	D	0.04	.	12.2401	0.54538	0.8581:0.1419:0.0:0.0	.	62;111	Q9H2R7;Q9Y266	.;NUDC_HUMAN	G	115;111;62	ENSP00000319664:E111G	ENSP00000319664:E111G	E	+	2	0	NUDC	27140707	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.148000	0.77389	2.111000	0.64477	0.533000	0.62120	GAG	.	.		0.637	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012172.2			G	27268120	A	G	27268120	3	3	73	1	0	0	0	0	1	0	0	0	10730	304	11	2	342	2	NUDC	1	27268120	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	573842	27268120	221982501	12	9338										
LAPTM5	7805	hgsc.bcm.edu	37	chr1	31215394	31215394	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atgaacaacaagacgctcatGatctggaggcaaagcaaagc	10	9	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:31215394G>C	ENST00000294507.3	-	2	164	c.90C>G	c.(88-90)atC>atG	p.I30M	LAPTM5_ENST00000476492.1_5'UTR	NM_006762.2	NP_006753.1	Q13571	LAPM5_HUMAN	lysosomal protein transmembrane 5	30					transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)				large_intestine(2)|lung(7)|skin(1)	10		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)		AGACGCTCATGATCTGGAGGC	0.587																																					p.I30M		Atlas-SNP	.											.	LAPTM5	30	.	0			c.C90G						.						84	66	72					1																	31215394		2203	4300	6503	SO:0001583	missense	7805	exon2			GCTCATGATCTGG	U51240	CCDS337.1	1p34	2009-07-20	2009-07-20		ENSG00000162511	ENSG00000162511			29612	protein-coding gene	gene with protein product		601476	"lysosomal multispanning membrane protein 5"			8661146, 12527926	Standard	NM_006762		Approved		uc001bsc.2	Q13571	OTTHUMG00000003707	ENST00000294507.3:c.90C>G	chr1.hg19:g.31215394G>C	ENSP00000294507:p.Ile30Met	102.0	0.0		59.0	27.0	NM_006762	Q13240|Q14698|Q3KP54	Missense_Mutation	SNP	ENST00000294507.3	hg19	CCDS337.1	.	.	.	.	.	.	.	.	.	.	G	17.84	3.488883	0.64074	.	.	ENSG00000162511	ENST00000294507;ENST00000424259	T	0.52295	0.67	5.05	2.9	0.33743	.	0.275088	0.29940	N	0.010806	T	0.51907	0.1702	L	0.51422	1.61	0.26252	N	0.978716	D	0.56746	0.977	P	0.58721	0.844	T	0.33059	-0.9883	10	0.44086	T	0.13	-30.0457	7.9368	0.29935	0.0:0.1722:0.6505:0.1773	.	30	Q13571	LAPM5_HUMAN	M	30	ENSP00000294507:I30M	ENSP00000294507:I30M	I	-	3	3	LAPTM5	30987981	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	0.985000	0.29578	2.363000	0.80096	0.462000	0.41574	ATC	.	.		0.587	LAPTM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010463.1	NM_006762		C	31215394	G	C	31215394	3	2	73	1	0	0	0	0	1	0	0	0	8635	1280	45	4	726	4	LAPTM5	1	31215394	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3947274	31215394	218035227	13	9339										
PEF1	553115	hgsc.bcm.edu	37	chr1	32101091	32101091	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tagtagctacccggaggggcTcctggtgcttgtcctgcagc	14	12	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:32101091T>A	ENST00000373703.4	-	2	79	c.57A>T	c.(55-57)ggA>ggT	p.G19G	PEF1_ENST00000440872.2_Silent_p.G19G|PEF1_ENST00000492061.1_5'UTR	NM_012392.3	NP_036524.1	Q9UBV8	PEF1_HUMAN	penta-EF-hand domain containing 1	19					proteolysis (GO:0006508)|response to calcium ion (GO:0051592)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|poly(A) RNA binding (GO:0044822)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)|all_neural(195;0.186)		STAD - Stomach adenocarcinoma(196;0.0546)		CCGGAGGGGCTCCTGGTGCTT	0.587																																					p.G19G		Atlas-SNP	.											.	PEF1	20	.	0			c.A57T						.						20	22	21					1																	32101091		2192	4289	6481	SO:0001819	synonymous_variant	553115	exon2			AGGGGCTCCTGGT		CCDS345.1	1p34	2013-01-10			ENSG00000162517	ENSG00000162517		"EF-hand domain containing"	30009	protein-coding gene	gene with protein product	"peflin"	610033				10486255, 11883899	Standard	NM_012392		Approved	PEF1A	uc001bth.2	Q9UBV8	OTTHUMG00000003877	ENST00000373703.4:c.57A>T	chr1.hg19:g.32101091T>A		308.0	0.0		270.0	106.0	NM_012392		Silent	SNP	ENST00000373703.4	hg19	CCDS345.1																																																																																			.	.		0.587	PEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011046.1	NM_012392		A	32101091	T	A	32101091	2	1	73	1	0	0	0	0	0	0	0	1	11727	1538	54	4		4	PEF1	1	32101091	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	885697	32101091	217149530	14	9340										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34174805	34174805	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gttattgtagttcacaggaaAgttgggggacagcaaagtac	13	5	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:34174805A>G	ENST00000373380.1	-	1	299	c.79T>C	c.(79-81)Ttt>Ctt	p.F27L	CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373381.4_Missense_Mutation_p.F1154L			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1114	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TTCACAGGAAAGTTGGGGGAC	0.483																																					p.F1114L		Atlas-SNP	.											CSMD2,NS,carcinoma,0,1	CSMD2	946	.	0			c.T3340C						.						102	92	95					1																	34174805		2203	4300	6503	SO:0001583	missense	114784	exon22			CAGGAAAGTTGGG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.79T>C	chr1.hg19:g.34174805A>G	ENSP00000362478:p.Phe27Leu	152.0	1.0		97.0	34.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	A	26.3	4.720707	0.89205	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.20200	2.09;2.09	5.6	5.6	0.85130	CUB (5);	0.067939	0.64402	D	0.000010	T	0.41119	0.1145	M	0.85041	2.73	0.80722	D	1	B;P;P	0.49358	0.133;0.923;0.866	B;P;P	0.50570	0.287;0.644;0.644	T	0.43245	-0.9403	10	0.48119	T	0.1	.	14.9681	0.71210	1.0:0.0:0.0:0.0	.	27;1114;1154	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	L	1154;27	ENSP00000362479:F1154L;ENSP00000362478:F27L	ENSP00000241312:F1114L	F	-	1	0	CSMD2	33947392	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.576000	0.82467	2.143000	0.66587	0.459000	0.35465	TTT	.	.		0.483	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		G	34174805	A	G	34174805	3	3	73	1	0	0	0	0	1	0	0	0	3947	72	3	2	7315	2	CSMD2	1	34174805	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2073714	34174805	215075816	15	9341										
C1orf94	84970	hgsc.bcm.edu	37	chr1	34663030	34663030	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggcagtaatgagcgccccagAgcctccatcattgtcggaga	12	12	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:34663030A>T	ENST00000488417.1	+	2	645	c.525A>T	c.(523-525)agA>agT	p.R175S	C1orf94_ENST00000373374.3_5'UTR	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	175										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				AGCGCCCCAGAGCCTCCATCA	0.597																																					p.R175S		Atlas-SNP	.											.	C1orf94	156	.	0			c.A525T						.						35	37	36					1																	34663030		2203	4300	6503	SO:0001583	missense	84970	exon2			CCCCAGAGCCTCC	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.525A>T	chr1.hg19:g.34663030A>T	ENSP00000435634:p.Arg175Ser	88.0	0.0		104.0	46.0	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	hg19	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	A	0.435	-0.901394	0.02453	.	.	ENSG00000142698	ENST00000488417	T	0.22134	1.97	4.5	0.84	0.18912	.	.	.	.	.	T	0.10508	0.0257	N	0.22421	0.69	0.09310	N	1	B	0.20780	0.048	B	0.19391	0.025	T	0.39057	-0.9632	9	0.12103	T	0.63	-29.7401	3.4935	0.07646	0.5887:0.2007:0.2107:0.0	.	175	Q6P1W5	CA094_HUMAN	S	175	ENSP00000435634:R175S	ENSP00000435634:R175S	R	+	3	2	C1orf94	34435617	0.000000	0.05858	0.017000	0.16124	0.172000	0.22775	0.468000	0.22051	0.309000	0.22966	0.533000	0.62120	AGA	.	.		0.597	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884		T	34663030	A	T	34663030	3	4	73	1	0	0	0	0	1	0	0	0	2073	301	11	4	531	4	C1orf94	1	34663030	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	488225	34663030	214587591	16	9342										
GRIK3	2899	hgsc.bcm.edu	37	chr1	37315910	37315910	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgcaggggctgcaggctcttAccagcactgtggtgacaatg	14	10	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:37315910A>G	ENST00000373091.3	-	9	1343		c.e9+1		GRIK3_ENST00000462621.1_Splice_Site|GRIK3_ENST00000373093.4_Splice_Site	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3						adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				GCAGGCTCTTACCAGCACTGT	0.612																																					.		Atlas-SNP	.											.	GRIK3	195	.	0			c.1326+2T>C						.						118	99	106					1																	37315910		2203	4300	6503	SO:0001630	splice_region_variant	2899	exon10			GCTCTTACCAGCA	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.1326+1T>C	chr1.hg19:g.37315910A>G		53.0	0.0		45.0	16.0	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Splice_Site	SNP	ENST00000373091.3	hg19	CCDS416.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.558367	0.86231	.	.	ENSG00000163873	ENST00000373091;ENST00000373093	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7583	0.78054	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GRIK3	37088497	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.962000	0.93254	2.116000	0.64780	0.454000	0.30748	.	.	.		0.612	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831	Intron	G	37315910	A	G	37315910	5	3	73	1	0	0	0	0	0	0	1	0	6784	405	14	2	1463	2	GRIK3	1	37315910	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2652880	37315910	211934711	17	9343										
NSUN4	387338	hgsc.bcm.edu	37	chr1	46810731	46810732	+	Frame_Shift_Ins	INS	-	-	T													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggtggccaatctgcagcccINScatcccctgcctcctgggcc							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:46810731_46810732insT	ENST00000474844.1	+	2	1002_1003	c.352_353insT	c.(352-354)ccafs	p.P118fs	NSUN4_ENST00000536062.1_Frame_Shift_Ins_p.P69fs|NSUN4_ENST00000498008.1_3'UTR|NSUN4_ENST00000537428.1_Frame_Shift_Ins_p.P69fs	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	118					rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)			endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					ATCTGCAGCCCCATCCCCTGCC	0.559																																					p.P118fs		Atlas-Indel,Pindel	.											.	NSUN4	26	.	0			c.352_353insT						.																																			SO:0001589	frameshift_variant	387338	exon2			.	AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"NOP2/Sun domain containing"	31802	protein-coding gene	gene with protein product	"sperm head and tail associated protein"	615394	"NOL1/NOP2/Sun domain family 4", "NOL1/NOP2/Sun domain family, member 4"				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	Exception_encountered	chr1.hg19:g.46810731_46810732insT	ENSP00000419740:p.Pro118fs	74.0	0.0		83.0	36.0	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Frame_Shift_Ins	INS	ENST00000474844.1	hg19	CCDS534.1																																																																																			.	.		0.559	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044		T	46810732	-	T	46810731	7	5	73	1	0	1	1	0	0	0	0	0	10689	623	22	0	358	0	NSUN4	1	46810731	Frame_Shift_Ins	INS	-	TCGA-CC-A7IH-01A-11D-A33K-10	9494821	46810731	202439890	18	9344										
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52761649	52761649	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	accatcatgaatcttcttgcAgtaagttgggaatttttttt	7	6	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:52761649A>G	ENST00000371591.1	+	11	3464	c.3333A>G	c.(3331-3333)gcA>gcG	p.A1111A	ZFYVE9_ENST00000357206.2_Splice_Site_p.A1052A|ZFYVE9_ENST00000469134.1_3'UTR|ZFYVE9_ENST00000287727.3_Splice_Site_p.A1111A	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	1111					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						ATCTTCTTGCAGTAAGTTGGG	0.398																																					p.A1111A		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.A3333G						.						196	179	185					1																	52761649		2203	4300	6503	SO:0001630	splice_region_variant	9372	exon12			TCTTGCAGTAAGT	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.3333+1A>G	chr1.hg19:g.52761649A>G		115.0	0.0		102.0	43.0	NM_004799	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Silent	SNP	ENST00000371591.1	hg19	CCDS563.1																																																																																			.	.		0.398	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	Silent	G	52761649	A	G	52761649	5	3	73	1	0	0	0	0	0	0	1	0	17686	202	7	2	3382	2	ZFYVE9	1	52761649	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	5950918	52761649	196488972	19	9345										
ROR1	4919	hgsc.bcm.edu	37	chr1	64515633	64515633	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtggtttcttccactggagTcttgtttgtcaagtttggta	12	6	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:64515633T>C	ENST00000371079.1	+	3	809	c.434T>C	c.(433-435)gTc>gCc	p.V145A	ROR1_ENST00000482426.1_3'UTR|ROR1_ENST00000371080.1_Missense_Mutation_p.V145A	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	145	Ig-like C2-type.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						TCCACTGGAGTCTTGTTTGTC	0.537																																					p.V145A		Atlas-SNP	.											.	ROR1	113	.	0			c.T434C						.						98	102	100					1																	64515633		2203	4300	6503	SO:0001583	missense	4919	exon3			CTGGAGTCTTGTT	M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"Immunoglobulin superfamily / I-set domain containing"	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.434T>C	chr1.hg19:g.64515633T>C	ENSP00000360120:p.Val145Ala	97.0	0.0		75.0	26.0	NM_001083592	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	hg19	CCDS626.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.149273	0.78001	.	.	ENSG00000185483	ENST00000371080;ENST00000371079;ENST00000544776	T;T	0.39229	1.09;1.09	5.79	5.79	0.91817	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.38778	N	0.001568	T	0.36220	0.0959	L	0.48218	1.51	0.80722	D	1	B;P	0.43024	0.3;0.798	B;P	0.48795	0.411;0.59	T	0.09530	-1.0670	10	0.36615	T	0.2	.	16.1341	0.81471	0.0:0.0:0.0:1.0	.	145;145	Q01973;Q66K77	ROR1_HUMAN;.	A	145;145;148	ENSP00000360121:V145A;ENSP00000360120:V145A	ENSP00000360120:V145A	V	+	2	0	ROR1	64288221	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.671000	0.83941	2.200000	0.70718	0.455000	0.32223	GTC	.	.		0.537	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		C	64515633	T	C	64515633	3	2	73	1	0	0	0	0	1	0	0	0	13541	1667	58	2	444	2	ROR1	1	64515633	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	11753984	64515633	184734988	20	9346										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70504419	70504419	+	Frame_Shift_Del	DEL	C	C	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caaaagcacagagaggctttCccccctaatgaaagatatca							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:70504419delC	ENST00000035383.5	+	19	2828	c.2798delC	c.(2797-2799)tccfs	p.S933fs	LRRC7_ENST00000415775.2_Frame_Shift_Del_p.S217fs|LRRC7_ENST00000310961.5_Frame_Shift_Del_p.S938fs	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	933						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						GAGAGGCTTTCCCCCCTAATG	0.368																																					p.S933fs		Pindel	.											.	LRRC7	400	.	0			c.2797delT						.						56	57	57					1																	70504419		2203	4300	6503	SO:0001589	frameshift_variant	57554	exon19			.		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2798delC	chr1.hg19:g.70504419delC	ENSP00000035383:p.Ser933fs	303.0	0.0		258.0	66.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Frame_Shift_Del	DEL	ENST00000035383.5	hg19	CCDS645.1																																																																																			.	.		0.368	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		-	70504419	C	-	70504419	7	5	73	1	0	1	0	1	0	0	0	0	9029	855	30	0	2872	0	LRRC7	1	70504419	Frame_Shift_Del	DEL	C	TCGA-CC-A7IH-01A-11D-A33K-10	5988786	70504419	178746202	21	9347										
LRRIQ3	127255	hgsc.bcm.edu	37	chr1	74621535	74621535	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tttaatattattaatttcctCttcataggttgttccctgta	4	7	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:74621535C>T	ENST00000395089.1	-	3	588	c.589G>A	c.(589-591)Gag>Aag	p.E197K	LRRIQ3_ENST00000468759.1_5'Flank|LRRIQ3_ENST00000370909.2_Missense_Mutation_p.E89K|LRRIQ3_ENST00000354431.4_Missense_Mutation_p.E197K			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	197										NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						TTAATTTCCTCTTCATAGGTT	0.239																																					p.E197K		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.G589A						.						28	26	27					1																	74621535		1763	4015	5778	SO:0001583	missense	127255	exon4			TTTCCTCTTCATA	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.589G>A	chr1.hg19:g.74621535C>T	ENSP00000378524:p.Glu197Lys	327.0	0.0		347.0	136.0	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	hg19	CCDS41350.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.07|17.07	3.295220|3.295220	0.60086|0.60086	.|.	.|.	ENSG00000162620|ENSG00000162620	ENST00000395089;ENST00000354431;ENST00000370909;ENST00000388972|ENST00000444984	T;T;T|.	0.33865|.	3.08;3.08;1.39|.	4.75|4.75	1.76|1.76	0.24704|0.24704	.|.	0.604283|.	0.15165|.	N|.	0.276963|.	T|T	0.14098|0.14098	0.0341|0.0341	L|L	0.27053|0.27053	0.805|0.805	0.21984|0.21984	N|N	0.999432|0.999432	B|.	0.29716|.	0.255|.	B|.	0.21360|.	0.034|.	T|T	0.26467|0.26467	-1.0102|-1.0102	10|5	0.62326|.	D|.	0.03|.	.|.	8.7276|8.7276	0.34478|0.34478	0.0:0.7282:0.0:0.2718|0.0:0.7282:0.0:0.2718	.|.	197|.	A6PVS8|.	LRIQ3_HUMAN|.	K|K	197;197;89;197|31	ENSP00000378524:E197K;ENSP00000346414:E197K;ENSP00000359946:E89K|.	ENSP00000346414:E197K|.	E|R	-|-	1|2	0|0	LRRIQ3|LRRIQ3	74394123|74394123	0.697000|0.697000	0.27767|0.27767	0.827000|0.827000	0.32855|0.32855	0.731000|0.731000	0.41821|0.41821	0.580000|0.580000	0.23803|0.23803	0.545000|0.545000	0.28902|0.28902	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.		0.239	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		T	74621535	C	T	74621535	3	4	73	1	0	0	0	0	1	0	0	0	9039	922	32	3	1305	3	LRRIQ3	1	74621535	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	4117116	74621535	174629086	22	9348										
TNNI3K	100526835	hgsc.bcm.edu	37	chr1	74833633	74833633	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	catcacccttggggaagattAaaagcatgacaaaaggtacc	9	9	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:74833633A>T	ENST00000370899.3	+	15	1646	c.1609A>T	c.(1609-1611)Aaa>Taa	p.K537*	FPGT-TNNI3K_ENST00000557284.2_Nonsense_Mutation_p.K550*|FPGT-TNNI3K_ENST00000370895.1_Nonsense_Mutation_p.K537*|TNNI3K_ENST00000370891.2_Nonsense_Mutation_p.K537*|RP11-439H8.4_ENST00000415549.2_RNA|TNNI3K_ENST00000326637.3_Nonsense_Mutation_p.K436*	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		GGGGAAGATTAAAAGCATGAC	0.289																																					p.K537X		Atlas-SNP	.											.	.	.	.	0			c.A1609T						.						66	67	67					1																	74833633		2203	4298	6501	SO:0001587	stop_gained	100526835	exon15			AAGATTAAAAGCA			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.1609A>T	chr1.hg19:g.74833633A>T	ENSP00000359936:p.Lys537*	379.0	0.0		332.0	114.0	NM_001112808		Nonsense_Mutation	SNP	ENST00000370899.3	hg19		.	.	.	.	.	.	.	.	.	.	A	37	6.086027	0.97271	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000534632;ENST00000557284;ENST00000370891;ENST00000326637	.	.	.	5.9	4.77	0.60923	.	0.046829	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.6637	0.51363	0.9311:0.0:0.0689:0.0	.	.	.	.	X	537;537;158;537;537;436	.	ENSP00000322251:K436X	K	+	1	0	RP11-653A5.2;AC093158.1	74606221	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.788000	0.75105	1.069000	0.40788	0.528000	0.53228	AAA	.	.		0.289	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			T	74833633	A	T	74833633	4	4	73	1	0	0	0	0	0	1	0	0	16344	363	13	4	1711	4	TNNI3K	1	74833633	Nonsense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	212098	74833633	174416988	23	9349										
GBP6	163351	hgsc.bcm.edu	37	chr1	89848365	89848365	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tttctctgttcctggagggcAcaagctctacatggaaacaa	9	10	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:89848365A>G	ENST00000370456.4	+	8	1388	c.1295A>G	c.(1294-1296)cAc>cGc	p.H432R	GBP6_ENST00000535065.1_Missense_Mutation_p.H302R	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	432					cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		CCTGGAGGGCACAAGCTCTAC	0.448																																					p.H432R		Atlas-SNP	.											.	GBP6	87	.	0			c.A1295G						.						81	83	82					1																	89848365		2203	4300	6503	SO:0001583	missense	163351	exon8			GAGGGCACAAGCT	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.1295A>G	chr1.hg19:g.89848365A>G	ENSP00000359485:p.His432Arg	200.0	0.0		169.0	54.0	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Missense_Mutation	SNP	ENST00000370456.4	hg19	CCDS723.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.118344	0.56505	.	.	ENSG00000183347	ENST00000544311;ENST00000370456;ENST00000535065	T;T	0.02258	4.37;4.37	5.12	3.98	0.46160	Guanylate-binding protein, C-terminal (3);	0.412335	0.24436	N	0.038550	T	0.04952	0.0133	M	0.86953	2.85	0.09310	N	1	D	0.53151	0.958	P	0.58780	0.845	T	0.16837	-1.0389	10	0.87932	D	0	-5.2703	9.5907	0.39543	0.8433:0.0:0.0:0.1567	.	432	Q6ZN66	GBP6_HUMAN	R	403;432;302	ENSP00000359485:H432R;ENSP00000442530:H302R	ENSP00000359485:H432R	H	+	2	0	GBP6	89620953	0.027000	0.19231	0.003000	0.11579	0.751000	0.42716	3.308000	0.51896	0.766000	0.33244	0.482000	0.46254	CAC	.	.		0.448	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460		G	89848365	A	G	89848365	3	3	73	1	0	0	0	0	1	0	0	0	6286	159	6	2	1321	2	GBP6	1	89848365	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	15014732	89848365	159402256	24	9350										
BRDT	676	hgsc.bcm.edu	37	chr1	92428482	92428482	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccctttcaacgtcctgtggaTgctgtgaaactacagttgcc	9	12	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:92428482T>C	ENST00000362005.3	+	3	589	c.171T>C	c.(169-171)gaT>gaC	p.D57D	BRDT_ENST00000370389.2_Intron|BRDT_ENST00000399546.2_Silent_p.D57D|BRDT_ENST00000402388.1_Silent_p.D57D|BRDT_ENST00000394530.3_Silent_p.D57D	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	57	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		GTCCTGTGGATGCTGTGAAAC	0.343																																					p.D57D		Atlas-SNP	.											.	BRDT	133	.	0			c.T171C						.						113	111	112					1																	92428482		2203	4300	6503	SO:0001819	synonymous_variant	676	exon2			TGTGGATGCTGTG	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"cancer/testis antigen 9"	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.171T>C	chr1.hg19:g.92428482T>C		124.0	0.0		128.0	46.0	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Silent	SNP	ENST00000362005.3	hg19	CCDS735.1																																																																																			.	.		0.343	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		C	92428482	T	C	92428482	2	2	73	1	0	0	0	0	0	0	0	1	1510	1461	51	2		2	BRDT	1	92428482	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2580117	92428482	156822139	25	9351										
ABCA4	24	hgsc.bcm.edu	37	chr1	94568641	94568641	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acaggccgatgtttttaatgAgaaatagtgtcagtgtttct	10	5	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:94568641A>C	ENST00000370225.3	-	5	586	c.500T>G	c.(499-501)cTc>cGc	p.L167R	ABCA4_ENST00000535735.1_Missense_Mutation_p.L167R	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	167					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GTTTTTAATGAGAAATAGTGT	0.443																																					p.L167R		Atlas-SNP	.											.	ABCA4	275	.	0			c.T500G						.						274	259	264					1																	94568641		2203	4300	6503	SO:0001583	missense	24	exon5			TTAATGAGAAATA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.500T>G	chr1.hg19:g.94568641A>C	ENSP00000359245:p.Leu167Arg	113.0	0.0		97.0	33.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.973951	0.74246	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.95853	-3.47;-3.83	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000002	D	0.97757	0.9264	M	0.88704	2.975	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.991	D	0.98866	1.0764	10	0.87932	D	0	.	15.1696	0.72862	1.0:0.0:0.0:0.0	.	167;167	F5H6E5;P78363	.;ABCA4_HUMAN	R	167	ENSP00000359245:L167R;ENSP00000437682:L167R	ENSP00000359245:L167R	L	-	2	0	ABCA4	94341229	1.000000	0.71417	0.900000	0.35374	0.486000	0.33341	8.308000	0.89966	2.058000	0.61347	0.533000	0.62120	CTC	.	.		0.443	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		C	94568641	A	C	94568641	3	2	73	1	0	0	0	0	1	0	0	0	34	304	11	5	6505	5	ABCA4	1	94568641	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2140159	94568641	154681980	26	9352										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103453234	103453234	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctgggtctccagttgggccTgctcgacctttgggtccttc	12	14	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:103453234T>A	ENST00000370096.3	-	30	2769	c.2457A>T	c.(2455-2457)gcA>gcT	p.A819A	COL11A1_ENST00000353414.4_Silent_p.A780A|COL11A1_ENST00000512756.1_Silent_p.A703A|COL11A1_ENST00000358392.2_Silent_p.A831A	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	819	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CAGTTGGGCCTGCTCGACCTT	0.473																																					p.A831A		Atlas-SNP	.											.	COL11A1	972	.	0			c.A2493T						.						93	87	89					1																	103453234		2203	4300	6503	SO:0001819	synonymous_variant	1301	exon30			TGGGCCTGCTCGA	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2457A>T	chr1.hg19:g.103453234T>A		113.0	0.0		91.0	35.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	9.460	1.092840	0.20471	.	.	ENSG00000060718	ENST00000370090	.	.	.	4.39	-1.07	0.09968	.	.	.	.	.	T	0.22975	0.0555	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10382	-1.0632	7	0.46703	T	0.11	.	5.7385	0.18079	0.4963:0.074:0.0:0.4297	.	34	F5H5Z5	.	L	34	.	ENSP00000359108:Q34L	Q	-	2	0	COL11A1	103225822	0.907000	0.30839	0.996000	0.52242	0.754000	0.42855	-0.121000	0.10643	-0.290000	0.09025	0.377000	0.23210	CAG	.	.		0.473	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103453234	T	A	103453234	2	1	73	1	0	0	0	0	0	0	0	1	3669	1567	55	4		4	COL11A1	1	103453234	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	8884593	103453234	145797387	27	9353										
WDR47	22911	hgsc.bcm.edu	37	chr1	109525342	109525342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agctcctccgctttctgggcCttccataaatgccaagtctc	7	15	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:109525342C>T	ENST00000369962.3	-	12	2377	c.2155G>A	c.(2155-2157)Ggc>Agc	p.G719S	WDR47_ENST00000369965.4_Missense_Mutation_p.G720S|WDR47_ENST00000357672.3_Missense_Mutation_p.G691S|WDR47_ENST00000400794.3_Missense_Mutation_p.G727S|WDR47_ENST00000361054.3_Missense_Mutation_p.G691S			O94967	WDR47_HUMAN	WD repeat domain 47	719					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		CTTTCTGGGCCTTCCATAAAT	0.403																																					p.G727S		Atlas-SNP	.											.	WDR47	56	.	0			c.G2179A						.						86	88	88					1																	109525342		2203	4300	6503	SO:0001583	missense	22911	exon12			CTGGGCCTTCCAT	AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433		"WD repeat domain containing"	29141	protein-coding gene	gene with protein product		615734				10048485	Standard	NM_014969		Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369962.3:c.2155G>A	chr1.hg19:g.109525342C>T	ENSP00000358979:p.Gly719Ser	133.0	0.0		138.0	61.0	NM_001142550	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Missense_Mutation	SNP	ENST00000369962.3	hg19	CCDS44187.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190473	0.78789	.	.	ENSG00000085433	ENST00000400794;ENST00000369962;ENST00000361054;ENST00000369965;ENST00000357672	T;T;T;T;T	0.56275	0.47;0.52;0.49;0.47;0.49	5.25	5.25	0.73442	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.051254	0.85682	D	0.000000	T	0.18551	0.0445	N	0.08118	0	0.80722	D	1	B;B;P;B	0.43633	0.332;0.156;0.813;0.086	B;B;B;B	0.35413	0.076;0.015;0.202;0.044	T	0.05954	-1.0854	10	0.30078	T	0.28	-9.8677	17.0163	0.86420	0.0:1.0:0.0:0.0	.	691;727;719;720	O94967-2;A8MX09;O94967;O94967-3	.;.;WDR47_HUMAN;.	S	727;719;691;720;691	ENSP00000383599:G727S;ENSP00000358979:G719S;ENSP00000354339:G691S;ENSP00000358982:G720S;ENSP00000350301:G691S	ENSP00000350301:G691S	G	-	1	0	WDR47	109326865	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.452000	0.82932	0.561000	0.74099	GGC	.	.		0.403	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032414.2	NM_014969		T	109525342	C	T	109525342	3	4	73	1	0	0	0	0	1	0	0	0	17315	681	24	3	620	3	WDR47	1	109525342	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	6072108	109525342	139725279	28	9354										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109801366	109801366	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctctgaggacctgcaggagcGcctatacctcaaccgcagcc	10	16	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:109801366G>C	ENST00000271332.3	+	2	3684	c.3623G>C	c.(3622-3624)cGc>cCc	p.R1208P		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1208					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CTGCAGGAGCGCCTATACCTC	0.701																																					p.R1208P	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.G3623C						.						17	16	16					1																	109801366		2195	4296	6491	SO:0001583	missense	1952	exon2			AGGAGCGCCTATA	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.3623G>C	chr1.hg19:g.109801366G>C	ENSP00000271332:p.Arg1208Pro	74.0	0.0		57.0	25.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.084118	0.76642	.	.	ENSG00000143126	ENST00000271332	T	0.69435	-0.4	4.43	4.43	0.53597	.	.	.	.	.	T	0.43478	0.1249	L	0.36672	1.1	0.51767	D	0.999934	P	0.45986	0.87	B	0.42625	0.393	T	0.47971	-0.9075	9	0.44086	T	0.13	.	8.6214	0.33864	0.1737:0.0:0.8263:0.0	.	1208	Q9HCU4	CELR2_HUMAN	P	1208	ENSP00000271332:R1208P	ENSP00000271332:R1208P	R	+	2	0	CELSR2	109602889	0.962000	0.33011	1.000000	0.80357	0.971000	0.66376	0.845000	0.27668	2.450000	0.82876	0.462000	0.41574	CGC	.	.		0.701	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		C	109801366	G	C	109801366	3	2	73	1	0	0	0	0	1	0	0	0	3224	1087	38	4	3629	4	CELSR2	1	109801366	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	276024	109801366	139449255	29	9355										
UBL4B	164153	hgsc.bcm.edu	37	chr1	110655547	110655547	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agataagcctggagcacctgGagcagctggcccagtacctc	12	13	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:110655547G>T	ENST00000334179.3	+	1	486	c.391G>T	c.(391-393)Gag>Tag	p.E131*		NM_203412.1	NP_981957.1	Q8N7F7	UBL4B_HUMAN	ubiquitin-like 4B	131						cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	7		all_cancers(81;1.14e-05)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0236)|all cancers(265;0.0823)|Epithelial(280;0.0917)|Colorectal(144;0.109)|LUSC - Lung squamous cell carcinoma(189;0.134)		GGAGCACCTGGAGCAGCTGGC	0.612																																					p.E131X		Atlas-SNP	.											UBL4B,right_upper_lobe,carcinoma,0,1	UBL4B	22	.	0			c.G391T						.						19	22	21					1																	110655547		2203	4299	6502	SO:0001587	stop_gained	164153	exon1			CACCTGGAGCAGC		CCDS820.1	1p13.3	2013-09-24			ENSG00000186150	ENSG00000186150			32309	protein-coding gene	gene with protein product		611127				16872915	Standard	NM_203412		Approved	FLJ25690	uc001dzc.3	Q8N7F7	OTTHUMG00000166989	ENST00000334179.3:c.391G>T	chr1.hg19:g.110655547G>T	ENSP00000334044:p.Glu131*	117.0	1.0		98.0	37.0	NM_203412		Nonsense_Mutation	SNP	ENST00000334179.3	hg19	CCDS820.1	.	.	.	.	.	.	.	.	.	.	G	33	5.250994	0.95305	.	.	ENSG00000186150	ENST00000334179	.	.	.	4.19	3.25	0.37280	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-8.1074	10.982	0.47499	0.0:0.1903:0.8097:0.0	.	.	.	.	X	131	.	ENSP00000334044:E131X	E	+	1	0	UBL4B	110457070	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.358000	0.59442	0.919000	0.36945	0.491000	0.48974	GAG	.	.		0.612	UBL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392303.1	NM_203412		T	110655547	G	T	110655547	4	4	73	1	0	0	0	0	0	1	0	0	16903	1175	41	3	393	3	UBL4B	1	110655547	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	854181	110655547	138595074	30	9356										
KCNA2	3737	hgsc.bcm.edu	37	chr1	111146974	111146974	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gccacacttgtctctgaaacTcattttcaggcagaggacgc	9	12	3	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:111146974T>A	ENST00000485317.1	-	3	1104	c.431A>T	c.(430-432)gAg>gTg	p.E144V	KCNA2_ENST00000316361.4_Missense_Mutation_p.E144V|KCNA2_ENST00000525120.1_Intron|KCNA2_ENST00000440270.1_Missense_Mutation_p.E144V|KCNA2_ENST00000369770.3_Missense_Mutation_p.E144V			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	144					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	TCTCTGAAACTCATTTTCAGG	0.458																																					p.E144V	Pancreas(18;568 735 10587 23710 36357)	Atlas-SNP	.											.	KCNA2	61	.	0			c.A431T						.						56	57	57					1																	111146974		2203	4300	6503	SO:0001583	missense	3737	exon3			TGAAACTCATTTT	L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.431A>T	chr1.hg19:g.111146974T>A	ENSP00000433109:p.Glu144Val	82.0	0.0		95.0	45.0	NM_001204269	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	hg19	CCDS827.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.343884	0.41498	.	.	ENSG00000177301	ENST00000369770;ENST00000485317;ENST00000440270;ENST00000316361	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	5.81	5.81	0.92471	.	0.636549	0.16168	N	0.226417	T	0.75064	0.3799	M	0.82193	2.58	0.80722	D	1	B;P	0.36392	0.002;0.551	B;P	0.49597	0.006;0.616	T	0.78064	-0.2350	10	0.72032	D	0.01	.	16.158	0.81680	0.0:0.0:0.0:1.0	.	144;144	Q86XG6;P16389	.;KCNA2_HUMAN	V	144	ENSP00000358785:E144V;ENSP00000433109:E144V;ENSP00000415257:E144V;ENSP00000314520:E144V	ENSP00000314520:E144V	E	-	2	0	KCNA2	110948497	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.883000	0.87264	2.220000	0.72140	0.496000	0.49642	GAG	.	.		0.458	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		A	111146974	T	A	111146974	3	1	73	1	0	0	0	0	1	0	0	0	8012	1551	54	4	1072	4	KCNA2	1	111146974	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	491427	111146974	138103647	31	9357										
KCNA3	3738	hgsc.bcm.edu	37	chr1	111216207	111216207	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgcgctggagaaaaggatgaCcccaataaagaggaagaaga	13	7	0	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:111216207C>A	ENST00000369769.2	-	1	1448	c.1225G>T	c.(1225-1227)Gtc>Ttc	p.V409F		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	409					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	AAAAGGATGACCCCAATAAAG	0.582																																					p.V409F		Atlas-SNP	.											.	KCNA3	91	.	0			c.G1225T						.						56	54	55					1																	111216207		2203	4300	6503	SO:0001583	missense	3738	exon1			GGATGACCCCAAT	L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.1225G>T	chr1.hg19:g.111216207C>A	ENSP00000358784:p.Val409Phe	92.0	0.0		70.0	28.0	NM_002232	Q5VWN2	Missense_Mutation	SNP	ENST00000369769.2	hg19	CCDS828.2	.	.	.	.	.	.	.	.	.	.	C	22.2	4.264204	0.80358	.	.	ENSG00000177272	ENST00000369769	D	0.97232	-4.3	5.71	5.71	0.89125	Ion transport (1);	0.000000	0.64402	U	0.000001	D	0.98804	0.9597	M	0.90145	3.09	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99552	1.0966	10	0.87932	D	0	.	19.8489	0.96731	0.0:1.0:0.0:0.0	.	409	P22001	KCNA3_HUMAN	F	409	ENSP00000358784:V409F	ENSP00000358784:V409F	V	-	1	0	KCNA3	111017730	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.814000	0.86154	2.689000	0.91719	0.655000	0.94253	GTC	.	.		0.582	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		A	111216207	C	A	111216207	3	1	73	1	0	0	0	0	1	0	0	0	8013	507	18	3	506	3	KCNA3	1	111216207	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	69233	111216207	138034414	32	9358										
SIKE1	80143	hgsc.bcm.edu	37	chr1	115318966	115318966	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctaaattagctacaatcttaCctctaattgggctaattttt	4	8	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:115318966C>G	ENST00000060969.5	-	4	592		c.e4+1		SIKE1_ENST00000369528.5_Splice_Site|SIKE1_ENST00000506320.1_5'Flank			Q9BRV8	SIKE1_HUMAN	suppressor of IKBKE 1						innate immune response (GO:0045087)	cytosol (GO:0005829)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6						TACAATCTTACCTCTAATTGG	0.373																																					.		Atlas-SNP	.											SIKE1,bladder,carcinoma,0,1	SIKE1	12	.	0			c.534+1G>C						.						150	146	147					1																	115318966		2203	4300	6503	SO:0001630	splice_region_variant	80143	exon5			ATCTTACCTCTAA	AK024821	CCDS878.1, CCDS41371.1	1p13.1	2009-08-13			ENSG00000052723	ENSG00000052723			26119	protein-coding gene	gene with protein product	"suppressor of IKK epsilon"	611656				16281057	Standard	NM_025073		Approved	FLJ21168, SIKE	uc001efp.4	Q9BRV8	OTTHUMG00000012061	ENST00000060969.5:c.522+1G>C	chr1.hg19:g.115318966C>G		106.0	1.0		118.0	9.0	NM_001102396	Q5TEZ7|Q5TEZ9|Q68DZ4|Q9H778	Splice_Site	SNP	ENST00000060969.5	hg19	CCDS878.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.628525	0.87560	.	.	ENSG00000052723	ENST00000369528;ENST00000060969	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6101	0.95602	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SIKE1	115120489	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.217000	0.77982	2.717000	0.92951	0.585000	0.79938	.	.	.		0.373	SIKE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033401.1	NM_025073	Intron	G	115318966	C	G	115318966	5	3	73	1	0	0	0	0	0	0	1	0	14335	521	18	4	108	4	SIKE1	1	115318966	Splice_Site	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	4102759	115318966	133931655	33	9359										
CD101	9398	hgsc.bcm.edu	37	chr1	117556093	117556093	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagggaaacccttagaactgGtttgcctggttgtaagcagt	12	7	0	1	rs201304832		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:117556093G>T	ENST00000256652.4	+	4	965	c.907G>T	c.(907-909)Gtt>Ttt	p.V303F	CD101_ENST00000369470.1_Missense_Mutation_p.V303F	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	303	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CTTAGAACTGGTTTGCCTGGT	0.468																																					p.V303F		Atlas-SNP	.											CD101,NS,lymphoid_neoplasm,0,1	CD101	95	.	0			c.G907T						.						128	132	130					1																	117556093		2203	4300	6503	SO:0001583	missense	9398	exon4			GAACTGGTTTGCC	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.907G>T	chr1.hg19:g.117556093G>T	ENSP00000256652:p.Val303Phe	136.0	0.0		108.0	42.0	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	hg19	CCDS891.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.594026	0.46214	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.02656	4.21;4.21	5.85	-3.41	0.04839	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.940590	0.08843	N	0.885539	T	0.01124	0.0037	M	0.65975	2.015	0.09310	N	0.999997	P	0.50369	0.934	P	0.47206	0.541	T	0.36553	-0.9743	10	0.09843	T	0.71	-3.2284	1.2286	0.01938	0.3934:0.2706:0.1991:0.137	.	303	Q93033	IGSF2_HUMAN	F	303	ENSP00000256652:V303F;ENSP00000358482:V303F	ENSP00000256652:V303F	V	+	1	0	CD101	117357616	0.000000	0.05858	0.066000	0.19879	0.792000	0.44763	-0.184000	0.09698	-0.426000	0.07360	-1.045000	0.02358	GTT	.	G|0.999;A|0.001		0.468	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		T	117556093	G	T	117556093	3	4	73	1	0	0	0	0	1	0	0	0	2964	1261	44	3	921	3	CD101	1	117556093	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	2237127	117556093	131694528	34	9360										
GPR89B	51463	hgsc.bcm.edu	37	chr1	147408746	147408746	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttctttctcctccagatactAttttttggatttgggtggct	8	8	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:147408746A>T	ENST00000314163.7	+	2	192	c.48A>T	c.(46-48)ctA>ctT	p.L16L		NM_016334.3	NP_057418.1	P0CG08	GPHRB_HUMAN	G protein-coupled receptor 89B	16					protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	voltage-gated ion channel activity (GO:0005244)			large_intestine(1)	1	all_hematologic(923;0.0276)					TCCAGATACTATTTTTTGGAT	0.308																																					p.L16L		Atlas-SNP	.											.	GPR89B	6	.	0			c.A48T						.						131	123	126					1																	147408746		2203	4298	6501	SO:0001819	synonymous_variant	51463	exon2			GATACTATTTTTT	U78723	CCDS930.1	1q21.1	2014-06-19	2007-06-06	2007-06-06	ENSG00000188092	ENSG00000188092			13840	protein-coding gene	gene with protein product		612806	"G protein-coupled receptor 89", "G protein-coupled receptor 89C"	GPR89, GPR89C		11042152	Standard	NM_016334		Approved	SH120	uc001epv.4	P0CG08	OTTHUMG00000013452	ENST00000314163.7:c.48A>T	chr1.hg19:g.147408746A>T		249.0	0.0		383.0	87.0	NM_016334	A6NN37|B2RUV3|B3KMN3|Q53FQ9|Q5T2V8|Q5T5P5|Q659E2|Q6NVY5|Q9P0S4|Q9Y302	Silent	SNP	ENST00000314163.7	hg19	CCDS930.1																																																																																			.	.		0.308	GPR89B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037481.2	NM_016334		T	147408746	A	T	147408746	2	4	73	1	0	0	0	0	0	0	0	1	6727	436	16	4		4	GPR89B	1	147408746	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	29852653	147408746	101841875	35	9361										
MTMR11	10903	hgsc.bcm.edu	37	chr1	149902441	149902441	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cttgtgtataggagtttaacTggacagaggaagcaagaaaa	12	4	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:149902441T>C	ENST00000439741.2	-	15	1715		c.e15-2		MTMR11_ENST00000492824.1_5'UTR|MTMR11_ENST00000369140.3_Splice_Site|MTMR11_ENST00000406732.3_Splice_Site|MTMR11_ENST00000361405.6_Splice_Site|SF3B4_ENST00000271628.8_5'Flank	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11								phosphatase activity (GO:0016791)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			GGAGTTTAACTGGACAGAGGA	0.463																																					.		Atlas-SNP	.											.	MTMR11	136	.	0			c.1249-2A>G						.						102	109	107					1																	149902441		2203	4300	6503	SO:0001630	splice_region_variant	10903	exon15			TTTAACTGGACAG	AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	24307	protein-coding gene	gene with protein product	"cisplatin resistance associated"					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.1465-2A>G	chr1.hg19:g.149902441T>C		35.0	0.0		76.0	11.0	NM_181873	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Splice_Site	SNP	ENST00000439741.2	hg19	CCDS53360.1	.	.	.	.	.	.	.	.	.	.	T	8.968	0.972170	0.18736	.	.	ENSG00000014914	ENST00000369140;ENST00000439741	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5219	0.50555	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MTMR11	148169065	0.997000	0.39634	0.591000	0.28745	0.258000	0.26162	3.989000	0.56958	2.209000	0.71365	0.533000	0.62120	.	.	.		0.463	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873	Intron	C	149902441	T	C	149902441	5	2	73	1	0	0	0	0	0	0	1	0	9949	1594	55	2	717	2	MTMR11	1	149902441	Splice_Site	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2493695	149902441	99348180	36	9362										
ZNF687	5298	hgsc.bcm.edu	37	chr1	151262629	151262630	+	IGR	INS	-	-	G													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttcccctgtcgcctgtgtgaINSgcgctccttctgctccgccc							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:151262629_151262630insG	ENST00000368873.1	-	0	3340				ZNF687_ENST00000368879.2_Frame_Shift_Ins_p.R1000fs			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta						phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CGCCTGTGTGAGCGCTCCTTCT	0.599																																					p.E999fs	Colon(154;765 1838 9854 28443 37492)	Atlas-Indel,Pindel	.											.	ZNF687	94	.	0			c.2996_2997insG						.																																			SO:0001628	intergenic_variant	57592	exon7			.	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348		chr1.hg19:g.151262630_151262630dupG		114.0	0.0		164.0	30.0	NM_020832	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	Frame_Shift_Ins	INS	ENST00000368873.1	hg19																																																																																				.	.		0.599	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651		G	151262630	-	G	151262629	6	5	73	0	1	1	1	0	0	0	0	0	18107	304	11	0		0	ZNF687	1	151262629	IGR	INS	-	TCGA-CC-A7IH-01A-11D-A33K-10	1360188	151262629	97987992	37	9363										
TCHH	7062	hgsc.bcm.edu	37	chr1	152081242	152081242	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctcctccaggaattttctgTcacgctcttggcggtgcagc	10	14	3	0	rs71582212		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:152081242T>C	ENST00000368804.1	-	2	4450	c.4451A>G	c.(4450-4452)gAc>gGc	p.D1484G		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1484	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAATTTTCTGTCACGCTCTTG	0.552																																					p.D1484G		Atlas-SNP	.											.	TCHH	275	.	0			c.A4451G						.						96	95	95					1																	152081242		1896	4105	6001	SO:0001583	missense	7062	exon3			TTTCTGTCACGCT	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.4451A>G	chr1.hg19:g.152081242T>C	ENSP00000357794:p.Asp1484Gly	147.0	0.0		246.0	49.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	N	10.48	1.360690	0.24598	.	.	ENSG00000159450	ENST00000368804	T	0.08807	3.05	3.51	3.51	0.40186	.	.	.	.	.	T	0.06096	0.0158	L	0.61218	1.895	0.09310	N	1	P	0.51791	0.948	P	0.48189	0.57	T	0.24657	-1.0154	9	0.33141	T	0.24	.	10.0217	0.42046	0.0:0.0:0.0:1.0	.	1484	Q07283	TRHY_HUMAN	G	1484	ENSP00000357794:D1484G	ENSP00000357794:D1484G	D	-	2	0	TCHH	150347866	0.001000	0.12720	0.011000	0.14972	0.044000	0.14063	0.426000	0.21363	1.461000	0.47929	0.164000	0.16699	GAC	.	.		0.552	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152081242	T	C	152081242	3	2	73	1	0	0	0	0	1	0	0	0	15715	1667	58	2	1384	2	TCHH	1	152081242	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	818613	152081242	97169379	38	9364										
FLG	2312	hgsc.bcm.edu	37	chr1	152280562	152280562	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctcctgagcagatccatgaTggtttctggacgcagaccca	11	12	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:152280562T>A	ENST00000368799.1	-	3	6835	c.6800A>T	c.(6799-6801)cAt>cTt	p.H2267L	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2267	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGATCCATGATGGTTTCTGGA	0.582									Ichthyosis																												p.H2267L		Atlas-SNP	.											.	FLG	900	.	0			c.A6800T						.						193	193	193					1																	152280562		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCATGATGGTTTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6800A>T	chr1.hg19:g.152280562T>A	ENSP00000357789:p.His2267Leu	245.0	0.0		367.0	71.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	T	3.954	-0.011622	0.07727	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.02140	4.43	3.41	-0.55	0.11825	.	.	.	.	.	T	0.00936	0.0031	M	0.72118	2.19	0.09310	N	1	B	0.29432	0.244	B	0.21151	0.033	T	0.39583	-0.9607	9	0.46703	T	0.11	.	5.4479	0.16546	0.0:0.1064:0.3284:0.5652	.	2267	P20930	FILA_HUMAN	L	2267;177	ENSP00000357789:H2267L	ENSP00000271820:H177L	H	-	2	0	FLG	150547186	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.175000	0.09825	-0.615000	0.05679	-2.091000	0.00372	CAT	.	.		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152280562	T	A	152280562	3	1	73	1	0	0	0	0	1	0	0	0	5930	1464	51	4	5389	4	FLG	1	152280562	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	199320	152280562	96970059	39	9365										
FLG2	388698	hgsc.bcm.edu	37	chr1	152329823	152329823	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acatttcacagttccccttgAgtgcccagaactatatccat	5	13	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:152329823A>T	ENST00000388718.5	-	3	511	c.439T>A	c.(439-441)Tca>Aca	p.S147T	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	147	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTTCCCCTTGAGTGCCCAGAA	0.463																																					p.S147T		Atlas-SNP	.											.	FLG2	431	.	0			c.T439A						.						235	232	233					1																	152329823		2203	4300	6503	SO:0001583	missense	388698	exon3			CCCTTGAGTGCCC	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.439T>A	chr1.hg19:g.152329823A>T	ENSP00000373370:p.Ser147Thr	266.0	0.0		388.0	272.0	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	hg19	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	A	1.564	-0.535914	0.04082	.	.	ENSG00000143520	ENST00000388718	T	0.00768	5.72	5.62	5.62	0.85841	.	.	.	.	.	T	0.00815	0.0027	L	0.46157	1.445	0.09310	N	1	D	0.61080	0.989	P	0.60068	0.868	T	0.58842	-0.7565	9	0.13470	T	0.59	0.2772	12.2215	0.54437	1.0:0.0:0.0:0.0	.	147	Q5D862	FILA2_HUMAN	T	147	ENSP00000373370:S147T	ENSP00000373370:S147T	S	-	1	0	FLG2	150596447	0.003000	0.15002	0.144000	0.22314	0.106000	0.19336	1.894000	0.39768	2.148000	0.66965	0.455000	0.32223	TCA	.	.		0.463	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152329823	A	T	152329823	3	4	73	1	0	0	0	0	1	0	0	0	5931	304	11	4	6740	4	FLG2	1	152329823	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	49261	152329823	96920798	40	9366										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842221	154842222	+	In_Frame_Ins	INS	-	-	CTGCTGCTGCTGCTGCTA													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgctgctgctgctgctgctgINSctgctgctgctgctgctgct							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:154842221_154842222insCTGCTGCTGCTGCTGCTA	ENST00000271915.4	-	1	534_535	c.219_220insTAGCAGCAGCAGCAGCAG	c.(217-222)cagcag>cagTAGCAGCAGCAGCAGCAGcag	p.72_73insQ*QQQQ	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	72	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	tgctgctgctgctgctgctgct	0.708																																					p.Q74delinsX		Atlas-Indel,Pindel	.											.	KCNN3	141	.	0			c.220_221insTAGCAGCAGCAGCAGCAG						.																																			SO:0001652	inframe_insertion	3782	exon1			.	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.219_220insTAGCAGCAGCAGCAGCAG	chr1.hg19:g.154842221_154842222insCTGCTGCTGCTGCTGCTA	ENSP00000271915:p.Gln72_Gln73insGln*GlnGlnGlnGln	73.0	0.0		136.0	41.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	In_Frame_Ins	INS	ENST00000271915.4	hg19	CCDS30880.1																																																																																			.	.		0.708	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		CTGCTGCTGCTGCTGCTA	154842222	-	CTGCTGCTGCTGCTGCTA	154842221	7	5	73	1	0	1	1	0	0	0	0	0	8089	1328	46	0	2029	0	KCNN3	1	154842221	In_Frame_Ins	INS	-	TCGA-CC-A7IH-01A-11D-A33K-10	2512398	154842221	94408400	41	9367										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158632708	158632708	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tatttcttcaaaatatgcagCcaggtctgtaaggatatcca	7	8	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:158632708C>G	ENST00000368147.4	-	17	2428	c.2248G>C	c.(2248-2250)Gct>Cct	p.A750P		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	750					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AAATATGCAGCCAGGTCTGTA	0.433																																					p.A750P		Atlas-SNP	.											.	SPTA1	720	.	0			c.G2248C						.						75	73	74					1																	158632708		1871	4092	5963	SO:0001583	missense	6708	exon17			ATGCAGCCAGGTC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2248G>C	chr1.hg19:g.158632708C>G	ENSP00000357129:p.Ala750Pro	148.0	0.0		209.0	10.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.640181	0.67244	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.42131	0.98;0.98	4.41	4.41	0.53225	.	0.267990	0.19856	N	0.104525	T	0.64091	0.2567	M	0.89904	3.07	0.51767	D	0.999932	D	0.76494	0.999	D	0.76575	0.988	T	0.72268	-0.4343	10	0.87932	D	0	.	13.8662	0.63590	0.0:1.0:0.0:0.0	.	750	P02549	SPTA1_HUMAN	P	750	ENSP00000357130:A750P;ENSP00000357129:A750P	ENSP00000357129:A750P	A	-	1	0	SPTA1	156899332	1.000000	0.71417	0.383000	0.26132	0.606000	0.37113	6.820000	0.75267	2.270000	0.75569	0.655000	0.94253	GCT	.	.		0.433	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		G	158632708	C	G	158632708	3	3	73	1	0	0	0	0	1	0	0	0	15131	739	26	4	5155	4	SPTA1	1	158632708	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	3790487	158632708	90617913	42	9368										
DARC	2532	hgsc.bcm.edu	37	chr1	159176146	159176146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tacgcccctgctcctcgcccTattctgccaccaggccaccc	6	22	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:159176146T>C	ENST00000368122.2	+	2	1596	c.917T>C	c.(916-918)cTa>cCa	p.L306P	DARC_ENST00000537147.1_Missense_Mutation_p.L306P|CTA-134P22.2_ENST00000609696.1_RNA|DARC_ENST00000368121.2_Missense_Mutation_p.L308P	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		306					chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.L308Q(1)		large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					CTCCTCGCCCTATTCTGCCAC	0.587																																					p.L308P		Atlas-SNP	.											DARC_ENST00000368121,NS,carcinoma,0,1	DARC	76	.	1	Substitution - Missense(1)	lung(1)	c.T923C						.						190	205	200					1																	159176146		2203	4300	6503	SO:0001583	missense	2532	exon1			TCGCCCTATTCTG																												ENST00000368122.2:c.917T>C	chr1.hg19:g.159176146T>C	ENSP00000357104:p.Leu306Pro	104.0	0.0		160.0	37.0	NM_001122951	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Missense_Mutation	SNP	ENST00000368122.2	hg19	CCDS1183.1	.	.	.	.	.	.	.	.	.	.	T	15.15	2.747346	0.49257	.	.	ENSG00000213088	ENST00000368122;ENST00000537147;ENST00000359381;ENST00000368121	T;T;T	0.49720	0.77;0.77;0.77	5.4	-0.0751	0.13728	.	0.547088	0.12038	U	0.505302	T	0.34164	0.0888	L	0.43923	1.385	0.19945	N	0.999943	D;D	0.62365	0.991;0.991	P;P	0.59643	0.861;0.861	T	0.09773	-1.0659	10	0.87932	D	0	-16.7268	5.3877	0.16227	0.2878:0.0:0.2979:0.4143	.	308;306	Q5Y7A1;Q16570	.;DUFFY_HUMAN	P	306;306;306;308	ENSP00000357104:L306P;ENSP00000441985:L306P;ENSP00000357103:L308P	ENSP00000352341:L306P	L	+	2	0	DARC	157442770	0.001000	0.12720	0.012000	0.15200	0.575000	0.36095	0.422000	0.21296	0.084000	0.17077	0.533000	0.62120	CTA	.	.		0.587	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2			C	159176146	T	C	159176146	3	2	73	1	0	0	0	0	1	0	0	0	4242	1522	53	2	950	2	DARC	1	159176146	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	543438	159176146	90074475	43	9369										
NCSTN	23385	hgsc.bcm.edu	37	chr1	160314603	160314606	+	Frame_Shift_Del	DEL	GATT	GATT	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgctcaacgccactcatcaGattggctgccagtgtgagtt							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	GATT	GATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:160314603_160314606delGATT	ENST00000294785.5	+	2	302_305	c.177_180delGATT	c.(175-180)cagattfs	p.QI59fs	COPA_ENST00000241704.7_5'Flank|NCSTN_ENST00000368063.1_Frame_Shift_Del_p.QI39fs|NCSTN_ENST00000535857.1_Frame_Shift_Del_p.QI59fs|NCSTN_ENST00000392212.4_Frame_Shift_Del_p.QI39fs|COPA_ENST00000368069.3_5'Flank	NM_015331.2	NP_056146.1	Q92542	NICA_HUMAN	nicastrin	59					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2)	34	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CCACTCATCAGATTGGCTGCCAGT	0.451																																					p.59_60del		Atlas-Indel,Pindel	.											.	NCSTN	64	.	0			c.176_179del						.																																			SO:0001589	frameshift_variant	23385	exon2			.	AF240468	CCDS1203.1	1q22-q23	2014-09-17			ENSG00000162736	ENSG00000162736			17091	protein-coding gene	gene with protein product		605254				9039502, 10993067	Standard	XM_005245053		Approved	KIAA0253, APH2	uc001fvx.3	Q92542	OTTHUMG00000033110	ENST00000294785.5:c.177_180delGATT	chr1.hg19:g.160314603_160314606delGATT	ENSP00000294785:p.Gln59fs	122.0	0.0		180.0	116.0	NM_015331	Q5T207|Q5T208|Q86VV5	Frame_Shift_Del	DEL	ENST00000294785.5	hg19	CCDS1203.1																																																																																			.	.		0.451	NCSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080622.1	NM_015331		-	160314606	GATT	-	160314603	7	5	73	1	0	1	0	1	0	0	0	0	10250	933	33	0	183	0	NCSTN	1	160314603	Frame_Shift_Del	DEL	GATT	TCGA-CC-A7IH-01A-11D-A33K-10	1138457	160314603	88936018	44	9370										
LY9	4063	hgsc.bcm.edu	37	chr1	160784465	160784465	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gaagatcagccagctgaagaTagaggacgccggcccctacc	12	13	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:160784465T>C	ENST00000263285.6	+	4	1016	c.986T>C	c.(985-987)aTa>aCa	p.I329T	LY9_ENST00000368037.5_Missense_Mutation_p.I329T|LY9_ENST00000368040.1_5'UTR|LY9_ENST00000341032.4_Missense_Mutation_p.I329T|LY9_ENST00000368041.2_Missense_Mutation_p.I289T|LY9_ENST00000392203.4_Missense_Mutation_p.I329T			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9	329	Ig-like V-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			CAGCTGAAGATAGAGGACGCC	0.577																																					p.I329T		Atlas-SNP	.											.	LY9	115	.	0			c.T986C						.						64	58	60					1																	160784465		2203	4300	6503	SO:0001583	missense	4063	exon4			TGAAGATAGAGGA	L42621	CCDS30916.1, CCDS30917.1, CCDS65695.1, CCDS65696.1	1q23.3	2013-01-11			ENSG00000122224	ENSG00000122224		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6730	protein-coding gene	gene with protein product		600684				8537117, 7797269	Standard	NM_001261457		Approved	CD229, mLY9, SLAMF3, hly9	uc001fwu.4	Q9HBG7	OTTHUMG00000024007	ENST00000263285.6:c.986T>C	chr1.hg19:g.160784465T>C	ENSP00000263285:p.Ile329Thr	164.0	1.0		265.0	163.0	NM_001261457	A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Missense_Mutation	SNP	ENST00000263285.6	hg19	CCDS30916.1	.	.	.	.	.	.	.	.	.	.	T	9.851	1.193695	0.22037	.	.	ENSG00000122224	ENST00000368041;ENST00000341032;ENST00000263285;ENST00000542780;ENST00000392203;ENST00000368037;ENST00000368036	T;T	0.01505	4.82;4.82	3.71	1.24	0.21308	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00468	0.0015	N	0.19112	0.55	0.18873	N	0.999982	P;P;B;P;P;P	0.43231	0.665;0.665;0.001;0.801;0.774;0.665	B;B;B;B;B;B	0.37780	0.119;0.119;0.001;0.258;0.236;0.119	T	0.49341	-0.8950	9	0.72032	D	0.01	-3.3458	4.1983	0.10453	0.0:0.1164:0.2068:0.6769	.	329;289;289;329;329;329	B4E0J5;Q5VYH7;Q5VYH9;E7EME5;Q9HBG7-2;Q9HBG7	.;.;.;.;.;LY9_HUMAN	T	329;329;329;329;289;289;231	ENSP00000342921:I329T;ENSP00000263285:I329T	ENSP00000263285:I329T	I	+	2	0	LY9	159051089	0.948000	0.32251	0.011000	0.14972	0.016000	0.09150	0.329000	0.19698	0.102000	0.17638	0.460000	0.39030	ATA	.	.		0.577	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348		C	160784465	T	C	160784465	3	2	73	1	0	0	0	0	1	0	0	0	9110	1406	49	2	1132	2	LY9	1	160784465	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	469862	160784465	88466156	45	9371										
FCGR2A	2212	hgsc.bcm.edu	37	chr1	161479767	161479767	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttggatcccaccttctccatCccacaagcaaaccacagtca	4	17	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:161479767C>T	ENST00000271450.6	+	4	560	c.522C>T	c.(520-522)atC>atT	p.I174I	FCGR2A_ENST00000367972.4_Silent_p.I173I	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	174	Ig-like C2-type 2.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CCTTCTCCATCCCACAAGCAA	0.498																																					p.I174I		Atlas-SNP	.											.	FCGR2A	38	.	0			c.C522T						.						137	120	126					1																	161479767		2203	4300	6503	SO:0001819	synonymous_variant	2212	exon4			CTCCATCCCACAA	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3616	protein-coding gene	gene with protein product	"Immunoglobulin G Fc receptor II"	146790	"Fc fragment of IgG, low affinity IIa, receptor for (CD32)"	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.522C>T	chr1.hg19:g.161479767C>T		853.0	1.0		1276.0	240.0	NM_001136219	Q8WUN1|Q8WW64	Silent	SNP	ENST00000271450.6	hg19	CCDS44264.1																																																																																			.	.		0.498	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642		T	161479767	C	T	161479767	2	4	73	1	0	0	0	0	0	0	0	1	5789	845	30	3		3	FCGR2A	1	161479767	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	695302	161479767	87770854	46	9372										
METTL13	51603	hgsc.bcm.edu	37	chr1	171753199	171753199	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtgggcggtcgctatctctGcatctccctggctcaggctc	13	14	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:171753199G>T	ENST00000361735.3	+	2	739	c.473G>T	c.(472-474)tGc>tTc	p.C158F	METTL13_ENST00000458517.1_Missense_Mutation_p.C157F|METTL13_ENST00000367737.5_Intron|METTL13_ENST00000362019.3_Missense_Mutation_p.C72F	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	158							methyltransferase activity (GO:0008168)			breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						CGCTATCTCTGCATCTCCCTG	0.597																																					p.C158F		Atlas-SNP	.											.	METTL13	67	.	0			c.G473T						.						86	75	78					1																	171753199		2203	4300	6503	SO:0001583	missense	51603	exon2			ATCTCTGCATCTC	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"KIAA0859"	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.473G>T	chr1.hg19:g.171753199G>T	ENSP00000354920:p.Cys158Phe	112.0	0.0		190.0	49.0	NM_015935	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Missense_Mutation	SNP	ENST00000361735.3	hg19	CCDS1299.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999889	0.74818	.	.	ENSG00000010165	ENST00000458517;ENST00000362019;ENST00000361735;ENST00000367736;ENST00000341850	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.49287	0.1548	L	0.39692	1.235	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.77557	0.984;0.99	T	0.46992	-0.9151	10	0.48119	T	0.1	-10.6217	18.6244	0.91332	0.0:0.0:1.0:0.0	.	157;158	B4E2X3;Q8N6R0	.;MTL13_HUMAN	F	157;72;158;75;72	ENSP00000401955:C157F;ENSP00000355393:C72F;ENSP00000354920:C158F;ENSP00000356710:C75F	ENSP00000341732:C72F	C	+	2	0	METTL13	170019822	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.443000	0.80521	2.454000	0.82982	0.655000	0.94253	TGC	.	.		0.597	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955		T	171753199	G	T	171753199	3	4	73	1	0	0	0	0	1	0	0	0	9506	1319	46	3	479	3	METTL13	1	171753199	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	10273432	171753199	77497422	47	9373										
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173526479	173526479	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgagacatgatctttcctacCatttgtggtacttccacttt	6	10	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:173526479C>A	ENST00000367714.3	-	10	1637	c.1215G>T	c.(1213-1215)atG>atT	p.M405I	SLC9C2_ENST00000536496.1_Splice_Site_p.M303I|RP3-436N22.3_ENST00000431459.1_RNA|SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	405					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TCTTTCCTACCATTTGTGGTA	0.353																																					p.M405I		Atlas-SNP	.											.	.	.	.	0			c.G1215T						.						93	101	98					1																	173526479		2203	4300	6503	SO:0001630	splice_region_variant	284525	exon10			TCCTACCATTTGT	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1215+1G>T	chr1.hg19:g.173526479C>A		262.0	0.0		445.0	95.0	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	hg19	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	C	0.767	-0.767252	0.02974	.	.	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.21361	2.01;2.01	5.26	5.26	0.73747	Cation/H+ exchanger (1);	0.478827	0.21379	N	0.075506	T	0.04861	0.0131	N	0.08118	0	0.29323	N	0.867211	B	0.29862	0.259	B	0.31946	0.138	T	0.30534	-0.9975	9	.	.	.	-11.0681	14.7399	0.69445	0.0:1.0:0.0:0.0	.	405	Q5TAH2	S9A11_HUMAN	I	405;303	ENSP00000356687:M405I;ENSP00000445437:M303I	.	M	-	3	0	SLC9A11	171793102	0.996000	0.38824	0.980000	0.43619	0.142000	0.21351	3.394000	0.52551	2.626000	0.88956	0.585000	0.79938	ATG	.	.		0.353	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	Missense_Mutation	A	173526479	C	A	173526479	5	1	73	1	0	0	0	0	0	0	1	0	14726	608	21	3	2235	3	SLC9A11	1	173526479	Splice_Site	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1773280	173526479	75724142	48	9374										
ZBTB37	84614	hgsc.bcm.edu	37	chr1	173842760	173842760	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggaggaattgctactgtgtAtgaatagaaaataatgaaaa	10	2	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:173842760A>T	ENST00000367701.5	+	3	1214				ZBTB37_ENST00000432989.1_Missense_Mutation_p.Y360F|ZBTB37_ENST00000427304.1_Intron|ZBTB37_ENST00000367702.1_Missense_Mutation_p.Y360F|ZBTB37_ENST00000367704.1_Intron			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						GCTACTGTGTATGAATAGAAA	0.408																																					p.Y360F		Atlas-SNP	.											.	ZBTB37	38	.	0			c.A1079T						.						76	74	75					1																	173842760		2203	4300	6503	SO:0001627	intron_variant	84614	exon4			CTGTGTATGAATA	AK057310	CCDS1312.1, CCDS44278.1	1q24.2	2013-01-08			ENSG00000185278	ENSG00000185278		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	28365	protein-coding gene	gene with protein product						12477932	Standard	NM_032522		Approved	MGC2629, ZNF908	uc009wwp.1	Q5TC79	OTTHUMG00000037274	ENST00000367701.5:c.1023+56A>T	chr1.hg19:g.173842760A>T		130.0	0.0		234.0	38.0	NM_032522	Q5TC80|Q96M87|Q9BQ88	Missense_Mutation	SNP	ENST00000367701.5	hg19	CCDS44278.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.791859	0.31685	.	.	ENSG00000185278	ENST00000432989;ENST00000367702	T;T	0.75050	-0.9;-0.9	3.64	-1.33	0.09172	.	.	.	.	.	T	0.29355	0.0731	.	.	.	0.09310	N	1	B	0.15141	0.012	B	0.14023	0.01	T	0.15235	-1.0444	7	.	.	.	.	3.9418	0.09331	0.3697:0.3753:0.2551:0.0	.	360	Q5TC79-2	.	F	360	ENSP00000409408:Y360F;ENSP00000356675:Y360F	.	Y	+	2	0	ZBTB37	172109383	0.918000	0.31147	0.002000	0.10522	0.035000	0.12851	0.326000	0.19646	-0.241000	0.09681	-0.250000	0.11733	TAT	.	.		0.408	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522		T	173842760	A	T	173842760	1	4	73	0	1	0	0	0	0	0	0	0	17553	449	16	4		4	ZBTB37	1	173842760	Intron	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	316281	173842760	75407861	49	9375										
ASTN1	460	hgsc.bcm.edu	37	chr1	176927577	176927577	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtggaatcacaaagctcttgCtgaggggcaaccacatgccc	11	12	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:176927577C>T	ENST00000367654.3	-	10	1875	c.1664G>A	c.(1663-1665)aGc>aAc	p.S555N	ASTN1_ENST00000424564.2_Missense_Mutation_p.S547N|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000367657.3_Missense_Mutation_p.S547N|ASTN1_ENST00000361833.2_Missense_Mutation_p.S547N	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	555					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						AAAGCTCTTGCTGAGGGGCAA	0.562																																					p.S547N		Atlas-SNP	.											.	ASTN1	314	.	0			c.G1640A						.						96	73	81					1																	176927577		2203	4300	6503	SO:0001583	missense	460	exon10			CTCTTGCTGAGGG	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1664G>A	chr1.hg19:g.176927577C>T	ENSP00000356626:p.Ser555Asn	206.0	0.0		278.0	72.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.352254	0.95830	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.21932	1.98;2.4;2.39;1.99	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.36936	0.0985	L	0.29908	0.895	0.80722	D	1	D;D;D	0.67145	0.996;0.989;0.989	D;D;D	0.75484	0.986;0.979;0.979	T	0.07177	-1.0786	10	0.49607	T	0.09	-31.6642	18.9852	0.92766	0.0:1.0:0.0:0.0	.	555;547;547	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	N	547;547;555;547;547	ENSP00000356629:S547N;ENSP00000354536:S547N;ENSP00000356626:S555N;ENSP00000395041:S547N	ENSP00000354536:S547N	S	-	2	0	ASTN1	175194200	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.695000	0.84257	2.572000	0.86782	0.655000	0.94253	AGC	.	.		0.562	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		T	176927577	C	T	176927577	3	4	73	1	0	0	0	0	1	0	0	0	1064	797	28	3	2304	3	ASTN1	1	176927577	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	3084817	176927577	72323044	50	9376										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177245534	177245534	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcctgctgcagatccaggacTcctgggccactcacaaccgg	11	16	1	1	rs368629885		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:177245534T>C	ENST00000361539.4	+	6	1288	c.976T>C	c.(976-978)Tcc>Ccc	p.S326P	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	326					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											GATCCAGGACTCCTGGGCCAC	0.567																																					p.S326P		Atlas-SNP	.											.	FAM5B	191	.	0			c.T976C						.						63	55	58					1																	177245534		2203	4300	6503	SO:0001583	missense	57795	exon6			CAGGACTCCTGGG		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.976T>C	chr1.hg19:g.177245534T>C	ENSP00000354481:p.Ser326Pro	495.0	0.0		691.0	69.0	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	hg19	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.871574	0.51695	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.15256	2.44	6.07	0.802	0.18686	.	0.390200	0.28209	N	0.016191	T	0.13114	0.0318	L	0.39898	1.24	0.36544	D	0.871453	B;P;B	0.37038	0.256;0.579;0.037	B;B;B	0.38755	0.189;0.281;0.029	T	0.12708	-1.0537	10	0.72032	D	0.01	-17.6413	6.0285	0.19667	0.3365:0.0:0.3715:0.2919	.	76;221;326	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	P	76;326	ENSP00000354481:S326P	ENSP00000354481:S326P	S	+	1	0	FAM5B	175512157	0.029000	0.19370	1.000000	0.80357	0.994000	0.84299	0.314000	0.19432	0.475000	0.27415	0.533000	0.62120	TCC	.	.		0.567	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		C	177245534	T	C	177245534	3	2	73	1	0	0	0	0	1	0	0	0	5601	1551	54	2	994	2	FAM5B	1	177245534	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	317957	177245534	72005087	51	9377										
FAM163A	148753	hgsc.bcm.edu	37	chr1	179783192	179783192	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggaggcgagaggctctccttTgctcccacatactacaaaga	10	12	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:179783192T>G	ENST00000341785.4	+	5	768	c.372T>G	c.(370-372)ttT>ttG	p.F124L	RP11-12M5.3_ENST00000453051.1_RNA|RP11-12M5.3_ENST00000415218.1_RNA	NM_173509.2	NP_775780.1	Q96GL9	F163A_HUMAN	family with sequence similarity 163, member A	124						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)	15						GGCTCTCCTTTGCTCCCACAT	0.617																																					p.F124L		Atlas-SNP	.											.	FAM163A	24	.	0			c.T372G						.						64	65	65					1																	179783192		2203	4300	6503	SO:0001583	missense	148753	exon5			CTCCTTTGCTCCC	BC009382	CCDS1333.1	1q25.2	2008-06-05	2008-06-05	2008-06-05	ENSG00000143340	ENSG00000143340			28274	protein-coding gene	gene with protein product		611727	"chromosome 1 open reading frame 76"	C1orf76		12477932	Standard	NM_173509		Approved	MGC16664	uc001gnj.3	Q96GL9	OTTHUMG00000035262	ENST00000341785.4:c.372T>G	chr1.hg19:g.179783192T>G	ENSP00000354891:p.Phe124Leu	229.0	0.0		356.0	37.0	NM_173509	A8K8R7	Missense_Mutation	SNP	ENST00000341785.4	hg19	CCDS1333.1	.	.	.	.	.	.	.	.	.	.	T	13.37	2.217662	0.39201	.	.	ENSG00000143340	ENST00000341785	.	.	.	4.57	-4.02	0.04034	.	0.134260	0.51477	N	0.000085	T	0.23210	0.0561	N	0.22421	0.69	0.28849	N	0.896145	B	0.02656	0.0	B	0.06405	0.002	T	0.05053	-1.0909	9	0.66056	D	0.02	-4.7195	9.1058	0.36696	0.0:0.7175:0.1263:0.1563	.	124	Q96GL9	F163A_HUMAN	L	124	.	ENSP00000354891:F124L	F	+	3	2	FAM163A	178049815	0.988000	0.35896	0.071000	0.20095	0.190000	0.23558	0.344000	0.19962	-1.001000	0.03434	0.460000	0.39030	TTT	.	.		0.617	FAM163A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085300.1	NM_173509		G	179783192	T	G	179783192	3	3	73	1	0	0	0	0	1	0	0	0	5481	1809	63	5	378	5	FAM163A	1	179783192	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2537658	179783192	69467429	52	9378										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181753861	181753861	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	accctagccatctggcctcaCctatcccagaagatgctgga	8	15	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:181753861C>A	ENST00000367573.2	+	41	5535	c.5535C>A	c.(5533-5535)caC>caA	p.H1845Q	CACNA1E_ENST00000358338.5_Missense_Mutation_p.H1777Q|CACNA1E_ENST00000360108.3_Missense_Mutation_p.H1826Q|CACNA1E_ENST00000367570.1_Missense_Mutation_p.H1845Q|CACNA1E_ENST00000526775.1_Missense_Mutation_p.H1826Q|CACNA1E_ENST00000367567.4_Missense_Mutation_p.H1452Q|CACNA1E_ENST00000357570.5_Missense_Mutation_p.H1796Q	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1845					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TCTGGCCTCACCTATCCCAGA	0.488																																					p.H1845Q		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C5535A						.						56	62	60					1																	181753861		1953	4138	6091	SO:0001583	missense	777	exon41			GCCTCACCTATCC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5535C>A	chr1.hg19:g.181753861C>A	ENSP00000356545:p.His1845Gln	152.0	0.0		202.0	42.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.280518	0.59758	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	T;T;T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02;0.02;0.02	5.57	5.57	0.84162	.	0.244272	0.47093	D	0.000250	T	0.46639	0.1403	N	0.08118	0	0.48511	D	0.999666	B;P	0.37276	0.018;0.589	B;B	0.41619	0.024;0.361	T	0.53711	-0.8400	10	0.54805	T	0.06	.	12.5104	0.56003	0.0:0.923:0.0:0.077	.	1826;1845	Q15878-2;Q15878-3	.;.	Q	1845;1826;1796;1777;1452;1826;1845	ENSP00000356542:H1845Q;ENSP00000434814:H1826Q;ENSP00000350183:H1796Q;ENSP00000351101:H1777Q;ENSP00000356539:H1452Q;ENSP00000353222:H1826Q;ENSP00000356545:H1845Q	ENSP00000350183:H1796Q	H	+	3	2	CACNA1E	180020484	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.902000	0.39848	2.610000	0.88304	0.563000	0.77884	CAC	.	.		0.488	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181753861	C	A	181753861	3	1	73	1	0	0	0	0	1	0	0	0	2544	506	18	3	5697	3	CACNA1E	1	181753861	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1970669	181753861	67496760	53	9379										
DHX9	1660	hgsc.bcm.edu	37	chr1	182836133	182836133	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttagaagcaggcattcgaggAatcagtcatgtaattgtaga	11	5	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:182836133A>T	ENST00000367549.3	+	14	1622	c.1512A>T	c.(1510-1512)ggA>ggT	p.G504G		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	504	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						GCATTCGAGGAATCAGTCATG	0.308																																					p.G504G	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.A1512T						.						176	159	164					1																	182836133		1824	4081	5905	SO:0001819	synonymous_variant	1660	exon14			TCGAGGAATCAGT	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.1512A>T	chr1.hg19:g.182836133A>T		117.0	0.0		167.0	35.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Silent	SNP	ENST00000367549.3	hg19	CCDS41444.1																																																																																			.	.		0.308	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		T	182836133	A	T	182836133	2	4	73	1	0	0	0	0	0	0	0	1	4518	233	9	4		4	DHX9	1	182836133	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1082272	182836133	66414488	54	9380										
GLT25D2	23127	hgsc.bcm.edu	37	chr1	183908097	183908097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccggctggcctgtgtagtgcGtagggtagatgagcaagggt	18	7	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:183908097G>A	ENST00000361927.4	-	12	2050	c.1679C>T	c.(1678-1680)aCg>aTg	p.T560M	COLGALT2_ENST00000486375.1_Intron|COLGALT2_ENST00000546159.1_Intron|COLGALT2_ENST00000367520.3_Missense_Mutation_p.T297M|COLGALT2_ENST00000367521.1_Missense_Mutation_p.T168M	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	560					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)	p.T560M(1)									TGTGTAGTGCGTAGGGTAGAT	0.557																																					p.T560M		Atlas-SNP	.											GLT25D2,colon,carcinoma,0,2	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1679T						.						124	117	119					1																	183908097		2203	4300	6503	SO:0001583	missense	23127	exon12			TAGTGCGTAGGGT	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.1679C>T	chr1.hg19:g.183908097G>A	ENSP00000354960:p.Thr560Met	277.0	2.0		472.0	321.0	NM_015101	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	hg19	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704101	0.88924	.	.	ENSG00000198756	ENST00000361927;ENST00000367521;ENST00000367520	T	0.79940	-1.32	5.21	5.21	0.72293	.	0.049946	0.85682	D	0.000000	D	0.90707	0.7084	M	0.84219	2.685	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	D	0.92015	0.5621	10	0.87932	D	0	.	18.7471	0.91797	0.0:0.0:1.0:0.0	.	560;297	Q8IYK4;Q5SXQ3	GT252_HUMAN;.	M	560;168;297	ENSP00000354960:T560M	ENSP00000354960:T560M	T	-	2	0	GLT25D2	182174720	1.000000	0.71417	0.919000	0.36401	0.853000	0.48598	7.694000	0.84235	2.411000	0.81874	0.563000	0.77884	ACG	.	.		0.557	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		A	183908097	G	A	183908097	3	1	73	1	0	0	0	0	1	0	0	0	6475	1145	40	1	205	1	GLT25D2	1	183908097	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1071964	183908097	65342524	55	9381										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190067337	190067337	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tttacacggtctctgatctcTagtagttgcaaaagtgctga	9	8	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:190067337T>A	ENST00000367462.3	-	8	2343	c.2112A>T	c.(2110-2112)ctA>ctT	p.L704L	BRINP3_ENST00000534846.1_Silent_p.L602L	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	704					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											CTCTGATCTCTAGTAGTTGCA	0.478																																					p.L704L		Atlas-SNP	.											.	FAM5C	343	.	0			c.A2112T						.						105	102	103					1																	190067337		2203	4300	6503	SO:0001819	synonymous_variant	339479	exon8			GATCTCTAGTAGT	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.2112A>T	chr1.hg19:g.190067337T>A		147.0	0.0		303.0	67.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Silent	SNP	ENST00000367462.3	hg19	CCDS1373.1																																																																																			.	.		0.478	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		A	190067337	T	A	190067337	2	1	73	1	0	0	0	0	0	0	0	1	5602	1509	53	4		4	FAM5C	1	190067337	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	6159240	190067337	59183284	56	9382										
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200817745	200817745	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	actggaattcacgttccttcAgaagatattcctgaaactat	6	9	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:200817745A>T	ENST00000236925.4	+	12	1930	c.1881A>T	c.(1879-1881)tcA>tcT	p.S627S	CAMSAP2_ENST00000413307.2_Silent_p.S600S|CAMSAP2_ENST00000358823.2_Silent_p.S616S			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	627					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										ACGTTCCTTCAGAAGATATTC	0.378																																					p.S616S		Atlas-SNP	.											.	.	.	.	0			c.A1848T						.						113	109	110					1																	200817745		2203	4300	6503	SO:0001819	synonymous_variant	23271	exon11			TCCTTCAGAAGAT	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.1881A>T	chr1.hg19:g.200817745A>T		80.0	0.0		219.0	42.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Silent	SNP	ENST00000236925.4	hg19																																																																																				.	.		0.378	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		T	200817745	A	T	200817745	2	4	73	1	0	0	0	0	0	0	0	1	2614	175	7	4		4	CAMSAP1L1	1	200817745	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	10750408	200817745	48432876	57	9383										
SYT2	127833	hgsc.bcm.edu	37	chr1	202571584	202571584	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcatatttcttcttcttgtcAggaaggaggaagaccttgac	9	8	5	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:202571584A>T	ENST00000367267.1	-	5	747	c.555T>A	c.(553-555)ccT>ccA	p.P185P	RP11-569A11.1_ENST00000428573.1_RNA|SYT2_ENST00000367268.4_Silent_p.P185P	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	185	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000250}.				neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	TCTTCTTGTCAGGAAGGAGGA	0.527																																					p.P185P		Atlas-SNP	.											.	SYT2	51	.	0			c.T555A						.						128	119	122					1																	202571584		2203	4300	6503	SO:0001819	synonymous_variant	127833	exon5			CTTGTCAGGAAGG	AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"Synaptotagmins"	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.555T>A	chr1.hg19:g.202571584A>T		77.0	0.0		132.0	99.0	NM_177402	Q496K5|Q8NBE5	Silent	SNP	ENST00000367267.1	hg19	CCDS1427.1																																																																																			.	.		0.527	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402		T	202571584	A	T	202571584	2	4	73	1	0	0	0	0	0	0	0	1	15489	175	7	4		4	SYT2	1	202571584	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1753839	202571584	46679037	58	9384										
FMOD	2331	hgsc.bcm.edu	37	chr1	203316593	203316593	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acagccgcacatacagcagcTtgggcgccccccggaagtag	12	15	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:203316593T>C	ENST00000354955.4	-	2	1269	c.806A>G	c.(805-807)aAg>aGg	p.K269R	FMOD_ENST00000493296.1_Intron	NM_002023.4	NP_002014.2	Q06828	FMOD_HUMAN	fibromodulin	269					carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor complex assembly (GO:0007181)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	17			BRCA - Breast invasive adenocarcinoma(75;0.171)			ATACAGCAGCTTGGGCGCCCC	0.577																																					p.K269R		Atlas-SNP	.											.	FMOD	49	.	0			c.A806G						.						114	112	112					1																	203316593		2203	4300	6503	SO:0001583	missense	2331	exon2			AGCAGCTTGGGCG	U05291	CCDS30976.1	1q32	2008-02-05			ENSG00000122176	ENSG00000122176		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	3774	protein-coding gene	gene with protein product	"fibromodulin proteoglycan"	600245				7851907	Standard	NM_002023		Approved	SLRR2E	uc001gzr.3	Q06828	OTTHUMG00000035910	ENST00000354955.4:c.806A>G	chr1.hg19:g.203316593T>C	ENSP00000347041:p.Lys269Arg	111.0	0.0		183.0	36.0	NM_002023	Q15331|Q8IV47	Missense_Mutation	SNP	ENST00000354955.4	hg19	CCDS30976.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.137207	0.37728	.	.	ENSG00000122176	ENST00000435105;ENST00000354955	T	0.58060	0.36	5.18	5.18	0.71444	.	0.153803	0.64402	D	0.000020	T	0.32556	0.0833	N	0.12569	0.235	0.39072	D	0.960734	B	0.14012	0.009	B	0.17098	0.017	T	0.19877	-1.0292	10	0.36615	T	0.2	-17.7863	8.5622	0.33518	0.0:0.0867:0.0:0.9133	.	269	Q06828	FMOD_HUMAN	R	256;269	ENSP00000347041:K269R	ENSP00000347041:K269R	K	-	2	0	FMOD	201583216	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.269000	0.51592	1.956000	0.56807	0.533000	0.62120	AAG	.	.		0.577	FMOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087472.1	NM_002023		C	203316593	T	C	203316593	3	2	73	1	0	0	0	0	1	0	0	0	5967	1609	56	2	332	2	FMOD	1	203316593	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	745009	203316593	45934028	59	9385										
AVPR1B	553	hgsc.bcm.edu	37	chr1	206230897	206230897	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctacatgggcttcaacagcCacctgttaccgcggcccctg	9	16	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:206230897C>A	ENST00000367126.4	+	2	1495	c.1030C>A	c.(1030-1032)Cac>Aac	p.H344N		NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	344					activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)|skin(2)	20			BRCA - Breast invasive adenocarcinoma(75;0.0312)		Desmopressin(DB00035)|Terlipressin(DB02638)|Vasopressin(DB00067)	CTTCAACAGCCACCTGTTACC	0.617																																					p.H344N		Atlas-SNP	.											.	AVPR1B	47	.	0			c.C1030A						.						49	43	45					1																	206230897		2203	4300	6503	SO:0001583	missense	553	exon2			AACAGCCACCTGT	D31833	CCDS73015.1	1q32	2014-05-06			ENSG00000198049	ENSG00000198049		"GPCR / Class A : Vasopressin and oxytocin receptors"	896	protein-coding gene	gene with protein product		600264		AVPR3		7929452, 8586456	Standard	NM_000707		Approved		uc001hds.2	P47901	OTTHUMG00000184377	ENST00000367126.4:c.1030C>A	chr1.hg19:g.206230897C>A	ENSP00000356094:p.His344Asn	138.0	0.0		257.0	72.0	NM_000707	B0M0J6|Q5TZ00	Missense_Mutation	SNP	ENST00000367126.4	hg19	CCDS30994.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.543997	0.65198	.	.	ENSG00000198049	ENST00000367126	T	0.35236	1.32	5.6	4.49	0.54785	.	0.528955	0.18918	N	0.127567	T	0.36635	0.0974	L	0.50333	1.59	0.31581	N	0.655118	B	0.24483	0.104	B	0.32805	0.153	T	0.35251	-0.9796	10	0.28530	T	0.3	-31.0318	14.3043	0.66375	0.0:0.9132:0.0:0.0868	.	344	P47901	V1BR_HUMAN	N	344	ENSP00000356094:H344N	ENSP00000356094:H344N	H	+	1	0	AVPR1B	204397520	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.727000	0.61993	2.632000	0.89209	0.563000	0.77884	CAC	.	.		0.617	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707		A	206230897	C	A	206230897	3	1	73	1	0	0	0	0	1	0	0	0	1232	594	21	3	1036	3	AVPR1B	1	206230897	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	2914304	206230897	43019724	60	9386										
CR2	1380	hgsc.bcm.edu	37	chr1	207646133	207646133	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctagaaatcacctgcccaccAccccctgttatctacaatgg	5	16	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:207646133A>T	ENST00000367058.3	+	10	1776	c.1587A>T	c.(1585-1587)ccA>ccT	p.P529P	CR2_ENST00000458541.2_Missense_Mutation_p.T504S|CR2_ENST00000367059.3_Silent_p.P529P|CR2_ENST00000367057.3_Silent_p.P529P	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	529	Sushi 9. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CCTGCCCACCACCCCCTGTTA	0.448																																					p.P529P		Atlas-SNP	.											.	CR2	164	.	0			c.A1587T						.						76	78	78					1																	207646133		2203	4300	6503	SO:0001819	synonymous_variant	1380	exon10			CCCACCACCCCCT	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1587A>T	chr1.hg19:g.207646133A>T		89.0	0.0		135.0	38.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Silent	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	A	6.234	0.411297	0.11812	.	.	ENSG00000117322	ENST00000458541	T	0.31510	1.49	5.75	0.449	0.16619	.	.	.	.	.	T	0.08537	0.0212	.	.	.	0.09310	N	0.999994	.	.	.	.	.	.	T	0.34403	-0.9830	6	0.02654	T	1	.	1.9435	0.03352	0.5071:0.1422:0.0773:0.2734	.	.	.	.	S	504	ENSP00000404222:T504S	ENSP00000404222:T504S	T	+	1	0	CR2	205712756	0.834000	0.29399	1.000000	0.80357	0.987000	0.75469	-0.180000	0.09754	0.095000	0.17434	0.533000	0.62120	ACC	.	.		0.448	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		T	207646133	A	T	207646133	2	4	73	1	0	0	0	0	0	0	0	1	3844	146	6	4		4	CR2	1	207646133	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1415236	207646133	41604488	61	9387										
LAMB3	3914	hgsc.bcm.edu	37	chr1	209789949	209789949	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tccttcaactcagcatacttTtgttttattctctcaaatcc	2	12	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:209789949T>A	ENST00000356082.4	-	22	3383	c.3249A>T	c.(3247-3249)caA>caT	p.Q1083H	LAMB3_ENST00000391911.1_Missense_Mutation_p.Q1083H|LAMB3_ENST00000367030.3_Missense_Mutation_p.Q1083H	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	1083	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		CAGCATACTTTTGTTTTATTC	0.478																																					p.Q1083H		Atlas-SNP	.											.	LAMB3	136	.	0			c.A3249T						.						101	97	99					1																	209789949		2203	4300	6503	SO:0001583	missense	3914	exon22			ATACTTTTGTTTT	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.3249A>T	chr1.hg19:g.209789949T>A	ENSP00000348384:p.Gln1083His	205.0	0.0		281.0	50.0	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	hg19	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.777043	0.31411	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030;ENST00000455193	T;T;T;T	0.65364	1.97;1.97;1.97;-0.15	4.43	0.632	0.17705	.	0.769070	0.11789	U	0.529406	T	0.42131	0.1189	L	0.29908	0.895	0.20764	N	0.999859	P	0.48162	0.906	B	0.38500	0.275	T	0.26985	-1.0087	10	0.45353	T	0.12	.	4.1608	0.10282	0.0:0.1933:0.1757:0.6309	.	1083	Q13751	LAMB3_HUMAN	H	1083;1083;1083;152	ENSP00000375778:Q1083H;ENSP00000348384:Q1083H;ENSP00000355997:Q1083H;ENSP00000398683:Q152H	ENSP00000348384:Q1083H	Q	-	3	2	LAMB3	207856572	0.997000	0.39634	0.133000	0.22050	0.624000	0.37722	0.177000	0.16801	-0.150000	0.11195	-0.486000	0.04755	CAA	.	.		0.478	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		A	209789949	T	A	209789949	3	1	73	1	0	0	0	0	1	0	0	0	8621	1838	64	4	277	4	LAMB3	1	209789949	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2143816	209789949	39460672	62	9388										
C1orf107	27042	hgsc.bcm.edu	37	chr1	210015611	210015611	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atattatttccactcaaagcAtttgatgaatcacatgaacc	4	9	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:210015611A>G	ENST00000491415.2	+	9	1544	c.1487A>G	c.(1486-1488)cAt>cGt	p.H496R		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	496					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						CACTCAAAGCATTTGATGAAT	0.408																																					p.H496R		Atlas-SNP	.											.	DIEXF	97	.	0			c.A1487G						.						79	71	74					1																	210015611		2203	4300	6503	SO:0001630	splice_region_variant	27042	exon9			CAAAGCATTTGAT	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.1486-1A>G	chr1.hg19:g.210015611A>G		93.0	0.0		162.0	44.0	NM_014388	O75992|Q4VY00|Q63HL9	Missense_Mutation	SNP	ENST00000491415.2	hg19	CCDS1493.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.7|23.7	4.442049|4.442049	0.83993|0.83993	.|.	.|.	ENSG00000117597|ENSG00000117597	ENST00000491415|ENST00000457820	T|.	0.38240|.	1.15|.	6.17|6.17	5.03|5.03	0.67393|0.67393	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71558|0.71558	0.3354|0.3354	M|M	0.70595|0.70595	2.14|2.14	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.70699|0.70699	-0.4800|-0.4800	10|5	0.31617|.	T|.	0.26|.	-19.2524|-19.2524	12.8532|12.8532	0.57869|0.57869	0.8777:0.0:0.0:0.1223|0.8777:0.0:0.0:0.1223	.|.	496|.	Q68CQ4|.	DIEXF_HUMAN|.	R|V	496|177	ENSP00000419005:H496R|.	ENSP00000419005:H496R|.	H|I	+|+	2|1	0|0	DIEXF|DIEXF	208082234|208082234	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	9.125000|9.125000	0.94402|0.94402	1.126000|1.126000	0.42016|0.42016	0.533000|0.533000	0.62120|0.62120	CAT|ATT	.	.		0.408	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388	Missense_Mutation	G	210015611	A	G	210015611	5	3	73	1	0	0	0	0	0	0	1	0	1983	231	8	2	1521	2	C1orf107	1	210015611	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	225662	210015611	39235010	63	9389										
KCNH1	3756	hgsc.bcm.edu	37	chr1	211192594	211192594	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggatgtctgagcccagctgtAggacctgtacagaaaaacat	11	9	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:211192594A>T	ENST00000271751.4	-	6	590	c.563T>A	c.(562-564)cTa>cAa	p.L188Q	KCNH1_ENST00000367007.4_Missense_Mutation_p.L188Q			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	188					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.L188P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		GCCCAGCTGTAGGACCTGTAC	0.428																																					p.L188Q		Atlas-SNP	.											KCNH1,NS,carcinoma,0,1	KCNH1	199	.	1	Substitution - Missense(1)	lung(1)	c.T563A						.						46	51	49					1																	211192594		2197	4281	6478	SO:0001583	missense	3756	exon6			AGCTGTAGGACCT	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.563T>A	chr1.hg19:g.211192594A>T	ENSP00000271751:p.Leu188Gln	25.0	0.0		58.0	29.0	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	hg19	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	A	18.72	3.684531	0.68157	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.99113	-5.44;-5.42	5.0	5.0	0.66597	.	0.000000	0.64402	D	0.000001	D	0.99202	0.9723	M	0.83483	2.645	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72338	0.943;0.977	D	0.99342	1.0912	10	0.87932	D	0	.	13.8759	0.63653	1.0:0.0:0.0:0.0	.	188;188	Q14CL3;O95259	.;KCNH1_HUMAN	Q	188	ENSP00000271751:L188Q;ENSP00000355974:L188Q	ENSP00000271751:L188Q	L	-	2	0	KCNH1	209259217	0.999000	0.42202	0.998000	0.56505	0.946000	0.59487	8.924000	0.92827	1.885000	0.54596	0.379000	0.24179	CTA	.	.		0.428	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		T	211192594	A	T	211192594	3	4	73	1	0	0	0	0	1	0	0	0	8040	420	15	4	2430	4	KCNH1	1	211192594	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1176983	211192594	38058027	64	9390										
SLC30A1	7779	hgsc.bcm.edu	37	chr1	211751602	211751602	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcagcccggccacgccgaccCcaaggaccaccagcggctgc	12	20	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:211751602C>A	ENST00000367001.4	-	1	482	c.353G>T	c.(352-354)gGg>gTg	p.G118V		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	118					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		CACGCCGACCCCAAGGACCAC	0.667																																					p.G118V		Atlas-SNP	.											.	SLC30A1	27	.	0			c.G353T						.						14	18	16					1																	211751602		2199	4292	6491	SO:0001583	missense	7779	exon1			CCGACCCCAAGGA	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.353G>T	chr1.hg19:g.211751602C>A	ENSP00000355968:p.Gly118Val	105.0	0.0		205.0	43.0	NM_021194	Q0VAK9|Q9BZF6	Missense_Mutation	SNP	ENST00000367001.4	hg19	CCDS1499.1	.	.	.	.	.	.	.	.	.	.	C	5.555	0.287263	0.10513	.	.	ENSG00000170385	ENST00000367001	T	0.64085	-0.08	4.13	-1.49	0.08718	.	0.462385	0.23928	N	0.043162	T	0.38295	0.1035	N	0.11818	0.18	0.80722	D	1	B	0.30870	0.298	B	0.40410	0.328	T	0.07290	-1.0780	10	0.12103	T	0.63	-0.0011	4.2683	0.10775	0.109:0.3585:0.3871:0.1454	.	118	Q9Y6M5	ZNT1_HUMAN	V	118	ENSP00000355968:G118V	ENSP00000355968:G118V	G	-	2	0	SLC30A1	209818225	1.000000	0.71417	0.197000	0.23402	0.954000	0.61252	2.028000	0.41088	-0.534000	0.06315	-0.519000	0.04390	GGG	.	.		0.667	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			A	211751602	C	A	211751602	3	1	73	1	0	0	0	0	1	0	0	0	14568	623	22	3	1178	3	SLC30A1	1	211751602	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	559008	211751602	37499019	65	9391										
C1orf227	149643	hgsc.bcm.edu	37	chr1	213009317	213009317	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctctttggttgtggtatcagTaaaggactgataggcatccg	12	7	2	1	rs372469118		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:213009317T>G	ENST00000332912.3	-	2	282	c.175A>C	c.(175-177)Act>Cct	p.T59P		NM_001024601.2	NP_001019772.1	Q537H7	SPT45_HUMAN		59										kidney(1)|large_intestine(1)|lung(1)	3						GTGGTATCAGTAAAGGACTGA	0.478																																					p.T59P		Atlas-SNP	.											.	C1orf227	9	.	0			c.A175C						.						154	144	147					1																	213009317		2203	4297	6500	SO:0001583	missense	149643	exon2			TATCAGTAAAGGA																												ENST00000332912.3:c.175A>C	chr1.hg19:g.213009317T>G	ENSP00000419160:p.Thr59Pro	204.0	1.0		302.0	213.0	NM_001024601		Missense_Mutation	SNP	ENST00000332912.3	hg19	CCDS31020.1	.	.	.	.	.	.	.	.	.	.	T	14.55	2.569324	0.45798	.	.	ENSG00000185523	ENST00000332912	T	0.48522	0.81	4.71	-9.43	0.00607	.	2.280910	0.01531	N	0.018794	T	0.28001	0.0690	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.13737	-1.0498	9	0.54805	T	0.06	3.0238	2.9603	0.05890	0.1029:0.3381:0.3126:0.2465	.	59	Q537H7	CA227_HUMAN	P	59	ENSP00000419160:T59P	ENSP00000419160:T59P	T	-	1	0	C1orf227	211075940	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.248000	0.08854	-1.987000	0.00982	-0.297000	0.09499	ACT	.	.		0.478	C1orf227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089672.2			G	213009317	T	G	213009317	3	3	73	1	0	0	0	0	1	0	0	0	2035	1638	57	5	129	5	C1orf227	1	213009317	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1257715	213009317	36241304	66	9392										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228462464	228462464	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gccacagcctgaccatctcaGacctggtgctggaggacgcg	13	14	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:228462464G>T	ENST00000422127.1	+	20	5919	c.5875G>T	c.(5875-5877)Gac>Tac	p.D1959Y	RP5-1139B12.3_ENST00000602529.1_RNA|OBSCN_ENST00000570156.2_Missense_Mutation_p.D2334Y|RP5-1139B12.2_ENST00000602517.1_RNA|OBSCN_ENST00000359599.6_Missense_Mutation_p.D806Y|RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000284548.11_Missense_Mutation_p.D1959Y|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1959	Ig-like 19.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GACCATCTCAGACCTGGTGCT	0.647																																					p.D2334Y		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G7000T						.						26	35	32					1																	228462464		2128	4249	6377	SO:0001583	missense	84033	exon24			ATCTCAGACCTGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.5875G>T	chr1.hg19:g.228462464G>T	ENSP00000409493:p.Asp1959Tyr	73.0	0.0		96.0	16.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	8.989	0.977320	0.18812	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.78126	0.86;0.86;-1.15	5.71	-6.2	0.02072	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.994904	0.08163	N	0.988239	T	0.78723	0.4328	M	0.67625	2.065	0.09310	N	0.999992	P;D	0.57257	0.56;0.979	B;P	0.53809	0.249;0.735	T	0.74954	-0.3488	10	0.62326	D	0.03	.	8.7186	0.34428	0.5091:0.0:0.3954:0.0955	.	1959;1959	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	Y	1959;1959;806	ENSP00000284548:D1959Y;ENSP00000409493:D1959Y;ENSP00000352613:D806Y	ENSP00000284548:D1959Y	D	+	1	0	OBSCN	226529087	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.811000	0.04500	-1.489000	0.01844	-0.263000	0.10527	GAC	.	.		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228462464	G	T	228462464	3	4	73	1	0	0	0	0	1	0	0	0	10821	942	33	3	5949	3	OBSCN	1	228462464	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	15453147	228462464	20788157	67	9393										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228559946	228559946	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggctggacccaggaggctgAggatctgtccgactccacac	14	13	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:228559946A>T	ENST00000422127.1	+	94	21511	c.21467A>T	c.(21466-21468)gAg>gTg	p.E7156V	OBSCN_ENST00000570156.2_Missense_Mutation_p.E8113V|OBSCN_ENST00000366707.4_Missense_Mutation_p.E4790V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7156					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CAGGAGGCTGAGGATCTGTCC	0.682																																					p.E8113V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A24338T						.						12	13	13					1																	228559946		2044	4175	6219	SO:0001583	missense	84033	exon105			AGGCTGAGGATCT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.21467A>T	chr1.hg19:g.228559946A>T	ENSP00000409493:p.Glu7156Val	113.0	0.0		192.0	39.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.28|17.28	3.348535|3.348535	0.61183|0.61183	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000422127;ENST00000366707|ENST00000441106	T;T|.	0.64618|.	-0.11;-0.03|.	4.31|4.31	-6.08|-6.08	0.02151|0.02151	.|.	.|.	.|.	.|.	.|.	T|.	0.24122|.	0.0584|.	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B|.	0.23128|.	0.08|.	B|.	0.19946|.	0.027|.	T|.	0.32640|.	-0.9899|.	9|.	0.29301|.	T|.	0.29|.	.|.	6.7903|6.7903	0.23695|0.23695	0.2233:0.3033:0.4734:0.0|0.2233:0.3033:0.4734:0.0	.|.	7156|.	Q5VST9|.	OBSCN_HUMAN|.	V|C	7156;4790|1772	ENSP00000409493:E7156V;ENSP00000355668:E4790V|.	ENSP00000355668:E4790V|.	E|X	+|+	2|3	0|0	OBSCN|OBSCN	226626569|226626569	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.018000|0.018000	0.13422|0.13422	-0.910000|-0.910000	0.03847|0.03847	-1.255000|-1.255000	0.01485|0.01485	GAG|TGA	.	.		0.682	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228559946	A	T	228559946	3	4	73	1	0	0	0	0	1	0	0	0	10821	304	11	4	23047	4	OBSCN	1	228559946	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	97482	228559946	20690675	68	9394										
TSNAX	7257	hgsc.bcm.edu	37	chr1	231700443	231700443	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgaagtgagccagtttttacGtcaggtttatgatgggtttt	12	4	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:231700443G>T	ENST00000366639.4	+	6	823	c.665G>T	c.(664-666)cGt>cTt	p.R222L	TSNAX-DISC1_ENST00000602962.1_Intron	NM_005999.2	NP_005990.1	Q99598	TSNAX_HUMAN	translin-associated factor X	222					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		all_cancers(173;0.0395)|Acute lymphoblastic leukemia(190;3.76e-06)|Prostate(94;0.116)				CAGTTTTTACGTCAGGTTTAT	0.438																																					p.R222L		Atlas-SNP	.											.	TSNAX	14	.	0			c.G665T						.						217	204	209					1																	231700443		2203	4300	6503	SO:0001583	missense	7257	exon6			TTTTACGTCAGGT	X95073	CCDS1596.1	1q42.2	2008-02-05			ENSG00000116918	ENSG00000116918			12380	protein-coding gene	gene with protein product		602964				9013868	Standard	NM_005999		Approved	TRAX	uc001huw.3	Q99598	OTTHUMG00000039486	ENST00000366639.4:c.665G>T	chr1.hg19:g.231700443G>T	ENSP00000355599:p.Arg222Leu	237.0	0.0		359.0	240.0	NM_005999	B1APC6	Missense_Mutation	SNP	ENST00000366639.4	hg19	CCDS1596.1	.	.	.	.	.	.	.	.	.	.	G	34	5.330927	0.95733	.	.	ENSG00000116918	ENST00000366639	.	.	.	5.77	5.77	0.91146	Translin, C-terminal (1);	0.094954	0.85682	D	0.000000	D	0.86573	0.5965	M	0.91920	3.255	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87894	0.2686	9	0.62326	D	0.03	.	20.3485	0.98803	0.0:0.0:1.0:0.0	.	222	Q99598	TSNAX_HUMAN	L	222	.	ENSP00000355599:R222L	R	+	2	0	TSNAX	229767066	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.316000	0.96319	2.885000	0.99019	0.650000	0.86243	CGT	.	.		0.438	TSNAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095267.2	NM_005999		T	231700443	G	T	231700443	3	4	73	1	0	0	0	0	1	0	0	0	16646	1145	40	1	687	1	TSNAX	1	231700443	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3140497	231700443	17550178	69	9395										
DISC1	27185	hgsc.bcm.edu	37	chr1	231829654	231829654	+	De_novo_Start_OutOfFrame	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggctacatgagaagctcgacAgggcctgggatcgggttcct	15	10	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:231829654A>T	ENST00000366637.3	+	0	203				TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000366633.3_Silent_p.T50T|DISC1_ENST00000535983.1_Silent_p.T50T|DISC1_ENST00000537876.1_Silent_p.T50T|DISC1_ENST00000439617.2_Silent_p.T50T|DISC1_ENST00000317586.4_Silent_p.T50T|DISC1_ENST00000602281.1_Silent_p.T50T|DISC1_ENST00000366636.4_Silent_p.T50T|DISC1_ENST00000539444.1_Silent_p.T50T	NM_001012957.1	NP_001012975.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1						canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				GAAGCTCGACAGGGCCTGGGA	0.637																																					p.T50T		Atlas-SNP	.											.	DISC1	207	.	0			c.A150T						.						46	46	46					1																	231829654		2203	4300	6503			27185	exon2			CTCGACAGGGCCT	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000366637.3:c.-1855A>T	chr1.hg19:g.231829654A>T		93.0	0.0		134.0	25.0	NM_001164541	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Silent	SNP	ENST00000366637.3	hg19																																																																																				.	.		0.637	DISC1-002	KNOWN	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000092352.2	NM_018662		T	231829654	A	T	231829654	1	4	73	1	0	1	0	0	0	0	0	0	4540	175	7	4		4	DISC1	1	231829654	De_novo_Start_OutOfFrame	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	129211	231829654	17420967	70	9396										
C1orf101	257044	hgsc.bcm.edu	37	chr1	244681971	244681971	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acagttctgaagagaaaagtTtattcttcaaatgagaaaat	7	4	3	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:244681971T>G	ENST00000366534.4	+	8	561	c.507T>G	c.(505-507)gtT>gtG	p.V169V	C1orf101_ENST00000473875.1_Intron|C1orf101_ENST00000366531.3_Silent_p.V18V|C1orf101_ENST00000366533.4_Silent_p.V169V	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	169						CatSper complex (GO:0036128)				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			AGAGAAAAGTTTATTCTTCAA	0.289																																					p.V169V		Atlas-SNP	.											.	C1orf101	158	.	0			c.T507G						.						45	51	49					1																	244681971		2197	4295	6492	SO:0001819	synonymous_variant	257044	exon8			AAAAGTTTATTCT	BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.507T>G	chr1.hg19:g.244681971T>G		387.0	0.0		623.0	137.0	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	hg19	CCDS44340.1																																																																																			.	.		0.289	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807		G	244681971	T	G	244681971	2	3	73	1	0	0	0	0	0	0	0	1	1978	1828	64	5		5	C1orf101	1	244681971	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	12852317	244681971	4568650	71	9397										
OR2G3	81469	hgsc.bcm.edu	37	chr1	247769234	247769234	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cactgaatgtatcctcttggCtgacatggccttggatcggt	11	10	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:247769234C>A	ENST00000320002.2	+	1	379	c.347C>A	c.(346-348)gCt>gAt	p.A116D	RP11-978I15.10_ENST00000435333.1_RNA|RNU6-691P_ENST00000516585.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(31)|skin(5)	50	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			ATCCTCTTGGCTGACATGGCC	0.498																																					p.A116D		Atlas-SNP	.											.	OR2G3	108	.	0			c.C347A						.						255	224	235					1																	247769234		2203	4300	6503	SO:0001583	missense	81469	exon1			TCTTGGCTGACAT	BK004417	CCDS31093.1	1q44	2012-08-09			ENSG00000177476	ENSG00000177476		"GPCR / Class A : Olfactory receptors"	15008	protein-coding gene	gene with protein product							Standard	NM_001001914		Approved		uc010pyz.2	Q8NGZ4	OTTHUMG00000040576	ENST00000320002.2:c.347C>A	chr1.hg19:g.247769234C>A	ENSP00000326301:p.Ala116Asp	186.0	1.0		288.0	202.0	NM_001001914	B2RN64|Q5JQT1|Q6IF45	Missense_Mutation	SNP	ENST00000320002.2	hg19	CCDS31093.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215100	0.79352	.	.	ENSG00000177476	ENST00000320002	T	0.02067	4.47	3.8	2.88	0.33553	GPCR, rhodopsin-like superfamily (1);	0.207947	0.22925	U	0.053964	T	0.16938	0.0407	H	0.98701	4.305	0.30885	N	0.730952	P	0.50369	0.934	P	0.55455	0.776	T	0.32134	-0.9918	10	0.87932	D	0	.	9.3439	0.38096	0.0:0.8908:0.0:0.1092	.	116	Q8NGZ4	OR2G3_HUMAN	D	116	ENSP00000326301:A116D	ENSP00000326301:A116D	A	+	2	0	OR2G3	245835857	0.003000	0.15002	0.965000	0.40720	0.936000	0.57629	1.559000	0.36320	0.940000	0.37473	0.492000	0.49549	GCT	.	.		0.498	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1			A	247769234	C	A	247769234	3	1	73	1	0	0	0	0	1	0	0	0	11008	797	28	3	349	3	OR2G3	1	247769234	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	3087263	247769234	1481387	72	9398										
OR2M3	127062	hgsc.bcm.edu	37	chr1	248366439	248366439	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcttcaatcacagccccaccCacaccttcctcttctttctg	2	19	6	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:248366439C>T	ENST00000456743.1	+	1	108	c.70C>T	c.(70-72)Cac>Tac	p.H24Y		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CAGCCCCACCCACACCTTCCT	0.498																																					p.H24Y		Atlas-SNP	.											.	OR2M3	116	.	0			c.C70T						.						203	209	207					1																	248366439		2203	4300	6503	SO:0001583	missense	127062	exon1			CCCACCCACACCT		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"GPCR / Class A : Olfactory receptors"	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.70C>T	chr1.hg19:g.248366439C>T	ENSP00000389625:p.His24Tyr	339.0	0.0		563.0	114.0	NM_001004689	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	hg19	CCDS31107.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.882650	0.51908	.	.	ENSG00000228198	ENST00000456743	T	0.00333	8.07	2.61	1.66	0.24008	.	0.000000	0.33401	U	0.004945	T	0.00328	0.0010	M	0.63428	1.95	0.09310	N	1	P	0.43857	0.819	P	0.46543	0.52	T	0.46020	-0.9221	10	0.59425	D	0.04	.	5.3991	0.16286	0.201:0.6769:0.0:0.1221	.	24	Q8NG83	OR2M3_HUMAN	Y	24	ENSP00000389625:H24Y	ENSP00000389625:H24Y	H	+	1	0	OR2M3	246433062	0.021000	0.18746	0.007000	0.13788	0.701000	0.40568	1.557000	0.36299	1.475000	0.48197	0.398000	0.26397	CAC	.	.		0.498	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		T	248366439	C	T	248366439	3	4	73	1	0	0	0	0	1	0	0	0	11020	594	21	3	72	3	OR2M3	1	248366439	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	597205	248366439	884182	73	9399										
OR2G6	391211	hgsc.bcm.edu	37	chr1	248685871	248685871	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aggaccctgatactgggtagTgctgctggacaaagccacaa	12	10	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr1:248685871T>C	ENST00000343414.4	+	1	956	c.924T>C	c.(922-924)agT>agC	p.S308S		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	308						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TACTGGGTAGTGCTGCTGGAC	0.473																																					p.S308S		Atlas-SNP	.											.	OR2G6	124	.	0			c.T924C						.						41	40	40					1																	248685871		2203	4297	6500	SO:0001819	synonymous_variant	391211	exon1			GGGTAGTGCTGCT		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"GPCR / Class A : Olfactory receptors"	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.924T>C	chr1.hg19:g.248685871T>C		37.0	0.0		74.0	8.0	NM_001013355	B2RP33	Silent	SNP	ENST00000343414.4	hg19	CCDS31119.1																																																																																			.	.		0.473	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842		C	248685871	T	C	248685871	2	2	73	1	0	0	0	0	0	0	0	1	11009	1693	59	2		2	OR2G6	1	248685871	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	319432	248685871	564750	74	9400										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1983303	1983303	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggcactaacctgaacagctCttgtatggctggttccacgg	11	11	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:1983303C>A	ENST00000399161.2	-	7	826	c.79G>T	c.(79-81)Gag>Tag	p.E27*	MYT1L_ENST00000428368.2_Nonsense_Mutation_p.E27*	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	27					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CTGAACAGCTCTTGTATGGCT	0.453																																					p.E27X		Atlas-SNP	.											.	MYT1L	241	.	0			c.G79T						.						95	98	97					2																	1983303		1919	4132	6051	SO:0001587	stop_gained	23040	exon7			ACAGCTCTTGTAT	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.79G>T	chr2.hg19:g.1983303C>A	ENSP00000382114:p.Glu27*	141.0	0.0		92.0	32.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Nonsense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	C	45	12.005629	0.99626	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	.	.	.	5.38	5.38	0.77491	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-42.2395	19.143	0.93452	0.0:1.0:0.0:0.0	.	.	.	.	X	27	.	ENSP00000295067:E27X	E	-	1	0	MYT1L	1962310	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	6.422000	0.73357	2.515000	0.84797	0.655000	0.94253	GAG	.	.		0.453	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1983303	C	A	1983303	4	1	73	1	0	0	0	0	0	1	0	0	10116	922	32	3	3551	3	MYT1L	2	1983303	Nonsense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10		1983303	241216070	75	9401										
OSR1	130497	hgsc.bcm.edu	37	chr2	19552136	19552136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agaatcctttcccacactctTgacacttgaagggcttctct	6	13	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:19552136T>C	ENST00000272223.2	-	3	1045	c.701A>G	c.(700-702)cAa>cGa	p.Q234R	OSR1_ENST00000536433.1_Missense_Mutation_p.Q234R	NM_145260.2	NP_660303.1	Q8TAX0	OSR1_HUMAN	odd-skipped related transciption factor 1	234					cell differentiation (GO:0030154)|cell proliferation involved in kidney development (GO:0072111)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|gonad development (GO:0008406)|heart development (GO:0007507)|intermediate mesoderm development (GO:0048389)|mesangial cell development (GO:0072143)|mesonephric duct morphogenesis (GO:0072180)|mesonephros development (GO:0001823)|metanephric cap mesenchymal cell proliferation involved in metanephros development (GO:0090094)|metanephric epithelium development (GO:0072207)|metanephric glomerulus vasculature development (GO:0072239)|metanephric interstitial fibroblast development (GO:0072259)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephric nephron tubule development (GO:0072234)|metanephric smooth muscle tissue development (GO:0072208)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of nephron tubule epithelial cell differentiation (GO:0072183)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|palate development (GO:0060021)|pattern specification involved in metanephros development (GO:0072268)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posterior mesonephric tubule development (GO:0072166)|pronephros development (GO:0048793)|renal vesicle progenitor cell differentiation (GO:0072184)|specification of anterior mesonephric tubule identity (GO:0072168)|specification of posterior mesonephric tubule identity (GO:0072169)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)|ureter urothelium development (GO:0072190)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|large_intestine(2)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)				CCCACACTCTTGACACTTGAA	0.453																																					p.Q234R		Atlas-SNP	.											.	OSR1	29	.	0			c.A701G						.						148	133	138					2																	19552136		2203	4300	6503	SO:0001583	missense	130497	exon3			CACTCTTGACACT	BC025712	CCDS1694.1	2p24.1	2013-10-17	2013-10-17	2004-11-26	ENSG00000143867	ENSG00000143867		"Zinc fingers, C2H2-type"	8111	protein-coding gene	gene with protein product		608891	"odd-skipped (Drosophila) homolog", "odd-skipped related 1 (Drosophila)"	ODD		2120051, 12119563	Standard	XM_006711942		Approved		uc002rdc.3	Q8TAX0	OTTHUMG00000088793	ENST00000272223.2:c.701A>G	chr2.hg19:g.19552136T>C	ENSP00000272223:p.Gln234Arg	108.0	0.0		115.0	48.0	NM_145260	B3KV97|D6W521	Missense_Mutation	SNP	ENST00000272223.2	hg19	CCDS1694.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.009850	0.54361	.	.	ENSG00000143867	ENST00000272223;ENST00000536433	T;T	0.03580	3.88;3.88	5.01	3.82	0.43975	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.054217	0.85682	D	0.000000	T	0.03053	0.0090	N	0.20986	0.625	0.45822	D	0.998693	B	0.14805	0.011	B	0.21360	0.034	T	0.50259	-0.8849	9	.	.	.	-10.781	10.7208	0.46040	0.143:0.0:0.0:0.857	.	234	Q8TAX0	OSR1_HUMAN	R	234	ENSP00000272223:Q234R;ENSP00000441801:Q234R	.	Q	-	2	0	OSR1	19415617	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.819000	0.86621	0.879000	0.35944	0.459000	0.35465	CAA	.	.		0.453	OSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000201432.2	NM_145260		C	19552136	T	C	19552136	3	2	73	1	0	0	0	0	1	0	0	0	11302	1812	63	2	103	2	OSR1	2	19552136	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	17568833	19552136	223647237	76	9402										
APOB	338	hgsc.bcm.edu	37	chr2	21229513	21229513	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagctcacagtactgttatgActaccctccacaaatttgtt	5	11	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:21229513A>T	ENST00000233242.1	-	26	10354	c.10227T>A	c.(10225-10227)agT>agA	p.S3409R		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3409	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TACTGTTATGACTACCCTCCA	0.413																																					p.S3409R		Atlas-SNP	.											.	APOB	761	.	0			c.T10227A						.						167	165	166					2																	21229513		2203	4300	6503	SO:0001583	missense	338	exon26			GTTATGACTACCC	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10227T>A	chr2.hg19:g.21229513A>T	ENSP00000233242:p.Ser3409Arg	103.0	0.0		109.0	48.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.597645	0.28445	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.38077	1.16	5.74	-0.997	0.10215	.	0.459902	0.21925	N	0.067102	T	0.32704	0.0838	M	0.85041	2.73	0.80722	D	1	P	0.37548	0.599	B	0.35607	0.206	T	0.17258	-1.0375	10	0.72032	D	0.01	.	0.8145	0.01100	0.3343:0.1458:0.301:0.2189	.	3409	P04114	APOB_HUMAN	R	3409	ENSP00000233242:S3409R	ENSP00000233242:S3409R	S	-	3	2	APOB	21083018	0.000000	0.05858	0.972000	0.41901	0.164000	0.22412	-0.225000	0.09151	-0.172000	0.10779	0.533000	0.62120	AGT	.	.		0.413	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21229513	A	T	21229513	3	4	73	1	0	0	0	0	1	0	0	0	785	272	10	4	3480	4	APOB	2	21229513	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1677377	21229513	221969860	77	9403										
EMILIN1	11117	hgsc.bcm.edu	37	chr2	27302028	27302028	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcctcgaggtttcagcctctAcacaggttccagtggggccc	11	14	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:27302028A>G	ENST00000380320.4	+	1	594	c.95A>G	c.(94-96)tAc>tGc	p.Y32C		NM_007046.3	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1	32					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(14)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	26	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCAGCCTCTACACAGGTTCC	0.711																																					p.Y32C		Atlas-SNP	.											.	EMILIN1	75	.	0			c.A95G						.						9	12	11					2																	27302028		2168	4273	6441	SO:0001583	missense	11117	exon1			GCCTCTACACAGG	AF088916	CCDS1733.1	2p23.3-p23.2	2008-02-05			ENSG00000138080	ENSG00000138080		"EMI domain containing"	19880	protein-coding gene	gene with protein product		130660					Standard	NM_007046		Approved	DKFZp586M121, gp115	uc002rii.4	Q9Y6C2	OTTHUMG00000097069	ENST00000380320.4:c.95A>G	chr2.hg19:g.27302028A>G	ENSP00000369677:p.Tyr32Cys	70.0	0.0		47.0	16.0	NM_007046	A5PL03|H0Y7A0|Q53SY9|Q96G58|Q96IH6|Q9UG76	Missense_Mutation	SNP	ENST00000380320.4	hg19	CCDS1733.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.607597	0.46527	.	.	ENSG00000138080	ENST00000380320	T	0.64085	-0.08	4.59	4.59	0.56863	.	0.358564	0.23883	N	0.043637	T	0.67173	0.2865	L	0.29908	0.895	0.44155	D	0.996956	D	0.76494	0.999	D	0.79784	0.993	T	0.66826	-0.5825	10	0.41790	T	0.15	-10.918	12.2161	0.54406	1.0:0.0:0.0:0.0	.	32	Q9Y6C2	EMIL1_HUMAN	C	32	ENSP00000369677:Y32C	ENSP00000369677:Y32C	Y	+	2	0	EMILIN1	27155532	1.000000	0.71417	0.989000	0.46669	0.261000	0.26267	3.306000	0.51881	1.849000	0.53698	0.379000	0.24179	TAC	.	.		0.711	EMILIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214185.1	NM_007046		G	27302028	A	G	27302028	3	3	73	1	0	0	0	0	1	0	0	0	5095	391	14	2	97	2	EMILIN1	2	27302028	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	6072515	27302028	215897345	78	9404										
WDR43	23160	hgsc.bcm.edu	37	chr2	29169340	29169340	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttctgaagaggagtctgatgAtgaaatagcagataaggatt	12	3	2	6			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:29169340A>T	ENST00000407426.3	+	17	1885	c.1829A>T	c.(1828-1830)gAt>gTt	p.D610V		NM_015131.1	NP_055946.1	Q15061	WDR43_HUMAN	WD repeat domain 43	610						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	20	Acute lymphoblastic leukemia(172;0.155)					GAGTCTGATGATGAAATAGCA	0.403																																					p.D610V		Atlas-SNP	.											.	WDR43	38	.	0			c.A1829T						.						80	73	75					2																	29169340		1833	4082	5915	SO:0001583	missense	23160	exon17			CTGATGATGAAAT	D87716	CCDS46251.1	2p23.3	2013-01-09			ENSG00000163811	ENSG00000163811		"WD repeat domain containing"	28945	protein-coding gene	gene with protein product	"UTP5, small subunit (SSU) processome component, homolog (yeast)"					7584026, 7584028, 17699751	Standard	NM_015131		Approved	KIAA0007, NET12, UTP5	uc002rmo.2	Q15061	OTTHUMG00000152015	ENST00000407426.3:c.1829A>T	chr2.hg19:g.29169340A>T	ENSP00000384302:p.Asp610Val	120.0	0.0		126.0	44.0	NM_015131	Q15395|Q92577	Missense_Mutation	SNP	ENST00000407426.3	hg19	CCDS46251.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.11|10.11	1.261619|1.261619	0.23051|0.23051	.|.	.|.	ENSG00000163811|ENSG00000163811	ENST00000407426|ENST00000446643	T|.	0.05081|.	3.5|.	5.77|5.77	4.62|4.62	0.57501|0.57501	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61949|0.61949	0.2388|0.2388	L|L	0.55481|0.55481	1.735|1.735	0.80722|0.80722	D|D	1|1	D|.	0.57899|.	0.981|.	P|.	0.49752|.	0.621|.	T|T	0.59150|0.59150	-0.7508|-0.7508	10|5	0.40728|.	T|.	0.16|.	-25.7841|-25.7841	11.7393|11.7393	0.51784|0.51784	0.9312:0.0:0.0688:0.0|0.9312:0.0:0.0688:0.0	.|.	610|.	Q15061|.	WDR43_HUMAN|.	V|L	610|162	ENSP00000384302:D610V|.	ENSP00000384302:D610V|.	D|M	+|+	2|1	0|0	WDR43|WDR43	29022844|29022844	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.104000|0.104000	0.19210|0.19210	6.249000|6.249000	0.72427|0.72427	1.123000|1.123000	0.41961|0.41961	0.533000|0.533000	0.62120|0.62120	GAT|ATG	.	.		0.403	WDR43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324865.1	XM_087089		T	29169340	A	T	29169340	3	4	73	1	0	0	0	0	1	0	0	0	17310	333	12	4	1895	4	WDR43	2	29169340	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1867312	29169340	214030033	79	9405										
QPCT	25797	hgsc.bcm.edu	37	chr2	37599570	37599570	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtatttccagaattacagtTatggaggtgtgattcaggat	12	4	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:37599570T>A	ENST00000338415.3	+	6	1053	c.895T>A	c.(895-897)Tat>Aat	p.Y299N	QPCT_ENST00000537448.1_Missense_Mutation_p.Y250N	NM_012413.3	NP_036545.1	Q16769	QPCT_HUMAN	glutaminyl-peptide cyclotransferase	299					cellular protein modification process (GO:0006464)|peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	extracellular vesicular exosome (GO:0070062)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|stomach(2)	17		Ovarian(717;0.051)|all_hematologic(82;0.21)				GAATTACAGTTATGGAGGTGT	0.403																																					p.Y299N		Atlas-SNP	.											.	QPCT	34	.	0			c.T895A						.						181	177	178					2																	37599570		2203	4300	6503	SO:0001583	missense	25797	exon6			TACAGTTATGGAG	X71125	CCDS1790.1	2p22	2008-07-31	2008-07-31		ENSG00000115828	ENSG00000115828	2.3.2.5		9753	protein-coding gene	gene with protein product	"glutaminyl cyclase"	607065				7999256	Standard	NM_012413		Approved	QC, GCT	uc002rqg.3	Q16769	OTTHUMG00000100963	ENST00000338415.3:c.895T>A	chr2.hg19:g.37599570T>A	ENSP00000344829:p.Tyr299Asn	119.0	0.0		99.0	41.0	NM_012413	Q16770|Q3KRG6|Q53TR4	Missense_Mutation	SNP	ENST00000338415.3	hg19	CCDS1790.1	.	.	.	.	.	.	.	.	.	.	T	6.423	0.446177	0.12164	.	.	ENSG00000115828	ENST00000338415;ENST00000404976;ENST00000537448;ENST00000444022	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.3	-0.053	0.13820	Peptidase M28 (1);	0.942842	0.09047	N	0.856433	T	0.28532	0.0706	L	0.31804	0.96	0.09310	N	1	B;B	0.12630	0.006;0.004	B;B	0.06405	0.002;0.002	T	0.21415	-1.0246	10	0.28530	T	0.3	-14.435	1.3634	0.02196	0.1854:0.3073:0.1135:0.3938	.	250;299	Q16769-2;Q16769	.;QPCT_HUMAN	N	299;250;250;64	ENSP00000344829:Y299N;ENSP00000385391:Y250N;ENSP00000441606:Y250N;ENSP00000389227:Y64N	ENSP00000344829:Y299N	Y	+	1	0	QPCT	37453074	0.000000	0.05858	0.001000	0.08648	0.596000	0.36781	-0.091000	0.11146	0.107000	0.17824	0.460000	0.39030	TAT	.	.		0.403	QPCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218572.2			A	37599570	T	A	37599570	3	1	73	1	0	0	0	0	1	0	0	0	12889	1754	61	4	917	4	QPCT	2	37599570	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	8430230	37599570	205599803	80	9406										
C2orf34	79823	hgsc.bcm.edu	37	chr2	44933426	44933426	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atttcttttctctctttcagGgcccttgctgtgtgtgagct	9	10	4	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:44933426G>A	ENST00000378494.3	+	5	482	c.438G>A	c.(436-438)agG>agA	p.R146R		NM_024766.4	NP_079042.1	Q7Z624	CMKMT_HUMAN	calmodulin-lysine N-methyltransferase	146						Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	calmodulin-lysine N-methyltransferase activity (GO:0018025)			breast(2)|large_intestine(3)|lung(5)	10						TCTCTTTCAGGGCCCTTGCTG	0.438																																					p.R146R		Atlas-SNP	.											.	CAMKMT	20	.	0			c.G438A						.						161	145	150					2																	44933426		2203	4300	6503	SO:0001630	splice_region_variant	79823	exon5			TTTCAGGGCCCTT		CCDS1820.1	2p21	2011-06-22	2011-03-10	2011-03-10	ENSG00000143919	ENSG00000143919	2.1.1.60		26276	protein-coding gene	gene with protein product	"CaM KMT"	609559	"chromosome 2 open reading frame 34"	C2orf34		20975703	Standard	NM_024766		Approved	CLNMT	uc002rum.3	Q7Z624	OTTHUMG00000128761	ENST00000378494.3:c.438-1G>A	chr2.hg19:g.44933426G>A		94.0	0.0		90.0	40.0	NM_024766	Q4ZG15|Q53SS6|Q8N6P5|Q9H5G8	Silent	SNP	ENST00000378494.3	hg19	CCDS1820.1																																																																																			.	.		0.438	CAMKMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250678.2	NM_024766	Silent	A	44933426	G	A	44933426	5	1	73	1	0	0	0	0	0	0	1	0	2165	1246	43	3	456	3	C2orf34	2	44933426	Splice_Site	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	7333856	44933426	198265947	81	9407										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50149221	50149221	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gactctcgtccacatggtatGagccttcatcccggtttctg	9	13	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:50149221G>T	ENST00000406316.2	-	22	5771	c.4295C>A	c.(4294-4296)tCa>tAa	p.S1432*	NRXN1_ENST00000406859.3_Nonsense_Mutation_p.S1432*|NRXN1_ENST00000401710.1_Nonsense_Mutation_p.S450*|NRXN1_ENST00000404971.1_Nonsense_Mutation_p.S1502*|NRXN1_ENST00000402717.3_Nonsense_Mutation_p.S1454*|NRXN1_ENST00000401669.2_Nonsense_Mutation_p.S1462*|NRXN1_ENST00000342183.5_Nonsense_Mutation_p.S397*|NRXN1_ENST00000405472.3_Nonsense_Mutation_p.S1454*	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1432					adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CACATGGTATGAGCCTTCATC	0.517																																					p.S1502X		Atlas-SNP	.											NRXN1_ENST00000536085,NS,carcinoma,0,3	NRXN1	1118	.	0			c.C4505A						.						218	174	189					2																	50149221		2203	4300	6503	SO:0001587	stop_gained	9378	exon24			TGGTATGAGCCTT	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.4295C>A	chr2.hg19:g.50149221G>T	ENSP00000384311:p.Ser1432*	126.0	0.0		125.0	53.0	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Nonsense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	50|50	16.278780|16.278780	0.99859|0.99859	.|.	.|.	ENSG00000179915|ENSG00000179915	ENST00000412315|ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	.|.	.|.	.|.	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	.|0.000000	.|0.48286	.|U	.|0.000185	T|.	0.47488|.	0.1448|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34004|.	-0.9846|.	4|.	.|0.02654	.|T	.|1	.|.	19.4586|19.4586	0.94906|0.94906	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	N|X	165|397;351;450;1502;1432;1454;1462;1503;1454;1432	.|.	.|ENSP00000341184:S397X	H|S	-|-	1|2	0|0	NRXN1|NRXN1	50002725|50002725	1.000000|1.000000	0.71417|0.71417	0.966000|0.966000	0.40874|0.40874	0.997000|0.997000	0.91878|0.91878	9.657000|9.657000	0.98554|0.98554	2.828000|2.828000	0.97474|0.97474	0.655000|0.655000	0.94253|0.94253	CAT|TCA	.	.		0.517	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50149221	G	T	50149221	4	4	73	1	0	0	0	0	0	1	0	0	10674	1294	45	3	142	3	NRXN1	2	50149221	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	5215795	50149221	193050152	82	9408										
CCT4	10575	hgsc.bcm.edu	37	chr2	62112155	62112155	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcaatgactcaactctttacCattttatccattccttttgg	3	11	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:62112155C>G	ENST00000394440.3	-	2	476	c.180G>C	c.(178-180)atG>atC	p.M60I	CCT4_ENST00000544079.1_Splice_Site_p.M60I|AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000538252.1_Splice_Site_p.M4I|CCT4_ENST00000544185.1_5'UTR	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	60					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			AACTCTTTACCATTTTATCCA	0.383																																					p.M60I		Atlas-SNP	.											.	CCT4	38	.	0			c.G180C						.						189	156	167					2																	62112155		2203	4300	6503	SO:0001630	splice_region_variant	10575	exon2			CTTTACCATTTTA		CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"Heat Shock Proteins / Chaperonins"	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.180+1G>C	chr2.hg19:g.62112155C>G		124.0	0.0		105.0	51.0	NM_001256721	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Missense_Mutation	SNP	ENST00000394440.3	hg19	CCDS33206.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.799156	0.90538	.	.	ENSG00000115484	ENST00000394440;ENST00000544079;ENST00000538252	T;T;T	0.81247	-1.47;2.69;-1.47	4.62	4.62	0.57501	Chaperonin TCP-1, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.88618	0.6485	M	0.72479	2.2	0.80722	D	1	D;D	0.89917	0.991;1.0	P;D	0.73708	0.853;0.981	D	0.88771	0.3264	9	.	.	.	-20.7995	17.451	0.87592	0.0:1.0:0.0:0.0	.	60;60	F5H5W3;P50991	.;TCPD_HUMAN	I	60;60;4	ENSP00000377958:M60I;ENSP00000443061:M60I;ENSP00000442174:M4I	.	M	-	3	0	CCT4	61965659	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.620000	0.83070	2.241000	0.73720	0.655000	0.94253	ATG	.	.		0.383	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2		Missense_Mutation	G	62112155	C	G	62112155	5	3	73	1	0	0	0	0	0	0	1	0	2957	608	21	4	1491	4	CCT4	2	62112155	Splice_Site	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	11962934	62112155	181087218	83	9409										
RAB11FIP5	26056	hgsc.bcm.edu	37	chr2	73315575	73315575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgagctgctgttgctacgacTgcctctgggccaggtgtcat	13	11	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:73315575T>C	ENST00000258098.6	-	3	1411	c.1171A>G	c.(1171-1173)Agt>Ggt	p.S391G	RAB11FIP5_ENST00000493523.2_5'UTR	NM_015470.2	NP_056285.1	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	391					cellular response to acidic pH (GO:0071468)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|regulation of protein localization to cell surface (GO:2000008)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)			biliary_tract(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	23						TTGCTACGACTGCCTCTGGGC	0.627																																					p.S391G		Atlas-SNP	.											.	RAB11FIP5	66	.	0			c.A1171G						.						46	49	48					2																	73315575		2203	4300	6503	SO:0001583	missense	26056	exon3			TACGACTGCCTCT	AF334812	CCDS1923.1	2p13	2008-02-05			ENSG00000135631	ENSG00000135631			24845	protein-coding gene	gene with protein product		605536				10048485, 11163216	Standard	NM_015470		Approved	GAF1, KIAA0857, RIP11, pp75	uc002sis.4	Q9BXF6	OTTHUMG00000129779	ENST00000258098.6:c.1171A>G	chr2.hg19:g.73315575T>C	ENSP00000258098:p.Ser391Gly	39.0	0.0		39.0	15.0	NM_015470	O94939|Q9P0M1	Missense_Mutation	SNP	ENST00000258098.6	hg19	CCDS1923.1	.	.	.	.	.	.	.	.	.	.	T	3.840	-0.034038	0.07543	.	.	ENSG00000135631	ENST00000258098	T	0.48522	0.81	3.66	1.26	0.21427	.	0.409242	0.25598	N	0.029578	T	0.34542	0.0901	L	0.47716	1.5	0.09310	N	0.999996	B;B	0.23591	0.0;0.088	B;B	0.22880	0.0;0.042	T	0.17107	-1.0380	10	0.26408	T	0.33	-3.8624	6.981	0.24704	0.0:0.303:0.0:0.697	.	391;391	Q9BXF6;Q2Z1P3	RFIP5_HUMAN;.	G	391	ENSP00000258098:S391G	ENSP00000258098:S391G	S	-	1	0	RAB11FIP5	73169083	0.006000	0.16342	0.766000	0.31476	0.280000	0.26924	0.419000	0.21247	0.269000	0.21961	-0.464000	0.05259	AGT	.	.		0.627	RAB11FIP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251995.1	NM_015470		C	73315575	T	C	73315575	3	2	73	1	0	0	0	0	1	0	0	0	12912	1580	55	2	802	2	RAB11FIP5	2	73315575	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	11203420	73315575	169883798	84	9410										
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74883712	74883712	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccctcacacatacaattactCtgttctccttgtggatcctg	5	14	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:74883712C>A	ENST00000357877.2	+	2	346	c.197C>A	c.(196-198)tCt>tAt	p.S66Y	SEMA4F_ENST00000339773.5_Missense_Mutation_p.S66Y	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	66	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						TACAATTACTCTGTTCTCCTT	0.562																																					p.S66Y		Atlas-SNP	.											.	SEMA4F	89	.	0			c.C197A						.						134	120	125					2																	74883712		2203	4300	6503	SO:0001583	missense	10505	exon2			ATTACTCTGTTCT	AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.197C>A	chr2.hg19:g.74883712C>A	ENSP00000350547:p.Ser66Tyr	148.0	0.0		119.0	52.0	NM_001271662	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	hg19	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.950111	0.73787	.	.	ENSG00000135622	ENST00000357877;ENST00000339773;ENST00000434486;ENST00000453930	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	4.9	4.9	0.64082	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.538685	0.19128	N	0.122017	T	0.30324	0.0761	M	0.68317	2.08	0.26711	N	0.970979	D;D;P;D	0.76494	0.999;0.999;0.693;0.987	D;D;P;D	0.74348	0.983;0.979;0.588;0.954	T	0.02885	-1.1098	10	0.72032	D	0.01	.	13.5155	0.61539	0.0:1.0:0.0:0.0	.	66;66;66;66	B7Z931;C9K0A1;O95754-2;O95754	.;.;.;SEM4F_HUMAN	Y	66	ENSP00000350547:S66Y;ENSP00000342675:S66Y;ENSP00000407698:S66Y;ENSP00000409141:S66Y	ENSP00000342675:S66Y	S	+	2	0	SEMA4F	74737220	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.347000	0.52200	2.568000	0.86640	0.650000	0.86243	TCT	.	.		0.562	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		A	74883712	C	A	74883712	3	1	73	1	0	0	0	0	1	0	0	0	14050	913	32	3	203	3	SEMA4F	2	74883712	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1568137	74883712	168315661	85	9411										
VWA3B	200403	hgsc.bcm.edu	37	chr2	98797635	98797635	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgctgatggggttgtggataTaaaagccaaaccggagaatg	14	6	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:98797635T>C	ENST00000477737.1	+	9	1475	c.1271T>C	c.(1270-1272)aTa>aCa	p.I424T	VWA3B_ENST00000451075.2_Missense_Mutation_p.I274T|VWA3B_ENST00000435344.1_Missense_Mutation_p.I424T	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	424										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						GTTGTGGATATAAAAGCCAAA	0.562																																					p.I424T		Atlas-SNP	.											.	VWA3B	138	.	0			c.T1271C						.						106	110	109					2																	98797635		2045	4197	6242	SO:0001583	missense	200403	exon9			TGGATATAAAAGC	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1271T>C	chr2.hg19:g.98797635T>C	ENSP00000417955:p.Ile424Thr	196.0	0.0		125.0	48.0	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.804736	0.31961	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.29142	1.58;2.9;2.33	5.31	5.31	0.75309	.	0.087235	0.48286	D	0.000196	T	0.32496	0.0831	L	0.48642	1.525	0.24157	N	0.99567	P;P;P	0.51449	0.595;0.945;0.776	B;B;B	0.44044	0.192;0.439;0.36	T	0.29579	-1.0007	10	0.72032	D	0.01	.	14.5317	0.67931	0.0:0.0:0.0:1.0	.	274;424;424	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	T	424;424;274	ENSP00000401959:I424T;ENSP00000417955:I424T;ENSP00000389463:I274T	ENSP00000388158:I424T	I	+	2	0	VWA3B	98164067	1.000000	0.71417	1.000000	0.80357	0.126000	0.20510	5.416000	0.66417	2.136000	0.66102	0.477000	0.44152	ATA	.	.		0.562	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		C	98797635	T	C	98797635	3	2	73	1	0	0	0	0	1	0	0	0	17256	1406	49	2	1301	2	VWA3B	2	98797635	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	23913923	98797635	144401738	86	9412										
IL18RAP	8807	hgsc.bcm.edu	37	chr2	103040730	103040730	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgttgtgtcaagatgattttAgaagttaagccccagacaaa	9	6	1	4	rs138125296		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:103040730A>T	ENST00000264260.2	+	5	1024	c.435A>T	c.(433-435)ttA>ttT	p.L145F	IL18RAP_ENST00000409369.1_Missense_Mutation_p.L3F	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	145					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						AGATGATTTTAGAAGTTAAGC	0.418																																					p.L145F		Atlas-SNP	.											.	IL18RAP	102	.	0			c.A435T						.						133	126	128					2																	103040730		2203	4300	6503	SO:0001583	missense	8807	exon5			GATTTTAGAAGTT	AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.435A>T	chr2.hg19:g.103040730A>T	ENSP00000264260:p.Leu145Phe	161.0	0.0		177.0	79.0	NM_003853	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Missense_Mutation	SNP	ENST00000264260.2	hg19	CCDS2061.1	.	.	.	.	.	.	.	.	.	.	A	18.71	3.681327	0.68042	.	.	ENSG00000115607	ENST00000264260;ENST00000409369	T;T	0.24350	1.86;3.87	5.69	-2.62	0.06152	.	0.133415	0.34223	N	0.004159	T	0.42200	0.1192	M	0.72894	2.215	0.21473	N	0.999677	D	0.89917	1.0	D	0.85130	0.997	T	0.28839	-1.0031	10	0.41790	T	0.15	.	10.657	0.45680	0.5309:0.0:0.4691:0.0	.	145	O95256	I18RA_HUMAN	F	145;3	ENSP00000264260:L145F;ENSP00000387201:L3F	ENSP00000264260:L145F	L	+	3	2	IL18RAP	102407162	0.360000	0.24964	0.007000	0.13788	0.834000	0.47266	-0.295000	0.08298	-0.616000	0.05671	0.533000	0.62120	TTA	.	A|1.000;G|0.000		0.418	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853		T	103040730	A	T	103040730	3	4	73	1	0	0	0	0	1	0	0	0	7657	417	15	4	445	4	IL18RAP	2	103040730	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4243095	103040730	140158643	87	9413										
GPR45	11250	hgsc.bcm.edu	37	chr2	105858393	105858393	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aacgcctcagactcggggtcCacccagttgcccgcacccct	9	19	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:105858393C>A	ENST00000258456.1	+	1	194	c.78C>A	c.(76-78)tcC>tcA	p.S26S		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	26						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						ACTCGGGGTCCACCCAGTTGC	0.597																																					p.S26S		Atlas-SNP	.											.	GPR45	73	.	0			c.C78A						.						105	98	100					2																	105858393		2203	4300	6503	SO:0001819	synonymous_variant	11250	exon1			GGGGTCCACCCAG	AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"GPCR / Class A : Orphans"	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.78C>A	chr2.hg19:g.105858393C>A		132.0	0.0		121.0	50.0	NM_007227	Q6NWS4|Q6NXU6	Silent	SNP	ENST00000258456.1	hg19	CCDS2066.1																																																																																			.	.		0.597	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227		A	105858393	C	A	105858393	2	1	73	1	0	0	0	0	0	0	0	1	6704	581	21	3		3	GPR45	2	105858393	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	2817663	105858393	137340980	88	9414										
ACOXL	55289	hgsc.bcm.edu	37	chr2	111556610	111556610	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggccccactgtttcatcgtTcctgtccgggatgaaaacgg	12	12	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:111556610T>A	ENST00000389811.4	+	7	704	c.480T>A	c.(478-480)gtT>gtA	p.V160V	ACOXL_ENST00000340561.4_Silent_p.V160V|ACOXL_ENST00000439055.1_Silent_p.V160V			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	160					fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						GTTTCATCGTTCCTGTCCGGG	0.473																																					p.V160V		Atlas-SNP	.											.	ACOXL	93	.	0			c.T480A						.						154	132	139					2																	111556610		2203	4300	6503	SO:0001819	synonymous_variant	55289	exon7			CATCGTTCCTGTC		CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"acyl-Coenzyme A oxidase-like"				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.480T>A	chr2.hg19:g.111556610T>A		115.0	0.0		118.0	62.0	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Silent	SNP	ENST00000389811.4	hg19		.	.	.	.	.	.	.	.	.	.	T	10.87	1.471854	0.26423	.	.	ENSG00000153093	ENST00000422487	.	.	.	5.35	-0.451	0.12214	.	.	.	.	.	T	0.54287	0.1849	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55283	-0.8165	5	0.87932	D	0	-40.3392	1.7734	0.03016	0.127:0.1613:0.1565:0.5552	.	.	.	.	Y	12	.	ENSP00000404255:F12Y	F	+	2	0	ACOXL	111273081	0.872000	0.30054	0.987000	0.45799	0.961000	0.63080	-0.409000	0.07160	0.057000	0.16193	0.528000	0.53228	TTC	.	.		0.473	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308		A	111556610	T	A	111556610	2	1	73	1	0	0	0	0	0	0	0	1	161	1770	62	4		4	ACOXL	2	111556610	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	5698217	111556610	131642763	89	9415										
DPP10	57628	hgsc.bcm.edu	37	chr2	116593732	116593732	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atatatatttttcccccccaGggttatggtggctatattgc	8	9	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:116593732G>T	ENST00000410059.1	+	22	2430		c.e22-1		DPP10_ENST00000310323.8_Splice_Site|DPP10_ENST00000393147.2_Splice_Site|DPP10_ENST00000409163.1_Splice_Site	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)							integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						TTCCCCCCCAGGGTTATGGTG	0.338																																					.		Atlas-SNP	.											.	DPP10	415	.	0			c.1951-1G>T						.						43	43	43					2																	116593732		2203	4300	6503	SO:0001630	splice_region_variant	57628	exon22			CCCCCAGGGTTAT	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1951-1G>T	chr2.hg19:g.116593732G>T		127.0	0.0		125.0	46.0	NM_020868	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Splice_Site	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.764343	0.49574	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7538	0.91825	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DPP10	116310202	1.000000	0.71417	0.995000	0.50966	0.508000	0.34012	7.900000	0.87376	2.649000	0.89929	0.655000	0.94253	.	.	.		0.338	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	Intron	T	116593732	G	T	116593732	5	4	73	1	0	0	0	0	0	0	1	0	4729	1014	35	3	2207	3	DPP10	2	116593732	Splice_Site	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	5037122	116593732	126605641	90	9416										
STEAP3	55240	hgsc.bcm.edu	37	chr2	120020691	120020691	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcacacgctcacctacggctGgacccgcgccttcgaggaga	12	16	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:120020691G>T	ENST00000354888.5	+	6	1748	c.1244G>T	c.(1243-1245)tGg>tTg	p.W415L	STEAP3_ENST00000425223.2_Missense_Mutation_p.W415L|STEAP3_ENST00000393108.2_Missense_Mutation_p.W415L|STEAP3_ENST00000409811.1_3'UTR|STEAP3_ENST00000393106.2_Missense_Mutation_p.W415L|STEAP3_ENST00000393107.2_Missense_Mutation_p.W415L|STEAP3_ENST00000393110.2_Missense_Mutation_p.W425L	NM_182915.2	NP_878919.2	Q658P3	STEA3_HUMAN	STEAP family member 3, metalloreductase	415					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cellular iron ion homeostasis (GO:0006879)|copper ion import (GO:0015677)|exosomal secretion (GO:1990182)|ferric iron import into cell (GO:0097461)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|protein secretion (GO:0009306)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	17						ACCTACGGCTGGACCCGCGCC	0.627																																					p.W425L		Atlas-SNP	.											.	STEAP3	44	.	0			c.G1274T						.						85	87	86					2																	120020691		2203	4300	6503	SO:0001583	missense	55240	exon6			ACGGCTGGACCCG	AY029585	CCDS2125.1, CCDS42738.1	2q14.2	2011-09-30	2011-09-30		ENSG00000115107	ENSG00000115107			24592	protein-coding gene	gene with protein product		609671				12606722	Standard	NM_182915		Approved	TSAP6, dudlin-2, STMP3	uc002tlr.3	Q658P3	OTTHUMG00000131402	ENST00000354888.5:c.1244G>T	chr2.hg19:g.120020691G>T	ENSP00000346961:p.Trp415Leu	41.0	0.0		47.0	21.0	NM_182915	A8K6E3|Q4VBR2|Q4ZG36|Q53SQ8|Q7Z389|Q86SF6|Q8NEW6|Q8TDP3|Q8TF03|Q9NVB5	Missense_Mutation	SNP	ENST00000354888.5	hg19	CCDS2125.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.025250	0.93518	.	.	ENSG00000115107	ENST00000393108;ENST00000354888;ENST00000393110;ENST00000393106;ENST00000393107;ENST00000425223;ENST00000546236	T;T;T;T;T;T	0.07114	3.23;3.23;3.22;3.23;3.23;3.23	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.31702	0.0805	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	T	0.03374	-1.1043	9	.	.	.	-14.2374	17.0672	0.86562	0.0:0.0:1.0:0.0	.	425;415	Q658P3-2;Q658P3	.;STEA3_HUMAN	L	415;415;425;415;415;415;59	ENSP00000376820:W415L;ENSP00000346961:W415L;ENSP00000376822:W425L;ENSP00000376818:W415L;ENSP00000376819:W415L;ENSP00000396214:W415L	.	W	+	2	0	STEAP3	119737161	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.263000	0.95617	2.527000	0.85204	0.561000	0.74099	TGG	.	.		0.627	STEAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254193.1	NM_018234		T	120020691	G	T	120020691	3	4	73	1	0	0	0	0	1	0	0	0	15294	1357	47	3	1292	3	STEAP3	2	120020691	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3426959	120020691	123178682	91	9417										
GLI2	2736	hgsc.bcm.edu	37	chr2	121743964	121743964	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atgccggggacggggcccggGagcctgggagacctgacggc	20	12	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:121743964G>T	ENST00000452319.1	+	13	2127	c.2067G>T	c.(2065-2067)ggG>ggT	p.G689G	GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_Silent_p.G361G|GLI2_ENST00000361492.4_Silent_p.G689G					GLI family zinc finger 2									p.G689G(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CGGGGCCCGGGAGCCTGGGAG	0.711																																					p.G689G		Atlas-SNP	.											GLI2,NS,carcinoma,0,1	GLI2	187	.	1	Substitution - coding silent(1)	lung(1)	c.G2067T						.						36	45	42					2																	121743964		2203	4299	6502	SO:0001819	synonymous_variant	2736	exon12			GCCCGGGAGCCTG		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.2067G>T	chr2.hg19:g.121743964G>T		160.0	0.0		138.0	66.0	NM_005270		Silent	SNP	ENST00000452319.1	hg19	CCDS33283.1																																																																																			.	.		0.711	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121743964	G	T	121743964	2	4	73	1	0	0	0	0	0	0	0	1	6446	1161	41	3		3	GLI2	2	121743964	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1723273	121743964	121455409	92	9418										
ARHGEF4	50649	hgsc.bcm.edu	37	chr2	131803692	131803692	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccagcagcaggtcctggtgcTggcggagcccaggcgcaagc	16	14	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:131803692T>C	ENST00000326016.5	+	14	2522	c.2003T>C	c.(2002-2004)cTg>cCg	p.L668P	ARHGEF4_ENST00000409303.1_Missense_Mutation_p.L608P|ARHGEF4_ENST00000525839.1_3'UTR|ARHGEF4_ENST00000428230.2_Missense_Mutation_p.L170P|ARHGEF4_ENST00000392953.3_3'UTR|ARHGEF4_ENST00000355771.3_Missense_Mutation_p.L597P	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	668					apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		GTCCTGGTGCTGGCGGAGCCC	0.672																																					p.L668P		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.T2003C						.						32	38	36					2																	131803692		2203	4300	6503	SO:0001583	missense	50649	exon14			TGGTGCTGGCGGA	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	684	protein-coding gene	gene with protein product	"APC-stimulated guanine nucleotide exchange factor"	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.2003T>C	chr2.hg19:g.131803692T>C	ENSP00000316845:p.Leu668Pro	57.0	0.0		50.0	13.0	NM_015320	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	hg19	CCDS2165.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.332512	0.81801	.	.	ENSG00000136002	ENST00000326016;ENST00000438985;ENST00000428230;ENST00000409303;ENST00000355771	T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000002	T	0.61311	0.2337	M	0.68317	2.08	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.68943	0.961;0.961	T	0.63585	-0.6604	10	0.56958	D	0.05	.	13.9228	0.63942	0.0:0.0:0.0:1.0	.	608;668	E9PEM0;Q9NR80	.;ARHG4_HUMAN	P	668;350;170;608;597	ENSP00000316845:L668P;ENSP00000389661:L350P;ENSP00000398455:L170P;ENSP00000387285:L608P;ENSP00000348017:L597P	ENSP00000316845:L668P	L	+	2	0	ARHGEF4	131520162	1.000000	0.71417	1.000000	0.80357	0.711000	0.40976	7.471000	0.80985	2.180000	0.69256	0.379000	0.24179	CTG	.	.		0.672	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			C	131803692	T	C	131803692	3	2	73	1	0	0	0	0	1	0	0	0	908	1580	55	2	2141	2	ARHGEF4	2	131803692	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	10059728	131803692	111395681	93	9419										
NEB	4703	hgsc.bcm.edu	37	chr2	152522831	152522831	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gattttggccacattcatgtAgtgaaccagtttaggatcat	9	7	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:152522831A>T	ENST00000172853.10	-	41	4951	c.4804T>A	c.(4804-4806)Tac>Aac	p.Y1602N	NEB_ENST00000603639.1_Missense_Mutation_p.Y1602N|NEB_ENST00000397345.3_Missense_Mutation_p.Y1602N|NEB_ENST00000604864.1_Missense_Mutation_p.Y1602N|NEB_ENST00000409198.1_Missense_Mutation_p.Y1602N|NEB_ENST00000427231.2_Missense_Mutation_p.Y1602N			P20929	NEBU_HUMAN	nebulin	1602					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		ACATTCATGTAGTGAACCAGT	0.438																																					p.Y1602N		Atlas-SNP	.											.	NEB	1697	.	0			c.T4804A						.						277	253	261					2																	152522831		1942	4150	6092	SO:0001583	missense	4703	exon41			TCATGTAGTGAAC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.4804T>A	chr2.hg19:g.152522831A>T	ENSP00000172853:p.Tyr1602Asn	93.0	0.0		86.0	34.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	A	23.9	4.469655	0.84533	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.76	5.76	0.90799	.	0.065584	0.64402	D	0.000006	T	0.61299	0.2336	M	0.68317	2.08	0.80722	D	1	D	0.60575	0.988	D	0.68483	0.958	T	0.57900	-0.7731	10	0.28530	T	0.3	.	16.0711	0.80936	1.0:0.0:0.0:0.0	.	1602	P20929	NEBU_HUMAN	N	1602	ENSP00000386259:Y1602N;ENSP00000380505:Y1602N;ENSP00000416578:Y1602N;ENSP00000172853:Y1602N	ENSP00000172853:Y1602N	Y	-	1	0	NEB	152231077	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.339000	0.96797	2.197000	0.70478	0.482000	0.46254	TAC	.	.		0.438	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152522831	A	T	152522831	3	4	73	1	0	0	0	0	1	0	0	0	10311	420	15	4	21450	4	NEB	2	152522831	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	20719139	152522831	90676542	94	9420										
TANC1	85461	hgsc.bcm.edu	37	chr2	160087091	160087091	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtacagctgagcacagaccCcgcaacacgccgttcatggg	12	14	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:160087091C>A	ENST00000263635.6	+	27	5391	c.5154C>A	c.(5152-5154)ccC>ccA	p.P1718P	TANC1_ENST00000454300.1_Silent_p.P1612P	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1718					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						AGCACAGACCCCGCAACACGC	0.547																																					p.P1718P		Atlas-SNP	.											.	TANC1	157	.	0			c.C5154A						.						107	115	112					2																	160087091		2070	4218	6288	SO:0001819	synonymous_variant	85461	exon27			CAGACCCCGCAAC	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.5154C>A	chr2.hg19:g.160087091C>A		135.0	0.0		111.0	43.0	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	hg19	CCDS42766.1																																																																																			.	.		0.547	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			A	160087091	C	A	160087091	2	1	73	1	0	0	0	0	0	0	0	1	15559	610	22	3		3	TANC1	2	160087091	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	7564260	160087091	83112282	95	9421										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166897949	166897949	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggaaaatttataccaacagGgtgggcatttctgcctggat	11	7	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:166897949G>A	ENST00000303395.4	-	13	2206	c.2207C>T	c.(2206-2208)cCc>cTc	p.P736L	SCN1A_ENST00000423058.2_Missense_Mutation_p.P736L|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.P725L|SCN1A_ENST00000409050.1_Missense_Mutation_p.P708L|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	736					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATACCAACAGGGTGGGCATTT	0.338																																					p.P736L		Atlas-SNP	.											.	SCN1A	641	.	0			c.C2207T						.						80	90	86					2																	166897949		2203	4300	6503	SO:0001583	missense	6323	exon13			CAACAGGGTGGGC	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2207C>T	chr2.hg19:g.166897949G>A	ENSP00000303540:p.Pro736Leu	72.0	0.0		73.0	30.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.406252	0.83230	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.96587	-4.06;-4.06;-3.99;-4.0	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000005	D	0.97929	0.9319	M	0.86864	2.845	0.80722	D	1	P;P;D	0.58970	0.904;0.845;0.984	P;B;P	0.55545	0.571;0.368;0.778	D	0.98481	1.0605	10	0.87932	D	0	.	19.8328	0.96642	0.0:0.0:1.0:0.0	.	725;708;736	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	L	736;736;725;708	ENSP00000407030:P736L;ENSP00000303540:P736L;ENSP00000364554:P725L;ENSP00000386312:P708L	ENSP00000303540:P736L	P	-	2	0	SCN1A	166606195	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.817000	0.86213	2.758000	0.94735	0.591000	0.81541	CCC	.	.		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		A	166897949	G	A	166897949	3	1	73	1	0	0	0	0	1	0	0	0	13929	1232	43	3	3878	3	SCN1A	2	166897949	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	6810858	166897949	76301424	96	9422										
NOSTRIN	115677	hgsc.bcm.edu	37	chr2	169681160	169681160	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acagggcaaacctggaaattAgctatgccaaaggacttcag	10	9	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:169681160A>C	ENST00000317647.7	+	3	359	c.130A>C	c.(130-132)Agc>Cgc	p.S44R	NOSTRIN_ENST00000445023.2_5'UTR|NOSTRIN_ENST00000397209.2_Intron|NOSTRIN_ENST00000458381.2_Missense_Mutation_p.S44R|NOSTRIN_ENST00000444448.2_Missense_Mutation_p.S44R|NOSTRIN_ENST00000421711.2_Intron|NOSTRIN_ENST00000397206.2_5'UTR	NM_001039724.3	NP_001034813.2	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficking	44	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				endocytosis (GO:0006897)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoskeleton (GO:0005856)|endocytic vesicle membrane (GO:0030666)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						CCTGGAAATTAGCTATGCCAA	0.453																																					p.S44R		Atlas-SNP	.											.	NOSTRIN	68	.	0			c.A130C						.						86	81	83					2																	169681160		1893	4127	6020	SO:0001583	missense	115677	exon3			GAAATTAGCTATG	AJ532842	CCDS42771.1, CCDS42772.1, CCDS54415.1, CCDS54416.1	2q31.1	2013-08-05	2013-08-05		ENSG00000163072	ENSG00000163072			20203	protein-coding gene	gene with protein product		607496	"nitric oxide synthase trafficker"			12446846	Standard	NM_001171631		Approved	MGC20702	uc002ueg.3	Q8IVI9	OTTHUMG00000153990	ENST00000317647.7:c.130A>C	chr2.hg19:g.169681160A>C	ENSP00000318921:p.Ser44Arg	701.0	0.0		600.0	221.0	NM_001039724	A8K2I9|B3KSF5|E7EPT9|Q27HG3|Q53S62|Q96CJ9	Missense_Mutation	SNP	ENST00000317647.7	hg19	CCDS42771.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.164663	0.78339	.	.	ENSG00000163072	ENST00000458381;ENST00000444448;ENST00000317647	T;T;T	0.17528	2.27;2.27;2.27	5.18	5.18	0.71444	Fps/Fes/Fer/CIP4 homology (2);	0.231859	0.50627	D	0.000103	T	0.25754	0.0627	L	0.56769	1.78	0.36811	D	0.885886	P;P	0.50369	0.81;0.934	B;P	0.50537	0.326;0.643	T	0.14008	-1.0488	10	0.23302	T	0.38	-11.5771	13.2758	0.60186	1.0:0.0:0.0:0.0	.	44;44	Q8IVI9;E7EPT9	NOSTN_HUMAN;.	R	44	ENSP00000402140:S44R;ENSP00000394051:S44R;ENSP00000318921:S44R	ENSP00000318921:S44R	S	+	1	0	NOSTRIN	169389406	1.000000	0.71417	0.978000	0.43139	0.993000	0.82548	6.214000	0.72200	2.088000	0.63022	0.533000	0.62120	AGC	.	.		0.453	NOSTRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333356.4	NM_052946		C	169681160	A	C	169681160	3	2	73	1	0	0	0	0	1	0	0	0	10555	420	15	5	140	5	NOSTRIN	2	169681160	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2783211	169681160	73518213	97	9423										
PPIG	9360	hgsc.bcm.edu	37	chr2	170465241	170465241	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtcaatggccaacagagggaAggatacaaatggttcacagt	12	7	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:170465241A>G	ENST00000260970.3	+	7	570	c.350A>G	c.(349-351)aAg>aGg	p.K117R	PPIG_ENST00000448752.2_Missense_Mutation_p.K117R|PPIG_ENST00000462903.1_Missense_Mutation_p.K117R|PPIG_ENST00000409714.3_Missense_Mutation_p.K102R	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	117	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	AACAGAGGGAAGGATACAAAT	0.373																																					p.K117R		Atlas-SNP	.											.	PPIG	100	.	0			c.A350G						.						85	84	85					2																	170465241		2203	4300	6503	SO:0001583	missense	9360	exon7			GAGGGAAGGATAC	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"SR-related CTD-associated factor 10"	606093	"peptidyl-prolyl isomerase G (cyclophilin G)"			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.350A>G	chr2.hg19:g.170465241A>G	ENSP00000260970:p.Lys117Arg	378.0	0.0		356.0	154.0	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	hg19	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	A	16.62	3.174157	0.57692	.	.	ENSG00000138398	ENST00000260970;ENST00000530133;ENST00000433207;ENST00000409714;ENST00000462903;ENST00000448752;ENST00000414307	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.06	3.91	0.45181	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.000000	0.85682	D	0.000000	T	0.37489	0.1005	L	0.31845	0.965	0.54753	D	0.999985	P;B;B;B;B	0.39480	0.675;0.447;0.447;0.098;0.402	P;B;B;B;B	0.45474	0.482;0.192;0.26;0.039;0.337	T	0.08126	-1.0737	10	0.33940	T	0.23	-17.2689	10.7459	0.46181	0.9244:0.0:0.0756:0.0	.	113;102;102;117;117	C9JM79;E9PG73;Q2NKQ6;Q13427-2;Q13427	.;.;.;.;PPIG_HUMAN	R	117;117;113;102;117;117;117	ENSP00000260970:K117R;ENSP00000408683:K113R;ENSP00000386245:K102R;ENSP00000435987:K117R;ENSP00000407083:K117R;ENSP00000402222:K117R	ENSP00000260970:K117R	K	+	2	0	PPIG	170173487	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.255000	0.95524	0.876000	0.35872	0.477000	0.44152	AAG	.	.		0.373	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			G	170465241	A	G	170465241	3	3	73	1	0	0	0	0	1	0	0	0	12336	72	3	2	368	2	PPIG	2	170465241	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	784081	170465241	72734132	98	9424										
CDCA7	83879	hgsc.bcm.edu	37	chr2	174230178	174230178	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttttgtattccttgtaatgcAggaagatgacctgcccagaa	9	8	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:174230178A>C	ENST00000347703.3	+	6	801		c.e6-1		CDCA7_ENST00000410101.3_Splice_Site|CDCA7_ENST00000306721.3_Splice_Site|CDCA7_ENST00000392567.2_Splice_Site|CDCA7_ENST00000410019.3_Splice_Site	NM_145810.2	NP_665809.1	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7						apoptotic process (GO:0006915)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.116)			CTTGTAATGCAGGAAGATGAC	0.408																																					.		Atlas-SNP	.											.	CDCA7	48	.	0			c.895-2A>C						.						66	68	67					2																	174230178		2203	4300	6503	SO:0001630	splice_region_variant	83879	exon7			TAATGCAGGAAGA	BG354580	CCDS2252.1, CCDS2253.1	2q31.1	2008-02-05			ENSG00000144354	ENSG00000144354			14628	protein-coding gene	gene with protein product		609937				11598121, 12188893	Standard	NM_145810		Approved	FLJ14736, JPO1	uc002uic.1	Q9BWT1	OTTHUMG00000132296	ENST00000347703.3:c.658-1A>C	chr2.hg19:g.174230178A>C		80.0	0.0		65.0	34.0	NM_031942	B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	Splice_Site	SNP	ENST00000347703.3	hg19	CCDS2253.1	.	.	.	.	.	.	.	.	.	.	A	16.09	3.025446	0.54683	.	.	ENSG00000144354	ENST00000347703;ENST00000392567;ENST00000306721;ENST00000410101;ENST00000410019	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3305	0.83010	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDCA7	173938424	1.000000	0.71417	0.963000	0.40424	0.450000	0.32258	4.038000	0.57318	2.317000	0.78254	0.459000	0.35465	.	.	.		0.408	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255400.1	NM_031942	Intron	C	174230178	A	C	174230178	5	2	73	1	0	0	0	0	0	0	1	0	3092	202	7	5	919	5	CDCA7	2	174230178	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3764937	174230178	68969195	99	9425										
TTN	7273	hgsc.bcm.edu	37	chr2	179431803	179431803	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaaacatattcattaccttcTaagagtttggtaactttcag	5	7	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:179431803T>C	ENST00000591111.1	-	276	74357	c.74133A>G	c.(74131-74133)ttA>ttG	p.L24711L	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.L17412L|TTN_ENST00000460472.2_Silent_p.L17287L|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Silent_p.L17479L|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Silent_p.L23784L|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Silent_p.L26352L|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24711	Fibronectin type-III 79. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATTACCTTCTAAGAGTTTGG	0.393																																					p.L26352L		Atlas-SNP	.											.	TTN	18412	.	0			c.A79056G						.						134	132	133					2																	179431803		1848	4096	5944	SO:0001819	synonymous_variant	7273	exon326			ACCTTCTAAGAGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.74133A>G	chr2.hg19:g.179431803T>C		120.0	0.0		119.0	43.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179431803	T	C	179431803	2	2	73	1	0	0	0	0	0	0	0	1	16750	1519	53	2		2	TTN	2	179431803	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	5201625	179431803	63767570	100	9426										
TTN	7273	hgsc.bcm.edu	37	chr2	179587117	179587117	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cattatctacaaatgaagtcTgtagattttcatcgtctctt	5	8	4	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:179587117T>G	ENST00000591111.1	-	75	21670	c.21446A>C	c.(21445-21447)cAg>cCg	p.Q7149P	RP11-171I2.1_ENST00000590024.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.Q6222P|TTN_ENST00000589042.1_Missense_Mutation_p.Q7466P			Q8WZ42	TITIN_HUMAN	titin	12724	Ig-like 53.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAATGAAGTCTGTAGATTTTC	0.418																																					p.Q7466P		Atlas-SNP	.											.	TTN	18412	.	0			c.A22397C						.						55	54	54					2																	179587117		1855	4107	5962	SO:0001583	missense	7273	exon77			GAAGTCTGTAGAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.21446A>C	chr2.hg19:g.179587117T>G	ENSP00000465570:p.Gln7149Pro	109.0	0.0		98.0	38.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	7.050	0.564201	0.13498	.	.	ENSG00000155657	ENST00000342992	T	0.68479	-0.33	6.16	6.16	0.99307	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.71584	0.3357	M	0.84511	2.7	0.80722	D	1	P	0.50443	0.935	B	0.40038	0.317	T	0.78961	-0.1997	9	0.87932	D	0	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	7149	Q8WZ42	TITIN_HUMAN	P	6222	ENSP00000343764:Q6222P	ENSP00000343764:Q6222P	Q	-	2	0	TTN	179295362	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	2.658000	0.46733	2.367000	0.80283	0.528000	0.53228	CAG	.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179587117	T	G	179587117	3	3	73	1	0	0	0	0	1	0	0	0	16750	1580	55	5	82276	5	TTN	2	179587117	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	155314	179587117	63612256	101	9427										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196913052	196913052	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	catttttaacactaaatggtTctggactctcatcatcctgc	5	11	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:196913052T>A	ENST00000312428.6	-	4	318	c.218A>T	c.(217-219)gAa>gTa	p.E73V	DNAH7_ENST00000410072.1_Missense_Mutation_p.E73V	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	73	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						ACTAAATGGTTCTGGACTCTC	0.358																																					p.E73V		Atlas-SNP	.											.	DNAH7	512	.	0			c.A218T						.						130	120	123					2																	196913052		1866	4112	5978	SO:0001583	missense	56171	exon4			AATGGTTCTGGAC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.218A>T	chr2.hg19:g.196913052T>A	ENSP00000311273:p.Glu73Val	61.0	0.0		59.0	25.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.953804	0.73902	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446;ENST00000427816	T;T	0.23348	1.91;2.7	4.81	4.81	0.61882	.	0.257338	0.30446	N	0.009615	T	0.21801	0.0525	L	0.46157	1.445	0.18873	N	0.999986	B	0.28128	0.201	B	0.21360	0.034	T	0.14200	-1.0481	10	0.45353	T	0.12	.	10.9236	0.47180	0.0:0.0:0.0:1.0	.	73	Q8WXX0	DYH7_HUMAN	V	73;73;73;48	ENSP00000311273:E73V;ENSP00000386260:E73V	ENSP00000311273:E73V	E	-	2	0	DNAH7	196621297	0.865000	0.29922	0.112000	0.21494	0.506000	0.33950	2.355000	0.44107	2.156000	0.67533	0.477000	0.44152	GAA	.	.		0.358	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196913052	T	A	196913052	3	1	73	1	0	0	0	0	1	0	0	0	4608	1783	62	4	12104	4	DNAH7	2	196913052	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	17325935	196913052	46286321	102	9428										
HECW2	57520	hgsc.bcm.edu	37	chr2	197183894	197183894	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgcgccacttgtgggctgatCtacctcttgagagccacaca	10	13	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:197183894C>T	ENST00000260983.3	-	9	1902	c.1720G>A	c.(1720-1722)Gat>Aat	p.D574N	HECW2_ENST00000409111.1_Missense_Mutation_p.D218N	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	574					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						GTGGGCTGATCTACCTCTTGA	0.612																																					p.D574N		Atlas-SNP	.											.	HECW2	239	.	0			c.G1720A						.						58	52	54					2																	197183894		2203	4300	6503	SO:0001583	missense	57520	exon9			GCTGATCTACCTC	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.1720G>A	chr2.hg19:g.197183894C>T	ENSP00000260983:p.Asp574Asn	108.0	0.0		101.0	39.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.960448	0.53400	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	T;T	0.34072	1.38;1.41	5.03	5.03	0.67393	.	0.930394	0.09133	N	0.844069	T	0.28433	0.0703	N	0.14661	0.345	0.37176	D	0.903272	B	0.26635	0.155	B	0.23716	0.048	T	0.16276	-1.0408	10	0.52906	T	0.07	.	16.7254	0.85421	0.0:1.0:0.0:0.0	.	574	Q9P2P5	HECW2_HUMAN	N	218;574	ENSP00000386775:D218N;ENSP00000260983:D574N	ENSP00000260983:D574N	D	-	1	0	HECW2	196892139	0.997000	0.39634	0.889000	0.34880	0.853000	0.48598	3.934000	0.56553	2.609000	0.88269	0.561000	0.74099	GAT	.	.		0.612	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		T	197183894	C	T	197183894	3	4	73	1	0	0	0	0	1	0	0	0	7052	913	32	3	3082	3	HECW2	2	197183894	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	270842	197183894	46015479	103	9429										
ALS2CR11	151254	hgsc.bcm.edu	37	chr2	202400648	202400648	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagcctgtgttctccctttcAgctaagtttagattgttgtt	8	8	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:202400648A>T	ENST00000286195.3	-	13	1551				ALS2CR11_ENST00000439140.1_Intron|ALS2CR11_ENST00000439802.1_Intron|ALS2CR11_ENST00000450242.1_Silent_p.A534A	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11											NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						TCTCCCTTTCAGCTAAGTTTA	0.398																																					p.A534A		Atlas-SNP	.											.	ALS2CR11	194	.	0			c.T1602A						.						146	109	120					2																	202400648		692	1590	2282	SO:0001627	intron_variant	151254	exon13			CCTTTCAGCTAAG	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.1506+95T>A	chr2.hg19:g.202400648A>T		33.0	0.0		28.0	12.0	NM_001168217	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Silent	SNP	ENST00000286195.3	hg19	CCDS2349.1																																																																																			.	.		0.398	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525		T	202400648	A	T	202400648	1	4	73	0	1	0	0	0	0	0	0	0	552	175	7	4		4	ALS2CR11	2	202400648	Intron	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	5216754	202400648	40798725	104	9430										
ALS2	57679	hgsc.bcm.edu	37	chr2	202593826	202593826	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cccagtgtgtattctgcttcCttccttttcctgccgagatg	8	13	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:202593826C>T	ENST00000264276.6	-	14	3033	c.2661G>A	c.(2659-2661)aaG>aaA	p.K887K	ALS2_ENST00000457679.2_Silent_p.K199K	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	887					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						ATTCTGCTTCCTTCCTTTTCC	0.453																																					p.K887K		Atlas-SNP	.											.	ALS2	172	.	0			c.G2661A						.						135	127	130					2																	202593826		1858	4102	5960	SO:0001819	synonymous_variant	57679	exon14			TGCTTCCTTCCTT	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.2661G>A	chr2.hg19:g.202593826C>T		180.0	0.0		162.0	86.0	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Silent	SNP	ENST00000264276.6	hg19	CCDS42800.1																																																																																			.	.		0.453	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		T	202593826	C	T	202593826	2	4	73	1	0	0	0	0	0	0	0	1	550	680	24	3		3	ALS2	2	202593826	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	193178	202593826	40605547	105	9431										
PARD3B	117583	hgsc.bcm.edu	37	chr2	206036933	206036933	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gttttcctttcttctgccttAggatggtcgtctgcgaatga	10	9	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:206036933A>T	ENST00000406610.2	+	12	1827		c.e12-1		PARD3B_ENST00000351153.1_Splice_Site|PARD3B_ENST00000358768.2_Splice_Site|PARD3B_ENST00000349953.3_Splice_Site|PARD3B_ENST00000462231.1_Splice_Site	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta						cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		CTTCTGCCTTAGGATGGTCGT	0.398																																					.		Atlas-SNP	.											.	PARD3B	314	.	0			c.1621-2A>T						.						99	91	94					2																	206036933		1902	4118	6020	SO:0001630	splice_region_variant	117583	exon12			TGCCTTAGGATGG	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19", "par-3 partitioning defective 3 homolog B (C. elegans)"	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.1621-1A>T	chr2.hg19:g.206036933A>T		148.0	0.0		128.0	50.0	NM_057177	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Splice_Site	SNP	ENST00000406610.2	hg19		.	.	.	.	.	.	.	.	.	.	A	17.86	3.493176	0.64186	.	.	ENSG00000116117	ENST00000406610;ENST00000358768;ENST00000351153;ENST00000349953	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8835	0.79222	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PARD3B	205745178	1.000000	0.71417	0.972000	0.41901	0.493000	0.33554	8.962000	0.93254	2.153000	0.67306	0.477000	0.44152	.	.	.		0.398	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	Intron	T	206036933	A	T	206036933	5	4	73	1	0	0	0	0	0	0	1	0	11453	434	15	4	1665	4	PARD3B	2	206036933	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3443107	206036933	37162440	106	9432										
MAP2	4133	hgsc.bcm.edu	37	chr2	210557752	210557752	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttagttgcccccatatctccTggccctctgactcccatgag	7	16	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:210557752T>A	ENST00000360351.4	+	7	1364	c.858T>A	c.(856-858)ccT>ccA	p.P286P	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000447185.1_Silent_p.P282P|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	286					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	CCATATCTCCTGGCCCTCTGA	0.463																																					p.P286P	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.T858A						.						51	52	51					2																	210557752		2203	4300	6503	SO:0001819	synonymous_variant	4133	exon7			ATCTCCTGGCCCT		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.858T>A	chr2.hg19:g.210557752T>A		165.0	0.0		141.0	60.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.		0.463	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		A	210557752	T	A	210557752	2	1	73	1	0	0	0	0	0	0	0	1	9244	1567	55	4		4	MAP2	2	210557752	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	4520819	210557752	32641621	107	9433										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215833480	215833480	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttggcagggactcctgttatAtcaaaacgaaggtcttttgt	10	7	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:215833480A>G	ENST00000272895.7	-	38	5961	c.5742T>C	c.(5740-5742)gaT>gaC	p.D1914D	ABCA12_ENST00000389661.4_Silent_p.D1596D	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1914					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CTCCTGTTATATCAAAACGAA	0.343																																					p.D1914D	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.T5742C						.						90	102	98					2																	215833480		2203	4300	6503	SO:0001819	synonymous_variant	26154	exon38			TGTTATATCAAAA	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5742T>C	chr2.hg19:g.215833480A>G		109.0	0.0		122.0	44.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	hg19	CCDS33372.1																																																																																			.	.		0.343	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215833480	A	G	215833480	2	3	73	1	0	0	0	0	0	0	0	1	30	446	16	2		2	ABCA12	2	215833480	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	5275728	215833480	27365893	108	9434										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215914355	215914355	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagatctacactcacctgggAgaactgtttgtttagttctt	8	8	3	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:215914355A>T	ENST00000272895.7	-	6	907	c.688T>A	c.(688-690)Tcc>Acc	p.S230T		NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	230					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CTCACCTGGGAGAACTGTTTG	0.383																																					p.S230T	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.T688A						.						76	74	74					2																	215914355		2203	4300	6503	SO:0001583	missense	26154	exon6			CCTGGGAGAACTG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.688T>A	chr2.hg19:g.215914355A>T	ENSP00000272895:p.Ser230Thr	111.0	0.0		95.0	43.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	16.84	3.235285	0.58886	.	.	ENSG00000144452	ENST00000272895	D	0.88664	-2.41	5.75	5.75	0.90469	.	0.196800	0.37219	N	0.002182	D	0.82884	0.5134	L	0.27053	0.805	0.80722	D	1	P	0.34562	0.457	B	0.36378	0.223	T	0.81317	-0.0987	10	0.30854	T	0.27	.	13.874	0.63643	1.0:0.0:0.0:0.0	.	230	Q86UK0	ABCAC_HUMAN	T	230	ENSP00000272895:S230T	ENSP00000272895:S230T	S	-	1	0	ABCA12	215622600	1.000000	0.71417	0.998000	0.56505	0.848000	0.48234	2.448000	0.44926	2.323000	0.78572	0.533000	0.62120	TCC	.	.		0.383	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215914355	A	T	215914355	3	4	73	1	0	0	0	0	1	0	0	0	30	304	11	4	7322	4	ABCA12	2	215914355	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	80875	215914355	27285018	109	9435										
TNS1	7145	hgsc.bcm.edu	37	chr2	218750502	218750502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caagagcagtcctggctcgaTggtgatgcagacgctagtct	13	10	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:218750502T>C	ENST00000171887.4	-	13	1158	c.706A>G	c.(706-708)Atc>Gtc	p.I236V	TNS1_ENST00000419504.1_Missense_Mutation_p.I236V|TNS1_ENST00000430930.1_Missense_Mutation_p.I236V|TNS1_ENST00000310858.6_Missense_Mutation_p.I267V	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	236	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CCTGGCTCGATGGTGATGCAG	0.542																																					p.I236V		Atlas-SNP	.											.	TNS1	251	.	0			c.A706G						.						146	127	133					2																	218750502		2203	4300	6503	SO:0001583	missense	7145	exon13			GCTCGATGGTGAT	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.706A>G	chr2.hg19:g.218750502T>C	ENSP00000171887:p.Ile236Val	72.0	0.0		74.0	29.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.22|15.22	2.769777|2.769777	0.49680|0.49680	.|.	.|.	ENSG00000079308|ENSG00000079308	ENST00000453356|ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554;ENST00000310858	.|D;D;D;D;D;D	.|0.86497	.|-2.13;-2.13;-2.13;-2.13;-2.13;-2.13	4.77|4.77	4.77|4.77	0.60923|0.60923	.|Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91610|0.91610	0.7349|0.7349	M|M	0.61703|0.61703	1.905|1.905	0.58432|0.58432	D|D	0.999999|0.999999	.|D;B;B;D;D;D	.|0.69078	.|0.997;0.115;0.363;0.996;0.958;0.993	.|D;B;B;D;D;D	.|0.80764	.|0.994;0.345;0.336;0.994;0.97;0.987	D|D	0.91191|0.91191	0.4984|0.4984	5|10	.|0.41790	.|T	.|0.15	.|.	14.118|14.118	0.65167|0.65167	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|236;290;267;236;236;236	.|B2RU35;A1L0S7;Q6IPI5;Q9HBL0;E9PGF5;E9PF55	.|.;.;.;TENS1_HUMAN;.;.	R|V	11|236;236;236;361;304;267	.|ENSP00000171887:I236V;ENSP00000408724:I236V;ENSP00000406016:I236V;ENSP00000405460:I361V;ENSP00000400383:I304V;ENSP00000308321:I267V	.|ENSP00000171887:I236V	H|I	-|-	2|1	0|0	TNS1|TNS1	218458747|218458747	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.912000|0.912000	0.54170|0.54170	3.976000|3.976000	0.56867|0.56867	1.992000|1.992000	0.58205|0.58205	0.379000|0.379000	0.24179|0.24179	CAT|ATC	.	.		0.542	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		C	218750502	T	C	218750502	3	2	73	1	0	0	0	0	1	0	0	0	16358	1464	51	2	4585	2	TNS1	2	218750502	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2836147	218750502	24448871	110	9436										
ACCN4	55515	hgsc.bcm.edu	37	chr2	220396495	220396495	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cccaggtctatactcgctatGggaagtgttacaccttcaac	8	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:220396495G>T	ENST00000347842.3	+	2	993	c.979G>T	c.(979-981)Ggg>Tgg	p.G327W	ASIC4_ENST00000358078.4_Missense_Mutation_p.G327W|ASIC4_ENST00000473709.1_3'UTR	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	327					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										TACTCGCTATGGGAAGTGTTA	0.632																																					p.G327W		Atlas-SNP	.											.	.	.	.	0			c.G979T						.						64	68	66					2																	220396495		2203	4300	6503	SO:0001583	missense	55515	exon2			CGCTATGGGAAGT	AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"Ion channels / Acid-sensing (proton-gated) ion channels"	21263	protein-coding gene	gene with protein product		606715	"amiloride-sensitive cation channel 4, pituitary", "amiloride-sensitive cation channel family member 4, pituitary"	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.979G>T	chr2.hg19:g.220396495G>T	ENSP00000326627:p.Gly327Trp	409.0	1.0		292.0	113.0	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Missense_Mutation	SNP	ENST00000347842.3	hg19	CCDS2442.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953766	0.73902	.	.	ENSG00000072182	ENST00000347842;ENST00000358078	D;D	0.88046	-2.33;-2.33	3.16	3.16	0.36331	.	0.000000	0.85682	D	0.000000	D	0.94761	0.8309	M	0.93283	3.4	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;1.0	D	0.96142	0.9101	10	0.87932	D	0	-14.9041	15.1743	0.72899	0.0:0.0:1.0:0.0	.	327;327;327	Q96FT7;Q96FT7-4;Q96FT7-2	ACCN4_HUMAN;.;.	W	327	ENSP00000326627:G327W;ENSP00000350786:G327W	ENSP00000326627:G327W	G	+	1	0	ACCN4	220104739	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.551000	0.98112	2.079000	0.62486	0.561000	0.74099	GGG	.	.		0.632	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674		T	220396495	G	T	220396495	3	4	73	1	0	0	0	0	1	0	0	0	131	1348	47	3	985	3	ACCN4	2	220396495	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1645993	220396495	22802878	111	9437										
SERPINE2	5270	hgsc.bcm.edu	37	chr2	224866418	224866418	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggtcctgccgtccgcccccAgctgaagcatccccaggacc	10	19	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:224866418A>T	ENST00000258405.4	-	2	442	c.200T>A	c.(199-201)cTg>cAg	p.L67Q	SERPINE2_ENST00000409840.3_Missense_Mutation_p.L67Q|SERPINE2_ENST00000409304.1_Missense_Mutation_p.L67Q|SERPINE2_ENST00000447280.2_Missense_Mutation_p.L79Q	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	67					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		GTCCGCCCCCAGCTGAAGCAT	0.567																																					p.L79Q		Atlas-SNP	.											.	SERPINE2	103	.	0			c.T236A						.						87	78	81					2																	224866418		2203	4300	6503	SO:0001583	missense	5270	exon2			GCCCCCAGCTGAA	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"Serine (or cysteine) peptidase inhibitors"	8951	protein-coding gene	gene with protein product	"glial-derived nexin 1"	177010	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.200T>A	chr2.hg19:g.224866418A>T	ENSP00000258405:p.Leu67Gln	63.0	0.0		63.0	27.0	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Missense_Mutation	SNP	ENST00000258405.4	hg19	CCDS2460.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.467241	0.84533	.	.	ENSG00000135919	ENST00000409304;ENST00000258405;ENST00000409840;ENST00000447280;ENST00000432738;ENST00000454956	D;D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18;-2.03	5.67	5.67	0.87782	Serpin domain (3);	0.135608	0.50627	D	0.000109	D	0.93874	0.8040	M	0.84585	2.705	0.52099	D	0.999947	D;D	0.71674	0.998;0.998	D;D	0.73380	0.98;0.98	D	0.94676	0.7861	10	0.72032	D	0.01	.	15.9132	0.79488	1.0:0.0:0.0:0.0	.	79;67	B4DIF2;P07093	.;GDN_HUMAN	Q	67;67;67;79;67;67	ENSP00000386412:L67Q;ENSP00000258405:L67Q;ENSP00000386969:L67Q;ENSP00000415786:L79Q;ENSP00000408452:L67Q;ENSP00000399655:L67Q	ENSP00000258405:L67Q	L	-	2	0	SERPINE2	224574662	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.387000	0.73191	2.148000	0.66965	0.533000	0.62120	CTG	.	.		0.567	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216		T	224866418	A	T	224866418	3	4	73	1	0	0	0	0	1	0	0	0	14127	188	7	4	1028	4	SERPINE2	2	224866418	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4469923	224866418	18332955	112	9438										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227886777	227886777	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctcatacctggtcctgagggGcctctcattccagggagccc	11	15	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:227886777G>A	ENST00000396625.3	-	44	4410	c.4203C>T	c.(4201-4203)ggC>ggT	p.G1401G	COL4A4_ENST00000329662.7_Silent_p.G1398G	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1401	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GTCCTGAGGGGCCTCTCATTC	0.483																																					p.G1401G		Atlas-SNP	.											.	COL4A4	215	.	0			c.C4203T						.						110	118	115					2																	227886777		1883	4105	5988	SO:0001819	synonymous_variant	1286	exon44			TGAGGGGCCTCTC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4203C>T	chr2.hg19:g.227886777G>A		240.0	1.0		247.0	105.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	hg19	CCDS42828.1																																																																																			.	.		0.483	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		A	227886777	G	A	227886777	2	1	73	1	0	0	0	0	0	0	0	1	3695	1190	42	3		3	COL4A4	2	227886777	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3020359	227886777	15312596	113	9439										
FARP2	9855	hgsc.bcm.edu	37	chr2	242380941	242380941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acacaccatcggcccagcccCtcgggccccccgcactccag	8	23	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr2:242380941C>T	ENST00000264042.3	+	13	1551	c.1381C>T	c.(1381-1383)Ctc>Ttc	p.L461F	FARP2_ENST00000373287.4_Missense_Mutation_p.L461F|FARP2_ENST00000545004.1_Missense_Mutation_p.L461F	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	461	Pro-rich.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GGCCCAGCCCCTCGGGCCCCC	0.637																																					p.L461F		Atlas-SNP	.											.	FARP2	92	.	0			c.C1381T						.						27	31	29					2																	242380941		2203	4298	6501	SO:0001583	missense	9855	exon13			CAGCCCCTCGGGC	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.1381C>T	chr2.hg19:g.242380941C>T	ENSP00000264042:p.Leu461Phe	96.0	0.0		89.0	40.0	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	hg19	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	C	2.836	-0.241528	0.05906	.	.	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287;ENST00000413432	T;D;D;T	0.81579	-0.92;-1.51;-1.51;-1.45	5.08	3.21	0.36854	.	4.117010	0.00357	N	0.000034	T	0.72112	0.3420	N	0.14661	0.345	0.09310	N	1	B;B;P	0.35600	0.259;0.259;0.511	B;B;B	0.29524	0.103;0.064;0.101	T	0.64896	-0.6299	10	0.56958	D	0.05	.	16.4196	0.83754	0.0:0.7516:0.2484:0.0	.	461;461;461	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	F	461;461;461;148	ENSP00000264042:L461F;ENSP00000443876:L461F;ENSP00000362384:L461F;ENSP00000412772:L148F	ENSP00000264042:L461F	L	+	1	0	FARP2	242029614	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	1.336000	0.33850	0.552000	0.29026	-0.795000	0.03280	CTC	.	.		0.637	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			T	242380941	C	T	242380941	3	4	73	1	0	0	0	0	1	0	0	0	5685	681	24	3	1427	3	FARP2	2	242380941	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	14494164	242380941	818432	114	9440										
CAND2	23066	hgsc.bcm.edu	37	chr3	12858225	12858225	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atttcctgcatgggccacctTgtaggccacctgggtgaccg	12	13	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:12858225T>A	ENST00000456430.2	+	10	1835	c.1794T>A	c.(1792-1794)ctT>ctA	p.L598L	CAND2_ENST00000295989.5_Silent_p.L505L	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	598					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TGGGCCACCTTGTAGGCCACC	0.627																																					p.L598L	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.T1794A						.						72	83	80					3																	12858225		2128	4227	6355	SO:0001819	synonymous_variant	23066	exon10			CCACCTTGTAGGC		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1794T>A	chr3.hg19:g.12858225T>A		149.0	1.0		124.0	105.0	NM_001162499	B9EGM9|E9KL24	Silent	SNP	ENST00000456430.2	hg19	CCDS54554.1																																																																																			.	.		0.627	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		A	12858225	T	A	12858225	2	1	73	1	0	0	0	0	0	0	0	1	2618	1799	63	4		4	CAND2	3	12858225	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10		12858225	185164205	115	9441										
NUP210	23225	hgsc.bcm.edu	37	chr3	13401819	13401819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggatccagtgttgctgataaTtccgggaggaatggggggca	17	6	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:13401819T>C	ENST00000254508.5	-	15	2187	c.2105A>G	c.(2104-2106)aAt>aGt	p.N702S		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	702					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TTGCTGATAATTCCGGGAGGA	0.582																																					p.N702S		Atlas-SNP	.											.	NUP210	182	.	0			c.A2105G						.						84	76	79					3																	13401819		2203	4300	6503	SO:0001583	missense	23225	exon15			TGATAATTCCGGG	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.2105A>G	chr3.hg19:g.13401819T>C	ENSP00000254508:p.Asn702Ser	161.0	0.0		115.0	101.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	T	11.31	1.600159	0.28534	.	.	ENSG00000132182	ENST00000254508	T	0.23950	1.88	5.66	4.5	0.54988	.	0.097784	0.64402	D	0.000002	T	0.15869	0.0382	L	0.35288	1.05	0.34934	D	0.749603	B;B	0.20887	0.049;0.029	B;B	0.17722	0.019;0.015	T	0.17745	-1.0359	10	0.09084	T	0.74	-13.2169	7.8484	0.29440	0.0:0.2213:0.0:0.7787	.	702;702	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	S	702	ENSP00000254508:N702S	ENSP00000254508:N702S	N	-	2	0	NUP210	13376819	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	1.605000	0.36815	0.984000	0.38629	0.533000	0.62120	AAT	.	.		0.582	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		C	13401819	T	C	13401819	3	2	73	1	0	0	0	0	1	0	0	0	10769	1493	52	2	3662	2	NUP210	3	13401819	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	543594	13401819	184620611	116	9442										
FGD5	152273	hgsc.bcm.edu	37	chr3	14860937	14860937	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tacaggagctggtgaggattCagtggcccctgctgctccgg	15	11	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:14860937C>A	ENST00000285046.5	+	1	469	c.359C>A	c.(358-360)tCa>tAa	p.S120*	FGD5_ENST00000543601.1_5'UTR	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	120	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						GGTGAGGATTCAGTGGCCCCT	0.632																																					p.S120X		Atlas-SNP	.											.	FGD5	248	.	0			c.C359A						.						18	22	20					3																	14860937		692	1590	2282	SO:0001587	stop_gained	152273	exon1			AGGATTCAGTGGC	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.359C>A	chr3.hg19:g.14860937C>A	ENSP00000285046:p.Ser120*	204.0	1.0		187.0	158.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Nonsense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.812810	0.90707	.	.	ENSG00000154783	ENST00000285046	.	.	.	5.66	-8.22	0.01037	.	2.531350	0.01468	N	0.016155	.	.	.	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	2.683	10.449	0.44511	0.0:0.5465:0.2488:0.2047	.	.	.	.	X	120	.	ENSP00000285046:S120X	S	+	2	0	FGD5	14835941	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.686000	0.05161	-2.428000	0.00559	-1.094000	0.02160	TCA	.	.		0.632	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		A	14860937	C	A	14860937	4	1	73	1	0	0	0	0	0	1	0	0	5844	838	29	3	361	3	FGD5	3	14860937	Nonsense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1459118	14860937	183161493	117	9443										
ITGA9	3680	hgsc.bcm.edu	37	chr3	37774280	37774280	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggatttcctttcatgaggtcAaagtcaaaggtaagggacac	11	7	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:37774280A>C	ENST00000264741.5	+	19	2401	c.2145A>C	c.(2143-2145)tcA>tcC	p.S715S		NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	715					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		TCATGAGGTCAAAGTCAAAGG	0.562																																					p.S715S		Atlas-SNP	.											.	ITGA9	98	.	0			c.A2145C						.						81	74	76					3																	37774280		2203	4299	6502	SO:0001819	synonymous_variant	3680	exon19			GAGGTCAAAGTCA	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2145A>C	chr3.hg19:g.37774280A>C		92.0	0.0		74.0	63.0	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	hg19	CCDS2669.1																																																																																			.	.		0.562	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		C	37774280	A	C	37774280	2	2	73	1	0	0	0	0	0	0	0	1	7892	117	5	5		5	ITGA9	3	37774280	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	22913343	37774280	160248150	118	9444										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38766700	38766700	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aggaacagactcatctttccAcgtctcacccagggatggag	10	12	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:38766700A>C	ENST00000449082.2	-	17	3192	c.3193T>G	c.(3193-3195)Tgg>Ggg	p.W1065G		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1065					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TCATCTTTCCACGTCTCACCC	0.592																																					p.W1065G		Atlas-SNP	.											.	SCN10A	359	.	0			c.T3193G						.						79	77	78					3																	38766700		2203	4300	6503	SO:0001583	missense	6336	exon17			CTTTCCACGTCTC	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.3193T>G	chr3.hg19:g.38766700A>C	ENSP00000390600:p.Trp1065Gly	140.0	1.0		60.0	45.0	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	hg19	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	A	5.985	0.365674	0.11352	.	.	ENSG00000185313	ENST00000449082	D	0.83755	-1.76	4.8	-4.2	0.03823	Sodium ion transport-associated (1);	12.276300	0.00166	N	0.000000	T	0.74959	0.3785	L	0.42245	1.32	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.57207	-0.7851	10	0.40728	T	0.16	.	5.8169	0.18497	0.381:0.2791:0.3399:0.0	.	1065	Q9Y5Y9	SCNAA_HUMAN	G	1065	ENSP00000390600:W1065G	ENSP00000390600:W1065G	W	-	1	0	SCN10A	38741704	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-0.416000	0.07097	-0.625000	0.05604	-0.369000	0.07265	TGG	.	.		0.592	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		C	38766700	A	C	38766700	3	2	73	1	0	0	0	0	1	0	0	0	13927	159	6	5	2721	5	SCN10A	3	38766700	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	992420	38766700	159255730	119	9445										
SCN11A	11280	hgsc.bcm.edu	37	chr3	38926834	38926834	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	accatctcaggtaaccatccAaagccatcctgaagatcaat	5	13	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:38926834A>G	ENST00000302328.3	-	17	3207	c.3009T>C	c.(3007-3009)ttT>ttC	p.F1003F	SCN11A_ENST00000444237.2_Silent_p.F1003F|SCN11A_ENST00000450244.1_Silent_p.F1003F|SCN11A_ENST00000456224.3_Silent_p.F965F	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1003					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GTAACCATCCAAAGCCATCCT	0.433																																					p.F1003F		Atlas-SNP	.											.	SCN11A	296	.	0			c.T3009C						.						158	145	149					3																	38926834		2203	4300	6503	SO:0001819	synonymous_variant	11280	exon17			CCATCCAAAGCCA	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.3009T>C	chr3.hg19:g.38926834A>G		144.0	1.0		118.0	102.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.		0.433	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		G	38926834	A	G	38926834	2	3	73	1	0	0	0	0	0	0	0	1	13928	127	5	2		2	SCN11A	3	38926834	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	160134	38926834	159095596	120	9446										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266127	41266150	+	In_Frame_Del	DEL	ACAGCTCCTTCTCTGAGTGGTAAA	ACAGCTCCTTCTCTGAGTGGTAAA	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tccattctggtgccactaccAcagctccttctctgagtggt					rs121913407|rs121913409		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	ACAGCTCCTTCTCTGAGTGGTAAA	ACAGCTCCTTCTCTGAGTGGTAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:41266127_41266150delACAGCTCCTTCTCTGAGTGGTAAA	ENST00000349496.5	+	3	404_427	c.124_147delACAGCTCCTTCTCTGAGTGGTAAA	c.(124-147)acagctccttctctgagtggtaaadel	p.TAPSLSGK42del	CTNNB1_ENST00000396185.3_In_Frame_Del_p.TAPSLSGK42del|CTNNB1_ENST00000396183.3_In_Frame_Del_p.TAPSLSGK42del|CTNNB1_ENST00000405570.1_In_Frame_Del_p.TAPSLSGK42del|CTNNB1_ENST00000453024.1_In_Frame_Del_p.TAPSLSGK35del	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	42					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45F(384)|p.S45P(168)|p.S45del(54)|p.A5_A80del(53)|p.S45C(19)|p.S45Y(17)|p.S45A(11)|p.K49R(9)|p.G48D(9)|p.A5_A80>D(7)|p.A5_Q143del(7)|p.T42R(5)|p.Q28_H134del(5)|p.A43V(5)|p.P44A(5)|p.A43T(4)|p.?(4)|p.P44S(4)|p.L46L(3)|p.S47N(3)|p.T42I(3)|p.W25_I140del(3)|p.T42fs*7(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.K49*(2)|p.D32_S47del(2)|p.G48V(2)|p.S45_S47>C(2)|p.P44_S45del(2)|p.S47T(2)|p.A43P(2)|p.A5_Y142>D(2)|p.A5fs*7(2)|p.T42_A43insSS(2)|p.L10_N141del(2)|p.P44L(2)|p.S37_G48>C(1)|p.Q28_Q61del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.K49E(1)|p.K49K(1)|p.Y30_A97del(1)|p.K49L(1)|p.T40_L46del(1)|p.Q28_A43del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.P44del(1)|p.A13_R151del(1)|p.M1_A87del(1)|p.L46_S47del(1)|p.P44_N51del(1)|p.V22_T102del(1)|p.S45fs*2(1)|p.T42T(1)|p.S45E(1)|p.T42S(1)|p.S45T(1)|p.A21_A80del(1)|p.S45S(1)|p.T42A(1)|p.A39_T42del(1)|p.I35_K170del(1)|p.L46V(1)|p.M14_S45del(1)|p.T42_G48del(1)|p.P44_S45insAP(1)|p.S45_G48del(1)|p.T42_K49>Q(1)|p.S45_D58del(1)|p.P16_K133del(1)|p.A20_A80del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.S47C(1)|p.S47G(1)|p.S47R(1)|p.A5_Q143>E(1)|p.H36_E53>L(1)|p.Y30_A80del(1)|p.A43del(1)|p.S45_L46del(1)|p.T41_N51del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.V22_S71>A(1)|p.V22_Y64del(1)|p.A20_S111del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTG	0.5	S45F(HCC15_LUNG)|S45F(LS180_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.41_49del	Colon(6;3 56 14213 18255)	Atlas-Indel,Pindel	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+2,3	CTNNB1	4904	.	866	Substitution - Missense(664)|Deletion - In frame(158)|Complex - deletion inframe(20)|Unknown(7)|Deletion - Frameshift(6)|Substitution - coding silent(6)|Insertion - In frame(3)|Substitution - Nonsense(2)	soft_tissue(284)|liver(213)|large_intestine(104)|kidney(98)|adrenal_gland(34)|endometrium(28)|thyroid(22)|skin(16)|haematopoietic_and_lymphoid_tissue(15)|stomach(12)|pituitary(7)|ovary(7)|biliary_tract(5)|lung(3)|cervix(3)|prostate(3)|central_nervous_system(2)|pancreas(2)|small_intestine(2)|bone(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	c.123_146del						.																																			SO:0001651	inframe_deletion	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	.	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.124_147delACAGCTCCTTCTCTGAGTGGTAAA	chr3.hg19:g.41266127_41266150delACAGCTCCTTCTCTGAGTGGTAAA	ENSP00000344456:p.Thr42_Lys49del	195.0	0.0		95.0	63.0	NM_001098210	A8K1L7|Q8NEW9|Q8NI94|Q9H391	In_Frame_Del	DEL	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.5	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		-	41266150	ACAGCTCCTTCTCTGAGTGGTAAA	-	41266127	7	5	73	1	0	1	0	1	0	0	0	0	4018	159	6	0	130	0	CTNNB1	3	41266127	In_Frame_Del	DEL	ACAGCTCCTTCTCTGAGTGGTAAA	TCGA-CC-A7IH-01A-11D-A33K-10	2339293	41266127	156756303	121	9447										
PTH1R	5745	hgsc.bcm.edu	37	chr3	46937344	46937344	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aggacaaggaggcacccactGgcagcaggtaccgaggtacg	15	11	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:46937344G>T	ENST00000313049.5	+	3	501	c.298G>T	c.(298-300)Ggc>Tgc	p.G100C	PTH1R_ENST00000490109.1_3'UTR|PTH1R_ENST00000430002.2_Missense_Mutation_p.G100C|PTH1R_ENST00000418619.1_Missense_Mutation_p.G100C|PTH1R_ENST00000449590.1_Missense_Mutation_p.G100C			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor	100					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|bone mineralization (GO:0030282)|bone resorption (GO:0045453)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|osteoblast development (GO:0002076)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|skeletal system development (GO:0001501)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	parathyroid hormone receptor activity (GO:0004991)|peptide hormone binding (GO:0017046)|protein self-association (GO:0043621)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(2)|stomach(1)|urinary_tract(2)	19					Preotact(DB05829)|Teriparatide(DB06285)	GGCACCCACTGGCAGCAGGTA	0.577											OREG0015543	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G100C		Atlas-SNP	.											.	PTH1R	49	.	0			c.G298T						.						122	86	98					3																	46937344		2203	4300	6503	SO:0001583	missense	5745	exon4			CCCACTGGCAGCA		CCDS2747.1	3p22-p21.1	2012-08-10	2008-11-18	2008-11-18	ENSG00000160801	ENSG00000160801		"GPCR / Class B : Parathyroid hormone receptors"	9608	protein-coding gene	gene with protein product		168468	"parathyroid hormone receptor 1"	PTHR, PTHR1		8020952	Standard	NM_001184744		Approved		uc021wxg.1	Q03431	OTTHUMG00000133515	ENST00000313049.5:c.298G>T	chr3.hg19:g.46937344G>T	ENSP00000321999:p.Gly100Cys	132.0	1.0	943	100.0	90.0	NM_001184744	Q2M1U3	Missense_Mutation	SNP	ENST00000313049.5	hg19	CCDS2747.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964705	0.53507	.	.	ENSG00000160801	ENST00000449590;ENST00000418619;ENST00000427125;ENST00000430002;ENST00000313049;ENST00000313063	T;T;T;T;T	0.52295	0.67;0.67;0.68;0.67;0.67	4.65	2.67	0.31697	GPCR, family 2, extracellular hormone receptor domain (1);	.	.	.	.	T	0.31670	0.0804	N	0.22421	0.69	0.42978	D	0.99445	D	0.54047	0.964	B	0.43754	0.43	T	0.10683	-1.0619	9	0.56958	D	0.05	.	5.6545	0.17635	0.2508:0.0:0.7492:0.0	.	100	Q03431	PTH1R_HUMAN	C	100;100;100;100;100;272	ENSP00000402723:G100C;ENSP00000411424:G100C;ENSP00000400977:G100C;ENSP00000413774:G100C;ENSP00000321999:G100C	ENSP00000321999:G100C	G	+	1	0	PTH1R	46912348	0.889000	0.30405	0.837000	0.33122	0.861000	0.49209	1.774000	0.38573	1.185000	0.42971	0.561000	0.74099	GGC	.	.		0.577	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316		T	46937344	G	T	46937344	3	4	73	1	0	0	0	0	1	0	0	0	12771	1348	47	3	308	3	PTH1R	3	46937344	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	5671217	46937344	151085086	122	9448										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47042832	47042832	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gaggcccccgtgggggtcctGgccagcctcacccagcaagc	14	17	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:47042832G>T	ENST00000450053.3	+	29	4727	c.4548G>T	c.(4546-4548)ctG>ctT	p.L1516L	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Silent_p.L1332L	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1516					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TGGGGGTCCTGGCCAGCCTCA	0.617																																					p.L1516L		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G4548T						.						40	49	46					3																	47042832		2088	4232	6320	SO:0001819	synonymous_variant	23218	exon29			GGTCCTGGCCAGC	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.4548G>T	chr3.hg19:g.47042832G>T		56.0	0.0		41.0	36.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	hg19	CCDS46817.1	.	.	.	.	.	.	.	.	.	.	G	6.564	0.472368	0.12461	.	.	ENSG00000160796	ENST00000416683	.	.	.	5.13	1.09	0.20402	.	.	.	.	.	T	0.44414	0.1292	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23297	-1.0192	4	.	.	.	.	3.4722	0.07571	0.1567:0.1332:0.573:0.1372	.	.	.	.	L	804	.	.	W	+	2	0	NBEAL2	47017836	1.000000	0.71417	0.999000	0.59377	0.758000	0.43043	3.318000	0.51975	0.323000	0.23307	-0.251000	0.11542	TGG	.	.		0.617	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47042832	G	T	47042832	2	4	73	1	0	0	0	0	0	0	0	1	10198	1335	47	3		3	NBEAL2	3	47042832	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	105488	47042832	150979598	123	9449										
STAB1	23166	hgsc.bcm.edu	37	chr3	52554842	52554842	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagccctgaggcctgctggcGcttctacccgaagttctgga	12	14	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:52554842G>T	ENST00000321725.6	+	55	5805	c.5729G>T	c.(5728-5730)cGc>cTc	p.R1910L		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1910					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GCCTGCTGGCGCTTCTACCCG	0.662																																					p.R1910L		Atlas-SNP	.											.	STAB1	178	.	0			c.G5729T						.						126	149	141					3																	52554842		2203	4300	6503	SO:0001583	missense	23166	exon55			GCTGGCGCTTCTA	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.5729G>T	chr3.hg19:g.52554842G>T	ENSP00000312946:p.Arg1910Leu	54.0	0.0		42.0	32.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.759652	0.31137	.	.	ENSG00000010327	ENST00000321725	D	0.85339	-1.97	5.49	2.16	0.27623	.	0.860267	0.10448	N	0.673413	T	0.74741	0.3756	L	0.44542	1.39	0.26403	N	0.976389	B	0.21905	0.062	B	0.19391	0.025	T	0.56998	-0.7886	10	0.11485	T	0.65	.	3.6654	0.08254	0.4212:0.1887:0.3901:0.0	.	1910	Q9NY15	STAB1_HUMAN	L	1910	ENSP00000312946:R1910L	ENSP00000312946:R1910L	R	+	2	0	STAB1	52529882	0.029000	0.19370	0.877000	0.34402	0.438000	0.31896	0.545000	0.23268	0.720000	0.32209	-0.137000	0.14449	CGC	.	.		0.662	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52554842	G	T	52554842	3	4	73	1	0	0	0	0	1	0	0	0	15252	1087	38	1	5947	1	STAB1	3	52554842	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	5512010	52554842	145467588	124	9450										
CACNA1D	776	hgsc.bcm.edu	37	chr3	53700544	53700544	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgcatcaccatggagggctgGacagatgtgctctactgggt	14	9	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:53700544G>A	ENST00000350061.5	+	7	1609	c.1098G>A	c.(1096-1098)tgG>tgA	p.W366*	CACNA1D_ENST00000288139.4_Nonsense_Mutation_p.W366*|CACNA1D_ENST00000422281.2_Nonsense_Mutation_p.W366*	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	366					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGAGGGCTGGACAGATGTGC	0.512																																					p.W366X		Atlas-SNP	.											.	CACNA1D	324	.	0			c.G1098A						.						160	161	161					3																	53700544		2203	4300	6503	SO:0001587	stop_gained	776	exon7			GGGCTGGACAGAT	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.1098G>A	chr3.hg19:g.53700544G>A	ENSP00000288133:p.Trp366*	123.0	0.0		128.0	6.0	NM_001128840	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Nonsense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.754693|5.754693	0.96890|0.96890	.|.	.|.	ENSG00000157388|ENSG00000157388	ENST00000481085|ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478	.|.	.|.	.|.	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|.	0.46756|.	0.1409|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34650|.	-0.9820|.	4|.	.|0.02654	.|T	.|1	.|.	18.8081|18.8081	0.92047|0.92047	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	E|X	52|366;366;366;39	.|.	.|ENSP00000288139:W366X	G|W	+|+	2|3	0|0	CACNA1D|CACNA1D	53675584|53675584	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.907000|0.907000	0.53573|0.53573	9.601000|9.601000	0.98297|0.98297	2.676000|2.676000	0.91093|0.91093	0.561000|0.561000	0.74099|0.74099	GGA|TGG	.	.		0.512	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		A	53700544	G	A	53700544	4	1	73	1	0	0	0	0	0	1	0	0	2543	1183	41	3	1124	3	CACNA1D	3	53700544	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1145702	53700544	144321886	125	9451										
LRTM1	57408	hgsc.bcm.edu	37	chr3	54958771	54958771	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccaggagcgctcgatcaagcTgctgaagctggttttgttga	13	9	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:54958771T>A	ENST00000273286.5	-	2	641	c.479A>T	c.(478-480)cAg>cTg	p.Q160L	CACNA2D3_ENST00000474759.1_Intron|CACNA2D3_ENST00000415676.2_Intron|LRTM1_ENST00000493075.1_Missense_Mutation_p.Q84L|CACNA2D3_ENST00000288197.5_Intron|CACNA2D3_ENST00000490478.1_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	160						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		TCGATCAAGCTGCTGAAGCTG	0.473																																					p.Q160L		Atlas-SNP	.											.	LRTM1	52	.	0			c.A479T						.						101	100	101					3																	54958771		2203	4300	6503	SO:0001583	missense	57408	exon2			TCAAGCTGCTGAA	AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.479A>T	chr3.hg19:g.54958771T>A	ENSP00000273286:p.Gln160Leu	187.0	0.0		140.0	123.0	NM_020678	Q8IUU2	Missense_Mutation	SNP	ENST00000273286.5	hg19	CCDS2876.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030178	0.35797	.	.	ENSG00000144771	ENST00000273286;ENST00000493075	T;D	0.89681	4.32;-2.55	5.96	4.79	0.61399	.	0.482604	0.24206	N	0.040575	T	0.77805	0.4185	N	0.13198	0.31	0.28999	N	0.887578	B	0.15473	0.013	B	0.12837	0.008	T	0.67833	-0.5568	10	0.39692	T	0.17	.	6.9224	0.24395	0.1339:0.0691:0.0:0.797	.	160	Q9HBL6	LRTM1_HUMAN	L	160;84	ENSP00000273286:Q160L;ENSP00000419772:Q84L	ENSP00000273286:Q160L	Q	-	2	0	LRTM1	54933811	1.000000	0.71417	0.962000	0.40283	0.660000	0.38997	2.717000	0.47227	1.041000	0.40125	0.533000	0.62120	CAG	.	.		0.473	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678		A	54958771	T	A	54958771	3	1	73	1	0	0	0	0	1	0	0	0	9053	1580	55	4	566	4	LRTM1	3	54958771	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1258227	54958771	143063659	126	9452										
KBTBD8	84541	hgsc.bcm.edu	37	chr3	67049479	67049479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcgatgccatggaccccttcCatgcttgcagtattcttaag	9	12	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:67049479C>T	ENST00000417314.2	+	2	140	c.91C>T	c.(91-93)Cat>Tat	p.H31Y	KBTBD8_ENST00000460576.1_Intron|KBTBD8_ENST00000469661.1_3'UTR|KBTBD8_ENST00000295568.4_Missense_Mutation_p.H5Y			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	31						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		GGACCCCTTCCATGCTTGCAG	0.443																																					p.H31Y		Atlas-SNP	.											.	KBTBD8	101	.	0			c.C91T						.						110	99	103					3																	67049479		2203	4300	6503	SO:0001583	missense	84541	exon2			CCCTTCCATGCTT	AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"BTB/POZ domain containing"	30691	protein-coding gene	gene with protein product	"T-cell activation kelch repeat protein"					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.91C>T	chr3.hg19:g.67049479C>T	ENSP00000401878:p.His31Tyr	208.0	0.0		271.0	93.0	NM_032505	B4DTW6|Q96JI5	Missense_Mutation	SNP	ENST00000417314.2	hg19	CCDS2906.2	.	.	.	.	.	.	.	.	.	.	C	16.05	3.013483	0.54468	.	.	ENSG00000163376	ENST00000295568;ENST00000417314;ENST00000460784	T;T;T	0.71817	-0.6;-0.6;-0.6	5.52	5.52	0.82312	BTB/POZ fold (2);	0.048699	0.85682	D	0.000000	T	0.76630	0.4014	L	0.29908	0.895	0.80722	D	1	D	0.57899	0.981	D	0.67900	0.954	T	0.73069	-0.4099	10	0.30854	T	0.27	.	19.7984	0.96495	0.0:1.0:0.0:0.0	.	31	Q8NFY9	KBTB8_HUMAN	Y	5;31;5	ENSP00000295568:H5Y;ENSP00000401878:H31Y;ENSP00000418075:H5Y	ENSP00000295568:H5Y	H	+	1	0	KBTBD8	67132169	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.666000	0.83877	2.753000	0.94483	0.467000	0.42956	CAT	.	.		0.443	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505		T	67049479	C	T	67049479	3	4	73	1	0	0	0	0	1	0	0	0	8008	594	21	3	97	3	KBTBD8	3	67049479	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	12090708	67049479	130972951	127	9453										
TMF1	7110	hgsc.bcm.edu	37	chr3	69097054	69097054	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctcgctgagctctcacttaTtacactttcatgatctaaaa	5	11	3	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:69097054T>C	ENST00000398559.2	-	2	1018	c.802A>G	c.(802-804)Ata>Gta	p.I268V	MIR3136_ENST00000583498.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.I268V|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	268					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		CTCTCACTTATTACACTTTCA	0.418																																					p.I268V		Atlas-SNP	.											.	TMF1	77	.	0			c.A802G						.						55	54	54					3																	69097054		1882	4112	5994	SO:0001583	missense	7110	exon2			CACTTATTACACT		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.802A>G	chr3.hg19:g.69097054T>C	ENSP00000381567:p.Ile268Val	58.0	0.0		68.0	30.0	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	hg19	CCDS43105.1	.	.	.	.	.	.	.	.	.	.	T	9.431	1.085664	0.20390	.	.	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248;ENST00000438636	T;T	0.77229	-1.08;-1.08	5.76	5.76	0.90799	.	0.184375	0.64402	D	0.000017	T	0.74092	0.3671	M	0.62723	1.935	0.38013	D	0.934615	P;B	0.40000	0.698;0.319	B;B	0.36030	0.216;0.107	T	0.75777	-0.3198	10	0.24483	T	0.36	-15.3798	16.0796	0.80995	0.0:0.0:0.0:1.0	.	268;268	P82094-2;P82094	.;TMF1_HUMAN	V	268;268;181;268	ENSP00000381567:I268V;ENSP00000438706:I268V	ENSP00000348582:I181V	I	-	1	0	TMF1	69179744	1.000000	0.71417	0.997000	0.53966	0.209000	0.24338	2.250000	0.43178	2.195000	0.70347	0.528000	0.53228	ATA	.	.		0.418	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		C	69097054	T	C	69097054	3	2	73	1	0	0	0	0	1	0	0	0	16243	1493	52	2	2543	2	TMF1	3	69097054	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2047575	69097054	128925376	128	9454										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78684981	78684981	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	actggtgccacttcttgtttCtgctgtcccagtggtttcca	9	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:78684981C>A	ENST00000464233.1	-	23	3428	c.3315G>T	c.(3313-3315)caG>caT	p.Q1105H	ROBO1_ENST00000495273.1_Missense_Mutation_p.Q1060H|ROBO1_ENST00000436010.2_Missense_Mutation_p.Q1066H|ROBO1_ENST00000467549.1_Missense_Mutation_p.Q1005H	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1105					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		CTTCTTGTTTCTGCTGTCCCA	0.488																																					p.Q1105H		Atlas-SNP	.											.	ROBO1	833	.	0			c.G3315T						.						190	184	186					3																	78684981		2114	4246	6360	SO:0001583	missense	6091	exon23			TTGTTTCTGCTGT	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.3315G>T	chr3.hg19:g.78684981C>A	ENSP00000420321:p.Gln1105His	275.0	0.0		326.0	95.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	10.71	1.427330	0.25726	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73	6.05	2.72	0.32119	.	0.228402	0.47455	D	0.000235	T	0.76933	0.4057	L	0.50333	1.59	0.42234	D	0.991909	P;B;P;B;B	0.41848	0.763;0.228;0.731;0.343;0.346	B;B;B;B;B	0.44224	0.444;0.322;0.342;0.126;0.382	T	0.73477	-0.3970	9	.	.	.	.	5.0071	0.14293	0.0:0.5705:0.1767:0.2528	.	1069;1105;1060;1005;1066	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	H	1066;1060;1105;1060;1005;1109	ENSP00000406043:Q1066H;ENSP00000420321:Q1105H;ENSP00000420637:Q1060H;ENSP00000417992:Q1005H	.	Q	-	3	2	ROBO1	78767671	1.000000	0.71417	1.000000	0.80357	0.157000	0.22087	2.333000	0.43912	1.562000	0.49601	0.650000	0.86243	CAG	.	.		0.488	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78684981	C	A	78684981	3	1	73	1	0	0	0	0	1	0	0	0	13528	912	32	3	1676	3	ROBO1	3	78684981	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	9587927	78684981	119337449	129	9455										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78711213	78711213	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtgcagaacagcatttcccAgctctctctggacctgcttg	10	13	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:78711213A>T	ENST00000464233.1	-	15	2131	c.2018T>A	c.(2017-2019)cTg>cAg	p.L673Q	ROBO1_ENST00000495273.1_Missense_Mutation_p.L637Q|ROBO1_ENST00000436010.2_Missense_Mutation_p.L634Q|ROBO1_ENST00000467549.1_Missense_Mutation_p.L637Q	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	673					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		AGCATTTCCCAGCTCTCTCTG	0.483																																					p.L673Q		Atlas-SNP	.											.	ROBO1	833	.	0			c.T2018A						.						77	86	83					3																	78711213		1971	4153	6124	SO:0001583	missense	6091	exon15			TTTCCCAGCTCTC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2018T>A	chr3.hg19:g.78711213A>T	ENSP00000420321:p.Leu673Gln	232.0	0.0		291.0	86.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677084	0.88445	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.66815	-0.19;-0.21;-0.23;-0.15	5.48	5.48	0.80851	Fibronectin, type III (2);	0.000000	0.85682	D	0.000000	T	0.81226	0.4778	M	0.73962	2.25	0.58432	D	0.999998	D;D;D;D;D;D	0.89917	0.997;1.0;1.0;1.0;1.0;0.987	D;D;D;D;D;D	0.91635	0.994;0.997;0.999;0.999;0.997;0.972	T	0.82014	-0.0667	9	.	.	.	.	15.5603	0.76240	1.0:0.0:0.0:0.0	.	637;637;673;637;637;634	Q9Y6N7-3;Q1RMC7;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;.;ROBO1_HUMAN;.;.;.	Q	634;637;673;637;637;677	ENSP00000406043:L634Q;ENSP00000420321:L673Q;ENSP00000420637:L637Q;ENSP00000417992:L637Q	.	L	-	2	0	ROBO1	78793903	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	9.322000	0.96357	2.072000	0.62099	0.454000	0.30748	CTG	.	.		0.483	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78711213	A	T	78711213	3	4	73	1	0	0	0	0	1	0	0	0	13528	188	7	4	3005	4	ROBO1	3	78711213	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	26232	78711213	119311217	130	9456										
ZBED2	79413	hgsc.bcm.edu	37	chr3	111312691	111312691	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggccttggatcctggcgctGcccagcctgaccatggccac	13	16	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:111312691G>T	ENST00000317012.4	-	2	1366	c.358C>A	c.(358-360)Cag>Aag	p.Q120K	CD96_ENST00000352690.4_Intron|CD96_ENST00000283285.5_Intron|CD96_ENST00000438817.2_Intron	NM_024508.4	NP_078784.2	Q9BTP6	ZBED2_HUMAN	zinc finger, BED-type containing 2	120							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(1)|skin(2)	6						TCCTGGCGCTGCCCAGCCTGA	0.642																																					p.Q120K		Atlas-SNP	.											.	ZBED2	22	.	0			c.C358A						.						37	37	37					3																	111312691		2203	4300	6503	SO:0001583	missense	79413	exon2			GGCGCTGCCCAGC	BC003536	CCDS2960.2	3p13-q13.2	2013-05-03			ENSG00000177494	ENSG00000177494		"Zinc fingers, BED-type"	20710	protein-coding gene	gene with protein product		615246				23533661	Standard	NM_024508		Approved	MGC10796	uc003dxy.3	Q9BTP6	OTTHUMG00000074061	ENST00000317012.4:c.358C>A	chr3.hg19:g.111312691G>T	ENSP00000321370:p.Gln120Lys	70.0	0.0		67.0	30.0	NM_024508	D3DN62	Missense_Mutation	SNP	ENST00000317012.4	hg19	CCDS2960.2	.	.	.	.	.	.	.	.	.	.	G	0.076	-1.192517	0.01607	.	.	ENSG00000177494	ENST00000317012	.	.	.	4.34	2.47	0.30058	.	0.389775	0.18529	U	0.138555	T	0.27419	0.0673	L	0.44542	1.39	0.09310	N	1	B	0.18310	0.027	B	0.09377	0.004	T	0.20371	-1.0277	9	0.12766	T	0.61	.	5.1522	0.15015	0.1076:0.0:0.6884:0.204	.	120	Q9BTP6	ZBED2_HUMAN	K	120	.	ENSP00000321370:Q120K	Q	-	1	0	ZBED2	112795381	0.120000	0.22244	0.084000	0.20598	0.231000	0.25187	1.955000	0.40372	0.535000	0.28714	0.467000	0.42956	CAG	.	.		0.642	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	NM_024508		T	111312691	G	T	111312691	3	4	73	1	0	0	0	0	1	0	0	0	17533	1328	46	3	302	3	ZBED2	3	111312691	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	32601478	111312691	86709739	131	9457										
PLCXD2	257068	hgsc.bcm.edu	37	chr3	111394182	111394182	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acaaagacatcatcggaggtCtgcaatgccgactggatggc	12	10	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:111394182C>A	ENST00000477665.1	+	1	414	c.90C>A	c.(88-90)gtC>gtA	p.V30V	PLCXD2_ENST00000393934.3_Silent_p.V30V|PLCXD2-AS1_ENST00000493131.1_RNA	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	30					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						CATCGGAGGTCTGCAATGCCG	0.562																																					p.V30V		Atlas-SNP	.											.	PLCXD2	36	.	0			c.C90A						.						160	142	148					3																	111394182		2203	4300	6503	SO:0001819	synonymous_variant	257068	exon1			GGAGGTCTGCAAT	AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.90C>A	chr3.hg19:g.111394182C>A		266.0	0.0		213.0	91.0	NM_001185106	Q96N12	Silent	SNP	ENST00000477665.1	hg19	CCDS54619.1																																																																																			.	.		0.562	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268		A	111394182	C	A	111394182	2	1	73	1	0	0	0	0	0	0	0	1	12051	900	32	3		3	PLCXD2	3	111394182	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	81491	111394182	86628248	132	9458										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112358178	112358178	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgcctccttcctcacctgccTggtggaagagcacaatctgt	9	14	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:112358178T>C	ENST00000206423.3	-	2	1528	c.575A>G	c.(574-576)cAg>cGg	p.Q192R	CCDC80_ENST00000439685.2_Missense_Mutation_p.Q192R|CCDC80_ENST00000475181.1_5'Flank	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	192					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						CTCACCTGCCTGGTGGAAGAG	0.587																																					p.Q192R		Atlas-SNP	.											.	CCDC80	100	.	0			c.A575G						.						86	66	73					3																	112358178		2203	4300	6503	SO:0001583	missense	151887	exon2			CCTGCCTGGTGGA	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.575A>G	chr3.hg19:g.112358178T>C	ENSP00000206423:p.Gln192Arg	126.0	0.0		130.0	63.0	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	hg19	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	T	17.78	3.473089	0.63737	.	.	ENSG00000091986	ENST00000206423;ENST00000439685	T;T	0.42513	0.97;0.97	5.55	3.02	0.34903	.	0.266613	0.38111	N	0.001816	T	0.24967	0.0606	N	0.21097	0.63	0.80722	D	1	B;B;B	0.15141	0.005;0.0;0.012	B;B;B	0.14578	0.004;0.003;0.011	T	0.05022	-1.0911	10	0.21014	T	0.42	-14.0638	8.0814	0.30748	0.0:0.0706:0.1354:0.794	.	203;192;192	Q76M96-2;A3KC71;Q76M96	.;.;CCD80_HUMAN	R	192	ENSP00000206423:Q192R;ENSP00000411814:Q192R	ENSP00000206423:Q192R	Q	-	2	0	CCDC80	113840868	1.000000	0.71417	0.999000	0.59377	0.838000	0.47535	4.113000	0.57851	0.932000	0.37266	0.528000	0.53228	CAG	.	.		0.587	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		C	112358178	T	C	112358178	3	2	73	1	0	0	0	0	1	0	0	0	2856	1580	55	2	2305	2	CCDC80	3	112358178	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	963996	112358178	85664252	133	9459										
BOC	91653	hgsc.bcm.edu	37	chr3	112993376	112993376	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctgcttccccgcagtgtccAggagagaaggggcagggggc	17	12	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:112993376A>T	ENST00000495514.1	+	9	2093	c.1389A>T	c.(1387-1389)ccA>ccT	p.P463P	BOC_ENST00000273395.4_Silent_p.P463P|BOC_ENST00000497495.1_3'UTR|BOC_ENST00000355385.3_Silent_p.P463P			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	463					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			CGCAGTGTCCAGGAGAGAAGG	0.662																																					p.P463P		Atlas-SNP	.											.	BOC	139	.	0			c.A1389T						.						24	28	26					3																	112993376		2203	4298	6501	SO:0001819	synonymous_variant	91653	exon9			GTGTCCAGGAGAG	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1389A>T	chr3.hg19:g.112993376A>T		182.0	0.0		129.0	61.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	hg19	CCDS2971.1																																																																																			.	.		0.662	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		T	112993376	A	T	112993376	2	4	73	1	0	0	0	0	0	0	0	1	1481	175	7	4		4	BOC	3	112993376	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	635198	112993376	85029054	134	9460										
C3orf30	152405	hgsc.bcm.edu	37	chr3	118865983	118865983	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agtgtacggccaagccactgAactagctgaacaccaggcta	10	12	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:118865983A>G	ENST00000295622.1	+	1	987	c.947A>G	c.(946-948)gAa>gGa	p.E316G	IGSF11_ENST00000441144.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	316										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		CAAGCCACTGAACTAGCTGAA	0.478																																					p.E316G		Atlas-SNP	.											.	C3orf30	64	.	0			c.A947G						.						94	80	84					3																	118865983		2203	4300	6503	SO:0001583	missense	152405	exon1			CCACTGAACTAGC	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.947A>G	chr3.hg19:g.118865983A>G	ENSP00000295622:p.Glu316Gly	130.0	0.0		136.0	57.0	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	hg19	CCDS2984.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.659|9.659	1.143729|1.143729	0.21205|0.21205	.|.	.|.	ENSG00000163424|ENSG00000163424	ENST00000295622;ENST00000470341|ENST00000460150;ENST00000473121;ENST00000492792	T|.	0.13307|.	2.6|.	4.6|4.6	-5.02|-5.02	0.02982|0.02982	.|.	1.587660|.	0.03610|.	N|.	0.234734|.	T|.	0.17916|.	0.0430|.	N|N	0.25647|0.25647	0.755|0.755	0.09310|0.09310	N|N	1|1	B;B|.	0.16802|.	0.017;0.019|.	B;B|.	0.14578|.	0.007;0.011|.	T|.	0.26744|.	-1.0094|.	10|.	0.22109|.	T|.	0.4|.	-0.2957|-0.2957	0.9074|0.9074	0.01287|0.01287	0.2442:0.1393:0.344:0.2725|0.2442:0.1393:0.344:0.2725	.|.	316;316|.	E9PFE5;Q96M34|.	.;CC030_HUMAN|.	G|W	316|279;108;50	ENSP00000295622:E316G|.	ENSP00000295622:E316G|.	E|X	+|+	2|3	0|0	C3orf30|C3orf30	120348673|120348673	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.727000|0.727000	0.25999|0.25999	-0.902000|-0.902000	0.03886|0.03886	-0.468000|-0.468000	0.05107|0.05107	GAA|TGA	.	.		0.478	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539		G	118865983	A	G	118865983	3	3	73	1	0	0	0	0	1	0	0	0	2222	246	9	2	949	2	C3orf30	3	118865983	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	5872607	118865983	79156447	135	9461										
POLQ	10721	hgsc.bcm.edu	37	chr3	121208148	121208148	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtctctctattatatttttCtgtttggtaatagtgcttgt	7	5	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:121208148C>T	ENST00000264233.5	-	16	3758	c.3630G>A	c.(3628-3630)caG>caA	p.Q1210Q		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1210					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TTATATTTTTCTGTTTGGTAA	0.338								DNA polymerases (catalytic subunits)																													p.Q1210Q	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G3630A						.						176	183	181					3																	121208148		2203	4300	6503	SO:0001819	synonymous_variant	10721	exon16			ATTTTTCTGTTTG	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.3630G>A	chr3.hg19:g.121208148C>T		109.0	0.0		121.0	53.0	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.338	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121208148	C	T	121208148	2	4	73	1	0	0	0	0	0	0	0	1	12217	912	32	3		3	POLQ	3	121208148	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	2342165	121208148	76814282	136	9462										
SLC41A3	54946	hgsc.bcm.edu	37	chr3	125775394	125775416	+	Intron	DEL	ATGGCCAGGCAATGCACCACGAT	ATGGCCAGGCAATGCACCACGAT	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gattcagctgggtgaccaccAtggccaggcaatgcaccacg					rs371771556|rs201025311|rs200888748|rs185228572	byFrequency	TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	ATGGCCAGGCAATGCACCACGAT	ATGGCCAGGCAATGCACCACGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:125775394_125775416delATGGCCAGGCAATGCACCACGAT	ENST00000315891.6	-	3	512				SLC41A3_ENST00000346785.5_Intron|SLC41A3_ENST00000383598.2_Start_Codon_Del|SLC41A3_ENST00000360370.4_Intron|SLC41A3_ENST00000508835.1_Intron|SLC41A3_ENST00000514023.1_Intron|RP11-158I23.1_ENST00000508263.1_RNA	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		GGTGACCACCATGGCCAGGCAATGCACCACGATCCCAGGAGCA	0.587																																					.		Atlas-Indel,Pindel	.											.	SLC41A3	80	.	0			.						.																																			SO:0001627	intron_variant	54946	wholegene			.		CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544		"Solute carriers"	31046	protein-coding gene	gene with protein product		610803					Standard	NM_001164475		Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000315891.6:c.274-5501ATCGTGGTGCATTGCCTGGCCAT>-	chr3.hg19:g.125775394_125775416delATGGCCAGGCAATGCACCACGAT		139.0	0.0		75.0	14.0	NM_001008487	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Frame_Shift_Del	DEL	ENST00000315891.6	hg19	CCDS33843.1																																																																																			.	.		0.587	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836		-	125775416	ATGGCCAGGCAATGCACCACGAT	-	125775394	6	5	73	0	1	1	0	1	0	0	0	0	14646	217	8	0		0	SLC41A3	3	125775394	Intron	DEL	ATGGCCAGGCAATGCACCACGAT	TCGA-CC-A7IH-01A-11D-A33K-10	4567246	125775394	72247036	137	9463										
KBTBD12	166348	hgsc.bcm.edu	37	chr3	127642796	127642796	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ataggagctatggggatgccAgtttttgttatgatcctgta	12	5	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:127642796A>T	ENST00000405109.1	+	2	1359	c.892A>T	c.(892-894)Agt>Tgt	p.S298C	KBTBD12_ENST00000405256.1_Missense_Mutation_p.S298C|KBTBD12_ENST00000343941.4_Intron|KBTBD12_ENST00000407609.3_Intron			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	298										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						TGGGGATGCCAGTTTTTGTTA	0.428																																					p.S298C		Atlas-SNP	.											.	KBTBD12	41	.	0			c.A892T						.						132	126	128					3																	127642796		1923	4118	6041	SO:0001583	missense	166348	exon1			GATGCCAGTTTTT		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.892A>T	chr3.hg19:g.127642796A>T	ENSP00000385957:p.Ser298Cys	162.0	0.0		131.0	60.0	NM_207335	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	hg19	CCDS33848.2	.	.	.	.	.	.	.	.	.	.	A	22.1	4.244133	0.79912	.	.	ENSG00000187715	ENST00000405109;ENST00000405256	T;T	0.66638	-0.22;-0.22	5.47	5.47	0.80525	Kelch-type beta propeller (1);	.	.	.	.	T	0.79435	0.4445	M	0.63843	1.955	0.58432	D	0.999996	D	0.89917	1.0	D	0.85130	0.997	T	0.78770	-0.2074	9	0.40728	T	0.16	.	15.8475	0.78903	1.0:0.0:0.0:0.0	.	298	Q3ZCT8	KBTBC_HUMAN	C	298	ENSP00000385957:S298C;ENSP00000385879:S298C	ENSP00000385957:S298C	S	+	1	0	KBTBD12	129125486	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.910000	0.92685	2.207000	0.71202	0.477000	0.44152	AGT	.	.		0.428	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		T	127642796	A	T	127642796	3	4	73	1	0	0	0	0	1	0	0	0	8000	188	7	4	894	4	KBTBD12	3	127642796	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1867402	127642796	70379634	138	9464										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130290136	130290136	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcccgtggagctgttagccaTggcaggatcaagcgacaagt	13	10	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:130290136T>G	ENST00000358511.6	+	6	2907	c.2876T>G	c.(2875-2877)aTg>aGg	p.M959R	COL6A6_ENST00000453409.2_Missense_Mutation_p.M959R	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	959	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CTGTTAGCCATGGCAGGATCA	0.498																																					p.M959R		Atlas-SNP	.											.	COL6A6	497	.	0			c.T2876G						.						54	53	53					3																	130290136		1978	4172	6150	SO:0001583	missense	131873	exon6			TAGCCATGGCAGG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.2876T>G	chr3.hg19:g.130290136T>G	ENSP00000351310:p.Met959Arg	240.0	0.0		193.0	80.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.974784	0.74360	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.79033	-1.23;-1.23	4.82	4.82	0.62117	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000002	D	0.85452	0.5700	M	0.78049	2.395	0.45272	D	0.998278	D	0.61080	0.989	P	0.58172	0.834	D	0.87838	0.2649	10	0.87932	D	0	.	14.3361	0.66592	0.0:0.0:0.0:1.0	.	959	A6NMZ7	CO6A6_HUMAN	R	959	ENSP00000351310:M959R;ENSP00000399236:M959R	ENSP00000351310:M959R	M	+	2	0	COL6A6	131772826	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.455000	0.80726	1.946000	0.56461	0.459000	0.35465	ATG	.	.		0.498	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		G	130290136	T	G	130290136	3	3	73	1	0	0	0	0	1	0	0	0	3705	1464	51	5	2898	5	COL6A6	3	130290136	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2647340	130290136	67732294	139	9465										
ACPP	55	hgsc.bcm.edu	37	chr3	132075574	132075574	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcggaatgagacgcagcacgAgccgtatcccctcatgctac	10	14	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:132075574A>T	ENST00000336375.5	+	10	1103	c.1013A>T	c.(1012-1014)gAg>gTg	p.E338V	ACPP_ENST00000475741.1_Missense_Mutation_p.E305V|ACPP_ENST00000351273.7_Missense_Mutation_p.E338V	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	338					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)	p.E334_Y340delETQHEPY(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						ACGCAGCACGAGCCGTATCCC	0.557																																					p.E338V		Atlas-SNP	.											.	ACPP	118	.	1	Deletion - In frame(1)	ovary(1)	c.A1013T						.						163	146	151					3																	132075574		2203	4300	6503	SO:0001583	missense	55	exon10			AGCACGAGCCGTA		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.1013A>T	chr3.hg19:g.132075574A>T	ENSP00000337471:p.Glu338Val	158.0	0.0		99.0	26.0	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Missense_Mutation	SNP	ENST00000336375.5	hg19	CCDS3073.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.21|13.21	2.170431|2.170431	0.38315|0.38315	.|.	.|.	ENSG00000014257|ENSG00000014257	ENST00000336375;ENST00000475741;ENST00000351273|ENST00000507647	T;T;T|.	0.17213|.	2.29;2.29;2.29|.	5.67|5.67	4.52|4.52	0.55395|0.55395	.|.	0.166448|.	0.41605|.	D|.	0.000857|.	T|T	0.61098|0.61098	0.2320|0.2320	M|M	0.84948|0.84948	2.725|2.725	0.25774|0.25774	N|N	0.9848|0.9848	P;P;D|.	0.56287|.	0.785;0.863;0.975|.	B;B;P|.	0.45660|.	0.197;0.359;0.489|.	T|T	0.57039|0.57039	-0.7879|-0.7879	10|5	0.72032|.	D|.	0.01|.	.|.	8.2264|8.2264	0.31570|0.31570	0.911:0.0:0.089:0.0|0.911:0.0:0.089:0.0	.|.	338;338;305|.	P15309;P15309-2;Q5FBY0|.	PPAP_HUMAN;.;.|.	V|C	338;305;338|23	ENSP00000337471:E338V;ENSP00000417744:E305V;ENSP00000323036:E338V|.	ENSP00000337471:E338V|.	E|S	+|+	2|1	0|0	ACPP|ACPP	133558264|133558264	0.999000|0.999000	0.42202|0.42202	0.081000|0.081000	0.20488|0.20488	0.121000|0.121000	0.20230|0.20230	2.867000|2.867000	0.48428|0.48428	0.997000|0.997000	0.38969|0.38969	0.533000|0.533000	0.62120|0.62120	GAG|AGC	.	.		0.557	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099		T	132075574	A	T	132075574	3	4	73	1	0	0	0	0	1	0	0	0	167	304	11	4	1051	4	ACPP	3	132075574	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1785438	132075574	65946856	140	9466										
C3orf36	80111	hgsc.bcm.edu	37	chr3	133647332	133647332	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtggttccccccaggtgagcAaggtgggggccccgtgggtg	19	11	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:133647332A>G	ENST00000408895.2	-	1	1324	c.316T>C	c.(316-318)Tgc>Cgc	p.C106R		NM_025041.2	NP_079317.2	Q3SXR2	CC036_HUMAN	chromosome 3 open reading frame 36	106										breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	6						CCAGGTGAGCAAGGTGGGGGC	0.677																																					p.C106R		Atlas-SNP	.											.	C3orf36	13	.	0			c.T316C						.						29	32	31					3																	133647332		2203	4299	6502	SO:0001583	missense	80111	exon1			GTGAGCAAGGTGG	AK025826	CCDS3083.1	3q22.1	2011-09-30			ENSG00000221972	ENSG00000221972			26170	protein-coding gene	gene with protein product						12477932	Standard	NM_025041		Approved	FLJ22173	uc003epz.1	Q3SXR2		ENST00000408895.2:c.316T>C	chr3.hg19:g.133647332A>G	ENSP00000386219:p.Cys106Arg	175.0	0.0		134.0	45.0	NM_025041	Q3SXR3|Q9H6K8	Missense_Mutation	SNP	ENST00000408895.2	hg19	CCDS3083.1	.	.	.	.	.	.	.	.	.	.	A	9.875	1.199951	0.22121	.	.	ENSG00000221972	ENST00000408895	.	.	.	1.96	-3.92	0.04155	.	.	.	.	.	T	0.15349	0.0370	N	0.08118	0	0.09310	N	1	B	0.15719	0.014	B	0.09377	0.004	T	0.16571	-1.0398	8	0.87932	D	0	.	4.0832	0.09935	0.4949:0.185:0.3201:0.0	.	106	Q3SXR2	CC036_HUMAN	R	106	.	ENSP00000386219:C106R	C	-	1	0	C3orf36	135130022	0.000000	0.05858	0.000000	0.03702	0.329000	0.28539	-1.058000	0.03482	-1.328000	0.02261	0.260000	0.18958	TGC	.	.		0.677	C3orf36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_025041		G	133647332	A	G	133647332	3	3	73	1	0	0	0	0	1	0	0	0	2228	130	5	2	185	2	C3orf36	3	133647332	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1571758	133647332	64375098	141	9467										
XRN1	54464	hgsc.bcm.edu	37	chr3	142145680	142145680	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttgtcttctgcctcctttgcTgaccttaaaggttaagggaa	9	9	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:142145680T>A	ENST00000264951.4	-	3	429	c.312A>T	c.(310-312)tcA>tcT	p.S104S	XRN1_ENST00000463916.1_Silent_p.S104S|XRN1_ENST00000392981.2_Silent_p.S104S|XRN1_ENST00000544157.1_Intron	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	104					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						CCTCCTTTGCTGACCTTAAAG	0.348																																					p.S104S		Atlas-SNP	.											.	XRN1	138	.	0			c.A312T						.						129	122	125					3																	142145680		2203	4300	6503	SO:0001819	synonymous_variant	54464	exon3			CTTTGCTGACCTT	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.312A>T	chr3.hg19:g.142145680T>A		94.0	0.0		68.0	40.0	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	hg19	CCDS3123.1																																																																																			.	.		0.348	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		A	142145680	T	A	142145680	2	1	73	1	0	0	0	0	0	0	0	1	17474	1567	55	4		4	XRN1	3	142145680	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	8498348	142145680	55876750	142	9468										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151160801	151160801	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggtcgaccacagccttggaTggtaacctccacattatttg	9	11	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:151160801T>C	ENST00000282466.3	-	5	5933	c.5934A>G	c.(5932-5934)ccA>ccG	p.P1978P	IGSF10_ENST00000495443.1_5'Flank	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1978	Ig-like C2-type 6.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CAGCCTTGGATGGTAACCTCC	0.438																																					p.P1978P		Atlas-SNP	.											.	IGSF10	279	.	0			c.A5934G						.						107	103	104					3																	151160801		2203	4300	6503	SO:0001819	synonymous_variant	285313	exon5			CTTGGATGGTAAC	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5934A>G	chr3.hg19:g.151160801T>C		108.0	0.0		94.0	38.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	hg19	CCDS3160.1																																																																																			.	.		0.438	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		C	151160801	T	C	151160801	2	2	73	1	0	0	0	0	0	0	0	1	7606	1451	51	2		2	IGSF10	3	151160801	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	9015121	151160801	46861629	143	9469										
VEPH1	79674	hgsc.bcm.edu	37	chr3	157031464	157031464	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtttcaaagctgtgagcaccCcctgcctgggtcttctccca	9	15	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:157031464C>A	ENST00000362010.2	-	11	2263	c.1956G>T	c.(1954-1956)ggG>ggT	p.G652G	RP11-550I24.2_ENST00000475102.1_RNA|RP11-550I24.2_ENST00000487238.1_RNA|RP11-550I24.2_ENST00000494885.1_RNA|VEPH1_ENST00000543418.1_Intron|VEPH1_ENST00000392832.2_Silent_p.G652G|VEPH1_ENST00000392833.2_Intron	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	652						plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			TGTGAGCACCCCCTGCCTGGG	0.483																																					p.G652G		Atlas-SNP	.											.	VEPH1	129	.	0			c.G1956T						.						73	75	74					3																	157031464		2203	4300	6503	SO:0001819	synonymous_variant	79674	exon11			AGCACCCCCTGCC	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"Pleckstrin homology (PH) domain containing"	25735	protein-coding gene	gene with protein product		609594	"ventricular zone expressed PH domain homolog 1 (zebrafish)"			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.1956G>T	chr3.hg19:g.157031464C>A		103.0	0.0		91.0	33.0	NM_001167912	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Silent	SNP	ENST00000362010.2	hg19	CCDS3179.1																																																																																			.	.		0.483	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621		A	157031464	C	A	157031464	2	1	73	1	0	0	0	0	0	0	0	1	17169	610	22	3		3	VEPH1	3	157031464	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	5870663	157031464	40990966	144	9470										
B3GALNT1	8706	hgsc.bcm.edu	37	chr3	160803874	160803874	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggatactcctggtaagaaatAtgggttttttggtaaaatcc	10	5	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:160803874A>G	ENST00000392781.2	-	8	1416	c.669T>C	c.(667-669)caT>caC	p.H223H	B3GALNT1_ENST00000320474.4_Silent_p.H223H|B3GALNT1_ENST00000392780.1_Silent_p.H223H|B3GALNT1_ENST00000392779.2_Silent_p.H223H|B3GALNT1_ENST00000417187.1_Intron|B3GALNT1_ENST00000473285.1_Silent_p.H223H|B3GALNT1_ENST00000488170.1_Silent_p.H223H	NM_001038628.1	NP_001033717.1	O75752	B3GL1_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	223					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity (GO:0047273)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)			GGTAAGAAATATGGGTTTTTT	0.363																																					p.H223H		Atlas-SNP	.											.	B3GALNT1	34	.	0			c.T669C						.						37	39	38					3																	160803874		2202	4295	6497	SO:0001819	synonymous_variant	8706	exon8			AGAAATATGGGTT	Y15062	CCDS3193.1	3q25	2014-07-18	2006-06-14	2006-05-09	ENSG00000169255	ENSG00000169255	2.4.1.79	"Blood group antigens", "Beta 3-glycosyltransferases"	918	protein-coding gene	gene with protein product	"globoside synthase", "P antigen synthase"	603094	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 (Globoside blood group)", "UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1 (Globoside blood group)"	B3GALT3		9582303, 10993897	Standard	XM_005247861		Approved	beta3Gal-T3, galT3, P1, GLOB	uc003fdv.3	O75752	OTTHUMG00000159064	ENST00000392781.2:c.669T>C	chr3.hg19:g.160803874A>G		84.0	0.0		69.0	25.0	NM_001038628	D3DNM4|Q3Y531|Q6IAI5|Q8NFM8|Q8NFM9|Q9HA06	Silent	SNP	ENST00000392781.2	hg19	CCDS3193.1																																																																																			.	.		0.363	B3GALNT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353125.1	NM_033167		G	160803874	A	G	160803874	2	3	73	1	0	0	0	0	0	0	0	1	1245	446	16	2		2	B3GALNT1	3	160803874	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3772410	160803874	37218556	145	9471										
SERPINI2	5276	hgsc.bcm.edu	37	chr3	167183368	167183368	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtcctcttttctgaatttcTgtttccaatctcctttgaaa	4	10	4	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:167183368T>A	ENST00000476257.1	-	5	870	c.572A>T	c.(571-573)cAg>cTg	p.Q191L	SERPINI2_ENST00000264677.4_Missense_Mutation_p.Q191L|SERPINI2_ENST00000461846.1_Missense_Mutation_p.Q191L|SERPINI2_ENST00000471111.1_Missense_Mutation_p.Q191L			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	191					cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						TCTGAATTTCTGTTTCCAATC	0.358																																					p.Q201L		Atlas-SNP	.											.	SERPINI2	85	.	0			c.A602T						.						74	72	72					3																	167183368		2203	4300	6503	SO:0001583	missense	5276	exon5			AATTTCTGTTTCC	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"Serine (or cysteine) peptidase inhibitors"	8945	protein-coding gene	gene with protein product		605587	"serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2", "serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.572A>T	chr3.hg19:g.167183368T>A	ENSP00000420621:p.Gln191Leu	106.0	0.0		102.0	43.0	NM_001012303		Missense_Mutation	SNP	ENST00000476257.1	hg19	CCDS3200.1	.	.	.	.	.	.	.	.	.	.	T	18.69	3.678571	0.68042	.	.	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111;ENST00000466903	D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86	5.74	5.74	0.90152	Serpin domain (3);	0.219004	0.46145	D	0.000310	D	0.85102	0.5620	L	0.28274	0.84	0.35423	D	0.793384	D;D	0.53619	0.961;0.961	P;P	0.57371	0.819;0.721	D	0.88946	0.3383	10	0.48119	T	0.1	.	14.0054	0.64461	0.0:0.0:0.0:1.0	.	191;191	B4DDY9;O75830	.;SPI2_HUMAN	L	191	ENSP00000420621:Q191L;ENSP00000417692:Q191L;ENSP00000264677:Q191L;ENSP00000419407:Q191L;ENSP00000417752:Q191L	ENSP00000264677:Q191L	Q	-	2	0	SERPINI2	168666062	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.413000	0.52686	2.196000	0.70406	0.533000	0.62120	CAG	.	.		0.358	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217		A	167183368	T	A	167183368	3	1	73	1	0	0	0	0	1	0	0	0	14134	1580	55	4	669	4	SERPINI2	3	167183368	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	6379494	167183368	30839062	146	9472										
PLD1	5337	hgsc.bcm.edu	37	chr3	171395376	171395376	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagcaaaaggtttatcaagtTgaacccagtctttgaagacg	9	8	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:171395376T>C	ENST00000351298.4	-	17	2102	c.1976A>G	c.(1975-1977)cAa>cGa	p.Q659R	PLD1_ENST00000340989.4_Missense_Mutation_p.Q659R|PLD1_ENST00000342215.6_Missense_Mutation_p.N550D|PLD1_ENST00000356327.5_Missense_Mutation_p.Q621R	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	659	Catalytic.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	TTTATCAAGTTGAACCCAGTC	0.428																																					p.Q659R	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.A1976G						.						195	171	179					3																	171395376		2203	4300	6503	SO:0001583	missense	5337	exon17			TCAAGTTGAACCC	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"Pleckstrin homology (PH) domain containing"	9067	protein-coding gene	gene with protein product	"choline phosphatase 1"	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.1976A>G	chr3.hg19:g.171395376T>C	ENSP00000342793:p.Gln659Arg	147.0	0.0		113.0	56.0	NM_002662		Missense_Mutation	SNP	ENST00000351298.4	hg19	CCDS3216.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.7|27.7	4.859087|4.859087	0.91433|0.91433	.|.	.|.	ENSG00000075651|ENSG00000075651	ENST00000342215|ENST00000356327;ENST00000351298;ENST00000340989	T|T;T;T	0.29655|0.06849	1.56|3.4;3.4;3.25	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.12774|0.12774	0.0310|0.0310	L|L	0.35414|0.35414	1.06|1.06	0.35158|0.35158	D|D	0.770378|0.770378	.|P;P	.|0.45283	.|0.822;0.855	.|P;P	.|0.48334	.|0.542;0.574	T|T	0.10291|0.10291	-1.0636|-1.0636	7|10	0.07325|0.39692	T|T	0.83|0.17	-21.8443|-21.8443	16.8061|16.8061	0.85666|0.85666	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|644;659	.|Q59EA4;Q13393	.|.;PLD1_HUMAN	D|R	550|621;659;659	ENSP00000339936:N550D|ENSP00000348681:Q621R;ENSP00000342793:Q659R;ENSP00000340326:Q659R	ENSP00000339936:N550D|ENSP00000340326:Q659R	N|Q	-|-	1|2	0|0	PLD1|PLD1	172878070|172878070	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.978000|0.978000	0.69477|0.69477	7.698000|7.698000	0.84413|0.84413	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	AAC|CAA	.	.		0.428	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		C	171395376	T	C	171395376	3	2	73	1	0	0	0	0	1	0	0	0	12054	1812	63	2	1292	2	PLD1	3	171395376	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	4212008	171395376	26627054	147	9473										
ABCC5	10057	hgsc.bcm.edu	37	chr3	183689367	183689367	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttacctcttggatctccagaTcgatgctgtgcagtgtcctc	9	12	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:183689367T>A	ENST00000334444.6	-	11	1985	c.1745A>T	c.(1744-1746)gAt>gTt	p.D582V	ABCC5_ENST00000265586.6_Missense_Mutation_p.D582V	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	582	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	GATCTCCAGATCGATGCTGTG	0.617																																					p.D582V		Atlas-SNP	.											.	ABCC5	142	.	0			c.A1745T						.						80	90	87					3																	183689367		2123	4219	6342	SO:0001583	missense	10057	exon11			TCCAGATCGATGC	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.1745A>T	chr3.hg19:g.183689367T>A	ENSP00000333926:p.Asp582Val	108.0	0.0		52.0	21.0	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Missense_Mutation	SNP	ENST00000334444.6	hg19	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	T	15.42	2.827194	0.50739	.	.	ENSG00000114770	ENST00000334444;ENST00000382495;ENST00000265586	D;D	0.94046	-3.34;-3.34	5.66	5.66	0.87406	ABC transporter, transmembrane domain, type 1 (1);ABC transporter-like (1);	0.050102	0.85682	D	0.000000	D	0.94588	0.8256	M	0.76002	2.32	0.80722	D	1	P;P	0.48589	0.786;0.912	P;P	0.49226	0.603;0.501	D	0.95122	0.8247	10	0.87932	D	0	-13.751	15.8935	0.79318	0.0:0.0:0.0:1.0	.	582;582	Q86UX3;O15440	.;MRP5_HUMAN	V	582;518;582	ENSP00000333926:D582V;ENSP00000265586:D582V	ENSP00000265586:D582V	D	-	2	0	ABCC5	185172061	1.000000	0.71417	1.000000	0.80357	0.128000	0.20619	6.889000	0.75627	2.155000	0.67459	0.533000	0.62120	GAT	.	.		0.617	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		A	183689367	T	A	183689367	3	1	73	1	0	0	0	0	1	0	0	0	56	1435	50	4	2648	4	ABCC5	3	183689367	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	12293991	183689367	14333063	148	9474										
LEPREL1	55214	hgsc.bcm.edu	37	chr3	189690681	189690681	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	accagacagggctgttcggcAgaccatgtgtgtataggaaa	13	8	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:189690681A>G	ENST00000319332.5	-	11	1878	c.1681T>C	c.(1681-1683)Tgc>Cgc	p.C561R	LEPREL1_ENST00000427335.2_Missense_Mutation_p.C380R	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1	561	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5)	41	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	GCTGTTCGGCAGACCATGTGT	0.418																																					p.C561R		Atlas-SNP	.											.	LEPREL1	95	.	0			c.T1681C						.						108	104	105					3																	189690681		2203	4300	6503	SO:0001583	missense	55214	exon11			TTCGGCAGACCAT		CCDS3294.1, CCDS46981.1	3q29	2014-01-28			ENSG00000090530	ENSG00000090530	1.14.11.7		19317	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 2"	610341				15063763, 21885030	Standard	NM_018192		Approved	FLJ10718, MLAT4, P3H2	uc011bsk.2	Q8IVL5	OTTHUMG00000156312	ENST00000319332.5:c.1681T>C	chr3.hg19:g.189690681A>G	ENSP00000316881:p.Cys561Arg	268.0	0.0		250.0	106.0	NM_018192	B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Missense_Mutation	SNP	ENST00000319332.5	hg19	CCDS3294.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.144373	0.77888	.	.	ENSG00000090530	ENST00000319332;ENST00000427335	T;T	0.72051	-0.62;-0.62	5.71	5.71	0.89125	Oxoglutarate/iron-dependent oxygenase (1);Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	T	0.81903	0.4921	M	0.88377	2.95	0.80722	D	1	P	0.50943	0.94	P	0.51297	0.665	D	0.85075	0.0942	9	.	.	.	-21.8233	15.1853	0.72996	1.0:0.0:0.0:0.0	.	561	Q8IVL5	P3H2_HUMAN	R	561;380	ENSP00000316881:C561R;ENSP00000408947:C380R	.	C	-	1	0	LEPREL1	191173375	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.941000	0.92964	2.171000	0.68590	0.528000	0.53228	TGC	.	.		0.418	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1	NM_018192		G	189690681	A	G	189690681	3	3	73	1	0	0	0	0	1	0	0	0	8739	188	7	2	465	2	LEPREL1	3	189690681	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	6001314	189690681	8331749	149	9475										
OPA1	4976	hgsc.bcm.edu	37	chr3	193332727	193332727	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tccaattaaatatggctaccAgcctcgcaggaatttttggc	8	10	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:193332727A>T	ENST00000392438.3	+	2	482	c.248A>T	c.(247-249)cAg>cTg	p.Q83L	OPA1_ENST00000487986.1_3'UTR|OPA1_ENST00000361908.3_Missense_Mutation_p.Q83L|OPA1_ENST00000361150.2_Missense_Mutation_p.Q83L|OPA1_ENST00000361510.2_Missense_Mutation_p.Q83L|OPA1_ENST00000361715.2_Missense_Mutation_p.Q83L|OPA1_ENST00000361828.2_Missense_Mutation_p.Q83L	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	83					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		TATGGCTACCAGCCTCGCAGG	0.443																																					p.Q83L		Atlas-SNP	.											.	OPA1	79	.	0			c.A248T						.						47	45	46					3																	193332727		2203	4300	6503	SO:0001583	missense	4976	exon2			GCTACCAGCCTCG	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.248A>T	chr3.hg19:g.193332727A>T	ENSP00000376233:p.Gln83Leu	280.0	0.0		246.0	17.0	NM_130832	D3DNW4	Missense_Mutation	SNP	ENST00000392438.3	hg19	CCDS43186.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.872623	0.91587	.	.	ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361715;ENST00000361828;ENST00000361150;ENST00000392437;ENST00000392436	D;D;D;D;D;D;D;T	0.95307	-3.25;-3.26;-3.3;-3.28;-3.21;-3.67;-2.02;-1.09	5.97	5.97	0.96955	.	0.287098	0.40144	N	0.001180	D	0.91868	0.7426	L	0.49350	1.555	0.58432	D	0.999999	B;B;B;B;B;B;B;B	0.33694	0.116;0.421;0.204;0.051;0.156;0.218;0.421;0.323	B;B;B;B;B;B;B;B	0.27380	0.073;0.073;0.055;0.016;0.073;0.035;0.05;0.079	D	0.91377	0.5124	10	0.66056	D	0.02	-13.7137	15.642	0.77012	1.0:0.0:0.0:0.0	.	83;83;83;83;83;83;83;83	E5KLK2;O60313;E5KLK0;E5KLK1;E5KLJ6;E5KLJ7;E5KLJ9;E5KLJ5	.;OPA1_HUMAN;.;.;.;.;.;.	L	83	ENSP00000354681:Q83L;ENSP00000376233:Q83L;ENSP00000355324:Q83L;ENSP00000355311:Q83L;ENSP00000354429:Q83L;ENSP00000354781:Q83L;ENSP00000376232:Q83L;ENSP00000376231:Q83L	ENSP00000354781:Q83L	Q	+	2	0	OPA1	194815421	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	4.383000	0.59600	2.288000	0.76882	0.533000	0.62120	CAG	.	.		0.443	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		T	193332727	A	T	193332727	3	4	73	1	0	0	0	0	1	0	0	0	10880	188	7	4	254	4	OPA1	3	193332727	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3642046	193332727	4689703	150	9476										
OPA1	4976	hgsc.bcm.edu	37	chr3	193374929	193374929	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgacagaaccgaaagggaaaGagcatgatgacatatttgat	11	5	0	6			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:193374929G>T	ENST00000392438.3	+	21	2308	c.2074G>T	c.(2074-2076)Gag>Tag	p.E692*	OPA1_ENST00000361510.2_Nonsense_Mutation_p.E747*|OPA1_ENST00000361715.2_Nonsense_Mutation_p.E711*|OPA1_ENST00000361828.2_Nonsense_Mutation_p.E710*|OPA1_ENST00000361150.2_Nonsense_Mutation_p.E693*|OPA1_ENST00000361908.3_Nonsense_Mutation_p.E729*	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	692					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		GAAAGGGAAAGAGCATGATGA	0.368																																					p.E747X		Atlas-SNP	.											.	OPA1	79	.	0			c.G2239T						.						88	92	91					3																	193374929		2203	4300	6503	SO:0001587	stop_gained	4976	exon23			GGGAAAGAGCATG	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.2074G>T	chr3.hg19:g.193374929G>T	ENSP00000376233:p.Glu692*	191.0	0.0		131.0	64.0	NM_130837	D3DNW4	Nonsense_Mutation	SNP	ENST00000392438.3	hg19	CCDS43186.1	.	.	.	.	.	.	.	.	.	.	G	42	9.437445	0.99171	.	.	ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361715;ENST00000361828;ENST00000361150	.	.	.	5.78	5.78	0.91487	.	0.043555	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-20.6863	18.996	0.92813	0.0:0.0:1.0:0.0	.	.	.	.	X	729;692;747;711;710;693	.	ENSP00000354781:E693X	E	+	1	0	OPA1	194857623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.751000	0.98889	2.722000	0.93159	0.655000	0.94253	GAG	.	.		0.368	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		T	193374929	G	T	193374929	4	4	73	1	0	0	0	0	0	1	0	0	10880	943	33	3	2329	3	OPA1	3	193374929	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	42202	193374929	4647501	151	9477										
ACAP2	23527	hgsc.bcm.edu	37	chr3	195112843	195112843	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcaagttttagttccaattcTgccacatcaccttctacttc	3	13	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr3:195112843T>A	ENST00000326793.6	-	2	317	c.87A>T	c.(85-87)gcA>gcT	p.A29A		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	29	BAR.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						GTTCCAATTCTGCCACATCAC	0.294																																					p.A29A		Atlas-SNP	.											.	ACAP2	72	.	0			c.A87T						.						81	84	83					3																	195112843		2201	4299	6500	SO:0001819	synonymous_variant	23527	exon2			CAATTCTGCCACA		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.87A>T	chr3.hg19:g.195112843T>A		806.0	1.0		775.0	294.0	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Silent	SNP	ENST00000326793.6	hg19	CCDS33924.1																																																																																			.	.		0.294	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287		A	195112843	T	A	195112843	2	1	73	1	0	0	0	0	0	0	0	1	119	1567	55	4		4	ACAP2	3	195112843	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1737914	195112843	2909587	152	9478										
EVC2	132884	hgsc.bcm.edu	37	chr4	5578129	5578129	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggcctgctgctgctgggctGcctcctgctgcaccagctgg	15	15	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:5578129G>A	ENST00000344408.5	-	18	3163	c.3110C>T	c.(3109-3111)gCa>gTa	p.A1037V	EVC2_ENST00000310917.2_Missense_Mutation_p.A957V|EVC2_ENST00000344938.1_Missense_Mutation_p.A1037V	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	1037					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CTGCTGGGCTGCCTCCTGCTG	0.642																																					p.A1037V		Atlas-SNP	.											.	EVC2	202	.	0			c.C3110T						.						27	25	26					4																	5578129		2203	4300	6503	SO:0001583	missense	132884	exon18			TGGGCTGCCTCCT	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.3110C>T	chr4.hg19:g.5578129G>A	ENSP00000342144:p.Ala1037Val	62.0	0.0		72.0	37.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	G	7.049	0.564160	0.13498	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74842	-0.88;-0.87;-0.88	5.38	1.31	0.21738	.	0.716774	0.13601	N	0.375878	T	0.53932	0.1827	N	0.24115	0.695	0.09310	N	1	B	0.14805	0.011	B	0.10450	0.005	T	0.34675	-0.9819	10	0.30078	T	0.28	-5.7468	3.1914	0.06618	0.0869:0.1381:0.3893:0.3857	.	1037	Q86UK5	LBN_HUMAN	V	1037;957;1037	ENSP00000339954:A1037V;ENSP00000311683:A957V;ENSP00000342144:A1037V	ENSP00000311683:A957V	A	-	2	0	EVC2	5629030	0.013000	0.17824	0.059000	0.19551	0.258000	0.26162	1.232000	0.32636	-0.084000	0.12595	0.491000	0.48974	GCA	.	.		0.642	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		A	5578129	G	A	5578129	3	1	73	1	0	0	0	0	1	0	0	0	5288	1319	46	3	836	3	EVC2	4	5578129	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10		5578129	185576147	153	9479										
ABLIM2	84448	hgsc.bcm.edu	37	chr4	8029484	8029484	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cccacatcactgcgtgccttAcctcggaagtaggggatgta	11	12	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:8029484A>T	ENST00000341937.5	-	11	1233				ABLIM2_ENST00000361581.5_Intron|ABLIM2_ENST00000546334.1_Intron|ABLIM2_ENST00000447017.2_Splice_Site|ABLIM2_ENST00000407564.3_Intron|ABLIM2_ENST00000428004.2_Intron|ABLIM2_ENST00000296372.8_Intron|ABLIM2_ENST00000318888.4_Intron|ABLIM2_ENST00000515079.1_Splice_Site|ABLIM2_ENST00000505872.1_Intron|ABLIM2_ENST00000545242.1_Intron|ABLIM2_ENST00000514025.1_Intron|ABLIM2_ENST00000361737.5_Intron	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2						actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|myofibril (GO:0030016)	zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|pancreas(3)|prostate(2)|urinary_tract(1)	25						TGCGTGCCTTACCTCGGAAGT	0.602																																					.		Atlas-SNP	.											.	ABLIM2	59	.	0			c.1267+2T>A						.						112	96	101					4																	8029484		1567	3582	5149	SO:0001627	intron_variant	84448	exon13			TGCCTTACCTCGG	AB058711	CCDS47011.1, CCDS47012.1, CCDS47013.1, CCDS47014.1, CCDS47015.1, CCDS47016.1, CCDS54719.1, CCDS68669.1	4p16.1	2012-05-16			ENSG00000163995	ENSG00000163995			19195	protein-coding gene	gene with protein product		612544	"actin binding LIM protein 2"				Standard	NM_001130083		Approved	KIAA1808	uc003gkj.4	Q6H8Q1	OTTHUMG00000057427	ENST00000341937.5:c.1168+1898T>A	chr4.hg19:g.8029484A>T		106.0	0.0		121.0	43.0	NM_001130083	E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Splice_Site	SNP	ENST00000341937.5	hg19	CCDS47013.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.234720	0.79800	.	.	ENSG00000163995	ENST00000400045;ENST00000447017;ENST00000510277	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2676	0.66129	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABLIM2	8080384	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.578000	0.60929	1.783000	0.52377	0.528000	0.53228	.	.	.		0.602	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083		T	8029484	A	T	8029484	1	4	73	0	1	0	0	0	0	0	0	0	95	405	14	4		4	ABLIM2	4	8029484	Intron	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2451355	8029484	183124792	154	9480										
FGFBP1	9982	hgsc.bcm.edu	37	chr4	15938116	15938116	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcctgcttttctgcttaatcTgggtgttgcccagagtgtcc	11	11	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:15938116T>A	ENST00000382333.1	-	3	434	c.140A>T	c.(139-141)cAg>cTg	p.Q47L	FGFBP1_ENST00000259988.2_Missense_Mutation_p.Q47L	NM_005130.4	NP_005121.1	Q14512	FGFP1_HUMAN	fibroblast growth factor binding protein 1	47					cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|prostate(2)|skin(1)	10						CTGCTTAATCTGGGTGTTGCC	0.517																																					p.Q47L		Atlas-SNP	.											.	FGFBP1	26	.	0			c.A140T						.						121	117	118					4																	15938116		2203	4300	6503	SO:0001583	missense	9982	exon3			TTAATCTGGGTGT	M60047	CCDS3418.1	4p15.32	2008-02-05			ENSG00000137440	ENSG00000137440			19695	protein-coding gene	gene with protein product		607737				11148217, 1885605	Standard	NM_005130		Approved	HBP17, FGFBP	uc003gom.3	Q14512	OTTHUMG00000097745	ENST00000382333.1:c.140A>T	chr4.hg19:g.15938116T>A	ENSP00000371770:p.Gln47Leu	149.0	0.0		219.0	128.0	NM_005130	A8K5J2	Missense_Mutation	SNP	ENST00000382333.1	hg19	CCDS3418.1	.	.	.	.	.	.	.	.	.	.	T	10.41	1.342527	0.24339	.	.	ENSG00000137440	ENST00000382333;ENST00000259988	T;T	0.14391	2.51;2.51	4.83	-3.36	0.04913	.	2.710420	0.01282	N	0.009760	T	0.11537	0.0281	L	0.47716	1.5	0.09310	N	1	B	0.14805	0.011	B	0.15052	0.012	T	0.28073	-1.0055	10	0.49607	T	0.09	-1.0224	0.798	0.01069	0.2522:0.1535:0.1303:0.4641	.	47	Q14512	FGFP1_HUMAN	L	47	ENSP00000371770:Q47L;ENSP00000259988:Q47L	ENSP00000259988:Q47L	Q	-	2	0	FGFBP1	15547214	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.931000	0.03967	-0.725000	0.04901	-0.462000	0.05337	CAG	.	.		0.517	FGFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214974.1	NM_005130		A	15938116	T	A	15938116	3	1	73	1	0	0	0	0	1	0	0	0	5868	1580	55	4	568	4	FGFBP1	4	15938116	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	7908632	15938116	175216160	155	9481										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20255500	20255500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gttagtgctggcgatcctgaAcaaggtggcaccgcaggcgt	15	10	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:20255500A>G	ENST00000504154.1	+	1	314	c.62A>G	c.(61-63)aAc>aGc	p.N21S	SLIT2_ENST00000503823.1_Missense_Mutation_p.N21S|SLIT2_ENST00000503837.1_Missense_Mutation_p.N21S|SLIT2_ENST00000273739.5_Missense_Mutation_p.N21S	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	21					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GCGATCCTGAACAAGGTGGCA	0.687																																					p.N21S		Atlas-SNP	.											.	SLIT2	290	.	0			c.A62G						.						95	75	82					4																	20255500		2203	4299	6502	SO:0001583	missense	9353	exon1			TCCTGAACAAGGT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.62A>G	chr4.hg19:g.20255500A>G	ENSP00000422591:p.Asn21Ser	17.0	0.0		42.0	11.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	A	2.048	-0.418427	0.04766	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.79845	-1.3;-1.31;-1.23;-1.28	3.99	-0.995	0.10222	.	0.279438	0.37095	N	0.002258	T	0.58595	0.2133	N	0.11756	0.17	0.21967	N	0.99945	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43669	-0.9377	10	0.18710	T	0.47	.	9.9968	0.41905	0.2806:0.0:0.7194:0.0	.	21;21	O94813-3;O94813	.;SLIT2_HUMAN	S	21	ENSP00000427548:N21S;ENSP00000422591:N21S;ENSP00000273739:N21S;ENSP00000422261:N21S	ENSP00000273739:N21S	N	+	2	0	SLIT2	19864598	0.669000	0.27502	0.274000	0.24659	0.538000	0.34931	1.255000	0.32909	-0.043000	0.13513	0.260000	0.18958	AAC	.	.		0.687	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			G	20255500	A	G	20255500	3	3	73	1	0	0	0	0	1	0	0	0	14755	43	2	2	64	2	SLIT2	4	20255500	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4317384	20255500	170898776	156	9482										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20525440	20525440	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gatgcttttcaggatctccaCaacttgaaccttctctccct	5	14	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:20525440C>A	ENST00000504154.1	+	13	1440	c.1188C>A	c.(1186-1188)caC>caA	p.H396Q	SLIT2_ENST00000503823.1_Missense_Mutation_p.H396Q|SLIT2_ENST00000503837.1_Missense_Mutation_p.H400Q|SLIT2_ENST00000273739.5_Missense_Mutation_p.H400Q	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	396					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						AGGATCTCCACAACTTGAACC	0.393																																					p.H396Q		Atlas-SNP	.											.	SLIT2	290	.	0			c.C1188A						.						165	156	159					4																	20525440		2203	4300	6503	SO:0001583	missense	9353	exon13			TCTCCACAACTTG	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1188C>A	chr4.hg19:g.20525440C>A	ENSP00000422591:p.His396Gln	208.0	0.0		251.0	15.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	C	2.785	-0.252590	0.05829	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.08	5.08	0.68730	.	0.099294	0.64402	D	0.000002	T	0.33352	0.0860	N	0.11818	0.18	0.54753	D	0.999988	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.27773	-1.0064	10	0.02654	T	1	.	18.8999	0.92439	0.0:1.0:0.0:0.0	.	396;396	O94813-3;O94813	.;SLIT2_HUMAN	Q	396;396;400;400;400	ENSP00000427548:H396Q;ENSP00000422591:H396Q;ENSP00000273739:H400Q;ENSP00000422261:H400Q	ENSP00000273739:H400Q	H	+	3	2	SLIT2	20134538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.953000	0.40352	2.529000	0.85273	0.644000	0.83932	CAC	.	.		0.393	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			A	20525440	C	A	20525440	3	1	73	1	0	0	0	0	1	0	0	0	14755	477	17	3	1238	3	SLIT2	4	20525440	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	269940	20525440	170628836	157	9483										
SEPSECS	51091	hgsc.bcm.edu	37	chr4	25160667	25160667	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaattgttgctgtccatgatTgcaagttcatgtaaaaagag	9	5	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:25160667T>G	ENST00000382103.2	-	2	249	c.177A>C	c.(175-177)gcA>gcC	p.A59A	SEPSECS_ENST00000302922.3_Intron|PI4K2B_ENST00000512921.1_5'Flank	NM_016955.3	NP_058651.3	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	59					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	pyridoxal phosphate binding (GO:0030170)|transferase activity, transferring selenium-containing groups (GO:0016785)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(2)|stomach(1)	8		Breast(46;0.173)				TGTCCATGATTGCAAGTTCAT	0.388																																					p.A59A		Atlas-SNP	.											.	SEPSECS	55	.	0			c.A177C						.						147	147	147					4																	25160667		1899	4129	6028	SO:0001819	synonymous_variant	51091	exon2			CATGATTGCAAGT	AJ238617	CCDS3432.1, CCDS3432.2	4p15.2	2008-10-27			ENSG00000109618	ENSG00000109618			30605	protein-coding gene	gene with protein product	"soluble liver antigen/liver pancreas antigen"	613009				16230358, 10931155, 17142313, 17194211	Standard	NM_016955		Approved	SLA/LP, SLA	uc003grg.3	Q9HD40	OTTHUMG00000128563	ENST00000382103.2:c.177A>C	chr4.hg19:g.25160667T>G		199.0	0.0		265.0	154.0	NM_016955	A8K8W1|Q0D2P3|Q17RT1|Q9NXZ5|Q9UGM9|Q9Y353	Silent	SNP	ENST00000382103.2	hg19	CCDS3432.2																																																																																			.	.		0.388	SEPSECS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250414.2	NM_016955		G	25160667	T	G	25160667	2	3	73	1	0	0	0	0	0	0	0	1	14073	1799	63	5		5	SEPSECS	4	25160667	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	4635227	25160667	165993609	158	9484										
KIT	3815	hgsc.bcm.edu	37	chr4	55564702	55564702	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggagggcaagtcagtgctgtCggaaaaattcatcctgaaag	13	7	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:55564702C>A	ENST00000288135.5	+	3	687	c.590C>A	c.(589-591)tCg>tAg	p.S197*		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	197	Ig-like C2-type 2.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCAGTGCTGTCGGAAAAATTC	0.498		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.S197X		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	KIT,NS,haematopoietic_neoplasm,0,1	KIT	7396	.	0			c.C590A						.						104	94	98					4																	55564702		2203	4300	6503	SO:0001587	stop_gained	3815	exon3	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	TGCTGTCGGAAAA	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.590C>A	chr4.hg19:g.55564702C>A	ENSP00000288135:p.Ser197*	100.0	0.0		75.0	34.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Nonsense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.628715	0.67015	.	.	ENSG00000157404	ENST00000288135;ENST00000412167;ENST00000536403	.	.	.	5.75	4.91	0.64330	.	0.113900	0.39834	N	0.001251	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9428	0.58354	0.0:0.9253:0.0:0.0747	.	.	.	.	X	197	.	ENSP00000288135:S197X	S	+	2	0	KIT	55259459	0.999000	0.42202	0.062000	0.19696	0.022000	0.10575	5.295000	0.65692	1.440000	0.47531	0.643000	0.83706	TCG	.	.		0.498	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			A	55564702	C	A	55564702	4	1	73	1	0	0	0	0	0	1	0	0	8338	893	31	1	600	1	KIT	4	55564702	Nonsense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	30404035	55564702	135589574	159	9485										
KDR	3791	hgsc.bcm.edu	37	chr4	55973948	55973948	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tccaactgccaataccagtgGatgtgatgcgggggaggaat	14	8	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:55973948G>C	ENST00000263923.4	-	10	1663	c.1368C>G	c.(1366-1368)atC>atG	p.I456M		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	456	Ig-like C2-type 5.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AATACCAGTGGATGTGATGCG	0.512			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.I456M		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.C1368G						.						201	171	181					4																	55973948		2203	4300	6503	SO:0001583	missense	3791	exon10			CCAGTGGATGTGA	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.1368C>G	chr4.hg19:g.55973948G>C	ENSP00000263923:p.Ile456Met	154.0	0.0		115.0	43.0	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	hg19	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	G	11.65	1.702795	0.30232	.	.	ENSG00000128052	ENST00000263923	T	0.12361	2.69	5.29	4.45	0.53987	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.530991	0.21343	N	0.076095	T	0.29158	0.0725	M	0.74467	2.265	0.21915	N	0.999475	D;D	0.59357	0.985;0.978	P;D	0.63703	0.838;0.917	T	0.25710	-1.0124	10	0.87932	D	0	.	3.548	0.07836	0.1491:0.1337:0.5792:0.138	.	456;456	P35968-2;P35968	.;VGFR2_HUMAN	M	456	ENSP00000263923:I456M	ENSP00000263923:I456M	I	-	3	3	KDR	55668705	0.956000	0.32656	0.051000	0.19133	0.274000	0.26718	1.215000	0.32431	1.235000	0.43724	0.313000	0.20887	ATC	.	.		0.512	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			C	55973948	G	C	55973948	3	2	73	1	0	0	0	0	1	0	0	0	8148	1164	41	4	2786	4	KDR	4	55973948	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	409246	55973948	135180328	160	9486										
AASDH	132949	hgsc.bcm.edu	37	chr4	57250311	57250311	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gaattccttgaaagtcacagTgtaacagcagaaaatttgat	8	6	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:57250311T>A	ENST00000205214.6	-	2	335	c.155A>T	c.(154-156)cAc>cTc	p.H52L	AASDH_ENST00000451613.1_Missense_Mutation_p.H52L|AASDH_ENST00000510762.1_Intron|AASDH_ENST00000513376.1_Intron|AASDH_ENST00000602986.1_5'UTR|AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000502617.1_Missense_Mutation_p.H52L	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	52					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				AAAGTCACAGTGTAACAGCAG	0.378																																					p.H52L		Atlas-SNP	.											.	AASDH	101	.	0			c.A155T						.						103	99	101					4																	57250311		2203	4300	6503	SO:0001583	missense	132949	exon2			TCACAGTGTAACA	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.155A>T	chr4.hg19:g.57250311T>A	ENSP00000205214:p.His52Leu	253.0	0.0		235.0	92.0	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	hg19	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.053740	0.55218	.	.	ENSG00000157426	ENST00000205214;ENST00000451613;ENST00000502617	T;T;T	0.49139	0.79;1.1;0.79	5.92	4.74	0.60224	AMP-dependent synthetase/ligase (1);	0.287343	0.44097	D	0.000488	T	0.49338	0.1551	L	0.38953	1.18	0.28835	N	0.896912	P;P;P;D	0.57899	0.855;0.766;0.855;0.981	B;P;B;P	0.54590	0.359;0.468;0.359;0.756	T	0.44832	-0.9302	10	0.35671	T	0.21	-2.8613	11.8177	0.52220	0.0:0.0689:0.0:0.9311	.	52;52;52;52	Q4L235-4;B4E2K0;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	L	52	ENSP00000205214:H52L;ENSP00000409656:H52L;ENSP00000421171:H52L	ENSP00000205214:H52L	H	-	2	0	AASDH	56945068	1.000000	0.71417	0.989000	0.46669	0.569000	0.35902	3.169000	0.50809	1.067000	0.40740	0.528000	0.53228	CAC	.	.		0.378	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		A	57250311	T	A	57250311	3	1	73	1	0	0	0	0	1	0	0	0	22	1696	59	4	3197	4	AASDH	4	57250311	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1276363	57250311	133903965	161	9487										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66467379	66467379	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cttgacaggtgccatttttcTcttcatatcctgccttgcac	6	13	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:66467379T>A	ENST00000273854.3	-	3	1490	c.890A>T	c.(889-891)gAg>gTg	p.E297V	EPHA5_ENST00000432638.2_Missense_Mutation_p.E297V|EPHA5_ENST00000354839.4_Missense_Mutation_p.E297V|EPHA5_ENST00000511294.1_Missense_Mutation_p.E297V	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	297	Cys-rich.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						GCCATTTTTCTCTTCATATCC	0.493										TSP Lung(17;0.13)																											p.E297V		Atlas-SNP	.											.	EPHA5	315	.	0			c.A890T						.						99	106	104					4																	66467379		2203	4300	6503	SO:0001583	missense	2044	exon3			TTTTTCTCTTCAT	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.890A>T	chr4.hg19:g.66467379T>A	ENSP00000273854:p.Glu297Val	58.0	0.0		55.0	23.0	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	hg19	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.929328	0.73327	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;D	0.97161	1.59;-0.89;1.59;-4.27	6.08	6.08	0.98989	.	0.186939	0.37393	N	0.002116	D	0.98115	0.9378	M	0.70787	2.145	0.58432	D	0.999997	D;D;D;D	0.76494	0.997;0.982;0.998;0.999	D;P;D;D	0.68621	0.911;0.898;0.959;0.931	D	0.99050	1.0827	10	0.87932	D	0	.	16.6438	0.85155	0.0:0.0:0.0:1.0	.	297;297;297;297	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	V	297	ENSP00000273854:E297V;ENSP00000389208:E297V;ENSP00000346899:E297V;ENSP00000427638:E297V	ENSP00000273854:E297V	E	-	2	0	EPHA5	66149974	1.000000	0.71417	1.000000	0.80357	0.635000	0.38103	6.275000	0.72594	2.333000	0.79357	0.533000	0.62120	GAG	.	.		0.493	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		A	66467379	T	A	66467379	3	1	73	1	0	0	0	0	1	0	0	0	5172	1551	54	4	2287	4	EPHA5	4	66467379	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	9217068	66467379	124686897	162	9488										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66467935	66467935	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gatccaactggtcaaaagccAgttattctgattctgttcca	7	10	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:66467935A>T	ENST00000273854.3	-	3	934	c.334T>A	c.(334-336)Tgg>Agg	p.W112R	EPHA5_ENST00000432638.2_Missense_Mutation_p.W112R|EPHA5_ENST00000354839.4_Missense_Mutation_p.W112R|EPHA5_ENST00000511294.1_Missense_Mutation_p.W112R	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	112	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						GTCAAAAGCCAGTTATTCTGA	0.438										TSP Lung(17;0.13)																											p.W112R		Atlas-SNP	.											.	EPHA5	315	.	0			c.T334A						.						123	129	127					4																	66467935		2203	4300	6503	SO:0001583	missense	2044	exon3			AAAGCCAGTTATT	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.334T>A	chr4.hg19:g.66467935A>T	ENSP00000273854:p.Trp112Arg	63.0	0.0		50.0	22.0	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	hg19	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.979272	0.74360	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.59638	0.25;0.25;0.25;0.25	5.68	5.68	0.88126	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.64402	D	0.000020	D	0.82737	0.5102	H	0.94183	3.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;0.999	D;D;D;D	0.97110	1.0;0.997;1.0;0.989	D	0.87809	0.2630	10	0.87932	D	0	.	15.9206	0.79562	1.0:0.0:0.0:0.0	.	112;112;112;112	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	R	112	ENSP00000273854:W112R;ENSP00000389208:W112R;ENSP00000346899:W112R;ENSP00000427638:W112R	ENSP00000273854:W112R	W	-	1	0	EPHA5	66150530	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.166000	0.68216	0.533000	0.62120	TGG	.	.		0.438	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		T	66467935	A	T	66467935	3	4	73	1	0	0	0	0	1	0	0	0	5172	188	7	4	2843	4	EPHA5	4	66467935	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	556	66467935	124686341	163	9489										
TMPRSS11A	339967	hgsc.bcm.edu	37	chr4	68780363	68780363	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagaacattccaggttttatAtcattgccatacacctgtgg	7	10	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:68780363A>G	ENST00000334830.7	-	9	1793	c.1047T>C	c.(1045-1047)gaT>gaC	p.D349D	TMPRSS11A_ENST00000396188.2_Silent_p.D346D|UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000508048.1_Silent_p.D345D			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	349	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						CAGGTTTTATATCATTGCCAT	0.383																																					p.D349D	NSCLC(26;2 894 10941 14480 22546)	Atlas-SNP	.											.	TMPRSS11A	74	.	0			c.T1047C						.						139	131	134					4																	68780363		2203	4300	6503	SO:0001819	synonymous_variant	339967	exon9			TTTTATATCATTG	AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.1047T>C	chr4.hg19:g.68780363A>G		251.0	0.0		235.0	30.0	NM_182606	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Silent	SNP	ENST00000334830.7	hg19	CCDS3519.1																																																																																			.	.		0.383	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606		G	68780363	A	G	68780363	2	3	73	1	0	0	0	0	0	0	0	1	16254	446	16	2		2	TMPRSS11A	4	68780363	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2312428	68780363	122373913	164	9490										
TMPRSS11A	339967	hgsc.bcm.edu	37	chr4	68795630	68795630	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgatgaggcatttattggcAaggctcttaaattccttatc	8	8	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:68795630A>G	ENST00000334830.7	-	5	1204	c.458T>C	c.(457-459)tTg>tCg	p.L153S	TMPRSS11A_ENST00000396188.2_Missense_Mutation_p.L150S|UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000508048.1_Missense_Mutation_p.L149S			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	153	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						ATTTATTGGCAAGGCTCTTAA	0.383																																					p.L153S	NSCLC(26;2 894 10941 14480 22546)	Atlas-SNP	.											.	TMPRSS11A	74	.	0			c.T458C						.						176	164	168					4																	68795630		2203	4300	6503	SO:0001583	missense	339967	exon5			ATTGGCAAGGCTC	AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.458T>C	chr4.hg19:g.68795630A>G	ENSP00000334611:p.Leu153Ser	213.0	0.0		165.0	80.0	NM_182606	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Missense_Mutation	SNP	ENST00000334830.7	hg19	CCDS3519.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.400682	0.62177	.	.	ENSG00000187054	ENST00000508048;ENST00000334830;ENST00000396188;ENST00000513536	T;T;T;T	0.51574	0.7;0.7;0.7;0.7	5.98	4.8	0.61643	SEA (1);	0.000000	0.43747	D	0.000527	T	0.67933	0.2946	M	0.83012	2.62	0.27428	N	0.954094	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.64287	-0.6443	10	0.72032	D	0.01	.	8.94	0.35725	0.916:0.0:0.084:0.0	.	150;153	B5MDI9;Q6ZMR5	.;TM11A_HUMAN	S	149;153;150;130	ENSP00000426911:L149S;ENSP00000334611:L153S;ENSP00000379491:L150S;ENSP00000427621:L130S	ENSP00000334611:L153S	L	-	2	0	TMPRSS11A	68478225	0.572000	0.26668	0.549000	0.28204	0.921000	0.55340	2.736000	0.47385	1.076000	0.40961	0.533000	0.62120	TTG	.	.		0.383	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606		G	68795630	A	G	68795630	3	3	73	1	0	0	0	0	1	0	0	0	16254	131	5	2	831	2	TMPRSS11A	4	68795630	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	15267	68795630	122358646	165	9491										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87732253	87732253	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tacaaagacacggaatggttCagacagaggtgagtcatggc	13	7	2	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:87732253C>A	ENST00000411767.2	+	47	7417	c.7354C>A	c.(7354-7356)Cag>Aag	p.Q2452K	PTPN13_ENST00000427191.2_Missense_Mutation_p.Q2433K|PTPN13_ENST00000511467.1_Missense_Mutation_p.Q2457K|PTPN13_ENST00000316707.6_Missense_Mutation_p.Q2261K|PTPN13_ENST00000436978.1_Missense_Mutation_p.Q2457K			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2452	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CGGAATGGTTCAGACAGAGGT	0.373																																					p.Q2457K		Atlas-SNP	.											.	PTPN13	203	.	0			c.C7369A						.						104	97	99					4																	87732253		1894	4122	6016	SO:0001583	missense	5783	exon47			ATGGTTCAGACAG		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.7354C>A	chr4.hg19:g.87732253C>A	ENSP00000407249:p.Gln2452Lys	46.0	0.0		42.0	12.0	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.918890	0.92249	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01	5.1	5.1	0.69264	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.46442	D	0.000300	D	0.94735	0.8301	H	0.94964	3.605	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.983;0.973;0.995;0.992	D	0.96020	0.9008	10	0.87932	D	0	.	18.8679	0.92300	0.0:1.0:0.0:0.0	.	2261;2433;2452;2457	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	K	2433;2457;2261;2452;2457;2401	ENSP00000408368:Q2433K;ENSP00000394794:Q2457K;ENSP00000322675:Q2261K;ENSP00000407249:Q2452K;ENSP00000426626:Q2457K	ENSP00000322675:Q2261K	Q	+	1	0	PTPN13	87951277	1.000000	0.71417	0.995000	0.50966	0.974000	0.67602	7.445000	0.80570	2.516000	0.84829	0.467000	0.42956	CAG	.	.		0.373	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87732253	C	A	87732253	3	1	73	1	0	0	0	0	1	0	0	0	12795	827	29	3	7551	3	PTPN13	4	87732253	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	18936623	87732253	103422023	166	9492										
FAM190A	401145	hgsc.bcm.edu	37	chr4	91229854	91229854	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggattttgaaagggaaaaagAgcactcaactaacaagaatg	10	5	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:91229854A>G	ENST00000509176.1	+	2	707	c.419A>G	c.(418-420)gAg>gGg	p.E140G	CCSER1_ENST00000333691.8_Missense_Mutation_p.E140G|CCSER1_ENST00000432775.2_Missense_Mutation_p.E140G	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	140																	AGGGAAAAAGAGCACTCAACT	0.368																																					p.E140G		Atlas-SNP	.											.	.	.	.	0			c.A419G						.						53	53	53					4																	91229854		1825	4083	5908	SO:0001583	missense	401145	exon2			AAAAAGAGCACTC		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.419A>G	chr4.hg19:g.91229854A>G	ENSP00000425040:p.Glu140Gly	131.0	0.0		126.0	56.0	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	hg19	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	A	16.60	3.168134	0.57476	.	.	ENSG00000184305	ENST00000509176;ENST00000432775;ENST00000333691;ENST00000458365	T;T;T	0.53423	1.14;0.62;1.14	5.18	2.64	0.31445	.	0.189801	0.46442	D	0.000297	T	0.51568	0.1682	L	0.43152	1.355	0.28186	N	0.927964	D;P;P	0.56287	0.975;0.51;0.649	P;B;B	0.58454	0.839;0.23;0.322	T	0.46091	-0.9216	10	0.72032	D	0.01	-20.7715	8.5104	0.33213	0.8002:0.1308:0.069:0.0	.	140;140;140	Q9C0I3-2;Q9C0I3;E7EUW0	.;F190A_HUMAN;.	G	140	ENSP00000425040:E140G;ENSP00000389283:E140G;ENSP00000329482:E140G	ENSP00000329482:E140G	E	+	2	0	FAM190A	91448877	1.000000	0.71417	0.964000	0.40570	0.989000	0.77384	5.517000	0.67061	0.458000	0.26988	0.533000	0.62120	GAG	.	.		0.368	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		G	91229854	A	G	91229854	3	3	73	1	0	0	0	0	1	0	0	0	5526	304	11	2	421	2	FAM190A	4	91229854	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3497601	91229854	99924422	167	9493										
BANK1	55024	hgsc.bcm.edu	37	chr4	102783820	102783820	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtctggtgcatgaaagctttAggtaagaatgtttatgattt	11	3	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:102783820A>T	ENST00000322953.4	+	4	1036	c.762A>T	c.(760-762)ttA>ttT	p.L254F	BANK1_ENST00000428908.1_Splice_Site_p.L121F|BANK1_ENST00000444316.2_Splice_Site_p.L224F|BANK1_ENST00000504592.1_Splice_Site_p.L239F|BANK1_ENST00000508653.1_Splice_Site_p.L121F	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	254	DBB. {ECO:0000255|PROSITE- ProRule:PRU00707}.				B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		TGAAAGCTTTAGGTAAGAATG	0.313																																					p.L254F		Atlas-SNP	.											.	BANK1	95	.	0			c.A762T						.						55	55	55					4																	102783820		2203	4297	6500	SO:0001630	splice_region_variant	55024	exon4			AGCTTTAGGTAAG	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.763+1A>T	chr4.hg19:g.102783820A>T		192.0	0.0		157.0	64.0	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	hg19	CCDS34038.1	.	.	.	.	.	.	.	.	.	.	A	17.16	3.318220	0.60524	.	.	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.20463	2.79;2.79;2.07;2.07;2.79	5.29	2.81	0.32909	DBB domain (1);	0.785218	0.10542	N	0.662562	T	0.31949	0.0813	L	0.50333	1.59	0.27041	N	0.964014	B;D;D	0.63880	0.385;0.993;0.993	B;P;P	0.61132	0.099;0.884;0.884	T	0.12066	-1.0562	10	0.39692	T	0.17	.	5.265	0.15593	0.751:0.0:0.0834:0.1656	.	121;254;239	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	F	239;254;121;121;224	ENSP00000421443:L239F;ENSP00000320509:L254F;ENSP00000412748:L121F;ENSP00000422314:L121F;ENSP00000388817:L224F	ENSP00000320509:L254F	L	+	3	2	BANK1	103002843	1.000000	0.71417	0.977000	0.42913	0.982000	0.71751	4.214000	0.58527	0.307000	0.22880	0.477000	0.44152	TTA	.	.		0.313	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	Missense_Mutation	T	102783820	A	T	102783820	5	4	73	1	0	0	0	0	0	0	1	0	1309	434	15	4	776	4	BANK1	4	102783820	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	11553966	102783820	88370456	168	9494										
EGF	1950	hgsc.bcm.edu	37	chr4	110904598	110904598	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtggtgaagttgatctaaagAaccaagtaacaccattggac	10	7	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:110904598A>G	ENST00000265171.5	+	16	2837	c.2392A>G	c.(2392-2394)Aac>Gac	p.N798D	EGF_ENST00000509793.1_Missense_Mutation_p.N756D|EGF_ENST00000503392.1_Missense_Mutation_p.N798D	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	798					activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	TGATCTAAAGAACCAAGTAAC	0.348																																					p.N798D		Atlas-SNP	.											.	EGF	113	.	0			c.A2392G						.						100	92	95					4																	110904598		2203	4300	6503	SO:0001583	missense	1950	exon16			CTAAAGAACCAAG	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.2392A>G	chr4.hg19:g.110904598A>G	ENSP00000265171:p.Asn798Asp	121.0	0.0		111.0	56.0	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	hg19	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	A	2.085	-0.409725	0.04799	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.88277	-2.36;-2.27;-1.94	5.31	-0.0968	0.13635	.	0.928471	0.09419	N	0.804668	T	0.69628	0.3132	N	0.04880	-0.145	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.09377	0.004;0.004;0.004	T	0.57659	-0.7773	10	0.02654	T	1	.	4.878	0.13665	0.6186:0.1482:0.2332:0.0	.	798;756;798	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	D	756;798;798	ENSP00000424316:N756D;ENSP00000265171:N798D;ENSP00000421384:N798D	ENSP00000265171:N798D	N	+	1	0	EGF	111124047	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.675000	0.25232	-0.221000	0.09973	-1.098000	0.02139	AAC	.	.		0.348	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			G	110904598	A	G	110904598	3	3	73	1	0	0	0	0	1	0	0	0	4964	246	9	2	2454	2	EGF	4	110904598	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	8120778	110904598	80249678	169	9495										
MAML3	55534	hgsc.bcm.edu	37	chr4	140651774	140651774	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctgagcctgggggcacggaGgactgcatggggcctgtggt	19	10	0	1	rs372122289		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:140651774G>T	ENST00000509479.2	-	3	2983	c.2127C>A	c.(2125-2127)tcC>tcA	p.S709S	MGST2_ENST00000515137.1_Intron	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					GGGGCACGGAGGACTGCATGG	0.632																																					p.S705S		Atlas-SNP	.											.	MAML3	192	.	0			c.C2115A						.						28	31	30					4																	140651774		2018	4174	6192	SO:0001819	synonymous_variant	55534	exon4			CACGGAGGACTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.2127C>A	chr4.hg19:g.140651774G>T		97.0	0.0		112.0	65.0	NM_018717		Silent	SNP	ENST00000509479.2	hg19	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	G	7.082	0.570365	0.13560	.	.	ENSG00000196782	ENST00000502696	.	.	.	5.74	-2.82	0.05787	.	.	.	.	.	T	0.18130	0.0435	.	.	.	0.28955	N	0.890201	.	.	.	.	.	.	T	0.27971	-1.0058	4	.	.	.	.	0.7201	0.00939	0.3438:0.1837:0.2852:0.1873	.	.	.	.	H	53	.	.	P	-	2	0	MAML3	140871224	0.128000	0.22383	0.001000	0.08648	0.812000	0.45895	-0.432000	0.06956	-0.735000	0.04837	-0.150000	0.13652	CCT	.	.		0.632	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140651774	G	T	140651774	2	4	73	1	0	0	0	0	0	0	0	1	9216	987	35	3		3	MAML3	4	140651774	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	29747176	140651774	50502502	170	9496										
ZNF330	27309	hgsc.bcm.edu	37	chr4	142145639	142145639	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtgatatttttatatgttacAggaatgtgacaagtgtcaga	10	3	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:142145639A>T	ENST00000262990.4	+	3	348		c.e3-1		ZNF330_ENST00000421169.2_Splice_Site	NM_014487.4	NP_055302.1	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330							chromosome, centromeric region (GO:0000775)|midbody (GO:0030496)|nucleolus (GO:0005730)	metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	14	all_hematologic(180;0.162)					TATATGTTACAGGAATGTGAC	0.269																																					.		Atlas-SNP	.											.	ZNF330	31	.	0			c.121-2A>T						.						77	84	82					4																	142145639		2199	4295	6494	SO:0001630	splice_region_variant	27309	exon3			TGTTACAGGAATG	AJ006591	CCDS3754.1	4q31.21	2008-05-15			ENSG00000109445	ENSG00000109445		"Zinc fingers, C2H2-type"	15462	protein-coding gene	gene with protein product		609550				11528117, 10593942	Standard	NM_001292002		Approved	NOA36, HSA6591	uc003iiq.4	Q9Y3S2	OTTHUMG00000133413	ENST00000262990.4:c.121-1A>T	chr4.hg19:g.142145639A>T		349.0	0.0		354.0	156.0	NM_014487	B2RDA3	Splice_Site	SNP	ENST00000262990.4	hg19	CCDS3754.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.453161	0.84209	.	.	ENSG00000109445	ENST00000262990;ENST00000512809;ENST00000503649;ENST00000512738;ENST00000421169	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF330	142365089	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	8.613000	0.90913	2.367000	0.80283	0.528000	0.53228	.	.	.		0.269	ZNF330-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257271.2	NM_014487	Intron	T	142145639	A	T	142145639	5	4	73	1	0	0	0	0	0	0	1	0	17863	202	7	4	125	4	ZNF330	4	142145639	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1493865	142145639	49008637	171	9497										
INPP4B	8821	hgsc.bcm.edu	37	chr4	142949992	142949992	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgtagtacttggggaaagcCatcagctgtagcatgttgaa	12	7	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:142949992C>A	ENST00000513000.1	-	27	3151	c.2718G>T	c.(2716-2718)atG>atT	p.M906I	INPP4B_ENST00000308502.4_Missense_Mutation_p.M906I|INPP4B_ENST00000508116.1_Missense_Mutation_p.M906I|INPP4B_ENST00000262992.4_Missense_Mutation_p.M906I	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	906					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					TGGGGAAAGCCATCAGCTGTA	0.408																																					p.M906I		Atlas-SNP	.											.	INPP4B	132	.	0			c.G2718T						.						167	150	156					4																	142949992		2203	4300	6503	SO:0001583	missense	8821	exon27			GAAAGCCATCAGC	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.2718G>T	chr4.hg19:g.142949992C>A	ENSP00000425487:p.Met906Ile	115.0	0.0		89.0	47.0	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	hg19	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.816722	0.50633	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000508116	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	5.58	5.58	0.84498	.	0.520991	0.21011	N	0.081687	T	0.22704	0.0548	L	0.42686	1.345	0.80722	D	1	P	0.39022	0.655	B	0.38264	0.269	T	0.02070	-1.1219	10	0.22706	T	0.39	.	19.5654	0.95390	0.0:1.0:0.0:0.0	.	906	O15327	INP4B_HUMAN	I	906	ENSP00000425487:M906I;ENSP00000262992:M906I;ENSP00000308441:M906I;ENSP00000423954:M906I	ENSP00000262992:M906I	M	-	3	0	INPP4B	143169442	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.956000	0.70315	2.641000	0.89580	0.585000	0.79938	ATG	.	.		0.408	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		A	142949992	C	A	142949992	3	1	73	1	0	0	0	0	1	0	0	0	7762	594	21	3	60	3	INPP4B	4	142949992	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	804353	142949992	48204284	172	9498										
MAB21L2	10586	hgsc.bcm.edu	37	chr4	151504564	151504564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctatctctcagcgcgtaagaTccgctcgcgtttccagacgc	9	15	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:151504564T>C	ENST00000317605.4	+	1	1488	c.383T>C	c.(382-384)aTc>aCc	p.I128T	LRBA_ENST00000357115.3_Intron|LRBA_ENST00000503716.1_5'Flank|LRBA_ENST00000510413.1_Intron|RP11-1336O20.2_ENST00000507934.1_RNA|LRBA_ENST00000507224.1_Intron|LRBA_ENST00000535741.1_Intron	NM_006439.4	NP_006430.1	Q9Y586	MB212_HUMAN	mab-21-like 2 (C. elegans)	128					camera-type eye development (GO:0043010)|embryonic body morphogenesis (GO:0010172)|eye development (GO:0001654)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	21	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.159)		GCGCGTAAGATCCGCTCGCGT	0.622																																					p.I128T		Atlas-SNP	.											.	MAB21L2	53	.	0			c.T383C						.						104	102	103					4																	151504564		2203	4300	6503	SO:0001583	missense	10586	exon1			GTAAGATCCGCTC	AF155219	CCDS3774.1	4q31.3	2013-10-22	2001-11-28		ENSG00000181541	ENSG00000181541			6758	protein-coding gene	gene with protein product		604357	"mab-21 (C. elegans)-like 2"				Standard	NM_006439		Approved		uc003ilw.3	Q9Y586	OTTHUMG00000161442	ENST00000317605.4:c.383T>C	chr4.hg19:g.151504564T>C	ENSP00000324701:p.Ile128Thr	55.0	0.0		58.0	20.0	NM_006439	B3KP37|Q9HBA7	Missense_Mutation	SNP	ENST00000317605.4	hg19	CCDS3774.1	.	.	.	.	.	.	.	.	.	.	T	19.96	3.923465	0.73213	.	.	ENSG00000181541	ENST00000317605	T	0.10005	2.92	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.31513	0.0799	M	0.80028	2.48	0.80722	D	1	D	0.57257	0.979	P	0.57425	0.82	T	0.08289	-1.0729	10	0.87932	D	0	-17.5434	15.8457	0.78887	0.0:0.0:0.0:1.0	.	128	Q9Y586	MB212_HUMAN	T	128	ENSP00000324701:I128T	ENSP00000324701:I128T	I	+	2	0	MAB21L2	151724014	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.040000	0.89188	2.131000	0.65755	0.459000	0.35465	ATC	.	.		0.622	MAB21L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364937.1	NM_006439		C	151504564	T	C	151504564	3	2	73	1	0	0	0	0	1	0	0	0	9151	1435	50	2	385	2	MAB21L2	4	151504564	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	8554572	151504564	39649712	173	9499										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155156385	155156385	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagataggcaggagagctggTctgagtccctcgggataccc	14	11	1	3	rs147174513		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:155156385T>A	ENST00000357232.4	-	25	8053	c.8054A>T	c.(8053-8055)gAc>gTc	p.D2685V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2685					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GGAGAGCTGGTCTGAGTCCCT	0.547																																					p.D2685V		Atlas-SNP	.											.	DCHS2	594	.	0			c.A8054T						.	T	VAL/ASP	0,4406		0,0,2203	82	74	77		8054	5.5	1	4	dbSNP_134	77	1,8599	1.2+/-3.3	0,1,4299	no	missense	DCHS2	NM_017639.3	152	0,1,6502	AA,AT,TT		0.0116,0.0,0.0077	probably-damaging	2685/2917	155156385	1,13005	2203	4300	6503	SO:0001583	missense	54798	exon25			AGCTGGTCTGAGT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.8054A>T	chr4.hg19:g.155156385T>A	ENSP00000349768:p.Asp2685Val	94.0	0.0		101.0	44.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185197	0.78677	0.0	1.16E-4	ENSG00000197410	ENST00000357232	T	0.62788	0.0	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000001	T	0.76800	0.4038	M	0.80982	2.52	0.80722	D	1	D	0.65815	0.995	P	0.59424	0.857	T	0.77148	-0.2694	10	0.34782	T	0.22	.	15.6877	0.77424	0.0:0.0:0.0:1.0	.	2685	Q6V1P9	PCD23_HUMAN	V	2685	ENSP00000349768:D2685V	ENSP00000349768:D2685V	D	-	2	0	DCHS2	155375835	1.000000	0.71417	0.999000	0.59377	0.956000	0.61745	5.906000	0.69900	2.101000	0.63845	0.377000	0.23210	GAC	.	T|1.000;A|0.000		0.547	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155156385	T	A	155156385	3	1	73	1	0	0	0	0	1	0	0	0	4290	1667	58	4	700	4	DCHS2	4	155156385	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3651821	155156385	35997891	174	9500										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155226268	155226268	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctcgaagggtgaagacttcTtgaatttctctgtcaagtat	9	8	3	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:155226268T>C	ENST00000357232.4	-	16	4010	c.4011A>G	c.(4009-4011)caA>caG	p.Q1337Q		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1337	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TGAAGACTTCTTGAATTTCTC	0.328																																					p.Q1337Q		Atlas-SNP	.											.	DCHS2	594	.	0			c.A4011G						.						44	43	44					4																	155226268		2203	4299	6502	SO:0001819	synonymous_variant	54798	exon16			GACTTCTTGAATT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4011A>G	chr4.hg19:g.155226268T>C		99.0	0.0		95.0	37.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	hg19	CCDS3785.1																																																																																			.	.		0.328	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		C	155226268	T	C	155226268	2	2	73	1	0	0	0	0	0	0	0	1	4290	1606	56	2		2	DCHS2	4	155226268	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	69883	155226268	35928008	175	9501										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183659668	183659668	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	catgggtggctggacattagAtaaacatcacgtgctggatg	13	7	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:183659668A>G	ENST00000511685.1	+	18	3473	c.3350A>G	c.(3349-3351)gAt>gGt	p.D1117G	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.D1117G			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1117					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TGGACATTAGATAAACATCAC	0.448																																					p.D1117G		Atlas-SNP	.											.	.	.	.	0			c.A3350G						.						203	196	198					4																	183659668		1987	4158	6145	SO:0001583	missense	55714	exon17			CATTAGATAAACA	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.3350A>G	chr4.hg19:g.183659668A>G	ENSP00000424226:p.Asp1117Gly	88.0	0.0		86.0	41.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	A	17.53	3.413584	0.62511	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.91351	-2.83;-2.83	5.35	5.35	0.76521	.	.	.	.	.	D	0.91862	0.7424	M	0.86740	2.835	0.51767	D	0.999939	B	0.16603	0.018	B	0.17098	0.017	D	0.90245	0.4289	9	0.87932	D	0	.	15.5001	0.75691	1.0:0.0:0.0:0.0	.	1117	Q9P273	TEN3_HUMAN	G	1117	ENSP00000424226:D1117G;ENSP00000385276:D1117G	ENSP00000385276:D1117G	D	+	2	0	ODZ3	183896662	1.000000	0.71417	0.880000	0.34516	0.364000	0.29643	7.385000	0.79763	2.250000	0.74265	0.533000	0.62120	GAT	.	.		0.448	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			G	183659668	A	G	183659668	3	3	73	1	0	0	0	0	1	0	0	0	10845	333	12	2	3416	2	ODZ3	4	183659668	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	28433400	183659668	7494608	176	9502										
TLR3	7098	hgsc.bcm.edu	37	chr4	186997908	186997908	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cacctgaagttgactcaggtAcccgatgatctacccacaaa	7	13	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr4:186997908A>C	ENST00000296795.3	+	2	239	c.135A>C	c.(133-135)gtA>gtC	p.V45V		NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	45	LRRNT.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		TGACTCAGGTACCCGATGATC	0.493																																					p.V45V		Atlas-SNP	.											.	TLR3	83	.	0			c.A135C						.						121	109	113					4																	186997908		2203	4300	6503	SO:0001819	synonymous_variant	7098	exon2			TCAGGTACCCGAT	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"CD molecules"	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.135A>C	chr4.hg19:g.186997908A>C		136.0	0.0		105.0	41.0	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Silent	SNP	ENST00000296795.3	hg19	CCDS3846.1																																																																																			.	.		0.493	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			C	186997908	A	C	186997908	2	2	73	1	0	0	0	0	0	0	0	1	15967	378	14	5		5	TLR3	4	186997908	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3338240	186997908	4156368	177	9503										
SLC6A3	6531	hgsc.bcm.edu	37	chr5	1409895	1409895	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gacgatgaagagcgtgaagaGctcacggtgtctgtgcagca	15	8	2	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:1409895G>T	ENST00000270349.9	-	10	1466	c.1339C>A	c.(1339-1341)Ctc>Atc	p.L447I	SLC6A3_ENST00000453492.2_Missense_Mutation_p.L447I	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	447					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	AGCGTGAAGAGCTCACGGTGT	0.592																																					p.L447I		Atlas-SNP	.											.	SLC6A3	102	.	0			c.C1339A						.						210	152	172					5																	1409895		2203	4300	6503	SO:0001583	missense	6531	exon10			TGAAGAGCTCACG		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"Solute carriers"	11049	protein-coding gene	gene with protein product	"dopamine transporter"	126455	"solute carrier family 6 (neurotransmitter transporter, dopamine), member 3", "dopamine transporter 1"	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1339C>A	chr5.hg19:g.1409895G>T	ENSP00000270349:p.Leu447Ile	74.0	0.0		51.0	29.0	NM_001044	A2RUN4|Q14996	Missense_Mutation	SNP	ENST00000270349.9	hg19	CCDS3863.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.055077	0.36277	.	.	ENSG00000142319	ENST00000270349;ENST00000453492	T;T	0.74842	-0.88;-0.88	4.19	4.19	0.49359	.	0.071928	0.56097	D	0.000028	T	0.68659	0.3025	L	0.28115	0.83	0.45502	D	0.998466	B	0.31227	0.314	B	0.42163	0.378	T	0.66874	-0.5813	10	0.31617	T	0.26	.	14.0096	0.64488	0.0:0.0:1.0:0.0	.	447	Q01959	SC6A3_HUMAN	I	447	ENSP00000270349:L447I;ENSP00000399806:L447I	ENSP00000270349:L447I	L	-	1	0	SLC6A3	1462895	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.738000	0.62073	1.880000	0.54463	0.478000	0.44815	CTC	.	.		0.592	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		T	1409895	G	T	1409895	3	4	73	1	0	0	0	0	1	0	0	0	14700	971	34	3	547	3	SLC6A3	5	1409895	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10		1409895	179505365	178	9504										
IRX1	79192	hgsc.bcm.edu	37	chr5	3600372	3600372	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccgcagcagccccacgctccCaggtacagctccaggccgcg	11	20	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:3600372C>A	ENST00000302006.3	+	2	1362	c.1310C>A	c.(1309-1311)cCa>cAa	p.P437Q	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	437					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CCCACGCTCCCAGGTACAGCT	0.682																																					p.P437Q		Atlas-SNP	.											.	IRX1	106	.	0			c.C1310A						.						11	13	13					5																	3600372		2200	4295	6495	SO:0001583	missense	79192	exon2			CGCTCCCAGGTAC	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.1310C>A	chr5.hg19:g.3600372C>A	ENSP00000305244:p.Pro437Gln	37.0	0.0		37.0	17.0	NM_024337	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	hg19	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	C	6.098	0.386366	0.11524	.	.	ENSG00000170549	ENST00000302006	T	0.57436	0.4	4.24	4.24	0.50183	.	1.389510	0.04033	N	0.301846	T	0.32496	0.0831	N	0.08118	0	0.34832	D	0.739757	B	0.29432	0.244	B	0.21546	0.035	T	0.26815	-1.0092	10	0.17369	T	0.5	.	8.4347	0.32780	0.0:0.8452:0.0:0.1548	.	437	P78414	IRX1_HUMAN	Q	437	ENSP00000305244:P437Q	ENSP00000305244:P437Q	P	+	2	0	IRX1	3653372	1.000000	0.71417	0.980000	0.43619	0.071000	0.16799	3.096000	0.50243	1.863000	0.54032	0.467000	0.42956	CCA	.	.		0.682	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		A	3600372	C	A	3600372	3	1	73	1	0	0	0	0	1	0	0	0	7852	594	21	3	1316	3	IRX1	5	3600372	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	2190477	3600372	177314888	179	9505										
C5orf22	55322	hgsc.bcm.edu	37	chr5	31534522	31534522	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tttgataaggaaacactcttTgggtaatatgtgattttatt	8	3	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:31534522T>C	ENST00000325366.9	+	2	352	c.225T>C	c.(223-225)ttT>ttC	p.F75F	DROSHA_ENST00000511367.2_5'Flank|C5orf22_ENST00000355907.3_5'UTR|DROSHA_ENST00000504361.1_5'Flank|DROSHA_ENST00000513349.1_5'Flank	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	75										kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						AAACACTCTTTGGGTAATATG	0.353																																					p.F75F		Atlas-SNP	.											.	C5orf22	48	.	0			c.T225C						.						119	112	114					5																	31534522		2203	4300	6503	SO:0001819	synonymous_variant	55322	exon2			ACTCTTTGGGTAA	AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.225T>C	chr5.hg19:g.31534522T>C		111.0	0.0		92.0	23.0	NM_018356	Q8ND28|Q8WU61|Q9NUR1	Silent	SNP	ENST00000325366.9	hg19	CCDS3895.1																																																																																			.	.		0.353	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356		C	31534522	T	C	31534522	2	2	73	1	0	0	0	0	0	0	0	1	2287	1809	63	2		2	C5orf22	5	31534522	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	27934150	31534522	149380738	180	9506										
BRIX1	55299	hgsc.bcm.edu	37	chr5	34922851	34922851	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaactgtttgaaaggttctcGgccccttttgtcttttgacc	8	10	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:34922851G>A	ENST00000336767.5	+	6	851	c.488G>A	c.(487-489)cGg>cAg	p.R163Q	BRIX1_ENST00000506023.1_3'UTR	NM_018321.3	NP_060791.3	Q8TDN6	BRX1_HUMAN	BRX1, biogenesis of ribosomes, homolog (S. cerevisiae)	163	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				ribosome biogenesis (GO:0042254)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|large_intestine(2)|lung(1)	4						AAAGGTTCTCGGCCCCTTTTG	0.348																																					p.R163Q		Atlas-SNP	.											.	BRIX1	21	.	0			c.G488A						.						107	113	111					5																	34922851		2203	4300	6503	SO:0001583	missense	55299	exon6			GTTCTCGGCCCCT		CCDS34143.1	5p13.2	2009-09-25	2009-09-25	2009-09-25	ENSG00000113460	ENSG00000113460			24170	protein-coding gene	gene with protein product			"brix domain containing 2"	BXDC2		12477932	Standard	NM_018321		Approved	BRIX, FLJ11100	uc003jja.3	Q8TDN6	OTTHUMG00000162021	ENST00000336767.5:c.488G>A	chr5.hg19:g.34922851G>A	ENSP00000338862:p.Arg163Gln	419.0	0.0		381.0	136.0	NM_018321	A8K0P5|Q3ZTT4|Q8N453|Q96DH1	Missense_Mutation	SNP	ENST00000336767.5	hg19	CCDS34143.1	.	.	.	.	.	.	.	.	.	.	G	36	5.846422	0.97016	.	.	ENSG00000113460	ENST00000336767	T	0.23754	1.89	6.16	6.16	0.99307	Brix domain (3);Anticodon-binding (1);	0.000000	0.85682	D	0.000000	T	0.67107	0.2858	H	0.95043	3.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.985	T	0.75175	-0.3410	10	0.72032	D	0.01	-3.4443	20.8598	0.99761	0.0:0.0:1.0:0.0	.	163;163	B4E0B8;Q8TDN6	.;BRX1_HUMAN	Q	163	ENSP00000338862:R163Q	ENSP00000338862:R163Q	R	+	2	0	BRIX1	34958608	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.291000	0.96070	2.937000	0.99478	0.650000	0.86243	CGG	.	.		0.348	BRIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366826.2	NM_018321		A	34922851	G	A	34922851	3	1	73	1	0	0	0	0	1	0	0	0	1517	1116	39	1	510	1	BRIX1	5	34922851	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3388329	34922851	145992409	181	9507										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37206332	37206332	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tatcacgtttacagaacagcTggaaagccacaccaattgaa	7	10	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:37206332T>A	ENST00000508244.1	-	16	3209	c.3116A>T	c.(3115-3117)cAg>cTg	p.Q1039L	C5orf42_ENST00000425232.2_Missense_Mutation_p.Q1039L|C5orf42_ENST00000274258.7_5'UTR			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1039						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			ACAGAACAGCTGGAAAGCCAC	0.363																																					p.Q1039L		Atlas-SNP	.											.	C5orf42	422	.	0			c.A3116T						.						117	99	104					5																	37206332		692	1591	2283	SO:0001583	missense	65250	exon17			AACAGCTGGAAAG		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.3116A>T	chr5.hg19:g.37206332T>A	ENSP00000421690:p.Gln1039Leu	343.0	0.0		306.0	30.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	T	12.63	1.996710	0.35226	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000514429	T;T;T	0.23754	1.9;1.9;1.89	4.96	3.81	0.43845	.	0.377537	0.20789	U	0.085641	T	0.21427	0.0516	L	0.50919	1.6	0.21822	N	0.999521	P	0.51933	0.949	B	0.43301	0.415	T	0.08889	-1.0700	10	0.16896	T	0.51	-0.6645	7.6902	0.28563	0.0:0.0748:0.1402:0.7851	.	1039	E9PH94	.	L	1039;1039;87	ENSP00000421690:Q1039L;ENSP00000389014:Q1039L;ENSP00000424223:Q87L	ENSP00000389014:Q1039L	Q	-	2	0	C5orf42	37242089	0.795000	0.28851	0.244000	0.24202	0.625000	0.37756	1.122000	0.31295	0.844000	0.35094	0.383000	0.25322	CAG	.	.		0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37206332	T	A	37206332	3	1	73	1	0	0	0	0	1	0	0	0	2303	1580	55	4	6621	4	C5orf42	5	37206332	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2283481	37206332	143708928	182	9508										
WDR70	55100	hgsc.bcm.edu	37	chr5	37721261	37721261	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccaaagctgaaccagatcatGgttggaactggaaatggatt	11	7	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:37721261G>A	ENST00000265107.4	+	14	1617	c.1461G>A	c.(1459-1461)atG>atA	p.M487I		NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	487							enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACCAGATCATGGTTGGAACTG	0.428																																					p.M487I		Atlas-SNP	.											.	WDR70	76	.	0			c.G1461A						.						153	146	149					5																	37721261		2203	4300	6503	SO:0001583	missense	55100	exon14			GATCATGGTTGGA	BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068		"WD repeat domain containing"	25495	protein-coding gene	gene with protein product						12477932	Standard	NM_018034		Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000265107.4:c.1461G>A	chr5.hg19:g.37721261G>A	ENSP00000265107:p.Met487Ile	176.0	0.0		153.0	63.0	NM_018034	Q9H053	Missense_Mutation	SNP	ENST00000265107.4	hg19	CCDS34147.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.533685	0.64972	.	.	ENSG00000082068	ENST00000265107	T	0.01197	5.19	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.01029	0.0034	N	0.10809	0.05	0.80722	D	1	B	0.14012	0.009	B	0.12837	0.008	T	0.58691	-0.7592	10	0.06236	T	0.91	-11.8932	20.8794	0.99867	0.0:0.0:1.0:0.0	.	487	Q9NW82	WDR70_HUMAN	I	487	ENSP00000265107:M487I	ENSP00000265107:M487I	M	+	3	0	WDR70	37757018	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.444000	0.97578	2.941000	0.99782	0.655000	0.94253	ATG	.	.		0.428	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034		A	37721261	G	A	37721261	3	1	73	1	0	0	0	0	1	0	0	0	17336	1348	47	3	1515	3	WDR70	5	37721261	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	514929	37721261	143193999	183	9509										
DEPDC1B	55789	hgsc.bcm.edu	37	chr5	59899225	59899225	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcctctcctttacctggactCttcgtagatgagccacacgc	7	15	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:59899225C>A	ENST00000265036.5	-	9	1302	c.1235G>T	c.(1234-1236)aGa>aTa	p.R412I	DEPDC1B_ENST00000453022.2_Missense_Mutation_p.R412I|DEPDC1B_ENST00000545085.1_Missense_Mutation_p.R385I|DEPDC1B_ENST00000509006.1_5'Flank	NM_018369.2	NP_060839.2	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B	412					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(2)|skin(2)	17		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				TACCTGGACTCTTCGTAGATG	0.418																																					p.R412I		Atlas-SNP	.											.	DEPDC1B	56	.	0			c.G1235T						.						68	68	68					5																	59899225		2203	4300	6503	SO:0001583	missense	55789	exon9			TGGACTCTTCGTA	AF303178	CCDS3977.1, CCDS47214.1	5q12	2008-02-05			ENSG00000035499	ENSG00000035499			24902	protein-coding gene	gene with protein product	"breast cancer cell 3"					12477932	Standard	NM_001145208		Approved	XTP1, BRCC3	uc003jsh.3	Q8WUY9	OTTHUMG00000097083	ENST00000265036.5:c.1235G>T	chr5.hg19:g.59899225C>A	ENSP00000265036:p.Arg412Ile	81.0	0.0		69.0	22.0	NM_001145208	A8K3R9|B4DUT4|Q86WJ3|Q8IZY6|Q9NUN3|Q9NW57	Missense_Mutation	SNP	ENST00000265036.5	hg19	CCDS3977.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946313	0.73672	.	.	ENSG00000035499	ENST00000265036;ENST00000453022;ENST00000545085	T;T;T	0.31510	1.49;1.49;1.49	5.03	5.03	0.67393	.	0.061085	0.85682	D	0.000000	T	0.42517	0.1206	M	0.63843	1.955	0.80722	D	1	P;P	0.42908	0.673;0.793	P;B	0.47251	0.542;0.439	T	0.19063	-1.0317	9	.	.	.	-21.5609	18.5461	0.91047	0.0:1.0:0.0:0.0	.	412;412	B4DUT4;Q8WUY9	.;DEP1B_HUMAN	I	412;412;385	ENSP00000265036:R412I;ENSP00000389101:R412I;ENSP00000438320:R385I	.	R	-	2	0	DEPDC1B	59934982	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.307000	0.59123	2.612000	0.88384	0.591000	0.81541	AGA	.	.		0.418	DEPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214207.1	NM_018369		A	59899225	C	A	59899225	3	1	73	1	0	0	0	0	1	0	0	0	4442	913	32	3	366	3	DEPDC1B	5	59899225	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	22177964	59899225	121016035	184	9510										
CARTPT	9607	hgsc.bcm.edu	37	chr5	71016426	71016426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aacctcctgcaattccttccTcctgaagtgcttatgaaggg	8	12	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:71016426T>C	ENST00000296777.4	+	3	466	c.335T>C	c.(334-336)cTc>cCc	p.L112P	CARTPT_ENST00000513096.1_3'UTR	NM_004291.3	NP_004282.1	Q16568	CART_HUMAN	CART prepropeptide	112					activation of MAPKK activity (GO:0000186)|adult feeding behavior (GO:0008343)|cell-cell signaling (GO:0007267)|cellular glucose homeostasis (GO:0001678)|cellular response to starvation (GO:0009267)|circadian regulation of gene expression (GO:0032922)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of appetite (GO:0032099)|negative regulation of bone resorption (GO:0045779)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of osteoclast differentiation (GO:0045671)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of epinephrine secretion (GO:0032812)|positive regulation of transmission of nerve impulse (GO:0051971)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|somatostatin secretion (GO:0070253)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|secretory granule (GO:0030141)				large_intestine(1)|lung(2)|ovary(1)	4		Lung NSC(167;0.00153)|Ovarian(174;0.0175)|Prostate(74;0.11)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;8.4e-56)	Amphetamine(DB00182)	AATTCCTTCCTCCTGAAGTGC	0.552																																					p.L112P		Atlas-SNP	.											.	CARTPT	10	.	0			c.T335C						.						148	116	127					5																	71016426		2203	4300	6503	SO:0001583	missense	9607	exon3			CCTTCCTCCTGAA	U16826	CCDS4011.1	5q13.2	2008-02-05			ENSG00000164326	ENSG00000164326			24323	protein-coding gene	gene with protein product	"cocaine and amphetamine regulated transcript"	602606				9590691, 8647455	Standard	NM_004291		Approved	CART	uc003kbv.2	Q16568	OTTHUMG00000131261	ENST00000296777.4:c.335T>C	chr5.hg19:g.71016426T>C	ENSP00000296777:p.Leu112Pro	114.0	0.0		88.0	42.0	NM_004291	Q6FG92	Missense_Mutation	SNP	ENST00000296777.4	hg19	CCDS4011.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185078	0.78677	.	.	ENSG00000164326	ENST00000296777	T	0.64085	-0.08	5.61	5.61	0.85477	.	0.152170	0.43579	D	0.000543	T	0.74092	0.3671	L	0.49126	1.545	0.80722	D	1	D	0.76494	0.999	D	0.72338	0.977	T	0.76753	-0.2843	10	0.87932	D	0	.	14.7866	0.69808	0.0:0.0:0.0:1.0	.	112	Q16568	CART_HUMAN	P	112	ENSP00000296777:L112P	ENSP00000296777:L112P	L	+	2	0	CARTPT	71052182	1.000000	0.71417	0.986000	0.45419	0.905000	0.53344	7.338000	0.79269	2.130000	0.65690	0.533000	0.62120	CTC	.	.		0.552	CARTPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254029.2	NM_004291		C	71016426	T	C	71016426	3	2	73	1	0	0	0	0	1	0	0	0	2661	1551	54	2	345	2	CARTPT	5	71016426	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	11117201	71016426	109898834	185	9511										
MRPS27	23107	hgsc.bcm.edu	37	chr5	71519592	71519592	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccaccagtttttctgaccccTggttgtcttcatcattttgg	7	12	4	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:71519592T>A	ENST00000261413.5	-	10	962	c.923A>T	c.(922-924)cAg>cTg	p.Q308L	MRPS27_ENST00000522562.1_5'Flank|MRPS27_ENST00000457646.4_Missense_Mutation_p.Q252L|MRPS27_ENST00000513900.1_Missense_Mutation_p.Q322L	NM_015084.2	NP_055899.2	Q92552	RT27_HUMAN	mitochondrial ribosomal protein S27	308						mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)		TTCTGACCCCTGGTTGTCTTC	0.502																																					p.Q308L		Atlas-SNP	.											.	MRPS27	23	.	0			c.A923T						.						153	145	148					5																	71519592		2203	4300	6503	SO:0001583	missense	23107	exon10			GACCCCTGGTTGT	D87453	CCDS4013.1, CCDS68890.1, CCDS75257.1	5q13.2	2012-09-13			ENSG00000113048	ENSG00000113048		"Mitochondrial ribosomal proteins / small subunits"	14512	protein-coding gene	gene with protein product		611989					Standard	NM_015084		Approved	KIAA0264	uc003kbz.4	Q92552	OTTHUMG00000100951	ENST00000261413.5:c.923A>T	chr5.hg19:g.71519592T>A	ENSP00000261413:p.Gln308Leu	121.0	0.0		97.0	48.0	NM_015084	B4DRT2|Q6P1S1	Missense_Mutation	SNP	ENST00000261413.5	hg19	CCDS4013.1	.	.	.	.	.	.	.	.	.	.	T	3.013	-0.203487	0.06180	.	.	ENSG00000113048	ENST00000261413;ENST00000457646;ENST00000513900;ENST00000508863	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	6.16	2.26	0.28386	.	0.516315	0.22348	N	0.061242	T	0.21962	0.0529	N	0.15975	0.35	0.27422	N	0.954276	B;B;B	0.15141	0.002;0.012;0.001	B;B;B	0.14578	0.002;0.011;0.007	T	0.16482	-1.0401	10	0.24483	T	0.36	-26.4815	7.0325	0.24975	0.2859:0.0:0.1263:0.5879	.	322;89;308	B4DRT2;E7ETN4;Q92552	.;.;RT27_HUMAN	L	308;252;322;252	ENSP00000261413:Q308L;ENSP00000428120:Q252L;ENSP00000426941:Q322L;ENSP00000426176:Q252L	ENSP00000261413:Q308L	Q	-	2	0	MRPS27	71555348	0.001000	0.12720	0.023000	0.16930	0.055000	0.15305	-0.226000	0.09139	0.137000	0.18759	0.528000	0.53228	CAG	.	.		0.502	MRPS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218560.2	NM_015084		A	71519592	T	A	71519592	3	1	73	1	0	0	0	0	1	0	0	0	9847	1580	55	4	329	4	MRPS27	5	71519592	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	503166	71519592	109395668	186	9512										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72188978	72188978	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cttcctagtgcctatcttcaGttgccacagcactgcagtct	7	14	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:72188978G>T	ENST00000337273.5	+	16	2227	c.1801G>T	c.(1801-1803)Gtt>Ttt	p.V601F	TNPO1_ENST00000523768.1_Missense_Mutation_p.V551F|TNPO1_ENST00000506351.2_Missense_Mutation_p.V593F|TNPO1_ENST00000454282.1_Missense_Mutation_p.V551F	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	601					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		CCTATCTTCAGTTGCCACAGC	0.433																																					p.V601F		Atlas-SNP	.											.	TNPO1	90	.	0			c.G1801T						.						173	160	164					5																	72188978		2203	4300	6503	SO:0001583	missense	3842	exon16			TCTTCAGTTGCCA	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.1801G>T	chr5.hg19:g.72188978G>T	ENSP00000336712:p.Val601Phe	80.0	0.0		104.0	45.0	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.866800	0.91511	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351;ENST00000519220	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.62	5.62	0.85841	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.86112	0.5855	M	0.92880	3.355	0.80722	D	1	D;D	0.54207	0.965;0.962	D;P	0.64237	0.923;0.841	D	0.88570	0.3129	10	0.87932	D	0	-25.0757	20.0205	0.97499	0.0:0.0:1.0:0.0	.	551;601	Q92973-3;Q92973	.;TNPO1_HUMAN	F	601;551;551;593;112	ENSP00000336712:V601F;ENSP00000398524:V551F;ENSP00000428899:V551F;ENSP00000425118:V593F	ENSP00000336712:V601F	V	+	1	0	TNPO1	72224734	1.000000	0.71417	0.999000	0.59377	0.894000	0.52154	9.439000	0.97543	2.801000	0.96364	0.650000	0.86243	GTT	.	.		0.433	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		T	72188978	G	T	72188978	3	4	73	1	0	0	0	0	1	0	0	0	16350	1029	36	3	1863	3	TNPO1	5	72188978	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	669386	72188978	108726282	187	9513										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72201205	72201205	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	accagtttcctcttcccttaAaagagcgtcttgcagctttt	6	12	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:72201205A>G	ENST00000337273.5	+	24	3091	c.2665A>G	c.(2665-2667)Aaa>Gaa	p.K889E	TNPO1_ENST00000523768.1_Missense_Mutation_p.K839E|TNPO1_ENST00000506351.2_Missense_Mutation_p.K881E|TNPO1_ENST00000454282.1_Missense_Mutation_p.K839E	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	889					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		TCTTCCCTTAAAAGAGCGTCT	0.358																																					p.K889E		Atlas-SNP	.											.	TNPO1	90	.	0			c.A2665G						.						103	109	107					5																	72201205		2203	4300	6503	SO:0001583	missense	3842	exon24			CCCTTAAAAGAGC	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.2665A>G	chr5.hg19:g.72201205A>G	ENSP00000336712:p.Lys889Glu	77.0	0.0		75.0	26.0	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	A	18.84	3.709181	0.68615	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.52	5.52	0.82312	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.38401	0.1039	M	0.79475	2.455	0.80722	D	1	P;P	0.36048	0.534;0.465	B;B	0.35550	0.205;0.059	T	0.33317	-0.9873	10	0.46703	T	0.11	-18.8819	15.7014	0.77544	1.0:0.0:0.0:0.0	.	839;889	Q92973-3;Q92973	.;TNPO1_HUMAN	E	889;839;839;881	ENSP00000336712:K889E;ENSP00000398524:K839E;ENSP00000428899:K839E;ENSP00000425118:K881E	ENSP00000336712:K889E	K	+	1	0	TNPO1	72236961	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.958000	0.93099	2.127000	0.65507	0.524000	0.50904	AAA	.	.		0.358	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		G	72201205	A	G	72201205	3	3	73	1	0	0	0	0	1	0	0	0	16350	15	1	2	2759	2	TNPO1	5	72201205	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	12227	72201205	108714055	188	9514										
BTF3	689	hgsc.bcm.edu	37	chr5	72798773	72798773	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acaaaccaaggaacagtgatCcactttaacaaccctaaagt	5	11	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:72798773C>A	ENST00000335895.8	+	4	367	c.216C>A	c.(214-216)atC>atA	p.I72I	BTF3_ENST00000380591.3_Silent_p.I116I|BTF3_ENST00000514505.2_3'UTR	NM_001207.4	NP_001198.2	O00478	BT3A3_HUMAN	basic transcription factor 3	0	Ig-like V-type 1.				T cell mediated immunity (GO:0002456)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(2)	5		Lung NSC(167;0.00405)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;2.73e-54)		GAACAGTGATCCACTTTAACA	0.373																																					p.I116I		Atlas-SNP	.											.	BTF3	10	.	0			c.C348A						.						58	62	61					5																	72798773		2203	4300	6503	SO:0001819	synonymous_variant	689	exon4			AGTGATCCACTTT	M90352	CCDS4019.1, CCDS34185.1	5q13.3	2010-06-17			ENSG00000145741	ENSG00000145741			1125	protein-coding gene	gene with protein product		602542	"nascent-polypeptide-associated complex beta polypeptide"	NACB		2320128, 1386332, 15716105	Standard	NM_001207		Approved	BTF3a, BTF3b	uc003kcr.1	P20290	OTTHUMG00000102031	ENST00000335895.8:c.216C>A	chr5.hg19:g.72798773C>A		42.0	0.0		36.0	15.0	NM_001037637	B4DWI7|E9PCP5	Silent	SNP	ENST00000335895.8	hg19	CCDS4019.1																																																																																			.	.		0.373	BTF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219815.2	NM_001207		A	72798773	C	A	72798773	2	1	73	1	0	0	0	0	0	0	0	1	1553	845	30	3		3	BTF3	5	72798773	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	597568	72798773	108116487	189	9515										
UTP15	84135	hgsc.bcm.edu	37	chr5	72868323	72868323	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctttttataggaggtcgttAtgttaaagtctgggacatgt	11	4	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:72868323A>G	ENST00000296792.4	+	7	938	c.683A>G	c.(682-684)tAt>tGt	p.Y228C	UTP15_ENST00000508491.1_Missense_Mutation_p.Y209C|UTP15_ENST00000543251.1_Missense_Mutation_p.Y38C	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	228			Y -> H (in dbSNP:rs16870608).		rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		GGAGGTCGTTATGTTAAAGTC	0.373																																					p.Y228C		Atlas-SNP	.											.	UTP15	30	.	0			c.A683G						.						189	194	192					5																	72868323		2203	4300	6503	SO:0001583	missense	84135	exon7			GTCGTTATGTTAA	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"WD repeat domain containing"	25758	protein-coding gene	gene with protein product			"UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.683A>G	chr5.hg19:g.72868323A>G	ENSP00000296792:p.Tyr228Cys	173.0	0.0		143.0	56.0	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Missense_Mutation	SNP	ENST00000296792.4	hg19	CCDS34186.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.01|18.01	3.528096|3.528096	0.64860|0.64860	.|.	.|.	ENSG00000164338|ENSG00000164338	ENST00000509005|ENST00000296792;ENST00000543251;ENST00000508491	.|T;T;T	.|0.59906	.|2.24;0.23;0.23	5.79|5.79	4.6|4.6	0.57074|0.57074	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.108667	.|0.64402	.|D	.|0.000004	T|T	0.67297|0.67297	0.2878|0.2878	L|L	0.47016|0.47016	1.485|1.485	0.58432|0.58432	D|D	0.999991|0.999991	.|B;D	.|0.76494	.|0.29;0.999	.|B;D	.|0.68943	.|0.261;0.961	T|T	0.66744|0.66744	-0.5846|-0.5846	5|10	.|0.49607	.|T	.|0.09	.|.	12.1613|12.1613	0.54105|0.54105	0.8717:0.0:0.0:0.1283|0.8717:0.0:0.0:0.1283	.|.	.|209;228	.|B4DXK8;Q8TED0	.|.;UTP15_HUMAN	V|C	255|228;38;209	.|ENSP00000296792:Y228C;ENSP00000440796:Y38C;ENSP00000424609:Y209C	.|ENSP00000296792:Y228C	M|Y	+|+	1|2	0|0	UTP15|UTP15	72904079|72904079	1.000000|1.000000	0.71417|0.71417	0.909000|0.909000	0.35828|0.35828	0.993000|0.993000	0.82548|0.82548	8.957000|8.957000	0.93082|0.93082	0.961000|0.961000	0.38030|0.38030	0.533000|0.533000	0.62120|0.62120	ATG|TAT	.	.		0.373	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175		G	72868323	A	G	72868323	3	3	73	1	0	0	0	0	1	0	0	0	17112	449	16	2	705	2	UTP15	5	72868323	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	69550	72868323	108046937	190	9516										
ANKRD32	84250	hgsc.bcm.edu	37	chr5	93989111	93989111	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agtaccttaagaaggcacatAtataatagagatcaggtaaa	8	5	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:93989111A>T	ENST00000265140.5	+	8	1436	c.1017A>T	c.(1015-1017)atA>atT	p.I339I		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	339						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		GAAGGCACATATATAATAGAG	0.308																																					p.I339I		Atlas-SNP	.											.	ANKRD32	117	.	0			c.A1017T						.						123	107	112					5																	93989111		692	1589	2281	SO:0001819	synonymous_variant	84250	exon8			GCACATATATAAT	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"Ankyrin repeat domain containing"	25408	protein-coding gene	gene with protein product			"BRCT domain containing 1"	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.1017A>T	chr5.hg19:g.93989111A>T		488.0	0.0		449.0	201.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Silent	SNP	ENST00000265140.5	hg19	CCDS4071.2																																																																																			.	.		0.308	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290		T	93989111	A	T	93989111	2	4	73	1	0	0	0	0	0	0	0	1	660	439	16	4		4	ANKRD32	5	93989111	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	21120788	93989111	86926149	191	9517										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128863439	128863439	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttttatttttatttgtttttAggtatttaaccttttccaac	3	5	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:128863439A>T	ENST00000274487.4	+	5	1213		c.e5-1		CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19							proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		ATTTGTTTTTAGGTATTTAAC	0.328																																					.		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.1069-2A>T						.						51	54	53					5																	128863439		2202	4299	6501	SO:0001630	splice_region_variant	171019	exon5			GTTTTTAGGTATT	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1069-1A>T	chr5.hg19:g.128863439A>T		315.0	1.0		247.0	104.0	NM_133638		Splice_Site	SNP	ENST00000274487.4	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.954233	0.53293	.	.	ENSG00000145808	ENST00000274487	.	.	.	4.41	4.41	0.53225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8637	0.46842	0.9217:0.0:0.0783:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADAMTS19	128891338	1.000000	0.71417	0.998000	0.56505	0.833000	0.47200	4.950000	0.63603	2.209000	0.71365	0.460000	0.39030	.	.	.		0.328	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	Intron	T	128863439	A	T	128863439	5	4	73	1	0	0	0	0	0	0	1	0	264	434	15	4	1085	4	ADAMTS19	5	128863439	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	34874328	128863439	52051821	192	9518										
FAM13B	51306	hgsc.bcm.edu	37	chr5	137284750	137284750	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttttctccttctgaatgaccTtgggttcatcttcattctct	5	11	6	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:137284750T>C	ENST00000033079.3	-	17	2439	c.1988A>G	c.(1987-1989)aAg>aGg	p.K663R	FAM13B_ENST00000425075.2_Missense_Mutation_p.K567R|FAM13B_ENST00000420893.2_Missense_Mutation_p.K663R	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	663					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						CTGAATGACCTTGGGTTCATC	0.393																																					p.K663R		Atlas-SNP	.											.	FAM13B	46	.	0			c.A1988G						.						178	169	172					5																	137284750		2203	4300	6503	SO:0001583	missense	51306	exon17			ATGACCTTGGGTT	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.1988A>G	chr5.hg19:g.137284750T>C	ENSP00000033079:p.Lys663Arg	63.0	0.0		77.0	35.0	NM_001101800	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	hg19	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.122786	0.00346	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.21932	3.05;1.98;3.09	5.06	3.21	0.36854	.	0.563214	0.18856	N	0.129261	T	0.05410	0.0143	N	0.00621	-1.32	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.39522	-0.9610	10	0.11182	T	0.66	-2.5308	8.8104	0.34963	0.0:0.7637:0.0:0.2363	.	567;663;663	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	R	663;567;663	ENSP00000033079:K663R;ENSP00000394669:K567R;ENSP00000388521:K663R	ENSP00000033079:K663R	K	-	2	0	FAM13B	137312649	0.007000	0.16637	0.167000	0.22817	0.007000	0.05969	0.283000	0.18846	0.639000	0.30564	-0.182000	0.12963	AAG	.	.		0.393	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			C	137284750	T	C	137284750	3	2	73	1	0	0	0	0	1	0	0	0	5458	1609	56	2	787	2	FAM13B	5	137284750	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	8421311	137284750	43630510	193	9519										
PCDHAC1	56135	hgsc.bcm.edu	37	chr5	140308412	140308412	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgggaccatggagacccaccActttcctcctctgtcactct	7	17	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:140308412A>G	ENST00000253807.2	+	1	1935	c.1935A>G	c.(1933-1935)ccA>ccG	p.P645P	PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHAC1_ENST00000409700.3_Silent_p.P645P|PCDHA13_ENST00000289272.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	645	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGACCCACCACTTTCCTCCT	0.532																																					p.P645P		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.A1935G						.						99	95	97					5																	140308412		2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			CCCACCACTTTCC	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"Cadherins / Protocadherins : Clustered"	8676	other	complex locus constituent	"PCDH-ALPHA-C1"	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1935A>G	chr5.hg19:g.140308412A>G		74.0	0.0		74.0	23.0	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	hg19	CCDS4241.1																																																																																			.	.		0.532	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		G	140308412	A	G	140308412	2	3	73	1	0	0	0	0	0	0	0	1	11541	146	6	2		2	PCDHAC1	5	140308412	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3023662	140308412	40606848	194	9520										
PCDHB6	56130	hgsc.bcm.edu	37	chr5	140531986	140531986	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cggctgtgcaggaggagcagGgcggcctcggtgggtcgcta	20	10	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:140531986G>T	ENST00000231136.1	+	1	2148	c.2148G>T	c.(2146-2148)agG>agT	p.R716S	PCDHB6_ENST00000543635.1_Missense_Mutation_p.R580S	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	716					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGAGGAGCAGGGCGGCCTCGG	0.652																																					p.R716S		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G2148T						.						77	91	86					5																	140531986		2202	4300	6502	SO:0001583	missense	56130	exon1			GAGCAGGGCGGCC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.2148G>T	chr5.hg19:g.140531986G>T	ENSP00000231136:p.Arg716Ser	57.0	0.0		45.0	22.0	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	hg19	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.301964	0.40694	.	.	ENSG00000113211	ENST00000543635;ENST00000231136	T;T	0.11495	2.77;2.77	4.45	0.241	0.15494	.	.	.	.	.	T	0.10337	0.0253	L	0.56340	1.77	0.09310	N	1	B	0.15141	0.012	B	0.18871	0.023	T	0.33111	-0.9881	9	0.72032	D	0.01	.	4.1725	0.10336	0.477:0.1746:0.3484:0.0	.	716	Q9Y5E3	PCDB6_HUMAN	S	580;716	ENSP00000438466:R580S;ENSP00000231136:R716S	ENSP00000231136:R716S	R	+	3	2	PCDHB6	140512170	0.054000	0.20591	0.001000	0.08648	0.209000	0.24338	1.689000	0.37700	0.046000	0.15833	0.556000	0.70494	AGG	.	.		0.652	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		T	140531986	G	T	140531986	3	4	73	1	0	0	0	0	1	0	0	0	11555	1223	43	3	2150	3	PCDHB6	5	140531986	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	223574	140531986	40383274	195	9521										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140572771	140572771	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcttaaccctcacagcgctgGatggtgggtctccatccagg	12	13	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:140572771G>T	ENST00000239446.4	+	1	830	c.646G>T	c.(646-648)Gat>Tat	p.D216Y		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	216	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CACAGCGCTGGATGGTGGGTC	0.542																																					p.D216Y		Atlas-SNP	.											.	PCDHB10	177	.	0			c.G646T						.						89	97	95					5																	140572771		2203	4300	6503	SO:0001583	missense	56126	exon1			GCGCTGGATGGTG	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.646G>T	chr5.hg19:g.140572771G>T	ENSP00000239446:p.Asp216Tyr	147.0	0.0		133.0	51.0	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	hg19	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509299	0.64522	.	.	ENSG00000120324	ENST00000239446	T	0.68903	-0.36	3.41	3.41	0.39046	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.89983	0.6873	H	0.99834	4.825	0.50813	D	0.99989	D	0.89917	1.0	D	0.97110	1.0	D	0.94526	0.7731	9	0.87932	D	0	.	15.0394	0.71777	0.0:0.0:1.0:0.0	.	216	Q9UN67	PCDBA_HUMAN	Y	216	ENSP00000239446:D216Y	ENSP00000239446:D216Y	D	+	1	0	PCDHB10	140552955	1.000000	0.71417	0.999000	0.59377	0.785000	0.44390	9.466000	0.97665	1.930000	0.55929	0.556000	0.70494	GAT	.	.		0.542	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		T	140572771	G	T	140572771	3	4	73	1	0	0	0	0	1	0	0	0	11544	1174	41	3	648	3	PCDHB10	5	140572771	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	40785	140572771	40342489	196	9522										
GRXCR2	643226	hgsc.bcm.edu	37	chr5	145239349	145239349	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	attctcattgcaggcagggcAcctcagggcccgataggact	12	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:145239349A>T	ENST00000377976.1	-	3	693	c.694T>A	c.(694-696)Tgc>Agc	p.C232S		NM_001080516.1	NP_001073985.1	A6NFK2	GRCR2_HUMAN	glutaredoxin, cysteine rich 2	232						cell projection (GO:0042995)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						CAGGCAGGGCACCTCAGGGCC	0.547																																					p.C232S		Atlas-SNP	.											.	GRXCR2	32	.	0			c.T694A						.						78	78	78					5																	145239349		2203	4300	6503	SO:0001583	missense	643226	exon3			CAGGGCACCTCAG		CCDS34263.1	5q32	2014-03-14			ENSG00000204928	ENSG00000204928			33862	protein-coding gene	gene with protein product		615762				24619944	Standard	NM_001080516		Approved	DFNB101	uc003lns.1	A6NFK2	OTTHUMG00000163417	ENST00000377976.1:c.694T>A	chr5.hg19:g.145239349A>T	ENSP00000367214:p.Cys232Ser	258.0	0.0		213.0	11.0	NM_001080516		Missense_Mutation	SNP	ENST00000377976.1	hg19	CCDS34263.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.779480	0.90195	.	.	ENSG00000204928	ENST00000377976	T	0.18338	2.22	5.84	5.84	0.93424	.	0.088546	0.85682	D	0.000000	T	0.52008	0.1708	M	0.91354	3.2	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.63301	-0.6668	10	0.87932	D	0	-44.7267	16.2045	0.82114	1.0:0.0:0.0:0.0	.	232	A6NFK2	GRCR2_HUMAN	S	232	ENSP00000367214:C232S	ENSP00000367214:C232S	C	-	1	0	GRXCR2	145219542	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.764000	0.91719	2.234000	0.73211	0.459000	0.35465	TGC	.	.		0.547	GRXCR2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373289.2			T	145239349	A	T	145239349	3	4	73	1	0	0	0	0	1	0	0	0	6822	159	6	4	56	4	GRXCR2	5	145239349	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4666578	145239349	35675911	197	9523										
FAT2	2196	hgsc.bcm.edu	37	chr5	150930189	150930189	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgggagggccccgagccgaGgtccaattttcccaccgtta	12	14	0	0	rs556459301		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:150930189G>A	ENST00000261800.5	-	7	4552	c.4540C>T	c.(4540-4542)Ctc>Ttc	p.L1514F		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1514	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L1514F(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCGAGCCGAGGTCCAATTTT	0.532													G|||	1	0.000199681	0	0	5008	,	,		21382	0		0	False		,,,				2504	0.001				p.L1514F		Atlas-SNP	.											FAT2,colon,carcinoma,0,1	FAT2	465	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4540T						.						94	87	89					5																	150930189		2203	4300	6503	SO:0001583	missense	2196	exon7			AGCCGAGGTCCAA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.4540C>T	chr5.hg19:g.150930189G>A	ENSP00000261800:p.Leu1514Phe	79.0	0.0		68.0	29.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	0.597	-0.830506	0.02734	.	.	ENSG00000086570	ENST00000261800	T	0.51071	0.72	5.23	3.26	0.37387	Cadherin (4);Cadherin-like (1);	0.362916	0.20546	N	0.090206	T	0.29914	0.0748	L	0.29908	0.895	0.29506	N	0.854592	B	0.22080	0.064	B	0.22880	0.042	T	0.11155	-1.0599	10	0.13470	T	0.59	.	7.5438	0.27755	0.1373:0.0:0.6924:0.1703	.	1514	Q9NYQ8	FAT2_HUMAN	F	1514	ENSP00000261800:L1514F	ENSP00000261800:L1514F	L	-	1	0	FAT2	150910382	1.000000	0.71417	0.980000	0.43619	0.021000	0.10359	3.138000	0.50570	2.425000	0.82216	0.650000	0.86243	CTC	.	.		0.532	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150930189	G	A	150930189	3	1	73	1	0	0	0	0	1	0	0	0	5698	1000	35	3	8577	3	FAT2	5	150930189	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	5690840	150930189	29985071	198	9524										
GEMIN5	25929	hgsc.bcm.edu	37	chr5	154311783	154311783	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctcctttcttactgatgtcAattatcaccactatgccatc	3	13	4	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:154311783A>G	ENST00000285873.7	-	4	612	c.537T>C	c.(535-537)atT>atC	p.I179I		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	179					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TACTGATGTCAATTATCACCA	0.378																																					p.I179I		Atlas-SNP	.											.	GEMIN5	120	.	0			c.T537C						.						135	136	136					5																	154311783		2203	4300	6503	SO:0001819	synonymous_variant	25929	exon4			GATGTCAATTATC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.537T>C	chr5.hg19:g.154311783A>G		155.0	0.0		158.0	70.0	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Silent	SNP	ENST00000285873.7	hg19	CCDS4330.1																																																																																			.	.		0.378	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			G	154311783	A	G	154311783	2	3	73	1	0	0	0	0	0	0	0	1	6339	126	5	2		2	GEMIN5	5	154311783	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3381594	154311783	26603477	199	9525										
FAM71B	153745	hgsc.bcm.edu	37	chr5	156590341	156590341	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgatagctgctcccgccagcGctgtggtcacttgacctggg	13	13	1	2	rs200982218		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:156590341G>T	ENST00000302938.4	-	2	1030	c.935C>A	c.(934-936)gCg>gAg	p.A312E		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	312	Ala-rich.					nucleus (GO:0005634)		p.A312G(1)		NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCCCGCCAGCGCTGTGGTCAC	0.517																																					p.A312E		Atlas-SNP	.											FAM71B,NS,carcinoma,0,1	FAM71B	145	.	1	Substitution - Missense(1)	lung(1)	c.C935A						.						114	111	112					5																	156590341		2203	4300	6503	SO:0001583	missense	153745	exon2			GCCAGCGCTGTGG		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.935C>A	chr5.hg19:g.156590341G>T	ENSP00000305596:p.Ala312Glu	52.0	0.0		53.0	29.0	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.636256	0.47049	.	.	ENSG00000170613	ENST00000302938	T	0.05319	3.46	3.85	2.96	0.34315	.	0.724337	0.11932	N	0.515623	T	0.15478	0.0373	L	0.57536	1.79	0.09310	N	1	D	0.71674	0.998	P	0.57152	0.814	T	0.07654	-1.0761	10	0.72032	D	0.01	-4.6405	9.7121	0.40251	0.0:0.2098:0.7902:0.0	.	312	Q8TC56	FA71B_HUMAN	E	312	ENSP00000305596:A312E	ENSP00000305596:A312E	A	-	2	0	FAM71B	156522919	0.020000	0.18652	0.002000	0.10522	0.003000	0.03518	2.432000	0.44784	1.154000	0.42482	0.655000	0.94253	GCG	.	G|1.000;A|0.000		0.517	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		T	156590341	G	T	156590341	3	4	73	1	0	0	0	0	1	0	0	0	5616	1087	38	1	886	1	FAM71B	5	156590341	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	2278558	156590341	24324919	200	9526										
ADRA1B	147	hgsc.bcm.edu	37	chr5	159344340	159344340	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtgcgccatctccatcgatcGctacatcggggtgcgctact	11	14	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:159344340G>A	ENST00000306675.3	+	1	551	c.428G>A	c.(427-429)cGc>cAc	p.R143H		NM_000679.3	NP_000670.1	P35368	ADA1B_HUMAN	adrenoceptor alpha 1B	143					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|adult heart development (GO:0007512)|behavioral response to cocaine (GO:0048148)|blood vessel remodeling (GO:0001974)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|multicellular organismal development (GO:0007275)|negative regulation of glycogen catabolic process (GO:0045818)|organ growth (GO:0035265)|positive regulation of glycogen catabolic process (GO:0045819)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of the force of heart contraction by epinephrine-norepinephrine (GO:0001997)|regulation of cardiac muscle contraction (GO:0055117)|regulation of vasoconstriction (GO:0019229)|response to amphetamine (GO:0001975)|response to morphine (GO:0043278)|vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure (GO:0001987)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)|protein heterodimerization activity (GO:0046982)			endometrium(3)|large_intestine(6)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acepromazine(DB01614)|Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Dapiprazole(DB00298)|Desipramine(DB01151)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Ziprasidone(DB00246)	TCCATCGATCGCTACATCGGG	0.607																																					p.R143H		Atlas-SNP	.											.	ADRA1B	39	.	0			c.G428A						.						107	90	96					5																	159344340		2203	4300	6503	SO:0001583	missense	147	exon1			TCGATCGCTACAT	L31773	CCDS4347.1	5q33.3	2012-08-08	2012-05-09		ENSG00000170214	ENSG00000170214		"GPCR / Class A : Adrenoceptors : alpha"	278	protein-coding gene	gene with protein product		104220	"adrenergic, alpha-1B-, receptor"				Standard	XM_005265818		Approved		uc003lxt.1	P35368	OTTHUMG00000130327	ENST00000306675.3:c.428G>A	chr5.hg19:g.159344340G>A	ENSP00000306662:p.Arg143His	60.0	0.0		56.0	25.0	NM_000679	B0LPE1	Missense_Mutation	SNP	ENST00000306675.3	hg19	CCDS4347.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.295953	0.81025	.	.	ENSG00000170214	ENST00000306675	D	0.97161	-4.27	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.99272	0.9746	H	0.99545	4.62	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.98479	1.0604	10	0.87932	D	0	.	17.7769	0.88511	0.0:0.0:1.0:0.0	rs61759420	143	P35368	ADA1B_HUMAN	H	143	ENSP00000306662:R143H	ENSP00000306662:R143H	R	+	2	0	ADRA1B	159276918	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.813000	0.99286	2.629000	0.89072	0.462000	0.41574	CGC	.	.		0.607	ADRA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252676.1			A	159344340	G	A	159344340	3	1	73	1	0	0	0	0	1	0	0	0	335	1087	38	1	430	1	ADRA1B	5	159344340	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	2753999	159344340	21570920	201	9527										
STK10	6793	hgsc.bcm.edu	37	chr5	171509351	171509351	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctttcttcatcagtttgagCtgctcttggaacctggtgta	9	9	5	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:171509351C>T	ENST00000176763.5	-	12	2311	c.1968G>A	c.(1966-1968)caG>caA	p.Q656Q	AC113342.1_ENST00000579783.1_RNA	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	656					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCAGTTTGAGCTGCTCTTGGA	0.587																																					p.Q656Q		Atlas-SNP	.											.	STK10	100	.	0			c.G1968A						.						129	122	124					5																	171509351		2203	4300	6503	SO:0001819	synonymous_variant	6793	exon12			TTTGAGCTGCTCT	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.1968G>A	chr5.hg19:g.171509351C>T		100.0	0.0		67.0	27.0	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	hg19	CCDS34290.1																																																																																			.	.		0.587	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		T	171509351	C	T	171509351	2	4	73	1	0	0	0	0	0	0	0	1	15301	796	28	3		3	STK10	5	171509351	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	12165011	171509351	9405909	202	9528										
HRH2	3274	hgsc.bcm.edu	37	chr5	175112498	175112498	+	IGR	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcattcatttgcaaacattcAtccaattcccaccacatgcc	2	15	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:175112498A>T	ENST00000231683.2	+	0	3095				HRH2_ENST00000377291.2_Missense_Mutation_p.H388L	NM_022304.2	NP_071640.1	P25021	HRH2_HUMAN	histamine receptor H2						digestive tract development (GO:0048565)|epithelial cell morphogenesis (GO:0003382)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|gastrin-induced gastric acid secretion (GO:0001698)|gland development (GO:0048732)|histamine-induced gastric acid secretion (GO:0001697)|immune response (GO:0006955)|memory (GO:0007613)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(10)|ovary(1)	22	all_cancers(89;0.00805)|Renal(175;0.000269)|Lung NSC(126;0.00419)|all_lung(126;0.00711)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Colorectal(1;0.0154)|COAD - Colon adenocarcinoma(1;0.149)	Amitriptyline(DB00321)|Asenapine(DB06216)|Betazole(DB00272)|Cimetidine(DB00501)|Doxepin(DB01142)|Epinastine(DB00751)|Famotidine(DB00927)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Methantheline(DB00940)|Nizatidine(DB00585)|Olanzapine(DB00334)|Ranitidine(DB00863)|Roxatidine acetate(DB08806)|Tolazoline(DB00797)	Gcaaacattcatccaattccc	0.398																																					p.H388L		Atlas-SNP	.											.	HRH2	108	.	0			c.A1163T						.						102	86	91					5																	175112498		692	1591	2283	SO:0001628	intergenic_variant	3274	exon3			ACATTCATCCAAT		CCDS4395.1, CCDS47344.1	5q35	2012-08-08			ENSG00000113749	ENSG00000113749		"GPCR / Class A : Histamine receptors"	5183	protein-coding gene	gene with protein product		142703				1714721	Standard	NM_022304		Approved		uc003mdc.4	P25021	OTTHUMG00000130660		chr5.hg19:g.175112498A>T		284.0	1.0		207.0	87.0	NM_001131055	B5BUP7|Q14464|Q7Z5R9	Missense_Mutation	SNP	ENST00000231683.2	hg19	CCDS4395.1	.	.	.	.	.	.	.	.	.	.	A	9.111	1.006671	0.19199	.	.	ENSG00000113749	ENST00000377291	T	0.62639	0.01	2.87	-4.6	0.03390	.	3.128170	0.01552	N	0.019706	T	0.48978	0.1530	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42258	-0.9462	9	0.87932	D	0	.	6.1699	0.20410	0.273:0.201:0.526:0.0	.	388	Q7Z5R9	.	L	388	ENSP00000366506:H388L	ENSP00000366506:H388L	H	+	2	0	HRH2	175045104	0.000000	0.05858	0.000000	0.03702	0.149000	0.21700	-1.347000	0.02632	-1.074000	0.03132	-0.589000	0.04120	CAT	.	.		0.398	HRH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253151.1			T	175112498	A	T	175112498	1	4	73	0	1	0	0	0	0	0	0	0	7365	217	8	4		4	HRH2	5	175112498	IGR	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3603147	175112498	5802762	203	9529										
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178548746	178548746	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cttcttggagggatctgagaTgtttcctagagggaggagag	16	5	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr5:178548746T>A	ENST00000251582.7	-	21	3195	c.3094A>T	c.(3094-3096)Atc>Ttc	p.I1032F		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	1032					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GGATCTGAGATGTTTCCTAGA	0.652																																					p.I1032F		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.A3094T						.						137	144	141					5																	178548746		2203	4300	6503	SO:0001583	missense	9509	exon21			CTGAGATGTTTCC	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.3094A>T	chr5.hg19:g.178548746T>A	ENSP00000251582:p.Ile1032Phe	84.0	0.0		67.0	23.0	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	hg19	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	T	7.766	0.706390	0.15239	.	.	ENSG00000087116	ENST00000251582	T	0.60040	0.22	5.74	-9.42	0.00610	.	1.619860	0.03460	N	0.212036	T	0.37999	0.1024	L	0.36672	1.1	0.31007	N	0.719683	B	0.23735	0.09	B	0.22601	0.04	T	0.06197	-1.0840	10	0.11794	T	0.64	.	6.8422	0.23969	0.1009:0.492:0.1038:0.3034	.	1032	O95450	ATS2_HUMAN	F	1032	ENSP00000251582:I1032F	ENSP00000251582:I1032F	I	-	1	0	ADAMTS2	178481352	0.000000	0.05858	0.001000	0.08648	0.298000	0.27526	-1.217000	0.02979	-1.798000	0.01250	-0.377000	0.06932	ATC	.	.		0.652	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		A	178548746	T	A	178548746	3	1	73	1	0	0	0	0	1	0	0	0	265	1464	51	4	549	4	ADAMTS2	5	178548746	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3436248	178548746	2366514	204	9530										
TUBB2B	347733	hgsc.bcm.edu	37	chr6	3227741	3227741	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cttggcgccgatctggttgcCgcactggcccgcctggatgt	14	14	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:3227741C>A	ENST00000259818.7	-	1	228	c.37G>T	c.(37-39)Ggc>Tgc	p.G13C	TUBB2B_ENST00000473006.1_Intron	NM_178012.4	NP_821080.1	Q9BVA1	TBB2B_HUMAN	tubulin, beta 2B class IIb	13					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|neuron migration (GO:0001764)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			kidney(2)|large_intestine(5)|lung(1)|prostate(1)|skin(1)	10	Ovarian(93;0.0386)	all_hematologic(90;0.108)				ATCTGGTTGCCGCACTGGCCC	0.726																																					p.G13C		Atlas-SNP	.											.	TUBB2B	25	.	0			c.G37T						.						40	41	41					6																	3227741		2200	4299	6499	SO:0001583	missense	347733	exon1			GGTTGCCGCACTG	BC001352	CCDS4485.1	6p25.2	2011-10-10	2011-10-10		ENSG00000137285	ENSG00000137285		"Tubulins"	30829	protein-coding gene	gene with protein product	"class IIb beta-tubulin"	612850	"tubulin, beta 2B"			8619474, 9110174	Standard	NM_178012		Approved	MGC8685, DKFZp566F223, bA506K6.1	uc003mvg.3	Q9BVA1	OTTHUMG00000014143	ENST00000259818.7:c.37G>T	chr6.hg19:g.3227741C>A	ENSP00000259818:p.Gly13Cys	21.0	0.0		37.0	11.0	NM_178012	A8K068	Missense_Mutation	SNP	ENST00000259818.7	hg19	CCDS4485.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.379008	0.82682	.	.	ENSG00000137285	ENST00000259818	D	0.90133	-2.62	4.34	4.34	0.51931	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.64402	D	0.000015	D	0.98108	0.9376	H	0.99977	5.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99640	1.0988	10	0.87932	D	0	.	17.4008	0.87459	0.0:1.0:0.0:0.0	.	13;13	Q8IZ29;Q9BVA1	.;TBB2B_HUMAN	C	13	ENSP00000259818:G13C	ENSP00000259818:G13C	G	-	1	0	TUBB2B	3172740	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.388000	0.79795	2.403000	0.81681	0.561000	0.74099	GGC	.	.		0.726	TUBB2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039680.2	NM_178012		A	3227741	C	A	3227741	3	1	73	1	0	0	0	0	1	0	0	0	16770	652	23	1	1316	1	TUBB2B	6	3227741	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10		3227741	167887326	205	9531										
PRPF4B	8899	hgsc.bcm.edu	37	chr6	4057278	4057278	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttttgttttcagttataggtAaaagctatgactatggtata	8	3	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:4057278A>G	ENST00000337659.6	+	13	2690	c.2590A>G	c.(2590-2592)Aaa>Gaa	p.K864E	PRPF4B_ENST00000538861.1_Missense_Mutation_p.K850E	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	864	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				AGTTATAGGTAAAAGCTATGA	0.328																																					p.K864E		Atlas-SNP	.											.	PRPF4B	140	.	0			c.A2590G						.						88	90	90					6																	4057278		2203	4300	6503	SO:0001583	missense	8899	exon13			ATAGGTAAAAGCT	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.2590A>G	chr6.hg19:g.4057278A>G	ENSP00000337194:p.Lys864Glu	64.0	0.0		122.0	25.0	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	hg19	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	A	16.81	3.224850	0.58668	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.65364	-0.15;-0.15	6.17	6.17	0.99709	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56277	0.1974	N	0.12611	0.24	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	T	0.64045	-0.6499	10	0.40728	T	0.16	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	864	Q13523	PRP4B_HUMAN	E	864;850	ENSP00000337194:K864E;ENSP00000439331:K850E	ENSP00000337194:K864E	K	+	1	0	PRPF4B	4002277	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.823000	0.92018	2.371000	0.80710	0.533000	0.62120	AAA	.	.		0.328	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			G	4057278	A	G	4057278	3	3	73	1	0	0	0	0	1	0	0	0	12585	363	13	2	2640	2	PRPF4B	6	4057278	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	829537	4057278	167057789	206	9532										
EEF1E1	9521	hgsc.bcm.edu	37	chr6	8097609	8097609	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cttctgcagtactccccagcAaatattctttgttggcttgc	7	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:8097609A>G	ENST00000379715.5	-	2	235	c.179T>C	c.(178-180)tTg>tCg	p.L60S	EEF1E1_ENST00000429723.2_Missense_Mutation_p.L60S|EEF1E1-BLOC1S5_ENST00000397456.2_Missense_Mutation_p.L60S|EEF1E1_ENST00000507463.1_Missense_Mutation_p.L60S	NM_004280.4	NP_004271.1	O43324	MCA3_HUMAN	eukaryotic translation elongation factor 1 epsilon 1	60	GST C-terminal.|Linker.				gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				endometrium(1)|prostate(1)	2	Ovarian(93;0.0398)					ACTCCCCAGCAAATATTCTTT	0.413																																					p.L60S		Atlas-SNP	.											.	EEF1E1	11	.	0			c.T179C						.						162	149	154					6																	8097609		2203	4300	6503	SO:0001583	missense	9521	exon2			CCCAGCAAATATT	AF054186	CCDS4507.1, CCDS47370.1	6p24.3	2009-05-20			ENSG00000124802	ENSG00000124802			3212	protein-coding gene	gene with protein product	"aminoacyl tRNA synthetase complex-interacting multifunctional protein 3"	609206		P18		9653160	Standard	NM_004280		Approved	AIMP3	uc003mxz.3	O43324	OTTHUMG00000014221	ENST00000379715.5:c.179T>C	chr6.hg19:g.8097609A>G	ENSP00000369038:p.Leu60Ser	150.0	0.0		227.0	60.0	NM_001135650	C9JLK5|Q5THS2	Missense_Mutation	SNP	ENST00000379715.5	hg19	CCDS4507.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.3|25.3	4.620200|4.620200	0.87460|0.87460	.|.	.|.	ENSG00000124802|ENSG00000124802	ENST00000502429|ENST00000429723;ENST00000379715;ENST00000507463;ENST00000488226	.|T;T;T	.|0.20598	.|3.29;3.29;2.06	5.62|5.62	5.62|5.62	0.85841|0.85841	.|Glutathione S-transferase, C-terminal-like (1);Glutathione S-transferase/chloride channel, C-terminal (1);Thioredoxin-like fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.44808|0.44808	0.1311|0.1311	M|M	0.87827|0.87827	2.91|2.91	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.999	T|T	0.53099|0.53099	-0.8486|-0.8486	5|9	.|.	.|.	.|.	-7.0642|-7.0642	15.827|15.827	0.78718|0.78718	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|60;60	.|C9JLK5;O43324	.|.;MCA3_HUMAN	R|S	47|60;60;60;72	.|ENSP00000414363:L60S;ENSP00000369038:L60S;ENSP00000425577:L72S	.|.	C|L	-|-	1|2	0|0	EEF1E1|EEF1E1	8042608|8042608	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.972000|0.972000	0.66771|0.66771	7.928000|7.928000	0.87587|0.87587	2.129000|2.129000	0.65627|0.65627	0.533000|0.533000	0.62120|0.62120	TGC|TTG	.	.		0.413	EEF1E1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039799.2	NM_004280		G	8097609	A	G	8097609	3	3	73	1	0	0	0	0	1	0	0	0	4929	131	5	2	397	2	EEF1E1	6	8097609	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4040331	8097609	163017458	207	9533										
SIRT5	23408	hgsc.bcm.edu	37	chr6	13588600	13588600	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagttttttgcaaaagcaaaGcacatagtcatcatctcagg	7	8	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:13588600G>A	ENST00000606117.1	+	4	449	c.153G>A	c.(151-153)aaG>aaA	p.K51K	SIRT5_ENST00000359782.3_Silent_p.K51K|SIRT5_ENST00000379262.4_Silent_p.K51K|SIRT5_ENST00000397350.2_Intron	NM_012241.4	NP_036373.1			sirtuin 5											breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	11	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)			CAAAAGCAAAGCACATAGTCA	0.413																																					p.K51K		Atlas-SNP	.											.	SIRT5	45	.	0			c.G153A						.						114	106	109					6																	13588600		2203	4300	6503	SO:0001819	synonymous_variant	23408	exon4			AGCAAAGCACATA	AF083110	CCDS4526.1, CCDS4527.1, CCDS54966.1, CCDS56398.1	6p23	2010-08-05	2010-06-25		ENSG00000124523	ENSG00000124523			14933	protein-coding gene	gene with protein product		604483	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 5", "sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae)"			10381378	Standard	NM_012241		Approved		uc003nay.3	Q9NXA8	OTTHUMG00000014278	ENST00000606117.1:c.153G>A	chr6.hg19:g.13588600G>A		173.0	0.0		367.0	86.0	NM_012241		Silent	SNP	ENST00000606117.1	hg19	CCDS4526.1																																																																																			.	.		0.413	SIRT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039908.2			A	13588600	G	A	13588600	2	1	73	1	0	0	0	0	0	0	0	1	14356	962	34	3		3	SIRT5	6	13588600	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	5490991	13588600	157526467	208	9534										
NUP153	9972	hgsc.bcm.edu	37	chr6	17706588	17706588	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccggatcttgccgccaccgcCccctccgactcctccggctc	8	23	1	0	rs373196566		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:17706588C>A	ENST00000262077.2	-	1	30	c.31G>T	c.(31-33)Ggc>Tgc	p.G11C	NUP153_ENST00000537253.1_Missense_Mutation_p.G11C|RP11-500C11.3_ENST00000606771.1_RNA	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	11	Gly-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			CCGCCACCGCCCCCTCCGACT	0.716																																					p.G11C		Atlas-SNP	.											.	NUP153	116	.	0			c.G31T						.						46	40	42					6																	17706588		2201	4299	6500	SO:0001583	missense	9972	exon1			CACCGCCCCCTCC	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"nucleoporin 153kD"			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.31G>T	chr6.hg19:g.17706588C>A	ENSP00000262077:p.Gly11Cys	57.0	0.0		87.0	9.0	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	hg19	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	C	19.63	3.864298	0.71949	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.08546	3.12;3.08	3.97	3.97	0.46021	.	0.000000	0.35525	N	0.003147	T	0.11452	0.0279	L	0.46157	1.445	0.32481	N	0.541469	D;D;D	0.71674	0.998;0.995;0.995	D;P;P	0.65874	0.939;0.871;0.871	T	0.00376	-1.1779	10	0.62326	D	0.03	-2.5652	11.8695	0.52513	0.0:1.0:0.0:0.0	.	11;33;11	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	C	11;33;11	ENSP00000262077:G11C;ENSP00000444029:G11C	ENSP00000262077:G11C	G	-	1	0	NUP153	17814567	0.997000	0.39634	1.000000	0.80357	0.808000	0.45660	1.803000	0.38863	2.503000	0.84419	0.591000	0.81541	GGC	.	.		0.716	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			A	17706588	C	A	17706588	3	1	73	1	0	0	0	0	1	0	0	0	10764	623	22	3	4484	3	NUP153	6	17706588	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	4117988	17706588	153408479	209	9535										
PRL	5617	hgsc.bcm.edu	37	chr6	22287693	22287693	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gagataattgtcgattttatGtgaatccctgcgtaggcagt	11	6	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:22287693G>T	ENST00000306482.1	-	5	1140	c.622C>A	c.(622-624)Cat>Aat	p.H208N	RP3-404K8.2_ENST00000561912.1_RNA	NM_000948.5|NM_001163558.2	NP_000939.1|NP_001157030.1	P01236	PRL_HUMAN	prolactin	208					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|circadian rhythm (GO:0007623)|female pregnancy (GO:0007565)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|multicellular organismal response to stress (GO:0033555)|ovulation cycle (GO:0042698)|parturition (GO:0007567)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of JAK-STAT cascade (GO:0046427)|regulation of multicellular organism growth (GO:0040014)|regulation of ossification (GO:0030278)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	prolactin receptor binding (GO:0005148)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)|prostate(1)	16	Ovarian(93;0.163)					TCGATTTTATGTGAATCCCTG	0.468																																					p.H208N		Atlas-SNP	.											.	PRL	41	.	0			c.C622A						.						249	220	230					6																	22287693		2203	4300	6503	SO:0001583	missense	5617	exon5			TTTTATGTGAATC	D00411	CCDS4548.1	6p22.3	2013-09-16			ENSG00000172179	ENSG00000172179			9445	protein-coding gene	gene with protein product		176760					Standard	NM_000948		Approved		uc003ndq.3	P01236	OTTHUMG00000016111	ENST00000306482.1:c.622C>A	chr6.hg19:g.22287693G>T	ENSP00000302150:p.His208Asn	63.0	0.0		143.0	43.0	NM_000948	Q15199|Q92996	Missense_Mutation	SNP	ENST00000306482.1	hg19	CCDS4548.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.944977	0.34283	.	.	ENSG00000172179	ENST00000306482;ENST00000438606	D	0.89123	-2.47	5.66	3.84	0.44239	Somatotropin hormone, conserved site (1);Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.128807	0.64402	N	0.000001	D	0.82282	0.5003	L	0.60012	1.86	0.53688	D	0.999979	B;B	0.15473	0.0;0.013	B;B	0.30401	0.014;0.115	T	0.77739	-0.2475	10	0.38643	T	0.18	0.0015	14.5109	0.67787	0.0:0.0:0.6167:0.3833	.	208;209	P01236;Q5I0G2	PRL_HUMAN;.	N	208;177	ENSP00000302150:H208N	ENSP00000302150:H208N	H	-	1	0	PRL	22395672	0.999000	0.42202	0.451000	0.26982	0.998000	0.95712	3.026000	0.49689	0.815000	0.34398	0.655000	0.94253	CAT	.	.		0.468	PRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043327.1	NM_000948		T	22287693	G	T	22287693	3	4	73	1	0	0	0	0	1	0	0	0	12540	1377	48	3	65	3	PRL	6	22287693	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	4581105	22287693	148827374	210	9536										
HIST1H2BJ	8970	hgsc.bcm.edu	37	chr6	27100194	27100194	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acggccttagtaccctcggaCacggcgtgcttggccaactc	11	15	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:27100194C>A	ENST00000607124.1	-	1	335	c.336G>T	c.(334-336)gtG>gtT	p.V112V	HIST1H2BJ_ENST00000339812.2_Silent_p.V112V|HIST1H2AG_ENST00000359193.2_5'Flank|HIST1H2BJ_ENST00000541790.1_Silent_p.V112V			P06899	H2B1J_HUMAN	histone cluster 1, H2bj	112					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(2)|lung(5)|ovary(1)|prostate(1)	10						TACCCTCGGACACGGCGTGCT	0.587																																					p.V112V		Atlas-SNP	.											HIST1H2BJ,NS,carcinoma,0,1	HIST1H2BJ	21	.	0			c.G336T						.						82	82	82					6																	27100194		2203	4300	6503	SO:0001819	synonymous_variant	8970	exon1			CTCGGACACGGCG	X00088	CCDS4618.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000124635	ENSG00000124635		"Histones / Replication-dependent"	4761	protein-coding gene	gene with protein product		615044	"H2B histone family, member R", "histone 1, H2bj"	H2BFR		6647026, 12408966	Standard	NM_021058		Approved	H2B/r	uc003niv.3	P06899	OTTHUMG00000014470	ENST00000607124.1:c.336G>T	chr6.hg19:g.27100194C>A		93.0	0.0		174.0	34.0	NM_021058	B2R4J4|O60816	Silent	SNP	ENST00000607124.1	hg19	CCDS4618.1																																																																																			.	.		0.587	HIST1H2BJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040138.2	NM_021058		A	27100194	C	A	27100194	2	1	73	1	0	0	0	0	0	0	0	1	7158	465	17	3		3	HIST1H2BJ	6	27100194	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	4812501	27100194	144014873	211	9537										
ZSCAN23	222696	hgsc.bcm.edu	37	chr6	28402633	28402633	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctcgataaggatggaattcTgggtgaagctttttccacat	11	7	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:28402633T>C	ENST00000289788.4	-	4	924	c.779A>G	c.(778-780)cAg>cGg	p.Q260R	ZSCAN23_ENST00000486481.1_5'Flank	NM_001012455.1	NP_001012458.1	Q3MJ62	ZSC23_HUMAN	zinc finger and SCAN domain containing 23	260					transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|prostate(1)|stomach(2)	4						GATGGAATTCTGGGTGAAGCT	0.502																																					p.Q260R		Atlas-SNP	.											.	ZSCAN23	18	.	0			c.A779G						.						87	76	79					6																	28402633		692	1591	2283	SO:0001583	missense	222696	exon4			GAATTCTGGGTGA	AK092117	CCDS47393.1	6p21.33	2013-01-08	2007-02-20	2007-02-20	ENSG00000187987	ENSG00000187987		"-", "Zinc fingers, C2H2-type"	21193	protein-coding gene	gene with protein product			"zinc finger protein 453", "zinc finger protein 390"	ZNF453, ZNF390			Standard	NM_001012455		Approved	dJ29K1.3.1	uc003nli.4	Q3MJ62	OTTHUMG00000016346	ENST00000289788.4:c.779A>G	chr6.hg19:g.28402633T>C	ENSP00000289788:p.Gln260Arg	148.0	0.0		275.0	66.0	NM_001012455	Q96KV9	Missense_Mutation	SNP	ENST00000289788.4	hg19	CCDS47393.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.123891	0.56613	.	.	ENSG00000187987	ENST00000289788	T	0.07444	3.19	4.56	4.56	0.56223	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47852	D	0.000207	T	0.01835	0.0058	N	0.16066	0.365	0.21473	N	0.999679	B	0.33807	0.426	B	0.37550	0.253	T	0.43798	-0.9369	10	0.27082	T	0.32	.	7.4644	0.27314	0.1924:0.0:0.0:0.8076	.	260	Q3MJ62	ZSC23_HUMAN	R	260	ENSP00000289788:Q260R	ENSP00000289788:Q260R	Q	-	2	0	ZSCAN23	28510612	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	-0.032000	0.12266	1.894000	0.54839	0.528000	0.53228	CAG	.	.		0.502	ZSCAN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043751.2	XM_167147		C	28402633	T	C	28402633	3	2	73	1	0	0	0	0	1	0	0	0	18250	1580	55	2	394	2	ZSCAN23	6	28402633	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1302439	28402633	142712434	212	9538										
ZNF311	282890	hgsc.bcm.edu	37	chr6	28962885	28962885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	actccatacttgatgttttcTtttcttatgtccagtaagat	5	8	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:28962885T>C	ENST00000377179.3	-	7	2406	c.1894A>G	c.(1894-1896)Aga>Gga	p.R632G	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	632					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						TGATGTTTTCTTTTCTTATGT	0.413																																					p.R632G		Atlas-SNP	.											.	ZNF311	59	.	0			c.A1894G						.						117	97	104					6																	28962885		1511	2709	4220	SO:0001583	missense	282890	exon7			GTTTTCTTTTCTT	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"Zinc fingers, C2H2-type", "-"	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.1894A>G	chr6.hg19:g.28962885T>C	ENSP00000366384:p.Arg632Gly	130.0	0.0		208.0	38.0	NM_001010877	A2BFK5|B0S7Y4|Q92971	Missense_Mutation	SNP	ENST00000377179.3	hg19	CCDS34357.1	.	.	.	.	.	.	.	.	.	.	T	17.29	3.352261	0.61183	.	.	ENSG00000197935	ENST00000377179;ENST00000535083	T	0.07688	3.17	3.13	3.13	0.36017	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	.	.	.	.	T	0.01387	0.0045	N	0.08118	0	0.27471	N	0.952865	P	0.47762	0.9	B	0.38954	0.286	T	0.45512	-0.9256	9	0.31617	T	0.26	-2.5445	8.0448	0.30542	0.0:0.0:0.0:1.0	.	632	Q5JNZ3	ZN311_HUMAN	G	632;540	ENSP00000366384:R632G	ENSP00000366384:R632G	R	-	1	2	ZNF311	29070864	0.040000	0.19996	0.995000	0.50966	0.930000	0.56654	0.913000	0.28611	1.666000	0.50821	0.477000	0.44152	AGA	.	.		0.413	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581		C	28962885	T	C	28962885	3	2	73	1	0	0	0	0	1	0	0	0	17849	1617	56	2	110	2	ZNF311	6	28962885	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	560252	28962885	142152182	213	9539										
GABBR1	2550	hgsc.bcm.edu	37	chr6	29591692	29591692	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgaggttccacatcctagcaGcctcagccaccagcgtggag	11	14	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:29591692G>T	ENST00000377034.4	-	7	1102	c.767C>A	c.(766-768)gCt>gAt	p.A256D	GABBR1_ENST00000377012.4_Missense_Mutation_p.A139D|GABBR1_ENST00000355973.3_Missense_Mutation_p.A139D|GABBR1_ENST00000376977.3_Missense_Mutation_p.A256D|GABBR1_ENST00000377016.4_Missense_Mutation_p.A194D	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	256					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	CATCCTAGCAGCCTCAGCCAC	0.537																																					p.A256D		Atlas-SNP	.											.	GABBR1	95	.	0			c.C767A						.						123	94	104					6																	29591692		1511	2709	4220	SO:0001583	missense	2550	exon7			CTAGCAGCCTCAG	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.767C>A	chr6.hg19:g.29591692G>T	ENSP00000366233:p.Ala256Asp	215.0	0.0		278.0	57.0	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	hg19	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	-	15.38	2.815807	0.50527	.	.	ENSG00000204681	ENST00000355973;ENST00000376977;ENST00000377016;ENST00000377012;ENST00000377034	D;D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67;-1.67	4.31	3.44	0.39384	Extracellular ligand-binding receptor (1);	0.061993	0.64402	D	0.000006	D	0.88742	0.6519	M	0.86343	2.81	0.80722	D	1	P;D;D;D	0.89917	0.86;1.0;1.0;1.0	P;D;D;D	0.91635	0.561;0.999;0.999;0.999	D	0.89744	0.3935	10	0.87932	D	0	-16.218	9.9893	0.41860	0.1005:0.0:0.8995:0.0	.	256;194;256;139	Q9UBS5-5;Q9UBS5-3;Q9UBS5;Q5SUJ9	.;.;GABR1_HUMAN;.	D	139;256;194;139;256	ENSP00000348248:A139D;ENSP00000366176:A256D;ENSP00000366215:A194D;ENSP00000366211:A139D;ENSP00000366233:A256D	ENSP00000348248:A139D	A	-	2	0	GABBR1	29699671	1.000000	0.71417	1.000000	0.80357	0.144000	0.21451	8.942000	0.92970	1.060000	0.40578	-0.293000	0.09583	GCT	.	.		0.537	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			T	29591692	G	T	29591692	3	4	73	1	0	0	0	0	1	0	0	0	6163	971	34	3	2186	3	GABBR1	6	29591692	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	628807	29591692	141523375	214	9540										
MUC21	394263	hgsc.bcm.edu	37	chr6	30955854	30955854	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctcaaccatggccttggtccAggccctggagggaatcatgg	13	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:30955854A>C	ENST00000376296.3	+	3	1825	c.1584A>C	c.(1582-1584)ccA>ccC	p.P528P	MUC21_ENST00000486149.2_Silent_p.P74P	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	528	Cytoplasmic tail.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GCCTTGGTCCAGGCCCTGGAG	0.537																																					p.P528P		Atlas-SNP	.											.	MUC21	98	.	0			c.A1584C						.						73	73	73					6																	30955854		1511	2708	4219	SO:0001819	synonymous_variant	394263	exon3			TGGTCCAGGCCCT	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1584A>C	chr6.hg19:g.30955854A>C		189.0	0.0		255.0	42.0	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	hg19	CCDS34388.1																																																																																			.	.		0.537	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		C	30955854	A	C	30955854	2	2	73	1	0	0	0	0	0	0	0	1	9986	175	7	5		5	MUC21	6	30955854	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1364162	30955854	140159213	215	9541										
C6orf47	57827	hgsc.bcm.edu	37	chr6	31627616	31627616	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccagtcacttcctgaattctCcgaggagctgtccacccgtc	8	16	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:31627616C>A	ENST00000375911.1	-	1	933	c.109G>T	c.(109-111)Gag>Tag	p.E37*	C6orf47-AS1_ENST00000422049.1_RNA	NM_021184.3	NP_067007.3	O95873	CF047_HUMAN	chromosome 6 open reading frame 47	37						cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9						CCTGAATTCTCCGAGGAGCTG	0.617																																					p.E37X		Atlas-SNP	.											.	C6orf47	15	.	0			c.G109T						.						38	36	37					6																	31627616		1511	2708	4219	SO:0001587	stop_gained	57827	exon1			AATTCTCCGAGGA	AF129756	CCDS34399.1	6p21.3	2011-12-13			ENSG00000204439	ENSG00000204439			19076	protein-coding gene	gene with protein product						2477242	Standard	NM_021184		Approved	D6S53E, G4	uc003nvm.1	O95873	OTTHUMG00000031172	ENST00000375911.1:c.109G>T	chr6.hg19:g.31627616C>A	ENSP00000365076:p.Glu37*	163.0	0.0		247.0	47.0	NM_021184	B0UXA1|B0UZ50|Q5SSS6|Q95IG0	Nonsense_Mutation	SNP	ENST00000375911.1	hg19	CCDS34399.1	.	.	.	.	.	.	.	.	.	.	C	44	10.893822	0.99484	.	.	ENSG00000204439	ENST00000375911;ENST00000538106	.	.	.	5.44	5.44	0.79542	.	0.000000	0.47093	D	0.000242	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-19.7986	14.6416	0.68729	0.0:1.0:0.0:0.0	.	.	.	.	X	37	.	ENSP00000365076:E37X	E	-	1	0	C6orf47	31735595	0.997000	0.39634	0.991000	0.47740	0.851000	0.48451	3.342000	0.52159	2.837000	0.97791	0.655000	0.94253	GAG	.	.		0.617	C6orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076324.1	NM_021184		A	31627616	C	A	31627616	4	1	73	1	0	0	0	0	0	1	0	0	2366	864	30	3	779	3	C6orf47	6	31627616	Nonsense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	671762	31627616	139487451	216	9542										
C6orf27	80737	hgsc.bcm.edu	37	chr6	31735467	31735467	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgtgatcttctggagcagcCcatccacgctgaacacaagt	9	13	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:31735467C>A	ENST00000375688.4	-	11	1768	c.1568G>T	c.(1567-1569)gGg>gTg	p.G523V	VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000375686.3_Missense_Mutation_p.G523V|SAPCD1-AS1_ENST00000419679.1_RNA|VWA7_ENST00000447450.1_Missense_Mutation_p.G523V			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	523						extracellular region (GO:0005576)											CTGGAGCAGCCCATCCACGCT	0.567																																					p.G523V		Atlas-SNP	.											.	.	.	.	0			c.G1568T						.						108	107	107					6																	31735467		2203	4300	6503	SO:0001583	missense	80737	exon11			AGCAGCCCATCCA		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"chromosome 6 open reading frame 27"	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.1568G>T	chr6.hg19:g.31735467C>A	ENSP00000364840:p.Gly523Val	108.0	0.0		190.0	42.0	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	hg19	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	C	9.767	1.171577	0.21704	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	T;T;T	0.29397	2.8;2.58;1.57	4.95	1.57	0.23409	.	0.920838	0.09417	N	0.804983	T	0.10981	0.0268	L	0.51422	1.61	0.39262	D	0.96422	B	0.22983	0.078	B	0.21917	0.037	T	0.23726	-1.0180	10	0.34782	T	0.22	-2.5619	3.6196	0.08090	0.0:0.4939:0.1933:0.3128	.	523	Q9Y334	G7C_HUMAN	V	523	ENSP00000364840:G523V;ENSP00000364838:G523V;ENSP00000390554:G523V	ENSP00000364838:G523V	G	-	2	0	C6orf27	31843446	0.254000	0.23992	0.993000	0.49108	0.535000	0.34838	0.647000	0.24812	0.531000	0.28639	0.561000	0.74099	GGG	.	.		0.567	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		A	31735467	C	A	31735467	3	1	73	1	0	0	0	0	1	0	0	0	2364	623	22	3	1134	3	C6orf27	6	31735467	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	107851	31735467	139379600	217	9543										
SLC44A4	80736	hgsc.bcm.edu	37	chr6	31839119	31839119	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccaataccaggactgggcaaAatcttcaaagatcttaacac	6	11	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:31839119A>C	ENST00000229729.6	-	9	693	c.673T>G	c.(673-675)Ttt>Gtt	p.F225V	SLC44A4_ENST00000544672.1_Missense_Mutation_p.F149V|SLC44A4_ENST00000375562.4_Missense_Mutation_p.F183V	NM_025257.2	NP_079533.2	Q53GD3	CTL4_HUMAN	solute carrier family 44, member 4	225					acetylcholine biosynthetic process (GO:0008292)|acetylcholine secretion (GO:0061526)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of cell growth (GO:0030307)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(1)|urinary_tract(2)	35					Choline(DB00122)	GACTGGGCAAAATCTTCAAAG	0.527																																					p.F225V		Atlas-SNP	.											SLC44A4,NS,carcinoma,0,1	SLC44A4	67	.	0			c.T673G						.						134	122	126					6																	31839119		2203	4300	6503	SO:0001583	missense	80736	exon9			GGGCAAAATCTTC	AF134726	CCDS4724.2, CCDS54989.1, CCDS54990.1	6p21.3	2014-02-17	2005-09-06	2005-09-06	ENSG00000204385	ENSG00000204385		"Solute carriers"	13941	protein-coding gene	gene with protein product		606107	"chromosome 6 open reading frame 29"	C6orf29		10677542, 15715662, 24379411	Standard	NM_025257		Approved	NG22, CTL4, FLJ14491, TPPT	uc010jti.3	Q53GD3	OTTHUMG00000031133	ENST00000229729.6:c.673T>G	chr6.hg19:g.31839119A>C	ENSP00000229729:p.Phe225Val	117.0	0.0		168.0	7.0	NM_025257	A2BED3|B0UXX8|B0UZY8|B4DU94|B4DWM2|E9PEK7|Q5JP84|Q5JQ93|Q658S8|Q6UX89|Q8TEW4|Q96C58|Q96K59|Q9Y332	Missense_Mutation	SNP	ENST00000229729.6	hg19	CCDS4724.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.45|17.45	3.392108|3.392108	0.62066|0.62066	.|.	.|.	ENSG00000204385|ENSG00000204385	ENST00000229729;ENST00000375562;ENST00000544672|ENST00000414427	T;T;T|.	0.10860|.	3.22;2.83;3.0|.	4.57|4.57	3.33|3.33	0.38152|0.38152	.|.	0.112173|.	0.64402|.	D|.	0.000010|.	T|T	0.47173|0.47173	0.1431|0.1431	L|L	0.54323|0.54323	1.7|1.7	0.45161|0.45161	D|D	0.998173|0.998173	B;B|.	0.09022|.	0.002;0.001|.	B;B|.	0.12156|.	0.007;0.003|.	T|T	0.46261|0.46261	-0.9204|-0.9204	10|5	0.28530|.	T|.	0.3|.	-17.2626|-17.2626	8.6008|8.6008	0.33742|0.33742	0.8169:0.0:0.0:0.1831|0.8169:0.0:0.0:0.1831	.|.	183;225|.	E9PEK7;Q53GD3|.	.;CTL4_HUMAN|.	V|M	225;183;149|220	ENSP00000229729:F225V;ENSP00000364712:F183V;ENSP00000444109:F149V|.	ENSP00000229729:F225V|.	F|I	-|-	1|3	0|3	SLC44A4|SLC44A4	31947098|31947098	0.996000|0.996000	0.38824|0.38824	0.999000|0.999000	0.59377|0.59377	0.982000|0.982000	0.71751|0.71751	3.844000|3.844000	0.55873|0.55873	1.934000|1.934000	0.56057|0.56057	0.459000|0.459000	0.35465|0.35465	TTT|ATT	.	.		0.527	SLC44A4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076234.3			C	31839119	A	C	31839119	3	2	73	1	0	0	0	0	1	0	0	0	14653	14	1	5	1511	5	SLC44A4	6	31839119	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	103652	31839119	139275948	218	9544										
GRM4	2914	hgsc.bcm.edu	37	chr6	34003458	34003458	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cactcaccttgtcggccgacTgcgaggtgccaaagaagatg	12	12	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:34003458T>A	ENST00000538487.2	-	9	2872	c.2429A>T	c.(2428-2430)cAg>cTg	p.Q810L	GRM4_ENST00000544773.2_Missense_Mutation_p.Q641L|GRM4_ENST00000535756.1_Missense_Mutation_p.Q677L|GRM4_ENST00000455714.2_Missense_Mutation_p.Q670L|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000374181.4_Missense_Mutation_p.Q810L|GRM4_ENST00000374177.3_Missense_Mutation_p.Q694L|GRM4_ENST00000609222.1_Missense_Mutation_p.Q677L	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	810					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GTCGGCCGACTGCGAGGTGCC	0.642																																					p.Q810L		Atlas-SNP	.											.	GRM4	317	.	0			c.A2429T						.						50	40	44					6																	34003458		2203	4300	6503	SO:0001583	missense	2914	exon9			GCCGACTGCGAGG	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.2429A>T	chr6.hg19:g.34003458T>A	ENSP00000440556:p.Gln810Leu	228.0	0.0		377.0	69.0	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	hg19	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	.	15.63	2.889505	0.52014	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000545715;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	D;D;D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43	4.37	4.37	0.52481	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.92665	0.7669	M	0.78916	2.43	0.80722	D	1	P;B;D;D;B	0.63046	0.797;0.02;0.992;0.959;0.045	B;B;D;P;B	0.72982	0.425;0.03;0.979;0.629;0.048	D	0.93788	0.7090	10	0.87932	D	0	.	13.7265	0.62761	0.0:0.0:0.0:1.0	.	763;641;670;810;677	B7ZLU9;B7Z1T9;F5GXM5;Q14833;B3KVL9	.;.;.;GRM4_HUMAN;.	L	810;694;502;677;641;810;670	ENSP00000363296:Q810L;ENSP00000363292:Q694L;ENSP00000445533:Q502L;ENSP00000437925:Q677L;ENSP00000437730:Q641L;ENSP00000440556:Q810L;ENSP00000398456:Q670L	ENSP00000363292:Q694L	Q	-	2	0	GRM4	34111436	1.000000	0.71417	0.991000	0.47740	0.503000	0.33858	7.795000	0.85887	1.823000	0.53134	0.379000	0.24179	CAG	.	.		0.642	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			A	34003458	T	A	34003458	3	1	73	1	0	0	0	0	1	0	0	0	6808	1580	55	4	321	4	GRM4	6	34003458	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2164339	34003458	137111609	219	9545										
ZNF76	7629	hgsc.bcm.edu	37	chr6	35260758	35260758	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gacatcccagcccaggtggcGatggtgactgaagaagatgg	15	9	0	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:35260758G>T	ENST00000373953.3	+	11	1532	c.1266G>T	c.(1264-1266)gcG>gcT	p.A422A	ZNF76_ENST00000440666.2_Silent_p.A396A|ZNF76_ENST00000339411.5_Silent_p.A422A	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	422					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						CCCAGGTGGCGATGGTGACTG	0.617																																					p.A422A	Esophageal Squamous(52;92 1039 20612 23956 34676)	Atlas-SNP	.											.	ZNF76	37	.	0			c.G1266T						.						74	86	82					6																	35260758		2203	4300	6503	SO:0001819	synonymous_variant	7629	exon11			GGTGGCGATGGTG	M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"Zinc fingers, C2H2-type"	13149	protein-coding gene	gene with protein product		194549	"zinc finger protein 76 (expressed in testis)"	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.1266G>T	chr6.hg19:g.35260758G>T		160.0	0.0		239.0	58.0	NM_003427	Q9BQB2	Silent	SNP	ENST00000373953.3	hg19	CCDS4801.1																																																																																			.	.		0.617	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427		T	35260758	G	T	35260758	2	4	73	1	0	0	0	0	0	0	0	1	18150	1045	37	1		1	ZNF76	6	35260758	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1257300	35260758	135854309	220	9546										
BRPF3	27154	hgsc.bcm.edu	37	chr6	36169160	36169160	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	attccatgtgacatgtgcacAgcgggctgggctcttcatga	12	10	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:36169160A>C	ENST00000357641.6	+	2	1314	c.1061A>C	c.(1060-1062)cAg>cCg	p.Q354P	BRPF3_ENST00000443324.2_Missense_Mutation_p.Q354P|BRPF3_ENST00000339717.7_Missense_Mutation_p.Q354P|BRPF3_ENST00000534694.1_Missense_Mutation_p.Q354P|BRPF3_ENST00000534400.1_Missense_Mutation_p.Q354P|BRPF3_ENST00000543502.1_Missense_Mutation_p.Q354P	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	354					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						ACATGTGCACAGCGGGCTGGG	0.532																																					p.Q354P		Atlas-SNP	.											.	BRPF3	93	.	0			c.A1061C						.						60	53	55					6																	36169160		2203	4300	6503	SO:0001583	missense	27154	exon2			GTGCACAGCGGGC	AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.1061A>C	chr6.hg19:g.36169160A>C	ENSP00000350267:p.Gln354Pro	89.0	0.0		131.0	21.0	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Missense_Mutation	SNP	ENST00000357641.6	hg19	CCDS34437.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.532647	0.64972	.	.	ENSG00000096070	ENST00000357641;ENST00000339717;ENST00000534694;ENST00000543502;ENST00000443324;ENST00000534400	D;T;T;T;T;D	0.84589	-1.87;0.98;0.98;0.98;0.98;-1.87	5.62	5.62	0.85841	Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.94407	0.8201	H	0.96239	3.79	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.996;0.996;0.999	D	0.96053	0.9033	10	0.87932	D	0	.	16.1189	0.81329	1.0:0.0:0.0:0.0	.	354;354;354	B7ZLN5;Q17RB6;Q9ULD4	.;.;BRPF3_HUMAN	P	354	ENSP00000350267:Q354P;ENSP00000345419:Q354P;ENSP00000434501:Q354P;ENSP00000445352:Q354P;ENSP00000387368:Q354P;ENSP00000436504:Q354P	ENSP00000345419:Q354P	Q	+	2	0	BRPF3	36277138	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.851000	0.92205	2.263000	0.75096	0.533000	0.62120	CAG	.	.		0.532	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695		C	36169160	A	C	36169160	3	2	73	1	0	0	0	0	1	0	0	0	1523	188	7	5	1063	5	BRPF3	6	36169160	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	908402	36169160	134945907	221	9547										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38994404	38994404	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtgaccatccacaatgaagtTctgagacagaccaaggagga	11	9	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:38994404T>A	ENST00000359357.3	+	90	13400	c.13146T>A	c.(13144-13146)gtT>gtA	p.V4382V	DNAH8_ENST00000441566.1_Silent_p.V4346V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4382					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ACAATGAAGTTCTGAGACAGA	0.517																																					p.V4599V		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T13797A						.						111	84	94					6																	38994404		2203	4300	6503	SO:0001819	synonymous_variant	1769	exon92			TGAAGTTCTGAGA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.13146T>A	chr6.hg19:g.38994404T>A		61.0	0.0		81.0	20.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	hg19																																																																																				.	.		0.517	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38994404	T	A	38994404	2	1	73	1	0	0	0	0	0	0	0	1	4609	1770	62	4		4	DNAH8	6	38994404	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2825244	38994404	132120663	222	9548										
GLP1R	2740	hgsc.bcm.edu	37	chr6	39040691	39040691	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gaacctgtttgcatccttcaTcctgcgagcattgtccgtct	8	13	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:39040691T>A	ENST00000373256.4	+	6	606	c.563T>A	c.(562-564)aTc>aAc	p.I188N		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	188					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)			breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	GCATCCTTCATCCTGCGAGCA	0.572																																					p.I188N		Atlas-SNP	.											.	GLP1R	64	.	0			c.T563A						.						224	179	194					6																	39040691		2203	4300	6503	SO:0001583	missense	2740	exon6			CCTTCATCCTGCG		CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"GPCR / Class B : Glucagon receptors"	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.563T>A	chr6.hg19:g.39040691T>A	ENSP00000362353:p.Ile188Asn	92.0	0.0		146.0	42.0	NM_002062	Q2M229|Q99669	Missense_Mutation	SNP	ENST00000373256.4	hg19	CCDS4839.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.811467	0.90707	.	.	ENSG00000112164	ENST00000373256	T	0.42900	0.96	5.71	5.71	0.89125	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000003	T	0.67692	0.2920	M	0.92923	3.36	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.77419	-0.2595	10	0.87932	D	0	.	15.988	0.80176	0.0:0.0:0.0:1.0	.	188	P43220	GLP1R_HUMAN	N	188	ENSP00000362353:I188N	ENSP00000362353:I188N	I	+	2	0	GLP1R	39148669	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.015000	0.88690	2.188000	0.69820	0.533000	0.62120	ATC	.	.		0.572	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1			A	39040691	T	A	39040691	3	1	73	1	0	0	0	0	1	0	0	0	6460	1435	50	4	585	4	GLP1R	6	39040691	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	46287	39040691	132074376	223	9549										
FRS3	10817	hgsc.bcm.edu	37	chr6	41739273	41739273	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgttgacataggtgtgggacTggggaaagagtccaagtgag	17	4	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:41739273T>A	ENST00000373018.3	-	7	816		c.e7-2		FRS3_ENST00000259748.2_Splice_Site	NM_006653.3	NP_006644.1	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3						fibroblast growth factor receptor signaling pathway (GO:0008543)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GGTGTGGGACTGGGGAAAGAG	0.592																																					.		Atlas-SNP	.											.	FRS3	53	.	0			c.565-2A>T						.						51	50	50					6																	41739273		2197	4269	6466	SO:0001630	splice_region_variant	10817	exon8			TGGGACTGGGGAA	AF036718	CCDS4860.1	6p21.1	2010-08-05			ENSG00000137218	ENSG00000137218			16970	protein-coding gene	gene with protein product		607744				8761293, 9660748	Standard	NM_006653		Approved	SNT-2, FRS2beta, FRS2B	uc003orc.1	O43559	OTTHUMG00000014686	ENST00000373018.3:c.565-2A>T	chr6.hg19:g.41739273T>A		16.0	0.0		37.0	11.0	NM_006653	Q5T3D5	Splice_Site	SNP	ENST00000373018.3	hg19	CCDS4860.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.310789	0.60414	.	.	ENSG00000137218	ENST00000373018;ENST00000259748	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1394	0.72599	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FRS3	41847251	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	7.400000	0.79949	2.073000	0.62155	0.533000	0.62120	.	.	.		0.592	FRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040532.2	NM_006653	Intron	A	41739273	T	A	41739273	5	1	73	1	0	0	0	0	0	0	1	0	6070	1594	55	4	919	4	FRS3	6	41739273	Splice_Site	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2698582	41739273	129375794	224	9550										
PTK7	5754	hgsc.bcm.edu	37	chr6	43109672	43109672	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtctcttttcttccagtttTtatcaccttcaaagtggaac	6	10	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:43109672T>A	ENST00000230419.4	+	12	1993	c.1772T>A	c.(1771-1773)tTt>tAt	p.F591Y	PTK7_ENST00000352931.2_Missense_Mutation_p.F591Y|PTK7_ENST00000481273.1_Missense_Mutation_p.F599Y|PTK7_ENST00000345201.2_Missense_Mutation_p.F551Y|PTK7_ENST00000349241.2_Missense_Mutation_p.F461Y	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	591	Ig-like C2-type 7.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			CTTCCAGTTTTTATCACCTTC	0.627																																					p.F599Y		Atlas-SNP	.											.	PTK7	101	.	0			c.T1796A						.						53	60	57					6																	43109672		2203	4300	6503	SO:0001583	missense	5754	exon12			CAGTTTTTATCAC	AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.1772T>A	chr6.hg19:g.43109672T>A	ENSP00000230419:p.Phe591Tyr	49.0	0.0		88.0	27.0	NM_001270398	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Missense_Mutation	SNP	ENST00000230419.4	hg19	CCDS4884.1	.	.	.	.	.	.	.	.	.	.	T	7.162	0.585833	0.13749	.	.	ENSG00000112655	ENST00000230419;ENST00000349241;ENST00000352931;ENST00000345201;ENST00000481273	T;T;T;T;T	0.73469	-0.67;-0.75;1.58;-0.68;-0.7	4.96	4.96	0.65561	Immunoglobulin-like (1);	0.163195	0.56097	D	0.000030	T	0.28599	0.0708	N	0.05441	-0.05	0.35271	D	0.780454	B;B;B;B;B	0.10296	0.0;0.003;0.001;0.003;0.0	B;B;B;B;B	0.13407	0.001;0.009;0.005;0.009;0.002	T	0.10177	-1.0641	10	0.02654	T	1	.	10.5783	0.45240	0.1532:0.0:0.0:0.8468	.	599;461;551;591;591	E9PFZ5;Q13308-3;Q13308-2;Q13308-4;Q13308	.;.;.;.;PTK7_HUMAN	Y	591;461;591;551;599	ENSP00000230419:F591Y;ENSP00000325462:F461Y;ENSP00000326029:F591Y;ENSP00000325992:F551Y;ENSP00000418754:F599Y	ENSP00000230418:F591Y	F	+	2	0	PTK7	43217650	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	2.778000	0.47726	1.859000	0.53934	0.459000	0.35465	TTT	.	.		0.627	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2			A	43109672	T	A	43109672	3	1	73	1	0	0	0	0	1	0	0	0	12778	1841	64	4	1818	4	PTK7	6	43109672	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1370399	43109672	128005395	225	9551										
CUL9	23113	hgsc.bcm.edu	37	chr6	43155101	43155101	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccaggctgaatggtgggagcTgcttttctttatcaaaaagt	11	7	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:43155101T>C	ENST00000252050.4	+	6	1589	c.1505T>C	c.(1504-1506)cTg>cCg	p.L502P	CUL9_ENST00000354495.3_Intron|CUL9_ENST00000372647.2_Missense_Mutation_p.L502P	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	502					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						TGGTGGGAGCTGCTTTTCTTT	0.478																																					p.L502P		Atlas-SNP	.											.	CUL9	248	.	0			c.T1505C						.						139	145	143					6																	43155101		2203	4300	6503	SO:0001583	missense	23113	exon6			GGGAGCTGCTTTT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.1505T>C	chr6.hg19:g.43155101T>C	ENSP00000252050:p.Leu502Pro	110.0	0.0		187.0	25.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.091403	0.76756	.	.	ENSG00000112659	ENST00000252050;ENST00000372647	T;T	0.80653	-1.4;-1.3	5.01	5.01	0.66863	.	0.143295	0.47852	D	0.000217	D	0.83876	0.5349	L	0.60455	1.87	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66196	0.942;0.942	D	0.86533	0.1823	10	0.87932	D	0	-10.7577	14.7211	0.69308	0.0:0.0:0.0:1.0	.	502;502	E9PEZ1;Q8IWT3	.;CUL9_HUMAN	P	502	ENSP00000252050:L502P;ENSP00000361730:L502P	ENSP00000252050:L502P	L	+	2	0	CUL9	43263079	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	7.132000	0.77251	1.883000	0.54544	0.383000	0.25322	CTG	.	.		0.478	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		C	43155101	T	C	43155101	3	2	73	1	0	0	0	0	1	0	0	0	4063	1580	55	2	1523	2	CUL9	6	43155101	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	45429	43155101	127959966	226	9552										
GPR116	221395	hgsc.bcm.edu	37	chr6	46826559	46826559	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tccacaactagacaggctgcCaagctcaagatggaaaagcc	9	12	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:46826559C>A	ENST00000283296.7	-	17	3369	c.3081G>T	c.(3079-3081)ttG>ttT	p.L1027F	GPR116_ENST00000545669.1_Missense_Mutation_p.L456F|GPR116_ENST00000362015.4_Missense_Mutation_p.L1027F|GPR116_ENST00000456426.2_Missense_Mutation_p.L885F|GPR116_ENST00000265417.7_Missense_Mutation_p.L1027F	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	1027					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			GACAGGCTGCCAAGCTCAAGA	0.507																																					p.L1027F	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											GPR116,right_lower_lobe,carcinoma,0,1	GPR116	133	.	0			c.G3081T						.						46	48	47					6																	46826559		2203	4300	6503	SO:0001583	missense	221395	exon17			GGCTGCCAAGCTC	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.3081G>T	chr6.hg19:g.46826559C>A	ENSP00000283296:p.Leu1027Phe	100.0	1.0		148.0	42.0	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	hg19	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.164409	0.57476	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000545557;ENST00000265417;ENST00000545669	T;T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5;-0.5	5.61	-0.631	0.11526	GPCR, family 2-like (1);	0.000000	0.47093	D	0.000246	T	0.80773	0.4687	M	0.90483	3.12	0.46927	D	0.999251	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.999;1.0	D	0.84268	0.0487	10	0.87932	D	0	-15.4006	12.83	0.57740	0.0:0.6171:0.0:0.3829	.	456;582;1027;885;1027	F5GWK9;B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;.;GP116_HUMAN	F	1027;1027;1027;885;398;1027;456	ENSP00000283296:L1027F;ENSP00000354563:L1027F;ENSP00000412866:L885F;ENSP00000265417:L1027F;ENSP00000441581:L456F	ENSP00000265417:L1027F	L	-	3	2	GPR116	46934518	1.000000	0.71417	0.995000	0.50966	0.883000	0.51084	0.715000	0.25822	-0.102000	0.12197	0.650000	0.86243	TTG	.	.		0.507	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		A	46826559	C	A	46826559	3	1	73	1	0	0	0	0	1	0	0	0	6641	593	21	3	979	3	GPR116	6	46826559	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	3671458	46826559	124288508	227	9553										
GPR110	266977	hgsc.bcm.edu	37	chr6	46976727	46976727	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	taacatgccaagccagattcTggctgtccactattgttcct	7	12	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:46976727T>A	ENST00000371253.2	-	11	2659	c.2444A>T	c.(2443-2445)cAg>cTg	p.Q815L	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.Q618L	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	815					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						AGCCAGATTCTGGCTGTCCAC	0.468																																					p.Q815L		Atlas-SNP	.											.	GPR110	102	.	0			c.A2444T						.						57	60	59					6																	46976727		2203	4300	6503	SO:0001583	missense	266977	exon11			AGATTCTGGCTGT	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.2444A>T	chr6.hg19:g.46976727T>A	ENSP00000360299:p.Gln815Leu	275.0	0.0		457.0	122.0	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	hg19	CCDS34471.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.015521	0.35511	.	.	ENSG00000153292	ENST00000371253;ENST00000283297	T;T	0.41065	1.01;1.01	5.9	3.48	0.39840	GPCR, family 2-like (1);	0.345458	0.25247	N	0.032044	T	0.15046	0.0363	L	0.49778	1.585	0.09310	N	1	B	0.17667	0.023	B	0.17979	0.02	T	0.22243	-1.0222	10	0.35671	T	0.21	0.0443	5.8397	0.18627	0.1192:0.1788:0.0:0.702	.	815	Q5T601	GP110_HUMAN	L	815;618	ENSP00000360299:Q815L;ENSP00000283297:Q618L	ENSP00000283297:Q618L	Q	-	2	0	GPR110	47084686	0.001000	0.12720	0.271000	0.24616	0.773000	0.43773	0.199000	0.17237	0.468000	0.27243	0.528000	0.53228	CAG	.	.		0.468	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		A	46976727	T	A	46976727	3	1	73	1	0	0	0	0	1	0	0	0	6635	1580	55	4	308	4	GPR110	6	46976727	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	150168	46976727	124138340	228	9554										
FAM83B	222584	hgsc.bcm.edu	37	chr6	54804890	54804890	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggtccaaacgcaatacgtcAgtttcaacccaatcagataa	6	11	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:54804890A>T	ENST00000306858.7	+	5	1237	c.1121A>T	c.(1120-1122)cAg>cTg	p.Q374L		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	374										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					GCAATACGTCAGTTTCAACCC	0.373																																					p.Q374L		Atlas-SNP	.											.	FAM83B	186	.	0			c.A1121T						.						68	67	67					6																	54804890		2203	4300	6503	SO:0001583	missense	222584	exon5			TACGTCAGTTTCA	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 143"	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.1121A>T	chr6.hg19:g.54804890A>T	ENSP00000304078:p.Gln374Leu	239.0	0.0		409.0	95.0	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	hg19	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	A	1.169	-0.641448	0.03531	.	.	ENSG00000168143	ENST00000306858	T	0.07800	3.16	5.33	2.84	0.33178	.	0.307924	0.32608	N	0.005862	T	0.03564	0.0102	M	0.62723	1.935	0.30000	N	0.816145	B	0.27498	0.18	B	0.26614	0.071	T	0.34304	-0.9834	10	0.26408	T	0.33	-0.2789	12.3569	0.55180	0.7329:0.2671:0.0:0.0	.	374	Q5T0W9	FA83B_HUMAN	L	374	ENSP00000304078:Q374L	ENSP00000304078:Q374L	Q	+	2	0	FAM83B	54912849	0.994000	0.37717	0.939000	0.37840	0.071000	0.16799	1.942000	0.40243	0.379000	0.24794	0.402000	0.26972	CAG	.	.		0.373	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		T	54804890	A	T	54804890	3	4	73	1	0	0	0	0	1	0	0	0	5642	188	7	4	1135	4	FAM83B	6	54804890	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	7828163	54804890	116310177	229	9555										
DST	667	hgsc.bcm.edu	37	chr6	56328485	56328485	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggatcttcggcctcggggtcGgaaagcagccataccctggc	14	13	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:56328485G>A	ENST00000361203.3	-	96	21884	c.21877C>T	c.(21877-21879)Cga>Tga	p.R7293*	DST_ENST00000312431.6_3'UTR|DST_ENST00000370754.5_Nonsense_Mutation_p.R7582*|DST_ENST00000370769.4_Nonsense_Mutation_p.R7404*|DST_ENST00000421834.2_Nonsense_Mutation_p.R5289*|DST_ENST00000370788.2_Nonsense_Mutation_p.R5207*|DST_ENST00000244364.6_Nonsense_Mutation_p.R4966*|DST_ENST00000446842.2_Nonsense_Mutation_p.R7078*			Q03001	DYST_HUMAN	dystonin	7402	GAR. {ECO:0000255|PROSITE- ProRule:PRU00792}.				axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CCTCGGGGTCGGAAAGCAGCC	0.562																																					p.R4966X		Atlas-SNP	.											.	DST	1427	.	0			c.C14896T						.						132	140	137					6																	56328485		2006	4153	6159	SO:0001587	stop_gained	667	exon81			GGGGTCGGAAAGC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.21877C>T	chr6.hg19:g.56328485G>A	ENSP00000354508:p.Arg7293*	83.0	0.0		168.0	30.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Nonsense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	G	59	34.662893	0.99982	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	.	.	.	5.82	5.82	0.92795	.	0.000000	0.45606	D	0.000354	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.3941	0.83550	0.0:0.0:0.8679:0.1321	.	.	.	.	X	4966;7582;7404;5289;7078;5207;7293	.	ENSP00000244364:R4966X	R	-	1	2	DST	56436444	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.531000	0.67148	2.748000	0.94277	0.655000	0.94253	CGA	.	.		0.562	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56328485	G	A	56328485	4	1	73	1	0	0	0	0	0	1	0	0	4785	1124	39	1	635	1	DST	6	56328485	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1523595	56328485	114786582	230	9556										
DST	667	hgsc.bcm.edu	37	chr6	56497806	56497806	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtagattacttagaacttgCtgatgttcaccaggtagcat	9	7	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:56497806C>A	ENST00000361203.3	-	24	3025	c.3018G>T	c.(3016-3018)caG>caT	p.Q1006H	DST_ENST00000312431.6_Missense_Mutation_p.Q1006H|DST_ENST00000370765.6_Missense_Mutation_p.Q680H|DST_ENST00000518935.1_Missense_Mutation_p.Q680H|DST_ENST00000370754.5_Missense_Mutation_p.Q1184H|DST_ENST00000370769.4_Missense_Mutation_p.Q1006H|DST_ENST00000421834.2_Missense_Mutation_p.Q1006H|DST_ENST00000370788.2_Missense_Mutation_p.Q1006H|DST_ENST00000244364.6_Missense_Mutation_p.Q680H|DST_ENST00000446842.2_Missense_Mutation_p.Q680H			Q03001	DYST_HUMAN	dystonin	1006					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTAGAACTTGCTGATGTTCAC	0.373																																					p.Q680H		Atlas-SNP	.											.	DST	1427	.	0			c.G2040T						.						101	99	100					6																	56497806		2203	4300	6503	SO:0001583	missense	667	exon14			AACTTGCTGATGT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.3018G>T	chr6.hg19:g.56497806C>A	ENSP00000354508:p.Gln1006His	94.0	0.0		136.0	26.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	C	17.12	3.309168	0.60414	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19	5.69	0.844	0.18943	.	0.000000	0.51477	D	0.000086	T	0.25082	0.0609	N	0.21617	0.685	0.32732	N	0.508842	D;D;D;B;B;D;D;D	0.89917	0.998;0.996;0.998;0.093;0.178;0.997;0.998;1.0	D;D;D;B;B;D;D;D	0.91635	0.993;0.986;0.993;0.028;0.234;0.991;0.993;0.999	T	0.05971	-1.0853	9	0.25106	T	0.35	.	10.9933	0.47561	0.0:0.6812:0.0:0.3188	.	1006;1006;1184;680;680;680;1006;680	Q5TBT1;E7ERU2;E9PEB9;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;DYST_HUMAN;.	H	680;1184;1006;1006;680;1006;1006;1006;680;1046;680;680	ENSP00000244364:Q680H;ENSP00000359790:Q1184H;ENSP00000359805:Q1006H;ENSP00000400883:Q1006H;ENSP00000393645:Q680H;ENSP00000307959:Q1006H;ENSP00000359824:Q1006H;ENSP00000354508:Q1006H;ENSP00000404924:Q680H;ENSP00000431030:Q1046H;ENSP00000359801:Q680H;ENSP00000431003:Q680H	ENSP00000244364:Q680H	Q	-	3	2	DST	56605765	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	1.341000	0.33907	0.154000	0.19237	-0.141000	0.14075	CAG	.	.		0.373	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56497806	C	A	56497806	3	1	73	1	0	0	0	0	1	0	0	0	4785	796	28	3	18399	3	DST	6	56497806	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	169321	56497806	114617261	231	9557										
KIAA1586	57691	hgsc.bcm.edu	37	chr6	56917944	56917944	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acatgatgtttctaaagcccAtggtaaaattcaggatttgt	8	6	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:56917944A>G	ENST00000370733.4	+	4	854	c.647A>G	c.(646-648)cAt>cGt	p.H216R	KIAA1586_ENST00000545356.1_Missense_Mutation_p.H189R	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	216							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TCTAAAGCCCATGGTAAAATT	0.294																																					p.H216R		Atlas-SNP	.											.	KIAA1586	59	.	0			c.A647G						.						45	48	47					6																	56917944		2201	4298	6499	SO:0001583	missense	57691	exon4			AAGCCCATGGTAA	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.647A>G	chr6.hg19:g.56917944A>G	ENSP00000359768:p.His216Arg	128.0	0.0		260.0	61.0	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	hg19	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	a	7.582	0.668909	0.14776	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.45276	0.93;0.9	4.02	1.49	0.22878	.	.	.	.	.	T	0.10723	0.0262	N	0.08118	0	0.21290	N	0.999735	P;P	0.51537	0.946;0.946	P;P	0.47603	0.551;0.551	T	0.04752	-1.0929	9	0.52906	T	0.07	.	3.2528	0.06820	0.6829:0.0:0.1135:0.2036	.	189;216	F5H2N6;Q9HCI6	.;K1586_HUMAN	R	216;189	ENSP00000359768:H216R;ENSP00000445507:H189R	ENSP00000359768:H216R	H	+	2	0	KIAA1586	57025903	0.999000	0.42202	0.956000	0.39512	0.007000	0.05969	2.587000	0.46128	0.195000	0.20347	-0.456000	0.05471	CAT	.	.		0.294	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		G	56917944	A	G	56917944	3	3	73	1	0	0	0	0	1	0	0	0	8254	217	8	2	661	2	KIAA1586	6	56917944	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	420138	56917944	114197123	232	9558										
LGSN	51557	hgsc.bcm.edu	37	chr6	63990332	63990334	+	In_Frame_Del	DEL	TCT	TCT	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	taggcacactcttcttcaggTctttcctgtccttggaataa							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:63990332_63990334delTCT	ENST00000370657.4	-	4	1155_1157	c.1122_1124delAGA	c.(1120-1125)aaagac>aac	p.374_375KD>N	LGSN_ENST00000370658.5_3'UTR			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	374					glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)			NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CTTCTTCAGGTCTTTCCTGTCCT	0.458																																					p.375_375del		Atlas-Indel,Pindel	.											.	LGSN	82	.	0			c.1123_1125del						.																																			SO:0001651	inframe_deletion	51557	exon4			.	AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"glutamate-ammonia ligase (glutamine synthetase) domain containing 1"	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.1122_1124delAGA	chr6.hg19:g.63990332_63990334delTCT	ENSP00000359691:p.Lys374_Asp375delinsAsn	74.0	0.0		76.0	39.0	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	In_Frame_Del	DEL	ENST00000370657.4	hg19	CCDS4964.1																																																																																			.	.		0.458	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571		-	63990334	TCT	-	63990332	7	5	73	1	0	1	0	1	0	0	0	0	8768	1667	58	0	409	0	LGSN	6	63990332	In_Frame_Del	DEL	TCT	TCGA-CC-A7IH-01A-11D-A33K-10	7072388	63990332	107124735	233	9559										
PHF3	23469	hgsc.bcm.edu	37	chr6	64389990	64389990	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagaactgattttacctaacAggaacttaagggacaaggta	9	6	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:64389990A>T	ENST00000262043.3	+	3	674	c.334A>T	c.(334-336)Agg>Tgg	p.R112W	PHF3_ENST00000393387.1_Missense_Mutation_p.R112W|PHF3_ENST00000509330.1_Missense_Mutation_p.R112W			Q92576	PHF3_HUMAN	PHD finger protein 3	112					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			TTTACCTAACAGGAACTTAAG	0.368																																					p.R112W	GBM(135;136 1820 29512 34071 46235)	Atlas-SNP	.											.	PHF3	191	.	0			c.A334T						.						148	147	147					6																	64389990		2203	4300	6503	SO:0001583	missense	23469	exon2			CCTAACAGGAACT	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.334A>T	chr6.hg19:g.64389990A>T	ENSP00000262043:p.Arg112Trp	149.0	0.0		124.0	60.0	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	hg19	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	A	16.01	3.001226	0.54254	.	.	ENSG00000118482	ENST00000481385;ENST00000262043;ENST00000494284;ENST00000509330;ENST00000393387;ENST00000514822	T;T;T;T;T	0.60424	1.17;1.55;1.22;0.19;1.55	5.34	5.34	0.76211	.	0.000000	0.44285	D	0.000464	T	0.66147	0.2760	M	0.62723	1.935	0.39866	D	0.973446	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	T	0.71474	-0.4582	10	0.87932	D	0	-16.0157	12.6212	0.56603	0.8624:0.1376:0.0:0.0	.	112;112	Q92576;D6R9X2	PHF3_HUMAN;.	W	24;112;65;112;112;42	ENSP00000425227:R24W;ENSP00000262043:R112W;ENSP00000424078:R65W;ENSP00000422841:R112W;ENSP00000377048:R112W	ENSP00000262043:R112W	R	+	1	2	PHF3	64447949	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.818000	0.62657	2.242000	0.73789	0.482000	0.46254	AGG	.	.		0.368	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			T	64389990	A	T	64389990	3	4	73	1	0	0	0	0	1	0	0	0	11845	179	7	4	340	4	PHF3	6	64389990	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	399658	64389990	106725077	234	9560										
LMBRD1	55788	hgsc.bcm.edu	37	chr6	70411411	70411411	+	Frame_Shift_Del	DEL	C	C	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttatgaaaccagaatctattCcagctgaatgaagagcttta							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:70411411delC	ENST00000370577.3	-	11	1236	c.1007delG	c.(1006-1008)ggafs	p.G336fs	LMBRD1_ENST00000370570.1_Frame_Shift_Del_p.G263fs	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	336					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						AGAATCTATTCCAGCTGAATG	0.249																																					p.G336fs		Atlas-Indel,Pindel	.											.	LMBRD1	61	.	0			c.1008delA						.						47	47	47					6																	70411411		2198	4288	6486	SO:0001589	frameshift_variant	55788	exon11			.	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1007delG	chr6.hg19:g.70411411delC	ENSP00000359609:p.Gly336fs	211.0	0.0		240.0	99.0	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Frame_Shift_Del	DEL	ENST00000370577.3	hg19	CCDS4969.1																																																																																			.	.		0.249	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		-	70411411	C	-	70411411	7	5	73	1	0	1	0	1	0	0	0	0	8851	855	30	0	639	0	LMBRD1	6	70411411	Frame_Shift_Del	DEL	C	TCGA-CC-A7IH-01A-11D-A33K-10	6021421	70411411	100703656	235	9561										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72892030	72892030	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agcagaatggcaaaggagccCtgaagagcgagcggaaacgc	15	9	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:72892030C>G	ENST00000521978.1	+	6	856	c.856C>G	c.(856-858)Ctg>Gtg	p.L286V	RIMS1_ENST00000520567.1_Missense_Mutation_p.L286V|RIMS1_ENST00000518273.1_Missense_Mutation_p.L286V|RIMS1_ENST00000491071.2_Missense_Mutation_p.L286V|RIMS1_ENST00000522291.1_Missense_Mutation_p.L286V|RIMS1_ENST00000517960.1_Missense_Mutation_p.L286V|RIMS1_ENST00000348717.5_Missense_Mutation_p.L286V|RIMS1_ENST00000264839.7_Missense_Mutation_p.L286V	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	286					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				CAAAGGAGCCCTGAAGAGCGA	0.527																																					p.L286V		Atlas-SNP	.											.	RIMS1	278	.	0			c.C856G						.						34	39	38					6																	72892030		1860	4105	5965	SO:0001583	missense	22999	exon6			GGAGCCCTGAAGA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.856C>G	chr6.hg19:g.72892030C>G	ENSP00000428417:p.Leu286Val	295.0	0.0		279.0	128.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	C	3.492	-0.103609	0.06967	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.13778	2.56;2.71;2.64;2.71;2.71;2.71;2.71;2.63	5.28	3.48	0.39840	.	0.839746	0.10019	N	0.726184	T	0.03915	0.0110	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38499	-0.9658	10	0.31617	T	0.26	3.3874	8.7095	0.34376	0.0:0.7562:0.0:0.2438	.	286	Q86UR5	RIMS1_HUMAN	V	286	ENSP00000430101:L286V;ENSP00000275037:L286V;ENSP00000264839:L286V;ENSP00000429959:L286V;ENSP00000430408:L286V;ENSP00000430502:L286V;ENSP00000430932:L286V;ENSP00000428417:L286V	ENSP00000264839:L286V	L	+	1	2	RIMS1	72948751	0.000000	0.05858	0.004000	0.12327	0.340000	0.28889	-0.160000	0.10041	1.238000	0.43771	0.462000	0.41574	CTG	.	.		0.527	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			G	72892030	C	G	72892030	3	3	73	1	0	0	0	0	1	0	0	0	13382	680	24	4	878	4	RIMS1	6	72892030	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	2480619	72892030	98223037	236	9562										
TTK	7272	hgsc.bcm.edu	37	chr6	80746315	80746315	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagtgttgttaaagattctcAggtaagacttaatgttggtt	10	3	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:80746315A>G	ENST00000369798.2	+	17	2159	c.2048A>G	c.(2047-2049)cAg>cGg	p.Q683R	TTK_ENST00000509894.1_Splice_Site_p.Q682R|TTK_ENST00000230510.3_Splice_Site_p.Q682R	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	683	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		AAAGATTCTCAGGTAAGACTT	0.328																																					p.Q683R		Atlas-SNP	.											.	TTK	199	.	0			c.A2048G						.						109	104	106					6																	80746315		2202	4299	6501	SO:0001630	splice_region_variant	7272	exon17			ATTCTCAGGTAAG		CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"cancer/testis antigen 96", "monopolar spindle 1 kinase"	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.2049+1A>G	chr6.hg19:g.80746315A>G		87.0	0.0		104.0	39.0	NM_003318	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	hg19	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	A	18.50	3.638097	0.67130	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798	T;T;T	0.64260	-0.09;-0.09;-0.09	6.08	6.08	0.98989	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.41949	0.1181	N	0.11789	0.175	0.80722	D	1	B;B	0.30211	0.273;0.269	B;B	0.41619	0.361;0.224	T	0.53236	-0.8467	10	0.49607	T	0.09	.	15.8323	0.78764	1.0:0.0:0.0:0.0	.	683;682	P33981;A8K8U5	TTK_HUMAN;.	R	682;682;683	ENSP00000422936:Q682R;ENSP00000230510:Q682R;ENSP00000358813:Q683R	ENSP00000230510:Q682R	Q	+	2	0	TTK	80803034	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.813000	0.69201	2.333000	0.79357	0.482000	0.46254	CAG	.	.		0.328	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2		Missense_Mutation	G	80746315	A	G	80746315	5	3	73	1	0	0	0	0	0	0	1	0	16735	202	7	2	2110	2	TTK	6	80746315	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	7854285	80746315	90368752	237	9563										
SPACA1	81833	hgsc.bcm.edu	37	chr6	88757710	88757710	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggcctccagtccgcgcgcggGaccaacgtcaccgctgccgt	13	18	1	0	rs376457887		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:88757710G>A	ENST00000237201.1	+	1	204	c.87G>A	c.(85-87)ggG>ggA	p.G29G		NM_030960.2	NP_112222.1	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1	29					acrosome assembly (GO:0001675)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	20		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.11)		CCGCGCGCGGGACCAACGTCA	0.706																																					p.G29G		Atlas-SNP	.											.	SPACA1	49	.	0			c.G87A						.	G		0,4334		0,0,2167	24	18	20		87	0.8	0	6		20	1,8505		0,1,4252	no	coding-synonymous	SPACA1	NM_030960.2		0,1,6419	AA,AG,GG		0.0118,0.0,0.0078		29/295	88757710	1,12839	2167	4253	6420	SO:0001819	synonymous_variant	81833	exon1			GCGCGGGACCAAC	AF203447	CCDS5014.1	6q15	2012-09-20			ENSG00000118434	ENSG00000118434			14967	protein-coding gene	gene with protein product		612739					Standard	NM_030960		Approved	SAMP32	uc003pmn.3	Q9HBV2	OTTHUMG00000015183	ENST00000237201.1:c.87G>A	chr6.hg19:g.88757710G>A		114.0	0.0		119.0	51.0	NM_030960		Silent	SNP	ENST00000237201.1	hg19	CCDS5014.1																																																																																			.	.		0.706	SPACA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041459.1			A	88757710	G	A	88757710	2	1	73	1	0	0	0	0	0	0	0	1	14987	1161	41	3		3	SPACA1	6	88757710	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	8011395	88757710	82357357	238	9564										
RTN4IP1	84816	hgsc.bcm.edu	37	chr6	107076839	107076839	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttggacaactttgcttctccAgaagcaaaccgcagtgcatg	9	11	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:107076839A>G	ENST00000369063.3	-	1	523	c.58T>C	c.(58-60)Tgg>Cgg	p.W20R	QRSL1_ENST00000369046.4_5'Flank|RTN4IP1_ENST00000539449.1_Missense_Mutation_p.W20R|QRSL1_ENST00000369044.1_5'Flank	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	20						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		TTGCTTCTCCAGAAGCAAACC	0.413																																					p.W20R		Atlas-SNP	.											.	RTN4IP1	31	.	0			c.T58C						.						87	84	85					6																	107076839		2203	4300	6503	SO:0001583	missense	84816	exon1			TTCTCCAGAAGCA	AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.58T>C	chr6.hg19:g.107076839A>G	ENSP00000358059:p.Trp20Arg	78.0	0.0		76.0	36.0	NM_032730	Q8N9B3|Q8WZ66|Q9BRA4	Missense_Mutation	SNP	ENST00000369063.3	hg19	CCDS5056.1	.	.	.	.	.	.	.	.	.	.	A	12.97	2.096137	0.36952	.	.	ENSG00000130347	ENST00000539449;ENST00000369063	T;T	0.44083	0.93;2.0	5.85	-0.778	0.10977	.	0.785180	0.12360	N	0.475779	T	0.10208	0.0250	L	0.36672	1.1	0.23192	N	0.998141	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.23511	-1.0186	10	0.30078	T	0.28	-0.9045	2.7538	0.05288	0.3685:0.4048:0.085:0.1417	.	20;20	G3V1R2;Q8WWV3	.;RT4I1_HUMAN	R	20	ENSP00000444261:W20R;ENSP00000358059:W20R	ENSP00000358059:W20R	W	-	1	0	RTN4IP1	107183532	0.997000	0.39634	0.989000	0.46669	0.961000	0.63080	0.417000	0.21214	0.427000	0.26145	0.533000	0.62120	TGG	.	.		0.413	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1			G	107076839	A	G	107076839	3	3	73	1	0	0	0	0	1	0	0	0	13744	188	7	2	1168	2	RTN4IP1	6	107076839	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	18319129	107076839	64038228	239	9565										
DSE	29940	hgsc.bcm.edu	37	chr6	116757673	116757673	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cactgtccacggagactctcAgcaactggatgtgttcatag	10	11	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:116757673A>T	ENST00000331677.3	+	7	2486	c.2042A>T	c.(2041-2043)cAg>cTg	p.Q681L	DSE_ENST00000537543.1_Missense_Mutation_p.Q700L|DSE_ENST00000452085.3_Missense_Mutation_p.Q681L|DSE_ENST00000359564.2_Missense_Mutation_p.Q681L			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	681					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		GGAGACTCTCAGCAACTGGAT	0.527																																					p.Q681L		Atlas-SNP	.											.	DSE	98	.	0			c.A2042T						.						102	98	99					6																	116757673		2203	4300	6503	SO:0001583	missense	29940	exon6			ACTCTCAGCAACT	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"squamous cell carcinoma antigen recognized by T cells 2"	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.2042A>T	chr6.hg19:g.116757673A>T	ENSP00000332151:p.Gln681Leu	110.0	0.0		118.0	55.0	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	hg19	CCDS5107.1	.	.	.	.	.	.	.	.	.	.	A	9.041	0.989636	0.18966	.	.	ENSG00000111817	ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T	0.62498	0.02;0.02;0.02;0.02	6.01	3.66	0.41972	.	0.287773	0.40469	N	0.001099	T	0.30541	0.0768	L	0.29908	0.895	0.46542	D	0.999093	B;B	0.21905	0.062;0.062	B;B	0.24701	0.055;0.037	T	0.28839	-1.0031	10	0.59425	D	0.04	-5.6812	6.2129	0.20640	0.6777:0.1293:0.193:0.0	.	700;681	B7Z765;Q9UL01	.;DSE_HUMAN	L	681;700;681;681	ENSP00000404049:Q681L;ENSP00000441152:Q700L;ENSP00000332151:Q681L;ENSP00000352567:Q681L	ENSP00000332151:Q681L	Q	+	2	0	DSE	116864366	1.000000	0.71417	0.546000	0.28166	0.558000	0.35554	4.160000	0.58164	1.098000	0.41479	0.528000	0.53228	CAG	.	.		0.527	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352		T	116757673	A	T	116757673	3	4	73	1	0	0	0	0	1	0	0	0	4776	188	7	4	2060	4	DSE	6	116757673	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	9680834	116757673	54357394	240	9566										
CLVS2	134829	hgsc.bcm.edu	37	chr6	123319264	123319264	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctggccaatctggaccactaTggcaggaagattctagtcct	10	11	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:123319264T>C	ENST00000275162.5	+	2	1677	c.342T>C	c.(340-342)taT>taC	p.Y114Y	CLVS2_ENST00000368438.1_Intron	NM_001010852.3	NP_001010852.2	Q5SYC1	CLVS2_HUMAN	clavesin 2	114	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	40						TGGACCACTATGGCAGGAAGA	0.483																																					p.Y114Y		Atlas-SNP	.											.	CLVS2	79	.	0			c.T342C						.						60	57	58					6																	123319264		2203	4300	6503	SO:0001819	synonymous_variant	134829	exon2			CCACTATGGCAGG	AK095527	CCDS34525.1	6q22.31	2009-10-14	2009-10-14	2009-10-14	ENSG00000146352	ENSG00000146352			23046	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 212", "chromosome 6 open reading frame 213", "retinaldehyde binding protein 1-like 2"	C6orf212, C6orf213, RLBP1L2		19651769	Standard	NM_001010852		Approved	bA160A10.4	uc003pzi.1	Q5SYC1	OTTHUMG00000015495	ENST00000275162.5:c.342T>C	chr6.hg19:g.123319264T>C		95.0	0.0		76.0	28.0	NM_001010852	B3KTG5|B4DHL0|C8UZT4|Q5SYC0	Silent	SNP	ENST00000275162.5	hg19	CCDS34525.1																																																																																			.	.		0.483	CLVS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042042.2	NM_001010852		C	123319264	T	C	123319264	2	2	73	1	0	0	0	0	0	0	0	1	3574	1471	51	2		2	CLVS2	6	123319264	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	6561591	123319264	47795803	241	9567										
ENPP3	5169	hgsc.bcm.edu	37	chr6	132006562	132006562	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	actgattattttcccagaatAaacttcttctacatgtacga	4	9	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:132006562A>T	ENST00000414305.1	+	14	1507	c.1179A>T	c.(1177-1179)atA>atT	p.I393I	ENPP3_ENST00000357639.3_Silent_p.I393I|ENPP3_ENST00000358229.5_Silent_p.I393I			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	393	Phosphodiesterase.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		TTCCCAGAATAAACTTCTTCT	0.348																																					p.I393I		Atlas-SNP	.											.	ENPP3	117	.	0			c.A1179T						.						132	147	142					6																	132006562		2203	4300	6503	SO:0001819	synonymous_variant	5169	exon13			CAGAATAAACTTC	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.1179A>T	chr6.hg19:g.132006562A>T		211.0	0.0		186.0	88.0	NM_005021	Q5JTL3	Silent	SNP	ENST00000414305.1	hg19	CCDS5148.1																																																																																			.	.		0.348	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2			T	132006562	A	T	132006562	2	4	73	1	0	0	0	0	0	0	0	1	5133	352	13	4		4	ENPP3	6	132006562	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	8687298	132006562	39108505	242	9568										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152765648	152765648	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gagccagaaattaattcttcGagagaatttttgactatttc	7	6	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:152765648G>T	ENST00000367255.5	-	30	4336	c.3735C>A	c.(3733-3735)ctC>ctA	p.L1245L	SYNE1_ENST00000413186.2_Silent_p.L1245L|SYNE1_ENST00000448038.1_Silent_p.L1252L|SYNE1_ENST00000367248.3_Silent_p.L1235L|SYNE1_ENST00000341594.5_Silent_p.L1311L|SYNE1_ENST00000367253.4_Silent_p.L1245L|SYNE1_ENST00000423061.1_Silent_p.L1252L|SYNE1_ENST00000265368.4_Silent_p.L1245L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1245					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.L1245L(2)|p.L1252L(1)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTAATTCTTCGAGAGAATTTT	0.348										HNSCC(10;0.0054)																											p.L1252L		Atlas-SNP	.											SYNE1_ENST00000423061,NS,carcinoma,0,3	SYNE1	3227	.	3	Substitution - coding silent(3)	lung(3)	c.C3756A						.						77	77	77					6																	152765648		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon30			TTCTTCGAGAGAA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.3735C>A	chr6.hg19:g.152765648G>T		101.0	0.0		60.0	33.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.348	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152765648	G	T	152765648	2	4	73	1	0	0	0	0	0	0	0	1	15460	1045	37	1		1	SYNE1	6	152765648	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	20759086	152765648	18349419	243	9569										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159654905	159654905	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agtctcccacaggcgcagggGcaggtggcgaccacaggtcc	15	14	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr6:159654905G>T	ENST00000297267.9	+	11	3561	c.3361G>T	c.(3361-3363)Gca>Tca	p.A1121S	FNDC1_ENST00000340366.6_Missense_Mutation_p.A1058S	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1121					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AGGCGCAGGGGCAGGTGGCGA	0.776																																					p.A1121S		Atlas-SNP	.											.	FNDC1	250	.	0			c.G3361T						.						5	8	7					6																	159654905		1714	3287	5001	SO:0001583	missense	84624	exon11			GCAGGGGCAGGTG	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3361G>T	chr6.hg19:g.159654905G>T	ENSP00000297267:p.Ala1121Ser	44.0	0.0		53.0	32.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	hg19	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.612|3.612	-0.079315|-0.079315	0.07141|0.07141	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000297267;ENST00000340366|ENST00000329629	T;T|T	0.06449|0.03065	3.3;4.13|4.06	0.235|0.235	0.235|0.235	0.15431|0.15431	.|.	1.560190|.	0.03980|.	N|.	0.293108|.	T|T	0.00967|0.00967	0.0032|0.0032	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	P;P|.	0.41597|.	0.756;0.643|.	P;B|.	0.48114|.	0.567;0.364|.	T|T	0.48210|0.48210	-0.9055|-0.9055	9|6	0.09338|0.62326	T|D	0.73|0.03	.|.	.|.	.|.	.|.	.|.	1058;1121|.	Q4ZHG4-2;Q4ZHG4|.	.;FNDC1_HUMAN|.	S|V	1121;1058|1016	ENSP00000297267:A1121S;ENSP00000342460:A1058S|ENSP00000333297:G1016V	ENSP00000297267:A1121S|ENSP00000333297:G1016V	A|G	+|+	1|2	0|0	FNDC1|FNDC1	159574895|159574895	0.022000|0.022000	0.18835|0.18835	0.002000|0.002000	0.10522|0.10522	0.002000|0.002000	0.02628|0.02628	0.364000|0.364000	0.20325|0.20325	0.308000|0.308000	0.22923|0.22923	0.313000|0.313000	0.20887|0.20887	GCA|GGC	.	.		0.776	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		T	159654905	G	T	159654905	3	4	73	1	0	0	0	0	1	0	0	0	5976	1203	42	3	3403	3	FNDC1	6	159654905	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	6889257	159654905	11460162	244	9570										
INTS1	26173	hgsc.bcm.edu	37	chr7	1513873	1513873	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgctcgctgcggaacacgtgCggctgcagcagctccagcag	14	14	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:1513873C>A	ENST00000404767.3	-	41	5845	c.5760G>T	c.(5758-5760)ccG>ccT	p.P1920P	INTS1_ENST00000389470.4_Silent_p.P2124P	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	1920					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GGAACACGTGCGGCTGCAGCA	0.687											OREG0017827	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P1920P		Atlas-SNP	.											.	INTS1	145	.	0			c.G5760T						.						19	27	24					7																	1513873		2110	4215	6325	SO:0001819	synonymous_variant	26173	exon41			CACGTGCGGCTGC	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.5760G>T	chr7.hg19:g.1513873C>A		19.0	0.0	596	21.0	11.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	hg19	CCDS47526.1																																																																																			.	.		0.687	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			A	1513873	C	A	1513873	2	1	73	1	0	0	0	0	0	0	0	1	7784	755	27	1		1	INTS1	7	1513873	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10		1513873	157624790	245	9571										
CARD11	84433	hgsc.bcm.edu	37	chr7	2968233	2968233	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tccctcacctgccacccaccTgcgatggggcgcgtcctcct	9	20	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:2968233T>A	ENST00000396946.4	-	13	2156	c.1753A>T	c.(1753-1755)Agc>Tgc	p.S585C		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	585					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GCCACCCACCTGCGATGGGGC	0.667			Mis		DLBCL																																p.S585C		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.A1753T						.						78	64	69					7																	2968233		2203	4300	6503	SO:0001630	splice_region_variant	84433	exon13			CCCACCTGCGATG	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1754+1A>T	chr7.hg19:g.2968233T>A		30.0	0.0		28.0	9.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	t	15.60	2.880610	0.51801	.	.	ENSG00000198286	ENST00000396946;ENST00000355508	T;T	0.53423	0.62;0.62	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.29716	0.0742	N	0.08118	0	0.54753	D	0.999985	B	0.17852	0.024	B	0.14578	0.011	T	0.12682	-1.0538	10	0.72032	D	0.01	-41.2281	13.2116	0.59828	0.0:0.0:0.0:1.0	.	585	Q9BXL7	CAR11_HUMAN	C	585;56	ENSP00000380150:S585C;ENSP00000347695:S56C	ENSP00000347695:S56C	S	-	1	0	CARD11	2934759	1.000000	0.71417	0.999000	0.59377	0.930000	0.56654	2.869000	0.48444	1.874000	0.54306	0.454000	0.30748	AGC	.	.		0.667	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	Missense_Mutation	A	2968233	T	A	2968233	5	1	73	1	0	0	0	0	0	0	1	0	2647	1594	55	4	1763	4	CARD11	7	2968233	Splice_Site	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1454360	2968233	156170430	246	9572										
HECW1	23072	hgsc.bcm.edu	37	chr7	43484497	43484497	+	Frame_Shift_Del	DEL	G	G	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcatgccctccgcccagggcGgcagcgcggcagaggaggag							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:43484497delG	ENST00000395891.2	+	11	2331	c.1726delG	c.(1726-1728)ggcfs	p.G576fs	HECW1_ENST00000453890.1_Frame_Shift_Del_p.G576fs	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	576					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CGCCCAGGGCGGCAGCGCGGC	0.697																																					p.G575fs		Pindel	.											.	HECW1	540	.	0			c.1725delC						.						29	35	33					7																	43484497		2136	4239	6375	SO:0001589	frameshift_variant	23072	exon11			.	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.1726delG	chr7.hg19:g.43484497delG	ENSP00000379228:p.Gly576fs	50.0	0.0		53.0	14.0	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Frame_Shift_Del	DEL	ENST00000395891.2	hg19	CCDS5469.2																																																																																			.	.		0.697	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		-	43484497	G	-	43484497	7	5	73	1	0	1	0	1	0	0	0	0	7051	1116	39	0	1760	0	HECW1	7	43484497	Frame_Shift_Del	DEL	G	TCGA-CC-A7IH-01A-11D-A33K-10	40516264	43484497	115654166	247	9573										
DBNL	28988	hgsc.bcm.edu	37	chr7	44096470	44096470	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctttcacaaggagagtggcCgcttccaggacgtgggaccc	14	12	1	1	rs145524590		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:44096470C>A	ENST00000448521.1	+	5	540	c.442C>A	c.(442-444)Cgc>Agc	p.R148S	DBNL_ENST00000497184.1_3'UTR|DBNL_ENST00000452943.1_Missense_Mutation_p.R123S|DBNL_ENST00000440166.1_Missense_Mutation_p.R45S|DBNL_ENST00000494774.1_Missense_Mutation_p.R148S|DBNL_ENST00000490734.2_Missense_Mutation_p.R53S|DBNL_ENST00000468694.1_Missense_Mutation_p.R148S|DBNL_ENST00000456905.1_Intron	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	148					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)			breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						GGAGAGTGGCCGCTTCCAGGA	0.617																																					p.R148S	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											.	DBNL	26	.	0			c.C442A						.						109	98	101					7																	44096470		2203	4300	6503	SO:0001583	missense	28988	exon5			AGTGGCCGCTTCC	AF151364	CCDS34622.1, CCDS34623.1, CCDS47579.1, CCDS64633.1, CCDS64634.1	7p13	2004-07-22			ENSG00000136279	ENSG00000136279			2696	protein-coding gene	gene with protein product		610106				10087302	Standard	NM_014063		Approved	SH3P7, HIP-55	uc003tjq.4	Q9UJU6	OTTHUMG00000155350	ENST00000448521.1:c.442C>A	chr7.hg19:g.44096470C>A	ENSP00000411701:p.Arg148Ser	81.0	0.0		90.0	13.0	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Missense_Mutation	SNP	ENST00000448521.1	hg19	CCDS34623.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.08|14.08	2.427840|2.427840	0.43122|0.43122	.|.	.|.	ENSG00000136279|ENSG00000136279	ENST00000432854|ENST00000448521;ENST00000440166;ENST00000452943;ENST00000468694;ENST00000494774;ENST00000490734;ENST00000539475	.|T;T;T;T;T;T	.|0.32272	.|1.9;2.16;2.18;1.46;1.92;2.16	4.9|4.9	1.93|1.93	0.25924|0.25924	.|.	.|0.240750	.|0.41605	.|N	.|0.000848	T|T	0.19446|0.19446	0.0467|0.0467	L|L	0.50333|0.50333	1.59|1.59	0.48571|0.48571	D|D	0.999675|0.999675	.|B;B;B;B;B;B;B;B	.|0.28378	.|0.209;0.065;0.063;0.147;0.051;0.107;0.013;0.015	.|B;B;B;B;B;B;B;B	.|0.26416	.|0.043;0.032;0.04;0.028;0.019;0.069;0.008;0.043	T|T	0.08411|0.08411	-1.0723|-1.0723	5|10	.|0.10636	.|T	.|0.68	-11.8848|-11.8848	3.1894|3.1894	0.06612|0.06612	0.4227:0.3492:0.1405:0.0876|0.4227:0.3492:0.1405:0.0876	.|.	.|45;96;78;53;123;148;148;148	.|B4DEM2;B4DXL9;B4DDU5;C9J7P1;B4DDD6;Q9UJU6-3;Q9UJU6;Q9UJU6-2	.|.;.;.;.;.;.;DBNL_HUMAN;.	Q|S	76|148;45;123;148;148;53;78	.|ENSP00000411701:R148S;ENSP00000415173:R45S;ENSP00000405343:R123S;ENSP00000417653:R148S;ENSP00000419992:R148S;ENSP00000417749:R53S	.|ENSP00000415173:R45S	P|R	+|+	2|1	0|0	DBNL|DBNL	44062995|44062995	1.000000|1.000000	0.71417|0.71417	0.724000|0.724000	0.30704|0.30704	0.873000|0.873000	0.50193|0.50193	2.321000|2.321000	0.43805|0.43805	0.090000|0.090000	0.17273|0.17273	0.456000|0.456000	0.33151|0.33151	CCG|CGC	.	C|1.000;T|0.000		0.617	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063		A	44096470	C	A	44096470	3	1	73	1	0	0	0	0	1	0	0	0	4257	652	23	1	460	1	DBNL	7	44096470	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	611973	44096470	115042193	248	9574										
TNS3	64759	hgsc.bcm.edu	37	chr7	47342734	47342734	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggtggctgcccgggcagggTcacaccctggccctgcaggc	17	15	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:47342734T>A	ENST00000398879.1	-	22	3637	c.3271A>T	c.(3271-3273)Acc>Tcc	p.T1091S	TNS3_ENST00000355730.3_Missense_Mutation_p.T851S|TNS3_ENST00000311160.9_Missense_Mutation_p.T1091S			Q68CZ2	TENS3_HUMAN	tensin 3	1091					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						CCGGGCAGGGTCACACCCTGG	0.662																																					p.T1091S		Atlas-SNP	.											.	TNS3	140	.	0			c.A3271T						.						21	26	24					7																	47342734		1978	4133	6111	SO:0001583	missense	64759	exon22			GCAGGGTCACACC	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.3271A>T	chr7.hg19:g.47342734T>A	ENSP00000381854:p.Thr1091Ser	112.0	0.0		100.0	11.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	hg19	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	T	0.102	-1.150754	0.01700	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000545849;ENST00000457718	D;D;D;D	0.93307	-2.78;-2.78;-3.2;-2.82	5.37	-2.45	0.06481	.	0.958022	0.08682	N	0.909361	T	0.78679	0.4321	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.69277	-0.5187	10	0.02654	T	1	-11.6978	5.192	0.15214	0.1412:0.3423:0.0:0.5166	.	1091	Q68CZ2	TENS3_HUMAN	S	1091;1201;1091;851;547;1194	ENSP00000312143:T1091S;ENSP00000381854:T1091S;ENSP00000347968:T851S;ENSP00000414358:T1194S	ENSP00000312143:T1091S	T	-	1	0	TNS3	47309259	0.005000	0.15991	0.001000	0.08648	0.309000	0.27889	1.062000	0.30555	-0.192000	0.10432	0.454000	0.30748	ACC	.	.		0.662	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		A	47342734	T	A	47342734	3	1	73	1	0	0	0	0	1	0	0	0	16359	1667	58	4	1106	4	TNS3	7	47342734	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3246264	47342734	111795929	249	9575										
IKZF1	10320	hgsc.bcm.edu	37	chr7	50467947	50467947	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcgtccccgagcaacagctgCcaagactccacggacaccga	10	17	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:50467947C>T	ENST00000331340.3	+	8	1337	c.1182C>T	c.(1180-1182)tgC>tgT	p.C394C	IKZF1_ENST00000343574.5_Silent_p.C307C|IKZF1_ENST00000357364.4_Silent_p.C307C|IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000346667.4_Silent_p.C164C|IKZF1_ENST00000439701.1_Silent_p.C352C|IKZF1_ENST00000349824.4_Silent_p.C251C|IKZF1_ENST00000438033.1_Silent_p.C307C|IKZF1_ENST00000359197.5_Silent_p.C352C	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	394					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(28)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				GCAACAGCTGCCAAGACTCCA	0.667			"D,T"	BCL6	"ALL, DLBCL"																																p.C394C		Atlas-SNP	.		"Rec,Dom"	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	28	Unknown(28)	haematopoietic_and_lymphoid_tissue(28)	c.C1182T						.						24	31	28					7																	50467947		2159	4242	6401	SO:0001819	synonymous_variant	10320	exon8			CAGCTGCCAAGAC	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13176	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 92"	603023	"zinc finger protein, subfamily 1A, 1 (Ikaros)"	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.1182C>T	chr7.hg19:g.50467947C>T		115.0	0.0		87.0	43.0	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Silent	SNP	ENST00000331340.3	hg19																																																																																				.	.		0.667	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060		T	50467947	C	T	50467947	2	4	73	1	0	0	0	0	0	0	0	1	7623	747	26	3		3	IKZF1	7	50467947	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	3125213	50467947	108670716	250	9576										
ZNF479	90827	hgsc.bcm.edu	37	chr7	57188114	57188115	+	Missense_Mutation	DNP	CC	CC	AA													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtctagtaaggtttgaggaCcagctaaaggctttgccaca					rs373275999		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:57188114_57188115CC>AA	ENST00000331162.4	-	5	1277_1278	c.1007_1008GG>TT	c.(1006-1008)tGG>tTT	p.W336F		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	336					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			GGTTTGAGGACCAGCTAAAGGC	0.455																																					p.W336C|p.W336L		Atlas-SNP	.											.	ZNF479	193	.	0			c.G1008T|c.G1007T						.																																			SO:0001583	missense	90827	exon5			TGAGGACCAGCTA|GAGGACCAGCTAA	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"Zinc fingers, C2H2-type", "-"	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.1007_1008delinsAA	chr7.hg19:g.57188114_57188115delinsAA	ENSP00000333776:p.Trp336Phe	202.0	0.0		188.0|187.0	67.0|68.0	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	hg19	CCDS43590.1																																																																																			.	.		0.455	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202		AA	57188115	CC	AA	57188114	3	1	73	1	0	0	0	0	1	0	0	0	17948	508	18	3	570	3	ZNF479	7	57188114	Missense_Mutation	DNP	CC	TCGA-CC-A7IH-01A-11D-A33K-10	6720167	57188114	101950549	251	9577										
DTX2	113878	hgsc.bcm.edu	37	chr7	76112438	76112438	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggaccgcagcacctgcccccAggatcctccacctccggtgc	10	20	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:76112438A>T	ENST00000324432.5	+	5	1392	c.882A>T	c.(880-882)ccA>ccT	p.P294P	DTX2_ENST00000446820.2_Silent_p.P294P|DTX2_ENST00000307569.8_Silent_p.P294P|DTX2_ENST00000446600.1_Silent_p.P203P|DTX2_ENST00000413936.2_Silent_p.P294P|DTX2_ENST00000430490.2_Silent_p.P294P	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	294					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						ACCTGCCCCCAGGATCCTCCA	0.652																																					p.P294P		Atlas-SNP	.											.	DTX2	64	.	0			c.A882T						.						21	23	22					7																	76112438		2196	4259	6455	SO:0001819	synonymous_variant	113878	exon2			GCCCCCAGGATCC		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"RING-type (C3HC4) zinc fingers"	15973	protein-coding gene	gene with protein product		613141	"deltex (Drosophila) homolog 2", "deltex homolog 2 (Drosophila)"			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.882A>T	chr7.hg19:g.76112438A>T		154.0	0.0		143.0	55.0	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	hg19	CCDS5587.1																																																																																			.	.		0.652	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2			T	76112438	A	T	76112438	2	4	73	1	0	0	0	0	0	0	0	1	4796	175	7	4		4	DTX2	7	76112438	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	18924324	76112438	83026225	252	9578										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81714106	81714106	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggataatatcgagctaggcCagtggcactgccaaaaacct	10	10	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:81714106C>A	ENST00000356253.5	-	7	892	c.637G>T	c.(637-639)Ggc>Tgc	p.G213C	CACNA2D1_ENST00000356860.3_Missense_Mutation_p.G213C|CACNA2D1_ENST00000423588.1_Missense_Mutation_p.G213C			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	213					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CGAGCTAGGCCAGTGGCACTG	0.423																																					p.G213C		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.G637T						.						100	98	99					7																	81714106		2203	4300	6503	SO:0001583	missense	781	exon7			CTAGGCCAGTGGC	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.637G>T	chr7.hg19:g.81714106C>A	ENSP00000348589:p.Gly213Cys	302.0	0.0		263.0	114.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	hg19		.	.	.	.	.	.	.	.	.	.	C	31	5.075395	0.94000	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000423588	T;T;T	0.71103	0.71;0.67;-0.54	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.88016	0.6324	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89273	0.3606	10	0.87932	D	0	-13.2343	20.0143	0.97474	0.0:1.0:0.0:0.0	.	213	P54289-2	.	C	213	ENSP00000349320:G213C;ENSP00000348589:G213C;ENSP00000405395:G213C	ENSP00000284088:G213C	G	-	1	0	CACNA2D1	81552042	1.000000	0.71417	0.974000	0.42286	0.995000	0.86356	7.673000	0.83973	2.831000	0.97527	0.650000	0.86243	GGC	.	.		0.423	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				A	81714106	C	A	81714106	3	1	73	1	0	0	0	0	1	0	0	0	2550	594	21	3	2770	3	CACNA2D1	7	81714106	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	5601668	81714106	77424557	253	9579										
PCLO	27445	hgsc.bcm.edu	37	chr7	82467649	82467649	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gagatttccaagatcatagtTaatttgaagctttaggagag	10	4	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:82467649T>C	ENST00000333891.9	-	15	14444	c.14107A>G	c.(14107-14109)Aac>Gac	p.N4703D	PCLO_ENST00000426442.2_5'UTR|PCLO_ENST00000423517.2_Missense_Mutation_p.N4703D	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AGATCATAGTTAATTTGAAGC	0.284																																					p.N4703D		Atlas-SNP	.											.	PCLO	1506	.	0			c.A14107G						.						41	39	40					7																	82467649		1796	4052	5848	SO:0001583	missense	27445	exon15			CATAGTTAATTTG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14107A>G	chr7.hg19:g.82467649T>C	ENSP00000334319:p.Asn4703Asp	72.0	0.0		66.0	22.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.992135	0.54041	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.41065	1.01;1.01	5.48	5.48	0.80851	.	.	.	.	.	T	0.51126	0.1656	N	0.21282	0.65	0.80722	D	1	D;D;P;P	0.69078	0.997;0.997;0.952;0.911	D;D;P;P	0.74348	0.983;0.983;0.817;0.662	T	0.56908	-0.7901	9	0.87932	D	0	.	15.5702	0.76330	0.0:0.0:0.0:1.0	.	4703;4703;133;200	Q9Y6V0-5;Q9Y6V0-6;Q9Y6V0-3;Q32P40	.;.;.;.	D	4703;4703;199	ENSP00000334319:N4703D;ENSP00000388393:N4703D	ENSP00000334319:N4703D	N	-	1	0	PCLO	82305585	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.579000	0.60936	2.060000	0.61445	0.533000	0.62120	AAC	.	.		0.284	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82467649	T	C	82467649	3	2	73	1	0	0	0	0	1	0	0	0	11592	1754	61	2	1382	2	PCLO	7	82467649	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	753543	82467649	76671014	254	9580										
PCLO	27445	hgsc.bcm.edu	37	chr7	82581285	82581285	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cttctgctaaatttgtgtcaGacatggaaggcttcattccc	8	10	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:82581285G>T	ENST00000333891.9	-	5	9321	c.8984C>A	c.(8983-8985)tCt>tAt	p.S2995Y	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Missense_Mutation_p.S2995Y	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ATTTGTGTCAGACATGGAAGG	0.413																																					p.S2995Y		Atlas-SNP	.											.	PCLO	1506	.	0			c.C8984A						.						183	176	178					7																	82581285		1862	4108	5970	SO:0001583	missense	27445	exon5			GTGTCAGACATGG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.8984C>A	chr7.hg19:g.82581285G>T	ENSP00000334319:p.Ser2995Tyr	161.0	0.0		168.0	85.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	9.990	1.230500	0.22542	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.55760	0.5;0.51	5.73	4.84	0.62591	.	.	.	.	.	T	0.71108	0.3301	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.75172	-0.3411	9	0.87932	D	0	.	16.0098	0.80391	0.0:0.0:0.8644:0.1356	.	2995;2995	Q9Y6V0-5;Q9Y6V0-6	.;.	Y	2926;2995;2995	ENSP00000334319:S2995Y;ENSP00000388393:S2995Y	ENSP00000334319:S2995Y	S	-	2	0	PCLO	82419221	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.867000	0.87062	1.375000	0.46248	0.557000	0.71058	TCT	.	.		0.413	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82581285	G	T	82581285	3	4	73	1	0	0	0	0	1	0	0	0	11592	942	33	3	6545	3	PCLO	7	82581285	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	113636	82581285	76557378	255	9581										
PCLO	27445	hgsc.bcm.edu	37	chr7	82764725	82764725	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggccttggctgaaggagagCcatgaagggttggttgtttc	16	6	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:82764725C>A	ENST00000333891.9	-	3	2478	c.2141G>T	c.(2140-2142)gGc>gTc	p.G714V	PCLO_ENST00000423517.2_Missense_Mutation_p.G714V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGAAGGAGAGCCATGAAGGGT	0.547																																					p.G714V		Atlas-SNP	.											.	PCLO	1506	.	0			c.G2141T						.						160	157	158					7																	82764725		1970	4157	6127	SO:0001583	missense	27445	exon3			GGAGAGCCATGAA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.2141G>T	chr7.hg19:g.82764725C>A	ENSP00000334319:p.Gly714Val	167.0	0.0		151.0	71.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	1.279	-0.610808	0.03690	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16897	2.31;2.31	5.79	4.91	0.64330	.	.	.	.	.	T	0.15955	0.0384	L	0.36672	1.1	0.42244	D	0.991943	P;P	0.42203	0.773;0.773	B;B	0.39465	0.3;0.3	T	0.02087	-1.1216	9	0.87932	D	0	.	13.0866	0.59144	0.0:0.9258:0.0:0.0742	.	714;714	Q9Y6V0-5;Q9Y6V0-6	.;.	V	660;714;714	ENSP00000334319:G714V;ENSP00000388393:G714V	ENSP00000334319:G714V	G	-	2	0	PCLO	82602661	0.004000	0.15560	0.124000	0.21820	0.150000	0.21749	1.702000	0.37836	1.444000	0.47605	0.591000	0.81541	GGC	.	.		0.547	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82764725	C	A	82764725	3	1	73	1	0	0	0	0	1	0	0	0	11592	739	26	3	13396	3	PCLO	7	82764725	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	183440	82764725	76373938	256	9582										
GRM3	2913	hgsc.bcm.edu	37	chr7	86416372	86416372	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctaccaagctttgtgatgctAtgaagatcctggatgggaag	12	7	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:86416372A>G	ENST00000361669.2	+	3	2363	c.1264A>G	c.(1264-1266)Atg>Gtg	p.M422V	AC005009.2_ENST00000452471.1_RNA|GRM3_ENST00000394720.2_Missense_Mutation_p.M420V|AC005009.2_ENST00000418031.1_RNA|GRM3_ENST00000536043.1_Missense_Mutation_p.M294V|GRM3_ENST00000546348.1_Intron|GRM3_ENST00000439827.1_Missense_Mutation_p.M422V	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	422					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					TTGTGATGCTATGAAGATCCT	0.463																																					p.M422V	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.A1264G						.						161	151	154					7																	86416372		2203	4300	6503	SO:0001583	missense	2913	exon3			GATGCTATGAAGA		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.1264A>G	chr7.hg19:g.86416372A>G	ENSP00000355316:p.Met422Val	135.0	0.0		89.0	9.0	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	hg19	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	A	18.69	3.677778	0.68042	.	.	ENSG00000198822	ENST00000361669;ENST00000536043;ENST00000439827;ENST00000394720	D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75	5.78	5.78	0.91487	Extracellular ligand-binding receptor (1);	0.037289	0.85682	D	0.000000	D	0.89543	0.6745	M	0.71581	2.175	0.80722	D	1	P;D;P	0.63880	0.669;0.993;0.717	B;D;P	0.63113	0.443;0.911;0.578	D	0.90671	0.4598	10	0.87932	D	0	.	15.287	0.73835	1.0:0.0:0.0:0.0	.	294;422;422	F5GYZ2;G5E9K2;Q14832	.;.;GRM3_HUMAN	V	422;294;422;420	ENSP00000355316:M422V;ENSP00000441407:M294V;ENSP00000398767:M422V;ENSP00000378209:M420V	ENSP00000355316:M422V	M	+	1	0	GRM3	86254308	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	5.896000	0.69822	2.196000	0.70406	0.533000	0.62120	ATG	.	.		0.463	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			G	86416372	A	G	86416372	3	3	73	1	0	0	0	0	1	0	0	0	6807	449	16	2	1270	2	GRM3	7	86416372	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3651647	86416372	72722291	257	9583										
FZD1	8321	hgsc.bcm.edu	37	chr7	90895564	90895564	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccgcctgggctgtgccggccAtcaagaccatcaccatcctg	10	17	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:90895564A>G	ENST00000287934.2	+	1	1782	c.1369A>G	c.(1369-1371)Atc>Gtc	p.I457V		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	457					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			TGTGCCGGCCATCAAGACCAT	0.637																																					p.I457V		Atlas-SNP	.											.	FZD1	64	.	0			c.A1369G						.						103	96	98					7																	90895564		2203	4300	6503	SO:0001583	missense	8321	exon1			CCGGCCATCAAGA	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"GPCR / Class F : Frizzled receptors"	4038	protein-coding gene	gene with protein product	"Wnt receptor", "frizzled, Drosophila, homolog of, 1"	603408	"frizzled (Drosophila) homolog 1", "frizzled homolog 1 (Drosophila)", "frizzled 1, seven transmembrane spanning receptor", "frizzled family receptor 1"			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.1369A>G	chr7.hg19:g.90895564A>G	ENSP00000287934:p.Ile457Val	57.0	0.0		56.0	20.0	NM_003505	A4D1E8|O94815|Q549T8	Missense_Mutation	SNP	ENST00000287934.2	hg19	CCDS5620.1	.	.	.	.	.	.	.	.	.	.	A	1.686	-0.505207	0.04261	.	.	ENSG00000157240	ENST00000287934	T	0.79454	-1.27	4.52	3.36	0.38483	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000004	T	0.43277	0.1240	N	0.01109	-1.01	0.47905	D	0.99954	B	0.12013	0.005	B	0.16289	0.015	T	0.47315	-0.9127	10	0.02654	T	1	.	9.8643	0.41134	0.9187:0.0:0.0813:0.0	.	457	Q9UP38	FZD1_HUMAN	V	457	ENSP00000287934:I457V	ENSP00000287934:I457V	I	+	1	0	FZD1	90733500	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.577000	0.53885	0.772000	0.33382	0.379000	0.24179	ATC	.	.		0.637	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		G	90895564	A	G	90895564	3	3	73	1	0	0	0	0	1	0	0	0	6136	217	8	2	1371	2	FZD1	7	90895564	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4479192	90895564	68243099	258	9584										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94040245	94040245	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctggagctgatggcagagcTggcgtcatggtaagctgtct	15	9	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:94040245T>C	ENST00000297268.6	+	22	1713	c.1242T>C	c.(1240-1242)gcT>gcC	p.A414A		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	414					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	ATGGCAGAGCTGGCGTCATGG	0.468										HNSCC(75;0.22)																											p.A414A		Atlas-SNP	.											.	COL1A2	240	.	0			c.T1242C						.						152	147	149					7																	94040245		2203	4300	6503	SO:0001819	synonymous_variant	1278	exon22			CAGAGCTGGCGTC	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1242T>C	chr7.hg19:g.94040245T>C		113.0	0.0		66.0	25.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	hg19	CCDS34682.1																																																																																			.	.		0.468	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		C	94040245	T	C	94040245	2	2	73	1	0	0	0	0	0	0	0	1	3680	1567	55	2		2	COL1A2	7	94040245	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3144681	94040245	65098418	259	9585										
GPR22	2845	hgsc.bcm.edu	37	chr7	107114661	107114661	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggatttcttatgttagaaatTgtgttgggacttggcagcaa	12	4	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:107114661T>A	ENST00000304402.4	+	3	1499	c.156T>A	c.(154-156)atT>atA	p.I52I	COG5_ENST00000475638.2_Intron|COG5_ENST00000393603.2_Intron|COG5_ENST00000347053.3_Intron|COG5_ENST00000297135.3_Intron	NM_005295.2	NP_005286.2	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	52					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(3)|lung(6)|ovary(2)|stomach(1)	12						TGTTAGAAATTGTGTTGGGAC	0.378																																					p.I52I		Atlas-SNP	.											.	GPR22	43	.	0			c.T156A						.						195	179	184					7																	107114661		2203	4300	6503	SO:0001819	synonymous_variant	2845	exon3			AGAAATTGTGTTG	U66581	CCDS5744.1	7q22-q31.1	2012-08-21			ENSG00000172209	ENSG00000172209		"GPCR / Class A : Orphans"	4477	protein-coding gene	gene with protein product		601910				9073069	Standard	NM_005295		Approved		uc003vef.3	Q99680	OTTHUMG00000154902	ENST00000304402.4:c.156T>A	chr7.hg19:g.107114661T>A		174.0	0.0		195.0	83.0	NM_005295	O14554	Silent	SNP	ENST00000304402.4	hg19	CCDS5744.1																																																																																			.	.		0.378	GPR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337598.1			A	107114661	T	A	107114661	2	1	73	1	0	0	0	0	0	0	0	1	6690	1800	63	4		4	GPR22	7	107114661	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	13074416	107114661	52024002	260	9586										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107706917	107706917	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acaagggcaagggtggcagcTgggaaatccaaagtagcctg	15	8	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:107706917T>A	ENST00000388781.3	-	20	2658	c.2575A>T	c.(2575-2577)Agc>Tgc	p.S859C	LAMB4_ENST00000205386.4_Missense_Mutation_p.S859C|LAMB4_ENST00000388780.3_Missense_Mutation_p.S859C	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	859	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						GGGTGGCAGCTGGGAAATCCA	0.532																																					p.S859C		Atlas-SNP	.											.	LAMB4	253	.	0			c.A2575T						.						65	58	60					7																	107706917		2203	4300	6503	SO:0001583	missense	22798	exon20			GGCAGCTGGGAAA	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2575A>T	chr7.hg19:g.107706917T>A	ENSP00000373433:p.Ser859Cys	125.0	0.0		117.0	48.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	hg19	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	T	16.68	3.191302	0.58017	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780	T;T;T	0.63255	-0.03;-0.03;-0.03	4.98	3.84	0.44239	EGF-like, laminin (4);	0.644454	0.14226	N	0.333070	T	0.71065	0.3296	M	0.87827	2.91	0.54753	D	0.999984	P	0.51537	0.946	P	0.49752	0.621	T	0.71761	-0.4495	10	0.62326	D	0.03	.	7.0636	0.25139	0.0:0.0837:0.193:0.7233	.	859	A4D0S4	LAMB4_HUMAN	C	859	ENSP00000205386:S859C;ENSP00000373433:S859C;ENSP00000373432:S859C	ENSP00000205386:S859C	S	-	1	0	LAMB4	107494153	0.000000	0.05858	0.673000	0.29887	0.806000	0.45545	-0.492000	0.06467	0.937000	0.37394	0.460000	0.39030	AGC	.	.		0.532	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		A	107706917	T	A	107706917	3	1	73	1	0	0	0	0	1	0	0	0	8622	1580	55	4	2770	4	LAMB4	7	107706917	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	592256	107706917	51431746	261	9587										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107820770	107820770	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggctaaagggctctagcccCggcaacatgccatgagtctt	11	12	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:107820770C>T	ENST00000425651.2	-	22	2747	c.2748G>A	c.(2746-2748)ccG>ccA	p.P916P	NRCAM_ENST00000413765.2_Silent_p.P897P|NRCAM_ENST00000379028.3_Silent_p.P916P|NRCAM_ENST00000379024.4_Silent_p.P897P|NRCAM_ENST00000351718.4_Silent_p.P900P|NRCAM_ENST00000379022.4_Silent_p.P916P	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	916	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GCTCTAGCCCCGGCAACATGC	0.493																																					p.P916P		Atlas-SNP	.											NRCAM_ENST00000379028,NS,carcinoma,0,2	NRCAM	267	.	0			c.G2748A						.						99	86	90					7																	107820770		2203	4300	6503	SO:0001819	synonymous_variant	4897	exon22			TAGCCCCGGCAAC		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.2748G>A	chr7.hg19:g.107820770C>T		105.0	0.0		104.0	62.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	hg19	CCDS47686.1																																																																																			.	.		0.493	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		T	107820770	C	T	107820770	2	4	73	1	0	0	0	0	0	0	0	1	10653	639	23	1		1	NRCAM	7	107820770	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	113853	107820770	51317893	262	9588										
ASZ1	136991	hgsc.bcm.edu	37	chr7	117003770	117003770	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acttcttcccttaattgtatAtgagttggatcattttcccg	6	9	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:117003770A>G	ENST00000284629.2	-	13	1370	c.1308T>C	c.(1306-1308)caT>caC	p.H436H		NM_130768.2	NP_570124.1			ankyrin repeat, SAM and basic leucine zipper domain containing 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(3)|skin(1)	24	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)			TTAATTGTATATGAGTTGGAT	0.308																																					p.H436H		Atlas-SNP	.											.	ASZ1	56	.	0			c.T1308C						.						88	85	86					7																	117003770		2202	4298	6500	SO:0001819	synonymous_variant	136991	exon13			TTGTATATGAGTT	AF461259	CCDS5772.1	7q31.2	2013-01-10	2005-03-15	2004-07-16	ENSG00000154438	ENSG00000154438		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	1350	protein-coding gene	gene with protein product		605797	"ankyrin-like 1"	C7orf7, ANKL1		12040005, 11279520	Standard	NM_130768		Approved	Orf3, GASZ, ALP1, CT1.19	uc003vjb.2	Q8WWH4	OTTHUMG00000064565	ENST00000284629.2:c.1308T>C	chr7.hg19:g.117003770A>G		73.0	0.0		85.0	26.0	NM_130768		Silent	SNP	ENST00000284629.2	hg19	CCDS5772.1																																																																																			.	.		0.308	ASZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000138907.7	NM_130768		G	117003770	A	G	117003770	2	3	73	1	0	0	0	0	0	0	0	1	1069	446	16	2		2	ASZ1	7	117003770	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	9183000	117003770	42134893	263	9589										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117407202	117407202	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcctttctggctcaagccctCcgtgcctacacaagatttct	6	15	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:117407202C>A	ENST00000160373.3	-	9	2898	c.2807G>T	c.(2806-2808)gGa>gTa	p.G936V		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	936					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		CTCAAGCCCTCCGTGCCTACA	0.443																																					p.G936V		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.G2807T						.						159	135	143					7																	117407202		2203	4300	6503	SO:0001583	missense	83992	exon9			AGCCCTCCGTGCC		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.2807G>T	chr7.hg19:g.117407202C>A	ENSP00000160373:p.Gly936Val	72.0	0.0		76.0	32.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.596853	0.46318	.	.	ENSG00000077063	ENST00000160373	T	0.68479	-0.33	5.64	2.85	0.33270	Ankyrin repeat-containing domain (2);	0.482216	0.27946	N	0.017217	T	0.74696	0.3750	H	0.96080	3.765	0.51482	D	0.999928	P	0.40000	0.698	B	0.38803	0.282	T	0.76623	-0.2891	10	0.72032	D	0.01	-1.6332	9.2559	0.37584	0.0:0.7483:0.1205:0.1312	.	936	Q8WZ74	CTTB2_HUMAN	V	936	ENSP00000160373:G936V	ENSP00000160373:G936V	G	-	2	0	CTTNBP2	117194438	0.990000	0.36364	0.236000	0.24074	0.657000	0.38888	2.282000	0.43461	0.412000	0.25729	0.561000	0.74099	GGA	.	.		0.443	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		A	117407202	C	A	117407202	3	1	73	1	0	0	0	0	1	0	0	0	4047	855	30	3	2244	3	CTTNBP2	7	117407202	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	403432	117407202	41731461	264	9590										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121653036	121653036	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccaaaaggaaggcatgtattTgctacacctgttttatcaat	7	8	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:121653036T>A	ENST00000393386.2	+	12	4347	c.3936T>A	c.(3934-3936)ttT>ttA	p.F1312L	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_3'UTR	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1312					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GGCATGTATTTGCTACACCTG	0.383																																					p.F1312L		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T3936A						.						79	71	73					7																	121653036		2203	4300	6503	SO:0001583	missense	5803	exon12			TGTATTTGCTACA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.3936T>A	chr7.hg19:g.121653036T>A	ENSP00000377047:p.Phe1312Leu	157.0	0.0		146.0	57.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	T	9.781	1.175386	0.21704	.	.	ENSG00000106278	ENST00000393386	T	0.39592	1.07	5.79	3.31	0.37934	.	0.597034	0.16565	N	0.208877	T	0.31670	0.0804	L	0.45137	1.4	0.30930	N	0.726991	B	0.22480	0.07	B	0.15870	0.014	T	0.25328	-1.0135	10	0.25751	T	0.34	.	8.5541	0.33469	0.1235:0.0:0.4066:0.4699	.	1312	P23471	PTPRZ_HUMAN	L	1312	ENSP00000377047:F1312L	ENSP00000377047:F1312L	F	+	3	2	PTPRZ1	121440272	0.170000	0.23016	0.799000	0.32177	0.059000	0.15707	0.637000	0.24659	0.377000	0.24735	0.454000	0.30748	TTT	.	.		0.383	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121653036	T	A	121653036	3	1	73	1	0	0	0	0	1	0	0	0	12829	1809	63	4	3982	4	PTPRZ1	7	121653036	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	4245834	121653036	37485627	265	9591										
FAM71F2	346653	hgsc.bcm.edu	37	chr7	128323061	128323061	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tagacaactgcagcagctacAagataccctctccagtggca	8	13	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:128323061A>G	ENST00000480462.1	+	5	884	c.778A>G	c.(778-780)Aag>Gag	p.K260E	FAM71F2_ENST00000378704.3_Missense_Mutation_p.K251E|FAM71F2_ENST00000477515.1_3'UTR			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	260										NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						CAGCAGCTACAAGATACCCTC	0.453																																					p.K260E		Atlas-SNP	.											.	FAM71F2	19	.	0			c.A778G						.						52	50	51					7																	128323061		1889	4116	6005	SO:0001583	missense	346653	exon5			AGCTACAAGATAC	BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"family with sequence similarity 137, member B"	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.778A>G	chr7.hg19:g.128323061A>G	ENSP00000420140:p.Lys260Glu	111.0	0.0		77.0	39.0	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	hg19	CCDS47701.1	.	.	.	.	.	.	.	.	.	.	A	10.87	1.473311	0.26423	.	.	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001	T;T;T;T	0.07444	3.19;3.19;3.19;3.19	3.41	-0.587	0.11690	.	3.223590	0.00866	N	0.001961	T	0.06962	0.0177	L	0.29908	0.895	0.09310	N	1	B;B	0.21606	0.058;0.035	B;B	0.22601	0.04;0.018	T	0.39057	-0.9632	10	0.72032	D	0.01	-12.1893	0.6937	0.00896	0.4624:0.2118:0.1208:0.2051	.	251;260	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	E	251;260;251;251	ENSP00000418907:K251E;ENSP00000420140:K260E;ENSP00000367976:K251E;ENSP00000401654:K251E	ENSP00000367976:K251E	K	+	1	0	FAM71F2	128110297	0.021000	0.18746	0.000000	0.03702	0.160000	0.22226	0.739000	0.26173	-0.090000	0.12462	0.456000	0.33151	AAG	.	.		0.453	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1			G	128323061	A	G	128323061	3	3	73	1	0	0	0	0	1	0	0	0	5621	131	5	2	796	2	FAM71F2	7	128323061	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	6670025	128323061	30815602	266	9592										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128434789	128434789	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tagccagcgcccagcaggcaGaggtgttcaccaagcagatc	12	13	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:128434789G>T	ENST00000297788.4	+	3	680	c.313G>T	c.(313-315)Gag>Tag	p.E105*	CCDC136_ENST00000378685.4_Nonsense_Mutation_p.E155*|CCDC136_ENST00000487361.1_Nonsense_Mutation_p.E105*|CCDC136_ENST00000464832.1_Nonsense_Mutation_p.E155*	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	105	Glu-rich.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CCAGCAGGCAGAGGTGTTCAC	0.597																																					p.E155X		Atlas-SNP	.											.	CCDC136	170	.	0			c.G463T						.						23	27	25					7																	128434789		1748	3622	5370	SO:0001587	stop_gained	64753	exon4			CAGGCAGAGGTGT		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.313G>T	chr7.hg19:g.128434789G>T	ENSP00000297788:p.Glu105*	314.0	1.0		222.0	83.0	NM_001201372	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Nonsense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	g	37	6.335248	0.97485	.	.	ENSG00000128596	ENST00000485998;ENST00000378685;ENST00000464832;ENST00000487361;ENST00000297788;ENST00000397697;ENST00000320524	.	.	.	4.45	4.45	0.53987	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-17.3837	14.6123	0.68524	0.0:0.0:1.0:0.0	.	.	.	.	X	105;155;155;105;105;105;105	.	ENSP00000297788:E105X	E	+	1	0	CCDC136	128222025	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	8.160000	0.89653	2.017000	0.59298	0.586000	0.80456	GAG	.	.		0.597	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		T	128434789	G	T	128434789	4	4	73	1	0	0	0	0	0	1	0	0	2772	943	33	3	323	3	CCDC136	7	128434789	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	111728	128434789	30703874	267	9593										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128450365	128450365	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtctcatttccaggaagtgtTggagaatcccgatgattcca	10	9	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:128450365T>G	ENST00000297788.4	+	12	2340	c.1973T>G	c.(1972-1974)tTg>tGg	p.L658W	CCDC136_ENST00000378685.4_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000464832.1_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	658						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CAGGAAGTGTTGGAGAATCCC	0.428																																					p.L658W		Atlas-SNP	.											.	CCDC136	170	.	0			c.T1973G						.						66	63	64					7																	128450365		1952	4151	6103	SO:0001583	missense	64753	exon12			AAGTGTTGGAGAA		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.1973T>G	chr7.hg19:g.128450365T>G	ENSP00000297788:p.Leu658Trp	149.0	0.0		158.0	69.0	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.15|19.15	3.771022|3.771022	0.69992|0.69992	.|.	.|.	ENSG00000128596|ENSG00000128596	ENST00000297788;ENST00000397697;ENST00000320524;ENST00000464672|ENST00000494552	T;T|.	0.45668|.	0.89;0.89|.	5.96|5.96	4.81|4.81	0.61882|0.61882	.|.	0.834039|.	0.10426|.	N|.	0.676027|.	T|T	0.47135|0.47135	0.1429|0.1429	M|M	0.62723|0.62723	1.935|1.935	0.19775|0.19775	N|N	0.999954|0.999954	D;D|.	0.76494|.	0.997;0.999|.	D;D|.	0.70935|.	0.958;0.971|.	T|T	0.38478|0.38478	-0.9659|-0.9659	10|5	0.66056|.	D|.	0.02|.	-1.4696|-1.4696	8.769|8.769	0.34719|0.34719	0.0:0.0847:0.0:0.9153|0.0:0.0847:0.0:0.9153	.|.	658;658|.	Q96JN2-2;Q96JN2|.	.;CC136_HUMAN|.	W|G	658;658;658;249|535	ENSP00000297788:L658W;ENSP00000417991:L249W|.	ENSP00000297788:L658W|.	L|W	+|+	2|1	0|0	CCDC136|CCDC136	128237601|128237601	1.000000|1.000000	0.71417|0.71417	0.959000|0.959000	0.39883|0.39883	0.031000|0.031000	0.12232|0.12232	2.138000|2.138000	0.42140|0.42140	1.080000|1.080000	0.41073|0.41073	0.533000|0.533000	0.62120|0.62120	TTG|TGG	.	.		0.428	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		G	128450365	T	G	128450365	3	3	73	1	0	0	0	0	1	0	0	0	2772	1821	63	5	2019	5	CCDC136	7	128450365	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	15576	128450365	30688298	268	9594										
ATP6V1F	9296	hgsc.bcm.edu	37	chr7	128505618	128505618	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccaggggcatgttcactgccGaagacctgcgctaggggact	14	12	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:128505618G>T	ENST00000249289.4	+	2	425	c.346G>T	c.(346-348)Gaa>Taa	p.E116*	RP11-309L24.2_ENST00000469965.1_RNA|RP11-309L24.4_ENST00000461420.1_lincRNA|ATP6V1F_ENST00000492758.1_Nonsense_Mutation_p.E144*	NM_004231.3	NP_004222.2	Q16864	VATF_HUMAN	ATPase, H+ transporting, lysosomal 14kDa, V1 subunit F	116					ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase activity, uncoupled (GO:0042624)|hydrogen ion transmembrane transporter activity (GO:0015078)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			lung(1)|ovary(1)|prostate(1)	3						GTTCACTGCCGAAGACCTGCG	0.612																																					p.E144X		Atlas-SNP	.											.	ATP6V1F	12	.	0			c.G430T						.						34	36	35					7																	128505618		2203	4300	6503	SO:0001587	stop_gained	9296	exon3			ACTGCCGAAGACC	D49400	CCDS5807.1, CCDS56511.1	7q32.1	2010-04-21	2002-08-29		ENSG00000128524	ENSG00000128524	3.6.3.14	"ATPases / V-type"	16832	protein-coding gene	gene with protein product		607160				8581736, 8621738	Standard	NM_004231		Approved	ATP6S14, VATF, Vma7	uc022all.1	Q16864	OTTHUMG00000158365	ENST00000249289.4:c.346G>T	chr7.hg19:g.128505618G>T	ENSP00000249289:p.Glu116*	79.0	0.0		64.0	27.0	NM_001198909	C9J2K4|Q6IBA8	Nonsense_Mutation	SNP	ENST00000249289.4	hg19	CCDS5807.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611828	0.66558	.	.	ENSG00000128524	ENST00000249289;ENST00000492758	.	.	.	4.84	4.84	0.62591	.	0.103516	0.64402	D	0.000005	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-17.0803	16.713	0.85389	0.0:0.0:1.0:0.0	.	.	.	.	X	116;144	.	ENSP00000249289:E116X	E	+	1	0	ATP6V1F	128292854	1.000000	0.71417	0.940000	0.37924	0.702000	0.40608	8.976000	0.93442	2.227000	0.72691	0.591000	0.81541	GAA	.	.		0.612	ATP6V1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350800.1	NM_004231		T	128505618	G	T	128505618	4	4	73	1	0	0	0	0	0	1	0	0	1185	1059	37	1	352	1	ATP6V1F	7	128505618	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	55253	128505618	30633045	269	9595										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131908376	131908376	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttacaccagtggcagcggtaTggactctccacgcaggacag	12	12	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:131908376T>C	ENST00000359827.3	-	9	2969	c.2007A>G	c.(2005-2007)ccA>ccG	p.P669P	PLXNA4_ENST00000321063.4_Silent_p.P669P			Q9HCM2	PLXA4_HUMAN	plexin A4	669	PSI 2.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						GGCAGCGGTATGGACTCTCCA	0.587																																					p.P669P		Atlas-SNP	.											.	PLXNA4	873	.	0			c.A2007G						.						38	41	40					7																	131908376		2105	4254	6359	SO:0001819	synonymous_variant	91584	exon9			GCGGTATGGACTC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2007A>G	chr7.hg19:g.131908376T>C		135.0	0.0		84.0	50.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	hg19	CCDS43646.1																																																																																			.	.		0.587	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		C	131908376	T	C	131908376	2	2	73	1	0	0	0	0	0	0	0	1	12131	1451	51	2		2	PLXNA4	7	131908376	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3402758	131908376	27230287	270	9596										
SLC37A3	84255	hgsc.bcm.edu	37	chr7	140048534	140048534	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccagaagaagaaggagtaatTcactaacttcaagcaggcgt	10	8	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:140048534T>C	ENST00000326232.9	-	10	1119	c.916A>G	c.(916-918)Aat>Gat	p.N306D	SLC37A3_ENST00000340308.3_Missense_Mutation_p.N306D|SLC37A3_ENST00000429996.2_3'UTR|SLC37A3_ENST00000447932.2_Missense_Mutation_p.N306D	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	306					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					AAGGAGTAATTCACTAACTTC	0.473																																					p.N306D	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.A916G						.						103	95	97					7																	140048534		2203	4300	6503	SO:0001583	missense	84255	exon10			AGTAATTCACTAA	AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"Solute carriers"	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.916A>G	chr7.hg19:g.140048534T>C	ENSP00000321498:p.Asn306Asp	120.0	0.0		90.0	44.0	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	hg19	CCDS5859.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	29.1|29.1	4.980061|4.980061	0.92982|0.92982	.|.	.|.	ENSG00000157800|ENSG00000157800	ENST00000340308;ENST00000447932;ENST00000326232|ENST00000485734;ENST00000485861	T;T;T|.	0.58210|.	0.35;0.35;0.35|.	5.02|5.02	5.02|5.02	0.67125|0.67125	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.098057|.	0.64402|.	D|.	0.000002|.	T|.	0.79358|.	0.4432|.	M|M	0.87900|0.87900	2.915|2.915	0.80722|0.80722	D|D	1|1	D;D;D|.	0.76494|.	0.994;0.972;0.999|.	D;P;D|.	0.67382|.	0.919;0.907;0.951|.	T|.	0.82772|.	-0.0292|.	10|.	0.62326|.	D|.	0.03|.	-30.227|-30.227	14.769|14.769	0.69662|0.69662	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	306;306;306|.	Q8NCC5-2;Q8NCC5-3;Q8NCC5|.	.;.;SPX3_HUMAN|.	D|W	306|84;142	ENSP00000343358:N306D;ENSP00000397481:N306D;ENSP00000321498:N306D|.	ENSP00000321498:N306D|.	N|X	-|-	1|3	0|0	SLC37A3|SLC37A3	139695003|139695003	1.000000|1.000000	0.71417|0.71417	0.945000|0.945000	0.38365|0.38365	0.917000|0.917000	0.54804|0.54804	7.897000|7.897000	0.87356|0.87356	1.898000|1.898000	0.54952|0.54952	0.379000|0.379000	0.24179|0.24179	AAT|TGA	.	.		0.473	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295		C	140048534	T	C	140048534	3	2	73	1	0	0	0	0	1	0	0	0	14614	1783	62	2	741	2	SLC37A3	7	140048534	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	8140158	140048534	19090129	271	9597										
DENND2A	27147	hgsc.bcm.edu	37	chr7	140285439	140285439	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggagaagcaggaaaattcaAgacacacttctttcccaggc	10	10	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:140285439A>G	ENST00000275884.6	-	4	1612	c.1195T>C	c.(1195-1197)Ttg>Ctg	p.L399L	DENND2A_ENST00000537639.1_Silent_p.L399L|DENND2A_ENST00000496613.1_Silent_p.L399L|DENND2A_ENST00000492720.1_Silent_p.L399L			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	399					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					GGAAAATTCAAGACACACTTC	0.527																																					p.L399L		Atlas-SNP	.											.	DENND2A	132	.	0			c.T1195C						.						173	174	174					7																	140285439		1988	4167	6155	SO:0001819	synonymous_variant	27147	exon3			AATTCAAGACACA	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.1195T>C	chr7.hg19:g.140285439A>G		144.0	0.0		134.0	51.0	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	hg19	CCDS43659.1																																																																																			.	.		0.527	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		G	140285439	A	G	140285439	2	3	73	1	0	0	0	0	0	0	0	1	4431	69	3	2		2	DENND2A	7	140285439	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	236905	140285439	18853224	272	9598										
MGAM	8972	hgsc.bcm.edu	37	chr7	141755835	141755835	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tatggtgtccacccctactaCatggggctggaggaggacgg	15	10	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:141755835C>T	ENST00000549489.2	+	29	3614	c.3519C>T	c.(3517-3519)taC>taT	p.Y1173Y	MGAM_ENST00000475668.2_Silent_p.Y1173Y	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1173	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ACCCCTACTACATGGGGCTGG	0.512																																					p.Y1173Y		Atlas-SNP	.											.	MGAM	767	.	0			c.C3519T						.						35	33	34					7																	141755835		1924	4129	6053	SO:0001819	synonymous_variant	8972	exon29			CTACTACATGGGG	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.3519C>T	chr7.hg19:g.141755835C>T		70.0	0.0		54.0	19.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	hg19	CCDS47727.1																																																																																			.	.		0.512	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141755835	C	T	141755835	2	4	73	1	0	0	0	0	0	0	0	1	9550	489	17	3		3	MGAM	7	141755835	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1470396	141755835	17382828	273	9599										
MGAM	8972	hgsc.bcm.edu	37	chr7	141764190	141764190	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttcttcctcctcagatttggAgtccagggacaggggcctga	12	11	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:141764190A>G	ENST00000549489.2	+	37	4447	c.4352A>G	c.(4351-4353)gAg>gGg	p.E1451G	MGAM_ENST00000475668.2_Missense_Mutation_p.E1451G	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1451	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCAGATTTGGAGTCCAGGGAC	0.552																																					p.E1451G		Atlas-SNP	.											.	MGAM	767	.	0			c.A4352G						.						27	29	28					7																	141764190		1941	4144	6085	SO:0001583	missense	8972	exon37			ATTTGGAGTCCAG	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4352A>G	chr7.hg19:g.141764190A>G	ENSP00000447378:p.Glu1451Gly	100.0	0.0		70.0	29.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	A	1.803	-0.476478	0.04414	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.90004	-2.6	4.26	1.56	0.23342	Glycoside hydrolase, superfamily (1);	.	.	.	.	T	0.76535	0.4001	N	0.05554	-0.025	0.32055	N	0.596443	B	0.26363	0.147	B	0.31751	0.135	T	0.70400	-0.4882	9	0.23302	T	0.38	.	8.6294	0.33911	0.6233:0.3767:0.0:0.0	.	1451	O43451	MGA_HUMAN	G	1451;1451;1328	ENSP00000447378:E1451G	ENSP00000316431:E1328G	E	+	2	0	MGAM	141410659	0.846000	0.29590	0.076000	0.20297	0.153000	0.21895	1.801000	0.38843	0.460000	0.27045	0.260000	0.18958	GAG	.	.		0.552	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			G	141764190	A	G	141764190	3	3	73	1	0	0	0	0	1	0	0	0	9550	304	11	2	4494	2	MGAM	7	141764190	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	8355	141764190	17374473	274	9600										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142563375	142563375	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agttccgacccaccagaggcCccctgcactggtgagttcct	10	16	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:142563375C>T	ENST00000392957.2	+	8	1879	c.1092C>T	c.(1090-1092)gcC>gcT	p.A364A	EPHB6_ENST00000442129.1_Silent_p.A364A|EPHB6_ENST00000411471.2_Silent_p.A87A	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	364	Cys-rich.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					CACCAGAGGCCCCCTGCACTG	0.652																																					p.A364A		Atlas-SNP	.											.	EPHB6	168	.	0			c.C1092T						.						25	26	25					7																	142563375		2203	4300	6503	SO:0001819	synonymous_variant	2051	exon8			AGAGGCCCCCTGC	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1092C>T	chr7.hg19:g.142563375C>T		97.0	0.0		44.0	13.0	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	hg19	CCDS5873.2																																																																																			.	.		0.652	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142563375	C	T	142563375	2	4	73	1	0	0	0	0	0	0	0	1	5180	610	22	3		3	EPHB6	7	142563375	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	799185	142563375	16575288	275	9601										
CLCN1	1180	hgsc.bcm.edu	37	chr7	143044041	143044041	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggataacatgtcacctgaagAggtgagtaagggaaatggaa	14	4	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:143044041A>T	ENST00000343257.2	+	20	2489	c.2402A>T	c.(2401-2403)gAg>gTg	p.E801V		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	801					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					TCACCTGAAGAGGTGAGTAAG	0.393																																					p.E801V		Atlas-SNP	.											.	CLCN1	141	.	0			c.A2402T						.						144	146	145					7																	143044041		2203	4300	6503	SO:0001630	splice_region_variant	1180	exon20			CTGAAGAGGTGAG	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.2403+1A>T	chr7.hg19:g.143044041A>T		118.0	0.0		64.0	30.0	NM_000083	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	hg19	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.315402	0.81358	.	.	ENSG00000188037	ENST00000343257	D	0.90900	-2.75	4.81	4.81	0.61882	.	0.058336	0.64402	D	0.000002	D	0.92658	0.7667	M	0.79805	2.47	0.52099	D	0.999947	D	0.56746	0.977	P	0.51266	0.664	D	0.93479	0.6826	10	0.87932	D	0	.	12.3956	0.55382	1.0:0.0:0.0:0.0	.	801	P35523	CLCN1_HUMAN	V	801	ENSP00000339867:E801V	ENSP00000339867:E801V	E	+	2	0	CLCN1	142754163	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	6.135000	0.71696	1.934000	0.56057	0.459000	0.35465	GAG	.	.		0.393	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083	Missense_Mutation	T	143044041	A	T	143044041	5	4	73	1	0	0	0	0	0	0	1	0	3464	318	11	4	2480	4	CLCN1	7	143044041	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	480666	143044041	16094622	276	9602										
OR2F2	135948	hgsc.bcm.edu	37	chr7	143633258	143633258	+	Frame_Shift_Del	DEL	A	A	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttagagaaattctctgggttAacatccaagctgggaacttg							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:143633258delA	ENST00000408955.2	+	1	1000	c.933delA	c.(931-933)ttafs	p.L311fs		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, member 2	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(19)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	32	Melanoma(164;0.0903)					TCTCTGGGTTAACATCCAAGC	0.413																																					p.L311X		Pindel	.											.	OR2F2	63	.	0			c.932delT						.						39	38	39					7																	143633258		1981	4209	6190	SO:0001589	frameshift_variant	135948	exon1			.		CCDS43666.1	7q33-q35	2012-08-09			ENSG00000221910	ENSG00000221910		"GPCR / Class A : Olfactory receptors"	8247	protein-coding gene	gene with protein product							Standard	NM_001004685		Approved	OR7-1	uc011ktv.2	O95006	OTTHUMG00000157768	ENST00000408955.2:c.933delA	chr7.hg19:g.143633258delA	ENSP00000386222:p.Leu311fs	50.0	0.0		59.0	19.0	NM_001004685	A4D2G0|Q6IFP8	Frame_Shift_Del	DEL	ENST00000408955.2	hg19	CCDS43666.1																																																																																			.	.		0.413	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1			-	143633258	A	-	143633258	7	5	73	1	0	1	0	1	0	0	0	0	11006	359	13	0	935	0	OR2F2	7	143633258	Frame_Shift_Del	DEL	A	TCGA-CC-A7IH-01A-11D-A33K-10	589217	143633258	15505405	277	9603										
OR2F1	26211	hgsc.bcm.edu	37	chr7	143657623	143657623	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	actcctagctgtggtcaggcTggcttgtgtggacacctcct	12	12	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:143657623T>A	ENST00000392899.1	+	1	597	c.560T>A	c.(559-561)cTg>cAg	p.L187Q	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	187					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					GTGGTCAGGCTGGCTTGTGTG	0.488																																					p.L187Q		Atlas-SNP	.											.	OR2F1	71	.	0			c.T560A						.						169	151	157					7																	143657623		2203	4300	6503	SO:0001583	missense	26211	exon1			TCAGGCTGGCTTG	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"GPCR / Class A : Olfactory receptors"	8246	protein-coding gene	gene with protein product		608497	"olfactory receptor, family 2, subfamily F, member 1"	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.560T>A	chr7.hg19:g.143657623T>A	ENSP00000376633:p.Leu187Gln	172.0	0.0		161.0	56.0	NM_012369	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	hg19	CCDS5887.1	.	.	.	.	.	.	.	.	.	.	T	18.43	3.621801	0.66787	.	.	ENSG00000213215	ENST00000392899	T	0.00411	7.53	5.53	5.53	0.82687	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41396	D	0.000881	T	0.02012	0.0063	H	0.95224	3.64	0.47407	D	0.99941	D	0.89917	1.0	D	0.97110	1.0	T	0.12218	-1.0556	10	0.87932	D	0	-16.5054	13.667	0.62401	0.0:0.0:0.0:1.0	.	187	Q13607	OR2F1_HUMAN	Q	187	ENSP00000376633:L187Q	ENSP00000376633:L187Q	L	+	2	0	OR2F1	143288556	0.389000	0.25205	0.986000	0.45419	0.604000	0.37047	3.867000	0.56047	2.315000	0.78130	0.533000	0.62120	CTG	.	.		0.488	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1			A	143657623	T	A	143657623	3	1	73	1	0	0	0	0	1	0	0	0	11005	1580	55	4	562	4	OR2F1	7	143657623	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	24365	143657623	15481040	278	9604										
OR6B1	135946	hgsc.bcm.edu	37	chr7	143701238	143701238	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gatcatcatcctattggtgcTgcaaaatcggccactgcaca	8	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:143701238T>A	ENST00000408922.2	+	1	217	c.149T>A	c.(148-150)cTg>cAg	p.L50Q		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|large_intestine(3)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	27	Melanoma(164;0.0783)					CTATTGGTGCTGCAAAATCGG	0.488																																					p.L50Q		Atlas-SNP	.											.	OR6B1	60	.	0			c.T149A						.						108	106	107					7																	143701238		2075	4246	6321	SO:0001583	missense	135946	exon1			TGGTGCTGCAAAA		CCDS43667.1	7q33-q35	2012-08-09			ENSG00000221813	ENSG00000221813		"GPCR / Class A : Olfactory receptors"	8354	protein-coding gene	gene with protein product							Standard	NM_001005281		Approved	OR7-3	uc003wdt.1	O95007	OTTHUMG00000157765	ENST00000408922.2:c.149T>A	chr7.hg19:g.143701238T>A	ENSP00000386151:p.Leu50Gln	204.0	0.0		165.0	64.0	NM_001005281	A4D2G2|B9EH47|Q6IFP6|Q96R38	Missense_Mutation	SNP	ENST00000408922.2	hg19	CCDS43667.1	.	.	.	.	.	.	.	.	.	.	T	1.959	-0.439292	0.04636	.	.	ENSG00000221813	ENST00000408922	T	0.01106	5.33	5.37	0.277	0.15668	GPCR, rhodopsin-like superfamily (1);	0.481200	0.15043	N	0.283733	T	0.00608	0.0020	N	0.10629	0.01	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47661	-0.9100	10	0.24483	T	0.36	.	1.1512	0.01786	0.4727:0.1444:0.2415:0.1414	.	50	O95007	OR6B1_HUMAN	Q	50	ENSP00000386151:L50Q	ENSP00000386151:L50Q	L	+	2	0	OR6B1	143332171	0.000000	0.05858	0.732000	0.30844	0.426000	0.31534	0.284000	0.18864	0.144000	0.18951	-0.399000	0.06403	CTG	.	.		0.488	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1			A	143701238	T	A	143701238	3	1	73	1	0	0	0	0	1	0	0	0	11196	1580	55	4	151	4	OR6B1	7	143701238	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	43615	143701238	15437425	279	9605										
OR2A12	346525	hgsc.bcm.edu	37	chr7	143792917	143792917	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgcagaaaggccttctctacCtgctcctcccacctctgcgt	7	18	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:143792917C>A	ENST00000408949.2	+	1	777	c.717C>A	c.(715-717)acC>acA	p.T239T		NM_001004135.1	NP_001004135.1	Q8NGT7	O2A12_HUMAN	olfactory receptor, family 2, subfamily A, member 12	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)	25	Melanoma(164;0.0783)					CCTTCTCTACCTGCTCCTCCC	0.587																																					p.T239T		Atlas-SNP	.											.	OR2A12	56	.	0			c.C717A						.						145	140	142					7																	143792917		1957	4149	6106	SO:0001819	synonymous_variant	346525	exon1			CTCTACCTGCTCC		CCDS43670.1	7q35	2013-09-20	2002-11-13	2002-11-13	ENSG00000221858	ENSG00000221858		"GPCR / Class A : Olfactory receptors"	15082	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 12 pseudogene"	OR2A12P			Standard	NM_001004135		Approved		uc011kty.2	Q8NGT7	OTTHUMG00000157996	ENST00000408949.2:c.717C>A	chr7.hg19:g.143792917C>A		173.0	0.0		136.0	44.0	NM_001004135	Q6IF43	Silent	SNP	ENST00000408949.2	hg19	CCDS43670.1																																																																																			.	.		0.587	OR2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349969.1			A	143792917	C	A	143792917	2	1	73	1	0	0	0	0	0	0	0	1	10984	668	24	3		3	OR2A12	7	143792917	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	91679	143792917	15345746	280	9606										
ZNF786	136051	hgsc.bcm.edu	37	chr7	148767562	148767562	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaacagttggctgagcctttTcttaatgtccagttcatttg	8	8	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:148767562T>C	ENST00000491431.1	-	4	2366	c.2302A>G	c.(2302-2304)Aaa>Gaa	p.K768E	ZNF786_ENST00000451334.3_Missense_Mutation_p.K731E|ZNF786_ENST00000316286.9_Missense_Mutation_p.K682E	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	768					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			CTGAGCCTTTTCTTAATGTCC	0.483																																					p.K768E		Atlas-SNP	.											.	ZNF786	69	.	0			c.A2302G						.						265	254	257					7																	148767562		1977	4180	6157	SO:0001583	missense	136051	exon4			GCCTTTTCTTAAT	AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"Zinc fingers, C2H2-type", "-"	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.2302A>G	chr7.hg19:g.148767562T>C	ENSP00000417470:p.Lys768Glu	111.0	0.0		138.0	58.0	NM_152411	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	hg19	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.986190	0.53934	.	.	ENSG00000197362	ENST00000316286;ENST00000491431;ENST00000451334	T;T;T	0.08807	3.05;3.2;3.1	4.62	0.63	0.17693	.	0.215648	0.23585	N	0.046607	T	0.04998	0.0134	N	0.22421	0.69	0.20074	N	0.999931	B	0.21821	0.061	B	0.18263	0.021	T	0.32375	-0.9909	10	0.66056	D	0.02	-4.7659	5.1927	0.15218	0.0:0.0962:0.3522:0.5515	.	768	Q8N393	ZN786_HUMAN	E	682;768;731	ENSP00000313516:K682E;ENSP00000417470:K768E;ENSP00000404984:K731E	ENSP00000313516:K682E	K	-	1	0	ZNF786	148398495	0.000000	0.05858	0.830000	0.32933	0.644000	0.38419	0.019000	0.13444	0.295000	0.22570	0.482000	0.46254	AAA	.	.		0.483	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411		C	148767562	T	C	148767562	3	2	73	1	0	0	0	0	1	0	0	0	18173	1792	62	2	50	2	ZNF786	7	148767562	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	4974645	148767562	10371101	281	9607										
FASTK	10922	hgsc.bcm.edu	37	chr7	150774867	150774867	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caatcagagcatgaggggtgCctgtggggaggcggggactg	20	7	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:150774867C>T	ENST00000297532.6	-	6	1117	c.1040G>A	c.(1039-1041)gGc>gAc	p.G347D	FASTK_ENST00000489884.1_5'UTR|RP11-148K1.12_ENST00000485974.1_RNA|FASTK_ENST00000482571.1_Splice_Site_p.G320D|FASTK_ENST00000540185.1_3'UTR|FASTK_ENST00000353841.2_Splice_Site_p.G206D	NM_006712.4	NP_006703.1	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase	347					apoptotic signaling pathway (GO:0097190)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|Fas-activated serine/threonine kinase activity (GO:0033867)|protein serine/threonine kinase activity (GO:0004674)			lung(4)|stomach(2)	6			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)		ATGAGGGGTGCCTGTGGGGAG	0.701																																					p.G347D		Atlas-SNP	.											.	FASTK	29	.	0			c.G1040A						.						31	38	36					7																	150774867		2202	4300	6502	SO:0001630	splice_region_variant	10922	exon6			GGGGTGCCTGTGG		CCDS5918.1, CCDS5919.1, CCDS59088.1	7q35	2006-07-06			ENSG00000164896	ENSG00000164896			24676	protein-coding gene	gene with protein product		606965				7544399, 15572676	Standard	NM_006712		Approved	FAST	uc003wix.2	Q14296	OTTHUMG00000158694	ENST00000297532.6:c.1040-1G>A	chr7.hg19:g.150774867C>T		101.0	0.0		88.0	36.0	NM_006712	A8K867|F8VTW9|Q59EM8|Q8IVA0	Missense_Mutation	SNP	ENST00000297532.6	hg19	CCDS5918.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.494606	0.44352	.	.	ENSG00000164896	ENST00000483105;ENST00000297530;ENST00000353841;ENST00000297532;ENST00000482571	T;T;T	0.30981	1.9;1.89;1.51	4.88	3.99	0.46301	.	0.240441	0.34700	N	0.003741	T	0.18257	0.0438	N	0.14661	0.345	0.80722	D	1	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.09377	0.004;0.002;0.002	T	0.04103	-1.0977	10	0.66056	D	0.02	.	9.5801	0.39481	0.0:0.8284:0.0:0.1716	.	320;206;347	F8VTW9;Q8IVA0;Q14296	.;.;FASTK_HUMAN	D	347;347;206;347;320	ENSP00000324817:G206D;ENSP00000297532:G347D;ENSP00000418516:G320D	ENSP00000297530:G347D	G	-	2	0	FASTK	150405800	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.023000	0.57211	1.184000	0.42957	0.655000	0.94253	GGC	.	.		0.701	FASTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351832.2	NM_006712	Missense_Mutation	T	150774867	C	T	150774867	5	4	73	1	0	0	0	0	0	0	1	0	5692	753	26	3	629	3	FASTK	7	150774867	Splice_Site	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	2007305	150774867	8363796	282	9608										
AGAP3	116988	hgsc.bcm.edu	37	chr7	150839513	150839513	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcctagatccagactgggccAgcctgaacctgggtgccctg	13	14	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr7:150839513A>T	ENST00000463381.1	+	14	1568	c.1072A>T	c.(1072-1074)Agc>Tgc	p.S358C	AGAP3_ENST00000397238.2_Missense_Mutation_p.S689C	NM_001281300.1	NP_001268229.1	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	653	Small GTPase-like.				cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						AGACTGGGCCAGCCTGAACCT	0.622																																					p.S689C		Atlas-SNP	.											.	AGAP3	121	.	0			c.A2065T						.						36	41	39					7																	150839513		2164	4284	6448	SO:0001583	missense	116988	exon16			TGGGCCAGCCTGA	AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16923	protein-coding gene	gene with protein product			"centaurin, gamma 3"	CENTG3			Standard	NM_001042535		Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000463381.1:c.1072A>T	chr7.hg19:g.150839513A>T	ENSP00000418016:p.Ser358Cys	110.0	0.0		76.0	9.0	NM_031946	B3KNZ8|E9PAL8|Q59EN0|Q96RK3	Missense_Mutation	SNP	ENST00000463381.1	hg19		.	.	.	.	.	.	.	.	.	.	A	26.5	4.748242	0.89663	.	.	ENSG00000133612	ENST00000463381;ENST00000397232;ENST00000397238;ENST00000335355	T;T	0.55930	0.49;0.49	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.80829	0.4698	H	0.96398	3.815	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	1.0;1.0;1.0;0.997	D	0.87022	0.2129	10	0.87932	D	0	.	14.2194	0.65815	1.0:0.0:0.0:0.0	.	653;188;689;358	Q96P47;E7ETI2;Q96P47-4;B3KNZ8	AGAP3_HUMAN;.;.;.	C	358;188;689;653	ENSP00000418016:S358C;ENSP00000380413:S689C	ENSP00000334157:S653C	S	+	1	0	AGAP3	150470446	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.207000	0.95064	1.948000	0.56530	0.533000	0.62120	AGC	.	.		0.622	AGAP3-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000351909.2	NM_031946		T	150839513	A	T	150839513	3	4	73	1	0	0	0	0	1	0	0	0	369	188	7	4	2194	4	AGAP3	7	150839513	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	64646	150839513	8299150	283	9609										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3889582	3889582	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttccatgcagaactcctttcAggatttctccaggatttcca	6	12	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:3889582A>T	ENST00000520002.1	-	4	1010	c.455T>A	c.(454-456)cTg>cAg	p.L152Q	CSMD1_ENST00000602557.1_Missense_Mutation_p.L152Q|CSMD1_ENST00000537824.1_Missense_Mutation_p.L152Q|CSMD1_ENST00000602723.1_Missense_Mutation_p.L152Q|CSMD1_ENST00000539096.1_Missense_Mutation_p.L152Q|CSMD1_ENST00000400186.3_Missense_Mutation_p.L152Q|CSMD1_ENST00000542608.1_Missense_Mutation_p.L152Q			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	152	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		AACTCCTTTCAGGATTTCTCC	0.443																																					p.L152Q		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T455A						.						89	94	92					8																	3889582		1999	4186	6185	SO:0001583	missense	64478	exon4			CCTTTCAGGATTT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.455T>A	chr8.hg19:g.3889582A>T	ENSP00000430733:p.Leu152Gln	117.0	0.0		50.0	41.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	A	0.197	-1.048257	0.01981	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04	5.52	5.52	0.82312	.	0.141721	0.27336	U	0.019829	T	0.44393	0.1291	N	0.16130	0.375	0.18873	N	0.999988	P	0.46784	0.884	P	0.46629	0.522	T	0.32693	-0.9897	10	0.13108	T	0.6	.	6.5804	0.22591	0.8285:0.0:0.1715:0.0	.	152	E5RIG2	.	Q	152;152;14;152;152;152	ENSP00000383047:L152Q;ENSP00000430733:L152Q;ENSP00000441462:L152Q;ENSP00000446243:L152Q;ENSP00000441675:L152Q	ENSP00000320445:L14Q	L	-	2	0	CSMD1	3876990	1.000000	0.71417	0.882000	0.34594	0.037000	0.13140	3.473000	0.53122	2.111000	0.64477	0.533000	0.62120	CTG	.	.		0.443	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3889582	A	T	3889582	3	4	73	1	0	0	0	0	1	0	0	0	3946	188	7	4	10320	4	CSMD1	8	3889582	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10		3889582	142474440	284	9610										
AGPAT5	55326	hgsc.bcm.edu	37	chr8	6612657	6612657	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccagaagaacaagaacatatGagaagatggctgcatgaacg	11	7	0	6			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:6612657G>A	ENST00000285518.6	+	7	1143	c.831G>A	c.(829-831)atG>atA	p.M277I	AGPAT5_ENST00000530716.1_3'UTR	NM_018361.3	NP_060831.2	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	277					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		AGPAT5/MCPH1(2)	endometrium(2)|kidney(2)|large_intestine(4)|lung(3)	11			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		AAGAACATATGAGAAGATGGC	0.358																																					p.M277I		Atlas-SNP	.											.	AGPAT5	31	.	0			c.G831A						.						91	76	81					8																	6612657		2203	4300	6503	SO:0001583	missense	55326	exon7			ACATATGAGAAGA	AF375789	CCDS34796.1	8p23.1	2013-02-05	2013-02-05		ENSG00000155189	ENSG00000155189	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20886	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, epsilon"	614796	"1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"				Standard	NM_018361		Approved	FLJ11210, LPAAT-e, LPAAT-epsilon	uc003wqo.3	Q9NUQ2	OTTHUMG00000163656	ENST00000285518.6:c.831G>A	chr8.hg19:g.6612657G>A	ENSP00000285518:p.Met277Ile	539.0	0.0		294.0	20.0	NM_018361	Q8IZ47|Q9BQG4	Missense_Mutation	SNP	ENST00000285518.6	hg19	CCDS34796.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.998007	0.74818	.	.	ENSG00000155189	ENST00000285518	T	0.39787	1.06	5.81	5.81	0.92471	.	0.168371	0.64402	D	0.000004	T	0.36496	0.0969	L	0.41124	1.26	0.52099	D	0.99994	B	0.09022	0.002	B	0.11329	0.006	T	0.11203	-1.0597	10	0.17832	T	0.49	-21.4045	17.585	0.87979	0.0:0.0:1.0:0.0	.	277	Q9NUQ2	PLCE_HUMAN	I	277	ENSP00000285518:M277I	ENSP00000285518:M277I	M	+	3	0	AGPAT5	6600065	1.000000	0.71417	0.880000	0.34516	0.794000	0.44872	5.574000	0.67424	2.746000	0.94184	0.591000	0.81541	ATG	.	.		0.358	AGPAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374684.1	NM_018361		A	6612657	G	A	6612657	3	1	73	1	0	0	0	0	1	0	0	0	390	1290	45	3	857	3	AGPAT5	8	6612657	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	2723075	6612657	139751365	285	9611										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10465648	10465648	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggcctccccttctgcctccTgggtctccacttcaacctcc	7	20	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:10465648T>A	ENST00000382483.3	-	4	6183	c.5960A>T	c.(5959-5961)cAg>cTg	p.Q1987L		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2067	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TTCTGCCTCCTGGGTCTCCAC	0.587																																					p.Q1987L		Atlas-SNP	.											.	RP1L1	453	.	0			c.A5960T						.						169	184	179					8																	10465648		1978	4162	6140	SO:0001583	missense	94137	exon4			GCCTCCTGGGTCT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5960A>T	chr8.hg19:g.10465648T>A	ENSP00000371923:p.Gln1987Leu	80.0	0.0		38.0	21.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	T	7.489	0.650263	0.14516	.	.	ENSG00000183638	ENST00000382483	T	0.05447	3.44	1.24	-0.879	0.10613	.	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.18263	0.021	T	0.44982	-0.9292	9	0.34782	T	0.22	.	4.8508	0.13537	0.2708:0.0:0.0:0.7292	.	1987	A6NKC6	.	L	1987	ENSP00000371923:Q1987L	ENSP00000371923:Q1987L	Q	-	2	0	RP1L1	10503058	0.000000	0.05858	0.041000	0.18516	0.028000	0.11728	0.052000	0.14163	0.450000	0.26774	0.254000	0.18369	CAG	.	.		0.587	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10465648	T	A	10465648	3	1	73	1	0	0	0	0	1	0	0	0	13548	1580	55	4	1246	4	RP1L1	8	10465648	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3852991	10465648	135898374	286	9612										
ASAH1	427	hgsc.bcm.edu	37	chr8	17933073	17933073	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtcctgaaggaggataggtTgattttctgcagtcctctgt	13	7	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:17933073T>A	ENST00000262097.6	-	2	413	c.102A>T	c.(100-102)tcA>tcT	p.S34S	ASAH1_ENST00000520051.1_5'UTR|ASAH1_ENST00000520781.1_Silent_p.S34S|ASAH1_ENST00000381733.4_Silent_p.S50S|ASAH1_ENST00000417108.2_5'UTR|ASAH1_ENST00000314146.10_Silent_p.S50S	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	34					cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		GAGGATAGGTTGATTTTCTGC	0.348																																					p.S50S		Atlas-SNP	.											.	ASAH1	71	.	0			c.A150T						.						177	173	175					8																	17933073		2203	4300	6503	SO:0001819	synonymous_variant	427	exon2			ATAGGTTGATTTT	U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"N-acylsphingosine amidohydrolase (acid ceramidase)"	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.102A>T	chr8.hg19:g.17933073T>A		141.0	0.0		65.0	55.0	NM_001127505	E9PDS0|Q6W898|Q96AS2	Silent	SNP	ENST00000262097.6	hg19	CCDS6006.1																																																																																			.	.		0.348	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315		A	17933073	T	A	17933073	2	1	73	1	0	0	0	0	0	0	0	1	1006	1799	63	4		4	ASAH1	8	17933073	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	7467425	17933073	128430949	287	9613										
CDCA2	157313	hgsc.bcm.edu	37	chr8	25319603	25319603	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctaccttaaaaaatgtagacGacgttctgcagtcggtgctc	9	10	1	1	rs149260399		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:25319603G>T	ENST00000330560.3	+	4	743	c.266G>T	c.(265-267)cGa>cTa	p.R89L	CDCA2_ENST00000380665.3_Missense_Mutation_p.R74L	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	89					mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R89Q(1)		breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		AAATGTAGACGACGTTCTGCA	0.403																																					p.R89L		Atlas-SNP	.											CDCA2,NS,carcinoma,0,1	CDCA2	78	.	1	Substitution - Missense(1)	cervix(1)	c.G266T						.						103	102	102					8																	25319603		2203	4300	6503	SO:0001583	missense	157313	exon4			GTAGACGACGTTC	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 81"					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.266G>T	chr8.hg19:g.25319603G>T	ENSP00000328228:p.Arg89Leu	120.0	1.0		53.0	40.0	NM_152562	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Missense_Mutation	SNP	ENST00000330560.3	hg19	CCDS6049.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.421180	0.42918	.	.	ENSG00000184661	ENST00000330560;ENST00000380665	T;T	0.66815	-0.23;-0.23	5.45	5.45	0.79879	.	0.000000	0.47455	D	0.000229	T	0.81211	0.4775	M	0.76002	2.32	0.42026	D	0.991006	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.83488	0.0068	10	0.87932	D	0	-11.0538	14.7814	0.69769	0.0:0.0:1.0:0.0	.	89;74;89	B7Z5Q5;E9PEI0;Q69YH5	.;.;CDCA2_HUMAN	L	89;74	ENSP00000328228:R89L;ENSP00000370040:R74L	ENSP00000328228:R89L	R	+	2	0	CDCA2	25375520	0.908000	0.30866	0.564000	0.28396	0.054000	0.15201	4.883000	0.63128	2.546000	0.85860	0.491000	0.48974	CGA	.	G|1.000;A|0.000		0.403	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562		T	25319603	G	T	25319603	3	4	73	1	0	0	0	0	1	0	0	0	3088	1058	37	1	276	1	CDCA2	8	25319603	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	7386530	25319603	121044419	288	9614										
FZD3	7976	hgsc.bcm.edu	37	chr8	28385435	28385435	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgcctgtatgtggtagttggGgtttctctcctcttagctgg	13	8	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:28385435G>C	ENST00000240093.3	+	5	1636	c.1158G>C	c.(1156-1158)ggG>ggC	p.G386G	FZD3_ENST00000537916.1_Silent_p.G386G|RNA5SP259_ENST00000365541.1_RNA	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	386					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		TGGTAGTTGGGGTTTCTCTCC	0.403																																					p.G386G		Atlas-SNP	.											.	FZD3	65	.	0			c.G1158C						.						129	127	127					8																	28385435		2203	4300	6503	SO:0001819	synonymous_variant	7976	exon5			AGTTGGGGTTTCT	AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"GPCR / Class F : Frizzled receptors"	4041	protein-coding gene	gene with protein product		606143	"frizzled (Drosophila) homolog 3", "frizzled homolog 3 (Drosophila)", "frizzled 3, seven transmembrane spanning receptor", "frizzled family receptor 3"			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.1158G>C	chr8.hg19:g.28385435G>C		142.0	0.0		69.0	50.0	NM_017412	A8K615	Silent	SNP	ENST00000240093.3	hg19	CCDS6069.1																																																																																			.	.		0.403	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866		C	28385435	G	C	28385435	2	2	73	1	0	0	0	0	0	0	0	1	6139	1219	43	4		4	FZD3	8	28385435	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3065832	28385435	117978587	289	9615										
IKBKB	3551	hgsc.bcm.edu	37	chr8	42171857	42171857	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caggcattcaaaagtgcggcAgaagagtgaggtggacattg	15	6	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:42171857A>G	ENST00000520810.1	+	9	896	c.710A>G	c.(709-711)cAg>cGg	p.Q237R	IKBKB_ENST00000416505.2_Missense_Mutation_p.Q178R|IKBKB_ENST00000520835.1_Missense_Mutation_p.Q235R|IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000379708.3_Missense_Mutation_p.Q14R	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	237	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	AAAGTGCGGCAGAAGAGTGAG	0.423																																					p.Q237R		Atlas-SNP	.											.	IKBKB	88	.	0			c.A710G						.						244	215	225					8																	42171857		2203	4300	6503	SO:0001583	missense	3551	exon9			TGCGGCAGAAGAG	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.710A>G	chr8.hg19:g.42171857A>G	ENSP00000430684:p.Gln237Arg	165.0	0.0		95.0	61.0	NM_001556	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	hg19	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	A	12.62	1.993766	0.35131	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	T;T;T;T	0.40225	1.04;1.04;1.04;2.94	5.95	5.95	0.96441	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.243392	0.43919	D	0.000519	T	0.28333	0.0700	N	0.12502	0.225	0.39360	D	0.965906	B;B;P;B;B;B	0.49090	0.006;0.007;0.919;0.004;0.009;0.016	B;B;B;B;B;B	0.40256	0.007;0.011;0.324;0.02;0.02;0.021	T	0.16660	-1.0395	10	0.45353	T	0.12	.	16.4159	0.83738	1.0:0.0:0.0:0.0	.	178;235;14;188;237;237	B4E0U4;O14920-2;B3KRB7;Q59GL9;O14920;Q32ND9	.;.;.;.;IKKB_HUMAN;.	R	237;178;235;14	ENSP00000430684:Q237R;ENSP00000404920:Q178R;ENSP00000430868:Q235R;ENSP00000369030:Q14R	ENSP00000369030:Q14R	Q	+	2	0	IKBKB	42291014	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.520000	0.60524	2.279000	0.76181	0.533000	0.62120	CAG	.	.		0.423	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			G	42171857	A	G	42171857	3	3	73	1	0	0	0	0	1	0	0	0	7620	188	7	2	740	2	IKBKB	8	42171857	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	13786422	42171857	104192165	290	9616										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52320842	52320842	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcaggactgagaaggtaggaGggtgcccgccatttagcagc	15	9	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:52320842G>C	ENST00000356297.4	-	17	3442	c.3342C>G	c.(3340-3342)ccC>ccG	p.P1114P	PXDNL_ENST00000543296.1_Silent_p.P1114P	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1114					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GAAGGTAGGAGGGTGCCCGCC	0.572																																					p.P1114P		Atlas-SNP	.											PXDNL_ENST00000356297,right_upper_lobe,carcinoma,-2,2	PXDNL	414	.	0			c.C3342G						.						53	59	57					8																	52320842		1913	4119	6032	SO:0001819	synonymous_variant	137902	exon17			GTAGGAGGGTGCC		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.3342C>G	chr8.hg19:g.52320842G>C		145.0	0.0		193.0	74.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.516802	0.00975	.	.	ENSG00000147485	ENST00000522933	T	0.68025	-0.3	3.82	-1.31	0.09230	.	0.136128	0.33515	N	0.004836	T	0.52629	0.1746	.	.	.	0.25024	N	0.991312	.	.	.	.	.	.	T	0.46978	-0.9152	7	0.51188	T	0.08	.	1.3668	0.02202	0.3297:0.1462:0.3762:0.1479	.	.	.	.	R	233	ENSP00000428114:P233R	ENSP00000428114:P233R	P	-	2	0	PXDNL	52483395	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-2.714000	0.00815	-0.192000	0.10432	0.655000	0.94253	CCT	.	.		0.572	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		C	52320842	G	C	52320842	2	2	73	1	0	0	0	0	0	0	0	1	12863	987	35	4		4	PXDNL	8	52320842	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	10148985	52320842	94043180	291	9617										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321428	52321428	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaggaaagcctgtcttcaggAgaccccgaggcaccgaaggg	14	11	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:52321428A>T	ENST00000356297.4	-	17	2856	c.2756T>A	c.(2755-2757)cTc>cAc	p.L919H	PXDNL_ENST00000543296.1_Missense_Mutation_p.L919H	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	919					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TGTCTTCAGGAGACCCCGAGG	0.612																																					p.L919H		Atlas-SNP	.											.	PXDNL	414	.	0			c.T2756A						.						28	32	30					8																	52321428		1949	4133	6082	SO:0001583	missense	137902	exon17			TTCAGGAGACCCC		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2756T>A	chr8.hg19:g.52321428A>T	ENSP00000348645:p.Leu919His	178.0	0.0		201.0	67.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.21|12.21	1.870622|1.870622	0.33069|0.33069	.|.	.|.	ENSG00000147485|ENSG00000147485	ENST00000356297;ENST00000543296|ENST00000522933	T;T|.	0.70986|.	-0.53;-0.53|.	4.02|4.02	4.02|4.02	0.46733|0.46733	.|.	0.000000|.	0.39909|.	N|.	0.001226|.	T|T	0.62853|0.62853	0.2462|0.2462	M|M	0.82323|0.82323	2.585|2.585	0.32991|0.32991	D|D	0.52495|0.52495	D|.	0.67145|.	0.996|.	D|.	0.66979|.	0.948|.	T|T	0.71876|0.71876	-0.4460|-0.4460	10|5	0.66056|.	D|.	0.02|.	.|.	6.1019|6.1019	0.20051|0.20051	0.88:0.0:0.12:0.0|0.88:0.0:0.12:0.0	.|.	919|.	A1KZ92|.	PXDNL_HUMAN|.	H|T	919|38	ENSP00000348645:L919H;ENSP00000444865:L919H|.	ENSP00000348645:L919H|.	L|S	-|-	2|1	0|0	PXDNL|PXDNL	52483981|52483981	0.986000|0.986000	0.35501|0.35501	0.073000|0.073000	0.20177|0.20177	0.072000|0.072000	0.16883|0.16883	3.951000|3.951000	0.56684|0.56684	1.447000|1.447000	0.47661|0.47661	0.533000|0.533000	0.62120|0.62120	CTC|TCC	.	.		0.612	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		T	52321428	A	T	52321428	3	4	73	1	0	0	0	0	1	0	0	0	12863	304	11	4	1663	4	PXDNL	8	52321428	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	586	52321428	94042594	292	9618										
FAM150A	389658	hgsc.bcm.edu	37	chr8	53451056	53451056	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcttgttaacaatctagcacAtcttttgtaatctaggaaaa	5	7	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:53451056A>G	ENST00000358543.4	-	4	587	c.337T>C	c.(337-339)Tgt>Cgt	p.C113R	FAM150A_ENST00000523939.1_Intron	NM_207413.3	NP_997296.1	Q6UXT8	F150A_HUMAN	family with sequence similarity 150, member A	113						extracellular region (GO:0005576)				lung(1)	1		Lung NSC(129;0.0919)|all_epithelial(80;0.125)|all_lung(136;0.17)				AATCTAGCACATCTTTTGTAA	0.308																																					p.C113R		Atlas-SNP	.											.	FAM150A	6	.	0			c.T337C						.						67	68	68					8																	53451056		2203	4299	6502	SO:0001583	missense	389658	exon4			TAGCACATCTTTT		CCDS6150.1	8q11.23	2007-12-18			ENSG00000196711	ENSG00000196711			33775	protein-coding gene	gene with protein product							Standard	NM_207413		Approved	UNQ9433	uc003xrd.3	Q6UXT8	OTTHUMG00000164256	ENST00000358543.4:c.337T>C	chr8.hg19:g.53451056A>G	ENSP00000351345:p.Cys113Arg	521.0	0.0		701.0	160.0	NM_207413	B7ZMG9	Missense_Mutation	SNP	ENST00000358543.4	hg19	CCDS6150.1	.	.	.	.	.	.	.	.	.	.	A	19.13	3.767787	0.69878	.	.	ENSG00000196711	ENST00000358543	.	.	.	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.77177	0.4092	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79916	-0.1601	9	0.87932	D	0	.	14.5285	0.67905	1.0:0.0:0.0:0.0	.	113	Q6UXT8	F150A_HUMAN	R	113	.	ENSP00000351345:C113R	C	-	1	0	FAM150A	53613609	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.772000	0.75001	2.128000	0.65567	0.528000	0.53228	TGT	.	.		0.308	FAM150A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377959.1	NM_207413		G	53451056	A	G	53451056	3	3	73	1	0	0	0	0	1	0	0	0	5461	217	8	2	56	2	FAM150A	8	53451056	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1129628	53451056	92912966	293	9619										
RGS20	8601	hgsc.bcm.edu	37	chr8	54764467	54764467	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttattgtgaaaacatgccccAgctttcccaagataaccaag	6	11	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:54764467A>T	ENST00000297313.3	+	1	100	c.8A>T	c.(7-9)cAg>cTg	p.Q3L	RGS20_ENST00000344277.6_Missense_Mutation_p.Q3L	NM_170587.2	NP_733466.1	O76081	RGS20_HUMAN	regulator of G-protein signaling 20	3					positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			AACATGCCCCAGCTTTCCCAA	0.458																																					p.Q3L		Atlas-SNP	.											.	RGS20	51	.	0			c.A8T						.						112	117	115					8																	54764467		2203	4300	6503	SO:0001583	missense	8601	exon1			TGCCCCAGCTTTC	AF074979	CCDS6155.1, CCDS6156.1, CCDS69482.1	8q11.23	2008-07-25	2007-08-14		ENSG00000147509	ENSG00000147509		"Regulators of G-protein signaling"	14600	protein-coding gene	gene with protein product		607193	"regulator of G-protein signalling 20"			9748279, 9748280	Standard	NM_003702		Approved	RGSZ1, ZGAP1	uc003xrp.3	O76081	OTTHUMG00000164750	ENST00000297313.3:c.8A>T	chr8.hg19:g.54764467A>T	ENSP00000297313:p.Gln3Leu	95.0	0.0		124.0	32.0	NM_170587	Q96BG9	Missense_Mutation	SNP	ENST00000297313.3	hg19	CCDS6155.1	.	.	.	.	.	.	.	.	.	.	A	9.494	1.101437	0.20632	.	.	ENSG00000147509	ENST00000297313;ENST00000344277	T;T	0.40225	1.07;1.04	4.84	-0.964	0.10326	.	.	.	.	.	T	0.25568	0.0622	L	0.29908	0.895	0.09310	N	1	B;B	0.10296	0.001;0.003	B;B	0.08055	0.002;0.003	T	0.25398	-1.0133	9	0.62326	D	0.03	.	2.9029	0.05712	0.3208:0.0:0.3564:0.3228	.	3;3	O76081-2;O76081	.;RGS20_HUMAN	L	3	ENSP00000297313:Q3L;ENSP00000344630:Q3L	ENSP00000297313:Q3L	Q	+	2	0	RGS20	54927020	0.000000	0.05858	0.000000	0.03702	0.613000	0.37349	0.202000	0.17295	-0.010000	0.14271	-1.093000	0.02169	CAG	.	.		0.458	RGS20-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380058.1			T	54764467	A	T	54764467	3	4	73	1	0	0	0	0	1	0	0	0	13318	188	7	4	10	4	RGS20	8	54764467	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1313411	54764467	91599555	294	9620										
CSPP1	10987	hgsc.bcm.edu	37	chr8	67976717	67976717	+	5'Flank	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtgtgtctccccggacgcgAgcccgctcccctgagtaaga	12	15	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:67976717A>T	ENST00000357849.4	-	0	0				CSPP1_ENST00000262210.5_Silent_p.R28R|COPS5_ENST00000519963.1_Intron|COPS5_ENST00000517736.1_5'UTR|CSPP1_ENST00000412460.1_5'UTR	NM_006837.2	NP_006828.2	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5						cullin deneddylation (GO:0010388)|exosomal secretion (GO:1990182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein deneddylation (GO:0000338)|protein deubiquitination (GO:0016579)|regulation of cell cycle (GO:0051726)|regulation of JNK cascade (GO:0046328)|transcription from RNA polymerase II promoter (GO:0006366)|translation (GO:0006412)|translational initiation (GO:0006413)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 3 complex (GO:0005852)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|transcription coactivator activity (GO:0003713)|translation initiation factor activity (GO:0003743)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(3)	14	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)			CCCGGACGCGAGCCCGCTCCC	0.672											OREG0018811	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R28R		Atlas-SNP	.											.	CSPP1	129	.	0			c.A84T						.						28	33	32					8																	67976717		2049	4189	6238	SO:0001631	upstream_gene_variant	79848	exon1			GACGCGAGCCCGC	U65928	CCDS6198.1	8q13.1	2013-03-14	2013-03-14		ENSG00000121022	ENSG00000121022			2240	protein-coding gene	gene with protein product		604850	"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 5", "COP9 constitutive photomorphogenic homolog subunit 5 (Arabidopsis)"			8837781, 9341143	Standard	NM_006837		Approved	JAB1, SGN5, MOV-34, CSN5	uc003xxe.3	Q92905	OTTHUMG00000164563		chr8.hg19:g.67976717A>T	Exception_encountered	85.0	0.0	1103	123.0	73.0	NM_024790	O15386|Q6AW95|Q86WQ4|Q9BQ17	Silent	SNP	ENST00000357849.4	hg19	CCDS6198.1																																																																																			.	.		0.672	COPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379245.2			T	67976717	A	T	67976717	1	4	73	0	1	0	0	0	0	0	0	0	3964	291	11	4		4	CSPP1	8	67976717	5'Flank	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	13212250	67976717	78387305	295	9621										
PREX2	80243	hgsc.bcm.edu	37	chr8	68965436	68965436	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caaaaacacctgaagagaagCatgaatggtttgaagctatt	9	6	0	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:68965436C>A	ENST00000288368.4	+	9	1325	c.1048C>A	c.(1048-1050)Cat>Aat	p.H350N	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	350	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TGAAGAGAAGCATGAATGGTT	0.383																																					p.H350N		Atlas-SNP	.											.	PREX2	614	.	0			c.C1048A						.						123	114	117					8																	68965436		2203	4300	6503	SO:0001583	missense	80243	exon9			GAGAAGCATGAAT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1048C>A	chr8.hg19:g.68965436C>A	ENSP00000288368:p.His350Asn	142.0	0.0		192.0	130.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.555438	0.65425	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	D	0.86694	-2.16	5.42	5.42	0.78866	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.063303	0.64402	D	0.000002	T	0.79924	0.4530	N	0.11064	0.09	0.54753	D	0.999986	B;B;B	0.24920	0.114;0.009;0.018	B;B;B	0.30943	0.122;0.012;0.043	T	0.75590	-0.3265	10	0.41790	T	0.15	.	19.2197	0.93791	0.0:1.0:0.0:0.0	.	350;350;350	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	N	350	ENSP00000288368:H350N	ENSP00000288368:H350N	H	+	1	0	PREX2	69127990	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.542000	0.85734	0.655000	0.94253	CAT	.	.		0.383	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		A	68965436	C	A	68965436	3	1	73	1	0	0	0	0	1	0	0	0	12489	710	25	3	1082	3	PREX2	8	68965436	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	988719	68965436	77398586	296	9622										
STMN2	11075	hgsc.bcm.edu	37	chr8	80553736	80553736	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tccaaagaagaaagacctgtCcctggaggagatccagaaga	11	9	0	6			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:80553736C>T	ENST00000220876.7	+	3	621	c.239C>T	c.(238-240)tCc>tTc	p.S80F	STMN2_ENST00000518491.1_Missense_Mutation_p.S69F|STMN2_ENST00000518111.1_Missense_Mutation_p.S80F	NM_001199214.1|NM_007029.3	NP_001186143.1|NP_008960.2	Q93045	STMN2_HUMAN	stathmin 2	80	Regulatory/phosphorylation domain. {ECO:0000255}.|SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				cellular response to nerve growth factor stimulus (GO:1990090)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|positive regulation of microtubule depolymerization (GO:0031117)|positive regulation of neuron projection development (GO:0010976)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)			AAAGACCTGTCCCTGGAGGAG	0.502																																					p.S80F		Atlas-SNP	.											.	STMN2	23	.	0			c.C239T						.						55	54	54					8																	80553736		1886	4125	6011	SO:0001583	missense	11075	exon3			ACCTGTCCCTGGA		CCDS43748.1, CCDS56542.1	8q21.13	2014-04-01	2014-04-01	2001-07-13	ENSG00000104435	ENSG00000104435			10577	protein-coding gene	gene with protein product		600621	"stathmin-like 2"	SCGN10		8622778, 12140291	Standard	NM_007029		Approved	SCG10	uc022awk.1	Q93045	OTTHUMG00000164610	ENST00000220876.7:c.239C>T	chr8.hg19:g.80553736C>T	ENSP00000220876:p.Ser80Phe	266.0	0.0		300.0	20.0	NM_007029	A8K9M2|G3V110|O14952|Q6PK68	Missense_Mutation	SNP	ENST00000220876.7	hg19	CCDS43748.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.696868	0.88830	.	.	ENSG00000104435	ENST00000220876;ENST00000414622;ENST00000518111;ENST00000518491	.	.	.	5.49	5.49	0.81192	.	0.095316	0.85682	D	0.000000	D	0.85923	0.5810	M	0.90145	3.09	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.998;0.997	D	0.88514	0.3091	9	0.87932	D	0	-6.5853	19.3806	0.94532	0.0:1.0:0.0:0.0	.	80;80	B7Z4K3;Q93045	.;STMN2_HUMAN	F	80;69;80;69	.	ENSP00000220876:S80F	S	+	2	0	STMN2	80716291	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.818000	0.86416	2.564000	0.86499	0.467000	0.42956	TCC	.	.		0.502	STMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379261.2	NM_007029		T	80553736	C	T	80553736	3	4	73	1	0	0	0	0	1	0	0	0	15324	855	30	3	249	3	STMN2	8	80553736	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	11588300	80553736	65810286	297	9623										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106813578	106813578	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagaagcgaacttccccagaGccaaaaggccatgcagacta	9	13	0	3	rs377466426		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:106813578G>A	ENST00000407775.2	+	8	1518	c.1268G>A	c.(1267-1269)aGc>aAc	p.S423N	RP11-152P17.2_ENST00000509144.2_RNA|ZFPM2_ENST00000517361.1_Missense_Mutation_p.S291N|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000520492.1_Missense_Mutation_p.S291N|ZFPM2_ENST00000378472.4_Missense_Mutation_p.S154N|RP11-152P17.2_ENST00000520594.1_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000524045.2_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	423					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			CTTCCCCAGAGCCAAAAGGCC	0.483																																					p.S423N		Atlas-SNP	.											.	ZFPM2	219	.	0			c.G1268A						.	G	ASN/SER	1,3929		0,1,1964	64	64	64		1268	4.1	1	8		64	0,8338		0,0,4169	no	missense	ZFPM2	NM_012082.3	46	0,1,6133	AA,AG,GG		0.0,0.0254,0.0082	benign	423/1152	106813578	1,12267	1965	4169	6134	SO:0001583	missense	23414	exon8			CCCAGAGCCAAAA	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.1268G>A	chr8.hg19:g.106813578G>A	ENSP00000384179:p.Ser423Asn	149.0	0.0		299.0	134.0	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	hg19	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.941878	0.34283	2.54E-4	0.0	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.20881	2.04;2.51;2.51;3.71	5.91	4.1	0.47936	.	0.168138	0.64402	D	0.000003	T	0.22003	0.0530	L	0.43152	1.355	0.45852	D	0.998716	P	0.46395	0.877	P	0.45829	0.494	T	0.01800	-1.1271	10	0.30078	T	0.28	.	12.0684	0.53601	0.0663:0.1267:0.807:0.0	.	423	Q8WW38	FOG2_HUMAN	N	423;291;291;154	ENSP00000384179:S423N;ENSP00000430757:S291N;ENSP00000428720:S291N;ENSP00000367733:S154N	ENSP00000367733:S154N	S	+	2	0	ZFPM2	106882754	1.000000	0.71417	0.986000	0.45419	0.722000	0.41435	2.503000	0.45407	1.492000	0.48499	0.655000	0.94253	AGC	.	.		0.483	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			A	106813578	G	A	106813578	3	1	73	1	0	0	0	0	1	0	0	0	17673	971	34	3	1298	3	ZFPM2	8	106813578	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	26259842	106813578	39550444	298	9624										
TRHR	7201	hgsc.bcm.edu	37	chr8	110100121	110100121	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cattgagaggtacatagcaaTctgtcaccccatcaaagccc	7	13	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:110100121T>G	ENST00000518632.1	+	2	731	c.380T>G	c.(379-381)aTc>aGc	p.I127S	TRHR_ENST00000311762.2_Missense_Mutation_p.I127S			P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	127					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thyrotropin-releasing hormone receptor activity (GO:0004997)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(12)|prostate(4)|skin(4)|urinary_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			TACATAGCAATCTGTCACCCC	0.423																																					p.I127S		Atlas-SNP	.											.	TRHR	74	.	0			c.T380G						.						135	116	122					8																	110100121		2203	4300	6503	SO:0001583	missense	7201	exon1			TAGCAATCTGTCA		CCDS6311.1	8q23.1	2013-09-20			ENSG00000174417	ENSG00000174417			12299	protein-coding gene	gene with protein product		188545				8128317	Standard	NM_003301		Approved		uc003ymz.4	P34981	OTTHUMG00000164910	ENST00000518632.1:c.380T>G	chr8.hg19:g.110100121T>G	ENSP00000430711:p.Ile127Ser	237.0	0.0		416.0	77.0	NM_003301	Q2M339	Missense_Mutation	SNP	ENST00000518632.1	hg19	CCDS6311.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.945878	0.73672	.	.	ENSG00000174417	ENST00000518632;ENST00000311762	D;D	0.82167	-1.58;-1.58	6.06	6.06	0.98353	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.95245	0.8458	H	0.99312	4.51	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97228	0.9882	10	0.87932	D	0	-46.8178	15.7905	0.78357	0.0:0.0:0.0:1.0	.	127	P34981	TRFR_HUMAN	S	127	ENSP00000430711:I127S;ENSP00000309818:I127S	ENSP00000309818:I127S	I	+	2	0	TRHR	110169297	1.000000	0.71417	0.991000	0.47740	0.990000	0.78478	8.033000	0.88852	2.324000	0.78689	0.533000	0.62120	ATC	.	.		0.423	TRHR-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380892.1			G	110100121	T	G	110100121	3	3	73	1	0	0	0	0	1	0	0	0	16495	1435	50	5	382	5	TRHR	8	110100121	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3286543	110100121	36263901	299	9625										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110509272	110509272	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggatttaccatttggacatgCtgggattatggaatttattt	10	4	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:110509272C>G	ENST00000378402.5	+	64	10556	c.10452C>G	c.(10450-10452)tgC>tgG	p.C3484W		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3484					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TTTGGACATGCTGGGATTATG	0.338										HNSCC(38;0.096)																											p.C3484W		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.C10452G						.						130	123	125					8																	110509272		1830	4087	5917	SO:0001583	missense	93035	exon64			GACATGCTGGGAT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.10452C>G	chr8.hg19:g.110509272C>G	ENSP00000367655:p.Cys3484Trp	140.0	0.0		318.0	68.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.071804	0.55646	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	T;T	0.80393	-1.37;-1.35	5.8	3.95	0.45737	Pectin lyase fold/virulence factor (1);	0.054481	0.64402	D	0.000001	D	0.85539	0.5720	M	0.62723	1.935	0.45378	D	0.998369	D	0.71674	0.998	D	0.74023	0.982	D	0.84274	0.0490	10	0.66056	D	0.02	.	7.3049	0.26443	0.0:0.7208:0.0:0.2792	.	3484	Q86WI1	PKHL1_HUMAN	W	3484;412	ENSP00000367655:C3484W;ENSP00000437376:C412W	ENSP00000367655:C3484W	C	+	3	2	PKHD1L1	110578448	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.451000	0.21779	0.741000	0.32674	0.650000	0.86243	TGC	.	.		0.338	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		G	110509272	C	G	110509272	3	3	73	1	0	0	0	0	1	0	0	0	11981	805	28	4	10706	4	PKHD1L1	8	110509272	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	409151	110509272	35854750	300	9626										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113326785	113326785	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agatttgggtaactgtcaggAtatccagggctcaatatgac	11	7	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:113326785A>T	ENST00000297405.5	-	48	7666	c.7422T>A	c.(7420-7422)taT>taA	p.Y2474*	CSMD3_ENST00000352409.3_Nonsense_Mutation_p.Y2404*|CSMD3_ENST00000343508.3_Nonsense_Mutation_p.Y2434*|CSMD3_ENST00000455883.2_Nonsense_Mutation_p.Y2370*	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2474	CUB 14. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AACTGTCAGGATATCCAGGGC	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.Y2474X		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T7422A						.						99	95	96					8																	113326785		2203	4300	6503	SO:0001587	stop_gained	114788	exon48			GTCAGGATATCCA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7422T>A	chr8.hg19:g.113326785A>T	ENSP00000297405:p.Tyr2474*	184.0	0.0		354.0	83.0	NM_198123	Q96PZ3	Nonsense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	48	14.907339	0.99815	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	.	.	.	4.98	2.6	0.31112	.	0.316121	0.28166	N	0.016342	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.6361	0.39809	0.8349:0.0:0.1651:0.0	.	.	.	.	X	2434;2474;1744;2370;2404	.	ENSP00000297405:Y2474X	Y	-	3	2	CSMD3	113395961	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	0.619000	0.24388	0.923000	0.37045	0.472000	0.43445	TAT	.	.		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113326785	A	T	113326785	4	4	73	1	0	0	0	0	0	1	0	0	3948	340	12	4	3797	4	CSMD3	8	113326785	Nonsense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2817513	113326785	33037237	301	9627										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113988150	113988150	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctggtactttgtgtatctgCtggatgaggagagagcccgt	14	8	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:113988150C>A	ENST00000297405.5	-	7	1502	c.1258G>T	c.(1258-1260)Gca>Tca	p.A420S	CSMD3_ENST00000352409.3_Missense_Mutation_p.A420S|CSMD3_ENST00000343508.3_Missense_Mutation_p.A380S|CSMD3_ENST00000455883.2_Intron	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	420						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TGTGTATCTGCTGGATGAGGA	0.458										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.A420S		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G1258T						.						202	178	186					8																	113988150		2203	4300	6503	SO:0001583	missense	114788	exon7			TATCTGCTGGATG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1258G>T	chr8.hg19:g.113988150C>A	ENSP00000297405:p.Ala420Ser	150.0	0.0		316.0	145.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.445554	0.63178	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000352409	T;T;T	0.19250	2.16;2.16;2.17	6.17	6.17	0.99709	.	0.277746	0.21304	N	0.076748	T	0.23532	0.0569	N	0.22421	0.69	0.32113	N	0.589046	P;P	0.45715	0.787;0.865	B;P	0.49361	0.404;0.608	T	0.02837	-1.1104	10	0.08837	T	0.75	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	420;380	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	S	380;420;420	ENSP00000345799:A380S;ENSP00000297405:A420S;ENSP00000343124:A420S	ENSP00000297405:A420S	A	-	1	0	CSMD3	114057326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.335000	0.65929	2.941000	0.99782	0.655000	0.94253	GCA	.	.		0.458	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113988150	C	A	113988150	3	1	73	1	0	0	0	0	1	0	0	0	3948	797	28	3	10125	3	CSMD3	8	113988150	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	661365	113988150	32375872	302	9628										
ENPP2	5168	hgsc.bcm.edu	37	chr8	120628551	120628551	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	taaatttctctcgccctcgcAgatgaaaagtggcatcaaat	7	10	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:120628551A>T	ENST00000075322.6	-	8	789	c.731T>A	c.(730-732)cTg>cAg	p.L244Q	ENPP2_ENST00000522826.1_Missense_Mutation_p.L244Q|ENPP2_ENST00000259486.6_Missense_Mutation_p.L244Q|ENPP2_ENST00000427067.2_Missense_Mutation_p.L240Q	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	244	Substrate binding. {ECO:0000250}.				cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TCGCCCTCGCAGATGAAAAGT	0.373																																					p.L244Q	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.T731A						.						123	110	114					8																	120628551		2203	4300	6503	SO:0001583	missense	5168	exon8			CCTCGCAGATGAA	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"autotaxin"	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.731T>A	chr8.hg19:g.120628551A>T	ENSP00000075322:p.Leu244Gln	71.0	0.0		195.0	93.0	NM_001130863	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	hg19	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.436096	0.83885	.	.	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522826;ENST00000075322;ENST00000520066	T;T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95;-0.95	5.55	5.55	0.83447	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.129957	0.53938	D	0.000042	D	0.82903	0.5138	L	0.49350	1.555	0.58432	D	0.999998	D;D;D	0.89917	0.999;1.0;0.998	D;D;D	0.76071	0.987;0.97;0.977	D	0.84756	0.0759	10	0.87932	D	0	.	15.7051	0.77573	1.0:0.0:0.0:0.0	.	244;244;244	E9PHP7;Q13822;Q13822-2	.;ENPP2_HUMAN;.	Q	244;240;244;244;226	ENSP00000259486:L244Q;ENSP00000403315:L240Q;ENSP00000428291:L244Q;ENSP00000075322:L244Q;ENSP00000428304:L226Q	ENSP00000075322:L244Q	L	-	2	0	ENPP2	120697732	1.000000	0.71417	0.997000	0.53966	0.694000	0.40290	9.339000	0.96797	2.106000	0.64143	0.460000	0.39030	CTG	.	.		0.373	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			T	120628551	A	T	120628551	3	4	73	1	0	0	0	0	1	0	0	0	5132	188	7	4	2171	4	ENPP2	8	120628551	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	6640401	120628551	25735471	303	9629										
GSDMC	56169	hgsc.bcm.edu	37	chr8	130778031	130778031	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gaaatgatggctctggatccAacagtttcctggggatttaa	11	7	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:130778031A>G	ENST00000276708.4	-	4	1294	c.413T>C	c.(412-414)tTg>tCg	p.L138S		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	138						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						CTCTGGATCCAACAGTTTCCT	0.517																																					p.L138S		Atlas-SNP	.											.	GSDMC	71	.	0			c.T413C						.						62	57	59					8																	130778031		2203	4300	6503	SO:0001583	missense	56169	exon4			GGATCCAACAGTT	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"melanoma-derived leucine zipper, extra-nuclear factor"	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.413T>C	chr8.hg19:g.130778031A>G	ENSP00000276708:p.Leu138Ser	73.0	0.0		117.0	29.0	NM_031415	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	hg19	CCDS6360.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.428422	0.43122	.	.	ENSG00000147697	ENST00000276708	T	0.25579	1.79	4.51	2.07	0.26955	.	0.981729	0.08288	N	0.968837	T	0.45054	0.1323	M	0.72118	2.19	0.09310	N	1	D	0.76494	0.999	D	0.73708	0.981	T	0.17440	-1.0369	10	0.62326	D	0.03	.	3.7426	0.08536	0.7084:0.0:0.1033:0.1883	.	138	Q9BYG8	GSDMC_HUMAN	S	138	ENSP00000276708:L138S	ENSP00000276708:L138S	L	-	2	0	GSDMC	130847213	0.001000	0.12720	0.000000	0.03702	0.101000	0.19017	0.884000	0.28214	0.255000	0.21593	0.482000	0.46254	TTG	.	.		0.517	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1			G	130778031	A	G	130778031	3	3	73	1	0	0	0	0	1	0	0	0	6827	131	5	2	1157	2	GSDMC	8	130778031	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	10149480	130778031	15585991	304	9630										
ADCY8	114	hgsc.bcm.edu	37	chr8	131955635	131955635	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctggcaaagagctcgttgaGcatcctgaccagctcctgag	11	12	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:131955635G>A	ENST00000286355.5	-	4	3407	c.1315C>T	c.(1315-1317)Ctc>Ttc	p.L439F	RP11-737F9.1_ENST00000523318.1_RNA|ADCY8_ENST00000377928.3_Missense_Mutation_p.L439F	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	439					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			AGCTCGTTGAGCATCCTGACC	0.473										HNSCC(32;0.087)																											p.L439F		Atlas-SNP	.											.	ADCY8	291	.	0			c.C1315T						.						61	57	58					8																	131955635		2203	4300	6503	SO:0001583	missense	114	exon4			CGTTGAGCATCCT	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1315C>T	chr8.hg19:g.131955635G>A	ENSP00000286355:p.Leu439Phe	116.0	0.0		175.0	77.0	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.385362	0.82792	.	.	ENSG00000155897	ENST00000286355;ENST00000377928;ENST00000522949	D;D;D	0.88277	-2.36;-2.36;-2.36	5.65	4.55	0.56014	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.96562	0.8878	H	0.99415	4.555	0.36593	D	0.874223	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.97262	0.9905	10	0.87932	D	0	.	8.863	0.35269	0.1918:0.0:0.8082:0.0	.	439;439	E7EVL1;P40145	.;ADCY8_HUMAN	F	439;439;54	ENSP00000286355:L439F;ENSP00000367161:L439F;ENSP00000428010:L54F	ENSP00000286355:L439F	L	-	1	0	ADCY8	132024817	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.278000	0.43426	2.825000	0.97269	0.655000	0.94253	CTC	.	.		0.473	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	131955635	G	A	131955635	3	1	73	1	0	0	0	0	1	0	0	0	300	971	34	3	2500	3	ADCY8	8	131955635	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1177604	131955635	14408387	305	9631										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139705929	139705929	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gagccccatgtgcaccttccTgtcccttggcaccctgcaca	8	18	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:139705929T>G	ENST00000303045.6	-	35	3160	c.2714A>C	c.(2713-2715)cAg>cCg	p.Q905P	COL22A1_ENST00000435777.1_Missense_Mutation_p.Q905P|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	905	Collagen-like 7.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TGCACCTTCCTGTCCCTTGGC	0.637										HNSCC(7;0.00092)																											p.Q905P		Atlas-SNP	.											.	COL22A1	390	.	0			c.A2714C						.						37	32	34					8																	139705929		2198	4297	6495	SO:0001583	missense	169044	exon35			CCTTCCTGTCCCT	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2714A>C	chr8.hg19:g.139705929T>G	ENSP00000303153:p.Gln905Pro	73.0	0.0		133.0	32.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	T	7.307	0.614116	0.14129	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.93307	-3.2;-3.2	3.71	3.71	0.42584	.	0.465293	0.17680	U	0.165657	T	0.82089	0.4961	N	0.02865	-0.47	0.24878	N	0.992246	P;B	0.40066	0.701;0.389	B;B	0.39738	0.126;0.308	T	0.74788	-0.3546	10	0.29301	T	0.29	.	9.0677	0.36473	0.0:0.0:0.0:1.0	.	905;905	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	P	905;905;618	ENSP00000303153:Q905P;ENSP00000387655:Q905P	ENSP00000303153:Q905P	Q	-	2	0	COL22A1	139775111	0.961000	0.32948	0.983000	0.44433	0.321000	0.28281	1.180000	0.32005	1.921000	0.55644	0.519000	0.50382	CAG	.	.		0.637	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		G	139705929	T	G	139705929	3	3	73	1	0	0	0	0	1	0	0	0	3683	1580	55	5	2290	5	COL22A1	8	139705929	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	7750294	139705929	6658093	306	9632										
BAI1	575	hgsc.bcm.edu	37	chr8	143558633	143558633	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtgcaacaactctgccgtgTgcccaggtgggtgggacctt	14	11	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:143558633T>G	ENST00000517894.1	+	5	2110	c.1216T>G	c.(1216-1218)Tgc>Ggc	p.C406G	BAI1_ENST00000323289.5_Missense_Mutation_p.C406G			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	406	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CTCTGCCGTGTGCCCAGGTGG	0.731																																					p.C406G		Atlas-SNP	.											.	BAI1	146	.	0			c.T1216G						.						15	19	18					8																	143558633		2048	4147	6195	SO:0001583	missense	575	exon4			GCCGTGTGCCCAG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.1216T>G	chr8.hg19:g.143558633T>G	ENSP00000430945:p.Cys406Gly	42.0	0.0		54.0	10.0	NM_001702		Missense_Mutation	SNP	ENST00000517894.1	hg19		.	.	.	.	.	.	.	.	.	.	T	23.1	4.380670	0.82792	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	D;D	0.96459	-4.02;-4.02	4.44	4.44	0.53790	.	0.000000	0.85682	U	0.000000	D	0.98131	0.9383	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.99023	1.0818	10	0.87932	D	0	.	13.1646	0.59562	0.0:0.0:0.0:1.0	.	406	E9PBK0	.	G	406	ENSP00000430945:C406G;ENSP00000313046:C406G	ENSP00000313046:C406G	C	+	1	0	BAI1	143555635	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.716000	0.84723	1.747000	0.51819	0.459000	0.35465	TGC	.	.		0.731	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		G	143558633	T	G	143558633	3	3	73	1	0	0	0	0	1	0	0	0	1298	1696	59	5	1230	5	BAI1	8	143558633	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3852704	143558633	2805389	307	9633										
ARC	23237	hgsc.bcm.edu	37	chr8	143694546	143694546	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtgggggccggccggctcggCcgcctgctccaggtcatcct	16	16	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:143694546C>A	ENST00000356613.2	-	1	2287	c.1087G>T	c.(1087-1089)Gcc>Tcc	p.A363S	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	0					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				GCCGGCTCGGCCGCCTGCTCC	0.711																																					p.A363S		Atlas-SNP	.											.	ARC	34	.	0			c.G1087T						.						14	17	16					8																	143694546		2196	4298	6494	SO:0001583	missense	23237	exon1			GCTCGGCCGCCTG	AF193421	CCDS34950.1	8q24.3	2008-08-01			ENSG00000198576	ENSG00000198576			648	protein-coding gene	gene with protein product		612461				10970730, 17466953	Standard	NM_015193		Approved	KIAA0278, Arg3.1	uc003ywn.2	Q7LC44	OTTHUMG00000134310	ENST00000356613.2:c.1087G>T	chr8.hg19:g.143694546C>A	ENSP00000349022:p.Ala363Ser	53.0	0.0		86.0	36.0	NM_015193	B4DFL0|O60937	Missense_Mutation	SNP	ENST00000356613.2	hg19	CCDS34950.1	.	.	.	.	.	.	.	.	.	.	C	4.022	0.001569	0.07819	.	.	ENSG00000198576	ENST00000356613	T	0.30182	1.54	4.61	-1.03	0.10102	.	0.294619	0.23476	U	0.047770	T	0.12305	0.0299	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32455	-0.9906	10	0.12103	T	0.63	.	10.164	0.42868	0.5094:0.3669:0.1237:0.0	.	363	Q7LC44	ARC_HUMAN	S	363	ENSP00000349022:A363S	ENSP00000349022:A363S	A	-	1	0	ARC	143691548	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.058000	0.11750	-0.652000	0.05408	-0.311000	0.09066	GCC	.	.		0.711	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2			A	143694546	C	A	143694546	3	1	73	1	0	0	0	0	1	0	0	0	841	739	26	3	107	3	ARC	8	143694546	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	135913	143694546	2669476	308	9634										
GLI4	2738	hgsc.bcm.edu	37	chr8	144351615	144351615	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccccttctgtcccgtcccctGtcagtctctcatcaccaggg	7	19	5	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:144351615G>T	ENST00000523522.1	+	1	88	c.49G>T	c.(49-51)Gtc>Ttc	p.V17F	GLI4_ENST00000517468.1_Missense_Mutation_p.V17F|GLI4_ENST00000344692.3_Missense_Mutation_p.V17F|GLI4_ENST00000521682.1_Missense_Mutation_p.V17F|GLI4_ENST00000340042.1_Missense_Mutation_p.V17F|ZFP41_ENST00000522452.1_Intron			P10075	GLI4_HUMAN	GLI family zinc finger 4	17					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(1)|lung(5)	9	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CCCGTCCCCTGTCAGTCTCTC	0.597																																					p.V17F		Atlas-SNP	.											.	GLI4	28	.	0			c.G49T						.						187	184	185					8																	144351615		2203	4300	6503	SO:0001583	missense	2738	exon2			TCCCCTGTCAGTC		CCDS6398.1	8q24.3	2013-01-08	2009-03-05		ENSG00000250571	ENSG00000250571		"Zinc fingers, C2H2-type"	4320	protein-coding gene	gene with protein product		165280	"GLI-Kruppel family member GLI4", "glioma-associated oncogene family zinc finger 4"			2850480	Standard	NM_138465		Approved	HKR4, ZNF928	uc003yxx.3	P10075	OTTHUMG00000164952	ENST00000523522.1:c.49G>T	chr8.hg19:g.144351615G>T	ENSP00000430987:p.Val17Phe	98.0	0.0		151.0	68.0	NM_138465	Q96CK9	Missense_Mutation	SNP	ENST00000523522.1	hg19	CCDS6398.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.342739	0.24339	.	.	ENSG00000250571	ENST00000521682;ENST00000340042;ENST00000344692;ENST00000517468;ENST00000523522;ENST00000520021	T;T	0.06528	3.29;3.29	4.1	0.876	0.19138	.	.	.	.	.	T	0.03477	0.0100	N	0.24115	0.695	0.09310	N	1	B	0.29085	0.232	B	0.24701	0.055	T	0.46190	-0.9209	9	0.09843	T	0.71	.	5.4408	0.16507	0.5044:0.0:0.4956:0.0	.	17	P10075	GLI4_HUMAN	F	17	ENSP00000345024:V17F;ENSP00000430987:V17F	ENSP00000345024:V17F	V	+	1	0	GLI4	144422990	0.000000	0.05858	0.002000	0.10522	0.253000	0.25986	-0.112000	0.10791	0.347000	0.23924	-0.244000	0.11960	GTC	.	.		0.597	GLI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381128.2			T	144351615	G	T	144351615	3	4	73	1	0	0	0	0	1	0	0	0	6448	1377	48	3	51	3	GLI4	8	144351615	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	657069	144351615	2012407	309	9635										
ZNF707	286075	hgsc.bcm.edu	37	chr8	144776308	144776308	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aggcctgcgggcaggcgttcAgcctgaaggaccgcctggct	16	13	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:144776308A>G	ENST00000532205.1	+	8	1623	c.724A>G	c.(724-726)Agc>Ggc	p.S242G	ZNF707_ENST00000454097.1_Missense_Mutation_p.S242G|ZNF707_ENST00000532158.1_Missense_Mutation_p.S242G|ZNF707_ENST00000358656.4_Missense_Mutation_p.S242G|RP11-429J17.2_ENST00000531565.1_RNA|ZNF707_ENST00000418203.2_Missense_Mutation_p.S242G			Q96C28	ZN707_HUMAN	zinc finger protein 707	242					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;5.6e-41)|Epithelial(56;1.02e-39)|all cancers(56;9.65e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GCAGGCGTTCAGCCTGAAGGA	0.642																																					p.S242G		Atlas-SNP	.											.	ZNF707	21	.	0			c.A724G						.						17	20	19					8																	144776308		2147	4246	6393	SO:0001583	missense	286075	exon6			GCGTTCAGCCTGA	AK001126	CCDS47932.1	8q24.3	2013-01-08				ENSG00000181135		"Zinc fingers, C2H2-type", "-"	27815	protein-coding gene	gene with protein product						12477932	Standard	NM_173831		Approved		uc010mfi.3	Q96C28		ENST00000532205.1:c.724A>G	chr8.hg19:g.144776308A>G	ENSP00000436212:p.Ser242Gly	49.0	0.0		89.0	10.0	NM_001100598	A8K317|B3KNY1|D3DWK7	Missense_Mutation	SNP	ENST00000532205.1	hg19	CCDS47932.1	.	.	.	.	.	.	.	.	.	.	A	12.96	2.094002	0.36952	.	.	ENSG00000181135	ENST00000454097;ENST00000358656;ENST00000532158;ENST00000532205;ENST00000418203	T;T;T;T;T	0.07688	3.17;3.17;3.17;3.17;3.17	2.99	0.242	0.15498	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05823	0.0152	N	0.20574	0.59	0.23632	N	0.997245	B;B	0.27997	0.197;0.108	B;B	0.36464	0.225;0.026	T	0.47661	-0.9100	8	.	.	.	-13.024	4.2736	0.10797	0.67:0.2033:0.1267:0.0	.	167;242	B4DV46;Q96C28	.;ZN707_HUMAN	G	242	ENSP00000409029:S242G;ENSP00000351482:S242G;ENSP00000436250:S242G;ENSP00000436212:S242G;ENSP00000413215:S242G	.	S	+	1	0	ZNF707	144848296	0.000000	0.05858	0.789000	0.31954	0.081000	0.17604	-1.674000	0.01949	0.217000	0.20800	0.460000	0.39030	AGC	.	.		0.642	ZNF707-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382197.1	NM_173831		G	144776308	A	G	144776308	3	3	73	1	0	0	0	0	1	0	0	0	18126	188	7	2	738	2	ZNF707	8	144776308	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	424693	144776308	1587714	310	9636										
DGAT1	8694	hgsc.bcm.edu	37	chr8	145540683	145540684	+	Splice_Site	INS	-	-	CC													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gatgccccccagagcactgaINScctcgtggaagaaggccgag							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr8:145540683_145540684insCC	ENST00000332324.4	-	15	1522		c.e15+1		GS1-393G12.12_ENST00000525023.1_RNA|DGAT1_ENST00000527438.1_Splice_Site	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1						acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	diacylglycerol O-acyltransferase activity (GO:0004144)|retinol O-fatty-acyltransferase activity (GO:0050252)|transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			CAGAGCACTGACCTCGTGGAAG	0.639																																					.		Atlas-Indel,Pindel	.											.	DGAT1	26	.	0			c.1248+2->GG						.																																			SO:0001630	splice_region_variant	8694	exon16			.	AF059202	CCDS6420.1	8q24.3	2014-05-06	2010-06-24	2001-11-09	ENSG00000185000	ENSG00000185000	2.3.1.20		2843	protein-coding gene	gene with protein product		604900	"diacylglycerol O-acyltransferase homolog 1 (mouse)"			9756920	Standard	NM_012079		Approved	ARGP1, DGAT	uc003zbv.3	O75907	OTTHUMG00000174606	ENST00000332324.4:c.1248+1->GG	chr8.hg19:g.145540684_145540685dupCC		68.0	0.0		116.0	58.0	NM_012079	B2RWQ2|D3DWL6|Q96BB8	Splice_Site	INS	ENST00000332324.4	hg19	CCDS6420.1																																																																																			.	.		0.639	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	NM_012079	Intron	CC	145540684	-	CC	145540683	8	5	73	1	0	1	1	0	0	0	1	0	4459	289	10	0	228	0	DGAT1	8	145540683	Splice_Site	INS	-	TCGA-CC-A7IH-01A-11D-A33K-10	764375	145540683	823339	311	9637										
FREM1	158326	hgsc.bcm.edu	37	chr9	14859459	14859459	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cccacaggataaaagtttctAtgaaggtatctctttcagta	7	8	3	1	rs375644504		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:14859459A>C	ENST00000380880.3	-	4	1136	c.353T>G	c.(352-354)aTa>aGa	p.I118R	FREM1_ENST00000422223.2_Missense_Mutation_p.I118R|FREM1_ENST00000380881.4_Missense_Mutation_p.I118R			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	118					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		AAAAGTTTCTATGAAGGTATC	0.423																																					p.I118R		Atlas-SNP	.											.	FREM1	261	.	0			c.T353G						.	A	ARG/ILE	1,3703		0,1,1851	105	102	103		353	-1	0.8	9		103	0,8184		0,0,4092	no	missense	FREM1	NM_144966.5	97	0,1,5943	CC,CA,AA		0.0,0.027,0.0084	benign	118/2180	14859459	1,11887	1852	4092	5944	SO:0001583	missense	158326	exon5			GTTTCTATGAAGG	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.353T>G	chr9.hg19:g.14859459A>C	ENSP00000370262:p.Ile118Arg	178.0	0.0		119.0	49.0	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	hg19	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	A	12.67	2.008270	0.35415	2.7E-4	0.0	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.11821	2.74;2.75;2.75	5.95	-1.02	0.10135	.	0.572649	0.21108	N	0.080025	T	0.11067	0.0270	L	0.36672	1.1	0.23515	N	0.997518	B	0.20164	0.042	B	0.22601	0.04	T	0.26224	-1.0109	10	0.66056	D	0.02	-0.0025	11.8127	0.52192	0.5406:0.0:0.4594:0.0	.	118	Q5H8C1	FREM1_HUMAN	R	118	ENSP00000370263:I118R;ENSP00000412940:I118R;ENSP00000370262:I118R	ENSP00000370257:I118R	I	-	2	0	FREM1	14849459	0.010000	0.17322	0.773000	0.31616	0.937000	0.57800	0.037000	0.13840	-0.223000	0.09943	-0.242000	0.12053	ATA	.	.		0.423	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		C	14859459	A	C	14859459	3	2	73	1	0	0	0	0	1	0	0	0	6052	449	16	5	6372	5	FREM1	9	14859459	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10		14859459	126353972	312	9638										
PTPLAD2	401494	hgsc.bcm.edu	37	chr9	21008034	21008034	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acttacctataaagagcatcAtgagatatattttcagcaca	5	8	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:21008034A>G	ENST00000495827.2	-	6	647	c.602T>C	c.(601-603)aTg>aCg	p.M201T	PTPLAD2_ENST00000513293.2_Missense_Mutation_p.M201T	NM_001010915.3	NP_001010915.2	Q5VWC8	HACD4_HUMAN	protein tyrosine phosphatase-like A domain containing 2	201					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)	10				Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10)		AAAGAGCATCATGAGATATAT	0.368																																					p.M201T		Atlas-SNP	.											.	PTPLAD2	26	.	0			c.T602C						.						107	101	103					9																	21008034		1865	4097	5962	SO:0001583	missense	401494	exon6			AGCATCATGAGAT		CCDS43791.1	9p21.3	2008-02-05			ENSG00000188921	ENSG00000188921			20920	protein-coding gene	gene with protein product		615941					Standard	NM_001010915		Approved	Em:AL662879.1, OTTHUMG00000021016	uc010mir.1	Q5VWC8	OTTHUMG00000021016	ENST00000495827.2:c.602T>C	chr9.hg19:g.21008034A>G	ENSP00000419503:p.Met201Thr	98.0	0.0		98.0	43.0	NM_001010915	Q7Z385	Missense_Mutation	SNP	ENST00000495827.2	hg19	CCDS43791.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.760240	0.31137	.	.	ENSG00000188921	ENST00000513293;ENST00000495827	T;T	0.28255	1.62;1.62	5.12	3.98	0.46160	.	0.330046	0.32918	N	0.005500	T	0.22126	0.0533	L	0.33485	1.01	0.36944	D	0.892527	B	0.09022	0.002	B	0.08055	0.003	T	0.09292	-1.0681	10	0.42905	T	0.14	-7.5059	8.8379	0.35123	0.8452:0.0:0.1548:0.0	.	201	Q5VWC8	HACD4_HUMAN	T	201	ENSP00000426475:M201T;ENSP00000419503:M201T	ENSP00000419503:M201T	M	-	2	0	PTPLAD2	20998034	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.076000	0.50081	0.902000	0.36520	0.528000	0.53228	ATG	.	.		0.368	PTPLAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055434.3	NM_001010915		G	21008034	A	G	21008034	3	3	73	1	0	0	0	0	1	0	0	0	12789	217	8	2	104	2	PTPLAD2	9	21008034	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	6148575	21008034	120205397	313	9639										
TEK	7010	hgsc.bcm.edu	37	chr9	27203079	27203079	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	catagggtcaagcaacccagCcttttctcatgaactggtga	9	11	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:27203079C>A	ENST00000380036.4	+	13	2613	c.2171C>A	c.(2170-2172)gCc>gAc	p.A724D	TEK_ENST00000519097.1_Missense_Mutation_p.A577D|TEK_ENST00000406359.4_Missense_Mutation_p.A681D	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	724	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		A -> T (in dbSNP:rs4631561). {ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	AGCAACCCAGCCTTTTCTCAT	0.473																																					p.A724D		Atlas-SNP	.											.	TEK	250	.	0			c.C2171A						.						79	76	77					9																	27203079		2203	4300	6503	SO:0001583	missense	7010	exon13			ACCCAGCCTTTTC	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2171C>A	chr9.hg19:g.27203079C>A	ENSP00000369375:p.Ala724Asp	185.0	0.0		134.0	56.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	C	6.709	0.499475	0.12762	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359	T;T;T	0.17691	2.26;2.26;2.26	5.58	3.62	0.41486	Fibronectin, type III (2);Immunoglobulin-like fold (1);	1.503030	0.04318	N	0.350123	T	0.15176	0.0366	N	0.08118	0	0.09310	N	1	B;B;B;B	0.23540	0.017;0.087;0.005;0.042	B;B;B;B	0.32928	0.062;0.155;0.016;0.089	T	0.42682	-0.9437	10	0.72032	D	0.01	.	13.6662	0.62396	0.4323:0.5677:0.0:0.0	.	577;757;681;724	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	D	577;724;681	ENSP00000430686:A577D;ENSP00000369375:A724D;ENSP00000383977:A681D	ENSP00000369375:A724D	A	+	2	0	TEK	27193079	0.005000	0.15991	0.401000	0.26359	0.955000	0.61496	1.573000	0.36472	1.476000	0.48215	0.637000	0.83480	GCC	.	.		0.473	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			A	27203079	C	A	27203079	3	1	73	1	0	0	0	0	1	0	0	0	15766	739	26	3	2221	3	TEK	9	27203079	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	6195045	27203079	114010352	314	9640										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32632432	32632432	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctgttctgttgacattgtgCgcaccacatcaatcacttcc	6	14	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:32632432C>G	ENST00000242310.4	-	1	3235	c.3146G>C	c.(3145-3147)cGc>cCc	p.R1049P	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1049					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TGACATTGTGCGCACCACATC	0.473																																					p.R1049P		Atlas-SNP	.											.	TAF1L	382	.	0			c.G3146C						.						224	222	223					9																	32632432		2203	4300	6503	SO:0001583	missense	138474	exon1			ATTGTGCGCACCA	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3146G>C	chr9.hg19:g.32632432C>G	ENSP00000418379:p.Arg1049Pro	215.0	0.0		217.0	81.0	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	hg19	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240544	0.79912	.	.	ENSG00000122728	ENST00000242310	T	0.17370	2.28	0.479	0.479	0.16796	.	0.000000	0.85682	D	0.000000	T	0.38639	0.1048	M	0.84511	2.7	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.23048	-1.0199	10	0.87932	D	0	.	6.6915	0.23174	0.0:0.9998:0.0:2.0E-4	.	1049	Q8IZX4	TAF1L_HUMAN	P	1049	ENSP00000418379:R1049P	ENSP00000418379:R1049P	R	-	2	0	TAF1L	32622432	1.000000	0.71417	0.998000	0.56505	0.882000	0.50991	4.928000	0.63447	0.507000	0.28148	0.195000	0.17529	CGC	.	.		0.473	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			G	32632432	C	G	32632432	3	3	73	1	0	0	0	0	1	0	0	0	15538	768	27	4	2338	4	TAF1L	9	32632432	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	5429353	32632432	108580999	315	9641										
NOL6	65083	hgsc.bcm.edu	37	chr9	33469275	33469275	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttggttggcagcaagcggcaCgggcggaagaagtcaggtgg	19	7	1	1	rs370042879		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:33469275C>G	ENST00000379471.2	-	6	879	c.792G>C	c.(790-792)ccG>ccC	p.P264P	NOL6_ENST00000455041.2_Silent_p.P204P|NOL6_ENST00000464829.1_5'UTR			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	264					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		GCAAGCGGCACGGGCGGAAGA	0.612																																					p.P264P		Atlas-SNP	.											.	NOL6	85	.	0			c.G792C						.						130	125	126					9																	33469275		2203	4300	6503	SO:0001819	synonymous_variant	65083	exon6			GCGGCACGGGCGG	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"nucleolar protein family 6 (RNA-associated)"			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.792G>C	chr9.hg19:g.33469275C>G		116.0	0.0		98.0	45.0	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Silent	SNP	ENST00000379471.2	hg19																																																																																				.	.		0.612	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		G	33469275	C	G	33469275	2	3	73	1	0	0	0	0	0	0	0	1	10534	523	19	4		4	NOL6	9	33469275	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	836843	33469275	107744156	316	9642										
KIF24	347240	hgsc.bcm.edu	37	chr9	34263160	34263160	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctgatccagtgctcggataCattccttcagctgcaaagtg	9	12	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:34263160C>A	ENST00000402558.2	-	8	1478	c.1454G>T	c.(1453-1455)tGt>tTt	p.C485F	KIF24_ENST00000345050.2_Missense_Mutation_p.C351F|KIF24_ENST00000379174.3_Missense_Mutation_p.C351F|KIF24_ENST00000379166.2_Missense_Mutation_p.C485F			Q5T7B8	KIF24_HUMAN	kinesin family member 24	485	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			TGCTCGGATACATTCCTTCAG	0.453																																					p.C485F		Atlas-SNP	.											.	KIF24	64	.	0			c.G1454T						.						180	167	171					9																	34263160		1991	4168	6159	SO:0001583	missense	347240	exon9			CGGATACATTCCT	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"Kinesins", "Sterile alpha motif (SAM) domain containing"	19916	protein-coding gene	gene with protein product		613747	"chromosome 9 open reading frame 48"	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.1454G>T	chr9.hg19:g.34263160C>A	ENSP00000384433:p.Cys485Phe	157.0	0.0		121.0	46.0	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Missense_Mutation	SNP	ENST00000402558.2	hg19	CCDS6551.2	.	.	.	.	.	.	.	.	.	.	C	18.88	3.716764	0.68844	.	.	ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188	T;T;T;T	0.19938	2.11;2.11;2.11;2.11	5.97	5.97	0.96955	Kinesin, motor domain (3);	0.000000	0.42172	D	0.000747	T	0.59649	0.2209	H	0.98111	4.15	0.58432	D	0.999999	P;P	0.49559	0.925;0.884	P;P	0.53490	0.727;0.712	T	0.75071	-0.3447	10	0.87932	D	0	.	20.4135	0.99023	0.0:1.0:0.0:0.0	.	485;485	Q5T7B8-4;Q5T7B8	.;KIF24_HUMAN	F	485;351;485;351;485	ENSP00000384433:C485F;ENSP00000368472:C351F;ENSP00000368464:C485F;ENSP00000340179:C351F	ENSP00000340179:C351F	C	-	2	0	KIF24	34253160	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	6.563000	0.73964	2.835000	0.97688	0.591000	0.81541	TGT	.	.		0.453	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5			A	34263160	C	A	34263160	3	1	73	1	0	0	0	0	1	0	0	0	8301	478	17	3	2672	3	KIF24	9	34263160	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	793885	34263160	106950271	317	9643										
DCAF10	79269	hgsc.bcm.edu	37	chr9	37861138	37861138	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctcccttctctccccctagtGtacttgtgtctatgaattcc	5	15	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:37861138G>T	ENST00000377724.3	+	7	1678	c.1313G>T	c.(1312-1314)tGt>tTt	p.C438F	DCAF10_ENST00000242323.7_Splice_Site_p.C401F|DCAF10_ENST00000483167.1_3'UTR|RP11-613M10.9_ENST00000540557.1_Intron	NM_024345.3	NP_077321.3	Q5QP82	DCA10_HUMAN	DDB1 and CUL4 associated factor 10	438					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	12						TCCCCCTAGTGTACTTGTGTC	0.448																																					p.C438F		Atlas-SNP	.											.	DCAF10	31	.	0			c.G1313T						.						129	124	125					9																	37861138		2203	4300	6503	SO:0001630	splice_region_variant	79269	exon7			CCTAGTGTACTTG	BC003520	CCDS6613.2, CCDS75835.1	9p13.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000122741	ENSG00000122741		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	23686	protein-coding gene	gene with protein product			"WD repeat domain 32"	WDR32			Standard	NM_001286810		Approved	MGC10765, FLJ23201	uc004aao.3	Q5QP82	OTTHUMG00000019934	ENST00000377724.3:c.1312-1G>T	chr9.hg19:g.37861138G>T		48.0	0.0		34.0	8.0	NM_024345	A4VCJ5|Q32NE2|Q8N2Q5|Q96ET5|Q9BTQ5|Q9H5P6	Missense_Mutation	SNP	ENST00000377724.3	hg19	CCDS6613.2	.	.	.	.	.	.	.	.	.	.	G	15.55	2.867707	0.51588	.	.	ENSG00000122741	ENST00000377724;ENST00000242323	T;T	0.72051	-0.27;-0.62	5.66	5.66	0.87406	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.052721	0.85682	D	0.000000	T	0.50752	0.1634	N	0.08118	0	0.43830	D	0.996405	B;B	0.10296	0.0;0.003	B;B	0.11329	0.0;0.006	T	0.49263	-0.8958	10	0.10111	T	0.7	.	17.2476	0.87032	0.0:0.0:1.0:0.0	.	401;438	Q5QP82-2;Q5QP82	.;DCA10_HUMAN	F	438;401	ENSP00000366953:C438F;ENSP00000242323:C401F	ENSP00000242323:C401F	C	+	2	0	DCAF10	37851138	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.441000	0.97557	2.690000	0.91761	0.655000	0.94253	TGT	.	.		0.448	DCAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052485.2	NM_024345	Missense_Mutation	T	37861138	G	T	37861138	5	4	73	1	0	0	0	0	0	0	1	0	4263	1391	48	3	1339	3	DCAF10	9	37861138	Splice_Site	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3597978	37861138	103352293	318	9644										
PIP5K1B	8395	hgsc.bcm.edu	37	chr9	71555562	71555562	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtgttgctttcgttcctagCcctgggatcccgacacaggc	11	13	0	0	rs201702261		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:71555562C>A	ENST00000265382.3	+	14	1663	c.1358C>A	c.(1357-1359)gCc>gAc	p.A453D	PIP5K1B_ENST00000541509.1_Splice_Site_p.A453D	NM_003558.2	NP_003549.1	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, beta	453					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			breast(1)|large_intestine(2)|stomach(1)	4				Lung(182;0.133)		TCGTTCCTAGCCCTGGGATCC	0.423																																					p.A453D		Atlas-SNP	.											.	PIP5K1B	40	.	0			c.C1358A						.						230	189	203					9																	71555562		2203	4300	6503	SO:0001630	splice_region_variant	8395	exon14			TCCTAGCCCTGGG	U78579	CCDS6624.1, CCDS65063.1	9q13	2008-02-05			ENSG00000107242	ENSG00000107242			8995	protein-coding gene	gene with protein product		602745				9177790, 8841185	Standard	NM_003558		Approved	STM7, MSS4	uc004agu.4	O14986	OTTHUMG00000019976	ENST00000265382.3:c.1358-1C>A	chr9.hg19:g.71555562C>A		146.0	0.0		147.0	64.0	NM_003558	A8K9L9|B4DIG7|P78518|P78519|Q5T5K6|Q5T5K8|Q5T5K9|Q5VZ00|Q7KYT5|Q8NHQ5|Q92749	Missense_Mutation	SNP	ENST00000265382.3	hg19	CCDS6624.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.525293	0.44969	.	.	ENSG00000107242	ENST00000541509;ENST00000377290;ENST00000265382;ENST00000419747	T;T	0.27256	1.7;1.68	5.78	5.78	0.91487	.	0.170855	0.51477	D	0.000083	T	0.17662	0.0424	L	0.29908	0.895	0.39940	D	0.974398	B	0.27068	0.167	B	0.22880	0.042	T	0.09378	-1.0677	9	.	.	.	.	11.0024	0.47614	0.0:0.8879:0.0:0.1121	.	453	O14986	PI51B_HUMAN	D	453;453;453;400	ENSP00000438082:A453D;ENSP00000265382:A453D	.	A	+	2	0	PIP5K1B	70745382	0.990000	0.36364	0.970000	0.41538	0.811000	0.45836	2.811000	0.47986	2.731000	0.93534	0.655000	0.94253	GCC	.	.		0.423	PIP5K1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052561.2	NM_003558	Missense_Mutation	A	71555562	C	A	71555562	5	1	73	1	0	0	0	0	0	0	1	0	11949	753	26	3	1400	3	PIP5K1B	9	71555562	Splice_Site	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	33694424	71555562	69657869	319	9645										
TMC1	117531	hgsc.bcm.edu	37	chr9	75404071	75404071	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gaagaaaaagcagcccaagtAgaagaaaacgtccacttgat	9	8	0	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:75404071A>T	ENST00000297784.5	+	15	1602	c.1062A>T	c.(1060-1062)gtA>gtT	p.V354V	TMC1_ENST00000340019.3_Silent_p.V354V|TMC1_ENST00000396237.3_Silent_p.V354V	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	354					auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						CAGCCCAAGTAGAAGAAAACG	0.383																																					p.V354V	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.A1062T						.						109	101	103					9																	75404071		2203	4300	6503	SO:0001819	synonymous_variant	117531	exon15			CCAAGTAGAAGAA	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"transmembrane, cochlear expressed, 1"	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.1062A>T	chr9.hg19:g.75404071A>T		130.0	0.0		139.0	8.0	NM_138691	A8MVZ2|B1AM91	Silent	SNP	ENST00000297784.5	hg19	CCDS6643.1																																																																																			.	.		0.383	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1			T	75404071	A	T	75404071	2	4	73	1	0	0	0	0	0	0	0	1	15999	407	15	4		4	TMC1	9	75404071	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3848509	75404071	65809360	320	9646										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79325463	79325463	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tttcagagttatctctgggaCtgtcttgtctctggacaaac	9	9	4	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:79325463C>A	ENST00000376718.3	-	8	1850	c.1727G>T	c.(1726-1728)aGt>aTt	p.S576I	PRUNE2_ENST00000428286.1_Missense_Mutation_p.S217I	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	576					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.S576N(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						ATCTCTGGGACTGTCTTGTCT	0.438																																					p.S576I		Atlas-SNP	.											PRUNE2_ENST00000376718,NS,carcinoma,0,1	PRUNE2	331	.	1	Substitution - Missense(1)	breast(1)	c.G1727T						.						54	48	50					9																	79325463		1568	3582	5150	SO:0001583	missense	158471	exon8			CTGGGACTGTCTT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.1727G>T	chr9.hg19:g.79325463C>A	ENSP00000365908:p.Ser576Ile	83.0	0.0		74.0	27.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.118210	0.37339	.	.	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.55234	0.53;0.55	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000010	T	0.62441	0.2428	M	0.67953	2.075	0.80722	D	1	D	0.64830	0.994	P	0.58077	0.832	T	0.66356	-0.5944	10	0.87932	D	0	-6.854	7.4756	0.27374	0.0:0.8025:0.0:0.1975	.	576	Q8WUY3	PRUN2_HUMAN	I	576;217;575	ENSP00000365908:S576I;ENSP00000397425:S217I	ENSP00000365908:S576I	S	-	2	0	PRUNE2	78515283	1.000000	0.71417	0.941000	0.38009	0.381000	0.30169	2.181000	0.42547	2.707000	0.92482	0.655000	0.94253	AGT	.	.		0.438	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79325463	C	A	79325463	3	1	73	1	0	0	0	0	1	0	0	0	12653	565	20	3	7587	3	PRUNE2	9	79325463	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	3921392	79325463	61887968	321	9647										
FOXB2	442425	hgsc.bcm.edu	37	chr9	79635447	79635447	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctggagggctgcccttggcgTccgtcatgcaccacctgggc	14	15	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:79635447T>A	ENST00000376708.1	+	1	877	c.877T>A	c.(877-879)Tcc>Acc	p.S293T		NM_001013735.1	NP_001013757.1	Q5VYV0	FOXB2_HUMAN	forkhead box B2	293					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|lung(8)|ovary(1)	10						GCCCTTGGCGTCCGTCATGCA	0.662																																					p.S293T		Atlas-SNP	.											.	FOXB2	71	.	0			c.T877A						.						38	37	38					9																	79635447		2203	4300	6503	SO:0001583	missense	442425	exon1			TTGGCGTCCGTCA		CCDS35045.1	9q21.2	2008-02-05			ENSG00000204612	ENSG00000204612		"Forkhead boxes"	23315	protein-coding gene	gene with protein product							Standard	NM_001013735		Approved	bA159H20.4	uc004ako.1	Q5VYV0	OTTHUMG00000020051	ENST00000376708.1:c.877T>A	chr9.hg19:g.79635447T>A	ENSP00000365898:p.Ser293Thr	43.0	0.0		40.0	20.0	NM_001013735		Missense_Mutation	SNP	ENST00000376708.1	hg19	CCDS35045.1	.	.	.	.	.	.	.	.	.	.	T	15.00	2.704253	0.48412	.	.	ENSG00000204612	ENST00000376708	D	0.96685	-4.09	3.41	3.41	0.39046	.	0.081596	0.51477	D	0.000086	D	0.95098	0.8412	L	0.28192	0.835	0.37325	D	0.909726	P	0.52842	0.956	D	0.65010	0.931	D	0.93350	0.6717	10	0.20046	T	0.44	.	10.9795	0.47486	0.0:0.0:0.0:1.0	.	293	Q5VYV0	FOXB2_HUMAN	T	293	ENSP00000365898:S293T	ENSP00000365898:S293T	S	+	1	0	FOXB2	78825267	0.946000	0.32159	0.976000	0.42696	0.844000	0.47949	1.728000	0.38105	1.400000	0.46741	0.379000	0.24179	TCC	.	.		0.662	FOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052745.1	NM_001013735		A	79635447	T	A	79635447	3	1	73	1	0	0	0	0	1	0	0	0	6001	1667	58	4	879	4	FOXB2	9	79635447	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	309984	79635447	61577984	322	9648										
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88292376	88292376	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtccaatctttgcaagaatAgaatgaatctgtaccattaa	7	7	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:88292376A>C	ENST00000357081.3	-	6	555	c.411T>G	c.(409-411)tcT>tcG	p.S137S	AGTPBP1_ENST00000432218.1_Silent_p.S19S|AGTPBP1_ENST00000376109.3_Silent_p.S189S|AGTPBP1_ENST00000337006.4_Silent_p.S79S|AGTPBP1_ENST00000376083.3_Silent_p.S137S|AGTPBP1_ENST00000491784.1_5'UTR|AGTPBP1_ENST00000376081.4_Silent_p.S137S|AGTPBP1_ENST00000376080.1_Silent_p.S79S			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	137					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						TTGCAAGAATAGAATGAATCT	0.358																																					p.S137S		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.T411G						.						130	129	129					9																	88292376		2203	4300	6503	SO:0001819	synonymous_variant	23287	exon6			AAGAATAGAATGA	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.411T>G	chr9.hg19:g.88292376A>C		110.0	0.0		122.0	6.0	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Silent	SNP	ENST00000357081.3	hg19																																																																																				.	.		0.358	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		C	88292376	A	C	88292376	2	2	73	1	0	0	0	0	0	0	0	1	400	407	15	5		5	AGTPBP1	9	88292376	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	8656929	88292376	52921055	323	9649										
ZCCHC6	79670	hgsc.bcm.edu	37	chr9	88961390	88961390	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aggtctggacctctgcttctTgttttcttaaggtgggggaa	13	7	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:88961390T>C	ENST00000375963.3	-	3	698	c.526A>G	c.(526-528)Aag>Gag	p.K176E	ZCCHC6_ENST00000375947.1_Missense_Mutation_p.K9E|ZCCHC6_ENST00000375961.2_Missense_Mutation_p.K176E|ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.K176E	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	176					RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						CTCTGCTTCTTGTTTTCTTAA	0.408																																					p.K176E		Atlas-SNP	.											.	ZCCHC6	105	.	0			c.A526G						.						153	145	148					9																	88961390		2203	4300	6503	SO:0001583	missense	79670	exon3			GCTTCTTGTTTTC	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.526A>G	chr9.hg19:g.88961390T>C	ENSP00000365130:p.Lys176Glu	118.0	0.0		90.0	28.0	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	hg19	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	T	15.29	2.788886	0.49997	.	.	ENSG00000083223	ENST00000375960;ENST00000375961;ENST00000375963;ENST00000427388;ENST00000375947	T;T;T;T	0.48522	1.14;1.14;1.14;0.81	5.29	5.29	0.74685	.	0.287586	0.34750	N	0.003718	T	0.30135	0.0755	L	0.27053	0.805	0.31182	N	0.701996	B;B;P;B	0.45474	0.037;0.023;0.859;0.227	B;B;B;B	0.38458	0.02;0.013;0.274;0.056	T	0.25916	-1.0118	10	0.19147	T	0.46	-15.7904	9.8269	0.40916	0.0:0.0762:0.0:0.9238	.	176;176;176;176	Q5VYS8-5;Q5VYS8-2;Q5VYS8-4;Q5VYS8	.;.;.;TUT7_HUMAN	E	176;176;176;9;9	ENSP00000365127:K176E;ENSP00000365128:K176E;ENSP00000365130:K176E;ENSP00000365114:K9E	ENSP00000365114:K9E	K	-	1	0	ZCCHC6	88151210	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	3.371000	0.52379	2.229000	0.72834	0.397000	0.26171	AAG	.	.		0.408	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		C	88961390	T	C	88961390	3	2	73	1	0	0	0	0	1	0	0	0	17607	1821	63	2	4061	2	ZCCHC6	9	88961390	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	669014	88961390	52252041	324	9650										
SYK	6850	hgsc.bcm.edu	37	chr9	93650165	93650165	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttctcctatgggcagaagccAtatcgagtgagccagtcctg	11	11	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:93650165A>G	ENST00000375754.4	+	12	1864	c.1716A>G	c.(1714-1716)ccA>ccG	p.P572P	SYK_ENST00000375751.4_Silent_p.P549P|SYK_ENST00000375747.1_Silent_p.P549P|SYK_ENST00000375746.1_Silent_p.P572P	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	572	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						GGCAGAAGCCATATCGAGTGA	0.463			T	"ETV6, ITK"	"MDS, peripheral T-cell lymphoma"																																p.P572P		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.A1716G						.						127	122	124					9																	93650165		2203	4300	6503	SO:0001819	synonymous_variant	6850	exon12			GAAGCCATATCGA	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"SH2 domain containing"	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1716A>G	chr9.hg19:g.93650165A>G		111.0	0.0		97.0	40.0	NM_003177		Silent	SNP	ENST00000375754.4	hg19	CCDS6688.1																																																																																			.	.		0.463	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1			G	93650165	A	G	93650165	2	3	73	1	0	0	0	0	0	0	0	1	15453	204	8	2		2	SYK	9	93650165	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4688775	93650165	47563266	325	9651										
ROR2	4920	hgsc.bcm.edu	37	chr9	94486208	94486208	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggtgtgagctgggcttgggGaccatctgaggaggcacctg	18	8	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:94486208G>T	ENST00000375708.3	-	9	2766	c.2568C>A	c.(2566-2568)gtC>gtA	p.V856V	ROR2_ENST00000375715.1_Intron|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	856	Pro-rich.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						TGGGCTTGGGGACCATCTGAG	0.657																																					p.V856V		Atlas-SNP	.											.	ROR2	167	.	0			c.C2568A						.						90	90	90					9																	94486208		2203	4300	6503	SO:0001819	synonymous_variant	4920	exon9			CTTGGGGACCATC	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.2568C>A	chr9.hg19:g.94486208G>T		73.0	0.0		39.0	16.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	hg19	CCDS6691.1																																																																																			.	.		0.657	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			T	94486208	G	T	94486208	2	4	73	1	0	0	0	0	0	0	0	1	13542	1161	41	3		3	ROR2	9	94486208	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	836043	94486208	46727223	326	9652										
BICD2	23299	hgsc.bcm.edu	37	chr9	95477644	95477644	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggtcagcgccagcttctgcTggatggccatgcgcagcagc	15	13	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:95477644T>A	ENST00000375512.3	-	7	2427	c.2360A>T	c.(2359-2361)cAg>cTg	p.Q787L	BICD2_ENST00000356884.6_Missense_Mutation_p.Q787L	NM_015250.3	NP_056065.1	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 (Drosophila)	787	Interacts with RAB6A. {ECO:0000250}.				cell death (GO:0008219)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase binding (GO:0017137)			cervix(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23						CAGCTTCTGCTGGATGGCCAT	0.642																																					p.Q787L		Atlas-SNP	.											.	BICD2	68	.	0			c.A2360T						.						32	31	31					9																	95477644		2203	4298	6501	SO:0001583	missense	23299	exon7			TTCTGCTGGATGG	AB014599	CCDS6700.1, CCDS35064.1	9q22.32	2008-02-05			ENSG00000185963	ENSG00000185963			17208	protein-coding gene	gene with protein product		609797				9734811	Standard	NM_001003800		Approved	KIAA0699	uc004asp.1	Q8TD16	OTTHUMG00000021036	ENST00000375512.3:c.2360A>T	chr9.hg19:g.95477644T>A	ENSP00000364662:p.Gln787Leu	85.0	0.0		81.0	35.0	NM_001003800	O75181|Q5TBQ2|Q5TBQ3|Q96LH2|Q9BT84|Q9H561	Missense_Mutation	SNP	ENST00000375512.3	hg19	CCDS6700.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.957566	0.92726	.	.	ENSG00000185963	ENST00000356884;ENST00000375512	T;T	0.62639	0.01;0.01	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.80210	0.4581	M	0.84948	2.725	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.80764	0.99;0.994	T	0.83346	-0.0005	10	0.66056	D	0.02	-41.7761	13.2901	0.60267	0.0:0.0:0.0:1.0	.	787;787	Q8TD16-2;Q8TD16	.;BICD2_HUMAN	L	787	ENSP00000349351:Q787L;ENSP00000364662:Q787L	ENSP00000349351:Q787L	Q	-	2	0	BICD2	94517465	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.085000	0.71343	2.092000	0.63282	0.528000	0.53228	CAG	.	.		0.642	BICD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055508.1	NM_015250		A	95477644	T	A	95477644	3	1	73	1	0	0	0	0	1	0	0	0	1429	1580	55	4	221	4	BICD2	9	95477644	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	991436	95477644	45735787	327	9653										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113168473	113168473	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cactttcataggtgtgtgccTctccagttgccactgcattg	9	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:113168473T>A	ENST00000401783.2	-	38	9743	c.9407A>T	c.(9406-9408)gAg>gTg	p.E3136V	SVEP1_ENST00000374469.1_Missense_Mutation_p.E3113V|SVEP1_ENST00000297826.5_Missense_Mutation_p.E1062V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3136	Sushi 29. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GGTGTGTGCCTCTCCAGTTGC	0.512																																					p.E3136V		Atlas-SNP	.											.	SVEP1	326	.	0			c.A9407T						.						95	99	98					9																	113168473		1978	4167	6145	SO:0001583	missense	79987	exon38			TGTGCCTCTCCAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.9407A>T	chr9.hg19:g.113168473T>A	ENSP00000384917:p.Glu3136Val	145.0	0.0		153.0	62.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	8.636	0.894774	0.17613	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.66995	-0.24;-0.24;-0.24	5.69	5.69	0.88448	Complement control module (2);Sushi/SCR/CCP (3);	0.368162	0.30003	N	0.010650	T	0.63498	0.2516	L	0.56199	1.76	0.80722	D	1	P	0.38677	0.642	B	0.40741	0.339	T	0.65216	-0.6222	10	0.46703	T	0.11	.	10.6138	0.45439	0.0:0.0806:0.0:0.9194	.	3136	Q4LDE5	SVEP1_HUMAN	V	3136;3113;1062	ENSP00000384917:E3136V;ENSP00000363593:E3113V;ENSP00000297826:E1062V	ENSP00000297826:E1062V	E	-	2	0	SVEP1	112208294	0.996000	0.38824	0.924000	0.36721	0.204000	0.24138	2.650000	0.46665	2.169000	0.68431	0.533000	0.62120	GAG	.	.		0.512	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113168473	T	A	113168473	3	1	73	1	0	0	0	0	1	0	0	0	15435	1551	54	4	1352	4	SVEP1	9	113168473	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	17690829	113168473	28044958	328	9654										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113341549	113341549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agttgacttcgcccacgctgGacgaatcatccaccaggaag	10	13	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:113341549G>A	ENST00000401783.2	-	1	611	c.275C>T	c.(274-276)tCc>tTc	p.S92F	SVEP1_ENST00000374469.1_Missense_Mutation_p.S69F|SVEP1_ENST00000302728.8_Missense_Mutation_p.S92F|SVEP1_ENST00000374461.1_Missense_Mutation_p.S69F	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	92	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GCCCACGCTGGACGAATCATC	0.677																																					p.S92F		Atlas-SNP	.											.	SVEP1	326	.	0			c.C275T						.						11	14	13					9																	113341549		2031	4138	6169	SO:0001583	missense	79987	exon1			ACGCTGGACGAAT	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.275C>T	chr9.hg19:g.113341549G>A	ENSP00000384917:p.Ser92Phe	60.0	0.0		51.0	21.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.930214	0.73327	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26	3.7	2.78	0.32641	von Willebrand factor, type A (3);	0.064576	0.64402	N	0.000005	D	0.87865	0.6285	M	0.87617	2.895	0.41978	D	0.990789	D;D;B	0.89917	0.999;1.0;0.09	D;D;B	0.91635	0.998;0.999;0.046	D	0.88326	0.2965	10	0.87932	D	0	.	10.8474	0.46751	0.0969:0.0:0.9031:0.0	.	92;92;92	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	F	92;69;92;69	ENSP00000384917:S92F;ENSP00000363593:S69F;ENSP00000304118:S92F;ENSP00000363585:S69F	ENSP00000304118:S92F	S	-	2	0	SVEP1	112381370	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.337000	0.96545	0.655000	0.30866	0.591000	0.81541	TCC	.	.		0.677	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113341549	G	A	113341549	3	1	73	1	0	0	0	0	1	0	0	0	15435	1174	41	3	10632	3	SVEP1	9	113341549	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	173076	113341549	27871882	329	9655										
ZNF483	158399	hgsc.bcm.edu	37	chr9	114289679	114289679	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctgcccctgagacacaatgCaagctgtagtgcccttgaac	9	14	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:114289679C>A	ENST00000309235.5	+	2	162	c.4C>A	c.(4-6)Caa>Aaa	p.Q2K	ZNF483_ENST00000355824.3_Missense_Mutation_p.Q2K|ZNF483_ENST00000374374.3_Missense_Mutation_p.Q2K|ZNF483_ENST00000358151.4_Missense_Mutation_p.Q2K	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						AGACACAATGCAAGCTGTAGT	0.488																																					p.Q2K		Atlas-SNP	.											.	ZNF483	78	.	0			c.C4A						.						93	89	90					9																	114289679		2203	4300	6503	SO:0001583	missense	158399	exon2			ACAATGCAAGCTG	AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"Zinc fingers, C2H2-type", "-", "-", "-"	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.4C>A	chr9.hg19:g.114289679C>A	ENSP00000311679:p.Gln2Lys	104.0	0.0		117.0	9.0	NM_133464	Q5VZN2|Q8NAE1	Missense_Mutation	SNP	ENST00000309235.5	hg19	CCDS35106.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763479	0.31228	.	.	ENSG00000173258	ENST00000358151;ENST00000355824;ENST00000374374;ENST00000309235	T;T;T;T	0.05925	5.74;5.7;3.37;3.61	5.55	0.126	0.14722	.	0.946056	0.08712	N	0.904800	T	0.02610	0.0079	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.14438	0.01;0.01;0.01;0.008	B;B;B;B	0.11329	0.002;0.006;0.003;0.004	T	0.45848	-0.9233	10	0.02654	T	1	-6.4721	1.2256	0.01932	0.3079:0.3728:0.1493:0.1699	.	2;2;2;2	Q6P088;Q5VZN3;Q8NAE1;Q8TF39	.;.;.;ZN483_HUMAN	K	2	ENSP00000350871:Q2K;ENSP00000438048:Q2K;ENSP00000363494:Q2K;ENSP00000311679:Q2K	ENSP00000311679:Q2K	Q	+	1	0	ZNF483	113329500	0.000000	0.05858	0.008000	0.14137	0.125000	0.20455	-0.209000	0.09358	0.363000	0.24346	-0.222000	0.12452	CAA	.	.		0.488	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567		A	114289679	C	A	114289679	3	1	73	1	0	0	0	0	1	0	0	0	17951	711	25	3	6	3	ZNF483	9	114289679	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	948130	114289679	26923752	330	9656										
OLFML2A	169611	hgsc.bcm.edu	37	chr9	127549471	127549471	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctcaacccctgtgagaacgAgtggaagatggagaaactca	11	9	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:127549471A>G	ENST00000373580.3	+	2	308	c.308A>G	c.(307-309)gAg>gGg	p.E103G		NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	103					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						TGTGAGAACGAGTGGAAGATG	0.592																																					p.E103G		Atlas-SNP	.											.	OLFML2A	61	.	0			c.A308G						.						53	61	58					9																	127549471		2065	4203	6268	SO:0001583	missense	169611	exon2			AGAACGAGTGGAA	AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.308A>G	chr9.hg19:g.127549471A>G	ENSP00000362682:p.Glu103Gly	76.0	0.0		70.0	35.0	NM_182487	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Missense_Mutation	SNP	ENST00000373580.3	hg19	CCDS6857.2	.	.	.	.	.	.	.	.	.	.	A	23.3	4.397688	0.83120	.	.	ENSG00000185585	ENST00000331715;ENST00000425732;ENST00000373580	T;T	0.46063	0.88;0.88	5.84	4.68	0.58851	.	0.115998	0.56097	D	0.000021	T	0.61123	0.2322	M	0.72894	2.215	0.80722	D	1	D;D	0.76494	0.999;0.995	D;P	0.73708	0.981;0.791	T	0.63386	-0.6649	10	0.72032	D	0.01	.	11.1721	0.48577	0.862:0.0:0.0:0.138	.	103;103	Q5JTM7;Q68BL7	.;OLM2A_HUMAN	G	103	ENSP00000336425:E103G;ENSP00000362682:E103G	ENSP00000336425:E103G	E	+	2	0	OLFML2A	126589292	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.063000	0.76714	0.995000	0.38917	0.533000	0.62120	GAG	.	.		0.592	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487		G	127549471	A	G	127549471	3	3	73	1	0	0	0	0	1	0	0	0	10866	304	11	2	314	2	OLFML2A	9	127549471	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	13259792	127549471	13663960	331	9657										
LMX1B	4010	hgsc.bcm.edu	37	chr9	129455877	129455877	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggtttcagaaccaaagagcAaaggtaagaggccacccccc	10	12	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:129455877A>T	ENST00000373474.4	+	5	823	c.816A>T	c.(814-816)gcA>gcT	p.A272A	LMX1B_ENST00000561065.1_Silent_p.A249A|LMX1B_ENST00000355497.5_Silent_p.A272A|LMX1B_ENST00000425646.2_Silent_p.A249A|LMX1B_ENST00000526117.1_Silent_p.A272A			O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	272					cell proliferation (GO:0008283)|central nervous system neuron development (GO:0021954)|cerebellum morphogenesis (GO:0021587)|collagen fibril organization (GO:0030199)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral pattern formation (GO:0009953)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|organ growth (GO:0035265)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|trabecular meshwork development (GO:0002930)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	15						ACCAAAGAGCAAAGGTAAGAG	0.647									Nail-Patella Syndrome																												p.A272A	Pancreas(110;1796 2278 18357 20466)	Atlas-SNP	.											.	LMX1B	86	.	0			c.A816T						.						43	47	46					9																	129455877		2203	4299	6502	SO:0001819	synonymous_variant	4010	exon5	Familial Cancer Database	Osteo-Onychodysplasia, Turner-Kieser syndrome, Fong disease	AAGAGCAAAGGTA	U77457	CCDS6866.1, CCDS6866.2, CCDS55342.1, CCDS55343.1	9q33.3	2011-06-20			ENSG00000136944	ENSG00000136944		"Homeoboxes / LIM class"	6654	protein-coding gene	gene with protein product		602575		NPS1		9441763, 9590287	Standard	NM_002316		Approved		uc004bqj.3	O60663	OTTHUMG00000020692	ENST00000373474.4:c.816A>T	chr9.hg19:g.129455877A>T		145.0	0.0		88.0	37.0	NM_001174146	F8W7W6|O75463|Q5JU95|Q6ISC9	Silent	SNP	ENST00000373474.4	hg19	CCDS55342.1																																																																																			.	.		0.647	LMX1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054123.2			T	129455877	A	T	129455877	2	4	73	1	0	0	0	0	0	0	0	1	8871	117	5	4		4	LMX1B	9	129455877	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1906406	129455877	11757554	332	9658										
FAM129B	64855	hgsc.bcm.edu	37	chr9	130279260	130279260	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acctcctcgaagcgcgccttGgcctgctcgtacaccatgtg	10	16	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:130279260G>T	ENST00000373312.3	-	8	1062	c.849C>A	c.(847-849)gcC>gcA	p.A283A	FAM129B_ENST00000468379.1_Intron|FAM129B_ENST00000373314.3_Silent_p.A270A	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	283					negative regulation of apoptotic process (GO:0043066)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						AGCGCGCCTTGGCCTGCTCGT	0.627																																					p.A283A		Atlas-SNP	.											.	FAM129B	84	.	0			c.C849A						.						146	132	136					9																	130279260		2203	4300	6503	SO:0001819	synonymous_variant	64855	exon8			CGCCTTGGCCTGC	AF151783	CCDS35144.1, CCDS35145.1	9q34.13	2010-02-01	2006-11-23	2006-11-23	ENSG00000136830	ENSG00000136830			25282	protein-coding gene	gene with protein product		614045	"chromosome 9 open reading frame 88"	C9orf88		14702039, 19362540	Standard	XM_005252135		Approved	DKFZP434H0820, FLJ13518, FLJ22151, FLJ22298, bA356B19.6, MINERVA	uc004brh.3	Q96TA1	OTTHUMG00000020705	ENST00000373312.3:c.849C>A	chr9.hg19:g.130279260G>T		81.0	0.0		57.0	21.0	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Silent	SNP	ENST00000373312.3	hg19	CCDS35145.1																																																																																			.	.		0.627	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833		T	130279260	G	T	130279260	2	4	73	1	0	0	0	0	0	0	0	1	5442	1335	47	3		3	FAM129B	9	130279260	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	823383	130279260	10934171	333	9659										
C9orf50	375759	hgsc.bcm.edu	37	chr9	132375462	132375471	+	Frame_Shift_Del	DEL	GAACAGAAGG	GAACAGAAGG	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gagcagcggccttcttccatGaacagaagggcaggctgctg							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	GAACAGAAGG	GAACAGAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:132375462_132375471delGAACAGAAGG	ENST00000372478.4	-	6	1304_1313	c.1103_1112delCCTTCTGTTC	c.(1102-1113)cccttctgttcafs	p.PFCS368fs	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	368				P -> S (in Ref. 3; AAI12354). {ECO:0000305}.						central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				CTTCTTCCATGAACAGAAGGGCAGGCTGCT	0.6																																					p.368_371del		Atlas-Indel,Pindel	.											.	C9orf50	25	.	0			c.1104_1113del						.																																			SO:0001589	frameshift_variant	375759	exon6			.	AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.1103_1112delCCTTCTGTTC	chr9.hg19:g.132375462_132375471delGAACAGAAGG	ENSP00000361556:p.Pro368fs	105.0	0.0		87.0	25.0	NM_199350	Q2M1I2|Q8NA65	Frame_Shift_Del	DEL	ENST00000372478.4	hg19	CCDS35159.1																																																																																			.	.		0.6	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350		-	132375471	GAACAGAAGG	-	132375462	7	5	73	1	0	1	0	1	0	0	0	0	2489	1294	45	0	191	0	C9orf50	9	132375462	Frame_Shift_Del	DEL	GAACAGAAGG	TCGA-CC-A7IH-01A-11D-A33K-10	2096202	132375462	8837969	334	9660										
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134526250	134526250	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cacctcagctggttttccctTctttgatggcgttctcttga	8	12	3	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:134526250T>C	ENST00000372189.3	-	2	220	c.97A>G	c.(97-99)Aag>Gag	p.K33E	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.K51E|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.K50E	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	33					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		GGTTTTCCCTTCTTTGATGGC	0.468																																					p.K51E		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.A151G						.						267	248	254					9																	134526250		1936	4140	6076	SO:0001583	missense	2889	exon2			TTCCCTTCTTTGA	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.97A>G	chr9.hg19:g.134526250T>C	ENSP00000361263:p.Lys33Glu	172.0	0.0		169.0	68.0	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	hg19	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.718762	0.89205	.	.	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000357686;ENST00000438647;ENST00000427994	T;T;T;T	0.50548	0.84;0.9;0.74;1.15	5.61	5.61	0.85477	.	0.265176	0.37393	N	0.002106	T	0.64778	0.2629	M	0.64997	1.995	0.58432	D	0.999991	D;D;D	0.67145	0.992;0.992;0.996	P;P;D	0.65987	0.872;0.872;0.94	T	0.67964	-0.5534	10	0.72032	D	0.01	.	14.9886	0.71368	0.0:0.0:0.0:1.0	.	50;33;51	Q68DL3;Q13905;Q13905-3	.;RPGF1_HUMAN;.	E	33;50;33;51;51;50;50;51	ENSP00000361269:K50E;ENSP00000361263:K33E;ENSP00000361264:K51E;ENSP00000410640:K50E	ENSP00000266110:K33E	K	-	1	0	RAPGEF1	133516071	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.694000	0.84235	2.127000	0.65507	0.533000	0.62120	AAG	.	.		0.468	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		C	134526250	T	C	134526250	3	2	73	1	0	0	0	0	1	0	0	0	13058	1792	62	2	3228	2	RAPGEF1	9	134526250	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2150788	134526250	6687181	335	9661										
GBGT1	26301	hgsc.bcm.edu	37	chr9	136029632	136029632	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggctgactccaggaaggactGgatgaaatgagtgtacctag	14	7	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:136029632G>C	ENST00000372040.3	-	7	687	c.376C>G	c.(376-378)Cag>Gag	p.Q126E	GBGT1_ENST00000372043.3_Intron|GBGT1_ENST00000372038.3_Missense_Mutation_p.P138R|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000540636.1_Missense_Mutation_p.Q109E	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	126					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		AGGAAGGACTGGATGAAATGA	0.607																																					p.Q126E		Atlas-SNP	.											.	GBGT1	25	.	0			c.C376G						.						42	44	43					9																	136029632		2203	4299	6502	SO:0001583	missense	26301	exon7			AGGACTGGATGAA	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"Glycosyltransferase family 6 domain containing"	20460	protein-coding gene	gene with protein product	"Forssman glycolipid synthetase (FS)", "Forssman synthetase"	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.376C>G	chr9.hg19:g.136029632G>C	ENSP00000361110:p.Gln126Glu	37.0	0.0		33.0	11.0	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Missense_Mutation	SNP	ENST00000372040.3	hg19	CCDS6960.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.620|7.620	0.676642|0.676642	0.14841|0.14841	.|.	.|.	ENSG00000148288|ENSG00000148288	ENST00000372038|ENST00000372040;ENST00000540636	T|T;T	0.39406|0.01139	1.08|5.28;5.28	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	.|0.220119	.|0.38778	.|N	.|0.001577	T|T	0.01029|0.01029	0.0034|0.0034	N|N	0.16368|0.16368	0.405|0.405	0.09310|0.09310	N|N	1|1	.|B;B	.|0.33777	.|0.244;0.425	.|B;B	.|0.34418	.|0.12;0.182	T|T	0.57636|0.57636	-0.7777|-0.7777	7|10	0.54805|0.17369	T|T	0.06|0.5	-16.1453|-16.1453	12.6992|12.6992	0.57022|0.57022	0.0:0.0:0.7217:0.2783|0.0:0.0:0.7217:0.2783	.|.	.|109;126	.|B7Z8S5;Q8N5D6	.|.;GBGT1_HUMAN	R|E	138|126;109	ENSP00000361108:P138R|ENSP00000361110:Q126E;ENSP00000437663:Q109E	ENSP00000361108:P138R|ENSP00000361110:Q126E	P|Q	-|-	2|1	0|0	GBGT1|GBGT1	135019453|135019453	0.000000|0.000000	0.05858|0.05858	0.840000|0.840000	0.33206|0.33206	0.328000|0.328000	0.28507|0.28507	-0.039000|-0.039000	0.12124|0.12124	2.513000|2.513000	0.84729|0.84729	0.491000|0.491000	0.48974|0.48974	CCA|CAG	.	.		0.607	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		C	136029632	G	C	136029632	3	2	73	1	0	0	0	0	1	0	0	0	6280	1357	47	4	671	4	GBGT1	9	136029632	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1503382	136029632	5183799	336	9662										
SOHLH1	402381	hgsc.bcm.edu	37	chr9	138589403	138589403	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctggcacacctgcttgaatcTgactcgacaacgtcaactgt	8	13	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr9:138589403T>A	ENST00000298466.5	-	4	476	c.416A>T	c.(415-417)cAg>cTg	p.Q139L	SOHLH1_ENST00000425225.1_Missense_Mutation_p.Q139L	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1	139					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(5)|prostate(1)	12		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		TGCTTGAATCTGACTCGACAA	0.537																																					p.Q139L		Atlas-SNP	.											.	SOHLH1	70	.	0			c.A416T						.						77	64	69					9																	138589403		2202	4300	6502	SO:0001583	missense	402381	exon4			TGAATCTGACTCG	BC031861	CCDS35174.1, CCDS48054.1	9q34.3	2013-05-21	2006-03-16	2006-03-16	ENSG00000165643	ENSG00000165643		"Basic helix-loop-helix proteins"	27845	protein-coding gene	gene with protein product	"spermatogenesis associated 27"	610224	"chromosome 9 open reading frame 157"	C9orf157		12477932	Standard	NM_001012415		Approved	NOHLH, TEB2, bA100C15.3, bHLHe80, SPATA27	uc010nbe.3	Q5JUK2	OTTHUMG00000020915	ENST00000298466.5:c.416A>T	chr9.hg19:g.138589403T>A	ENSP00000298466:p.Gln139Leu	98.0	0.0		67.0	30.0	NM_001012415	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Missense_Mutation	SNP	ENST00000298466.5	hg19	CCDS35174.1	.	.	.	.	.	.	.	.	.	.	T	14.38	2.518717	0.44763	.	.	ENSG00000165643	ENST00000298466;ENST00000425225	T;T	0.36520	1.25;1.26	4.24	1.86	0.25419	.	0.283495	0.19157	N	0.121285	T	0.42337	0.1198	L	0.50333	1.59	0.09310	N	0.999999	D;D	0.65815	0.991;0.995	P;P	0.61070	0.883;0.763	T	0.14896	-1.0456	10	0.51188	T	0.08	-20.5323	3.9756	0.09473	0.0:0.1163:0.2406:0.6431	.	139;139	Q5JUK2-2;Q5JUK2	.;SOLH1_HUMAN	L	139	ENSP00000298466:Q139L;ENSP00000404438:Q139L	ENSP00000298466:Q139L	Q	-	2	0	SOHLH1	137729224	0.005000	0.15991	0.012000	0.15200	0.009000	0.06853	0.125000	0.15749	0.615000	0.30124	0.459000	0.35465	CAG	.	.		0.537	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		A	138589403	T	A	138589403	3	1	73	1	0	0	0	0	1	0	0	0	14938	1580	55	4	808	4	SOHLH1	9	138589403	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2559771	138589403	2624028	337	9663										
C10orf18	54906	hgsc.bcm.edu	37	chr10	5789185	5789185	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaacaaacaagcctgtctgtGagtagagaggtcagcctaga	11	8	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:5789185G>T	ENST00000328090.5	+	15	4426	c.3801G>T	c.(3799-3801)gtG>gtT	p.V1267V		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1267																	GCCTGTCTGTGAGTAGAGAGG	0.393																																					p.V1267V		Atlas-SNP	.											.	.	.	.	0			c.G3801T						.						83	86	85					10																	5789185		1875	4118	5993	SO:0001819	synonymous_variant	54906	exon15			GTCTGTGAGTAGA	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.3801G>T	chr10.hg19:g.5789185G>T		90.0	0.0		132.0	13.0	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Silent	SNP	ENST00000328090.5	hg19	CCDS41485.1																																																																																			.	.		0.393	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		T	5789185	G	T	5789185	2	4	73	1	0	0	0	0	0	0	0	1	1598	1277	45	3		3	C10orf18	10	5789185	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10		5789185	129745562	338	9664										
CELF2	10659	hgsc.bcm.edu	37	chr10	11207586	11207586	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agaactttttgagccttacgGagccgtctaccagatcaacg	9	11	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:11207586G>A	ENST00000379261.4	+	2	283	c.191G>A	c.(190-192)gGa>gAa	p.G64E	CELF2_ENST00000417956.2_Missense_Mutation_p.G40E|CELF2_ENST00000609692.1_Missense_Mutation_p.G40E|CELF2_ENST00000450189.1_Missense_Mutation_p.G71E|CELF2_ENST00000354440.2_Missense_Mutation_p.G40E|CELF2_ENST00000399850.3_Missense_Mutation_p.G40E|CELF2_ENST00000416382.2_Missense_Mutation_p.G64E|CELF2_ENST00000315874.4_Missense_Mutation_p.G40E|CELF2_ENST00000537122.1_5'UTR|CELF2_ENST00000427450.1_Missense_Mutation_p.G40E|CELF2_ENST00000608830.1_Missense_Mutation_p.G40E|CELF2_ENST00000354897.3_Missense_Mutation_p.G40E|CELF2_ENST00000542579.1_Missense_Mutation_p.G71E	NM_001025077.2	NP_001020248.1	O95319	CELF2_HUMAN	CUGBP, Elav-like family member 2	64	Necessary for RNA-binding, TNNT2 exon 5 and NMDA R1 exon 21 inclusion.|RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of heart contraction (GO:0008016)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	16						GAGCCTTACGGAGCCGTCTAC	0.587																																					p.G71E		Atlas-SNP	.											.	CELF2	78	.	0			c.G212A						.						61	64	63					10																	11207586		1934	4150	6084	SO:0001583	missense	10659	exon2			CTTACGGAGCCGT	U69546	CCDS41488.1, CCDS44354.1, CCDS44355.1, CCDS44356.1	10p13	2013-02-12	2010-02-19	2010-02-19	ENSG00000048740	ENSG00000048740		"RNA binding motif (RRM) containing"	2550	protein-coding gene	gene with protein product		602538	"CUG triplet repeat, RNA-binding protein 2", "CUG triplet repeat, RNA binding protein 2"	CUGBP2		7869393, 9887331	Standard	NM_006561		Approved	Etr-3, NAPOR-2, BRUNOL3	uc001ikl.4	O95319	OTTHUMG00000017668	ENST00000379261.4:c.191G>A	chr10.hg19:g.11207586G>A	ENSP00000368563:p.Gly64Glu	91.0	0.0		115.0	69.0	NM_006561	B7ZAN9|Q7KYU4|Q8N499|Q92950|Q96NW9|Q96RQ5|Q96RQ6|Q9UL67	Missense_Mutation	SNP	ENST00000379261.4	hg19	CCDS44354.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939129	0.92526	.	.	ENSG00000048740	ENST00000379261;ENST00000416382;ENST00000450189;ENST00000542579;ENST00000399850;ENST00000417956;ENST00000315874;ENST00000354440;ENST00000354897;ENST00000427450	T;T;T;T;T;T;T;T;T	0.77098	-1.07;-1.07;0.96;0.96;-1.07;-1.07;-1.07;-1.07;-1.07	5.51	5.51	0.81932	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.91928	0.7444	H	0.94925	3.6	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.93522	0.6862	10	0.87932	D	0	-6.4706	19.807	0.96535	0.0:0.0:1.0:0.0	.	48;64;40;59;71;59;64	B4DDE7;B4DS31;B4DSZ2;B2RA86;E9PC62;O95319-3;O95319	.;.;.;.;.;.;CELF2_HUMAN	E	64;64;71;71;40;40;40;40;40;40	ENSP00000368563:G64E;ENSP00000406451:G64E;ENSP00000389951:G71E;ENSP00000443926:G71E;ENSP00000382743:G40E;ENSP00000404834:G40E;ENSP00000315328:G40E;ENSP00000346426:G40E;ENSP00000388530:G40E	ENSP00000315328:G40E	G	+	2	0	CELF2	11247592	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.658000	0.98594	2.759000	0.94783	0.563000	0.77884	GGA	.	.		0.587	CELF2-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	11207586	G	A	11207586	3	1	73	1	0	0	0	0	1	0	0	0	3218	1174	41	3	275	3	CELF2	10	11207586	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	5418401	11207586	124327161	339	9665										
PTER	9317	hgsc.bcm.edu	37	chr10	16553155	16553155	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcacggctattctcatatacTcaccaatgttgttcctaaaa	4	11	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:16553155T>C	ENST00000378000.1	+	6	1196	c.950T>C	c.(949-951)cTc>cCc	p.L317P	PTER_ENST00000298942.3_Missense_Mutation_p.L317P|PTER_ENST00000423462.2_Missense_Mutation_p.L270P|PTER_ENST00000535784.2_Missense_Mutation_p.L317P	NM_001001484.2|NM_001261838.1|NM_030664.4	NP_001001484.1|NP_001248767.1|NP_109589.2	Q96BW5	PTER_HUMAN	phosphotriesterase related	317					catabolic process (GO:0009056)|epithelial cell differentiation (GO:0030855)	extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)	15						TCTCATATACTCACCAATGTT	0.413																																					p.L317P	Ovarian(2;46 150 15648 38137 47908)	Atlas-SNP	.											.	PTER	40	.	0			c.T950C						.						159	148	151					10																	16553155		2203	4300	6503	SO:0001583	missense	9317	exon6			ATATACTCACCAA	BC015092	CCDS7111.1, CCDS58070.1, CCDS73070.1	10p12	2003-11-05			ENSG00000165983	ENSG00000165983			9590	protein-coding gene	gene with protein product		604446				9925913	Standard	NM_001001484		Approved		uc001ioi.2	Q96BW5	OTTHUMG00000017737	ENST00000378000.1:c.950T>C	chr10.hg19:g.16553155T>C	ENSP00000367239:p.Leu317Pro	123.0	0.0		156.0	31.0	NM_030664	B0YJ77|B3KTF5|D3DRU0|Q9BY46	Missense_Mutation	SNP	ENST00000378000.1	hg19	CCDS7111.1	.	.	.	.	.	.	.	.	.	.	T	16.97	3.268659	0.59540	.	.	ENSG00000165983	ENST00000343656;ENST00000535784;ENST00000423462;ENST00000378000;ENST00000298942	T;T;T;T	0.50548	0.74;0.88;0.74;0.74	5.86	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.67730	0.2924	M	0.82716	2.605	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79108	0.99;0.992	T	0.67169	-0.5738	10	0.26408	T	0.33	-4.0769	12.0599	0.53557	0.0:0.0672:0.0:0.9328	.	270;317	Q96BW5-2;Q96BW5	.;PTER_HUMAN	P	317;317;270;317;317	ENSP00000439485:L317P;ENSP00000389535:L270P;ENSP00000367239:L317P;ENSP00000298942:L317P	ENSP00000298942:L317P	L	+	2	0	PTER	16593161	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	4.661000	0.61518	1.046000	0.40249	0.491000	0.48974	CTC	.	.		0.413	PTER-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047001.2	NM_030664		C	16553155	T	C	16553155	3	2	73	1	0	0	0	0	1	0	0	0	12751	1551	54	2	964	2	PTER	10	16553155	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	5345569	16553155	118981592	340	9666										
NEBL	10529	hgsc.bcm.edu	37	chr10	21178773	21178773	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgcaagcttttgataccttaCctcagaaataaaagcaccga	6	10	1	2	rs139581346		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:21178773C>A	ENST00000377122.4	-	3	655		c.e3+1		NEBL_ENST00000377159.4_Intron|NEBL_ENST00000377119.1_Splice_Site|NEBL_ENST00000417816.2_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette						cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TGATACCTTACCTCAGAAATA	0.299																																					.		Atlas-SNP	.											.	NEBL	199	.	0			c.258+1G>T						.						83	84	84					10																	21178773		2203	4298	6501	SO:0001630	splice_region_variant	10529	exon4			ACCTTACCTCAGA	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.258+1G>T	chr10.hg19:g.21178773C>A		208.0	0.0		299.0	170.0	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Splice_Site	SNP	ENST00000377122.4	hg19	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.180208	0.78564	.	.	ENSG00000078114	ENST00000377122;ENST00000377119;ENST00000434381	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NEBL	21218779	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	5.471000	0.66762	2.941000	0.99782	0.655000	0.94253	.	.	C|0.999;T|0.001		0.299	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	Intron	A	21178773	C	A	21178773	5	1	73	1	0	0	0	0	0	0	1	0	10312	521	18	3	2889	3	NEBL	10	21178773	Splice_Site	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	4625618	21178773	114355974	341	9667										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24833078	24833078	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccaagcgcttcgaaatcgctAggtctcaacctgaagacacc	8	14	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:24833078A>T	ENST00000376454.3	+	19	4909	c.4879A>T	c.(4879-4881)Agg>Tgg	p.R1627W	KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376451.2_Missense_Mutation_p.R1310W|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000376462.1_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1627					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						CGAAATCGCTAGGTCTCAACC	0.463																																					p.R1627W		Atlas-SNP	.											.	KIAA1217	235	.	0			c.A4879T						.						98	98	98					10																	24833078		2203	4300	6503	SO:0001583	missense	56243	exon19			ATCGCTAGGTCTC	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.4879A>T	chr10.hg19:g.24833078A>T	ENSP00000365637:p.Arg1627Trp	84.0	0.0		119.0	64.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	A	9.895	1.205285	0.22205	.	.	ENSG00000120549	ENST00000442879;ENST00000376454;ENST00000450158;ENST00000376451	T;T	0.36520	1.65;1.25	5.25	-0.304	0.12788	.	0.323538	0.27447	N	0.019329	T	0.45316	0.1336	M	0.62723	1.935	0.19300	N	0.999978	P;P;P	0.47484	0.896;0.896;0.896	P;P;P	0.51355	0.667;0.667;0.487	T	0.50717	-0.8795	10	0.87932	D	0	.	14.4529	0.67397	0.475:0.525:0.0:0.0	.	1310;1310;1627	C9JRK3;Q5T5P2-3;Q5T5P2	.;.;SKT_HUMAN	W	1310;1627;1310;1310	ENSP00000365637:R1627W;ENSP00000365634:R1310W	ENSP00000365634:R1310W	R	+	1	2	KIAA1217	24873084	0.000000	0.05858	0.001000	0.08648	0.072000	0.16883	-0.554000	0.06006	-0.320000	0.08640	-0.396000	0.06452	AGG	.	.		0.463	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		T	24833078	A	T	24833078	3	4	73	1	0	0	0	0	1	0	0	0	8225	411	15	4	4953	4	KIAA1217	10	24833078	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3654305	24833078	110701669	342	9668										
PRTFDC1	56952	hgsc.bcm.edu	37	chr10	25145922	25145922	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtcctcccagttccgacaacAtcctttgcaaaaaggacaga	7	13	0	1	rs148662493		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:25145922A>T	ENST00000320152.6	-	6	454	c.426T>A	c.(424-426)gaT>gaA	p.D142E	PRTFDC1_ENST00000376378.1_Missense_Mutation_p.D142E	NM_020200.5	NP_064585.1	Q9NRG1	PRDC1_HUMAN	phosphoribosyl transferase domain containing 1	142					nucleoside metabolic process (GO:0009116)	cytosol (GO:0005829)	magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9						TTCCGACAACATCCTTTGCAA	0.403																																					p.D142E		Atlas-SNP	.											.	PRTFDC1	29	.	0			c.T426A						.	A	GLU/ASP	1,4405	2.1+/-5.4	0,1,2202	230	188	203		426	3.1	0.9	10	dbSNP_134	203	0,8600		0,0,4300	no	missense	PRTFDC1	NM_020200.5	45	0,1,6502	TT,TA,AA		0.0,0.0227,0.0077	probably-damaging	142/226	25145922	1,13005	2203	4300	6503	SO:0001583	missense	56952	exon6			GACAACATCCTTT	AF226056	CCDS7145.1, CCDS60506.1	10p12.31	2003-11-10			ENSG00000099256	ENSG00000099256			23333	protein-coding gene	gene with protein product		610751					Standard	XM_005252537		Approved	HHGP	uc001ise.1	Q9NRG1	OTTHUMG00000017829	ENST00000320152.6:c.426T>A	chr10.hg19:g.25145922A>T	ENSP00000318602:p.Asp142Glu	136.0	0.0		164.0	12.0	NM_020200	B7Z1Z3|Q53HA7|Q59EL9|Q5VV18|Q5VV20	Missense_Mutation	SNP	ENST00000320152.6	hg19	CCDS7145.1	.	.	.	.	.	.	.	.	.	.	A	11.17	1.560524	0.27827	2.27E-4	0.0	ENSG00000099256	ENST00000320152;ENST00000358336;ENST00000376378	D;D	0.99928	-8.07;-8.07	5.59	3.14	0.36123	Phosphoribosyltransferase (1);	0.210015	0.48767	D	0.000176	D	0.99924	0.9965	H	0.94385	3.53	0.80722	D	1	D;D	0.89917	0.992;1.0	P;D	0.80764	0.768;0.994	D	0.96886	0.9649	10	0.87932	D	0	.	10.3543	0.43954	0.8633:0.0:0.1367:0.0	.	142;142	Q9NRG1-2;Q9NRG1	.;PRDC1_HUMAN	E	142	ENSP00000318602:D142E;ENSP00000365558:D142E	ENSP00000318602:D142E	D	-	3	2	PRTFDC1	25185928	1.000000	0.71417	0.874000	0.34290	0.080000	0.17528	1.140000	0.31516	0.356000	0.24157	0.454000	0.30748	GAT	.	A|1.000;T|0.000		0.403	PRTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047243.2	NM_020200		T	25145922	A	T	25145922	3	4	73	1	0	0	0	0	1	0	0	0	12649	214	8	4	267	4	PRTFDC1	10	25145922	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	312844	25145922	110388825	343	9669										
PRTFDC1	56952	hgsc.bcm.edu	37	chr10	25226147	25226147	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtctgatgaaatcaaccttcAttgagacaaatcgatctgaa	7	8	4	4	rs368309249		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:25226147A>G	ENST00000320152.6	-	3	333	c.305T>C	c.(304-306)aTg>aCg	p.M102T	PRTFDC1_ENST00000376378.1_Missense_Mutation_p.M102T|PRTFDC1_ENST00000376376.3_Missense_Mutation_p.M102T	NM_020200.5	NP_064585.1	Q9NRG1	PRDC1_HUMAN	phosphoribosyl transferase domain containing 1	102					nucleoside metabolic process (GO:0009116)	cytosol (GO:0005829)	magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9						ATCAACCTTCATTGAGACAAA	0.353													A|||	1	0.000199681	0	0.0014	5008	,	,		18668	0		0	False		,,,				2504	0				p.M102T		Atlas-SNP	.											.	PRTFDC1	29	.	0			c.T305C						.	A	THR/MET	1,4405	2.1+/-5.4	0,1,2202	102	98	100		305	5.6	1	10		100	0,8600		0,0,4300	no	missense	PRTFDC1	NM_020200.5	81	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign	102/226	25226147	1,13005	2203	4300	6503	SO:0001583	missense	56952	exon3			ACCTTCATTGAGA	AF226056	CCDS7145.1, CCDS60506.1	10p12.31	2003-11-10			ENSG00000099256	ENSG00000099256			23333	protein-coding gene	gene with protein product		610751					Standard	XM_005252537		Approved	HHGP	uc001ise.1	Q9NRG1	OTTHUMG00000017829	ENST00000320152.6:c.305T>C	chr10.hg19:g.25226147A>G	ENSP00000318602:p.Met102Thr	79.0	0.0		86.0	22.0	NM_020200	B7Z1Z3|Q53HA7|Q59EL9|Q5VV18|Q5VV20	Missense_Mutation	SNP	ENST00000320152.6	hg19	CCDS7145.1	.	.	.	.	.	.	.	.	.	.	A	14.09	2.430588	0.43122	2.27E-4	0.0	ENSG00000099256	ENST00000320152;ENST00000358336;ENST00000376378;ENST00000376376	D;D;D	0.99695	-5.67;-5.67;-6.43	5.63	5.63	0.86233	Phosphoribosyltransferase (1);	0.116803	0.85682	D	0.000000	D	0.98438	0.9480	N	0.21617	0.685	0.54753	D	0.999986	B;B	0.28900	0.054;0.227	B;B	0.29862	0.007;0.108	D	0.99029	1.0820	10	0.49607	T	0.09	.	15.87	0.79108	1.0:0.0:0.0:0.0	.	102;102	Q9NRG1-2;Q9NRG1	.;PRDC1_HUMAN	T	102	ENSP00000318602:M102T;ENSP00000365558:M102T;ENSP00000365556:M102T	ENSP00000318602:M102T	M	-	2	0	PRTFDC1	25266153	1.000000	0.71417	0.997000	0.53966	0.944000	0.59088	4.803000	0.62546	2.145000	0.66743	0.533000	0.62120	ATG	.	.		0.353	PRTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047243.2	NM_020200		G	25226147	A	G	25226147	3	3	73	1	0	0	0	0	1	0	0	0	12649	217	8	2	400	2	PRTFDC1	10	25226147	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	80225	25226147	110308600	344	9670										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26377316	26377316	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atatctcctggaaaaatcccGagttatccaccaagctatgt	6	11	1	0	rs200209381		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:26377316G>T	ENST00000265944.5	+	15	1710	c.1544G>T	c.(1543-1545)cGa>cTa	p.R515L	MYO3A_ENST00000543632.1_Missense_Mutation_p.R515L	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	515	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GAAAAATCCCGAGTTATCCAC	0.358																																					p.R515L		Atlas-SNP	.											MYO3A,bladder,carcinoma,0,1	MYO3A	371	.	0			c.G1544T						.						59	61	60					10																	26377316		2203	4300	6503	SO:0001583	missense	53904	exon15			AATCCCGAGTTAT	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1544G>T	chr10.hg19:g.26377316G>T	ENSP00000265944:p.Arg515Leu	106.0	0.0		166.0	42.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	32	5.180708	0.94846	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	D;D	0.96885	-4.16;-4.16	5.78	5.78	0.91487	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.99070	0.9681	H	0.98446	4.235	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.97110	0.996;0.998;1.0	D	0.98869	1.0765	10	0.87932	D	0	.	20.3668	0.98882	0.0:0.0:1.0:0.0	.	515;515;515	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	L	515	ENSP00000265944:R515L;ENSP00000445909:R515L	ENSP00000265944:R515L	R	+	2	0	MYO3A	26417322	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.813000	0.99286	2.894000	0.99253	0.655000	0.94253	CGA	.	G|1.000;A|0.000		0.358	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26377316	G	T	26377316	3	4	73	1	0	0	0	0	1	0	0	0	10085	1058	37	1	1594	1	MYO3A	10	26377316	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1151169	26377316	109157431	345	9671										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26465717	26465717	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aactgaagtcactttatctgGgtgtctcgcaccataagcca	8	11	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:26465717G>T	ENST00000265944.5	+	31	4547	c.4381G>T	c.(4381-4383)Ggt>Tgt	p.G1461C	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1461					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ACTTTATCTGGGTGTCTCGCA	0.358																																					p.G1461C		Atlas-SNP	.											.	MYO3A	371	.	0			c.G4381T						.						91	86	88					10																	26465717		2203	4300	6503	SO:0001583	missense	53904	exon31			TATCTGGGTGTCT	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.4381G>T	chr10.hg19:g.26465717G>T	ENSP00000265944:p.Gly1461Cys	87.0	0.0		98.0	5.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.951157	0.53186	.	.	ENSG00000095777	ENST00000265944	D	0.81659	-1.52	5.91	3.85	0.44370	.	0.317210	0.37304	N	0.002160	T	0.77075	0.4077	L	0.46157	1.445	0.09310	N	0.999997	D	0.61697	0.99	P	0.47673	0.554	T	0.70799	-0.4774	10	0.72032	D	0.01	.	9.8688	0.41162	0.2029:0.0:0.7971:0.0	.	1461	Q8NEV4	MYO3A_HUMAN	C	1461	ENSP00000265944:G1461C	ENSP00000265944:G1461C	G	+	1	0	MYO3A	26505723	0.108000	0.22018	0.415000	0.26534	0.928000	0.56348	0.681000	0.25320	1.508000	0.48769	0.650000	0.86243	GGT	.	.		0.358	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26465717	G	T	26465717	3	4	73	1	0	0	0	0	1	0	0	0	10085	1232	43	3	4495	3	MYO3A	10	26465717	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	88401	26465717	109069030	346	9672										
PARD3	56288	hgsc.bcm.edu	37	chr10	34759158	34759158	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggagaggccaattagagctGggtcactactgcgtcgaaca	13	9	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:34759158G>A	ENST00000374789.3	-	4	762	c.437C>T	c.(436-438)cCa>cTa	p.P146L	PARD3_ENST00000374776.1_Missense_Mutation_p.P146L|PARD3_ENST00000340077.5_Missense_Mutation_p.P146L|PARD3_ENST00000545693.1_Missense_Mutation_p.P146L|PARD3_ENST00000350537.4_Missense_Mutation_p.P146L|PARD3_ENST00000374773.1_Missense_Mutation_p.P146L|PARD3_ENST00000374794.3_Missense_Mutation_p.P146L|PARD3_ENST00000545260.1_Missense_Mutation_p.P146L|PARD3_ENST00000374790.3_Missense_Mutation_p.P146L|PARD3_ENST00000346874.4_Missense_Mutation_p.P146L|PARD3_ENST00000374788.3_Missense_Mutation_p.P146L	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	146					apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				AATTAGAGCTGGGTCACTACT	0.418																																					p.P146L		Atlas-SNP	.											.	PARD3	131	.	0			c.C437T						.						121	120	120					10																	34759158		2203	4300	6503	SO:0001583	missense	56288	exon4			AGAGCTGGGTCAC	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"atypical PKC isotype-specific interacting protein", "par-3 family cell polarity regulator alpha", "protein phosphatase 1, regulatory subunit 118"	606745	"par-3 (partitioning defective 3, C.elegans) homolog", "par-3 partitioning defective 3 homolog (C. elegans)"			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.437C>T	chr10.hg19:g.34759158G>A	ENSP00000363921:p.Pro146Leu	117.0	0.0		130.0	34.0	NM_001184788	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Missense_Mutation	SNP	ENST00000374789.3	hg19	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	G	31	5.096345	0.94197	.	.	ENSG00000148498	ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790;ENST00000374776;ENST00000340077;ENST00000374773	T;T;T;T;T;T;T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.74891	0.3776	M	0.75777	2.31	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.963;1.0	D;D;D;D;D;D;D;D;D;D;D;P;D	0.97110	1.0;0.997;1.0;1.0;1.0;1.0;1.0;0.998;1.0;1.0;1.0;0.827;0.999	T	0.75587	-0.3266	10	0.87932	D	0	.	20.1617	0.98138	0.0:0.0:1.0:0.0	.	146;146;146;146;146;146;146;146;146;146;146;146;146	Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q5VWV2;Q6IQ47;Q8TEW0-8;Q8TEW0-9;Q8TEW0-10	.;.;.;.;.;.;.;PARD3_HUMAN;.;.;.;.;.	L	146	ENSP00000443147:P146L;ENSP00000440857:P146L;ENSP00000363921:P146L;ENSP00000363920:P146L;ENSP00000340591:P146L;ENSP00000363926:P146L;ENSP00000311986:P146L;ENSP00000363922:P146L;ENSP00000363908:P146L;ENSP00000341844:P146L;ENSP00000363905:P146L	ENSP00000341844:P146L	P	-	2	0	PARD3	34799164	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.839000	0.92120	2.854000	0.98071	0.655000	0.94253	CCA	.	.		0.418	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619		A	34759158	G	A	34759158	3	1	73	1	0	0	0	0	1	0	0	0	11452	1348	47	3	3756	3	PARD3	10	34759158	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	8293441	34759158	100775589	347	9673										
MBL2	4153	hgsc.bcm.edu	37	chr10	54528161	54528161	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcattcctgggggtggccacAgaggcctggaacttgacaca	14	11	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:54528161A>C	ENST00000373968.3	-	4	547	c.483T>G	c.(481-483)tcT>tcG	p.S161S		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	161	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						GGGTGGCCACAGAGGCCTGGA	0.493																																					p.S161S		Atlas-SNP	.											.	MBL2	55	.	0			c.T483G						.						137	140	139					10																	54528161		2202	4300	6502	SO:0001819	synonymous_variant	4153	exon4			GGCCACAGAGGCC	AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"Collectins"	6922	protein-coding gene	gene with protein product		154545	"mannose-binding lectin (protein C) 2, soluble (opsonic defect)"	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.483T>G	chr10.hg19:g.54528161A>C		144.0	0.0		153.0	46.0	NM_000242	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Silent	SNP	ENST00000373968.3	hg19	CCDS7247.1																																																																																			.	.		0.493	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242		C	54528161	A	C	54528161	2	2	73	1	0	0	0	0	0	0	0	1	9359	175	7	5		5	MBL2	10	54528161	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	19769003	54528161	81006586	348	9674										
SLC16A9	220963	hgsc.bcm.edu	37	chr10	61443920	61443920	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttttccttttccttcaccaaAggcatccagccattctatgt	4	13	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:61443920A>G	ENST00000395348.3	-	2	766	c.130T>C	c.(130-132)Ttt>Ctt	p.F44L	SLC16A9_ENST00000490066.1_5'UTR|SLC16A9_ENST00000395347.1_Missense_Mutation_p.F44L	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	44					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						CCTTCACCAAAGGCATCCAGC	0.463																																					p.F44L		Atlas-SNP	.											.	SLC16A9	58	.	0			c.T130C						.						130	127	128					10																	61443920		2203	4300	6503	SO:0001583	missense	220963	exon2			CACCAAAGGCATC	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.130T>C	chr10.hg19:g.61443920A>G	ENSP00000378757:p.Phe44Leu	213.0	0.0		243.0	12.0	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	hg19	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	A	33	5.229247	0.95173	.	.	ENSG00000165449	ENST00000395348;ENST00000395347;ENST00000490066	T;T	0.55588	0.51;0.51	5.33	5.33	0.75918	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.100645	0.64402	D	0.000002	T	0.58366	0.2117	L	0.60067	1.865	0.80722	D	1	P	0.52692	0.955	P	0.48770	0.589	T	0.63001	-0.6734	10	0.59425	D	0.04	.	15.2955	0.73902	1.0:0.0:0.0:0.0	.	44	Q7RTY1	MOT9_HUMAN	L	44	ENSP00000378757:F44L;ENSP00000378756:F44L	ENSP00000378756:F44L	F	-	1	0	SLC16A9	61113926	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.320000	0.89995	2.014000	0.59158	0.533000	0.62120	TTT	.	.		0.463	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		G	61443920	A	G	61443920	3	3	73	1	0	0	0	0	1	0	0	0	14430	72	3	2	1419	2	SLC16A9	10	61443920	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	6915759	61443920	74090827	349	9675										
ANK3	288	hgsc.bcm.edu	37	chr10	61829030	61829030	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggaaggtatcttttggtgaaGtggcctttatgggaagtttg	15	3	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:61829030G>T	ENST00000280772.2	-	37	11800	c.11609C>A	c.(11608-11610)aCt>aAt	p.T3870N	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3870					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTTTGGTGAAGTGGCCTTTAT	0.398																																					p.T3870N		Atlas-SNP	.											.	ANK3	703	.	0			c.C11609A						.						303	298	300					10																	61829030		2203	4300	6503	SO:0001583	missense	288	exon37			GGTGAAGTGGCCT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11609C>A	chr10.hg19:g.61829030G>T	ENSP00000280772:p.Thr3870Asn	252.0	0.0		354.0	202.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	7.952	0.745070	0.15710	.	.	ENSG00000151150	ENST00000280772	T	0.16897	2.31	5.07	5.07	0.68467	.	0.000000	0.43416	D	0.000571	T	0.08223	0.0205	N	0.14661	0.345	0.80722	D	1	P	0.37015	0.578	B	0.24701	0.055	T	0.14008	-1.0488	10	0.52906	T	0.07	.	9.1159	0.36758	0.0812:0.1602:0.7586:0.0	.	3870	Q12955	ANK3_HUMAN	N	3870	ENSP00000280772:T3870N	ENSP00000280772:T3870N	T	-	2	0	ANK3	61499036	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.154000	0.50693	2.511000	0.84671	0.650000	0.86243	ACT	.	.		0.398	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61829030	G	T	61829030	3	4	73	1	0	0	0	0	1	0	0	0	622	1029	36	3	1865	3	ANK3	10	61829030	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	385110	61829030	73705717	350	9676										
RUFY2	55680	hgsc.bcm.edu	37	chr10	70141014	70141014	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acttttgatacatctctatgTtaattgctttaacttcctct	3	9	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:70141014T>A	ENST00000602465.1	-	11	1182	c.1082A>T	c.(1081-1083)aAc>aTc	p.N361I	RUFY2_ENST00000454950.2_Missense_Mutation_p.N303I|RUFY2_ENST00000472394.2_5'UTR|RUFY2_ENST00000388768.2_Missense_Mutation_p.N396I|RUFY2_ENST00000399200.2_Missense_Mutation_p.N327I			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	410						nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						CATCTCTATGTTAATTGCTTT	0.328																																					p.N396I		Atlas-SNP	.											.	RUFY2	58	.	0			c.A1187T						.						159	144	149					10																	70141014		1835	4095	5930	SO:0001583	missense	55680	exon11			TCTATGTTAATTG	AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130		"Zinc fingers, FYVE domain containing"	19761	protein-coding gene	gene with protein product		610328				11877430	Standard	NM_001042417		Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.1082A>T	chr10.hg19:g.70141014T>A	ENSP00000473462:p.Asn361Ile	81.0	0.0		116.0	37.0	NM_017987	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Missense_Mutation	SNP	ENST00000602465.1	hg19		.	.	.	.	.	.	.	.	.	.	T	25.0	4.597404	0.87055	.	.	ENSG00000204130	ENST00000388768;ENST00000399200;ENST00000454950	T;T;T	0.57436	0.4;1.31;0.87	5.29	5.29	0.74685	.	0.089619	0.85682	D	0.000000	T	0.72170	0.3427	M	0.76170	2.325	0.80722	D	1	D;D;D;D	0.89917	0.998;0.999;0.999;1.0	D;D;D;D	0.85130	0.991;0.996;0.996;0.997	T	0.74942	-0.3492	10	0.56958	D	0.05	.	15.3935	0.74767	0.0:0.0:0.0:1.0	.	303;361;327;396	B4DFR0;Q8WXA3-2;Q8WXA3-4;Q8WXA3-3	.;.;.;.	I	396;327;303	ENSP00000373420:N396I;ENSP00000382151:N327I;ENSP00000404986:N303I	ENSP00000373420:N396I	N	-	2	0	RUFY2	69811020	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.674000	0.68117	2.225000	0.72522	0.477000	0.44152	AAC	.	.		0.328	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987		A	70141014	T	A	70141014	3	1	73	1	0	0	0	0	1	0	0	0	13754	1725	60	4	883	4	RUFY2	10	70141014	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	8311984	70141014	65393733	351	9677										
SAR1A	56681	hgsc.bcm.edu	37	chr10	71917592	71917592	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agaaagacaatcccattaatTgctgggagataatttttcca	7	7	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:71917592T>G	ENST00000373242.2	-	6	472	c.276A>C	c.(274-276)gcA>gcC	p.A92A	SAR1A_ENST00000431664.2_Silent_p.A92A|SAR1A_ENST00000373236.1_Silent_p.A92A|SAR1A_ENST00000373241.4_Silent_p.A92A|SAR1A_ENST00000373238.1_Silent_p.A92A|SAR1A_ENST00000458634.2_Silent_p.A49A	NM_001142648.1	NP_001136120.1	Q9NR31	SAR1A_HUMAN	secretion associated, Ras related GTPase 1A	92					intracellular protein transport (GO:0006886)|negative regulation of cargo loading into COPII-coated vesicle (GO:1901303)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)	6						TCCCATTAATTGCTGGGAGAT	0.353																																					p.A92A		Atlas-SNP	.											.	SAR1A	19	.	0			c.A276C						.						81	72	75					10																	71917592		2203	4300	6503	SO:0001819	synonymous_variant	56681	exon5			ATTAATTGCTGGG		CCDS7298.1	10q22.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000079332	ENSG00000079332			10534	protein-coding gene	gene with protein product		607691	"SAR1a gene homolog (S. cerevisiae) 1", "SAR1a gene homolog 1 (S. cerevisiae)", "SAR1 homolog A (S. cerevisiae)"	SARA1		10871277	Standard	NM_020150		Approved	SAR1, Sara	uc010qji.2	Q9NR31	OTTHUMG00000018400	ENST00000373242.2:c.276A>C	chr10.hg19:g.71917592T>G		92.0	0.0		127.0	43.0	NM_020150	B4DQ19	Silent	SNP	ENST00000373242.2	hg19	CCDS7298.1																																																																																			.	.		0.353	SAR1A-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048500.2			G	71917592	T	G	71917592	2	3	73	1	0	0	0	0	0	0	0	1	13854	1799	63	5		5	SAR1A	10	71917592	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1776578	71917592	63617155	352	9678										
PSAP	5660	hgsc.bcm.edu	37	chr10	73591653	73591653	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agctgcggtgacaacgtcttTgcatatgtcgcagggaaggg	15	8	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:73591653T>C	ENST00000394936.3	-	3	346	c.199A>G	c.(199-201)Aaa>Gaa	p.K67E	PSAP_ENST00000394934.1_Missense_Mutation_p.K67E			P07602	SAP_HUMAN	prosaposin	67	Saposin B-type 1. {ECO:0000255|PROSITE- ProRule:PRU00415}.				blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						ACAACGTCTTTGCATATGTCG	0.527																																					p.K67E		Atlas-SNP	.											.	PSAP	43	.	0			c.A199G						.						180	166	171					10																	73591653		2203	4300	6503	SO:0001583	missense	5660	exon3			CGTCTTTGCATAT	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"Endogenous ligands"	9498	protein-coding gene	gene with protein product	"variant Gaucher disease and variant metachromatic leukodystrophy"	176801	"sphingolipid activator protein-1"	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.199A>G	chr10.hg19:g.73591653T>C	ENSP00000378394:p.Lys67Glu	85.0	0.0		116.0	19.0	NM_001042466	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Missense_Mutation	SNP	ENST00000394936.3	hg19	CCDS7311.1	.	.	.	.	.	.	.	.	.	.	T	18.51	3.639215	0.67244	.	.	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000394929;ENST00000404083	D;D	0.82803	-1.65;-1.65	5.2	4.05	0.47172	Saposin-like (2);Saposin-like type B, 1 (1);Saposin B (2);	0.044717	0.85682	D	0.000000	T	0.82107	0.4965	L	0.51914	1.62	0.58432	D	0.999999	P	0.36125	0.538	P	0.44811	0.461	T	0.78388	-0.2223	10	0.33940	T	0.23	-10.186	12.1935	0.54284	0.0:0.0:0.143:0.857	.	67	P07602	SAP_HUMAN	E	67;67;67;67;67;70	ENSP00000378394:K67E;ENSP00000378392:K67E	ENSP00000350063:K67E	K	-	1	0	PSAP	73261659	1.000000	0.71417	0.810000	0.32431	0.508000	0.34012	4.184000	0.58323	0.909000	0.36697	0.460000	0.39030	AAA	.	.		0.527	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778		C	73591653	T	C	73591653	3	2	73	1	0	0	0	0	1	0	0	0	12655	1821	63	2	1439	2	PSAP	10	73591653	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1674061	73591653	61943094	353	9679										
SEC24C	9632	hgsc.bcm.edu	37	chr10	75525661	75525661	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tatgaattcttggccactgtAgattactgcaaggtgaggga	12	6	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:75525661A>T	ENST00000339365.2	+	11	1632	c.1470A>T	c.(1468-1470)gtA>gtT	p.V490V	SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000411652.2_Silent_p.V371V|SEC24C_ENST00000345254.4_Silent_p.V490V|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000546025.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	490					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					TGGCCACTGTAGATTACTGCA	0.502																																					p.V490V		Atlas-SNP	.											.	SEC24C	86	.	0			c.A1470T						.						160	147	151					10																	75525661		2203	4300	6503	SO:0001819	synonymous_variant	9632	exon10			CACTGTAGATTAC	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"SEC24 (S. cerevisiae) related gene family, member C", "SEC24 family, member C (S. cerevisiae)"			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.1470A>T	chr10.hg19:g.75525661A>T		123.0	0.0		108.0	34.0	NM_198597	B4DZT4|Q8WV25	Silent	SNP	ENST00000339365.2	hg19	CCDS7332.1																																																																																			.	.		0.502	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			T	75525661	A	T	75525661	2	4	73	1	0	0	0	0	0	0	0	1	14011	407	15	4		4	SEC24C	10	75525661	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1934008	75525661	60009086	354	9680										
SFTPA1	653509	hgsc.bcm.edu	37	chr10	81371581	81371581	+	De_novo_Start_InFrame	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcagcgactggacccagagcCatgtggctgtgccctctggc	14	14	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:81371581C>A	ENST00000398636.3	+	0	138				SFTPA1_ENST00000372308.3_De_novo_Start_InFrame|SFTPA1_ENST00000419470.2_Silent_p.A15A|SFTPA1_ENST00000372313.5_Intron|SFTPA1_ENST00000428376.2_De_novo_Start_InFrame	NM_001164644.1|NM_001164646.1|NM_005411.4	NP_001158116.1|NP_001158118.1|NP_005402.3	Q8IWL2	SFTA1_HUMAN	surfactant protein A1						lipid transport (GO:0006869)|respiratory gaseous exchange (GO:0007585)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|lipid transporter activity (GO:0005319)			endometrium(1)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			GACCCAGAGCCATGTGGCTGT	0.607																																					p.A15A		Atlas-SNP	.											.	SFTPA1	23	.	0			c.C45A						.						189	184	186					10																	81371581		2203	4296	6499			653509	exon3			CAGAGCCATGTGG	BC026229	CCDS44444.1, CCDS44445.1, CCDS44444.2	10q22.3	2012-11-02	2008-08-26			ENSG00000122852		"Collectins"	10798	protein-coding gene	gene with protein product	"surfactant, pulmonary-associated protein A1A"	178630	"surfactant, pulmonary-associated protein A1"	SFTP1			Standard	NM_001093770		Approved	SP-A, SP-A1, COLEC4	uc009xry.3	Q8IWL2			chr10.hg19:g.81371581C>A		332.0	1.0		421.0	152.0	NM_001093770	A8K3T8|B7ZW50|E3VLD8|E3VLD9|E3VLE0|E3VLE1|G5E9J3|P07714|Q14DV4|Q5RIR5|Q5RIR7|Q6PIT0|Q8TC19	Silent	SNP	ENST00000398636.3	hg19	CCDS44445.1																																																																																			.	.		0.607	SFTPA1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_005411		A	81371581	C	A	81371581	1	1	73	1	0	1	0	0	0	0	0	0	14204	581	21	3		3	SFTPA1	10	81371581	De_novo_Start_InFrame	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	5845920	81371581	54163166	355	9681										
LDB3	11155	hgsc.bcm.edu	37	chr10	88441277	88441277	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcccaggcaccccaggcaccCcggagctcaggcccaccttt	10	20	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:88441277C>A	ENST00000361373.4	+	4	427	c.406C>A	c.(406-408)Ccg>Acg	p.P136T	LDB3_ENST00000372056.4_Missense_Mutation_p.P136T|LDB3_ENST00000352360.5_Intron|LDB3_ENST00000458213.2_Intron|LDB3_ENST00000310944.6_Missense_Mutation_p.P136T|LDB3_ENST00000372066.3_Intron|LDB3_ENST00000263066.6_Intron|LDB3_ENST00000429277.2_Missense_Mutation_p.P136T|LDB3_ENST00000542786.1_Missense_Mutation_p.P136T	NM_007078.2	NP_009009.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						CCCAGGCACCCCGGAGCTCAG	0.736																																					p.P136T		Atlas-SNP	.											.	LDB3	164	.	0			c.C406A						.						33	33	33					10																	88441277		2200	4295	6495	SO:0001583	missense	11155	exon4			GGCACCCCGGAGC	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"cypher", "oracle", "Z-band alternatively spliced PDZ motif protein"	605906	"cardiomyopathy, dilated 1C (autosomal dominant)"	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.406C>A	chr10.hg19:g.88441277C>A	ENSP00000355296:p.Pro136Thr	35.0	0.0		63.0	19.0	NM_007078		Missense_Mutation	SNP	ENST00000361373.4	hg19	CCDS7377.1	.	.	.	.	.	.	.	.	.	.	C	0.039	-1.292907	0.01375	.	.	ENSG00000122367	ENST00000539402;ENST00000429277;ENST00000372056;ENST00000310944;ENST00000361373;ENST00000542786	T;T;T;T;T	0.56611	0.78;0.93;1.04;0.45;1.0	4.82	1.84	0.25277	.	0.712444	0.10992	N	0.611475	T	0.35595	0.0937	L	0.27053	0.805	0.21802	N	0.999533	B;B;B;B;B	0.15719	0.0;0.003;0.007;0.0;0.014	B;B;B;B;B	0.16722	0.001;0.016;0.006;0.001;0.007	T	0.25676	-1.0125	10	0.41790	T	0.15	.	4.3292	0.11055	0.1384:0.6151:0.1144:0.132	.	136;136;136;136;136	B4E3K3;F5H0C2;O75112-4;O75112;O75112-5	.;.;.;LDB3_HUMAN;.	T	136	ENSP00000401437:P136T;ENSP00000361126:P136T;ENSP00000311913:P136T;ENSP00000355296:P136T;ENSP00000438866:P136T	ENSP00000311913:P136T	P	+	1	0	LDB3	88431257	1.000000	0.71417	0.202000	0.23494	0.035000	0.12851	1.071000	0.30666	0.156000	0.19299	-0.471000	0.05019	CCG	.	.		0.736	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2			A	88441277	C	A	88441277	3	1	73	1	0	0	0	0	1	0	0	0	8706	623	22	3	420	3	LDB3	10	88441277	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	7069696	88441277	47093470	356	9682										
IFIT5	24138	hgsc.bcm.edu	37	chr10	91174557	91174558	+	Start_Codon_Ins	INS	-	-	GA													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgcagagcgctgccatcatINSgaggtaagggttttcctttg							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:91174557_91174558insGA	ENST00000371795.4	+	0	215_216				IFIT5_ENST00000416601.1_Start_Codon_Ins|LIPA_ENST00000371837.1_5'Flank	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5						defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						GCTGCCATCATGAGGTAAGGGT	0.649																																					p.M1fs		Atlas-Indel,Pindel	.											.	IFIT5	32	.	0			c.2_3insGA						.																																			SO:0001582	initiator_codon_variant	24138	exon1			.	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.3_4dupGA	chr10.hg19:g.91174558_91174559dupGA		40.0	0.0		78.0	45.0	NM_012420	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Frame_Shift_Ins	INS	ENST00000371795.4	hg19	CCDS7403.1																																																																																			.	.		0.649	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		GA	91174558	-	GA	91174557	7	5	73	1	0	1	1	0	0	0	0	0	7534	1464	51	0	4	0	IFIT5	10	91174557	Start_Codon_Ins	INS	-	TCGA-CC-A7IH-01A-11D-A33K-10	2733280	91174557	44360190	357	9683										
SUFU	51684	hgsc.bcm.edu	37	chr10	104268957	104268957	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagaccccttggactatgttAgcatgtacaggaatgtgggg	13	8	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:104268957A>T	ENST00000369902.3	+	2	380	c.214A>T	c.(214-216)Agc>Tgc	p.S72C	SUFU_ENST00000369899.2_Missense_Mutation_p.S72C|SUFU_ENST00000423559.2_Missense_Mutation_p.S72C	NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	72					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		GGACTATGTTAGCATGTACAG	0.512			"D, F, S"		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation																												p.S72C		Atlas-SNP	.	yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	.	SUFU	44	.	0			c.A214T						.						158	137	145					10																	104268957		2203	4300	6503	SO:0001583	missense	51684	exon2	Familial Cancer Database		TATGTTAGCATGT	AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.214A>T	chr10.hg19:g.104268957A>T	ENSP00000358918:p.Ser72Cys	150.0	0.0		130.0	89.0	NM_001178133	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Missense_Mutation	SNP	ENST00000369902.3	hg19	CCDS7537.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.552887	0.86127	.	.	ENSG00000107882	ENST00000369902;ENST00000369899;ENST00000423559	D;D;D	0.83837	-1.77;-1.77;-1.77	5.44	5.44	0.79542	Suppressor of fused domain (1);	0.000000	0.85682	D	0.000000	D	0.93501	0.7926	H	0.94462	3.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.993;0.988;0.996	D	0.95223	0.8335	10	0.87932	D	0	-23.4494	15.4866	0.75573	1.0:0.0:0.0:0.0	.	72;72;72	Q9UMX1;Q9UMX1-2;Q9UMX1-3	SUFU_HUMAN;.;.	C	72	ENSP00000358918:S72C;ENSP00000358915:S72C;ENSP00000411597:S72C	ENSP00000358915:S72C	S	+	1	0	SUFU	104258947	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.474000	0.90413	2.056000	0.61249	0.459000	0.35465	AGC	.	.		0.512	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050089.1	NM_016169		T	104268957	A	T	104268957	3	4	73	1	0	0	0	0	1	0	0	0	15383	420	15	4	220	4	SUFU	10	104268957	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	13094400	104268957	31265790	358	9684										
SHOC2	8036	hgsc.bcm.edu	37	chr10	112724768	112724768	+	Frame_Shift_Del	DEL	A	A	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcaaaaacttgtcaaaactcAgcatgcttagcattcgagag							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:112724768delA	ENST00000369452.4	+	2	997	c.652delA	c.(652-654)agcfs	p.S218fs	SHOC2_ENST00000489390.1_Intron|SHOC2_ENST00000265277.5_Frame_Shift_Del_p.S218fs	NM_007373.3	NP_031399.2	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog (C. elegans)	218					fibroblast growth factor receptor signaling pathway (GO:0008543)|positive regulation of Ras protein signal transduction (GO:0046579)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase binding (GO:0019903)|protein phosphatase regulator activity (GO:0019888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(2)	17				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		GTCAAAACTCAGCATGCTTAG	0.358																																					p.L217fs		Atlas-Indel,Pindel	.											.	SHOC2	49	.	0			c.651delC						.						68	69	69					10																	112724768		2203	4299	6502	SO:0001589	frameshift_variant	8036	exon2			.	AB020669	CCDS7568.1, CCDS58095.1	10q25	2014-09-17	2001-11-28		ENSG00000108061	ENSG00000108061			15454	protein-coding gene	gene with protein product		602775	"soc-2 (suppressor of clear, C.elegans) homolog"			9618511, 9674433, 10783161	Standard	NM_007373		Approved	KIAA0862, SOC2, SUR-8, SOC-2, SUR8	uc001kzl.4	Q9UQ13	OTTHUMG00000019047	ENST00000369452.4:c.652delA	chr10.hg19:g.112724768delA	ENSP00000358464:p.Ser218fs	99.0	0.0		132.0	42.0	NM_007373	A8K9W8|B3KR23|O76063|Q5VZS8|Q5VZS9	Frame_Shift_Del	DEL	ENST00000369452.4	hg19	CCDS7568.1																																																																																			.	.		0.358	SHOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050355.1	NM_007373		-	112724768	A	-	112724768	7	5	73	1	0	1	0	1	0	0	0	0	14302	188	7	0	654	0	SHOC2	10	112724768	Frame_Shift_Del	DEL	A	TCGA-CC-A7IH-01A-11D-A33K-10	8455811	112724768	22809979	359	9685										
KCNK18	338567	hgsc.bcm.edu	37	chr10	118969679	118969679	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acttcttcctgttcttctccAtttatatcatcgttggaatg	5	10	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:118969679A>G	ENST00000334549.1	+	3	1024	c.1024A>G	c.(1024-1026)Att>Gtt	p.I342V		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	342					cellular response to pH (GO:0071467)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41		Colorectal(252;0.19)		all cancers(201;0.0211)		GTTCTTCTCCATTTATATCAT	0.383																																					p.I342V		Atlas-SNP	.											.	KCNK18	70	.	0			c.A1024G						.						275	244	254					10																	118969679		2203	4300	6503	SO:0001583	missense	338567	exon3			TTCTCCATTTATA	AB087138	CCDS7598.1	10q26.11	2012-03-07			ENSG00000186795	ENSG00000186795		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	19439	protein-coding gene	gene with protein product	"TWIK related spinal cord K+ channel"	613655				16382106	Standard	NM_181840		Approved	K2p18.1, TRESK-2, TRESK2, TRESK, TRIK	uc010qsr.2	Q7Z418	OTTHUMG00000019120	ENST00000334549.1:c.1024A>G	chr10.hg19:g.118969679A>G	ENSP00000334650:p.Ile342Val	107.0	0.0		132.0	36.0	NM_181840	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	hg19	CCDS7598.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.697672	0.30142	.	.	ENSG00000186795	ENST00000334549	T	0.28255	1.62	5.4	-1.39	0.08997	Ion transport 2 (1);	0.566111	0.18791	N	0.131041	T	0.15132	0.0365	N	0.16602	0.42	0.19575	N	0.999968	B	0.17465	0.022	B	0.32149	0.141	T	0.37776	-0.9691	10	0.02654	T	1	.	8.7547	0.34639	0.2775:0.5242:0.1983:0.0	.	342	Q7Z418	KCNKI_HUMAN	V	342	ENSP00000334650:I342V	ENSP00000334650:I342V	I	+	1	0	KCNK18	118959669	0.558000	0.26554	0.174000	0.22961	0.995000	0.86356	0.342000	0.19926	-0.415000	0.07484	0.533000	0.62120	ATT	.	.		0.383	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840		G	118969679	A	G	118969679	3	3	73	1	0	0	0	0	1	0	0	0	8074	217	8	2	1034	2	KCNK18	10	118969679	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	6244911	118969679	16565068	360	9686										
GPR123	84435	hgsc.bcm.edu	37	chr10	134910562	134910562	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgtgcacggccgtcatgctgCtctgcctcctggcctccttc	10	18	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr10:134910562C>A	ENST00000392607.3	+	3	524	c.88C>A	c.(88-90)Ctc>Atc	p.L30I	GPR123_ENST00000607359.1_Missense_Mutation_p.L750I	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	30					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L30F(1)|p.L750F(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CGTCATGCTGCTCTGCCTCCT	0.612																																					p.L30I		Atlas-SNP	.											GPR123,NS,carcinoma,0,1	GPR123	118	.	2	Substitution - Missense(2)	kidney(2)	c.C88A						.						151	116	128					10																	134910562		2203	4300	6503	SO:0001583	missense	84435	exon3			ATGCTGCTCTGCC	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"-", "GPCR / Class B : Orphans"	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.88C>A	chr10.hg19:g.134910562C>A	ENSP00000376384:p.Leu30Ile	44.0	0.0		54.0	32.0	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Missense_Mutation	SNP	ENST00000392607.3	hg19	CCDS41580.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.330859	0.60853	.	.	ENSG00000197177	ENST00000368577;ENST00000392609;ENST00000392607	T	0.38077	1.16	3.85	3.85	0.44370	GPCR, family 2-like (1);	0.330102	0.20831	N	0.084884	T	0.43322	0.1242	M	0.74881	2.28	0.80722	D	1	B;P	0.36633	0.242;0.562	B;B	0.44224	0.259;0.444	T	0.43893	-0.9363	10	0.52906	T	0.07	-21.8247	7.7121	0.28684	0.0:0.8809:0.0:0.1191	.	30;750	Q86SQ6;Q86SQ6-1	GP123_HUMAN;.	I	750;750;30	ENSP00000376384:L30I	ENSP00000357566:L750I	L	+	1	0	GPR123	134760552	1.000000	0.71417	0.994000	0.49952	0.894000	0.52154	2.077000	0.41557	1.892000	0.54788	0.436000	0.28706	CTC	.	.		0.612	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2			A	134910562	C	A	134910562	3	1	73	1	0	0	0	0	1	0	0	0	6645	797	28	3	94	3	GPR123	10	134910562	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	15940883	134910562	624185	361	9687										
MUC6	4588	hgsc.bcm.edu	37	chr11	1031239	1031239	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agcccgcacatctgacccatGtacttccgctccaccagaac	6	18	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:1031239G>C	ENST00000421673.2	-	5	554	c.504C>G	c.(502-504)taC>taG	p.Y168*		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	168	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCTGACCCATGTACTTCCGCT	0.662																																					p.Y168X		Atlas-SNP	.											.	MUC6	408	.	0			c.C504G						.						17	16	16					11																	1031239		1823	4050	5873	SO:0001587	stop_gained	4588	exon5			ACCCATGTACTTC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.504C>G	chr11.hg19:g.1031239G>C	ENSP00000406861:p.Tyr168*	121.0	0.0		124.0	51.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Nonsense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	g	16.82	3.228453	0.58777	.	.	ENSG00000184956	ENST00000421673	.	.	.	3.66	3.66	0.41972	.	0.725673	0.10516	U	0.665538	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7734	0.51972	0.0:0.1782:0.8218:0.0	.	.	.	.	X	168	.	ENSP00000406861:Y168X	Y	-	3	2	MUC6	1021239	1.000000	0.71417	0.983000	0.44433	0.256000	0.26092	2.098000	0.41757	1.778000	0.52293	0.197000	0.17608	TAC	.	.		0.662	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		C	1031239	G	C	1031239	4	2	73	1	0	0	0	0	0	1	0	0	9989	1372	48	4	6931	4	MUC6	11	1031239	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10		1031239	133975277	362	9688										
MUC2	4583	hgsc.bcm.edu	37	chr11	1087958	1087958	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggaaccggagcttcgagaccTgcaggaccatcaacggcatc	12	13	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:1087958T>C	ENST00000441003.2	+	25	3460	c.3433T>C	c.(3433-3435)Tgc>Cgc	p.C1145R	MUC2_ENST00000359061.5_Missense_Mutation_p.C1145R	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1145					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CTTCGAGACCTGCAGGACCAT	0.622																																					p.C1145R		Atlas-SNP	.											.	MUC2	614	.	0			c.T3433C						.						64	69	68					11																	1087958		2145	4251	6396	SO:0001583	missense	4583	exon25			GAGACCTGCAGGA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3433T>C	chr11.hg19:g.1087958T>C	ENSP00000415183:p.Cys1145Arg	94.0	0.0		61.0	25.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	t	11.51	1.660052	0.29515	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	D;D	0.92397	-3.03;-3.03	3.98	3.98	0.46160	.	0.158163	0.40818	N	0.001003	D	0.96334	0.8804	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.96973	0.9710	10	0.87932	D	0	.	13.0893	0.59158	0.0:0.0:0.0:1.0	.	1145	E7EUV1	.	R	1145	ENSP00000415183:C1145R;ENSP00000351956:C1145R	ENSP00000351956:C1145R	C	+	1	0	MUC2	1077958	1.000000	0.71417	0.091000	0.20842	0.339000	0.28857	5.925000	0.70062	1.688000	0.51068	0.450000	0.29827	TGC	.	.		0.622	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1087958	T	C	1087958	3	2	73	1	0	0	0	0	1	0	0	0	9984	1580	55	2	3531	2	MUC2	11	1087958	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	56719	1087958	133918558	363	9689										
KRTAP5-3	387266	hgsc.bcm.edu	37	chr11	1629498	1629498	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcacacgggcttgcagcagcAgacaggtacacagcagccgg	14	13	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:1629498A>T	ENST00000399685.1	-	1	195	c.118T>A	c.(118-120)Tgc>Agc	p.C40S		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	40	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		TTGCAGCAGCAGACAGGTACA	0.677																																					p.C40S		Atlas-SNP	.											.	KRTAP5-3	33	.	0			c.T118A						.						65	83	77					11																	1629498		2201	4298	6499	SO:0001583	missense	387266	exon1			AGCAGCAGACAGG	AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"Keratin associated proteins"	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.118T>A	chr11.hg19:g.1629498A>T	ENSP00000382592:p.Cys40Ser	126.0	0.0		93.0	39.0	NM_001012708	Q6PL44|Q701N3	Missense_Mutation	SNP	ENST00000399685.1	hg19	CCDS41591.1	.	.	.	.	.	.	.	.	.	.	A	0.150	-1.092695	0.01858	.	.	ENSG00000196224	ENST00000399685	T	0.01113	5.32	2.19	2.19	0.27852	.	.	.	.	.	T	0.01454	0.0047	L	0.51853	1.615	0.22996	N	0.998458	P	0.34684	0.463	B	0.38683	0.279	T	0.43097	-0.9412	9	0.12430	T	0.62	.	6.3642	0.21445	1.0:0.0:0.0:0.0	.	40	Q6L8H2	KRA53_HUMAN	S	40	ENSP00000382592:C40S	ENSP00000382592:C40S	C	-	1	0	KRTAP5-3	1586074	0.011000	0.17503	0.985000	0.45067	0.092000	0.18411	-0.602000	0.05680	1.259000	0.44117	0.248000	0.18094	TGC	.	.		0.677	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1			T	1629498	A	T	1629498	3	4	73	1	0	0	0	0	1	0	0	0	8571	188	7	4	602	4	KRTAP5-3	11	1629498	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	541540	1629498	133377018	364	9690										
KRTAP5-6	440023	hgsc.bcm.edu	37	chr11	1718512	1718532	+	In_Frame_Del	DEL	GGCTGTGGGGGCTGTGGCTCT	GGCTGTGGGGGCTGTGGCTCT	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctctggaggctgtggctccGgctgtgggggctgtggctct					rs545751292		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	GGCTGTGGGGGCTGTGGCTCT	GGCTGTGGGGGCTGTGGCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:1718512_1718532delGGCTGTGGGGGCTGTGGCTCT	ENST00000382160.1	+	1	88_108	c.37_57delGGCTGTGGGGGCTGTGGCTCT	c.(37-57)ggctgtgggggctgtggctctdel	p.GCGGCGS20del		NM_001012416.1	NP_001012416.1	Q6L8G9	KRA56_HUMAN	keratin associated protein 5-6	20						keratin filament (GO:0045095)		p.G16C(1)|p.G15G(1)		endometrium(1)|large_intestine(2)|lung(6)|skin(1)	10		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CTGTGGCTCCGGCTGTGGGGGCTGTGGCTCTGGCTGTGGGG	0.643																																					p.12_19del		Atlas-Indel,Pindel	.											.	KRTAP5-6	18	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)	c.36_56del						.			394,3824		8,378,1723						3.1	1			76	270,7968		4,262,3853	no	coding	KRTAP5-6	NM_001012416.1		12,640,5576	A1A1,A1R,RR		3.2775,9.3409,5.3308				664,11792				SO:0001651	inframe_deletion	440023	exon1			.	AB126075	CCDS31332.1	11p15.5	2008-02-05			ENSG00000205864	ENSG00000205864		"Keratin associated proteins"	23600	protein-coding gene	gene with protein product						15144888	Standard	NM_001012416		Approved	KRTAP5.6	uc001lua.3	Q6L8G9	OTTHUMG00000043932	ENST00000382160.1:c.37_57delGGCTGTGGGGGCTGTGGCTCT	chr11.hg19:g.1718512_1718532delGGCTGTGGGGGCTGTGGCTCT	ENSP00000371595:p.Gly20_Ser26del	154.0	0.0		140.0	44.0	NM_001012416	A1L452	In_Frame_Del	DEL	ENST00000382160.1	hg19	CCDS31332.1																																																																																			.	.		0.643	KRTAP5-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102339.2			-	1718532	GGCTGTGGGGGCTGTGGCTCT	-	1718512	7	5	73	1	0	1	0	1	0	0	0	0	8574	1116	39	0	39	0	KRTAP5-6	11	1718512	In_Frame_Del	DEL	GGCTGTGGGGGCTGTGGCTCT	TCGA-CC-A7IH-01A-11D-A33K-10	89014	1718512	133288004	365	9691										
OR56A5	0	hgsc.bcm.edu	37	chr11	5988980	5988980	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtgaagaagaggatgaggaTgaagtgggaaccacaagtac	16	4	0	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:5988980T>A								OR56A3 (19389 upstream) : OR52L1 (18141 downstream)																							AGGATGAGGATGAAGTGGGAA	0.468																																					p.I249F		Atlas-SNP	.											.	.	.	.	0			c.A745T						.						169	164	166					11																	5988980		692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			TGAGGATGAAGTG																													chr11.hg19:g.5988980T>A		195.0	0.0		157.0	63.0	NM_001146033		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.468									A	5988980	T	A	5988980	1	1	73	0	1	0	0	0	0	0	0	0	11145	1464	51	4		4	OR56A5	11	5988980	IGR	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	4270468	5988980	129017536	366	9692										
CCKBR	887	hgsc.bcm.edu	37	chr11	6292239	6292239	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	accgcccaccctttgtgctcAggggctgttcaccagaacgg	11	15	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:6292239A>G	ENST00000334619.2	+	5	1004		c.e5-1		CCKBR_ENST00000525462.1_Silent_p.S339S|CCKBR_ENST00000532715.1_Splice_Site|CCKBR_ENST00000532396.1_Splice_Site	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor						cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	CTTTGTGCTCAGGGGCTGTTC	0.642																																					.		Atlas-SNP	.											.	CCKBR	232	.	0			c.812-2A>G						.						40	42	42					11																	6292239		2201	4296	6497	SO:0001630	splice_region_variant	887	exon5			GTGCTCAGGGGCT	D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"GPCR / Class A : Cholecystokinin receptors"	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.812-1A>G	chr11.hg19:g.6292239A>G		50.0	0.0		40.0	25.0	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Splice_Site	SNP	ENST00000334619.2	hg19	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	A	0.329	-0.957110	0.02267	.	.	ENSG00000110148	ENST00000334619;ENST00000532715	.	.	.	4.69	3.58	0.41010	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.426	0.21770	0.8932:0.0:0.1068:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCKBR	6248815	0.181000	0.23161	0.216000	0.23742	0.014000	0.08584	1.964000	0.40462	2.091000	0.63221	0.533000	0.62120	.	.	.		0.642	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875	Intron	G	6292239	A	G	6292239	5	3	73	1	0	0	0	0	0	0	1	0	2883	202	7	2	828	2	CCKBR	11	6292239	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	303259	6292239	128714277	367	9693										
OR2AG1	144125	hgsc.bcm.edu	37	chr11	6806883	6806883	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtatatgtgatgggtgtgacCttcctgattccctctcttgc	10	10	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:6806883C>T	ENST00000307401.4	+	1	636	c.615C>T	c.(613-615)acC>acT	p.T205T		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	205						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGGGTGTGACCTTCCTGATTC	0.488																																					p.T205T		Atlas-SNP	.											.	OR2AG1	57	.	0			c.C615T						.						243	204	217					11																	6806883		2201	4296	6497	SO:0001819	synonymous_variant	144125	exon1			TGTGACCTTCCTG	AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"GPCR / Class A : Olfactory receptors"	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.615C>T	chr11.hg19:g.6806883C>T		83.0	0.0		104.0	43.0	NM_001004489	B9EKV7|Q6IFG7|Q96R26	Silent	SNP	ENST00000307401.4	hg19	CCDS31414.1																																																																																			.	.		0.488	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385980.1	NM_001004489		T	6806883	C	T	6806883	2	4	73	1	0	0	0	0	0	0	0	1	10993	668	24	3		3	OR2AG1	11	6806883	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	514644	6806883	128199633	368	9694										
OR10A5	144124	hgsc.bcm.edu	37	chr11	6867208	6867208	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccatctccttccttggctgtGccactcagatgtatttcttc	6	14	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:6867208G>T	ENST00000299454.4	+	1	326	c.295G>T	c.(295-297)Gcc>Tcc	p.A99S	OR10A5_ENST00000379831.2_Missense_Mutation_p.A103S			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	99					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CCTTGGCTGTGCCACTCAGAT	0.502																																					p.A99S	Pancreas(44;21 1072 25662 28041 45559)	Atlas-SNP	.											.	OR10A5	48	.	0			c.G295T						.						91	93	93					11																	6867208		2201	4296	6497	SO:0001583	missense	144124	exon1			GGCTGTGCCACTC	AF324499	CCDS7773.1	11p15.4	2012-08-09			ENSG00000166363	ENSG00000166363		"GPCR / Class A : Olfactory receptors"	15131	protein-coding gene	gene with protein product		608493		OR10A1			Standard	NM_178168		Approved	OR11-403, JCG6	uc001met.1	Q9H207	OTTHUMG00000165738	ENST00000299454.4:c.295G>T	chr11.hg19:g.6867208G>T	ENSP00000299454:p.Ala99Ser	237.0	0.0		222.0	92.0	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Missense_Mutation	SNP	ENST00000299454.4	hg19	CCDS7773.1	.	.	.	.	.	.	.	.	.	.	.	15.71	2.914575	0.52546	.	.	ENSG00000166363	ENST00000299454;ENST00000379831	T;T	0.00402	7.56;7.56	3.42	3.42	0.39159	GPCR, rhodopsin-like superfamily (1);	0.215458	0.32640	N	0.005838	T	0.00666	0.0022	M	0.81942	2.565	0.29091	N	0.882099	P	0.48089	0.905	P	0.46975	0.533	T	0.31641	-0.9936	10	0.66056	D	0.02	.	13.1066	0.59252	0.0:0.0:1.0:0.0	.	99	Q9H207	O10A5_HUMAN	S	99;103	ENSP00000299454:A99S;ENSP00000369159:A103S	ENSP00000299454:A99S	A	+	1	0	OR10A5	6823784	0.506000	0.26139	1.000000	0.80357	0.989000	0.77384	1.120000	0.31271	2.176000	0.68965	0.591000	0.81541	GCC	.	.		0.502	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168		T	6867208	G	T	6867208	3	4	73	1	0	0	0	0	1	0	0	0	10902	1319	46	3	297	3	OR10A5	11	6867208	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	60325	6867208	128139308	369	9695										
NLRP10	338322	hgsc.bcm.edu	37	chr11	7981937	7981937	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcacagactcctcaggacccTgtgccgggaaagctcggagc	13	14	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:7981937T>A	ENST00000328600.2	-	2	1383	c.1222A>T	c.(1222-1224)Agg>Tgg	p.R408W		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	408	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CTCAGGACCCTGTGCCGGGAA	0.532																																					p.R408W		Atlas-SNP	.											.	NLRP10	146	.	0			c.A1222T						.						49	49	49					11																	7981937		2201	4296	6497	SO:0001583	missense	338322	exon2			GGACCCTGTGCCG	AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"Nucleotide-binding domain and leucine rich repeat containing"	21464	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"	609662	"NACHT, leucine rich repeat and PYD containing 10"	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.1222A>T	chr11.hg19:g.7981937T>A	ENSP00000327763:p.Arg408Trp	57.0	0.0		57.0	23.0	NM_176821	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	hg19	CCDS7784.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.819281	0.32145	.	.	ENSG00000182261	ENST00000328600	D	0.88124	-2.34	4.93	1.09	0.20402	.	0.532689	0.15896	N	0.239292	D	0.86201	0.5876	L	0.40543	1.245	0.09310	N	0.999997	D	0.65815	0.995	P	0.61070	0.883	T	0.75028	-0.3462	10	0.66056	D	0.02	.	4.8344	0.13456	0.0:0.1011:0.3839:0.515	.	408	Q86W26	NAL10_HUMAN	W	408	ENSP00000327763:R408W	ENSP00000327763:R408W	R	-	1	2	NLRP10	7938513	0.201000	0.23410	0.269000	0.24586	0.031000	0.12232	0.564000	0.23563	0.825000	0.34637	-0.316000	0.08728	AGG	.	.		0.532	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821		A	7981937	T	A	7981937	3	1	73	1	0	0	0	0	1	0	0	0	10481	1579	55	4	749	4	NLRP10	11	7981937	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1114729	7981937	127024579	370	9696										
ZNF143	7702	hgsc.bcm.edu	37	chr11	9499989	9499989	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagctggaagatggtaccacAgcttatatccaccatgcagt	9	11	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:9499989A>T	ENST00000396602.2	+	6	545	c.426A>T	c.(424-426)acA>acT	p.T142T	ZNF143_ENST00000299606.2_Silent_p.T114T|ZNF143_ENST00000396597.3_Silent_p.T111T|ZNF143_ENST00000530463.1_Silent_p.T141T|ZNF143_ENST00000396604.1_Silent_p.T141T	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	142					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		ATGGTACCACAGCTTATATCC	0.478																																					p.T142T		Atlas-SNP	.											.	ZNF143	38	.	0			c.A426T						.						154	128	137					11																	9499989		2201	4294	6495	SO:0001819	synonymous_variant	7702	exon6			TACCACAGCTTAT	U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"Zinc fingers, C2H2-type"	12928	protein-coding gene	gene with protein product		603433	"zinc finger protein 143 (clone pHZ-1)"				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.426A>T	chr11.hg19:g.9499989A>T		98.0	0.0		75.0	22.0	NM_003442	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Silent	SNP	ENST00000396602.2	hg19	CCDS7799.2	.	.	.	.	.	.	.	.	.	.	A	11.66	1.703887	0.30232	.	.	ENSG00000166478	ENST00000526657	T	0.48522	0.81	5.04	-4.05	0.03998	.	.	.	.	.	T	0.47377	0.1442	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57051	-0.7877	6	0.87932	D	0	.	6.18	0.20465	0.2293:0.0:0.4313:0.3394	.	.	.	.	L	141	ENSP00000435881:Q141L	ENSP00000435881:Q141L	Q	+	2	0	ZNF143	9456565	0.023000	0.18921	0.987000	0.45799	0.976000	0.68499	-0.726000	0.04936	-0.291000	0.09012	-0.468000	0.05107	CAG	.	.		0.478	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442		T	9499989	A	T	9499989	2	4	73	1	0	0	0	0	0	0	0	1	17747	175	7	4		4	ZNF143	11	9499989	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1518052	9499989	125506527	371	9697										
ZDHHC13	54503	hgsc.bcm.edu	37	chr11	19170802	19170802	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccccactcttattgatggagAgggattcagcagcatccacc	9	13	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:19170802A>C	ENST00000446113.2	+	5	564	c.443A>C	c.(442-444)gAg>gCg	p.E148A	ZDHHC13_ENST00000399351.3_Missense_Mutation_p.E18A|ZDHHC13_ENST00000532812.1_3'UTR	NM_019028.2	NP_061901.2	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC-type containing 13	148					metabolic process (GO:0008152)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	magnesium ion transmembrane transporter activity (GO:0015095)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6						ATTGATGGAGAGGGATTCAGC	0.408																																					p.E148A		Atlas-SNP	.											.	ZDHHC13	40	.	0			c.A443C						.						93	82	85					11																	19170802		1893	4110	6003	SO:0001583	missense	54503	exon5			ATGGAGAGGGATT	AB024495	CCDS44550.1, CCDS44551.1	11p15.1	2013-01-10			ENSG00000177054	ENSG00000177054		"Zinc fingers, DHHC-type", "Ankyrin repeat domain containing"	18413	protein-coding gene	gene with protein product		612815				18794299	Standard	NM_001001483		Approved	FLJ10852, FLJ10941, HIP14L	uc001mpi.3	Q8IUH4	OTTHUMG00000166099	ENST00000446113.2:c.443A>C	chr11.hg19:g.19170802A>C	ENSP00000400113:p.Glu148Ala	135.0	0.0		134.0	51.0	NM_019028	Q7Z2D3|Q86VK2|Q9NV30|Q9NV99	Missense_Mutation	SNP	ENST00000446113.2	hg19	CCDS44550.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.785333	0.90282	.	.	ENSG00000177054	ENST00000446113;ENST00000399351	T;T	0.65732	-0.17;0.62	5.79	5.79	0.91817	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.69620	0.3131	N	0.26092	0.79	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.73474	-0.3971	10	0.72032	D	0.01	-2.3789	15.7882	0.78326	1.0:0.0:0.0:0.0	.	148	Q8IUH4	ZDH13_HUMAN	A	148;18	ENSP00000400113:E148A;ENSP00000382288:E18A	ENSP00000382288:E18A	E	+	2	0	ZDHHC13	19127378	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.205000	0.71048	0.455000	0.32223	GAG	.	.		0.408	ZDHHC13-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387821.1	NM_019028		C	19170802	A	C	19170802	3	2	73	1	0	0	0	0	1	0	0	0	17618	304	11	5	461	5	ZDHHC13	11	19170802	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	9670813	19170802	115835714	372	9698										
SLC6A5	9152	hgsc.bcm.edu	37	chr11	20652295	20652295	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcatctttgccggcttcgtcAtcttctccgttatcggcttc	8	14	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:20652295A>C	ENST00000525748.1	+	10	1831	c.1558A>C	c.(1558-1560)Atc>Ctc	p.I520L	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	520					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	CGGCTTCGTCATCTTCTCCGT	0.502																																					p.I520L		Atlas-SNP	.											.	SLC6A5	151	.	0			c.A1558C						.						201	169	180					11																	20652295		2203	4300	6503	SO:0001583	missense	9152	exon10			TTCGTCATCTTCT	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"Solute carriers"	11051	protein-coding gene	gene with protein product	"glycine transporter 2"	604159	"solute carrier family 6 (neurotransmitter transporter, glycine), member 5"	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.1558A>C	chr11.hg19:g.20652295A>C	ENSP00000434364:p.Ile520Leu	151.0	0.0		134.0	52.0	NM_004211	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	hg19	CCDS7854.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.330292	0.81690	.	.	ENSG00000165970	ENST00000525748	T	0.78003	-1.14	5.57	5.57	0.84162	.	0.044671	0.85682	D	0.000000	D	0.90655	0.7069	M	0.93283	3.4	0.80722	D	1	D	0.71674	0.998	D	0.69479	0.964	D	0.93083	0.6493	10	0.87932	D	0	.	15.7239	0.77736	1.0:0.0:0.0:0.0	.	520	Q9Y345	SC6A5_HUMAN	L	520	ENSP00000434364:I520L	ENSP00000434364:I520L	I	+	1	0	SLC6A5	20608871	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	7.576000	0.82467	2.116000	0.64780	0.533000	0.62120	ATC	.	.		0.502	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211		C	20652295	A	C	20652295	3	2	73	1	0	0	0	0	1	0	0	0	14702	217	8	5	1596	5	SLC6A5	11	20652295	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1481493	20652295	114354221	373	9699										
HIPK3	10114	hgsc.bcm.edu	37	chr11	33358716	33358716	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttttgcaaagaaacagatatGtctcattctggttggagatt	9	5	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:33358716G>T	ENST00000303296.4	+	4	1622	c.1317G>T	c.(1315-1317)atG>atT	p.M439I	HIPK3_ENST00000379016.3_Missense_Mutation_p.M439I|HIPK3_ENST00000534262.1_3'UTR|HIPK3_ENST00000456517.1_Missense_Mutation_p.M439I|HIPK3_ENST00000525975.1_Missense_Mutation_p.M439I	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	439	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						AAACAGATATGTCTCATTCTG	0.328																																					p.M439I		Atlas-SNP	.											.	HIPK3	92	.	0			c.G1317T						.						57	58	58					11																	33358716		2201	4294	6495	SO:0001583	missense	10114	exon4			AGATATGTCTCAT	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.1317G>T	chr11.hg19:g.33358716G>T	ENSP00000304226:p.Met439Ile	91.0	0.0		60.0	27.0	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	G	8.226	0.803583	0.16467	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.19250	2.16;2.16;2.16;2.16	4.88	0.0826	0.14429	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.477607	0.19356	N	0.116264	T	0.06735	0.0172	N	0.04686	-0.185	0.28635	N	0.907454	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21930	-1.0231	10	0.25106	T	0.35	.	0.2865	0.00252	0.3784:0.2143:0.1758:0.2316	.	439;439	Q9H422-2;Q9H422	.;HIPK3_HUMAN	I	439	ENSP00000431710:M439I;ENSP00000304226:M439I;ENSP00000368301:M439I;ENSP00000398241:M439I	ENSP00000304226:M439I	M	+	3	0	HIPK3	33315292	0.962000	0.33011	0.993000	0.49108	0.916000	0.54674	0.096000	0.15147	-0.163000	0.10946	0.563000	0.77884	ATG	.	.		0.328	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		T	33358716	G	T	33358716	3	4	73	1	0	0	0	0	1	0	0	0	7127	1377	48	3	1327	3	HIPK3	11	33358716	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	12706421	33358716	101647800	374	9700										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33628353	33628353	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aggagccaggagtcatcggcAgtcctcaacggcgaggtaag	15	10	2	0	rs557858789		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:33628353A>T	ENST00000321505.4	+	13	4335	c.4155A>T	c.(4153-4155)gcA>gcT	p.A1385A	KIAA1549L_ENST00000389726.3_Silent_p.A1391A			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1385						integral component of membrane (GO:0016021)											AGTCATCGGCAGTCCTCAACG	0.587																																					p.A1385A		Atlas-SNP	.											.	.	.	.	0			c.A4155T						.						22	24	23					11																	33628353		2040	4202	6242	SO:0001819	synonymous_variant	25758	exon13			ATCGGCAGTCCTC	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.4155A>T	chr11.hg19:g.33628353A>T		119.0	0.0		118.0	47.0	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	hg19	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	A	2.326	-0.354567	0.05138	.	.	ENSG00000110427	ENST00000526400	.	.	.	5.43	-10.9	0.00192	.	.	.	.	.	T	0.16041	0.0386	.	.	.	0.24382	N	0.994786	.	.	.	.	.	.	T	0.06162	-1.0842	4	.	.	.	-2.331	3.9237	0.09254	0.0963:0.3948:0.2214:0.2876	.	.	.	.	L	783	.	.	Q	+	2	0	C11orf41	33584929	0.000000	0.05858	0.000000	0.03702	0.210000	0.24377	-2.036000	0.01421	-3.562000	0.00141	-1.560000	0.00886	CAG	.	.		0.587	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		T	33628353	A	T	33628353	2	4	73	1	0	0	0	0	0	0	0	1	1642	175	7	4		4	C11orf41	11	33628353	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	269637	33628353	101378163	375	9701										
ELF5	2001	hgsc.bcm.edu	37	chr11	34515128	34515128	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctgcacagctgcaggccacTgatgttgaagttgcagaagg	14	9	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:34515128T>A	ENST00000312319.2	-	3	512	c.283A>T	c.(283-285)Agt>Tgt	p.S95C	ELF5_ENST00000429939.2_Intron|ELF5_ENST00000532417.1_Missense_Mutation_p.S85C|ELF5_ENST00000528709.1_Intron|ELF5_ENST00000257832.2_Missense_Mutation_p.S85C	NM_001243081.1|NM_198381.1	NP_001230010.1|NP_938195.1	Q9UKW6	ELF5_HUMAN	E74-like factor 5 (ets domain transcription factor)	95	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|ectoderm development (GO:0007398)|mammary gland epithelial cell differentiation (GO:0060644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			large_intestine(4)|skin(1)	5		Acute lymphoblastic leukemia(5;0.0087)|all_hematologic(20;0.0384)				TGCAGGCCACTGATGTTGAAG	0.547											OREG0020879	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S95C	Melanoma(61;202 1660 4348 21594)	Atlas-SNP	.											.	ELF5	21	.	0			c.A283T						.						88	73	78					11																	34515128		2202	4298	6500	SO:0001583	missense	2001	exon3			GGCCACTGATGTT	AF049703	CCDS7892.1, CCDS7893.1, CCDS58129.1, CCDS73273.1	11p13-p12	2008-05-14			ENSG00000135374	ENSG00000135374			3320	protein-coding gene	gene with protein product		605169				9840936	Standard	NM_001422		Approved		uc001mvp.2	Q9UKW6	OTTHUMG00000166451	ENST00000312319.2:c.283A>T	chr11.hg19:g.34515128T>A	ENSP00000311010:p.Ser95Cys	117.0	0.0	848	95.0	45.0	NM_198381	A6XAE6|A8K452|O95175|Q8N2K9|Q96QY3|Q9UKW5	Missense_Mutation	SNP	ENST00000312319.2	hg19	CCDS7892.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.027915	0.75390	.	.	ENSG00000135374	ENST00000257832;ENST00000312319;ENST00000532417	T;T;T	0.33438	1.41;1.41;1.41	4.66	4.66	0.58398	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.321577	0.30714	N	0.009030	T	0.40522	0.1120	L	0.50333	1.59	0.39319	D	0.965214	D;D	0.59357	0.985;0.975	P;P	0.55999	0.789;0.756	T	0.40001	-0.9586	10	0.87932	D	0	.	9.5285	0.39180	0.157:0.0:0.0:0.843	.	85;95	Q9UKW6-3;Q9UKW6	.;ELF5_HUMAN	C	85;95;85	ENSP00000257832:S85C;ENSP00000311010:S95C;ENSP00000436386:S85C	ENSP00000257832:S85C	S	-	1	0	ELF5	34471704	0.993000	0.37304	1.000000	0.80357	0.985000	0.73830	1.801000	0.38843	1.745000	0.51790	0.459000	0.35465	AGT	.	.		0.547	ELF5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389845.1	NM_198381		A	34515128	T	A	34515128	3	1	73	1	0	0	0	0	1	0	0	0	5059	1580	55	4	534	4	ELF5	11	34515128	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	886775	34515128	100491388	376	9702										
OR8H2	390151	hgsc.bcm.edu	37	chr11	55873220	55873220	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	attaattccacttcaggaaaGcagaaagctttctctacttg	6	9	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:55873220G>T	ENST00000313503.1	+	1	702	c.702G>T	c.(700-702)aaG>aaT	p.K234N		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	234						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					CTTCAGGAAAGCAGAAAGCTT	0.373										HNSCC(53;0.14)																											p.K234N		Atlas-SNP	.											OR8H2,NS,carcinoma,0,1	OR8H2	117	.	0			c.G702T						.						113	110	111					11																	55873220		2201	4296	6497	SO:0001583	missense	390151	exon1			AGGAAAGCAGAAA	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"GPCR / Class A : Olfactory receptors"	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.702G>T	chr11.hg19:g.55873220G>T	ENSP00000323982:p.Lys234Asn	157.0	1.0		182.0	73.0	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	hg19	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	g	12.26	1.885103	0.33255	.	.	ENSG00000181767	ENST00000313503	T	0.00169	8.63	3.58	2.65	0.31530	GPCR, rhodopsin-like superfamily (1);	0.111644	0.40728	N	0.001028	T	0.00356	0.0011	M	0.87038	2.855	0.09310	N	1	P	0.44195	0.828	P	0.50934	0.654	T	0.21793	-1.0235	10	0.87932	D	0	.	5.4631	0.16627	0.1892:0.2773:0.5335:0.0	.	234	Q8N162	OR8H2_HUMAN	N	234	ENSP00000323982:K234N	ENSP00000323982:K234N	K	+	3	2	OR8H2	55629796	0.019000	0.18553	0.850000	0.33497	0.662000	0.39071	1.254000	0.32897	1.952000	0.56665	0.440000	0.28878	AAG	.	.		0.373	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200		T	55873220	G	T	55873220	3	4	73	1	0	0	0	0	1	0	0	0	11247	962	34	3	704	3	OR8H2	11	55873220	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	21358092	55873220	79133296	377	9703										
OR8J3	81168	hgsc.bcm.edu	37	chr11	55904587	55904587	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaaaaaccaaatttgttgctGcagatataaagactattgtt	6	5	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:55904587G>T	ENST00000301529.1	-	1	607	c.608C>A	c.(607-609)gCa>gAa	p.A203E		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					ATTTGTTGCTGCAGATATAAA	0.308																																					p.A203E		Atlas-SNP	.											.	OR8J3	112	.	0			c.C608A						.						105	108	107					11																	55904587		2201	4296	6497	SO:0001583	missense	81168	exon1			GTTGCTGCAGATA		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"GPCR / Class A : Olfactory receptors"	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.608C>A	chr11.hg19:g.55904587G>T	ENSP00000301529:p.Ala203Glu	53.0	0.0		76.0	33.0	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	hg19	CCDS31520.1	.	.	.	.	.	.	.	.	.	.	G	11.05	1.524384	0.27299	.	.	ENSG00000167822	ENST00000301529	T	0.39229	1.09	3.27	2.31	0.28768	GPCR, rhodopsin-like superfamily (1);	0.430233	0.22264	N	0.062364	T	0.64616	0.2614	M	0.91818	3.245	0.09310	N	1	D	0.53619	0.961	P	0.59825	0.864	T	0.58177	-0.7682	10	0.87932	D	0	.	10.7899	0.46426	0.1057:0.0:0.8943:0.0	.	203	Q8NGG0	OR8J3_HUMAN	E	203	ENSP00000301529:A203E	ENSP00000301529:A203E	A	-	2	0	OR8J3	55661163	0.000000	0.05858	0.021000	0.16686	0.253000	0.25986	0.141000	0.16076	1.553000	0.49476	0.297000	0.19635	GCA	.	.		0.308	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064		T	55904587	G	T	55904587	3	4	73	1	0	0	0	0	1	0	0	0	11251	1319	46	3	341	3	OR8J3	11	55904587	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	31367	55904587	79101929	378	9704										
OR8K1	390157	hgsc.bcm.edu	37	chr11	56113774	56113774	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cactgtcattgccccgaagaTgttagtaaacttcatagtgc	8	10	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:56113774T>A	ENST00000279783.2	+	1	354	c.260T>A	c.(259-261)aTg>aAg	p.M87K		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	87						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					GCCCCGAAGATGTTAGTAAAC	0.393										HNSCC(65;0.19)																											p.M87K		Atlas-SNP	.											.	OR8K1	93	.	0			c.T260A						.						171	164	167					11																	56113774		2201	4296	6497	SO:0001583	missense	390157	exon1			CGAAGATGTTAGT	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.260T>A	chr11.hg19:g.56113774T>A	ENSP00000279783:p.Met87Lys	145.0	0.0		149.0	53.0	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	hg19	CCDS31528.1	.	.	.	.	.	.	.	.	.	.	T	9.680	1.148943	0.21288	.	.	ENSG00000150261	ENST00000279783	T	0.06068	3.35	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.093959	0.46758	D	0.000278	T	0.14485	0.0350	M	0.90595	3.13	0.09310	N	0.999999	P	0.50710	0.938	B	0.41764	0.366	T	0.35276	-0.9795	10	0.87932	D	0	-19.0734	10.8159	0.46575	0.0:0.0773:0.0:0.9227	.	87	Q8NGG5	OR8K1_HUMAN	K	87	ENSP00000279783:M87K	ENSP00000279783:M87K	M	+	2	0	OR8K1	55870350	0.127000	0.22367	0.428000	0.26697	0.046000	0.14306	2.552000	0.45828	1.862000	0.54008	0.448000	0.29417	ATG	.	.		0.393	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		A	56113774	T	A	56113774	3	1	73	1	0	0	0	0	1	0	0	0	11252	1464	51	4	262	4	OR8K1	11	56113774	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	209187	56113774	78892742	379	9705										
RAB3IL1	5866	hgsc.bcm.edu	37	chr11	61675695	61675695	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggctcctggggactccctgTggccttggcaggggtccgtg	18	12	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:61675695T>C	ENST00000394836.2	-	2	252	c.95A>G	c.(94-96)cAc>cGc	p.H32R	RAB3IL1_ENST00000301773.5_Missense_Mutation_p.H79R	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	32					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						GGACTCCCTGTGGCCTTGGCA	0.721																																					p.H79R		Atlas-SNP	.											.	RAB3IL1	39	.	0			c.A236G						.						6	7	7					11																	61675695		2159	4244	6403	SO:0001583	missense	5866	exon2			TCCCTGTGGCCTT	AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.95A>G	chr11.hg19:g.61675695T>C	ENSP00000378313:p.His32Arg	47.0	0.0		19.0	14.0	NM_001271686	Q86V32|Q9P1Q8	Missense_Mutation	SNP	ENST00000394836.2	hg19	CCDS8014.1	.	.	.	.	.	.	.	.	.	.	T	4.930	0.172721	0.09391	.	.	ENSG00000167994	ENST00000394836;ENST00000301773;ENST00000531922	T;T;T	0.42900	1.58;1.52;0.96	4.87	-6.26	0.02033	.	1.632430	0.02955	N	0.142221	T	0.23532	0.0569	N	0.14661	0.345	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.10450	0.005;0.0	T	0.15607	-1.0431	10	0.19590	T	0.45	-15.0784	9.0866	0.36586	0.1117:0.1832:0.0:0.7051	.	79;32	Q8TBN0-2;Q8TBN0	.;R3GEF_HUMAN	R	32;79;79	ENSP00000378313:H32R;ENSP00000301773:H79R;ENSP00000435444:H79R	ENSP00000301773:H79R	H	-	2	0	RAB3IL1	61432271	0.000000	0.05858	0.008000	0.14137	0.629000	0.37895	-1.854000	0.01664	-1.506000	0.01805	-0.441000	0.05720	CAC	.	.		0.721	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401		C	61675695	T	C	61675695	3	2	73	1	0	0	0	0	1	0	0	0	12952	1696	59	2	1089	2	RAB3IL1	11	61675695	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	5561921	61675695	73330821	380	9706										
SLC22A24	283238	hgsc.bcm.edu	37	chr11	62886696	62886696	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atagtcatggtggagaacccTgccaagaagcgcagtatgca	12	9	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:62886696T>A	ENST00000417740.1	-	3	1059	c.618A>T	c.(616-618)gcA>gcT	p.A206A	SLC22A24_ENST00000326192.5_Silent_p.A206A	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	206					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						TGGAGAACCCTGCCAAGAAGC	0.423																																					p.A206A		Atlas-SNP	.											.	SLC22A24	31	.	0			c.A618T						.						131	115	120					11																	62886696		692	1591	2283	SO:0001819	synonymous_variant	283238	exon3			GAACCCTGCCAAG		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"Solute carriers"	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.618A>T	chr11.hg19:g.62886696T>A		205.0	0.0		213.0	76.0	NM_001136506		Silent	SNP	ENST00000417740.1	hg19																																																																																				.	.		0.423	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586		A	62886696	T	A	62886696	2	1	73	1	0	0	0	0	0	0	0	1	14468	1567	55	4		4	SLC22A24	11	62886696	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1211001	62886696	72119820	381	9707										
PYGM	5837	hgsc.bcm.edu	37	chr11	64527129	64527129	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccaggctccccagcagcaccTtggggtccttctcatagtag	10	15	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:64527129T>C	ENST00000164139.3	-	1	640	c.242A>G	c.(241-243)aAg>aGg	p.K81R	PYGM_ENST00000377432.3_Splice_Site_p.K81R	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	81					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CAGCAGCACCTTGGGGTCCTT	0.627																																					p.K81R		Atlas-SNP	.											.	PYGM	77	.	0			c.A242G						.						81	92	88					11																	64527129		2201	4297	6498	SO:0001630	splice_region_variant	5837	exon1			AGCACCTTGGGGT		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.243+1A>G	chr11.hg19:g.64527129T>C		51.0	0.0		26.0	20.0	NM_001164716	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	hg19	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.264669	0.80358	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.92752	-3.1;-2.15	5.42	5.42	0.78866	.	0.071781	0.56097	D	0.000040	D	0.92364	0.7577	M	0.77820	2.39	0.80722	D	1	B;B	0.30179	0.079;0.271	B;B	0.37091	0.232;0.241	D	0.90777	0.4676	10	0.37606	T	0.19	-38.0183	13.41	0.60938	0.0:0.0:0.0:1.0	.	81;81	A6NDY6;P11217	.;PYGM_HUMAN	R	81	ENSP00000366650:K81R;ENSP00000164139:K81R	ENSP00000164139:K81R	K	-	2	0	PYGM	64283705	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.781000	0.85668	2.069000	0.61940	0.533000	0.62120	AAG	.	.		0.627	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609	Missense_Mutation	C	64527129	T	C	64527129	5	2	73	1	0	0	0	0	0	0	1	0	12877	1623	56	2	2366	2	PYGM	11	64527129	Splice_Site	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1640433	64527129	70479387	382	9708										
MEN1	4221	hgsc.bcm.edu	37	chr11	64573793	64573793	+	Frame_Shift_Del	DEL	G	G	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tagccagccaggtacatgtaGgggtagatgtgttcatcccg							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:64573793delG	ENST00000337652.1	-	7	1478	c.975delC	c.(973-975)cccfs	p.P325fs	MEN1_ENST00000315422.4_Frame_Shift_Del_p.P320fs|MEN1_ENST00000377313.1_Frame_Shift_Del_p.P325fs|MEN1_ENST00000394376.1_Frame_Shift_Del_p.P325fs|MEN1_ENST00000478548.1_5'UTR|MEN1_ENST00000377321.1_Frame_Shift_Del_p.P285fs|MEN1_ENST00000377316.2_Frame_Shift_Del_p.P320fs|MEN1_ENST00000394374.2_Frame_Shift_Del_p.P325fs|MEN1_ENST00000312049.6_Frame_Shift_Del_p.P320fs|MEN1_ENST00000377326.3_Frame_Shift_Del_p.P320fs|MEN1_ENST00000443283.1_Frame_Shift_Del_p.P325fs	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	325	Interaction with FANCD2.		P -> L (in MEN1). {ECO:0000269|PubMed:9506756}.|P -> R (in MEN1). {ECO:0000269|PubMed:15714081}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.Y321fs*47(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						GGTACATGTAGGGGTAGATGT	0.622			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated		OREG0004014	type=REGULATORY REGION|Gene=MEN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.Y326fs	Esophageal Squamous(1;83 158 15500 18603 18803 29295)	Pindel	.	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	.	MEN1	442	.	1	Deletion - Frameshift(1)	pancreas(1)	c.976delT						.						264	230	241					11																	64573793		2201	4297	6498	SO:0001589	frameshift_variant	4221	exon7	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	.	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.975delC	chr11.hg19:g.64573793delG	ENSP00000337088:p.Pro325fs	201.0	0.0	1077	94.0	45.0	NM_130800	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Frame_Shift_Del	DEL	ENST00000337652.1	hg19	CCDS8083.1																																																																																			.	.		0.622	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			-	64573793	G	-	64573793	7	5	73	1	0	1	0	1	0	0	0	0	9481	987	35	0	888	0	MEN1	11	64573793	Frame_Shift_Del	DEL	G	TCGA-CC-A7IH-01A-11D-A33K-10	46664	64573793	70432723	383	9709										
MEN1	4221	hgsc.bcm.edu	37	chr11	64575092	64575092	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agggttgatggcacacaccaTgaacgccacctccatcttgc	9	14	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:64575092T>C	ENST00000337652.1	-	4	1233	c.730A>G	c.(730-732)Atg>Gtg	p.M244V	MEN1_ENST00000315422.4_Missense_Mutation_p.M239V|MEN1_ENST00000377313.1_Missense_Mutation_p.M244V|MEN1_ENST00000394376.1_Missense_Mutation_p.M244V|MEN1_ENST00000478548.1_5'Flank|MEN1_ENST00000377321.1_Missense_Mutation_p.M204V|MEN1_ENST00000377316.2_Missense_Mutation_p.M239V|MEN1_ENST00000394374.2_Missense_Mutation_p.M244V|MEN1_ENST00000312049.6_Missense_Mutation_p.M239V|MEN1_ENST00000377326.3_Missense_Mutation_p.M239V|MEN1_ENST00000443283.1_Missense_Mutation_p.M244V	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	244	Interaction with FANCD2.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						GCACACACCATGAACGCCACC	0.572			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												p.M244V	Esophageal Squamous(1;83 158 15500 18603 18803 29295)	Atlas-SNP	.	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	.	MEN1	442	.	0			c.A730G						.						134	115	122					11																	64575092		2201	4297	6498	SO:0001583	missense	4221	exon4	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	ACACCATGAACGC	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.730A>G	chr11.hg19:g.64575092T>C	ENSP00000337088:p.Met244Val	99.0	0.0		42.0	31.0	NM_130800	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	hg19	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	T	17.00	3.277464	0.59758	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873;ENST00000450708;ENST00000413626	D;D;D;D;D;D;D;D;D;D;D;D;D	0.99292	-5.7;-5.7;-5.7;-5.7;-5.7;-5.7;-5.7;-5.7;-5.7;-5.7;-5.7;-5.7;-5.7	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	D	0.98817	0.9601	L	0.47716	1.5	0.58432	D	0.999999	B;P;B	0.43578	0.291;0.811;0.339	B;P;B	0.57846	0.064;0.828;0.105	D	0.99353	1.0915	10	0.66056	D	0.02	-40.1896	12.62	0.56597	0.0:0.0:0.0:1.0	.	239;204;244	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	V	239;204;239;239;239;244;244;244;244;244;239;239;239	ENSP00000366533:M239V;ENSP00000366538:M204V;ENSP00000366543:M239V;ENSP00000308975:M239V;ENSP00000323747:M239V;ENSP00000337088:M244V;ENSP00000377901:M244V;ENSP00000377899:M244V;ENSP00000396940:M244V;ENSP00000366530:M244V;ENSP00000413944:M239V;ENSP00000394933:M239V;ENSP00000411218:M239V	ENSP00000308975:M239V	M	-	1	0	MEN1	64331668	1.000000	0.71417	0.969000	0.41365	0.941000	0.58515	6.984000	0.76186	1.934000	0.56057	0.379000	0.24179	ATG	.	.		0.572	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			C	64575092	T	C	64575092	3	2	73	1	0	0	0	0	1	0	0	0	9481	1464	51	2	1145	2	MEN1	11	64575092	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1299	64575092	70431424	384	9710										
KLC2	64837	hgsc.bcm.edu	37	chr11	66029592	66029592	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctcatcctgtcttccttcccAggaggagaagggggacgtcc	12	13	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:66029592A>T	ENST00000417856.1	+	4	702		c.e4-1		KLC2_ENST00000421552.1_Splice_Site|KLC2_ENST00000394067.2_Splice_Site|KLC2_ENST00000394066.2_Splice_Site|KLC2_ENST00000394078.1_Splice_Site|KLC2_ENST00000394065.2_Splice_Site|KLC2_ENST00000316924.5_Splice_Site|RP11-867G23.1_ENST00000530805.1_RNA|RP11-755F10.3_ENST00000533576.1_RNA	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon cargo transport (GO:0008088)|blood coagulation (GO:0007596)|microtubule-based movement (GO:0007018)	ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinesin I complex (GO:0016938)|membrane (GO:0016020)|microtubule (GO:0005874)|neuron projection (GO:0043005)|protein complex (GO:0043234)	kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						CTTCCTTCCCAGGAGGAGAAG	0.627																																					.		Atlas-SNP	.											.	KLC2	50	.	0			c.460-2A>T						.						84	69	74					11																	66029592		2200	4295	6495	SO:0001630	splice_region_variant	64837	exon4			CTTCCCAGGAGGA	AK022449	CCDS8130.1, CCDS44653.1	11q13.1	2013-01-10			ENSG00000174996	ENSG00000174996		"Tetratricopeptide (TTC) repeat domain containing"	20716	protein-coding gene	gene with protein product		611729				9624122	Standard	NM_022822		Approved	FLJ12387	uc001ohb.2	Q9H0B6	OTTHUMG00000133757	ENST00000417856.1:c.460-1A>T	chr11.hg19:g.66029592A>T		115.0	0.0		109.0	45.0	NM_001134775	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Splice_Site	SNP	ENST00000417856.1	hg19	CCDS8130.1	.	.	.	.	.	.	.	.	.	.	A	15.40	2.823039	0.50739	.	.	ENSG00000174996	ENST00000417856;ENST00000440228;ENST00000394067;ENST00000316924;ENST00000421552;ENST00000394078;ENST00000461611;ENST00000475757;ENST00000394066;ENST00000394065	.	.	.	4.04	4.04	0.47022	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.1024	0.53792	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KLC2	65786168	1.000000	0.71417	0.960000	0.40013	0.609000	0.37215	6.812000	0.75226	1.691000	0.51100	0.459000	0.35465	.	.	.		0.627	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822	Intron	T	66029592	A	T	66029592	5	4	73	1	0	0	0	0	0	0	1	0	8343	202	7	4	468	4	KLC2	11	66029592	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1454500	66029592	68976924	385	9711										
ADRBK1	156	hgsc.bcm.edu	37	chr11	67047308	67047308	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aacttccagcttcctcccttAgccatacatcgaagagattt	5	13	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:67047308A>T	ENST00000308595.5	+	6	731		c.e6-1		ADRBK1_ENST00000526285.1_Splice_Site	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1						activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	TTCCTCCCTTAGCCATACATC	0.582																																					.		Atlas-SNP	.											.	ADRBK1	51	.	0			c.442-2A>T						.						85	87	86					11																	67047308		2200	4295	6495	SO:0001630	splice_region_variant	156	exon6			TCCCTTAGCCATA	X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"Pleckstrin homology (PH) domain containing"	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.442-1A>T	chr11.hg19:g.67047308A>T		94.0	0.0		176.0	80.0	NM_001619	B0ZBE1|Q13837|Q6GTT3	Splice_Site	SNP	ENST00000308595.5	hg19	CCDS8156.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.947167	0.73672	.	.	ENSG00000173020	ENST00000308595;ENST00000526285	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2535	0.73568	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADRBK1	66803884	0.998000	0.40836	0.968000	0.41197	0.842000	0.47809	4.034000	0.57289	2.073000	0.62155	0.482000	0.46254	.	.	.		0.582	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619	Intron	T	67047308	A	T	67047308	5	4	73	1	0	0	0	0	0	0	1	0	343	434	15	4	462	4	ADRBK1	11	67047308	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1017716	67047308	67959208	386	9712										
P2RY6	5031	hgsc.bcm.edu	37	chr11	73007940	73007940	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	catcagcttccagcgctaccTgggcatctgccacccgctgg	10	17	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:73007940T>A	ENST00000393590.2	+	2	676	c.377T>A	c.(376-378)cTg>cAg	p.L126Q	P2RY6_ENST00000349767.2_Missense_Mutation_p.L126Q|P2RY6_ENST00000542092.1_Missense_Mutation_p.L126Q|P2RY6_ENST00000540124.1_Missense_Mutation_p.L126Q|P2RY6_ENST00000393592.2_Missense_Mutation_p.L126Q|P2RY6_ENST00000540342.1_Missense_Mutation_p.L126Q|P2RY6_ENST00000393591.1_Missense_Mutation_p.L126Q|P2RY6_ENST00000538328.1_Missense_Mutation_p.L126Q	NM_001277207.1|NM_001277208.1	NP_001264136.1|NP_001264137.1	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 6	126					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)	14						CAGCGCTACCTGGGCATCTGC	0.662																																					p.L126Q		Atlas-SNP	.											.	P2RY6	45	.	0			c.T377A						.						68	67	68					11																	73007940		2200	4293	6493	SO:0001583	missense	5031	exon4			GCTACCTGGGCAT		CCDS8220.1	11q13.5	2012-08-08				ENSG00000171631		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8543	protein-coding gene	gene with protein product		602451				8670200	Standard	NM_176797		Approved	P2Y6	uc001otr.4	Q15077		ENST00000393590.2:c.377T>A	chr11.hg19:g.73007940T>A	ENSP00000377215:p.Leu126Gln	25.0	0.0		38.0	8.0	NM_176796	Q15754	Missense_Mutation	SNP	ENST00000393590.2	hg19	CCDS8220.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.325702	0.81580	.	.	ENSG00000171631	ENST00000540342;ENST00000542092;ENST00000349767;ENST00000393592;ENST00000544437;ENST00000393591;ENST00000540124;ENST00000393590;ENST00000535931;ENST00000538328	T;T;T;T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85	4.18	4.18	0.49190	GPCR, rhodopsin-like superfamily (1);	0.185989	0.42682	D	0.000675	T	0.66107	0.2756	M	0.79258	2.445	0.41722	D	0.989516	D	0.64830	0.994	D	0.64410	0.925	T	0.72214	-0.4358	10	0.87932	D	0	.	12.8465	0.57833	0.0:0.0:0.0:1.0	.	126	Q15077	P2RY6_HUMAN	Q	126	ENSP00000443427:L126Q;ENSP00000445652:L126Q;ENSP00000309771:L126Q;ENSP00000377217:L126Q;ENSP00000441079:L126Q;ENSP00000377216:L126Q;ENSP00000442551:L126Q;ENSP00000377215:L126Q;ENSP00000440770:L126Q;ENSP00000442990:L126Q	ENSP00000309771:L126Q	L	+	2	0	P2RY6	72685588	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.984000	0.70548	1.865000	0.54081	0.402000	0.26972	CTG	.	.		0.662	P2RY6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397349.1			A	73007940	T	A	73007940	3	1	73	1	0	0	0	0	1	0	0	0	11363	1580	55	4	379	4	P2RY6	11	73007940	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	5960632	73007940	61998576	387	9713										
PRKRIR	5612	hgsc.bcm.edu	37	chr11	76063253	76063253	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttaatccccacttctcagttAtcatagtgtgaaatttcaca	4	10	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:76063253A>T	ENST00000260045.3	-	5	1046	c.941T>A	c.(940-942)aTa>aAa	p.I314K	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	314					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						CTTCTCAGTTATCATAGTGTG	0.383																																					p.I314K		Atlas-SNP	.											.	PRKRIR	65	.	0			c.T941A						.						47	49	48					11																	76063253		2187	4275	6462	SO:0001583	missense	5612	exon5			TCAGTTATCATAG	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"THAP (C2CH-type zinc finger) domain containing"	9440	protein-coding gene	gene with protein product	"THAP domain containing 12"	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.941T>A	chr11.hg19:g.76063253A>T	ENSP00000260045:p.Ile314Lys	401.0	1.0		387.0	135.0	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	ENST00000260045.3	hg19	CCDS8243.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.094067	0.56075	.	.	ENSG00000137492	ENST00000529901;ENST00000260045	T;T	0.26518	1.73;1.73	4.99	4.99	0.66335	Ribonuclease H-like (1);	0.144523	0.64402	D	0.000006	T	0.24044	0.0582	L	0.43152	1.355	0.80722	D	1	B	0.31153	0.31	B	0.29942	0.109	T	0.03354	-1.1045	10	0.36615	T	0.2	.	15.1171	0.72410	1.0:0.0:0.0:0.0	.	314	O43422	P52K_HUMAN	K	139;314	ENSP00000436249:I139K;ENSP00000260045:I314K	ENSP00000260045:I314K	I	-	2	0	PRKRIR	75740901	1.000000	0.71417	0.983000	0.44433	0.923000	0.55619	8.521000	0.90569	2.043000	0.60533	0.524000	0.50904	ATA	.	.		0.383	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705		T	76063253	A	T	76063253	3	4	73	1	0	0	0	0	1	0	0	0	12538	449	16	4	1348	4	PRKRIR	11	76063253	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3055313	76063253	58943263	388	9714										
THRSP	7069	hgsc.bcm.edu	37	chr11	77775013	77775013	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgaggtgcacaacatggagcAggtggtgatgatccccagcc	14	11	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:77775013A>G	ENST00000281030.2	+	1	107	c.86A>G	c.(85-87)cAg>cGg	p.Q29R	NDUFC2-KCTD14_ENST00000528251.1_Intron|NDUFC2-KCTD14_ENST00000530054.1_Intron	NM_003251.3	NP_003242.1	Q92748	THRSP_HUMAN	thyroid hormone responsive	29					lipid metabolic process (GO:0006629)|regulation of lipid biosynthetic process (GO:0046890)|regulation of transcription, DNA-templated (GO:0006355)|regulation of triglyceride biosynthetic process (GO:0010866)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7	all_cancers(14;2.23e-19)|all_epithelial(13;7.49e-22)|Breast(9;6.38e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;2.15e-25)			AACATGGAGCAGGTGGTGATG	0.607																																					p.Q29R		Atlas-SNP	.											.	THRSP	18	.	0			c.A86G						.						98	85	90					11																	77775013		2200	4292	6492	SO:0001583	missense	7069	exon1			TGGAGCAGGTGGT	Y08409	CCDS8256.1	11q14.1	2012-06-19	2010-06-25		ENSG00000151365	ENSG00000151365			11800	protein-coding gene	gene with protein product	"SPOT14 homolog (rat)"	601926	"thyroid hormone responsive SPOT14 (rat) homolog", "lipogenic protein 1"	LPGP1		9003802	Standard	NM_003251		Approved	SPOT14, Lpgp, S14, THRP	uc001oyx.3	Q92748	OTTHUMG00000166632	ENST00000281030.2:c.86A>G	chr11.hg19:g.77775013A>G	ENSP00000281030:p.Gln29Arg	63.0	0.0		70.0	32.0	NM_003251	B2R4W7	Missense_Mutation	SNP	ENST00000281030.2	hg19	CCDS8256.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.214524	0.79352	.	.	ENSG00000151365	ENST00000281030	.	.	.	5.21	5.21	0.72293	.	0.591520	0.16932	N	0.193637	T	0.79275	0.4418	.	.	.	0.40981	D	0.984774	D	0.89917	1.0	D	0.77557	0.99	T	0.81831	-0.0752	8	0.87932	D	0	-15.4818	14.1992	0.65690	1.0:0.0:0.0:0.0	.	29	Q92748	THRSP_HUMAN	R	29	.	ENSP00000281030:Q29R	Q	+	2	0	THRSP	77452661	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.945000	0.63568	2.199000	0.70637	0.459000	0.35465	CAG	.	.		0.607	THRSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390939.1	NM_003251		G	77775013	A	G	77775013	3	3	73	1	0	0	0	0	1	0	0	0	15891	188	7	2	88	2	THRSP	11	77775013	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1711760	77775013	57231503	389	9715										
CCDC83	220047	hgsc.bcm.edu	37	chr11	85622367	85622411	+	In_Frame_Del	DEL	TTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTAT	TTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTAT	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgaagaattaaaaaatgctaTtcatgaactggaagcagaaa					rs143833799|rs141851299|rs537726488		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	TTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTAT	TTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:85622367_85622411delTTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTAT	ENST00000342404.3	+	8	932_976	c.716_760delTTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTAT	c.(715-762)attcatgaactggaagcagaaaatttggtgcttattgatcaactatcc>acc	p.239_254IHELEAENLVLIDQLS>T	CCDC83_ENST00000280245.4_In_Frame_Del_p.239_254IHELEAENLVLIDQLS>T|CCDC83_ENST00000529676.2_3'UTR|CCDC83_ENST00000376067.1_In_Frame_Del_p.140_155IHELEAENLVLIDQLS>T			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	239										breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				AAAAATGCTATTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTATCCAACTGTAG	0.318																																					p.239_253del		Atlas-Indel,Pindel	.											.	CCDC83	48	.	0			c.715_759del						.																																			SO:0001651	inframe_deletion	220047	exon8			.	AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.716_760delTTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTAT	chr11.hg19:g.85622367_85622411delTTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTAT	ENSP00000344512:p.Ile239_Ser254delinsThr	228.0	0.0		139.0	15.0	NM_173556	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	In_Frame_Del	DEL	ENST00000342404.3	hg19																																																																																				.	.		0.318	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556		-	85622411	TTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTAT	-	85622367	7	5	73	1	0	1	0	1	0	0	0	0	2859	1493	52	0	742	0	CCDC83	11	85622367	In_Frame_Del	DEL	TTCATGAACTGGAAGCAGAAAATTTGGTGCTTATTGATCAACTAT	TCGA-CC-A7IH-01A-11D-A33K-10	7847354	85622367	49384149	390	9716										
GRM5	2915	hgsc.bcm.edu	37	chr11	88338049	88338049	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggacatctgcatgttgtggaGcccataggccatcgaataga	12	9	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:88338049G>T	ENST00000305447.4	-	4	1380	c.1231C>A	c.(1231-1233)Ctc>Atc	p.L411I	GRM5_ENST00000455756.2_Missense_Mutation_p.L411I|GRM5_ENST00000305432.5_Missense_Mutation_p.L411I|GRM5_ENST00000418177.2_Missense_Mutation_p.L411I|GRM5_ENST00000393297.1_Missense_Mutation_p.L411I	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	411					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	ATGTTGTGGAGCCCATAGGCC	0.463																																					p.L411I		Atlas-SNP	.											.	GRM5	414	.	0			c.C1231A						.						97	84	88					11																	88338049		2201	4299	6500	SO:0001583	missense	2915	exon5			TGTGGAGCCCATA	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1231C>A	chr11.hg19:g.88338049G>T	ENSP00000306138:p.Leu411Ile	140.0	0.0		117.0	52.0	NM_000842	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	hg19	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.303319	0.81136	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.88509	-2.39;-2.39;-2.39;-2.39;-2.39	5.89	4.98	0.66077	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.94006	0.8080	M	0.78285	2.405	0.58432	D	0.99999	D;D	0.69078	0.996;0.997	D;D	0.87578	0.998;0.997	D	0.94006	0.7280	9	.	.	.	.	14.7898	0.69830	0.0689:0.0:0.9311:0.0	.	411;411	P41594-2;P41594	.;GRM5_HUMAN	I	411	ENSP00000402912:L411I;ENSP00000405690:L411I;ENSP00000305905:L411I;ENSP00000306138:L411I;ENSP00000376975:L411I	.	L	-	1	0	GRM5	87977697	1.000000	0.71417	0.631000	0.29282	0.990000	0.78478	4.875000	0.63072	1.497000	0.48584	0.544000	0.68410	CTC	.	.		0.463	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		T	88338049	G	T	88338049	3	4	73	1	0	0	0	0	1	0	0	0	6809	971	34	3	2431	3	GRM5	11	88338049	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	2715682	88338049	46668467	391	9717										
TYR	7299	hgsc.bcm.edu	37	chr11	88911129	88911129	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gactagaggaagaatgctccTggctgttttgtactgcctgc	12	9	0	2	rs375229194		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:88911129T>A	ENST00000263321.5	+	1	510	c.8T>A	c.(7-9)cTg>cAg	p.L3Q	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	3					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	AGAATGCTCCTGGCTGTTTTG	0.488																																					p.L3Q		Atlas-SNP	.											.	TYR	130	.	0			c.T8A						.						92	91	92					11																	88911129		2201	4299	6500	SO:0001583	missense	7299	exon1			TGCTCCTGGCTGT	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"oculocutaneous albinism IA"	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.8T>A	chr11.hg19:g.88911129T>A	ENSP00000263321:p.Leu3Gln	103.0	0.0		57.0	28.0	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	hg19	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	T	13.65	2.299275	0.40694	.	.	ENSG00000077498	ENST00000263321	D	0.99329	-5.75	6.07	3.78	0.43462	.	0.222277	0.39274	N	0.001404	D	0.98582	0.9526	L	0.60455	1.87	0.09310	N	1	P	0.52170	0.951	P	0.54706	0.759	D	0.95751	0.8792	9	.	.	.	.	8.2322	0.31605	0.0:0.2143:0.0:0.7857	.	3	P14679	TYRO_HUMAN	Q	3	ENSP00000263321:L3Q	.	L	+	2	0	TYR	88550777	0.922000	0.31269	0.013000	0.15412	0.645000	0.38454	1.761000	0.38440	0.541000	0.28827	0.533000	0.62120	CTG	.	.		0.488	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		A	88911129	T	A	88911129	3	1	73	1	0	0	0	0	1	0	0	0	16828	1580	55	4	10	4	TYR	11	88911129	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	573080	88911129	46095387	392	9718										
FAT3	120114	hgsc.bcm.edu	37	chr11	92498202	92498202	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgatagagtgactgaaattgTaggggtggtgtctgtgcagc	16	4	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:92498202T>C	ENST00000298047.6	+	5	4159	c.4142T>C	c.(4141-4143)gTa>gCa	p.V1381A	RP11-203F8.1_ENST00000529884.1_RNA|FAT3_ENST00000409404.2_Missense_Mutation_p.V1381A|FAT3_ENST00000525166.1_Missense_Mutation_p.V1231A			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1381	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ACTGAAATTGTAGGGGTGGTG	0.433										TCGA Ovarian(4;0.039)																											p.V1381A		Atlas-SNP	.											.	FAT3	1822	.	0			c.T4142C						.						105	106	106					11																	92498202		1922	4111	6033	SO:0001583	missense	120114	exon5			AAATTGTAGGGGT	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.4142T>C	chr11.hg19:g.92498202T>C	ENSP00000298047:p.Val1381Ala	143.0	0.0		115.0	46.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	T	22.0	4.223651	0.79576	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.65916	-0.18;-0.18;-0.18	5.97	5.97	0.96955	.	.	.	.	.	T	0.76601	0.4010	M	0.89785	3.06	0.80722	D	1	P	0.46859	0.885	P	0.48524	0.58	T	0.82301	-0.0525	9	0.87932	D	0	.	16.4608	0.84044	0.0:0.0:0.0:1.0	.	1381	Q8TDW7-3	.	A	1381;1381;1231	ENSP00000298047:V1381A;ENSP00000387040:V1381A;ENSP00000432586:V1231A	ENSP00000298047:V1381A	V	+	2	0	FAT3	92137850	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	7.633000	0.83260	2.288000	0.76882	0.533000	0.62120	GTA	.	.		0.433	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		C	92498202	T	C	92498202	3	2	73	1	0	0	0	0	1	0	0	0	5699	1638	57	2	4160	2	FAT3	11	92498202	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3587073	92498202	42508314	393	9719										
TRPC6	7225	hgsc.bcm.edu	37	chr11	101375282	101375282	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagatgctcattggccactgCcaactgtagggcattctggc	11	12	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:101375282C>A	ENST00000344327.3	-	2	842	c.418G>T	c.(418-420)Gca>Tca	p.A140S	TRPC6_ENST00000532133.1_Missense_Mutation_p.A140S|TRPC6_ENST00000348423.4_Missense_Mutation_p.A140S|TRPC6_ENST00000526713.1_5'Flank|TRPC6_ENST00000360497.4_Missense_Mutation_p.A140S	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	140					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		TTGGCCACTGCCAACTGTAGG	0.438																																					p.A140S	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											.	TRPC6	132	.	0			c.G418T						.						103	89	94					11																	101375282		2203	4299	6502	SO:0001583	missense	7225	exon2			CCACTGCCAACTG	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.418G>T	chr11.hg19:g.101375282C>A	ENSP00000340913:p.Ala140Ser	120.0	0.0		97.0	40.0	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	hg19	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087510	0.94100	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	5.96	5.96	0.96718	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.91287	0.7253	M	0.85630	2.765	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.90630	0.4566	10	0.51188	T	0.08	-16.3923	20.422	0.99049	0.0:1.0:0.0:0.0	.	140;140;140	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	S	140	ENSP00000340913:A140S;ENSP00000435574:A140S;ENSP00000343672:A140S;ENSP00000353687:A140S	ENSP00000340913:A140S	A	-	1	0	TRPC6	100880492	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.818000	0.86416	2.832000	0.97577	0.655000	0.94253	GCA	.	.		0.438	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		A	101375282	C	A	101375282	3	1	73	1	0	0	0	0	1	0	0	0	16598	739	26	3	2425	3	TRPC6	11	101375282	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	8877080	101375282	33631234	394	9720										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103026215	103026215	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctgatacaattgtagccaaAgctgccgaccttaaagtatg	9	9	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:103026215A>T	ENST00000375735.2	+	25	3873	c.3729A>T	c.(3727-3729)aaA>aaT	p.K1243N	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.K1243N|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1243	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TTGTAGCCAAAGCTGCCGACC	0.358																																					p.K1243N		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A3729T						.						57	56	56					11																	103026215		1815	4075	5890	SO:0001583	missense	79659	exon25			AGCCAAAGCTGCC	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.3729A>T	chr11.hg19:g.103026215A>T	ENSP00000364887:p.Lys1243Asn	139.0	0.0		125.0	49.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	A	10.43	1.348687	0.24426	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.60672	0.17;0.17	5.48	5.48	0.80851	Dynein heavy chain, domain-2 (1);	0.182320	0.26275	U	0.025310	T	0.36386	0.0965	N	0.11000	0.08	0.40058	D	0.975862	B;B	0.16802	0.004;0.019	B;B	0.24155	0.04;0.051	T	0.27640	-1.0068	10	0.19147	T	0.46	.	10.0007	0.41927	0.9246:0.0:0.0754:0.0	.	1243;1243	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	N	1243	ENSP00000364887:K1243N;ENSP00000381167:K1243N	ENSP00000364887:K1243N	K	+	3	2	DYNC2H1	102531425	1.000000	0.71417	1.000000	0.80357	0.425000	0.31504	1.484000	0.35508	2.084000	0.62774	0.528000	0.53228	AAA	.	.		0.358	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103026215	A	T	103026215	3	4	73	1	0	0	0	0	1	0	0	0	4848	69	3	4	3827	4	DYNC2H1	11	103026215	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1650933	103026215	31980301	395	9721										
ELMOD1	55531	hgsc.bcm.edu	37	chr11	107526788	107526788	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttgtctcactttcagcaaacAttctgtaagtatcctgttgt	6	9	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:107526788A>G	ENST00000265840.7	+	11	1093	c.828A>G	c.(826-828)acA>acG	p.T276T	ELMOD1_ENST00000531234.1_Silent_p.T270T|ELMOD1_ENST00000443271.2_Silent_p.T268T	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	276	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)	cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)			endometrium(2)|large_intestine(5)|liver(2)|lung(7)|pancreas(2)|prostate(1)	19		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		TTCAGCAAACATTCTGTAAGT	0.458																																					p.T276T		Atlas-SNP	.											.	ELMOD1	40	.	0			c.A828G						.						75	68	70					11																	107526788		1849	4051	5900	SO:0001819	synonymous_variant	55531	exon11			GCAAACATTCTGT	AL359601	CCDS44723.1, CCDS44724.1	11q23.1	2012-10-15	2006-01-20		ENSG00000110675	ENSG00000110675			25334	protein-coding gene	gene with protein product		615456	"ELMO domain containing 1"			12477932	Standard	NM_018712		Approved	DKFZp547C176	uc010rvs.2	Q8N336	OTTHUMG00000166361	ENST00000265840.7:c.828A>G	chr11.hg19:g.107526788A>G		84.0	0.0		59.0	30.0	NM_018712	B4E167|G5E9S5|Q9NPW3	Silent	SNP	ENST00000265840.7	hg19	CCDS44723.1																																																																																			.	.		0.458	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389406.1	NM_018712		G	107526788	A	G	107526788	2	3	73	1	0	0	0	0	0	0	0	1	5070	204	8	2		2	ELMOD1	11	107526788	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4500573	107526788	27479728	396	9722										
DDX10	1662	hgsc.bcm.edu	37	chr11	108709284	108709284	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agaagataacatttactgatGaaggggaggtaagattctag	12	3	1	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:108709284G>A	ENST00000322536.3	+	14	2206	c.2077G>A	c.(2077-2079)Gaa>Aaa	p.E693K	DDX10_ENST00000526794.1_Missense_Mutation_p.E693K	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	693					metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		ATTTACTGATGAAGGGGAGGT	0.328			T	NUP98	AML*																																p.E693K		Atlas-SNP	.		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	.	DDX10	70	.	0			c.G2077A						.						105	118	113					11																	108709284		2201	4297	6498	SO:0001583	missense	1662	exon14			ACTGATGAAGGGG	U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"DEAD-boxes"	2735	protein-coding gene	gene with protein product		601235	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.2077G>A	chr11.hg19:g.108709284G>A	ENSP00000314348:p.Glu693Lys	236.0	0.0		186.0	62.0	NM_004398	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	hg19	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.661182	0.67700	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.55234	0.54;0.53	5.87	5.87	0.94306	.	0.202030	0.42172	D	0.000743	T	0.52306	0.1726	M	0.64404	1.975	0.48901	D	0.999728	P;P	0.34562	0.457;0.457	B;B	0.31390	0.129;0.129	T	0.56607	-0.7951	10	0.72032	D	0.01	-12.6355	16.9184	0.86157	0.0:0.0:1.0:0.0	.	693;693	Q13206;E9PIF2	DDX10_HUMAN;.	K	693;599;693	ENSP00000314348:E693K;ENSP00000432032:E693K	ENSP00000314348:E693K	E	+	1	0	DDX10	108214494	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	6.104000	0.71498	2.775000	0.95449	0.650000	0.86243	GAA	.	.		0.328	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398		A	108709284	G	A	108709284	3	1	73	1	0	0	0	0	1	0	0	0	4344	1291	45	3	2131	3	DDX10	11	108709284	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1182496	108709284	26297232	397	9723										
RNF214	257160	hgsc.bcm.edu	37	chr11	117109396	117109396	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caataaccaaggagaataacAgaaatgtccatttggagcac	8	8	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:117109396A>T	ENST00000531452.1	+	3	233	c.187A>T	c.(187-189)Aga>Tga	p.R63*	RNF214_ENST00000530849.1_Intron|RNF214_ENST00000531287.1_Intron|RNF214_ENST00000300650.4_Nonsense_Mutation_p.R63*	NM_001077239.1|NM_001278249.1	NP_001070707.1|NP_001265178.1	Q8ND24	RN214_HUMAN	ring finger protein 214	63							zinc ion binding (GO:0008270)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		GGAGAATAACAGAAATGTCCA	0.453																																					p.R63X		Atlas-SNP	.											.	RNF214	54	.	0			c.A187T						.						187	196	193					11																	117109396		1944	4140	6084	SO:0001587	stop_gained	257160	exon3			AATAACAGAAATG	AL834448	CCDS41720.1, CCDS60976.1	11q23.3	2014-02-12	2007-02-16		ENSG00000167257	ENSG00000167257		"RING-type (C3HC4) zinc fingers"	25335	protein-coding gene	gene with protein product							Standard	NM_001077239		Approved	DKFZp547C195	uc001pqt.4	Q8ND24	OTTHUMG00000167069	ENST00000531452.1:c.187A>T	chr11.hg19:g.117109396A>T	ENSP00000431643:p.Arg63*	150.0	0.0		137.0	58.0	NM_207343	B2RUW0|B4DTD1	Nonsense_Mutation	SNP	ENST00000531452.1	hg19	CCDS41720.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.566449	0.86439	.	.	ENSG00000167257	ENST00000534428;ENST00000531452;ENST00000300650	.	.	.	5.5	4.31	0.51392	.	2.214490	0.02025	N	0.048065	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.6742	8.8752	0.35340	0.8111:0.1889:0.0:0.0	.	.	.	.	X	63	.	ENSP00000300650:R63X	R	+	1	2	RNF214	116614606	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.142000	0.42177	2.091000	0.63221	0.482000	0.46254	AGA	.	.		0.453	RNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392884.1	NM_001077239		T	117109396	A	T	117109396	4	4	73	1	0	0	0	0	0	1	0	0	13493	180	7	4	193	4	RNF214	11	117109396	Nonsense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	8400112	117109396	17897120	398	9724										
OR8G2	0	hgsc.bcm.edu	37	chr11	124095466	124095466	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggaaaccattcctcagtgacTgagttcattctggctgggct	11	10	3	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:124095466T>A								OR10D3 (38514 upstream) : OR8G1 (24956 downstream)																							CCTCAGTGACTGAGTTCATTC	0.478																																					p.T23T		Atlas-SNP	.											.	.	.	.	0			c.T69A						.						82	82	82					11																	124095466		2017	4203	6220	SO:0001628	intergenic_variant	26492	exon1			AGTGACTGAGTTC																													chr11.hg19:g.124095466T>A		168.0	0.0		127.0	54.0	NM_001007249		Silent	SNP		hg19																																																																																				.	.	0	0.478									A	124095466	T	A	124095466	1	1	73	0	1	0	0	0	0	0	0	0	11244	1567	55	4		4	OR8G2	11	124095466	IGR	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	6986070	124095466	10911050	399	9725										
CDON	50937	hgsc.bcm.edu	37	chr11	125891234	125891234	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cccaaaagagaggagttgagAgaaagaattgtcagagtccc	12	7	1	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:125891234A>G	ENST00000392693.3	-	3	385	c.258T>C	c.(256-258)tcT>tcC	p.S86S	CDON_ENST00000263577.7_Silent_p.S86S	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	86	Ig-like C2-type 1.				anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		AGGAGTTGAGAGAAAGAATTG	0.468																																					p.S86S		Atlas-SNP	.											.	CDON	137	.	0			c.T258C						.						86	84	85					11																	125891234		2201	4299	6500	SO:0001819	synonymous_variant	50937	exon3			GTTGAGAGAAAGA	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17104	protein-coding gene	gene with protein product	"cell adhesion molecule-related/down-regulated by oncogenes"	608707	"Cdon homolog (mouse)"			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.258T>C	chr11.hg19:g.125891234A>G		82.0	0.0		58.0	17.0	NM_016952	O14631	Silent	SNP	ENST00000392693.3	hg19	CCDS58192.1	.	.	.	.	.	.	.	.	.	.	A	1.213	-0.628996	0.03610	.	.	ENSG00000064309	ENST00000534661	T	0.40476	1.03	5.4	3.09	0.35607	.	0.000000	0.48767	D	0.000171	T	0.50292	0.1607	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47355	-0.9124	7	0.72032	D	0.01	-23.5902	8.1026	0.30865	0.6793:0.0:0.3207:0.0	.	.	.	.	P	62	ENSP00000436755:S62P	ENSP00000436755:S62P	S	-	1	0	CDON	125396444	1.000000	0.71417	0.988000	0.46212	0.060000	0.15804	0.965000	0.29319	0.369000	0.24510	0.450000	0.29827	TCT	.	.		0.468	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		G	125891234	A	G	125891234	2	3	73	1	0	0	0	0	0	0	0	1	3172	291	11	2		2	CDON	11	125891234	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1795768	125891234	9115282	400	9726										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133807314	133807314	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggacagcctccccctgaatGctgtacgctcggcaggtgta	12	13	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr11:133807314G>A	ENST00000321016.8	-	5	866	c.636C>T	c.(634-636)agC>agT	p.S212S	IGSF9B_ENST00000533871.2_Silent_p.S212S			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	212	Ig-like 2.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CCCCCTGAATGCTGTACGCTC	0.617																																					p.S212S		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C636T						.						84	96	92					11																	133807314		2108	4214	6322	SO:0001819	synonymous_variant	22997	exon5			CTGAATGCTGTAC	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.636C>T	chr11.hg19:g.133807314G>A		104.0	0.0		83.0	28.0	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	hg19																																																																																				.	.		0.617	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133807314	G	A	133807314	2	1	73	1	0	0	0	0	0	0	0	1	7615	1310	46	3		3	IGSF9B	11	133807314	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	7916080	133807314	1199202	401	9727										
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	666812	666812	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggtacagcaattcatcaaaGacatggaaaacctgttccag	9	9	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:666812G>T	ENST00000266383.5	+	16	2432	c.2419G>T	c.(2419-2421)Gac>Tac	p.D807Y		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	807					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			ATTCATCAAAGACATGGAAAA	0.517																																					p.D807Y		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G2419T						.						84	76	79					12																	666812		2203	4300	6503	SO:0001583	missense	283358	exon16			ATCAAAGACATGG	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.2419G>T	chr12.hg19:g.666812G>T	ENSP00000266383:p.Asp807Tyr	165.0	0.0		147.0	54.0	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.656311	0.88056	.	.	ENSG00000139044	ENST00000266383	T	0.34472	1.36	4.97	4.97	0.65823	.	0.085141	0.85682	D	0.000000	T	0.61060	0.2317	M	0.70842	2.15	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.65425	-0.6171	10	0.87932	D	0	-19.6504	18.199	0.89832	0.0:0.0:1.0:0.0	.	807	Q6L9W6	B4GN3_HUMAN	Y	807	ENSP00000266383:D807Y	ENSP00000266383:D807Y	D	+	1	0	B4GALNT3	537073	1.000000	0.71417	0.982000	0.44146	0.919000	0.55068	9.368000	0.97152	2.462000	0.83206	0.555000	0.69702	GAC	.	.		0.517	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		T	666812	G	T	666812	3	4	73	1	0	0	0	0	1	0	0	0	1268	942	33	3	2481	3	B4GALNT3	12	666812	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10		666812	133185083	402	9728										
ENO2	2026	hgsc.bcm.edu	37	chr12	7026812	7026812	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaggcaggggcagctgagcgGgaactgcccctgtatcgcca	15	12	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:7026812G>C	ENST00000535366.1	+	5	1004	c.378G>C	c.(376-378)cgG>cgC	p.R126R	ENO2_ENST00000544774.1_Silent_p.R83R|ENO2_ENST00000538763.1_Silent_p.R83R|ENO2_ENST00000545045.2_Intron|ENO2_ENST00000229277.1_Silent_p.R126R|ENO2_ENST00000541477.1_Silent_p.R126R			P09104	ENOG_HUMAN	enolase 2 (gamma, neuronal)	126					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perikaryon (GO:0043204)|phosphopyruvate hydratase complex (GO:0000015)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			endometrium(3)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						CAGCTGAGCGGGAACTGCCCC	0.602																																					p.R126R		Atlas-SNP	.											.	ENO2	20	.	0			c.G378C						.						81	68	72					12																	7026812		2203	4300	6503	SO:0001819	synonymous_variant	2026	exon6			TGAGCGGGAACTG	M22349	CCDS8570.1	12p13	2012-10-02				ENSG00000111674	4.2.1.11		3353	protein-coding gene	gene with protein product		131360					Standard	NM_001975		Approved		uc001qru.1	P09104		ENST00000535366.1:c.378G>C	chr12.hg19:g.7026812G>C		50.0	0.0		42.0	16.0	NM_001975	B7Z2X9|Q96J33	Silent	SNP	ENST00000535366.1	hg19	CCDS8570.1																																																																																			.	.		0.602	ENO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401786.1			C	7026812	G	C	7026812	2	2	73	1	0	0	0	0	0	0	0	1	5124	1219	43	4		4	ENO2	12	7026812	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	6360000	7026812	126825083	403	9729										
A2ML1	144568	hgsc.bcm.edu	37	chr12	8990976	8990976	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcacctgtggacatggccacCtttgacctcattggatatgc	10	12	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:8990976C>T	ENST00000299698.7	+	9	1080	c.900C>T	c.(898-900)acC>acT	p.T300T		NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1									p.T300T(1)		NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						ACATGGCCACCTTTGACCTCA	0.458																																					p.T300T		Atlas-SNP	.											A2ML1,caecum,carcinoma,0,1	A2ML1	199	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C900T						.						180	169	172					12																	8990976		1965	4166	6131	SO:0001819	synonymous_variant	144568	exon9			GGCCACCTTTGAC	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.900C>T	chr12.hg19:g.8990976C>T		197.0	1.0		111.0	50.0	NM_144670		Silent	SNP	ENST00000299698.7	hg19	CCDS8596.2																																																																																			.	.		0.458	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		T	8990976	C	T	8990976	2	4	73	1	0	0	0	0	0	0	0	1	5	668	24	3		3	A2ML1	12	8990976	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1964164	8990976	124860919	404	9730										
PHC1	1911	hgsc.bcm.edu	37	chr12	9083485	9083485	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggcatgaacctgacacggaCagccacacctgcgcccagcc	11	17	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:9083485C>A	ENST00000543824.1	+	8	1399	c.1067C>A	c.(1066-1068)aCa>aAa	p.T356K	PHC1_ENST00000433847.2_3'UTR|PHC1_ENST00000433083.2_Missense_Mutation_p.T311K|PHC1_ENST00000536844.1_Missense_Mutation_p.T135K|PHC1_ENST00000544916.1_Missense_Mutation_p.T356K			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	356					cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						CTGACACGGACAGCCACACCT	0.498																																					p.T356K		Atlas-SNP	.											.	PHC1	67	.	0			c.C1067A						.						21	23	23					12																	9083485		2198	4291	6489	SO:0001583	missense	1911	exon7			CACGGACAGCCAC	U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"Sterile alpha motif (SAM) domain containing"	3182	protein-coding gene	gene with protein product		602978	"early development regulator 1 (homolog of polyhomeotic 1)", "polyhomeotic-like 1 (Drosophila)"	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.1067C>A	chr12.hg19:g.9083485C>A	ENSP00000440674:p.Thr356Lys	79.0	0.0		121.0	36.0	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Missense_Mutation	SNP	ENST00000543824.1	hg19	CCDS8597.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.453440	0.84209	.	.	ENSG00000111752	ENST00000543824;ENST00000251757;ENST00000433083;ENST00000544916;ENST00000536844	T;T;T;T;D	0.83673	1.66;1.66;1.64;1.66;-1.75	5.38	5.38	0.77491	.	0.072582	0.64402	D	0.000019	D	0.88280	0.6394	L	0.47190	1.495	0.34457	D	0.701358	D;D;D	0.61697	0.99;0.981;0.981	D;D;D	0.69824	0.962;0.966;0.966	D	0.91388	0.5133	10	0.72032	D	0.01	-13.8727	17.0895	0.86618	0.0:1.0:0.0:0.0	.	356;356;356	B4DF21;P78364;B2RXH1	.;PHC1_HUMAN;.	K	356;356;311;356;135	ENSP00000440674:T356K;ENSP00000251757:T356K;ENSP00000399194:T311K;ENSP00000437659:T356K;ENSP00000440488:T135K	ENSP00000251757:T356K	T	+	2	0	PHC1	8974752	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	4.825000	0.62708	2.802000	0.96397	0.655000	0.94253	ACA	.	.		0.498	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426		A	9083485	C	A	9083485	3	1	73	1	0	0	0	0	1	0	0	0	11825	478	17	3	1089	3	PHC1	12	9083485	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	92509	9083485	124768410	405	9731										
CD69	969	hgsc.bcm.edu	37	chr12	9907785	9907785	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctggtagccaacccagtccTcagagcatgaagaaacatgg	10	11	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:9907785T>C	ENST00000228434.3	-	3	340	c.260A>G	c.(259-261)gAg>gGg	p.E87G	CD69_ENST00000536709.1_Missense_Mutation_p.E87G	NM_001781.2	NP_001772.1	Q07108	CD69_HUMAN	CD69 molecule	87					cellular response to drug (GO:0035690)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)	10						AACCCAGTCCTCAGAGCATGA	0.438																																					p.E87G		Atlas-SNP	.											.	CD69	23	.	0			c.A260G						.						117	123	121					12																	9907785		2203	4300	6503	SO:0001583	missense	969	exon3			CAGTCCTCAGAGC	Z22576	CCDS8604.1	12p13	2011-08-30	2006-03-28		ENSG00000110848	ENSG00000110848		"C-type lectin domain containing", "CD molecules"	1694	protein-coding gene	gene with protein product		107273	"CD69 antigen (p60, early T-cell activation antigen)"			1612643	Standard	NM_001781		Approved	CLEC2C	uc001qwk.3	Q07108	OTTHUMG00000168481	ENST00000228434.3:c.260A>G	chr12.hg19:g.9907785T>C	ENSP00000228434:p.Glu87Gly	131.0	0.0		103.0	42.0	NM_001781		Missense_Mutation	SNP	ENST00000228434.3	hg19	CCDS8604.1	.	.	.	.	.	.	.	.	.	.	T	3.200	-0.163832	0.06502	.	.	ENSG00000110848	ENST00000228434;ENST00000536709	T;T	0.62788	0.0;0.0	5.22	-0.15	0.13416	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (1);	0.893166	0.09789	N	0.755588	T	0.35799	0.0944	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.18808	-1.0325	9	.	.	.	-3.5921	6.7106	0.23274	0.0:0.0863:0.4784:0.4352	.	87;87	B4E0H7;Q07108	.;CD69_HUMAN	G	87	ENSP00000228434:E87G;ENSP00000442597:E87G	.	E	-	2	0	CD69	9799052	0.003000	0.15002	0.009000	0.14445	0.059000	0.15707	0.571000	0.23669	-0.155000	0.11098	-0.435000	0.05868	GAG	.	.		0.438	CD69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399876.1			C	9907785	T	C	9907785	3	2	73	1	0	0	0	0	1	0	0	0	3033	1551	54	2	351	2	CD69	12	9907785	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	824300	9907785	123944110	406	9732										
CLEC1B	51266	hgsc.bcm.edu	37	chr12	10147839	10147839	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	taaatgagtcctggctttgaTgtactcctattgtaaacata	7	7	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:10147839T>A	ENST00000298527.6	-	5	624	c.445A>T	c.(445-447)Atc>Ttc	p.I149F	CLEC1B_ENST00000348658.4_Missense_Mutation_p.I116F|CLEC1B_ENST00000428126.2_Missense_Mutation_p.I116F	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	149	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						CTGGCTTTGATGTACTCCTAT	0.408																																					p.I149F		Atlas-SNP	.											.	CLEC1B	39	.	0			c.A445T						.						211	202	205					12																	10147839		1859	4091	5950	SO:0001583	missense	51266	exon5			CTTTGATGTACTC	AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"C-type lectin domain containing"	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.445A>T	chr12.hg19:g.10147839T>A	ENSP00000298527:p.Ile149Phe	55.0	0.0		40.0	13.0	NM_016509	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	hg19	CCDS41752.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.192446	0.38707	.	.	ENSG00000165682	ENST00000398937;ENST00000428126;ENST00000298527;ENST00000348658	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	3.83	-5.6	0.02497	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.633406	0.13753	N	0.365175	T	0.10423	0.0255	L	0.38531	1.155	0.09310	N	1	B;B	0.28055	0.166;0.199	B;B	0.25140	0.031;0.058	T	0.17684	-1.0361	10	0.52906	T	0.07	.	1.2104	0.01903	0.2781:0.1023:0.3606:0.259	.	116;149	Q9P126-2;Q9P126	.;CLC1B_HUMAN	F	56;116;149;116	ENSP00000381910:I56F;ENSP00000406338:I116F;ENSP00000298527:I149F;ENSP00000327169:I116F	ENSP00000298527:I149F	I	-	1	0	CLEC1B	10039106	0.001000	0.12720	0.000000	0.03702	0.561000	0.35649	-0.998000	0.03701	-0.869000	0.04052	0.248000	0.18094	ATC	.	.		0.408	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509		A	10147839	T	A	10147839	3	1	73	1	0	0	0	0	1	0	0	0	3508	1464	51	4	252	4	CLEC1B	12	10147839	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	240054	10147839	123704056	407	9733										
PRB2	653247	hgsc.bcm.edu	37	chr12	11546400	11546400	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttgttgcctccttgtgggggTggtccttgtggctttcctgg	15	9	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:11546400T>A	ENST00000389362.4	-	3	647	c.612A>T	c.(610-612)ccA>ccT	p.P204P	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	204	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			CTTGTGGGGGTGGTCCTTGTG	0.597																																					p.P204P		Atlas-SNP	.											.	PRB2	168	.	0			c.A612T						.						71	79	77					12																	11546400		2085	4138	6223	SO:0001819	synonymous_variant	653247	exon3			TGGGGGTGGTCCT	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.612A>T	chr12.hg19:g.11546400T>A		369.0	0.0		322.0	46.0	NM_006248	O00599|P02811|P04281	Silent	SNP	ENST00000389362.4	hg19	CCDS41757.2																																																																																			.	.		0.597	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248		A	11546400	T	A	11546400	2	1	73	1	0	0	0	0	0	0	0	1	12455	1683	59	4		4	PRB2	12	11546400	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1398561	11546400	122305495	408	9734										
CASC1	55259	hgsc.bcm.edu	37	chr12	25267703	25267703	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	catgttaatatgagcatcttGaatcaaggtaacagggccaa	9	7	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:25267703G>A	ENST00000320267.9	-	12	1561	c.1480C>T	c.(1480-1482)Caa>Taa	p.Q494*	CASC1_ENST00000395987.3_Nonsense_Mutation_p.Q500*|CASC1_ENST00000537577.1_Nonsense_Mutation_p.Q382*|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000395990.2_Nonsense_Mutation_p.Q454*|CASC1_ENST00000354189.5_Nonsense_Mutation_p.Q558*|CASC1_ENST00000545133.1_Nonsense_Mutation_p.Q435*	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	494										breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			TGAGCATCTTGAATCAAGGTA	0.383																																					p.Q558X		Atlas-SNP	.											.	CASC1	146	.	0			c.C1672T						.						149	127	134					12																	25267703		2203	4300	6503	SO:0001587	stop_gained	55259	exon13			CATCTTGAATCAA	AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 54"					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.1480C>T	chr12.hg19:g.25267703G>A	ENSP00000313141:p.Gln494*	165.0	0.0		113.0	45.0	NM_001082972	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Nonsense_Mutation	SNP	ENST00000320267.9	hg19	CCDS41762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.497693|5.497693	0.96355|0.96355	.|.	.|.	ENSG00000118307|ENSG00000118307	ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395990;ENST00000537577;ENST00000545133;ENST00000389246|ENST00000556006	.|.	.|.	.|.	5.62|5.62	4.73|4.73	0.59995|0.59995	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.61837	.|0.2379	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69892	.|-0.5022	.|3	0.30078|.	T|.	0.28|.	-27.8804|-27.8804	12.1148|12.1148	0.53860|0.53860	0.0791:0.0:0.9209:0.0|0.0791:0.0:0.9209:0.0	.|.	.|.	.|.	.|.	X|L	558;500;494;454;382;435;304|330	.|.	ENSP00000313141:Q494X|.	Q|S	-|-	1|2	0|0	CASC1|CASC1	25158970|25158970	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.992000|0.992000	0.81027|0.81027	6.627000|6.627000	0.74258|0.74258	1.519000|1.519000	0.48950|0.48950	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.	.		0.383	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272		A	25267703	G	A	25267703	4	1	73	1	0	0	0	0	0	1	0	0	2662	1299	45	3	686	3	CASC1	12	25267703	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	13721303	25267703	108584192	409	9735										
RASSF8	11228	hgsc.bcm.edu	37	chr12	26217535	26217535	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	taaacaaatgggggcagtatGctagtgatgtgcagctcatt	12	6	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:26217535G>T	ENST00000405154.2	+	3	407	c.208G>T	c.(208-210)Gct>Tct	p.A70S	RASSF8_ENST00000381352.3_Missense_Mutation_p.A70S|RASSF8_ENST00000282884.9_Missense_Mutation_p.A70S|RASSF8_ENST00000541490.1_Missense_Mutation_p.A70S|RASSF8_ENST00000542865.1_Missense_Mutation_p.A70S	NM_001164748.1	NP_001158220.1	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	70	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				signal transduction (GO:0007165)					cervix(2)|endometrium(1)|large_intestine(6)|lung(15)|urinary_tract(1)	25	Colorectal(261;0.0847)					GGGGCAGTATGCTAGTGATGT	0.448																																					p.A70S		Atlas-SNP	.											.	RASSF8	56	.	0			c.G208T						.						127	126	126					12																	26217535		2203	4300	6503	SO:0001583	missense	11228	exon4			CAGTATGCTAGTG	U82396	CCDS8705.1, CCDS53765.1	12p12.3	2013-05-30	2008-02-22	2005-09-14	ENSG00000123094	ENSG00000123094			13232	protein-coding gene	gene with protein product		608231	"chromosome 12 open reading frame 2"	C12orf2			Standard	NM_007211		Approved	HoJ-1	uc001rgx.3	Q8NHQ8	OTTHUMG00000169087	ENST00000405154.2:c.208G>T	chr12.hg19:g.26217535G>T	ENSP00000384491:p.Ala70Ser	119.0	0.0		100.0	42.0	NM_007211	A8K1Z0|O95647|Q5SCI2|Q76KB6	Missense_Mutation	SNP	ENST00000405154.2	hg19	CCDS53765.1	.	.	.	.	.	.	.	.	.	.	G	18.59	3.656559	0.67586	.	.	ENSG00000123094	ENST00000381352;ENST00000535907;ENST00000405154;ENST00000542865;ENST00000541490;ENST00000542004;ENST00000542315;ENST00000541218;ENST00000282884;ENST00000545413;ENST00000541934	T;T;T;T;T;T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23;2.23;2.23;2.23;2.23;2.23	5.39	5.39	0.77823	Ras-association (3);	0.000000	0.85682	D	0.000000	T	0.24122	0.0584	N	0.17594	0.5	0.80722	D	1	P;D	0.54397	0.867;0.966	P;P	0.62813	0.79;0.907	T	0.05178	-1.0901	10	0.17369	T	0.5	-31.9131	18.5154	0.90934	0.0:0.0:1.0:0.0	.	70;70	Q8NHQ8-2;Q8NHQ8	.;RASF8_HUMAN	S	70	ENSP00000370756:A70S;ENSP00000442036:A70S;ENSP00000384491:A70S;ENSP00000439839:A70S;ENSP00000443096:A70S;ENSP00000442485:A70S;ENSP00000441294:A70S;ENSP00000445970:A70S;ENSP00000282884:A70S;ENSP00000443696:A70S	ENSP00000282884:A70S	A	+	1	0	RASSF8	26108802	1.000000	0.71417	0.997000	0.53966	0.594000	0.36715	9.403000	0.97302	2.710000	0.92621	0.655000	0.94253	GCT	.	.		0.448	RASSF8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402209.2	NM_007211		T	26217535	G	T	26217535	3	4	73	1	0	0	0	0	1	0	0	0	13107	1319	46	3	214	3	RASSF8	12	26217535	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	949832	26217535	107634360	410	9736										
PPFIBP1	8496	hgsc.bcm.edu	37	chr12	27832961	27832961	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggcaaccgcggggccccgatTaggttggtctcgagacttgg	16	11	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:27832961T>A	ENST00000318304.8	+	20	2163	c.1880T>A	c.(1879-1881)tTa>tAa	p.L627*	PPFIBP1_ENST00000542629.1_Nonsense_Mutation_p.L596*|PPFIBP1_ENST00000228425.6_Nonsense_Mutation_p.L621*|PPFIBP1_ENST00000537927.1_Nonsense_Mutation_p.L474*	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	627					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					GGGCCCCGATTAGGTTGGTCT	0.478																																					p.L627X		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.T1880A						.						76	83	81					12																	27832961		2203	4300	6503	SO:0001587	stop_gained	8496	exon20			CCCGATTAGGTTG	AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.1880T>A	chr12.hg19:g.27832961T>A	ENSP00000314724:p.Leu627*	90.0	0.0		74.0	39.0	NM_177444	O75336|Q86X70|Q9NY03|Q9ULJ0	Nonsense_Mutation	SNP	ENST00000318304.8	hg19	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	T	43	9.894552	0.99289	.	.	ENSG00000110841	ENST00000540114;ENST00000537927;ENST00000318304;ENST00000542629;ENST00000228425	.	.	.	5.91	5.91	0.95273	.	0.000000	0.28290	U	0.015888	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.8816	16.0127	0.80413	0.0:0.0:0.0:1.0	.	.	.	.	X	458;474;627;596;621	.	ENSP00000228425:L621X	L	+	2	0	PPFIBP1	27724228	1.000000	0.71417	0.710000	0.30468	0.832000	0.47134	7.593000	0.82686	2.266000	0.75297	0.533000	0.62120	TTA	.	.		0.478	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622		A	27832961	T	A	27832961	4	1	73	1	0	0	0	0	0	1	0	0	12322	1764	61	4	1978	4	PPFIBP1	12	27832961	Nonsense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1615426	27832961	106018934	411	9737										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32137297	32137297	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagttggcagaacctcagaaAgaagagcccatcacagaagt	10	9	2	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:32137297A>G	ENST00000312561.4	+	4	3822	c.3408A>G	c.(3406-3408)aaA>aaG	p.K1136K	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1136																	AACCTCAGAAAGAAGAGCCCA	0.413																																					p.K1136K		Atlas-SNP	.											.	.	.	.	0			c.A3408G						.						101	105	104					12																	32137297		2203	4300	6503	SO:0001819	synonymous_variant	55196	exon4			TCAGAAAGAAGAG	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3408A>G	chr12.hg19:g.32137297A>G		101.0	0.0		90.0	35.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	hg19	CCDS8725.2																																																																																			.	.		0.413	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		G	32137297	A	G	32137297	2	3	73	1	0	0	0	0	0	0	0	1	1684	69	3	2		2	C12orf35	12	32137297	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4304336	32137297	101714598	412	9738										
BICD1	636	hgsc.bcm.edu	37	chr12	32369200	32369200	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggcatttgggcagtccttctCcatccaccggaaggttgctg	12	12	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:32369200C>G	ENST00000281474.5	+	2	336	c.233C>G	c.(232-234)tCc>tGc	p.S78C	BICD1_ENST00000548411.1_Missense_Mutation_p.S78C	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	78					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			CAGTCCTTCTCCATCCACCGG	0.463																																					p.S78C		Atlas-SNP	.											.	BICD1	89	.	0			c.C233G						.						72	74	73					12																	32369200		2203	4300	6503	SO:0001583	missense	636	exon2			CCTTCTCCATCCA	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.233C>G	chr12.hg19:g.32369200C>G	ENSP00000281474:p.Ser78Cys	163.0	0.0		150.0	58.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	C	19.25	3.791503	0.70452	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	T;T	0.53857	0.6;0.6	5.45	5.45	0.79879	.	0.147996	0.48286	D	0.000188	T	0.72795	0.3505	M	0.77103	2.36	0.80722	D	1	D;D	0.67145	0.992;0.996	P;P	0.62649	0.789;0.905	T	0.75657	-0.3242	10	0.62326	D	0.03	.	19.2981	0.94131	0.0:1.0:0.0:0.0	.	78;78	F8W113;Q96G01	.;BICD1_HUMAN	C	78	ENSP00000446793:S78C;ENSP00000281474:S78C	ENSP00000281474:S78C	S	+	2	0	BICD1	32260467	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	3.771000	0.55318	2.546000	0.85860	0.655000	0.94253	TCC	.	.		0.463	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		G	32369200	C	G	32369200	3	3	73	1	0	0	0	0	1	0	0	0	1428	855	30	4	239	4	BICD1	12	32369200	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	231903	32369200	101482695	413	9739										
BICD1	636	hgsc.bcm.edu	37	chr12	32490444	32490444	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggttccagatgtgatgaatAtgtcacccagttggatgaga	12	6	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:32490444A>G	ENST00000281474.5	+	7	2367	c.2264A>G	c.(2263-2265)tAt>tGt	p.Y755C	BICD1_ENST00000548411.1_Missense_Mutation_p.Y755C	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	755	Interacts with RAB6A.				anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			TGTGATGAATATGTCACCCAG	0.408																																					p.Y755C		Atlas-SNP	.											.	BICD1	89	.	0			c.A2264G						.						92	87	89					12																	32490444		2203	4300	6503	SO:0001583	missense	636	exon7			ATGAATATGTCAC	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.2264A>G	chr12.hg19:g.32490444A>G	ENSP00000281474:p.Tyr755Cys	130.0	0.0		114.0	50.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.329189	0.60743	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	T;T	0.60171	0.21;0.21	4.66	4.66	0.58398	.	0.000000	0.64402	D	0.000001	T	0.78830	0.4345	M	0.89214	3.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.82354	-0.0499	10	0.51188	T	0.08	.	14.2757	0.66179	1.0:0.0:0.0:0.0	.	755;755	F8W113;Q96G01	.;BICD1_HUMAN	C	755	ENSP00000446793:Y755C;ENSP00000281474:Y755C	ENSP00000281474:Y755C	Y	+	2	0	BICD1	32381711	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.822000	0.92013	1.968000	0.57251	0.482000	0.46254	TAT	.	.		0.408	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		G	32490444	A	G	32490444	3	3	73	1	0	0	0	0	1	0	0	0	1428	449	16	2	2290	2	BICD1	12	32490444	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	121244	32490444	101361451	414	9740										
MLL2	8085	hgsc.bcm.edu	37	chr12	49432023	49432023	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgtctccattgagcaggtcaTccaagtgggggtcattggtc	13	10	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:49432023T>C	ENST00000301067.7	-	34	9115	c.9116A>G	c.(9115-9117)gAt>gGt	p.D3039G	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3039					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GAGCAGGTCATCCAAGTGGGG	0.522																																					p.D3039G		Atlas-SNP	.											.	MLL2	1173	.	0			c.A9116G						.						101	101	101					12																	49432023		2024	4190	6214	SO:0001583	missense	8085	exon34			AGGTCATCCAAGT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.9116A>G	chr12.hg19:g.49432023T>C	ENSP00000301067:p.Asp3039Gly	143.0	0.0		138.0	59.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	T	11.92	1.783706	0.31593	.	.	ENSG00000167548	ENST00000301067	D	0.95622	-3.76	5.11	5.11	0.69529	.	0.000000	0.39834	N	0.001253	D	0.96614	0.8895	L	0.49126	1.545	0.58432	D	0.999997	D	0.89917	1.0	D	0.83275	0.996	D	0.97199	0.9863	10	0.87932	D	0	.	14.2014	0.65707	0.0:0.0:0.0:1.0	.	3039	O14686	MLL2_HUMAN	G	3039	ENSP00000301067:D3039G	ENSP00000301067:D3039G	D	-	2	0	MLL2	47718290	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.926000	0.87569	2.062000	0.61559	0.533000	0.62120	GAT	.	.		0.522	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49432023	T	C	49432023	3	2	73	1	0	0	0	0	1	0	0	0	9630	1435	50	2	7581	2	MLL2	12	49432023	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	16941579	49432023	84419872	415	9741										
KRT5	3852	hgsc.bcm.edu	37	chr12	52913903	52913903	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtagaggctccggctgccatAgccacccactccacaagcac	9	17	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:52913903A>T	ENST00000252242.4	-	1	568	c.178T>A	c.(178-180)Tat>Aat	p.Y60N		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	60	Gly-rich.|Head.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		CGGCTGCCATAGCCACCCACT	0.647																																					p.Y60N		Atlas-SNP	.											.	KRT5	88	.	0			c.T178A						.						45	60	55					12																	52913903		2201	4293	6494	SO:0001583	missense	3852	exon1			TGCCATAGCCACC		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"-", "Intermediate filaments type II, keratins (basic)"	6442	protein-coding gene	gene with protein product		148040	"epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types", "keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.178T>A	chr12.hg19:g.52913903A>T	ENSP00000252242:p.Tyr60Asn	81.0	0.0		68.0	26.0	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	hg19	CCDS8830.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.27|11.27	1.589772|1.589772	0.28357|0.28357	.|.	.|.	ENSG00000186081|ENSG00000186081	ENST00000456000|ENST00000252242;ENST00000546577	.|D;T	.|0.85411	.|-1.98;2.09	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	.|0.759830	.|0.11612	.|N	.|0.546660	.|T	.|0.81475	.|0.4830	L|L	0.32530|0.32530	0.975|0.975	0.34396|0.34396	D|D	0.694722|0.694722	.|B	.|0.06786	.|0.001	.|B	.|0.09377	.|0.004	.|T	.|0.79867	.|-0.1622	.|10	.|0.87932	.|D	.|0	.|.	16.3797|16.3797	0.83452|0.83452	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|60	.|P13647	.|K2C5_HUMAN	.|N	-1|60	.|ENSP00000252242:Y60N;ENSP00000449651:Y60N	.|ENSP00000252242:Y60N	.|Y	-|-	.|1	.|0	KRT5|KRT5	51200170|51200170	0.991000|0.991000	0.36638|0.36638	0.765000|0.765000	0.31456|0.31456	0.087000|0.087000	0.18053|0.18053	4.226000|4.226000	0.58606|0.58606	2.271000|2.271000	0.75665|0.75665	0.533000|0.533000	0.62120|0.62120	.|TAT	.	.		0.647	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1			T	52913903	A	T	52913903	3	4	73	1	0	0	0	0	1	0	0	0	8488	420	15	4	1630	4	KRT5	12	52913903	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3481880	52913903	80937992	416	9742										
MAP3K12	7786	hgsc.bcm.edu	37	chr12	53878895	53878895	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcaactggagggcacgggcaGatggagactgttgcttccca	15	10	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:53878895G>A	ENST00000267079.2	-	7	1210	c.985C>T	c.(985-987)Ctg>Ttg	p.L329L	MAP3K12_ENST00000547151.1_5'Flank|MAP3K12_ENST00000547488.1_Silent_p.L362L|MAP3K12_ENST00000547035.1_Silent_p.L362L	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	329	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						GGCACGGGCAGATGGAGACTG	0.552																																					p.L362L		Atlas-SNP	.											.	MAP3K12	160	.	0			c.C1084T						.						122	102	108					12																	53878895		2203	4300	6503	SO:0001819	synonymous_variant	7786	exon6			CGGGCAGATGGAG	U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.985C>T	chr12.hg19:g.53878895G>A		126.0	0.0		123.0	52.0	NM_001193511	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Silent	SNP	ENST00000267079.2	hg19	CCDS8860.1																																																																																			.	.		0.552	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		A	53878895	G	A	53878895	2	1	73	1	0	0	0	0	0	0	0	1	9255	933	33	3		3	MAP3K12	12	53878895	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	964992	53878895	79973000	417	9743										
OBFC2B	79035	hgsc.bcm.edu	37	chr12	56619991	56619991	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggtttattctgaggttcctAacttcagtgagccaaaccca	8	10	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:56619991A>G	ENST00000380198.2	+	4	817	c.319A>G	c.(319-321)Aac>Gac	p.N107D	NABP2_ENST00000341463.5_Missense_Mutation_p.N107D|NABP2_ENST00000267023.4_Missense_Mutation_p.N107D			Q9BQ15	SOSB1_HUMAN	nucleic acid binding protein 2	107					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)|SOSS complex (GO:0070876)	single-stranded DNA binding (GO:0003697)										TGAGGTTCCTAACTTCAGTGA	0.517																																					p.N107D		Atlas-SNP	.											.	.	.	.	0			c.A319G						.						111	107	109					12																	56619991		2203	4300	6503	SO:0001583	missense	79035	exon5			GTTCCTAACTTCA	BC006171	CCDS8911.1	12q13.3	2012-06-19	2012-06-19	2012-06-19	ENSG00000139579	ENSG00000139579			28412	protein-coding gene	gene with protein product	"single strand DNA-binding protein 1", "sensor of single-strand DNA complex subunit B1"	612104	"oligonucleotide/oligosaccharide-binding fold containing 2B"	OBFC2B			Standard	NM_024068		Approved	MGC2731, SSB1, hSSB1, SOSS-B1	uc001ski.3	Q9BQ15	OTTHUMG00000152527	ENST00000380198.2:c.319A>G	chr12.hg19:g.56619991A>G	ENSP00000369545:p.Asn107Asp	188.0	0.0		165.0	65.0	NM_024068	A6NDF8|Q6XYC8	Missense_Mutation	SNP	ENST00000380198.2	hg19	CCDS8911.1	.	.	.	.	.	.	.	.	.	.	A	18.41	3.618898	0.66787	.	.	ENSG00000139579	ENST00000447747;ENST00000399713;ENST00000267023;ENST00000380198;ENST00000341463	D;D;D;D;D	0.90676	-2.71;-2.71;-2.71;-2.71;-2.71	4.32	4.32	0.51571	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	D	0.89217	0.6652	M	0.65498	2.005	0.51482	D	0.999927	B;P;B	0.36683	0.233;0.565;0.165	B;B;B	0.37091	0.174;0.217;0.241	D	0.90098	0.4182	10	0.87932	D	0	-16.7133	12.834	0.57763	1.0:0.0:0.0:0.0	.	107;107;107	C9JT95;C9JMP5;Q9BQ15	.;.;SOSB1_HUMAN	D	107	ENSP00000413902:N107D;ENSP00000408616:N107D;ENSP00000267023:N107D;ENSP00000369545:N107D;ENSP00000368862:N107D	ENSP00000267023:N107D	N	+	1	0	OBFC2B	54906258	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.970000	0.93415	1.741000	0.51731	0.370000	0.22315	AAC	.	.		0.517	NABP2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326610.1	NM_024068		G	56619991	A	G	56619991	3	3	73	1	0	0	0	0	1	0	0	0	10818	362	13	2	333	2	OBFC2B	12	56619991	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2741096	56619991	77231904	418	9744										
ZBTB39	9880	hgsc.bcm.edu	37	chr12	57397645	57397645	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gatcagttgaatgttgggctCtagaactttcttgcacacct	9	9	3	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:57397645C>G	ENST00000300101.2	-	2	1142	c.1057G>C	c.(1057-1059)Gag>Cag	p.E353Q		NM_014830.2	NP_055645.1	O15060	ZBT39_HUMAN	zinc finger and BTB domain containing 39	353					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|prostate(1)	16						ATGTTGGGCTCTAGAACTTTC	0.537																																					p.E353Q		Atlas-SNP	.											.	ZBTB39	58	.	0			c.G1057C						.						164	148	154					12																	57397645		2203	4300	6503	SO:0001583	missense	9880	exon2			TGGGCTCTAGAAC	AB002350	CCDS31839.1	12q13.3	2013-01-09				ENSG00000166860		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	29014	protein-coding gene	gene with protein product						9205841	Standard	NM_014830		Approved	KIAA0352, ZNF922	uc001sml.2	O15060		ENST00000300101.2:c.1057G>C	chr12.hg19:g.57397645C>G	ENSP00000300101:p.Glu353Gln	128.0	0.0		117.0	48.0	NM_014830	A7MD38|Q9UD98	Missense_Mutation	SNP	ENST00000300101.2	hg19	CCDS31839.1	.	.	.	.	.	.	.	.	.	.	C	9.439	1.087549	0.20390	.	.	ENSG00000166860	ENST00000300101	T	0.08193	3.12	5.22	5.22	0.72569	.	0.348186	0.29172	N	0.012923	T	0.05868	0.0153	N	0.16903	0.455	0.33269	D	0.560731	P	0.35272	0.493	B	0.29942	0.109	T	0.33007	-0.9885	10	0.23302	T	0.38	-22.7362	16.3249	0.82975	0.0:1.0:0.0:0.0	.	353	O15060	ZBT39_HUMAN	Q	353	ENSP00000300101:E353Q	ENSP00000300101:E353Q	E	-	1	0	ZBTB39	55683912	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.921000	0.56454	2.720000	0.93068	0.655000	0.94253	GAG	.	.		0.537	ZBTB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411214.1	NM_014830		G	57397645	C	G	57397645	3	3	73	1	0	0	0	0	1	0	0	0	17555	922	32	4	1085	4	ZBTB39	12	57397645	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	777654	57397645	76454250	419	9745										
IRAK3	11213	hgsc.bcm.edu	37	chr12	66638446	66638446	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaactttccattaaaacagaTgtctacagctttggaattgt	6	7	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:66638446T>A	ENST00000261233.4	+	9	1489	c.1068T>A	c.(1066-1068)gaT>gaA	p.D356E	IRAK3_ENST00000457197.2_Missense_Mutation_p.D295E	NM_007199.2	NP_009130.2			interleukin-1 receptor-associated kinase 3											breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(28;0.0203)		TTAAAACAGATGTCTACAGCT	0.368																																					p.D356E		Atlas-SNP	.											.	IRAK3	75	.	0			c.T1068A						.						95	87	90					12																	66638446		2203	4300	6503	SO:0001583	missense	11213	exon9			AACAGATGTCTAC	AF113136	CCDS8975.1, CCDS44937.1	12q13.13	2008-05-02			ENSG00000090376	ENSG00000090376			17020	protein-coding gene	gene with protein product		604459				10383454	Standard	NM_001142523		Approved	IRAK-M	uc001sth.3	Q9Y616	OTTHUMG00000169002	ENST00000261233.4:c.1068T>A	chr12.hg19:g.66638446T>A	ENSP00000261233:p.Asp356Glu	117.0	0.0		101.0	35.0	NM_007199		Missense_Mutation	SNP	ENST00000261233.4	hg19	CCDS8975.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.004124	0.54254	.	.	ENSG00000090376	ENST00000261233;ENST00000457197	T;T	0.74526	-0.85;-0.85	5.84	-4.29	0.03721	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.88629	0.6488	H	0.96861	3.895	0.32145	N	0.585008	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.88317	0.2960	9	.	.	.	-26.1063	14.6965	0.69126	0.0:0.3232:0.0:0.6768	.	295;356	Q9Y616-2;Q9Y616	.;IRAK3_HUMAN	E	356;295	ENSP00000261233:D356E;ENSP00000409852:D295E	.	D	+	3	2	IRAK3	64924713	0.001000	0.12720	0.030000	0.17652	0.541000	0.35023	-2.325000	0.01115	-1.109000	0.02996	-0.733000	0.03571	GAT	.	.		0.368	IRAK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401908.1			A	66638446	T	A	66638446	3	1	73	1	0	0	0	0	1	0	0	0	7833	1461	51	4	1102	4	IRAK3	12	66638446	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	9240801	66638446	67213449	420	9746										
TPH2	121278	hgsc.bcm.edu	37	chr12	72425319	72425319	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agggactttgcaaagtcaatTacccgtcccttctcagtata	7	11	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:72425319T>C	ENST00000333850.3	+	11	1458	c.1317T>C	c.(1315-1317)atT>atC	p.I439I		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	439					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	CAAAGTCAATTACCCGTCCCT	0.423																																					p.I439I		Atlas-SNP	.											.	TPH2	81	.	0			c.T1317C						.						95	81	86					12																	72425319		2203	4300	6503	SO:0001819	synonymous_variant	121278	exon11			GTCAATTACCCGT	AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.1317T>C	chr12.hg19:g.72425319T>C		156.0	0.0		141.0	60.0	NM_173353	A6NGA4|Q14CB0	Silent	SNP	ENST00000333850.3	hg19	CCDS31859.1																																																																																			.	.		0.423	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353		C	72425319	T	C	72425319	2	2	73	1	0	0	0	0	0	0	0	1	16417	1742	61	2		2	TPH2	12	72425319	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	5786873	72425319	61426576	421	9747										
NAV3	89795	hgsc.bcm.edu	37	chr12	78513452	78513452	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aggaggccacagatccagtaCcagcagtattgattccaacg	10	11	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:78513452C>G	ENST00000397909.2	+	15	3649	c.3476C>G	c.(3475-3477)aCc>aGc	p.T1159S	NAV3_ENST00000536525.2_Missense_Mutation_p.T1159S|NAV3_ENST00000266692.7_Missense_Mutation_p.T1159S|NAV3_ENST00000228327.6_Missense_Mutation_p.T1159S			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1159	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						AGATCCAGTACCAGCAGTATT	0.542										HNSCC(70;0.22)																											p.T1159S		Atlas-SNP	.											.	NAV3	506	.	0			c.C3476G						.						70	72	72					12																	78513452		1981	4158	6139	SO:0001583	missense	89795	exon15			CCAGTACCAGCAG	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.3476C>G	chr12.hg19:g.78513452C>G	ENSP00000381007:p.Thr1159Ser	169.0	0.0		132.0	56.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.16|16.16	3.043916|3.043916	0.55110|0.55110	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692|ENST00000552895	T;T;T;T|.	0.18657|.	2.2;2.2;2.2;2.2|.	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.000000|.	0.41294|.	U|.	0.000913|.	T|.	0.46639|.	0.1403|.	N|N	0.04880|0.04880	-0.145|-0.145	0.80722|0.80722	D|D	1|1	B;P;B;B|.	0.34412|.	0.347;0.453;0.077;0.1|.	B;B;B;B|.	0.42062|.	0.145;0.374;0.03;0.084|.	T|.	0.42258|.	-0.9462|.	10|.	0.09338|.	T|.	0.73|.	-19.8387|-19.8387	19.949|19.949	0.97192|0.97192	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1159;1159;1159;1159|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	S|X	1159|230	ENSP00000446132:T1159S;ENSP00000381007:T1159S;ENSP00000228327:T1159S;ENSP00000266692:T1159S|.	ENSP00000228327:T1159S|.	T|Y	+|+	2|3	0|2	NAV3|NAV3	77037583|77037583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.960000|0.960000	0.62799|0.62799	7.594000|7.594000	0.82698|0.82698	2.706000|2.706000	0.92434|0.92434	0.655000|0.655000	0.94253|0.94253	ACC|TAC	.	.		0.542	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		G	78513452	C	G	78513452	3	3	73	1	0	0	0	0	1	0	0	0	10194	507	18	4	3534	4	NAV3	12	78513452	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	6088133	78513452	55338443	422	9748										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80750668	80750668	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gattcaagttcgacaggaagAaccttgttgtttttcccctt	8	9	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:80750668A>T	ENST00000547103.1	+	48	5936	c.5930A>T	c.(5929-5931)gAa>gTa	p.E1977V	OTOGL_ENST00000546620.1_Missense_Mutation_p.E8V|OTOGL_ENST00000458043.2_Missense_Mutation_p.E1989V			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1977	Cys-rich.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						CGACAGGAAGAACCTTGTTGT	0.353																																					p.E1989V		Atlas-SNP	.											.	OTOGL	235	.	0			c.A5966T						.						109	97	101					12																	80750668		2203	4300	6503	SO:0001583	missense	283310	exon48			AGGAAGAACCTTG	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5930A>T	chr12.hg19:g.80750668A>T	ENSP00000447211:p.Glu1977Val	247.0	1.0		269.0	120.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.5|22.5	4.299202|4.299202	0.81025|0.81025	.|.	.|.	ENSG00000165899|ENSG00000165899	ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182|ENST00000298820	T;T;T;T|.	0.33654|.	1.4;1.4;1.4;1.4|.	5.36|5.36	4.18|4.18	0.49190|0.49190	.|.	0.424311|.	0.21815|.	N|.	0.068713|.	T|T	0.59252|0.59252	0.2180|0.2180	M|M	0.62723|0.62723	1.935|1.935	0.31953|0.31953	N|N	0.609369|0.609369	D|.	0.54601|.	0.967|.	P|.	0.53689|.	0.732|.	T|T	0.64719|0.64719	-0.6341|-0.6341	10|5	0.37606|.	T|.	0.19|.	.|.	12.2377|12.2377	0.54524|0.54524	0.8576:0.1424:0.0:0.0|0.8576:0.1424:0.0:0.0	.|.	354|.	Q3ZCN5|.	OTOGL_HUMAN|.	V|Y	1977;1989;8;6|432	ENSP00000447211:E1977V;ENSP00000400895:E1989V;ENSP00000449094:E8V;ENSP00000449641:E6V|.	ENSP00000400895:E1989V|.	E|N	+|+	2|1	0|0	OTOGL|OTOGL	79274799|79274799	1.000000|1.000000	0.71417|0.71417	0.890000|0.890000	0.34922|0.34922	0.987000|0.987000	0.75469|0.75469	5.491000|5.491000	0.66887|0.66887	0.831000|0.831000	0.34780|0.34780	0.455000|0.455000	0.32223|0.32223	GAA|AAC	.	.		0.353	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		T	80750668	A	T	80750668	3	4	73	1	0	0	0	0	1	0	0	0	1709	246	9	4	6156	4	C12orf64	12	80750668	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2237216	80750668	53101227	423	9749										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	82147865	82147865	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtctcccgaagggtgtctaGaagacgatccctttcatcta	10	11	4	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:82147865G>C	ENST00000549396.1	-	3	296	c.136C>G	c.(136-138)Cta>Gta	p.L46V	PPFIA2_ENST00000550584.2_Missense_Mutation_p.L46V|PPFIA2_ENST00000548586.1_Missense_Mutation_p.L46V|PPFIA2_ENST00000549325.1_Missense_Mutation_p.L46V|PPFIA2_ENST00000552948.1_Missense_Mutation_p.L46V|PPFIA2_ENST00000333447.7_Missense_Mutation_p.L46V	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	46					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						AGGGTGTCTAGAAGACGATCC	0.522																																					p.L46V		Atlas-SNP	.											.	PPFIA2	207	.	0			c.C136G						.						65	67	67					12																	82147865		1935	4146	6081	SO:0001583	missense	8499	exon2			TGTCTAGAAGACG	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.136C>G	chr12.hg19:g.82147865G>C	ENSP00000450337:p.Leu46Val	138.0	0.0		120.0	49.0	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	hg19	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.792964	0.90453	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000552948;ENST00000551442;ENST00000547623	T;T;T;T;T;T;T	0.58652	0.32;0.32;0.32;0.32;0.32;0.32;0.32	5.95	5.95	0.96441	.	0.189534	0.35466	N	0.003196	T	0.73521	0.3597	L	0.58969	1.84	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.70178	-0.4943	10	0.45353	T	0.12	.	20.3812	0.98933	0.0:0.0:1.0:0.0	.	46	O75334	LIPA2_HUMAN	V	46;46;57;46;46;46;46;46	ENSP00000450337:L46V;ENSP00000450298:L46V;ENSP00000327416:L46V;ENSP00000449338:L46V;ENSP00000447868:L46V;ENSP00000449469:L46V;ENSP00000447918:L46V	ENSP00000327416:L46V	L	-	1	2	PPFIA2	80671996	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.931000	0.63469	2.821000	0.97095	0.650000	0.86243	CTA	.	.		0.522	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			C	82147865	G	C	82147865	3	2	73	1	0	0	0	0	1	0	0	0	12319	933	33	4	3757	4	PPFIA2	12	82147865	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1397197	82147865	51704030	424	9750										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85518207	85518207	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agaagacagcaaggcaagcaGtattcccaccataagaatcc	8	11	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:85518207G>T	ENST00000393217.2	+	17	3978	c.3917G>T	c.(3916-3918)aGt>aTt	p.S1306I		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1306										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		AAGGCAAGCAGTATTCCCACC	0.378																																					p.S1306I		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.G3917T						.						167	183	178					12																	85518207		2203	4300	6503	SO:0001583	missense	84125	exon17			CAAGCAGTATTCC	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.3917G>T	chr12.hg19:g.85518207G>T	ENSP00000376910:p.Ser1306Ile	70.0	0.0		76.0	32.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.194009	0.38707	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.55052	0.54	5.33	1.98	0.26296	.	1.848560	0.02908	N	0.136304	T	0.35508	0.0934	N	0.14661	0.345	0.09310	N	1	B;B	0.21905	0.028;0.062	B;B	0.19148	0.01;0.024	T	0.29274	-1.0017	10	0.66056	D	0.02	.	2.384	0.04361	0.3696:0.0:0.2409:0.3895	.	1306;1281	Q96JM4;C9JI57	LRIQ1_HUMAN;.	I	1306;1281;1306	ENSP00000376910:S1306I	ENSP00000256007:S1306I	S	+	2	0	LRRIQ1	84042338	0.000000	0.05858	0.000000	0.03702	0.462000	0.32619	-0.065000	0.11617	0.178000	0.19917	0.591000	0.81541	AGT	.	.		0.378	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85518207	G	T	85518207	3	4	73	1	0	0	0	0	1	0	0	0	9038	1029	36	3	3979	3	LRRIQ1	12	85518207	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3370342	85518207	48333688	425	9751										
KITLG	4254	hgsc.bcm.edu	37	chr12	88910260	88910260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgggctcttgaatgattttTttagatcctagaagaaaaaa	8	5	1	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:88910260T>C	ENST00000228280.5	-	5	553	c.371A>G	c.(370-372)aAa>aGa	p.K124R	KITLG_ENST00000347404.5_Missense_Mutation_p.K124R|KITLG_ENST00000378535.4_5'UTR|KITLG_ENST00000357116.4_Intron	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand	124					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|negative regulation of mast cell apoptotic process (GO:0033026)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of myeloid leukocyte differentiation (GO:0002763)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	stem cell factor receptor binding (GO:0005173)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)	9						GAATGATTTTTTTAGATCCTA	0.333									Testicular Cancer, Familial Clustering of																												p.K124R		Atlas-SNP	.											.	KITLG	26	.	0			c.A371G						.						28	31	30					12																	88910260		2187	4288	6475	SO:0001583	missense	4254	exon5	Familial Cancer Database		GATTTTTTTAGAT	M59964	CCDS31867.1, CCDS31868.1	12q22	2010-11-23			ENSG00000049130	ENSG00000049130			6343	protein-coding gene	gene with protein product	"mast cell growth factor", "stem cell factor", "steel factor", "familial progressive hyperpigmentation 2"	184745		MGF		2208279, 1707188, 19375057	Standard	NM_003994		Approved	SCF, SF, Kitl, KL-1, FPH2	uc001tav.3	P21583	OTTHUMG00000169888	ENST00000228280.5:c.371A>G	chr12.hg19:g.88910260T>C	ENSP00000228280:p.Lys124Arg	69.0	0.0		44.0	22.0	NM_003994	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Missense_Mutation	SNP	ENST00000228280.5	hg19	CCDS31868.1	.	.	.	.	.	.	.	.	.	.	T	10.89	1.479636	0.26511	.	.	ENSG00000049130	ENST00000378535;ENST00000228280;ENST00000347404	T;T	0.70749	-0.51;-0.51	4.96	2.16	0.27623	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.581480	0.19732	N	0.107326	T	0.56062	0.1960	L	0.45581	1.43	0.19300	N	0.999971	B;B	0.14012	0.007;0.009	B;B	0.12156	0.002;0.007	T	0.40794	-0.9544	10	0.32370	T	0.25	-3.6834	3.2753	0.06896	0.3762:0.1519:0.0:0.4719	.	124;124	P21583-2;P21583	.;SCF_HUMAN	R	89;124;124	ENSP00000228280:K124R;ENSP00000054216:K124R	ENSP00000228280:K124R	K	-	2	0	KITLG	87434391	0.994000	0.37717	0.928000	0.36995	0.291000	0.27294	0.230000	0.17852	0.701000	0.31803	0.482000	0.46254	AAA	.	.		0.333	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406424.2	NM_003994		C	88910260	T	C	88910260	3	2	73	1	0	0	0	0	1	0	0	0	8339	1841	64	2	470	2	KITLG	12	88910260	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3392053	88910260	44941635	426	9752										
DCN	1634	hgsc.bcm.edu	37	chr12	91546950	91546950	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccatcaagatgtaattccgtAagggaaggaggaagacctgg	13	7	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:91546950A>T	ENST00000052754.5	-	6	1170	c.669T>A	c.(667-669)ctT>ctA	p.L223L	DCN_ENST00000456569.2_Intron|DCN_ENST00000425043.1_Silent_p.L76L|DCN_ENST00000547568.2_Silent_p.L76L|DCN_ENST00000393155.1_Silent_p.L223L|DCN_ENST00000441303.2_Intron|DCN_ENST00000228329.5_Silent_p.L114L|DCN_ENST00000420120.2_Silent_p.L114L|DCN_ENST00000303320.3_Intron|DCN_ENST00000552962.1_Silent_p.L223L	NM_001920.3	NP_001911.1	P07585	PGS2_HUMAN	decorin	223					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|kidney development (GO:0001822)|organ morphogenesis (GO:0009887)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|placenta development (GO:0001890)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	collagen type VI trimer (GO:0005589)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|skin(1)	20						GTAATTCCGTAAGGGAAGGAG	0.353																																					p.L223L		Atlas-SNP	.											.	DCN	61	.	0			c.T669A						.						123	117	119					12																	91546950		2203	4300	6503	SO:0001819	synonymous_variant	1634	exon6			TTCCGTAAGGGAA	AF138300	CCDS9039.1, CCDS9040.1, CCDS9041.1, CCDS9042.1, CCDS44951.1	12q21.33	2014-04-16			ENSG00000011465	ENSG00000011465		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	2705	protein-coding gene	gene with protein product	"decorin proteoglycan"	125255				8432526	Standard	NM_133507		Approved	DSPG2, SLRR1B	uc001tbt.3	P07585	OTTHUMG00000169998	ENST00000052754.5:c.669T>A	chr12.hg19:g.91546950A>T		100.0	0.0		82.0	37.0	NM_001920	Q9P0Z0|Q9P0Z1|Q9Y5N8|Q9Y5N9	Silent	SNP	ENST00000052754.5	hg19	CCDS9039.1																																																																																			.	.		0.353	DCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406799.3	NM_133507		T	91546950	A	T	91546950	2	4	73	1	0	0	0	0	0	0	0	1	4299	349	13	4		4	DCN	12	91546950	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2636690	91546950	42304945	427	9753										
IFT81	28981	hgsc.bcm.edu	37	chr12	110565247	110565247	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggagccctttaggaagaactAtaatttaatcacgtttgatt	8	6	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:110565247A>G	ENST00000242591.5	+	2	568	c.62A>G	c.(61-63)tAt>tGt	p.Y21C	IFT81_ENST00000361948.4_Missense_Mutation_p.Y21C|IFT81_ENST00000552912.1_Missense_Mutation_p.Y21C	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	21	CH (calponin-homology)-like region.				cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|spermatogenesis (GO:0007283)	centrosome (GO:0005813)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)	tubulin binding (GO:0015631)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)	10						AGGAAGAACTATAATTTAATC	0.328																																					p.Y21C		Atlas-SNP	.											.	IFT81	86	.	0			c.A62G						.						51	49	50					12																	110565247		2203	4300	6503	SO:0001583	missense	28981	exon2			AGAACTATAATTT	AF139540	CCDS9142.1, CCDS41831.1	12q24.13	2014-07-03	2014-07-03	2005-11-02		ENSG00000122970		"Intraflagellar transport homologs"	14313	protein-coding gene	gene with protein product		605489	"carnitine deficiency-associated, expressed in ventricle 1", "intraflagellar transport 81 homolog (Chlamydomonas)"	CDV1		11130971	Standard	NM_014055		Approved	CDV-1R, MGC4027	uc001tqi.3	Q8WYA0	OTTHUMG00000169326	ENST00000242591.5:c.62A>G	chr12.hg19:g.110565247A>G	ENSP00000242591:p.Tyr21Cys	249.0	0.0		249.0	83.0	NM_014055	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Missense_Mutation	SNP	ENST00000242591.5	hg19	CCDS41831.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.628421	0.67015	.	.	ENSG00000122970	ENST00000361948;ENST00000552912;ENST00000242591;ENST00000546374	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	6.11	6.11	0.99139	.	0.051364	0.85682	D	0.000000	D	0.85410	0.5690	M	0.71036	2.16	0.80722	D	1	D;D	0.71674	0.995;0.998	P;D	0.63113	0.893;0.911	D	0.86884	0.2044	10	0.87932	D	0	-13.764	12.3276	0.55020	0.8735:0.0:0.0:0.1265	.	21;21	Q8WYA0;Q8WYA0-3	IFT81_HUMAN;.	C	21	ENSP00000355372:Y21C;ENSP00000449718:Y21C;ENSP00000242591:Y21C;ENSP00000446950:Y21C	ENSP00000242591:Y21C	Y	+	2	0	IFT81	109049630	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.063000	0.64332	2.343000	0.79666	0.533000	0.62120	TAT	.	.		0.328	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055		G	110565247	A	G	110565247	3	3	73	1	0	0	0	0	1	0	0	0	7574	449	16	2	64	2	IFT81	12	110565247	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	19018297	110565247	23286648	428	9754										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112688787	112688787	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tttgttacctttgtaaaagtTtggaccgcaatagctcctga	8	8	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:112688787T>A	ENST00000430131.2	-	23	3583	c.2438A>T	c.(2437-2439)aAa>aTa	p.K813I	HECTD4_ENST00000550722.1_Missense_Mutation_p.K1089I|HECTD4_ENST00000377560.5_Missense_Mutation_p.K1063I			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	813					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TTGTAAAAGTTTGGACCGCAA	0.393																																					p.K1101I		Atlas-SNP	.											.	.	.	.	0			c.A3302T						.						84	77	79					12																	112688787		2203	4300	6503	SO:0001583	missense	283450	exon24			AAAAGTTTGGACC	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.2438A>T	chr12.hg19:g.112688787T>A	ENSP00000404379:p.Lys813Ile	158.0	0.0		127.0	58.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	T	21.1	4.096356	0.76870	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.57107	0.42;0.42;0.59	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.59487	0.2197	N	0.19112	0.55	0.53005	D	0.999964	D;P;D	0.69078	0.997;0.769;0.997	D;P;D	0.78314	0.991;0.451;0.991	T	0.65195	-0.6227	10	0.87932	D	0	.	15.3625	0.74492	0.0:0.0:0.0:1.0	.	813;813;803	Q9Y4D8-2;Q9Y4D8;Q9Y4D8-3	.;K0614_HUMAN;.	I	1063;813;1089	ENSP00000366783:K1063I;ENSP00000404379:K813I;ENSP00000449784:K1089I	ENSP00000366783:K1063I	K	-	2	0	C12orf51	111173170	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.671000	0.83941	2.234000	0.73211	0.533000	0.62120	AAA	.	.		0.393	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		A	112688787	T	A	112688787	3	1	73	1	0	0	0	0	1	0	0	0	1698	1841	64	4	9764	4	C12orf51	12	112688787	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2123540	112688787	21163108	429	9755										
MED13L	23389	hgsc.bcm.edu	37	chr12	116446847	116446847	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gaagcaggaggtggtaaagaTgaagatgatgatggtcctgc	16	4	0	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:116446847T>C	ENST00000281928.3	-	10	1577	c.1371A>G	c.(1369-1371)tcA>tcG	p.S457S		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	457						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		GTGGTAAAGATGAAGATGATG	0.453																																					p.S457S		Atlas-SNP	.											.	MED13L	193	.	0			c.A1371G						.						209	202	205					12																	116446847		2203	4300	6503	SO:0001819	synonymous_variant	23389	exon10			TAAAGATGAAGAT	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.1371A>G	chr12.hg19:g.116446847T>C		123.0	0.0		123.0	41.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	hg19	CCDS9177.1																																																																																			.	.		0.453	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			C	116446847	T	C	116446847	2	2	73	1	0	0	0	0	0	0	0	1	9440	1451	51	2		2	MED13L	12	116446847	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3758060	116446847	17405048	430	9756										
SRRM4	84530	hgsc.bcm.edu	37	chr12	119554788	119554788	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcaagaaaaagaagaagaaaAgttccaagaaacacaagcga	8	6	1	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:119554788A>T	ENST00000267260.4	+	4	800	c.412A>T	c.(412-414)Agt>Tgt	p.S138C	RP11-364C11.2_ENST00000537730.1_RNA	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	138	Lys-rich.|Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						GAAGAAGAAAAGTTCCAAGAA	0.493																																					p.S138C		Atlas-SNP	.											.	SRRM4	131	.	0			c.A412T						.						76	71	72					12																	119554788		1851	4093	5944	SO:0001583	missense	84530	exon4			AAGAAAAGTTCCA	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"neural-specific SR-related protein of 100 kDa"	613103	"KIAA1853"	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.412A>T	chr12.hg19:g.119554788A>T	ENSP00000267260:p.Ser138Cys	70.0	0.0		60.0	25.0	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	hg19	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	A	15.48	2.844623	0.51164	.	.	ENSG00000139767	ENST00000267260	T	0.32988	1.43	5.46	1.8	0.24995	.	0.251456	0.44285	D	0.000475	T	0.38852	0.1056	L	0.61218	1.895	0.28639	N	0.907261	D	0.53885	0.963	P	0.54026	0.74	T	0.25916	-1.0118	10	0.54805	T	0.06	-2.6946	7.5081	0.27558	0.7401:0.0:0.2599:0.0	.	138	A7MD48	SRRM4_HUMAN	C	138	ENSP00000267260:S138C	ENSP00000267260:S138C	S	+	1	0	SRRM4	118039171	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	1.570000	0.36439	0.115000	0.18071	-0.264000	0.10439	AGT	.	.		0.493	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		T	119554788	A	T	119554788	3	4	73	1	0	0	0	0	1	0	0	0	15186	72	3	4	426	4	SRRM4	12	119554788	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3107941	119554788	14297107	431	9757										
CIT	11113	hgsc.bcm.edu	37	chr12	120271925	120271925	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atcagatgaacgctgtgaacAgccaaaatcagctcagctag	9	10	3	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:120271925A>T	ENST00000261833.7	-	6	676	c.624T>A	c.(622-624)gcT>gcA	p.A208A	CIT_ENST00000392521.2_Silent_p.A208A	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	208	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		CGCTGTGAACAGCCAAAATCA	0.438																																					p.A208A		Atlas-SNP	.											.	CIT	535	.	0			c.T624A						.						129	111	117					12																	120271925		2203	4300	6503	SO:0001819	synonymous_variant	11113	exon6			GTGAACAGCCAAA	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.624T>A	chr12.hg19:g.120271925A>T		147.0	0.0		122.0	45.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	hg19	CCDS9192.1																																																																																			.	.		0.438	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120271925	A	T	120271925	2	4	73	1	0	0	0	0	0	0	0	1	3440	175	7	4		4	CIT	12	120271925	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	717137	120271925	13579970	432	9758										
WDR66	144406	hgsc.bcm.edu	37	chr12	122413230	122413230	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtctggtggccgggaaggaaAattctacagggtaattgtcc	14	7	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:122413230A>G	ENST00000288912.4	+	18	3706	c.2852A>G	c.(2851-2853)aAa>aGa	p.K951R		NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	951							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		CGGGAAGGAAAATTCTACAGG	0.463																																					p.K951R	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.A2852G						.						81	83	83					12																	122413230		2021	4185	6206	SO:0001583	missense	144406	exon18			AAGGAAAATTCTA	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"WD repeat domain containing"	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.2852A>G	chr12.hg19:g.122413230A>G	ENSP00000288912:p.Lys951Arg	200.0	0.0		156.0	55.0	NM_144668	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	hg19	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	A	13.65	2.299165	0.40694	.	.	ENSG00000158023	ENST00000288912	T	0.05139	3.49	5.41	4.26	0.50523	.	0.643093	0.16036	N	0.232659	T	0.04182	0.0116	N	0.22421	0.69	0.80722	D	1	B	0.22211	0.066	B	0.17098	0.017	T	0.38908	-0.9639	10	0.13108	T	0.6	.	6.9235	0.24401	0.7937:0.0:0.0729:0.1334	.	951	Q8TBY9	WDR66_HUMAN	R	951	ENSP00000288912:K951R	ENSP00000288912:K951R	K	+	2	0	WDR66	120897613	0.997000	0.39634	0.999000	0.59377	0.981000	0.71138	2.124000	0.42006	0.892000	0.36259	0.460000	0.39030	AAA	.	.		0.463	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		G	122413230	A	G	122413230	3	3	73	1	0	0	0	0	1	0	0	0	17332	14	1	2	2977	2	WDR66	12	122413230	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2141305	122413230	11438665	433	9759										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126138603	126138603	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagggaagaataagttactcAaaagtggtggtccagatgcc	12	6	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:126138603A>G	ENST00000299308.3	+	9	2592	c.2584A>G	c.(2584-2586)Aaa>Gaa	p.K862E	TMEM132B_ENST00000535886.1_Missense_Mutation_p.K374E	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	862						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		TAAGTTACTCAAAAGTGGTGG	0.522																																					p.K862E		Atlas-SNP	.											.	TMEM132B	207	.	0			c.A2584G						.						62	61	61					12																	126138603		1937	4125	6062	SO:0001583	missense	114795	exon9			TTACTCAAAAGTG	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.2584A>G	chr12.hg19:g.126138603A>G	ENSP00000299308:p.Lys862Glu	132.0	0.0		91.0	44.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	hg19	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	A	2.696	-0.271980	0.05716	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.13657	2.57;2.57	5.15	2.78	0.32641	.	1.853410	0.02513	N	0.091793	T	0.07188	0.0182	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.35001	-0.9806	10	0.06365	T	0.9	.	0.2151	0.00161	0.2959:0.2961:0.1783:0.2297	.	862	Q14DG7	T132B_HUMAN	E	862;374	ENSP00000299308:K862E;ENSP00000440436:K374E	ENSP00000299308:K862E	K	+	1	0	TMEM132B	124704556	0.975000	0.34042	0.007000	0.13788	0.718000	0.41266	3.214000	0.51161	0.777000	0.33496	0.533000	0.62120	AAA	.	.		0.522	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		G	126138603	A	G	126138603	3	3	73	1	0	0	0	0	1	0	0	0	16061	131	5	2	2618	2	TMEM132B	12	126138603	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3725373	126138603	7713292	434	9760										
GPR133	283383	hgsc.bcm.edu	37	chr12	131456098	131456098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtacaacagctcctgcatcAgcaagccagagcagtgtggc	12	12	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:131456098A>G	ENST00000261654.5	+	4	842	c.283A>G	c.(283-285)Agc>Ggc	p.S95G	GPR133_ENST00000535015.1_Missense_Mutation_p.S127G	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	95					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		CTCCTGCATCAGCAAGCCAGA	0.512																																					p.S95G		Atlas-SNP	.											.	GPR133	136	.	0			c.A283G						.						73	60	64					12																	131456098		2203	4300	6503	SO:0001583	missense	283383	exon4			TGCATCAGCAAGC	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"-", "GPCR / Class B : Orphans"	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.283A>G	chr12.hg19:g.131456098A>G	ENSP00000261654:p.Ser95Gly	85.0	0.0		77.0	34.0	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	hg19	CCDS9272.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.852193	0.51270	.	.	ENSG00000111452	ENST00000261654;ENST00000542091;ENST00000535015	T;T;T	0.60040	0.5;0.22;0.52	4.73	4.73	0.59995	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.100619	0.64402	D	0.000003	T	0.69762	0.3147	M	0.70595	2.14	0.80722	D	1	D;D	0.58620	0.983;0.979	P;P	0.59171	0.853;0.807	T	0.73783	-0.3874	10	0.72032	D	0.01	.	11.9648	0.53029	1.0:0.0:0.0:0.0	.	127;95	B7ZLF7;Q6QNK2	.;GP133_HUMAN	G	95;95;127	ENSP00000261654:S95G;ENSP00000442501:S95G;ENSP00000444425:S127G	ENSP00000261654:S95G	S	+	1	0	GPR133	130022051	1.000000	0.71417	0.018000	0.16275	0.002000	0.02628	6.032000	0.70918	1.775000	0.52247	0.533000	0.62120	AGC	.	.		0.512	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		G	131456098	A	G	131456098	3	3	73	1	0	0	0	0	1	0	0	0	6651	188	7	2	297	2	GPR133	12	131456098	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	5317495	131456098	2395797	435	9761										
ULK1	8408	hgsc.bcm.edu	37	chr12	132393332	132393332	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccaaccccgccggccgccgcGccaaccccaacagcatccgc	8	24	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:132393332G>T	ENST00000321867.4	+	6	811	c.460G>T	c.(460-462)Gcc>Tcc	p.A154S		NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	154	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		CGGCCGCCGCGCCAACCCCAA	0.721																																					p.A154S		Atlas-SNP	.											.	ULK1	92	.	0			c.G460T						.						19	23	21					12																	132393332		2197	4290	6487	SO:0001583	missense	8408	exon6			CGCCGCGCCAACC	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"ATG1 autophagy related 1 homolog (S. cerevisiae)"	603168	"unc-51 (C. elegans)-like kinase 1", "unc-51-like kinase 1 (C. elegans)"			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.460G>T	chr12.hg19:g.132393332G>T	ENSP00000324560:p.Ala154Ser	44.0	0.0		37.0	19.0	NM_003565	Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	hg19	CCDS9274.1	.	.	.	.	.	.	.	.	.	.	G	8.845	0.943181	0.18281	.	.	ENSG00000177169	ENST00000321867;ENST00000537421;ENST00000542313	T;T;T	0.72942	-0.29;-0.7;-0.27	5.51	2.36	0.29203	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.067840	0.64402	D	0.000011	T	0.43188	0.1236	N	0.10874	0.06	0.80722	D	1	B	0.13145	0.007	B	0.15052	0.012	T	0.18178	-1.0345	10	0.07482	T	0.82	-30.3342	7.4252	0.27094	0.0878:0.0:0.3662:0.546	.	154	O75385	ULK1_HUMAN	S	154;71;48	ENSP00000324560:A154S;ENSP00000438953:A71S;ENSP00000444983:A48S	ENSP00000324560:A154S	A	+	1	0	ULK1	130959285	0.998000	0.40836	0.902000	0.35471	0.960000	0.62799	2.453000	0.44970	0.676000	0.31285	0.455000	0.32223	GCC	.	.		0.721	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			T	132393332	G	T	132393332	3	4	73	1	0	0	0	0	1	0	0	0	16990	1087	38	1	482	1	ULK1	12	132393332	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	937234	132393332	1458563	436	9762										
PUS1	80324	hgsc.bcm.edu	37	chr12	132423731	132423731	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tttacagggtgtgtccgcagCcggccaggtggtatccctga	14	11	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr12:132423731C>A	ENST00000376649.3	+	4	955	c.455C>A	c.(454-456)gCc>gAc	p.A152D	PUS1_ENST00000440818.2_Missense_Mutation_p.A124D|PUS1_ENST00000542167.2_Missense_Mutation_p.A99D|PUS1_ENST00000443358.2_Missense_Mutation_p.A124D|PUS1_ENST00000535067.1_Intron	NM_025215.5	NP_079491.2	Q9Y606	TRUA_HUMAN	pseudouridylate synthase 1	152					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|tRNA pseudouridine synthesis (GO:0031119)	mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)|pseudouridylate synthase activity (GO:0004730)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	11	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.05e-08)|Epithelial(86;2.51e-07)|all cancers(50;2.94e-07)		GTGTCCGCAGCCGGCCAGGTG	0.557																																					p.A152D	Esophageal Squamous(102;671 2009 17384 45666)	Atlas-SNP	.											.	PUS1	47	.	0			c.C455A						.						78	53	62					12																	132423731		2192	4274	6466	SO:0001583	missense	80324	exon4			CCGCAGCCGGCCA	AF116238	CCDS9275.2, CCDS31928.1	12q24	2004-05-17			ENSG00000177192	ENSG00000177192			15508	protein-coding gene	gene with protein product		608109				10094309	Standard	NM_001002019		Approved		uc001ujf.3	Q9Y606	OTTHUMG00000128507	ENST00000376649.3:c.455C>A	chr12.hg19:g.132423731C>A	ENSP00000365837:p.Ala152Asp	100.0	0.0		88.0	42.0	NM_025215	A8K877|B3KQC1|Q8WYT2|Q9BU44	Missense_Mutation	SNP	ENST00000376649.3	hg19	CCDS9275.2	.	.	.	.	.	.	.	.	.	.	C	18.22	3.575321	0.65878	.	.	ENSG00000177192	ENST00000443358;ENST00000376649;ENST00000322060;ENST00000440818;ENST00000542167;ENST00000538037	T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38	4.83	3.94	0.45596	Pseudouridine synthase I, TruA, N-terminal (1);Pseudouridine synthase, catalytic domain (1);Pseudouridine synthase I, TruA, alpha/beta domain (1);	0.052313	0.85682	D	0.000000	T	0.74816	0.3766	M	0.89478	3.035	0.58432	D	0.999996	D;D	0.67145	0.996;0.994	D;D	0.71656	0.956;0.974	T	0.79964	-0.1581	10	0.62326	D	0.03	-22.042	13.6514	0.62312	0.0:0.9242:0.0:0.0758	.	99;152	F5H1S9;Q9Y606	.;TRUA_HUMAN	D	124;152;124;124;99;124	ENSP00000392451:A124D;ENSP00000365837:A152D;ENSP00000324726:A124D;ENSP00000400032:A124D;ENSP00000438948:A99D;ENSP00000440326:A124D	ENSP00000324726:A124D	A	+	2	0	PUS1	130989684	0.999000	0.42202	0.124000	0.21820	0.764000	0.43329	4.009000	0.57110	1.167000	0.42706	0.305000	0.20034	GCC	.	.		0.557	PUS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250313.2	NM_025215		A	132423731	C	A	132423731	3	1	73	1	0	0	0	0	1	0	0	0	12845	739	26	3	469	3	PUS1	12	132423731	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	30399	132423731	1428164	437	9763										
MTUS2	23281	hgsc.bcm.edu	37	chr13	30066785	30066785	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttaatgtcttctttccagaaTtgatgtccactcatgagctt	6	9	3	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr13:30066785T>C	ENST00000380808.2	+	5	661	c.445T>C	c.(445-447)Ttg>Ctg	p.L149L	MTUS2-AS1_ENST00000323380.5_RNA|MTUS2_ENST00000431530.3_Silent_p.L1180L|MTUS2_ENST00000542829.1_Silent_p.L59L	NM_015233.5	NP_056048.1	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	1170						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CTTTCCAGAATTGATGTCCAC	0.348																																					p.L1180L		Atlas-SNP	.											.	MTUS2	279	.	0			c.T3538C						.						88	80	82					13																	30066785		1812	4075	5887	SO:0001819	synonymous_variant	23281	exon10			CCAGAATTGATGT	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000380808.2:c.445T>C	chr13.hg19:g.30066785T>C		99.0	0.0		98.0	35.0	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Silent	SNP	ENST00000380808.2	hg19	CCDS41874.1																																																																																			.	.		0.348	MTUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044335.2	XM_166270		C	30066785	T	C	30066785	2	2	73	1	0	0	0	0	0	0	0	1	9975	1490	52	2		2	MTUS2	13	30066785	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10		30066785	85103093	438	9764										
NBEA	26960	hgsc.bcm.edu	37	chr13	35729982	35729982	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccagattctacagtgaaaatTcagaatccaagtgagcaaat	7	8	2	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr13:35729982T>A	ENST00000400445.3	+	19	3051	c.2517T>A	c.(2515-2517)atT>atA	p.I839I	NBEA_ENST00000379939.2_Silent_p.I839I|NBEA_ENST00000310336.4_Silent_p.I839I|NBEA_ENST00000540320.1_Silent_p.I839I	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	839					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CAGTGAAAATTCAGAATCCAA	0.373																																					p.I839I		Atlas-SNP	.											.	NBEA	340	.	0			c.T2517A						.						110	105	107					13																	35729982		1897	4124	6021	SO:0001819	synonymous_variant	26960	exon19			GAAAATTCAGAAT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.2517T>A	chr13.hg19:g.35729982T>A		62.0	0.0		90.0	18.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.373	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35729982	T	A	35729982	2	1	73	1	0	0	0	0	0	0	0	1	10196	1771	62	4		4	NBEA	13	35729982	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	5663197	35729982	79439896	439	9765										
MAB21L1	4081	hgsc.bcm.edu	37	chr13	36049699	36049699	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccggttgggtcccggccaggGgatgtggggaagtggccagt	20	9	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr13:36049699G>T	ENST00000379919.4	-	1	1133	c.577C>A	c.(577-579)Ccc>Acc	p.P193T	NBEA_ENST00000400445.3_Intron|NBEA_ENST00000379939.2_Intron|NBEA_ENST00000310336.4_Intron|NBEA_ENST00000537702.1_5'Flank|NBEA_ENST00000540320.1_Intron	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)	193					anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		CCCGGCCAGGGGATGTGGGGA	0.622																																					p.P193T		Atlas-SNP	.											.	MAB21L1	52	.	0			c.C577A						.						44	51	48					13																	36049699		2203	4299	6502	SO:0001583	missense	4081	exon1			GCCAGGGGATGTG	BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"mab-21 (C. elegans)-like 1"			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.577C>A	chr13.hg19:g.36049699G>T	ENSP00000369251:p.Pro193Thr	55.0	0.0		34.0	12.0	NM_005584	Q6I9T5	Missense_Mutation	SNP	ENST00000379919.4	hg19	CCDS9353.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.440279	0.43326	.	.	ENSG00000180660	ENST00000379919	T	0.07688	3.17	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.08846	0.0219	L	0.35414	1.06	0.80722	D	1	B	0.18013	0.025	B	0.22601	0.04	T	0.26360	-1.0105	10	0.09338	T	0.73	-14.4518	19.9576	0.97228	0.0:0.0:1.0:0.0	.	193	Q13394	MB211_HUMAN	T	193	ENSP00000369251:P193T	ENSP00000369251:P193T	P	-	1	0	MAB21L1	34947699	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.736000	0.93811	0.655000	0.94253	CCC	.	.		0.622	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584		T	36049699	G	T	36049699	3	4	73	1	0	0	0	0	1	0	0	0	9150	1232	43	3	506	3	MAB21L1	13	36049699	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	319717	36049699	79120179	440	9766										
SLITRK6	84189	hgsc.bcm.edu	37	chr13	86368800	86368800	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caatagtgatgaacataatcAgaagtcccaatattagaaca	6	7	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr13:86368800A>C	ENST00000400286.2	-	2	2442	c.1844T>G	c.(1843-1845)cTg>cGg	p.L615R		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	615					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		GAACATAATCAGAAGTCCCAA	0.413																																					p.L615R		Atlas-SNP	.											.	SLITRK6	150	.	0			c.T1844G						.						131	125	127					13																	86368800		1975	4162	6137	SO:0001583	missense	84189	exon2			ATAATCAGAAGTC	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.1844T>G	chr13.hg19:g.86368800A>C	ENSP00000383143:p.Leu615Arg	194.0	0.0		173.0	69.0	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	hg19	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.183236	0.57800	.	.	ENSG00000184564	ENST00000400286	T	0.66460	-0.21	5.65	5.65	0.86999	.	0.000000	0.56097	U	0.000022	T	0.81749	0.4888	M	0.76838	2.35	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.83790	0.0230	10	0.62326	D	0.03	-3.8014	14.6942	0.69110	1.0:0.0:0.0:0.0	.	615	Q9H5Y7	SLIK6_HUMAN	R	615	ENSP00000383143:L615R	ENSP00000383143:L615R	L	-	2	0	SLITRK6	85266801	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	9.339000	0.96797	2.146000	0.66826	0.533000	0.62120	CTG	.	.		0.413	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		C	86368800	A	C	86368800	3	2	73	1	0	0	0	0	1	0	0	0	14762	188	7	5	685	5	SLITRK6	13	86368800	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	50319101	86368800	28801078	441	9767										
ABCC4	10257	hgsc.bcm.edu	37	chr13	95858957	95858957	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtgaaggtcacaaacacgatGattttgcttgcactgaaaaa	9	7	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr13:95858957G>T	ENST00000376887.4	-	8	1104	c.990C>A	c.(988-990)atC>atA	p.I330I	ABCC4_ENST00000431522.1_Silent_p.I330I|ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000536256.1_Silent_p.I255I|ABCC4_ENST00000412704.1_Silent_p.I330I	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	330	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	CAAACACGATGATTTTGCTTG	0.502																																					p.I330I		Atlas-SNP	.											.	ABCC4	248	.	0			c.C990A						.						166	152	157					13																	95858957		2203	4300	6503	SO:0001819	synonymous_variant	10257	exon8			CACGATGATTTTG	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"ATP binding cassette transporters / subfamily C"	55	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter (ABC superfamily)", "bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)", "multidrug resistance-associated protein 4", "multispecific organic anion transporter B"	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.990C>A	chr13.hg19:g.95858957G>T		168.0	0.0		120.0	58.0	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	hg19	CCDS9474.1																																																																																			.	.		0.502	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845		T	95858957	G	T	95858957	2	4	73	1	0	0	0	0	0	0	0	1	55	1280	45	3		3	ABCC4	13	95858957	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	9490157	95858957	19310921	442	9768										
DZIP1	22873	hgsc.bcm.edu	37	chr13	96237036	96237036	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aatgcgccccaggcatttagCacatgagcaaaatgtggttc	10	10	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr13:96237036C>A	ENST00000376829.2	-	22	3329	c.2478G>T	c.(2476-2478)gtG>gtT	p.V826V	DZIP1_ENST00000347108.3_Silent_p.V826V|DZIP1_ENST00000361396.2_Silent_p.V807V|DZIP1_ENST00000361156.3_Silent_p.V807V	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	826					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			AGGCATTTAGCACATGAGCAA	0.428																																					p.V826V		Atlas-SNP	.											.	DZIP1	195	.	0			c.G2478T						.						119	119	119					13																	96237036		2203	4300	6503	SO:0001819	synonymous_variant	22873	exon22			ATTTAGCACATGA	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.2478G>T	chr13.hg19:g.96237036C>A		181.0	0.0		123.0	50.0	NM_198968	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Silent	SNP	ENST00000376829.2	hg19	CCDS9478.1																																																																																			.	.		0.428	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		A	96237036	C	A	96237036	2	1	73	1	0	0	0	0	0	0	0	1	4865	697	25	3		3	DZIP1	13	96237036	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	378079	96237036	18932842	443	9769										
EFNB2	1948	hgsc.bcm.edu	37	chr13	107145427	107145427	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttcgccgggctctgcgggggCatctcctggacgatgtacac	14	13	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr13:107145427C>T	ENST00000245323.4	-	5	1112	c.963G>A	c.(961-963)atG>atA	p.M321I		NM_004093.3	NP_004084.1	P52799	EFNB2_HUMAN	ephrin-B2	321					anatomical structure morphogenesis (GO:0009653)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|lymph vessel development (GO:0001945)|negative regulation of keratinocyte proliferation (GO:0010839)|organ morphogenesis (GO:0009887)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|regulation of chemotaxis (GO:0050920)|viral process (GO:0016032)	focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)	p.M321I(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					TCTGCGGGGGCATCTCCTGGA	0.587																																					p.M321I		Atlas-SNP	.											EFNB2,NS,carcinoma,0,1	EFNB2	39	.	1	Substitution - Missense(1)	lung(1)	c.G963A						.						68	64	65					13																	107145427		2203	4300	6503	SO:0001583	missense	1948	exon5			CGGGGGCATCTCC	L38734	CCDS9507.1	13q33	2011-03-09			ENSG00000125266	ENSG00000125266		"Ephrins"	3227	protein-coding gene	gene with protein product	"HTK ligand", "ligand of eph-related kinase 5", "eph-related receptor tyrosine kinase ligand 5"	600527		EPLG5		7833926	Standard	NM_004093		Approved	LERK5, Htk-L, HTKL, MGC126226, MGC126227, MGC126228	uc001vqi.3	P52799	OTTHUMG00000017324	ENST00000245323.4:c.963G>A	chr13.hg19:g.107145427C>T	ENSP00000245323:p.Met321Ile	32.0	0.0		32.0	9.0	NM_004093	Q5JV56	Missense_Mutation	SNP	ENST00000245323.4	hg19	CCDS9507.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.874887	0.72180	.	.	ENSG00000125266	ENST00000245323	D	0.91124	-2.79	5.6	5.6	0.85130	.	0.142496	0.85682	D	0.000000	D	0.87188	0.6115	L	0.54323	1.7	0.80722	D	1	P	0.37276	0.589	B	0.32393	0.145	D	0.85115	0.0965	10	0.10902	T	0.67	.	19.6251	0.95674	0.0:1.0:0.0:0.0	.	321	P52799	EFNB2_HUMAN	I	321	ENSP00000245323:M321I	ENSP00000245323:M321I	M	-	3	0	EFNB2	105943428	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.020000	0.70826	2.636000	0.89361	0.655000	0.94253	ATG	.	.		0.587	EFNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045733.4	NM_004093		T	107145427	C	T	107145427	3	4	73	1	0	0	0	0	1	0	0	0	4958	710	25	3	42	3	EFNB2	13	107145427	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	10908391	107145427	8024451	444	9770										
ARHGEF7	8874	hgsc.bcm.edu	37	chr13	111938504	111938504	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctttccctaggatcttagtaAgagccctaagaccatgaaaa	7	10	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr13:111938504A>G	ENST00000375741.2	+	18	2274	c.2024A>G	c.(2023-2025)aAg>aGg	p.K675R	ARHGEF7_ENST00000317133.5_Missense_Mutation_p.K654R|ARHGEF7_ENST00000375739.2_Missense_Mutation_p.K625R|ARHGEF7_ENST00000375736.4_Missense_Mutation_p.K497R|ARHGEF7_ENST00000478679.1_Missense_Mutation_p.K419R|ARHGEF7_ENST00000375723.1_Missense_Mutation_p.K497R|ARHGEF7_ENST00000426073.2_Missense_Mutation_p.K497R|ARHGEF7_ENST00000218789.5_Missense_Mutation_p.K497R|ARHGEF7_ENST00000375737.5_Missense_Mutation_p.K572R|ARHGEF7_ENST00000370623.3_Missense_Mutation_p.K582R	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	675					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			GATCTTAGTAAGAGCCCTAAG	0.458																																					p.K675R		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.A2024G						.						78	76	76					13																	111938504		2203	4300	6503	SO:0001583	missense	8874	exon18			TTAGTAAGAGCCC	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.2024A>G	chr13.hg19:g.111938504A>G	ENSP00000364893:p.Lys675Arg	80.0	0.0		78.0	8.0	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Missense_Mutation	SNP	ENST00000375741.2	hg19	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.290528	0.40494	.	.	ENSG00000102606	ENST00000317133;ENST00000375741;ENST00000375739;ENST00000370623;ENST00000545635;ENST00000218789;ENST00000375736;ENST00000426073;ENST00000375737;ENST00000375723;ENST00000478679	T;T;T;T;T;T;T;T;T;T	0.65178	0.43;0.41;0.42;0.44;0.42;0.45;0.45;0.47;0.38;-0.14	4.6	3.36	0.38483	.	0.050134	0.85682	N	0.000000	T	0.58293	0.2112	M	0.65498	2.005	0.80722	D	1	B;B;B;B;B;B	0.32620	0.058;0.378;0.006;0.012;0.058;0.029	B;B;B;B;B;B	0.35727	0.102;0.115;0.033;0.034;0.162;0.209	T	0.50915	-0.8771	10	0.24483	T	0.36	.	10.241	0.43312	0.9198:0.0:0.0802:0.0	.	419;572;497;625;675;654	E9PDQ5;B7Z6G2;Q14155-6;Q14155-2;Q14155;Q14155-3	.;.;.;.;ARHG7_HUMAN;.	R	654;675;625;582;652;497;497;497;572;497;419	ENSP00000325994:K654R;ENSP00000364893:K675R;ENSP00000364891:K625R;ENSP00000359657:K582R;ENSP00000218789:K497R;ENSP00000364888:K497R;ENSP00000397068:K497R;ENSP00000364889:K572R;ENSP00000364875:K497R;ENSP00000417596:K419R	ENSP00000218789:K497R	K	+	2	0	ARHGEF7	110736505	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.646000	0.74348	0.578000	0.29487	0.459000	0.35465	AAG	.	.		0.458	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511		G	111938504	A	G	111938504	3	3	73	1	0	0	0	0	1	0	0	0	911	72	3	2	2094	2	ARHGEF7	13	111938504	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4793077	111938504	3231374	445	9771										
MYH6	4624	hgsc.bcm.edu	37	chr14	23865974	23865974	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagcttctctgtccccttccTgctatcaatgaactgtccct	5	16	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:23865974T>G	ENST00000356287.3	-	18	2250	c.2221A>C	c.(2221-2223)Agg>Cgg	p.R741R	MYH6_ENST00000405093.3_Silent_p.R741R			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	741	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		GTCCCCTTCCTGCTATCAATG	0.547																																					p.R741R		Atlas-SNP	.											.	MYH6	274	.	0			c.A2221C						.						118	94	102					14																	23865974		2203	4300	6503	SO:0001819	synonymous_variant	4624	exon19			CCTTCCTGCTATC	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.2221A>C	chr14.hg19:g.23865974T>G		124.0	0.0		110.0	40.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	hg19	CCDS9600.1																																																																																			.	.		0.547	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			G	23865974	T	G	23865974	2	3	73	1	0	0	0	0	0	0	0	1	10047	1579	55	5		5	MYH6	14	23865974	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10		23865974	83483566	446	9772										
MYH7	4625	hgsc.bcm.edu	37	chr14	23901694	23901694	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcagctacactcacgtgatcAggatggactggttttctctg	11	10	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:23901694A>C	ENST00000355349.3	-	6	686	c.524T>G	c.(523-525)cTg>cGg	p.L175R		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	175	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCACGTGATCAGGATGGACTG	0.577																																					p.L175R		Atlas-SNP	.											MYH7,NS,carcinoma,0,1	MYH7	349	.	0			c.T524G						.						211	183	193					14																	23901694		2203	4300	6503	SO:0001583	missense	4625	exon6			GTGATCAGGATGG	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.524T>G	chr14.hg19:g.23901694A>C	ENSP00000347507:p.Leu175Arg	148.0	2.0		121.0	52.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.862269	0.71949	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.90004	-2.6	3.81	2.65	0.31530	Myosin head, motor domain (3);	.	.	.	.	D	0.96697	0.8922	H	0.99863	4.86	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.95429	0.8514	9	0.87932	D	0	.	8.6083	0.33786	0.9058:0.0:0.0942:0.0	.	175	P12883	MYH7_HUMAN	R	175	ENSP00000347507:L175R	ENSP00000347507:L175R	L	-	2	0	MYH7	22971534	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.043000	0.71004	1.503000	0.48686	0.379000	0.24179	CTG	.	.		0.577	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		C	23901694	A	C	23901694	3	2	73	1	0	0	0	0	1	0	0	0	10048	188	7	5	5423	5	MYH7	14	23901694	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	35720	23901694	83447846	447	9773										
RIPK3	11035	hgsc.bcm.edu	37	chr14	24806550	24806550	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gaaaccatgacatcattacgAgagtgctggttttctatggt	10	7	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:24806550A>T	ENST00000216274.5	-	8	1235	c.1017T>A	c.(1015-1017)tcT>tcA	p.S339S	ADCY4_ENST00000396747.3_5'Flank|RP11-934B9.3_ENST00000555591.1_Silent_p.S13S|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000418030.2_5'Flank|ADCY4_ENST00000554068.2_5'Flank|RIPK3_ENST00000554338.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	339					activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		CATCATTACGAGAGTGCTGGT	0.478																																					p.S339S	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.T1017A						.						145	152	150					14																	24806550		2203	4300	6503	SO:0001819	synonymous_variant	11035	exon8			ATTACGAGAGTGC	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.1017T>A	chr14.hg19:g.24806550A>T		52.0	0.0		28.0	13.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	hg19	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	A	3.581	-0.085654	0.07097	.	.	ENSG00000129465	ENST00000554569	.	.	.	2.42	1.19	0.21007	.	.	.	.	.	T	0.25382	0.0617	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23976	-1.0173	4	.	.	.	-2.5216	5.3014	0.15780	0.6998:0.3002:0.0:0.0	.	.	.	.	H	20	.	.	L	-	2	0	RIPK3	23876390	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	-0.381000	0.07417	0.308000	0.22923	0.533000	0.62120	CTC	.	.		0.478	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		T	24806550	A	T	24806550	2	4	73	1	0	0	0	0	0	0	0	1	13397	291	11	4		4	RIPK3	14	24806550	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	904856	24806550	82542990	448	9774										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31641123	31641123	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atgtaatgatgatgacctttGacctctattaacatctgcac	6	9	2	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:31641123G>A	ENST00000399332.1	-	8	1764	c.1276C>T	c.(1276-1278)Caa>Taa	p.Q426*	HECTD1_ENST00000553700.1_Nonsense_Mutation_p.Q426*	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	426					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		GATGACCTTTGACCTCTATTA	0.299																																					p.Q426X		Atlas-SNP	.											.	HECTD1	159	.	0			c.C1276T						.						96	91	92					14																	31641123		1833	4088	5921	SO:0001587	stop_gained	25831	exon8			ACCTTTGACCTCT	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.1276C>T	chr14.hg19:g.31641123G>A	ENSP00000382269:p.Gln426*	352.0	1.0		312.0	121.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Nonsense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	G	43	10.057843	0.99327	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000556224	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-2.0412	19.328	0.94270	0.0:0.0:1.0:0.0	.	.	.	.	X	426	.	ENSP00000261312:Q426X	Q	-	1	0	HECTD1	30710874	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.840000	0.99478	2.570000	0.86706	0.585000	0.79938	CAA	.	.		0.299	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			A	31641123	G	A	31641123	4	1	73	1	0	0	0	0	0	1	0	0	7048	1299	45	3	6700	3	HECTD1	14	31641123	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	6834573	31641123	75708417	449	9775										
NPAS3	64067	hgsc.bcm.edu	37	chr14	34269082	34269082	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggccacagctccagtaacccGgacagccgcgacagcgacga	12	16	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:34269082G>C	ENST00000356141.4	+	12	1569	c.1569G>C	c.(1567-1569)ccG>ccC	p.P523P	NPAS3_ENST00000551492.1_Silent_p.P528P|NPAS3_ENST00000346562.2_Silent_p.P491P|NPAS3_ENST00000548645.1_Silent_p.P493P|NPAS3_ENST00000357798.5_Silent_p.P510P			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	523					locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		CCAGTAACCCGGACAGCCGCG	0.637																																					p.P523P		Atlas-SNP	.											.	NPAS3	266	.	0			c.G1569C						.						51	54	53					14																	34269082		2203	4300	6503	SO:0001819	synonymous_variant	64067	exon12			TAACCCGGACAGC	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.1569G>C	chr14.hg19:g.34269082G>C		152.0	0.0		121.0	54.0	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Silent	SNP	ENST00000356141.4	hg19	CCDS53891.1																																																																																			.	.		0.637	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			C	34269082	G	C	34269082	2	2	73	1	0	0	0	0	0	0	0	1	10573	1103	39	4		4	NPAS3	14	34269082	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	2627959	34269082	73080458	450	9776										
CLEC14A	161198	hgsc.bcm.edu	37	chr14	38724410	38724410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccagctcgaagcccgtagcaCattcgcaggcaaagcctccc	9	17	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:38724410C>T	ENST00000342213.2	-	1	1164	c.818G>A	c.(817-819)tGt>tAt	p.C273Y		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	273	EGF-like.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		GCCCGTAGCACATTCGCAGGC	0.662																																					p.C273Y		Atlas-SNP	.											.	CLEC14A	83	.	0			c.G818A						.						65	71	69					14																	38724410		2203	4300	6503	SO:0001583	missense	161198	exon1			GTAGCACATTCGC		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"C-type lectin domain containing"	19832	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 27"	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.818G>A	chr14.hg19:g.38724410C>T	ENSP00000353013:p.Cys273Tyr	77.0	0.0		59.0	30.0	NM_175060	Q695G9|Q6PWT6|Q8N5V5	Missense_Mutation	SNP	ENST00000342213.2	hg19	CCDS9667.1	.	.	.	.	.	.	.	.	.	.	C	16.38	3.106350	0.56291	.	.	ENSG00000176435	ENST00000342213;ENST00000546356	D	0.99942	-8.46	3.91	3.91	0.45181	Epidermal growth factor-like (1);	0.000000	0.51477	D	0.000085	D	0.99851	0.9931	L	0.32530	0.975	0.39636	D	0.970256	D	0.89917	1.0	D	0.85130	0.997	D	0.94571	0.7771	10	0.87932	D	0	-7.9173	11.7127	0.51635	0.0:1.0:0.0:0.0	.	273	Q86T13	CLC14_HUMAN	Y	273;38	ENSP00000353013:C273Y	ENSP00000353013:C273Y	C	-	2	0	CLEC14A	37794161	0.997000	0.39634	0.985000	0.45067	0.740000	0.42216	2.690000	0.47001	2.498000	0.84270	0.591000	0.81541	TGT	.	.		0.662	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		T	38724410	C	T	38724410	3	4	73	1	0	0	0	0	1	0	0	0	3501	478	17	3	658	3	CLEC14A	14	38724410	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	4455328	38724410	68625130	451	9777										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42356398	42356398	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gataacattcctaaggggacCttctcccatttgcacaagat	7	11	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:42356398C>A	ENST00000298119.4	+	3	1759	c.570C>A	c.(568-570)acC>acA	p.T190T	LRFN5_ENST00000554171.1_Silent_p.T190T|LRFN5_ENST00000554120.1_Silent_p.T190T	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	190						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		CTAAGGGGACCTTCTCCCATT	0.423										HNSCC(30;0.082)																											p.T190T		Atlas-SNP	.											.	LRFN5	269	.	0			c.C570A						.						73	64	67					14																	42356398		2203	4300	6503	SO:0001819	synonymous_variant	145581	exon3			GGGGACCTTCTCC	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.570C>A	chr14.hg19:g.42356398C>A		86.0	0.0		91.0	38.0	NM_152447	B3KU78|Q86XL2	Silent	SNP	ENST00000298119.4	hg19	CCDS9678.1																																																																																			.	.		0.423	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		A	42356398	C	A	42356398	2	1	73	1	0	0	0	0	0	0	0	1	8950	668	24	3		3	LRFN5	14	42356398	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	3631988	42356398	64993142	452	9778										
DLGAP5	9787	hgsc.bcm.edu	37	chr14	55629758	55629758	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cacccagattcctcaagtttGatcagattgttgaatttgtg	8	8	2	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:55629758G>C	ENST00000247191.2	-	13	1800	c.1584C>G	c.(1582-1584)atC>atG	p.I528M	DLGAP5_ENST00000395425.2_Missense_Mutation_p.I528M	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	528					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						CCTCAAGTTTGATCAGATTGT	0.299																																					p.I528M		Atlas-SNP	.											.	DLGAP5	84	.	0			c.C1584G						.						93	91	92					14																	55629758		2203	4291	6494	SO:0001583	missense	9787	exon13			AAGTTTGATCAGA	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.1584C>G	chr14.hg19:g.55629758G>C	ENSP00000247191:p.Ile528Met	72.0	0.0		47.0	14.0	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	hg19	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	G	1.553	-0.538824	0.04053	.	.	ENSG00000126787	ENST00000395425;ENST00000247191	T;T	0.17054	2.3;2.3	4.83	-0.549	0.11829	.	0.981615	0.08346	N	0.960066	T	0.09774	0.0240	N	0.19112	0.55	0.09310	N	0.999995	B;B	0.14012	0.009;0.009	B;B	0.19666	0.026;0.016	T	0.38090	-0.9677	10	0.40728	T	0.16	.	3.2593	0.06843	0.221:0.3681:0.3117:0.0992	.	528;528	A8MTM6;Q15398	.;DLGP5_HUMAN	M	528	ENSP00000378815:I528M;ENSP00000247191:I528M	ENSP00000247191:I528M	I	-	3	3	DLGAP5	54699511	0.653000	0.27358	0.629000	0.29254	0.040000	0.13550	-0.031000	0.12287	-0.058000	0.13177	-0.237000	0.12165	ATC	.	.		0.299	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		C	55629758	G	C	55629758	3	2	73	1	0	0	0	0	1	0	0	0	4565	1280	45	4	1079	4	DLGAP5	14	55629758	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	13273360	55629758	51719782	453	9779										
ZFP36L1	677	hgsc.bcm.edu	37	chr14	69256435	69256435	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctcggacatgggccggaagaGgaaggtggtcggggagccac	19	9	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:69256435G>T	ENST00000439696.2	-	2	1133	c.832C>A	c.(832-834)Ctc>Atc	p.L278I	ZFP36L1_ENST00000336440.3_Missense_Mutation_p.L278I|ZFP36L1_ENST00000555997.1_3'UTR	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1	278					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GGCCGGAAGAGGAAGGTGGTC	0.632											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L347I		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.C1039A						.						54	65	61					14																	69256435		2203	4300	6503	SO:0001583	missense	677	exon3			GGAAGAGGAAGGT	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"RING-type (C3HC4) zinc fingers"	1107	protein-coding gene	gene with protein product		601064	"zinc finger protein, C3H type, 36-like 1", "zinc finger protein 36, C3H type-like 1"	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.832C>A	chr14.hg19:g.69256435G>T	ENSP00000388402:p.Leu278Ile	96.0	0.0	1113	63.0	34.0	NM_001244701	Q13851	Missense_Mutation	SNP	ENST00000439696.2	hg19	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759275	0.49468	.	.	ENSG00000185650	ENST00000439696;ENST00000336440;ENST00000435246	T;T	0.31247	1.5;1.5	4.38	4.38	0.52667	.	0.262799	0.32287	N	0.006310	T	0.21227	0.0511	L	0.33485	1.01	0.80722	D	1	P	0.37688	0.605	B	0.35039	0.194	T	0.03807	-1.1002	10	0.18276	T	0.48	-8.0209	12.6439	0.56723	0.0825:0.0:0.9175:0.0	.	278	Q07352	TISB_HUMAN	I	278;278;261	ENSP00000388402:L278I;ENSP00000337386:L278I	ENSP00000337386:L278I	L	-	1	0	ZFP36L1	68326188	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.780000	0.47742	2.271000	0.75665	0.591000	0.81541	CTC	.	.		0.632	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1			T	69256435	G	T	69256435	3	4	73	1	0	0	0	0	1	0	0	0	17661	1000	35	3	188	3	ZFP36L1	14	69256435	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	13626677	69256435	38093105	454	9780										
C14orf115	55237	hgsc.bcm.edu	37	chr14	74825421	74825421	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cggatgctggtgatggacatGatcgctaccacgaagttcaa	12	9	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:74825421G>T	ENST00000256362.4	+	2	2176	c.1935G>T	c.(1933-1935)atG>atT	p.M645I		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	645					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						TGATGGACATGATCGCTACCA	0.617																																					p.M645I		Atlas-SNP	.											.	VRTN	79	.	0			c.G1935T						.						69	53	58					14																	74825421		2203	4300	6503	SO:0001583	missense	55237	exon2			GGACATGATCGCT	AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 115", "vertebrae development homolog (pig)"	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.1935G>T	chr14.hg19:g.74825421G>T	ENSP00000256362:p.Met645Ile	125.0	0.0		126.0	49.0	NM_018228	Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	hg19	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	G	6.672	0.492606	0.12702	.	.	ENSG00000133980	ENST00000256362	T	0.40476	1.03	4.28	2.39	0.29439	.	0.075039	0.53938	U	0.000043	T	0.26557	0.0649	N	0.24115	0.695	0.28102	N	0.931388	B	0.10296	0.003	B	0.08055	0.003	T	0.18304	-1.0341	10	0.48119	T	0.1	-18.2477	9.1098	0.36720	0.1763:0.0:0.8237:0.0	.	645	Q9H8Y1	VRTN_HUMAN	I	645	ENSP00000256362:M645I	ENSP00000256362:M645I	M	+	3	0	VRTN	73895174	1.000000	0.71417	0.670000	0.29842	0.099000	0.18886	1.133000	0.31430	1.036000	0.39998	0.485000	0.47835	ATG	.	.		0.617	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228		T	74825421	G	T	74825421	3	4	73	1	0	0	0	0	1	0	0	0	1742	1290	45	3	1937	3	C14orf115	14	74825421	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	5568986	74825421	32524119	455	9781										
C14orf174	161394	hgsc.bcm.edu	37	chr14	77843998	77843998	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagaacgtgcagctgaaaccTggcgggacgtcccaggaagg	15	10	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:77843998T>A	ENST00000216471.4	+	1	523	c.237T>A	c.(235-237)ccT>ccA	p.P79P	SAMD15_ENST00000533095.2_Intron|TMED8_ENST00000216468.7_5'Flank	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	79										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						AGCTGAAACCTGGCGGGACGT	0.532																																					p.P79P		Atlas-SNP	.											.	SAMD15	60	.	0			c.T237A						.						107	105	105					14																	77843998		2203	4300	6503	SO:0001819	synonymous_variant	161394	exon1			GAAACCTGGCGGG	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"Sterile alpha motif (SAM) domain containing"	18631	protein-coding gene	gene with protein product			"family with sequence similarity 15, member A", "chromosome 14 open reading frame 174"	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.237T>A	chr14.hg19:g.77843998T>A		129.0	0.0		127.0	53.0	NM_001010860	Q2M3P3	Silent	SNP	ENST00000216471.4	hg19	CCDS32126.1																																																																																			.	.		0.532	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		A	77843998	T	A	77843998	2	1	73	1	0	0	0	0	0	0	0	1	1761	1567	55	4		4	C14orf174	14	77843998	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3018577	77843998	29505542	456	9782										
CATSPERB	79820	hgsc.bcm.edu	37	chr14	92126218	92126218	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acctttccacgttgagaaacAaaagtaatagctgatgtata	7	7	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:92126218A>G	ENST00000256343.3	-	15	1551	c.1395T>C	c.(1393-1395)ttT>ttC	p.F465F		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	465					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				GTTGAGAAACAAAAGTAATAG	0.348																																					p.F465F		Atlas-SNP	.											.	CATSPERB	114	.	0			c.T1395C						.						72	71	72					14																	92126218		2203	4300	6503	SO:0001819	synonymous_variant	79820	exon15			AGAAACAAAAGTA	AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.1395T>C	chr14.hg19:g.92126218A>G		52.0	0.0		34.0	13.0	NM_024764	A0AV51	Silent	SNP	ENST00000256343.3	hg19	CCDS32142.1																																																																																			.	.		0.348	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		G	92126218	A	G	92126218	2	3	73	1	0	0	0	0	0	0	0	1	2693	127	5	2		2	CATSPERB	14	92126218	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	14282220	92126218	15223322	457	9783										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94046694	94046694	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttgtgaactcctggagagacTagctcctaaagaagaaagcc	10	9	0	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:94046694T>A	ENST00000393151.2	+	19	2633	c.2633T>A	c.(2632-2634)cTa>cAa	p.L878Q	UNC79_ENST00000256339.4_Missense_Mutation_p.L701Q|UNC79_ENST00000553484.1_Missense_Mutation_p.L878Q|UNC79_ENST00000555664.1_Missense_Mutation_p.L878Q			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	878					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CTGGAGAGACTAGCTCCTAAA	0.458																																					p.L701Q		Atlas-SNP	.											.	UNC79	366	.	0			c.T2102A						.						75	80	78					14																	94046694		2203	4300	6503	SO:0001583	missense	57578	exon19			AGAGACTAGCTCC	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.2633T>A	chr14.hg19:g.94046694T>A	ENSP00000376858:p.Leu878Gln	102.0	0.0		104.0	53.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	T	23.0	4.366899	0.82463	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.25250	1.81;1.81;1.81;1.81	5.11	5.11	0.69529	.	0.000000	0.64402	D	0.000001	T	0.45856	0.1363	L	0.50333	1.59	0.49483	D	0.999797	D	0.76494	0.999	D	0.83275	0.996	T	0.44667	-0.9313	10	0.87932	D	0	-8.628	14.9032	0.70696	0.0:0.0:0.0:1.0	.	878	C9JQL1	.	Q	701;878;878;878;878	ENSP00000256339:L701Q;ENSP00000450868:L878Q;ENSP00000451360:L878Q;ENSP00000376858:L878Q	ENSP00000256339:L701Q	L	+	2	0	KIAA1409	93116447	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.817000	0.86213	1.938000	0.56188	0.459000	0.35465	CTA	.	.		0.458	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94046694	T	A	94046694	3	1	73	1	0	0	0	0	1	0	0	0	8239	1522	53	4	2164	4	KIAA1409	14	94046694	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1920476	94046694	13302846	458	9784										
DICER1	23405	hgsc.bcm.edu	37	chr14	95560494	95560494	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttctaagcgctggtaacaatCtgaggggatccgaagtggaa	13	7	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:95560494C>A	ENST00000526495.1	-	26	5387		c.e26-1		DICER1_ENST00000527414.1_Splice_Site|DICER1_ENST00000343455.3_Splice_Site|DICER1_ENST00000527416.2_5'Flank|DICER1_ENST00000556045.1_Splice_Site|DICER1_ENST00000393063.1_Splice_Site|DICER1_ENST00000541352.1_Splice_Site			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III						angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		TGGTAACAATCTGAGGGGATC	0.488			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												.		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.5096-1G>T						.						55	59	57					14																	95560494		2203	4300	6503	SO:0001630	splice_region_variant	23405	exon25	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	AACAATCTGAGGG	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.5096-1G>T	chr14.hg19:g.95560494C>A		60.0	0.0		47.0	17.0	NM_177438	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Splice_Site	SNP	ENST00000526495.1	hg19	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.008776	0.75046	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000556045;ENST00000541352	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2735	0.94021	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DICER1	94630247	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.421000	0.80204	2.549000	0.85964	0.655000	0.94253	.	.	.		0.488	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1		Intron	A	95560494	C	A	95560494	5	1	73	1	0	0	0	0	0	0	1	0	4523	927	32	3	689	3	DICER1	14	95560494	Splice_Site	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1513800	95560494	11789046	459	9785										
BDKRB2	624	hgsc.bcm.edu	37	chr14	96707662	96707662	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcctcaacccactggtgtacGtgatcgtgggcaagcgcttc	12	13	1	1	rs201791629		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:96707662G>T	ENST00000306005.3	+	3	1193	c.997G>T	c.(997-999)Gtg>Ttg	p.V333L	RP11-404P21.8_ENST00000553811.1_Intron|BDKRB2_ENST00000539359.1_Missense_Mutation_p.V306L|BDKRB2_ENST00000542454.2_Missense_Mutation_p.V306L|BDKRB2_ENST00000554311.1_Missense_Mutation_p.V333L	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	333					arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	ACTGGTGTACGTGATCGTGGG	0.562																																					p.V333L		Atlas-SNP	.											.	BDKRB2	56	.	0			c.G997T						.						77	67	71					14																	96707662		2203	4300	6503	SO:0001583	missense	624	exon3			GTGTACGTGATCG	S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"GPCR / Class A : Bradykinin receptors"	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.997G>T	chr14.hg19:g.96707662G>T	ENSP00000307713:p.Val333Leu	117.0	0.0		99.0	44.0	NM_000623		Missense_Mutation	SNP	ENST00000306005.3	hg19	CCDS9942.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.637872	0.87760	.	.	ENSG00000168398	ENST00000542454;ENST00000554311;ENST00000306005;ENST00000539359	T;T;T;T	0.19532	2.14;2.14;2.14;2.14	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.35480	0.0933	M	0.68952	2.095	0.58432	D	0.999994	D	0.56521	0.976	P	0.49999	0.628	T	0.30504	-0.9976	10	0.66056	D	0.02	-28.6288	17.779	0.88518	0.0:0.0:1.0:0.0	.	333	P30411	BKRB2_HUMAN	L	306;333;333;306	ENSP00000439459:V306L;ENSP00000450482:V333L;ENSP00000307713:V333L;ENSP00000438376:V306L	ENSP00000307713:V333L	V	+	1	0	BDKRB2	95777415	1.000000	0.71417	0.767000	0.31495	0.896000	0.52359	7.904000	0.87408	2.196000	0.70406	0.561000	0.74099	GTG	.	.		0.562	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1			T	96707662	G	T	96707662	3	4	73	1	0	0	0	0	1	0	0	0	1393	1145	40	1	1003	1	BDKRB2	14	96707662	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1147168	96707662	10641878	460	9786										
SETD3	84193	hgsc.bcm.edu	37	chr14	99865385	99865385	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	actgctttttccaaaatctcTttctcacctaagcgcaattt	3	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:99865385T>C	ENST00000331768.5	-	13	1575	c.1416A>G	c.(1414-1416)aaA>aaG	p.K472K		NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	472					histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				CCAAAATCTCTTTCTCACCTA	0.413																																					p.K472K		Atlas-SNP	.											.	SETD3	56	.	0			c.A1416G						.						96	97	96					14																	99865385		2203	4300	6503	SO:0001819	synonymous_variant	84193	exon13			AATCTCTTTCTCA	AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"chromosome 14 open reading frame 154"	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.1416A>G	chr14.hg19:g.99865385T>C		148.0	0.0		142.0	57.0	NM_032233	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Silent	SNP	ENST00000331768.5	hg19	CCDS9951.1																																																																																			.	.		0.413	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233		C	99865385	T	C	99865385	2	2	73	1	0	0	0	0	0	0	0	1	14147	1606	56	2		2	SETD3	14	99865385	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3157723	99865385	7484155	461	9787										
TDRD9	122402	hgsc.bcm.edu	37	chr14	104460669	104460669	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tccacttttttcttccctagGtctgggtgaaataaattata	6	8	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:104460669G>T	ENST00000409874.4	+	10	1229	c.1181G>T	c.(1180-1182)gGt>gTt	p.G394V	TDRD9_ENST00000339063.5_Splice_Site_p.G394V	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	394	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TCTTCCCTAGGTCTGGGTGAA	0.353																																					p.G394V		Atlas-SNP	.											.	TDRD9	175	.	0			c.G1181T						.						166	173	171					14																	104460669		2203	4300	6503	SO:0001630	splice_region_variant	122402	exon10			CCCTAGGTCTGGG	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1181-1G>T	chr14.hg19:g.104460669G>T		63.0	0.0		77.0	29.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Missense_Mutation	SNP	ENST00000409874.4	hg19	CCDS9987.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.2|23.2	4.384969|4.384969	0.82792|0.82792	.|.	.|.	ENSG00000156414|ENSG00000156414	ENST00000409874;ENST00000339063|ENST00000557332	T;T|.	0.06608|.	3.28;3.28|.	5.72|5.72	5.72|5.72	0.89469|0.89469	Helicase, C-terminal (1);|.	0.000000|.	0.64402|.	D|.	0.000011|.	D|D	0.91670|0.91670	0.7367|0.7367	H|H	0.99104|0.99104	4.43|4.43	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.998|.	D|D	0.94776|0.94776	0.7949|0.7949	9|5	.|.	.|.	.|.	.|.	19.4897|19.4897	0.95046|0.95046	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	394;394|.	Q8NDG6-2;Q8NDG6|.	.;TDRD9_HUMAN|.	V|S	394|120	ENSP00000387303:G394V;ENSP00000343545:G394V|.	.|.	G|R	+|+	2|3	0|2	TDRD9|TDRD9	103530422|103530422	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.943000|0.943000	0.58893|0.58893	7.849000|7.849000	0.86908|0.86908	2.711000|2.711000	0.92665|0.92665	0.655000|0.655000	0.94253|0.94253	GGT|AGG	.	.		0.353	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	Missense_Mutation	T	104460669	G	T	104460669	5	4	73	1	0	0	0	0	0	0	1	0	15751	1275	44	3	1219	3	TDRD9	14	104460669	Splice_Site	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	4595284	104460669	2888871	462	9788										
TMEM179	388021	hgsc.bcm.edu	37	chr14	105070865	105070865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctggcgagcaggctgaagcGgcaggcggccggcgggcccc	20	14	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr14:105070865G>A	ENST00000556573.1	-	1	455	c.214C>T	c.(214-216)Cgc>Tgc	p.R72C	TMEM179_ENST00000341595.3_Missense_Mutation_p.R72C			Q6ZVK1	T179A_HUMAN	transmembrane protein 179	72						integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|skin(1)	4			all cancers(16;0.00276)|OV - Ovarian serous cystadenocarcinoma(23;0.0262)|Epithelial(46;0.058)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.129)		AGGCTGAAGCGGCAGGCGGCC	0.701																																					p.R72C		Atlas-SNP	.											.	TMEM179	9	.	0			c.C214T						.						4	6	6					14																	105070865		1999	3949	5948	SO:0001583	missense	388021	exon1			TGAAGCGGCAGGC	AK124477	CCDS66723.1, CCDS73688.1	14q32.33	2012-04-11	2006-10-16	2006-10-16	ENSG00000258986	ENSG00000258986			20137	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 90"	C14orf90			Standard	NM_001286390		Approved	FLJ42486, TMEM179A	uc001yox.1	Q6ZVK1	OTTHUMG00000170829	ENST00000556573.1:c.214C>T	chr14.hg19:g.105070865G>A	ENSP00000450958:p.Arg72Cys	63.0	0.0		43.0	19.0	NM_207379		Missense_Mutation	SNP	ENST00000556573.1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.06	3.754837	0.69648	.	.	ENSG00000189203;ENSG00000258986;ENSG00000258986	ENST00000415614;ENST00000556573;ENST00000341595	T;T;T	0.19394	2.15;2.15;2.15	2.75	2.75	0.32379	.	0.246648	0.40144	N	0.001175	T	0.32436	0.0829	L	0.47716	1.5	0.54753	D	0.99998	D	0.89917	1.0	D	0.63703	0.917	T	0.04767	-1.0928	10	0.62326	D	0.03	.	9.233	0.37448	0.0:0.0:0.7836:0.2164	.	72	Q6ZVK1-2	.	C	72	ENSP00000397763:R72C;ENSP00000450958:R72C;ENSP00000340477:R72C	ENSP00000340477:R72C	R	-	1	0	RP11-614O9.3;TMEM179	104141910	1.000000	0.71417	0.999000	0.59377	0.945000	0.59286	4.372000	0.59530	1.352000	0.45808	0.462000	0.41574	CGC	.	.		0.701	TMEM179-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410585.1	NM_207379		A	105070865	G	A	105070865	3	1	73	1	0	0	0	0	1	0	0	0	16111	1116	39	1	391	1	TMEM179	14	105070865	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	610196	105070865	2278675	463	9789										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24921224	24921224	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atcttcgtcgcccctaagagGccgtgtcctctccctcgggc	10	17	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:24921224G>T	ENST00000329468.2	+	1	684	c.210G>T	c.(208-210)agG>agT	p.R70S		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	70					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CCCCTAAGAGGCCGTGTCCTC	0.706																																					p.R70S		Atlas-SNP	.											.	.	.	.	0			c.G210T						.						17	21	20					15																	24921224		2189	4273	6462	SO:0001583	missense	23742	exon1			TAAGAGGCCGTGT	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.210G>T	chr15.hg19:g.24921224G>T	ENSP00000333735:p.Arg70Ser	39.0	0.0		46.0	21.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	13.47	2.248089	0.39697	.	.	ENSG00000185823	ENST00000329468	T	0.29917	1.55	2.45	1.51	0.23008	.	0.209142	0.24238	N	0.040283	T	0.36026	0.0952	L	0.34521	1.04	0.09310	N	1	D	0.76494	0.999	D	0.74023	0.982	T	0.05225	-1.0898	10	0.59425	D	0.04	.	5.2401	0.15467	0.1721:0.0:0.8279:0.0	.	70	Q9NZP6	CO002_HUMAN	S	70	ENSP00000333735:R70S	ENSP00000333735:R70S	R	+	3	2	C15orf2	22472317	0.001000	0.12720	0.004000	0.12327	0.003000	0.03518	0.422000	0.21296	0.594000	0.29761	0.484000	0.47621	AGG	.	.		0.706	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24921224	G	T	24921224	3	4	73	1	0	0	0	0	1	0	0	0	1786	1194	42	3	212	3	C15orf2	15	24921224	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10		24921224	77610168	464	9790										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24921716	24921716	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctccagcgagctcctgcttGgaaggccctgccatgcccag	11	16	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:24921716G>A	ENST00000329468.2	+	1	1176	c.702G>A	c.(700-702)ttG>ttA	p.L234L		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	234					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											GCTCCTGCTTGGAAGGCCCTG	0.612																																					p.L234L		Atlas-SNP	.											.	.	.	.	0			c.G702A						.						30	32	31					15																	24921716		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			CTGCTTGGAAGGC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.702G>A	chr15.hg19:g.24921716G>A		57.0	0.0		61.0	32.0	NM_018958		Silent	SNP	ENST00000329468.2	hg19	CCDS10015.1																																																																																			.	.		0.612	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24921716	G	A	24921716	2	1	73	1	0	0	0	0	0	0	0	1	1786	1339	47	3		3	C15orf2	15	24921716	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	492	24921716	77609676	465	9791										
GABRA5	2558	hgsc.bcm.edu	37	chr15	27114454	27114454	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaacctccttctcttttgtaTttccatgaacttatccagtc	3	12	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:27114454T>A	ENST00000335625.5	+	3	947	c.59T>A	c.(58-60)aTt>aAt	p.I20N	GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000400081.3_Missense_Mutation_p.I20N|GABRA5_ENST00000355395.5_Missense_Mutation_p.I20N|GABRA5_ENST00000557449.1_3'UTR	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	20					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	CTCTTTTGTATTTCCATGAAC	0.388																																					p.I20N		Atlas-SNP	.											.	GABRA5	127	.	0			c.T59A						.						205	198	200					15																	27114454		1901	4127	6028	SO:0001583	missense	2558	exon3			TTTGTATTTCCAT		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.59T>A	chr15.hg19:g.27114454T>A	ENSP00000335592:p.Ile20Asn	139.0	0.0		132.0	45.0	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	hg19	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	T	14.46	2.540737	0.45280	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000557484;ENST00000400081;ENST00000554038;ENST00000554596;ENST00000554599	T;T;T;T;T;T	0.81247	-0.62;-0.62;-0.62;-1.21;-1.15;-1.47	5.82	2.31	0.28768	.	0.502130	0.20995	N	0.081974	T	0.59770	0.2218	N	0.08118	0	0.24078	N	0.995958	B	0.15473	0.013	B	0.11329	0.006	T	0.51702	-0.8672	10	0.49607	T	0.09	.	6.8613	0.24067	0.0:0.2596:0.0:0.7404	.	20	P31644	GBRA5_HUMAN	N	20	ENSP00000335592:I20N;ENSP00000347557:I20N;ENSP00000382953:I20N;ENSP00000451527:I20N;ENSP00000450806:I20N;ENSP00000450717:I20N	ENSP00000335592:I20N	I	+	2	0	GABRA5	24665547	1.000000	0.71417	0.972000	0.41901	0.985000	0.73830	2.894000	0.48640	0.461000	0.27071	0.533000	0.62120	ATT	.	.		0.388	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			A	27114454	T	A	27114454	3	1	73	1	0	0	0	0	1	0	0	0	6172	1493	52	4	61	4	GABRA5	15	27114454	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2192738	27114454	75416938	466	9792										
CHRM5	1133	hgsc.bcm.edu	37	chr15	34355220	34355220	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acgctgggctctcgggagtcTggcttgtgacctttggcttg	15	10	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:34355220T>G	ENST00000383263.5	+	3	972	c.302T>G	c.(301-303)cTg>cGg	p.L101R	CHRM5_ENST00000557872.1_Missense_Mutation_p.L101R	NM_012125.3	NP_036257.1	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	101					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|dopamine transport (GO:0015872)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|gastric acid secretion (GO:0001696)|metabolic process (GO:0008152)|regulation of phosphatidylinositol dephosphorylation (GO:0060304)|transmission of nerve impulse (GO:0019226)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	20		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Imipramine(DB00458)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CTCGGGAGTCTGGCTTGTGAC	0.507																																					p.L101R		Atlas-SNP	.											.	CHRM5	59	.	0			c.T302G						.						83	71	75					15																	34355220		2201	4298	6499	SO:0001583	missense	1133	exon3			GGAGTCTGGCTTG		CCDS10031.1	15q26	2012-08-08			ENSG00000184984	ENSG00000184984		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1954	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 5"	118496					Standard	NM_012125		Approved		uc001zhk.1	P08912	OTTHUMG00000129369	ENST00000383263.5:c.302T>G	chr15.hg19:g.34355220T>G	ENSP00000372750:p.Leu101Arg	172.0	0.0		138.0	54.0	NM_012125	Q96RG7	Missense_Mutation	SNP	ENST00000383263.5	hg19	CCDS10031.1	.	.	.	.	.	.	.	.	.	.	T	17.05	3.289524	0.59976	.	.	ENSG00000184984	ENST00000383263	T	0.73363	-0.74	5.64	5.64	0.86602	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.83862	0.5346	L	0.60067	1.865	0.51012	D	0.999904	D	0.63880	0.993	D	0.72982	0.979	D	0.85389	0.1124	10	0.87932	D	0	-8.7407	16.0238	0.80522	0.0:0.0:0.0:1.0	.	101	P08912	ACM5_HUMAN	R	101	ENSP00000372750:L101R	ENSP00000372750:L101R	L	+	2	0	CHRM5	32142512	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.975000	0.63777	2.367000	0.80283	0.528000	0.53228	CTG	.	.		0.507	CHRM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251521.2			G	34355220	T	G	34355220	3	3	73	1	0	0	0	0	1	0	0	0	3382	1580	55	5	304	5	CHRM5	15	34355220	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	7240766	34355220	68176172	467	9793										
ATPBD4	89978	hgsc.bcm.edu	37	chr15	35830633	35830633	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aatggcatggtgccccactgTctgatacatgtagctatcca	9	11	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:35830633T>A	ENST00000256538.4	-	3	180	c.154A>T	c.(154-156)Aca>Tca	p.T52S	DPH6_ENST00000440392.2_Missense_Mutation_p.T52S	NM_080650.3	NP_542381.1	Q7L8W6	DPH6_HUMAN	diphthamine biosynthesis 6	52					peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		ATP binding (GO:0005524)|diphthine-ammonia ligase activity (GO:0017178)										TGCCCCACTGTCTGATACATG	0.438																																					p.T52S		Atlas-SNP	.											.	ATPBD4	30	.	0			c.A154T						.						122	100	107					15																	35830633		2201	4298	6499	SO:0001583	missense	89978	exon3			CCACTGTCTGATA		CCDS10043.1, CCDS45213.1	15q14	2013-06-19	2013-06-19	2013-05-02	ENSG00000134146	ENSG00000134146	6.3.1.14		30543	protein-coding gene	gene with protein product	"diphthine--ammonia ligase"		"ATP binding domain 4", "DPH6 homolog (S. cerevisiae)"	ATPBD4		23169644, 23468660	Standard	NM_080650		Approved	MGC14798		Q7L8W6	OTTHUMG00000129759	ENST00000256538.4:c.154A>T	chr15.hg19:g.35830633T>A	ENSP00000256538:p.Thr52Ser	151.0	0.0		157.0	70.0	NM_001141972	B3KWG1|Q96HJ6	Missense_Mutation	SNP	ENST00000256538.4	hg19	CCDS10043.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.554891	0.86231	.	.	ENSG00000134146	ENST00000256538;ENST00000440392	T;T	0.40756	1.54;1.02	5.8	5.8	0.92144	Domain of unknown function DUF71, ATP-binding domain (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.48409	0.1498	L	0.33245	0.995	0.58432	D	0.999999	P;P	0.47191	0.891;0.881	P;P	0.55303	0.773;0.598	T	0.36286	-0.9754	10	0.35671	T	0.21	-20.2853	16.1559	0.81666	0.0:0.0:0.0:1.0	.	52;52	B3KWG1;Q7L8W6	.;ATBD4_HUMAN	S	52	ENSP00000256538:T52S;ENSP00000406976:T52S	ENSP00000256538:T52S	T	-	1	0	ATPBD4	33617925	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.991000	0.88244	2.229000	0.72834	0.528000	0.53228	ACA	.	.		0.438	DPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251973.1	NM_080650		A	35830633	T	A	35830633	3	1	73	1	0	0	0	0	1	0	0	0	1202	1667	58	4	867	4	ATPBD4	15	35830633	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1475413	35830633	66700759	468	9794										
FAM98B	283742	hgsc.bcm.edu	37	chr15	38773693	38773693	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttcagtacagtggaaaatgaAttgatgatatcttacttaat	7	4	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:38773693A>C	ENST00000491535.1	+	7	938	c.930A>C	c.(928-930)gaA>gaC	p.E310D	FAM98B_ENST00000397609.2_Intron	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B	310						cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		TGGAAAATGAATTGATGATAT	0.378																																					p.E310D		Atlas-SNP	.											.	FAM98B	53	.	0			c.A930C						.						143	136	139					15																	38773693		2200	4297	6497	SO:0001583	missense	283742	exon7			AAATGAATTGATG		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831	ENST00000491535.1:c.930A>C	chr15.hg19:g.38773693A>C	ENSP00000453166:p.Glu310Asp	149.0	0.0		150.0	60.0	NM_001042429	A8MUW5|Q8N935	Missense_Mutation	SNP	ENST00000491535.1	hg19	CCDS42015.1	.	.	.	.	.	.	.	.	.	.	A	11.40	1.627715	0.28978	.	.	ENSG00000171262	ENST00000305752	.	.	.	4.38	2.07	0.26955	.	.	.	.	.	T	0.15089	0.0364	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26815	-1.0092	7	.	.	.	.	2.9128	0.05743	0.613:0.0:0.2031:0.1839	.	310	Q52LJ0	FA98B_HUMAN	D	310	.	.	E	+	3	2	FAM98B	36560985	0.017000	0.18338	0.006000	0.13384	0.029000	0.11900	0.720000	0.25896	0.323000	0.23307	0.383000	0.25322	GAA	.	.		0.378	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		C	38773693	A	C	38773693	3	2	73	1	0	0	0	0	1	0	0	0	5665	98	4	5	956	5	FAM98B	15	38773693	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2943060	38773693	63757699	469	9795										
GATM	2628	hgsc.bcm.edu	37	chr15	45668899	45668899	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtaagaagagacagggcagTccttgggcagaggctcagtg	16	7	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:45668899T>G	ENST00000396659.3	-	2	527	c.188A>C	c.(187-189)gAc>gCc	p.D63A	GATM_ENST00000558336.1_Missense_Mutation_p.D63A|GATM_ENST00000458245.5_5'Flank	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	63					cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|embryo development (GO:0009790)|response to mercury ion (GO:0046689)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	glycine amidinotransferase activity (GO:0015068)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines (GO:0016813)			biliary_tract(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	15		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Glycine(DB00145)|L-Ornithine(DB00129)	GACAGGGCAGTCCTTGGGCAG	0.572																																					p.D63A		Atlas-SNP	.											.	GATM	34	.	0			c.A188C						.						115	104	108					15																	45668899		2198	4298	6496	SO:0001583	missense	2628	exon2			GGGCAGTCCTTGG	S68805	CCDS10122.1	15q15.1	2007-12-06			ENSG00000171766	ENSG00000171766	2.1.4.1		4175	protein-coding gene	gene with protein product		602360				8313955	Standard	NM_001482		Approved	AGAT	uc001zvc.3	P50440	OTTHUMG00000131427	ENST00000396659.3:c.188A>C	chr15.hg19:g.45668899T>G	ENSP00000379895:p.Asp63Ala	99.0	0.0		100.0	37.0	NM_001482	B4DH99|B4DPI3|Q53EQ4	Missense_Mutation	SNP	ENST00000396659.3	hg19	CCDS10122.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.087547	0.55968	.	.	ENSG00000171766	ENST00000396659	T	0.50813	0.73	5.81	4.65	0.58169	.	0.047245	0.85682	D	0.000000	T	0.21761	0.0524	N	0.03154	-0.405	0.39540	D	0.968802	B;B	0.19706	0.038;0.022	B;B	0.18561	0.022;0.01	T	0.14364	-1.0475	10	0.11182	T	0.66	-20.0193	10.6538	0.45663	0.1426:0.0:0.0:0.8574	.	63;63	P50440-3;P50440	.;GATM_HUMAN	A	63	ENSP00000379895:D63A	ENSP00000379895:D63A	D	-	2	0	GATM	43456191	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.930000	0.56522	2.210000	0.71456	0.533000	0.62120	GAC	.	.		0.572	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482		G	45668899	T	G	45668899	3	3	73	1	0	0	0	0	1	0	0	0	6271	1667	58	5	1115	5	GATM	15	45668899	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	6895206	45668899	56862493	470	9796										
SPATA5L1	79029	hgsc.bcm.edu	37	chr15	45694903	45694903	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggggcgtcgagatcccggagGagtctcagcctgaatcgcct	15	12	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:45694903G>C	ENST00000305560.6	+	1	375	c.276G>C	c.(274-276)agG>agC	p.R92S	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.R92S|GATM_ENST00000458245.5_5'Flank	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	92						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		GATCCCGGAGGAGTCTCAGCC	0.756																																					p.R92S		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.G276C						.						4	6	6					15																	45694903		2002	4026	6028	SO:0001583	missense	79029	exon1			CCGGAGGAGTCTC	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"ATPases / AAA-type"	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.276G>C	chr15.hg19:g.45694903G>C	ENSP00000305494:p.Arg92Ser	10.0	0.0		14.0	8.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	hg19	CCDS10123.1	.	.	.	.	.	.	.	.	.	.	G	3.572	-0.087476	0.07097	.	.	ENSG00000171763	ENST00000305560	D	0.93488	-3.23	4.98	-1.74	0.08056	.	1.021240	0.07819	N	0.959485	D	0.82674	0.5088	N	0.08118	0	0.09310	N	1	B	0.15473	0.013	B	0.11329	0.006	T	0.70059	-0.4976	10	0.42905	T	0.14	-11.0034	4.9695	0.14108	0.414:0.0:0.4521:0.1339	.	92	Q9BVQ7	SPA5L_HUMAN	S	92	ENSP00000305494:R92S	ENSP00000305494:R92S	R	+	3	2	SPATA5L1	43482195	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	-0.390000	0.07332	-0.208000	0.10171	0.645000	0.84053	AGG	.	.		0.756	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		C	45694903	G	C	45694903	3	2	73	1	0	0	0	0	1	0	0	0	15027	1165	41	4	278	4	SPATA5L1	15	45694903	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	26004	45694903	56836489	471	9797										
FBN1	2200	hgsc.bcm.edu	37	chr15	48741033	48741033	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggcaataaaagcttccaactGtgtcaatgcactgcccatga	8	11	1	1	rs145082616		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:48741033G>T	ENST00000316623.5	-	46	6058	c.5603C>A	c.(5602-5604)aCa>aAa	p.T1868K		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1868	EGF-like 31; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GCTTCCAACTGTGTCAATGCA	0.343																																					p.T1868K		Atlas-SNP	.											.	FBN1	310	.	0			c.C5603A						.						102	96	98					15																	48741033		2197	4296	6493	SO:0001583	missense	2200	exon46			CCAACTGTGTCAA	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5603C>A	chr15.hg19:g.48741033G>T	ENSP00000325527:p.Thr1868Lys	60.0	0.0		69.0	7.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305187	0.60305	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.92495	-3.05	6.16	5.25	0.73442	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.210306	0.53938	D	0.000052	D	0.90601	0.7053	M	0.68593	2.085	0.80722	D	1	P	0.38617	0.64	B	0.40602	0.334	D	0.88397	0.3012	10	0.29301	T	0.29	.	11.403	0.49880	0.0683:0.1269:0.8049:0.0	.	1868	P35555	FBN1_HUMAN	K	1868;436;758	ENSP00000325527:T1868K	ENSP00000325527:T1868K	T	-	2	0	FBN1	46528325	0.998000	0.40836	0.999000	0.59377	0.996000	0.88848	2.632000	0.46511	1.612000	0.50221	0.650000	0.86243	ACA	.	G|1.000;A|0.000		0.343	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48741033	G	T	48741033	3	4	73	1	0	0	0	0	1	0	0	0	5710	1377	48	3	3096	3	FBN1	15	48741033	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3046130	48741033	53790359	472	9798										
GABPB1	2553	hgsc.bcm.edu	37	chr15	50578223	50578223	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaaaaaaattgaatttatttTggatgactgcggcaaagcac	8	5	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:50578223T>A	ENST00000220429.8	-	8	1204				GABPB1_ENST00000560825.1_Silent_p.P346P|GABPB1_ENST00000429662.2_Silent_p.P359P|GABPB1_ENST00000543881.1_Intron|GABPB1_ENST00000380877.3_Intron|GABPB1_ENST00000359031.4_Silent_p.P347P|GABPB1_ENST00000396464.3_Silent_p.P347P			Q06547	GABP1_HUMAN	GA binding protein transcription factor, beta subunit 1						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(1)|large_intestine(7)|lung(5)	14						GAATTTATTTTGGATGACTGC	0.328																																					p.P359P		Atlas-SNP	.											.	GABPB1	33	.	0			c.A1077T						.						87	92	90					15																	50578223		2196	4294	6490	SO:0001627	intron_variant	2553	exon8			TTATTTTGGATGA	D13316	CCDS10135.1, CCDS10136.1, CCDS32239.1, CCDS45258.1	15q21.2	2013-01-10	2008-02-25	2008-02-25	ENSG00000104064	ENSG00000104064		"Ankyrin repeat domain containing"	4074	protein-coding gene	gene with protein product		600610	"GA binding protein transcription factor, beta subunit 2"	GABPB2		7958862	Standard	NM_016655		Approved	E4TF1-47, GABPB	uc001zyb.3	Q06547	OTTHUMG00000131642	ENST00000220429.8:c.1035+41A>T	chr15.hg19:g.50578223T>A		130.0	0.0		104.0	45.0	NM_002041	A8IE52|Q06545|Q12940|Q12941|Q12942|Q8IYD0	Silent	SNP	ENST00000220429.8	hg19	CCDS32239.1																																																																																			.	.		0.328	GABPB1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000418294.1			A	50578223	T	A	50578223	1	1	73	0	1	0	0	0	0	0	0	0	6166	1799	63	4		4	GABPB1	15	50578223	Intron	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1837190	50578223	51953169	473	9799										
PRTG	283659	hgsc.bcm.edu	37	chr15	55971629	55971629	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	taaactttctggccattcaaCaaatgaaggaggagctattt	8	7	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:55971629C>A	ENST00000389286.4	-	7	1035	c.988G>T	c.(988-990)Gtt>Ttt	p.V330F	RP11-420M1.2_ENST00000561155.1_RNA	NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		GGCCATTCAACAAATGAAGGA	0.393																																					p.V330F		Atlas-SNP	.											.	PRTG	110	.	0			c.G988T						.						67	59	61					15																	55971629		1817	4079	5896	SO:0001583	missense	283659	exon7			ATTCAACAAATGA	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.988G>T	chr15.hg19:g.55971629C>A	ENSP00000373937:p.Val330Phe	88.0	0.0		104.0	44.0	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	hg19	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.032989	0.75504	.	.	ENSG00000166450	ENST00000389286	T	0.28255	1.62	5.72	4.81	0.61882	Immunoglobulin I-set (1);Immunoglobulin-like (1);	0.065857	0.64402	D	0.000010	T	0.51058	0.1652	M	0.77103	2.36	0.80722	D	1	D	0.67145	0.996	D	0.63113	0.911	T	0.54721	-0.8251	10	0.62326	D	0.03	-14.4704	9.8531	0.41068	0.0:0.846:0.0:0.154	.	330	Q2VWP7	PRTG_HUMAN	F	330	ENSP00000373937:V330F	ENSP00000373937:V330F	V	-	1	0	PRTG	53758921	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.747000	0.55134	1.416000	0.47057	0.591000	0.81541	GTT	.	.		0.393	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		A	55971629	C	A	55971629	3	1	73	1	0	0	0	0	1	0	0	0	12650	478	17	3	2520	3	PRTG	15	55971629	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	5393406	55971629	46559763	474	9800										
CLN6	54982	hgsc.bcm.edu	37	chr15	68504126	68504126	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtcacccaccaggtggatgcTggcacccatgatgaagatga	12	11	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:68504126T>A	ENST00000249806.5	-	4	530	c.373A>T	c.(373-375)Agc>Tgc	p.S125C	CLN6_ENST00000564752.1_Missense_Mutation_p.S125C|CLN6_ENST00000566347.1_Intron|CLN6_ENST00000565471.1_Intron|RP11-315D16.2_ENST00000562767.1_Intron|CLN6_ENST00000418702.2_Intron|CLN6_ENST00000538696.1_Missense_Mutation_p.S157C	NM_017882.2	NP_060352.1	Q9NWW5	CLN6_HUMAN	ceroid-lipofuscinosis, neuronal 6, late infantile, variant	125					cell death (GO:0008219)|cellular macromolecule catabolic process (GO:0044265)|cholesterol metabolic process (GO:0008203)|ganglioside metabolic process (GO:0001573)|glycosaminoglycan metabolic process (GO:0030203)|locomotion involved in locomotory behavior (GO:0031987)|lysosomal lumen acidification (GO:0007042)|positive regulation of proteolysis (GO:0045862)|protein catabolic process (GO:0030163)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						AGGTGGATGCTGGCACCCATG	0.587																																					p.S125C		Atlas-SNP	.											.	CLN6	16	.	0			c.A373T						.						127	119	121					15																	68504126		2200	4298	6498	SO:0001583	missense	54982	exon4			GGATGCTGGCACC	AK000568	CCDS10227.1	15q23	2014-09-17			ENSG00000128973	ENSG00000128973			2077	protein-coding gene	gene with protein product		606725				9097964, 11727201	Standard	NM_017882		Approved	FLJ20561, HsT18960, nclf	uc002arf.3	Q9NWW5	OTTHUMG00000133286	ENST00000249806.5:c.373A>T	chr15.hg19:g.68504126T>A	ENSP00000249806:p.Ser125Cys	105.0	0.0		57.0	30.0	NM_017882	A8K560|B4DDH6|Q6IAB1|Q96SR0	Missense_Mutation	SNP	ENST00000249806.5	hg19	CCDS10227.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.760773	0.89932	.	.	ENSG00000128973	ENST00000249806;ENST00000538696	D;D	0.96011	-3.88;-3.88	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.96706	0.8925	L	0.59436	1.845	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66497	0.939;0.944	D	0.97317	0.9941	10	0.87932	D	0	-40.8627	14.9797	0.71303	0.0:0.0:0.0:1.0	.	157;125	B4DDH6;Q9NWW5	.;CLN6_HUMAN	C	125;157	ENSP00000249806:S125C;ENSP00000445770:S157C	ENSP00000249806:S125C	S	-	1	0	CLN6	66291180	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.576000	0.82467	1.935000	0.56089	0.418000	0.28097	AGC	.	.		0.587	CLN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257066.1	NM_017882		A	68504126	T	A	68504126	3	1	73	1	0	0	0	0	1	0	0	0	3547	1580	55	4	578	4	CLN6	15	68504126	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	12532497	68504126	34027266	475	9801										
ITGA11	22801	hgsc.bcm.edu	37	chr15	68609680	68609680	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctctcctcgttcacacactCaatgctaccgtctgagtcct	5	17	4	1	rs546078018		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:68609680C>A	ENST00000315757.7	-	21	2724	c.2638G>T	c.(2638-2640)Gag>Tag	p.E880*	ITGA11_ENST00000423218.2_Nonsense_Mutation_p.E880*	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	880					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						TTCACACACTCAATGCTACCG	0.607																																					p.E880X		Atlas-SNP	.											.	ITGA11	110	.	0			c.G2638T						.						123	135	131					15																	68609680		2083	4207	6290	SO:0001587	stop_gained	22801	exon21			CACACTCAATGCT	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.2638G>T	chr15.hg19:g.68609680C>A	ENSP00000327290:p.Glu880*	130.0	0.0		101.0	39.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Nonsense_Mutation	SNP	ENST00000315757.7	hg19	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	C	37	6.039429	0.97226	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	.	.	.	4.79	4.79	0.61399	.	0.152015	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	16.8386	0.85962	0.0:1.0:0.0:0.0	.	.	.	.	X	880;880;515	.	ENSP00000327290:E880X	E	-	1	0	ITGA11	66396734	1.000000	0.71417	1.000000	0.80357	0.021000	0.10359	6.039000	0.70972	2.214000	0.71695	0.561000	0.74099	GAG	.	.		0.607	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		A	68609680	C	A	68609680	4	1	73	1	0	0	0	0	0	1	0	0	7883	835	29	3	968	3	ITGA11	15	68609680	Nonsense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	105554	68609680	33921712	476	9802										
NEO1	4756	hgsc.bcm.edu	37	chr15	73564819	73564819	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgacttctccacccaaggatGtgactgttgtgagtaaagag	11	9	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:73564819G>C	ENST00000339362.5	+	20	3328	c.2881G>C	c.(2881-2883)Gtg>Ctg	p.V961L	NEO1_ENST00000558964.1_Missense_Mutation_p.V961L|NEO1_ENST00000560262.1_Missense_Mutation_p.V961L|NEO1_ENST00000261908.6_Missense_Mutation_p.V961L			Q92859	NEO1_HUMAN	neogenin 1	961	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						ACCCAAGGATGTGACTGTTGT	0.373																																					p.V961L		Atlas-SNP	.											.	NEO1	102	.	0			c.G2881C						.						91	86	88					15																	73564819		2198	4297	6495	SO:0001583	missense	4756	exon19			AAGGATGTGACTG	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.2881G>C	chr15.hg19:g.73564819G>C	ENSP00000341198:p.Val961Leu	123.0	0.0		91.0	35.0	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	hg19	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	G	9.741	1.164897	0.21538	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.50548	0.74;0.74	6.02	6.02	0.97574	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.18676	0.0448	N	0.01410	-0.885	0.80722	D	1	P;B;B;B	0.37015	0.578;0.043;0.087;0.087	B;B;B;B	0.29598	0.104;0.018;0.06;0.06	T	0.40683	-0.9550	10	0.02654	T	1	-14.7626	20.5407	0.99260	0.0:0.0:1.0:0.0	.	961;961;683;961	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	L	961;683;961	ENSP00000341198:V961L;ENSP00000261908:V961L	ENSP00000261908:V961L	V	+	1	0	NEO1	71351872	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.876000	0.87215	2.865000	0.98341	0.655000	0.94253	GTG	.	.		0.373	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		C	73564819	G	C	73564819	3	2	73	1	0	0	0	0	1	0	0	0	10345	1377	48	4	2955	4	NEO1	15	73564819	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	4955139	73564819	28966573	477	9803										
ISLR2	57611	hgsc.bcm.edu	37	chr15	74426996	74426996	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gatcctgcggcctcaggcccCtgaccctatggagaagcgca	12	15	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:74426996C>G	ENST00000361742.3	+	4	2670	c.1901C>G	c.(1900-1902)cCt>cGt	p.P634R	ISLR2_ENST00000435464.1_Missense_Mutation_p.P634R|ISLR2_ENST00000565159.1_Missense_Mutation_p.P634R|ISLR2_ENST00000453268.2_Missense_Mutation_p.P634R|ISLR2_ENST00000419208.1_Missense_Mutation_p.P634R|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000445793.1_Missense_Mutation_p.P634R|ISLR2_ENST00000565540.1_Missense_Mutation_p.P634R	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	634					positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						CCTCAGGCCCCTGACCCTATG	0.682											OREG0023277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P634R		Atlas-SNP	.											.	ISLR2	78	.	0			c.C1901G						.						35	35	35					15																	74426996		2198	4297	6495	SO:0001583	missense	57611	exon4			AGGCCCCTGACCC		CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.1901C>G	chr15.hg19:g.74426996C>G	ENSP00000355402:p.Pro634Arg	112.0	0.0	1152	89.0	40.0	NM_001130138	A8K352|Q9P263	Missense_Mutation	SNP	ENST00000361742.3	hg19	CCDS10259.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.026369	0.35701	.	.	ENSG00000167178	ENST00000445793;ENST00000361742;ENST00000435464;ENST00000453268;ENST00000395121;ENST00000419208	T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35	4.84	3.92	0.45320	.	0.132655	0.51477	D	0.000094	T	0.38904	0.1058	L	0.29908	0.895	0.48696	D	0.99969	B	0.34103	0.437	B	0.29267	0.1	T	0.37478	-0.9704	10	0.87932	D	0	.	12.1086	0.53825	0.0:0.9126:0.0:0.0874	.	634	Q6UXK2	ISLR2_HUMAN	R	634;634;634;634;223;634	ENSP00000403244:P634R;ENSP00000355402:P634R;ENSP00000411443:P634R;ENSP00000411834:P634R;ENSP00000408872:P634R	ENSP00000355402:P634R	P	+	2	0	ISLR2	72214049	0.998000	0.40836	0.950000	0.38849	0.850000	0.48378	3.993000	0.56987	1.024000	0.39682	0.313000	0.20887	CCT	.	.		0.682	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851		G	74426996	C	G	74426996	3	3	73	1	0	0	0	0	1	0	0	0	7868	681	24	4	1903	4	ISLR2	15	74426996	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	862177	74426996	28104396	478	9804										
PSMA4	5685	hgsc.bcm.edu	37	chr15	78837269	78837269	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agttggttacagcgctgtgtGatatcaaacaagcttataca	9	7	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:78837269G>A	ENST00000044462.7	+	6	496	c.346G>A	c.(346-348)Gat>Aat	p.D116N	PSMA4_ENST00000413382.2_Missense_Mutation_p.D45N|PSMA4_ENST00000557929.1_3'UTR|PSMA4_ENST00000559082.1_Missense_Mutation_p.D116N|PSMA4_ENST00000558341.1_Intron|PSMA4_ENST00000558281.1_Missense_Mutation_p.D116N|PSMA4_ENST00000560217.1_Missense_Mutation_p.D85N|PSMA4_ENST00000558094.1_Missense_Mutation_p.D28N	NM_002789.4	NP_002780.1	P25789	PSA4_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 4	116					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						AGCGCTGTGTGATATCAAACA	0.323																																					p.D116N		Atlas-SNP	.											.	PSMA4	17	.	0			c.G346A						.						96	92	93					15																	78837269		2196	4293	6489	SO:0001583	missense	5685	exon6			CTGTGTGATATCA	BC005361	CCDS10303.1, CCDS45319.1	15q24.1	2004-01-19			ENSG00000041357	ENSG00000041357		"Proteasome (prosome, macropain) subunits"	9533	protein-coding gene	gene with protein product		176846				2025653	Standard	NM_002789		Approved	HC9, HsT17706	uc010blf.3	P25789	OTTHUMG00000143859	ENST00000044462.7:c.346G>A	chr15.hg19:g.78837269G>A	ENSP00000044462:p.Asp116Asn	129.0	0.0		99.0	39.0	NM_001102667	D3DW86|Q53XP2|Q567Q5|Q8TBD1	Missense_Mutation	SNP	ENST00000044462.7	hg19	CCDS10303.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.302273	0.81136	.	.	ENSG00000041357	ENST00000413382;ENST00000044462	T;T	0.22743	1.94;1.94	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.34193	0.0889	L	0.53617	1.68	0.80722	D	1	B	0.33748	0.423	B	0.43889	0.435	T	0.02015	-1.1229	10	0.44086	T	0.13	-37.7379	20.0825	0.97783	0.0:0.0:1.0:0.0	.	116	P25789	PSA4_HUMAN	N	45;116	ENSP00000402118:D45N;ENSP00000044462:D116N	ENSP00000044462:D116N	D	+	1	0	PSMA4	76624324	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	9.586000	0.98226	2.746000	0.94184	0.655000	0.94253	GAT	.	.		0.323	PSMA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290107.5	NM_002789		A	78837269	G	A	78837269	3	1	73	1	0	0	0	0	1	0	0	0	12681	1290	45	3	364	3	PSMA4	15	78837269	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	4410273	78837269	23694123	479	9805										
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79080627	79080627	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggaccaggtgaggggagcgGcgtcgtacaggagctgtgga	21	7	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:79080627G>A	ENST00000388820.4	-	8	1478	c.1268C>T	c.(1267-1269)gCc>gTc	p.A423V	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	423	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GAGGGGAGCGGCGTCGTACAG	0.572																																					p.A423V		Atlas-SNP	.											ADAMTS7,neck,malignant_melanoma,0,1	ADAMTS7	142	.	0			c.C1268T						.						130	114	119					15																	79080627		2196	4293	6489	SO:0001583	missense	11173	exon8			GGAGCGGCGTCGT	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.1268C>T	chr15.hg19:g.79080627G>A	ENSP00000373472:p.Ala423Val	121.0	1.0		84.0	41.0	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	hg19	CCDS32303.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.93|17.93	3.508621|3.508621	0.64410|0.64410	.|.	.|.	ENSG00000136378|ENSG00000136378	ENST00000388820|ENST00000456326	T|.	0.03635|.	3.86|.	5.37|5.37	4.44|4.44	0.53790|0.53790	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);|.	0.273612|.	0.33916|.	N|.	0.004437|.	T|T	0.31544|0.31544	0.0800|0.0800	L|L	0.27053|0.27053	0.805|0.805	0.26492|0.26492	N|N	0.974925|0.974925	B;B|B	0.32467|0.24258	0.372;0.367|0.1	B;B|B	0.39771|0.18561	0.309;0.253|0.022	T|T	0.15093|0.15093	-1.0449|-1.0449	10|8	0.42905|0.35671	T|T	0.14|0.21	.|.	13.4868|13.4868	0.61371|0.61371	0.0:0.1645:0.8355:0.0|0.0:0.1645:0.8355:0.0	.|.	423;423|398	A8MQ00;Q9UKP4|E7EP58	.;ATS7_HUMAN|.	V|S	423|398	ENSP00000373472:A423V|.	ENSP00000373472:A423V|ENSP00000396177:P398S	A|P	-|-	2|1	0|0	ADAMTS7|ADAMTS7	76867682|76867682	1.000000|1.000000	0.71417|0.71417	0.060000|0.060000	0.19600|0.19600	0.903000|0.903000	0.53119|0.53119	4.457000|4.457000	0.60088|0.60088	1.238000|1.238000	0.43771|0.43771	0.491000|0.491000	0.48974|0.48974	GCC|CCG	.	.		0.572	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		A	79080627	G	A	79080627	3	1	73	1	0	0	0	0	1	0	0	0	271	1203	42	3	3860	3	ADAMTS7	15	79080627	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	243358	79080627	23450765	480	9806										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88472454	88472454	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgtgctgtagacatctctggAcatgccgaagtccccaatct	9	13	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:88472454A>T	ENST00000360948.2	-	16	2262	c.2101T>A	c.(2101-2103)Tcc>Acc	p.S701T	NTRK3_ENST00000355254.2_Missense_Mutation_p.S701T|NTRK3_ENST00000557856.1_Missense_Mutation_p.S693T|NTRK3_ENST00000357724.2_Missense_Mutation_p.S693T|NTRK3_ENST00000542733.2_Missense_Mutation_p.S603T|NTRK3_ENST00000394480.2_Missense_Mutation_p.S701T|NTRK3_ENST00000558676.1_Missense_Mutation_p.S693T	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	701	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			ACATCTCTGGACATGCCGAAG	0.532			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.S701T		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.T2101A						.						112	104	107					15																	88472454		2201	4299	6500	SO:0001583	missense	4916	exon17			CTCTGGACATGCC	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.2101T>A	chr15.hg19:g.88472454A>T	ENSP00000354207:p.Ser701Thr	197.0	0.0		162.0	70.0	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.758218	0.89843	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733	D;D;D;D;D	0.90563	-2.69;-2.69;-2.69;-2.69;-2.69	5.16	5.16	0.70880	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93475	0.7918	L	0.52266	1.64	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.992;1.0;0.99;1.0	D;D;D;D;D	0.85130	0.995;0.987;0.997;0.979;0.997	D	0.94155	0.7409	10	0.87932	D	0	.	14.1992	0.65690	1.0:0.0:0.0:0.0	.	603;693;693;701;701	B7Z7U4;E9PG56;B7Z4C5;Q16288-3;Q16288	.;.;.;.;NTRK3_HUMAN	T	701;701;693;701;603	ENSP00000377990:S701T;ENSP00000354207:S701T;ENSP00000350356:S693T;ENSP00000347397:S701T;ENSP00000437773:S603T	ENSP00000347397:S701T	S	-	1	0	NTRK3	86273458	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.118000	0.94355	1.952000	0.56665	0.533000	0.62120	TCC	.	.		0.532	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				T	88472454	A	T	88472454	3	4	73	1	0	0	0	0	1	0	0	0	10717	275	10	4	434	4	NTRK3	15	88472454	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	9391827	88472454	14058938	481	9807										
WDR93	56964	hgsc.bcm.edu	37	chr15	90272996	90272996	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaccgaactctaaaggataaAgctggtactttactgctgag	9	8	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:90272996A>G	ENST00000268130.7	+	11	1307	c.1206A>G	c.(1204-1206)aaA>aaG	p.K402K	WDR93_ENST00000560294.1_Silent_p.K402K|WDR93_ENST00000444934.2_Silent_p.K119K	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	402					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TAAAGGATAAAGCTGGTACTT	0.493																																					p.K402K		Atlas-SNP	.											.	WDR93	63	.	0			c.A1206G						.						74	66	69					15																	90272996		2200	4299	6499	SO:0001819	synonymous_variant	56964	exon11			GGATAAAGCTGGT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"WD repeat domain containing"	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1206A>G	chr15.hg19:g.90272996A>G		135.0	0.0		93.0	5.0	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	hg19	CCDS32326.1																																																																																			.	.		0.493	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212		G	90272996	A	G	90272996	2	3	73	1	0	0	0	0	0	0	0	1	17355	69	3	2		2	WDR93	15	90272996	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1800542	90272996	12258396	482	9808										
FURIN	5045	hgsc.bcm.edu	37	chr15	91423153	91423153	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcgccatggtggccctggccCagaattggaccacagtggcc	14	14	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:91423153C>T	ENST00000268171.3	+	12	1594	c.1315C>T	c.(1315-1317)Cag>Tag	p.Q439*		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	439					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GGCCCTGGCCCAGAATTGGAC	0.642																																					p.Q439X		Atlas-SNP	.											.	FURIN	85	.	0			c.C1315T						.						33	36	35					15																	91423153		2198	4298	6496	SO:0001587	stop_gained	5045	exon12			CTGGCCCAGAATT	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1315C>T	chr15.hg19:g.91423153C>T	ENSP00000268171:p.Gln439*	174.0	0.0		122.0	56.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Nonsense_Mutation	SNP	ENST00000268171.3	hg19	CCDS10364.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.117177	0.56505	.	.	ENSG00000140564	ENST00000268171	.	.	.	4.65	3.68	0.42216	.	0.270928	0.40064	N	0.001185	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-11.2263	13.4155	0.60966	0.3159:0.6841:0.0:0.0	.	.	.	.	X	439	.	ENSP00000268171:Q439X	Q	+	1	0	FURIN	89224157	1.000000	0.71417	1.000000	0.80357	0.734000	0.41952	1.703000	0.37846	2.410000	0.81850	0.485000	0.47835	CAG	.	.		0.642	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		T	91423153	C	T	91423153	4	4	73	1	0	0	0	0	0	1	0	0	6107	595	21	3	1357	3	FURIN	15	91423153	Nonsense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1150157	91423153	11108239	483	9809										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101523888	101523888	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acggcagttgtgcaggaattGcttgagtccttaccaggtaa	12	8	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:101523888G>T	ENST00000388948.3	+	4	776	c.417G>T	c.(415-417)ttG>ttT	p.L139F	LRRK1_ENST00000532029.2_Missense_Mutation_p.L139F|LRRK1_ENST00000284395.5_Missense_Mutation_p.L112F	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGCAGGAATTGCTTGAGTCCT	0.532																																					p.L139F		Atlas-SNP	.											.	LRRK1	310	.	0			c.G417T						.						88	88	88					15																	101523888		2043	4179	6222	SO:0001583	missense	79705	exon4			GGAATTGCTTGAG	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.417G>T	chr15.hg19:g.101523888G>T	ENSP00000373600:p.Leu139Phe	89.0	0.0		65.0	24.0	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099661	0.56183	.	.	ENSG00000154237	ENST00000388948;ENST00000284395;ENST00000532029	D;T;D	0.84070	-1.8;-0.88;-1.8	5.71	-3.15	0.05233	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000017	D	0.88890	0.6560	M	0.86651	2.83	0.34026	D	0.653296	D;D	0.89917	0.995;1.0	D;D	0.91635	0.982;0.999	D	0.87677	0.2545	10	0.72032	D	0.01	.	7.9177	0.29827	0.4544:0.0:0.4448:0.1008	.	139;139	Q38SD2;Q38SD2-2	LRRK1_HUMAN;.	F	139;112;139	ENSP00000373600:L139F;ENSP00000284395:L112F;ENSP00000433268:L139F	ENSP00000284395:L112F	L	+	3	2	LRRK1	99341411	0.970000	0.33590	0.025000	0.17156	0.625000	0.37756	0.047000	0.14056	-0.435000	0.07264	0.591000	0.81541	TTG	.	.		0.532	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		T	101523888	G	T	101523888	3	4	73	1	0	0	0	0	1	0	0	0	9041	1310	46	3	427	3	LRRK1	15	101523888	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	10100735	101523888	1007504	484	9810										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101595197	101595197	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atgctcacccaaaaaatagcCtaccagatcgcctcgggcct	7	15	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr15:101595197C>A	ENST00000388948.3	+	27	4460	c.4101C>A	c.(4099-4101)gcC>gcA	p.A1367A	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Silent_p.A1364A	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AAAAAATAGCCTACCAGATCG	0.433																																					p.A1367A		Atlas-SNP	.											.	LRRK1	310	.	0			c.C4101A						.						120	116	117					15																	101595197		1947	4126	6073	SO:0001819	synonymous_variant	79705	exon27			AATAGCCTACCAG	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.4101C>A	chr15.hg19:g.101595197C>A		156.0	0.0		125.0	57.0	NM_024652		Silent	SNP	ENST00000388948.3	hg19	CCDS42086.1																																																																																			.	.		0.433	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101595197	C	A	101595197	2	1	73	1	0	0	0	0	0	0	0	1	9041	668	24	3		3	LRRK1	15	101595197	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	71309	101595197	936195	485	9811										
CCNF	899	hgsc.bcm.edu	37	chr16	2499281	2499281	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acaccccgtcccggctgtctAggtccccactgtggtggatt	11	15	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:2499281A>T	ENST00000397066.4	+	12	1306		c.e12-1			NM_001761.2	NP_001752.2	P41002	CCNF_HUMAN	cyclin F						mitotic nuclear division (GO:0007067)|negative regulation of centrosome duplication (GO:0010826)|placenta development (GO:0001890)|protein ubiquitination (GO:0016567)|re-entry into mitotic cell cycle (GO:0000320)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	centriole (GO:0005814)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(2)|lung(5)|prostate(4)|skin(1)	20		Ovarian(90;0.17)				CCGGCTGTCTAGGTCCCCACT	0.652																																					.		Atlas-SNP	.											.	CCNF	110	.	0			c.1219-2A>T						.						54	56	55					16																	2499281		2198	4300	6498	SO:0001630	splice_region_variant	899	exon12			CTGTCTAGGTCCC	Z36714	CCDS10467.1	16p13.3	2008-02-05			ENSG00000162063	ENSG00000162063		"F-boxes /  "other""	1591	protein-coding gene	gene with protein product		600227				7896286	Standard	NM_001761		Approved	FBX1, FBXO1	uc002cqd.1	P41002	OTTHUMG00000128858	ENST00000397066.4:c.1219-1A>T	chr16.hg19:g.2499281A>T		82.0	0.0		60.0	25.0	NM_001761	B2R8H3|Q96EG9	Splice_Site	SNP	ENST00000397066.4	hg19	CCDS10467.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.236391	0.58886	.	.	ENSG00000162063	ENST00000397066;ENST00000293968	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.312	0.66422	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCNF	2439282	1.000000	0.71417	0.906000	0.35671	0.602000	0.36980	8.232000	0.89796	2.057000	0.61298	0.460000	0.39030	.	.	.		0.652	CCNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250801.1	NM_001761	Intron	T	2499281	A	T	2499281	5	4	73	1	0	0	0	0	0	0	1	0	2924	434	15	4	1263	4	CCNF	16	2499281	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10		2499281	87855472	486	9812										
USP7	7874	hgsc.bcm.edu	37	chr16	8988707	8988707	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttcatcacttctcgaaaatgCtcgccctagaatggcaaagg	8	11	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:8988707C>A	ENST00000344836.4	-	29	3243	c.3045G>T	c.(3043-3045)gaG>gaT	p.E1015D	USP7_ENST00000535863.1_Missense_Mutation_p.E916D|USP7_ENST00000381886.4_Missense_Mutation_p.E999D	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	1015					maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						CTCGAAAATGCTCGCCCTAGA	0.597																																					p.E1015D		Atlas-SNP	.											.	USP7	116	.	0			c.G3045T						.						95	90	92					16																	8988707		2197	4300	6497	SO:0001583	missense	7874	exon29			AAAATGCTCGCCC	Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"Ubiquitin-specific peptidases"	12630	protein-coding gene	gene with protein product		602519	"ubiquitin specific protease 7 (herpes virus-associated)"	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.3045G>T	chr16.hg19:g.8988707C>A	ENSP00000343535:p.Glu1015Asp	104.0	0.0		88.0	33.0	NM_003470	A6NMY8|B7Z815|H0Y3G8	Missense_Mutation	SNP	ENST00000344836.4	hg19	CCDS32385.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.869092	0.51588	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863	T;T	0.20200	2.09;2.17	5.35	1.86	0.25419	.	0.052181	0.85682	D	0.000000	T	0.23451	0.0567	M	0.84156	2.68	0.58432	D	0.999999	P;P	0.46064	0.872;0.872	B;B	0.39185	0.293;0.293	T	0.05632	-1.0873	10	0.52906	T	0.07	.	6.9685	0.24637	0.0:0.5238:0.0:0.4762	.	1015;999	Q93009;B7Z815	UBP7_HUMAN;.	D	1015;1023;916	ENSP00000343535:E1015D;ENSP00000443646:E916D	ENSP00000343535:E1015D	E	-	3	2	USP7	8896208	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	1.413000	0.34725	0.647000	0.30713	0.305000	0.20034	GAG	.	.		0.597	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			A	8988707	C	A	8988707	3	1	73	1	0	0	0	0	1	0	0	0	17103	796	28	3	275	3	USP7	16	8988707	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	6489426	8988707	81366046	487	9813										
ERCC4	2072	hgsc.bcm.edu	37	chr16	14020498	14020498	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcctctttcgccagaaaaacAaacgtggttttattaaagct	7	9	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:14020498A>T	ENST00000311895.7	+	3	478	c.469A>T	c.(469-471)Aaa>Taa	p.K157*	ERCC4_ENST00000575156.1_Nonsense_Mutation_p.K157*	NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	157	Helicase-like.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						CCAGAAAAACAAACGTGGTTT	0.403			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.K157X		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"excision repair cross-complementing rodent repair deficiency, complementation group 4"		E	.	ERCC4	100	.	0			c.A469T						.						160	151	154					16																	14020498		2197	4300	6497	SO:0001587	stop_gained	2072	exon3	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AAAAACAAACGTG	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"xeroderma pigmentosum, complementation group F"	133520	"excision repair cross-complementing rodent repair deficiency, complementation group 4"	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.469A>T	chr16.hg19:g.14020498A>T	ENSP00000310520:p.Lys157*	87.0	0.0		80.0	31.0	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Nonsense_Mutation	SNP	ENST00000311895.7	hg19	CCDS32390.1	.	.	.	.	.	.	.	.	.	.	A	37	6.025265	0.97211	.	.	ENSG00000175595	ENST00000311895;ENST00000439007;ENST00000389138	.	.	.	5.34	4.24	0.50183	.	0.045329	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.9587	11.7328	0.51748	0.8521:0.1478:0.0:0.0	.	.	.	.	X	157;146;146	.	ENSP00000310520:K157X	K	+	1	0	ERCC4	13927999	1.000000	0.71417	0.985000	0.45067	0.991000	0.79684	8.962000	0.93254	0.846000	0.35142	0.533000	0.62120	AAA	.	.		0.403	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236		T	14020498	A	T	14020498	4	4	73	1	0	0	0	0	0	1	0	0	5217	131	5	4	479	4	ERCC4	16	14020498	Nonsense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	5031791	14020498	76334255	488	9814										
MKL2	57496	hgsc.bcm.edu	37	chr16	14341108	14341108	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagccacgctgtaggccagcCcgtctctacaggtggccaga	12	15	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:14341108C>T	ENST00000341243.5	+	10	1958	c.1958C>T	c.(1957-1959)cCc>cTc	p.P653L	MKL2_ENST00000318282.5_Missense_Mutation_p.P664L|MKL2_ENST00000571589.1_Missense_Mutation_p.P664L|MKL2_ENST00000574045.1_Missense_Mutation_p.P664L			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	653					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GTAGGCCAGCCCGTCTCTACA	0.607																																					p.P664L		Atlas-SNP	.											.	MKL2	103	.	0			c.C1991T						.						47	49	48					16																	14341108		2197	4300	6497	SO:0001583	missense	57496	exon12			GCCAGCCCGTCTC	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.1958C>T	chr16.hg19:g.14341108C>T	ENSP00000345841:p.Pro653Leu	99.0	0.0		72.0	26.0	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Missense_Mutation	SNP	ENST00000341243.5	hg19		.	.	.	.	.	.	.	.	.	.	C	16.22	3.062940	0.55432	.	.	ENSG00000186260	ENST00000318282;ENST00000341243	.	.	.	4.98	4.98	0.66077	.	0.237331	0.42548	D	0.000686	T	0.72645	0.3486	M	0.62723	1.935	0.45515	D	0.998473	B;D	0.56746	0.003;0.977	B;P	0.55923	0.004;0.787	T	0.74559	-0.3625	9	0.51188	T	0.08	-11.2743	17.5646	0.87916	0.0:1.0:0.0:0.0	.	664;664	B4DGT8;Q9ULH7-4	.;.	L	664;653	.	ENSP00000339086:P664L	P	+	2	0	MKL2	14248609	0.993000	0.37304	0.989000	0.46669	0.484000	0.33280	4.074000	0.57577	2.466000	0.83321	0.655000	0.94253	CCC	.	.		0.607	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		T	14341108	C	T	14341108	3	4	73	1	0	0	0	0	1	0	0	0	9611	623	22	3	2029	3	MKL2	16	14341108	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	320610	14341108	76013645	489	9815										
ARL6IP1	23204	hgsc.bcm.edu	37	chr16	18810100	18810100	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cggaggactttatcagccatCagcatcacttctccccatcc	6	16	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:18810100C>T	ENST00000304414.7	-	2	304	c.93G>A	c.(91-93)ctG>ctA	p.L31L	ARL6IP1_ENST00000562819.1_Silent_p.L31L|ARL6IP1_ENST00000546206.2_Silent_p.L2L|RP11-1035H13.3_ENST00000567078.2_Silent_p.L31L	NM_015161.1	NP_055976.1	Q15041	AR6P1_HUMAN	ADP-ribosylation factor-like 6 interacting protein 1	31					cell death (GO:0008219)|cotranslational protein targeting to membrane (GO:0006613)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|Sec61 translocon complex (GO:0005784)				breast(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)	11						TATCAGCCATCAGCATCACTT	0.453																																					p.L31L		Atlas-SNP	.											.	ARL6IP1	23	.	0			c.G93A						.						231	200	211					16																	18810100		2197	4300	6497	SO:0001819	synonymous_variant	23204	exon2			AGCCATCAGCATC	BC010281	CCDS10572.1	16p12-p11.2	2014-03-12	2006-09-26	2006-09-26	ENSG00000170540	ENSG00000170540			697	protein-coding gene	gene with protein product		607669	"ADP-ribosylation factor-like 6 interacting protein"	ARL6IP		24482476	Standard	NM_015161		Approved	AIP1, ARMER, KIAA0069, SPG61	uc002dfl.1	Q15041	OTTHUMG00000131367	ENST00000304414.7:c.93G>A	chr16.hg19:g.18810100C>T		132.0	0.0		120.0	48.0	NM_015161		Silent	SNP	ENST00000304414.7	hg19	CCDS10572.1																																																																																			.	.		0.453	ARL6IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254156.2	NM_015161		T	18810100	C	T	18810100	2	4	73	1	0	0	0	0	0	0	0	1	942	813	29	3		3	ARL6IP1	16	18810100	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	4468992	18810100	71544653	490	9816										
C16orf62	57020	hgsc.bcm.edu	37	chr16	19640035	19640035	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgaccgacttcagattctcaAcgaagcttggaaagtcatca	8	10	4	2	rs370460906		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:19640035A>C	ENST00000251143.5	+	17	1472	c.1460A>C	c.(1459-1461)aAc>aCc	p.N487T	C16orf62_ENST00000543152.1_Missense_Mutation_p.N236T|C16orf62_ENST00000417362.2_Missense_Mutation_p.N420T|C16orf62_ENST00000448695.1_Missense_Mutation_p.N337T|C16orf62_ENST00000438132.3_Missense_Mutation_p.N576T|C16orf62_ENST00000542263.1_Missense_Mutation_p.N509T			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	487						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						CAGATTCTCAACGAAGCTTGG	0.353																																					p.N576T		Atlas-SNP	.											.	C16orf62	164	.	0			c.A1727C						.						118	113	115					16																	19640035		2197	4300	6497	SO:0001583	missense	57020	exon17			TTCTCAACGAAGC		CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.1460A>C	chr16.hg19:g.19640035A>C	ENSP00000251143:p.Asn487Thr	107.0	0.0		82.0	26.0	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Missense_Mutation	SNP	ENST00000251143.5	hg19		.	.	.	.	.	.	.	.	.	.	A	20.7	4.036077	0.75617	.	.	ENSG00000103544	ENST00000438132;ENST00000542263;ENST00000251143;ENST00000417362;ENST00000448695	T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39	5.96	3.67	0.42095	.	0.000000	0.85682	D	0.000000	T	0.67804	0.2932	M	0.74258	2.255	0.58432	D	0.999999	B;D	0.71674	0.031;0.998	B;D	0.78314	0.017;0.991	T	0.65348	-0.6190	9	.	.	.	-20.4469	8.5778	0.33609	0.8018:0.1306:0.0677:0.0	.	509;487	F5H7K1;Q7Z3J2	.;CP062_HUMAN	T	576;509;487;420;337	ENSP00000400815:N576T;ENSP00000442468:N509T;ENSP00000251143:N487T;ENSP00000395973:N420T;ENSP00000398009:N337T	.	N	+	2	0	C16orf62	19547536	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	6.750000	0.74888	0.468000	0.27243	0.533000	0.62120	AAC	.	.		0.353	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314		C	19640035	A	C	19640035	3	2	73	1	0	0	0	0	1	0	0	0	1827	43	2	5	1526	5	C16orf62	16	19640035	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	829935	19640035	70714718	491	9817										
ACSM5	54988	hgsc.bcm.edu	37	chr16	20432662	20432663	+	Frame_Shift_Ins	INS	-	-	C													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	taccagcggaaccaccggggINScccccaagatggtcgagcac							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:20432662_20432663insC	ENST00000331849.4	+	5	853_854	c.706_707insC	c.(706-708)gccfs	p.A236fs		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	236					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						AACCACCGGGGCCCCCAAGATG	0.545																																					p.A236fs		Atlas-Indel,Pindel	.											.	ACSM5	101	.	0			c.706_707insC						.																																			SO:0001589	frameshift_variant	54988	exon5			.		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"Acyl-CoA synthetase family"	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.711dupC	chr16.hg19:g.20432667_20432667dupC	ENSP00000327916:p.Ala236fs	86.0	0.0		67.0	30.0	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Frame_Shift_Ins	INS	ENST00000331849.4	hg19	CCDS10585.1																																																																																			.	.		0.545	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888		C	20432663	-	C	20432662	7	5	73	1	0	1	1	0	0	0	0	0	187	1203	42	0	720	0	ACSM5	16	20432662	Frame_Shift_Ins	INS	-	TCGA-CC-A7IH-01A-11D-A33K-10	792627	20432662	69922091	492	9818										
NSMCE1	197370	hgsc.bcm.edu	37	chr16	27268833	27268833	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgccatgggtcatcagcaacTggaggaagcgccggtggaca	15	11	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:27268833T>C	ENST00000361439.4	-	2	158	c.59A>G	c.(58-60)cAg>cGg	p.Q20R		NM_145080.3	NP_659547.2	Q8WV22	NSE1_HUMAN	non-SMC element 1 homolog (S. cerevisiae)	20	Interaction with NDNL2.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|intracellular signal transduction (GO:0035556)|positive regulation of response to DNA damage stimulus (GO:2001022)|protein ubiquitination (GO:0016567)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)	7						CATCAGCAACTGGAGGAAGCG	0.547																																					p.Q20R		Atlas-SNP	.											.	NSMCE1	28	.	0			c.A59G						.						97	103	101					16																	27268833		2117	4226	6343	SO:0001583	missense	197370	exon2			AGCAACTGGAGGA	AF161451	CCDS10628.2	16p12.1	2010-03-23	2006-07-05		ENSG00000169189	ENSG00000169189			29897	protein-coding gene	gene with protein product						11927594	Standard	XM_005255163		Approved	NSE1	uc002doi.1	Q8WV22	OTTHUMG00000131674	ENST00000361439.4:c.59A>G	chr16.hg19:g.27268833T>C	ENSP00000355077:p.Gln20Arg	146.0	0.0		106.0	49.0	NM_145080	D3DWF6|Q9P045|Q9P049	Missense_Mutation	SNP	ENST00000361439.4	hg19	CCDS10628.2	.	.	.	.	.	.	.	.	.	.	T	20.6	4.013620	0.75161	.	.	ENSG00000169189	ENST00000361439	T	0.41065	1.01	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.57710	0.2072	L	0.58510	1.815	0.48040	D	0.999576	D	0.67145	0.996	D	0.83275	0.996	T	0.57985	-0.7716	10	0.48119	T	0.1	.	10.7581	0.46249	0.0:0.0:0.0:1.0	.	20	Q8WV22	NSE1_HUMAN	R	20	ENSP00000355077:Q20R	ENSP00000355077:Q20R	Q	-	2	0	NSMCE1	27176334	1.000000	0.71417	0.993000	0.49108	0.970000	0.65996	3.278000	0.51662	2.024000	0.59613	0.460000	0.39030	CAG	.	.		0.547	NSMCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254577.3	NM_145080		C	27268833	T	C	27268833	3	2	73	1	0	0	0	0	1	0	0	0	10684	1580	55	2	769	2	NSMCE1	16	27268833	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	6836171	27268833	63085920	493	9819										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27472839	27472839	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagagcgagacaggccttggCtttctcagccagcgcttccg	12	13	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:27472839C>A	ENST00000356183.4	-	37	6177	c.6162G>T	c.(6160-6162)aaG>aaT	p.K2054N	GTF3C1_ENST00000561623.1_Missense_Mutation_p.K2029N|GTF3C1_ENST00000567806.1_5'Flank	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	2054					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CAGGCCTTGGCTTTCTCAGCC	0.612																																					p.K2054N		Atlas-SNP	.											.	GTF3C1	210	.	0			c.G6162T						.						87	75	79					16																	27472839		2197	4300	6497	SO:0001583	missense	2975	exon37			CCTTGGCTTTCTC	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.6162G>T	chr16.hg19:g.27472839C>A	ENSP00000348510:p.Lys2054Asn	68.0	0.0		45.0	18.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.146558	0.57044	.	.	ENSG00000077235	ENST00000356183	T	0.26518	1.73	5.12	5.12	0.69794	.	0.345333	0.29900	N	0.010906	T	0.45074	0.1324	M	0.70595	2.14	0.36818	D	0.886269	P;D	0.59357	0.907;0.985	B;P	0.56563	0.372;0.801	T	0.56001	-0.8051	10	0.66056	D	0.02	-7.4463	15.3242	0.74147	0.0:1.0:0.0:0.0	.	2054;2029	Q12789;Q12789-3	TF3C1_HUMAN;.	N	2054	ENSP00000348510:K2054N	ENSP00000348510:K2054N	K	-	3	2	GTF3C1	27380340	0.997000	0.39634	0.833000	0.33012	0.125000	0.20455	0.989000	0.29629	2.393000	0.81446	0.556000	0.70494	AAG	.	.		0.612	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		A	27472839	C	A	27472839	3	1	73	1	0	0	0	0	1	0	0	0	6881	796	28	3	171	3	GTF3C1	16	27472839	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	204006	27472839	62881914	494	9820										
XPO6	23214	hgsc.bcm.edu	37	chr16	28137133	28137141	+	In_Frame_Del	DEL	CGGCAGTCG	CGGCAGTCG	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcagggagcagtgcagccgcCggcagtcgttctccgccgtg							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	CGGCAGTCG	CGGCAGTCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:28137133_28137141delCGGCAGTCG	ENST00000304658.5	-	13	2135_2143	c.1635_1643delCGACTGCCG	c.(1633-1644)aacgactgccgg>aag	p.545_548NDCR>K	XPO6_ENST00000565698.1_In_Frame_Del_p.531_534NDCR>K	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	545					protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						GTGCAGCCGCCGGCAGTCGTTCTCCGCCG	0.565																																					p.546_548del		Atlas-Indel,Pindel	.											.	XPO6	177	.	0			c.1636_1644del						.																																			SO:0001651	inframe_deletion	23214	exon13			.	AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"Exportins"	19733	protein-coding gene	gene with protein product		608411	"RAN binding protein 20"	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.1635_1643delCGACTGCCG	chr16.hg19:g.28137133_28137141delCGGCAGTCG	ENSP00000302790:p.Asn545_Arg548delinsLys	70.0	0.0		50.0	17.0	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	In_Frame_Del	DEL	ENST00000304658.5	hg19	CCDS42135.1																																																																																			.	.		0.565	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		-	28137141	CGGCAGTCG	-	28137133	7	5	73	1	0	1	0	1	0	0	0	0	17463	652	23	0	1782	0	XPO6	16	28137133	In_Frame_Del	DEL	CGGCAGTCG	TCGA-CC-A7IH-01A-11D-A33K-10	664294	28137133	62217620	495	9821										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30749727	30749727	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgagactagtgccagcccggGaagcccgtctgtccgcagca	13	14	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:30749727G>A	ENST00000262518.4	+	34	8751	c.8366G>A	c.(8365-8367)gGa>gAa	p.G2789E	RP11-2C24.4_ENST00000483578.1_lincRNA|SRCAP_ENST00000395059.2_Missense_Mutation_p.G2727E|SRCAP_ENST00000344771.4_Missense_Mutation_p.G2631E	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2789	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GCCAGCCCGGGAAGCCCGTCT	0.652																																					p.G2789E		Atlas-SNP	.											.	SRCAP	298	.	0			c.G8366A						.						53	61	58					16																	30749727		2197	4300	6497	SO:0001583	missense	10847	exon34			GCCCGGGAAGCCC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.8366G>A	chr16.hg19:g.30749727G>A	ENSP00000262518:p.Gly2789Glu	79.0	0.0		66.0	9.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	5.004	0.186388	0.09495	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.95272	-3.63;-3.66;-3.66	5.04	5.04	0.67666	.	0.129031	0.35585	N	0.003102	D	0.88621	0.6486	N	0.08118	0	0.33117	D	0.541292	P;P	0.50272	0.933;0.802	P;B	0.44811	0.461;0.272	D	0.91772	0.5428	10	0.56958	D	0.05	-2.9378	13.7558	0.62935	0.0:0.0:1.0:0.0	.	2727;2789	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	E	2789;2727;2631	ENSP00000262518:G2789E;ENSP00000378499:G2727E;ENSP00000343042:G2631E	ENSP00000262518:G2789E	G	+	2	0	SRCAP	30657228	1.000000	0.71417	0.994000	0.49952	0.064000	0.16182	4.661000	0.61518	2.629000	0.89072	0.591000	0.81541	GGA	.	.		0.652	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30749727	G	A	30749727	3	1	73	1	0	0	0	0	1	0	0	0	15150	1174	41	3	8492	3	SRCAP	16	30749727	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	2612594	30749727	59605026	496	9822										
C16orf93	90835	hgsc.bcm.edu	37	chr16	30771751	30771751	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggctctgctcaggacaccctAgctccagcagctcagccagc	10	17	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:30771751A>T	ENST00000543610.1	-	4	1284	c.323T>A	c.(322-324)cTa>cAa	p.L108Q	RNF40_ENST00000357890.5_5'Flank|C16orf93_ENST00000541260.1_Missense_Mutation_p.L108Q|RNF40_ENST00000563683.1_5'Flank|RNF40_ENST00000402121.3_5'Flank|PHKG2_ENST00000563588.1_3'UTR|C16orf93_ENST00000545825.1_Missense_Mutation_p.L108Q|RNF40_ENST00000324685.6_5'Flank	NM_001014979.2	NP_001014979.2	A1A4V9	CP093_HUMAN	chromosome 16 open reading frame 93	108										breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)	11						AGGACACCCTAGCTCCAGCAG	0.607																																					p.L108Q		Atlas-SNP	.											.	C16orf93	33	.	0			c.T323A						.						63	68	66					16																	30771751		2197	4300	6497	SO:0001583	missense	90835	exon4			CACCCTAGCTCCA	BC042548	CCDS32434.1, CCDS32434.2, CCDS55993.1	16p11.2	2012-10-10			ENSG00000196118	ENSG00000196118			28078	protein-coding gene	gene with protein product							Standard	NM_001195620		Approved	MGC104706	uc002dzm.3	A1A4V9	OTTHUMG00000167926	ENST00000543610.1:c.323T>A	chr16.hg19:g.30771751A>T	ENSP00000437532:p.Leu108Gln	115.0	0.0		98.0	35.0	NM_001195620	A1A4V8|F5GX13|Q569G2	Missense_Mutation	SNP	ENST00000543610.1	hg19	CCDS32434.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.68|16.68	3.191227|3.191227	0.58017|0.58017	.|.	.|.	ENSG00000196118|ENSG00000196118	ENST00000354963;ENST00000543610;ENST00000545825|ENST00000535476	.|.	.|.	.|.	4.48|4.48	4.48|4.48	0.54585|0.54585	.|.	0.219797|.	0.30201|.	N|.	0.010173|.	T|.	0.54983|.	0.1892|.	L|L	0.46157|0.46157	1.445|1.445	0.34591|0.34591	D|D	0.715468|0.715468	D;D;D|.	0.89917|.	1.0;0.999;0.999|.	D;D;D|.	0.70016|.	0.967;0.943;0.943|.	T|.	0.64659|.	-0.6355|.	9|.	0.62326|.	D|.	0.03|.	-5.0472|-5.0472	12.9117|12.9117	0.58182|0.58182	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	108;71;108|.	F5GX13;A1A4V9-2;A1A4V9|.	.;.;CP093_HUMAN|.	Q|K	71;108;108|5	.|.	ENSP00000347050:L71Q|.	L|X	-|-	2|1	0|0	C16orf93|C16orf93	30679252|30679252	0.879000|0.879000	0.30193|0.30193	0.834000|0.834000	0.33040|0.33040	0.354000|0.354000	0.29330|0.29330	5.885000|5.885000	0.69736|0.69736	1.890000|1.890000	0.54733|0.54733	0.379000|0.379000	0.24179|0.24179	CTA|TAG	.	.		0.607	C16orf93-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397089.1	NM_001014979		T	30771751	A	T	30771751	3	4	73	1	0	0	0	0	1	0	0	0	1848	420	15	4	696	4	C16orf93	16	30771751	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	22024	30771751	59583002	497	9823										
PHKB	5257	hgsc.bcm.edu	37	chr16	47622887	47622887	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gatgatgaagttctttttagCcagacacttgataaagtggt	10	5	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:47622887C>G	ENST00000323584.5	+	10	966	c.942C>G	c.(940-942)agC>agG	p.S314R	PHKB_ENST00000455779.1_Missense_Mutation_p.S307R|PHKB_ENST00000567402.1_3'UTR|PHKB_ENST00000566044.1_Missense_Mutation_p.S307R|PHKB_ENST00000299167.8_Missense_Mutation_p.S314R	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	314					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				TTCTTTTTAGCCAGACACTTG	0.403																																					p.S314R		Atlas-SNP	.											.	PHKB	298	.	0			c.C942G						.						89	88	88					16																	47622887		2201	4300	6501	SO:0001583	missense	5257	exon10			TTTTAGCCAGACA		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.942C>G	chr16.hg19:g.47622887C>G	ENSP00000313504:p.Ser314Arg	68.0	0.0		73.0	26.0	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	C	9.856	1.194993	0.22037	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.93659	-3.26;-3.26	6.07	1.49	0.22878	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.253140	0.51477	D	0.000087	D	0.85622	0.5739	L	0.28192	0.835	0.49389	D	0.999789	B;B	0.18610	0.005;0.029	B;B	0.25759	0.063;0.049	T	0.74512	-0.3641	10	0.29301	T	0.29	-0.7234	5.8152	0.18488	0.1413:0.5562:0.0:0.3025	.	314;307	Q93100;Q93100-4	KPBB_HUMAN;.	R	307;307;314	ENSP00000414345:S307R;ENSP00000313504:S314R	ENSP00000299167:S307R	S	+	3	2	PHKB	46180388	0.258000	0.24033	0.550000	0.28217	0.986000	0.74619	0.702000	0.25631	0.441000	0.26529	-0.237000	0.12165	AGC	.	.		0.403	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			G	47622887	C	G	47622887	3	3	73	1	0	0	0	0	1	0	0	0	11854	738	26	4	1039	4	PHKB	16	47622887	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	16851136	47622887	42731866	498	9824										
RBL2	5934	hgsc.bcm.edu	37	chr16	53515713	53515713	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aatgctttctcctcgagaaaAgattttctattacttcagca	5	9	3	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:53515713A>C	ENST00000262133.6	+	21	3352	c.3215A>C	c.(3214-3216)aAg>aCg	p.K1072T	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Missense_Mutation_p.K451T	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	1072					chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CCTCGAGAAAAGATTTTCTAT	0.398																																					p.K1072T		Atlas-SNP	.											.	RBL2	115	.	0			c.A3215C						.						103	101	101					16																	53515713		2198	4300	6498	SO:0001583	missense	5934	exon21			GAGAAAAGATTTT	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.3215A>C	chr16.hg19:g.53515713A>C	ENSP00000262133:p.Lys1072Thr	121.0	0.0		111.0	57.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	hg19	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	A	15.79	2.938204	0.52972	.	.	ENSG00000103479	ENST00000262133;ENST00000379935;ENST00000544545	T;T	0.58060	0.36;0.36	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.72724	0.3496	M	0.78049	2.395	0.33951	D	0.644424	D;B;D	0.76494	0.998;0.409;0.999	D;B;D	0.78314	0.991;0.082;0.986	T	0.81276	-0.1006	10	0.46703	T	0.11	-16.0336	15.8276	0.78727	1.0:0.0:0.0:0.0	.	451;782;1072	B7Z913;E9PG04;Q08999	.;.;RBL2_HUMAN	T	1072;782;451	ENSP00000262133:K1072T;ENSP00000444685:K451T	ENSP00000262133:K1072T	K	+	2	0	RBL2	52073214	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.525000	0.67110	2.195000	0.70347	0.533000	0.62120	AAG	.	.		0.398	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		C	53515713	A	C	53515713	3	2	73	1	0	0	0	0	1	0	0	0	13125	72	3	5	3297	5	RBL2	16	53515713	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	5892826	53515713	36839040	499	9825										
CCDC135	84229	hgsc.bcm.edu	37	chr16	57760018	57760018	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttccgcaacccagcgaagccCgcggaggaggacgtggcaga	15	13	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:57760018C>A	ENST00000360716.3	+	14	2018	c.1797C>A	c.(1795-1797)ccC>ccA	p.P599P	CCDC135_ENST00000336825.8_Silent_p.P534P|CCDC135_ENST00000394337.4_Silent_p.P599P			Q8IY82	CC135_HUMAN		599					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						CAGCGAAGCCCGCGGAGGAGG	0.607																																					p.P599P		Atlas-SNP	.											.	CCDC135	97	.	0			c.C1797A						.						43	38	40					16																	57760018		2198	4298	6496	SO:0001819	synonymous_variant	84229	exon13			GAAGCCCGCGGAG																												ENST00000360716.3:c.1797C>A	chr16.hg19:g.57760018C>A		294.0	0.0		239.0	116.0	NM_032269	A8K943|Q8NAA0|Q9H080	Silent	SNP	ENST00000360716.3	hg19	CCDS10787.1																																																																																			.	.		0.607	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2			A	57760018	C	A	57760018	2	1	73	1	0	0	0	0	0	0	0	1	2771	639	23	1		1	CCDC135	16	57760018	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	4244305	57760018	32594735	500	9826										
NFAT5	10725	hgsc.bcm.edu	37	chr16	69703941	69703943	+	In_Frame_Del	DEL	AGA	AGA	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	catagctgttcagtgaaaggAgaagaagaagtgtttttaat							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:69703941_69703943delAGA	ENST00000354436.2	+	7	1695_1697	c.1377_1379delAGA	c.(1375-1380)ggagaa>gga	p.E462del	NFAT5_ENST00000567239.1_In_Frame_Del_p.E480del|NFAT5_ENST00000349945.1_In_Frame_Del_p.E386del|NFAT5_ENST00000393742.2_In_Frame_Del_p.E386del|NFAT5_ENST00000566899.1_In_Frame_Del_p.E386del|NFAT5_ENST00000432919.1_In_Frame_Del_p.E480del	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	462					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						CAGTGAAAGGAGAAGAAGAAGTG	0.374																																					p.477_478del		Atlas-Indel,Pindel	.											.	NFAT5	184	.	0			c.1430_1432del						.																																			SO:0001651	inframe_deletion	10725	exon8			.	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.1377_1379delAGA	chr16.hg19:g.69703947_69703949delAGA	ENSP00000346420:p.Glu462del	305.0	0.0		233.0	85.0	NM_001113178	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	In_Frame_Del	DEL	ENST00000354436.2	hg19	CCDS10881.1																																																																																			.	.		0.374	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		-	69703943	AGA	-	69703941	7	5	73	1	0	1	0	1	0	0	0	0	10369	291	11	0	1461	0	NFAT5	16	69703941	In_Frame_Del	DEL	AGA	TCGA-CC-A7IH-01A-11D-A33K-10	11943923	69703941	20650812	501	9827										
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76509861	76509861	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgcccaactattgtgaacacGgtggggagtgttcccagtcc	12	11	0	1	rs150806968		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:76509861G>A	ENST00000476707.1	+	10	1829	c.1690G>A	c.(1690-1692)Ggt>Agt	p.G564S	CNTNAP4_ENST00000377504.4_Missense_Mutation_p.G512S|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.G560S|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.G488S			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	561	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)		p.G488R(1)|p.G560R(1)|p.G536R(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						TTGTGAACACGGTGGGGAGTG	0.428													G|||	1	0.000199681	8e-04	0	5008	,	,		21415	0		0	False		,,,				2504	0				p.G488S		Atlas-SNP	.											CNTNAP4_ENST00000478060,neck,malignant_melanoma,0,6	CNTNAP4	600	.	3	Substitution - Missense(3)	lung(3)	c.G1462A						.	G	SER/GLY,SER/GLY	0,4396		0,0,2198	159	140	147		1680,1462	5.3	0.2	16	dbSNP_134	147	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	CNTNAP4	NM_033401.3,NM_138994.3	56,56	0,2,6496	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	561/1309,488/1236	76509861	2,12994	2198	4300	6498	SO:0001583	missense	85445	exon10			GAACACGGTGGGG	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.1690G>A	chr16.hg19:g.76509861G>A	ENSP00000417628:p.Gly564Ser	112.0	0.0		75.0	29.0	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	hg19		.	.	.	.	.	.	.	.	.	.	G	18.15	3.560997	0.65538	0.0	2.33E-4	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.32	5.32	0.75619	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.40469	N	0.001099	T	0.70046	0.3179	.	.	.	0.51012	D	0.9999	D;D;D;D	0.89917	1.0;1.0;0.999;0.999	D;D;D;D	0.71414	0.953;0.973;0.953;0.911	T	0.72487	-0.4278	9	0.72032	D	0.01	.	12.5047	0.55975	0.0756:0.0:0.9244:0.0	.	488;564;536;561	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	S	560;512;488;564	ENSP00000306893:G560S;ENSP00000439733:G512S;ENSP00000418741:G488S;ENSP00000417628:G564S	ENSP00000306893:G560S	G	+	1	0	CNTNAP4	75067362	1.000000	0.71417	0.239000	0.24122	0.130000	0.20726	5.579000	0.67457	2.773000	0.95371	0.655000	0.94253	GGT	.	G|1.000;A|0.000		0.428	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		A	76509861	G	A	76509861	3	1	73	1	0	0	0	0	1	0	0	0	3651	1116	39	1	1736	1	CNTNAP4	16	76509861	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	6805920	76509861	13844892	502	9828										
OSGIN1	29948	hgsc.bcm.edu	37	chr16	83998905	83998905	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgctgtgggcccgcaacgtgGtcctcgccacaggcacgttc	13	16	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:83998905G>A	ENST00000343939.2	+	7	1359	c.976G>A	c.(976-978)Gtc>Atc	p.V326I	OSGIN1_ENST00000361711.3_Missense_Mutation_p.V243I|OSGIN1_ENST00000393306.1_Missense_Mutation_p.V243I			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	326					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						CCGCAACGTGGTCCTCGCCAC	0.706																																					p.V243I		Atlas-SNP	.											.	OSGIN1	33	.	0			c.G727A						.						29	34	32					16																	83998905		2199	4298	6497	SO:0001583	missense	29948	exon6			AACGTGGTCCTCG	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"bone marrow stromal cell-derived growth inhibitor", "pregnancy induced growth inhibitor"	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.976G>A	chr16.hg19:g.83998905G>A	ENSP00000343376:p.Val326Ile	42.0	0.0		35.0	15.0	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	hg19		.	.	.	.	.	.	.	.	.	.	G	28.2	4.900108	0.92035	.	.	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.42900	0.96;0.96;0.96	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.55305	0.1912	L	0.38838	1.175	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.55872	-0.8072	10	0.46703	T	0.11	-7.2067	16.8408	0.85968	0.0:0.0:1.0:0.0	.	326	Q9UJX0	OSGI1_HUMAN	I	326;243;243	ENSP00000343376:V326I;ENSP00000355374:V243I;ENSP00000376983:V243I	ENSP00000343376:V326I	V	+	1	0	OSGIN1	82556406	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	9.713000	0.98740	2.211000	0.71520	0.467000	0.42956	GTC	.	.		0.706	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		A	83998905	G	A	83998905	3	1	73	1	0	0	0	0	1	0	0	0	11298	1261	44	3	1002	3	OSGIN1	16	83998905	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	7489044	83998905	6355848	503	9829										
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84459339	84459339	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gatgtttttgtctcttccccAggtctcatcatgctcattgg	8	11	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:84459339A>T	ENST00000262429.4	+	11	1008		c.e11-1		ATP2C2_ENST00000420010.2_Splice_Site|ATP2C2_ENST00000416219.2_Splice_Site	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2						ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						TCTCTTCCCCAGGTCTCATCA	0.498																																					.		Atlas-SNP	.											.	ATP2C2	75	.	0			c.920-2A>T						.						254	249	251					16																	84459339		2010	4185	6195	SO:0001630	splice_region_variant	9914	exon11			TTCCCCAGGTCTC	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"ATPases / P-type"	29103	protein-coding gene	gene with protein product	"secretory pathway calcium ATPase 2"	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.920-1A>T	chr16.hg19:g.84459339A>T		152.0	0.0		168.0	64.0	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Splice_Site	SNP	ENST00000262429.4	hg19	CCDS42207.1	.	.	.	.	.	.	.	.	.	.	A	12.01	1.809797	0.31961	.	.	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5089	0.61499	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP2C2	83016840	1.000000	0.71417	0.949000	0.38748	0.127000	0.20565	8.213000	0.89758	1.883000	0.54544	0.533000	0.62120	.	.	.		0.498	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	Intron	T	84459339	A	T	84459339	5	4	73	1	0	0	0	0	0	0	1	0	1144	202	7	4	960	4	ATP2C2	16	84459339	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	460434	84459339	5895414	504	9830										
FOXF1	2294	hgsc.bcm.edu	37	chr16	86544400	86544400	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgacgctgagcgagatctaCcagttcctgcagagccgctt	11	13	1	4	rs121909336		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:86544400C>A	ENST00000262426.4	+	1	268	c.225C>A	c.(223-225)taC>taA	p.Y75*	FENDRR_ENST00000595886.1_lincRNA	NM_001451.2	NP_001442.2	Q12946	FOXF1_HUMAN	forkhead box F1	75					blood vessel development (GO:0001568)|branching involved in open tracheal system development (GO:0060446)|cardiac left ventricle morphogenesis (GO:0003214)|cellular response to cytokine stimulus (GO:0071345)|cellular response to organic cyclic compound (GO:0071407)|detection of wounding (GO:0014822)|determination of left/right symmetry (GO:0007368)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic ectodermal digestive tract morphogenesis (GO:0048613)|embryonic foregut morphogenesis (GO:0048617)|endocardial cushion development (GO:0003197)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lateral mesodermal cell differentiation (GO:0048371)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung vasculature development (GO:0060426)|mesenchyme migration (GO:0090131)|midgut development (GO:0007494)|morphogenesis of a branching structure (GO:0001763)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smooth muscle cell differentiation (GO:0051150)|renal system development (GO:0072001)|respiratory tube development (GO:0030323)|right lung morphogenesis (GO:0060461)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|smoothened signaling pathway (GO:0007224)|somitogenesis (GO:0001756)|trachea development (GO:0060438)|ureter development (GO:0072189)|vasculogenesis (GO:0001570)|venous blood vessel development (GO:0060841)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(1)	12						GCGAGATCTACCAGTTCCTGC	0.617																																					p.Y75X		Atlas-SNP	.											.	FOXF1	59	.	0			c.C225A						.						60	64	63					16																	86544400		2198	4300	6498	SO:0001587	stop_gained	2294	exon1			GATCTACCAGTTC	U13219	CCDS10957.2	16q24	2008-02-05			ENSG00000103241	ENSG00000103241		"Forkhead boxes"	3809	protein-coding gene	gene with protein product		601089		FKHL5		8825632, 7957066	Standard	NM_001451		Approved	FREAC1	uc002fjl.3	Q12946	OTTHUMG00000137651	ENST00000262426.4:c.225C>A	chr16.hg19:g.86544400C>A	ENSP00000262426:p.Tyr75*	136.0	0.0		121.0	43.0	NM_001451	B2RAF4|Q5FWE5	Nonsense_Mutation	SNP	ENST00000262426.4	hg19	CCDS10957.2	.	.	.	.	.	.	.	.	.	.	C	37	6.200035	0.97371	.	.	ENSG00000103241	ENST00000262426	.	.	.	4.21	4.21	0.49690	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8897	0.79286	0.0:1.0:0.0:0.0	.	.	.	.	X	75	.	ENSP00000262426:Y75X	Y	+	3	2	FOXF1	85101901	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.392000	0.44433	2.052000	0.61016	0.650000	0.86243	TAC	.	.		0.617	FOXF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000269103.2	NM_001451		A	86544400	C	A	86544400	4	1	73	1	0	0	0	0	0	1	0	0	6013	518	18	3	227	3	FOXF1	16	86544400	Nonsense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	2085061	86544400	3810353	505	9831										
IL17C	27189	hgsc.bcm.edu	37	chr16	88705453	88705453	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggcccaccatgacccctcccTcagggggcacccccacagtc	9	21	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr16:88705453T>A	ENST00000244241.4	+	2	120	c.71T>A	c.(70-72)cTc>cAc	p.L24H		NM_013278.3	NP_037410.1	Q9P0M4	IL17C_HUMAN	interleukin 17C	24					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|neutrophil differentiation (GO:0030223)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)			large_intestine(1)|lung(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0477)		GACCCCTCCCTCAGGGGGCAC	0.672																																					p.L24H		Atlas-SNP	.											.	IL17C	6	.	0			c.T71A						.						85	95	92					16																	88705453		1973	4163	6136	SO:0001583	missense	27189	exon2			CCTCCCTCAGGGG	AF152099	CCDS42217.1	16q24	2011-07-14			ENSG00000124391	ENSG00000124391		"Interleukins and interleukin receptors"	5983	protein-coding gene	gene with protein product		604628				10639155	Standard	NM_013278		Approved	IL-17C, CX2, IL-21, MGC126884, MGC138401	uc002fla.3	Q9P0M4		ENST00000244241.4:c.71T>A	chr16.hg19:g.88705453T>A	ENSP00000244241:p.Leu24His	79.0	0.0		71.0	8.0	NM_013278	Q3MIG8|Q9HC75	Missense_Mutation	SNP	ENST00000244241.4	hg19	CCDS42217.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.142756	0.57044	.	.	ENSG00000124391	ENST00000244241	T	0.49432	0.78	4.74	-0.698	0.11280	.	1.476710	0.04236	N	0.336041	T	0.34571	0.0902	L	0.29908	0.895	0.09310	N	1	D	0.58620	0.983	B	0.43783	0.431	T	0.26087	-1.0113	10	0.72032	D	0.01	-5.876	1.436	0.02343	0.1416:0.165:0.1467:0.5467	.	24	Q9P0M4	IL17C_HUMAN	H	24	ENSP00000244241:L24H	ENSP00000244241:L24H	L	+	2	0	IL17C	87232954	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.519000	0.06260	-0.090000	0.12462	0.454000	0.30748	CTC	.	.		0.672	IL17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422575.1	NM_013278		A	88705453	T	A	88705453	3	1	73	1	0	0	0	0	1	0	0	0	7645	1551	54	4	77	4	IL17C	16	88705453	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2161053	88705453	1649300	506	9832										
OR1A1	8383	hgsc.bcm.edu	37	chr17	3119514	3119514	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tttcatgtgaagatgatgtaCctaggggttggcattttctc	11	6	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:3119514C>A	ENST00000304094.1	+	1	600	c.600C>A	c.(598-600)taC>taA	p.Y200*		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						AGATGATGTACCTAGGGGTTG	0.478																																					p.Y200X		Atlas-SNP	.											OR1A1,NS,neuroblastoma,0,1	OR1A1	54	.	0			c.C600A						.						276	237	250					17																	3119514		2203	4300	6503	SO:0001587	stop_gained	8383	exon1			GATGTACCTAGGG	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"GPCR / Class A : Olfactory receptors"	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.600C>A	chr17.hg19:g.3119514C>A	ENSP00000305207:p.Tyr200*	99.0	0.0		85.0	36.0	NM_014565	A5D914|Q6IFM1|Q6NTA9|Q96R87	Nonsense_Mutation	SNP	ENST00000304094.1	hg19	CCDS11022.1	.	.	.	.	.	.	.	.	.	.	C	3.660	-0.069746	0.07228	.	.	ENSG00000172146	ENST00000304094	.	.	.	4.96	-5.26	0.02772	.	0.148494	0.31897	N	0.006899	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.4587	0.67433	0.0:0.2699:0.0:0.7301	.	.	.	.	X	200	.	ENSP00000305207:Y200X	Y	+	3	2	OR1A1	3066264	0.000000	0.05858	0.069000	0.20011	0.038000	0.13279	-1.588000	0.02106	-0.827000	0.04278	-2.560000	0.00174	TAC	.	.		0.478	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565		A	3119514	C	A	3119514	4	1	73	1	0	0	0	0	0	1	0	0	10958	518	18	3	602	3	OR1A1	17	3119514	Nonsense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10		3119514	78075696	507	9833										
SPATA22	84690	hgsc.bcm.edu	37	chr17	3349813	3349813	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctgtgcatgttcacgccaaTacttcatgctttcaataact	5	11	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:3349813T>C	ENST00000573128.1	-	7	1238	c.755A>G	c.(754-756)tAt>tGt	p.Y252C	SPATA22_ENST00000268981.5_Missense_Mutation_p.Y252C|SPATA22_ENST00000397168.3_Missense_Mutation_p.Y252C|SPATA22_ENST00000355380.4_Missense_Mutation_p.Y209C|SPATA22_ENST00000575375.1_Missense_Mutation_p.Y252C|SPATA22_ENST00000541913.1_Missense_Mutation_p.Y236C|SPATA22_ENST00000572969.1_Missense_Mutation_p.Y252C			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	252					fertilization (GO:0009566)|gamete generation (GO:0007276)|meiotic DNA repair synthesis (GO:0000711)|regulation of meiotic cell cycle (GO:0051445)|reproductive system development (GO:0061458)|synapsis (GO:0007129)	chromosome (GO:0005694)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)	19						TTCACGCCAATACTTCATGCT	0.308																																					p.Y252C		Atlas-SNP	.											.	SPATA22	49	.	0			c.A755G						.						82	80	81					17																	3349813		2202	4295	6497	SO:0001583	missense	84690	exon7			CGCCAATACTTCA	AY035868	CCDS11027.1, CCDS54066.1, CCDS54067.1	17p13.3	2005-12-19							30705	protein-coding gene	gene with protein product						12477932	Standard	NM_001170696		Approved	NYD-SP20	uc002fvn.3	Q8NHS9		ENST00000573128.1:c.755A>G	chr17.hg19:g.3349813T>C	ENSP00000459580:p.Tyr252Cys	423.0	0.0		409.0	155.0	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Missense_Mutation	SNP	ENST00000573128.1	hg19	CCDS11027.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.584582	0.65992	.	.	ENSG00000141255	ENST00000355380;ENST00000397168;ENST00000268981;ENST00000541913	T;T;T;T	0.80738	-1.41;-1.41;1.83;-1.41	5.26	5.26	0.73747	.	0.089874	0.44285	D	0.000462	D	0.83524	0.5273	L	0.27053	0.805	0.36068	D	0.841956	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.992;0.997;0.992;0.999	D	0.88270	0.2929	10	0.72032	D	0.01	-20.0111	14.6709	0.68942	0.0:0.0:0.0:1.0	.	236;252;209;252	F5GWB9;B4DXB1;Q8NHS9-2;Q8NHS9	.;.;.;SPT22_HUMAN	C	209;252;252;236	ENSP00000347541:Y209C;ENSP00000380354:Y252C;ENSP00000268981:Y252C;ENSP00000441920:Y236C	ENSP00000268981:Y252C	Y	-	2	0	SPATA22	3296563	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	4.567000	0.60850	2.128000	0.65567	0.533000	0.62120	TAT	.	.		0.308	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598		C	3349813	T	C	3349813	3	2	73	1	0	0	0	0	1	0	0	0	15023	1406	49	2	348	2	SPATA22	17	3349813	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	230299	3349813	77845397	508	9834										
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3937451	3937451	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggcgtctacctctgctggcaAaagacggataattaactggc	11	10	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:3937451A>G	ENST00000381638.2	-	40	6566	c.6442T>C	c.(6442-6444)Ttg>Ctg	p.L2148L		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2148							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						TCTGCTGGCAAAAGACGGATA	0.512																																					p.L2148L		Atlas-SNP	.											.	ZZEF1	195	.	0			c.T6442C						.						153	143	147					17																	3937451		2203	4300	6503	SO:0001819	synonymous_variant	23140	exon40			CTGGCAAAAGACG	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.6442T>C	chr17.hg19:g.3937451A>G		199.0	0.0		202.0	78.0	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	hg19	CCDS11043.1																																																																																			.	.		0.512	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		G	3937451	A	G	3937451	2	3	73	1	0	0	0	0	0	0	0	1	18270	11	1	2		2	ZZEF1	17	3937451	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	587638	3937451	77257759	509	9835										
ZMYND15	84225	hgsc.bcm.edu	37	chr17	4649179	4649179	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agggagcggggcccgcccggCgcccgggcccccacccccat	15	21	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:4649179C>A	ENST00000433935.1	+	14	2180	c.2123C>A	c.(2122-2124)gCg>gAg	p.A708E	ZMYND15_ENST00000269289.6_Missense_Mutation_p.A669E|ZMYND15_ENST00000592813.1_Missense_Mutation_p.A669E|ZMYND15_ENST00000573751.2_Missense_Mutation_p.A716E	NM_001136046.2|NM_001267822.1	NP_001129518.1|NP_001254751.1	Q9H091	ZMY15_HUMAN	zinc finger, MYND-type containing 15	708	Pro-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)	18						gcccgcccggcgcccgggccc	0.726																																					p.A716E		Atlas-SNP	.											.	ZMYND15	87	.	0			c.C2147A						.						4	5	5					17																	4649179		1979	3967	5946	SO:0001583	missense	84225	exon14			GCCCGGCGCCCGG	AL136893	CCDS11053.1, CCDS45584.1, CCDS58506.1	17p13.3	2008-05-02			ENSG00000141497	ENSG00000141497		"Zinc fingers, MYND-type"	20997	protein-coding gene	gene with protein product		614312				11230166	Standard	NM_001136046		Approved	DKFZp434N127	uc002fyu.3	Q9H091	OTTHUMG00000090760	ENST00000433935.1:c.2123C>A	chr17.hg19:g.4649179C>A	ENSP00000391742:p.Ala708Glu	315.0	0.0		245.0	129.0	NM_001267822	B4DXY5|I3L296	Missense_Mutation	SNP	ENST00000433935.1	hg19	CCDS45584.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.188734	0.38609	.	.	ENSG00000141497	ENST00000433935;ENST00000269289	T;T	0.55930	0.49;0.58	4.37	1.2	0.21068	.	0.163809	0.28834	N	0.013983	T	0.41119	0.1145	L	0.29908	0.895	0.09310	N	1	P;P	0.43431	0.807;0.807	P;P	0.45377	0.478;0.478	T	0.29671	-1.0004	10	0.87932	D	0	-1.7672	6.7105	0.23274	0.0:0.6913:0.0:0.3087	.	708;669	B4DXY5;Q9H091	.;ZMY15_HUMAN	E	708;669	ENSP00000391742:A708E;ENSP00000269289:A669E	ENSP00000269289:A669E	A	+	2	0	ZMYND15	4595928	0.119000	0.22226	0.001000	0.08648	0.003000	0.03518	1.854000	0.39368	0.199000	0.20427	0.655000	0.94253	GCG	.	.		0.726	ZMYND15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439580.1	NM_032265		A	4649179	C	A	4649179	3	1	73	1	0	0	0	0	1	0	0	0	17723	768	27	1	2173	1	ZMYND15	17	4649179	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	711728	4649179	76546031	510	9836										
SAT2	112483	hgsc.bcm.edu	37	chr17	7530941	7530941	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctccttggcctctcggatccGcacggaagccatccggatcc	10	17	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:7530941G>T	ENST00000269298.5	-	1	232	c.13C>A	c.(13-15)Cgg>Agg	p.R5R	SHBG_ENST00000340624.5_5'Flank|SHBG_ENST00000574539.1_Intron|SAT2_ENST00000380466.2_5'UTR|SHBG_ENST00000441599.2_5'Flank|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000575903.1_5'Flank|SAT2_ENST00000573566.1_Silent_p.R5R|SHBG_ENST00000576728.1_Intron|SHBG_ENST00000572262.1_Intron|SHBG_ENST00000380450.4_5'Flank|SHBG_ENST00000416273.3_5'Flank|SHBG_ENST00000570547.1_Intron|SHBG_ENST00000575314.1_Intron|SHBG_ENST00000576478.1_Intron	NM_133491.3	NP_597998.1	Q96F10	SAT2_HUMAN	spermidine/spermine N1-acetyltransferase family member 2	5	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				nor-spermidine metabolic process (GO:0046204)|putrescine acetylation (GO:0032920)|putrescine catabolic process (GO:0009447)|spermidine acetylation (GO:0032918)|spermine acetylation (GO:0032919)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	diamine N-acetyltransferase activity (GO:0004145)	p.?(1)		kidney(1)|large_intestine(2)	3				READ - Rectum adenocarcinoma(115;0.166)	Spermine(DB00127)	TCTCGGATCCGCACGGAAGCC	0.622																																					p.R5R		Atlas-SNP	.											.	SAT2	8	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.C13A						.						48	44	45					17																	7530941		2203	4300	6503	SO:0001819	synonymous_variant	112483	exon1			GGATCCGCACGGA	AF348524	CCDS11116.1	17p13.2	2011-11-16	2008-01-07		ENSG00000141504	ENSG00000141504	2.3.1.57		23160	protein-coding gene	gene with protein product	"diamine N-acetyltransferase 2"	611463	"spermidine/spermine N1-acetyltransferase 2"			15283699, 17558023	Standard	NM_133491		Approved	SSAT2	uc002gic.2	Q96F10	OTTHUMG00000108152	ENST00000269298.5:c.13C>A	chr17.hg19:g.7530941G>T		101.0	0.0		89.0	31.0	NM_133491		Silent	SNP	ENST00000269298.5	hg19	CCDS11116.1	.	.	.	.	.	.	.	.	.	.	G	9.451	1.090525	0.20471	.	.	ENSG00000141504	ENST00000380466	.	.	.	4.71	1.28	0.21552	.	0.297139	0.18269	N	0.146396	T	0.52175	0.1718	.	.	.	0.54753	D	0.999983	.	.	.	.	.	.	T	0.31336	-0.9947	6	0.19147	T	0.46	-33.8505	10.6193	0.45470	0.0:0.0:0.4035:0.5965	.	.	.	.	E	78	.	ENSP00000369833:A78E	A	-	2	0	SAT2	7471666	0.764000	0.28473	0.857000	0.33713	0.626000	0.37791	0.542000	0.23222	0.094000	0.17404	0.655000	0.94253	GCG	.	.		0.622	SAT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440078.1	NM_133491		T	7530941	G	T	7530941	2	4	73	1	0	0	0	0	0	0	0	1	13867	1086	38	1		1	SAT2	17	7530941	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	2881762	7530941	73664269	511	9837										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7644139	7644139	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cttccctaggctatcaagcgGacttatgacaagaaggcggt	11	10	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:7644139G>A	ENST00000572933.1	+	11	2978	c.1518G>A	c.(1516-1518)cgG>cgA	p.R506R	DNAH2_ENST00000082259.3_Silent_p.R588R|DNAH2_ENST00000570791.1_Silent_p.R588R|DNAH2_ENST00000389173.2_Silent_p.R506R			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	506	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTATCAAGCGGACTTATGACA	0.587																																					p.R506R		Atlas-SNP	.											.	DNAH2	498	.	0			c.G1518A						.						110	103	105					17																	7644139		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon10			CAAGCGGACTTAT	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.1518G>A	chr17.hg19:g.7644139G>A		51.0	0.0		52.0	18.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.		0.587	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7644139	G	A	7644139	2	1	73	1	0	0	0	0	0	0	0	1	4604	1161	41	3		3	DNAH2	17	7644139	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	113198	7644139	73551071	512	9838										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7660453	7660453	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aattgactactgggagcggcTgctgtttgagacgccccatt	12	10	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:7660453T>A	ENST00000572933.1	+	13	3409	c.1949T>A	c.(1948-1950)cTg>cAg	p.L650Q	RPL29P2_ENST00000498671.1_RNA|DNAH2_ENST00000389173.2_Missense_Mutation_p.L650Q			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	650	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TGGGAGCGGCTGCTGTTTGAG	0.542																																					p.L650Q		Atlas-SNP	.											.	DNAH2	498	.	0			c.T1949A						.						186	181	183					17																	7660453		2203	4300	6503	SO:0001583	missense	146754	exon12			AGCGGCTGCTGTT	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.1949T>A	chr17.hg19:g.7660453T>A	ENSP00000458355:p.Leu650Gln	146.0	0.0		73.0	29.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.118057	0.77323	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.62498	0.02	4.96	4.96	0.65561	Dynein heavy chain, domain-1 (1);	0.084157	0.48767	D	0.000171	T	0.80276	0.4593	M	0.85299	2.745	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.83547	0.0099	10	0.66056	D	0.02	.	13.7444	0.62865	0.0:0.0:0.0:1.0	.	650	Q9P225	DYH2_HUMAN	Q	650	ENSP00000373825:L650Q	ENSP00000353818:L650Q	L	+	2	0	DNAH2	7601178	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.044000	0.64214	2.084000	0.62774	0.402000	0.26972	CTG	.	.		0.542	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7660453	T	A	7660453	3	1	73	1	0	0	0	0	1	0	0	0	4604	1580	55	4	1995	4	DNAH2	17	7660453	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	16314	7660453	73534757	513	9839										
ALOX12B	242	hgsc.bcm.edu	37	chr17	7989531	7989531	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gagggcactgcacggtgtacTggcccacctaggcaggatgc	15	12	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:7989531T>A	ENST00000319144.4	-	2	415	c.155A>T	c.(154-156)cAg>cTg	p.Q52L	MIR4314_ENST00000583321.1_RNA	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	52	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						CACGGTGTACTGGCCCACCTA	0.642										Multiple Myeloma(8;0.094)																											p.Q52L		Atlas-SNP	.											.	ALOX12B	61	.	0			c.A155T						.						69	58	62					17																	7989531		2203	4300	6503	SO:0001583	missense	242	exon2			GTGTACTGGCCCA	AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"Arachidonate lipoxygenases"	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.155A>T	chr17.hg19:g.7989531T>A	ENSP00000315167:p.Gln52Leu	102.0	0.0		74.0	33.0	NM_001139		Missense_Mutation	SNP	ENST00000319144.4	hg19	CCDS11129.1	.	.	.	.	.	.	.	.	.	.	T	8.070	0.770089	0.15983	.	.	ENSG00000179477	ENST00000319144	T	0.63744	-0.06	4.58	3.47	0.39725	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.806849	0.11961	N	0.512771	T	0.43188	0.1236	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31447	-0.9943	10	0.52906	T	0.07	-7.375	9.5306	0.39191	0.0:0.0881:0.0:0.9119	.	52	O75342	LX12B_HUMAN	L	52	ENSP00000315167:Q52L	ENSP00000315167:Q52L	Q	-	2	0	ALOX12B	7930256	0.001000	0.12720	0.038000	0.18304	0.310000	0.27922	0.867000	0.27968	1.930000	0.55929	0.529000	0.55759	CAG	.	.		0.642	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3			A	7989531	T	A	7989531	3	1	73	1	0	0	0	0	1	0	0	0	537	1580	55	4	2006	4	ALOX12B	17	7989531	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	329078	7989531	73205679	514	9840										
ARHGEF15	22899	hgsc.bcm.edu	37	chr17	8215862	8215862	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaggccgggctcaggatgcaGatgccccggagccaggtctc	15	13	2	1	rs536515839		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:8215862G>C	ENST00000361926.3	+	2	615	c.505G>C	c.(505-507)Gat>Cat	p.D169H	ARHGEF15_ENST00000421050.1_Missense_Mutation_p.D169H	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	169					negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						TCAGGATGCAGATGCCCCGGA	0.637																																					p.D169H		Atlas-SNP	.											.	ARHGEF15	97	.	0			c.G505C						.						36	39	38					17																	8215862		2203	4299	6502	SO:0001583	missense	22899	exon2			GATGCAGATGCCC	AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"Rho guanine nucleotide exchange factors"	15590	protein-coding gene	gene with protein product	"Rho guanine exchange factor (GEF) 15"	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.505G>C	chr17.hg19:g.8215862G>C	ENSP00000355026:p.Asp169His	39.0	0.0		38.0	14.0	NM_025014	A8K6G1|Q8N449|Q9H8B4	Missense_Mutation	SNP	ENST00000361926.3	hg19	CCDS11139.1	.	.	.	.	.	.	.	.	.	.	G	3.434	-0.115403	0.06881	.	.	ENSG00000198844	ENST00000361926;ENST00000455564;ENST00000421050	T;T	0.75367	-0.93;-0.93	5.51	5.51	0.81932	.	0.586739	0.16625	N	0.206297	T	0.68550	0.3013	L	0.27053	0.805	0.09310	N	1	P;P;D	0.56746	0.612;0.612;0.977	B;B;P	0.46718	0.259;0.259;0.525	T	0.64275	-0.6446	10	0.49607	T	0.09	-3.8974	14.9567	0.71120	0.0:0.0:1.0:0.0	.	169;169;70	D3DTR7;O94989;B4DTR5	.;ARHGF_HUMAN;.	H	169;70;169	ENSP00000355026:D169H;ENSP00000412505:D169H	ENSP00000355026:D169H	D	+	1	0	ARHGEF15	8156587	0.024000	0.19004	0.007000	0.13788	0.012000	0.07955	2.249000	0.43169	2.600000	0.87896	0.555000	0.69702	GAT	.	.		0.637	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728		C	8215862	G	C	8215862	3	2	73	1	0	0	0	0	1	0	0	0	898	942	33	4	507	4	ARHGEF15	17	8215862	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	226331	8215862	72979348	515	9841										
RCVRN	5957	hgsc.bcm.edu	37	chr17	9804355	9804355	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atcttctcggctcgcttttcCggcgtgttttcatcgtctgg	10	12	4	0	rs144667256		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:9804355C>T	ENST00000226193.5	-	2	884	c.444G>A	c.(442-444)ccG>ccA	p.P148P	RCVRN_ENST00000570909.3_5'UTR	NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin	148	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of calcium ion transport (GO:0051924)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	dendrite (GO:0030425)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						CTCGCTTTTCCGGCGTGTTTT	0.438																																					p.P148P		Atlas-SNP	.											.	RCVRN	34	.	0			c.G444A						.	C		0,4406		0,0,2203	109	101	104		444	-11.8	0.3	17	dbSNP_134	104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RCVRN	NM_002903.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		148/201	9804355	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5957	exon2			CTTTTCCGGCGTG	BC001720	CCDS11151.1	17p13.1	2013-01-10		2006-09-26	ENSG00000109047	ENSG00000109047		"EF-hand domain containing"	9937	protein-coding gene	gene with protein product		179618		RCV1		1387789, 12507501, 1467959, 12789533	Standard	NM_002903		Approved		uc002gme.1	P35243	OTTHUMG00000130268	ENST00000226193.5:c.444G>A	chr17.hg19:g.9804355C>T		101.0	0.0		99.0	49.0	NM_002903	Q53XL0	Silent	SNP	ENST00000226193.5	hg19	CCDS11151.1																																																																																			.	C|1.000;T|0.000		0.438	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252600.2	NM_002903		T	9804355	C	T	9804355	2	4	73	1	0	0	0	0	0	0	0	1	13201	639	23	1		1	RCVRN	17	9804355	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1588493	9804355	71390855	516	9842										
MYH13	8735	hgsc.bcm.edu	37	chr17	10212854	10212854	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctcaccttgagctggccctgGaccgtgcgcagatgcttctg	12	14	2	2	rs371037408		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:10212854G>C	ENST00000418404.3	-	33	5113	c.4950C>G	c.(4948-4950)gtC>gtG	p.V1650V	RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Silent_p.V1650V			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1650					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						GCTGGCCCTGGACCGTGCGCA	0.637																																					p.V1650V		Atlas-SNP	.											.	MYH13	533	.	0			c.C4950G						.						32	33	33					17																	10212854		2154	4274	6428	SO:0001819	synonymous_variant	8735	exon34			GCCCTGGACCGTG	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.4950C>G	chr17.hg19:g.10212854G>C		49.0	0.0		47.0	21.0	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	hg19	CCDS45613.1																																																																																			.	.		0.637	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		C	10212854	G	C	10212854	2	2	73	1	0	0	0	0	0	0	0	1	10041	1161	41	4		4	MYH13	17	10212854	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	408499	10212854	70982356	517	9843										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11696953	11696953	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgatctttttgataaaatccAgacagaagtgctcaagaaaa	7	6	2	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:11696953A>G	ENST00000262442.4	+	42	8263	c.8195A>G	c.(8194-8196)cAg>cGg	p.Q2732R	DNAH9_ENST00000454412.2_Missense_Mutation_p.Q2732R	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2732					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GATAAAATCCAGACAGAAGTG	0.333																																					p.Q2732R		Atlas-SNP	.											.	DNAH9	695	.	0			c.A8195G						.						100	106	104					17																	11696953		2203	4300	6503	SO:0001583	missense	1770	exon42			AAATCCAGACAGA	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.8195A>G	chr17.hg19:g.11696953A>G	ENSP00000262442:p.Gln2732Arg	111.0	0.0		102.0	40.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	5.283	0.237578	0.10023	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.25912	1.81;1.77	5.76	5.76	0.90799	.	0.198640	0.44902	D	0.000406	T	0.24198	0.0586	L	0.53249	1.67	0.80722	D	1	B	0.12013	0.005	B	0.15870	0.014	T	0.05971	-1.0853	10	0.21014	T	0.42	.	11.204	0.48758	0.8632:0.0:0.0:0.1368	.	2732	Q9NYC9	DYH9_HUMAN	R	2732;2732;1314	ENSP00000262442:Q2732R;ENSP00000414874:Q2732R	ENSP00000262442:Q2732R	Q	+	2	0	DNAH9	11637678	1.000000	0.71417	1.000000	0.80357	0.555000	0.35460	7.130000	0.77235	2.191000	0.70037	0.533000	0.62120	CAG	.	.		0.333	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		G	11696953	A	G	11696953	3	3	73	1	0	0	0	0	1	0	0	0	4610	188	7	2	8361	2	DNAH9	17	11696953	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1484099	11696953	69498257	518	9844										
RAI1	10743	hgsc.bcm.edu	37	chr17	17698925	17698925	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgagcagaggcctggcatgcAggacccgctgtcacccaagg	14	14	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:17698925A>T	ENST00000353383.1	+	3	3132	c.2663A>T	c.(2662-2664)cAg>cTg	p.Q888L	RAI1_ENST00000261641.6_Missense_Mutation_p.Q888L	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	888					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CCTGGCATGCAGGACCCGCTG	0.657																																					p.Q888L		Atlas-SNP	.											.	RAI1	121	.	0			c.A2663T						.						30	28	29					17																	17698925		2203	4300	6503	SO:0001583	missense	10743	exon3			GCATGCAGGACCC	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"Smith-Magenis syndrome chromosome region"	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.2663A>T	chr17.hg19:g.17698925A>T	ENSP00000323074:p.Gln888Leu	80.0	0.0		66.0	33.0	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.829464	0.50845	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.67345	-0.26;2.47;0.34	5.03	5.03	0.67393	.	0.290760	0.28382	N	0.015559	T	0.63438	0.2511	L	0.54323	1.7	0.37563	D	0.919154	B	0.19817	0.039	B	0.21360	0.034	T	0.65948	-0.6044	10	0.52906	T	0.07	.	14.772	0.69688	1.0:0.0:0.0:0.0	.	888	Q7Z5J4	RAI1_HUMAN	L	888;888;888;888;888;840	ENSP00000323074:Q888L;ENSP00000379120:Q888L;ENSP00000261641:Q888L	ENSP00000261641:Q888L	Q	+	2	0	RAI1	17639650	0.996000	0.38824	1.000000	0.80357	0.982000	0.71751	1.680000	0.37607	1.909000	0.55274	0.459000	0.35465	CAG	.	.		0.657	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		T	17698925	A	T	17698925	3	4	73	1	0	0	0	0	1	0	0	0	13022	188	7	4	2665	4	RAI1	17	17698925	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	6001972	17698925	63496285	519	9845										
MFAP4	4239	hgsc.bcm.edu	37	chr17	19289686	19289686	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acaggcacactggggcccgaGgggtagatgaggtacacgcc	16	11	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:19289686G>C	ENST00000299610.4	-	3	261	c.177C>G	c.(175-177)ccC>ccG	p.P59P	MFAP4_ENST00000574313.2_5'Flank|MFAP4_ENST00000395592.2_Silent_p.P83P|MFAP4_ENST00000497081.2_Silent_p.P84P	NM_002404.2	NP_002395.1	P55083	MFAP4_HUMAN	microfibrillar-associated protein 4	59	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|cellular response to UV-B (GO:0071493)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|regulation of collagen metabolic process (GO:0010712)|UV protection (GO:0009650)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)				large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	10	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					TGGGGCCCGAGGGGTAGATGA	0.617																																					p.P83P		Atlas-SNP	.											.	MFAP4	33	.	0			c.C249G						.						79	59	66					17																	19289686		2203	4300	6503	SO:0001819	synonymous_variant	4239	exon3			GCCCGAGGGGTAG	L38486	CCDS11208.1, CCDS56023.1	17p11.2	2013-02-06			ENSG00000166482	ENSG00000166482		"Fibrinogen C domain containing"	7035	protein-coding gene	gene with protein product	"microfibril-associated glycoprotein 4"	600596				7633408	Standard	NM_001198695		Approved		uc002gvs.3	P55083	OTTHUMG00000059585	ENST00000299610.4:c.177C>G	chr17.hg19:g.19289686G>C		137.0	0.0		137.0	59.0	NM_001198695	A8KAJ1|A8MVM2|B4E317|Q6P680	Silent	SNP	ENST00000299610.4	hg19	CCDS11208.1																																																																																			.	.		0.617	MFAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132493.2	NM_002404		C	19289686	G	C	19289686	2	2	73	1	0	0	0	0	0	0	0	1	9526	987	35	4		4	MFAP4	17	19289686	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1590761	19289686	61905524	520	9846										
SLC6A4	6532	hgsc.bcm.edu	37	chr17	28534791	28534791	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggccacccagcagatcctccAgaaccaccccgggctgaagc	10	18	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:28534791A>T	ENST00000401766.2	-	12	2121	c.1609T>A	c.(1609-1611)Tgg>Agg	p.W537R	SLC6A4_ENST00000261707.3_Missense_Mutation_p.W537R|RP11-354P11.4_ENST00000581633.1_RNA			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	537					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	CAGATCCTCCAGAACCACCCC	0.572																																					p.W537R		Atlas-SNP	.											.	SLC6A4	60	.	0			c.T1609A						.						83	70	74					17																	28534791		2203	4300	6503	SO:0001583	missense	6532	exon13			TCCTCCAGAACCA	L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"Solute carriers"	11050	protein-coding gene	gene with protein product	"serotonin transporter 1"	182138	"solute carrier family 6 (neurotransmitter transporter, serotonin), member 4", "5-hydroxytryptamine (serotonin) transporter", "obsessive-compulsive disorder 1"	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.1609T>A	chr17.hg19:g.28534791A>T	ENSP00000385822:p.Trp537Arg	205.0	0.0		117.0	43.0	NM_001045	Q5EE02	Missense_Mutation	SNP	ENST00000401766.2	hg19	CCDS11256.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.736301	0.89482	.	.	ENSG00000108576	ENST00000394821;ENST00000401766;ENST00000261707	T;T	0.78816	-1.21;-1.21	5.64	5.64	0.86602	.	0.114577	0.64402	D	0.000004	D	0.92024	0.7473	H	0.97158	3.95	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94492	0.7702	10	0.87932	D	0	.	15.0294	0.71694	1.0:0.0:0.0:0.0	.	537	P31645	SC6A4_HUMAN	R	579;537;537	ENSP00000385822:W537R;ENSP00000261707:W537R	ENSP00000261707:W537R	W	-	1	0	SLC6A4	25558917	1.000000	0.71417	0.993000	0.49108	0.874000	0.50279	9.339000	0.96797	2.153000	0.67306	0.482000	0.46254	TGG	.	.		0.572	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045		T	28534791	A	T	28534791	3	4	73	1	0	0	0	0	1	0	0	0	14701	188	7	4	295	4	SLC6A4	17	28534791	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	9245105	28534791	52660419	521	9847										
MYO1D	4642	hgsc.bcm.edu	37	chr17	31048069	31048069	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaacttctcgtatgtctggcGgaaggcaaatcctgcccgac	10	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:31048069G>A	ENST00000318217.5	-	15	2189	c.1885C>T	c.(1885-1887)Cgc>Tgc	p.R629C	MYO1D_ENST00000579584.1_Missense_Mutation_p.R629C|MYO1D_ENST00000394649.4_Missense_Mutation_p.R541C	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	629	Myosin motor.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			TATGTCTGGCGGAAGGCAAAT	0.478																																					p.R629C		Atlas-SNP	.											.	MYO1D	93	.	0			c.C1885T						.						140	139	139					17																	31048069		2203	4300	6503	SO:0001583	missense	4642	exon15			TCTGGCGGAAGGC	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"Myosins / Myosin superfamily : Class I"	7598	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 108"	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.1885C>T	chr17.hg19:g.31048069G>A	ENSP00000324527:p.Arg629Cys	155.0	0.0		125.0	10.0	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	hg19	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.651361	0.88056	.	.	ENSG00000176658	ENST00000318217	D	0.92699	-3.09	5.21	5.21	0.72293	Myosin head, motor domain (2);	0.000000	0.38381	U	0.001715	D	0.98178	0.9398	H	0.99800	4.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99198	1.0872	10	0.87932	D	0	.	16.289	0.82738	0.0:0.0:1.0:0.0	.	540;629	Q7Z3N6;O94832	.;MYO1D_HUMAN	C	629	ENSP00000324527:R629C	ENSP00000324527:R629C	R	-	1	0	MYO1D	28072182	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.028000	0.70889	2.716000	0.92895	0.561000	0.74099	CGC	.	.		0.478	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			A	31048069	G	A	31048069	3	1	73	1	0	0	0	0	1	0	0	0	10080	1116	39	1	1167	1	MYO1D	17	31048069	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	2513278	31048069	50147141	522	9848										
SLFN13	146857	hgsc.bcm.edu	37	chr17	33767910	33767910	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tggagaatagcccctttcaaAgaagcacctgcaggtgtctg	11	10	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:33767910A>T	ENST00000285013.6	-	6	2673	c.2398T>A	c.(2398-2400)Ttt>Att	p.F800I	SLFN13_ENST00000526861.1_Missense_Mutation_p.F800I|SLFN13_ENST00000534689.1_Missense_Mutation_p.F482I|SLFN13_ENST00000542635.1_Missense_Mutation_p.F800I|SLFN13_ENST00000533791.1_Missense_Mutation_p.F800I|SLFN13_ENST00000360502.2_Missense_Mutation_p.F482I	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	800						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CCCCTTTCAAAGAAGCACCTG	0.443																																					p.F800I		Atlas-SNP	.											.	SLFN13	79	.	0			c.T2398A						.						98	92	94					17																	33767910		2203	4300	6503	SO:0001583	missense	146857	exon6			TTTCAAAGAAGCA	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.2398T>A	chr17.hg19:g.33767910A>T	ENSP00000285013:p.Phe800Ile	92.0	0.0		114.0	52.0	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	hg19	CCDS32620.1	.	.	.	.	.	.	.	.	.	.	a	12.47	1.949071	0.34377	.	.	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	T;T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42;-1.42	3.26	3.26	0.37387	.	0.455607	0.18595	N	0.136640	D	0.82440	0.5037	M	0.80183	2.485	0.09310	N	1	P;P	0.46457	0.878;0.689	P;B	0.47402	0.546;0.091	T	0.75317	-0.3360	10	0.66056	D	0.02	.	8.1098	0.30907	1.0:0.0:0.0:0.0	.	482;800	Q68D06-2;Q68D06	.;SLN13_HUMAN	I	800;482;800;800;482	ENSP00000285013:F800I;ENSP00000353692:F482I;ENSP00000434439:F800I;ENSP00000444016:F800I;ENSP00000435442:F482I	ENSP00000285013:F800I	F	-	1	0	SLFN13	30792023	0.000000	0.05858	0.013000	0.15412	0.002000	0.02628	0.396000	0.20867	1.472000	0.48140	0.329000	0.21502	TTT	.	.		0.443	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		T	33767910	A	T	33767910	3	4	73	1	0	0	0	0	1	0	0	0	14751	72	3	4	299	4	SLFN13	17	33767910	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2719841	33767910	47427300	523	9849										
CCL14	6358	hgsc.bcm.edu	37	chr17	34311402	34311402	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggcttggagcactggctgtTggtctcatagtaatccataa	12	8	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:34311402T>C	ENST00000394509.4	-	2	274	c.166A>G	c.(166-168)Aac>Gac	p.N56D	CCL14_ENST00000586216.1_Missense_Mutation_p.N56D|CTB-186H2.3_ENST00000593057.1_Intron|CCL14_ENST00000435911.2_Missense_Mutation_p.N72D|CCL14_ENST00000536149.1_Missense_Mutation_p.N72D|CTB-186H2.3_ENST00000591669.1_5'Flank|CCL14_ENST00000480944.2_Missense_Mutation_p.N78D|CCL16_ENST00000293275.3_5'Flank|CCL15-CCL14_ENST00000481427.2_3'UTR			Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14	56					cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)	extracellular space (GO:0005615)				large_intestine(1)|lung(6)	7		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CACTGGCTGTTGGTCTCATAG	0.577																																					p.N72D		Atlas-SNP	.											.	CCL14	22	.	0			c.A214G						.						108	92	97					17																	34311402		2203	4300	6503	SO:0001583	missense	6358	exon3			GGCTGTTGGTCTC	Z49270	CCDS32624.1, CCDS45652.1	17q11.2	2014-04-10	2002-08-22	2002-08-23	ENSG00000213494	ENSG00000276409		"Chemokine ligands", "Endogenous ligands"	10612	protein-coding gene	gene with protein product		601392	"small inducible cytokine subfamily A (Cys-Cys), member 14"	SCYA14		8661057	Standard	NM_032963		Approved	HCC-1, HCC-3, NCC-2, SCYL2, CKb1, MCIF	uc010wcq.1	Q16627	OTTHUMG00000188403	ENST00000394509.4:c.166A>G	chr17.hg19:g.34311402T>C	ENSP00000378017:p.Asn56Asp	111.0	0.0		98.0	38.0	NM_032962	E1P649|E1P650|Q13954	Missense_Mutation	SNP	ENST00000394509.4	hg19	CCDS32624.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.143852	0.57044	.	.	ENSG00000213494	ENST00000394509;ENST00000536149;ENST00000435911	T;T;T	0.13657	2.57;2.57;2.57	5.14	4.06	0.47325	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.326818	0.21475	U	0.073932	T	0.11836	0.0288	.	.	.	0.19945	N	0.999942	B;B	0.28820	0.224;0.187	B;B	0.31495	0.131;0.08	T	0.19844	-1.0293	9	0.52906	T	0.07	.	8.1132	0.30926	0.0:0.0936:0.0:0.9064	.	56;72	Q16627;Q16627-2	CCL14_HUMAN;.	D	56;72;72	ENSP00000378017:N56D;ENSP00000441771:N72D;ENSP00000409197:N72D	ENSP00000378017:N56D	N	-	1	0	CCL14	31335515	1.000000	0.71417	0.952000	0.39060	0.509000	0.34042	2.749000	0.47492	0.894000	0.36317	0.460000	0.39030	AAC	.	.		0.577	CCL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272892.2	NM_032962		C	34311402	T	C	34311402	3	2	73	1	0	0	0	0	1	0	0	0	2887	1812	63	2	123	2	CCL14	17	34311402	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	543492	34311402	46883808	524	9850										
KRT23	25984	hgsc.bcm.edu	37	chr17	39084545	39084545	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctggaatgtgcgcttcagtTcgtggatgtcaccttgtctg	12	10	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:39084545T>C	ENST00000209718.3	-	6	1290	c.866A>G	c.(865-867)gAa>gGa	p.E289G	KRT23_ENST00000436344.3_Missense_Mutation_p.E152G|AC004231.2_ENST00000418393.1_RNA	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)	289	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000301)|Ovarian(249;0.15)				GCGCTTCAGTTCGTGGATGTC	0.572																																					p.E289G		Atlas-SNP	.											KRT23,NS,malignant_melanoma,-1,1	KRT23	59	.	0			c.A866G						.						267	215	233					17																	39084545		2203	4300	6503	SO:0001583	missense	25984	exon6			TTCAGTTCGTGGA	AF102848	CCDS11380.1, CCDS62182.1	17q21.2	2013-01-16			ENSG00000108244	ENSG00000108244		"-", "Intermediate filaments type I, keratins (acidic)"	6438	protein-coding gene	gene with protein product		606194				11135429, 16831889	Standard	NM_015515		Approved	K23, DKFZP434G032, HAIK1, CK23, MGC26158	uc002hvm.1	Q9C075	OTTHUMG00000133376	ENST00000209718.3:c.866A>G	chr17.hg19:g.39084545T>C	ENSP00000209718:p.Glu289Gly	89.0	0.0		57.0	28.0	NM_015515	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Missense_Mutation	SNP	ENST00000209718.3	hg19	CCDS11380.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.958305	0.73902	.	.	ENSG00000108244	ENST00000209718;ENST00000436344	D;D	0.91237	-2.81;-2.81	5.79	5.79	0.91817	Filament (1);	0.000000	0.52532	D	0.000073	D	0.95793	0.8631	M	0.86864	2.845	0.58432	D	0.999998	D	0.76494	0.999	D	0.75020	0.985	D	0.96418	0.9309	10	0.87932	D	0	.	16.1252	0.81386	0.0:0.0:0.0:1.0	.	289	Q9C075	K1C23_HUMAN	G	289;152	ENSP00000209718:E289G;ENSP00000414056:E152G	ENSP00000209718:E289G	E	-	2	0	KRT23	36338071	1.000000	0.71417	1.000000	0.80357	0.226000	0.24999	5.970000	0.70431	2.214000	0.71695	0.533000	0.62120	GAA	.	.		0.572	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1			C	39084545	T	C	39084545	3	2	73	1	0	0	0	0	1	0	0	0	8469	1783	62	2	418	2	KRT23	17	39084545	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	4773143	39084545	42110665	525	9851										
KRT34	3885	hgsc.bcm.edu	37	chr17	39538297	39538297	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caccttctccaggtagctggCcaggcggtcgttcaggaact	12	13	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:39538297C>T	ENST00000394001.1	-	1	358	c.328G>A	c.(328-330)Gcc>Acc	p.A110T		NM_021013.3	NP_066293.2	O76011	KRT34_HUMAN	keratin 34	110	Coil 1A.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Breast(137;0.000496)				AGGTAGCTGGCCAGGCGGTCG	0.607																																					p.A110T		Atlas-SNP	.											.	KRT34	71	.	0			c.G328A						.						91	86	88					17																	39538297		2203	4297	6500	SO:0001583	missense	3885	exon1			AGCTGGCCAGGCG	Y16790	CCDS11390.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131737	ENSG00000131737		"-", "Intermediate filaments type I, keratins (acidic)"	6452	protein-coding gene	gene with protein product	"hard keratin type I 4"	602763	"keratin, hair, acidic, 4"	KRTHA4		2431943, 9756910, 16831889	Standard	NM_021013		Approved	Ha-4	uc002hwm.3	O76011	OTTHUMG00000133436	ENST00000394001.1:c.328G>A	chr17.hg19:g.39538297C>T	ENSP00000377570:p.Ala110Thr	175.0	0.0		179.0	69.0	NM_021013	Q8IUT8|Q8N4W2	Missense_Mutation	SNP	ENST00000394001.1	hg19	CCDS11390.1	.	.	.	.	.	.	.	.	.	.	c	35	5.525983	0.96431	.	.	ENSG00000131737	ENST00000394001;ENST00000251648	.	.	.	5.82	5.82	0.92795	Filament (1);	0.000000	0.64402	D	0.000005	D	0.86142	0.5862	M	0.93106	3.38	0.50632	D	0.999885	D	0.76494	0.999	D	0.67382	0.951	D	0.88794	0.3280	9	0.87932	D	0	.	19.141	0.93446	0.0:1.0:0.0:0.0	.	110	O76011	KRT34_HUMAN	T	68;110	.	ENSP00000251648:A110T	A	-	1	0	KRT34	36791823	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.986000	0.70563	2.764000	0.94973	0.650000	0.86243	GCC	.	.		0.607	KRT34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257304.3	NM_021013		T	39538297	C	T	39538297	3	4	73	1	0	0	0	0	1	0	0	0	8480	739	26	3	1010	3	KRT34	17	39538297	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	453752	39538297	41656913	526	9852										
MLX	6945	hgsc.bcm.edu	37	chr17	40721541	40721541	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctagccattgactacattcaGtttttgcacaaggagaagaa	8	8	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:40721541G>T	ENST00000246912.4	+	6	608	c.555G>T	c.(553-555)caG>caT	p.Q185H	MLX_ENST00000346833.4_Missense_Mutation_p.Q101H|MLX_ENST00000435881.2_Missense_Mutation_p.Q131H	NM_170607.2	NP_733752.1	Q9UH92	MLX_HUMAN	MLX, MAX dimerization protein	185	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				energy reserve metabolic process (GO:0006112)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|positive regulation of cellular metabolic process (GO:0031325)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(3)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	10		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		ACTACATTCAGTTTTTGCACA	0.468																																					p.Q185H	GBM(121;657 1601 4665 24731 34640)	Atlas-SNP	.											.	MLX	17	.	0			c.G555T						.						104	98	100					17																	40721541		2203	4300	6503	SO:0001583	missense	6945	exon6			CATTCAGTTTTTG	AF213668	CCDS11430.1, CCDS42341.1, CCDS45687.1	17q21.1	2013-05-21	2012-11-15	2005-02-11		ENSG00000108788		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	11645	protein-coding gene	gene with protein product		602976	"transcription factor-like 4", "MAX-like protein X"	TCFL4		8973301	Standard	NM_170607		Approved	MAD7, MXD7, bHLHd13	uc002iag.3	Q9UH92		ENST00000246912.4:c.555G>T	chr17.hg19:g.40721541G>T	ENSP00000246912:p.Gln185His	83.0	0.0		79.0	32.0	NM_170607	A8K2J3|B2RAV8|B2RD73|Q53XM6|Q96FL2|Q9H2V0|Q9H2V1|Q9H2V2|Q9NXN3	Missense_Mutation	SNP	ENST00000246912.4	hg19	CCDS11430.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.320597	0.41096	.	.	ENSG00000108788	ENST00000346833;ENST00000246912;ENST00000435881	D;D;D	0.98028	-4.67;-4.67;-4.67	5.69	5.69	0.88448	Helix-loop-helix DNA-binding (5);	0.051071	0.85682	D	0.000000	D	0.95223	0.8451	L	0.39020	1.185	0.58432	D	0.999991	B;B;B	0.19445	0.036;0.012;0.016	B;B;B	0.24269	0.052;0.03;0.028	D	0.92081	0.5672	10	0.40728	T	0.16	-16.8961	14.0233	0.64571	0.0721:0.0:0.9279:0.0	.	101;185;131	Q9UH92-2;Q9UH92;Q9UH92-3	.;MLX_HUMAN;.	H	101;185;131	ENSP00000320913:Q101H;ENSP00000246912:Q185H;ENSP00000416627:Q131H	ENSP00000246912:Q185H	Q	+	3	2	MLX	37975067	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.922000	0.48860	2.696000	0.92011	0.655000	0.94253	CAG	.	.		0.468	MLX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450415.1	NM_170607		T	40721541	G	T	40721541	3	4	73	1	0	0	0	0	1	0	0	0	9644	1020	36	3	577	3	MLX	17	40721541	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1183244	40721541	40473669	527	9853										
RPL27	6155	hgsc.bcm.edu	37	chr17	41150829	41150829	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggctggacgctactccggacGcaaagctgtcatcgtgaagg	14	11	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:41150829G>A	ENST00000589913.1	+	1	336	c.62G>A	c.(61-63)cGc>cAc	p.R21H	RPL27_ENST00000253788.5_Missense_Mutation_p.R21H|Y_RNA_ENST00000363257.1_RNA|RPL27_ENST00000590864.1_5'Flank|RPL27_ENST00000589037.1_Missense_Mutation_p.R21H			P61353	RL27_HUMAN	ribosomal protein L27	21	KOW.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)	3		Breast(137;0.000717)|Ovarian(249;0.0776)		BRCA - Breast invasive adenocarcinoma(366;0.157)		TACTCCGGACGCAAAGCTGTC	0.587																																					p.R21H		Atlas-SNP	.											.	RPL27	6	.	0			c.G62A						.						89	83	85					17																	41150829		2203	4300	6503	SO:0001583	missense	6155	exon2			CCGGACGCAAAGC		CCDS11449.1	17q21	2011-04-06				ENSG00000131469		"L ribosomal proteins"	10328	protein-coding gene	gene with protein product	"60S ribosomal protein L27"	607526				1302024	Standard	NM_000988		Approved	L27	uc002icj.3	P61353		ENST00000589913.1:c.62G>A	chr17.hg19:g.41150829G>A	ENSP00000464813:p.Arg21His	50.0	0.0		42.0	19.0	NM_000988	P08526|Q4G0A9	Missense_Mutation	SNP	ENST00000589913.1	hg19	CCDS11449.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.921541	0.52653	.	.	ENSG00000131469	ENST00000253788	.	.	.	4.54	3.57	0.40892	KOW (2);Translation protein SH3-like, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.53465	0.1798	L	0.42744	1.35	0.80722	D	1	B	0.18968	0.032	B	0.19391	0.025	T	0.52990	-0.8501	9	0.44086	T	0.13	.	12.5238	0.56075	0.0822:0.0:0.9178:0.0	.	21	P61353	RL27_HUMAN	H	21	.	ENSP00000253788:R21H	R	+	2	0	RPL27	38404355	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	9.283000	0.95860	1.276000	0.44395	-0.350000	0.07774	CGC	.	.		0.587	RPL27-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452472.1	NM_000988		A	41150829	G	A	41150829	3	1	73	1	0	0	0	0	1	0	0	0	13590	1087	38	1	64	1	RPL27	17	41150829	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	429288	41150829	40044381	528	9854										
IFI35	3430	hgsc.bcm.edu	37	chr17	41166312	41166312	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agtcttcacctctgagtcagGctaggggcctccccttctca	9	15	5	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:41166312G>T	ENST00000415816.2	+	7	1080	c.857G>T	c.(856-858)gGc>gTc	p.G286V	IFI35_ENST00000438323.2_Missense_Mutation_p.G288V	NM_005533.4	NP_005524.2	P80217	IN35_HUMAN	interferon-induced protein 35	286				EVEALTVVPQGQQGLAVFTSESG -> GRGPDSRTPRTAGP SSLHL (in Ref. 1; no nucleotide entry). {ECO:0000305}.	cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)	8		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.157)		TCTGAGTCAGGCTAGGGGCCT	0.627																																					p.G288V		Atlas-SNP	.											.	IFI35	23	.	0			c.G863T						.						48	41	44					17																	41166312		2203	4300	6503	SO:0001583	missense	3430	exon7			AGTCAGGCTAGGG	BC001356	CCDS11450.1	17q21	2006-04-05			ENSG00000068079	ENSG00000068079			5399	protein-coding gene	gene with protein product		600735					Standard	NM_005533		Approved	IFP35	uc021txx.1	P80217	OTTHUMG00000167720	ENST00000415816.2:c.857G>T	chr17.hg19:g.41166312G>T	ENSP00000394579:p.Gly286Val	80.0	0.0		52.0	29.0	NM_005533	C9JGX1|Q92984|Q99537|Q9BV98	Missense_Mutation	SNP	ENST00000415816.2	hg19		.	.	.	.	.	.	.	.	.	.	G	16.87	3.241189	0.58995	.	.	ENSG00000068079	ENST00000415816;ENST00000438323	T;T	0.54479	0.57;0.58	5.8	-1.38	0.09027	.	1.557740	0.03200	N	0.174660	T	0.37972	0.1023	L	0.36672	1.1	0.09310	N	0.999999	B	0.30406	0.278	B	0.24155	0.051	T	0.32693	-0.9897	10	0.72032	D	0.01	0.1825	1.8675	0.03201	0.2172:0.2493:0.4054:0.1281	.	286	P80217	IN35_HUMAN	V	286;288	ENSP00000394579:G286V;ENSP00000395590:G288V	ENSP00000394579:G286V	G	+	2	0	IFI35	38419838	0.002000	0.14202	0.005000	0.12908	0.002000	0.02628	0.060000	0.14342	0.075000	0.16796	0.462000	0.41574	GGC	.	.		0.627	IFI35-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000395851.1	NM_005533		T	41166312	G	T	41166312	3	4	73	1	0	0	0	0	1	0	0	0	7525	1203	42	3	889	3	IFI35	17	41166312	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	15483	41166312	40028898	529	9855										
NBR1	4077	hgsc.bcm.edu	37	chr17	41349033	41349033	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagaagaagacctgagtgggAcccagtttgtgtgtgagaca	14	7	0	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:41349033A>G	ENST00000422280.1	+	16	2395	c.1936A>G	c.(1936-1938)Acc>Gcc	p.T646A	NBR1_ENST00000590996.1_Missense_Mutation_p.T646A|NBR1_ENST00000589872.1_Missense_Mutation_p.T646A|NBR1_ENST00000542611.1_Missense_Mutation_p.T625A|NBR1_ENST00000341165.6_Missense_Mutation_p.T646A|NBR1_ENST00000389312.4_Missense_Mutation_p.T646A	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	646					macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		CCTGAGTGGGACCCAGTTTGT	0.502																																					p.T646A		Atlas-SNP	.											.	NBR1	55	.	0			c.A1936G						.						149	130	136					17																	41349033		1568	3582	5150	SO:0001583	missense	4077	exon16			AGTGGGACCCAGT	X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.1936A>G	chr17.hg19:g.41349033A>G	ENSP00000411250:p.Thr646Ala	201.0	0.0		187.0	11.0	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	hg19	CCDS45694.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.053575	0.55218	.	.	ENSG00000188554	ENST00000422280;ENST00000542611;ENST00000341165;ENST00000389312;ENST00000389311	T;T;T;T	0.17691	2.26;2.26;2.26;2.26	5.77	5.77	0.91146	.	.	.	.	.	T	0.25827	0.0629	L	0.49126	1.545	0.45747	D	0.998642	D;P;D	0.58620	0.983;0.569;0.983	P;B;P	0.49887	0.625;0.269;0.625	T	0.00735	-1.1588	9	0.36615	T	0.2	-10.8015	16.084	0.81025	1.0:0.0:0.0:0.0	.	625;646;646	B7Z5R6;Q14596-2;Q14596	.;.;NBR1_HUMAN	A	646;625;646;646;646	ENSP00000411250:T646A;ENSP00000437545:T625A;ENSP00000343479:T646A;ENSP00000373963:T646A	ENSP00000343479:T646A	T	+	1	0	NBR1	38704559	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.192000	0.58378	2.202000	0.70862	0.482000	0.46254	ACC	.	.		0.502	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		G	41349033	A	G	41349033	3	3	73	1	0	0	0	0	1	0	0	0	10209	275	10	2	1994	2	NBR1	17	41349033	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	182721	41349033	39846177	530	9856										
SLC4A1	6521	hgsc.bcm.edu	37	chr17	42328926	42328926	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtacagccagggggatgcggGacaggatgggctccatgagg	19	8	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:42328926G>A	ENST00000262418.6	-	18	2497	c.2342C>T	c.(2341-2343)tCc>tTc	p.S781F	AC003102.1_ENST00000399246.2_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	781	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GGGGATGCGGGACAGGATGGG	0.627																																					p.S781F		Atlas-SNP	.											.	SLC4A1	104	.	0			c.C2342T						.						81	76	78					17																	42328926		2203	4300	6503	SO:0001583	missense	6521	exon18			ATGCGGGACAGGA		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"CD molecules", "Blood group antigens", "Solute carriers"	11027	protein-coding gene	gene with protein product	"Froese blood group", "Swann blood group", "Wright blood group"	109270	"Waldner blood group", "erythrocyte membrane protein band 3", "Diego blood group", "solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)", "solute carrier family 4 (anion exchanger), member 1"	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.2342C>T	chr17.hg19:g.42328926G>A	ENSP00000262418:p.Ser781Phe	153.0	0.0		135.0	47.0	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	hg19	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858482	0.71834	.	.	ENSG00000004939	ENST00000262418	T	0.79352	-1.26	5.22	0.579	0.17397	Bicarbonate transporter, C-terminal (1);	0.557954	0.18498	N	0.139441	T	0.79563	0.4467	M	0.68317	2.08	0.31234	N	0.69596	D	0.58970	0.984	P	0.57009	0.811	T	0.76364	-0.2986	10	0.87932	D	0	.	4.5335	0.12017	0.0754:0.2345:0.4791:0.211	.	781	P02730	B3AT_HUMAN	F	781	ENSP00000262418:S781F	ENSP00000262418:S781F	S	-	2	0	SLC4A1	39684452	0.615000	0.27026	0.985000	0.45067	0.983000	0.72400	0.431000	0.21444	0.277000	0.22141	0.561000	0.74099	TCC	.	.		0.627	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		A	42328926	G	A	42328926	3	1	73	1	0	0	0	0	1	0	0	0	14665	1174	41	3	405	3	SLC4A1	17	42328926	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	979893	42328926	38866284	531	9857										
FMNL1	752	hgsc.bcm.edu	37	chr17	43311537	43311537	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagcaagggtccaccctcctCcgtgcccaaaagccgccacc	8	20	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:43311537C>A	ENST00000331495.3	+	6	920	c.584C>A	c.(583-585)tCc>tAc	p.S195Y	FMNL1_ENST00000328118.3_Missense_Mutation_p.S195Y|FMNL1_ENST00000592006.1_3'UTR	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	195	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						CCACCCTCCTCCGTGCCCAAA	0.567																																					p.S195Y	GBM(164;1247 1997 8702 11086 51972)	Atlas-SNP	.											.	FMNL1	78	.	0			c.C584A						.						66	70	69					17																	43311537		2203	4300	6503	SO:0001583	missense	752	exon6			CCTCCTCCGTGCC	AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"formin-like"	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.584C>A	chr17.hg19:g.43311537C>A	ENSP00000329219:p.Ser195Tyr	89.0	0.0		63.0	11.0	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Missense_Mutation	SNP	ENST00000331495.3	hg19	CCDS11497.1	.	.	.	.	.	.	.	.	.	.	C	9.570	1.120749	0.20877	.	.	ENSG00000184922	ENST00000328118;ENST00000331495	T;T	0.81078	-1.45;-1.45	5.03	5.03	0.67393	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);	0.777035	0.12224	N	0.488034	D	0.85835	0.5789	M	0.62723	1.935	0.09310	N	1	P;B	0.51537	0.946;0.145	P;B	0.54026	0.74;0.123	T	0.78293	-0.2260	10	0.45353	T	0.12	.	17.1037	0.86656	0.0:1.0:0.0:0.0	.	195;195	O95466-2;O95466	.;FMNL_HUMAN	Y	195	ENSP00000327442:S195Y;ENSP00000329219:S195Y	ENSP00000327442:S195Y	S	+	2	0	FMNL1	40667320	0.241000	0.23857	0.008000	0.14137	0.088000	0.18126	4.175000	0.58263	2.615000	0.88500	0.555000	0.69702	TCC	.	.		0.567	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892		A	43311537	C	A	43311537	3	1	73	1	0	0	0	0	1	0	0	0	5959	855	30	3	606	3	FMNL1	17	43311537	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	982611	43311537	37883673	532	9858										
NME1	4830	hgsc.bcm.edu	37	chr17	49239133	49239133	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtggagagtgcagagaaggAgatcggcttgtggtttcacc	16	6	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:49239133A>T	ENST00000393196.3	+	5	517	c.386A>T	c.(385-387)gAg>gTg	p.E129V	NME2_ENST00000393193.2_Intron|NME1_ENST00000336097.3_Missense_Mutation_p.E154V|NME1_ENST00000013034.3_Missense_Mutation_p.E154V|NME1-NME2_ENST00000393198.3_Intron|NME1_ENST00000511355.1_3'UTR|NME2_ENST00000376392.6_Intron|NME2_ENST00000555572.1_Intron|NME1-NME2_ENST00000608447.1_Intron	NM_000269.2	NP_000260.1	P15531	NDKA_HUMAN	NME/NM23 nucleoside diphosphate kinase 1	129					cellular response to drug (GO:0035690)|cellular response to fatty acid (GO:0071398)|cellular response to glucose stimulus (GO:0071333)|CTP biosynthetic process (GO:0006241)|DNA catabolic process (GO:0006308)|endocytosis (GO:0006897)|GTP biosynthetic process (GO:0006183)|hippocampus development (GO:0021766)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amine (GO:0014075)|response to cAMP (GO:0051591)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|deoxyribonuclease activity (GO:0004536)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|nucleoside diphosphate kinase activity (GO:0004550)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|single-stranded DNA binding (GO:0003697)			endometrium(1)|large_intestine(1)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)		Adefovir Dipivoxil(DB00718)|Lamivudine(DB00709)|Tenofovir(DB00300)	GCAGAGAAGGAGATCGGCTTG	0.478																																					p.E154V	GBM(176;1298 2890 6639 30062)	Atlas-SNP	.											.	NME1	12	.	0			c.A461T						.						128	116	120					17																	49239133		2203	4300	6503	SO:0001583	missense	4830	exon6			AGAAGGAGATCGG	AL360191, X17620	CCDS11578.1, CCDS11579.1	17q21.33	2013-04-29	2012-05-18		ENSG00000239672	ENSG00000239672			7849	protein-coding gene	gene with protein product		156490	"non-metastatic cells 1, protein (NM23A) expressed in"			8270257, 19852809	Standard	NM_000269		Approved	NM23, NM23-H1, NDPKA		P15531	OTTHUMG00000137474	ENST00000393196.3:c.386A>T	chr17.hg19:g.49239133A>T	ENSP00000376892:p.Glu129Val	131.0	0.0		104.0	53.0	NM_198175	Q6FGK3|Q86XQ2|Q9UDJ6	Missense_Mutation	SNP	ENST00000393196.3	hg19	CCDS11579.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.413568	0.83449	.	.	ENSG00000239672	ENST00000393196;ENST00000336097;ENST00000013034	T;T;T	0.67698	-0.28;-0.28;-0.28	5.81	5.81	0.92471	.	.	.	.	.	D	0.91355	0.7273	H	0.99958	5.055	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95534	0.8606	9	0.87932	D	0	-12.0086	16.4563	0.84015	1.0:0.0:0.0:0.0	.	129;154	P15531;P15531-2	NDKA_HUMAN;.	V	129;154;154	ENSP00000376892:E129V;ENSP00000337060:E154V;ENSP00000013034:E154V	ENSP00000013034:E154V	E	+	2	0	NME1	46594132	1.000000	0.71417	1.000000	0.80357	0.477000	0.33069	8.823000	0.92018	2.343000	0.79666	0.533000	0.62120	GAG	.	.		0.478	NME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268662.2	NM_000269		T	49239133	A	T	49239133	3	4	73	1	0	0	0	0	1	0	0	0	10498	304	11	4	479	4	NME1	17	49239133	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	5927596	49239133	31956077	533	9859										
OR4D2	124538	hgsc.bcm.edu	37	chr17	56247411	56247411	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	catctcccggcccctccgctAtgtcaccgtcatgaacactc	6	19	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:56247411A>G	ENST00000545221.1	+	1	395	c.395A>G	c.(394-396)tAt>tGt	p.Y132C		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						CCCCTCCGCTATGTCACCGTC	0.572																																					p.Y132C		Atlas-SNP	.											.	OR4D2	48	.	0			c.A395G						.						88	88	88					17																	56247411		2203	4300	6503	SO:0001583	missense	124538	exon1			TCCGCTATGTCAC		CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"GPCR / Class A : Olfactory receptors"	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.395A>G	chr17.hg19:g.56247411A>G	ENSP00000441354:p.Tyr132Cys	74.0	0.0		73.0	28.0	NM_001004707	Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	hg19	CCDS32688.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.053735	0.55218	.	.	ENSG00000255713	ENST00000545221	T	0.33865	1.39	5.5	5.5	0.81552	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000140	T	0.51584	0.1683	M	0.92784	3.345	0.45205	D	0.998213	B	0.31859	0.343	B	0.33620	0.167	T	0.61267	-0.7097	10	0.87932	D	0	-15.1891	13.8478	0.63479	1.0:0.0:0.0:0.0	.	132	P58180	OR4D2_HUMAN	C	132	ENSP00000441354:Y132C	ENSP00000441354:Y132C	Y	+	2	0	OR4D2	53602410	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.283000	0.95860	2.220000	0.72140	0.496000	0.49642	TAT	.	.		0.572	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1			G	56247411	A	G	56247411	3	3	73	1	0	0	0	0	1	0	0	0	11065	449	16	2	397	2	OR4D2	17	56247411	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	7008278	56247411	24947799	534	9860										
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56384317	56384317	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtagaagccatcggcatcctTgtccccaaacacctggaggc	10	14	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:56384317T>C	ENST00000343736.4	-	25	5159	c.4996A>G	c.(4996-4998)Aag>Gag	p.K1666E	BZRAP1_ENST00000268893.6_Missense_Mutation_p.K1606E|BZRAP1_ENST00000355701.3_Missense_Mutation_p.K1666E			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1666	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCGGCATCCTTGTCCCCAAAC	0.612																																					p.K1666E		Atlas-SNP	.											.	BZRAP1	287	.	0			c.A4996G						.						57	49	52					17																	56384317		2203	4300	6503	SO:0001583	missense	9256	exon25			CATCCTTGTCCCC	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4996A>G	chr17.hg19:g.56384317T>C	ENSP00000345824:p.Lys1666Glu	48.0	0.0		43.0	17.0	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	hg19	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.040915	0.93685	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.09073	3.02;3.02;3.02	5.64	5.64	0.86602	Src homology-3 domain (3);Variant SH3 (1);	0.047833	0.85682	D	0.000000	T	0.17023	0.0409	N	0.20304	0.555	0.51482	D	0.999921	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.996;0.996	T	0.04115	-1.0976	10	0.66056	D	0.02	.	15.0407	0.71788	0.0:0.0:0.0:1.0	.	1666;1606;1666	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	E	1666;1666;1606	ENSP00000347929:K1666E;ENSP00000345824:K1666E;ENSP00000268893:K1606E	ENSP00000268893:K1606E	K	-	1	0	BZRAP1	53739316	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.051000	0.71072	2.162000	0.67917	0.421000	0.28195	AAG	.	.		0.612	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		C	56384317	T	C	56384317	3	2	73	1	0	0	0	0	1	0	0	0	1579	1821	63	2	605	2	BZRAP1	17	56384317	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	136906	56384317	24810893	535	9861										
GDPD1	284161	hgsc.bcm.edu	37	chr17	57351120	57351120	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agcttagggattttttacatAacttttcagcatagaaaaag	7	5	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:57351120A>T	ENST00000284116.4	+	10	1068	c.931A>T	c.(931-933)Aac>Tac	p.N311Y	GDPD1_ENST00000581140.1_Intron	NM_182569.3	NP_872375.2	Q8N9F7	GDPD1_HUMAN	glycerophosphodiester phosphodiesterase domain containing 1	311					glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)					TTTTTTACATAACTTTTCAGC	0.333																																					p.N311Y		Atlas-SNP	.											.	GDPD1	39	.	0			c.A931T						.						47	52	50					17																	57351120		2203	4295	6498	SO:0001583	missense	284161	exon10			TTACATAACTTTT	AK094770	CCDS11616.1, CCDS58583.1, CCDS58584.1	17q23.2	2011-01-25				ENSG00000153982			20883	protein-coding gene	gene with protein product						14612981	Standard	NM_182569		Approved	FLJ37451, GDE4	uc002ixk.2	Q8N9F7		ENST00000284116.4:c.931A>T	chr17.hg19:g.57351120A>T	ENSP00000284116:p.Asn311Tyr	44.0	0.0		65.0	25.0	NM_182569	A8W735|Q56VR1|Q8N4E3	Missense_Mutation	SNP	ENST00000284116.4	hg19	CCDS11616.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.719723	0.30503	.	.	ENSG00000153982	ENST00000284116	T	0.33654	1.4	5.81	4.71	0.59529	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.397035	0.33023	N	0.005364	T	0.43722	0.1260	M	0.78456	2.415	0.80722	D	1	B	0.22480	0.07	B	0.31016	0.123	T	0.40459	-0.9562	10	0.72032	D	0.01	.	11.5207	0.50549	0.8658:0.0:0.0:0.1342	.	311	Q8N9F7	GDPD1_HUMAN	Y	311	ENSP00000284116:N311Y	ENSP00000284116:N311Y	N	+	1	0	GDPD1	54705902	0.999000	0.42202	0.592000	0.28758	0.267000	0.26476	2.089000	0.41672	0.978000	0.38470	0.477000	0.44152	AAC	.	.		0.333	GDPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446024.1	NM_182569		T	57351120	A	T	57351120	3	4	73	1	0	0	0	0	1	0	0	0	6331	362	13	4	1020	4	GDPD1	17	57351120	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	966803	57351120	23844090	536	9862										
NACA2	342538	hgsc.bcm.edu	37	chr17	59667968	59667968	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agctcggactgcctttgctcTcgacacatttgcttgtgaca	9	12	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:59667968T>A	ENST00000521764.1	-	1	595	c.574A>T	c.(574-576)Aga>Tga	p.R192*		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	192	UBA.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					GCCTTTGCTCTCGACACATTT	0.408																																					p.R192X		Atlas-SNP	.											.	NACA2	33	.	0			c.A574T						.						267	237	247					17																	59667968		2203	4300	6503	SO:0001587	stop_gained	342538	exon1			TTGCTCTCGACAC	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"alpha-NAC protein"	609274	"nascent-polypeptide-associated complex alpha polypeptide-like"	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.574A>T	chr17.hg19:g.59667968T>A	ENSP00000427802:p.Arg192*	109.0	0.0		110.0	43.0	NM_199290	Q2VIR9	Nonsense_Mutation	SNP	ENST00000521764.1	hg19	CCDS11630.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.916270	0.73098	.	.	ENSG00000253506	ENST00000521764	.	.	.	0.753	0.753	0.18404	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7201	0.17982	0.0:0.0:0.0:1.0	.	.	.	.	X	192	.	.	R	-	1	2	NACA2	57022750	1.000000	0.71417	0.992000	0.48379	0.878000	0.50629	1.591000	0.36665	0.588000	0.29660	0.338000	0.21704	AGA	.	.		0.408	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290		A	59667968	T	A	59667968	4	1	73	1	0	0	0	0	0	1	0	0	10143	1559	54	4	77	4	NACA2	17	59667968	Nonsense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2316848	59667968	21527242	537	9863										
ACE	1636	hgsc.bcm.edu	37	chr17	61566056	61566056	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggaaatatgaagacctgttaTgggcatgggagggctggcga	17	5	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:61566056T>G	ENST00000290866.4	+	16	2377	c.2353T>G	c.(2353-2355)Tgg>Ggg	p.W785G	ACE_ENST00000577647.1_Missense_Mutation_p.W211G|ACE_ENST00000490216.2_Missense_Mutation_p.W211G|ACE_ENST00000413513.3_Missense_Mutation_p.W211G|ACE_ENST00000290863.6_Missense_Mutation_p.W211G|ACE_ENST00000428043.1_Missense_Mutation_p.W785G|ACE_ENST00000421982.2_Missense_Mutation_p.W95G	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	785	Peptidase M2 2.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	AGACCTGTTATGGGCATGGGA	0.552																																					p.W785G		Atlas-SNP	.											.	ACE	187	.	0			c.T2353G						.						119	112	114					17																	61566056		2203	4300	6503	SO:0001583	missense	1636	exon16			CTGTTATGGGCAT	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.2353T>G	chr17.hg19:g.61566056T>G	ENSP00000290866:p.Trp785Gly	68.0	0.0		70.0	29.0	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	T	7.029	0.560216	0.13498	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863;ENST00000413513;ENST00000421982	T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.37	5.93	5.93	0.95920	.	0.101295	0.64402	D	0.000002	T	0.62648	0.2445	M	0.91972	3.26	0.23331	N	0.997899	D;P;D;D	0.59767	0.976;0.941;0.986;0.984	P;P;P;P	0.59424	0.649;0.857;0.745;0.666	T	0.65417	-0.6173	10	0.66056	D	0.02	-23.2778	11.5969	0.50979	0.0:0.0:0.1484:0.8516	.	95;211;211;785	F6X3S4;B4DXI3;P12821-3;P12821	.;.;.;ACE_HUMAN	G	785;785;211;211;95	ENSP00000290866:W785G;ENSP00000397593:W785G;ENSP00000290863:W211G;ENSP00000392247:W211G;ENSP00000387760:W95G	ENSP00000290863:W211G	W	+	1	0	ACE	58919788	1.000000	0.71417	0.926000	0.36857	0.035000	0.12851	4.956000	0.63645	2.271000	0.75665	0.459000	0.35465	TGG	.	.		0.552	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			G	61566056	T	G	61566056	3	3	73	1	0	0	0	0	1	0	0	0	136	1464	51	5	2618	5	ACE	17	61566056	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1898088	61566056	19629154	538	9864										
GH2	2689	hgsc.bcm.edu	37	chr17	61957713	61957713	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctgccctccacagagcggcActgcacgatgcgcaggaatg	13	14	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:61957713A>G	ENST00000423893.2	-	5	683	c.622T>C	c.(622-624)Tgc>Cgc	p.C208R	GH2_ENST00000332800.7_3'UTR|GH2_ENST00000449787.2_Missense_Mutation_p.C193R|GH2_ENST00000456543.2_Silent_p.S206S			P01242	SOM2_HUMAN	growth hormone 2	208					JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	24						ACAGAGCGGCACTGCACGATG	0.592																																					p.C208R		Atlas-SNP	.											.	GH2	73	.	0			c.T622C						.						107	89	95					17																	61957713		2202	4279	6481	SO:0001583	missense	2689	exon5			AGCGGCACTGCAC	J03756	CCDS11647.1, CCDS11648.1, CCDS45757.1, CCDS45758.1	17q22-q24	2014-01-30						"Endogenous ligands"	4262	protein-coding gene	gene with protein product	"placental-specific growth hormone", "placenta-specific growth hormone"	139240				6306568	Standard	NM_002059		Approved	GH-V, GHV, GHL, hGH-V	uc002jcl.2	P01242		ENST00000423893.2:c.622T>C	chr17.hg19:g.61957713A>G	ENSP00000409294:p.Cys208Arg	114.0	0.0		91.0	11.0	NM_002059	B1A4H5|B1A4H7|O14643|O14644|P09587	Missense_Mutation	SNP	ENST00000423893.2	hg19	CCDS11647.1	.	.	.	.	.	.	.	.	.	.	a	11.37	1.618543	0.28801	.	.	ENSG00000136487	ENST00000423893;ENST00000449787	D;D	0.99194	-5.54;-5.54	2.74	2.74	0.32292	Somatotropin hormone, conserved site (1);Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	.	.	.	.	D	0.99086	0.9686	.	.	.	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99364	1.0918	8	0.87932	D	0	.	9.9433	0.41593	1.0:0.0:0.0:0.0	.	208;193	P01242;O14643	SOM2_HUMAN;.	R	208;193	ENSP00000409294:C208R;ENSP00000410618:C193R	ENSP00000409294:C208R	C	-	1	0	GH2	59311445	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	2.950000	0.49081	1.255000	0.44051	0.254000	0.18369	TGC	.	.		0.592	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1	NM_002059		G	61957713	A	G	61957713	3	3	73	1	0	0	0	0	1	0	0	0	6376	159	6	2	123	2	GH2	17	61957713	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	391657	61957713	19237497	539	9865										
CSHL1	1444	hgsc.bcm.edu	37	chr17	61987231	61987231	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acttgctgtaggtctgcttgAgggtctgcccagtcaggtgg	15	9	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:61987231A>T	ENST00000309894.5	-	5	508	c.509T>A	c.(508-510)cTc>cAc	p.L170H	CSHL1_ENST00000259003.10_Missense_Mutation_p.L108H|CSHL1_ENST00000346606.6_Missense_Mutation_p.L76H|CSHL1_ENST00000558099.1_5'UTR|CSHL1_ENST00000561003.1_Silent_p.P171P|CSHL1_ENST00000450719.3_Silent_p.P160P|CSHL1_ENST00000438387.2_Missense_Mutation_p.L87H	NM_022579.1	NP_072101.1	Q14406	CSHL_HUMAN	chorionic somatomammotropin hormone-like 1	170						extracellular region (GO:0005576)	hormone activity (GO:0005179)|metal ion binding (GO:0046872)			endometrium(3)|lung(6)	9						GGTCTGCTTGAGGGTCTGCCC	0.552																																					p.L170H		Atlas-SNP	.											.	CSHL1	42	.	0			c.T509A						.						194	172	179					17																	61987231		2203	4300	6503	SO:0001583	missense	1444	exon5			TGCTTGAGGGTCT	BC029365	CCDS11652.1, CCDS42370.1, CCDS45759.1	17q22-q24	2012-10-02							2442	protein-coding gene	gene with protein product	"chorionic somatomammotropin CS-5"	603515		CSHP1		8083227	Standard	NM_001318		Approved	hCS-L, CSL, CS-5, MGC149868	uc002jda.1	Q14406		ENST00000309894.5:c.509T>A	chr17.hg19:g.61987231A>T	ENSP00000309524:p.Leu170His	137.0	0.0		150.0	71.0	NM_022579	D3DU26|D3DU27|Q0VDB2	Missense_Mutation	SNP	ENST00000309894.5	hg19	CCDS11652.1	.	.	.	.	.	.	.	.	.	.	a	13.04	2.119610	0.37436	.	.	ENSG00000204414	ENST00000309894;ENST00000438387;ENST00000259003;ENST00000346606	D;D;D	0.91124	-2.79;-2.79;-2.79	3.6	3.6	0.41247	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.454500	0.04305	N	0.347916	D	0.94843	0.8334	M	0.70275	2.135	0.80722	D	1	D;D;D;D	0.67145	0.983;0.996;0.996;0.996	P;P;D;P	0.64687	0.796;0.882;0.928;0.882	D	0.87053	0.2148	10	0.87932	D	0	.	11.3009	0.49304	1.0:0.0:0.0:0.0	.	76;87;170;147	Q14406-4;Q14406-3;Q14406;Q14406-2	.;.;CSHL_HUMAN;.	H	170;87;165;76	ENSP00000309524:L170H;ENSP00000402632:L87H;ENSP00000316360:L76H	ENSP00000259003:L165H	L	-	2	0	GH1	59340963	1.000000	0.71417	0.982000	0.44146	0.017000	0.09413	5.526000	0.67116	1.412000	0.46977	0.254000	0.18369	CTC	.	.		0.552	CSHL1-009	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444557.1	NM_022579		T	61987231	A	T	61987231	3	4	73	1	0	0	0	0	1	0	0	0	3944	304	11	4	163	4	CSHL1	17	61987231	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	29518	61987231	19207979	540	9866										
MGAT5B	146664	hgsc.bcm.edu	37	chr17	74921070	74921070	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acttaggggtaccgccaggcCggggaagctgcccgctcacc	14	15	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:74921070C>A	ENST00000569840.2	+	9	1622	c.1048C>A	c.(1048-1050)Cgg>Agg	p.R350R	MGAT5B_ENST00000301618.4_Silent_p.R350R|MGAT5B_ENST00000428789.2_Silent_p.R361R	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	350					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ACCGCCAGGCCGGGGAAGCTG	0.612																																					p.R361R		Atlas-SNP	.											.	MGAT5B	98	.	0			c.C1081A						.						80	85	83					17																	74921070		2203	4300	6503	SO:0001819	synonymous_variant	146664	exon8			CCAGGCCGGGGAA	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	24140	protein-coding gene	gene with protein product		612441	"mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1048C>A	chr17.hg19:g.74921070C>A		78.0	0.0		54.0	20.0	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	hg19	CCDS59299.1																																																																																			.	.		0.612	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677		A	74921070	C	A	74921070	2	1	73	1	0	0	0	0	0	0	0	1	9558	643	23	1		1	MGAT5B	17	74921070	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	12933839	74921070	6274140	541	9867										
AZI1	22994	hgsc.bcm.edu	37	chr17	79170793	79170793	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acctccagcttcagccgcatCacagacgtgctcacctcgga	8	17	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:79170793C>G	ENST00000269392.4	-	14	1966	c.1719G>C	c.(1717-1719)gtG>gtC	p.V573V	AZI1_ENST00000374782.3_Silent_p.V570V|AZI1_ENST00000450824.2_Silent_p.V570V|AZI1_ENST00000575907.1_Silent_p.V573V|RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000570482.2_5'Flank	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		573					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TCAGCCGCATCACAGACGTGC	0.682																																					p.V570V		Atlas-SNP	.											.	AZI1	145	.	0			c.G1710C						.						63	48	53					17																	79170793		2189	4292	6481	SO:0001819	synonymous_variant	22994	exon14			CCGCATCACAGAC																												ENST00000269392.4:c.1719G>C	chr17.hg19:g.79170793C>G		240.0	0.0		240.0	109.0	NM_014984	A6NHI8|B2RN11|Q96F50	Silent	SNP	ENST00000269392.4	hg19																																																																																				.	.		0.682	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			G	79170793	C	G	79170793	2	3	73	1	0	0	0	0	0	0	0	1	1240	813	29	4		4	AZI1	17	79170793	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	4249723	79170793	2024417	542	9868										
FN3KRP	79672	hgsc.bcm.edu	37	chr17	80674715	80674715	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggcgggtgcatcagccagggCcggagctacgacacggatca	16	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr17:80674715C>T	ENST00000269373.6	+	1	157	c.84C>T	c.(82-84)ggC>ggT	p.G28G	FN3KRP_ENST00000535965.1_5'UTR|RP11-388C12.1_ENST00000574471.1_lincRNA	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	28							kinase activity (GO:0016301)			breast(1)|large_intestine(2)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	7	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			TCAGCCAGGGCCGGAGCTACG	0.701																																					p.G28G		Atlas-SNP	.											.	FN3KRP	31	.	0			c.C84T						.						28	30	29					17																	80674715		2199	4295	6494	SO:0001819	synonymous_variant	79672	exon1			CCAGGGCCGGAGC	AY360465	CCDS11817.1	17q25.3	2014-08-12			ENSG00000141560	ENSG00000141560			25700	protein-coding gene	gene with protein product		611683				14633848	Standard	NM_024619		Approved	FLJ12171, FN3KL	uc002kfu.3	Q9HA64	OTTHUMG00000177846	ENST00000269373.6:c.84C>T	chr17.hg19:g.80674715C>T		586.0	2.0		449.0	206.0	NM_024619	Q969F4|Q9H0U7	Silent	SNP	ENST00000269373.6	hg19	CCDS11817.1																																																																																			.	.		0.701	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619		T	80674715	C	T	80674715	2	4	73	1	0	0	0	0	0	0	0	1	5972	726	26	3		3	FN3KRP	17	80674715	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1503922	80674715	520495	543	9869										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5397253	5397253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgcctgtgaatgcgggctgtGctgcagcatccccgctgtct	13	13	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr18:5397253G>T	ENST00000341928.2	-	18	2985	c.2645C>A	c.(2644-2646)gCa>gAa	p.A882E	EPB41L3_ENST00000544123.1_Missense_Mutation_p.A713E|EPB41L3_ENST00000542146.1_Missense_Mutation_p.A187E|EPB41L3_ENST00000427684.2_Missense_Mutation_p.A179E|EPB41L3_ENST00000400111.3_Missense_Mutation_p.A660E|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000342933.3_Missense_Mutation_p.A882E|EPB41L3_ENST00000540638.2_Missense_Mutation_p.A660E	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	882	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.A882E(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						TGCGGGCTGTGCTGCAGCATC	0.612																																					p.A882E		Atlas-SNP	.											EPB41L3,NS,carcinoma,0,1	EPB41L3	222	.	1	Substitution - Missense(1)	lung(1)	c.C2645A						.						89	77	81					18																	5397253		2203	4300	6503	SO:0001583	missense	23136	exon18			GGCTGTGCTGCAG	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2645C>A	chr18.hg19:g.5397253G>T	ENSP00000343158:p.Ala882Glu	90.0	0.0		81.0	24.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	3.284	-0.146491	0.06627	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89	5.73	1.82	0.25136	.	2.044370	0.01726	N	0.028594	T	0.28267	0.0698	N	0.17474	0.49	0.09310	N	1	B;P;B;B;B;B;B;B	0.35433	0.0;0.501;0.0;0.001;0.0;0.001;0.0;0.002	B;B;B;B;B;B;B;B	0.35550	0.003;0.205;0.007;0.003;0.001;0.005;0.003;0.002	T	0.16247	-1.0409	10	0.19147	T	0.46	.	6.0818	0.19944	0.0927:0.1145:0.6684:0.1245	.	713;179;187;274;551;660;882;117	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	E	882;551;713;551;179;187;882;660	ENSP00000343158:A882E;ENSP00000441174:A713E;ENSP00000392195:A179E;ENSP00000442233:A187E;ENSP00000341138:A882E;ENSP00000382981:A660E	ENSP00000343158:A882E	A	-	2	0	EPB41L3	5387253	0.010000	0.17322	0.000000	0.03702	0.044000	0.14063	1.103000	0.31062	0.040000	0.15660	0.591000	0.81541	GCA	.	.		0.612	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		T	5397253	G	T	5397253	3	4	73	1	0	0	0	0	1	0	0	0	5156	1319	46	3	638	3	EPB41L3	18	5397253	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10		5397253	72679995	544	9870										
IMPA2	3613	hgsc.bcm.edu	37	chr18	12009936	12009936	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagtgtgtgctcacccacagCccgacgtggatcatcgaccc	10	15	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr18:12009936C>A	ENST00000269159.3	+	3	527	c.285C>A	c.(283-285)agC>agA	p.S95R	IMPA2_ENST00000588752.1_3'UTR|IMPA2_ENST00000589238.1_5'UTR|IMPA2_ENST00000588927.1_5'UTR	NM_014214.2	NP_055029.1	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	95					inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)|stomach(2)|urinary_tract(1)	12					Lithium(DB01356)	TCACCCACAGCCCGACGTGGA	0.572																																					p.S95R		Atlas-SNP	.											.	IMPA2	27	.	0			c.C285A						.						120	117	118					18																	12009936		2203	4300	6503	SO:0001583	missense	3613	exon3			CCACAGCCCGACG	AF014398	CCDS11855.1	18p11.2	2008-03-18			ENSG00000141401	ENSG00000141401	3.1.3.25		6051	protein-coding gene	gene with protein product		605922				9322233	Standard	NM_014214		Approved		uc002kqp.2	O14732	OTTHUMG00000131693	ENST00000269159.3:c.285C>A	chr18.hg19:g.12009936C>A	ENSP00000269159:p.Ser95Arg	101.0	0.0		92.0	42.0	NM_014214	B0YJ29|Q9UJT3	Missense_Mutation	SNP	ENST00000269159.3	hg19	CCDS11855.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.102921	0.37145	.	.	ENSG00000141401	ENST00000269159	T	0.42513	0.97	5.48	4.61	0.57282	.	0.240021	0.47093	D	0.000245	T	0.30665	0.0772	N	0.25825	0.765	0.80722	D	1	B	0.21225	0.053	B	0.21546	0.035	T	0.10800	-1.0614	10	0.62326	D	0.03	-8.4541	10.1515	0.42796	0.0:0.8377:0.0:0.1623	.	95	O14732	IMPA2_HUMAN	R	95	ENSP00000269159:S95R	ENSP00000269159:S95R	S	+	3	2	IMPA2	11999936	0.997000	0.39634	0.996000	0.52242	0.733000	0.41908	0.309000	0.19332	1.314000	0.45095	0.491000	0.48974	AGC	.	.		0.572	IMPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254601.1			A	12009936	C	A	12009936	3	1	73	1	0	0	0	0	1	0	0	0	7732	738	26	3	295	3	IMPA2	18	12009936	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	6612683	12009936	66067312	545	9871										
CEP192	55125	hgsc.bcm.edu	37	chr18	13113583	13113583	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctcttctgtatgtatttcgtAggtctccatcacatttttgc	6	10	4	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr18:13113583A>T	ENST00000325971.8	+	39	6852		c.e39-1		CEP192_ENST00000506447.1_Splice_Site|CEP192_ENST00000430049.2_Splice_Site|CEP192_ENST00000540847.2_Splice_Site			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa						centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TGTATTTCGTAGGTCTCCATC	0.398																																					.		Atlas-SNP	.											.	CEP192	340	.	0			c.7048-2A>T						.						112	112	112					18																	13113583		2203	4300	6503	SO:0001630	splice_region_variant	55125	exon41			TTTCGTAGGTCTC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.5260-1A>T	chr18.hg19:g.13113583A>T		62.0	0.0		70.0	32.0	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Splice_Site	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	A	19.81	3.897005	0.72639	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049;ENST00000540847	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3039	0.73976	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CEP192	13103583	1.000000	0.71417	0.994000	0.49952	0.868000	0.49771	7.407000	0.80029	2.084000	0.62774	0.460000	0.39030	.	.	.		0.398	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	Intron	T	13113583	A	T	13113583	5	4	73	1	0	0	0	0	0	0	1	0	3253	434	15	4	7204	4	CEP192	18	13113583	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1103647	13113583	64963665	546	9872										
MC5R	4161	hgsc.bcm.edu	37	chr18	13826194	13826194	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagtggataggtacgtcaccAtcttctacgccctgcgctac	9	14	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr18:13826194A>C	ENST00000324750.3	+	1	652	c.430A>C	c.(430-432)Atc>Ctc	p.I144L	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	144					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|melanocortin receptor activity (GO:0004977)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|upper_aerodigestive_tract(1)	41						GTACGTCACCATCTTCTACGC	0.567																																					p.I144L		Atlas-SNP	.											.	MC5R	83	.	0			c.A430C						.						149	129	136					18																	13826194		2203	4300	6503	SO:0001583	missense	4161	exon1			GTCACCATCTTCT	AY268429	CCDS11868.1	18p11.2	2012-08-10			ENSG00000176136	ENSG00000176136		"GPCR / Class A : Melanocortin receptors"	6933	protein-coding gene	gene with protein product		600042				8396929	Standard	NM_005913		Approved		uc010xaf.2	P33032	OTTHUMG00000131720	ENST00000324750.3:c.430A>C	chr18.hg19:g.13826194A>C	ENSP00000318077:p.Ile144Leu	105.0	0.0		84.0	32.0	NM_005913	B0YJ34|Q502V1	Missense_Mutation	SNP	ENST00000324750.3	hg19	CCDS11868.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.009062	0.54361	.	.	ENSG00000176136	ENST00000324750	T	0.81078	-1.45	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.91499	0.7316	M	0.92833	3.35	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	D	0.93422	0.6778	10	0.87932	D	0	.	13.8852	0.63704	1.0:0.0:0.0:0.0	.	144	P33032	MC5R_HUMAN	L	144	ENSP00000318077:I144L	ENSP00000318077:I144L	I	+	1	0	MC5R	13816194	1.000000	0.71417	1.000000	0.80357	0.369000	0.29798	7.068000	0.76748	1.873000	0.54277	0.374000	0.22700	ATC	.	.		0.567	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913		C	13826194	A	C	13826194	3	2	73	1	0	0	0	0	1	0	0	0	9376	217	8	5	432	5	MC5R	18	13826194	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	712611	13826194	64251054	547	9873										
HRH4	59340	hgsc.bcm.edu	37	chr18	22057255	22057255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	actgcttagagccaggagatTagccaagtcactggccattc	10	11	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr18:22057255T>C	ENST00000256906.4	+	3	1002	c.902T>C	c.(901-903)tTa>tCa	p.L301S	HRH4_ENST00000426880.2_Missense_Mutation_p.L213S	NM_001160166.1|NM_021624.3	NP_001153638.1|NP_067637.2	Q9H3N8	HRH4_HUMAN	histamine receptor H4	301					inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of MAPK cascade (GO:0043408)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Amitriptyline(DB00321)|Amoxapine(DB00543)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Mianserin(DB06148)|Olanzapine(DB00334)	GCCAGGAGATTAGCCAAGTCA	0.428																																					p.L301S		Atlas-SNP	.											.	HRH4	46	.	0			c.T902C						.						199	197	198					18																	22057255		2203	4300	6503	SO:0001583	missense	59340	exon3			GGAGATTAGCCAA	AF312230	CCDS11887.1, CCDS45841.1	18q11.2	2012-08-08			ENSG00000134489	ENSG00000134489		"GPCR / Class A : Histamine receptors"	17383	protein-coding gene	gene with protein product		606792				11118334, 10973974	Standard	NM_021624		Approved	H4R, HH4R, AXOR35, GPCR105, GPRv53	uc002kvi.3	Q9H3N8	OTTHUMG00000131945	ENST00000256906.4:c.902T>C	chr18.hg19:g.22057255T>C	ENSP00000256906:p.Leu301Ser	172.0	0.0		142.0	55.0	NM_021624	B0YJ19|B2KJ48|Q4G0I6|Q9GZQ0	Missense_Mutation	SNP	ENST00000256906.4	hg19	CCDS11887.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.557582	0.86231	.	.	ENSG00000134489	ENST00000256906;ENST00000426880	T;T	0.39406	1.08;1.08	5.78	5.78	0.91487	GPCR, rhodopsin-like superfamily (1);	0.316936	0.29205	N	0.012837	T	0.60130	0.2245	L	0.53617	1.68	0.42626	D	0.993365	D;P	0.76494	0.999;0.943	D;P	0.75020	0.985;0.867	T	0.62651	-0.6809	10	0.66056	D	0.02	-18.0601	15.3026	0.73966	0.0:0.0:0.0:1.0	.	213;301	B2KJ48;Q9H3N8	.;HRH4_HUMAN	S	301;213	ENSP00000256906:L301S;ENSP00000402526:L213S	ENSP00000256906:L301S	L	+	2	0	HRH4	20311253	0.996000	0.38824	0.984000	0.44739	0.842000	0.47809	6.176000	0.71955	2.208000	0.71279	0.528000	0.53228	TTA	.	.		0.428	HRH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254904.1			C	22057255	T	C	22057255	3	2	73	1	0	0	0	0	1	0	0	0	7367	1764	61	2	912	2	HRH4	18	22057255	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	8231061	22057255	56019993	548	9874										
KCTD1	284252	hgsc.bcm.edu	37	chr18	24126984	24126984	+	5'UTR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgttccccagcgagggcggcTgggggcggtggtggtgggag	23	8	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr18:24126984T>A	ENST00000580059.1	-	0	98				KCTD1_ENST00000417602.1_Missense_Mutation_p.Q506L|KCTD1_ENST00000317932.7_Intron|KCTD1_ENST00000408011.3_Intron|KCTD1_ENST00000579973.1_Intron			Q719H9	KCTD1_HUMAN	potassium channel tetramerization domain containing 1						negative regulation of transcription, DNA-templated (GO:0045892)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(3)	12	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			CGAGGGCGGCTGGGGGCGGTG	0.711																																					p.Q506L		Atlas-SNP	.											.	KCTD1	76	.	0			c.A1517T						.						3	3	3					18																	24126984		625	1460	2085	SO:0001623	5_prime_UTR_variant	284252	exon1			GGCGGCTGGGGGC	AF542549	CCDS11888.1	18q11.2	2013-09-20	2013-06-20		ENSG00000134504	ENSG00000134504			18249	protein-coding gene	gene with protein product		613420	"potassium channel tetramerisation domain containing 1"	C18orf5			Standard	NM_001142730		Approved		uc010xbj.3	Q719H9	OTTHUMG00000131947	ENST00000580059.1:c.-308A>T	chr18.hg19:g.24126984T>A		26.0	0.0		26.0	15.0	NM_001142730	A8K1F5	Missense_Mutation	SNP	ENST00000580059.1	hg19	CCDS11888.1	.	.	.	.	.	.	.	.	.	.	T	10.74	1.436339	0.25813	.	.	ENSG00000134504	ENST00000417602	T	0.78924	-1.22	5.13	2.66	0.31614	.	.	.	.	.	T	0.78342	0.4268	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.75918	-0.3148	6	0.62326	D	0.03	.	5.4448	0.16529	0.0:0.0948:0.3863:0.5189	.	.	.	.	L	506	ENSP00000408405:Q506L	ENSP00000408405:Q506L	Q	-	2	0	KCTD1	22380982	0.170000	0.23016	1.000000	0.80357	0.996000	0.88848	0.893000	0.28336	0.735000	0.32537	0.374000	0.22700	CAG	.	.		0.711	KCTD1-005	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000446266.1	XM_209091		A	24126984	T	A	24126984	1	1	73	0	1	0	0	0	0	0	0	0	8105	1580	55	4		4	KCTD1	18	24126984	5'UTR	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2069729	24126984	53950264	549	9875										
MEP1B	4225	hgsc.bcm.edu	37	chr18	29793483	29793483	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acattcgacagcgtatgtccAatcagcggagtataactaca	8	10	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr18:29793483A>C	ENST00000269202.6	+	11	1587	c.1540A>C	c.(1540-1542)Aat>Cat	p.N514H	MEP1B_ENST00000581447.1_Missense_Mutation_p.N514H	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	514	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						GCGTATGTCCAATCAGCGGAG	0.418																																					p.N514H		Atlas-SNP	.											.	MEP1B	54	.	0			c.A1540C						.						78	73	74					18																	29793483		1920	4130	6050	SO:0001583	missense	4225	exon11			ATGTCCAATCAGC	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.1540A>C	chr18.hg19:g.29793483A>C	ENSP00000269202:p.Asn514His	89.0	0.0		89.0	35.0	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	hg19	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	A	15.13	2.740691	0.49045	.	.	ENSG00000141434	ENST00000269202	T	0.20463	2.07	5.53	5.53	0.82687	TRAF-type (1);TRAF-like (1);MATH (3);	0.040424	0.85682	D	0.000000	T	0.36744	0.0978	M	0.74881	2.28	0.47009	D	0.999282	B	0.30563	0.285	B	0.42625	0.393	T	0.14254	-1.0479	10	0.40728	T	0.16	-11.6089	15.6384	0.76973	1.0:0.0:0.0:0.0	.	514	Q16820	MEP1B_HUMAN	H	514	ENSP00000269202:N514H	ENSP00000269202:N514H	N	+	1	0	MEP1B	28047481	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	6.999000	0.76283	2.102000	0.63906	0.383000	0.25322	AAT	.	.		0.418	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		C	29793483	A	C	29793483	3	2	73	1	0	0	0	0	1	0	0	0	9485	130	5	5	1582	5	MEP1B	18	29793483	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	5666499	29793483	48283765	550	9876										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30554635	30554635	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtgtgtgcatccttctctgcAgctgacagagctaaagggaa	12	9	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr18:30554635A>T	ENST00000383096.3	-	22	2581	c.2399T>A	c.(2398-2400)cTg>cAg	p.L800Q	CCDC178_ENST00000406524.2_Missense_Mutation_p.L824Q|CCDC178_ENST00000583930.1_Missense_Mutation_p.L824Q|CCDC178_ENST00000403303.1_Missense_Mutation_p.L800Q|CCDC178_ENST00000402325.1_Missense_Mutation_p.L750Q|CCDC178_ENST00000579947.1_Missense_Mutation_p.L800Q|CCDC178_ENST00000300227.8_Missense_Mutation_p.L762Q|CCDC178_ENST00000579916.1_Missense_Mutation_p.L120Q|CCDC178_ENST00000581852.1_Missense_Mutation_p.L5Q			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	800																	CCTTCTCTGCAGCTGACAGAG	0.498																																					p.L800Q		Atlas-SNP	.											.	.	.	.	0			c.T2399A						.						48	43	45					18																	30554635		2203	4300	6503	SO:0001583	missense	374864	exon21			CTCTGCAGCTGAC	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.2399T>A	chr18.hg19:g.30554635A>T	ENSP00000372576:p.Leu800Gln	48.0	0.0		43.0	15.0	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	hg19	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	A	9.820	1.185447	0.21870	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.51817	0.69;0.69;0.83;0.91;1.78	5.59	5.59	0.84812	.	.	.	.	.	T	0.62258	0.2413	L	0.43152	1.355	0.47308	D	0.999388	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;0.999;0.999;0.999	T	0.64943	-0.6288	9	0.72032	D	0.01	-7.2632	15.7575	0.78046	1.0:0.0:0.0:0.0	.	824;800;750;800;762;800	F8W7A7;A1L4G8;Q5BJE1-3;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;.;.;CR034_HUMAN	Q	800;800;762;824;750	ENSP00000385591:L800Q;ENSP00000372576:L800Q;ENSP00000300227:L762Q;ENSP00000385867:L824Q;ENSP00000385234:L750Q	ENSP00000300227:L762Q	L	-	2	0	C18orf34	28808633	1.000000	0.71417	1.000000	0.80357	0.684000	0.39900	5.639000	0.67868	2.118000	0.64928	0.460000	0.39030	CTG	.	.		0.498	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		T	30554635	A	T	30554635	3	4	73	1	0	0	0	0	1	0	0	0	1904	188	7	4	212	4	C18orf34	18	30554635	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	761152	30554635	47522613	551	9877										
DCC	1630	hgsc.bcm.edu	37	chr18	50923756	50923756	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atgaattctcggtcatggtaAcaaaaaacagaaggtccagt	9	7	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr18:50923756A>T	ENST00000442544.2	+	18	3383	c.2767A>T	c.(2767-2769)Aca>Tca	p.T923S	DCC_ENST00000581580.1_Missense_Mutation_p.T558S|DCC_ENST00000412726.1_Missense_Mutation_p.T751S	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	923	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GGTCATGGTAACAAAAAACAG	0.418																																					p.T923S		Atlas-SNP	.											.	DCC	360	.	0			c.A2767T						.						123	105	111					18																	50923756		2203	4300	6503	SO:0001583	missense	1630	exon18			ATGGTAACAAAAA	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.2767A>T	chr18.hg19:g.50923756A>T	ENSP00000389140:p.Thr923Ser	184.0	0.0		145.0	60.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.772607	0.49680	.	.	ENSG00000187323	ENST00000442544;ENST00000412726	T;T	0.56941	0.43;0.43	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.63212	0.2492	L	0.49778	1.585	0.47862	D	0.999539	P;P;D	0.64830	0.462;0.462;0.994	P;P;D	0.67900	0.464;0.464;0.954	T	0.57608	-0.7782	10	0.11794	T	0.64	.	15.1301	0.72517	1.0:0.0:0.0:0.0	.	751;751;923	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	S	923;751	ENSP00000389140:T923S;ENSP00000397322:T751S	ENSP00000397322:T751S	T	+	1	0	DCC	49177754	1.000000	0.71417	0.458000	0.27068	0.877000	0.50540	9.220000	0.95180	2.213000	0.71641	0.528000	0.53228	ACA	.	.		0.418	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	50923756	A	T	50923756	3	4	73	1	0	0	0	0	1	0	0	0	4284	43	2	4	2837	4	DCC	18	50923756	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	20369121	50923756	27153492	552	9878										
ADNP2	22850	hgsc.bcm.edu	37	chr18	77896097	77896097	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctggctgccatcgccgtccAtttggtgcgctgcagaagtg	13	13	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr18:77896097A>G	ENST00000262198.4	+	4	3256	c.2801A>G	c.(2800-2802)cAt>cGt	p.H934R		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	934					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		ATCGCCGTCCATTTGGTGCGC	0.562																																					p.H934R		Atlas-SNP	.											.	ADNP2	102	.	0			c.A2801G						.						88	86	87					18																	77896097		2202	4298	6500	SO:0001583	missense	22850	exon4			CCGTCCATTTGGT	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	23803	protein-coding gene	gene with protein product			"zinc finger protein 508"	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.2801A>G	chr18.hg19:g.77896097A>G	ENSP00000262198:p.His934Arg	57.0	0.0		78.0	31.0	NM_014913	A8K951|O94943|Q9H9P3	Missense_Mutation	SNP	ENST00000262198.4	hg19	CCDS32853.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.802419	0.50315	.	.	ENSG00000101544	ENST00000262198	.	.	.	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000001	T	0.77445	0.4131	M	0.72894	2.215	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.78391	-0.2222	8	.	.	.	-27.7232	14.9181	0.70812	1.0:0.0:0.0:0.0	.	934	Q6IQ32	ADNP2_HUMAN	R	934	.	.	H	+	2	0	ADNP2	75997088	1.000000	0.71417	0.824000	0.32777	0.170000	0.22686	8.031000	0.88826	2.110000	0.64415	0.533000	0.62120	CAT	.	.		0.562	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913		G	77896097	A	G	77896097	3	3	73	1	0	0	0	0	1	0	0	0	324	217	8	2	2811	2	ADNP2	18	77896097	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	26972341	77896097	181151	553	9879										
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1434882	1434882	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gacgagggcagaaccacaacGtgcaagggttccacccctac	11	14	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:1434882G>C	ENST00000233078.4	+	12	1356	c.1195G>C	c.(1195-1197)Gtg>Ctg	p.V399L	DAZAP1_ENST00000336761.6_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	399					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAACCACAACGTGCAAGGGTT	0.682																																					p.V399L		Atlas-SNP	.											.	DAZAP1	52	.	0			c.G1195C						.						12	14	14					19																	1434882		2179	4254	6433	SO:0001583	missense	26528	exon12			CACAACGTGCAAG		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"RNA binding motif (RRM) containing"	2683	protein-coding gene	gene with protein product	"deleted in azoospermia associated protein 1"	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.1195G>C	chr19.hg19:g.1434882G>C	ENSP00000233078:p.Val399Leu	96.0	0.0		80.0	29.0	NM_018959	Q96MJ3|Q9NRR9	Missense_Mutation	SNP	ENST00000233078.4	hg19	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.269513	0.80469	.	.	ENSG00000071626	ENST00000233078	T	0.29917	1.55	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.43211	0.1237	L	0.27053	0.805	0.80722	D	1	P;P;D	0.53312	0.931;0.931;0.959	P;P;D	0.65987	0.872;0.872;0.94	T	0.33369	-0.9871	10	0.51188	T	0.08	.	17.8389	0.88709	0.0:0.0:1.0:0.0	.	466;399;165	Q5IRN4;Q96EP5;B3KS63	.;DAZP1_HUMAN;.	L	399	ENSP00000233078:V399L	ENSP00000233078:V399L	V	+	1	0	DAZAP1	1385882	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.039000	0.93777	2.454000	0.82982	0.561000	0.74099	GTG	.	.		0.682	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		C	1434882	G	C	1434882	3	2	73	1	0	0	0	0	1	0	0	0	4246	1145	40	4	1334	4	DAZAP1	19	1434882	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10		1434882	57694101	554	9880										
THOP1	7064	hgsc.bcm.edu	37	chr19	2810300	2810300	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aggctctgccccatccctgcAggcggagttcgccatgttca	11	15	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:2810300A>T	ENST00000307741.6	+	10	1658		c.e10-1		THOP1_ENST00000395212.4_De_novo_Start_OutOfFrame|THOP1_ENST00000586677.1_Splice_Site|THOP1_ENST00000591149.1_Splice_Site	NM_003249.3	NP_003240.1	P52888	THOP1_HUMAN	thimet oligopeptidase 1						intracellular signal transduction (GO:0035556)|peptide metabolic process (GO:0006518)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			NS(1)|central_nervous_system(1)|endometrium(1)|lung(8)|ovary(2)|skin(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCATCCCTGCAGGCGGAGTTC	0.677																																					.		Atlas-SNP	.											.	THOP1	49	.	0			c.1456-2A>T						.						34	35	35					19																	2810300		2196	4299	6495	SO:0001630	splice_region_variant	7064	exon10			CCCTGCAGGCGGA		CCDS12095.1	19p13.3	2008-02-05				ENSG00000172009	3.4.24.15		11793	protein-coding gene	gene with protein product		601117				9790774	Standard	NM_003249		Approved		uc002lwj.3	P52888		ENST00000307741.6:c.1456-1A>T	chr19.hg19:g.2810300A>T		61.0	0.0		45.0	19.0	NM_003249	B3KSE2|Q9UCB3	Splice_Site	SNP	ENST00000307741.6	hg19	CCDS12095.1	.	.	.	.	.	.	.	.	.	.	A	11.40	1.627522	0.28978	.	.	ENSG00000172009	ENST00000307741	.	.	.	4.4	4.4	0.53042	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4333	0.55584	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	THOP1	2761300	1.000000	0.71417	0.980000	0.43619	0.084000	0.17831	8.610000	0.90902	1.615000	0.50252	0.260000	0.18958	.	.	.		0.677	THOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451587.2		Intron	T	2810300	A	T	2810300	5	4	73	1	0	0	0	0	0	0	1	0	15886	202	7	4	1492	4	THOP1	19	2810300	Splice_Site	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1375418	2810300	56318683	555	9881										
PLIN4	729359	hgsc.bcm.edu	37	chr19	4510630	4510630	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gccacgtcagtcgcaaggccCttggtagtggctgcggcttc	14	13	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:4510630C>A	ENST00000301286.3	-	3	3299	c.3300G>T	c.(3298-3300)aaG>aaT	p.K1100N		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1100						cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TCGCAAGGCCCTTGGTAGTGG	0.692																																					p.K1100N		Atlas-SNP	.											.	PLIN4	191	.	0			c.G3300T						.						22	26	24					19																	4510630		2148	4244	6392	SO:0001583	missense	729359	exon3			AAGGCCCTTGGTA	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"Perilipins"	29393	protein-coding gene	gene with protein product		613247	"KIAA1881"	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.3300G>T	chr19.hg19:g.4510630C>A	ENSP00000301286:p.Lys1100Asn	65.0	0.0		63.0	30.0	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	hg19	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	c	9.306	1.054457	0.19907	.	.	ENSG00000167676	ENST00000301286	T	0.04862	3.54	3.6	0.916	0.19373	.	0.604873	0.12274	U	0.483576	T	0.03178	0.0093	N	0.19112	0.55	0.09310	N	1	P	0.38978	0.652	B	0.27887	0.084	T	0.42068	-0.9473	10	0.51188	T	0.08	0.2631	5.0018	0.14268	0.0:0.5713:0.0:0.4287	.	1100	Q96Q06	PLIN4_HUMAN	N	1100	ENSP00000301286:K1100N	ENSP00000301286:K1100N	K	-	3	2	PLIN4	4461630	0.012000	0.17670	0.000000	0.03702	0.003000	0.03518	0.810000	0.27183	-0.095000	0.12351	0.506000	0.49869	AAG	.	.		0.692	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		A	4510630	C	A	4510630	3	1	73	1	0	0	0	0	1	0	0	0	12101	680	24	3	789	3	PLIN4	19	4510630	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1700330	4510630	54618353	556	9882										
ZNRF4	148066	hgsc.bcm.edu	37	chr19	5455751	5455751	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggccgagccctcgtggcagtCaaagccttgctggtcttgtc	13	13	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:5455751C>T	ENST00000222033.4	+	1	326	c.249C>T	c.(247-249)gtC>gtT	p.V83V		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	83						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		TCGTGGCAGTCAAAGCCTTGC	0.667																																					p.V83V		Atlas-SNP	.											.	ZNRF4	59	.	0			c.C249T						.						45	55	51					19																	5455751		2114	4203	6317	SO:0001819	synonymous_variant	148066	exon1			GGCAGTCAAAGCC	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"RING-type (C3HC4) zinc fingers"	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.249C>T	chr19.hg19:g.5455751C>T		31.0	0.0		25.0	11.0	NM_181710	A8K886|O75866	Silent	SNP	ENST00000222033.4	hg19	CCDS42475.1																																																																																			.	.		0.667	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710		T	5455751	C	T	5455751	2	4	73	1	0	0	0	0	0	0	0	1	18229	813	29	3		3	ZNRF4	19	5455751	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	945121	5455751	53673232	557	9883										
CCL25	6370	hgsc.bcm.edu	37	chr19	8117950	8117950	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagcatgaacctgtggctccTggcctgcctggtggccggct	14	14	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:8117950T>A	ENST00000390669.3	+	1	67	c.17T>A	c.(16-18)cTg>cAg	p.L6Q	CCL25_ENST00000315626.4_Missense_Mutation_p.L6Q|CCL25_ENST00000253451.4_Missense_Mutation_p.L6Q			O15444	CCL25_HUMAN	chemokine (C-C motif) ligand 25	6					cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|negative regulation of leukocyte tethering or rolling (GO:1903237)|positive regulation of cell-matrix adhesion (GO:0001954)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR10 chemokine receptor binding (GO:0031735)|chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|hormone activity (GO:0005179)			NS(1)|endometrium(1)|lung(1)|skin(1)|urinary_tract(1)	5						CTGTGGCTCCTGGCCTGCCTG	0.662																																					p.L6Q		Atlas-SNP	.											.	CCL25	12	.	0			c.T17A						.						7	12	10					19																	8117950		1818	3955	5773	SO:0001583	missense	6370	exon2			GGCTCCTGGCCTG	U86358	CCDS12194.1, CCDS56080.1	19p13.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000131142	ENSG00000131142		"Chemokine ligands", "Endogenous ligands"	10624	protein-coding gene	gene with protein product	"Ck beta-15", "thymus expressed chemokine", "TECKvar"	602565	"small inducible cytokine subfamily A (Cys-Cys), member 25"	SCYA25		9285413, 9722960	Standard	NM_005624		Approved	TECK, Ckb15	uc002mjd.3	O15444	OTTHUMG00000141287	ENST00000390669.3:c.17T>A	chr19.hg19:g.8117950T>A	ENSP00000375086:p.Leu6Gln	71.0	0.0		46.0	22.0	NM_001201359	A1L4J4|A6NI52|A8K9E7|B5MCA5|Q96KJ7	Missense_Mutation	SNP	ENST00000390669.3	hg19	CCDS12194.1	.	.	.	.	.	.	.	.	.	.	T	17.57	3.423641	0.62733	.	.	ENSG00000131142	ENST00000253451;ENST00000315626;ENST00000390669	T;T;T	0.58506	1.93;0.33;1.91	3.72	2.69	0.31865	.	0.270670	0.30538	N	0.009401	T	0.62624	0.2443	L	0.42245	1.32	0.22666	N	0.998874	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.74023	0.98;0.981;0.982	T	0.50841	-0.8780	10	0.72032	D	0.01	-20.7157	5.9428	0.19201	0.0:0.1199:0.0:0.8801	.	6;6;6	C9JDZ7;O15444;A6NI52	.;CCL25_HUMAN;.	Q	6	ENSP00000253451:L6Q;ENSP00000324756:L6Q;ENSP00000375086:L6Q	ENSP00000253451:L6Q	L	+	2	0	CCL25	8023950	0.400000	0.25295	0.678000	0.29963	0.372000	0.29890	1.595000	0.36708	0.781000	0.33589	0.533000	0.62120	CTG	.	.		0.662	CCL25-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280522.1	NM_005624		A	8117950	T	A	8117950	3	1	73	1	0	0	0	0	1	0	0	0	2899	1580	55	4	19	4	CCL25	19	8117950	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2662199	8117950	51011033	558	9884										
MUC16	94025	hgsc.bcm.edu	37	chr19	9048117	9048117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctctggttcatcagaagaaaTagtcagagttggaatagttg	11	5	4	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:9048117T>C	ENST00000397910.4	-	5	33717	c.33514A>G	c.(33514-33516)Att>Gtt	p.I11172V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11174	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCAGAAGAAATAGTCAGAGTT	0.448																																					p.I11172V		Atlas-SNP	.											.	MUC16	4315	.	0			c.A33514G						.						72	66	68					19																	9048117		1927	4131	6058	SO:0001583	missense	94025	exon5			AAGAAATAGTCAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33514A>G	chr19.hg19:g.9048117T>C	ENSP00000381008:p.Ile11172Val	112.0	0.0		71.0	28.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	6.171	0.399806	0.11696	.	.	ENSG00000181143	ENST00000397910	T	0.02236	4.38	3.59	-6.02	0.02192	.	.	.	.	.	T	0.01765	0.0056	L	0.29908	0.895	.	.	.	B	0.16396	0.017	B	0.13407	0.009	T	0.46484	-0.9188	8	0.87932	D	0	.	5.5142	0.16898	0.0:0.2179:0.2804:0.5017	.	11172	B5ME49	.	V	11172	ENSP00000381008:I11172V	ENSP00000381008:I11172V	I	-	1	0	MUC16	8909117	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.046000	0.00156	-1.231000	0.02557	-0.373000	0.07131	ATT	.	.		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9048117	T	C	9048117	3	2	73	1	0	0	0	0	1	0	0	0	9982	1406	49	2	10329	2	MUC16	19	9048117	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	930167	9048117	50080866	559	9885										
RDH8	50700	hgsc.bcm.edu	37	chr19	10129508	10129508	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttttcggagctgtccgtctcGtcaaagctgtgcttccaggc	11	12	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:10129508G>T	ENST00000171214.1	+	3	613	c.364G>T	c.(364-366)Gtc>Ttc	p.V122F	RDH8_ENST00000591589.1_Missense_Mutation_p.V142F	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	122					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	TGTCCGTCTCGTCAAAGCTGT	0.597																																					p.V142F		Atlas-SNP	.											.	RDH8	51	.	0			c.G424T						.						95	91	92					19																	10129508		2203	4300	6503	SO:0001583	missense	50700	exon3			CGTCTCGTCAAAG	AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	14423	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 28C, member 2"	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.364G>T	chr19.hg19:g.10129508G>T	ENSP00000171214:p.Val122Phe	81.0	0.0		77.0	25.0	NM_015725	Q9H838	Missense_Mutation	SNP	ENST00000171214.1	hg19		.	.	.	.	.	.	.	.	.	.	G	20.8	4.042827	0.75732	.	.	ENSG00000080511	ENST00000171214	D	0.87729	-2.29	5.34	4.29	0.51040	NAD(P)-binding domain (1);	0.123412	0.53938	D	0.000050	D	0.89594	0.6760	L	0.50333	1.59	0.38422	D	0.946217	D	0.59357	0.985	D	0.69479	0.964	D	0.90106	0.4188	10	0.72032	D	0.01	.	8.7599	0.34667	0.1741:0.0:0.8259:0.0	.	122	Q9NYR8	RDH8_HUMAN	F	122	ENSP00000171214:V122F	ENSP00000171214:V122F	V	+	1	0	RDH8	9990508	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.472000	0.35376	2.492000	0.84095	0.491000	0.48974	GTC	.	.		0.597	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				T	10129508	G	T	10129508	3	4	73	1	0	0	0	0	1	0	0	0	13211	1145	40	1	374	1	RDH8	19	10129508	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1081391	10129508	48999475	560	9886										
ICAM5	7087	hgsc.bcm.edu	37	chr19	10404581	10404581	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgcgaagccaccaaccctcGgggctctgcggccaaaaatg	11	15	1	0	rs147604357		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:10404581G>T	ENST00000221980.4	+	7	1736	c.1673G>T	c.(1672-1674)cGg>cTg	p.R558L		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	558	Ig-like C2-type 6.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			ACCAACCCTCGGGGCTCTGCG	0.652																																					p.R558L		Atlas-SNP	.											ICAM5,NS,carcinoma,0,1	ICAM5	53	.	0			c.G1673T						.						42	49	47					19																	10404581		2202	4300	6502	SO:0001583	missense	7087	exon7			ACCCTCGGGGCTC	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5348	protein-coding gene	gene with protein product	"telencephalin"	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1673G>T	chr19.hg19:g.10404581G>T	ENSP00000221980:p.Arg558Leu	52.0	0.0		41.0	19.0	NM_003259	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	hg19	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	G	8.334	0.827139	0.16749	.	.	ENSG00000105376	ENST00000221980	T	0.13196	2.61	5.37	1.59	0.23543	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.627732	0.13598	N	0.376087	T	0.03608	0.0103	N	0.00630	-1.315	0.09310	N	1	B	0.28128	0.201	B	0.32149	0.141	T	0.42155	-0.9468	10	0.23891	T	0.37	-1.8771	4.8381	0.13474	0.1404:0.0:0.6901:0.1695	.	558	Q9UMF0	ICAM5_HUMAN	L	558	ENSP00000221980:R558L	ENSP00000221980:R558L	R	+	2	0	ICAM5	10265581	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.409000	0.02483	0.486000	0.27676	0.448000	0.29417	CGG	.	G|1.000;A|0.000		0.652	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		T	10404581	G	T	10404581	3	4	73	1	0	0	0	0	1	0	0	0	7492	1116	39	1	1699	1	ICAM5	19	10404581	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	275073	10404581	48724402	561	9887										
NANOS3	342977	hgsc.bcm.edu	37	chr19	13988465	13988465	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcccacttactggccagggcTacacctccgtctacagccac	8	18	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:13988465T>A	ENST00000397555.2	+	2	346	c.346T>A	c.(346-348)Tac>Aac	p.Y116N	NANOS3_ENST00000339133.5_Missense_Mutation_p.Y135N|MIR181C_ENST00000384881.1_RNA|MIR181D_ENST00000384853.1_RNA|NANOS3_ENST00000591727.1_Intron	NM_001098622.2	NP_001092092.1	P60323	NANO3_HUMAN	nanos homolog 3 (Drosophila)	116					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	7			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			TGGCCAGGGCTACACCTCCGT	0.662																																					p.Y135N		Atlas-SNP	.											.	NANOS3	19	.	0			c.T403A						.						16	21	20					19																	13988465		2120	4219	6339	SO:0001583	missense	342977	exon1			CAGGGCTACACCT	BM702754	CCDS42511.1	19p13.13	2003-12-01				ENSG00000187556			22048	protein-coding gene	gene with protein product		608229					Standard	NM_001098622		Approved	NANOS1L, NOS3	uc002mxj.4	P60323		ENST00000397555.2:c.346T>A	chr19.hg19:g.13988465T>A	ENSP00000380687:p.Tyr116Asn	77.0	0.0		52.0	29.0	NM_001098622	Q495E5	Missense_Mutation	SNP	ENST00000397555.2	hg19		.	.	.	.	.	.	.	.	.	.	T	19.73	3.881759	0.72294	.	.	ENSG00000187556	ENST00000339133;ENST00000397555	T;T	0.46063	0.88;0.89	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.59878	0.2226	.	.	.	0.51012	D	0.9999	D	0.89917	1.0	D	0.91635	0.999	T	0.57271	-0.7840	9	0.29301	T	0.29	-3.6142	12.7228	0.57152	0.0:0.0:0.0:1.0	.	135	P60323-2	.	N	135;116	ENSP00000341992:Y135N;ENSP00000380687:Y116N	ENSP00000341992:Y135N	Y	+	1	0	NANOS3	13849465	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.808000	0.75206	2.119000	0.64992	0.533000	0.62120	TAC	.	.		0.662	NANOS3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_292819		A	13988465	T	A	13988465	3	1	73	1	0	0	0	0	1	0	0	0	10162	1522	53	4	405	4	NANOS3	19	13988465	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	3583884	13988465	45140518	562	9888										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14029727	14029727	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tccccctgtccggcccagagGtgcccccacccccgaggacc	10	22	0	1	rs369829647		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:14029727G>T	ENST00000318003.7	+	10	1262	c.1021G>T	c.(1021-1023)Gtg>Ttg	p.V341L	CC2D1A_ENST00000589606.1_Missense_Mutation_p.V341L	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	341	Pro-rich.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			CGGCCCAGAGGTGCCCCCACC	0.672																																					p.V341L		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G1021T						.						14	22	19					19																	14029727		2013	4163	6176	SO:0001583	missense	54862	exon10			CCAGAGGTGCCCC	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.1021G>T	chr19.hg19:g.14029727G>T	ENSP00000313601:p.Val341Leu	211.0	0.0		167.0	64.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	hg19	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.615512	0.28801	.	.	ENSG00000132024	ENST00000318003;ENST00000397486	T	0.43294	0.95	4.75	3.66	0.41972	.	0.930752	0.09169	N	0.839224	T	0.24314	0.0589	N	0.12182	0.205	0.35106	D	0.765706	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.004;0.002;0.002	T	0.23691	-1.0181	10	0.28530	T	0.3	-5.7378	7.5154	0.27598	0.1017:0.1742:0.7241:0.0	.	341;341;95	Q6P1N0-2;Q6P1N0;C9J1T8	.;C2D1A_HUMAN;.	L	341;95	ENSP00000313601:V341L	ENSP00000313601:V341L	V	+	1	0	CC2D1A	13890727	0.133000	0.22466	0.951000	0.38953	0.349000	0.29174	0.838000	0.27572	2.472000	0.83506	0.561000	0.74099	GTG	.	.		0.672	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		T	14029727	G	T	14029727	3	4	73	1	0	0	0	0	1	0	0	0	2728	1261	44	3	1059	3	CC2D1A	19	14029727	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	41262	14029727	45099256	563	9889										
EMR3	84658	hgsc.bcm.edu	37	chr19	14772862	14772862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acattgacagtagaaacttcCttcgacattgtaacacacag	6	10	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:14772862C>T	ENST00000253673.5	-	4	368	c.268G>A	c.(268-270)Gga>Aga	p.G90R	EMR3_ENST00000599900.1_5'UTR|EMR3_ENST00000344373.4_Intron|EMR3_ENST00000443157.2_Intron	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	90	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						TAGAAACTTCCTTCGACATTG	0.383																																					p.G90R		Atlas-SNP	.											.	EMR3	99	.	0			c.G268A						.						203	169	181					19																	14772862		2203	4300	6503	SO:0001583	missense	84658	exon4			AACTTCCTTCGAC	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"-", "GPCR / Class B : Orphans"	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.268G>A	chr19.hg19:g.14772862C>T	ENSP00000253673:p.Gly90Arg	122.0	0.0		109.0	47.0	NM_032571		Missense_Mutation	SNP	ENST00000253673.5	hg19	CCDS12315.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.968362	0.53614	.	.	ENSG00000131355	ENST00000253673	D	0.99557	-6.16	4.12	4.12	0.48240	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.99739	0.9897	H	0.97587	4.035	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	D	0.97276	0.9914	9	0.87932	D	0	.	11.7465	0.51823	0.0:1.0:0.0:0.0	.	90	Q9BY15	EMR3_HUMAN	R	90	ENSP00000253673:G90R	ENSP00000253673:G90R	G	-	1	0	EMR3	14633862	0.155000	0.22806	0.034000	0.17996	0.034000	0.12701	1.486000	0.35530	2.133000	0.65898	0.508000	0.49915	GGA	.	.		0.383	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571		T	14772862	C	T	14772862	3	4	73	1	0	0	0	0	1	0	0	0	5108	690	24	3	1742	3	EMR3	19	14772862	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	743135	14772862	44356121	564	9890										
CCDC105	126402	hgsc.bcm.edu	37	chr19	15122107	15122107	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtgcgacagctgctgcgccAgcgcgaggtcaccgaccaca	14	15	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:15122107A>G	ENST00000292574.3	+	1	552	c.470A>G	c.(469-471)cAg>cGg	p.Q157R	SLC1A6_ENST00000430939.2_5'Flank	NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	157						extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						CTGCTGCGCCAGCGCGAGGTC	0.687																																					p.Q157R		Atlas-SNP	.											.	CCDC105	53	.	0			c.A470G						.						7	8	8					19																	15122107		1974	4131	6105	SO:0001583	missense	126402	exon1			TGCGCCAGCGCGA	AK097684	CCDS12322.1	19p13.12	2008-02-05				ENSG00000160994			26866	protein-coding gene	gene with protein product						12477932	Standard	NM_173482		Approved	FLJ40365	uc002nae.2	Q8IYK2		ENST00000292574.3:c.470A>G	chr19.hg19:g.15122107A>G	ENSP00000292574:p.Gln157Arg	58.0	0.0		73.0	26.0	NM_173482	Q8N7T5|Q8NDL5	Missense_Mutation	SNP	ENST00000292574.3	hg19	CCDS12322.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.661198	0.47572	.	.	ENSG00000160994	ENST00000292574	T	0.02552	4.25	3.82	2.8	0.32819	.	0.000000	0.48286	D	0.000195	T	0.07683	0.0193	M	0.67953	2.075	0.26848	N	0.968221	D	0.63046	0.992	P	0.59643	0.861	T	0.18618	-1.0331	10	0.25106	T	0.35	-22.4254	5.8611	0.18747	0.8726:0.0:0.1274:0.0	.	157	Q8IYK2	CC105_HUMAN	R	157	ENSP00000292574:Q157R	ENSP00000292574:Q157R	Q	+	2	0	CCDC105	14983107	0.900000	0.30661	0.993000	0.49108	0.694000	0.40290	0.984000	0.29565	0.372000	0.24591	-0.464000	0.05259	CAG	.	.		0.687	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482		G	15122107	A	G	15122107	3	3	73	1	0	0	0	0	1	0	0	0	2742	188	7	2	472	2	CCDC105	19	15122107	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	349245	15122107	44006876	565	9891										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15281192	15281192	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcccgccggcccttgtgaccAgaggccacgtccttgtgcag	12	16	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:15281192A>G	ENST00000263388.2	-	27	5139	c.5064T>C	c.(5062-5064)tcT>tcC	p.S1688S		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1688					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CCTTGTGACCAGAGGCCACGT	0.652																																					p.S1688S		Atlas-SNP	.											.	NOTCH3	340	.	0			c.T5064C						.						41	44	43					19																	15281192		2203	4300	6503	SO:0001819	synonymous_variant	4854	exon27			GTGACCAGAGGCC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.5064T>C	chr19.hg19:g.15281192A>G		86.0	0.0		51.0	24.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	hg19	CCDS12326.1																																																																																			.	.		0.652	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		G	15281192	A	G	15281192	2	3	73	1	0	0	0	0	0	0	0	1	10559	175	7	2		2	NOTCH3	19	15281192	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	159085	15281192	43847791	566	9892										
ANO8	57719	hgsc.bcm.edu	37	chr19	17441186	17441186	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctggaagcagccaagcatgAgcaagaagacacagacgagg	14	9	0	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:17441186A>G	ENST00000159087.4	-	9	1279	c.1121T>C	c.(1120-1122)cTc>cCc	p.L374P		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	374	Leu-rich.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						GCCAAGCATGAGCAAGAAGAC	0.642																																					p.L374P		Atlas-SNP	.											.	ANO8	67	.	0			c.T1121C						.						29	28	28					19																	17441186		2198	4297	6495	SO:0001583	missense	57719	exon9			AGCATGAGCAAGA	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	29329	protein-coding gene	gene with protein product		610216	"KIAA1623", "transmembrane protein 16H"	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.1121T>C	chr19.hg19:g.17441186A>G	ENSP00000159087:p.Leu374Pro	92.0	0.0		74.0	31.0	NM_020959	A6NIJ0	Missense_Mutation	SNP	ENST00000159087.4	hg19	CCDS32949.1	.	.	.	.	.	.	.	.	.	.	A	18.71	3.682471	0.68157	.	.	ENSG00000074855	ENST00000159087	T	0.66460	-0.21	5.26	5.26	0.73747	.	0.391639	0.23552	N	0.046943	T	0.80523	0.4639	M	0.78637	2.42	0.53005	D	0.999966	D	0.58268	0.982	D	0.66979	0.948	T	0.82540	-0.0406	10	0.62326	D	0.03	.	13.0825	0.59121	1.0:0.0:0.0:0.0	.	374	Q9HCE9	ANO8_HUMAN	P	374	ENSP00000159087:L374P	ENSP00000159087:L374P	L	-	2	0	ANO8	17302186	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.386000	0.44380	1.981000	0.57761	0.402000	0.26972	CTC	.	.		0.642	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644		G	17441186	A	G	17441186	3	3	73	1	0	0	0	0	1	0	0	0	703	304	11	2	2617	2	ANO8	19	17441186	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	2159994	17441186	41687797	567	9893										
PIK3R2	5296	hgsc.bcm.edu	37	chr19	18273890	18273890	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	catcaatcactaccgccacgAgtctctggcccagtacaatg	7	15	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:18273890A>G	ENST00000593731.1	+	10	1783	c.1223A>G	c.(1222-1224)gAg>gGg	p.E408G	PIK3R2_ENST00000222254.8_Missense_Mutation_p.E408G			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	408	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	TACCGCCACGAGTCTCTGGCC	0.572																																					p.E408G		Atlas-SNP	.											.	PIK3R2	48	.	0			c.A1223G						.						106	84	92					19																	18273890		2203	4300	6503	SO:0001583	missense	5296	exon10			GCCACGAGTCTCT		CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"SH2 domain containing"	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.1223A>G	chr19.hg19:g.18273890A>G	ENSP00000471914:p.Glu408Gly	178.0	0.0		147.0	50.0	NM_005027	Q5EAT5|Q9UPH9	Missense_Mutation	SNP	ENST00000593731.1	hg19	CCDS12371.1	.	.	.	.	.	.	.	.	.	.	A	14.11	2.436878	0.43224	.	.	ENSG00000105647	ENST00000222254	T	0.63417	-0.04	3.69	3.69	0.42338	SH2 motif (3);	0.113373	0.64402	D	0.000014	T	0.67221	0.2870	M	0.63428	1.95	0.58432	D	0.999994	D	0.61080	0.989	P	0.52514	0.701	T	0.70601	-0.4827	10	0.52906	T	0.07	-26.517	12.2662	0.54679	1.0:0.0:0.0:0.0	.	408	O00459	P85B_HUMAN	G	408	ENSP00000222254:E408G	ENSP00000222254:E408G	E	+	2	0	PIK3R2	18134890	1.000000	0.71417	0.808000	0.32385	0.044000	0.14063	7.135000	0.77276	1.641000	0.50575	0.459000	0.35465	GAG	.	.		0.572	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027		G	18273890	A	G	18273890	3	3	73	1	0	0	0	0	1	0	0	0	11928	304	11	2	1257	2	PIK3R2	19	18273890	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	832704	18273890	40855093	568	9894										
ZNF708	7562	hgsc.bcm.edu	37	chr19	21477081	21477081	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gactggttaaaagcttttccAcattcttcacatttgtaggg	8	8	2	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:21477081A>T	ENST00000356929.3	-	4	884	c.687T>A	c.(685-687)tgT>tgA	p.C229*		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	165					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						AAGCTTTTCCACATTCTTCAC	0.348																																					p.C229X		Atlas-SNP	.											.	ZNF708	66	.	0			c.T687A						.						40	43	42					19																	21477081		2180	4284	6464	SO:0001587	stop_gained	7562	exon4			TTTTCCACATTCT	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"Zinc fingers, C2H2-type", "-"	12945	protein-coding gene	gene with protein product			"zinc finger protein 15-like 1 (KOX 8)", "zinc finger protein 708", "zinc finger protein 708 (KOX8)"	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.687T>A	chr19.hg19:g.21477081A>T	ENSP00000349401:p.Cys229*	27.0	0.0		32.0	15.0	NM_021269	Q6ZMR0	Nonsense_Mutation	SNP	ENST00000356929.3	hg19	CCDS32980.1	.	.	.	.	.	.	.	.	.	.	.	13.12	2.141164	0.37825	.	.	ENSG00000182141	ENST00000356929	.	.	.	1.05	1.05	0.20165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.1942	0.10435	0.7718:0.0:0.2282:0.0	.	.	.	.	X	229	.	ENSP00000349401:C229X	C	-	3	2	ZNF708	21268921	0.793000	0.28825	0.010000	0.14722	0.009000	0.06853	1.090000	0.30902	0.408000	0.25621	0.397000	0.26171	TGT	.	.		0.348	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269		T	21477081	A	T	21477081	4	4	73	1	0	0	0	0	0	1	0	0	18127	157	6	4	1008	4	ZNF708	19	21477081	Nonsense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3203191	21477081	37651902	569	9895										
CD22	933	hgsc.bcm.edu	37	chr19	35823773	35823773	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acagtggtcagctggggctgAggatggagtccaagactgag	17	7	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:35823773A>T	ENST00000085219.5	+	3	424	c.358A>T	c.(358-360)Agg>Tgg	p.R120W	CD22_ENST00000419549.2_De_novo_Start_OutOfFrame|CD22_ENST00000536635.2_Missense_Mutation_p.R120W|CD22_ENST00000595419.1_3'UTR|CD22_ENST00000594250.1_Missense_Mutation_p.R120W|CD22_ENST00000341773.6_Missense_Mutation_p.R120W|U62631.5_ENST00000597110.1_RNA|CD22_ENST00000544992.2_Missense_Mutation_p.R120W|CD22_ENST00000270311.6_De_novo_Start_InFrame	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	120	Ig-like V-type.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GCTGGGGCTGAGGATGGAGTC	0.537																																					p.R120W	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.A358T						.						90	79	83					19																	35823773		2203	4300	6503	SO:0001583	missense	933	exon3			GGGCTGAGGATGG	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1643	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 2"	107266	"CD22 antigen"			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.358A>T	chr19.hg19:g.35823773A>T	ENSP00000085219:p.Arg120Trp	89.0	0.0		76.0	26.0	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	hg19	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	A	17.76	3.469521	0.63625	.	.	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	5.26	4.23	0.50019	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000028	T	0.67059	0.2853	M	0.79805	2.47	0.45634	D	0.998566	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	T	0.68622	-0.5360	10	0.87932	D	0	.	9.1319	0.36850	0.8154:0.1846:0.0:0.0	.	120;120;120;120	F5GYU4;F5H7U3;P20273;P20273-2	.;.;CD22_HUMAN;.	W	120	ENSP00000085219:R120W;ENSP00000442279:R120W;ENSP00000339349:R120W;ENSP00000441237:R120W	ENSP00000085219:R120W	R	+	1	2	CD22	40515613	1.000000	0.71417	0.981000	0.43875	0.506000	0.33950	2.744000	0.47450	0.819000	0.34492	0.460000	0.39030	AGG	.	.		0.537	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		T	35823773	A	T	35823773	3	4	73	1	0	0	0	0	1	0	0	0	2987	295	11	4	364	4	CD22	19	35823773	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	14346692	35823773	23305210	570	9896										
APLP1	333	hgsc.bcm.edu	37	chr19	36370026	36370026	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctgtgtcgggtctgctgatCatgggagcgggcggaggctc	19	9	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:36370026C>A	ENST00000221891.4	+	16	1956	c.1764C>A	c.(1762-1764)atC>atA	p.I588I	APLP1_ENST00000537454.2_Silent_p.I548I|RN7SL402P_ENST00000465059.1_RNA|APLP1_ENST00000586861.1_Silent_p.I581I	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	587					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTCTGCTGATCATGGGAGCGG	0.642																																					p.I588I		Atlas-SNP	.											.	APLP1	77	.	0			c.C1764A						.						50	50	50					19																	36370026		2203	4300	6503	SO:0001819	synonymous_variant	333	exon16			GCTGATCATGGGA	U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"amyloid-like protein 1", "amyloid precursor-like protein 1"	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.1764C>A	chr19.hg19:g.36370026C>A		44.0	0.0		21.0	9.0	NM_001024807	O00113|Q96A92	Silent	SNP	ENST00000221891.4	hg19	CCDS32997.1																																																																																			.	.		0.642	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807		A	36370026	C	A	36370026	2	1	73	1	0	0	0	0	0	0	0	1	778	816	29	3		3	APLP1	19	36370026	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	546253	36370026	22758957	571	9897										
HKR1	284459	hgsc.bcm.edu	37	chr19	37854185	37854185	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcacacacgggggagaagccAtttgtatgtacggagtgtgg	15	7	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:37854185A>T	ENST00000324411.4	+	6	1757	c.1488A>T	c.(1486-1488)ccA>ccT	p.P496P	HKR1_ENST00000544914.1_Silent_p.P223P|HKR1_ENST00000541583.2_Silent_p.P435P|HKR1_ENST00000589392.1_Silent_p.P478P|HKR1_ENST00000591471.1_Silent_p.P223P|HKR1_ENST00000591134.1_Intron|HKR1_ENST00000392153.3_Silent_p.P477P	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	496					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGGAGAAGCCATTTGTATGTA	0.527																																					p.P496P		Atlas-SNP	.											.	HKR1	74	.	0			c.A1488T						.						83	81	82					19																	37854185		2203	4300	6503	SO:0001819	synonymous_variant	284459	exon6			GAAGCCATTTGTA	M20675	CCDS12502.1	19q13.13	2013-01-08	2010-05-04			ENSG00000181666		"Zinc fingers, C2H2-type", "-"	4928	protein-coding gene	gene with protein product	"oncogene HKR1"	165250	"GLI-Kruppel family member HKR1"			2850480, 9813242	Standard	NM_181786		Approved	ZNF875	uc002ogb.3	P10072		ENST00000324411.4:c.1488A>T	chr19.hg19:g.37854185A>T		103.0	0.0		128.0	50.0	NM_181786	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Silent	SNP	ENST00000324411.4	hg19	CCDS12502.1																																																																																			.	.		0.527	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786		T	37854185	A	T	37854185	2	4	73	1	0	0	0	0	0	0	0	1	7203	204	8	4		4	HKR1	19	37854185	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1484159	37854185	21274798	572	9898										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41071395	41071395	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagactgagctggaggcgcgGgtgcctgagctgaccacctg	16	11	0	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:41071395G>A	ENST00000352632.3	+	28	6068	c.5982G>A	c.(5980-5982)cgG>cgA	p.R1994R	SPTBN4_ENST00000338932.3_Silent_p.R1994R|SPTBN4_ENST00000598249.1_Silent_p.R1994R|SPTBN4_ENST00000392025.1_Silent_p.R737R			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1994					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TGGAGGCGCGGGTGCCTGAGC	0.632																																					p.R1994R		Atlas-SNP	.											.	SPTBN4	213	.	0			c.G5982A						.						63	63	63					19																	41071395		2203	4300	6503	SO:0001819	synonymous_variant	57731	exon28			GGCGCGGGTGCCT	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.5982G>A	chr19.hg19:g.41071395G>A		110.0	0.0		116.0	48.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	hg19	CCDS12559.1																																																																																			.	.		0.632	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			A	41071395	G	A	41071395	2	1	73	1	0	0	0	0	0	0	0	1	15136	1219	43	3		3	SPTBN4	19	41071395	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	3217210	41071395	18057588	573	9899										
GRIK5	2901	hgsc.bcm.edu	37	chr19	42510881	42510881	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aggtcatcggccgactccacAggcacctccatgcgctgcac	10	17	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:42510881A>G	ENST00000262895.3	-	15	1952	c.1953T>C	c.(1951-1953)ccT>ccC	p.P651P	GRIK5_ENST00000593562.1_Silent_p.P651P|GRIK5_ENST00000301218.4_Silent_p.P651P	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	651					cellular response to glucose stimulus (GO:0071333)|establishment of localization in cell (GO:0051649)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|positive regulation of neuron apoptotic process (GO:0043525)|protein retention in ER lumen (GO:0006621)|receptor clustering (GO:0043113)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	35		Prostate(69;0.059)				CCGACTCCACAGGCACCTCCA	0.622																																					p.P651P		Atlas-SNP	.											.	GRIK5	220	.	0			c.T1953C						.						82	65	70					19																	42510881		2203	4300	6503	SO:0001819	synonymous_variant	2901	exon15			CTCCACAGGCACC		CCDS12595.1	19q13.2	2012-08-29			ENSG00000105737	ENSG00000105737		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4583	protein-coding gene	gene with protein product		600283		GRIK2		7527545	Standard	NM_002088		Approved	GluK5, KA2	uc002osj.2	Q16478	OTTHUMG00000044573	ENST00000262895.3:c.1953T>C	chr19.hg19:g.42510881A>G		59.0	0.0		49.0	17.0	NM_002088	Q8WWG8	Silent	SNP	ENST00000262895.3	hg19	CCDS12595.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.550132	0.27652	.	.	ENSG00000105737	ENST00000454993	.	.	.	5.18	-10.1	0.00402	.	.	.	.	.	T	0.47135	0.1429	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57602	-0.7783	4	.	.	.	.	9.4213	0.38553	0.1047:0.094:0.6266:0.1747	.	.	.	.	R	28	.	.	C	-	1	0	GRIK5	47202721	0.000000	0.05858	0.855000	0.33649	0.993000	0.82548	-1.786000	0.01766	-1.611000	0.01581	-0.376000	0.06991	TGT	.	.		0.622	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1			G	42510881	A	G	42510881	2	3	73	1	0	0	0	0	0	0	0	1	6786	175	7	2		2	GRIK5	19	42510881	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1439486	42510881	16618102	574	9900										
CIC	23152	hgsc.bcm.edu	37	chr19	42795109	42795109	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gggtgtcagcttagtgtattCggacaagaagtcggcagcag	15	7	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:42795109C>G	ENST00000575354.2	+	10	2229	c.2189C>G	c.(2188-2190)tCg>tGg	p.S730W	CIC_ENST00000160740.3_Missense_Mutation_p.S730W|CIC_ENST00000572681.2_Missense_Mutation_p.S1639W	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	730	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				TTAGTGTATTCGGACAAGAAG	0.627			"Mis, F, S"		oligodendroglioma																																p.S730W		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.C2189G						.						30	31	30					19																	42795109		2202	4299	6501	SO:0001583	missense	23152	exon10			TGTATTCGGACAA	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"capicua (Drosophila) homolog", "capicua homolog (Drosophila)"			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.2189C>G	chr19.hg19:g.42795109C>G	ENSP00000458663:p.Ser730Trp	109.0	0.0		104.0	46.0	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	hg19	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.122842	0.37436	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.78	4.78	0.61160	.	.	.	.	.	T	0.49830	0.1580	N	0.14661	0.345	0.54753	D	0.999984	D	0.63880	0.993	P	0.54590	0.756	T	0.57900	-0.7731	8	0.87932	D	0	-8.5816	15.3429	0.74311	0.0:1.0:0.0:0.0	.	730	Q96RK0	CIC_HUMAN	W	730	.	ENSP00000160740:S730W	S	+	2	0	CIC	47486949	0.711000	0.27906	1.000000	0.80357	0.997000	0.91878	4.611000	0.61162	2.480000	0.83734	0.561000	0.74099	TCG	.	.		0.627	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			G	42795109	C	G	42795109	3	3	73	1	0	0	0	0	1	0	0	0	3426	893	31	4	2227	4	CIC	19	42795109	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	284228	42795109	16333874	575	9901										
CEACAM1	634	hgsc.bcm.edu	37	chr19	43013273	43013273	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aggtttcattactgctttttTacttctgaataaattatttc	4	6	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:43013273T>C	ENST00000161559.6	-	9	1703	c.1569A>G	c.(1567-1569)gtA>gtG	p.V523V	CEACAM1_ENST00000351134.3_Silent_p.V249V|CEACAM1_ENST00000358394.3_Silent_p.V458V|CEACAM1_ENST00000403444.3_3'UTR|CEACAM1_ENST00000403461.1_3'UTR|LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000308072.4_Intron|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000488639.2_5'UTR|CEACAM1_ENST00000352591.5_Silent_p.V427V	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	523					angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	ACTGCTTTTTTACTTCTGAAT	0.443																																					p.V523V		Atlas-SNP	.											.	CEACAM1	43	.	0			c.A1569G						.						154	138	143					19																	43013273		2203	4300	6503	SO:0001819	synonymous_variant	634	exon9			CTTTTTTACTTCT	M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.1569A>G	chr19.hg19:g.43013273T>C		154.0	0.0		126.0	61.0	NM_001712	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Silent	SNP	ENST00000161559.6	hg19	CCDS12609.1																																																																																			.	.		0.443	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712		C	43013273	T	C	43013273	2	2	73	1	0	0	0	0	0	0	0	1	3189	1741	61	2		2	CEACAM1	19	43013273	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	218164	43013273	16115710	576	9902										
IRGC	56269	hgsc.bcm.edu	37	chr19	44223324	44223324	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgccgagcggctgcgggaggCcggcgtggctgaccctcgca	18	14	0	1	rs574684743	byFrequency	TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:44223324C>A	ENST00000244314.5	+	2	813	c.614C>A	c.(613-615)gCc>gAc	p.A205D		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	205	IRG-type G.					membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				CTGCGGGAGGCCGGCGTGGCT	0.706																																					p.A205D	Colon(189;350 2037 11447 13433 38914)	Atlas-SNP	.											.	IRGC	67	.	0			c.C614A						.						25	27	26					19																	44223324		2156	4231	6387	SO:0001583	missense	56269	exon2			GGGAGGCCGGCGT	BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"immunity-related GTPase family, cinema 1"	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.614C>A	chr19.hg19:g.44223324C>A	ENSP00000244314:p.Ala205Asp	33.0	0.0		34.0	14.0	NM_019612	Q05BR8	Missense_Mutation	SNP	ENST00000244314.5	hg19	CCDS12629.1	.	.	.	.	.	.	.	.	.	.	C	5.968	0.362555	0.11296	.	.	ENSG00000124449	ENST00000244314	T	0.11604	2.76	4.82	0.33	0.15929	.	1.159190	0.06269	N	0.695258	T	0.10809	0.0264	L	0.46819	1.47	0.09310	N	1	B	0.27316	0.175	B	0.30943	0.122	T	0.45011	-0.9290	10	0.15952	T	0.53	.	7.5731	0.27920	0.0:0.5674:0.0:0.4326	.	205	Q6NXR0	IIGP5_HUMAN	D	205	ENSP00000244314:A205D	ENSP00000244314:A205D	A	+	2	0	IRGC	48915164	0.993000	0.37304	0.000000	0.03702	0.078000	0.17371	-0.229000	0.09098	0.079000	0.16929	0.655000	0.94253	GCC	.	.		0.706	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612		A	44223324	C	A	44223324	3	1	73	1	0	0	0	0	1	0	0	0	7847	739	26	3	616	3	IRGC	19	44223324	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1210051	44223324	14905659	577	9903										
C19orf61	56006	hgsc.bcm.edu	37	chr19	44241827	44241827	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgaaaaggaaggcagcaatcTggagtgactgagggtgggca	17	5	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:44241827T>A	ENST00000270066.6	-	9	1259	c.917A>T	c.(916-918)cAg>cTg	p.Q306L	SMG9_ENST00000601170.1_Missense_Mutation_p.Q306L	NM_019108.2	NP_061981.2	Q9H0W8	SMG9_HUMAN	SMG9 nonsense mediated mRNA decay factor	306					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|intracellular (GO:0005622)	identical protein binding (GO:0042802)			kidney(1)|large_intestine(5)|liver(1)|lung(7)|pancreas(1)|prostate(2)|urinary_tract(2)	19						GGCAGCAATCTGGAGTGACTG	0.562																																					p.Q306L		Atlas-SNP	.											.	SMG9	39	.	0			c.A917T						.						139	106	117					19																	44241827		2203	4300	6503	SO:0001583	missense	56006	exon9			GCAATCTGGAGTG	BC008869	CCDS33043.2	19q13.31	2013-07-02	2013-07-02	2011-06-21	ENSG00000105771	ENSG00000105771			25763	protein-coding gene	gene with protein product		613176	"chromosome 19 open reading frame 61", "smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C19orf61		11230166, 19417104	Standard	NM_019108		Approved	FLJ12886	uc002oxj.2	Q9H0W8	OTTHUMG00000150337	ENST00000270066.6:c.917A>T	chr19.hg19:g.44241827T>A	ENSP00000270066:p.Gln306Leu	94.0	0.0		70.0	26.0	NM_019108	O60429|Q9H9A9	Missense_Mutation	SNP	ENST00000270066.6	hg19	CCDS33043.2	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145193	0.77888	.	.	ENSG00000105771	ENST00000270066	T	0.38722	1.12	4.07	4.07	0.47477	.	0.000000	0.85682	D	0.000000	T	0.64193	0.2576	M	0.85542	2.76	0.58432	D	0.999999	D	0.67145	0.996	D	0.67382	0.951	T	0.70022	-0.4986	10	0.72032	D	0.01	-8.8864	11.052	0.47896	0.0:0.0:0.0:1.0	.	306	Q9H0W8	SMG9_HUMAN	L	306	ENSP00000270066:Q306L	ENSP00000270066:Q306L	Q	-	2	0	SMG9	48933667	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.810000	0.75216	1.709000	0.51313	0.528000	0.53228	CAG	.	.		0.562	SMG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317668.1	NM_019108		A	44241827	T	A	44241827	3	1	73	1	0	0	0	0	1	0	0	0	1945	1580	55	4	669	4	C19orf61	19	44241827	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	18503	44241827	14887156	578	9904										
LYPD5	284348	hgsc.bcm.edu	37	chr19	44306498	44306498	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agagcgcagccccaaagaggCagagcagaatgactctgggg	15	10	1	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:44306498C>A	ENST00000377950.3	-	1	115	c.35G>T	c.(34-36)tGc>tTc	p.C12F	LYPD5_ENST00000414615.2_Intron|LYPD5_ENST00000594013.1_5'Flank	NM_001031749.2	NP_001026919.2	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5	12						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	8		Prostate(69;0.0352)				CCCAAAGAGGCAGAGCAGAAT	0.597																																					p.C12F		Atlas-SNP	.											.	LYPD5	22	.	0			c.G35T						.						65	72	70					19																	44306498		692	1591	2283	SO:0001583	missense	284348	exon1			AAGAGGCAGAGCA	AK055031	CCDS12631.1, CCDS46096.1	19q13.31	2008-02-05				ENSG00000159871			26397	protein-coding gene	gene with protein product						12477932	Standard	NM_182573		Approved	FLJ30469	uc002oxm.4	Q6UWN5		ENST00000377950.3:c.35G>T	chr19.hg19:g.44306498C>A	ENSP00000367185:p.Cys12Phe	68.0	0.0		38.0	15.0	NM_001031749	Q6PEX9|Q96DR2	Missense_Mutation	SNP	ENST00000377950.3	hg19	CCDS46096.1	.	.	.	.	.	.	.	.	.	.	C	1.408	-0.576207	0.03882	.	.	ENSG00000159871	ENST00000377950	T	0.06933	3.24	3.73	-2.17	0.07059	.	0.719989	0.11799	U	0.528350	T	0.04137	0.0115	N	0.19112	0.55	0.09310	N	0.999997	B	0.18461	0.028	B	0.09377	0.004	T	0.39522	-0.9610	10	0.33940	T	0.23	-3.5099	3.3955	0.07304	0.1802:0.4009:0.0:0.4189	.	12	Q6UWN5	LYPD5_HUMAN	F	12	ENSP00000367185:C12F	ENSP00000367185:C12F	C	-	2	0	LYPD5	48998338	0.641000	0.27251	0.030000	0.17652	0.227000	0.25037	-0.435000	0.06931	-0.280000	0.09154	-0.196000	0.12772	TGC	.	.		0.597	LYPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463611.1	NM_182573		A	44306498	C	A	44306498	3	1	73	1	0	0	0	0	1	0	0	0	9122	710	25	3	740	3	LYPD5	19	44306498	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	64671	44306498	14822485	579	9905										
ZNF285	26974	hgsc.bcm.edu	37	chr19	44892183	44892183	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggatcctttgtttccaaatcTgccagcaatgaagcacttct	7	11	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:44892183T>G	ENST00000330997.4	-	4	288	c.224A>C	c.(223-225)cAg>cCg	p.Q75P	CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000591679.1_Missense_Mutation_p.Q82P|ZNF285_ENST00000544719.2_Missense_Mutation_p.Q75P	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	75	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						TTTCCAAATCTGCCAGCAATG	0.408																																					p.Q75P		Atlas-SNP	.											.	ZNF285	86	.	0			c.A224C						.						90	93	92					19																	44892183		2203	4300	6503	SO:0001583	missense	26974	exon4			CAAATCTGCCAGC	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.224A>C	chr19.hg19:g.44892183T>G	ENSP00000333595:p.Gln75Pro	197.0	0.0		175.0	67.0	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	hg19	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	T	13.65	2.299170	0.40694	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.07114	3.22	3.44	1.18	0.20946	Krueppel-associated box (1);	.	.	.	.	T	0.04634	0.0126	N	0.17082	0.46	0.09310	N	1	B;B	0.15473	0.013;0.013	B;B	0.09377	0.004;0.004	T	0.41645	-0.9497	9	0.34782	T	0.22	.	3.9353	0.09304	0.0:0.129:0.2183:0.6528	.	99;75	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	P	98;75	ENSP00000333595:Q75P	ENSP00000333595:Q75P	Q	-	2	0	ZNF285	49584023	0.001000	0.12720	0.952000	0.39060	0.668000	0.39293	0.269000	0.18589	0.329000	0.23460	0.373000	0.22412	CAG	.	.		0.408	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		G	44892183	T	G	44892183	3	3	73	1	0	0	0	0	1	0	0	0	17837	1580	55	5	1552	5	ZNF285	19	44892183	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	585685	44892183	14236800	580	9906										
CYTH2	9266	hgsc.bcm.edu	37	chr19	48978146	48978146	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcaagattcctgaggatgacGggaatgacctgacccacacc	10	12	1	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:48978146G>T	ENST00000452733.2	+	8	1224	c.748G>T	c.(748-750)Ggg>Tgg	p.G250W	CYTH2_ENST00000427476.1_Missense_Mutation_p.G250W			Q99418	CYH2_HUMAN	cytohesin 2	250					actin cytoskeleton organization (GO:0030036)|endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|inositol 1,4,5 trisphosphate binding (GO:0070679)|lipid binding (GO:0008289)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						TGAGGATGACGGGAATGACCT	0.622																																					p.G250W		Atlas-SNP	.											.	CYTH2	33	.	0			c.G748T						.						157	130	139					19																	48978146		2203	4300	6503	SO:0001583	missense	9266	exon8			GATGACGGGAATG	X99753	CCDS12722.1	19q13.32	2014-05-02	2008-08-14	2008-08-14	ENSG00000105443	ENSG00000105443		"Pleckstrin homology (PH) domain containing"	9502	protein-coding gene	gene with protein product		602488	"pleckstrin homology, Sec7 and coiled/coil domains 2 (cytohesin-2)", "pleckstrin homology, Sec7 and coiled-coil domains 2"	PSCD2L, PSCD2		8706128, 8945478, 20525696	Standard	NM_004228		Approved	CTS18.1, Sec7p-L, ARNO, Sec7p-like, cytohesin-2	uc002pjj.4	Q99418	OTTHUMG00000150245	ENST00000452733.2:c.748G>T	chr19.hg19:g.48978146G>T	ENSP00000408236:p.Gly250Trp	127.0	0.0		97.0	4.0	NM_017457	A8K8P0|Q8IXY9|Q92958	Missense_Mutation	SNP	ENST00000452733.2	hg19	CCDS12722.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.469237	0.84533	.	.	ENSG00000105443	ENST00000452733;ENST00000427476	T;T	0.31769	1.48;1.48	4.35	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.63177	0.2489	M	0.91717	3.235	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.72871	-0.4161	10	0.87932	D	0	.	14.7596	0.69596	0.0:0.0:1.0:0.0	.	250	Q99418-2	.	W	250	ENSP00000408236:G250W;ENSP00000391648:G250W	ENSP00000375753:G250W	G	+	1	0	CYTH2	53669958	1.000000	0.71417	0.711000	0.30485	0.949000	0.60115	9.648000	0.98483	2.421000	0.82119	0.491000	0.48974	GGG	.	.		0.622	CYTH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317060.1	NM_004228		T	48978146	G	T	48978146	3	4	73	1	0	0	0	0	1	0	0	0	4206	1116	39	1	778	1	CYTH2	19	48978146	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	4085963	48978146	10150837	581	9907										
BCAT2	587	hgsc.bcm.edu	37	chr19	49309901	49309901	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtggtcggtaaatgtcttcCcaaacaccaggggctcgccg	12	12	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:49309901C>G	ENST00000316273.6	-	3	185	c.173G>C	c.(172-174)gGg>gCg	p.G58A	BCAT2_ENST00000599246.1_Intron|BCAT2_ENST00000597011.1_Missense_Mutation_p.G18A|BCAT2_ENST00000598162.1_Missense_Mutation_p.G58A|BCAT2_ENST00000545387.2_Intron|BCAT2_ENST00000402551.1_Missense_Mutation_p.G18A|BCAT2_ENST00000601496.1_5'Flank	NM_001190.3	NP_001181.2	O15382	BCAT2_HUMAN	branched chain amino-acid transaminase 2, mitochondrial	58					branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|isoleucine catabolic process (GO:0006550)|leucine metabolic process (GO:0006551)|regulation of hormone levels (GO:0010817)|small molecule metabolic process (GO:0044281)|valine metabolic process (GO:0006573)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	12		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.000366)|Epithelial(262;0.0195)|GBM - Glioblastoma multiforme(486;0.0224)	L-Isoleucine(DB00167)|L-Leucine(DB00149)	AAATGTCTTCCCAAACACCAG	0.582																																					p.G58A		Atlas-SNP	.											.	BCAT2	35	.	0			c.G173C						.						115	118	117					19																	49309901		2203	4300	6503	SO:0001583	missense	587	exon3			GTCTTCCCAAACA	U68418	CCDS12735.1, CCDS54290.1, CCDS74416.1	19q13.33	2013-09-20	2010-05-07		ENSG00000105552	ENSG00000105552	2.6.1.42		977	protein-coding gene	gene with protein product		113530	"branched chain aminotransferase 2, mitochondrial"	BCT2		9165094	Standard	NM_001190		Approved	BCAM	uc002pkr.3	O15382	OTTHUMG00000183327	ENST00000316273.6:c.173G>C	chr19.hg19:g.49309901C>G	ENSP00000322991:p.Gly58Ala	60.0	0.0		60.0	22.0	NM_001190	B2RB87|O00269|Q96KG1|Q9BTB6|Q9BUU6	Missense_Mutation	SNP	ENST00000316273.6	hg19	CCDS12735.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890544	0.91889	.	.	ENSG00000105552	ENST00000316273;ENST00000402551	T;T	0.66995	-0.24;-0.24	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.86422	0.5929	M	0.93328	3.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89734	0.3928	10	0.87932	D	0	-34.067	16.7525	0.85489	0.0:1.0:0.0:0.0	.	58;58	Q53EW7;O15382	.;BCAT2_HUMAN	A	58;18	ENSP00000322991:G58A;ENSP00000385161:G18A	ENSP00000322991:G58A	G	-	2	0	BCAT2	54001713	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.059000	0.76684	2.626000	0.88956	0.650000	0.86243	GGG	.	.		0.582	BCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466202.1			G	49309901	C	G	49309901	3	3	73	1	0	0	0	0	1	0	0	0	1355	623	22	4	1041	4	BCAT2	19	49309901	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	331755	49309901	9819082	582	9908										
LRRC4B	94030	hgsc.bcm.edu	37	chr19	51022208	51022208	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atgagccacagcttgcgcagGctggtgagaccctggaagga	15	10	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:51022208G>A	ENST00000599957.1	-	3	959	c.762C>T	c.(760-762)agC>agT	p.S254S	LRRC4B_ENST00000389201.3_Silent_p.S254S			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	254					positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		GCTTGCGCAGGCTGGTGAGAC	0.657																																					p.S254S		Atlas-SNP	.											.	LRRC4B	89	.	0			c.C762T						.						36	44	41					19																	51022208		2143	4243	6386	SO:0001819	synonymous_variant	94030	exon3			GCGCAGGCTGGTG	BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"Immunoglobulin superfamily / I-set domain containing", "Endogenous ligands"	25042	protein-coding gene	gene with protein product	"netrin-G3 ligand"		"leucine-rich repeats and immunoglobulin-like domains 4"	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.762C>T	chr19.hg19:g.51022208G>A		77.0	0.0		66.0	21.0	NM_001080457	Q3ZCQ4|Q58F20	Silent	SNP	ENST00000599957.1	hg19	CCDS42595.1																																																																																			.	.		0.657	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457		A	51022208	G	A	51022208	2	1	73	1	0	0	0	0	0	0	0	1	9016	1194	42	3		3	LRRC4B	19	51022208	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1712307	51022208	8106775	583	9909										
SYT3	84258	hgsc.bcm.edu	37	chr19	51128790	51128790	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgcttcttcagacgccgcccCtcgctgatcagggaggcctt	11	16	3	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:51128790C>A	ENST00000338916.4	-	6	2067	c.1434G>T	c.(1432-1434)gaG>gaT	p.E478D	SYT3_ENST00000593901.1_Missense_Mutation_p.E478D|SYT3_ENST00000544769.1_Missense_Mutation_p.E478D|SYT3_ENST00000600079.1_Missense_Mutation_p.E478D	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	478	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		GACGCCGCCCCTCGCTGATCA	0.597																																					p.E478D		Atlas-SNP	.											.	SYT3	85	.	0			c.G1434T						.						53	48	50					19																	51128790		2203	4300	6503	SO:0001583	missense	84258	exon6			CCGCCCCTCGCTG	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.1434G>T	chr19.hg19:g.51128790C>A	ENSP00000340914:p.Glu478Asp	114.0	0.0		84.0	27.0	NM_032298	Q8N5Z1|Q8N640	Missense_Mutation	SNP	ENST00000338916.4	hg19	CCDS12798.1	.	.	.	.	.	.	.	.	.	.	C	0.752	-0.772578	0.02951	.	.	ENSG00000213023	ENST00000338916;ENST00000544769	T;T	0.69806	-0.43;-0.43	3.47	2.42	0.29668	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.289846	0.26103	U	0.026337	T	0.36386	0.0965	N	0.10782	0.045	0.39903	D	0.973925	B	0.06786	0.001	B	0.09377	0.004	T	0.28396	-1.0045	10	0.02654	T	1	.	5.8191	0.18518	0.0:0.6568:0.0:0.3432	.	478	Q9BQG1	SYT3_HUMAN	D	478	ENSP00000340914:E478D;ENSP00000438883:E478D	ENSP00000340914:E478D	E	-	3	2	SYT3	55820602	0.499000	0.26083	1.000000	0.80357	0.798000	0.45092	-0.257000	0.08745	0.600000	0.29862	0.549000	0.68633	GAG	.	.		0.597	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		A	51128790	C	A	51128790	3	1	73	1	0	0	0	0	1	0	0	0	15490	680	24	3	350	3	SYT3	19	51128790	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	106582	51128790	8000193	584	9910										
SIGLEC7	27036	hgsc.bcm.edu	37	chr19	51645871	51645871	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggctccagtggccacaaacaAcccagcttgggcagtgcagg	13	13	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:51645871A>T	ENST00000317643.6	+	1	314	c.245A>T	c.(244-246)aAc>aTc	p.N82I	SIGLEC7_ENST00000305628.7_Missense_Mutation_p.N82I|SIGLEC7_ENST00000600577.1_Missense_Mutation_p.N82I	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	82	Ig-like V-type.				cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		GCCACAAACAACCCAGCTTGG	0.557																																					p.N82I		Atlas-SNP	.											.	SIGLEC7	74	.	0			c.A245T						.						114	106	109					19																	51645871		2203	4300	6503	SO:0001583	missense	27036	exon1			CAAACAACCCAGC	AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10876	protein-coding gene	gene with protein product		604410	"sialic acid binding Ig-like lectin 19, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 2"	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.245A>T	chr19.hg19:g.51645871A>T	ENSP00000323328:p.Asn82Ile	139.0	0.0		95.0	9.0	NM_016543	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Missense_Mutation	SNP	ENST00000317643.6	hg19	CCDS12826.1	.	.	.	.	.	.	.	.	.	.	.	11.84	1.758486	0.31137	.	.	ENSG00000168995	ENST00000317643;ENST00000305628;ENST00000536156	T;T;T	0.49139	0.79;0.79;0.79	2.71	-1.34	0.09143	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	1.309180	0.05595	N	0.575386	T	0.62514	0.2434	M	0.78049	2.395	0.09310	N	1	D;B;P	0.89917	1.0;0.091;0.511	D;B;P	0.85130	0.997;0.13;0.525	T	0.50363	-0.8837	10	0.72032	D	0.01	.	0.3232	0.00306	0.4013:0.2289:0.1459:0.2239	.	82;82;82	Q9Y286-4;Q9Y286-2;Q9Y286	.;.;SIGL7_HUMAN	I	82	ENSP00000323328:N82I;ENSP00000306757:N82I;ENSP00000437609:N82I	ENSP00000306757:N82I	N	+	2	0	SIGLEC7	56337683	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.851000	0.27751	-0.078000	0.12730	-0.525000	0.04345	AAC	.	.		0.557	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543		T	51645871	A	T	51645871	3	4	73	1	0	0	0	0	1	0	0	0	14328	43	2	4	247	4	SIGLEC7	19	51645871	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	517081	51645871	7483112	585	9911										
HAS1	3036	hgsc.bcm.edu	37	chr19	52219555	52219555	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcggttggtgaggtgccggtCatccccaaaagtacagtggg	16	9	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:52219555C>A	ENST00000222115.1	-	4	1049	c.1015G>T	c.(1015-1017)Gac>Tac	p.D339Y	HAS1_ENST00000601714.1_Missense_Mutation_p.D346Y|HAS1_ENST00000594621.1_Intron|HAS1_ENST00000540069.2_Missense_Mutation_p.D338Y	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	339					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		AGGTGCCGGTCATCCCCAAAA	0.532																																					p.D339Y	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.G1015T						.						117	106	110					19																	52219555		2203	4300	6503	SO:0001583	missense	3036	exon4			GCCGGTCATCCCC	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.1015G>T	chr19.hg19:g.52219555C>A	ENSP00000222115:p.Asp339Tyr	163.0	0.0		103.0	38.0	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	hg19	CCDS12838.1	.	.	.	.	.	.	.	.	.	.	c	16.53	3.148197	0.57151	.	.	ENSG00000105509	ENST00000540069;ENST00000222115	T;T	0.76186	-1.0;-1.0	3.35	3.35	0.38373	.	0.188629	0.44097	U	0.000494	D	0.89406	0.6706	H	0.96301	3.8	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.985;0.992;0.992	D	0.92135	0.5715	10	0.87932	D	0	-12.7644	12.592	0.56447	0.0:1.0:0.0:0.0	.	338;339;338	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	Y	338;339	ENSP00000445021:D338Y;ENSP00000222115:D339Y	ENSP00000222115:D339Y	D	-	1	0	HAS1	56911367	1.000000	0.71417	1.000000	0.80357	0.558000	0.35554	7.614000	0.82996	1.608000	0.50180	0.165000	0.16767	GAC	.	.		0.532	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		A	52219555	C	A	52219555	3	1	73	1	0	0	0	0	1	0	0	0	6970	826	29	3	729	3	HAS1	19	52219555	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	573684	52219555	6909428	586	9912										
ZNF28	7576	hgsc.bcm.edu	37	chr19	53303548	53303548	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtatggtttctctccagtaTgaactctctgatgttctgta	8	8	3	2	rs369691107		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:53303548T>C	ENST00000457749.2	-	4	1669	c.1550A>G	c.(1549-1551)cAt>cGt	p.H517R	ZNF28_ENST00000438150.2_Missense_Mutation_p.H464R|ZNF28_ENST00000414252.2_Missense_Mutation_p.H464R|ZNF28_ENST00000360272.4_Missense_Mutation_p.H464R	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	517					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		CTCTCCAGTATGAACTCTCTG	0.398																																					p.H517R		Atlas-SNP	.											.	ZNF28	191	.	0			c.A1550G						.	T	ARG/HIS	1,4405		0,1,2202	106	107	107		1550	1.9	0	19		107	0,8600		0,0,4300	no	missense	ZNF28	NM_006969.3	29	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	possibly-damaging	517/719	53303548	1,13005	2203	4300	6503	SO:0001583	missense	7576	exon4			CCAGTATGAACTC	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.1550A>G	chr19.hg19:g.53303548T>C	ENSP00000397693:p.His517Arg	104.0	0.0		65.0	21.0	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	hg19	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	14.01	2.408932	0.42715	2.27E-4	0.0	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27	1.89	1.89	0.25635	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.81650	0.4867	M	0.92026	3.265	0.26204	N	0.979409	D	0.89917	1.0	D	0.70935	0.971	T	0.68522	-0.5386	9	0.87932	D	0	.	5.838	0.18617	0.0:0.0:0.2728:0.7272	.	517	P17035	ZNF28_HUMAN	R	464;517;464;464;464	ENSP00000412143:H464R;ENSP00000397693:H517R;ENSP00000353410:H464R;ENSP00000444965:H464R;ENSP00000375661:H464R	ENSP00000353410:H464R	H	-	2	0	ZNF28	57995360	0.978000	0.34361	0.028000	0.17463	0.057000	0.15508	2.163000	0.42377	0.861000	0.35504	0.333000	0.21579	CAT	.	.		0.398	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		C	53303548	T	C	53303548	3	2	73	1	0	0	0	0	1	0	0	0	17828	1464	51	2	610	2	ZNF28	19	53303548	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1083993	53303548	5825435	587	9913										
LILRB3	11025	hgsc.bcm.edu	37	chr19	54721082	54721082	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgcagctgggcgtaggtcacAtcctgggaggcttcagatgc	15	10	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:54721082A>G	ENST00000391750.1	-	14	1912	c.1776T>C	c.(1774-1776)gaT>gaC	p.D592D	LILRB3_ENST00000346401.6_Silent_p.D604D|LILRA6_ENST00000270464.5_Silent_p.D593D|LILRB3_ENST00000469273.1_5'UTR|LILRB3_ENST00000407860.2_Silent_p.D609D|LILRB3_ENST00000245620.9_Silent_p.D593D|LILRB3_ENST00000424807.1_Silent_p.D592D|LILRA6_ENST00000419410.2_Silent_p.D593D|LILRA6_ENST00000440558.2_Silent_p.D592D|LILRA6_ENST00000391735.3_3'UTR			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	592					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CGTAGGTCACATCCTGGGAGG	0.632																																					p.D593D		Atlas-SNP	.											.	LILRB3	67	.	0			c.T1779C						.						87	90	89					19																	54721082		2203	4300	6503	SO:0001819	synonymous_variant	11025	exon13			GGTCACATCCTGG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1776T>C	chr19.hg19:g.54721082A>G		176.0	0.0		166.0	80.0	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	hg19	CCDS33105.1																																																																																			.	.		0.632	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		G	54721082	A	G	54721082	2	3	73	1	0	0	0	0	0	0	0	1	8801	214	8	2		2	LILRB3	19	54721082	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1417534	54721082	4407901	588	9914										
LILRA3	11026	hgsc.bcm.edu	37	chr19	54803147	54803147	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cggagaagatggcccgggatGacccacgggcatgggaatgg	18	9	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:54803147G>C	ENST00000251390.3	-	4	621	c.530C>G	c.(529-531)tCa>tGa	p.S177*	LILRA3_ENST00000391745.1_Nonsense_Mutation_p.S194*|LILRA3_ENST00000391744.3_Intron	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	177	Ig-like C2-type 2.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGCCCGGGATGACCCACGGGC	0.562																																					p.S177X		Atlas-SNP	.											.	LILRA3	65	.	0			c.C530G						.						147	120	129					19																	54803147		2195	4162	6357	SO:0001587	stop_gained	11026	exon4			CGGGATGACCCAC	U91926		19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.530C>G	chr19.hg19:g.54803147G>C	ENSP00000251390:p.Ser177*	167.0	0.0		129.0	46.0	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Nonsense_Mutation	SNP	ENST00000251390.3	hg19	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.004390	0.74932	.	.	ENSG00000170866	ENST00000251390;ENST00000391745	.	.	.	2.21	-4.29	0.03721	.	0.915817	0.09155	N	0.840975	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	4.8661	0.13609	0.0:0.4858:0.2096:0.3046	.	.	.	.	X	177;194	.	ENSP00000251390:S177X	S	-	2	0	LILRA3	59494959	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.222000	0.02965	-1.079000	0.03113	-1.081000	0.02215	TCA	.	.		0.562	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1			C	54803147	G	C	54803147	4	2	73	1	0	0	0	0	0	1	0	0	8795	1294	45	4	805	4	LILRA3	19	54803147	Nonsense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	82065	54803147	4325836	589	9915										
U2AF2	11338	hgsc.bcm.edu	37	chr19	56173908	56173908	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caacgcccagatgcgcctggGggggctgacccaggcccctg	15	16	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:56173908G>T	ENST00000308924.4	+	6	567	c.527G>T	c.(526-528)gGg>gTg	p.G176V	U2AF2_ENST00000590551.1_Missense_Mutation_p.G12V|CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.12_ENST00000589456.1_RNA|U2AF2_ENST00000450554.2_Missense_Mutation_p.G176V			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	176	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G176E(1)|p.G176V(1)		biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		ATGCGCCTGGGGGGGCTGACC	0.607																																					p.G176V		Atlas-SNP	.											U2AF2,NS,carcinoma,0,2	U2AF2	62	.	2	Substitution - Missense(2)	lung(2)	c.G527T						.						40	48	45					19																	56173908		2203	4300	6503	SO:0001583	missense	11338	exon6			GCCTGGGGGGGCT	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"RNA binding motif (RRM) containing"	23156	protein-coding gene	gene with protein product	"U2 small nuclear ribonucleoprotein auxiliary factor (65kD)", "splicing factor U2AF 65 kD subunit", "U2 snRNP auxiliary factor large subunit"	191318	"U2 (RNU2) small nuclear RNA auxiliary factor 2"			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.527G>T	chr19.hg19:g.56173908G>T	ENSP00000307863:p.Gly176Val	156.0	1.0		131.0	52.0	NM_001012478	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	hg19	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	G	8.764	0.924203	0.18056	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	T;T	0.11604	2.76;2.76	4.13	3.06	0.35304	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.04998	0.0134	N	0.05441	-0.05	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.34477	-0.9827	10	0.11182	T	0.66	-22.3889	11.8012	0.52128	0.0965:0.0:0.9035:0.0	.	176;176	P26368;P26368-2	U2AF2_HUMAN;.	V	176	ENSP00000307863:G176V;ENSP00000388475:G176V	ENSP00000307863:G176V	G	+	2	0	U2AF2	60865720	1.000000	0.71417	0.984000	0.44739	0.967000	0.64934	7.171000	0.77595	2.023000	0.59567	0.585000	0.79938	GGG	.	.		0.607	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		T	56173908	G	T	56173908	3	4	73	1	0	0	0	0	1	0	0	0	16838	1232	43	3	549	3	U2AF2	19	56173908	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	1370761	56173908	2955075	590	9916										
PEG3	5178	hgsc.bcm.edu	37	chr19	57327366	57327366	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctccagcacgaactctctgaTggttgatagcatcgaagctc	9	12	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:57327366T>C	ENST00000326441.9	-	10	2807	c.2444A>G	c.(2443-2445)cAt>cGt	p.H815R	ZIM2_ENST00000601070.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.H689R|PEG3_ENST00000423103.2_Missense_Mutation_p.H815R|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.H691R	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	815					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		AACTCTCTGATGGTTGATAGC	0.468																																					p.H815R		Atlas-SNP	.											.	PEG3	414	.	0			c.A2444G						.						134	127	129					19																	57327366		2203	4300	6503	SO:0001583	missense	5178	exon9			CTCTGATGGTTGA	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.2444A>G	chr19.hg19:g.57327366T>C	ENSP00000326581:p.His815Arg	177.0	0.0		148.0	6.0	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	hg19	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.533271	0.27387	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02579	4.24;4.24	3.96	2.85	0.33270	.	1.141450	0.06613	N	0.756038	T	0.04182	0.0116	M	0.61703	1.905	.	.	.	P;B;B	0.37015	0.578;0.0;0.002	B;B;B	0.28305	0.088;0.001;0.002	T	0.34428	-0.9829	9	0.87932	D	0	-1.1202	6.8699	0.24115	0.0:0.1351:0.0:0.8649	.	691;815;750	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	R	815	ENSP00000326581:H815R;ENSP00000403051:H815R	ENSP00000326581:H815R	H	-	2	0	ZIM2	62019178	0.001000	0.12720	0.001000	0.08648	0.011000	0.07611	0.951000	0.29135	0.805000	0.34159	0.477000	0.44152	CAT	.	.		0.468	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			C	57327366	T	C	57327366	3	2	73	1	0	0	0	0	1	0	0	0	11729	1464	51	2	2326	2	PEG3	19	57327366	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1153458	57327366	1801617	591	9917										
ZIM3	114026	hgsc.bcm.edu	37	chr19	57646378	57646378	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acatccataaggtttttgtcCagtatgggtttttttatgca	8	6	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:57646378C>A	ENST00000269834.1	-	5	1712	c.1327G>T	c.(1327-1329)Gga>Tga	p.G443*	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	443					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GGTTTTTGTCCAGTATGGGTT	0.418																																					p.G443X		Atlas-SNP	.											.	ZIM3	107	.	0			c.G1327T						.						139	142	141					19																	57646378		2203	4300	6503	SO:0001587	stop_gained	114026	exon5			TTTGTCCAGTATG	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.1327G>T	chr19.hg19:g.57646378C>A	ENSP00000269834:p.Gly443*	143.0	0.0		127.0	50.0	NM_052882	Q14CA6	Nonsense_Mutation	SNP	ENST00000269834.1	hg19	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	C	38	7.017602	0.98006	.	.	ENSG00000141946	ENST00000269834	.	.	.	2.16	1.11	0.20524	.	.	.	.	.	.	.	.	.	.	.	0.53005	D	0.999966	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	6.5562	0.22462	0.0:0.8376:0.0:0.1624	.	.	.	.	X	443	.	ENSP00000269834:G443X	G	-	1	0	ZIM3	62338190	0.000000	0.05858	0.002000	0.10522	0.281000	0.26958	0.080000	0.14802	0.458000	0.26988	0.313000	0.20887	GGA	.	.		0.418	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			A	57646378	C	A	57646378	4	1	73	1	0	0	0	0	0	1	0	0	17700	603	21	3	95	3	ZIM3	19	57646378	Nonsense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	319012	57646378	1482605	592	9918										
ZNF256	10172	hgsc.bcm.edu	37	chr19	58452722	58452722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cataaggccttgctccagtaTgaactttccagtgtgagatg	10	9	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:58452722T>C	ENST00000282308.3	-	3	1650	c.1454A>G	c.(1453-1455)cAt>cGt	p.H485R	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	485					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		TGCTCCAGTATGAACTTTCCA	0.453																																					p.H485R	NSCLC(55;1313 1552 8040 11996)	Atlas-SNP	.											.	ZNF256	117	.	0			c.A1454G						.						87	86	86					19																	58452722		2203	4300	6503	SO:0001583	missense	10172	exon3			CCAGTATGAACTT	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"Zinc fingers, C2H2-type", "-"	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.1454A>G	chr19.hg19:g.58452722T>C	ENSP00000282308:p.His485Arg	60.0	0.0		56.0	21.0	NM_005773	B2RA92|Q53Y85|Q9BV71	Missense_Mutation	SNP	ENST00000282308.3	hg19	CCDS12966.1	.	.	.	.	.	.	.	.	.	.	.	23.2	4.384159	0.82792	.	.	ENSG00000152454	ENST00000282308	T	0.67523	-0.27	2.96	2.96	0.34315	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.84492	0.5484	H	0.94964	3.605	0.36779	D	0.884254	D	0.89917	1.0	D	0.77004	0.989	D	0.89023	0.3436	9	0.87932	D	0	.	10.4264	0.44380	0.0:0.0:0.0:1.0	.	485	Q9Y2P7	ZN256_HUMAN	R	485	ENSP00000282308:H485R	ENSP00000282308:H485R	H	-	2	0	ZNF256	63144534	1.000000	0.71417	0.165000	0.22776	0.798000	0.45092	3.644000	0.54381	1.341000	0.45600	0.383000	0.25322	CAT	.	.		0.453	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1			C	58452722	T	C	58452722	3	2	73	1	0	0	0	0	1	0	0	0	17814	1464	51	2	433	2	ZNF256	19	58452722	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	806344	58452722	676261	593	9919										
SLC27A5	10998	hgsc.bcm.edu	37	chr19	59022230	59022230	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggtgtaggggaggtatggctGaggtagaagcagcggatgtt	20	3	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr19:59022230G>A	ENST00000263093.2	-	2	865	c.756C>T	c.(754-756)ctC>ctT	p.L252L	SLC27A5_ENST00000601355.1_Silent_p.L168L	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	252					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		AGGTATGGCTGAGGTAGAAGC	0.632																																					p.L252L		Atlas-SNP	.											SLC27A5,bladder,carcinoma,0,1	SLC27A5	58	.	0			c.C756T						.						34	35	34					19																	59022230		2203	4300	6503	SO:0001819	synonymous_variant	10998	exon2			ATGGCTGAGGTAG	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"Acyl-CoA synthetase family", "Solute carriers"	10999	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 3"	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.756C>T	chr19.hg19:g.59022230G>A		55.0	0.0		52.0	25.0	NM_012254	B3KVP6|B4DPQ1	Silent	SNP	ENST00000263093.2	hg19	CCDS12983.1																																																																																			.	.		0.632	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		A	59022230	G	A	59022230	2	1	73	1	0	0	0	0	0	0	0	1	14544	1277	45	3		3	SLC27A5	19	59022230	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	569508	59022230	106753	594	9920										
SOX12	6666	hgsc.bcm.edu	37	chr20	306791	306791	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ccgagatctccaagcgcctgGgccgccgctggcagctgctg	14	16	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:306791G>A	ENST00000342665.2	+	1	553	c.223G>A	c.(223-225)Ggc>Agc	p.G75S	RP5-1103G7.4_ENST00000442637.1_RNA|RP5-1103G7.4_ENST00000414676.1_RNA|SOX12_ENST00000544632.1_Missense_Mutation_p.G75S	NM_006943.2	NP_008874.2	O15370	SOX12_HUMAN	SRY (sex determining region Y)-box 12	75					cell fate commitment (GO:0045165)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord development (GO:0021510)	nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		all_cancers(10;0.000331)|Lung NSC(37;0.0496)|all_lung(30;0.0831)|all_epithelial(17;0.0868)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			CAAGCGCCTGGGCCGCCGCTG	0.642																																					p.G75S		Atlas-SNP	.											.	SOX12	8	.	0			c.G223A						.						25	24	24					20																	306791		2191	4288	6479	SO:0001583	missense	6666	exon1			CGCCTGGGCCGCC	U35612	CCDS12995.1	20p13	2008-07-28	2002-07-22	2002-07-26	ENSG00000177732	ENSG00000177732		"SRY (sex determining region Y)-boxes"	11198	protein-coding gene	gene with protein product		601947	"SRY (sex determining region Y)-box 22"	SOX22		9215677	Standard	NM_006943		Approved		uc002wdh.4	O15370	OTTHUMG00000031623	ENST00000342665.2:c.223G>A	chr20.hg19:g.306791G>A	ENSP00000347646:p.Gly75Ser	155.0	0.0		123.0	51.0	NM_006943	Q5D038|Q9NUD4	Missense_Mutation	SNP	ENST00000342665.2	hg19	CCDS12995.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.617762	0.87359	.	.	ENSG00000177732	ENST00000544632;ENST00000342665	D;D	0.98947	-5.26;-5.26	3.63	3.63	0.41609	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.52532	U	0.000070	D	0.99108	0.9693	M	0.89478	3.035	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99126	1.0851	10	0.87932	D	0	.	12.8184	0.57679	0.0:0.0:1.0:0.0	.	75	O15370	SOX12_HUMAN	S	75	ENSP00000441671:G75S;ENSP00000347646:G75S	ENSP00000347646:G75S	G	+	1	0	SOX12	254791	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	6.883000	0.75595	1.858000	0.53909	0.313000	0.20887	GGC	.	.		0.642	SOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077435.2	NM_006943		A	306791	G	A	306791	3	1	73	1	0	0	0	0	1	0	0	0	14958	1232	43	3	225	3	SOX12	20	306791	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10		306791	62718729	595	9921										
STK35	140901	hgsc.bcm.edu	37	chr20	2097911	2097911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cccaaaaacgcaggacttccAtgtctgaggggatcaagcag	11	11	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:2097911A>G	ENST00000381482.3	+	3	1763	c.1492A>G	c.(1492-1494)Atg>Gtg	p.M498V	STK35_ENST00000246032.3_Missense_Mutation_p.M365V|STK35_ENST00000400064.3_Intron			Q8TDR2	STK35_HUMAN	serine/threonine kinase 35	498	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(2)|liver(2)|lung(6)|ovary(1)|prostate(2)	13						CAGGACTTCCATGTCTGAGGG	0.507																																					p.M498V		Atlas-SNP	.											.	STK35	31	.	0			c.A1492G						.						82	79	80					20																	2097911		2203	4300	6503	SO:0001583	missense	140901	exon3			ACTTCCATGTCTG	AL359916	CCDS13024.1, CCDS13024.2	20p13	2008-07-02			ENSG00000125834	ENSG00000125834			16254	protein-coding gene	gene with protein product	"CLP-36 interacting kinase"	609370				11973348	Standard	NM_080836		Approved	bA550O8.2, CLIK1	uc002wfw.4	Q8TDR2	OTTHUMG00000031688	ENST00000381482.3:c.1492A>G	chr20.hg19:g.2097911A>G	ENSP00000370891:p.Met498Val	127.0	0.0		80.0	40.0	NM_080836	B2RBM3|C7ENV8|Q2NKW6|Q5T3R1|Q5T3R2|Q96AB4|Q9BZ06	Missense_Mutation	SNP	ENST00000381482.3	hg19	CCDS13024.2	.	.	.	.	.	.	.	.	.	.	A	9.602	1.128964	0.21041	.	.	ENSG00000125834	ENST00000381482;ENST00000246032	D;D	0.92595	-3.07;-3.07	5.5	5.5	0.81552	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81683	0.4874	N	0.02420	-0.555	0.80722	D	1	B	0.17852	0.024	B	0.28385	0.089	T	0.77474	-0.2574	10	0.28530	T	0.3	-16.879	13.6097	0.62071	1.0:0.0:0.0:0.0	.	498	Q8TDR2	STK35_HUMAN	V	498;365	ENSP00000370891:M498V;ENSP00000246032:M365V	ENSP00000246032:M365V	M	+	1	0	STK35	2045911	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.139000	0.94554	2.308000	0.77769	0.533000	0.62120	ATG	.	.		0.507	STK35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077574.3	NM_080836		G	2097911	A	G	2097911	3	3	73	1	0	0	0	0	1	0	0	0	15316	217	8	2	1502	2	STK35	20	2097911	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	1791120	2097911	60927609	596	9922										
SMOX	54498	hgsc.bcm.edu	37	chr20	4155893	4155893	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagccacatcggaggccgtgTgcagagtgtgaaacttggta	14	9	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:4155893T>C	ENST00000305958.4	+	2	416	c.191T>C	c.(190-192)gTg>gCg	p.V64A	SMOX_ENST00000346595.2_Missense_Mutation_p.V64A|SMOX_ENST00000484515.1_3'UTR|SMOX_ENST00000379460.2_Missense_Mutation_p.V64A|SMOX_ENST00000339123.6_Missense_Mutation_p.V64A|SMOX_ENST00000278795.3_Missense_Mutation_p.V64A	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	64					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	GGAGGCCGTGTGCAGAGTGTG	0.582																																					p.V64A		Atlas-SNP	.											.	SMOX	119	.	0			c.T191C						.						64	60	61					20																	4155893		2203	4300	6503	SO:0001583	missense	54498	exon2			GCCGTGTGCAGAG	AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"chromosome 20 open reading frame 16"	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.191T>C	chr20.hg19:g.4155893T>C	ENSP00000307252:p.Val64Ala	106.0	0.0		95.0	36.0	NM_175839	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Missense_Mutation	SNP	ENST00000305958.4	hg19	CCDS13075.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.300427	0.81136	.	.	ENSG00000088826	ENST00000339123;ENST00000305958;ENST00000278795;ENST00000346595;ENST00000379460	D;D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24;-3.24	4.91	4.91	0.64330	Amine oxidase (1);	0.000000	0.85682	D	0.000000	D	0.93527	0.7934	L	0.31371	0.925	0.80722	D	1	D;D;P;D;D;D	0.69078	0.997;0.997;0.909;0.997;0.994;0.987	D;D;P;D;D;D	0.79108	0.992;0.96;0.777;0.992;0.954;0.945	D	0.92618	0.6105	9	.	.	.	-15.1479	12.7905	0.57530	0.0:0.0:0.0:1.0	.	64;64;64;64;64;64	B4DE63;Q9NWM0-6;Q9NWM0-3;Q9NWM0;Q9NWM0-2;Q9NWM0-4	.;.;.;SMOX_HUMAN;.;.	A	64	ENSP00000344595:V64A;ENSP00000307252:V64A;ENSP00000278795:V64A;ENSP00000341775:V64A;ENSP00000368773:V64A	.	V	+	2	0	SMOX	4103893	1.000000	0.71417	0.990000	0.47175	0.970000	0.65996	7.838000	0.86804	1.961000	0.56991	0.455000	0.32223	GTG	.	.		0.582	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842		C	4155893	T	C	4155893	3	2	73	1	0	0	0	0	1	0	0	0	14818	1696	59	2	193	2	SMOX	20	4155893	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2057982	4155893	58869627	597	9923										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9288511	9288511	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gaaggaagttccctccttttTgcaagaaggagcagtttttg	11	7	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:9288511T>G	ENST00000378493.1	+	1	65	c.50T>G	c.(49-51)tTg>tGg	p.L17W	PLCB4_ENST00000378473.3_Missense_Mutation_p.L17W|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000414679.2_Missense_Mutation_p.L17W|PLCB4_ENST00000278655.4_Missense_Mutation_p.L17W|PLCB4_ENST00000378501.2_Missense_Mutation_p.L17W|PLCB4_ENST00000334005.3_Missense_Mutation_p.L17W			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	17					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						CCCTCCTTTTTGCAAGAAGGA	0.299																																					p.L17W		Atlas-SNP	.											.	PLCB4	204	.	0			c.T50G						.						63	59	61					20																	9288511		2203	4298	6501	SO:0001583	missense	5332	exon2			CCTTTTTGCAAGA		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.50T>G	chr20.hg19:g.9288511T>G	ENSP00000367754:p.Leu17Trp	80.0	0.0		80.0	51.0	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	hg19	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.138684	0.77775	.	.	ENSG00000101333	ENST00000407043;ENST00000441846;ENST00000334005;ENST00000378473;ENST00000437503;ENST00000416836;ENST00000278655;ENST00000378493;ENST00000378501	T;T;T;T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	5.87	5.87	0.94306	Pleckstrin homology-type (1);	0.118259	0.64402	D	0.000010	T	0.80099	0.4561	M	0.80847	2.515	0.38024	D	0.934958	P;P;D	0.67145	0.95;0.661;0.996	P;B;D	0.76071	0.621;0.221;0.987	D	0.84824	0.0798	10	0.87932	D	0	.	15.2632	0.73640	0.0:0.0:0.0:1.0	.	17;17;17	E2QRH8;Q15147;Q15147-4	.;PLCB4_HUMAN;.	W	17	ENSP00000385805:L17W;ENSP00000412982:L17W;ENSP00000334105:L17W;ENSP00000367734:L17W;ENSP00000391614:L17W;ENSP00000395753:L17W;ENSP00000278655:L17W;ENSP00000367754:L17W;ENSP00000367762:L17W	ENSP00000278655:L17W	L	+	2	0	PLCB4	9236511	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.792000	0.69052	2.248000	0.74166	0.533000	0.62120	TTG	.	.		0.299	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			G	9288511	T	G	9288511	3	3	73	1	0	0	0	0	1	0	0	0	12039	1821	63	5	52	5	PLCB4	20	9288511	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	5132618	9288511	53737009	598	9924										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9352961	9352961	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tccttacagaatgatgaaatTgagcccacagcattttctta	6	9	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:9352961T>A	ENST00000378493.1	+	8	612	c.597T>A	c.(595-597)atT>atA	p.I199I	PLCB4_ENST00000378473.3_Silent_p.I199I|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000414679.2_Silent_p.I199I|PLCB4_ENST00000278655.4_Silent_p.I199I|PLCB4_ENST00000378501.2_Silent_p.I199I|PLCB4_ENST00000334005.3_Silent_p.I199I			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	199					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						ATGATGAAATTGAGCCCACAG	0.373																																					p.I199I		Atlas-SNP	.											.	PLCB4	204	.	0			c.T597A						.						78	79	79					20																	9352961		2202	4300	6502	SO:0001819	synonymous_variant	5332	exon9			TGAAATTGAGCCC		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.597T>A	chr20.hg19:g.9352961T>A		186.0	0.0		165.0	80.0	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Silent	SNP	ENST00000378493.1	hg19	CCDS13105.1																																																																																			.	.		0.373	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			A	9352961	T	A	9352961	2	1	73	1	0	0	0	0	0	0	0	1	12039	1800	63	4		4	PLCB4	20	9352961	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	64450	9352961	53672559	599	9925										
PAK7	57144	hgsc.bcm.edu	37	chr20	9525119	9525119	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctttggaaacttgagcacagAaaccaaaatcagacaacttt	6	9	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:9525119A>G	ENST00000378429.3	-	9	2312	c.1766T>C	c.(1765-1767)tTc>tCc	p.F589S	PAK7_ENST00000353224.5_Missense_Mutation_p.F589S|PAK7_ENST00000378423.1_Missense_Mutation_p.F589S	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	589	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TTGAGCACAGAAACCAAAATC	0.413																																					p.F589S		Atlas-SNP	.											.	PAK7	194	.	0			c.T1766C						.						96	93	94					20																	9525119		2203	4300	6503	SO:0001583	missense	57144	exon8			GCACAGAAACCAA	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1766T>C	chr20.hg19:g.9525119A>G	ENSP00000367686:p.Phe589Ser	169.0	0.0		139.0	48.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.011681	0.93346	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423	T;T;T	0.64803	-0.12;-0.12;-0.12	5.97	5.97	0.96955	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73125	0.3547	L	0.42686	1.345	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.71411	-0.4601	9	.	.	.	.	16.4608	0.84044	1.0:0.0:0.0:0.0	.	589	Q9P286	PAK7_HUMAN	S	589	ENSP00000367686:F589S;ENSP00000322957:F589S;ENSP00000367679:F589S	.	F	-	2	0	PAK7	9473119	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.278000	0.95766	2.288000	0.76882	0.533000	0.62120	TTC	.	.		0.413	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			G	9525119	A	G	9525119	3	3	73	1	0	0	0	0	1	0	0	0	11414	246	9	2	405	2	PAK7	20	9525119	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	172158	9525119	53500401	600	9926										
SEC23B	10483	hgsc.bcm.edu	37	chr20	18491619	18491619	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctccttactcctttgaaagAacgtccagacctacctcctg	5	15	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:18491619A>G	ENST00000336714.3	+	2	572	c.140A>G	c.(139-141)gAa>gGa	p.E47G	SEC23B_ENST00000377475.3_Missense_Mutation_p.E47G|SEC23B_ENST00000262544.2_Missense_Mutation_p.E47G|SEC23B_ENST00000377465.1_Missense_Mutation_p.E47G	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	47					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						CCTTTGAAAGAACGTCCAGAC	0.493																																					p.E47G		Atlas-SNP	.											.	SEC23B	70	.	0			c.A140G						.						169	149	155					20																	18491619		2203	4300	6503	SO:0001583	missense	10483	exon2			TGAAAGAACGTCC	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"Sec23 (S. cerevisiae) homolog B", "congenital dyserythropoietic anemia, type II"	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.140A>G	chr20.hg19:g.18491619A>G	ENSP00000338844:p.Glu47Gly	216.0	0.0		239.0	106.0	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	hg19	CCDS13137.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.908899	0.92107	.	.	ENSG00000101310	ENST00000450074;ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	D;D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7;-1.7	5.29	5.29	0.74685	Zinc finger, Sec23/Sec24-type (1);	0.000000	0.85682	D	0.000000	D	0.83087	0.5178	M	0.78916	2.43	0.80722	D	1	B;B	0.27316	0.175;0.01	B;B	0.24269	0.052;0.019	T	0.82833	-0.0262	10	0.66056	D	0.02	-20.9293	14.5693	0.68202	1.0:0.0:0.0:0.0	.	47;47	B4DJW8;Q15437	.;SC23B_HUMAN	G	47	ENSP00000403971:E47G;ENSP00000338844:E47G;ENSP00000262544:E47G;ENSP00000366695:E47G;ENSP00000366685:E47G	ENSP00000262544:E47G	E	+	2	0	SEC23B	18439619	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.087000	0.94110	2.234000	0.73211	0.533000	0.62120	GAA	.	.		0.493	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			G	18491619	A	G	18491619	3	3	73	1	0	0	0	0	1	0	0	0	14007	246	9	2	142	2	SEC23B	20	18491619	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	8966500	18491619	44533901	601	9927										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20144825	20144825	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atctacaggggagcctcagcTgctttttgtattcagctgtt	10	9	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:20144825T>A	ENST00000245957.5	+	11	1234	c.1158T>A	c.(1156-1158)gcT>gcA	p.A386A	C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000451767.2_Silent_p.A386A|C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000377306.1_Silent_p.A386A	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		386										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		GAGCCTCAGCTGCTTTTTGTA	0.493																																					p.A386A		Atlas-SNP	.											.	C20orf26	188	.	0			c.T1158A						.						116	116	116					20																	20144825		2203	4300	6503	SO:0001819	synonymous_variant	26074	exon11			CTCAGCTGCTTTT																												ENST00000245957.5:c.1158T>A	chr20.hg19:g.20144825T>A		77.0	0.0		60.0	19.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Silent	SNP	ENST00000245957.5	hg19	CCDS33447.1																																																																																			.	.		0.493	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			A	20144825	T	A	20144825	2	1	73	1	0	0	0	0	0	0	0	1	2108	1567	55	4		4	C20orf26	20	20144825	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1653206	20144825	42880695	602	9928										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20269371	20269371	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caacttccacaccaacgacaTagccatcagagctgctggct	7	15	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:20269371T>C	ENST00000245957.5	+	23	2991	c.2915T>C	c.(2914-2916)aTa>aCa	p.I972T	C20orf26_ENST00000377309.2_Intron	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		972										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		ACCAACGACATAGCCATCAGA	0.428																																					p.I972T		Atlas-SNP	.											.	C20orf26	188	.	0			c.T2915C						.						157	144	149					20																	20269371		2203	4300	6503	SO:0001583	missense	26074	exon23			ACGACATAGCCAT																												ENST00000245957.5:c.2915T>C	chr20.hg19:g.20269371T>C	ENSP00000245957:p.Ile972Thr	218.0	0.0		166.0	66.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	hg19	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	T	8.966	0.971824	0.18736	.	.	ENSG00000089101	ENST00000343997;ENST00000389655;ENST00000245957	T	0.40225	1.04	5.75	5.75	0.90469	.	0.750513	0.13155	N	0.409512	T	0.30355	0.0762	L	0.40543	1.245	0.25111	N	0.990712	B	0.26547	0.152	B	0.21708	0.036	T	0.24190	-1.0167	10	0.14252	T	0.57	.	7.0755	0.25201	0.1316:0.0709:0.0:0.7975	.	972	Q8NHU2	CT026_HUMAN	T	912;938;972	ENSP00000245957:I972T	ENSP00000245957:I972T	I	+	2	0	C20orf26	20217371	0.000000	0.05858	0.780000	0.31762	0.913000	0.54294	0.860000	0.27871	2.205000	0.71048	0.528000	0.53228	ATA	.	.		0.428	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			C	20269371	T	C	20269371	3	2	73	1	0	0	0	0	1	0	0	0	2108	1406	49	2	3033	2	C20orf26	20	20269371	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	124546	20269371	42756149	603	9929										
NANP	140838	hgsc.bcm.edu	37	chr20	25596957	25596957	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcctttcgaagttcagtaagCatggctttgacgtcttctgc	9	10	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:25596957C>A	ENST00000304788.3	-	2	577	c.351G>T	c.(349-351)atG>atT	p.M117I		NM_152667.2	NP_689880.1	Q8TBE9	NANP_HUMAN	N-acetylneuraminic acid phosphatase	117					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate biosynthetic process (GO:0046380)		N-acylneuraminate-9-phosphatase activity (GO:0050124)			endometrium(2)|lung(2)|prostate(1)	5						GTTCAGTAAGCATGGCTTTGA	0.448																																					p.M117I		Atlas-SNP	.											.	NANP	10	.	0			c.G351T						.						116	114	115					20																	25596957		2203	4300	6503	SO:0001583	missense	140838	exon2			AGTAAGCATGGCT	AL031673	CCDS13173.1	20p11.1	2006-10-24	2006-01-24	2006-01-24	ENSG00000170191	ENSG00000170191			16140	protein-coding gene	gene with protein product		610763	"chromosome 20 open reading frame 147", "haloacid dehalogenase-like hydrolase domain containing 4"	C20orf147, HDHD4		16237198	Standard	NM_152667		Approved	dJ694B14.3, MGC26833	uc002wuy.3	Q8TBE9	OTTHUMG00000032132	ENST00000304788.3:c.351G>T	chr20.hg19:g.25596957C>A	ENSP00000302441:p.Met117Ile	121.0	0.0		89.0	37.0	NM_152667	B3KP12|Q5JYN8|Q8TE97|Q9Y3N0	Missense_Mutation	SNP	ENST00000304788.3	hg19	CCDS13173.1	.	.	.	.	.	.	.	.	.	.	C	19.10	3.762103	0.69763	.	.	ENSG00000170191	ENST00000304788	T	0.04862	3.54	5.4	5.4	0.78164	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.043012	0.85682	D	0.000000	T	0.16981	0.0408	L	0.56199	1.76	0.48762	D	0.999702	P	0.47545	0.897	P	0.55112	0.769	T	0.00088	-1.2091	10	0.48119	T	0.1	-7.247	16.7324	0.85438	0.0:1.0:0.0:0.0	.	117	Q8TBE9	NANP_HUMAN	I	117	ENSP00000302441:M117I	ENSP00000302441:M117I	M	-	3	0	NANP	25544957	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	4.290000	0.59019	2.528000	0.85240	0.485000	0.47835	ATG	.	.		0.448	NANP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078457.2	NM_152667		A	25596957	C	A	25596957	3	1	73	1	0	0	0	0	1	0	0	0	10163	710	25	3	399	3	NANP	20	25596957	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	5327586	25596957	37428563	604	9930										
TM9SF4	9777	hgsc.bcm.edu	37	chr20	30738606	30738606	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgccattttcccacagggtGtttggcggattttctgctgg	12	10	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:30738606G>T	ENST00000398022.2	+	12	1408	c.1173G>T	c.(1171-1173)gtG>gtT	p.V391V	TM9SF4_ENST00000217315.5_Silent_p.V374V	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	391						integral component of membrane (GO:0016021)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			CCCACAGGGTGTTTGGCGGAT	0.567																																					p.V391V		Atlas-SNP	.											.	TM9SF4	65	.	0			c.G1173T						.						120	113	115					20																	30738606		2203	4300	6503	SO:0001819	synonymous_variant	9777	exon12			CAGGGTGTTTGGC	BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.1173G>T	chr20.hg19:g.30738606G>T		133.0	0.0		110.0	50.0	NM_014742	B0QYT7|Q9NUA3	Silent	SNP	ENST00000398022.2	hg19	CCDS13196.2																																																																																			.	.		0.567	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742		T	30738606	G	T	30738606	2	4	73	1	0	0	0	0	0	0	0	1	15995	1364	48	3		3	TM9SF4	20	30738606	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	5141649	30738606	32286914	605	9931										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31023559	31023580	+	Frame_Shift_Del	DEL	AGGCTGACACTAGAGAAGCTGC	AGGCTGACACTAGAGAAGCTGC	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctcacggaggacagcagtgAggctgacactagagaagctg					rs527562446|rs560170731|rs545071926		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	AGGCTGACACTAGAGAAGCTGC	AGGCTGACACTAGAGAAGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:31023559_31023580delAGGCTGACACTAGAGAAGCTGC	ENST00000375687.4	+	13	3468_3489	c.3044_3065delAGGCTGACACTAGAGAAGCTGC	c.(3043-3066)gaggctgacactagagaagctgcafs	p.EADTREAA1015fs	ASXL1_ENST00000306058.5_Frame_Shift_Del_p.EADTREAA1010fs	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1015					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.D1017A(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						GACAGCAGTGAGGCTGACACTAGAGAAGCTGCAGTGACAAAG	0.518			"F, N, Mis"		"MDS, CMML"																																p.1015_1022del		Atlas-Indel,Pindel	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.3043_3064del						.																																			SO:0001589	frameshift_variant	171023	exon12			.	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3044_3065delAGGCTGACACTAGAGAAGCTGC	chr20.hg19:g.31023559_31023580delAGGCTGACACTAGAGAAGCTGC	ENSP00000364839:p.Glu1015fs	75.0	0.0		59.0	24.0	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Frame_Shift_Del	DEL	ENST00000375687.4	hg19	CCDS13201.1																																																																																			.	.		0.518	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		-	31023580	AGGCTGACACTAGAGAAGCTGC	-	31023559	7	5	73	1	0	1	0	1	0	0	0	0	1066	304	11	0	3100	0	ASXL1	20	31023559	Frame_Shift_Del	DEL	AGGCTGACACTAGAGAAGCTGC	TCGA-CC-A7IH-01A-11D-A33K-10	284953	31023559	32001961	606	9932										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33324500	33324500	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aaagtacgccttacctggtcTggcaacagaggcctgcagtg	12	11	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:33324500T>A	ENST00000374796.2	-	13	8526	c.5956A>T	c.(5956-5958)Aga>Tga	p.R1986*	NCOA6_ENST00000359003.2_Nonsense_Mutation_p.R1986*			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1986	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						TTACCTGGTCTGGCAACAGAG	0.453																																					p.R1986X		Atlas-SNP	.											.	NCOA6	219	.	0			c.A5956T						.						93	82	86					20																	33324500		2203	4300	6503	SO:0001587	stop_gained	23054	exon12			CTGGTCTGGCAAC	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.5956A>T	chr20.hg19:g.33324500T>A	ENSP00000363929:p.Arg1986*	146.0	0.0		123.0	54.0	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Nonsense_Mutation	SNP	ENST00000374796.2	hg19	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	57	29.943585	0.99976	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	.	.	.	5.82	4.72	0.59763	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.0306	8.9205	0.35607	0.0:0.084:0.0:0.916	.	.	.	.	X	1986	.	ENSP00000351894:R1986X	R	-	1	2	NCOA6	32788161	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	2.001000	0.40825	2.232000	0.73038	0.482000	0.46254	AGA	.	.		0.453	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		A	33324500	T	A	33324500	4	1	73	1	0	0	0	0	0	1	0	0	10242	1588	55	4	251	4	NCOA6	20	33324500	Nonsense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	2300941	33324500	29701020	607	9933										
RBM12	10137	hgsc.bcm.edu	37	chr20	34242510	34242510	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acaggtggcggattcaagggCggcatgcccgacatgggtgg	18	9	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:34242510C>T	ENST00000374114.3	-	3	998	c.735G>A	c.(733-735)ccG>ccA	p.P245P	CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317677.5_5'Flank|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000317619.3_Intron|RBM12_ENST00000374104.3_Silent_p.P245P|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000359646.1_Silent_p.P245P|CPNE1_ENST00000352393.4_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	245	Pro-rich.					nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			GATTCAAGGGCGGCATGCCCG	0.552																																					p.P245P		Atlas-SNP	.											RBM12,NS,carcinoma,0,1	RBM12	93	.	0			c.G735A						.						73	72	72					20																	34242510		2203	4300	6503	SO:0001819	synonymous_variant	10137	exon2			CAAGGGCGGCATG	AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"RNA binding motif (RRM) containing"	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.735G>A	chr20.hg19:g.34242510C>T		81.0	2.0		72.0	26.0	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Silent	SNP	ENST00000374114.3	hg19	CCDS13261.1																																																																																			.	.		0.552	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		T	34242510	C	T	34242510	2	4	73	1	0	0	0	0	0	0	0	1	13128	755	27	1		1	RBM12	20	34242510	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	918010	34242510	28783010	608	9934										
RBL1	5933	hgsc.bcm.edu	37	chr20	35632146	35632146	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cttgtacagcagagcgcttcTtggtgtaaggcctgacccat	11	11	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:35632146T>A	ENST00000373664.3	-	21	3061	c.2995A>T	c.(2995-2997)Aga>Tga	p.R999*	RBL1_ENST00000344359.3_Nonsense_Mutation_p.R999*	NM_002895.2	NP_002886.2	P28749	RBL1_HUMAN	retinoblastoma-like 1	999					chromatin modification (GO:0016568)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(7)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	42		Myeloproliferative disorder(115;0.00878)				AGAGCGCTTCTTGGTGTAAGG	0.453																																					p.R999X		Atlas-SNP	.											.	RBL1	114	.	0			c.A2995T						.						136	127	130					20																	35632146		2203	4300	6503	SO:0001587	stop_gained	5933	exon21			CGCTTCTTGGTGT	L14812	CCDS13289.1, CCDS13290.1	20q11.23	2014-03-11	2014-03-11		ENSG00000080839	ENSG00000080839			9893	protein-coding gene	gene with protein product		116957				1833063	Standard	NM_183404		Approved	p107, cp107, PRB1	uc002xgi.3	P28749	OTTHUMG00000032406	ENST00000373664.3:c.2995A>T	chr20.hg19:g.35632146T>A	ENSP00000362768:p.Arg999*	213.0	0.0		228.0	97.0	NM_183404	A8K2W5|Q4VXA0|Q8N5K6|Q9H1L5|Q9H1M1	Nonsense_Mutation	SNP	ENST00000373664.3	hg19	CCDS13289.1	.	.	.	.	.	.	.	.	.	.	T	38	7.228267	0.98150	.	.	ENSG00000080839	ENST00000373664;ENST00000344359	.	.	.	5.04	3.92	0.45320	.	0.401929	0.25651	N	0.029218	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.8928	6.6761	0.23095	0.0:0.0875:0.261:0.6515	.	.	.	.	X	999	.	ENSP00000343646:R999X	R	-	1	2	RBL1	35065560	0.238000	0.23825	1.000000	0.80357	0.984000	0.73092	1.003000	0.29809	0.927000	0.37143	0.528000	0.53228	AGA	.	.		0.453	RBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079067.2	NM_002895		A	35632146	T	A	35632146	4	1	73	1	0	0	0	0	0	1	0	0	13124	1617	56	4	228	4	RBL1	20	35632146	Nonsense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1389636	35632146	27393374	609	9935										
WFDC3	140686	hgsc.bcm.edu	37	chr20	44405762	44405762	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gccacagccggtgctgcagcAtttatgcccctggggacagg	14	13	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:44405762A>T	ENST00000243938.4	-	5	528	c.445T>A	c.(445-447)Tgc>Agc	p.C149S	WFDC3_ENST00000372632.2_Intron|RNU6ATAC38P_ENST00000408119.1_RNA|WFDC3_ENST00000481847.1_Intron|WFDC3_ENST00000372630.2_Intron	NM_080614.1	NP_542181.1	Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3	149	WAP 3. {ECO:0000255|PROSITE- ProRule:PRU00722}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				GTGCTGCAGCATTTATGCCCC	0.547																																					p.C149S		Atlas-SNP	.											.	WFDC3	18	.	0			c.T445A						.						71	57	62					20																	44405762		2203	4300	6503	SO:0001583	missense	140686	exon5			TGCAGCATTTATG	AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116		"WAP four-disulfide core domain containing"	15957	protein-coding gene	gene with protein product						12206714, 10680116	Standard	NM_080614		Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000243938.4:c.445T>A	chr20.hg19:g.44405762A>T	ENSP00000243938:p.Cys149Ser	190.0	0.0		151.0	62.0	NM_080614	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	Missense_Mutation	SNP	ENST00000243938.4	hg19	CCDS33478.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.5|21.5	4.152045|4.152045	0.78001|0.78001	.|.	.|.	ENSG00000124116|ENSG00000124116	ENST00000243938|ENST00000337205	D|.	0.99239|.	-5.61|.	4.62|4.62	4.62|4.62	0.57501|0.57501	Whey acidic protein, 4-disulphide core (4);|.	0.000000|.	0.44097|.	D|.	0.000482|.	D|D	0.86372|0.86372	0.5917|0.5917	H|H	0.96833|0.96833	3.89|3.89	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	D|D	0.89494|0.89494	0.3759|0.3759	10|5	0.87932|.	D|.	0|.	-9.9257|-9.9257	10.6189|10.6189	0.45467|0.45467	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	149|.	Q8IUB2|.	WFDC3_HUMAN|.	S|K	149|142	ENSP00000243938:C149S|.	ENSP00000243938:C149S|.	C|N	-|-	1|3	0|2	WFDC3|WFDC3	43839169|43839169	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.991000|0.991000	0.79684|0.79684	3.903000|3.903000	0.56318|0.56318	2.096000|2.096000	0.63516|0.63516	0.533000|0.533000	0.62120|0.62120	TGC|AAT	.	.		0.547	WFDC3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316858.1			T	44405762	A	T	44405762	3	4	73	1	0	0	0	0	1	0	0	0	17368	217	8	4	262	4	WFDC3	20	44405762	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	8773616	44405762	18619758	610	9936										
WFDC3	140686	hgsc.bcm.edu	37	chr20	44418554	44418554	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atgttctcctgcagttatccAggattccagagacccaagag	9	11	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:44418554A>T	ENST00000243938.4	-	2	144	c.61T>A	c.(61-63)Tgg>Agg	p.W21R	WFDC3_ENST00000372632.2_Missense_Mutation_p.W21R|DNTTIP1_ENST00000372622.3_5'Flank|WFDC3_ENST00000481847.1_Intron|WFDC3_ENST00000372630.2_Missense_Mutation_p.W21R	NM_080614.1	NP_542181.1	Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3	21						extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				GCAGTTATCCAGGATTCCAGA	0.488																																					p.W21R		Atlas-SNP	.											.	WFDC3	18	.	0			c.T61A						.						116	98	104					20																	44418554		2203	4300	6503	SO:0001583	missense	140686	exon2			TTATCCAGGATTC	AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116		"WAP four-disulfide core domain containing"	15957	protein-coding gene	gene with protein product						12206714, 10680116	Standard	NM_080614		Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000243938.4:c.61T>A	chr20.hg19:g.44418554A>T	ENSP00000243938:p.Trp21Arg	115.0	0.0		66.0	20.0	NM_080614	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	Missense_Mutation	SNP	ENST00000243938.4	hg19	CCDS33478.1	.	.	.	.	.	.	.	.	.	.	A	13.49	2.253518	0.39797	.	.	ENSG00000124116	ENST00000243938;ENST00000372630;ENST00000372632	T;T;T	0.25085	1.82;1.94;1.91	4.13	3.02	0.34903	Whey acidic protein, 4-disulphide core (1);	0.000000	0.36034	N	0.002827	T	0.18467	0.0443	L	0.48877	1.53	0.24784	N	0.992799	P	0.41673	0.759	B	0.35899	0.213	T	0.12268	-1.0554	10	0.48119	T	0.1	-19.2611	6.9637	0.24611	0.7969:0.0:0.0:0.2031	.	21	Q8IUB2	WFDC3_HUMAN	R	21	ENSP00000243938:W21R;ENSP00000361713:W21R;ENSP00000361715:W21R	ENSP00000243938:W21R	W	-	1	0	WFDC3	43851961	0.956000	0.32656	0.994000	0.49952	0.782000	0.44232	1.869000	0.39519	0.913000	0.36797	0.533000	0.62120	TGG	.	.		0.488	WFDC3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316858.1			T	44418554	A	T	44418554	3	4	73	1	0	0	0	0	1	0	0	0	17368	188	7	4	658	4	WFDC3	20	44418554	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	12792	44418554	18606966	611	9937										
ZNF334	55713	hgsc.bcm.edu	37	chr20	45130946	45130946	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cattcgtaaggcttctccccTgtgtgtgacctgaaatgttc	9	11	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:45130946T>A	ENST00000347606.4	-	5	1214	c.1032A>T	c.(1030-1032)acA>acT	p.T344T	ZNF334_ENST00000457685.2_Silent_p.T306T|ZNF334_ENST00000593880.1_Silent_p.T367T	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	344					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				GCTTCTCCCCTGTGTGTGACC	0.438																																					p.T344T		Atlas-SNP	.											.	ZNF334	101	.	0			c.A1032T						.						158	162	161					20																	45130946		2203	4300	6503	SO:0001819	synonymous_variant	55713	exon5			CTCCCCTGTGTGT	AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"Zinc fingers, C2H2-type", "-"	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.1032A>T	chr20.hg19:g.45130946T>A		107.0	0.0		97.0	40.0	NM_018102	Q5T6U2|Q9NVW4	Silent	SNP	ENST00000347606.4	hg19	CCDS33480.1																																																																																			.	.		0.438	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			A	45130946	T	A	45130946	2	1	73	1	0	0	0	0	0	0	0	1	17866	1567	55	4		4	ZNF334	20	45130946	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	712392	45130946	17894574	612	9938										
PSMA7	5688	hgsc.bcm.edu	37	chr20	60718284	60718284	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cgcggtcgagcccttcttgaCggcctcctgcgcgtactcca	11	17	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:60718284C>G	ENST00000370873.4	-	1	202	c.76G>C	c.(76-78)Gtc>Ctc	p.V26L	SS18L1_ENST00000421564.1_5'Flank|SS18L1_ENST00000331758.3_5'Flank|PSMA7_ENST00000370858.3_Missense_Mutation_p.V26L|PSMA7_ENST00000370861.1_5'Flank|PSMA7_ENST00000484488.1_5'UTR	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 7	26					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	identical protein binding (GO:0042802)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|lung(2)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			CCCTTCTTGACGGCCTCCTGC	0.766																																					p.V26L		Atlas-SNP	.											.	PSMA7	13	.	0			c.G76C						.						6	7	7					20																	60718284		2122	4182	6304	SO:0001583	missense	5688	exon1			TCTTGACGGCCTC	AF022815	CCDS13489.1	20q13.33	2008-07-02			ENSG00000101182	ENSG00000101182		"Proteasome (prosome, macropain) subunits"	9536	protein-coding gene	gene with protein product	"proteasome subunit XAPC7", "proteasome subunit RC6-1"	606607				8764072	Standard	NM_002792		Approved	XAPC7, C6, HSPC, RC6-1	uc002ybx.2	O14818	OTTHUMG00000032895	ENST00000370873.4:c.76G>C	chr20.hg19:g.60718284C>G	ENSP00000359910:p.Val26Leu	9.0	0.0		18.0	14.0	NM_002792	B2R515|Q5JXJ2|Q9BR53|Q9H4K5|Q9UEU8	Missense_Mutation	SNP	ENST00000370873.4	hg19	CCDS13489.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427494	0.62733	.	.	ENSG00000101182	ENST00000370873;ENST00000370858	T;T	0.26957	1.7;1.7	4.66	0.327	0.15913	.	0.080710	0.48767	U	0.000161	T	0.64238	0.2580	H	0.99922	4.955	0.45962	D	0.998784	D	0.76494	0.999	D	0.75484	0.986	T	0.58423	-0.7639	10	0.72032	D	0.01	.	3.6509	0.08203	0.1367:0.58:0.1322:0.1512	.	26	O14818	PSA7_HUMAN	L	26	ENSP00000359910:V26L;ENSP00000359895:V26L	ENSP00000359895:V26L	V	-	1	0	PSMA7	60151679	1.000000	0.71417	0.006000	0.13384	0.004000	0.04260	4.785000	0.62418	-0.176000	0.10707	-1.368000	0.01194	GTC	.	.		0.766	PSMA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079975.1	NM_002792		G	60718284	C	G	60718284	3	3	73	1	0	0	0	0	1	0	0	0	12684	536	19	4	698	4	PSMA7	20	60718284	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	15587338	60718284	2307236	613	9939										
PSMA7	5688	hgsc.bcm.edu	37	chr20	60718296	60718296	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cttcttgacggcctcctgcgCgtactccacttggaagaggt	11	13	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:60718296C>A	ENST00000370873.4	-	1	190	c.64G>T	c.(64-66)Gcg>Tcg	p.A22S	SS18L1_ENST00000421564.1_5'Flank|SS18L1_ENST00000331758.3_5'Flank|PSMA7_ENST00000370858.3_Missense_Mutation_p.A22S|PSMA7_ENST00000370861.1_5'Flank|PSMA7_ENST00000484488.1_5'UTR	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 7	22					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	identical protein binding (GO:0042802)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|lung(2)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			GCCTCCTGCGCGTACTCCACT	0.751																																					p.A22S		Atlas-SNP	.											.	PSMA7	13	.	0			c.G64T						.						8	9	9					20																	60718296		2158	4227	6385	SO:0001583	missense	5688	exon1			CCTGCGCGTACTC	AF022815	CCDS13489.1	20q13.33	2008-07-02			ENSG00000101182	ENSG00000101182		"Proteasome (prosome, macropain) subunits"	9536	protein-coding gene	gene with protein product	"proteasome subunit XAPC7", "proteasome subunit RC6-1"	606607				8764072	Standard	NM_002792		Approved	XAPC7, C6, HSPC, RC6-1	uc002ybx.2	O14818	OTTHUMG00000032895	ENST00000370873.4:c.64G>T	chr20.hg19:g.60718296C>A	ENSP00000359910:p.Ala22Ser	11.0	0.0		16.0	12.0	NM_002792	B2R515|Q5JXJ2|Q9BR53|Q9H4K5|Q9UEU8	Missense_Mutation	SNP	ENST00000370873.4	hg19	CCDS13489.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558143	0.65538	.	.	ENSG00000101182	ENST00000370873;ENST00000370858	T;T	0.57273	0.41;0.41	4.84	1.81	0.25067	Proteasome, alpha-subunit, conserved site (3);	0.000000	0.64402	U	0.000001	T	0.73745	0.3626	M	0.93808	3.46	0.44694	D	0.997681	D	0.67145	0.996	D	0.71870	0.975	T	0.72250	-0.4348	10	0.87932	D	0	.	6.6484	0.22949	0.145:0.6986:0.0:0.1564	.	22	O14818	PSA7_HUMAN	S	22	ENSP00000359910:A22S;ENSP00000359895:A22S	ENSP00000359895:A22S	A	-	1	0	PSMA7	60151691	1.000000	0.71417	0.022000	0.16811	0.005000	0.04900	4.707000	0.61852	0.119000	0.18210	-0.443000	0.05667	GCG	.	.		0.751	PSMA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079975.1	NM_002792		A	60718296	C	A	60718296	3	1	73	1	0	0	0	0	1	0	0	0	12684	768	27	1	710	1	PSMA7	20	60718296	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	12	60718296	2307224	614	9940										
COL20A1	57642	hgsc.bcm.edu	37	chr20	61947981	61947981	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ggcgtggccatggagccctcTgccttcggtgggaccccgac	15	15	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:61947981T>C	ENST00000358894.6	+	21	2701	c.2601T>C	c.(2599-2601)tcT>tcC	p.S867S	COL20A1_ENST00000326996.6_Silent_p.S867S|COL20A1_ENST00000422202.1_Silent_p.S874S|COL20A1_ENST00000435874.1_Silent_p.S874S	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	867	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					TGGAGCCCTCTGCCTTCGGTG	0.642																																					p.S867S		Atlas-SNP	.											.	COL20A1	137	.	0			c.T2601C						.						29	32	31					20																	61947981		2024	4154	6178	SO:0001819	synonymous_variant	57642	exon21			GCCCTCTGCCTTC	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.2601T>C	chr20.hg19:g.61947981T>C		77.0	0.0		38.0	16.0	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Silent	SNP	ENST00000358894.6	hg19	CCDS46628.1																																																																																			.	.		0.642	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		C	61947981	T	C	61947981	2	2	73	1	0	0	0	0	0	0	0	1	3681	1567	55	2		2	COL20A1	20	61947981	Silent	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	1229685	61947981	1077539	615	9941										
PRIC285	85441	hgsc.bcm.edu	37	chr20	62203527	62203527	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctcccagggcagggcctggTcgaaggccaccatctgtgcg	15	14	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:62203527T>A	ENST00000467148.1	-	1	281	c.212A>T	c.(211-213)gAc>gTc	p.D71V	HELZ2_ENST00000479540.1_5'UTR	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	71					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CAGGGCCTGGTCGAAGGCCAC	0.642																																					p.D71V		Atlas-SNP	.											.	.	.	.	0			c.A212T						.						36	31	33					20																	62203527		2184	4294	6478	SO:0001583	missense	85441	exon2			GCCTGGTCGAAGG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.212A>T	chr20.hg19:g.62203527T>A	ENSP00000417401:p.Asp71Val	79.0	0.0		83.0	23.0	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.494512	0.26774	.	.	ENSG00000130589	ENST00000467148	T	0.02472	4.28	3.91	2.8	0.32819	.	0.328568	0.28952	U	0.013616	T	0.12220	0.0297	M	0.79475	2.455	0.51767	D	0.999932	D;D	0.89917	1.0;0.967	D;P	0.70016	0.967;0.622	T	0.00205	-1.1922	10	0.87932	D	0	-21.1577	8.9447	0.35751	0.0:0.0908:0.0:0.9092	.	71;71	Q4VXQ0;Q9BYK8	.;PR285_HUMAN	V	71	ENSP00000417401:D71V	ENSP00000417401:D71V	D	-	2	0	RP4-697K14.7	61673971	1.000000	0.71417	0.138000	0.22173	0.002000	0.02628	3.195000	0.51013	0.409000	0.25649	0.533000	0.62120	GAC	.	.		0.642	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		A	62203527	T	A	62203527	3	1	73	1	0	0	0	0	1	0	0	0	12497	1667	58	4	7836	4	PRIC285	20	62203527	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	255546	62203527	821993	616	9942										
ZGPAT	84619	hgsc.bcm.edu	37	chr20	62366141	62366141	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cacgcgaggtataggctccaGactcctcaccaagatgggct	11	13	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr20:62366141G>T	ENST00000328969.5	+	5	1143	c.1016G>T	c.(1015-1017)aGa>aTa	p.R339I	RP4-583P15.15_ENST00000490623.2_Missense_Mutation_p.D225Y|ZGPAT_ENST00000357119.4_Missense_Mutation_p.R310I|LIME1_ENST00000309546.3_5'Flank|ZGPAT_ENST00000478385.1_3'UTR|ZGPAT_ENST00000369967.3_Missense_Mutation_p.R319I|ZGPAT_ENST00000448100.2_Missense_Mutation_p.R319I|ZGPAT_ENST00000355969.6_Missense_Mutation_p.R319I	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	339	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					ATAGGCTCCAGACTCCTCACC	0.597																																					p.R339I		Atlas-SNP	.											.	ZGPAT	57	.	0			c.G1016T						.						90	74	79					20																	62366141		2203	4300	6503	SO:0001583	missense	84619	exon5			GCTCCAGACTCCT	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"Zinc fingers, CCCH-type domain containing", "G patch domain containing"	15948	protein-coding gene	gene with protein product			"KIAA1847"	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.1016G>T	chr20.hg19:g.62366141G>T	ENSP00000332013:p.Arg339Ile	88.0	0.0		94.0	35.0	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Missense_Mutation	SNP	ENST00000328969.5	hg19	CCDS13534.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290266	0.59976	.	.	ENSG00000197114	ENST00000448100;ENST00000355969;ENST00000357119;ENST00000369967;ENST00000328969	T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23	5.06	-0.654	0.11443	D111/G-patch (3);	0.196141	0.52532	D	0.000076	T	0.48241	0.1489	M	0.75447	2.3	0.47037	D	0.999299	P;D;P	0.60575	0.875;0.988;0.938	P;P;P	0.57846	0.571;0.828;0.555	T	0.50759	-0.8790	10	0.87932	D	0	-10.9626	8.9195	0.35604	0.7729:0.0:0.2271:0.0	.	310;339;319	Q8N5A5-3;Q8N5A5;Q8N5A5-2	.;ZGPAT_HUMAN;.	I	319;319;310;319;339	ENSP00000391176:R319I;ENSP00000348242:R319I;ENSP00000349634:R310I;ENSP00000358984:R319I;ENSP00000332013:R339I	ENSP00000332013:R339I	R	+	2	0	ZGPAT	61836585	0.999000	0.42202	0.598000	0.28837	0.983000	0.72400	2.479000	0.45197	0.014000	0.14944	0.563000	0.77884	AGA	.	.		0.597	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		T	62366141	G	T	62366141	3	4	73	1	0	0	0	0	1	0	0	0	17689	942	33	3	1030	3	ZGPAT	20	62366141	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	162614	62366141	659379	617	9943										
HSPA13	6782	hgsc.bcm.edu	37	chr21	15746215	15746215	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gctgaatgggtaccagtattTtctgaaagaggtcttcatta	10	6	3	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr21:15746215T>G	ENST00000285667.3	-	5	1206	c.1139A>C	c.(1138-1140)aAa>aCa	p.K380T	HSPA13_ENST00000544452.1_Missense_Mutation_p.K172T	NM_006948.4	NP_008879.3	P48723	HSP13_HUMAN	heat shock protein 70kDa family, member 13	380						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						TACCAGTATTTTCTGAAAGAG	0.418																																					p.K380T		Atlas-SNP	.											.	HSPA13	44	.	0			c.A1139C						.						147	159	155					21																	15746215		2203	4300	6503	SO:0001583	missense	6782	exon5			AGTATTTTCTGAA		CCDS13567.1	21q11.1	2011-09-02	2008-06-17	2008-06-17	ENSG00000155304	ENSG00000155304		"Heat shock proteins / HSP70"	11375	protein-coding gene	gene with protein product		601100	"stress 70 protein chaperone, microsome-associated, 60kD", "stress 70 protein chaperone, microsome-associated, 60kDa"	STCH		8825657	Standard	NM_006948		Approved		uc002yjt.3	P48723	OTTHUMG00000074261	ENST00000285667.3:c.1139A>C	chr21.hg19:g.15746215T>G	ENSP00000285667:p.Lys380Thr	153.0	0.0		149.0	71.0	NM_006948	B2R616|Q8NE40	Missense_Mutation	SNP	ENST00000285667.3	hg19	CCDS13567.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.993556	0.54041	.	.	ENSG00000155304	ENST00000285667;ENST00000544452	T;T	0.01119	5.31;5.31	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.08980	0.0222	M	0.88031	2.925	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.04678	-1.0934	10	0.38643	T	0.18	-25.6802	16.215	0.82206	0.0:0.0:0.0:1.0	.	380	P48723	HSP13_HUMAN	T	380;172	ENSP00000285667:K380T;ENSP00000441986:K172T	ENSP00000285667:K380T	K	-	2	0	HSPA13	14668086	1.000000	0.71417	1.000000	0.80357	0.106000	0.19336	6.295000	0.72744	2.288000	0.76882	0.533000	0.62120	AAA	.	.		0.418	HSPA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157815.1			G	15746215	T	G	15746215	3	3	73	1	0	0	0	0	1	0	0	0	7415	1841	64	5	280	5	HSPA13	21	15746215	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10		15746215	32383680	618	9944										
CCT8	10694	hgsc.bcm.edu	37	chr21	30437364	30437364	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tctttgacagatgttacatcAccttcggtttccttcttaaa	5	10	3	2	rs143385323		TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr21:30437364A>C	ENST00000286788.4	-	7	893	c.687T>G	c.(685-687)ggT>ggG	p.G229G	CCT8_ENST00000470450.1_5'UTR|CCT8_ENST00000540844.1_Silent_p.G156G|CCT8_ENST00000542732.1_Silent_p.G210G	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	229					'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						ATGTTACATCACCTTCGGTTT	0.388																																					p.G229G		Atlas-SNP	.											.	CCT8	38	.	0			c.T687G						.						173	157	162					21																	30437364		2203	4300	6503	SO:0001819	synonymous_variant	10694	exon7			TACATCACCTTCG	Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"Heat Shock Proteins / Chaperonins"	1623	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 112"	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595	ENST00000286788.4:c.687T>G	chr21.hg19:g.30437364A>C		90.0	0.0		75.0	38.0	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Silent	SNP	ENST00000286788.4	hg19	CCDS33528.1																																																																																			.	A|0.999;G|0.001		0.388	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1			C	30437364	A	C	30437364	2	2	73	1	0	0	0	0	0	0	0	1	2962	146	6	5		5	CCT8	21	30437364	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	14691149	30437364	17692531	619	9945										
IFNAR1	3454	hgsc.bcm.edu	37	chr21	34715660	34715660	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctggaacaaaagatagtgttAtgtgggctttggatggttta	13	3	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr21:34715660A>T	ENST00000270139.3	+	4	615	c.463A>T	c.(463-465)Atg>Ttg	p.M155L	IFNAR1_ENST00000442357.2_Missense_Mutation_p.M155L|IFNAR1_ENST00000416947.2_Missense_Mutation_p.M86L	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	155	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""Interferon Alfa-2a(DB00034)|""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"	AGATAGTGTTATGTGGGCTTT	0.358																																					p.M155L	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											.	IFNAR1	44	.	0			c.A463T						.						170	173	172					21																	34715660		2203	4300	6503	SO:0001583	missense	3454	exon4			AGTGTTATGTGGG		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"Interferons"	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.463A>T	chr21.hg19:g.34715660A>T	ENSP00000270139:p.Met155Leu	98.0	0.0		113.0	48.0	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Missense_Mutation	SNP	ENST00000270139.3	hg19	CCDS13624.1	.	.	.	.	.	.	.	.	.	.	A	10.71	1.427283	0.25726	.	.	ENSG00000142166	ENST00000416947;ENST00000270139;ENST00000442357	T;T;T	0.27104	1.69;1.69;1.69	5.86	4.64	0.57946	Fibronectin, type III (2);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	0.388090	0.33364	N	0.005000	T	0.22551	0.0544	M	0.64997	1.995	0.35502	D	0.799853	P	0.36874	0.572	B	0.31751	0.135	T	0.27262	-1.0079	10	0.33940	T	0.23	-20.2627	8.6037	0.33760	0.8294:0.0:0.0:0.1705	.	155	P17181	INAR1_HUMAN	L	86;155;155	ENSP00000395606:M86L;ENSP00000270139:M155L;ENSP00000407406:M155L	ENSP00000270139:M155L	M	+	1	0	IFNAR1	33637530	0.941000	0.31946	0.927000	0.36925	0.090000	0.18270	1.975000	0.40569	2.237000	0.73441	0.528000	0.53228	ATG	.	.		0.358	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4			T	34715660	A	T	34715660	3	4	73	1	0	0	0	0	1	0	0	0	7553	449	16	4	477	4	IFNAR1	21	34715660	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	4278296	34715660	13414235	620	9946										
UMODL1	89766	hgsc.bcm.edu	37	chr21	43496123	43496123	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcctctttcagaaaaaggccTctccctgttgggctaccagc	9	14	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr21:43496123T>A	ENST00000408910.2	+	2	86	c.86T>A	c.(85-87)cTc>cAc	p.L29H	UMODL1_ENST00000400427.1_5'UTR|UMODL1_ENST00000400424.2_5'UTR|UMODL1_ENST00000408989.2_Missense_Mutation_p.L29H	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	29					adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						GAAAAAGGCCTCTCCCTGTTG	0.577																																					p.L29H	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.T86A						.						128	139	135					21																	43496123		2048	4192	6240	SO:0001583	missense	89766	exon2			AAGGCCTCTCCCT		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.86T>A	chr21.hg19:g.43496123T>A	ENSP00000386147:p.Leu29His	131.0	0.0		92.0	34.0	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	hg19	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	T	15.91	2.971243	0.53614	.	.	ENSG00000177398	ENST00000408989;ENST00000408910	D;D	0.81996	-1.56;-1.53	4.44	3.31	0.37934	.	0.000000	0.40554	N	0.001070	T	0.81875	0.4915	N	0.19112	0.55	0.44946	D	0.997961	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.82230	-0.0560	10	0.87932	D	0	-32.1966	7.4516	0.27242	0.0:0.1031:0.0:0.8969	.	29;29	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	H	29	ENSP00000386126:L29H;ENSP00000386147:L29H	ENSP00000386147:L29H	L	+	2	0	UMODL1	42369192	1.000000	0.71417	0.967000	0.41034	0.496000	0.33645	3.115000	0.50391	1.939000	0.56221	0.533000	0.62120	CTC	.	.		0.577	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			A	43496123	T	A	43496123	3	1	73	1	0	0	0	0	1	0	0	0	16995	1551	54	4	92	4	UMODL1	21	43496123	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	8780463	43496123	4633772	621	9947										
TRPM2	7226	hgsc.bcm.edu	37	chr21	45811258	45811258	+	Frame_Shift_Del	DEL	C	C	-													0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gcagctgaaggagtttgtcaCctgggacaccttgctctacc							TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr21:45811258delC	ENST00000397928.1	+	11	1989	c.1544delC	c.(1543-1545)accfs	p.T515fs	TRPM2_ENST00000300481.9_Frame_Shift_Del_p.T515fs|TRPM2_ENST00000300482.5_Frame_Shift_Del_p.T515fs|TRPM2_ENST00000397932.2_Frame_Shift_Del_p.T515fs|TRPM2_ENST00000498430.1_3'UTR	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	515					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GAGTTTGTCACCTGGGACACC	0.582																																					p.T515fs		Pindel	.											.	TRPM2	196	.	0			c.1543delA						.						155	113	127					21																	45811258		2203	4300	6503	SO:0001589	frameshift_variant	7226	exon11			.	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.1544delC	chr21.hg19:g.45811258delC	ENSP00000381023:p.Thr515fs	140.0	0.0		98.0	29.0	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Frame_Shift_Del	DEL	ENST00000397928.1	hg19	CCDS13710.1																																																																																			.	.		0.582	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		-	45811258	C	-	45811258	7	5	73	1	0	1	0	1	0	0	0	0	16601	507	18	0	1586	0	TRPM2	21	45811258	Frame_Shift_Del	DEL	C	TCGA-CC-A7IH-01A-11D-A33K-10	2315135	45811258	2318637	622	9948										
ARVCF	421	hgsc.bcm.edu	37	chr22	19969151	19969151	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aatgccggtccagggcaccaTctgcaaaagggcctagtggg	14	11	1	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr22:19969151T>C	ENST00000263207.3	-	5	770	c.479A>G	c.(478-480)gAt>gGt	p.D160G	ARVCF_ENST00000487793.1_5'UTR|ARVCF_ENST00000344269.3_Missense_Mutation_p.D97G|ARVCF_ENST00000406259.1_Missense_Mutation_p.D160G|ARVCF_ENST00000406522.1_Missense_Mutation_p.D97G|ARVCF_ENST00000401994.1_Missense_Mutation_p.D97G	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	160					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CAGGGCACCATCTGCAAAAGG	0.662																																					p.D160G		Atlas-SNP	.											.	ARVCF	54	.	0			c.A479G						.						32	39	36					22																	19969151		2174	4253	6427	SO:0001583	missense	421	exon5			GCACCATCTGCAA		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"Armadillo repeat containing"	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.479A>G	chr22.hg19:g.19969151T>C	ENSP00000263207:p.Asp160Gly	44.0	0.0		38.0	19.0	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	hg19	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.471749	0.63737	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47	4.43	4.43	0.53597	.	3.396280	0.03899	N	0.279958	T	0.51449	0.1675	L	0.41236	1.265	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.07908	-1.0748	9	.	.	.	-14.2188	14.1392	0.65308	0.0:0.0:0.0:1.0	.	160	O00192	ARVC_HUMAN	G	160;97;97;97;160	ENSP00000263207:D160G;ENSP00000342042:D97G;ENSP00000384341:D97G;ENSP00000384732:D97G;ENSP00000385444:D160G	.	D	-	2	0	ARVCF	18349151	1.000000	0.71417	0.930000	0.37139	0.841000	0.47740	7.263000	0.78421	1.984000	0.57885	0.450000	0.29827	GAT	.	.		0.662	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		C	19969151	T	C	19969151	3	2	73	1	0	0	0	0	1	0	0	0	1003	1435	50	2	2469	2	ARVCF	22	19969151	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10		19969151	31335415	623	9949										
HPS4	89781	hgsc.bcm.edu	37	chr22	26860234	26860234	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agagggtctgctctgggaatGggggcttggctgctatggcc	18	8	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr22:26860234G>C	ENST00000398145.2	-	11	1978	c.1362C>G	c.(1360-1362)ccC>ccG	p.P454P	HPS4_ENST00000493455.2_5'Flank|HPS4_ENST00000402105.3_Silent_p.P449P|HPS4_ENST00000336873.5_Silent_p.P454P|HPS4_ENST00000398141.1_Silent_p.P467P	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	454					blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						CTCTGGGAATGGGGGCTTGGC	0.607									Hermansky-Pudlak syndrome																												p.P454P		Atlas-SNP	.											.	HPS4	123	.	0			c.C1362G						.						113	112	113					22																	26860234		2203	4300	6503	SO:0001819	synonymous_variant	89781	exon11	Familial Cancer Database	HPS, HPS1-8	GGGAATGGGGGCT		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099			15844	protein-coding gene	gene with protein product		606682				11836498, 12663659	Standard	NM_022081		Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.1362C>G	chr22.hg19:g.26860234G>C		82.0	0.0		52.0	20.0	NM_022081	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Silent	SNP	ENST00000398145.2	hg19	CCDS13835.1																																																																																			.	.		0.607	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081		C	26860234	G	C	26860234	2	2	73	1	0	0	0	0	0	0	0	1	7350	1335	47	4		4	HPS4	22	26860234	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	6891083	26860234	24444332	624	9950										
PLA2G3	50487	hgsc.bcm.edu	37	chr22	31533830	31533830	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	accctttctgatgtggtggcCccttccgaaggtgctgcttc	11	13	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr22:31533830C>A	ENST00000215885.3	-	4	1184	c.932G>T	c.(931-933)gGg>gTg	p.G311V		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	311					acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						ATGTGGTGGCCCCTTCCGAAG	0.647																																					p.G311V		Atlas-SNP	.											.	PLA2G3	85	.	0			c.G932T						.						102	113	109					22																	31533830		2203	4300	6503	SO:0001583	missense	50487	exon4			GGTGGCCCCTTCC	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.932G>T	chr22.hg19:g.31533830C>A	ENSP00000215885:p.Gly311Val	144.0	0.0		90.0	37.0	NM_015715	O95768	Missense_Mutation	SNP	ENST00000215885.3	hg19	CCDS13889.1	.	.	.	.	.	.	.	.	.	.	C	5.061	0.196859	0.09599	.	.	ENSG00000100078	ENST00000215885	T	0.11169	2.8	4.16	3.11	0.35812	.	1.421980	0.04002	N	0.296604	T	0.07638	0.0192	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32214	-0.9915	10	0.27785	T	0.31	-0.2407	11.2433	0.48982	0.0:0.8136:0.1864:0.0	.	311	Q9NZ20	PA2G3_HUMAN	V	311	ENSP00000215885:G311V	ENSP00000215885:G311V	G	-	2	0	PLA2G3	29863830	0.000000	0.05858	0.023000	0.16930	0.005000	0.04900	0.613000	0.24299	1.050000	0.40346	0.655000	0.94253	GGG	.	.		0.647	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715		A	31533830	C	A	31533830	3	1	73	1	0	0	0	0	1	0	0	0	12009	623	22	3	613	3	PLA2G3	22	31533830	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	4673596	31533830	19770736	625	9951										
RFPL2	10739	hgsc.bcm.edu	37	chr22	32586882	32586882	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gccaaaaatgggcgcaatggCtcctcagcagatacgctcct	10	13	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr22:32586882C>T	ENST00000400237.1	-	5	1949	c.1014G>A	c.(1012-1014)gaG>gaA	p.E338E	RFPL2_ENST00000489846.1_5'UTR|RFPL2_ENST00000400236.3_Silent_p.E248E|RFPL2_ENST00000248980.4_Silent_p.E277E|RFPL2_ENST00000248983.4_Silent_p.E248E			O75678	RFPL2_HUMAN	ret finger protein-like 2	338	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	21						GGCGCAATGGCTCCTCAGCAG	0.473																																					p.E338E		Atlas-SNP	.											.	RFPL2	81	.	0			c.G1014A						.						50	73	65					22																	32586882		2203	4299	6502	SO:0001819	synonymous_variant	10739	exon5			CAATGGCTCCTCA	AJ010231	CCDS43009.1, CCDS46694.1, CCDS43009.2	22q12.3	2008-06-12				ENSG00000128253		"RING-type (C3HC4) zinc fingers"	9979	protein-coding gene	gene with protein product		605969				10508838	Standard	NM_001098527		Approved	RNF79	uc003amg.3	O75678		ENST00000400237.1:c.1014G>A	chr22.hg19:g.32586882C>T		250.0	1.0		264.0	116.0	NM_001098527		Silent	SNP	ENST00000400237.1	hg19	CCDS43009.2																																																																																			.	.		0.473	RFPL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075262.2	NM_006605		T	32586882	C	T	32586882	2	4	73	1	0	0	0	0	0	0	0	1	13269	796	28	3		3	RFPL2	22	32586882	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	1053052	32586882	18717684	626	9952										
ENTHD1	150350	hgsc.bcm.edu	37	chr22	40257983	40257983	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atccatcagcaatgtgatgaCttgcttagatttttcccgga	8	9	1	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr22:40257983C>A	ENST00000325157.6	-	3	629	c.379G>T	c.(379-381)Gtc>Ttc	p.V127F		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	127	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.									breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					AATGTGATGACTTGCTTAGAT	0.363																																					p.V127F		Atlas-SNP	.											.	ENTHD1	83	.	0			c.G379T						.						58	50	53					22																	40257983		2203	4300	6503	SO:0001583	missense	150350	exon3			TGATGACTTGCTT	AK093154	CCDS13998.1	22q13.1	2006-06-26			ENSG00000176177	ENSG00000176177			26352	protein-coding gene	gene with protein product						12477932	Standard	NM_152512		Approved	FLJ25421	uc003ayg.3	Q8IYW4	OTTHUMG00000151098	ENST00000325157.6:c.379G>T	chr22.hg19:g.40257983C>A	ENSP00000317431:p.Val127Phe	209.0	0.0		194.0	81.0	NM_152512	B0QYD5|Q5H9F7|Q96LK3	Missense_Mutation	SNP	ENST00000325157.6	hg19	CCDS13998.1	.	.	.	.	.	.	.	.	.	.	C	19.16	3.773075	0.69992	.	.	ENSG00000176177	ENST00000325157	T	0.50001	0.76	6.17	1.65	0.23941	Epsin domain, N-terminal (1);ENTH/VHS (2);Epsin-like, N-terminal (2);	0.351702	0.25164	N	0.032645	T	0.55305	0.1912	M	0.75777	2.31	0.40263	D	0.978202	P	0.46656	0.882	P	0.53146	0.719	T	0.58819	-0.7569	10	0.87932	D	0	-3.336	6.8145	0.23822	0.0:0.5406:0.3319:0.1275	.	127	Q8IYW4	ENTD1_HUMAN	F	127	ENSP00000317431:V127F	ENSP00000317431:V127F	V	-	1	0	ENTHD1	38587929	0.995000	0.38212	0.999000	0.59377	0.823000	0.46562	0.046000	0.14035	0.874000	0.35823	0.655000	0.94253	GTC	.	.		0.363	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512		A	40257983	C	A	40257983	3	1	73	1	0	0	0	0	1	0	0	0	5139	565	20	3	1464	3	ENTHD1	22	40257983	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	7671101	40257983	11046583	627	9953										
TNRC6B	23112	hgsc.bcm.edu	37	chr22	40708962	40708962	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctggtgcctggccctacagtGcctctgacaactcctttacc	8	16	1	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr22:40708962G>T	ENST00000454349.2	+	19	4850	c.4639G>T	c.(4639-4641)Gcc>Tcc	p.A1547S	TNRC6B_ENST00000301923.9_Missense_Mutation_p.A743S|TNRC6B_ENST00000335727.9_Missense_Mutation_p.A1437S|TNRC6B_ENST00000402203.1_Missense_Mutation_p.A743S	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	1547	Silencing domain; interaction with CNOT1 and PAN3.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						GCCCTACAGTGCCTCTGACAA	0.428																																					p.A1547S		Atlas-SNP	.											.	TNRC6B	195	.	0			c.G4639T						.						93	87	89					22																	40708962		2002	4169	6171	SO:0001583	missense	23112	exon19			TACAGTGCCTCTG	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.4639G>T	chr22.hg19:g.40708962G>T	ENSP00000401946:p.Ala1547Ser	110.0	0.0		106.0	39.0	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Missense_Mutation	SNP	ENST00000454349.2	hg19	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286900	0.80803	.	.	ENSG00000100354	ENST00000301923;ENST00000402203;ENST00000454349;ENST00000400140;ENST00000335727	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.50616	0.1626	L	0.31752	0.955	0.80722	D	1	D;D;D;D	0.76494	0.995;0.999;0.999;0.996	D;D;D;D	0.80764	0.978;0.987;0.994;0.987	T	0.28681	-1.0036	10	0.07030	T	0.85	-7.5731	19.516	0.95165	0.0:0.0:1.0:0.0	.	1547;1437;1437;743	Q9UPQ9;A8MYY3;Q9UPQ9-1;Q9UPQ9-2	TNR6B_HUMAN;.;.;.	S	743;743;1547;1437;1437	ENSP00000306759:A743S;ENSP00000384795:A743S;ENSP00000401946:A1547S;ENSP00000338371:A1437S	ENSP00000306759:A743S	A	+	1	0	TNRC6B	39038908	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.361000	0.97122	2.623000	0.88846	0.655000	0.94253	GCC	.	.		0.428	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				T	40708962	G	T	40708962	3	4	73	1	0	0	0	0	1	0	0	0	16356	1319	46	3	4834	3	TNRC6B	22	40708962	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	450979	40708962	10595604	628	9954										
FBLN1	2192	hgsc.bcm.edu	37	chr22	45970507	45970507	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caccgtcatctcgctgcctaCcttccgcgagttcacccgcc	7	20	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr22:45970507C>T	ENST00000327858.6	+	15	1909	c.1814C>T	c.(1813-1815)aCc>aTc	p.T605I	FBLN1_ENST00000348697.2_Intron	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	605					embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TCGCTGCCTACCTTCCGCGAG	0.647																																					p.T605I		Atlas-SNP	.											.	FBLN1	143	.	0			c.C1814T						.						170	96	121					22																	45970507		2203	4300	6503	SO:0001583	missense	2192	exon15			TGCCTACCTTCCG		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1814C>T	chr22.hg19:g.45970507C>T	ENSP00000331544:p.Thr605Ile	82.0	0.0		57.0	22.0	NM_006486	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	hg19	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434874	0.83885	.	.	ENSG00000077942	ENST00000327858	D	0.83837	-1.77	5.12	5.12	0.69794	.	0.247951	0.39834	N	0.001258	D	0.86485	0.5944	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.86268	0.1659	10	0.41790	T	0.15	.	16.3351	0.83056	0.0:1.0:0.0:0.0	.	605	P23142	FBLN1_HUMAN	I	605	ENSP00000331544:T605I	ENSP00000331544:T605I	T	+	2	0	FBLN1	44349171	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.453000	0.73488	2.371000	0.80710	0.563000	0.77884	ACC	.	.		0.647	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		T	45970507	C	T	45970507	3	4	73	1	0	0	0	0	1	0	0	0	5706	507	18	3	2352	3	FBLN1	22	45970507	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	5261545	45970507	5334059	629	9955										
GTSE1	51512	hgsc.bcm.edu	37	chr22	46719148	46719148	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cagcggccgcagtcgtgcacGtcagttggcaggtgagtgac	16	11	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr22:46719148G>T	ENST00000454366.1	+	8	1706	c.1494G>T	c.(1492-1494)acG>acT	p.T498T		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	479					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		AGTCGTGCACGTCAGTTGGCA	0.542																																					p.T498T	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.G1494T						.						144	146	145					22																	46719148		2203	4300	6503	SO:0001819	synonymous_variant	51512	exon8			GTGCACGTCAGTT	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1494G>T	chr22.hg19:g.46719148G>T		82.0	0.0		57.0	23.0	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	hg19	CCDS14074.2																																																																																			.	.		0.542	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		T	46719148	G	T	46719148	2	4	73	1	0	0	0	0	0	0	0	1	6894	1132	40	1		1	GTSE1	22	46719148	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	748641	46719148	4585418	630	9956										
MOV10L1	54456	hgsc.bcm.edu	37	chr22	50580530	50580530	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aataggaaaacaatgacggaCcaagctgagcatggaacaga	11	7	0	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr22:50580530C>T	ENST00000262794.5	+	16	2174	c.2091C>T	c.(2089-2091)gaC>gaT	p.D697D	MOV10L1_ENST00000540615.1_Silent_p.D677D|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Silent_p.D697D|MOV10L1_ENST00000395858.3_Silent_p.D697D	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	697					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		CAATGACGGACCAAGCTGAGC	0.453																																					p.D697D		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C2091T						.						93	82	86					22																	50580530		2203	4300	6503	SO:0001819	synonymous_variant	54456	exon16			GACGGACCAAGCT	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2091C>T	chr22.hg19:g.50580530C>T		85.0	0.0		79.0	37.0	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	hg19	CCDS14084.1																																																																																			.	.		0.453	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50580530	C	T	50580530	2	4	73	1	0	0	0	0	0	0	0	1	9728	506	18	3		3	MOV10L1	22	50580530	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	3861382	50580530	724036	631	9957										
ACR	49	hgsc.bcm.edu	37	chr22	51178223	51178223	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	agagagatatgtggagaaaaTcatcattcatgaaaaataca	8	4	3	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chr22:51178223T>C	ENST00000216139.5	+	3	423	c.383T>C	c.(382-384)aTc>aCc	p.I128T	AC002056.5_ENST00000532913.1_RNA|AC000036.4_ENST00000449652.1_RNA|ACR_ENST00000529621.1_Missense_Mutation_p.I128T	NM_001097.2	NP_001088.2	P10323	ACRO_HUMAN	acrosin	128	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acrosome matrix dispersal (GO:0002077)|acrosome reaction (GO:0007340)|activation of adenylate cyclase activity (GO:0007190)|binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|response to steroid hormone (GO:0048545)|single fertilization (GO:0007338)	acrosomal matrix (GO:0043159)|extracellular region (GO:0005576)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|protein complex (GO:0043234)	amidase activity (GO:0004040)|copper ion binding (GO:0005507)|DNA binding (GO:0003677)|drug binding (GO:0008144)|fucose binding (GO:0042806)|mannose binding (GO:0005537)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	7		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)		GTGGAGAAAATCATCATTCAT	0.473																																					p.I128T		Atlas-SNP	.											.	ACR	28	.	0			c.T383C						.						81	87	85					22																	51178223		2203	4300	6503	SO:0001583	missense	49	exon3			AGAAAATCATCAT	CR456366	CCDS14101.1	22q13.33	2012-10-23	2012-10-23		ENSG00000100312	ENSG00000100312	3.4.21.10		126	protein-coding gene	gene with protein product	"preproacrosin", "acrosin light and heavy chain prepropeptide"	102480				2298447, 12398221	Standard	NM_001097		Approved		uc003bnh.4	P10323	OTTHUMG00000150155	ENST00000216139.5:c.383T>C	chr22.hg19:g.51178223T>C	ENSP00000216139:p.Ile128Thr	156.0	0.0		126.0	58.0	NM_001097	Q6ICK2	Missense_Mutation	SNP	ENST00000216139.5	hg19	CCDS14101.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.724271	0.48728	.	.	ENSG00000100312	ENST00000216139;ENST00000529621	D;D	0.90004	-2.6;-2.6	4.52	4.52	0.55395	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.39985	N	0.001219	D	0.91855	0.7422	L	0.51853	1.615	0.36578	D	0.873397	D;D	0.89917	0.997;1.0	D;D	0.81914	0.978;0.995	D	0.94054	0.7320	10	0.87932	D	0	-25.7551	12.1301	0.53938	0.0:0.0:0.0:1.0	.	128;128	E9PLV5;P10323	.;ACRO_HUMAN	T	128	ENSP00000216139:I128T;ENSP00000435120:I128T	ENSP00000216139:I128T	I	+	2	0	ACR	49525089	0.202000	0.23423	0.779000	0.31741	0.393000	0.30537	3.915000	0.56409	2.043000	0.60533	0.374000	0.22700	ATC	.	.		0.473	ACR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000316605.2	NM_001097		C	51178223	T	C	51178223	3	2	73	1	0	0	0	0	1	0	0	0	169	1435	50	2	393	2	ACR	22	51178223	Missense_Mutation	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	597693	51178223	126343	632	9958										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	6069058	6069058	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tcttccgtgggcacgtagatGtttaagtaaaggcagtcttc	11	8	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:6069058G>T	ENST00000381095.3	-	2	1077	c.450C>A	c.(448-450)aaC>aaA	p.N150K	NLGN4X_ENST00000275857.6_Missense_Mutation_p.N150K|NLGN4X_ENST00000469740.1_5'UTR|NLGN4X_ENST00000381093.2_Missense_Mutation_p.N150K|NLGN4X_ENST00000381092.1_Missense_Mutation_p.N150K|NLGN4X_ENST00000538097.1_Missense_Mutation_p.N150K	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	150					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						GCACGTAGATGTTTAAGTAAA	0.423																																					p.N150K		Atlas-SNP	.											.	NLGN4X	191	.	0			c.C450A						.						134	114	121					X																	6069058		2203	4300	6503	SO:0001583	missense	57502	exon2			GTAGATGTTTAAG	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.450C>A	chrX.hg19:g.6069058G>T	ENSP00000370485:p.Asn150Lys	74.0	0.0		51.0	41.0	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.504444	0.64410	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74	4.08	2.27	0.28462	Carboxylesterase type B, conserved site (1);Carboxylesterase, type B (1);	.	.	.	.	D	0.93874	0.8040	H	0.99668	4.69	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.994;1.0;0.995	D	0.90293	0.4324	9	0.87932	D	0	.	4.8961	0.13751	0.4897:0.0:0.5103:0.0	.	150;150;150	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	K	150	ENSP00000370485:N150K;ENSP00000370483:N150K;ENSP00000275857:N150K;ENSP00000370482:N150K;ENSP00000439203:N150K	ENSP00000275857:N150K	N	-	3	2	NLGN4X	6079058	1.000000	0.71417	0.962000	0.40283	0.962000	0.63368	1.917000	0.39996	0.582000	0.29556	0.594000	0.82650	AAC	.	.		0.423	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		T	6069058	G	T	6069058	3	4	73	1	0	0	0	0	1	0	0	0	10473	1368	48	3	2020	3	NLGN4X	23	6069058	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10		6069058	149201502	633	9959										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23397834	23397834	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tagtgcacgtcctggaagagCtaaagaatgctcgggccacc	12	11	0	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:23397834C>T	ENST00000379361.4	+	2	1338	c.478C>T	c.(478-480)Cta>Tta	p.L160L		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	160					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						CCTGGAAGAGCTAAAGAATGC	0.468																																					p.L160L		Atlas-SNP	.											.	PTCHD1	213	.	0			c.C478T						.						99	85	89					X																	23397834		2203	4300	6503	SO:0001819	synonymous_variant	139411	exon2			GAAGAGCTAAAGA	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.478C>T	chrX.hg19:g.23397834C>T		358.0	0.0		242.0	204.0	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Silent	SNP	ENST00000379361.4	hg19	CCDS35215.2																																																																																			.	.		0.468	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		T	23397834	C	T	23397834	2	4	73	1	0	0	0	0	0	0	0	1	12744	796	28	3		3	PTCHD1	23	23397834	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	17328776	23397834	131872726	634	9960										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24383280	24383280	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aagctgcaactgcaaccgcaGtggcagccaaagccacggca	11	14	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:24383280G>T								AC004552.1 (16257 upstream) : PDK3 (100057 downstream)																							tgcaaccgcagtggcagccaa	0.637																																					p.Q801H		Atlas-SNP	.											.	.	.	.	0			c.G2403T						.						4	7	6					X																	24383280		1344	3106	4450	SO:0001628	intergenic_variant	100130302	exon1			ACCGCAGTGGCAG																													chrX.hg19:g.24383280G>T		121.0	1.0		77.0	66.0	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.637									T	24383280	G	T	24383280	1	4	73	0	1	0	0	0	0	0	0	0	5581	1020	36	3		3	FAM48B1	23	24383280	IGR	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	985446	24383280	130887280	635	9961										
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49143177	49143177	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gccgggacagaagcccagatAgaggtcaccagtgagtgggc	16	10	1	4			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:49143177A>G	ENST00000055335.6	+	4	2041	c.2025A>G	c.(2023-2025)atA>atG	p.I675M	PPP1R3F_ENST00000495799.1_Missense_Mutation_p.I329M|PPP1R3F_ENST00000376188.1_Missense_Mutation_p.I329M|PPP1R3F_ENST00000466508.1_Missense_Mutation_p.I329M|PPP1R3F_ENST00000438316.1_Missense_Mutation_p.I346M	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	675					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					AAGCCCAGATAGAGGTCACCA	0.592																																					p.I675M		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.A2025G						.						47	32	37					X																	49143177		2202	4299	6501	SO:0001583	missense	89801	exon4			CCAGATAGAGGTC		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14944	protein-coding gene	gene with protein product			"protein phosphatase 1, regulatory (inhibitor) subunit 3F"			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.2025A>G	chrX.hg19:g.49143177A>G	ENSP00000055335:p.Ile675Met	134.0	0.0		115.0	99.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	hg19	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.035642	0.00040	.	.	ENSG00000049769	ENST00000466508;ENST00000438316;ENST00000055335;ENST00000495799;ENST00000376188	T;T;T;T;T	0.53206	1.06;1.05;0.63;1.06;1.06	4.8	1.92	0.25849	.	0.639785	0.15112	N	0.279920	T	0.14013	0.0339	N	0.01352	-0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33085	-0.9882	10	0.02654	T	1	-3.8068	5.6646	0.17689	0.3537:0.0:0.6463:0.0	.	346;360;675	F5H262;A2VDJ8;Q6ZSY5	.;.;PPR3F_HUMAN	M	329;346;675;329;329	ENSP00000420687:I329M;ENSP00000415548:I346M;ENSP00000055335:I675M;ENSP00000417535:I329M;ENSP00000365359:I329M	ENSP00000055335:I675M	I	+	3	3	PPP1R3F	49030121	.	.	0.074000	0.20217	0.375000	0.29983	.	.	0.520000	0.28426	-0.383000	0.06682	ATA	.	.		0.592	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		G	49143177	A	G	49143177	3	3	73	1	0	0	0	0	1	0	0	0	12387	410	15	2	2039	2	PPP1R3F	23	49143177	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	24759897	49143177	106127383	636	9962										
APEX2	27301	hgsc.bcm.edu	37	chrX	55033578	55033578	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cactgatgagcgccctcatgAccccgaagactccagaagag	10	14	1	6			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:55033578A>T	ENST00000374987.3	+	6	1333	c.1267A>T	c.(1267-1269)Acc>Tcc	p.T423S	ALAS2_ENST00000498636.1_5'Flank	NM_014481.2	NP_055296.2	Q9UBZ4	APEX2_HUMAN	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	423					base-excision repair (GO:0006284)|cell cycle (GO:0007049)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1)	21						CGCCCTCATGACCCCGAAGAC	0.547								Other BER factors																													p.T423S		Atlas-SNP	.											.	APEX2	50	.	0			c.A1267T						.						53	47	49					X																	55033578		2203	4300	6503	SO:0001583	missense	27301	exon6			CTCATGACCCCGA	AB021260	CCDS14365.1	Xp11.23	2014-02-18			ENSG00000169188	ENSG00000169188	4.2.99.18		17889	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 2"	300773				11376153	Standard	NM_014481		Approved	APEXL2, APE2, XTH2, ZGRF2	uc004dtz.4	Q9UBZ4	OTTHUMG00000021642	ENST00000374987.3:c.1267A>T	chrX.hg19:g.55033578A>T	ENSP00000364126:p.Thr423Ser	124.0	0.0		86.0	62.0	NM_014481	Q9Y5X7	Missense_Mutation	SNP	ENST00000374987.3	hg19	CCDS14365.1	.	.	.	.	.	.	.	.	.	.	A	0.485	-0.877881	0.02550	.	.	ENSG00000169188	ENST00000374987	T	0.59364	0.27	4.46	1.76	0.24704	.	0.831979	0.11053	N	0.604765	T	0.40297	0.1111	L	0.38838	1.175	0.09310	N	1	B	0.16166	0.016	B	0.09377	0.004	T	0.23119	-1.0197	10	0.15066	T	0.55	-3.4926	5.0712	0.14608	0.6345:0.1841:0.0:0.1813	.	423	Q9UBZ4	APEX2_HUMAN	S	423	ENSP00000364126:T423S	ENSP00000364126:T423S	T	+	1	0	APEX2	55050303	0.000000	0.05858	0.002000	0.10522	0.018000	0.09664	0.544000	0.23253	0.621000	0.30232	-0.527000	0.04329	ACC	.	.		0.547	APEX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056845.1			T	55033578	A	T	55033578	3	4	73	1	0	0	0	0	1	0	0	0	770	275	10	4	1289	4	APEX2	23	55033578	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	5890401	55033578	100236982	637	9963										
KIF4A	24137	hgsc.bcm.edu	37	chrX	69572476	69572476	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	actgttgcttgcatggctgcAgccattgatactgcggtgga	13	9	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:69572476A>G	ENST00000374403.3	+	14	1540	c.1458A>G	c.(1456-1458)gcA>gcG	p.A486A	KIF4A_ENST00000374388.3_Silent_p.A486A	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	486					anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						GCATGGCTGCAGCCATTGATA	0.418																																					p.A486A		Atlas-SNP	.											.	KIF4A	118	.	0			c.A1458G						.						97	87	90					X																	69572476		2203	4300	6503	SO:0001819	synonymous_variant	24137	exon14			GGCTGCAGCCATT	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"Kinesins"	13339	protein-coding gene	gene with protein product	"chromokinesin"	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1458A>G	chrX.hg19:g.69572476A>G		104.0	0.0		152.0	77.0	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Silent	SNP	ENST00000374403.3	hg19	CCDS14401.1																																																																																			.	.		0.418	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310		G	69572476	A	G	69572476	2	3	73	1	0	0	0	0	0	0	0	1	8312	175	7	2		2	KIF4A	23	69572476	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	14538898	69572476	85698084	638	9964										
TEX11	56159	hgsc.bcm.edu	37	chrX	69772028	69772028	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aatagccccaaacttcttccAggggacagagctctacattc	7	13	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:69772028A>T	ENST00000395889.2	-	29	2668	c.2513T>A	c.(2512-2514)cTg>cAg	p.L838Q	TEX11_ENST00000374320.2_Missense_Mutation_p.L513Q|TEX11_ENST00000374333.2_Missense_Mutation_p.L823Q|TEX11_ENST00000344304.3_Missense_Mutation_p.L838Q	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	838					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					AACTTCTTCCAGGGGACAGAG	0.403																																					p.L838Q		Atlas-SNP	.											.	TEX11	132	.	0			c.T2513A						.						80	71	74					X																	69772028		2203	4300	6503	SO:0001583	missense	56159	exon29			TCTTCCAGGGGAC	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.2513T>A	chrX.hg19:g.69772028A>T	ENSP00000379226:p.Leu838Gln	326.0	1.0		467.0	215.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	hg19	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	A	9.317	1.057101	0.19907	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	T;T;T;T	0.52295	1.23;1.24;0.67;1.24	4.96	2.52	0.30459	.	0.444700	0.20340	N	0.094244	T	0.36413	0.0966	L	0.49350	1.555	0.09310	N	1	P;P	0.46512	0.879;0.807	B;B	0.41571	0.36;0.197	T	0.23833	-1.0177	9	.	.	.	0.1952	3.4912	0.07638	0.5497:0.0:0.097:0.3532	.	823;838	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	Q	823;838;513;838	ENSP00000363453:L823Q;ENSP00000379226:L838Q;ENSP00000363440:L513Q;ENSP00000340995:L838Q	.	L	-	2	0	TEX11	69688753	0.956000	0.32656	0.006000	0.13384	0.828000	0.46876	3.147000	0.50639	0.226000	0.20979	-0.396000	0.06452	CTG	.	.		0.403	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			T	69772028	A	T	69772028	3	4	73	1	0	0	0	0	1	0	0	0	15789	188	7	4	321	4	TEX11	23	69772028	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	199552	69772028	85498532	639	9965										
P2RY10	27334	hgsc.bcm.edu	37	chrX	78216943	78216943	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	aattctttattactttatggCttcagagtttcgtgaccaac	6	8	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:78216943C>A	ENST00000171757.2	+	4	1206	c.926C>A	c.(925-927)gCt>gAt	p.A309D	P2RY10_ENST00000544091.1_Missense_Mutation_p.A309D	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2)	42						TACTTTATGGCTTCAGAGTTT	0.473																																					p.A309D		Atlas-SNP	.											.	P2RY10	99	.	0			c.C926A						.						153	140	144					X																	78216943		2203	4300	6503	SO:0001583	missense	27334	exon2			TTATGGCTTCAGA	AF000545	CCDS14442.1	Xq21.1	2012-08-23			ENSG00000078589	ENSG00000078589		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	19906	protein-coding gene	gene with protein product		300529				11004484, 9755289	Standard	NM_014499		Approved	P2Y10	uc004edf.3	O00398	OTTHUMG00000021896	ENST00000171757.2:c.926C>A	chrX.hg19:g.78216943C>A	ENSP00000171757:p.Ala309Asp	125.0	0.0		188.0	84.0	NM_198333	D3DTE5|Q4VBN7|Q86V16	Missense_Mutation	SNP	ENST00000171757.2	hg19	CCDS14442.1	.	.	.	.	.	.	.	.	.	.	C	16.92	3.255739	0.59321	.	.	ENSG00000078589	ENST00000544091;ENST00000171757	T;T	0.36340	1.26;1.26	4.99	4.99	0.66335	.	0.588494	0.17181	N	0.183871	T	0.23532	0.0569	N	0.08118	0	0.44395	D	0.9973	P	0.38020	0.615	B	0.38156	0.266	T	0.12837	-1.0532	10	0.37606	T	0.19	.	15.8593	0.79009	0.0:1.0:0.0:0.0	.	309	O00398	P2Y10_HUMAN	D	309	ENSP00000443138:A309D;ENSP00000171757:A309D	ENSP00000171757:A309D	A	+	2	0	P2RY10	78103599	0.997000	0.39634	1.000000	0.80357	0.991000	0.79684	3.518000	0.53451	2.311000	0.77944	0.597000	0.82753	GCT	.	.		0.473	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1			A	78216943	C	A	78216943	3	1	73	1	0	0	0	0	1	0	0	0	11356	797	28	3	928	3	P2RY10	23	78216943	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	8444915	78216943	77053617	640	9966										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91131828	91131828	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttgaaacaccagaaggagacAagatgccacaactgattgtt	9	8	0	5			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:91131828A>T	ENST00000373094.1	+	2	1434	c.589A>T	c.(589-591)Aag>Tag	p.K197*	PCDH11X_ENST00000373088.1_Nonsense_Mutation_p.K197*|PCDH11X_ENST00000373097.1_Nonsense_Mutation_p.K197*|PCDH11X_ENST00000406881.1_Nonsense_Mutation_p.K197*|PCDH11X_ENST00000395337.2_Nonsense_Mutation_p.K197*|PCDH11X_ENST00000298274.8_Nonsense_Mutation_p.K197*|PCDH11X_ENST00000504220.2_Nonsense_Mutation_p.K197*|PCDH11X_ENST00000361724.1_Nonsense_Mutation_p.K197*|PCDH11X_ENST00000361655.2_Nonsense_Mutation_p.K197*	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	197	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						AGAAGGAGACAAGATGCCACA	0.358																																					p.K197X	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.A589T						.						79	72	75					X																	91131828		2202	4296	6498	SO:0001587	stop_gained	27328	exon2			GGAGACAAGATGC	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.589A>T	chrX.hg19:g.91131828A>T	ENSP00000362186:p.Lys197*	333.0	1.0		554.0	238.0	NM_001168363	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Nonsense_Mutation	SNP	ENST00000373094.1	hg19	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	A	16.29	3.080250	0.55753	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	.	.	.	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.4567	0.55708	1.0:0.0:0.0:0.0	.	.	.	.	X	197	.	ENSP00000298274:K197X	K	+	1	0	PCDH11X	91018484	1.000000	0.71417	0.878000	0.34440	0.172000	0.22775	8.999000	0.93557	1.526000	0.49068	0.441000	0.28932	AAG	.	.		0.358	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		T	91131828	A	T	91131828	4	4	73	1	0	0	0	0	0	1	0	0	11517	131	5	4	595	4	PCDH11X	23	91131828	Nonsense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	12914885	91131828	64138732	641	9967										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91873264	91873264	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tttttcctcaccccaacagcTgcagaaataactgttcaacc	4	14	2	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:91873264T>A	ENST00000373094.1	+	7	4214	c.3369T>A	c.(3367-3369)gcT>gcA	p.A1123A	PCDH11X_ENST00000373088.1_Splice_Site_p.A1086A|PCDH11X_ENST00000373097.1_Splice_Site_p.A1113A|PCDH11X_ENST00000406881.1_Splice_Site_p.T1115T|PCDH11X_ENST00000298274.8_Silent_p.A1086A|PCDH11X_ENST00000504220.2_3'UTR|PCDH11X_ENST00000361655.2_Splice_Site_p.T1105T	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1123					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						CCCCAACAGCTGCAGAAATAA	0.378																																					p.A1123A	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.T3369A						.						34	28	30					X																	91873264		2201	4297	6498	SO:0001630	splice_region_variant	27328	exon7			AACAGCTGCAGAA	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3368-1T>A	chrX.hg19:g.91873264T>A		112.0	0.0		245.0	116.0	NM_032968	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Silent	SNP	ENST00000373094.1	hg19	CCDS14461.1																																																																																			.	.		0.378	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969	Silent	A	91873264	T	A	91873264	5	1	73	1	0	0	0	0	0	0	1	0	11517	1594	55	4	3517	4	PCDH11X	23	91873264	Splice_Site	SNP	T	TCGA-CC-A7IH-01A-11D-A33K-10	741436	91873264	63397296	642	9968										
COL4A6	1288	hgsc.bcm.edu	37	chrX	107464587	107464587	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	cctgttgggccttgaattccAattggtccaggtcgtcccta	10	12	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:107464587A>G	ENST00000372216.4	-	4	265	c.165T>C	c.(163-165)atT>atC	p.I55I	COL4A6_ENST00000538570.1_Silent_p.I54I|COL4A6_ENST00000545689.1_Silent_p.I54I|COL4A6_ENST00000394872.2_Silent_p.I54I|COL4A6_ENST00000334504.7_Silent_p.I54I	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	55	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						CTTGAATTCCAATTGGTCCAG	0.478									Alport syndrome with Diffuse Leiomyomatosis																												p.I55I	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.T165C						.						114	98	103					X																	107464587		2203	4300	6503	SO:0001819	synonymous_variant	1288	exon4	Familial Cancer Database		AATTCCAATTGGT	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.165T>C	chrX.hg19:g.107464587A>G		89.0	0.0		153.0	73.0	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Silent	SNP	ENST00000372216.4	hg19	CCDS14541.1																																																																																			.	.		0.478	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			G	107464587	A	G	107464587	2	3	73	1	0	0	0	0	0	0	0	1	3697	126	5	2		2	COL4A6	23	107464587	Silent	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	15591323	107464587	47805973	643	9969										
GPC4	2239	hgsc.bcm.edu	37	chrX	132458433	132458433	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	caggttcacatttcccaccaCgtagtaacgtttcaactcta	5	13	3	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:132458433C>A	ENST00000370828.3	-	3	975	c.451G>T	c.(451-453)Gtg>Ttg	p.V151L	GPC4_ENST00000535467.1_Missense_Mutation_p.V81L	NM_001448.2	NP_001439.2	O75487	GPC4_HUMAN	glypican 4	151					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					TTTCCCACCACGTAGTAACGT	0.433																																					p.V151L		Atlas-SNP	.											.	GPC4	58	.	0			c.G451T						.						173	176	175					X																	132458433		2203	4300	6503	SO:0001583	missense	2239	exon3			CCACCACGTAGTA	AF030186	CCDS14637.1	Xq26.1	2008-02-05			ENSG00000076716	ENSG00000076716		"Proteoglycans / Cell Surface : Glypicans"	4452	protein-coding gene	gene with protein product	"glypican proteoglycan 4"	300168				9787072	Standard	NM_001448		Approved	K-glypican	uc004exc.1	O75487	OTTHUMG00000022434	ENST00000370828.3:c.451G>T	chrX.hg19:g.132458433C>A	ENSP00000359864:p.Val151Leu	118.0	0.0		200.0	91.0	NM_001448	B2R6J7|B4E2C0|Q6ZMA6|Q96L43|Q9NU08|Q9UJN1|Q9UPD9	Missense_Mutation	SNP	ENST00000370828.3	hg19	CCDS14637.1	.	.	.	.	.	.	.	.	.	.	C	9.882	1.201945	0.22121	.	.	ENSG00000076716	ENST00000370828;ENST00000536418;ENST00000535467	T;T	0.46819	0.86;0.86	5.94	5.94	0.96194	.	0.398190	0.28766	N	0.014206	T	0.44644	0.1303	L	0.39898	1.24	0.39044	D	0.960181	B	0.13594	0.008	B	0.20577	0.03	T	0.33266	-0.9875	10	0.48119	T	0.1	0.1747	18.1511	0.89675	0.0:1.0:0.0:0.0	.	151	O75487	GPC4_HUMAN	L	151;149;81	ENSP00000359864:V151L;ENSP00000444959:V81L	ENSP00000359864:V151L	V	-	1	0	GPC4	132286099	0.022000	0.18835	0.880000	0.34516	0.412000	0.31113	1.003000	0.29809	2.509000	0.84616	0.529000	0.55759	GTG	.	.		0.433	GPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058338.1	NM_001448		A	132458433	C	A	132458433	3	1	73	1	0	0	0	0	1	0	0	0	6608	536	19	1	1247	1	GPC4	23	132458433	Missense_Mutation	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	24993846	132458433	22812127	644	9970										
GPR112	139378	hgsc.bcm.edu	37	chrX	135488040	135488040	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	acaatgagcctgacattcttActtggcctcacctgggggtt	10	11	2	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:135488040A>T	ENST00000394143.1	+	23	9135	c.8844A>T	c.(8842-8844)ttA>ttT	p.L2948F	GPR112_ENST00000412101.1_Missense_Mutation_p.L2743F|GPR112_ENST00000287534.4_Missense_Mutation_p.L2701F|GPR112_ENST00000370652.1_Missense_Mutation_p.L2948F|GPR112_ENST00000394141.1_Missense_Mutation_p.L2743F	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2948					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TGACATTCTTACTTGGCCTCA	0.438																																					p.L2948F		Atlas-SNP	.											.	GPR112	459	.	0			c.A8844T						.						159	141	147					X																	135488040		2203	4300	6503	SO:0001583	missense	139378	exon23			ATTCTTACTTGGC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.8844A>T	chrX.hg19:g.135488040A>T	ENSP00000377699:p.Leu2948Phe	76.0	0.0		157.0	26.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.626427	0.66901	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	4.71	-2.15	0.07102	GPCR, family 2-like (1);	.	.	.	.	D	0.84497	0.5485	H	0.96833	3.89	0.32878	D	0.510135	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.83267	-0.0045	9	0.87932	D	0	.	8.3267	0.32162	0.4221:0.1183:0.4596:0.0	.	2743;2948	Q8IZF6-3;Q8IZF6	.;GP112_HUMAN	F	2948;2948;2743;2701;2743	ENSP00000377699:L2948F;ENSP00000359686:L2948F;ENSP00000416526:L2743F;ENSP00000287534:L2701F;ENSP00000377697:L2743F	ENSP00000287534:L2701F	L	+	3	2	GPR112	135315706	0.346000	0.24844	0.978000	0.43139	0.978000	0.69477	-0.176000	0.09811	-0.441000	0.07201	-0.314000	0.08810	TTA	.	.		0.438	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			T	135488040	A	T	135488040	3	4	73	1	0	0	0	0	1	0	0	0	6637	388	14	4	8922	4	GPR112	23	135488040	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	3029607	135488040	19782520	645	9971										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140969387	140969387	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ttcatagagattctttttggCatttccctgacagaagtgga	9	7	2	3			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:140969387C>T	ENST00000298296.1	+	4	714	c.714C>T	c.(712-714)ggC>ggT	p.G238G	MAGEC3_ENST00000443323.2_Intron|MAGEC3_ENST00000448920.1_Intron|MAGEC3_ENST00000536088.1_Intron	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	238	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					TTCTTTTTGGCATTTCCCTGA	0.473																																					p.G238G		Atlas-SNP	.											.	MAGEC3	228	.	0			c.C714T						.						154	138	144					X																	140969387		2203	4300	6503	SO:0001819	synonymous_variant	139081	exon4			TTTTGGCATTTCC	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.714C>T	chrX.hg19:g.140969387C>T		89.0	0.0		141.0	60.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Silent	SNP	ENST00000298296.1	hg19	CCDS14676.1																																																																																			.	.		0.473	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		T	140969387	C	T	140969387	2	4	73	1	0	0	0	0	0	0	0	1	9191	697	25	3		3	MAGEC3	23	140969387	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	5481347	140969387	14301173	646	9972										
AFF2	2334	hgsc.bcm.edu	37	chrX	147743516	147743516	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	atttgctaactaaccattctAatcagaatcacctagtggga	6	9	3	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:147743516A>G	ENST00000370460.2	+	3	747	c.268A>G	c.(268-270)Aat>Gat	p.N90D	AFF2_ENST00000370457.5_Missense_Mutation_p.N86D|AFF2_ENST00000342251.3_Missense_Mutation_p.N86D|AFF2_ENST00000370458.1_Missense_Mutation_p.N86D	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	90					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					TAACCATTCTAATCAGAATCA	0.368																																					p.N90D		Atlas-SNP	.											.	AFF2	679	.	0			c.A268G						.						130	132	131					X																	147743516		2203	4300	6503	SO:0001583	missense	2334	exon3			CATTCTAATCAGA	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.268A>G	chrX.hg19:g.147743516A>G	ENSP00000359489:p.Asn90Asp	248.0	0.0		394.0	176.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	hg19	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.560822	0.65538	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000370458	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	5.63	5.63	0.86233	.	0.053377	0.64402	D	0.000001	T	0.60379	0.2264	L	0.39898	1.24	0.80722	D	1	P;P;P;P;P;P	0.49862	0.592;0.592;0.592;0.787;0.822;0.929	B;B;B;B;P;P	0.46419	0.322;0.322;0.322;0.322;0.451;0.516	T	0.64266	-0.6448	10	0.59425	D	0.04	.	14.8595	0.70369	1.0:0.0:0.0:0.0	.	90;86;86;86;90;86	P51816-6;P51816-3;P51816-2;P51816-5;P51816;P51816-4	.;.;.;.;AFF2_HUMAN;.	D	90;86;86;86	ENSP00000359489:N90D;ENSP00000359486:N86D;ENSP00000345459:N86D;ENSP00000359487:N86D	ENSP00000345459:N86D	N	+	1	0	AFF2	147551208	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.983000	0.93477	1.891000	0.54761	0.486000	0.48141	AAT	.	.		0.368	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		G	147743516	A	G	147743516	3	3	73	1	0	0	0	0	1	0	0	0	357	362	13	2	278	2	AFF2	23	147743516	Missense_Mutation	SNP	A	TCGA-CC-A7IH-01A-11D-A33K-10	6774129	147743516	7527044	647	9973										
EMD	2010	hgsc.bcm.edu	37	chrX	153607910	153607910	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	ctgcgccggtacaacatcccGcacgggcctgtagtaggtac	12	14	0	0			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:153607910G>T	ENST00000369842.4	+	1	354	c.66G>T	c.(64-66)ccG>ccT	p.P22P	EMD_ENST00000369835.3_Silent_p.P22P	NM_000117.2	NP_000108.1	P50402	EMD_HUMAN	emerin	22	LEM. {ECO:0000255|PROSITE- ProRule:PRU00313}.				cellular response to growth factor stimulus (GO:0071363)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fibroblast proliferation (GO:0048147)|positive regulation of protein export from nucleus (GO:0046827)|regulation of canonical Wnt signaling pathway (GO:0060828)|skeletal muscle cell differentiation (GO:0035914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	actin binding (GO:0003779)|beta-tubulin binding (GO:0048487)			lung(5)	5	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ACAACATCCCGCACGGGCCTG	0.726																																					p.P22P		Atlas-SNP	.											.	EMD	25	.	0			c.G66T						.						25	20	22					X																	153607910		2075	4069	6144	SO:0001819	synonymous_variant	2010	exon1			CATCCCGCACGGG	X82434	CCDS14745.1	Xq27.3-q28	2014-09-17	2008-07-29		ENSG00000102119	ENSG00000102119			3331	protein-coding gene	gene with protein product	"LEM domain containing 5"	300384	"Emery-Dreifuss muscular dystrophy"				Standard	NM_000117		Approved	STA, LEMD5	uc004fkl.3	P50402	OTTHUMG00000033186	ENST00000369842.4:c.66G>T	chrX.hg19:g.153607910G>T		77.0	0.0		100.0	46.0	NM_000117	Q6FI02	Silent	SNP	ENST00000369842.4	hg19	CCDS14745.1																																																																																			.	.		0.726	EMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080921.1			T	153607910	G	T	153607910	2	4	73	1	0	0	0	0	0	0	0	1	5089	1074	38	1		1	EMD	23	153607910	Silent	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	5864394	153607910	1662650	648	9974										
CTAG2	30848	hgsc.bcm.edu	37	chrX	153880820	153880820	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	gtccttcagaaccgcccctgGtcgggggagaggtgcggcat	16	12	1	2			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:153880820G>T	ENST00000247306.4	-	2	418	c.355C>A	c.(355-357)Cca>Aca	p.P119T	CTAG2_ENST00000369585.3_Missense_Mutation_p.P119T	NM_020994.3	NP_066274.2	O75638	CTAG2_HUMAN	cancer/testis antigen 2	119						centrosome (GO:0005813)				central_nervous_system(1)|endometrium(1)|lung(6)|ovary(1)|pancreas(1)	10	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ACCGCCCCTGGTCGGGGGAGA	0.647																																					p.P119T		Atlas-SNP	.											.	CTAG2	88	.	0			c.C355A						.						48	47	47					X																	153880820		2203	4298	6501	SO:0001583	missense	30848	exon2			CCCCTGGTCGGGG	AJ012833	CCDS14759.1, CCDS35455.1	Xq28	2009-08-18			ENSG00000126890	ENSG00000126890			2492	protein-coding gene	gene with protein product	"CTL-recognized antigen on melanoma", "LAGE-1a protein", "cancer/testis antigen family 6, member 2a", "cancer/testis antigen family 6, member 2b"	300396				9626360, 10399963	Standard	NM_020994		Approved	LAGE-1, CAMEL, LAGE1, ESO2, MGC3803, MGC138724, CT6.2a, CT6.2b, LAGE-1a, LAGE-1b	uc004fmi.2	O75638	OTTHUMG00000024239	ENST00000247306.4:c.355C>A	chrX.hg19:g.153880820G>T	ENSP00000247306:p.Pro119Thr	134.0	0.0		178.0	88.0	NM_020994	O75637|Q0VIL6|Q14CD6|Q2Z1N4|Q9BU80|Q9UJ89|Q9Y479	Missense_Mutation	SNP	ENST00000247306.4	hg19	CCDS14759.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.570117	0.28003	.	.	ENSG00000126890	ENST00000247306;ENST00000369585;ENST00000454505	T;T	0.31247	1.5;1.5	1.59	1.59	0.23543	.	.	.	.	.	T	0.22126	0.0533	L	0.51422	1.61	0.09310	N	1	P;P	0.47350	0.894;0.689	B;B	0.32762	0.152;0.065	T	0.17653	-1.0362	9	0.72032	D	0.01	1.1791	8.7212	0.34441	0.0:0.0:1.0:0.0	.	119;119	O75638;O75638-2	CTAG2_HUMAN;.	T	119;119;61	ENSP00000247306:P119T;ENSP00000358598:P119T	ENSP00000247306:P119T	P	-	1	0	CTAG2	153534014	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.804000	0.27098	1.110000	0.41699	0.377000	0.23210	CCA	.	.		0.647	CTAG2-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061176.1	NM_020994		T	153880820	G	T	153880820	3	4	73	1	0	0	0	0	1	0	0	0	3993	1261	44	3	420	3	CTAG2	23	153880820	Missense_Mutation	SNP	G	TCGA-CC-A7IH-01A-11D-A33K-10	272910	153880820	1389740	649	9975										
VBP1	7411	hgsc.bcm.edu	37	chrX	154444801	154444801	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0292307692307692	19	1	1.25420569987888	1.36253115843792	1.19861763561832	0.293305800181552	0.979516806722687	0	tgtggcaaaggagaaatggcCacagggaatgggcggcggct	18	7	0	1			TCGA-CC-A7IH-01A-11D-A33K-10	TCGA-CC-A7IH-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d3ad3bc-b5be-4233-a04b-909afa0302cf	aa24c0b3-7197-431d-b840-98fb061c54f6	g.chrX:154444801C>G	ENST00000286428.5	+	1	159	c.42C>G	c.(40-42)gcC>gcG	p.A14A	VBP1_ENST00000535916.1_Intron	NM_003372.5	NP_003363.1	P61758	PFD3_HUMAN	von Hippel-Lindau binding protein 1	14					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)				NS(1)|endometrium(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GAGAAATGGCCACAGGGAATG	0.642																																					p.A14A		Atlas-SNP	.											.	VBP1	20	.	0			c.C42G						.						46	34	38					X																	154444801		2154	4200	6354	SO:0001819	synonymous_variant	7411	exon1			AATGGCCACAGGG	U56833	CCDS14765.1	Xq28	2008-07-07			ENSG00000155959	ENSG00000155959			12662	protein-coding gene	gene with protein product	"prefoldin 3"	300133				8674032, 9339366	Standard	NM_003372		Approved	PFD3, PFDN3	uc004fnc.3	P61758	OTTHUMG00000022666	ENST00000286428.5:c.42C>G	chrX.hg19:g.154444801C>G		69.0	0.0		130.0	72.0	NM_003372	B2R8L5|O55228|Q15765|Q5JT81|Q86X96	Silent	SNP	ENST00000286428.5	hg19	CCDS14765.1																																																																																			.	.		0.642	VBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058806.1			G	154444801	C	G	154444801	2	3	73	1	0	0	0	0	0	0	0	1	17151	581	21	4		4	VBP1	23	154444801	Silent	SNP	C	TCGA-CC-A7IH-01A-11D-A33K-10	563981	154444801	825759	650	9976										
PRAMEF17	391004	hgsc.bcm.edu	37	chr1	13716967	13716967	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agcccttgaaggtgttcataGacctctgccaaaaggaaagt	10	9	2	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:13716967G>T	ENST00000376098.4	+	2	480	c.454G>T	c.(454-456)Gac>Tac	p.D152Y		NM_001099851.1	NP_001093321.1	Q5VTA0	PRA17_HUMAN	PRAME family member 17	152					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					kidney(1)|lung(2)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GGTGTTCATAGACCTCTGCCA	0.537																																					p.D152Y		Atlas-SNP	.											PRAMEF17,right_upper_lobe,carcinoma,0,1	PRAMEF17	12	.	0			c.G454T						.						39	47	44					1																	13716967		2122	4224	6346	SO:0001583	missense	391004	exon2			TTCATAGACCTCT		CCDS41264.1	1p36.21	2013-01-17			ENSG00000204479	ENSG00000204479		"-"	29485	protein-coding gene	gene with protein product							Standard	NM_001099851		Approved	OTTHUMG00000007909	uc009vnz.1	Q5VTA0	OTTHUMG00000007909	ENST00000376098.4:c.454G>T	chr1.hg19:g.13716967G>T	ENSP00000365266:p.Asp152Tyr	209.0	0.0		212.0	96.0	NM_001099851	B2RUU4	Missense_Mutation	SNP	ENST00000376098.4	hg19	CCDS41264.1	.	.	.	.	.	.	.	.	.	.	G	8.520	0.868451	0.17322	.	.	ENSG00000204479	ENST00000376098	T	0.44881	0.91	1.09	0.124	0.14714	.	0.377307	0.21405	N	0.075061	T	0.61899	0.2384	M	0.92026	3.265	0.09310	N	1	D	0.69078	0.997	D	0.68192	0.956	T	0.52442	-0.8575	10	0.87932	D	0	.	3.641	0.08166	0.2714:0.0:0.7286:0.0	.	152	Q5VTA0	PRA17_HUMAN	Y	152	ENSP00000365266:D152Y	ENSP00000365266:D152Y	D	+	1	0	PRAMEF17	13589554	0.004000	0.15560	0.004000	0.12327	0.006000	0.05464	0.457000	0.21875	0.047000	0.15862	-0.391000	0.06502	GAC	.	.		0.537	PRAMEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021780.2	NM_001099851		T	13716967	G	T	13716967	3	4	74	1	0	0	0	0	1	0	0	0	12444	942	33	3	460	3	PRAMEF17	1	13716967	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10		13716967	235533654	1	9977										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22172730	22172730	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cggggacacatggtgcagccGcagccgtgagccgcgggtct	17	13	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:22172730G>A	ENST00000374695.3	-	64	8414	c.8335C>T	c.(8335-8337)Cgg>Tgg	p.R2779W	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2779	Ig-like C2-type 13.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGGTGCAGCCGCAGCCGTGAG	0.642																																					p.R2779W		Atlas-SNP	.											.	HSPG2	311	.	0			c.C8335T						.						14	17	16					1																	22172730		2182	4258	6440	SO:0001583	missense	3339	exon64			GCAGCCGCAGCCG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.8335C>T	chr1.hg19:g.22172730G>A	ENSP00000363827:p.Arg2779Trp	76.0	0.0		104.0	5.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.162458	0.38217	.	.	ENSG00000142798	ENST00000374695;ENST00000453796	T;T	0.69306	-0.39;-0.39	5.22	0.337	0.15966	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.259363	0.20276	N	0.095560	T	0.82010	0.4944	M	0.86502	2.82	0.37636	D	0.921858	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.989	D	0.85944	0.1460	10	0.72032	D	0.01	.	14.1814	0.65577	0.0:0.0:0.5057:0.4943	.	719;2779	Q59EG0;P98160	.;PGBM_HUMAN	W	2779;194	ENSP00000363827:R2779W;ENSP00000396310:R194W	ENSP00000363827:R2779W	R	-	1	2	HSPG2	22045317	0.998000	0.40836	0.267000	0.24556	0.085000	0.17905	1.384000	0.34396	0.165000	0.19558	0.561000	0.74099	CGG	.	.		0.642	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22172730	G	A	22172730	3	1	74	1	0	0	0	0	1	0	0	0	7439	1086	38	1	4976	1	HSPG2	1	22172730	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	8455763	22172730	227077891	2	9978										
CELA3B	23436	hgsc.bcm.edu	37	chr1	22304871	22304871	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ctcccctctagcctcaggctAtggcccaccttcctctcgcc	6	21	3	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:22304871A>G	ENST00000337107.6	+	2	72	c.53A>G	c.(52-54)tAt>tGt	p.Y18C	RN7SL421P_ENST00000582599.1_RNA	NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	18					cholesterol metabolic process (GO:0008203)|proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			breast(2)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						GCCTCAGGCTATGGCCCACCT	0.617																																					p.Y18C		Atlas-SNP	.											.	CELA3B	24	.	0			c.A53G						.						147	95	113					1																	22304871		2203	4300	6503	SO:0001583	missense	23436	exon2			CAGGCTATGGCCC	M18692	CCDS219.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000219073	ENSG00000219073	3.4.21.70		15945	protein-coding gene	gene with protein product	"proteinase E", "elastase 1", "cholesterol-binding pancreatic protease", "pancreatic endopeptidase E"		"elastase 3B, pancreatic"	ELA3B		2826474, 2460440	Standard	NM_007352		Approved	CBPP	uc001bfk.3	P08861	OTTHUMG00000002758	ENST00000337107.6:c.53A>G	chr1.hg19:g.22304871A>G	ENSP00000338369:p.Tyr18Cys	102.0	0.0		108.0	42.0	NM_007352	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	Missense_Mutation	SNP	ENST00000337107.6	hg19	CCDS219.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.219679	0.00286	.	.	ENSG00000219073	ENST00000337107;ENST00000374666	D;D	0.87491	-2.26;-1.97	4.87	-0.968	0.10313	Peptidase cysteine/serine, trypsin-like (1);	0.351400	0.33290	N	0.005062	T	0.43612	0.1255	N	0.00089	-2.185	0.23689	N	0.997105	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.59532	-0.7437	10	0.02654	T	1	-3.9411	2.807	0.05430	0.1603:0.2802:0.4313:0.1282	.	18;18	B1AQ52;P08861	.;CEL3B_HUMAN	C	18;34	ENSP00000338369:Y18C;ENSP00000363798:Y34C	ENSP00000338369:Y18C	Y	+	2	0	CELA3B	22177458	1.000000	0.71417	0.549000	0.28204	0.008000	0.06430	3.343000	0.52167	-0.445000	0.07159	-1.080000	0.02220	TAT	.	.		0.617	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007797.1	NM_007352		G	22304871	A	G	22304871	3	3	74	1	0	0	0	0	1	0	0	0	3216	449	16	2	59	2	CELA3B	1	22304871	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	132141	22304871	226945750	3	9979										
FGR	2268	hgsc.bcm.edu	37	chr1	27939760	27939760	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gattcggcccttggtgatgaGctcagtgagcaggatcccaa	13	10	1	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:27939760G>T	ENST00000374005.3	-	12	1639	c.1351C>A	c.(1351-1353)Ctc>Atc	p.L451I	FGR_ENST00000399173.1_Missense_Mutation_p.L451I|FGR_ENST00000374004.1_Missense_Mutation_p.L451I|FGR_ENST00000545953.1_Missense_Mutation_p.L385I	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	451	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		TTGGTGATGAGCTCAGTGAGC	0.602																																					p.L451I		Atlas-SNP	.											.	FGR	39	.	0			c.C1351A						.						87	87	87					1																	27939760		2203	4300	6503	SO:0001583	missense	2268	exon12			TGATGAGCTCAGT	BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"SH2 domain containing"	3697	protein-coding gene	gene with protein product		164940	"Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog", "v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog", "feline Gardner-Rasheed sarcoma viral oncogene homolog"	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.1351C>A	chr1.hg19:g.27939760G>T	ENSP00000363117:p.Leu451Ile	111.0	0.0		127.0	62.0	NM_001042729	D3DPL7|Q9UIQ3	Missense_Mutation	SNP	ENST00000374005.3	hg19	CCDS305.1	.	.	.	.	.	.	.	.	.	.	g	10.98	1.503947	0.26949	.	.	ENSG00000000938	ENST00000374005;ENST00000545953;ENST00000399173;ENST00000374004;ENST00000374003	T;T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49;-1.49	4.65	3.7	0.42460	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.45867	D	0.000331	T	0.56746	0.2006	N	0.02379	-0.575	0.30346	N	0.785278	B	0.11235	0.004	B	0.28553	0.091	T	0.48747	-0.9008	10	0.06365	T	0.9	.	12.8845	0.58036	0.0:0.0:0.8356:0.1643	.	451	P09769	FGR_HUMAN	I	451;385;451;451;451	ENSP00000363117:L451I;ENSP00000445302:L385I;ENSP00000382126:L451I;ENSP00000363116:L451I;ENSP00000363115:L451I	ENSP00000363115:L451I	L	-	1	0	FGR	27812347	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	5.693000	0.68264	1.053000	0.40415	0.586000	0.80456	CTC	.	.		0.602	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248		T	27939760	G	T	27939760	3	4	74	1	0	0	0	0	1	0	0	0	5882	971	34	3	246	3	FGR	1	27939760	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	5634889	27939760	221310861	4	9980										
NCDN	23154	hgsc.bcm.edu	37	chr1	36025987	36025987	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ctcggcggcggatcttcgatGctgtcggcttcaccttcccc	11	16	2	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:36025987G>T	ENST00000373243.2	+	3	618	c.235G>T	c.(235-237)Gct>Tct	p.A79S	KIAA0319L_ENST00000325722.3_5'Flank|NCDN_ENST00000373253.3_Missense_Mutation_p.A62S|NCDN_ENST00000356090.4_Missense_Mutation_p.A79S|NCDN_ENST00000459931.1_3'UTR	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	79					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GATCTTCGATGCTGTCGGCTT	0.572																																					p.A79S		Atlas-SNP	.											.	NCDN	79	.	0			c.G235T						.						142	141	141					1																	36025987		2203	4300	6503	SO:0001583	missense	23154	exon3			TTCGATGCTGTCG	AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.235G>T	chr1.hg19:g.36025987G>T	ENSP00000362340:p.Ala79Ser	129.0	0.0		109.0	36.0	NM_014284	D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Missense_Mutation	SNP	ENST00000373243.2	hg19	CCDS392.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.388735	0.82902	.	.	ENSG00000020129	ENST00000373253;ENST00000356090;ENST00000373243;ENST00000437806	T;T;T	0.70749	-0.51;-0.51;-0.51	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.82646	0.5082	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80686	-0.1272	10	0.33141	T	0.24	-11.8617	17.9511	0.89053	0.0:0.0:1.0:0.0	.	79	Q9UBB6	NCDN_HUMAN	S	62;79;79;62	ENSP00000362350:A62S;ENSP00000348394:A79S;ENSP00000362340:A79S	ENSP00000348394:A79S	A	+	1	0	NCDN	35798574	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	8.955000	0.93058	2.480000	0.83734	0.561000	0.74099	GCT	.	.		0.572	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284		T	36025987	G	T	36025987	3	4	74	1	0	0	0	0	1	0	0	0	10223	1319	46	3	245	3	NCDN	1	36025987	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	8086227	36025987	213224634	5	9981										
UQCRH	7388	hgsc.bcm.edu	37	chr1	46782226	46782226	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tttctttcccccatctaggtGgcccacaaactctttaacaa	4	14	3	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:46782226G>T	ENST00000311672.5	+	4	382	c.246G>T	c.(244-246)gtG>gtT	p.V82V		NM_001089591.1|NM_006004.2	NP_001083060.1|NP_005995.2	P07919	QCR6_HUMAN	ubiquinol-cytochrome c reductase hinge protein	82					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|protein heterooligomerization (GO:0051291)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	4	Acute lymphoblastic leukemia(166;0.155)					CCATCTAGGTGGCCCACAAAC	0.418																																					p.V82V		Atlas-SNP	.											.	UQCRH	4	.	0			c.G246T						.						163	156	158					1																	46782226		2203	4300	6503	SO:0001819	synonymous_variant	7388	exon4			CTAGGTGGCCCAC	BC001934	CCDS30704.1	1p34.1	2011-07-04			ENSG00000173660	ENSG00000173660	1.10.2.2	"Mitochondrial respiratory chain complex / Complex III"	12590	protein-coding gene	gene with protein product	"ubiquinol-cytochrome c reductase, complex III subunit VIII"	613844				2826252	Standard	XM_005271167		Approved	QCR6, UQCR8	uc001cpp.3	P07919	OTTHUMG00000007813	ENST00000311672.5:c.246G>T	chr1.hg19:g.46782226G>T		217.0	0.0		228.0	118.0	NM_006004	B2R4V9|D3DQ18|Q5TDF6|Q6LDB8|Q9BQ91	Silent	SNP	ENST00000311672.5	hg19	CCDS30704.1																																																																																			.	.		0.418	UQCRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021451.1	NM_006004		T	46782226	G	T	46782226	2	4	74	1	0	0	0	0	0	0	0	1	17037	1335	47	3		3	UQCRH	1	46782226	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	10756239	46782226	202468395	6	9982										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109810616	109810616	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	taccagctggccacgcggctGctggcccacgagagcaccca	12	17	0	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:109810616G>T	ENST00000271332.3	+	17	6313	c.6252G>T	c.(6250-6252)ctG>ctT	p.L2084L		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2084					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CCACGCGGCTGCTGGCCCACG	0.667																																					p.L2084L	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.G6252T						.						30	32	31					1																	109810616		2203	4300	6503	SO:0001819	synonymous_variant	1952	exon17			GCGGCTGCTGGCC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.6252G>T	chr1.hg19:g.109810616G>T		45.0	0.0		32.0	9.0	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	hg19	CCDS796.1																																																																																			.	.		0.667	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		T	109810616	G	T	109810616	2	4	74	1	0	0	0	0	0	0	0	1	3224	1306	46	3		3	CELSR2	1	109810616	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	63028390	109810616	139440005	7	9983										
FLG	2312	hgsc.bcm.edu	37	chr1	152280060	152280060	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gatccttgtcttcctccagtGctggtcccggtccgtccatg	10	15	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:152280060G>T	ENST00000368799.1	-	3	7337	c.7302C>A	c.(7300-7302)agC>agA	p.S2434R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2434	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTCCTCCAGTGCTGGTCCCGG	0.602									Ichthyosis																												p.S2434R		Atlas-SNP	.											.	FLG	900	.	0			c.C7302A						.						273	250	258					1																	152280060		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCCAGTGCTGGTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7302C>A	chr1.hg19:g.152280060G>T	ENSP00000357789:p.Ser2434Arg	145.0	0.0		156.0	47.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	10.52	1.373430	0.24857	.	.	ENSG00000143631	ENST00000368799	T	0.01767	4.65	4.03	-8.05	0.01106	.	.	.	.	.	T	0.00754	0.0025	M	0.81682	2.555	0.09310	N	1	B	0.19331	0.035	B	0.09377	0.004	T	0.44034	-0.9354	9	0.52906	T	0.07	.	2.9885	0.05975	0.5332:0.1246:0.2159:0.1262	.	2434	P20930	FILA_HUMAN	R	2434	ENSP00000357789:S2434R	ENSP00000357789:S2434R	S	-	3	2	FLG	150546684	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.532000	0.02217	-1.568000	0.01670	-0.300000	0.09419	AGC	.	.		0.602	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152280060	G	T	152280060	3	4	74	1	0	0	0	0	1	0	0	0	5930	1310	46	3	4887	3	FLG	1	152280060	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	42469444	152280060	96970561	8	9984										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201021743	201021743	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gttgttgttccggtttatttGggtcccatccaccaaggcga	11	10	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:201021743G>T	ENST00000362061.3	-	32	4121	c.3895C>A	c.(3895-3897)Caa>Aaa	p.Q1299K	CACNA1S_ENST00000367338.3_Missense_Mutation_p.Q1280K	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1299					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGGTTTATTTGGGTCCCATCC	0.562																																					p.Q1299K		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C3895A						.						266	228	241					1																	201021743		2203	4300	6503	SO:0001583	missense	779	exon32			TTATTTGGGTCCC	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.3895C>A	chr1.hg19:g.201021743G>T	ENSP00000355192:p.Gln1299Lys	123.0	0.0		113.0	38.0	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	16.64	3.178620	0.57692	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.98419	-4.92;-4.92	4.68	4.68	0.58851	Ion transport (1);	0.116892	0.64402	D	0.000017	D	0.97476	0.9174	M	0.72894	2.215	0.39160	D	0.962395	P	0.38473	0.633	B	0.42959	0.403	D	0.98619	1.0666	10	0.49607	T	0.09	.	13.6846	0.62508	0.0:0.1548:0.8451:0.0	.	1299	Q13698	CAC1S_HUMAN	K	1299;1280	ENSP00000355192:Q1299K;ENSP00000356307:Q1280K	ENSP00000355192:Q1299K	Q	-	1	0	CACNA1S	199288366	1.000000	0.71417	0.579000	0.28588	0.957000	0.61999	4.616000	0.61197	2.299000	0.77371	0.551000	0.68910	CAA	.	.		0.562	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		T	201021743	G	T	201021743	3	4	74	1	0	0	0	0	1	0	0	0	2549	1357	47	3	1778	3	CACNA1S	1	201021743	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	48741683	201021743	48228878	9	9985										
TATDN3	128387	hgsc.bcm.edu	37	chr1	212965299	212965315	+	Frame_Shift_Del	DEL	CTGCCACCTCTCCGCCC	CTGCCACCTCTCCGCCC	-													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gtaggcttggtggactgtcaCtgccacctctccgccccgga					rs377084448		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	CTGCCACCTCTCCGCCC	CTGCCACCTCTCCGCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:212965299_212965315delCTGCCACCTCTCCGCCC	ENST00000366974.4	+	1	130_146	c.36_52delCTGCCACCTCTCCGCCC	c.(34-54)cactgccacctctccgccccgfs	p.CHLSAP13fs	NSL1_ENST00000473995.1_5'Flank|TATDN3_ENST00000531963.1_Frame_Shift_Del_p.CHLSAP13fs|TATDN3_ENST00000530441.1_Frame_Shift_Del_p.CHLSAP13fs|TATDN3_ENST00000532324.1_Frame_Shift_Del_p.CHLSAP13fs|TATDN3_ENST00000366973.4_Frame_Shift_Del_p.CHLSAP13fs|TATDN3_ENST00000526997.1_Frame_Shift_Del_p.CHLSAP13fs|NSL1_ENST00000422588.2_5'Flank|NSL1_ENST00000366976.1_5'Flank|TATDN3_ENST00000526641.1_Frame_Shift_Del_p.CHLSAP13fs|NSL1_ENST00000366975.6_5'Flank|NSL1_ENST00000366978.1_5'Flank|NSL1_ENST00000366977.3_5'Flank	NM_001042552.2|NM_001042553.2|NM_001146169.1|NM_001146171.1	NP_001036017.1|NP_001036018.1|NP_001139641.1|NP_001139643.1	Q17R31	TATD3_HUMAN	TatD DNase domain containing 3	13					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00699)|all cancers(67;0.0118)|GBM - Glioblastoma multiforme(131;0.0801)|Epithelial(68;0.104)		TGGACTGTCACTGCCACCTCTCCGCCCCGGACTTTGA	0.659																																					p.12_17del		Atlas-Indel,Pindel	.											.	TATDN3	23	.	0			c.35_51del						.																																			SO:0001589	frameshift_variant	128387	exon1			.	AL832248	CCDS31019.1, CCDS41465.1, CCDS53475.1, CCDS53476.1, CCDS53477.1	1q32.3	2008-02-05			ENSG00000203705	ENSG00000203705			27010	protein-coding gene	gene with protein product							Standard	NM_001042552		Approved		uc001hjo.2	Q17R31	OTTHUMG00000036805	ENST00000366974.4:c.36_52delCTGCCACCTCTCCGCCC	chr1.hg19:g.212965299_212965315delCTGCCACCTCTCCGCCC	ENSP00000355941:p.Cys13fs	180.0	0.0		140.0	25.0	NM_001042552	A6NGS3|B7Z1C1|B7Z978|B7ZLQ6|E9PJE5|E9PNH3|G3V151|Q4G0L1	Frame_Shift_Del	DEL	ENST00000366974.4	hg19	CCDS31019.1																																																																																			.	.		0.659	TATDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089396.2	XM_375838		-	212965315	CTGCCACCTCTCCGCCC	-	212965299	7	5	74	1	0	1	0	1	0	0	0	0	15608	564	20	0	38	0	TATDN3	1	212965299	Frame_Shift_Del	DEL	CTGCCACCTCTCCGCCC	TCGA-CC-A7II-01A-11D-A33K-10	11943556	212965299	36285322	10	9986										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228525079	228525079	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cagaggacggcgatgcccgaGgcgaggtgggcggctggaac	20	10	0	1	rs34771878		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:228525079G>A	ENST00000422127.1	+	66	16839	c.16795G>A	c.(16795-16797)Ggc>Agc	p.G5599S	OBSCN_ENST00000570156.2_Missense_Mutation_p.G6556S|OBSCN_ENST00000284548.11_Missense_Mutation_p.G5599S|OBSCN_ENST00000366707.4_Missense_Mutation_p.G3233S|OBSCN_ENST00000366709.4_Missense_Mutation_p.G2718S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5599					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CGATGCCCGAGGCGAGGTGGG	0.652																																					p.G6556S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G19666A						.						20	23	22					1																	228525079		2052	4173	6225	SO:0001583	missense	84033	exon77			GCCCGAGGCGAGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.16795G>A	chr1.hg19:g.228525079G>A	ENSP00000409493:p.Gly5599Ser	223.0	0.0		165.0	55.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.4|21.4	4.139130|4.139130	0.77775|0.77775	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709|ENST00000441106	T;T;T;T|T	0.62941|0.66638	0.33;-0.01;0.04;0.48|-0.22	4.37|4.37	4.37|4.37	0.52481|0.52481	Src homology-3 domain (1);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.74801|0.74801	0.3764|0.3764	L|L	0.54323|0.54323	1.7|1.7	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.999;1.0|.	T|T	0.77395|0.77395	-0.2604|-0.2604	10|7	0.45353|0.59425	T|D	0.12|0.04	.|.	17.4671|17.4671	0.87635|0.87635	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	5599;5599|.	Q5VST9;Q5VST9-3|.	OBSCN_HUMAN;.|.	S|K	5599;5599;3233;2718|214	ENSP00000284548:G5599S;ENSP00000409493:G5599S;ENSP00000355668:G3233S;ENSP00000355670:G2718S|ENSP00000388554:R214K	ENSP00000284548:G5599S|ENSP00000388554:R214K	G|R	+|+	1|2	0|0	OBSCN|OBSCN	226591702|226591702	1.000000|1.000000	0.71417|0.71417	0.407000|0.407000	0.26434|0.26434	0.003000|0.003000	0.03518|0.03518	8.939000|8.939000	0.92951|0.92951	2.437000|2.437000	0.82529|0.82529	0.655000|0.655000	0.94253|0.94253	GGC|AGG	.	.		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228525079	G	A	228525079	3	1	74	1	0	0	0	0	1	0	0	0	10821	1000	35	3	17053	3	OBSCN	1	228525079	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	15559780	228525079	20725542	11	9987										
RYR2	6262	hgsc.bcm.edu	37	chr1	237947437	237947437	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	catcgaaatcatgggaagcgCcaaacgcatcgagagggtct	12	10	2	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr1:237947437C>T	ENST00000366574.2	+	90	12742	c.12425C>T	c.(12424-12426)gCc>gTc	p.A4142V	RYR2_ENST00000542537.1_Missense_Mutation_p.A4126V|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Missense_Mutation_p.A4148V	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4142					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATGGGAAGCGCCAAACGCATC	0.498																																					p.A4142V		Atlas-SNP	.											.	RYR2	1273	.	0			c.C12425T						.						76	76	76					1																	237947437		1916	4139	6055	SO:0001583	missense	6262	exon90			GAAGCGCCAAACG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.12425C>T	chr1.hg19:g.237947437C>T	ENSP00000355533:p.Ala4142Val	155.0	0.0		106.0	43.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.221274	0.79464	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.97850	-4.57;-4.57;-4.57	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000006	D	0.97936	0.9321	L	0.47716	1.5	0.80722	D	1	D;D	0.69078	0.997;0.987	D;P	0.79784	0.993;0.87	D	0.98561	1.0641	10	0.72032	D	0.01	.	15.0213	0.71632	0.0:0.8581:0.1419:0.0	.	1116;4142	B4DGV4;Q92736	.;RYR2_HUMAN	V	4142;4148;4126;1116	ENSP00000355533:A4142V;ENSP00000353174:A4148V;ENSP00000443798:A4126V	ENSP00000353174:A4148V	A	+	2	0	RYR2	236014060	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	4.853000	0.62911	2.610000	0.88304	0.655000	0.94253	GCC	.	.		0.498	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237947437	C	T	237947437	3	4	74	1	0	0	0	0	1	0	0	0	13784	739	26	3	12783	3	RYR2	1	237947437	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	9422358	237947437	11303184	12	9988										
FAM84A	151354	hgsc.bcm.edu	37	chr2	14774404	14774404	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcatcttttccaaagtgagcGgtggccctcagggcgccgac	13	13	2	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:14774404G>T	ENST00000295092.2	+	2	589	c.301G>T	c.(301-303)Ggt>Tgt	p.G101C	AC011897.1_ENST00000581929.1_5'Flank|FAM84A_ENST00000331243.4_Missense_Mutation_p.G101C	NM_145175.2	NP_660158.2	Q96KN4	FA84A_HUMAN	family with sequence similarity 84, member A	101										endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(1;0.00969)			CAAAGTGAGCGGTGGCCCTCA	0.667																																					p.G101C		Atlas-SNP	.											.	FAM84A	23	.	0			c.G301T						.						14	16	15					2																	14774404		2196	4291	6487	SO:0001583	missense	151354	exon2			GTGAGCGGTGGCC	AJ417080, BC026346	CCDS1684.1	2p24.3	2005-08-09			ENSG00000162981	ENSG00000162981			20743	protein-coding gene	gene with protein product	"neurological/sensory 1"	611234				14702039	Standard	NM_145175		Approved	NSE1, FLJ35392	uc002rbz.2	Q96KN4	OTTHUMG00000119093	ENST00000295092.2:c.301G>T	chr2.hg19:g.14774404G>T	ENSP00000295092:p.Gly101Cys	13.0	0.0		14.0	7.0	NM_145175	A6NP76|Q86UZ2|Q8NAH7|Q8TAM5	Missense_Mutation	SNP	ENST00000295092.2	hg19	CCDS1684.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.46|16.46	3.128805|3.128805	0.56721|0.56721	.|.	.|.	ENSG00000162981|ENSG00000162981	ENST00000295092;ENST00000331243;ENST00000359969|ENST00000540701	T;T|.	0.03801|.	3.8;3.8|.	4.44|4.44	3.55|3.55	0.40652|0.40652	.|.	0.106113|.	0.64402|.	D|.	0.000005|.	T|T	0.55321|0.55321	0.1913|0.1913	L|L	0.39898|0.39898	1.24|1.24	0.39690|0.39690	D|D	0.971026|0.971026	D|.	0.64830|.	0.994|.	P|.	0.51385|.	0.668|.	T|T	0.59558|0.59558	-0.7432|-0.7432	10|6	0.49607|0.87932	T|D	0.09|0	-27.4376|-27.4376	8.3319|8.3319	0.32191|0.32191	0.2027:0.0:0.7973:0.0|0.2027:0.0:0.7973:0.0	.|.	101|.	Q96KN4|.	FA84A_HUMAN|.	C|L	101|8	ENSP00000295092:G101C;ENSP00000330681:G101C|.	ENSP00000295092:G101C|ENSP00000443261:R8L	G|R	+|+	1|2	0|0	FAM84A|FAM84A	14691855|14691855	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	2.756000|2.756000	0.47549|0.47549	1.190000|1.190000	0.43042|0.43042	0.655000|0.655000	0.94253|0.94253	GGT|CGG	.	.		0.667	FAM84A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239308.2	NM_145175		T	14774404	G	T	14774404	3	4	74	1	0	0	0	0	1	0	0	0	5649	1116	39	1	303	1	FAM84A	2	14774404	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10		14774404	228424969	13	9989										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25464487	25464487	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	catgatcttcccctggtgccGcaccatgcccaccgtgatgg	10	16	1	2	rs375399431		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:25464487G>A	ENST00000264709.3	-	17	2363	c.2026C>T	c.(2026-2028)Cgg>Tgg	p.R676W	DNMT3A_ENST00000380746.4_Missense_Mutation_p.R487W|DNMT3A_ENST00000402667.1_Missense_Mutation_p.R453W|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000321117.5_Missense_Mutation_p.R676W	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	676	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.R676W(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCTGGTGCCGCACCATGCCC	0.627			"Mis, F, N, S"		AML																																p.R676W		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	DNMT3A_ENST00000380746,NS,carcinoma,+2,1	DNMT3A	1807	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2026T						.	G	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	149	95	113		2026,1459,2026	5.4	1	2		113	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	DNMT3A	NM_022552.3,NM_153759.2,NM_175629.1	101,101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	676/913,487/724,676/913	25464487	1,13005	2203	4300	6503	SO:0001583	missense	1788	exon17			GGTGCCGCACCAT		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2026C>T	chr2.hg19:g.25464487G>A	ENSP00000264709:p.Arg676Trp	101.0	0.0		80.0	4.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	ENST00000264709.3	hg19	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.837170	0.91117	0.0	1.16E-4	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.96619	-4.07;-4.07;-4.07;-4.07	5.44	5.44	0.79542	.	0.115412	0.64402	D	0.000013	D	0.98074	0.9365	M	0.88105	2.93	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.66602	0.935;0.945	D	0.98657	1.0682	10	0.87932	D	0	-10.3061	13.6788	0.62472	0.0:0.0:0.845:0.155	.	676;487	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	W	487;676;676;453	ENSP00000370122:R487W;ENSP00000324375:R676W;ENSP00000264709:R676W;ENSP00000384237:R453W	ENSP00000264709:R676W	R	-	1	2	DNMT3A	25317991	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.995000	0.57001	2.568000	0.86640	0.555000	0.69702	CGG	.	.		0.627	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		A	25464487	G	A	25464487	3	1	74	1	0	0	0	0	1	0	0	0	4678	1086	38	1	740	1	DNMT3A	2	25464487	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	10690083	25464487	217734886	14	9990										
OTOF	9381	hgsc.bcm.edu	37	chr2	26699163	26699163	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcactgtccagcctgccgagCcgaagccccgcttccctggc	11	19	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:26699163C>A	ENST00000272371.2	-	23	2825	c.2699G>T	c.(2698-2700)gGc>gTc	p.G900V	OTOF_ENST00000402415.3_Missense_Mutation_p.G210V|OTOF_ENST00000338581.6_Missense_Mutation_p.G153V|OTOF_ENST00000403946.3_Missense_Mutation_p.G900V|OTOF_ENST00000339598.3_Missense_Mutation_p.G153V	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	900					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCTGCCGAGCCGAAGCCCCG	0.697																																					p.G900V	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.G2699T						.						25	25	25					2																	26699163		2089	4116	6205	SO:0001583	missense	9381	exon23			GCCGAGCCGAAGC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2699G>T	chr2.hg19:g.26699163C>A	ENSP00000272371:p.Gly900Val	27.0	0.0		27.0	10.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.856946	0.71834	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	5.41	5.41	0.78517	Ferlin B-domain (1);	0.000000	0.85682	D	0.000000	D	0.91670	0.7367	M	0.84326	2.69	0.80722	D	1	D;D;D;D	0.89917	1.0;0.994;1.0;1.0	D;P;D;D	0.97110	1.0;0.828;1.0;0.999	D	0.91667	0.5347	10	0.48119	T	0.1	-40.8975	17.7511	0.88434	0.0:1.0:0.0:0.0	.	900;153;210;153	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	V	153;153;210;900;900	ENSP00000345137:G153V;ENSP00000344521:G153V;ENSP00000383906:G210V;ENSP00000272371:G900V;ENSP00000385255:G900V	ENSP00000272371:G900V	G	-	2	0	OTOF	26552667	1.000000	0.71417	1.000000	0.80357	0.383000	0.30230	7.630000	0.83225	2.546000	0.85860	0.561000	0.74099	GGC	.	.		0.697	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			A	26699163	C	A	26699163	3	1	74	1	0	0	0	0	1	0	0	0	11312	739	26	3	3575	3	OTOF	2	26699163	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	1234676	26699163	216500210	15	9991										
C2orf16	84226	hgsc.bcm.edu	37	chr2	27804122	27804122	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gagagaacccgtcataacccCtcttggagaaaccatcgcag	9	13	2	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:27804122C>A	ENST00000408964.2	+	1	4734	c.4683C>A	c.(4681-4683)ccC>ccA	p.P1561P	ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000416005.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000355467.4_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000379717.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1561	Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GTCATAACCCCTCTTGGAGAA	0.527																																					p.P1561P		Atlas-SNP	.											.	C2orf16	357	.	0			c.C4683A						.						117	118	118					2																	27804122		1891	4109	6000	SO:0001819	synonymous_variant	84226	exon1			TAACCCCTCTTGG	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4683C>A	chr2.hg19:g.27804122C>A		79.0	0.0		100.0	21.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	hg19	CCDS42666.1																																																																																			.	.		0.527	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		A	27804122	C	A	27804122	2	1	74	1	0	0	0	0	0	0	0	1	2159	668	24	3		3	C2orf16	2	27804122	Silent	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	1104959	27804122	215395251	16	9992										
ADD2	119	hgsc.bcm.edu	37	chr2	70933425	70933425	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgaagtcctgccgcaggtccGccgcccggttgcgaaggcgc	15	15	0	1	rs373392326		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:70933425G>T	ENST00000264436.4	-	3	560	c.116C>A	c.(115-117)gCg>gAg	p.A39E	ADD2_ENST00000473232.1_5'Flank|ADD2_ENST00000413157.2_Missense_Mutation_p.A39E|ADD2_ENST00000430656.1_Missense_Mutation_p.A55E|ADD2_ENST00000355733.3_Missense_Mutation_p.A39E|ADD2_ENST00000407644.2_Missense_Mutation_p.A39E	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	39					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						CCGCAGGTCCGCCGCCCGGTT	0.687																																					p.A55E		Atlas-SNP	.											.	ADD2	261	.	0			c.C164A						.						51	52	52					2																	70933425		2203	4300	6503	SO:0001583	missense	119	exon2			AGGTCCGCCGCCC	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.116C>A	chr2.hg19:g.70933425G>T	ENSP00000264436:p.Ala39Glu	104.0	0.0		74.0	31.0	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	hg19	CCDS1906.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126225	0.37533	.	.	ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000456320;ENST00000355733;ENST00000522886;ENST00000264439;ENST00000356565;ENST00000517596;ENST00000413157;ENST00000430656;ENST00000415348;ENST00000425976	T;T;T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53	4.89	4.89	0.63831	.	0.148379	0.44902	D	0.000412	T	0.46639	0.1403	M	0.66297	2.02	0.29846	N	0.828861	P;P;D;P;P;P	0.63046	0.645;0.631;0.992;0.505;0.623;0.904	B;B;P;B;B;B	0.54026	0.177;0.387;0.74;0.177;0.247;0.411	T	0.50841	-0.8780	10	0.87932	D	0	-14.2279	15.9349	0.79694	0.0:0.0:1.0:0.0	.	55;39;39;39;39;39	B4DM17;P35612-4;E9PAN1;Q05DK5;P35612;P35612-3	.;.;.;.;ADDB_HUMAN;.	E	39;39;39;39;39;39;39;39;39;55;39;39	ENSP00000264436:A39E;ENSP00000384677:A39E;ENSP00000347972:A39E;ENSP00000430243:A39E;ENSP00000388072:A39E;ENSP00000398112:A55E;ENSP00000412357:A39E;ENSP00000412681:A39E	ENSP00000264436:A39E	A	-	2	0	ADD2	70786933	0.998000	0.40836	0.018000	0.16275	0.076000	0.17211	5.317000	0.65822	2.690000	0.91761	0.591000	0.81541	GCG	.	.		0.687	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		T	70933425	G	T	70933425	3	4	74	1	0	0	0	0	1	0	0	0	305	1087	38	1	2301	1	ADD2	2	70933425	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	43129303	70933425	172265948	17	9993										
ACOXL	55289	hgsc.bcm.edu	37	chr2	111556210	111556210	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tttgtaattgacacgccgtgTgaaaatgcggagaagatgta	12	5	0	4			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:111556210T>C	ENST00000389811.4	+	6	593	c.369T>C	c.(367-369)tgT>tgC	p.C123C	ACOXL_ENST00000439055.1_Silent_p.C123C|ACOXL_ENST00000340561.4_Silent_p.C123C			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	123					fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						ACACGCCGTGTGAAAATGCGG	0.438																																					p.C123C		Atlas-SNP	.											.	ACOXL	93	.	0			c.T369C						.						130	123	125					2																	111556210		1926	4137	6063	SO:0001819	synonymous_variant	55289	exon6			GCCGTGTGAAAAT		CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"acyl-Coenzyme A oxidase-like"				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.369T>C	chr2.hg19:g.111556210T>C		75.0	0.0		48.0	17.0	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Silent	SNP	ENST00000389811.4	hg19																																																																																				.	.		0.438	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308		C	111556210	T	C	111556210	2	2	74	1	0	0	0	0	0	0	0	1	161	1702	59	2		2	ACOXL	2	111556210	Silent	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	40622785	111556210	131643163	18	9994										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148684674	148684674	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ggcaatgctctgtgaaaccaTtgaagaatgttgggatcacg	12	7	2	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:148684674T>C	ENST00000241416.7	+	11	2009	c.1373T>C	c.(1372-1374)aTt>aCt	p.I458T	ACVR2A_ENST00000404590.1_Missense_Mutation_p.I458T|ACVR2A_ENST00000535787.1_Missense_Mutation_p.I350T|ACVR2A_ENST00000495775.1_3'UTR	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	458	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.I458T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TGTGAAACCATTGAAGAATGT	0.378																																					p.I458T		Atlas-SNP	.											ACVR2A,NS,carcinoma,0,1	ACVR2A	125	.	1	Substitution - Missense(1)	breast(1)	c.T1373C						.						106	101	103					2																	148684674		2203	4299	6502	SO:0001583	missense	92	exon11			AAACCATTGAAGA		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1373T>C	chr2.hg19:g.148684674T>C	ENSP00000241416:p.Ile458Thr	121.0	1.0		73.0	18.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.688428	0.68271	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	T;T;T	0.71341	-0.56;-0.56;-0.56	6.06	6.06	0.98353	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.80706	0.4674	M	0.76727	2.345	0.80722	D	1	P	0.41345	0.746	P	0.51550	0.673	T	0.82466	-0.0443	10	0.87932	D	0	.	16.6245	0.84952	0.0:0.0:0.0:1.0	.	458	P27037	AVR2A_HUMAN	T	458;350;458	ENSP00000241416:I458T;ENSP00000439988:I350T;ENSP00000384338:I458T	ENSP00000241416:I458T	I	+	2	0	ACVR2A	148401144	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	8.040000	0.89188	2.323000	0.78572	0.528000	0.53228	ATT	.	.		0.378	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		C	148684674	T	C	148684674	3	2	74	1	0	0	0	0	1	0	0	0	223	1493	52	2	1415	2	ACVR2A	2	148684674	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	37128464	148684674	94514699	19	9995										
CCDC141	285025	hgsc.bcm.edu	37	chr2	179701999	179701999	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgctctctggatgttcagcaCtgattctgtgtaaggcagta	11	8	3	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:179701999C>A	ENST00000420890.2	-	23	4064	c.3947G>T	c.(3946-3948)aGt>aTt	p.S1316I	CCDC141_ENST00000295723.5_Missense_Mutation_p.S741I|CCDC141_ENST00000480419.1_5'UTR	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	1316										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			ATGTTCAGCACTGATTCTGTG	0.483																																					p.S1316I		Atlas-SNP	.											CCDC141_ENST00000420890,NS,malignant_melanoma,0,2	CCDC141	362	.	0			c.G3947T						.						120	105	110					2																	179701999		2203	4300	6503	SO:0001583	missense	285025	exon23			TCAGCACTGATTC	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.3947G>T	chr2.hg19:g.179701999C>A	ENSP00000395995:p.Ser1316Ile	117.0	0.0		81.0	28.0	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	hg19		.	.	.	.	.	.	.	.	.	.	C	11.13	1.546935	0.27652	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723	T;T;T	0.49139	0.79;1.35;1.34	5.71	-0.467	0.12150	.	0.737124	0.13245	N	0.402553	T	0.48077	0.1480	L	0.50333	1.59	0.09310	N	1	D;D	0.59767	0.986;0.958	P;P	0.54312	0.66;0.748	T	0.38023	-0.9680	10	0.87932	D	0	-1.0937	5.3175	0.15864	0.0:0.3511:0.1499:0.499	.	741;741	Q6ZP82;Q6ZP82-2	CC141_HUMAN;.	I	1316;760;741	ENSP00000395995:S1316I;ENSP00000344627:S760I;ENSP00000295723:S741I	ENSP00000295723:S741I	S	-	2	0	CCDC141	179410244	0.897000	0.30589	0.021000	0.16686	0.476000	0.33039	0.025000	0.13577	0.052000	0.16007	0.655000	0.94253	AGT	.	.		0.483	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		A	179701999	C	A	179701999	3	1	74	1	0	0	0	0	1	0	0	0	2777	565	20	3	409	3	CCDC141	2	179701999	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	31017325	179701999	63497374	20	9996										
ITGAV	3685	hgsc.bcm.edu	37	chr2	187455211	187455222	+	In_Frame_Del	DEL	TCGGCTTCGCCG	TCGGCTTCGCCG	-													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tggccccgagggaagttactTcggcttcgccgtggatttct					rs61763606	byFrequency	TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	TCGGCTTCGCCG	TCGGCTTCGCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:187455211_187455222delTCGGCTTCGCCG	ENST00000261023.3	+	1	420_431	c.146_157delTCGGCTTCGCCG	c.(145-159)ttcggcttcgccgtg>ttg	p.49_53FGFAV>L	ITGAV_ENST00000374907.3_In_Frame_Del_p.49_53FGFAV>L	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	49					angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)	p.F51F(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	GGAAGTTACTTCGGCTTCGCCGTGGATTTCTT	0.637																																					p.49_52del	Melanoma(58;108 1995 6081)	Atlas-Indel,Pindel	.											.	ITGAV	124	.	1	Substitution - coding silent(1)	urinary_tract(1)	c.145_156del						.																																			SO:0001651	inframe_deletion	3685	exon1			.		CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"CD molecules", "Integrins"	6150	protein-coding gene	gene with protein product		193210	"antigen identified by monoclonal antibody L230", "vitronectin receptor", "integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.146_157delTCGGCTTCGCCG	chr2.hg19:g.187455211_187455222delTCGGCTTCGCCG	ENSP00000261023:p.Phe49_Val53delinsLeu	219.0	0.0		175.0	36.0	NM_001145000	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	In_Frame_Del	DEL	ENST00000261023.3	hg19	CCDS2292.1																																																																																			.	.		0.637	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		-	187455222	TCGGCTTCGCCG	-	187455211	7	5	74	1	0	1	0	1	0	0	0	0	7897	1783	62	0	148	0	ITGAV	2	187455211	In_Frame_Del	DEL	TCGGCTTCGCCG	TCGA-CC-A7II-01A-11D-A33K-10	7753212	187455211	55744162	21	9997										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189850437	189850437	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tggtgaccctggtattccagGacaaccagggtcccctggtt	12	12	0	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:189850437G>C	ENST00000304636.3	+	4	550	c.380G>C	c.(379-381)gGa>gCa	p.G127A	COL3A1_ENST00000317840.5_Missense_Mutation_p.G127A	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	127					aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	GGTATTCCAGGACAACCAGGG	0.443																																					p.G127A		Atlas-SNP	.											.	COL3A1	292	.	0			c.G380C						.						41	44	43					2																	189850437		2203	4300	6503	SO:0001583	missense	1281	exon4			TTCCAGGACAACC	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.380G>C	chr2.hg19:g.189850437G>C	ENSP00000304408:p.Gly127Ala	232.0	0.0		192.0	74.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	hg19	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.486957	0.84854	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.99329	-5.75;-5.75	4.62	4.62	0.57501	.	0.000000	0.47455	D	0.000238	D	0.99504	0.9823	M	0.91768	3.24	0.49798	D	0.999828	D	0.89917	1.0	D	0.91635	0.999	D	0.98179	1.0456	10	0.87932	D	0	.	15.8159	0.78599	0.0:0.0:1.0:0.0	.	127	P02461	CO3A1_HUMAN	A	127	ENSP00000304408:G127A;ENSP00000315243:G127A	ENSP00000304408:G127A	G	+	2	0	COL3A1	189558682	1.000000	0.71417	0.997000	0.53966	0.976000	0.68499	9.010000	0.93611	2.414000	0.81942	0.313000	0.20887	GGA	.	.		0.443	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		C	189850437	G	C	189850437	3	2	74	1	0	0	0	0	1	0	0	0	3690	1174	41	4	394	4	COL3A1	2	189850437	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	2395226	189850437	53348936	22	9998										
ESPNL	339768	hgsc.bcm.edu	37	chr2	239010624	239010624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ccccgctgcacctggccgccCgttttggacacccagtgctg	11	18	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:239010624C>T	ENST00000343063.3	+	2	600	c.337C>T	c.(337-339)Cgt>Tgt	p.R113C	ESPNL_ENST00000409169.1_Missense_Mutation_p.R113C	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	113										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		CCTGGCCGCCCGTTTTGGACA	0.697																																					p.R113C		Atlas-SNP	.											.	ESPNL	63	.	0			c.C337T						.						18	21	20					2																	239010624		2202	4299	6501	SO:0001583	missense	339768	exon2			GCCGCCCGTTTTG	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"Ankyrin repeat domain containing"	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.337C>T	chr2.hg19:g.239010624C>T	ENSP00000339115:p.Arg113Cys	59.0	0.0		46.0	18.0	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	hg19	CCDS2525.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.500345	0.85176	.	.	ENSG00000144488	ENST00000343063;ENST00000409169	T;T	0.66460	-0.21;-0.21	4.45	4.45	0.53987	Ankyrin repeat-containing domain (4);	0.099656	0.40302	U	0.001123	T	0.77425	0.4128	L	0.54908	1.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79490	-0.1782	10	0.62326	D	0.03	-35.566	14.0307	0.64613	0.0:1.0:0.0:0.0	.	113	Q6ZVH7	ESPNL_HUMAN	C	113	ENSP00000339115:R113C;ENSP00000386577:R113C	ENSP00000339115:R113C	R	+	1	0	ESPNL	238675363	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.561000	0.45905	2.039000	0.60335	0.484000	0.47621	CGT	.	.		0.697	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312		T	239010624	C	T	239010624	3	4	74	1	0	0	0	0	1	0	0	0	5257	652	23	1	343	1	ESPNL	2	239010624	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	49160187	239010624	4188749	23	9999										
HDLBP	3069	hgsc.bcm.edu	37	chr2	242202212	242202212	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	catgatggagaggccttggtCtttggccaaagacagctcca	12	10	1	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr2:242202212C>T	ENST00000391975.1	-	5	591	c.364G>A	c.(364-366)Gac>Aac	p.D122N	HDLBP_ENST00000391976.2_Missense_Mutation_p.D122N|HDLBP_ENST00000310931.4_Missense_Mutation_p.D122N|HDLBP_ENST00000427183.2_Missense_Mutation_p.D158N	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	122					cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		AGGCCTTGGTCTTTGGCCAAA	0.488																																					p.D158N		Atlas-SNP	.											.	HDLBP	118	.	0			c.G472A						.						214	180	191					2																	242202212		2203	4300	6503	SO:0001583	missense	3069	exon6			CTTGGTCTTTGGC		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.364G>A	chr2.hg19:g.242202212C>T	ENSP00000375836:p.Asp122Asn	130.0	0.0		96.0	38.0	NM_001243900	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	hg19	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	C	32	5.168116	0.94768	.	.	ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183;ENST00000422933;ENST00000428482;ENST00000452065;ENST00000444092;ENST00000430918;ENST00000441124	T;T;T;T;T;T;T;T;T;T	0.62941	2.32;2.32;2.32;2.2;1.28;0.69;-0.01;0.08;0.08;0.1	5.93	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.73938	0.3651	L	0.53780	1.695	0.80722	D	1	P;D	0.89917	0.614;1.0	P;D	0.97110	0.474;1.0	T	0.71457	-0.4587	10	0.27785	T	0.31	-47.1993	15.192	0.73053	0.0:0.9329:0.0:0.0671	.	158;122	E7EM71;Q00341	.;VIGLN_HUMAN	N	122;122;122;158;122;122;122;122;122;122	ENSP00000375836:D122N;ENSP00000375837:D122N;ENSP00000312042:D122N;ENSP00000399139:D158N;ENSP00000403807:D122N;ENSP00000405109:D122N;ENSP00000387782:D122N;ENSP00000416559:D122N;ENSP00000403913:D122N;ENSP00000396964:D122N	ENSP00000312042:D122N	D	-	1	0	HDLBP	241850885	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.755000	0.85180	1.538000	0.49270	0.655000	0.94253	GAC	.	.		0.488	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		T	242202212	C	T	242202212	3	4	74	1	0	0	0	0	1	0	0	0	7034	913	32	3	3538	3	HDLBP	2	242202212	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	3191588	242202212	997161	24	10000										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38743417	38743417	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	caaagcgaacatcttcatgaCacattcgcctgtgaagacgg	9	11	2	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr3:38743417C>A	ENST00000449082.2	-	26	4569	c.4570G>T	c.(4570-4572)Gtc>Ttc	p.V1524F		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1524					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	ATCTTCATGACACATTCGCCT	0.458																																					p.V1524F		Atlas-SNP	.											.	SCN10A	359	.	0			c.G4570T						.						151	126	135					3																	38743417		2203	4300	6503	SO:0001583	missense	6336	exon26			TCATGACACATTC	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4570G>T	chr3.hg19:g.38743417C>A	ENSP00000390600:p.Val1524Phe	111.0	0.0		97.0	28.0	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	hg19	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.311079	0.60414	.	.	ENSG00000185313	ENST00000449082	D	0.98807	-5.15	4.96	4.06	0.47325	Ion transport (1);	0.224065	0.38663	N	0.001603	D	0.98757	0.9582	M	0.64630	1.985	0.42012	D	0.990943	D	0.76494	0.999	D	0.74348	0.983	D	0.99881	1.1113	10	0.87932	D	0	.	15.1927	0.73060	0.0:0.8585:0.1415:0.0	.	1524	Q9Y5Y9	SCNAA_HUMAN	F	1524	ENSP00000390600:V1524F	ENSP00000390600:V1524F	V	-	1	0	SCN10A	38718421	0.319000	0.24607	0.994000	0.49952	0.978000	0.69477	0.651000	0.24873	1.261000	0.44149	0.557000	0.71058	GTC	.	.		0.458	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		A	38743417	C	A	38743417	3	1	74	1	0	0	0	0	1	0	0	0	13927	478	17	3	1308	3	SCN10A	3	38743417	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10		38743417	159279013	25	10001										
CCDC13	152206	hgsc.bcm.edu	37	chr3	42750569	42750569	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tccggaagtcctcctcctttCcccgcagggcactgcccagg	10	18	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr3:42750569C>A	ENST00000310232.6	-	16	2134	c.2051G>T	c.(2050-2052)gGa>gTa	p.G684V	HHATL-AS1_ENST00000600839.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	684										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						CTCCTCCTTTCCCCGCAGGGC	0.587																																					p.G684V		Atlas-SNP	.											.	CCDC13	71	.	0			c.G2051T						.						93	81	85					3																	42750569		2203	4300	6503	SO:0001583	missense	152206	exon16			TCCTTTCCCCGCA	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.2051G>T	chr3.hg19:g.42750569C>A	ENSP00000309836:p.Gly684Val	82.0	0.0		60.0	19.0	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	C	9.128	1.010651	0.19277	.	.	ENSG00000244607	ENST00000310232	T	0.23754	1.89	4.58	3.63	0.41609	.	0.474521	0.20779	N	0.085822	T	0.14787	0.0357	L	0.36672	1.1	0.28566	N	0.910859	B	0.27882	0.192	B	0.24541	0.054	T	0.06534	-1.0821	10	0.31617	T	0.26	.	1.6896	0.02849	0.2154:0.4638:0.1796:0.1412	.	684	Q8IYE1	CCD13_HUMAN	V	684	ENSP00000309836:G684V	ENSP00000309836:G684V	G	-	2	0	CCDC13	42725573	0.003000	0.15002	0.967000	0.41034	0.991000	0.79684	0.212000	0.17497	2.374000	0.81015	0.563000	0.77884	GGA	.	.		0.587	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		A	42750569	C	A	42750569	3	1	74	1	0	0	0	0	1	0	0	0	2767	855	30	3	100	3	CCDC13	3	42750569	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	4007152	42750569	155271861	26	10002										
CCDC71	64925	hgsc.bcm.edu	37	chr3	49201424	49201424	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gattagctgtgcatgaactaTagccatagacatcaccactg	8	10	1	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr3:49201424T>C	ENST00000321895.6	-	2	324	c.218A>G	c.(217-219)tAt>tGt	p.Y73C		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	73										endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCATGAACTATAGCCATAGAC	0.582																																					p.Y73C		Atlas-SNP	.											.	CCDC71	33	.	0			c.A218G						.						109	88	95					3																	49201424		2203	4300	6503	SO:0001583	missense	64925	exon2			GAACTATAGCCAT	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.218A>G	chr3.hg19:g.49201424T>C	ENSP00000319006:p.Tyr73Cys	164.0	0.0		116.0	44.0	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Missense_Mutation	SNP	ENST00000321895.6	hg19	CCDS2790.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.018752	0.54576	.	.	ENSG00000177352	ENST00000321895	T	0.67698	-0.28	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000003	T	0.80844	0.4701	M	0.68952	2.095	0.58432	D	0.999992	D	0.89917	1.0	D	0.91635	0.999	T	0.82762	-0.0297	10	0.87932	D	0	-5.2511	16.1997	0.82060	0.0:0.0:0.0:1.0	.	73	Q8IV32	CCD71_HUMAN	C	73	ENSP00000319006:Y73C	ENSP00000319006:Y73C	Y	-	2	0	CCDC71	49176428	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.204000	0.77872	2.240000	0.73641	0.528000	0.53228	TAT	.	.		0.582	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903		C	49201424	T	C	49201424	3	2	74	1	0	0	0	0	1	0	0	0	2846	1406	49	2	1189	2	CCDC71	3	49201424	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	6450855	49201424	148821006	27	10003										
RNF123	63891	hgsc.bcm.edu	37	chr3	49744294	49744294	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	aaagctggaccacctgagccGccgtcttgcctgggtccatg	12	14	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr3:49744294G>T	ENST00000327697.6	+	26	2603	c.2459G>T	c.(2458-2460)cGc>cTc	p.R820L	RNF123_ENST00000432042.1_Missense_Mutation_p.R674L	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	820					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		CACCTGAGCCGCCGTCTTGCC	0.567																																					p.R820L		Atlas-SNP	.											.	RNF123	100	.	0			c.G2459T						.						151	125	134					3																	49744294		2203	4300	6503	SO:0001583	missense	63891	exon26			TGAGCCGCCGTCT	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.2459G>T	chr3.hg19:g.49744294G>T	ENSP00000328287:p.Arg820Leu	115.0	0.0		92.0	25.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.602678	0.87157	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	D;D	0.94897	-2.95;-3.55	5.3	5.3	0.74995	.	0.162806	0.41294	D	0.000912	D	0.95300	0.8475	L	0.32530	0.975	0.80722	D	1	D;D	0.63880	0.993;0.993	D;D	0.74023	0.982;0.982	D	0.95987	0.8982	10	0.87932	D	0	-22.7933	16.0911	0.81090	0.0:0.0:1.0:0.0	.	674;820	C9J266;Q5XPI4	.;RN123_HUMAN	L	820;820;674	ENSP00000328287:R820L;ENSP00000392443:R674L	ENSP00000328287:R820L	R	+	2	0	RNF123	49719298	1.000000	0.71417	1.000000	0.80357	0.660000	0.38997	8.678000	0.91211	2.460000	0.83146	0.491000	0.48974	CGC	.	.		0.567	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		T	49744294	G	T	49744294	3	4	74	1	0	0	0	0	1	0	0	0	13448	1087	38	1	2557	1	RNF123	3	49744294	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	542870	49744294	148278136	28	10004										
NPHP3	27031	hgsc.bcm.edu	37	chr3	132438610	132438610	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ttgctgctctctccattgctTggtatttcgcttctaaagca	7	11	2	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr3:132438610T>G	ENST00000337331.5	-	2	544	c.458A>C	c.(457-459)cAa>cCa	p.Q153P	NPHP3-AS1_ENST00000489343.1_RNA|NPHP3_ENST00000343113.4_Missense_Mutation_p.Q153P|NPHP3_ENST00000326682.8_Missense_Mutation_p.Q153P|NPHP3_ENST00000476742.1_5'Flank|NPHP3-AS1_ENST00000504440.1_RNA	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	153					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CTCCATTGCTTGGTATTTCGC	0.333																																					p.Q153P		Atlas-SNP	.											.	NPHP3	110	.	0			c.A458C						.						149	141	144					3																	132438610		2203	4299	6502	SO:0001583	missense	27031	exon2			ATTGCTTGGTATT	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"Tetratricopeptide (TTC) repeat domain containing"	7907	protein-coding gene	gene with protein product	"nephrocystin-3", "Meckel syndrome, type 7", "cilia and flagella associated protein 31"	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.458A>C	chr3.hg19:g.132438610T>G	ENSP00000338766:p.Gln153Pro	107.0	0.0		64.0	28.0	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	hg19	CCDS3078.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.453686	0.84209	.	.	ENSG00000113971	ENST00000326682;ENST00000337331;ENST00000343113	D;D;D	0.93763	-3.28;-3.23;-2.01	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.94568	0.8250	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.95442	0.8526	10	0.87932	D	0	-21.2615	15.689	0.77436	0.0:0.0:0.0:1.0	.	153	Q7Z494	NPHP3_HUMAN	P	153	ENSP00000319909:Q153P;ENSP00000338766:Q153P;ENSP00000344802:Q153P	ENSP00000319909:Q153P	Q	-	2	0	NPHP3	133921300	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.102000	0.63906	0.455000	0.32223	CAA	.	.		0.333	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		G	132438610	T	G	132438610	3	3	74	1	0	0	0	0	1	0	0	0	10589	1812	63	5	3638	5	NPHP3	3	132438610	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	82694316	132438610	65583820	29	10005										
SMC4	10051	hgsc.bcm.edu	37	chr3	160134114	160134114	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	caaccagaaacaatgccctcGagaaggaaaaagagaaagaa	9	8	0	4			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr3:160134114G>T	ENST00000357388.3	+	10	1799	c.1348G>T	c.(1348-1350)Gag>Tag	p.E450*	SMC4_ENST00000344722.5_Nonsense_Mutation_p.E450*|SMC4_ENST00000360111.2_Nonsense_Mutation_p.E450*|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000462787.1_Nonsense_Mutation_p.E450*|SMC4_ENST00000469762.1_Nonsense_Mutation_p.E425*	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	450					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CAATGCCCTCGAGAAGGAAAA	0.313																																					p.E450X		Atlas-SNP	.											.	SMC4	135	.	0			c.G1348T						.						57	63	61					3																	160134114		2201	4291	6492	SO:0001587	stop_gained	10051	exon9			GCCCTCGAGAAGG	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.1348G>T	chr3.hg19:g.160134114G>T	ENSP00000349961:p.Glu450*	374.0	0.0		306.0	119.0	NM_005496	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Nonsense_Mutation	SNP	ENST00000357388.3	hg19	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	G	37	6.020685	0.97211	.	.	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000469762;ENST00000462787;ENST00000344722;ENST00000545277	.	.	.	6.07	5.2	0.72013	.	0.087770	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-22.4133	16.5359	0.84373	0.0:0.0:0.8682:0.1318	.	.	.	.	X	450;450;425;450;450;44	.	ENSP00000341382:E450X	E	+	1	0	SMC4	161616808	1.000000	0.71417	0.977000	0.42913	0.135000	0.20990	6.667000	0.74451	1.567000	0.49668	-0.169000	0.13324	GAG	.	.		0.313	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			T	160134114	G	T	160134114	4	4	74	1	0	0	0	0	0	1	0	0	14800	1059	37	1	1382	1	SMC4	3	160134114	Nonsense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	27695504	160134114	37888316	30	10006										
KLHL6	89857	hgsc.bcm.edu	37	chr3	183210427	183210427	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ttcccattgggccctcccccGatcacatacagcttcttctt	5	17	3	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr3:183210427G>T	ENST00000341319.3	-	6	1454	c.1419C>A	c.(1417-1419)atC>atA	p.I473I		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	473					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			GCCCTCCCCCGATCACATACA	0.557																																					p.I473I		Atlas-SNP	.											.	KLHL6	100	.	0			c.C1419A						.						164	135	145					3																	183210427		2203	4300	6503	SO:0001819	synonymous_variant	89857	exon6			TCCCCCGATCACA	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"Kelch-like", "BTB/POZ domain containing"	18653	protein-coding gene	gene with protein product	"kelch-like protein KLHL6"	614214	"kelch-like 6 (Drosophila)"			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.1419C>A	chr3.hg19:g.183210427G>T		160.0	0.0		118.0	31.0	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	hg19	CCDS3245.2																																																																																			.	.		0.557	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		T	183210427	G	T	183210427	2	4	74	1	0	0	0	0	0	0	0	1	8402	1048	37	1		1	KLHL6	3	183210427	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	23076313	183210427	14812003	31	10007										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	143613	143613	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ctgctgtacttccatagcatCcccaggtgggacggggggca	14	12	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr5:143613C>A	ENST00000283426.6	+	3	788	c.738C>A	c.(736-738)atC>atA	p.I246I	Y_RNA_ENST00000362670.1_RNA	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	246							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		TCCATAGCATCCCCAGGTGGG	0.662																																					p.I246I		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.C738A						.						44	46	45					5																	143613		2202	4298	6500	SO:0001819	synonymous_variant	153478	exon3			TAGCATCCCCAGG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.738C>A	chr5.hg19:g.143613C>A		74.0	0.0		64.0	15.0	NM_052909		Silent	SNP	ENST00000283426.6	hg19	CCDS34124.1																																																																																			.	.		0.662	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		A	143613	C	A	143613	2	1	74	1	0	0	0	0	0	0	0	1	12081	845	30	3		3	PLEKHG4B	5	143613	Silent	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10		143613	180771647	32	10008										
SLC6A3	6531	hgsc.bcm.edu	37	chr5	1411361	1411361	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cggtgcgggttactcacggcGctgtcgatacccagggtgag	16	11	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr5:1411361G>T	ENST00000270349.9	-	9	1393	c.1266C>A	c.(1264-1266)agC>agA	p.S422R	SLC6A3_ENST00000453492.2_Missense_Mutation_p.S422R	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	422					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	TACTCACGGCGCTGTCGATAC	0.647																																					p.S422R		Atlas-SNP	.											SLC6A3,colon,carcinoma,0,2	SLC6A3	102	.	0			c.C1266A						.						70	55	60					5																	1411361		2117	4150	6267	SO:0001583	missense	6531	exon9			CACGGCGCTGTCG		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"Solute carriers"	11049	protein-coding gene	gene with protein product	"dopamine transporter"	126455	"solute carrier family 6 (neurotransmitter transporter, dopamine), member 3", "dopamine transporter 1"	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1266C>A	chr5.hg19:g.1411361G>T	ENSP00000270349:p.Ser422Arg	54.0	0.0		41.0	26.0	NM_001044	A2RUN4|Q14996	Missense_Mutation	SNP	ENST00000270349.9	hg19	CCDS3863.1	.	.	.	.	.	.	.	.	.	.	G	10.12	1.264169	0.23136	.	.	ENSG00000142319	ENST00000270349;ENST00000453492	T;T	0.81163	-1.46;-1.46	4.5	-9.01	0.00744	.	0.000000	0.85682	D	0.000000	D	0.91975	0.7458	H	0.98218	4.175	0.39335	D	0.965488	D	0.65815	0.995	D	0.74674	0.984	D	0.94058	0.7324	10	0.87932	D	0	.	20.113	0.97915	0.8189:0.0:0.1811:0.0	.	422	Q01959	SC6A3_HUMAN	R	422	ENSP00000270349:S422R;ENSP00000399806:S422R	ENSP00000270349:S422R	S	-	3	2	SLC6A3	1464361	0.004000	0.15560	0.020000	0.16555	0.120000	0.20174	-0.956000	0.03865	-3.115000	0.00240	-2.612000	0.00159	AGC	.	.		0.647	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		T	1411361	G	T	1411361	3	4	74	1	0	0	0	0	1	0	0	0	14700	1078	38	1	624	1	SLC6A3	5	1411361	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	1267748	1411361	179503899	33	10009										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38438475	38438475	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgtgtgagagccccttgtgcCcatgggggcagctgccggcc	16	13	0	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr5:38438475C>T	ENST00000354891.3	+	17	2728	c.2382C>T	c.(2380-2382)gcC>gcT	p.A794A	EGFLAM_ENST00000397202.2_Silent_p.A160A|EGFLAM_ENST00000322350.5_Silent_p.A794A|EGFLAM_ENST00000336740.6_Silent_p.A560A	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	794	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					CCCCTTGTGCCCATGGGGGCA	0.592																																					p.A794A	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C2382T						.						43	45	44					5																	38438475		2203	4300	6503	SO:0001819	synonymous_variant	133584	exon17			TTGTGCCCATGGG	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.2382C>T	chr5.hg19:g.38438475C>T		151.0	0.0		177.0	104.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	hg19	CCDS56363.1																																																																																			.	.		0.592	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		T	38438475	C	T	38438475	2	4	74	1	0	0	0	0	0	0	0	1	4968	610	22	3		3	EGFLAM	5	38438475	Silent	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	37027114	38438475	142476785	34	10010										
PTGER4	5734	hgsc.bcm.edu	37	chr5	40692406	40692406	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gtgggagcggcagggctgggCctgcccctaaggggagctcc	19	12	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr5:40692406C>A	ENST00000302472.3	+	3	2417	c.1393C>A	c.(1393-1395)Cct>Act	p.P465T		NM_000958.2	NP_000949.1	P35408	PE2R4_HUMAN	prostaglandin E receptor 4 (subtype EP4)	465				GPA -> WAC (in Ref. 2; AAA36438). {ECO:0000305}.	adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|bone development (GO:0060348)|cellular response to mechanical stimulus (GO:0071260)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|JNK cascade (GO:0007254)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of eosinophil extravasation (GO:2000420)|negative regulation of inflammatory response (GO:0050728)|negative regulation of integrin activation (GO:0033624)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|regulation of ossification (GO:0030278)|regulation of stress fiber assembly (GO:0051492)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|T-helper cell differentiation (GO:0042093)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)			breast(1)|endometrium(3)|liver(1)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23					Dinoprostone(DB00917)|Misoprostol(DB00929)	CAGGGCTGGGCCTGCCCCTAA	0.498																																					p.P465T		Atlas-SNP	.											.	PTGER4	49	.	0			c.C1393A						.						30	32	31					5																	40692406		2203	4300	6503	SO:0001583	missense	5734	exon3			GCTGGGCCTGCCC	L28175	CCDS3930.1	5p13.1	2012-08-08			ENSG00000171522	ENSG00000171522		"GPCR / Class A : Prostanoid receptors"	9596	protein-coding gene	gene with protein product		601586				7759114, 8661119	Standard	NM_000958		Approved	EP4	uc003jlz.3	P35408	OTTHUMG00000094769	ENST00000302472.3:c.1393C>A	chr5.hg19:g.40692406C>A	ENSP00000302846:p.Pro465Thr	114.0	0.0		111.0	30.0	NM_000958	Q3MJ87	Missense_Mutation	SNP	ENST00000302472.3	hg19	CCDS3930.1	.	.	.	.	.	.	.	.	.	.	C	8.588	0.883973	0.17467	.	.	ENSG00000171522	ENST00000302472	T	0.51325	0.71	5.81	0.569	0.17340	.	0.216989	0.39909	N	0.001236	T	0.29850	0.0746	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.16041	-1.0416	10	0.54805	T	0.06	-1.3758	2.4748	0.04573	0.1178:0.4355:0.1158:0.3309	.	465	P35408	PE2R4_HUMAN	T	465	ENSP00000302846:P465T	ENSP00000302846:P465T	P	+	1	0	PTGER4	40728163	0.000000	0.05858	0.030000	0.17652	0.614000	0.37383	-0.284000	0.08422	0.055000	0.16094	0.655000	0.94253	CCT	.	.		0.498	PTGER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211578.2	NM_000958		A	40692406	C	A	40692406	3	1	74	1	0	0	0	0	1	0	0	0	12758	739	26	3	1399	3	PTGER4	5	40692406	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	2253931	40692406	140222854	35	10011										
XRCC4	7518	hgsc.bcm.edu	37	chr5	82406962	82406962	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ggaccagctgatgtatacacGtttaatttttctaaagagtc	8	7	1	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr5:82406962G>C	ENST00000511817.1	+	3	335	c.255G>C	c.(253-255)acG>acC	p.T85T	XRCC4_ENST00000396027.4_Silent_p.T85T|XRCC4_ENST00000338635.6_Silent_p.T85T|XRCC4_ENST00000282268.3_Silent_p.T85T|XRCC4_ENST00000509268.1_3'UTR			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	85					cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		ATGTATACACGTTTAATTTTT	0.348								Non-homologous end-joining																													p.T85T		Atlas-SNP	.											.	XRCC4	37	.	0			c.G255C						.						96	96	96					5																	82406962		2203	4300	6503	SO:0001819	synonymous_variant	7518	exon3			ATACACGTTTAAT	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"X-ray repair, complementing defective, repair in Chinese hamster", "DNA repair protein XRCC4"	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.255G>C	chr5.hg19:g.82406962G>C		111.0	0.0		93.0	20.0	NM_003401	A8K3X4|Q9BS72|Q9UP94	Silent	SNP	ENST00000511817.1	hg19	CCDS4059.1																																																																																			.	.		0.348	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550		C	82406962	G	C	82406962	2	2	74	1	0	0	0	0	0	0	0	1	17470	1132	40	4		4	XRCC4	5	82406962	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	41714556	82406962	98508298	36	10012										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222692	140222692	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	acgtggtagcgaaggtgcgcGcagtggacgccgactcgggc	18	11	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr5:140222692G>T	ENST00000531613.1	+	1	1786	c.1786G>T	c.(1786-1788)Gca>Tca	p.A596S	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.A596S	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	596	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGGTGCGCGCAGTGGACGC	0.701																																					p.A596S		Atlas-SNP	.											.	PCDHA8	366	.	0			c.G1786T						.						70	72	71					5																	140222692		2196	4266	6462	SO:0001583	missense	56140	exon1			GTGCGCGCAGTGG	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1786G>T	chr5.hg19:g.140222692G>T	ENSP00000434655:p.Ala596Ser	64.0	0.0		42.0	21.0	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	hg19	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.479331	0.63849	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.61510	0.1;0.1	3.71	3.71	0.42584	Cadherin (4);Cadherin-like (1);	0.000000	0.36444	U	0.002583	D	0.83018	0.5163	H	0.98178	4.165	0.43372	D	0.99546	D;D	0.71674	0.998;0.99	P;P	0.62435	0.902;0.782	D	0.90541	0.4502	10	0.87932	D	0	.	15.9009	0.79377	0.0:0.0:1.0:0.0	.	596;596	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	S	596	ENSP00000434655:A596S;ENSP00000367363:A596S	ENSP00000367363:A596S	A	+	1	0	PCDHA8	140202876	1.000000	0.71417	1.000000	0.80357	0.024000	0.10985	5.926000	0.70070	1.789000	0.52484	0.306000	0.20318	GCA	.	.		0.701	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		T	140222692	G	T	140222692	3	4	74	1	0	0	0	0	1	0	0	0	11539	1087	38	1	1788	1	PCDHA8	5	140222692	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	57815730	140222692	40692568	37	10013										
GEMIN5	25929	hgsc.bcm.edu	37	chr5	154287212	154287212	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgctcctccccttcttggtcTgacacaccattctcaacagg	6	16	3	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr5:154287212T>C	ENST00000285873.7	-	16	2409	c.2334A>G	c.(2332-2334)tcA>tcG	p.S778S		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	778					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTTCTTGGTCTGACACACCAT	0.498																																					p.S778S		Atlas-SNP	.											.	GEMIN5	120	.	0			c.A2334G						.						167	149	155					5																	154287212		2203	4300	6503	SO:0001819	synonymous_variant	25929	exon16			TTGGTCTGACACA	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.2334A>G	chr5.hg19:g.154287212T>C		172.0	0.0		131.0	44.0	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Silent	SNP	ENST00000285873.7	hg19	CCDS4330.1																																																																																			.	.		0.498	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			C	154287212	T	C	154287212	2	2	74	1	0	0	0	0	0	0	0	1	6339	1567	55	2		2	GEMIN5	5	154287212	Silent	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	14064520	154287212	26628048	38	10014										
COL23A1	91522	hgsc.bcm.edu	37	chr5	177669082	177669082	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	aggcctggtggtcccggctcGcccttctggcccttcactcc	11	18	2	0	rs551123931		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr5:177669082G>T	ENST00000390654.3	-	27	1899	c.1542C>A	c.(1540-1542)ggC>ggA	p.G514G		NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	514	Collagen-like 5.|Gly-rich.				collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		GTCCCGGCTCGCCCTTCTGGC	0.662																																					p.G514G		Atlas-SNP	.											.	COL23A1	47	.	0			c.C1542A						.						14	19	18					5																	177669082		1929	4066	5995	SO:0001819	synonymous_variant	91522	exon27			CGGCTCGCCCTTC	AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767		"Collagens"	22990	protein-coding gene	gene with protein product		610043				12644459	Standard	NM_173465		Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.1542C>A	chr5.hg19:g.177669082G>T		53.0	0.0		46.0	8.0	NM_173465	Q8IVR4|Q9NT93	Silent	SNP	ENST00000390654.3	hg19	CCDS4436.1																																																																																			.	.		0.662	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465		T	177669082	G	T	177669082	2	4	74	1	0	0	0	0	0	0	0	1	3684	1074	38	1		1	COL23A1	5	177669082	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	23381870	177669082	3246178	39	10015										
GNMT	27232	hgsc.bcm.edu	37	chr6	42928679	42928679	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ctgctgcgccagcacggctgCcagcgggtgctcgacgtagc	15	15	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr6:42928679C>T	ENST00000372808.3	+	1	184	c.174C>T	c.(172-174)tgC>tgT	p.C58C		NM_018960.4	NP_061833.1	Q14749	GNMT_HUMAN	glycine N-methyltransferase	58					cellular protein modification process (GO:0006464)|glycogen metabolic process (GO:0005977)|methionine metabolic process (GO:0006555)|one-carbon metabolic process (GO:0006730)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|S-adenosylmethionine metabolic process (GO:0046500)	cytoplasm (GO:0005737)	folic acid binding (GO:0005542)|glycine binding (GO:0016594)|glycine N-methyltransferase activity (GO:0017174)			kidney(2)|large_intestine(1)|lung(1)	4	Colorectal(47;0.196)		all cancers(41;0.00196)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0461)		Glycine(DB00145)|S-Adenosylmethionine(DB00118)	AGCACGGCTGCCAGCGGGTGC	0.706																																					p.C58C		Atlas-SNP	.											.	GNMT	13	.	0			c.C174T						.						4	5	5					6																	42928679		1887	3821	5708	SO:0001819	synonymous_variant	27232	exon1			CGGCTGCCAGCGG	AF101475	CCDS4876.1	6p12	2008-02-05			ENSG00000124713	ENSG00000124713			4415	protein-coding gene	gene with protein product		606628				10843803, 9495250	Standard	NM_018960		Approved		uc003otd.3	Q14749	OTTHUMG00000014712	ENST00000372808.3:c.174C>T	chr6.hg19:g.42928679C>T		17.0	0.0		24.0	10.0	NM_018960	Q5T8W2|Q9NNZ1|Q9NS24	Silent	SNP	ENST00000372808.3	hg19	CCDS4876.1																																																																																			.	.		0.706	GNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040568.1	NM_018960		T	42928679	C	T	42928679	2	4	74	1	0	0	0	0	0	0	0	1	6548	747	26	3		3	GNMT	6	42928679	Silent	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10		42928679	128186388	40	10016										
DLK2	65989	hgsc.bcm.edu	37	chr6	43418725	43418725	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agccactggggcagaggcagTcgaagtcgtggacacggtcc	16	11	0	1	rs80187636		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr6:43418725T>A	ENST00000357338.3	-	6	1404	c.704A>T	c.(703-705)gAc>gTc	p.D235V	DLK2_ENST00000414245.1_Missense_Mutation_p.D229V|DLK2_ENST00000372488.3_Missense_Mutation_p.D235V|DLK2_ENST00000372485.1_Missense_Mutation_p.D229V	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	235	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			GCAGAGGCAGTCGAAGTCGTG	0.632																																					p.D235V		Atlas-SNP	.											.	DLK2	22	.	0			c.A704T						.						61	65	63					6																	43418725		2203	4300	6503	SO:0001583	missense	65989	exon6			AGGCAGTCGAAGT	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"EGF-like-domain, multiple 9"	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.704A>T	chr6.hg19:g.43418725T>A	ENSP00000349893:p.Asp235Val	102.0	0.0		114.0	50.0	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Missense_Mutation	SNP	ENST00000357338.3	hg19	CCDS4897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.51|15.51	2.854689|2.854689	0.51376|0.51376	.|.	.|.	ENSG00000171462|ENSG00000171462	ENST00000372485;ENST00000372488;ENST00000357338;ENST00000414245|ENST00000430324	D;D;D;D|.	0.91407|.	-2.84;-2.84;-2.84;-2.84|.	4.94|4.94	3.77|3.77	0.43336|0.43336	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);|.	0.359485|.	0.32120|.	N|.	0.006554|.	T|T	0.08403|0.08403	0.0209|0.0209	N|N	0.01473|0.01473	-0.845|-0.845	0.50813|0.50813	D|D	0.999896|0.999896	B|.	0.25272|.	0.122|.	B|.	0.25614|.	0.062|.	T|T	0.13629|0.13629	-1.0502|-1.0502	10|5	0.18276|.	T|.	0.48|.	.|.	10.4748|10.4748	0.44659|0.44659	0.0:0.0776:0.0:0.9224|0.0:0.0776:0.0:0.9224	.|.	235|.	Q6UY11|.	DLK2_HUMAN|.	V|S	229;235;235;229|141	ENSP00000361563:D229V;ENSP00000361566:D235V;ENSP00000349893:D235V;ENSP00000398906:D229V|.	ENSP00000349893:D235V|.	D|T	-|-	2|1	0|0	DLK2|DLK2	43526703|43526703	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.693000|0.693000	0.40251|0.40251	2.411000|2.411000	0.44600|0.44600	0.844000|0.844000	0.35094|0.35094	0.379000|0.379000	0.24179|0.24179	GAC|ACT	.	.		0.632	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932		A	43418725	T	A	43418725	3	1	74	1	0	0	0	0	1	0	0	0	4567	1667	58	4	451	4	DLK2	6	43418725	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	490046	43418725	127696342	41	10017										
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90577673	90577673	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	aacaccatctacctcttctgGccttaaacagagtatgatgc	6	12	3	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr6:90577673G>A	ENST00000551025.1	+	0	6101									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		ACCTCTTCTGGCCTTAAACAG	0.408																																					p.G1555D	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.G4664A						.						158	141	146					6																	90577673		1926	4129	6055			9994	exon8			CTTCTGGCCTTAA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90577673G>A		84.0	0.0		68.0	21.0	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	hg19																																																																																				.	.		0.408	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		A	90577673	G	A	90577673	1	1	74	0	1	0	0	0	0	0	0	0	2680	1203	42	3		3	CASP8AP2	6	90577673	RNA	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	47158948	90577673	80537394	42	10018										
ESR1	2099	hgsc.bcm.edu	37	chr6	152129176	152129176	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cggcccctgggcgaggtgtaCctggacagcagcaagcccgc	15	15	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr6:152129176C>A	ENST00000206249.3	+	1	491	c.129C>A	c.(127-129)taC>taA	p.Y43*	ESR1_ENST00000427531.2_5'Flank|ESR1_ENST00000443427.1_Nonsense_Mutation_p.Y43*|ESR1_ENST00000406599.1_Nonsense_Mutation_p.Y43*|ESR1_ENST00000338799.5_Nonsense_Mutation_p.Y43*|ESR1_ENST00000456483.2_Nonsense_Mutation_p.Y43*|ESR1_ENST00000440973.1_Nonsense_Mutation_p.Y43*	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	43	Interaction with DDX5; self-association.|Modulating (transactivation AF-1); mediates interaction with MACROD1.|Required for interaction with NCOA1.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	GCGAGGTGTACCTGGACAGCA	0.677																																					p.Y43X		Atlas-SNP	.											.	ESR1	94	.	0			c.C129A						.						24	27	26					6																	152129176		2203	4300	6503	SO:0001587	stop_gained	2099	exon1			GGTGTACCTGGAC	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"Nuclear hormone receptors"	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.129C>A	chr6.hg19:g.152129176C>A	ENSP00000206249:p.Tyr43*	57.0	0.0		62.0	26.0	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Nonsense_Mutation	SNP	ENST00000206249.3	hg19	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	C	39	7.630277	0.98399	.	.	ENSG00000091831	ENST00000404742;ENST00000440973;ENST00000338799;ENST00000456483;ENST00000446550;ENST00000443427;ENST00000206249;ENST00000406599	.	.	.	5.06	4.18	0.49190	.	0.242112	0.43919	D	0.000507	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.9107	0.35552	0.0:0.7734:0.0:0.2265	.	.	.	.	X	43	.	ENSP00000206249:Y43X	Y	+	3	2	ESR1	152170869	0.960000	0.32886	1.000000	0.80357	0.985000	0.73830	-0.056000	0.11787	2.359000	0.80004	0.563000	0.77884	TAC	.	.		0.677	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1			A	152129176	C	A	152129176	4	1	74	1	0	0	0	0	0	1	0	0	5258	518	18	3	131	3	ESR1	6	152129176	Nonsense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	61551503	152129176	18985891	43	10019										
EZR	7430	hgsc.bcm.edu	37	chr6	159210363	159210363	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ttgtatttggctggattgcaAactccagctctgcatccatg	9	10	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr6:159210363A>T	ENST00000367075.3	-	3	221	c.53T>A	c.(52-54)tTt>tAt	p.F18Y	EZR_ENST00000476189.1_5'UTR|EZR_ENST00000337147.7_Missense_Mutation_p.F18Y|EZR_ENST00000392177.4_Missense_Mutation_p.F18Y	NM_001111077.1	NP_001104547.1	P15311	EZRI_HUMAN	ezrin	18	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of endothelial barrier (GO:0061028)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|filopodium assembly (GO:0046847)|leukocyte cell-cell adhesion (GO:0007159)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|receptor internalization (GO:0031623)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|astrocyte projection (GO:0097449)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell tip (GO:0051286)|ciliary basal body (GO:0036064)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|microspike (GO:0044393)|microvillus (GO:0005902)|microvillus membrane (GO:0031528)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|Schwann cell microvillus (GO:0097454)|T-tubule (GO:0030315)|uropod (GO:0001931)|vesicle (GO:0031982)	actin filament binding (GO:0051015)|cell adhesion molecule binding (GO:0050839)|poly(A) RNA binding (GO:0044822)		EZR/ROS1(4)	breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	15		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)		CTGGATTGCAAACTCCAGCTC	0.378			T	ROS1	NSCLC																																p.F18Y		Atlas-SNP	.		Dom	yes		6	6q25.3	7430	ezrin		E	.	EZR	44	.	0			c.T53A						.						102	92	95					6																	159210363		2203	4300	6503	SO:0001583	missense	7430	exon2			ATTGCAAACTCCA	AF187552	CCDS5258.1	6q25.3	2010-12-10	2007-11-29	2007-11-29	ENSG00000092820	ENSG00000092820		"A-kinase anchor proteins"	12691	protein-coding gene	gene with protein product	"cytovillin 2"	123900	"villin 2 (ezrin)"	VIL2			Standard	NM_003379		Approved		uc003qrt.4	P15311	OTTHUMG00000015917	ENST00000367075.3:c.53T>A	chr6.hg19:g.159210363A>T	ENSP00000356042:p.Phe18Tyr	140.0	0.0		126.0	36.0	NM_003379	E1P5A8|P23714|Q4VX75|Q96CU8|Q9NSJ4	Missense_Mutation	SNP	ENST00000367075.3	hg19	CCDS5258.1	.	.	.	.	.	.	.	.	.	.	A	31	5.097975	0.94197	.	.	ENSG00000092820	ENST00000337147;ENST00000367075;ENST00000392177	T;T;T	0.78924	-1.22;-1.22;-1.15	4.78	4.78	0.61160	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.89001	0.6591	M	0.92784	3.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91709	0.5380	10	0.87932	D	0	.	14.7544	0.69552	1.0:0.0:0.0:0.0	.	18;18	E7EQR4;P15311	.;EZRI_HUMAN	Y	18	ENSP00000338934:F18Y;ENSP00000356042:F18Y;ENSP00000376016:F18Y	ENSP00000338934:F18Y	F	-	2	0	EZR	159130351	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.644000	0.91044	2.131000	0.65755	0.454000	0.30748	TTT	.	.		0.378	EZR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042878.1	NM_003379		T	159210363	A	T	159210363	3	4	74	1	0	0	0	0	1	0	0	0	5337	14	1	4	1755	4	EZR	6	159210363	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	7081187	159210363	11904704	44	10020										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161507445	161507445	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agatcagtcgagccctgaagGagctcttccatgaagccaga	11	11	2	4			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr6:161507445G>T	ENST00000392142.4	+	8	2555	c.2407G>T	c.(2407-2409)Gag>Tag	p.E803*	MAP3K4_ENST00000366919.2_Nonsense_Mutation_p.E803*|MAP3K4_ENST00000348824.7_Nonsense_Mutation_p.E803*|MAP3K4_ENST00000366920.2_Nonsense_Mutation_p.E803*	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	803					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AGCCCTGAAGGAGCTCTTCCA	0.433																																					p.E803X		Atlas-SNP	.											.	MAP3K4	364	.	0			c.G2407T						.						57	61	59					6																	161507445		2203	4300	6503	SO:0001587	stop_gained	4216	exon8			CTGAAGGAGCTCT	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.2407G>T	chr6.hg19:g.161507445G>T	ENSP00000375986:p.Glu803*	80.0	0.0		95.0	34.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Nonsense_Mutation	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	G	40	8.251123	0.98727	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-36.3925	19.6017	0.95566	0.0:0.0:1.0:0.0	.	.	.	.	X	803	.	ENSP00000297332:E803X	E	+	1	0	MAP3K4	161427435	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	9.476000	0.97823	2.622000	0.88805	0.655000	0.94253	GAG	.	.		0.433	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			T	161507445	G	T	161507445	4	4	74	1	0	0	0	0	0	1	0	0	9261	1175	41	3	2437	3	MAP3K4	6	161507445	Nonsense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	2297082	161507445	9607622	45	10021										
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4825905	4825905	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agcggctgcagtggactcggAagccgtctaccagcacctgt	13	13	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr7:4825905A>T	ENST00000348624.4	+	10	1251	c.1157A>T	c.(1156-1158)gAa>gTa	p.E386V	MIR4656_ENST00000579503.1_RNA|AP5Z1_ENST00000401897.1_Missense_Mutation_p.E386V	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	386					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											GTGGACTCGGAAGCCGTCTAC	0.627																																					p.E386V		Atlas-SNP	.											.	.	.	.	0			c.A1157T						.						41	49	46					7																	4825905		1986	4145	6131	SO:0001583	missense	9907	exon10			ACTCGGAAGCCGT	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"KIAA0415"	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1157A>T	chr7.hg19:g.4825905A>T	ENSP00000297562:p.Glu386Val	64.0	0.0		73.0	30.0	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	hg19	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.044372	0.75732	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.53206	0.65;0.63	5.29	2.89	0.33648	.	0.408719	0.26079	N	0.026467	T	0.58623	0.2135	M	0.78049	2.395	0.38295	D	0.94281	D	0.59357	0.985	P	0.55713	0.782	T	0.62110	-0.6923	10	0.72032	D	0.01	.	7.7425	0.28849	0.8331:0.0:0.1669:0.0	.	386	O43299	K0415_HUMAN	V	386	ENSP00000297562:E386V;ENSP00000384980:E386V	ENSP00000297562:E386V	E	+	2	0	KIAA0415	4792431	1.000000	0.71417	0.007000	0.13788	0.968000	0.65278	4.534000	0.60622	0.327000	0.23409	0.459000	0.35465	GAA	.	.		0.627	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			T	4825905	A	T	4825905	3	4	74	1	0	0	0	0	1	0	0	0	8184	246	9	4	1195	4	KIAA0415	7	4825905	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10		4825905	154312758	46	10022										
IGF2BP3	10643	hgsc.bcm.edu	37	chr7	23509624	23509624	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cacgaacgcgtagccagtctTcaccaggaagggtcccgaca	11	14	2	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr7:23509624T>A	ENST00000258729.3	-	1	462	c.106A>T	c.(106-108)Aag>Tag	p.K36*	IGF2BP3_ENST00000491719.1_5'Flank	NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	36	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						TAGCCAGTCTTCACCAGGAAG	0.637																																					p.K36X		Atlas-SNP	.											.	IGF2BP3	71	.	0			c.A106T						.						57	64	62					7																	23509624		2203	4300	6503	SO:0001587	stop_gained	10643	exon1			CAGTCTTCACCAG	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"RNA binding motif (RRM) containing"	28868	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 3", "cancer/testis antigen 98"	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.106A>T	chr7.hg19:g.23509624T>A	ENSP00000258729:p.Lys36*	87.0	0.0		80.0	30.0	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Nonsense_Mutation	SNP	ENST00000258729.3	hg19	CCDS5382.1	.	.	.	.	.	.	.	.	.	.	T	41	9.041004	0.99046	.	.	ENSG00000136231	ENST00000258729	.	.	.	3.82	2.59	0.31030	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.4517	9.817	0.40858	0.0:0.0:0.1736:0.8264	.	.	.	.	X	36	.	ENSP00000258729:K36X	K	-	1	0	IGF2BP3	23476149	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	7.613000	0.82986	0.305000	0.22832	0.455000	0.32223	AAG	.	.		0.637	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547		A	23509624	T	A	23509624	4	1	74	1	0	0	0	0	0	1	0	0	7584	1792	62	4	1693	4	IGF2BP3	7	23509624	Nonsense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	18683719	23509624	135629039	47	10023										
AMPH	273	hgsc.bcm.edu	37	chr7	38457451	38457451	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ctcctccactggctcctcagCccgagtgtccattccaaggt	8	17	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr7:38457451C>A	ENST00000356264.2	-	17	1587	c.1372G>T	c.(1372-1374)Gct>Tct	p.A458S	AMPH_ENST00000471913.1_Intron|AMPH_ENST00000325590.5_Intron|AMPH_ENST00000428293.2_Intron	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	458					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						GGCTCCTCAGCCCGAGTGTCC	0.597																																					p.A458S		Atlas-SNP	.											.	AMPH	157	.	0			c.G1372T						.						115	92	100					7																	38457451		2203	4300	6503	SO:0001583	missense	273	exon17			CCTCAGCCCGAGT		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1372G>T	chr7.hg19:g.38457451C>A	ENSP00000348602:p.Ala458Ser	74.0	0.0		67.0	19.0	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	hg19	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	C	14.07	2.424877	0.43020	.	.	ENSG00000078053	ENST00000356264	T	0.59083	0.29	4.75	2.87	0.33458	.	.	.	.	.	T	0.25457	0.0619	N	0.08118	0	0.80722	D	1	B	0.32245	0.361	B	0.24155	0.051	T	0.10359	-1.0633	9	0.07030	T	0.85	9.8062	5.0881	0.14693	0.0:0.4882:0.2886:0.2231	.	458	P49418	AMPH_HUMAN	S	458	ENSP00000348602:A458S	ENSP00000348602:A458S	A	-	1	0	AMPH	38423976	0.164000	0.22935	0.920000	0.36463	0.973000	0.67179	0.102000	0.15272	0.990000	0.38787	0.609000	0.83330	GCT	.	.		0.597	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		A	38457451	C	A	38457451	3	1	74	1	0	0	0	0	1	0	0	0	588	739	26	3	735	3	AMPH	7	38457451	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	14947827	38457451	120681212	48	10024										
NPTX2	4885	hgsc.bcm.edu	37	chr7	98256508	98256508	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcccctgtttgtcagtgacgGcaagtggcaccacatctgtg	12	12	2	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr7:98256508G>T	ENST00000265634.3	+	4	1085	c.920G>T	c.(919-921)gGc>gTc	p.G307V		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	307	Pentaxin.				synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			GTCAGTGACGGCAAGTGGCAC	0.642																																					p.G307V		Atlas-SNP	.											.	NPTX2	45	.	0			c.G920T						.						86	72	76					7																	98256508		2203	4300	6503	SO:0001583	missense	4885	exon4			GTGACGGCAAGTG		CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"apexin"	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.920G>T	chr7.hg19:g.98256508G>T	ENSP00000265634:p.Gly307Val	64.0	0.0		64.0	30.0	NM_002523	A4D267|Q86XV7|Q96G70	Missense_Mutation	SNP	ENST00000265634.3	hg19	CCDS5657.1	.	.	.	.	.	.	.	.	.	.	G	31	5.099807	0.94197	.	.	ENSG00000106236	ENST00000265634	T	0.66099	-0.19	5.38	5.38	0.77491	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.86661	0.5986	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90623	0.4561	10	0.66056	D	0.02	-12.8195	18.4772	0.90797	0.0:0.0:1.0:0.0	.	307	P47972	NPTX2_HUMAN	V	307	ENSP00000265634:G307V	ENSP00000265634:G307V	G	+	2	0	NPTX2	98094444	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.813000	0.99286	2.677000	0.91161	0.650000	0.86243	GGC	.	.		0.642	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523		T	98256508	G	T	98256508	3	4	74	1	0	0	0	0	1	0	0	0	10612	1203	42	3	934	3	NPTX2	7	98256508	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	59799057	98256508	60882155	49	10025										
DGKI	9162	hgsc.bcm.edu	37	chr7	137080389	137080389	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gctcctgcatccaccagaagCtggcacacagcccggttccg	10	17	0	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr7:137080389C>A	ENST00000288490.5	-	33	3036	c.3036G>T	c.(3034-3036)caG>caT	p.Q1012H	DGKI_ENST00000494390.1_5'UTR|DGKI_ENST00000424189.2_Missense_Mutation_p.Q1025H|DGKI_ENST00000453654.2_Missense_Mutation_p.Q681H|DGKI_ENST00000446122.1_Missense_Mutation_p.Q994H	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	1012					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						CCACCAGAAGCTGGCACACAG	0.567																																					p.Q1012H		Atlas-SNP	.											.	DGKI	335	.	0			c.G3036T						.						77	67	71					7																	137080389		2203	4300	6503	SO:0001583	missense	9162	exon33			CAGAAGCTGGCAC	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.3036G>T	chr7.hg19:g.137080389C>A	ENSP00000288490:p.Gln1012His	132.0	0.0		142.0	37.0	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	hg19	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	C	4.387	0.071385	0.08436	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.65916	-0.18;-0.18;-0.18	5.35	3.16	0.36331	Ankyrin repeat-containing domain (3);	0.127182	0.53938	D	0.000053	T	0.48714	0.1515	L	0.45744	1.44	0.35490	D	0.798896	B;B	0.09022	0.001;0.002	B;B	0.14023	0.006;0.01	T	0.48747	-0.9008	10	0.12103	T	0.63	.	8.9371	0.35706	0.0:0.7282:0.0:0.2718	.	681;1012	E9PFX6;O75912	.;DGKI_HUMAN	H	681;929;1015;1012;994	ENSP00000392161:Q681H;ENSP00000288490:Q1012H;ENSP00000399131:Q994H	ENSP00000288490:Q1012H	Q	-	3	2	DGKI	136730929	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.585000	0.23879	1.384000	0.46424	-0.145000	0.13849	CAG	.	.		0.567	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		A	137080389	C	A	137080389	3	1	74	1	0	0	0	0	1	0	0	0	4473	796	28	3	169	3	DGKI	7	137080389	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	38823881	137080389	22058274	50	10026										
TPK1	27010	hgsc.bcm.edu	37	chr7	144150676	144150676	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ggtccagaggagtgggtggtCagtttccacagtcacaacac	13	10	2	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr7:144150676C>A	ENST00000360057.3	-	9	796	c.694G>T	c.(694-696)Gac>Tac	p.D232Y	RNU6ATAC40P_ENST00000408580.1_RNA|TPK1_ENST00000378099.3_Missense_Mutation_p.D183Y|TPK1_ENST00000549981.1_3'UTR|TPK1_ENST00000547966.1_5'UTR|TPK1_ENST00000538212.2_Missense_Mutation_p.D178Y	NM_022445.3	NP_071890.2	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1	232					small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788)			large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2)	19					Thiamine(DB00152)	AGTGGGTGGTCAGTTTCCACA	0.453																																					p.D232Y	Ovarian(45;88 1034 2073 5829 28455)	Atlas-SNP	.											.	TPK1	41	.	0			c.G694T						.						204	180	188					7																	144150676		2203	4300	6503	SO:0001583	missense	27010	exon9			GGTGGTCAGTTTC	AB028138	CCDS5888.1, CCDS55178.1	7q34-q35	2008-07-18			ENSG00000196511	ENSG00000196511			17358	protein-coding gene	gene with protein product	"placental protein 20", "thiamine pyrophosphokinase 1", "thiamine kinase", "thiamine diphosphokinase"	606370				11342111	Standard	NM_022445		Approved	HTPK1, PP20	uc003weq.3	Q9H3S4	OTTHUMG00000152774	ENST00000360057.3:c.694G>T	chr7.hg19:g.144150676C>A	ENSP00000353165:p.Asp232Tyr	119.0	0.0		122.0	29.0	NM_022445	A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602	Missense_Mutation	SNP	ENST00000360057.3	hg19	CCDS5888.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.563419	0.86335	.	.	ENSG00000196511	ENST00000360057;ENST00000538212;ENST00000378099	T;T;T	0.78707	-1.2;-1.2;-1.2	5.79	5.79	0.91817	Thiamin pyrophosphokinase, vitamin B1-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.90738	0.7093	M	0.91872	3.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.994;0.999;0.995	D	0.92218	0.5782	10	0.87932	D	0	-24.9542	17.5252	0.87798	0.0:1.0:0.0:0.0	.	183;232;178	F5GZG6;Q9H3S4;Q6ZQX6	.;TPK1_HUMAN;.	Y	232;178;183	ENSP00000353165:D232Y;ENSP00000438813:D178Y;ENSP00000367339:D183Y	ENSP00000353165:D232Y	D	-	1	0	TPK1	143781609	0.977000	0.34250	0.969000	0.41365	0.967000	0.64934	3.298000	0.51818	2.746000	0.94184	0.655000	0.94253	GAC	.	.		0.453	TPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327777.1	NM_022445		A	144150676	C	A	144150676	3	1	74	1	0	0	0	0	1	0	0	0	16419	826	29	3	41	3	TPK1	7	144150676	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	7070287	144150676	14987987	51	10027										
NOS3	4846	hgsc.bcm.edu	37	chr7	150696315	150696315	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ccctgggcctgcgctggtacGccctcccggcagtgtccaac	12	18	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr7:150696315G>C	ENST00000484524.1	+	8	994	c.994G>C	c.(994-996)Gcc>Ccc	p.A332P	NOS3_ENST00000467517.1_Missense_Mutation_p.A332P|NOS3_ENST00000461406.1_Missense_Mutation_p.A126P|NOS3_ENST00000297494.3_Missense_Mutation_p.A332P	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCGCTGGTACGCCCTCCCGGC	0.642																																					p.A332P		Atlas-SNP	.											.	NOS3	131	.	0			c.G994C						.						61	68	66					7																	150696315		2201	4295	6496	SO:0001583	missense	4846	exon8			TGGTACGCCCTCC		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.994G>C	chr7.hg19:g.150696315G>C	ENSP00000420215:p.Ala332Pro	42.0	0.0		51.0	32.0	NM_001160111	Q495E5	Missense_Mutation	SNP	ENST00000484524.1	hg19	CCDS55182.1	.	.	.	.	.	.	.	.	.	.	N	28.3	4.911772	0.92178	.	.	ENSG00000164867	ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517	T;T;T;T	0.35605	1.3;1.47;1.3;1.3	5.59	5.59	0.84812	Nitric oxide synthase, oxygenase domain (2);	0.000000	0.64402	D	0.000014	T	0.67373	0.2886	M	0.89353	3.025	0.58432	D	0.999996	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.997;0.995;0.973	T	0.73681	-0.3906	10	0.87932	D	0	-9.7199	17.0996	0.86645	0.0:0.0:1.0:0.0	.	332;332;332;126;332	A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474	.;.;.;.;NOS3_HUMAN	P	332;126;332;332	ENSP00000297494:A332P;ENSP00000417143:A126P;ENSP00000420215:A332P;ENSP00000420551:A332P	ENSP00000297494:A332P	A	+	1	0	NOS3	150327248	0.997000	0.39634	0.958000	0.39756	0.847000	0.48162	6.771000	0.74996	2.620000	0.88729	0.639000	0.83563	GCC	.	.		0.642	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		C	150696315	G	C	150696315	3	2	74	1	0	0	0	0	1	0	0	0	10553	1087	38	4	1024	4	NOS3	7	150696315	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	6545639	150696315	8442348	52	10028										
POLR3D	661	hgsc.bcm.edu	37	chr8	22105780	22105780	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	aacagatcttgcgtatgctgGagaaggacgatgtgggtacc	14	7	1	2	rs199704064		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr8:22105780G>T	ENST00000397802.4	+	4	690	c.475G>T	c.(475-477)Gag>Tag	p.E159*	POLR3D_ENST00000306433.4_Nonsense_Mutation_p.E159*			P05423	RPC4_HUMAN	polymerase (RNA) III (DNA directed) polypeptide D, 44kDa	159					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	13				Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		GCGTATGCTGGAGAAGGACGA	0.502																																					p.E159X		Atlas-SNP	.											.	POLR3D	26	.	0			c.G475T						.						102	109	107					8																	22105780		2203	4300	6503	SO:0001587	stop_gained	661	exon5			ATGCTGGAGAAGG	M17754	CCDS34858.1	8q21	2013-01-21	2003-04-01	2003-04-04	ENSG00000168495	ENSG00000168495		"RNA polymerase subunits"	1080	protein-coding gene	gene with protein product		187280	"BN51 (BHK21) temperature sensitivity complementing"	BN51T		12391170, 11279001	Standard	NM_001722		Approved	TSBN51, RPC4	uc003xbl.3	P05423	OTTHUMG00000163778	ENST00000397802.4:c.475G>T	chr8.hg19:g.22105780G>T	ENSP00000380904:p.Glu159*	117.0	0.0		966.0	46.0	NM_001722	Q6FI28|Q9BPV7|Q9BPZ1|Q9BXB3	Nonsense_Mutation	SNP	ENST00000397802.4	hg19	CCDS34858.1	.	.	.	.	.	.	.	.	.	.	G	38	6.713816	0.97784	.	.	ENSG00000168495	ENST00000306433;ENST00000519237;ENST00000397802	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-36.3725	18.7009	0.91620	0.0:0.0:1.0:0.0	.	.	.	.	X	159	.	ENSP00000303088:E159X	E	+	1	0	POLR3D	22161725	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	7.373000	0.79623	2.695000	0.91970	0.655000	0.94253	GAG	.	G|1.000;A|0.000		0.502	POLR3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375434.2	NM_001722		T	22105780	G	T	22105780	4	4	74	1	0	0	0	0	0	1	0	0	12240	1175	41	3	489	3	POLR3D	8	22105780	Nonsense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10		22105780	124258242	53	10029										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125074249	125074249	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cccttgcccccatcacacagGtggatggaacccagcctggg	11	16	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr8:125074249G>T	ENST00000522917.1	+	25	3510	c.3304G>T	c.(3304-3306)Gtg>Ttg	p.V1102L	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6-AS2_ENST00000601180.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.V1102L	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1102						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CATCACACAGGTGGATGGAAC	0.517																																					p.V1102L		Atlas-SNP	.											.	FER1L6	268	.	0			c.G3304T						.						82	85	84					8																	125074249		1956	4151	6107	SO:0001583	missense	654463	exon25			ACACAGGTGGATG	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.3304G>T	chr8.hg19:g.125074249G>T	ENSP00000428280:p.Val1102Leu	111.0	0.0		268.0	213.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	2.569	-0.300040	0.05532	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.80824	-1.42;-1.42	5.51	0.735	0.18300	C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.62380	0.2423	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46857	-0.9161	9	0.27785	T	0.31	0.0988	9.3562	0.38168	0.3681:0.0:0.6319:0.0	.	1102	Q2WGJ9	FR1L6_HUMAN	L	1102	ENSP00000428280:V1102L;ENSP00000381982:V1102L	ENSP00000381982:V1102L	V	+	1	0	FER1L6	125143430	0.402000	0.25311	0.003000	0.11579	0.001000	0.01503	0.134000	0.15932	0.142000	0.18901	-0.122000	0.15005	GTG	.	.		0.517	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		T	125074249	G	T	125074249	3	4	74	1	0	0	0	0	1	0	0	0	5823	1261	44	3	3398	3	FER1L6	8	125074249	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	102968469	125074249	21289773	54	10030										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139737668	139737668	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	aggggggcctgggacaccagGgggtcctggagggccctgta	20	10	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr8:139737668G>A	ENST00000303045.6	-	24	2601	c.2155C>T	c.(2155-2157)Cct>Tct	p.P719S	COL22A1_ENST00000435777.1_Missense_Mutation_p.P719S	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	719	Collagen-like 5.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GGGACACCAGGGGGTCCTGGA	0.582										HNSCC(7;0.00092)																											p.P719S		Atlas-SNP	.											COL22A1,mucosal,malignant_melanoma,0,1	COL22A1	390	.	0			c.C2155T						.						51	59	56					8																	139737668		2203	4300	6503	SO:0001583	missense	169044	exon24			CACCAGGGGGTCC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2155C>T	chr8.hg19:g.139737668G>A	ENSP00000303153:p.Pro719Ser	92.0	0.0		212.0	10.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.054787	0.36277	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.98649	-5.05;-5.05	4.94	4.07	0.47477	.	0.000000	0.49916	D	0.000132	D	0.97414	0.9154	M	0.77820	2.39	0.44485	D	0.997428	B;B	0.31931	0.347;0.186	B;B	0.35859	0.135;0.212	D	0.96101	0.9069	10	0.20046	T	0.44	.	9.9387	0.41567	0.0965:0.0:0.9035:0.0	.	719;719	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	S	719;719;432	ENSP00000303153:P719S;ENSP00000387655:P719S	ENSP00000303153:P719S	P	-	1	0	COL22A1	139806850	0.982000	0.34865	0.638000	0.29380	0.820000	0.46376	2.896000	0.48656	1.390000	0.46547	-0.140000	0.14226	CCT	.	.		0.582	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139737668	G	A	139737668	3	1	74	1	0	0	0	0	1	0	0	0	3683	1232	43	3	2893	3	COL22A1	8	139737668	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	14663419	139737668	6626354	55	10031										
KCNK9	51305	hgsc.bcm.edu	37	chr8	140631020	140631020	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgcagggccacgtagtccccGaacccaatggtagtcaacgt	11	13	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr8:140631020G>T	ENST00000520439.1	-	2	669	c.606C>A	c.(604-606)ttC>ttA	p.F202L	KCNK9_ENST00000303015.1_Missense_Mutation_p.F202L|KCNK9_ENST00000523477.1_5'Flank	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	202					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	CGTAGTCCCCGAACCCAATGG	0.587																																					p.F202L		Atlas-SNP	.											.	KCNK9	100	.	0			c.C606A						.						75	76	75					8																	140631020		2203	4300	6503	SO:0001583	missense	51305	exon2			GTCCCCGAACCCA	AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.606C>A	chr8.hg19:g.140631020G>T	ENSP00000430676:p.Phe202Leu	93.0	0.0		283.0	214.0	NM_016601	Q2M290|Q540F2	Missense_Mutation	SNP	ENST00000520439.1	hg19	CCDS6377.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.813097	0.70912	.	.	ENSG00000169427	ENST00000522317;ENST00000303015;ENST00000520439	T;T;T	0.28069	1.63;1.63;1.63	5.85	1.55	0.23275	Ion transport 2 (1);	0.000000	0.85682	D	0.000000	T	0.40743	0.1129	L	0.56340	1.77	0.80722	D	1	D	0.64830	0.994	D	0.64237	0.923	T	0.11743	-1.0575	10	0.41790	T	0.15	.	6.5738	0.22553	0.5716:0.0:0.4284:0.0	.	202	Q9NPC2	KCNK9_HUMAN	L	202	ENSP00000429847:F202L;ENSP00000302166:F202L;ENSP00000430676:F202L	ENSP00000302166:F202L	F	-	3	2	KCNK9	140700202	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.107000	0.31110	0.382000	0.24878	0.655000	0.94253	TTC	.	.		0.587	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601		T	140631020	G	T	140631020	3	4	74	1	0	0	0	0	1	0	0	0	8081	1049	37	1	522	1	KCNK9	8	140631020	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	893352	140631020	5733002	56	10032										
SCRIB	23513	hgsc.bcm.edu	37	chr8	144891811	144891811	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcctcagccgacgggccctcGggctcagcctcagagactgt	13	16	3	1	rs546935238		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr8:144891811G>A	ENST00000320476.3	-	14	1614	c.1608C>T	c.(1606-1608)ccC>ccT	p.P536P	SCRIB_ENST00000356994.2_Silent_p.P536P|SCRIB_ENST00000377533.3_Silent_p.P455P	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	536	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			ACGGGCCCTCGGGCTCAGCCT	0.662													G|||	1	0.000199681	0	0	5008	,	,		16028	0		0	False		,,,				2504	0.001				p.P536P	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C1608T						.						57	55	55					8																	144891811		2203	4300	6503	SO:0001819	synonymous_variant	23513	exon14			GCCCTCGGGCTCA	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.1608C>T	chr8.hg19:g.144891811G>A		51.0	0.0		121.0	94.0	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	hg19	CCDS6411.1																																																																																			.	.		0.662	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		A	144891811	G	A	144891811	2	1	74	1	0	0	0	0	0	0	0	1	13952	1103	39	1		1	SCRIB	8	144891811	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	4260791	144891811	1472211	57	10033										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2097384	2097385	+	Splice_Site	DNP	GG	GG	TC													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tccctttccactggttcttaGgggaaaggaggtgctaagac							TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr9:2097384_2097385GG>TC	ENST00000382203.1	+	21	3200_3201	c.2991_2992GG>TC	c.(2989-2994)aaGGgg>aaTCgg	p.997_998KG>NR	SMARCA2_ENST00000357248.2_Splice_Site_p.997_998KG>NR|SMARCA2_ENST00000349721.2_Splice_Site_p.997_998KG>NR|SMARCA2_ENST00000382194.1_Splice_Site_p.997_998KG>NR			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	997					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		CTGGTTCTTAGGGGAAAGGAGG	0.381																																					.|p.G998R		Atlas-SNP	.											.	SMARCA2	313	.	0			c.2992-1G>T|c.G2992C						.																																			SO:0001630	splice_region_variant	6595	exon21			TTCTTAGGGGAAA|TCTTAGGGGAAAG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	Exception_encountered	chr9.hg19:g.2097384_2097385delinsTC		50.0	0.0		84.0	38.0	NM_003070|NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Splice_Site|Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1																																																																																			.	.		0.381	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	Missense_Mutation	TC	2097385	GG	TC	2097384	5	4	74	1	0	0	0	0	0	0	1	0	14784	1014	35	3	3069	3	SMARCA2	9	2097384	Splice_Site	DNP	GG	TCGA-CC-A7II-01A-11D-A33K-10		2097384	139116047	58	10034										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5923025	5923025	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agacactggtactgaatccaAtgaggcaaatgactctggaa	10	8	1	4			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr9:5923025A>G	ENST00000399933.3	-	8	2970	c.2971T>C	c.(2971-2973)Ttg>Ctg	p.L991L	KIAA2026_ENST00000381461.2_Silent_p.L961L	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	991										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		ACTGAATCCAATGAGGCAAAT	0.398																																					p.L991L		Atlas-SNP	.											.	KIAA2026	231	.	0			c.T2971C						.						144	135	137					9																	5923025		1903	4127	6030	SO:0001819	synonymous_variant	158358	exon8			AATCCAATGAGGC	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.2971T>C	chr9.hg19:g.5923025A>G		146.0	0.0		167.0	61.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	hg19																																																																																				.	.		0.398	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		G	5923025	A	G	5923025	2	3	74	1	0	0	0	0	0	0	0	1	8279	98	4	2		2	KIAA2026	9	5923025	Silent	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	3825641	5923025	135290406	59	10035										
VCP	7415	hgsc.bcm.edu	37	chr9	35068346	35068346	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gagaatggctgttgataggtCatcaccttttgaactagaag	11	6	2	4			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr9:35068346C>T	ENST00000358901.6	-	2	926	c.31G>A	c.(31-33)Gac>Aac	p.D11N		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	11					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GTTGATAGGTCATCACCTTTT	0.458																																					p.D11N		Atlas-SNP	.											.	VCP	64	.	0			c.G31A						.						222	202	209					9																	35068346		2203	4300	6503	SO:0001583	missense	7415	exon2			ATAGGTCATCACC	AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"ATPases / AAA-type"	12666	protein-coding gene	gene with protein product		601023	"valosin-containing protein"			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.31G>A	chr9.hg19:g.35068346C>T	ENSP00000351777:p.Asp11Asn	57.0	0.0		93.0	34.0	NM_007126	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Missense_Mutation	SNP	ENST00000358901.6	hg19	CCDS6573.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168585	0.78339	.	.	ENSG00000165280	ENST00000358901	D	0.95137	-3.62	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.94778	0.8314	M	0.80746	2.51	0.80722	D	1	B	0.15719	0.014	B	0.19946	0.027	D	0.91181	0.4976	10	0.52906	T	0.07	-6.7381	18.8014	0.92018	0.0:1.0:0.0:0.0	.	11	P55072	TERA_HUMAN	N	11	ENSP00000351777:D11N	ENSP00000351777:D11N	D	-	1	0	VCP	35058346	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.703000	0.84585	2.882000	0.98803	0.655000	0.94253	GAC	.	.		0.458	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126		T	35068346	C	T	35068346	3	4	74	1	0	0	0	0	1	0	0	0	17155	826	29	3	2453	3	VCP	9	35068346	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	29145321	35068346	106145085	60	10036										
KIAA1958	158405	hgsc.bcm.edu	37	chr9	115421771	115421771	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gtaaggcaggcatgtcgggcGcgcgttctcgcaacatcgtc	14	12	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr9:115421771G>A	ENST00000337530.6	+	4	1869	c.1573G>A	c.(1573-1575)Gcg>Acg	p.A525T	KIAA1958_ENST00000536272.1_Missense_Mutation_p.A553T	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	525										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						CATGTCGGGCGCGCGTTCTCG	0.577																																					p.A525T		Atlas-SNP	.											.	KIAA1958	52	.	0			c.G1573A						.						61	50	54					9																	115421771		2203	4300	6503	SO:0001583	missense	158405	exon4			TCGGGCGCGCGTT	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.1573G>A	chr9.hg19:g.115421771G>A	ENSP00000336940:p.Ala525Thr	117.0	0.0		159.0	69.0	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Missense_Mutation	SNP	ENST00000337530.6	hg19	CCDS35108.1	.	.	.	.	.	.	.	.	.	.	G	9.400	1.077732	0.20227	.	.	ENSG00000165185	ENST00000337530;ENST00000536272	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	T	0.17577	0.0422	N	0.08118	0	0.23972	N	0.996306	P;B	0.35226	0.491;0.198	B;B	0.25405	0.06;0.016	T	0.07849	-1.0751	8	0.13853	T	0.58	.	14.2383	0.65941	0.0:0.0:0.8507:0.1493	.	553;525	B7ZKW6;Q8N8K9	.;K1958_HUMAN	T	525;553	.	ENSP00000336940:A525T	A	+	1	0	KIAA1958	114461592	1.000000	0.71417	0.961000	0.40146	0.924000	0.55760	4.771000	0.62318	2.676000	0.91093	0.655000	0.94253	GCG	.	.		0.577	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465		A	115421771	G	A	115421771	3	1	74	1	0	0	0	0	1	0	0	0	8273	1087	38	1	1583	1	KIAA1958	9	115421771	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	80353425	115421771	25791660	61	10037										
MRPS2	51116	hgsc.bcm.edu	37	chr9	138392921	138392921	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ctcggccgagccgcaggacgCttggaagcgcgacggccctt	15	15	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr9:138392921C>T	ENST00000371785.1	+	3	330	c.121C>T	c.(121-123)Ctt>Ttt	p.L41F	MRPS2_ENST00000488610.1_3'UTR|RP11-426A6.5_ENST00000415062.1_RNA|C9orf116_ENST00000429260.2_5'Flank|C9orf116_ENST00000371789.3_5'Flank|MRPS2_ENST00000241600.5_Missense_Mutation_p.L41F|C9orf116_ENST00000371791.1_Intron			Q9Y399	RT02_HUMAN	mitochondrial ribosomal protein S2	41					translation (GO:0006412)	mitochondrion (GO:0005739)|small ribosomal subunit (GO:0015935)	structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(1)|prostate(2)|urinary_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.46e-53)|Epithelial(140;2.04e-47)|all cancers(34;1.23e-42)		CCGCAGGACGCTTGGAAGCGC	0.701																																					p.L41F		Atlas-SNP	.											.	MRPS2	17	.	0			c.C121T						.						9	11	10					9																	138392921		2146	4231	6377	SO:0001583	missense	51116	exon2			AGGACGCTTGGAA	AB051627	CCDS6990.1	9q34	2012-09-13			ENSG00000122140	ENSG00000122140		"Mitochondrial ribosomal proteins / small subunits"	14495	protein-coding gene	gene with protein product		611971					Standard	NM_016034		Approved	CGI-91	uc004cfv.5	Q9Y399	OTTHUMG00000020910	ENST00000371785.1:c.121C>T	chr9.hg19:g.138392921C>T	ENSP00000360850:p.Leu41Phe	68.0	0.0		89.0	29.0	NM_016034	Q5T899|Q9BSQ4	Missense_Mutation	SNP	ENST00000371785.1	hg19	CCDS6990.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.306675	0.40795	.	.	ENSG00000122140	ENST00000371785;ENST00000241600;ENST00000453385	T;T;T	0.34667	1.84;1.84;1.35	4.17	-2.89	0.05665	.	2.045970	0.02694	U	0.111049	T	0.24812	0.0602	L	0.48642	1.525	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.06954	-1.0798	10	0.10636	T	0.68	-1.7267	1.6937	0.02857	0.1388:0.3989:0.1476:0.3147	.	41	Q9Y399	RT02_HUMAN	F	41;41;55	ENSP00000360850:L41F;ENSP00000241600:L41F;ENSP00000400082:L55F	ENSP00000241600:L41F	L	+	1	0	MRPS2	137532742	0.000000	0.05858	0.002000	0.10522	0.091000	0.18340	-0.389000	0.07342	-0.154000	0.11118	0.484000	0.47621	CTT	.	.		0.701	MRPS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054998.1			T	138392921	C	T	138392921	3	4	74	1	0	0	0	0	1	0	0	0	9840	797	28	3	127	3	MRPS2	9	138392921	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	22971150	138392921	2820510	62	10038										
PTGDS	5730	hgsc.bcm.edu	37	chr9	139873558	139873558	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcccctgccacggatggtggCctcaacctgacctccacctt	9	18	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr9:139873558C>A	ENST00000371625.3	+	2	302	c.228C>A	c.(226-228)ggC>ggA	p.G76G	RP11-229P13.19_ENST00000413913.2_RNA|PTGDS_ENST00000460340.1_3'UTR|PTGDS_ENST00000224167.2_Silent_p.G76G	NM_000954.5	NP_000945.3	P41222	PTGDS_HUMAN	prostaglandin D2 synthase 21kDa (brain)	76					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|prostaglandin biosynthetic process (GO:0001516)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|rough endoplasmic reticulum (GO:0005791)	fatty acid binding (GO:0005504)|prostaglandin-D synthase activity (GO:0004667)|retinoid binding (GO:0005501)|transporter activity (GO:0005215)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CGGATGGTGGCCTCAACCTGA	0.662																																					p.G76G		Atlas-SNP	.											.	PTGDS	15	.	0			c.C228A						.						70	71	71					9																	139873558		2203	4300	6503	SO:0001819	synonymous_variant	5730	exon2			TGGTGGCCTCAAC	AA621632	CCDS7019.1	9q34.2-q34.3	2011-11-15	2002-08-29		ENSG00000107317	ENSG00000107317	5.3.99.2	"Lipocalins"	9592	protein-coding gene	gene with protein product	"lipocalin-type prostaglandin D synthase"	176803	"prostaglandin D2 synthase (21kD, brain)"			1902577	Standard	NM_000954		Approved	PGDS, L-PGDS	uc004cke.3	P41222	OTTHUMG00000020957	ENST00000371625.3:c.228C>A	chr9.hg19:g.139873558C>A		67.0	0.0		79.0	28.0	NM_000954	B2R727|Q5SQ10|Q7M4P3|Q9UC22|Q9UCC9|Q9UCD9	Silent	SNP	ENST00000371625.3	hg19	CCDS7019.1	.	.	.	.	.	.	.	.	.	.	c	7.848	0.723455	0.15439	.	.	ENSG00000107317	ENST00000446677	.	.	.	4.44	-2.1	0.07210	.	.	.	.	.	T	0.20901	0.0503	.	.	.	0.09310	N	0.999994	.	.	.	.	.	.	T	0.28933	-1.0028	4	.	.	.	-7.4149	3.3462	0.07136	0.4232:0.3251:0.1661:0.0856	.	.	.	.	T	99	.	.	P	+	1	0	PTGDS	138993379	0.001000	0.12720	0.004000	0.12327	0.050000	0.14768	0.583000	0.23849	-0.016000	0.14127	0.457000	0.33378	CCT	.	.		0.662	PTGDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055188.1	NM_000954		A	139873558	C	A	139873558	2	1	74	1	0	0	0	0	0	0	0	1	12754	726	26	3		3	PTGDS	9	139873558	Silent	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	1480637	139873558	1339873	63	10039										
C10orf18	54906	hgsc.bcm.edu	37	chr10	5803296	5803296	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agaacataatgttgaagtcaTttcagagtgcaaatatcatt	7	5	3	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr10:5803296T>C	ENST00000328090.5	+	19	7661	c.7036T>C	c.(7036-7038)Ttt>Ctt	p.F2346L		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2346																	GTTGAAGTCATTTCAGAGTGC	0.318																																					p.F2346L		Atlas-SNP	.											.	.	.	.	0			c.T7036C						.						114	108	110					10																	5803296		1876	4107	5983	SO:0001583	missense	54906	exon19			AAGTCATTTCAGA	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.7036T>C	chr10.hg19:g.5803296T>C	ENSP00000328426:p.Phe2346Leu	54.0	0.0		35.0	13.0	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	hg19	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	T	11.66	1.705558	0.30232	.	.	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.44083	0.93	6.06	6.06	0.98353	.	0.546345	0.18169	N	0.149519	T	0.27933	0.0688	N	0.08118	0	0.09310	N	1	B	0.16802	0.019	B	0.14023	0.01	T	0.23691	-1.0181	10	0.49607	T	0.09	.	16.2741	0.82634	0.0:0.0:0.0:1.0	.	2346	Q5VWN6	F208B_HUMAN	L	2346;1541	ENSP00000328426:F2346L	ENSP00000328426:F2346L	F	+	1	0	C10orf18	5843302	0.304000	0.24472	0.026000	0.17262	0.115000	0.19883	3.773000	0.55333	2.322000	0.78497	0.528000	0.53228	TTT	.	.		0.318	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		C	5803296	T	C	5803296	3	2	74	1	0	0	0	0	1	0	0	0	1598	1493	52	2	7098	2	C10orf18	10	5803296	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10		5803296	129731451	64	10040										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7679202	7679202	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	aggactcaccttccccgcgcCcactgcccctctgcctgctg	8	21	2	0	rs374950629		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr10:7679202C>A	ENST00000256861.6	-	5	719	c.641G>T	c.(640-642)gGg>gTg	p.G214V	ITIH5_ENST00000397146.2_Missense_Mutation_p.G214V|ITIH5_ENST00000446830.2_5'UTR|ITIH5_ENST00000397145.2_Missense_Mutation_p.G214V|ITIH5_ENST00000434980.1_5'UTR	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	214					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TTCCCCGCGCCCACTGCCCCT	0.622																																					p.G214V		Atlas-SNP	.											ITIH5_ENST00000397145,right_upper_lobe,carcinoma,0,2	ITIH5	343	.	0			c.G641T						.						97	102	100					10																	7679202		2203	4300	6503	SO:0001583	missense	80760	exon5			CCGCGCCCACTGC			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.641G>T	chr10.hg19:g.7679202C>A	ENSP00000256861:p.Gly214Val	51.0	1.0		37.0	15.0	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	C	2.503	-0.314641	0.05422	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000397145	T;T;T	0.02579	4.78;4.24;4.25	5.88	3.99	0.46301	.	0.601900	0.19381	N	0.115661	T	0.02571	0.0078	.	.	.	0.30486	N	0.771832	B;B	0.14438	0.01;0.009	B;B	0.20384	0.029;0.01	T	0.25779	-1.0122	9	0.30078	T	0.28	-25.4834	7.8408	0.29397	0.0:0.726:0.1343:0.1397	.	214;214	G5E9D8;Q86UX2	.;ITIH5_HUMAN	V	214	ENSP00000256861:G214V;ENSP00000380333:G214V;ENSP00000380332:G214V	ENSP00000256861:G214V	G	-	2	0	ITIH5	7719208	0.000000	0.05858	0.047000	0.18901	0.181000	0.23173	0.735000	0.26115	0.783000	0.33636	0.655000	0.94253	GGG	.	.		0.622	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		A	7679202	C	A	7679202	3	1	74	1	0	0	0	0	1	0	0	0	7916	623	22	3	2364	3	ITIH5	10	7679202	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	1875906	7679202	127855545	65	10041										
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49450281	49450281	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ggctgggtagacagacacttCtttctcatgaacccgacaag	10	11	2	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr10:49450281C>T	ENST00000374201.3	-	5	792	c.490G>A	c.(490-492)Gaa>Aaa	p.E164K	FRMPD2_ENST00000305531.3_Missense_Mutation_p.E140K|FRMPD2_ENST00000407470.4_Missense_Mutation_p.E133K	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	164	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)	p.E164K(1)		NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		ACAGACACTTCTTTCTCATGA	0.557																																					p.E164K		Atlas-SNP	.											FRMPD2,NS,NS,0,1	FRMPD2	157	.	1	Substitution - Missense(1)	NS(1)	c.G490A						.						105	102	103					10																	49450281		2203	4300	6503	SO:0001583	missense	143162	exon5			ACACTTCTTTCTC	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.490G>A	chr10.hg19:g.49450281C>T	ENSP00000363317:p.Glu164Lys	178.0	0.0		112.0	40.0	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	hg19	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.244293	0.79912	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.32988	1.43;1.43;1.43	5.19	5.19	0.71726	KIND (2);	.	.	.	.	T	0.38374	0.1038	L	0.46157	1.445	0.24214	N	0.99546	D;P;D	0.55385	0.971;0.839;0.971	P;B;P	0.49752	0.621;0.298;0.621	T	0.25676	-1.0125	9	0.66056	D	0.02	.	14.2141	0.65781	0.0:1.0:0.0:0.0	.	140;164;133	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	K	164;140;133	ENSP00000363317:E164K;ENSP00000307079:E140K;ENSP00000384339:E133K	ENSP00000307079:E140K	E	-	1	0	FRMPD2	49120287	0.989000	0.36119	0.213000	0.23690	0.979000	0.70002	2.979000	0.49313	2.430000	0.82344	0.655000	0.94253	GAA	.	.		0.557	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		T	49450281	C	T	49450281	3	4	74	1	0	0	0	0	1	0	0	0	6066	922	32	3	3539	3	FRMPD2	10	49450281	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	41771079	49450281	86084466	66	10042										
TET1	80312	hgsc.bcm.edu	37	chr10	70405127	70405127	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	aaccaagtctcttatcgttaAtgaaagataggagattaaca	7	6	1	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr10:70405127A>G	ENST00000373644.4	+	4	2850	c.2641A>G	c.(2641-2643)Atg>Gtg	p.M881V		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	881					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CTTATCGTTAATGAAAGATAG	0.418																																					p.M881V		Atlas-SNP	.											.	TET1	255	.	0			c.A2641G						.						114	119	117					10																	70405127		2203	4300	6503	SO:0001583	missense	80312	exon4			TCGTTAATGAAAG	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.2641A>G	chr10.hg19:g.70405127A>G	ENSP00000362748:p.Met881Val	71.0	0.0		62.0	24.0	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	A	7.620	0.676566	0.14841	.	.	ENSG00000138336	ENST00000373644	T	0.06608	3.28	5.79	3.43	0.39272	.	0.315990	0.29884	N	0.010949	T	0.05456	0.0144	L	0.34521	1.04	0.28600	N	0.909208	B	0.09022	0.002	B	0.08055	0.003	T	0.27606	-1.0069	10	0.31617	T	0.26	.	9.2148	0.37339	0.8572:0.0:0.1428:0.0	.	881	Q8NFU7	TET1_HUMAN	V	881	ENSP00000362748:M881V	ENSP00000362748:M881V	M	+	1	0	TET1	70075133	1.000000	0.71417	0.477000	0.27303	0.555000	0.35460	4.048000	0.57390	0.449000	0.26747	0.455000	0.32223	ATG	.	.		0.418	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		G	70405127	A	G	70405127	3	3	74	1	0	0	0	0	1	0	0	0	15784	101	4	2	2651	2	TET1	10	70405127	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	20954846	70405127	65129620	67	10043										
CHST3	9469	hgsc.bcm.edu	37	chr10	73767615	73767615	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	acatggccctcaaggcggtgCgcatccggcagctggagttc	14	13	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr10:73767615C>A	ENST00000373115.4	+	3	1263	c.826C>A	c.(826-828)Cgc>Agc	p.R276S		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	276					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						CAAGGCGGTGCGCATCCGGCA	0.721																																					p.R276S		Atlas-SNP	.											.	CHST3	36	.	0			c.C826A						.						8	9	9					10																	73767615		2161	4181	6342	SO:0001583	missense	9469	exon3			GCGGTGCGCATCC	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"Sulfotransferases, membrane-bound"	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.826C>A	chr10.hg19:g.73767615C>A	ENSP00000362207:p.Arg276Ser	19.0	0.0		25.0	10.0	NM_004273	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	hg19	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.066645	0.76301	.	.	ENSG00000122863	ENST00000373115	D	0.84146	-1.81	5.8	5.8	0.92144	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.94112	0.8112	M	0.91663	3.23	0.80722	D	1	D	0.71674	0.998	D	0.70716	0.97	D	0.94771	0.7945	10	0.87932	D	0	-29.025	19.0419	0.93004	0.0:1.0:0.0:0.0	.	276	Q7LGC8	CHST3_HUMAN	S	276	ENSP00000362207:R276S	ENSP00000362207:R276S	R	+	1	0	CHST3	73437621	0.998000	0.40836	0.994000	0.49952	0.980000	0.70556	3.110000	0.50352	2.758000	0.94735	0.561000	0.74099	CGC	.	.		0.721	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273		A	73767615	C	A	73767615	3	1	74	1	0	0	0	0	1	0	0	0	3407	768	27	1	832	1	CHST3	10	73767615	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	3362488	73767615	61767132	68	10044										
SLC16A12	387700	hgsc.bcm.edu	37	chr10	91196032	91196032	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gatagcagagcccatccattCccacggcaaagaggtagcaa	10	12	0	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr10:91196032C>A	ENST00000341233.4	-	7	1373	c.983G>T	c.(982-984)gGa>gTa	p.G328V	SLC16A12_ENST00000371790.4_Missense_Mutation_p.G358V	NM_213606.3	NP_998771.3	Q6ZSM3	MOT12_HUMAN	solute carrier family 16, member 12	328						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|skin(1)|stomach(1)	14						CCCATCCATTCCCACGGCAAA	0.458																																					p.G358V		Atlas-SNP	.											.	SLC16A12	40	.	0			c.G1073T						.						124	110	115					10																	91196032		2203	4300	6503	SO:0001583	missense	387700	exon7			TCCATTCCCACGG		CCDS7404.1, CCDS7404.2	10q23.32	2013-07-18	2013-07-18		ENSG00000152779	ENSG00000152779		"Solute carriers"	23094	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 12"	611910	"solute carrier family 16 (monocarboxylic acid transporters), member 12", "solute carrier family 16, member 12 (monocarboxylic acid transporter 12)"				Standard	NM_213606		Approved	MCT12	uc001kgm.3	Q6ZSM3	OTTHUMG00000018714	ENST00000341233.4:c.983G>T	chr10.hg19:g.91196032C>A	ENSP00000343022:p.Gly328Val	122.0	0.0		80.0	37.0	NM_213606	Q5M9M9|Q5T7J2|Q6ZV76	Missense_Mutation	SNP	ENST00000341233.4	hg19		.	.	.	.	.	.	.	.	.	.	C	19.04	3.749959	0.69533	.	.	ENSG00000152779	ENST00000341233;ENST00000371790	T;T	0.79554	-1.28;-1.28	5.81	4.9	0.64082	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.352154	0.29165	N	0.012949	T	0.77691	0.4168	L	0.39898	1.24	0.80722	D	1	P	0.41748	0.761	P	0.48368	0.575	T	0.72962	-0.4132	10	0.07175	T	0.84	.	15.6609	0.77188	0.0:0.8579:0.1421:0.0	.	328	Q6ZSM3	MOT12_HUMAN	V	328;358	ENSP00000343022:G328V;ENSP00000360855:G358V	ENSP00000343022:G328V	G	-	2	0	SLC16A12	91186012	0.980000	0.34600	1.000000	0.80357	0.972000	0.66771	1.655000	0.37345	1.418000	0.47098	0.591000	0.81541	GGA	.	.		0.458	SLC16A12-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_213606		A	91196032	C	A	91196032	3	1	74	1	0	0	0	0	1	0	0	0	14420	855	30	3	485	3	SLC16A12	10	91196032	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	17428417	91196032	44338715	69	10045										
NEURL	9148	hgsc.bcm.edu	37	chr10	105350084	105350084	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cacgcctgctgccccatctgCcgccgccccatcaaggacat	8	20	2	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr10:105350084C>A	ENST00000369780.4	+	6	2089	c.1680C>A	c.(1678-1680)tgC>tgA	p.C560*	NEURL_ENST00000369777.2_Nonsense_Mutation_p.C543*|SH3PXD2A_ENST00000427662.2_Intron	NM_004210.4	NP_004201.3	O76050	NEUL1_HUMAN		560					brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Notch signaling pathway (GO:0045746)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse maturation (GO:0090129)|protein monoubiquitination (GO:0006513)|skeletal muscle tissue development (GO:0007519)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|translation factor activity, non-nucleic acid binding (GO:0045183)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	17				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)		GCCCCATCTGCCGCCGCCCCA	0.637																																					p.C560X		Atlas-SNP	.											.	NEURL	38	.	0			c.C1680A						.						67	55	59					10																	105350084		2203	4300	6503	SO:0001587	stop_gained	9148	exon6			CATCTGCCGCCGC																												ENST00000369780.4:c.1680C>A	chr10.hg19:g.105350084C>A	ENSP00000358795:p.Cys560*	77.0	0.0		63.0	17.0	NM_004210	Q5TDR2|Q5TDR3|Q8TAN0|Q9H463	Nonsense_Mutation	SNP	ENST00000369780.4	hg19	CCDS7551.1	.	.	.	.	.	.	.	.	.	.	C	36	5.739640	0.96873	.	.	ENSG00000107954	ENST00000369780;ENST00000369777	.	.	.	5.84	4.89	0.63831	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.168	10.3372	0.43856	0.0:0.8432:0.0:0.1568	.	.	.	.	X	560;543	.	ENSP00000358792:C543X	C	+	3	2	NEURL	105340074	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.507000	0.45442	1.383000	0.46405	-0.367000	0.07326	TGC	.	.		0.637	NEURL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050170.1			A	105350084	C	A	105350084	4	1	74	1	0	0	0	0	0	1	0	0	10354	747	26	3	1702	3	NEURL	10	105350084	Nonsense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	14154052	105350084	30184663	70	10046										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108431023	108431023	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	atcagcctcagtgcagacacAgggttcagattccatagctc	9	12	3	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr10:108431023A>G	ENST00000263054.6	-	16	2168	c.2161T>C	c.(2161-2163)Tgt>Cgt	p.C721R	SORCS1_ENST00000344440.6_Missense_Mutation_p.C721R|SORCS1_ENST00000369698.1_Missense_Mutation_p.C256R	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	721					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GTGCAGACACAGGGTTCAGAT	0.433																																					p.C721R		Atlas-SNP	.											.	SORCS1	534	.	0			c.T2161C						.						224	192	203					10																	108431023		2203	4300	6503	SO:0001583	missense	114815	exon16			AGACACAGGGTTC	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2161T>C	chr10.hg19:g.108431023A>G	ENSP00000263054:p.Cys721Arg	129.0	0.0		83.0	26.0	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.192206	0.78902	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.61274	0.12;0.32;0.31	5.45	5.45	0.79879	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.81074	0.4747	M	0.91561	3.22	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;1.0	D	0.85414	0.1139	9	.	.	.	-16.8096	15.8205	0.78638	1.0:0.0:0.0:0.0	.	721;721;721;721;721	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	R	256;721;721	ENSP00000358712:C256R;ENSP00000263054:C721R;ENSP00000345964:C721R	.	C	-	1	0	SORCS1	108421013	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.910000	0.92685	2.201000	0.70794	0.533000	0.62120	TGT	.	.		0.433	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		G	108431023	A	G	108431023	3	3	74	1	0	0	0	0	1	0	0	0	14945	188	7	2	1623	2	SORCS1	10	108431023	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	3080939	108431023	27103724	71	10047										
CTBP2	1488	hgsc.bcm.edu	37	chr10	126715003	126715003	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gctgtcagggcgcaaggggtGggagagctgtacccggagtt	19	8	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr10:126715003G>A	ENST00000337195.5	-	3	458				CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000309035.6_Silent_p.P442P|CTBP2_ENST00000531469.1_Intron	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		CGCAAGGGGTGGGAGAGCTGT	0.677																																					p.P442P		Atlas-SNP	.											.	CTBP2	100	.	0			c.C1326T						.						35	38	37					10																	126715003		2202	4300	6502	SO:0001627	intron_variant	1488	exon1			AGGGGTGGGAGAG	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12562C>T	chr10.hg19:g.126715003G>A		117.0	0.0		99.0	44.0	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Silent	SNP	ENST00000337195.5	hg19	CCDS7643.1																																																																																			.	.		0.677	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914		A	126715003	G	A	126715003	1	1	74	0	1	0	0	0	0	0	0	0	4000	1335	47	3		3	CTBP2	10	126715003	Intron	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	18283980	126715003	8819744	72	10048										
OR51G1	79324	hgsc.bcm.edu	37	chr11	4945191	4945191	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	atgcagtgggttgcagacggCcacgtagcggtcaatggaca	15	9	1	1	rs148836962	byFrequency	TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr11:4945191C>A	ENST00000321961.2	-	1	446	c.379G>T	c.(379-381)Gcc>Tcc	p.A127S	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	127						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTGCAGACGGCCACGTAGCGG	0.517																																					p.A127S		Atlas-SNP	.											.	OR51G1	74	.	0			c.G379T						.						112	98	103					11																	4945191		2201	4298	6499	SO:0001583	missense	79324	exon1			AGACGGCCACGTA	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"GPCR / Class A : Olfactory receptors"	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.379G>T	chr11.hg19:g.4945191C>A	ENSP00000322546:p.Ala127Ser	103.0	0.0		104.0	26.0	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	hg19	CCDS31366.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.678186	0.47886	.	.	ENSG00000176879	ENST00000321961	T	0.52983	0.64	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39020	U	0.001481	T	0.77994	0.4214	H	0.96175	3.78	0.38309	D	0.943194	D	0.89917	1.0	D	0.91635	0.999	D	0.87237	0.2264	10	0.87932	D	0	.	15.2651	0.73654	0.0:1.0:0.0:0.0	.	127	Q8NGK1	O51G1_HUMAN	S	127	ENSP00000322546:A127S	ENSP00000322546:A127S	A	-	1	0	OR51G1	4901767	1.000000	0.71417	1.000000	0.80357	0.090000	0.18270	4.450000	0.60041	2.169000	0.68431	0.557000	0.71058	GCC	.	C|0.999;T|0.001		0.517	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237		A	4945191	C	A	4945191	3	1	74	1	0	0	0	0	1	0	0	0	11107	739	26	3	588	3	OR51G1	11	4945191	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10		4945191	130061325	73	10049										
IGSF22	283284	hgsc.bcm.edu	37	chr11	18743087	18743087	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcttggcccccgcaccttcaGcacgtgttccttgttaatgc	9	15	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr11:18743087G>A	ENST00000513874.1	-	4	512	c.373C>T	c.(373-375)Ctg>Ttg	p.L125L	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	125	Ig-like 1.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CGCACCTTCAGCACGTGTTCC	0.602											OREG0020822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L125L		Atlas-SNP	.											.	IGSF22	211	.	0			c.C373T						.						125	128	127					11																	18743087		1951	4135	6086	SO:0001819	synonymous_variant	283284	exon4			CCTTCAGCACGTG	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.373C>T	chr11.hg19:g.18743087G>A		83.0	0.0	90	101.0	30.0	NM_173588	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	hg19	CCDS41625.2																																																																																			.	.		0.602	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		A	18743087	G	A	18743087	2	1	74	1	0	0	0	0	0	0	0	1	7609	962	34	3		3	IGSF22	11	18743087	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	13797896	18743087	116263429	74	10050										
FSHB	2488	hgsc.bcm.edu	37	chr11	30255242	30255242	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gattccttgtatacatacccAgtggccacccagtgtcactg	8	13	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr11:30255242A>T	ENST00000417547.1	+	3	324	c.285A>T	c.(283-285)ccA>ccT	p.P95P	FSHB_ENST00000254122.3_Silent_p.P95P|FSHB_ENST00000533718.1_Silent_p.P95P	NM_001018080.1	NP_001018090.1	P01225	FSHB_HUMAN	follicle stimulating hormone, beta polypeptide	95					cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|female pregnancy (GO:0007565)|follicle-stimulating hormone signaling pathway (GO:0042699)|peptide hormone processing (GO:0016486)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone biosynthetic process (GO:0006701)|regulation of osteoclast differentiation (GO:0045670)|Sertoli cell proliferation (GO:0060011)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	12						ATACATACCCAGTGGCCACCC	0.522																																					p.P95P		Atlas-SNP	.											.	FSHB	28	.	0			c.A285T						.						102	83	90					11																	30255242		2202	4299	6501	SO:0001819	synonymous_variant	2488	exon3			ATACCCAGTGGCC		CCDS7868.1	11p13	2013-02-26				ENSG00000131808		"Endogenous ligands"	3964	protein-coding gene	gene with protein product	"follitropin, beta chain", "follicle-stimulating hormone beta subunit"	136530				2885163, 3151250	Standard	NM_000510		Approved		uc001msm.3	P01225		ENST00000417547.1:c.285A>T	chr11.hg19:g.30255242A>T		117.0	0.0		152.0	32.0	NM_000510	A2TF08|A5JVV3|Q14D61	Silent	SNP	ENST00000417547.1	hg19	CCDS7868.1																																																																																			.	.		0.522	FSHB-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389757.1	NM_000510		T	30255242	A	T	30255242	2	4	74	1	0	0	0	0	0	0	0	1	6080	175	7	4		4	FSHB	11	30255242	Silent	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	11512155	30255242	104751274	75	10051										
PACSIN3	29763	hgsc.bcm.edu	37	chr11	47201773	47201773	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcacagcgttccacccgttcCtgcagtttgcgcagctgctc	10	16	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr11:47201773C>A	ENST00000539589.1	-	6	909	c.567G>T	c.(565-567)caG>caT	p.Q189H	PACSIN3_ENST00000298838.6_Missense_Mutation_p.Q189H	NM_001184975.1	NP_001171904.1	Q9UKS6	PACN3_HUMAN	protein kinase C and casein kinase substrate in neurons 3	189	F-BAR domain. {ECO:0000250}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endocytosis (GO:0045806)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium channel inhibitor activity (GO:0019855)|cytoskeletal protein binding (GO:0008092)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)	11						CCACCCGTTCCTGCAGTTTGC	0.652											OREG0020952	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q189H		Atlas-SNP	.											.	PACSIN3	28	.	0			c.G567T						.						105	90	95					11																	47201773		2201	4298	6499	SO:0001583	missense	29763	exon6			CCGTTCCTGCAGT	AF130979	CCDS31481.1	11p12-p11	2008-02-05				ENSG00000165912			8572	protein-coding gene	gene with protein product	"syndapin III"	606513				10531379	Standard	NM_016223		Approved	SDPIII	uc001ndx.3	Q9UKS6		ENST00000539589.1:c.567G>T	chr11.hg19:g.47201773C>A	ENSP00000440945:p.Gln189His	23.0	0.0	945	30.0	13.0	NM_016223	A6NH84|Q9H331|Q9NWV9	Missense_Mutation	SNP	ENST00000539589.1	hg19	CCDS31481.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.25|13.25	2.180563|2.180563	0.38511|0.38511	.|.	.|.	ENSG00000165912|ENSG00000165912	ENST00000298838;ENST00000539589;ENST00000528462|ENST00000415232	T;T;T|.	0.45668|.	0.89;0.89;0.89|.	5.52|5.52	3.31|3.31	0.37934|0.37934	.|.	0.186773|.	0.53938|.	D|.	0.000053|.	T|T	0.56659|0.56659	0.2000|0.2000	L|L	0.34521|0.34521	1.04|1.04	0.39448|0.39448	D|D	0.967355|0.967355	P|.	0.46327|.	0.876|.	B|.	0.34093|.	0.175|.	T|T	0.62927|0.62927	-0.6750|-0.6750	10|6	0.41790|0.62326	T|D	0.15|0.03	-40.0996|-40.0996	13.0496|13.0496	0.58948|0.58948	0.0:0.8465:0.0:0.1535|0.0:0.8465:0.0:0.1535	.|.	189|.	Q9UKS6|.	PACN3_HUMAN|.	H|M	189|188	ENSP00000298838:Q189H;ENSP00000440945:Q189H;ENSP00000437252:Q189H|.	ENSP00000298838:Q189H|ENSP00000405352:R188M	Q|R	-|-	3|2	2|0	PACSIN3|PACSIN3	47158349|47158349	0.937000|0.937000	0.31787|0.31787	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	0.134000|0.134000	0.15932|0.15932	1.351000|1.351000	0.45789|0.45789	0.561000|0.561000	0.74099|0.74099	CAG|AGG	.	.		0.652	PACSIN3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391632.1	NM_016223		A	47201773	C	A	47201773	3	1	74	1	0	0	0	0	1	0	0	0	11385	680	24	3	731	3	PACSIN3	11	47201773	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	16946531	47201773	87804743	76	10052										
ZFP91	80829	hgsc.bcm.edu	37	chr11	58384203	58384203	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tcatagatcaaagggattatAtctgtgaatattgtgctcgg	10	5	3	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr11:58384203A>G	ENST00000316059.6	+	10	1288	c.1117A>G	c.(1117-1119)Atc>Gtc	p.I373V	ZFP91-CNTF_ENST00000389919.4_Missense_Mutation_p.I373V	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	373					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				AAGGGATTATATCTGTGAATA	0.408																																					p.I373V		Atlas-SNP	.											.	ZFP91	66	.	0			c.A1117G						.						69	68	69					11																	58384203		2201	4295	6496	SO:0001583	missense	80829	exon10			GATTATATCTGTG	AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"Zinc fingers, C2H2-type"	14983	protein-coding gene	gene with protein product			"zinc finger protein homologous to Zfp91 in mouse", "zinc finger protein 91 homolog (mouse)"			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.1117A>G	chr11.hg19:g.58384203A>G	ENSP00000339030:p.Ile373Val	81.0	0.0		102.0	21.0	NM_053023	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Missense_Mutation	SNP	ENST00000316059.6	hg19	CCDS31553.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.480550	0.84747	.	.	ENSG00000186660	ENST00000316059;ENST00000389918	T	0.14391	2.51	5.79	5.79	0.91817	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.16085	0.0387	N	0.03084	-0.415	0.58432	D	0.999993	P;D	0.53151	0.948;0.958	D;D	0.70716	0.949;0.97	T	0.45991	-0.9223	10	0.25106	T	0.35	-10.1966	15.127	0.72489	1.0:0.0:0.0:0.0	.	373;373	Q96JP5-2;Q96JP5	.;ZFP91_HUMAN	V	373	ENSP00000339030:I373V	ENSP00000374569:I373V	I	+	1	0	ZFP91	58140779	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.223000	0.72356	0.455000	0.32223	ATC	.	.		0.408	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023		G	58384203	A	G	58384203	3	3	74	1	0	0	0	0	1	0	0	0	17670	449	16	2	1155	2	ZFP91	11	58384203	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	11182430	58384203	76622313	77	10053										
MPEG1	219972	hgsc.bcm.edu	37	chr11	58980026	58980026	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ggtgctactctggtaatttgCccaggattccaggatttctg	11	9	2	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr11:58980026C>T	ENST00000361050.3	-	1	398	c.313G>A	c.(313-315)Gca>Aca	p.A105T	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	105	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.					integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				TGGTAATTTGCCCAGGATTCC	0.448																																					p.A105T		Atlas-SNP	.											.	MPEG1	72	.	0			c.G313A						.						207	194	198					11																	58980026		1913	4121	6034	SO:0001583	missense	219972	exon1			AATTTGCCCAGGA	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"macrophage expressed gene 1"	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.313G>A	chr11.hg19:g.58980026C>T	ENSP00000354335:p.Ala105Thr	84.0	0.0		83.0	7.0	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	hg19	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	C	0.198	-1.047352	0.01981	.	.	ENSG00000197629	ENST00000361050;ENST00000545098	T	0.21932	1.98	5.05	-3.91	0.04168	Membrane attack complex component/perforin (MACPF) domain (1);	0.467745	0.21099	N	0.080188	T	0.07908	0.0198	N	0.08118	0	0.24352	N	0.994912	B	0.02656	0.0	B	0.01281	0.0	T	0.36696	-0.9737	10	0.14252	T	0.57	-1.897	11.2463	0.48998	0.0:0.2422:0.0:0.7578	.	105	Q2M385	MPEG1_HUMAN	T	105	ENSP00000354335:A105T	ENSP00000354335:A105T	A	-	1	0	MPEG1	58736602	0.050000	0.20438	0.174000	0.22961	0.009000	0.06853	0.176000	0.16782	-0.545000	0.06224	-0.825000	0.03093	GCA	.	.		0.448	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		T	58980026	C	T	58980026	3	4	74	1	0	0	0	0	1	0	0	0	9732	739	26	3	1841	3	MPEG1	11	58980026	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	595823	58980026	76026490	78	10054										
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117789435	117789449	+	In_Frame_Del	DEL	GCTGGAGATGCCTGG	GCTGGAGATGCCTGG	-													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cccggcccggaggtgtcccaGctggagatgcctgggctgga							TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	GCTGGAGATGCCTGG	GCTGGAGATGCCTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr11:117789435_117789449delGCTGGAGATGCCTGG	ENST00000430170.2	-	2	213_227	c.126_140delCCAGGCATCTCCAGC	c.(124-141)gcccaggcatctccagct>gct	p.42_47AQASPA>A	TMPRSS13_ENST00000445164.2_In_Frame_Del_p.42_47AQASPA>A|TMPRSS13_ENST00000524993.1_In_Frame_Del_p.42_47AQASPA>A|TMPRSS13_ENST00000528626.1_In_Frame_Del_p.42_47AQASPA>A|TMPRSS13_ENST00000526090.1_In_Frame_Del_p.42_47AQASPA>A	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	42	13 X 5 AA repeats of A-S-P-A-[GLQR].|4 X 5 AA repeats of T-P-P-G-R.|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		AGGTGTCCCAGCTGGAGATGCCTGGGCTGGAGATG	0.66																																					p.43_47del		Atlas-INDEL	.											.	TMPRSS13	75	.	0			c.127_141del						.																																			SO:0001651	inframe_deletion	84000	exon2			.	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"Serine peptidases / Transmembrane"	29808	protein-coding gene	gene with protein product		610050	"transmembrane protease, serine 11"	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.126_140delCCAGGCATCTCCAGC	chr11.hg19:g.117789435_117789449delGCTGGAGATGCCTGG	ENSP00000387702:p.Ala42_Pro46del	42.0	0.0		29.0	11.0	NM_001206789	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	In_Frame_Del	DEL	ENST00000430170.2	hg19	CCDS58185.1																																																																																			.	.		0.66	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		-	117789449	GCTGGAGATGCCTGG	-	117789435	7	5	74	1	0	1	0	1	0	0	0	0	16260	971	34	0	1611	0	TMPRSS13	11	117789435	In_Frame_Del	DEL	GCTGGAGATGCCTGG	TCGA-CC-A7II-01A-11D-A33K-10	58809409	117789435	17217081	79	10055										
TECTA	7007	hgsc.bcm.edu	37	chr11	120996428	120996428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgtgggagtgtggcactgtcGtggaccccactgcttttgtg	15	9	0	0	rs370652301		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr11:120996428G>A	ENST00000392793.1	+	8	1892	c.1621G>A	c.(1621-1623)Gtg>Atg	p.V541M	TECTA_ENST00000264037.2_Missense_Mutation_p.V541M			O75443	TECTA_HUMAN	tectorin alpha	541					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGGCACTGTCGTGGACCCCAC	0.587																																					p.V541M		Atlas-SNP	.											.	TECTA	329	.	0			c.G1621A						.	G	MET/VAL	0,4406		0,0,2203	136	135	135		1621	3	0.5	11		135	1,8597	1.2+/-3.3	0,1,4298	no	missense	TECTA	NM_005422.2	21	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	541/2156	120996428	1,13003	2203	4299	6502	SO:0001583	missense	7007	exon7			ACTGTCGTGGACC	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1621G>A	chr11.hg19:g.120996428G>A	ENSP00000376543:p.Val541Met	88.0	0.0		77.0	11.0	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.030471	0.54790	0.0	1.16E-4	ENSG00000109927	ENST00000392793;ENST00000264037	D;D	0.83419	-1.72;-1.72	4.91	3.04	0.35103	Uncharacterised domain, cysteine-rich (2);	0.136631	0.49305	N	0.000153	D	0.91019	0.7175	M	0.91510	3.215	0.34529	D	0.708962	D	0.76494	0.999	D	0.63192	0.912	D	0.93874	0.7165	10	0.72032	D	0.01	.	11.3331	0.49487	0.1492:0.0:0.8508:0.0	.	541	O75443	TECTA_HUMAN	M	541	ENSP00000376543:V541M;ENSP00000264037:V541M	ENSP00000264037:V541M	V	+	1	0	TECTA	120501638	1.000000	0.71417	0.546000	0.28166	0.829000	0.46940	3.367000	0.52350	0.613000	0.30089	-0.251000	0.11542	GTG	.	.		0.587	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	120996428	G	A	120996428	3	1	74	1	0	0	0	0	1	0	0	0	15762	1145	40	1	1647	1	TECTA	11	120996428	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	3206993	120996428	14010088	80	10056										
OR4D5	219875	hgsc.bcm.edu	37	chr11	123811018	123811018	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ccgaagccactcacgggaggGccgcagcaaggccctgtcta	13	15	2	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr11:123811018G>T	ENST00000307033.2	+	1	769	c.695G>T	c.(694-696)gGc>gTc	p.G232V		NM_001001965.1	NP_001001965.1	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D, member 5	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		TCACGGGAGGGCCGCAGCAAG	0.527																																					p.G232V		Atlas-SNP	.											.	OR4D5	94	.	0			c.G695T						.						224	194	204					11																	123811018		2202	4299	6501	SO:0001583	missense	219875	exon1			GGGAGGGCCGCAG	BK004316	CCDS31699.1	11q24.1	2012-08-09			ENSG00000171014	ENSG00000171014		"GPCR / Class A : Olfactory receptors"	14852	protein-coding gene	gene with protein product							Standard	NM_001001965		Approved		uc001pzk.1	Q8NGN0	OTTHUMG00000165961	ENST00000307033.2:c.695G>T	chr11.hg19:g.123811018G>T	ENSP00000305970:p.Gly232Val	145.0	0.0		143.0	35.0	NM_001001965	B9EGZ4|Q6IFE6	Missense_Mutation	SNP	ENST00000307033.2	hg19	CCDS31699.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.891291	0.33442	.	.	ENSG00000171014	ENST00000307033	T	0.00299	8.22	5.49	-0.146	0.13432	GPCR, rhodopsin-like superfamily (1);	0.720448	0.12266	N	0.484316	T	0.00754	0.0025	H	0.94964	3.605	0.48571	D	0.999678	P	0.46020	0.871	D	0.64687	0.928	T	0.59542	-0.7435	10	0.87932	D	0	0.0461	5.36	0.16083	0.3139:0.1613:0.5248:0.0	.	232	Q8NGN0	OR4D5_HUMAN	V	232	ENSP00000305970:G232V	ENSP00000305970:G232V	G	+	2	0	OR4D5	123316228	0.004000	0.15560	0.176000	0.23000	0.284000	0.27059	0.438000	0.21559	-0.323000	0.08602	-0.355000	0.07637	GGC	.	.		0.527	OR4D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387263.1	NM_001001965		T	123811018	G	T	123811018	3	4	74	1	0	0	0	0	1	0	0	0	11066	1203	42	3	697	3	OR4D5	11	123811018	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	2814590	123811018	11195498	81	10057										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40714888	40714889	+	Frame_Shift_Ins	INS	-	-	T													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ccattgtgagaactctgaaaINSttatcatccgactatatgaa							TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr12:40714888_40714889insT	ENST00000298910.7	+	35	5126_5127	c.5068_5069insT	c.(5068-5070)attfs	p.I1690fs		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1690					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GAACTCTGAAATTATCATCCGA	0.396																																					p.I1690fs		Atlas-Indel,Pindel	.											.	LRRK2	763	.	0			c.5068_5069insT						.																																			SO:0001589	frameshift_variant	120892	exon35			.	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.5070dupT	chr12.hg19:g.40714890_40714890dupT	ENSP00000298910:p.Ile1690fs	108.0	0.0		74.0	33.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Frame_Shift_Ins	INS	ENST00000298910.7	hg19	CCDS31774.1																																																																																			.	.		0.396	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40714889	-	T	40714888	7	5	74	1	0	1	1	0	0	0	0	0	9042	101	4	0	5206	0	LRRK2	12	40714888	Frame_Shift_Ins	INS	-	TCGA-CC-A7II-01A-11D-A33K-10		40714888	93137007	82	10058										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41966302	41966302	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ctcagagcaggagaatgcagCcgaggaccccaatagcacat	11	12	1	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr12:41966302C>A	ENST00000402685.2	+	10	1729	c.1721C>A	c.(1720-1722)gCc>gAc	p.A574D	PDZRN4_ENST00000539469.2_Missense_Mutation_p.A316D|PDZRN4_ENST00000298919.7_Missense_Mutation_p.A314D	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	574							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				GAGAATGCAGCCGAGGACCCC	0.498																																					p.A574D		Atlas-SNP	.											.	PDZRN4	346	.	0			c.C1721A						.						101	89	93					12																	41966302		2203	4300	6503	SO:0001583	missense	29951	exon10			ATGCAGCCGAGGA	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1721C>A	chr12.hg19:g.41966302C>A	ENSP00000384197:p.Ala574Asp	200.0	1.0		161.0	81.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	C	7.081	0.570320	0.13560	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.72505	-0.66;3.83;3.82	5.05	3.21	0.36854	.	1.424160	0.04150	N	0.321150	T	0.68192	0.2974	L	0.50333	1.59	0.09310	N	1	P;B;B	0.34462	0.454;0.061;0.061	B;B;B	0.32022	0.105;0.139;0.139	T	0.57763	-0.7755	10	0.59425	D	0.04	-3.8108	11.4137	0.49939	0.0:0.8482:0.0:0.1518	.	574;314;316	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	D	574;316;314	ENSP00000384197:A574D;ENSP00000439990:A316D;ENSP00000298919:A314D	ENSP00000298919:A314D	A	+	2	0	PDZRN4	40252569	0.186000	0.23225	0.006000	0.13384	0.505000	0.33919	1.444000	0.35068	0.776000	0.33473	-0.143000	0.13931	GCC	.	.		0.498	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		A	41966302	C	A	41966302	3	1	74	1	0	0	0	0	1	0	0	0	11719	739	26	3	1832	3	PDZRN4	12	41966302	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	1251414	41966302	91885593	83	10059										
KRT76	51350	hgsc.bcm.edu	37	chr12	53170525	53170525	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgagggtcttgatctgttccCgctcctgggcctttacttgc	11	12	2	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr12:53170525C>A	ENST00000332411.2	-	1	604	c.551G>T	c.(550-552)cGg>cTg	p.R184L		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	184	Coil 1A.|Rod.				cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GATCTGTTCCCGCTCCTGGGC	0.557																																					p.R184L		Atlas-SNP	.											.	KRT76	72	.	0			c.G551T						.						109	113	112					12																	53170525		2203	4298	6501	SO:0001583	missense	51350	exon1			TGTTCCCGCTCCT	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"-", "Intermediate filaments type II, keratins (basic)"	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.551G>T	chr12.hg19:g.53170525C>A	ENSP00000330101:p.Arg184Leu	136.0	0.0		116.0	38.0	NM_015848	B4DRR3|Q7Z795	Missense_Mutation	SNP	ENST00000332411.2	hg19	CCDS8838.1	.	.	.	.	.	.	.	.	.	.	C	17.69	3.451878	0.63290	.	.	ENSG00000185069	ENST00000332411	D	0.90133	-2.62	4.2	2.38	0.29361	Filament (1);	0.187921	0.26140	N	0.026104	D	0.94801	0.8321	M	0.87547	2.89	0.33466	D	0.585523	D	0.89917	1.0	D	0.85130	0.997	D	0.95259	0.8367	10	0.87932	D	0	.	9.2398	0.37489	0.0:0.7323:0.0:0.2677	.	184	Q01546	K22O_HUMAN	L	184	ENSP00000330101:R184L	ENSP00000330101:R184L	R	-	2	0	KRT76	51456792	0.992000	0.36948	0.955000	0.39395	0.985000	0.73830	1.362000	0.34148	0.730000	0.32425	0.462000	0.41574	CGG	.	.		0.557	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848		A	53170525	C	A	53170525	3	1	74	1	0	0	0	0	1	0	0	0	8498	652	23	1	1401	1	KRT76	12	53170525	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	11204223	53170525	80681370	84	10060										
KRT4	3851	hgsc.bcm.edu	37	chr12	53207647	53207647	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ggcaccttgtcgtgacccagCcacactcatggagatgcttt	10	13	1	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr12:53207647C>T	ENST00000551956.1	-	1	688	c.196G>A	c.(196-198)Gct>Act	p.A66T	KRT4_ENST00000458244.2_Intron|KRT4_ENST00000293774.4_Missense_Mutation_p.A140T			P19013	K2C4_HUMAN	keratin 4	66	Gly-rich.|Head.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CGTGACCCAGCCACACTCATG	0.587																																					p.A66T	Pancreas(190;284 2995 41444 45903)	Atlas-SNP	.											.	KRT4	110	.	0			c.G196A						.						112	130	124					12																	53207647		2101	4247	6348	SO:0001583	missense	3851	exon1			ACCCAGCCACACT		CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"-", "Intermediate filaments type II, keratins (basic)"	6441	protein-coding gene	gene with protein product	"cytokeratin 4", "keratin, type II cytoskeletal 4"	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.196G>A	chr12.hg19:g.53207647C>T	ENSP00000448220:p.Ala66Thr	93.0	0.0		70.0	38.0	NM_002272	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Missense_Mutation	SNP	ENST00000551956.1	hg19	CCDS41787.2	.	.	.	.	.	.	.	.	.	.	C	18.97	3.735155	0.69189	.	.	ENSG00000170477	ENST00000551956;ENST00000293774	T;T	0.80653	-1.4;2.14	5.0	5.0	0.66597	.	0.000000	0.47852	D	0.000220	D	0.88485	0.6449	M	0.83384	2.64	0.80722	D	1	.	.	.	.	.	.	D	0.89183	0.3545	8	0.56958	D	0.05	.	14.6034	0.68460	0.0:0.8424:0.1576:0.0	.	.	.	.	T	66;140	ENSP00000448220:A66T;ENSP00000293774:A140T	ENSP00000293774:A140T	A	-	1	0	KRT4	51493914	0.000000	0.05858	0.981000	0.43875	0.591000	0.36615	1.006000	0.29847	2.705000	0.92388	0.585000	0.79938	GCT	.	.		0.587	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272		T	53207647	C	T	53207647	3	4	74	1	0	0	0	0	1	0	0	0	8486	739	26	3	1402	3	KRT4	12	53207647	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	37122	53207647	80644248	85	10061										
DTX3	196403	hgsc.bcm.edu	37	chr12	58002913	58002913	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ggtgcaagaggagctgagagCgaagggtatcacagatgact	16	6	1	4			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr12:58002913C>T	ENST00000548198.1	+	5	2526	c.1022C>T	c.(1021-1023)gCg>gTg	p.A341V	DTX3_ENST00000551632.1_Missense_Mutation_p.A344V|ARHGEF25_ENST00000333972.7_5'Flank|AC025165.8_ENST00000356672.3_RNA|ARHGEF25_ENST00000286494.4_5'Flank|DTX3_ENST00000337737.3_Missense_Mutation_p.A341V|DTX3_ENST00000548804.1_Missense_Mutation_p.A341V			Q8N9I9	DTX3_HUMAN	deltex 3, E3 ubiquitin ligase	341					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(6)|urinary_tract(1)	12	Melanoma(17;0.122)					GAGCTGAGAGCGAAGGGTATC	0.562																																					p.A341V		Atlas-SNP	.											.	DTX3	27	.	0			c.C1022T						.						117	119	118					12																	58002913		1991	4159	6150	SO:0001583	missense	196403	exon7			TGAGAGCGAAGGG	AK094385	CCDS41800.1, CCDS66410.1	12q13.2	2014-01-28	2014-01-28			ENSG00000178498		"RING-type (C3HC4) zinc fingers"	24457	protein-coding gene	gene with protein product		613142	"deltex 3 homolog (Drosophila)", "deltex homolog 3 (Drosophila)"			12670957	Standard	XM_005268697		Approved	FLJ34766, RNF154	uc001sow.1	Q8N9I9		ENST00000548198.1:c.1022C>T	chr12.hg19:g.58002913C>T	ENSP00000447873:p.Ala341Val	94.0	0.0		87.0	38.0	NM_178502	Q53ZZ2|Q8NAU6|Q8NDS8	Missense_Mutation	SNP	ENST00000548198.1	hg19	CCDS41800.1	.	.	.	.	.	.	.	.	.	.	c	10.18	1.278463	0.23307	.	.	ENSG00000178498	ENST00000548804;ENST00000337737;ENST00000548198;ENST00000551632	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	3.19	3.19	0.36642	.	0.522770	0.16601	U	0.207326	T	0.41050	0.1142	M	0.71920	2.185	0.32394	N	0.552796	P	0.40302	0.712	B	0.18263	0.021	T	0.63950	-0.6521	10	0.87932	D	0	.	13.9819	0.64310	0.0:1.0:0.0:0.0	.	341	Q8N9I9	DTX3_HUMAN	V	341;341;341;344	ENSP00000449294:A341V;ENSP00000338050:A341V;ENSP00000447873:A341V;ENSP00000448696:A344V	ENSP00000338050:A341V	A	+	2	0	DTX3	56289180	0.999000	0.42202	1.000000	0.80357	0.132000	0.20833	2.113000	0.41902	1.751000	0.51876	0.586000	0.80456	GCG	.	.		0.562	DTX3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407848.1	NM_178502		T	58002913	C	T	58002913	3	4	74	1	0	0	0	0	1	0	0	0	4797	768	27	1	1036	1	DTX3	12	58002913	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	4795266	58002913	75848982	86	10062										
WIF1	11197	hgsc.bcm.edu	37	chr12	65449809	65449854	+	Splice_Site	DEL	GTAGCCCAGATTGGCAATGTGTATGGGGTACTTACGCTTTGAACAG	GTAGCCCAGATTGGCAATGTGTATGGGGTACTTACGCTTTGAACAG	-													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcaatgtgtatggggtacttAcgctttgaacagaggtctcc					rs201141383		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	GTAGCCCAGATTGGCAATGTGTATGGGGTACTTACGCTTTGAACAG	GTAGCCCAGATTGGCAATGTGTATGGGGTACTTACGCTTTGAACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr12:65449809_65449854delGTAGCCCAGATTGGCAATGTGTATGGGGTACTTACGCTTTGAACAG	ENST00000286574.4	-	8	1253_1297	c.879_923delCTGTTCAAAGCGTAAGTACCCCATACACATTGCCAATCTGGGCTAC	c.(877-924)aactgttcaaagcgtaagtaccccatacacattgccaatctgggctac>aac	p.CSKRKYPIHIANLGY294fs		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	294	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)		p.G299C(2)		cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		TGGGGTACTTACGCTTTGAACAGAGGTCTCCCTGGTAACCTTTGGAACACTTACATTTGCTTTTAC	0.455			T	HMGA2	pleomorphic salivary gland adenoma																																p.305_308del	Esophageal Squamous(148;1595 1816 48559 49439 49664)	Pindel	.		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	WIF1	96	.	2	Substitution - Missense(2)	lung(2)	c.913_922del						.																																			SO:0001630	splice_region_variant	11197	exon8			.	AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.922+1CTGTTCAAAGCGTAAGTACCCCATACACATTGCCAATCTGGGCTAC>-	chr12.hg19:g.65449809_65449854delGTAGCCCAGATTGGCAATGTGTATGGGGTACTTACGCTTTGAACAG		65.0	0.0		55.0	14.0	NM_007191	Q6UXI1|Q8WVG4	Frame_Shift_Del	DEL	ENST00000286574.4	hg19	CCDS8971.1																																																																																			.	.		0.455	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2		Frame_Shift_Del	-	65449854	GTAGCCCAGATTGGCAATGTGTATGGGGTACTTACGCTTTGAACAG	-	65449809	8	5	74	1	0	1	0	1	0	0	1	0	17381	405	14	0	227	0	WIF1	12	65449809	Splice_Site	DEL	GTAGCCCAGATTGGCAATGTGTATGGGGTACTTACGCTTTGAACAG	TCGA-CC-A7II-01A-11D-A33K-10	7446896	65449809	68402086	87	10063										
SYT1	6857	hgsc.bcm.edu	37	chr12	79689884	79689884	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	attcaggctgccgaactgccCgccttggacatggggggcac	14	13	1	0	rs369758844		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr12:79689884C>T	ENST00000261205.4	+	7	1167	c.510C>T	c.(508-510)ccC>ccT	p.P170P	SYT1_ENST00000393240.3_Silent_p.P170P|SYT1_ENST00000457153.2_Silent_p.P167P|SYT1_ENST00000552744.1_Silent_p.P170P	NM_005639.2	NP_005630.1	P21579	SYT1_HUMAN	synaptotagmin I	170	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000305}.				calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|detection of calcium ion (GO:0005513)|glutamate secretion (GO:0014047)|neurotransmitter secretion (GO:0007269)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of vesicle fusion (GO:0031340)|protein homooligomerization (GO:0051260)|regulation of exocytosis (GO:0017157)|regulation of regulated secretory pathway (GO:1903305)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|vesicle docking (GO:0048278)	cell junction (GO:0030054)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|endocytic vesicle membrane (GO:0030666)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol binding (GO:0005545)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|transporter activity (GO:0005215)	p.P170P(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|pancreas(2)|skin(6)	25						CCGAACTGCCCGCCTTGGACA	0.428																																					p.P170P		Atlas-SNP	.											SYT1,NS,NS,0,1	SYT1	70	.	1	Substitution - coding silent(1)	pancreas(1)	c.C510T						.	C	,,	0,4406		0,0,2203	97	92	94		510,510,510	-5.2	0.9	12		94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SYT1	NM_001135805.1,NM_001135806.1,NM_005639.2	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	170/423,170/423,170/423	79689884	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6857	exon8			ACTGCCCGCCTTG		CCDS9017.1	12q21.2	2013-09-20			ENSG00000067715	ENSG00000067715		"Synaptotagmins"	11509	protein-coding gene	gene with protein product		185605		SYT, SVP65		1840599	Standard	NM_001135805		Approved	P65	uc001syv.3	P21579	OTTHUMG00000134326	ENST00000261205.4:c.510C>T	chr12.hg19:g.79689884C>T		107.0	1.0		71.0	28.0	NM_001135805	Q6AI31	Silent	SNP	ENST00000261205.4	hg19	CCDS9017.1	.	.	.	.	.	.	.	.	.	.	C	8.327	0.825609	0.16749	0.0	1.16E-4	ENSG00000067715	ENST00000549559	T	0.16897	2.31	5.52	-5.19	0.02832	.	0.000000	0.85682	D	0.000000	T	0.25457	0.0619	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.13176	-1.0519	7	0.72032	D	0.01	.	11.069	0.47993	0.1104:0.1236:0.0:0.766	.	.	.	.	L	72	ENSP00000449415:P72L	ENSP00000449415:P72L	P	+	2	0	SYT1	78214015	0.004000	0.15560	0.919000	0.36401	0.947000	0.59692	-1.268000	0.02836	-0.888000	0.03956	-1.134000	0.01955	CCG	.	.		0.428	SYT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259415.1	NM_005639		T	79689884	C	T	79689884	2	4	74	1	0	0	0	0	0	0	0	1	15480	639	23	1		1	SYT1	12	79689884	Silent	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	14240075	79689884	54162011	88	10064										
STAB2	55576	hgsc.bcm.edu	37	chr12	104077060	104077060	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	acttcatgcttggaacaaacCgggaaatgtcatccattggt	9	9	2	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr12:104077060C>A	ENST00000388887.2	+	26	3087	c.2883C>A	c.(2881-2883)acC>acA	p.T961T		NM_017564.9	NP_060034.9			stabilin 2									p.T961T(2)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TGGAACAAACCGGGAAATGTC	0.333																																					p.T961T		Atlas-SNP	.											STAB2,NS,carcinoma,0,2	STAB2	370	.	2	Substitution - coding silent(2)	lung(2)	c.C2883A						.						171	156	161					12																	104077060		2203	4300	6503	SO:0001819	synonymous_variant	55576	exon26			ACAAACCGGGAAA	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.2883C>A	chr12.hg19:g.104077060C>A		141.0	0.0		183.0	59.0	NM_017564		Silent	SNP	ENST00000388887.2	hg19	CCDS31888.1																																																																																			.	.		0.333	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104077060	C	A	104077060	2	1	74	1	0	0	0	0	0	0	0	1	15253	639	23	1		1	STAB2	12	104077060	Silent	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	24387176	104077060	29774835	89	10065										
SSH1	54434	hgsc.bcm.edu	37	chr12	109192797	109192797	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ttgcatccaagatgccttcaTactcagacagctgcctcata	6	13	3	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr12:109192797T>C	ENST00000326495.5	-	13	1421	c.1328A>G	c.(1327-1329)tAt>tGt	p.Y443C	SSH1_ENST00000326470.5_Missense_Mutation_p.Y454C|SSH1_ENST00000360239.3_Missense_Mutation_p.Y131C|SSH1_ENST00000551165.1_Missense_Mutation_p.Y443C	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	443	Tyrosine-protein phosphatase.				actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GATGCCTTCATACTCAGACAG	0.577																																					p.Y454C		Atlas-SNP	.											.	SSH1	144	.	0			c.A1361G						.						72	70	70					12																	109192797		2203	4300	6503	SO:0001583	missense	54434	exon12			CCTTCATACTCAG	BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30579	protein-coding gene	gene with protein product		606778	"slingshot homolog 1 (Drosophila)"			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.1328A>G	chr12.hg19:g.109192797T>C	ENSP00000315713:p.Tyr443Cys	55.0	0.0		60.0	18.0	NM_001161331	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Missense_Mutation	SNP	ENST00000326495.5	hg19	CCDS9121.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.445052	0.83993	.	.	ENSG00000084112	ENST00000360239;ENST00000326495;ENST00000551165;ENST00000326470	T;T;T;T	0.63096	1.01;-0.02;-0.02;-0.02	5.11	5.11	0.69529	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.84955	0.5587	H	0.95574	3.69	0.58432	D	0.999991	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.89698	0.3903	10	0.87932	D	0	-20.7526	15.2215	0.73313	0.0:0.0:0.0:1.0	.	454;443;443;131	Q8WYL5-5;Q8WYL5-2;Q8WYL5;Q8WYL5-4	.;.;SSH1_HUMAN;.	C	131;443;443;454	ENSP00000353374:Y131C;ENSP00000315713:Y443C;ENSP00000448824:Y443C;ENSP00000326107:Y454C	ENSP00000326107:Y454C	Y	-	2	0	SSH1	107716926	1.000000	0.71417	0.950000	0.38849	0.988000	0.76386	8.040000	0.89188	2.066000	0.61787	0.533000	0.62120	TAT	.	.		0.577	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984		C	109192797	T	C	109192797	3	2	74	1	0	0	0	0	1	0	0	0	15199	1406	49	2	2019	2	SSH1	12	109192797	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	5115737	109192797	24659098	90	10066										
EP400	57634	hgsc.bcm.edu	37	chr12	132445446	132445446	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cagatcacactggccccactGccgctccccagccccacctc	6	23	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr12:132445446G>T	ENST00000333577.4	+	2	391	c.282G>T	c.(280-282)ctG>ctT	p.L94L	EP400_ENST00000332482.4_Silent_p.L94L|EP400_ENST00000330386.6_Silent_p.L94L|EP400_ENST00000389561.2_Silent_p.L94L|EP400_ENST00000389562.2_Silent_p.L94L			Q96L91	EP400_HUMAN	E1A binding protein p400	94					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		TGGCCCCACTGCCGCTCCCCA	0.617																																					p.L94L		Atlas-SNP	.											.	EP400	370	.	0			c.G282T						.						44	44	44					12																	132445446		2203	4300	6503	SO:0001819	synonymous_variant	57634	exon2			CCCACTGCCGCTC	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.282G>T	chr12.hg19:g.132445446G>T		304.0	1.0		245.0	126.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.		0.617	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		T	132445446	G	T	132445446	2	4	74	1	0	0	0	0	0	0	0	1	5151	1306	46	3		3	EP400	12	132445446	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	23252649	132445446	1406449	91	10067										
RNF17	56163	hgsc.bcm.edu	37	chr13	25416232	25416232	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ttttcgattctcttggtgctCctgaaatgactactactagt	7	9	1	2	rs140457030		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr13:25416232C>T	ENST00000255324.5	+	19	2588	c.2536C>T	c.(2536-2538)Cct>Tct	p.P846S	RNF17_ENST00000339524.3_5'Flank|RNF17_ENST00000381921.1_Missense_Mutation_p.P846S	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	846					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		TCTTGGTGCTCCTGAAATGAC	0.343																																					p.P846S		Atlas-SNP	.											.	RNF17	259	.	0			c.C2536T						.	C	SER/PRO,SER/PRO	4,4402	8.1+/-20.4	0,4,2199	158	149	152		2536,2536	5.3	1	13	dbSNP_134	152	0,8600		0,0,4300	yes	missense,missense	RNF17	NM_001184993.1,NM_031277.2	74,74	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	possibly-damaging,possibly-damaging	846/1620,846/1624	25416232	4,13002	2203	4300	6503	SO:0001583	missense	56163	exon19			GGTGCTCCTGAAA	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.2536C>T	chr13.hg19:g.25416232C>T	ENSP00000255324:p.Pro846Ser	78.0	0.0		63.0	20.0	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	hg19	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	C	8.103	0.777141	0.16120	9.08E-4	0.0	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000418120	T;T;T	0.11712	3.55;3.55;2.75	5.29	5.29	0.74685	Staphylococcal nuclease (SNase-like) (1);	0.277119	0.29459	N	0.012097	T	0.19366	0.0465	L	0.27053	0.805	0.80722	D	1	B;D;B	0.89917	0.068;1.0;0.083	B;D;B	0.87578	0.014;0.998;0.02	T	0.07233	-1.0783	10	0.12430	T	0.62	-8.1118	16.2019	0.82087	0.0:1.0:0.0:0.0	.	846;846;846	B7Z7S1;Q9BXT8-5;Q9BXT8	.;.;RNF17_HUMAN	S	846;846;705;170	ENSP00000255324:P846S;ENSP00000371346:P846S;ENSP00000388892:P170S	ENSP00000255324:P846S	P	+	1	0	RNF17	24314232	0.663000	0.27448	0.996000	0.52242	0.013000	0.08279	0.689000	0.25437	2.638000	0.89438	0.585000	0.79938	CCT	.	C|1.000;T|0.000		0.343	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		T	25416232	C	T	25416232	3	4	74	1	0	0	0	0	1	0	0	0	13476	855	30	3	2610	3	RNF17	13	25416232	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10		25416232	89753646	92	10068										
ADPRHL1	113622	hgsc.bcm.edu	37	chr13	114107605	114107632	+	Frame_Shift_Del	DEL	GCGAGAGTACGAGGTGGTCCAGGCCCCC	GCGAGAGTACGAGGTGGTCCAGGCCCCC	-													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	actcacgggccattctcctgGcgagagtacgaggtggtcca					rs34085933|rs546248843|rs35745409|rs141431509|rs148683938|rs558010517	byFrequency	TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	GCGAGAGTACGAGGTGGTCCAGGCCCCC	GCGAGAGTACGAGGTGGTCCAGGCCCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr13:114107605_114107632delGCGAGAGTACGAGGTGGTCCAGGCCCCC	ENST00000375418.3	-	1	207_234	c.121_148delGGGGGCCTGGACCACCTCGTACTCTCGC	c.(121-150)gggggcctggaccacctcgtactctcgccafs	p.GGLDHLVLSP41fs		NM_138430.3	NP_612439.2	Q8NDY3	ARHL1_HUMAN	ADP-ribosylhydrolase like 1	41					protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)	p.L46L(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	11	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.0195)|GBM - Glioblastoma multiforme(44;0.116)			CATTCTCCTGGCGAGAGTACGAGGTGGTCCAGGCCCCCGGAACGTTGC	0.623																																					p.41_50del		Pindel	.											.	ADPRHL1	30	.	1	Substitution - coding silent(1)	lung(1)	c.122_149del						.																																			SO:0001589	frameshift_variant	113622	exon1			.	AJ313429	CCDS9535.1, CCDS9536.1	13q34	2003-06-19			ENSG00000153531	ENSG00000153531			21303	protein-coding gene	gene with protein product		610620				12070318	Standard	NM_138430		Approved	ARH2	uc001vtq.1	Q8NDY3	OTTHUMG00000017386	ENST00000375418.3:c.121_148delGGGGGCCTGGACCACCTCGTACTCTCGC	chr13.hg19:g.114107605_114107632delGCGAGAGTACGAGGTGGTCCAGGCCCCC	ENSP00000364567:p.Gly41fs	114.0	0.0		97.0	15.0	NM_138430	Q5JUG2|Q96GD1	Frame_Shift_Del	DEL	ENST00000375418.3	hg19	CCDS9535.1																																																																																			.	.		0.623	ADPRHL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045915.2	NM_138430		-	114107632	GCGAGAGTACGAGGTGGTCCAGGCCCCC	-	114107605	7	5	74	1	0	1	0	1	0	0	0	0	332	1203	42	0	944	0	ADPRHL1	13	114107605	Frame_Shift_Del	DEL	GCGAGAGTACGAGGTGGTCCAGGCCCCC	TCGA-CC-A7II-01A-11D-A33K-10	88691373	114107605	1062273	93	10069										
PRKD1	5587	hgsc.bcm.edu	37	chr14	30100159	30100159	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	atttcgaaacaatgaggattGgccccattaggaattaaagc	9	7	0	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr14:30100159G>A	ENST00000331968.5	-	10	1690	c.1461C>T	c.(1459-1461)gcC>gcT	p.A487A	PRKD1_ENST00000415220.2_Silent_p.A495A	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	487	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		AATGAGGATTGGCCCCATTAG	0.363																																					p.A487A		Atlas-SNP	.											.	PRKD1	316	.	0			c.C1461T						.						115	111	112					14																	30100159		2203	4300	6503	SO:0001819	synonymous_variant	5587	exon10			AGGATTGGCCCCA		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.1461C>T	chr14.hg19:g.30100159G>A		188.0	0.0		130.0	43.0	NM_002742	A6NL64|B2RAF6	Silent	SNP	ENST00000331968.5	hg19	CCDS9637.1																																																																																			.	.		0.363	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		A	30100159	G	A	30100159	2	1	74	1	0	0	0	0	0	0	0	1	12530	1335	47	3		3	PRKD1	14	30100159	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10		30100159	77249381	94	10070										
ESR2	2100	hgsc.bcm.edu	37	chr14	64727461	64727461	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gtacccacatctctctctccGggagcctgaagaggaaagca	10	13	2	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr14:64727461G>T	ENST00000341099.4	-	5	1075	c.658C>A	c.(658-660)Cgg>Agg	p.R220R	ESR2_ENST00000353772.3_Silent_p.R220R|ESR2_ENST00000357782.2_Silent_p.R220R|ESR2_ENST00000555278.1_Silent_p.R220R|ESR2_ENST00000554572.1_Silent_p.R220R|ESR2_ENST00000542956.1_Silent_p.R220R|ESR2_ENST00000557772.1_Silent_p.R220R|ESR2_ENST00000555483.1_5'UTR|ESR2_ENST00000358599.5_Silent_p.R220R|ESR2_ENST00000267525.6_Silent_p.R220R|ESR2_ENST00000553796.1_Silent_p.R220R	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	220	Steroid-binding.				brain development (GO:0007420)|cell-cell signaling (GO:0007267)|epithelial cell maturation involved in prostate gland development (GO:0060743)|extracellular negative regulation of signal transduction (GO:1900116)|gene expression (GO:0010467)|hormone-mediated apoptotic signaling pathway (GO:0008628)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|ovarian follicle development (GO:0001541)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|uterus development (GO:0060065)|vagina development (GO:0060068)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor antagonist activity (GO:0048019)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	CTCTCTCTCCGGGAGCCTGAA	0.577																																					p.R220R		Atlas-SNP	.											.	ESR2	82	.	0			c.C658A						.						28	29	29					14																	64727461		2191	4281	6472	SO:0001819	synonymous_variant	2100	exon4			CTCTCCGGGAGCC	X99101	CCDS9762.1, CCDS32096.1, CCDS55920.1, CCDS61469.1, CCDS61470.1	14q21-q22	2013-01-16			ENSG00000140009	ENSG00000140009		"Nuclear hormone receptors"	3468	protein-coding gene	gene with protein product		601663				8769313	Standard	NM_001214902		Approved	NR3A2, Erb	uc001xha.1	Q92731	OTTHUMG00000141306	ENST00000341099.4:c.658C>A	chr14.hg19:g.64727461G>T		45.0	0.0		39.0	7.0	NM_001214902	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Silent	SNP	ENST00000341099.4	hg19	CCDS9762.1																																																																																			.	.		0.577	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1			T	64727461	G	T	64727461	2	4	74	1	0	0	0	0	0	0	0	1	5259	1115	39	1		1	ESR2	14	64727461	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	34627302	64727461	42622079	95	10071										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105413999	105413999	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgtcacttccgccttggggcCtttcaggtccagcttggggc	13	13	2	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr14:105413999C>A	ENST00000333244.5	-	7	7908	c.7789G>T	c.(7789-7791)Ggc>Tgc	p.G2597C	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2597						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCCTTGGGGCCTTTCAGGTCC	0.617																																					p.G2597C		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G7789T						.						123	135	131					14																	105413999		1861	4092	5953	SO:0001583	missense	113146	exon7			TGGGGCCTTTCAG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7789G>T	chr14.hg19:g.105413999C>A	ENSP00000353114:p.Gly2597Cys	198.0	0.0		183.0	76.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	11.90	1.777164	0.31411	.	.	ENSG00000185567	ENST00000333244	T	0.03468	3.92	3.56	3.56	0.40772	.	.	.	.	.	T	0.19248	0.0462	M	0.88775	2.98	0.09310	N	1	D	0.63046	0.992	P	0.60473	0.875	T	0.04103	-1.0977	9	0.54805	T	0.06	.	14.1715	0.65512	0.0:1.0:0.0:0.0	.	2597	Q8IVF2	AHNK2_HUMAN	C	2597	ENSP00000353114:G2597C	ENSP00000353114:G2597C	G	-	1	0	AHNAK2	104485044	0.000000	0.05858	0.059000	0.19551	0.263000	0.26337	0.184000	0.16939	1.543000	0.49345	0.485000	0.47835	GGC	.	.		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105413999	C	A	105413999	3	1	74	1	0	0	0	0	1	0	0	0	415	681	24	3	9602	3	AHNAK2	14	105413999	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	40686538	105413999	1935541	96	10072										
GABRA5	2558	hgsc.bcm.edu	37	chr15	27128577	27128577	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcctccctctcaacaacctcCttgccagcaagatctggacc	6	18	2	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr15:27128577C>A	ENST00000335625.5	+	6	1258	c.370C>A	c.(370-372)Ctt>Att	p.L124I	GABRA5_ENST00000355395.5_Missense_Mutation_p.L124I|GABRA5_ENST00000400081.3_Missense_Mutation_p.L124I|GABRA5_ENST00000557449.1_Intron|GABRB3_ENST00000541819.2_Intron	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	124					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	CAACAACCTCCTTGCCAGCAA	0.547																																					p.L124I		Atlas-SNP	.											.	GABRA5	127	.	0			c.C370A						.						91	102	98					15																	27128577		2195	4296	6491	SO:0001583	missense	2558	exon6			AACCTCCTTGCCA		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.370C>A	chr15.hg19:g.27128577C>A	ENSP00000335592:p.Leu124Ile	119.0	0.0		89.0	40.0	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	hg19	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.109478	0.77096	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000555182;ENST00000400081;ENST00000554596;ENST00000554599	T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	5.4	4.47	0.54385	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.83119	0.5185	L	0.50919	1.6	0.53688	D	0.999974	P	0.51147	0.942	P	0.60068	0.868	D	0.85076	0.0943	10	0.87932	D	0	.	14.8695	0.70444	0.1446:0.8554:0.0:0.0	.	124	P31644	GBRA5_HUMAN	I	124;124;92;124;124;124	ENSP00000335592:L124I;ENSP00000347557:L124I;ENSP00000450653:L92I;ENSP00000382953:L124I;ENSP00000450806:L124I;ENSP00000450717:L124I	ENSP00000335592:L124I	L	+	1	0	GABRA5	24679670	0.991000	0.36638	0.042000	0.18584	0.969000	0.65631	2.953000	0.49105	1.384000	0.46424	0.561000	0.74099	CTT	.	.		0.547	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			A	27128577	C	A	27128577	3	1	74	1	0	0	0	0	1	0	0	0	6172	681	24	3	384	3	GABRA5	15	27128577	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10		27128577	75402815	97	10073										
DUOX1	53905	hgsc.bcm.edu	37	chr15	45437120	45437120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgtttaacttggaggaagagCggcaggcgctggtggaaaat	16	5	0	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr15:45437120C>T	ENST00000321429.4	+	19	2571	c.2164C>T	c.(2164-2166)Cgg>Tgg	p.R722W	DUOX1_ENST00000561166.1_Missense_Mutation_p.R368W|DUOX1_ENST00000389037.3_Missense_Mutation_p.R722W	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	722					cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GGAGGAAGAGCGGCAGGCGCT	0.567																																					p.R722W		Atlas-SNP	.											.	DUOX1	125	.	0			c.C2164T						.						83	97	92					15																	45437120		2198	4298	6496	SO:0001583	missense	53905	exon19			GAAGAGCGGCAGG	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.2164C>T	chr15.hg19:g.45437120C>T	ENSP00000317997:p.Arg722Trp	84.0	0.0		59.0	25.0	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	hg19	CCDS32221.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.111177	0.56398	.	.	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	D;D	0.87887	-2.31;-2.31	4.81	2.88	0.33553	.	0.155171	0.53938	D	0.000048	D	0.90445	0.7008	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.88917	0.3363	10	0.62326	D	0.03	-35.7814	8.1009	0.30857	0.1809:0.6448:0.1743:0.0	.	722	Q9NRD9	DUOX1_HUMAN	W	722	ENSP00000317997:R722W;ENSP00000373689:R722W	ENSP00000317997:R722W	R	+	1	2	DUOX1	43224412	0.999000	0.42202	0.997000	0.53966	0.507000	0.33981	1.990000	0.40717	0.713000	0.32060	-0.181000	0.13052	CGG	.	.		0.567	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		T	45437120	C	T	45437120	3	4	74	1	0	0	0	0	1	0	0	0	4802	759	27	1	2230	1	DUOX1	15	45437120	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	18308543	45437120	57094272	98	10074										
ANKDD1A	348094	hgsc.bcm.edu	37	chr15	65208032	65208032	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcagctccacgaggccgcccGccagaacaatgtcggcagga	13	15	0	1	rs553148491		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr15:65208032G>A	ENST00000380230.3	+	2	100	c.71G>A	c.(70-72)cGc>cAc	p.R24H	ANKDD1A_ENST00000491145.1_3'UTR|ANKDD1A_ENST00000496660.1_Intron|ANKDD1A_ENST00000357698.3_Missense_Mutation_p.R24H|AC069368.3_ENST00000437723.1_Intron|ANKDD1A_ENST00000395720.1_Missense_Mutation_p.R24H|ANKDD1A_ENST00000319580.8_Intron	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	24					signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						GAGGCCGCCCGCCAGAACAAT	0.597													G|||	1	0.000199681	8e-04	0	5008	,	,		18846	0		0	False		,,,				2504	0				p.R24H		Atlas-SNP	.											ANKDD1A,NS,carcinoma,0,3	ANKDD1A	47	.	0			c.G71A						.						34	38	37					15																	65208032		1925	4132	6057	SO:0001583	missense	348094	exon2			CCGCCCGCCAGAA		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.71G>A	chr15.hg19:g.65208032G>A	ENSP00000369579:p.Arg24His	57.0	0.0		43.0	13.0	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Missense_Mutation	SNP	ENST00000380230.3	hg19	CCDS10197.2	.	.	.	.	.	.	.	.	.	.	G	15.22	2.769437	0.49680	.	.	ENSG00000166839	ENST00000380230;ENST00000357698;ENST00000395720	T;T;T	0.66460	-0.21;-0.21;-0.21	3.94	2.06	0.26882	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.66147	0.2760	L	0.37697	1.125	0.09310	N	0.999997	D;D	0.76494	0.999;0.999	D;D	0.66847	0.947;0.911	T	0.53858	-0.8379	9	0.14656	T	0.56	-9.5593	6.0201	0.19625	0.238:0.0:0.762:0.0	.	24;24	Q495B1;Q495B1-1	AKD1A_HUMAN;.	H	24	ENSP00000369579:R24H;ENSP00000350329:R24H;ENSP00000379070:R24H	ENSP00000350329:R24H	R	+	2	0	ANKDD1A	62995085	0.098000	0.21812	0.018000	0.16275	0.787000	0.44495	1.223000	0.32527	0.363000	0.24346	0.484000	0.47621	CGC	.	.		0.597	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703		A	65208032	G	A	65208032	3	1	74	1	0	0	0	0	1	0	0	0	624	1087	38	1	77	1	ANKDD1A	15	65208032	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	19770912	65208032	37323360	99	10075										
LOXL1	4016	hgsc.bcm.edu	37	chr15	74235272	74235272	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gagcccacctgtactccctgCgctgtgctgcggaggagaag	14	13	0	1	rs566197761		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr15:74235272C>T	ENST00000261921.7	+	2	1506	c.1180C>T	c.(1180-1182)Cgc>Tgc	p.R394C		NM_005576.2	NP_005567.2	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1	394	Lysyl-oxidase like.				extracellular matrix organization (GO:0030198)|oxidation-reduction process (GO:0055114)|protein deamination (GO:0018277)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor (GO:0016641)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						GTACTCCCTGCGCTGTGCTGC	0.587													C|||	1	0.000199681	0	0.0014	5008	,	,		20777	0		0	False		,,,				2504	0				p.R394C		Atlas-SNP	.											.	LOXL1	25	.	0			c.C1180T						.						174	163	166					15																	74235272		2198	4297	6495	SO:0001583	missense	4016	exon2			TCCCTGCGCTGTG	L21186	CCDS10253.1	15q24-q25	2008-07-18			ENSG00000129038	ENSG00000129038			6665	protein-coding gene	gene with protein product		153456				7689553	Standard	NM_005576		Approved	LOXL, LOL	uc002awc.1	Q08397	OTTHUMG00000137595	ENST00000261921.7:c.1180C>T	chr15.hg19:g.74235272C>T	ENSP00000261921:p.Arg394Cys	136.0	0.0		91.0	29.0	NM_005576	Q6NUL3|Q96BW7	Missense_Mutation	SNP	ENST00000261921.7	hg19	CCDS10253.1	.	.	.	.	.	.	.	.	.	.	C	19.01	3.744866	0.69418	.	.	ENSG00000129038	ENST00000261921;ENST00000395162	T	0.33438	1.41	3.91	3.91	0.45181	.	0.067785	0.64402	D	0.000019	T	0.53174	0.1780	M	0.80982	2.52	0.58432	D	0.999994	D	0.89917	1.0	D	0.81914	0.995	T	0.57653	-0.7774	10	0.87932	D	0	.	9.0924	0.36619	0.2186:0.7814:0.0:0.0	.	394	Q08397	LOXL1_HUMAN	C	394;256	ENSP00000261921:R394C	ENSP00000261921:R394C	R	+	1	0	LOXL1	72022325	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.752000	0.38349	2.180000	0.69256	0.561000	0.74099	CGC	.	.		0.587	LOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268995.2	NM_005576		T	74235272	C	T	74235272	3	4	74	1	0	0	0	0	1	0	0	0	8908	768	27	1	1186	1	LOXL1	15	74235272	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	9027240	74235272	28296120	100	10076										
ISLR	3671	hgsc.bcm.edu	37	chr15	74467261	74467261	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cctggctcaggcctgccctgAgccctgcgactgtggggaaa	14	14	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr15:74467261A>G	ENST00000249842.3	+	2	419	c.62A>G	c.(61-63)gAg>gGg	p.E21G	RP11-665J16.1_ENST00000561647.1_RNA|ISLR_ENST00000395118.1_Missense_Mutation_p.E21G	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	21	LRRNT.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						GCCTGCCCTGAGCCCTGCGAC	0.627																																					p.E21G		Atlas-SNP	.											.	ISLR	49	.	0			c.A62G						.						46	43	44					15																	74467261		2198	4297	6495	SO:0001583	missense	3671	exon2			GCCCTGAGCCCTG	AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"Immunoglobulin superfamily / I-set domain containing"	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.62A>G	chr15.hg19:g.74467261A>G	ENSP00000249842:p.Glu21Gly	57.0	0.0		41.0	10.0	NM_201526		Missense_Mutation	SNP	ENST00000249842.3	hg19	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	A	10.78	1.446065	0.25987	.	.	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.62105	0.05;0.05	3.91	2.67	0.31697	Leucine-rich repeat-containing N-terminal (1);	0.252672	0.25922	U	0.027435	T	0.43277	0.1240	L	0.28054	0.825	0.45354	D	0.998349	B	0.09022	0.002	B	0.11329	0.006	T	0.32428	-0.9907	10	0.36615	T	0.2	.	6.0472	0.19766	0.6112:0.2978:0.091:0.0	.	21	O14498	ISLR_HUMAN	G	21	ENSP00000249842:E21G;ENSP00000378550:E21G	ENSP00000249842:E21G	E	+	2	0	ISLR	72254314	0.997000	0.39634	0.952000	0.39060	0.597000	0.36814	2.940000	0.49003	1.413000	0.46997	0.260000	0.18958	GAG	.	.		0.627	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545		G	74467261	A	G	74467261	3	3	74	1	0	0	0	0	1	0	0	0	7867	304	11	2	64	2	ISLR	15	74467261	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	231989	74467261	28064131	101	10077										
ARID3B	10620	hgsc.bcm.edu	37	chr15	74836781	74836781	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tccaaggcctcaccttctgtCtccacagcaggacagccgaa	8	16	3	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr15:74836781C>T	ENST00000346246.5	+	2	735	c.504C>T	c.(502-504)gtC>gtT	p.V168V		NM_006465.2	NP_006456.1	Q8IVW6	ARI3B_HUMAN	AT rich interactive domain 3B (BRIGHT-like)	168						nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(2)	14						CACCTTCTGTCTCCACAGCAG	0.517																																					p.V168V		Atlas-SNP	.											.	ARID3B	35	.	0			c.C504T						.						70	56	61					15																	74836781		2197	4296	6493	SO:0001819	synonymous_variant	10620	exon2			TTCTGTCTCCACA		CCDS10264.1	15q24	2013-02-07	2006-11-08		ENSG00000179361	ENSG00000179361		"-"	14350	protein-coding gene	gene with protein product		612457	"AT rich interactive domain 3B (BRIGHT- like)"				Standard	NM_006465		Approved	BDP, DRIL2	uc002ayd.3	Q8IVW6	OTTHUMG00000141321	ENST00000346246.5:c.504C>T	chr15.hg19:g.74836781C>T		104.0	0.0		77.0	27.0	NM_006465	O95443|Q59HC9|Q6P9C9	Silent	SNP	ENST00000346246.5	hg19	CCDS10264.1																																																																																			.	.		0.517	ARID3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280688.2	NM_006465		T	74836781	C	T	74836781	2	4	74	1	0	0	0	0	0	0	0	1	917	900	32	3		3	ARID3B	15	74836781	Silent	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	369520	74836781	27694611	102	10078										
PDE8A	5151	hgsc.bcm.edu	37	chr15	85681082	85681082	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgacaacaactttaaatactGgaaaggactggacgaaatga	9	6	0	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr15:85681082G>T	ENST00000310298.4	+	23	2690	c.2438G>T	c.(2437-2439)tGg>tTg	p.W813L	PDE8A_ENST00000394553.1_Missense_Mutation_p.W813L|PDE8A_ENST00000339708.5_Missense_Mutation_p.W767L|PDE8A_ENST00000557957.1_Missense_Mutation_p.W741L			O60658	PDE8A_HUMAN	phosphodiesterase 8A	813	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	TTTAAATACTGGAAAGGACTG	0.468																																					p.W813L		Atlas-SNP	.											.	PDE8A	50	.	0			c.G2438T						.						101	85	91					15																	85681082		2203	4299	6502	SO:0001583	missense	5151	exon22			AATACTGGAAAGG	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"Phosphodiesterases"	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.2438G>T	chr15.hg19:g.85681082G>T	ENSP00000311453:p.Trp813Leu	146.0	0.0		103.0	36.0	NM_002605	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Missense_Mutation	SNP	ENST00000310298.4	hg19	CCDS10336.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725813	0.69074	.	.	ENSG00000073417	ENST00000310298;ENST00000394553;ENST00000339708	T;T;T	0.81330	-1.48;-1.48;-1.48	5.49	5.49	0.81192	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	D	0.90068	0.6898	M	0.80746	2.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.90735	0.4645	10	0.87932	D	0	.	16.9239	0.86170	0.0:0.0:1.0:0.0	.	767;813	O60658-2;O60658	.;PDE8A_HUMAN	L	813;813;767	ENSP00000311453:W813L;ENSP00000378056:W813L;ENSP00000340679:W767L	ENSP00000311453:W813L	W	+	2	0	PDE8A	83482086	1.000000	0.71417	1.000000	0.80357	0.013000	0.08279	9.185000	0.94900	2.865000	0.98341	0.655000	0.94253	TGG	.	.		0.468	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		T	85681082	G	T	85681082	3	4	74	1	0	0	0	0	1	0	0	0	11662	1357	47	3	2524	3	PDE8A	15	85681082	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	10844301	85681082	16850310	103	10079										
AGBL1	123624	hgsc.bcm.edu	37	chr15	87097615	87097615	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cttcccaaaatccttgataaGctagcaccagcattcacaat	4	13	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr15:87097615G>A	ENST00000441037.2	+	20	2798	c.2703G>A	c.(2701-2703)aaG>aaA	p.K901K	AGBL1_ENST00000389298.3_Silent_p.K632K|AGBL1_ENST00000421325.2_Silent_p.K901K	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	901					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TCCTTGATAAGCTAGCACCAG	0.463																																					p.K901K		Atlas-SNP	.											.	AGBL1	151	.	0			c.G2703A						.						31	31	31					15																	87097615		1870	4103	5973	SO:0001819	synonymous_variant	123624	exon20			TGATAAGCTAGCA	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2703G>A	chr15.hg19:g.87097615G>A		72.0	0.0		61.0	23.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	hg19	CCDS58398.1																																																																																			.	.		0.463	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		A	87097615	G	A	87097615	2	1	74	1	0	0	0	0	0	0	0	1	375	962	34	3		3	AGBL1	15	87097615	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	1416533	87097615	15433777	104	10080										
SSTR5	6755	hgsc.bcm.edu	37	chr16	1129560	1129560	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cgtggtgaaggtgagggcggCgggcgtgcgcgtgggctgcg	24	8	0	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr16:1129560C>A	ENST00000293897.4	+	1	780	c.692C>A	c.(691-693)gCg>gAg	p.A231E	SSTR5-AS1_ENST00000569832.1_RNA|SSTR5_ENST00000397547.2_Missense_Mutation_p.A231E|SSTR5_ENST00000562758.1_Intron	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	231					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytokinesis (GO:0032467)|regulation of insulin secretion (GO:0050796)|somatostatin signaling pathway (GO:0038170)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			endometrium(2)|lung(5)|prostate(1)|skin(1)	9		Hepatocellular(780;0.00369)			Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	GTGAGGGCGGCGGGCGTGCGC	0.672																																					p.A231E		Atlas-SNP	.											.	SSTR5	36	.	0			c.C692A						.						78	75	76					16																	1129560		2190	4294	6484	SO:0001583	missense	6755	exon2			GGGCGGCGGGCGT	D16827	CCDS10429.1	16p13.3	2012-08-08			ENSG00000162009	ENSG00000162009		"GPCR / Class A : Somatostatin receptors"	11334	protein-coding gene	gene with protein product		182455				7607700	Standard	NM_001053		Approved		uc021taf.1	P35346	OTTHUMG00000047842	ENST00000293897.4:c.692C>A	chr16.hg19:g.1129560C>A	ENSP00000293897:p.Ala231Glu	70.0	0.0		63.0	46.0	NM_001172560	P34988|Q541E0|Q9UJI5	Missense_Mutation	SNP	ENST00000293897.4	hg19	CCDS10429.1	.	.	.	.	.	.	.	.	.	.	C	11.16	1.556218	0.27827	.	.	ENSG00000162009	ENST00000397547;ENST00000293897	T;T	0.39056	1.1;1.1	4.76	3.79	0.43588	GPCR, rhodopsin-like superfamily (1);	0.229561	0.37955	N	0.001875	T	0.48132	0.1483	L	0.45744	1.44	0.09310	N	1	P	0.40107	0.703	P	0.50570	0.644	T	0.41106	-0.9527	10	0.56958	D	0.05	.	12.4082	0.55451	0.0:0.9164:0.0:0.0836	.	231	P35346	SSR5_HUMAN	E	231	ENSP00000380680:A231E;ENSP00000293897:A231E	ENSP00000293897:A231E	A	+	2	0	SSTR5	1069561	0.017000	0.18338	0.002000	0.10522	0.004000	0.04260	2.500000	0.45381	0.980000	0.38523	0.561000	0.74099	GCG	.	.		0.672	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1			A	1129560	C	A	1129560	3	1	74	1	0	0	0	0	1	0	0	0	15216	768	27	1	694	1	SSTR5	16	1129560	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10		1129560	89225193	105	10081										
ALG1	56052	hgsc.bcm.edu	37	chr16	5121883	5121883	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgcttggtcctgctggcgctGtgtctgctgctgccgctgct	14	13	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr16:5121883G>A	ENST00000262374.5	+	1	64	c.33G>A	c.(31-33)ctG>ctA	p.L11L	ALG1_ENST00000544428.1_5'Flank|ALG1_ENST00000588623.1_Intron	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	11					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				TGCTGGCGCTGTGTctgctgc	0.721																																					p.L11L		Atlas-SNP	.											.	ALG1	35	.	0			c.G33A						.						11	12	11					16																	5121883		2174	4256	6430	SO:0001819	synonymous_variant	56052	exon1			GGCGCTGTGTCTG	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"Glycosyltransferase group 1 domain containing"	18294	protein-coding gene	gene with protein product		605907	"asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)", "asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.33G>A	chr16.hg19:g.5121883G>A		29.0	0.0		18.0	14.0	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Silent	SNP	ENST00000262374.5	hg19	CCDS10528.1																																																																																			.	.		0.721	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109		A	5121883	G	A	5121883	2	1	74	1	0	0	0	0	0	0	0	1	510	1364	48	3		3	ALG1	16	5121883	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	3992323	5121883	85232870	106	10082										
GSG1L	146395	hgsc.bcm.edu	37	chr16	27840186	27840186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gccctgctcaaagaccttgcGcttgtgccggaactcaatga	10	13	2	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr16:27840186G>A	ENST00000447459.2	-	5	838	c.754C>T	c.(754-756)Cgc>Tgc	p.R252C	GSG1L_ENST00000569166.1_Missense_Mutation_p.R97C|GSG1L_ENST00000380898.2_Missense_Mutation_p.R97C|GSG1L_ENST00000380897.3_Missense_Mutation_p.R97C|GSG1L_ENST00000395724.3_Missense_Mutation_p.R201C	NM_001109763.1	NP_001103233.1	Q6UXU4	GSG1L_HUMAN	GSG1-like	252					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	asymmetric synapse (GO:0032279)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(4)	17						AAGACCTTGCGCTTGTGCCGG	0.587																																					p.R252C		Atlas-SNP	.											.	GSG1L	82	.	0			c.C754T						.						103	76	85					16																	27840186		2197	4300	6497	SO:0001583	missense	146395	exon5			CCTTGCGCTTGTG	AK128775	CCDS10631.1, CCDS45450.1	16p11.2	2014-01-20			ENSG00000169181	ENSG00000169181			28283	protein-coding gene	gene with protein product						22813734	Standard	NM_001109763		Approved	MGC18079, PRO19651, KTSR5831	uc002doz.2	Q6UXU4	OTTHUMG00000131676	ENST00000447459.2:c.754C>T	chr16.hg19:g.27840186G>A	ENSP00000394954:p.Arg252Cys	159.0	0.0		145.0	41.0	NM_001109763	Q7Z6F8|Q8TB81	Missense_Mutation	SNP	ENST00000447459.2	hg19	CCDS45450.1	.	.	.	.	.	.	.	.	.	.	G	33	5.207335	0.95033	.	.	ENSG00000169181	ENST00000447459;ENST00000395724;ENST00000380898;ENST00000380897	T;T	0.35605	1.33;1.3	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.55940	0.1952	L	0.49778	1.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.949;0.967;0.99	T	0.58188	-0.7680	10	0.87932	D	0	0.6619	17.5938	0.88005	0.0:0.0:1.0:0.0	.	201;97;252	Q6UXU4-3;Q6UXU4-4;Q6UXU4	.;.;GSG1L_HUMAN	C	252;201;97;97	ENSP00000394954:R252C;ENSP00000379074:R201C	ENSP00000370282:R97C	R	-	1	0	GSG1L	27747687	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.898000	0.87363	2.455000	0.83008	0.650000	0.86243	CGC	.	.		0.587	GSG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433832.2	NM_144675		A	27840186	G	A	27840186	3	1	74	1	0	0	0	0	1	0	0	0	6830	1087	38	1	253	1	GSG1L	16	27840186	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	22718303	27840186	62514567	107	10083										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31405619	31405619	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ctacgatcttccaggaggatGcaggcggctttgggcagagc	15	10	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr16:31405619G>T	ENST00000389202.2	+	2	143	c.94G>T	c.(94-96)Gca>Tca	p.A32S		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	32					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CCAGGAGGATGCAGGCGGCTT	0.572																																					p.A32S		Atlas-SNP	.											.	ITGAD	154	.	0			c.G94T						.						103	86	91					16																	31405619		2197	4300	6497	SO:0001583	missense	3681	exon2			GAGGATGCAGGCG	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.94G>T	chr16.hg19:g.31405619G>T	ENSP00000373854:p.Ala32Ser	132.0	0.0		104.0	15.0	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	G	9.722	1.160041	0.21454	.	.	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.72394	-0.65	4.54	4.54	0.55810	.	.	.	.	.	T	0.60856	0.2301	L	0.42581	1.335	0.09310	N	1	B;B;B	0.29590	0.25;0.038;0.021	B;B;B	0.25506	0.061;0.056;0.056	T	0.48258	-0.9051	9	0.20046	T	0.44	.	12.7695	0.57412	0.0:0.0:1.0:0.0	.	32;48;32	B7Z6V7;Q59H14;Q13349	.;.;ITAD_HUMAN	S	48;32	ENSP00000373854:A32S	ENSP00000373854:A32S	A	+	1	0	ITGAD	31313120	0.030000	0.19436	0.048000	0.18961	0.505000	0.33919	2.474000	0.45154	2.064000	0.61679	0.561000	0.74099	GCA	.	.		0.572	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		T	31405619	G	T	31405619	3	4	74	1	0	0	0	0	1	0	0	0	7893	1319	46	3	100	3	ITGAD	16	31405619	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	3565433	31405619	58949134	108	10084										
ABCC12	94160	hgsc.bcm.edu	37	chr16	48119516	48119516	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tttcttacctttgaattacgGagaagagctcgggccacaca	9	10	1	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr16:48119516G>T	ENST00000311303.3	-	27	4161	c.3816C>A	c.(3814-3816)ctC>ctA	p.L1272L	ABCC12_ENST00000448542.1_3'UTR|ABCC12_ENST00000532355.1_5'UTR|ABCC12_ENST00000416054.1_3'UTR	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	1272	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				TTGAATTACGGAGAAGAGCTC	0.453																																					p.L1272L		Atlas-SNP	.											.	ABCC12	190	.	0			c.C3816A						.						151	148	149					16																	48119516		2201	4300	6501	SO:0001819	synonymous_variant	94160	exon27			ATTACGGAGAAGA	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.3816C>A	chr16.hg19:g.48119516G>T		191.0	0.0		144.0	43.0	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	hg19	CCDS10730.1																																																																																			.	.		0.453	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		T	48119516	G	T	48119516	2	4	74	1	0	0	0	0	0	0	0	1	52	1161	41	3		3	ABCC12	16	48119516	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	16713897	48119516	42235237	109	10085										
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76592443	76592443	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tcactgccatagctgttcgcAtttatcagcagaaaaggtta	8	9	2	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr16:76592443A>G	ENST00000476707.1	+	23	3938	c.3799A>G	c.(3799-3801)Att>Gtt	p.I1267V	CNTNAP4_ENST00000478060.1_Missense_Mutation_p.I1191V|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.I1263V|RP11-58C22.1_ENST00000563764.1_Intron|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.I1215V			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	1264					cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						AGCTGTTCGCATTTATCAGCA	0.358																																					p.I1191V		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.A3571G						.						85	84	84					16																	76592443		1959	4197	6156	SO:0001583	missense	85445	exon23			GTTCGCATTTATC	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.3799A>G	chr16.hg19:g.76592443A>G	ENSP00000417628:p.Ile1267Val	172.0	0.0		176.0	52.0	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.32	1.902010	0.33535	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	5.65	4.54	0.55810	.	0.000000	0.42053	D	0.000772	T	0.43831	0.1265	.	.	.	0.36153	D	0.84761	B;B;B	0.26547	0.017;0.046;0.152	B;B;B	0.25987	0.02;0.023;0.065	T	0.49263	-0.8958	9	0.38643	T	0.18	.	12.1231	0.53903	0.8716:0.0:0.0:0.1284	.	1191;1267;1264	E9PFZ6;E9PDN6;Q9C0A0	.;.;CNTP4_HUMAN	V	1263;1215;1191;1267	ENSP00000306893:I1263V;ENSP00000439733:I1215V;ENSP00000418741:I1191V;ENSP00000417628:I1267V	ENSP00000306893:I1263V	I	+	1	0	CNTNAP4	75149944	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.984000	0.56923	1.111000	0.41721	0.533000	0.62120	ATT	.	.		0.358	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		G	76592443	A	G	76592443	3	3	74	1	0	0	0	0	1	0	0	0	3651	217	8	2	3897	2	CNTNAP4	16	76592443	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	28472927	76592443	13762310	110	10086										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77355100	77355100	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tcatgatcacatcccactagCtgtgacaaaaacaaaaaacg	5	11	2	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr16:77355100C>T	ENST00000282849.5	-	15	2582		c.e15-1			NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18						eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						ATCCCACTAGCTGTGACAAAA	0.378																																					.		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.2164-1G>A						.						73	73	73					16																	77355100		2198	4300	6498	SO:0001630	splice_region_variant	170692	exon16			CACTAGCTGTGAC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2164-1G>A	chr16.hg19:g.77355100C>T		102.0	0.0		111.0	34.0	NM_199355	Q6P4R5|Q6ZWJ9	Splice_Site	SNP	ENST00000282849.5	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.019772	0.54576	.	.	ENSG00000140873	ENST00000282849	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8324	0.92145	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADAMTS18	75912601	1.000000	0.71417	1.000000	0.80357	0.529000	0.34654	7.409000	0.80053	2.696000	0.92011	0.655000	0.94253	.	.	.		0.378	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		Intron	T	77355100	C	T	77355100	5	4	74	1	0	0	0	0	0	0	1	0	263	811	28	3	1538	3	ADAMTS18	16	77355100	Splice_Site	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	762657	77355100	12999653	111	10087										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77401346	77401346	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ttccttacatacatttcttgCgtcgtccacaaaaatgctgc	5	12	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr16:77401346C>T	ENST00000282849.5	-	4	1188	c.770G>A	c.(769-771)cGc>cAc	p.R257H	ADAMTS18_ENST00000567121.1_5'Flank	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	257					eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						ACATTTCTTGCGTCGTCCACA	0.443																																					p.R257H		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G770A						.						77	76	76					16																	77401346		2198	4300	6498	SO:0001583	missense	170692	exon4			TTCTTGCGTCGTC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.770G>A	chr16.hg19:g.77401346C>T	ENSP00000282849:p.Arg257His	91.0	0.0		76.0	32.0	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	32	5.175432	0.94807	.	.	ENSG00000140873	ENST00000282849;ENST00000449265	T;T	0.61392	0.11;2.09	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.76608	0.4011	M	0.78049	2.395	0.58432	D	0.999999	D	0.89917	1.0	D	0.79784	0.993	T	0.78242	-0.2280	10	0.52906	T	0.07	.	17.4456	0.87577	0.0:1.0:0.0:0.0	.	257	Q8TE60	ATS18_HUMAN	H	257	ENSP00000282849:R257H;ENSP00000392540:R257H	ENSP00000282849:R257H	R	-	2	0	ADAMTS18	75958847	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.447000	0.66606	2.603000	0.88011	0.555000	0.69702	CGC	.	.		0.443	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			T	77401346	C	T	77401346	3	4	74	1	0	0	0	0	1	0	0	0	263	768	27	1	2975	1	ADAMTS18	16	77401346	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	46246	77401346	12953407	112	10088										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000420246.2_Missense_Mutation_p.R249S|TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.R249S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	87.0	0.0		50.0	22.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	74	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10		7577534	73617676	113	10089										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7721980	7721980	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gggcctggaggcccagctgcTgggcattgtggtgcggaagg	20	9	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr17:7721980T>C	ENST00000572933.1	+	70	12016	c.10556T>C	c.(10555-10557)cTg>cCg	p.L3519P	DNAH2_ENST00000389173.2_Missense_Mutation_p.L3519P			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3519	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GCCCAGCTGCTGGGCATTGTG	0.592																																					p.L3519P		Atlas-SNP	.											.	DNAH2	498	.	0			c.T10556C						.						101	97	98					17																	7721980		2203	4300	6503	SO:0001583	missense	146754	exon69			AGCTGCTGGGCAT	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.10556T>C	chr17.hg19:g.7721980T>C	ENSP00000458355:p.Leu3519Pro	47.0	0.0		24.0	13.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	T	19.41	3.821380	0.71028	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.35789	1.29	4.34	4.34	0.51931	.	0.000000	0.64402	D	0.000014	T	0.75657	0.3879	H	0.99444	4.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85621	0.1264	10	0.87932	D	0	.	12.6744	0.56884	0.0:0.0:0.0:1.0	.	3480;3519	Q9P225-2;Q9P225	.;DYH2_HUMAN	P	3480;3519	ENSP00000373825:L3519P	ENSP00000353818:L3480P	L	+	2	0	DNAH2	7662705	1.000000	0.71417	0.980000	0.43619	0.854000	0.48673	4.435000	0.59941	1.819000	0.53055	0.460000	0.39030	CTG	.	.		0.592	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		C	7721980	T	C	7721980	3	2	74	1	0	0	0	0	1	0	0	0	4604	1580	55	2	10830	2	DNAH2	17	7721980	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	144446	7721980	73473230	114	10090										
MYH3	4621	hgsc.bcm.edu	37	chr17	10534941	10534941	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gccttacgtccgtgatggccTtcttggccttctcctcagcg	10	15	3	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr17:10534941T>C	ENST00000583535.1	-	36	5360	c.5273A>G	c.(5272-5274)aAg>aGg	p.K1758R	MYH3_ENST00000226209.7_Missense_Mutation_p.K1758R	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1758					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						CGTGATGGCCTTCTTGGCCTT	0.567											OREG0024180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K1758R		Atlas-SNP	.											.	MYH3	227	.	0			c.A5273G						.						173	118	137					17																	10534941		2203	4300	6503	SO:0001583	missense	4621	exon36			ATGGCCTTCTTGG		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.5273A>G	chr17.hg19:g.10534941T>C	ENSP00000464317:p.Lys1758Arg	122.0	0.0	665	48.0	25.0	NM_002470	Q15492	Missense_Mutation	SNP	ENST00000583535.1	hg19	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.040387	0.93630	.	.	ENSG00000109063	ENST00000226209	T	0.80214	-1.35	5.0	5.0	0.66597	Myosin tail (1);	.	.	.	.	D	0.87791	0.6266	M	0.82433	2.59	0.42409	D	0.992596	P	0.45212	0.853	P	0.53760	0.734	D	0.90043	0.4143	9	0.87932	D	0	.	15.1557	0.72739	0.0:0.0:0.0:1.0	.	1758	P11055	MYH3_HUMAN	R	1758	ENSP00000226209:K1758R	ENSP00000226209:K1758R	K	-	2	0	MYH3	10475666	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.864000	0.87037	2.216000	0.71823	0.459000	0.35465	AAG	.	.		0.567	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		C	10534941	T	C	10534941	3	2	74	1	0	0	0	0	1	0	0	0	10045	1609	56	2	573	2	MYH3	17	10534941	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	2812961	10534941	70660269	115	10091										
TBX21	30009	hgsc.bcm.edu	37	chr17	45820045	45820045	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agccactacaggatgtttgtGgacgtggtcttggtggacca	14	8	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr17:45820045G>A	ENST00000177694.1	+	2	772	c.561G>A	c.(559-561)gtG>gtA	p.V187V		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	187					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						GGATGTTTGTGGACGTGGTCT	0.632																																					p.V187V		Atlas-SNP	.											.	TBX21	50	.	0			c.G561A						.						46	37	40					17																	45820045		2203	4300	6503	SO:0001819	synonymous_variant	30009	exon2			GTTTGTGGACGTG	AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"T-boxes"	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.561G>A	chr17.hg19:g.45820045G>A		93.0	0.0		56.0	7.0	NM_013351		Silent	SNP	ENST00000177694.1	hg19	CCDS11514.1																																																																																			.	.		0.632	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351		A	45820045	G	A	45820045	2	1	74	1	0	0	0	0	0	0	0	1	15672	1335	47	3		3	TBX21	17	45820045	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	35285104	45820045	35375165	116	10092										
EVPL	2125	hgsc.bcm.edu	37	chr17	74014602	74014602	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cgggagcacgcttggtctccCcgccagggccctgcacgacc	13	18	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr17:74014602C>A	ENST00000301607.3	-	12	1617	c.1364G>T	c.(1363-1365)gGg>gTg	p.G455V	EVPL_ENST00000586740.1_Missense_Mutation_p.G455V	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	455	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CTTGGTCTCCCCGCCAGGGCC	0.652																																					p.G455V		Atlas-SNP	.											.	EVPL	155	.	0			c.G1364T						.						20	21	21					17																	74014602		2202	4298	6500	SO:0001583	missense	2125	exon12			GTCTCCCCGCCAG	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.1364G>T	chr17.hg19:g.74014602C>A	ENSP00000301607:p.Gly455Val	108.0	0.0		104.0	32.0	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	hg19	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.768759	0.90020	.	.	ENSG00000167880	ENST00000301607	T	0.74002	-0.8	5.12	5.12	0.69794	.	0.052170	0.85682	D	0.000000	D	0.87334	0.6151	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.945	D	0.88852	0.3320	10	0.87932	D	0	-59.6834	18.9474	0.92627	0.0:1.0:0.0:0.0	.	455;455	B7ZLH8;Q92817	.;EVPL_HUMAN	V	455	ENSP00000301607:G455V	ENSP00000301607:G455V	G	-	2	0	EVPL	71526197	0.983000	0.35010	0.954000	0.39281	0.781000	0.44180	3.524000	0.53495	2.573000	0.86826	0.561000	0.74099	GGG	.	.		0.652	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		A	74014602	C	A	74014602	3	1	74	1	0	0	0	0	1	0	0	0	5294	623	22	3	4781	3	EVPL	17	74014602	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	28194557	74014602	7180608	117	10093										
DUS1L	64118	hgsc.bcm.edu	37	chr17	80019565	80019565	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cctgcaggcactggatgttcCcgttagcaaacacagggatg	12	11	0	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr17:80019565C>T	ENST00000354321.7	-	6	1111	c.626G>A	c.(625-627)gGg>gAg	p.G209E	DUS1L_ENST00000306796.5_Missense_Mutation_p.G209E			Q6P1R4	DUS1L_HUMAN	dihydrouridine synthase 1-like (S. cerevisiae)	209							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	6	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			CTGGATGTTCCCGTTAGCAAA	0.657																																					p.G209E		Atlas-SNP	.											.	DUS1L	25	.	0			c.G626A						.						96	91	93					17																	80019565		2203	4300	6503	SO:0001583	missense	64118	exon7			ATGTTCCCGTTAG		CCDS32775.1	17q25.3	2005-08-09				ENSG00000169718			30086	protein-coding gene	gene with protein product						12477932	Standard	NM_022156		Approved	PP3111, DUS1	uc002kdr.4	Q6P1R4		ENST00000354321.7:c.626G>A	chr17.hg19:g.80019565C>T	ENSP00000346280:p.Gly209Glu	81.0	0.0		50.0	18.0	NM_022156	A6NHV4|Q96AI3	Missense_Mutation	SNP	ENST00000354321.7	hg19	CCDS32775.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.883179	0.51908	.	.	ENSG00000169718	ENST00000354321;ENST00000306796;ENST00000542088;ENST00000538833	T;T;T	0.70869	-0.52;-0.52;-0.52	3.83	3.83	0.44106	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.90734	0.7092	H	0.99225	4.475	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.94905	0.8060	10	0.87932	D	0	-39.3762	16.2497	0.82475	0.0:1.0:0.0:0.0	.	82;209;78	B4DPG7;Q6P1R4;Q9BTJ3	.;DUS1L_HUMAN;.	E	209;209;82;77	ENSP00000346280:G209E;ENSP00000303515:G209E;ENSP00000445110:G77E	ENSP00000303515:G209E	G	-	2	0	DUS1L	77612854	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	7.093000	0.76937	2.126000	0.65437	0.563000	0.77884	GGG	.	.		0.657	DUS1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442347.1	NM_022156		T	80019565	C	T	80019565	3	4	74	1	0	0	0	0	1	0	0	0	4807	623	22	3	827	3	DUS1L	17	80019565	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	6004963	80019565	1175645	118	10094										
CDH20	28316	hgsc.bcm.edu	37	chr18	59217241	59217241	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	acggattctaaccaggaggtCtggtttccggcagcaggagc	14	10	2	0	rs373889945		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr18:59217241C>A	ENST00000262717.4	+	11	2077	c.1679C>A	c.(1678-1680)tCt>tAt	p.S560Y	CDH20_ENST00000536675.2_Missense_Mutation_p.S560Y|CDH20_ENST00000538374.1_Missense_Mutation_p.S560Y			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	560	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				ACCAGGAGGTCTGGTTTCCGG	0.512																																					p.S560Y		Atlas-SNP	.											.	CDH20	117	.	0			c.C1679A						.						47	49	49					18																	59217241		2203	4300	6503	SO:0001583	missense	28316	exon10			GGAGGTCTGGTTT	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1679C>A	chr18.hg19:g.59217241C>A	ENSP00000262717:p.Ser560Tyr	95.0	0.0		117.0	48.0	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	hg19	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.909440	0.72868	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.53640	0.61;0.61;0.61	5.93	5.93	0.95920	Cadherin (4);Cadherin-like (1);	0.257806	0.40818	N	0.001002	T	0.70002	0.3174	M	0.76574	2.34	0.42829	D	0.99401	D	0.55385	0.971	D	0.65323	0.934	T	0.70769	-0.4782	10	0.66056	D	0.02	.	20.3539	0.98825	0.0:1.0:0.0:0.0	.	560	Q9HBT6	CAD20_HUMAN	Y	560	ENSP00000444767:S560Y;ENSP00000442226:S560Y;ENSP00000262717:S560Y	ENSP00000262717:S560Y	S	+	2	0	CDH20	57368221	0.999000	0.42202	0.998000	0.56505	0.992000	0.81027	5.413000	0.66399	2.826000	0.97356	0.655000	0.94253	TCT	.	.		0.512	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		A	59217241	C	A	59217241	3	1	74	1	0	0	0	0	1	0	0	0	3108	913	32	3	1717	3	CDH20	18	59217241	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10		59217241	18860007	119	10095										
MYO1F	4542	hgsc.bcm.edu	37	chr19	8619381	8619395	+	In_Frame_Del	DEL	CTCACAGTCGATAAG	CTCACAGTCGATAAG	-													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ctaatgatgacacactggttCtcacagtcgataagcatgtt					rs201539438		TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	CTCACAGTCGATAAG	CTCACAGTCGATAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:8619381_8619395delCTCACAGTCGATAAG	ENST00000338257.8	-	4	559_573	c.292_306delCTTATCGACTGTGAG	c.(292-306)cttatcgactgtgagdel	p.LIDCE98del		NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	98	Myosin motor.				defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						CACACTGGTTCTCACAGTCGATAAGCATGTTCCGG	0.609																																					p.98_103del		Atlas-Indel,Pindel	.											.	MYO1F	128	.	0			c.293_307del						.																																			SO:0001651	inframe_deletion	4542	exon4			.	X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"Myosins / Myosin superfamily : Class I"	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.292_306delCTTATCGACTGTGAG	chr19.hg19:g.8619381_8619395delCTCACAGTCGATAAG	ENSP00000344871:p.Leu98_Glu102del	55.0	0.0		46.0	14.0	NM_012335	Q8WWN7	In_Frame_Del	DEL	ENST00000338257.8	hg19	CCDS42494.1																																																																																			.	.		0.609	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			-	8619395	CTCACAGTCGATAAG	-	8619381	7	5	74	1	0	1	0	1	0	0	0	0	10082	912	32	0	3090	0	MYO1F	19	8619381	In_Frame_Del	DEL	CTCACAGTCGATAAG	TCGA-CC-A7II-01A-11D-A33K-10		8619381	50509602	120	10096										
FAM129C	199786	hgsc.bcm.edu	37	chr19	17657556	17657556	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ccaggctctgaccactgaggGcatctatgaggacgtcatcc	11	13	3	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:17657556G>T	ENST00000335393.4	+	14	1847	c.1709G>T	c.(1708-1710)gGc>gTc	p.G570V	FAM129C_ENST00000332386.5_Missense_Mutation_p.G570V|FAM129C_ENST00000601861.1_Missense_Mutation_p.G539V|FAM129C_ENST00000595684.1_Missense_Mutation_p.G570V|FAM129C_ENST00000600871.1_Missense_Mutation_p.G516V|FAM129C_ENST00000599124.1_Missense_Mutation_p.G503V|FAM129C_ENST00000599164.1_Missense_Mutation_p.G539V|FAM129C_ENST00000449408.2_Missense_Mutation_p.G296V|FAM129C_ENST00000352727.3_Missense_Mutation_p.G534V	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	570										autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						ACCACTGAGGGCATCTATGAG	0.637																																					p.G570V		Atlas-SNP	.											.	FAM129C	110	.	0			c.G1709T						.						71	48	56					19																	17657556		2203	4299	6502	SO:0001583	missense	199786	exon14			CTGAGGGCATCTA	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.1709G>T	chr19.hg19:g.17657556G>T	ENSP00000335040:p.Gly570Val	42.0	0.0		42.0	12.0	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	hg19	CCDS12362.1	.	.	.	.	.	.	.	.	.	.	G	10.38	1.335235	0.24253	.	.	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000449408;ENST00000435646	T;T;T;T	0.38077	2.09;2.1;1.16;1.73	4.62	1.09	0.20402	.	0.744958	0.11957	N	0.513183	T	0.51312	0.1667	M	0.72479	2.2	0.09310	N	0.999993	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.77557	0.985;0.99;0.99;0.99;0.985	T	0.29579	-1.0007	10	0.56958	D	0.05	-17.2637	3.9466	0.09350	0.2199:0.2004:0.5797:0.0	.	516;570;570;534;570	E7ENP6;Q86XR2;Q86XR2-3;Q86XR2-4;Q86XR2-2	.;NIBL2_HUMAN;.;.;.	V	570;570;534;296;516	ENSP00000335040:G570V;ENSP00000333447:G570V;ENSP00000341067:G534V;ENSP00000394929:G296V	ENSP00000333447:G570V	G	+	2	0	FAM129C	17518556	0.239000	0.23836	0.006000	0.13384	0.067000	0.16453	0.880000	0.28159	1.086000	0.41228	-0.275000	0.10095	GGC	.	.		0.637	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544		T	17657556	G	T	17657556	3	4	74	1	0	0	0	0	1	0	0	0	5443	1203	42	3	1763	3	FAM129C	19	17657556	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	9038175	17657556	41471427	121	10097										
ANKRD27	84079	hgsc.bcm.edu	37	chr19	33096767	33096767	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cagcagtgccacaagctcgtGatggccaccggagcaggcgt	14	13	0	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:33096767G>A	ENST00000306065.4	-	24	2625	c.2467C>T	c.(2467-2469)Cac>Tac	p.H823Y	SNORA68_ENST00000364518.1_RNA	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	823					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					ACAAGCTCGTGATGGCCACCG	0.587																																					p.H823Y		Atlas-SNP	.											.	ANKRD27	86	.	0			c.C2467T						.						123	109	114					19																	33096767		2203	4300	6503	SO:0001583	missense	84079	exon24			GCTCGTGATGGCC	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"Ankyrin repeat domain containing"	25310	protein-coding gene	gene with protein product	"Vps9 domain and ankyrin-repeat-containing protein"					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.2467C>T	chr19.hg19:g.33096767G>A	ENSP00000304292:p.His823Tyr	166.0	0.0		454.0	292.0	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	hg19	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	G	0.416	-0.910890	0.02434	.	.	ENSG00000105186	ENST00000306065	T	0.64438	-0.1	5.92	5.92	0.95590	Ankyrin repeat-containing domain (4);	0.095833	0.45606	D	0.000348	T	0.38348	0.1037	N	0.04132	-0.27	0.80722	D	1	B	0.13145	0.007	B	0.14578	0.011	T	0.34625	-0.9821	10	0.10902	T	0.67	-29.3388	14.4765	0.67548	0.072:0.0:0.928:0.0	.	823	Q96NW4	ANR27_HUMAN	Y	823	ENSP00000304292:H823Y	ENSP00000304292:H823Y	H	-	1	0	ANKRD27	37788607	1.000000	0.71417	0.784000	0.31847	0.024000	0.10985	6.296000	0.72751	2.809000	0.96659	0.650000	0.86243	CAC	.	.		0.587	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		A	33096767	G	A	33096767	3	1	74	1	0	0	0	0	1	0	0	0	655	1290	45	3	709	3	ANKRD27	19	33096767	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	15439211	33096767	26032216	122	10098										
MLL4	9757	hgsc.bcm.edu	37	chr19	36222992	36222992	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcccaactactcgccatcccGgaggcccttggggggtgtct	13	15	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:36222992G>T	ENST00000222270.7	+	27	5621	c.5621G>T	c.(5620-5622)cGg>cTg	p.R1874L	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.R1874L	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1874					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TCGCCATCCCGGAGGCCCTTG	0.687																																					p.R1874L		Atlas-SNP	.											.	MLL4	229	.	0			c.G5621T						.						12	14	13					19																	36222992		1865	4087	5952	SO:0001583	missense	8085	exon27			CATCCCGGAGGCC	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5621G>T	chr19.hg19:g.36222992G>T	ENSP00000222270:p.Arg1874Leu	71.0	0.0		218.0	50.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	G	4.654	0.121565	0.08881	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.86562	-2.14;-2.14	5.33	4.29	0.51040	.	0.000000	0.40554	N	0.001069	D	0.83695	0.5310	M	0.63843	1.955	0.51012	D	0.999906	P	0.37122	0.583	B	0.29353	0.101	D	0.84772	0.0768	10	0.66056	D	0.02	.	14.5411	0.67995	0.0:0.0:0.8519:0.1481	.	1874	Q9UMN6	MLL4_HUMAN	L	1874	ENSP00000222270:R1874L;ENSP00000398837:R1874L	ENSP00000222270:R1874L	R	+	2	0	AD000671.1	40914832	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	5.498000	0.66931	1.366000	0.46076	-0.181000	0.13052	CGG	.	.		0.687	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		T	36222992	G	T	36222992	3	4	74	1	0	0	0	0	1	0	0	0	9632	1116	39	1	5727	1	MLL4	19	36222992	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	3126225	36222992	22905991	123	10099										
ZNF829	374899	hgsc.bcm.edu	37	chr19	37383281	37383281	+	Frame_Shift_Del	DEL	T	T	-													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	aataagaaatgtgggctgaaTaaaagtagacatgtcttcac							TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:37383281delT	ENST00000391711.3	-	6	776	c.412delA	c.(412-414)attfs	p.I138fs	ZNF345_ENST00000526123.1_Intron|ZNF829_ENST00000520965.1_Frame_Shift_Del_p.I219fs|ZNF345_ENST00000432005.2_Intron	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	138					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTGGGCTGAATAAAAGTAGAC	0.338																																					p.I219fs		Atlas-Indel,Pindel	.											.	ZNF829	70	.	0			c.656delT						.						63	55	58					19																	37383281		1837	4084	5921	SO:0001589	frameshift_variant	374899	exon6			.	BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"Zinc fingers, C2H2-type", "-"	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.412delA	chr19.hg19:g.37383281delT	ENSP00000429266:p.Ile138fs	39.0	0.0		96.0	15.0	NM_001171979	Q3KNS7|Q6ZNN0|Q7Z657	Frame_Shift_Del	DEL	ENST00000391711.3	hg19	CCDS42557.1																																																																																			.	.		0.338	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232		-	37383281	T	-	37383281	7	5	74	1	0	1	0	1	0	0	0	0	18197	1406	49	0	890	0	ZNF829	19	37383281	Frame_Shift_Del	DEL	T	TCGA-CC-A7II-01A-11D-A33K-10	1160289	37383281	21745702	124	10100										
MAP4K1	11184	hgsc.bcm.edu	37	chr19	39105049	39105049	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cctggagcacttcccggcagAcatagctaatctggagctct	10	13	2	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:39105049A>G	ENST00000591517.1	-	5	378	c.350T>C	c.(349-351)gTc>gCc	p.V117A	MAP4K1_ENST00000589002.1_5'Flank|MAP4K1_ENST00000586296.1_Missense_Mutation_p.V117A|MAP4K1_ENST00000423454.2_5'Flank|MAP4K1_ENST00000396857.2_Missense_Mutation_p.V117A|MAP4K1_ENST00000589130.1_Missense_Mutation_p.V113A	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	117	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TTCCCGGCAGACATAGCTAAT	0.632																																					p.V117A		Atlas-SNP	.											.	MAP4K1	165	.	0			c.T350C						.						98	104	102					19																	39105049		1926	4141	6067	SO:0001583	missense	11184	exon5			CGGCAGACATAGC	U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6863	protein-coding gene	gene with protein product	"hematopoietic progenitor kinase 1"	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.350T>C	chr19.hg19:g.39105049A>G	ENSP00000465039:p.Val117Ala	63.0	0.0		206.0	23.0	NM_007181		Missense_Mutation	SNP	ENST00000591517.1	hg19	CCDS59385.1	.	.	.	.	.	.	.	.	.	.	A	16.75	3.208738	0.58343	.	.	ENSG00000104814	ENST00000396857;ENST00000221409	T	0.25912	1.77	4.87	4.87	0.63330	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.140996	0.47455	D	0.000239	T	0.33614	0.0869	L	0.60067	1.865	0.80722	D	1	P;P	0.43857	0.571;0.819	B;P	0.45913	0.229;0.497	T	0.17018	-1.0383	10	0.87932	D	0	.	13.7588	0.62952	1.0:0.0:0.0:0.0	.	117;117	Q92918-2;Q92918	.;M4K1_HUMAN	A	117	ENSP00000380066:V117A	ENSP00000221409:V117A	V	-	2	0	MAP4K1	43796889	0.992000	0.36948	1.000000	0.80357	0.950000	0.60333	5.549000	0.67261	1.958000	0.56883	0.368000	0.22195	GTC	.	.		0.632	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600		G	39105049	A	G	39105049	3	3	74	1	0	0	0	0	1	0	0	0	9268	275	10	2	2325	2	MAP4K1	19	39105049	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	1721768	39105049	20023934	125	10101										
ATP1A3	478	hgsc.bcm.edu	37	chr19	42492257	42492257	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gtgcgttaggcccatcccggGccaggatctcctgggctttg	14	13	1	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:42492257G>T	ENST00000302102.5	-	4	338	c.188C>A	c.(187-189)gCc>gAc	p.A63D	ATP1A3_ENST00000545399.1_Missense_Mutation_p.A76D|ATP1A3_ENST00000543770.1_Missense_Mutation_p.A74D|ATP1A3_ENST00000602133.1_Missense_Mutation_p.A33D|ATP1A3_ENST00000468774.2_5'UTR	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	63					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						CCCATCCCGGGCCAGGATCTC	0.632																																					p.A76D		Atlas-SNP	.											.	ATP1A3	117	.	0			c.C227A						.						92	96	95					19																	42492257		2203	4300	6503	SO:0001583	missense	478	exon4			TCCCGGGCCAGGA		CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"ATPases / P-type"	801	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-3", "sodium pump subunit alpha-3", "sodium-potassium ATPase catalytic subunit alpha-3"	182350	"dystonia 12"	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.188C>A	chr19.hg19:g.42492257G>T	ENSP00000302397:p.Ala63Asp	96.0	0.0		63.0	49.0	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	hg19	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	G	8.773	0.926333	0.18056	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000543770;ENST00000448429	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	4.09	3.02	0.34903	ATPase, P-type cation-transporter, N-terminal (2);	0.057698	0.64402	D	0.000002	T	0.74711	0.3752	L	0.56396	1.775	0.47547	D	0.999451	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.13407	0.003;0.001;0.009;0.002	T	0.67530	-0.5647	10	0.24483	T	0.36	.	11.67	0.51395	0.0:0.1816:0.8184:0.0	.	76;74;63;63	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	D	63;63;76;33;74;76	ENSP00000302397:A63D;ENSP00000411503:A63D;ENSP00000444688:A76D;ENSP00000437577:A74D	ENSP00000302397:A63D	A	-	2	0	ATP1A3	47184097	1.000000	0.71417	1.000000	0.80357	0.302000	0.27658	3.247000	0.51422	0.822000	0.34565	-0.479000	0.04858	GCC	.	.		0.632	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		T	42492257	G	T	42492257	3	4	74	1	0	0	0	0	1	0	0	0	1130	1203	42	3	2933	3	ATP1A3	19	42492257	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	3387208	42492257	16636726	126	10102										
HIF3A	64344	hgsc.bcm.edu	37	chr19	46825090	46825090	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gccttccctgagcgaggctgCcctggccgctgacccccgcc	12	20	0	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:46825090C>A	ENST00000377670.4	+	10	1233	c.1202C>A	c.(1201-1203)gCc>gAc	p.A401D	HIF3A_ENST00000339613.2_Missense_Mutation_p.A345D|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000472815.1_Missense_Mutation_p.A332D|HIF3A_ENST00000420102.2_Missense_Mutation_p.A350D|HIF3A_ENST00000244303.6_Missense_Mutation_p.A332D|HIF3A_ENST00000600383.1_Missense_Mutation_p.A332D|HIF3A_ENST00000300862.3_Missense_Mutation_p.A399D	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	401					cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		AGCGAGGCTGCCCTGGCCGCT	0.687																																					p.A401D		Atlas-SNP	.											.	HIF3A	154	.	0			c.C1202A						.						41	49	47					19																	46825090		2203	4298	6501	SO:0001583	missense	64344	exon10			AGGCTGCCCTGGC	AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"Basic helix-loop-helix proteins"	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1202C>A	chr19.hg19:g.46825090C>A	ENSP00000366898:p.Ala401Asp	91.0	0.0		123.0	68.0	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Missense_Mutation	SNP	ENST00000377670.4	hg19	CCDS12681.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.441|8.441	0.850781|0.850781	0.17034|0.17034	.|.	.|.	ENSG00000124440|ENSG00000124440	ENST00000244302;ENST00000377670;ENST00000244303;ENST00000339613;ENST00000291300;ENST00000300862;ENST00000420102|ENST00000472815	T;T;T;T;T|.	0.64438|.	0.62;-0.09;0.51;0.62;-0.1|.	4.45|4.45	2.33|2.33	0.28932|0.28932	.|.	1.084810|.	0.07166|.	N|.	0.851496|.	T|.	0.20618|.	0.0496|.	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	P;B;B;B;B;B;B|.	0.37276|.	0.589;0.089;0.152;0.089;0.201;0.201;0.089|.	B;B;B;B;B;B;B|.	0.33454|.	0.164;0.055;0.058;0.055;0.039;0.039;0.016|.	T|.	0.23476|.	-1.0187|.	10|.	0.27082|.	T|.	0.32|.	.|.	6.9583|6.9583	0.24583|0.24583	0.0:0.7906:0.0:0.2094|0.0:0.7906:0.0:0.2094	.|.	350;332;399;350;345;401;401|.	F5H884;B4DNA2;Q9Y2N7-2;B4DSD9;A8MPQ1;Q9Y2N7;B0M185|.	.;.;.;.;.;HIF3A_HUMAN;.|.	D|X	401;401;332;345;345;399;350|373	ENSP00000366898:A401D;ENSP00000244303:A332D;ENSP00000341877:A345D;ENSP00000300862:A399D;ENSP00000407771:A350D|.	ENSP00000244302:A401D|.	A|C	+|+	2|3	0|2	HIF3A|HIF3A	51516930|51516930	0.023000|0.023000	0.18921|0.18921	0.355000|0.355000	0.25773|0.25773	0.799000|0.799000	0.45148|0.45148	0.921000|0.921000	0.28718|0.28718	0.634000|0.634000	0.30469|0.30469	-0.140000|-0.140000	0.14226|0.14226	GCC|TGC	.	.		0.687	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3			A	46825090	C	A	46825090	3	1	74	1	0	0	0	0	1	0	0	0	7114	739	26	3	1264	3	HIF3A	19	46825090	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	4332833	46825090	12303893	127	10103										
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47424838	47424838	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	caccaccgaagaggtgtttaActccccccgggcaggatcac	10	15	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:47424838A>T	ENST00000404338.3	+	1	2906	c.2906A>T	c.(2905-2907)aAc>aTc	p.N969I		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	969					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										GAGGTGTTTAACTCCCCCCGG	0.473																																					p.N969I		Atlas-SNP	.											.	.	.	.	0			c.A2906T						.						55	55	55					19																	47424838		1926	4130	6056	SO:0001583	missense	2909	exon1			TGTTTAACTCCCC	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.2906A>T	chr19.hg19:g.47424838A>T	ENSP00000385720:p.Asn969Ile	111.0	0.0		130.0	68.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.506344	0.26949	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	T	0.07216	3.21	5.86	3.79	0.43588	.	0.300009	0.33272	N	0.005086	T	0.03959	0.0111	N	0.08118	0	0.32820	D	0.50265	P	0.36465	0.554	B	0.31869	0.137	T	0.19745	-1.0296	10	0.72032	D	0.01	-39.5541	7.3702	0.26798	0.7635:0.0:0.2365:0.0	.	969	Q9NRY4-2	.	I	969	ENSP00000385720:N969I	ENSP00000324820:N969I	N	+	2	0	ARHGAP35	52116678	0.621000	0.27077	0.992000	0.48379	0.975000	0.68041	1.285000	0.33261	1.058000	0.40530	0.533000	0.62120	AAC	.	.		0.473	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		T	47424838	A	T	47424838	3	4	74	1	0	0	0	0	1	0	0	0	6804	43	2	4	2908	4	ARHGAP35	19	47424838	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	599748	47424838	11704145	128	10104										
FAM83E	54854	hgsc.bcm.edu	37	chr19	49104612	49104613	+	Missense_Mutation	DNP	CC	CC	AA													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gctggagtgtccttggagccCcaggatttcttgagctgtgg							TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:49104612_49104613CC>AA	ENST00000263266.3	-	5	1379_1380	c.1190_1191GG>TT	c.(1189-1191)tGG>tTT	p.W397F		NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	397										NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		CCTTGGAGCCCCAGGATTTCTT	0.673																																					p.W397C|p.W397L		Atlas-SNP	.											FAM83E,NS,carcinoma,0,1|.	FAM83E	34	.	0			c.G1191T|c.G1190T						.																																			SO:0001583	missense	54854	exon5			GGAGCCCCAGGAT|GAGCCCCAGGATT	AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523			25972	protein-coding gene	gene with protein product							Standard	NM_017708		Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.1190_1191delinsAA	chr19.hg19:g.49104612_49104613delinsAA	ENSP00000263266:p.Trp397Phe	146.0|147.0	0.0		175.0|176.0	38.0	NM_017708	Q9NXK1	Missense_Mutation	SNP	ENST00000263266.3	hg19	CCDS42587.1																																																																																			.	.		0.673	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708		AA	49104613	CC	AA	49104612	3	1	74	1	0	0	0	0	1	0	0	0	5645	624	22	3	249	3	FAM83E	19	49104612	Missense_Mutation	DNP	CC	TCGA-CC-A7II-01A-11D-A33K-10	1679774	49104612	10024371	129	10105										
ZNF28	7576	hgsc.bcm.edu	37	chr19	53302982	53302982	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	aagtctatgatggtatacaaGgtttgacatctgactgaagg	11	5	2	4			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:53302982G>C	ENST00000457749.2	-	4	2235	c.2116C>G	c.(2116-2118)Ctt>Gtt	p.L706V	ZNF28_ENST00000414252.2_Missense_Mutation_p.L653V|ZNF28_ENST00000438150.2_Missense_Mutation_p.L653V|ZNF28_ENST00000360272.4_Missense_Mutation_p.L653V	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	706					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		TGGTATACAAGGTTTGACATC	0.413																																					p.L706V		Atlas-SNP	.											.	ZNF28	191	.	0			c.C2116G						.						111	105	107					19																	53302982		2203	4298	6501	SO:0001583	missense	7576	exon4			ATACAAGGTTTGA	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.2116C>G	chr19.hg19:g.53302982G>C	ENSP00000397693:p.Leu706Val	73.0	0.0		71.0	41.0	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	hg19	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	7.267	0.606462	0.14002	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	1.65	0.473	0.16763	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23094	0.0558	M	0.85299	2.745	0.09310	N	1	P	0.38223	0.623	B	0.41666	0.363	T	0.12811	-1.0533	9	0.87932	D	0	.	8.8067	0.34943	0.0:0.2347:0.7653:0.0	.	706	P17035	ZNF28_HUMAN	V	653;706;653;653	ENSP00000412143:L653V;ENSP00000397693:L706V;ENSP00000353410:L653V;ENSP00000444965:L653V	ENSP00000353410:L653V	L	-	1	0	ZNF28	57994794	0.381000	0.25140	0.001000	0.08648	0.001000	0.01503	0.308000	0.19314	0.041000	0.15688	-0.989000	0.02550	CTT	.	.		0.413	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		C	53302982	G	C	53302982	3	2	74	1	0	0	0	0	1	0	0	0	17828	1000	35	4	44	4	ZNF28	19	53302982	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	4198370	53302982	5826001	130	10106										
ZNF677	342926	hgsc.bcm.edu	37	chr19	53740851	53740851	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ggctttgtcacattcattacAtttgtaaggtttctctccag	7	9	3	0			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:53740851A>G	ENST00000598513.1	-	5	1279	c.1129T>C	c.(1129-1131)Tgt>Cgt	p.C377R	ZNF677_ENST00000333952.4_Missense_Mutation_p.C377R	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		CATTCATTACATTTGTAAGGT	0.393																																					p.C377R		Atlas-SNP	.											.	ZNF677	94	.	0			c.T1129C						.						92	85	87					19																	53740851		2203	4300	6503	SO:0001583	missense	342926	exon5			CATTACATTTGTA	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1129T>C	chr19.hg19:g.53740851A>G	ENSP00000469391:p.Cys377Arg	122.0	0.0		118.0	25.0	NM_182609		Missense_Mutation	SNP	ENST00000598513.1	hg19	CCDS12861.1	.	.	.	.	.	.	.	.	.	.	A	16.58	3.162684	0.57368	.	.	ENSG00000197928	ENST00000333952	D	0.85258	-1.96	2.14	2.14	0.27477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38111	N	0.001810	D	0.94308	0.8171	H	0.98594	4.275	0.54753	D	0.999981	D	0.89917	1.0	D	0.97110	1.0	D	0.93465	0.6814	10	0.87932	D	0	.	8.2235	0.31556	1.0:0.0:0.0:0.0	.	377	Q86XU0	ZN677_HUMAN	R	377	ENSP00000334394:C377R	ENSP00000334394:C377R	C	-	1	0	ZNF677	58432663	1.000000	0.71417	0.977000	0.42913	0.976000	0.68499	7.473000	0.81007	1.249000	0.43950	0.496000	0.49642	TGT	.	.		0.393	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		G	53740851	A	G	53740851	3	3	74	1	0	0	0	0	1	0	0	0	18099	217	8	2	629	2	ZNF677	19	53740851	Missense_Mutation	SNP	A	TCGA-CC-A7II-01A-11D-A33K-10	437869	53740851	5388132	131	10107										
ZNF71	58491	hgsc.bcm.edu	37	chr19	57133835	57133835	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gcaagaagcacttcacggggCgctcgtccctcatcgtgcac	11	15	2	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr19:57133835C>A	ENST00000328070.6	+	3	1414	c.1180C>A	c.(1180-1182)Cgc>Agc	p.R394S		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R394S(1)		endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		CTTCACGGGGCGCTCGTCCCT	0.627																																					p.R394S		Atlas-SNP	.											ZNF71,NS,carcinoma,0,1	ZNF71	69	.	1	Substitution - Missense(1)	prostate(1)	c.C1180A						.						88	70	76					19																	57133835		2203	4300	6503	SO:0001583	missense	58491	exon3			ACGGGGCGCTCGT	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"Zinc fingers, C2H2-type"	13141	protein-coding gene	gene with protein product		194545	"zinc finger protein 71 (Cos26)"			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.1180C>A	chr19.hg19:g.57133835C>A	ENSP00000328245:p.Arg394Ser	56.0	0.0		55.0	28.0	NM_021216	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	hg19	CCDS12947.1	.	.	.	.	.	.	.	.	.	.	C	2.611	-0.290711	0.05568	.	.	ENSG00000197951	ENST00000328070	T	0.08102	3.13	3.58	2.45	0.29901	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02119	0.0066	N	0.01209	-0.955	0.09310	N	1	B	0.29301	0.241	B	0.20184	0.028	T	0.34453	-0.9828	9	0.02654	T	1	.	8.5263	0.33307	0.3659:0.6341:0.0:0.0	.	394	Q9NQZ8	ZNF71_HUMAN	S	394	ENSP00000328245:R394S	ENSP00000328245:R394S	R	+	1	0	ZNF71	61825647	0.000000	0.05858	0.994000	0.49952	0.995000	0.86356	-0.497000	0.06428	1.815000	0.52974	0.561000	0.74099	CGC	.	.		0.627	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		A	57133835	C	A	57133835	3	1	74	1	0	0	0	0	1	0	0	0	18129	768	27	1	1182	1	ZNF71	19	57133835	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	3392984	57133835	1995148	132	10108										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33329288	33329288	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ttatttgatttgggggcaagGgagtggaaatggaggaagag	18	1	0	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr20:33329288G>A	ENST00000374796.2	-	12	7342	c.4772C>T	c.(4771-4773)cCc>cTc	p.P1591L	NCOA6_ENST00000359003.2_Missense_Mutation_p.P1591L			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1591					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						TGGGGGCAAGGGAGTGGAAAT	0.468																																					p.P1591L		Atlas-SNP	.											NCOA6,NS,haematopoietic_neoplasm,0,3	NCOA6	219	.	0			c.C4772T						.						130	117	122					20																	33329288		2203	4300	6503	SO:0001583	missense	23054	exon11			GGCAAGGGAGTGG	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.4772C>T	chr20.hg19:g.33329288G>A	ENSP00000363929:p.Pro1591Leu	71.0	0.0		130.0	54.0	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	hg19	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.532212	0.64972	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.25579	1.79;1.79	5.55	5.55	0.83447	.	0.077816	0.56097	D	0.000034	T	0.21590	0.0520	N	0.24115	0.695	0.80722	D	1	P	0.43094	0.799	B	0.38378	0.272	T	0.02391	-1.1166	10	0.62326	D	0.03	-7.102	19.7069	0.96076	0.0:0.0:1.0:0.0	.	1591	Q14686	NCOA6_HUMAN	L	1591	ENSP00000363929:P1591L;ENSP00000351894:P1591L	ENSP00000351894:P1591L	P	-	2	0	NCOA6	32792949	1.000000	0.71417	0.982000	0.44146	0.910000	0.53928	8.686000	0.91250	2.894000	0.99253	0.591000	0.81541	CCC	.	.		0.468	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		A	33329288	G	A	33329288	3	1	74	1	0	0	0	0	1	0	0	0	10242	1232	43	3	1439	3	NCOA6	20	33329288	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10		33329288	29696232	133	10109										
GDF5	8200	hgsc.bcm.edu	37	chr20	34025505	34025505	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ctggcattggcattggtggcCcccccaccatagctgtgacc	11	15	0	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr20:34025505C>G	ENST00000374372.1	-	3	707	c.204G>C	c.(202-204)ggG>ggC	p.G68G	GDF5_ENST00000374369.3_Silent_p.G68G			P43026	GDF5_HUMAN	growth differentiation factor 5	68					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			CATTGGTGGCCCCCCCACCAT	0.662																																					p.G68G		Atlas-SNP	.											.	GDF5	66	.	0			c.G204C						.						29	28	28					20																	34025505		2203	4300	6503	SO:0001819	synonymous_variant	8200	exon1			GGTGGCCCCCCCA	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"cartilage-derived morphogenetic protein-1"	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.204G>C	chr20.hg19:g.34025505C>G		60.0	0.0		89.0	38.0	NM_000557	E1P5Q2|Q96SB1	Silent	SNP	ENST00000374372.1	hg19	CCDS13254.1																																																																																			.	.		0.662	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2			G	34025505	C	G	34025505	2	3	74	1	0	0	0	0	0	0	0	1	6324	610	22	4		4	GDF5	20	34025505	Silent	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	696217	34025505	29000015	134	10110										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57768554	57768554	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agagaggaagaagctgaaagTggaggacctgcacagctgga	16	6	0	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr20:57768554T>C	ENST00000371030.2	+	1	2480	c.2480T>C	c.(2479-2481)gTg>gCg	p.V827A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	827							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					AAGCTGAAAGTGGAGGACCTG	0.622																																					p.V827A		Atlas-SNP	.											.	ZNF831	287	.	0			c.T2480C						.						33	41	39					20																	57768554		2039	4193	6232	SO:0001583	missense	128611	exon1			TGAAAGTGGAGGA	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.2480T>C	chr20.hg19:g.57768554T>C	ENSP00000360069:p.Val827Ala	81.0	0.0		140.0	62.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.208871	0.39003	.	.	ENSG00000124203	ENST00000371030	T	0.13538	2.58	4.92	3.82	0.43975	.	0.389415	0.21720	N	0.070134	T	0.14570	0.0352	L	0.36672	1.1	0.19300	N	0.999977	P	0.51791	0.948	P	0.47786	0.557	T	0.06661	-1.0814	10	0.66056	D	0.02	-11.5444	8.2457	0.31686	0.0:0.0909:0.0:0.9091	.	827	Q5JPB2	ZN831_HUMAN	A	827	ENSP00000360069:V827A	ENSP00000360069:V827A	V	+	2	0	ZNF831	57201949	0.984000	0.35163	0.952000	0.39060	0.150000	0.21749	1.615000	0.36922	0.737000	0.32582	0.368000	0.22195	GTG	.	.		0.622	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		C	57768554	T	C	57768554	3	2	74	1	0	0	0	0	1	0	0	0	18200	1696	59	2	2482	2	ZNF831	20	57768554	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	23743049	57768554	5256966	135	10111										
C21orf63	59271	hgsc.bcm.edu	37	chr21	33829933	33829933	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	ggacgaatgccagaaccagcGggcctgccacctcctggtca	12	15	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr21:33829933G>A	ENST00000300255.2	+	3	859	c.386G>A	c.(385-387)cGg>cAg	p.R129Q	EVA1C_ENST00000382699.3_Missense_Mutation_p.R129Q|EVA1C_ENST00000401402.3_Missense_Mutation_p.R129Q	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	129	SUEL-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00260}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										CAGAACCAGCGGGCCTGCCAC	0.527																																					p.R129Q		Atlas-SNP	.											.	.	.	.	0			c.G386A						.						110	94	100					21																	33829933		2203	4300	6503	SO:0001583	missense	59271	exon3			ACCAGCGGGCCTG	AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 64", "chromosome 21 open reading frame 63", "family with sequence similarity 176, member C"	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.386G>A	chr21.hg19:g.33829933G>A	ENSP00000300255:p.Arg129Gln	205.0	0.0		160.0	28.0	NM_058187	A6ND58|Q8IXZ0	Missense_Mutation	SNP	ENST00000300255.2	hg19	CCDS13614.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.712689	0.89112	.	.	ENSG00000166979	ENST00000300255;ENST00000401402;ENST00000382699;ENST00000412833	T;T;T;T	0.16073	2.37;2.37;2.37;2.37	5.07	5.07	0.68467	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.000000	0.85682	D	0.000000	T	0.29556	0.0737	N	0.21324	0.655	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.05273	-1.0895	10	0.34782	T	0.22	-15.943	18.4733	0.90782	0.0:0.0:1.0:0.0	.	129;129;129	A6ND58;P58658;B5MC74	.;CU063_HUMAN;.	Q	129;129;129;34	ENSP00000300255:R129Q;ENSP00000384594:R129Q;ENSP00000372146:R129Q;ENSP00000389269:R34Q	ENSP00000300255:R129Q	R	+	2	0	C21orf63	32751804	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.446000	0.97590	2.349000	0.79799	0.462000	0.41574	CGG	.	.		0.527	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187		A	33829933	G	A	33829933	3	1	74	1	0	0	0	0	1	0	0	0	2133	1116	39	1	396	1	C21orf63	21	33829933	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10		33829933	14299962	136	10112										
DSCAM	1826	hgsc.bcm.edu	37	chr21	42064797	42064797	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gtgatgtacgcctccaccgaGgaggggataatgcacttgaa	13	9	0	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr21:42064797G>A	ENST00000400454.1	-	3	924	c.447C>T	c.(445-447)tcC>tcT	p.S149S		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	149	Ig-like C2-type 2.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CCTCCACCGAGGAGGGGATAA	0.532																																					p.S149S	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C447T						.						138	134	136					21																	42064797		2018	4173	6191	SO:0001819	synonymous_variant	1826	exon3			CACCGAGGAGGGG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.447C>T	chr21.hg19:g.42064797G>A		104.0	0.0		64.0	19.0	NM_001271534	O60468	Silent	SNP	ENST00000400454.1	hg19	CCDS42929.1																																																																																			.	.		0.532	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	42064797	G	A	42064797	2	1	74	1	0	0	0	0	0	0	0	1	4770	987	35	3		3	DSCAM	21	42064797	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	8234864	42064797	6065098	137	10113										
TRPM2	7226	hgsc.bcm.edu	37	chr21	45820191	45820191	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gctctccgtggacaatgggcTgtggcgtgtgaccctgtgca	15	11	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr21:45820191T>A	ENST00000397928.1	+	15	2703	c.2258T>A	c.(2257-2259)cTg>cAg	p.L753Q	TRPM2_ENST00000397932.2_Missense_Mutation_p.L753Q|TRPM2_ENST00000300481.9_Missense_Mutation_p.L733Q|TRPM2_ENST00000300482.5_Missense_Mutation_p.L753Q|TRPM2_ENST00000498430.1_3'UTR	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	753					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GACAATGGGCTGTGGCGTGTG	0.677																																					p.L753Q		Atlas-SNP	.											.	TRPM2	196	.	0			c.T2258A						.						121	86	98					21																	45820191		2203	4299	6502	SO:0001583	missense	7226	exon15			ATGGGCTGTGGCG	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2258T>A	chr21.hg19:g.45820191T>A	ENSP00000381023:p.Leu753Gln	53.0	0.0		47.0	16.0	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	hg19	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	T	9.357	1.066995	0.20067	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	4.87	2.45	0.29901	.	0.510940	0.18958	N	0.126464	T	0.71367	0.3331	M	0.72894	2.215	0.09310	N	1	D;P;D	0.60160	0.987;0.918;0.977	P;P;P	0.50896	0.653;0.472;0.653	T	0.61969	-0.6953	10	0.46703	T	0.11	-14.3568	5.8132	0.18477	0.1486:0.0837:0.0:0.7678	.	753;539;753	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	Q	753;753;733;753	ENSP00000300482:L753Q;ENSP00000381023:L753Q;ENSP00000300481:L733Q;ENSP00000381026:L753Q	ENSP00000300481:L733Q	L	+	2	0	TRPM2	44644619	0.039000	0.19947	0.096000	0.21009	0.272000	0.26649	1.619000	0.36965	0.217000	0.20800	0.496000	0.49642	CTG	.	.		0.677	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		A	45820191	T	A	45820191	3	1	74	1	0	0	0	0	1	0	0	0	16601	1580	55	4	2316	4	TRPM2	21	45820191	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10	3755394	45820191	2309704	138	10114										
ZNF74	7625	hgsc.bcm.edu	37	chr22	20749677	20749677	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agagaatctcgaggatatatCgggttggggtcttcccgaag	14	7	2	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr22:20749677C>G	ENST00000400451.2	+	2	603	c.89C>G	c.(88-90)tCg>tGg	p.S30W	ZNF74_ENST00000403682.3_Intron|ZNF74_ENST00000357502.5_Missense_Mutation_p.I35M|ZNF74_ENST00000356671.5_Missense_Mutation_p.S30W|ZNF74_ENST00000405993.1_Missense_Mutation_p.S30W	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	30					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GAGGATATATCGGGTTGGGGT	0.542																																					p.S30W		Atlas-SNP	.											ZNF74,NS,carcinoma,0,1	ZNF74	54	.	0			c.C89G						.						141	147	145					22																	20749677		1964	4140	6104	SO:0001583	missense	7625	exon2			ATATATCGGGTTG	X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"Zinc fingers, C2H2-type", "-"	13144	protein-coding gene	gene with protein product		194548	"zinc finger protein 74 (Cos52)"			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.89C>G	chr22.hg19:g.20749677C>G	ENSP00000383301:p.Ser30Trp	161.0	0.0		138.0	62.0	NM_003426	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Missense_Mutation	SNP	ENST00000400451.2	hg19	CCDS42982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	9.387|9.387	1.074424|1.074424	0.20227|0.20227	.|.	.|.	ENSG00000185252|ENSG00000185252	ENST00000357502|ENST00000400451;ENST00000356671;ENST00000405993	.|T;T;T	.|0.06068	.|3.41;3.41;3.35	3.8|3.8	0.075|0.075	0.14397|0.14397	.|.	.|1.382960	.|0.05998	.|N	.|0.647249	T|T	0.03263|0.03263	0.0095|0.0095	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.12630	.|0.006	.|B	.|0.06405	.|0.002	T|T	0.44390|0.44390	-0.9331|-0.9331	6|10	0.56958|0.37606	D|T	0.05|0.19	-0.2226|-0.2226	2.9108|2.9108	0.05736|0.05736	0.0:0.2863:0.2435:0.4702|0.0:0.2863:0.2435:0.4702	.|.	.|30	.|Q16587	.|ZNF74_HUMAN	M|W	35|30	.|ENSP00000383301:S30W;ENSP00000349098:S30W;ENSP00000385855:S30W	ENSP00000350101:I35M|ENSP00000349098:S30W	I|S	+|+	3|2	3|0	ZNF74|ZNF74	19079677|19079677	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.010000|0.010000	0.07245|0.07245	0.130000|0.130000	0.15850|0.15850	0.037000|0.037000	0.15575|0.15575	0.591000|0.591000	0.81541|0.81541	ATC|TCG	.	.		0.542	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426		G	20749677	C	G	20749677	3	3	74	1	0	0	0	0	1	0	0	0	18142	893	31	4	95	4	ZNF74	22	20749677	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10		20749677	30554889	139	10115										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26298603	26298603	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tgacctgcagctggcccaggCcctaggtgagtcagtgtttg	14	11	1	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr22:26298603C>A	ENST00000407587.2	+	30	5019	c.4850C>A	c.(4849-4851)gCc>gAc	p.A1617D	CTA-125H2.2_ENST00000597548.1_RNA|CTA-125H2.2_ENST00000609889.1_RNA|CTA-125H2.2_ENST00000599792.1_RNA|MYO18B_ENST00000335473.7_Missense_Mutation_p.A1616D|CTA-125H2.2_ENST00000609570.1_RNA|CTA-125H2.2_ENST00000609275.1_RNA|CTA-125H2.2_ENST00000597284.1_RNA|CTA-125H2.2_ENST00000607895.1_RNA|MYO18B_ENST00000536101.1_Missense_Mutation_p.A1616D|CTA-125H2.2_ENST00000609823.1_RNA|CTA-125H2.2_ENST00000594585.1_RNA|CTA-125H2.2_ENST00000608257.1_RNA|CTA-125H2.2_ENST00000600211.1_RNA|CTA-125H2.2_ENST00000453457.3_RNA|MYO18B_ENST00000536204.1_3'UTR|CTA-125H2.2_ENST00000595093.1_RNA|CTA-125H2.2_ENST00000599080.1_RNA|CTA-125H2.2_ENST00000609157.1_RNA|CTA-125H2.2_ENST00000600269.1_RNA|CTA-125H2.2_ENST00000608115.1_RNA			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1616	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CTGGCCCAGGCCCTAGGTGAG	0.622																																					p.A1616D		Atlas-SNP	.											.	MYO18B	322	.	0			c.C4847A						.						41	44	43					22																	26298603		1981	4162	6143	SO:0001583	missense	84700	exon30			CCCAGGCCCTAGG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.4850C>A	chr22.hg19:g.26298603C>A	ENSP00000386096:p.Ala1617Asp	66.0	0.0		50.0	13.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	26.7	4.760173	0.89932	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.87729	-2.27;-2.27;-2.29	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.93481	0.7920	M	0.80422	2.495	0.52501	D	0.999956	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.993;0.989;0.988;0.995	D	0.94151	0.7405	10	0.72032	D	0.01	.	16.4582	0.84029	0.0:1.0:0.0:0.0	.	1129;1616;1617;1616	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	D	1616;1616;1617	ENSP00000441229:A1616D;ENSP00000334563:A1616D;ENSP00000386096:A1617D	ENSP00000334563:A1616D	A	+	2	0	MYO18B	24628603	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.860000	0.62961	2.464000	0.83262	0.655000	0.94253	GCC	.	.		0.622	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26298603	C	A	26298603	3	1	74	1	0	0	0	0	1	0	0	0	10075	739	26	3	4961	3	MYO18B	22	26298603	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	5548926	26298603	25005963	140	10116										
TCF20	6942	hgsc.bcm.edu	37	chr22	42608089	42608089	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agaattcaaacctgcgttagGgtccccataagcatgagccc	9	12	1	2			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr22:42608089G>C	ENST00000359486.3	-	1	3359	c.3223C>G	c.(3223-3225)Cct>Gct	p.P1075A	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Missense_Mutation_p.P1075A	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1075					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						CCTGCGTTAGGGTCCCCATAA	0.493																																					p.P1075A		Atlas-SNP	.											.	TCF20	164	.	0			c.C3223G						.						68	68	68					22																	42608089		2203	4300	6503	SO:0001583	missense	6942	exon1			CGTTAGGGTCCCC	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.3223C>G	chr22.hg19:g.42608089G>C	ENSP00000352463:p.Pro1075Ala	101.0	0.0		115.0	54.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.123331	0.77436	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.72394	-0.65;-0.65	5.81	5.81	0.92471	.	0.000000	0.64402	D	0.000002	T	0.77545	0.4146	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	T	0.79923	-0.1598	10	0.87932	D	0	-14.2081	20.0628	0.97684	0.0:0.0:1.0:0.0	.	1075;1075	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	A	1075	ENSP00000352463:P1075A;ENSP00000335561:P1075A	ENSP00000335561:P1075A	P	-	1	0	TCF20	40938033	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	6.716000	0.74702	2.745000	0.94114	0.655000	0.94253	CCT	.	.		0.493	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		C	42608089	G	C	42608089	3	2	74	1	0	0	0	0	1	0	0	0	15705	1232	43	4	2697	4	TCF20	22	42608089	Missense_Mutation	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	16309486	42608089	8696477	141	10117										
POLDIP3	84271	hgsc.bcm.edu	37	chr22	42983538	42983538	+	Frame_Shift_Del	DEL	A	A	-													0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	atgggctggtctgaggtgatAacattcccattcatgtgaag							TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr22:42983538delA	ENST00000252115.5	-	8	1166	c.1062delT	c.(1060-1062)gttfs	p.V354fs	POLDIP3_ENST00000491021.1_5'UTR|POLDIP3_ENST00000451060.2_Intron|POLDIP3_ENST00000339677.6_Intron|POLDIP3_ENST00000348657.2_Frame_Shift_Del_p.V325fs	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	354					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						CTGAGGTGATAACATTCCCAT	0.512																																					p.I355fs	Ovarian(52;967 1128 5875 19997 42537)	Atlas-Indel,Pindel	.											.	POLDIP3	58	.	0			c.1063delA						.						157	156	156					22																	42983538		2203	4300	6503	SO:0001589	frameshift_variant	84271	exon8			.		CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"RNA binding motif (RRM) containing"	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.1062delT	chr22.hg19:g.42983538delA	ENSP00000252115:p.Val354fs	140.0	0.0		124.0	37.0	NM_032311	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Frame_Shift_Del	DEL	ENST00000252115.5	hg19	CCDS14038.1																																																																																			.	.		0.512	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311		-	42983538	A	-	42983538	7	5	74	1	0	1	0	1	0	0	0	0	12204	349	13	0	211	0	POLDIP3	22	42983538	Frame_Shift_Del	DEL	A	TCGA-CC-A7II-01A-11D-A33K-10	375449	42983538	8321028	142	10118										
KIAA1644	85352	hgsc.bcm.edu	37	chr22	44681337	44681337	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	gaactctggaaggtcatcagCggtgggctgtgagcatctcc	14	10	4	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr22:44681337C>A	ENST00000381176.4	-	4	702	c.570G>T	c.(568-570)ccG>ccT	p.P190P		NM_001099294.1	NP_001092764.1	Q3SXP7	K1644_HUMAN	KIAA1644	190						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)				AGGTCATCAGCGGTGGGCTGT	0.617																																					p.P190P		Atlas-SNP	.											KIAA1644,colon,carcinoma,0,1	KIAA1644	39	.	0			c.G570T						.						68	71	70					22																	44681337		2117	4237	6354	SO:0001819	synonymous_variant	85352	exon4			CATCAGCGGTGGG	AB051431	CCDS43025.1	22q13	2009-02-06	2009-02-06		ENSG00000138944	ENSG00000138944			29335	protein-coding gene	gene with protein product						11258795	Standard	NM_001099294		Approved		uc003bet.2	Q3SXP7	OTTHUMG00000030991	ENST00000381176.4:c.570G>T	chr22.hg19:g.44681337C>A		137.0	1.0		130.0	34.0	NM_001099294	A6NHP0|A9Z1Z0|Q3SXP8|Q5JZ71|Q9BYB5	Silent	SNP	ENST00000381176.4	hg19	CCDS43025.1																																																																																			.	.		0.617	KIAA1644-006	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075879.2	NM_001099294		A	44681337	C	A	44681337	2	1	74	1	0	0	0	0	0	0	0	1	8259	755	27	1		1	KIAA1644	22	44681337	Silent	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	1697799	44681337	6623229	143	10119										
PHF21B	112885	hgsc.bcm.edu	37	chr22	45279146	45279146	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	agggatgactgggtgcccctCtggcgggccagcaggcttgt	17	11	1	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr22:45279146C>A	ENST00000313237.5	-	13	1566	c.1416G>T	c.(1414-1416)caG>caT	p.Q472H	PHF21B_ENST00000404079.2_Missense_Mutation_p.Q418H|PHF21B_ENST00000403565.1_Missense_Mutation_p.Q268H|PHF21B_ENST00000396103.3_Missense_Mutation_p.Q430H	NM_138415.4	NP_612424.1	Q96EK2	PF21B_HUMAN	PHD finger protein 21B	472							zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(14)|ovary(2)|prostate(1)|skin(2)	25		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		GGGTGCCCCTCTGGCGGGCCA	0.627																																					p.Q472H		Atlas-SNP	.											.	PHF21B	61	.	0			c.G1416T						.						44	51	48					22																	45279146		2203	4300	6503	SO:0001583	missense	112885	exon13			GCCCCTCTGGCGG	AK091480	CCDS14061.1, CCDS56234.1, CCDS63504.1	22q13.31	2013-01-28			ENSG00000056487	ENSG00000056487		"Zinc fingers, PHD-type"	25161	protein-coding gene	gene with protein product			"PHD finger protein 4"	PHF4		12477932	Standard	NM_138415		Approved	BHC80L, FLJ34161	uc011aql.2	Q96EK2	OTTHUMG00000151199	ENST00000313237.5:c.1416G>T	chr22.hg19:g.45279146C>A	ENSP00000324403:p.Gln472His	29.0	0.0		38.0	10.0	NM_138415	B0QYW3|B0QYW4|B3KRU4|B7Z4F8|Q5TFL2|Q6ICC0	Missense_Mutation	SNP	ENST00000313237.5	hg19	CCDS14061.1	.	.	.	.	.	.	.	.	.	.	c	17.64	3.439142	0.63067	.	.	ENSG00000056487	ENST00000403565;ENST00000313237;ENST00000396103;ENST00000404079	D;D;D;D	0.88046	-2.33;-1.66;-1.71;-1.71	3.49	0.682	0.17992	.	0.094539	0.42420	U	0.000705	D	0.89315	0.6680	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.58970	0.984;0.973;0.973;0.966	P;P;P;P	0.62740	0.906;0.807;0.807;0.751	D	0.86671	0.1910	10	0.87932	D	0	-28.2465	7.8319	0.29347	0.0:0.7522:0.0:0.2478	.	430;418;472;268	Q96EK2-3;B7Z4F8;Q96EK2;B1AHC5	.;.;PF21B_HUMAN;.	H	268;472;430;418	ENSP00000385053:Q268H;ENSP00000324403:Q472H;ENSP00000379410:Q430H;ENSP00000385105:Q418H	ENSP00000324403:Q472H	Q	-	3	2	PHF21B	43657810	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	2.556000	0.45862	-0.002000	0.14469	0.299000	0.19835	CAG	.	.		0.627	PHF21B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321731.2	NM_138415		A	45279146	C	A	45279146	3	1	74	1	0	0	0	0	1	0	0	0	11843	912	32	3	183	3	PHF21B	22	45279146	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	597809	45279146	6025420	144	10120										
CRELD2	79174	hgsc.bcm.edu	37	chr22	50312939	50312939	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cacggcttgggaggaaaagaCgctgtccaagtacgagtcca	13	10	0	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chr22:50312939C>T	ENST00000328268.4	+	2	265	c.191C>T	c.(190-192)aCg>aTg	p.T64M	CRELD2_ENST00000407217.3_Missense_Mutation_p.T64M|ALG12_ENST00000330817.6_5'Flank|CRELD2_ENST00000403427.3_Missense_Mutation_p.T64M|CRELD2_ENST00000404488.3_Missense_Mutation_p.T64M	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	64						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		GAGGAAAAGACGCTGTCCAAG	0.612																																					p.T64M		Atlas-SNP	.											.	CRELD2	57	.	0			c.C191T						.						77	66	70					22																	50312939		2203	4300	6503	SO:0001583	missense	79174	exon2			AAAAGACGCTGTC	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.191C>T	chr22.hg19:g.50312939C>T	ENSP00000332223:p.Thr64Met	182.0	0.0		268.0	17.0	NM_024324	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Missense_Mutation	SNP	ENST00000328268.4	hg19	CCDS14082.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305788	0.81247	.	.	ENSG00000184164	ENST00000450207;ENST00000404488;ENST00000328268;ENST00000407217;ENST00000403427	T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27	4.51	4.51	0.55191	.	0.170117	0.50627	D	0.000102	T	0.58018	0.2093	M	0.63428	1.95	0.38075	D	0.936483	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.73380	0.972;0.976;0.972;0.98;0.976;0.978	T	0.65928	-0.6049	10	0.66056	D	0.02	.	17.5664	0.87921	0.0:1.0:0.0:0.0	.	64;64;64;64;64;64	Q6UXH1-2;Q6UXH1-5;Q6UXH1-4;A5GZA6;Q6UXH1;Q6UXH1-3	.;.;.;.;CREL2_HUMAN;.	M	64	ENSP00000387769:T64M;ENSP00000383938:T64M;ENSP00000332223:T64M;ENSP00000386034:T64M;ENSP00000384111:T64M	ENSP00000332223:T64M	T	+	2	0	CRELD2	48698943	0.613000	0.27009	0.940000	0.37924	0.991000	0.79684	1.204000	0.32296	2.216000	0.71823	0.655000	0.94253	ACG	.	.		0.612	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324		T	50312939	C	T	50312939	3	4	74	1	0	0	0	0	1	0	0	0	3869	536	19	1	197	1	CRELD2	22	50312939	Missense_Mutation	SNP	C	TCGA-CC-A7II-01A-11D-A33K-10	5033793	50312939	991627	145	10121										
DMD	1756	hgsc.bcm.edu	37	chrX	32834720	32834720	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	tcttttcactgttggtttgtTgcaatccagccatgatattt	7	8	2	1			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chrX:32834720T>A	ENST00000357033.4	-	6	601	c.395A>T	c.(394-396)cAa>cTa	p.Q132L	DMD_ENST00000288447.4_Missense_Mutation_p.Q124L|DMD_ENST00000378677.2_Missense_Mutation_p.Q128L	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	132	Actin-binding.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GTTGGTTTGTTGCAATCCAGC	0.373																																					p.Q132L		Atlas-SNP	.											.	DMD	2127	.	0			c.A395T						.						163	141	149					X																	32834720		2202	4300	6502	SO:0001583	missense	1756	exon6			GTTTGTTGCAATC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.395A>T	chrX.hg19:g.32834720T>A	ENSP00000354923:p.Gln132Leu	107.0	0.0		87.0	56.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.528591	0.85706	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	D;D;D	0.95724	-3.79;-3.79;-3.79	5.44	5.44	0.79542	Calponin homology domain (2);	0.000000	0.35495	U	0.003162	D	0.96809	0.8958	M	0.63169	1.94	0.80722	D	1	D;D;D;P;D	0.61080	0.989;0.979;0.988;0.892;0.979	P;P;D;B;P	0.65233	0.841;0.858;0.933;0.237;0.858	D	0.97321	0.9944	10	0.87932	D	0	.	14.5467	0.68035	0.0:0.0:0.0:1.0	.	132;124;124;132;128	F5H6K1;Q4G0X0;P11532-4;P11532;E9PDN5	.;.;.;DMD_HUMAN;.	L	124;128;132;132;9;124	ENSP00000367948:Q128L;ENSP00000354923:Q132L;ENSP00000288447:Q124L	ENSP00000288447:Q124L	Q	-	2	0	DMD	32744641	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.036000	0.88901	1.816000	0.52996	0.486000	0.48141	CAA	.	.		0.373	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32834720	T	A	32834720	3	1	74	1	0	0	0	0	1	0	0	0	4582	1812	63	4	11201	4	DMD	23	32834720	Missense_Mutation	SNP	T	TCGA-CC-A7II-01A-11D-A33K-10		32834720	122435840	146	10122										
NXF3	56000	hgsc.bcm.edu	37	chrX	102334693	102334693	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0340136054421769	5	1	1.04458722741433	0	1.22293138819239	0.0294117647058824	0.304738562091504	0	cggagctgtgatactcacggGgctgagtcctcaggattgaa	14	9	2	3			TCGA-CC-A7II-01A-11D-A33K-10	TCGA-CC-A7II-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	38404863-430b-43e1-9349-5e50adbe47bd	67f74191-95ad-4192-a479-4cd21b1cdfa4	g.chrX:102334693G>A	ENST00000395065.3	-	13	1259	c.1158C>T	c.(1156-1158)gcC>gcT	p.A386A	NXF3_ENST00000425644.1_Silent_p.A58A	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	386	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)			NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						ATACTCACGGGGCTGAGTCCT	0.572																																					p.A386A		Atlas-SNP	.											.	NXF3	81	.	0			c.C1158T						.						99	91	94					X																	102334693		2203	4300	6503	SO:0001819	synonymous_variant	56000	exon13			TCACGGGGCTGAG	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.1158C>T	chrX.hg19:g.102334693G>A		108.0	0.0		77.0	58.0	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Silent	SNP	ENST00000395065.3	hg19	CCDS14503.1	.	.	.	.	.	.	.	.	.	.	G	7.117	0.577203	0.13686	.	.	ENSG00000147206	ENST00000427570	.	.	.	4.44	0.315	0.15852	.	.	.	.	.	T	0.32406	0.0828	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.27971	-1.0058	4	.	.	.	12.3355	8.1428	0.31093	0.4187:0.0:0.5813:0.0	.	.	.	.	S	263	.	.	P	-	1	0	NXF3	102221349	0.331000	0.24713	0.000000	0.03702	0.026000	0.11368	0.695000	0.25527	-0.202000	0.10268	-0.380000	0.06706	CCC	.	.		0.572	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		A	102334693	G	A	102334693	2	1	74	1	0	0	0	0	0	0	0	1	10794	1219	43	3		3	NXF3	23	102334693	Silent	SNP	G	TCGA-CC-A7II-01A-11D-A33K-10	69499973	102334693	52935867	147	10123										
KLHL21	9903	hgsc.bcm.edu	37	chr1	6661948	6661948	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aggtagcgccactgacccgtCtgcgggttgtagcagtcgac	14	12	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:6661948C>A	ENST00000377658.4	-	1	981	c.930G>T	c.(928-930)caG>caT	p.Q310H	KLHL21_ENST00000377663.3_Missense_Mutation_p.Q310H|KLHL21_ENST00000467612.1_Intron|KLHL21_ENST00000463043.1_Intron	NM_014851.2	NP_055666.2	Q9UJP4	KLH21_HUMAN	kelch-like family member 21	310					chromosome passenger complex localization to spindle midzone (GO:0035853)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|regulation of cytokinesis (GO:0032465)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|polar microtubule (GO:0005827)				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|prostate(2)	8	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)		ACTGACCCGTCTGCGGGTTGT	0.662																																					p.Q310H		Atlas-SNP	.											.	KLHL21	27	.	0			c.G930T						.						23	23	23					1																	6661948		2190	4284	6474	SO:0001583	missense	9903	exon1			ACCCGTCTGCGGG	AK090472	CCDS30575.1	1p36	2013-01-30	2013-01-30		ENSG00000162413	ENSG00000162413		"Kelch-like", "BTB/POZ domain containing"	29041	protein-coding gene	gene with protein product			"kelch-like 21 (Drosophila)"				Standard	XM_005263542		Approved	KIAA0469	uc001aoa.3	Q9UJP4	OTTHUMG00000001437	ENST00000377658.4:c.930G>T	chr1.hg19:g.6661948C>A	ENSP00000366886:p.Gln310His	135.0	0.0		113.0	31.0	NM_014851	B3KQP2|O75057|Q5SY26|Q5SY28|Q8N4I6|Q8NF10	Missense_Mutation	SNP	ENST00000377658.4	hg19	CCDS30575.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.351149	0.41599	.	.	ENSG00000162413	ENST00000377658;ENST00000377663	T;T	0.77877	-1.13;-1.13	4.55	4.55	0.56014	Galactose oxidase, beta-propeller (1);	0.064498	0.64402	D	0.000005	T	0.70439	0.3224	L	0.31157	0.91	0.80722	D	1	P;P	0.48998	0.918;0.899	P;P	0.49301	0.606;0.568	T	0.71297	-0.4635	10	0.54805	T	0.06	.	6.8845	0.24191	0.0:0.7103:0.1941:0.0955	.	310;310	Q9UJP4;Q9UJP4-2	KLH21_HUMAN;.	H	310	ENSP00000366886:Q310H;ENSP00000366891:Q310H	ENSP00000366886:Q310H	Q	-	3	2	KLHL21	6584535	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	0.623000	0.24447	2.517000	0.84864	0.561000	0.74099	CAG	.	.		0.662	KLHL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004188.1	NM_014851		A	6661948	C	A	6661948	3	1	75	1	0	0	0	0	1	0	0	0	8385	912	32	3	879	3	KLHL21	1	6661948	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10		6661948	242588673	1	10124										
SLC2A7	155184	hgsc.bcm.edu	37	chr1	9078428	9078428	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	acatgggaagggcgctgtagGagatgcctggtttgggcaca	17	7	0	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:9078428G>C	ENST00000400906.1	-	5	442	c.443C>G	c.(442-444)tCc>tGc	p.S148C		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	148					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			NS(1)|breast(1)|endometrium(4)|large_intestine(10)|lung(4)|prostate(2)|skin(2)	24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		GGCGCTGTAGGAGATGCCTGG	0.542																																					p.S148C		Atlas-SNP	.											.	SLC2A7	56	.	0			c.C443G						.						72	64	67					1																	9078428		2203	4300	6503	SO:0001583	missense	155184	exon5			CTGTAGGAGATGC	AL356306	CCDS98.2	1p36.2	2013-05-22			ENSG00000197241	ENSG00000197241		"Solute carriers"	13445	protein-coding gene	gene with protein product	"intestinal facilitative glucose transporter 7"	610371				11780753	Standard	NM_207420		Approved	GLUT7	uc009vmo.1	Q6PXP3	OTTHUMG00000057499	ENST00000400906.1:c.443C>G	chr1.hg19:g.9078428G>C	ENSP00000383698:p.Ser148Cys	87.0	0.0		84.0	14.0	NM_207420	A2A333	Missense_Mutation	SNP	ENST00000400906.1	hg19	CCDS98.2	.	.	.	.	.	.	.	.	.	.	G	18.28	3.590181	0.66105	.	.	ENSG00000197241	ENST00000400906	T	0.74315	-0.83	4.51	3.58	0.41010	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Sugar transporter, conserved site (1);	0.220221	0.38959	N	0.001501	T	0.80949	0.4722	L	0.48986	1.54	0.30630	N	0.757569	D	0.76494	0.999	D	0.73708	0.981	T	0.78922	-0.2013	10	0.37606	T	0.19	.	13.5965	0.61994	0.0:0.157:0.843:0.0	.	148	Q6PXP3	GTR7_HUMAN	C	148	ENSP00000383698:S148C	ENSP00000383698:S148C	S	-	2	0	SLC2A7	9001015	0.996000	0.38824	0.977000	0.42913	0.988000	0.76386	4.926000	0.63433	1.080000	0.41073	0.561000	0.74099	TCC	.	.		0.542	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420		C	9078428	G	C	9078428	3	2	75	1	0	0	0	0	1	0	0	0	14565	1174	41	4	1127	4	SLC2A7	1	9078428	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	2416480	9078428	240172193	2	10125										
SPEN	23013	hgsc.bcm.edu	37	chr1	16256548	16256548	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cgacatggttccttccatgaAgatgaggatcccataggctc	10	11	0	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:16256548A>C	ENST00000375759.3	+	11	4017	c.3813A>C	c.(3811-3813)gaA>gaC	p.E1271D		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1271					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CCTTCCATGAAGATGAGGATC	0.478																																					p.E1271D		Atlas-SNP	.											.	SPEN	374	.	0			c.A3813C						.						86	90	88					1																	16256548		2203	4300	6503	SO:0001583	missense	23013	exon11			CCATGAAGATGAG		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.3813A>C	chr1.hg19:g.16256548A>C	ENSP00000364912:p.Glu1271Asp	126.0	0.0		81.0	22.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	9.043	0.990191	0.18966	.	.	ENSG00000065526	ENST00000375759	T	0.10477	2.87	5.02	-6.46	0.01908	.	.	.	.	.	T	0.04048	0.0113	N	0.17082	0.46	0.31076	N	0.71248	B	0.06786	0.001	B	0.04013	0.001	T	0.45396	-0.9264	9	0.13853	T	0.58	-22.692	2.9756	0.05936	0.3566:0.195:0.3521:0.0963	.	1271	Q96T58	MINT_HUMAN	D	1271	ENSP00000364912:E1271D	ENSP00000364912:E1271D	E	+	3	2	SPEN	16129135	0.000000	0.05858	0.883000	0.34634	0.980000	0.70556	-1.681000	0.01937	-1.017000	0.03367	0.455000	0.32223	GAA	.	.		0.478	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		C	16256548	A	C	16256548	3	2	75	1	0	0	0	0	1	0	0	0	15053	69	3	5	3855	5	SPEN	1	16256548	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	7178120	16256548	232994073	3	10126										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43896050	43896050	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttttcagaggctgagcttatGggagaagaaggtatgtgggc	16	4	1	4			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:43896050G>A	ENST00000562955.1	+	30	4299	c.4299G>A	c.(4297-4299)atG>atA	p.M1433I	SZT2_ENST00000372442.1_Missense_Mutation_p.M591I	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1490					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CTGAGCTTATGGGAGAAGAAG	0.522																																					p.M1433I		Atlas-SNP	.											.	SZT2	383	.	0			c.G4299A						.						125	124	124					1																	43896050		2203	4300	6503	SO:0001583	missense	23334	exon30			GCTTATGGGAGAA	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.4299G>A	chr1.hg19:g.43896050G>A	ENSP00000457168:p.Met1433Ile	72.0	0.0		47.0	16.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	hg19	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	G	8.120	0.780663	0.16120	.	.	ENSG00000198198	ENST00000372442	.	.	.	6.07	-2.47	0.06442	.	0.923284	0.09352	N	0.814025	T	0.13628	0.0330	N	0.02011	-0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.32666	-0.9898	9	0.17369	T	0.5	.	12.4571	0.55710	0.695:0.0:0.305:0.0	.	1433	Q5T011-5	.	I	591	.	ENSP00000361519:M591I	M	+	3	0	SZT2	43668637	0.944000	0.32072	0.094000	0.20943	0.890000	0.51754	0.410000	0.21098	-0.342000	0.08363	-0.136000	0.14681	ATG	.	.		0.522	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		A	43896050	G	A	43896050	3	1	75	1	0	0	0	0	1	0	0	0	8187	1348	47	3	1827	3	KIAA0467	1	43896050	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	27639502	43896050	205354571	4	10127										
DNAJC6	9829	hgsc.bcm.edu	37	chr1	65874377	65874377	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tactctctggtcaaggtttcAatgctcacaaagacaaaaag	7	9	4	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:65874377A>T	ENST00000395325.3	+	17	2531	c.2374A>T	c.(2374-2376)Aat>Tat	p.N792Y	DNAJC6_ENST00000371069.4_Missense_Mutation_p.N849Y|DNAJC6_ENST00000263441.7_Missense_Mutation_p.N779Y	NM_014787.3	NP_055602.1	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	792					cell death (GO:0008219)|clathrin coat disassembly (GO:0072318)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytosol (GO:0005829)|synapse (GO:0045202)	protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(22)|ovary(1)|prostate(2)|skin(1)	39						TCAAGGTTTCAATGCTCACAA	0.388																																					p.N849Y		Atlas-SNP	.											.	DNAJC6	104	.	0			c.A2545T						.						90	94	92					1																	65874377		2203	4300	6503	SO:0001583	missense	9829	exon17			GGTTTCAATGCTC	AB007942	CCDS30739.1, CCDS58004.1, CCDS58005.1	1p31.3	2011-09-02			ENSG00000116675	ENSG00000116675		"Heat shock proteins / DNAJ (HSP40)"	15469	protein-coding gene	gene with protein product	"auxilin"	608375				9455484, 11147971	Standard	NM_001256864		Approved	KIAA0473	uc001dce.2	O75061	OTTHUMG00000009066	ENST00000395325.3:c.2374A>T	chr1.hg19:g.65874377A>T	ENSP00000378735:p.Asn792Tyr	361.0	0.0		260.0	71.0	NM_001256864	B7Z3V8|D3DQ65|D3DQ66|Q32M66|Q4G0K1|Q5T614|Q5T615	Missense_Mutation	SNP	ENST00000395325.3	hg19	CCDS30739.1	.	.	.	.	.	.	.	.	.	.	A	19.02	3.745735	0.69418	.	.	ENSG00000116675	ENST00000263441;ENST00000395325;ENST00000371069	T;T;T	0.23754	1.89;1.89;1.89	5.37	5.37	0.77165	Heat shock protein DnaJ, N-terminal (2);	0.225310	0.46442	D	0.000283	T	0.32793	0.0841	L	0.44542	1.39	0.47153	D	0.999337	D;D	0.60575	0.988;0.961	D;P	0.65874	0.939;0.784	T	0.08973	-1.0696	10	0.72032	D	0.01	.	15.5421	0.76062	1.0:0.0:0.0:0.0	.	849;792	O75061-2;O75061	.;AUXI_HUMAN	Y	779;792;849	ENSP00000263441:N779Y;ENSP00000378735:N792Y;ENSP00000360108:N849Y	ENSP00000263441:N779Y	N	+	1	0	DNAJC6	65646965	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.549000	0.45803	2.254000	0.74563	0.460000	0.39030	AAT	.	.		0.388	DNAJC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025134.1			T	65874377	A	T	65874377	3	4	75	1	0	0	0	0	1	0	0	0	4655	130	5	4	2440	4	DNAJC6	1	65874377	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	21978327	65874377	183376244	5	10128										
BNIPL	149428	hgsc.bcm.edu	37	chr1	151015463	151015463	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cgggcagagggtctgggcacCagtgagacagctgaaaggct	17	9	1	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:151015463C>A	ENST00000368931.3	+	5	621	c.465C>A	c.(463-465)acC>acA	p.T155T	BNIPL_ENST00000295294.7_Silent_p.T73T	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	155					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GTCTGGGCACCAGTGAGACAG	0.532																																					p.T155T		Atlas-SNP	.											.	BNIPL	45	.	0			c.C465A						.						125	118	120					1																	151015463		2203	4300	6503	SO:0001819	synonymous_variant	149428	exon5			GGGCACCAGTGAG	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.465C>A	chr1.hg19:g.151015463C>A		178.0	0.0		105.0	22.0	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Silent	SNP	ENST00000368931.3	hg19	CCDS978.2																																																																																			.	.		0.532	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279		A	151015463	C	A	151015463	2	1	75	1	0	0	0	0	0	0	0	1	1480	581	21	3		3	BNIPL	1	151015463	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	85141086	151015463	98235158	6	10129										
FLG	2312	hgsc.bcm.edu	37	chr1	152276077	152276077	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttcctcctctccttgaccccGggtgtccacgaatggtgtcc	9	16	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:152276077G>T	ENST00000368799.1	-	3	11320	c.11285C>A	c.(11284-11286)cCg>cAg	p.P3762Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3762	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTTGACCCCGGGTGTCCACG	0.602									Ichthyosis																												p.P3762Q		Atlas-SNP	.											.	FLG	900	.	0			c.C11285A						.						354	348	350					1																	152276077		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GACCCCGGGTGTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11285C>A	chr1.hg19:g.152276077G>T	ENSP00000357789:p.Pro3762Gln	121.0	0.0		96.0	25.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	9.136	1.012635	0.19277	.	.	ENSG00000143631	ENST00000368799	T	0.01647	4.71	3.25	2.28	0.28536	.	.	.	.	.	T	0.02193	0.0068	M	0.75447	2.3	0.09310	N	1	D	0.71674	0.998	P	0.61201	0.885	T	0.43909	-0.9362	9	0.15066	T	0.55	.	8.2723	0.31851	0.0:0.2459:0.7541:0.0	.	3762	P20930	FILA_HUMAN	Q	3762	ENSP00000357789:P3762Q	ENSP00000357789:P3762Q	P	-	2	0	FLG	150542701	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.054000	0.11826	0.659000	0.30945	0.552000	0.68991	CCG	.	.		0.602	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152276077	G	T	152276077	3	4	75	1	0	0	0	0	1	0	0	0	5930	1116	39	1	904	1	FLG	1	152276077	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	1260614	152276077	96974544	7	10130										
CRTC2	200186	hgsc.bcm.edu	37	chr1	153920605	153920605	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tcattggagccggtcactgcGgaatgactcctccacagcag	11	13	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:153920605G>T	ENST00000368633.1	-	14	2189	c.2062C>A	c.(2062-2064)Cgc>Agc	p.R688S	DENND4B_ENST00000361217.4_5'Flank|CRTC2_ENST00000368630.3_Missense_Mutation_p.R368S	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	688					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CGGTCACTGCGGAATGACTCC	0.602																																					p.R688S		Atlas-SNP	.											.	CRTC2	58	.	0			c.C2062A						.						83	71	75					1																	153920605		2203	4300	6503	SO:0001583	missense	200186	exon14			CACTGCGGAATGA	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.2062C>A	chr1.hg19:g.153920605G>T	ENSP00000357622:p.Arg688Ser	150.0	0.0		77.0	14.0	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	hg19	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.156510	0.78114	.	.	ENSG00000160741	ENST00000368630;ENST00000368633	D;T	0.81659	-1.52;0.45	4.65	4.65	0.58169	Transducer of regulated CREB activity, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85741	0.5767	M	0.64170	1.965	0.46609	D	0.999124	D;D	0.89917	1.0;0.967	D;P	0.87578	0.998;0.777	D	0.87363	0.2345	10	0.87932	D	0	-13.0267	15.0504	0.71865	0.0:0.0:1.0:0.0	.	688;368	Q53ET0;Q5T4K5	CRTC2_HUMAN;.	S	368;688	ENSP00000357619:R368S;ENSP00000357622:R688S	ENSP00000357619:R368S	R	-	1	0	CRTC2	152187229	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.454000	0.73493	2.419000	0.82065	0.462000	0.41574	CGC	.	.		0.602	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		T	153920605	G	T	153920605	3	4	75	1	0	0	0	0	1	0	0	0	3902	1116	39	1	23	1	CRTC2	1	153920605	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	1644528	153920605	95330016	8	10131										
ASPM	259266	hgsc.bcm.edu	37	chr1	197072361	197072361	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tctgttctcttccaatactgTaagccctataatacttttga	4	10	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:197072361T>G	ENST00000367409.4	-	18	6276	c.6020A>C	c.(6019-6021)tAc>tCc	p.Y2007S	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2007					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TCCAATACTGTAAGCCCTATA	0.328																																					p.Y2007S		Atlas-SNP	.											.	ASPM	444	.	0			c.A6020C						.						87	91	89					1																	197072361		2203	4299	6502	SO:0001583	missense	259266	exon18			ATACTGTAAGCCC	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.6020A>C	chr1.hg19:g.197072361T>G	ENSP00000356379:p.Tyr2007Ser	67.0	0.0		56.0	11.0	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	t	9.770	1.172510	0.21704	.	.	ENSG00000066279	ENST00000367409	T	0.73363	-0.74	5.6	5.6	0.85130	.	0.261257	0.33253	N	0.005103	D	0.84101	0.5398	M	0.91459	3.21	0.09310	N	0.999999	D	0.55605	0.972	P	0.52267	0.694	T	0.80885	-0.1182	10	0.66056	D	0.02	.	11.5511	0.50721	0.1338:0.0:0.0:0.8662	.	2007	Q8IZT6	ASPM_HUMAN	S	2007	ENSP00000356379:Y2007S	ENSP00000356379:Y2007S	Y	-	2	0	ASPM	195338984	0.485000	0.25972	0.077000	0.20336	0.232000	0.25224	1.367000	0.34204	2.136000	0.66102	0.524000	0.50904	TAC	.	.		0.328	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		G	197072361	T	G	197072361	3	3	75	1	0	0	0	0	1	0	0	0	1056	1638	57	5	4457	5	ASPM	1	197072361	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	43151756	197072361	52178260	9	10132										
CRB1	23418	hgsc.bcm.edu	37	chr1	197404289	197404289	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cctgcaagggtgtctaagtaCaatagaaatcggaggcattt	11	7	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:197404289C>A	ENST00000367400.3	+	9	3431	c.3296C>A	c.(3295-3297)aCa>aAa	p.T1099K	CRB1_ENST00000367399.2_Missense_Mutation_p.T987K|CRB1_ENST00000538660.1_Intron|RP11-75C23.1_ENST00000422250.1_RNA|CRB1_ENST00000535699.1_Missense_Mutation_p.T1075K|CRB1_ENST00000544212.1_Missense_Mutation_p.T580K|CRB1_ENST00000367397.1_Missense_Mutation_p.T480K	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	1099	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		T -> K (in RP12). {ECO:0000269|PubMed:21987686}.		cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TGTCTAAGTACAATAGAAATC	0.358																																					p.T1099K		Atlas-SNP	.											.	CRB1	284	.	0			c.C3296A						.						59	64	62					1																	197404289		2203	4300	6503	SO:0001583	missense	23418	exon9			TAAGTACAATAGA		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.3296C>A	chr1.hg19:g.197404289C>A	ENSP00000356370:p.Thr1099Lys	66.0	0.0		55.0	14.0	NM_201253	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	hg19	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837562	0.50951	.	.	ENSG00000134376	ENST00000535699;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	T;T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32;-0.32	5.7	5.7	0.88788	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.79269	0.4417	M	0.70595	2.14	0.45777	D	0.998664	D;D;D;D	0.89917	1.0;1.0;0.992;0.982	D;D;P;P	0.85130	0.997;0.996;0.73;0.824	T	0.76743	-0.2847	9	0.32370	T	0.25	.	13.0831	0.59125	0.0:0.9268:0.0:0.0732	.	1075;987;748;1099	F5H0L2;P82279-3;P82279-4;P82279	.;.;.;CRUM1_HUMAN	K	1075;1099;987;580;480;748	ENSP00000438786:T1075K;ENSP00000356370:T1099K;ENSP00000356369:T987K;ENSP00000444556:T580K;ENSP00000356367:T480K	ENSP00000356367:T480K	T	+	2	0	CRB1	195670912	1.000000	0.71417	0.995000	0.50966	0.345000	0.29048	4.441000	0.59981	2.681000	0.91329	0.650000	0.86243	ACA	.	.		0.358	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		A	197404289	C	A	197404289	3	1	75	1	0	0	0	0	1	0	0	0	3850	478	17	3	3330	3	CRB1	1	197404289	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	331928	197404289	51846332	10	10133										
TP53BP2	7159	hgsc.bcm.edu	37	chr1	223983912	223983912	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cacagaagctgacttggatgGgtatgatgggacagagatgg	16	5	0	4			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:223983912G>C	ENST00000343537.7	-	13	2620	c.2329C>G	c.(2329-2331)Cca>Gca	p.P777A	TP53BP2_ENST00000391878.2_Missense_Mutation_p.P648A|TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391879.2_Missense_Mutation_p.P10A	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	771					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		GACTTGGATGGGTATGATGGG	0.483																																					p.P777A		Atlas-SNP	.											.	TP53BP2	144	.	0			c.C2329G						.						154	162	159					1																	223983912		2203	4300	6503	SO:0001583	missense	7159	exon13			TGGATGGGTATGA	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.2329C>G	chr1.hg19:g.223983912G>C	ENSP00000341957:p.Pro777Ala	99.0	0.0		69.0	6.0	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	hg19	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.920866	0.33908	.	.	ENSG00000143514	ENST00000391878;ENST00000343537;ENST00000391879	T;T;T	0.49720	0.82;1.0;0.77	5.47	2.02	0.26589	.	0.200971	0.53938	D	0.000052	T	0.32556	0.0833	L	0.36672	1.1	0.41222	D	0.986515	B;B	0.28055	0.199;0.0	B;B	0.23716	0.048;0.001	T	0.14309	-1.0477	10	0.54805	T	0.06	.	6.7283	0.23369	0.0783:0.1279:0.6623:0.1314	.	777;771	B4DG66;Q13625	.;ASPP2_HUMAN	A	648;777;10	ENSP00000375750:P648A;ENSP00000341957:P777A;ENSP00000375751:P10A	ENSP00000341957:P777A	P	-	1	0	TP53BP2	222050535	1.000000	0.71417	0.183000	0.23137	0.997000	0.91878	2.982000	0.49337	0.661000	0.30985	0.655000	0.94253	CCA	.	.		0.483	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		C	223983912	G	C	223983912	3	2	75	1	0	0	0	0	1	0	0	0	16399	1232	43	4	1099	4	TP53BP2	1	223983912	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	26579623	223983912	25266709	11	10134										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228474027	228474027	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttgaggcgggtgaccagcggGcctcggccgccctgcgggtc	18	14	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:228474027G>T	ENST00000422127.1	+	34	9297	c.9253G>T	c.(9253-9255)Gcc>Tcc	p.A3085S	OBSCN_ENST00000570156.2_Missense_Mutation_p.A3514S|OBSCN_ENST00000366707.4_Missense_Mutation_p.A204S|OBSCN_ENST00000366709.4_Missense_Mutation_p.A204S|OBSCN_ENST00000359599.6_Missense_Mutation_p.A1932S|OBSCN_ENST00000284548.11_Missense_Mutation_p.A3085S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3085	Ig-like 30.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGACCAGCGGGCCTCGGCCGC	0.657																																					p.A3514S		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,4	OBSCN	2142	.	0			c.G10540T						.						10	13	12					1																	228474027		1983	4140	6123	SO:0001583	missense	84033	exon39			CAGCGGGCCTCGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.9253G>T	chr1.hg19:g.228474027G>T	ENSP00000409493:p.Ala3085Ser	65.0	0.0		46.0	15.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.435484	0.43224	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	5.67	-5.2	0.02823	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.597925	0.16713	N	0.202571	T	0.14356	0.0347	N	0.02985	-0.445	0.09310	N	0.999995	B;B	0.11235	0.004;0.002	B;B	0.26310	0.068;0.048	T	0.19031	-1.0318	10	0.27785	T	0.31	.	5.772	0.18259	0.515:0.0:0.1789:0.3061	.	3085;3085	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	3085;3085;204;204;1932	ENSP00000284548:A3085S;ENSP00000409493:A3085S;ENSP00000355668:A204S;ENSP00000355670:A204S;ENSP00000352613:A1932S	ENSP00000284548:A3085S	A	+	1	0	OBSCN	226540650	0.993000	0.37304	0.258000	0.24420	0.122000	0.20287	0.348000	0.20031	-0.812000	0.04363	0.561000	0.74099	GCC	.	.		0.657	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228474027	G	T	228474027	3	4	75	1	0	0	0	0	1	0	0	0	10821	1203	42	3	9383	3	OBSCN	1	228474027	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	4490115	228474027	20776594	12	10135										
IRF2BP2	359948	hgsc.bcm.edu	37	chr1	234743411	234743411	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tgggccgcttcaggcggtgtGgtccggttggaatgaggtga	19	7	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:234743411G>A	ENST00000366609.3	-	2	1266	c.1236C>T	c.(1234-1236)acC>acT	p.T412T	RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000491430.1_5'UTR|IRF2BP2_ENST00000366610.3_Silent_p.T396T	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			CAGGCGGTGTGGTCCGGTTGG	0.587																																					p.T412T		Atlas-SNP	.											.	IRF2BP2	37	.	0			c.C1236T						.						95	102	100					1																	234743411		2203	4300	6503	SO:0001819	synonymous_variant	359948	exon2			CGGTGTGGTCCGG	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.1236C>T	chr1.hg19:g.234743411G>A		118.0	0.0		105.0	19.0	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	hg19	CCDS1602.1																																																																																			.	.		0.587	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972		A	234743411	G	A	234743411	2	1	75	1	0	0	0	0	0	0	0	1	7839	1335	47	3		3	IRF2BP2	1	234743411	Silent	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	6269384	234743411	14507210	13	10136										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247587376	247587376	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agatggagttgctgtttgacCccgatgatgagcattctgag	13	7	1	5			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr1:247587376C>A	ENST00000336119.3	+	3	1377	c.631C>A	c.(631-633)Ccc>Acc	p.P211T	NLRP3_ENST00000348069.2_Missense_Mutation_p.P211T|NLRP3_ENST00000366496.2_Missense_Mutation_p.P211T|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000366497.2_Missense_Mutation_p.P211T|NLRP3_ENST00000391828.3_Missense_Mutation_p.P211T|NLRP3_ENST00000391827.2_Missense_Mutation_p.P211T	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	211					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			GCTGTTTGACCCCGATGATGA	0.587																																					p.P211T		Atlas-SNP	.											.	NLRP3	286	.	0			c.C631A						.						92	82	86					1																	247587376		2203	4300	6503	SO:0001583	missense	114548	exon3			TTTGACCCCGATG	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.631C>A	chr1.hg19:g.247587376C>A	ENSP00000337383:p.Pro211Thr	175.0	0.0		130.0	24.0	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	C	7.627	0.678092	0.14841	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	T;T;T;T;T;T	0.78003	-1.06;-1.07;-1.06;-1.14;-1.07;-1.1	4.27	3.34	0.38264	.	0.131978	0.35555	N	0.003123	D	0.84804	0.5553	M	0.72894	2.215	0.20764	N	0.999852	B;P;D;P;P	0.76494	0.35;0.937;0.999;0.896;0.914	B;P;D;P;P	0.72625	0.071;0.543;0.978;0.66;0.517	T	0.75317	-0.3360	10	0.66056	D	0.02	.	9.9683	0.41738	0.0:0.7671:0.2329:0.0	.	211;211;211;211;211	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	T	211	ENSP00000375704:P211T;ENSP00000355453:P211T;ENSP00000337383:P211T;ENSP00000294752:P211T;ENSP00000355452:P211T;ENSP00000375703:P211T	ENSP00000337383:P211T	P	+	1	0	NLRP3	245653999	0.000000	0.05858	0.046000	0.18839	0.008000	0.06430	-0.046000	0.11983	1.362000	0.46000	0.655000	0.94253	CCC	.	.		0.587	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		A	247587376	C	A	247587376	3	1	75	1	0	0	0	0	1	0	0	0	10487	623	22	3	641	3	NLRP3	1	247587376	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	12843965	247587376	1663245	14	10137										
CAD	790	hgsc.bcm.edu	37	chr2	27456323	27456323	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cctgaagccattgactcggcTgagaaccgtttcaagttttc	9	11	1	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr2:27456323T>G	ENST00000403525.1	+	19	3090	c.2946T>G	c.(2944-2946)gcT>gcG	p.A982A	CAD_ENST00000264705.4_Silent_p.A1045A			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGACTCGGCTGAGAACCGTT	0.607																																					p.A1045A		Atlas-SNP	.											.	CAD	199	.	0			c.T3135G						.						52	51	51					2																	27456323		2203	4300	6503	SO:0001819	synonymous_variant	790	exon20			CTCGGCTGAGAAC	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.2946T>G	chr2.hg19:g.27456323T>G		66.0	0.0		54.0	7.0	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	hg19																																																																																				.	.		0.607	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			G	27456323	T	G	27456323	2	3	75	1	0	0	0	0	0	0	0	1	2567	1567	55	5		5	CAD	2	27456323	Silent	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10		27456323	215743050	15	10138										
XDH	7498	hgsc.bcm.edu	37	chr2	31596741	31596741	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tacactgaccgtactcacttGgaagagctggacatcggctg	11	11	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr2:31596741G>T	ENST00000379416.3	-	16	1732	c.1684C>A	c.(1684-1686)Caa>Aaa	p.Q562K		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	562					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GTACTCACTTGGAAGAGCTGG	0.483																																					p.Q562K	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.C1684A						.						48	45	46					2																	31596741		2203	4300	6503	SO:0001583	missense	7498	exon16			TCACTTGGAAGAG	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.1684C>A	chr2.hg19:g.31596741G>T	ENSP00000368727:p.Gln562Lys	57.0	0.0		46.0	9.0	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	hg19	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.188959	0.57909	.	.	ENSG00000158125	ENST00000379416	T	0.10960	2.82	5.75	5.75	0.90469	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead (1);	0.000000	0.85682	D	0.000000	T	0.24736	0.0600	M	0.88105	2.93	0.80722	D	1	B	0.18863	0.031	B	0.19148	0.024	T	0.06250	-1.0837	10	0.62326	D	0.03	.	19.5652	0.95390	0.0:0.0:1.0:0.0	.	562	P47989	XDH_HUMAN	K	562	ENSP00000368727:Q562K	ENSP00000368727:Q562K	Q	-	1	0	XDH	31450245	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	7.111000	0.77077	2.714000	0.92807	0.655000	0.94253	CAA	.	.		0.483	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		T	31596741	G	T	31596741	3	4	75	1	0	0	0	0	1	0	0	0	17441	1357	47	3	2401	3	XDH	2	31596741	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	4140418	31596741	211602632	16	10139										
ZFP36L2	678	hgsc.bcm.edu	37	chr2	43452474	43452474	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ctcgaagggccggcacagctCggtcttgtagcgcgtggagt	16	11	1	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr2:43452474C>G	ENST00000282388.3	-	2	762	c.469G>C	c.(469-471)Gag>Cag	p.E157Q	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	157					cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E157Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				CGGCACAGCTCGGTCTTGTAG	0.652																																					p.E157Q		Atlas-SNP	.											ZFP36L2,NS,carcinoma,0,2	ZFP36L2	56	.	1	Substitution - Missense(1)	lung(1)	c.G469C						.						37	37	37					2																	43452474		2202	4300	6502	SO:0001583	missense	678	exon2			ACAGCTCGGTCTT	X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"RING-type (C3HC4) zinc fingers"	1108	protein-coding gene	gene with protein product		612053	"zinc finger protein 36, C3H type-like 1", "zinc finger protein 36, C3H type-like 2"	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.469G>C	chr2.hg19:g.43452474C>G	ENSP00000282388:p.Glu157Gln	45.0	0.0		30.0	7.0	NM_006887	Q53TB4|Q9BSJ3	Missense_Mutation	SNP	ENST00000282388.3	hg19	CCDS1811.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.861249	0.91433	.	.	ENSG00000152518	ENST00000282388	T	0.52526	0.66	4.76	4.76	0.60689	Zinc finger, CCCH-type (3);	0.063998	0.64402	D	0.000010	T	0.70736	0.3258	M	0.80332	2.49	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76364	-0.2986	10	0.87932	D	0	-28.709	16.6213	0.84931	0.0:1.0:0.0:0.0	.	157	P47974	TISD_HUMAN	Q	157	ENSP00000282388:E157Q	ENSP00000282388:E157Q	E	-	1	0	ZFP36L2	43305978	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.308000	0.78929	2.202000	0.70862	0.555000	0.69702	GAG	.	.		0.652	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887		G	43452474	C	G	43452474	3	3	75	1	0	0	0	0	1	0	0	0	17662	893	31	4	1019	4	ZFP36L2	2	43452474	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	11855733	43452474	199746899	17	10140										
AHSA2	9736	hgsc.bcm.edu	37	chr2	61413791	61413791	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	actgaattttgtgcctactcTagggcaaacagaattacaat	7	8	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr2:61413791T>A	ENST00000398571.2	-	0	11357				AHSA2_ENST00000357022.2_Missense_Mutation_p.L95Q|AHSA2_ENST00000489653.1_3'UTR|AHSA2_ENST00000394457.3_Missense_Mutation_p.L95Q|AHSA2_ENST00000410073.1_Missense_Mutation_p.L104Q	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34						positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			GTGCCTACTCTAGGGCAAACA	0.338																																					p.L95Q		Atlas-SNP	.											.	AHSA2	26	.	0			c.T284A						.						72	70	71					2																	61413791		2203	4300	6503	SO:0001628	intergenic_variant	130872	exon6			CTACTCTAGGGCA	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265		chr2.hg19:g.61413791T>A		118.0	0.0		84.0	22.0	NM_152392	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	.	10.56	1.385599	0.25031	.	.	ENSG00000173209	ENST00000357022;ENST00000394457;ENST00000430934;ENST00000410073	.	.	.	5.92	-4.97	0.03029	.	0.719989	0.12745	N	0.442708	T	0.19005	0.0456	L	0.36672	1.1	0.09310	N	1	P	0.38642	0.641	B	0.35413	0.202	T	0.33879	-0.9851	9	0.11485	T	0.65	.	8.4476	0.32852	0.0:0.5488:0.1178:0.3334	.	257	Q719I0	AHSA2_HUMAN	Q	95;95;258;104	.	ENSP00000349525:L95Q	L	+	2	0	AHSA2	61267295	0.000000	0.05858	0.054000	0.19295	0.934000	0.57294	-0.980000	0.03770	-0.561000	0.06094	-0.250000	0.11733	CTA	.	.		0.338	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			A	61413791	T	A	61413791	1	1	75	0	1	0	0	0	0	0	0	0	419	1522	53	4		4	AHSA2	2	61413791	IGR	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	17961317	61413791	181785582	18	10141										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84775472	84775472	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	accacatgagttgcccacttAtggagactctgagaaaatga	9	9	1	4			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr2:84775472A>T	ENST00000237449.6	+	7	1255	c.1247A>T	c.(1246-1248)tAt>tTt	p.Y416F	DNAH6_ENST00000389394.3_Missense_Mutation_p.Y416F|DNAH6_ENST00000398278.2_Missense_Mutation_p.Y416F			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	416	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTGCCCACTTATGGAGACTCT	0.373																																					p.Y416F		Atlas-SNP	.											.	DNAH6	194	.	0			c.A1247T						.						118	116	116					2																	84775472		2203	4300	6503	SO:0001583	missense	1768	exon8			CCACTTATGGAGA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.1247A>T	chr2.hg19:g.84775472A>T	ENSP00000237449:p.Tyr416Phe	125.0	0.0		112.0	19.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	6.679	0.493778	0.12702	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.24538	1.85;1.99;1.85	4.92	-0.481	0.12082	.	.	.	.	.	T	0.10594	0.0259	N	0.15975	0.35	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36040	-0.9764	9	0.13470	T	0.59	.	2.5006	0.04632	0.4652:0.3124:0.0827:0.1396	.	416	Q9C0G6	DYH6_HUMAN	F	416	ENSP00000374045:Y416F;ENSP00000381326:Y416F;ENSP00000237449:Y416F	ENSP00000237449:Y416F	Y	+	2	0	DNAH6	84628983	0.042000	0.20092	0.000000	0.03702	0.078000	0.17371	0.430000	0.21428	-0.225000	0.09913	0.482000	0.46254	TAT	.	.		0.373	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84775472	A	T	84775472	3	4	75	1	0	0	0	0	1	0	0	0	4607	449	16	4	1273	4	DNAH6	2	84775472	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	23361681	84775472	158423901	19	10142										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99013018	99013018	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ggtgctcaagagcctcccagAcaagctgaaggctgagatcg	13	11	1	4			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr2:99013018A>G	ENST00000272602.2	+	7	1424	c.1385A>G	c.(1384-1386)gAc>gGc	p.D462G	CNGA3_ENST00000409937.1_Missense_Mutation_p.D466G|CNGA3_ENST00000436404.2_Missense_Mutation_p.D444G|CNGA3_ENST00000393504.1_Missense_Mutation_p.D462G			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	462					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AGCCTCCCAGACAAGCTGAAG	0.577																																					p.D462G		Atlas-SNP	.											.	CNGA3	118	.	0			c.A1385G						.						62	56	58					2																	99013018		2203	4300	6503	SO:0001583	missense	1261	exon8			TCCCAGACAAGCT	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.1385A>G	chr2.hg19:g.99013018A>G	ENSP00000272602:p.Asp462Gly	102.0	0.0		106.0	17.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	A	18.48	3.633103	0.67015	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.96716	-4.1;-4.1;-4.1;-4.1	4.92	4.92	0.64577	Cyclic nucleotide-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.98220	0.9411	M	0.93062	3.375	0.80722	D	1	D;D;P	0.63046	0.983;0.992;0.681	P;D;B	0.63703	0.889;0.917;0.189	D	0.98745	1.0718	10	0.52906	T	0.07	.	13.7295	0.62779	1.0:0.0:0.0:0.0	.	466;444;462	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	G	462;444;462;466	ENSP00000377140:D462G;ENSP00000410070:D444G;ENSP00000272602:D462G;ENSP00000386761:D466G	ENSP00000272602:D462G	D	+	2	0	CNGA3	98379450	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.758000	0.91663	2.076000	0.62316	0.456000	0.33151	GAC	.	.		0.577	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		G	99013018	A	G	99013018	3	3	75	1	0	0	0	0	1	0	0	0	3600	275	10	2	1411	2	CNGA3	2	99013018	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	14237546	99013018	144186355	20	10143										
IL1RL2	8808	hgsc.bcm.edu	37	chr2	102808473	102808473	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ccataggtggtttaccaaatTtatcagatgagtacaagcaa	8	7	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr2:102808473T>A	ENST00000264257.2	+	4	508	c.382T>A	c.(382-384)Tta>Ata	p.L128I	IL1RL2_ENST00000481806.1_Intron|IL1RL2_ENST00000441515.2_Intron|IL1RL2_ENST00000539491.1_Missense_Mutation_p.L128I	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	128	Ig-like C2-type 2.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						TTTACCAAATTTATCAGATGA	0.378																																					p.L128I		Atlas-SNP	.											.	IL1RL2	118	.	0			c.T382A						.						103	100	101					2																	102808473		2203	4300	6503	SO:0001583	missense	8808	exon4			CCAAATTTATCAG	U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.382T>A	chr2.hg19:g.102808473T>A	ENSP00000264257:p.Leu128Ile	201.0	0.0		210.0	42.0	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	hg19	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	T	14.74	2.625992	0.46840	.	.	ENSG00000115598	ENST00000264257;ENST00000421464;ENST00000539491	T;T;T	0.17854	2.25;2.25;2.25	5.4	1.56	0.23342	Immunoglobulin-like (1);	1.365760	0.05222	N	0.508661	T	0.16471	0.0396	L	0.44542	1.39	0.09310	N	1	P	0.41420	0.749	B	0.41691	0.364	T	0.26224	-1.0109	10	0.21540	T	0.41	.	6.0967	0.20025	0.0:0.0881:0.3321:0.5798	.	128	Q9HB29	ILRL2_HUMAN	I	128	ENSP00000264257:L128I;ENSP00000387611:L128I;ENSP00000442184:L128I	ENSP00000264257:L128I	L	+	1	2	IL1RL2	102174905	0.000000	0.05858	0.003000	0.11579	0.594000	0.36715	-0.377000	0.07456	0.403000	0.25479	0.533000	0.62120	TTA	.	.		0.378	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		A	102808473	T	A	102808473	3	1	75	1	0	0	0	0	1	0	0	0	7673	1838	64	4	392	4	IL1RL2	2	102808473	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	3795455	102808473	140390900	21	10144										
GALNT13	114805	hgsc.bcm.edu	37	chr2	155098670	155098670	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	atcgttccccacactatctaCtctcagaggtcatcttggta	6	13	4	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr2:155098670C>A	ENST00000392825.3	+	5	1006	c.439C>A	c.(439-441)Ctc>Atc	p.L147I	GALNT13_ENST00000409237.1_Missense_Mutation_p.L147I	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	147	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						ACACTATCTACTCTCAGAGGT	0.353																																					p.L147I		Atlas-SNP	.											.	GALNT13	170	.	0			c.C439A						.						128	118	121					2																	155098670		2203	4300	6503	SO:0001583	missense	114805	exon5			TATCTACTCTCAG	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23242	protein-coding gene	gene with protein product	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13", "polypeptide GalNAc transferase 13"	608369	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.439C>A	chr2.hg19:g.155098670C>A	ENSP00000376570:p.Leu147Ile	95.0	0.0		81.0	31.0	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Missense_Mutation	SNP	ENST00000392825.3	hg19	CCDS2199.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.257670	0.39896	.	.	ENSG00000144278	ENST00000392825;ENST00000409237	T;T	0.61510	0.1;0.1	5.56	5.56	0.83823	Glycosyl transferase, family 2 (1);	0.130565	0.50627	D	0.000108	T	0.51432	0.1674	L	0.49455	1.56	0.58432	D	0.999998	B;B	0.33755	0.424;0.224	B;B	0.37015	0.239;0.239	T	0.44360	-0.9333	10	0.19590	T	0.45	.	11.5969	0.50979	0.0:0.918:0.0:0.082	.	147;147	Q08ER7;Q8IUC8	.;GLT13_HUMAN	I	147	ENSP00000376570:L147I;ENSP00000387239:L147I	ENSP00000376570:L147I	L	+	1	0	GALNT13	154806916	1.000000	0.71417	0.970000	0.41538	0.974000	0.67602	4.819000	0.62664	2.621000	0.88768	0.579000	0.79373	CTC	.	.		0.353	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917		A	155098670	C	A	155098670	3	1	75	1	0	0	0	0	1	0	0	0	6219	565	20	3	449	3	GALNT13	2	155098670	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	52290197	155098670	88100703	22	10145										
TTN	7273	hgsc.bcm.edu	37	chr2	179604561	179604561	+	Frame_Shift_Del	DEL	C	C	-													0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aagttccattttcaggttagCcatttgaggatcaacatctt							TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr2:179604561delC	ENST00000591111.1	-	46	12672	c.12448delG	c.(12448-12450)gctfs	p.A4150fs	TTN_ENST00000589042.1_Frame_Shift_Del_p.A4467fs|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.A4229fs|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.A4104fs|TTN_ENST00000342175.6_Frame_Shift_Del_p.A4296fs			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCAGGTTAGCCATTTGAGGA	0.413																																					p.A4467fs		Atlas-Indel,Pindel	.											.	TTN	18412	.	0			c.13400delC						.						155	152	153					2																	179604561		1924	4145	6069	SO:0001589	frameshift_variant	7273	exon48			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.12448delG	chr2.hg19:g.179604561delC	ENSP00000465570:p.Ala4150fs	122.0	0.0		107.0	25.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179604561	C	-	179604561	7	5	75	1	0	1	0	1	0	0	0	0	16750	739	26	0	91390	0	TTN	2	179604561	Frame_Shift_Del	DEL	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	24505891	179604561	63594812	23	10146										
ALS2CR12	130540	hgsc.bcm.edu	37	chr2	202211384	202211384	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	acaagttgatagccaggtgaCacgttgatcacttcctaggc	10	10	1	3	rs552883600		TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr2:202211384C>A	ENST00000286190.5	-	4	295	c.249G>T	c.(247-249)gtG>gtT	p.V83V	ALS2CR12_ENST00000392257.3_Silent_p.V83V|ALS2CR12_ENST00000448967.1_5'UTR|ALS2CR12_ENST00000439709.1_Silent_p.V83V|ALS2CR12_ENST00000405148.2_Silent_p.V83V			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12	83					regulation of GTPase activity (GO:0043087)	outer dense fiber (GO:0001520)|sperm fibrous sheath (GO:0035686)|sperm flagellum (GO:0036126)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)	21						AGCCAGGTGACACGTTGATCA	0.453																																					p.V83V		Atlas-SNP	.											.	ALS2CR12	54	.	0			c.G249T						.						134	111	119					2																	202211384		2203	4300	6503	SO:0001819	synonymous_variant	130540	exon5			AGGTGACACGTTG	AB053314	CCDS2346.1, CCDS46488.1	2q33.1	2009-10-06			ENSG00000155749	ENSG00000155749			14439	protein-coding gene	gene with protein product							Standard	XM_006712272		Approved		uc002uya.4	Q96Q35	OTTHUMG00000132824	ENST00000286190.5:c.249G>T	chr2.hg19:g.202211384C>A		63.0	0.0		46.0	11.0	NM_001127391	G5E9S3|Q53TT6|Q8N1B6	Silent	SNP	ENST00000286190.5	hg19	CCDS2346.1																																																																																			.	.		0.453	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256286.1	NM_139163		A	202211384	C	A	202211384	2	1	75	1	0	0	0	0	0	0	0	1	553	465	17	3		3	ALS2CR12	2	202211384	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	22606823	202211384	40987989	24	10147										
LRRC3B	116135	hgsc.bcm.edu	37	chr3	26751375	26751375	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tgaaacagtcttactgtatcTggactccaatcagatcacat	6	10	4	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr3:26751375T>A	ENST00000396641.2	+	2	804	c.212T>A	c.(211-213)cTg>cAg	p.L71Q	AC114877.3_ENST00000446601.1_lincRNA|LRRC3B_ENST00000456208.2_Missense_Mutation_p.L71Q|LRRC3B_ENST00000417744.1_Missense_Mutation_p.L71Q	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	71						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						TTACTGTATCTGGACTCCAAT	0.398																																					p.L71Q		Atlas-SNP	.											.	LRRC3B	51	.	0			c.T212A						.						91	88	89					3																	26751375		2203	4300	6503	SO:0001583	missense	116135	exon2			TGTATCTGGACTC	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.212T>A	chr3.hg19:g.26751375T>A	ENSP00000379880:p.Leu71Gln	89.0	0.0		69.0	19.0	NM_052953	Q5M8T0	Missense_Mutation	SNP	ENST00000396641.2	hg19	CCDS2644.1	.	.	.	.	.	.	.	.	.	.	T	19.01	3.743233	0.69418	.	.	ENSG00000179796	ENST00000396641;ENST00000432040;ENST00000417744;ENST00000456208	D;D;D;D	0.96885	-4.16;-4.16;-4.16;-4.16	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.99020	0.9665	H	0.99026	4.405	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.99198	1.0872	10	0.87932	D	0	-7.7357	16.0034	0.80327	0.0:0.0:0.0:1.0	.	71	Q96PB8	LRC3B_HUMAN	Q	71	ENSP00000379880:L71Q;ENSP00000398184:L71Q;ENSP00000406370:L71Q;ENSP00000394940:L71Q	ENSP00000379880:L71Q	L	+	2	0	LRRC3B	26726379	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	CTG	.	.		0.398	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953		A	26751375	T	A	26751375	3	1	75	1	0	0	0	0	1	0	0	0	9005	1580	55	4	214	4	LRRC3B	3	26751375	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10		26751375	171271055	25	10148										
SCN11A	11280	hgsc.bcm.edu	37	chr3	38938564	38938564	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ctcttttgggaattgaagctAcggccaaaaagctgcatgcc	10	10	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr3:38938564A>T	ENST00000302328.3	-	14	2373	c.2175T>A	c.(2173-2175)cgT>cgA	p.R725R	SCN11A_ENST00000456224.3_Silent_p.R725R|SCN11A_ENST00000444237.2_Silent_p.R725R|SCN11A_ENST00000450244.1_Silent_p.R725R	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	725					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AATTGAAGCTACGGCCAAAAA	0.502																																					p.R725R		Atlas-SNP	.											.	SCN11A	296	.	0			c.T2175A						.						88	82	84					3																	38938564		2203	4300	6503	SO:0001819	synonymous_variant	11280	exon14			GAAGCTACGGCCA	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.2175T>A	chr3.hg19:g.38938564A>T		194.0	0.0		94.0	46.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.		0.502	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		T	38938564	A	T	38938564	2	4	75	1	0	0	0	0	0	0	0	1	13928	378	14	4		4	SCN11A	3	38938564	Silent	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	12187189	38938564	159083866	26	10149										
CHDH	55349	hgsc.bcm.edu	37	chr3	53851839	53851839	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cagcgtcctgggcttgtagaCagggacatctttgtcccaga	12	11	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr3:53851839C>T	ENST00000315251.6	-	9	2187	c.1750G>A	c.(1750-1752)Gtc>Atc	p.V584I		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	584					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	GGCTTGTAGACAGGGACATCT	0.592																																					p.V584I		Atlas-SNP	.											.	CHDH	34	.	0			c.G1750A						.						74	59	64					3																	53851839		2203	4300	6503	SO:0001583	missense	55349	exon9			TGTAGACAGGGAC	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.1750G>A	chr3.hg19:g.53851839C>T	ENSP00000319851:p.Val584Ile	46.0	0.0		55.0	16.0	NM_018397	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	hg19	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.762909	0.49574	.	.	ENSG00000016391	ENST00000315251	T	0.22743	1.94	5.54	3.76	0.43208	.	0.143052	0.46758	N	0.000264	T	0.14313	0.0346	N	0.19112	0.55	0.54753	D	0.999983	B	0.22003	0.063	B	0.21917	0.037	T	0.05099	-1.0906	10	0.42905	T	0.14	-39.1715	11.7443	0.51811	0.0:0.8587:0.0:0.1413	.	584	Q8NE62	CHDH_HUMAN	I	584	ENSP00000319851:V584I	ENSP00000319851:V584I	V	-	1	0	CHDH	53826879	0.983000	0.35010	0.938000	0.37757	0.974000	0.67602	2.298000	0.43602	0.719000	0.32188	0.655000	0.94253	GTC	.	.		0.592	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		T	53851839	C	T	53851839	3	4	75	1	0	0	0	0	1	0	0	0	3335	478	17	3	38	3	CHDH	3	53851839	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	14913275	53851839	144170591	27	10150										
IQCB1	9657	hgsc.bcm.edu	37	chr3	121514404	121514404	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttgaatcaagcatgctgcttGatgtagtttctgaaatgccg	10	7	2	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr3:121514404G>A	ENST00000310864.6	-	10	1100	c.886C>T	c.(886-888)Caa>Taa	p.Q296*	IQCB1_ENST00000349820.6_Intron	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	296	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.				cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)			NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		CATGCTGCTTGATGTAGTTTC	0.358																																					p.Q296X		Atlas-SNP	.											.	IQCB1	50	.	0			c.C886T						.						59	60	60					3																	121514404		2203	4298	6501	SO:0001587	stop_gained	9657	exon10			CTGCTTGATGTAG	D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"nephrocystin-5"	609237	"IQ calmodulin-binding motif containing 1"			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.886C>T	chr3.hg19:g.121514404G>A	ENSP00000311505:p.Gln296*	231.0	0.0		212.0	14.0	NM_001023570	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Nonsense_Mutation	SNP	ENST00000310864.6	hg19	CCDS33837.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.386735	0.82902	.	.	ENSG00000173226	ENST00000310864;ENST00000460108	.	.	.	4.71	1.65	0.23941	.	0.465951	0.21437	N	0.074556	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-0.6546	12.0879	0.53708	0.0:0.0:0.3142:0.6858	.	.	.	.	X	296;112	.	ENSP00000311505:Q296X	Q	-	1	0	IQCB1	122997094	1.000000	0.71417	0.995000	0.50966	0.946000	0.59487	1.372000	0.34261	0.208000	0.20626	0.467000	0.42956	CAA	.	.		0.358	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642		A	121514404	G	A	121514404	4	1	75	1	0	0	0	0	0	1	0	0	7812	1299	45	3	934	3	IQCB1	3	121514404	Nonsense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	67662565	121514404	76508026	28	10151										
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135721147	135721147	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agtgaaggaagtggtaatgaTacaatttctagctctgaaac	10	5	2	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr3:135721147T>C	ENST00000264977.3	+	2	1424	c.807T>C	c.(805-807)gaT>gaC	p.D269D	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	269					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GTGGTAATGATACAATTTCTA	0.343																																					p.D269D		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T807C						.						72	74	73					3																	135721147		2203	4300	6503	SO:0001819	synonymous_variant	5523	exon2			TAATGATACAATT	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.807T>C	chr3.hg19:g.135721147T>C		118.0	0.0		120.0	25.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	hg19	CCDS3087.1																																																																																			.	.		0.343	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		C	135721147	T	C	135721147	2	2	75	1	0	0	0	0	0	0	0	1	12400	1403	49	2		2	PPP2R3A	3	135721147	Silent	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	14206743	135721147	62301283	29	10152										
SSR3	6747	hgsc.bcm.edu	37	chr3	156271447	156271447	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttgaaaaacatacttacttgTgcttgagaacaaatttcaca	5	7	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr3:156271447T>G	ENST00000265044.2	-	2	351	c.257A>C	c.(256-258)cAc>cCc	p.H86P	SSR3_ENST00000467789.1_Missense_Mutation_p.H86P|SSR3_ENST00000478842.1_5'Flank|SSR3_ENST00000496050.1_Missense_Mutation_p.H34P|SSR3_ENST00000476217.1_Missense_Mutation_p.H86P|SSR3_ENST00000463503.1_Missense_Mutation_p.H34P	NM_007107.3	NP_009038.1	Q9UNL2	SSRG_HUMAN	signal sequence receptor, gamma (translocon-associated protein gamma)	86					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	integral component of endoplasmic reticulum membrane (GO:0030176)|Sec61 translocon complex (GO:0005784)				endometrium(1)|prostate(2)	3			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TACTTACTTGTGCTTGAGAAC	0.313																																					p.H86P		Atlas-SNP	.											.	SSR3	17	.	0			c.A257C						.						104	96	98					3																	156271447		2203	4300	6503	SO:0001583	missense	6747	exon2			TACTTGTGCTTGA	BC017203	CCDS3176.1	3q25.31	2004-02-27			ENSG00000114850	ENSG00000114850			11325	protein-coding gene	gene with protein product		606213					Standard	NM_007107		Approved	TRAPG	uc003fau.3	Q9UNL2	OTTHUMG00000158632	ENST00000265044.2:c.257A>C	chr3.hg19:g.156271447T>G	ENSP00000265044:p.His86Pro	135.0	0.0		99.0	21.0	NM_007107	B2R7D0|B4E2P2|D3DNK5|Q549M4	Missense_Mutation	SNP	ENST00000265044.2	hg19	CCDS3176.1	.	.	.	.	.	.	.	.	.	.	T	17.69	3.451855	0.63290	.	.	ENSG00000114850	ENST00000265044;ENST00000467789;ENST00000476217;ENST00000463503;ENST00000496050	.	.	.	5.03	5.03	0.67393	.	0.141527	0.64402	D	0.000005	T	0.72391	0.3454	M	0.89095	3.005	0.80722	D	1	B;B	0.16802	0.019;0.018	B;B	0.19391	0.022;0.025	T	0.72030	-0.4413	9	0.40728	T	0.16	.	15.0687	0.72017	0.0:0.0:0.0:1.0	.	86;86	B4E2P2;Q9UNL2	.;SSRG_HUMAN	P	86;86;86;34;34	.	ENSP00000265044:H86P	H	-	2	0	SSR3	157754141	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.758000	0.85224	2.017000	0.59298	0.528000	0.53228	CAC	.	.		0.313	SSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351521.1	NM_007107		G	156271447	T	G	156271447	3	3	75	1	0	0	0	0	1	0	0	0	15207	1696	59	5	316	5	SSR3	3	156271447	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	20550300	156271447	41750983	30	10153										
TP63	8626	hgsc.bcm.edu	37	chr3	189590736	189590736	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tcctcagcacacaattgaaaCgtacaggcaacagcaacagc	7	13	1	1	rs558374141		TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr3:189590736C>T	ENST00000264731.3	+	10	1390	c.1301C>T	c.(1300-1302)aCg>aTg	p.T434M	TP63_ENST00000456148.1_Missense_Mutation_p.T336M|TP63_ENST00000382063.4_Missense_Mutation_p.T349M|TP63_ENST00000418709.2_Missense_Mutation_p.T434M|TP63_ENST00000392463.2_Missense_Mutation_p.T340M|TP63_ENST00000437221.1_Missense_Mutation_p.T340M|TP63_ENST00000392460.3_Missense_Mutation_p.T434M|TP63_ENST00000449992.1_Missense_Mutation_p.T255M|TP63_ENST00000320472.5_Missense_Mutation_p.T434M|TP63_ENST00000440651.2_Missense_Mutation_p.T430M|TP63_ENST00000392461.3_Missense_Mutation_p.T340M|TP63_ENST00000354600.5_Missense_Mutation_p.T340M	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	434	Oligomerization.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		ACAATTGAAACGTACAGGCAA	0.463										HNSCC(45;0.13)			C|||	1	0.000199681	0	0	5008	,	,		21745	0		0	False		,,,				2504	0.001				p.T434M		Atlas-SNP	.											.	TP63	187	.	0			c.C1301T						.						184	149	161					3																	189590736		2203	4300	6503	SO:0001583	missense	8626	exon10			TTGAAACGTACAG	AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"tumor protein p73-like", "tumor protein p53-like", "tumor protein p53-competing protein"	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.1301C>T	chr3.hg19:g.189590736C>T	ENSP00000264731:p.Thr434Met	288.0	0.0		297.0	117.0	NM_001114979	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Missense_Mutation	SNP	ENST00000264731.3	hg19	CCDS3293.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152904	0.57259	.	.	ENSG00000073282	ENST00000264731;ENST00000418709;ENST00000320472;ENST00000392460;ENST00000440651;ENST00000382063;ENST00000354600;ENST00000437221;ENST00000392463;ENST00000392461;ENST00000449992;ENST00000456148	D;D;D;D;D;D;D;D;D;D;D;D	0.99680	-6.05;-6.32;-6.29;-6.29;-6.06;-6.37;-6.04;-6.32;-6.28;-6.28;-6.38;-6.04	5.81	4.94	0.65067	.	0.105498	0.64402	D	0.000002	D	0.99143	0.9704	L	0.34521	1.04	0.52099	D	0.999946	D;D;D;D;D;D;D;D;D	0.71674	0.996;0.996;0.996;0.993;0.997;0.977;0.996;0.994;0.998	P;P;P;P;P;P;P;P;D	0.64042	0.855;0.897;0.855;0.855;0.888;0.677;0.897;0.791;0.921	D	0.98400	1.0567	9	.	.	.	-19.9144	9.7402	0.40413	0.0:0.7865:0.1399:0.0736	.	255;434;340;340;340;340;434;434;434	Q9H3D4-10;Q9H3D4-7;Q9H3D4-4;Q9H3D4-2;Q9H3D4-6;C9D7C9;Q9H3D4-3;Q9H3D4;Q9H3D4-5	.;.;.;.;.;.;.;P63_HUMAN;.	M	434;434;434;434;430;349;340;340;340;340;255;336	ENSP00000264731:T434M;ENSP00000407144:T434M;ENSP00000317510:T434M;ENSP00000376253:T434M;ENSP00000394337:T430M;ENSP00000371495:T349M;ENSP00000346614:T340M;ENSP00000392488:T340M;ENSP00000376256:T340M;ENSP00000376254:T340M;ENSP00000387839:T255M;ENSP00000389485:T336M	.	T	+	2	0	TP63	191073430	1.000000	0.71417	0.818000	0.32626	0.916000	0.54674	4.479000	0.60236	1.455000	0.47813	0.655000	0.94253	ACG	.	.		0.463	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722		T	189590736	C	T	189590736	3	4	75	1	0	0	0	0	1	0	0	0	16407	536	19	1	1385	1	TP63	3	189590736	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	33319289	189590736	8431694	31	10154										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	193025125	193025125	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tttctactcaccccacagtcGttagctccatctccacacat	3	17	3	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr3:193025125G>A	ENST00000342358.4	-	22	2676	c.2559C>T	c.(2557-2559)aaC>aaT	p.N853N	ATP13A5_ENST00000495496.1_5'UTR|ATP13A5-AS1_ENST00000414634.1_RNA	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	853						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		CCCCACAGTCGTTAGCTCCAT	0.458																																					p.N853N		Atlas-SNP	.											ATP13A5,NS,neuroblastoma,0,1	ATP13A5	171	.	0			c.C2559T						.						104	90	95					3																	193025125		2203	4300	6503	SO:0001819	synonymous_variant	344905	exon22			ACAGTCGTTAGCT	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.2559C>T	chr3.hg19:g.193025125G>A		91.0	0.0		114.0	38.0	NM_198505	Q6UWS4|Q6ZWL0	Silent	SNP	ENST00000342358.4	hg19	CCDS33914.1																																																																																			.	.		0.458	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		A	193025125	G	A	193025125	2	1	75	1	0	0	0	0	0	0	0	1	1127	1136	40	1		1	ATP13A5	3	193025125	Silent	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	3434389	193025125	4997305	32	10155										
GPR125	166647	hgsc.bcm.edu	37	chr4	22425952	22425952	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gccaacatgatgttacttgcAatgtcaaccatcacgtcacc	6	13	3	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr4:22425952A>G	ENST00000334304.5	-	11	1736	c.1467T>C	c.(1465-1467)atT>atC	p.I489I	GPR125_ENST00000508133.1_Silent_p.I263I|GPR125_ENST00000282943.5_5'UTR|GPR125_ENST00000502482.1_Silent_p.I489I	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	489					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				TGTTACTTGCAATGTCAACCA	0.448																																					p.I489I		Atlas-SNP	.											.	GPR125	118	.	0			c.T1467C						.						137	121	126					4																	22425952		2203	4300	6503	SO:0001819	synonymous_variant	166647	exon11			ACTTGCAATGTCA	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.1467T>C	chr4.hg19:g.22425952A>G		182.0	0.0		172.0	100.0	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Silent	SNP	ENST00000334304.5	hg19	CCDS33964.1																																																																																			.	.		0.448	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			G	22425952	A	G	22425952	2	3	75	1	0	0	0	0	0	0	0	1	6647	126	5	2		2	GPR125	4	22425952	Silent	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10		22425952	168728324	33	10156										
ATP10D	57205	hgsc.bcm.edu	37	chr4	47525056	47525056	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aaaaaatacattgaccgatgCtggaaagacgttactgttgg	10	6	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr4:47525056C>G	ENST00000273859.3	+	4	782	c.513C>G	c.(511-513)tgC>tgG	p.C171W	ATP10D_ENST00000504445.1_Missense_Mutation_p.C171W	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	171			C -> R (in dbSNP:rs7683838).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						TTGACCGATGCTGGAAAGACG	0.338																																					p.C171W		Atlas-SNP	.											.	ATP10D	168	.	0			c.C513G						.						86	78	81					4																	47525056		2203	4300	6503	SO:0001583	missense	57205	exon4			CCGATGCTGGAAA	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.513C>G	chr4.hg19:g.47525056C>G	ENSP00000273859:p.Cys171Trp	136.0	0.0		77.0	20.0	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	hg19	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.129973	0.37630	.	.	ENSG00000145246	ENST00000273859;ENST00000504445	T;T	0.74737	-0.87;-0.87	5.94	2.21	0.28008	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.173510	0.52532	D	0.000077	T	0.79563	0.4467	M	0.66939	2.045	0.49051	D	0.999748	D;P	0.65815	0.995;0.886	P;P	0.61275	0.886;0.762	T	0.74731	-0.3566	10	0.38643	T	0.18	-9.2528	8.3469	0.32279	0.0:0.6113:0.0:0.3887	.	171;171	Q9P241;Q6PEW3	AT10D_HUMAN;.	W	171	ENSP00000273859:C171W;ENSP00000420909:C171W	ENSP00000273859:C171W	C	+	3	2	ATP10D	47219813	1.000000	0.71417	0.932000	0.37286	0.540000	0.34992	1.258000	0.32944	0.095000	0.17434	-0.439000	0.05793	TGC	.	.		0.338	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		G	47525056	C	G	47525056	3	3	75	1	0	0	0	0	1	0	0	0	1118	805	28	4	523	4	ATP10D	4	47525056	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	25099104	47525056	143629220	34	10157										
RNF150	57484	hgsc.bcm.edu	37	chr4	141888999	141888999	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tccttcccttttggctcaggAatcattatggccacgatgtc	8	12	2	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr4:141888999A>G	ENST00000515673.2	-	2	546	c.513T>C	c.(511-513)atT>atC	p.I171I	RNF150_ENST00000515057.1_5'UTR|RNF150_ENST00000507500.1_Silent_p.I171I|RNF150_ENST00000420921.2_Silent_p.I30I|RNF150_ENST00000379512.2_Silent_p.I30I|RNF150_ENST00000306799.3_Silent_p.I171I			Q9ULK6	RN150_HUMAN	ring finger protein 150	171	PA.					integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					TTGGCTCAGGAATCATTATGG	0.473																																					p.I171I		Atlas-SNP	.											.	RNF150	94	.	0			c.T513C						.						217	185	196					4																	141888999		2203	4300	6503	SO:0001819	synonymous_variant	57484	exon2			CTCAGGAATCATT	AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"RING-type (C3HC4) zinc fingers"	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.513T>C	chr4.hg19:g.141888999A>G		88.0	0.0		49.0	25.0	NM_020724	Q3T1D0|Q6ZNW6	Silent	SNP	ENST00000515673.2	hg19	CCDS34065.1																																																																																			.	.		0.473	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090		G	141888999	A	G	141888999	2	3	75	1	0	0	0	0	0	0	0	1	13466	242	9	2		2	RNF150	4	141888999	Silent	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	94363943	141888999	49265277	35	10158										
ASB5	140458	hgsc.bcm.edu	37	chr4	177146466	177146466	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	accttgacttgctgcttcatGtagtggtgatcgatctgccc	10	11	2	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr4:177146466G>A	ENST00000296525.3	-	2	336	c.223C>T	c.(223-225)Cat>Tat	p.H75Y	ASB5_ENST00000512254.1_Missense_Mutation_p.H22Y|ASB5_ENST00000511879.1_5'UTR	NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	75					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		GCTGCTTCATGTAGTGGTGAT	0.373																																					p.H75Y		Atlas-SNP	.											.	ASB5	88	.	0			c.C223T						.						91	95	94					4																	177146466		2203	4300	6503	SO:0001583	missense	140458	exon2			CTTCATGTAGTGG	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"Ankyrin repeat domain containing"	17180	protein-coding gene	gene with protein product		615050	"ankyrin repeat and SOCS box-containing 5"				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.223C>T	chr4.hg19:g.177146466G>A	ENSP00000296525:p.His75Tyr	174.0	0.0		109.0	47.0	NM_080874	Q8N7B5	Missense_Mutation	SNP	ENST00000296525.3	hg19	CCDS3827.1	.	.	.	.	.	.	.	.	.	.	G	31	5.085281	0.94100	.	.	ENSG00000164122	ENST00000296525;ENST00000512254	T;T	0.70399	-0.48;-0.48	6.16	6.16	0.99307	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.84692	0.5528	M	0.71871	2.18	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.985;0.993	D	0.83855	0.0265	10	0.62326	D	0.03	-27.2356	20.8598	0.99761	0.0:0.0:1.0:0.0	.	75;22	Q8WWX0;Q8N7B5	ASB5_HUMAN;.	Y	75;22	ENSP00000296525:H75Y;ENSP00000422877:H22Y	ENSP00000296525:H75Y	H	-	1	0	ASB5	177383460	1.000000	0.71417	0.978000	0.43139	0.938000	0.57974	9.110000	0.94302	2.937000	0.99478	0.650000	0.86243	CAT	.	.		0.373	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1			A	177146466	G	A	177146466	3	1	75	1	0	0	0	0	1	0	0	0	1026	1377	48	3	790	3	ASB5	4	177146466	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	35257467	177146466	14007810	36	10159										
CLPTM1L	81037	hgsc.bcm.edu	37	chr5	1330438	1330438	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ccgggaccagcaccagcaggCtcgtctgctcgtccagcagg	13	16	1	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr5:1330438C>G	ENST00000320895.5	-	9	1294	c.1037G>C	c.(1036-1038)aGc>aCc	p.S346T	CLPTM1L_ENST00000507807.1_Intron|CLPTM1L_ENST00000320927.6_Intron	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	346					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		CACCAGCAGGCTCGTCTGCTC	0.642																																					p.S346T		Atlas-SNP	.											.	CLPTM1L	60	.	0			c.G1037C						.						84	78	80					5																	1330438		2203	4299	6502	SO:0001583	missense	81037	exon9			AGCAGGCTCGTCT	AK027306	CCDS3862.1	5p15.33	2008-02-05			ENSG00000049656	ENSG00000049656			24308	protein-coding gene	gene with protein product	"cisplatin resistance related protein"	612585				11162647	Standard	NM_030782		Approved	FLJ14400, CRR9	uc003jch.3	Q96KA5	OTTHUMG00000131015	ENST00000320895.5:c.1037G>C	chr5.hg19:g.1330438C>G	ENSP00000313854:p.Ser346Thr	221.0	0.0		166.0	9.0	NM_030782	D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Missense_Mutation	SNP	ENST00000320895.5	hg19	CCDS3862.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.908983	0.92107	.	.	ENSG00000049656	ENST00000320895	T	0.59083	0.29	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.80994	0.4731	M	0.90922	3.16	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85161	0.0992	10	0.54805	T	0.06	-33.4482	16.7303	0.85433	0.0:1.0:0.0:0.0	.	346	Q96KA5	CLP1L_HUMAN	T	346	ENSP00000313854:S346T	ENSP00000313854:S346T	S	-	2	0	CLPTM1L	1383438	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	7.254000	0.78329	2.213000	0.71641	0.655000	0.94253	AGC	.	.		0.642	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2	NM_030782		G	1330438	C	G	1330438	3	3	75	1	0	0	0	0	1	0	0	0	3557	797	28	4	615	4	CLPTM1L	5	1330438	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10		1330438	179584822	37	10160										
RGNEF	64283	hgsc.bcm.edu	37	chr5	73069858	73069858	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tccaagctggtggaagacgtCacaaagtgagtttagctact	11	8	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr5:73069858C>A	ENST00000426542.2	+	4	674	c.654C>A	c.(652-654)gtC>gtA	p.V218V	ARHGEF28_ENST00000437974.1_Silent_p.V218V|ARHGEF28_ENST00000287898.5_Silent_p.V218V|ARHGEF28_ENST00000545377.1_Silent_p.V218V|ARHGEF28_ENST00000296794.6_Silent_p.V218V|ARHGEF28_ENST00000513042.2_Silent_p.V218V			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	218					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										TGGAAGACGTCACAAAGTGAG	0.453																																					p.V218V		Atlas-SNP	.											.	.	.	.	0			c.C654A						.						24	23	23					5																	73069858		1893	4113	6006	SO:0001819	synonymous_variant	64283	exon5			AGACGTCACAAAG		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.654C>A	chr5.hg19:g.73069858C>A		81.0	0.0		65.0	17.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	hg19	CCDS54870.1																																																																																			.	.		0.453	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			A	73069858	C	A	73069858	2	1	75	1	0	0	0	0	0	0	0	1	13298	813	29	3		3	RGNEF	5	73069858	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	71739420	73069858	107845402	38	10161										
BRD8	10902	hgsc.bcm.edu	37	chr5	137485482	137485482	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ctttggattcttgctgagccTccccctaggaatgccaggaa	10	12	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr5:137485482T>C	ENST00000254900.5	-	23	3496	c.3125A>G	c.(3124-3126)gAg>gGg	p.E1042G		NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	1042					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTGCTGAGCCTCCCCCTAGGA	0.458																																					p.E1042G		Atlas-SNP	.											.	BRD8	192	.	0			c.A3125G						.						125	111	115					5																	137485482		2203	4300	6503	SO:0001583	missense	10902	exon23			TGAGCCTCCCCCT	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.3125A>G	chr5.hg19:g.137485482T>C	ENSP00000254900:p.Glu1042Gly	93.0	0.0		72.0	5.0	NM_139199	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Missense_Mutation	SNP	ENST00000254900.5	hg19	CCDS4198.1	.	.	.	.	.	.	.	.	.	.	T	1.823	-0.471730	0.04445	.	.	ENSG00000112983	ENST00000254900;ENST00000427976	T;T	0.28454	1.88;1.61	4.84	2.45	0.29901	.	0.925692	0.08964	N	0.868328	T	0.17152	0.0412	N	0.14661	0.345	0.19575	N	0.999967	B	0.02656	0.0	B	0.04013	0.001	T	0.26849	-1.0091	10	0.23891	T	0.37	.	7.0267	0.24944	0.0:0.2081:0.0:0.7919	.	1042	Q9H0E9	BRD8_HUMAN	G	1042;148	ENSP00000254900:E1042G;ENSP00000392646:E148G	ENSP00000254900:E1042G	E	-	2	0	BRD8	137513381	0.001000	0.12720	0.289000	0.24876	0.126000	0.20510	0.967000	0.29344	0.871000	0.35750	0.528000	0.53228	GAG	.	.		0.458	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		C	137485482	T	C	137485482	3	2	75	1	0	0	0	0	1	0	0	0	1508	1551	54	2	602	2	BRD8	5	137485482	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	64415624	137485482	43429778	39	10162										
DCDC2	51473	hgsc.bcm.edu	37	chr6	24278324	24278324	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tctttaattttacattttgtTtcaatttcgtcagtttttct	3	6	4	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:24278324T>A	ENST00000378454.3	-	7	1176	c.875A>T	c.(874-876)aAa>aTa	p.K292I		NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	292					cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TACATTTTGTTTCAATTTCGT	0.328																																					p.K292I		Atlas-SNP	.											.	DCDC2	53	.	0			c.A875T						.						143	138	140					6																	24278324		2203	4300	6503	SO:0001583	missense	51473	exon8			TTTTGTTTCAATT	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.875A>T	chr6.hg19:g.24278324T>A	ENSP00000367715:p.Lys292Ile	112.0	0.0		71.0	13.0	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Missense_Mutation	SNP	ENST00000378454.3	hg19	CCDS4550.1	.	.	.	.	.	.	.	.	.	.	T	16.73	3.205264	0.58234	.	.	ENSG00000146038	ENST00000378454	T	0.02890	4.12	4.75	4.75	0.60458	.	0.339687	0.34700	N	0.003748	T	0.03220	0.0094	L	0.39397	1.21	0.80722	D	1	D	0.58970	0.984	P	0.55161	0.77	T	0.56798	-0.7919	10	0.44086	T	0.13	0.0289	12.5327	0.56124	0.0:0.0:0.0:1.0	.	292	Q9UHG0	DCDC2_HUMAN	I	292	ENSP00000367715:K292I	ENSP00000367715:K292I	K	-	2	0	DCDC2	24386303	1.000000	0.71417	0.891000	0.34965	0.432000	0.31715	4.054000	0.57434	2.120000	0.65058	0.533000	0.62120	AAA	.	.		0.328	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356		A	24278324	T	A	24278324	3	1	75	1	0	0	0	0	1	0	0	0	4287	1841	64	4	571	4	DCDC2	6	24278324	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10		24278324	146836743	40	10163										
SLC17A1	6568	hgsc.bcm.edu	37	chr6	25799088	25799088	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	actataaggtagaaaattagGccagtcacattaatggctgc	9	7	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:25799088G>C	ENST00000244527.4	-	12	1444	c.1329C>G	c.(1327-1329)ggC>ggG	p.G443G	SLC17A1_ENST00000468082.1_Silent_p.G389G|SLC17A1_ENST00000476801.1_Silent_p.G443G|SLC17A1_ENST00000427328.1_Silent_p.G389G	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	443					ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						AGAAAATTAGGCCAGTCACAT	0.388																																					p.G443G		Atlas-SNP	.											.	SLC17A1	71	.	0			c.C1329G						.						94	92	93					6																	25799088		2203	4300	6503	SO:0001819	synonymous_variant	6568	exon12			AATTAGGCCAGTC		CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"Solute carriers"	10929	protein-coding gene	gene with protein product		182308	"solute carrier family 17 (sodium phosphate), member 1"	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.1329C>G	chr6.hg19:g.25799088G>C		61.0	0.0		36.0	13.0	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Silent	SNP	ENST00000244527.4	hg19	CCDS4565.1																																																																																			.	.		0.388	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2			C	25799088	G	C	25799088	2	2	75	1	0	0	0	0	0	0	0	1	14431	1190	42	4		4	SLC17A1	6	25799088	Silent	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	1520764	25799088	145315979	41	10164										
HIST1H4C	8364	hgsc.bcm.edu	37	chr6	26104441	26104441	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cacagccatggatgtagtatAtgccctaaaacgtcaggggc	11	10	1	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:26104441A>G	ENST00000377803.2	+	1	338	c.266A>G	c.(265-267)tAt>tGt	p.Y89C		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	89					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7						GATGTAGTATATGCCCTAAAA	0.478																																					p.Y89C		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.A266G						.						65	58	61					6																	26104441		2203	4300	6503	SO:0001583	missense	8364	exon1			TAGTATATGCCCT	X60486	CCDS4583.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000197061	ENSG00000197061		"Histones / Replication-dependent"	4787	protein-coding gene	gene with protein product		602827	"H4 histone family, member G", "histone 1, H4c"	H4FG		9119399, 12408966	Standard	NM_003542		Approved	H4/g, dJ221C16.1	uc003ngi.3	P62805	OTTHUMG00000014429	ENST00000377803.2:c.266A>G	chr6.hg19:g.26104441A>G	ENSP00000367034:p.Tyr89Cys	79.0	0.0		83.0	16.0	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377803.2	hg19	CCDS4583.1	.	.	.	.	.	.	.	.	.	.	.	15.35	2.807103	0.50421	.	.	ENSG00000197061	ENST00000377803	T	0.68025	-0.3	4.56	4.56	0.56223	.	0.000000	0.64402	D	0.000001	T	0.70430	0.3223	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.75207	-0.3399	7	0.66056	D	0.02	.	13.5381	0.61657	1.0:0.0:0.0:0.0	.	.	.	.	C	89	ENSP00000367034:Y89C	ENSP00000367034:Y89C	Y	+	2	0	HIST1H4C	26212420	1.000000	0.71417	1.000000	0.80357	0.068000	0.16541	9.139000	0.94554	2.049000	0.60858	0.454000	0.30748	TAT	.	.		0.478	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542		G	26104441	A	G	26104441	3	3	75	1	0	0	0	0	1	0	0	0	7176	449	16	2	268	2	HIST1H4C	6	26104441	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	305353	26104441	145010626	42	10165										
BTN2A1	11120	hgsc.bcm.edu	37	chr6	26468554	26468554	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttgccgggtgggcgtcttccTggactatgaagctggagatg	16	8	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:26468554T>A	ENST00000312541.5	+	8	1609	c.1361T>A	c.(1360-1362)cTg>cAg	p.L454Q	BTN2A1_ENST00000429381.1_3'UTR|BTN2A1_ENST00000541522.1_Missense_Mutation_p.L393Q|BTN2A1_ENST00000469185.1_Intron	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	454	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						GGCGTCTTCCTGGACTATGAA	0.547																																					p.L454Q		Atlas-SNP	.											.	BTN2A1	118	.	0			c.T1361A						.						136	119	125					6																	26468554		2203	4298	6501	SO:0001583	missense	11120	exon8			TCTTCCTGGACTA	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.1361T>A	chr6.hg19:g.26468554T>A	ENSP00000312158:p.Leu454Gln	132.0	0.0		121.0	24.0	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	hg19	CCDS4613.1	.	.	.	.	.	.	.	.	.	.	T	16.68	3.191563	0.58017	.	.	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000265424	T;T	0.79940	-1.32;-1.32	2.72	1.54	0.23209	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.39687	N	0.001285	D	0.88894	0.6561	H	0.97365	3.99	0.32474	N	0.542464	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.85022	0.0912	10	0.87932	D	0	.	6.2113	0.20631	0.0:0.1339:0.0:0.8661	.	393;454	B4DLP9;Q7KYR7	.;BT2A1_HUMAN	Q	454;393;440	ENSP00000312158:L454Q;ENSP00000443909:L393Q	ENSP00000265424:L440Q	L	+	2	0	BTN2A1	26576533	1.000000	0.71417	0.918000	0.36340	0.743000	0.42351	6.022000	0.70839	0.462000	0.27095	0.402000	0.26972	CTG	.	.		0.547	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049		A	26468554	T	A	26468554	3	1	75	1	0	0	0	0	1	0	0	0	1562	1580	55	4	1414	4	BTN2A1	6	26468554	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	364113	26468554	144646513	43	10166										
NKAPL	222698	hgsc.bcm.edu	37	chr6	28227197	28227197	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tccgaggacatcgtgggctcTcggagaaggcgacgcagctc	15	12	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:28227197T>C	ENST00000343684.3	+	1	100	c.48T>C	c.(46-48)tcT>tcC	p.S16S	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	16										breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						TCGTGGGCTCTCGGAGAAGGC	0.662																																					p.S16S		Atlas-SNP	.											.	NKAPL	72	.	0			c.T48C						.						32	30	30					6																	28227197		2201	4295	6496	SO:0001819	synonymous_variant	222698	exon1			GGGCTCTCGGAGA	BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 194"	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.48T>C	chr6.hg19:g.28227197T>C		91.0	0.0		98.0	19.0	NM_001007531	Q3MIV1|Q9H4Q7	Silent	SNP	ENST00000343684.3	hg19	CCDS34353.1																																																																																			.	.		0.662	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1			C	28227197	T	C	28227197	2	2	75	1	0	0	0	0	0	0	0	1	10449	1538	54	2		2	NKAPL	6	28227197	Silent	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	1758643	28227197	142887870	44	10167										
BAT3	7917	hgsc.bcm.edu	37	chr6	31608213	31608213	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tcagctgaagctccatcctgTtcatcccgggagcccccctc	8	18	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:31608213T>C	ENST00000375964.6	-	22	3310	c.2997A>G	c.(2995-2997)gaA>gaG	p.E999E	BAG6_ENST00000211379.5_Silent_p.E993E|BAG6_ENST00000375976.4_Silent_p.E993E|BAG6_ENST00000470875.1_5'Flank|BAG6_ENST00000404765.2_Silent_p.E1029E|BAG6_ENST00000439687.2_Intron|BAG6_ENST00000362049.6_Silent_p.E993E	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	999					brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						CTCCATCCTGTTCATCCCGGG	0.597																																					p.E999E		Atlas-SNP	.											.	BAG6	73	.	0			c.A2997G						.						112	131	124					6																	31608213		1511	2709	4220	SO:0001819	synonymous_variant	7917	exon22			ATCCTGTTCATCC	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"HLA-B associated transcript 3"	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.2997A>G	chr6.hg19:g.31608213T>C		82.0	0.0		68.0	11.0	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Silent	SNP	ENST00000375964.6	hg19	CCDS47403.1	.	.	.	.	.	.	.	.	.	.	T	6.876	0.531031	0.13127	.	.	ENSG00000204463	ENST00000441793	.	.	.	5.54	-5.72	0.02406	.	.	.	.	.	T	0.20700	0.0498	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42531	-0.9446	4	.	.	.	.	2.6061	0.04878	0.1032:0.3374:0.2112:0.3482	.	.	.	.	S	142	.	.	N	-	2	0	BAG6	31716192	0.976000	0.34144	0.841000	0.33234	0.944000	0.59088	-0.251000	0.08818	-0.639000	0.05502	-0.327000	0.08410	AAC	.	.		0.597	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703		C	31608213	T	C	31608213	2	2	75	1	0	0	0	0	0	0	0	1	1322	1722	60	2		2	BAT3	6	31608213	Silent	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	3381016	31608213	139506854	45	10168										
MSH5	4439	hgsc.bcm.edu	37	chr6	31726650	31726650	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gcagtgtcatctacatccctCtggtgagggcaggagagtgg	15	9	3	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:31726650C>G	ENST00000375755.3	+	15	1610	c.1324C>G	c.(1324-1326)Ctg>Gtg	p.L442V	MSH5_ENST00000431848.2_Missense_Mutation_p.L141V|MSH5_ENST00000534153.4_Missense_Mutation_p.L459V|MSH5-SAPCD1_ENST00000493662.2_Missense_Mutation_p.L459V|RNU6-850P_ENST00000516934.1_RNA|MSH5_ENST00000375750.3_Missense_Mutation_p.L442V|MSH5_ENST00000395853.1_Missense_Mutation_p.L116V|MSH5_ENST00000375742.3_Missense_Mutation_p.L459V|MSH5_ENST00000375740.3_Missense_Mutation_p.L459V|MSH5_ENST00000375703.3_Missense_Mutation_p.L442V	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	442					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						CTACATCCCTCTGGTGAGGGC	0.493								Direct reversal of damage;Mismatch excision repair (MMR)																													p.L459V		Atlas-SNP	.											.	MSH5	108	.	0			c.C1375G						.						82	78	79					6																	31726650		2203	4300	6503	SO:0001583	missense	4439	exon15			ATCCCTCTGGTGA	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"mutS (E. coli) homolog 5", "mutS homolog 5 (E. coli)"			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.1324C>G	chr6.hg19:g.31726650C>G	ENSP00000364908:p.Leu442Val	128.0	0.0		93.0	22.0	NM_025259	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Missense_Mutation	SNP	ENST00000375755.3	hg19	CCDS4720.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631813	0.46944	.	.	ENSG00000204410	ENST00000375755;ENST00000375742;ENST00000375750;ENST00000534153;ENST00000375703;ENST00000375740;ENST00000450148;ENST00000431848;ENST00000395853	D;D;D;D;D;D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47	5.42	3.29	0.37713	DNA mismatch repair protein MutS, clamp (1);DNA mismatch repair protein MutS, core (3);	0.000000	0.64402	D	0.000005	T	0.75852	0.3906	L	0.53249	1.67	0.45390	D	0.998374	P;P;P;B;P	0.39071	0.498;0.475;0.531;0.02;0.658	B;B;P;B;P	0.45428	0.211;0.259;0.479;0.07;0.48	T	0.73594	-0.3933	9	0.02654	T	1	-18.1329	7.6032	0.28087	0.0:0.7142:0.0:0.2858	.	127;459;442;442;459	Q59EC5;O43196-4;O43196;O43196-2;O43196-3	.;.;MSH5_HUMAN;.;.	V	442;459;442;459;442;459;284;141;116	ENSP00000364908:L442V;ENSP00000364894:L459V;ENSP00000364903:L442V;ENSP00000431693:L459V;ENSP00000364855:L442V;ENSP00000364892:L459V;ENSP00000394971:L284V;ENSP00000416784:L141V;ENSP00000379194:L116V	ENSP00000364855:L442V	L	+	1	2	MSH5	31834629	0.972000	0.33761	1.000000	0.80357	0.982000	0.71751	0.692000	0.25482	1.293000	0.44690	0.591000	0.81541	CTG	.	.		0.493	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4			G	31726650	C	G	31726650	3	3	75	1	0	0	0	0	1	0	0	0	9882	912	32	4	1429	4	MSH5	6	31726650	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	118437	31726650	139388417	46	10169										
CYP39A1	51302	hgsc.bcm.edu	37	chr6	46609971	46609971	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	attttagaaacacattaattCcttcttcttcagtaacaaag	3	8	3	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:46609971C>T	ENST00000275016.2	-	2	445	c.242G>A	c.(241-243)gGa>gAa	p.G81E		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	81					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						CACATTAATTCCTTCTTCTTC	0.308																																					p.G81E		Atlas-SNP	.											.	CYP39A1	41	.	0			c.G242A						.						70	72	72					6																	46609971		2203	4295	6498	SO:0001583	missense	51302	exon2			TTAATTCCTTCTT	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"Cytochrome P450s"	17449	protein-coding gene	gene with protein product		605994	"cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.242G>A	chr6.hg19:g.46609971C>T	ENSP00000275016:p.Gly81Glu	79.0	0.0		48.0	4.0	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	hg19	CCDS4916.1	.	.	.	.	.	.	.	.	.	.	C	18.85	3.711223	0.68730	.	.	ENSG00000146233	ENST00000275016	T	0.68624	-0.34	4.7	4.7	0.59300	.	0.066550	0.64402	D	0.000014	T	0.76154	0.3948	M	0.70275	2.135	0.49483	D	0.999797	D;D	0.76494	0.999;0.999	D;D	0.68621	0.959;0.959	T	0.78290	-0.2261	10	0.54805	T	0.06	-10.742	16.7908	0.85589	0.0:1.0:0.0:0.0	.	81;81	B7Z786;Q9NYL5	.;CP39A_HUMAN	E	81	ENSP00000275016:G81E	ENSP00000275016:G81E	G	-	2	0	CYP39A1	46717930	0.977000	0.34250	1.000000	0.80357	0.980000	0.70556	2.232000	0.43018	2.321000	0.78463	0.563000	0.77884	GGA	.	.		0.308	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1			T	46609971	C	T	46609971	3	4	75	1	0	0	0	0	1	0	0	0	4179	855	30	3	1211	3	CYP39A1	6	46609971	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	14883321	46609971	124505096	47	10170										
RHAG	6005	hgsc.bcm.edu	37	chr6	49583450	49583450	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agccaaagtaggccccaaagGcatggatcgtcattgatgct	11	10	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:49583450G>T	ENST00000371175.4	-	4	553	c.527C>A	c.(526-528)gCc>gAc	p.A176D	RHAG_ENST00000229810.7_Missense_Mutation_p.A176D	NM_000324.2	NP_000315.2	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	176					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|carbon dioxide transport (GO:0015670)|cellular ion homeostasis (GO:0006873)|erythrocyte development (GO:0048821)|multicellular organismal iron ion homeostasis (GO:0060586)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	39	Lung NSC(77;0.0255)					GGCCCCAAAGGCATGGATCGT	0.468																																					p.A176D	Ovarian(176;476 2003 7720 43408 44749)	Atlas-SNP	.											RHAG,NS,carcinoma,+1,1	RHAG	85	.	0			c.C527A						.						117	110	113					6																	49583450		2203	4300	6503	SO:0001583	missense	6005	exon4			CCAAAGGCATGGA		CCDS4927.1	6p12.3	2014-07-19	2006-02-23		ENSG00000112077	ENSG00000112077		"CD molecules", "Blood group antigens", "Solute carriers"	10006	protein-coding gene	gene with protein product		180297	"Rhesus blood group-associated glycoprotein"			9479501	Standard	NM_000324		Approved	RH50A, CD241, SLC42A1	uc003ozk.4	Q02094	OTTHUMG00000016377	ENST00000371175.4:c.527C>A	chr6.hg19:g.49583450G>T	ENSP00000360217:p.Ala176Asp	109.0	0.0		108.0	20.0	NM_000324	B2R8T8|O43514|O43515|Q7L8L3|Q9H454	Missense_Mutation	SNP	ENST00000371175.4	hg19	CCDS4927.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.778013	0.90195	.	.	ENSG00000112077	ENST00000371175;ENST00000229810;ENST00000418071;ENST00000539403	T;T	0.25250	1.81;1.81	5.76	5.76	0.90799	Ammonium transporter AmtB-like (3);	0.091506	0.85682	D	0.000000	T	0.52322	0.1727	M	0.91196	3.185	0.80722	D	1	D;P;P	0.52996	0.957;0.87;0.87	P;P;P	0.60345	0.873;0.824;0.824	T	0.62440	-0.6854	10	0.87932	D	0	-8.7584	18.9695	0.92709	0.0:0.0:1.0:0.0	.	176;176;176	O43515;Q9UHG9;Q02094	.;.;RHAG_HUMAN	D	176	ENSP00000360217:A176D;ENSP00000229810:A176D	ENSP00000229810:A176D	A	-	2	0	RHAG	49691409	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	9.410000	0.97335	2.726000	0.93360	0.655000	0.94253	GCC	.	.		0.468	RHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043806.1			T	49583450	G	T	49583450	3	4	75	1	0	0	0	0	1	0	0	0	13330	1203	42	3	730	3	RHAG	6	49583450	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	2973479	49583450	121531617	48	10171										
EYS	346007	hgsc.bcm.edu	37	chr6	65622636	65622636	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	catccagatgtacactcacaTctgaaataaaatattaaaat	3	8	2	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:65622636T>A	ENST00000370621.3	-	16	2908	c.2382A>T	c.(2380-2382)cgA>cgT	p.R794R	EYS_ENST00000370616.2_Splice_Site_p.R794R|EYS_ENST00000503581.1_Splice_Site_p.R794R			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	794	EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TACACTCACATCTGaaataaa	0.318																																					p.R794R		Atlas-SNP	.											.	EYS	527	.	0			c.A2382T						.						80	62	67					6																	65622636		692	1591	2283	SO:0001630	splice_region_variant	346007	exon16			CTCACATCTGAAA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2382-1A>T	chr6.hg19:g.65622636T>A		50.0	0.0		48.0	5.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	hg19																																																																																				.	.		0.318	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	Silent	A	65622636	T	A	65622636	5	1	75	1	0	0	0	0	0	0	1	0	5334	1449	50	4	7009	4	EYS	6	65622636	Splice_Site	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	16039186	65622636	105492431	49	10172										
MTO1	25821	hgsc.bcm.edu	37	chr6	74202034	74202034	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tccagagcccttgaagaagtAtactaaatgtagagagctgg	11	7	0	4			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:74202034A>G	ENST00000370300.4	+	11	1880	c.1790A>G	c.(1789-1791)tAt>tGt	p.Y597C	MTO1_ENST00000370305.1_Missense_Mutation_p.Y523C|MTO1_ENST00000498286.1_Missense_Mutation_p.Y572C|RP11-505P4.6_ENST00000423099.1_RNA|MTO1_ENST00000415954.2_Missense_Mutation_p.Y612C	NM_012123.3|NM_133645.2	NP_036255.2|NP_598400.1	Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	597					mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						TTGAAGAAGTATACTAAATGT	0.348																																					p.Y612C		Atlas-SNP	.											.	MTO1	59	.	0			c.A1835G						.						81	83	82					6																	74202034		2203	4300	6503	SO:0001583	missense	25821	exon11			AGAAGTATACTAA	AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297			19261	protein-coding gene	gene with protein product		614667	"mitochondrial translation optimization 1 homolog (S. cerevisiae)"			12011058, 22608499	Standard	NM_012123		Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000370300.4:c.1790A>G	chr6.hg19:g.74202034A>G	ENSP00000359323:p.Tyr597Cys	58.0	0.0		68.0	21.0	NM_001123226	B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	Missense_Mutation	SNP	ENST00000370300.4	hg19	CCDS4979.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.083815	0.36758	.	.	ENSG00000135297	ENST00000415954;ENST00000498286;ENST00000357845;ENST00000370305;ENST00000370300;ENST00000521156	.	.	.	5.39	4.17	0.49024	.	0.201325	0.34986	N	0.003537	T	0.34221	0.0890	L	0.39898	1.24	0.32282	N	0.567452	D;D;P;P	0.61697	0.967;0.99;0.893;0.9	P;P;P;P	0.55161	0.77;0.73;0.694;0.593	T	0.23797	-1.0178	9	0.40728	T	0.16	-14.812	7.7139	0.28694	0.669:0.0:0.0:0.331	.	612;475;572;597	Q9Y2Z2-6;Q9Y2Z2-2;Q9Y2Z2-4;Q9Y2Z2	.;.;.;MTO1_HUMAN	C	612;572;475;523;597;127	.	ENSP00000350506:Y475C	Y	+	2	0	MTO1	74258755	0.996000	0.38824	0.930000	0.37139	0.136000	0.21042	3.524000	0.53495	2.035000	0.60131	0.477000	0.44152	TAT	.	.		0.348	MTO1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041215.2	NM_012123		G	74202034	A	G	74202034	3	3	75	1	0	0	0	0	1	0	0	0	9962	449	16	2	1956	2	MTO1	6	74202034	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	8579398	74202034	96913033	50	10173										
FUT9	10690	hgsc.bcm.edu	37	chr6	96651384	96651384	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agacatcagttgggatctgaCaaatttacctcagcaagcta	8	9	3	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:96651384C>A	ENST00000302103.5	+	3	679	c.353C>A	c.(352-354)aCa>aAa	p.T118K		NM_006581.3	NP_006572.2	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3) fucosyltransferase)	118					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	34		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		TGGGATCTGACAAATTTACCT	0.463																																					p.T118K	Melanoma(98;1369 1476 6592 22940 26587)	Atlas-SNP	.											.	FUT9	79	.	0			c.C353A						.						116	103	107					6																	96651384		2203	4300	6503	SO:0001583	missense	10690	exon3			ATCTGACAAATTT	AB023021	CCDS5033.1	6q16	2013-02-26			ENSG00000172461	ENSG00000172461		"Fucosyltransferases"	4020	protein-coding gene	gene with protein product		606865				10386598, 10575236	Standard	NM_006581		Approved	Fuc-TIX	uc003pop.4	Q9Y231	OTTHUMG00000015236	ENST00000302103.5:c.353C>A	chr6.hg19:g.96651384C>A	ENSP00000302599:p.Thr118Lys	106.0	0.0		96.0	17.0	NM_006581	Q5T0W4	Missense_Mutation	SNP	ENST00000302103.5	hg19	CCDS5033.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.034890	0.35893	.	.	ENSG00000172461	ENST00000302103	T	0.21361	2.01	5.3	5.3	0.74995	.	0.098721	0.64402	D	0.000001	T	0.07413	0.0187	N	0.26042	0.785	0.54753	D	0.999986	B	0.13594	0.008	B	0.19666	0.026	T	0.11567	-1.0582	10	0.09084	T	0.74	-15.1735	18.3049	0.90177	0.0:1.0:0.0:0.0	.	118	Q9Y231	FUT9_HUMAN	K	118	ENSP00000302599:T118K	ENSP00000302599:T118K	T	+	2	0	FUT9	96758105	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	5.705000	0.68355	2.643000	0.89663	0.655000	0.94253	ACA	.	.		0.463	FUT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041554.2	NM_006581		A	96651384	C	A	96651384	3	1	75	1	0	0	0	0	1	0	0	0	6119	478	17	3	355	3	FUT9	6	96651384	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	22449350	96651384	74463683	51	10174										
AIM1	202	hgsc.bcm.edu	37	chr6	106969168	106969168	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	attttctgaattgtcaaaacTgaagaatgatgatatggaaa	8	3	2	5			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:106969168T>C	ENST00000369066.3	+	2	3348	c.2861T>C	c.(2860-2862)cTg>cCg	p.L954P		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TTGTCAAAACTGAAGAATGAT	0.363																																					p.L954P		Atlas-SNP	.											.	AIM1	161	.	0			c.T2861C						.						64	68	67					6																	106969168		2203	4300	6503	SO:0001583	missense	202	exon2			CAAAACTGAAGAA	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.2861T>C	chr6.hg19:g.106969168T>C	ENSP00000358062:p.Leu954Pro	99.0	0.0		111.0	45.0	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	T	5.771	0.326576	0.10900	.	.	ENSG00000112297	ENST00000369066	T	0.73469	-0.75	5.99	0.803	0.18691	.	1.097930	0.06923	N	0.809750	T	0.40196	0.1107	L	0.28192	0.835	0.24198	N	0.995521	B	0.17465	0.022	B	0.14578	0.011	T	0.30880	-0.9963	10	0.33940	T	0.23	.	9.1582	0.37005	0.0:0.3804:0.0:0.6196	.	954	Q9Y4K1	AIM1_HUMAN	P	954	ENSP00000358062:L954P	ENSP00000358062:L954P	L	+	2	0	AIM1	107075861	0.062000	0.20869	0.681000	0.30009	0.486000	0.33341	0.018000	0.13422	-0.074000	0.12820	0.533000	0.62120	CTG	.	.		0.363	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			C	106969168	T	C	106969168	3	2	75	1	0	0	0	0	1	0	0	0	430	1580	55	2	2867	2	AIM1	6	106969168	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	10317784	106969168	64145899	52	10175										
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117128020	117128020	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ctttattgaagagatcaaaaAcatggaattgcctcagaaat	7	6	2	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:117128020A>T	ENST00000310357.3	-	3	869	c.848T>A	c.(847-849)gTt>gAt	p.V283D	GPRC6A_ENST00000530250.1_Intron|GPRC6A_ENST00000368549.3_Missense_Mutation_p.V283D	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	283					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V283A(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		GAGATCAAAAACATGGAATTG	0.348																																					p.V283D		Atlas-SNP	.											GPRC6A,NS,carcinoma,0,1	GPRC6A	152	.	1	Substitution - Missense(1)	lung(1)	c.T848A						.						85	89	87					6																	117128020		2203	4299	6502	SO:0001583	missense	222545	exon3			TCAAAAACATGGA	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.848T>A	chr6.hg19:g.117128020A>T	ENSP00000309493:p.Val283Asp	45.0	0.0		47.0	12.0	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	hg19	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.002811	0.54254	.	.	ENSG00000173612	ENST00000310357;ENST00000368549	D;D	0.84070	-1.8;-1.8	6.17	6.17	0.99709	Extracellular ligand-binding receptor (1);	0.136963	0.32769	N	0.005669	D	0.89146	0.6632	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.965;0.998	D	0.89911	0.4052	10	0.62326	D	0.03	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	283;283	Q5T6X5-3;Q5T6X5	.;GPC6A_HUMAN	D	283	ENSP00000309493:V283D;ENSP00000357537:V283D	ENSP00000309493:V283D	V	-	2	0	GPRC6A	117234713	0.760000	0.28428	0.995000	0.50966	0.336000	0.28762	4.900000	0.63252	2.371000	0.80710	0.533000	0.62120	GTT	.	.		0.348	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			T	117128020	A	T	117128020	3	4	75	1	0	0	0	0	1	0	0	0	6737	43	2	4	1948	4	GPRC6A	6	117128020	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	10158852	117128020	53987047	53	10176										
FBXO30	84085	hgsc.bcm.edu	37	chr6	146127013	146127013	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ataaagtgcaccataagattCttcatcaacagacactaaac	4	10	3	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr6:146127013C>G	ENST00000237281.4	-	2	695	c.529G>C	c.(529-531)Gaa>Caa	p.E177Q		NM_032145.4	NP_115521.3	Q8TB52	FBX30_HUMAN	F-box protein 30	177							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		CCATAAGATTCTTCATCAACA	0.378																																					p.E177Q		Atlas-SNP	.											.	FBXO30	56	.	0			c.G529C						.						170	168	169					6																	146127013		2203	4300	6503	SO:0001583	missense	84085	exon2			AAGATTCTTCATC	AF248640	CCDS5208.1	6q24	2008-02-05	2004-06-15		ENSG00000118496	ENSG00000118496		"F-boxes /  "other""	15600	protein-coding gene	gene with protein product		609101	"F-box only protein, helicase, 18"				Standard	XM_005267159		Approved	MGC21674, Fbx30	uc003qla.3	Q8TB52	OTTHUMG00000015749	ENST00000237281.4:c.529G>C	chr6.hg19:g.146127013C>G	ENSP00000237281:p.Glu177Gln	55.0	0.0		63.0	21.0	NM_032145	Q9BXZ7	Missense_Mutation	SNP	ENST00000237281.4	hg19	CCDS5208.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.701985	0.30232	.	.	ENSG00000118496	ENST00000237281	T	0.20598	2.06	5.82	4.96	0.65561	.	0.146153	0.64402	D	0.000008	T	0.08133	0.0203	L	0.33485	1.01	0.46749	D	0.99918	B	0.20052	0.041	B	0.17433	0.018	T	0.08743	-1.0707	10	0.26408	T	0.33	-16.8672	15.2103	0.73219	0.0:0.9321:0.0:0.0679	.	177	Q8TB52	FBX30_HUMAN	Q	177	ENSP00000237281:E177Q	ENSP00000237281:E177Q	E	-	1	0	FBXO30	146168706	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.751000	0.68720	1.460000	0.47911	0.591000	0.81541	GAA	.	.		0.378	FBXO30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042570.2			G	146127013	C	G	146127013	3	3	75	1	0	0	0	0	1	0	0	0	5748	922	32	4	1716	4	FBXO30	6	146127013	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	28998993	146127013	24988054	54	10177										
SCIN	85477	hgsc.bcm.edu	37	chr7	12666242	12666242	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cagaaggaggtgaaacaccaAtcttcaaacagttttttaag	8	7	2	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr7:12666242A>C	ENST00000297029.5	+	8	1116	c.1015A>C	c.(1015-1017)Atc>Ctc	p.I339L	SCIN_ENST00000445618.2_Missense_Mutation_p.I92L|SCIN_ENST00000519209.1_Missense_Mutation_p.I92L|SCIN_ENST00000473722.1_3'UTR	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	339	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TGAAACACCAATCTTCAAACA	0.328																																					p.I339L		Atlas-SNP	.											.	SCIN	105	.	0			c.A1015C						.						38	34	35					7																	12666242		1750	3908	5658	SO:0001583	missense	85477	exon8			ACACCAATCTTCA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.1015A>C	chr7.hg19:g.12666242A>C	ENSP00000297029:p.Ile339Leu	82.0	0.0		78.0	51.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	hg19	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	A	4.200	0.035872	0.08148	.	.	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.55234	0.53;0.53;0.53	5.94	0.056	0.14317	Gelsolin domain (1);	0.156002	0.56097	D	0.000027	T	0.20659	0.0497	N	0.04768	-0.165	0.34707	D	0.727358	B	0.06786	0.001	B	0.13407	0.009	T	0.35325	-0.9793	10	0.02654	T	1	-8.572	5.822	0.18532	0.5879:0.25:0.1621:0.0	.	339	Q9Y6U3	ADSV_HUMAN	L	339;92;92	ENSP00000297029:I339L;ENSP00000430997:I92L;ENSP00000390189:I92L	ENSP00000297029:I339L	I	+	1	0	SCIN	12632767	0.788000	0.28762	0.988000	0.46212	0.986000	0.74619	1.593000	0.36686	0.377000	0.24735	0.460000	0.39030	ATC	.	.		0.328	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		C	12666242	A	C	12666242	3	2	75	1	0	0	0	0	1	0	0	0	13920	101	4	5	1045	5	SCIN	7	12666242	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10		12666242	146472421	55	10178										
ANLN	54443	hgsc.bcm.edu	37	chr7	36435972	36435972	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gtctatgactcatgctaagcGagctagacagccactttcag	9	11	3	2	rs555242135		TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr7:36435972G>T	ENST00000265748.2	+	2	337	c.116G>T	c.(115-117)cGa>cTa	p.R39L	ANLN_ENST00000396068.2_Missense_Mutation_p.R39L	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	39	Interaction with CD2AP.|Nuclear localization.|Required for ubiquitination.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						CATGCTAAGCGAGCTAGACAG	0.473																																					p.R39L		Atlas-SNP	.											.	ANLN	101	.	0			c.G116T						.						69	71	71					7																	36435972		2203	4300	6503	SO:0001583	missense	54443	exon2			CTAAGCGAGCTAG	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.116G>T	chr7.hg19:g.36435972G>T	ENSP00000265748:p.Arg39Leu	165.0	0.0		163.0	33.0	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	hg19	CCDS5447.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.356902	0.82243	.	.	ENSG00000011426	ENST00000265748;ENST00000396068;ENST00000424865;ENST00000418118	T;T;T	0.55234	0.53;0.53;3.95	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.74550	0.3731	M	0.75264	2.295	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.76462	-0.2950	10	0.87932	D	0	-13.6627	19.774	0.96385	0.0:0.0:1.0:0.0	.	39;39;39	A8K5D9;Q9NQW6-2;Q9NQW6	.;.;ANLN_HUMAN	L	39;39;17;17	ENSP00000265748:R39L;ENSP00000379380:R39L;ENSP00000404979:R17L	ENSP00000265748:R39L	R	+	2	0	ANLN	36402497	1.000000	0.71417	0.467000	0.27180	0.321000	0.28281	8.351000	0.90072	2.679000	0.91253	0.591000	0.81541	CGA	.	.		0.473	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		T	36435972	G	T	36435972	3	4	75	1	0	0	0	0	1	0	0	0	694	1058	37	1	122	1	ANLN	7	36435972	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	23769730	36435972	122702691	56	10179										
CD36	948	hgsc.bcm.edu	37	chr7	80295781	80295781	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	atctgtcctattgggaaagtCactgcgacatgattaatggt	10	7	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr7:80295781C>G	ENST00000435819.1	+	11	1408	c.724C>G	c.(724-726)Cac>Gac	p.H242D	CD36_ENST00000447544.2_Missense_Mutation_p.H242D|CD36_ENST00000432207.1_Missense_Mutation_p.H242D|CD36_ENST00000538969.1_Missense_Mutation_p.H182D|CD36_ENST00000433696.2_Intron|CD36_ENST00000309881.7_Missense_Mutation_p.H242D|CD36_ENST00000394788.3_Missense_Mutation_p.H242D|CD36_ENST00000534394.1_Missense_Mutation_p.H166D|CD36_ENST00000544133.1_Missense_Mutation_p.H242D			P16671	CD36_HUMAN	CD36 molecule (thrombospondin receptor)	242					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular lipid metabolic process (GO:0044255)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to hydroperoxide (GO:0071447)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cGMP-mediated signaling (GO:0019934)|cholesterol transport (GO:0030301)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|lipoprotein transport (GO:0042953)|long-chain fatty acid import (GO:0044539)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle mediated signaling (GO:0055096)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitric oxide mediated signal transduction (GO:0007263)|phagocytosis, recognition (GO:0006910)|plasma lipoprotein particle clearance (GO:0034381)|plasma membrane long-chain fatty acid transport (GO:0015911)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood microparticle formation (GO:2000334)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of removal of superoxide radicals (GO:2000121)|response to stilbenoid (GO:0035634)|small molecule metabolic process (GO:0044281)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|lipoteichoic acid receptor activity (GO:0070892)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|thrombospondin receptor activity (GO:0070053)|transforming growth factor beta binding (GO:0050431)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(10)|large_intestine(1)|lung(6)|ovary(1)	21						TTGGGAAAGTCACTGCGACAT	0.338																																					p.H242D		Atlas-SNP	.											.	CD36	185	.	0			c.C724G						.						152	144	147					7																	80295781		2203	4300	6503	SO:0001583	missense	948	exon6			GAAAGTCACTGCG	Z32770	CCDS34673.1	7q11.2	2010-02-26	2006-03-28		ENSG00000135218	ENSG00000135218		"CD molecules"	1663	protein-coding gene	gene with protein product		173510	"CD36 antigen (collagen type I receptor, thrombospondin receptor)"			7503937	Standard	NM_001001548		Approved	SCARB3, GPIV, FAT, GP4, GP3B	uc003uhg.4	P16671	OTTHUMG00000155383	ENST00000435819.1:c.724C>G	chr7.hg19:g.80295781C>G	ENSP00000399421:p.His242Asp	36.0	0.0		33.0	13.0	NM_001127444	D9IX66|D9IX67|D9IX68|D9IX69|Q13966|Q16093|Q8TCV7|Q9BPZ8|Q9BQC2|Q9BZM8|Q9BZN3|Q9BZN4|Q9BZN5	Missense_Mutation	SNP	ENST00000435819.1	hg19	CCDS34673.1	.	.	.	.	.	.	.	.	.	.	C	2.907	-0.226254	0.06022	.	.	ENSG00000135218	ENST00000435819;ENST00000309881;ENST00000534394;ENST00000394788;ENST00000447544;ENST00000432207;ENST00000419819;ENST00000538969;ENST00000544133	T;T;T;T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	5.01	2.58	0.30949	.	0.116287	0.64402	D	0.000010	T	0.49150	0.1540	N	0.19112	0.55	0.20074	N	0.999938	B	0.22746	0.074	B	0.23852	0.049	T	0.26950	-1.0088	9	.	.	.	-11.1083	5.4882	0.16761	0.0:0.1496:0.2744:0.576	.	242	P16671	CD36_HUMAN	D	242;242;166;242;242;242;242;182;242	ENSP00000399421:H242D;ENSP00000308165:H242D;ENSP00000431296:H166D;ENSP00000378268:H242D;ENSP00000415743:H242D;ENSP00000411411:H242D;ENSP00000392298:H242D;ENSP00000439543:H182D;ENSP00000441956:H242D	.	H	+	1	0	CD36	80133717	0.965000	0.33210	0.196000	0.23383	0.746000	0.42486	1.614000	0.36911	0.313000	0.23062	-0.294000	0.09567	CAC	.	.		0.338	CD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339767.6	NM_001001547		G	80295781	C	G	80295781	3	3	75	1	0	0	0	0	1	0	0	0	3009	826	29	4	746	4	CD36	7	80295781	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	43859809	80295781	78842882	57	10180										
SMURF1	57154	hgsc.bcm.edu	37	chr7	98645348	98645348	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cacttcgatgcggcaatgacCagcttggggctgctgaagcg	14	11	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr7:98645348C>A	ENST00000361125.1	-	11	1508	c.1189G>T	c.(1189-1191)Ggt>Tgt	p.G397C	AC004893.11_ENST00000482799.2_RNA|SMURF1_ENST00000361368.2_Missense_Mutation_p.G371C|AC004893.11_ENST00000468960.2_RNA	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	397					BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			CGGCAATGACCAGCTTGGGGC	0.512																																					p.G397C		Atlas-SNP	.											.	SMURF1	58	.	0			c.G1189T						.						113	110	111					7																	98645348		2203	4300	6503	SO:0001583	missense	57154	exon11			AATGACCAGCTTG	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.1189G>T	chr7.hg19:g.98645348C>A	ENSP00000354621:p.Gly397Cys	71.0	0.0		77.0	20.0	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Missense_Mutation	SNP	ENST00000361125.1	hg19	CCDS34690.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.859752	0.91433	.	.	ENSG00000198742	ENST00000361368;ENST00000361125	T;T	0.46063	0.88;0.88	5.44	5.44	0.79542	HECT (1);	0.000000	0.85682	D	0.000000	T	0.71204	0.3312	M	0.87617	2.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.76656	-0.2879	10	0.87932	D	0	.	19.2699	0.94004	0.0:1.0:0.0:0.0	.	371;397;371	Q9HCE7-2;Q9HCE7;B9EGV3	.;SMUF1_HUMAN;.	C	371;397	ENSP00000355326:G371C;ENSP00000354621:G397C	ENSP00000354621:G397C	G	-	1	0	SMURF1	98483284	1.000000	0.71417	0.769000	0.31535	0.843000	0.47879	7.814000	0.86154	2.527000	0.85204	0.563000	0.77884	GGT	.	.		0.512	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429		A	98645348	C	A	98645348	3	1	75	1	0	0	0	0	1	0	0	0	14834	594	21	3	1120	3	SMURF1	7	98645348	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	18349567	98645348	60493315	58	10181										
MUC17	140453	hgsc.bcm.edu	37	chr7	100677761	100677761	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ccacttctactgaagccagtTcacctcctcccactgctgaa	5	17	2	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr7:100677761T>A	ENST00000306151.4	+	3	3128	c.3064T>A	c.(3064-3066)Tca>Aca	p.S1022T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1022	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TGAAGCCAGTTCACCTCCTCC	0.527																																					p.S1022T		Atlas-SNP	.											.	MUC17	804	.	0			c.T3064A						.						471	378	409					7																	100677761		2203	4300	6503	SO:0001583	missense	140453	exon3			GCCAGTTCACCTC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3064T>A	chr7.hg19:g.100677761T>A	ENSP00000302716:p.Ser1022Thr	205.0	0.0		197.0	34.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.020498	0.00418	.	.	ENSG00000169876	ENST00000306151	T	0.02498	4.27	0.74	-1.48	0.08745	.	.	.	.	.	T	0.01661	0.0053	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.49588	-0.8924	9	0.09338	T	0.73	.	0.8792	0.01230	0.1724:0.1616:0.3449:0.321	.	1022	Q685J3	MUC17_HUMAN	T	1022	ENSP00000302716:S1022T	ENSP00000302716:S1022T	S	+	1	0	MUC17	100464481	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-3.018000	0.00644	-3.296000	0.00193	-1.668000	0.00747	TCA	.	.		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100677761	T	A	100677761	3	1	75	1	0	0	0	0	1	0	0	0	9983	1783	62	4	3074	4	MUC17	7	100677761	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	2032413	100677761	58460902	59	10182										
LHFPL3	375612	hgsc.bcm.edu	37	chr7	104377307	104377307	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	catttctagcatttgtgcttGgtaatcgacaagacagcttg	9	8	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr7:104377307G>C	ENST00000401970.2	+	2	711	c.589G>C	c.(589-591)Ggt>Cgt	p.G197R	LHFPL3_ENST00000535008.1_Missense_Mutation_p.G211R|LHFPL3-AS1_ENST00000449764.1_RNA|LHFPL3-AS1_ENST00000433514.1_RNA|LHFPL3_ENST00000424859.1_Missense_Mutation_p.G197R|LHFPL3_ENST00000543266.1_Missense_Mutation_p.G211R			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	211						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(6)	9						ATTTGTGCTTGGTAATCGACA	0.448																																					p.G211R		Atlas-SNP	.											.	LHFPL3	24	.	0			c.G631C						.						69	67	67					7																	104377307		1931	4158	6089	SO:0001583	missense	375612	exon2			GTGCTTGGTAATC	AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416			6589	protein-coding gene	gene with protein product		609719	"lipoma HMGIC fusion partner-like 4"	LHFPL4		10329012	Standard	NM_199000		Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000401970.2:c.589G>C	chr7.hg19:g.104377307G>C	ENSP00000385374:p.Gly197Arg	73.0	0.0		65.0	16.0	NM_199000	A1L383|A4D0Q5	Missense_Mutation	SNP	ENST00000401970.2	hg19		.	.	.	.	.	.	.	.	.	.	G	28.1	4.895096	0.91962	.	.	ENSG00000187416	ENST00000424859;ENST00000535008;ENST00000401970;ENST00000543266	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.87529	0.6200	M	0.88450	2.955	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.88720	0.3229	10	0.72032	D	0.01	-36.019	20.0845	0.97795	0.0:0.0:1.0:0.0	.	211;211	A1L384;A4D0Q5	.;.	R	197;211;197;211	ENSP00000393128:G197R;ENSP00000444350:G211R;ENSP00000385374:G197R;ENSP00000445976:G211R	ENSP00000385374:G197R	G	+	1	0	LHFPL3	104164543	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.813000	0.99286	2.821000	0.97095	0.650000	0.86243	GGT	.	.		0.448	LHFPL3-002	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000348284.1	NM_199000		C	104377307	G	C	104377307	3	2	75	1	0	0	0	0	1	0	0	0	8775	1348	47	4	637	4	LHFPL3	7	104377307	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	3699546	104377307	54761356	60	10183										
PNPLA8	50640	hgsc.bcm.edu	37	chr7	108113028	108113028	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tgatccagcttttcatttcgActttcatctagaggtatgtt	7	8	3	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr7:108113028A>G	ENST00000422087.1	-	12	2572	c.2166T>C	c.(2164-2166)agT>agC	p.S722S	PNPLA8_ENST00000453144.1_Silent_p.S622S|PNPLA8_ENST00000257694.8_Silent_p.S722S|PNPLA8_ENST00000436062.1_Silent_p.S722S|PNPLA8_ENST00000388728.5_Silent_p.S660S|PNPLA8_ENST00000426128.2_Silent_p.S660S	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	722					arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						TTTCATTTCGACTTTCATCTA	0.338																																					p.S722S		Atlas-SNP	.											.	PNPLA8	82	.	0			c.T2166C						.						64	66	65					7																	108113028		2203	4300	6503	SO:0001819	synonymous_variant	50640	exon10			ATTTCGACTTTCA	AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"Patatin-like phospholipase domain containing"	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.2166T>C	chr7.hg19:g.108113028A>G		84.0	0.0		97.0	15.0	NM_001256008	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Silent	SNP	ENST00000422087.1	hg19	CCDS34733.1																																																																																			.	.		0.338	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		G	108113028	A	G	108113028	2	3	75	1	0	0	0	0	0	0	0	1	12180	272	10	2		2	PNPLA8	7	108113028	Silent	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	3735721	108113028	51025635	61	10184										
FLNC	2318	hgsc.bcm.edu	37	chr7	128485033	128485033	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tggagcgcggcaaggtcggtGaggcagccaccttcactgtg	16	11	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr7:128485033G>A	ENST00000325888.8	+	21	3775	c.3514G>A	c.(3514-3516)Gag>Aag	p.E1172K	FLNC_ENST00000346177.6_Missense_Mutation_p.E1172K	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1172					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CAAGGTCGGTGAGGCAGCCAC	0.652																																					p.E1172K		Atlas-SNP	.											.	FLNC	339	.	0			c.G3514A						.						41	48	45					7																	128485033		2167	4261	6428	SO:0001583	missense	2318	exon21			GTCGGTGAGGCAG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.3514G>A	chr7.hg19:g.128485033G>A	ENSP00000327145:p.Glu1172Lys	82.0	0.0		97.0	22.0	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	hg19	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.873070	0.91664	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.86297	-2.1;-2.1	5.56	5.56	0.83823	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.91925	0.7443	L	0.52759	1.655	0.80722	D	1	D;P	0.76494	0.999;0.923	D;P	0.85130	0.997;0.836	D	0.91049	0.4877	10	0.44086	T	0.13	.	19.5273	0.95212	0.0:0.0:1.0:0.0	.	1172;1172	Q14315-2;Q14315	.;FLNC_HUMAN	K	1172	ENSP00000327145:E1172K;ENSP00000344002:E1172K	ENSP00000327145:E1172K	E	+	1	0	FLNC	128272269	1.000000	0.71417	0.964000	0.40570	0.835000	0.47333	6.690000	0.74567	2.615000	0.88500	0.555000	0.69702	GAG	.	.		0.652	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128485033	G	A	128485033	3	1	75	1	0	0	0	0	1	0	0	0	5943	1291	45	3	3596	3	FLNC	7	128485033	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	20372005	128485033	30653630	62	10185										
ABP1	26	hgsc.bcm.edu	37	chr7	150554178	150554178	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gcttatcatacagcgctatgTagaaggctactttctgcacc	8	11	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr7:150554178T>C	ENST00000493429.1	+	4	1204	c.620T>C	c.(619-621)gTa>gCa	p.V207A	AOC1_ENST00000467291.1_Missense_Mutation_p.V207A|AOC1_ENST00000416793.2_Missense_Mutation_p.V207A|AOC1_ENST00000360937.4_Missense_Mutation_p.V207A			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	207					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	CAGCGCTATGTAGAAGGCTAC	0.612																																					p.V207A		Atlas-SNP	.											.	ABP1	92	.	0			c.T620C						.						76	79	78					7																	150554178		2024	4178	6202	SO:0001583	missense	26	exon2			GCTATGTAGAAGG	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"diamine oxidase"	104610	"amiloride binding protein 1 (amine oxidase (copper-containing))"	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.620T>C	chr7.hg19:g.150554178T>C	ENSP00000418614:p.Val207Ala	34.0	0.0		32.0	8.0	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	hg19	CCDS43679.1	.	.	.	.	.	.	.	.	.	.	T	19.30	3.801593	0.70682	.	.	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000460213;ENST00000360937;ENST00000416793;ENST00000437714;ENST00000483043	T;T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16;2.16	4.88	4.88	0.63580	Copper amine oxidase, N3-terminal (1);Copper amine oxidase, N2/N3-terminal (1);Copper amine oxidase, N-terminal (1);	0.125519	0.53938	D	0.000060	T	0.42854	0.1221	M	0.76328	2.33	0.50813	D	0.999891	P;D	0.58620	0.931;0.983	P;P	0.62649	0.527;0.905	T	0.37549	-0.9701	10	0.56958	D	0.05	-19.2859	12.497	0.55933	0.0:0.0:0.0:1.0	.	207;207	C9J690;P19801	.;ABP1_HUMAN	A	207;207;207;207;207;83;207	ENSP00000418614:V207A;ENSP00000418328:V207A;ENSP00000418557:V207A;ENSP00000354193:V207A;ENSP00000411613:V207A;ENSP00000417392:V207A	ENSP00000354193:V207A	V	+	2	0	ABP1	150185111	1.000000	0.71417	0.068000	0.19968	0.607000	0.37147	4.662000	0.61525	2.056000	0.61249	0.459000	0.35465	GTA	.	.		0.612	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		C	150554178	T	C	150554178	3	2	75	1	0	0	0	0	1	0	0	0	98	1638	57	2	622	2	ABP1	7	150554178	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	22069145	150554178	8584485	63	10186										
DNAJB6	10049	hgsc.bcm.edu	37	chr7	157155965	157155965	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	atatgaagtgctgtcggatgGtgagtgacagcgagctgctg	16	6	0	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr7:157155965G>T	ENST00000262177.4	+	3	380		c.e3+1		DNAJB6_ENST00000429029.2_Splice_Site|DNAJB6_ENST00000443280.1_Splice_Site|DNAJB6_ENST00000452797.2_Intron	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6						intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		CTGTCGGATGGTGAGTGACAG	0.517																																					.	Esophageal Squamous(46;195 967 1350 20350 43814)	Atlas-SNP	.											.	DNAJB6	39	.	0			c.175+1G>T						.						53	50	51					7																	157155965		2203	4299	6502	SO:0001630	splice_region_variant	10049	exon3			CGGATGGTGAGTG	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"Heat shock proteins / DNAJ (HSP40)"	14888	protein-coding gene	gene with protein product		611332	"limb girdle muscular dystrophy 1D (autosomal dominant)"	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.175+1G>T	chr7.hg19:g.157155965G>T		81.0	0.0		61.0	14.0	NM_005494	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Splice_Site	SNP	ENST00000262177.4	hg19	CCDS5946.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.485859	0.44147	.	.	ENSG00000105993	ENST00000441561;ENST00000429029;ENST00000262177;ENST00000417758;ENST00000443280;ENST00000421417;ENST00000437030;ENST00000412557;ENST00000453383	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5382	0.87840	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAJB6	156848726	1.000000	0.71417	0.997000	0.53966	0.233000	0.25261	8.947000	0.93000	2.217000	0.71921	0.557000	0.71058	.	.	.		0.517	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2		Intron	T	157155965	G	T	157155965	5	4	75	1	0	0	0	0	0	0	1	0	4626	1275	44	3	182	3	DNAJB6	7	157155965	Splice_Site	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	6601787	157155965	1982698	64	10187										
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8748999	8748999	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cgcgtggggcactctcgcccCgacccgatgcaagaaggagc	14	15	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr8:8748999C>T	ENST00000276282.6	-	1	2156	c.1570G>A	c.(1570-1572)Ggg>Agg	p.G524R		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	524	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.									endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		ACTCTCGCCCCGACCCGATGC	0.632																																					p.G524R	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											MFHAS1,NS,carcinoma,0,1	MFHAS1	58	.	0			c.G1570A						.						30	28	28					8																	8748999		2201	4297	6498	SO:0001583	missense	9258	exon1			TCGCCCCGACCCG	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"leucine rich repeat containing 65", "malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.1570G>A	chr8.hg19:g.8748999C>T	ENSP00000276282:p.Gly524Arg	68.0	0.0		49.0	2.0	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	hg19	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.614917	0.28712	.	.	ENSG00000147324	ENST00000276282	T	0.78364	-1.17	5.42	4.55	0.56014	ROC GTPase (1);	0.339314	0.28921	N	0.013720	T	0.57740	0.2074	L	0.29908	0.895	0.31402	N	0.676526	P	0.35155	0.487	B	0.18871	0.023	T	0.59085	-0.7520	10	0.15952	T	0.53	.	8.7735	0.34747	0.0:0.7697:0.0:0.2303	.	524	Q9Y4C4	MFHA1_HUMAN	R	524	ENSP00000276282:G524R	ENSP00000276282:G524R	G	-	1	0	MFHAS1	8786409	0.890000	0.30428	1.000000	0.80357	0.746000	0.42486	1.676000	0.37565	1.525000	0.49052	0.563000	0.77884	GGG	.	.		0.632	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		T	8748999	C	T	8748999	3	4	75	1	0	0	0	0	1	0	0	0	9530	652	23	1	1600	1	MFHAS1	8	8748999	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10		8748999	137615023	65	10188										
ZDHHC2	51201	hgsc.bcm.edu	37	chr8	17072756	17072756	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tattattcagtctcgaaaacCatcagtttcctgcaaagcca	5	11	3	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr8:17072756C>T	ENST00000262096.8	+	11	1656	c.961C>T	c.(961-963)Cat>Tat	p.H321Y		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	321					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|recycling endosome membrane (GO:0055038)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|pancreas(1)|stomach(1)	8				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		TCTCGAAAACCATCAGTTTCC	0.378																																					p.H321Y		Atlas-SNP	.											.	ZDHHC2	25	.	0			c.C961T						.						76	72	73					8																	17072756		1850	4101	5951	SO:0001583	missense	51201	exon11			GAAAACCATCAGT	AB023584	CCDS47810.1	8p22	2008-05-15			ENSG00000104219	ENSG00000104219		"Zinc fingers, DHHC-type"	18469	protein-coding gene	gene with protein product						10918388	Standard	NM_016353		Approved	ZNF372	uc003wxe.3	Q9UIJ5	OTTHUMG00000163860	ENST00000262096.8:c.961C>T	chr8.hg19:g.17072756C>T	ENSP00000262096:p.His321Tyr	86.0	0.0		59.0	30.0	NM_016353	D3DSP5	Missense_Mutation	SNP	ENST00000262096.8	hg19	CCDS47810.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.023878	0.54683	.	.	ENSG00000104219	ENST00000262096	T	0.43688	0.94	5.53	5.53	0.82687	.	0.218907	0.47093	D	0.000259	T	0.45337	0.1337	M	0.65975	2.015	0.54753	D	0.999988	P	0.37781	0.608	B	0.37650	0.255	T	0.47849	-0.9085	10	0.56958	D	0.05	-3.1576	15.4426	0.75200	0.1394:0.8606:0.0:0.0	.	321	Q9UIJ5	ZDHC2_HUMAN	Y	321	ENSP00000262096:H321Y	ENSP00000262096:H321Y	H	+	1	0	ZDHHC2	17117127	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	6.455000	0.73497	2.773000	0.95371	0.585000	0.79938	CAT	.	.		0.378	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	NM_016353		T	17072756	C	T	17072756	3	4	75	1	0	0	0	0	1	0	0	0	17625	594	21	3	1003	3	ZDHHC2	8	17072756	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	8323757	17072756	129291266	66	10189										
CHMP4C	92421	hgsc.bcm.edu	37	chr8	82670408	82670408	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ggcagaacttgaagaattggAacaggaggaattaaataaga	12	3	0	4			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr8:82670408A>T	ENST00000297265.4	+	4	708	c.515A>T	c.(514-516)gAa>gTa	p.E172V		NM_152284.3	NP_689497.1	Q96CF2	CHM4C_HUMAN	charged multivesicular body protein 4C	172	Intramolecular interaction with N- terminus. {ECO:0000250}.				abscission (GO:0009838)|cytokinesis checkpoint (GO:0031565)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|negative regulation of cytokinesis (GO:0032466)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|membrane (GO:0016020)|midbody (GO:0030496)	protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	10						GAAGAATTGGAACAGGAGGAA	0.418																																					p.E172V		Atlas-SNP	.											.	CHMP4C	28	.	0			c.A515T						.						107	107	107					8																	82670408		2203	4300	6503	SO:0001583	missense	92421	exon4			AATTGGAACAGGA	AK000049	CCDS6233.1	8q21.13	2011-09-21	2011-09-21		ENSG00000164695	ENSG00000164695		"Charged multivesicular body proteins"	30599	protein-coding gene	gene with protein product	"Snf7 homologue associated with Alix 3"	610899	"chromatin modifying protein 4C"			12860994 , 14678797	Standard	NM_152284		Approved	MGC22825, Shax3, VPS32C	uc003ycl.3	Q96CF2	OTTHUMG00000164726	ENST00000297265.4:c.515A>T	chr8.hg19:g.82670408A>T	ENSP00000297265:p.Glu172Val	72.0	0.0		94.0	18.0	NM_152284	B2RBZ1	Missense_Mutation	SNP	ENST00000297265.4	hg19	CCDS6233.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.417224	0.83449	.	.	ENSG00000164695	ENST00000297265	T	0.74106	-0.81	6.17	6.17	0.99709	.	0.042099	0.85682	D	0.000000	D	0.88058	0.6335	M	0.92367	3.3	0.80722	D	1	P	0.51057	0.941	P	0.58210	0.835	D	0.90135	0.4209	10	0.59425	D	0.04	-31.8189	16.8222	0.85835	1.0:0.0:0.0:0.0	.	172	Q96CF2	CHM4C_HUMAN	V	172	ENSP00000297265:E172V	ENSP00000297265:E172V	E	+	2	0	CHMP4C	82832963	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.078000	0.76821	2.371000	0.80710	0.533000	0.62120	GAA	.	.		0.418	CHMP4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379927.1	NM_152284		T	82670408	A	T	82670408	3	4	75	1	0	0	0	0	1	0	0	0	3360	246	9	4	529	4	CHMP4C	8	82670408	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	65597652	82670408	63693614	67	10190										
LRRCC1	85444	hgsc.bcm.edu	37	chr8	86041583	86041583	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aaaaacattagaaaaaatggAgagacaaaaaaggcagcagc	9	5	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr8:86041583A>G	ENST00000360375.3	+	10	1744	c.1595A>G	c.(1594-1596)gAg>gGg	p.E532G	LRRCC1_ENST00000414626.2_Missense_Mutation_p.E512G	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	532					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						GAAAAAATGGAGAGACAAAAA	0.333																																					p.E532G		Atlas-SNP	.											.	LRRCC1	212	.	0			c.A1595G						.						89	93	92					8																	86041583		1848	4094	5942	SO:0001583	missense	85444	exon10			AAATGGAGAGACA	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.1595A>G	chr8.hg19:g.86041583A>G	ENSP00000353538:p.Glu532Gly	291.0	0.0		289.0	105.0	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	hg19	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.413291	0.83449	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	T;T	0.38887	1.11;1.11	5.58	5.58	0.84498	.	0.000000	0.39759	N	0.001274	T	0.65344	0.2682	M	0.73598	2.24	0.54753	D	0.999986	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.972	T	0.67707	-0.5601	10	0.54805	T	0.06	-19.004	16.0742	0.80958	1.0:0.0:0.0:0.0	.	439;512;439;532	B4DV06;Q9C099-2;E9PE41;Q9C099	.;.;.;LRCC1_HUMAN	G	532;512	ENSP00000353538:E532G;ENSP00000394695:E512G	ENSP00000353538:E532G	E	+	2	0	LRRCC1	86228835	1.000000	0.71417	0.995000	0.50966	0.943000	0.58893	6.317000	0.72862	2.259000	0.74868	0.528000	0.53228	GAG	.	.		0.333	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		G	86041583	A	G	86041583	3	3	75	1	0	0	0	0	1	0	0	0	9035	304	11	2	1633	2	LRRCC1	8	86041583	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	3371175	86041583	60322439	68	10191										
FBXO43	286151	hgsc.bcm.edu	37	chr8	101153047	101153047	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cagtcctgcaagtatacactGcagtacagctattttctccc	6	13	1	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr8:101153047G>A	ENST00000428847.2	-	2	1751	c.1435C>T	c.(1435-1437)Cag>Tag	p.Q479*		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	479					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			AGTATACACTGCAGTACAGCT	0.363																																					p.Q479X		Atlas-SNP	.											.	FBXO43	155	.	0			c.C1435T						.						213	199	203					8																	101153047		1836	4099	5935	SO:0001587	stop_gained	286151	exon2			TACACTGCAGTAC	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"F-boxes /  "other""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.1435C>T	chr8.hg19:g.101153047G>A	ENSP00000403293:p.Gln479*	128.0	0.0		105.0	24.0	NM_001029860		Nonsense_Mutation	SNP	ENST00000428847.2	hg19	CCDS47904.1	.	.	.	.	.	.	.	.	.	.	G	37	6.049687	0.97236	.	.	ENSG00000156509	ENST00000428847	.	.	.	5.06	1.76	0.24704	.	0.410465	0.26140	N	0.026107	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-2.092	6.8315	0.23913	0.0:0.3179:0.3124:0.3697	.	.	.	.	X	479	.	ENSP00000403293:Q479X	Q	-	1	0	FBXO43	101222223	0.004000	0.15560	0.224000	0.23877	0.799000	0.45148	0.532000	0.23067	0.569000	0.29329	0.655000	0.94253	CAG	.	.		0.363	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918		A	101153047	G	A	101153047	4	1	75	1	0	0	0	0	0	1	0	0	5760	1328	46	3	707	3	FBXO43	8	101153047	Nonsense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	15111464	101153047	45210975	69	10192										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113326812	113326812	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gggctcaatatgactccagtAgaatctagccgtaattcatt	8	9	3	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr8:113326812A>G	ENST00000297405.5	-	48	7639	c.7395T>C	c.(7393-7395)tcT>tcC	p.S2465S	CSMD3_ENST00000343508.3_Silent_p.S2425S|CSMD3_ENST00000352409.3_Silent_p.S2395S|CSMD3_ENST00000455883.2_Silent_p.S2361S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2465	CUB 14. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TGACTCCAGTAGAATCTAGCC	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S2465S		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T7395C						.						64	62	63					8																	113326812		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon48			TCCAGTAGAATCT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7395T>C	chr8.hg19:g.113326812A>G		112.0	0.0		101.0	13.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113326812	A	G	113326812	2	3	75	1	0	0	0	0	0	0	0	1	3948	407	15	2		2	CSMD3	8	113326812	Silent	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	12173765	113326812	33037210	70	10193										
SNTB1	6641	hgsc.bcm.edu	37	chr8	121706115	121706115	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cggatactggggatcctttcTtcacatagggcgtggcttct	12	10	3	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr8:121706115T>C	ENST00000395601.3	-	3	1019	c.605A>G	c.(604-606)aAg>aGg	p.K202R	SNTB1_ENST00000519177.1_5'UTR|SNTB1_ENST00000517992.1_Missense_Mutation_p.K202R	NM_021021.3	NP_066301.1	Q13884	SNTB1_HUMAN	syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)	202	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|protein complex (GO:0043234)|synapse (GO:0045202)				NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(6)	24	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			GGATCCTTTCTTCACATAGGG	0.522																																					p.K202R		Atlas-SNP	.											.	SNTB1	54	.	0			c.A605G						.						87	92	90					8																	121706115		2203	4300	6503	SO:0001583	missense	6641	exon2			CCTTTCTTCACAT	AF028828	CCDS6334.1	8q23-q24	2013-01-10	2002-08-29		ENSG00000172164	ENSG00000172164		"Pleckstrin homology (PH) domain containing"	11168	protein-coding gene	gene with protein product	"tax interaction protein 43"	600026	"syntrophin, beta 1 (dystrophin-associated protein A1, 59kD, basic component 1)"	SNT2B1		8183929, 9482110	Standard	NM_021021		Approved	59-DAP, A1B, BSYN2, TIP-43, SNT2	uc010mdg.3	Q13884	OTTHUMG00000165041	ENST00000395601.3:c.605A>G	chr8.hg19:g.121706115T>C	ENSP00000378965:p.Lys202Arg	85.0	0.0		69.0	17.0	NM_021021	A8K9E0|O14912|Q4KMG8	Missense_Mutation	SNP	ENST00000395601.3	hg19	CCDS6334.1	.	.	.	.	.	.	.	.	.	.	T	19.74	3.883690	0.72410	.	.	ENSG00000172164	ENST00000395601;ENST00000517992	T;T	0.58506	0.33;0.33	5.44	3.03	0.35002	PDZ/DHR/GLGF (1);Pleckstrin homology domain (2);	0.047720	0.85682	D	0.000000	T	0.42426	0.1202	L	0.35723	1.085	0.54753	D	0.999988	B;B	0.27166	0.076;0.17	B;B	0.23419	0.034;0.046	T	0.15549	-1.0433	10	0.27785	T	0.31	.	8.4	0.32581	0.0:0.0682:0.1324:0.7994	.	202;202	Q13884;Q13884-2	SNTB1_HUMAN;.	R	202	ENSP00000378965:K202R;ENSP00000431124:K202R	ENSP00000378965:K202R	K	-	2	0	SNTB1	121775296	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.452000	0.60054	0.484000	0.27630	0.533000	0.62120	AAG	.	.		0.522	SNTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381535.1	NM_021021		C	121706115	T	C	121706115	3	2	75	1	0	0	0	0	1	0	0	0	14887	1609	56	2	1035	2	SNTB1	8	121706115	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	8379303	121706115	24657907	71	10194										
FBXO32	114907	hgsc.bcm.edu	37	chr8	124553194	124553194	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	atccaggaagcgcttccagcCgtcggccgtcttcacccagt	10	16	2	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr8:124553194C>T	ENST00000517956.1	-	1	252	c.61G>A	c.(61-63)Ggc>Agc	p.G21S	FBXO32_ENST00000443022.2_Missense_Mutation_p.G21S	NM_058229.3|NM_148177.2	NP_478136.1|NP_680482.1	Q969P5	FBX32_HUMAN	F-box protein 32	21					cellular response to dexamethasone stimulus (GO:0071549)|protein ubiquitination (GO:0016567)|response to denervation involved in regulation of muscle adaptation (GO:0014894)	nucleolus (GO:0005730)|Z disc (GO:0030018)				autonomic_ganglia(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)|stomach(1)	21	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			CGCTTCCAGCCGTCGGCCGTC	0.672																																					p.G21S		Atlas-SNP	.											.	FBXO32	39	.	0			c.G61A						.						36	38	37					8																	124553194		2203	4300	6503	SO:0001583	missense	114907	exon1			TCCAGCCGTCGGC	AJ420108	CCDS6345.1, CCDS56553.1	8q24.13	2008-01-28	2004-06-15		ENSG00000156804	ENSG00000156804		"F-boxes /  "other""	16731	protein-coding gene	gene with protein product		606604	"F-box only protein 32"			11679633, 11717410	Standard	NM_058229		Approved	MAFbx, ATROGIN1, Fbx32	uc003yqr.3	Q969P5	OTTHUMG00000164981	ENST00000517956.1:c.61G>A	chr8.hg19:g.124553194C>T	ENSP00000428205:p.Gly21Ser	78.0	0.0		95.0	29.0	NM_001242463	A4KYM0	Missense_Mutation	SNP	ENST00000517956.1	hg19	CCDS6345.1	.	.	.	.	.	.	.	.	.	.	C	37	6.009963	0.97200	.	.	ENSG00000156804	ENST00000517956;ENST00000443022	T;T	0.23950	1.88;1.88	4.47	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.54224	0.1845	M	0.80982	2.52	0.42809	D	0.993959	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.987	T	0.62473	-0.6847	10	0.72032	D	0.01	-1.3489	16.9246	0.86173	0.0:1.0:0.0:0.0	.	21;21	A4KYM0;Q969P5	.;FBX32_HUMAN	S	21	ENSP00000428205:G21S;ENSP00000390790:G21S	ENSP00000390790:G21S	G	-	1	0	FBXO32	124622375	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.957000	0.76019	2.319000	0.78375	0.561000	0.74099	GGC	.	.		0.672	FBXO32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381281.1			T	124553194	C	T	124553194	3	4	75	1	0	0	0	0	1	0	0	0	5750	652	23	1	1042	1	FBXO32	8	124553194	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	2847079	124553194	21810828	72	10195										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2039815	2039815	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cagcagcagcagcagcagcaGcaacagcagccgcagcagca	12	15	0	0	rs574062756	byFrequency	TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr9:2039815G>A	ENST00000382203.1	+	4	914	c.705G>A	c.(703-705)caG>caA	p.Q235Q	SMARCA2_ENST00000349721.2_Silent_p.Q235Q|SMARCA2_ENST00000357248.2_Silent_p.Q235Q|SMARCA2_ENST00000491574.1_3'UTR|RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000382194.1_Silent_p.Q235Q			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	235	Poly-Gln.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		agcagcagcagcaacagcagc	0.587													G|||	41	0.0081869	0.0151	0.0029	5008	,	,		10366	0.0089		0	False		,,,				2504	0.0102				p.Q235Q		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G705A						.						10	13	12					9																	2039815		2161	4205	6366	SO:0001819	synonymous_variant	6595	exon4			GCAGCAGCAACAG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.705G>A	chr9.hg19:g.2039815G>A		43.0	0.0		219.0	10.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	hg19	CCDS34977.1																																																																																			.	.		0.587	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2039815	G	A	2039815	2	1	75	1	0	0	0	0	0	0	0	1	14784	962	34	3		3	SMARCA2	9	2039815	Silent	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10		2039815	139173616	73	10196										
GLIS3	169792	hgsc.bcm.edu	37	chr9	4117860	4117860	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cttgtatcttcgagggcaacCggcccagaagcaagtgaagt	12	10	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr9:4117860C>G	ENST00000324333.10	-	3	1346	c.1153G>C	c.(1153-1155)Ggt>Cgt	p.G385R	GLIS3_ENST00000381971.3_Missense_Mutation_p.G540R	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	385					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		CGAGGGCAACCGGCCCAGAAG	0.577																																					p.G540R		Atlas-SNP	.											.	GLIS3	152	.	0			c.G1618C						.						150	136	141					9																	4117860		2203	4300	6503	SO:0001583	missense	169792	exon4			GGCAACCGGCCCA	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"Zinc fingers, C2H2-type"	28510	protein-coding gene	gene with protein product		610192	"zinc finger protein 515"	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.1153G>C	chr9.hg19:g.4117860C>G	ENSP00000325494:p.Gly385Arg	69.0	0.0		262.0	232.0	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	hg19	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.401272	0.83120	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	D;T	0.93859	-3.3;2.41	5.51	5.51	0.81932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.52532	D	0.000066	D	0.97108	0.9055	M	0.84585	2.705	0.80722	D	1	D;D;D;D;D	0.89917	0.991;0.999;0.999;1.0;1.0	P;D;D;D;D	0.77557	0.801;0.935;0.974;0.99;0.99	D	0.97502	1.0061	10	0.87932	D	0	.	19.4269	0.94746	0.0:1.0:0.0:0.0	.	48;53;53;540;385	Q1PHK4;Q1PHK2;Q1PHK3;Q8NEA6-2;Q8NEA6	.;.;.;.;GLIS3_HUMAN	R	385;540	ENSP00000325494:G385R;ENSP00000371398:G540R	ENSP00000325494:G385R	G	-	1	0	GLIS3	4107860	1.000000	0.71417	0.912000	0.35992	0.613000	0.37349	7.792000	0.85828	2.595000	0.87683	0.655000	0.94253	GGT	.	.		0.577	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		G	4117860	C	G	4117860	3	3	75	1	0	0	0	0	1	0	0	0	6455	652	23	4	1206	4	GLIS3	9	4117860	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	2078045	4117860	137095571	74	10197										
RANBP6	26953	hgsc.bcm.edu	37	chr9	6015579	6015579	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gcttttctgacacggtcgccGgcacccctgcagacgcggtt	12	15	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr9:6015579G>A	ENST00000259569.5	-	1	39	c.29C>T	c.(28-30)cCg>cTg	p.P10L	RANBP6_ENST00000485372.1_5'UTR	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	10					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.P10L(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		CACGGTCGCCGGCACCCCTGC	0.567																																					p.P10L		Atlas-SNP	.											RANBP6,NS,carcinoma,0,1	RANBP6	127	.	1	Substitution - Missense(1)	endometrium(1)	c.C29T						.						39	45	43					9																	6015579		2203	4299	6502	SO:0001583	missense	26953	exon1			GTCGCCGGCACCC	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.29C>T	chr9.hg19:g.6015579G>A	ENSP00000259569:p.Pro10Leu	14.0	0.0		61.0	56.0	NM_001243203	Q5T7X4|Q7Z3V2|Q96E78	Missense_Mutation	SNP	ENST00000259569.5	hg19	CCDS6467.1	.	.	.	.	.	.	.	.	.	.	G	16.18	3.049115	0.55110	.	.	ENSG00000137040	ENST00000259569	T	0.09350	2.99	4.54	4.54	0.55810	.	0.654725	0.13929	N	0.353051	T	0.06645	0.0170	N	0.03608	-0.345	0.41703	D	0.98941	B	0.13594	0.008	B	0.12156	0.007	T	0.38499	-0.9658	10	0.72032	D	0.01	-0.2399	15.5945	0.76569	0.0:0.0:1.0:0.0	.	10	O60518	RNBP6_HUMAN	L	10	ENSP00000259569:P10L	ENSP00000259569:P10L	P	-	2	0	RANBP6	6005579	0.998000	0.40836	0.885000	0.34714	0.457000	0.32468	5.100000	0.64560	2.813000	0.96785	0.561000	0.74099	CCG	.	.		0.567	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		A	6015579	G	A	6015579	3	1	75	1	0	0	0	0	1	0	0	0	13046	1116	39	1	3292	1	RANBP6	9	6015579	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	1897719	6015579	135197852	75	10198										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20944661	20944661	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gggagttggacttgttctgtCcctcatgagccacagcagcc	12	12	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr9:20944661C>T	ENST00000380249.1	+	31	3807	c.3443C>T	c.(3442-3444)tCc>tTc	p.S1148F	FOCAD_ENST00000338382.6_Missense_Mutation_p.S1148F|FOCAD_ENST00000605086.1_Missense_Mutation_p.S584F	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1148						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											CTTGTTCTGTCCCTCATGAGC	0.502																																					p.S1148F		Atlas-SNP	.											.	.	.	.	0			c.C3443T						.						139	119	126					9																	20944661		2203	4300	6503	SO:0001583	missense	54914	exon31			TTCTGTCCCTCAT	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.3443C>T	chr9.hg19:g.20944661C>T	ENSP00000369599:p.Ser1148Phe	75.0	0.0		56.0	12.0	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	hg19	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.338875	0.81911	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.70399	-0.48;-0.48	5.73	4.82	0.62117	Armadillo-type fold (1);	0.476902	0.24732	N	0.036046	T	0.80686	0.4670	M	0.69823	2.125	0.52501	D	0.999954	D	0.58970	0.984	P	0.56700	0.804	D	0.83669	0.0165	10	0.87932	D	0	-11.97	16.8704	0.86039	0.0:0.8622:0.1378:0.0	.	1148	Q5VW36	K1797_HUMAN	F	1148	ENSP00000369599:S1148F;ENSP00000344307:S1148F	ENSP00000344307:S1148F	S	+	2	0	KIAA1797	20934661	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.039000	0.49791	1.500000	0.48636	0.655000	0.94253	TCC	.	.		0.502	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		T	20944661	C	T	20944661	3	4	75	1	0	0	0	0	1	0	0	0	8267	855	30	3	3553	3	KIAA1797	9	20944661	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	14929082	20944661	120268770	76	10199										
GNE	10020	hgsc.bcm.edu	37	chr9	36223377	36223377	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tttacaatcttacctactccCaaaattctgcagttcagttt	3	11	3	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr9:36223377C>T	ENST00000539815.1	-	7	1444	c.1404G>A	c.(1402-1404)ttG>ttA	p.L468L	GNE_ENST00000543356.2_Silent_p.L463L|GNE_ENST00000396594.3_Silent_p.L499L|GNE_ENST00000377902.5_Silent_p.L468L|GNE_ENST00000539208.1_Silent_p.L358L|GNE_ENST00000447283.2_Silent_p.L468L			Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	468	N-acetylmannosamine kinase.				carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)			endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			TACCTACTCCCAAAATTCTGC	0.358																																					p.L499L	GBM(184;106 2118 20004 35750 50727)	Atlas-SNP	.											.	GNE	141	.	0			c.G1497A						.						100	104	103					9																	36223377		2202	4299	6501	SO:0001819	synonymous_variant	10020	exon8			TACTCCCAAAATT	AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921			23657	protein-coding gene	gene with protein product		603824	"UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase"	IBM2		9305887, 9305888	Standard	NM_005476		Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539815.1:c.1404G>A	chr9.hg19:g.36223377C>T		73.0	0.0		62.0	15.0	NM_001128227	A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	Silent	SNP	ENST00000539815.1	hg19	CCDS6602.1																																																																																			.	.		0.358	GNE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052412.4	NM_005476		T	36223377	C	T	36223377	2	4	75	1	0	0	0	0	0	0	0	1	6530	593	21	3		3	GNE	9	36223377	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	15278716	36223377	104990054	77	10200										
ZNF510	22869	hgsc.bcm.edu	37	chr9	99525914	99525914	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gtccttgaatgacactgatgCctgtaacagtacatttctat	7	9	1	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr9:99525914C>T	ENST00000375231.1	-	4	780	c.130G>A	c.(130-132)Gca>Aca	p.A44T	ZNF510_ENST00000223428.4_Splice_Site_p.A44T|ZNF510_ENST00000472201.1_5'UTR			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	44					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				GACACTGATGCCTGTAACAGT	0.398																																					p.A44T		Atlas-SNP	.											.	ZNF510	59	.	0			c.G130A						.						86	82	83					9																	99525914		2203	4300	6503	SO:0001630	splice_region_variant	22869	exon4			CTGATGCCTGTAA	AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"Zinc fingers, C2H2-type", "-"	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.130-1G>A	chr9.hg19:g.99525914C>T		66.0	0.0		54.0	27.0	NM_014930	Q5SZP5	Missense_Mutation	SNP	ENST00000375231.1	hg19	CCDS35074.1	.	.	.	.	.	.	.	.	.	.	c	19.09	3.760827	0.69763	.	.	ENSG00000081386	ENST00000375231;ENST00000223428;ENST00000374641	T;T;T	0.00808	5.67;5.67;5.67	3.29	1.35	0.21983	Krueppel-associated box (1);	.	.	.	.	T	0.00608	0.0020	N	0.08118	0	0.09310	N	1	P	0.36065	0.535	B	0.34301	0.179	T	0.51585	-0.8687	9	0.39692	T	0.17	.	5.4816	0.16727	0.199:0.6869:0.0:0.1141	.	44	Q9Y2H8	ZN510_HUMAN	T	44	ENSP00000364379:A44T;ENSP00000223428:A44T;ENSP00000363772:A44T	ENSP00000223428:A44T	A	-	1	0	ZNF510	98565735	0.771000	0.28555	0.016000	0.15963	0.404000	0.30871	1.147000	0.31602	0.376000	0.24707	0.655000	0.94253	GCA	.	.		0.398	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930	Missense_Mutation	T	99525914	C	T	99525914	5	4	75	1	0	0	0	0	0	0	1	0	17969	753	26	3	1933	3	ZNF510	9	99525914	Splice_Site	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	63302537	99525914	41687517	78	10201										
ABCA1	19	hgsc.bcm.edu	37	chr9	107595004	107595004	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ggctgtccaatctaagccatCcaactgctgttcccaaaagt	7	13	1	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr9:107595004C>T	ENST00000374736.3	-	12	1754	c.1360G>A	c.(1360-1362)Gat>Aat	p.D454N	ABCA1_ENST00000494467.1_5'Flank	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	454					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	TCTAAGCCATCCAACTGCTGT	0.488																																					p.D454N		Atlas-SNP	.											.	ABCA1	244	.	0			c.G1360A						.						201	159	173					9																	107595004		2203	4300	6503	SO:0001583	missense	19	exon12			AGCCATCCAACTG	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.1360G>A	chr9.hg19:g.107595004C>T	ENSP00000363868:p.Asp454Asn	158.0	0.0		105.0	24.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.392658	0.25118	.	.	ENSG00000165029	ENST00000374736	D	0.84873	-1.91	5.37	1.47	0.22746	.	0.966711	0.08613	N	0.919758	T	0.56891	0.2016	N	0.00707	-1.245	0.44523	D	0.99747	B	0.02656	0.0	B	0.01281	0.0	T	0.51482	-0.8700	10	0.20046	T	0.44	.	5.0513	0.14511	0.0:0.4026:0.1613:0.4362	.	454	O95477	ABCA1_HUMAN	N	454	ENSP00000363868:D454N	ENSP00000363868:D454N	D	-	1	0	ABCA1	106634825	0.032000	0.19561	0.776000	0.31678	0.982000	0.71751	0.824000	0.27379	0.659000	0.30945	-0.251000	0.11542	GAT	.	.		0.488	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107595004	C	T	107595004	3	4	75	1	0	0	0	0	1	0	0	0	28	855	30	3	5581	3	ABCA1	9	107595004	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	8069090	107595004	33618427	79	10202										
DBC1	1620	hgsc.bcm.edu	37	chr9	121930349	121930349	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ctgcacatggcgcagctgttGttcccgcctatcacgcaggg	12	14	1	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr9:121930349G>C	ENST00000265922.3	-	8	1760	c.1299C>G	c.(1297-1299)aaC>aaG	p.N433K	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	433					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											CGCAGCTGTTGTTCCCGCCTA	0.632																																					p.N433K		Atlas-SNP	.											.	DBC1	194	.	0			c.C1299G						.						29	29	29					9																	121930349		2203	4300	6503	SO:0001583	missense	1620	exon8			GCTGTTGTTCCCG	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1299C>G	chr9.hg19:g.121930349G>C	ENSP00000265922:p.Asn433Lys	45.0	0.0		36.0	13.0	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	hg19	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.233538	0.79688	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.52754	0.65	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	L	0.36672	1.1	0.80722	D	1	D	0.53885	0.963	P	0.47402	0.546	T	0.52003	-0.8633	10	0.72032	D	0.01	-34.6636	19.8211	0.96595	0.0:0.0:1.0:0.0	.	433	O60477	DBC1_HUMAN	K	433	ENSP00000265922:N433K	ENSP00000265922:N433K	N	-	3	2	DBC1	120970170	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.771000	0.98977	2.687000	0.91594	0.655000	0.94253	AAC	.	.		0.632	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		C	121930349	G	C	121930349	3	2	75	1	0	0	0	0	1	0	0	0	4249	1368	48	4	990	4	DBC1	9	121930349	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	14335345	121930349	19283082	80	10203										
DBC1	1620	hgsc.bcm.edu	37	chr9	121976358	121976358	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ggcacaggtactccccctccCcattgcacatgatatagctc	7	16	0	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr9:121976358C>T	ENST00000265922.3	-	6	1222	c.761G>A	c.(760-762)gGg>gAg	p.G254E	BRINP1_ENST00000373964.2_Missense_Mutation_p.G254E	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	254					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											CTCCCCCTCCCCATTGCACAT	0.517																																					p.G254E		Atlas-SNP	.											DBC1,NS,carcinoma,0,1	DBC1	194	.	0			c.G761A						.						114	94	101					9																	121976358		2203	4300	6503	SO:0001583	missense	1620	exon6			CCCTCCCCATTGC	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.761G>A	chr9.hg19:g.121976358C>T	ENSP00000265922:p.Gly254Glu	110.0	0.0		70.0	40.0	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	hg19	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.290940	0.59976	.	.	ENSG00000078725	ENST00000373969;ENST00000265922;ENST00000373964	T;T	0.47869	2.41;0.83	5.59	4.68	0.58851	.	0.048659	0.85682	D	0.000000	T	0.55273	0.1910	L	0.42245	1.32	0.80722	D	1	P;D	0.71674	0.918;0.998	P;P	0.56823	0.604;0.807	T	0.57318	-0.7832	10	0.52906	T	0.07	-13.9737	14.8812	0.70534	0.1445:0.8555:0.0:0.0	.	254;254	O60477-2;O60477	.;DBC1_HUMAN	E	254	ENSP00000265922:G254E;ENSP00000363075:G254E	ENSP00000265922:G254E	G	-	2	0	DBC1	121016179	1.000000	0.71417	0.715000	0.30552	0.986000	0.74619	7.482000	0.81143	1.337000	0.45525	0.558000	0.71614	GGG	.	.		0.517	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		T	121976358	C	T	121976358	3	4	75	1	0	0	0	0	1	0	0	0	4249	623	22	3	1536	3	DBC1	9	121976358	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	46009	121976358	19237073	81	10204										
TTF1	7270	hgsc.bcm.edu	37	chr9	135276847	135276847	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ccactccctcgttaccttggCgcctcttgcacgtgcttgct	8	17	1	0	rs61741946	byFrequency	TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr9:135276847C>T	ENST00000334270.2	-	2	1401	c.1362G>A	c.(1360-1362)gcG>gcA	p.A454A		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	454					chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		GTTACCTTGGCGCCTCTTGCA	0.458													c|||	2	0.000399361	0.0015	0	5008	,	,		13701	0		0	False		,,,				2504	0				p.A454A		Atlas-SNP	.											.	TTF1	82	.	0			c.G1362A						.						99	99	99					9																	135276847		2203	4300	6503	SO:0001819	synonymous_variant	7270	exon2			CCTTGGCGCCTCT	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.1362G>A	chr9.hg19:g.135276847C>T		112.0	0.0		86.0	50.0	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Silent	SNP	ENST00000334270.2	hg19	CCDS6948.1																																																																																			.	C|0.987;T|0.013		0.458	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344		T	135276847	C	T	135276847	2	4	75	1	0	0	0	0	0	0	0	1	16733	755	27	1		1	TTF1	9	135276847	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	13300489	135276847	5936584	82	10205										
FAM171A1	221061	hgsc.bcm.edu	37	chr10	15290660	15290660	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agcttctggtcaaaccgccaCgccgcgacataggcattgtg	11	13	2	0	rs151163427	byFrequency	TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr10:15290660C>A	ENST00000378116.4	-	5	738	c.732G>T	c.(730-732)gcG>gcT	p.A244A	FAM171A1_ENST00000477161.1_5'UTR	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	244						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						CAAACCGCCACGCCGCGACAT	0.552																																					p.A244A		Atlas-SNP	.											.	FAM171A1	252	.	0			c.G732T						.						78	72	74					10																	15290660		2203	4300	6503	SO:0001819	synonymous_variant	221061	exon5			CCGCCACGCCGCG	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 38"	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.732G>T	chr10.hg19:g.15290660C>A		113.0	0.0		81.0	26.0	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Silent	SNP	ENST00000378116.4	hg19	CCDS31154.1																																																																																			.	C|1.000;T|0.000		0.552	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		A	15290660	C	A	15290660	2	1	75	1	0	0	0	0	0	0	0	1	5495	523	19	1		1	FAM171A1	10	15290660	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10		15290660	120244087	83	10206										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26455035	26455035	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aagtcgagcgaggagccccgCatgagccctgacacctgtgc	13	14	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr10:26455035C>G	ENST00000265944.5	+	27	3205	c.3039C>G	c.(3037-3039)cgC>cgG	p.R1013R	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1013	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AGGAGCCCCGCATGAGCCCTG	0.448																																					p.R1013R		Atlas-SNP	.											.	MYO3A	371	.	0			c.C3039G						.						158	171	166					10																	26455035		2203	4300	6503	SO:0001819	synonymous_variant	53904	exon27			GCCCCGCATGAGC	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3039C>G	chr10.hg19:g.26455035C>G		81.0	0.0		46.0	19.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	hg19	CCDS7148.1																																																																																			.	.		0.448	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		G	26455035	C	G	26455035	2	3	75	1	0	0	0	0	0	0	0	1	10085	697	25	4		4	MYO3A	10	26455035	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	11164375	26455035	109079712	84	10207										
DLG5	9231	hgsc.bcm.edu	37	chr10	79569437	79569437	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agctccagctgggactttttGatgaagacaacgcgtggctc	12	10	0	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr10:79569437G>A	ENST00000372391.2	-	24	4520	c.4515C>T	c.(4513-4515)atC>atT	p.I1505I	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Silent_p.I1165I	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1505	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			GGGACTTTTTGATGAAGACAA	0.542																																					p.I1505I		Atlas-SNP	.											.	DLG5	154	.	0			c.C4515T						.						190	190	190					10																	79569437		2203	4300	6503	SO:0001819	synonymous_variant	9231	exon24			CTTTTTGATGAAG	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"discs, large (Drosophila) homolog 5"			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.4515C>T	chr10.hg19:g.79569437G>A		240.0	0.0		207.0	55.0	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	hg19	CCDS7353.2																																																																																			.	.		0.542	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			A	79569437	G	A	79569437	2	1	75	1	0	0	0	0	0	0	0	1	4560	1280	45	3		3	DLG5	10	79569437	Silent	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	53114402	79569437	55965310	85	10208										
HECTD2	143279	hgsc.bcm.edu	37	chr10	93252211	93252211	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ctaaagaatggttccttcttCtaattcgccaaatttttcat	4	9	3	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr10:93252211C>G	ENST00000298068.5	+	13	1496	c.1402C>G	c.(1402-1404)Cta>Gta	p.L468V	HECTD2_ENST00000446394.1_Missense_Mutation_p.L472V|HECTD2_ENST00000371667.1_Missense_Mutation_p.L118V|HECTD2_ENST00000536715.1_Missense_Mutation_p.L57V	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	468	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						GTTCCTTCTTCTAATTCGCCA	0.338																																					p.L468V	NSCLC(12;376 469 1699 39910 41417)	Atlas-SNP	.											.	HECTD2	60	.	0			c.C1402G						.						112	110	111					10																	93252211		2203	4299	6502	SO:0001583	missense	143279	exon13			CTTCTTCTAATTC	AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"HECT domain containing 2"			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.1402C>G	chr10.hg19:g.93252211C>G	ENSP00000298068:p.Leu468Val	73.0	0.0		104.0	39.0	NM_182765	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Missense_Mutation	SNP	ENST00000298068.5	hg19	CCDS7414.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.154727	0.78114	.	.	ENSG00000165338	ENST00000446394;ENST00000298068;ENST00000536715;ENST00000371667	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	5.28	4.37	0.52481	HECT (4);	0.000000	0.64402	D	0.000002	T	0.64046	0.2563	L	0.61218	1.895	0.54753	D	0.999986	P;D	0.71674	0.844;0.998	P;D	0.69307	0.842;0.963	T	0.66196	-0.5984	10	0.51188	T	0.08	.	14.4632	0.67465	0.0:0.9284:0.0:0.0716	.	472;468	E7ERR3;Q5U5R9	.;HECD2_HUMAN	V	472;468;57;118	ENSP00000401023:L472V;ENSP00000298068:L468V;ENSP00000439687:L57V;ENSP00000360731:L118V	ENSP00000298068:L468V	L	+	1	2	HECTD2	93242191	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.134000	0.57990	1.359000	0.45940	0.655000	0.94253	CTA	.	.		0.338	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1			G	93252211	C	G	93252211	3	3	75	1	0	0	0	0	1	0	0	0	7049	912	32	4	1476	4	HECTD2	10	93252211	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	13682774	93252211	42282536	86	10209										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6550235	6550235	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tggtcccatcaagaactacgTgacgctggtgagccgcctga	12	12	1	4			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr11:6550235T>A	ENST00000527990.2	+	10	2231	c.2231T>A	c.(2230-2232)gTg>gAg	p.V744E	DNHD1_ENST00000254579.6_Missense_Mutation_p.V744E			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	744					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AAGAACTACGTGACGCTGGTG	0.522																																					p.V744E		Atlas-SNP	.											.	DNHD1	198	.	0			c.T2231A						.						150	139	142					11																	6550235		692	1591	2283	SO:0001583	missense	144132	exon12			ACTACGTGACGCT	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.2231T>A	chr11.hg19:g.6550235T>A	ENSP00000436180:p.Val744Glu	95.0	0.0		81.0	14.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.017813	0.35606	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210	T;T	0.25414	1.8;1.8	5.54	0.0919	0.14470	.	.	.	.	.	T	0.12518	0.0304	L	0.32530	0.975	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.37820	-0.9689	9	0.02654	T	1	.	2.489	0.04606	0.1418:0.0809:0.2942:0.4831	.	744	Q96M86	DNHD1_HUMAN	E	744;744;10	ENSP00000254579:V744E;ENSP00000436180:V744E	ENSP00000254579:V744E	V	+	2	0	DNHD1	6506811	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.332000	0.07904	-0.242000	0.09667	0.528000	0.53228	GTG	.	.		0.522	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6550235	T	A	6550235	3	1	75	1	0	0	0	0	1	0	0	0	4670	1696	59	4	2278	4	DNHD1	11	6550235	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10		6550235	128456281	87	10210										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6644337	6644337	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tctggttaataccaaaatagGgggaagaggtggcaagggaa	15	4	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr11:6644337G>T	ENST00000299441.3	-	21	8981	c.8570C>A	c.(8569-8571)cCc>cAc	p.P2857H	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2857	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCAAAATAGGGGGAAGAGGT	0.637																																					p.P2857H		Atlas-SNP	.											.	DCHS1	277	.	0			c.C8570A						.						32	30	31					11																	6644337		2201	4294	6495	SO:0001583	missense	8642	exon21			AAATAGGGGGAAG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.8570C>A	chr11.hg19:g.6644337G>T	ENSP00000299441:p.Pro2857His	35.0	0.0		44.0	17.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	G	16.46	3.130236	0.56721	.	.	ENSG00000166341	ENST00000299441	T	0.64991	-0.13	4.97	4.97	0.65823	Cadherin (3);Cadherin-like (1);	0.000000	0.39146	N	0.001444	T	0.79381	0.4436	M	0.82132	2.575	0.58432	D	0.999997	D	0.89917	1.0	D	0.76071	0.987	T	0.78094	-0.2338	10	0.33141	T	0.24	.	16.9706	0.86298	0.0:0.0:1.0:0.0	.	2857	Q96JQ0	PCD16_HUMAN	H	2857	ENSP00000299441:P2857H	ENSP00000299441:P2857H	P	-	2	0	DCHS1	6600913	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.860000	0.86993	2.587000	0.87381	0.655000	0.94253	CCC	.	.		0.637	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		T	6644337	G	T	6644337	3	4	75	1	0	0	0	0	1	0	0	0	4289	1232	43	3	1330	3	DCHS1	11	6644337	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	94102	6644337	128362179	88	10211										
SLC6A5	9152	hgsc.bcm.edu	37	chr11	20622906	20622906	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ctgagcggccaggagtggggTcttgcaaactcagtagcccg	15	11	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr11:20622906T>A	ENST00000525748.1	+	2	508	c.235T>A	c.(235-237)Tct>Act	p.S79T		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	79					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	AGGAGTGGGGTCTTGCAAACT	0.726																																					p.S79T		Atlas-SNP	.											.	SLC6A5	151	.	0			c.T235A						.						6	8	7					11																	20622906		2157	4220	6377	SO:0001583	missense	9152	exon2			GTGGGGTCTTGCA	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"Solute carriers"	11051	protein-coding gene	gene with protein product	"glycine transporter 2"	604159	"solute carrier family 6 (neurotransmitter transporter, glycine), member 5"	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.235T>A	chr11.hg19:g.20622906T>A	ENSP00000434364:p.Ser79Thr	25.0	0.0		15.0	7.0	NM_004211	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	hg19	CCDS7854.1	.	.	.	.	.	.	.	.	.	.	T	9.749	1.166952	0.21621	.	.	ENSG00000165970	ENST00000525748	T	0.70986	-0.53	5.7	2.15	0.27550	.	1.035280	0.07660	N	0.933577	T	0.47801	0.1465	N	0.08118	0	0.20403	N	0.999904	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	10	0.33141	T	0.24	.	5.0054	0.14286	0.1471:0.0:0.359:0.4938	.	79	Q9Y345	SC6A5_HUMAN	T	79	ENSP00000434364:S79T	ENSP00000298923:S79T	S	+	1	0	SLC6A5	20579482	0.606000	0.26949	0.332000	0.25469	0.993000	0.82548	0.764000	0.26532	0.611000	0.30052	0.379000	0.24179	TCT	.	.		0.726	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211		A	20622906	T	A	20622906	3	1	75	1	0	0	0	0	1	0	0	0	14702	1667	58	4	241	4	SLC6A5	11	20622906	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	13978569	20622906	114383610	89	10212										
PAMR1	25891	hgsc.bcm.edu	37	chr11	35513688	35513688	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tacccccccatgagccatttCggcagctcttgcagttttca	7	15	2	1	rs377041707		TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr11:35513688C>A	ENST00000378880.2	-	3	729	c.284G>T	c.(283-285)cGa>cTa	p.R95L	PAMR1_ENST00000378878.3_Missense_Mutation_p.R95L|PAMR1_ENST00000534803.1_5'UTR|PAMR1_ENST00000532848.1_Missense_Mutation_p.R55L|PAMR1_ENST00000278360.3_Missense_Mutation_p.R95L	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	95						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						TGAGCCATTTCGGCAGCTCTT	0.522																																					p.R95L		Atlas-SNP	.											.	PAMR1	85	.	0			c.G284T						.						186	181	183					11																	35513688		2202	4298	6500	SO:0001583	missense	25891	exon3			CCATTTCGGCAGC		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"regeneration-associated muscle protease"					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.284G>T	chr11.hg19:g.35513688C>A	ENSP00000368158:p.Arg95Leu	68.0	0.0		74.0	25.0	NM_001001991	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	hg19	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.644264	0.67244	.	.	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605;ENST00000529303	D;D;D;D;D;D	0.90620	-2.27;-2.31;-2.47;-2.28;-2.27;-2.7	5.25	4.33	0.51752	Epidermal growth factor-like (1);	0.459441	0.22469	N	0.059650	D	0.82481	0.5046	N	0.14661	0.345	0.23620	N	0.997279	P;D;P	0.54207	0.533;0.965;0.477	B;B;B	0.43123	0.097;0.409;0.061	T	0.76124	-0.3074	10	0.87932	D	0	.	10.0175	0.42022	0.0:0.8448:0.0:0.1552	.	95;95;95	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	L	95;95;95;55;55;95	ENSP00000278360:R95L;ENSP00000368158:R95L;ENSP00000368156:R95L;ENSP00000433868:R55L;ENSP00000432591:R55L;ENSP00000433024:R95L	ENSP00000278360:R95L	R	-	2	0	PAMR1	35470264	0.992000	0.36948	0.953000	0.39169	0.882000	0.50991	2.398000	0.44486	1.212000	0.43366	0.491000	0.48974	CGA	.	.		0.522	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430		A	35513688	C	A	35513688	3	1	75	1	0	0	0	0	1	0	0	0	11422	884	31	1	1969	1	PAMR1	11	35513688	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	14890782	35513688	99492828	90	10213										
OR4P4	81300	hgsc.bcm.edu	37	chr11	55405983	55405983	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	atgatttctatcacgtgcacCcagctcattcaccaacccat	4	15	4	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr11:55405983C>A	ENST00000314612.2	+	1	150	c.150C>A	c.(148-150)acC>acA	p.T50T		NM_001004124.1	NP_001004124.1	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P, member 4	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|central_nervous_system(1)|kidney(4)|large_intestine(4)|lung(28)|ovary(1)|upper_aerodigestive_tract(1)	40						TCACGTGCACCCAGCTCATTC	0.388																																					p.T50T		Atlas-SNP	.											.	OR4P4	84	.	0			c.C150A						.						180	156	164					11																	55405983		2180	4035	6215	SO:0001819	synonymous_variant	81300	exon1			GTGCACCCAGCTC	AB065775	CCDS31504.1	11q11	2012-08-09			ENSG00000181927	ENSG00000181927		"GPCR / Class A : Olfactory receptors"	15180	protein-coding gene	gene with protein product				OR4P3P			Standard	NM_001004124		Approved		uc010rij.2	Q8NGL7	OTTHUMG00000165300	ENST00000314612.2:c.150C>A	chr11.hg19:g.55405983C>A		66.0	0.0		68.0	24.0	NM_001004124		Silent	SNP	ENST00000314612.2	hg19	CCDS31504.1																																																																																			.	.		0.388	OR4P4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383356.1	NM_001004124		A	55405983	C	A	55405983	2	1	75	1	0	0	0	0	0	0	0	1	11089	610	22	3		3	OR4P4	11	55405983	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	19892295	55405983	79600533	91	10214										
CASP4	837	hgsc.bcm.edu	37	chr11	104819283	104819283	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gcgttgaagagcagaaagcaAtgaagtccttctccacgtgg	12	9	1	4			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr11:104819283A>G	ENST00000444739.2	-	6	1812	c.902T>C	c.(901-903)aTt>aCt	p.I301T	CASP4_ENST00000393150.3_Missense_Mutation_p.I245T|CASP4_ENST00000531333.1_5'Flank	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	301					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		GCAGAAAGCAATGAAGTCCTT	0.468																																					p.I301T		Atlas-SNP	.											.	CASP4	57	.	0			c.T902C						.						162	117	132					11																	104819283		2202	4299	6501	SO:0001583	missense	837	exon6			AAAGCAATGAAGT	U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"Caspases"	1505	protein-coding gene	gene with protein product		602664	"caspase 4, apoptosis-related cysteine protease"			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.902T>C	chr11.hg19:g.104819283A>G	ENSP00000388566:p.Ile301Thr	78.0	0.0		48.0	21.0	NM_001225	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	hg19	CCDS8327.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.861050	0.71949	.	.	ENSG00000196954	ENST00000444739;ENST00000393150;ENST00000355546	T;T	0.27402	1.67;1.67	5.08	5.08	0.68730	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.177207	0.47093	D	0.000256	T	0.57577	0.2063	M	0.93016	3.37	0.40390	D	0.979531	P	0.51147	0.942	P	0.55222	0.771	T	0.70132	-0.4956	10	0.87932	D	0	.	12.7845	0.57496	1.0:0.0:0.0:0.0	.	301	P49662	CASP4_HUMAN	T	301;245;254	ENSP00000388566:I301T;ENSP00000376857:I245T	ENSP00000347741:I254T	I	-	2	0	CASP4	104324493	1.000000	0.71417	0.993000	0.49108	0.934000	0.57294	6.209000	0.72171	1.904000	0.55121	0.397000	0.26171	ATT	.	.		0.468	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225		G	104819283	A	G	104819283	3	3	75	1	0	0	0	0	1	0	0	0	2675	101	4	2	243	2	CASP4	11	104819283	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	49413300	104819283	30187233	92	10215										
CASP5	838	hgsc.bcm.edu	37	chr11	104872821	104872821	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tgaagcagccttttcatcccCacgatgtcatagtgagcccc	8	14	2	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr11:104872821C>A	ENST00000260315.3	-	5	650	c.651G>T	c.(649-651)gtG>gtT	p.V217V	CASP5_ENST00000393141.2_Silent_p.V230V|CASP5_ENST00000526056.1_Silent_p.V230V|CASP5_ENST00000531367.1_Silent_p.V75V|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000418434.1_Silent_p.V75V|CASP5_ENST00000444749.2_Silent_p.V159V			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	217			V -> L (in dbSNP:rs3181326). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.7}.		apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		TTTTCATCCCCACGATGTCAT	0.493																																					p.V230V		Atlas-SNP	.											.	CASP5	213	.	0			c.G690T						.						153	131	139					11																	104872821		2202	4299	6501	SO:0001819	synonymous_variant	838	exon5			CATCCCCACGATG		CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"Caspases"	1506	protein-coding gene	gene with protein product		602665	"caspase 5, apoptosis-related cysteine protease"			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.651G>T	chr11.hg19:g.104872821C>A		121.0	0.0		93.0	26.0	NM_001136112	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Silent	SNP	ENST00000260315.3	hg19	CCDS8328.2																																																																																			.	.		0.493	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347		A	104872821	C	A	104872821	2	1	75	1	0	0	0	0	0	0	0	1	2676	581	21	3		3	CASP5	11	104872821	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	53538	104872821	30133695	93	10216										
PDZD3	79849	hgsc.bcm.edu	37	chr11	119059407	119059407	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ggctcccgcctcgccccgggGcagcagctcagcctcactgg	13	19	2	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr11:119059407G>C	ENST00000531114.1	+	7	1865	c.1316G>C	c.(1315-1317)gGc>gCc	p.G439A	PDZD3_ENST00000392817.2_Missense_Mutation_p.G439A|PDZD3_ENST00000322712.4_Missense_Mutation_p.G359A|PDZD3_ENST00000525131.1_Missense_Mutation_p.G360A|PDZD3_ENST00000355547.5_Missense_Mutation_p.G373A			Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	439					cGMP-mediated signaling (GO:0019934)|ion transport (GO:0006811)|negative regulation of cGMP biosynthetic process (GO:0030827)|negative regulation of guanylate cyclase activity (GO:0031283)|receptor guanylyl cyclase signaling pathway (GO:0007168)|response to toxic substance (GO:0009636)|water transport (GO:0006833)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|subapical complex (GO:0035003)	guanylate cyclase inhibitor activity (GO:0030251)|ion channel inhibitor activity (GO:0008200)|protein C-terminus binding (GO:0008022)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	14	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)		TCGCCCCGGGGCAGCAGCTCA	0.607																																					p.G373A		Atlas-SNP	.											.	PDZD3	42	.	0			c.G1118C						.						62	57	59					11																	119059407		2200	4295	6495	SO:0001583	missense	79849	exon9			CCCGGGGCAGCAG	AK091966	CCDS8417.1, CCDS53719.1	11q23.3	2008-02-05	2006-01-24	2006-01-24	ENSG00000172367	ENSG00000172367			19891	protein-coding gene	gene with protein product		607146	"PDZ domain containing 2"	PDZK2		11950846	Standard	NM_024791		Approved	FLJ22756, IKEPP	uc001pvz.3	Q86UT5	OTTHUMG00000166224	ENST00000531114.1:c.1316G>C	chr11.hg19:g.119059407G>C	ENSP00000431164:p.Gly439Ala	178.0	0.0		102.0	44.0	NM_001168468	Q8N6R4|Q8NAW7|Q8NEX7|Q9H5Z3	Missense_Mutation	SNP	ENST00000531114.1	hg19		.	.	.	.	.	.	.	.	.	.	G	3.342	-0.134380	0.06711	.	.	ENSG00000172367	ENST00000525131;ENST00000531114;ENST00000355547;ENST00000322712;ENST00000454065;ENST00000392817	T;T;T;T;T	0.72725	1.68;1.64;1.68;-0.68;1.64	5.21	0.106	0.14540	PDZ/DHR/GLGF (1);	2.366130	0.01524	N	0.018466	T	0.49236	0.1545	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.23226	-1.0194	10	0.07990	T	0.79	-2.0671	0.9742	0.01422	0.4383:0.142:0.2639:0.1558	.	360;439;373;359	E9PPZ1;Q86UT5;Q86UT5-2;B0YJ61	.;NHRF4_HUMAN;.;.	A	360;439;373;359;373;439	ENSP00000434559:G360A;ENSP00000431164:G439A;ENSP00000347742:G373A;ENSP00000327107:G359A;ENSP00000376564:G439A	ENSP00000327107:G359A	G	+	2	0	PDZD3	118564617	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.103000	0.15292	-0.238000	0.09724	-0.302000	0.09304	GGC	.	.		0.607	PDZD3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388471.1	NM_024791		C	119059407	G	C	119059407	3	2	75	1	0	0	0	0	1	0	0	0	11711	1203	42	4	1152	4	PDZD3	11	119059407	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	14186586	119059407	15947109	94	10217										
GRIK4	2900	hgsc.bcm.edu	37	chr11	120811107	120811107	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttacagctgaacgggagaagGtgattgatttctctaagcca	11	7	1	4			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr11:120811107G>T	ENST00000527524.2	+	14	1815	c.1528G>T	c.(1528-1530)Gtg>Ttg	p.V510L	GRIK4_ENST00000438375.2_Missense_Mutation_p.V510L	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	510					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		ACGGGAGAAGGTGATTGATTT	0.443																																					p.V510L		Atlas-SNP	.											.	GRIK4	149	.	0			c.G1528T						.						104	104	104					11																	120811107		2203	4299	6502	SO:0001583	missense	2900	exon12			GAGAAGGTGATTG	S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1528G>T	chr11.hg19:g.120811107G>T	ENSP00000435648:p.Val510Leu	75.0	0.0		55.0	15.0	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	hg19	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267073	0.80469	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.12465	2.68;2.68	5.56	5.56	0.83823	Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.23688	0.0573	M	0.77616	2.38	0.80722	D	1	B;B	0.31026	0.304;0.199	B;B	0.29785	0.107;0.093	T	0.03374	-1.1043	10	0.87932	D	0	.	19.1145	0.93332	0.0:0.0:1.0:0.0	.	510;510	A6H8K8;Q16099	.;GRIK4_HUMAN	L	510	ENSP00000435648:V510L;ENSP00000404063:V510L	ENSP00000404063:V510L	V	+	1	0	GRIK4	120316317	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.809000	0.99208	2.626000	0.88956	0.655000	0.94253	GTG	.	.		0.443	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		T	120811107	G	T	120811107	3	4	75	1	0	0	0	0	1	0	0	0	6785	1261	44	3	1574	3	GRIK4	11	120811107	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	1751700	120811107	14195409	95	10218										
ERC1	23085	hgsc.bcm.edu	37	chr12	1192448	1192448	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	accttgtgtagcagagctgaCagaggagaactttcagaggc	13	8	1	5			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:1192448C>G	ENST00000397203.2	+	3	1194	c.788C>G	c.(787-789)aCa>aGa	p.T263R	ERC1_ENST00000546231.2_Missense_Mutation_p.T263R|ERC1_ENST00000543086.3_Missense_Mutation_p.T263R|ERC1_ENST00000589028.1_Missense_Mutation_p.T263R|ERC1_ENST00000360905.4_Missense_Mutation_p.T263R|ERC1_ENST00000355446.5_Missense_Mutation_p.T263R			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	263					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			GCAGAGCTGACAGAGGAGAAC	0.517																																					p.T263R		Atlas-SNP	.											.	ERC1	95	.	0			c.C788G						.						85	77	79					12																	1192448		2203	4300	6503	SO:0001583	missense	23085	exon3			AGCTGACAGAGGA	AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"RAB6 interacting protein 2"	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.788C>G	chr12.hg19:g.1192448C>G	ENSP00000380386:p.Thr263Arg	76.0	0.0		107.0	13.0	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	hg19	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168205	0.78339	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000543086;ENST00000542302;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394;ENST00000538971	T;T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89	5.62	5.62	0.85841	.	0.050212	0.85682	D	0.000000	T	0.60741	0.2292	L	0.59436	1.845	0.58432	D	0.99999	D;D;D;D	0.76494	0.995;0.982;0.994;0.999	D;P;P;D	0.76071	0.962;0.837;0.84;0.987	T	0.49341	-0.8950	10	0.15066	T	0.55	-15.5413	20.0247	0.97519	0.0:1.0:0.0:0.0	.	39;263;263;263	F5H327;Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;.;RB6I2_HUMAN	R	263;263;263;263;263;263;263;263;263;263;39	ENSP00000340054:T263R;ENSP00000380386:T263R;ENSP00000438546:T263R;ENSP00000445336:T263R;ENSP00000442739:T263R;ENSP00000347621:T263R;ENSP00000354158:T263R;ENSP00000410064:T263R	ENSP00000340054:T263R	T	+	2	0	ERC1	1062709	1.000000	0.71417	0.965000	0.40720	0.955000	0.61496	4.759000	0.62227	2.804000	0.96469	0.655000	0.94253	ACA	.	.		0.517	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		G	1192448	C	G	1192448	3	3	75	1	0	0	0	0	1	0	0	0	5212	478	17	4	794	4	ERC1	12	1192448	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10		1192448	132659447	96	10219										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26752255	26752255	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	taattgttcatgaagatgtgCcgcatggtttctgcttcaag	10	7	3	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:26752255C>T	ENST00000381340.3	-	30	4241	c.3825G>A	c.(3823-3825)cgG>cgA	p.R1275R		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1275					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TGAAGATGTGCCGCATGGTTT	0.433																																					p.R1275R		Atlas-SNP	.											.	ITPR2	270	.	0			c.G3825A						.						185	169	174					12																	26752255		1981	4183	6164	SO:0001819	synonymous_variant	3709	exon30			GATGTGCCGCATG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.3825G>A	chr12.hg19:g.26752255C>T		87.0	0.0		84.0	14.0	NM_002223	O94773	Silent	SNP	ENST00000381340.3	hg19	CCDS41764.1																																																																																			.	.		0.433	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		T	26752255	C	T	26752255	2	4	75	1	0	0	0	0	0	0	0	1	7930	726	26	3		3	ITPR2	12	26752255	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	25559807	26752255	107099640	97	10220										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40740721	40740721	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttagaaatacaaggaaaattAcctggtaagttctgttttct	7	5	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:40740721A>T	ENST00000298910.7	+	42	6334	c.6276A>T	c.(6274-6276)ttA>ttT	p.L2092F		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2092	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AAGGAAAATTACCTGGTAAGT	0.299																																					p.L2092F		Atlas-SNP	.											.	LRRK2	763	.	0			c.A6276T						.						49	51	50					12																	40740721		2203	4300	6503	SO:0001583	missense	120892	exon42			AAAATTACCTGGT	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.6276A>T	chr12.hg19:g.40740721A>T	ENSP00000298910:p.Leu2092Phe	43.0	0.0		42.0	17.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	A	17.93	3.509423	0.64522	.	.	ENSG00000188906	ENST00000298910	T	0.66099	-0.19	5.6	-2.78	0.05859	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70081	0.3183	L	0.59436	1.845	0.46203	D	0.998924	P;D	0.76494	0.914;0.999	P;D	0.75484	0.685;0.986	T	0.66917	-0.5802	10	0.41790	T	0.15	.	12.8915	0.58073	0.4936:0.0:0.5064:0.0	.	2092;2092	Q17RV3;Q5S007	.;LRRK2_HUMAN	F	2092	ENSP00000298910:L2092F	ENSP00000298910:L2092F	L	+	3	2	LRRK2	39026988	0.985000	0.35326	0.965000	0.40720	0.986000	0.74619	0.277000	0.18734	-0.788000	0.04504	-0.269000	0.10298	TTA	.	.		0.299	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40740721	A	T	40740721	3	4	75	1	0	0	0	0	1	0	0	0	9042	388	14	4	6442	4	LRRK2	12	40740721	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	13988466	40740721	93111174	98	10221										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43769295	43769295	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttctactcccattaaaaggaCattgatatggattttttagt	6	6	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:43769295C>T	ENST00000389420.3	-	36	5332	c.5333G>A	c.(5332-5334)tGt>tAt	p.C1778Y		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1778	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ATTAAAAGGACATTGATATGG	0.358																																					p.C1778Y		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.G5333A						.						146	146	146					12																	43769295		2203	4300	6503	SO:0001583	missense	80070	exon36			AAAGGACATTGAT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.5333G>A	chr12.hg19:g.43769295C>T	ENSP00000374071:p.Cys1778Tyr	94.0	0.0		83.0	23.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	C	15.79	2.936072	0.52972	.	.	ENSG00000173157	ENST00000389420	T	0.39406	1.08	4.8	4.8	0.61643	Peptidase M12B, GON-ADAMTSs (2);	0.000000	0.56097	D	0.000038	T	0.71333	0.3327	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78006	-0.2373	10	0.87932	D	0	.	18.7512	0.91816	0.0:1.0:0.0:0.0	.	1778	P59510	ATS20_HUMAN	Y	1778	ENSP00000374071:C1778Y	ENSP00000374071:C1778Y	C	-	2	0	ADAMTS20	42055562	1.000000	0.71417	0.992000	0.48379	0.378000	0.30076	6.409000	0.73289	2.596000	0.87737	0.460000	0.39030	TGT	.	.		0.358	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43769295	C	T	43769295	3	4	75	1	0	0	0	0	1	0	0	0	266	478	17	3	414	3	ADAMTS20	12	43769295	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	3028574	43769295	90082600	99	10222										
AMIGO2	91523	hgsc.bcm.edu	37	chr12	47471425	47471425	+	5'Flank	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ctgccttccgttcatcagcgGaggcatcactagcggggcca	12	14	3	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:47471425G>A	ENST00000546455.1	+	0	0				AMIGO2_ENST00000321382.3_Missense_Mutation_p.S454F|AMIGO2_ENST00000266581.4_Missense_Mutation_p.S454F|AMIGO2_ENST00000550413.1_Missense_Mutation_p.S454F|AMIGO2_ENST00000429635.1_Missense_Mutation_p.S454F			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)										TTCATCAGCGGAGGCATCACT	0.517																																					p.S454F		Atlas-SNP	.											.	AMIGO2	50	.	0			c.C1361T						.						140	140	140					12																	47471425		2203	4300	6503	SO:0001631	upstream_gene_variant	347902	exon2			TCAGCGGAGGCAT	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617		chr12.hg19:g.47471425G>A	Exception_encountered	135.0	0.0		126.0	20.0	NM_181847	Q96B20	Missense_Mutation	SNP	ENST00000546455.1	hg19	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	G	9.285	1.049226	0.19827	.	.	ENSG00000139211	ENST00000266581;ENST00000550413;ENST00000429635;ENST00000321382	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.08	-0.142	0.13448	.	0.434925	0.21612	N	0.071766	T	0.30823	0.0777	L	0.39898	1.24	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.27434	-1.0074	10	0.10377	T	0.69	-0.2165	8.4226	0.32710	0.1357:0.3563:0.508:0.0	.	454	Q86SJ2	AMGO2_HUMAN	F	454	ENSP00000266581:S454F;ENSP00000449034:S454F;ENSP00000406020:S454F;ENSP00000320848:S454F	ENSP00000266581:S454F	S	-	2	0	AMIGO2	45757692	0.616000	0.27035	0.000000	0.03702	0.789000	0.44602	1.086000	0.30853	-0.126000	0.11682	-0.273000	0.10243	TCC	.	.		0.517	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		A	47471425	G	A	47471425	1	1	75	0	1	0	0	0	0	0	0	0	576	1174	41	3		3	AMIGO2	12	47471425	5'Flank	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	3702130	47471425	86380470	100	10223										
DNAJC22	79962	hgsc.bcm.edu	37	chr12	49743205	49743205	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cgctcagtgtgcggctctatCgtctgggcttggcttacctt	12	12	3	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:49743205C>G	ENST00000549441.2	+	3	1754	c.550C>G	c.(550-552)Cgt>Ggt	p.R184G	DNAJC22_ENST00000395069.3_Missense_Mutation_p.R184G			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	184						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						GCGGCTCTATCGTCTGGGCTT	0.577																																					p.R184G		Atlas-SNP	.											.	DNAJC22	29	.	0			c.C550G						.						76	74	75					12																	49743205		2203	4300	6503	SO:0001583	missense	79962	exon2			CTCTATCGTCTGG	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"Heat shock proteins / DNAJ (HSP40)"	25802	protein-coding gene	gene with protein product	"wurst homolog (Drosophila)"					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.550C>G	chr12.hg19:g.49743205C>G	ENSP00000446830:p.Arg184Gly	37.0	0.0		42.0	19.0	NM_024902	B3KP54	Missense_Mutation	SNP	ENST00000549441.2	hg19	CCDS8785.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.501000	0.44455	.	.	ENSG00000178401	ENST00000549441;ENST00000395069	T;T	0.46451	0.87;0.87	4.87	2.03	0.26663	.	0.095437	0.64402	D	0.000001	T	0.35770	0.0943	M	0.66939	2.045	0.48696	D	0.999699	P	0.44578	0.838	B	0.40199	0.322	T	0.07731	-1.0757	10	0.41790	T	0.15	-3.595	5.5044	0.16846	0.1384:0.6221:0.0:0.2395	.	184	Q8N4W6	DJC22_HUMAN	G	184	ENSP00000446830:R184G;ENSP00000378508:R184G	ENSP00000378508:R184G	R	+	1	0	DNAJC22	48029472	0.653000	0.27358	0.991000	0.47740	0.775000	0.43874	0.700000	0.25601	0.203000	0.20529	0.561000	0.74099	CGT	.	.		0.577	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902		G	49743205	C	G	49743205	3	3	75	1	0	0	0	0	1	0	0	0	4643	884	31	4	552	4	DNAJC22	12	49743205	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	2271780	49743205	84108690	101	10224										
LARP4	113251	hgsc.bcm.edu	37	chr12	50869325	50869325	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aaaggaaccccgaaagttaaGttatgctgaagtgtgccaga	11	7	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:50869325G>T	ENST00000398473.2	+	16	1965	c.1853G>T	c.(1852-1854)aGt>aTt	p.S618I	LARP4_ENST00000293618.8_Missense_Mutation_p.S547I|LARP4_ENST00000429001.3_Missense_Mutation_p.S624I|LARP4_ENST00000518444.1_Missense_Mutation_p.S617I|LARP4_ENST00000347328.5_Missense_Mutation_p.S547I	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	618					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						CGAAAGTTAAGTTATGCTGAA	0.378																																					p.S618I		Atlas-SNP	.											.	LARP4	58	.	0			c.G1853T						.						201	200	200					12																	50869325		1812	4087	5899	SO:0001583	missense	113251	exon16			AGTTAAGTTATGC	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.1853G>T	chr12.hg19:g.50869325G>T	ENSP00000381490:p.Ser618Ile	103.0	0.0		82.0	14.0	NM_052879	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Missense_Mutation	SNP	ENST00000398473.2	hg19	CCDS41782.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153560	0.78114	.	.	ENSG00000161813	ENST00000293618;ENST00000429001;ENST00000398473;ENST00000518444;ENST00000520064;ENST00000347328	T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.74344	0.3704	M	0.75777	2.31	0.80722	D	1	P;B;P;D;D;B;B	0.89917	0.468;0.117;0.766;1.0;1.0;0.134;0.178	P;B;P;D;D;B;B	0.85130	0.453;0.082;0.527;0.997;0.997;0.124;0.173	T	0.76476	-0.2945	10	0.87932	D	0	.	19.6351	0.95728	0.0:0.0:1.0:0.0	.	499;28;617;547;547;618;624	Q71RC2-2;Q8WVX5;Q71RC2-3;G3XAA8;G5E976;Q71RC2;Q71RC2-4	.;.;.;.;.;LARP4_HUMAN;.	I	547;624;618;617;499;547	ENSP00000293618:S547I;ENSP00000415464:S624I;ENSP00000381490:S618I;ENSP00000429077:S617I;ENSP00000340901:S547I	ENSP00000293618:S547I	S	+	2	0	LARP4	49155592	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.089000	0.94137	2.728000	0.93425	0.643000	0.83706	AGT	.	.		0.378	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879		T	50869325	G	T	50869325	3	4	75	1	0	0	0	0	1	0	0	0	8639	1029	36	3	1919	3	LARP4	12	50869325	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	1126120	50869325	82982570	102	10225										
SCN8A	6334	hgsc.bcm.edu	37	chr12	52056683	52056683	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cactggcaaacattgagaggCgcattgctgagagcaagctc	12	10	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:52056683C>T	ENST00000354534.6	+	2	260	c.82C>T	c.(82-84)Cgc>Tgc	p.R28C	SCN8A_ENST00000550891.1_Missense_Mutation_p.R28C|SCN8A_ENST00000545061.1_Missense_Mutation_p.R28C	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	28					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	CATTGAGAGGCGCATTGCTGA	0.572																																					p.R28C		Atlas-SNP	.											.	SCN8A	331	.	0			c.C82T						.						106	107	107					12																	52056683		2029	4205	6234	SO:0001583	missense	6334	exon2			GAGAGGCGCATTG	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10596	protein-coding gene	gene with protein product		600702	"sodium channel, voltage gated, type VIII, alpha polypeptide"	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.82C>T	chr12.hg19:g.52056683C>T	ENSP00000346534:p.Arg28Cys	94.0	0.0		80.0	20.0	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	hg19	CCDS44891.1	.	.	.	.	.	.	.	.	.	.	C	32	5.150210	0.94645	.	.	ENSG00000196876	ENST00000550891;ENST00000354534;ENST00000545061;ENST00000355133	D;D;D;D	0.97772	-4.51;-4.53;-4.49;-4.39	4.97	4.97	0.65823	.	.	.	.	.	D	0.98692	0.9561	M	0.92738	3.34	0.80722	D	1	D	0.89917	1.0	P	0.54706	0.759	D	0.99751	1.1018	9	0.87932	D	0	.	18.7994	0.92010	0.0:1.0:0.0:0.0	.	28	Q9UQD0	SCN8A_HUMAN	C	28	ENSP00000448415:R28C;ENSP00000346534:R28C;ENSP00000440360:R28C;ENSP00000347255:R28C	ENSP00000346534:R28C	R	+	1	0	SCN8A	50342950	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.651000	0.83577	2.760000	0.94817	0.655000	0.94253	CGC	.	.		0.572	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		T	52056683	C	T	52056683	3	4	75	1	0	0	0	0	1	0	0	0	13939	768	27	1	84	1	SCN8A	12	52056683	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	1187358	52056683	81795212	103	10226										
GPR84	53831	hgsc.bcm.edu	37	chr12	54757483	54757483	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agcaggttgaatcgggtacgGagcttgggctggatggccaa	17	7	0	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:54757483G>C	ENST00000551809.1	-	1	788	c.153C>G	c.(151-153)ctC>ctG	p.L51L	GPR84_ENST00000267015.3_Silent_p.L51L|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						ATCGGGTACGGAGCTTGGGCT	0.587																																					p.L51L		Atlas-SNP	.											.	GPR84	38	.	0			c.C153G						.						185	157	166					12																	54757483		2203	4300	6503	SO:0001819	synonymous_variant	53831	exon2			GGTACGGAGCTTG	AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.153C>G	chr12.hg19:g.54757483G>C		68.0	0.0		66.0	23.0	NM_020370	B6V9G7	Silent	SNP	ENST00000551809.1	hg19	CCDS8878.1																																																																																			.	.		0.587	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			C	54757483	G	C	54757483	2	2	75	1	0	0	0	0	0	0	0	1	6722	1161	41	4		4	GPR84	12	54757483	Silent	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	2700800	54757483	79094412	104	10227										
LACRT	90070	hgsc.bcm.edu	37	chr12	55024698	55024698	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	atgcccatggttttaatagaCtgaatttcttcagtaatttt	6	6	2	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:55024698C>T	ENST00000257867.4	-	5	448	c.395G>A	c.(394-396)aGt>aAt	p.S132N	LACRT_ENST00000547511.1_Missense_Mutation_p.S121N	NM_033277.1	NP_150593.1	Q9GZZ8	LACRT_HUMAN	lacritin	132					calcineurin-NFAT signaling cascade (GO:0033173)|calcium-mediated signaling (GO:0019722)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of secretion (GO:0051047)|protein localization to Golgi apparatus (GO:0034067)|tear secretion (GO:0070075)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule (GO:0030141)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|growth factor activity (GO:0008083)|laminin-1 binding (GO:0043237)|protein N-terminus binding (GO:0047485)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(1)	10						TTTTAATAGACTGAATTTCTT	0.413																																					p.S132N		Atlas-SNP	.											.	LACRT	26	.	0			c.G395A						.						148	123	132					12																	55024698		2203	4300	6503	SO:0001583	missense	90070	exon5			AATAGACTGAATT	AF238867	CCDS8883.1	12q13.2	2014-06-13			ENSG00000135413				16430	protein-coding gene	gene with protein product		607360				11419941	Standard	NM_033277		Approved	LACRITIN	uc001sgi.1	Q9GZZ8	OTTHUMG00000169936	ENST00000257867.4:c.395G>A	chr12.hg19:g.55024698C>T	ENSP00000257867:p.Ser132Asn	133.0	0.0		128.0	13.0	NM_033277		Missense_Mutation	SNP	ENST00000257867.4	hg19	CCDS8883.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.755326	0.00663	.	.	ENSG00000135413	ENST00000547511;ENST00000257867	.	.	.	2.79	-5.58	0.02512	.	9.302310	0.00166	N	0.000008	T	0.18676	0.0448	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.30534	-0.9975	9	0.87932	D	0	.	3.3959	0.07305	0.4706:0.3363:0.0884:0.1047	.	132	Q9GZZ8	LACRT_HUMAN	N	121;132	.	ENSP00000257867:S132N	S	-	2	0	LACRT	53310965	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.838000	0.00052	-5.554000	0.00012	-0.471000	0.05019	AGT	.	.		0.413	LACRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406615.1	NM_033277		T	55024698	C	T	55024698	3	4	75	1	0	0	0	0	1	0	0	0	8605	565	20	3	25	3	LACRT	12	55024698	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	267215	55024698	78827197	105	10228										
HCFC2	29915	hgsc.bcm.edu	37	chr12	104480666	104480666	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aagtacagctgatcaaagccActaccaactcctttcatgtc	5	13	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:104480666A>G	ENST00000229330.4	+	8	1209	c.1105A>G	c.(1105-1107)Act>Gct	p.T369A		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	369	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						GATCAAAGCCACTACCAACTC	0.408																																					p.T369A	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-SNP	.											.	HCFC2	94	.	0			c.A1105G						.						171	151	158					12																	104480666		2203	4300	6503	SO:0001583	missense	29915	exon8			AAAGCCACTACCA	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1105A>G	chr12.hg19:g.104480666A>G	ENSP00000229330:p.Thr369Ala	91.0	0.0		116.0	28.0	NM_013320	B2R8Q5|C0H5X3	Missense_Mutation	SNP	ENST00000229330.4	hg19	CCDS9097.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.243258	0.79912	.	.	ENSG00000111727	ENST00000229330	T	0.56941	0.43	5.43	5.43	0.79202	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.52661	0.1748	L	0.53249	1.67	0.42186	D	0.991704	D	0.55172	0.97	P	0.48627	0.584	T	0.51364	-0.8715	10	0.08837	T	0.75	-19.468	15.4817	0.75534	1.0:0.0:0.0:0.0	.	369	Q9Y5Z7	HCFC2_HUMAN	A	369	ENSP00000229330:T369A	ENSP00000229330:T369A	T	+	1	0	HCFC2	103004796	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	7.919000	0.87513	2.054000	0.61138	0.528000	0.53228	ACT	.	.		0.408	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		G	104480666	A	G	104480666	3	3	75	1	0	0	0	0	1	0	0	0	7002	159	6	2	1135	2	HCFC2	12	104480666	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	49455968	104480666	29371229	106	10229										
MVK	4598	hgsc.bcm.edu	37	chr12	110032905	110032905	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cctctctggaccagctctgcCaggtgaccagggcccgcgga	13	16	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:110032905C>A	ENST00000228510.3	+	10	1034	c.958C>A	c.(958-960)Cag>Aag	p.Q320K	MVK_ENST00000539696.1_Missense_Mutation_p.Q39K|MVK_ENST00000392727.3_Missense_Mutation_p.Q268K|MVK_ENST00000541384.1_Missense_Mutation_p.Q126K|MVK_ENST00000539575.1_Missense_Mutation_p.Q268K	NM_000431.2|NM_001114185.1	NP_000422.1|NP_001107657.1	Q03426	KIME_HUMAN	mevalonate kinase	320					cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|negative regulation of inflammatory response (GO:0050728)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|mevalonate kinase activity (GO:0004496)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8						CCAGCTCTGCCAGGTGACCAG	0.627																																					p.Q320K		Atlas-SNP	.											.	MVK	42	.	0			c.C958A						.						83	78	80					12																	110032905		2203	4300	6503	SO:0001583	missense	4598	exon10			CTCTGCCAGGTGA	M88468	CCDS9132.1, CCDS73522.1	12q24	2014-09-17	2008-01-30		ENSG00000110921	ENSG00000110921	2.7.1.36		7530	protein-coding gene	gene with protein product	"LH receptor mRNA-binding protein", "mevalonic aciduria"	251170	"mevalonate kinase (mevalonic aciduria)"			1377680	Standard	XM_005253883		Approved	LRBP, MK	uc001toy.4	Q03426	OTTHUMG00000169256	ENST00000228510.3:c.958C>A	chr12.hg19:g.110032905C>A	ENSP00000228510:p.Gln320Lys	73.0	0.0		51.0	7.0	NM_000431		Missense_Mutation	SNP	ENST00000228510.3	hg19	CCDS9132.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.958252	0.53400	.	.	ENSG00000110921	ENST00000539696;ENST00000228510;ENST00000392727;ENST00000539575;ENST00000541384;ENST00000540353	D;D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59;-2.59	4.51	4.51	0.55191	GHMP kinase, C-terminal (1);	0.196139	0.43747	D	0.000527	T	0.77260	0.4104	N	0.17345	0.48	0.34003	D	0.650532	B;B	0.26744	0.002;0.158	B;B	0.21151	0.007;0.033	T	0.75470	-0.3306	10	0.09338	T	0.73	-11.6459	12.577	0.56369	0.0:1.0:0.0:0.0	.	268;320	F5H8H2;Q03426	.;KIME_HUMAN	K	39;320;268;268;126;39	ENSP00000439134:Q39K;ENSP00000228510:Q320K;ENSP00000376487:Q268K;ENSP00000443551:Q268K;ENSP00000443182:Q126K	ENSP00000228510:Q320K	Q	+	1	0	MVK	108517288	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.668000	0.61568	2.340000	0.79590	0.563000	0.77884	CAG	.	.		0.627	MVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403143.1	NM_000431		A	110032905	C	A	110032905	3	1	75	1	0	0	0	0	1	0	0	0	10004	595	21	3	992	3	MVK	12	110032905	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	5552239	110032905	23818990	107	10230										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130015669	130015669	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ggtgcatactttccagtataAtccgtgcgctccttgacatc	8	12	0	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:130015669A>T	ENST00000422113.2	-	3	1376	c.1050T>A	c.(1048-1050)gaT>gaA	p.D350E		NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	350					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TTCCAGTATAATCCGTGCGCT	0.517																																					p.D350E		Atlas-SNP	.											.	TMEM132D	299	.	0			c.T1050A						.						112	101	105					12																	130015669		2203	4300	6503	SO:0001583	missense	121256	exon3			AGTATAATCCGTG	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1050T>A	chr12.hg19:g.130015669A>T	ENSP00000408581:p.Asp350Glu	58.0	0.0		48.0	13.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	A	0.168	-1.074855	0.01903	.	.	ENSG00000151952	ENST00000422113	T	0.13089	2.62	5.09	-2.54	0.06307	.	0.339943	0.24559	N	0.037482	T	0.07593	0.0191	N	0.25890	0.77	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.34054	-0.9844	9	.	.	.	-5.9146	9.9494	0.41630	0.2388:0.6065:0.1547:0.0	.	350	Q14C87	T132D_HUMAN	E	350	ENSP00000408581:D350E	.	D	-	3	2	TMEM132D	128581622	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-0.802000	0.04545	-0.827000	0.04278	-0.290000	0.09829	GAT	.	.		0.517	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	130015669	A	T	130015669	3	4	75	1	0	0	0	0	1	0	0	0	16062	98	4	4	2277	4	TMEM132D	12	130015669	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	19982764	130015669	3836226	108	10231										
EP400	57634	hgsc.bcm.edu	37	chr12	132522532	132522532	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gctgtttgaagtttattctcCcatggatgatgctggcttcc	10	9	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr12:132522532C>A	ENST00000333577.4	+	33	6315	c.6206C>A	c.(6205-6207)cCc>cAc	p.P2069H	EP400_ENST00000332482.4_Missense_Mutation_p.P1996H|EP400_ENST00000330386.6_Missense_Mutation_p.P1952H|EP400_ENST00000389562.2_Missense_Mutation_p.P2032H|EP400_ENST00000389561.2_Missense_Mutation_p.P2033H			Q96L91	EP400_HUMAN	E1A binding protein p400	2069					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		GTTTATTCTCCCATGGATGAT	0.498																																					p.P2033H		Atlas-SNP	.											.	EP400	370	.	0			c.C6098A						.						229	208	215					12																	132522532		2203	4300	6503	SO:0001583	missense	57634	exon32			ATTCTCCCATGGA	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.6206C>A	chr12.hg19:g.132522532C>A	ENSP00000333602:p.Pro2069His	123.0	0.0		90.0	4.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	hg19		.	.	.	.	.	.	.	.	.	.	C	11.01	1.514410	0.27123	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.90563	-2.68;-2.68;-2.69;-2.68;-2.68	5.43	5.43	0.79202	.	0.000000	0.64402	D	0.000002	D	0.94149	0.8123	L	0.52573	1.65	0.44330	D	0.997216	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.94481	0.7693	10	0.72032	D	0.01	.	19.2486	0.93913	0.0:1.0:0.0:0.0	.	2033;1952;2032	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	H	2069;2033;2032;1996;1952;2033	ENSP00000333602:P2069H;ENSP00000374212:P2033H;ENSP00000374213:P2032H;ENSP00000331737:P1996H;ENSP00000330620:P1952H	ENSP00000330620:P1952H	P	+	2	0	EP400	131088485	0.978000	0.34361	0.449000	0.26957	0.365000	0.29674	3.737000	0.55060	2.534000	0.85438	0.650000	0.86243	CCC	.	.		0.498	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132522532	C	A	132522532	3	1	75	1	0	0	0	0	1	0	0	0	5151	623	22	3	6217	3	EP400	12	132522532	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	2506863	132522532	1329363	109	10232										
FREM2	341640	hgsc.bcm.edu	37	chr13	39422758	39422758	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	atgcctatgaacgcagccctTggcgagcccagcaaagccac	10	15	0	1	rs112083916	byFrequency	TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr13:39422758T>C	ENST00000280481.7	+	8	6546	c.6330T>C	c.(6328-6330)ctT>ctC	p.L2110L	FREM2_ENST00000482551.1_3'UTR	NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2110					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		ACGCAGCCCTTGGCGAGCCCA	0.433																																					p.L2110L		Atlas-SNP	.											.	FREM2	385	.	0			c.T6330C						.						88	86	87					13																	39422758		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon8			AGCCCTTGGCGAG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.6330T>C	chr13.hg19:g.39422758T>C		56.0	0.0		34.0	16.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	T|0.995;G|0.005		0.433	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39422758	T	C	39422758	2	2	75	1	0	0	0	0	0	0	0	1	6053	1799	63	2		2	FREM2	13	39422758	Silent	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10		39422758	75747120	110	10233										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42875560	42875560	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aactttagagtcaatgacatCattggaagttacaaaaatgg	8	5	2	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr13:42875560C>T	ENST00000025301.2	+	8	2853	c.2678C>T	c.(2677-2679)tCa>tTa	p.S893L		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	893					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TCAATGACATCATTGGAAGTT	0.368																																					p.S893L		Atlas-SNP	.											.	AKAP11	146	.	0			c.C2678T						.						33	33	33					13																	42875560		2203	4299	6502	SO:0001583	missense	11215	exon8			TGACATCATTGGA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.2678C>T	chr13.hg19:g.42875560C>T	ENSP00000025301:p.Ser893Leu	69.0	0.0		54.0	26.0	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.468526	0.63625	.	.	ENSG00000023516	ENST00000025301	T	0.19938	2.11	6.03	6.03	0.97812	.	0.163542	0.38897	N	0.001533	T	0.42154	0.1190	M	0.65975	2.015	0.47407	D	0.999411	D	0.56746	0.977	P	0.55923	0.787	T	0.02625	-1.1132	10	0.40728	T	0.16	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	893	Q9UKA4	AKA11_HUMAN	L	893	ENSP00000025301:S893L	ENSP00000025301:S893L	S	+	2	0	AKAP11	41773560	0.780000	0.28664	0.272000	0.24630	0.376000	0.30014	7.111000	0.77077	2.861000	0.98227	0.655000	0.94253	TCA	.	.		0.368	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		T	42875560	C	T	42875560	3	4	75	1	0	0	0	0	1	0	0	0	447	838	29	3	2700	3	AKAP11	13	42875560	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	3452802	42875560	72294318	111	10234										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42356467	42356467	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttgcagaagctaccacctgaCcctctctttcagcgagctca	7	15	3	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr14:42356467C>T	ENST00000298119.4	+	3	1828	c.639C>T	c.(637-639)gaC>gaT	p.D213D	LRFN5_ENST00000554120.1_Silent_p.D213D|LRFN5_ENST00000554171.1_Silent_p.D213D	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	213						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TACCACCTGACCCTCTCTTTC	0.428										HNSCC(30;0.082)																											p.D213D		Atlas-SNP	.											.	LRFN5	269	.	0			c.C639T						.						72	70	71					14																	42356467		2203	4300	6503	SO:0001819	synonymous_variant	145581	exon3			ACCTGACCCTCTC	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.639C>T	chr14.hg19:g.42356467C>T		91.0	0.0		57.0	28.0	NM_152447	B3KU78|Q86XL2	Silent	SNP	ENST00000298119.4	hg19	CCDS9678.1																																																																																			.	.		0.428	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		T	42356467	C	T	42356467	2	4	75	1	0	0	0	0	0	0	0	1	8950	506	18	3		3	LRFN5	14	42356467	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10		42356467	64993073	112	10235										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64491167	64491167	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agcttgaagactccttgcagCagctactgaggtaggaaata	11	8	0	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr14:64491167C>G	ENST00000344113.4	+	39	6042	c.5830C>G	c.(5830-5832)Cag>Gag	p.Q1944E	SYNE2_ENST00000554584.1_Missense_Mutation_p.Q1944E|SYNE2_ENST00000358025.3_Missense_Mutation_p.Q1944E|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	1944					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		CTCCTTGCAGCAGCTACTGAG	0.438																																					p.Q1944E		Atlas-SNP	.											.	SYNE2	577	.	0			c.C5830G						.						55	53	54					14																	64491167		1890	4120	6010	SO:0001583	missense	23224	exon39			TTGCAGCAGCTAC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.5830C>G	chr14.hg19:g.64491167C>G	ENSP00000341781:p.Gln1944Glu	30.0	0.0		44.0	9.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	C	7.103	0.574529	0.13623	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.35789	1.29;1.29;1.29	5.14	5.14	0.70334	.	0.000000	0.50627	D	0.000118	T	0.27278	0.0669	L	0.29908	0.895	0.80722	D	1	B;B	0.21905	0.037;0.062	B;B	0.26969	0.034;0.075	T	0.06445	-1.0826	10	0.06625	T	0.88	.	16.776	0.85550	0.0:1.0:0.0:0.0	.	1944;1944	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	E	1944	ENSP00000350719:Q1944E;ENSP00000341781:Q1944E;ENSP00000452570:Q1944E	ENSP00000261678:Q1944E	Q	+	1	0	SYNE2	63560920	1.000000	0.71417	0.987000	0.45799	0.004000	0.04260	3.168000	0.50801	2.386000	0.81285	0.585000	0.79938	CAG	.	.		0.438	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64491167	C	G	64491167	3	3	75	1	0	0	0	0	1	0	0	0	15461	711	25	4	5980	4	SYNE2	14	64491167	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	22134700	64491167	42858373	113	10236										
GPHN	10243	hgsc.bcm.edu	37	chr14	67647566	67647566	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gagcatgcgcagtgccaatgGattgttgatgctacctccaa	11	10	0	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr14:67647566G>C	ENST00000315266.5	+	22	3244	c.2123G>C	c.(2122-2124)gGa>gCa	p.G708A	GPHN_ENST00000543237.1_Missense_Mutation_p.G754A|GPHN_ENST00000478722.1_Missense_Mutation_p.G741A|GPHN_ENST00000305960.9_Missense_Mutation_p.G677A|GPHN_ENST00000544752.2_3'UTR	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	708	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		AGTGCCAATGGATTGTTGATG	0.478			T	MLL	AL																																p.G741A		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.G2222C						.						172	134	147					14																	67647566		2203	4300	6503	SO:0001583	missense	10243	exon23			CCAATGGATTGTT	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.2123G>C	chr14.hg19:g.67647566G>C	ENSP00000312771:p.Gly708Ala	77.0	0.0		56.0	10.0	NM_020806	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	hg19	CCDS32103.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.232|5.232	0.228381|0.228381	0.09916|0.09916	.|.	.|.	ENSG00000171723|ENSG00000171723	ENST00000556240|ENST00000315266;ENST00000478722;ENST00000543237;ENST00000305960	.|.	.|.	.|.	5.83|5.83	5.83|5.83	0.93111|0.93111	.|MoeA, C-terminal, domain IV (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.34803|0.34803	0.0910|0.0910	N|N	0.04090|0.04090	-0.28|-0.28	0.80722|0.80722	D|D	1|1	.|B;B;B;B	.|0.24186	.|0.047;0.099;0.058;0.099	.|B;B;B;B	.|0.19391	.|0.017;0.025;0.018;0.019	T|T	0.38735|0.38735	-0.9647|-0.9647	5|9	.|0.02654	.|T	.|1	-10.6074|-10.6074	20.1307|20.1307	0.97998|0.97998	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|677;754;708;741	.|F8W7D6;F5H039;Q9NQX3;Q9NQX3-2	.|.;.;GEPH_HUMAN;.	H|A	1|708;741;754;677	.|.	.|ENSP00000303019:G677A	D|G	+|+	1|2	0|0	GPHN|GPHN	66717319|66717319	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.713000|9.713000	0.98740|0.98740	2.768000|2.768000	0.95171|0.95171	0.467000|0.467000	0.42956|0.42956	GAT|GGA	.	.		0.478	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		C	67647566	G	C	67647566	3	2	75	1	0	0	0	0	1	0	0	0	6618	1174	41	4	2312	4	GPHN	14	67647566	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	3156399	67647566	39701974	114	10237										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102508727	102508727	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ctttgtgtgtgcaggtgggtGatgctgaagaatgtgcatct	15	5	1	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr14:102508727G>A	ENST00000360184.4	+	68	12446	c.12282G>A	c.(12280-12282)gtG>gtA	p.V4094V	RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557242.1_RNA|RP11-1017G21.4_ENST00000557551.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4094	AAA 6. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GCAGGTGGGTGATGCTGAAGA	0.562																																					p.V4094V		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.G12282A						.						93	82	86					14																	102508727		2203	4300	6503	SO:0001819	synonymous_variant	1778	exon68			GTGGGTGATGCTG	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.12282G>A	chr14.hg19:g.102508727G>A		50.0	0.0		57.0	14.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	hg19	CCDS9966.1																																																																																			.	.		0.562	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		A	102508727	G	A	102508727	2	1	75	1	0	0	0	0	0	0	0	1	4843	1277	45	3		3	DYNC1H1	14	102508727	Silent	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	34861161	102508727	4840813	115	10238										
LCMT2	9836	hgsc.bcm.edu	37	chr15	43622597	43622597	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aaaggggtcctgcacgtaccCgcgcgcggccagggaacgct	15	14	0	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr15:43622597C>T	ENST00000305641.5	-	1	206	c.91G>A	c.(91-93)Ggg>Agg	p.G31R	ADAL_ENST00000428046.3_5'Flank|ADAL_ENST00000389651.4_5'Flank|LCMT2_ENST00000544735.1_5'UTR|LCMT2_ENST00000567039.1_Splice_Site_p.G31R|ADAL_ENST00000422466.2_5'Flank	NM_014793.4	NP_055608.2	O60294	TYW4_HUMAN	leucine carboxyl methyltransferase 2	31					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)	p.G31W(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(1)|urinary_tract(1)	20		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)	TGCACGTACCCGCGCGCGGCC	0.716																																					p.G31R		Atlas-SNP	.											.	LCMT2	48	.	1	Substitution - Missense(1)	lung(1)	c.G91A						.						19	23	22					15																	43622597		2110	4118	6228	SO:0001583	missense	9836	exon1			CGTACCCGCGCGC	AF265443	CCDS10094.1	15q15.3	2007-01-26			ENSG00000168806	ENSG00000168806			17558	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 4"	611246				9628581, 17150819	Standard	NM_014793		Approved	KIAA0547, MGC9534, TYW4, PPM2	uc001zrg.3	O60294	OTTHUMG00000130705	ENST00000305641.5:c.91G>A	chr15.hg19:g.43622597C>T	ENSP00000307214:p.Gly31Arg	28.0	0.0		29.0	4.0	NM_014793	Q4JFT6|Q96B55|Q9NR10	Missense_Mutation	SNP	ENST00000305641.5	hg19	CCDS10094.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.037875	0.75617	.	.	ENSG00000168806	ENST00000305641	T	0.26373	1.74	5.55	5.55	0.83447	.	0.057403	0.64402	D	0.000002	T	0.47764	0.1463	M	0.69358	2.11	0.80722	D	1	D	0.76494	0.999	D	0.67725	0.953	T	0.31696	-0.9934	10	0.51188	T	0.08	.	14.877	0.70501	0.0:1.0:0.0:0.0	.	31	O60294	LCMT2_HUMAN	R	31	ENSP00000307214:G31R	ENSP00000307214:G31R	G	-	1	0	LCMT2	41409889	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	3.788000	0.55446	2.894000	0.99253	0.655000	0.94253	GGG	.	.		0.716	LCMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253205.1	NM_014793		T	43622597	C	T	43622597	3	4	75	1	0	0	0	0	1	0	0	0	8688	652	23	1	1973	1	LCMT2	15	43622597	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10		43622597	58908795	116	10239										
SIN3A	25942	hgsc.bcm.edu	37	chr15	75705145	75705145	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gggctgaggagctggctgggCaggagctggggctgactggg	23	7	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr15:75705145C>T	ENST00000394947.3	-	5	1029	c.715G>A	c.(715-717)Gcc>Acc	p.A239T	SIN3A_ENST00000360439.4_Missense_Mutation_p.A239T|SIN3A_ENST00000394949.4_Missense_Mutation_p.A239T	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						gctggctgggcaggagctggg	0.562																																					p.A239T		Atlas-SNP	.											.	SIN3A	152	.	0			c.G715A						.						93	82	86					15																	75705145		2197	4294	6491	SO:0001583	missense	25942	exon5			GCTGGGCAGGAGC	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.715G>A	chr15.hg19:g.75705145C>T	ENSP00000378402:p.Ala239Thr	82.0	0.0		87.0	44.0	NM_001145358		Missense_Mutation	SNP	ENST00000394947.3	hg19	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	C	14.57	2.575316	0.45902	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.44083	0.93;0.93;0.93	6.04	6.04	0.98038	.	0.057302	0.64402	D	0.000002	T	0.26846	0.0657	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.10590	-1.0623	10	0.17369	T	0.5	-1.2736	19.5674	0.95401	0.0:1.0:0.0:0.0	.	239	Q96ST3	SIN3A_HUMAN	T	239	ENSP00000378402:A239T;ENSP00000378403:A239T;ENSP00000353622:A239T	ENSP00000353622:A239T	A	-	1	0	SIN3A	73492198	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.327000	0.52045	2.873000	0.98535	0.561000	0.74099	GCC	.	.		0.562	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		T	75705145	C	T	75705145	3	4	75	1	0	0	0	0	1	0	0	0	14340	710	25	3	3174	3	SIN3A	15	75705145	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	32082548	75705145	26826247	117	10240										
TSC2	7249	hgsc.bcm.edu	37	chr16	2138085	2138088	+	Frame_Shift_Del	DEL	TCGT	TCGT	-													0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ggacaccagcgtggccaagaTcgtgtctgaccgcaacctgc					rs397515227|rs45483700|rs45498401	byFrequency	TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	TCGT	TCGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr16:2138085_2138088delTCGT	ENST00000219476.3	+	40	5735_5738	c.5105_5108delTCGT	c.(5104-5109)atcgtgfs	p.IV1702fs	MIR1225_ENST00000408729.1_RNA|TSC2_ENST00000568454.1_Frame_Shift_Del_p.IV1646fs|TSC2_ENST00000401874.2_Frame_Shift_Del_p.IV1635fs|TSC2_ENST00000350773.4_Frame_Shift_Del_p.IV1679fs|TSC2_ENST00000353929.4_Frame_Shift_Del_p.IV1659fs|TSC2_ENST00000382538.6_Frame_Shift_Del_p.IV1587fs|TSC2_ENST00000439673.2_Frame_Shift_Del_p.IV1599fs	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1702	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				GTGGCCAAGATCGTGTCTGACCGC	0.676			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.1702_1703del		Atlas-Indel,Pindel	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.5104_5107del	GRCh37	CM010517	TSC2	M	rs45498401	.																																			SO:0001589	frameshift_variant	7249	exon40	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	.	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.5105_5108delTCGT	chr16.hg19:g.2138085_2138088delTCGT	ENSP00000219476:p.Ile1702fs	53.0	0.0		33.0	12.0	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Frame_Shift_Del	DEL	ENST00000219476.3	hg19	CCDS10458.1																																																																																			.	.		0.676	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		-	2138088	TCGT	-	2138085	7	5	75	1	0	1	0	1	0	0	0	0	16621	1435	50	0	5259	0	TSC2	16	2138085	Frame_Shift_Del	DEL	TCGT	TCGA-CC-A7IJ-01A-11D-A33Q-10		2138085	88216668	118	10241										
ZC3H7A	29066	hgsc.bcm.edu	37	chr16	11876180	11876180	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttccttaatgttctgctgccTttttcttctctcctcggaca	5	13	3	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr16:11876180T>C	ENST00000396516.2	-	1	228	c.31A>G	c.(31-33)Agg>Ggg	p.R11G	ZC3H7A_ENST00000575170.1_5'UTR|ZC3H7A_ENST00000355758.4_Missense_Mutation_p.R11G			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	11						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						TTCTGCTGCCTTTTTCTTCTC	0.413																																					p.R11G		Atlas-SNP	.											.	ZC3H7A	72	.	0			c.A31G						.						261	221	235					16																	11876180		2197	4300	6497	SO:0001583	missense	29066	exon2			GCTGCCTTTTTCT	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30959	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 7", "zinc finger CCCH-type containing 7"	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.31A>G	chr16.hg19:g.11876180T>C	ENSP00000379773:p.Arg11Gly	104.0	0.0		76.0	4.0	NM_014153	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	hg19	CCDS10550.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.986262	0.74589	.	.	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.28454	1.61;1.61	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.54775	0.1879	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.57464	-0.7807	10	0.56958	D	0.05	.	14.6773	0.68989	0.0:0.0:0.0:1.0	.	11	Q8IWR0	Z3H7A_HUMAN	G	11	ENSP00000347999:R11G;ENSP00000379773:R11G	ENSP00000347999:R11G	R	-	1	2	ZC3H7A	11783681	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.960000	0.56752	2.124000	0.65301	0.402000	0.26972	AGG	.	.		0.413	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153		C	11876180	T	C	11876180	3	2	75	1	0	0	0	0	1	0	0	0	17587	1608	56	2	2972	2	ZC3H7A	16	11876180	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	9738095	11876180	78478573	119	10242										
GPRC5B	51704	hgsc.bcm.edu	37	chr16	19883202	19883202	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gcccgcggcagctgcacgtcCtcctcgaaggccgtctcccg	12	19	1	0	rs199935784		TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr16:19883202C>T	ENST00000300571.2	-	2	1157	c.966G>A	c.(964-966)gaG>gaA	p.E322E	GPRC5B_ENST00000537135.1_Silent_p.E348E|GPRC5B_ENST00000569479.1_Silent_p.E322E|GPRC5B_ENST00000569847.1_Silent_p.E322E|GPRC5B_ENST00000535671.1_Silent_p.E322E	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	322					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						GCTGCACGTCCTCCTCGAAGG	0.627																																					p.E322E		Atlas-SNP	.											.	GPRC5B	54	.	0			c.G966A						.						78	73	74					16																	19883202		2197	4300	6497	SO:0001819	synonymous_variant	51704	exon2			CACGTCCTCCTCG	AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"GPCR / Class C : Orphans"	13308	protein-coding gene	gene with protein product		605948	"G protein-coupled receptor, family C, group 1, member B", "G protein-coupled receptor, family C, group 5, member B"			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.966G>A	chr16.hg19:g.19883202C>T		62.0	0.0		42.0	19.0	NM_016235	D2DFB0|O75205|Q8NBZ8	Silent	SNP	ENST00000300571.2	hg19	CCDS10581.1																																																																																			.	C|1.000;G|0.000		0.627	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1			T	19883202	C	T	19883202	2	4	75	1	0	0	0	0	0	0	0	1	6734	680	24	3		3	GPRC5B	16	19883202	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	8007022	19883202	70471551	120	10243										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58589731	58589731	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gtggtggatgattatatattCgctggaaatagctgtttgct	12	4	0	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr16:58589731C>A	ENST00000317147.5	-	20	2893	c.2561G>T	c.(2560-2562)cGa>cTa	p.R854L	CNOT1_ENST00000569732.1_5'UTR|CNOT1_ENST00000441024.2_Missense_Mutation_p.R854L|CNOT1_ENST00000569240.1_Missense_Mutation_p.R849L	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	854	Interaction with ZFP36.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		ATTATATATTCGCTGGAAATA	0.403																																					p.R854L		Atlas-SNP	.											.	CNOT1	359	.	0			c.G2561T						.						209	165	180					16																	58589731		2198	4300	6498	SO:0001583	missense	23019	exon20			TATATTCGCTGGA	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.2561G>T	chr16.hg19:g.58589731C>A	ENSP00000320949:p.Arg854Leu	31.0	0.0		26.0	13.0	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	C	36	5.869921	0.97049	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000394200;ENST00000441024	T;T	0.52754	0.7;0.65	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.75459	0.3852	M	0.88105	2.93	0.80722	D	1	D;P;P	0.63046	0.992;0.91;0.929	D;P;P	0.72982	0.979;0.492;0.82	T	0.79090	-0.1946	10	0.72032	D	0.01	.	20.0308	0.97536	0.0:1.0:0.0:0.0	.	854;854;849	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	L	854;283;849;854	ENSP00000320949:R854L;ENSP00000413113:R854L	ENSP00000320949:R854L	R	-	2	0	CNOT1	57147232	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.732000	0.93576	0.585000	0.79938	CGA	.	.		0.403	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		A	58589731	C	A	58589731	3	1	75	1	0	0	0	0	1	0	0	0	3619	884	31	1	4911	1	CNOT1	16	58589731	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	38706529	58589731	31765022	121	10244										
JPH3	57338	hgsc.bcm.edu	37	chr16	87723913	87723913	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	caccgccccgaggaccggggCttcggggtgcagagactgcg	17	14	0	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr16:87723913C>A	ENST00000284262.2	+	4	2189	c.1947C>A	c.(1945-1947)ggC>ggA	p.G649G	JPH3_ENST00000563609.1_3'UTR	NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	649					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		AGGACCGGGGCTTCGGGGTGC	0.687																																					p.G649G		Atlas-SNP	.											.	JPH3	95	.	0			c.C1947A						.						9	11	10					16																	87723913		2165	4270	6435	SO:0001819	synonymous_variant	57338	exon4			CCGGGGCTTCGGG	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"trinucleotide repeat containing 22"	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.1947C>A	chr16.hg19:g.87723913C>A		100.0	0.0		79.0	52.0	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Silent	SNP	ENST00000284262.2	hg19	CCDS10962.1																																																																																			.	.		0.687	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2			A	87723913	C	A	87723913	2	1	75	1	0	0	0	0	0	0	0	1	7971	784	28	3		3	JPH3	16	87723913	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	29134182	87723913	2630840	122	10245										
TP53	7157	hgsc.bcm.edu	37	chr17	7578461	7578461	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gtagatggccatggcgcggaCgcgggtgccgggcgggggtg	23	9	0	1	rs121912654		TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr17:7578461C>A	ENST00000269305.4	-	5	658	c.469G>T	c.(469-471)Gtc>Ttc	p.V157F	TP53_ENST00000455263.2_Missense_Mutation_p.V157F|TP53_ENST00000420246.2_Missense_Mutation_p.V157F|TP53_ENST00000445888.2_Missense_Mutation_p.V157F|TP53_ENST00000413465.2_Missense_Mutation_p.V157F|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.V157F	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	157	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> A (in sporadic cancers; somatic mutation).|V -> D (in sporadic cancers; somatic mutation).|V -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|V -> G (in sporadic cancers; somatic mutation).|V -> I (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9419979}.|V -> L (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V157F(161)|p.V157I(10)|p.0?(8)|p.V157L(6)|p.V64F(6)|p.V25F(6)|p.R156_I162delRVRAMAI(2)|p.T155fs*23(2)|p.V157del(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.V157fs*22(2)|p.V157fs*24(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156_V157del(1)|p.R156_V157insV(1)|p.R156_R158delRVR(1)|p.R156fs*12(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.V157_M160delVRAM(1)|p.D148fs*23(1)|p.V157_R158delVR(1)|p.S149fs*72(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*20(1)|p.V157_I162delVRAMAI(1)|p.V157fs*23(1)|p.V157fs*21(1)|p.V157fs*25(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGCGCGGACGCGGGTGCCG	0.617		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.V157F	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,+1,5	TP53	33396	.	231	Substitution - Missense(189)|Deletion - Frameshift(15)|Deletion - In frame(14)|Whole gene deletion(8)|Insertion - Frameshift(3)|Insertion - In frame(1)|Complex - frameshift(1)	lung(69)|liver(30)|upper_aerodigestive_tract(26)|breast(19)|oesophagus(14)|ovary(13)|stomach(9)|large_intestine(7)|haematopoietic_and_lymphoid_tissue(7)|central_nervous_system(6)|bone(5)|vulva(4)|urinary_tract(4)|skin(3)|pancreas(3)|endometrium(2)|kidney(2)|biliary_tract(2)|soft_tissue(2)|prostate(1)|adrenal_gland(1)|salivary_gland(1)|thymus(1)	c.G469T						.						50	52	51					17																	7578461		2202	4300	6502	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CGCGGACGCGGGT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.469G>T	chr17.hg19:g.7578461C>A	ENSP00000269305:p.Val157Phe	75.0	0.0		63.0	39.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.865109	0.32977	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99822	-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94	5.47	2.42	0.29668	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.216722	0.39210	N	0.001429	D	0.99718	0.9891	M	0.86420	2.815	0.33606	D	0.603	D;D;D;D;D;D;D	0.89917	1.0;0.998;0.999;0.999;0.999;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.997;0.994;0.984;0.981;0.996;0.998;0.996	D	0.97998	1.0358	10	0.72032	D	0.01	-16.7152	5.3541	0.16051	0.0:0.6119:0.146:0.2421	.	118;157;157;64;157;157;157	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	F	157;157;157;157;157;157;146;64;25;64;25;157	ENSP00000410739:V157F;ENSP00000352610:V157F;ENSP00000269305:V157F;ENSP00000398846:V157F;ENSP00000391127:V157F;ENSP00000391478:V157F;ENSP00000425104:V25F;ENSP00000423862:V64F;ENSP00000424104:V157F	ENSP00000269305:V157F	V	-	1	0	TP53	7519186	0.137000	0.22531	0.013000	0.15412	0.150000	0.21749	0.548000	0.23314	0.386000	0.24997	-0.253000	0.11424	GTC	.	.		0.617	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578461	C	A	7578461	3	1	75	1	0	0	0	0	1	0	0	0	16396	536	19	1	829	1	TP53	17	7578461	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10		7578461	73616749	123	10246										
KRT32	3882	hgsc.bcm.edu	37	chr17	39622138	39622138	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gatcctgcgcaggccattgaTgtcggcctccaccagctgcc	11	16	0	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr17:39622138T>C	ENST00000225899.3	-	3	698	c.595A>G	c.(595-597)Atc>Gtc	p.I199V	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	199	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				AGGCCATTGATGTCGGCCTCC	0.577																																					p.I199V		Atlas-SNP	.											.	KRT32	57	.	0			c.A595G						.						77	68	71					17																	39622138		2203	4300	6503	SO:0001583	missense	3882	exon3			CATTGATGTCGGC	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"-", "Intermediate filaments type I, keratins (acidic)"	6449	protein-coding gene	gene with protein product	"hard keratin type I"	602760	"keratin, hair, acidic, 2"	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.595A>G	chr17.hg19:g.39622138T>C	ENSP00000225899:p.Ile199Val	71.0	0.0		62.0	12.0	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	hg19	CCDS11393.1	.	.	.	.	.	.	.	.	.	.	T	12.61	1.988642	0.35131	.	.	ENSG00000108759	ENST00000225899	D	0.89050	-2.46	4.93	3.85	0.44370	Filament (1);	0.397757	0.18265	N	0.146516	D	0.90249	0.6951	M	0.69523	2.12	0.25084	N	0.990903	B	0.29716	0.255	B	0.43194	0.411	D	0.83606	0.0131	10	0.48119	T	0.1	.	10.083	0.42401	0.0:0.0797:0.0:0.9203	.	199	Q14532	K1H2_HUMAN	V	199	ENSP00000225899:I199V	ENSP00000225899:I199V	I	-	1	0	KRT32	36875664	1.000000	0.71417	0.992000	0.48379	0.221000	0.24807	5.159000	0.64923	0.858000	0.35431	0.456000	0.33151	ATC	.	.		0.577	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278		C	39622138	T	C	39622138	3	2	75	1	0	0	0	0	1	0	0	0	8477	1464	51	2	771	2	KRT32	17	39622138	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	32043677	39622138	41573072	124	10247										
CIDEA	1149	hgsc.bcm.edu	37	chr18	12277129	12277129	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gcctctgccacaggagtctgCtgcggttcctgtcctactcc	10	16	2	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr18:12277129C>A	ENST00000320477.9	+	5	585	c.520C>A	c.(520-522)Ctg>Atg	p.L174M	CIDEA_ENST00000521296.1_3'UTR	NM_001279.3	NP_001270.1	O60543	CIDEA_HUMAN	cell death-inducing DFFA-like effector a	174					apoptotic process (GO:0006915)|cell death (GO:0008219)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of execution phase of apoptosis (GO:1900118)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of sequestering of triglyceride (GO:0010890)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|response to stilbenoid (GO:0035634)|temperature homeostasis (GO:0001659)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|mitochondrial envelope (GO:0005740)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)	13						CAGGAGTCTGCTGCGGTTCCT	0.562																																					p.L174M		Atlas-SNP	.											.	CIDEA	32	.	0			c.C520A						.						98	83	88					18																	12277129		2203	4300	6503	SO:0001583	missense	1149	exon5			AGTCTGCTGCGGT	AF041378	CCDS11856.1	18p11.21	2008-08-01			ENSG00000176194	ENSG00000176194			1976	protein-coding gene	gene with protein product		604440				9564035, 18509062	Standard	NM_001279		Approved	CIDE-A	uc002kqt.4	O60543	OTTHUMG00000131691	ENST00000320477.9:c.520C>A	chr18.hg19:g.12277129C>A	ENSP00000320209:p.Leu174Met	75.0	0.0		74.0	32.0	NM_001279	B0YIY7|Q6UPR7	Missense_Mutation	SNP	ENST00000320477.9	hg19	CCDS11856.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.940687	0.34283	.	.	ENSG00000176194	ENST00000320477	D	0.84223	-1.82	4.87	2.69	0.31865	.	0.095899	0.42420	D	0.000701	D	0.90741	0.7094	M	0.86028	2.79	0.36724	D	0.88132	D;D	0.76494	0.999;0.998	D;D	0.66716	0.946;0.928	D	0.91596	0.5291	10	0.72032	D	0.01	-24.1273	7.7978	0.29158	0.0:0.7729:0.0:0.2271	.	208;174	Q8N5P9;O60543	.;CIDEA_HUMAN	M	174	ENSP00000320209:L174M	ENSP00000320209:L174M	L	+	1	2	CIDEA	12267129	0.990000	0.36364	0.990000	0.47175	0.270000	0.26580	-0.019000	0.12546	1.035000	0.39972	0.462000	0.41574	CTG	.	.		0.562	CIDEA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254599.2	NM_001279		A	12277129	C	A	12277129	3	1	75	1	0	0	0	0	1	0	0	0	3427	796	28	3	682	3	CIDEA	18	12277129	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10		12277129	65800119	125	10248										
DSG2	1829	hgsc.bcm.edu	37	chr18	29126582	29126582	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	taggaacaccacggtgtctgGagctggagtccctggccctc	13	13	1	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr18:29126582G>C	ENST00000261590.8	+	15	3442	c.3233G>C	c.(3232-3234)gGa>gCa	p.G1078A	RP11-75N4.2_ENST00000583706.1_RNA	NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	1078					apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			ACGGTGTCTGGAGCTGGAGTC	0.478																																					p.G1078A		Atlas-SNP	.											.	DSG2	115	.	0			c.G3233C						.						87	84	85					18																	29126582		1899	4140	6039	SO:0001583	missense	1829	exon15			TGTCTGGAGCTGG	Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"Cadherins / Major cadherins"	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.3233G>C	chr18.hg19:g.29126582G>C	ENSP00000261590:p.Gly1078Ala	95.0	0.0		103.0	15.0	NM_001943	Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	hg19	CCDS42423.1	.	.	.	.	.	.	.	.	.	.	G	2.670	-0.277769	0.05679	.	.	ENSG00000046604	ENST00000261590	T	0.63417	-0.04	4.4	0.393	0.16294	.	0.493791	0.18306	N	0.145241	T	0.42177	0.1191	N	0.24115	0.695	0.09310	N	0.999998	B	0.14012	0.009	B	0.12156	0.007	T	0.21449	-1.0245	10	0.24483	T	0.36	.	9.0184	0.36184	0.0838:0.4231:0.4931:0.0	.	1078	Q14126	DSG2_HUMAN	A	1078	ENSP00000261590:G1078A	ENSP00000261590:G1078A	G	+	2	0	DSG2	27380580	0.003000	0.15002	0.000000	0.03702	0.067000	0.16453	1.094000	0.30951	0.057000	0.16193	-0.229000	0.12294	GGA	.	.		0.478	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943		C	29126582	G	C	29126582	3	2	75	1	0	0	0	0	1	0	0	0	4779	1174	41	4	3291	4	DSG2	18	29126582	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	16849453	29126582	48950666	126	10249										
KIAA0427	9811	hgsc.bcm.edu	37	chr18	46287965	46287965	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agaaggctgtgtccgaccgcAgcttcgccttcaccgctgcc	11	16	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr18:46287965A>G	ENST00000256413.3	+	9	1571	c.1276A>G	c.(1276-1278)Agc>Ggc	p.S426G	CTIF_ENST00000382998.4_Missense_Mutation_p.S428G	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	426	MIF4G.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						GTCCGACCGCAGCTTCGCCTT	0.597																																					p.S428G		Atlas-SNP	.											.	CTIF	102	.	0			c.A1282G						.						124	96	106					18																	46287965		2203	4300	6503	SO:0001583	missense	9811	exon10			GACCGCAGCTTCG	AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"KIAA0427"	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.1276A>G	chr18.hg19:g.46287965A>G	ENSP00000256413:p.Ser426Gly	64.0	0.0		68.0	29.0	NM_001142397	B3KTR8|Q8IVD5	Missense_Mutation	SNP	ENST00000256413.3	hg19	CCDS11935.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.702561	0.88924	.	.	ENSG00000134030	ENST00000256413;ENST00000382998;ENST00000420275	T;T	0.24908	1.83;1.83	5.75	5.75	0.90469	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.082208	0.85682	D	0.000000	T	0.43411	0.1246	L	0.45581	1.43	0.58432	D	0.999998	D;D	0.69078	0.993;0.997	P;D	0.65140	0.888;0.932	T	0.27872	-1.0061	10	0.59425	D	0.04	-14.5574	15.7442	0.77926	1.0:0.0:0.0:0.0	.	428;426	O43310-2;O43310	.;CTIF_HUMAN	G	426;428;378	ENSP00000256413:S426G;ENSP00000372459:S428G	ENSP00000256413:S426G	S	+	1	0	CTIF	44541963	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.927000	0.92846	2.194000	0.70268	0.533000	0.62120	AGC	.	.		0.597	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772		G	46287965	A	G	46287965	3	3	75	1	0	0	0	0	1	0	0	0	8185	188	7	2	1312	2	KIAA0427	18	46287965	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	17161383	46287965	31789283	127	10250										
SERPINB8	5271	hgsc.bcm.edu	37	chr18	61645627	61645627	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aggacaactcaagaaacgtaTtcttctctcccatgagcatc	6	12	3	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr18:61645627T>C	ENST00000397985.2	+	2	341	c.85T>C	c.(85-87)Ttc>Ctc	p.F29L	SERPINB8_ENST00000542677.1_Intron|HMSD_ENST00000481726.1_3'UTR|SERPINB8_ENST00000397988.3_Missense_Mutation_p.F29L|SERPINB8_ENST00000353706.2_Missense_Mutation_p.F29L	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	29					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				AAGAAACGTATTCTTCTCTCC	0.493																																					p.F29L		Atlas-SNP	.											.	SERPINB8	42	.	0			c.T85C						.						100	88	92					18																	61645627		2203	4300	6503	SO:0001583	missense	5271	exon2			AACGTATTCTTCT	L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"Serine (or cysteine) peptidase inhibitors"	8952	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase 2"	601697	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.85T>C	chr18.hg19:g.61645627T>C	ENSP00000381072:p.Phe29Leu	58.0	0.0		66.0	6.0	NM_001031848	B4DTW2|Q7Z2V6|Q8N178	Missense_Mutation	SNP	ENST00000397985.2	hg19	CCDS11991.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.021314	0.35701	.	.	ENSG00000166401	ENST00000397985;ENST00000353706;ENST00000397988;ENST00000448851;ENST00000441827	D;D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9;-1.9	5.03	3.81	0.43845	Serpin domain (3);	0.090413	0.85682	D	0.000000	D	0.82949	0.5148	M	0.72624	2.21	0.80722	D	1	B;P	0.38250	0.367;0.624	B;B	0.37144	0.242;0.242	D	0.84560	0.0649	10	0.54805	T	0.06	.	11.3882	0.49798	0.0:0.0:0.1507:0.8493	.	29;29	P50452;Q8N178	SPB8_HUMAN;.	L	29	ENSP00000381072:F29L;ENSP00000331368:F29L;ENSP00000381075:F29L;ENSP00000414580:F29L;ENSP00000393456:F29L	ENSP00000331368:F29L	F	+	1	0	SERPINB8	59796607	1.000000	0.71417	0.147000	0.22382	0.025000	0.11179	3.751000	0.55165	2.108000	0.64289	0.533000	0.62120	TTC	.	.		0.493	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848		C	61645627	T	C	61645627	3	2	75	1	0	0	0	0	1	0	0	0	14122	1493	52	2	87	2	SERPINB8	18	61645627	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	15357662	61645627	16431621	128	10251										
OR7A17	26333	hgsc.bcm.edu	37	chr19	14991644	14991644	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	taagttcacagaaaaagtggGggatttccaagtctgtgcag	12	6	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr19:14991644G>A	ENST00000327462.2	-	1	620	c.524C>T	c.(523-525)cCc>cTc	p.P175L		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					GAAAAAGTGGGGGATTTCCAA	0.483																																					p.P175L		Atlas-SNP	.											.	OR7A17	37	.	0			c.C524T						.						91	86	88					19																	14991644		2203	4300	6503	SO:0001583	missense	26333	exon1			AAGTGGGGGATTT	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"GPCR / Class A : Olfactory receptors"	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.524C>T	chr19.hg19:g.14991644G>A	ENSP00000328144:p.Pro175Leu	68.0	0.0		60.0	25.0	NM_030901	Q6IFQ6|Q96R98	Missense_Mutation	SNP	ENST00000327462.2	hg19	CCDS12319.1	.	.	.	.	.	.	.	.	.	.	g	12.15	1.851824	0.32699	.	.	ENSG00000185385	ENST00000327462	T	0.37752	1.18	3.37	-2.81	0.05805	GPCR, rhodopsin-like superfamily (1);	0.200782	0.24594	U	0.037186	T	0.50616	0.1626	M	0.67569	2.06	0.09310	N	1	D	0.69078	0.997	D	0.79108	0.992	T	0.48210	-0.9055	10	0.66056	D	0.02	.	11.233	0.48923	0.0:0.0:0.2462:0.7537	.	175	O14581	OR7AH_HUMAN	L	175	ENSP00000328144:P175L	ENSP00000328144:P175L	P	-	2	0	OR7A17	14852644	0.000000	0.05858	0.640000	0.29408	0.420000	0.31355	0.068000	0.14531	-0.090000	0.12462	0.454000	0.30748	CCC	.	.		0.483	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901		A	14991644	G	A	14991644	3	1	75	1	0	0	0	0	1	0	0	0	11224	1232	43	3	407	3	OR7A17	19	14991644	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10		14991644	44137339	129	10252										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15298796	15298796	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cgtccagctgacacgtggagCcgctgaagcctggggtgggg	18	11	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr19:15298796C>A	ENST00000263388.2	-	10	1577	c.1502G>T	c.(1501-1503)gGc>gTc	p.G501V		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	501	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			ACACGTGGAGCCGCTGAAGCC	0.642																																					p.G501V		Atlas-SNP	.											.	NOTCH3	340	.	0			c.G1502T						.						20	15	17					19																	15298796		1900	3592	5492	SO:0001583	missense	4854	exon10			GTGGAGCCGCTGA	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1502G>T	chr19.hg19:g.15298796C>A	ENSP00000263388:p.Gly501Val	98.0	0.0		82.0	38.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	c	25.3	4.628567	0.87560	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.98249	-4.82	4.87	4.87	0.63330	EGF (1);EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.32703	N	0.005745	D	0.99513	0.9826	H	0.99746	4.745	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97622	1.0136	10	0.87932	D	0	.	16.7979	0.85607	0.0:1.0:0.0:0.0	.	504;501	Q59FL3;Q9UM47	.;NOTC3_HUMAN	V	501;503	ENSP00000263388:G501V	ENSP00000263388:G501V	G	-	2	0	NOTCH3	15159796	0.990000	0.36364	1.000000	0.80357	0.855000	0.48748	6.019000	0.70818	2.258000	0.74832	0.306000	0.20318	GGC	.	.		0.642	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		A	15298796	C	A	15298796	3	1	75	1	0	0	0	0	1	0	0	0	10559	739	26	3	5559	3	NOTCH3	19	15298796	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	307152	15298796	43830187	130	10253										
FXYD3	5349	hgsc.bcm.edu	37	chr19	35614352	35614352	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tcacttcccgcaggctcagcCcaaagctgatgaggacagac	10	14	2	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr19:35614352C>T	ENST00000344013.6	+	9	451	c.255C>T	c.(253-255)gcC>gcT	p.A85A	FXYD3_ENST00000604255.1_Silent_p.A142A|LGI4_ENST00000493050.1_5'Flank|FXYD3_ENST00000604404.1_Silent_p.A85A|FXYD3_ENST00000346446.5_Silent_p.A111A|FXYD3_ENST00000406988.1_Silent_p.A85A|FXYD3_ENST00000603524.1_Silent_p.A114A|FXYD3_ENST00000435734.2_Silent_p.A111A|FXYD3_ENST00000603181.1_Silent_p.A85A|FXYD3_ENST00000604621.1_Silent_p.A85A|FXYD3_ENST00000604804.1_Silent_p.A114A|FXYD3_ENST00000535103.1_Silent_p.A142A			Q14802	FXYD3_HUMAN	FXYD domain containing ion transport regulator 3	85					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of catalytic activity (GO:0050790)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			endometrium(1)|lung(2)|prostate(1)	4	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CAGGCTCAGCCCAAAGCTGAT	0.517																																					p.A142A		Atlas-SNP	.											.	FXYD3	15	.	0			c.C426T						.						132	112	119					19																	35614352		2203	4300	6503	SO:0001819	synonymous_variant	5349	exon11			CTCAGCCCAAAGC	X93036	CCDS12442.1, CCDS12443.1, CCDS46048.1, CCDS46049.1, CCDS46050.1	19q13.11-q13.12	2008-05-14	2002-01-14			ENSG00000089356			4027	protein-coding gene	gene with protein product		604996	"FXYD domain-containing ion transport regulator 3"	PLML		7836447, 10950925	Standard	NM_005971		Approved	MAT-8	uc010xsm.2	Q14802		ENST00000344013.6:c.255C>T	chr19.hg19:g.35614352C>T		82.0	0.0		57.0	10.0	NM_001136007	A6NDE0|C9JDU2|F5H174|F8WB34|Q13211|Q6IB59	Silent	SNP	ENST00000344013.6	hg19	CCDS12442.1																																																																																			.	.		0.517	FXYD3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000468985.1	NM_021910		T	35614352	C	T	35614352	2	4	75	1	0	0	0	0	0	0	0	1	6127	610	22	3		3	FXYD3	19	35614352	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	20315556	35614352	23514631	131	10254										
CEACAM8	1088	hgsc.bcm.edu	37	chr19	43098936	43098936	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	cctgtgagcaggagcccctgCcaggggatgcgccatctgca	14	14	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr19:43098936C>T	ENST00000244336.5	-	1	146	c.45G>A	c.(43-45)tgG>tgA	p.W15*	LIPE-AS1_ENST00000594688.1_RNA|CEACAM8_ENST00000599005.1_Nonsense_Mutation_p.W15*|LIPE-AS1_ENST00000594624.2_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	15					immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				GGAGCCCCTGCCAGGGGATGC	0.622																																					p.W15X		Atlas-SNP	.											.	CEACAM8	44	.	0			c.G45A						.						102	94	97					19																	43098936		2203	4300	6503	SO:0001587	stop_gained	1088	exon1			CCCCTGCCAGGGG	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.45G>A	chr19.hg19:g.43098936C>T	ENSP00000244336:p.Trp15*	29.0	0.0		32.0	8.0	NM_001816	O60399|Q16574	Nonsense_Mutation	SNP	ENST00000244336.5	hg19	CCDS12610.1	.	.	.	.	.	.	.	.	.	.	c	15.64	2.892220	0.52014	.	.	ENSG00000124469	ENST00000244336	.	.	.	1.4	1.4	0.22301	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.1898	0.20518	0.0:1.0:0.0:0.0	.	.	.	.	X	15	.	ENSP00000244336:W15X	W	-	3	0	CEACAM8	47790776	0.033000	0.19621	0.020000	0.16555	0.016000	0.09150	0.359000	0.20233	1.063000	0.40649	0.313000	0.20887	TGG	.	.		0.622	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1			T	43098936	C	T	43098936	4	4	75	1	0	0	0	0	0	1	0	0	3200	740	26	3	1024	3	CEACAM8	19	43098936	Nonsense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	7484584	43098936	16030047	132	10255										
FUT1	2523	hgsc.bcm.edu	37	chr19	49253562	49253562	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agtctggcagggtgaagttgGccaggtagacagtgtctccg	16	8	2	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr19:49253562G>C	ENST00000310160.3	-	4	1951	c.977C>G	c.(976-978)gCc>gGc	p.A326G	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	326					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		GGTGAAGTTGGCCAGGTAGAC	0.572																																					p.A326G		Atlas-SNP	.											.	FUT1	44	.	0			c.C977G						.						100	76	84					19																	49253562		2203	4300	6503	SO:0001583	missense	2523	exon4			AAGTTGGCCAGGT		CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"Blood group antigens", "Fucosyltransferases"	4012	protein-coding gene	gene with protein product		211100	"fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)", "fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.977C>G	chr19.hg19:g.49253562G>C	ENSP00000312021:p.Ala326Gly	41.0	0.0		52.0	27.0	NM_000148	O14505|O14506|O14507	Missense_Mutation	SNP	ENST00000310160.3	hg19	CCDS12733.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.932742	0.73442	.	.	ENSG00000174951	ENST00000310160;ENST00000539428	D	0.97553	-4.43	4.5	4.5	0.54988	.	0.102806	0.43260	D	0.000584	D	0.98068	0.9363	M	0.73430	2.235	0.35613	D	0.808809	D	0.89917	1.0	D	0.91635	0.999	D	0.99954	1.1593	10	0.49607	T	0.09	-5.5389	15.0977	0.72247	0.0:0.0:1.0:0.0	.	326	P19526	FUT1_HUMAN	G	326;316	ENSP00000312021:A326G	ENSP00000312021:A326G	A	-	2	0	FUT1	53945374	1.000000	0.71417	0.999000	0.59377	0.889000	0.51656	5.751000	0.68720	2.517000	0.84864	0.561000	0.74099	GCC	.	.		0.572	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148		C	49253562	G	C	49253562	3	2	75	1	0	0	0	0	1	0	0	0	6109	1203	42	4	124	4	FUT1	19	49253562	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	6154626	49253562	9875421	133	10256										
ZNF586	54807	hgsc.bcm.edu	37	chr19	58290133	58290133	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttttaggttgttggcatggaGgggaagatgaggcagcacct	16	5	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr19:58290133G>A	ENST00000396154.2	+	3	351	c.178G>A	c.(178-180)Ggg>Agg	p.G60R	ZNF586_ENST00000391702.3_Missense_Mutation_p.G17R|ZNF586_ENST00000396150.4_Silent_p.E17E|ZNF586_ENST00000598183.1_Intron|ZNF586_ENST00000598885.1_Intron|ZNF586_ENST00000599802.1_Intron	NM_017652.3	NP_060122.2	Q9NXT0	ZN586_HUMAN	zinc finger protein 586	60	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)	15		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTGGCATGGAGGGGAAGATGA	0.443																																					p.G60R		Atlas-SNP	.											.	ZNF586	31	.	0			c.G178A						.						70	67	68					19																	58290133		2042	4217	6259	SO:0001583	missense	54807	exon3			CATGGAGGGGAAG	AK095993	CCDS42640.1, CCDS56107.1, CCDS56108.1	19q13.43	2013-01-08				ENSG00000083828		"Zinc fingers, C2H2-type", "-"	25949	protein-coding gene	gene with protein product						12477932	Standard	NM_017652		Approved	FLJ20070	uc002qqd.3	Q9NXT0		ENST00000396154.2:c.178G>A	chr19.hg19:g.58290133G>A	ENSP00000379458:p.Gly60Arg	28.0	0.0		38.0	7.0	NM_017652	A0JLV8|A8MY63|B3KTS9|E7ERT1|G3XAH3	Missense_Mutation	SNP	ENST00000396154.2	hg19	CCDS42640.1	.	.	.	.	.	.	.	.	.	.	G	7.250	0.603058	0.13939	.	.	ENSG00000083828	ENST00000449441;ENST00000391702;ENST00000396154	T;T	0.09163	3.01;5.74	1.89	-0.389	0.12455	Krueppel-associated box (3);	.	.	.	.	T	0.08758	0.0217	.	.	.	0.09310	N	1	P	0.51057	0.941	B	0.43251	0.413	T	0.25328	-1.0135	8	0.59425	D	0.04	.	3.8261	0.08855	0.4528:0.0:0.5472:0.0	.	60	Q9NXT0	ZN586_HUMAN	R	60;17;60	ENSP00000375583:G17R;ENSP00000379458:G60R	ENSP00000375583:G17R	G	+	1	0	ZNF586	62981945	0.001000	0.12720	0.034000	0.17996	0.975000	0.68041	-0.032000	0.12266	0.115000	0.18071	-0.136000	0.14681	GGG	.	.		0.443	ZNF586-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466825.2	NM_017652		A	58290133	G	A	58290133	3	1	75	1	0	0	0	0	1	0	0	0	18034	1000	35	3	188	3	ZNF586	19	58290133	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	9036571	58290133	838850	134	10257										
ZNF256	10172	hgsc.bcm.edu	37	chr19	58453067	58453067	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ttgtaccagtgtgaactctcTggtgtgtaataaggctagaa	11	6	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr19:58453067T>C	ENST00000282308.3	-	3	1305	c.1109A>G	c.(1108-1110)cAg>cGg	p.Q370R	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	370					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		GTGAACTCTCTGGTGTGTAAT	0.433																																					p.Q370R	NSCLC(55;1313 1552 8040 11996)	Atlas-SNP	.											.	ZNF256	117	.	0			c.A1109G						.						74	68	70					19																	58453067		2203	4300	6503	SO:0001583	missense	10172	exon3			ACTCTCTGGTGTG	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"Zinc fingers, C2H2-type", "-"	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.1109A>G	chr19.hg19:g.58453067T>C	ENSP00000282308:p.Gln370Arg	60.0	0.0		42.0	8.0	NM_005773	B2RA92|Q53Y85|Q9BV71	Missense_Mutation	SNP	ENST00000282308.3	hg19	CCDS12966.1	.	.	.	.	.	.	.	.	.	.	.	4.844	0.156988	0.09236	.	.	ENSG00000152454	ENST00000282308	T	0.17691	2.26	2.51	1.47	0.22746	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08133	0.0203	N	0.04355	-0.22	0.09310	N	1	P	0.44478	0.836	B	0.43018	0.405	T	0.21280	-1.0250	9	0.37606	T	0.19	.	5.6763	0.17751	0.0:0.1471:0.0:0.8529	.	370	Q9Y2P7	ZN256_HUMAN	R	370	ENSP00000282308:Q370R	ENSP00000282308:Q370R	Q	-	2	0	ZNF256	63144879	0.000000	0.05858	0.004000	0.12327	0.006000	0.05464	-0.442000	0.06871	0.214000	0.20742	-0.376000	0.06991	CAG	.	.		0.433	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1			C	58453067	T	C	58453067	3	2	75	1	0	0	0	0	1	0	0	0	17814	1580	55	2	778	2	ZNF256	19	58453067	Missense_Mutation	SNP	T	TCGA-CC-A7IJ-01A-11D-A33Q-10	162934	58453067	675916	135	10258										
ANGPT4	51378	hgsc.bcm.edu	37	chr20	869031	869031	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gttctccagcttgttggtggAcagaaaggtctctggcatct	12	9	3	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr20:869031A>G	ENST00000381922.3	-	3	619	c.517T>C	c.(517-519)Tcc>Ccc	p.S173P	ANGPT4_ENST00000546022.1_Missense_Mutation_p.S173P	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	173					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						TTGTTGGTGGACAGAAAGGTC	0.577																																					p.S173P	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											.	ANGPT4	77	.	0			c.T517C						.						98	86	90					20																	869031		2203	4300	6503	SO:0001583	missense	51378	exon3			TGGTGGACAGAAA	AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"Fibrinogen C domain containing"	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.517T>C	chr20.hg19:g.869031A>G	ENSP00000371347:p.Ser173Pro	34.0	0.0		22.0	10.0	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Missense_Mutation	SNP	ENST00000381922.3	hg19	CCDS13009.1	.	.	.	.	.	.	.	.	.	.	a	12.57	1.979052	0.34942	.	.	ENSG00000101280	ENST00000381922;ENST00000546022	T;T	0.14516	2.5;2.5	4.44	3.31	0.37934	.	0.260965	0.30723	N	0.009019	T	0.31199	0.0789	M	0.75615	2.305	0.42985	D	0.994474	D;D	0.76494	0.999;0.999	D;D	0.66196	0.942;0.942	T	0.02417	-1.1162	10	0.56958	D	0.05	.	8.3884	0.32514	0.8244:0.0:0.0:0.1755	.	173;173	B4E3J9;Q9Y264	.;ANGP4_HUMAN	P	173	ENSP00000371347:S173P;ENSP00000439605:S173P	ENSP00000371347:S173P	S	-	1	0	ANGPT4	817031	1.000000	0.71417	0.975000	0.42487	0.024000	0.10985	4.734000	0.62043	0.712000	0.32039	0.248000	0.18094	TCC	.	.		0.577	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985		G	869031	A	G	869031	3	3	75	1	0	0	0	0	1	0	0	0	612	275	10	2	1022	2	ANGPT4	20	869031	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10		869031	62156489	136	10259										
MACROD2	140733	hgsc.bcm.edu	37	chr20	13983050	13983050	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agggcaagggccaaaatgatGgtaagtttctcggaacattt	12	6	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr20:13983050G>A	ENST00000310348.4	+	2	163	c.163G>A	c.(163-165)Gaa>Aaa	p.E55K	MACROD2_ENST00000217246.4_Splice_Site_p.E55K			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	55					brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				CCAAAATGATGGTAAGTTTCT	0.373																																					p.E55K		Atlas-SNP	.											.	MACROD2	34	.	0			c.G163A						.						134	134	134					20																	13983050		2203	4300	6503	SO:0001630	splice_region_variant	140733	exon2			AATGATGGTAAGT	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"chromosome 20 open reading frame 133"	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.163+1G>A	chr20.hg19:g.13983050G>A		97.0	0.0		85.0	45.0	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	hg19	CCDS13120.2	.	.	.	.	.	.	.	.	.	.	G	13.84	2.358541	0.41801	.	.	ENSG00000172264	ENST00000217246;ENST00000310348	T;T	0.42900	0.96;0.96	5.87	5.87	0.94306	.	0.483364	0.20494	N	0.091228	T	0.28234	0.0697	N	0.16602	0.42	0.80722	D	1	P;B	0.40970	0.734;0.02	B;B	0.37731	0.257;0.023	T	0.07404	-1.0774	10	0.07813	T	0.8	-6.426	18.8026	0.92023	0.0:0.0:1.0:0.0	.	55;55	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	K	55	ENSP00000217246:E55K;ENSP00000309809:E55K	ENSP00000217246:E55K	E	+	1	0	MACROD2	13931050	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.377000	0.73145	2.770000	0.95276	0.650000	0.86243	GAA	.	.		0.373	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	Missense_Mutation	A	13983050	G	A	13983050	5	1	75	1	0	0	0	0	0	0	1	0	9155	1362	47	3	169	3	MACROD2	20	13983050	Splice_Site	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	13114019	13983050	49042470	137	10260										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61522428	61522428	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	caacaccaaagcggccacggCtgctgaaataggagtagaga	12	10	0	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr20:61522428C>T	ENST00000266070.4	-	15	3750	c.3425G>A	c.(3424-3426)aGc>aAc	p.S1142N	DIDO1_ENST00000395340.1_Missense_Mutation_p.S1142N|DIDO1_ENST00000395343.1_Missense_Mutation_p.S1142N|DIDO1_ENST00000395335.2_Missense_Mutation_p.S1142N	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1142					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GCGGCCACGGCTGCTGAAATA	0.552																																					p.S1142N	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.G3425A						.						98	97	97					20																	61522428		2203	4300	6503	SO:0001583	missense	11083	exon15			CCACGGCTGCTGA	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.3425G>A	chr20.hg19:g.61522428C>T	ENSP00000266070:p.Ser1142Asn	114.0	0.0		76.0	16.0	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	C	35	5.441265	0.96187	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.16597	2.65;2.65;2.33;2.33	5.31	5.31	0.75309	Spen paralogue and orthologue SPOC, C-terminal (1);	0.000000	0.51477	D	0.000090	T	0.40546	0.1121	L	0.56124	1.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.14531	-1.0469	10	0.87932	D	0	-39.6478	19.3406	0.94339	0.0:1.0:0.0:0.0	.	1142;1142	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	N	1142	ENSP00000266070:S1142N;ENSP00000378752:S1142N;ENSP00000378749:S1142N;ENSP00000378744:S1142N	ENSP00000266070:S1142N	S	-	2	0	DIDO1	60992873	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.624000	0.83124	2.636000	0.89361	0.655000	0.94253	AGC	.	.		0.552	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		T	61522428	C	T	61522428	3	4	75	1	0	0	0	0	1	0	0	0	4524	797	28	3	3334	3	DIDO1	20	61522428	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	47539378	61522428	1503092	138	10261										
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62044867	62044867	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ggctgagtactgctcgatgaCgtccatcacgtcgtagggcc	13	12	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr20:62044867C>A	ENST00000359125.2	-	15	1873	c.1699G>T	c.(1699-1701)Gtc>Ttc	p.V567F	KCNQ2_ENST00000359689.1_Missense_Mutation_p.V567F|KCNQ2_ENST00000370224.1_Missense_Mutation_p.V539F|KCNQ2_ENST00000357249.2_Missense_Mutation_p.V549F|KCNQ2_ENST00000354587.3_Missense_Mutation_p.V539F|KCNQ2_ENST00000360480.3_Missense_Mutation_p.V539F|KCNQ2_ENST00000344462.4_Missense_Mutation_p.V536F	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	567					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TGCTCGATGACGTCCATCACG	0.637																																					p.V567F		Atlas-SNP	.											.	KCNQ2	201	.	0			c.G1699T						.						111	99	103					20																	62044867		2203	4300	6503	SO:0001583	missense	3785	exon15			CGATGACGTCCAT	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1699G>T	chr20.hg19:g.62044867C>A	ENSP00000352035:p.Val567Phe	235.0	0.0		128.0	35.0	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	hg19	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	c	28.3	4.905377	0.92107	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222	D;D;D;D;D;D;D;D;D;D	0.99861	-7.26;-7.26;-7.26;-7.26;-7.26;-7.26;-7.26;-7.26;-7.26;-7.26	4.99	4.99	0.66335	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.142336	0.46442	D	0.000283	D	0.99871	0.9939	M	0.87381	2.88	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96360	0.9265	10	0.87932	D	0	-18.2624	18.2551	0.90017	0.0:1.0:0.0:0.0	.	539;549;536;567	O43526-3;O43526-2;O43526-4;O43526	.;.;.;KCNQ2_HUMAN	F	549;567;537;539;567;536;539;527;539;539	ENSP00000349789:V549F;ENSP00000352035:V567F;ENSP00000359246:V537F;ENSP00000346601:V539F;ENSP00000352718:V567F;ENSP00000399612:V536F;ENSP00000353668:V539F;ENSP00000339611:V527F;ENSP00000359244:V539F;ENSP00000359242:V539F	ENSP00000339611:V527F	V	-	1	0	KCNQ2	61515311	1.000000	0.71417	0.995000	0.50966	0.823000	0.46562	7.581000	0.82535	2.323000	0.78572	0.556000	0.70494	GTC	.	.		0.637	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		A	62044867	C	A	62044867	3	1	75	1	0	0	0	0	1	0	0	0	8092	536	19	1	931	1	KCNQ2	20	62044867	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	522439	62044867	980653	139	10262										
CLDN17	26285	hgsc.bcm.edu	37	chr21	31538834	31538834	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ataatgttgctgccaacaaaAgctgatactctccactgagg	8	10	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr21:31538834A>C	ENST00000286808.3	-	1	137	c.102T>G	c.(100-102)gcT>gcG	p.A34A		NM_012131.2	NP_036263.1	P56750	CLD17_HUMAN	claudin 17	34					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	23						TGCCAACAAAAGCTGATACTC	0.502																																					p.A34A		Atlas-SNP	.											CLDN17,NS,carcinoma,0,1	CLDN17	61	.	0			c.T102G						.						68	71	70					21																	31538834		2203	4300	6503	SO:0001819	synonymous_variant	26285	exon1			AACAAAAGCTGAT	AJ250712	CCDS13586.1	21q22.1	2008-07-31			ENSG00000156282	ENSG00000156282		"Claudins"	2038	protein-coding gene	gene with protein product						12736707	Standard	NM_012131		Approved	MGC126552, MGC126554	uc011acv.2	P56750	OTTHUMG00000081873	ENST00000286808.3:c.102T>G	chr21.hg19:g.31538834A>C		113.0	0.0		75.0	14.0	NM_012131	Q3MJB5|Q6UY37	Silent	SNP	ENST00000286808.3	hg19	CCDS13586.1																																																																																			.	.		0.502	CLDN17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182261.1	NM_012131		C	31538834	A	C	31538834	2	2	75	1	0	0	0	0	0	0	0	1	3480	59	3	5		5	CLDN17	21	31538834	Silent	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10		31538834	16591061	140	10263										
TTC3	7267	hgsc.bcm.edu	37	chr21	38461097	38461097	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aaaaaataaatttgtctttaAgcaattcacgtgcttctgag	6	6	3	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr21:38461097A>T	ENST00000399017.2	+	5	3085		c.e5-1		TTC3_ENST00000355666.1_Splice_Site|TTC3_ENST00000354749.2_Splice_Site|TTC3_ENST00000399010.1_Splice_Site|TTC3_ENST00000540756.1_Intron|TTC3_ENST00000479930.1_Splice_Site	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3						negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TTTGTCTTTAAGCAATTCACG	0.284																																					.	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.339-2A>T						.						46	46	46					21																	38461097		2203	4300	6503	SO:0001630	splice_region_variant	7267	exon5			TCTTTAAGCAATT	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.339-1A>T	chr21.hg19:g.38461097A>T		103.0	0.0		67.0	22.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Splice_Site	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	A	18.53	3.643191	0.67244	.	.	ENSG00000182670	ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000399010;ENST00000399017;ENST00000354749	.	.	.	5.17	5.17	0.71159	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5353	0.56138	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TTC3	37382967	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	5.008000	0.63991	1.957000	0.56846	0.528000	0.53228	.	.	.		0.284	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		Intron	T	38461097	A	T	38461097	5	4	75	1	0	0	0	0	0	0	1	0	16712	86	3	4	351	4	TTC3	21	38461097	Splice_Site	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10	6922263	38461097	9668798	141	10264										
PDE9A	5152	hgsc.bcm.edu	37	chr21	44108091	44108091	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	ccatcgaccccaccatgcccGcgaattcagaacggtaagag	9	15	1	2			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr21:44108091G>A	ENST00000291539.6	+	3	265	c.205G>A	c.(205-207)Gcg>Acg	p.A69T	PDE9A_ENST00000398232.3_Intron|PDE9A_ENST00000335440.6_Missense_Mutation_p.R45H|PDE9A_ENST00000398229.3_Missense_Mutation_p.A28T|PDE9A_ENST00000539837.1_Missense_Mutation_p.A34T|PDE9A_ENST00000398224.3_Intron|PDE9A_ENST00000335512.4_Missense_Mutation_p.A69T|PDE9A_ENST00000398236.3_Intron|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000328862.6_Intron|PDE9A_ENST00000349112.3_Intron|PDE9A_ENST00000398234.3_Missense_Mutation_p.A28T|PDE9A_ENST00000380328.2_Missense_Mutation_p.A69T|PDE9A_ENST00000398227.3_Intron|PDE9A_ENST00000398225.3_Missense_Mutation_p.A28T	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	69					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	CACCATGCCCGCGAATTCAGA	0.577																																					p.A69T		Atlas-SNP	.											.	PDE9A	69	.	0			c.G205A						.						83	69	73					21																	44108091		2203	4300	6503	SO:0001583	missense	5152	exon3			ATGCCCGCGAATT	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"Phosphodiesterases"	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.205G>A	chr21.hg19:g.44108091G>A	ENSP00000291539:p.Ala69Thr	55.0	0.0		32.0	12.0	NM_001001570	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	hg19	CCDS13690.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	7.029|7.029	0.560319|0.560319	0.13498|0.13498	.|.	.|.	ENSG00000160191|ENSG00000160191	ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328;ENST00000398234;ENST00000398225;ENST00000398229|ENST00000335440	T;T;T;T;T;T;T|T	0.69306|0.70282	-0.35;-0.32;-0.36;-0.35;-0.33;-0.38;-0.39|-0.47	4.98|4.98	4.08|4.08	0.47627|0.47627	.|.	0.599027|.	0.17297|.	N|.	0.179402|.	T|T	0.47192|0.47192	0.1432|0.1432	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B;B;B;B;B;B|P	0.31485|0.40660	0.021;0.265;0.1;0.037;0.325;0.282|0.726	B;B;B;B;B;B|B	0.24269|0.32465	0.009;0.03;0.016;0.009;0.052;0.016|0.146	T|T	0.21621|0.21621	-1.0240|-1.0240	9|8	0.26408|0.13108	T|T	0.33|0.6	.|.	9.8363|9.8363	0.40971|0.40971	0.1003:0.0:0.8997:0.0|0.1003:0.0:0.8997:0.0	.|.	28;28;69;28;69;69|45	O76083-6;O76083-14;O76083-2;O76083-11;O76083-5;O76083|O76083-12	.;.;.;.;.;PDE9A_HUMAN|.	T|H	69;34;69;69;28;28;28|45	ENSP00000335242:A69T;ENSP00000441899:A34T;ENSP00000291539:A69T;ENSP00000369685:A69T;ENSP00000381289:A28T;ENSP00000381281:A28T;ENSP00000381285:A28T|ENSP00000335365:R45H	ENSP00000291539:A69T|ENSP00000335365:R45H	A|R	+|+	1|2	0|0	PDE9A|PDE9A	42981160|42981160	0.855000|0.855000	0.29742|0.29742	0.097000|0.097000	0.21041|0.21041	0.104000|0.104000	0.19210|0.19210	1.672000|1.672000	0.37523|0.37523	2.467000|2.467000	0.83353|0.83353	0.655000|0.655000	0.94253|0.94253	GCG|CGC	.	.		0.577	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			A	44108091	G	A	44108091	3	1	75	1	0	0	0	0	1	0	0	0	11664	1087	38	1	215	1	PDE9A	21	44108091	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	5646994	44108091	4021804	142	10265										
SIK1	150094	hgsc.bcm.edu	37	chr21	44845966	44845966	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	aagttgcctttgcccagggtCcgctcgatgtcgtaaaaacc	10	12	0	0			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr21:44845966C>T	ENST00000270162.6	-	2	225	c.93G>A	c.(91-93)cgG>cgA	p.R31R		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	31	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	TGCCCAGGGTCCGCTCGATGT	0.682																																					p.R31R		Atlas-SNP	.											.	SIK1	65	.	0			c.G93A						.						23	25	24					21																	44845966		2200	4296	6496	SO:0001819	synonymous_variant	150094	exon2			CAGGGTCCGCTCG	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"myocardial SNF1-like kinase"	605705	"SNF1-like kinase"	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.93G>A	chr21.hg19:g.44845966C>T		67.0	0.0		45.0	15.0	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Silent	SNP	ENST00000270162.6	hg19	CCDS33575.1																																																																																			.	.		0.682	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		T	44845966	C	T	44845966	2	4	75	1	0	0	0	0	0	0	0	1	14332	842	30	3		3	SIK1	21	44845966	Silent	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	737875	44845966	3283929	143	10266										
XPNPEP3	63929	hgsc.bcm.edu	37	chr22	41318489	41318489	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	taaagacttggggatcatgaAgaacattaaggaaaataatg	10	3	1	3			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr22:41318489A>C	ENST00000357137.4	+	8	1292	c.1208A>C	c.(1207-1209)aAg>aCg	p.K403T	XPNPEP3_ENST00000544094.1_Missense_Mutation_p.K380T	NM_022098.3	NP_071381.1	Q9NQH7	XPP3_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 3, putative	403					glomerular filtration (GO:0003094)|protein processing (GO:0016485)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metallopeptidase activity (GO:0008237)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	17						GGGATCATGAAGAACATTAAG	0.443																																					p.K403T	Ovarian(145;306 1841 7037 21878 30110)	Atlas-SNP	.											.	XPNPEP3	46	.	0			c.A1208C						.						204	201	202					22																	41318489		2203	4300	6503	SO:0001583	missense	63929	exon8			TCATGAAGAACAT		CCDS14007.1, CCDS74869.1	22q13.2	2010-07-20			ENSG00000196236	ENSG00000196236			28052	protein-coding gene	gene with protein product		613553				15708373, 20179356	Standard	NM_022098		Approved	APP3, NPHPL1	uc003azh.3	Q9NQH7	OTTHUMG00000151312	ENST00000357137.4:c.1208A>C	chr22.hg19:g.41318489A>C	ENSP00000349658:p.Lys403Thr	53.0	0.0		71.0	6.0	NM_022098	B2R9G1|B7Z790|B7Z7B2|Q6I9V9|Q8NDA6|Q9BV27|Q9BVH0	Missense_Mutation	SNP	ENST00000357137.4	hg19	CCDS14007.1	.	.	.	.	.	.	.	.	.	.	A	14.70	2.613923	0.46631	.	.	ENSG00000196236	ENST00000357137;ENST00000544094	T;T	0.76968	-1.06;-1.06	5.59	-2.74	0.05932	Peptidase M24, structural domain (3);	0.783877	0.12363	N	0.475427	T	0.65112	0.2660	L	0.41124	1.26	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.54098	-0.8344	10	0.48119	T	0.1	-5.8035	8.6855	0.34234	0.5088:0.1106:0.3805:0.0	.	403	Q9NQH7	XPP3_HUMAN	T	403;380	ENSP00000349658:K403T;ENSP00000441942:K380T	ENSP00000349658:K403T	K	+	2	0	XPNPEP3	39648435	0.479000	0.25925	0.007000	0.13788	0.650000	0.38633	0.293000	0.19029	-0.399000	0.07668	0.533000	0.62120	AAG	.	.		0.443	XPNPEP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322201.2	NM_022098		C	41318489	A	C	41318489	3	2	75	1	0	0	0	0	1	0	0	0	17459	72	3	5	1238	5	XPNPEP3	22	41318489	Missense_Mutation	SNP	A	TCGA-CC-A7IJ-01A-11D-A33Q-10		41318489	9986077	144	10267										
MEI1	150365	hgsc.bcm.edu	37	chr22	42177763	42177763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	tggccctcaccttggcaaagGcagattctcccaggactgca	10	14	2	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr22:42177763G>A	ENST00000401548.3	+	24	3041	c.3001G>A	c.(3001-3003)Gca>Aca	p.A1001T	MEI1_ENST00000476893.1_3'UTR|MEI1_ENST00000540880.1_3'UTR|MEI1_ENST00000400107.1_Missense_Mutation_p.A334T|MEI1_ENST00000300398.4_Missense_Mutation_p.A9T	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTTGGCAAAGGCAGATTCTCC	0.602																																					p.A1001T		Atlas-SNP	.											.	MEI1	87	.	0			c.G3001A						.						49	50	50					22																	42177763		2060	4239	6299	SO:0001583	missense	150365	exon24			GCAAAGGCAGATT	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"spermatogenesis associated 38"	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.3001G>A	chr22.hg19:g.42177763G>A	ENSP00000384115:p.Ala1001Thr	109.0	0.0		132.0	77.0	NM_152513		Missense_Mutation	SNP	ENST00000401548.3	hg19	CCDS46718.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312490	0.23908	.	.	ENSG00000167077	ENST00000401548;ENST00000400107;ENST00000300398;ENST00000419798;ENST00000403492	T;T;T;T	0.64803	-0.12;-0.12;0.0;0.0	6.03	-2.42	0.06542	.	1.419210	0.04213	N	0.332173	T	0.38612	0.1047	N	0.12182	0.205	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B	0.10450	0.005;0.003;0.002;0.002;0.002;0.005;0.002	T	0.25152	-1.0140	10	0.08179	T	0.78	-3.206	7.7499	0.28890	0.2335:0.2441:0.5223:0.0	.	15;111;334;111;244;369;1001	B7Z735;Q6ZRK7;Q5TIA1-3;E9PB79;Q5TIA1-5;Q5TIA1-2;Q5TIA1	.;.;.;.;.;.;MEI1_HUMAN	T	1001;334;9;111;9	ENSP00000384115:A1001T;ENSP00000382978:A334T;ENSP00000300398:A9T;ENSP00000385298:A9T	ENSP00000300398:A9T	A	+	1	0	MEI1	40507709	0.000000	0.05858	0.000000	0.03702	0.144000	0.21451	0.123000	0.15708	-0.135000	0.11495	0.655000	0.94253	GCA	.	.		0.602	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513		A	42177763	G	A	42177763	3	1	75	1	0	0	0	0	1	0	0	0	9474	1203	42	3	3095	3	MEI1	22	42177763	Missense_Mutation	SNP	G	TCGA-CC-A7IJ-01A-11D-A33Q-10	859274	42177763	9126803	145	10268										
SCUBE1	80274	hgsc.bcm.edu	37	chr22	43608598	43608598	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	agaagcctggagaacactggCctgaaagtcagaggtcatgg	14	8	2	4			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr22:43608598C>A	ENST00000360835.4	-	17	2180	c.2054G>T	c.(2053-2055)gGc>gTc	p.G685V	Z82214.3_ENST00000420269.1_RNA	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	685					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				AGAACACTGGCCTGAAAGTCA	0.701																																					p.G685V		Atlas-SNP	.											.	SCUBE1	105	.	0			c.G2054T						.						29	31	30					22																	43608598		2182	4274	6456	SO:0001630	splice_region_variant	80274	exon17			CACTGGCCTGAAA		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.2054-1G>T	chr22.hg19:g.43608598C>A		44.0	0.0		37.0	13.0	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	hg19	CCDS14048.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.586109	0.86851	.	.	ENSG00000159307	ENST00000360835;ENST00000381243	T	0.62364	0.03	4.3	4.3	0.51218	Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	T	0.72471	0.3464	L	0.43701	1.375	0.80722	D	1	D	0.76494	0.999	D	0.68621	0.959	T	0.76418	-0.2966	10	0.87932	D	0	.	17.3317	0.87267	0.0:1.0:0.0:0.0	.	685	Q8IWY4	SCUB1_HUMAN	V	685;315	ENSP00000354080:G685V	ENSP00000354080:G685V	G	-	2	0	SCUBE1	41938542	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.378000	0.66190	2.390000	0.81377	0.655000	0.94253	GGC	.	.		0.701	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	Missense_Mutation	A	43608598	C	A	43608598	5	1	75	1	0	0	0	0	0	0	1	0	13959	753	26	3	936	3	SCUBE1	22	43608598	Splice_Site	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10	1430835	43608598	7695968	146	10269										
TYMP	1890	hgsc.bcm.edu	37	chr22	50967719	50967743	+	Frame_Shift_Del	DEL	GTCTCCTCCAGATCCATGCCCCGAA	GTCTCCTCCAGATCCATGCCCCGAA	-													0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	gggcctgggtcagcaccgagGtctcctccagatccatgccc					rs143789597|rs553915679	byFrequency	TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	GTCTCCTCCAGATCCATGCCCCGAA	GTCTCCTCCAGATCCATGCCCCGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chr22:50967719_50967743delGTCTCCTCCAGATCCATGCCCCGAA	ENST00000252029.3	-	3	401_425	c.239_263delTTCGGGGCATGGATCTGGAGGAGAC	c.(238-264)cttcggggcatggatctggaggagaccfs	p.LRGMDLEET80fs	TYMP_ENST00000395678.3_Frame_Shift_Del_p.LRGMDLEET80fs|TYMP_ENST00000395680.1_Frame_Shift_Del_p.LRGMDLEET80fs|TYMP_ENST00000395681.1_Frame_Shift_Del_p.LRGMDLEET80fs|SCO2_ENST00000543927.1_5'Flank	NM_001113755.2|NM_001113756.2|NM_001257988.1|NM_001257989.1|NM_001953.4	NP_001107227.1|NP_001107228.1|NP_001244917.1|NP_001244918.1|NP_001944.1	P19971	TYPH_HUMAN	thymidine phosphorylase	80					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)|DNA replication (GO:0006260)|mitochondrial genome maintenance (GO:0000002)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphorylase activity (GO:0004645)|platelet-derived growth factor receptor binding (GO:0005161)|pyrimidine-nucleoside phosphorylase activity (GO:0016154)|thymidine phosphorylase activity (GO:0009032)|transferase activity, transferring pentosyl groups (GO:0016763)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Cidofovir(DB00369)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Trifluridine(DB00432)	CAGCACCGAGGTCTCCTCCAGATCCATGCCCCGAAGTCGGATGGC	0.68																																					p.80_88del		Atlas-Indel,Pindel	.											.	TYMP	25	.	0			c.240_264del	GRCh37	CM055158	TYMP	M		.																																			SO:0001589	frameshift_variant	1890	exon2			.	M63193	CCDS14096.1, CCDS58811.1	22q13	2014-09-17	2008-01-21	2008-01-21	ENSG00000025708	ENSG00000025708	2.4.2.4		3148	protein-coding gene	gene with protein product	"gliostatin"	131222	"endothelial cell growth factor 1 (platelet-derived)"	MNGIE, ECGF1		1590793, 11733540	Standard	NM_001113755		Approved		uc003bme.5	P19971	OTTHUMG00000150249	ENST00000252029.3:c.239_263delTTCGGGGCATGGATCTGGAGGAGAC	chr22.hg19:g.50967719_50967743delGTCTCCTCCAGATCCATGCCCCGAA	ENSP00000252029:p.Leu80fs	68.0	0.0		46.0	20.0	NM_001113756	A8MW15|H9KVA0|Q13390|Q8WVB7	Frame_Shift_Del	DEL	ENST00000252029.3	hg19	CCDS14096.1																																																																																			.	.		0.68	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317081.1	NM_001953		-	50967743	GTCTCCTCCAGATCCATGCCCCGAA	-	50967719	7	5	75	1	0	1	0	1	0	0	0	0	16826	1261	44	0	1217	0	TYMP	22	50967719	Frame_Shift_Del	DEL	GTCTCCTCCAGATCCATGCCCCGAA	TCGA-CC-A7IJ-01A-11D-A33Q-10	7359121	50967719	336847	147	10270										
UPRT	139596	hgsc.bcm.edu	37	chrX	74494412	74494412	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0608108108108108	9	1	0.959408554831896	1.25982941543582	0.805704858708956	1	1	0	actctcccggcagatcggggCgcagcttaagctgctgccta	12	14	1	1			TCGA-CC-A7IJ-01A-11D-A33Q-10	TCGA-CC-A7IJ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4daabef7-38d1-4a34-882c-1a78de6fe252	0d941ca8-539e-4a09-827d-7089b997f42e	g.chrX:74494412C>T	ENST00000373383.4	+	1	490	c.323C>T	c.(322-324)gCg>gTg	p.A108V	UPRT_ENST00000373379.1_Missense_Mutation_p.A108V|UPRT_ENST00000530743.1_5'Flank|UPRT_ENST00000531704.1_3'UTR	NM_145052.3	NP_659489.1	Q96BW1	UPP_HUMAN	uracil phosphoribosyltransferase (FUR1) homolog (S. cerevisiae)	108					female pregnancy (GO:0007565)|lactation (GO:0007595)|response to insulin (GO:0032868)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(4)|lung(4)	18						CAGATCGGGGCGCAGCTTAAG	0.557																																					p.A108V		Atlas-SNP	.											.	UPRT	46	.	0			c.C323T						.						28	22	24					X																	74494412		2203	4300	6503	SO:0001583	missense	139596	exon1			TCGGGGCGCAGCT	BC015116	CCDS14429.1	Xq13.3	2009-01-14			ENSG00000094841	ENSG00000094841			28334	protein-coding gene	gene with protein product		300656				12477932	Standard	NM_145052		Approved	DKFZp781E1243, MGC23937, FUR1, RP11-311P8.3	uc004ecb.2	Q96BW1	OTTHUMG00000021864	ENST00000373383.4:c.323C>T	chrX.hg19:g.74494412C>T	ENSP00000362481:p.Ala108Val	98.0	0.0		128.0	88.0	NM_145052	Q5JRL1|Q5JRL3|Q68DN0|Q96MW2	Missense_Mutation	SNP	ENST00000373383.4	hg19	CCDS14429.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.299813	0.81136	.	.	ENSG00000094841	ENST00000373383;ENST00000373379	D;D	0.91521	-2.86;-2.86	5.38	2.51	0.30379	.	0.566544	0.18568	N	0.137402	T	0.81578	0.4852	L	0.35854	1.095	0.18873	N	0.999989	P;B;B	0.39022	0.655;0.145;0.145	B;B;B	0.28709	0.093;0.05;0.05	T	0.68538	-0.5382	10	0.34782	T	0.22	-7.9436	9.1085	0.36712	0.1541:0.5532:0.2927:0.0	.	108;108;108	Q96BW1-2;A8KAF9;Q96BW1	.;.;UPP_HUMAN	V	108	ENSP00000362481:A108V;ENSP00000362477:A108V	ENSP00000362471:A108V	A	+	2	0	UPRT	74411137	0.706000	0.27856	0.001000	0.08648	0.941000	0.58515	2.545000	0.45769	0.191000	0.20236	0.600000	0.82982	GCG	.	.		0.557	UPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057278.1	NM_145052		T	74494412	C	T	74494412	3	4	75	1	0	0	0	0	1	0	0	0	17029	768	27	1	325	1	UPRT	23	74494412	Missense_Mutation	SNP	C	TCGA-CC-A7IJ-01A-11D-A33Q-10		74494412	80776148	148	10271										
MXRA8	54587	hgsc.bcm.edu	37	chr1	1290242	1290242	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctccagcggctcgatacgcaGtgagaagtcaccgcgctcaa	11	14	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:1290242G>T	ENST00000309212.6	-	5	799	c.769C>A	c.(769-771)Ctg>Atg	p.L257M	MXRA8_ENST00000445648.2_Missense_Mutation_p.L257M|MXRA8_ENST00000477278.2_Missense_Mutation_p.L248M|MXRA8_ENST00000342753.4_Missense_Mutation_p.L156M	NM_001282582.1|NM_032348.2	NP_001269511.1|NP_115724.1	Q9BRK3	MXRA8_HUMAN	matrix-remodelling associated 8	257	Ig-like V-type 2.				establishment of glial blood-brain barrier (GO:0060857)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TCGATACGCAGTGAGAAGTCA	0.677																																					p.L257M		Atlas-SNP	.											.	MXRA8	28	.	0			c.C769A						.						21	24	23					1																	1290242		2194	4291	6485	SO:0001583	missense	54587	exon5			TACGCAGTGAGAA	BC006213	CCDS24.1, CCDS59950.1, CCDS59951.1, CCDS59952.1	1p36.33	2013-01-11			ENSG00000162576	ENSG00000162576		"Immunoglobulin superfamily / V-set domain containing"	7542	protein-coding gene	gene with protein product	"limitrin"					14603461	Standard	XM_005244758		Approved	DKFZp586E2023	uc001aew.3	Q9BRK3	OTTHUMG00000002973	ENST00000309212.6:c.769C>A	chr1.hg19:g.1290242G>T	ENSP00000307887:p.Leu257Met	111.0	0.0		118.0	49.0	NM_032348	B3KTR6|B4DE34|Q5TA39|Q96KC3	Missense_Mutation	SNP	ENST00000309212.6	hg19	CCDS24.1	.	.	.	.	.	.	.	.	.	.	.	15.93	2.976807	0.53720	.	.	ENSG00000162576	ENST00000309212;ENST00000378864;ENST00000342753;ENST00000445648	T;T;T	0.67865	-0.29;-0.29;-0.29	4.24	3.3	0.37823	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	U	0.000001	T	0.77896	0.4199	M	0.67625	2.065	0.58432	D	0.999993	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;0.999;0.999;0.999	T	0.80067	-0.1537	10	0.72032	D	0.01	-1.1561	11.4826	0.50335	0.092:0.0:0.908:0.0	.	248;156;235;257;257	B3KTR6;B4DE34;B4E385;Q9BRK3-2;Q9BRK3	.;.;.;.;MXRA8_HUMAN	M	257;248;156;257	ENSP00000307887:L257M;ENSP00000344998:L156M;ENSP00000399229:L257M	ENSP00000307887:L257M	L	-	1	2	MXRA8	1280105	1.000000	0.71417	0.978000	0.43139	0.307000	0.27823	4.615000	0.61190	1.897000	0.54924	0.298000	0.19748	CTG	.	.		0.677	MXRA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008282.2	NM_032348		T	1290242	G	T	1290242	3	4	76	1	0	0	0	0	1	0	0	0	10014	1020	36	3	583	3	MXRA8	1	1290242	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10		1290242	247960379	1	10272										
CHD5	26038	hgsc.bcm.edu	37	chr1	6206301	6206301	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aggattcggtgaatcatcatCcactctggcttgatgccata	9	10	3	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:6206301C>T	ENST00000262450.3	-	11	1872	c.1773G>A	c.(1771-1773)tgG>tgA	p.W591*	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GAATCATCATCCACTCTGGCT	0.577																																					p.W591X		Atlas-SNP	.											.	CHD5	267	.	0			c.G1773A						.						137	134	135					1																	6206301		2203	4300	6503	SO:0001587	stop_gained	26038	exon11			CATCATCCACTCT	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.1773G>A	chr1.hg19:g.6206301C>T	ENSP00000262450:p.Trp591*	57.0	0.0		73.0	15.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Nonsense_Mutation	SNP	ENST00000262450.3	hg19	CCDS57.1	.	.	.	.	.	.	.	.	.	.	C	37	6.243051	0.97408	.	.	ENSG00000116254	ENST00000262450;ENST00000378006	.	.	.	3.85	3.85	0.44370	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.8543	16.3262	0.82983	0.0:1.0:0.0:0.0	.	.	.	.	X	591;107	.	ENSP00000262450:W591X	W	-	3	0	CHD5	6128888	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	7.600000	0.82769	2.138000	0.66242	0.462000	0.41574	TGG	.	.		0.577	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6206301	C	T	6206301	4	4	76	1	0	0	0	0	0	1	0	0	3330	856	30	3	4215	3	CHD5	1	6206301	Nonsense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	4916059	6206301	243044320	2	10273										
PRDM2	7799	hgsc.bcm.edu	37	chr1	14108238	14108238	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cccatggggattggtgtgacAgccacaaatttcactacaca	9	11	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:14108238A>T	ENST00000235372.7	+	8	4804	c.3948A>T	c.(3946-3948)acA>acT	p.T1316T	PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000413440.1_Silent_p.T1115T|PRDM2_ENST00000311066.5_Silent_p.T1316T|PRDM2_ENST00000343137.4_Silent_p.T1115T|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1316					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TTGGTGTGACAGCCACAAATT	0.468																																					p.T1316T		Atlas-SNP	.											.	PRDM2	147	.	0			c.A3948T						.						137	132	134					1																	14108238		2203	4300	6503	SO:0001819	synonymous_variant	7799	exon8			TGTGACAGCCACA	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"Chromatin-modifying enzymes / K-methyltransferases"	9347	protein-coding gene	gene with protein product	"retinoblastoma protein-binding zinc finger protein", "retinoblastoma protein-interacting zinc finger protein", "MTE-binding protein", "zinc-finger DNA-binding protein", "GATA-3 binding protein G3B"	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.3948A>T	chr1.hg19:g.14108238A>T		79.0	0.0		83.0	38.0	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Silent	SNP	ENST00000235372.7	hg19	CCDS150.1																																																																																			.	.		0.468	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		T	14108238	A	T	14108238	2	4	76	1	0	0	0	0	0	0	0	1	12470	175	7	4		4	PRDM2	1	14108238	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	7901937	14108238	235142383	3	10274										
EPHA8	2046	hgsc.bcm.edu	37	chr1	22895781	22895781	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctcttgtctcctgttttacaGtgaatttgctggacacgtcg	9	10	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:22895781G>A	ENST00000166244.3	+	2	166		c.e2-1		EPHA8_ENST00000538803.1_Splice_Site|EPHA8_ENST00000374644.4_Splice_Site	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CTGTTTTACAGTGAATTTGCT	0.602																																					.		Atlas-SNP	.											.	EPHA8	221	.	0			c.95-1G>A						.						137	129	132					1																	22895781		2203	4300	6503	SO:0001630	splice_region_variant	2046	exon2			TTTACAGTGAATT	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.95-1G>A	chr1.hg19:g.22895781G>A		62.0	0.0		55.0	11.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Splice_Site	SNP	ENST00000166244.3	hg19	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.711469	0.48517	.	.	ENSG00000070886	ENST00000166244;ENST00000374644;ENST00000538803	.	.	.	3.58	3.58	0.41010	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.043	0.58910	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EPHA8	22768368	1.000000	0.71417	0.997000	0.53966	0.551000	0.35334	8.840000	0.92125	1.999000	0.58509	0.297000	0.19635	.	.	.		0.602	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	Intron	A	22895781	G	A	22895781	5	1	76	1	0	0	0	0	0	0	1	0	5175	1043	36	3	100	3	EPHA8	1	22895781	Splice_Site	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	8787543	22895781	226354840	4	10275										
ASAP3	55616	hgsc.bcm.edu	37	chr1	23762387	23762387	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gctgtccaaagtcctgcccaTtggcaaaggcctccagtacc	9	15	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:23762387T>G	ENST00000336689.3	-	17	1750	c.1706A>C	c.(1705-1707)aAt>aCt	p.N569T	ASAP3_ENST00000437606.2_Missense_Mutation_p.N560T|ASAP3_ENST00000495646.1_Missense_Mutation_p.N73T	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	569					cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						GTCCTGCCCATTGGCAAAGGC	0.582																																					p.N569T		Atlas-SNP	.											.	ASAP3	65	.	0			c.A1706C						.						105	110	108					1																	23762387		2203	4300	6503	SO:0001583	missense	55616	exon17			TGCCCATTGGCAA	AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	14987	protein-coding gene	gene with protein product	"centaurin, beta 6"		"development and differentiation enhancing factor-like 1"	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.1706A>C	chr1.hg19:g.23762387T>G	ENSP00000338769:p.Asn569Thr	114.0	0.0		117.0	21.0	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Missense_Mutation	SNP	ENST00000336689.3	hg19	CCDS235.1	.	.	.	.	.	.	.	.	.	.	T	12.97	2.097053	0.37048	.	.	ENSG00000088280	ENST00000538685;ENST00000495646;ENST00000336689;ENST00000437606	T;T;T	0.52983	2.1;0.64;0.65	3.88	0.193	0.15139	Ankyrin repeat-containing domain (1);	0.289987	0.32204	N	0.006424	T	0.38134	0.1029	L	0.52011	1.625	0.27052	N	0.963765	B;B;B;B	0.18461	0.024;0.028;0.004;0.012	B;B;B;B	0.23419	0.014;0.046;0.046;0.024	T	0.37126	-0.9719	10	0.87932	D	0	.	7.4275	0.27107	0.0:0.4004:0.0:0.5996	.	560;438;92;569	Q8TDY4-3;B4DRP2;Q9NXH7;Q8TDY4	.;.;.;ASAP3_HUMAN	T	92;73;569;560	ENSP00000436150:N73T;ENSP00000338769:N569T;ENSP00000408826:N560T	ENSP00000338769:N569T	N	-	2	0	ASAP3	23634974	0.999000	0.42202	0.958000	0.39756	0.936000	0.57629	3.110000	0.50352	-0.063000	0.13065	0.363000	0.22086	AAT	.	.		0.582	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		G	23762387	T	G	23762387	3	3	76	1	0	0	0	0	1	0	0	0	1012	1493	52	5	1041	5	ASAP3	1	23762387	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	866606	23762387	225488234	5	10276										
GPR3	2827	hgsc.bcm.edu	37	chr1	27720703	27720703	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	actggccatcactgtcgaccGctacctttctctgtacaatg	7	14	2	0	rs372066479		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:27720703G>C	ENST00000374024.3	+	2	500	c.401G>C	c.(400-402)cGc>cCc	p.R134P		NM_005281.3	NP_005272.1	P46089	GPR3_HUMAN	G protein-coupled receptor 3	134					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|regulation of meiosis (GO:0040020)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(3)|ovary(1)|skin(1)	8		Breast(348;1.53e-05)|Ovarian(437;0.0606)|all_lung(284;0.157)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;2.81e-26)|Colorectal(126;1.24e-08)|KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;4.45e-06)|Lung(427;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|LUSC - Lung squamous cell carcinoma(448;0.008)|READ - Rectum adenocarcinoma(331;0.0419)		ACTGTCGACCGCTACCTTTCT	0.577																																					p.R134P		Atlas-SNP	.											.	GPR3	23	.	0			c.G401C						.						150	138	142					1																	27720703		2203	4300	6503	SO:0001583	missense	2827	exon2			TCGACCGCTACCT	BC032702	CCDS303.1	1p36.1-p35	2012-08-21			ENSG00000181773	ENSG00000181773		"GPCR / Class A : Orphans"	4484	protein-coding gene	gene with protein product		600241				7851889	Standard	NM_005281		Approved	ACCA	uc001bod.4	P46089	OTTHUMG00000003397	ENST00000374024.3:c.401G>C	chr1.hg19:g.27720703G>C	ENSP00000363136:p.Arg134Pro	39.0	0.0		31.0	13.0	NM_005281	A8K570	Missense_Mutation	SNP	ENST00000374024.3	hg19	CCDS303.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.005142	0.74932	.	.	ENSG00000181773	ENST00000374024	D	0.97161	-4.27	5.46	5.46	0.80206	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	D	0.99165	0.9711	H	0.98111	4.15	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.98979	1.0804	10	0.87932	D	0	.	18.9204	0.92523	0.0:0.0:1.0:0.0	.	134	P46089	GPR3_HUMAN	P	134	ENSP00000363136:R134P	ENSP00000363136:R134P	R	+	2	0	GPR3	27593290	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.866000	0.99616	2.561000	0.86390	0.462000	0.41574	CGC	.	.		0.577	GPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009522.1	NM_005281		C	27720703	G	C	27720703	3	2	76	1	0	0	0	0	1	0	0	0	6694	1087	38	4	403	4	GPR3	1	27720703	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	3958316	27720703	221529918	6	10277										
SPOCD1	90853	hgsc.bcm.edu	37	chr1	32265012	32265012	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aaggcctcaccgagtccataGtacctcctgcatggaacgga	10	13	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:32265012G>T	ENST00000360482.2	-	7	1987	c.1858C>A	c.(1858-1860)Cta>Ata	p.L620I	SPOCD1_ENST00000533231.1_Missense_Mutation_p.L620I|SPOCD1_ENST00000373648.2_Intron|SPOCD1_ENST00000257100.3_Missense_Mutation_p.L113I	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	620	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		CGAGTCCATAGTACCTCCTGC	0.622																																					p.L620I		Atlas-SNP	.											.	SPOCD1	109	.	0			c.C1858A						.						72	49	57					1																	32265012		2202	4300	6502	SO:0001583	missense	90853	exon7			TCCATAGTACCTC	AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 146"					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.1858C>A	chr1.hg19:g.32265012G>T	ENSP00000353670:p.Leu620Ile	191.0	0.0		238.0	110.0	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	hg19	CCDS347.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.729591	0.30684	.	.	ENSG00000134668	ENST00000257100;ENST00000360482;ENST00000533231;ENST00000449266;ENST00000529396	T;T;T	0.65364	-0.15;-0.15;-0.15	4.14	2.26	0.28386	Transcription elongation factor S-II, central domain (4);	.	.	.	.	T	0.64271	0.2583	M	0.83312	2.635	0.49299	D	0.999778	B;B	0.24043	0.078;0.096	B;B	0.34346	0.112;0.18	T	0.60959	-0.7159	9	0.48119	T	0.1	-0.8669	6.5776	0.22575	0.2205:0.0:0.7795:0.0	.	620;620	Q6ZMY3-2;Q6ZMY3	.;SPOC1_HUMAN	I	113;620;620;5;41	ENSP00000257100:L113I;ENSP00000353670:L620I;ENSP00000435851:L620I	ENSP00000257100:L113I	L	-	1	2	SPOCD1	32037599	0.779000	0.28652	0.633000	0.29310	0.321000	0.28281	0.752000	0.26362	0.524000	0.28502	0.544000	0.68410	CTA	.	.		0.622	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		T	32265012	G	T	32265012	3	4	76	1	0	0	0	0	1	0	0	0	15093	1020	36	3	1832	3	SPOCD1	1	32265012	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	4544309	32265012	216985609	7	10278										
EIF2C3	192669	hgsc.bcm.edu	37	chr1	36439043	36439043	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	accaccctctgggagggggcAgggaagtgtggtttggattc	17	8	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:36439043A>T	ENST00000373191.4	+	5	938	c.589A>T	c.(589-591)Agg>Tgg	p.R197W	AGO3_ENST00000397828.2_Missense_Mutation_p.R197W|AGO3_ENST00000246314.6_Intron|AGO3_ENST00000324350.5_Missense_Mutation_p.R197W	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	197					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										GGGAGGGGGCAGGGAAGTGTG	0.453																																					p.R197W		Atlas-SNP	.											.	.	.	.	0			c.A589T						.						162	163	162					1																	36439043		2203	4300	6503	SO:0001583	missense	192669	exon5			GGGGGCAGGGAAG	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"Argonaute/PIWI family"	18421	protein-coding gene	gene with protein product	"argonaute 3"	607355	"eukaryotic translation initiation factor 2C, 3"	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.589A>T	chr1.hg19:g.36439043A>T	ENSP00000362287:p.Arg197Trp	110.0	0.0		177.0	27.0	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	hg19	CCDS399.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.251485	0.80135	.	.	ENSG00000126070	ENST00000324350;ENST00000373191;ENST00000397828	T	0.10099	2.91	5.62	4.45	0.53987	Domain of unknown function DUF1785 (1);	0.000000	0.85682	D	0.000000	T	0.37489	0.1005	M	0.88450	2.955	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.984	T	0.38650	-0.9651	10	0.72032	D	0.01	.	12.2039	0.54340	0.7355:0.2645:0.0:0.0	.	197;197	Q9H9G7;Q5TA56	AGO3_HUMAN;.	W	197	ENSP00000362287:R197W	ENSP00000317425:R197W	R	+	1	2	EIF2C3	36211630	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.335000	0.52105	2.141000	0.66446	0.460000	0.39030	AGG	.	.		0.453	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852		T	36439043	A	T	36439043	3	4	76	1	0	0	0	0	1	0	0	0	5009	179	7	4	607	4	EIF2C3	1	36439043	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	4174031	36439043	212811578	8	10279										
SMAP2	64744	hgsc.bcm.edu	37	chr1	40882562	40882562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgatgcctccaccagtaggcAtggttgctcagccaggagct	12	12	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:40882562A>G	ENST00000539317.1	+	9	911	c.718A>G	c.(718-720)Atg>Gtg	p.M240V		NM_001198980.1	NP_001185909.1	Q8WU79	SMAP2_HUMAN	small ArfGAP2	320					regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			central_nervous_system(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			ACCAGTAGGCATGGTTGCTCA	0.592																																					p.M320V		Atlas-SNP	.											.	SMAP2	48	.	0			c.A958G						.						61	54	56					1																	40882562		2203	4300	6503	SO:0001583	missense	64744	exon9			GTAGGCATGGTTG	AL137764	CCDS451.1, CCDS55592.1, CCDS55593.1, CCDS72763.1	1p35.3-p34.1	2008-09-22	2008-09-05	2008-01-09	ENSG00000084070	ENSG00000084070		"ADP-ribosylation factor GTPase activating proteins"	25082	protein-coding gene	gene with protein product			"stromal membrane-associated protein 1-like", "stromal membrane-associated GTPase-activating protein 2"	SMAP1L		16571680	Standard	NM_001198978		Approved		uc001cfj.3	Q8WU79	OTTHUMG00000007301	ENST00000539317.1:c.718A>G	chr1.hg19:g.40882562A>G	ENSP00000442835:p.Met240Val	213.0	0.0		276.0	40.0	NM_022733	B2R7T1|B7Z5B5|B7Z8V2|D3DPV2|Q5QPL2|Q96C93|Q9NST2|Q9UJL8	Missense_Mutation	SNP	ENST00000539317.1	hg19	CCDS55593.1	.	.	.	.	.	.	.	.	.	.	A	7.556	0.663789	0.14710	.	.	ENSG00000084070	ENST00000372718;ENST00000372708;ENST00000539317	T;T;T	0.29917	2.25;2.26;1.55	6.02	4.9	0.64082	.	0.427371	0.31589	N	0.007389	T	0.12475	0.0303	N	0.03324	-0.35	0.45914	D	0.998756	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.16988	-1.0384	10	0.13853	T	0.58	-9.0976	9.6694	0.40004	0.9196:0.0:0.0804:0.0	.	290;320	Q8WU79-2;Q8WU79	.;SMAP2_HUMAN	V	320;290;240	ENSP00000361803:M320V;ENSP00000361793:M290V;ENSP00000442835:M240V	ENSP00000361793:M290V	M	+	1	0	SMAP2	40655149	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.407000	0.59754	2.311000	0.77944	0.533000	0.62120	ATG	.	.		0.592	SMAP2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022733		G	40882562	A	G	40882562	3	3	76	1	0	0	0	0	1	0	0	0	14782	217	8	2	992	2	SMAP2	1	40882562	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	4443519	40882562	208368059	9	10280										
CCDC30	728621	hgsc.bcm.edu	37	chr1	43110399	43110399	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	taaagaaaataagcaattacAggaaaatagtcttcgtctca	6	6	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:43110399A>T	ENST00000340612.4	+	12	1811	c.1811A>T	c.(1810-1812)cAg>cTg	p.Q604L	CCDC30_ENST00000390640.4_Missense_Mutation_p.Q393L|CCDC30_ENST00000342022.4_Missense_Mutation_p.Q604L|CCDC30_ENST00000428554.2_Missense_Mutation_p.Q604L|CCDC30_ENST00000507855.1_Missense_Mutation_p.Q393L			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	604						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						AAGCAATTACAGGAAAATAGT	0.368																																					p.Q604L		Atlas-SNP	.											.	CCDC30	78	.	0			c.A1811T						.						105	96	99					1																	43110399		2203	4300	6503	SO:0001583	missense	728621	exon13			AATTACAGGAAAA	AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"prefoldin 6-like"					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1811A>T	chr1.hg19:g.43110399A>T	ENSP00000340378:p.Gln604Leu	21.0	0.0		30.0	9.0	NM_001080850	Q14F06|Q5VVM5	Missense_Mutation	SNP	ENST00000340612.4	hg19	CCDS30690.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.073588	0.36566	.	.	ENSG00000186409	ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.36	4.23	0.50019	.	0.184752	0.48767	D	0.000176	T	0.33059	0.0850	N	0.24115	0.695	0.36838	D	0.887249	P;B	0.39250	0.665;0.027	B;B	0.43728	0.429;0.015	T	0.38887	-0.9640	10	0.72032	D	0.01	.	8.3208	0.32128	0.9094:0.0:0.0906:0.0	.	604;393	Q5VVM6;Q5VVM6-2	CCD30_HUMAN;.	L	604;393;604;604;393	ENSP00000397035:Q604L;ENSP00000426711:Q393L;ENSP00000340378:Q604L;ENSP00000339280:Q604L;ENSP00000375051:Q393L	ENSP00000340378:Q604L	Q	+	2	0	CCDC30	42882986	1.000000	0.71417	0.554000	0.28268	0.752000	0.42762	2.432000	0.44784	0.963000	0.38082	0.533000	0.62120	CAG	.	.		0.368	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030		T	43110399	A	T	43110399	3	4	76	1	0	0	0	0	1	0	0	0	2807	188	7	4	1857	4	CCDC30	1	43110399	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	2227837	43110399	206140222	10	10281										
ST3GAL3	6487	hgsc.bcm.edu	37	chr1	44395833	44395833	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cacaatatccagcgagagaaAgagtttctgcggaagctggt	12	8	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:44395833A>G	ENST00000361392.4	+	12	1245	c.1068A>G	c.(1066-1068)aaA>aaG	p.K356K	ST3GAL3_ENST00000351035.3_Silent_p.K394K|ST3GAL3_ENST00000533933.1_Silent_p.K258K|ST3GAL3_ENST00000361746.4_Silent_p.K425K|ST3GAL3_ENST00000361400.4_Silent_p.K340K|ST3GAL3_ENST00000545417.1_Missense_Mutation_p.R158G|ST3GAL3_ENST00000531451.1_Missense_Mutation_p.R127G|ST3GAL3_ENST00000330208.2_Missense_Mutation_p.R143G|ST3GAL3_ENST00000372377.4_3'UTR|ST3GAL3_ENST00000372374.2_Silent_p.K325K|ST3GAL3_ENST00000531816.1_Missense_Mutation_p.K95R|ST3GAL3_ENST00000361812.4_Missense_Mutation_p.R158G|ST3GAL3_ENST00000372365.1_3'UTR|ST3GAL3_ENST00000528371.1_Missense_Mutation_p.K180R|ST3GAL3_ENST00000372375.2_Silent_p.K410K|ST3GAL3_ENST00000372369.1_Silent_p.K326K|ST3GAL3_ENST00000262915.3_Silent_p.K425K|ST3GAL3_ENST00000347631.2_Silent_p.K371K|ST3GAL3_ENST00000335430.6_3'UTR|ST3GAL3_ENST00000332628.6_Silent_p.K325K|ST3GAL3_ENST00000372362.2_Missense_Mutation_p.R143G|ST3GAL3_ENST00000372367.1_Missense_Mutation_p.K195R|ST3GAL3_ENST00000372366.1_3'UTR|ST3GAL3_ENST00000372368.2_Silent_p.K410K|ST3GAL3_ENST00000353126.3_Silent_p.K258K|ST3GAL3_ENST00000372372.2_Silent_p.K394K|ST3GAL3_ENST00000531993.1_Silent_p.K242K	NM_001270459.1|NM_006279.3|NM_174964.2	NP_001257388.1|NP_006270.1|NP_777624.1	Q11203	SIAT6_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	356					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|N-acetyllactosaminide alpha-2,3-sialyltransferase activity (GO:0008118)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(3)|skin(1)	19	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				AGCGAGAGAAAGAGTTTCTGC	0.552																																					p.K195R		Atlas-SNP	.											.	ST3GAL3	56	.	0			c.A584G						.						197	181	187					1																	44395833		2203	4300	6503	SO:0001819	synonymous_variant	6487	exon8			AGAGAAAGAGTTT	L23768	CCDS492.1, CCDS493.1, CCDS494.1, CCDS495.1, CCDS496.1, CCDS497.1, CCDS498.1, CCDS499.1, CCDS500.1, CCDS53310.1, CCDS57988.1, CCDS57989.1, CCDS57990.1, CCDS57991.1, CCDS57992.1, CCDS57993.1, CCDS57994.1	1p34.1	2014-01-31	2005-02-07	2005-02-07	ENSG00000126091	ENSG00000126091	2.4.99.6	"Sialyltransferases"	10866	protein-coding gene	gene with protein product	"ST3Gal III"	606494	"sialyltransferase 6 (N-acetyllacosaminide alpha 2,3-sialyltransferase)", "mental retardation, non-syndromic, autosomal recessive, 12"	SIAT6, MRT12		8333853, 21907012	Standard	NM_174963		Approved		uc001cjz.4	Q11203	OTTHUMG00000007561	ENST00000361392.4:c.1068A>G	chr1.hg19:g.44395833A>G		57.0	0.0		61.0	15.0	NM_001270463	A9Z1W2|D3DPX8|Q5T4W9|Q5T4X0|Q5T4X7|Q5T4X8|Q5T4X9|Q5T4Y0|Q5T4Y2|Q5T4Y3|Q5T4Y4|Q86UR6|Q86UR7|Q86UR8|Q86UR9|Q86US0|Q86US1|Q86US2|Q8IX41|Q8IX42|Q8IX43|Q8IX44|Q8IX45|Q8IX46|Q8IX47|Q8IX48|Q8IX49|Q8IX50|Q8IX51|Q8IX52|Q8IX53|Q8IX54|Q8IX55|Q8IX56|Q8IX57|Q8IX58	Missense_Mutation	SNP	ENST00000361392.4	hg19	CCDS492.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.84|17.84	3.488833|3.488833	0.64074|0.64074	.|.	.|.	ENSG00000126091|ENSG00000126091	ENST00000372367;ENST00000528371;ENST00000531816|ENST00000545417;ENST00000330208;ENST00000361812;ENST00000372362;ENST00000531451;ENST00000490502	T;T;T|T;T;T;T;T	0.77750|0.77877	-0.16;0.43;-1.12|-1.13;-1.13;-1.13;-1.13;-1.11	4.5|4.5	-2.06|-2.06	0.07298|0.07298	.|.	0.057637|.	0.64402|.	D|.	0.000002|.	T|T	0.67571|0.67571	0.2907|0.2907	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B;B;B|B;B;B	0.02656|0.02656	0.0;0.0;0.0|0.0;0.0;0.0	B;B;B|B;B;B	0.04013|0.01281	0.001;0.001;0.001|0.0;0.0;0.0	T|T	0.58999|0.58999	-0.7536|-0.7536	9|8	0.87932|0.87932	D|D	0|0	.|.	11.1695|11.1695	0.48563|0.48563	0.2712:0.0:0.7288:0.0|0.2712:0.0:0.7288:0.0	.|.	95;180;195|143;158;127	Q11203-22;Q11203-17;Q11203-24|Q11203-12;Q5T4Y1;Q11203-18	.;.;.|.;.;.	R|G	195;180;95|158;143;158;143;127;193	ENSP00000361442:K195R;ENSP00000434876:K180R;ENSP00000434378:K95R|ENSP00000439634:R158G;ENSP00000333494:R143G;ENSP00000355201:R158G;ENSP00000361437:R143G;ENSP00000435603:R127G	ENSP00000361442:K195R|ENSP00000333494:R143G	K|R	+|+	2|1	0|2	ST3GAL3|ST3GAL3	44168420|44168420	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.984000|0.984000	0.73092|0.73092	1.759000|1.759000	0.38420|0.38420	-0.208000|-0.208000	0.10171|0.10171	-0.462000|-0.462000	0.05337|0.05337	AAG|AGA	.	.		0.552	ST3GAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019964.1	NM_174963		G	44395833	A	G	44395833	2	3	76	1	0	0	0	0	0	0	0	1	15231	73	3	2		2	ST3GAL3	1	44395833	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	1285434	44395833	204854788	11	10282										
DMRTB1	63948	hgsc.bcm.edu	37	chr1	53932266	53932266	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctaccttctttgtccttcacAgatgaccaggatgcagaggt	9	11	2	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:53932266A>T	ENST00000371445.3	+	4	1016		c.e4-1			NM_033067.1	NP_149056.1	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal, 1						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(5)|ovary(1)|skin(1)	10						TGTCCTTCACAGATGACCAGG	0.468																																					.		Atlas-SNP	.											.	DMRTB1	38	.	0			c.962-2A>T						.						164	179	174					1																	53932266		2203	4300	6503	SO:0001630	splice_region_variant	63948	exon4			CTTCACAGATGAC	AJ291671	CCDS581.1	1p32	2008-08-29			ENSG00000143006	ENSG00000143006			13913	protein-coding gene	gene with protein product		614805					Standard	NM_033067		Approved		uc001cvq.1	Q96MA1	OTTHUMG00000008080	ENST00000371445.3:c.962-1A>T	chr1.hg19:g.53932266A>T		209.0	0.0		233.0	112.0	NM_033067	Q96SD2	Splice_Site	SNP	ENST00000371445.3	hg19	CCDS581.1	.	.	.	.	.	.	.	.	.	.	A	14.95	2.688133	0.48097	.	.	ENSG00000143006	ENST00000371445	.	.	.	4.63	3.52	0.40303	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.3459	0.21349	0.8914:0.0:0.1086:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DMRTB1	53704854	0.998000	0.40836	0.649000	0.29536	0.444000	0.32077	1.392000	0.34486	2.075000	0.62263	0.459000	0.35465	.	.	.		0.468	DMRTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022110.1		Intron	T	53932266	A	T	53932266	5	4	76	1	0	0	0	0	0	0	1	0	4592	202	7	4	974	4	DMRTB1	1	53932266	Splice_Site	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	9536433	53932266	195318355	12	10283										
YIPF1	54432	hgsc.bcm.edu	37	chr1	54332055	54332055	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctgggggataatccacagtaTctgaaagaagagaaaaggag	13	5	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:54332055T>C	ENST00000072644.1	-	9	985	c.649A>G	c.(649-651)Ata>Gta	p.I217V	YIPF1_ENST00000539954.1_Splice_Site_p.I242V|YIPF1_ENST00000469457.1_5'UTR|YIPF1_ENST00000371399.1_Splice_Site_p.I34V	NM_018982.4	NP_061855.1	Q9Y548	YIPF1_HUMAN	Yip1 domain family, member 1	217						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|skin(1)|urinary_tract(2)	19						ATCCACAGTATCTGAAAGAAG	0.493																																					p.I217V		Atlas-SNP	.											.	YIPF1	30	.	0			c.A649G						.						34	37	36					1																	54332055		2203	4300	6503	SO:0001630	splice_region_variant	54432	exon9			ACAGTATCTGAAA	BC009674	CCDS584.1	1p33-p32.1	2008-02-05			ENSG00000058799	ENSG00000058799		"Yip1 domain family"	25231	protein-coding gene	gene with protein product						12477932	Standard	NM_018982		Approved	DJ167A19.1, FinGER1	uc001cvu.3	Q9Y548	OTTHUMG00000008074	ENST00000072644.1:c.649-1A>G	chr1.hg19:g.54332055T>C		282.0	0.0		313.0	136.0	NM_018982	B2RCM7|D3DQ40|Q9NWJ1	Missense_Mutation	SNP	ENST00000072644.1	hg19	CCDS584.1	.	.	.	.	.	.	.	.	.	.	T	3.386	-0.125275	0.06795	.	.	ENSG00000058799	ENST00000371399;ENST00000072644;ENST00000539954	T;T	0.40756	1.02;1.02	5.54	3.2	0.36748	Yip1 domain (1);	0.144208	0.64402	N	0.000009	T	0.19167	0.0460	N	0.11724	0.165	0.47183	D	0.999342	B	0.02656	0.0	B	0.08055	0.003	T	0.15838	-1.0423	10	0.02654	T	1	-24.2691	8.753	0.34629	0.0:0.1615:0.0:0.8385	.	217	Q9Y548	YIPF1_HUMAN	V	34;217;242	ENSP00000072644:I217V;ENSP00000439926:I242V	ENSP00000072644:I217V	I	-	1	0	YIPF1	54104643	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	1.846000	0.39289	0.396000	0.25283	0.482000	0.46254	ATA	.	.		0.493	YIPF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022103.5	NM_018982	Missense_Mutation	C	54332055	T	C	54332055	5	2	76	1	0	0	0	0	0	0	1	0	17492	1449	50	2	279	2	YIPF1	1	54332055	Splice_Site	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	399789	54332055	194918566	13	10284										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79411969	79411969	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccgaacttacctatacagacGgttccatcattagtgataaa	6	10	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:79411969G>T	ENST00000370742.3	-	3	378	c.315C>A	c.(313-315)acC>acA	p.T105T		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	105	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		CTATACAGACGGTTCCATCAT	0.358																																					p.T105T		Atlas-SNP	.											.	ELTD1	143	.	0			c.C315A						.						94	89	90					1																	79411969		1871	4106	5977	SO:0001819	synonymous_variant	64123	exon3			ACAGACGGTTCCA	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.315C>A	chr1.hg19:g.79411969G>T		101.0	0.0		128.0	54.0	NM_022159	B1AR71|Q5KU34	Silent	SNP	ENST00000370742.3	hg19	CCDS41352.1																																																																																			.	.		0.358	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		T	79411969	G	T	79411969	2	4	76	1	0	0	0	0	0	0	0	1	5086	1103	39	1		1	ELTD1	1	79411969	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	25079914	79411969	169838652	14	10285										
ABCA4	24	hgsc.bcm.edu	37	chr1	94543350	94543350	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctggctttcccgagggccctTgtagaggaagtttaggatgg	15	8	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:94543350T>C	ENST00000370225.3	-	11	1536	c.1450A>G	c.(1450-1452)Aag>Gag	p.K484E	ABCA4_ENST00000535735.1_Missense_Mutation_p.K484E	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	484					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.K484E(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CGAGGGCCCTTGTAGAGGAAG	0.498																																					p.K484E		Atlas-SNP	.											ABCA4,NS,carcinoma,0,1	ABCA4	275	.	1	Substitution - Missense(1)	lung(1)	c.A1450G						.						172	167	169					1																	94543350		2203	4300	6503	SO:0001583	missense	24	exon11			GGCCCTTGTAGAG	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.1450A>G	chr1.hg19:g.94543350T>C	ENSP00000359245:p.Lys484Glu	126.0	0.0		129.0	37.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	T	13.20	2.166960	0.38217	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.85171	-1.95;-1.95	5.24	5.24	0.73138	.	0.471455	0.23813	N	0.044308	T	0.70988	0.3287	L	0.39147	1.195	0.18873	N	0.999983	P;B	0.39940	0.696;0.001	B;B	0.41412	0.356;0.003	T	0.65331	-0.6194	10	0.19590	T	0.45	.	15.3047	0.73982	0.0:0.0:0.0:1.0	.	484;484	F5H6E5;P78363	.;ABCA4_HUMAN	E	484	ENSP00000359245:K484E;ENSP00000437682:K484E	ENSP00000359245:K484E	K	-	1	0	ABCA4	94315938	0.910000	0.30920	0.007000	0.13788	0.318000	0.28184	5.572000	0.67411	2.202000	0.70862	0.533000	0.62120	AAG	.	.		0.498	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		C	94543350	T	C	94543350	3	2	76	1	0	0	0	0	1	0	0	0	34	1821	63	2	5531	2	ABCA4	1	94543350	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	15131381	94543350	154707271	15	10286										
PTBP2	58155	hgsc.bcm.edu	37	chr1	97271990	97271990	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	taaagatggttacgccccaaAgtctgtttaccctcttcggt	8	11	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:97271990A>G	ENST00000426398.2	+	10	1103	c.1060A>G	c.(1060-1062)Agt>Ggt	p.S354G	PTBP2_ENST00000370198.1_Missense_Mutation_p.S359G|PTBP2_ENST00000370197.1_Missense_Mutation_p.S359G|PTBP2_ENST00000609116.1_Missense_Mutation_p.S354G|PTBP2_ENST00000541987.1_Intron|PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000394184.3_Missense_Mutation_p.S370G	NM_021190.2	NP_067013.1	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	354	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splice site selection (GO:0006376)|negative regulation of RNA splicing (GO:0033119)|regulation of neural precursor cell proliferation (GO:2000177)	spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|skin(1)	26		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)		TACGCCCCAAAGTCTGTTTAC	0.388																																					p.S354G		Atlas-SNP	.											.	PTBP2	62	.	0			c.A1060G						.						222	204	210					1																	97271990		2203	4300	6503	SO:0001583	missense	58155	exon10			CCCCAAAGTCTGT	AB051232	CCDS754.1, CCDS72828.1, CCDS72829.1, CCDS72830.1	1p21.3	2013-07-16			ENSG00000117569	ENSG00000117569		"RNA binding motif (RRM) containing"	17662	protein-coding gene	gene with protein product		608449				11003644	Standard	XM_005271084		Approved	brPTB, nPTB, PTB, PTBLP	uc001drq.3	Q9UKA9	OTTHUMG00000010685	ENST00000426398.2:c.1060A>G	chr1.hg19:g.97271990A>G	ENSP00000412788:p.Ser354Gly	59.0	0.0		65.0	23.0	NM_021190	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	Missense_Mutation	SNP	ENST00000426398.2	hg19	CCDS754.1	.	.	.	.	.	.	.	.	.	.	A	9.628	1.135614	0.21123	.	.	ENSG00000117569	ENST00000236228;ENST00000543738;ENST00000370198;ENST00000370197;ENST00000426398;ENST00000394184	T;T;T;T;T	0.46451	0.88;0.89;0.87;0.9;0.87	5.65	5.65	0.86999	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.21881	0.0527	L	0.35644	1.08	0.80722	D	1	B;P;P;B;B;B	0.40619	0.001;0.603;0.724;0.001;0.0;0.001	B;B;B;B;B;B	0.40534	0.006;0.178;0.332;0.006;0.008;0.008	T	0.03922	-1.0992	10	0.17832	T	0.49	.	15.8653	0.79060	1.0:0.0:0.0:0.0	.	362;370;359;354;354;359	B4DSU5;B4DSS8;Q9UKA9-4;Q9UKA9;Q9UKA9-2;Q9UKA9-3	.;.;.;PTBP2_HUMAN;.;.	G	354;26;359;359;354;370	ENSP00000236228:S354G;ENSP00000359217:S359G;ENSP00000359216:S359G;ENSP00000412788:S354G;ENSP00000377738:S370G	ENSP00000236228:S354G	S	+	1	0	PTBP2	97044578	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.752000	0.68728	2.149000	0.67028	0.460000	0.39030	AGT	.	.		0.388	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1			G	97271990	A	G	97271990	3	3	76	1	0	0	0	0	1	0	0	0	12738	72	3	2	1098	2	PTBP2	1	97271990	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	2728640	97271990	151978631	16	10287										
OLFM3	118427	hgsc.bcm.edu	37	chr1	102269846	102269846	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aaagggtgacattgaacagcAcctggtggccattgttccag	12	9	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:102269846A>T	ENST00000338858.5	-	6	1384	c.1385T>A	c.(1384-1386)gTg>gAg	p.V462E	OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000536598.1_3'UTR|OLFM3_ENST00000370103.4_Missense_Mutation_p.V442E			Q96PB7	NOE3_HUMAN	olfactomedin 3	462	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		ATTGAACAGCACCTGGTGGCC	0.403																																					p.V442E		Atlas-SNP	.											.	OLFM3	178	.	0			c.T1325A						.						153	145	148					1																	102269846		2203	4300	6503	SO:0001583	missense	118427	exon6			AACAGCACCTGGT	AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"optimedin"	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.1385T>A	chr1.hg19:g.102269846A>T	ENSP00000345192:p.Val462Glu	67.0	0.0		86.0	33.0	NM_058170	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Missense_Mutation	SNP	ENST00000338858.5	hg19		.	.	.	.	.	.	.	.	.	.	A	19.80	3.895036	0.72639	.	.	ENSG00000118733	ENST00000370103;ENST00000338858	D;D	0.90955	-2.76;-2.76	5.47	5.47	0.80525	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.95812	0.8637	M	0.91090	3.175	0.80722	D	1	D;D	0.76494	0.992;0.999	D;D	0.81914	0.961;0.995	D	0.96761	0.9561	10	0.87932	D	0	.	15.8388	0.78824	1.0:0.0:0.0:0.0	.	442;462	Q5T3V6;Q96PB7	.;NOE3_HUMAN	E	442;462	ENSP00000359121:V442E;ENSP00000345192:V462E	ENSP00000345192:V462E	V	-	2	0	OLFM3	102042434	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.910000	0.92685	2.202000	0.70862	0.528000	0.53228	GTG	.	.		0.403	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1			T	102269846	A	T	102269846	3	4	76	1	0	0	0	0	1	0	0	0	10863	159	6	4	55	4	OLFM3	1	102269846	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	4997856	102269846	146980775	17	10288										
SLC25A24	29957	hgsc.bcm.edu	37	chr1	108742645	108742645	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cctgcagctcgccgatgtccAccactccgtccccattgcgg	9	19	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:108742645A>T	ENST00000565488.1	-	1	335	c.116T>A	c.(115-117)gTg>gAg	p.V39E	RP11-483I13.5_ENST00000564063.1_RNA|SLC25A24_ENST00000569674.1_Missense_Mutation_p.V39E	NM_013386.4	NP_037518.3	Q6NUK1	SCMC1_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24	39	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				ATP transport (GO:0015867)|cellular response to calcium ion (GO:0071277)|cellular response to oxidative stress (GO:0034599)|mitochondrial transport (GO:0006839)|regulation of cell death (GO:0010941)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP transmembrane transporter activity (GO:0005347)|calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)		GCCGATGTCCACCACTCCGTC	0.721																																					p.V39E		Atlas-SNP	.											.	SLC25A24	65	.	0			c.T116A						.						18	24	22					1																	108742645		2024	4168	6192	SO:0001583	missense	29957	exon1			ATGTCCACCACTC	AJ619961	CCDS786.1, CCDS41361.1	1p13.2	2013-05-22			ENSG00000085491	ENSG00000085491		"Solute carriers", "EF-hand domain containing"	20662	protein-coding gene	gene with protein product		608744				15123600	Standard	NM_013386		Approved	DKFZp586G0123, APC1	uc001dvn.5	Q6NUK1	OTTHUMG00000011013	ENST00000565488.1:c.116T>A	chr1.hg19:g.108742645A>T	ENSP00000457733:p.Val39Glu	76.0	0.0		108.0	63.0	NM_013386	B7ZAI9|Q5T331|Q5T485|Q6PJJ9|Q705K4|Q9P129	Missense_Mutation	SNP	ENST00000565488.1	hg19	CCDS41361.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.882113	0.91740	.	.	ENSG00000085491	ENST00000264128	T	0.73047	-0.71	4.65	4.65	0.58169	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.71443	0.3340	M	0.93898	3.47	0.52501	D	0.999957	B	0.18013	0.025	B	0.26969	0.075	T	0.77691	-0.2493	10	0.87932	D	0	-27.6067	13.4165	0.60972	1.0:0.0:0.0:0.0	.	39	Q6NUK1	SCMC1_HUMAN	E	39	ENSP00000264128:V39E	ENSP00000264128:V39E	V	-	2	0	SLC25A24	108544168	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	5.527000	0.67123	1.940000	0.56252	0.374000	0.22700	GTG	.	.		0.721	SLC25A24-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030280.2	NM_013386		T	108742645	A	T	108742645	3	4	76	1	0	0	0	0	1	0	0	0	14502	159	6	4	1487	4	SLC25A24	1	108742645	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	6472799	108742645	140507976	18	10289										
PHTF1	10745	hgsc.bcm.edu	37	chr1	114240970	114240970	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gatattgtagattaagggatTcattgtcagtccatagagtc	10	5	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:114240970T>A	ENST00000369604.1	-	18	2665	c.2182A>T	c.(2182-2184)Aat>Tat	p.N728Y	PHTF1_ENST00000393357.2_Missense_Mutation_p.N728Y|PHTF1_ENST00000474926.1_5'UTR|PHTF1_ENST00000369600.1_Missense_Mutation_p.N675Y|PHTF1_ENST00000369596.2_Missense_Mutation_p.N675Y|PHTF1_ENST00000369598.1_Missense_Mutation_p.N683Y			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	728					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATTAAGGGATTCATTGTCAGT	0.353																																					p.N728Y		Atlas-SNP	.											.	PHTF1	69	.	0			c.A2182T						.						139	137	138					1																	114240970		2203	4300	6503	SO:0001583	missense	10745	exon17			AGGGATTCATTGT	AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.2182A>T	chr1.hg19:g.114240970T>A	ENSP00000358617:p.Asn728Tyr	67.0	0.0		70.0	18.0	NM_006608	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Missense_Mutation	SNP	ENST00000369604.1	hg19	CCDS861.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.312855	0.81358	.	.	ENSG00000116793	ENST00000369597;ENST00000393357;ENST00000369596;ENST00000369598;ENST00000369600;ENST00000369604	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.71771	0.3379	M	0.65975	2.015	0.80722	D	1	D	0.71674	0.998	D	0.63488	0.915	T	0.75593	-0.3264	9	0.87932	D	0	-26.9547	16.8222	0.85835	0.0:0.0:0.0:1.0	.	728	Q9UMS5	PHTF1_HUMAN	Y	683;728;675;683;675;728	.	ENSP00000358609:N675Y	N	-	1	0	PHTF1	114042493	1.000000	0.71417	0.999000	0.59377	0.587000	0.36485	7.984000	0.88150	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.353	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608		A	114240970	T	A	114240970	3	1	76	1	0	0	0	0	1	0	0	0	11871	1783	62	4	114	4	PHTF1	1	114240970	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	5498325	114240970	135009651	19	10290										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117142910	117142910	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgatacactgcaagtcaaagGagtcgctgtaggtcaccccc	10	12	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:117142910G>C	ENST00000369486.3	-	7	2447	c.1682C>G	c.(1681-1683)tCc>tGc	p.S561C	IGSF3_ENST00000369483.1_Missense_Mutation_p.S581C|IGSF3_ENST00000318837.6_Missense_Mutation_p.S581C	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	561	Ig-like C2-type 5.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		CAAGTCAAAGGAGTCGCTGTA	0.592																																					p.S581C		Atlas-SNP	.											.	IGSF3	294	.	0			c.C1742G						.						29	34	32					1																	117142910		2203	4298	6501	SO:0001583	missense	3321	exon8			TCAAAGGAGTCGC	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.1682C>G	chr1.hg19:g.117142910G>C	ENSP00000358498:p.Ser561Cys	46.0	0.0		44.0	19.0	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.963270	0.74016	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.03272	3.99;3.99;3.99	4.57	4.57	0.56435	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.062103	0.64402	D	0.000003	T	0.06962	0.0177	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.984;0.999;0.991	T	0.24693	-1.0153	10	0.87932	D	0	-40.0587	14.8994	0.70666	0.0:0.0:1.0:0.0	.	581;561;581	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	C	561;581;581	ENSP00000358498:S561C;ENSP00000358495:S581C;ENSP00000321184:S581C	ENSP00000321184:S581C	S	-	2	0	IGSF3	116944433	1.000000	0.71417	0.980000	0.43619	0.861000	0.49209	9.017000	0.93651	2.354000	0.79902	0.455000	0.32223	TCC	.	.		0.592	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		C	117142910	G	C	117142910	3	2	76	1	0	0	0	0	1	0	0	0	7610	1174	41	4	1922	4	IGSF3	1	117142910	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	2901940	117142910	132107711	20	10291										
SF3B4	10262	hgsc.bcm.edu	37	chr1	149898428	149898428	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gagccatggcgctcacccttGgagtccttcttgaaggcata	11	12	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:149898428G>A	ENST00000271628.8	-	3	1130	c.546C>T	c.(544-546)tcC>tcT	p.S182S	MTMR11_ENST00000492824.1_5'Flank	NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	182					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)	17	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			GCTCACCCTTGGAGTCCTTCT	0.537																																					p.S182S		Atlas-SNP	.											.	SF3B4	37	.	0			c.C546T						.						84	82	83					1																	149898428		2203	4300	6503	SO:0001819	synonymous_variant	10262	exon3			ACCCTTGGAGTCC	L35013	CCDS72900.1	1q21.2	2013-02-12	2002-08-29		ENSG00000143368	ENSG00000143368		"RNA binding motif (RRM) containing"	10771	protein-coding gene	gene with protein product		605593	"splicing factor 3b, subunit 4, 49kD"			7958871	Standard	NM_005850		Approved	SAP49, SF3b49, Hsh49	uc001etk.2	Q15427	OTTHUMG00000012208	ENST00000271628.8:c.546C>T	chr1.hg19:g.149898428G>A		89.0	0.0		135.0	25.0	NM_005850	Q5SZ63	Silent	SNP	ENST00000271628.8	hg19	CCDS941.1																																																																																			.	.		0.537	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033753.1	NM_005850		A	149898428	G	A	149898428	2	1	76	1	0	0	0	0	0	0	0	1	14168	1335	47	3		3	SF3B4	1	149898428	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	32755518	149898428	99352193	21	10292										
MRPS21	54460	hgsc.bcm.edu	37	chr1	150266814	150266814	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aacatctgaagttcatcgccAggactgtgatggtacaggaa	11	8	2	2	rs376189902		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:150266814A>T	ENST00000369084.5	+	1	475	c.28A>T	c.(28-30)Agg>Tgg	p.R10W	MRPS21_ENST00000309092.7_Missense_Mutation_p.R10W	NM_018997.3	NP_061870.1	P82921	RT21_HUMAN	mitochondrial ribosomal protein S21	10					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(1)|pancreas(1)	4	Lung NSC(24;5.57e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GTTCATCGCCAGGACTGTGAT	0.473																																					p.R10W		Atlas-SNP	.											.	MRPS21	8	.	0			c.A28T						.						110	96	100					1																	150266814		2203	4300	6503	SO:0001583	missense	54460	exon1			ATCGCCAGGACTG	AB051353	CCDS950.1	1q21	2012-09-13			ENSG00000187145			"Mitochondrial ribosomal proteins / small subunits"	14046	protein-coding gene	gene with protein product		611984					Standard	NM_031901		Approved		uc001euk.3	P82921	OTTHUMG00000012544	ENST00000369084.5:c.28A>T	chr1.hg19:g.150266814A>T	ENSP00000358080:p.Arg10Trp	196.0	0.0		309.0	27.0	NM_018997	Q5TB11|Q9BST6	Missense_Mutation	SNP	ENST00000369084.5	hg19	CCDS950.1	.	.	.	.	.	.	.	.	.	.	A	18.72	3.684518	0.68157	.	.	ENSG00000187145	ENST00000309092;ENST00000369084	T;T	0.38077	1.16;1.16	5.41	4.25	0.50352	.	.	.	.	.	T	0.30039	0.0752	.	.	.	0.49051	D	0.999745	P	0.48764	0.915	P	0.49226	0.603	T	0.15665	-1.0429	8	0.87932	D	0	.	9.623	0.39732	0.6576:0.3424:0.0:0.0	.	10	P82921	RT21_HUMAN	W	10	ENSP00000312395:R10W;ENSP00000358080:R10W	ENSP00000312395:R10W	R	+	1	2	MRPS21	148533438	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	1.643000	0.37217	1.030000	0.39839	0.533000	0.62120	AGG	.	.		0.473	MRPS21-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035813.1	NM_018997		T	150266814	A	T	150266814	3	4	76	1	0	0	0	0	1	0	0	0	9841	179	7	4	30	4	MRPS21	1	150266814	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	368386	150266814	98983807	22	10293										
HORMAD1	84072	hgsc.bcm.edu	37	chr1	150676627	150676627	+	Frame_Shift_Del	DEL	T	T	-													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atagaaagatctggactttcTttagacctcataatttcatc							TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:150676627delT	ENST00000361824.2	-	12	1020	c.915delA	c.(913-915)aaafs	p.K305fs	RNU6-1042P_ENST00000384204.1_RNA|HORMAD1_ENST00000368995.4_Frame_Shift_Del_p.K225fs|HORMAD1_ENST00000368993.2_Frame_Shift_Del_p.K305fs|HORMAD1_ENST00000322343.7_Frame_Shift_Del_p.K298fs	NM_032132.4	NP_115508.2	Q86X24	HORM1_HUMAN	HORMA domain containing 1	305				K -> E (in Ref. 1; CAG38536). {ECO:0000305}.	blastocyst development (GO:0001824)|meiotic DNA double-strand break formation (GO:0042138)|meiotic nuclear division (GO:0007126)|meiotic recombination checkpoint (GO:0051598)|meiotic sister chromatid cohesion (GO:0051177)|oogenesis (GO:0048477)|regulation of homologous chromosome segregation (GO:0060629)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(3)	16	all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			CTGGACTTTCTTTAGACCTCA	0.318																																					p.E306fs		Atlas-Indel,Pindel	.											.	HORMAD1	59	.	0			c.916delG						.						33	33	33					1																	150676627		2198	4294	6492	SO:0001589	frameshift_variant	84072	exon12			.	AL136755	CCDS967.1, CCDS55633.1	1q21.2	2009-03-09			ENSG00000143452	ENSG00000143452			25245	protein-coding gene	gene with protein product	"cancer/testis antigen 46"	609824				11230166, 15999985	Standard	NM_032132		Approved	DKFZP434A1315, CT46	uc001evk.2	Q86X24	OTTHUMG00000035005	ENST00000361824.2:c.915delA	chr1.hg19:g.150676627delT	ENSP00000355167:p.Lys305fs	181.0	0.0		190.0	28.0	NM_032132	A6NMK2|B3KUK1|Q4G114|Q5T5I3|Q5T5I4|Q5T5I5|Q6FIC1|Q9H0K8	Frame_Shift_Del	DEL	ENST00000361824.2	hg19	CCDS967.1																																																																																			.	.		0.318	HORMAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084722.1	NM_032132		-	150676627	T	-	150676627	7	5	76	1	0	1	0	1	0	0	0	0	7295	1606	56	0	285	0	HORMAD1	1	150676627	Frame_Shift_Del	DEL	T	TCGA-CC-A7IK-01A-12D-A33Q-10	409813	150676627	98573994	23	10294										
FLG	2312	hgsc.bcm.edu	37	chr1	152284916	152284917	+	Missense_Mutation	DNP	CT	CT	GA													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atggtgggatccttgtcttaCtccagtgctgggccctgtcc							TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:152284916_152284917CT>GA	ENST00000368799.1	-	3	2480_2481	c.2445_2446AG>TC	c.(2443-2448)ggAGta>ggTCta	p.V816L	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	816	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTTGTCTTACTCCAGTGCTGG	0.569									Ichthyosis																												p.V816L|p.G815G		Atlas-SNP	.											.	FLG	900	.	0			c.G2446C|c.A2445T						.																																			SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCTTACTCCAGT|TCTTACTCCAGTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2445_2446delinsGA	chr1.hg19:g.152284916_152284917delinsGA	ENSP00000357789:p.Val816Leu	124.0|123.0	0.0		148.0|150.0	37.0|40.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation|Silent	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.569	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		GA	152284917	CT	GA	152284916	3	3	76	1	0	0	0	0	1	0	0	0	5930	565	20	4	9743	4	FLG	1	152284916	Missense_Mutation	DNP	CT	TCGA-CC-A7IK-01A-12D-A33Q-10	1608289	152284916	96965705	24	10295										
FLG2	388698	hgsc.bcm.edu	37	chr1	152326656	152326656	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccatattggccaaatccagtGgactgacctgagtcagatat	9	10	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:152326656G>T	ENST00000388718.5	-	3	3678	c.3606C>A	c.(3604-3606)tcC>tcA	p.S1202S	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1202	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAAATCCAGTGGACTGACCTG	0.483																																					p.S1202S		Atlas-SNP	.											.	FLG2	431	.	0			c.C3606A						.						116	114	115					1																	152326656		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			TCCAGTGGACTGA	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.3606C>A	chr1.hg19:g.152326656G>T		96.0	0.0		124.0	26.0	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	hg19	CCDS30861.1																																																																																			.	.		0.483	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152326656	G	T	152326656	2	4	76	1	0	0	0	0	0	0	0	1	5931	1335	47	3		3	FLG2	1	152326656	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	41740	152326656	96923965	25	10296										
SPRR4	163778	hgsc.bcm.edu	37	chr1	152944448	152944448	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agcaagtgaagcagccttgtCagccaccccctgttaaatgt	9	12	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:152944448C>T	ENST00000328051.2	+	2	131	c.82C>T	c.(82-84)Cag>Tag	p.Q28*		NM_173080.1	NP_775103.1	Q96PI1	SPRR4_HUMAN	small proline-rich protein 4	28	Gln-rich.				keratinization (GO:0031424)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)				lung(1)|prostate(1)	2	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCAGCCTTGTCAGCCACCCCC	0.572																																					p.Q28X		Atlas-SNP	.											.	SPRR4	8	.	0			c.C82T						.						132	118	122					1																	152944448		2203	4300	6503	SO:0001587	stop_gained	163778	exon2			CCTTGTCAGCCAC	AF335109	CCDS1031.1	1q21.3	2008-02-05	2006-11-29		ENSG00000184148	ENSG00000184148			23173	protein-coding gene	gene with protein product						11719550, 11279051	Standard	NM_173080		Approved		uc001fav.1	Q96PI1	OTTHUMG00000012450	ENST00000328051.2:c.82C>T	chr1.hg19:g.152944448C>T	ENSP00000332163:p.Gln28*	174.0	0.0		238.0	69.0	NM_173080	Q2M1Y7|Q5T522	Nonsense_Mutation	SNP	ENST00000328051.2	hg19	CCDS1031.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.155425	0.57259	.	.	ENSG00000184148	ENST00000328051	.	.	.	4.86	4.86	0.63082	.	0.000000	0.31134	U	0.008188	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-0.0046	13.3677	0.60694	0.0:1.0:0.0:0.0	.	.	.	.	X	28	.	ENSP00000332163:Q28X	Q	+	1	0	SPRR4	151211072	0.999000	0.42202	1.000000	0.80357	0.372000	0.29890	3.312000	0.51927	2.532000	0.85374	0.460000	0.39030	CAG	.	.		0.572	SPRR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034663.1	NM_173080		T	152944448	C	T	152944448	4	4	76	1	0	0	0	0	0	1	0	0	15119	827	29	3	84	3	SPRR4	1	152944448	Nonsense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	617792	152944448	96306173	26	10297										
AQP10	89872	hgsc.bcm.edu	37	chr1	154296109	154296109	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gtggggctcttggccatcctGgacagacggaacaagggagt	16	9	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:154296109G>C	ENST00000324978.3	+	5	574	c.534G>C	c.(532-534)ctG>ctC	p.L178L	AQP10_ENST00000484864.1_Silent_p.L178L|ATP8B2_ENST00000368487.3_5'Flank|AQP10_ENST00000355197.4_3'UTR	NM_080429.2	NP_536354.2	Q96PS8	AQP10_HUMAN	aquaporin 10	178					response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|stomach(2)|upper_aerodigestive_tract(1)	23	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGGCCATCCTGGACAGACGGA	0.617																																					p.L178L		Atlas-SNP	.											.	AQP10	44	.	0			c.G534C						.						141	145	144					1																	154296109		2203	4300	6503	SO:0001819	synonymous_variant	89872	exon5			CATCCTGGACAGA	AF159174	CCDS1065.1	1q21.3	2008-02-05			ENSG00000143595	ENSG00000143595		"Ion channels / Aquaporins"	16029	protein-coding gene	gene with protein product		606578				11573934	Standard	NM_080429		Approved		uc001feu.3	Q96PS8	OTTHUMG00000035980	ENST00000324978.3:c.534G>C	chr1.hg19:g.154296109G>C		98.0	0.0		114.0	16.0	NM_080429	Q5VYD3|Q5VYD4|Q8NG70	Silent	SNP	ENST00000324978.3	hg19	CCDS1065.1																																																																																			.	.		0.617	AQP10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087661.1	NM_080429		C	154296109	G	C	154296109	2	2	76	1	0	0	0	0	0	0	0	1	822	1335	47	4		4	AQP10	1	154296109	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	1351661	154296109	94954512	27	10298										
ADAR	103	hgsc.bcm.edu	37	chr1	154569745	154569745	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgcaacacagtattggaaccTgacaggagatgaagcacgta	11	8	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:154569745T>C	ENST00000368474.4	-	5	2134		c.e5-2		ADAR_ENST00000368471.3_Splice_Site|ADAR_ENST00000292205.5_Splice_Site	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific						adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		TATTGGAACCTGACAGGAGAT	0.512																																					.		Atlas-SNP	.											.	ADAR	113	.	0			c.1935-2A>G	GRCh37	CS090036	ADAR	S		.						62	61	61					1																	154569745		2203	4300	6503	SO:0001630	splice_region_variant	103	exon6			GGAACCTGACAGG	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.1935-2A>G	chr1.hg19:g.154569745T>C		63.0	0.0		79.0	36.0	NM_015840	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Splice_Site	SNP	ENST00000368474.4	hg19	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	T	12.01	1.810656	0.32053	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3898	0.74735	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADAR	152836369	1.000000	0.71417	0.995000	0.50966	0.075000	0.17131	7.384000	0.79751	2.270000	0.75569	0.533000	0.62120	.	.	.		0.512	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	Intron	C	154569745	T	C	154569745	5	2	76	1	0	0	0	0	0	0	1	0	281	1594	55	2	1791	2	ADAR	1	154569745	Splice_Site	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	273636	154569745	94680876	28	10299										
ATP1A2	477	hgsc.bcm.edu	37	chr1	160098468	160098468	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctgaccctgacagccaagcgCatggcacggaagaactgcct	11	14	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:160098468C>A	ENST00000361216.3	+	9	1133	c.1044C>A	c.(1042-1044)cgC>cgA	p.R348R	ATP1A2_ENST00000392233.3_Silent_p.R348R	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	348					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CAGCCAAGCGCATGGCACGGA	0.577																																					p.R348R		Atlas-SNP	.											.	ATP1A2	167	.	0			c.C1044A						.						96	88	91					1																	160098468		2203	4300	6503	SO:0001819	synonymous_variant	477	exon9			CAAGCGCATGGCA	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.1044C>A	chr1.hg19:g.160098468C>A		104.0	0.0		154.0	31.0	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	hg19	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	C	10.30	1.311026	0.23821	.	.	ENSG00000018625	ENST00000447527	.	.	.	4.77	2.76	0.32466	.	.	.	.	.	T	0.42381	0.1200	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35276	-0.9795	4	.	.	.	.	7.3329	0.26592	0.2651:0.6483:0.0:0.0866	.	.	.	.	E	59	.	.	A	+	2	0	ATP1A2	158365092	0.190000	0.23276	1.000000	0.80357	0.966000	0.64601	-0.427000	0.06999	1.135000	0.42183	0.561000	0.74099	GCA	.	.		0.577	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160098468	C	A	160098468	2	1	76	1	0	0	0	0	0	0	0	1	1129	697	25	3		3	ATP1A2	1	160098468	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	5528723	160098468	89152153	29	10300										
RCSD1	92241	hgsc.bcm.edu	37	chr1	167659345	167659345	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gtcaagagctcgcctctgatTgagaagcttcaggtaagtgc	12	9	3	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:167659345T>A	ENST00000367854.3	+	4	589	c.258T>A	c.(256-258)atT>atA	p.I86I	RCSD1_ENST00000537350.1_Silent_p.I56I	NM_052862.3	NP_443094.3	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	86					cellular hyperosmotic response (GO:0071474)|skeletal muscle contraction (GO:0003009)	actin filament (GO:0005884)	actin filament binding (GO:0051015)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	24	all_hematologic(923;0.215)					CGCCTCTGATTGAGAAGCTTC	0.423																																					p.I86I		Atlas-SNP	.											.	RCSD1	64	.	0			c.T258A						.						134	122	126					1																	167659345		2203	4300	6503	SO:0001819	synonymous_variant	92241	exon4			TCTGATTGAGAAG	BC072399	CCDS1263.1	1q24.2	2008-02-05			ENSG00000198771	ENSG00000198771			28310	protein-coding gene	gene with protein product		610579				12477932	Standard	NM_052862		Approved	MK2S4, MGC21854	uc001gem.3	Q6JBY9	OTTHUMG00000035318	ENST00000367854.3:c.258T>A	chr1.hg19:g.167659345T>A		98.0	0.0		114.0	39.0	NM_052862	B1AK48|Q4G0E7|Q6IN93|Q8IZM2|Q96DX0|Q9NST4	Silent	SNP	ENST00000367854.3	hg19	CCDS1263.1																																																																																			.	.		0.423	RCSD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085451.1	NM_052862		A	167659345	T	A	167659345	2	1	76	1	0	0	0	0	0	0	0	1	13200	1800	63	4		4	RCSD1	1	167659345	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	7560877	167659345	81591276	30	10301										
GPR161	23432	hgsc.bcm.edu	37	chr1	168054803	168054803	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagctaaaacatctccttctTcgatgctctgcaactgcagc	6	14	3	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:168054803T>G	ENST00000367838.1	-	8	1869	c.1556A>C	c.(1555-1557)gAa>gCa	p.E519A	GPR161_ENST00000546300.1_Missense_Mutation_p.E405A|GPR161_ENST00000537209.1_Missense_Mutation_p.E539A|GPR161_ENST00000367835.1_Missense_Mutation_p.E519A|GPR161_ENST00000271357.5_Missense_Mutation_p.E519A|GPR161_ENST00000361697.2_Missense_Mutation_p.E519A|GPR161_ENST00000367836.1_Missense_Mutation_p.E387A|GPR161_ENST00000539777.1_Missense_Mutation_p.E441A	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	519					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					ATCTCCTTCTTCGATGCTCTG	0.657																																					p.E539A		Atlas-SNP	.											.	GPR161	56	.	0			c.A1616C						.						52	61	58					1																	168054803		2203	4300	6503	SO:0001583	missense	23432	exon7			CCTTCTTCGATGC	AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"GPCR / Class A : Orphans"	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.1556A>C	chr1.hg19:g.168054803T>G	ENSP00000356812:p.Glu519Ala	85.0	0.0		139.0	67.0	NM_001267609	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Missense_Mutation	SNP	ENST00000367838.1	hg19	CCDS1268.1	.	.	.	.	.	.	.	.	.	.	t	11.37	1.618595	0.28801	.	.	ENSG00000143147	ENST00000367838;ENST00000271357;ENST00000367836;ENST00000367835;ENST00000546300;ENST00000539777;ENST00000537209;ENST00000361697	T;T;D;T;T;T;T;T	0.82344	-0.13;-0.13;-1.6;-0.13;-1.14;-1.12;-0.05;-0.13	5.75	1.89	0.25635	.	0.269080	0.40728	N	0.001024	T	0.57359	0.2048	N	0.22421	0.69	0.23758	N	0.996924	B;B;B;B;B	0.15141	0.0;0.0;0.001;0.0;0.012	B;B;B;B;B	0.15870	0.002;0.001;0.004;0.001;0.014	T	0.40040	-0.9584	9	0.51188	T	0.08	4.0E-4	13.125	0.59349	0.0:0.0:0.3801:0.6199	.	539;405;441;539;519	F5GXD6;B7Z5E8;F5H6J7;B7Z5Z6;Q8N6U8	.;.;.;.;GP161_HUMAN	A	519;519;387;519;405;441;539;519	ENSP00000356812:E519A;ENSP00000271357:E519A;ENSP00000356810:E387A;ENSP00000356809:E519A;ENSP00000444348:E405A;ENSP00000437576:E441A;ENSP00000441039:E539A;ENSP00000355194:E519A	ENSP00000271357:E519A	E	-	2	0	GPR161	166321427	0.999000	0.42202	0.008000	0.14137	0.257000	0.26127	3.938000	0.56583	0.052000	0.16007	0.524000	0.50904	GAA	.	.		0.657	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369		G	168054803	T	G	168054803	3	3	76	1	0	0	0	0	1	0	0	0	6673	1783	62	5	37	5	GPR161	1	168054803	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	395458	168054803	81195818	31	10302										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177250137	177250137	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcatgcctgtgaatgagggcAgctttcctgactgggaaagg	14	8	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:177250137A>C	ENST00000361539.4	+	8	2137	c.1825A>C	c.(1825-1827)Agc>Cgc	p.S609R	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	609					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											GAATGAGGGCAGCTTTCCTGA	0.537																																					p.S609R		Atlas-SNP	.											.	FAM5B	191	.	0			c.A1825C						.						74	70	71					1																	177250137		2203	4300	6503	SO:0001583	missense	57795	exon8			GAGGGCAGCTTTC		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1825A>C	chr1.hg19:g.177250137A>C	ENSP00000354481:p.Ser609Arg	65.0	0.0		84.0	13.0	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	hg19	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	A	9.572	1.121187	0.20877	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.14893	2.47	5.25	-4.17	0.03857	.	0.792587	0.12706	N	0.445980	T	0.09468	0.0233	N	0.14661	0.345	0.09310	N	1	B;B	0.33266	0.404;0.037	B;B	0.36335	0.222;0.01	T	0.30238	-0.9985	10	0.62326	D	0.03	-1.3116	9.5077	0.39058	0.4115:0.1097:0.4788:0.0	.	504;609	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	R	362;609	ENSP00000354481:S609R	ENSP00000354481:S609R	S	+	1	0	FAM5B	175516760	0.000000	0.05858	0.029000	0.17559	0.947000	0.59692	-0.159000	0.10056	-0.554000	0.06150	0.260000	0.18958	AGC	.	.		0.537	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		C	177250137	A	C	177250137	3	2	76	1	0	0	0	0	1	0	0	0	5601	188	7	5	1851	5	FAM5B	1	177250137	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	9195334	177250137	72000484	32	10303										
ASPM	259266	hgsc.bcm.edu	37	chr1	197102525	197102525	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttttcgaacaattaaccgccTagcttcaatttcaatttcaa	3	10	3	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:197102525T>A	ENST00000367409.4	-	6	2630	c.2374A>T	c.(2374-2376)Agg>Tgg	p.R792W	ASPM_ENST00000367408.1_Missense_Mutation_p.R42W|ASPM_ENST00000294732.7_Missense_Mutation_p.R792W	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	792					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						ATTAACCGCCTAGCTTCAATT	0.348																																					p.R792W		Atlas-SNP	.											.	ASPM	444	.	0			c.A2374T						.						73	73	73					1																	197102525		2203	4300	6503	SO:0001583	missense	259266	exon6			ACCGCCTAGCTTC	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.2374A>T	chr1.hg19:g.197102525T>A	ENSP00000356379:p.Arg792Trp	115.0	0.0		175.0	62.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	T	17.57	3.422176	0.62622	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408	T;T;T	0.60040	0.22;0.22;0.22	5.27	0.922	0.19408	Calponin homology domain (1);	0.224829	0.38837	N	0.001549	T	0.64929	0.2643	L	0.53249	1.67	0.09310	N	1	D;D	0.76494	0.993;0.999	P;D	0.66497	0.849;0.944	T	0.57093	-0.7870	10	0.66056	D	0.02	.	8.8774	0.35354	0.0:0.0922:0.5359:0.3719	.	792;792	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	W	792;792;42	ENSP00000356379:R792W;ENSP00000294732:R792W;ENSP00000356378:R42W	ENSP00000294732:R792W	R	-	1	2	ASPM	195369148	0.991000	0.36638	0.012000	0.15200	0.972000	0.66771	1.131000	0.31406	-0.031000	0.13781	0.528000	0.53228	AGG	.	.		0.348	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		A	197102525	T	A	197102525	3	1	76	1	0	0	0	0	1	0	0	0	1056	1521	53	4	8151	4	ASPM	1	197102525	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	19852388	197102525	52148096	33	10304										
IGFN1	91156	hgsc.bcm.edu	37	chr1	201196213	201196213	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	accccgcggtgtacagcactGacctgctgggcgtgtgctcc	13	15	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:201196213G>T	ENST00000335211.4	+	23	11120	c.10990G>T	c.(10990-10992)Gac>Tac	p.D3664Y	IGFN1_ENST00000295591.8_3'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	1207						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GTACAGCACTGACCTGCTGGG	0.652																																					p.D3664Y		Atlas-SNP	.											.	IGFN1	220	.	0			c.G10990T						.						71	48	55					1																	201196213		2203	4300	6503	SO:0001583	missense	91156	exon23			AGCACTGACCTGC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.10990G>T	chr1.hg19:g.201196213G>T	ENSP00000334714:p.Asp3664Tyr	171.0	0.0		225.0	72.0	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	hg19	CCDS53455.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.17|10.17	1.276300|1.276300	0.23307|0.23307	.|.	.|.	ENSG00000163395|ENSG00000163395	ENST00000335211|ENST00000412892	T|.	0.66099|.	-0.19|.	5.06|5.06	2.14|2.14	0.27477|0.27477	.|.	0.115963|.	0.56097|.	D|.	0.000024|.	T|.	0.40347|.	0.1113|.	L|L	0.27944|0.27944	0.81|0.81	0.45676|0.45676	D|D	0.998599|0.998599	D|.	0.69078|.	0.997|.	D|.	0.79108|.	0.992|.	T|.	0.07385|.	-1.0775|.	10|.	0.87932|.	D|.	0|.	.|.	7.2076|7.2076	0.25915|0.25915	0.381:0.0:0.619:0.0|0.381:0.0:0.619:0.0	.|.	3664|.	F8WAI1|.	.|.	Y|L	3664|1081	ENSP00000334714:D3664Y|.	ENSP00000334714:D3664Y|.	D|X	+|+	1|2	0|2	IGFN1|IGFN1	199462836|199462836	0.936000|0.936000	0.31750|0.31750	0.009000|0.009000	0.14445|0.14445	0.014000|0.014000	0.08584|0.08584	1.765000|1.765000	0.38481|0.38481	0.173000|0.173000	0.19788|0.19788	0.561000|0.561000	0.74099|0.74099	GAC|TGA	.	.		0.652	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		T	201196213	G	T	201196213	3	4	76	1	0	0	0	0	1	0	0	0	7599	1290	45	3	11076	3	IGFN1	1	201196213	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	4093688	201196213	48054408	34	10305										
NAV1	89796	hgsc.bcm.edu	37	chr1	201757764	201757764	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cttccgagaccccacggacgAtggtgagacttcatgctagc	11	13	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:201757764A>G	ENST00000367296.4	+	10	3584	c.3164A>G	c.(3163-3165)gAt>gGt	p.D1055G	IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000367300.3_Intron|NAV1_ENST00000367297.4_Missense_Mutation_p.D1055G|NAV1_ENST00000469130.1_3'UTR|NAV1_ENST00000295624.6_Missense_Mutation_p.D1055G|NAV1_ENST00000367302.1_Intron|NAV1_ENST00000367295.1_Missense_Mutation_p.D664G	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1055					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						CCCACGGACGATGGTGAGACT	0.602																																					p.D1055G		Atlas-SNP	.											.	NAV1	143	.	0			c.A3164G						.						104	81	89					1																	201757764		2203	4300	6503	SO:0001583	missense	89796	exon10			CGGACGATGGTGA	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"neuron navigator-1", "pore membrane and/or filament interacting like protein 3"	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.3164A>G	chr1.hg19:g.201757764A>G	ENSP00000356265:p.Asp1055Gly	36.0	0.0		48.0	12.0	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	hg19	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	A	19.61	3.860703	0.71834	.	.	ENSG00000134369	ENST00000367296;ENST00000295624;ENST00000367297;ENST00000391966;ENST00000367295	T;T;T;T	0.09538	2.99;3.02;2.97;3.02	5.54	5.54	0.83059	.	0.056958	0.64402	D	0.000002	T	0.26231	0.0640	L	0.46157	1.445	0.80722	D	1	B;B;P;D;B	0.67145	0.181;0.099;0.669;0.996;0.181	B;B;B;D;B	0.67103	0.074;0.041;0.175;0.949;0.041	T	0.00630	-1.1636	10	0.87932	D	0	-25.0053	15.3514	0.74389	1.0:0.0:0.0:0.0	.	1055;664;1055;563;1055	Q8NEY1-6;Q8NEY1-5;Q8NEY1;A8MYI2;Q8NEY1-3	.;.;NAV1_HUMAN;.;.	G	1055;1055;1055;563;664	ENSP00000356265:D1055G;ENSP00000295624:D1055G;ENSP00000356266:D1055G;ENSP00000356264:D664G	ENSP00000295624:D1055G	D	+	2	0	NAV1	200024387	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	7.259000	0.78381	2.098000	0.63641	0.533000	0.62120	GAT	.	.		0.602	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		G	201757764	A	G	201757764	3	3	76	1	0	0	0	0	1	0	0	0	10192	333	12	2	3259	2	NAV1	1	201757764	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	561551	201757764	47492857	35	10306										
TMEM183A	92703	hgsc.bcm.edu	37	chr1	202987649	202987649	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aaagattgttgggaacagacAggaaccaatgtgggaattca	12	5	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:202987649A>C	ENST00000367242.3	+	6	829	c.749A>C	c.(748-750)cAg>cCg	p.Q250P		NM_001079809.1|NM_138391.4	NP_001073277.1|NP_612400.3	Q8IXX5	T183A_HUMAN	transmembrane protein 183A	250						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)|skin(3)	7			BRCA - Breast invasive adenocarcinoma(75;0.18)			GGGAACAGACAGGAACCAATG	0.313																																					p.Q250P		Atlas-SNP	.											.	.	.	.	0			c.A749C						.						127	128	128					1																	202987649		2203	4300	6503	SO:0001583	missense	653659	exon6			ACAGACAGGAACC	BC013073	CCDS1432.1	1q31.1	2008-09-09	2006-12-18	2006-12-18	ENSG00000163444	ENSG00000163444			20173	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 37"	C1orf37			Standard	NM_138391		Approved		uc001gyu.1	Q8IXX5	OTTHUMG00000042051	ENST00000367242.3:c.749A>C	chr1.hg19:g.202987649A>C	ENSP00000356211:p.Gln250Pro	250.0	0.0		302.0	124.0	NM_001079809	A8K5W1|Q6NW15|Q96E06	Missense_Mutation	SNP	ENST00000367242.3	hg19	CCDS1432.1	.	.	.	.	.	.	.	.	.	.	A	9.169	1.020576	0.19433	.	.	ENSG00000163444	ENST00000367242	T	0.24350	1.86	5.71	5.71	0.89125	.	0.221153	0.47455	D	0.000234	T	0.17365	0.0417	N	0.22421	0.69	0.43076	D	0.994727	B;B	0.12013	0.003;0.005	B;B	0.08055	0.002;0.003	T	0.07102	-1.0790	10	0.30854	T	0.27	-15.8121	11.1552	0.48484	0.846:0.154:0.0:0.0	.	250;250	Q1AE95;Q8IXX5	T183B_HUMAN;T183A_HUMAN	P	250	ENSP00000356211:Q250P	ENSP00000356211:Q250P	Q	+	2	0	TMEM183A	201254272	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.539000	0.45718	2.307000	0.77673	0.528000	0.53228	CAG	.	.		0.313	TMEM183A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100129.1	NM_138391		C	202987649	A	C	202987649	3	2	76	1	0	0	0	0	1	0	0	0	16117	188	7	5	771	5	TMEM183A	1	202987649	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	1229885	202987649	46262972	36	10307										
CR2	1380	hgsc.bcm.edu	37	chr1	207649619	207649620	+	Missense_Mutation	DNP	GA	GA	TC													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccgcctaagacccctaacggGaaccatactggtggaaacat							TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:207649619_207649620GA>TC	ENST00000367058.3	+	14	2769_2770	c.2580_2581GA>TC	c.(2578-2583)ggGAac>ggTCac	p.N861H	CR2_ENST00000367057.3_Missense_Mutation_p.N920H|CR2_ENST00000458541.2_Missense_Mutation_p.N834H|CR2_ENST00000367059.3_Intron	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	861	Sushi 14. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CCCCTAACGGGAACCATACTGG	0.5																																					p.G919G|p.N920H		Atlas-SNP	.											.	CR2	164	.	0			c.G2757T|c.A2758C						.																																			SO:0001583	missense	1380	exon15			TAACGGGAACCAT|AACGGGAACCATA	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	Exception_encountered	chr1.hg19:g.207649619_207649620delinsTC	ENSP00000356025:p.Asn861His	79.0	0.0		115.0|117.0	61.0|63.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Silent|Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1																																																																																			.	.		0.5	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		TC	207649620	GA	TC	207649619	3	4	76	1	0	0	0	0	1	0	0	0	3844	1161	41	3	2815	3	CR2	1	207649619	Missense_Mutation	DNP	GA	TCGA-CC-A7IK-01A-12D-A33Q-10	4661970	207649619	41601002	37	10308										
TMEM206	55248	hgsc.bcm.edu	37	chr1	212558622	212558622	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagacaggaattaccacagtCtgattggagaaggggtccgt	13	8	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:212558622C>A	ENST00000261455.4	-	4	626	c.489G>T	c.(487-489)caG>caT	p.Q163H	TMEM206_ENST00000471937.1_5'UTR|TMEM206_ENST00000535273.1_Missense_Mutation_p.Q224H	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	163						cell surface (GO:0009986)|integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		TTACCACAGTCTGATTGGAGA	0.552																																					p.Q224H		Atlas-SNP	.											.	TMEM206	41	.	0			c.G672T						.						121	115	117					1																	212558622		2203	4300	6503	SO:0001583	missense	55248	exon5			CACAGTCTGATTG	AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 75"	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.489G>T	chr1.hg19:g.212558622C>A	ENSP00000261455:p.Gln163His	225.0	0.0		313.0	50.0	NM_001198862	B7Z4D6|Q6IA87|Q9NV85	Missense_Mutation	SNP	ENST00000261455.4	hg19	CCDS1504.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.624233	0.28889	.	.	ENSG00000065600	ENST00000261455;ENST00000535273	.	.	.	5.43	2.08	0.27032	.	0.345356	0.34223	N	0.004159	T	0.32041	0.0816	L	0.27053	0.805	0.35461	D	0.796485	B;B	0.14438	0.01;0.0	B;B	0.16289	0.015;0.001	T	0.17684	-1.0361	9	0.40728	T	0.16	-16.7474	2.8675	0.05605	0.0:0.3206:0.2611:0.4183	.	224;163	B7Z4D6;Q9H813	.;TM206_HUMAN	H	163;224	.	ENSP00000261455:Q163H	Q	-	3	2	TMEM206	210625245	0.995000	0.38212	0.987000	0.45799	0.538000	0.34931	0.179000	0.16840	0.628000	0.30357	0.655000	0.94253	CAG	.	.		0.552	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252		A	212558622	C	A	212558622	3	1	76	1	0	0	0	0	1	0	0	0	16146	912	32	3	583	3	TMEM206	1	212558622	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	4909003	212558622	36691999	38	10309										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214537999	214537999	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttggtatggcgacggaccgaCtggatctcctccaagtaggc	13	11	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:214537999C>A	ENST00000366956.5	-	18	3485	c.3291G>T	c.(3289-3291)caG>caT	p.Q1097H	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	1097	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GACGGACCGACTGGATCTCCT	0.587																																					p.Q1097H	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											.	PTPN14	168	.	0			c.G3291T						.						99	86	91					1																	214537999		2203	4300	6503	SO:0001583	missense	5784	exon18			GACCGACTGGATC	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.3291G>T	chr1.hg19:g.214537999C>A	ENSP00000355923:p.Gln1097His	146.0	0.0		227.0	36.0	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.928431	0.73327	.	.	ENSG00000152104	ENST00000366956	D	0.83673	-1.75	5.7	4.79	0.61399	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.061995	0.64402	D	0.000002	T	0.81592	0.4855	L	0.33753	1.03	0.80722	D	1	D	0.71674	0.998	P	0.55965	0.788	T	0.79778	-0.1660	10	0.35671	T	0.21	.	10.1845	0.42988	0.0:0.7924:0.1362:0.0714	.	1097	Q15678	PTN14_HUMAN	H	1097	ENSP00000355923:Q1097H	ENSP00000355923:Q1097H	Q	-	3	2	PTPN14	212604622	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	4.563000	0.60823	1.403000	0.46800	0.655000	0.94253	CAG	.	.		0.587	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		A	214537999	C	A	214537999	3	1	76	1	0	0	0	0	1	0	0	0	12796	564	20	3	280	3	PTPN14	1	214537999	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	1979377	214537999	34712622	39	10310										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228550304	228550304	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cctggagcgagcggaccaggAggtcacatctgtcctgaaga	14	11	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:228550304A>C	ENST00000422127.1	+	80	18733	c.18689A>C	c.(18688-18690)gAg>gCg	p.E6230A	OBSCN_ENST00000570156.2_Missense_Mutation_p.E7187A|OBSCN_ENST00000366707.4_Missense_Mutation_p.E3864A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6230					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCGGACCAGGAGGTCACATCT	0.687																																					p.E7187A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A21560C						.						43	48	46					1																	228550304		1942	4141	6083	SO:0001583	missense	84033	exon91			ACCAGGAGGTCAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18689A>C	chr1.hg19:g.228550304A>C	ENSP00000409493:p.Glu6230Ala	194.0	0.0		278.0	103.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	12.27	1.888321	0.33348	.	.	ENSG00000154358	ENST00000422127;ENST00000366707	T;T	0.62105	0.05;0.08	4.06	1.55	0.23275	.	0.146689	0.43919	D	0.000514	T	0.37489	0.1005	N	0.24115	0.695	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.16571	-1.0398	10	0.08837	T	0.75	.	5.5178	0.16916	0.6453:0.1812:0.0:0.1735	.	6230	Q5VST9	OBSCN_HUMAN	A	6230;3864	ENSP00000409493:E6230A;ENSP00000355668:E3864A	ENSP00000355668:E3864A	E	+	2	0	OBSCN	226616927	0.090000	0.21635	0.000000	0.03702	0.005000	0.04900	1.068000	0.30629	0.192000	0.20272	-0.619000	0.04042	GAG	.	.		0.687	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228550304	A	C	228550304	3	2	76	1	0	0	0	0	1	0	0	0	10821	304	11	5	20213	5	OBSCN	1	228550304	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	14012305	228550304	20700317	40	10311										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245850812	245850812	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	actgacaacttcaggagggtCgtggatgggtgtgagatggc	17	6	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr1:245850812C>A	ENST00000407071.2	+	12	4967	c.4527C>A	c.(4525-4527)gtC>gtA	p.V1509V	KIF26B_ENST00000366518.4_Silent_p.V1128V	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1509					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TCAGGAGGGTCGTGGATGGGT	0.637																																					p.V1509V		Atlas-SNP	.											.	KIF26B	343	.	0			c.C4527A						.						31	37	35					1																	245850812		2120	4217	6337	SO:0001819	synonymous_variant	55083	exon12			GAGGGTCGTGGAT	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.4527C>A	chr1.hg19:g.245850812C>A		157.0	0.0		213.0	117.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	.		0.637	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245850812	C	A	245850812	2	1	76	1	0	0	0	0	0	0	0	1	8304	871	31	1		1	KIF26B	1	245850812	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	17300508	245850812	3399809	41	10312										
CAD	790	hgsc.bcm.edu	37	chr2	27455440	27455440	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tatacctaacgtattggggcAccacccatgacctcaccttt	6	14	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:27455440A>G	ENST00000403525.1	+	17	2725	c.2581A>G	c.(2581-2583)Acc>Gcc	p.T861A	CAD_ENST00000264705.4_Missense_Mutation_p.T924A|CAD_ENST00000464159.1_3'UTR			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTATTGGGGCACCACCCATGA	0.522																																					p.T924A		Atlas-SNP	.											.	CAD	199	.	0			c.A2770G						.						205	138	161					2																	27455440		2203	4300	6503	SO:0001583	missense	790	exon18			TGGGGCACCACCC	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.2581A>G	chr2.hg19:g.27455440A>G	ENSP00000384510:p.Thr861Ala	151.0	0.0		164.0	82.0	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.	.	.	.	.	.	.	.	.	.	A	8.423	0.846812	0.17034	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.97328	-4.34;-4.34	5.37	5.37	0.77165	Pre-ATP-grasp fold (1);Carbamoyl-phosphate synthetase, large subunit, oligomerisation (1);	0.245691	0.47455	D	0.000238	D	0.93481	0.7920	L	0.41573	1.285	0.36886	D	0.88966	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	D	0.90860	0.4738	10	0.25751	T	0.34	0.0865	9.4816	0.38904	0.9176:0.0:0.0824:0.0	.	861;924	F8VPD4;P27708	.;PYR1_HUMAN	A	924;861	ENSP00000264705:T924A;ENSP00000384510:T861A	ENSP00000264705:T924A	T	+	1	0	CAD	27308944	0.992000	0.36948	0.994000	0.49952	0.099000	0.18886	2.807000	0.47955	2.256000	0.74724	0.528000	0.53228	ACC	.	.		0.522	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			G	27455440	A	G	27455440	3	3	76	1	0	0	0	0	1	0	0	0	2567	159	6	2	2840	2	CAD	2	27455440	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10		27455440	215743933	42	10313										
SPAST	6683	hgsc.bcm.edu	37	chr2	32314626	32314626	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gagctagacgccttcaagctAaaatgatgactaatttggtt	9	7	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:32314626A>G	ENST00000315285.3	+	3	663	c.538A>G	c.(538-540)Aaa>Gaa	p.K180E	SPAST_ENST00000345662.1_Missense_Mutation_p.K180E|AL121655.1_ENST00000577299.1_RNA	NM_014946.3	NP_055761.2			spastin											breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					CCTTCAAGCTAAAATGATGAC	0.318																																					p.K180E		Atlas-SNP	.											.	SPAST	61	.	0			c.A538G						.						107	103	104					2																	32314626		2203	4300	6503	SO:0001583	missense	6683	exon3			CAAGCTAAAATGA	AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"ATPases / AAA-type"	11233	protein-coding gene	gene with protein product		604277	"spastic paraplegia 4 (autosomal dominant; spastin)"	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.538A>G	chr2.hg19:g.32314626A>G	ENSP00000320885:p.Lys180Glu	81.0	0.0		103.0	26.0	NM_199436		Missense_Mutation	SNP	ENST00000315285.3	hg19	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.671563	0.88348	.	.	ENSG00000021574	ENST00000345662;ENST00000315285	T;T	0.77358	-1.09;-1.09	5.77	5.77	0.91146	MIT (2);	0.526955	0.23260	N	0.050148	D	0.87478	0.6187	M	0.80982	2.52	0.58432	D	0.999999	D;D	0.71674	0.984;0.998	P;D	0.66979	0.865;0.948	D	0.86378	0.1727	10	0.32370	T	0.25	-12.8061	15.8048	0.78491	1.0:0.0:0.0:0.0	.	180;180	E5KRP6;Q9UBP0	.;SPAST_HUMAN	E	180	ENSP00000340817:K180E;ENSP00000320885:K180E	ENSP00000320885:K180E	K	+	1	0	SPAST	32168130	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.268000	0.78473	2.212000	0.71576	0.529000	0.55759	AAA	.	.		0.318	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436		G	32314626	A	G	32314626	3	3	76	1	0	0	0	0	1	0	0	0	15012	363	13	2	548	2	SPAST	2	32314626	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	4859186	32314626	210884747	43	10314										
FER1L5	90342	hgsc.bcm.edu	37	chr2	97335890	97335890	+	RNA	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgttagggatggtttagcttAtcgaggccgagtcttcctgg	14	7	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:97335890A>T	ENST00000457909.1	+	0	0							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						GGTTTAGCTTATCGAGGCCGA	0.468																																					p.Y461F		Atlas-SNP	.											.	FER1L5	113	.	0			c.A1382T						.						143	113	122					2																	97335890		692	1591	2283			90342	exon17			TAGCTTATCGAGG	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		chr2.hg19:g.97335890A>T		125.0	0.0		134.0	35.0	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.56	2.870933	0.51695	.	.	ENSG00000214272	ENST00000414152;ENST00000436930	.	.	.	4.89	4.89	0.63831	.	.	.	.	.	T	0.62648	0.2445	L	0.50333	1.59	.	.	.	D	0.67145	0.996	D	0.63381	0.914	T	0.73585	-0.3936	7	0.87932	D	0	.	10.8235	0.46619	1.0:0.0:0.0:0.0	.	461	A0AVI2	FR1L5_HUMAN	F	461;454	.	ENSP00000444148:Y461F	Y	+	2	0	FER1L5	96699617	1.000000	0.71417	0.958000	0.39756	0.961000	0.63080	5.685000	0.68204	2.057000	0.61298	0.528000	0.53228	TAT	.	.		0.468	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		T	97335890	A	T	97335890	1	4	76	0	1	0	0	0	0	0	0	0	5822	449	16	4		4	FER1L5	2	97335890	RNA	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	65021264	97335890	145863483	44	10315										
TMEM131	23505	hgsc.bcm.edu	37	chr2	98429012	98429012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tatgatatgccaactttttaTagccaactttaaaaaaagat	4	6	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:98429012T>C	ENST00000186436.5	-	17	1963	c.1735A>G	c.(1735-1737)Ata>Gta	p.I579V		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	579						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						CAACTTTTTATAGCCAACTTT	0.313																																					p.I579V		Atlas-SNP	.											.	TMEM131	258	.	0			c.A1735G						.						86	78	80					2																	98429012		1806	4071	5877	SO:0001583	missense	23505	exon17			TTTTTATAGCCAA	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.1735A>G	chr2.hg19:g.98429012T>C	ENSP00000186436:p.Ile579Val	191.0	0.0		246.0	52.0	NM_015348		Missense_Mutation	SNP	ENST00000186436.5	hg19	CCDS46368.1	.	.	.	.	.	.	.	.	.	.	T	11.83	1.755953	0.31137	.	.	ENSG00000075568	ENST00000186436	T	0.42513	0.97	5.14	2.75	0.32379	.	0.040649	0.85682	N	0.000000	T	0.31638	0.0803	L	0.45228	1.405	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.07177	-1.0786	10	0.29301	T	0.29	-16.3249	8.6277	0.33899	0.0:0.151:0.0:0.849	.	579	Q92545	TM131_HUMAN	V	579	ENSP00000186436:I579V	ENSP00000186436:I579V	I	-	1	0	TMEM131	97795444	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	2.218000	0.42889	0.507000	0.28148	-0.250000	0.11733	ATA	.	.		0.313	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		C	98429012	T	C	98429012	3	2	76	1	0	0	0	0	1	0	0	0	16059	1406	49	2	4016	2	TMEM131	2	98429012	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	1093122	98429012	144770361	45	10316										
C2orf55	343990	hgsc.bcm.edu	37	chr2	99449345	99449345	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctgcagagctttaatccgatCacacacattttcttgggaaa	7	10	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:99449345C>A	ENST00000397899.2	-	4	686	c.355G>T	c.(355-357)Gat>Tat	p.D119Y	KIAA1211L_ENST00000462314.1_Intron	NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	119																	TTAATCCGATCACACACATTT	0.478																																					p.D119Y		Atlas-SNP	.											.	.	.	.	0			c.G355T						.						224	234	231					2																	99449345		1916	4140	6056	SO:0001583	missense	343990	exon4			TCCGATCACACAC	BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 55"	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.355G>T	chr2.hg19:g.99449345C>A	ENSP00000380996:p.Asp119Tyr	64.0	0.0		63.0	12.0	NM_207362		Missense_Mutation	SNP	ENST00000397899.2	hg19	CCDS42720.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.890353	0.72524	.	.	ENSG00000196872	ENST00000397899;ENST00000423771;ENST00000428096;ENST00000415261	T	0.53640	0.61	4.96	4.96	0.65561	.	0.000000	0.49305	D	0.000155	T	0.66752	0.2821	M	0.63843	1.955	0.33945	D	0.643781	D	0.89917	1.0	D	0.81914	0.995	T	0.76291	-0.3013	10	0.72032	D	0.01	-13.0498	17.3797	0.87401	0.0:1.0:0.0:0.0	.	119	Q6NV74	CB055_HUMAN	Y	119;147;133;133	ENSP00000380996:D119Y	ENSP00000380996:D119Y	D	-	1	0	C2orf55	98815777	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.508000	0.67006	2.556000	0.86216	0.655000	0.94253	GAT	.	.		0.478	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362		A	99449345	C	A	99449345	3	1	76	1	0	0	0	0	1	0	0	0	2178	826	29	3	2561	3	C2orf55	2	99449345	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	1020333	99449345	143750028	46	10317										
REV1	51455	hgsc.bcm.edu	37	chr2	100058804	100058804	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gttgttgagctgtttggctaTattgcttggacctggcagag	14	6	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:100058804T>C	ENST00000258428.3	-	5	706	c.478A>G	c.(478-480)Ata>Gta	p.I160V	REV1_ENST00000465835.1_5'UTR|REV1_ENST00000393445.3_Missense_Mutation_p.I160V	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	160					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGTTTGGCTATATTGCTTGGA	0.418								Direct reversal of damage																													p.I160V		Atlas-SNP	.											.	REV1	100	.	0			c.A478G						.						95	88	90					2																	100058804		2203	4300	6503	SO:0001583	missense	51455	exon5			TGGCTATATTGCT	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.478A>G	chr2.hg19:g.100058804T>C	ENSP00000258428:p.Ile160Val	100.0	0.0		141.0	33.0	NM_001037872	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	hg19	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	T	12.18	1.860774	0.32884	.	.	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.26810	1.71;1.71	5.28	0.229	0.15368	.	0.538788	0.22649	N	0.057348	T	0.21427	0.0516	M	0.61703	1.905	0.24908	N	0.992068	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.09377	0.002;0.001;0.004	T	0.32107	-0.9919	10	0.16896	T	0.51	.	9.1772	0.37118	0.0:0.2761:0.0:0.7239	.	139;160;160	Q9UBZ9-3;Q9UBZ9;Q9UBZ9-2	.;REV1_HUMAN;.	V	160	ENSP00000377091:I160V;ENSP00000258428:I160V	ENSP00000258428:I160V	I	-	1	0	REV1	99425236	0.999000	0.42202	0.781000	0.31783	0.996000	0.88848	0.765000	0.26546	-0.174000	0.10743	0.459000	0.35465	ATA	.	.		0.418	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		C	100058804	T	C	100058804	3	2	76	1	0	0	0	0	1	0	0	0	13254	1406	49	2	3353	2	REV1	2	100058804	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	609459	100058804	143140569	47	10318										
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105914979	105914979	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aatgagtaccttcaaagtccTgtaggatatggccctcctta	8	10	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:105914979T>G	ENST00000393359.2	-	3	1298	c.872A>C	c.(871-873)cAg>cCg	p.Q291P	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.Q291P			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	291	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						TTCAAAGTCCTGTAGGATATG	0.423																																					p.Q291P	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.A872C						.						113	109	110					2																	105914979		2203	4300	6503	SO:0001583	missense	9392	exon3			AAGTCCTGTAGGA	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.872A>C	chr2.hg19:g.105914979T>G	ENSP00000377027:p.Gln291Pro	83.0	0.0		88.0	23.0	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	hg19	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.711566	0.68730	.	.	ENSG00000135966	ENST00000393359;ENST00000258449	T;T	0.44881	0.91;0.91	5.65	5.65	0.86999	Citron-like (1);	0.000000	0.85682	D	0.000000	T	0.53981	0.1830	M	0.63428	1.95	0.80722	D	1	D	0.61080	0.989	P	0.54544	0.755	T	0.50448	-0.8827	10	0.27785	T	0.31	-30.2906	15.8909	0.79296	0.0:0.0:0.0:1.0	.	291	Q8WUH2	TGFA1_HUMAN	P	291	ENSP00000377027:Q291P;ENSP00000258449:Q291P	ENSP00000258449:Q291P	Q	-	2	0	TGFBRAP1	105281411	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.825000	0.86693	2.146000	0.66826	0.533000	0.62120	CAG	.	.		0.423	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		G	105914979	T	G	105914979	3	3	76	1	0	0	0	0	1	0	0	0	15839	1580	55	5	1750	5	TGFBRAP1	2	105914979	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	5856175	105914979	137284394	48	10319										
IL1F9	56300	hgsc.bcm.edu	37	chr2	113742493	113742493	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctaccgtgccaagactggtaGgacctccacccttgagtctg	10	14	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:113742493G>T	ENST00000259205.4	+	5	446	c.377G>T	c.(376-378)aGg>aTg	p.R126M	IL36G_ENST00000376489.2_Missense_Mutation_p.R91M	NM_019618.2	NP_062564.1	Q9NZH8	IL36G_HUMAN	interleukin 36, gamma	126					cell-cell signaling (GO:0007267)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|skin(1)	14						AAGACTGGTAGGACCTCCACC	0.522																																					p.R126M		Atlas-SNP	.											IL36G,NS,malignant_melanoma,0,1	IL36G	26	.	0			c.G377T						.						142	126	131					2																	113742493		2203	4300	6503	SO:0001583	missense	56300	exon5			CTGGTAGGACCTC	AF200492	CCDS2108.1, CCDS62992.1	2q12-q21	2011-07-14	2011-06-06	2011-06-06	ENSG00000136688	ENSG00000136688		"Interleukins and interleukin receptors"	15741	protein-coding gene	gene with protein product	"interleukin-1 homolog 1", "interleukin 1-related protein 2", "interleukin-1 epsilon"	605542	"interleukin 1 family, member 9"	IL1F9		10860666, 10744718, 11991722, 11991723	Standard	NM_019618		Approved	IL-1H1, IL-1RP2, IL-1F9, IL1H1, IL1E	uc002tio.1	Q9NZH8	OTTHUMG00000131336	ENST00000259205.4:c.377G>T	chr2.hg19:g.113742493G>T	ENSP00000259205:p.Arg126Met	117.0	0.0		189.0	43.0	NM_019618	Q56B91|Q6UVX7|Q7RTZ9	Missense_Mutation	SNP	ENST00000259205.4	hg19	CCDS2108.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.745572	0.49151	.	.	ENSG00000136688	ENST00000376489;ENST00000259205	T;T	0.18016	2.24;2.27	4.52	0.409	0.16382	.	1.005840	0.07990	N	0.987024	T	0.31136	0.0787	L	0.59436	1.845	0.09310	N	1	D;D	0.61080	0.989;0.972	P;P	0.60345	0.769;0.873	T	0.21415	-1.0246	10	0.52906	T	0.07	-3.4433	7.9277	0.29885	0.0926:0.475:0.4323:0.0	.	91;126	Q9NZH8-2;Q9NZH8	.;IL36G_HUMAN	M	91;126	ENSP00000365672:R91M;ENSP00000259205:R126M	ENSP00000259205:R126M	R	+	2	0	IL36G	113458964	0.000000	0.05858	0.014000	0.15608	0.144000	0.21451	-0.118000	0.10692	-0.037000	0.13646	0.561000	0.74099	AGG	.	.		0.522	IL36G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330713.2	NM_019618		T	113742493	G	T	113742493	3	4	76	1	0	0	0	0	1	0	0	0	7666	1000	35	3	391	3	IL1F9	2	113742493	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	7827514	113742493	129456880	49	10320										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141459798	141459798	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caccatctcgcgattccctcCagtctcaaggtcgattctct	6	16	3	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:141459798C>A	ENST00000389484.3	-	39	7185	c.6214G>T	c.(6214-6216)Gga>Tga	p.G2072*		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2072					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CGATTCCCTCCAGTCTCAAGG	0.403										TSP Lung(27;0.18)																											p.G2072X	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G6214T						.						199	175	183					2																	141459798		2203	4300	6503	SO:0001587	stop_gained	53353	exon39			TCCCTCCAGTCTC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.6214G>T	chr2.hg19:g.141459798C>A	ENSP00000374135:p.Gly2072*	168.0	0.0		263.0	60.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Nonsense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	53	20.898001	0.99935	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	.	.	.	5.49	5.49	0.81192	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.3684	0.94473	0.0:1.0:0.0:0.0	.	.	.	.	X	2072;2010	.	ENSP00000374135:G2072X	G	-	1	0	LRP1B	141176268	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.710000	0.84655	2.582000	0.87167	0.557000	0.71058	GGA	.	.		0.403	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141459798	C	A	141459798	4	1	76	1	0	0	0	0	0	1	0	0	8964	603	21	3	7797	3	LRP1B	2	141459798	Nonsense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	27717305	141459798	101739575	50	10321										
NEB	4703	hgsc.bcm.edu	37	chr2	152512686	152512686	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	catcactctgtatgcgattcAtattcctggtcagctcaatg	7	11	5	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:152512686A>G	ENST00000172853.10	-	49	6623	c.6476T>C	c.(6475-6477)aTg>aCg	p.M2159T	NEB_ENST00000409198.1_Missense_Mutation_p.M2159T|NEB_ENST00000604864.1_Missense_Mutation_p.M2159T|NEB_ENST00000603639.1_Missense_Mutation_p.M2159T|NEB_ENST00000427231.2_Missense_Mutation_p.M2159T|NEB_ENST00000397345.3_Missense_Mutation_p.M2159T			P20929	NEBU_HUMAN	nebulin	2159					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TATGCGATTCATATTCCTGGT	0.448																																					p.M2159T		Atlas-SNP	.											.	NEB	1697	.	0			c.T6476C						.						394	384	387					2																	152512686		2069	4203	6272	SO:0001583	missense	4703	exon49			CGATTCATATTCC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.6476T>C	chr2.hg19:g.152512686A>G	ENSP00000172853:p.Met2159Thr	95.0	0.0		108.0	20.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	A	15.88	2.964020	0.53507	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.83	5.83	0.93111	.	0.133804	0.64402	D	0.000004	T	0.41926	0.1180	L	0.47716	1.5	0.80722	D	1	P	0.51351	0.944	P	0.55455	0.776	T	0.08576	-1.0715	10	0.20046	T	0.44	.	16.194	0.82011	1.0:0.0:0.0:0.0	.	2159	P20929	NEBU_HUMAN	T	2159	ENSP00000386259:M2159T;ENSP00000380505:M2159T;ENSP00000416578:M2159T;ENSP00000172853:M2159T	ENSP00000172853:M2159T	M	-	2	0	NEB	152220932	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	6.220000	0.72237	2.225000	0.72522	0.460000	0.39030	ATG	.	.		0.448	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152512686	A	G	152512686	3	3	76	1	0	0	0	0	1	0	0	0	10311	217	8	2	19746	2	NEB	2	152512686	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	11052888	152512686	90686687	51	10322										
STK39	27347	hgsc.bcm.edu	37	chr2	169020389	169020389	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tttatgatatccaacattgaAcctaagtagacaaacagaag	6	7	0	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:169020389A>T	ENST00000355999.4	-	4	1137	c.432T>A	c.(430-432)ggT>ggA	p.G144G		NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	144	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						CCAACATTGAACCTAAGTAGA	0.318																																					p.G144G		Atlas-SNP	.											.	STK39	95	.	0			c.T432A						.						106	96	99					2																	169020389		1844	4089	5933	SO:0001630	splice_region_variant	27347	exon4			CATTGAACCTAAG	AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648			17717	protein-coding gene	gene with protein product	"STE20/SPS1 homolog (yeast)"	607648				10980603	Standard	NM_013233		Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.431-1T>A	chr2.hg19:g.169020389A>T		83.0	0.0		91.0	16.0	NM_013233	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	Silent	SNP	ENST00000355999.4	hg19	CCDS42770.1																																																																																			.	.		0.318	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258112.2	NM_013233	Silent	T	169020389	A	T	169020389	5	4	76	1	0	0	0	0	0	0	1	0	15320	57	2	4	1265	4	STK39	2	169020389	Splice_Site	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	16507703	169020389	74178984	52	10323										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178769916	178769916	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gaagatacatctgcataaccTgggacaaagagagtagtaag	11	6	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:178769916T>A	ENST00000286063.6	-	3	1389		c.e3-2		PDE11A_ENST00000358450.4_Splice_Site|PDE11A_ENST00000449286.2_Splice_Site|PDE11A_ENST00000497003.1_Splice_Site|PDE11A_ENST00000409504.1_Splice_Site	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A						blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	CTGCATAACCTGGGACAAAGA	0.368									Primary Pigmented Nodular Adrenocortical Disease, Familial																												.		Atlas-SNP	.											.	PDE11A	283	.	0			c.322-2A>T						.						92	81	85					2																	178769916		2203	4300	6503	SO:0001630	splice_region_variant	50940	exon5	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	ATAACCTGGGACA	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.1072-2A>T	chr2.hg19:g.178769916T>A		40.0	0.0		57.0	14.0	NM_001077197	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Splice_Site	SNP	ENST00000286063.6	hg19	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	T	18.30	3.593438	0.66219	.	.	ENSG00000128655	ENST00000286063;ENST00000358450;ENST00000431253	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.357	0.74434	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDE11A	178478162	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	7.646000	0.83445	2.033000	0.60031	0.460000	0.39030	.	.	.		0.368	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		Intron	A	178769916	T	A	178769916	5	1	76	1	0	0	0	0	0	0	1	0	11640	1594	55	4	1803	4	PDE11A	2	178769916	Splice_Site	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	9749527	178769916	64429457	53	10324										
TTN	7273	hgsc.bcm.edu	37	chr2	179642164	179642164	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	taccttccacagttaaaatcActgaaattgaagatctgcct	5	10	2	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:179642164A>T	ENST00000591111.1	-	26	4852	c.4628T>A	c.(4627-4629)gTg>gAg	p.V1543E	TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.V1543E|TTN_ENST00000342175.6_Missense_Mutation_p.V1497E|TTN_ENST00000359218.5_Missense_Mutation_p.V1497E|TTN_ENST00000342992.6_Missense_Mutation_p.V1543E|TTN_ENST00000460472.2_Missense_Mutation_p.V1497E|TTN_ENST00000589042.1_Missense_Mutation_p.V1543E|RP11-88L24.4_ENST00000582038.2_RNA			Q8WZ42	TITIN_HUMAN	titin	12404	Ig-like 6.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTTAAAATCACTGAAATTGA	0.378																																					p.V1543E		Atlas-SNP	.											.	TTN	18412	.	0			c.T4628A						.						46	45	46					2																	179642164		2203	4300	6503	SO:0001583	missense	7273	exon26			AAAATCACTGAAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.4628T>A	chr2.hg19:g.179642164A>T	ENSP00000465570:p.Val1543Glu	48.0	0.0		52.0	34.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.47	2.842610	0.51057	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43	5.9	5.9	0.94986	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.83261	0.5216	M	0.89478	3.035	0.36166	D	0.848423	P;P;P;P;D	0.61080	0.773;0.773;0.773;0.879;0.989	P;P;P;P;P	0.61201	0.583;0.583;0.583;0.583;0.885	D	0.89596	0.3831	9	0.87932	D	0	.	16.3228	0.82958	1.0:0.0:0.0:0.0	.	1497;1497;1497;1543;1543	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	E	1543;1497;1497;1497;1497;1543	ENSP00000343764:V1543E;ENSP00000434586:V1497E;ENSP00000340554:V1497E;ENSP00000352154:V1497E;ENSP00000354117:V1543E	ENSP00000340554:V1497E	V	-	2	0	TTN	179350409	1.000000	0.71417	0.996000	0.52242	0.890000	0.51754	7.439000	0.80444	2.262000	0.75019	0.528000	0.53228	GTG	.	.		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179642164	A	T	179642164	3	4	76	1	0	0	0	0	1	0	0	0	16750	159	6	4	106708	4	TTN	2	179642164	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	872248	179642164	63557209	54	10325										
MFSD6	54842	hgsc.bcm.edu	37	chr2	191362167	191362167	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	acattcttttctctccagacAagacaatgttggcagaaaga	7	9	2	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:191362167A>G	ENST00000392328.1	+	7	2218	c.1894A>G	c.(1894-1896)Aag>Gag	p.K632E	MFSD6_ENST00000535751.1_Missense_Mutation_p.K94E|MFSD6_ENST00000281416.7_Missense_Mutation_p.K632E	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	632					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						CTCTCCAGACAAGACAATGTT	0.373																																					p.K632E		Atlas-SNP	.											.	MFSD6	58	.	0			c.A1894G						.						116	113	114					2																	191362167		2203	4300	6503	SO:0001583	missense	54842	exon7			CCAGACAAGACAA		CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.1894A>G	chr2.hg19:g.191362167A>G	ENSP00000376141:p.Lys632Glu	40.0	0.0		63.0	14.0	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Missense_Mutation	SNP	ENST00000392328.1	hg19	CCDS2306.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.11|10.11	1.261132|1.261132	0.23051|0.23051	.|.	.|.	ENSG00000151690|ENSG00000151690	ENST00000392328;ENST00000281416;ENST00000444317;ENST00000542423;ENST00000535751|ENST00000434582	T;T;T;T|.	0.58210|.	0.35;0.35;0.35;0.35|.	5.98|5.98	5.98|5.98	0.97165|0.97165	Major facilitator superfamily domain, general substrate transporter (1);|.	0.198371|.	0.56097|.	D|.	0.000034|.	T|T	0.44095|0.44095	0.1277|0.1277	N|N	0.22421|0.22421	0.69|0.69	0.37982|0.37982	D|D	0.933614|0.933614	B|.	0.20164|.	0.042|.	B|.	0.25405|.	0.06|.	T|T	0.48234|0.48234	-0.9053|-0.9053	10|5	0.22109|.	T|.	0.4|.	-25.9069|-25.9069	10.0367|10.0367	0.42133|0.42133	0.9258:0.0:0.0742:0.0|0.9258:0.0:0.0742:0.0	.|.	632|.	Q6ZSS7|.	MFSD6_HUMAN|.	E|R	632;632;94;94;94|167	ENSP00000376141:K632E;ENSP00000281416:K632E;ENSP00000406837:K94E;ENSP00000440917:K94E|.	ENSP00000281416:K632E|.	K|Q	+|+	1|2	0|0	MFSD6|MFSD6	191070412|191070412	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	5.019000|5.019000	0.64060|0.64060	2.288000|2.288000	0.76882|0.76882	0.528000|0.528000	0.53228|0.53228	AAG|CAA	.	.		0.373	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1			G	191362167	A	G	191362167	3	3	76	1	0	0	0	0	1	0	0	0	9544	131	5	2	1912	2	MFSD6	2	191362167	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	11720003	191362167	51837206	55	10326										
ALS2CR11	151254	hgsc.bcm.edu	37	chr2	202356442	202356442	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atactgcttcaggtttttccTgaacagtccatttatagatg	7	8	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:202356442T>A	ENST00000286195.3	-	15	1626				ALS2CR11_ENST00000482942.1_Intron|ALS2CR11_ENST00000439802.1_Intron|ALS2CR11_ENST00000439140.1_Missense_Mutation_p.Q1541L	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11											NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						AGGTTTTTCCTGAACAGTCCA	0.368																																					p.Q1541L		Atlas-SNP	.											.	ALS2CR11	194	.	0			c.A4622T						.						140	107	117					2																	202356442		692	1591	2283	SO:0001627	intron_variant	151254	exon15			TTTTCCTGAACAG	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.1582-3817A>T	chr2.hg19:g.202356442T>A		0.0	0.0		4.0	4.0	NM_001168221	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Missense_Mutation	SNP	ENST00000286195.3	hg19	CCDS2349.1	.	.	.	.	.	.	.	.	.	.	T	5.976	0.364043	0.11296	.	.	ENSG00000155754	ENST00000439140	T	0.52754	0.65	5.15	2.78	0.32641	.	.	.	.	.	T	0.44993	0.1320	L	0.42245	1.32	0.09310	N	0.999999	D	0.58268	0.982	P	0.48677	0.586	T	0.29640	-1.0005	9	0.87932	D	0	.	7.374	0.26818	0.0:0.1763:0.0:0.8237	.	1541	E9PGG4	.	L	1541	ENSP00000409937:Q1541L	ENSP00000409937:Q1541L	Q	-	2	0	ALS2CR11	202064687	0.017000	0.18338	0.001000	0.08648	0.072000	0.16883	1.684000	0.37649	0.426000	0.26116	0.455000	0.32223	CAG	.	.		0.368	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525		A	202356442	T	A	202356442	1	1	76	0	1	0	0	0	0	0	0	0	552	1580	55	4		4	ALS2CR11	2	202356442	Intron	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	10994275	202356442	40842931	56	10327										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222301134	222301134	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cttaccctggtggtgtaagcTgcttccggatcatcctcaag	10	12	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:222301134T>A	ENST00000281821.2	-	13	2372	c.2331A>T	c.(2329-2331)gcA>gcT	p.A777A	EPHA4_ENST00000409938.1_Silent_p.A777A|EPHA4_ENST00000392071.4_Silent_p.A726A|EPHA4_ENST00000409854.1_Silent_p.A777A	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	777	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		TGGTGTAAGCTGCTTCCGGAT	0.488																																					p.A777A		Atlas-SNP	.											.	EPHA4	263	.	0			c.A2331T						.						81	65	71					2																	222301134		2203	4300	6503	SO:0001819	synonymous_variant	2043	exon13			GTAAGCTGCTTCC	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.2331A>T	chr2.hg19:g.222301134T>A		84.0	0.0		93.0	23.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Silent	SNP	ENST00000281821.2	hg19	CCDS2447.1																																																																																			.	.		0.488	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			A	222301134	T	A	222301134	2	1	76	1	0	0	0	0	0	0	0	1	5171	1567	55	4		4	EPHA4	2	222301134	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	19944692	222301134	20898239	57	10328										
ALPP	250	hgsc.bcm.edu	37	chr2	233243696	233243696	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gccagttgaggaggagaaccCggacttctggaaccgcgagg	16	10	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:233243696C>A	ENST00000392027.2	+	2	361	c.92C>A	c.(91-93)cCg>cAg	p.P31Q	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	31					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GAGGAGAACCCGGACTTCTGG	0.642																																					p.P31Q		Atlas-SNP	.											.	ALPP	53	.	0			c.C92A						.						68	84	79					2																	233243696		2203	4300	6503	SO:0001583	missense	250	exon2			AGAACCCGGACTT	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"Regan isozyme"	171800	"alkaline phosphatase, placental (Regan isozyme)"			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.92C>A	chr2.hg19:g.233243696C>A	ENSP00000375881:p.Pro31Gln	77.0	0.0		109.0	16.0	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	hg19	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	.	14.32	2.498901	0.44455	.	.	ENSG00000163283	ENST00000392027	T	0.64438	-0.1	2.32	2.32	0.28847	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.170635	0.52532	D	0.000070	T	0.81307	0.4795	M	0.91090	3.175	0.54753	D	0.999989	D	0.69078	0.997	D	0.76071	0.987	D	0.85840	0.1397	10	0.87932	D	0	.	13.0087	0.58720	0.0:1.0:0.0:0.0	.	31	P05187	PPB1_HUMAN	Q	31	ENSP00000375881:P31Q	ENSP00000375881:P31Q	P	+	2	0	ALPP	232951940	0.998000	0.40836	0.226000	0.23910	0.417000	0.31264	7.107000	0.77047	1.294000	0.44707	0.306000	0.20318	CCG	.	.		0.642	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632		A	233243696	C	A	233243696	3	1	76	1	0	0	0	0	1	0	0	0	548	652	23	1	98	1	ALPP	2	233243696	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	10942562	233243696	9955677	58	10329										
SH3BP4	23677	hgsc.bcm.edu	37	chr2	235951205	235951205	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttcaggtgaaggacgaccagGaggccatcctcacccagttt	11	12	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr2:235951205G>T	ENST00000409212.1	+	4	2299	c.1792G>T	c.(1792-1794)Gag>Tag	p.E598*	SH3BP4_ENST00000392011.2_Nonsense_Mutation_p.E598*|SH3BP4_ENST00000344528.4_Nonsense_Mutation_p.E598*			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	598					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		GGACGACCAGGAGGCCATCCT	0.572																																					p.E598X		Atlas-SNP	.											.	SH3BP4	109	.	0			c.G1792T						.						61	61	61					2																	235951205		2203	4300	6503	SO:0001587	stop_gained	23677	exon4			GACCAGGAGGCCA	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.1792G>T	chr2.hg19:g.235951205G>T	ENSP00000386862:p.Glu598*	116.0	0.0		130.0	94.0	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Nonsense_Mutation	SNP	ENST00000409212.1	hg19	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	G	43	10.258404	0.99370	.	.	ENSG00000130147	ENST00000392011;ENST00000409212;ENST00000344528	.	.	.	5.08	5.08	0.68730	.	0.252860	0.42053	D	0.000776	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-18.5127	17.0389	0.86483	0.0:0.0:1.0:0.0	.	.	.	.	X	598	.	ENSP00000340237:E598X	E	+	1	0	SH3BP4	235615944	1.000000	0.71417	0.993000	0.49108	0.963000	0.63663	9.458000	0.97634	2.354000	0.79902	0.655000	0.94253	GAG	.	.		0.572	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			T	235951205	G	T	235951205	4	4	76	1	0	0	0	0	0	1	0	0	14261	1175	41	3	1798	3	SH3BP4	2	235951205	Nonsense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	2707509	235951205	7248168	59	10330										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10382000	10382000	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagctgcagtggagagcagcTgaatggcttccctccaaact	11	12	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:10382000T>A	ENST00000352432.4	-	20	3232	c.3163A>T	c.(3163-3165)Agc>Tgc	p.S1055C	ATP2B2_ENST00000360273.2_Missense_Mutation_p.S1055C|ATP2B2_ENST00000343816.4_Missense_Mutation_p.S1041C|ATP2B2_ENST00000383800.4_Missense_Mutation_p.S1010C|ATP2B2_ENST00000397077.1_Missense_Mutation_p.S1010C			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	1055					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						GGAGAGCAGCTGAATGGCTTC	0.567																																					p.S1055C	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A3163T						.						91	81	84					3																	10382000		2203	4300	6503	SO:0001583	missense	491	exon21			AGCAGCTGAATGG	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.3163A>T	chr3.hg19:g.10382000T>A	ENSP00000324172:p.Ser1055Cys	69.0	0.0		73.0	16.0	NM_001001331	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.211153	0.79240	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000429937;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52;-2.52	4.08	4.08	0.47627	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.95249	0.8459	M	0.93062	3.375	0.80722	D	1	D;B;B	0.76494	0.999;0.057;0.372	D;B;B	0.80764	0.994;0.152;0.371	D	0.95814	0.8844	10	0.62326	D	0.03	-23.103	13.0807	0.59112	0.0:0.0:0.0:1.0	.	990;1022;1055	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	C	1055;1010;1010;1055;1041;990;244;911;1055	ENSP00000324172:S1055C;ENSP00000373311:S1010C;ENSP00000380267:S1010C;ENSP00000353414:S1055C;ENSP00000344677:S1041C;ENSP00000414854:S911C	ENSP00000342954:S1055C	S	-	1	0	ATP2B2	10357000	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.792000	0.85828	1.487000	0.48415	0.460000	0.39030	AGC	.	.		0.567	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10382000	T	A	10382000	3	1	76	1	0	0	0	0	1	0	0	0	1140	1580	55	4	580	4	ATP2B2	3	10382000	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10		10382000	187640430	60	10331										
UBP1	7342	hgsc.bcm.edu	37	chr3	33441756	33441756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttgctgtgtttcctggatcgTagctgaaggctgaatttgct	12	7	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:33441756T>C	ENST00000283629.3	-	11	1634	c.1105A>G	c.(1105-1107)Acg>Gcg	p.T369A	UBP1_ENST00000283628.5_Missense_Mutation_p.T369A|UBP1_ENST00000486388.1_5'UTR|UBP1_ENST00000447368.2_Missense_Mutation_p.T333A	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	369					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						TCCTGGATCGTAGCTGAAGGC	0.368																																					p.T369A		Atlas-SNP	.											.	UBP1	42	.	0			c.A1105G						.						135	121	126					3																	33441756		2203	4300	6503	SO:0001583	missense	7342	exon11			GGATCGTAGCTGA	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.1105A>G	chr3.hg19:g.33441756T>C	ENSP00000283629:p.Thr369Ala	60.0	0.0		54.0	6.0	NM_014517	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	hg19	CCDS2659.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.810728	0.50421	.	.	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628	T;T;T	0.20069	2.1;2.16;2.1	6.16	6.16	0.99307	Sterile alpha motif/pointed domain (1);	0.099426	0.64402	D	0.000001	T	0.26810	0.0656	M	0.66297	2.02	0.49299	D	0.999779	P;B	0.37207	0.587;0.228	B;B	0.38156	0.266;0.146	T	0.04078	-1.0979	10	0.72032	D	0.01	-16.0228	11.8297	0.52288	0.1306:0.0:0.0:0.8694	.	333;369	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	A	369;333;369	ENSP00000283629:T369A;ENSP00000395558:T333A;ENSP00000283628:T369A	ENSP00000283628:T369A	T	-	1	0	UBP1	33416760	1.000000	0.71417	0.994000	0.49952	0.800000	0.45204	4.104000	0.57790	2.367000	0.80283	0.528000	0.53228	ACG	.	.		0.368	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517		C	33441756	T	C	33441756	3	2	76	1	0	0	0	0	1	0	0	0	16910	1638	57	2	541	2	UBP1	3	33441756	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	23059756	33441756	164580674	61	10332										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:41266098A>T	ENST00000349496.5	+	3	375	c.95A>T	c.(94-96)gAc>gTc	p.D32V	CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32V|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25V|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32V	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95T						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>T	chr3.hg19:g.41266098A>T	ENSP00000344456:p.Asp32Val	160.0	0.0		167.0	34.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184569	0.78677	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70037	0.3178	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.74325	-0.3702	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	V	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25V;ENSP00000385604:D32V;ENSP00000412219:D32V;ENSP00000379486:D32V;ENSP00000344456:D32V;ENSP00000411226:D25V;ENSP00000379488:D32V;ENSP00000409302:D32V;ENSP00000401599:D32V	ENSP00000344456:D32V	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266098	A	T	41266098	3	4	76	1	0	0	0	0	1	0	0	0	4018	275	10	4	101	4	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	7824342	41266098	156756332	62	10333										
CDCP1	64866	hgsc.bcm.edu	37	chr3	45187699	45187699	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tccaaagcccggcactcaccTgccccgcgcggcaggcgcgc	12	20	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:45187699T>A	ENST00000296129.1	-	1	215	c.81A>T	c.(79-81)gcA>gcT	p.A27A	CDCP1_ENST00000425231.2_Splice_Site_p.A27A	NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	27						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		GGCACTCACCTGCCCCGCGCG	0.731																																					p.A27A		Atlas-SNP	.											.	CDCP1	61	.	0			c.A81T						.						12	14	14					3																	45187699		2184	4268	6452	SO:0001630	splice_region_variant	64866	exon1			CTCACCTGCCCCG	AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"CD molecules"	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.82+1A>T	chr3.hg19:g.45187699T>A		89.0	0.0		83.0	14.0	NM_178181	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Silent	SNP	ENST00000296129.1	hg19	CCDS2727.1																																																																																			.	.		0.731	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842	Silent	A	45187699	T	A	45187699	5	1	76	1	0	0	0	0	0	0	1	0	3095	1594	55	4	2473	4	CDCP1	3	45187699	Splice_Site	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	3921601	45187699	152834731	63	10334										
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48455150	48455150	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	acccccaagcccacctgggcTgccacaggaaaagccccagg	10	18	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:48455150T>A	ENST00000358536.4	-	23	4733	c.4464A>T	c.(4462-4464)gcA>gcT	p.A1488A	PLXNB1_ENST00000448774.2_Silent_p.A99A|PLXNB1_ENST00000465117.1_5'Flank|PLXNB1_ENST00000358459.4_Silent_p.A1305A|PLXNB1_ENST00000456774.1_Silent_p.A1305A|PLXNB1_ENST00000296440.6_Silent_p.A1488A	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1488					axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CCACCTGGGCTGCCACAGGAA	0.617																																					p.A1488A		Atlas-SNP	.											.	PLXNB1	150	.	0			c.A4464T						.						41	45	44					3																	48455150		2203	4300	6503	SO:0001819	synonymous_variant	5364	exon23			CTGGGCTGCCACA	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.4464A>T	chr3.hg19:g.48455150T>A		75.0	0.0		74.0	14.0	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.		0.617	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		A	48455150	T	A	48455150	2	1	76	1	0	0	0	0	0	0	0	1	12132	1567	55	4		4	PLXNB1	3	48455150	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	3267451	48455150	149567280	64	10335										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48689876	48689876	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atgctgacccccacctggatGcagccaaccagaccctgagg	10	16	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:48689876G>T	ENST00000164024.4	-	11	6025	c.5745C>A	c.(5743-5745)tgC>tgA	p.C1915*	CELSR3_ENST00000544264.1_Nonsense_Mutation_p.C1915*	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1915	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CCACCTGGATGCAGCCAACCA	0.622																																					p.C1915X		Atlas-SNP	.											.	CELSR3	237	.	0			c.C5745A						.						71	67	68					3																	48689876		2203	4300	6503	SO:0001587	stop_gained	1951	exon11			CTGGATGCAGCCA	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.5745C>A	chr3.hg19:g.48689876G>T	ENSP00000164024:p.Cys1915*	109.0	0.0		85.0	11.0	NM_001407	O75092	Nonsense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	G	47	13.866750	0.99767	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	.	.	.	5.1	0.298	0.15766	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.2746	0.31864	0.4053:0.0:0.5947:0.0	.	.	.	.	X	1915	.	ENSP00000164024:C1915X	C	-	3	2	CELSR3	48664880	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	2.428000	0.44749	0.309000	0.22966	-0.367000	0.07326	TGC	.	.		0.622	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		T	48689876	G	T	48689876	4	4	76	1	0	0	0	0	0	1	0	0	3225	1311	46	3	4293	3	CELSR3	3	48689876	Nonsense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	234726	48689876	149332554	65	10336										
QRICH1	54870	hgsc.bcm.edu	37	chr3	49095208	49095208	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gggctgctgactgtggtgccTggccttggatctgcacctgg	16	11	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:49095208T>A	ENST00000395443.2	-	3	897	c.425A>T	c.(424-426)cAg>cTg	p.Q142L	QRICH1_ENST00000424300.1_Missense_Mutation_p.Q142L|QRICH1_ENST00000357496.2_Missense_Mutation_p.Q142L|QRICH1_ENST00000479449.1_Intron	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	142	Gln-rich.					nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CTGTGGTGCCTGGCCTTGGAT	0.617																																					p.Q142L		Atlas-SNP	.											.	QRICH1	48	.	0			c.A425T						.						182	156	165					3																	49095208		2203	4300	6503	SO:0001583	missense	54870	exon3			GGTGCCTGGCCTT		CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.425A>T	chr3.hg19:g.49095208T>A	ENSP00000378830:p.Gln142Leu	76.0	0.0		75.0	18.0	NM_198880	Q4G0F7|Q7L621|Q8TEA5	Missense_Mutation	SNP	ENST00000395443.2	hg19	CCDS2787.1	.	.	.	.	.	.	.	.	.	.	T	16.16	3.045726	0.55110	.	.	ENSG00000198218	ENST00000395443;ENST00000357496;ENST00000424300	.	.	.	5.99	5.99	0.97316	.	0.159496	0.56097	D	0.000023	T	0.25232	0.0613	N	0.08118	0	0.53688	D	0.999976	P	0.43477	0.808	B	0.27887	0.084	T	0.25398	-1.0133	9	0.66056	D	0.02	-2.5159	15.7232	0.77732	0.0:0.0:0.0:1.0	.	142	Q2TAL8	QRIC1_HUMAN	L	142	.	ENSP00000350094:Q142L	Q	-	2	0	QRICH1	49070212	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.299000	0.33424	2.305000	0.77605	0.529000	0.55759	CAG	.	.		0.617	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		A	49095208	T	A	49095208	3	1	76	1	0	0	0	0	1	0	0	0	12894	1580	55	4	1937	4	QRICH1	3	49095208	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	405332	49095208	148927222	66	10337										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49166551	49166551	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcgtcgcccaaccatgtgctGgcggcagtggcattgacctg	14	13	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:49166551G>C	ENST00000418109.1	-	14	1797	c.1633C>G	c.(1633-1635)Cag>Gag	p.Q545E	LAMB2_ENST00000305544.4_Missense_Mutation_p.Q545E	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	545	Laminin EGF-like 5; truncated. {ECO:0000255|PROSITE-ProRule:PRU00460}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ACCATGTGCTGGCGGCAGTGG	0.582																																					p.Q545E		Atlas-SNP	.											.	LAMB2	156	.	0			c.C1633G						.						73	67	69					3																	49166551		2203	4300	6503	SO:0001583	missense	3913	exon13			TGTGCTGGCGGCA		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.1633C>G	chr3.hg19:g.49166551G>C	ENSP00000388325:p.Gln545Glu	45.0	0.0		53.0	26.0	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	hg19	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	G	9.192	1.026250	0.19512	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.59906	0.23;0.23	5.27	4.34	0.51931	EGF-like, laminin (3);EGF-like region, conserved site (1);	0.296128	0.33217	N	0.005144	T	0.22126	0.0533	N	0.00677	-1.265	0.30083	N	0.809	B	0.21309	0.054	B	0.19148	0.024	T	0.15037	-1.0451	10	0.09843	T	0.71	.	11.178	0.48612	0.0:0.0:0.6447:0.3553	.	545	P55268	LAMB2_HUMAN	E	545	ENSP00000388325:Q545E;ENSP00000307156:Q545E	ENSP00000307156:Q545E	Q	-	1	0	LAMB2	49141555	0.854000	0.29725	0.999000	0.59377	0.985000	0.73830	1.538000	0.36094	2.465000	0.83290	0.655000	0.94253	CAG	.	.		0.582	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		C	49166551	G	C	49166551	3	2	76	1	0	0	0	0	1	0	0	0	8620	1357	47	4	3843	4	LAMB2	3	49166551	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	71343	49166551	148855879	67	10338										
BSN	8927	hgsc.bcm.edu	37	chr3	49698355	49698355	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gctgcggctccagggctgcaCcactcccgctggccagtttg	13	16	0	0	rs141830771		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:49698355C>G	ENST00000296452.4	+	6	9191	c.9077C>G	c.(9076-9078)aCc>aGc	p.T3026S		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3026					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CAGGGCTGCACCACTCCCGCT	0.662																																					p.T3026S		Atlas-SNP	.											.	BSN	272	.	0			c.C9077G						.						49	45	46					3																	49698355		2203	4300	6503	SO:0001583	missense	8927	exon6			GCTGCACCACTCC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.9077C>G	chr3.hg19:g.49698355C>G	ENSP00000296452:p.Thr3026Ser	46.0	0.0		49.0	13.0	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	hg19	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	5.711	0.315736	0.10789	.	.	ENSG00000164061	ENST00000296452	T	0.16743	2.32	4.61	4.61	0.57282	.	0.578373	0.16382	N	0.216857	T	0.08802	0.0218	N	0.03608	-0.345	0.35544	D	0.803308	B	0.12630	0.006	B	0.14578	0.011	T	0.22347	-1.0219	10	0.30078	T	0.28	-1.447	13.9181	0.63914	0.0:0.8465:0.1535:0.0	.	3026	Q9UPA5	BSN_HUMAN	S	3026	ENSP00000296452:T3026S	ENSP00000296452:T3026S	T	+	2	0	BSN	49673359	0.164000	0.22935	0.004000	0.12327	0.039000	0.13416	3.871000	0.56077	2.120000	0.65058	0.561000	0.74099	ACC	.	C|1.000;T|0.000		0.662	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		G	49698355	C	G	49698355	3	3	76	1	0	0	0	0	1	0	0	0	1532	507	18	4	9099	4	BSN	3	49698355	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	531804	49698355	148324075	68	10339										
CDHR4	389118	hgsc.bcm.edu	37	chr3	49832413	49832413	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcataaaggcagaggctggcAgggttggaagagctgcggaa	17	6	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:49832413A>T	ENST00000412678.2	-	9	1160	c.1152T>A	c.(1150-1152)ccT>ccA	p.P384P	CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	384	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						AGAGGCTGGCAGGGTTGGAAG	0.612																																					p.P384P		Atlas-SNP	.											.	CDHR4	37	.	0			c.T1152A						.						47	58	54					3																	49832413		692	1591	2283	SO:0001819	synonymous_variant	389118	exon9			GCTGGCAGGGTTG		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"Cadherins / Cadherin-related"	34527	protein-coding gene	gene with protein product			"cadherin-like 29"	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.1152T>A	chr3.hg19:g.49832413A>T		121.0	0.0		139.0	35.0	NM_001007540	Q6UXT0	Silent	SNP	ENST00000412678.2	hg19	CCDS46829.1																																																																																			.	.		0.612	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540		T	49832413	A	T	49832413	2	4	76	1	0	0	0	0	0	0	0	1	3123	175	7	4		4	CDHR4	3	49832413	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	134058	49832413	148190017	69	10340										
LRTM1	57408	hgsc.bcm.edu	37	chr3	54952542	54952542	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caccttcccaggatcattggTttgagccaagggtcccccat	9	14	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:54952542T>C	ENST00000273286.5	-	3	1144	c.982A>G	c.(982-984)Acc>Gcc	p.T328A	CACNA2D3_ENST00000490478.1_Intron|CACNA2D3_ENST00000288197.5_Intron|LRTM1_ENST00000493075.1_Missense_Mutation_p.T252A|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000474759.1_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	328						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		GGATCATTGGTTTGAGCCAAG	0.507																																					p.T328A		Atlas-SNP	.											.	LRTM1	52	.	0			c.A982G						.						164	157	160					3																	54952542		2203	4300	6503	SO:0001583	missense	57408	exon3			CATTGGTTTGAGC	AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.982A>G	chr3.hg19:g.54952542T>C	ENSP00000273286:p.Thr328Ala	145.0	0.0		141.0	38.0	NM_020678	Q8IUU2	Missense_Mutation	SNP	ENST00000273286.5	hg19	CCDS2876.1	.	.	.	.	.	.	.	.	.	.	T	2.869	-0.234511	0.05983	.	.	ENSG00000144771	ENST00000273286;ENST00000493075	T;T	0.46819	0.86;1.2	5.48	-1.74	0.08056	.	0.817548	0.11312	N	0.576991	T	0.22322	0.0538	N	0.12887	0.27	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.25779	-1.0122	10	0.12766	T	0.61	.	6.4576	0.21938	0.1194:0.409:0.0:0.4716	.	328	Q9HBL6	LRTM1_HUMAN	A	328;252	ENSP00000273286:T328A;ENSP00000419772:T252A	ENSP00000273286:T328A	T	-	1	0	LRTM1	54927582	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.085000	0.14912	-0.223000	0.09943	-0.441000	0.05720	ACC	.	.		0.507	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678		C	54952542	T	C	54952542	3	2	76	1	0	0	0	0	1	0	0	0	9053	1725	60	2	59	2	LRTM1	3	54952542	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	5120129	54952542	143069888	70	10341										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57394214	57394214	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggagggcccattgcagcaatCagctctatgtccaccagcgt	11	13	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:57394214C>A	ENST00000351747.2	-	40	6192	c.6012G>T	c.(6010-6012)ctG>ctT	p.L2004L		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	2004	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TTGCAGCAATCAGCTCTATGT	0.388																																					p.L2004L		Atlas-SNP	.											.	DNAH12	182	.	0			c.G6012T						.						84	75	78					3																	57394214		692	1591	2283	SO:0001819	synonymous_variant	201625	exon40			AGCAATCAGCTCT	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.6012G>T	chr3.hg19:g.57394214C>A		112.0	0.0		117.0	67.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Silent	SNP	ENST00000351747.2	hg19																																																																																				.	.		0.388	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		A	57394214	C	A	57394214	2	1	76	1	0	0	0	0	0	0	0	1	4602	813	29	3		3	DNAH12	3	57394214	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	2441672	57394214	140628216	71	10342										
MITF	4286	hgsc.bcm.edu	37	chr3	70008478	70008478	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcatccgtggactatatccgAaagttgcaacgagaacagca	10	10	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:70008478A>G	ENST00000448226.2	+	9	1213	c.1086A>G	c.(1084-1086)cgA>cgG	p.R362R	MITF_ENST00000394351.3_Silent_p.R255R|MITF_ENST00000314557.6_Silent_p.R249R|MITF_ENST00000314589.5_Silent_p.R340R|MITF_ENST00000472437.1_Silent_p.R304R|MITF_ENST00000352241.4_Silent_p.R356R|MITF_ENST00000531774.1_Silent_p.R193R|MITF_ENST00000394355.2_Silent_p.R331R|MITF_ENST00000328528.6_Silent_p.R355R			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	362	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		ACTATATCCGAAAGTTGCAAC	0.453			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														p.R356R	Melanoma(29;269 969 31479 41502 42961)	Atlas-SNP	.		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	.	MITF	156	.	0			c.A1068G						.						89	80	83					3																	70008478		2203	4300	6503	SO:0001819	synonymous_variant	4286	exon9			TATCCGAAAGTTG		CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.1086A>G	chr3.hg19:g.70008478A>G		216.0	0.0		216.0	32.0	NM_198159	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Silent	SNP	ENST00000448226.2	hg19																																																																																				.	.		0.453	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		G	70008478	A	G	70008478	2	3	76	1	0	0	0	0	0	0	0	1	9605	233	9	2		2	MITF	3	70008478	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	12614264	70008478	128013952	72	10343										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77666666	77666666	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tttctcatttaatttcagctAtgacagtgatagctggtgcc	8	8	2	2	rs372099694		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:77666666A>G	ENST00000461745.1	+	22	4196	c.3296A>G	c.(3295-3297)tAt>tGt	p.Y1099C	ROBO2_ENST00000332191.8_Missense_Mutation_p.Y1099C|ROBO2_ENST00000487694.3_Missense_Mutation_p.Y1115C|ROBO2_ENST00000469233.1_3'UTR	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1099					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		AATTTCAGCTATGACAGTGAT	0.393													A|||	1	0.000199681	0	0.0014	5008	,	,		20664	0		0	False		,,,				2504	0				p.Y1099C		Atlas-SNP	.											.	ROBO2	527	.	0			c.A3296G						.	A	CYS/TYR,CYS/TYR	1,3897		0,1,1948	114	101	105		3344,3296	5.6	1	3		105	0,8296		0,0,4148	no	missense,missense	ROBO2	NM_001128929.2,NM_002942.4	194,194	0,1,6096	GG,GA,AA		0.0,0.0257,0.0082	possibly-damaging,possibly-damaging	1115/1395,1099/1379	77666666	1,12193	1949	4148	6097	SO:0001583	missense	6092	exon22			TCAGCTATGACAG	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3296A>G	chr3.hg19:g.77666666A>G	ENSP00000417164:p.Tyr1099Cys	64.0	0.0		63.0	44.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.0|20.0	3.930858|3.930858	0.73327|0.73327	2.57E-4|2.57E-4	0.0|0.0	ENSG00000185008|ENSG00000185008	ENST00000490991|ENST00000487694;ENST00000403211;ENST00000461745;ENST00000332191	.|T;T;T	.|0.62941	.|-0.01;0.02;0.01	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	.|0.000000	.|0.41823	.|D	.|0.000813	T|T	0.73528|0.73528	0.3598|0.3598	L|L	0.52573|0.52573	1.65|1.65	.|.	.|.	.|.	.|D;D;D	.|0.76494	.|0.99;0.999;0.99	.|P;D;P	.|0.67382	.|0.73;0.951;0.693	T|T	0.77120|0.77120	-0.2705|-0.2705	4|9	.|0.52906	.|T	.|0.07	.|.	15.7589|15.7589	0.78063|0.78063	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1115;1099;1099	.|Q19AB5;F8W703;Q9HCK4	.|.;.;ROBO2_HUMAN	V|C	256|1115;1115;1099;1099	.|ENSP00000417335:Y1115C;ENSP00000417164:Y1099C;ENSP00000327536:Y1099C	.|ENSP00000327536:Y1099C	M|Y	+|+	1|2	0|0	ROBO2|ROBO2	77749356|77749356	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.883000|0.883000	0.51084|0.51084	8.962000|8.962000	0.93254|0.93254	2.120000|2.120000	0.65058|0.65058	0.533000|0.533000	0.62120|0.62120	ATG|TAT	.	.		0.393	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		G	77666666	A	G	77666666	3	3	76	1	0	0	0	0	1	0	0	0	13529	449	16	2	3384	2	ROBO2	3	77666666	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	7658188	77666666	120355764	73	10344										
IMPG2	50939	hgsc.bcm.edu	37	chr3	100948247	100948247	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tctggaaagctcactgctctCatacatctgtctgatttctt	6	11	6	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:100948247C>A	ENST00000193391.7	-	17	3797	c.3610G>T	c.(3610-3612)Gag>Tag	p.E1204*		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	1204					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	TCACTGCTCTCATACATCTGT	0.537																																					p.E1204X		Atlas-SNP	.											.	IMPG2	164	.	0			c.G3610T						.						159	138	145					3																	100948247		2203	4300	6503	SO:0001587	stop_gained	50939	exon17			TGCTCTCATACAT	AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.3610G>T	chr3.hg19:g.100948247C>A	ENSP00000193391:p.Glu1204*	91.0	0.0		74.0	9.0	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Nonsense_Mutation	SNP	ENST00000193391.7	hg19	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	42	9.699379	0.99241	.	.	ENSG00000081148	ENST00000193391	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-13.6036	19.8965	0.96963	0.0:1.0:0.0:0.0	.	.	.	.	X	1204	.	ENSP00000193391:E1204X	E	-	1	0	IMPG2	102430937	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.451000	0.44952	2.717000	0.92951	0.655000	0.94253	GAG	.	.		0.537	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			A	100948247	C	A	100948247	4	1	76	1	0	0	0	0	0	1	0	0	7738	835	29	3	127	3	IMPG2	3	100948247	Nonsense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	23281581	100948247	97074183	74	10345										
IMPG2	50939	hgsc.bcm.edu	37	chr3	100976471	100976471	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caatataatctctgaagttaCtgattgtataaacaacagtg	6	6	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:100976471C>A	ENST00000193391.7	-	10	1242	c.1055G>T	c.(1054-1056)aGt>aTt	p.S352I		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	352	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	TCTGAAGTTACTGATTGTATA	0.433																																					p.S352I		Atlas-SNP	.											.	IMPG2	164	.	0			c.G1055T						.						106	106	106					3																	100976471		2203	4300	6503	SO:0001583	missense	50939	exon10			AAGTTACTGATTG	AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.1055G>T	chr3.hg19:g.100976471C>A	ENSP00000193391:p.Ser352Ile	92.0	0.0		92.0	60.0	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	hg19	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.415402	0.62511	.	.	ENSG00000081148	ENST00000193391	T	0.26223	1.75	5.51	1.45	0.22620	.	0.190595	0.47093	D	0.000247	T	0.23965	0.0580	L	0.56769	1.78	0.30623	N	0.758262	P;P	0.50272	0.933;0.933	B;B	0.42882	0.401;0.401	T	0.24584	-1.0156	10	0.72032	D	0.01	-2.9849	7.7492	0.28888	0.0:0.6073:0.2496:0.143	.	352;352	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	I	352	ENSP00000193391:S352I	ENSP00000193391:S352I	S	-	2	0	IMPG2	102459161	0.970000	0.33590	0.997000	0.53966	0.963000	0.63663	1.156000	0.31712	0.671000	0.31185	0.462000	0.41574	AGT	.	.		0.433	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			A	100976471	C	A	100976471	3	1	76	1	0	0	0	0	1	0	0	0	7738	565	20	3	2710	3	IMPG2	3	100976471	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	28224	100976471	97045959	75	10346										
BTLA	151888	hgsc.bcm.edu	37	chr3	112185077	112185077	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aacaatgcctggtttgttttCttccaggcatggattagaat	9	7	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:112185077C>A	ENST00000334529.5	-	5	950	c.748G>T	c.(748-750)Gaa>Taa	p.E250*	BTLA_ENST00000474965.1_5'UTR|BTLA_ENST00000383680.4_Nonsense_Mutation_p.E202*	NM_181780.3	NP_861445	Q7Z6A9	BTLA_HUMAN	B and T lymphocyte associated	250					immune response-regulating cell surface receptor signaling pathway (GO:0002768)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of B cell proliferation (GO:0030889)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|cervix(2)|large_intestine(1)|lung(5)|prostate(1)	11		Acute lymphoblastic leukemia(4;1.34e-07)|all_hematologic(4;0.000361)				GGTTTGTTTTCTTCCAGGCAT	0.413																																					p.E250X		Atlas-SNP	.											.	BTLA	22	.	0			c.G748T						.						125	120	122					3																	112185077		2203	4300	6503	SO:0001587	stop_gained	151888	exon5			TGTTTTCTTCCAG	AY293286	CCDS33819.1, CCDS43130.1	3q13.2	2013-01-11			ENSG00000186265	ENSG00000186265		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21087	protein-coding gene	gene with protein product		607925				12796776	Standard	NM_001085357		Approved	BTLA1, CD272	uc003dza.4	Q7Z6A9	OTTHUMG00000159255	ENST00000334529.5:c.748G>T	chr3.hg19:g.112185077C>A	ENSP00000333919:p.Glu250*	63.0	0.0		74.0	21.0	NM_181780	Q3B831|Q3HS85|Q6ZNH9	Nonsense_Mutation	SNP	ENST00000334529.5	hg19	CCDS33819.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.624481	0.66901	.	.	ENSG00000186265	ENST00000334529;ENST00000383680	.	.	.	5.13	3.32	0.38043	.	0.426359	0.19352	N	0.116375	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-5.4371	7.885	0.29644	0.0:0.8117:0.0:0.1883	.	.	.	.	X	250;202	.	ENSP00000333919:E250X	E	-	1	0	BTLA	113667767	0.038000	0.19896	0.342000	0.25602	0.263000	0.26337	0.427000	0.21379	0.725000	0.32318	0.591000	0.81541	GAA	.	.		0.413	BTLA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354101.1	NM_181780		A	112185077	C	A	112185077	4	1	76	1	0	0	0	0	0	1	0	0	1560	922	32	3	125	3	BTLA	3	112185077	Nonsense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	11208606	112185077	85837353	76	10347										
C3orf17	25871	hgsc.bcm.edu	37	chr3	112736436	112736436	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tggcattctttaattacagcTgcaatgcaaaggtctgaagc	9	8	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:112736436T>A	ENST00000314400.5	-	2	311	c.120A>T	c.(118-120)gcA>gcT	p.A40A	RP11-572M11.4_ENST00000467342.1_RNA|C3orf17_ENST00000393857.2_Intron|C3orf17_ENST00000383675.2_Silent_p.A40A|RP11-572M11.4_ENST00000460707.1_RNA|RP11-572M11.4_ENST00000496389.1_RNA|RP11-572M11.4_ENST00000470313.1_RNA	NM_015412.3	NP_056227.2	Q6NW34	CC017_HUMAN	chromosome 3 open reading frame 17	40					negative regulation of neuron differentiation (GO:0045665)|positive regulation of Notch signaling pathway (GO:0045747)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|lung(6)|prostate(2)|skin(1)	13						TAATTACAGCTGCAATGCAAA	0.353																																					p.A40A		Atlas-SNP	.											.	C3orf17	37	.	0			c.A120T						.						151	135	141					3																	112736436		2203	4300	6503	SO:0001819	synonymous_variant	25871	exon2			TACAGCTGCAATG	AL117573	CCDS33824.1	3q13.2	2009-11-06			ENSG00000163608	ENSG00000163608			24496	protein-coding gene	gene with protein product						12477932	Standard	NR_027794		Approved	DKFZP434F2021, NET17	uc003dzr.3	Q6NW34	OTTHUMG00000159286	ENST00000314400.5:c.120A>T	chr3.hg19:g.112736436T>A		93.0	0.0		99.0	42.0	NM_015412	D3DN69|Q68DM6|Q9H7U0|Q9UFM4	Silent	SNP	ENST00000314400.5	hg19	CCDS33824.1																																																																																			.	.		0.353	C3orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354405.3	NM_015412		A	112736436	T	A	112736436	2	1	76	1	0	0	0	0	0	0	0	1	2212	1567	55	4		4	C3orf17	3	112736436	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	551359	112736436	85285994	77	10348										
BOC	91653	hgsc.bcm.edu	37	chr3	113004363	113004363	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagtcaggggtgaggagagcCcccgacagtcctgtcctgga	15	12	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:113004363C>T	ENST00000495514.1	+	19	3812	c.3108C>T	c.(3106-3108)gcC>gcT	p.A1036A	BOC_ENST00000273395.4_Silent_p.A1037A|BOC_ENST00000355385.3_Silent_p.A1036A			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	1036					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGAGGAGAGCCCCCGACAGTC	0.622																																					p.A1036A		Atlas-SNP	.											.	BOC	139	.	0			c.C3108T						.						44	42	42					3																	113004363		2203	4300	6503	SO:0001819	synonymous_variant	91653	exon19			GAGAGCCCCCGAC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.3108C>T	chr3.hg19:g.113004363C>T		95.0	0.0		112.0	69.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	hg19	CCDS2971.1																																																																																			.	.		0.622	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		T	113004363	C	T	113004363	2	4	76	1	0	0	0	0	0	0	0	1	1481	610	22	3		3	BOC	3	113004363	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	267927	113004363	85018067	78	10349										
CCDC52	152185	hgsc.bcm.edu	37	chr3	113187199	113187199	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcagaggttgtgctacctgaTgatatgtttttcttcggctt	11	7	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:113187199T>C	ENST00000295872.4	-	10	1201	c.942A>G	c.(940-942)tcA>tcG	p.S314S		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	314					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						TGCTACCTGATGATATGTTTT	0.373																																					p.S314S		Atlas-SNP	.											.	SPICE1	130	.	0			c.A942G						.						122	122	122					3																	113187199		2203	4300	6503	SO:0001819	synonymous_variant	152185	exon10			ACCTGATGATATG	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.942A>G	chr3.hg19:g.113187199T>C		86.0	0.0		102.0	24.0	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	hg19	CCDS2973.1																																																																																			.	.		0.373	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		C	113187199	T	C	113187199	2	2	76	1	0	0	0	0	0	0	0	1	2824	1451	51	2		2	CCDC52	3	113187199	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	182836	113187199	84835231	79	10350										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140281142	140281142	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	taattctactgcaggctactCcatctacggtaaggccacac	7	13	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr3:140281142C>A	ENST00000458420.3	+	13	2394	c.2204C>A	c.(2203-2205)tCc>tAc	p.S735Y		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	735					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						GCAGGCTACTCCATCTACGGT	0.552										HNSCC(16;0.037)																											p.S735Y	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.C2204A						.						106	97	100					3																	140281142		2203	4300	6503	SO:0001583	missense	64084	exon13			GCTACTCCATCTA	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2204C>A	chr3.hg19:g.140281142C>A	ENSP00000402460:p.Ser735Tyr	33.0	0.0		35.0	20.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.663967	0.67700	.	.	ENSG00000158258	ENST00000458420	T	0.30448	1.53	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.57403	0.2051	M	0.74258	2.255	0.58432	D	0.999999	D	0.76494	0.999	D	0.83275	0.996	T	0.54892	-0.8225	9	.	.	.	-25.8184	17.5547	0.87887	0.0:1.0:0.0:0.0	.	735	Q9H4D0	CSTN2_HUMAN	Y	735	ENSP00000402460:S735Y	.	S	+	2	0	CLSTN2	141763832	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.227000	0.78070	2.755000	0.94549	0.655000	0.94253	TCC	.	.		0.552	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		A	140281142	C	A	140281142	3	1	76	1	0	0	0	0	1	0	0	0	3564	855	30	3	2254	3	CLSTN2	3	140281142	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	27093943	140281142	57741288	80	10351										
WFS1	7466	hgsc.bcm.edu	37	chr4	6288867	6288867	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cctttgaagaagtcctggagAgggccaaggccggggacccc	15	12	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:6288867A>T	ENST00000226760.1	+	3	450	c.280A>T	c.(280-282)Agg>Tgg	p.R94W	WFS1_ENST00000503569.1_Missense_Mutation_p.R94W	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	94					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		AGTCCTGGAGAGGGCCAAGGC	0.582																																					p.R94W		Atlas-SNP	.											WFS1,caecum,carcinoma,0,3	WFS1	71	.	0			c.A280T						.						52	50	51					4																	6288867		2176	4249	6425	SO:0001583	missense	7466	exon3			CTGGAGAGGGCCA	AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.280A>T	chr4.hg19:g.6288867A>T	ENSP00000226760:p.Arg94Trp	108.0	0.0		32.0	16.0	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Missense_Mutation	SNP	ENST00000226760.1	hg19	CCDS3386.1	.	.	.	.	.	.	.	.	.	.	A	17.57	3.421883	0.62622	.	.	ENSG00000109501	ENST00000503569;ENST00000226760	D;D	0.94000	-3.33;-3.33	3.84	3.84	0.44239	.	0.284353	0.38778	N	0.001564	D	0.94085	0.8104	L	0.52573	1.65	0.30760	N	0.744201	D	0.56968	0.978	P	0.62089	0.898	D	0.92021	0.5626	10	0.62326	D	0.03	-22.206	10.6348	0.45558	1.0:0.0:0.0:0.0	.	94	O76024	WFS1_HUMAN	W	94	ENSP00000423337:R94W;ENSP00000226760:R94W	ENSP00000226760:R94W	R	+	1	2	WFS1	6339768	1.000000	0.71417	1.000000	0.80357	0.316000	0.28119	6.802000	0.75175	1.623000	0.50342	0.459000	0.35465	AGG	.	.		0.582	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1			T	6288867	A	T	6288867	3	4	76	1	0	0	0	0	1	0	0	0	17375	295	11	4	286	4	WFS1	4	6288867	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10		6288867	184865409	81	10352										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13616094	13616094	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	acatccttatttagcagaatTaaattattatgctcttttgt	4	6	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:13616094T>C	ENST00000040738.5	-	4	1035	c.900A>G	c.(898-900)ttA>ttG	p.L300L		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	300						nucleus (GO:0005634)	DNA binding (GO:0003677)										TTAGCAGAATTAAATTATTAT	0.388																																					p.L300L		Atlas-SNP	.											.	.	.	.	0			c.A900G						.						73	69	70					4																	13616094		2203	4300	6503	SO:0001819	synonymous_variant	259282	exon4			CAGAATTAAATTA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.900A>G	chr4.hg19:g.13616094T>C		75.0	0.0		33.0	21.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Silent	SNP	ENST00000040738.5	hg19	CCDS3411.2																																																																																			.	.		0.388	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		C	13616094	T	C	13616094	2	2	76	1	0	0	0	0	0	0	0	1	1483	1751	61	2		2	BOD1L	4	13616094	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	7327227	13616094	177538182	82	10353										
RFC1	5981	hgsc.bcm.edu	37	chr4	39313096	39313096	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctgctatttcatacttggatTtcttgcctggcatagtccga	8	10	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:39313096T>C	ENST00000381897.1	-	12	1590	c.1457A>G	c.(1456-1458)aAa>aGa	p.K486R	RFC1_ENST00000349703.2_Missense_Mutation_p.K486R	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	486	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						ATACTTGGATTTCTTGCCTGG	0.348																																					p.K486R	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.A1457G						.						133	126	128					4																	39313096		2203	4300	6503	SO:0001583	missense	5981	exon12			TTGGATTTCTTGC	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.1457A>G	chr4.hg19:g.39313096T>C	ENSP00000371321:p.Lys486Arg	50.0	0.0		38.0	7.0	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	hg19	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.769326	0.49680	.	.	ENSG00000035928	ENST00000381897;ENST00000349703;ENST00000504554	T;T;T	0.44083	2.6;2.59;0.93	5.71	4.49	0.54785	.	0.407857	0.28958	N	0.013594	T	0.27663	0.0680	L	0.28344	0.845	0.36907	D	0.890683	B;B	0.12630	0.0;0.006	B;B	0.20384	0.005;0.029	T	0.15492	-1.0435	10	0.16896	T	0.51	-9.0652	9.1711	0.37081	0.0:0.1419:0.0:0.8581	.	486;486	P35251;P35251-2	RFC1_HUMAN;.	R	486;486;118	ENSP00000371321:K486R;ENSP00000261424:K486R;ENSP00000422129:K118R	ENSP00000261424:K486R	K	-	2	0	RFC1	38989491	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	4.017000	0.57167	0.956000	0.37904	0.533000	0.62120	AAA	.	.		0.348	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		C	39313096	T	C	39313096	3	2	76	1	0	0	0	0	1	0	0	0	13259	1841	64	2	2042	2	RFC1	4	39313096	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	25697002	39313096	151841180	83	10354										
GABRA4	2557	hgsc.bcm.edu	37	chr4	46967019	46967019	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttcaggatgcttctctctctGcactggagcagcgggaactt	11	11	3	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:46967019G>A	ENST00000264318.3	-	8	2084	c.1102C>T	c.(1102-1104)Cag>Tag	p.Q368*		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	368					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TTCTCTCTCTGCACTGGAGCA	0.423																																					p.Q368X	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											.	GABRA4	129	.	0			c.C1102T						.						89	96	93					4																	46967019		2203	4299	6502	SO:0001587	stop_gained	2557	exon8			CTCTCTGCACTGG		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4078	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 4"	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.1102C>T	chr4.hg19:g.46967019G>A	ENSP00000264318:p.Gln368*	138.0	0.0		72.0	16.0	NM_000809	Q8IYR7	Nonsense_Mutation	SNP	ENST00000264318.3	hg19	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	G	43	9.996373	0.99313	.	.	ENSG00000109158	ENST00000264318	.	.	.	4.81	3.97	0.46021	.	2.531910	0.01013	N	0.003874	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	11.8776	0.52556	0.0836:0.0:0.9164:0.0	.	.	.	.	X	368	.	ENSP00000264318:Q368X	Q	-	1	0	GABRA4	46661776	0.336000	0.24757	0.173000	0.22940	0.003000	0.03518	2.576000	0.46033	1.238000	0.43771	0.591000	0.81541	CAG	.	.		0.423	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			A	46967019	G	A	46967019	4	1	76	1	0	0	0	0	0	1	0	0	6171	1328	46	3	570	3	GABRA4	4	46967019	Nonsense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	7653923	46967019	144187257	84	10355										
SPATA18	132671	hgsc.bcm.edu	37	chr4	52943036	52943036	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cctccaccgctgtcaaggtcAggagaccgtccccaaaccgc	9	18	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:52943036A>T	ENST00000295213.4	+	7	1224	c.850A>T	c.(850-852)Agg>Tgg	p.R284W	SPATA18_ENST00000419395.2_Missense_Mutation_p.R252W	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	284	Ser-rich.				cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			TGTCAAGGTCAGGAGACCGTC	0.667																																					p.R284W		Atlas-SNP	.											.	SPATA18	222	.	0			c.A850T						.						56	48	51					4																	52943036		2203	4300	6503	SO:0001583	missense	132671	exon7			AAGGTCAGGAGAC	BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"spermatogenesis associated 18 homolog (rat)"			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.850A>T	chr4.hg19:g.52943036A>T	ENSP00000295213:p.Arg284Trp	264.0	0.0		129.0	67.0	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	hg19	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	A	13.69	2.312873	0.40895	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	T;T	0.23348	1.91;3.76	4.09	2.78	0.32641	.	0.178843	0.49916	D	0.000134	T	0.46814	0.1412	M	0.77103	2.36	0.50813	D	0.999899	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.46105	-0.9215	10	0.54805	T	0.06	-19.7729	8.6137	0.33817	0.807:0.1929:0.0:0.0	.	252;284;284	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	W	284;252	ENSP00000295213:R284W;ENSP00000415309:R252W	ENSP00000295213:R284W	R	+	1	2	SPATA18	52637793	0.676000	0.27567	0.090000	0.20809	0.004000	0.04260	0.793000	0.26944	1.783000	0.52377	0.379000	0.24179	AGG	.	.		0.667	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263		T	52943036	A	T	52943036	3	4	76	1	0	0	0	0	1	0	0	0	15018	179	7	4	876	4	SPATA18	4	52943036	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	5976017	52943036	138211240	85	10356										
SULT1B1	27284	hgsc.bcm.edu	37	chr4	70620914	70620914	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caacttcagatcttttcgcaGaatatcttttggggaaagca	8	8	3	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:70620914G>A	ENST00000310613.3	-	2	319	c.22C>T	c.(22-24)Ctg>Ttg	p.L8L		NM_014465.3	NP_055280.2	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member 1	8					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|cellular biogenic amine metabolic process (GO:0006576)|epithelial cell differentiation (GO:0030855)|flavonoid metabolic process (GO:0009812)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|thyroid hormone metabolic process (GO:0042403)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|sulfotransferase activity (GO:0008146)			breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(14)|prostate(1)|upper_aerodigestive_tract(1)	24						TCTTTTCGCAGAATATCTTTT	0.353																																					p.L8L		Atlas-SNP	.											.	SULT1B1	46	.	0			c.C22T						.						91	92	92					4																	70620914		2203	4300	6503	SO:0001819	synonymous_variant	27284	exon2			TTCGCAGAATATC	D89479	CCDS3530.1	4q13.3	2008-02-05			ENSG00000173597	ENSG00000173597		"Sulfotransferases, cytosolic"	17845	protein-coding gene	gene with protein product		608436				11688987, 9443824	Standard	NM_014465		Approved	ST1B2	uc003hen.3	O43704	OTTHUMG00000129407	ENST00000310613.3:c.22C>T	chr4.hg19:g.70620914G>A		125.0	0.0		74.0	38.0	NM_014465	O15497|Q96FI1|Q9UK34	Silent	SNP	ENST00000310613.3	hg19	CCDS3530.1																																																																																			.	.		0.353	SULT1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251563.2	NM_014465		A	70620914	G	A	70620914	2	1	76	1	0	0	0	0	0	0	0	1	15391	933	33	3		3	SULT1B1	4	70620914	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	17677878	70620914	120533362	86	10357										
ANKRD56	345079	hgsc.bcm.edu	37	chr4	77818168	77818168	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccggtctccgcggggagcggGgccgggcaggagagcaggcg	22	12	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:77818168G>A	ENST00000334306.2	-	1	834	c.835C>T	c.(835-837)Ccc>Tcc	p.P279S		NM_001029870.1	NP_001025041.1	A6NEL2	SWAHB_HUMAN	sosondowah ankyrin repeat domain family member B	279																	CGGGGAGCGGGGCCGGGCAGG	0.716																																					p.P279S		Atlas-SNP	.											.	.	.	.	0			c.C835T						.						4	6	5					4																	77818168		1959	3964	5923	SO:0001583	missense	345079	exon1			GAGCGGGGCCGGG		CCDS34017.1	4q21.1	2013-01-10	2012-01-12	2012-01-12	ENSG00000186212	ENSG00000186212		"Ankyrin repeat domain containing"	32958	protein-coding gene	gene with protein product			"ankyrin repeat domain 56"	ANKRD56		22234889	Standard	NM_001029870		Approved		uc003hki.3	A6NEL2	OTTHUMG00000160876	ENST00000334306.2:c.835C>T	chr4.hg19:g.77818168G>A	ENSP00000334879:p.Pro279Ser	19.0	0.0		14.0	9.0	NM_001029870	B2RP29	Missense_Mutation	SNP	ENST00000334306.2	hg19	CCDS34017.1	.	.	.	.	.	.	.	.	.	.	G	9.796	1.179323	0.21787	.	.	ENSG00000186212	ENST00000334306	T	0.05382	3.45	4.32	0.521	0.17046	.	1.751880	0.03913	U	0.282258	T	0.03348	0.0097	N	0.12182	0.205	0.09310	N	1	B	0.30068	0.267	B	0.28139	0.086	T	0.37407	-0.9707	10	0.10111	T	0.7	-1.9297	2.9578	0.05882	0.1649:0.1407:0.5493:0.1451	.	279	A6NEL2	ANR56_HUMAN	S	279	ENSP00000334879:P279S	ENSP00000334879:P279S	P	-	1	0	ANKRD56	78037192	0.229000	0.23729	0.000000	0.03702	0.004000	0.04260	1.675000	0.37555	-0.136000	0.11475	0.561000	0.74099	CCC	.	.		0.716	SOWAHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362762.1	NM_001029870		A	77818168	G	A	77818168	3	1	76	1	0	0	0	0	1	0	0	0	682	1232	43	3	1550	3	ANKRD56	4	77818168	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	7197254	77818168	113336108	87	10358										
SEC31A	22872	hgsc.bcm.edu	37	chr4	83793196	83793196	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cctcggaggcaaggaccatcTgagtagcaacatcaggatgc	12	11	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:83793196T>G	ENST00000395310.2	-	7	865	c.683A>C	c.(682-684)cAg>cCg	p.Q228P	SEC31A_ENST00000443462.2_Missense_Mutation_p.Q223P|SEC31A_ENST00000508479.1_Missense_Mutation_p.Q228P|SEC31A_ENST00000348405.4_Missense_Mutation_p.Q228P|SEC31A_ENST00000448323.1_Missense_Mutation_p.Q228P|SEC31A_ENST00000509142.1_Missense_Mutation_p.Q228P|SEC31A_ENST00000432794.1_Missense_Mutation_p.Q228P|SEC31A_ENST00000326950.5_Missense_Mutation_p.Q228P|SEC31A_ENST00000505984.1_Missense_Mutation_p.Q228P|SEC31A_ENST00000436790.2_5'UTR|SEC31A_ENST00000513858.1_Missense_Mutation_p.Q228P|SEC31A_ENST00000264405.5_5'Flank|SEC31A_ENST00000311785.7_Missense_Mutation_p.Q228P|SEC31A_ENST00000508502.1_Missense_Mutation_p.Q228P|SEC31A_ENST00000355196.2_Missense_Mutation_p.Q228P|SEC31A_ENST00000500777.2_Missense_Mutation_p.Q228P|SEC31A_ENST00000505472.1_Missense_Mutation_p.Q228P	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	228	Interaction with SEC13.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				AAGGACCATCTGAGTAGCAAC	0.453																																					p.Q228P		Atlas-SNP	.											.	SEC31A	227	.	0			c.A683C						.						117	91	100					4																	83793196		2203	4300	6503	SO:0001583	missense	22872	exon7			ACCATCTGAGTAG	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.683A>C	chr4.hg19:g.83793196T>G	ENSP00000378721:p.Gln228Pro	212.0	0.0		108.0	41.0	NM_001077206	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Missense_Mutation	SNP	ENST00000395310.2	hg19	CCDS3596.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.779214	0.90195	.	.	ENSG00000138674	ENST00000348405;ENST00000513858;ENST00000395310;ENST00000443462;ENST00000509142;ENST00000432794;ENST00000448323;ENST00000326950;ENST00000311785;ENST00000505472;ENST00000500777;ENST00000508502;ENST00000355196;ENST00000505984;ENST00000508479;ENST00000503058	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.63913	1.64;1.64;1.64;1.55;1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64;-0.07	5.65	5.65	0.86999	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84247	0.5430	M	0.93197	3.39	0.80722	D	1	P;P;D;D;D;P;D;D;P	0.76494	0.897;0.93;0.986;0.976;0.992;0.864;0.999;0.958;0.885	P;P;P;P;D;P;D;P;P	0.75484	0.756;0.529;0.744;0.701;0.956;0.771;0.986;0.72;0.691	D	0.88582	0.3137	10	0.87932	D	0	-9.1846	15.8687	0.79091	0.0:0.0:0.0:1.0	.	223;228;228;228;228;228;228;228;228	B4DIW6;B7ZL00;O94979-5;D6RHZ5;O94979-6;O94979-4;O94979-3;O94979-2;O94979	.;.;.;.;.;.;.;.;SC31A_HUMAN	P	228;228;228;223;228;228;228;228;228;228;228;228;228;228;228;199	ENSP00000337602:Q228P;ENSP00000426886:Q228P;ENSP00000378721:Q228P;ENSP00000408027:Q223P;ENSP00000426569:Q228P;ENSP00000407944:Q228P;ENSP00000400926:Q228P;ENSP00000325087:Q228P;ENSP00000309070:Q228P;ENSP00000421633:Q228P;ENSP00000421464:Q228P;ENSP00000424635:Q228P;ENSP00000347329:Q228P;ENSP00000424451:Q228P;ENSP00000425999:Q228P;ENSP00000425056:Q199P	ENSP00000309070:Q228P	Q	-	2	0	SEC31A	84012220	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.036000	0.88901	2.136000	0.66102	0.477000	0.44152	CAG	.	.		0.453	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		G	83793196	T	G	83793196	3	3	76	1	0	0	0	0	1	0	0	0	14013	1580	55	5	3063	5	SEC31A	4	83793196	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	5975028	83793196	107361080	88	10359										
THAP9	79725	hgsc.bcm.edu	37	chr4	83838969	83838969	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aaagggacttaaagggcctcTgttgcctgaaacttacagta	10	8	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:83838969T>A	ENST00000302236.5	+	5	1655	c.1604T>A	c.(1603-1605)cTg>cAg	p.L535Q	LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	535					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				AAAGGGCCTCTGTTGCCTGAA	0.318																																					p.L535Q		Atlas-SNP	.											.	THAP9	65	.	0			c.T1604A						.						89	93	91					4																	83838969		2203	4299	6502	SO:0001583	missense	79725	exon5			GGCCTCTGTTGCC	AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"THAP (C2CH-type zinc finger) domain containing"	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.1604T>A	chr4.hg19:g.83838969T>A	ENSP00000305533:p.Leu535Gln	70.0	0.0		33.0	16.0	NM_024672	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	hg19	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	T	9.728	1.161373	0.21538	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	D	0.91894	-2.93	3.87	3.87	0.44632	.	0.000000	0.38326	N	0.001732	D	0.94128	0.8117	L	0.58810	1.83	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.93365	0.6730	10	0.45353	T	0.12	-9.6715	11.3618	0.49648	0.0:0.0:0.0:1.0	.	535	Q9H5L6	THAP9_HUMAN	Q	535	ENSP00000305533:L535Q	ENSP00000305533:L535Q	L	+	2	0	THAP9	84057993	0.208000	0.23494	0.116000	0.21606	0.017000	0.09413	4.766000	0.62279	1.983000	0.57843	0.533000	0.62120	CTG	.	.		0.318	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672		A	83838969	T	A	83838969	3	1	76	1	0	0	0	0	1	0	0	0	15866	1580	55	4	1622	4	THAP9	4	83838969	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	45773	83838969	107315307	89	10360										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85623579	85623579	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gggataagttcttttacatcTgccatattgtgctttgacgc	9	8	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:85623579T>G	ENST00000295888.4	-	56	8930	c.8523A>C	c.(8521-8523)gcA>gcC	p.A2841A	WDFY3_ENST00000322366.6_Silent_p.A2824A	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2841	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.|Interaction with SQSTM1.|Sufficient for translocalization to p62 bodies/ALIS.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CTTTTACATCTGCCATATTGT	0.458																																					p.A2841A		Atlas-SNP	.											.	WDFY3	314	.	0			c.A8523C						.						88	95	92					4																	85623579		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon56			TACATCTGCCATA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.8523A>C	chr4.hg19:g.85623579T>G		200.0	0.0		84.0	43.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.		0.458	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		G	85623579	T	G	85623579	2	3	76	1	0	0	0	0	0	0	0	1	17285	1567	55	5		5	WDFY3	4	85623579	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	1784610	85623579	105530697	90	10361										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123185451	123185451	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	taccctcagcctcagatttcAacactgtcttgtctagtgac	6	13	5	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:123185451A>C	ENST00000264501.4	+	45	7559	c.7186A>C	c.(7186-7188)Aac>Cac	p.N2396H	KIAA1109_ENST00000388738.3_Missense_Mutation_p.N2396H|KIAA1109_ENST00000455637.1_Missense_Mutation_p.N2396H			Q2LD37	K1109_HUMAN	KIAA1109	2396					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CTCAGATTTCAACACTGTCTT	0.398																																					p.N2396H		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A7186C						.						104	101	102					4																	123185451		1918	4132	6050	SO:0001583	missense	84162	exon43			GATTTCAACACTG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.7186A>C	chr4.hg19:g.123185451A>C	ENSP00000264501:p.Asn2396His	130.0	0.0		60.0	16.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.3|26.3	4.724386|4.724386	0.89298|0.89298	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000419325	T;T;T|.	0.26518|.	2.33;2.33;1.73|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.000000|.	0.56097|.	U|.	0.000040|.	T|T	0.52108|0.52108	0.1714|0.1714	N|N	0.19112|0.19112	0.55|0.55	0.51767|0.51767	D|D	0.999937|0.999937	D;D;D|.	0.76494|.	0.999;0.999;0.999|.	D;D;D|.	0.83275|.	0.996;0.996;0.994|.	T|T	0.49021|0.49021	-0.8982|-0.8982	10|5	0.42905|.	T|.	0.14|.	.|.	16.3782|16.3782	0.83418|0.83418	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	2396;2395;2396|.	Q2LD37-6;Q2LD37-2;Q2LD37|.	.;.;K1109_HUMAN|.	H|P	2396|353	ENSP00000264501:N2396H;ENSP00000373390:N2396H;ENSP00000389925:N2396H|.	ENSP00000264501:N2396H|.	N|Q	+|+	1|2	0|0	KIAA1109|KIAA1109	123404901|123404901	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.117000|9.117000	0.94347|0.94347	2.277000|2.277000	0.76020|0.76020	0.528000|0.528000	0.53228|0.53228	AAC|CAA	.	.		0.398	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123185451	A	C	123185451	3	2	76	1	0	0	0	0	1	0	0	0	8217	130	5	5	7356	5	KIAA1109	4	123185451	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	37561872	123185451	67968825	91	10362										
FGA	2243	hgsc.bcm.edu	37	chr4	155507589	155507589	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcccagagttccagcttccaGtacttccaggtccagagctc	8	15	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr4:155507589G>T	ENST00000302053.3	-	5	1070	c.992C>A	c.(991-993)aCt>aAt	p.T331N	FGA_ENST00000403106.3_Missense_Mutation_p.T331N	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	331			T -> A (in dbSNP:rs6050). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	CCAGCTTCCAGTACTTCCAGG	0.577																																					p.T331N	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.C992A						.						91	99	96					4																	155507589		2203	4300	6503	SO:0001583	missense	2243	exon5			CTTCCAGTACTTC		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.992C>A	chr4.hg19:g.155507589G>T	ENSP00000306361:p.Thr331Asn	136.0	0.0		75.0	16.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	9.600	1.128378	0.21041	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.72051	-0.62;-0.62	4.95	2.0	0.26442	.	3.217810	0.01539	N	0.019120	T	0.61185	0.2327	L	0.47190	1.495	0.09310	N	1	B;P	0.39216	0.218;0.664	B;B	0.35353	0.124;0.201	T	0.47058	-0.9146	10	0.29301	T	0.29	.	3.162	0.06523	0.0923:0.1295:0.418:0.3602	.	331;331	P02671-2;P02671	.;FIBA_HUMAN	N	331	ENSP00000306361:T331N;ENSP00000385981:T331N	ENSP00000306361:T331N	T	-	2	0	FGA	155727039	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.576000	0.05854	0.485000	0.27652	0.650000	0.86243	ACT	.	.		0.577	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		T	155507589	G	T	155507589	3	4	76	1	0	0	0	0	1	0	0	0	5838	1029	36	3	1660	3	FGA	4	155507589	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	32322138	155507589	35646687	92	10363										
PRKAA1	5562	hgsc.bcm.edu	37	chr5	40763061	40763061	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cactcctttggcaagatcgaTagttgctaactgatcccgat	8	11	0	2	rs373496949		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:40763061T>C	ENST00000397128.2	-	9	1507	c.1499A>G	c.(1498-1500)tAt>tGt	p.Y500C	PRKAA1_ENST00000354209.3_Missense_Mutation_p.Y515C	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	500					activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)			breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	GCAAGATCGATAGTTGCTAAC	0.408																																					p.Y515C		Atlas-SNP	.											.	PRKAA1	27	.	0			c.A1544G						.	T	CYS/TYR,CYS/TYR	1,3751		0,1,1875	105	100	101		1499,1544	5.9	1	5		101	0,8228		0,0,4114	no	missense,missense	PRKAA1	NM_006251.5,NM_206907.3	194,194	0,1,5989	CC,CT,TT		0.0,0.0267,0.0083	possibly-damaging,possibly-damaging	500/560,515/575	40763061	1,11979	1876	4114	5990	SO:0001583	missense	5562	exon10			GATCGATAGTTGC		CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"AMPK, alpha, 1"	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.1499A>G	chr5.hg19:g.40763061T>C	ENSP00000380317:p.Tyr500Cys	117.0	0.0		101.0	27.0	NM_206907	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Missense_Mutation	SNP	ENST00000397128.2	hg19	CCDS3932.2	.	.	.	.	.	.	.	.	.	.	T	19.88	3.909502	0.72868	2.67E-4	0.0	ENSG00000132356	ENST00000397128;ENST00000354209	T;T	0.08807	3.05;3.05	5.93	5.93	0.95920	.	0.053936	0.85682	D	0.000000	T	0.15998	0.0385	L	0.36672	1.1	0.80722	D	1	P;D	0.58268	0.926;0.982	P;P	0.55345	0.599;0.774	T	0.00849	-1.1541	10	0.41790	T	0.15	-20.2903	16.3839	0.83495	0.0:0.0:0.0:1.0	.	500;515	Q13131;Q13131-2	AAPK1_HUMAN;.	C	500;515	ENSP00000380317:Y500C;ENSP00000346148:Y515C	ENSP00000346148:Y515C	Y	-	2	0	AC008810.1	40798818	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.964000	0.56780	2.258000	0.74832	0.533000	0.62120	TAT	.	.		0.408	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251		C	40763061	T	C	40763061	3	2	76	1	0	0	0	0	1	0	0	0	12505	1406	49	2	184	2	PRKAA1	5	40763061	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10		40763061	140152199	93	10364										
SFRS12IP1	285672	hgsc.bcm.edu	37	chr5	64023956	64023956	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tttccttttttttttcaattTgattttttctttgctttttt	2	5	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:64023956T>A	ENST00000513458.4	-	4	423	c.256A>T	c.(256-258)Aaa>Taa	p.K86*		NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	86	Lys-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						tttttcaatttgattttttct	0.269																																					p.K86X		Atlas-SNP	.											.	SREK1IP1	28	.	0			c.A256T						.						17	21	19					5																	64023956		2129	4184	6313	SO:0001587	stop_gained	285672	exon4			TCAATTTGATTTT	AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006			26716	protein-coding gene	gene with protein product	"p18 splicing regulatory protein"		"SFRS12-interacting protein 1"	SFRS12IP1		15456940	Standard	NM_173829		Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.256A>T	chr5.hg19:g.64023956T>A	ENSP00000427401:p.Lys86*	236.0	0.0		203.0	51.0	NM_173829	Q32NC8	Nonsense_Mutation	SNP	ENST00000513458.4	hg19	CCDS34171.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433650	0.83776	.	.	ENSG00000153006	ENST00000513458	.	.	.	4.17	2.98	0.34508	.	0.404164	0.27236	N	0.020290	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.87	6.9743	0.24666	0.203:0.0:0.0:0.797	.	.	.	.	X	86	.	ENSP00000427401:K86X	K	-	1	0	SREK1IP1	64059712	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	3.061000	0.49963	0.731000	0.32448	0.533000	0.62120	AAA	.	.		0.269	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829		A	64023956	T	A	64023956	4	1	76	1	0	0	0	0	0	1	0	0	14183	1821	63	4	219	4	SFRS12IP1	5	64023956	Nonsense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	23260895	64023956	116891304	94	10365										
MARVELD2	153562	hgsc.bcm.edu	37	chr5	68715680	68715680	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gctgacgcagtgtttccccgGgatccctatggatctctaga	11	12	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:68715680G>A	ENST00000325631.5	+	2	542	c.468G>A	c.(466-468)cgG>cgA	p.R156R	MARVELD2_ENST00000413223.2_Silent_p.R156R	NM_001038603.2|NM_001244734.1	NP_001033692.2|NP_001231663.1	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	156					cell-cell junction organization (GO:0045216)|establishment of endothelial barrier (GO:0061028)|sensory perception of sound (GO:0007605)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(4)|skin(1)|urinary_tract(1)	15		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		TGTTTCCCCGGGATCCCTATG	0.522																																					p.R156R		Atlas-SNP	.											.	MARVELD2	49	.	0			c.G468A						.						63	64	64					5																	68715680		2203	4300	6503	SO:0001819	synonymous_variant	153562	exon2			TCCCCGGGATCCC	AK055094	CCDS34175.1, CCDS58956.1	5q13.1	2007-05-01	2004-07-12	2004-07-14	ENSG00000152939	ENSG00000152939			26401	protein-coding gene	gene with protein product	"tricellulin"	610572	"MARVEL (membrane-associating) domain containing 2", "deafness, autosomal recessive 49"	MRVLDC2, DFNB49		17186462	Standard	NM_001038603		Approved	FLJ30532, TRIC	uc003jwq.3	Q8N4S9	OTTHUMG00000162512	ENST00000325631.5:c.468G>A	chr5.hg19:g.68715680G>A		106.0	0.0		105.0	39.0	NM_001244734	A1BQX0|A1BQX1|A8KA97|Q96NM9	Silent	SNP	ENST00000325631.5	hg19	CCDS34175.1																																																																																			.	.		0.522	MARVELD2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369583.1	NM_144724		A	68715680	G	A	68715680	2	1	76	1	0	0	0	0	0	0	0	1	9327	1219	43	3		3	MARVELD2	5	68715680	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	4691724	68715680	112199580	95	10366										
ELL2	22936	hgsc.bcm.edu	37	chr5	95236690	95236690	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctgactccaatgaccgtctgTctatttcactgtatccaggc	7	13	3	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:95236690T>C	ENST00000237853.4	-	6	1185	c.836A>G	c.(835-837)gAc>gGc	p.D279G	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	279					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		TGACCGTCTGTCTATTTCACT	0.328																																					p.D279G		Atlas-SNP	.											.	ELL2	63	.	0			c.A836G						.						86	92	90					5																	95236690		2203	4299	6502	SO:0001583	missense	22936	exon6			CGTCTGTCTATTT	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.836A>G	chr5.hg19:g.95236690T>C	ENSP00000237853:p.Asp279Gly	217.0	0.0		163.0	73.0	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	hg19	CCDS4080.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.991118	0.74703	.	.	ENSG00000118985	ENST00000237853;ENST00000513343	T;T	0.37058	1.22;1.22	5.52	5.52	0.82312	.	0.044252	0.85682	D	0.000000	T	0.61198	0.2328	M	0.79475	2.455	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	T	0.66528	-0.5901	10	0.87932	D	0	-4.9508	15.2931	0.73882	0.0:0.0:0.0:1.0	.	279	O00472	ELL2_HUMAN	G	279;97	ENSP00000237853:D279G;ENSP00000423915:D97G	ENSP00000237853:D279G	D	-	2	0	ELL2	95262446	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	7.115000	0.77110	2.086000	0.62901	0.459000	0.35465	GAC	.	.		0.328	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		C	95236690	T	C	95236690	3	2	76	1	0	0	0	0	1	0	0	0	5065	1667	58	2	1114	2	ELL2	5	95236690	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	26521010	95236690	85678570	96	10367										
SLCO4C1	353189	hgsc.bcm.edu	37	chr5	101631729	101631729	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cccctcctcaaactcggacaGcgacagtgaccggagcttct	9	16	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:101631729G>C	ENST00000310954.6	-	1	524	c.238C>G	c.(238-240)Ctg>Gtg	p.L80V		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		AACTCGGACAGCGACAGTGAC	0.577																																					p.L80V		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.C238G						.						89	90	90					5																	101631729		2203	4300	6503	SO:0001583	missense	353189	exon1			CGGACAGCGACAG	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"Solute carriers"	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.238C>G	chr5.hg19:g.101631729G>C	ENSP00000309741:p.Leu80Val	147.0	0.0		99.0	29.0	NM_180991		Missense_Mutation	SNP	ENST00000310954.6	hg19	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	G	3.319	-0.139058	0.06669	.	.	ENSG00000173930	ENST00000310954	T	0.38077	1.16	3.81	0.412	0.16397	.	1.188650	0.06781	N	0.785336	T	0.24890	0.0604	L	0.38531	1.155	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.25779	-1.0122	10	0.29301	T	0.29	.	3.1762	0.06569	0.106:0.4243:0.3049:0.1648	.	80	Q6ZQN7	SO4C1_HUMAN	V	80	ENSP00000309741:L80V	ENSP00000309741:L80V	L	-	1	2	SLCO4C1	101659628	0.000000	0.05858	0.003000	0.11579	0.060000	0.15804	0.563000	0.23547	0.295000	0.22570	0.591000	0.81541	CTG	.	.		0.577	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991		C	101631729	G	C	101631729	3	2	76	1	0	0	0	0	1	0	0	0	14745	962	34	4	1988	4	SLCO4C1	5	101631729	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	6395039	101631729	79283531	97	10368										
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109049407	109049407	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atcttctgccctcacaattaTccctctcagttgacactgca	4	15	4	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:109049407T>G	ENST00000261483.4	+	2	1374	c.322T>G	c.(322-324)Tcc>Gcc	p.S108A		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	108					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		CTCACAATTATCCCTCTCAGT	0.443																																					p.S108A		Atlas-SNP	.											.	MAN2A1	136	.	0			c.T322G						.						140	127	132					5																	109049407		2202	4300	6502	SO:0001583	missense	4124	exon2			CAATTATCCCTCT		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.322T>G	chr5.hg19:g.109049407T>G	ENSP00000261483:p.Ser108Ala	97.0	0.0		85.0	23.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	T	10.78	1.447905	0.26074	.	.	ENSG00000112893	ENST00000261483	T	0.76709	-1.04	5.26	-0.755	0.11061	.	0.899783	0.09637	N	0.775522	T	0.64136	0.2571	L	0.42245	1.32	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.44682	-0.9312	10	0.11485	T	0.65	-0.188	7.0347	0.24987	0.0:0.2008:0.2567:0.5425	.	108	Q16706	MA2A1_HUMAN	A	108	ENSP00000261483:S108A	ENSP00000261483:S108A	S	+	1	0	MAN2A1	109077306	0.000000	0.05858	0.000000	0.03702	0.968000	0.65278	0.181000	0.16880	-0.017000	0.14103	0.378000	0.23410	TCC	.	.		0.443	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			G	109049407	T	G	109049407	3	3	76	1	0	0	0	0	1	0	0	0	9223	1435	50	5	328	5	MAN2A1	5	109049407	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	7417678	109049407	71865853	98	10369										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112849665	112849665	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gaggcggcggcccctcgcctTgtggccctgggggcggcggc	20	15	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:112849665T>C	ENST00000161863.4	+	1	286	c.73T>C	c.(73-75)Tgt>Cgt	p.C25R	YTHDC2_ENST00000515883.1_Missense_Mutation_p.C25R	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	25	Gly-rich.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		CCCCTCGCCTTGTGGCCCTGG	0.682																																					p.C25R		Atlas-SNP	.											.	YTHDC2	118	.	0			c.T73C						.						10	11	10					5																	112849665		2185	4284	6469	SO:0001583	missense	64848	exon1			TCGCCTTGTGGCC	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.73T>C	chr5.hg19:g.112849665T>C	ENSP00000161863:p.Cys25Arg	86.0	0.0		70.0	21.0	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	T	3.576	-0.086703	0.07097	.	.	ENSG00000047188	ENST00000161863;ENST00000515883	T;T	0.06068	4.36;3.35	3.28	2.03	0.26663	.	.	.	.	.	T	0.03608	0.0103	N	0.14661	0.345	0.21915	N	0.999476	B	0.02656	0.0	B	0.01281	0.0	T	0.42224	-0.9464	9	0.45353	T	0.12	.	3.3528	0.07158	0.0:0.13:0.2437:0.6263	.	25	Q9H6S0	YTDC2_HUMAN	R	25	ENSP00000161863:C25R;ENSP00000423101:C25R	ENSP00000161863:C25R	C	+	1	0	YTHDC2	112877564	.	.	0.086000	0.20670	0.040000	0.13550	.	.	0.428000	0.26173	0.260000	0.18958	TGT	.	.		0.682	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		C	112849665	T	C	112849665	3	2	76	1	0	0	0	0	1	0	0	0	17512	1812	63	2	75	2	YTHDC2	5	112849665	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	3800258	112849665	68065595	99	10370										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118513717	118513717	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cttgtctaattcgacttttgAattcttctggcgaggaagcc	9	9	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:118513717A>T	ENST00000311085.8	+	28	6993	c.6913A>T	c.(6913-6915)Aat>Tat	p.N2305Y	DMXL1_ENST00000539542.1_Missense_Mutation_p.N2305Y	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2305										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		TCGACTTTTGAATTCTTCTGG	0.373																																					p.N2305Y		Atlas-SNP	.											.	DMXL1	268	.	0			c.A6913T						.						67	67	67					5																	118513717		2202	4300	6502	SO:0001583	missense	1657	exon28			CTTTTGAATTCTT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.6913A>T	chr5.hg19:g.118513717A>T	ENSP00000309690:p.Asn2305Tyr	102.0	0.0		89.0	15.0	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	17.61	3.433327	0.62844	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.10005	2.92;2.92	5.72	5.72	0.89469	.	0.117593	0.85682	D	0.000000	T	0.23886	0.0578	M	0.72479	2.2	0.53688	D	0.999979	D;D	0.54397	0.963;0.966	P;P	0.50440	0.632;0.641	T	0.00899	-1.1522	10	0.72032	D	0.01	-21.876	16.0205	0.80486	1.0:0.0:0.0:0.0	.	2305;2305	F5H269;Q9Y485	.;DMXL1_HUMAN	Y	2305	ENSP00000309690:N2305Y;ENSP00000439479:N2305Y	ENSP00000309690:N2305Y	N	+	1	0	DMXL1	118541616	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.194000	0.70268	0.533000	0.62120	AAT	.	.		0.373	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		T	118513717	A	T	118513717	3	4	76	1	0	0	0	0	1	0	0	0	4596	246	9	4	7023	4	DMXL1	5	118513717	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	5664052	118513717	62401543	100	10371										
SLC12A2	6558	hgsc.bcm.edu	37	chr5	127484507	127484507	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgctaaaggttatgggaaaaAtaatgaacctcttcgtggct	10	6	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:127484507A>G	ENST00000262461.2	+	12	2132	c.1943A>G	c.(1942-1944)aAt>aGt	p.N648S	SLC12A2_ENST00000343225.4_Missense_Mutation_p.N648S	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	648					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	TATGGGAAAAATAATGAACCT	0.308																																					p.N648S		Atlas-SNP	.											.	SLC12A2	119	.	0			c.A1943G						.						178	181	180					5																	127484507		2203	4299	6502	SO:0001583	missense	6558	exon12			GGAAAAATAATGA		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.1943A>G	chr5.hg19:g.127484507A>G	ENSP00000262461:p.Asn648Ser	92.0	0.0		74.0	9.0	NM_001046	Q8N713|Q8WWH7	Missense_Mutation	SNP	ENST00000262461.2	hg19	CCDS4144.1	.	.	.	.	.	.	.	.	.	.	A	17.12	3.308423	0.60305	.	.	ENSG00000064651	ENST00000262461;ENST00000343225	D;D	0.98512	-4.97;-4.97	4.8	4.8	0.61643	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.97564	0.9202	L	0.43923	1.385	0.80722	D	1	P;D	0.53462	0.95;0.96	P;P	0.54210	0.628;0.745	D	0.98304	1.0520	10	0.87932	D	0	.	14.7822	0.69774	1.0:0.0:0.0:0.0	.	648;648	P55011-3;P55011	.;S12A2_HUMAN	S	648	ENSP00000262461:N648S;ENSP00000340878:N648S	ENSP00000262461:N648S	N	+	2	0	SLC12A2	127512406	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.268000	0.78473	2.142000	0.66516	0.477000	0.44152	AAT	.	.		0.308	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		G	127484507	A	G	127484507	3	3	76	1	0	0	0	0	1	0	0	0	14398	101	4	2	1989	2	SLC12A2	5	127484507	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	8970790	127484507	53430753	101	10372										
P4HA2	8974	hgsc.bcm.edu	37	chr5	131552947	131552947	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aggccagtctgtgtttagccGcttcaccagtttgtaggcat	11	10	2	0	rs370556720		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:131552947G>A	ENST00000401867.1	-	5	842	c.274C>T	c.(274-276)Cgg>Tgg	p.R92W	P4HA2_ENST00000166534.4_Missense_Mutation_p.R92W|P4HA2_ENST00000379086.1_Missense_Mutation_p.R92W|P4HA2_ENST00000379104.2_Missense_Mutation_p.R92W|P4HA2_ENST00000360568.3_Missense_Mutation_p.R92W|P4HA2_ENST00000379100.2_Missense_Mutation_p.R92W			O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha polypeptide II	92					peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|procollagen-proline 4-dioxygenase complex (GO:0016222)	electron carrier activity (GO:0009055)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)	GTGTTTAGCCGCTTCACCAGT	0.567																																					p.R92W	Esophageal Squamous(68;117 1135 17362 19256 34242)	Atlas-SNP	.											.	P4HA2	72	.	0			c.C274T						.	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	137	116	123		274,274,274,274,274	4.3	1	5		123	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	P4HA2	NM_001017973.1,NM_001017974.1,NM_001142598.1,NM_001142599.1,NM_004199.2	101,101,101,101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	92/534,92/534,92/534,92/536,92/536	131552947	1,13005	2203	4300	6503	SO:0001583	missense	8974	exon4			TTAGCCGCTTCAC	U90441	CCDS4151.1, CCDS34230.1	5q31	2008-12-09	2008-12-09		ENSG00000072682	ENSG00000072682	1.14.11.2		8547	protein-coding gene	gene with protein product	"4-PH alpha 2", "collagen prolyl 4-hydroxylase alpha(II)"	600608	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II"			9211872, 9149945	Standard	NM_001142598		Approved	C-P4Halpha(II)	uc003kwl.3	O15460	OTTHUMG00000059647	ENST00000401867.1:c.274C>T	chr5.hg19:g.131552947G>A	ENSP00000384999:p.Arg92Trp	73.0	0.0		49.0	18.0	NM_001017974	D3DQ85|D3DQ86|Q8WWN0	Missense_Mutation	SNP	ENST00000401867.1	hg19	CCDS4151.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.431817	0.83776	0.0	1.16E-4	ENSG00000072682	ENST00000401867;ENST00000379086;ENST00000166534;ENST00000360568;ENST00000379104;ENST00000379100;ENST00000417528;ENST00000431054;ENST00000439698;ENST00000395164;ENST00000453286;ENST00000428369;ENST00000418055;ENST00000416053	T;T;T;T;T;T	0.68181	-0.3;-0.31;-0.3;-0.31;-0.3;-0.31	6.17	4.35	0.52113	Prolyl 4-hydroxylase alpha-subunit, N-terminal (1);	0.046090	0.85682	D	0.000000	D	0.86644	0.5982	H	0.95679	3.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89956	0.4083	10	0.87932	D	0	-2.9059	14.4187	0.67168	0.0:0.0:0.6133:0.3867	.	92;92	O15460;O15460-2	P4HA2_HUMAN;.	W	92;92;92;92;92;92;92;124;92;92;92;92;92;92	ENSP00000384999:R92W;ENSP00000368379:R92W;ENSP00000166534:R92W;ENSP00000353772:R92W;ENSP00000368398:R92W;ENSP00000368394:R92W	ENSP00000166534:R92W	R	-	1	2	P4HA2	131580846	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	3.972000	0.56838	0.873000	0.35799	0.655000	0.94253	CGG	.	.		0.567	P4HA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132653.4	NM_004199		A	131552947	G	A	131552947	3	1	76	1	0	0	0	0	1	0	0	0	11366	1086	38	1	1445	1	P4HA2	5	131552947	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	4068440	131552947	49362313	102	10373										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140432008	140432008	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cattgaaacatacgacattgAcattcaagctacagatggtg	8	8	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:140432008A>G	ENST00000306549.3	+	1	1030	c.953A>G	c.(952-954)gAc>gGc	p.D318G		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	318	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TACGACATTGACATTCAAGCT	0.473																																					p.D318G		Atlas-SNP	.											.	PCDHB1	148	.	0			c.A953G						.						121	117	118					5																	140432008		2203	4300	6503	SO:0001583	missense	29930	exon1			ACATTGACATTCA	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.953A>G	chr5.hg19:g.140432008A>G	ENSP00000307234:p.Asp318Gly	129.0	0.0		89.0	22.0	NM_013340	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	hg19	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	A	12.06	1.823468	0.32237	.	.	ENSG00000171815	ENST00000306549	T	0.01685	4.69	6.17	5.0	0.66597	Cadherin (5);Cadherin-like (1);	0.000000	0.49916	D	0.000129	T	0.02156	0.0067	L	0.50919	1.6	0.09310	N	1	P	0.38677	0.642	B	0.34418	0.182	T	0.46830	-0.9163	10	0.49607	T	0.09	.	7.3612	0.26748	0.6223:0.1293:0.0:0.2484	.	318	Q9Y5F3	PCDB1_HUMAN	G	318	ENSP00000307234:D318G	ENSP00000307234:D318G	D	+	2	0	PCDHB1	140412192	0.000000	0.05858	0.998000	0.56505	0.997000	0.91878	0.036000	0.13819	1.120000	0.41904	0.533000	0.62120	GAC	.	.		0.473	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		G	140432008	A	G	140432008	3	3	76	1	0	0	0	0	1	0	0	0	11543	275	10	2	955	2	PCDHB1	5	140432008	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	8879061	140432008	40483252	103	10374										
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140558117	140558117	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tagatataggccaaaacaatAttgagaactatataatcagc	6	6	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:140558117A>G	ENST00000239444.2	+	1	747	c.502A>G	c.(502-504)Att>Gtt	p.I168V	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	168	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCAAAACAATATTGAGAACTA	0.468																																					p.I168V		Atlas-SNP	.											.	PCDHB8	199	.	0			c.A502G						.						64	99	87					5																	140558117		2203	4300	6503	SO:0001583	missense	56128	exon1			AACAATATTGAGA	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.502A>G	chr5.hg19:g.140558117A>G	ENSP00000239444:p.Ile168Val	512.0	0.0		352.0	71.0	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	hg19	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	a	0.202	-1.043999	0.01997	.	.	ENSG00000120322	ENST00000239444	T	0.50001	0.76	4.25	-1.6	0.08426	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.19046	0.0457	N	0.03016	-0.435	0.09310	N	1	B	0.10296	0.003	B	0.17979	0.02	T	0.23261	-1.0193	9	0.25106	T	0.35	.	5.2872	0.15708	0.507:0.2613:0.2317:0.0	.	168	Q9UN66	PCDB8_HUMAN	V	168	ENSP00000239444:I168V	ENSP00000239444:I168V	I	+	1	0	PCDHB8	140538301	0.000000	0.05858	0.002000	0.10522	0.183000	0.23260	-2.354000	0.01089	0.076000	0.16826	0.477000	0.44152	ATT	.	.		0.468	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		G	140558117	A	G	140558117	3	3	76	1	0	0	0	0	1	0	0	0	11557	449	16	2	504	2	PCDHB8	5	140558117	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	126109	140558117	40357143	104	10375										
JAKMIP2	9832	hgsc.bcm.edu	37	chr5	147030071	147030071	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggtctccagttccttttccaGggaaaagatgatcctgtcct	9	11	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:147030071G>A	ENST00000265272.5	-	4	1134	c.667C>T	c.(667-669)Ctg>Ttg	p.L223L	JAKMIP2_ENST00000507386.1_Silent_p.L223L|JAKMIP2_ENST00000333010.6_Silent_p.L181L	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	223						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTTTTCCAGGGAAAAGATG	0.413																																					p.L223L		Atlas-SNP	.											.	JAKMIP2	154	.	0			c.C667T						.						88	86	86					5																	147030071		2203	4300	6503	SO:0001819	synonymous_variant	9832	exon4			TTTCCAGGGAAAA	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.667C>T	chr5.hg19:g.147030071G>A		163.0	0.0		138.0	51.0	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Silent	SNP	ENST00000265272.5	hg19	CCDS4285.1																																																																																			.	.		0.413	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790		A	147030071	G	A	147030071	2	1	76	1	0	0	0	0	0	0	0	1	7950	991	35	3		3	JAKMIP2	5	147030071	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	6471954	147030071	33885189	105	10376										
SLC36A3	285641	hgsc.bcm.edu	37	chr5	150678223	150678223	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccaatgttgcatttcaacaaGtggatcaaagtttgcatcat	7	8	3	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:150678223G>T	ENST00000335230.3	-	2	561	c.150C>A	c.(148-150)caC>caA	p.H50Q	SLC36A3_ENST00000377713.3_Missense_Mutation_p.H50Q	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	50						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATTTCAACAAGTGGATCAAAG	0.532																																					p.H50Q		Atlas-SNP	.											.	SLC36A3	54	.	0			c.C150A						.						112	98	103					5																	150678223		2203	4300	6503	SO:0001583	missense	285641	exon2			CAACAAGTGGATC	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"Solute carriers"	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.150C>A	chr5.hg19:g.150678223G>T	ENSP00000334750:p.His50Gln	94.0	0.0		73.0	15.0	NM_181774	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Missense_Mutation	SNP	ENST00000335230.3	hg19	CCDS4314.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.920714	0.52653	.	.	ENSG00000186334	ENST00000335230;ENST00000377713	T;T	0.02446	4.29;4.29	4.62	0.254	0.15557	.	0.000000	0.85682	D	0.000000	T	0.18425	0.0442	H	0.96048	3.76	0.38161	D	0.939034	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.02202	-1.1196	10	0.87932	D	0	.	7.0277	0.24950	0.4824:0.0:0.5176:0.0	.	50;50	Q495N2-3;Q495N2	.;S36A3_HUMAN	Q	50	ENSP00000334750:H50Q;ENSP00000366942:H50Q	ENSP00000334750:H50Q	H	-	3	2	SLC36A3	150658416	0.976000	0.34144	0.335000	0.25508	0.966000	0.64601	0.619000	0.24388	0.085000	0.17107	0.655000	0.94253	CAC	.	.		0.532	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774		T	150678223	G	T	150678223	3	4	76	1	0	0	0	0	1	0	0	0	14610	1020	36	3	1425	3	SLC36A3	5	150678223	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	3648152	150678223	30237037	106	10377										
SPARC	6678	hgsc.bcm.edu	37	chr5	151045983	151045983	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tacagggaagatgtacatgtTatagttcttctcgaagtccc	9	8	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:151045983T>A	ENST00000231061.4	-	8	986	c.673A>T	c.(673-675)Aac>Tac	p.N225Y	SPARC_ENST00000537849.1_5'Flank	NM_003118.3	NP_003109.1	P09486	SPRC_HUMAN	secreted protein, acidic, cysteine-rich (osteonectin)	225					blood coagulation (GO:0007596)|bone development (GO:0060348)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|inner ear development (GO:0048839)|lung development (GO:0030324)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|regulation of cell morphogenesis (GO:0022604)|response to cadmium ion (GO:0046686)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to gravity (GO:0009629)|response to L-ascorbic acid (GO:0033591)|response to lead ion (GO:0010288)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nuclear matrix (GO:0016363)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|platelet alpha granule membrane (GO:0031092)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)			central_nervous_system(3)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(196;0.109)|all_hematologic(541;0.122)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;0.00118)		ATGTACATGTTATAGTTCTTC	0.562																																					p.N225Y		Atlas-SNP	.											.	SPARC	38	.	0			c.A673T						.						87	80	82					5																	151045983		2203	4300	6503	SO:0001583	missense	6678	exon8			ACATGTTATAGTT		CCDS4318.1	5q31-q33	2012-10-02			ENSG00000113140	ENSG00000113140			11219	protein-coding gene	gene with protein product	"cysteine-rich protein", "osteonectin"	182120		ON		2838412, 3410046	Standard	NM_003118		Approved		uc003lui.4	P09486	OTTHUMG00000130122	ENST00000231061.4:c.673A>T	chr5.hg19:g.151045983T>A	ENSP00000231061:p.Asn225Tyr	97.0	0.0		88.0	46.0	NM_003118	D3DQH9|Q6IBK4	Missense_Mutation	SNP	ENST00000231061.4	hg19	CCDS4318.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.323168	0.81580	.	.	ENSG00000113140	ENST00000231061;ENST00000538026	T	0.24350	1.86	5.64	4.43	0.53597	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.122706	0.85682	N	0.000000	T	0.39410	0.1077	M	0.78223	2.4	0.58432	D	0.999999	P	0.46784	0.884	P	0.47864	0.559	T	0.43327	-0.9398	10	0.59425	D	0.04	-25.2967	14.0277	0.64594	0.0:0.0:0.1341:0.8659	.	225	P09486	SPRC_HUMAN	Y	225;134	ENSP00000231061:N225Y	ENSP00000231061:N225Y	N	-	1	0	SPARC	151026176	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.602000	0.61098	2.143000	0.66587	0.533000	0.62120	AAC	.	.		0.562	SPARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252430.1	NM_003118		A	151045983	T	A	151045983	3	1	76	1	0	0	0	0	1	0	0	0	15010	1754	61	4	250	4	SPARC	5	151045983	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	367760	151045983	29869277	107	10378										
FAM114A2	10827	hgsc.bcm.edu	37	chr5	153413430	153413430	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tctgccttctcgatgacattTgaaatgccttgtcctaatga	7	10	2	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr5:153413430T>C	ENST00000351797.4	-	4	400	c.324A>G	c.(322-324)tcA>tcG	p.S108S	FAM114A2_ENST00000522858.1_Silent_p.S108S|FAM114A2_ENST00000520313.1_Silent_p.S38S|FAM114A2_ENST00000520667.1_Silent_p.S108S	NM_018691.2	NP_061161.2	Q9NRY5	F1142_HUMAN	family with sequence similarity 114, member A2	108							purine nucleotide binding (GO:0017076)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)|urinary_tract(1)	18						CGATGACATTTGAAATGCCTT	0.333																																					p.S108S		Atlas-SNP	.											.	FAM114A2	51	.	0			c.A324G						.						80	75	77					5																	153413430		2202	4300	6502	SO:0001819	synonymous_variant	10827	exon4			GACATTTGAAATG	AF159700	CCDS4323.1	5q31-q33	2008-06-13	2008-06-13	2008-06-13	ENSG00000055147	ENSG00000055147			1333	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 3"	C5orf3		10843801	Standard	XM_005268359		Approved	133K02	uc003lvc.3	Q9NRY5	OTTHUMG00000130147	ENST00000351797.4:c.324A>G	chr5.hg19:g.153413430T>C		166.0	0.0		151.0	41.0	NM_018691	B2R8D8|Q9H7E0	Silent	SNP	ENST00000351797.4	hg19	CCDS4323.1																																																																																			.	.		0.333	FAM114A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252455.1	NM_018691		C	153413430	T	C	153413430	2	2	76	1	0	0	0	0	0	0	0	1	5409	1799	63	2		2	FAM114A2	5	153413430	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	2367447	153413430	27501830	108	10379										
JARID2	3720	hgsc.bcm.edu	37	chr6	15501254	15501254	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagacatgctgcgcatccccAgaactgcccaggaccggctg	11	16	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:15501254A>G	ENST00000341776.2	+	8	2306	c.2062A>G	c.(2062-2064)Aga>Gga	p.R688G	JARID2_ENST00000397311.3_Missense_Mutation_p.R516G|JARID2_ENST00000541660.1_Missense_Mutation_p.R650G	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	688	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.			R -> K (in Ref. 1; AAC50822). {ECO:0000305}.	central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				GCGCATCCCCAGAACTGCCCA	0.582																																					p.R688G		Atlas-SNP	.											.	JARID2	135	.	0			c.A2062G						.						71	80	77					6																	15501254		2203	4300	6503	SO:0001583	missense	3720	exon8			ATCCCCAGAACTG	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.2062A>G	chr6.hg19:g.15501254A>G	ENSP00000341280:p.Arg688Gly	99.0	0.0		80.0	9.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	hg19	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	A	15.22	2.767569	0.49574	.	.	ENSG00000008083	ENST00000341776;ENST00000397311;ENST00000541660	T;T;T	0.62498	0.02;0.02;0.02	5.15	5.15	0.70609	ARID/BRIGHT DNA-binding domain (5);	0.138580	0.64402	D	0.000005	T	0.38241	0.1033	L	0.48642	1.525	0.32039	N	0.598512	P;B	0.36465	0.554;0.175	B;B	0.26770	0.073;0.037	T	0.52624	-0.8551	10	0.72032	D	0.01	-2.5951	14.9738	0.71254	1.0:0.0:0.0:0.0	.	650;688	F5H590;Q92833	.;JARD2_HUMAN	G	688;516;650	ENSP00000341280:R688G;ENSP00000380478:R516G;ENSP00000444623:R650G	ENSP00000341280:R688G	R	+	1	2	JARID2	15609233	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.836000	0.69375	1.941000	0.56285	0.459000	0.35465	AGA	.	.		0.582	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		G	15501254	A	G	15501254	3	3	76	1	0	0	0	0	1	0	0	0	7954	180	7	2	2092	2	JARID2	6	15501254	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10		15501254	155613813	109	10380										
HIST1H3I	8354	hgsc.bcm.edu	37	chr6	27839739	27839739	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gatgtctttaggcataatagTgacgcgtttggcgtgaatgg	14	5	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:27839739T>G	ENST00000328488.2	-	1	360	c.355A>C	c.(355-357)Act>Cct	p.T119P		NM_003533.2	NP_003524.1	P68431	H31_HUMAN	histone cluster 1, H3i	119					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GGCATAATAGTGACGCGTTTG	0.572																																					p.T119P		Atlas-SNP	.											.	HIST1H3I	28	.	0			c.A355C						.						131	142	138					6																	27839739		2203	4300	6503	SO:0001583	missense	8354	exon1			TAATAGTGACGCG	X83550	CCDS4636.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000182572	ENSG00000275379		"Histones / Replication-dependent"	4771	protein-coding gene	gene with protein product		602814	"H3 histone family, member F", "histone 1, H3i"	H3FF		9031620, 9439656, 12408966	Standard	NM_003533		Approved	H3/f, H3.f	uc003njy.3	P68431	OTTHUMG00000016184	ENST00000328488.2:c.355A>C	chr6.hg19:g.27839739T>G	ENSP00000329554:p.Thr119Pro	111.0	0.0		101.0	39.0	NM_003533	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000328488.2	hg19	CCDS4636.1	.	.	.	.	.	.	.	.	.	.	T	11.96	1.795799	0.31777	.	.	ENSG00000182572	ENST00000328488	T	0.75367	-0.93	4.12	4.12	0.48240	.	.	.	.	.	T	0.77485	0.4137	.	.	.	0.42515	D	0.992982	.	.	.	.	.	.	T	0.81337	-0.0978	6	0.87932	D	0	.	13.3331	0.60500	0.0:0.0:0.0:1.0	.	.	.	.	P	119	ENSP00000329554:T119P	ENSP00000329554:T119P	T	-	1	0	HIST1H3I	27947718	1.000000	0.71417	1.000000	0.80357	0.415000	0.31203	7.579000	0.82511	2.086000	0.62901	0.528000	0.53228	ACT	.	.		0.572	HIST1H3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043452.1	NM_003533		G	27839739	T	G	27839739	3	3	76	1	0	0	0	0	1	0	0	0	7172	1696	59	5	59	5	HIST1H3I	6	27839739	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	12338485	27839739	143275328	110	10381										
OR2B2	81697	hgsc.bcm.edu	37	chr6	27879561	27879561	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttgagcagagcagggacttcAcagaagaagtgatccacttc	11	9	1	5			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:27879561A>G	ENST00000303324.2	-	1	613	c.537T>C	c.(535-537)tgT>tgC	p.C179C		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						CAGGGACTTCACAGAAGAAGT	0.453																																					p.C179C		Atlas-SNP	.											.	OR2B2	54	.	0			c.T537C						.						99	92	94					6																	27879561		2203	4300	6503	SO:0001819	synonymous_variant	81697	exon1			GACTTCACAGAAG	Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"GPCR / Class A : Olfactory receptors"	13966	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily B, member 9"	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.537T>C	chr6.hg19:g.27879561A>G		75.0	0.0		76.0	28.0	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Silent	SNP	ENST00000303324.2	hg19	CCDS4641.1																																																																																			.	.		0.453	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1			G	27879561	A	G	27879561	2	3	76	1	0	0	0	0	0	0	0	1	10998	157	6	2		2	OR2B2	6	27879561	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	39822	27879561	143235506	111	10382										
TRIM27	5987	hgsc.bcm.edu	37	chr6	28876789	28876789	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctccgtcaagaatagacattTttgggcaaaaatgtggattt	9	6	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:28876789T>A	ENST00000377199.3	-	5	1203	c.847A>T	c.(847-849)Aaa>Taa	p.K283*	TRIM27_ENST00000498117.1_5'Flank|TRIM27_ENST00000377194.3_Nonsense_Mutation_p.K283*	NM_006510.4	NP_006501.1	P14373	TRI27_HUMAN	tripartite motif containing 27	283					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell proliferation (GO:0008283)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|negative regulation of adaptive immune response (GO:0002820)|negative regulation of calcium ion import (GO:0090281)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of interleukin-2 secretion (GO:1900041)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						AATAGACATTTTTGGGCAAAA	0.393			T	RET	papillary thyroid																																p.K283X		Atlas-SNP	.		Dom	yes		6	6p22	5987	tripartite motif-containing 27		E	.	TRIM27	26	.	0			c.A847T						.						81	83	82					6																	28876789		2203	4300	6503	SO:0001587	stop_gained	5987	exon5			GACATTTTTGGGC	Z58939	CCDS4654.1	6p22	2013-01-09	2011-01-25	2006-09-26	ENSG00000204713	ENSG00000204713		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9975	protein-coding gene	gene with protein product		602165	"ret finger protein", "tripartite motif-containing 27"	RFP		8114113	Standard	NM_006510		Approved	RNF76	uc003nlr.3	P14373	OTTHUMG00000031215	ENST00000377199.3:c.847A>T	chr6.hg19:g.28876789T>A	ENSP00000366404:p.Lys283*	135.0	0.0		201.0	45.0	NM_006510	A2BE15|Q5RJA8|Q5ST26|Q6LA73|Q6NXR9|Q9BZY6|Q9UJL3	Nonsense_Mutation	SNP	ENST00000377199.3	hg19	CCDS4654.1	.	.	.	.	.	.	.	.	.	.	T	42	9.282718	0.99123	.	.	ENSG00000204713	ENST00000377199;ENST00000377194	.	.	.	4.47	4.47	0.54385	.	0.000000	0.56097	D	0.000021	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4452	0.44490	0.0:0.0:0.0:1.0	.	.	.	.	X	283	.	ENSP00000366399:K283X	K	-	1	0	TRIM27	28984768	0.993000	0.37304	1.000000	0.80357	0.959000	0.62525	1.997000	0.40786	2.241000	0.73720	0.533000	0.62120	AAA	.	.		0.393	TRIM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076442.2	NM_030950		A	28876789	T	A	28876789	4	1	76	1	0	0	0	0	0	1	0	0	16516	1850	64	4	710	4	TRIM27	6	28876789	Nonsense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	997228	28876789	142238278	112	10383										
ZNF311	282890	hgsc.bcm.edu	37	chr6	28963167	28963167	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	attggtcaagtttgacttccCactgaaagctttcccacact	6	12	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:28963167C>A	ENST00000377179.3	-	7	2124	c.1612G>T	c.(1612-1614)Ggg>Tgg	p.G538W	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	538					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						TTTGACTTCCCACTGAAAGCT	0.443																																					p.G538W		Atlas-SNP	.											.	ZNF311	59	.	0			c.G1612T						.						93	87	89					6																	28963167		1511	2709	4220	SO:0001583	missense	282890	exon7			ACTTCCCACTGAA	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"Zinc fingers, C2H2-type", "-"	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.1612G>T	chr6.hg19:g.28963167C>A	ENSP00000366384:p.Gly538Trp	121.0	0.0		87.0	8.0	NM_001010877	A2BFK5|B0S7Y4|Q92971	Missense_Mutation	SNP	ENST00000377179.3	hg19	CCDS34357.1	.	.	.	.	.	.	.	.	.	.	C	9.143	1.014365	0.19277	.	.	ENSG00000197935	ENST00000377179;ENST00000535083	T	0.07688	3.17	3.59	1.44	0.22558	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00875	0.0029	N	0.02985	-0.445	0.09310	N	1	B	0.15141	0.012	B	0.12156	0.007	T	0.47923	-0.9079	9	0.33940	T	0.23	-6.2223	1.7053	0.02881	0.2174:0.4475:0.2117:0.1234	.	538	Q5JNZ3	ZN311_HUMAN	W	538;446	ENSP00000366384:G538W	ENSP00000366384:G538W	G	-	1	0	ZNF311	29071146	0.000000	0.05858	0.424000	0.26647	0.547000	0.35210	-0.965000	0.03829	0.744000	0.32741	0.585000	0.79938	GGG	.	.		0.443	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581		A	28963167	C	A	28963167	3	1	76	1	0	0	0	0	1	0	0	0	17849	594	21	3	392	3	ZNF311	6	28963167	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	86378	28963167	142151900	113	10384										
OR12D3	81797	hgsc.bcm.edu	37	chr6	29342442	29342442	+	Frame_Shift_Del	DEL	G	G	-													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agagaagagtcagaaagaaaGctcccatggatatgctgcct							TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:29342442delG	ENST00000396806.3	-	1	626	c.623delC	c.(622-624)gctfs	p.A208fs	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						CAGAAAGAAAGCTCCCATGGA	0.453																																					p.A208fs		Atlas-Indel,Pindel	.											.	OR12D3	55	.	0			c.624delT						.						77	82	80					6																	29342442		1511	2709	4220	SO:0001589	frameshift_variant	81797	exon1			.		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"GPCR / Class A : Olfactory receptors"	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.623delC	chr6.hg19:g.29342442delG	ENSP00000380023:p.Ala208fs	74.0	0.0		67.0	16.0	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Frame_Shift_Del	DEL	ENST00000396806.3	hg19	CCDS4658.1																																																																																			.	.		0.453	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3			-	29342442	G	-	29342442	7	5	76	1	0	1	0	1	0	0	0	0	10941	971	34	0	331	0	OR12D3	6	29342442	Frame_Shift_Del	DEL	G	TCGA-CC-A7IK-01A-12D-A33Q-10	379275	29342442	141772625	114	10385										
ATF6B	1388	hgsc.bcm.edu	37	chr6	32085719	32085719	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agaggttcaactccctgaacTggctcttgctctgagaaccc	9	13	3	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:32085719T>A	ENST00000375203.3	-	12	1373	c.1341A>T	c.(1339-1341)ccA>ccT	p.P447P	ATF6B_ENST00000375201.4_Silent_p.P444P	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	447					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						CTCCCTGAACTGGCTCTTGCT	0.607																																					p.P447P		Atlas-SNP	.											.	ATF6B	40	.	0			c.A1341T						.						47	49	48					6																	32085719		2203	4300	6503	SO:0001819	synonymous_variant	1388	exon12			CTGAACTGGCTCT		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"basic leucine zipper proteins"	2349	protein-coding gene	gene with protein product		600984	"cAMP responsive element binding protein-like 1"	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.1341A>T	chr6.hg19:g.32085719T>A		90.0	0.0		107.0	32.0	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Silent	SNP	ENST00000375203.3	hg19	CCDS4737.1																																																																																			.	.		0.607	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2			A	32085719	T	A	32085719	2	1	76	1	0	0	0	0	0	0	0	1	1085	1567	55	4		4	ATF6B	6	32085719	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	2743277	32085719	139029348	115	10386										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32163815	32163815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tacgttggtgagcgacgtccGccggcgctagcccagcctgg	15	14	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:32163815G>A	ENST00000375023.3	-	30	5549	c.5411C>T	c.(5410-5412)gCg>gTg	p.A1804V	GPSM3_ENST00000375043.3_5'Flank|NOTCH4_ENST00000443903.2_Silent_p.G180G	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1804					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						AGCGACGTCCGCCGGCGCTAG	0.701																																					p.A1804V		Atlas-SNP	.											.	NOTCH4	201	.	0			c.C5411T						.						8	10	10					6																	32163815		1393	2625	4018	SO:0001583	missense	4855	exon30			ACGTCCGCCGGCG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.5411C>T	chr6.hg19:g.32163815G>A	ENSP00000364163:p.Ala1804Val	9.0	0.0		21.0	13.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.528618	0.27299	.	.	ENSG00000204301	ENST00000375023	T	0.70986	-0.53	4.71	-6.15	0.02105	Ankyrin repeat-containing domain (3);	1.684020	0.03641	N	0.239512	T	0.33990	0.0882	N	0.16833	0.445	0.09310	N	0.999995	B;P	0.37158	0.207;0.585	B;B	0.24848	0.056;0.036	T	0.32719	-0.9896	10	0.62326	D	0.03	.	18.8395	0.92177	0.0:0.1482:0.7799:0.0719	.	1804;1803	Q99466;B0S882	NOTC4_HUMAN;.	V	1804	ENSP00000364163:A1804V	ENSP00000364163:A1804V	A	-	2	0	NOTCH4	32271793	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	0.383000	0.20651	-0.972000	0.03559	-0.344000	0.07964	GCG	.	.		0.701	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32163815	G	A	32163815	3	1	76	1	0	0	0	0	1	0	0	0	10560	1087	38	1	604	1	NOTCH4	6	32163815	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	78096	32163815	138951252	116	10387										
PRICKLE4	29964	hgsc.bcm.edu	37	chr6	41754576	41754595	+	Frame_Shift_Del	DEL	CGCTGCTGCCGGCGGTTCCA	CGCTGCTGCCGGCGGTTCCA	-													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	accctctcccgaacactcctCgctgctgccggcggttccag					rs9381093|rs201760202|rs191020519	byFrequency	TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	CGCTGCTGCCGGCGGTTCCA	CGCTGCTGCCGGCGGTTCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:41754576_41754595delCGCTGCTGCCGGCGGTTCCA	ENST00000394260.1	+	5	744_763	c.744_763delCGCTGCTGCCGGCGGTTCCA	c.(742-765)ctcgctgctgccggcggttccagcfs	p.AAAGGSS249fs	PRICKLE4_ENST00000394263.1_Frame_Shift_Del_p.AAAGGSS289fs|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000458694.1_Frame_Shift_Del_p.AAAGGSS289fs|TOMM6_ENST00000398884.3_5'Flank			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	249						nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.A289T(2)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GAACACTCCTCGCTGCTGCCGGCGGTTCCAGCCTGCAAAC	0.641											OREG0017435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.288_294del		Pindel	.											.,2	PRICKLE4	29	.	2	Substitution - Missense(2)	central_nervous_system(2)	c.863_882del						.																																			SO:0001589	frameshift_variant	29964	exon8			.	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"chromosome 6 open reading frame 49"	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.744_763delCGCTGCTGCCGGCGGTTCCA	chr6.hg19:g.41754576_41754595delCGCTGCTGCCGGCGGTTCCA	ENSP00000377803:p.Ala249fs	63.0	0.0	903	72.0	18.0	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Frame_Shift_Del	DEL	ENST00000394260.1	hg19																																																																																				.	.		0.641	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397		-	41754595	CGCTGCTGCCGGCGGTTCCA	-	41754576	7	5	76	1	0	1	0	1	0	0	0	0	12501	871	31	0	886	0	PRICKLE4	6	41754576	Frame_Shift_Del	DEL	CGCTGCTGCCGGCGGTTCCA	TCGA-CC-A7IK-01A-12D-A33Q-10	9590761	41754576	129360491	117	10388										
PRICKLE4	29964	hgsc.bcm.edu	37	chr6	41754595	41754596	+	Frame_Shift_Ins	INS	-	-	GC													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cgctgctgccggcggttccaINSgcctgcaaactcagaggggg							TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:41754595_41754596insGC	ENST00000394260.1	+	5	763_764	c.763_764insGC	c.(763-765)agcfs	p.S255fs	PRICKLE4_ENST00000394263.1_Frame_Shift_Ins_p.S295fs|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000458694.1_Frame_Shift_Ins_p.S295fs|TOMM6_ENST00000398884.3_5'Flank			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	255						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CGGCGGTTCCAGCCTGCAAACT	0.629											OREG0017435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S295fs		Atlas-INDEL	.											.	PRICKLE4	29	.	0			c.883_884insGC						.																																			SO:0001589	frameshift_variant	29964	exon8			.	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"chromosome 6 open reading frame 49"	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.764_765dupGC	chr6.hg19:g.41754596_41754597dupGC	ENSP00000377803:p.Ser255fs	57.0	0.0	903	76.0	39.0	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Frame_Shift_Ins	INS	ENST00000394260.1	hg19																																																																																				.	.		0.629	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397		GC	41754596	-	GC	41754595	7	5	76	1	0	1	1	0	0	0	0	0	12501	188	7	0	905	0	PRICKLE4	6	41754595	Frame_Shift_Ins	INS	-	TCGA-CC-A7IK-01A-12D-A33Q-10	19	41754595	129360472	118	10389										
GPR116	221395	hgsc.bcm.edu	37	chr6	46828555	46828555	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aagagctgatttcatgttccGctttgtctatgctaatagaa	8	7	2	3	rs375753155		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:46828555G>A	ENST00000283296.7	-	16	2564	c.2276C>T	c.(2275-2277)gCg>gTg	p.A759V	GPR116_ENST00000545669.1_Missense_Mutation_p.A188V|GPR116_ENST00000456426.2_Missense_Mutation_p.A617V|GPR116_ENST00000265417.7_Missense_Mutation_p.A759V|GPR116_ENST00000362015.4_Missense_Mutation_p.A759V	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	759					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			TTCATGTTCCGCTTTGTCTAT	0.428																																					p.A759V	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.C2276T						.	G	VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	128	124	126		2276,2276	-4.1	0	6		126	0,8600		0,0,4300	no	missense,missense	GPR116	NM_001098518.1,NM_015234.4	64,64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	759/1347,759/1347	46828555	1,13005	2203	4300	6503	SO:0001583	missense	221395	exon16			TGTTCCGCTTTGT	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.2276C>T	chr6.hg19:g.46828555G>A	ENSP00000283296:p.Ala759Val	91.0	0.0		78.0	37.0	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	hg19	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	G	4.745	0.138528	0.09083	2.27E-4	0.0	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000545557;ENST00000265417;ENST00000545669	T;T;T;T;T	0.27402	1.73;2.11;1.73;1.73;1.67	5.68	-4.13	0.03904	.	1.380720	0.04734	N	0.421705	T	0.02304	0.0071	N	0.01576	-0.805	0.09310	N	1	B;B;B;B;B	0.15719	0.0;0.0;0.001;0.014;0.001	B;B;B;B;B	0.11329	0.001;0.001;0.0;0.006;0.0	T	0.28202	-1.0051	10	0.26408	T	0.33	-0.3707	0.8708	0.01213	0.4398:0.1117:0.165:0.2835	.	188;314;759;617;759	F5GWK9;B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;.;GP116_HUMAN	V	759;759;759;617;130;759;188	ENSP00000283296:A759V;ENSP00000354563:A759V;ENSP00000412866:A617V;ENSP00000265417:A759V;ENSP00000441581:A188V	ENSP00000265417:A759V	A	-	2	0	GPR116	46936514	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.357000	0.07651	-0.490000	0.06707	-1.119000	0.02030	GCG	.	.		0.428	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		A	46828555	G	A	46828555	3	1	76	1	0	0	0	0	1	0	0	0	6641	1087	38	1	1788	1	GPR116	6	46828555	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	5073960	46828555	124286512	119	10390										
DEFB113	245927	hgsc.bcm.edu	37	chr6	49937328	49937328	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caaaggtcagaaaaatacaaAgtatcttcattgctgatgca	7	7	3	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:49937328A>C	ENST00000398718.1	-	1	10	c.11T>G	c.(10-12)cTt>cGt	p.L4R		NM_001037729.1	NP_001032818.1	Q30KQ7	DB113_HUMAN	defensin, beta 113	4					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Lung NSC(77;0.042)					AAAAATACAAAGTATCTTCAT	0.343																																					p.L4R		Atlas-SNP	.											.	DEFB113	18	.	0			c.T11G						.						104	103	103					6																	49937328		1857	4087	5944	SO:0001583	missense	245927	exon1			ATACAAAGTATCT	DQ012017	CCDS43472.1	6p12.3	2010-03-30			ENSG00000214642	ENSG00000214642		"Defensins, beta"	18094	protein-coding gene	gene with protein product						11854508, 16033865	Standard	NM_001037729		Approved	DEFB-13	uc011dwq.2	Q30KQ7	OTTHUMG00000160210	ENST00000398718.1:c.11T>G	chr6.hg19:g.49937328A>C	ENSP00000381703:p.Leu4Arg	52.0	0.0		89.0	8.0	NM_001037729		Missense_Mutation	SNP	ENST00000398718.1	hg19	CCDS43472.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.820101	0.32145	.	.	ENSG00000214642	ENST00000398718	.	.	.	4.06	4.06	0.47325	.	.	.	.	.	T	0.38719	0.1051	.	.	.	0.09310	N	1	D	0.58970	0.984	P	0.57371	0.819	T	0.12682	-1.0538	6	.	.	.	-2.1036	9.5877	0.39526	1.0:0.0:0.0:0.0	.	4	Q30KQ7	DB113_HUMAN	R	4	.	.	L	-	2	0	DEFB113	50045287	0.173000	0.23056	0.015000	0.15790	0.347000	0.29111	3.461000	0.53035	1.834000	0.53371	0.482000	0.46254	CTT	.	.		0.343	DEFB113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359666.1			C	49937328	A	C	49937328	3	2	76	1	0	0	0	0	1	0	0	0	4404	72	3	5	237	5	DEFB113	6	49937328	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	3108773	49937328	121177739	120	10391										
BAI3	577	hgsc.bcm.edu	37	chr6	70092727	70092727	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttgttcttttttgcagaaggTcatgcatacaaggaagaggc	11	6	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:70092727T>C	ENST00000370598.1	+	31	5101	c.4280T>C	c.(4279-4281)gTc>gCc	p.V1427A	BAI3_ENST00000238918.8_Missense_Mutation_p.V633A|BAI3_ENST00000546190.1_Missense_Mutation_p.V391A	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1427					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V1427G(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TTGCAGAAGGTCATGCATACA	0.328																																					p.V1427A		Atlas-SNP	.											BAI3,NS,carcinoma,0,1	BAI3	451	.	1	Substitution - Missense(1)	lung(1)	c.T4280C						.						98	97	97					6																	70092727		2203	4300	6503	SO:0001583	missense	577	exon31			AGAAGGTCATGCA	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.4280T>C	chr6.hg19:g.70092727T>C	ENSP00000359630:p.Val1427Ala	83.0	0.0		74.0	26.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.515019	0.85389	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.15017	2.46;2.46;2.46	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.27419	0.0673	L	0.52573	1.65	0.51233	D	0.999918	P;D	0.69078	0.924;0.997	P;D	0.72625	0.857;0.978	T	0.02646	-1.1129	10	0.87932	D	0	.	15.708	0.77602	0.0:0.0:0.0:1.0	.	633;1427	B7Z356;O60242	.;BAI3_HUMAN	A	1427;633;391	ENSP00000359630:V1427A;ENSP00000238918:V633A;ENSP00000441821:V391A	ENSP00000238918:V633A	V	+	2	0	BAI3	70149448	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.668000	0.83897	2.104000	0.64026	0.482000	0.46254	GTC	.	.		0.328	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			C	70092727	T	C	70092727	3	2	76	1	0	0	0	0	1	0	0	0	1300	1667	58	2	4394	2	BAI3	6	70092727	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	20155399	70092727	101022340	121	10392										
C6orf57	135154	hgsc.bcm.edu	37	chr6	71289154	71289154	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cattctctgaggaaaacaagTtcttctcaaggaggaaagtc	9	8	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:71289154T>G	ENST00000370474.3	+	2	126	c.102T>G	c.(100-102)agT>agG	p.S34R		NM_145267.2	NP_660310.2	Q5VUM1	SDHF4_HUMAN	chromosome 6 open reading frame 57	34					innate immune response (GO:0045087)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)				kidney(1)|lung(1)|skin(1)	3						GGAAAACAAGTTCTTCTCAAG	0.393																																					p.S34R		Atlas-SNP	.											.	C6orf57	13	.	0			c.T102G						.						100	99	99					6																	71289154		2203	4300	6503	SO:0001583	missense	135154	exon2			AACAAGTTCTTCT	BC018085	CCDS4972.1	6q12	2011-12-13			ENSG00000154079	ENSG00000154079			20957	protein-coding gene	gene with protein product							Standard	NM_145267		Approved		uc003pfq.1	Q5VUM1	OTTHUMG00000014992	ENST00000370474.3:c.102T>G	chr6.hg19:g.71289154T>G	ENSP00000359505:p.Ser34Arg	94.0	0.0		102.0	30.0	NM_145267	E1P532	Missense_Mutation	SNP	ENST00000370474.3	hg19	CCDS4972.1	.	.	.	.	.	.	.	.	.	.	T	12.51	1.958672	0.34565	.	.	ENSG00000154079	ENST00000370474	T	0.33654	1.4	4.47	3.3	0.37823	.	0.811929	0.11927	N	0.516110	T	0.09642	0.0237	N	0.24115	0.695	0.29679	N	0.841869	P	0.48911	0.917	B	0.38655	0.278	T	0.07009	-1.0795	10	0.52906	T	0.07	-0.7049	5.2358	0.15445	0.0:0.2001:0.0:0.7999	.	34	Q5VUM1	CF057_HUMAN	R	34	ENSP00000359505:S34R	ENSP00000359505:S34R	S	+	3	2	C6orf57	71345875	0.998000	0.40836	0.985000	0.45067	0.672000	0.39443	0.267000	0.18552	1.768000	0.52137	0.472000	0.43445	AGT	.	.		0.393	C6orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041140.1	NM_145267		G	71289154	T	G	71289154	3	3	76	1	0	0	0	0	1	0	0	0	2368	1722	60	5	108	5	C6orf57	6	71289154	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	1196427	71289154	99825913	122	10393										
CD109	135228	hgsc.bcm.edu	37	chr6	74407156	74407156	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gtgacagccccagggatcatCaggcccggaggaaatgtgac	14	11	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:74407156C>T	ENST00000287097.5	+	2	220	c.108C>T	c.(106-108)atC>atT	p.I36I	CD109_ENST00000437994.2_Silent_p.I36I|CD109_ENST00000422508.2_Silent_p.I36I|RP11-553A21.3_ENST00000428865.2_RNA			Q6YHK3	CD109_HUMAN	CD109 molecule	36					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CAGGGATCATCAGGCCCGGAG	0.507																																					p.I36I		Atlas-SNP	.											.	CD109	170	.	0			c.C108T						.						112	111	111					6																	74407156		2203	4300	6503	SO:0001819	synonymous_variant	135228	exon2			GATCATCAGGCCC	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.108C>T	chr6.hg19:g.74407156C>T		71.0	0.0		71.0	23.0	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	hg19	CCDS4982.1																																																																																			.	.		0.507	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		T	74407156	C	T	74407156	2	4	76	1	0	0	0	0	0	0	0	1	2965	816	29	3		3	CD109	6	74407156	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	3118002	74407156	96707911	123	10394										
HTR1B	3351	hgsc.bcm.edu	37	chr6	78172967	78172967	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gagcgccaatagcataaccaGcagtactttccagggtaggg	12	10	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:78172967G>T	ENST00000369947.2	-	1	523	c.154C>A	c.(154-156)Ctg>Atg	p.L52M		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	52					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	AGCATAACCAGCAGTACTTTC	0.547																																					p.L52M		Atlas-SNP	.											.	HTR1B	55	.	0			c.C154A						.						233	208	216					6																	78172967		2203	4300	6503	SO:0001583	missense	3351	exon1			TAACCAGCAGTAC	BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5287	protein-coding gene	gene with protein product		182131	"5-hydroxytryptamine (serotonin) receptor 1B"			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.154C>A	chr6.hg19:g.78172967G>T	ENSP00000358963:p.Leu52Met	162.0	0.0		149.0	95.0	NM_000863	Q4VAY7	Missense_Mutation	SNP	ENST00000369947.2	hg19	CCDS4986.1	.	.	.	.	.	.	.	.	.	.	G	5.405	0.259832	0.10239	.	.	ENSG00000135312	ENST00000369947	T	0.00551	6.65	4.88	2.12	0.27331	.	0.179711	0.37095	N	0.002248	T	0.00178	0.0005	N	0.24115	0.695	0.46798	D	0.999205	P	0.36065	0.535	B	0.42959	0.403	T	0.71220	-0.4657	9	.	.	.	.	4.9734	0.14127	0.2463:0.1543:0.5994:0.0	.	52	P28222	5HT1B_HUMAN	M	52	ENSP00000358963:L52M	.	L	-	1	2	HTR1B	78229686	0.997000	0.39634	0.248000	0.24265	0.353000	0.29299	1.508000	0.35769	0.269000	0.21961	0.561000	0.74099	CTG	.	.		0.547	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863		T	78172967	G	T	78172967	3	4	76	1	0	0	0	0	1	0	0	0	7446	962	34	3	1022	3	HTR1B	6	78172967	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	3765811	78172967	92942100	124	10395										
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83862023	83862023	+	Silent	SNP	A	A	G													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atagatatgttatcacctgcAatggaaaccgcaaacataac							TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:83862023A>G	ENST00000349129.2	+	30	6326	c.6066A>G	c.(6064-6066)gcA>gcG	p.A2022A	DOPEY1_ENST00000369739.3_Silent_p.A2013A|DOPEY1_ENST00000237163.5_Intron|DOPEY1_ENST00000484282.1_3'UTR	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2022					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TATCACCTGCAATGGAAACCG	0.318																																					p.A2022A		Atlas-SNP	.											.	DOPEY1	190	.	0			c.A6066G						.						62	62	62					6																	83862023		2203	4294	6497	SO:0001819	synonymous_variant	23033	exon30			ACCTGCAATGGAA	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.6066A>G	chr6.hg19:g.83862023A>G		124.0	0.0		109.0	36.0	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	hg19	CCDS4996.1																																																																																			.	.		0.318	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		G	83862023	A	G	83862023	2	3	76	1	0	0	0	0	0	0	0	1	4709	117	5	2		2	DOPEY1	6	83862023	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	5689056	83862023	87253044	125	10396	42	2								
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83862028	83862028	+	Missense_Mutation	SNP	A	A	C													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tatgttatcacctgcaatggAaaccgcaaacataactcctt							TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:83862028A>C	ENST00000349129.2	+	30	6331	c.6071A>C	c.(6070-6072)gAa>gCa	p.E2024A	DOPEY1_ENST00000369739.3_Missense_Mutation_p.E2015A|DOPEY1_ENST00000237163.5_Intron|DOPEY1_ENST00000484282.1_3'UTR	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2024					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CCTGCAATGGAAACCGCAAAC	0.328																																					p.E2024A		Atlas-SNP	.											.	DOPEY1	190	.	0			c.A6071C						.						64	64	64					6																	83862028		2203	4294	6497	SO:0001583	missense	23033	exon30			CAATGGAAACCGC	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.6071A>C	chr6.hg19:g.83862028A>C	ENSP00000195654:p.Glu2024Ala	124.0	0.0		108.0	37.0	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	hg19	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	A	2.077	-0.411745	0.04799	.	.	ENSG00000083097	ENST00000349129	T	0.24151	1.87	6.06	4.89	0.63831	.	0.145312	0.64402	D	0.000011	T	0.07818	0.0196	L	0.43152	1.355	0.80722	D	1	P;B;B	0.41080	0.737;0.278;0.278	B;B;B	0.31290	0.127;0.057;0.057	T	0.13980	-1.0489	10	0.21014	T	0.42	.	10.7188	0.46028	0.9282:0.0:0.0718:0.0	.	1915;2015;2024	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	A	2024	ENSP00000195654:E2024A	ENSP00000195654:E2024A	E	+	2	0	DOPEY1	83918747	1.000000	0.71417	1.000000	0.80357	0.194000	0.23727	6.600000	0.74132	1.105000	0.41606	0.533000	0.62120	GAA	.	.		0.328	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		C	83862028	A	C	83862028	3	2	76	1	0	0	0	0	1	0	0	0	4709	246	9	5	6181	5	DOPEY1	6	83862028	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	5	83862028	87253039	126	10397	42	2								
FUT9	10690	hgsc.bcm.edu	37	chr6	96651917	96651917	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tggaagattataactctcccAgtgagctagcaaagtatctg	9	8	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:96651917A>T	ENST00000302103.5	+	3	1212	c.886A>T	c.(886-888)Agt>Tgt	p.S296C		NM_006581.3	NP_006572.2	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3) fucosyltransferase)	296					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	34		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		TAACTCTCCCAGTGAGCTAGC	0.388																																					p.S296C	Melanoma(98;1369 1476 6592 22940 26587)	Atlas-SNP	.											FUT9,colon,carcinoma,0,1	FUT9	79	.	0			c.A886T						.						69	68	68					6																	96651917		2203	4300	6503	SO:0001583	missense	10690	exon3			TCTCCCAGTGAGC	AB023021	CCDS5033.1	6q16	2013-02-26			ENSG00000172461	ENSG00000172461		"Fucosyltransferases"	4020	protein-coding gene	gene with protein product		606865				10386598, 10575236	Standard	NM_006581		Approved	Fuc-TIX	uc003pop.4	Q9Y231	OTTHUMG00000015236	ENST00000302103.5:c.886A>T	chr6.hg19:g.96651917A>T	ENSP00000302599:p.Ser296Cys	51.0	0.0		56.0	8.0	NM_006581	Q5T0W4	Missense_Mutation	SNP	ENST00000302103.5	hg19	CCDS5033.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.302826	0.60195	.	.	ENSG00000172461	ENST00000302103	T	0.26518	1.73	5.5	4.35	0.52113	.	0.134780	0.64402	D	0.000002	T	0.23572	0.0570	L	0.56199	1.76	0.32758	N	0.505442	P	0.45240	0.854	P	0.52627	0.704	T	0.05666	-1.0871	10	0.87932	D	0	-15.2491	10.0915	0.42449	0.9217:0.0:0.0783:0.0	.	296	Q9Y231	FUT9_HUMAN	C	296	ENSP00000302599:S296C	ENSP00000302599:S296C	S	+	1	0	FUT9	96758638	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.049000	0.64244	2.091000	0.63221	0.383000	0.25322	AGT	.	.		0.388	FUT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041554.2	NM_006581		T	96651917	A	T	96651917	3	4	76	1	0	0	0	0	1	0	0	0	6119	188	7	4	888	4	FUT9	6	96651917	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	12789889	96651917	74463150	127	10398										
MICAL1	64780	hgsc.bcm.edu	37	chr6	109766714	109766714	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	attcatggtgcctgaggtctTggcaaaggtctgcagggcct	14	9	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:109766714T>A	ENST00000358807.3	-	21	3003	c.2692A>T	c.(2692-2694)Aag>Tag	p.K898*	MICAL1_ENST00000368952.4_Nonsense_Mutation_p.K917*|MICAL1_ENST00000358577.3_Nonsense_Mutation_p.K812*	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	898					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		CCTGAGGTCTTGGCAAAGGTC	0.567																																					p.K898X		Atlas-SNP	.											.	MICAL1	79	.	0			c.A2692T						.						70	71	70					6																	109766714		2203	4300	6503	SO:0001587	stop_gained	64780	exon21			AGGTCTTGGCAAA	AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"NEDD9 interacting protein with calponin homology and LIM domains"	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.2692A>T	chr6.hg19:g.109766714T>A	ENSP00000351664:p.Lys898*	47.0	0.0		67.0	26.0	NM_022765	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Nonsense_Mutation	SNP	ENST00000358807.3	hg19	CCDS5076.1	.	.	.	.	.	.	.	.	.	.	T	37	6.495916	0.97612	.	.	ENSG00000135596	ENST00000358807;ENST00000368952;ENST00000358577;ENST00000368957;ENST00000335266	.	.	.	5.51	0.524	0.17066	.	0.952738	0.08798	N	0.892250	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.3632	0.26758	0.0:0.3601:0.0:0.6399	.	.	.	.	X	898;917;812;422;154	.	ENSP00000335372:K154X	K	-	1	0	MICAL1	109873407	0.996000	0.38824	0.009000	0.14445	0.029000	0.11900	1.132000	0.31418	0.078000	0.16900	-0.256000	0.11100	AAG	.	.		0.567	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765		A	109766714	T	A	109766714	4	1	76	1	0	0	0	0	0	1	0	0	9578	1821	63	4	531	4	MICAL1	6	109766714	Nonsense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	13114797	109766714	61348353	128	10399										
FIG4	9896	hgsc.bcm.edu	37	chr6	110081565	110081565	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tattgtttatattccctgggAcatggccaagtataccaaaa	7	8	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:110081565A>T	ENST00000230124.3	+	11	1374	c.1250A>T	c.(1249-1251)gAc>gTc	p.D417V	FIG4_ENST00000441478.2_Missense_Mutation_p.D140V	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	417	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		ATTCCCTGGGACATGGCCAAG	0.413																																					p.D417V		Atlas-SNP	.											.	FIG4	77	.	0			c.A1250T						.						184	147	160					6																	110081565		2203	4300	6503	SO:0001583	missense	9896	exon11			CCTGGGACATGGC	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"KIAA0274", "FIG4 homolog (S. cerevisiae)", "FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.1250A>T	chr6.hg19:g.110081565A>T	ENSP00000230124:p.Asp417Val	94.0	0.0		81.0	20.0	NM_014845	Q53H49|Q5TCS6	Missense_Mutation	SNP	ENST00000230124.3	hg19	CCDS5078.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.116988	0.77323	.	.	ENSG00000112367	ENST00000441478;ENST00000230124	T;T	0.77750	-1.12;-1.12	5.49	4.34	0.51931	Synaptojanin, N-terminal (2);	0.107962	0.64402	D	0.000009	D	0.89001	0.6591	H	0.96333	3.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.91111	0.4922	10	0.87932	D	0	-25.2145	11.11	0.48226	0.9276:0.0:0.0724:0.0	.	140;417	F5H8L9;Q92562	.;FIG4_HUMAN	V	140;417	ENSP00000399443:D140V;ENSP00000230124:D417V	ENSP00000230124:D417V	D	+	2	0	FIG4	110188258	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	5.979000	0.70508	0.926000	0.37118	0.460000	0.39030	GAC	.	.		0.413	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845		T	110081565	A	T	110081565	3	4	76	1	0	0	0	0	1	0	0	0	5896	275	10	4	1292	4	FIG4	6	110081565	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	314851	110081565	61033502	129	10400										
REV3L	5980	hgsc.bcm.edu	37	chr6	111696479	111696479	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggttgcaggggagtcgggaaCttttggccaaaagtccttca	14	8	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:111696479C>A	ENST00000358835.3	-	14	3533	c.3079G>T	c.(3079-3081)Gtt>Ttt	p.V1027F	REV3L_ENST00000368802.3_Missense_Mutation_p.V1027F|REV3L_ENST00000368805.1_Missense_Mutation_p.V1027F|REV3L_ENST00000435970.1_Missense_Mutation_p.V949F			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1027					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		GAGTCGGGAACTTTTGGCCAA	0.343								DNA polymerases (catalytic subunits)																													p.V1027F		Atlas-SNP	.											.	REV3L	386	.	0			c.G3079T						.						118	117	117					6																	111696479		2203	4300	6503	SO:0001583	missense	5980	exon13			CGGGAACTTTTGG	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.3079G>T	chr6.hg19:g.111696479C>A	ENSP00000351697:p.Val1027Phe	45.0	0.0		52.0	12.0	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	16.78	3.218137	0.58560	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01787	4.74;4.74;4.74;4.64	5.84	5.84	0.93424	Ribonuclease H-like (1);	0.000000	0.64402	D	0.000001	T	0.05823	0.0152	L	0.56769	1.78	0.44825	D	0.997837	D	0.76494	0.999	D	0.68765	0.96	T	0.31336	-0.9947	10	0.87932	D	0	.	20.139	0.98050	0.0:1.0:0.0:0.0	.	1027	O60673	DPOLZ_HUMAN	F	1027;1027;1027;949	ENSP00000357792:V1027F;ENSP00000357795:V1027F;ENSP00000351697:V1027F;ENSP00000402003:V949F	ENSP00000351697:V1027F	V	-	1	0	REV3L	111803172	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.614000	0.67695	2.764000	0.94973	0.655000	0.94253	GTT	.	.		0.343	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111696479	C	A	111696479	3	1	76	1	0	0	0	0	1	0	0	0	13255	565	20	3	6393	3	REV3L	6	111696479	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	1614914	111696479	59418588	130	10401										
L3MBTL3	84456	hgsc.bcm.edu	37	chr6	130415451	130415451	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cttcagaacatggtggatgcTcaaccccgggatgtaaaggg	13	9	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:130415451T>C	ENST00000529410.1	+	20	2154	c.1675T>C	c.(1675-1677)Tca>Cca	p.S559P	L3MBTL3_ENST00000368139.2_Missense_Mutation_p.S534P|L3MBTL3_ENST00000361794.2_Missense_Mutation_p.S559P|L3MBTL3_ENST00000526019.1_Missense_Mutation_p.S534P|L3MBTL3_ENST00000533560.1_Missense_Mutation_p.S534P|L3MBTL3_ENST00000368136.2_Missense_Mutation_p.S559P			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	559					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		TGGTGGATGCTCAACCCCGGG	0.448																																					p.S559P		Atlas-SNP	.											.	L3MBTL3	99	.	0			c.T1675C						.						83	80	81					6																	130415451		2203	4300	6503	SO:0001583	missense	84456	exon18			GGATGCTCAACCC	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"Sterile alpha motif (SAM) domain containing"	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.1675T>C	chr6.hg19:g.130415451T>C	ENSP00000431962:p.Ser559Pro	70.0	0.0		79.0	10.0	NM_032438	Q4VXE1|Q5VUM9|Q6P9B5	Missense_Mutation	SNP	ENST00000529410.1	hg19	CCDS34537.1	.	.	.	.	.	.	.	.	.	.	T	5.288	0.238493	0.10023	.	.	ENSG00000198945	ENST00000529410;ENST00000533560;ENST00000361794;ENST00000368139;ENST00000526019;ENST00000368136	T;T;T;T;T;T	0.11385	2.81;2.78;2.81;2.78;2.78;2.81	5.81	-2.75	0.05914	.	0.171080	0.52532	N	0.000067	T	0.00384	0.0012	N	0.00143	-2	0.25394	N	0.988506	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35699	-0.9778	10	0.02654	T	1	.	3.9649	0.09426	0.4596:0.3132:0.0:0.2272	.	534;559	Q96JM7-2;Q96JM7	.;LMBL3_HUMAN	P	559;534;559;534;534;559	ENSP00000431962:S559P;ENSP00000437185:S534P;ENSP00000354526:S559P;ENSP00000357121:S534P;ENSP00000436706:S534P;ENSP00000357118:S559P	ENSP00000354526:S559P	S	+	1	0	L3MBTL3	130457144	0.997000	0.39634	0.950000	0.38849	0.840000	0.47671	0.544000	0.23253	-0.101000	0.12219	0.528000	0.53228	TCA	.	.		0.448	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074		C	130415451	T	C	130415451	3	2	76	1	0	0	0	0	1	0	0	0	8602	1551	54	2	1737	2	L3MBTL3	6	130415451	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	18718972	130415451	40699616	131	10402										
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143090697	143090697	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agtatttgttacctgagtaaActgcttccaagcacttgatg	8	8	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:143090697A>G	ENST00000367604.1	-	4	5818	c.5179T>C	c.(5179-5181)Ttt>Ctt	p.F1727L	HIVEP2_ENST00000012134.2_Missense_Mutation_p.F1727L|HIVEP2_ENST00000367603.2_Missense_Mutation_p.F1727L			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1727					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		ACCTGAGTAAACTGCTTCCAA	0.388																																					p.F1727L	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.T5179C						.						93	85	88					6																	143090697		1864	4120	5984	SO:0001583	missense	3097	exon5			GAGTAAACTGCTT	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.5179T>C	chr6.hg19:g.143090697A>G	ENSP00000356576:p.Phe1727Leu	55.0	0.0		70.0	52.0	NM_006734	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	hg19	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	A	0.678	-0.799165	0.02841	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02280	4.36;4.36;4.36	5.79	4.65	0.58169	.	0.136027	0.64402	D	0.000002	T	0.00666	0.0022	N	0.21583	0.68	0.44373	D	0.997278	B	0.10296	0.003	B	0.09377	0.004	T	0.49214	-0.8963	10	0.10636	T	0.68	-15.9816	10.1907	0.43024	0.8691:0.0:0.1309:0.0	.	1727	P31629	ZEP2_HUMAN	L	1727	ENSP00000356576:F1727L;ENSP00000356575:F1727L;ENSP00000012134:F1727L	ENSP00000012134:F1727L	F	-	1	0	HIVEP2	143132390	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	4.327000	0.59247	2.208000	0.71279	0.533000	0.62120	TTT	.	.		0.388	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			G	143090697	A	G	143090697	3	3	76	1	0	0	0	0	1	0	0	0	7196	43	2	2	2185	2	HIVEP2	6	143090697	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	12675246	143090697	28024370	132	10403										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152652650	152652650	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttggcctccagttcactgcaGatggccaggtgatccatgag	12	11	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:152652650G>A	ENST00000367255.5	-	78	13771	c.13170C>T	c.(13168-13170)atC>atT	p.I4390I	SYNE1_ENST00000341594.5_Silent_p.I4255I|SYNE1_ENST00000265368.4_Silent_p.I4390I|SYNE1_ENST00000423061.1_Silent_p.I4319I|SYNE1_ENST00000448038.1_Silent_p.I4319I	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4390					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GTTCACTGCAGATGGCCAGGT	0.542										HNSCC(10;0.0054)																											p.I4390I		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C13170T						.						80	77	78					6																	152652650		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon78			ACTGCAGATGGCC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.13170C>T	chr6.hg19:g.152652650G>A		133.0	0.0		104.0	71.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.542	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152652650	G	A	152652650	2	1	76	1	0	0	0	0	0	0	0	1	15460	932	33	3		3	SYNE1	6	152652650	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	9561953	152652650	18462417	133	10404										
NOX3	50508	hgsc.bcm.edu	37	chr6	155776020	155776020	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agcatgcagttaaaattcagGcacagtgcggatgctcgtgc	12	9	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:155776020G>A	ENST00000159060.2	-	3	282	c.180C>T	c.(178-180)tgC>tgT	p.C60C		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	60	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		TAAAATTCAGGCACAGTGCGG	0.368																																					p.C60C		Atlas-SNP	.											.	NOX3	93	.	0			c.C180T						.						55	57	56					6																	155776020		2203	4300	6503	SO:0001819	synonymous_variant	50508	exon3			ATTCAGGCACAGT	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.180C>T	chr6.hg19:g.155776020G>A		74.0	0.0		98.0	32.0	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	hg19	CCDS5250.1																																																																																			.	.		0.368	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			A	155776020	G	A	155776020	2	1	76	1	0	0	0	0	0	0	0	1	10566	1195	42	3		3	NOX3	6	155776020	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	3123370	155776020	15339047	134	10405										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159650876	159650876	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tttcatacgccccggctctcAaaccatttggagcaaagtcc	7	14	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:159650876A>C	ENST00000297267.9	+	10	1410	c.1210A>C	c.(1210-1212)Aaa>Caa	p.K404Q	FNDC1_ENST00000340366.6_Intron	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	404	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CCCGGCTCTCAAACCATTTGG	0.493																																					p.K404Q		Atlas-SNP	.											.	FNDC1	250	.	0			c.A1210C						.						164	169	168					6																	159650876		1911	4117	6028	SO:0001583	missense	84624	exon10			GCTCTCAAACCAT	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.1210A>C	chr6.hg19:g.159650876A>C	ENSP00000297267:p.Lys404Gln	60.0	0.0		82.0	22.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	hg19	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.674920	0.67928	.	.	ENSG00000164694	ENST00000297267	T	0.53206	0.63	5.82	5.82	0.92795	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.61198	0.2328	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.62656	-0.6808	10	0.45353	T	0.12	-21.3403	16.1814	0.81903	1.0:0.0:0.0:0.0	.	404	Q4ZHG4	FNDC1_HUMAN	Q	404	ENSP00000297267:K404Q	ENSP00000297267:K404Q	K	+	1	0	FNDC1	159570864	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.004000	0.76317	2.234000	0.73211	0.533000	0.62120	AAA	.	.		0.493	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		C	159650876	A	C	159650876	3	2	76	1	0	0	0	0	1	0	0	0	5976	131	5	5	1248	5	FNDC1	6	159650876	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	3874856	159650876	11464191	135	10406										
MLLT4	4301	hgsc.bcm.edu	37	chr6	168352222	168352222	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tccatggatttgcctctcccAccacccccttccgccaacca	4	21	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr6:168352222A>T	ENST00000447894.2	+	29	4167	c.4167A>T	c.(4165-4167)ccA>ccT	p.P1389P	MLLT4_ENST00000392112.1_Silent_p.P1372P|MLLT4_ENST00000366806.2_Silent_p.P1389P|MLLT4_ENST00000351017.4_Silent_p.P1396P|MLLT4_ENST00000400822.3_Silent_p.P1388P|MLLT4_ENST00000344191.4_Silent_p.P1389P|MLLT4_ENST00000392108.3_Silent_p.P1389P			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1389	Pro-rich.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		TGCCTCTCCCACCACCCCCTT	0.587			T	MLL	AL																																p.P1389P		Atlas-SNP	.		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	.	MLLT4	351	.	0			c.A4167T						.						76	84	82					6																	168352222		2203	4300	6503	SO:0001819	synonymous_variant	4301	exon29			TCTCCCACCACCC	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.4167A>T	chr6.hg19:g.168352222A>T		50.0	0.0		71.0	7.0	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	hg19																																																																																				.	.		0.587	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		T	168352222	A	T	168352222	2	4	76	1	0	0	0	0	0	0	0	1	9638	146	6	4		4	MLLT4	6	168352222	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	8701346	168352222	2762845	136	10407										
LFNG	3955	hgsc.bcm.edu	37	chr7	2565185	2565185	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	catccaggccatggagcgggTcagcgagaacaaggtggtga	16	9	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:2565185T>A	ENST00000222725.5	+	4	739	c.719T>A	c.(718-720)gTc>gAc	p.V240D	LFNG_ENST00000402506.1_Missense_Mutation_p.V169D|LFNG_ENST00000402045.1_Missense_Mutation_p.V111D|LFNG_ENST00000338732.3_Missense_Mutation_p.V111D|MIR4648_ENST00000580107.1_RNA|LFNG_ENST00000359574.3_Missense_Mutation_p.V240D	NM_001040167.1	NP_001035257.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	240					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		ATGGAGCGGGTCAGCGAGAAC	0.726																																					p.V240D		Atlas-SNP	.											.	LFNG	57	.	0			c.T719A						.						33	33	33					7																	2565185		2199	4298	6497	SO:0001583	missense	3955	exon4			AGCGGGTCAGCGA	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"Beta 3-glycosyltransferases"	6560	protein-coding gene	gene with protein product		602576	"lunatic fringe (Drosophila) homolog", "lunatic fringe homolog (Drosophila)"			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000222725.5:c.719T>A	chr7.hg19:g.2565185T>A	ENSP00000222725:p.Val240Asp	46.0	0.0		39.0	13.0	NM_001040167	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Missense_Mutation	SNP	ENST00000222725.5	hg19	CCDS34587.1	.	.	.	.	.	.	.	.	.	.	T	11.68	1.712092	0.30322	.	.	ENSG00000106003	ENST00000402506;ENST00000402045;ENST00000338732;ENST00000222725;ENST00000359574	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04	4.95	4.95	0.65309	.	0.386317	0.28343	N	0.015682	T	0.58850	0.2151	L	0.56199	1.76	0.58432	D	0.999998	B;B	0.24721	0.08;0.11	B;B	0.28553	0.017;0.091	T	0.56189	-0.8020	10	0.30854	T	0.27	-17.9401	14.6327	0.68668	0.0:0.0:0.0:1.0	.	240;240	Q8NES3-3;Q8NES3	.;LFNG_HUMAN	D	169;111;111;240;240	ENSP00000385764:V169D;ENSP00000384786:V111D;ENSP00000343095:V111D;ENSP00000222725:V240D;ENSP00000352579:V240D	ENSP00000222725:V240D	V	+	2	0	LFNG	2531711	1.000000	0.71417	0.032000	0.17829	0.679000	0.39708	7.463000	0.80869	1.871000	0.54225	0.459000	0.35465	GTC	.	.		0.726	LFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325021.1	NM_002304		A	2565185	T	A	2565185	3	1	76	1	0	0	0	0	1	0	0	0	8746	1667	58	4	1009	4	LFNG	7	2565185	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10		2565185	156573478	137	10408										
FOXK1	221937	hgsc.bcm.edu	37	chr7	4801902	4801902	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggtgtgcgaggtggggcccaAggagccagcagcagccgtcg	19	11	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:4801902A>T	ENST00000328914.4	+	9	2009	c.2009A>T	c.(2008-2010)aAg>aTg	p.K670M	FOXK1_ENST00000446823.1_Missense_Mutation_p.K507M	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GTGGGGCCCAAGGAGCCAGCA	0.692																																					p.K670M		Atlas-SNP	.											.	FOXK1	64	.	0			c.A2009T						.						23	18	20					7																	4801902		2039	4004	6043	SO:0001583	missense	221937	exon9			GGCCCAAGGAGCC	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.2009A>T	chr7.hg19:g.4801902A>T	ENSP00000328720:p.Lys670Met	124.0	0.0		129.0	38.0	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	hg19	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	a	17.31	3.357941	0.61403	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.95821	-3.46;-3.82	4.82	4.82	0.62117	.	0.342066	0.26765	N	0.022618	D	0.89808	0.6822	N	0.08118	0	0.28571	N	0.910627	P;B	0.44195	0.828;0.101	B;B	0.43155	0.41;0.015	D	0.86762	0.1967	10	0.87932	D	0	.	12.1388	0.53986	1.0:0.0:0.0:0.0	.	670;507	P85037;P85037-2	FOXK1_HUMAN;.	M	507;426;670;553	ENSP00000394442:K507M;ENSP00000328720:K670M	ENSP00000328720:K670M	K	+	2	0	FOXK1	4768428	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.730000	0.74780	1.812000	0.52913	0.454000	0.30748	AAG	.	.		0.692	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			T	4801902	A	T	4801902	3	4	76	1	0	0	0	0	1	0	0	0	6022	72	3	4	2043	4	FOXK1	7	4801902	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	2236717	4801902	154336761	138	10409										
FSCN1	6624	hgsc.bcm.edu	37	chr7	5643005	5643005	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cacgggcaagtactggacgcTgacggccaccgggggcgtgc	17	13	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:5643005T>A	ENST00000382361.3	+	2	1064	c.950T>A	c.(949-951)cTg>cAg	p.L317Q	FSCN1_ENST00000340250.6_Missense_Mutation_p.L296Q	NM_003088.3	NP_003079.1	Q16658	FSCN1_HUMAN	fascin actin-bundling protein 1	317					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|cell motility (GO:0048870)|cell proliferation (GO:0008283)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|invadopodium (GO:0071437)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|drug binding (GO:0008144)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)		TACTGGACGCTGACGGCCACC	0.652																																					p.L317Q		Atlas-SNP	.											.	FSCN1	29	.	0			c.T950A						.						82	59	67					7																	5643005		2203	4300	6503	SO:0001583	missense	6624	exon2			GGACGCTGACGGC	U03057	CCDS5342.1	7p22	2014-02-03	2014-02-03	2002-09-20	ENSG00000075618	ENSG00000075618		"Fascins"	11148	protein-coding gene	gene with protein product	"Singed, drosophila, homolog-like", "actin bundling protein"	602689	"singed (Drosophila)-like (sea urchin fascin homolog like)", "fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus)"	SNL		8068206, 10783262	Standard	NM_003088		Approved	p55, FLJ38511	uc003sou.3	Q16658	OTTHUMG00000090599	ENST00000382361.3:c.950T>A	chr7.hg19:g.5643005T>A	ENSP00000371798:p.Leu317Gln	70.0	0.0		62.0	10.0	NM_003088	A6NI89|B2RE97|Q96IC5|Q96IH1|Q9BRF1	Missense_Mutation	SNP	ENST00000382361.3	hg19	CCDS5342.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411012	0.83340	.	.	ENSG00000075618	ENST00000340250;ENST00000382361;ENST00000444748;ENST00000447103;ENST00000405801;ENST00000535097	T;T	0.51071	0.72;1.3	4.75	4.75	0.60458	Fascin domain (1);Actin cross-linking (1);	0.000000	0.64402	D	0.000006	T	0.72301	0.3443	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.78534	-0.2167	10	0.87932	D	0	-4.2061	13.0869	0.59146	0.0:0.0:0.0:1.0	.	296;317	B3KTA3;Q16658	.;FSCN1_HUMAN	Q	296;317;39;39;39;39	ENSP00000339729:L296Q;ENSP00000371798:L317Q	ENSP00000339729:L296Q	L	+	2	0	FSCN1	5609531	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	7.997000	0.88414	1.764000	0.52075	0.459000	0.35465	CTG	.	.		0.652	FSCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207153.3	NM_003088		A	5643005	T	A	5643005	3	1	76	1	0	0	0	0	1	0	0	0	6075	1580	55	4	956	4	FSCN1	7	5643005	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	841103	5643005	153495658	139	10410										
STK31	56164	hgsc.bcm.edu	37	chr7	23766879	23766879	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gatttatggtggattattttCtgaagatcagtgttggtaca	11	3	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:23766879C>T	ENST00000355870.3	+	5	388	c.269C>T	c.(268-270)tCt>tTt	p.S90F	STK31_ENST00000428484.1_Missense_Mutation_p.S67F|STK31_ENST00000433467.2_Missense_Mutation_p.S90F|STK31_ENST00000354639.3_Missense_Mutation_p.S67F|STK31_ENST00000405627.3_3'UTR	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	90	Tudor. {ECO:0000255|PROSITE- ProRule:PRU00211}.					acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GGATTATTTTCTGAAGATCAG	0.318																																					p.S90F		Atlas-SNP	.											.	STK31	175	.	0			c.C269T						.						117	112	113					7																	23766879		2203	4299	6502	SO:0001583	missense	56164	exon5			TATTTTCTGAAGA	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.269C>T	chr7.hg19:g.23766879C>T	ENSP00000348132:p.Ser90Phe	109.0	0.0		78.0	36.0	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	hg19	CCDS5386.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.266221	0.80358	.	.	ENSG00000196335	ENST00000355870;ENST00000422637;ENST00000456014;ENST00000433467;ENST00000354639;ENST00000444333;ENST00000428484	T;T;T;T;T;T;T	0.11277	2.79;2.79;2.79;2.79;2.79;2.79;2.79	5.37	5.37	0.77165	Tudor subgroup (1);Maternal tudor protein (1);Tudor domain (1);	0.067201	0.64402	D	0.000008	T	0.36468	0.0968	M	0.78049	2.395	0.53005	D	0.99996	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	T	0.09400	-1.0676	10	0.87932	D	0	-10.2652	18.2362	0.89950	0.0:1.0:0.0:0.0	.	90;90	B4DZ06;Q9BXU1	.;STK31_HUMAN	F	90;46;67;90;67;67;67	ENSP00000348132:S90F;ENSP00000414087:S46F;ENSP00000389340:S67F;ENSP00000411852:S90F;ENSP00000346660:S67F;ENSP00000398413:S67F;ENSP00000406146:S67F	ENSP00000346660:S67F	S	+	2	0	STK31	23733404	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.619000	0.67729	2.677000	0.91161	0.650000	0.86243	TCT	.	.		0.318	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		T	23766879	C	T	23766879	3	4	76	1	0	0	0	0	1	0	0	0	15311	913	32	3	287	3	STK31	7	23766879	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	18123874	23766879	135371784	140	10411										
HOXA11	3207	hgsc.bcm.edu	37	chr7	27224509	27224509	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tctctgtgcacgagctcctcCgcggagtagcagtgggccag	14	13	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:27224509C>A	ENST00000006015.3	-	1	326	c.255G>T	c.(253-255)gcG>gcT	p.A85A	HOXA11-AS_ENST00000522674.1_RNA|HOXA11-AS_ENST00000522863.1_RNA|HOXA11-AS_ENST00000520360.1_RNA|HOXA11-AS_ENST00000520395.1_RNA|HOXA11-AS_ENST00000479766.1_RNA|RP1-170O19.14_ENST00000523331.1_lincRNA	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	85					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal joint morphogenesis (GO:0060272)|male gonad development (GO:0008584)|mesodermal cell fate specification (GO:0007501)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)	nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	16						CGAGCTCCTCCGCGGAGTAGC	0.677			T	NUP98	CML																																p.A85A		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.G255T						.						40	46	44					7																	27224509		2203	4300	6503	SO:0001819	synonymous_variant	3207	exon1			CTCCTCCGCGGAG		CCDS5411.1	7p15.2	2014-09-17	2005-12-22		ENSG00000005073	ENSG00000005073		"Homeoboxes / ANTP class : HOXL subclass"	5101	protein-coding gene	gene with protein product		142958	"homeo box A11"	HOX1I, HOX1		1973146, 1358459	Standard	NM_005523		Approved		uc003syx.3	P31270	OTTHUMG00000023437	ENST00000006015.3:c.255G>T	chr7.hg19:g.27224509C>A		96.0	0.0		73.0	37.0	NM_005523	A4D190	Silent	SNP	ENST00000006015.3	hg19	CCDS5411.1	.	.	.	.	.	.	.	.	.	.	C	11.96	1.795895	0.31777	.	.	ENSG00000005073	ENST00000517402	.	.	.	5.49	0.966	0.19667	.	.	.	.	.	T	0.52370	0.1730	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40001	-0.9586	4	.	.	.	.	6.2155	0.20653	0.0:0.4812:0.2695:0.2493	.	.	.	.	L	55	.	.	R	-	2	0	HOXA11	27191034	0.994000	0.37717	1.000000	0.80357	0.996000	0.88848	0.344000	0.19962	0.249000	0.21456	0.650000	0.86243	CGG	.	.		0.677	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1			A	27224509	C	A	27224509	2	1	76	1	0	0	0	0	0	0	0	1	7299	639	23	1		1	HOXA11	7	27224509	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	3457630	27224509	131914154	141	10412										
STK17A	9263	hgsc.bcm.edu	37	chr7	43647961	43647961	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agattttagaaggtgttcacTttttacacactcgtgatgta	8	6	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:43647961T>G	ENST00000319357.5	+	3	705	c.526T>G	c.(526-528)Ttt>Gtt	p.F176V	STK17A_ENST00000462448.1_3'UTR	NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						AGGTGTTCACTTTTTACACAC	0.333																																					p.F176V		Atlas-SNP	.											.	STK17A	31	.	0			c.T526G						.						123	121	122					7																	43647961		2203	4300	6503	SO:0001583	missense	9263	exon3			GTTCACTTTTTAC	AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"death-associated protein kinase-related 1"	604726	"serine/threonine kinase 17a (apoptosis-inducing)"			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.526T>G	chr7.hg19:g.43647961T>G	ENSP00000319192:p.Phe176Val	164.0	0.0		134.0	59.0	NM_004760	A4D1V6|Q8IVC8	Missense_Mutation	SNP	ENST00000319357.5	hg19	CCDS5470.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.485009	0.84854	.	.	ENSG00000164543	ENST00000319357	T	0.67698	-0.28	4.57	4.57	0.56435	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.42964	U	0.000628	T	0.72724	0.3496	L	0.39397	1.21	0.58432	D	0.999999	D	0.58970	0.984	D	0.63113	0.911	T	0.74931	-0.3496	10	0.54805	T	0.06	.	14.2605	0.66083	0.0:0.0:0.0:1.0	.	176	Q9UEE5	ST17A_HUMAN	V	176	ENSP00000319192:F176V	ENSP00000319192:F176V	F	+	1	0	STK17A	43614486	1.000000	0.71417	0.898000	0.35279	0.995000	0.86356	6.900000	0.75687	1.822000	0.53115	0.528000	0.53228	TTT	.	.		0.333	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760		G	43647961	T	G	43647961	3	3	76	1	0	0	0	0	1	0	0	0	15305	1609	56	5	536	5	STK17A	7	43647961	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	16423452	43647961	115490702	142	10413										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47870917	47870917	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gctgaagggcccttgaccacTggggcattagtccctccaaa	11	13	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:47870917T>C	ENST00000289672.2	-	42	6421	c.6371A>G	c.(6370-6372)cAg>cGg	p.Q2124R		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2124					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CCTTGACCACTGGGGCATTAG	0.577																																					p.Q2124R		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A6371G						.						87	79	82					7																	47870917		2203	4300	6503	SO:0001583	missense	168507	exon42			GACCACTGGGGCA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.6371A>G	chr7.hg19:g.47870917T>C	ENSP00000289672:p.Gln2124Arg	121.0	0.0		96.0	36.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.797068	0.00617	.	.	ENSG00000158683	ENST00000289672	T	0.18810	2.19	5.1	-10.2	0.00374	.	5.626960	0.00397	N	0.000054	T	0.07279	0.0184	N	0.05441	-0.05	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.20571	-1.0271	10	0.02654	T	1	0.4993	5.7735	0.18267	0.0761:0.1292:0.2271:0.5676	.	2124	Q8TDX9	PK1L1_HUMAN	R	2124	ENSP00000289672:Q2124R	ENSP00000289672:Q2124R	Q	-	2	0	PKD1L1	47837442	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.200000	0.01237	-4.757000	0.00033	-2.497000	0.00192	CAG	.	.		0.577	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		C	47870917	T	C	47870917	3	2	76	1	0	0	0	0	1	0	0	0	11973	1580	55	2	2242	2	PKD1L1	7	47870917	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	4222956	47870917	111267746	143	10414										
FIGNL1	63979	hgsc.bcm.edu	37	chr7	50514059	50514060	+	Frame_Shift_Ins	INS	-	-	T													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cacgctgaggttggtggtacINStttttttgctgatctaccca							TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:50514059_50514060insT	ENST00000419119.1	-	2	2479_2480	c.926_927insA	c.(925-927)aagfs	p.K309fs	FIGNL1_ENST00000395556.2_Frame_Shift_Ins_p.K309fs|FIGNL1_ENST00000356889.4_Frame_Shift_Ins_p.K309fs|FIGNL1_ENST00000433017.1_Frame_Shift_Ins_p.K309fs			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	309	Necessary and sufficient for interaction with RAD51.				ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				GTTGGTGGTACTTTTTTTGCTG	0.426																																					p.K309fs		Atlas-Indel,Pindel	.											.	FIGNL1	73	.	0			c.927_928insA						.																																			SO:0001589	frameshift_variant	63979	exon4			.	AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"ATPases / AAA-type"	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.927dupA	chr7.hg19:g.50514066_50514066dupT	ENSP00000410811:p.Lys309fs	148.0	0.0		113.0	28.0	NM_022116	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Frame_Shift_Ins	INS	ENST00000419119.1	hg19	CCDS5510.1																																																																																			.	.		0.426	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762		T	50514060	-	T	50514059	7	5	76	1	0	1	1	0	0	0	0	0	5900	564	20	0	1101	0	FIGNL1	7	50514059	Frame_Shift_Ins	INS	-	TCGA-CC-A7IK-01A-12D-A33Q-10	2643142	50514059	108624604	144	10415										
ZNF273	10793	hgsc.bcm.edu	37	chr7	64388967	64388967	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccacaactcttactaaacatAagagaatttatactaaagag	4	8	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:64388967A>G	ENST00000476120.1	+	4	1332	c.1261A>G	c.(1261-1263)Aag>Gag	p.K421E	ZNF273_ENST00000319636.5_Missense_Mutation_p.K356E|ZNF273_ENST00000527278.1_3'UTR	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	421					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				TACTAAACATAAGAGAATTTA	0.338																																					p.K421E	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-SNP	.											.	ZNF273	45	.	0			c.A1261G						.						37	40	39					7																	64388967		2203	4298	6501	SO:0001583	missense	10793	exon4			AAACATAAGAGAA	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"Zinc fingers, C2H2-type", "-"	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.1261A>G	chr7.hg19:g.64388967A>G	ENSP00000418719:p.Lys421Glu	143.0	0.0		148.0	22.0	NM_021148	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	hg19	CCDS5528.2	.	.	.	.	.	.	.	.	.	.	.	17.81	3.480294	0.63849	.	.	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.18016	2.24;2.24	1.16	-2.32	0.06745	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18425	0.0442	N	0.20807	0.61	0.21220	N	0.999759	D	0.61697	0.99	D	0.73380	0.98	T	0.19614	-1.0300	9	0.59425	D	0.04	.	2.2335	0.04002	0.4355:0.3136:0.2509:0.0	.	421	Q14593	ZN273_HUMAN	E	421;356	ENSP00000418719:K421E;ENSP00000324518:K356E	ENSP00000324518:K356E	K	+	1	0	ZNF273	64026402	0.000000	0.05858	0.800000	0.32199	0.797000	0.45037	-0.346000	0.07760	0.175000	0.19841	0.172000	0.16884	AAG	.	.		0.338	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1			G	64388967	A	G	64388967	3	3	76	1	0	0	0	0	1	0	0	0	17823	363	13	2	1275	2	ZNF273	7	64388967	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	13874908	64388967	94749696	145	10416										
CYP3A5	1577	hgsc.bcm.edu	37	chr7	99272195	99272195	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttttatagcactctgtgtcaAatttccagagaccctgggag	9	9	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:99272195A>C	ENST00000222982.4	-	3	278	c.179T>G	c.(178-180)tTt>tGt	p.F60C	CYP3A5_ENST00000439761.1_Missense_Mutation_p.F60C|CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000480723.1_5'UTR|CYP3A5_ENST00000343703.5_Missense_Mutation_p.F50C	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	60					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	CTCTGTGTCAAATTTCCAGAG	0.408																																					p.F60C		Atlas-SNP	.											.	CYP3A5	46	.	0			c.T179G						.						80	77	78					7																	99272195		2203	4300	6503	SO:0001583	missense	1577	exon3			GTGTCAAATTTCC	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"Cytochrome P450s"	2638	protein-coding gene	gene with protein product		605325	"cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.179T>G	chr7.hg19:g.99272195A>C	ENSP00000222982:p.Phe60Cys	69.0	0.0		42.0	22.0	NM_001190484	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Missense_Mutation	SNP	ENST00000222982.4	hg19	CCDS5672.1	.	.	.	.	.	.	.	.	.	.	A	14.96	2.691428	0.48097	.	.	ENSG00000106258	ENST00000222982;ENST00000343703;ENST00000439761	T;T;T	0.70399	-0.48;-0.48;-0.48	3.48	0.667	0.17907	.	0.220302	0.47093	N	0.000252	T	0.81446	0.4824	M	0.91612	3.225	0.80722	D	1	D;B;D	0.57257	0.974;0.418;0.979	P;B;P	0.61328	0.82;0.383;0.887	T	0.77544	-0.2548	10	0.72032	D	0.01	.	4.8896	0.13721	0.6254:0.1906:0.0:0.184	.	50;60;60	F5H4S0;B7Z5I7;P20815	.;.;CP3A5_HUMAN	C	60;50;60	ENSP00000222982:F60C;ENSP00000342969:F50C;ENSP00000401269:F60C	ENSP00000222982:F60C	F	-	2	0	CYP3A5	99110131	1.000000	0.71417	0.005000	0.12908	0.028000	0.11728	4.534000	0.60622	-0.095000	0.12351	0.379000	0.24179	TTT	.	.		0.408	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1			C	99272195	A	C	99272195	3	2	76	1	0	0	0	0	1	0	0	0	4182	14	1	5	1373	5	CYP3A5	7	99272195	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	34883228	99272195	59866468	146	10417										
AZGP1	563	hgsc.bcm.edu	37	chr7	99569527	99569527	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcctgtctttactgttgtatCtaaagaactggaggtcattg	9	7	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:99569527C>A	ENST00000292401.4	-	2	315	c.179G>T	c.(178-180)aGa>aTa	p.R60I	AZGP1_ENST00000411734.1_Missense_Mutation_p.R57I	NM_001185.3	NP_001176.1	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc-binding	60					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell adhesion (GO:0007155)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein transmembrane transport (GO:0071806)|retina homeostasis (GO:0001895)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|MHC class I protein complex (GO:0042612)|nucleus (GO:0005634)	glycoprotein binding (GO:0001948)|peptide antigen binding (GO:0042605)|protein transmembrane transporter activity (GO:0008320)|ribonuclease activity (GO:0004540)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|stomach(1)	16	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					ACTGTTGTATCTAAAGAACTG	0.517																																					p.R60I		Atlas-SNP	.											.	AZGP1	41	.	0			c.G179T						.						115	109	111					7																	99569527		2203	4300	6503	SO:0001583	missense	563	exon2			TTGTATCTAAAGA	BC005306	CCDS5680.1	7q22.1	2013-01-11	2006-11-07		ENSG00000160862	ENSG00000160862		"Immunoglobulin superfamily / C1-set domain containing"	910	protein-coding gene	gene with protein product		194460	"alpha-2-glycoprotein 1, zinc"			2049092	Standard	NM_001185		Approved	ZA2G, ZAG	uc003ush.3	P25311	OTTHUMG00000023066	ENST00000292401.4:c.179G>T	chr7.hg19:g.99569527C>A	ENSP00000292401:p.Arg60Ile	79.0	0.0		81.0	18.0	NM_001185	D6W5T8|O60386|Q5XKQ4|Q8N4N0	Missense_Mutation	SNP	ENST00000292401.4	hg19	CCDS5680.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.14|11.14	1.552511|1.552511	0.27739|0.27739	.|.	.|.	ENSG00000160862|ENSG00000160862	ENST00000419575|ENST00000292401;ENST00000411734	.|T;T	.|0.00940	.|5.52;5.52	1.51|1.51	-2.16|-2.16	0.07080|0.07080	.|MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|0.983094	.|0.08225	.|U	.|0.978571	T|T	0.02012|0.02012	0.0063|0.0063	M|M	0.90082|0.90082	3.085|3.085	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.27971	.|0.196	.|B	.|0.23852	.|0.049	T|T	0.30060|0.30060	-0.9991|-0.9991	5|10	.|0.87932	.|D	.|0	.|.	5.346|5.346	0.16010|0.16010	0.0:0.1966:0.0:0.8034|0.0:0.1966:0.0:0.8034	.|.	.|60	.|P25311	.|ZA2G_HUMAN	Y|I	31|60;57	.|ENSP00000292401:R60I;ENSP00000396093:R57I	.|ENSP00000292401:R60I	D|R	-|-	1|2	0|0	AZGP1|AZGP1	99407463|99407463	0.341000|0.341000	0.24801|0.24801	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.417000|-0.417000	0.07088|0.07088	-0.371000|-0.371000	0.08004|0.08004	-1.745000|-1.745000	0.00682|0.00682	GAT|AGA	.	.		0.517	AZGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059387.4	NM_001185		A	99569527	C	A	99569527	3	1	76	1	0	0	0	0	1	0	0	0	1239	913	32	3	729	3	AZGP1	7	99569527	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	297332	99569527	59569136	147	10418										
TMEM168	64418	hgsc.bcm.edu	37	chr7	112412840	112412840	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccaaaggtgagtttacctgcTagagcccactctcctgtacc	8	14	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:112412840T>A	ENST00000312814.6	-	4	2102	c.1542A>T	c.(1540-1542)ctA>ctT	p.L514L	TMEM168_ENST00000480969.1_5'Flank|TMEM168_ENST00000454074.1_Silent_p.L514L	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	514						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						GTTTACCTGCTAGAGCCCACT	0.413																																					p.L514L		Atlas-SNP	.											.	TMEM168	84	.	0			c.A1542T						.						93	80	84					7																	112412840		2203	4300	6503	SO:0001819	synonymous_variant	64418	exon4			ACCTGCTAGAGCC		CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.1542A>T	chr7.hg19:g.112412840T>A		194.0	0.0		139.0	37.0	NM_022484	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Silent	SNP	ENST00000312814.6	hg19	CCDS5757.1																																																																																			.	.		0.413	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		A	112412840	T	A	112412840	2	1	76	1	0	0	0	0	0	0	0	1	16098	1509	53	4		4	TMEM168	7	112412840	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	12843313	112412840	46725823	148	10419										
CFTR	1080	hgsc.bcm.edu	37	chr7	117175426	117175426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tttcctgatagtccttgcccTttttcaggctgggctaggga	11	10	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:117175426T>C	ENST00000003084.6	+	6	836	c.704T>C	c.(703-705)cTt>cCt	p.L235P	CFTR_ENST00000454343.1_Missense_Mutation_p.L235P	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	235	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	GTCCTTGCCCTTTTTCAGGCT	0.438									Cystic Fibrosis																												p.L235P		Atlas-SNP	.											.	CFTR	171	.	0			c.T704C						.						128	119	122					7																	117175426		2203	4300	6503	SO:0001583	missense	1080	exon6	Familial Cancer Database	CF	TTGCCCTTTTTCA	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.704T>C	chr7.hg19:g.117175426T>C	ENSP00000003084:p.Leu235Pro	121.0	0.0		96.0	4.0	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	hg19	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	T	12.14	1.849389	0.32699	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.91351	-2.83;-2.83;-2.83	5.37	4.2	0.49525	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.563956	0.20074	N	0.099787	T	0.77025	0.4070	N	0.01438	-0.865	0.22982	N	0.998476	B	0.16166	0.016	B	0.25884	0.064	T	0.66180	-0.5988	10	0.34782	T	0.22	-0.328	12.4979	0.55940	0.0:0.0:0.1397:0.8603	.	235	P13569	CFTR_HUMAN	P	235;235;205	ENSP00000003084:L235P;ENSP00000403677:L235P;ENSP00000389119:L205P	ENSP00000003084:L235P	L	+	2	0	CFTR	116962662	0.900000	0.30661	0.016000	0.15963	0.989000	0.77384	4.475000	0.60210	0.864000	0.35578	0.528000	0.53228	CTT	.	.		0.438	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		C	117175426	T	C	117175426	3	2	76	1	0	0	0	0	1	0	0	0	3296	1609	56	2	726	2	CFTR	7	117175426	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	4762586	117175426	41963237	149	10420										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121653534	121653534	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccaatctcatactcactatcTgagaattctgaagaagataa	5	9	4	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:121653534T>A	ENST00000393386.2	+	12	4845	c.4434T>A	c.(4432-4434)tcT>tcA	p.S1478S	PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1478					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						ACTCACTATCTGAGAATTCTG	0.393																																					p.S1478S		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T4434A						.						79	78	78					7																	121653534		2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			ACTATCTGAGAAT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.4434T>A	chr7.hg19:g.121653534T>A		92.0	0.0		69.0	27.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	hg19	CCDS34740.1																																																																																			.	.		0.393	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121653534	T	A	121653534	2	1	76	1	0	0	0	0	0	0	0	1	12829	1567	55	4		4	PTPRZ1	7	121653534	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	4478108	121653534	37485129	150	10421										
GCC1	79571	hgsc.bcm.edu	37	chr7	127222729	127222729	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggagctgctgcagccgggccAgctcctgcttccagtcatca	12	15	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:127222729A>T	ENST00000321407.2	-	2	2091	c.1667T>A	c.(1666-1668)cTg>cAg	p.L556Q	GCC1_ENST00000497650.1_5'Flank	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	556					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CAGCCGGGCCAGCTCCTGCTT	0.627																																					p.L556Q		Atlas-SNP	.											.	GCC1	83	.	0			c.T1667A						.						31	34	33					7																	127222729		2202	4299	6501	SO:0001583	missense	79571	exon2			CGGGCCAGCTCCT	AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"golgi coiled-coil 1"			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.1667T>A	chr7.hg19:g.127222729A>T	ENSP00000318821:p.Leu556Gln	48.0	0.0		34.0	5.0	NM_024523	Q9H6N7	Missense_Mutation	SNP	ENST00000321407.2	hg19	CCDS5796.1	.	.	.	.	.	.	.	.	.	.	A	15.78	2.935037	0.52866	.	.	ENSG00000179562	ENST00000321407	T	0.15256	2.44	5.5	4.32	0.51571	.	0.485370	0.22030	N	0.065603	T	0.17831	0.0428	L	0.50333	1.59	0.38342	D	0.944104	P	0.49961	0.93	P	0.44732	0.459	T	0.09100	-1.0690	10	0.17369	T	0.5	-6.5626	11.051	0.47889	0.8442:0.1558:0.0:0.0	.	556	Q96CN9	GCC1_HUMAN	Q	556	ENSP00000318821:L556Q	ENSP00000318821:L556Q	L	-	2	0	GCC1	127009965	0.946000	0.32159	1.000000	0.80357	0.960000	0.62799	2.563000	0.45922	0.983000	0.38602	0.533000	0.62120	CTG	.	.		0.627	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523		T	127222729	A	T	127222729	3	4	76	1	0	0	0	0	1	0	0	0	6293	188	7	4	664	4	GCC1	7	127222729	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	5569195	127222729	31915934	151	10422										
CHRM2	1129	hgsc.bcm.edu	37	chr7	136700208	136700208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgcagccttctatttgccagTgatcatcatgactgtgctat	8	10	3	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:136700208T>C	ENST00000445907.2	+	3	1124	c.596T>C	c.(595-597)gTg>gCg	p.V199A	hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000439694.1_RNA|CHRM2_ENST00000401861.1_Missense_Mutation_p.V199A|hsa-mir-490_ENST00000593789.1_RNA|CHRM2_ENST00000397608.3_Missense_Mutation_p.V199A|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000453373.1_Missense_Mutation_p.V199A|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000402486.3_Missense_Mutation_p.V199A|hsa-mir-490_ENST00000598184.1_RNA|CHRM2_ENST00000320658.5_Missense_Mutation_p.V199A	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	199					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TATTTGCCAGTGATCATCATG	0.488																																					p.V199A		Atlas-SNP	.											.	CHRM2	167	.	0			c.T596C						.						72	64	67					7																	136700208		2203	4300	6503	SO:0001583	missense	1129	exon3			TGCCAGTGATCAT		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.596T>C	chr7.hg19:g.136700208T>C	ENSP00000399745:p.Val199Ala	69.0	0.0		58.0	30.0	NM_001006632	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	hg19	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.027227	0.75390	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	T;T;T;T;T;T	0.38240	1.15;1.15;1.15;1.15;1.15;1.15	5.51	5.51	0.81932	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.57636	0.2067	M	0.70842	2.15	0.80722	D	1	D	0.64830	0.994	D	0.64237	0.923	T	0.60073	-0.7334	10	0.52906	T	0.07	-5.7288	15.6399	0.76989	0.0:0.0:0.0:1.0	.	199	P08172	ACM2_HUMAN	A	199	ENSP00000399745:V199A;ENSP00000415386:V199A;ENSP00000319984:V199A;ENSP00000380733:V199A;ENSP00000384937:V199A;ENSP00000384401:V199A	ENSP00000319984:V199A	V	+	2	0	CHRM2	136350748	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.991000	0.88244	2.103000	0.63969	0.533000	0.62120	GTG	.	.		0.488	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			C	136700208	T	C	136700208	3	2	76	1	0	0	0	0	1	0	0	0	3379	1696	59	2	598	2	CHRM2	7	136700208	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	9477479	136700208	22438455	152	10423										
AKR1D1	6718	hgsc.bcm.edu	37	chr7	137776523	137776523	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gattctttcagctatgggctAcaaatcatgtcccagagatg	9	9	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:137776523A>G	ENST00000242375.3	+	3	313	c.271A>G	c.(271-273)Aca>Gca	p.T91A	AKR1D1_ENST00000468877.2_Intron|RN7SKP223_ENST00000410582.1_RNA|AKR1D1_ENST00000411726.2_Missense_Mutation_p.T91A|AKR1D1_ENST00000432161.1_Missense_Mutation_p.T91A	NM_005989.3	NP_005980.1	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1	91					androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|C21-steroid hormone metabolic process (GO:0008207)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|steroid binding (GO:0005496)			endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	23					Azelaic Acid(DB00548)|Finasteride(DB01216)	GCTATGGGCTACAAATCATGT	0.448																																					p.T91A		Atlas-SNP	.											.	AKR1D1	52	.	0			c.A271G						.						96	93	94					7																	137776523		2203	4300	6503	SO:0001583	missense	6718	exon3			TGGGCTACAAATC	Z28339	CCDS5846.1, CCDS55169.1, CCDS55170.1	7q32-q33	2012-12-04	2012-12-04		ENSG00000122787	ENSG00000122787	1.3.99.6	"Aldo-keto reductases"	388	protein-coding gene	gene with protein product	"delta 4-3-ketosteroid-5-beta-reductase"	604741	"aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5-beta-reductase)"	SRD5B1		7508385, 10343119	Standard	NM_005989		Approved		uc003vtz.3	P51857	OTTHUMG00000155787	ENST00000242375.3:c.271A>G	chr7.hg19:g.137776523A>G	ENSP00000242375:p.Thr91Ala	67.0	0.0		75.0	14.0	NM_001190907	A1L4P6|A8K060|B4DPN3|B4DPN8	Missense_Mutation	SNP	ENST00000242375.3	hg19	CCDS5846.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.956940	0.73902	.	.	ENSG00000122787	ENST00000432161;ENST00000411726;ENST00000242375;ENST00000438242	T;T;T;T	0.51325	1.93;1.93;1.93;0.71	5.4	5.4	0.78164	NADP-dependent oxidoreductase domain (3);	0.000000	0.85682	D	0.000000	T	0.63236	0.2494	L	0.54965	1.715	0.58432	D	0.999999	D;D;D	0.69078	0.997;0.996;0.982	D;D;P	0.76575	0.988;0.943;0.768	T	0.65734	-0.6096	10	0.72032	D	0.01	.	13.4313	0.61057	1.0:0.0:0.0:0.0	.	91;91;91	B4DPN8;B4DPN3;P51857	.;.;AK1D1_HUMAN	A	91;91;91;35	ENSP00000389197:T91A;ENSP00000402374:T91A;ENSP00000242375:T91A;ENSP00000397042:T35A	ENSP00000242375:T91A	T	+	1	0	AKR1D1	137427063	1.000000	0.71417	0.680000	0.29994	0.701000	0.40568	8.184000	0.89702	2.271000	0.75665	0.533000	0.62120	ACA	.	.		0.448	AKR1D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341637.1	NM_005989		G	137776523	A	G	137776523	3	3	76	1	0	0	0	0	1	0	0	0	473	391	14	2	281	2	AKR1D1	7	137776523	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	1076315	137776523	21362140	153	10424										
CLCN1	1180	hgsc.bcm.edu	37	chr7	143021573	143021573	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gagtcggctgttgttttgggAcaccacttggaggcaagtga	15	7	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:143021573A>G	ENST00000343257.2	+	7	928	c.841A>G	c.(841-843)Aca>Gca	p.T281A	CLCN1_ENST00000495612.1_Intron	NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	281					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					TTGTTTTGGGACACCACTTGG	0.527																																					p.T281A		Atlas-SNP	.											.	CLCN1	141	.	0			c.A841G						.						194	148	164					7																	143021573		2203	4300	6503	SO:0001583	missense	1180	exon7			TTTGGGACACCAC	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.841A>G	chr7.hg19:g.143021573A>G	ENSP00000339867:p.Thr281Ala	98.0	0.0		98.0	29.0	NM_000083	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	hg19	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	.	7.025	0.559449	0.13436	.	.	ENSG00000188037	ENST00000343257	D	0.89485	-2.52	4.61	4.61	0.57282	Chloride channel, core (2);	0.147082	0.64402	N	0.000012	T	0.64360	0.2591	N	0.00380	-1.58	0.46416	D	0.99903	B	0.15473	0.013	B	0.22386	0.039	T	0.68074	-0.5505	10	0.02654	T	1	.	14.0642	0.64819	1.0:0.0:0.0:0.0	.	281	P35523	CLCN1_HUMAN	A	281	ENSP00000339867:T281A	ENSP00000339867:T281A	T	+	1	0	CLCN1	142731695	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.919000	0.92770	1.738000	0.51689	0.454000	0.30748	ACA	.	.		0.527	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		G	143021573	A	G	143021573	3	3	76	1	0	0	0	0	1	0	0	0	3464	275	10	2	867	2	CLCN1	7	143021573	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	5245050	143021573	16117090	154	10425										
GALNT11	63917	hgsc.bcm.edu	37	chr7	151810421	151810421	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gaccatatggatctcccgaaGgccaggacaccatgacacac	9	14	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr7:151810421G>C	ENST00000434507.1	+	10	1608	c.1171G>C	c.(1171-1173)Ggc>Cgc	p.G391R	GALNT11_ENST00000430044.2_Missense_Mutation_p.G391R|GALNT11_ENST00000320311.2_Missense_Mutation_p.G391R|GALNT11_ENST00000452146.2_Missense_Mutation_p.G310R			Q8NCW6	GLT11_HUMAN	polypeptide N-acetylgalactosaminyltransferase 11	391					cellular protein metabolic process (GO:0044267)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via threonine (GO:0018243)|regulation of Notch signaling pathway (GO:0008593)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|Notch binding (GO:0005112)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|prostate(5)|skin(2)	27	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		ATCTCCCGAAGGCCAGGACAC	0.468																																					p.G391R		Atlas-SNP	.											.	GALNT11	59	.	0			c.G1171C						.						166	155	159					7																	151810421		2203	4300	6503	SO:0001583	missense	63917	exon8			CCCGAAGGCCAGG	AC006017	CCDS5930.1	7q36.1	2014-05-09	2014-05-09		ENSG00000178234	ENSG00000178234	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19875	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 11"	615130	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)"			11925450	Standard	NM_022087		Approved	GalNAc-T11	uc010lqg.1	Q8NCW6	OTTHUMG00000157251	ENST00000434507.1:c.1171G>C	chr7.hg19:g.151810421G>C	ENSP00000416787:p.Gly391Arg	125.0	0.0		104.0	14.0	NM_022087	B3KWF4|Q6PCD1|Q9H6C2|Q9H6Z5|Q9UDR8	Missense_Mutation	SNP	ENST00000434507.1	hg19	CCDS5930.1	.	.	.	.	.	.	.	.	.	.	G	32	5.109135	0.94292	.	.	ENSG00000178234	ENST00000430044;ENST00000452146;ENST00000443352;ENST00000434507;ENST00000320311	T;T;T;T	0.56275	0.47;0.47;0.47;0.47	5.59	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.72293	0.3442	M	0.87456	2.885	0.80722	D	1	D;D;D	0.59357	0.985;0.967;0.985	P;P;P	0.59643	0.861;0.597;0.861	T	0.77464	-0.2578	10	0.62326	D	0.03	.	14.8638	0.70399	0.07:0.0:0.93:0.0	.	310;391;391	B7Z5G5;B3KWF4;Q8NCW6	.;.;GLT11_HUMAN	R	391;310;391;391;391	ENSP00000395122:G391R;ENSP00000393399:G310R;ENSP00000416787:G391R;ENSP00000315835:G391R	ENSP00000315835:G391R	G	+	1	0	GALNT11	151441354	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.770000	0.98971	2.622000	0.88805	0.561000	0.74099	GGC	.	.		0.468	GALNT11-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348184.1	NM_022087		C	151810421	G	C	151810421	3	2	76	1	0	0	0	0	1	0	0	0	6217	1000	35	4	1197	4	GALNT11	7	151810421	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	8788848	151810421	7328242	155	10426										
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24254913	24254913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	accacacatgtggtgtgaagAgcactgacgggaaacaaggc	13	9	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:24254913A>G	ENST00000256412.4	+	6	791	c.571A>G	c.(571-573)Agc>Ggc	p.S191G	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.S112G|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.S112G	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	191					immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TGGTGTGAAGAGCACTGACGG	0.443																																					p.S191G	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.A571G						.						213	206	208					8																	24254913		2203	4300	6503	SO:0001583	missense	27299	exon6			GTGAAGAGCACTG	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.571A>G	chr8.hg19:g.24254913A>G	ENSP00000256412:p.Ser191Gly	115.0	0.0		88.0	34.0	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	hg19	CCDS6044.1	.	.	.	.	.	.	.	.	.	.	A	10.04	1.240511	0.22711	.	.	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.02863	4.13;4.13;4.13	5.53	0.121	0.14695	.	1.186920	0.05939	N	0.636654	T	0.01523	0.0049	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.48843	-0.8999	10	0.16896	T	0.51	-9.9204	2.1959	0.03911	0.3917:0.3701:0.0917:0.1466	.	191	O15204	ADEC1_HUMAN	G	191;112;112	ENSP00000256412:S191G;ENSP00000442592:S112G;ENSP00000428993:S112G	ENSP00000256412:S191G	S	+	1	0	ADAMDEC1	24310858	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	0.938000	0.28965	0.071000	0.16664	0.455000	0.32223	AGC	.	.		0.443	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		G	24254913	A	G	24254913	3	3	76	1	0	0	0	0	1	0	0	0	254	304	11	2	593	2	ADAMDEC1	8	24254913	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10		24254913	122109109	156	10427										
PTK2B	2185	hgsc.bcm.edu	37	chr8	27293843	27293843	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aggcttttttggggaggtctAtgaaggtgtctacacaaatc	12	6	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:27293843A>G	ENST00000397501.1	+	20	2127	c.1319A>G	c.(1318-1320)tAt>tGt	p.Y440C	PTK2B_ENST00000397497.4_Missense_Mutation_p.Y186C|PTK2B_ENST00000338238.4_Missense_Mutation_p.Y440C|PTK2B_ENST00000420218.2_Missense_Mutation_p.Y440C|PTK2B_ENST00000517339.1_Missense_Mutation_p.Y440C|PTK2B_ENST00000544172.1_Missense_Mutation_p.Y440C|PTK2B_ENST00000346049.5_Missense_Mutation_p.Y440C	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	440	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	GGGGAGGTCTATGAAGGTGTC	0.493																																					p.Y440C		Atlas-SNP	.											.	PTK2B	304	.	0			c.A1319G						.						286	259	268					8																	27293843		2203	4300	6503	SO:0001583	missense	2185	exon20			AGGTCTATGAAGG	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"protein tyrosine kinase 2 beta", "PTK2B protein tyrosine kinase 2 beta"	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.1319A>G	chr8.hg19:g.27293843A>G	ENSP00000380638:p.Tyr440Cys	129.0	0.0		90.0	12.0	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Missense_Mutation	SNP	ENST00000397501.1	hg19	CCDS6057.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.573343	0.86542	.	.	ENSG00000120899	ENST00000397501;ENST00000539100;ENST00000338238;ENST00000544172;ENST00000346049;ENST00000420218;ENST00000517339;ENST00000397497	T;T;T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37;-0.37;-0.37	5.44	5.44	0.79542	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.115243	0.64402	D	0.000009	T	0.78541	0.4299	M	0.62723	1.935	0.80722	D	1	P;P;D;D	0.76494	0.646;0.787;0.999;0.999	B;P;D;D	0.71870	0.308;0.453;0.958;0.975	T	0.80888	-0.1181	10	0.87932	D	0	.	13.4604	0.61223	1.0:0.0:0.0:0.0	.	445;186;440;440	Q59GM4;E9PBI4;Q14289-2;Q14289	.;.;.;FAK2_HUMAN	C	440;445;440;440;440;440;440;186	ENSP00000380638:Y440C;ENSP00000342242:Y440C;ENSP00000440926:Y440C;ENSP00000332816:Y440C;ENSP00000391995:Y440C;ENSP00000427931:Y440C;ENSP00000380634:Y186C	ENSP00000342242:Y440C	Y	+	2	0	PTK2B	27349760	1.000000	0.71417	0.986000	0.45419	0.999000	0.98932	6.636000	0.74299	2.068000	0.61886	0.533000	0.62120	TAT	.	.		0.493	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103		G	27293843	A	G	27293843	3	3	76	1	0	0	0	0	1	0	0	0	12776	449	16	2	1373	2	PTK2B	8	27293843	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	3038930	27293843	119070179	157	10428										
NRG1	3084	hgsc.bcm.edu	37	chr8	31498128	31498128	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcaggtacatcttcttcatgGagcccgacgccaacagcacc	9	15	3	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:31498128G>A	ENST00000520407.1	+	1	858	c.628G>A	c.(628-630)Gag>Aag	p.E210K	NRG1_ENST00000519301.1_Intron	NM_013962.2	NP_039256.2	Q02297	NRG1_HUMAN	neuregulin 1	593	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CTTCTTCATGGAGCCCGACGC	0.687																																					p.E210K		Atlas-SNP	.											.	NRG1	260	.	0			c.G628A						.						15	19	17					8																	31498128		1995	4133	6128	SO:0001583	missense	3084	exon1			TTCATGGAGCCCG	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000520407.1:c.628G>A	chr8.hg19:g.31498128G>A	ENSP00000434640:p.Glu210Lys	78.0	0.0		68.0	34.0	NM_013962	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000520407.1	hg19	CCDS47836.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.291804	0.59976	.	.	ENSG00000157168	ENST00000520407;ENST00000523534	T;T	0.74632	-0.86;-0.65	4.53	4.53	0.55603	.	.	.	.	.	T	0.79046	0.4380	.	.	.	0.80722	D	1	D	0.61697	0.99	P	0.53313	0.723	T	0.80079	-0.1532	8	0.44086	T	0.13	.	14.7546	0.69554	0.0:0.0:1.0:0.0	.	210	Q02297-9	.	K	210;63	ENSP00000434640:E210K;ENSP00000429067:E63K	ENSP00000434640:E210K	E	+	1	0	NRG1	31617670	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.844000	0.69430	2.075000	0.62263	0.563000	0.77884	GAG	.	.		0.687	NRG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376412.2			A	31498128	G	A	31498128	3	1	76	1	0	0	0	0	1	0	0	0	10656	1175	41	3	630	3	NRG1	8	31498128	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	4204285	31498128	114865894	158	10429										
ADAM32	203102	hgsc.bcm.edu	37	chr8	39018462	39018462	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcctctttatctagaaatgcAtattgtggtggacaaaactt	7	7	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:39018462A>G	ENST00000379907.4	+	7	699	c.572A>G	c.(571-573)cAt>cGt	p.H191R	ADAM32_ENST00000519315.1_Missense_Mutation_p.H191R|ADAM32_ENST00000437682.2_Missense_Mutation_p.H198R	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	191	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			CTAGAAATGCATATTGTGGTG	0.303																																					p.H191R		Atlas-SNP	.											.	ADAM32	70	.	0			c.A572G						.						151	130	136					8																	39018462		1819	4078	5897	SO:0001583	missense	203102	exon7			AAATGCATATTGT	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"ADAM metallopeptidase domain containing"	15479	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 32"			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.572A>G	chr8.hg19:g.39018462A>G	ENSP00000369238:p.His191Arg	64.0	0.0		79.0	31.0	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	hg19	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.452154	0.63290	.	.	ENSG00000197140	ENST00000399831;ENST00000437682;ENST00000519315;ENST00000379907;ENST00000399826	T;T;T;T	0.63096	2.65;-0.02;-0.02;2.97	5.6	3.21	0.36854	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.769546	0.10651	N	0.649899	T	0.75788	0.3897	M	0.85542	2.76	0.22240	N	0.999267	P;D;D	0.58970	0.888;0.984;0.969	P;D;D	0.65010	0.762;0.917;0.931	T	0.59984	-0.7351	10	0.27082	T	0.32	.	5.6166	0.17434	0.7389:0.173:0.0882:0.0	.	198;191;191	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	R	150;198;191;191;192	ENSP00000382727:H150R;ENSP00000405978:H198R;ENSP00000429422:H191R;ENSP00000369238:H191R	ENSP00000369238:H191R	H	+	2	0	ADAM32	39137619	0.306000	0.24490	0.756000	0.31282	0.766000	0.43426	0.771000	0.26633	0.408000	0.25621	0.533000	0.62120	CAT	.	.		0.303	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		G	39018462	A	G	39018462	3	3	76	1	0	0	0	0	1	0	0	0	249	217	8	2	598	2	ADAM32	8	39018462	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	7520334	39018462	107345560	159	10430										
AGPAT6	137964	hgsc.bcm.edu	37	chr8	41469773	41469773	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cgatgtgatcatcttggccaGcgatggctattatgccatgg	12	9	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:41469773G>A	ENST00000396987.3	+	7	1703	c.776G>A	c.(775-777)aGc>aAc	p.S259N	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	259					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			ATCTTGGCCAGCGATGGCTAT	0.498																																					p.S259N		Atlas-SNP	.											.	AGPAT6	32	.	0			c.G776A						.						145	126	132					8																	41469773		2203	4300	6503	SO:0001583	missense	137964	exon7			TGGCCAGCGATGG	AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	20880	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, zeta"	608143	"1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.776G>A	chr8.hg19:g.41469773G>A	ENSP00000380184:p.Ser259Asn	107.0	0.0		91.0	33.0	NM_178819	Q86V89	Missense_Mutation	SNP	ENST00000396987.3	hg19	CCDS6117.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.612688	0.46631	.	.	ENSG00000158669	ENST00000396987	D	0.97232	-4.3	5.03	5.03	0.67393	Phospholipid/glycerol acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.92583	0.7644	N	0.11651	0.15	0.80722	D	1	B	0.11235	0.004	B	0.20384	0.029	D	0.88395	0.3011	10	0.33940	T	0.23	.	17.5492	0.87871	0.0:0.0:1.0:0.0	.	259	Q86UL3	GPAT4_HUMAN	N	259	ENSP00000380184:S259N	ENSP00000380184:S259N	S	+	2	0	AGPAT6	41588930	1.000000	0.71417	0.986000	0.45419	0.962000	0.63368	7.816000	0.86201	2.620000	0.88729	0.655000	0.94253	AGC	.	.		0.498	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819		A	41469773	G	A	41469773	3	1	76	1	0	0	0	0	1	0	0	0	391	971	34	3	798	3	AGPAT6	8	41469773	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	2451311	41469773	104894249	160	10431										
C8orf22	492307	hgsc.bcm.edu	37	chr8	49986888	49986888	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gaataaaagatctgtctgctActgggtgagttttagccttc	10	7	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:49986888A>G	ENST00000303202.8	+	4	402	c.229A>G	c.(229-231)Act>Gct	p.T77A	C8orf22_ENST00000517663.1_Missense_Mutation_p.T77A|C8orf22_ENST00000399653.4_Missense_Mutation_p.T77A|C8orf22_ENST00000522267.1_Missense_Mutation_p.T77A	NM_001256598.1	NP_001243527.1	Q8WWR9	PDPFL_HUMAN	chromosome 8 open reading frame 22	77					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)					large_intestine(1)|lung(7)|prostate(1)	9		all_cancers(86;0.0452)|all_epithelial(80;0.000863)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				TCTGTCTGCTACTGGGTGAGT	0.398																																					p.T77A		Atlas-SNP	.											.	C8orf22	20	.	0			c.A229G						.						73	69	70					8																	49986888		1891	4112	6003	SO:0001583	missense	492307	exon4			TCTGCTACTGGGT	BC017981	CCDS47854.1, CCDS59101.1, CCDS59102.1	8q11.21	2012-04-11			ENSG00000168333	ENSG00000168333			31745	protein-coding gene	gene with protein product							Standard	NM_001007176		Approved		uc031tba.1	Q8WWR9	OTTHUMG00000164217	ENST00000303202.8:c.229A>G	chr8.hg19:g.49986888A>G	ENSP00000304926:p.Thr77Ala	64.0	0.0		63.0	17.0	NM_001256598	G3V137|Q8WVI1	Missense_Mutation	SNP	ENST00000303202.8	hg19	CCDS59101.1	.	.	.	.	.	.	.	.	.	.	A	0.567	-0.842714	0.02671	.	.	ENSG00000168333	ENST00000517663;ENST00000522267;ENST00000399653;ENST00000303202	.	.	.	4.15	-3.47	0.04753	.	0.737822	0.11828	U	0.525484	T	0.15262	0.0368	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.21724	-1.0237	7	.	.	.	-16.8682	3.0681	0.06221	0.3377:0.0:0.3175:0.3448	.	77	Q8WWR9-2	.	A	77	.	.	T	+	1	0	C8orf22	50149441	0.003000	0.15002	0.001000	0.08648	0.002000	0.02628	0.250000	0.18235	-0.237000	0.09739	0.421000	0.28195	ACT	.	.		0.398	C8orf22-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377837.1	NM_001007176		G	49986888	A	G	49986888	3	3	76	1	0	0	0	0	1	0	0	0	2421	391	14	2	239	2	C8orf22	8	49986888	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	8517115	49986888	96377134	161	10432										
CSPP1	10565	hgsc.bcm.edu	37	chr8	68107738	68107738	+	IGR	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcagaaacgctgaaacgtttCatggcagagcagctgaacca	10	10	2	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:68107738C>T	ENST00000262215.3	-	0	7225				CSPP1_ENST00000262210.5_Silent_p.F1192F|CSPP1_ENST00000412460.1_Silent_p.F847F|ARFGEF1_ENST00000520381.1_Intron|CSPP1_ENST00000521168.1_3'UTR|ARFGEF1_ENST00000517955.1_5'Flank	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)						endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TGAAACGTTTCATGGCAGAGC	0.517																																					p.F1192F		Atlas-SNP	.											.	CSPP1	129	.	0			c.C3576T						.						96	96	96					8																	68107738		2001	4187	6188	SO:0001628	intergenic_variant	79848	exon29			ACGTTTCATGGCA	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626		chr8.hg19:g.68107738C>T		163.0	0.0		174.0	89.0	NM_024790	Q9NV46|Q9UFV2|Q9UNL0	Silent	SNP	ENST00000262215.3	hg19	CCDS6199.1																																																																																			.	.		0.517	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		T	68107738	C	T	68107738	1	4	76	0	1	0	0	0	0	0	0	0	3964	825	29	3		3	CSPP1	8	68107738	IGR	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	18120850	68107738	78256284	162	10433										
NCOA2	10499	hgsc.bcm.edu	37	chr8	71036125	71036125	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccttgggcactcacctgctcGggacccatggaggacagccc	12	16	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:71036125G>A	ENST00000452400.2	-	21	4468	c.4287C>T	c.(4285-4287)ccC>ccT	p.P1429P	NCOA2_ENST00000267974.4_Silent_p.P517P	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	1429					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TCACCTGCTCGGGACCCATGG	0.507			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.P1429P		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.C4287T						.						74	72	73					8																	71036125		2113	4231	6344	SO:0001819	synonymous_variant	10499	exon21			CTGCTCGGGACCC	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.4287C>T	chr8.hg19:g.71036125G>A		103.0	0.0		126.0	34.0	NM_006540	Q14CD2	Silent	SNP	ENST00000452400.2	hg19	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	G	9.294	1.051388	0.19827	.	.	ENSG00000140396	ENST00000518363	.	.	.	5.8	-0.043	0.13861	.	0.102095	0.64402	D	0.000002	T	0.56920	0.2018	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54417	-0.8297	6	0.87932	D	0	.	3.9919	0.09541	0.3857:0.0:0.3562:0.2581	.	.	.	.	L	530	.	ENSP00000429132:P530L	P	-	2	0	NCOA2	71198679	0.183000	0.23186	0.999000	0.59377	0.995000	0.86356	-0.353000	0.07691	0.040000	0.15660	0.655000	0.94253	CCG	.	.		0.507	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			A	71036125	G	A	71036125	2	1	76	1	0	0	0	0	0	0	0	1	10238	1103	39	1		1	NCOA2	8	71036125	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	2928387	71036125	75327897	163	10434										
EYA1	2138	hgsc.bcm.edu	37	chr8	72229893	72229893	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gactgagactgtgacaatccAccttcagtcttgatgcctgc	9	12	2	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:72229893A>T	ENST00000340726.3	-	7	1089	c.450T>A	c.(448-450)ggT>ggA	p.G150G	EYA1_ENST00000388742.4_Silent_p.G150G|EYA1_ENST00000388740.3_Silent_p.G117G|EYA1_ENST00000388743.2_Silent_p.G149G|EYA1_ENST00000388741.2_Silent_p.G116G|EYA1_ENST00000303824.7_Silent_p.G144G|EYA1_ENST00000419131.1_Silent_p.G145G	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	150					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			GTGACAATCCACCTTCAGTCT	0.443																																					p.G150G		Atlas-SNP	.											.	EYA1	108	.	0			c.T450A						.						281	256	264					8																	72229893		2203	4300	6503	SO:0001819	synonymous_variant	2138	exon7			CAATCCACCTTCA	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"Protein tyrosine phosphatases / Asp-based PTPs"	3519	protein-coding gene	gene with protein product		601653	"eyes absent (Drosophila) homolog 1", "eyes absent homolog 1 (Drosophila)"	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.450T>A	chr8.hg19:g.72229893A>T		55.0	0.0		58.0	23.0	NM_000503	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Silent	SNP	ENST00000340726.3	hg19	CCDS34906.1																																																																																			.	.		0.443	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		T	72229893	A	T	72229893	2	4	76	1	0	0	0	0	0	0	0	1	5330	146	6	4		4	EYA1	8	72229893	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	1193768	72229893	74134129	164	10435										
IMPA1	3612	hgsc.bcm.edu	37	chr8	82572837	82572837	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agtgaattcccatttcataaTatgcatctgctccgccagtt	6	11	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:82572837T>C	ENST00000256108.5	-	8	1097	c.632A>G	c.(631-633)tAt>tGt	p.Y211C	IMPA1_ENST00000523710.1_5'UTR|IMPA1_ENST00000449740.2_Missense_Mutation_p.Y270C|IMPA1_ENST00000311489.4_Missense_Mutation_p.I175V	NM_005536.3	NP_005527.1	P29218	IMPA1_HUMAN	inositol(myo)-1(or 4)-monophosphatase 1	211					inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|inositol monophosphate phosphatase activity (GO:0052834)|lithium ion binding (GO:0031403)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|stomach(1)	18					Lithium(DB01356)	CATTTCATAATATGCATCTGC	0.413																																					p.Y270C		Atlas-SNP	.											.	IMPA1	46	.	0			c.A809G						.						97	88	91					8																	82572837		2203	4299	6502	SO:0001583	missense	3612	exon9			TCATAATATGCAT		CCDS6231.1, CCDS47883.1, CCDS47884.1	8q21.1-q21.3	2008-01-28			ENSG00000133731	ENSG00000133731	3.1.3.25		6050	protein-coding gene	gene with protein product		602064		IMPA		1377913	Standard	NM_005536		Approved		uc011lfq.1	P29218	OTTHUMG00000164682	ENST00000256108.5:c.632A>G	chr8.hg19:g.82572837T>C	ENSP00000256108:p.Tyr211Cys	290.0	0.0		453.0	53.0	NM_001144878	B2R733|B4DLN3|B7Z6Q4|J3KQT7|Q9UK71	Missense_Mutation	SNP	ENST00000256108.5	hg19	CCDS6231.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	19.47|19.47|19.47	3.834114|3.834114|3.834114	0.71373|0.71373|0.71373	.|.|.	.|.|.	ENSG00000133731|ENSG00000133731|ENSG00000133731	ENST00000523942|ENST00000311489|ENST00000256108;ENST00000449740	.|T|T;T	.|0.52295|0.60424	.|0.67|0.19;0.19	4.23|4.23|4.23	4.23|4.23|4.23	0.50019|0.50019|0.50019	.|.|.	.|.|0.127142	.|.|0.56097	.|.|D	.|.|0.000038	T|T|T	0.74756|0.74756|0.74756	0.3758|0.3758|0.3758	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|B|D;D	.|0.19331|0.89917	.|0.035|1.0;1.0	.|B|D;D	.|0.27380|0.75484	.|0.079|0.986;0.98	T|T|T	0.78229|0.78229|0.78229	-0.2285|-0.2285|-0.2285	4|8|9	.|0.25751|0.59425	.|T|D	.|0.34|0.04	-25.0445|-25.0445|-25.0445	13.5125|13.5125|13.5125	0.61522|0.61522|0.61522	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|175|270;211	.|B4DLN3|B7Z6Q4;P29218	.|.|.;IMPA1_HUMAN	M|V|C	235|175|211;270	.|ENSP00000311803:I175V|ENSP00000256108:Y211C;ENSP00000408526:Y270C	.|ENSP00000311803:I175V|ENSP00000256108:Y211C	I|I|Y	-|-|-	3|1|2	3|0|0	IMPA1|IMPA1|IMPA1	82735392|82735392|82735392	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.952000|0.952000|0.952000	0.39060|0.39060|0.39060	0.981000|0.981000|0.981000	0.71138|0.71138|0.71138	4.450000|4.450000|4.450000	0.60041|0.60041|0.60041	1.764000|1.764000|1.764000	0.52075|0.52075|0.52075	0.445000|0.445000|0.445000	0.29226|0.29226|0.29226	ATA|ATT|TAT	.	.		0.413	IMPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379723.1			C	82572837	T	C	82572837	3	2	76	1	0	0	0	0	1	0	0	0	7731	1406	49	2	209	2	IMPA1	8	82572837	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	10342944	82572837	63791185	165	10436										
CA1	759	hgsc.bcm.edu	37	chr8	86250479	86250479	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcagaagggtctttcagctcAcctgatcggttatcgttgtc	10	10	4	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:86250479A>T	ENST00000523953.1	-	4	1282		c.e4+1		CA1_ENST00000256119.5_Splice_Site|CA1_ENST00000523022.1_Splice_Site|CA1_ENST00000431316.1_Splice_Site|CA1_ENST00000542576.1_Splice_Site|CA1_ENST00000518341.1_Splice_Site|CA1_ENST00000432364.2_Splice_Site|CA1_ENST00000522389.1_Intron			P00915	CAH1_HUMAN	carbonic anhydrase I						bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	13		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Diclofenamide(DB01144)|Dorzolamide(DB00869)|Ethinamate(DB01031)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methazolamide(DB00703)|Methocarbamol(DB00423)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Zonisamide(DB00909)	CTTTCAGCTCACCTGATCGGT	0.388																																					.		Atlas-SNP	.											.	CA1	41	.	0			c.235+2T>A						.						165	167	166					8																	86250479		2203	4300	6503	SO:0001630	splice_region_variant	759	exon5			CAGCTCACCTGAT	M33987	CCDS6237.1	8q21.2	2006-03-10				ENSG00000133742	4.2.1.1	"Carbonic anhydrases"	1368	protein-coding gene	gene with protein product		114800				1916821	Standard	NM_001164830		Approved	Car1	uc003ydi.3	P00915		ENST00000523953.1:c.235+1T>A	chr8.hg19:g.86250479A>T		60.0	0.0		92.0	13.0	NM_001738		Splice_Site	SNP	ENST00000523953.1	hg19	CCDS6237.1	.	.	.	.	.	.	.	.	.	.	A	10.84	1.462683	0.26248	.	.	ENSG00000133742	ENST00000523953;ENST00000256119;ENST00000431316;ENST00000542576;ENST00000432364;ENST00000523022;ENST00000521679;ENST00000517618;ENST00000517590;ENST00000521846;ENST00000522579;ENST00000522814;ENST00000522662;ENST00000523858	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1693	0.65497	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CA1	86437731	1.000000	0.71417	0.868000	0.34077	0.066000	0.16364	8.123000	0.89586	2.020000	0.59435	0.482000	0.46254	.	.	.		0.388	CA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381067.1	NM_001738	Intron	T	86250479	A	T	86250479	5	4	76	1	0	0	0	0	0	0	1	0	2512	173	6	4	572	4	CA1	8	86250479	Splice_Site	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	3677642	86250479	60113543	166	10437										
ADCY8	114	hgsc.bcm.edu	37	chr8	131797638	131797638	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gagtcctttacctgtttttcAggtgacaggcctgacacggc	11	11	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:131797638A>T	ENST00000286355.5	-	16	5236	c.3144T>A	c.(3142-3144)ccT>ccA	p.P1048P	ADCY8_ENST00000377928.3_Silent_p.P917P	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	1048					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CCTGTTTTTCAGGTGACAGGC	0.502										HNSCC(32;0.087)																											p.P1048P		Atlas-SNP	.											.	ADCY8	291	.	0			c.T3144A						.						107	88	94					8																	131797638		2203	4300	6503	SO:0001819	synonymous_variant	114	exon16			TTTTTCAGGTGAC	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.3144T>A	chr8.hg19:g.131797638A>T		49.0	0.0		75.0	6.0	NM_001115		Silent	SNP	ENST00000286355.5	hg19	CCDS6363.1																																																																																			.	.		0.502	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			T	131797638	A	T	131797638	2	4	76	1	0	0	0	0	0	0	0	1	300	175	7	4		4	ADCY8	8	131797638	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	45547159	131797638	14566384	167	10438										
ADCY8	114	hgsc.bcm.edu	37	chr8	131848557	131848557	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gaggttgtcataacgcagaaAgaggcctgcgtagacggtct	14	8	2	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:131848557A>G	ENST00000286355.5	-	12	4733	c.2641T>C	c.(2641-2643)Ttt>Ctt	p.F881L	ADCY8_ENST00000377928.3_Missense_Mutation_p.F750L	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	881			F -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TAACGCAGAAAGAGGCCTGCG	0.532										HNSCC(32;0.087)																											p.F881L		Atlas-SNP	.											ADCY8,colon,carcinoma,0,1	ADCY8	291	.	0			c.T2641C						.						149	119	129					8																	131848557		2203	4300	6503	SO:0001583	missense	114	exon12			GCAGAAAGAGGCC	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.2641T>C	chr8.hg19:g.131848557A>G	ENSP00000286355:p.Phe881Leu	98.0	0.0		130.0	46.0	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	A	17.76	3.469130	0.63625	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.80480	-1.38;-1.38	5.29	5.29	0.74685	.	0.058536	0.64402	D	0.000002	D	0.83792	0.5331	L	0.50333	1.59	0.35480	D	0.798077	D;P	0.67145	0.996;0.93	P;P	0.58721	0.844;0.449	D	0.86288	0.1672	10	0.31617	T	0.26	.	14.4064	0.67086	1.0:0.0:0.0:0.0	.	750;881	E7EVL1;P40145	.;ADCY8_HUMAN	L	881;750	ENSP00000286355:F881L;ENSP00000367161:F750L	ENSP00000286355:F881L	F	-	1	0	ADCY8	131917739	1.000000	0.71417	0.999000	0.59377	0.203000	0.24098	8.691000	0.91279	2.000000	0.58554	0.459000	0.35465	TTT	.	.		0.532	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			G	131848557	A	G	131848557	3	3	76	1	0	0	0	0	1	0	0	0	300	72	3	2	1142	2	ADCY8	8	131848557	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	50919	131848557	14515465	168	10439										
TG	7038	hgsc.bcm.edu	37	chr8	133935748	133935748	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccctcttgaggactcacagtGtttgagtaggtgctgggggt	15	8	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:133935748G>C	ENST00000220616.4	+	22	4734	c.4694G>C	c.(4693-4695)tGt>tCt	p.C1565S	TG_ENST00000377869.1_Intron|TG_ENST00000542445.1_5'UTR	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1565	Thyroglobulin type-1 11. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GACTCACAGTGTTTGAGTAGG	0.577																																					p.C1565S		Atlas-SNP	.											.	TG	416	.	0			c.G4694C						.						53	51	52					8																	133935748		2203	4300	6503	SO:0001583	missense	7038	exon22			CACAGTGTTTGAG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4694G>C	chr8.hg19:g.133935748G>C	ENSP00000220616:p.Cys1565Ser	67.0	0.0		89.0	24.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.072203	0.55646	.	.	ENSG00000042832	ENST00000543313;ENST00000220616	T	0.78481	-1.18	4.84	4.84	0.62591	Thyroglobulin type-1 (3);	0.100524	0.45606	D	0.000343	D	0.87309	0.6145	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88849	0.3318	10	0.87932	D	0	.	13.429	0.61044	0.0:0.0:1.0:0.0	.	1565	P01266	THYG_HUMAN	S	371;1565	ENSP00000220616:C1565S	ENSP00000220616:C1565S	C	+	2	0	TG	134004930	1.000000	0.71417	1.000000	0.80357	0.543000	0.35085	5.563000	0.67352	2.247000	0.74100	0.555000	0.69702	TGT	.	.		0.577	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	133935748	G	C	133935748	3	2	76	1	0	0	0	0	1	0	0	0	15828	1377	48	4	4780	4	TG	8	133935748	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	2087191	133935748	12428274	169	10440										
PTK2	5747	hgsc.bcm.edu	37	chr8	141889628	141889628	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cctcacactggagacgcccaTatccacgtgaagccagtgaa	9	14	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:141889628T>C	ENST00000522684.1	-	4	533	c.304A>G	c.(304-306)Atg>Gtg	p.M102V	PTK2_ENST00000520892.1_Missense_Mutation_p.M102V|PTK2_ENST00000535192.1_Missense_Mutation_p.M102V|PTK2_ENST00000395218.2_Missense_Mutation_p.M102V|PTK2_ENST00000519419.1_Missense_Mutation_p.M146V|PTK2_ENST00000517887.1_Missense_Mutation_p.M146V|PTK2_ENST00000340930.3_Missense_Mutation_p.M102V|PTK2_ENST00000521059.1_Missense_Mutation_p.M102V|PTK2_ENST00000519881.1_Missense_Mutation_p.M102V	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	102	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			GAGACGCCCATATCCACGTGA	0.507																																					p.M124V		Atlas-SNP	.											.	PTK2	311	.	0			c.A370G						.						290	272	278					8																	141889628		2203	4300	6503	SO:0001583	missense	5747	exon4			CGCCCATATCCAC	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9611	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 71"	600758	"PTK2 protein tyrosine kinase 2"			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.304A>G	chr8.hg19:g.141889628T>C	ENSP00000429911:p.Met102Val	128.0	0.0		194.0	92.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.23|14.23	2.474467|2.474467	0.43942|0.43942	.|.	.|.	ENSG00000169398|ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000517887;ENST00000521059;ENST00000395218;ENST00000340930;ENST00000519419;ENST00000520828;ENST00000520475;ENST00000519881;ENST00000520892;ENST00000523803;ENST00000521907;ENST00000517453;ENST00000520045;ENST00000521395|ENST00000519654	T;T;T;T;T;T;T|.	0.75154|.	-0.89;-0.88;-0.91;-0.89;-0.88;-0.88;-0.91|.	5.36|5.36	5.36|5.36	0.76844|0.76844	Band 4.1 domain (1);FERM domain (1);|.	0.037553|.	0.85682|.	D|.	0.000000|.	T|T	0.69287|0.69287	0.3094|0.3094	L|L	0.55481|0.55481	1.735|1.735	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.13145|.	0.004;0.007;0.002;0.002|.	B;B;B;B|.	0.06405|.	0.002;0.002;0.001;0.0|.	T|T	0.67776|0.67776	-0.5583|-0.5583	10|5	0.42905|.	T|.	0.14|.	.|.	15.6584|15.6584	0.77162|0.77162	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	102;102;124;102|.	B4E2N6;Q05397;Q658W2;Q8IYN9|.	.;FAK1_HUMAN;.;.|.	V|C	102;102;146;102;102;102;146;1;102;102;102;102;102;102;102;102|112	ENSP00000429911:M102V;ENSP00000438009:M102V;ENSP00000429082:M146V;ENSP00000429474:M102V;ENSP00000378644:M102V;ENSP00000341189:M102V;ENSP00000429129:M146V|.	ENSP00000341189:M102V|.	M|Y	-|-	1|2	0|0	PTK2|PTK2	141958810|141958810	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.990000|0.990000	0.78478|0.78478	3.679000|3.679000	0.54634|0.54634	2.160000|2.160000	0.67779|0.67779	0.528000|0.528000	0.53228|0.53228	ATG|TAT	.	.		0.507	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		C	141889628	T	C	141889628	3	2	76	1	0	0	0	0	1	0	0	0	12775	1406	49	2	2970	2	PTK2	8	141889628	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	7953880	141889628	4474394	170	10441										
ZFP41	286128	hgsc.bcm.edu	37	chr8	144332183	144332183	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctgcctgagtcctgaagacgAagagcacgtctttgatgcct	11	11	1	5			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:144332183A>T	ENST00000330701.4	+	2	539	c.170A>T	c.(169-171)gAa>gTa	p.E57V	ZFP41_ENST00000522452.1_Missense_Mutation_p.E57V|ZFP41_ENST00000520584.1_Missense_Mutation_p.E57V	NM_173832.4	NP_776193.1	Q8N8Y5	ZFP41_HUMAN	ZFP41 zinc finger protein	57					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|lung(4)|ovary(1)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CCTGAAGACGAAGAGCACGTC	0.552																																					p.E57V		Atlas-SNP	.											.	ZFP41	25	.	0			c.A170T						.						62	69	66					8																	144332183		2203	4300	6503	SO:0001583	missense	286128	exon2			AAGACGAAGAGCA		CCDS6397.1	8q24.3	2013-01-08	2012-11-27		ENSG00000181638	ENSG00000181638		"Zinc fingers, C2H2-type"	26786	protein-coding gene	gene with protein product			"zinc finger protein 41 homolog (mouse)"			11214971	Standard	NM_173832		Approved	FLJ38705, FLJ00028, ZNF753	uc003yxw.4	Q8N8Y5	OTTHUMG00000164951	ENST00000330701.4:c.170A>T	chr8.hg19:g.144332183A>T	ENSP00000327427:p.Glu57Val	79.0	0.0		97.0	7.0	NM_173832	D3DWJ5	Missense_Mutation	SNP	ENST00000330701.4	hg19	CCDS6397.1	.	.	.	.	.	.	.	.	.	.	A	19.95	3.921081	0.73213	.	.	ENSG00000181638	ENST00000520584;ENST00000330701;ENST00000522452	T;T;T	0.07216	3.21;3.21;3.21	2.82	1.66	0.24008	.	.	.	.	.	T	0.08313	0.0207	N	0.24115	0.695	0.09310	N	1	D	0.61080	0.989	P	0.50825	0.651	T	0.27365	-1.0076	9	0.72032	D	0.01	-10.2381	4.5313	0.12006	0.7139:0.0:0.2861:0.0	.	57	Q8N8Y5	ZFP41_HUMAN	V	57	ENSP00000430465:E57V;ENSP00000327427:E57V;ENSP00000428966:E57V	ENSP00000327427:E57V	E	+	2	0	ZFP41	144403558	0.001000	0.12720	0.001000	0.08648	0.710000	0.40934	0.272000	0.18644	0.499000	0.27970	0.383000	0.25322	GAA	.	.		0.552	ZFP41-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381114.2	NM_173832		T	144332183	A	T	144332183	3	4	76	1	0	0	0	0	1	0	0	0	17664	246	9	4	172	4	ZFP41	8	144332183	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	2442555	144332183	2031839	171	10442										
PLEC	5339	hgsc.bcm.edu	37	chr8	145001890	145001890	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccccgcagctcatcccgcagGgcgtcgaacgtgggctgctg	14	16	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:145001890G>A	ENST00000322810.4	-	27	4024	c.3855C>T	c.(3853-3855)gcC>gcT	p.A1285A	PLEC_ENST00000527096.1_Silent_p.A1171A|PLEC_ENST00000354589.3_Silent_p.A1148A|PLEC_ENST00000357649.2_Silent_p.A1152A|PLEC_ENST00000345136.3_Silent_p.A1148A|PLEC_ENST00000356346.3_Silent_p.A1134A|PLEC_ENST00000354958.2_Silent_p.A1126A|PLEC_ENST00000398774.2_Silent_p.A1116A|PLEC_ENST00000436759.2_Silent_p.A1175A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1285	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CATCCCGCAGGGCGTCGAACG	0.731																																					p.A1285A		Atlas-SNP	.											.	PLEC	1144	.	0			c.C3855T						.						7	8	8					8																	145001890		2028	4131	6159	SO:0001819	synonymous_variant	5339	exon27			CCGCAGGGCGTCG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.3855C>T	chr8.hg19:g.145001890G>A		48.0	0.0		59.0	11.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.		0.731	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	145001890	G	A	145001890	2	1	76	1	0	0	0	0	0	0	0	1	12061	1219	43	3		3	PLEC	8	145001890	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	669707	145001890	1362132	172	10443										
ARHGAP39	80728	hgsc.bcm.edu	37	chr8	145758592	145758592	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cacccagggcagctggcgctCggggtagcgctctctctgca	14	15	2	0	rs144988605		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:145758592C>T	ENST00000276826.5	-	7	2914	c.2713G>A	c.(2713-2715)Gag>Aag	p.E905K	ARHGAP39_ENST00000377307.2_Missense_Mutation_p.E936K|ARHGAP39_ENST00000540274.1_Missense_Mutation_p.E905K			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	905	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						AGCTGGCGCTCGGGGTAGCGC	0.657																																					p.E936K		Atlas-SNP	.											.	ARHGAP39	80	.	0			c.G2806A						.						71	66	67					8																	145758592		2203	4300	6503	SO:0001583	missense	80728	exon10			GGCGCTCGGGGTA		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"Rho GTPase activating proteins"	29351	protein-coding gene	gene with protein product	"RhoGAP93B homolog (Drosophila)", "crossGAP homolog (Drosophila)"	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.2713G>A	chr8.hg19:g.145758592C>T	ENSP00000276826:p.Glu905Lys	41.0	0.0		62.0	24.0	NM_025251	B4E1I1	Missense_Mutation	SNP	ENST00000276826.5	hg19		.	.	.	.	.	.	.	.	.	.	C	19.87	3.906975	0.72868	.	.	ENSG00000147799	ENST00000276826;ENST00000377307;ENST00000540274	T;T;T	0.68181	-0.31;-0.08;-0.31	4.94	4.94	0.65067	Rho GTPase-activating protein domain (2);Rho GTPase activation protein (1);	0.275541	0.38111	N	0.001802	T	0.48114	0.1482	N	0.21142	0.635	0.38315	D	0.943359	B;B	0.30526	0.069;0.283	B;B	0.22152	0.009;0.038	T	0.50457	-0.8826	10	0.07482	T	0.82	-22.2584	16.014	0.80422	0.0:1.0:0.0:0.0	.	905;936	Q9C0H5;Q9C0H5-2	RHG39_HUMAN;.	K	905;936;905	ENSP00000276826:E905K;ENSP00000366522:E936K;ENSP00000445075:E905K	ENSP00000276826:E905K	E	-	1	0	ARHGAP39	145729400	0.996000	0.38824	0.355000	0.25773	0.728000	0.41692	5.999000	0.70665	2.448000	0.82819	0.563000	0.77884	GAG	.	C|1.000;G|0.000		0.657	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			T	145758592	C	T	145758592	3	4	76	1	0	0	0	0	1	0	0	0	884	893	31	1	554	1	ARHGAP39	8	145758592	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	756702	145758592	605430	173	10444										
ARHGAP39	80728	hgsc.bcm.edu	37	chr8	145806392	145806392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggctgctctccgccgaggcgCgcggggactccgtgttctgc	16	15	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr8:145806392C>T	ENST00000276826.5	-	2	551	c.350G>A	c.(349-351)cGc>cAc	p.R117H	ARHGAP39_ENST00000377307.2_Missense_Mutation_p.R117H|ARHGAP39_ENST00000540274.1_Missense_Mutation_p.R117H			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	117					axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						CGCCGAGGCGCGCGGGGACTC	0.711																																					p.R117H		Atlas-SNP	.											.	ARHGAP39	80	.	0			c.G350A						.						10	11	11					8																	145806392		2181	4268	6449	SO:0001583	missense	80728	exon4			GAGGCGCGCGGGG		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"Rho GTPase activating proteins"	29351	protein-coding gene	gene with protein product	"RhoGAP93B homolog (Drosophila)", "crossGAP homolog (Drosophila)"	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.350G>A	chr8.hg19:g.145806392C>T	ENSP00000276826:p.Arg117His	42.0	0.0		55.0	23.0	NM_025251	B4E1I1	Missense_Mutation	SNP	ENST00000276826.5	hg19		.	.	.	.	.	.	.	.	.	.	C	16.60	3.168355	0.57584	.	.	ENSG00000147799	ENST00000276826;ENST00000377307;ENST00000540274	T;T;T	0.03242	4.0;4.0;4.0	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000006	T	0.09113	0.0225	L	0.34521	1.04	0.25764	N	0.984919	D;D	0.76494	0.998;0.999	P;D	0.63877	0.781;0.919	T	0.15235	-1.0444	10	0.41790	T	0.15	-30.7916	12.4416	0.55627	0.0:0.8309:0.1691:0.0	.	117;117	Q9C0H5;Q9C0H5-2	RHG39_HUMAN;.	H	117	ENSP00000276826:R117H;ENSP00000366522:R117H;ENSP00000445075:R117H	ENSP00000276826:R117H	R	-	2	0	ARHGAP39	145777200	0.324000	0.24652	0.309000	0.25155	0.030000	0.12068	3.676000	0.54612	2.526000	0.85167	0.557000	0.71058	CGC	.	.		0.711	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			T	145806392	C	T	145806392	3	4	76	1	0	0	0	0	1	0	0	0	884	768	27	1	3034	1	ARHGAP39	8	145806392	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	47800	145806392	557630	174	10445										
CHMP5	51510	hgsc.bcm.edu	37	chr9	33271184	33271184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	actgggagtaaaggaaatgaAgaaggcatacaagcaagtga	13	4	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr9:33271184A>G	ENST00000223500.8	+	5	487	c.350A>G	c.(349-351)aAg>aGg	p.K117R	CHMP5_ENST00000419016.2_Missense_Mutation_p.K117R	NM_016410.5	NP_057494.3	Q9NZZ3	CHMP5_HUMAN	charged multivesicular body protein 5	117					endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of receptor recycling (GO:0001919)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10			LUSC - Lung squamous cell carcinoma(29;0.00506)			AAGGAAATGAAGAAGGCATAC	0.363																																					p.K117R		Atlas-SNP	.											.	CHMP5	15	.	0			c.A350G						.						170	149	156					9																	33271184		2203	4300	6503	SO:0001583	missense	51510	exon5			AAATGAAGAAGGC	AF132968	CCDS6537.1, CCDS56569.1	9p13.3	2011-09-21	2011-09-21	2005-08-09	ENSG00000086065	ENSG00000086065		"Charged multivesicular body proteins"	26942	protein-coding gene	gene with protein product		610900	"chromosome 9 open reading frame 83", "chromatin modifying protein 5"	C9orf83, SNF7DC2		15644320, 11559748	Standard	NM_016410		Approved	HSPC177, CGI-34, Vps60	uc003zsm.4	Q9NZZ3	OTTHUMG00000019765	ENST00000223500.8:c.350A>G	chr9.hg19:g.33271184A>G	ENSP00000223500:p.Lys117Arg	57.0	0.0		49.0	25.0	NM_016410	B2RD95|B4DIR6|Q5VXW2|Q96AV2|Q9HB68|Q9NYS4|Q9Y323	Missense_Mutation	SNP	ENST00000223500.8	hg19	CCDS6537.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.656726	0.88154	.	.	ENSG00000086065	ENST00000223500;ENST00000419016	T;T	0.77750	-1.12;-1.12	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.83677	0.5306	M	0.81802	2.56	0.58432	D	0.999995	P;P	0.50066	0.931;0.763	P;P	0.50659	0.647;0.529	D	0.85690	0.1306	10	0.56958	D	0.05	-8.693	14.049	0.64725	1.0:0.0:0.0:0.0	.	117;117	B4DIR6;Q9NZZ3	.;CHMP5_HUMAN	R	117	ENSP00000223500:K117R;ENSP00000442725:K117R	ENSP00000223500:K117R	K	+	2	0	CHMP5	33261184	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.879000	0.92398	2.259000	0.74868	0.529000	0.55759	AAG	.	.		0.363	CHMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052040.3	NM_016410		G	33271184	A	G	33271184	3	3	76	1	0	0	0	0	1	0	0	0	3361	72	3	2	368	2	CHMP5	9	33271184	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10		33271184	107942247	175	10446										
FBXO10	26267	hgsc.bcm.edu	37	chr9	37541574	37541574	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caagactcaggctccacatcTggctggttgggccaattggg	13	11	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr9:37541574T>C	ENST00000432825.2	-	2	240	c.192A>G	c.(190-192)ccA>ccG	p.P64P	FBXO10_ENST00000541829.1_Intron|RP11-613M10.8_ENST00000544475.1_5'UTR|RP11-613M10.8_ENST00000537239.2_3'UTR	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	64					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		GCTCCACATCTGGCTGGTTGG	0.567																																					p.P64P		Atlas-SNP	.											.	FBXO10	75	.	0			c.A192G						.						47	48	47					9																	37541574		2007	4171	6178	SO:0001819	synonymous_variant	26267	exon2			CACATCTGGCTGG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"F-boxes /  "other""	13589	protein-coding gene	gene with protein product		609092	"F-box only protein 10"			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.192A>G	chr9.hg19:g.37541574T>C		132.0	0.0		127.0	36.0	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Silent	SNP	ENST00000432825.2	hg19	CCDS47966.1																																																																																			.	.		0.567	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3			C	37541574	T	C	37541574	2	2	76	1	0	0	0	0	0	0	0	1	5734	1567	55	2		2	FBXO10	9	37541574	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	4270390	37541574	103671857	176	10447										
TMC1	117531	hgsc.bcm.edu	37	chr9	75431065	75431065	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgtgtctcctctagccttcaTacaccgaattcgacatcagt	6	13	4	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr9:75431065T>G	ENST00000297784.5	+	19	2242	c.1702T>G	c.(1702-1704)Tac>Gac	p.Y568D	TMC1_ENST00000486417.1_3'UTR|TMC1_ENST00000396237.3_Missense_Mutation_p.Y568D|TMC1_ENST00000340019.3_Missense_Mutation_p.Y568D	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	568					auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						CTAGCCTTCATACACCGAATT	0.453																																					p.Y568D	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.T1702G						.						205	155	172					9																	75431065		2203	4300	6503	SO:0001583	missense	117531	exon19			CCTTCATACACCG	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"transmembrane, cochlear expressed, 1"	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.1702T>G	chr9.hg19:g.75431065T>G	ENSP00000297784:p.Tyr568Asp	97.0	0.0		95.0	13.0	NM_138691	A8MVZ2|B1AM91	Missense_Mutation	SNP	ENST00000297784.5	hg19	CCDS6643.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461157	0.63513	.	.	ENSG00000165091	ENST00000297784;ENST00000340019;ENST00000396235;ENST00000537917;ENST00000538054;ENST00000542143;ENST00000396237	T;T;T	0.63096	-0.02;-0.02;-0.02	6.16	5.03	0.67393	.	0.066732	0.64402	D	0.000007	T	0.78880	0.4353	M	0.82193	2.58	0.53688	D	0.999971	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.79108	0.986;0.986;0.992	T	0.79196	-0.1903	10	0.41790	T	0.15	-19.4271	12.2288	0.54476	0.0:0.0659:0.0:0.9341	.	535;535;568	A5D8Y1;A4FUA6;Q8TDI8	.;.;TMC1_HUMAN	D	568;568;535;535;535;562;568	ENSP00000297784:Y568D;ENSP00000341433:Y568D;ENSP00000379538:Y568D	ENSP00000297784:Y568D	Y	+	1	0	TMC1	74620885	1.000000	0.71417	0.980000	0.43619	0.364000	0.29643	8.040000	0.89188	1.148000	0.42385	0.528000	0.53228	TAC	.	.		0.453	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1			G	75431065	T	G	75431065	3	3	76	1	0	0	0	0	1	0	0	0	15999	1406	49	5	1760	5	TMC1	9	75431065	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	37889491	75431065	65782366	177	10448										
OGN	4969	hgsc.bcm.edu	37	chr9	95148565	95148565	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggtccaagtagaggaaggtgAggttattcagtttctgtaag	14	4	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr9:95148565A>T	ENST00000262551.4	-	6	1064	c.644T>A	c.(643-645)cTc>cAc	p.L215H	OGN_ENST00000375561.5_Missense_Mutation_p.L215H|CENPP_ENST00000375587.3_Intron	NM_033014.2	NP_148935.1	P20774	MIME_HUMAN	osteoglycin	215					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|negative regulation of smooth muscle cell proliferation (GO:0048662)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	13						GAGGAAGGTGAGGTTATTCAG	0.368																																					p.L215H		Atlas-SNP	.											.	OGN	26	.	0			c.T644A						.						193	186	189					9																	95148565		2203	4300	6503	SO:0001583	missense	4969	exon6			AAGGTGAGGTTAT	AI424992	CCDS6695.1	9q22	2008-02-05	2007-02-16		ENSG00000106809	ENSG00000106809		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8126	protein-coding gene	gene with protein product	"mimecan proteoglycan"	602383	"osteoglycin (osteoinductive factor)"			2372374	Standard	NM_033014		Approved	mimecan, OIF, SLRR3A	uc004asa.3	P20774	OTTHUMG00000020224	ENST00000262551.4:c.644T>A	chr9.hg19:g.95148565A>T	ENSP00000262551:p.Leu215His	50.0	0.0		64.0	29.0	NM_033014	Q6FIB0|Q9UF90|Q9UNK5	Missense_Mutation	SNP	ENST00000262551.4	hg19	CCDS6695.1	.	.	.	.	.	.	.	.	.	.	A	15.98	2.993261	0.54041	.	.	ENSG00000106809	ENST00000262551;ENST00000375561	D;D	0.94897	-3.55;-3.55	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.98425	0.9476	H	0.98370	4.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.99;0.994	D	0.99780	1.1027	10	0.87932	D	0	.	15.7668	0.78131	1.0:0.0:0.0:0.0	.	273;215	B4DI63;P20774	.;MIME_HUMAN	H	215	ENSP00000262551:L215H;ENSP00000364711:L215H	ENSP00000262551:L215H	L	-	2	0	OGN	94188386	1.000000	0.71417	0.580000	0.28601	0.082000	0.17680	8.606000	0.90888	2.266000	0.75297	0.533000	0.62120	CTC	.	.		0.368	OGN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053087.1	NM_024416		T	95148565	A	T	95148565	3	4	76	1	0	0	0	0	1	0	0	0	10855	304	11	4	260	4	OGN	9	95148565	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	19717500	95148565	46064866	178	10449										
NIPSNAP3B	55335	hgsc.bcm.edu	37	chr9	107533137	107533137	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctccctattctaggagtctaTgaactagctgtttttcagat	7	9	3	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr9:107533137T>A	ENST00000374762.3	+	4	509	c.438T>A	c.(436-438)taT>taA	p.Y146*	NIPSNAP3B_ENST00000461177.1_3'UTR	NM_018376.2	NP_060846.2	Q9BS92	NPS3B_HUMAN	nipsnap homolog 3B (C. elegans)	146										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	11						TAGGAGTCTATGAACTAGCTG	0.378																																					p.Y146X		Atlas-SNP	.											.	NIPSNAP3B	22	.	0			c.T438A						.						106	103	104					9																	107533137		2203	4300	6503	SO:0001587	stop_gained	55335	exon4			AGTCTATGAACTA	BC017914	CCDS6761.1	9q31.3	2003-11-27			ENSG00000165028	ENSG00000165028			23641	protein-coding gene	gene with protein product		608872				12477932	Standard	NM_018376		Approved	FLJ11275	uc004bci.3	Q9BS92	OTTHUMG00000020414	ENST00000374762.3:c.438T>A	chr9.hg19:g.107533137T>A	ENSP00000363894:p.Tyr146*	74.0	0.0		88.0	31.0	NM_018376	Q5VX30|Q9NUM2	Nonsense_Mutation	SNP	ENST00000374762.3	hg19	CCDS6761.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.397855	0.62177	.	.	ENSG00000165028	ENST00000374762	.	.	.	4.06	0.227	0.15359	.	0.067660	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2509	4.7884	0.13236	0.1383:0.159:0.0:0.7027	.	.	.	.	X	146	.	ENSP00000363894:Y146X	Y	+	3	2	NIPSNAP3B	106572958	1.000000	0.71417	0.987000	0.45799	0.509000	0.34042	0.501000	0.22578	-0.054000	0.13266	0.533000	0.62120	TAT	.	.		0.378	NIPSNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053486.1	NM_018376		A	107533137	T	A	107533137	4	1	76	1	0	0	0	0	0	1	0	0	10440	1471	51	4	452	4	NIPSNAP3B	9	107533137	Nonsense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	12384572	107533137	33680294	179	10450										
PPP6C	5537	hgsc.bcm.edu	37	chr9	127920663	127920663	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctctgtctacaaaatcacccTgtgaagtaaaagtttacagt	6	9	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr9:127920663T>A	ENST00000373547.4	-	4	337		c.e4-2		PPP6C_ENST00000415905.1_Splice_Site|PPP6C_ENST00000451402.1_Splice_Site|PPP6C_ENST00000373546.3_Intron	NM_002721.4	NP_002712.1	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit						G1/S transition of mitotic cell cycle (GO:0000082)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(3)	14						AAAATCACCCTGTGAAGTAAA	0.323																																					.		Atlas-SNP	.											.	PPP6C	108	.	0			c.238-2A>T						.						100	105	103					9																	127920663		2203	4300	6503	SO:0001630	splice_region_variant	5537	exon5			TCACCCTGTGAAG	AF035158	CCDS6861.1, CCDS48018.1, CCDS48019.1	9q33.3	2010-03-17			ENSG00000119414	ENSG00000119414		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9323	protein-coding gene	gene with protein product		612725				9143513	Standard	NM_002721		Approved	PP6	uc004bpg.4	O00743	OTTHUMG00000020671	ENST00000373547.4:c.238-2A>T	chr9.hg19:g.127920663T>A		58.0	0.0		102.0	8.0	NM_002721	B2R5V6|B7Z2W9|B7Z5K9|Q5U0A2|Q9UIC9	Splice_Site	SNP	ENST00000373547.4	hg19	CCDS6861.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420089	0.83559	.	.	ENSG00000119414	ENST00000373547;ENST00000451402;ENST00000415905;ENST00000456642	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8897	0.70600	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PPP6C	126960484	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.599000	0.82757	2.113000	0.64589	0.528000	0.53228	.	.	.		0.323	PPP6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054060.1	NM_016294	Intron	A	127920663	T	A	127920663	5	1	76	1	0	0	0	0	0	0	1	0	12419	1594	55	4	697	4	PPP6C	9	127920663	Splice_Site	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	20387526	127920663	13292768	180	10451										
LMX1B	4010	hgsc.bcm.edu	37	chr9	129458665	129458665	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cctcagacgtgggctccctgCaggcccgcgtggggaacccc	14	17	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr9:129458665C>A	ENST00000373474.4	+	8	1151	c.1144C>A	c.(1144-1146)Cag>Aag	p.Q382K	LMX1B_ENST00000355497.5_Missense_Mutation_p.Q386K|LMX1B_ENST00000526117.1_Missense_Mutation_p.Q375K|LMX1B_ENST00000561065.1_Missense_Mutation_p.Q363K|LMX1B_ENST00000425646.2_Missense_Mutation_p.Q352K			O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	382					cell proliferation (GO:0008283)|central nervous system neuron development (GO:0021954)|cerebellum morphogenesis (GO:0021587)|collagen fibril organization (GO:0030199)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral pattern formation (GO:0009953)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|organ growth (GO:0035265)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|trabecular meshwork development (GO:0002930)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	15						GGGCTCCCTGCAGGCCCGCGT	0.647									Nail-Patella Syndrome																												p.Q386K	Pancreas(110;1796 2278 18357 20466)	Atlas-SNP	.											.	LMX1B	86	.	0			c.C1156A						.						106	109	108					9																	129458665		2203	4300	6503	SO:0001583	missense	4010	exon8	Familial Cancer Database	Osteo-Onychodysplasia, Turner-Kieser syndrome, Fong disease	TCCCTGCAGGCCC	U77457	CCDS6866.1, CCDS6866.2, CCDS55342.1, CCDS55343.1	9q33.3	2011-06-20			ENSG00000136944	ENSG00000136944		"Homeoboxes / LIM class"	6654	protein-coding gene	gene with protein product		602575		NPS1		9441763, 9590287	Standard	NM_002316		Approved		uc004bqj.3	O60663	OTTHUMG00000020692	ENST00000373474.4:c.1144C>A	chr9.hg19:g.129458665C>A	ENSP00000362573:p.Gln382Lys	114.0	0.0		108.0	35.0	NM_001174146	F8W7W6|O75463|Q5JU95|Q6ISC9	Missense_Mutation	SNP	ENST00000373474.4	hg19	CCDS55342.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055847	0.76074	.	.	ENSG00000136944	ENST00000526117;ENST00000373474;ENST00000355497;ENST00000425646	T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.77082	0.4078	M	0.61703	1.905	0.80722	D	1	B;P;P	0.44429	0.415;0.745;0.835	B;B;B	0.41691	0.194;0.298;0.364	T	0.77381	-0.2609	10	0.34782	T	0.22	.	17.6964	0.88282	0.0:1.0:0.0:0.0	.	363;359;375	B7ZLH2;O60663;F8VYP0	.;LMX1B_HUMAN;.	K	375;382;386;352	ENSP00000436930:Q375K;ENSP00000362573:Q382K;ENSP00000347684:Q386K;ENSP00000390923:Q352K	ENSP00000347684:Q386K	Q	+	1	0	LMX1B	128498486	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.469000	0.80959	2.420000	0.82092	0.561000	0.74099	CAG	.	.		0.647	LMX1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054123.2			A	129458665	C	A	129458665	3	1	76	1	0	0	0	0	1	0	0	0	8871	711	25	3	1207	3	LMX1B	9	129458665	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	1538002	129458665	11754766	181	10452										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138642869	138642869	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcgcgtcctgctcgatgaccCggccctgggcatcggatggt	15	14	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr9:138642869C>A	ENST00000263604.3	+	4	359	c.359C>A	c.(358-360)cCg>cAg	p.P120Q	KCNT1_ENST00000298480.5_Missense_Mutation_p.P139Q|KCNT1_ENST00000371757.2_Missense_Mutation_p.P139Q|KCNT1_ENST00000486577.2_Missense_Mutation_p.P100Q|KCNT1_ENST00000490355.2_Missense_Mutation_p.P120Q|KCNT1_ENST00000491806.2_Missense_Mutation_p.P106Q|KCNT1_ENST00000487664.1_Missense_Mutation_p.P91Q|KCNT1_ENST00000488444.2_Missense_Mutation_p.P120Q			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	120					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		CTCGATGACCCGGCCCTGGGC	0.692																																					p.P139Q		Atlas-SNP	.											.	KCNT1	139	.	0			c.C416A						.						74	66	69					9																	138642869		2203	4300	6503	SO:0001583	missense	57582	exon4			ATGACCCGGCCCT	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.359C>A	chr9.hg19:g.138642869C>A	ENSP00000263604:p.Pro120Gln	38.0	0.0		27.0	10.0	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	.	14.40	2.523120	0.44866	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000473941;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T;T	0.44482	1.92;1.86;1.86;0.92;1.9	4.68	4.68	0.58851	.	0.070231	0.64402	D	0.000019	T	0.57080	0.2029	L	0.60455	1.87	0.80722	D	1	P;D	0.54601	0.935;0.967	P;D	0.63381	0.535;0.914	T	0.52358	-0.8586	10	0.23302	T	0.38	-34.6371	16.5626	0.84570	0.0:1.0:0.0:0.0	.	139;91	B9EGP2;G5E9V0	.;.	Q	91;139;139;86;100;106;120;120;120	ENSP00000417851:P91Q;ENSP00000298480:P139Q;ENSP00000360822:P139Q;ENSP00000420764:P86Q;ENSP00000263604:P120Q	ENSP00000263604:P120Q	P	+	2	0	KCNT1	137782690	0.997000	0.39634	0.920000	0.36463	0.014000	0.08584	3.610000	0.54125	2.149000	0.67028	0.561000	0.74099	CCG	.	.		0.692	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		A	138642869	C	A	138642869	3	1	76	1	0	0	0	0	1	0	0	0	8100	652	23	1	430	1	KCNT1	9	138642869	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	9184204	138642869	2570562	182	10453										
C9orf172	389813	hgsc.bcm.edu	37	chr9	139740383	139740383	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcccagacgctacgccgcacTgtccctgtccgagacgtcgc	10	18	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr9:139740383T>C	ENST00000436881.1	+	1	1517	c.1517T>C	c.(1516-1518)cTg>cCg	p.L506P	PHPT1_ENST00000545326.1_5'Flank|PHPT1_ENST00000371661.1_5'Flank	NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	506										endometrium(2)|large_intestine(1)|lung(6)	9						TACGCCGCACTGTCCCTGTCC	0.711																																					p.L506P		Atlas-SNP	.											.	C9orf172	23	.	0			c.T1517C						.						7	8	8					9																	139740383		1957	4063	6020	SO:0001583	missense	389813	exon1			CCGCACTGTCCCT		CCDS48059.1	9q34.3	2012-04-03			ENSG00000232434	ENSG00000232434			37284	protein-coding gene	gene with protein product							Standard	NM_001080482		Approved		uc011meh.2	C9J069		ENST00000436881.1:c.1517T>C	chr9.hg19:g.139740383T>C	ENSP00000412388:p.Leu506Pro	41.0	0.0		51.0	26.0	NM_001080482		Missense_Mutation	SNP	ENST00000436881.1	hg19	CCDS48059.1	.	.	.	.	.	.	.	.	.	.	.	17.66	3.445762	0.63178	.	.	ENSG00000232434	ENST00000436881	.	.	.	3.84	2.66	0.31614	.	.	.	.	.	T	0.62368	0.2422	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60890	-0.7173	8	0.87932	D	0	-9.1052	8.4829	0.33054	0.1738:0.0:0.0:0.8262	.	506	C9J069	CI172_HUMAN	P	506	.	ENSP00000412388:L506P	L	+	2	0	C9orf172	138860204	1.000000	0.71417	0.298000	0.25002	0.906000	0.53458	5.598000	0.67585	0.339000	0.23719	0.387000	0.25754	CTG	.	.		0.711	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482		C	139740383	T	C	139740383	3	2	76	1	0	0	0	0	1	0	0	0	2473	1580	55	2	1519	2	C9orf172	9	139740383	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	1097514	139740383	1473048	183	10454										
DIP2C	22982	hgsc.bcm.edu	37	chr10	329356	329356	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tccgtaaatagtgaaataacCgctggcattgtgggcactgt	11	8	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:329356C>A	ENST00000280886.6	-	35	4237	c.4150G>T	c.(4150-4152)Ggt>Tgt	p.G1384C	RNA5SP298_ENST00000364991.1_RNA	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1384						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GTGAAATAACCGCTGGCATTG	0.463																																					p.G1384C		Atlas-SNP	.											.	DIP2C	195	.	0			c.G4150T						.						145	134	138					10																	329356		2203	4300	6503	SO:0001583	missense	22982	exon35			AATAACCGCTGGC	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.4150G>T	chr10.hg19:g.329356C>A	ENSP00000280886:p.Gly1384Cys	128.0	0.0		82.0	4.0	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.589301	0.66105	.	.	ENSG00000151240	ENST00000280886;ENST00000535541	T	0.24538	1.85	5.81	5.81	0.92471	AMP-dependent synthetase/ligase (1);	0.050095	0.85682	D	0.000000	T	0.60170	0.2248	M	0.87381	2.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65220	-0.6221	10	0.87932	D	0	-19.4154	20.0748	0.97738	0.0:1.0:0.0:0.0	.	1384	Q9Y2E4	DIP2C_HUMAN	C	1384;309	ENSP00000280886:G1384C	ENSP00000280886:G1384C	G	-	1	0	DIP2C	319356	1.000000	0.71417	0.843000	0.33291	0.063000	0.16089	7.776000	0.85560	2.747000	0.94245	0.549000	0.68633	GGT	.	.		0.463	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		A	329356	C	A	329356	3	1	76	1	0	0	0	0	1	0	0	0	4531	652	23	1	532	1	DIP2C	10	329356	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10		329356	135205391	184	10455										
RAB18	22931	hgsc.bcm.edu	37	chr10	27822715	27822715	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	taaactggataattggttaaAtgaattggaaacatactgta	8	3	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:27822715A>G	ENST00000356940.6	+	5	413	c.311A>G	c.(310-312)aAt>aGt	p.N104S	RAB18_ENST00000375802.3_Missense_Mutation_p.N59S|RAB18_ENST00000535776.1_Intron|RAB18_ENST00000465772.1_3'UTR	NM_001256410.1|NM_001256415.1|NM_021252.4	NP_001243339.1|NP_001243344.1|NP_067075.1	Q9NP72	RAB18_HUMAN	RAB18, member RAS oncogene family	104					brain development (GO:0007420)|endoplasmic reticulum tubular network organization (GO:0071786)|eye development (GO:0001654)|GTP catabolic process (GO:0006184)|lipid particle organization (GO:0034389)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|large_intestine(1)|lung(1)	3						AATTGGTTAAATGAATTGGAA	0.303																																					p.N133S		Atlas-SNP	.											.	RAB18	18	.	0			c.A398G						.						115	113	114					10																	27822715		2203	4298	6501	SO:0001583	missense	22931	exon6			GGTTAAATGAATT	AJ277145	CCDS7155.1, CCDS58073.1, CCDS73080.1, CCDS73081.1	10p12	2011-03-07			ENSG00000099246	ENSG00000099246		"RAB, member RAS oncogene"	14244	protein-coding gene	gene with protein product		602207				10648831	Standard	NM_021252		Approved		uc001itw.4	Q9NP72	OTTHUMG00000017861	ENST00000356940.6:c.311A>G	chr10.hg19:g.27822715A>G	ENSP00000349415:p.Asn104Ser	61.0	0.0		67.0	18.0	NM_001256410	B3KMC7|B7Z333|D3DRW1|Q53FX8|Q56UN9|Q6FIH1	Missense_Mutation	SNP	ENST00000356940.6	hg19	CCDS7155.1	.	.	.	.	.	.	.	.	.	.	A	11.89	1.773832	0.31411	.	.	ENSG00000099246	ENST00000356940;ENST00000540268;ENST00000375802	T;T	0.75938	-0.98;-0.98	5.87	3.48	0.39840	Small GTP-binding protein domain (1);	.	.	.	.	T	0.55689	0.1936	N	0.17764	0.52	0.80722	D	1	B;B;B	0.18013	0.019;0.025;0.001	B;B;B	0.24269	0.012;0.052;0.003	T	0.41378	-0.9512	9	0.14252	T	0.57	.	8.2976	0.31995	0.7979:0.1324:0.0696:0.0	.	104;133;104	B7Z4P9;Q56UN9;Q9NP72	.;.;RAB18_HUMAN	S	104;82;59	ENSP00000349415:N104S;ENSP00000364960:N59S	ENSP00000349415:N104S	N	+	2	0	RAB18	27862721	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.575000	0.46025	1.014000	0.39417	0.528000	0.53228	AAT	.	.		0.303	RAB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047326.2	NM_021252		G	27822715	A	G	27822715	3	3	76	1	0	0	0	0	1	0	0	0	12918	101	4	2	329	2	RAB18	10	27822715	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	27493359	27822715	107712032	185	10456										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49687731	49687731	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atggcctgcacccagtcctcCatgtcacgctgggagctggc	12	15	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:49687731C>T	ENST00000249601.4	-	4	695	c.399G>A	c.(397-399)atG>atA	p.M133I	ARHGAP22_ENST00000374172.1_Missense_Mutation_p.M8I|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.M43I|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.M139I|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.M133I|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.M43I	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	133	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCCAGTCCTCCATGTCACGCT	0.677																																					p.M139I		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.G417A						.						30	29	30					10																	49687731		2202	4299	6501	SO:0001583	missense	58504	exon4			GTCCTCCATGTCA	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.399G>A	chr10.hg19:g.49687731C>T	ENSP00000249601:p.Met133Ile	71.0	0.0		73.0	21.0	NM_001256025	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	hg19	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	C	32	5.151917	0.94645	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T	0.76316	-1.01;2.21;2.21;2.21;-1.01;-1.01	4.71	4.71	0.59529	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.049134	0.85682	D	0.000000	D	0.89438	0.6715	M	0.89287	3.02	0.80722	D	1	P;P;D;P	0.69078	0.738;0.906;0.997;0.72	P;D;D;P	0.87578	0.869;0.973;0.998;0.537	D	0.89692	0.3898	10	0.39692	T	0.17	.	16.8225	0.85922	0.0:1.0:0.0:0.0	.	139;133;133;43	B4DED8;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3	.;.;RHG22_HUMAN;.	I	133;8;43;43;139;133	ENSP00000249601:M133I;ENSP00000363287:M8I;ENSP00000363285:M43I;ENSP00000410054:M43I;ENSP00000416701:M139I;ENSP00000412461:M133I	ENSP00000249601:M133I	M	-	3	0	ARHGAP22	49357737	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.500000	0.81588	2.456000	0.83038	0.655000	0.94253	ATG	.	.		0.677	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		T	49687731	C	T	49687731	3	4	76	1	0	0	0	0	1	0	0	0	872	594	21	3	1725	3	ARHGAP22	10	49687731	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	21865016	49687731	85847016	186	10457										
CHAT	1103	hgsc.bcm.edu	37	chr10	50873041	50873041	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccgcctactgagagcaagccAttggcaacaaaggaaaaagc	10	11	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:50873041A>G	ENST00000337653.2	+	15	2349	c.2196A>G	c.(2194-2196)ccA>ccG	p.P732P	CHAT_ENST00000351556.3_Silent_p.P614P|CHAT_ENST00000395559.2_Silent_p.P614P|CHAT_ENST00000339797.1_Silent_p.P614P|CHAT_ENST00000395562.2_Silent_p.P650P|CHAT_ENST00000455728.2_Intron	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	732					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	AGAGCAAGCCATTGGCAACAA	0.527																																					p.P732P		Atlas-SNP	.											.	CHAT	162	.	0			c.A2196G						.						87	86	86					10																	50873041		2203	4300	6503	SO:0001819	synonymous_variant	1103	exon15			CAAGCCATTGGCA	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.2196A>G	chr10.hg19:g.50873041A>G		79.0	0.0		64.0	45.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Silent	SNP	ENST00000337653.2	hg19	CCDS7232.1																																																																																			.	.		0.527	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		G	50873041	A	G	50873041	2	3	76	1	0	0	0	0	0	0	0	1	3315	204	8	2		2	CHAT	10	50873041	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	1185310	50873041	84661706	187	10458										
DNA2	1763	hgsc.bcm.edu	37	chr10	70190319	70190319	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgacccaaacgcaaaaatccTattttaaacttggctaactt	4	10	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:70190319T>C	ENST00000358410.3	-	14	2132	c.2082A>G	c.(2080-2082)atA>atG	p.I694M	DNA2_ENST00000399179.2_Intron|DNA2_ENST00000399180.2_Missense_Mutation_p.I780M	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	694	Helicase activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						GCAAAAATCCTATTTTAAACT	0.383																																					p.I694M		Atlas-SNP	.											.	DNA2	76	.	0			c.A2082G						.						75	70	71					10																	70190319		1825	4087	5912	SO:0001583	missense	1763	exon14			AAATCCTATTTTA	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"DNA2 DNA replication helicase 2-like (yeast)", "DNA replication helicase 2 homolog (yeast)"	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.2082A>G	chr10.hg19:g.70190319T>C	ENSP00000351185:p.Ile694Met	111.0	0.0		85.0	23.0	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Missense_Mutation	SNP	ENST00000358410.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.73|17.73	3.460855|3.460855	0.63513|0.63513	.|.	.|.	ENSG00000138346|ENSG00000138346	ENST00000399180;ENST00000358410|ENST00000440722	D;D|.	0.82711|.	-1.64;-1.64|.	5.61|5.61	-6.98|-6.98	0.01611|0.01611	.|.	0.314198|.	0.33875|.	N|.	0.004477|.	T|T	0.44871|0.44871	0.1314|0.1314	L|L	0.37466|0.37466	1.105|1.105	0.80722|0.80722	D|D	1|1	P|.	0.49307|.	0.922|.	P|.	0.51866|.	0.682|.	T|T	0.47736|0.47736	-0.9094|-0.9094	10|5	0.51188|.	T|.	0.08|.	.|.	8.0606|8.0606	0.30631|0.30631	0.4912:0.0:0.2817:0.2271|0.4912:0.0:0.2817:0.2271	.|.	694|.	P51530|.	DNA2L_HUMAN|.	M|G	780;694|16	ENSP00000382133:I780M;ENSP00000351185:I694M|.	ENSP00000351185:I694M|.	I|R	-|-	3|1	3|2	DNA2|DNA2	69860325|69860325	0.005000|0.005000	0.15991|0.15991	0.940000|0.940000	0.37924|0.37924	0.988000|0.988000	0.76386|0.76386	-1.356000|-1.356000	0.02609|0.02609	-1.035000|-1.035000	0.03291|0.03291	0.529000|0.529000	0.55759|0.55759	ATA|AGG	.	.		0.383	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			C	70190319	T	C	70190319	3	2	76	1	0	0	0	0	1	0	0	0	4598	1512	53	2	1132	2	DNA2	10	70190319	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	19317278	70190319	65344428	188	10459										
ASCC1	51008	hgsc.bcm.edu	37	chr10	73892879	73892879	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agtttcacactattccactcTttcactattagtccagatgc	4	12	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:73892879T>C	ENST00000342444.4	-	9	992	c.891A>G	c.(889-891)aaA>aaG	p.K297K	ASCC1_ENST00000394915.3_Silent_p.K297K|ASCC1_ENST00000317168.6_Silent_p.K269K|ASCC1_ENST00000545550.1_Silent_p.K291K|ASCC1_ENST00000394919.1_Silent_p.K269K|ASCC1_ENST00000317126.4_Silent_p.K269K	NM_001198799.2	NP_001185728.1	Q8N9N2	ASCC1_HUMAN	activating signal cointegrator 1 complex subunit 1	297					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|transcription factor complex (GO:0005667)	catalytic activity (GO:0003824)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(2)|skin(1)	7						TATTCCACTCTTTCACTATTA	0.398																																					p.K297K		Atlas-SNP	.											.	ASCC1	18	.	0			c.A891G						.						131	121	124					10																	73892879		2203	4300	6503	SO:0001819	synonymous_variant	51008	exon9			CCACTCTTTCACT	AY013290	CCDS31219.1, CCDS55713.1	10q22.1	2012-09-20			ENSG00000138303	ENSG00000138303			24268	protein-coding gene	gene with protein product		614215				10810093, 12077347	Standard	NM_001198799		Approved	CGI-18, ASC1p50, Em:AC022392.3	uc001jst.2	Q8N9N2	OTTHUMG00000018434	ENST00000342444.4:c.891A>G	chr10.hg19:g.73892879T>C		97.0	0.0		85.0	23.0	NM_001198799	Q5SW06|Q5SW07|Q96EI8|Q9Y307	Silent	SNP	ENST00000342444.4	hg19	CCDS55713.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.822|9.822	1.185968|1.185968	0.21870|0.21870	.|.	.|.	ENSG00000138303|ENSG00000138303	ENST00000530394;ENST00000525286|ENST00000486689	T|.	0.63744|.	-0.06|.	5.75|5.75	0.849|0.849	0.18972|0.18972	.|.	0.046120|.	0.85682|.	D|.	0.000000|.	T|T	0.55561|0.55561	0.1928|0.1928	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49123|0.49123	-0.8972|-0.8972	7|4	0.19590|.	T|.	0.45|.	.|.	8.6068|8.6068	0.33778|0.33778	0.0:0.3013:0.0:0.6987|0.0:0.3013:0.0:0.6987	.|.	.|.	.|.	.|.	R|G	67;126|201	ENSP00000436409:K67R|.	ENSP00000435147:K126R|.	K|R	-|-	2|1	0|2	ASCC1|ASCC1	73562885|73562885	0.809000|0.809000	0.29036|0.29036	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	-0.323000|-0.323000	0.07997|0.07997	0.418000|0.418000	0.25898|0.25898	0.533000|0.533000	0.62120|0.62120	AAG|AGA	.	.		0.398	ASCC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048573.2	NM_015947		C	73892879	T	C	73892879	2	2	76	1	0	0	0	0	0	0	0	1	1031	1606	56	2		2	ASCC1	10	73892879	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	3702560	73892879	61641868	189	10460										
GOLGA7B	401647	hgsc.bcm.edu	37	chr10	99623744	99623744	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcaacggattttacgcagagGctgagaagattgggggcagc	15	7	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:99623744G>A	ENST00000370602.1	+	3	261	c.196G>A	c.(196-198)Gct>Act	p.A66T		NM_001010917.2	NP_001010917.1	Q2TAP0	GOG7B_HUMAN	golgin A7 family, member B	66						Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|prostate(1)	5						TTACGCAGAGGCTGAGAAGAT	0.587																																					p.A66T		Atlas-SNP	.											.	GOLGA7B	11	.	0			c.G196A						.						56	59	58					10																	99623744		2203	4300	6503	SO:0001583	missense	401647	exon3			GCAGAGGCTGAGA	BC008047	CCDS31265.1	10q24.2	2011-10-25	2010-02-12	2008-10-03	ENSG00000155265	ENSG00000155265			31668	protein-coding gene	gene with protein product		614189	"chromosome 10 open reading frame 133", "chromosome 10 open reading frame 132", "golgi autoantigen, golgin subfamily a, 7B"	C10orf133, C10orf132			Standard	NM_001010917		Approved	bA459F3.4, bA451M19.3	uc001kos.3	Q2TAP0	OTTHUMG00000018869	ENST00000370602.1:c.196G>A	chr10.hg19:g.99623744G>A	ENSP00000359634:p.Ala66Thr	81.0	0.0		63.0	15.0	NM_001010917	Q5T4F5	Missense_Mutation	SNP	ENST00000370602.1	hg19	CCDS31265.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.062979	0.76187	.	.	ENSG00000155265	ENST00000370602	.	.	.	5.18	5.18	0.71444	Golgin subfamily A member 7/ERF4 (1);	0.000000	0.85682	D	0.000000	D	0.84624	0.5513	M	0.88450	2.955	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	D	0.86875	0.2038	9	0.62326	D	0.03	-28.5351	17.6285	0.88099	0.0:0.0:1.0:0.0	.	66	Q2TAP0	GOG7B_HUMAN	T	66	.	ENSP00000359634:A66T	A	+	1	0	GOLGA7B	99613734	1.000000	0.71417	0.981000	0.43875	0.049000	0.14656	9.657000	0.98554	2.711000	0.92665	0.563000	0.77884	GCT	.	.		0.587	GOLGA7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049752.1	NM_001010917		A	99623744	G	A	99623744	3	1	76	1	0	0	0	0	1	0	0	0	6570	1203	42	3	206	3	GOLGA7B	10	99623744	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	25730865	99623744	35911003	190	10461										
ABCC2	1244	hgsc.bcm.edu	37	chr10	101556936	101556936	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agatgaaaaccaagacattaGtgagcaagtttgaaacgcac	9	7	0	5			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:101556936G>T	ENST00000370449.4	+	7	828	c.715G>T	c.(715-717)Gtg>Ttg	p.V239L	ABCC2_ENST00000370434.1_Missense_Mutation_p.V239L	NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	239					cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CAAGACATTAGTGAGCAAGTT	0.517																																					p.V239L		Atlas-SNP	.											.	ABCC2	160	.	0			c.G715T						.						78	77	77					10																	101556936		2203	4300	6503	SO:0001583	missense	1244	exon7			ACATTAGTGAGCA	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.715G>T	chr10.hg19:g.101556936G>T	ENSP00000359478:p.Val239Leu	79.0	0.0		63.0	32.0	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	hg19	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	G	12.88	2.070020	0.36566	.	.	ENSG00000023839	ENST00000370449;ENST00000370434	D;D	0.88586	-2.4;-2.4	5.62	-2.54	0.06307	.	1.373150	0.04252	N	0.338734	T	0.80412	0.4618	L	0.39245	1.2	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.60306	-0.7289	10	0.28530	T	0.3	-12.4658	0.7802	0.01039	0.2073:0.2454:0.1552:0.3921	.	239	Q92887	MRP2_HUMAN	L	239	ENSP00000359478:V239L;ENSP00000359463:V239L	ENSP00000359463:V239L	V	+	1	0	ABCC2	101546926	0.000000	0.05858	0.061000	0.19648	0.018000	0.09664	-0.030000	0.12308	0.016000	0.14998	-0.397000	0.06425	GTG	.	.		0.517	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		T	101556936	G	T	101556936	3	4	76	1	0	0	0	0	1	0	0	0	53	1029	36	3	741	3	ABCC2	10	101556936	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	1933192	101556936	33977811	191	10462										
SUFU	51684	hgsc.bcm.edu	37	chr10	104389884	104389884	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gaaggtctccatcctgcctgAcgtggtgttcgacagtccgc	12	13	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:104389884A>T	ENST00000369902.3	+	12	1593	c.1427A>T	c.(1426-1428)gAc>gTc	p.D476V		NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	476					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		ATCCTGCCTGACGTGGTGTTC	0.577			"D, F, S"		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation																												p.D476V		Atlas-SNP	.	yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	.	SUFU	44	.	0			c.A1427T						.						196	167	177					10																	104389884		2203	4300	6503	SO:0001583	missense	51684	exon12	Familial Cancer Database		TGCCTGACGTGGT	AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.1427A>T	chr10.hg19:g.104389884A>T	ENSP00000358918:p.Asp476Val	75.0	0.0		51.0	23.0	NM_016169	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Missense_Mutation	SNP	ENST00000369902.3	hg19	CCDS7537.1	.	.	.	.	.	.	.	.	.	.	A	17.54	3.415788	0.62511	.	.	ENSG00000107882	ENST00000369902	T	0.72051	-0.62	5.59	5.59	0.84812	.	0.128884	0.64402	D	0.000001	T	0.74921	0.3780	L	0.43923	1.385	0.80722	D	1	D	0.56746	0.977	P	0.55871	0.786	T	0.77928	-0.2404	10	0.87932	D	0	-16.554	14.3445	0.66651	1.0:0.0:0.0:0.0	.	476	Q9UMX1	SUFU_HUMAN	V	476	ENSP00000358918:D476V	ENSP00000358918:D476V	D	+	2	0	SUFU	104379874	1.000000	0.71417	0.027000	0.17364	0.626000	0.37791	8.001000	0.88508	2.136000	0.66102	0.459000	0.35465	GAC	.	.		0.577	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050089.1	NM_016169		T	104389884	A	T	104389884	3	4	76	1	0	0	0	0	1	0	0	0	15383	275	10	4	1483	4	SUFU	10	104389884	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	2832948	104389884	31144863	192	10463										
C10orf79	80217	hgsc.bcm.edu	37	chr10	105900629	105900629	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agaattcaagtcttcaattaTgttcttgttgatgagaattg	8	4	4	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:105900629T>A	ENST00000357060.3	-	34	4517	c.4402A>T	c.(4402-4404)Ata>Tta	p.I1468L	WDR96_ENST00000428666.1_Missense_Mutation_p.I1440L|WDR96_ENST00000479392.1_5'UTR	NM_025145.5	NP_079421.5														NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TCTTCAATTATGTTCTTGTTG	0.333																																					p.I1468L		Atlas-SNP	.											.	WDR96	183	.	0			c.A4402T						.						83	79	81					10																	105900629		2203	4299	6502	SO:0001583	missense	80217	exon34			CAATTATGTTCTT																												ENST00000357060.3:c.4402A>T	chr10.hg19:g.105900629T>A	ENSP00000349568:p.Ile1468Leu	82.0	0.0		69.0	7.0	NM_025145		Missense_Mutation	SNP	ENST00000357060.3	hg19	CCDS31281.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.786802	0.31593	.	.	ENSG00000197748	ENST00000357060;ENST00000428666	T;T	0.14022	2.54;2.55	5.51	3.07	0.35406	.	0.112103	0.64402	D	0.000012	T	0.08802	0.0218	L	0.29908	0.895	0.32488	N	0.54064	B;B	0.02656	0.0;0.0	B;B	0.11329	0.003;0.006	T	0.12218	-1.0556	10	0.26408	T	0.33	.	6.3415	0.21324	0.139:0.076:0.0:0.785	.	1440;1468	G5E9L1;Q8NDM7	.;WDR96_HUMAN	L	1468;1440	ENSP00000349568:I1468L;ENSP00000400289:I1440L	ENSP00000349568:I1468L	I	-	1	0	WDR96	105890619	0.935000	0.31712	0.923000	0.36655	0.857000	0.48899	1.281000	0.33214	0.925000	0.37094	-0.274000	0.10170	ATA	.	.		0.333	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	105900629	T	A	105900629	3	1	76	1	0	0	0	0	1	0	0	0	1620	1464	51	4	615	4	C10orf79	10	105900629	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	1510745	105900629	29634118	193	10464										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106924072	106924072	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atgtttcaggcaacattggcCcggagctctcatatactgat	9	10	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:106924072C>G	ENST00000369701.3	+	12	1971	c.1744C>G	c.(1744-1746)Ccg>Gcg	p.P582A		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	582					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CAACATTGGCCCGGAGCTCTC	0.478																																					p.P582A	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.C1744G						.						110	97	101					10																	106924072		2203	4300	6503	SO:0001583	missense	22986	exon12			ATTGGCCCGGAGC	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1744C>G	chr10.hg19:g.106924072C>G	ENSP00000358715:p.Pro582Ala	44.0	0.0		46.0	6.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	C	9.548	1.115129	0.20795	.	.	ENSG00000156395	ENST00000369701;ENST00000393176	T;T	0.21543	2.0;2.0	6.17	-4.12	0.03916	VPS10 (1);	0.721094	0.14149	N	0.338102	T	0.07234	0.0183	N	0.11845	0.185	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.30208	-0.9986	9	.	.	.	.	2.5836	0.04825	0.1135:0.2532:0.1706:0.4626	.	582	Q9UPU3	SORC3_HUMAN	A	582;27	ENSP00000358715:P582A;ENSP00000376876:P27A	.	P	+	1	0	SORCS3	106914062	0.021000	0.18746	0.303000	0.25071	0.997000	0.91878	-0.549000	0.06041	-0.548000	0.06199	0.655000	0.94253	CCG	.	.		0.478	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		G	106924072	C	G	106924072	3	3	76	1	0	0	0	0	1	0	0	0	14947	623	22	4	1790	4	SORCS3	10	106924072	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	1023443	106924072	28610675	194	10465										
EIF3A	8661	hgsc.bcm.edu	37	chr10	120819149	120819149	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cctggctgcatctactatggCccgttccagttggaaagcat	10	12	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:120819149C>T	ENST00000369144.3	-	10	1535	c.1408G>A	c.(1408-1410)Gcc>Acc	p.A470T	EIF3A_ENST00000541549.1_Missense_Mutation_p.A436T|SNORA19_ENST00000410656.1_RNA|SNORA19_ENST00000384737.1_RNA	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A	0					mature ribosome assembly (GO:0042256)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal subunit export from nucleus (GO:0000054)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lamin filament (GO:0005638)|nucleus (GO:0005634)	ribosomal large subunit binding (GO:0043023)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)			endometrium(8)|kidney(4)|large_intestine(14)|lung(22)|prostate(1)|skin(4)|urinary_tract(3)	56		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		TCTACTATGGCCCGTTCCAGT	0.463																																					p.A470T		Atlas-SNP	.											.	EIF3A	142	.	0			c.G1408A						.						94	86	89					10																	120819149		2203	4300	6503	SO:0001583	missense	8661	exon10			CTATGGCCCGTTC	U78311	CCDS7608.1	10q26.11	2007-08-03	2007-07-27	2007-07-27	ENSG00000107581	ENSG00000107581			3271	protein-coding gene	gene with protein product		602039	"eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa"	EIF3, EIF3S10		9054404, 8590280	Standard	NM_003750		Approved	eIF3-theta, eIF3-p170, KIAA0139, eIF3a, TIF32	uc001ldu.3	Q14152	OTTHUMG00000019144	ENST00000369144.3:c.1408G>A	chr10.hg19:g.120819149C>T	ENSP00000358140:p.Ala470Thr	281.0	0.0		256.0	63.0	NM_003750	B7ZBG9|Q6IBN8|Q96TD5	Missense_Mutation	SNP	ENST00000369144.3	hg19	CCDS7608.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.501556	0.64298	.	.	ENSG00000107581	ENST00000369144;ENST00000541549	T;T	0.30981	1.51;1.51	5.78	5.78	0.91487	Winged helix-turn-helix transcription repressor DNA-binding (1);Proteasome component (PCI) domain (2);	0.000000	0.39083	N	0.001474	T	0.19644	0.0472	N	0.22421	0.69	0.40110	D	0.976476	P	0.34462	0.454	B	0.31946	0.138	T	0.07309	-1.0779	10	0.28530	T	0.3	-12.2681	10.7099	0.45977	0.1334:0.7973:0.0:0.0693	.	470	Q14152	EIF3A_HUMAN	T	470;436	ENSP00000358140:A470T;ENSP00000438178:A436T	ENSP00000358140:A470T	A	-	1	0	EIF3A	120809139	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.251000	0.43187	2.730000	0.93505	0.655000	0.94253	GCC	.	.		0.463	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750		T	120819149	C	T	120819149	3	4	76	1	0	0	0	0	1	0	0	0	5014	739	26	3	2792	3	EIF3A	10	120819149	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	13895077	120819149	14715598	195	10466										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123276887	123276887	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tatcccaatagaattacccgCcaagcacgtatattccccag	5	14	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:123276887C>A	ENST00000358487.5	-	8	1302	c.1030G>T	c.(1030-1032)Gcg>Tcg	p.A344S	FGFR2_ENST00000360144.3_Intron|FGFR2_ENST00000369056.1_Intron|FGFR2_ENST00000369060.4_Intron|FGFR2_ENST00000369061.4_Intron|FGFR2_ENST00000457416.2_Intron|FGFR2_ENST00000356226.4_Missense_Mutation_p.A229S|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000346997.2_Missense_Mutation_p.A344S|FGFR2_ENST00000351936.6_Missense_Mutation_p.A344S|FGFR2_ENST00000369059.1_Intron|FGFR2_ENST00000357555.5_Missense_Mutation_p.A255S|FGFR2_ENST00000478859.1_Missense_Mutation_p.A116S	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	344	Ig-like C2-type 3.		A -> G (in CS and JWS). {ECO:0000269|PubMed:7581378, ECO:0000269|PubMed:7874170}.|A -> P (in CS and PS). {ECO:0000269|PubMed:8644708}.		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GAATTACCCGCCAAGCACGTA	0.438		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																												p.A344S		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.G1030T	GRCh37	CM960649	FGFR2	M		.						128	113	118					10																	123276887		2203	4300	6503	SO:0001583	missense	2263	exon8	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	TACCCGCCAAGCA	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1030G>T	chr10.hg19:g.123276887C>A	ENSP00000351276:p.Ala344Ser	102.0	0.0		86.0	22.0	NM_000141	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	hg19	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	C	34	5.360031	0.95877	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000358487;ENST00000356226;ENST00000346997;ENST00000351936;ENST00000336553	T;T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03;-1.03	5.86	5.86	0.93980	.	.	.	.	.	D	0.89942	0.6861	M	0.84683	2.71	0.80722	D	1	P;D;B;D;P	0.69078	0.9;0.996;0.087;0.997;0.64	D;D;B;D;P	0.79784	0.916;0.993;0.444;0.942;0.716	D	0.90539	0.4501	9	0.87932	D	0	.	20.1865	0.98220	0.0:1.0:0.0:0.0	.	229;344;363;255;229	B5A963;B5A960;D3DRD5;P21802-21;P21802-20	.;.;.;.;.	S	255;347;344;229;344;344;255	ENSP00000350166:A255S;ENSP00000351276:A344S;ENSP00000348559:A229S;ENSP00000263451:A344S;ENSP00000309878:A344S;ENSP00000337665:A255S	ENSP00000337665:A255S	A	-	1	0	FGFR2	123266877	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.764000	0.85297	2.775000	0.95449	0.655000	0.94253	GCG	.	.		0.438	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		A	123276887	C	A	123276887	3	1	76	1	0	0	0	0	1	0	0	0	5874	739	26	3	1583	3	FGFR2	10	123276887	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	2457738	123276887	12257860	196	10467										
FAM196A	642938	hgsc.bcm.edu	37	chr10	128973670	128973670	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggactaggctggttccccagCcccggcggggtgtgagtctg	17	12	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:128973670C>G	ENST00000522781.1	-	4	1545	c.990G>C	c.(988-990)ggG>ggC	p.G330G	FAM196A_ENST00000424811.2_Silent_p.G330G|DOCK1_ENST00000280333.6_Intron	NM_001039762.2	NP_001034851.1	Q6ZSG2	F196A_HUMAN	family with sequence similarity 196, member A	330										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						GGTTCCCCAGCCCCGGCGGGG	0.622																																					p.G330G		Atlas-SNP	.											.	FAM196A	55	.	0			c.G990C						.						82	91	88					10																	128973670		2203	4300	6503	SO:0001819	synonymous_variant	642938	exon4			CCCCAGCCCCGGC		CCDS31312.1	10q26.2	2009-09-11	2009-09-11	2009-09-11		ENSG00000188916			33859	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 141"	C10orf141			Standard	NM_001039762		Approved	FLJ45557	uc001ljv.1	Q6ZSG2		ENST00000522781.1:c.990G>C	chr10.hg19:g.128973670C>G		30.0	0.0		37.0	9.0	NM_001039762	B2RNT4|B7ZME7	Silent	SNP	ENST00000522781.1	hg19	CCDS31312.1																																																																																			.	.		0.622	FAM196A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050978.2	NM_001039762		G	128973670	C	G	128973670	2	3	76	1	0	0	0	0	0	0	0	1	5533	726	26	4		4	FAM196A	10	128973670	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	5696783	128973670	6561077	197	10468										
VENTX	27287	hgsc.bcm.edu	37	chr10	135053333	135053333	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagggagatgcagctctcagAggtccaggtgaggtgggccg	18	9	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr10:135053333A>T	ENST00000325980.9	+	2	906	c.395A>T	c.(394-396)gAg>gTg	p.E132V		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	132					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(1)	14		all_cancers(35;4.15e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)|all cancers(32;1.19e-05)		CAGCTCTCAGAGGTCCAGGtg	0.647																																					p.E132V		Atlas-SNP	.											.	VENTX	24	.	0			c.A395T						.						18	22	20					10																	135053333		2203	4295	6498	SO:0001583	missense	27287	exon2			TCTCAGAGGTCCA	AF068006	CCDS7675.1	10q26.3	2011-06-20	2011-06-01	2005-09-27	ENSG00000151650	ENSG00000151650		"Homeoboxes / ANTP class : NKL subclass"	13639	protein-coding gene	gene with protein product		607158	"VENT-like homeobox 2", "VENT homeobox homolog (Xenopus laevis)"	VENTX2		10790436	Standard	NM_014468		Approved	HPX42B	uc010quy.1	O95231	OTTHUMG00000019307	ENST00000325980.9:c.395A>T	chr10.hg19:g.135053333A>T	ENSP00000357556:p.Glu132Val	42.0	0.0		44.0	12.0	NM_014468	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	hg19	CCDS7675.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.434279	0.62955	.	.	ENSG00000151650	ENST00000325980	D	0.97041	-4.22	3.36	3.36	0.38483	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.130587	0.48767	U	0.000162	D	0.98362	0.9456	M	0.91510	3.215	0.47905	D	0.999543	D	0.89917	1.0	D	0.83275	0.996	D	0.98417	1.0575	10	0.87932	D	0	.	8.4583	0.32912	1.0:0.0:0.0:0.0	.	132	O95231	VENTX_HUMAN	V	132	ENSP00000357556:E132V	ENSP00000357556:E132V	E	+	2	0	VENTX	134903323	1.000000	0.71417	0.681000	0.30009	0.682000	0.39822	6.170000	0.71920	1.316000	0.45131	0.363000	0.22086	GAG	.	.		0.647	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468		T	135053333	A	T	135053333	3	4	76	1	0	0	0	0	1	0	0	0	17168	304	11	4	401	4	VENTX	10	135053333	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	6079663	135053333	481414	198	10469										
LRRC56	115399	hgsc.bcm.edu	37	chr11	552109	552109	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggccagggagccccccgagcAgctgccccaacacaggccag	13	18	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:552109A>T	ENST00000270115.7	+	12	1558	c.1058A>T	c.(1057-1059)cAg>cTg	p.Q353L		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	353										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCCCCCGAGCAGCTGCCCCAA	0.672																																					p.Q353L		Atlas-SNP	.											.	LRRC56	23	.	0			c.A1058T						.						37	46	43					11																	552109		2201	4300	6501	SO:0001583	missense	115399	exon12			CCGAGCAGCTGCC		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.1058A>T	chr11.hg19:g.552109A>T	ENSP00000270115:p.Gln353Leu	107.0	0.0		76.0	37.0	NM_198075	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	hg19	CCDS7700.1	.	.	.	.	.	.	.	.	.	.	A	10.36	1.327543	0.24080	.	.	ENSG00000161328	ENST00000270115	T	0.09255	3.0	4.38	-0.874	0.10631	.	0.158927	0.30068	N	0.010483	T	0.04363	0.0120	L	0.27053	0.805	0.09310	N	1	B	0.33694	0.421	B	0.27500	0.08	T	0.43426	-0.9392	10	0.08179	T	0.78	-22.0255	4.9868	0.14194	0.4647:0.1657:0.3696:0.0	.	353	Q8IYG6	LRC56_HUMAN	L	353	ENSP00000270115:Q353L	ENSP00000270115:Q353L	Q	+	2	0	LRRC56	542109	0.238000	0.23825	0.057000	0.19452	0.079000	0.17450	-0.068000	0.11561	-0.242000	0.09667	0.459000	0.35465	CAG	.	.		0.672	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075		T	552109	A	T	552109	3	4	76	1	0	0	0	0	1	0	0	0	9021	188	7	4	1092	4	LRRC56	11	552109	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10		552109	134454407	199	10470										
OR52A1	23538	hgsc.bcm.edu	37	chr11	5172674	5172674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gtggattttatgaacagaacAtttttaccacatgaatgcga	8	6	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:5172674A>G	ENST00000380367.1	-	2	1343	c.926T>C	c.(925-927)aTg>aCg	p.M309T	OR52A1_ENST00000328942.1_Missense_Mutation_p.M309T			Q9UKL2	O52A1_HUMAN	olfactory receptor, family 52, subfamily A, member 1	309					sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	19		Medulloblastoma(188;0.00106)|Breast(177;0.0155)|all_neural(188;0.0189)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGAACAGAACATTTTTACCAC	0.338																																					p.M309T		Atlas-SNP	.											.	OR52A1	58	.	0			c.T926C						.						118	128	125					11																	5172674		2201	4297	6498	SO:0001583	missense	23538	exon1			CAGAACATTTTTA	AF154673	CCDS31374.1	11p15.4	2012-08-09			ENSG00000182070	ENSG00000182070		"GPCR / Class A : Olfactory receptors"	8318	protein-coding gene	gene with protein product						10512676	Standard	NM_012375		Approved	HPFH1OR	uc010qyy.2	Q9UKL2	OTTHUMG00000066603	ENST00000380367.1:c.926T>C	chr11.hg19:g.5172674A>G	ENSP00000369725:p.Met309Thr	92.0	0.0		58.0	19.0	NM_012375	Q6IF31	Missense_Mutation	SNP	ENST00000380367.1	hg19	CCDS31374.1	.	.	.	.	.	.	.	.	.	.	A	12.65	2.000225	0.35320	.	.	ENSG00000182070	ENST00000380367;ENST00000328942	T;T	0.37235	1.21;1.21	5.36	5.36	0.76844	.	0.304873	0.28470	N	0.015226	T	0.28632	0.0709	L	0.29908	0.895	0.22468	N	0.999075	B	0.26120	0.142	B	0.20184	0.028	T	0.23547	-1.0185	10	0.54805	T	0.06	.	14.3327	0.66569	1.0:0.0:0.0:0.0	.	309	Q9UKL2	O52A1_HUMAN	T	309	ENSP00000369725:M309T;ENSP00000333684:M309T	ENSP00000333684:M309T	M	-	2	0	OR52A1	5129250	0.653000	0.27358	0.481000	0.27354	0.193000	0.23685	1.419000	0.34793	2.254000	0.74563	0.528000	0.53228	ATG	.	.		0.338	OR52A1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142810.2	NM_012375		G	5172674	A	G	5172674	3	3	76	1	0	0	0	0	1	0	0	0	11117	217	8	2	14	2	OR52A1	11	5172674	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	4620565	5172674	129833842	200	10471										
TRIM6	117854	hgsc.bcm.edu	37	chr11	5624771	5624771	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctaatcggcatctggccaacAtagtgaggcggctcagagag	13	10	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:5624771A>G	ENST00000278302.5	+	2	369	c.229A>G	c.(229-231)Ata>Gta	p.I77V	TRIM6_ENST00000445329.1_Intron|HBG2_ENST00000380259.2_Intron|TRIM6_ENST00000515022.1_Intron|TRIM6-TRIM34_ENST00000354852.5_Missense_Mutation_p.I105V|TRIM6_ENST00000380097.3_Missense_Mutation_p.I105V|TRIM6_ENST00000380107.1_Missense_Mutation_p.I77V|TRIM6_ENST00000507320.1_Intron|AC015691.13_ENST00000394793.2_RNA|TRIM6_ENST00000506134.1_Intron	NM_001198645.1|NM_058166.4	NP_001185574.1|NP_477514.1	Q9C030	TRIM6_HUMAN	tripartite motif containing 6	77					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|prostate(2)|stomach(1)	22		Lung NSC(207;2.23e-07)|all_lung(207;1.81e-06)|Medulloblastoma(188;0.00225)|Breast(177;0.0101)|all_neural(188;0.0212)		Epithelial(150;1.12e-45)|BRCA - Breast invasive adenocarcinoma(625;0.00101)|LUSC - Lung squamous cell carcinoma(625;0.192)		TCTGGCCAACATAGTGAGGCG	0.552																																					p.I105V		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.A313G						.						84	84	84					11																	5624771		2201	4297	6498	SO:0001583	missense	445372	exon2			GCCAACATAGTGA	AF220030	CCDS31389.1, CCDS31390.1, CCDS55738.1	11p15	2013-01-09	2011-01-25		ENSG00000121236	ENSG00000121236		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16277	protein-coding gene	gene with protein product		607564	"tripartite motif-containing 6"			11331580	Standard	NM_058166		Approved	RNF89		Q9C030	OTTHUMG00000150029	ENST00000278302.5:c.229A>G	chr11.hg19:g.5624771A>G	ENSP00000278302:p.Ile77Val	68.0	0.0		31.0	15.0	NM_001003819	A8K2A7|B4DDQ5|Q86WZ8|Q9HCR1	Missense_Mutation	SNP	ENST00000278302.5	hg19	CCDS31390.1	.	.	.	.	.	.	.	.	.	.	A	13.61	2.287440	0.40494	.	.	ENSG00000121236;ENSG00000121236;ENSG00000121236;ENSG00000258659;ENSG00000258588	ENST00000278302;ENST00000380107;ENST00000380097;ENST00000337072;ENST00000354852	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	4.04	4.04	0.47022	Zinc finger, RING/FYVE/PHD-type (1);	.	.	.	.	D	0.88669	0.6499	M	0.62016	1.91	0.19945	N	0.999945	D;P;D;D	0.62365	0.977;0.55;0.991;0.985	P;B;D;D	0.72625	0.836;0.241;0.978;0.952	T	0.77707	-0.2487	9	0.21540	T	0.41	.	7.7915	0.29123	0.7876:0.2124:0.0:0.0	.	77;105;105;77	E9PFM0;B2RNG4;Q9C030-2;Q9C030	.;.;.;TRIM6_HUMAN	V	77;77;105;105;105	ENSP00000278302:I77V;ENSP00000369450:I77V;ENSP00000369440:I105V;ENSP00000346916:I105V	ENSP00000278302:I77V	I	+	1	0	TRIM34;TRIM6;TRIM6-TRIM34	5581347	0.022000	0.18835	1.000000	0.80357	0.731000	0.41821	1.625000	0.37029	2.037000	0.60232	0.533000	0.62120	ATA	.	.		0.552	TRIM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143376.2	NM_001003818		G	5624771	A	G	5624771	3	3	76	1	0	0	0	0	1	0	0	0	16548	217	8	2	319	2	TRIM6	11	5624771	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	452097	5624771	129381745	201	10472										
NR1H3	10062	hgsc.bcm.edu	37	chr11	47289839	47289839	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caacgtgcaggaccagctccAggtagagaggctgcagcaca	13	12	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:47289839A>C	ENST00000467728.1	+	8	2368	c.1130A>C	c.(1129-1131)cAg>cCg	p.Q377P	MADD_ENST00000402799.1_5'Flank|NR1H3_ENST00000395397.3_Missense_Mutation_p.Q332P|NR1H3_ENST00000407404.1_Missense_Mutation_p.Q317P|NR1H3_ENST00000527949.1_Missense_Mutation_p.Q226P|RP11-17G12.3_ENST00000545474.1_RNA|NR1H3_ENST00000481889.2_Missense_Mutation_p.Q396P|MADD_ENST00000407859.3_5'Flank|NR1H3_ENST00000405576.1_Missense_Mutation_p.Q272P|RP11-17G12.3_ENST00000543925.1_RNA|NR1H3_ENST00000441012.2_Missense_Mutation_p.Q377P|NR1H3_ENST00000405853.3_Missense_Mutation_p.Q317P|MADD_ENST00000395344.3_5'Flank|MADD_ENST00000311027.5_5'Flank|MADD_ENST00000406482.1_5'Flank|MADD_ENST00000342922.4_5'Flank|MADD_ENST00000402192.2_5'Flank|NR1H3_ENST00000529540.1_3'UTR|MADD_ENST00000395336.3_5'Flank|MADD_ENST00000349238.3_5'Flank			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	377	Ligand-binding. {ECO:0000255}.				apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						GACCAGCTCCAGGTAGAGAGG	0.552																																					p.Q383P		Atlas-SNP	.											.	NR1H3	52	.	0			c.A1148C						.						99	83	88					11																	47289839		2201	4298	6499	SO:0001583	missense	10062	exon9			AGCTCCAGGTAGA	U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434		"Nuclear hormone receptors"	7966	protein-coding gene	gene with protein product	"liver X receptor-alpha"	602423				8621574, 7744246	Standard	NM_005693		Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.1130A>C	chr11.hg19:g.47289839A>C	ENSP00000420656:p.Gln377Pro	100.0	0.0		62.0	27.0	NM_001251934	A8K3J9|D3DQR1|Q8IW13|Q96H87	Missense_Mutation	SNP	ENST00000467728.1	hg19	CCDS7929.1	.	.	.	.	.	.	.	.	.	.	A	19.47	3.833615	0.71258	.	.	ENSG00000025434	ENST00000395397;ENST00000405576;ENST00000481889;ENST00000407404;ENST00000441012;ENST00000467728;ENST00000405853;ENST00000527949	D;D;D;D;D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13	5.4	5.4	0.78164	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.063133	0.64402	D	0.000003	D	0.94241	0.8151	N	0.11560	0.145	0.43421	D	0.995573	B;P;D;P;P	0.54047	0.032;0.847;0.964;0.799;0.892	B;P;P;P;P	0.62813	0.086;0.625;0.907;0.63;0.491	D	0.93652	0.6974	10	0.46703	T	0.11	.	9.4075	0.38471	0.7331:0.0:0.0:0.2669	.	383;272;377;396;317	B4DXU5;B5MBY7;Q13133;E9PLL4;Q13133-2	.;.;NR1H3_HUMAN;.;.	P	332;272;396;317;377;377;317;226	ENSP00000378793:Q332P;ENSP00000385073:Q272P;ENSP00000433271:Q396P;ENSP00000385801:Q317P;ENSP00000387946:Q377P;ENSP00000420656:Q377P;ENSP00000384745:Q317P;ENSP00000432073:Q226P	ENSP00000378793:Q332P	Q	+	2	0	NR1H3	47246415	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.460000	0.73518	2.181000	0.69327	0.533000	0.62120	CAG	.	.		0.552	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319214.3			C	47289839	A	C	47289839	3	2	76	1	0	0	0	0	1	0	0	0	10627	188	7	5	1160	5	NR1H3	11	47289839	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	41665068	47289839	87716677	202	10473										
OR5B17	219965	hgsc.bcm.edu	37	chr11	58126348	58126348	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gagtaaccaatgcctgcaagAgacaggttactgagaaaaaa	10	7	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:58126348A>G	ENST00000357377.3	-	1	194	c.195T>C	c.(193-195)tcT>tcC	p.S65S		NM_001005489.1	NP_001005489.1	Q8NGF7	OR5BH_HUMAN	olfactory receptor, family 5, subfamily B, member 17	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TGCCTGCAAGAGACAGGTTAC	0.468																																					p.S65S		Atlas-SNP	.											.	OR5B17	64	.	0			c.T195C						.						76	73	74					11																	58126348		2201	4295	6496	SO:0001819	synonymous_variant	219965	exon1			TGCAAGAGACAGG	AB065849	CCDS31548.1	11q12.1	2012-08-09			ENSG00000197786	ENSG00000197786		"GPCR / Class A : Olfactory receptors"	15267	protein-coding gene	gene with protein product				OR5B20P			Standard	NM_001005489		Approved		uc010rke.2	Q8NGF7	OTTHUMG00000167465	ENST00000357377.3:c.195T>C	chr11.hg19:g.58126348A>G		85.0	0.0		27.0	10.0	NM_001005489	Q6IEX1	Silent	SNP	ENST00000357377.3	hg19	CCDS31548.1																																																																																			.	.		0.468	OR5B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394708.2	NM_001005489		G	58126348	A	G	58126348	2	3	76	1	0	0	0	0	0	0	0	1	11158	291	11	2		2	OR5B17	11	58126348	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	10836509	58126348	76880168	203	10474										
FLRT1	28992	hgsc.bcm.edu	37	chr11	63883947	63883947	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcttcatctactgcaacgacCggggactcacatccatcccc	7	17	3	0	rs139162750		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:63883947C>A	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Silent_p.R70R	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						CTGCAACGACCGGGGACTCAC	0.607																																					p.R70R		Atlas-SNP	.											.	FLRT1	46	.	0			c.C208A						.						124	80	95					11																	63883947		2201	4297	6498	SO:0001627	intron_variant	23769	exon2			AACGACCGGGGAC	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+34763G>T	chr11.hg19:g.63883947C>A		53.0	0.0		26.0	18.0	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	hg19	CCDS8056.1																																																																																			.	C|1.000;T|0.000		0.607	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		A	63883947	C	A	63883947	1	1	76	0	1	0	0	0	0	0	0	0	5946	643	23	1		1	FLRT1	11	63883947	Intron	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	5757599	63883947	71122569	204	10475										
CCDC88B	283234	hgsc.bcm.edu	37	chr11	64111953	64111953	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gttgagacaggagggccctgAgcacaagccagggccttcgg	16	11	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:64111953A>G	ENST00000356786.5	+	14	1984	c.1940A>G	c.(1939-1941)gAg>gGg	p.E647G	CCDC88B_ENST00000301897.4_5'UTR|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	647						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GAGGGCCCTGAGCACAAGCCA	0.662																																					p.E647G		Atlas-SNP	.											.	CCDC88B	89	.	0			c.A1940G						.						22	27	26					11																	64111953		2193	4296	6489	SO:0001583	missense	283234	exon14			GCCCTGAGCACAA	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"brain leucine zipper protein", "GRP78-interacting protein induced by ER stress"	611205	"coiled-coil domain containing 88"	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.1940A>G	chr11.hg19:g.64111953A>G	ENSP00000349238:p.Glu647Gly	89.0	0.0		58.0	22.0	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Missense_Mutation	SNP	ENST00000356786.5	hg19	CCDS8072.2	.	.	.	.	.	.	.	.	.	.	a	9.992	1.231216	0.22626	.	.	ENSG00000168071	ENST00000377638;ENST00000356786	T	0.25579	1.79	3.45	-1.24	0.09435	.	.	.	.	.	T	0.10937	0.0267	N	0.08118	0	0.30548	N	0.765723	B;B;B	0.12630	0.0;0.006;0.0	B;B;B	0.14578	0.001;0.011;0.001	T	0.18903	-1.0322	9	0.49607	T	0.09	.	4.3185	0.11005	0.5934:0.1696:0.237:0.0	.	647;296;647	B2RTU8;A6NC98-3;A6NC98	.;.;CC88B_HUMAN	G	647	ENSP00000349238:E647G	ENSP00000349238:E647G	E	+	2	0	CCDC88B	63868529	0.000000	0.05858	0.006000	0.13384	0.376000	0.30014	-0.378000	0.07446	-0.334000	0.08463	0.249000	0.18162	GAG	.	.		0.662	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251		G	64111953	A	G	64111953	3	3	76	1	0	0	0	0	1	0	0	0	2866	304	11	2	1994	2	CCDC88B	11	64111953	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	228006	64111953	70894563	205	10476										
INPPL1	3636	hgsc.bcm.edu	37	chr11	71948760	71948760	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agctgcagcccccccggggaCtgccctcggactatggccgg	14	17	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:71948760C>T	ENST00000298229.2	+	26	3676	c.3472C>T	c.(3472-3474)Ctg>Ttg	p.L1158L	INPPL1_ENST00000538751.1_Silent_p.L916L|INPPL1_ENST00000541756.1_Silent_p.L916L|PHOX2A_ENST00000544057.1_5'Flank	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1158					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CCCCCGGGGACTGCCCTCGGA	0.697																																					p.L1158L		Atlas-SNP	.											.	INPPL1	120	.	0			c.C3472T						.						10	12	12					11																	71948760		2150	4245	6395	SO:0001819	synonymous_variant	3636	exon26			CGGGGACTGCCCT	Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"Sterile alpha motif (SAM) domain containing", "SH2 domain containing"	6080	protein-coding gene	gene with protein product	"51C protein"	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.3472C>T	chr11.hg19:g.71948760C>T		105.0	0.0		59.0	25.0	NM_001567	B2RTX5|Q13577|Q13578	Silent	SNP	ENST00000298229.2	hg19	CCDS8213.1																																																																																			.	.		0.697	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		T	71948760	C	T	71948760	2	4	76	1	0	0	0	0	0	0	0	1	7770	564	20	3		3	INPPL1	11	71948760	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	7836807	71948760	63057756	206	10477										
MMP27	64066	hgsc.bcm.edu	37	chr11	102573828	102573828	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tccacagcagctcgtgccatAtccggagtatagtttattat	8	10	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:102573828A>T	ENST00000260229.4	-	3	454	c.363T>A	c.(361-363)gaT>gaA	p.D121E		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	121					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	CTCGTGCCATATCCGGAGTAT	0.353																																					p.D121E		Atlas-SNP	.											.	MMP27	84	.	0			c.T363A						.						73	70	71					11																	102573828		2203	4299	6502	SO:0001583	missense	64066	exon3			TGCCATATCCGGA	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"matrix metalloprotease 27"		"matrix metalloproteinase 27"			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.363T>A	chr11.hg19:g.102573828A>T	ENSP00000260229:p.Asp121Glu	100.0	0.0		59.0	34.0	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	hg19	CCDS8319.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.338976	0.41398	.	.	ENSG00000137675	ENST00000260229	T	0.53857	0.6	5.11	-2.76	0.05896	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.110120	0.40908	D	0.000999	T	0.64371	0.2592	M	0.86953	2.85	0.52099	D	0.999947	D	0.53885	0.963	P	0.58454	0.839	T	0.64123	-0.6481	10	0.72032	D	0.01	.	6.9973	0.24789	0.4854:0.0:0.4007:0.1139	.	121	Q9H306	MMP27_HUMAN	E	121	ENSP00000260229:D121E	ENSP00000260229:D121E	D	-	3	2	MMP27	102079038	0.991000	0.36638	0.412000	0.26496	0.017000	0.09413	0.514000	0.22786	-0.737000	0.04824	-1.258000	0.01471	GAT	.	.		0.353	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		T	102573828	A	T	102573828	3	4	76	1	0	0	0	0	1	0	0	0	9673	446	16	4	1210	4	MMP27	11	102573828	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	30625068	102573828	32432688	207	10478										
ZC3H12C	85463	hgsc.bcm.edu	37	chr11	110033998	110033998	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttttattatctccatgacagGttcatgccccctgatgaccc	6	13	2	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:110033998G>T	ENST00000278590.3	+	5	1200	c.1149G>T	c.(1147-1149)aaG>aaT	p.K383N	ZC3H12C_ENST00000453089.2_Splice_Site_p.K352N|ZC3H12C_ENST00000528673.1_Splice_Site_p.K384N	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	383							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		TCCATGACAGGTTCATGCCCC	0.383																																					p.K383N		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.G1149T						.						50	44	46					11																	110033998		1818	4078	5896	SO:0001630	splice_region_variant	85463	exon5			TGACAGGTTCATG		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1149-1G>T	chr11.hg19:g.110033998G>T		93.0	0.0		56.0	26.0	NM_033390	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	hg19	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702546	0.68501	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.43688	0.94;0.94;0.94	5.78	2.58	0.30949	Ribonuclease Zc3h12a-like (1);	0.000000	0.85682	D	0.000000	T	0.58566	0.2131	M	0.76574	2.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	T	0.56171	-0.8023	9	.	.	.	.	7.5219	0.27633	0.4263:0.0:0.5737:0.0	.	384;383;383	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	N	383;384;352	ENSP00000278590:K383N;ENSP00000431821:K384N;ENSP00000413094:K352N	.	K	+	3	2	ZC3H12C	109539208	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	0.990000	0.29642	0.606000	0.29965	0.561000	0.74099	AAG	.	.		0.383	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	Missense_Mutation	T	110033998	G	T	110033998	5	4	76	1	0	0	0	0	0	0	1	0	17578	1275	44	3	1167	3	ZC3H12C	11	110033998	Splice_Site	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	7460170	110033998	24972518	208	10479										
NCAM1	4684	hgsc.bcm.edu	37	chr11	113102431	113102431	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gtcgctgaccctgaagagcaTccagtacactgatgccggag	12	12	0	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr11:113102431T>C	ENST00000533760.1	+	9	1369	c.770T>C	c.(769-771)aTc>aCc	p.I257T	NCAM1_ENST00000401611.2_Missense_Mutation_p.I384T|NCAM1_ENST00000316851.7_Missense_Mutation_p.I375T|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	385	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CTGAAGAGCATCCAGTACACT	0.582																																					p.I411T		Atlas-SNP	.											.	NCAM1	372	.	0			c.T1232C						.						79	83	82					11																	113102431		2174	4280	6454	SO:0001583	missense	4684	exon12			AGAGCATCCAGTA		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.770T>C	chr11.hg19:g.113102431T>C	ENSP00000473281:p.Ile257Thr	97.0	0.0		68.0	4.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.85	3.712183	0.68730	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.70164	-0.46;-0.46	4.71	4.71	0.59529	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.145674	0.46442	U	0.000282	T	0.65544	0.2701	.	.	.	0.80722	D	1	P;P;P;P	0.43094	0.692;0.799;0.536;0.551	B;B;B;B	0.42738	0.364;0.364;0.396;0.364	T	0.71434	-0.4594	9	0.72032	D	0.01	-38.685	14.6379	0.68702	0.0:0.0:0.0:1.0	.	385;375;385;375	P13591-5;P13591-1;P13591;P13591-3	.;.;NCAM1_HUMAN;.	T	257;384;375	ENSP00000384055:I384T;ENSP00000318472:I375T	ENSP00000318472:I375T	I	+	2	0	NCAM1	112607641	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.796000	0.85898	2.110000	0.64415	0.402000	0.26972	ATC	.	.		0.582	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		C	113102431	T	C	113102431	3	2	76	1	0	0	0	0	1	0	0	0	10211	1435	50	2	1193	2	NCAM1	11	113102431	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	3068433	113102431	21904085	209	10480										
MFAP5	8076	hgsc.bcm.edu	37	chr12	8800721	8800721	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gtctctgcaaatccacatttTcacagggaggaagtcggaag	11	9	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:8800721T>C	ENST00000359478.2	-	10	675	c.488A>G	c.(487-489)gAa>gGa	p.E163G	MFAP5_ENST00000540087.1_Missense_Mutation_p.E153G|MFAP5_ENST00000433590.2_Missense_Mutation_p.E138G|MFAP5_ENST00000535336.1_Missense_Mutation_p.E99G|MFAP5_ENST00000543369.1_Missense_Mutation_p.E141G|MFAP5_ENST00000396549.2_Missense_Mutation_p.E153G	NM_003480.2	NP_003471.1	Q13361	MFAP5_HUMAN	microfibrillar associated protein 5	163					extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|skin(1)	13	Lung SC(5;0.184)					ATCCACATTTTCACAGGGAGG	0.473																																					p.E163G		Atlas-SNP	.											.	MFAP5	34	.	0			c.A488G						.						90	87	88					12																	8800721		2203	4300	6503	SO:0001583	missense	8076	exon10			ACATTTTCACAGG	AK124368	CCDS8595.1, CCDS73437.1	12p13.1-p12.3	2004-04-05				ENSG00000197614			29673	protein-coding gene	gene with protein product		601103				9792630, 8557636	Standard	XM_005253485		Approved	MAGP2, MP25	uc001qut.1	Q13361		ENST00000359478.2:c.488A>G	chr12.hg19:g.8800721T>C	ENSP00000352455:p.Glu163Gly	166.0	0.0		85.0	70.0	NM_003480	B0AZL6|D3DUV1|Q7Z490	Missense_Mutation	SNP	ENST00000359478.2	hg19	CCDS8595.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.18|17.18	3.322561|3.322561	0.60634|0.60634	.|.	.|.	ENSG00000197614|ENSG00000197614	ENST00000543467;ENST00000359478;ENST00000433590;ENST00000396549;ENST00000543369;ENST00000535336;ENST00000540087|ENST00000535411	.|.	.|.	.|.	4.79|4.79	4.79|4.79	0.61399|0.61399	.|.	0.572443|.	0.18358|.	N|.	0.143656|.	T|T	0.38772|0.38772	0.1053|0.1053	N|N	0.24115|0.24115	0.695|0.695	0.32269|0.32269	N|N	0.569079|0.569079	P;P;P|.	0.46395|.	0.792;0.877;0.877|.	B;B;B|.	0.37731|.	0.257;0.257;0.257|.	T|T	0.47315|0.47315	-0.9127|-0.9127	9|5	0.72032|.	D|.	0.01|.	-3.4876|-3.4876	10.894|10.894	0.47012|0.47012	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	138;163;153|.	B3KW70;Q13361;Q7Z490|.	.;MFAP5_HUMAN;.|.	G|E	69;163;138;153;141;99;153|153	.|.	ENSP00000352455:E163G|.	E|K	-|-	2|1	0|0	MFAP5|MFAP5	8691988|8691988	0.922000|0.922000	0.31269|0.31269	0.926000|0.926000	0.36857|0.36857	0.930000|0.930000	0.56654|0.56654	2.337000|2.337000	0.43947|0.43947	2.138000|2.138000	0.66242|0.66242	0.460000|0.460000	0.39030|0.39030	GAA|AAA	.	.		0.473	MFAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400656.2	NM_003480		C	8800721	T	C	8800721	3	2	76	1	0	0	0	0	1	0	0	0	9527	1783	62	2	37	2	MFAP5	12	8800721	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10		8800721	125051174	210	10481										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22676443	22676443	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tccagagtacacgccgttccTatggctcgcaccactaaccc	7	17	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:22676443T>A	ENST00000333957.4	-	7	972	c.717A>T	c.(715-717)atA>atT	p.I239I	C2CD5_ENST00000542676.1_Silent_p.I239I|C2CD5_ENST00000540703.1_5'UTR|C2CD5_ENST00000396028.2_Silent_p.I239I|C2CD5_ENST00000545552.1_Silent_p.I239I|C2CD5_ENST00000544930.1_Silent_p.I41I|C2CD5_ENST00000446597.1_Silent_p.I239I|C2CD5_ENST00000536386.1_Silent_p.I239I	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	239					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										ACGCCGTTCCTATGGCTCGCA	0.453																																					p.I239I		Atlas-SNP	.											.	.	.	.	0			c.A717T						.						132	121	124					12																	22676443		2203	4300	6503	SO:0001819	synonymous_variant	9847	exon7			CGTTCCTATGGCT	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.717A>T	chr12.hg19:g.22676443T>A		91.0	0.0		54.0	19.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	hg19	CCDS31758.1																																																																																			.	.		0.453	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		A	22676443	T	A	22676443	2	1	76	1	0	0	0	0	0	0	0	1	8191	1512	53	4		4	KIAA0528	12	22676443	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	13875722	22676443	111175452	211	10482										
RPAP3	79657	hgsc.bcm.edu	37	chr12	48064026	48064026	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgctattacatttgctagatTaataggattattctctggag	8	5	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:48064026T>A	ENST00000005386.3	-	13	1505	c.1390A>T	c.(1390-1392)Aat>Tat	p.N464Y	RPAP3_ENST00000380650.4_Missense_Mutation_p.N430Y|RPAP3_ENST00000432584.3_Missense_Mutation_p.N305Y	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	464										endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					TTTGCTAGATTAATAGGATTA	0.388																																					p.N464Y		Atlas-SNP	.											.	RPAP3	45	.	0			c.A1390T						.						142	138	139					12																	48064026		2203	4300	6503	SO:0001583	missense	79657	exon13			CTAGATTAATAGG	AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"Tetratricopeptide (TTC) repeat domain containing"	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.1390A>T	chr12.hg19:g.48064026T>A	ENSP00000005386:p.Asn464Tyr	55.0	0.0		55.0	20.0	NM_024604	B4DRW9|Q6PHR5	Missense_Mutation	SNP	ENST00000005386.3	hg19	CCDS8753.1	.	.	.	.	.	.	.	.	.	.	T	15.45	2.836414	0.50951	.	.	ENSG00000005175	ENST00000005386;ENST00000432584;ENST00000380650	T;T;T	0.15487	2.86;2.42;2.86	5.47	1.59	0.23543	.	1.972720	0.01659	N	0.024987	T	0.19485	0.0468	L	0.34521	1.04	0.09310	N	1	P;B	0.40875	0.731;0.412	B;B	0.44224	0.444;0.259	T	0.18524	-1.0334	10	0.49607	T	0.09	.	7.0278	0.24950	0.0:0.0753:0.2816:0.6432	.	430;464	Q9H6T3-2;Q9H6T3	.;RPAP3_HUMAN	Y	464;305;430	ENSP00000005386:N464Y;ENSP00000401823:N305Y;ENSP00000370024:N430Y	ENSP00000005386:N464Y	N	-	1	0	RPAP3	46350293	0.000000	0.05858	0.000000	0.03702	0.730000	0.41778	0.412000	0.21131	0.026000	0.15269	0.455000	0.32223	AAT	.	.		0.388	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604		A	48064026	T	A	48064026	3	1	76	1	0	0	0	0	1	0	0	0	13558	1754	61	4	627	4	RPAP3	12	48064026	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	25387583	48064026	85787869	212	10483										
DDN	23109	hgsc.bcm.edu	37	chr12	49391094	49391094	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccccgcggcccccgccgggcTggtgtaaaaggcgactgctc	14	17	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:49391094T>A	ENST00000421952.2	-	2	1586	c.1565A>T	c.(1564-1566)cAg>cTg	p.Q522L	RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	522	Interaction with CD2AP and NPHS1. {ECO:0000250}.					cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						cccgccgggcTGGTGTAAAAG	0.687																																					p.Q522L		Atlas-SNP	.											.	DDN	54	.	0			c.A1565T						.						8	10	9					12																	49391094		2172	4222	6394	SO:0001583	missense	23109	exon2			CCGGGCTGGTGTA	AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.1565A>T	chr12.hg19:g.49391094T>A	ENSP00000390590:p.Gln522Leu	195.0	0.0		180.0	89.0	NM_015086		Missense_Mutation	SNP	ENST00000421952.2	hg19	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	T	8.484	0.860409	0.17178	.	.	ENSG00000181418	ENST00000421952	T	0.56275	0.47	3.68	-0.121	0.13535	.	0.631666	0.13163	N	0.408907	T	0.33962	0.0881	L	0.32530	0.975	0.09310	N	1	P	0.36535	0.557	B	0.33750	0.169	T	0.19647	-1.0299	10	0.62326	D	0.03	-2.0503	3.8991	0.09152	0.0:0.3649:0.2045:0.4306	.	522	O94850	DEND_HUMAN	L	522	ENSP00000390590:Q522L	ENSP00000390590:Q522L	Q	-	2	0	DDN	47677361	0.001000	0.12720	0.001000	0.08648	0.249000	0.25844	0.160000	0.16462	-0.020000	0.14032	0.402000	0.26972	CAG	.	.		0.687	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			A	49391094	T	A	49391094	3	1	76	1	0	0	0	0	1	0	0	0	4335	1580	55	4	574	4	DDN	12	49391094	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	1327068	49391094	84460801	213	10484										
RACGAP1	29127	hgsc.bcm.edu	37	chr12	50388003	50388003	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cttttagaaggctacagataGcatggatatcatccactttg	8	8	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:50388003G>A	ENST00000427314.2	-	14	1473	c.1250C>T	c.(1249-1251)gCt>gTt	p.A417V	RACGAP1_ENST00000434422.1_Missense_Mutation_p.A417V|RACGAP1_ENST00000548961.1_5'Flank|RACGAP1_ENST00000312377.5_Missense_Mutation_p.A417V|RACGAP1_ENST00000547905.1_Missense_Mutation_p.A417V|RACGAP1_ENST00000547061.1_5'Flank|RACGAP1_ENST00000551016.1_Missense_Mutation_p.A417V|RACGAP1_ENST00000454520.2_Missense_Mutation_p.A417V	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						GCTACAGATAGCATGGATATC	0.448																																					p.A417V		Atlas-SNP	.											.	RACGAP1	36	.	0			c.C1250T						.						138	136	137					12																	50388003		2203	4300	6503	SO:0001583	missense	29127	exon14			CAGATAGCATGGA		CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000427314.2:c.1250C>T	chr12.hg19:g.50388003G>A	ENSP00000404190:p.Ala417Val	96.0	0.0		104.0	42.0	NM_013277		Missense_Mutation	SNP	ENST00000427314.2	hg19	CCDS8795.1	.	.	.	.	.	.	.	.	.	.	G	8.867	0.948407	0.18356	.	.	ENSG00000161800	ENST00000427314;ENST00000312377;ENST00000434422;ENST00000454520;ENST00000551016;ENST00000547905;ENST00000549342	T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22	5.35	4.44	0.53790	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.149779	0.64402	N	0.000013	T	0.07683	0.0193	N	0.04880	-0.145	0.58432	D	0.999994	B	0.12630	0.006	B	0.09377	0.004	T	0.13602	-1.0503	10	0.02654	T	1	-7.9733	14.4667	0.67490	0.0721:0.0:0.9279:0.0	.	417	Q9H0H5	RGAP1_HUMAN	V	417;417;417;417;417;417;153	ENSP00000404190:A417V;ENSP00000309871:A417V;ENSP00000413241:A417V;ENSP00000404808:A417V;ENSP00000449374:A417V;ENSP00000449370:A417V;ENSP00000449565:A153V	ENSP00000309871:A417V	A	-	2	0	RACGAP1	48674270	1.000000	0.71417	0.930000	0.37139	0.978000	0.69477	4.024000	0.57218	1.206000	0.43276	0.555000	0.69702	GCT	.	.		0.448	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277		A	50388003	G	A	50388003	3	1	76	1	0	0	0	0	1	0	0	0	12992	971	34	3	672	3	RACGAP1	12	50388003	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	996909	50388003	83463892	214	10485										
KRT71	112802	hgsc.bcm.edu	37	chr12	52938508	52938508	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aagccatagacactgccgccActggtgctgctgatgatggc	12	12	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:52938508A>C	ENST00000267119.5	-	9	1449	c.1380T>G	c.(1378-1380)agT>agG	p.S460R		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	460	Tail.				hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		CACTGCCGCCACTGGTGCTGC	0.627																																					p.S460R		Atlas-SNP	.											.	KRT71	70	.	0			c.T1380G						.						18	16	17					12																	52938508		2163	4240	6403	SO:0001583	missense	112802	exon9			GCCGCCACTGGTG	AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"-", "Intermediate filaments type II, keratins (basic)"	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.1380T>G	chr12.hg19:g.52938508A>C	ENSP00000267119:p.Ser460Arg	36.0	0.0		22.0	7.0	NM_033448	B3KVC1|Q3SY85|Q96DU2	Missense_Mutation	SNP	ENST00000267119.5	hg19	CCDS8831.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.979847	0.34942	.	.	ENSG00000139648	ENST00000267119	D	0.81659	-1.52	4.16	-4.95	0.03048	.	0.000000	0.43579	U	0.000544	T	0.74053	0.3666	L	0.53249	1.67	0.31237	N	0.695594	D	0.56746	0.977	P	0.50192	0.634	T	0.75587	-0.3266	10	0.09338	T	0.73	.	12.419	0.55510	0.8442:0.0:0.1558:0.0	.	460	Q3SY84	K2C71_HUMAN	R	460	ENSP00000267119:S460R	ENSP00000267119:S460R	S	-	3	2	KRT71	51224775	0.009000	0.17119	0.314000	0.25224	0.630000	0.37929	-0.695000	0.05109	-0.772000	0.04602	-0.232000	0.12228	AGT	.	.		0.627	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448		C	52938508	A	C	52938508	3	2	76	1	0	0	0	0	1	0	0	0	8493	156	6	5	195	5	KRT71	12	52938508	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	2550505	52938508	80913387	215	10486										
KRT1	3848	hgsc.bcm.edu	37	chr12	53073703	53073703	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	accaggagggcagacaggacCataaccacccccatatccac	8	16	0	1	rs557388955		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:53073703C>A	ENST00000252244.3	-	1	488	c.430G>T	c.(430-432)Ggt>Tgt	p.G144C		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	144	Gly/Phe/Ser-rich.|Head.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						CAGACAGGACCATAACCACCC	0.547													C|||	1	0.000199681	0	0.0014	5008	,	,		15897	0		0	False		,,,				2504	0				p.G144C		Atlas-SNP	.											.	KRT1	110	.	0			c.G430T						.						356	325	336					12																	53073703		2203	4300	6503	SO:0001583	missense	3848	exon1			CAGGACCATAACC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.430G>T	chr12.hg19:g.53073703C>A	ENSP00000252244:p.Gly144Cys	191.0	0.0		113.0	26.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	hg19	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.732565	0.30684	.	.	ENSG00000167768	ENST00000252244	D	0.95821	-3.82	4.33	3.42	0.39159	.	.	.	.	.	D	0.97526	0.9190	M	0.86420	2.815	0.36679	D	0.878936	D	0.89917	1.0	D	0.77557	0.99	D	0.98630	1.0671	9	0.38643	T	0.18	.	13.1255	0.59351	0.0:0.8374:0.1626:0.0	.	144	P04264	K2C1_HUMAN	C	144	ENSP00000252244:G144C	ENSP00000252244:G144C	G	-	1	0	KRT1	51359970	0.028000	0.19301	0.470000	0.27216	0.793000	0.44817	1.691000	0.37721	0.941000	0.37499	0.448000	0.29417	GGT	.	.		0.547	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		A	53073703	C	A	53073703	3	1	76	1	0	0	0	0	1	0	0	0	8456	594	21	3	1540	3	KRT1	12	53073703	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	135195	53073703	80778192	216	10487										
CAND1	55832	hgsc.bcm.edu	37	chr12	67691234	67691234	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tccttcaattctgacctgtcTacttccccagttgaccagcc	5	16	3	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:67691234T>C	ENST00000545606.1	+	5	976	c.539T>C	c.(538-540)cTa>cCa	p.L180P		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	180					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		CTGACCTGTCTACTTCCCCAG	0.378																																					p.L180P		Atlas-SNP	.											.	CAND1	100	.	0			c.T539C						.						136	138	137					12																	67691234		2203	4300	6503	SO:0001583	missense	55832	exon5			CCTGTCTACTTCC		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.539T>C	chr12.hg19:g.67691234T>C	ENSP00000442318:p.Leu180Pro	114.0	0.0		112.0	51.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.279023	0.80692	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047	T	0.75367	-0.93	5.34	5.34	0.76211	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88742	0.6519	M	0.91663	3.23	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.91254	0.5031	9	.	.	.	-5.6922	15.3337	0.74234	0.0:0.0:0.0:1.0	.	180	Q86VP6	CAND1_HUMAN	P	180;180;22	ENSP00000442318:L180P	.	L	+	2	0	CAND1	65977501	1.000000	0.71417	0.926000	0.36857	0.980000	0.70556	7.809000	0.86057	2.030000	0.59900	0.533000	0.62120	CTA	.	.		0.378	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		C	67691234	T	C	67691234	3	2	76	1	0	0	0	0	1	0	0	0	2617	1522	53	2	557	2	CAND1	12	67691234	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	14617531	67691234	66160661	217	10488										
NAV3	89795	hgsc.bcm.edu	37	chr12	78362415	78362415	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccttggtggaacttcagcagCgagttactcacgcttcccct	9	14	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:78362415C>A	ENST00000397909.2	+	5	777	c.604C>A	c.(604-606)Cga>Aga	p.R202R	NAV3_ENST00000266692.7_Silent_p.R202R|NAV3_ENST00000228327.6_Silent_p.R202R|NAV3_ENST00000536525.2_Silent_p.R202R			Q8IVL0	NAV3_HUMAN	neuron navigator 3	202						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.R202*(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						ACTTCAGCAGCGAGTTACTCA	0.473										HNSCC(70;0.22)																											p.R202R		Atlas-SNP	.											NAV3,NS,carcinoma,0,2	NAV3	506	.	1	Substitution - Nonsense(1)	prostate(1)	c.C604A						.						74	78	77					12																	78362415		1989	4177	6166	SO:0001819	synonymous_variant	89795	exon5			CAGCAGCGAGTTA	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.604C>A	chr12.hg19:g.78362415C>A		194.0	0.0		213.0	87.0	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	C	4.797	0.148139	0.09134	.	.	ENSG00000067798	ENST00000550503	.	.	.	5.7	-1.95	0.07548	.	.	.	.	.	T	0.55924	0.1951	.	.	.	0.50467	D	0.999871	.	.	.	.	.	.	T	0.52830	-0.8523	4	.	.	.	-1.6834	10.8941	0.47012	0.4901:0.3039:0.206:0.0	.	.	.	.	E	48	.	.	A	+	2	0	NAV3	76886546	1.000000	0.71417	0.051000	0.19133	0.485000	0.33311	1.317000	0.33631	-0.313000	0.08728	0.637000	0.83480	GCG	.	.		0.473	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78362415	C	A	78362415	2	1	76	1	0	0	0	0	0	0	0	1	10194	760	27	1		1	NAV3	12	78362415	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	10671181	78362415	55489480	218	10489										
NEDD1	121441	hgsc.bcm.edu	37	chr12	97337446	97337446	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcttaatgtttttatgggatCtccagggaaagaggaaaatg	11	4	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:97337446C>A	ENST00000266742.4	+	12	1742	c.1403C>A	c.(1402-1404)tCt>tAt	p.S468Y	NEDD1_ENST00000557644.1_Missense_Mutation_p.S475Y|NEDD1_ENST00000429527.2_Missense_Mutation_p.S468Y|NEDD1_ENST00000457368.2_Missense_Mutation_p.S379Y|NEDD1_ENST00000411739.2_Missense_Mutation_p.S379Y	NM_152905.3	NP_690869.1	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally down-regulated 1	468					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	apical part of cell (GO:0045177)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|pericentriolar material (GO:0000242)|spindle pole (GO:0000922)				breast(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)	22						TTTATGGGATCTCCAGGGAAA	0.363																																					p.S475Y		Atlas-SNP	.											.	NEDD1	47	.	0			c.C1424A						.						99	97	97					12																	97337446		2203	4300	6503	SO:0001583	missense	121441	exon11			TGGGATCTCCAGG		CCDS9063.1, CCDS44955.1, CCDS44956.1	12q23.1	2013-01-10			ENSG00000139350	ENSG00000139350		"WD repeat domain containing"	7723	protein-coding gene	gene with protein product		600372					Standard	NM_001135175		Approved	GCP-WD, TUBGCP7	uc001tev.4	Q8NHV4	OTTHUMG00000170604	ENST00000266742.4:c.1403C>A	chr12.hg19:g.97337446C>A	ENSP00000266742:p.Ser468Tyr	61.0	0.0		55.0	19.0	NM_001135175	B0AZN0|B4E145|G3V3F1|Q8NA30	Missense_Mutation	SNP	ENST00000266742.4	hg19	CCDS9063.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.885104	0.51908	.	.	ENSG00000139350	ENST00000266742;ENST00000429527;ENST00000411739;ENST00000557644;ENST00000457368	T;T;T;T;T	0.50277	0.76;0.76;1.53;0.75;1.53	5.25	2.98	0.34508	.	0.389844	0.31909	N	0.006869	T	0.40347	0.1113	L	0.51422	1.61	0.39434	D	0.96712	P;P	0.42620	0.785;0.498	P;B	0.46253	0.509;0.312	T	0.42999	-0.9418	10	0.02654	T	1	.	9.2259	0.37407	0.1466:0.7667:0.0:0.0867	.	475;468	G3V3F1;Q8NHV4	.;NEDD1_HUMAN	Y	468;468;379;475;379	ENSP00000266742:S468Y;ENSP00000404978:S468Y;ENSP00000411307:S379Y;ENSP00000451211:S475Y;ENSP00000407964:S379Y	ENSP00000266742:S468Y	S	+	2	0	NEDD1	95861577	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	2.370000	0.44240	1.148000	0.42385	0.650000	0.86243	TCT	.	.		0.363	NEDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409792.1			A	97337446	C	A	97337446	3	1	76	1	0	0	0	0	1	0	0	0	10318	913	32	3	1466	3	NEDD1	12	97337446	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	18975031	97337446	36514449	219	10490										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120575521	120575521	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagcttgcctcatgcccaccTcagggctgcgggtggcctcc	12	17	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr12:120575521T>C	ENST00000300648.6	-	49	6503	c.6491A>G	c.(6490-6492)gAg>gGg	p.E2164G		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	2164					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CATGCCCACCTCAGGGCTGCG	0.597																																					p.E2164G		Atlas-SNP	.											.	GCN1L1	207	.	0			c.A6491G						.						40	47	45					12																	120575521		2122	4239	6361	SO:0001583	missense	10985	exon49			CCCACCTCAGGGC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.6491A>G	chr12.hg19:g.120575521T>C	ENSP00000300648:p.Glu2164Gly	91.0	0.0		69.0	10.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.487321	0.63962	.	.	ENSG00000089154	ENST00000300648	T	0.65732	-0.17	5.26	5.26	0.73747	Armadillo-like helical (1);Armadillo-type fold (1);	0.056886	0.64402	D	0.000002	T	0.55337	0.1914	L	0.40543	1.245	0.54753	D	0.999984	B	0.19445	0.036	B	0.18263	0.021	T	0.54695	-0.8255	10	0.59425	D	0.04	.	15.1699	0.72862	0.0:0.0:0.0:1.0	.	2164	Q92616	GCN1L_HUMAN	G	2164	ENSP00000300648:E2164G	ENSP00000300648:E2164G	E	-	2	0	GCN1L1	119059904	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.484000	0.81180	1.968000	0.57251	0.460000	0.39030	GAG	.	.		0.597	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			C	120575521	T	C	120575521	3	2	76	1	0	0	0	0	1	0	0	0	6307	1551	54	2	1564	2	GCN1L1	12	120575521	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	23238075	120575521	13276374	220	10491										
LATS2	26524	hgsc.bcm.edu	37	chr13	21549409	21549409	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cattccgccccaggcggtggTctgcggagcagcacagcttg	14	14	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr13:21549409T>A	ENST00000382592.4	-	8	3272	c.2867A>T	c.(2866-2868)gAc>gTc	p.D956V	LATS2_ENST00000542899.1_Missense_Mutation_p.D956V	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CAGGCGGTGGTCTGCGGAGCA	0.627																																					p.D956V		Atlas-SNP	.											.	LATS2	176	.	0			c.A2867T						.						46	48	47					13																	21549409		2203	4300	6503	SO:0001583	missense	26524	exon8			CGGTGGTCTGCGG	AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"LATS (large tumor suppressor, Drosophila) homolog 2", "LATS, large tumor suppressor, homolog 2 (Drosophila)"			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.2867A>T	chr13.hg19:g.21549409T>A	ENSP00000372035:p.Asp956Val	88.0	0.0		71.0	25.0	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	hg19	CCDS9294.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.461274	0.43736	.	.	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.64438	-0.1;-0.1	5.96	5.96	0.96718	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.255793	0.32593	N	0.005898	T	0.57125	0.2032	L	0.28274	0.84	0.80722	D	1	P	0.45212	0.853	P	0.45138	0.471	T	0.62895	-0.6757	10	0.87932	D	0	.	16.4338	0.83864	0.0:0.0:0.0:1.0	.	956	Q9NRM7	LATS2_HUMAN	V	956	ENSP00000372035:D956V;ENSP00000441817:D956V	ENSP00000372035:D956V	D	-	2	0	LATS2	20447409	1.000000	0.71417	0.242000	0.24170	0.239000	0.25481	6.198000	0.72106	2.270000	0.75569	0.533000	0.62120	GAC	.	.		0.627	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			A	21549409	T	A	21549409	3	1	76	1	0	0	0	0	1	0	0	0	8656	1667	58	4	403	4	LATS2	13	21549409	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10		21549409	93620469	221	10492										
MIPEP	4285	hgsc.bcm.edu	37	chr13	24410481	24410481	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcagcaaaatcagtagggcaCctggtccctaaaacaagaaa	8	10	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr13:24410481C>T	ENST00000382172.3	-	14	1649	c.1551G>A	c.(1549-1551)agG>agA	p.R517R		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	517					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		CAGTAGGGCACCTGGTCCCTA	0.343																																					p.R517R		Atlas-SNP	.											.	MIPEP	53	.	0			c.G1551A						.						78	80	79					13																	24410481		2203	4300	6503	SO:0001819	synonymous_variant	4285	exon14			AGGGCACCTGGTC		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1551G>A	chr13.hg19:g.24410481C>T		53.0	0.0		50.0	16.0	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Silent	SNP	ENST00000382172.3	hg19	CCDS9303.1																																																																																			.	.		0.343	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1			T	24410481	C	T	24410481	2	4	76	1	0	0	0	0	0	0	0	1	9601	506	18	3		3	MIPEP	13	24410481	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	2861072	24410481	90759397	222	10493										
ATP12A	479	hgsc.bcm.edu	37	chr13	25284608	25284608	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccattaacagacaaggtaccAgagggaatacctagaatgga	10	8	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr13:25284608A>G	ENST00000381946.3	+	20	2941	c.2774A>G	c.(2773-2775)cAg>cGg	p.Q925R	ATP12A_ENST00000218548.6_Missense_Mutation_p.Q931R			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	925					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		ACAAGGTACCAGAGGGAATAC	0.453																																					p.Q931R	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.A2792G						.						89	87	88					13																	25284608		2203	4300	6503	SO:0001583	missense	479	exon20			GGTACCAGAGGGA	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2774A>G	chr13.hg19:g.25284608A>G	ENSP00000371372:p.Gln925Arg	164.0	0.0		80.0	39.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.863029	0.51482	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.88431	-2.38;-2.38	5.19	5.19	0.71726	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.95519	0.8544	M	0.93283	3.4	0.58432	D	0.999996	D;D	0.64830	0.994;0.99	D;D	0.72625	0.978;0.947	D	0.96223	0.9162	10	0.62326	D	0.03	.	13.3136	0.60394	1.0:0.0:0.0:0.0	.	931;925	P54707-2;P54707	.;AT12A_HUMAN	R	931;925	ENSP00000218548:Q931R;ENSP00000371372:Q925R	ENSP00000218548:Q931R	Q	+	2	0	ATP12A	24182608	1.000000	0.71417	0.996000	0.52242	0.047000	0.14425	8.892000	0.92491	2.076000	0.62316	0.533000	0.62120	CAG	.	.		0.453	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		G	25284608	A	G	25284608	3	3	76	1	0	0	0	0	1	0	0	0	1122	188	7	2	2870	2	ATP12A	13	25284608	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	874127	25284608	89885270	223	10494										
WBP4	11193	hgsc.bcm.edu	37	chr13	41656941	41656941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agtggtatttaaagaaaaaaCagtcacttctcttggagtta	8	5	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr13:41656941C>T	ENST00000379487.3	+	10	1422	c.1022C>T	c.(1021-1023)aCa>aTa	p.T341I	WBP4_ENST00000542082.1_Missense_Mutation_p.T320I	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	341					mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		AAAGAAAAAACAGTCACTTCT	0.408																																					p.T341I		Atlas-SNP	.											WBP4,NS,carcinoma,0,1	WBP4	40	.	0			c.C1022T						.						75	75	75					13																	41656941		2203	4300	6503	SO:0001583	missense	11193	exon10			AAAAAACAGTCAC	AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"formin binding protein 21"	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.1022C>T	chr13.hg19:g.41656941C>T	ENSP00000368801:p.Thr341Ile	100.0	0.0		75.0	17.0	NM_007187	B7Z4M2|Q32P29	Missense_Mutation	SNP	ENST00000379487.3	hg19	CCDS9375.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.162527	0.57368	.	.	ENSG00000120688	ENST00000379487;ENST00000542082	.	.	.	6.06	6.06	0.98353	.	0.157440	0.56097	D	0.000027	T	0.79753	0.4500	M	0.71581	2.175	0.49687	D	0.999815	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.973	T	0.80122	-0.1514	9	0.87932	D	0	-28.5545	18.8049	0.92032	0.0:1.0:0.0:0.0	.	320;341	B7Z4M2;O75554	.;WBP4_HUMAN	I	341;320	.	ENSP00000368801:T341I	T	+	2	0	WBP4	40554941	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.295000	0.51794	2.879000	0.98667	0.650000	0.86243	ACA	.	.		0.408	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187		T	41656941	C	T	41656941	3	4	76	1	0	0	0	0	1	0	0	0	17276	478	17	3	1060	3	WBP4	13	41656941	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	16372333	41656941	73512937	224	10495										
TNFSF11	8600	hgsc.bcm.edu	37	chr13	43174893	43174893	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcctttttatttcaggaattAcaacatatcgttggatcaca	5	8	2	0	rs375216189		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr13:43174893A>G	ENST00000239849.6	+	3	544	c.393A>G	c.(391-393)ttA>ttG	p.L131L	TNFSF11_ENST00000405262.2_Silent_p.L58L|TNFSF11_ENST00000544862.1_Silent_p.L58L|TNFSF11_ENST00000398795.2_Silent_p.L58L|TNFSF11_ENST00000358545.2_Silent_p.L58L			O14788	TNF11_HUMAN	tumor necrosis factor (ligand) superfamily, member 11	131					activation of JUN kinase activity (GO:0007257)|bone resorption (GO:0045453)|calcium ion homeostasis (GO:0055074)|cytokine-mediated signaling pathway (GO:0019221)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|monocyte chemotaxis (GO:0002548)|organ morphogenesis (GO:0009887)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of bone resorption (GO:0045780)|positive regulation of corticotropin-releasing hormone secretion (GO:0051466)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast development (GO:2001206)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	cytokine activity (GO:0005125)|tumor necrosis factor receptor binding (GO:0005164)|tumor necrosis factor receptor superfamily binding (GO:0032813)			kidney(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	10		Lung NSC(96;1.11e-05)|Breast(139;0.00868)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000249)|GBM - Glioblastoma multiforme(144;0.00119)|BRCA - Breast invasive adenocarcinoma(63;0.073)	Denosumab(DB06643)|Lenalidomide(DB00480)	TTCAGGAATTACAACATATCG	0.333																																					p.L131L		Atlas-SNP	.											.	TNFSF11	43	.	0			c.A393G						.	A	,	1,4405	2.1+/-5.4	0,1,2202	69	66	67		393,174	0.2	1	13		67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TNFSF11	NM_003701.3,NM_033012.3	,	0,2,6501	GG,GA,AA		0.0116,0.0227,0.0154	,	131/318,58/245	43174893	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	8600	exon3			GGAATTACAACAT	AF013171	CCDS9384.1, CCDS9385.1	13q14	2008-02-05			ENSG00000120659	ENSG00000120659		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11926	protein-coding gene	gene with protein product		602642				9312132, 9367155	Standard	NM_003701		Approved	TRANCE, RANKL, OPGL, ODF, CD254	uc001uyu.2	O14788	OTTHUMG00000016807	ENST00000239849.6:c.393A>G	chr13.hg19:g.43174893A>G		46.0	0.0		38.0	13.0	NM_003701	O14723|Q96Q17|Q9P2Q3	Silent	SNP	ENST00000239849.6	hg19	CCDS9384.1																																																																																			.	.		0.333	TNFSF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044702.2			G	43174893	A	G	43174893	2	3	76	1	0	0	0	0	0	0	0	1	16317	388	14	2		2	TNFSF11	13	43174893	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	1517952	43174893	71994985	225	10496										
GAS6	2621	hgsc.bcm.edu	37	chr13	114535616	114535616	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cacctcctcacctggtgggcTgcagcctcttgaagcgcagt	11	15	2	1	rs200744856		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr13:114535616T>A	ENST00000327773.6	-	9	1090	c.944A>T	c.(943-945)cAg>cTg	p.Q315L	GAS6_ENST00000450766.1_Missense_Mutation_p.Q42L|GAS6_ENST00000355761.4_Missense_Mutation_p.Q261L|GAS6-AS1_ENST00000458001.1_RNA|GAS6_ENST00000357389.3_Missense_Mutation_p.Q358L|GAS6_ENST00000418959.3_Missense_Mutation_p.Q16L	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	358					activation of protein kinase B activity (GO:0032148)|apoptotic cell clearance (GO:0043277)|B cell chemotaxis (GO:0035754)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to interferon-alpha (GO:0035457)|cellular response to starvation (GO:0009267)|cellular response to vitamin K (GO:0071307)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|extracellular matrix assembly (GO:0085029)|fusion of virus membrane with host plasma membrane (GO:0019064)|hematopoietic stem cell migration to bone marrow (GO:0097241)|leukocyte migration (GO:0050900)|macrophage cytokine production (GO:0010934)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of oligodendrocyte apoptotic process (GO:1900142)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of renal albumin absorption (GO:2000533)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|peptidyl-serine phosphorylation (GO:0018105)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phagocytosis (GO:0050766)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of TOR signaling (GO:0032008)|post-translational protein modification (GO:0043687)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein targeting to plasma membrane (GO:0072661)|proteolysis (GO:0006508)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|viral entry into host cell (GO:0046718)|viral genome replication (GO:0019079)	cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|platelet alpha granule lumen (GO:0031093)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|phosphatidylserine binding (GO:0001786)|protein tyrosine kinase activator activity (GO:0030296)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(4)|ovary(1)	5	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)				CCTGGTGGGCTGCAGCCTCTT	0.632																																					p.Q315L		Atlas-SNP	.											.	GAS6	75	.	0			c.A944T						.						99	82	88					13																	114535616		2197	4290	6487	SO:0001583	missense	2621	exon9			GTGGGCTGCAGCC		CCDS45072.1	13q34	2008-07-18			ENSG00000183087	ENSG00000183087			4168	protein-coding gene	gene with protein product	"AXL stimulatory factor"	600441		AXLLG		8336730	Standard	NM_000820		Approved	AXSF, FLJ34709, DKFZp666G247	uc001vud.3	Q14393	OTTHUMG00000017395	ENST00000327773.6:c.944A>T	chr13.hg19:g.114535616T>A	ENSP00000331831:p.Gln315Leu	40.0	0.0		40.0	4.0	NM_000820	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Missense_Mutation	SNP	ENST00000327773.6	hg19	CCDS45072.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.382482	0.82792	.	.	ENSG00000183087	ENST00000357389;ENST00000355761;ENST00000450766;ENST00000418959;ENST00000327773	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	4.75	4.75	0.60458	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	T	0.80138	0.4568	M	0.65975	2.015	0.50313	D	0.999868	P;B;D	0.56746	0.875;0.231;0.977	B;B;P	0.48488	0.375;0.068;0.579	T	0.82544	-0.0404	9	0.56958	D	0.05	-37.6214	14.2588	0.66070	0.0:0.0:0.0:1.0	.	358;42;315	Q14393;B3KVL4;Q14393-2	GAS6_HUMAN;.;.	L	358;261;42;16;315	ENSP00000349962:Q358L;ENSP00000348003:Q261L;ENSP00000416498:Q42L;ENSP00000400117:Q16L;ENSP00000331831:Q315L	ENSP00000331831:Q315L	Q	-	2	0	GAS6	113578327	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.386000	0.73186	1.761000	0.52028	0.379000	0.24179	CAG	.	T|1.000;C|0.000		0.632	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2	NM_000820		A	114535616	T	A	114535616	3	1	76	1	0	0	0	0	1	0	0	0	6257	1580	55	4	1120	4	GAS6	13	114535616	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	71360723	114535616	634262	226	10497										
RASA3	22821	hgsc.bcm.edu	37	chr13	114766318	114766318	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttacctttgcttttgtggtaGgtaaattcatggttggtcaa	10	5	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr13:114766318G>T	ENST00000334062.7	-	19	1954	c.1833C>A	c.(1831-1833)acC>acA	p.T611T	RASA3_ENST00000389544.4_Silent_p.T579T	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	611	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			TTTTGTGGTAGGTAAATTCAT	0.512																																					p.T611T		Atlas-SNP	.											.	RASA3	83	.	0			c.C1833A						.						128	122	124					13																	114766318		2203	4300	6503	SO:0001819	synonymous_variant	22821	exon19			GTGGTAGGTAAAT		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"Pleckstrin homology (PH) domain containing"	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.1833C>A	chr13.hg19:g.114766318G>T		124.0	0.0		85.0	37.0	NM_007368	A6NL15|F8W6X8|Q8IUY2	Silent	SNP	ENST00000334062.7	hg19	CCDS32016.1																																																																																			.	.		0.512	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368		T	114766318	G	T	114766318	2	4	76	1	0	0	0	0	0	0	0	1	13077	987	35	3		3	RASA3	13	114766318	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	230702	114766318	403560	227	10498										
RNASE10	338879	hgsc.bcm.edu	37	chr14	20979115	20979115	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgtcattgcctgtgagctcaAggggggaaaatgtcacaaaa	12	7	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr14:20979115A>T	ENST00000328444.5	+	1	504	c.485A>T	c.(484-486)aAg>aTg	p.K162M	RNASE10_ENST00000430083.1_Missense_Mutation_p.K190M	NM_001012975.1	NP_001012993.1	Q5GAN6	RNS10_HUMAN	ribonuclease, RNase A family, 10 (non-active)	162					epithelial cell morphogenesis (GO:0003382)|heterotypic cell-cell adhesion (GO:0034113)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of sperm motility (GO:1902093)|regulation of fertilization (GO:0080154)|seminiferous tubule development (GO:0072520)|single fertilization (GO:0007338)	extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	12	all_cancers(95;0.00123)		Epithelial(56;1.81e-07)|all cancers(55;1.86e-06)	GBM - Glioblastoma multiforme(265;0.022)|READ - Rectum adenocarcinoma(17;0.191)		TGTGAGCTCAAGGGGGGAAAA	0.478																																					p.K162M		Atlas-SNP	.											.	RNASE10	28	.	0			c.A485T						.						100	82	88					14																	20979115		2203	4300	6503	SO:0001583	missense	338879	exon1			AGCTCAAGGGGGG		CCDS32035.1	14q11.1	2004-11-16				ENSG00000182545		"Ribonucleases, RNase A"	19275	protein-coding gene	gene with protein product						12920233	Standard	XM_005267584		Approved	RNASE9	uc010tlj.2	Q5GAN6		ENST00000328444.5:c.485A>T	chr14.hg19:g.20979115A>T	ENSP00000333358:p.Lys162Met	108.0	0.0		66.0	9.0	NM_001012975	A2RUQ3|B4DKY4	Missense_Mutation	SNP	ENST00000328444.5	hg19	CCDS32035.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.879509	0.33162	.	.	ENSG00000182545	ENST00000430083;ENST00000328444	T;T	0.14893	2.47;2.47	4.71	3.54	0.40534	Ribonuclease A, domain (3);	0.283892	0.31577	N	0.007403	T	0.27027	0.0662	M	0.85099	2.735	0.30982	N	0.72239	P;D	0.53312	0.892;0.959	B;P	0.46389	0.377;0.515	T	0.36768	-0.9734	10	0.46703	T	0.11	-29.4925	7.8351	0.29365	0.8161:0.0:0.0:0.1838	.	162;190	Q5GAN6;B4DKY4	RNS10_HUMAN;.	M	190;162	ENSP00000392996:K190M;ENSP00000333358:K162M	ENSP00000333358:K162M	K	+	2	0	RNASE10	20048955	0.997000	0.39634	0.708000	0.30435	0.801000	0.45260	1.587000	0.36622	0.894000	0.36317	0.533000	0.62120	AAG	.	.		0.478	RNASE10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411088.1	XM_292225		T	20979115	A	T	20979115	3	4	76	1	0	0	0	0	1	0	0	0	13415	72	3	4	487	4	RNASE10	14	20979115	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10		20979115	86370425	228	10499										
GZMB	3002	hgsc.bcm.edu	37	chr14	25101298	25101298	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agcctgaggggctgcacagcTctggtccgcttggcctttct	13	13	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr14:25101298T>A	ENST00000216341.4	-	4	472	c.366A>T	c.(364-366)agA>agT	p.R122S	GZMB_ENST00000526004.1_Missense_Mutation_p.E77V|GZMB_ENST00000382540.1_Missense_Mutation_p.R77S|GZMB_ENST00000382542.1_Missense_Mutation_p.R156S|RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000415355.3_Missense_Mutation_p.R110S|RP11-104E19.1_ENST00000555300.1_RNA			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	122	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		GCTGCACAGCTCTGGTCCGCT	0.637																																					p.R122S		Atlas-SNP	.											.	GZMB	73	.	0			c.A366T						.						53	51	52					14																	25101298		2203	4300	6503	SO:0001583	missense	3002	exon4			CACAGCTCTGGTC	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"fragmentin 2", "cytotoxic serine protease B", "cathepsin G-like 1", "T-cell serine protease 1-3E"	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.366A>T	chr14.hg19:g.25101298T>A	ENSP00000216341:p.Arg122Ser	55.0	0.0		55.0	16.0	NM_004131	Q8N1D2|Q9UCC1	Missense_Mutation	SNP	ENST00000216341.4	hg19	CCDS9633.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	9.891|9.891	1.204238|1.204238	0.22205|0.22205	.|.	.|.	ENSG00000100453|ENSG00000100453	ENST00000526004|ENST00000415355;ENST00000216341;ENST00000382542;ENST00000382540;ENST00000382539	T|T;D;D;T	0.79554|0.92397	-1.28|0.37;-3.03;-3.03;1.66	5.3|5.3	-1.58|-1.58	0.08479|0.08479	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.|1.940520	.|0.03235	.|N	.|0.179487	T|T	0.78966|0.78966	0.4367|0.4367	N|N	0.10945|0.10945	0.07|0.07	0.18873|0.18873	N|N	0.999989|0.999989	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.06405	.|0.002;0.001	T|T	0.70037|0.70037	-0.4982|-0.4982	7|10	0.66056|0.07644	D|T	0.02|0.81	.|.	1.0882|1.0882	0.01658|0.01658	0.1426:0.2469:0.1479:0.4626|0.1426:0.2469:0.1479:0.4626	.|.	.|110;122	.|Q6XGZ4;P10144	.|.;GRAB_HUMAN	V|S	77|110;122;156;77;27	ENSP00000434213:E77V|ENSP00000387385:R110S;ENSP00000216341:R122S;ENSP00000371982:R156S;ENSP00000371980:R77S	ENSP00000434213:E77V|ENSP00000216341:R122S	E|R	-|-	2|3	0|2	GZMB|GZMB	24171138|24171138	0.000000|0.000000	0.05858|0.05858	0.024000|0.024000	0.17045|0.17045	0.019000|0.019000	0.09904|0.09904	-2.083000|-2.083000	0.01364|0.01364	-0.414000|-0.414000	0.07495|0.07495	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.637	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131		A	25101298	T	A	25101298	3	1	76	1	0	0	0	0	1	0	0	0	6925	1548	54	4	385	4	GZMB	14	25101298	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	4122183	25101298	82248242	229	10500										
FAM179B	23116	hgsc.bcm.edu	37	chr14	45433642	45433642	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tggaatcatgggagaaaaccAgacctccacttccaaggata	9	10	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr14:45433642A>T	ENST00000361577.3	+	1	2232	c.2018A>T	c.(2017-2019)cAg>cTg	p.Q673L	KLHL28_ENST00000553817.1_Intron|KLHL28_ENST00000396128.4_5'Flank|FAM179B_ENST00000382233.2_Missense_Mutation_p.Q673L|FAM179B_ENST00000361462.2_Missense_Mutation_p.Q673L	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	673										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						GGAGAAAACCAGACCTCCACT	0.393																																					p.Q673L		Atlas-SNP	.											.	FAM179B	115	.	0			c.A2018T						.						46	46	46					14																	45433642		2203	4300	6503	SO:0001583	missense	23116	exon1			AAAACCAGACCTC	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.2018A>T	chr14.hg19:g.45433642A>T	ENSP00000355045:p.Gln673Leu	46.0	0.0		32.0	25.0	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	A	9.494	1.101480	0.20632	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233	T;T;T	0.05717	3.4;3.4;3.4	5.01	-0.416	0.12351	Armadillo-type fold (1);	0.671044	0.13208	N	0.405422	T	0.03390	0.0098	N	0.14661	0.345	0.24132	N	0.995768	B;B;B;B	0.23990	0.095;0.066;0.039;0.095	B;B;B;B	0.20955	0.032;0.032;0.032;0.032	T	0.44375	-0.9332	10	0.30078	T	0.28	-0.0656	7.1182	0.25429	0.5096:0.3812:0.1091:0.0	.	673;673;673;673	Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2	.;.;F179B_HUMAN;.	L	673	ENSP00000355045:Q673L;ENSP00000354917:Q673L;ENSP00000371668:Q673L	ENSP00000354917:Q673L	Q	+	2	0	FAM179B	44503392	0.281000	0.24258	0.978000	0.43139	0.759000	0.43091	0.496000	0.22499	0.337000	0.23665	0.379000	0.24179	CAG	.	.		0.393	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		T	45433642	A	T	45433642	3	4	76	1	0	0	0	0	1	0	0	0	5511	188	7	4	2020	4	FAM179B	14	45433642	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	20332344	45433642	61915898	230	10501										
PPP2R5E	5529	hgsc.bcm.edu	37	chr14	63860613	63860613	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	accagaaactgtttgtgttcTgccttaagaggtaaagcaaa	9	7	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr14:63860613T>C	ENST00000337537.3	-	8	1376	c.774A>G	c.(772-774)gcA>gcG	p.A258A	PPP2R5E_ENST00000553266.1_5'UTR|PPP2R5E_ENST00000422769.2_Silent_p.A182A|PPP2R5E_ENST00000555899.1_Silent_p.A258A	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	258					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		GTTTGTGTTCTGCCTTAAGAG	0.388																																					p.A258A		Atlas-SNP	.											.	PPP2R5E	43	.	0			c.A774G						.						100	98	99					14																	63860613		2203	4300	6503	SO:0001819	synonymous_variant	5529	exon8			GTGTTCTGCCTTA	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9313	protein-coding gene	gene with protein product		601647	"protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.774A>G	chr14.hg19:g.63860613T>C		82.0	0.0		76.0	13.0	NM_006246	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Silent	SNP	ENST00000337537.3	hg19	CCDS9758.1																																																																																			.	.		0.388	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246		C	63860613	T	C	63860613	2	2	76	1	0	0	0	0	0	0	0	1	12408	1567	55	2		2	PPP2R5E	14	63860613	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	18426971	63860613	43488927	231	10502										
FAM161B	145483	hgsc.bcm.edu	37	chr14	74411141	74411141	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gctgtggctgccaagtctctCtgtcgagcagcttcctttag	11	12	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr14:74411141C>G	ENST00000534936.1	-	3	927	c.822G>C	c.(820-822)caG>caC	p.Q274H	FAM161B_ENST00000286544.3_Missense_Mutation_p.Q337H			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	274										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						CCAAGTCTCTCTGTCGAGCAG	0.552																																					p.Q337H		Atlas-SNP	.											.	FAM161B	67	.	0			c.G1011C						.						82	83	82					14																	74411141		2203	4300	6503	SO:0001583	missense	145483	exon3			GTCTCTCTGTCGA	AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 44"	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.822G>C	chr14.hg19:g.74411141C>G	ENSP00000445326:p.Gln274His	70.0	0.0		56.0	13.0	NM_152445	B7Z882|J3KNA2	Missense_Mutation	SNP	ENST00000534936.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.27	2.186049	0.38609	.	.	ENSG00000156050	ENST00000286544;ENST00000534936	T;T	0.25085	1.82;1.82	5.12	2.26	0.28386	.	0.262495	0.32518	N	0.005986	T	0.18882	0.0453	L	0.49350	1.555	0.32345	N	0.559188	B	0.22003	0.063	B	0.25759	0.063	T	0.17684	-1.0361	10	0.54805	T	0.06	-3.458	0.6848	0.00881	0.1807:0.3764:0.1765:0.2665	.	274	Q96MY7	F161B_HUMAN	H	337;274	ENSP00000286544:Q337H;ENSP00000445326:Q274H	ENSP00000286544:Q337H	Q	-	3	2	FAM161B	73480894	0.068000	0.21057	0.975000	0.42487	0.981000	0.71138	0.360000	0.20250	0.295000	0.22570	0.563000	0.77884	CAG	.	.		0.552	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445		G	74411141	C	G	74411141	3	3	76	1	0	0	0	0	1	0	0	0	5478	912	32	4	1149	4	FAM161B	14	74411141	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	10550528	74411141	32938399	232	10503										
BDKRB2	624	hgsc.bcm.edu	37	chr14	96707630	96707630	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gatcgcctccttcatggcctAcagcaacagctgcctcaacc	7	17	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr14:96707630A>G	ENST00000306005.3	+	3	1161	c.965A>G	c.(964-966)tAc>tGc	p.Y322C	RP11-404P21.8_ENST00000553811.1_Intron|BDKRB2_ENST00000554311.1_Missense_Mutation_p.Y322C|BDKRB2_ENST00000542454.2_Missense_Mutation_p.Y295C|BDKRB2_ENST00000539359.1_Missense_Mutation_p.Y295C	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	322					arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	TTCATGGCCTACAGCAACAGC	0.582																																					p.Y322C		Atlas-SNP	.											BDKRB2,NS,carcinoma,0,1	BDKRB2	56	.	0			c.A965G						.						81	70	74					14																	96707630		2203	4300	6503	SO:0001583	missense	624	exon3			TGGCCTACAGCAA	S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"GPCR / Class A : Bradykinin receptors"	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.965A>G	chr14.hg19:g.96707630A>G	ENSP00000307713:p.Tyr322Cys	111.0	0.0		61.0	7.0	NM_000623		Missense_Mutation	SNP	ENST00000306005.3	hg19	CCDS9942.1	.	.	.	.	.	.	.	.	.	.	A	9.295	1.051571	0.19827	.	.	ENSG00000168398	ENST00000542454;ENST00000554311;ENST00000306005;ENST00000539359	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	4.62	2.13	0.27403	GPCR, rhodopsin-like superfamily (1);	0.285276	0.34580	N	0.003860	T	0.24774	0.0601	M	0.80422	2.495	0.38013	D	0.934619	B	0.20459	0.045	B	0.27076	0.076	T	0.09975	-1.0650	10	0.54805	T	0.06	-21.3378	5.3404	0.15981	0.5878:0.0:0.0835:0.3286	.	322	P30411	BKRB2_HUMAN	C	295;322;322;295	ENSP00000439459:Y295C;ENSP00000450482:Y322C;ENSP00000307713:Y322C;ENSP00000438376:Y295C	ENSP00000307713:Y322C	Y	+	2	0	BDKRB2	95777383	0.824000	0.29247	0.991000	0.47740	0.527000	0.34593	1.515000	0.35845	0.597000	0.29811	0.459000	0.35465	TAC	.	.		0.582	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1			G	96707630	A	G	96707630	3	3	76	1	0	0	0	0	1	0	0	0	1393	391	14	2	971	2	BDKRB2	14	96707630	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	22296489	96707630	10641910	233	10504										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105408806	105408806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gaggctcacgtcagcctccaCcttcagcgcagacacatcca	8	17	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr14:105408806C>T	ENST00000333244.5	-	7	13101	c.12982G>A	c.(12982-12984)Gtg>Atg	p.V4328M	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4328						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TCAGCCTCCACCTTCAGCGCA	0.602																																					p.V4328M		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G12982A						.						163	177	172					14																	105408806		1970	4141	6111	SO:0001583	missense	113146	exon7			CCTCCACCTTCAG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.12982G>A	chr14.hg19:g.105408806C>T	ENSP00000353114:p.Val4328Met	93.0	0.0		82.0	54.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	10.48	1.363160	0.24684	.	.	ENSG00000185567	ENST00000333244	T	0.00932	5.53	3.16	1.19	0.21007	.	0.685869	0.10634	U	0.651821	T	0.02156	0.0067	M	0.63208	1.945	0.09310	N	1	P	0.44776	0.843	P	0.53006	0.715	T	0.46091	-0.9216	10	0.30078	T	0.28	.	4.1107	0.10057	0.1836:0.614:0.0:0.2023	.	4328	Q8IVF2	AHNK2_HUMAN	M	4328	ENSP00000353114:V4328M	ENSP00000353114:V4328M	V	-	1	0	AHNAK2	104479851	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.525000	0.06214	-0.086000	0.12550	-0.665000	0.03846	GTG	.	.		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105408806	C	T	105408806	3	4	76	1	0	0	0	0	1	0	0	0	415	507	18	3	4409	3	AHNAK2	14	105408806	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	8701176	105408806	1940734	234	10505										
OTUD7A	161725	hgsc.bcm.edu	37	chr15	31776404	31776404	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccccctgcatggcggcgcgcAggatgttgaggctcagcttc	14	14	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr15:31776404A>C	ENST00000307050.4	-	11	1966	c.1874T>G	c.(1873-1875)cTg>cGg	p.L625R	OTUD7A_ENST00000382902.1_Missense_Mutation_p.L632R	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	625					protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		GGCGGCGCGCAGGATGTTGAG	0.672																																					p.L625R		Atlas-SNP	.											.	OTUD7A	89	.	0			c.T1874G						.						17	17	17					15																	31776404		2198	4294	6492	SO:0001583	missense	161725	exon11			GCGCGCAGGATGT	AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918		"OTU domain containing"	20718	protein-coding gene	gene with protein product		612024	"chromosome 15 open reading frame 16", "OTU domain containing 7", "OTU domain containing 7A"	C15orf16, OTUD7		23827681	Standard	NM_130901		Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.1874T>G	chr15.hg19:g.31776404A>C	ENSP00000305926:p.Leu625Arg	22.0	0.0		20.0	10.0	NM_130901	Q8IWK5	Missense_Mutation	SNP	ENST00000307050.4	hg19	CCDS10026.1	.	.	.	.	.	.	.	.	.	.	A	19.86	3.905257	0.72868	.	.	ENSG00000169918	ENST00000307050;ENST00000382902	T;T	0.38722	1.12;1.12	4.61	4.61	0.57282	.	0.148435	0.44902	D	0.000411	T	0.53222	0.1783	L	0.34521	1.04	0.43050	D	0.994653	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.996	T	0.58526	-0.7621	10	0.87932	D	0	-16.4006	14.0325	0.64624	1.0:0.0:0.0:0.0	.	632;625	Q8TE49-2;Q8TE49	.;OTU7A_HUMAN	R	625;632	ENSP00000305926:L625R;ENSP00000372358:L632R	ENSP00000305926:L625R	L	-	2	0	OTUD7A	29563696	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.379000	0.90146	1.693000	0.51124	0.459000	0.35465	CTG	.	.		0.672	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901		C	31776404	A	C	31776404	3	2	76	1	0	0	0	0	1	0	0	0	11327	188	7	5	910	5	OTUD7A	15	31776404	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10		31776404	70754988	235	10506										
CEP152	22995	hgsc.bcm.edu	37	chr15	49033896	49033896	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagcattcataatctttttcTcagccctgtggggaattcca	7	11	3	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr15:49033896T>A	ENST00000380950.2	-	26	4182	c.3995A>T	c.(3994-3996)gAg>gTg	p.E1332V	CEP152_ENST00000399334.3_Missense_Mutation_p.E1276V|CEP152_ENST00000325747.5_Missense_Mutation_p.E1239V	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1332					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		AATCTTTTTCTCAGCCCTGTG	0.383																																					p.E1332V		Atlas-SNP	.											.	CEP152	145	.	0			c.A3995T						.						149	137	141					15																	49033896		1807	4077	5884	SO:0001583	missense	22995	exon26			TTTTTCTCAGCCC	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.3995A>T	chr15.hg19:g.49033896T>A	ENSP00000370337:p.Glu1332Val	55.0	0.0		45.0	10.0	NM_001194998	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	hg19	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.552871	0.65425	.	.	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334	T;T;T	0.66638	0.05;-0.03;-0.22	5.87	5.87	0.94306	.	0.065981	0.64402	D	0.000015	T	0.79678	0.4487	M	0.68593	2.085	0.80722	D	1	D;D;D	0.67145	0.992;0.996;0.996	P;D;D	0.64410	0.894;0.925;0.925	T	0.81835	-0.0750	10	0.87932	D	0	-15.8868	16.2774	0.82651	0.0:0.0:0.0:1.0	.	1239;1332;1276	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	V	1332;1239;1276	ENSP00000370337:E1332V;ENSP00000321000:E1239V;ENSP00000382271:E1276V	ENSP00000321000:E1239V	E	-	2	0	CEP152	46821188	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.451000	0.80668	2.247000	0.74100	0.482000	0.46254	GAG	.	.		0.383	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		A	49033896	T	A	49033896	3	1	76	1	0	0	0	0	1	0	0	0	3250	1551	54	4	1145	4	CEP152	15	49033896	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	17257492	49033896	53497496	236	10507										
HERC1	8925	hgsc.bcm.edu	37	chr15	63970246	63970246	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagctgcagctctgagaggtCagcgaggccatgcctagtat	13	11	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr15:63970246C>A	ENST00000443617.2	-	37	6955	c.6868G>T	c.(6868-6870)Gac>Tac	p.D2290Y	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2290					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TCTGAGAGGTCAGCGAGGCCA	0.527																																					p.D2290Y		Atlas-SNP	.											.	HERC1	624	.	0			c.G6868T						.						148	156	153					15																	63970246		2084	4200	6284	SO:0001583	missense	8925	exon37			AGAGGTCAGCGAG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.6868G>T	chr15.hg19:g.63970246C>A	ENSP00000390158:p.Asp2290Tyr	83.0	0.0		70.0	28.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.109313	0.56398	.	.	ENSG00000103657	ENST00000443617	T	0.25912	1.77	5.6	5.6	0.85130	.	0.127571	0.50627	D	0.000102	T	0.28466	0.0704	L	0.34521	1.04	0.58432	D	0.999997	B	0.31790	0.34	B	0.37091	0.241	T	0.07328	-1.0778	10	0.87932	D	0	.	19.605	0.95577	0.0:1.0:0.0:0.0	.	2290	Q15751	HERC1_HUMAN	Y	2290	ENSP00000390158:D2290Y	ENSP00000390158:D2290Y	D	-	1	0	HERC1	61757299	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.739000	0.62080	2.635000	0.89317	0.655000	0.94253	GAC	.	.		0.527	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63970246	C	A	63970246	3	1	76	1	0	0	0	0	1	0	0	0	7066	826	29	3	7885	3	HERC1	15	63970246	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	14936350	63970246	38561146	237	10508										
HERC1	8925	hgsc.bcm.edu	37	chr15	63986548	63986548	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aatctggagcaaccttgtacTggccactttcaaagctgtgc	9	11	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr15:63986548T>A	ENST00000443617.2	-	29	5530	c.5443A>T	c.(5443-5445)Agt>Tgt	p.S1815C	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1815					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						AACCTTGTACTGGCCACTTTC	0.463																																					p.S1815C		Atlas-SNP	.											.	HERC1	624	.	0			c.A5443T						.						64	62	62					15																	63986548		1945	4140	6085	SO:0001583	missense	8925	exon29			TTGTACTGGCCAC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.5443A>T	chr15.hg19:g.63986548T>A	ENSP00000390158:p.Ser1815Cys	119.0	0.0		65.0	13.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461780	0.63513	.	.	ENSG00000103657	ENST00000443617	T	0.34472	1.36	5.92	5.92	0.95590	.	0.190841	0.45867	D	0.000332	T	0.36082	0.0954	N	0.20986	0.625	0.58432	D	0.999991	D	0.56287	0.975	P	0.49708	0.62	T	0.10730	-1.0617	10	0.45353	T	0.12	.	16.3662	0.83325	0.0:0.0:0.0:1.0	.	1815	Q15751	HERC1_HUMAN	C	1815	ENSP00000390158:S1815C	ENSP00000390158:S1815C	S	-	1	0	HERC1	61773601	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.184000	0.72008	2.274000	0.75844	0.533000	0.62120	AGT	.	.		0.463	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63986548	T	A	63986548	3	1	76	1	0	0	0	0	1	0	0	0	7066	1580	55	4	9342	4	HERC1	15	63986548	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	16302	63986548	38544844	238	10509										
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79059245	79059245	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agccgctgcctgagccttcaGggcccagtgtgcccaggggc	15	15	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr15:79059245G>T	ENST00000388820.4	-	19	3218	c.3008C>A	c.(3007-3009)cCt>cAt	p.P1003H	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1003					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						TGAGCCTTCAGGGCCCAGTGT	0.667																																					p.P1003H		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C3008A						.						19	20	19					15																	79059245		2185	4278	6463	SO:0001583	missense	11173	exon19			CCTTCAGGGCCCA	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3008C>A	chr15.hg19:g.79059245G>T	ENSP00000373472:p.Pro1003His	83.0	0.0		55.0	21.0	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	hg19	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.159885	0.57368	.	.	ENSG00000136378	ENST00000388820	T	0.59906	0.23	4.83	2.95	0.34219	.	0.824928	0.11097	N	0.600108	T	0.63224	0.2493	M	0.64997	1.995	0.09310	N	1	D	0.65815	0.995	P	0.53185	0.72	T	0.50898	-0.8773	10	0.52906	T	0.07	.	7.7336	0.28802	0.2653:0.0:0.7347:0.0	.	1003	Q9UKP4	ATS7_HUMAN	H	1003	ENSP00000373472:P1003H	ENSP00000373472:P1003H	P	-	2	0	ADAMTS7	76846300	0.001000	0.12720	0.026000	0.17262	0.153000	0.21895	0.955000	0.29188	0.457000	0.26962	-0.205000	0.12727	CCT	.	.		0.667	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		T	79059245	G	T	79059245	3	4	76	1	0	0	0	0	1	0	0	0	271	1000	35	3	2076	3	ADAMTS7	15	79059245	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	15072697	79059245	23472147	239	10510										
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84568428	84568428	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagtggaagcaaaattgcctTggctgaaacaagcacaagaa	10	8	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr15:84568428T>A	ENST00000286744.5	+	15	1869	c.1645T>A	c.(1645-1647)Tgg>Agg	p.W549R	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.W549R	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	549						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AAAATTGCCTTGGCTGAAACA	0.383																																					p.W549R		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.T1645A						.						115	95	102					15																	84568428		2203	4300	6503	SO:0001583	missense	57188	exon15			TTGCCTTGGCTGA	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.1645T>A	chr15.hg19:g.84568428T>A	ENSP00000286744:p.Trp549Arg	232.0	0.0		174.0	66.0	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	hg19	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.295405	0.81025	.	.	ENSG00000156218	ENST00000286744	T	0.64085	-0.08	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.70237	0.3201	L	0.32530	0.975	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.997	T	0.73717	-0.3895	10	0.72032	D	0.01	.	14.3507	0.66699	0.0:0.0:0.0:1.0	.	549;549	P82987-2;P82987	.;ATL3_HUMAN	R	549	ENSP00000286744:W549R	ENSP00000286744:W549R	W	+	1	0	ADAMTSL3	82359432	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.007000	0.76335	1.985000	0.57927	0.519000	0.50382	TGG	.	.		0.383	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		A	84568428	T	A	84568428	3	1	76	1	0	0	0	0	1	0	0	0	276	1812	63	4	1699	4	ADAMTSL3	15	84568428	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	5509183	84568428	17962964	240	10511										
PRC1	9055	hgsc.bcm.edu	37	chr15	91522459	91522460	+	Frame_Shift_Ins	INS	-	-	A													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aagagttccttgtgaacttcINSatagtagttttttaaccgca							TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr15:91522459_91522460insA	ENST00000361188.5	-	8	2246_2247	c.1035_1036insT	c.(1033-1038)tatgaafs	p.E346fs	PRC1_ENST00000442656.2_Frame_Shift_Ins_p.E305fs|PRC1_ENST00000394249.3_Frame_Shift_Ins_p.E346fs|PRC1_ENST00000361919.3_Frame_Shift_Ins_p.E346fs|Y_RNA_ENST00000363272.1_RNA|PRC1-AS1_ENST00000554388.1_RNA					protein regulator of cytokinesis 1											endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					TTGTGAACTTCATAGTAGTTTT	0.406																																					p.E346_V347delinsX		Atlas-INDEL	.											.	PRC1	51	.	0			c.1036_1037insT						.																																			SO:0001589	frameshift_variant	9055	exon8			.	AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"anaphase spindle elongation 1 homolog (S. cerevisiae)"	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.1036dupT	chr15.hg19:g.91522460_91522460dupA	ENSP00000354679:p.Glu346fs	79.0	0.0		42.0	10.0	NM_199413		Frame_Shift_Ins	INS	ENST00000361188.5	hg19	CCDS45352.1																																																																																			.	.		0.406	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981		A	91522460	-	A	91522459	7	5	76	1	0	1	1	0	0	0	0	0	12458	835	29	0	858	0	PRC1	15	91522459	Frame_Shift_Ins	INS	-	TCGA-CC-A7IK-01A-12D-A33Q-10	6954031	91522459	11008933	241	10512										
MEF2A	4205	hgsc.bcm.edu	37	chr15	100214726	100214726	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcagccagctcaacgttaacAgattcaagcatgctctctcc	7	14	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr15:100214726A>G	ENST00000557785.1	+	6	868	c.519A>G	c.(517-519)acA>acG	p.T173T	MEF2A_ENST00000557942.1_Silent_p.T173T|MEF2A_ENST00000354410.5_Silent_p.T175T|MEF2A_ENST00000338042.6_Silent_p.T173T|MEF2A_ENST00000558812.1_Silent_p.T105T|MEF2A_ENST00000449277.2_Silent_p.T105T|MEF2A_ENST00000453228.2_Silent_p.T173T	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	175	Ser/Thr-rich.				apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			CAACGTTAACAGATTCAAGCA	0.498																																					p.T175T		Atlas-SNP	.											.	MEF2A	138	.	0			c.A525G						.						196	187	190					15																	100214726		1953	4153	6106	SO:0001819	synonymous_variant	4205	exon6			GTTAACAGATTCA		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"Myocyte enhancer factors"	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.519A>G	chr15.hg19:g.100214726A>G		119.0	0.0		89.0	39.0	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Silent	SNP	ENST00000557785.1	hg19	CCDS53978.1																																																																																			.	.		0.498	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1			G	100214726	A	G	100214726	2	3	76	1	0	0	0	0	0	0	0	1	9464	175	7	2		2	MEF2A	15	100214726	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	8692267	100214726	2316666	242	10513										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101562141	101562141	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	acctgaccatcagcaatgtgCctgcagaaatccaaaaagaa	7	11	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr15:101562141C>A	ENST00000388948.3	+	14	2190	c.1831C>A	c.(1831-1833)Cct>Act	p.P611T	LRRK1_ENST00000284395.5_Missense_Mutation_p.P608T	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CAGCAATGTGCCTGCAGAAAT	0.577																																					p.P611T		Atlas-SNP	.											.	LRRK1	310	.	0			c.C1831A						.						52	56	55					15																	101562141		2044	4195	6239	SO:0001583	missense	79705	exon14			AATGTGCCTGCAG	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.1831C>A	chr15.hg19:g.101562141C>A	ENSP00000373600:p.Pro611Thr	77.0	0.0		35.0	18.0	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.542835	0.86022	.	.	ENSG00000154237	ENST00000388948;ENST00000284395	T;T	0.77877	-1.13;-1.13	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.90383	0.6990	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88877	0.3337	10	0.27785	T	0.31	.	18.9334	0.92576	0.0:1.0:0.0:0.0	.	611	Q38SD2	LRRK1_HUMAN	T	611;608	ENSP00000373600:P611T;ENSP00000284395:P608T	ENSP00000284395:P608T	P	+	1	0	LRRK1	99379664	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	7.535000	0.82014	2.782000	0.95742	0.655000	0.94253	CCT	.	.		0.577	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101562141	C	A	101562141	3	1	76	1	0	0	0	0	1	0	0	0	9041	739	26	3	1881	3	LRRK1	15	101562141	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	1347415	101562141	969251	243	10514										
OR4F6	390648	hgsc.bcm.edu	37	chr15	102346471	102346471	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttcttttgtgatcttcctcgAtttatcaaactggcttgcat	6	9	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr15:102346471A>G	ENST00000328882.4	+	1	570	c.549A>G	c.(547-549)cgA>cgG	p.R183R		NM_001005326.1	NP_001005326.1	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F, member 6	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(1)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			ATCTTCCTCGATTTATCAAAC	0.363																																					p.R183R		Atlas-SNP	.											.	OR4F6	45	.	0			c.A549G						.						183	180	181					15																	102346471		2203	4299	6502	SO:0001819	synonymous_variant	390648	exon1			TCCTCGATTTATC	AC025234	CCDS32341.1	15q26.3	2014-02-19	2002-02-28		ENSG00000184140	ENSG00000184140		"GPCR / Class A : Olfactory receptors"	15372	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily F, member 12"	OR4F12			Standard	NM_001005326		Approved		uc010utr.2	Q8NGB9	OTTHUMG00000172267	ENST00000328882.4:c.549A>G	chr15.hg19:g.102346471A>G		80.0	0.0		74.0	34.0	NM_001005326	B9EH28|Q6IF95	Silent	SNP	ENST00000328882.4	hg19	CCDS32341.1																																																																																			.	.		0.363	OR4F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417593.1			G	102346471	A	G	102346471	2	3	76	1	0	0	0	0	0	0	0	1	11075	320	12	2		2	OR4F6	15	102346471	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	784330	102346471	184921	244	10515										
MEFV	4210	hgsc.bcm.edu	37	chr16	3304779	3304779	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atcatctgtgccgttttcttGtgtggaatattctggaagga	11	6	4	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr16:3304779G>C	ENST00000219596.1	-	2	328	c.289C>G	c.(289-291)Caa>Gaa	p.Q97E	MEFV_ENST00000339854.4_Intron|MEFV_ENST00000536379.1_Intron|MEFV_ENST00000541159.1_Intron	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	97					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						CCGTTTTCTTGTGTGGAATAT	0.547																																					p.Q97E		Atlas-SNP	.											.	MEFV	170	.	0			c.C289G						.						47	52	50					16																	3304779		2146	4213	6359	SO:0001583	missense	4210	exon2			TTTCTTGTGTGGA	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.289C>G	chr16.hg19:g.3304779G>C	ENSP00000219596:p.Gln97Glu	31.0	0.0		36.0	10.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	hg19	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	G	1.208	-0.630620	0.03584	.	.	ENSG00000103313	ENST00000545159;ENST00000219596	T	0.62788	-0.0	3.75	0.58	0.17402	.	0.673936	0.13268	N	0.400749	T	0.35422	0.0931	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20672	-1.0268	10	0.09338	T	0.73	-37.9873	7.0377	0.25002	0.0:0.3807:0.4379:0.1814	.	97	O15553	MEFV_HUMAN	E	97	ENSP00000219596:Q97E	ENSP00000219596:Q97E	Q	-	1	0	MEFV	3244780	0.025000	0.19082	0.020000	0.16555	0.007000	0.05969	0.187000	0.16998	0.170000	0.19704	-0.257000	0.10917	CAA	.	.		0.547	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		C	3304779	G	C	3304779	3	2	76	1	0	0	0	0	1	0	0	0	9468	1386	48	4	2092	4	MEFV	16	3304779	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10		3304779	87049974	245	10516										
SEC14L5	9717	hgsc.bcm.edu	37	chr16	5050737	5050737	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cgtgggggaggaggcgctgcTgcggcatgtgagtcaggggc	22	8	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr16:5050737T>A	ENST00000251170.7	+	9	1232	c.1052T>A	c.(1051-1053)cTg>cAg	p.L351Q		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	351	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						GAGGCGCTGCTGCGGCATGTG	0.667																																					p.L351Q		Atlas-SNP	.											.	SEC14L5	79	.	0			c.T1052A						.						14	16	16					16																	5050737		2020	4134	6154	SO:0001583	missense	9717	exon9			CGCTGCTGCGGCA	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1052T>A	chr16.hg19:g.5050737T>A	ENSP00000251170:p.Leu351Gln	66.0	0.0		57.0	23.0	NM_014692		Missense_Mutation	SNP	ENST00000251170.7	hg19	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.277525	0.80580	.	.	ENSG00000103184	ENST00000251170	T	0.76839	-1.05	4.36	4.36	0.52297	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.000000	0.49916	D	0.000126	D	0.86686	0.5992	M	0.75150	2.29	0.80722	D	1	D	0.71674	0.998	D	0.77004	0.989	D	0.88112	0.2826	10	0.62326	D	0.03	-23.454	13.7221	0.62735	0.0:0.0:0.0:1.0	.	351	O43304	S14L5_HUMAN	Q	351	ENSP00000251170:L351Q	ENSP00000251170:L351Q	L	+	2	0	SEC14L5	4990738	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	7.349000	0.79376	1.841000	0.53522	0.379000	0.24179	CTG	.	.		0.667	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1			A	5050737	T	A	5050737	3	1	76	1	0	0	0	0	1	0	0	0	14000	1580	55	4	1082	4	SEC14L5	16	5050737	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	1745958	5050737	85304016	246	10517										
IGSF6	10261	hgsc.bcm.edu	37	chr16	21654919	21654919	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcttagagggttggattttgActgccaagaagagaaggaaa	13	4	1	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr16:21654919A>T	ENST00000268389.4	-	4	596	c.535T>A	c.(535-537)Tca>Aca	p.S179T	METTL9_ENST00000396014.4_Intron|RNU6-196P_ENST00000384315.1_RNA|METTL9_ENST00000358154.3_Intron|RNU6-1005P_ENST00000384519.1_RNA	NM_005849.3	NP_005840.2	O95976	IGSF6_HUMAN	immunoglobulin superfamily, member 6	179					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(48;0.066)		TTGGATTTTGACTGCCAAGAA	0.318																																					p.S179T		Atlas-SNP	.											.	IGSF6	19	.	0			c.T535A						.						105	94	98					16																	21654919		2199	4298	6497	SO:0001630	splice_region_variant	10261	exon4			ATTTTGACTGCCA	AJ223183	CCDS10599.1	16p12.2	2013-01-11			ENSG00000140749	ENSG00000140749		"Immunoglobulin superfamily / V-set domain containing"	5953	protein-coding gene	gene with protein product		606222				9809579	Standard	NM_005849		Approved	DORA	uc002djg.2	O95976	OTTHUMG00000090709	ENST00000268389.4:c.535-1T>A	chr16.hg19:g.21654919A>T		57.0	0.0		73.0	14.0	NM_005849	Q8WWD8	Missense_Mutation	SNP	ENST00000268389.4	hg19	CCDS10599.1	.	.	.	.	.	.	.	.	.	.	A	9.480	1.097861	0.20552	.	.	ENSG00000140749	ENST00000268389	T	0.24350	1.86	5.53	1.84	0.25277	.	0.995451	0.08146	N	0.990877	T	0.21631	0.0521	L	0.46157	1.445	0.28520	N	0.913107	B	0.28082	0.2	B	0.28385	0.089	T	0.33624	-0.9861	10	0.23302	T	0.38	-24.8375	6.3715	0.21483	0.5051:0.3483:0.0:0.1466	.	179	O95976	IGSF6_HUMAN	T	179	ENSP00000268389:S179T	ENSP00000268389:S179T	S	-	1	0	IGSF6	21562420	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	1.170000	0.31883	0.088000	0.17205	0.528000	0.53228	TCA	.	.		0.318	IGSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207400.1		Missense_Mutation	T	21654919	A	T	21654919	5	4	76	1	0	0	0	0	0	0	1	0	7612	289	10	4	202	4	IGSF6	16	21654919	Splice_Site	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	16604182	21654919	68699834	247	10518										
CES7	221223	hgsc.bcm.edu	37	chr16	55897346	55897346	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggctttgtggaataagccttTggccatgggagacagtatct	13	7	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr16:55897346T>A	ENST00000290567.9	-	6	845	c.724A>T	c.(724-726)Aaa>Taa	p.K242*	CES5A_ENST00000521992.1_Nonsense_Mutation_p.K271*|CES5A_ENST00000518005.1_Nonsense_Mutation_p.K136*|CES5A_ENST00000319165.9_Nonsense_Mutation_p.K242*|CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000520435.1_Nonsense_Mutation_p.K212*	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	242						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						AATAAGCCTTTGGCCATGGGA	0.488																																					p.K271X		Atlas-SNP	.											.	CES5A	206	.	0			c.A811T						.						140	112	121					16																	55897346		2198	4300	6498	SO:0001587	stop_gained	221223	exon7			AGCCTTTGGCCAT	AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"Carboxylesterases"	26459	protein-coding gene	gene with protein product			"carboxylesterase 7"	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.724A>T	chr16.hg19:g.55897346T>A	ENSP00000290567:p.Lys242*	104.0	0.0		122.0	15.0	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Nonsense_Mutation	SNP	ENST00000290567.9	hg19	CCDS45490.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.994017	0.74703	.	.	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	.	.	.	5.28	-0.599	0.11645	.	1.749360	0.02591	N	0.099945	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.4339	0.21813	0.0:0.1824:0.1302:0.6875	.	.	.	.	X	271;242;136;242;212;23	.	ENSP00000290567:K242X	K	-	1	0	CES5A	54454847	0.002000	0.14202	0.008000	0.14137	0.384000	0.30261	0.809000	0.27168	-0.222000	0.09958	-1.078000	0.02229	AAA	.	.		0.488	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024		A	55897346	T	A	55897346	4	1	76	1	0	0	0	0	0	1	0	0	3274	1821	63	4	1035	4	CES7	16	55897346	Nonsense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	34242427	55897346	34457407	248	10519										
AMFR	267	hgsc.bcm.edu	37	chr16	56435757	56435757	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tggagttgcaactgcaaaccTgtggaaacaaaacaagccca	9	10	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr16:56435757T>A	ENST00000290649.5	-	8	1185		c.e8-2			NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase						aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						ACTGCAAACCTGTGGAAACAA	0.522																																					.	Pancreas(2;144 323 39528)	Atlas-SNP	.											.	AMFR	40	.	0			c.975-2A>T						.						73	69	70					16																	56435757		2198	4300	6498	SO:0001630	splice_region_variant	267	exon9			CAAACCTGTGGAA	L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"RING-type (C3HC4) zinc fingers"	463	protein-coding gene	gene with protein product		603243	"autocrine motility factor receptor"			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.975-2A>T	chr16.hg19:g.56435757T>A		43.0	0.0		40.0	8.0	NM_001144	P26442|Q8IZ70	Splice_Site	SNP	ENST00000290649.5	hg19	CCDS10758.1	.	.	.	.	.	.	.	.	.	.	T	19.28	3.796699	0.70567	.	.	ENSG00000159461	ENST00000290649	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8526	0.78943	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	AMFR	54993258	1.000000	0.71417	0.993000	0.49108	0.853000	0.48598	7.862000	0.87013	2.141000	0.66446	0.528000	0.53228	.	.	.		0.522	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2		Intron	A	56435757	T	A	56435757	5	1	76	1	0	0	0	0	0	0	1	0	571	1594	55	4	986	4	AMFR	16	56435757	Splice_Site	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	538411	56435757	33918996	249	10520										
CMIP	80790	hgsc.bcm.edu	37	chr16	81691394	81691394	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctttagaacacaaacttgacCacccaggagcatgaaaacat	6	11	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr16:81691394C>A	ENST00000537098.3	+	5	726	c.654C>A	c.(652-654)acC>acA	p.T218T	CMIP_ENST00000539778.2_Silent_p.T124T|CMIP_ENST00000566513.1_3'UTR|CMIP_ENST00000398040.4_Silent_p.T65T	NM_198390.2	NP_938204.2	Q8IY22	CMIP_HUMAN	c-Maf inducing protein	218						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(5)|kidney(1)|lung(7)	13						CAAACTTGACCACCCAGGAGC	0.453																																					p.T218T		Atlas-SNP	.											.	CMIP	37	.	0			c.C654A						.						64	62	63					16																	81691394		1915	4130	6045	SO:0001819	synonymous_variant	80790	exon5			CTTGACCACCCAG	AB051481	CCDS54044.1, CCDS54045.1	16q23	2011-08-04			ENSG00000153815	ENSG00000153815			24319	protein-coding gene	gene with protein product		610112				11214970, 12939343	Standard	NM_030629		Approved		uc002fgp.3	Q8IY22		ENST00000537098.3:c.654C>A	chr16.hg19:g.81691394C>A		136.0	0.0		120.0	25.0	NM_198390	Q9C0G9	Silent	SNP	ENST00000537098.3	hg19	CCDS54044.1																																																																																			.	.		0.453	CMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432399.2	NM_030629		A	81691394	C	A	81691394	2	1	76	1	0	0	0	0	0	0	0	1	3580	581	21	3		3	CMIP	16	81691394	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	25255637	81691394	8663359	250	10521										
OR3A1	4994	hgsc.bcm.edu	37	chr17	3195335	3195335	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agagctgtgggaggtcacagTagaagtgattgatcacattg	14	5	2	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:3195335T>C	ENST00000323404.1	-	1	541	c.542A>G	c.(541-543)tAc>tGc	p.Y181C	RP11-64J4.2_ENST00000573491.1_RNA	NM_002550.2	NP_002541.2	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A, member 1	181					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	20						GAGGTCACAGTAGAAGTGATT	0.547																																					p.Y181C	GBM(20;287 516 18743 28660 36594)	Atlas-SNP	.											.	OR3A1	46	.	0			c.A542G						.						163	150	155					17																	3195335		2203	4300	6503	SO:0001583	missense	4994	exon1			TCACAGTAGAAGT	X80391	CCDS11023.1	17p13.3	2012-08-09			ENSG00000180090	ENSG00000180090		"GPCR / Class A : Olfactory receptors"	8282	protein-coding gene	gene with protein product						8921386, 8647456	Standard	NM_002550		Approved	OLFRA03, OR40, OR17-40	uc002fvh.1	P47881	OTTHUMG00000090642	ENST00000323404.1:c.542A>G	chr17.hg19:g.3195335T>C	ENSP00000313803:p.Tyr181Cys	169.0	0.0		79.0	62.0	NM_002550	Q4VB06|Q6IFM4	Missense_Mutation	SNP	ENST00000323404.1	hg19	CCDS11023.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.867826	0.51588	.	.	ENSG00000180090	ENST00000323404	T	0.00024	8.97	5.01	3.85	0.44370	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45867	D	0.000329	T	0.00300	0.0009	M	0.62266	1.93	0.32648	N	0.519729	D	0.89917	1.0	D	0.83275	0.996	T	0.62426	-0.6857	10	0.87932	D	0	-30.8067	9.516	0.39106	0.199:0.0:0.0:0.801	.	181	P47881	OR3A1_HUMAN	C	181	ENSP00000313803:Y181C	ENSP00000313803:Y181C	Y	-	2	0	OR3A1	3142085	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	1.126000	0.31344	2.223000	0.72356	0.528000	0.53228	TAC	.	.		0.547	OR3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207302.2			C	3195335	T	C	3195335	3	2	76	1	0	0	0	0	1	0	0	0	11046	1638	57	2	409	2	OR3A1	17	3195335	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10		3195335	77999875	251	10522										
TP53	7157	hgsc.bcm.edu	37	chr17	7576866	7576897	+	Frame_Shift_Del	DEL	TATTCTCCATCCAGTGGTTTCTTCTTTGGCTG	TATTCTCCATCCAGTGGTTTCTTCTTTGGCTG	-													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttagtacctgaagggtgaaaTattctccatccagtggtttc					rs121912659		TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	TATTCTCCATCCAGTGGTTTCTTCTTTGGCTG	TATTCTCCATCCAGTGGTTTCTTCTTTGGCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:7576866_7576897delTATTCTCCATCCAGTGGTTTCTTCTTTGGCTG	ENST00000269305.4	-	9	1138_1169	c.949_980delCAGCCAAAGAAGAAACCACTGGATGGAGAATA	c.(949-981)cagccaaagaagaaaccactggatggagaatatfs	p.QPKKKPLDGEY317fs	TP53_ENST00000455263.2_Frame_Shift_Del_p.QPKKKPLDGEY317fs|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Frame_Shift_Del_p.QPKKKPLDGEY317fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.QPKKKPLDGEY317fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.QPKKKPLDGEY317fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	317	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		Q -> H (in a kidney cancer with no family history; germline mutation and in a sporadic cancer; somatic mutation).|Q -> K (in sporadic cancers; somatic mutation).|Q -> L (in a sporadic cancer; somatic mutation).|Q -> P (in a sporadic cancer; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q317*(29)|p.0?(8)|p.K319*(8)|p.E326*(4)|p.K321fs*24(4)|p.Q317K(3)|p.P322fs*23(3)|p.K320*(3)|p.K320N(3)|p.K321_P322insK(2)|p.K319N(2)|p.Q317R(2)|p.P318fs*15(2)|p.D324E(2)|p.K319E(2)|p.K320fs*26(2)|p.K319fs*19(2)|p.P322L(2)|p.P318A(2)|p.P322R(2)|p.K321*(2)|p.G325*(1)|p.S315fs*22(1)|p.S314fs*25(1)|p.Q317P(1)|p.L323fs*22(1)|p.K319R(1)|p.K321K(1)|p.P318fs*21(1)|p.K320fs*25(1)|p.Y327fs*10(1)|p.G325fs*23(1)|p.D324fs*29(1)|p.L323V(1)|p.Y327fs*9(1)|p.L323R(1)|p.?(1)|p.L323P(1)|p.D324fs*21(1)|p.Y327D(1)|p.Y327fs*1(1)|p.L308fs*15(1)|p.L323G(1)|p.Q317fs*28(1)|p.Q317fs*45(1)|p.L323M(1)|p.K320K(1)|p.G325A(1)|p.D324D(1)|p.G325E(1)|p.E326K(1)|p.D324S(1)|p.G325V(1)|p.K320fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAG	0.466		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.317_327del	Pancreas(47;798 1329 9957 10801)	Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000269305,NS,carcinoma,0,2	TP53	33396	.	122	Substitution - Nonsense(47)|Substitution - Missense(33)|Deletion - Frameshift(17)|Insertion - Frameshift(10)|Whole gene deletion(8)|Substitution - coding silent(3)|Insertion - In frame(2)|Unknown(1)|Complex - frameshift(1)	upper_aerodigestive_tract(15)|large_intestine(15)|urinary_tract(13)|breast(13)|ovary(13)|skin(9)|haematopoietic_and_lymphoid_tissue(7)|central_nervous_system(5)|liver(5)|bone(5)|oesophagus(4)|lung(4)|soft_tissue(3)|pancreas(3)|stomach(2)|endometrium(2)|NS(2)|thyroid(1)|peritoneum(1)	c.950_981del	GRCh37	CM920680	TP53	M	rs121912659	.																																			SO:0001589	frameshift_variant	7157	exon9	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.949_980delCAGCCAAAGAAGAAACCACTGGATGGAGAATA	chr17.hg19:g.7576866_7576897delTATTCTCCATCCAGTGGTTTCTTCTTTGGCTG	ENSP00000269305:p.Gln317fs	81.0	0.0		15.0	13.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.466	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7576897	TATTCTCCATCCAGTGGTTTCTTCTTTGGCTG	-	7576866	7	5	76	1	0	1	0	1	0	0	0	0	16396	1406	49	0	302	0	TP53	17	7576866	Frame_Shift_Del	DEL	TATTCTCCATCCAGTGGTTTCTTCTTTGGCTG	TCGA-CC-A7IK-01A-12D-A33Q-10	4381531	7576866	73618344	252	10523										
GLP2R	9340	hgsc.bcm.edu	37	chr17	9739777	9739777	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	taccctgcccttcatacttaCcttggtggagtgaaggtaat	9	10	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:9739777C>T	ENST00000262441.5	+	3	880	c.367C>T	c.(367-369)Cct>Tct	p.P123S	GLP2R_ENST00000574745.1_5'UTR	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	123					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	TTCATACTTACCTTGGTGGAG	0.443																																					p.P123S		Atlas-SNP	.											.	GLP2R	90	.	0			c.C367T						.						263	238	246					17																	9739777		2203	4300	6503	SO:0001583	missense	9340	exon3			TACTTACCTTGGT	AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"GPCR / Class B : Glucagon receptors"	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.367C>T	chr17.hg19:g.9739777C>T	ENSP00000262441:p.Pro123Ser	118.0	0.0		40.0	26.0	NM_004246	Q4VAT3	Missense_Mutation	SNP	ENST00000262441.5	hg19	CCDS11150.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.777862	0.90195	.	.	ENSG00000065325	ENST00000396206;ENST00000304773;ENST00000262441	T	0.54071	0.59	5.48	5.48	0.80851	GPCR, family 2, extracellular hormone receptor domain (2);	0.000000	0.37857	N	0.001916	T	0.68869	0.3048	L	0.50919	1.6	0.58432	D	0.999999	D	0.71674	0.998	D	0.83275	0.996	T	0.70200	-0.4937	10	0.66056	D	0.02	.	18.1188	0.89565	0.0:1.0:0.0:0.0	.	123	O95838	GLP2R_HUMAN	S	123;98;123	ENSP00000262441:P123S	ENSP00000262441:P123S	P	+	1	0	GLP2R	9680502	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.114000	0.64648	2.582000	0.87167	0.563000	0.77884	CCT	.	.		0.443	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4			T	9739777	C	T	9739777	3	4	76	1	0	0	0	0	1	0	0	0	6461	507	18	3	377	3	GLP2R	17	9739777	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	2162911	9739777	71455433	253	10524										
FBXW10	10517	hgsc.bcm.edu	37	chr17	18653121	18653121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	acataaccaagccagggtacGatccctgcaatctattggtt	8	11	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:18653121G>A	ENST00000395665.4	+	3	978	c.757G>A	c.(757-759)Gat>Aat	p.D253N	FBXW10_ENST00000395667.1_Missense_Mutation_p.D253N|FBXW10_ENST00000301938.4_Missense_Mutation_p.D253N|FBXW10_ENST00000308799.4_Missense_Mutation_p.D253N			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	253										NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GCCAGGGTACGATCCCTGCAA	0.483																																					p.D253N		Atlas-SNP	.											.	FBXW10	82	.	0			c.G757A						.						182	140	155					17																	18653121		2203	4300	6503	SO:0001583	missense	10517	exon3			GGGTACGATCCCT	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"F-boxes / WD-40 domains", "WD repeat domain containing"	1211	protein-coding gene	gene with protein product		611679	"chromosome 17 open reading frame 1A", "F-box and WD-40 domain protein 10"	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.757G>A	chr17.hg19:g.18653121G>A	ENSP00000379025:p.Asp253Asn	315.0	0.0		344.0	15.0	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	hg19	CCDS11199.3	.	.	.	.	.	.	.	.	.	.	G	15.08	2.727553	0.48833	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	2.49	-1.02	0.10135	.	1.171610	0.06794	U	0.787558	T	0.17789	0.0427	L	0.29908	0.895	0.09310	N	1	P;P;P;P	0.47106	0.89;0.89;0.824;0.89	B;B;B;B	0.37047	0.24;0.173;0.121;0.24	T	0.20306	-1.0279	10	0.48119	T	0.1	.	4.1575	0.10268	0.2727:0.1998:0.5275:0.0	.	253;253;253;253	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	N	253	ENSP00000379026:D253N;ENSP00000310382:D253N;ENSP00000306937:D253N;ENSP00000379025:D253N	ENSP00000306937:D253N	D	+	1	0	FBXW10	18593846	0.000000	0.05858	0.000000	0.03702	0.955000	0.61496	-0.250000	0.08830	-0.029000	0.13827	0.405000	0.27470	GAT	.	.		0.483	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456		A	18653121	G	A	18653121	3	1	76	1	0	0	0	0	1	0	0	0	5771	1058	37	1	767	1	FBXW10	17	18653121	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	8913344	18653121	62542089	254	10525										
ULK2	9706	hgsc.bcm.edu	37	chr17	19741841	19741841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cattctatctttttggtttcTctgaagcaaacccaaaagga	6	9	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:19741841T>C	ENST00000395544.4	-	10	1259	c.760A>G	c.(760-762)Aga>Gga	p.R254G	ULK2_ENST00000361658.2_Missense_Mutation_p.R254G|ULK2_ENST00000580130.1_5'Flank	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	254	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					TTTTGGTTTCTCTGAAGCAAA	0.318																																					p.R254G		Atlas-SNP	.											.	ULK2	142	.	0			c.A760G						.						58	61	60					17																	19741841		2203	4299	6502	SO:0001583	missense	9706	exon10			GGTTTCTCTGAAG	AB014523	CCDS11213.1	17p11.2	2014-02-12	2013-07-02		ENSG00000083290	ENSG00000083290	2.7.11.1		13480	protein-coding gene	gene with protein product		608650	"unc-51 (C. elegans)-like kinase 2", "unc-51-like kinase 2 (C. elegans)"			10557072	Standard	NM_014683		Approved	KIAA0623, Unc51.2, ATG1B	uc002gwn.3	Q8IYT8	OTTHUMG00000059511	ENST00000395544.4:c.760A>G	chr17.hg19:g.19741841T>C	ENSP00000378914:p.Arg254Gly	180.0	0.0		172.0	84.0	NM_001142610	A8MY69|O75119	Missense_Mutation	SNP	ENST00000395544.4	hg19	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.219041	0.79464	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	T;T	0.25414	1.8;1.8	5.79	4.65	0.58169	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	L	0.55834	1.745	0.54753	D	0.999981	P	0.40578	0.722	B	0.37015	0.239	T	0.07731	-1.0757	10	0.87932	D	0	-19.7372	11.9521	0.52961	0.0:0.0:0.1448:0.8552	.	254	Q8IYT8	ULK2_HUMAN	G	254	ENSP00000354877:R254G;ENSP00000378914:R254G	ENSP00000354877:R254G	R	-	1	2	ULK2	19682433	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.532000	0.60608	2.215000	0.71742	0.528000	0.53228	AGA	.	.		0.318	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683		C	19741841	T	C	19741841	3	2	76	1	0	0	0	0	1	0	0	0	16991	1559	54	2	2422	2	ULK2	17	19741841	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	1088720	19741841	61453369	255	10526										
NOS2	4843	hgsc.bcm.edu	37	chr17	26089920	26089920	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gtagaacctgggcttcagaaTggggagctgggaaagcagga	17	6	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:26089920T>A	ENST00000313735.6	-	22	2937	c.2704A>T	c.(2704-2706)Att>Ttt	p.I902F		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	902	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GGCTTCAGAATGGGGAGCTGG	0.602																																					p.I902F		Atlas-SNP	.											.	NOS2	113	.	0			c.A2704T						.						28	26	27					17																	26089920		2202	4299	6501	SO:0001583	missense	4843	exon22			TCAGAATGGGGAG	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"nitric oxide synthase 2A (inducible, hepatocytes)"	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2704A>T	chr17.hg19:g.26089920T>A	ENSP00000327251:p.Ile902Phe	60.0	0.0		58.0	24.0	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	hg19	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	T	13.83	2.353507	0.41700	.	.	ENSG00000007171	ENST00000313735;ENST00000379105	T	0.33216	1.42	4.9	-0.729	0.11158	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.653207	0.14699	N	0.303707	T	0.18087	0.0434	N	0.22421	0.69	0.21527	N	0.999658	B	0.06786	0.001	B	0.14578	0.011	T	0.18461	-1.0336	10	0.51188	T	0.08	.	7.8613	0.29511	0.0:0.1889:0.5534:0.2577	.	902	P35228	NOS2_HUMAN	F	902;863	ENSP00000327251:I902F	ENSP00000327251:I902F	I	-	1	0	NOS2	23114047	0.001000	0.12720	0.054000	0.19295	0.952000	0.60782	0.254000	0.18314	-0.095000	0.12351	0.374000	0.22700	ATT	.	.		0.602	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		A	26089920	T	A	26089920	3	1	76	1	0	0	0	0	1	0	0	0	10552	1464	51	4	781	4	NOS2	17	26089920	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	6348079	26089920	55105290	256	10527										
VTN	7448	hgsc.bcm.edu	37	chr17	26695961	26695961	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gggccaaggctgcatccacgTtgtccgggatgccatcgaag	14	12	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:26695961T>A	ENST00000226218.4	-	5	1376	c.758A>T	c.(757-759)aAc>aTc	p.N253I	TMEM199_ENST00000509083.1_Intron|SARM1_ENST00000379061.4_Intron|VTN_ENST00000438614.1_5'Flank|CTB-96E2.2_ENST00000555059.2_5'Flank|VTN_ENST00000536498.1_5'UTR|SARM1_ENST00000457710.3_5'Flank|CTB-96E2.3_ENST00000591482.1_RNA	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	253					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	TGCATCCACGTTGTCCGGGAT	0.597																																					p.N253I		Atlas-SNP	.											.	VTN	45	.	0			c.A758T						.						95	91	92					17																	26695961		2203	4300	6503	SO:0001583	missense	7448	exon5			TCCACGTTGTCCG	BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"Endogenous ligands"	12724	protein-coding gene	gene with protein product	"serum spreading factor", "somatomedin B", "complement S-protein"	193190	"vitronectin (serum spreading factor, somatomedin B, complement S-protein)"			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500	ENST00000226218.4:c.758A>T	chr17.hg19:g.26695961T>A	ENSP00000226218:p.Asn253Ile	131.0	0.0		130.0	63.0	NM_000638	B2R7G0|P01141|Q9BSH7	Missense_Mutation	SNP	ENST00000226218.4	hg19	CCDS11229.1	.	.	.	.	.	.	.	.	.	.	T	16.80	3.224358	0.58668	.	.	ENSG00000255604	ENST00000226218	T	0.09073	3.02	5.92	5.92	0.95590	Hemopexin/matrixin (2);	0.368951	0.36167	N	0.002757	T	0.34978	0.0916	M	0.92367	3.3	0.21105	N	0.999787	D	0.59357	0.985	P	0.58266	0.836	T	0.46442	-0.9191	10	0.87932	D	0	-14.1232	16.3648	0.83312	0.0:0.0:0.0:1.0	.	253	P04004	VTNC_HUMAN	I	253	ENSP00000226218:N253I	ENSP00000226218:N253I	N	-	2	0	AC002094.1	23720088	0.902000	0.30710	0.006000	0.13384	0.027000	0.11550	5.895000	0.69814	2.263000	0.75096	0.533000	0.62120	AAC	.	.		0.597	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638		A	26695961	T	A	26695961	3	1	76	1	0	0	0	0	1	0	0	0	17252	1725	60	4	694	4	VTN	17	26695961	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	606041	26695961	54499249	257	10528										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27017150	27017150	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gacatccgggcagagctgagCtgtcgatataaggacctccg	13	11	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:27017150C>T	ENST00000314616.6	+	26	3676	c.3393C>T	c.(3391-3393)agC>agT	p.S1131S	SUPT6H_ENST00000347486.4_Silent_p.S1131S	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1131	Interaction with KDM6A. {ECO:0000250}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CAGAGCTGAGCTGTCGATATA	0.512																																					p.S1131S		Atlas-SNP	.											.	SUPT6H	165	.	0			c.C3393T						.						125	121	122					17																	27017150		2203	4300	6503	SO:0001819	synonymous_variant	6830	exon26			GCTGAGCTGTCGA	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.3393C>T	chr17.hg19:g.27017150C>T		209.0	0.0		205.0	98.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.512	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27017150	C	T	27017150	2	4	76	1	0	0	0	0	0	0	0	1	15415	796	28	3		3	SUPT6H	17	27017150	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	321189	27017150	54178060	258	10529										
TAOK1	57551	hgsc.bcm.edu	37	chr17	27829620	27829620	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttcctaggaggaagaaaattAcagagaagagggagatccta	12	5	0	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:27829620A>G	ENST00000261716.3	+	13	1736	c.1217A>G	c.(1216-1218)tAc>tGc	p.Y406C	TAOK1_ENST00000536202.1_Missense_Mutation_p.Y406C	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	406					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|execution phase of apoptosis (GO:0097194)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of cytoskeleton organization (GO:0051493)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28			Colorectal(6;0.198)			GAAGAAAATTACAGAGAAGAG	0.348																																					p.Y406C		Atlas-SNP	.											.	TAOK1	151	.	0			c.A1217G						.						101	89	93					17																	27829620		2203	4300	6503	SO:0001583	missense	57551	exon13			AAAATTACAGAGA	AB037782	CCDS32601.1, CCDS56024.1	17q11.2	2014-01-28				ENSG00000160551			29259	protein-coding gene	gene with protein product		610266				10718198, 14517247	Standard	NM_020791		Approved	KIAA1361, MARKK, PSK2, MAP3K16, FLJ14314, TAO1	uc002hdz.2	Q7L7X3		ENST00000261716.3:c.1217A>G	chr17.hg19:g.27829620A>G	ENSP00000261716:p.Tyr406Cys	88.0	0.0		91.0	15.0	NM_025142	A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Missense_Mutation	SNP	ENST00000261716.3	hg19	CCDS32601.1	.	.	.	.	.	.	.	.	.	.	A	14.58	2.578212	0.45902	.	.	ENSG00000160551	ENST00000261716;ENST00000536202	T;T	0.41758	0.99;0.99	6.03	6.03	0.97812	Protein kinase-like domain (1);	0.260256	0.39834	N	0.001260	T	0.46444	0.1393	M	0.72118	2.19	0.54753	D	0.999988	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.10450	0.0;0.005;0.002	T	0.34700	-0.9818	10	0.41790	T	0.15	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	406;232;406	B7ZLV6;Q7L7X3-2;Q7L7X3	.;.;TAOK1_HUMAN	C	406	ENSP00000261716:Y406C;ENSP00000438819:Y406C	ENSP00000261716:Y406C	Y	+	2	0	TAOK1	24853746	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.014000	0.64029	2.302000	0.77476	0.533000	0.62120	TAC	.	.		0.348	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791		G	27829620	A	G	27829620	3	3	76	1	0	0	0	0	1	0	0	0	15562	391	14	2	1263	2	TAOK1	17	27829620	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	812470	27829620	53365590	259	10530										
NF1	4763	hgsc.bcm.edu	37	chr17	29554603	29554603	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctaatccttaactatccaaaAgccaaaatggaagatggcca	6	10	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:29554603A>C	ENST00000358273.4	+	20	2771	c.2388A>C	c.(2386-2388)aaA>aaC	p.K796N	NF1_ENST00000356175.3_Missense_Mutation_p.K796N	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	796					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		ACTATCCAAAAGCCAAAATGG	0.353			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.K796N		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.A2388C						.						89	77	81					17																	29554603		2203	4300	6503	SO:0001583	missense	4763	exon20	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	TCCAAAAGCCAAA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.2388A>C	chr17.hg19:g.29554603A>C	ENSP00000351015:p.Lys796Asn	131.0	0.0		144.0	18.0	NM_000267	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	.	20.4	3.978953	0.74360	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.10573	3.02;3.16;2.86	4.83	2.52	0.30459	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.21550	0.0519	L	0.45352	1.415	0.80722	D	1	D;D;D	0.89917	1.0;0.989;0.998	D;D;D	0.91635	0.999;0.978;0.919	T	0.00327	-1.1814	10	0.72032	D	0.01	.	8.7724	0.34740	0.7526:0.0:0.2474:0.0	.	796;796;796	E1P657;P21359-2;P21359	.;.;NF1_HUMAN	N	796;796;462	ENSP00000351015:K796N;ENSP00000348498:K796N;ENSP00000389907:K462N	ENSP00000348498:K796N	K	+	3	2	NF1	26578729	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.752000	0.62176	0.258000	0.21686	0.528000	0.53228	AAA	.	.		0.353	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29554603	A	C	29554603	3	2	76	1	0	0	0	0	1	0	0	0	10365	69	3	5	2527	5	NF1	17	29554603	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	1724983	29554603	51640607	260	10531										
AP2B1	163	hgsc.bcm.edu	37	chr17	33921086	33921086	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atttcacaaccaataaaaaaGgtaagtatgagaatacaatc	5	6	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:33921086G>T	ENST00000262325.7	+	2	590	c.37G>T	c.(37-39)Gga>Tga	p.G13*	AP2B1_ENST00000537622.2_Splice_Site_p.G13*|AP2B1_ENST00000312678.8_Splice_Site_p.G13*|AP2B1_ENST00000589344.1_Splice_Site_p.G13*|AP2B1_ENST00000538556.1_5'UTR|AP2B1_ENST00000592545.1_Splice_Site_p.G13*	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	13					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		CAATAAAAAAGGTAAGTATGA	0.353																																					p.G13X		Atlas-SNP	.											.	AP2B1	70	.	0			c.G37T						.						48	44	45					17																	33921086		2196	4297	6493	SO:0001630	splice_region_variant	163	exon2			AAAAAAGGTAAGT	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.37+1G>T	chr17.hg19:g.33921086G>T		338.0	0.0		314.0	59.0	NM_001282	A6NJP3|P21851|Q7Z451|Q96J19	Nonsense_Mutation	SNP	ENST00000262325.7	hg19	CCDS32622.1	.	.	.	.	.	.	.	.	.	.	G	38	6.654516	0.97739	.	.	ENSG00000006125	ENST00000262325;ENST00000312678;ENST00000537622	.	.	.	4.28	4.28	0.50868	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-24.2509	15.8086	0.78538	0.0:0.0:1.0:0.0	.	.	.	.	X	13	.	ENSP00000262325:G13X	G	+	1	0	AP2B1	30945199	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.362000	0.90100	2.380000	0.81148	0.467000	0.42956	GGA	.	.		0.353	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1		Nonsense_Mutation	T	33921086	G	T	33921086	5	4	76	1	0	0	0	0	0	0	1	0	741	1014	35	3	39	3	AP2B1	17	33921086	Splice_Site	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	4366483	33921086	47274124	261	10532										
KRT31	3881	hgsc.bcm.edu	37	chr17	39553767	39553767	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gctggtgcggcagctcaggcTgggcaggcagaagttgtagg	19	8	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:39553767T>A	ENST00000251645.2	-	1	77	c.25A>T	c.(25-27)Agc>Tgc	p.S9C		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	9	Head.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				CAGCTCAGGCTGGGCAGGCAG	0.652																																					p.S9C		Atlas-SNP	.											.	KRT31	158	.	0			c.A25T						.						15	18	17					17																	39553767		2192	4286	6478	SO:0001583	missense	3881	exon1			TCAGGCTGGGCAG	X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"-", "Intermediate filaments type I, keratins (acidic)"	6448	protein-coding gene	gene with protein product	"hard keratin type I 1"	601077	"keratin, hair, acidic, 1"	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.25A>T	chr17.hg19:g.39553767T>A	ENSP00000251645:p.Ser9Cys	52.0	0.0		55.0	16.0	NM_002277	Q9UE12	Missense_Mutation	SNP	ENST00000251645.2	hg19	CCDS11391.1	.	.	.	.	.	.	.	.	.	.	t	11.12	1.546548	0.27652	.	.	ENSG00000094796	ENST00000251645	D	0.83335	-1.71	5.82	3.62	0.41486	.	0.710043	0.14100	N	0.341450	D	0.83376	0.5241	M	0.76170	2.325	0.21105	N	0.999784	B	0.33448	0.412	B	0.40101	0.319	T	0.75679	-0.3234	10	0.87932	D	0	.	7.2684	0.26242	0.0:0.3291:0.0:0.6709	.	9	Q15323	K1H1_HUMAN	C	9	ENSP00000251645:S9C	ENSP00000251645:S9C	S	-	1	0	KRT31	36807293	0.634000	0.27190	0.818000	0.32626	0.345000	0.29048	0.815000	0.27253	0.493000	0.27837	0.533000	0.62120	AGC	.	.		0.652	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277		A	39553767	T	A	39553767	3	1	76	1	0	0	0	0	1	0	0	0	8476	1580	55	4	1253	4	KRT31	17	39553767	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	5632681	39553767	41641443	262	10533										
KRT19	3880	hgsc.bcm.edu	37	chr17	39684180	39684180	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cgcggatcttcacctctagcTcgccgttggccgcctccagg	11	17	3	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:39684180T>C	ENST00000361566.3	-	1	380	c.320A>G	c.(319-321)gAg>gGg	p.E107G		NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	107	Coil 1A.|Rod.				cell differentiation involved in embryonic placenta development (GO:0060706)|response to estrogen (GO:0043627)|sarcomere organization (GO:0045214)|viral process (GO:0016032)	cell periphery (GO:0071944)|costamere (GO:0043034)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12		Breast(137;0.00038)				CACCTCTAGCTCGCCGTTGGC	0.652																																					p.E107G		Atlas-SNP	.											.	KRT19	41	.	0			c.A320G						.						47	54	51					17																	39684180		2203	4299	6502	SO:0001583	missense	3880	exon1			TCTAGCTCGCCGT		CCDS11399.1	17q21.2	2013-06-20			ENSG00000171345	ENSG00000171345		"-", "Intermediate filaments type I, keratins (acidic)"	6436	protein-coding gene	gene with protein product	"keratin, type I cytoskeletal 19", "keratin, type I, 40-kd", "cytokeratin 19", "40-kDa keratin intermediate filament"	148020				16831889	Standard	NM_002276		Approved	K19, CK19, K1CS, MGC15366		P08727	OTTHUMG00000133422	ENST00000361566.3:c.320A>G	chr17.hg19:g.39684180T>C	ENSP00000355124:p.Glu107Gly	85.0	0.0		93.0	18.0	NM_002276	B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Missense_Mutation	SNP	ENST00000361566.3	hg19	CCDS11399.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.337675	0.60963	.	.	ENSG00000171345	ENST00000361566;ENST00000455635	D;D	0.89415	-2.51;-2.12	4.83	4.83	0.62350	Filament (1);	0.274046	0.25759	N	0.028491	D	0.86952	0.6057	M	0.66297	2.02	0.27078	N	0.963164	B	0.10296	0.003	B	0.13407	0.009	T	0.80750	-0.1243	10	0.62326	D	0.03	.	10.8182	0.46589	0.0:0.0777:0.0:0.9223	.	107	P08727	K1C19_HUMAN	G	107	ENSP00000355124:E107G;ENSP00000408759:E107G	ENSP00000355124:E107G	E	-	2	0	KRT19	36937706	0.548000	0.26473	1.000000	0.80357	0.991000	0.79684	3.253000	0.51469	1.933000	0.56026	0.379000	0.24179	GAG	.	.		0.652	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257285.1	NM_002276		C	39684180	T	C	39684180	3	2	76	1	0	0	0	0	1	0	0	0	8465	1551	54	2	906	2	KRT19	17	39684180	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	130413	39684180	41511030	263	10534										
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42949889	42949889	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctgggagctggagaagcagaCgttacccaggagtggggaaa	17	7	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:42949889C>T	ENST00000426333.2	-	11	1216	c.919G>A	c.(919-921)Gtc>Atc	p.V307I	EFTUD2_ENST00000402521.3_Missense_Mutation_p.V272I|EFTUD2_ENST00000592576.1_Missense_Mutation_p.V297I|EFTUD2_ENST00000591382.1_Missense_Mutation_p.V307I	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	307	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				GAGAAGCAGACGTTACCCAGG	0.557																																					p.V307I	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.G919A						.						187	164	172					17																	42949889		2203	4300	6503	SO:0001583	missense	9343	exon11			AGCAGACGTTACC	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.919G>A	chr17.hg19:g.42949889C>T	ENSP00000392094:p.Val307Ile	112.0	0.0		116.0	49.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Missense_Mutation	SNP	ENST00000426333.2	hg19	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	C	36	5.771722	0.96922	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	T;T	0.76448	-1.02;-1.02	5.94	5.94	0.96194	Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	D	0.86678	0.5990	M	0.78801	2.425	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.55923	0.787;0.787	D	0.86809	0.1997	10	0.59425	D	0.04	-33.336	20.3736	0.98901	0.0:1.0:0.0:0.0	.	297;307	B4DMC0;Q15029	.;U5S1_HUMAN	I	307;297;272	ENSP00000392094:V307I;ENSP00000385873:V272I	ENSP00000262414:V297I	V	-	1	0	EFTUD2	40305415	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.820000	0.97059	0.650000	0.86243	GTC	.	.		0.557	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		T	42949889	C	T	42949889	3	4	76	1	0	0	0	0	1	0	0	0	4963	536	19	1	2071	1	EFTUD2	17	42949889	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	3265709	42949889	38245321	264	10535										
CRHR1	1394	hgsc.bcm.edu	37	chr17	43910820	43910820	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggtgtgctcaaattgcagatCaatttcatcttccttttcaa	6	9	5	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:43910820C>A	ENST00000398285.3	+	11	933	c.933C>A	c.(931-933)atC>atA	p.I311I	CRHR1_ENST00000352855.5_Silent_p.I242I|CRHR1_ENST00000577353.1_Silent_p.I282I|CRHR1_ENST00000314537.5_Silent_p.I282I|CRHR1_ENST00000293493.7_Silent_p.I107I|CRHR1_ENST00000339069.5_Silent_p.I181I	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	311	Important for antagonist binding.				activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		AATTGCAGATCAATTTCATCT	0.567																																					p.I311I	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.C933A						.						122	126	125					17																	43910820		2145	4251	6396	SO:0001819	synonymous_variant	1394	exon11			GCAGATCAATTTC	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"GPCR / Class B : Corticotropin-releasing factor receptors"	2357	protein-coding gene	gene with protein product	"corticotropin-releasing factor receptor"	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.933C>A	chr17.hg19:g.43910820C>A		92.0	0.0		79.0	19.0	NM_001145146	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Silent	SNP	ENST00000398285.3	hg19	CCDS45712.1																																																																																			.	.		0.567	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3			A	43910820	C	A	43910820	2	1	76	1	0	0	0	0	0	0	0	1	3873	816	29	3		3	CRHR1	17	43910820	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	960931	43910820	37284390	265	10536										
LPO	4025	hgsc.bcm.edu	37	chr17	56343575	56343575	+	Frame_Shift_Del	DEL	T	T	-													0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tccaagctgatgaaacagaaTaaaatgatgactggagagct							TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:56343575delT	ENST00000262290.4	+	11	1897	c.1581delT	c.(1579-1581)aatfs	p.N527fs	LPO_ENST00000421678.2_Frame_Shift_Del_p.N444fs|LPO_ENST00000543544.1_Frame_Shift_Del_p.N468fs|LPO_ENST00000582328.1_Frame_Shift_Del_p.N444fs	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	527					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						TGAAACAGAATAAAATGATGA	0.547																																					p.N527fs		Atlas-Indel,Pindel	.											.	LPO	73	.	0			c.1580delA						.						64	58	60					17																	56343575		2203	4300	6503	SO:0001589	frameshift_variant	4025	exon11			.	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1581delT	chr17.hg19:g.56343575delT	ENSP00000262290:p.Asn527fs	91.0	0.0		82.0	27.0	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Frame_Shift_Del	DEL	ENST00000262290.4	hg19	CCDS32689.1																																																																																			.	.		0.547	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1			-	56343575	T	-	56343575	7	5	76	1	0	1	0	1	0	0	0	0	8931	1403	49	0	1619	0	LPO	17	56343575	Frame_Shift_Del	DEL	T	TCGA-CC-A7IK-01A-12D-A33Q-10	12432755	56343575	24851635	266	10537										
MPO	4353	hgsc.bcm.edu	37	chr17	56349142	56349142	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgtcgatgttgttgggcgtgCcatactgctccatcagtttc	11	10	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:56349142C>A	ENST00000225275.3	-	11	2080	c.1904G>T	c.(1903-1905)gGc>gTc	p.G635V	MPO_ENST00000340482.3_Missense_Mutation_p.G667V	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	635					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	GTTGGGCGTGCCATACTGCTC	0.627																																					p.G635V		Atlas-SNP	.											.	MPO	114	.	0			c.G1904T						.						126	85	99					17																	56349142		2203	4300	6503	SO:0001583	missense	4353	exon11			GGCGTGCCATACT		CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.1904G>T	chr17.hg19:g.56349142C>A	ENSP00000225275:p.Gly635Val	82.0	0.0		74.0	22.0	NM_000250	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	hg19	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.274898	0.80580	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.77358	-1.09;-1.09	5.16	4.2	0.49525	.	0.162930	0.56097	D	0.000037	D	0.89213	0.6651	M	0.90252	3.1	0.80722	D	1	D	0.71674	0.998	D	0.77004	0.989	D	0.90874	0.4748	10	0.87932	D	0	-24.8157	12.7965	0.57562	0.0:0.9214:0.0:0.0786	.	635	P05164	PERM_HUMAN	V	667;635	ENSP00000344419:G667V;ENSP00000225275:G635V	ENSP00000225275:G635V	G	-	2	0	MPO	53704141	0.955000	0.32602	0.918000	0.36340	0.902000	0.53008	4.039000	0.57325	1.193000	0.43086	0.563000	0.77884	GGC	.	.		0.627	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			A	56349142	C	A	56349142	3	1	76	1	0	0	0	0	1	0	0	0	9741	739	26	3	341	3	MPO	17	56349142	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	5567	56349142	24846068	267	10538										
TEX14	56155	hgsc.bcm.edu	37	chr17	56663388	56663388	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agactactctgaggatgccaAggaggtactgtgagctgtcc	13	9	1	3	rs576022136	byFrequency	TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:56663388A>T	ENST00000240361.8	-	18	2947	c.2862T>A	c.(2860-2862)ccT>ccA	p.P954P	TEX14_ENST00000349033.5_Silent_p.P948P|TEX14_ENST00000389934.3_Silent_p.P948P			Q8IWB6	TEX14_HUMAN	testis expressed 14	954					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GAGGATGCCAAGGAGGTACTG	0.498													A|||	2	0.000399361	0.0015	0	5008	,	,		19006	0		0	False		,,,				2504	0				p.P954P		Atlas-SNP	.											.	TEX14	343	.	0			c.T2862A						.						143	145	144					17																	56663388		2203	4300	6503	SO:0001819	synonymous_variant	56155	exon18			ATGCCAAGGAGGT	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2862T>A	chr17.hg19:g.56663388A>T		70.0	0.0		73.0	32.0	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Silent	SNP	ENST00000240361.8	hg19	CCDS56042.1																																																																																			.	.		0.498	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56663388	A	T	56663388	2	4	76	1	0	0	0	0	0	0	0	1	15793	59	3	4		4	TEX14	17	56663388	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	314246	56663388	24531822	268	10539										
GH2	2689	hgsc.bcm.edu	37	chr17	61958465	61958465	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agagggaggtctgggggttcTgcaggaatgaatacttctgc	16	6	3	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:61958465T>G	ENST00000423893.2	-	3	276	c.215A>C	c.(214-216)cAg>cCg	p.Q72P	GH2_ENST00000449787.2_Splice_Site|GH2_ENST00000456543.2_Missense_Mutation_p.Q72P|GH2_ENST00000332800.7_Missense_Mutation_p.Q72P			P01242	SOM2_HUMAN	growth hormone 2	72					JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	24						CTGGGGGTTCTGCAGGAATGA	0.517																																					p.Q72P		Atlas-SNP	.											.	GH2	73	.	0			c.A215C						.						198	210	206					17																	61958465		2203	4300	6503	SO:0001583	missense	2689	exon3			GGGTTCTGCAGGA	J03756	CCDS11647.1, CCDS11648.1, CCDS45757.1, CCDS45758.1	17q22-q24	2014-01-30						"Endogenous ligands"	4262	protein-coding gene	gene with protein product	"placental-specific growth hormone", "placenta-specific growth hormone"	139240				6306568	Standard	NM_002059		Approved	GH-V, GHV, GHL, hGH-V	uc002jcl.2	P01242		ENST00000423893.2:c.215A>C	chr17.hg19:g.61958465T>G	ENSP00000409294:p.Gln72Pro	65.0	0.0		67.0	35.0	NM_022557	B1A4H5|B1A4H7|O14643|O14644|P09587	Missense_Mutation	SNP	ENST00000423893.2	hg19	CCDS11647.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|t	1.542|1.542	-0.541618|-0.541618	0.04053|0.04053	.|.	.|.	ENSG00000136487|ENSG00000136487	ENST00000449787|ENST00000332800;ENST00000456543;ENST00000423893	.|D;D;D	.|0.88896	.|-2.44;-2.44;-2.44	3.1|3.1	2.0|2.0	0.26442|0.26442	.|Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	.|0.164006	.|0.51477	.|D	.|0.000091	.|D	.|0.91284	.|0.7252	M|M	0.68593|0.68593	2.085|2.085	0.28790|0.28790	N|N	0.899386|0.899386	.|D;D;D;D	.|0.69078	.|0.994;0.981;0.997;0.994	.|D;P;D;D	.|0.67900	.|0.954;0.797;0.947;0.954	.|D	.|0.84799	.|0.0783	.|10	.|0.72032	.|D	.|0.01	.|.	6.6537|6.6537	0.22977|0.22977	0.0:0.1241:0.0:0.8759|0.0:0.1241:0.0:0.8759	.|.	.|72;72;72;72	.|P01242;O14644;B1A4H7;B1A4H5	.|SOM2_HUMAN;.;.;.	.|P	-1|72	.|ENSP00000333157:Q72P;ENSP00000394122:Q72P;ENSP00000409294:Q72P	.|ENSP00000333157:Q72P	.|Q	-|-	.|2	.|0	GH2|GH2	59312197|59312197	1.000000|1.000000	0.71417|0.71417	0.180000|0.180000	0.23079|0.23079	0.004000|0.004000	0.04260|0.04260	2.960000|2.960000	0.49161|0.49161	0.392000|0.392000	0.25172|0.25172	-0.611000|-0.611000	0.04053|0.04053	.|CAG	.	.		0.517	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1	NM_002059		G	61958465	T	G	61958465	3	3	76	1	0	0	0	0	1	0	0	0	6376	1594	55	5	787	5	GH2	17	61958465	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	5295077	61958465	19236745	269	10540										
SDK2	54549	hgsc.bcm.edu	37	chr17	71348683	71348683	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccgcgatgacccggaagtcaTagctcacgcccggcttcagg	12	15	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:71348683T>G	ENST00000392650.3	-	41	5687	c.5687A>C	c.(5686-5688)tAt>tCt	p.Y1896S	SDK2_ENST00000388726.3_Missense_Mutation_p.Y1877S|SDK2_ENST00000410094.1_5'UTR	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1896	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CCGGAAGTCATAGCTCACGCC	0.617																																					p.Y1896S		Atlas-SNP	.											.	SDK2	219	.	0			c.A5687C						.						101	77	85					17																	71348683		2203	4300	6503	SO:0001583	missense	54549	exon41			AAGTCATAGCTCA	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.5687A>C	chr17.hg19:g.71348683T>G	ENSP00000376421:p.Tyr1896Ser	63.0	0.0		57.0	18.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.725783	0.89298	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893;ENST00000410094	D;D;D	0.89343	-2.5;-2.5;-2.5	5.37	5.37	0.77165	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.96815	0.8960	H	0.98594	4.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98448	1.0590	10	0.87932	D	0	.	15.3709	0.74564	0.0:0.0:0.0:1.0	.	1896;1877	Q58EX2;Q58EX2-3	SDK2_HUMAN;.	S	1520;1896;1877;1053;1896;237	ENSP00000376421:Y1896S;ENSP00000373378:Y1877S;ENSP00000407098:Y1053S	ENSP00000324967:Y1896S	Y	-	2	0	SDK2	68860278	1.000000	0.71417	0.938000	0.37757	0.992000	0.81027	7.903000	0.87398	2.031000	0.59945	0.533000	0.62120	TAT	.	.		0.617	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		G	71348683	T	G	71348683	3	3	76	1	0	0	0	0	1	0	0	0	13984	1406	49	5	851	5	SDK2	17	71348683	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	9390218	71348683	9846527	270	10541										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76446801	76446801	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tggctgtgtgcttggtggtcTccagattctccaccaaggcc	12	12	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr17:76446801T>A	ENST00000585328.1	-	67	10971	c.10847A>T	c.(10846-10848)gAg>gTg	p.E3616V	DNAH17_ENST00000389840.5_Missense_Mutation_p.E3607V|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3607	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CTTGGTGGTCTCCAGATTCTC	0.607																																					p.E3621V		Atlas-SNP	.											.	DNAH17	347	.	0			c.A10862T						.						81	67	72					17																	76446801		2203	4300	6503	SO:0001583	missense	8632	exon67			GTGGTCTCCAGAT	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.10847A>T	chr17.hg19:g.76446801T>A	ENSP00000465516:p.Glu3616Val	60.0	0.0		62.0	35.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	T	31	5.067709	0.93950	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.69040	-0.37	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000005	D	0.89245	0.6660	H	0.98833	4.345	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	D	0.93562	0.6896	10	0.87932	D	0	.	15.3576	0.74440	0.0:0.0:0.0:1.0	.	3616	E7EUM8	.	V	3616;3607	ENSP00000374490:E3607V	ENSP00000300671:E3616V	E	-	2	0	DNAH17	73958396	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.848000	0.86902	2.018000	0.59344	0.528000	0.53228	GAG	.	.		0.607	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76446801	T	A	76446801	3	1	76	1	0	0	0	0	1	0	0	0	4603	1551	54	4	2586	4	DNAH17	17	76446801	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	5098118	76446801	4748409	271	10542										
ATP9B	374868	hgsc.bcm.edu	37	chr18	76966943	76966943	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gtctccctgcacaggaagacAgtgacccgcccattcatgaa	9	14	2	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr18:76966943A>T	ENST00000426216.2	+	10	978	c.961A>T	c.(961-963)Agt>Tgt	p.S321C	ATP9B_ENST00000307671.7_Missense_Mutation_p.S321C	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	321					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		ACAGGAAGACAGTGACCCGCC	0.408																																					p.S321C		Atlas-SNP	.											.	ATP9B	96	.	0			c.A961T						.						113	102	105					18																	76966943		2203	4300	6503	SO:0001583	missense	374868	exon10			GAAGACAGTGACC	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"ATPases / P-type"	13541	protein-coding gene	gene with protein product		614446	"ATPase, Class II, type 9B"			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.961A>T	chr18.hg19:g.76966943A>T	ENSP00000398076:p.Ser321Cys	40.0	0.0		23.0	17.0	NM_198531	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	hg19	CCDS12014.1	.	.	.	.	.	.	.	.	.	.	A	12.21	1.868232	0.32977	.	.	ENSG00000166377	ENST00000426216;ENST00000307671	T;T	0.67345	-0.23;-0.26	5.42	2.93	0.34026	ATPase, P-type, ATPase-associated domain (1);	0.476053	0.23270	N	0.050021	T	0.58779	0.2146	L	0.54323	1.7	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.51841	-0.8654	10	0.42905	T	0.14	.	9.728	0.40344	0.7031:0.0:0.0:0.2969	.	321;321	O43861;O43861-2	ATP9B_HUMAN;.	C	321	ENSP00000398076:S321C;ENSP00000304500:S321C	ENSP00000304500:S321C	S	+	1	0	ATP9B	75067931	1.000000	0.71417	0.998000	0.56505	0.772000	0.43724	2.073000	0.41519	0.314000	0.23086	0.374000	0.22700	AGT	.	.		0.408	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531		T	76966943	A	T	76966943	3	4	76	1	0	0	0	0	1	0	0	0	1199	188	7	4	999	4	ATP9B	18	76966943	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10		76966943	1110305	272	10543										
ATCAY	85300	hgsc.bcm.edu	37	chr19	3918830	3918830	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gccccagccggagtttgtgcTgcccaggtctgaagagaagc	14	12	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:3918830T>C	ENST00000450849.2	+	11	1495	c.1028T>C	c.(1027-1029)cTg>cCg	p.L343P	ATCAY_ENST00000398448.3_Missense_Mutation_p.L349P|RN7SL202P_ENST00000584410.1_RNA|ATCAY_ENST00000600960.1_Missense_Mutation_p.L343P|ATCAY_ENST00000301260.6_Missense_Mutation_p.L343P	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	343	Mediates interaction with GLS.				apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)			breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		GAGTTTGTGCTGCCCAGGTCT	0.617																																					p.L343P		Atlas-SNP	.											.	ATCAY	84	.	0			c.T1028C						.						60	64	63					19																	3918830		2037	4198	6235	SO:0001583	missense	85300	exon11			TTGTGCTGCCCAG		CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"Cayman ataxia", "caytaxin"	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.1028T>C	chr19.hg19:g.3918830T>C	ENSP00000390941:p.Leu343Pro	115.0	0.0		63.0	38.0	NM_033064	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Missense_Mutation	SNP	ENST00000450849.2	hg19	CCDS45923.1	.	.	.	.	.	.	.	.	.	.	T	2.902	-0.227324	0.06022	.	.	ENSG00000167654	ENST00000450849;ENST00000301260;ENST00000357694;ENST00000398448;ENST00000539301	T;T;T	0.38240	1.18;1.17;1.15	2.89	1.86	0.25419	.	2.793970	0.01702	N	0.027256	T	0.27098	0.0664	L	0.27053	0.805	0.30623	N	0.758292	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.21930	-1.0231	10	0.35671	T	0.21	-14.2741	4.6217	0.12455	0.0:0.153:0.0:0.847	.	349;343;343	B4DS11;Q86WG3-3;Q86WG3	.;.;ATCAY_HUMAN	P	343;343;343;349;321	ENSP00000390941:L343P;ENSP00000301260:L343P;ENSP00000381466:L349P	ENSP00000301260:L343P	L	+	2	0	ATCAY	3869830	0.799000	0.28903	0.394000	0.26270	0.015000	0.08874	0.783000	0.26802	0.513000	0.28278	0.459000	0.35465	CTG	.	.		0.617	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457872.2			C	3918830	T	C	3918830	3	2	76	1	0	0	0	0	1	0	0	0	1077	1580	55	2	1066	2	ATCAY	19	3918830	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10		3918830	55210153	273	10544										
SHD	56961	hgsc.bcm.edu	37	chr19	4280338	4280338	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggccagagccaaggcccttcTgggcggccccggggaggagg	19	13	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:4280338T>A	ENST00000543264.2	+	1	1741	c.278T>A	c.(277-279)cTg>cAg	p.L93Q	SHD_ENST00000599689.1_Missense_Mutation_p.L93Q	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	93										breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGGCCCTTCTGGGCGGCCCC	0.637																																					p.L93Q		Atlas-SNP	.											.	SHD	33	.	0			c.T278A						.						8	9	8					19																	4280338		2157	4252	6409	SO:0001583	missense	56961	exon1			CCCTTCTGGGCGG	BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"SH2 domain containing"	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.278T>A	chr19.hg19:g.4280338T>A	ENSP00000446058:p.Leu93Gln	52.0	0.0		33.0	15.0	NM_020209	Q96NC2	Missense_Mutation	SNP	ENST00000543264.2	hg19	CCDS12125.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.278260	0.80692	.	.	ENSG00000105251	ENST00000543264;ENST00000221852	T	0.39229	1.09	4.75	3.73	0.42828	.	0.485585	0.18019	U	0.154302	T	0.48822	0.1521	L	0.56769	1.78	0.38409	D	0.945878	B;P	0.46578	0.265;0.88	B;P	0.53313	0.229;0.723	T	0.49360	-0.8948	10	0.52906	T	0.07	-18.7318	7.1806	0.25770	0.0:0.1047:0.0:0.8953	.	7;93	Q9NPN8;Q96IW2	.;SHD_HUMAN	Q	93;8	ENSP00000446058:L93Q	ENSP00000221852:L8Q	L	+	2	0	SHD	4231338	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	1.985000	0.40668	0.773000	0.33404	0.397000	0.26171	CTG	.	.		0.637	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209		A	4280338	T	A	4280338	3	1	76	1	0	0	0	0	1	0	0	0	14290	1580	55	4	280	4	SHD	19	4280338	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	361508	4280338	54848645	274	10545										
PLIN4	729359	hgsc.bcm.edu	37	chr19	4511838	4511838	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	actggtctggacagtcccttTggcgacattcactgccccca	9	15	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:4511838T>A	ENST00000301286.3	-	3	2091	c.2092A>T	c.(2092-2094)Aaa>Taa	p.K698*		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	698	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						ACAGTCCCTTTGGCGACATTC	0.597																																					p.K698X		Atlas-SNP	.											.	PLIN4	191	.	0			c.A2092T						.						254	275	268					19																	4511838		2155	4248	6403	SO:0001587	stop_gained	729359	exon3			TCCCTTTGGCGAC	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"Perilipins"	29393	protein-coding gene	gene with protein product		613247	"KIAA1881"	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2092A>T	chr19.hg19:g.4511838T>A	ENSP00000301286:p.Lys698*	198.0	0.0		113.0	41.0	NM_001080400	A6NEI2	Nonsense_Mutation	SNP	ENST00000301286.3	hg19	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	T	37	6.172217	0.97348	.	.	ENSG00000167676	ENST00000301286	.	.	.	5.31	4.26	0.50523	.	0.133397	0.33290	N	0.005066	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.4698	11.2107	0.48797	0.0:0.0:0.1541:0.8459	.	.	.	.	X	698	.	ENSP00000301286:K698X	K	-	1	0	PLIN4	4462838	0.001000	0.12720	0.993000	0.49108	0.196000	0.23810	0.571000	0.23669	0.811000	0.34303	0.386000	0.25728	AAA	.	.		0.597	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		A	4511838	T	A	4511838	4	1	76	1	0	0	0	0	0	1	0	0	12101	1821	63	4	1997	4	PLIN4	19	4511838	Nonsense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	231500	4511838	54617145	275	10546										
FUT3	2525	hgsc.bcm.edu	37	chr19	5843806	5843806	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gctgcgcaccgtctggtaccTggattcctgctgcagtttcc	11	14	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:5843806T>A	ENST00000303225.6	-	3	1679	c.1045A>T	c.(1045-1047)Agg>Tgg	p.R349W	FUT3_ENST00000458379.2_Missense_Mutation_p.R349W|FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000589620.1_Missense_Mutation_p.R349W|FUT3_ENST00000589918.1_Missense_Mutation_p.R349W	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	349					cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						GTCTGGTACCTGGATTCCTGC	0.637																																					p.R349W	Esophageal Squamous(82;745 1728 24593 44831)	Atlas-SNP	.											.	FUT3	30	.	0			c.A1045T						.						61	64	63					19																	5843806		2203	4300	6503	SO:0001583	missense	2525	exon3			GGTACCTGGATTC		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"CD molecules", "Blood group antigens", "Fucosyltransferases"	4014	protein-coding gene	gene with protein product		111100	"fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.1045A>T	chr19.hg19:g.5843806T>A	ENSP00000305603:p.Arg349Trp	220.0	0.0		127.0	70.0	NM_001097640	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	hg19	CCDS12153.1	.	.	.	.	.	.	.	.	.	.	T	16.76	3.212015	0.58452	.	.	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.26067	1.76;1.76	2.29	1.2	0.21068	.	4.574480	0.01087	N	0.005103	T	0.53802	0.1819	M	0.86651	2.83	0.09310	N	1	D;D;D;D	0.67145	0.987;0.996;0.996;0.996	D;D;D;D	0.66602	0.945;0.926;0.926;0.926	T	0.04976	-1.0914	10	0.72032	D	0.01	.	4.7674	0.13139	0.0:0.332:0.0:0.668	.	349;349;349;349	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	W	349	ENSP00000305603:R349W;ENSP00000416443:R349W	ENSP00000305603:R349W	R	-	1	2	FUT3	5794806	0.000000	0.05858	0.120000	0.21714	0.559000	0.35586	-1.868000	0.01644	0.112000	0.17975	0.163000	0.16589	AGG	.	.		0.637	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149		A	5843806	T	A	5843806	3	1	76	1	0	0	0	0	1	0	0	0	6113	1579	55	4	44	4	FUT3	19	5843806	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	1331968	5843806	53285177	276	10547										
KHSRP	8570	hgsc.bcm.edu	37	chr19	6416517	6416517	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccacctcgatcttttcctcgAtaagctgcttggcgtggtca	9	13	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:6416517A>G	ENST00000398148.3	-	14	1564	c.1472T>C	c.(1471-1473)aTc>aCc	p.I491T	MIR3940_ENST00000579148.1_RNA	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	491	Gly-rich.|KH 4. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						CTTTTCCTCGATAAGCTGCTT	0.582																																					p.I491T	Colon(55;593 1006 2067 9135 22980)	Atlas-SNP	.											.	KHSRP	51	.	0			c.T1472C						.						30	32	32					19																	6416517		1887	4107	5994	SO:0001583	missense	8570	exon14			TCCTCGATAAGCT	U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247			6316	protein-coding gene	gene with protein product	"FUSE binding protein 2"	603445				9136930, 8940189	Standard	NM_003685		Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945		ENST00000398148.3:c.1472T>C	chr19.hg19:g.6416517A>G	ENSP00000381216:p.Ile491Thr	108.0	0.0		60.0	24.0	NM_003685	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Missense_Mutation	SNP	ENST00000398148.3	hg19	CCDS45936.1	.	.	.	.	.	.	.	.	.	.	A	15.89	2.967133	0.53507	.	.	ENSG00000088247	ENST00000398148;ENST00000201886	T	0.74737	-0.87	5.21	5.21	0.72293	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.89801	0.6820	H	0.95780	3.72	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.92670	0.6149	10	0.87932	D	0	.	14.0772	0.64897	1.0:0.0:0.0:0.0	.	491	Q92945	FUBP2_HUMAN	T	491	ENSP00000381216:I491T	ENSP00000201886:I491T	I	-	2	0	KHSRP	6367517	1.000000	0.71417	0.952000	0.39060	0.766000	0.43426	9.022000	0.93678	1.963000	0.57068	0.533000	0.62120	ATC	.	.		0.582	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1			G	6416517	A	G	6416517	3	3	76	1	0	0	0	0	1	0	0	0	8160	333	12	2	691	2	KHSRP	19	6416517	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	572711	6416517	52712466	277	10548										
MUC16	94025	hgsc.bcm.edu	37	chr19	9065588	9065588	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccagagatggatgttctgctAgaggaggtgacttctgtcct	13	8	2	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:9065588A>T	ENST00000397910.4	-	3	22061	c.21858T>A	c.(21856-21858)tcT>tcA	p.S7286S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7288	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATGTTCTGCTAGAGGAGGTGA	0.478																																					p.S7286S		Atlas-SNP	.											.	MUC16	4315	.	0			c.T21858A						.						130	125	127					19																	9065588		1976	4152	6128	SO:0001819	synonymous_variant	94025	exon3			TCTGCTAGAGGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21858T>A	chr19.hg19:g.9065588A>T		51.0	0.0		21.0	11.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9065588	A	T	9065588	2	4	76	1	0	0	0	0	0	0	0	1	9982	407	15	4		4	MUC16	19	9065588	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	2649071	9065588	50063395	278	10549										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10602745	10602745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gctgcatctgcaggaagttcGgcgtcaacgagtggcagcgc	15	11	2	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:10602745G>A	ENST00000171111.5	-	3	1380	c.833C>T	c.(832-834)cCg>cTg	p.P278L	CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000393623.2_Missense_Mutation_p.P278L|KEAP1_ENST00000588024.1_5'UTR	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	278	BACK.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CAGGAAGTTCGGCGTCAACGA	0.612																																					p.P278L		Atlas-SNP	.											KEAP1,middle_lobe,carcinoma,-1,1	KEAP1	182	.	0			c.C833T						.						61	60	61					19																	10602745		2203	4300	6503	SO:0001583	missense	9817	exon3			AAGTTCGGCGTCA	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.833C>T	chr19.hg19:g.10602745G>A	ENSP00000171111:p.Pro278Leu	78.0	0.0		36.0	17.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	G	31	5.103735	0.94245	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.70516	-0.49;-0.49	5.61	5.61	0.85477	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	D	0.82595	0.5071	M	0.69248	2.105	0.80722	D	1	D	0.89917	1.0	D	0.69142	0.962	D	0.84027	0.0357	10	0.87932	D	0	.	17.1459	0.86766	0.0:0.0:1.0:0.0	.	278	Q14145	KEAP1_HUMAN	L	278	ENSP00000171111:P278L;ENSP00000377245:P278L	ENSP00000171111:P278L	P	-	2	0	KEAP1	10463745	1.000000	0.71417	0.951000	0.38953	0.987000	0.75469	7.675000	0.84002	2.656000	0.90262	0.561000	0.74099	CCG	.	.		0.612	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		A	10602745	G	A	10602745	3	1	76	1	0	0	0	0	1	0	0	0	8150	1116	39	1	1057	1	KEAP1	19	10602745	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	1537157	10602745	48526238	279	10550										
CCDC151	115948	hgsc.bcm.edu	37	chr19	11545698	11545698	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tggaacggcctggggtccacGcctgggctgtgcccttgcct	15	14	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:11545698G>T	ENST00000356392.4	-	1	227	c.140C>A	c.(139-141)gCg>gAg	p.A47E	PRKCSH_ENST00000587327.1_5'Flank|CCDC151_ENST00000545100.1_Intron|CCDC151_ENST00000591179.1_Missense_Mutation_p.A47E|PRKCSH_ENST00000592741.1_5'Flank|PRKCSH_ENST00000591462.1_5'Flank|PRKCSH_ENST00000412601.1_5'Flank|CCDC151_ENST00000586836.1_Intron|PRKCSH_ENST00000252455.2_5'Flank|PRKCSH_ENST00000589838.1_5'Flank	NM_145045.4	NP_659482.3	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	47										endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	12						TGGGGTCCACGCCTGGGCTGT	0.617											OREG0025257	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A47E		Atlas-SNP	.											.	CCDC151	44	.	0			c.C140A						.						63	68	67					19																	11545698		1970	4143	6113	SO:0001583	missense	115948	exon1			GTCCACGCCTGGG		CCDS42501.1	19p13.2	2014-02-20				ENSG00000198003			28303	protein-coding gene	gene with protein product		615956				24067530	Standard	NM_145045		Approved	MGC20983	uc002mrs.3	A5D8V7		ENST00000356392.4:c.140C>A	chr19.hg19:g.11545698G>T	ENSP00000348757:p.Ala47Glu	79.0	0.0	673	31.0	22.0	NM_145045	B4DXT0|Q96CG5	Missense_Mutation	SNP	ENST00000356392.4	hg19	CCDS42501.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486550	0.63962	.	.	ENSG00000198003	ENST00000356392;ENST00000543934	T	0.16073	2.37	4.54	0.89	0.19218	.	0.200197	0.25011	N	0.033831	T	0.26085	0.0636	L	0.60455	1.87	0.58432	D	0.999998	D;D	0.67145	0.989;0.996	P;D	0.63192	0.865;0.912	T	0.08452	-1.0721	10	0.22706	T	0.39	-8.6531	6.2124	0.20636	0.1021:0.3662:0.5317:0.0	.	47;47	B3KPH7;A5D8V7	.;CC151_HUMAN	E	47;26	ENSP00000348757:A47E	ENSP00000348757:A47E	A	-	2	0	CCDC151	11406698	0.998000	0.40836	0.805000	0.32314	0.002000	0.02628	1.709000	0.37909	0.592000	0.29728	-0.165000	0.13383	GCG	.	.		0.617	CCDC151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458800.1	NM_145045		T	11545698	G	T	11545698	3	4	76	1	0	0	0	0	1	0	0	0	2788	1087	38	1	1699	1	CCDC151	19	11545698	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	942953	11545698	47583285	280	10551										
CYP4F22	126410	hgsc.bcm.edu	37	chr19	15636153	15636153	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctgtgtgtccccaggatgctGcccatcacagaccgcctgct	10	16	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:15636153G>A	ENST00000269703.3	+	3	205	c.6G>A	c.(4-6)ctG>ctA	p.L2L	CYP4F22_ENST00000601005.2_Silent_p.L2L	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	2						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						CCAGGATGCTGCCCATCACAG	0.602																																					p.L2L		Atlas-SNP	.											.	CYP4F22	74	.	0			c.G6A						.						87	58	68					19																	15636153		2203	4300	6503	SO:0001819	synonymous_variant	126410	exon3			GATGCTGCCCATC		CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"Cytochrome P450s"	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.6G>A	chr19.hg19:g.15636153G>A		34.0	0.0		28.0	7.0	NM_173483	Q8N8H4	Silent	SNP	ENST00000269703.3	hg19	CCDS12331.1																																																																																			.	.		0.602	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483		A	15636153	G	A	15636153	2	1	76	1	0	0	0	0	0	0	0	1	4191	1306	46	3		3	CYP4F22	19	15636153	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	4090455	15636153	43492830	281	10552										
OR10H1	26539	hgsc.bcm.edu	37	chr19	15917916	15917916	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcattacatttttttctgggTagagtttactgaagaaggtc	9	5	2	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:15917916T>G	ENST00000334920.2	-	1	1020	c.932A>C	c.(931-933)tAc>tCc	p.Y311S		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						TTTTTCTGGGTAGAGTTTACT	0.443																																					p.Y311S		Atlas-SNP	.											.	OR10H1	59	.	0			c.A932C						.						90	87	88					19																	15917916		2203	4300	6503	SO:0001583	missense	26539	exon1			TCTGGGTAGAGTT	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"GPCR / Class A : Olfactory receptors"	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.932A>C	chr19.hg19:g.15917916T>G	ENSP00000335596:p.Tyr311Ser	105.0	0.0		56.0	9.0	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	hg19	CCDS12335.1	.	.	.	.	.	.	.	.	.	.	.	5.422	0.262931	0.10294	.	.	ENSG00000186723	ENST00000334920	T	0.35421	1.31	4.42	-3.51	0.04696	.	1.317390	0.05459	N	0.550803	T	0.10121	0.0248	N	0.01188	-0.97	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16158	-1.0412	10	0.22706	T	0.39	.	0.9319	0.01337	0.2696:0.3674:0.16:0.2031	.	311	Q9Y4A9	O10H1_HUMAN	S	311	ENSP00000335596:Y311S	ENSP00000335596:Y311S	Y	-	2	0	OR10H1	15778916	0.032000	0.19561	0.000000	0.03702	0.001000	0.01503	1.451000	0.35145	-0.170000	0.10816	-0.263000	0.10527	TAC	.	.		0.443	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1			G	15917916	T	G	15917916	3	3	76	1	0	0	0	0	1	0	0	0	10914	1638	57	5	28	5	OR10H1	19	15917916	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	281763	15917916	43211067	282	10553										
CHERP	84167	hgsc.bcm.edu	37	chr19	16634007	16634007	+	IGR	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	aagccatgggggggagggccGaagtcagggtgctggggtcc	21	8	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:16634007G>A	ENST00000221671.3	+	0	3427				CHERP_ENST00000544299.1_5'UTR|CTD-3222D19.2_ENST00000409035.1_Intron|CHERP_ENST00000198939.6_Silent_p.F623F|CHERP_ENST00000546361.2_Silent_p.F612F	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44											endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						GGGGAGGGCCGAAGTCAGGGT	0.672																																					p.F612F		Atlas-SNP	.											.	CHERP	70	.	0			c.C1836T						.						43	55	51					19																	16634007		2129	4242	6371	SO:0001628	intergenic_variant	10523	exon11			AGGGCCGAAGTCA	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5			chr19.hg19:g.16634007G>A		74.0	0.0		45.0	27.0	NM_006387	Q8N6Y7	Silent	SNP	ENST00000221671.3	hg19	CCDS12345.1																																																																																			.	.		0.672	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207		A	16634007	G	A	16634007	1	1	76	0	1	0	0	0	0	0	0	0	3338	1049	37	1		1	CHERP	19	16634007	IGR	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	716091	16634007	42494976	283	10554										
SIN3B	23309	hgsc.bcm.edu	37	chr19	16973709	16973709	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gtttagcttgaccattggacActtctccagggttcgtggac	11	10	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:16973709A>C	ENST00000379803.1	+	10	1295	c.1281A>C	c.(1279-1281)acA>acC	p.T427T	SIN3B_ENST00000248054.5_Intron|SIN3B_ENST00000595541.1_5'Flank	NM_015260.2	NP_056075.1			SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						ACCATTGGACACTTCTCCAGG	0.473																																					p.T427T		Atlas-SNP	.											.	SIN3B	90	.	0			c.A1281C						.						279	261	267					19																	16973709		2203	4300	6503	SO:0001819	synonymous_variant	23309	exon10			TTGGACACTTCTC	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000379803.1:c.1281A>C	chr19.hg19:g.16973709A>C		94.0	0.0		41.0	13.0	NM_015260		Silent	SNP	ENST00000379803.1	hg19	CCDS32946.1																																																																																			.	.		0.473	SIN3B-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462848.1	NM_015260		C	16973709	A	C	16973709	2	2	76	1	0	0	0	0	0	0	0	1	14341	146	6	5		5	SIN3B	19	16973709	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	339702	16973709	42155274	284	10555										
IL12RB1	3594	hgsc.bcm.edu	37	chr19	18186614	18186614	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caggaacttccttggctcccCagctgccgtcgtcggagctg	12	15	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:18186614C>A	ENST00000600835.2	-	8	943	c.645G>T	c.(643-645)ctG>ctT	p.L215L	IL12RB1_ENST00000593993.2_Silent_p.L215L|IL12RB1_ENST00000322153.7_Silent_p.L215L			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	215	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						CTTGGCTCCCCAGCTGCCGTC	0.582																																					p.L215L		Atlas-SNP	.											.	IL12RB1	92	.	0			c.G645T	GRCh37	CI067578	IL12RB1	I		.						59	61	60					19																	18186614		2203	4300	6503	SO:0001819	synonymous_variant	3594	exon7			GCTCCCCAGCTGC	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.645G>T	chr19.hg19:g.18186614C>A		70.0	0.0		39.0	7.0	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Silent	SNP	ENST00000600835.2	hg19	CCDS54232.1																																																																																			.	.		0.582	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3			A	18186614	C	A	18186614	2	1	76	1	0	0	0	0	0	0	0	1	7635	581	21	3		3	IL12RB1	19	18186614	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	1212905	18186614	40942369	285	10556										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22157397	22157397	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gacatttgcatatttgccacGttgaaatactttgctctgtg	8	8	1	1	rs530559517	byFrequency	TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:22157397G>T	ENST00000397126.4	-	4	587	c.439C>A	c.(439-441)Cgt>Agt	p.R147S	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	147					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TATTTGCCACGTTGAAATACT	0.328																																					p.R147S		Atlas-SNP	.											.	ZNF208	817	.	0			c.C439A						.						131	128	129					19																	22157397		2052	4230	6282	SO:0001583	missense	7757	exon4			TGCCACGTTGAAA	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.439C>A	chr19.hg19:g.22157397G>T	ENSP00000380315:p.Arg147Ser	93.0	0.0		50.0	16.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	G	0.889	-0.726286	0.03158	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.06687	3.27	1.44	-2.88	0.05682	.	.	.	.	.	T	0.06554	0.0168	.	.	.	0.09310	N	1	P	0.43314	0.803	B	0.40602	0.334	T	0.25537	-1.0129	8	0.52906	T	0.07	.	6.3092	0.21154	0.4659:0.0:0.5341:0.0	.	147	O43345	ZN208_HUMAN	S	147	ENSP00000380315:R147S	ENSP00000380315:R147S	R	-	1	0	ZNF208	21949237	0.000000	0.05858	0.004000	0.12327	0.027000	0.11550	-0.464000	0.06688	-0.603000	0.05767	-0.763000	0.03452	CGT	.	.		0.328	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22157397	G	T	22157397	3	4	76	1	0	0	0	0	1	0	0	0	17781	1145	40	1	3407	1	ZNF208	19	22157397	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	3970783	22157397	36971586	286	10557										
HPN	3249	hgsc.bcm.edu	37	chr19	35551262	35551262	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gtcccacagactgtggccgcAggaagctgcccgtggaccgc	14	15	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:35551262A>T	ENST00000262626.2	+	8	1291	c.466A>T	c.(466-468)Agg>Tgg	p.R156W	HPN_ENST00000597419.1_Intron|HPN-AS1_ENST00000392227.2_RNA|HPN_ENST00000392226.1_Missense_Mutation_p.R156W	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin	156					basement membrane disassembly (GO:0034769)|cholesterol homeostasis (GO:0042632)|cochlea morphogenesis (GO:0090103)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|epithelium development (GO:0060429)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pilomotor reflex (GO:0097195)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|positive regulation of gene expression (GO:0010628)|positive regulation of hepatocyte proliferation (GO:2000347)|positive regulation of plasminogen activation (GO:0010756)|positive regulation of thyroid hormone generation (GO:2000611)|potassium ion transmembrane transport (GO:0071805)|proteolysis (GO:0006508)|regulation of cell shape (GO:0008360)|response to thyroid hormone (GO:0097066)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	CTGTGGCCGCAGGAAGCTGCC	0.692																																					p.R156W		Atlas-SNP	.											.	HPN	45	.	0			c.A466T						.						33	38	36					19																	35551262		2203	4298	6501	SO:0001583	missense	3249	exon8			GGCCGCAGGAAGC		CCDS32993.1	19q13.12	2013-04-25	2008-12-08		ENSG00000105707	ENSG00000105707		"Serine peptidases / Transmembrane"	5155	protein-coding gene	gene with protein product	"transmembrane protease, serine 1"	142440				2835076	Standard	NM_182983		Approved	TMPRSS1	uc002nxq.2	P05981	OTTHUMG00000182474	ENST00000262626.2:c.466A>T	chr19.hg19:g.35551262A>T	ENSP00000262626:p.Arg156Trp	25.0	0.0		21.0	4.0	NM_182983	B2RDS4	Missense_Mutation	SNP	ENST00000262626.2	hg19	CCDS32993.1	.	.	.	.	.	.	.	.	.	.	A	18.93	3.727960	0.69074	.	.	ENSG00000105707	ENST00000262626;ENST00000392226;ENST00000541345	T;T	0.63744	-0.06;-0.06	4.68	1.25	0.21368	Peptidase cysteine/serine, trypsin-like (1);Speract/scavenger receptor-related (1);Hepsin, SRCR (1);	0.053179	0.64402	D	0.000001	T	0.67524	0.2902	L	0.36672	1.1	0.48901	D	0.999728	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.997	T	0.66089	-0.6010	10	0.87932	D	0	.	11.001	0.47604	0.5381:0.4619:0.0:0.0	.	128;156;156	B7Z1L4;B2ZDQ2;P05981	.;.;HEPS_HUMAN	W	156;156;128	ENSP00000262626:R156W;ENSP00000376060:R156W	ENSP00000262626:R156W	R	+	1	2	HPN	40243102	0.253000	0.23982	0.524000	0.27887	0.987000	0.75469	0.870000	0.28010	-0.024000	0.13941	0.454000	0.30748	AGG	.	.		0.692	HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1	NM_002151		T	35551262	A	T	35551262	3	4	76	1	0	0	0	0	1	0	0	0	7345	179	7	4	492	4	HPN	19	35551262	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	13393865	35551262	23577721	287	10558										
POLR2I	5438	hgsc.bcm.edu	37	chr19	36604924	36604924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcgcgccacttacctcggccCgcgcactgtgtgactggaag	12	15	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:36604924C>T	ENST00000221859.4	-	5	797	c.308G>A	c.(307-309)cGg>cAg	p.R103Q	TBCB_ENST00000586868.1_5'Flank|TBCB_ENST00000221855.3_5'Flank|TBCB_ENST00000589996.1_5'Flank|TBCB_ENST00000585746.1_5'Flank	NM_006233.4	NP_006224.1	P36954	RPB9_HUMAN	polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa	103					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter (GO:0001193)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|ovary(1)	3	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TACCTCGGCCCGCGCACTGTG	0.612											OREG0025437	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R103Q		Atlas-SNP	.											.	POLR2I	10	.	0			c.G308A						.						98	102	100					19																	36604924		2203	4300	6503	SO:0001583	missense	5438	exon5			TCGGCCCGCGCAC		CCDS12487.1	19q13.12	2013-10-17	2002-08-29		ENSG00000105258	ENSG00000105258	2.7.7.6	"RNA polymerase subunits"	9196	protein-coding gene	gene with protein product		180662	"polymerase (RNA) II (DNA directed) polypeptide I (14.5kD)"			8034326	Standard	NM_006233		Approved	RPB9, hRPB14.5	uc002ode.3	P36954	OTTHUMG00000181749	ENST00000221859.4:c.308G>A	chr19.hg19:g.36604924C>T	ENSP00000221859:p.Arg103Gln	82.0	0.0	864	49.0	15.0	NM_006233	B2R5J2|Q6NW05	Missense_Mutation	SNP	ENST00000221859.4	hg19	CCDS12487.1	.	.	.	.	.	.	.	.	.	.	C	15.19	2.759403	0.49468	.	.	ENSG00000105258	ENST00000221859	T	0.43294	0.95	5.0	3.96	0.45880	Zinc finger, TFIIS-type (4);	0.050022	0.85682	D	0.000000	T	0.54532	0.1864	M	0.77406	2.37	0.44168	D	0.996976	P	0.43633	0.813	P	0.50825	0.651	T	0.59478	-0.7447	10	0.56958	D	0.05	-27.055	11.5104	0.50490	0.0:0.9124:0.0:0.0876	.	103	P36954	RPB9_HUMAN	Q	103	ENSP00000221859:R103Q	ENSP00000221859:R103Q	R	-	2	0	POLR2I	41296764	1.000000	0.71417	0.993000	0.49108	0.071000	0.16799	3.460000	0.53028	1.474000	0.48178	-0.140000	0.14226	CGG	.	.		0.612	POLR2I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457442.1	NM_006233		T	36604924	C	T	36604924	3	4	76	1	0	0	0	0	1	0	0	0	12231	652	23	1	77	1	POLR2I	19	36604924	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	1053662	36604924	22524059	288	10559										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40376756	40376756	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccaggcagagatcaaagatgCaatctttcaagggaccctgg	11	10	3	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:40376756C>A	ENST00000221347.6	-	24	11673	c.11666G>T	c.(11665-11667)tGc>tTc	p.C3889F	FCGBP_ENST00000595713.1_5'Flank	NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3889						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			ATCAAAGATGCAATCTTTCAA	0.587																																					p.C3889F		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	.	0			c.G11666T						.						15	20	18					19																	40376756		2160	4205	6365	SO:0001583	missense	8857	exon24			AAGATGCAATCTT	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.11666G>T	chr19.hg19:g.40376756C>A	ENSP00000221347:p.Cys3889Phe	624.0	0.0		301.0	38.0	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	c	13.29	2.193133	0.38707	.	.	ENSG00000090920	ENST00000221347	D	0.90133	-2.62	3.75	3.75	0.43078	Uncharacterised domain, cysteine-rich (2);	.	.	.	.	D	0.97256	0.9103	H	0.98866	4.355	0.43334	D	0.995378	D	0.89917	1.0	D	0.91635	0.999	D	0.98740	1.0716	9	0.87932	D	0	.	14.6972	0.69132	0.0:1.0:0.0:0.0	.	3889	Q9Y6R7	FCGBP_HUMAN	F	3889	ENSP00000221347:C3889F	ENSP00000221347:C3889F	C	-	2	0	FCGBP	45068596	1.000000	0.71417	0.042000	0.18584	0.044000	0.14063	7.600000	0.82769	1.792000	0.52537	0.313000	0.20887	TGC	.	.		0.587	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40376756	C	A	40376756	3	1	76	1	0	0	0	0	1	0	0	0	5786	710	25	3	4603	3	FCGBP	19	40376756	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	3771832	40376756	18752227	289	10560										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42853717	42853717	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggctgcagcgccctgggtctGctcgcctcttccctctgcct	11	18	3	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:42853717G>T	ENST00000251268.6	+	14	2365	c.2365G>T	c.(2365-2367)Gct>Tct	p.A789S	MEGF8_ENST00000334370.4_Missense_Mutation_p.A722S	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	789					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CCCTGGGTCTGCTCGCCTCTT	0.657																																					p.A789S		Atlas-SNP	.											.	MEGF8	358	.	0			c.G2365T						.						38	43	41					19																	42853717		2203	4299	6502	SO:0001583	missense	1954	exon14			GGGTCTGCTCGCC	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.2365G>T	chr19.hg19:g.42853717G>T	ENSP00000251268:p.Ala789Ser	39.0	0.0		14.0	10.0	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	G	9.706	1.155671	0.21454	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.20738	2.05;2.06	4.64	-0.0615	0.13784	.	0.949193	0.08752	N	0.898904	T	0.06735	0.0172	N	0.02539	-0.55	0.09310	N	0.999992	B;B	0.21381	0.001;0.055	B;B	0.12156	0.001;0.007	T	0.37454	-0.9705	10	0.06236	T	0.91	.	8.1339	0.31043	0.3519:0.0:0.6481:0.0	.	789;722	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	S	722;789	ENSP00000334219:A722S;ENSP00000251268:A789S	ENSP00000251268:A789S	A	+	1	0	MEGF8	47545557	0.001000	0.12720	0.115000	0.21578	0.943000	0.58893	0.445000	0.21677	-0.162000	0.10964	0.491000	0.48974	GCT	.	.		0.657	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		T	42853717	G	T	42853717	3	4	76	1	0	0	0	0	1	0	0	0	9472	1319	46	3	2214	3	MEGF8	19	42853717	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	2476961	42853717	16275266	290	10561										
PSG2	5670	hgsc.bcm.edu	37	chr19	43576075	43576075	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cctgaacggtaattggtgtaTgaagggtgaattctggggag	16	4	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:43576075T>C	ENST00000406487.1	-	4	839	c.741A>G	c.(739-741)tcA>tcG	p.S247S		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	247	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				AATTGGTGTATGAAGGGTGAA	0.483																																					p.S247S		Atlas-SNP	.											.	PSG2	84	.	0			c.A741G						.						150	164	159					19																	43576075		2203	4299	6502	SO:0001819	synonymous_variant	5670	exon4			GGTGTATGAAGGG		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9519	protein-coding gene	gene with protein product	"pregnancy-specific beta-1 glycoprotein", "pregnancy-specific beta-1-glycoprotein 7", "carcinoembryonic antigen SG8"	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.741A>G	chr19.hg19:g.43576075T>C		148.0	0.0		108.0	17.0	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	hg19	CCDS12616.1																																																																																			.	C|0.570;A|0.430		0.483	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246		C	43576075	T	C	43576075	2	2	76	1	0	0	0	0	0	0	0	1	12667	1451	51	2		2	PSG2	19	43576075	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	722358	43576075	15552908	291	10562										
CLPTM1	1209	hgsc.bcm.edu	37	chr19	45480646	45480646	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	catccacgtttacttcaccaAgagtggcttccacccagacc	6	16	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:45480646A>G	ENST00000337392.5	+	5	665	c.515A>G	c.(514-516)aAg>aGg	p.K172R	CLPTM1_ENST00000546079.1_Missense_Mutation_p.K70R|CLPTM1_ENST00000541297.2_Missense_Mutation_p.K158R	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	172					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)		p.K172R(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		TACTTCACCAAGAGTGGCTTC	0.617																																					p.K172R		Atlas-SNP	.											CLPTM1_ENST00000347493,NS,lymphoid_neoplasm,0,3	CLPTM1	109	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A515G						.						119	119	119					19																	45480646		2203	4300	6503	SO:0001583	missense	1209	exon5			TCACCAAGAGTGG	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.515A>G	chr19.hg19:g.45480646A>G	ENSP00000336994:p.Lys172Arg	49.0	0.0		58.0	11.0	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	hg19	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.943858	0.73672	.	.	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.41719	0.1171	N	0.20483	0.58	0.80722	D	1	P;B;B	0.44627	0.839;0.363;0.363	P;B;B	0.46452	0.517;0.434;0.434	T	0.21930	-1.0231	9	0.10377	T	0.69	-33.936	13.5943	0.61979	1.0:0.0:0.0:0.0	.	158;172;172	F5H8J3;B3KQH2;O96005	.;.;CLPT1_HUMAN	R	70;158;172;172	.	ENSP00000336994:K172R	K	+	2	0	CLPTM1	50172486	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.646000	0.91053	2.099000	0.63709	0.456000	0.33151	AAG	.	.		0.617	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294		G	45480646	A	G	45480646	3	3	76	1	0	0	0	0	1	0	0	0	3556	72	3	2	533	2	CLPTM1	19	45480646	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	1904571	45480646	13648337	292	10563										
TRAPPC6A	79090	hgsc.bcm.edu	37	chr19	45668133	45668133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ggtgattggtgcgcaggctgTccatctgcttctggaacacc	13	11	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:45668133T>C	ENST00000585934.1	-	3	266	c.248A>G	c.(247-249)gAc>gGc	p.D83G	TRAPPC6A_ENST00000006275.4_Missense_Mutation_p.D97G|TRAPPC6A_ENST00000588062.1_Silent_p.G60G|TRAPPC6A_ENST00000592647.1_Silent_p.G74G	NM_001270891.1	NP_001257820.1	O75865	TPC6A_HUMAN	trafficking protein particle complex 6A	83					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	8		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00872)|GBM - Glioblastoma multiforme(486;0.233)		GCGCAGGCTGTCCATCTGCTT	0.647																																					p.D97G		Atlas-SNP	.											.	TRAPPC6A	16	.	0			c.A290G						.						78	77	77					19																	45668133		2203	4300	6503	SO:0001583	missense	79090	exon3			AGGCTGTCCATCT	AF161407	CCDS12655.1, CCDS59395.1, CCDS59396.1, CCDS59397.1	19q13.32	2012-10-02				ENSG00000007255		"Trafficking protein particle complex"	23069	protein-coding gene	gene with protein product		610396					Standard	NM_024108		Approved	TRS33, MGC2650, HSPC289	uc002pav.4	O75865		ENST00000585934.1:c.248A>G	chr19.hg19:g.45668133T>C	ENSP00000468612:p.Asp83Gly	80.0	0.0		88.0	19.0	NM_024108	K7ERB1|K7ERQ4|Q9BQ45|Q9P092	Missense_Mutation	SNP	ENST00000585934.1	hg19	CCDS59397.1	.	.	.	.	.	.	.	.	.	.	t	17.01	3.278119	0.59758	.	.	ENSG00000007255	ENST00000006275	T	0.57436	0.4	4.78	4.78	0.61160	NO signalling/Golgi transport  ligand-binding domain (1);	0.113453	0.56097	D	0.000028	T	0.76097	0.3940	M	0.92169	3.28	0.80722	D	1	D;D	0.76494	0.999;0.994	D;P	0.71870	0.975;0.903	T	0.81385	-0.0957	10	0.87932	D	0	-25.0331	10.6947	0.45892	0.0:0.0:0.0:1.0	.	83;97	O75865;O75865-2	TPC6A_HUMAN;.	G	97	ENSP00000006275:D97G	ENSP00000006275:D97G	D	-	2	0	TRAPPC6A	50359973	1.000000	0.71417	0.886000	0.34754	0.495000	0.33615	2.253000	0.43205	1.784000	0.52394	0.460000	0.39030	GAC	.	.		0.647	TRAPPC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457556.1	NM_024108		C	45668133	T	C	45668133	3	2	76	1	0	0	0	0	1	0	0	0	16478	1667	58	2	247	2	TRAPPC6A	19	45668133	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	187487	45668133	13460850	293	10564										
MARK4	57787	hgsc.bcm.edu	37	chr19	45783689	45783689	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caaagagtccttgaccagccAgaagtacaacgaagtgaccg	10	11	0	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:45783689A>T	ENST00000262891.4	+	11	1395	c.1064A>T	c.(1063-1065)cAg>cTg	p.Q355L	MARK4_ENST00000300843.4_Missense_Mutation_p.Q355L	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	355	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)			NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		TTGACCAGCCAGAAGTACAAC	0.597																																					p.Q355L		Atlas-SNP	.											.	MARK4	132	.	0			c.A1064T						.						137	133	134					19																	45783689		2203	4300	6503	SO:0001583	missense	57787	exon11			CCAGCCAGAAGTA	AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"MAP/microtubule affinity-regulating kinase like 1"	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.1064A>T	chr19.hg19:g.45783689A>T	ENSP00000262891:p.Gln355Leu	226.0	0.0		277.0	22.0	NM_001199867	Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Missense_Mutation	SNP	ENST00000262891.4	hg19	CCDS56097.1	.	.	.	.	.	.	.	.	.	.	A	19.03	3.748242	0.69533	.	.	ENSG00000007047	ENST00000262893;ENST00000262891;ENST00000300843	T;T	0.22134	1.97;1.97	5.16	5.16	0.70880	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);	0.000000	0.64402	D	0.000001	T	0.33265	0.0857	M	0.79805	2.47	0.58432	D	0.999997	B;P;P	0.52170	0.359;0.951;0.891	B;P;B	0.47573	0.182;0.55;0.295	T	0.14839	-1.0458	10	0.31617	T	0.26	.	12.9784	0.58549	1.0:0.0:0.0:0.0	.	221;355;355	Q8N2N5;Q96L34;Q96L34-2	.;MARK4_HUMAN;.	L	385;355;355	ENSP00000262891:Q355L;ENSP00000300843:Q355L	ENSP00000262891:Q355L	Q	+	2	0	MARK4	50475529	0.388000	0.25197	1.000000	0.80357	0.998000	0.95712	1.332000	0.33805	2.174000	0.68829	0.459000	0.35465	CAG	.	.		0.597	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417		T	45783689	A	T	45783689	3	4	76	1	0	0	0	0	1	0	0	0	9324	188	7	4	1106	4	MARK4	19	45783689	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	115556	45783689	13345294	294	10565										
ELSPBP1	64100	hgsc.bcm.edu	37	chr19	48523032	48523032	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcccctccatctacagaaatAatgtggtctctgattgcatg	7	11	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:48523032A>T	ENST00000339841.2	+	5	590	c.412A>T	c.(412-414)Aat>Tat	p.N138Y	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	138	Fibronectin type-II 3. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		CTACAGAAATAATGTGGTCTC	0.473																																					p.N138Y		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.A412T						.						96	87	90					19																	48523032		2203	4300	6503	SO:0001583	missense	64100	exon5			AGAAATAATGTGG	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"epididymal protein 12"	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.412A>T	chr19.hg19:g.48523032A>T	ENSP00000340660:p.Asn138Tyr	129.0	0.0		148.0	28.0	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	hg19	CCDS12708.1	.	.	.	.	.	.	.	.	.	.	A	1.906	-0.451955	0.04540	.	.	ENSG00000169393	ENST00000339841	T	0.50548	0.74	3.76	0.191	0.15130	Fibronectin, type II, collagen-binding (4);Kringle-like fold (1);	1.385230	0.04759	N	0.425942	T	0.37705	0.1013	L	0.52905	1.665	0.09310	N	1	P	0.36392	0.551	B	0.31614	0.133	T	0.30937	-0.9961	10	0.72032	D	0.01	.	1.0922	0.01665	0.5097:0.1922:0.1121:0.1859	.	138	Q96BH3	ESPB1_HUMAN	Y	138	ENSP00000340660:N138Y	ENSP00000340660:N138Y	N	+	1	0	ELSPBP1	53214844	0.000000	0.05858	0.002000	0.10522	0.025000	0.11179	-0.462000	0.06704	-0.170000	0.10816	0.459000	0.35465	AAT	.	.		0.473	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1			T	48523032	A	T	48523032	3	4	76	1	0	0	0	0	1	0	0	0	5085	362	13	4	426	4	ELSPBP1	19	48523032	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	2739343	48523032	10605951	295	10566										
KCNJ14	3770	hgsc.bcm.edu	37	chr19	48967700	48967700	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctacctccctggtgaactgcTctggggccatcgttttgagc	11	13	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:48967700T>C	ENST00000391884.1	+	2	1453	c.977T>C	c.(976-978)cTc>cCc	p.L326P	CTC-273B12.5_ENST00000596497.1_RNA|CTC-273B12.5_ENST00000593476.1_RNA|CTC-273B12.5_ENST00000600650.1_RNA|CTC-273B12.6_ENST00000597574.1_lincRNA|CTC-273B12.5_ENST00000600529.1_RNA|KCNJ14_ENST00000342291.2_Missense_Mutation_p.L326P|CTC-273B12.7_ENST00000595676.1_5'Flank			Q9UNX9	KCJ14_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 14	326					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|skin(2)|urinary_tract(1)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000109)|all cancers(93;0.000129)|Epithelial(262;0.0081)|GBM - Glioblastoma multiforme(486;0.0222)	Yohimbine(DB01392)	GGTGAACTGCTCTGGGGCCAT	0.587																																					p.D326A	NSCLC(148;170 3504 35216)	Atlas-SNP	.											.	KCNJ14	28	.	0			c.A977C						.						88	73	78					19																	48967700		2203	4300	6503	SO:0001583	missense	3770	exon3			AACTGCTCTGGGG	BC042033	CCDS12721.1	19q13	2011-07-05				ENSG00000182324		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6260	protein-coding gene	gene with protein product		603953				9592090, 10723734, 16382105	Standard	NM_013348		Approved	Kir2.4, IRK4	uc002pje.2	Q9UNX9		ENST00000391884.1:c.977T>C	chr19.hg19:g.48967700T>C	ENSP00000375756:p.Leu326Pro	96.0	0.0		101.0	11.0	NM_013348		Missense_Mutation	SNP	ENST00000391884.1	hg19	CCDS12721.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.292364	0.80914	.	.	ENSG00000182324	ENST00000342291;ENST00000391884	D;D	0.95482	-3.72;-3.72	5.24	5.24	0.73138	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.98372	0.9459	H	0.96015	3.755	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.99418	1.0932	10	0.87932	D	0	.	13.733	0.62799	0.0:0.0:0.0:1.0	.	326	Q9UNX9	IRK14_HUMAN	P	326	ENSP00000341479:L326P;ENSP00000375756:L326P	ENSP00000341479:L326P	L	+	2	0	KCNJ14	53659512	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.345000	0.52182	2.288000	0.76882	0.533000	0.62120	CTC	.	.		0.587	KCNJ14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466127.1	NM_013348		C	48967700	T	C	48967700	3	2	76	1	0	0	0	0	1	0	0	0	8057	1551	54	2	983	2	KCNJ14	19	48967700	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	444668	48967700	10161283	296	10567										
SIGLEC9	27180	hgsc.bcm.edu	37	chr19	51630384	51630384	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcagttgacagcaatcccccTgccaggctgagcctgagctg	12	14	0	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:51630384T>A	ENST00000250360.3	+	4	913	c.846T>A	c.(844-846)ccT>ccA	p.P282P	SIGLEC9_ENST00000440804.3_Silent_p.P282P	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	282	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		GCAATCCCCCTGCCAGGCTGA	0.617																																					p.P282P		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.T846A						.						97	93	94					19																	51630384		2203	4300	6503	SO:0001819	synonymous_variant	27180	exon4			TCCCCCTGCCAGG	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.846T>A	chr19.hg19:g.51630384T>A		64.0	0.0		80.0	19.0	NM_001198558	Q6GTU4|Q9BYI9	Silent	SNP	ENST00000250360.3	hg19	CCDS12825.1																																																																																			.	.		0.617	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		A	51630384	T	A	51630384	2	1	76	1	0	0	0	0	0	0	0	1	14330	1567	55	4		4	SIGLEC9	19	51630384	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	2662684	51630384	7498599	297	10568										
IGLON5	402665	hgsc.bcm.edu	37	chr19	51830988	51830988	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gacccggatccctggcaggcTgagcagcggcacggccgaag	16	14	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:51830988T>A	ENST00000270642.8	+	7	770	c.770T>A	c.(769-771)cTg>cAg	p.L257Q		NM_001101372.1	NP_001094842.1	A6NGN9	IGLO5_HUMAN	IgLON family member 5	257	Ig-like C2-type 3.					extracellular region (GO:0005576)				large_intestine(5)|lung(6)|prostate(1)	12						CCTGGCAGGCTGAGCAGCGGC	0.692																																					p.L257Q		Atlas-SNP	.											.	IGLON5	31	.	0			c.T770A						.						8	8	8					19																	51830988		1912	4062	5974	SO:0001583	missense	402665	exon7			GCAGGCTGAGCAG		CCDS46158.1	19q13.33	2013-01-29			ENSG00000142549	ENSG00000142549		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	34550	protein-coding gene	gene with protein product							Standard	NM_001101372		Approved	LOC402665	uc002pwc.2	A6NGN9	OTTHUMG00000154422	ENST00000270642.8:c.770T>A	chr19.hg19:g.51830988T>A	ENSP00000270642:p.Leu257Gln	24.0	0.0		19.0	5.0	NM_001101372		Missense_Mutation	SNP	ENST00000270642.8	hg19	CCDS46158.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.974130	0.92919	.	.	ENSG00000142549	ENST00000270642	T	0.18016	2.24	5.2	5.2	0.72013	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.392349	0.26549	N	0.023753	T	0.46698	0.1406	M	0.87328	2.875	0.44302	D	0.997171	D	0.89917	1.0	D	0.83275	0.996	T	0.53301	-0.8458	10	0.62326	D	0.03	-12.171	13.0257	0.58814	0.0:0.0:0.0:1.0	.	257	A6NGN9	IGLO5_HUMAN	Q	257	ENSP00000270642:L257Q	ENSP00000270642:L257Q	L	+	2	0	IGLON5	56522800	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.553000	0.67287	1.982000	0.57802	0.455000	0.32223	CTG	.	.		0.692	IGLON5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335149.1	NM_001101372		A	51830988	T	A	51830988	3	1	76	1	0	0	0	0	1	0	0	0	7604	1580	55	4	796	4	IGLON5	19	51830988	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	200604	51830988	7297995	298	10569										
SIGLEC10	89790	hgsc.bcm.edu	37	chr19	51918290	51918290	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcagagagggggccgggctgGcctgggaggagcagctgcag	22	9	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:51918290G>T	ENST00000339313.5	-	8	1519	c.1403C>A	c.(1402-1404)gCc>gAc	p.A468D	SIGLEC10_ENST00000441969.3_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000353836.5_Intron|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000432469.2_Intron|SIGLEC10_ENST00000525998.1_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000436984.2_Intron|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.A410D|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.A468D			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	468					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		GGCCGGGCTGGCCTGGGAGGA	0.701																																					p.A468D		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C1403A						.						10	12	11					19																	51918290		2180	4253	6433	SO:0001583	missense	89790	exon8			GGGCTGGCCTGGG	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15620	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 10 Ig-like lectin 7", "siglec-like gene 2"	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.1403C>A	chr19.hg19:g.51918290G>T	ENSP00000345243:p.Ala468Asp	35.0	0.0		54.0	7.0	NM_033130	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	hg19	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	11.85	1.761401	0.31228	.	.	ENSG00000142512	ENST00000356298;ENST00000439889;ENST00000339313	D;D;D	0.85702	-2.02;-2.02;-2.02	4.83	3.78	0.43462	.	0.000000	0.56097	D	0.000028	D	0.92496	0.7617	M	0.88181	2.935	0.09310	N	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.991;0.999	D	0.85652	0.1283	10	0.87932	D	0	.	11.0884	0.48102	0.0:0.188:0.812:0.0	.	410;468	Q96LC7-3;Q96LC7	.;SIG10_HUMAN	D	468;410;468	ENSP00000348646:A468D;ENSP00000389132:A410D;ENSP00000345243:A468D	ENSP00000345243:A468D	A	-	2	0	SIGLEC10	56610102	0.686000	0.27661	0.126000	0.21872	0.004000	0.04260	2.994000	0.49433	1.020000	0.39573	0.561000	0.74099	GCC	.	.		0.701	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		T	51918290	G	T	51918290	3	4	76	1	0	0	0	0	1	0	0	0	14321	1203	42	3	706	3	SIGLEC10	19	51918290	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	87302	51918290	7210693	299	10570										
ZNF578	147660	hgsc.bcm.edu	37	chr19	53013987	53013987	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgactttgagtttcagtcacAaaaagatgaaagaaatggcc	9	6	2	5			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:53013987A>G	ENST00000421239.2	+	6	597	c.353A>G	c.(352-354)cAa>cGa	p.Q118R	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	118					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		TTTCAGTCACAAAAAGATGAA	0.398																																					p.Q118R		Atlas-SNP	.											.,1	.	.	.	0			c.A353G						.						99	104	102					19																	53013987		2201	4300	6501	SO:0001583	missense	147660	exon6			AGTCACAAAAAGA	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.353A>G	chr19.hg19:g.53013987A>G	ENSP00000459216:p.Gln118Arg	175.0	0.0		191.0	58.0	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	hg19	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	1.815	-0.473611	0.04414	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.72	-3.43	0.04810	.	.	.	.	.	T	0.26882	0.0658	N	0.17723	0.515	0.09310	N	1	D	0.57899	0.981	D	0.67900	0.954	T	0.12319	-1.0552	7	.	.	.	.	0.2444	0.00196	0.3715:0.2054:0.217:0.206	.	118	G3V4F6	.	R	118	.	.	Q	+	2	0	ZNF578	57705799	0.000000	0.05858	0.001000	0.08648	0.277000	0.26821	-1.667000	0.01961	-0.679000	0.05217	0.113000	0.15668	CAA	.	.		0.398	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		G	53013987	A	G	53013987	3	3	76	1	0	0	0	0	1	0	0	0	18025	130	5	2	363	2	ZNF578	19	53013987	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	1095697	53013987	6114996	300	10571										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53645692	53645692	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttttctggacttccctgaagGaacatccttcaatgtcttgg	8	10	3	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:53645692G>T	ENST00000334197.7	-	5	457	c.389C>A	c.(388-390)tCc>tAc	p.S130Y	ZNF347_ENST00000452676.2_Missense_Mutation_p.S131Y|ZNF347_ENST00000601469.2_Missense_Mutation_p.S131Y|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	130					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		TTCCCTGAAGGAACATCCTTC	0.403																																					p.S131Y	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.C392A						.						129	110	116					19																	53645692		2203	4299	6502	SO:0001583	missense	84671	exon5			CTGAAGGAACATC	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.389C>A	chr19.hg19:g.53645692G>T	ENSP00000334146:p.Ser130Tyr	71.0	0.0		85.0	10.0	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	hg19	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.979416	0.00448	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.07114	3.23;3.22	2.64	-3.02	0.05446	.	.	.	.	.	T	0.02688	0.0081	N	0.08118	0	0.09310	N	1	P;B	0.37207	0.587;0.183	B;B	0.36922	0.236;0.054	T	0.32134	-0.9918	9	0.02654	T	1	.	3.7249	0.08470	0.3157:0.0:0.4528:0.2315	.	131;130	G5E9N4;Q96SE7	.;ZN347_HUMAN	Y	130;131	ENSP00000334146:S130Y;ENSP00000405218:S131Y	ENSP00000334146:S130Y	S	-	2	0	ZNF347	58337504	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.894000	0.00707	-0.156000	0.11079	-0.244000	0.11960	TCC	.	.		0.403	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		T	53645692	G	T	53645692	3	4	76	1	0	0	0	0	1	0	0	0	17876	1174	41	3	2134	3	ZNF347	19	53645692	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	631705	53645692	5483291	301	10572										
VSTM1	284415	hgsc.bcm.edu	37	chr19	54561741	54561741	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tcgttcaccttgcgcagcacAaatgtcacattctgggaatg	9	11	3	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr19:54561741A>T	ENST00000338372.2	-	3	349	c.174T>A	c.(172-174)ttT>ttA	p.F58L	VSTM1_ENST00000376626.1_Missense_Mutation_p.F58L|VSTM1_ENST00000366170.2_Intron|VSTM1_ENST00000425006.2_Missense_Mutation_p.F58L	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	58	Ig-like V-type.				immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		TGCGCAGCACAAATGTCACAT	0.567																																					p.F58L		Atlas-SNP	.											.	VSTM1	30	.	0			c.T174A						.						138	129	132					19																	54561741		2203	4300	6503	SO:0001583	missense	284415	exon3			CAGCACAAATGTC	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.174T>A	chr19.hg19:g.54561741A>T	ENSP00000343366:p.Phe58Leu	122.0	0.0		133.0	17.0	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Missense_Mutation	SNP	ENST00000338372.2	hg19	CCDS12872.1	.	.	.	.	.	.	.	.	.	.	A	16.25	3.069137	0.55539	.	.	ENSG00000189068	ENST00000338372;ENST00000376626;ENST00000425006	T;T;T	0.11821	2.74;2.74;2.74	3.49	1.34	0.21922	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.401900	0.15870	N	0.240598	T	0.26340	0.0643	M	0.84948	2.725	0.09310	N	1	P;P	0.46395	0.877;0.877	P;P	0.51615	0.675;0.675	T	0.06338	-1.0832	9	.	.	.	-5.0435	5.1123	0.14815	0.2773:0.0:0.7227:0.0	.	58;58	D2DJS4;Q6UX27	.;VSTM1_HUMAN	L	58	ENSP00000343366:F58L;ENSP00000365813:F58L;ENSP00000413006:F58L	.	F	-	3	2	VSTM1	59253553	0.011000	0.17503	0.007000	0.13788	0.014000	0.08584	0.420000	0.21263	0.825000	0.34637	-0.375000	0.07067	TTT	.	.		0.567	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481		T	54561741	A	T	54561741	3	4	76	1	0	0	0	0	1	0	0	0	17243	127	5	4	564	4	VSTM1	19	54561741	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	916049	54561741	4567242	302	10573										
PTPRA	5786	hgsc.bcm.edu	37	chr20	2987988	2987988	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	atattgttggtttgtttcctAgatgaccactctagagtcca	8	8	1	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr20:2987988A>T	ENST00000216877.6	+	10	1202		c.e10-1		PTPRA_ENST00000399903.2_Splice_Site|PTPRA_ENST00000356147.3_Splice_Site|PTPRA_ENST00000425918.2_Splice_Site|PTPRA_ENST00000358719.4_Splice_Site|PTPRA_ENST00000318266.5_Splice_Site|PTPRA_ENST00000380393.3_Splice_Site	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A						axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TTTGTTTCCTAGATGACCACT	0.433																																					.		Atlas-SNP	.											.	PTPRA	75	.	0			c.830-2A>T						.						155	146	149					20																	2987988		2203	4300	6503	SO:0001630	splice_region_variant	5786	exon15			TTTCCTAGATGAC		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.803-1A>T	chr20.hg19:g.2987988A>T		50.0	0.0		41.0	9.0	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Splice_Site	SNP	ENST00000216877.6	hg19	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.452151	0.84209	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000425918;ENST00000318266;ENST00000356147	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5026	0.75713	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTPRA	2935988	1.000000	0.71417	0.964000	0.40570	0.875000	0.50365	8.058000	0.89460	2.202000	0.70862	0.533000	0.62120	.	.	.		0.433	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3		Intron	T	2987988	A	T	2987988	5	4	76	1	0	0	0	0	0	0	1	0	12810	434	15	4	858	4	PTPRA	20	2987988	Splice_Site	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10		2987988	60037532	303	10574										
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3674260	3674260	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	catgtgtaggtgagctgggcCgggtgagtggtccacacaag	17	8	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr20:3674260C>A	ENST00000344754.4	-	13	3341	c.3342G>T	c.(3340-3342)ccG>ccT	p.P1114P	SIGLEC1_ENST00000202578.4_Silent_p.P1114P	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1114	Ig-like C2-type 11.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						TGAGCTGGGCCGGGTGAGTGG	0.657																																					p.P1114P		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.G3342T						.						72	50	58					20																	3674260		2203	4300	6503	SO:0001819	synonymous_variant	6614	exon13			CTGGGCCGGGTGA	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.3342G>T	chr20.hg19:g.3674260C>A		57.0	0.0		37.0	8.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	hg19	CCDS13060.1																																																																																			.	.		0.657	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		A	3674260	C	A	3674260	2	1	76	1	0	0	0	0	0	0	0	1	14320	639	23	1		1	SIGLEC1	20	3674260	Silent	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	686272	3674260	59351260	304	10575										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9364907	9364907	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cagatgaaaacgccccagtcTtcctagatcgtttagaactt	7	11	1	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr20:9364907T>A	ENST00000378493.1	+	11	928	c.913T>A	c.(913-915)Ttc>Atc	p.F305I	PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378501.2_Missense_Mutation_p.F305I|PLCB4_ENST00000278655.4_Missense_Mutation_p.F305I|PLCB4_ENST00000334005.3_Missense_Mutation_p.F305I|PLCB4_ENST00000414679.2_Missense_Mutation_p.F305I|PLCB4_ENST00000378473.3_Missense_Mutation_p.F305I			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	305					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						CGCCCCAGTCTTCCTAGATCG	0.433																																					p.F305I		Atlas-SNP	.											.	PLCB4	204	.	0			c.T913A						.						178	169	172					20																	9364907		2203	4300	6503	SO:0001583	missense	5332	exon12			CCAGTCTTCCTAG		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.913T>A	chr20.hg19:g.9364907T>A	ENSP00000367754:p.Phe305Ile	80.0	0.0		81.0	23.0	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	hg19	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	T	32	5.166947	0.94768	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	T;T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3;2.3	5.93	5.93	0.95920	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.42381	0.1200	M	0.78637	2.42	0.80722	D	1	D;P;D;D	0.71674	0.998;0.795;0.985;0.997	D;B;D;D	0.72338	0.959;0.443;0.977;0.931	T	0.21930	-1.0231	10	0.22706	T	0.39	.	16.3756	0.83387	0.0:0.0:0.0:1.0	.	305;152;305;305	E2QRH8;Q15147-2;Q15147;Q15147-4	.;.;PLCB4_HUMAN;.	I	305;305;305;305;305;141	ENSP00000334105:F305I;ENSP00000367734:F305I;ENSP00000278655:F305I;ENSP00000367754:F305I;ENSP00000367762:F305I;ENSP00000390616:F141I	ENSP00000278655:F305I	F	+	1	0	PLCB4	9312907	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.984000	0.70548	2.270000	0.75569	0.460000	0.39030	TTC	.	.		0.433	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			A	9364907	T	A	9364907	3	1	76	1	0	0	0	0	1	0	0	0	12039	1609	56	4	955	4	PLCB4	20	9364907	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	5690647	9364907	53660613	305	10576										
TNNC2	7125	hgsc.bcm.edu	37	chr20	44453043	44453043	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctcgaagtcgatggtgccgcTgcctgcgggcagcaggtggc	17	12	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr20:44453043T>G	ENST00000372555.3	-	4	294	c.202A>C	c.(202-204)Agc>Cgc	p.S68R	TNNC2_ENST00000372557.1_Missense_Mutation_p.S53R	NM_003279.2	NP_003270.1	P02585	TNNC2_HUMAN	troponin C type 2 (fast)	68	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				muscle filament sliding (GO:0030049)|regulation of muscle contraction (GO:0006937)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(115;0.0122)			Felodipine(DB01023)	ATGGTGCCGCTGCCTGCGGGC	0.657																																					p.S68R		Atlas-SNP	.											.	TNNC2	12	.	0			c.A202C						.						66	59	62					20																	44453043		2203	4300	6503	SO:0001583	missense	7125	exon4			TGCCGCTGCCTGC		CCDS13375.1	20q12-q13.11	2013-01-10	2005-09-12		ENSG00000101470	ENSG00000101470		"EF-hand domain containing"	11944	protein-coding gene	gene with protein product		191039	"troponin C2, fast"			2373703	Standard	NM_003279		Approved		uc002xpr.3	P02585	OTTHUMG00000032623	ENST00000372555.3:c.202A>C	chr20.hg19:g.44453043T>G	ENSP00000361636:p.Ser68Arg	40.0	0.0		33.0	20.0	NM_003279	Q6FH92	Missense_Mutation	SNP	ENST00000372555.3	hg19	CCDS13375.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.163407	0.78226	.	.	ENSG00000101470	ENST00000372557;ENST00000372555	T;T	0.79749	-1.3;-1.3	4.49	4.49	0.54785	EF-hand-like domain (1);	0.083853	0.85682	D	0.000000	D	0.86192	0.5874	L	0.54863	1.705	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	D	0.87529	0.2451	10	0.87932	D	0	-30.5273	12.7774	0.57457	0.0:0.0:0.0:1.0	.	68	P02585	TNNC2_HUMAN	R	53;68	ENSP00000361638:S53R;ENSP00000361636:S68R	ENSP00000361636:S68R	S	-	1	0	TNNC2	43886450	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	7.863000	0.87023	1.892000	0.54788	0.455000	0.32223	AGC	.	.		0.657	TNNC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079524.3	NM_003279		G	44453043	T	G	44453043	3	3	76	1	0	0	0	0	1	0	0	0	16340	1580	55	5	292	5	TNNC2	20	44453043	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	35088136	44453043	18572477	306	10577										
ZNF334	55713	hgsc.bcm.edu	37	chr20	45130957	45130957	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cttctcccctgtgtgtgaccTgaaatgttcagccagggctg	11	12	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr20:45130957T>A	ENST00000347606.4	-	5	1203	c.1021A>T	c.(1021-1023)Agg>Tgg	p.R341W	ZNF334_ENST00000457685.2_Missense_Mutation_p.R303W|ZNF334_ENST00000593880.1_Missense_Mutation_p.R364W	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	341					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				GTGTGTGACCTGAAATGTTCA	0.433																																					p.R341W		Atlas-SNP	.											.	ZNF334	101	.	0			c.A1021T						.						148	151	150					20																	45130957		2203	4300	6503	SO:0001583	missense	55713	exon5			GTGACCTGAAATG	AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"Zinc fingers, C2H2-type", "-"	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.1021A>T	chr20.hg19:g.45130957T>A	ENSP00000255129:p.Arg341Trp	70.0	0.0		49.0	16.0	NM_018102	Q5T6U2|Q9NVW4	Missense_Mutation	SNP	ENST00000347606.4	hg19	CCDS33480.1	.	.	.	.	.	.	.	.	.	.	T	18.83	3.707875	0.68615	.	.	ENSG00000198185	ENST00000457685;ENST00000347606	T;T	0.25579	1.79;1.79	3.3	2.15	0.27550	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.52092	0.1713	M	0.89030	3	0.36092	D	0.843496	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.61332	-0.7084	9	0.87932	D	0	.	8.0599	0.30627	0.0:0.0:0.205:0.795	.	303;341;364	B3KQ93;Q9HCZ1;Q8N3P8	.;ZN334_HUMAN;.	W	303;341	ENSP00000402582:R303W;ENSP00000255129:R341W	ENSP00000255129:R341W	R	-	1	2	ZNF334	44564364	0.000000	0.05858	0.244000	0.24202	0.986000	0.74619	-0.558000	0.05978	0.419000	0.25927	0.482000	0.46254	AGG	.	.		0.433	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			A	45130957	T	A	45130957	3	1	76	1	0	0	0	0	1	0	0	0	17866	1579	55	4	1025	4	ZNF334	20	45130957	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	677914	45130957	17894563	307	10578										
PREX1	57580	hgsc.bcm.edu	37	chr20	47296240	47296240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gccttgtaggtgccatcgtcGtagcggaagcgatacatcac	12	11	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr20:47296240G>A	ENST00000371941.3	-	12	1510	c.1488C>T	c.(1486-1488)taC>taT	p.Y496Y	PREX1_ENST00000396220.1_Silent_p.Y496Y	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	496	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TGCCATCGTCGTAGCGGAAGC	0.607																																					p.Y496Y		Atlas-SNP	.											.	PREX1	441	.	0			c.C1488T						.						184	139	154					20																	47296240		2203	4300	6503	SO:0001819	synonymous_variant	57580	exon12			ATCGTCGTAGCGG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1488C>T	chr20.hg19:g.47296240G>A		82.0	0.0		86.0	32.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.		0.607	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47296240	G	A	47296240	2	1	76	1	0	0	0	0	0	0	0	1	12488	1140	40	1		1	PREX1	20	47296240	Silent	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	2165283	47296240	15729280	308	10579										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50255968	50255968	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caggatctggtcgccaggggTcctcagctgcatggaagact	14	11	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr20:50255968T>C	ENST00000338821.5	-	15	1846	c.1582A>G	c.(1582-1584)Acc>Gcc	p.T528A	ATP9A_ENST00000402822.1_Missense_Mutation_p.T407A|ATP9A_ENST00000311637.5_Missense_Mutation_p.T392A	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	528					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TCGCCAGGGGTCCTCAGCTGC	0.532											OREG0026043	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T528A		Atlas-SNP	.											.	ATP9A	135	.	0			c.A1582G						.						153	126	135					20																	50255968		2203	4300	6503	SO:0001583	missense	10079	exon15			CAGGGGTCCTCAG	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1582A>G	chr20.hg19:g.50255968T>C	ENSP00000342481:p.Thr528Ala	147.0	0.0	968	144.0	18.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	hg19	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	T	15.65	2.896052	0.52121	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	T;T;T	0.77877	-1.08;-1.13;-1.08	5.32	5.32	0.75619	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.82001	0.4942	L	0.33137	0.985	0.80722	D	1	D;B	0.56035	0.974;0.005	D;B	0.70487	0.969;0.014	T	0.82633	-0.0361	10	0.46703	T	0.11	-41.2446	15.2837	0.73810	0.0:0.0:0.0:1.0	.	407;528	O75110-2;O75110	.;ATP9A_HUMAN	A	392;528;407	ENSP00000309086:T392A;ENSP00000342481:T528A;ENSP00000385875:T407A	ENSP00000309086:T392A	T	-	1	0	ATP9A	49689375	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.937000	0.87672	2.013000	0.59113	0.533000	0.62120	ACC	.	.		0.532	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		C	50255968	T	C	50255968	3	2	76	1	0	0	0	0	1	0	0	0	1198	1667	58	2	1617	2	ATP9A	20	50255968	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	2959728	50255968	12769552	309	10580										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60890246	60890246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cacagccttggcatgtgcgaTcttcttgcttgtctcgtctg	10	12	4	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr20:60890246T>C	ENST00000252999.3	-	59	7951	c.7885A>G	c.(7885-7887)Atc>Gtc	p.I2629V		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2629	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCATGTGCGATCTTCTTGCTT	0.637																																					p.I2629V		Atlas-SNP	.											.	LAMA5	268	.	0			c.A7885G						.						36	37	36					20																	60890246		2196	4288	6484	SO:0001583	missense	3911	exon59			GTGCGATCTTCTT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7885A>G	chr20.hg19:g.60890246T>C	ENSP00000252999:p.Ile2629Val	46.0	0.0		21.0	8.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	t	15.63	2.891056	0.52014	.	.	ENSG00000130702	ENST00000252999	T	0.20200	2.09	4.02	2.87	0.33458	.	0.113197	0.56097	U	0.000025	T	0.17152	0.0412	L	0.44542	1.39	0.80722	D	1	B	0.26363	0.147	B	0.24701	0.055	T	0.04413	-1.0953	10	0.39692	T	0.17	.	9.2461	0.37527	0.0:0.0:0.183:0.817	.	2629	O15230	LAMA5_HUMAN	V	2629	ENSP00000252999:I2629V	ENSP00000252999:I2629V	I	-	1	0	LAMA5	60323641	0.016000	0.18221	0.963000	0.40424	0.649000	0.38597	0.544000	0.23253	0.403000	0.25479	0.375000	0.23000	ATC	.	.		0.637	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		C	60890246	T	C	60890246	3	2	76	1	0	0	0	0	1	0	0	0	8618	1435	50	2	3290	2	LAMA5	20	60890246	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	10634278	60890246	2135274	310	10581										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61512777	61512777	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	cgacaccgagaagtgggccaTggagaccccgacggcggccc	15	15	0	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr20:61512777T>C	ENST00000266070.4	-	16	4856	c.4531A>G	c.(4531-4533)Atg>Gtg	p.M1511V	DIDO1_ENST00000395343.1_Missense_Mutation_p.M1511V	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1511					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					AAGTGGGCCATGGAGACCCCG	0.577																																					p.M1511V	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.A4531G						.						95	94	94					20																	61512777		2203	4300	6503	SO:0001583	missense	11083	exon16			GGGCCATGGAGAC	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.4531A>G	chr20.hg19:g.61512777T>C	ENSP00000266070:p.Met1511Val	33.0	0.0		33.0	5.0	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.392700	0.83011	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.09163	3.01;3.01	5.69	5.69	0.88448	.	0.000000	0.52532	D	0.000073	T	0.26593	0.0650	M	0.77820	2.39	0.80722	D	1	D	0.56521	0.976	P	0.52109	0.69	T	0.01869	-1.1257	10	0.52906	T	0.07	-43.8188	15.9481	0.79809	0.0:0.0:0.0:1.0	.	1511	Q9BTC0	DIDO1_HUMAN	V	1511	ENSP00000266070:M1511V;ENSP00000378752:M1511V	ENSP00000266070:M1511V	M	-	1	0	DIDO1	60983222	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	5.771000	0.68881	2.153000	0.67306	0.533000	0.62120	ATG	.	.		0.577	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		C	61512777	T	C	61512777	3	2	76	1	0	0	0	0	1	0	0	0	4524	1464	51	2	2195	2	DIDO1	20	61512777	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	622531	61512777	1512743	311	10582										
PRPF6	57473	hgsc.bcm.edu	37	chr20	62612637	62612637	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccgttcctagggatgcccgcGcccctcggctacgtgccggg	14	17	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr20:62612637G>T	ENST00000450537.1	-	2	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Silent_p.A13A|SAMD10_ENST00000498830.1_5'Flank|SAMD10_ENST00000369886.3_5'Flank			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GGATGCCCGCGCCCCTCGGCT	0.677																																					p.A13A		Atlas-SNP	.											.	PRPF6	88	.	0			c.G39T						.						20	20	20					20																	62612637		2191	4286	6477	SO:0001627	intron_variant	24148	exon1			GCCCGCGCCCCTC	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.5-13329C>A	chr20.hg19:g.62612637G>T		110.0	0.0		112.0	66.0	NM_012469	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	.		0.677	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		T	62612637	G	T	62612637	1	4	76	0	1	0	0	0	0	0	0	0	12586	1074	38	1		1	PRPF6	20	62612637	Intron	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	1099860	62612637	412883	312	10583										
LIPI	149998	hgsc.bcm.edu	37	chr21	15537598	15537598	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	acagtccacacataagctagTcttgtaatctttgtatgaac	6	9	2	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr21:15537598T>A	ENST00000536861.1	-	6	846	c.847A>T	c.(847-849)Act>Tct	p.T283S	LIPI_ENST00000344577.2_Missense_Mutation_p.T304S			Q6XZB0	LIPI_HUMAN	lipase, member I	283					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		CATAAGCTAGTCTTGTAATCT	0.338																																					p.T304S		Atlas-SNP	.											.	LIPI	95	.	0			c.A910T						.						95	92	93					21																	15537598		2203	4300	6503	SO:0001583	missense	149998	exon6			AGCTAGTCTTGTA	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.847A>T	chr21.hg19:g.15537598T>A	ENSP00000440381:p.Thr283Ser	103.0	0.0		59.0	32.0	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.301|8.301	0.819954|0.819954	0.16678|0.16678	.|.	.|.	ENSG00000188992|ENSG00000188992	ENST00000400211|ENST00000344577;ENST00000536861;ENST00000382981	.|D;D	.|0.89746	.|-2.56;-2.56	5.73|5.73	-0.758|-0.758	0.11049|0.11049	.|.	.|1.158660	.|0.06041	.|N	.|0.654905	T|T	0.71736|0.71736	0.3375|0.3375	N|N	0.02665|0.02665	-0.54|-0.54	0.09310|0.09310	N|N	1|1	.|B;B	.|0.10296	.|0.003;0.001	.|B;B	.|0.11329	.|0.006;0.006	T|T	0.58233|0.58233	-0.7672|-0.7672	5|10	.|0.10636	.|T	.|0.68	.|.	9.3844|9.3844	0.38333|0.38333	0.0:0.3968:0.0:0.6032|0.0:0.3968:0.0:0.6032	.|.	.|253;304	.|G1JSG6;Q6XZB0-2	.|.;.	V|S	132|304;283;148	.|ENSP00000343331:T304S;ENSP00000440381:T283S	.|ENSP00000343331:T304S	D|T	-|-	2|1	0|0	LIPI|LIPI	14459469|14459469	0.003000|0.003000	0.15002|0.15002	0.206000|0.206000	0.23566|0.23566	0.911000|0.911000	0.54048|0.54048	0.568000|0.568000	0.23623|0.23623	-0.276000|-0.276000	0.09206|0.09206	-0.274000|-0.274000	0.10170|0.10170	GAC|ACT	.	.		0.338	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		A	15537598	T	A	15537598	3	1	76	1	0	0	0	0	1	0	0	0	8834	1667	58	4	555	4	LIPI	21	15537598	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10		15537598	32592297	313	10584										
LIPI	149998	hgsc.bcm.edu	37	chr21	15537634	15537634	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tgaacgacaaggaaatgaaaTaaaattgcagtttgtttcta	8	4	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr21:15537634T>G	ENST00000536861.1	-	6	810	c.811A>C	c.(811-813)Att>Ctt	p.I271L	LIPI_ENST00000344577.2_Missense_Mutation_p.I292L			Q6XZB0	LIPI_HUMAN	lipase, member I	271					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		GGAAATGAAATAAAATTGCAG	0.353																																					p.I292L		Atlas-SNP	.											.	LIPI	95	.	0			c.A874C						.						86	86	86					21																	15537634		2203	4299	6502	SO:0001583	missense	149998	exon6			ATGAAATAAAATT	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.811A>C	chr21.hg19:g.15537634T>G	ENSP00000440381:p.Ile271Leu	103.0	0.0		61.0	38.0	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.17|14.17	2.456127|2.456127	0.43634|0.43634	.|.	.|.	ENSG00000188992|ENSG00000188992	ENST00000344577;ENST00000536861;ENST00000382981|ENST00000400211	D;D|.	0.90324|.	-2.65;-2.65|.	5.73|5.73	2.22|2.22	0.28083|0.28083	.|.	0.360153|.	0.32563|.	N|.	0.005923|.	T|T	0.25865|0.25865	0.0630|0.0630	N|N	0.25890|0.25890	0.77|0.77	0.20307|0.20307	N|N	0.999916|0.999916	B;B|.	0.31383|.	0.321;0.321|.	B;B|.	0.34652|.	0.187;0.132|.	T|T	0.23154|0.23154	-1.0196|-1.0196	10|5	0.14656|.	T|.	0.56|.	.|.	7.4006|7.4006	0.26962|0.26962	0.0:0.2458:0.0:0.7542|0.0:0.2458:0.0:0.7542	.|.	241;292|.	G1JSG6;Q6XZB0-2|.	.;.|.	L|S	292;271;136|120	ENSP00000343331:I292L;ENSP00000440381:I271L|.	ENSP00000343331:I292L|.	I|Y	-|-	1|2	0|0	LIPI|LIPI	14459505|14459505	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.067000|1.067000	0.30616|0.30616	0.204000|0.204000	0.20548|0.20548	0.528000|0.528000	0.53228|0.53228	ATT|TAT	.	.		0.353	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		G	15537634	T	G	15537634	3	3	76	1	0	0	0	0	1	0	0	0	8834	1406	49	5	591	5	LIPI	21	15537634	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	36	15537634	32592261	314	10585										
ABCG1	9619	hgsc.bcm.edu	37	chr21	43646020	43646020	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gaaggaccctggtggaggaaGaaaggtagggagggcggctg	21	5	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr21:43646020G>T	ENST00000361802.2	+	2	427	c.282G>T	c.(280-282)aaG>aaT	p.K94N	ABCG1_ENST00000398449.3_Missense_Mutation_p.K94N|ABCG1_ENST00000398457.2_Missense_Mutation_p.K96N|ABCG1_ENST00000343687.3_Missense_Mutation_p.K105N|ABCG1_ENST00000462050.1_3'UTR|ABCG1_ENST00000347800.2_Missense_Mutation_p.K91N	NM_004915.3	NP_004906.3	P45844	ABCG1_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 1	94	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				amyloid precursor protein catabolic process (GO:0042987)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|detection of hormone stimulus (GO:0009720)|glycoprotein transport (GO:0034436)|high-density lipoprotein particle remodeling (GO:0034375)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of cholesterol efflux (GO:0010875)|regulation of cholesterol esterification (GO:0010872)|regulation of transcription, DNA-templated (GO:0006355)|response to high density lipoprotein particle (GO:0055099)|response to lipid (GO:0033993)|response to organic substance (GO:0010033)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|glycoprotein transporter activity (GO:0034437)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sterol-transporting ATPase activity (GO:0034041)|toxin transporter activity (GO:0019534)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(3)|prostate(2)|stomach(1)	29					Adenosine triphosphate(DB00171)	GGTGGAGGAAGAAAGGTAGGG	0.567																																					p.K105N		Atlas-SNP	.											.	ABCG1	140	.	0			c.G315T						.						58	66	63					21																	43646020		2203	4300	6503	SO:0001583	missense	9619	exon2			GAGGAAGAAAGGT	U34919	CCDS13681.1, CCDS13682.1, CCDS13683.1, CCDS42937.1, CCDS42938.1	21q22.3	2012-03-14			ENSG00000160179	ENSG00000160179		"ATP binding cassette transporters / subfamily G"	73	protein-coding gene	gene with protein product	"ATP-binding cassette transporter 8"	603076				8659545, 16870176	Standard	NM_016818		Approved	ABC8	uc002zaq.3	P45844	OTTHUMG00000086791	ENST00000361802.2:c.282G>T	chr21.hg19:g.43646020G>T	ENSP00000354995:p.Lys94Asn	64.0	0.0		31.0	24.0	NM_207174	Q86SU8|Q96L76|Q9BXK6|Q9BXK7|Q9BXK8|Q9BXK9|Q9BXL0|Q9BXL1|Q9BXL2|Q9BXL3|Q9BXL4	Missense_Mutation	SNP	ENST00000361802.2	hg19	CCDS13682.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.220676	0.58560	.	.	ENSG00000160179	ENST00000398457;ENST00000347800;ENST00000450121;ENST00000398449;ENST00000361802;ENST00000343687	D;D;D;D;D;D	0.86627	-2.15;-2.14;-1.84;-2.14;-2.11;-2.15	4.99	4.11	0.48088	ABC transporter-like (1);	.	.	.	.	T	0.78780	0.4337	L	0.33245	0.995	0.80722	D	1	P;B;B;B;B;B	0.36660	0.564;0.081;0.301;0.065;0.071;0.081	B;B;B;B;B;B	0.34242	0.168;0.02;0.178;0.03;0.073;0.094	T	0.74509	-0.3642	8	.	.	.	.	10.8834	0.46953	0.1525:0.0:0.8475:0.0	.	105;105;94;94;91;96	B4DPT7;P45844-2;P45844;P45844-4;P45844-5;P45844-3	.;.;ABCG1_HUMAN;.;.;.	N	96;91;94;94;94;105	ENSP00000381475:K96N;ENSP00000291524:K91N;ENSP00000414541:K94N;ENSP00000381467:K94N;ENSP00000354995:K94N;ENSP00000339744:K105N	.	K	+	3	2	ABCG1	42519089	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.261000	0.58841	1.234000	0.43709	0.561000	0.74099	AAG	.	.		0.567	ABCG1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195318.2	NM_207174		T	43646020	G	T	43646020	3	4	76	1	0	0	0	0	1	0	0	0	68	933	33	3	456	3	ABCG1	21	43646020	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	28108386	43646020	4483875	315	10586										
MLC1	23209	hgsc.bcm.edu	37	chr22	50506909	50506909	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	catctccacgattctcatgaTgctgaatgacagatatccag	7	11	2	4			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chr22:50506909T>G	ENST00000311597.5	-	10	1453	c.847A>C	c.(847-849)Atc>Ctc	p.I283L	MLC1_ENST00000535444.1_Missense_Mutation_p.I204L|MLC1_ENST00000450140.2_Missense_Mutation_p.I231L|MLC1_ENST00000431262.2_Missense_Mutation_p.I253L|MLC1_ENST00000538737.1_Missense_Mutation_p.I249L|MLC1_ENST00000395876.2_Missense_Mutation_p.I283L|MLC1_ENST00000483836.1_5'UTR	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	283					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		ATTCTCATGATGCTGAATGAC	0.502																																					p.I283L		Atlas-SNP	.											.	MLC1	48	.	0			c.A847C						.						117	117	117					22																	50506909		2203	4300	6503	SO:0001583	missense	23209	exon10			TCATGATGCTGAA	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.847A>C	chr22.hg19:g.50506909T>G	ENSP00000310375:p.Ile283Leu	114.0	0.0		50.0	34.0	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	hg19	CCDS14083.1	.	.	.	.	.	.	.	.	.	.	T	8.730	0.916523	0.17907	.	.	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140	D;D;D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14;-2.14;-2.14	4.63	-5.71	0.02413	.	0.350237	0.27595	N	0.018673	T	0.79482	0.4453	L	0.48642	1.525	0.09310	N	0.999999	B;B;B;B	0.15930	0.015;0.015;0.015;0.004	B;B;B;B	0.15870	0.012;0.012;0.014;0.012	T	0.64888	-0.6301	10	0.66056	D	0.02	-14.5954	12.7472	0.57287	0.0:0.1848:0.0:0.8152	.	249;253;231;283	F5H1B9;B7Z659;B7Z1X1;Q15049	.;.;.;MLC1_HUMAN	L	283;283;249;253;204;231	ENSP00000379216:I283L;ENSP00000310375:I283L;ENSP00000445805:I249L;ENSP00000415877:I253L;ENSP00000438910:I204L;ENSP00000412448:I231L	ENSP00000310375:I283L	I	-	1	0	MLC1	48849036	0.991000	0.36638	0.006000	0.13384	0.002000	0.02628	0.691000	0.25467	-0.903000	0.03881	-1.006000	0.02489	ATC	.	.		0.502	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166		G	50506909	T	G	50506909	3	3	76	1	0	0	0	0	1	0	0	0	9621	1464	51	5	298	5	MLC1	22	50506909	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10		50506909	797657	316	10587										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3240280	3240280	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tccttctcccgttgggtctcCttcgagaagggtgagtgctc	12	12	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:3240280C>A	ENST00000217939.6	-	5	3600	c.3446G>T	c.(3445-3447)aGg>aTg	p.R1149M		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1149						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GTTGGGTCTCCTTCGAGAAGG	0.512																																					p.R1149M		Atlas-SNP	.											.	MXRA5	815	.	0			c.G3446T						.						121	112	115					X																	3240280		2203	4300	6503	SO:0001583	missense	25878	exon5			GGTCTCCTTCGAG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.3446G>T	chrX.hg19:g.3240280C>A	ENSP00000217939:p.Arg1149Met	108.0	0.0		79.0	65.0	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	c	10.65	1.408504	0.25378	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.70749	-0.51	3.61	0.371	0.16168	.	0.159238	0.28659	U	0.014570	T	0.58452	0.2123	N	0.19112	0.55	0.09310	N	1	D	0.63046	0.992	P	0.49561	0.615	T	0.56727	-0.7931	10	0.66056	D	0.02	.	8.6847	0.34229	0.0:0.6362:0.0:0.3638	.	1149	Q9NR99	MXRA5_HUMAN	M	1149	ENSP00000217939:R1149M	ENSP00000217939:R1149M	R	-	2	0	MXRA5	3250280	0.797000	0.28877	0.000000	0.03702	0.003000	0.03518	0.262000	0.18460	-0.429000	0.07329	0.519000	0.50382	AGG	.	.		0.512	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3240280	C	A	3240280	3	1	76	1	0	0	0	0	1	0	0	0	10012	681	24	3	5052	3	MXRA5	23	3240280	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10		3240280	152030280	317	10588										
KAL1	3730	hgsc.bcm.edu	37	chrX	8503725	8503725	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gcccaagtcacttgaaacccAgtcatgggctgatagagatt	10	10	2	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:8503725A>T	ENST00000262648.3	-	12	1898	c.1749T>A	c.(1747-1749)acT>acA	p.T583T	KAL1_ENST00000481896.1_5'UTR	NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	583	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						CTTGAAACCCAGTCATGGGCT	0.502																																					p.T583T		Atlas-SNP	.											.	KAL1	78	.	0			c.T1749A						.						121	92	102					X																	8503725		2203	4299	6502	SO:0001819	synonymous_variant	3730	exon12			AAACCCAGTCATG		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"WAP four-disulfide core domain containing", "Fibronectin type III domain containing"	6211	protein-coding gene	gene with protein product	"anosmin-1", "WAP four-disulfide core domain 19"	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.1749T>A	chrX.hg19:g.8503725A>T		170.0	0.0		92.0	37.0	NM_000216	B2RPF8	Silent	SNP	ENST00000262648.3	hg19	CCDS14130.1																																																																																			.	.		0.502	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216		T	8503725	A	T	8503725	2	4	76	1	0	0	0	0	0	0	0	1	7983	175	7	4		4	KAL1	23	8503725	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	5263445	8503725	146766835	318	10589										
DMD	1756	hgsc.bcm.edu	37	chrX	32481605	32481605	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	taagttctttgagttctgtcTcaagtctcgaagcaaactct	7	9	5	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:32481605T>A	ENST00000357033.4	-	25	3589	c.3383A>T	c.(3382-3384)gAg>gTg	p.E1128V	DMD_ENST00000378677.2_Missense_Mutation_p.E1124V	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1128					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GAGTTCTGTCTCAAGTCTCGA	0.428																																					p.E1128V		Atlas-SNP	.											.	DMD	2127	.	0			c.A3383T						.						260	167	199					X																	32481605		2202	4300	6502	SO:0001583	missense	1756	exon25			TCTGTCTCAAGTC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.3383A>T	chrX.hg19:g.32481605T>A	ENSP00000354923:p.Glu1128Val	59.0	0.0		46.0	20.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	T	9.032	0.987577	0.18966	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.53640	0.61;0.61	5.43	5.43	0.79202	.	0.446950	0.15801	U	0.243978	T	0.41834	0.1176	L	0.36672	1.1	0.58432	D	0.999997	B;B;B	0.20368	0.023;0.044;0.029	B;B;B	0.27608	0.049;0.077;0.081	T	0.31194	-0.9952	10	0.56958	D	0.05	.	11.8017	0.52130	0.0:0.0:0.1441:0.8559	.	1120;1128;1124	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	V	1120;1124;1128;1128;1005	ENSP00000367948:E1124V;ENSP00000354923:E1128V	ENSP00000354923:E1128V	E	-	2	0	DMD	32391526	1.000000	0.71417	0.184000	0.23157	0.028000	0.11728	6.110000	0.71535	1.825000	0.53177	0.356000	0.21956	GAG	.	.		0.428	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32481605	T	A	32481605	3	1	76	1	0	0	0	0	1	0	0	0	4582	1551	54	4	8137	4	DMD	23	32481605	Missense_Mutation	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	23977880	32481605	122788955	319	10590										
RBM3	5935	hgsc.bcm.edu	37	chrX	48433627	48433627	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caactttaacaccgacgagcAggcactggaagaccacttca	8	13	1	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:48433627A>T	ENST00000376759.3	+	2	122	c.59A>T	c.(58-60)cAg>cTg	p.Q20L	AC115618.1_ENST00000376775.2_5'Flank|RBM3_ENST00000376755.1_Missense_Mutation_p.Q20L|RBM3_ENST00000354480.2_5'Flank|RBM3_ENST00000430348.2_De_novo_Start_OutOfFrame|RBM3_ENST00000466764.1_3'UTR	NM_006743.4	NP_006734.1	P98179	RBM3_HUMAN	RNA binding motif (RNP1, RRM) protein 3	20	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				positive regulation of translation (GO:0045727)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of translation (GO:0006417)|response to cold (GO:0009409)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						ACCGACGAGCAGGCACTGGAA	0.527											OREG0019765	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q20L		Atlas-SNP	.											.	RBM3	20	.	0			c.A59T						.						83	60	68					X																	48433627		2203	4300	6503	SO:0001583	missense	5935	exon2			ACGAGCAGGCACT	BC006825	CCDS14301.1	Xp11.2	2014-05-19	2004-04-23		ENSG00000102317	ENSG00000102317		"RNA binding motif (RRM) containing"	9900	protein-coding gene	gene with protein product		300027	"RNA binding motif protein 3"			8634703	Standard	NM_006743		Approved	IS1-RNPL	uc004dkf.2	P98179	OTTHUMG00000024121	ENST00000376759.3:c.59A>T	chrX.hg19:g.48433627A>T	ENSP00000365950:p.Gln20Leu	57.0	0.0	954	30.0	13.0	NM_006743		Missense_Mutation	SNP	ENST00000376759.3	hg19	CCDS14301.1	.	.	.	.	.	.	.	.	.	.	A	18.07	3.540966	0.65085	.	.	ENSG00000102317	ENST00000376759;ENST00000376755	D;D	0.85773	-2.03;-2.03	4.74	3.58	0.41010	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.296885	0.22745	U	0.056144	D	0.85022	0.5602	L	0.37750	1.13	0.80722	D	1	D	0.55385	0.971	P	0.59357	0.856	D	0.83595	0.0125	10	0.66056	D	0.02	-5.2225	7.7588	0.28940	0.8983:0.0:0.1017:0.0	.	20	P98179	RBM3_HUMAN	L	20	ENSP00000365950:Q20L;ENSP00000365946:Q20L	ENSP00000365946:Q20L	Q	+	2	0	RBM3	48318571	1.000000	0.71417	0.995000	0.50966	0.335000	0.28730	5.446000	0.66600	0.752000	0.32923	0.417000	0.27973	CAG	.	.		0.527	RBM3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060755.1	NM_006743		T	48433627	A	T	48433627	3	4	76	1	0	0	0	0	1	0	0	0	13144	188	7	4	61	4	RBM3	23	48433627	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	15952022	48433627	106836933	320	10591										
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54783989	54783989	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	caagaggattccaggccccaGgtgtggcatgttgtttcggg	15	9	0	1			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:54783989G>C	ENST00000218436.6	-	8	2547	c.2518C>G	c.(2518-2520)Ctg>Gtg	p.L840V		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	840	Pro-rich.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CCAGGCCCCAGGTGTGGCATG	0.493																																					p.L840V		Atlas-SNP	.											.	.	.	.	0			c.C2518G						.						107	101	103					X																	54783989		2203	4300	6503	SO:0001583	missense	347365	exon8			GCCCCAGGTGTGG	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.2518C>G	chrX.hg19:g.54783989G>C	ENSP00000218436:p.Leu840Val	83.0	0.0		55.0	47.0	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	hg19	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	G	0.045	-1.268525	0.01433	.	.	ENSG00000102313	ENST00000218436	T	0.02395	4.31	3.91	2.1	0.27182	.	9.083100	0.01492	U	0.017158	T	0.01976	0.0062	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.44982	-0.9292	10	0.16896	T	0.51	.	4.129	0.10141	0.2151:0.0:0.6028:0.1822	.	840	Q6UXX5	ITH5L_HUMAN	V	840	ENSP00000218436:L840V	ENSP00000218436:L840V	L	-	1	2	ITIH5L	54800714	0.051000	0.20477	0.001000	0.08648	0.013000	0.08279	0.962000	0.29280	0.061000	0.16311	0.466000	0.42574	CTG	.	.		0.493	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		C	54783989	G	C	54783989	3	2	76	1	0	0	0	0	1	0	0	0	7917	991	35	4	1447	4	ITIH5L	23	54783989	Missense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	6350362	54783989	100486571	321	10592										
RLIM	51132	hgsc.bcm.edu	37	chrX	73812676	73812676	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ccactagaacgtcttgcagaTggctcattttcattctctga	7	11	4	3			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:73812676T>C	ENST00000332687.6	-	4	692	c.474A>G	c.(472-474)ccA>ccG	p.P158P	RLIM_ENST00000349225.2_Silent_p.P158P	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	158					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTCTTGCAGATGGCTCATTTT	0.408																																					p.P158P	Esophageal Squamous(169;1899 1923 14997 18818 32118)	Atlas-SNP	.											.	RLIM	90	.	0			c.A474G						.						143	132	135					X																	73812676		2203	4299	6502	SO:0001819	synonymous_variant	51132	exon5			TGCAGATGGCTCA	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.474A>G	chrX.hg19:g.73812676T>C		105.0	0.0		52.0	43.0	NM_183353	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Silent	SNP	ENST00000332687.6	hg19	CCDS14427.1																																																																																			.	.		0.408	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		C	73812676	T	C	73812676	2	2	76	1	0	0	0	0	0	0	0	1	13405	1451	51	2		2	RLIM	23	73812676	Silent	SNP	T	TCGA-CC-A7IK-01A-12D-A33Q-10	19028687	73812676	81457884	322	10593										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128470	83128470	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ttgatttcctcatgttagtgGgacagtctgatgatgaatcc	10	7	2	4	rs146830604	byFrequency	TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:83128470G>T	ENST00000329312.4	+	4	791	c.754G>T	c.(754-756)Gga>Tga	p.G252*		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	252					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						CATGTTAGTGGGACAGTCTGA	0.308																																					p.G252X		Atlas-SNP	.											.	CYLC1	272	.	0			c.G754T						.						40	37	38					X																	83128470		2195	4291	6486	SO:0001587	stop_gained	1538	exon4			TTAGTGGGACAGT	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.754G>T	chrX.hg19:g.83128470G>T	ENSP00000331556:p.Gly252*	220.0	0.0		110.0	98.0	NM_021118	A0AVQ8|Q5JQQ9	Nonsense_Mutation	SNP	ENST00000329312.4	hg19	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	g	16.29	3.082382	0.55861	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	.	.	.	4.92	-1.13	0.09775	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-1.018	4.3552	0.11174	0.3748:0.3054:0.3198:0.0	.	.	.	.	X	252	.	ENSP00000331556:G252X	G	+	1	0	CYLC1	83015126	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.148000	0.10219	-0.537000	0.06290	0.600000	0.82982	GGA	.	G|0.999;A|0.001		0.308	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		T	83128470	G	T	83128470	4	4	76	1	0	0	0	0	0	1	0	0	4143	1233	43	3	768	3	CYLC1	23	83128470	Nonsense_Mutation	SNP	G	TCGA-CC-A7IK-01A-12D-A33Q-10	9315794	83128470	72142090	323	10594										
RPS6KA6	27330	hgsc.bcm.edu	37	chrX	83352788	83352788	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	tatgtttcttacccagccaaCattgtgtaaaaaaggactcc	6	10	1	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:83352788C>T	ENST00000262752.2	-	19	1852	c.1845G>A	c.(1843-1845)atG>atA	p.M615I	RPS6KA6_ENST00000495332.1_5'UTR|RPS6KA6_ENST00000543399.1_Missense_Mutation_p.M615I	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	615	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						ACCCAGCCAACATTGTGTAAA	0.303																																					p.M615I		Atlas-SNP	.											.	RPS6KA6	116	.	0			c.G1845A						.						122	118	120					X																	83352788		2203	4293	6496	SO:0001583	missense	27330	exon19			AGCCAACATTGTG	AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.1845G>A	chrX.hg19:g.83352788C>T	ENSP00000262752:p.Met615Ile	269.0	2.0		146.0	123.0	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	hg19	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	C	32	5.113361	0.94339	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.41758	0.99;0.99	5.46	5.46	0.80206	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.57359	0.2048	L	0.48986	1.54	0.80722	D	1	D;P	0.57899	0.981;0.931	P;P	0.59703	0.862;0.704	T	0.59989	-0.7350	10	0.72032	D	0.01	.	18.392	0.90486	0.0:1.0:0.0:0.0	.	615;615	B7ZL90;Q9UK32	.;KS6A6_HUMAN	I	615	ENSP00000262752:M615I;ENSP00000440830:M615I	ENSP00000262752:M615I	M	-	3	0	RPS6KA6	83239444	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.548000	0.82154	2.284000	0.76573	0.600000	0.82982	ATG	.	.		0.303	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		T	83352788	C	T	83352788	3	4	76	1	0	0	0	0	1	0	0	0	13670	478	17	3	408	3	RPS6KA6	23	83352788	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	224318	83352788	71917772	324	10595										
ARMCX6	54470	hgsc.bcm.edu	37	chrX	100871178	100871178	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	ctggctaaatggaaagcccgCatccttgggctcggcaaaca	11	12	0	0			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:100871178C>A	ENST00000361910.4	-	3	777	c.433G>T	c.(433-435)Gcg>Tcg	p.A145S	ARMCX6_ENST00000539247.1_Missense_Mutation_p.A145S|ARMCX6_ENST00000497931.1_Intron|ARMCX6_ENST00000538627.1_Missense_Mutation_p.A145S	NM_019007.3	NP_061880.2	Q7L4S7	ARMX6_HUMAN	armadillo repeat containing, X-linked 6	145						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|liver(2)|lung(3)	9						GGAAAGCCCGCATCCTTGGGC	0.478																																					p.A145S		Atlas-SNP	.											.	ARMCX6	21	.	0			c.G433T						.						38	42	40					X																	100871178		2201	4293	6494	SO:0001583	missense	54470	exon4			AGCCCGCATCCTT	BC007677	CCDS14488.1	Xq21.33-q22.3	2014-03-21			ENSG00000198960	ENSG00000198960		"Armadillo repeat containing"	26094	protein-coding gene	gene with protein product						16221301, 22569362	Standard	NM_001184768		Approved	FLJ20811, GASP10	uc004ehy.3	Q7L4S7	OTTHUMG00000022034	ENST00000361910.4:c.433G>T	chrX.hg19:g.100871178C>A	ENSP00000354708:p.Ala145Ser	200.0	0.0		99.0	67.0	NM_001184768	Q9NWJ3	Missense_Mutation	SNP	ENST00000361910.4	hg19	CCDS14488.1	.	.	.	.	.	.	.	.	.	.	.	10.31	1.314640	0.23908	.	.	ENSG00000198960	ENST00000361910;ENST00000539247;ENST00000538627	T;T;T	0.37058	1.22;1.22;1.22	3.91	2.12	0.27331	.	0.000000	0.49916	D	0.000128	T	0.53302	0.1788	M	0.79258	2.445	0.09310	N	0.999999	D	0.76494	0.999	D	0.85130	0.997	T	0.37150	-0.9718	10	0.44086	T	0.13	-6.8423	5.782	0.18312	0.0:0.748:0.0:0.252	.	145	Q7L4S7	ARMX6_HUMAN	S	145	ENSP00000354708:A145S;ENSP00000444537:A145S;ENSP00000440648:A145S	ENSP00000354708:A145S	A	-	1	0	ARMCX6	100757834	0.051000	0.20477	0.005000	0.12908	0.027000	0.11550	0.978000	0.29488	0.449000	0.26747	0.476000	0.43555	GCG	.	.		0.478	ARMCX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057562.1	NM_019007		A	100871178	C	A	100871178	3	1	76	1	0	0	0	0	1	0	0	0	963	710	25	3	473	3	ARMCX6	23	100871178	Missense_Mutation	SNP	C	TCGA-CC-A7IK-01A-12D-A33Q-10	17518390	100871178	54399382	325	10596										
IL13RA2	3598	hgsc.bcm.edu	37	chrX	114244204	114244204	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	gaactctcccgagtaaaagtAagatagactggcggcaaagg	12	8	1	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:114244204A>G	ENST00000371936.1	-	8	981	c.732T>C	c.(730-732)ctT>ctC	p.L244L	IL13RA2_ENST00000243213.1_Silent_p.L244L			Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2	244	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	23						GAGTAAAAGTAAGATAGACTG	0.398																																					p.L244L		Atlas-SNP	.											.	IL13RA2	66	.	0			c.T732C						.						73	67	69					X																	114244204		2203	4300	6503	SO:0001819	synonymous_variant	3598	exon7			AAAAGTAAGATAG	X95302	CCDS14565.1	Xq23	2014-01-21			ENSG00000123496	ENSG00000123496		"Interleukins and interleukin receptors", "CD molecules"	5975	protein-coding gene	gene with protein product	"cancer/testis antigen 19"	300130				8663118, 9083087	Standard	NM_000640		Approved	IL-13R, IL13BP, CD213a2, CT19	uc004epx.3	Q14627	OTTHUMG00000022229	ENST00000371936.1:c.732T>C	chrX.hg19:g.114244204A>G		145.0	0.0		74.0	25.0	NM_000640	A8K7E2|O00667	Silent	SNP	ENST00000371936.1	hg19	CCDS14565.1																																																																																			.	.		0.398	IL13RA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057966.1	NM_000640		G	114244204	A	G	114244204	2	3	76	1	0	0	0	0	0	0	0	1	7639	349	13	2		2	IL13RA2	23	114244204	Silent	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	13373026	114244204	41026356	326	10597										
SAGE1	55511	hgsc.bcm.edu	37	chrX	134986663	134986663	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0214723926380368	7	1	0.947159090909091	0.572458791208791	1.06313775510204	0.087683284457478	0.605664168567394	0	agtcactcacagcatttgtgAagagaggataaataacggcc	10	8	2	2			TCGA-CC-A7IK-01A-12D-A33Q-10	TCGA-CC-A7IK-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93a9dd15-d593-4dcb-bf89-401618ca141b	437320c7-d091-4bee-9776-417b93833127	g.chrX:134986663A>T	ENST00000370709.3	+	3	248	c.248A>T	c.(247-249)gAa>gTa	p.E83V	SAGE1_ENST00000324447.3_Missense_Mutation_p.E83V|SAGE1_ENST00000537770.1_Missense_Mutation_p.E83V|SAGE1_ENST00000535938.1_Missense_Mutation_p.E83V			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	83						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					AGCATTTGTGAAGAGAGGATA	0.468																																					p.E83V		Atlas-SNP	.											.	SAGE1	160	.	0			c.A248T						.						176	143	154					X																	134986663		2203	4300	6503	SO:0001583	missense	55511	exon4			TTTGTGAAGAGAG	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.248A>T	chrX.hg19:g.134986663A>T	ENSP00000359743:p.Glu83Val	197.0	0.0		140.0	53.0	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	hg19	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	A	12.90	2.075079	0.36566	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000537770;ENST00000370709	T;T;T;T	0.36878	1.23;1.23;1.27;1.23	1.65	1.65	0.23941	.	0.204172	0.31531	U	0.007496	T	0.41119	0.1145	L	0.34521	1.04	0.09310	N	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.979;0.999	T	0.07214	-1.0784	10	0.87932	D	0	.	4.8128	0.13351	1.0:0.0:0.0:0.0	.	83;83	F5H2Z8;Q9NXZ1	.;SAGE1_HUMAN	V	83	ENSP00000323191:E83V;ENSP00000445959:E83V;ENSP00000438276:E83V;ENSP00000359743:E83V	ENSP00000323191:E83V	E	+	2	0	SAGE1	134814329	0.539000	0.26402	0.081000	0.20488	0.013000	0.08279	2.529000	0.45632	0.891000	0.36235	0.235000	0.17854	GAA	.	.		0.468	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		T	134986663	A	T	134986663	3	4	76	1	0	0	0	0	1	0	0	0	13824	246	9	4	258	4	SAGE1	23	134986663	Missense_Mutation	SNP	A	TCGA-CC-A7IK-01A-12D-A33Q-10	20742459	134986663	20283897	327	10598										
IL23R	149233	hgsc.bcm.edu	37	chr1	67724414	67724414	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tctgcctgagggaagccatcTcagcaataataatgaaatta	8	8	2	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:67724414T>G	ENST00000347310.5	+	11	1664	c.1493T>G	c.(1492-1494)cTc>cGc	p.L498R	IL23R_ENST00000371002.1_3'UTR|IL23R_ENST00000395227.1_Missense_Mutation_p.L243R|IL23R_ENST00000473881.1_3'UTR	NM_144701.2	NP_653302.2	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor	498					defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|interleukin-23-mediated signaling pathway (GO:0038155)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)	interleukin-23 receptor complex (GO:0072536)|receptor complex (GO:0043235)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	21						GGAAGCCATCTCAGCAATAAT	0.358																																					p.L498R		Atlas-SNP	.											.	IL23R	52	.	0			c.T1493G						.						59	61	60					1																	67724414		2203	4300	6503	SO:0001583	missense	149233	exon11			GCCATCTCAGCAA	AF461422	CCDS637.1	1p31.2	2008-02-05			ENSG00000162594	ENSG00000162594			19100	protein-coding gene	gene with protein product		607562				12023369	Standard	NM_144701		Approved	IL-23R	uc001ddo.3	Q5VWK5	OTTHUMG00000009092	ENST00000347310.5:c.1493T>G	chr1.hg19:g.67724414T>G	ENSP00000321345:p.Leu498Arg	257.0	0.0		169.0	79.0	NM_144701	C9JGX4|Q4VGP1|Q4VGP2|Q4VGP3|Q4VGP4|Q4VGP5|Q4VGP6|Q5VWK7|Q8IW84|Q8NFQ9|Q96AS1	Missense_Mutation	SNP	ENST00000347310.5	hg19	CCDS637.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.98|13.98	2.398180|2.398180	0.42512|0.42512	.|.	.|.	ENSG00000162594|ENSG00000162594	ENST00000347310;ENST00000395227|ENST00000425614	T;T|.	0.34275|.	1.37;1.43|.	5.62|5.62	1.79|1.79	0.24919|0.24919	.|.	0.518502|.	0.18862|.	N|.	0.129107|.	T|T	0.18635|0.18635	0.0447|0.0447	L|L	0.46157|0.46157	1.445|1.445	0.09310|0.09310	N|N	1|1	B;P;D;B;B|.	0.58620|.	0.356;0.496;0.983;0.356;0.091|.	B;B;P;B;B|.	0.56700|.	0.104;0.178;0.804;0.104;0.022|.	T|T	0.18999|0.18999	-1.0319|-1.0319	10|5	0.66056|.	D|.	0.02|.	-19.0109|-19.0109	4.3881|4.3881	0.11327|0.11327	0.0:0.1794:0.17:0.6506|0.0:0.1794:0.17:0.6506	.|.	244;133;96;243;498|.	Q5VWK5-2;Q5VWK5-5;Q5VWK5-7;Q5VWK5-6;Q5VWK5|.	.;.;.;.;IL23R_HUMAN|.	R|A	498;243|260	ENSP00000321345:L498R;ENSP00000378652:L243R|.	ENSP00000321345:L498R|.	L|S	+|+	2|1	0|0	IL23R|IL23R	67497002|67497002	0.000000|0.000000	0.05858|0.05858	0.011000|0.011000	0.14972|0.14972	0.007000|0.007000	0.05969|0.05969	0.279000|0.279000	0.18771|0.18771	0.971000|0.971000	0.38288|0.38288	0.528000|0.528000	0.53228|0.53228	CTC|TCA	.	.		0.358	IL23R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025199.2	NM_144701		G	67724414	T	G	67724414	3	3	77	1	0	0	0	0	1	0	0	0	7685	1551	54	5	1531	5	IL23R	1	67724414	Missense_Mutation	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10		67724414	181526207	1	10599										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79472325	79472325	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gctgagcactcacctaggagCgggaggcgtttcattggcgg	16	10	2	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:79472325C>A	ENST00000370742.3	-	1	78	c.15G>T	c.(13-15)ccG>ccT	p.P5P		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	5					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		CACCTAGGAGCGGGAGGCGTT	0.682																																					p.P5P		Atlas-SNP	.											.	ELTD1	143	.	0			c.G15T						.						13	17	16					1																	79472325		1965	4126	6091	SO:0001819	synonymous_variant	64123	exon1			TAGGAGCGGGAGG	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.15G>T	chr1.hg19:g.79472325C>A		138.0	0.0		178.0	81.0	NM_022159	B1AR71|Q5KU34	Silent	SNP	ENST00000370742.3	hg19	CCDS41352.1																																																																																			.	.		0.682	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		A	79472325	C	A	79472325	2	1	77	1	0	0	0	0	0	0	0	1	5086	755	27	1		1	ELTD1	1	79472325	Silent	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	11747911	79472325	169778296	2	10600										
AGL	178	hgsc.bcm.edu	37	chr1	100356775	100356775	+	Splice_Site	SNP	G	G	T													0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gacatgtctctgaattttcaGgtttaatgtctgtattggca							TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:100356775G>T	ENST00000294724.4	+	22	3290		c.e22-1		AGL_ENST00000361302.3_Splice_Site|AGL_ENST00000370165.3_Splice_Site|AGL_ENST00000370163.3_Splice_Site|AGL_ENST00000370161.2_Splice_Site|AGL_ENST00000361915.3_Splice_Site|AGL_ENST00000361522.4_Splice_Site	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase						carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TGAATTTTCAGGTTTAATGTC	0.368																																					.		Atlas-SNP	.											.	AGL	137	.	0			c.2813-1G>T						.						84	84	84					1																	100356775		2203	4300	6503	SO:0001630	splice_region_variant	178	exon22			TTTTCAGGTTTAA	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.2813-1G>T	chr1.hg19:g.100356775G>T		62.0	0.0		80.0	37.0	NM_000642	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Splice_Site	SNP	ENST00000294724.4	hg19	CCDS759.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.966920	0.34659	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.852	0.96744	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AGL	100129363	1.000000	0.71417	1.000000	0.80357	0.019000	0.09904	8.952000	0.93031	2.703000	0.92315	0.579000	0.79373	.	.	.		0.368	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	Intron	T	100356775	G	T	100356775	5	4	77	1	0	0	0	0	0	0	1	0	384	1014	35	3	2963	3	AGL	1	100356775	Splice_Site	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	20884450	100356775	148893846	3	10601	43	2								
AGL	178	hgsc.bcm.edu	37	chr1	100356784	100356784	+	Missense_Mutation	SNP	T	T	G													0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ctgaattttcaggtttaatgTctgtattggcagaaataaga							TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:100356784T>G	ENST00000294724.4	+	22	3299	c.2821T>G	c.(2821-2823)Tct>Gct	p.S941A	AGL_ENST00000361302.3_Missense_Mutation_p.S925A|AGL_ENST00000370165.3_Missense_Mutation_p.S941A|AGL_ENST00000370163.3_Missense_Mutation_p.S941A|AGL_ENST00000370161.2_Missense_Mutation_p.S925A|AGL_ENST00000361915.3_Missense_Mutation_p.S941A|AGL_ENST00000361522.4_Missense_Mutation_p.S924A	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	941					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		AGGTTTAATGTCTGTATTGGC	0.373																																					p.S941A		Atlas-SNP	.											.	AGL	137	.	0			c.T2821G						.						89	90	89					1																	100356784		2203	4300	6503	SO:0001583	missense	178	exon22			TTAATGTCTGTAT	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.2821T>G	chr1.hg19:g.100356784T>G	ENSP00000294724:p.Ser941Ala	70.0	0.0		86.0	41.0	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	hg19	CCDS759.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.642920	0.47153	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	T;T;T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28;1.28;1.28	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.55705	0.1937	M	0.83223	2.63	0.58432	D	0.999999	D;D;D	0.69078	0.997;0.997;0.995	D;D;D	0.68765	0.96;0.96;0.913	T	0.63413	-0.6643	10	0.66056	D	0.02	.	15.9785	0.80089	0.0:0.0:0.0:1.0	.	924;925;941	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	A	941;941;941;941;925;925;924	ENSP00000355106:S941A;ENSP00000359184:S941A;ENSP00000359182:S941A;ENSP00000294724:S941A;ENSP00000354971:S925A;ENSP00000359180:S925A;ENSP00000354635:S924A	ENSP00000294724:S941A	S	+	1	0	AGL	100129372	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	5.570000	0.67398	2.183000	0.69458	0.472000	0.43445	TCT	.	.		0.373	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		G	100356784	T	G	100356784	3	3	77	1	0	0	0	0	1	0	0	0	384	1667	58	5	2972	5	AGL	1	100356784	Missense_Mutation	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	9	100356784	148893837	4	10602	43	2								
ADORA3	140	hgsc.bcm.edu	37	chr1	112031572	112031572	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ggggtgattcttgtagtgggCattgtagttgcagatggcag	17	4	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:112031572C>A	ENST00000369716.4	-	3	665	c.532G>T	c.(532-534)Gcc>Tcc	p.A178S	ADORA3_ENST00000369717.4_Missense_Mutation_p.A97S|RNU6-792P_ENST00000363490.1_RNA	NM_020683.6	NP_065734.5	P33765	AA3R_HUMAN	adenosine A3 receptor	0					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	TTGTAGTGGGCATTGTAGTTG	0.502																																					p.A178S		Atlas-SNP	.											.	ADORA3	104	.	0			c.G532T						.						217	199	205					1																	112031572		2203	4300	6503	SO:0001583	missense	140	exon3			AGTGGGCATTGTA	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"GPCR / Class A : Adenosine receptors", "Immunoglobulin superfamily / V-set domain containing"	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000369716.4:c.532G>T	chr1.hg19:g.112031572C>A	ENSP00000358730:p.Ala178Ser	237.0	0.0		280.0	128.0	NM_020683	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000369716.4	hg19	CCDS838.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.601|2.601	-0.292967|-0.292967	0.05568|0.05568	.|.	.|.	ENSG00000121933|ENSG00000121933	ENST00000369717;ENST00000369716|ENST00000414219	T;T|.	0.03951|.	3.75;3.75|.	4.85|4.85	-0.947|-0.947	0.10382|0.10382	.|.	0.727104|.	0.12401|.	N|.	0.472129|.	T|T	0.07638|0.07638	0.0192|0.0192	N|N	0.20807|0.20807	0.61|0.61	0.09310|0.09310	N|N	0.999999|0.999999	P;B|.	0.36909|.	0.573;0.419|.	B;B|.	0.38378|.	0.272;0.118|.	T|T	0.37663|0.37663	-0.9696|-0.9696	10|5	0.39692|.	T|.	0.17|.	-7.5827|-7.5827	4.946|4.946	0.13989|0.13989	0.0:0.4504:0.151:0.3986|0.0:0.4504:0.151:0.3986	.|.	97;178|.	Q5QNY7;P33765-2|.	.;.|.	S|I	97;178|37	ENSP00000358731:A97S;ENSP00000358730:A178S|.	ENSP00000358730:A178S|.	A|M	-|-	1|3	0|0	ADORA3|ADORA3	111833095|111833095	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.151000|0.151000	0.21798|0.21798	0.021000|0.021000	0.13489|0.13489	-0.066000|-0.066000	0.12998|0.12998	0.462000|0.462000	0.41574|0.41574	GCC|ATG	.	.		0.502	ADORA3-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157679.1	NM_000677, NM_020683		A	112031572	C	A	112031572	3	1	77	1	0	0	0	0	1	0	0	0	329	710	25	3	527	3	ADORA3	1	112031572	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	11674788	112031572	137219049	5	10603										
PRRX1	5396	hgsc.bcm.edu	37	chr1	170633465	170633465	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	aggcgaaaaagaacttctccGtcagtcacctgctagacctg	9	12	3	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:170633465G>T	ENST00000239461.6	+	1	419	c.106G>T	c.(106-108)Gtc>Ttc	p.V36F	PRRX1_ENST00000367760.3_Missense_Mutation_p.V36F|PRRX1_ENST00000497230.2_Missense_Mutation_p.V36F	NM_022716.2	NP_073207.1	P54821	PRRX1_HUMAN	paired related homeobox 1	36					artery morphogenesis (GO:0048844)|cartilage development (GO:0051216)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)	nucleolus (GO:0005730)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			large_intestine(2)|ovary(1)	3	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GAACTTCTCCGTCAGTCACCT	0.682																																					p.V36F		Atlas-SNP	.											.	PRRX1	81	.	0			c.G106T						.						44	42	42					1																	170633465		2203	4300	6503	SO:0001583	missense	5396	exon1			TTCTCCGTCAGTC	M95929	CCDS1290.1, CCDS1291.1	1q24.3	2011-06-20	2003-11-12	2003-11-14	ENSG00000116132	ENSG00000116132		"Homeoboxes / PRD class"	9142	protein-coding gene	gene with protein product		167420	"paired mesoderm homeo box 1"	PMX1		1509260	Standard	NM_006902		Approved	PHOX1	uc001ghf.3	P54821	OTTHUMG00000035231	ENST00000239461.6:c.106G>T	chr1.hg19:g.170633465G>T	ENSP00000239461:p.Val36Phe	259.0	0.0		356.0	209.0	NM_006902	B5BUM7|O60807	Missense_Mutation	SNP	ENST00000239461.6	hg19	CCDS1290.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.576999	0.65878	.	.	ENSG00000116132	ENST00000367760;ENST00000239461;ENST00000497230	D;D;D	0.92397	-2.93;-3.03;-2.92	4.63	3.72	0.42706	.	0.067852	0.64402	D	0.000013	D	0.90885	0.7136	L	0.32530	0.975	0.80722	D	1	D;D	0.64830	0.989;0.994	D;D	0.77004	0.975;0.989	D	0.92077	0.5669	10	0.87932	D	0	.	11.4981	0.50422	0.0883:0.0:0.9117:0.0	.	36;36	P54821;P54821-2	PRRX1_HUMAN;.	F	36	ENSP00000356734:V36F;ENSP00000239461:V36F;ENSP00000450762:V36F	ENSP00000239461:V36F	V	+	1	0	PRRX1	168900089	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.656000	0.91102	1.175000	0.42826	0.555000	0.69702	GTC	.	.		0.682	PRRX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085236.3	NM_006902		T	170633465	G	T	170633465	3	4	77	1	0	0	0	0	1	0	0	0	12624	1145	40	1	108	1	PRRX1	1	170633465	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	58601893	170633465	78617156	6	10604										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181701871	181701871	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ggccagcgggagccaccatgGctggccaggccctgtcatgg	16	14	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:181701871G>T	ENST00000367573.2	+	20	2649	c.2649G>T	c.(2647-2649)tgG>tgT	p.W883C	CACNA1E_ENST00000367570.1_Missense_Mutation_p.W883C|CACNA1E_ENST00000367567.4_Missense_Mutation_p.W490C|CACNA1E_ENST00000526775.1_Missense_Mutation_p.W864C|CACNA1E_ENST00000360108.3_Missense_Mutation_p.W864C|CACNA1E_ENST00000357570.5_Missense_Mutation_p.W834C|CACNA1E_ENST00000358338.5_Missense_Mutation_p.W815C	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	883					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AGCCACCATGGCTGGCCAGGC	0.667																																					p.W883C		Atlas-SNP	.											.	CACNA1E	778	.	0			c.G2649T						.						21	26	25					1																	181701871		2018	4170	6188	SO:0001583	missense	777	exon20			ACCATGGCTGGCC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2649G>T	chr1.hg19:g.181701871G>T	ENSP00000356545:p.Trp883Cys	159.0	0.0		231.0	132.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.213460	0.39102	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96011	-3.82;-3.82;-3.82;-3.82;-3.88;-3.83;-3.82	4.13	4.13	0.48395	.	0.908022	0.09802	N	0.753923	D	0.93953	0.8064	N	0.08118	0	0.58432	D	0.999999	D;D;D	0.69078	0.997;0.994;0.997	P;P;P	0.60173	0.823;0.87;0.823	D	0.92193	0.5761	10	0.52906	T	0.07	.	15.4265	0.75055	0.0:0.0:1.0:0.0	.	864;883;883	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	C	883;864;834;815;490;864;883	ENSP00000356542:W883C;ENSP00000434814:W864C;ENSP00000350183:W834C;ENSP00000351101:W815C;ENSP00000356539:W490C;ENSP00000353222:W864C;ENSP00000356545:W883C	ENSP00000350183:W834C	W	+	3	0	CACNA1E	179968494	1.000000	0.71417	1.000000	0.80357	0.308000	0.27856	3.352000	0.52239	2.592000	0.87571	0.555000	0.69702	TGG	.	.		0.667	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181701871	G	T	181701871	3	4	77	1	0	0	0	0	1	0	0	0	2544	1212	42	3	2727	3	CACNA1E	1	181701871	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	11068406	181701871	67548750	7	10605										
F13B	2165	hgsc.bcm.edu	37	chr1	197032133	197032133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	agtaaaagcttttaaaagtaTagtaatattgggcaattctt	7	3	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:197032133T>C	ENST00000367412.1	-	2	162	c.119A>G	c.(118-120)tAt>tGt	p.Y40C		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	40	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						TTTAAAAGTATAGTAATATTG	0.338																																					p.Y40C		Atlas-SNP	.											.	F13B	137	.	0			c.A119G						.						108	121	117					1																	197032133		2203	4300	6503	SO:0001583	missense	2165	exon2			AAAGTATAGTAAT	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.119A>G	chr1.hg19:g.197032133T>C	ENSP00000356382:p.Tyr40Cys	134.0	0.0		227.0	121.0	NM_001994	A8K3E5|Q5VYL5	Missense_Mutation	SNP	ENST00000367412.1	hg19	CCDS1388.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.152946	0.57259	.	.	ENSG00000143278	ENST00000367412	T	0.28069	1.63	5.58	5.58	0.84498	Complement control module (2);Sushi/SCR/CCP (1);	0.000000	0.30401	N	0.009712	T	0.57344	0.2047	M	0.78223	2.4	0.54753	D	0.999985	D	0.89917	1.0	D	0.91635	0.999	T	0.59456	-0.7451	10	0.46703	T	0.11	.	15.7383	0.77863	0.0:0.0:0.0:1.0	.	40	P05160	F13B_HUMAN	C	40	ENSP00000356382:Y40C	ENSP00000356382:Y40C	Y	-	2	0	F13B	195298756	1.000000	0.71417	0.966000	0.40874	0.450000	0.32258	5.217000	0.65252	2.120000	0.65058	0.533000	0.62120	TAT	.	.		0.338	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994		C	197032133	T	C	197032133	3	2	77	1	0	0	0	0	1	0	0	0	5343	1406	49	2	1910	2	F13B	1	197032133	Missense_Mutation	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	15330262	197032133	52218488	8	10606										
NAV1	89796	hgsc.bcm.edu	37	chr1	201752875	201752875	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	cctccccagtgccttccccaGcagtactcccgtccccaccc	5	24	0	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:201752875G>A	ENST00000367296.4	+	7	3119	c.2699G>A	c.(2698-2700)aGc>aAc	p.S900N	IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000295624.6_Missense_Mutation_p.S900N|NAV1_ENST00000367295.1_Missense_Mutation_p.S509N|NAV1_ENST00000367300.3_Missense_Mutation_p.S900N|NAV1_ENST00000367302.1_Missense_Mutation_p.S913N|NAV1_ENST00000469130.1_3'UTR|NAV1_ENST00000367297.4_Missense_Mutation_p.S900N	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	900					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						GCCTTCCCCAGCAGTACTCCC	0.612																																					p.S900N		Atlas-SNP	.											.	NAV1	143	.	0			c.G2699A						.						53	54	54					1																	201752875		2203	4300	6503	SO:0001583	missense	89796	exon7			TCCCCAGCAGTAC	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"neuron navigator-1", "pore membrane and/or filament interacting like protein 3"	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.2699G>A	chr1.hg19:g.201752875G>A	ENSP00000356265:p.Ser900Asn	57.0	0.0		111.0	34.0	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	hg19	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	G	13.95	2.390760	0.42410	.	.	ENSG00000134369	ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000391966;ENST00000367295	T;T;T;T;T;T	0.07567	3.18;3.21;3.21;3.21;3.18;3.21	5.28	5.28	0.74379	.	0.157867	0.43416	D	0.000561	T	0.06188	0.0160	N	0.14661	0.345	0.30559	N	0.76467	B;B;B;P;B	0.41848	0.257;0.095;0.046;0.763;0.231	B;B;B;B;B	0.39027	0.098;0.037;0.067;0.288;0.075	T	0.20472	-1.0274	10	0.18710	T	0.47	-28.688	16.7189	0.85405	0.0:0.0:1.0:0.0	.	900;509;900;408;900	Q8NEY1-6;Q8NEY1-5;Q8NEY1;A8MYI2;Q8NEY1-3	.;.;NAV1_HUMAN;.;.	N	913;900;900;900;900;408;509	ENSP00000356271:S913N;ENSP00000356265:S900N;ENSP00000295624:S900N;ENSP00000356266:S900N;ENSP00000356269:S900N;ENSP00000356264:S509N	ENSP00000295624:S900N	S	+	2	0	NAV1	200019498	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.164000	0.58190	2.480000	0.83734	0.460000	0.39030	AGC	.	.		0.612	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		A	201752875	G	A	201752875	3	1	77	1	0	0	0	0	1	0	0	0	10192	971	34	3	2782	3	NAV1	1	201752875	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	4720742	201752875	47497746	9	10607										
ELF3	1999	hgsc.bcm.edu	37	chr1	201982370	201982370	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gaagcggaaacgaggccggcCccgaaagctgagcaaagagt	15	10	0	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:201982370C>G	ENST00000359651.3	+	6	3941	c.749C>G	c.(748-750)cCc>cGc	p.P250R	RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367284.5_Missense_Mutation_p.P250R|RP11-465N4.4_ENST00000419190.1_RNA|ELF3_ENST00000367283.3_Missense_Mutation_p.P250R					E74-like factor 3 (ets domain transcription factor, epithelial-specific )											breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						CGAGGCCGGCCCCGAAAGCTG	0.637																																					p.P250R		Atlas-SNP	.											.	ELF3	92	.	0			c.C749G						.						73	78	76					1																	201982370		2203	4300	6503	SO:0001583	missense	1999	exon7			GCCGGCCCCGAAA	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.749C>G	chr1.hg19:g.201982370C>G	ENSP00000352673:p.Pro250Arg	185.0	0.0		258.0	161.0	NM_001114309		Missense_Mutation	SNP	ENST00000359651.3	hg19	CCDS1419.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.119787	0.77323	.	.	ENSG00000163435	ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044	T;T;T	0.18174	2.23;2.23;2.23	5.63	4.73	0.59995	AT hook, DNA-binding motif (1);	2.375910	0.01495	N	0.017244	T	0.39682	0.1087	M	0.69823	2.125	0.47994	D	0.999565	D	0.60160	0.987	P	0.55871	0.786	T	0.01323	-1.1385	10	0.72032	D	0.01	.	9.4021	0.38440	0.0:0.7786:0.1437:0.0777	.	250	P78545	ELF3_HUMAN	R	250;250;250;227	ENSP00000352673:P250R;ENSP00000356253:P250R;ENSP00000356252:P250R	ENSP00000311348:P227R	P	+	2	0	ELF3	200248993	0.886000	0.30341	1.000000	0.80357	0.987000	0.75469	1.057000	0.30492	1.396000	0.46663	0.561000	0.74099	CCC	.	.		0.637	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		G	201982370	C	G	201982370	3	3	77	1	0	0	0	0	1	0	0	0	5057	623	22	4	771	4	ELF3	1	201982370	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	229495	201982370	47268251	10	10608										
USH2A	7399	hgsc.bcm.edu	37	chr1	216173882	216173882	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	catgcacttagtagaaactgGtggggtgtaaatactgctaa	11	6	0	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:216173882G>C	ENST00000307340.3	-	33	6734	c.6348C>G	c.(6346-6348)caC>caG	p.H2116Q	USH2A_ENST00000366943.2_Missense_Mutation_p.H2116Q	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2116	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GTAGAAACTGGTGGGGTGTAA	0.458										HNSCC(13;0.011)																											p.H2116Q		Atlas-SNP	.											.	USH2A	1168	.	0			c.C6348G						.						106	100	102					1																	216173882		2203	4300	6503	SO:0001583	missense	7399	exon33			AAACTGGTGGGGT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.6348C>G	chr1.hg19:g.216173882G>C	ENSP00000305941:p.His2116Gln	87.0	0.0		119.0	39.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	10.02	1.235871	0.22626	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.54071	0.59;0.59	5.79	1.25	0.21368	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.143577	0.31566	N	0.007431	T	0.46776	0.1410	L	0.56396	1.775	0.33080	D	0.536452	B	0.18863	0.031	B	0.15870	0.014	T	0.56335	-0.7996	10	0.54805	T	0.06	.	12.0995	0.53774	0.2729:0.0:0.7271:0.0	.	2116	O75445	USH2A_HUMAN	Q	2116	ENSP00000305941:H2116Q;ENSP00000355910:H2116Q	ENSP00000305941:H2116Q	H	-	3	2	USH2A	214240505	1.000000	0.71417	0.540000	0.28089	0.366000	0.29705	1.139000	0.31504	0.358000	0.24211	0.650000	0.86243	CAC	.	.		0.458	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	216173882	G	C	216173882	3	2	77	1	0	0	0	0	1	0	0	0	17051	1252	44	4	9420	4	USH2A	1	216173882	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	14191512	216173882	33076739	11	10609										
EXO1	9156	hgsc.bcm.edu	37	chr1	242048690	242048690	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	aaacctctaggacctgccagAgccagtgggctgagcaagaa	12	11	1	3			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:242048690A>C	ENST00000366548.3	+	15	2879	c.2286A>C	c.(2284-2286)agA>agC	p.R762S	EXO1_ENST00000348581.5_Missense_Mutation_p.R762S|EXO1_ENST00000518483.1_Missense_Mutation_p.R762S	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	762	Interaction with MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			GACCTGCCAGAGCCAGTGGGC	0.473								Editing and processing nucleases																													p.R762S		Atlas-SNP	.											.	EXO1	103	.	0			c.A2286C						.						58	63	61					1																	242048690		2203	4300	6503	SO:0001583	missense	9156	exon13			TGCCAGAGCCAGT	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.2286A>C	chr1.hg19:g.242048690A>C	ENSP00000355506:p.Arg762Ser	87.0	0.0		133.0	62.0	NM_006027	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	hg19	CCDS1620.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.42|16.42	3.117412|3.117412	0.56505|0.56505	.|.	.|.	ENSG00000174371|ENSG00000174371	ENST00000366548;ENST00000348581;ENST00000518483|ENST00000521202	T;T;T|.	0.70164|.	-0.46;-0.46;-0.46|.	5.87|5.87	2.16|2.16	0.27623|0.27623	.|.	0.225948|.	0.47455|.	D|.	0.000239|.	T|T	0.59891|0.59891	0.2227|0.2227	L|L	0.60455|0.60455	1.87|1.87	0.38282|0.38282	D|D	0.942459|0.942459	P;P;P|.	0.39782|.	0.561;0.688;0.561|.	B;B;B|.	0.34242|.	0.053;0.178;0.116|.	T|T	0.56920|0.56920	-0.7899|-0.7899	10|5	0.72032|.	D|.	0.01|.	-36.6227|-36.6227	9.5309|9.5309	0.39193|0.39193	0.7902:0.0:0.2098:0.0|0.7902:0.0:0.2098:0.0	.|.	761;762;762|.	A8K5H6;Q9UQ84-4;Q9UQ84|.	.;.;EXO1_HUMAN|.	S|R	762|127	ENSP00000355506:R762S;ENSP00000311873:R762S;ENSP00000430251:R762S|.	ENSP00000311873:R762S|.	R|S	+|+	3|1	2|0	EXO1|EXO1	240115313|240115313	1.000000|1.000000	0.71417|0.71417	0.849000|0.849000	0.33467|0.33467	0.985000|0.985000	0.73830|0.73830	1.906000|1.906000	0.39887|0.39887	0.102000|0.102000	0.17638|0.17638	0.460000|0.460000	0.39030|0.39030	AGA|AGC	.	.		0.473	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027		C	242048690	A	C	242048690	3	2	77	1	0	0	0	0	1	0	0	0	5302	301	11	5	2332	5	EXO1	1	242048690	Missense_Mutation	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10	25874808	242048690	7201931	12	10610										
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458206	248458206	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	cgggcttctgtagagcgcatGagcagaacagcagcgaggat	15	9	1	3			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr1:248458206G>A	ENST00000317996.1	-	1	674	c.675C>T	c.(673-675)ctC>ctT	p.L225L		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			TAGAGCGCATGAGCAGAACAG	0.507																																					p.L225L		Atlas-SNP	.											.	OR2T12	113	.	0			c.C675T						.						139	122	128					1																	248458206		2203	4300	6503	SO:0001819	synonymous_variant	127064	exon1			GCGCATGAGCAGA	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.675C>T	chr1.hg19:g.248458206G>A		322.0	0.0		497.0	188.0	NM_001004692		Silent	SNP	ENST00000317996.1	hg19	CCDS31110.1																																																																																			.	.		0.507	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		A	248458206	G	A	248458206	2	1	77	1	0	0	0	0	0	0	0	1	11028	1277	45	3		3	OR2T12	1	248458206	Silent	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	6409516	248458206	792415	13	10611										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25467466	25467466	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ggcccccacagcagatggtgCagtaggactggtagccgtcg	15	12	0	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr2:25467466C>A	ENST00000264709.3	-	14	1947	c.1610G>T	c.(1609-1611)tGc>tTc	p.C537F	DNMT3A_ENST00000402667.1_Missense_Mutation_p.C314F|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000321117.5_Missense_Mutation_p.C537F|DNMT3A_ENST00000380746.4_Missense_Mutation_p.C348F	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	537	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCAGATGGTGCAGTAGGACTG	0.602			"Mis, F, N, S"		AML																																p.C537F		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.G1610T						.						122	104	110					2																	25467466		2203	4300	6503	SO:0001583	missense	1788	exon14			ATGGTGCAGTAGG		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1610G>T	chr2.hg19:g.25467466C>A	ENSP00000264709:p.Cys537Phe	73.0	0.0		56.0	24.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	ENST00000264709.3	hg19	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892617	0.91889	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.99376	-5.79;-5.79;-5.79;-5.79	5.65	5.65	0.86999	Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.99369	0.9778	M	0.78916	2.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.97	D	0.99211	1.0876	10	0.87932	D	0	-10.7178	17.2343	0.86994	0.0:1.0:0.0:0.0	.	537;348	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	F	348;537;537;314	ENSP00000370122:C348F;ENSP00000324375:C537F;ENSP00000264709:C537F;ENSP00000384237:C314F	ENSP00000264709:C537F	C	-	2	0	DNMT3A	25320970	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.818000	0.86416	2.655000	0.90218	0.655000	0.94253	TGC	.	.		0.602	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		A	25467466	C	A	25467466	3	1	77	1	0	0	0	0	1	0	0	0	4678	710	25	3	1168	3	DNMT3A	2	25467466	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10		25467466	217731907	14	10612										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25467523	25467523	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	cacactccagaaagcagttcTagacagcagcgggaagggtc	12	11	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr2:25467523T>C	ENST00000264709.3	-	14	1892		c.e14-2		DNMT3A_ENST00000402667.1_Splice_Site|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000321117.5_Splice_Site|DNMT3A_ENST00000380746.4_Splice_Site	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha						C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAAGCAGTTCTAGACAGCAGC	0.612			"Mis, F, N, S"		AML																																.		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.988-2A>G						.						78	71	74					2																	25467523		2203	4300	6503	SO:0001630	splice_region_variant	1788	exon11			CAGTTCTAGACAG		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1555-2A>G	chr2.hg19:g.25467523T>C		62.0	0.0		35.0	21.0	NM_153759	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Splice_Site	SNP	ENST00000264709.3	hg19	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	T	19.73	3.881731	0.72294	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5913	0.61961	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNMT3A	25321027	1.000000	0.71417	0.750000	0.31169	0.850000	0.48378	8.015000	0.88690	2.146000	0.66826	0.533000	0.62120	.	.	.		0.612	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	Intron	C	25467523	T	C	25467523	5	2	77	1	0	0	0	0	0	0	1	0	4678	1536	53	2	1225	2	DNMT3A	2	25467523	Splice_Site	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	57	25467523	217731850	15	10613										
DQX1	165545	hgsc.bcm.edu	37	chr2	74751076	74751076	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	actgggcaggaacactagcaCatctcctggaagctccttcc	9	14	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr2:74751076C>T	ENST00000404568.3	-	4	1009	c.790G>A	c.(790-792)Gtg>Atg	p.V264M	DQX1_ENST00000393951.2_Missense_Mutation_p.V264M|DQX1_ENST00000495597.1_5'UTR	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	264	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						AACACTAGCACATCTCCTGGA	0.493																																					p.V264M		Atlas-SNP	.											.	DQX1	95	.	0			c.G790A						.						29	29	29					2																	74751076		2203	4300	6503	SO:0001583	missense	165545	exon4			CTAGCACATCTCC	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.790G>A	chr2.hg19:g.74751076C>T	ENSP00000384621:p.Val264Met	102.0	0.0		68.0	26.0	NM_133637	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	hg19	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	C	18.91	3.724610	0.68959	.	.	ENSG00000144045	ENST00000393951;ENST00000404568	T;T	0.03717	3.83;3.83	5.53	5.53	0.82687	Helicase, C-terminal (1);	0.077842	0.53938	D	0.000056	T	0.07007	0.0178	L	0.45470	1.425	0.44789	D	0.997791	P	0.47350	0.894	B	0.43950	0.437	T	0.09185	-1.0686	10	0.62326	D	0.03	-20.7461	16.9468	0.86232	0.0:1.0:0.0:0.0	.	264	Q8TE96	DQX1_HUMAN	M	264	ENSP00000377523:V264M;ENSP00000384621:V264M	ENSP00000377523:V264M	V	-	1	0	DQX1	74604584	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	3.780000	0.55386	2.601000	0.87937	0.609000	0.83330	GTG	.	.		0.493	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		T	74751076	C	T	74751076	3	4	77	1	0	0	0	0	1	0	0	0	4753	478	17	3	1399	3	DQX1	2	74751076	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	49283553	74751076	168448297	16	10614										
HTRA2	27429	hgsc.bcm.edu	37	chr2	74757927	74757927	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gatcccgtggcagacatcgcAacgctgaggattcagactaa	11	11	1	3			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr2:74757927A>G	ENST00000258080.3	+	2	1320	c.690A>G	c.(688-690)gcA>gcG	p.A230A	HTRA2_ENST00000467961.1_3'UTR|AUP1_ENST00000377526.3_5'Flank|HTRA2_ENST00000352222.3_Silent_p.A230A	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN	HtrA serine peptidase 2	230	Serine protease.				adult walking behavior (GO:0007628)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|ceramide metabolic process (GO:0006672)|execution phase of apoptosis (GO:0097194)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitochondrion organization (GO:0007005)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|pentacyclic triterpenoid metabolic process (GO:0019742)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell death (GO:0010942)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of mitochondrion degradation (GO:1903146)|regulation of multicellular organism growth (GO:0040014)|response to herbicide (GO:0009635)	CD40 receptor complex (GO:0035631)|chromatin (GO:0000785)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)|unfolded protein binding (GO:0051082)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12						CAGACATCGCAACGCTGAGGA	0.577																																					p.A230A		Atlas-SNP	.											.	HTRA2	22	.	0			c.A690G						.						80	86	84					2																	74757927		2203	4300	6503	SO:0001819	synonymous_variant	27429	exon2			CATCGCAACGCTG		CCDS1951.1, CCDS1952.1	2p13.1	2011-07-21	2005-08-19	2005-08-19	ENSG00000115317	ENSG00000115317		"Serine peptidases / Serine peptidases", "Parkinson disease"	14348	protein-coding gene	gene with protein product		606441	"protease, serine, 25"	PRSS25		10644717, 10971580	Standard	XM_005264266		Approved	OMI, PARK13	uc002smi.1	O43464	OTTHUMG00000129957	ENST00000258080.3:c.690A>G	chr2.hg19:g.74757927A>G		64.0	0.0		49.0	25.0	NM_013247	Q9HBZ4|Q9P0Y3|Q9P0Y4	Silent	SNP	ENST00000258080.3	hg19	CCDS1951.1																																																																																			.	.		0.577	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247		G	74757927	A	G	74757927	2	3	77	1	0	0	0	0	0	0	0	1	7463	117	5	2		2	HTRA2	2	74757927	Silent	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10	6851	74757927	168441446	17	10615										
ACTR1B	10120	hgsc.bcm.edu	37	chr2	98275016	98275016	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tccacccgcatgatggagtgAggcatggcaaagccctcata	11	12	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr2:98275016A>C	ENST00000289228.5	-	6	747	c.531T>G	c.(529-531)ccT>ccG	p.P177P		NM_005735.3	NP_005726.1	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	177					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)			endometrium(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	15						TGATGGAGTGAGGCATGGCAA	0.607																																					p.P177P		Atlas-SNP	.											ACTR1B,caecum,carcinoma,0,1	ACTR1B	34	.	0			c.T531G						.						172	150	157					2																	98275016		2203	4300	6503	SO:0001819	synonymous_variant	10120	exon6			GGAGTGAGGCATG	X82207	CCDS2033.1	2q11.1-q11.2	2008-05-20	2001-11-28		ENSG00000115073	ENSG00000115073			168	protein-coding gene	gene with protein product		605144	"ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"	CTRN2		7696711, 10343100	Standard	NM_005735		Approved		uc002syb.2	P42025	OTTHUMG00000130549	ENST00000289228.5:c.531T>G	chr2.hg19:g.98275016A>C		96.0	0.0		69.0	33.0	NM_005735	D3DVH2|Q53SK5|Q9BRB7	Silent	SNP	ENST00000289228.5	hg19	CCDS2033.1																																																																																			.	.		0.607	ACTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252973.1	NM_005735		C	98275016	A	C	98275016	2	2	77	1	0	0	0	0	0	0	0	1	210	291	11	5		5	ACTR1B	2	98275016	Silent	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10	23517089	98275016	144924357	18	10616										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141665624	141665624	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tcaatatctccatcacacacCcatgctttgttgatgcatct	4	13	4	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr2:141665624C>A	ENST00000389484.3	-	22	4313	c.3342G>T	c.(3340-3342)tgG>tgT	p.W1114C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1114	LDL-receptor class A 9. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.W1114*(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CATCACACACCCATGCTTTGT	0.398										TSP Lung(27;0.18)																											p.W1114C	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,0,1	LRP1B	1315	.	1	Substitution - Nonsense(1)	liver(1)	c.G3342T						.						180	143	156					2																	141665624		2203	4300	6503	SO:0001583	missense	53353	exon22			ACACACCCATGCT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3342G>T	chr2.hg19:g.141665624C>A	ENSP00000374135:p.Trp1114Cys	150.0	0.0		183.0	96.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.552808	0.86127	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.96300	-3.97;-3.97	5.58	5.58	0.84498	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.64402	D	0.000001	D	0.98861	0.9615	H	0.96269	3.795	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.971;0.999	D	0.99349	1.0914	10	0.72032	D	0.01	.	19.5654	0.95390	0.0:1.0:0.0:0.0	.	297;1114	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	C	1114;1052;259	ENSP00000374135:W1114C;ENSP00000413239:W259C	ENSP00000374135:W1114C	W	-	3	0	LRP1B	141382094	1.000000	0.71417	0.993000	0.49108	0.980000	0.70556	7.729000	0.84864	2.641000	0.89580	0.585000	0.79938	TGG	.	.		0.398	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141665624	C	A	141665624	3	1	77	1	0	0	0	0	1	0	0	0	8964	624	22	3	10737	3	LRP1B	2	141665624	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	43390608	141665624	101533749	19	10617										
TTN	7273	hgsc.bcm.edu	37	chr2	179496878	179496878	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tttaaaaagcacttaccaagCacagtgagtttagcttctga	7	8	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr2:179496878C>T	ENST00000591111.1	-	186	39044	c.38820G>A	c.(38818-38820)gtG>gtA	p.V12940V	TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Silent_p.V14581V|TTN_ENST00000359218.5_Silent_p.V5641V|TTN_ENST00000342175.6_Silent_p.V5708V|TTN_ENST00000460472.2_Silent_p.V5516V|TTN_ENST00000342992.6_Silent_p.V12013V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12940					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTTACCAAGCACAGTGAGTT	0.333																																					p.V14581V		Atlas-SNP	.											.	TTN	18412	.	0			c.G43743A						.						63	55	58					2																	179496878		1831	4097	5928	SO:0001819	synonymous_variant	7273	exon236			ACCAAGCACAGTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.38820G>A	chr2.hg19:g.179496878C>T		64.0	0.0		59.0	32.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.333	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179496878	C	T	179496878	2	4	77	1	0	0	0	0	0	0	0	1	16750	697	25	3		3	TTN	2	179496878	Silent	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	37831254	179496878	63702495	20	10618										
ITGA4	3676	hgsc.bcm.edu	37	chr2	182323028	182323028	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	aagaatcccggccagacgtgCgaacagctccagctgggtga	13	12	0	3			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr2:182323028C>T	ENST00000397033.2	+	2	733	c.303C>T	c.(301-303)tgC>tgT	p.C101C	ITGA4_ENST00000478440.1_3'UTR|ITGA4_ENST00000339307.4_Silent_p.C101C	NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	101					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	GCCAGACGTGCGAACAGCTCC	0.587																																					p.C101C		Atlas-SNP	.											.	ITGA4	142	.	0			c.C303T						.						31	36	34					2																	182323028		2005	4160	6165	SO:0001819	synonymous_variant	3676	exon2			GACGTGCGAACAG		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.303C>T	chr2.hg19:g.182323028C>T		140.0	0.0		117.0	44.0	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	hg19	CCDS42788.1																																																																																			.	.		0.587	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			T	182323028	C	T	182323028	2	4	77	1	0	0	0	0	0	0	0	1	7887	776	27	1		1	ITGA4	2	182323028	Silent	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	2826150	182323028	60876345	21	10619										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr3:41266098A>T	ENST00000349496.5	+	3	375	c.95A>T	c.(94-96)gAc>gTc	p.D32V	CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32V|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25V|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32V	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95T						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>T	chr3.hg19:g.41266098A>T	ENSP00000344456:p.Asp32Val	188.0	0.0		164.0	41.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184569	0.78677	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70037	0.3178	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.74325	-0.3702	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	V	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25V;ENSP00000385604:D32V;ENSP00000412219:D32V;ENSP00000379486:D32V;ENSP00000344456:D32V;ENSP00000411226:D25V;ENSP00000379488:D32V;ENSP00000409302:D32V;ENSP00000401599:D32V	ENSP00000344456:D32V	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266098	A	T	41266098	3	4	77	1	0	0	0	0	1	0	0	0	4018	275	10	4	101	4	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10		41266098	156756332	22	10620										
PTPN23	25930	hgsc.bcm.edu	37	chr3	47449186	47449186	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ccacaattcccacccccccaGgagcccccttggtgaagccc	7	21	0	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr3:47449186G>T	ENST00000265562.4	+	13	1080		c.e13-1		PTPN23_ENST00000431726.1_Splice_Site	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23						cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CACCCCCCCAGGAGCCCCCTT	0.637																																					.		Atlas-SNP	.											.	PTPN23	85	.	0			c.1004-1G>T						.						57	62	60					3																	47449186		2203	4300	6503	SO:0001630	splice_region_variant	25930	exon13			CCCCCAGGAGCCC	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.1004-1G>T	chr3.hg19:g.47449186G>T		91.0	0.0		91.0	54.0	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Splice_Site	SNP	ENST00000265562.4	hg19	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.975735	0.74360	.	.	ENSG00000076201	ENST00000456408;ENST00000265562	.	.	.	5.09	5.09	0.68999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4365	0.87554	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTPN23	47424190	1.000000	0.71417	0.999000	0.59377	0.801000	0.45260	7.605000	0.82844	2.633000	0.89246	0.655000	0.94253	.	.	.		0.637	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	Intron	T	47449186	G	T	47449186	5	4	77	1	0	0	0	0	0	0	1	0	12803	1014	35	3	1053	3	PTPN23	3	47449186	Splice_Site	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	6183088	47449186	150573244	23	10621										
GMPPB	29925	hgsc.bcm.edu	37	chr3	49759578	49759578	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tggccgatgcgggcacttggGtcctgagagcggtgggaaaa	18	8	0	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr3:49759578G>A	ENST00000480687.1	-	9	887	c.771C>T	c.(769-771)gaC>gaT	p.D257D	GMPPB_ENST00000308388.6_Silent_p.D257D|AMIGO3_ENST00000535833.1_5'UTR|GMPPB_ENST00000308375.6_Silent_p.D257D|AMIGO3_ENST00000320431.7_5'Flank			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B	257					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGGCACTTGGGTCCTGAGAGC	0.612																																					p.D257D		Atlas-SNP	.											.	GMPPB	14	.	0			c.C771T						.						57	57	57					3																	49759578		2203	4300	6503	SO:0001819	synonymous_variant	29925	exon8			ACTTGGGTCCTGA	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.771C>T	chr3.hg19:g.49759578G>A		76.0	0.0		69.0	25.0	NM_021971	A8K6N5|Q9H7U3	Silent	SNP	ENST00000480687.1	hg19	CCDS2803.1																																																																																			.	.		0.612	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334		A	49759578	G	A	49759578	2	1	77	1	0	0	0	0	0	0	0	1	6503	1252	44	3		3	GMPPB	3	49759578	Silent	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	2310392	49759578	148262852	24	10622										
APPL1	26060	hgsc.bcm.edu	37	chr3	57271521	57271521	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ttgaatgctttttccatagaAtgaattaagtgcagcaacac	7	7	0	3			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr3:57271521A>G	ENST00000288266.3	+	3	302	c.155A>G	c.(154-156)aAt>aGt	p.N52S		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	52	Required for RAB5A binding.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)			breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		TTTCCATAGAATGAATTAAGT	0.229																																					p.N52S		Atlas-SNP	.											.	APPL1	59	.	0			c.A155G						.						23	24	23					3																	57271521		2188	4261	6449	SO:0001630	splice_region_variant	26060	exon3			CATAGAATGAATT	AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"Pleckstrin homology (PH) domain containing"	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.154-1A>G	chr3.hg19:g.57271521A>G		548.0	0.0		469.0	149.0	NM_012096	Q9P2B9	Missense_Mutation	SNP	ENST00000288266.3	hg19	CCDS2882.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.470027	0.84533	.	.	ENSG00000157500	ENST00000288266;ENST00000495803;ENST00000444459	T;T;T	0.29917	1.55;3.71;1.55	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.47728	0.1461	L	0.51422	1.61	0.80722	D	1	P;D;P	0.63046	0.636;0.992;0.757	B;P;B	0.62649	0.075;0.905;0.132	T	0.33471	-0.9867	10	0.39692	T	0.17	.	16.0347	0.80617	1.0:0.0:0.0:0.0	.	35;35;52	B4DQX8;C9JAB0;Q9UKG1	.;.;DP13A_HUMAN	S	52;52;35	ENSP00000288266:N52S;ENSP00000419644:N52S;ENSP00000406095:N35S	ENSP00000288266:N52S	N	+	2	0	APPL1	57246561	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.770000	0.91746	2.179000	0.69175	0.528000	0.53228	AAT	.	.		0.229	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096	Missense_Mutation	G	57271521	A	G	57271521	5	3	77	1	0	0	0	0	0	0	1	0	817	115	4	2	165	2	APPL1	3	57271521	Splice_Site	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10	7511943	57271521	140750909	25	10623										
C3orf17	25871	hgsc.bcm.edu	37	chr3	112732231	112732231	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ggggacaacacatactttggTagttaagggctgattttcac	11	7	1	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr3:112732231T>C	ENST00000314400.5	-	4	552	c.361A>G	c.(361-363)Acc>Gcc	p.T121A	C3orf17_ENST00000383675.2_Intron|C3orf17_ENST00000393857.2_5'UTR|C3orf17_ENST00000472762.1_5'Flank	NM_015412.3	NP_056227.2	Q6NW34	CC017_HUMAN	chromosome 3 open reading frame 17	121					negative regulation of neuron differentiation (GO:0045665)|positive regulation of Notch signaling pathway (GO:0045747)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|lung(6)|prostate(2)|skin(1)	13						CATACTTTGGTAGTTAAGGGC	0.368																																					p.T121A		Atlas-SNP	.											.	C3orf17	37	.	0			c.A361G						.						103	106	105					3																	112732231		2203	4300	6503	SO:0001583	missense	25871	exon4			CTTTGGTAGTTAA	AL117573	CCDS33824.1	3q13.2	2009-11-06			ENSG00000163608	ENSG00000163608			24496	protein-coding gene	gene with protein product						12477932	Standard	NR_027794		Approved	DKFZP434F2021, NET17	uc003dzr.3	Q6NW34	OTTHUMG00000159286	ENST00000314400.5:c.361A>G	chr3.hg19:g.112732231T>C	ENSP00000320251:p.Thr121Ala	544.0	0.0		541.0	335.0	NM_015412	D3DN69|Q68DM6|Q9H7U0|Q9UFM4	Missense_Mutation	SNP	ENST00000314400.5	hg19	CCDS33824.1	.	.	.	.	.	.	.	.	.	.	T	5.833	0.337870	0.11013	.	.	ENSG00000163608	ENST00000314400;ENST00000472166	T;T	0.41400	1.0;1.0	5.9	-4.84	0.03151	.	1.066830	0.07101	N	0.840417	T	0.26991	0.0661	L	0.56769	1.78	0.09310	N	0.999998	B	0.20052	0.041	B	0.14578	0.011	T	0.34153	-0.9840	10	0.09843	T	0.71	2.238	0.6485	0.00823	0.2361:0.2877:0.2426:0.2337	.	121	Q6NW34	CC017_HUMAN	A	121;46	ENSP00000320251:T121A;ENSP00000417613:T46A	ENSP00000320251:T121A	T	-	1	0	C3orf17	114214921	0.000000	0.05858	0.000000	0.03702	0.241000	0.25554	-0.191000	0.09601	-0.697000	0.05092	-0.313000	0.08912	ACC	.	.		0.368	C3orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354405.3	NM_015412		C	112732231	T	C	112732231	3	2	77	1	0	0	0	0	1	0	0	0	2212	1638	57	2	1366	2	C3orf17	3	112732231	Missense_Mutation	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	55460710	112732231	85290199	26	10624										
MECOM	2122	hgsc.bcm.edu	37	chr3	168806927	168806927	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tatctgtgaagtgccttataTgatctagagcagaaagtcca	9	7	2	4			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr3:168806927T>C	ENST00000464456.1	-	14	4055	c.2855A>G	c.(2854-2856)cAt>cGt	p.H952R	MECOM_ENST00000460814.1_Missense_Mutation_p.H952R|MECOM_ENST00000494292.1_Missense_Mutation_p.H1140R|MECOM_ENST00000264674.3_Missense_Mutation_p.H1026R|MECOM_ENST00000472280.1_Missense_Mutation_p.H962R|MECOM_ENST00000392736.3_Missense_Mutation_p.H961R|MECOM_ENST00000468789.1_Missense_Mutation_p.H961R|MECOM_ENST00000433243.2_Missense_Mutation_p.H962R	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						GTGCCTTATATGATCTAGAGC	0.338																																					p.H1149R		Atlas-SNP	.											.	MECOM	216	.	0			c.A3446G						.						99	97	98					3																	168806927		2203	4300	6503	SO:0001583	missense	2122	exon16			CTTATATGATCTA	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2855A>G	chr3.hg19:g.168806927T>C	ENSP00000419770:p.His952Arg	111.0	0.0		123.0	74.0	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	hg19	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.969814	0.53614	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243	T;T;T;T;T;T;T;T	0.05447	3.49;3.48;3.45;3.59;3.44;3.48;3.44;3.59	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000004	T	0.16938	0.0407	L	0.43152	1.355	0.80722	D	1	D;D;D;D;D	0.67145	0.991;0.996;0.985;0.993;0.994	P;D;P;P;P	0.63793	0.852;0.918;0.622;0.857;0.829	T	0.00573	-1.1664	10	0.44086	T	0.13	-13.9098	15.9147	0.79503	0.0:0.0:0.0:1.0	.	1149;953;1140;1026;961	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	R	1026;961;952;962;1140;961;952;962	ENSP00000264674:H1026R;ENSP00000376493:H961R;ENSP00000419770:H952R;ENSP00000420048:H962R;ENSP00000417899:H1140R;ENSP00000419995:H961R;ENSP00000420466:H952R;ENSP00000394302:H962R	ENSP00000264674:H1026R	H	-	2	0	MECOM	170289621	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	6.977000	0.76141	2.227000	0.72691	0.460000	0.39030	CAT	.	.		0.338	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		C	168806927	T	C	168806927	3	2	77	1	0	0	0	0	1	0	0	0	9431	1464	51	2	281	2	MECOM	3	168806927	Missense_Mutation	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	56074696	168806927	29215503	27	10625										
NCEH1	57552	hgsc.bcm.edu	37	chr3	172351796	172351796	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ttcacattttgctgataagaTggtgtgttaaaatctaaagc	8	5	2	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr3:172351796T>C	ENST00000475381.1	-	5	929	c.696A>G	c.(694-696)ccA>ccG	p.P232P	NCEH1_ENST00000273512.3_Silent_p.P264P|NCEH1_ENST00000538775.1_Silent_p.P272P|NCEH1_ENST00000543711.1_Silent_p.P99P			Q6PIU2	NCEH1_HUMAN	neutral cholesterol ester hydrolase 1	232					lipid catabolic process (GO:0016042)|protein dephosphorylation (GO:0006470)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carboxylic ester hydrolase activity (GO:0052689)|phosphate ion binding (GO:0042301)|serine hydrolase activity (GO:0017171)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15						GCTGATAAGATGGTGTGTTAA	0.398																																					p.P272P		Atlas-SNP	.											.	NCEH1	63	.	0			c.A816G						.						106	99	102					3																	172351796		2203	4300	6503	SO:0001819	synonymous_variant	57552	exon5			ATAAGATGGTGTG	AB037784	CCDS54681.1, CCDS54682.1	3q26.31	2009-07-23	2009-07-23	2009-07-23	ENSG00000144959	ENSG00000144959			29260	protein-coding gene	gene with protein product		613234	"arylacetamide deacetylase-like 1"	AADACL1		10718198	Standard	NM_001146276		Approved	KIAA1363, NCEH	uc011bpx.2	Q6PIU2	OTTHUMG00000156872	ENST00000475381.1:c.696A>G	chr3.hg19:g.172351796T>C		121.0	0.0		134.0	42.0	NM_001146276	B7Z2K4|B7Z3A1|B7Z5U2|B7Z906|B7ZAW6|F5H7K4|Q86WZ1|Q9P2I4	Silent	SNP	ENST00000475381.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.539	-0.854617	0.02630	.	.	ENSG00000144959	ENST00000424772	.	.	.	5.67	0.583	0.17417	.	.	.	.	.	T	0.50803	0.1637	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35871	-0.9771	4	.	.	.	-29.6019	5.0145	0.14330	0.2723:0.0:0.495:0.2327	.	.	.	.	R	263	.	.	H	-	2	0	NCEH1	173834490	0.969000	0.33509	0.997000	0.53966	0.031000	0.12232	0.027000	0.13621	0.065000	0.16485	-1.260000	0.01463	CAT	.	.		0.398	NCEH1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346367.3	NM_020792		C	172351796	T	C	172351796	2	2	77	1	0	0	0	0	0	0	0	1	10224	1451	51	2		2	NCEH1	3	172351796	Silent	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	3544869	172351796	25670634	28	10626										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30724307	30724307	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	attgaaatccgcaagattggGcgcatccccctcaaggacgg	11	12	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr4:30724307G>T	ENST00000361762.2	+	1	2271	c.1263G>T	c.(1261-1263)ggG>ggT	p.G421G	PCDH7_ENST00000543491.1_Silent_p.G421G	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	421					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						GCAAGATTGGGCGCATCCCCC	0.632																																					p.G421G		Atlas-SNP	.											.	PCDH7	215	.	0			c.G1263T						.						44	44	44					4																	30724307		2203	4300	6503	SO:0001819	synonymous_variant	5099	exon1			GATTGGGCGCATC	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1263G>T	chr4.hg19:g.30724307G>T		189.0	0.0		150.0	57.0	NM_032457	O60246|O60247|Q4W5C4	Silent	SNP	ENST00000361762.2	hg19	CCDS33971.1	.	.	.	.	.	.	.	.	.	.	G	5.264	0.234177	0.09969	.	.	ENSG00000169851	ENST00000511884	.	.	.	5.48	-1.44	0.08856	.	.	.	.	.	T	0.54127	0.1839	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49995	-0.8879	4	.	.	.	.	8.7181	0.34423	0.1976:0.479:0.3234:0.0	.	.	.	.	S	111	.	.	A	+	1	0	PCDH7	30333405	0.004000	0.15560	0.998000	0.56505	0.919000	0.55068	-1.060000	0.03475	-0.051000	0.13334	-0.140000	0.14226	GCG	.	.		0.632	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		T	30724307	G	T	30724307	2	4	77	1	0	0	0	0	0	0	0	1	11525	1190	42	3		3	PCDH7	4	30724307	Silent	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10		30724307	160429969	29	10627										
DKK2	27123	hgsc.bcm.edu	37	chr4	107845304	107845304	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ttttggtccagaaatgacgaGcacagcaaaacccttcaatg	8	10	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr4:107845304G>A	ENST00000285311.3	-	4	1292	c.587C>T	c.(586-588)gCt>gTt	p.A196V	DKK2_ENST00000513208.1_Missense_Mutation_p.A96V|DKK2_ENST00000510463.1_Missense_Mutation_p.A150V	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	196	DKK-type Cys-2.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		GAAATGACGAGCACAGCAAAA	0.488																																					p.A196V		Atlas-SNP	.											.	DKK2	96	.	0			c.C587T						.						125	115	118					4																	107845304		2203	4300	6503	SO:0001583	missense	27123	exon4			TGACGAGCACAGC	AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"dickkopf (Xenopus laevis) homolog 2", "dickkopf 2 homolog (Xenopus laevis)"			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.587C>T	chr4.hg19:g.107845304G>A	ENSP00000285311:p.Ala196Val	206.0	0.0		127.0	55.0	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Missense_Mutation	SNP	ENST00000285311.3	hg19	CCDS3675.1	.	.	.	.	.	.	.	.	.	.	G	35	5.474217	0.96291	.	.	ENSG00000155011	ENST00000285311;ENST00000513208;ENST00000510463	T;T;T	0.64085	-0.08;0.06;0.12	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.81664	0.4870	M	0.82823	2.61	0.80722	D	1	D	0.63880	0.993	D	0.70227	0.968	D	0.83701	0.0182	10	0.87932	D	0	-13.917	19.6876	0.95986	0.0:0.0:1.0:0.0	.	196	Q9UBU2	DKK2_HUMAN	V	196;96;150	ENSP00000285311:A196V;ENSP00000421255:A96V;ENSP00000423797:A150V	ENSP00000285311:A196V	A	-	2	0	DKK2	108064753	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.476000	0.97823	2.657000	0.90304	0.585000	0.79938	GCT	.	.		0.488	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4			A	107845304	G	A	107845304	3	1	77	1	0	0	0	0	1	0	0	0	4547	971	34	3	196	3	DKK2	4	107845304	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	77120997	107845304	83308972	30	10628										
QRFPR	84109	hgsc.bcm.edu	37	chr4	122251638	122251638	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ccagcacacagcaaagagagCcaccactgtcaccatcataa	6	15	2	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr4:122251638C>A	ENST00000394427.2	-	5	1249	c.838G>T	c.(838-840)Gct>Tct	p.A280S	QRFPR_ENST00000334383.5_Missense_Mutation_p.G242V|Y_RNA_ENST00000384419.1_RNA	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	280					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						GCAAAGAGAGCCACCACTGTC	0.413																																					p.A280S		Atlas-SNP	.											.	QRFPR	65	.	0			c.G838T						.						157	149	152					4																	122251638		2203	4300	6503	SO:0001583	missense	84109	exon5			AGAGAGCCACCAC	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"GPCR / Class A : RF amide peptide receptors"	15565	protein-coding gene	gene with protein product		606925	"G protein-coupled receptor 103"	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.838G>T	chr4.hg19:g.122251638C>A	ENSP00000377948:p.Ala280Ser	119.0	0.0		64.0	27.0	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	hg19	CCDS3719.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.73|13.73	2.324117|2.324117	0.41197|0.41197	.|.	.|.	ENSG00000186867|ENSG00000186867	ENST00000394427|ENST00000334383	T|T	0.37584|0.69926	1.19|-0.44	5.66|5.66	3.7|3.7	0.42460|0.42460	GPCR, rhodopsin-like superfamily (1);|.	0.457827|.	0.23955|.	N|.	0.042906|.	T|T	0.56108|0.56108	0.1963|0.1963	L|L	0.28014|0.28014	0.82|0.82	0.36549|0.36549	D|D	0.871734|0.871734	B|.	0.06786|.	0.001|.	B|.	0.11329|.	0.006|.	T|T	0.63292|0.63292	-0.6670|-0.6670	10|7	0.38643|0.72032	T|D	0.18|0.01	.|.	4.7779|4.7779	0.13189|0.13189	0.3172:0.4973:0.1067:0.0789|0.3172:0.4973:0.1067:0.0789	.|.	280|.	Q96P65|.	QRFPR_HUMAN|.	S|V	280|242	ENSP00000377948:A280S|ENSP00000335610:G242V	ENSP00000377948:A280S|ENSP00000335610:G242V	A|G	-|-	1|2	0|0	QRFPR|QRFPR	122471088|122471088	0.987000|0.987000	0.35691|0.35691	1.000000|1.000000	0.80357|0.80357	0.892000|0.892000	0.51952|0.51952	0.800000|0.800000	0.27042|0.27042	1.350000|1.350000	0.45770|0.45770	0.655000|0.655000	0.94253|0.94253	GCT|GGC	.	.		0.413	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		A	122251638	C	A	122251638	3	1	77	1	0	0	0	0	1	0	0	0	12893	739	26	3	465	3	QRFPR	4	122251638	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	14406334	122251638	68902638	31	10629										
MEGF10	84466	hgsc.bcm.edu	37	chr5	126774132	126774132	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tccatacctgtaatttcagcAtgtccacctgcccactgggg	8	14	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr5:126774132A>C	ENST00000274473.6	+	18	2373	c.2106A>C	c.(2104-2106)ccA>ccC	p.P702P	MEGF10_ENST00000503335.2_Splice_Site_p.P702P	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	702	Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		TAATTTCAGCATGTCCACCTG	0.512																																					p.P702P		Atlas-SNP	.											.	MEGF10	152	.	0			c.A2106C						.						128	116	120					5																	126774132		2203	4300	6503	SO:0001630	splice_region_variant	84466	exon18			TTCAGCATGTCCA	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.2105-1A>C	chr5.hg19:g.126774132A>C		76.0	0.0		95.0	28.0	NM_032446	Q68DE5|Q8WUL3	Silent	SNP	ENST00000274473.6	hg19	CCDS4142.1																																																																																			.	.		0.512	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	Silent	C	126774132	A	C	126774132	5	2	77	1	0	0	0	0	0	0	1	0	9469	231	8	5	2168	5	MEGF10	5	126774132	Splice_Site	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10		126774132	54141128	32	10630										
PCDHB2	56133	hgsc.bcm.edu	37	chr5	140476384	140476385	+	Missense_Mutation	DNP	GC	GC	TG													0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ctggtggacggcttctcccaGccctacctgctgctcccgga							TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr5:140476384_140476385GC>TG	ENST00000194155.4	+	1	2158_2159	c.2010_2011GC>TG	c.(2008-2013)caGCcc>caTGcc	p.670_671QP>HA		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	670	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCTTCTCCCAGCCCTACCTGCT	0.688																																					p.Q670H|p.P671A		Atlas-SNP	.											.	PCDHB2	163	.	0			c.G2010T|c.C2011G						.																																			SO:0001583	missense	56133	exon1			CTCCCAGCCCTAC|TCCCAGCCCTACC	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"Cadherins / Protocadherins : Clustered"	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	Exception_encountered	chr5.hg19:g.140476384_140476385delinsTG	ENSP00000194155:p.Q670_P671delinsHA	17.0	0.0		22.0	9.0|10.0	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	hg19	CCDS4244.1																																																																																			.	.		0.688	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		TG	140476385	GC	TG	140476384	3	4	77	1	0	0	0	0	1	0	0	0	11551	962	34	3	2012	3	PCDHB2	5	140476384	Missense_Mutation	DNP	GC	TCGA-CC-A7IL-01A-11D-A33Q-10	13702252	140476384	40438876	33	10631										
PCDHGB7	56099	hgsc.bcm.edu	37	chr5	140798888	140798888	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tcgggctcaacggccgtgtcTcctactctctcattgccagc	9	16	4	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr5:140798888T>G	ENST00000398594.2	+	1	1462	c.1462T>G	c.(1462-1464)Tcc>Gcc	p.S488A	PCDHGA9_ENST00000573521.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGB2_ENST00000522605.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	488	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCCGTGTCTCCTACTCTCT	0.632																																					p.S488A		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.T1462G						.						74	85	82					5																	140798888		2138	4242	6380	SO:0001583	missense	56099	exon1			CGTGTCTCCTACT	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1462T>G	chr5.hg19:g.140798888T>G	ENSP00000381594:p.Ser488Ala	86.0	0.0		111.0	50.0	NM_018927	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	hg19	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	t	10.90	1.480387	0.26598	.	.	ENSG00000254122	ENST00000398594	T	0.52754	0.65	5.19	4.01	0.46588	Cadherin (4);Cadherin-like (1);	0.000000	0.32884	U	0.005523	T	0.53498	0.1800	L	0.60957	1.885	0.19775	N	0.999959	P;D	0.55172	0.933;0.97	P;P	0.55577	0.777;0.779	T	0.47509	-0.9112	10	0.59425	D	0.04	.	6.9361	0.24466	0.1886:0.0:0.1317:0.6797	.	488;488	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	A	488	ENSP00000381594:S488A	ENSP00000381594:S488A	S	+	1	0	PCDHGB7	140779072	0.000000	0.05858	0.740000	0.30986	0.021000	0.10359	0.241000	0.18065	0.791000	0.33826	0.402000	0.26972	TCC	.	.		0.632	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		G	140798888	T	G	140798888	3	3	77	1	0	0	0	0	1	0	0	0	11577	1551	54	5	1464	5	PCDHGB7	5	140798888	Missense_Mutation	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	322504	140798888	40116372	34	10632										
ZNF184	7738	hgsc.bcm.edu	37	chr6	27419760	27419760	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ttacattcataagctttctcTtgagtatgagttttctgatg	7	6	3	3	rs371959671		TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr6:27419760T>C	ENST00000211936.6	-	6	1862	c.1578A>G	c.(1576-1578)caA>caG	p.Q526Q	ZNF184_ENST00000377419.1_Silent_p.Q526Q	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	526				Q -> G (in Ref. 4; AAC51180). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						AAGCTTTCTCTTGAGTATGAG	0.383																																					p.Q526Q		Atlas-SNP	.											.	ZNF184	89	.	0			c.A1578G						.	T		0,4406		0,0,2203	66	68	67		1578	-2.3	1	6		67	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	ZNF184	NM_007149.2		0,2,6500	CC,CT,TT		0.0233,0.0,0.0154		526/752	27419760	2,13002	2203	4299	6502	SO:0001819	synonymous_variant	7738	exon6			TTTCTCTTGAGTA	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1578A>G	chr6.hg19:g.27419760T>C		51.0	0.0		107.0	28.0	NM_007149	B2R715|O60792|Q8TBA9	Silent	SNP	ENST00000211936.6	hg19	CCDS4624.1																																																																																			.	.		0.383	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		C	27419760	T	C	27419760	2	2	77	1	0	0	0	0	0	0	0	1	17766	1606	56	2		2	ZNF184	6	27419760	Silent	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10		27419760	143695307	35	10633										
HLA-G	3135	hgsc.bcm.edu	37	chr6	29797329	29797329	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gggaggaccagacccaggacGtggagctcgtggagaccagg	18	10	0	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr6:29797329G>T	ENST00000360323.6	+	4	778	c.754G>T	c.(754-756)Gtg>Ttg	p.V252L	HLA-G_ENST00000376818.3_Missense_Mutation_p.V160L|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000428701.1_Missense_Mutation_p.V252L|HLA-G_ENST00000376828.2_Missense_Mutation_p.V257L			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	252	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						GACCCAGGACGTGGAGCTCGT	0.617																																					p.V252L		Atlas-SNP	.											.	HLA-G	90	.	0			c.G754T						.						79	72	75					6																	29797329		2203	4300	6503	SO:0001583	missense	3135	exon5			CAGGACGTGGAGC		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4964	protein-coding gene	gene with protein product	"b2 microglobulin"	142871	"HLA-G histocompatibility antigen, class I, G"				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.754G>T	chr6.hg19:g.29797329G>T	ENSP00000353472:p.Val252Leu	81.0	0.0		172.0	44.0	NM_002127		Missense_Mutation	SNP	ENST00000360323.6	hg19	CCDS4668.1	.	.	.	.	.	.	.	.	.	.	.	2.104	-0.405355	0.04832	.	.	ENSG00000204632	ENST00000376828;ENST00000428701;ENST00000360323;ENST00000376818	T;T;T;T	0.03580	3.88;3.88;3.88;3.88	1.72	0.423	0.16463	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.519636	0.15656	U	0.251124	T	0.01835	0.0058	M	0.79258	2.445	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.0	T	0.37244	-0.9714	10	0.87932	D	0	.	5.0576	0.14540	0.822:0.0:0.178:0.0	.	257;160;252	Q5RJ85;Q31611;P17693	.;.;HLAG_HUMAN	L	257;252;252;160	ENSP00000366024:V257L;ENSP00000412927:V252L;ENSP00000353472:V252L;ENSP00000366014:V160L	ENSP00000353472:V252L	V	+	1	0	HLA-G	29905308	0.001000	0.12720	0.128000	0.21923	0.006000	0.05464	-0.276000	0.08514	-0.037000	0.13646	-1.054000	0.02325	GTG	.	.		0.617	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		T	29797329	G	T	29797329	3	4	77	1	0	0	0	0	1	0	0	0	7221	1145	40	1	768	1	HLA-G	6	29797329	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	2377569	29797329	141317738	36	10634										
TUBB	203068	hgsc.bcm.edu	37	chr6	30691141	30691162	+	Frame_Shift_Del	DEL	GGGCCAAAGGCCACTACACAGA	GGGCCAAAGGCCACTACACAGA	-													0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gtctggggcaggtaacaactGggccaaaggccactacacag							TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	GGGCCAAAGGCCACTACACAGA	GGGCCAAAGGCCACTACACAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr6:30691141_30691162delGGGCCAAAGGCCACTACACAGA	ENST00000327892.8	+	4	608_629	c.302_323delGGGCCAAAGGCCACTACACAGA	c.(301-324)tgggccaaaggccactacacagagfs	p.WAKGHYTE101fs	TUBB_ENST00000396384.1_Frame_Shift_Del_p.WAKGHYTE29fs|TUBB_ENST00000396389.1_Frame_Shift_Del_p.WAKGHYTE83fs|TUBB_ENST00000435534.1_Frame_Shift_Del_p.WAKGHYTE101fs|XXbac-BPG252P9.9_ENST00000607476.1_RNA|TUBB_ENST00000330914.3_Frame_Shift_Del_p.WAKGHYTE29fs	NM_178014.2	NP_821133.1	P07437	TBB5_HUMAN	tubulin, beta class I	101					cell division (GO:0051301)|cellular component movement (GO:0006928)|cellular process (GO:0009987)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cell body (GO:0044297)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|kidney(8)|large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	16					Colchicine(DB01394)|Podofilox(DB01179)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	GGTAACAACTGGGCCAAAGGCCACTACACAGAGGGCGCCGAG	0.536																																					p.101_108del		Atlas-Indel,Pindel	.											.	TUBB	30	.	0			c.301_322del						.																																			SO:0001589	frameshift_variant	203068	exon4			.	AB062393	CCDS4687.1	6p21.33	2011-10-10	2011-10-10		ENSG00000196230	ENSG00000196230		"Tubulins"	20778	protein-coding gene	gene with protein product	"class I beta-tubulin", "beta1-tubulin"	191130	"tubulin, beta polypeptide", "tubulin, beta"			11504633, 8270253	Standard	NM_001293212		Approved	OK/SW-cl.56, MGC16435, M40, Tubb5	uc003nrl.3	P07437	OTTHUMG00000031059	ENST00000327892.8:c.302_323delGGGCCAAAGGCCACTACACAGA	chr6.hg19:g.30691141_30691162delGGGCCAAAGGCCACTACACAGA	ENSP00000339001:p.Trp101fs	191.0	0.0		293.0	38.0	NM_178014	P05218|Q8WUC1|Q9CY33	Frame_Shift_Del	DEL	ENST00000327892.8	hg19	CCDS4687.1																																																																																			.	.		0.536	TUBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076074.2	NM_178014		-	30691162	GGGCCAAAGGCCACTACACAGA	-	30691141	7	5	77	1	0	1	0	1	0	0	0	0	16767	1357	47	0	316	0	TUBB	6	30691141	Frame_Shift_Del	DEL	GGGCCAAAGGCCACTACACAGA	TCGA-CC-A7IL-01A-11D-A33Q-10	893812	30691141	140423926	37	10635										
KLC4	89953	hgsc.bcm.edu	37	chr6	43039049	43039049	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	aacagggcaaatatgctgagGctgagacactatacaaagag	11	7	0	3			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr6:43039049G>T	ENST00000394056.2	+	10	1687	c.1192G>T	c.(1192-1194)Gct>Tct	p.A398S	KLC4_ENST00000394058.1_Missense_Mutation_p.A398S|KLC4_ENST00000453940.2_Missense_Mutation_p.A321S|KLC4_ENST00000479388.1_Missense_Mutation_p.A398S|KLC4_ENST00000347162.5_Missense_Mutation_p.A398S|KLC4_ENST00000259708.3_Missense_Mutation_p.A416S			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	398						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			ATATGCTGAGGCTGAGACACT	0.502																																					p.A416S		Atlas-SNP	.											.	KLC4	89	.	0			c.G1246T						.						81	78	79					6																	43039049		2203	4300	6503	SO:0001583	missense	89953	exon9			GCTGAGGCTGAGA	AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"Tetratricopeptide (TTC) repeat domain containing"	21624	protein-coding gene	gene with protein product			"kinesin-like 8"	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.1192G>T	chr6.hg19:g.43039049G>T	ENSP00000377620:p.Ala398Ser	107.0	0.0		186.0	123.0	NM_201523	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	hg19	CCDS4883.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.782598	0.70222	.	.	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	D;T;D;D;D;D	0.88201	-2.35;-0.62;-2.35;-2.35;-2.35;-2.35	5.43	5.43	0.79202	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.097761	0.45606	D	0.000357	D	0.93719	0.7993	M	0.93720	3.45	0.80722	D	1	P;P;P	0.42357	0.777;0.687;0.733	P;P;P	0.53006	0.715;0.468;0.517	D	0.94521	0.7727	10	0.87932	D	0	-23.6703	13.6474	0.62290	0.0758:0.0:0.9242:0.0	.	321;416;398	B4DME9;Q9NSK0-3;Q9NSK0	.;.;KLC4_HUMAN	S	398;321;416;398;398;398	ENSP00000340221:A398S;ENSP00000395806:A321S;ENSP00000259708:A416S;ENSP00000418031:A398S;ENSP00000377620:A398S;ENSP00000377622:A398S	ENSP00000259708:A416S	A	+	1	0	KLC4	43147027	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.632000	0.83247	2.810000	0.96702	0.650000	0.86243	GCT	.	.		0.502	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		T	43039049	G	T	43039049	3	4	77	1	0	0	0	0	1	0	0	0	8345	1203	42	3	1349	3	KLC4	6	43039049	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	12347908	43039049	128076018	38	10636										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76024770	76024770	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ctggctttgcaggccaagttGttcaatgtgcatttgtcttt	10	8	2	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr6:76024770G>A	ENST00000237172.7	-	5	1108	c.778C>T	c.(778-780)Caa>Taa	p.Q260*	FILIP1_ENST00000393004.2_Nonsense_Mutation_p.Q260*|FILIP1_ENST00000370020.1_Nonsense_Mutation_p.Q161*|FILIP1_ENST00000498523.1_5'UTR	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	260										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						AGGCCAAGTTGTTCAATGTGC	0.403																																					p.Q260X		Atlas-SNP	.											.	FILIP1	173	.	0			c.C778T						.						200	190	194					6																	76024770		2203	4300	6503	SO:0001587	stop_gained	27145	exon5			CAAGTTGTTCAAT	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.778C>T	chr6.hg19:g.76024770G>A	ENSP00000237172:p.Gln260*	80.0	0.0		48.0	42.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Nonsense_Mutation	SNP	ENST00000237172.7	hg19	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	G	38	6.680395	0.97759	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-32.4465	20.3046	0.98621	0.0:0.0:1.0:0.0	.	.	.	.	X	260;260;161	.	ENSP00000237172:Q260X	Q	-	1	0	FILIP1	76081490	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.420000	0.97426	2.878000	0.98634	0.650000	0.86243	CAA	.	.		0.403	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76024770	G	A	76024770	4	1	77	1	0	0	0	0	0	1	0	0	5902	1386	48	3	2871	3	FILIP1	6	76024770	Nonsense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	32985721	76024770	95090297	39	10637										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121434235	121434235	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	agattttatggaagtttgctGctgtttcaggaatctctcac	9	7	3	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr6:121434235G>A	ENST00000398212.2	-	28	3191	c.3142C>T	c.(3142-3144)Cag>Tag	p.Q1048*	TBC1D32_ENST00000275159.6_Nonsense_Mutation_p.Q1089*|TBC1D32_ENST00000398197.2_5'UTR	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	1048					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										GAAGTTTGCTGCTGTTTCAGG	0.313																																					p.Q1048X		Atlas-SNP	.											.	C6orf170	146	.	0			c.C3142T						.						156	149	151					6																	121434235		1806	4083	5889	SO:0001587	stop_gained	221322	exon28			TTTGCTGCTGTTT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.3142C>T	chr6.hg19:g.121434235G>A	ENSP00000381270:p.Gln1048*	183.0	0.0		89.0	79.0	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Nonsense_Mutation	SNP	ENST00000398212.2	hg19	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	G	39	7.389046	0.98252	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	17.5884	0.87989	0.0:0.0:1.0:0.0	.	.	.	.	X	1089;1048	.	ENSP00000275159:Q1089X	Q	-	1	0	C6orf170	121475934	1.000000	0.71417	1.000000	0.80357	0.354000	0.29330	4.575000	0.60908	2.833000	0.97629	0.585000	0.79938	CAG	.	.		0.313	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		A	121434235	G	A	121434235	4	1	77	1	0	0	0	0	0	1	0	0	2346	1328	46	3	651	3	C6orf170	6	121434235	Nonsense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	45409465	121434235	49680832	40	10638										
L3MBTL3	84456	hgsc.bcm.edu	37	chr6	130374111	130374111	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gaaagctgacaccaaggaggAtggagaagagagagatgatg	16	4	0	5			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr6:130374111A>C	ENST00000529410.1	+	9	1036	c.557A>C	c.(556-558)gAt>gCt	p.D186A	L3MBTL3_ENST00000533560.1_Missense_Mutation_p.D161A|L3MBTL3_ENST00000361794.2_Missense_Mutation_p.D186A|L3MBTL3_ENST00000368136.2_Missense_Mutation_p.D186A|L3MBTL3_ENST00000368139.2_Missense_Mutation_p.D161A|L3MBTL3_ENST00000526019.1_Missense_Mutation_p.D161A			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	186					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		ACCAAGGAGGATGGAGAAGAG	0.458																																					p.D186A		Atlas-SNP	.											.	L3MBTL3	99	.	0			c.A557C						.						82	70	74					6																	130374111		2203	4300	6503	SO:0001583	missense	84456	exon7			AGGAGGATGGAGA	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"Sterile alpha motif (SAM) domain containing"	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.557A>C	chr6.hg19:g.130374111A>C	ENSP00000431962:p.Asp186Ala	81.0	0.0		72.0	61.0	NM_032438	Q4VXE1|Q5VUM9|Q6P9B5	Missense_Mutation	SNP	ENST00000529410.1	hg19	CCDS34537.1	.	.	.	.	.	.	.	.	.	.	A	17.81	3.479597	0.63849	.	.	ENSG00000198945	ENST00000529410;ENST00000533560;ENST00000361794;ENST00000528385;ENST00000368139;ENST00000526019;ENST00000368136	T;T;T;T;T;T;T	0.54675	2.47;2.47;2.47;0.56;2.47;2.47;2.47	5.13	5.13	0.70059	.	0.247429	0.40144	N	0.001167	T	0.43678	0.1258	L	0.51422	1.61	0.42742	D	0.993748	D;B	0.55385	0.971;0.009	P;B	0.49752	0.621;0.011	T	0.39375	-0.9617	10	0.37606	T	0.19	.	13.4676	0.61263	1.0:0.0:0.0:0.0	.	161;186	Q96JM7-2;Q96JM7	.;LMBL3_HUMAN	A	186;161;186;186;161;161;186	ENSP00000431962:D186A;ENSP00000437185:D161A;ENSP00000354526:D186A;ENSP00000433257:D186A;ENSP00000357121:D161A;ENSP00000436706:D161A;ENSP00000357118:D186A	ENSP00000354526:D186A	D	+	2	0	L3MBTL3	130415804	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	4.249000	0.58766	2.068000	0.61886	0.460000	0.39030	GAT	.	.		0.458	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074		C	130374111	A	C	130374111	3	2	77	1	0	0	0	0	1	0	0	0	8602	333	12	5	575	5	L3MBTL3	6	130374111	Missense_Mutation	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10	8939876	130374111	40740956	41	10639										
UST	10090	hgsc.bcm.edu	37	chr6	149285691	149285691	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ccagcatgaggcaggaggagCgctacctggtaagtcctgtc	14	11	0	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr6:149285691C>A	ENST00000367463.4	+	5	776	c.673C>A	c.(673-675)Cgc>Agc	p.R225S	RP11-162J8.2_ENST00000413845.1_RNA	NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	225					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		GCAGGAGGAGCGCTACCTGGT	0.567																																					p.R225S		Atlas-SNP	.											UST,colon,carcinoma,0,1	UST	42	.	0			c.C673A						.						69	62	64					6																	149285691		2203	4300	6503	SO:0001583	missense	10090	exon5			GAGGAGCGCTACC	AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"Sulfotransferases, membrane-bound"	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.673C>A	chr6.hg19:g.149285691C>A	ENSP00000356433:p.Arg225Ser	76.0	0.0		56.0	50.0	NM_005715	B2RCX6	Missense_Mutation	SNP	ENST00000367463.4	hg19	CCDS5213.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.542122	0.85917	.	.	ENSG00000111962	ENST00000367463	T	0.72051	-0.62	5.91	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.74535	0.3729	M	0.78049	2.395	0.80722	D	1	D	0.60575	0.988	D	0.66351	0.943	T	0.71122	-0.4684	10	0.13470	T	0.59	-19.565	12.3424	0.55101	0.3226:0.6774:0.0:0.0	.	225	Q9Y2C2	UST_HUMAN	S	225	ENSP00000356433:R225S	ENSP00000356433:R225S	R	+	1	0	UST	149327384	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.424000	0.66464	2.793000	0.96121	0.655000	0.94253	CGC	.	.		0.567	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715		A	149285691	C	A	149285691	3	1	77	1	0	0	0	0	1	0	0	0	17108	768	27	1	691	1	UST	6	149285691	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	18911580	149285691	21829376	42	10640										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44573141	44573141	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gcaaaggtccgcacagctggCatgggggtcagggcccctgt	16	12	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr7:44573141C>T	ENST00000289547.4	-	8	2353	c.2298G>A	c.(2296-2298)atG>atA	p.M766I	NPC1L1_ENST00000546276.1_Missense_Mutation_p.M766I|NPC1L1_ENST00000423141.1_3'UTR|NPC1L1_ENST00000381160.3_Missense_Mutation_p.M766I	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	766	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	GCACAGCTGGCATGGGGGTCA	0.632																																					p.M766I		Atlas-SNP	.											NPC1L1,bladder,carcinoma,0,1	NPC1L1	141	.	0			c.G2298A						.						58	58	58					7																	44573141		2203	4300	6503	SO:0001583	missense	29881	exon8			AGCTGGCATGGGG		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.2298G>A	chr7.hg19:g.44573141C>T	ENSP00000289547:p.Met766Ile	188.0	0.0		190.0	112.0	NM_001101648	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	hg19	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	c	27.1	4.801563	0.90538	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276	D;D;D	0.95518	-3.73;-3.73;-3.73	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	D	0.96923	0.8995	M	0.67625	2.065	0.58432	D	0.999997	P;D;D	0.76494	0.678;0.988;0.999	P;D;D	0.71656	0.835;0.934;0.974	D	0.96522	0.9386	10	0.40728	T	0.16	-46.062	15.2998	0.73940	0.0:1.0:0.0:0.0	.	766;766;766	B7ZLE6;Q17RV5;D3DVK9	.;.;.	I	766	ENSP00000289547:M766I;ENSP00000370552:M766I;ENSP00000438033:M766I	ENSP00000289547:M766I	M	-	3	0	NPC1L1	44539666	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.207000	0.77899	2.197000	0.70478	0.511000	0.50034	ATG	.	.		0.632	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		T	44573141	C	T	44573141	3	4	77	1	0	0	0	0	1	0	0	0	10580	710	25	3	1833	3	NPC1L1	7	44573141	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10		44573141	114565522	43	10641										
GNAT3	346562	hgsc.bcm.edu	37	chr7	80123960	80123960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tacttttcccagattctcctGctcctgcaacataaaaagag	5	12	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr7:80123960G>A	ENST00000398291.3	-	2	215	c.122C>T	c.(121-123)gCa>gTa	p.A41V	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	41					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						AGATTCTCCTGCTCCTGCAAC	0.279																																					p.A41V		Atlas-SNP	.											.	GNAT3	65	.	0			c.C122T						.						76	69	71					7																	80123960		1811	4071	5882	SO:0001583	missense	346562	exon2			TCTCCTGCTCCTG		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.122C>T	chr7.hg19:g.80123960G>A	ENSP00000381339:p.Ala41Val	296.0	0.0		316.0	103.0	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Missense_Mutation	SNP	ENST00000398291.3	hg19	CCDS47625.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.772410	0.90108	.	.	ENSG00000214415	ENST00000398291	D	0.89415	-2.51	4.87	4.87	0.63330	G protein alpha subunit, helical insertion (1);	0.129764	0.51477	U	0.000100	D	0.95674	0.8593	M	0.93808	3.46	0.80722	D	1	D	0.62365	0.991	D	0.65684	0.937	D	0.96841	0.9618	9	.	.	.	.	17.1202	0.86700	0.0:0.0:1.0:0.0	.	41	A8MTJ3	GNAT3_HUMAN	V	41	ENSP00000381339:A41V	.	A	-	2	0	GNAT3	79961896	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	9.023000	0.93683	2.415000	0.81967	0.585000	0.79938	GCA	.	.		0.279	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370		A	80123960	G	A	80123960	3	1	77	1	0	0	0	0	1	0	0	0	6521	1319	46	3	968	3	GNAT3	7	80123960	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	35550819	80123960	79014703	44	10642										
DYNC1I1	1780	hgsc.bcm.edu	37	chr7	95705439	95705439	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tgtcatgtggtcccccgtgcAtcctgcgctttttgcctgcg	11	14	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr7:95705439A>G	ENST00000324972.6	+	15	1824	c.1631A>G	c.(1630-1632)cAt>cGt	p.H544R	DYNC1I1_ENST00000447467.2_Missense_Mutation_p.H527R|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.H527R|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.H524R|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.H507R|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.H507R	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	544					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			TCCCCCGTGCATCCTGCGCTT	0.582											OREG0018174	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H544R		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.A1631G						.						135	115	122					7																	95705439		2203	4300	6503	SO:0001583	missense	1780	exon15			CCGTGCATCCTGC	AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"Cytoplasmic dyneins", "WD repeat domain containing"	2963	protein-coding gene	gene with protein product		603772	"dynein, cytoplasmic, intermediate polypeptide 1"	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.1631A>G	chr7.hg19:g.95705439A>G	ENSP00000320130:p.His544Arg	101.0	0.0	1315	89.0	66.0	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	hg19	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.296044	0.81025	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.06294	3.32;3.32;3.32;3.32;3.32;3.32	4.38	4.38	0.52667	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.19604	0.0471	M	0.70595	2.14	0.80722	D	1	D;D;D;D;P	0.69078	0.995;0.997;0.997;0.978;0.928	P;D;D;P;P	0.66602	0.882;0.945;0.945;0.742;0.614	T	0.04650	-1.0936	10	0.20519	T	0.43	-2.995	13.7249	0.62752	1.0:0.0:0.0:0.0	.	527;524;527;544;507	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	R	527;544;507;524;507;527	ENSP00000392337:H527R;ENSP00000320130:H544R;ENSP00000438377:H507R;ENSP00000398118:H524R;ENSP00000352348:H507R;ENSP00000412444:H527R	ENSP00000320130:H544R	H	+	2	0	DYNC1I1	95543375	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.005000	0.93587	1.984000	0.57885	0.260000	0.18958	CAT	.	.		0.582	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		G	95705439	A	G	95705439	3	3	77	1	0	0	0	0	1	0	0	0	4844	217	8	2	1685	2	DYNC1I1	7	95705439	Missense_Mutation	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10	15581479	95705439	63433224	45	10643										
RAD54B	25788	hgsc.bcm.edu	37	chr8	95399347	95399347	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gcaagcctttgtatagactcTtttcttcatttttatcacaa	4	9	4	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr8:95399347T>C	ENST00000336148.5	-	11	1974	c.1850A>G	c.(1849-1851)aAg>aGg	p.K617R		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	617					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			GTATAGACTCTTTTCTTCATT	0.378								Direct reversal of damage;Homologous recombination																													p.K617R		Atlas-SNP	.											.	RAD54B	88	.	0			c.A1850G						.						129	119	123					8																	95399347		2203	4300	6503	SO:0001583	missense	25788	exon11			AGACTCTTTTCTT	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.1850A>G	chr8.hg19:g.95399347T>C	ENSP00000336606:p.Lys617Arg	55.0	0.0		92.0	54.0	NM_012415	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	hg19	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	T	5.615	0.298218	0.10622	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	D	0.88975	-2.45	5.39	-2.57	0.06248	.	1.152260	0.05915	N	0.632357	T	0.66297	0.2775	N	0.01705	-0.755	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.58098	-0.7696	10	0.14656	T	0.56	-0.0335	1.8742	0.03215	0.1189:0.2476:0.1903:0.4431	.	617	Q9Y620	RA54B_HUMAN	R	617;289	ENSP00000336606:K617R	ENSP00000336606:K617R	K	-	2	0	RAD54B	95468523	0.000000	0.05858	0.056000	0.19401	0.883000	0.51084	-0.206000	0.09398	0.009000	0.14813	-0.472000	0.04984	AAG	.	.		0.378	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		C	95399347	T	C	95399347	3	2	77	1	0	0	0	0	1	0	0	0	13007	1609	56	2	902	2	RAD54B	8	95399347	Missense_Mutation	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10		95399347	50964675	46	10644										
LRP12	29967	hgsc.bcm.edu	37	chr8	105511591	105511591	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tttctagagatgttgtcatcCgaatgaaacctaatccagat	7	8	2	3			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr8:105511591C>A	ENST00000276654.5	-	4	537	c.429G>T	c.(427-429)tcG>tcT	p.S143S	LRP12_ENST00000424843.2_Silent_p.S124S	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	143	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			TGTTGTCATCCGAATGAAACC	0.353																																					p.S143S		Atlas-SNP	.											LRP12,NS,carcinoma,0,1	LRP12	124	.	0			c.G429T						.						151	150	150					8																	105511591		2203	4300	6503	SO:0001819	synonymous_variant	29967	exon4			GTCATCCGAATGA	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.429G>T	chr8.hg19:g.105511591C>A		96.0	0.0		147.0	41.0	NM_013437	A8K137|B4DRQ2	Silent	SNP	ENST00000276654.5	hg19	CCDS6303.1																																																																																			.	.		0.353	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		A	105511591	C	A	105511591	2	1	77	1	0	0	0	0	0	0	0	1	8963	639	23	1		1	LRP12	8	105511591	Silent	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	10112244	105511591	40852431	47	10645										
EIF3H	8667	hgsc.bcm.edu	37	chr8	117658834	117658834	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	atattctcctgctggcgacgCtgctgatactaaaattcaaa	7	10	2	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr8:117658834C>T	ENST00000276682.4	-	9	1645	c.879G>A	c.(877-879)caG>caA	p.Q293Q	EIF3H_ENST00000521861.1_Silent_p.Q279Q					eukaryotic translation initiation factor 3, subunit H											large_intestine(2)|lung(10)|skin(1)	13	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)					GCTGGCGACGCTGCTGATACT	0.522																																					p.Q279Q		Atlas-SNP	.											.	EIF3H	28	.	0			c.G837A						.						118	126	124					8																	117658834		2203	4300	6503	SO:0001819	synonymous_variant	8667	exon7			GCGACGCTGCTGA	U54559	CCDS6319.1	8q24.11	2007-07-27	2007-07-27	2007-07-27	ENSG00000147677	ENSG00000147677			3273	protein-coding gene	gene with protein product		603912	"eukaryotic translation initiation factor 3, subunit 3 gamma, 40kDa"	EIF3S3		9341143	Standard	NM_003756		Approved	eIF3-gamma, eIF3-p40, eIF3h	uc003yoa.3	O15372	OTTHUMG00000164919	ENST00000276682.4:c.879G>A	chr8.hg19:g.117658834C>T		60.0	0.0		50.0	20.0	NM_003756		Silent	SNP	ENST00000276682.4	hg19																																																																																				.	.		0.522	EIF3H-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000380913.1	NM_003756		T	117658834	C	T	117658834	2	4	77	1	0	0	0	0	0	0	0	1	5020	796	28	3		3	EIF3H	8	117658834	Silent	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	12147243	117658834	28705188	48	10646										
IFNA14	3448	hgsc.bcm.edu	37	chr9	21239412	21239412	+	Frame_Shift_Del	DEL	G	G	-													0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	caagtttgttgaaaaagagaGggatctcatgatttctgctc					rs702212	byFrequency	TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr9:21239412delG	ENST00000380222.2	-	1	566	c.523delC	c.(523-525)ctcfs	p.L175fs		NM_002172.2	NP_002163.2	P01570	IFN14_HUMAN	interferon, alpha 14	175				L -> F (in Ref. 1; CAA23803). {ECO:0000305}.	adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)	p.L175I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)	11				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		GAAAAAGAGAGGGATCTCATG	0.388																																					p.L175fs		Atlas-Indel,Pindel	.											.	IFNA14	29	.	1	Substitution - Missense(1)	lung(1)	c.524delT						.						267	267	267					9																	21239412		2203	4300	6503	SO:0001589	frameshift_variant	3448	exon1			.		CCDS6501.1	9p22	2010-08-24			ENSG00000228083	ENSG00000228083		"Interferons"	5420	protein-coding gene	gene with protein product		147579				1385305	Standard	NM_002172		Approved	LEIF2H, IFN-alphaH	uc010mis.3	P01570	OTTHUMG00000019665	ENST00000380222.2:c.523delC	chr9.hg19:g.21239412delG	ENSP00000369571:p.Leu175fs	159.0	0.0		128.0	45.0	NM_002172	Q5VZ56|Q7M4S1	Frame_Shift_Del	DEL	ENST00000380222.2	hg19	CCDS6501.1																																																																																			.	.		0.388	IFNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051894.1	NM_002172		-	21239412	G	-	21239412	7	5	77	1	0	1	0	1	0	0	0	0	7543	1000	35	0	50	0	IFNA14	9	21239412	Frame_Shift_Del	DEL	G	TCGA-CC-A7IL-01A-11D-A33Q-10		21239412	119974019	49	10647										
EXOSC3	51010	hgsc.bcm.edu	37	chr9	37783971	37783971	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gacaagtaagacaaagaagcTggctcactccctccaacatc	7	13	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr9:37783971T>C	ENST00000327304.5	-	2	426	c.414A>G	c.(412-414)ccA>ccG	p.P138P	EXOSC3_ENST00000396521.3_Silent_p.P138P|RP11-613M10.9_ENST00000540557.1_3'UTR|EXOSC3_ENST00000490516.1_5'UTR	NM_016042.3	NP_057126.2	Q9NQT5	EXOS3_HUMAN	exosome component 3	138					CUT catabolic process (GO:0071034)|DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|isotype switching (GO:0045190)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of isotype switching (GO:0045830)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(1)	4				GBM - Glioblastoma multiforme(29;0.00771)|Lung(182;0.221)		ACAAAGAAGCTGGCTCACTCC	0.393																																					p.P138P		Atlas-SNP	.											.	EXOSC3	8	.	0			c.A414G						.						145	136	139					9																	37783971		2203	4300	6503	SO:0001819	synonymous_variant	51010	exon2			AGAAGCTGGCTCA	BC002437	CCDS35016.1, CCDS43805.1	9p11	2009-01-20			ENSG00000107371	ENSG00000107371			17944	protein-coding gene	gene with protein product	"exosome component Rrp40", "CGI-102 protein"	606489				10810093, 11110791	Standard	NM_016042		Approved	hRrp40p, Rrp40p, RRP40, CGI-102, p10, hRrp-40	uc004aal.3	Q9NQT5	OTTHUMG00000019932	ENST00000327304.5:c.414A>G	chr9.hg19:g.37783971T>C		82.0	0.0		41.0	17.0	NM_016042	A8K0K6|Q5QP85|Q9Y3A8	Silent	SNP	ENST00000327304.5	hg19	CCDS35016.1																																																																																			.	.		0.393	EXOSC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052478.3	NM_016042		C	37783971	T	C	37783971	2	2	77	1	0	0	0	0	0	0	0	1	5318	1567	55	2		2	EXOSC3	9	37783971	Silent	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	16544559	37783971	103429460	50	10648										
NR4A3	8013	hgsc.bcm.edu	37	chr9	102595735	102595735	+	Splice_Site	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	cagagatcttgattattccaGagtaagttttatgatttcct	7	6	1	4			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr9:102595735G>C	ENST00000395097.2	+	5	1982	c.1253G>C	c.(1252-1254)aGa>aCa	p.R418T	NR4A3_ENST00000338488.4_Missense_Mutation_p.R418T|NR4A3_ENST00000330847.1_Splice_Site_p.R429T	NM_006981.3|NM_173200.2	NP_008912.2|NP_775292.1	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3	418					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)		TCF12/NR4A3(2)|TAF15/NR4A3(33)|EWSR1/NR4A3(146)|TFG/NR4A3(2)				Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				GATTATTCCAGAGTAAGTTTT	0.413			T	EWSR1	extraskeletal myxoid chondrosarcoma																																p.R429T		Atlas-SNP	.		Dom	yes		9	9q22	8013	"nuclear receptor subfamily 4, group A, member 3 (NOR1)"		M	.	NR4A3	80	.	0			c.G1286C						.						135	133	134					9																	102595735		2203	4300	6503	SO:0001630	splice_region_variant	8013	exon6			ATTCCAGAGTAAG	U12767	CCDS6742.1, CCDS6743.1, CCDS6744.1	9q22	2013-01-16			ENSG00000119508	ENSG00000119508		"Nuclear hormone receptors"	7982	protein-coding gene	gene with protein product		600542				8614405	Standard	NM_006981		Approved	CSMF, CHN, NOR1, MINOR	uc004baf.1	Q92570	OTTHUMG00000021030	ENST00000395097.2:c.1254+1G>C	chr9.hg19:g.102595735G>C		123.0	0.0		108.0	48.0	NM_173200	A2A3I7|Q12935|Q14979|Q16420|Q4VXA8|Q4VXA9|Q9UEK2|Q9UEK3	Missense_Mutation	SNP	ENST00000395097.2	hg19	CCDS6743.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.893608	0.52121	.	.	ENSG00000119508	ENST00000395097;ENST00000338488;ENST00000395096;ENST00000330847	T;D;T	0.88741	0.76;-2.42;0.76	5.71	5.71	0.89125	Nuclear hormone receptor, ligand-binding (2);	0.499688	0.18576	N	0.137192	D	0.86997	0.6068	N	0.08118	0	0.47621	D	0.999478	D;B;D	0.55800	0.973;0.135;0.964	P;B;P	0.55222	0.481;0.01;0.771	D	0.88169	0.2863	10	0.46703	T	0.11	.	20.2245	0.98337	0.0:0.0:1.0:0.0	.	429;418;418	Q92570-3;Q92570;Q92570-2	.;NR4A3_HUMAN;.	T	418;418;242;429	ENSP00000378531:R418T;ENSP00000340301:R418T;ENSP00000333122:R429T	ENSP00000333122:R429T	R	+	2	0	NR4A3	101635556	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.954000	0.76001	2.861000	0.98227	0.650000	0.86243	AGA	.	.		0.413	NR4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055482.1		Missense_Mutation	C	102595735	G	C	102595735	5	2	77	1	0	0	0	0	0	0	1	0	10643	956	33	4	1300	4	NR4A3	9	102595735	Splice_Site	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	64811764	102595735	38617696	51	10649										
RGS3	5998	hgsc.bcm.edu	37	chr9	116268749	116268749	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gcctgtggagcactggaaatGtgtggagctggcccacgaga	16	9	0	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr9:116268749G>A	ENST00000374140.2	+	13	1270	c.1061G>A	c.(1060-1062)tGt>tAt	p.C354Y	RGS3_ENST00000374136.1_5'UTR|RGS3_ENST00000317613.6_Missense_Mutation_p.C242Y|RGS3_ENST00000350696.5_Missense_Mutation_p.C354Y|RGS3_ENST00000343817.5_Missense_Mutation_p.C73Y|RGS3_ENST00000394646.3_Missense_Mutation_p.C73Y	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	354	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						CACTGGAAATGTGTGGAGCTG	0.662																																					p.C354Y		Atlas-SNP	.											.	RGS3	251	.	0			c.G1061A						.						35	30	32					9																	116268749		2202	4297	6499	SO:0001583	missense	5998	exon13			GGAAATGTGTGGA	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"Regulators of G-protein signaling"	9999	protein-coding gene	gene with protein product		602189	"regulator of G-protein signalling 3"			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.1061G>A	chr9.hg19:g.116268749G>A	ENSP00000363255:p.Cys354Tyr	307.0	0.0		176.0	64.0	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	hg19	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.870930	0.91587	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613;ENST00000343817;ENST00000394646	T;T;T;T;T	0.26518	1.73;1.73;1.73;1.73;1.73	5.27	5.27	0.74061	PDZ/DHR/GLGF (4);	0.092297	0.85682	D	0.000000	T	0.35248	0.0925	N	0.12961	0.28	0.80722	D	1	D;D;D;D;D	0.89917	0.997;1.0;1.0;0.989;0.999	D;D;D;P;D	0.87578	0.996;0.998;0.998;0.894;0.994	T	0.30995	-0.9959	10	0.87932	D	0	.	16.2171	0.82237	0.0:0.0:1.0:0.0	.	73;73;244;242;354	B3KUB2;P49796-4;B3KWG8;P49796-5;P49796	.;.;.;.;RGS3_HUMAN	Y	354;354;242;73;73	ENSP00000363255:C354Y;ENSP00000259406:C354Y;ENSP00000312844:C242Y;ENSP00000340284:C73Y;ENSP00000378141:C73Y	ENSP00000312844:C242Y	C	+	2	0	RGS3	115308570	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.774000	0.91767	2.735000	0.93741	0.655000	0.94253	TGT	.	.		0.662	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		A	116268749	G	A	116268749	3	1	77	1	0	0	0	0	1	0	0	0	13321	1377	48	3	1248	3	RGS3	9	116268749	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	13673014	116268749	24944682	52	10650										
NPFFR1	64106	hgsc.bcm.edu	37	chr10	72015502	72015502	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ggacacatgatgagcagcgcCagggcccagatgacggcgat	15	11	0	4			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr10:72015502C>A	ENST00000277942.6	-	4	503	c.504G>T	c.(502-504)ctG>ctT	p.L168L		NM_022146.4	NP_071429.1	Q9GZQ6	NPFF1_HUMAN	neuropeptide FF receptor 1	168					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			endometrium(2)|lung(1)	3						TGAGCAGCGCCAGGGCCCAGA	0.662																																					p.L168L		Atlas-SNP	.											.	NPFFR1	21	.	0			c.G504T						.						23	29	27					10																	72015502		2202	4296	6498	SO:0001819	synonymous_variant	64106	exon4			CAGCGCCAGGGCC	AB040104	CCDS53539.1	10q21-q22	2012-08-10	2006-02-15	2006-02-15	ENSG00000148734	ENSG00000148734		"GPCR / Class A :  Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors"	17425	protein-coding gene	gene with protein product	"neuropeptide FF 1"	607448	"G protein-coupled receptor 147"	GPR147		11024015	Standard	NM_022146		Approved	OT7T022, NPFF1R1	uc021psj.1	Q9GZQ6	OTTHUMG00000018404	ENST00000277942.6:c.504G>T	chr10.hg19:g.72015502C>A		105.0	0.0		97.0	32.0	NM_022146	A2RRF0|Q8NGR0|Q96RN3	Silent	SNP	ENST00000277942.6	hg19	CCDS53539.1																																																																																			.	.		0.662	NPFFR1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048504.2	NM_022146		A	72015502	C	A	72015502	2	1	77	1	0	0	0	0	0	0	0	1	10586	581	21	3		3	NPFFR1	10	72015502	Silent	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10		72015502	63519245	53	10651										
PRF1	5551	hgsc.bcm.edu	37	chr10	72360312	72360312	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gagccgcatcccgggccacaGcttcagtggagctgactttg	13	13	1	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr10:72360312G>T	ENST00000441259.1	-	2	507	c.347C>A	c.(346-348)gCt>gAt	p.A116D	PRF1_ENST00000373209.2_Missense_Mutation_p.A116D	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	116	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CCGGGCCACAGCTTCAGTGGA	0.662			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.A116D		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.C347A						.						40	38	39					10																	72360312		2203	4300	6503	SO:0001583	missense	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCCACAGCTTCAG	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"Perforin", "perforin 1 (preforming protein)"	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.347C>A	chr10.hg19:g.72360312G>T	ENSP00000398568:p.Ala116Asp	88.0	0.0		65.0	20.0	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	hg19	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.321184	0.23994	.	.	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.91295	-2.82;-2.82	5.65	-11.3	0.00108	Membrane attack complex component/perforin (MACPF) domain (1);	1.476590	0.04138	N	0.319109	T	0.76421	0.3985	N	0.16743	0.435	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.64575	-0.6375	10	0.05351	T	0.99	2.0238	11.0522	0.47896	0.0:0.2942:0.1926:0.5132	.	116	P14222	PERF_HUMAN	D	116	ENSP00000362305:A116D;ENSP00000398568:A116D	ENSP00000316746:A116D	A	-	2	0	PRF1	72030318	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.354000	0.07681	-2.204000	0.00743	-0.181000	0.13052	GCT	.	.		0.662	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		T	72360312	G	T	72360312	3	4	77	1	0	0	0	0	1	0	0	0	12490	971	34	3	1328	3	PRF1	10	72360312	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	344810	72360312	63174435	54	10652										
KCNIP2	30819	hgsc.bcm.edu	37	chr10	103589645	103589645	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gggggcggagggaggctgggGcggctaatgctgaagggagc	24	6	0	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr10:103589645G>T	ENST00000356640.2	-	3	454	c.179C>A	c.(178-180)gCc>gAc	p.A60D	KCNIP2_ENST00000461105.1_Missense_Mutation_p.A75D|KCNIP2_ENST00000353068.3_Intron|KCNIP2_ENST00000348850.5_Intron|KCNIP2-AS1_ENST00000412353.1_RNA|KCNIP2_ENST00000343195.4_Intron|KCNIP2_ENST00000370046.1_Intron|KCNIP2_ENST00000355657.2_5'UTR|KCNIP2_ENST00000358038.3_Intron	NM_014591.4|NM_173191.2	NP_055406.2|NP_775283.1	Q9NS61	KCIP2_HUMAN	Kv channel interacting protein 2	60					clustering of voltage-gated potassium channels (GO:0045163)|detection of calcium ion (GO:0005513)|membrane repolarization (GO:0086009)|muscle contraction (GO:0006936)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of cation channel activity (GO:2001257)|regulation of heart contraction (GO:0008016)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|calcium ion binding (GO:0005509)|ER retention sequence binding (GO:0046923)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein N-terminus binding (GO:0047485)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.122)		Epithelial(162;4.93e-09)|all cancers(201;2.63e-07)		GGAGGCTGGGGCGGCTAATGC	0.662																																					p.A75D		Atlas-SNP	.											.	KCNIP2	45	.	0			c.C224A						.						61	55	57					10																	103589645		2140	4228	6368	SO:0001583	missense	30819	exon3			GCTGGGGCGGCTA		CCDS7521.1, CCDS7522.1, CCDS7523.1, CCDS7524.1, CCDS7525.1, CCDS7526.1, CCDS41562.1	10q24.32	2013-09-20	2001-11-29		ENSG00000120049	ENSG00000120049		"EF-hand domain containing"	15522	protein-coding gene	gene with protein product		604661	"Kv channel-interacting protein 2"			10676964	Standard	NM_173192		Approved	KCHIP2	uc001kuc.3	Q9NS61	OTTHUMG00000018937	ENST00000356640.2:c.179C>A	chr10.hg19:g.103589645G>T	ENSP00000349055:p.Ala60Asp	39.0	0.0		28.0	13.0	NM_014591	A6NJE5|A8MQ75|Q3YAC6|Q3YAC8|Q3YAC9|Q7Z6F1|Q96K86|Q96T41|Q96T42|Q96T43|Q96T44|Q9H0N4|Q9HD10|Q9HD11|Q9NS60|Q9NY10|Q9NZI1	Missense_Mutation	SNP	ENST00000356640.2	hg19	CCDS7522.1	.	.	.	.	.	.	.	.	.	.	g	13.67	2.305205	0.40795	.	.	ENSG00000120049	ENST00000356640;ENST00000461105	T;T	0.69435	-0.27;-0.4	3.87	0.787	0.18596	.	0.936579	0.08816	N	0.889542	T	0.45935	0.1367	N	0.14661	0.345	0.50171	D	0.999853	B;B	0.14805	0.011;0.0	B;B	0.17433	0.018;0.0	T	0.36529	-0.9744	10	0.87932	D	0	.	3.4681	0.07557	0.3142:0.0:0.5055:0.1803	.	75;60	Q9NS61-6;Q9NS61	.;KCIP2_HUMAN	D	60;75	ENSP00000349055:A60D;ENSP00000420040:A75D	ENSP00000349055:A60D	A	-	2	0	KCNIP2	103579635	1.000000	0.71417	0.893000	0.35052	0.993000	0.82548	0.938000	0.28965	0.032000	0.15435	0.457000	0.33378	GCC	.	.		0.662	KCNIP2-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049973.1			T	103589645	G	T	103589645	3	4	77	1	0	0	0	0	1	0	0	0	8049	1203	42	3	733	3	KCNIP2	10	103589645	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	31229333	103589645	31945102	55	10653										
PCGF6	84108	hgsc.bcm.edu	37	chr10	105104793	105104793	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gtactcacccaatgaactccAgtaataaagacatatcaagt	5	10	2	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr10:105104793A>G	ENST00000369847.3	-	6	837	c.770T>C	c.(769-771)cTg>cCg	p.L257P	PCGF6_ENST00000490296.1_5'UTR|PCGF6_ENST00000337211.4_Intron	NM_001011663.1	NP_001011663.1	Q9BYE7	PCGF6_HUMAN	polycomb group ring finger 6	257				L -> P (in Ref. 2; BAF83368). {ECO:0000305}.	negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(3)	8		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)		AATGAACTCCAGTAATAAAGA	0.348																																					p.L257P		Atlas-SNP	.											.	PCGF6	23	.	0			c.T770C						.						104	102	103					10																	105104793		2203	4300	6503	SO:0001583	missense	84108	exon6			AACTCCAGTAATA	AB047006	CCDS7546.1, CCDS31275.1	10q24.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000156374	ENSG00000156374		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	21156	protein-coding gene	gene with protein product		607816	"ring finger protein 134"	RNF134		12167161	Standard	NM_032154		Approved	MBLR	uc001kwt.3	Q9BYE7	OTTHUMG00000018982	ENST00000369847.3:c.770T>C	chr10.hg19:g.105104793A>G	ENSP00000358862:p.Leu257Pro	171.0	0.0		142.0	44.0	NM_001011663	A8K3R4|Q5SYD1|Q5SYD6|Q96ID9|Q96SJ1	Missense_Mutation	SNP	ENST00000369847.3	hg19	CCDS31275.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.977370	0.74360	.	.	ENSG00000156374	ENST00000369847	T	0.38240	1.15	5.67	5.67	0.87782	.	0.140599	0.48767	D	0.000166	T	0.66346	0.2780	M	0.88105	2.93	0.80722	D	1	D	0.71674	0.998	D	0.81914	0.995	T	0.72874	-0.4160	10	0.59425	D	0.04	.	15.5854	0.76479	1.0:0.0:0.0:0.0	.	257	Q9BYE7	PCGF6_HUMAN	P	257	ENSP00000358862:L257P	ENSP00000358862:L257P	L	-	2	0	PCGF6	105094783	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.409000	0.80053	2.163000	0.67991	0.459000	0.35465	CTG	.	.		0.348	PCGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050132.1	NM_032154		G	105104793	A	G	105104793	3	3	77	1	0	0	0	0	1	0	0	0	11587	188	7	2	302	2	PCGF6	10	105104793	Missense_Mutation	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10	1515148	105104793	30429954	56	10654										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124335940	124335940	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gattctggtttggccctgagGctggtgaatggagatggcag	17	6	1	3			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr10:124335940G>T	ENST00000338354.3	+	7	415	c.309G>T	c.(307-309)agG>agT	p.R103S	DMBT1_ENST00000368909.3_Missense_Mutation_p.R103S|DMBT1_ENST00000368956.2_Missense_Mutation_p.R103S|DMBT1_ENST00000330163.4_Missense_Mutation_p.R103S|DMBT1_ENST00000368955.3_Missense_Mutation_p.R103S|DMBT1_ENST00000344338.3_Missense_Mutation_p.R103S|DMBT1_ENST00000359586.6_Missense_Mutation_p.R103S			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	103	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TGGCCCTGAGGCTGGTGAATG	0.562																																					p.R103S	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G309T						.						131	134	133					10																	124335940		2020	4213	6233	SO:0001583	missense	1755	exon7			CCTGAGGCTGGTG		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.309G>T	chr10.hg19:g.124335940G>T	ENSP00000342210:p.Arg103Ser	30.0	0.0		37.0	13.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	g	10.35	1.326100	0.24080	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63	4.54	-2.95	0.05564	Speract/scavenger receptor (1);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.75517	0.3860	H	0.99347	4.525	0.09310	N	0.999998	D;P;P;D;D	0.76494	0.995;0.879;0.827;0.999;0.999	D;P;B;D;D	0.85130	0.964;0.605;0.177;0.997;0.937	T	0.63060	-0.6721	9	0.87932	D	0	.	3.526	0.07760	0.5256:0.1148:0.2547:0.1049	.	103;103;103;103;103	F8WEF7;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	S	103	ENSP00000342210:R103S;ENSP00000343175:R103S;ENSP00000327747:R103S;ENSP00000357905:R103S;ENSP00000357951:R103S;ENSP00000357952:R103S;ENSP00000352593:R103S	ENSP00000331522:R103S	R	+	3	2	DMBT1	124325930	0.308000	0.24509	0.094000	0.20943	0.011000	0.07611	-0.372000	0.07504	-0.726000	0.04895	-1.094000	0.02160	AGG	.	.		0.562	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		T	124335940	G	T	124335940	3	4	77	1	0	0	0	0	1	0	0	0	4579	1194	42	3	335	3	DMBT1	10	124335940	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	19231147	124335940	11198807	57	10655										
CTBP2	1488	hgsc.bcm.edu	37	chr10	126714944	126714944	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	aggggcccgggttagtcaagGccacccctgcctgcaggggg	17	13	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr10:126714944G>A	ENST00000337195.5	-	3	458				CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000309035.6_Missense_Mutation_p.A462V	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		GTTAGTCAAGGCCACCCCTGC	0.662																																					p.A462V		Atlas-SNP	.											.	CTBP2	100	.	0			c.C1385T						.						37	43	41					10																	126714944		2202	4300	6502	SO:0001627	intron_variant	1488	exon1			GTCAAGGCCACCC	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12621C>T	chr10.hg19:g.126714944G>A		67.0	0.0		58.0	36.0	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	hg19	CCDS7643.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.662585	0.67700	.	.	ENSG00000175029	ENST00000309035	D	0.84442	-1.85	4.31	4.31	0.51392	.	0.741433	0.11399	N	0.568022	D	0.82476	0.5045	.	.	.	0.80722	D	1	B	0.31548	0.328	B	0.31101	0.124	T	0.81415	-0.0943	9	0.72032	D	0.01	.	15.5276	0.75923	0.0:0.0:1.0:0.0	.	462	P56545-2	.	V	462	ENSP00000311825:A462V	ENSP00000311825:A462V	A	-	2	0	CTBP2	126704934	1.000000	0.71417	0.997000	0.53966	0.790000	0.44656	8.470000	0.90399	2.396000	0.81511	0.467000	0.42956	GCC	.	.		0.662	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914		A	126714944	G	A	126714944	1	1	77	0	1	0	0	0	0	0	0	0	4000	1203	42	3		3	CTBP2	10	126714944	Intron	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	2379004	126714944	8819803	58	10656										
GUCY1A2	2977	hgsc.bcm.edu	37	chr11	106810594	106810594	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tttgcaacctgttccacttcCacatccagccgatagatctt	5	14	1	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr11:106810594C>A	ENST00000526355.2	-	4	1266	c.798G>T	c.(796-798)gtG>gtT	p.V266V	GUCY1A2_ENST00000282249.2_Silent_p.V266V|GUCY1A2_ENST00000347596.2_Silent_p.V266V	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	266					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	GTTCCACTTCCACATCCAGCC	0.438																																					p.V266V		Atlas-SNP	.											.	GUCY1A2	180	.	0			c.G798T						.						100	96	97					11																	106810594		2201	4298	6499	SO:0001819	synonymous_variant	2977	exon4			CACTTCCACATCC	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.798G>T	chr11.hg19:g.106810594C>A		88.0	0.0		71.0	50.0	NM_000855	A1L4C4|B7ZLT5	Silent	SNP	ENST00000526355.2	hg19	CCDS8335.1																																																																																			.	.		0.438	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			A	106810594	C	A	106810594	2	1	77	1	0	0	0	0	0	0	0	1	6902	581	21	3		3	GUCY1A2	11	106810594	Silent	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10		106810594	28195922	59	10657										
ZNF202	7753	hgsc.bcm.edu	37	chr11	123600474	123600474	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tcattaggtgactcaggctcCactcctaaatgcaccgtctc	7	14	3	1	rs143645376	byFrequency	TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr11:123600474C>A	ENST00000529691.1	-	3	681	c.462G>T	c.(460-462)gtG>gtT	p.V154V	ZNF202_ENST00000530393.1_Silent_p.V154V|ZNF202_ENST00000336139.4_Silent_p.V154V			O95125	ZN202_HUMAN	zinc finger protein 202	154			V -> A (in dbSNP:rs1144507). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9790754, ECO:0000269|Ref.2, ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		ACTCAGGCTCCACTCCTAAAT	0.567																																					p.V154V		Atlas-SNP	.											.	ZNF202	72	.	0			c.G462T						.						81	74	76					11																	123600474		2202	4299	6501	SO:0001819	synonymous_variant	7753	exon5			AGGCTCCACTCCT	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"Zinc fingers, C2H2-type", "-", "-", "-"	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.462G>T	chr11.hg19:g.123600474C>A		72.0	0.0		51.0	11.0	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Silent	SNP	ENST00000529691.1	hg19	CCDS8443.1																																																																																			.	C|0.998;T|0.002		0.567	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		A	123600474	C	A	123600474	2	1	77	1	0	0	0	0	0	0	0	1	17778	581	21	3		3	ZNF202	11	123600474	Silent	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	16789880	123600474	11406042	60	10658										
GALNT8	26290	hgsc.bcm.edu	37	chr12	4848403	4848403	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	attcgtgaatgaagctctgtCcattatacaacgggccatca	8	10	2	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr12:4848403C>G	ENST00000252318.2	+	3	921	c.584C>G	c.(583-585)tCc>tGc	p.S195C	RP11-234B24.6_ENST00000544741.2_3'UTR	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	195	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						GAAGCTCTGTCCATTATACAA	0.428																																					p.S195C	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											.	GALNT8	89	.	0			c.C584G						.						141	126	131					12																	4848403		2203	4300	6503	SO:0001583	missense	26290	exon3			CTCTGTCCATTAT	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4130	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 8"	606250	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.584C>G	chr12.hg19:g.4848403C>G	ENSP00000252318:p.Ser195Cys	112.0	0.0		75.0	37.0	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	hg19	CCDS8533.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.233228	0.58886	.	.	ENSG00000130035	ENST00000252318	T	0.60548	0.18	4.36	4.36	0.52297	Glycosyl transferase, family 2 (1);	0.000000	0.64402	D	0.000001	T	0.78323	0.4265	M	0.86573	2.825	0.51012	D	0.999901	D	0.89917	1.0	D	0.97110	1.0	T	0.82912	-0.0222	10	0.87932	D	0	.	14.4135	0.67132	0.0:1.0:0.0:0.0	.	195	Q9NY28	GALT8_HUMAN	C	195	ENSP00000252318:S195C	ENSP00000252318:S195C	S	+	2	0	GALNT8	4718664	0.998000	0.40836	0.861000	0.33841	0.259000	0.26198	4.073000	0.57570	2.251000	0.74343	0.561000	0.74099	TCC	.	.		0.428	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417		G	4848403	C	G	4848403	3	3	77	1	0	0	0	0	1	0	0	0	6227	855	30	4	594	4	GALNT8	12	4848403	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10		4848403	129003492	61	10659										
A2ML1	144568	hgsc.bcm.edu	37	chr12	8988264	8988264	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ttcagtgtggaggaatatggTaggtggggaaatggacaggc	18	3	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr12:8988264T>C	ENST00000299698.7	+	6	823		c.e6+2			NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						AGGAATATGGTAGGTGGGGAA	0.537																																					.		Atlas-SNP	.											.	A2ML1	199	.	0			c.643+2T>C						.						90	90	90					12																	8988264		1963	4153	6116	SO:0001630	splice_region_variant	144568	exon6			ATATGGTAGGTGG	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.643+2T>C	chr12.hg19:g.8988264T>C		133.0	0.0		80.0	32.0	NM_144670		Splice_Site	SNP	ENST00000299698.7	hg19	CCDS8596.2	.	.	.	.	.	.	.	.	.	.	T	14.04	2.416756	0.42918	.	.	ENSG00000166535	ENST00000299698;ENST00000539161	.	.	.	3.88	3.88	0.44766	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3814	0.38316	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	A2ML1	8879531	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	4.342000	0.59341	1.984000	0.57885	0.459000	0.35465	.	.	.		0.537	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	Intron	C	8988264	T	C	8988264	5	2	77	1	0	0	0	0	0	0	1	0	5	1652	57	2	667	2	A2ML1	12	8988264	Splice_Site	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	4139861	8988264	124863631	62	10660										
HOXC6	3223	hgsc.bcm.edu	37	chr12	54423561	54423561	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ggcgccggcgcatcgagatcGccaacgcgctttgcctgacc	13	16	0	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr12:54423561G>T	ENST00000243108.4	+	2	687	c.523G>T	c.(523-525)Gcc>Tcc	p.A175S	RP11-834C11.14_ENST00000512206.1_RNA|HOXC4_ENST00000303406.4_Intron|RP11-834C11.12_ENST00000513209.1_Intron|HOXC6_ENST00000394331.3_Missense_Mutation_p.A93S	NM_004503.3	NP_004494.1	P09630	HXC6_HUMAN	homeobox C6	175					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CATCGAGATCGCCAACGCGCT	0.562																																					p.A175S		Atlas-SNP	.											.	HOXC6	30	.	0			c.G523T						.						90	96	94					12																	54423561		2203	4300	6503	SO:0001583	missense	3223	exon2			GAGATCGCCAACG		CCDS8871.1, CCDS41792.1	12q13.13	2011-06-20	2005-12-22		ENSG00000197757	ENSG00000197757		"Homeoboxes / ANTP class : HOXL subclass"	5128	protein-coding gene	gene with protein product		142972	"homeo box C6"	HOX3C, HOX3		1973146, 1358459	Standard	NM_153693		Approved		uc001sev.3	P09630	OTTHUMG00000160027	ENST00000243108.4:c.523G>T	chr12.hg19:g.54423561G>T	ENSP00000243108:p.Ala175Ser	86.0	0.0		50.0	25.0	NM_004503	B2RBV2|Q6DK09	Missense_Mutation	SNP	ENST00000243108.4	hg19	CCDS8871.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.290494	0.80914	.	.	ENSG00000197757	ENST00000394331;ENST00000243108	D;D	0.97888	-4.59;-4.59	4.69	4.69	0.59074	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97303	0.9118	L	0.28115	0.83	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.97151	0.9831	10	0.37606	T	0.19	.	16.5532	0.84477	0.0:0.0:1.0:0.0	.	175	P09630	HXC6_HUMAN	S	93;175	ENSP00000377864:A93S;ENSP00000243108:A175S	ENSP00000243108:A175S	A	+	1	0	HOXC6	52709828	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.578000	0.98200	2.434000	0.82447	0.561000	0.74099	GCC	.	.		0.562	HOXC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358943.2			T	54423561	G	T	54423561	3	4	77	1	0	0	0	0	1	0	0	0	7324	1087	38	1	529	1	HOXC6	12	54423561	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	45435297	54423561	79428334	63	10661										
LRIG3	121227	hgsc.bcm.edu	37	chr12	59284530	59284539	+	Frame_Shift_Del	DEL	AAACTCTTTC	AAACTCTTTC	-													0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tccaaagtttcaagggactgAaactctttcagatgttcagg					rs144966301		TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	AAACTCTTTC	AAACTCTTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr12:59284530_59284539delAAACTCTTTC	ENST00000320743.3	-	4	709_718	c.423_432delGAAAGAGTTT	c.(421-432)ctgaaagagtttfs	p.LKEF141fs	LRIG3_ENST00000379141.4_Frame_Shift_Del_p.LKEF81fs	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	141					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			CAAGGGACTGAAACTCTTTCAGATGTTCAG	0.381			T	ROS1	NSCLC																																p.142_145del		Atlas-Indel,Pindel	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.424_433del						.																																			SO:0001589	frameshift_variant	121227	exon4			.	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.423_432delGAAAGAGTTT	chr12.hg19:g.59284530_59284539delAAACTCTTTC	ENSP00000326759:p.Leu141fs	86.0	0.0		49.0	12.0	NM_153377	Q6UXL7|Q8NC72	Frame_Shift_Del	DEL	ENST00000320743.3	hg19	CCDS8960.1																																																																																			.	.		0.381	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		-	59284539	AAACTCTTTC	-	59284530	7	5	77	1	0	1	0	1	0	0	0	0	8955	243	9	0	2991	0	LRIG3	12	59284530	Frame_Shift_Del	DEL	AAACTCTTTC	TCGA-CC-A7IL-01A-11D-A33Q-10	4860969	59284530	74567365	64	10662										
SMAD9	4093	hgsc.bcm.edu	37	chr13	37446983	37446983	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	cactgtgcagggaggcgctgCggaacttggccaggaggctg	18	10	0	0	rs200651392		TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr13:37446983C>A	ENST00000399275.2	-	2	621	c.482G>T	c.(481-483)cGc>cTc	p.R161L	SMAD9_ENST00000379826.4_Missense_Mutation_p.R161L|SMAD9_ENST00000350148.5_Missense_Mutation_p.R161L			O15198	SMAD9_HUMAN	SMAD family member 9	161					BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cartilage development (GO:0051216)|cellular response to organic cyclic compound (GO:0071407)|hindbrain development (GO:0030902)|intracellular signal transduction (GO:0035556)|midbrain development (GO:0030901)|Mullerian duct regression (GO:0001880)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)	18		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)		GGAGGCGCTGCGGAACTTGGC	0.577																																					p.R161L		Atlas-SNP	.											SMAD9_ENST00000379826,NS,carcinoma,0,2	SMAD9	91	.	0			c.G482T						.						131	113	119					13																	37446983		2203	4300	6503	SO:0001583	missense	4093	exon3			GCGCTGCGGAACT		CCDS9360.1, CCDS45032.1	13q12-q14	2014-09-17	2006-11-06	2004-05-26	ENSG00000120693	ENSG00000120693		"SMADs"	6774	protein-coding gene	gene with protein product		603295	"MAD, mothers against decapentaplegic homolog 9 (Drosophila)", "SMAD, mothers against DPP homolog 9 (Drosophila)"	MADH6, MADH9		9205116	Standard	NM_001127217		Approved		uc001uvw.3	O15198	OTTHUMG00000016740	ENST00000399275.2:c.482G>T	chr13.hg19:g.37446983C>A	ENSP00000382216:p.Arg161Leu	89.0	0.0		65.0	22.0	NM_005905	A2A2Y6|O14989|Q5TBA1	Missense_Mutation	SNP	ENST00000399275.2	hg19	CCDS45032.1	.	.	.	.	.	.	.	.	.	.	C	17.30	3.354459	0.61293	.	.	ENSG00000120693	ENST00000399275;ENST00000350148;ENST00000379826	D;D;D	0.94280	-3.39;-3.38;-3.39	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.94361	0.8187	M	0.74258	2.255	0.80722	D	1	B;B	0.31548	0.023;0.328	B;B	0.42625	0.105;0.393	D	0.92068	0.5662	10	0.20046	T	0.44	.	18.4945	0.90860	0.0:1.0:0.0:0.0	.	161;161	O15198-2;O15198	.;SMAD9_HUMAN	L	161	ENSP00000382216:R161L;ENSP00000239885:R161L;ENSP00000369154:R161L	ENSP00000239885:R161L	R	-	2	0	SMAD9	36344983	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.469000	0.80959	2.670000	0.90874	0.563000	0.77884	CGC	.	C|0.999;T|0.001		0.577	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905		A	37446983	C	A	37446983	3	1	77	1	0	0	0	0	1	0	0	0	14779	768	27	1	941	1	SMAD9	13	37446983	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10		37446983	77722895	65	10663										
DACH1	1602	hgsc.bcm.edu	37	chr13	72049330	72049330	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gcggtcagcctctatctctgGggtcagagagtctaaaagca	12	10	5	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr13:72049330G>T	ENST00000359684.2	-	11	2187	c.2188C>A	c.(2188-2190)Cca>Aca	p.P730T	DACH1_ENST00000354591.4_Missense_Mutation_p.P476T|DACH1_ENST00000313174.7_Missense_Mutation_p.P530T|DACH1_ENST00000305425.4_Missense_Mutation_p.P678T			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	730					cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		TCTATCTCTGGGGTCAGAGAG	0.408																																					p.P678T		Atlas-SNP	.											.	DACH1	123	.	0			c.C2032A						.						87	84	85					13																	72049330		1850	4108	5958	SO:0001583	missense	1602	exon10			TCTCTGGGGTCAG	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.2188C>A	chr13.hg19:g.72049330G>T	ENSP00000352712:p.Pro730Thr	103.0	0.0		59.0	26.0	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Missense_Mutation	SNP	ENST00000359684.2	hg19		.	.	.	.	.	.	.	.	.	.	G	18.86	3.712457	0.68730	.	.	ENSG00000165659	ENST00000305425;ENST00000313174;ENST00000354591;ENST00000359684;ENST00000377826	T;T;T;T	0.33216	1.46;1.5;1.49;1.42	5.61	4.76	0.60689	.	0.057000	0.64402	D	0.000001	T	0.50274	0.1606	L	0.55481	1.735	0.33128	D	0.542748	D;D;P	0.69078	0.996;0.997;0.551	P;D;B	0.70716	0.866;0.97;0.431	T	0.63651	-0.6589	10	0.49607	T	0.09	-3.3432	15.9357	0.79704	0.0:0.0:0.8639:0.1361	.	474;528;676	Q9UI36-4;Q9UI36-3;Q9UI36-2	.;.;.	T	678;530;476;730;730	ENSP00000304994:P678T;ENSP00000318506:P530T;ENSP00000346604:P476T;ENSP00000352712:P730T	ENSP00000304994:P678T	P	-	1	0	DACH1	70947331	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.415000	0.80131	1.343000	0.45638	0.650000	0.86243	CCA	.	.		0.408	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		T	72049330	G	T	72049330	3	4	77	1	0	0	0	0	1	0	0	0	4222	1232	43	3	102	3	DACH1	13	72049330	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	34602347	72049330	43120548	66	10664										
C14orf93	60686	hgsc.bcm.edu	37	chr14	23456717	23456717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ccggaaacggggagggcgggCcacccacacacctggctcgt	15	15	0	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr14:23456717C>T	ENST00000299088.6	-	7	1753	c.1324G>A	c.(1324-1326)Gcc>Acc	p.A442T	C14orf93_ENST00000397379.3_Missense_Mutation_p.A442T|C14orf93_ENST00000341470.4_Intron|C14orf93_ENST00000397382.4_Missense_Mutation_p.A442T|RP11-298I3.4_ENST00000556503.1_RNA|RP11-298I3.4_ENST00000555294.1_RNA|RP11-298I3.4_ENST00000557615.1_RNA|C14orf93_ENST00000406429.2_Intron|C14orf93_ENST00000397377.1_Missense_Mutation_p.A262T	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93	442						extracellular region (GO:0005576)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	17	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		GGAGGGCGGGCCACCCACACA	0.572																																					p.A442T		Atlas-SNP	.											.	C14orf93	33	.	0			c.G1324A						.						94	86	89					14																	23456717		2203	4300	6503	SO:0001583	missense	60686	exon7			GGCGGGCCACCCA	AK023026	CCDS9583.1, CCDS61399.1, CCDS61400.1	14q11.1	2012-09-25			ENSG00000100802	ENSG00000100802			20162	protein-coding gene	gene with protein product							Standard	XM_005267971		Approved	FLJ12154	uc001wih.3	Q9H972	OTTHUMG00000028712	ENST00000299088.6:c.1324G>A	chr14.hg19:g.23456717C>T	ENSP00000299088:p.Ala442Thr	62.0	0.0		72.0	49.0	NM_021944	B7WP03|D3DS38|D3DS39|Q86SE6|Q96CF7|Q9HA68	Missense_Mutation	SNP	ENST00000299088.6	hg19	CCDS9583.1	.	.	.	.	.	.	.	.	.	.	c	35	5.517139	0.96416	.	.	ENSG00000100802	ENST00000299088;ENST00000397379;ENST00000397382;ENST00000397377	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000018	T	0.61048	0.2316	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.69731	-0.5066	10	0.72032	D	0.01	-15.3837	18.7998	0.92011	0.0:1.0:0.0:0.0	.	442	Q9H972	CN093_HUMAN	T	442;442;442;262	ENSP00000299088:A442T;ENSP00000380535:A442T;ENSP00000380538:A442T;ENSP00000380533:A262T	ENSP00000299088:A442T	A	-	1	0	C14orf93	22526557	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.562000	0.67346	2.737000	0.93849	0.645000	0.84053	GCC	.	.		0.572	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	NM_021944		T	23456717	C	T	23456717	3	4	77	1	0	0	0	0	1	0	0	0	1784	739	26	3	296	3	C14orf93	14	23456717	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10		23456717	83892823	67	10665										
NFKBIA	4792	hgsc.bcm.edu	37	chr14	35871694	35871694	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gaaggttttctagtgtcagcTggcccagctgctgctgtatc	12	10	2	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr14:35871694T>A	ENST00000216797.5	-	5	913	c.812A>T	c.(811-813)cAg>cTg	p.Q271L	NFKBIA_ENST00000557389.1_Missense_Mutation_p.Q181L|NFKBIA_ENST00000557140.1_Missense_Mutation_p.Q228L|NFKBIA_ENST00000557100.1_5'UTR	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	271					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	TAGTGTCAGCTGGCCCAGCTG	0.557																																					p.Q271L		Atlas-SNP	.											.	NFKBIA	28	.	0			c.A812T						.						88	91	90					14																	35871694		2203	4300	6503	SO:0001583	missense	4792	exon5			GTCAGCTGGCCCA		CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"Ankyrin repeat domain containing"	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.812A>T	chr14.hg19:g.35871694T>A	ENSP00000216797:p.Gln271Leu	106.0	0.0		91.0	35.0	NM_020529	B2R8L6	Missense_Mutation	SNP	ENST00000216797.5	hg19	CCDS9656.1	.	.	.	.	.	.	.	.	.	.	T	15.72	2.917344	0.52546	.	.	ENSG00000100906	ENST00000216797;ENST00000557140;ENST00000557389	T;T;T	0.35973	1.28;1.28;1.28	5.76	5.76	0.90799	Ankyrin repeat-containing domain (1);	.	.	.	.	T	0.27098	0.0664	L	0.28115	0.83	0.39503	D	0.968227	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.0	T	0.06935	-1.0799	9	0.41790	T	0.15	-12.2413	12.3378	0.55077	0.1263:0.0:0.0:0.8737	.	228;271	G3V3I4;P25963	.;IKBA_HUMAN	L	271;228;181	ENSP00000216797:Q271L;ENSP00000451257:Q228L;ENSP00000450514:Q181L	ENSP00000216797:Q271L	Q	-	2	0	NFKBIA	34941445	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.174000	0.50847	2.195000	0.70347	0.533000	0.62120	CAG	.	.		0.557	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529		A	35871694	T	A	35871694	3	1	77	1	0	0	0	0	1	0	0	0	10386	1580	55	4	149	4	NFKBIA	14	35871694	Missense_Mutation	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	12414977	35871694	71477846	68	10666										
C14orf106	55320	hgsc.bcm.edu	37	chr14	45693923	45693923	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ccttgaggttagaatatcaaTggatacatccaattcttcag	7	8	3	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr14:45693923T>C	ENST00000310806.4	-	11	2325	c.1867A>G	c.(1867-1869)Att>Gtt	p.I623V		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	623					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						AGAATATCAATGGATACATCC	0.299																																					p.I623V		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.A1867G						.						57	57	57					14																	45693923		2202	4297	6499	SO:0001583	missense	55320	exon11			TATCAATGGATAC	AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"kinetochore null 2 homolog (C. elegans)"		"chromosome 14 open reading frame 106"	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.1867A>G	chr14.hg19:g.45693923T>C	ENSP00000309790:p.Ile623Val	66.0	0.0		63.0	15.0	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	hg19	CCDS9684.1	.	.	.	.	.	.	.	.	.	.	T	0.554	-0.847955	0.02651	.	.	ENSG00000129534	ENST00000310806	T	0.17528	2.27	5.25	2.84	0.33178	.	0.857102	0.10489	N	0.668608	T	0.11580	0.0282	N	0.25647	0.755	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.36768	-0.9734	10	0.25751	T	0.34	-0.7599	7.3375	0.26617	0.0:0.177:0.0:0.823	.	623	Q6P0N0	M18BP_HUMAN	V	623	ENSP00000309790:I623V	ENSP00000309790:I623V	I	-	1	0	MIS18BP1	44763673	0.015000	0.18098	0.076000	0.20297	0.975000	0.68041	-0.022000	0.12480	0.383000	0.24910	0.477000	0.44152	ATT	.	.		0.299	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			C	45693923	T	C	45693923	3	2	77	1	0	0	0	0	1	0	0	0	1740	1464	51	2	1559	2	C14orf106	14	45693923	Missense_Mutation	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	9822229	45693923	61655617	69	10667										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63174666	63174667	+	Missense_Mutation	DNP	CC	CC	AG													0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tgaatcactgctcttggggtCctcagacaatagccccattg							TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr14:63174666_63174667CC>AG	ENST00000322893.7	-	11	2794_2795	c.2526_2527GG>CT	c.(2524-2529)gaGGac>gaCTac	p.842_843ED>DY	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	842					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CTCTTGGGGTCCTCAGACAATA	0.436																																					p.D843Y|p.E842D		Atlas-SNP	.											.	KCNH5	320	.	0			c.G2527T|c.G2526C						.																																			SO:0001583	missense	27133	exon11			TGGGGTCCTCAGA|GGGGTCCTCAGAC	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2526_2527delinsAG	chr14.hg19:g.63174666_63174667delinsAG	ENSP00000321427:p.E842_D843delinsDY	111.0|112.0	0.0		117.0|119.0	66.0|67.0	NM_139318	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	hg19	CCDS9756.1																																																																																			.	.		0.436	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		AG	63174667	CC	AG	63174666	3	1	77	1	0	0	0	0	1	0	0	0	8044	855	30	3	443	3	KCNH5	14	63174666	Missense_Mutation	DNP	CC	TCGA-CC-A7IL-01A-11D-A33Q-10	17480743	63174666	44174874	70	10668										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68273376	68273376	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	agcattgcccgctcaggatcTagatgatccggtgagactga	12	10	2	4			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr14:68273376T>C	ENST00000347230.4	-	6	1041	c.903A>G	c.(901-903)ctA>ctG	p.L301L	ZFYVE26_ENST00000555452.1_Silent_p.L301L	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	301					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		GCTCAGGATCTAGATGATCCG	0.478																																					p.L301L		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A903G						.						79	75	77					14																	68273376		2203	4300	6503	SO:0001819	synonymous_variant	23503	exon6			AGGATCTAGATGA	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.903A>G	chr14.hg19:g.68273376T>C		95.0	0.0		80.0	47.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	hg19	CCDS9788.1																																																																																			.	.		0.478	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		C	68273376	T	C	68273376	2	2	77	1	0	0	0	0	0	0	0	1	17683	1509	53	2		2	ZFYVE26	14	68273376	Silent	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	5098710	68273376	39076164	71	10669										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92472209	92472209	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	caatagtgtttttttccagaGaaagctgattgttaccagca	8	7	0	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr14:92472209G>T	ENST00000267622.4	-	11	2484	c.2111C>A	c.(2110-2112)tCt>tAt	p.S704Y		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	704					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TTTTTCCAGAGAAAGCTGATT	0.373			T	PDGFRB	AML																																p.S704Y	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.C2111A						.						106	112	110					14																	92472209		2203	4299	6502	SO:0001583	missense	9321	exon11			TCCAGAGAAAGCT	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.2111C>A	chr14.hg19:g.92472209G>T	ENSP00000267622:p.Ser704Tyr	131.0	0.0		114.0	40.0	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	hg19	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.921|5.921	0.354062|0.354062	0.11182|0.11182	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000554357|ENST00000267622;ENST00000542257	.|T	.|0.04360	.|3.64	6.16|6.16	5.22|5.22	0.72569|0.72569	.|.	.|0.386281	.|0.29444	.|N	.|0.012127	T|T	0.07683|0.07683	0.0193|0.0193	M|M	0.66939|0.66939	2.045|2.045	0.31504|0.31504	N|N	0.664407|0.664407	.|B;B	.|0.19200	.|0.007;0.034	.|B;B	.|0.18561	.|0.016;0.022	T|T	0.01869|0.01869	-1.1257|-1.1257	5|10	.|0.26408	.|T	.|0.33	.|.	12.8277|12.8277	0.57728|0.57728	0.0:0.2069:0.678:0.1151|0.0:0.2069:0.678:0.1151	.|.	.|440;704	.|F5H1Z0;Q15643	.|.;TRIPB_HUMAN	L|Y	419|704;440	.|ENSP00000267622:S704Y	.|ENSP00000267622:S704Y	F|S	-|-	3|2	2|0	TRIP11|TRIP11	91541962|91541962	0.974000|0.974000	0.33945|0.33945	0.993000|0.993000	0.49108|0.49108	0.302000|0.302000	0.27658|0.27658	1.706000|1.706000	0.37878|0.37878	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	TTC|TCT	.	.		0.373	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			T	92472209	G	T	92472209	3	4	77	1	0	0	0	0	1	0	0	0	16570	942	33	3	3872	3	TRIP11	14	92472209	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	24198833	92472209	14877331	72	10670										
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23889234	23889234	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	cccactcacactctgcgagcGcttcaaggtaatggaatggc	10	13	3	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr15:23889234G>A	ENST00000532292.1	-	1	1941	c.1847C>T	c.(1846-1848)gCg>gTg	p.A616V		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	499					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		CTCTGCGAGCGCTTCAAGGTA	0.562																																					p.A1219V		Atlas-SNP	.											.	MAGEL2	108	.	0			c.C3656T						.						61	64	63					15																	23889234		2035	4193	6228	SO:0001583	missense	54551	exon1			GCGAGCGCTTCAA	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.1847C>T	chr15.hg19:g.23889234G>A	ENSP00000433433:p.Ala616Val	81.0	0.0		67.0	35.0	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.61	3.170309	0.57584	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	T	0.63355	0.2504	M	0.81112	2.525	0.09310	N	1	.	.	.	.	.	.	T	0.57429	-0.7813	5	.	.	.	.	13.5932	0.61971	0.0:0.0:1.0:0.0	.	.	.	.	C	648	.	.	R	-	1	0	MAGEL2	21440327	0.341000	0.24801	0.017000	0.16124	0.637000	0.38172	4.118000	0.57884	2.671000	0.90904	0.563000	0.77884	CGC	.	.		0.562	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		A	23889234	G	A	23889234	3	1	77	1	0	0	0	0	1	0	0	0	9198	1087	38	1	97	1	MAGEL2	15	23889234	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10		23889234	78642158	73	10671										
DNAJC17	55192	hgsc.bcm.edu	37	chr15	41060161	41060161	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	cgtaggcggcccctcctggtCttcctgctgcatccgtgcga	12	16	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr15:41060161C>T	ENST00000220496.4	-	11	922	c.892G>A	c.(892-894)Gac>Aac	p.D298N	C15orf62_ENST00000344320.6_5'Flank|DNAJC17_ENST00000558727.1_5'UTR	NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	298					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)		nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|skin(1)	6		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		CCCTCCTGGTCTTCCTGCTGC	0.557																																					p.D298N		Atlas-SNP	.											.	DNAJC17	18	.	0			c.G892A						.						73	67	69					15																	41060161		2203	4300	6503	SO:0001583	missense	55192	exon11			CCTGGTCTTCCTG	AK001496	CCDS10065.1	15q15.1	2014-02-12			ENSG00000104129	ENSG00000104129		"Heat shock proteins / DNAJ (HSP40)", "RNA binding motif (RRM) containing"	25556	protein-coding gene	gene with protein product						12477932	Standard	NM_018163		Approved	FLJ10634	uc001zms.2	Q9NVM6	OTTHUMG00000130065	ENST00000220496.4:c.892G>A	chr15.hg19:g.41060161C>T	ENSP00000220496:p.Asp298Asn	14.0	0.0		21.0	16.0	NM_018163		Missense_Mutation	SNP	ENST00000220496.4	hg19	CCDS10065.1	.	.	.	.	.	.	.	.	.	.	C	31	5.077981	0.94000	.	.	ENSG00000104129	ENST00000220496	T	0.26518	1.73	5.74	5.74	0.90152	.	0.092864	0.64402	D	0.000001	T	0.52741	0.1753	M	0.83223	2.63	0.80722	D	1	D	0.58970	0.984	P	0.59357	0.856	T	0.56323	-0.7998	10	0.87932	D	0	.	18.055	0.89362	0.0:1.0:0.0:0.0	.	298	Q9NVM6	DJC17_HUMAN	N	298	ENSP00000220496:D298N	ENSP00000220496:D298N	D	-	1	0	DNAJC17	38847453	1.000000	0.71417	0.948000	0.38648	0.454000	0.32378	6.446000	0.73460	2.873000	0.98535	0.561000	0.74099	GAC	.	.		0.557	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163		T	41060161	C	T	41060161	3	4	77	1	0	0	0	0	1	0	0	0	4638	913	32	3	26	3	DNAJC17	15	41060161	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	17170927	41060161	61471231	74	10672										
FBN1	2200	hgsc.bcm.edu	37	chr15	48888574	48888574	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	agacagccactttcacaaacAgctgtaaaataaggagagag	9	8	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr15:48888574A>G	ENST00000316623.5	-	6	899	c.444T>C	c.(442-444)ccT>ccC	p.P148P		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	148	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TTTCACAAACAGCTGTAAAAT	0.428																																					p.P148P		Atlas-SNP	.											.	FBN1	310	.	0			c.T444C						.						87	81	83					15																	48888574		2197	4296	6493	SO:0001630	splice_region_variant	2200	exon6			ACAAACAGCTGTA	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.443-1T>C	chr15.hg19:g.48888574A>G		63.0	0.0		55.0	11.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	hg19	CCDS32232.1																																																																																			.	.		0.428	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		Silent	G	48888574	A	G	48888574	5	3	77	1	0	0	0	0	0	0	1	0	5710	202	7	2	8415	2	FBN1	15	48888574	Splice_Site	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10	7828413	48888574	53642818	75	10673										
TRIP4	9325	hgsc.bcm.edu	37	chr15	64686298	64686298	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	atttcggatcctttgcagcaGtgcttcaaaaaagatggtaa	9	7	1	1	rs115051562	byFrequency	TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr15:64686298G>T	ENST00000261884.3	+	2	315	c.255G>T	c.(253-255)caG>caT	p.Q85H	TRIP4_ENST00000559565.1_3'UTR	NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	85					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						CTTTGCAGCAGTGCTTCAAAA	0.328																																					p.Q85H		Atlas-SNP	.											.	TRIP4	43	.	0			c.G255T						.						77	76	76					15																	64686298		2203	4300	6503	SO:0001583	missense	9325	exon2			GCAGCAGTGCTTC	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"-"	12310	protein-coding gene	gene with protein product	"zinc finger, C2HC5-type"	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.255G>T	chr15.hg19:g.64686298G>T	ENSP00000261884:p.Gln85His	180.0	0.0		155.0	8.0	NM_016213	B2RAS0|Q96ED7|Q9UKH0	Missense_Mutation	SNP	ENST00000261884.3	hg19	CCDS10194.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.416659	0.42918	.	.	ENSG00000103671	ENST00000261884	.	.	.	5.68	2.76	0.32466	.	0.719058	0.14356	N	0.324751	T	0.31765	0.0807	L	0.36672	1.1	0.23089	N	0.998312	B	0.29162	0.235	B	0.31812	0.136	T	0.22173	-1.0224	9	0.45353	T	0.12	-16.4616	6.7238	0.23345	0.2764:0.1228:0.6008:0.0	.	85	Q15650	TRIP4_HUMAN	H	85	.	ENSP00000261884:Q85H	Q	+	3	2	TRIP4	62473351	0.000000	0.05858	0.992000	0.48379	0.985000	0.73830	-0.539000	0.06113	0.875000	0.35847	0.655000	0.94253	CAG	.	G|0.986;A|0.014		0.328	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213		T	64686298	G	T	64686298	3	4	77	1	0	0	0	0	1	0	0	0	16573	1020	36	3	261	3	TRIP4	15	64686298	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	15797724	64686298	37845094	76	10674										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9934503	9934503	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gtcactatgaaattcacacaCctagaaaagcagaaggtgag	9	8	2	4			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr16:9934503C>A	ENST00000396573.2	-	8	1961		c.e8+1		GRIN2A_ENST00000396575.2_Splice_Site|GRIN2A_ENST00000562109.1_Splice_Site|GRIN2A_ENST00000404927.2_Splice_Site|GRIN2A_ENST00000330684.3_Splice_Site|GRIN2A_ENST00000535259.1_Splice_Site	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A						directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AATTCACACACCTAGAAAAGC	0.433																																					.		Atlas-SNP	.											.	GRIN2A	366	.	0			c.1651+1G>T						.						107	91	97					16																	9934503		2197	4300	6497	SO:0001630	splice_region_variant	2903	exon8			CACACACCTAGAA		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.1651+1G>T	chr16.hg19:g.9934503C>A		138.0	0.0		137.0	41.0	NM_001134407	O00669|Q17RZ6	Splice_Site	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.771776	0.90108	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9735	0.89120	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GRIN2A	9842004	1.000000	0.71417	0.985000	0.45067	0.955000	0.61496	7.388000	0.79795	2.469000	0.83416	0.655000	0.94253	.	.	.		0.433	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		Intron	A	9934503	C	A	9934503	5	1	77	1	0	0	0	0	0	0	1	0	6788	521	18	3	2770	3	GRIN2A	16	9934503	Splice_Site	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10		9934503	80420250	77	10675										
TMC7	79905	hgsc.bcm.edu	37	chr16	19049311	19049311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tattgttctggctgttttagGggcatgcttttatgcaatat	10	5	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr16:19049311G>A	ENST00000304381.5	+	8	1251	c.1121G>A	c.(1120-1122)gGg>gAg	p.G374E	TMC7_ENST00000421369.3_Missense_Mutation_p.G264E|TMC7_ENST00000569532.1_Missense_Mutation_p.G374E|TMC7_ENST00000561963.1_3'UTR	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	374					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						GCTGTTTTAGGGGCATGCTTT	0.398																																					p.G374E		Atlas-SNP	.											.	TMC7	75	.	0			c.G1121A						.						217	187	197					16																	19049311		2197	4300	6497	SO:0001583	missense	79905	exon8			TTTTAGGGGCATG	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1121G>A	chr16.hg19:g.19049311G>A	ENSP00000304710:p.Gly374Glu	108.0	0.0		80.0	26.0	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Missense_Mutation	SNP	ENST00000304381.5	hg19	CCDS10573.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.533866	0.45073	.	.	ENSG00000170537	ENST00000304381;ENST00000421369	T;T	0.52057	0.68;0.68	5.5	-0.185	0.13276	.	0.422877	0.25319	N	0.031530	T	0.33847	0.0877	L	0.52126	1.63	0.20403	N	0.999908	B;P	0.37612	0.229;0.602	B;B	0.38296	0.128;0.27	T	0.14671	-1.0464	10	0.42905	T	0.14	.	2.2645	0.04075	0.1252:0.5038:0.1472:0.2238	.	374;374	Q7Z402;B3KSZ3	TMC7_HUMAN;.	E	374;264	ENSP00000304710:G374E;ENSP00000397081:G264E	ENSP00000304710:G374E	G	+	2	0	TMC7	18956812	0.016000	0.18221	0.016000	0.15963	0.511000	0.34104	0.277000	0.18734	0.211000	0.20683	-0.284000	0.09977	GGG	.	.		0.398	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847		A	19049311	G	A	19049311	3	1	77	1	0	0	0	0	1	0	0	0	16005	1232	43	3	1151	3	TMC7	16	19049311	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	9114808	19049311	71305442	78	10676										
VWA3A	146177	hgsc.bcm.edu	37	chr16	22149725	22149725	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	aagaaccattcaggaaaagtActgggaagttcagccctccc	9	11	2	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr16:22149725A>G	ENST00000389398.5	+	22	2280	c.2184A>G	c.(2182-2184)gtA>gtG	p.V728V	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	728						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		CAGGAAAAGTACTGGGAAGTT	0.577																																					p.V728V		Atlas-SNP	.											.	VWA3A	115	.	0			c.A2184G						.						40	44	43					16																	22149725		1957	4147	6104	SO:0001819	synonymous_variant	146177	exon22			AAAAGTACTGGGA	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2184A>G	chr16.hg19:g.22149725A>G		85.0	0.0		62.0	37.0	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Silent	SNP	ENST00000389398.5	hg19	CCDS45441.1																																																																																			.	.		0.577	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			G	22149725	A	G	22149725	2	3	77	1	0	0	0	0	0	0	0	1	17255	378	14	2		2	VWA3A	16	22149725	Silent	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10	3100414	22149725	68205028	79	10677										
SCNN1G	6340	hgsc.bcm.edu	37	chr16	23226546	23226546	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ccgccgccagtggcagaaagCcaaggagtggtgggcctgga	17	11	0	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr16:23226546C>A	ENST00000300061.2	+	13	1849	c.1706C>A	c.(1705-1707)gCc>gAc	p.A569D	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	569					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	TGGCAGAAAGCCAAGGAGTGG	0.567																																					p.A569D		Atlas-SNP	.											.	SCNN1G	82	.	0			c.C1706A						.						93	89	90					16																	23226546		2197	4300	6497	SO:0001583	missense	6340	exon13			AGAAAGCCAAGGA	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.1706C>A	chr16.hg19:g.23226546C>A	ENSP00000300061:p.Ala569Asp	53.0	0.0		64.0	43.0	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Missense_Mutation	SNP	ENST00000300061.2	hg19	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	C	17.87	3.495716	0.64186	.	.	ENSG00000166828	ENST00000300061	T	0.71579	-0.58	5.22	5.22	0.72569	.	0.246452	0.35555	N	0.003128	T	0.51227	0.1662	N	0.08118	0	0.42033	D	0.991032	P	0.50272	0.933	P	0.44860	0.462	T	0.51332	-0.8719	10	0.19590	T	0.45	-0.3453	11.2783	0.49180	0.0:0.9165:0.0:0.0835	.	569	P51170	SCNNG_HUMAN	D	569	ENSP00000300061:A569D	ENSP00000300061:A569D	A	+	2	0	SCNN1G	23134047	0.889000	0.30405	1.000000	0.80357	0.954000	0.61252	1.803000	0.38863	2.411000	0.81874	0.561000	0.74099	GCC	.	.		0.567	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		A	23226546	C	A	23226546	3	1	77	1	0	0	0	0	1	0	0	0	13945	739	26	3	1752	3	SCNN1G	16	23226546	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	1076821	23226546	67128207	80	10678										
CES1	1066	hgsc.bcm.edu	37	chr16	55862715	55862715	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tggcattcttcacaaagctcCatggttctgcaggctgcggt	11	11	3	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr16:55862715C>T	ENST00000361503.4	-	2	351	c.221G>A	c.(220-222)tGg>tAg	p.W74*	CES1_ENST00000566555.1_5'Flank|CES1_ENST00000422046.2_Nonsense_Mutation_p.W74*|CES1_ENST00000360526.3_Nonsense_Mutation_p.W75*			P23141	EST1_HUMAN	carboxylesterase 1	74					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	CACAAAGCTCCATGGTTCTGC	0.537																																					p.W75X	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.G224A						.						110	109	110					16																	55862715		2198	4300	6498	SO:0001587	stop_gained	1066	exon2			AAGCTCCATGGTT	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"Carboxylesterases"	1863	protein-coding gene	gene with protein product	"human monocyte/macrophage serine esterase 1"	114835	"carboxylesterase 1 (monocyte/macrophage serine esterase 1)"			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.221G>A	chr16.hg19:g.55862715C>T	ENSP00000355193:p.Trp74*	153.0	0.0		131.0	12.0	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Nonsense_Mutation	SNP	ENST00000361503.4	hg19	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	19.73	3.881416	0.72294	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	.	.	.	4.48	4.48	0.54585	.	0.000000	0.45606	D	0.000354	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.6933	0.69101	0.0:1.0:0.0:0.0	.	.	.	.	X	75;74;74	.	ENSP00000353720:W75X	W	-	2	0	CES1	54420216	1.000000	0.71417	0.371000	0.25978	0.013000	0.08279	7.126000	0.77201	2.051000	0.60960	0.393000	0.25936	TGG	.	.		0.537	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266		T	55862715	C	T	55862715	4	4	77	1	0	0	0	0	0	1	0	0	3271	595	21	3	1534	3	CES1	16	55862715	Nonsense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	32636169	55862715	34492038	81	10679										
CES2	8824	hgsc.bcm.edu	37	chr16	66976621	66976621	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ctcaagaacatcaggccaccGcacatgaaggcagaccatgg	10	13	2	3			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr16:66976621G>A	ENST00000317091.4	+	10	2529	c.1545G>A	c.(1543-1545)ccG>ccA	p.P515P	CES2_ENST00000417689.1_Silent_p.P515P|RP11-361L15.4_ENST00000566869.1_RNA	NM_003869.5	NP_003860.2	O00748	EST2_HUMAN	carboxylesterase 2	451					catabolic process (GO:0009056)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)			breast(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|urinary_tract(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0663)|Epithelial(162;0.166)	Dabigatran etexilate(DB06695)|Irinotecan(DB00762)|Mycophenolate mofetil(DB00688)|Prasugrel(DB06209)	TCAGGCCACCGCACATGAAGG	0.562																																					p.P515P	Ovarian(70;1230 1691 37888 38351)	Atlas-SNP	.											.	CES2	43	.	0			c.G1545A						.						92	85	88					16																	66976621		2200	4300	6500	SO:0001819	synonymous_variant	8824	exon10			GCCACCGCACATG	BC032095	CCDS10825.1, CCDS45507.1	16q22.1	2010-10-12	2010-10-12		ENSG00000172831	ENSG00000172831		"Carboxylesterases"	1864	protein-coding gene	gene with protein product		605278	"carboxylesterase 2 (intestine, liver)"			9169443, 9144407, 20931200	Standard	NM_198061		Approved	CE-2, iCE, CES2A1	uc002eqr.3	O00748	OTTHUMG00000137517	ENST00000317091.4:c.1545G>A	chr16.hg19:g.66976621G>A		76.0	0.0		99.0	31.0	NM_003869	A8K367|Q16859|Q5MAB8|Q7Z366|Q8IUP4|Q8TCP8	Silent	SNP	ENST00000317091.4	hg19	CCDS10825.1																																																																																			.	.		0.562	CES2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268838.2	NM_003869		A	66976621	G	A	66976621	2	1	77	1	0	0	0	0	0	0	0	1	3272	1074	38	1		1	CES2	16	66976621	Silent	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	11113906	66976621	23378132	82	10680										
CTCF	10664	hgsc.bcm.edu	37	chr16	67650677	67650677	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ctcacaagtgcccagactgcGacatggcctttgtgaccagt	10	13	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr16:67650677G>T	ENST00000264010.4	+	5	1426	c.982G>T	c.(982-984)Gac>Tac	p.D328Y	AC009095.4_ENST00000388909.4_RNA|CTCF_ENST00000401394.1_5'UTR	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	328					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		CCCAGACTGCGACATGGCCTT	0.498																																					p.D328Y	Colon(175;1200 1966 6945 23069 27405)	Atlas-SNP	.											.	CTCF	193	.	0			c.G982T						.						301	254	270					16																	67650677		2198	4300	6498	SO:0001583	missense	10664	exon5			GACTGCGACATGG	U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"Zinc fingers, C2H2-type"	13723	protein-coding gene	gene with protein product	"11 zinc finger transcriptional repressor"	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.982G>T	chr16.hg19:g.67650677G>T	ENSP00000264010:p.Asp328Tyr	112.0	0.0		134.0	36.0	NM_006565	B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	ENST00000264010.4	hg19	CCDS10841.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831258	0.91036	.	.	ENSG00000102974	ENST00000264010	T	0.07688	3.17	4.89	4.89	0.63831	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.153953	0.43919	D	0.000502	T	0.34745	0.0908	M	0.85299	2.745	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.20672	-1.0268	10	0.59425	D	0.04	.	18.2991	0.90157	0.0:0.0:1.0:0.0	.	328	P49711	CTCF_HUMAN	Y	328	ENSP00000264010:D328Y	ENSP00000264010:D328Y	D	+	1	0	CTCF	66208178	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	9.397000	0.97276	2.553000	0.86117	0.555000	0.69702	GAC	.	.		0.498	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2	NM_006565		T	67650677	G	T	67650677	3	4	77	1	0	0	0	0	1	0	0	0	4002	1058	37	1	992	1	CTCF	16	67650677	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	674056	67650677	22704076	83	10681										
ZNF23	7571	hgsc.bcm.edu	37	chr16	71482852	71482852	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	actgatagggcttttctcctGtgtggatgctctgatgctgc	12	9	2	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr16:71482852G>C	ENST00000393539.2	-	6	1889	c.1076C>G	c.(1075-1077)aCa>aGa	p.T359R	ZNF23_ENST00000564528.1_Missense_Mutation_p.T301R|ZNF23_ENST00000539742.1_5'UTR|ZNF23_ENST00000358700.2_3'UTR|AC010547.9_ENST00000561908.1_3'UTR|ZNF23_ENST00000428724.2_Missense_Mutation_p.T301R|ZNF23_ENST00000497160.1_3'UTR|ZNF23_ENST00000417828.1_Missense_Mutation_p.T359R|ZNF23_ENST00000357254.4_Missense_Mutation_p.T359R	NM_145911.1	NP_666016.1	P17027	ZNF23_HUMAN	zinc finger protein 23	359					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(14)|stomach(1)|urinary_tract(1)	29		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		CTTTTCTCCTGTGTGGATGCT	0.428																																					p.T359R		Atlas-SNP	.											.	ZNF23	65	.	0			c.C1076G						.						70	65	67					16																	71482852		2198	4300	6498	SO:0001583	missense	7571	exon6			TCTCCTGTGTGGA	X52347	CCDS10900.1	16q22.2	2013-03-28	2012-07-12		ENSG00000167377	ENSG00000167377		"Zinc fingers, C2H2-type"	13023	protein-coding gene	gene with protein product		194527	"zinc finger protein 359"	ZNF359			Standard	NM_145911		Approved	KOX16, Zfp612, ZNF612	uc002faf.3	P17027	OTTHUMG00000176797	ENST00000393539.2:c.1076C>G	chr16.hg19:g.71482852G>C	ENSP00000377171:p.Thr359Arg	77.0	0.0		60.0	23.0	NM_145911	Q8NDP5|Q96IT3|Q9UG42	Missense_Mutation	SNP	ENST00000393539.2	hg19	CCDS10900.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534941	0.64972	.	.	ENSG00000167377	ENST00000393539;ENST00000357254;ENST00000417828;ENST00000428724;ENST00000539742;ENST00000358700	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	4.15	3.18	0.36537	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45606	D	0.000343	T	0.45155	0.1328	M	0.62016	1.91	0.42091	D	0.991292	D;D	0.89917	1.0;0.995	D;D	0.80764	0.994;0.91	T	0.47368	-0.9123	10	0.87932	D	0	-23.2998	11.4521	0.50158	0.0:0.0:0.8182:0.1818	.	359;359	B3KR55;P17027	.;ZNF23_HUMAN	R	359;359;359;301;301;159	ENSP00000377171:T359R;ENSP00000349796:T359R;ENSP00000395712:T359R;ENSP00000387673:T301R	ENSP00000349796:T359R	T	-	2	0	ZNF23	70040353	0.994000	0.37717	0.998000	0.56505	0.975000	0.68041	2.119000	0.41958	1.298000	0.44778	0.561000	0.74099	ACA	.	.		0.428	ZNF23-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268985.23	NM_145911		C	71482852	G	C	71482852	3	2	77	1	0	0	0	0	1	0	0	0	17798	1377	48	4	859	4	ZNF23	16	71482852	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	3832175	71482852	18871901	84	10682										
CRISPLD2	83716	hgsc.bcm.edu	37	chr16	84884214	84884214	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	caagatcggttgtgctgtgaAcacctgccggaagatgactg	13	9	0	4			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr16:84884214A>G	ENST00000262424.5	+	5	757	c.533A>G	c.(532-534)aAc>aGc	p.N178S	AC025280.1_ENST00000584136.1_RNA|CRISPLD2_ENST00000567845.1_Missense_Mutation_p.N178S|CRISPLD2_ENST00000564567.1_Missense_Mutation_p.N178S|CRISPLD2_ENST00000566431.1_3'UTR	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	178	SCP.				extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)			endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						TGTGCTGTGAACACCTGCCGG	0.463																																					p.N178S		Atlas-SNP	.											.	CRISPLD2	36	.	0			c.A533G						.						164	150	155					16																	84884214		2199	4300	6499	SO:0001583	missense	83716	exon5			CTGTGAACACCTG	AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"LCCL domain containing cysteine-rich secretory protein 2"	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.533A>G	chr16.hg19:g.84884214A>G	ENSP00000262424:p.Asn178Ser	96.0	0.0		85.0	20.0	NM_031476	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Missense_Mutation	SNP	ENST00000262424.5	hg19	CCDS10949.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.130502	0.56828	.	.	ENSG00000103196	ENST00000262424	T	0.07021	3.23	5.84	4.72	0.59763	CAP domain (3);	0.250702	0.45867	D	0.000338	T	0.07593	0.0191	N	0.20530	0.585	0.80722	D	1	B;B;P	0.44044	0.0;0.022;0.825	B;B;B	0.42625	0.011;0.041;0.393	T	0.21552	-1.0242	10	0.66056	D	0.02	.	12.0712	0.53618	0.8559:0.1441:0.0:0.0	.	178;178;178	Q9H0B8;Q9H0B8-2;Q9H0B8-3	CRLD2_HUMAN;.;.	S	178	ENSP00000262424:N178S	ENSP00000262424:N178S	N	+	2	0	CRISPLD2	83441715	1.000000	0.71417	0.995000	0.50966	0.871000	0.50021	6.956000	0.76013	1.002000	0.39104	0.459000	0.35465	AAC	.	.		0.463	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476		G	84884214	A	G	84884214	3	3	77	1	0	0	0	0	1	0	0	0	3885	43	2	2	547	2	CRISPLD2	16	84884214	Missense_Mutation	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10	13401362	84884214	5470539	85	10683										
KRTAP4-7	100132476	hgsc.bcm.edu	37	chr17	39240735	39240735	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gccccagctgctgtatgtccAgctgctgcaagccccagtgc	11	16	0	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr17:39240735A>C	ENST00000391417.4	+	1	277	c.277A>C	c.(277-279)Agc>Cgc	p.S93R		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	118	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						ctgtatgtccagctgctgcaa	0.682																																					p.S93R		Atlas-SNP	.											.	KRTAP4-7	49	.	0			c.A277C						.						10	16	14					17																	39240735		683	1572	2255	SO:0001583	missense	100132476	exon1			ATGTCCAGCTGCT	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"Keratin associated proteins"	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.277A>C	chr17.hg19:g.39240735A>C	ENSP00000375236:p.Ser93Arg	21.0	0.0		40.0	34.0	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	hg19	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	12.99	2.103902	0.37145	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00642	6.02	3.69	2.56	0.30785	.	.	.	.	.	T	0.01558	0.0050	.	.	.	0.30411	N	0.779047	D	0.53462	0.96	P	0.54815	0.761	T	0.41215	-0.9521	8	0.62326	D	0.03	.	8.1351	0.31050	0.6023:0.3977:0.0:0.0	.	93	Q9BYR0	KRA47_HUMAN	R	93;84	ENSP00000375236:S93R	ENSP00000375236:S93R	S	+	1	0	KRTAP4-9;KRTAP4-7	36494261	0.987000	0.35691	0.998000	0.56505	0.882000	0.50991	0.768000	0.26590	0.356000	0.24157	0.254000	0.18369	AGC	.	.		0.682	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1			C	39240735	A	C	39240735	3	2	77	1	0	0	0	0	1	0	0	0	8564	188	7	5	279	5	KRTAP4-7	17	39240735	Missense_Mutation	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10		39240735	41954475	86	10684										
C19orf21	126353	hgsc.bcm.edu	37	chr19	763554	763554	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	aacgccatggcagagcgctgGgaatcccgcatctacgccag	12	14	1	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr19:763554G>T	ENST00000215582.6	+	5	2107	c.2004G>T	c.(2002-2004)tgG>tgT	p.W668C		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	668					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CAGAGCGCTGGGAATCCCGCA	0.627																																					p.W668C		Atlas-SNP	.											.	C19orf21	56	.	0			c.G2004T						.						54	49	51					19																	763554		2203	4300	6503	SO:0001583	missense	126353	exon5			GCGCTGGGAATCC	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.2004G>T	chr19.hg19:g.763554G>T	ENSP00000215582:p.Trp668Cys	43.0	0.0		26.0	12.0	NM_173481		Missense_Mutation	SNP	ENST00000215582.6	hg19	CCDS12042.1	.	.	.	.	.	.	.	.	.	.	G	19.41	3.822688	0.71028	.	.	ENSG00000099812	ENST00000215582	D	0.84442	-1.85	4.62	4.62	0.57501	.	0.000000	0.56097	D	0.000038	D	0.90758	0.7099	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91778	0.5433	10	0.87932	D	0	-24.4772	14.9823	0.71319	0.0:0.0:1.0:0.0	.	668	Q8IVT2	CS021_HUMAN	C	668	ENSP00000215582:W668C	ENSP00000215582:W668C	W	+	3	0	C19orf21	714554	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.281000	0.72632	2.306000	0.77630	0.561000	0.74099	TGG	.	.		0.627	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		T	763554	G	T	763554	3	4	77	1	0	0	0	0	1	0	0	0	1915	1241	43	3	2018	3	C19orf21	19	763554	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10		763554	58365429	87	10685										
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11553327	11553327	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	agcagcaccagaagctgtggGaaggtatggcagaaatggcc	15	8	0	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr19:11553327G>A	ENST00000589838.1	+	6	595	c.595G>A	c.(595-597)Gaa>Aaa	p.E199K	PRKCSH_ENST00000252455.2_Missense_Mutation_p.E199K|PRKCSH_ENST00000412601.1_Missense_Mutation_p.E199K|PRKCSH_ENST00000591462.1_Missense_Mutation_p.E199K|PRKCSH_ENST00000592741.1_Missense_Mutation_p.E199K|PRKCSH_ENST00000587327.1_Missense_Mutation_p.E199K			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	199					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						GAAGCTGTGGGAAGGTATGGC	0.552																																					p.E199K		Atlas-SNP	.											.	PRKCSH	55	.	0			c.G595A						.						98	75	83					19																	11553327		2203	4300	6503	SO:0001583	missense	5589	exon7			CTGTGGGAAGGTA		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"EF-hand domain containing"	9411	protein-coding gene	gene with protein product		177060	"polycystic liver disease"	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.595G>A	chr19.hg19:g.11553327G>A	ENSP00000465461:p.Glu199Lys	66.0	0.0		40.0	16.0	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Missense_Mutation	SNP	ENST00000589838.1	hg19	CCDS32911.1	.	.	.	.	.	.	.	.	.	.	G	31	5.072765	0.93950	.	.	ENSG00000130175	ENST00000252455;ENST00000412601	T;T	0.73897	1.12;-0.79	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.84897	0.5574	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;0.996;1.0	D;P;D	0.87578	0.998;0.885;0.997	T	0.82102	-0.0623	10	0.20046	T	0.44	-24.0032	17.2438	0.87021	0.0:0.0:1.0:0.0	.	199;199;199	E7EQZ9;A8K318;P14314	.;.;GLU2B_HUMAN	K	199	ENSP00000252455:E199K;ENSP00000395616:E199K	ENSP00000252455:E199K	E	+	1	0	PRKCSH	11414327	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.467000	0.90390	2.372000	0.80975	0.655000	0.94253	GAA	.	.		0.552	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			A	11553327	G	A	11553327	3	1	77	1	0	0	0	0	1	0	0	0	12528	1175	41	3	617	3	PRKCSH	19	11553327	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	10789773	11553327	47575656	88	10686										
ZNF507	22847	hgsc.bcm.edu	37	chr19	32845521	32845524	+	Frame_Shift_Del	DEL	AGAA	AGAA	-													0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	accgtcattgaaaaattgagAgaaaggacagaccaaaacgc					rs367792223		TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	AGAA	AGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr19:32845521_32845524delAGAA	ENST00000311921.4	+	2	1977_1980	c.1785_1788delAGAA	c.(1783-1788)agagaafs	p.RE595fs	ZNF507_ENST00000355898.5_Frame_Shift_Del_p.RE595fs|ZNF507_ENST00000544431.1_Frame_Shift_Del_p.RE595fs	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	595					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					AAAAATTGAGAGAAAGGACAGACC	0.485																																					p.595_596del		Atlas-Indel,Pindel	.											.	ZNF507	92	.	0			c.1784_1787del						.																																			SO:0001589	frameshift_variant	22847	exon3			.	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"Zinc fingers, C2H2-type"	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.1785_1788delAGAA	chr19.hg19:g.32845521_32845524delAGAA	ENSP00000312277:p.Arg595fs	116.0	0.0		72.0	37.0	NM_001136156	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Frame_Shift_Del	DEL	ENST00000311921.4	hg19	CCDS32985.1																																																																																			.	.		0.485	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910		-	32845524	AGAA	-	32845521	7	5	77	1	0	1	0	1	0	0	0	0	17968	301	11	0	1787	0	ZNF507	19	32845521	Frame_Shift_Del	DEL	AGAA	TCGA-CC-A7IL-01A-11D-A33Q-10	21292194	32845521	26283462	89	10687										
ZNF793	390927	hgsc.bcm.edu	37	chr19	38028629	38028629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	agaagtcatgcctcaataaaCattggagaactcacacagga	8	9	3	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr19:38028629C>T	ENST00000587143.1	+	6	1304	c.1069C>T	c.(1069-1071)Cat>Tat	p.H357Y	ZNF793_ENST00000588578.1_3'UTR|ZNF793_ENST00000445217.1_Missense_Mutation_p.H357Y|ZNF793_ENST00000589319.1_Intron|ZNF793_ENST00000542455.1_Missense_Mutation_p.H357Y			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	357					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCTCAATAAACATTGGAGAAC	0.443																																					p.H357Y	Melanoma(44;400 1431 1499 19093)	Atlas-SNP	.											.	ZNF793	50	.	0			c.C1069T						.						76	84	81					19																	38028629		2156	4288	6444	SO:0001583	missense	390927	exon8			AATAAACATTGGA	AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.1069C>T	chr19.hg19:g.38028629C>T	ENSP00000468605:p.His357Tyr	98.0	0.0		51.0	18.0	NM_001013659	E9PGN4|Q7Z3Q9	Missense_Mutation	SNP	ENST00000587143.1	hg19	CCDS46062.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.708892	0.68615	.	.	ENSG00000188227	ENST00000542455;ENST00000418827;ENST00000445217;ENST00000322299	D;D	0.86769	-2.17;-2.17	4.13	3.04	0.35103	.	0.000000	0.38837	N	0.001543	D	0.94909	0.8354	H	0.95114	3.625	0.33293	D	0.563767	D	0.89917	1.0	D	0.87578	0.998	D	0.97021	0.9743	10	0.87932	D	0	.	12.7454	0.57278	0.0:0.8325:0.1675:0.0	.	357	E9PGN4	.	Y	357;357;357;356	ENSP00000444355:H357Y;ENSP00000396402:H357Y	ENSP00000318811:H356Y	H	+	1	0	ZNF793	42720469	0.998000	0.40836	0.983000	0.44433	0.951000	0.60555	5.043000	0.64208	1.007000	0.39238	0.650000	0.86243	CAT	.	.		0.443	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		T	38028629	C	T	38028629	3	4	77	1	0	0	0	0	1	0	0	0	18180	478	17	3	1083	3	ZNF793	19	38028629	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	5183108	38028629	21100354	90	10688										
CKM	1158	hgsc.bcm.edu	37	chr19	45810804	45810804	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tgcgccagcttcacatgcacGcctccacgcagcccagtgcc	9	19	1	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr19:45810804G>T	ENST00000221476.3	-	7	1056	c.882C>A	c.(880-882)ggC>ggA	p.G294G		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	294	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	TCACATGCACGCCTCCACGCA	0.607																																					p.G294G		Atlas-SNP	.											.	CKM	40	.	0			c.C882A						.						80	70	73					19																	45810804		2203	4300	6503	SO:0001819	synonymous_variant	1158	exon7			ATGCACGCCTCCA	M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.882C>A	chr19.hg19:g.45810804G>T		65.0	0.0		42.0	16.0	NM_001824	Q96QL9	Silent	SNP	ENST00000221476.3	hg19	CCDS12659.1																																																																																			.	.		0.607	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1			T	45810804	G	T	45810804	2	4	77	1	0	0	0	0	0	0	0	1	3450	1074	38	1		1	CKM	19	45810804	Silent	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	7782175	45810804	13318179	91	10689										
ALDH16A1	126133	hgsc.bcm.edu	37	chr19	49962955	49962955	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	aggtgatccagaagcaccagCggctgctgtggaccctggaa	14	11	0	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr19:49962955C>T	ENST00000293350.4	+	4	512	c.349C>T	c.(349-351)Cgg>Tgg	p.R117W	ALDH16A1_ENST00000433981.2_5'UTR|ALDH16A1_ENST00000598015.1_3'UTR|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.R117W|ALDH16A1_ENST00000540132.1_Intron	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	117						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		GAAGCACCAGCGGCTGCTGTG	0.622																																					p.R117W		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.C349T						.						44	48	47					19																	49962955		2203	4299	6502	SO:0001583	missense	126133	exon4			CACCAGCGGCTGC	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"Aldehyde dehydrogenases"	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.349C>T	chr19.hg19:g.49962955C>T	ENSP00000293350:p.Arg117Trp	90.0	0.0		65.0	27.0	NM_001145396	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	hg19	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.220844	0.79464	.	.	ENSG00000161618	ENST00000293350;ENST00000455361	T;T	0.76578	-1.03;-1.03	5.32	2.87	0.33458	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.247502	0.40640	N	0.001053	D	0.85617	0.5738	M	0.86268	2.805	0.80722	D	1	D;D	0.76494	0.999;0.998	P;P	0.60886	0.88;0.87	D	0.86934	0.2075	10	0.87932	D	0	-8.6509	9.913	0.41417	0.4416:0.5584:0.0:0.0	.	117;117	B4DLQ1;Q8IZ83	.;A16A1_HUMAN	W	117	ENSP00000293350:R117W;ENSP00000410142:R117W	ENSP00000293350:R117W	R	+	1	2	ALDH16A1	54654767	0.844000	0.29557	1.000000	0.80357	0.948000	0.59901	0.466000	0.22019	1.355000	0.45865	0.460000	0.39030	CGG	.	.		0.622	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		T	49962955	C	T	49962955	3	4	77	1	0	0	0	0	1	0	0	0	488	759	27	1	363	1	ALDH16A1	19	49962955	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	4152151	49962955	9166028	92	10690										
NLRP4	147945	hgsc.bcm.edu	37	chr19	56372857	56372857	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	agcaccctcagcgagtcgacCtttgtgacctggtgtaacca	10	13	1	1	rs200258143		TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr19:56372857C>A	ENST00000301295.6	+	4	2384	c.1962C>A	c.(1960-1962)acC>acA	p.T654T	NLRP4_ENST00000587891.1_Silent_p.T579T|NLRP4_ENST00000346986.5_Silent_p.T654T	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	654					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GCGAGTCGACCTTTGTGACCT	0.557																																					p.T654T		Atlas-SNP	.											.	NLRP4	331	.	0			c.C1962A						.						118	99	106					19																	56372857		2203	4300	6503	SO:0001819	synonymous_variant	147945	exon4			GTCGACCTTTGTG	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1962C>A	chr19.hg19:g.56372857C>A		85.0	0.0		43.0	20.0	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	hg19	CCDS12936.1																																																																																			.	C|1.000;G|0.000		0.557	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		A	56372857	C	A	56372857	2	1	77	1	0	0	0	0	0	0	0	1	10488	668	24	3		3	NLRP4	19	56372857	Silent	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	6409902	56372857	2756126	93	10691										
ZIM3	114026	hgsc.bcm.edu	37	chr19	57647323	57647323	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tacatcatctatgcccagtgGaagtattttcttagatccgt	7	9	3	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr19:57647323G>A	ENST00000269834.1	-	5	767	c.382C>T	c.(382-384)Cca>Tca	p.P128S	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	128					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ATGCCCAGTGGAAGTATTTTC	0.388																																					p.P128S		Atlas-SNP	.											.	ZIM3	107	.	0			c.C382T						.						224	216	219					19																	57647323		2203	4300	6503	SO:0001583	missense	114026	exon5			CCAGTGGAAGTAT	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.382C>T	chr19.hg19:g.57647323G>A	ENSP00000269834:p.Pro128Ser	146.0	0.0		84.0	40.0	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	hg19	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	G	2.902	-0.227190	0.06022	.	.	ENSG00000141946	ENST00000269834	T	0.04083	3.71	2.18	2.18	0.27775	.	.	.	.	.	T	0.02494	0.0076	N	0.12182	0.205	0.09310	N	1	B	0.23377	0.084	B	0.19148	0.024	T	0.43734	-0.9373	9	0.07325	T	0.83	.	8.2657	0.31813	0.0:0.0:0.7631:0.2369	.	128	Q96PE6	ZIM3_HUMAN	S	128	ENSP00000269834:P128S	ENSP00000269834:P128S	P	-	1	0	ZIM3	62339135	0.011000	0.17503	0.003000	0.11579	0.100000	0.18952	0.737000	0.26144	1.523000	0.49018	0.313000	0.20887	CCA	.	.		0.388	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			A	57647323	G	A	57647323	3	1	77	1	0	0	0	0	1	0	0	0	17700	1174	41	3	1040	3	ZIM3	19	57647323	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	1274466	57647323	1481660	94	10692										
ZNF417	147687	hgsc.bcm.edu	37	chr19	58420786	58420786	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	tctttccagtgtggactcgcTgatgttgaataaggctgctc	11	9	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr19:58420786T>A	ENST00000312026.5	-	3	1024	c.860A>T	c.(859-861)cAg>cTg	p.Q287L	ZNF417_ENST00000595559.1_Missense_Mutation_p.Q286L|CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000536263.1_Missense_Mutation_p.Q88L	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	287					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		GTGGACTCGCTGATGTTGAAT	0.463																																					p.Q287L		Atlas-SNP	.											.	ZNF417	44	.	0			c.A860T						.						158	156	156					19																	58420786		2203	4300	6503	SO:0001583	missense	147687	exon3			ACTCGCTGATGTT	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"Zinc fingers, C2H2-type", "-"	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.860A>T	chr19.hg19:g.58420786T>A	ENSP00000311319:p.Gln287Leu	270.0	0.0		188.0	72.0	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	hg19	CCDS12965.1	.	.	.	.	.	.	.	.	.	.	.	7.949	0.744362	0.15710	.	.	ENSG00000173480	ENST00000312026;ENST00000536263	T;T	0.27256	2.51;1.68	1.68	0.577	0.17385	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.14657	0.0354	N	0.17631	0.505	0.09310	N	1	B;P	0.50272	0.403;0.933	B;B	0.41271	0.111;0.352	T	0.13548	-1.0505	9	0.66056	D	0.02	.	5.5656	0.17168	0.0:0.1624:0.0:0.8376	.	287;287	F5H0M9;Q8TAU3	.;ZN417_HUMAN	L	287;88	ENSP00000311319:Q287L;ENSP00000442760:Q88L	ENSP00000311319:Q287L	Q	-	2	0	ZNF417	63112598	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.070000	0.14573	-0.036000	0.13669	0.155000	0.16302	CAG	.	.		0.463	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475		A	58420786	T	A	58420786	3	1	77	1	0	0	0	0	1	0	0	0	17909	1580	55	4	871	4	ZNF417	19	58420786	Missense_Mutation	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	773463	58420786	708197	95	10693										
ZSCAN18	65982	hgsc.bcm.edu	37	chr19	58597611	58597611	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gtgtccagcctggaggcagcGtcaggctgggaaagctgata	16	9	1	1	rs147947490	byFrequency	TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr19:58597611G>A	ENST00000240727.6	-	6	1167	c.768C>T	c.(766-768)gaC>gaT	p.D256D	ZSCAN18_ENST00000421612.2_Silent_p.D121D|ZSCAN18_ENST00000600404.1_Silent_p.D312D|ZSCAN18_ENST00000601144.1_Silent_p.D256D	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	256					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|skin(3)	19		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		TGGAGGCAGCGTCAGGCTGGG	0.542																																					p.D312D		Atlas-SNP	.											.	ZSCAN18	104	.	0			c.C936T						.						74	64	67					19																	58597611		2203	4300	6503	SO:0001819	synonymous_variant	65982	exon6			GGCAGCGTCAGGC	AY280799, AY279352	CCDS12971.1, CCDS46214.1, CCDS46215.1	19q13.43	2013-01-09	2007-02-20	2007-02-20		ENSG00000121413		"-", "Zinc fingers, C2H2-type"	21037	protein-coding gene	gene with protein product			"zinc finger protein 447"	ZNF447			Standard	NM_001145542		Approved	FLJ12895	uc010yht.1	Q8TBC5		ENST00000240727.6:c.768C>T	chr19.hg19:g.58597611G>A		208.0	0.0		102.0	48.0	NM_001145542	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	Silent	SNP	ENST00000240727.6	hg19	CCDS12971.1																																																																																			.	G|0.993;C|0.007		0.542	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926		A	58597611	G	A	58597611	2	1	77	1	0	0	0	0	0	0	0	1	18245	1136	40	1		1	ZSCAN18	19	58597611	Silent	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	176825	58597611	531372	96	10694										
ANKRD5	63926	hgsc.bcm.edu	37	chr20	10030419	10030424	+	In_Frame_Del	DEL	ATTTAA	ATTTAA	-													0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	attctttaaaggaaccagatAtttaaacaagtcttttgtct							TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	ATTTAA	ATTTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr20:10030419_10030424delATTTAA	ENST00000378380.3	+	6	1531_1536	c.1202_1207delATTTAA	c.(1201-1209)tatttaaac>tac	p.LN402del	ANKEF1_ENST00000488991.1_3'UTR|SNAP25-AS1_ENST00000603542.1_RNA|SNAP25-AS1_ENST00000421143.2_RNA|ANKEF1_ENST00000378392.1_In_Frame_Del_p.LN402del	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	402							calcium ion binding (GO:0005509)										GGAACCAGATATTTAAACAAGTCTTT	0.413																																					p.401_402del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1201_1206del						.																																			SO:0001651	inframe_deletion	63926	exon6			.	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.1202_1207delATTTAA	chr20.hg19:g.10030419_10030424delATTTAA	ENSP00000367631:p.Leu402_Asn403del	126.0	0.0		81.0	27.0	NM_198798	B3KUQ0|Q9H6Y9	In_Frame_Del	DEL	ENST00000378380.3	hg19	CCDS13108.1																																																																																			.	.		0.413	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		-	10030424	ATTTAA	-	10030419	7	5	77	1	0	1	0	1	0	0	0	0	676	449	16	0	1220	0	ANKRD5	20	10030419	In_Frame_Del	DEL	ATTTAA	TCGA-CC-A7IL-01A-11D-A33Q-10		10030419	52995101	97	10695										
CST9	128822	hgsc.bcm.edu	37	chr20	23584366	23584366	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	atggagaacaccatcttaccTcgccactgttggacaaaaga	8	11	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr20:23584366T>A	ENST00000376971.3	-	2	272	c.261A>T	c.(259-261)cgA>cgT	p.R87R		NM_001008693.2	NP_001008693.2	Q5W186	CST9_HUMAN	cystatin 9 (testatin)	87						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			central_nervous_system(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Colorectal(13;0.0993)					CCATCTTACCTCGCCACTGTT	0.468																																					p.R87R		Atlas-SNP	.											.	CST9	26	.	0			c.A261T						.						150	136	140					20																	23584366		2203	4300	6503	SO:0001819	synonymous_variant	128822	exon2			CTTACCTCGCCAC	AF494536	CCDS33450.1	20p11.21	2012-08-14			ENSG00000173335	ENSG00000173335			13261	protein-coding gene	gene with protein product						20565543	Standard	NM_001008693		Approved	CLM, CTES7A	uc002wtl.3	Q5W186	OTTHUMG00000032076	ENST00000376971.3:c.261A>T	chr20.hg19:g.23584366T>A		41.0	0.0		33.0	16.0	NM_001008693	B2RP76|Q8TD53	Silent	SNP	ENST00000376971.3	hg19	CCDS33450.1																																																																																			.	.		0.468	CST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078341.1	NM_001008693.1		A	23584366	T	A	23584366	2	1	77	1	0	0	0	0	0	0	0	1	3981	1538	54	4		4	CST9	20	23584366	Silent	SNP	T	TCGA-CC-A7IL-01A-11D-A33Q-10	13553947	23584366	39441154	98	10696										
C20orf4	25980	hgsc.bcm.edu	37	chr20	34832689	34832689	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	gcatttgagcattggaagcgGctcctgaacctcctgtgccg	12	12	0	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr20:34832689G>T	ENST00000373932.3	+	3	1174	c.828G>T	c.(826-828)cgG>cgT	p.R276R	AAR2_ENST00000397286.3_Silent_p.R276R|AAR2_ENST00000320849.4_Silent_p.R276R	NM_015511.3	NP_056326.2	Q9Y312	AAR2_HUMAN	AAR2 splicing factor homolog (S. cerevisiae)	276																	ATTGGAAGCGGCTCCTGAACC	0.522																																					p.R276R		Atlas-SNP	.											.	.	.	.	0			c.G828T						.						213	177	189					20																	34832689		2203	4300	6503	SO:0001819	synonymous_variant	25980	exon3			GAAGCGGCTCCTG		CCDS13273.1	20q11.23	2012-07-20	2012-07-20	2012-07-20	ENSG00000131043	ENSG00000131043			15886	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 4"	C20orf4			Standard	NM_015511		Approved	bA234K24.2	uc002xfc.3	Q9Y312	OTTHUMG00000032380	ENST00000373932.3:c.828G>T	chr20.hg19:g.34832689G>T		137.0	0.0		189.0	129.0	NM_001271874	E1P5S7|Q9H4F9|Q9P1P3|Q9UFK9	Silent	SNP	ENST00000373932.3	hg19	CCDS13273.1																																																																																			.	.		0.522	AAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079001.2	NM_015511		T	34832689	G	T	34832689	2	4	77	1	0	0	0	0	0	0	0	1	2113	1190	42	3		3	C20orf4	20	34832689	Silent	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	11248323	34832689	28192831	99	10697										
CHD6	84181	hgsc.bcm.edu	37	chr20	40049157	40049157	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	acatactgtaccttgactatGgcagtttccgtctctatcat	6	11	2	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr20:40049157G>A	ENST00000373233.3	-	31	6295	c.6118C>T	c.(6118-6120)Cat>Tat	p.H2040Y		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2040					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CCTTGACTATGGCAGTTTCCG	0.413																																					p.H2040Y		Atlas-SNP	.											.	CHD6	312	.	0			c.C6118T						.						133	124	127					20																	40049157		2203	4300	6503	SO:0001583	missense	84181	exon31			GACTATGGCAGTT	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.6118C>T	chr20.hg19:g.40049157G>A	ENSP00000362330:p.His2040Tyr	36.0	0.0		39.0	8.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	G	13.96	2.392189	0.42410	.	.	ENSG00000124177	ENST00000373233	D	0.85702	-2.02	5.97	5.97	0.96955	.	0.552403	0.17827	N	0.160672	T	0.80691	0.4671	L	0.29908	0.895	0.80722	D	1	B	0.27068	0.167	B	0.25614	0.062	T	0.76924	-0.2779	10	0.66056	D	0.02	-0.9564	18.6044	0.91261	0.0:0.0:1.0:0.0	.	2040	Q8TD26	CHD6_HUMAN	Y	2040	ENSP00000362330:H2040Y	ENSP00000362330:H2040Y	H	-	1	0	CHD6	39482571	0.999000	0.42202	0.990000	0.47175	0.839000	0.47603	4.313000	0.59160	2.828000	0.97474	0.655000	0.94253	CAT	.	.		0.413	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40049157	G	A	40049157	3	1	77	1	0	0	0	0	1	0	0	0	3331	1348	47	3	2057	3	CHD6	20	40049157	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	5216468	40049157	22976363	100	10698										
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38865317	38865317	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	actattttgaaatatatttcAgatataccagtatattcaga	4	5	2	3			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr21:38865317A>T	ENST00000398960.2	+	7	1026		c.e7-1		DYRK1A_ENST00000451934.1_Splice_Site|DYRK1A_ENST00000338785.3_Splice_Site|DYRK1A_ENST00000398956.2_Splice_Site|DYRK1A_ENST00000321219.8_Splice_Site|DYRK1A_ENST00000339659.4_Splice_Site|DYRK1A_ENST00000455387.2_Splice_Site	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A						circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AATATATTTCAGATATACCAG	0.358																																					.	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.952-2A>T						.						78	78	78					21																	38865317		2203	4300	6503	SO:0001630	splice_region_variant	1859	exon9			TATTTCAGATATA	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.952-1A>T	chr21.hg19:g.38865317A>T		68.0	0.0		62.0	31.0	NM_101395	O60769|Q92582|Q92810|Q9UNM5	Splice_Site	SNP	ENST00000398960.2	hg19	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	.	24.5	4.535165	0.85812	.	.	ENSG00000157540	ENST00000338785;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956;ENST00000455387	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0172	0.80450	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DYRK1A	37787187	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.287000	0.95975	2.239000	0.73571	0.528000	0.53228	.	.	.		0.358	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396	Intron	T	38865317	A	T	38865317	5	4	77	1	0	0	0	0	0	0	1	0	4856	202	7	4	976	4	DYRK1A	21	38865317	Splice_Site	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10		38865317	9264578	101	10699										
PPM1F	9647	hgsc.bcm.edu	37	chr22	22277762	22277762	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	aagaagccatcacaggcaagCagcaggtagtcctcggagcc	12	12	1	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chr22:22277762C>T	ENST00000263212.5	-	8	1173	c.1068G>A	c.(1066-1068)ctG>ctA	p.L356L	PPM1F_ENST00000538191.1_Silent_p.L252L|PPM1F_ENST00000407142.1_Silent_p.L188L	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	356					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		CACAGGCAAGCAGCAGGTAGT	0.642																																					p.L356L		Atlas-SNP	.											.	PPM1F	34	.	0			c.G1068A						.						51	54	53					22																	22277762		2203	4300	6503	SO:0001819	synonymous_variant	9647	exon8			GGCAAGCAGCAGG	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19388	protein-coding gene	gene with protein product	"partner of PIX 2", "Ca(2+)/calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1F (PP2C domain containing)"			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.1068G>A	chr22.hg19:g.22277762C>T		106.0	0.0		139.0	52.0	NM_014634	A8K6G3|B7Z2C3|Q96PM2	Silent	SNP	ENST00000263212.5	hg19	CCDS13796.1																																																																																			.	.		0.642	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634		T	22277762	C	T	22277762	2	4	77	1	0	0	0	0	0	0	0	1	12351	697	25	3		3	PPM1F	22	22277762	Silent	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10		22277762	29026804	102	10700										
ARSF	416	hgsc.bcm.edu	37	chrX	3019189	3019189	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	aacacccttgtctactttacAtcagatcacggagggcattt	7	11	3	1			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chrX:3019189A>G	ENST00000381127.1	+	8	1250	c.1029A>G	c.(1027-1029)acA>acG	p.T343T	ARSF_ENST00000537104.1_Silent_p.T343T|ARSF_ENST00000359361.2_Silent_p.T343T	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	343					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TCTACTTTACATCAGATCACG	0.413																																					p.T343T		Atlas-SNP	.											.	ARSF	97	.	0			c.A1029G						.						154	128	137					X																	3019189		2203	4299	6502	SO:0001819	synonymous_variant	416	exon8			CTTTACATCAGAT	X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"Arylsulfatase family"	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.1029A>G	chrX.hg19:g.3019189A>G		276.0	0.0		131.0	110.0	NM_004042	Q8TCC5	Silent	SNP	ENST00000381127.1	hg19	CCDS14123.1																																																																																			.	.		0.413	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1			G	3019189	A	G	3019189	2	3	77	1	0	0	0	0	0	0	0	1	991	204	8	2		2	ARSF	23	3019189	Silent	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10		3019189	152251371	103	10701										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23410846	23410846	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ggcagccaggattttctgctGcaattcctgtattgcaatct	9	10	2	0			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chrX:23410846G>A	ENST00000379361.4	+	3	2071	c.1211G>A	c.(1210-1212)tGc>tAc	p.C404Y		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	404	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						ATTTTCTGCTGCAATTCCTGT	0.463																																					p.C404Y		Atlas-SNP	.											.	PTCHD1	213	.	0			c.G1211A						.						127	111	116					X																	23410846		2203	4300	6503	SO:0001583	missense	139411	exon3			TCTGCTGCAATTC	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.1211G>A	chrX.hg19:g.23410846G>A	ENSP00000368666:p.Cys404Tyr	69.0	0.0		45.0	40.0	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	hg19	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	G	11.01	1.514265	0.27123	.	.	ENSG00000165186	ENST00000379361	D	0.91407	-2.84	5.32	5.32	0.75619	Sterol-sensing domain (1);	0.113194	0.64402	D	0.000005	T	0.81479	0.4831	N	0.14661	0.345	0.38181	D	0.939612	B	0.02656	0.0	B	0.06405	0.002	T	0.77487	-0.2569	10	0.26408	T	0.33	-19.1593	11.8355	0.52321	0.0829:0.0:0.9171:0.0	.	404	Q96NR3	PTHD1_HUMAN	Y	404	ENSP00000368666:C404Y	ENSP00000368666:C404Y	C	+	2	0	PTCHD1	23320767	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.313000	0.72844	2.353000	0.79882	0.600000	0.82982	TGC	.	.		0.463	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		A	23410846	G	A	23410846	3	1	77	1	0	0	0	0	1	0	0	0	12744	1319	46	3	1221	3	PTCHD1	23	23410846	Missense_Mutation	SNP	G	TCGA-CC-A7IL-01A-11D-A33Q-10	20391657	23410846	131859714	104	10702										
SAGE1	55511	hgsc.bcm.edu	37	chrX	134988645	134988645	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	acctgataacgtgttgttgaCtcttcgaccacggcgtatta	9	10	1	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chrX:134988645C>G	ENST00000370709.3	+	6	671	c.671C>G	c.(670-672)aCt>aGt	p.T224S	SAGE1_ENST00000537770.1_Intron|SAGE1_ENST00000535938.1_Missense_Mutation_p.T224S|SAGE1_ENST00000324447.3_Missense_Mutation_p.T224S			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	224						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					GTGTTGTTGACTCTTCGACCA	0.428																																					p.T224S		Atlas-SNP	.											.	SAGE1	160	.	0			c.C671G						.						206	170	182					X																	134988645		2203	4300	6503	SO:0001583	missense	55511	exon7			TGTTGACTCTTCG	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.671C>G	chrX.hg19:g.134988645C>G	ENSP00000359743:p.Thr224Ser	134.0	0.0		96.0	89.0	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	hg19	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	C	5.227	0.227336	0.09916	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000370709	T;T;T	0.38560	1.13;1.13;1.13	1.22	1.22	0.21188	.	0.178696	0.37715	U	0.001962	T	0.22322	0.0538	N	0.17082	0.46	0.09310	N	0.999997	P	0.39022	0.655	B	0.38264	0.269	T	0.08391	-1.0724	10	0.44086	T	0.13	.	5.406	0.16323	0.0:1.0:0.0:0.0	.	224	Q9NXZ1	SAGE1_HUMAN	S	224	ENSP00000323191:T224S;ENSP00000445959:T224S;ENSP00000359743:T224S	ENSP00000323191:T224S	T	+	2	0	SAGE1	134816311	0.301000	0.24444	0.039000	0.18376	0.030000	0.12068	0.507000	0.22675	0.891000	0.36235	0.292000	0.19580	ACT	.	.		0.428	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		G	134988645	C	G	134988645	3	3	77	1	0	0	0	0	1	0	0	0	13824	565	20	4	693	4	SAGE1	23	134988645	Missense_Mutation	SNP	C	TCGA-CC-A7IL-01A-11D-A33Q-10	111577799	134988645	20281915	105	10703										
TBL1Y	90665	hgsc.bcm.edu	37	chrY	6939610	6939610	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	3	1	0.66096256684492	1.24848484848485	0.535064935064935	1	1	0	ctggccctcagagtgatggaAcactattggctatgggttca	12	9	2	2			TCGA-CC-A7IL-01A-11D-A33Q-10	TCGA-CC-A7IL-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e30b274-44cd-410b-a15b-08a2080a3ba4	f75b1d6b-8497-4452-b100-4b5bda7ff6e7	g.chrY:6939610A>C	ENST00000383032.1	+	11	1389	c.742A>C	c.(742-744)Aca>Cca	p.T248P	TBL1Y_ENST00000355162.2_Missense_Mutation_p.T248P|TBL1Y_ENST00000346432.3_Missense_Mutation_p.T248P	NM_033284.1	NP_150600.1	Q9BQ87	TBL1Y_HUMAN	transducin (beta)-like 1, Y-linked	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(1)|large_intestine(4)|lung(2)|skin(1)	8						GAGTGATGGAACACTATTGGC	0.488																																					p.T248P		Atlas-SNP	.											.	TBL1Y	15	.	0			c.A742C						.						84	73	75					Y																	6939610		598	1951	2549	SO:0001583	missense	90665	exon10			GATGGAACACTAT	AF332220	CCDS14779.1	Yp11.2	2013-01-10	2009-12-17		ENSG00000092377	ENSG00000092377		"WD repeat domain containing"	18502	protein-coding gene	gene with protein product		400033					Standard	NM_033284		Approved	TBL1	uc004frd.3	Q9BQ87	OTTHUMG00000035299	ENST00000383032.1:c.742A>C	chrY.hg19:g.6939610A>C	ENSP00000372499:p.Thr248Pro	94.0	0.0		38.0	34.0	NM_134258	A1L4B3	Missense_Mutation	SNP	ENST00000383032.1	hg19	CCDS14779.1																																																																																			.	.		0.488	TBL1Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085360.1	NM_033284		C	6939610	A	C	6939610	3	2	77	1	0	0	0	0	1	0	0	0	15656	43	2	5	764	5	TBL1Y	24	6939610	Missense_Mutation	SNP	A	TCGA-CC-A7IL-01A-11D-A33Q-10		6939610	52433956	106	10704										
GCLM	2730	hgsc.bcm.edu	37	chr1	94362176	94362176	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	gatcctgccatccctcacctGtgcccactgatacagctgtt	7	16	1	1			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr1:94362176G>C	ENST00000370238.3	-	5	784	c.538C>G	c.(538-540)Cag>Gag	p.Q180E	GCLM_ENST00000467772.1_5'UTR	NM_002061.2	NP_002052.1	P48507	GSH0_HUMAN	glutamate-cysteine ligase, modifier subunit	180					apoptotic mitochondrial changes (GO:0008637)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of glutamate-cysteine ligase activity (GO:0035229)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	glutamate-cysteine ligase activity (GO:0004357)|glutamate-cysteine ligase catalytic subunit binding (GO:0035226)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_lung(203;0.000815)|Lung NSC(277;0.00363)		all cancers(265;0.00566)|GBM - Glioblastoma multiforme(16;0.0203)|Epithelial(280;0.131)	L-Cysteine(DB00151)	TCCCTCACCTGTGCCCACTGA	0.478																																					p.Q180E		Atlas-SNP	.											.	GCLM	20	.	0			c.C538G						.						210	180	190					1																	94362176		2203	4300	6503	SO:0001583	missense	2730	exon5			TCACCTGTGCCCA	L35546	CCDS746.1	1p21	2008-02-05			ENSG00000023909	ENSG00000023909	6.3.2.2		4312	protein-coding gene	gene with protein product	"gamma-glutamylcysteine synthetase"	601176		GLCLR		7826375	Standard	NM_002061		Approved		uc001dqg.1	P48507	OTTHUMG00000010562	ENST00000370238.3:c.538C>G	chr1.hg19:g.94362176G>C	ENSP00000359258:p.Gln180Glu	114.0	0.0		162.0	76.0	NM_002061	A8K334|D3DT45|M5A959|Q6FHC1|Q9NPX9|Q9NU74	Missense_Mutation	SNP	ENST00000370238.3	hg19	CCDS746.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.903022	0.52227	.	.	ENSG00000023909	ENST00000370238	T	0.21932	1.98	5.32	4.39	0.52855	NADP-dependent oxidoreductase domain (3);	0.156175	0.64402	D	0.000018	T	0.06142	0.0159	L	0.37750	1.13	0.58432	D	0.999998	B	0.30146	0.27	B	0.25506	0.061	T	0.05241	-1.0897	10	0.06891	T	0.86	.	15.6097	0.76707	0.0:0.0:0.8613:0.1387	.	180	P48507	GSH0_HUMAN	E	180	ENSP00000359258:Q180E	ENSP00000359258:Q180E	Q	-	1	0	GCLM	94134764	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	6.242000	0.72376	1.343000	0.45638	0.655000	0.94253	CAG	.	.		0.478	GCLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029169.1	NM_002061		C	94362176	G	C	94362176	3	2	78	1	0	0	0	0	1	0	0	0	6304	1386	48	4	298	4	GCLM	1	94362176	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10		94362176	154888445	1	10705										
CGN	57530	hgsc.bcm.edu	37	chr1	151506476	151506476	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	gaggctgcggcaggccctgcAggcatcccaggctgagcggg	18	13	0	1			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr1:151506476A>G	ENST00000271636.7	+	15	2901	c.2768A>G	c.(2767-2769)cAg>cGg	p.Q923R		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	917					transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			CAGGCCCTGCAGGCATCCCAG	0.632																																					p.Q923R		Atlas-SNP	.											.	CGN	106	.	0			c.A2768G						.						29	32	31					1																	151506476		2195	4290	6485	SO:0001583	missense	57530	exon15			CCCTGCAGGCATC	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.2768A>G	chr1.hg19:g.151506476A>G	ENSP00000271636:p.Gln923Arg	391.0	0.0		563.0	70.0	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	hg19	CCDS999.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.179826	0.57800	.	.	ENSG00000143375	ENST00000271636	T	0.78246	-1.16	5.25	5.25	0.73442	Myosin tail (1);	0.261922	0.38326	N	0.001736	T	0.72510	0.3469	L	0.31420	0.93	0.44454	D	0.997384	D	0.71674	0.998	D	0.67900	0.954	T	0.71331	-0.4625	10	0.21014	T	0.42	-27.2151	13.994	0.64386	1.0:0.0:0.0:0.0	.	917	Q9P2M7	CING_HUMAN	R	923	ENSP00000271636:Q923R	ENSP00000271636:Q923R	Q	+	2	0	CGN	149773100	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	4.166000	0.58203	1.990000	0.58119	0.460000	0.39030	CAG	.	.		0.632	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		G	151506476	A	G	151506476	3	3	78	1	0	0	0	0	1	0	0	0	3305	188	7	2	2822	2	CGN	1	151506476	Missense_Mutation	SNP	A	TCGA-CC-A8HS-01A-11D-A35Z-10	57144300	151506476	97744145	2	10706										
CELF3	11189	hgsc.bcm.edu	37	chr1	151678725	151678725	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ctttgctgctgctgctgttgCtgctgctgctgctgctgctg	13	12	0	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr1:151678725C>T	ENST00000290583.4	-	10	1894	c.1101G>A	c.(1099-1101)caG>caA	p.Q367Q	CELF3_ENST00000392706.3_Silent_p.Q162Q|CELF3_ENST00000290585.4_Silent_p.Q317Q|RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000470688.1_5'UTR	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	367	Gln-rich.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.Q367Q(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						gctgctgttgctgctgctgct	0.657																																					p.Q367Q		Atlas-SNP	.											CELF3,caecum,carcinoma,0,1	CELF3	49	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1101A						.						18	19	19					1																	151678725		2200	4292	6492	SO:0001819	synonymous_variant	11189	exon10			CTGTTGCTGCTGC	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.1101G>A	chr1.hg19:g.151678725C>T		39.0	0.0		85.0	4.0	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Silent	SNP	ENST00000290583.4	hg19	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	6.031	0.374049	0.11409	.	.	ENSG00000159409	ENST00000420342	.	.	.	4.11	2.19	0.27852	.	.	.	.	.	T	0.38719	0.1051	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23583	-1.0184	4	.	.	.	-4.4657	5.9572	0.19279	0.0:0.755:0.0:0.245	.	.	.	.	N	368	.	.	S	-	2	0	CELF3	149945349	0.942000	0.31987	1.000000	0.80357	0.747000	0.42532	-0.032000	0.12266	0.496000	0.27904	-0.258000	0.10820	AGC	.	.		0.657	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		T	151678725	C	T	151678725	2	4	78	1	0	0	0	0	0	0	0	1	3219	796	28	3		3	CELF3	1	151678725	Silent	SNP	C	TCGA-CC-A8HS-01A-11D-A35Z-10	172249	151678725	97571896	3	10707										
OR10J1	26476	hgsc.bcm.edu	37	chr1	159409832	159409832	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tctcccaagaatgctctccaGcctcgtaggtatgagccagc	9	14	2	2			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr1:159409832G>T	ENST00000423932.3	+	1	321	c.284G>T	c.(283-285)aGc>aTc	p.S95I	RP11-550P17.5_ENST00000431862.1_RNA	NM_012351.2	NP_036483.2	P30954	O10J1_HUMAN	olfactory receptor, family 10, subfamily J, member 1	95					G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|single fertilization (GO:0007338)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|stomach(1)	25	all_hematologic(112;0.0429)					ATGCTCTCCAGCCTCGTAGGT	0.468																																					p.S95I		Atlas-SNP	.											.	OR10J1	118	.	0			c.G284T						.						105	92	96					1																	159409832		2203	4300	6503	SO:0001583	missense	26476	exon1			TCTCCAGCCTCGT	X64995	CCDS1185.1	1q23.2	2012-08-09			ENSG00000196184	ENSG00000196184		"GPCR / Class A : Olfactory receptors"	8175	protein-coding gene	gene with protein product						1370859	Standard	NM_012351		Approved	HGMP07J, HSHGMP07J	uc010piv.2	P30954	OTTHUMG00000022737	ENST00000423932.3:c.284G>T	chr1.hg19:g.159409832G>T	ENSP00000399078:p.Ser95Ile	101.0	0.0		166.0	7.0	NM_012351	Q2M1M8|Q5VSV1|Q6IET5|Q96R56	Missense_Mutation	SNP	ENST00000423932.3	hg19	CCDS1185.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.299844	0.40694	.	.	ENSG00000196184	ENST00000423932	T	0.00411	7.53	4.48	2.99	0.34606	GPCR, rhodopsin-like superfamily (1);	0.132994	0.34314	N	0.004077	T	0.00144	0.0004	N	0.11789	0.175	0.09310	N	1	P	0.49447	0.924	P	0.55345	0.774	T	0.40979	-0.9534	10	0.87932	D	0	.	3.7354	0.08508	0.1838:0.0:0.6112:0.205	.	95	P30954	O10J1_HUMAN	I	95	ENSP00000399078:S95I	ENSP00000399078:S95I	S	+	2	0	OR10J1	157676456	0.000000	0.05858	0.673000	0.29887	0.698000	0.40448	-0.517000	0.06275	0.736000	0.32559	0.655000	0.94253	AGC	.	.		0.468	OR10J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059020.1	NM_012351		T	159409832	G	T	159409832	3	4	78	1	0	0	0	0	1	0	0	0	10919	971	34	3	286	3	OR10J1	1	159409832	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	7731107	159409832	89840789	4	10708										
PTPRC	5788	hgsc.bcm.edu	37	chr1	198698298	198698298	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	acagcaggagcttgttgaaaGgggtaagtatgtatattttt	12	3	0	1			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr1:198698298G>A	ENST00000367376.2	+	17	2027	c.1856G>A	c.(1855-1857)aGg>aAg	p.R619K	PTPRC_ENST00000442510.2_Missense_Mutation_p.R621K|PTPRC_ENST00000352140.3_Missense_Mutation_p.R571K|PTPRC_ENST00000348564.6_Missense_Mutation_p.R460K|PTPRC_ENST00000594404.1_Missense_Mutation_p.R458K	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	619					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						CTTGTTGAAAGGGGTAAGTAT	0.279																																					p.R621K		Atlas-SNP	.											.	PTPRC	229	.	0			c.G1862A						.						95	99	98					1																	198698298		2203	4300	6503	SO:0001583	missense	5788	exon17			TTGAAAGGGGTAA	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1856G>A	chr1.hg19:g.198698298G>A	ENSP00000356346:p.Arg619Lys	312.0	0.0		431.0	247.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	hg19		.	.	.	.	.	.	.	.	.	.	G	12.49	1.953134	0.34471	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.02369	4.32	5.37	4.45	0.53987	.	0.275703	0.25925	N	0.027419	T	0.02727	0.0082	L	0.36672	1.1	0.40426	D	0.979895	B;B;B;B;B	0.23806	0.019;0.091;0.001;0.002;0.004	B;B;B;B;B	0.21708	0.034;0.036;0.01;0.01;0.01	T	0.39820	-0.9595	10	0.08381	T	0.77	.	11.3741	0.49717	0.0856:0.0:0.9144:0.0	.	555;555;460;571;619	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	K	621;555;571;571;505;619;553;458	ENSP00000193532:R571K	ENSP00000306782:R458K	R	+	2	0	PTPRC	196964921	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	2.000000	0.40816	1.406000	0.46857	0.650000	0.86243	AGG	.	.		0.279	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				A	198698298	G	A	198698298	3	1	78	1	0	0	0	0	1	0	0	0	12812	1000	35	3	1929	3	PTPRC	1	198698298	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	39288466	198698298	50552323	5	10709										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245771032	245771032	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tggctgcgtgttctgtttcgGccacgccaaactgggttcgt	13	11	1	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr1:245771032G>A	ENST00000407071.2	+	7	2077	c.1637G>A	c.(1636-1638)gGc>gAc	p.G546D	KIF26B_ENST00000366518.4_Missense_Mutation_p.G165D	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	546	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TTCTGTTTCGGCCACGCCAAA	0.567																																					p.G546D		Atlas-SNP	.											.	KIF26B	343	.	0			c.G1637A						.						88	103	98					1																	245771032		2136	4239	6375	SO:0001583	missense	55083	exon7			GTTTCGGCCACGC	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.1637G>A	chr1.hg19:g.245771032G>A	ENSP00000385545:p.Gly546Asp	79.0	0.0		99.0	59.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564695	0.86439	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.79749	-1.3;-1.3	5.73	5.73	0.89815	Kinesin, motor domain (5);	.	.	.	.	D	0.94634	0.8270	H	0.98701	4.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.96404	0.9299	9	0.87932	D	0	.	19.9747	0.97299	0.0:0.0:1.0:0.0	.	165;546	B7WPD9;Q2KJY2	.;KI26B_HUMAN	D	546;165;162	ENSP00000385545:G546D;ENSP00000355475:G165D	ENSP00000355475:G165D	G	+	2	0	KIF26B	243837655	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.869000	0.99810	2.715000	0.92844	0.551000	0.68910	GGC	.	.		0.567	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245771032	G	A	245771032	3	1	78	1	0	0	0	0	1	0	0	0	8304	1203	42	3	1663	3	KIF26B	1	245771032	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	47072734	245771032	3479589	6	10710										
OR6F1	343169	hgsc.bcm.edu	37	chr1	247875822	247875822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	gtaggatggccagtgctttgGgcactgctgctgtggtatac	15	8	0	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr1:247875822G>A	ENST00000302084.2	-	1	283	c.236C>T	c.(235-237)cCc>cTc	p.P79L	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	79						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			CAGTGCTTTGGGCACTGCTGC	0.473																																					p.P79L		Atlas-SNP	.											.	OR6F1	88	.	0			c.C236T						.						111	111	111					1																	247875822		2203	4300	6503	SO:0001583	missense	343169	exon1			GCTTTGGGCACTG	BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"GPCR / Class A : Olfactory receptors"	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.236C>T	chr1.hg19:g.247875822G>A	ENSP00000305640:p.Pro79Leu	70.0	0.0		87.0	22.0	NM_001005286	B2RNV6|Q6IF02|Q96R39	Missense_Mutation	SNP	ENST00000302084.2	hg19	CCDS31095.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.020799	0.54576	.	.	ENSG00000169214	ENST00000302084	T	0.01854	4.6	3.99	3.99	0.46301	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43416	D	0.000567	T	0.18923	0.0454	H	0.94620	3.56	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.14200	-1.0481	10	0.87932	D	0	-56.0078	15.174	0.72896	0.0:0.0:1.0:0.0	.	79	Q8NGZ6	OR6F1_HUMAN	L	79	ENSP00000305640:P79L	ENSP00000305640:P79L	P	-	2	0	OR6F1	245942445	1.000000	0.71417	0.971000	0.41717	0.013000	0.08279	5.044000	0.64214	2.209000	0.71365	0.591000	0.81541	CCC	.	.		0.473	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286		A	247875822	G	A	247875822	3	1	78	1	0	0	0	0	1	0	0	0	11210	1232	43	3	694	3	OR6F1	1	247875822	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	2104790	247875822	1374799	7	10711										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525807	248525807	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	aggacatgatggtatctgtcTtctataccatcctcactcca	6	12	4	1			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr1:248525807T>C	ENST00000366475.1	+	1	925	c.925T>C	c.(925-927)Ttc>Ctc	p.F309L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGTATCTGTCTTCTATACCAT	0.488																																					p.F309L		Atlas-SNP	.											.	OR2T4	126	.	0			c.T925C						.						144	142	143					1																	248525807		2203	4300	6503	SO:0001583	missense	127074	exon1			TCTGTCTTCTATA	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.925T>C	chr1.hg19:g.248525807T>C	ENSP00000355431:p.Phe309Leu	716.0	0.0		792.0	234.0	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.700971	0.48307	.	.	ENSG00000196944	ENST00000366475	T	0.00032	8.88	3.0	1.8	0.24995	GPCR, rhodopsin-like superfamily (1);	0.147942	0.31636	N	0.007317	T	0.00144	0.0004	L	0.37630	1.12	0.09310	N	1	P	0.40180	0.705	P	0.46975	0.533	T	0.32107	-0.9919	10	0.62326	D	0.03	.	4.8151	0.13363	0.0:0.4364:0.0:0.5636	.	309	Q8NH00	OR2T4_HUMAN	L	309	ENSP00000355431:F309L	ENSP00000355431:F309L	F	+	1	0	OR2T4	246592430	0.000000	0.05858	1.000000	0.80357	0.674000	0.39518	-0.523000	0.06230	1.228000	0.43614	0.477000	0.44152	TTC	.	.		0.488	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		C	248525807	T	C	248525807	3	2	78	1	0	0	0	0	1	0	0	0	11036	1609	56	2	927	2	OR2T4	1	248525807	Missense_Mutation	SNP	T	TCGA-CC-A8HS-01A-11D-A35Z-10	649985	248525807	724814	8	10712										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50280467	50280467	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tggctgtgctagtagccaggGtcgtggtagtctccataatt	13	8	1	0	rs200974417		TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr2:50280467G>C	ENST00000406316.2	-	20	5456	c.3980C>G	c.(3979-3981)aCc>aGc	p.T1327S	NRXN1_ENST00000401669.2_Missense_Mutation_p.T1357S|NRXN1_ENST00000404971.1_Missense_Mutation_p.T1397S|NRXN1_ENST00000402717.3_Missense_Mutation_p.T1349S|NRXN1_ENST00000342183.5_Missense_Mutation_p.T292S|NRXN1_ENST00000405472.3_Missense_Mutation_p.T1349S|NRXN1_ENST00000406859.3_Missense_Mutation_p.T1327S|NRXN1_ENST00000401710.1_Missense_Mutation_p.T345S	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1327	Poly-Thr.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			AGTAGCCAGGGTCGTGGTAGT	0.473																																					p.T1397S		Atlas-SNP	.											.	NRXN1	1118	.	0			c.C4190G						.						136	133	134					2																	50280467		2203	4300	6503	SO:0001583	missense	9378	exon22			GCCAGGGTCGTGG	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3980C>G	chr2.hg19:g.50280467G>C	ENSP00000384311:p.Thr1327Ser	84.0	0.0		77.0	30.0	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.061504	0.76187	.	.	ENSG00000179915	ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T;T;T	0.73152	0.79;1.96;-0.0;-0.07;-0.72;-0.61;-0.33;-0.21	5.5	5.5	0.81552	.	0.217355	0.28098	U	0.016618	T	0.80188	0.4577	M	0.72118	2.19	0.44946	D	0.997961	P;D;B;B	0.55172	0.889;0.97;0.324;0.068	P;P;B;B	0.53102	0.686;0.718;0.389;0.097	T	0.81938	-0.0704	10	0.62326	D	0.03	.	19.3964	0.94608	0.0:0.0:1.0:0.0	.	1397;292;1327;1349	Q9ULB1-3;P58400;F8WB18;A7E294	.;NRX1B_HUMAN;.;.	S	292;246;345;1397;1327;1349;1357;1398;1349;1327	ENSP00000341184:T292S;ENSP00000385580:T345S;ENSP00000385142:T1397S;ENSP00000384311:T1327S;ENSP00000434015:T1349S;ENSP00000385017:T1357S;ENSP00000385434:T1349S;ENSP00000385681:T1327S	ENSP00000341184:T292S	T	-	2	0	NRXN1	50133971	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.866000	0.99616	2.582000	0.87167	0.655000	0.94253	ACC	.	.		0.473	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			C	50280467	G	C	50280467	3	2	78	1	0	0	0	0	1	0	0	0	10674	1261	44	4	465	4	NRXN1	2	50280467	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10		50280467	192918906	9	10713										
AAK1	22848	hgsc.bcm.edu	37	chr2	69784077	69784077	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	aggcacatttcatcccattgCttgtcctcaccagaaataca	5	13	2	1	rs371902412		TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr2:69784077C>T	ENST00000409085.4	-	3	573	c.197G>A	c.(196-198)aGc>aAc	p.S66N	AAK1_ENST00000406297.3_Missense_Mutation_p.S66N|AAK1_ENST00000409068.1_Missense_Mutation_p.S66N	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	66	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						CATCCCATTGCTTGTCCTCAC	0.433																																					p.S66N		Atlas-SNP	.											.	AAK1	121	.	0			c.G197A						.	C	ASN/SER	0,3984		0,0,1992	133	121	125		197	5.2	1	2		125	1,8365		0,1,4182	no	missense	AAK1	NM_014911.3	46	0,1,6174	TT,TC,CC		0.012,0.0,0.0081	benign	66/962	69784077	1,12349	1992	4183	6175	SO:0001583	missense	22848	exon3			CCATTGCTTGTCC	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.197G>A	chr2.hg19:g.69784077C>T	ENSP00000386456:p.Ser66Asn	75.0	0.0		84.0	33.0	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Missense_Mutation	SNP	ENST00000409085.4	hg19	CCDS1893.2	.	.	.	.	.	.	.	.	.	.	C	11.49	1.653154	0.29425	0.0	1.2E-4	ENSG00000115977	ENST00000409068;ENST00000409085;ENST00000406297	T;T;T	0.29397	1.57;1.57;1.57	5.25	5.25	0.73442	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.248350	0.47093	D	0.000254	T	0.21801	0.0525	N	0.11927	0.2	0.35491	D	0.799012	B;B;B;B	0.25007	0.052;0.052;0.042;0.116	B;B;B;B	0.30401	0.055;0.115;0.07;0.057	T	0.20107	-1.0285	10	0.33141	T	0.24	-12.2002	16.3823	0.83472	0.0:1.0:0.0:0.0	.	66;66;66;66	B7ZLC4;D6W5G0;Q2M2I8-2;Q2M2I8	.;.;.;AAK1_HUMAN	N	66	ENSP00000386342:S66N;ENSP00000386456:S66N;ENSP00000385181:S66N	ENSP00000385181:S66N	S	-	2	0	AAK1	69637581	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	2.452000	0.44961	2.724000	0.93272	0.655000	0.94253	AGC	.	.		0.433	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911		T	69784077	C	T	69784077	3	4	78	1	0	0	0	0	1	0	0	0	16	797	28	3	2768	3	AAK1	2	69784077	Missense_Mutation	SNP	C	TCGA-CC-A8HS-01A-11D-A35Z-10	19503610	69784077	173415296	10	10714										
SPEG	10290	hgsc.bcm.edu	37	chr2	220352988	220352988	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ggaggcagccaccctgctctGcctgccagcggcctgccctg	13	18	1	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr2:220352988G>A	ENST00000312358.7	+	32	7946	c.7814G>A	c.(7813-7815)tGc>tAc	p.C2605Y	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2605	Ig-like 9.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		ACCCTGCTCTGCCTGCCAGCG	0.612																																					p.C2605Y		Atlas-SNP	.											.	SPEG	272	.	0			c.G7814A						.						53	57	55					2																	220352988		2053	4206	6259	SO:0001583	missense	10290	exon32			TGCTCTGCCTGCC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.7814G>A	chr2.hg19:g.220352988G>A	ENSP00000311684:p.Cys2605Tyr	55.0	0.0		67.0	32.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149030	0.57151	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	D	0.84873	-1.91	4.89	4.89	0.63831	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.42682	D	0.000670	D	0.95582	0.8564	H	0.98027	4.13	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97596	1.0120	10	0.87932	D	0	.	18.0612	0.89378	0.0:0.0:1.0:0.0	.	2605	Q15772	SPEG_HUMAN	Y	2605	ENSP00000311684:C2605Y	ENSP00000265327:C2605Y	C	+	2	0	SPEG	220061232	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	9.697000	0.98697	2.282000	0.76494	0.591000	0.81541	TGC	.	.		0.612	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220352988	G	A	220352988	3	1	78	1	0	0	0	0	1	0	0	0	15051	1319	46	3	7952	3	SPEG	2	220352988	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	150568911	220352988	22846385	11	10715										
C2orf57	165100	hgsc.bcm.edu	37	chr2	232458829	232458829	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ctcaccccacgccaggcccaGgctgaccccaactatgatta	7	18	1	2			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr2:232458829G>A	ENST00000313965.2	+	1	1255	c.1167G>A	c.(1165-1167)caG>caA	p.Q389Q		NM_152614.2	NP_689827.2	Q53QW1	CB057_HUMAN	chromosome 2 open reading frame 57	389										endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	19		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)		GCCAGGCCCAGGCTGACCCCA	0.657																																					p.Q389Q		Atlas-SNP	.											.	C2orf57	35	.	0			c.G1167A						.						31	30	30					2																	232458829		2202	4300	6502	SO:0001819	synonymous_variant	165100	exon1			GGCCCAGGCTGAC	BC034405	CCDS2487.1	2q37.1	2008-02-05			ENSG00000177673	ENSG00000177673			28563	protein-coding gene	gene with protein product						12477932	Standard	NM_152614		Approved	MGC35154	uc002vrz.3	Q53QW1	OTTHUMG00000133226	ENST00000313965.2:c.1167G>A	chr2.hg19:g.232458829G>A		107.0	0.0		74.0	35.0	NM_152614	Q8N4F2	Silent	SNP	ENST00000313965.2	hg19	CCDS2487.1																																																																																			.	.		0.657	C2orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256962.1	NM_152614		A	232458829	G	A	232458829	2	1	78	1	0	0	0	0	0	0	0	1	2180	991	35	3		3	C2orf57	2	232458829	Silent	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	12105841	232458829	10740544	12	10716										
SUSD5	26032	hgsc.bcm.edu	37	chr3	33194727	33194727	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	gtagagttgactggtacttcGtcaagtcaccatccccaatg	9	11	2	2	rs377664152		TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr3:33194727G>A	ENST00000309558.3	-	5	1814	c.1397C>T	c.(1396-1398)aCg>aTg	p.T466M		NM_015551.1	NP_056366.1	O60279	SUSD5_HUMAN	sushi domain containing 5	466					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	hyaluronic acid binding (GO:0005540)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						CTGGTACTTCGTCAAGTCACC	0.507																																					p.T466M		Atlas-SNP	.											.	SUSD5	53	.	0			c.C1397T						.	G	MET/THR	1,4017		0,1,2008	93	94	94		1397	2.1	0	3		94	0,8356		0,0,4178	no	missense	SUSD5	NM_015551.1	81	0,1,6186	AA,AG,GG		0.0,0.0249,0.0081	possibly-damaging	466/630	33194727	1,12373	2009	4178	6187	SO:0001583	missense	26032	exon5			TACTTCGTCAAGT	AB011099	CCDS46787.1	3p23	2014-02-12	2006-01-13		ENSG00000173705	ENSG00000173705			29061	protein-coding gene	gene with protein product							Standard	NM_015551		Approved	KIAA0527	uc003cfo.1	O60279	OTTHUMG00000155829	ENST00000309558.3:c.1397C>T	chr3.hg19:g.33194727G>A	ENSP00000308727:p.Thr466Met	67.0	0.0		48.0	12.0	NM_015551		Missense_Mutation	SNP	ENST00000309558.3	hg19	CCDS46787.1	.	.	.	.	.	.	.	.	.	.	G	13.46	2.245184	0.39697	2.49E-4	0.0	ENSG00000173705	ENST00000309558	T	0.08102	3.13	5.29	2.06	0.26882	.	0.514704	0.18978	N	0.125958	T	0.07593	0.0191	L	0.57536	1.79	0.09310	N	1	B	0.30211	0.273	B	0.20184	0.028	T	0.25916	-1.0118	10	0.72032	D	0.01	-6.1251	4.3885	0.11328	0.1302:0.1397:0.5873:0.1428	.	466	O60279	SUSD5_HUMAN	M	466	ENSP00000308727:T466M	ENSP00000308727:T466M	T	-	2	0	SUSD5	33169731	0.001000	0.12720	0.009000	0.14445	0.696000	0.40369	0.703000	0.25646	1.206000	0.43276	0.650000	0.86243	ACG	.	.		0.507	SUSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341902.1	XM_171054		A	33194727	G	A	33194727	3	1	78	1	0	0	0	0	1	0	0	0	15426	1145	40	1	496	1	SUSD5	3	33194727	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10		33194727	164827703	13	10717										
HTR1F	3355	hgsc.bcm.edu	37	chr3	88040772	88040772	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ggtacaagagaacggaaagcAgccactaccctgggattaat	11	9	0	1			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr3:88040772A>G	ENST00000319595.4	+	1	927	c.873A>G	c.(871-873)gcA>gcG	p.A291A		NM_000866.3	NP_000857.1	P30939	5HT1F_HUMAN	5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled	291					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(8;0.147)	Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00664)	Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Ketamine(DB01221)|Methysergide(DB00247)|Mianserin(DB06148)|Naratriptan(DB00952)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Zolmitriptan(DB00315)	AACGGAAAGCAGCCACTACCC	0.363																																					p.A291A		Atlas-SNP	.											.	HTR1F	66	.	0			c.A873G						.						70	80	76					3																	88040772		2203	4300	6503	SO:0001819	synonymous_variant	3355	exon2			GAAAGCAGCCACT	L05597	CCDS2920.1	3p12	2012-08-08	2012-02-03		ENSG00000179097	ENSG00000179097		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5292	protein-coding gene	gene with protein product		182134	"5-hydroxytryptamine (serotonin) receptor 1F"			8384716, 8380639	Standard	NM_000866		Approved	HTR1EL, 5-HT1F	uc003dqr.2	P30939	OTTHUMG00000159008	ENST00000319595.4:c.873A>G	chr3.hg19:g.88040772A>G		91.0	0.0		87.0	29.0	NM_000866		Silent	SNP	ENST00000319595.4	hg19	CCDS2920.1																																																																																			.	.		0.363	HTR1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352890.1	NM_000866		G	88040772	A	G	88040772	2	3	78	1	0	0	0	0	0	0	0	1	7449	175	7	2		2	HTR1F	3	88040772	Silent	SNP	A	TCGA-CC-A8HS-01A-11D-A35Z-10	54846045	88040772	109981658	14	10718										
BOC	91653	hgsc.bcm.edu	37	chr3	112991482	112991482	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ggaggactcaggcacctaccGctgcatggccgacaatgggg	15	12	1	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr3:112991482G>A	ENST00000495514.1	+	7	1597	c.893G>A	c.(892-894)cGc>cAc	p.R298H	BOC_ENST00000273395.4_Missense_Mutation_p.R298H|BOC_ENST00000355385.3_Missense_Mutation_p.R298H			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	298	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			GGCACCTACCGCTGCATGGCC	0.602																																					p.R298H		Atlas-SNP	.											.	BOC	139	.	0			c.G893A						.						106	94	98					3																	112991482		2203	4300	6503	SO:0001583	missense	91653	exon7			CCTACCGCTGCAT	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.893G>A	chr3.hg19:g.112991482G>A	ENSP00000418663:p.Arg298His	120.0	0.0		95.0	22.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	hg19	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	g	19.88	3.910048	0.72983	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.30981	1.51;1.51;1.51	5.92	5.05	0.67936	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.407363	0.26911	N	0.021874	T	0.37461	0.1004	L	0.35341	1.055	0.27754	N	0.944064	D;D	0.61697	0.987;0.99	P;P	0.59595	0.781;0.86	T	0.16276	-1.0408	10	0.37606	T	0.19	.	10.8782	0.46923	0.0678:0.1293:0.8028:0.0	.	298;298	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	H	298	ENSP00000418663:R298H;ENSP00000273395:R298H;ENSP00000347546:R298H	ENSP00000273395:R298H	R	+	2	0	BOC	114474172	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	2.175000	0.42491	1.530000	0.49136	-0.127000	0.14921	CGC	.	.		0.602	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		A	112991482	G	A	112991482	3	1	78	1	0	0	0	0	1	0	0	0	1481	1087	38	1	911	1	BOC	3	112991482	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	24950710	112991482	85030948	15	10719										
GPR149	344758	hgsc.bcm.edu	37	chr3	154146570	154146570	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	agccccagcggcagcgggcgCacccggtccgaacacggtgt	15	16	0	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr3:154146570C>G	ENST00000389740.2	-	1	934	c.835G>C	c.(835-837)Gcg>Ccg	p.A279P		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	279					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			GCAGCGGGCGCACCCGGTCCG	0.682																																					p.A279P		Atlas-SNP	.											.	GPR149	134	.	0			c.G835C						.						34	37	36					3																	154146570		1898	4116	6014	SO:0001583	missense	344758	exon1			CGGGCGCACCCGG	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.835G>C	chr3.hg19:g.154146570C>G	ENSP00000374390:p.Ala279Pro	181.0	0.0		177.0	95.0	NM_001038705		Missense_Mutation	SNP	ENST00000389740.2	hg19	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	C	6.852	0.526405	0.13066	.	.	ENSG00000174948	ENST00000389740	.	.	.	4.51	1.53	0.23141	GPCR, rhodopsin-like superfamily (1);	1.526850	0.03495	N	0.217157	T	0.12305	0.0299	N	0.00155	-1.965	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.25293	-1.0136	9	0.10902	T	0.67	5.8061	17.5242	0.87795	0.0:0.6386:0.3614:0.0	.	279	Q86SP6	GP149_HUMAN	P	279	.	ENSP00000374390:A279P	A	-	1	0	GPR149	155629264	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	1.404000	0.34623	0.517000	0.28361	0.655000	0.94253	GCG	.	.		0.682	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		G	154146570	C	G	154146570	3	3	78	1	0	0	0	0	1	0	0	0	6662	710	25	4	1376	4	GPR149	3	154146570	Missense_Mutation	SNP	C	TCGA-CC-A8HS-01A-11D-A35Z-10	41155088	154146570	43875860	16	10720										
C4orf43	55319	hgsc.bcm.edu	37	chr4	164436503	164436503	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	cagtgagctggagcagattgAgttacataacagtatcaggg	13	6	1	3			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr4:164436503A>G	ENST00000358572.5	+	5	619	c.278A>G	c.(277-279)gAg>gGg	p.E93G	TMA16_ENST00000508268.1_Missense_Mutation_p.E93G|TMA16_ENST00000513134.1_Intron|TMA16_ENST00000511562.1_3'UTR|TMA16_ENST00000513272.1_Intron	NM_018352.2	NP_060822.2	Q96EY4	TMA16_HUMAN	translation machinery associated 16 homolog (S. cerevisiae)	93						nucleus (GO:0005634)											GAGCAGATTGAGTTACATAAC	0.463																																					p.E93G		Atlas-SNP	.											.	.	.	.	0			c.A278G						.						115	117	116					4																	164436503		1949	4138	6087	SO:0001583	missense	55319	exon5			AGATTGAGTTACA		CCDS43278.1	4q32.3	2012-03-02	2012-03-02	2012-03-02	ENSG00000198498	ENSG00000198498			25638	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 43"	C4orf43		12477932	Standard	NM_018352		Approved	FLJ11184	uc003iqq.4	Q96EY4	OTTHUMG00000161528	ENST00000358572.5:c.278A>G	chr4.hg19:g.164436503A>G	ENSP00000351380:p.Glu93Gly	378.0	0.0		230.0	90.0	NM_018352	Q0P6E4|Q0P6J1|Q9NUR7	Missense_Mutation	SNP	ENST00000358572.5	hg19	CCDS43278.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.73|19.73	3.882904|3.882904	0.72410|0.72410	.|.	.|.	ENSG00000198498|ENSG00000198498	ENST00000358572;ENST00000508268|ENST00000509657	T;T|.	0.32753|.	1.44;1.44|.	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	0.085246|.	0.85682|.	D|.	0.000000|.	T|.	0.76948|.	0.4059|.	M|M	0.81239|0.81239	2.535|2.535	0.80722|0.80722	D|D	1|1	B|.	0.06786|.	0.001|.	B|.	0.06405|.	0.002|.	T|.	0.78440|.	-0.2203|.	10|.	0.48119|.	T|.	0.1|.	-20.9634|-20.9634	15.2636|15.2636	0.73643|0.73643	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	93|.	Q96EY4|.	CD043_HUMAN|.	G|W	93|131	ENSP00000351380:E93G;ENSP00000423375:E93G|.	ENSP00000351380:E93G|.	E|X	+|+	2|3	0|0	C4orf43|C4orf43	164655953|164655953	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.997000|0.997000	0.91878|0.91878	8.124000|8.124000	0.89588|0.89588	2.307000|2.307000	0.77673|0.77673	0.528000|0.528000	0.53228|0.53228	GAG|TGA	.	.		0.463	TMA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365208.1	NM_018352		G	164436503	A	G	164436503	3	3	78	1	0	0	0	0	1	0	0	0	2273	304	11	2	296	2	C4orf43	4	164436503	Missense_Mutation	SNP	A	TCGA-CC-A8HS-01A-11D-A35Z-10		164436503	26717773	17	10721										
HPGD	3248	hgsc.bcm.edu	37	chr4	175414376	175414376	+	Frame_Shift_Del	DEL	T	T	-													0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tattgtcccatgttttcttcTttttcaattgattcaaggat							TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr4:175414376delT	ENST00000296522.6	-	6	1034	c.588delA	c.(586-588)aaafs	p.K196fs	HPGD_ENST00000296521.7_Intron|HPGD_ENST00000510901.1_Frame_Shift_Del_p.K75fs|HPGD_ENST00000542498.1_Intron|HPGD_ENST00000541923.1_Frame_Shift_Del_p.K75fs|HPGD_ENST00000422112.2_Frame_Shift_Del_p.K128fs	NM_000860.5|NM_001145816.2|NM_001256301.1|NM_001256307.1	NP_000851.2|NP_001139288.1|NP_001243230.1|NP_001243236.1	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)	196					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|ductus arteriosus closure (GO:0097070)|female pregnancy (GO:0007565)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|ovulation (GO:0030728)|parturition (GO:0007567)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|thrombin receptor signaling pathway (GO:0070493)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|catalytic activity (GO:0003824)|NAD binding (GO:0051287)|NAD+ binding (GO:0070403)|prostaglandin E receptor activity (GO:0004957)|protein homodimerization activity (GO:0042803)			kidney(1)|lung(3)|prostate(3)	7		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)		TGTTTTCTTCTTTTTCAATTG	0.333																																					p.E197fs		Atlas-INDEL	.											.	HPGD	19	.	0			c.589delG						.						91	89	90					4																	175414376		2203	4299	6502	SO:0001589	frameshift_variant	3248	exon6			.		CCDS3821.1, CCDS54821.1, CCDS58933.1, CCDS58934.1, CCDS58935.1	4q34-q35	2011-09-14			ENSG00000164120	ENSG00000164120	1.1.1.141	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	5154	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 36C, member 1"	601688				19027726	Standard	NM_000860		Approved	SDR36C1	uc003itu.3	P15428	OTTHUMG00000160772	ENST00000296522.6:c.588delA	chr4.hg19:g.175414376delT	ENSP00000296522:p.Lys196fs	66.0	0.0		56.0	37.0	NM_000860	B4DTA4|B4DU74|B4DV57|D3DP43|E7EV11|O00749|Q06F08|Q12998	Frame_Shift_Del	DEL	ENST00000296522.6	hg19	CCDS3821.1																																																																																			.	.		0.333	HPGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362228.3			-	175414376	T	-	175414376	7	5	78	1	0	1	0	1	0	0	0	0	7343	1606	56	0	220	0	HPGD	4	175414376	Frame_Shift_Del	DEL	T	TCGA-CC-A8HS-01A-11D-A35Z-10	10977873	175414376	15739900	18	10722										
MYO10	4651	hgsc.bcm.edu	37	chr5	16689975	16689975	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	caatcaggtggaaagtcctaTcggccataatgatgtcgatc	10	9	1	1			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr5:16689975T>A	ENST00000513610.1	-	28	4308	c.3854A>T	c.(3853-3855)gAt>gTt	p.D1285V	MYO10_ENST00000505695.1_Missense_Mutation_p.D624V|MYO10_ENST00000274203.9_Missense_Mutation_p.D642V|MYO10_ENST00000427430.2_Missense_Mutation_p.D642V|MYO10_ENST00000515803.1_Missense_Mutation_p.D624V	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1285	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GAAAGTCCTATCGGCCATAAT	0.483																																					p.D1285V		Atlas-SNP	.											.	MYO10	198	.	0			c.A3854T						.						172	172	172					5																	16689975		2098	4225	6323	SO:0001583	missense	4651	exon28			GTCCTATCGGCCA	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.3854A>T	chr5.hg19:g.16689975T>A	ENSP00000421280:p.Asp1285Val	77.0	0.0		105.0	33.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	hg19	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.867102	0.51588	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.14266	2.52;2.52;2.52;2.52;2.52	5.52	5.52	0.82312	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	T	0.29223	0.0727	L	0.57130	1.785	0.80722	D	1	B;P;D	0.60575	0.14;0.813;0.988	B;B;P	0.58077	0.066;0.413;0.832	T	0.00907	-1.1519	9	0.46703	T	0.11	.	15.307	0.74001	0.0:0.0:0.0:1.0	.	164;926;1285	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	V	1285;624;642;624;642	ENSP00000421280:D1285V;ENSP00000425051:D624V;ENSP00000274203:D642V;ENSP00000421170:D624V;ENSP00000391106:D642V	ENSP00000274203:D642V	D	-	2	0	MYO10	16742975	1.000000	0.71417	0.454000	0.27019	0.045000	0.14185	6.258000	0.72487	2.104000	0.64026	0.533000	0.62120	GAT	.	.		0.483	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16689975	T	A	16689975	3	1	78	1	0	0	0	0	1	0	0	0	10071	1435	50	4	2378	4	MYO10	5	16689975	Missense_Mutation	SNP	T	TCGA-CC-A8HS-01A-11D-A35Z-10		16689975	164225285	19	10723										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167654929	167654929	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ggaacagctaccagctctgtAataatggtaccctgagggtg	12	9	1	1			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr5:167654929A>T	ENST00000518659.1	+	25	5353	c.5314A>T	c.(5314-5316)Aat>Tat	p.N1772Y	TENM2_ENST00000545108.1_Missense_Mutation_p.N1771Y|TENM2_ENST00000519204.1_Missense_Mutation_p.N1651Y|TENM2_ENST00000403607.2_Missense_Mutation_p.N1596Y|TENM2_ENST00000520394.1_Missense_Mutation_p.N1533Y|CTB-178M22.2_ENST00000519795.1_RNA	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1772					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										CCAGCTCTGTAATAATGGTAC	0.488																																					p.N1763Y		Atlas-SNP	.											.	.	.	.	0			c.A5287T						.						57	57	57					5																	167654929		1923	4146	6069	SO:0001583	missense	57451	exon25			CTCTGTAATAATG	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.5314A>T	chr5.hg19:g.167654929A>T	ENSP00000429430:p.Asn1772Tyr	169.0	0.0		95.0	32.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	A	1.128	-0.653277	0.03480	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89270	-2.02;-2.01;-2.12;-2.49;-2.49	5.66	5.66	0.87406	.	0.172324	0.64402	N	0.000008	T	0.78685	0.4322	N	0.05510	-0.035	0.41217	D	0.986487	B;B;B	0.30146	0.0;0.0;0.27	B;B;B	0.25140	0.001;0.001;0.058	T	0.77851	-0.2434	10	0.40728	T	0.16	.	15.8895	0.79286	1.0:0.0:0.0:0.0	.	1771;1772;1533	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	Y	1772;1771;1651;1533;1596	ENSP00000429430:N1772Y;ENSP00000438635:N1771Y;ENSP00000428964:N1651Y;ENSP00000427874:N1533Y;ENSP00000384905:N1596Y	ENSP00000384905:N1596Y	N	+	1	0	ODZ2	167587507	1.000000	0.71417	0.149000	0.22428	0.840000	0.47671	6.097000	0.71452	2.153000	0.67306	0.459000	0.35465	AAT	.	.		0.488	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	167654929	A	T	167654929	3	4	78	1	0	0	0	0	1	0	0	0	10844	362	13	4	5385	4	ODZ2	5	167654929	Missense_Mutation	SNP	A	TCGA-CC-A8HS-01A-11D-A35Z-10	150964954	167654929	13260331	20	10724										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30919613	30919613	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	atcacctcatctgcagcagaGtctacagaacatagagatag	8	10	4	3			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr6:30919613G>C	ENST00000462446.1	+	2	3400	c.3372G>C	c.(3370-3372)gaG>gaC	p.E1124D	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	297						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CTGCAGCAGAGTCTACAGAAC	0.488																																					p.E1124D		Atlas-SNP	.											.	DPCR1	99	.	0			c.G3372C						.						185	165	171					6																	30919613		692	1591	2283	SO:0001583	missense	135656	exon2			AGCAGAGTCTACA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.3372G>C	chr6.hg19:g.30919613G>C	ENSP00000417182:p.Glu1124Asp	69.0	0.0		69.0	33.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	g	5.334	0.246863	0.10130	.	.	ENSG00000168631	ENST00000462446	T	0.48522	0.81	1.86	-1.96	0.07525	.	.	.	.	.	T	0.30293	0.0760	L	0.44542	1.39	0.09310	N	0.999999	D	0.61697	0.99	D	0.72982	0.979	T	0.10660	-1.0620	9	0.21014	T	0.42	0.0038	1.9518	0.03368	0.3889:0.0:0.3475:0.2636	.	1124	E9PEI6	.	D	1124	ENSP00000417182:E1124D	ENSP00000417182:E1124D	E	+	3	2	DPCR1	31027592	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-0.329000	0.07935	-0.267000	0.09325	-0.408000	0.06270	GAG	.	.		0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		C	30919613	G	C	30919613	3	2	78	1	0	0	0	0	1	0	0	0	4714	1020	36	4	3378	4	DPCR1	6	30919613	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10		30919613	140195454	21	10725										
KLHDC3	116138	hgsc.bcm.edu	37	chr6	42986657	42986657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	aggggccatgtccccgccggCgccagtgctgctgtattgtt	14	13	0	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr6:42986657C>T	ENST00000326974.4	+	8	1072	c.877C>T	c.(877-879)Cgc>Tgc	p.R293C	KLHDC3_ENST00000332245.8_Missense_Mutation_p.R234C|RRP36_ENST00000244496.5_5'Flank|KLHDC3_ENST00000244670.8_Missense_Mutation_p.R159C	NM_057161.3	NP_476502.1	Q9BQ90	KLDC3_HUMAN	kelch domain containing 3	293					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|reciprocal meiotic recombination (GO:0007131)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)	chromatin binding (GO:0003682)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			TCCCCGCCGGCGCCAGTGCTG	0.512																																					p.R293C		Atlas-SNP	.											.	KLHDC3	23	.	0			c.C877T						.						65	77	73					6																	42986657		2202	4299	6501	SO:0001583	missense	116138	exon8			CGCCGGCGCCAGT	AB055925	CCDS4880.1	6p21.1	2003-06-12			ENSG00000124702	ENSG00000124702			20704	protein-coding gene	gene with protein product		611248				12444059, 12606021	Standard	NM_057161		Approved	PEAS, hPeas, dJ20C7.3	uc003otl.3	Q9BQ90	OTTHUMG00000014714	ENST00000326974.4:c.877C>T	chr6.hg19:g.42986657C>T	ENSP00000313995:p.Arg293Cys	121.0	0.0		106.0	20.0	NM_057161	A8K2W9	Missense_Mutation	SNP	ENST00000326974.4	hg19	CCDS4880.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.297416	0.60086	.	.	ENSG00000124702	ENST00000326974;ENST00000432243;ENST00000244670;ENST00000394096;ENST00000426116;ENST00000332245	T;T;T	0.66638	-0.22;-0.22;-0.22	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.76219	0.3957	M	0.93197	3.39	0.80722	D	1	P;P;P;P	0.52170	0.951;0.861;0.489;0.917	P;B;B;B	0.50708	0.648;0.391;0.105;0.391	T	0.82703	-0.0326	10	0.72032	D	0.01	-7.2709	12.9393	0.58333	0.2828:0.7172:0.0:0.0	.	293;234;159;293	E7ENU0;E7ERR0;F8W6A4;Q9BQ90	.;.;.;KLDC3_HUMAN	C	293;293;159;293;266;234	ENSP00000313995:R293C;ENSP00000244670:R159C;ENSP00000331562:R234C	ENSP00000244670:R159C	R	+	1	0	KLHDC3	43094635	1.000000	0.71417	0.999000	0.59377	0.919000	0.55068	1.762000	0.38451	2.648000	0.89879	0.205000	0.17691	CGC	.	.		0.512	KLHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040570.1	NM_057161		T	42986657	C	T	42986657	3	4	78	1	0	0	0	0	1	0	0	0	8366	768	27	1	903	1	KLHDC3	6	42986657	Missense_Mutation	SNP	C	TCGA-CC-A8HS-01A-11D-A35Z-10	12067044	42986657	128128410	22	10726										
ROS1	6098	hgsc.bcm.edu	37	chr6	117746713	117746713	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ttaccagattagttacacacGactttaggcagctatttaaa	6	8	0	1	rs371523377		TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr6:117746713G>T	ENST00000368508.3	-	1	305	c.107C>A	c.(106-108)tCg>tAg	p.S36*	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Nonsense_Mutation_p.S36*	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	36					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AGTTACACACGACTTTAGGCA	0.363			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.S36X		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.C107A						.						140	135	137					6																	117746713		2203	4300	6503	SO:0001587	stop_gained	6098	exon1			ACACACGACTTTA	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.107C>A	chr6.hg19:g.117746713G>T	ENSP00000357494:p.Ser36*	120.0	0.0		103.0	53.0	NM_002944	Q15368|Q5TDB5	Nonsense_Mutation	SNP	ENST00000368508.3	hg19	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	G	37	6.304748	0.97458	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	.	.	.	5.11	2.4	0.29515	.	0.309329	0.23953	N	0.042923	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	8.0708	0.30689	0.205:0.0:0.795:0.0	.	.	.	.	X	36	.	ENSP00000357493:S36X	S	-	2	0	ROS1	117853406	0.998000	0.40836	0.995000	0.50966	0.702000	0.40608	0.848000	0.27710	0.435000	0.26365	-1.202000	0.01658	TCG	.	.		0.363	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			T	117746713	G	T	117746713	4	4	78	1	0	0	0	0	0	1	0	0	13546	1059	37	1	7108	1	ROS1	6	117746713	Nonsense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	74760056	117746713	53368354	23	10727										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48443322	48443322	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	actcagcatcagcacaaacaGacccgagctctgtctggagg	10	13	4	1			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr7:48443322G>C	ENST00000435803.1	+	39	11940	c.11916G>C	c.(11914-11916)caG>caC	p.Q3972H		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3972	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AGCACAAACAGACCCGAGCTC	0.493																																					p.Q3972H		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G11916C						.						105	105	105					7																	48443322		1956	4142	6098	SO:0001583	missense	154664	exon39			CAAACAGACCCGA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11916G>C	chr7.hg19:g.48443322G>C	ENSP00000411096:p.Gln3972His	90.0	0.0		63.0	26.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	6.187	0.402590	0.11696	.	.	ENSG00000179869	ENST00000435803	D	0.93366	-3.21	6.17	-5.84	0.02318	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.467204	0.18100	N	0.151724	D	0.83774	0.5327	L	0.39397	1.21	0.09310	N	1	B;B	0.23128	0.006;0.08	B;B	0.23716	0.01;0.048	T	0.70648	-0.4814	10	0.35671	T	0.21	.	1.37	0.02209	0.4404:0.1644:0.1071:0.2881	.	1674;3972	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	H	3972	ENSP00000411096:Q3972H	ENSP00000411096:Q3972H	Q	+	3	2	ABCA13	48413868	0.000000	0.05858	0.000000	0.03702	0.110000	0.19582	-1.642000	0.02006	-0.498000	0.06632	0.655000	0.94253	CAG	.	.		0.493	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48443322	G	C	48443322	3	2	78	1	0	0	0	0	1	0	0	0	31	933	33	4	11899	4	ABCA13	7	48443322	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10		48443322	110695341	24	10728										
RPL7A	6130	hgsc.bcm.edu	37	chr9	136216547	136216547	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	gttcacccaggccctggaccGccaaacaggtgaggttctgt	12	13	2	1			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr9:136216547G>T	ENST00000323345.6	+	3	296	c.266G>T	c.(265-267)cGc>cTc	p.R89L	MED22_ENST00000343730.5_5'Flank|SNORD36A_ENST00000362874.1_RNA|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000344469.5_5'Flank|MED22_ENST00000371999.1_5'Flank|RPL7A_ENST00000463740.1_3'UTR|SNORD36B_ENST00000363961.1_RNA|RPL7A_ENST00000315731.4_Intron|MED22_ENST00000491289.1_5'Flank|MED22_ENST00000471524.1_5'Flank|SURF1_ENST00000495952.1_5'Flank|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000476080.1_5'Flank	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	89					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		GCCCTGGACCGCCAAACAGGT	0.527																																					p.R89L		Atlas-SNP	.											.	RPL7A	9	.	0			c.G266T						.						47	53	51					9																	136216547		2196	4299	6495	SO:0001583	missense	6130	exon3			TGGACCGCCAAAC	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"L ribosomal proteins"	10364	protein-coding gene	gene with protein product	"surfeit 3", "PLA-X polypeptide", "surfeit locus protein 3", "60S ribosomal protein L7a", ";", "thyroid hormone receptor uncoupling protein"	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.266G>T	chr9.hg19:g.136216547G>T	ENSP00000361076:p.Arg89Leu	131.0	0.0		115.0	5.0	NM_000972	P11518|Q5T8U4	Missense_Mutation	SNP	ENST00000323345.6	hg19	CCDS6965.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.593234	0.66219	.	.	ENSG00000148303	ENST00000323345;ENST00000426651	T;T	0.58506	0.33;0.7	4.03	4.03	0.46877	.	0.000000	0.85682	D	0.000000	T	0.67590	0.2909	M	0.92970	3.365	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	T	0.73341	-0.4013	10	0.87932	D	0	.	15.1827	0.72972	0.0:0.0:1.0:0.0	.	89	P62424	RL7A_HUMAN	L	89;116	ENSP00000361076:R89L;ENSP00000416638:R116L	ENSP00000361076:R89L	R	+	2	0	RPL7A	135206368	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	8.833000	0.92089	1.816000	0.52996	0.313000	0.20887	CGC	.	.		0.527	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972		T	136216547	G	T	136216547	3	4	78	1	0	0	0	0	1	0	0	0	13615	1087	38	1	276	1	RPL7A	9	136216547	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10		136216547	4996884	25	10729										
RNF208	727800	hgsc.bcm.edu	37	chr9	140115059	140115059	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	gacgtgttgacagccagcgcGgccaggccgtagtcggtgaa	16	11	0	2	rs540686797		TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr9:140115059G>A	ENST00000392827.1	-	2	774	c.606C>T	c.(604-606)gcC>gcT	p.A202A	RNF208_ENST00000391553.1_Silent_p.A202A			Q9H0X6	RN208_HUMAN	ring finger protein 208	202					protein autoubiquitination (GO:0051865)		ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			lung(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		CAGCCAGCGCGGCCAGGCCGT	0.667													G|||	1	0.000199681	8e-04	0	5008	,	,		14448	0		0	False		,,,				2504	0				p.A202A		Atlas-SNP	.											.	RNF208	11	.	0			c.C606T						.						51	40	44					9																	140115059		2190	4293	6483	SO:0001819	synonymous_variant	727800	exon1			CAGCGCGGCCAGG	AF416715	CCDS7037.2	9q34.3	2007-01-19				ENSG00000212864		"RING-type (C3HC4) zinc fingers"	25420	protein-coding gene	gene with protein product						11230166	Standard	NM_031297		Approved	DKFZP761H1710	uc004clz.2	Q9H0X6		ENST00000392827.1:c.606C>T	chr9.hg19:g.140115059G>A		247.0	0.0		356.0	18.0	NM_031297	A2BFA0	Silent	SNP	ENST00000392827.1	hg19	CCDS7037.2																																																																																			.	.		0.667	RNF208-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254714.1	NM_031297		A	140115059	G	A	140115059	2	1	78	1	0	0	0	0	0	0	0	1	13490	1103	39	1		1	RNF208	9	140115059	Silent	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	3898512	140115059	1098372	26	10730										
NLRP10	338322	hgsc.bcm.edu	37	chr11	7981277	7981277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tgttcctgctatattatcttTgccctccttctgtccatgga	6	12	2	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr11:7981277T>C	ENST00000328600.2	-	2	2043	c.1882A>G	c.(1882-1884)Aaa>Gaa	p.K628E		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	628					defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATATTATCTTTGCCCTCCTTC	0.388																																					p.K628E		Atlas-SNP	.											.	NLRP10	146	.	0			c.A1882G						.						97	90	92					11																	7981277		2201	4294	6495	SO:0001583	missense	338322	exon2			TATCTTTGCCCTC	AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"Nucleotide-binding domain and leucine rich repeat containing"	21464	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"	609662	"NACHT, leucine rich repeat and PYD containing 10"	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.1882A>G	chr11.hg19:g.7981277T>C	ENSP00000327763:p.Lys628Glu	103.0	0.0		96.0	5.0	NM_176821	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	hg19	CCDS7784.1	.	.	.	.	.	.	.	.	.	.	T	6.341	0.431031	0.12045	.	.	ENSG00000182261	ENST00000328600	T	0.80566	-1.39	3.02	-4.18	0.03846	.	.	.	.	.	T	0.54208	0.1844	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46373	-0.9196	9	0.07482	T	0.82	.	5.0267	0.14389	0.0:0.3562:0.3729:0.2709	.	628	Q86W26	NAL10_HUMAN	E	628	ENSP00000327763:K628E	ENSP00000327763:K628E	K	-	1	0	NLRP10	7937853	0.000000	0.05858	0.000000	0.03702	0.189000	0.23516	-0.276000	0.08514	-0.935000	0.03728	0.383000	0.25322	AAA	.	.		0.388	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821		C	7981277	T	C	7981277	3	2	78	1	0	0	0	0	1	0	0	0	10481	1821	63	2	89	2	NLRP10	11	7981277	Missense_Mutation	SNP	T	TCGA-CC-A8HS-01A-11D-A35Z-10		7981277	127025239	27	10731										
GALNTL4	374378	hgsc.bcm.edu	37	chr11	11643115	11643115	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tcacgcaagtggacaccaaaGttttggtcttcctggtgcac	10	11	2	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr11:11643115G>A	ENST00000227756.4	-	1	437	c.26C>T	c.(25-27)aCt>aTt	p.T9I	GALNT18_ENST00000526064.1_5'UTR	NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	9					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										GGACACCAAAGTTTTGGTCTT	0.597																																					p.T9I		Atlas-SNP	.											.	.	.	.	0			c.C26T						.						74	58	63					11																	11643115		2201	4294	6495	SO:0001583	missense	374378	exon1			ACCAAAGTTTTGG	AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"Glycosyltransferase family 2 domain containing"	30488	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 18"	615136	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.26C>T	chr11.hg19:g.11643115G>A	ENSP00000227756:p.Thr9Ile	76.0	0.0		106.0	40.0	NM_198516	O95903|Q8NDY9	Missense_Mutation	SNP	ENST00000227756.4	hg19	CCDS7807.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.885978	0.91814	.	.	ENSG00000110328	ENST00000227756	T	0.58060	0.36	4.95	4.95	0.65309	.	0.183891	0.36628	N	0.002489	T	0.62780	0.2456	L	0.41492	1.28	0.52099	D	0.999942	D	0.71674	0.998	D	0.73708	0.981	T	0.55897	-0.8068	10	0.22109	T	0.4	.	16.9065	0.86130	0.0:0.0:1.0:0.0	.	9	Q6P9A2	GLTL4_HUMAN	I	9	ENSP00000227756:T9I	ENSP00000227756:T9I	T	-	2	0	GALNTL4	11599691	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.263000	0.95617	2.572000	0.86782	0.561000	0.74099	ACT	.	.		0.597	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516		A	11643115	G	A	11643115	3	1	78	1	0	0	0	0	1	0	0	0	6231	1029	36	3	1841	3	GALNTL4	11	11643115	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	3661838	11643115	123363401	28	10732										
WDR74	54663	hgsc.bcm.edu	37	chr11	62607038	62607038	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tccagcgtgcagcagcagccGccatgacaaagcctggaggc	13	14	0	1	rs545160528	byFrequency	TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr11:62607038G>A	ENST00000525239.1	-	2	542	c.5C>T	c.(4-6)gCg>gTg	p.A2V	WDR74_ENST00000529106.1_Missense_Mutation_p.A2V|WDR74_ENST00000540620.1_5'UTR|RNU2-2P_ENST00000410396.1_RNA|WDR74_ENST00000311713.7_Missense_Mutation_p.A2V|WDR74_ENST00000278856.4_Missense_Mutation_p.A2V|WDR74_ENST00000525752.1_5'UTR			Q6RFH5	WDR74_HUMAN	WD repeat domain 74	2					blastocyst formation (GO:0001825)|RNA metabolic process (GO:0016070)	nucleolus (GO:0005730)|nucleus (GO:0005634)				kidney(2)|large_intestine(1)|liver(1)|lung(3)|ovary(1)	8						AGCAGCAGCCGCCATGACAAA	0.642													G|||	3	0.000599042	0	0	5008	,	,		17818	0		0	False		,,,				2504	0.0031				p.A2V		Atlas-SNP	.											.	WDR74	36	.	0			c.C5T						.						34	40	38					11																	62607038		2161	4262	6423	SO:0001583	missense	54663	exon2			GCAGCCGCCATGA		CCDS44630.1	11q12.3	2013-01-09				ENSG00000133316		"WD repeat domain containing"	25529	protein-coding gene	gene with protein product							Standard	NM_018093		Approved	FLJ10439	uc001nvm.2	Q6RFH5		ENST00000525239.1:c.5C>T	chr11.hg19:g.62607038G>A	ENSP00000432119:p.Ala2Val	69.0	0.0		80.0	33.0	NM_018093	A8K8G5|Q9BRC9|Q9H6X8|Q9NVY2	Missense_Mutation	SNP	ENST00000525239.1	hg19	CCDS44630.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.116044	0.56505	.	.	ENSG00000133316	ENST00000311713;ENST00000529106;ENST00000525239;ENST00000278856;ENST00000538098	.	.	.	4.28	3.34	0.38264	.	0.124803	0.50627	D	0.000113	T	0.23846	0.0577	N	0.22421	0.69	0.26885	N	0.967456	D;P;P	0.56287	0.975;0.814;0.883	B;B;B	0.43082	0.407;0.148;0.285	T	0.08932	-1.0698	9	0.34782	T	0.22	-18.1912	10.2014	0.43087	0.1017:0.0:0.8983:0.0	.	2;2;2	B4E018;Q6RFH5;Q6RFH5-2	.;WDR74_HUMAN;.	V	2	.	ENSP00000278856:A2V	A	-	2	0	WDR74	62363614	0.993000	0.37304	0.850000	0.33497	0.007000	0.05969	2.105000	0.41825	2.213000	0.71641	0.655000	0.94253	GCG	.	.		0.642	WDR74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395678.1	NM_018093		A	62607038	G	A	62607038	3	1	78	1	0	0	0	0	1	0	0	0	17339	1087	38	1	1196	1	WDR74	11	62607038	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	50963923	62607038	72399478	29	10733										
SUV420H1	51111	hgsc.bcm.edu	37	chr11	67957487	67957487	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tgatggtcattagacaacttGcctccatttctcctgccatt	6	12	2	2			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr11:67957487G>T	ENST00000304363.4	-	2	410	c.57C>A	c.(55-57)ggC>ggA	p.G19G	SUV420H1_ENST00000402789.1_Silent_p.G19G|SUV420H1_ENST00000401547.2_Silent_p.G19G|SUV420H1_ENST00000402185.2_Silent_p.G19G|SUV420H1_ENST00000405515.1_Silent_p.G19G	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	19					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TAGACAACTTGCCTCCATTTC	0.488																																					p.G19G		Atlas-SNP	.											.	SUV420H1	125	.	0			c.C57A						.						330	279	296					11																	67957487		2200	4294	6494	SO:0001819	synonymous_variant	51111	exon2			CAACTTGCCTCCA	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.57C>A	chr11.hg19:g.67957487G>T		76.0	0.0		66.0	4.0	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Silent	SNP	ENST00000304363.4	hg19	CCDS31623.1																																																																																			.	.		0.488	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		T	67957487	G	T	67957487	2	4	78	1	0	0	0	0	0	0	0	1	15429	1306	46	3		3	SUV420H1	11	67957487	Silent	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	5350449	67957487	67049029	30	10734										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20782946	20782946	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tttctgcagtgcagtttccaGaatctgctgacacaactgcc	8	12	2	2			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr12:20782946G>C	ENST00000359062.3	+	6	1685	c.1645G>C	c.(1645-1647)Gaa>Caa	p.E549Q	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	549					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	GCAGTTTCCAGAATCTGCTGA	0.522																																					p.E549Q		Atlas-SNP	.											.	PDE3A	184	.	0			c.G1645C						.						131	131	131					12																	20782946		2203	4300	6503	SO:0001583	missense	5139	exon6			TTTCCAGAATCTG		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.1645G>C	chr12.hg19:g.20782946G>C	ENSP00000351957:p.Glu549Gln	87.0	0.0		54.0	20.0	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.455775	0.84209	.	.	ENSG00000172572	ENST00000359062	T	0.54479	0.57	5.44	5.44	0.79542	.	0.702082	0.14966	N	0.288062	T	0.51873	0.1700	L	0.48642	1.525	0.43708	D	0.996178	P	0.48764	0.915	B	0.42771	0.397	T	0.55854	-0.8075	10	0.56958	D	0.05	.	17.2299	0.86982	0.0:0.0:1.0:0.0	.	549	Q14432	PDE3A_HUMAN	Q	549	ENSP00000351957:E549Q	ENSP00000351957:E549Q	E	+	1	0	PDE3A	20674213	1.000000	0.71417	0.996000	0.52242	0.855000	0.48748	8.421000	0.90259	2.834000	0.97654	0.650000	0.86243	GAA	.	.		0.522	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			C	20782946	G	C	20782946	3	2	78	1	0	0	0	0	1	0	0	0	11646	943	33	4	1667	4	PDE3A	12	20782946	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10		20782946	113068949	31	10735										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112685925	112685925	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ttgttctccagtttcccctgCatggcatcatcaacttcact	5	14	4	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr12:112685925C>G	ENST00000430131.2	-	26	4073	c.2928G>C	c.(2926-2928)atG>atC	p.M976I	HECTD4_ENST00000377560.5_Missense_Mutation_p.M1226I|HECTD4_ENST00000550722.1_Missense_Mutation_p.M1252I			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	976					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GTTTCCCCTGCATGGCATCAT	0.338																																					p.M1264I		Atlas-SNP	.											.	.	.	.	0			c.G3792C						.						101	95	97					12																	112685925		1893	4131	6024	SO:0001583	missense	283450	exon27			CCCCTGCATGGCA	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.2928G>C	chr12.hg19:g.112685925C>G	ENSP00000404379:p.Met976Ile	135.0	0.0		151.0	7.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	C	9.595	1.127237	0.20959	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.41758	0.99;0.99;0.99	5.79	-2.1	0.07210	.	.	.	.	.	T	0.16041	0.0386	N	0.08118	0	0.23903	N	0.996516	B	0.02656	0.0	B	0.01281	0.0	T	0.22382	-1.0218	9	0.16896	T	0.51	.	2.045	0.03558	0.205:0.4615:0.0996:0.2339	.	976	Q9Y4D8	K0614_HUMAN	I	1226;976;1252	ENSP00000366783:M1226I;ENSP00000404379:M976I;ENSP00000449784:M1252I	ENSP00000366783:M1226I	M	-	3	0	C12orf51	111170308	0.955000	0.32602	0.883000	0.34634	0.870000	0.49936	0.126000	0.15769	-0.415000	0.07484	-0.263000	0.10527	ATG	.	.		0.338	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		G	112685925	C	G	112685925	3	3	78	1	0	0	0	0	1	0	0	0	1698	710	25	4	9262	4	C12orf51	12	112685925	Missense_Mutation	SNP	C	TCGA-CC-A8HS-01A-11D-A35Z-10	91902979	112685925	21165970	32	10736										
STOML3	161003	hgsc.bcm.edu	37	chr13	39564842	39564842	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tatcttgcttctcaggtgaaGacaccctagaatccatctca	6	12	3	3			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr13:39564842G>A	ENST00000379631.4	-	1	361	c.17C>T	c.(16-18)tCt>tTt	p.S6F	STOML3_ENST00000423210.1_5'UTR	NM_145286.2	NP_660329.1	Q8TAV4	STML3_HUMAN	stomatin (EPB72)-like 3	6					signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	11		Lung NSC(96;1.42e-05)|Prostate(109;0.00851)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;2.93e-08)|Epithelial(112;3.64e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00107)|BRCA - Breast invasive adenocarcinoma(63;0.00349)|GBM - Glioblastoma multiforme(144;0.0137)		CTCAGGTGAAGACACCCTAGA	0.403																																					p.S6F		Atlas-SNP	.											.	STOML3	47	.	0			c.C17T						.						138	132	134					13																	39564842		2203	4300	6503	SO:0001583	missense	161003	exon1			GGTGAAGACACCC	BC025760	CCDS9367.1, CCDS45040.1	13q13.2	2004-03-05			ENSG00000133115	ENSG00000133115			19420	protein-coding gene	gene with protein product		608327				12122055	Standard	NM_145286		Approved	SRO, Epb7.2l	uc001uwx.3	Q8TAV4	OTTHUMG00000016763	ENST00000379631.4:c.17C>T	chr13.hg19:g.39564842G>A	ENSP00000368952:p.Ser6Phe	87.0	0.0		56.0	37.0	NM_145286	B4E285|Q5JS35	Missense_Mutation	SNP	ENST00000379631.4	hg19	CCDS9367.1	.	.	.	.	.	.	.	.	.	.	G	8.222	0.802790	0.16397	.	.	ENSG00000133115	ENST00000379631	D	0.98567	-5.0	4.71	4.71	0.59529	.	2.132240	0.01386	N	0.013090	D	0.95373	0.8498	N	0.08118	0	0.25424	N	0.98824	B	0.22480	0.07	B	0.28011	0.085	D	0.87485	0.2423	10	0.59425	D	0.04	0.2834	10.481	0.44693	0.0:0.0:0.8061:0.1939	.	6	Q8TAV4	STML3_HUMAN	F	6	ENSP00000368952:S6F	ENSP00000368952:S6F	S	-	2	0	STOML3	38462842	0.256000	0.24012	0.097000	0.21041	0.300000	0.27592	0.354000	0.20146	2.153000	0.67306	0.650000	0.86243	TCT	.	.		0.403	STOML3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044604.2			A	39564842	G	A	39564842	3	1	78	1	0	0	0	0	1	0	0	0	15330	942	33	3	915	3	STOML3	13	39564842	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10		39564842	75605036	33	10737										
DZIP1	22873	hgsc.bcm.edu	37	chr13	96239841	96239841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ctcgatttcgcttccctcggTcccgtccgcgtcacttttca	7	17	2	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr13:96239841T>C	ENST00000376829.2	-	20	3021	c.2170A>G	c.(2170-2172)Acc>Gcc	p.T724A	DZIP1_ENST00000347108.3_Missense_Mutation_p.T724A|DZIP1_ENST00000361156.3_Missense_Mutation_p.T705A|DZIP1_ENST00000361396.2_Missense_Mutation_p.T705A	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	724					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			CTTCCCTCGGTCCCGTCCGCG	0.552																																					p.T724A		Atlas-SNP	.											.	DZIP1	195	.	0			c.A2170G						.						183	155	164					13																	96239841		2203	4300	6503	SO:0001583	missense	22873	exon20			CCTCGGTCCCGTC	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.2170A>G	chr13.hg19:g.96239841T>C	ENSP00000366025:p.Thr724Ala	90.0	0.0		142.0	69.0	NM_198968	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	hg19	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	T	7.446	0.641623	0.14451	.	.	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	5.35	4.15	0.48705	.	0.571979	0.18370	N	0.143293	T	0.34716	0.0907	M	0.72894	2.215	0.25802	N	0.984495	P;B	0.35307	0.494;0.361	B;B	0.32465	0.146;0.069	T	0.35276	-0.9795	10	0.59425	D	0.04	-13.0104	7.2039	0.25897	0.1452:0.0:0.152:0.7029	.	705;724	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	A	724;705;705;724	ENSP00000257312:T724A;ENSP00000355018:T705A;ENSP00000355175:T705A;ENSP00000366025:T724A	ENSP00000257312:T724A	T	-	1	0	DZIP1	95037842	1.000000	0.71417	0.916000	0.36221	0.003000	0.03518	2.004000	0.40854	0.845000	0.35118	-0.316000	0.08728	ACC	.	.		0.552	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		C	96239841	T	C	96239841	3	2	78	1	0	0	0	0	1	0	0	0	4865	1667	58	2	449	2	DZIP1	13	96239841	Missense_Mutation	SNP	T	TCGA-CC-A8HS-01A-11D-A35Z-10	56674999	96239841	18930037	34	10738										
ZIC2	7546	hgsc.bcm.edu	37	chr13	100637726	100637726	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	gcggcggcagcggcggcggcGgctgcggcggcggcggccgc	24	15	0	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr13:100637726G>T	ENST00000376335.3	+	3	1682	c.1389G>T	c.(1387-1389)gcG>gcT	p.A463A	ZIC2_ENST00000477213.1_3'UTR	NM_007129.3	NP_009060.2	O95409	ZIC2_HUMAN	Zic family member 2	463	Poly-Ala.				brain development (GO:0007420)|developmental pigmentation (GO:0048066)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|retinal ganglion cell axon guidance (GO:0031290)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(2)|liver(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					cggcggcggcggctgcggcgg	0.816																																					p.A463A	Pancreas(97;119 1522 31925 44771 48764)	Atlas-SNP	.											.	ZIC2	25	.	0			c.G1389T						.						2	3	3					13																	100637726		765	1850	2615	SO:0001819	synonymous_variant	7546	exon3			GGCGGCGGCTGCG	AF104902	CCDS9495.1	13q32	2013-01-08	2011-05-19		ENSG00000043355	ENSG00000043355		"Zinc fingers, C2H2-type"	12873	protein-coding gene	gene with protein product	"Zinc finger protein of the cerebellum 2"	603073	"Zic family member 2 (odd-paired Drosophila homolog)", "Zic family member 2 (odd-paired homolog, Drosophila)"			9771712	Standard	NM_007129		Approved	HPE5	uc001von.3	O95409	OTTHUMG00000017279	ENST00000376335.3:c.1389G>T	chr13.hg19:g.100637726G>T		92.0	0.0		113.0	5.0	NM_007129	Q5VYA9|Q9H309	Silent	SNP	ENST00000376335.3	hg19	CCDS9495.1																																																																																			.	.		0.816	ZIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045618.2	NM_007129		T	100637726	G	T	100637726	2	4	78	1	0	0	0	0	0	0	0	1	17694	1103	39	1		1	ZIC2	13	100637726	Silent	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	4397885	100637726	14532152	35	10739										
TEP1	7011	hgsc.bcm.edu	37	chr14	20850191	20850191	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ggtagtgtccgccacacactCagcactccgtgcagctggtc	11	15	1	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr14:20850191C>T	ENST00000262715.5	-	30	4345	c.4305G>A	c.(4303-4305)ctG>ctA	p.L1435L	TEP1_ENST00000545983.1_5'UTR|TEP1_ENST00000556935.1_Silent_p.L1327L	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1435	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GCCACACACTCAGCACTCCGT	0.597																																					p.L1435L		Atlas-SNP	.											.	TEP1	224	.	0			c.G4305A						.						127	105	113					14																	20850191		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon30			CACACTCAGCACT		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.4305G>A	chr14.hg19:g.20850191C>T		67.0	0.0		112.0	60.0	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	.		0.597	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20850191	C	T	20850191	2	4	78	1	0	0	0	0	0	0	0	1	15774	813	29	3		3	TEP1	14	20850191	Silent	SNP	C	TCGA-CC-A8HS-01A-11D-A35Z-10		20850191	86499349	36	10740										
OR5AU1	390445	hgsc.bcm.edu	37	chr14	21623890	21623890	+	Frame_Shift_Del	DEL	G	G	-													0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ggtggcactcacatggatcaGgaggaacatgaccaggttcc							TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr14:21623890delG	ENST00000304418.3	-	1	332	c.295delC	c.(295-297)ctgfs	p.L99fs		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(12)|pancreas(1)	21	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		ACATGGATCAGGAGGAACATG	0.587																																					p.L99fs		Atlas-INDEL	.											.	OR5AU1	46	.	0			c.296delT						.						107	87	94					14																	21623890		2203	4300	6503	SO:0001589	frameshift_variant	390445	exon1			.	AL157687	CCDS32042.1	14q11.2	2013-09-23			ENSG00000169327	ENSG00000169327		"GPCR / Class A : Olfactory receptors"	15362	protein-coding gene	gene with protein product							Standard	NM_001004731		Approved		uc010tlp.2	Q8NGC0	OTTHUMG00000170753	ENST00000304418.3:c.295delC	chr14.hg19:g.21623890delG	ENSP00000302057:p.Leu99fs	134.0	0.0		149.0	11.0	NM_001004731	B2RP78|Q6IEU2|Q96R10	Frame_Shift_Del	DEL	ENST00000304418.3	hg19	CCDS32042.1																																																																																			.	.		0.587	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1			-	21623890	G	-	21623890	7	5	78	1	0	1	0	1	0	0	0	0	11156	991	35	0	796	0	OR5AU1	14	21623890	Frame_Shift_Del	DEL	G	TCGA-CC-A8HS-01A-11D-A35Z-10	773699	21623890	85725650	37	10741	44	2								
OR5AU1	390445	hgsc.bcm.edu	37	chr14	21623894	21623895	+	Frame_Shift_Ins	INS	-	-	GA													0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	cactcacatggatcaggaggINSaacatgaccaggttccccag							TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr14:21623894_21623895insGA	ENST00000304418.3	-	1	327_328	c.290_291insTC	c.(289-291)ttcfs	p.F97fs		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	97						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(12)|pancreas(1)	21	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		GGATCAGGAGGAACATGACCAG	0.589																																					p.F97fs		Atlas-INDEL	.											.	OR5AU1	46	.	0			c.291_292insTC						.																																			SO:0001589	frameshift_variant	390445	exon1			.	AL157687	CCDS32042.1	14q11.2	2013-09-23			ENSG00000169327	ENSG00000169327		"GPCR / Class A : Olfactory receptors"	15362	protein-coding gene	gene with protein product							Standard	NM_001004731		Approved		uc010tlp.2	Q8NGC0	OTTHUMG00000170753	ENST00000304418.3:c.290_291insTC	chr14.hg19:g.21623894_21623895insGA	ENSP00000302057:p.Phe97fs	136.0	0.0		149.0	11.0	NM_001004731	B2RP78|Q6IEU2|Q96R10	Frame_Shift_Ins	INS	ENST00000304418.3	hg19	CCDS32042.1																																																																																			.	.		0.589	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1			GA	21623895	-	GA	21623894	7	5	78	1	0	1	1	0	0	0	0	0	11156	1165	41	0	800	0	OR5AU1	14	21623894	Frame_Shift_Ins	INS	-	TCGA-CC-A8HS-01A-11D-A35Z-10	4	21623894	85725646	38	10742	44	2								
PTPN21	11099	hgsc.bcm.edu	37	chr14	88970830	88970830	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ttccaatactttttcatcttGtaaccatccctgaagaaaac	3	11	2	2			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr14:88970830G>C	ENST00000556564.1	-	6	810	c.526C>G	c.(526-528)Caa>Gaa	p.Q176E	PTPN21_ENST00000328736.3_Missense_Mutation_p.Q176E|PTPN21_ENST00000554628.1_5'UTR|RP11-507K2.2_ENST00000555444.1_RNA	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	176	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TTTTCATCTTGTAACCATCCC	0.383																																					p.Q176E		Atlas-SNP	.											.	PTPN21	113	.	0			c.C526G						.						166	154	158					14																	88970830		2203	4299	6502	SO:0001583	missense	11099	exon6			CATCTTGTAACCA	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.526C>G	chr14.hg19:g.88970830G>C	ENSP00000452414:p.Gln176Glu	113.0	0.0		76.0	59.0	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	hg19	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	G	9.674	1.147392	0.21288	.	.	ENSG00000070778	ENST00000328736;ENST00000556564;ENST00000555243	T;T;T	0.26957	1.7;1.7;1.7	5.18	5.18	0.71444	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.148278	0.47455	D	0.000240	T	0.41719	0.1171	M	0.78916	2.43	0.46901	D	0.999244	B;P	0.43938	0.022;0.822	B;P	0.46718	0.022;0.525	T	0.28396	-1.0045	10	0.34782	T	0.22	.	19.0577	0.93072	0.0:0.0:1.0:0.0	.	176;176	G3V3S6;Q16825	.;PTN21_HUMAN	E	176	ENSP00000330276:Q176E;ENSP00000452414:Q176E;ENSP00000451401:Q176E	ENSP00000330276:Q176E	Q	-	1	0	PTPN21	88040583	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.124000	0.94394	2.574000	0.86865	0.655000	0.94253	CAA	.	.		0.383	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			C	88970830	G	C	88970830	3	2	78	1	0	0	0	0	1	0	0	0	12801	1386	48	4	3054	4	PTPN21	14	88970830	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10	67346936	88970830	18378710	39	10743										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105408769	105408769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tgaggtgagtggtcttcaggTccccctgcatggaggggagg	18	8	2	2			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr14:105408769T>C	ENST00000333244.5	-	7	13138	c.13019A>G	c.(13018-13020)gAc>gGc	p.D4340G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4340						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGTCTTCAGGTCCCCCTGCAT	0.622																																					p.D4340G		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A13019G						.						146	155	152					14																	105408769		1979	4145	6124	SO:0001583	missense	113146	exon7			TTCAGGTCCCCCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.13019A>G	chr14.hg19:g.105408769T>C	ENSP00000353114:p.Asp4340Gly	110.0	0.0		93.0	4.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	13.44	2.238841	0.39598	.	.	ENSG00000185567	ENST00000333244	T	0.02177	4.41	3.31	2.14	0.27477	.	.	.	.	.	T	0.09642	0.0237	M	0.75884	2.315	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.13150	-1.0520	9	0.45353	T	0.12	.	7.3174	0.26507	0.0:0.1144:0.0:0.8856	.	4340	Q8IVF2	AHNK2_HUMAN	G	4340	ENSP00000353114:D4340G	ENSP00000353114:D4340G	D	-	2	0	AHNAK2	104479814	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.336000	0.19823	0.218000	0.20820	0.254000	0.18369	GAC	.	.		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105408769	T	C	105408769	3	2	78	1	0	0	0	0	1	0	0	0	415	1667	58	2	4372	2	AHNAK2	14	105408769	Missense_Mutation	SNP	T	TCGA-CC-A8HS-01A-11D-A35Z-10	16437939	105408769	1940771	40	10744										
RPL4	6124	hgsc.bcm.edu	37	chr15	66795056	66795056	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tgccaacggcgccaggttttGgttggtgcaaacattcggcc	13	11	0	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr15:66795056G>C	ENST00000307961.6	-	4	407	c.315C>G	c.(313-315)acC>acG	p.T105T	SNORD16_ENST00000362803.1_RNA|ZWILCH_ENST00000307897.5_5'Flank|SNORD18C_ENST00000362704.1_RNA|SNORD18B_ENST00000365659.1_RNA|ZWILCH_ENST00000446801.2_5'Flank|RPL4_ENST00000564517.1_5'Flank|RPL4_ENST00000568588.1_Silent_p.T11T|ZWILCH_ENST00000535141.2_5'Flank|ZWILCH_ENST00000565627.1_5'Flank|SNORD18A_ENST00000363753.1_RNA	NM_000968.3	NP_000959.2	P36578	RL4_HUMAN	ribosomal protein L4	105					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)|urinary_tract(1)	17						GCCAGGTTTTGGTTGGTGCAA	0.463																																					p.T105T		Atlas-SNP	.											.	RPL4	29	.	0			c.C315G						.						117	108	111					15																	66795056		2201	4299	6500	SO:0001819	synonymous_variant	6124	exon4			GGTTTTGGTTGGT	AB007167	CCDS10218.1	15q22	2011-04-06			ENSG00000174444	ENSG00000174444		"L ribosomal proteins"	10353	protein-coding gene	gene with protein product	"60S ribosomal protein L4"	180479				9582194, 8268230	Standard	NM_000968		Approved	L4	uc002apv.3	P36578	OTTHUMG00000133193	ENST00000307961.6:c.315C>G	chr15.hg19:g.66795056G>C		189.0	0.0		123.0	49.0	NM_000968	A8K502|P39029|Q4VBR0|Q969Z9	Silent	SNP	ENST00000307961.6	hg19	CCDS10218.1																																																																																			.	.		0.463	RPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256903.2	NM_000968		C	66795056	G	C	66795056	2	2	78	1	0	0	0	0	0	0	0	1	13610	1335	47	4		4	RPL4	15	66795056	Silent	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10		66795056	35736336	41	10745										
SCNN1B	6338	hgsc.bcm.edu	37	chr16	23364163	23364163	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	gctgaaggacctggatgagcTgatggaagctgtcctggaga	16	7	0	4			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr16:23364163T>A	ENST00000343070.2	+	3	529	c.353T>A	c.(352-354)cTg>cAg	p.L118Q	SCNN1B_ENST00000569789.1_3'UTR|SCNN1B_ENST00000307331.5_Missense_Mutation_p.L163Q|SCNN1B_ENST00000568923.1_Missense_Mutation_p.L118Q|SCNN1B_ENST00000568085.1_Missense_Mutation_p.L118Q	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	118					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	CTGGATGAGCTGATGGAAGCT	0.517																																					p.L118Q		Atlas-SNP	.											.	SCNN1B	81	.	0			c.T353A						.						107	96	100					16																	23364163		2197	4300	6497	SO:0001583	missense	6338	exon3			ATGAGCTGATGGA	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10600	protein-coding gene	gene with protein product	"Liddle syndrome"	600760	"sodium channel, nonvoltage-gated 1, beta", "sodium channel, non-voltage-gated 1, beta"				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.353T>A	chr16.hg19:g.23364163T>A	ENSP00000345751:p.Leu118Gln	95.0	0.0		57.0	23.0	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Missense_Mutation	SNP	ENST00000343070.2	hg19	CCDS10609.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.050835	0.75960	.	.	ENSG00000168447	ENST00000343070;ENST00000307331	T;T	0.61392	0.11;0.11	5.0	5.0	0.66597	.	3.762580	0.00935	N	0.002776	T	0.80681	0.4669	M	0.78637	2.42	0.46376	D	0.999018	D	0.89917	1.0	D	0.97110	1.0	T	0.59804	-0.7385	10	0.62326	D	0.03	-6.5618	13.8924	0.63747	0.0:0.0:0.0:1.0	.	118	P51168	SCNNB_HUMAN	Q	118;163	ENSP00000345751:L118Q;ENSP00000302874:L163Q	ENSP00000302874:L163Q	L	+	2	0	SCNN1B	23271664	1.000000	0.71417	0.987000	0.45799	0.970000	0.65996	5.028000	0.64115	1.857000	0.53885	0.460000	0.39030	CTG	.	.		0.517	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			A	23364163	T	A	23364163	3	1	78	1	0	0	0	0	1	0	0	0	13943	1580	55	4	359	4	SCNN1B	16	23364163	Missense_Mutation	SNP	T	TCGA-CC-A8HS-01A-11D-A35Z-10		23364163	66990590	42	10746										
GLG1	2734	hgsc.bcm.edu	37	chr16	74640738	74640739	+	Missense_Mutation	DNP	AG	AG	CT													0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	aaaggcggctgcggcggctgAggctgctgttgctgttgctg							TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr16:74640738_74640739AG>CT	ENST00000422840.2	-	1	253_254	c.254_255CT>AG	c.(253-255)cCT>cAG	p.P85Q	GLG1_ENST00000447066.2_Missense_Mutation_p.P85Q|GLG1_ENST00000205061.5_Missense_Mutation_p.P85Q	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	85	Poly-Gln.			P -> L (in Ref. 1; AAB06460). {ECO:0000305}.	blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						gcggcggctgaggctgctgttg	0.733																																					p.P85P|p.P85H		Atlas-SNP	.											.	GLG1	106	.	0			c.T255G|c.C254A						.																																			SO:0001583	missense	2734	exon1			CGGCTGAGGCTGC|GGCTGAGGCTGCT		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.254_255delinsCT	chr16.hg19:g.74640738_74640739delinsCT	ENSP00000405984:p.Pro85Gln	77.0	0.0		52.0|53.0	15.0|16.0	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Silent|Missense_Mutation	SNP	ENST00000422840.2	hg19	CCDS45527.1																																																																																			.	.		0.733	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		CT	74640739	AG	CT	74640738	3	2	78	1	0	0	0	0	1	0	0	0	6444	291	11	5	3468	5	GLG1	16	74640738	Missense_Mutation	DNP	AG	TCGA-CC-A8HS-01A-11D-A35Z-10	51276575	74640738	15714015	43	10747			1	12		3	3	40	N	T_AG_AA	1.856445e-09
GLG1	2734	hgsc.bcm.edu	37	chr16	74640753	74640753	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ggctgaggctgctgttgctgTtgctgctgctgctgttgctg	16	9	0	1	rs546611688|rs374123768	byFrequency	TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr16:74640753T>C	ENST00000422840.2	-	1	239	c.240A>G	c.(238-240)caA>caG	p.Q80Q	GLG1_ENST00000447066.2_Silent_p.Q80Q|GLG1_ENST00000205061.5_Silent_p.Q80Q	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	80	Poly-Gln.				blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						gctgttgctgttgctgctgct	0.736																																					p.Q80Q		Atlas-SNP	.											.	GLG1	106	.	0			c.A240G						.						5	6	6					16																	74640753		2053	4079	6132	SO:0001819	synonymous_variant	2734	exon1			TTGCTGTTGCTGC		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.240A>G	chr16.hg19:g.74640753T>C		72.0	0.0		53.0	22.0	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Silent	SNP	ENST00000422840.2	hg19	CCDS45527.1																																																																																			.	.		0.736	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		C	74640753	T	C	74640753	2	2	78	1	0	0	0	0	0	0	0	1	6444	1722	60	2		2	GLG1	16	74640753	Silent	SNP	T	TCGA-CC-A8HS-01A-11D-A35Z-10	15	74640753	15714000	44	10748			1	12		3	3	40	N	T_AG_AA	1.856445e-09
GLG1	2734	hgsc.bcm.edu	37	chr16	74640777	74640778	+	Missense_Mutation	DNP	AA	AA	CT													0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tgctgctgctgttgctgctgAagctgcgatgactgaggcag							TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr16:74640777_74640778AA>CT	ENST00000422840.2	-	1	214_215	c.215_216TT>AG	c.(214-216)cTT>cAG	p.L72Q	GLG1_ENST00000447066.2_Missense_Mutation_p.L72Q|GLG1_ENST00000205061.5_Missense_Mutation_p.L72Q	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	72	Poly-Gln.				blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						gttgctgctgAAGCTGCGATGA	0.733																																					p.L72L|p.L72H		Atlas-SNP	.											.	GLG1	106	.	0			c.T216G|c.T215A						.																																			SO:0001583	missense	2734	exon1			CTGCTGAAGCTGC|TGCTGAAGCTGCG		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.215_216delinsCT	chr16.hg19:g.74640777_74640778delinsCT	ENSP00000405984:p.Leu72Gln	75.0	0.0		53.0|54.0	14.0	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Silent|Missense_Mutation	SNP	ENST00000422840.2	hg19	CCDS45527.1																																																																																			.	.		0.733	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		CT	74640778	AA	CT	74640777	3	2	78	1	0	0	0	0	1	0	0	0	6444	233	9	5	3507	5	GLG1	16	74640777	Missense_Mutation	DNP	AA	TCGA-CC-A8HS-01A-11D-A35Z-10	24	74640777	15713976	45	10749			1	12		3	3	40	N	T_AG_AA	1.856445e-09
MUC16	94025	hgsc.bcm.edu	37	chr19	9074011	9074011	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	aactgaagtcgcagaaacagGagaggatgtatgttgccctt	12	7	0	3			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr19:9074011G>T	ENST00000397910.4	-	3	13638	c.13435C>A	c.(13435-13437)Cct>Act	p.P4479T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4481	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCAGAAACAGGAGAGGATGTA	0.473																																					p.P4479T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C13435A						.						137	130	132					19																	9074011		2031	4174	6205	SO:0001583	missense	94025	exon3			AAACAGGAGAGGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.13435C>A	chr19.hg19:g.9074011G>T	ENSP00000381008:p.Pro4479Thr	129.0	0.0		121.0	63.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	2.511	-0.312868	0.05422	.	.	ENSG00000181143	ENST00000397910	T	0.23348	1.91	2.22	-0.211	0.13172	.	.	.	.	.	T	0.25531	0.0621	L	0.55481	1.735	.	.	.	P	0.40282	0.711	P	0.45276	0.475	T	0.31971	-0.9924	8	0.87932	D	0	.	3.1	0.06323	0.1824:0.2895:0.5281:0.0	.	4479	B5ME49	.	T	4479	ENSP00000381008:P4479T	ENSP00000381008:P4479T	P	-	1	0	MUC16	8935011	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.866000	0.04245	0.024000	0.15214	0.313000	0.20887	CCT	.	.		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9074011	G	T	9074011	3	4	78	1	0	0	0	0	1	0	0	0	9982	1174	41	3	30416	3	MUC16	19	9074011	Missense_Mutation	SNP	G	TCGA-CC-A8HS-01A-11D-A35Z-10		9074011	50054972	46	10750										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363152	22363152	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ttgaggaccaggtgaaggctTtgccacattcttcacatttg	10	9	2	2			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr19:22363152T>G	ENST00000397121.2	-	3	1684	c.1367A>C	c.(1366-1368)aAa>aCa	p.K456T		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	456					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				GGTGAAGGCTTTGCCACATTC	0.433																																					p.K456T		Atlas-SNP	.											.	ZNF676	146	.	0			c.A1367C						.						119	123	122					19																	22363152		2152	4274	6426	SO:0001583	missense	163223	exon3			AAGGCTTTGCCAC	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.1367A>C	chr19.hg19:g.22363152T>G	ENSP00000380310:p.Lys456Thr	52.0	0.0		63.0	19.0	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	hg19	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	12.19	1.862253	0.32884	.	.	ENSG00000196109	ENST00000397121	T	0.35236	1.32	0.85	0.85	0.18980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.61223	0.2330	M	0.90019	3.08	0.28590	N	0.909714	D	0.76494	0.999	D	0.87578	0.998	T	0.52719	-0.8538	9	0.72032	D	0.01	.	6.592	0.22651	0.0:0.0:0.0:1.0	.	456	Q8N7Q3	ZN676_HUMAN	T	456	ENSP00000380310:K456T	ENSP00000380310:K456T	K	-	2	0	ZNF676	22154992	0.957000	0.32711	0.098000	0.21074	0.098000	0.18820	2.902000	0.48703	0.166000	0.19597	0.164000	0.16699	AAA	.	.		0.433	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		G	22363152	T	G	22363152	3	3	78	1	0	0	0	0	1	0	0	0	18098	1841	64	5	403	5	ZNF676	19	22363152	Missense_Mutation	SNP	T	TCGA-CC-A8HS-01A-11D-A35Z-10	13289141	22363152	36765831	47	10751										
C19orf33	64073	hgsc.bcm.edu	37	chr19	38795301	38795301	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	ttccgactccagcagcagctCcagcgattcggacacggatg	11	14	0	0			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr19:38795301C>A	ENST00000301246.5	+	3	277	c.176C>A	c.(175-177)tCc>tAc	p.S59Y	C19orf33_ENST00000588605.1_Missense_Mutation_p.P79T|CTB-102L5.4_ENST00000591889.1_Silent_p.L146L	NM_033520.1	NP_277055.1	Q9GZP8	IMUP_HUMAN	chromosome 19 open reading frame 33	59						nucleus (GO:0005634)						all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AGCAGCAGCTCCAGCGATTCG	0.667																																					p.S59Y		Atlas-SNP	.											.	C19orf33	9	.	0			c.C176A						.						41	46	44					19																	38795301		2203	4300	6503	SO:0001583	missense	64073	exon3			GCAGCTCCAGCGA	AF213678	CCDS12511.1	19q13.2	2012-10-26			ENSG00000167644	ENSG00000167644			16668	protein-coding gene	gene with protein product	"immortalization-upregulated protein", "HAI-2 related small protein", "hepatocyte growth factor activator inhibitor type 2-related small protein"					11080599	Standard	NM_033520		Approved	IMUP-1, IMUP-2, H2RSP, IMUP	uc002ohu.1	Q9GZP8	OTTHUMG00000181894	ENST00000301246.5:c.176C>A	chr19.hg19:g.38795301C>A	ENSP00000301246:p.Ser59Tyr	150.0	0.0		231.0	165.0	NM_033520	Q0P6G2|Q96H58|Q9HCR4	Missense_Mutation	SNP	ENST00000301246.5	hg19	CCDS12511.1	.	.	.	.	.	.	.	.	.	.	C	12.37	1.918526	0.33908	.	.	ENSG00000167644	ENST00000301246	.	.	.	4.23	0.63	0.17693	.	1.043110	0.07588	N	0.921454	T	0.41696	0.1170	L	0.34521	1.04	0.22803	N	0.998719	D	0.67145	0.996	P	0.60286	0.872	T	0.31613	-0.9937	9	0.87932	D	0	-10.0071	6.1672	0.20396	0.0:0.5283:0.3666:0.105	.	59	Q9GZP8	IMUP_HUMAN	Y	59	.	ENSP00000301246:S59Y	S	+	2	0	C19orf33	43487141	1.000000	0.71417	0.989000	0.46669	0.330000	0.28571	0.826000	0.27407	0.129000	0.18514	0.555000	0.69702	TCC	.	.		0.667	C19orf33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458168.1	NM_033520		A	38795301	C	A	38795301	3	1	78	1	0	0	0	0	1	0	0	0	1921	855	30	3	186	3	C19orf33	19	38795301	Missense_Mutation	SNP	C	TCGA-CC-A8HS-01A-11D-A35Z-10	16432149	38795301	20333682	48	10752										
NLRP5	126206	hgsc.bcm.edu	37	chr19	56539531	56539531	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	tttggcctcgtgagcgaagaCgtaaggaggccactggaggt	16	8	0	2			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr19:56539531C>T	ENST00000390649.3	+	7	1932	c.1932C>T	c.(1930-1932)gaC>gaT	p.D644D		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	644					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		TGAGCGAAGACGTAAGGAGGC	0.552																																					p.D644D		Atlas-SNP	.											.	NLRP5	217	.	0			c.C1932T						.						61	63	62					19																	56539531		1976	4149	6125	SO:0001819	synonymous_variant	126206	exon7			CGAAGACGTAAGG	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1932C>T	chr19.hg19:g.56539531C>T		80.0	0.0		75.0	8.0	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	hg19	CCDS12938.1																																																																																			.	.		0.552	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		T	56539531	C	T	56539531	2	4	78	1	0	0	0	0	0	0	0	1	10489	535	19	1		1	NLRP5	19	56539531	Silent	SNP	C	TCGA-CC-A8HS-01A-11D-A35Z-10	17744230	56539531	2589452	49	10753										
ZNF814	730051	hgsc.bcm.edu	37	chr19	58386258	58386258	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	4	1	1.5207476635514	2.11214953271028	1.18808411214953	1	1	0	cactgaagacagatgactccCctgacacatgcaacttacac	6	14	0	5			TCGA-CC-A8HS-01A-11D-A35Z-10	TCGA-CC-A8HS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eec73def-9c6d-487a-b4b5-d9e879138027	4de9ebd4-2594-4178-b695-344708a55698	g.chr19:58386258C>A	ENST00000435989.2	-	3	734	c.500G>T	c.(499-501)gGg>gTg	p.G167V	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	167					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AGATGACTCCCCTGACACATG	0.498																																					p.G167V		Atlas-SNP	.											ZNF814,NS,carcinoma,0,1	ZNF814	93	.	0			c.G500T						.						108	81	89					19																	58386258		692	1590	2282	SO:0001583	missense	730051	exon3			GACTCCCCTGACA		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.500G>T	chr19.hg19:g.58386258C>A	ENSP00000410545:p.Gly167Val	327.0	0.0		310.0	159.0	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	11.16	1.555809	0.27827	.	.	ENSG00000204514	ENST00000435989;ENST00000376205	T	0.07688	3.17	2.27	-4.54	0.03452	.	.	.	.	.	T	0.05090	0.0136	N	0.14661	0.345	0.09310	N	1	P	0.50528	0.936	P	0.47827	0.558	T	0.13282	-1.0515	9	0.66056	D	0.02	.	1.3582	0.02186	0.1613:0.1936:0.16:0.4851	.	167	B7Z6K7	ZN814_HUMAN	V	167	ENSP00000410545:G167V	ENSP00000365378:G167V	G	-	2	0	ZNF814	63078070	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-2.636000	0.00867	-1.214000	0.02614	-1.152000	0.01820	GGG	.	.		0.498	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		A	58386258	C	A	58386258	3	1	78	1	0	0	0	0	1	0	0	0	18191	623	22	3	2071	3	ZNF814	19	58386258	Missense_Mutation	SNP	C	TCGA-CC-A8HS-01A-11D-A35Z-10	1846727	58386258	742725	50	10754										
SCNN1D	6339	hgsc.bcm.edu	37	chr1	1222594	1222594	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tggatatcctggccctgctgCccgcggcatgggaggacagc	15	13	0	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:1222594C>G	ENST00000338555.2	+	6	1877	c.733C>G	c.(733-735)Ccc>Gcc	p.P245A	SCNN1D_ENST00000400928.3_Missense_Mutation_p.P245A|SCNN1D_ENST00000379116.5_Missense_Mutation_p.P409A|SCNN1D_ENST00000325425.8_Missense_Mutation_p.P311A			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	245					ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	GGCCCTGCTGCCCGCGGCATG	0.662																																					p.P409A		Atlas-SNP	.											.	SCNN1D	60	.	0			c.C1225G						.						31	26	28					1																	1222594		2186	4288	6474	SO:0001583	missense	6339	exon9			CTGCTGCCCGCGG	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10601	protein-coding gene	gene with protein product		601328	"sodium channel, nonvoltage-gated 1, delta", "sodium channel, non-voltage-gated 1, delta"			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.733C>G	chr1.hg19:g.1222594C>G	ENSP00000339504:p.Pro245Ala	100.0	0.0		83.0	11.0	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Missense_Mutation	SNP	ENST00000338555.2	hg19		.	.	.	.	.	.	.	.	.	.	C	14.51	2.556297	0.45487	.	.	ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928;ENST00000379099	T;T;T;T	0.70399	-0.48;-0.44;-0.48;-0.44	4.06	4.06	0.47325	.	0.508245	0.14308	U	0.327889	D	0.83473	0.5262	M	0.76002	2.32	0.43965	D	0.996647	P;D	0.89917	0.943;1.0	P;D	0.83275	0.874;0.996	D	0.84095	0.0392	10	0.56958	D	0.05	.	14.8084	0.69974	0.0:1.0:0.0:0.0	.	245;409	P51172;A6NNF7	SCNND_HUMAN;.	A	276;409;245;311;245;36	ENSP00000368411:P409A;ENSP00000339504:P245A;ENSP00000321594:P311A;ENSP00000383717:P245A	ENSP00000321594:P311A	P	+	1	0	SCNN1D	1212457	0.374000	0.25081	0.135000	0.22099	0.024000	0.10985	2.055000	0.41345	1.819000	0.53055	0.313000	0.20887	CCC	.	.		0.662	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978		G	1222594	C	G	1222594	3	3	79	1	0	0	0	0	1	0	0	0	13944	739	26	4	953	4	SCNN1D	1	1222594	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10		1222594	248028027	1	10755										
C1orf127	148345	hgsc.bcm.edu	37	chr1	11008817	11008817	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	aggctggggacctcgctgagCttgcaccactctggggagaa	15	11	1	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:11008817C>T	ENST00000377008.4	-	11	1320	c.874G>A	c.(874-876)Gct>Act	p.A292T	C1orf127_ENST00000377004.4_Missense_Mutation_p.A459T			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	292	Pro-rich.									NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CCTCGCTGAGCTTGCACCACT	0.627																																					p.A459T		Atlas-SNP	.											.	C1orf127	134	.	0			c.G1375A						.						54	63	60					1																	11008817		2203	4300	6503	SO:0001583	missense	148345	exon12			GCTGAGCTTGCAC	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.874G>A	chr1.hg19:g.11008817C>T	ENSP00000366207:p.Ala292Thr	73.0	0.0		64.0	19.0	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	hg19		.	.	.	.	.	.	.	.	.	.	C	14.57	2.575797	0.45902	.	.	ENSG00000175262	ENST00000377004;ENST00000377008	T;T	0.25250	1.81;1.81	4.5	1.35	0.21983	.	2.265380	0.02351	N	0.075942	T	0.24736	0.0600	N	0.19112	0.55	0.09310	N	1	P;P;P	0.45827	0.867;0.764;0.867	P;B;P	0.47645	0.553;0.399;0.553	T	0.21177	-1.0253	10	0.54805	T	0.06	0.958	6.8922	0.24236	0.0:0.5576:0.3416:0.1008	.	310;284;292	B7ZLG7;Q8N9H9-2;Q8N9H9	.;.;CA127_HUMAN	T	459;292	ENSP00000366203:A459T;ENSP00000366207:A292T	ENSP00000366203:A459T	A	-	1	0	C1orf127	10931404	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.083000	0.11286	0.392000	0.25172	-0.479000	0.04858	GCT	.	.		0.627	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		T	11008817	C	T	11008817	3	4	79	1	0	0	0	0	1	0	0	0	1996	797	28	3	1100	3	C1orf127	1	11008817	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	9786223	11008817	238241804	2	10756										
C1orf94	84970	hgsc.bcm.edu	37	chr1	34684343	34684343	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cccctatttttcttccagtgGgaatggcataaacttttaga	7	9	1	1	rs373403037		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:34684343G>T	ENST00000488417.1	+	7	1898	c.1778G>T	c.(1777-1779)gGg>gTg	p.G593V	C1orf94_ENST00000373374.3_Missense_Mutation_p.G403V	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	593										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				TCTTCCAGTGGGAATGGCATA	0.502																																					p.G593V		Atlas-SNP	.											C1orf94_ENST00000488417,mucosal,malignant_melanoma,0,2	C1orf94	156	.	0			c.G1778T						.						134	129	131					1																	34684343		2203	4300	6503	SO:0001583	missense	84970	exon7			CCAGTGGGAATGG	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.1778G>T	chr1.hg19:g.34684343G>T	ENSP00000435634:p.Gly593Val	79.0	0.0		76.0	19.0	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	hg19	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.042661	0.75732	.	.	ENSG00000142698	ENST00000373374;ENST00000488417	T;T	0.49720	0.88;0.77	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000004	T	0.67496	0.2899	M	0.72118	2.19	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.70777	-0.4780	10	0.87932	D	0	-11.7657	14.5004	0.67716	0.0:0.0:1.0:0.0	.	593	Q6P1W5	CA094_HUMAN	V	403;593	ENSP00000362472:G403V;ENSP00000435634:G593V	ENSP00000362472:G403V	G	+	2	0	C1orf94	34456930	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.600000	0.54052	2.487000	0.83934	0.655000	0.94253	GGG	.	.		0.502	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884		T	34684343	G	T	34684343	3	4	79	1	0	0	0	0	1	0	0	0	2073	1232	43	3	1804	3	C1orf94	1	34684343	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	23675526	34684343	214566278	3	10757										
MFSD2A	84879	hgsc.bcm.edu	37	chr1	40431615	40431615	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cagacacgccttgtttccagGacctcaatagctctacagta	7	13	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:40431615G>T	ENST00000372809.5	+	6	825	c.682G>T	c.(682-684)Gac>Tac	p.D228Y	MFSD2A_ENST00000480630.1_3'UTR|MFSD2A_ENST00000372811.5_Missense_Mutation_p.D215Y|MFSD2A_ENST00000420632.2_Missense_Mutation_p.D59Y	NM_001136493.1	NP_001129965.1	Q8NA29	NLS1_HUMAN	major facilitator superfamily domain containing 2A	228					establishment of blood-brain barrier (GO:0060856)|fatty acid transport (GO:0015908)|lipid transport across blood brain barrier (GO:1990379)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phospholipid transporter activity (GO:0005548)|symporter activity (GO:0015293)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						TTGTTTCCAGGACCTCAATAG	0.572																																					p.D228Y		Atlas-SNP	.											.	MFSD2A	53	.	0			c.G682T						.						126	100	109					1																	40431615		2203	4300	6503	SO:0001583	missense	84879	exon6			TTCCAGGACCTCA	AK093223	CCDS446.1, CCDS44118.1, CCDS72762.1	1p34.2	2009-09-08	2009-09-08	2009-09-08	ENSG00000168389	ENSG00000168389			25897	protein-coding gene	gene with protein product		614397	"major facilitator superfamily domain containing 2"	MFSD2		18694395	Standard	XM_005271285		Approved	FLJ14490	uc001cev.3	Q8NA29	OTTHUMG00000009293	ENST00000372809.5:c.682G>T	chr1.hg19:g.40431615G>T	ENSP00000361895:p.Asp228Tyr	173.0	0.0		178.0	37.0	NM_001136493	A8K675|Q6UWU5|Q96F59|Q9BRC8	Missense_Mutation	SNP	ENST00000372809.5	hg19	CCDS44118.1	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592290	0.28357	.	.	ENSG00000168389	ENST00000372811;ENST00000420632;ENST00000434861;ENST00000372809	D;D;D;D	0.87809	-2.3;-2.3;-2.3;-2.3	5.94	-1.04	0.10068	Major facilitator superfamily domain, general substrate transporter (1);	0.895788	0.10030	N	0.724829	T	0.80783	0.4689	L	0.29908	0.895	0.09310	N	1	P;P;P	0.41393	0.748;0.743;0.565	B;P;B	0.49140	0.446;0.601;0.317	T	0.69304	-0.5180	10	0.44086	T	0.13	-1.4567	0.7006	0.00907	0.398:0.1261:0.2195:0.2564	.	178;228;215	B4DNN7;Q8NA29;Q8NA29-2	.;MFS2A_HUMAN;.	Y	215;59;213;228	ENSP00000361898:D215Y;ENSP00000391261:D59Y;ENSP00000407606:D213Y;ENSP00000361895:D228Y	ENSP00000361895:D228Y	D	+	1	0	MFSD2A	40204202	0.524000	0.26282	0.079000	0.20413	0.707000	0.40811	0.907000	0.28531	-0.207000	0.10187	0.563000	0.77884	GAC	.	.		0.572	MFSD2A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025756.1	NM_032793		T	40431615	G	T	40431615	3	4	79	1	0	0	0	0	1	0	0	0	9539	1174	41	3	704	3	MFSD2A	1	40431615	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	5747272	40431615	208819006	4	10758										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42047556	42047556	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	acagtcaacatgtgggtgccCaggggtttggggcgcatgtc	16	9	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:42047556C>T	ENST00000372583.1	-	4	3798	c.2913G>A	c.(2911-2913)ctG>ctA	p.L971L	HIVEP3_ENST00000247584.5_Silent_p.L971L|HIVEP3_ENST00000372584.1_Silent_p.L971L|HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000429157.2_Silent_p.L971L	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	971	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TGTGGGTGCCCAGGGGTTTGG	0.617																																					p.L971L		Atlas-SNP	.											.	HIVEP3	235	.	0			c.G2913A						.						54	58	57					1																	42047556		2203	4300	6503	SO:0001819	synonymous_variant	59269	exon4			GGTGCCCAGGGGT	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.2913G>A	chr1.hg19:g.42047556C>T		132.0	0.0		119.0	26.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.		0.617	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	42047556	C	T	42047556	2	4	79	1	0	0	0	0	0	0	0	1	7197	581	21	3		3	HIVEP3	1	42047556	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	1615941	42047556	207203065	5	10759										
TMEM53	79639	hgsc.bcm.edu	37	chr1	45120308	45120308	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gtagtcacggaggtggctgaCgtgtgcagatgacacgaaat	15	7	1	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:45120308C>T	ENST00000372237.3	-	3	920	c.757G>A	c.(757-759)Gtc>Atc	p.V253I	TMEM53_ENST00000476724.1_5'UTR|TMEM53_ENST00000372243.3_Intron|TMEM53_ENST00000372244.3_Intron|TMEM53_ENST00000372242.3_Intron|TMEM53_ENST00000372235.3_Missense_Mutation_p.V223I	NM_024587.2	NP_078863.2	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	253						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(3)|ovary(2)|urinary_tract(1)	10	Acute lymphoblastic leukemia(166;0.155)					AGGTGGCTGACGTGTGCAGAT	0.582																																					p.V253I		Atlas-SNP	.											.	TMEM53	40	.	0			c.G757A						.						97	106	103					1																	45120308		2203	4300	6503	SO:0001583	missense	79639	exon3			GGCTGACGTGTGC		CCDS511.1, CCDS72773.1	1p34.1	2008-02-26			ENSG00000126106	ENSG00000126106			26186	protein-coding gene	gene with protein product						12958361	Standard	XR_425151		Approved	FLJ22353, NET4	uc001cmc.3	Q6P2H8	OTTHUMG00000007833	ENST00000372237.3:c.757G>A	chr1.hg19:g.45120308C>T	ENSP00000361311:p.Val253Ile	67.0	0.0		88.0	4.0	NM_024587	B4DKG0|Q5JPH2|Q6IA07|Q9H6E2	Missense_Mutation	SNP	ENST00000372237.3	hg19	CCDS511.1	.	.	.	.	.	.	.	.	.	.	C	33	5.218833	0.95104	.	.	ENSG00000126106	ENST00000372237;ENST00000372235	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.85712	0.5760	M	0.90309	3.105	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87759	0.2597	9	0.56958	D	0.05	.	19.1769	0.93605	0.0:1.0:0.0:0.0	.	253	Q6P2H8	TMM53_HUMAN	I	253;223	.	ENSP00000361309:V223I	V	-	1	0	TMEM53	44892895	1.000000	0.71417	0.987000	0.45799	0.942000	0.58702	7.690000	0.84178	2.533000	0.85409	0.462000	0.41574	GTC	.	.		0.582	TMEM53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021599.1	NM_024587		T	45120308	C	T	45120308	3	4	79	1	0	0	0	0	1	0	0	0	16194	536	19	1	80	1	TMEM53	1	45120308	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	3072752	45120308	204130313	6	10760										
PTGER3	5733	hgsc.bcm.edu	37	chr1	71478137	71478137	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cttgcagtgctcaactgatgTctgattgaagatcattttca	8	8	4	4			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:71478137T>A	ENST00000306666.5	-	2	1138	c.928A>T	c.(928-930)Aca>Tca	p.T310S	PTGER3_ENST00000460330.1_Missense_Mutation_p.T310S|PTGER3_ENST00000356595.4_Missense_Mutation_p.T310S|PTGER3_ENST00000354608.5_Missense_Mutation_p.T310S|PTGER3_ENST00000370932.2_Missense_Mutation_p.T310S|PTGER3_ENST00000370924.4_Missense_Mutation_p.T310S|PTGER3_ENST00000351052.5_Missense_Mutation_p.T310S|PTGER3_ENST00000414819.1_Missense_Mutation_p.T310S|PTGER3_ENST00000370931.3_Missense_Mutation_p.T310S	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	310					cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	TCAACTGATGTCTGATTGAAG	0.393																																					p.T310S		Atlas-SNP	.											.	PTGER3	246	.	0			c.A928T						.						108	101	103					1																	71478137		2203	4300	6503	SO:0001583	missense	5733	exon2			CTGATGTCTGATT	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.928A>T	chr1.hg19:g.71478137T>A	ENSP00000302313:p.Thr310Ser	57.0	0.0		60.0	15.0	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Missense_Mutation	SNP	ENST00000306666.5	hg19	CCDS657.1	.	.	.	.	.	.	.	.	.	.	T	13.69	2.312343	0.40895	.	.	ENSG00000050628	ENST00000370931;ENST00000370932;ENST00000351052;ENST00000460330;ENST00000370934;ENST00000354608;ENST00000356595;ENST00000414819;ENST00000306666;ENST00000370924	T;T;T;T;T;T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54;-0.54;-0.54;-0.54;-0.54;-0.54	5.65	4.45	0.53987	GPCR, rhodopsin-like superfamily (1);	0.313747	0.33792	N	0.004557	T	0.48259	0.1490	L	0.38838	1.175	0.28415	N	0.918008	P;P;P;D;P;P;P;P	0.53151	0.863;0.858;0.911;0.958;0.918;0.9;0.9;0.858	B;P;P;P;B;P;P;P	0.52386	0.338;0.609;0.571;0.697;0.42;0.474;0.571;0.609	T	0.46484	-0.9188	10	0.05721	T	0.95	-5.8685	11.3451	0.49556	0.136:0.0:0.0:0.864	.	310;310;310;310;310;310;310;310	Q147U0;Q6TTN3;F5H821;B1AK19;Q147X8;P43115-3;P43115-4;P43115	.;.;.;.;.;.;.;PE2R3_HUMAN	S	310	ENSP00000359969:T310S;ENSP00000359970:T310S;ENSP00000280208:T310S;ENSP00000418073:T310S;ENSP00000346624:T310S;ENSP00000349003:T310S;ENSP00000401423:T310S;ENSP00000302313:T310S;ENSP00000359962:T310S	ENSP00000302313:T310S	T	-	1	0	PTGER3	71250725	1.000000	0.71417	0.995000	0.50966	0.779000	0.44077	3.451000	0.52964	2.156000	0.67533	0.402000	0.26972	ACA	.	.		0.393	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957		A	71478137	T	A	71478137	3	1	79	1	0	0	0	0	1	0	0	0	12757	1667	58	4	559	4	PTGER3	1	71478137	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	26357829	71478137	177772484	7	10761										
C1orf173	127254	hgsc.bcm.edu	37	chr1	75065587	75065587	+	Silent	SNP	C	C	T													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gatttttcaccttgtttctcCtcatctacttcaaagtcttc							TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:75065587C>T	ENST00000326665.5	-	11	1736	c.1518G>A	c.(1516-1518)gaG>gaA	p.E506E	C1orf173_ENST00000420661.2_Silent_p.E309E|RP4-612J11.1_ENST00000416017.1_RNA	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		506	Glu-rich.							p.E506D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CTTGTTTCTCCTCATCTACTT	0.338																																					p.E506E		Atlas-SNP	.											C1orf173,NS,carcinoma,0,1	C1orf173	380	.	1	Substitution - Missense(1)	lung(1)	c.G1518A						.						154	163	160					1																	75065587		2203	4300	6503	SO:0001819	synonymous_variant	127254	exon11			TTTCTCCTCATCT																												ENST00000326665.5:c.1518G>A	chr1.hg19:g.75065587C>T		67.0	0.0		83.0	19.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	hg19	CCDS30755.1																																																																																			.	.		0.338	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			T	75065587	C	T	75065587	2	4	79	1	0	0	0	0	0	0	0	1	2016	680	24	3		3	C1orf173	1	75065587	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	3587450	75065587	174185034	8	10762	45	2								
C1orf173	127254	hgsc.bcm.edu	37	chr1	75065589	75065589	+	Nonsense_Mutation	SNP	C	C	A													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tttttcaccttgtttctcctCatctacttcaaagtcttctt							TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:75065589C>A	ENST00000326665.5	-	11	1734	c.1516G>T	c.(1516-1518)Gag>Tag	p.E506*	C1orf173_ENST00000420661.2_Nonsense_Mutation_p.E309*|RP4-612J11.1_ENST00000416017.1_RNA	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		506	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TGTTTCTCCTCATCTACTTCA	0.333																																					p.E506X		Atlas-SNP	.											.	C1orf173	380	.	0			c.G1516T						.						151	159	156					1																	75065589		2203	4300	6503	SO:0001587	stop_gained	127254	exon11			TCTCCTCATCTAC																												ENST00000326665.5:c.1516G>T	chr1.hg19:g.75065589C>A	ENSP00000322609:p.Glu506*	66.0	0.0		83.0	19.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Nonsense_Mutation	SNP	ENST00000326665.5	hg19	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.138970	0.77775	.	.	ENSG00000178965	ENST00000326665;ENST00000420661	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	-7.5709	19.5202	0.95182	0.0:1.0:0.0:0.0	.	.	.	.	X	506;309	.	ENSP00000322609:E506X	E	-	1	0	C1orf173	74838177	1.000000	0.71417	0.977000	0.42913	0.006000	0.05464	5.308000	0.65768	2.715000	0.92844	0.650000	0.86243	GAG	.	.		0.333	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75065589	C	A	75065589	4	1	79	1	0	0	0	0	0	1	0	0	2016	835	29	3	3092	3	C1orf173	1	75065589	Nonsense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	2	75065589	174185032	9	10763	45	2								
CELF3	11189	hgsc.bcm.edu	37	chr1	151680335	151680335	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgaacatgcccaactgggtgGccacctgctgcatgcggcgg	14	13	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:151680335G>T	ENST00000290583.4	-	6	1356	c.563C>A	c.(562-564)gCc>gAc	p.A188D	RP11-98D18.1_ENST00000457548.1_RNA|RIIAD1_ENST00000326413.3_5'Flank|AL589765.1_ENST00000442233.2_5'Flank|CELF3_ENST00000392706.3_Missense_Mutation_p.A5D|CELF3_ENST00000290585.4_Missense_Mutation_p.A188D|CELF3_ENST00000470688.1_5'UTR	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	188					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						CAACTGGGTGGCCACCTGCTG	0.662																																					p.A188D		Atlas-SNP	.											.	CELF3	49	.	0			c.C563A						.						59	52	54					1																	151680335		2203	4300	6503	SO:0001583	missense	11189	exon6			TGGGTGGCCACCT	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.563C>A	chr1.hg19:g.151680335G>T	ENSP00000290583:p.Ala188Asp	106.0	0.0		129.0	23.0	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	hg19	CCDS1002.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	26.6|26.6	4.753921|4.753921	0.89843|0.89843	.|.	.|.	ENSG00000159409|ENSG00000159409	ENST00000290585;ENST00000290583;ENST00000392706;ENST00000368833|ENST00000420342	T;T;T|.	0.18338|.	2.23;2.22;2.96|.	3.75|3.75	3.75|3.75	0.43078|0.43078	.|.	0.061993|.	0.64402|.	D|.	0.000004|.	T|T	0.71204|0.71204	0.3312|0.3312	M|M	0.83603|0.83603	2.65|2.65	0.80722|0.80722	D|D	1|1	P;D;D;P;D|.	0.58268|.	0.911;0.974;0.977;0.947;0.982|.	P;P;P;P;P|.	0.61800|.	0.536;0.894;0.848;0.599;0.837|.	T|T	0.75033|0.75033	-0.3460|-0.3460	10|5	0.72032|.	D|.	0.01|.	-10.5358|-10.5358	14.6626|14.6626	0.68882|0.68882	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	188;188;187;188;187|.	Q5SZQ7;Q5SZQ8-2;F8W6B7;Q5SZQ8;Q5SZQ8-3|.	.;.;.;CELF3_HUMAN;.|.	D|T	188;188;5;187|189	ENSP00000290585:A188D;ENSP00000290583:A188D;ENSP00000376470:A5D|.	ENSP00000290583:A188D|.	A|P	-|-	2|1	0|0	CELF3|CELF3	149946959|149946959	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.519000|5.519000	0.67074|0.67074	2.098000|2.098000	0.63641|0.63641	0.655000|0.655000	0.94253|0.94253	GCC|CCA	.	.		0.662	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		T	151680335	G	T	151680335	3	4	79	1	0	0	0	0	1	0	0	0	3219	1203	42	3	862	3	CELF3	1	151680335	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	76614746	151680335	97570286	10	10764										
RPTN	126638	hgsc.bcm.edu	37	chr1	152127436	152127436	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tcatggctgtgtctatcccaAgtttgatggccctgctcttc	9	12	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:152127436A>C	ENST00000316073.3	-	3	2203	c.2139T>G	c.(2137-2139)acT>acG	p.T713T		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	713	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						GTCTATCCCAAGTTTGATGGC	0.552																																					p.T713T		Atlas-SNP	.											RPTN,NS,carcinoma,0,1	RPTN	123	.	0			c.T2139G						.						337	274	293					1																	152127436		1568	3582	5150	SO:0001819	synonymous_variant	126638	exon3			ATCCCAAGTTTGA	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.2139T>G	chr1.hg19:g.152127436A>C		87.0	0.0		107.0	11.0	NM_001122965	B7ZBZ3	Silent	SNP	ENST00000316073.3	hg19	CCDS41397.1																																																																																			.	.		0.552	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		C	152127436	A	C	152127436	2	2	79	1	0	0	0	0	0	0	0	1	13679	59	3	5		5	RPTN	1	152127436	Silent	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	447101	152127436	97123185	11	10765										
IVL	3713	hgsc.bcm.edu	37	chr1	152883199	152883199	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gccagagctcccagagcagcAgatggggcagctgaagcacc	14	13	0	4			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:152883199A>G	ENST00000368764.3	+	2	990	c.926A>G	c.(925-927)cAg>cGg	p.Q309R	IVL_ENST00000392667.2_Missense_Mutation_p.Q163R			P07476	INVO_HUMAN	involucrin	309	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCAGagcagcagatggggcag	0.637																																					p.Q309R		Atlas-SNP	.											.	IVL	100	.	0			c.A926G						.						18	18	18					1																	152883199		2088	4122	6210	SO:0001583	missense	3713	exon2			AGCAGCAGATGGG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.926A>G	chr1.hg19:g.152883199A>G	ENSP00000357753:p.Gln309Arg	219.0	0.0		246.0	32.0	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	hg19	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	A	11.96	1.794373	0.31777	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.11385	3.0;2.78	2.9	2.9	0.33743	.	.	.	.	.	T	0.09113	0.0225	M	0.62723	1.935	0.09310	N	1	P	0.52170	0.951	P	0.54431	0.752	T	0.17961	-1.0352	9	0.24483	T	0.36	.	9.1968	0.37233	1.0:0.0:0.0:0.0	.	309	P07476	INVO_HUMAN	R	309;163	ENSP00000357753:Q309R;ENSP00000376435:Q163R	ENSP00000357753:Q309R	Q	+	2	0	IVL	151149823	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.990000	0.03732	1.088000	0.41272	0.374000	0.22700	CAG	.	.		0.637	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		G	152883199	A	G	152883199	3	3	79	1	0	0	0	0	1	0	0	0	7938	188	7	2	928	2	IVL	1	152883199	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	755763	152883199	96367422	12	10766										
SHE	126669	hgsc.bcm.edu	37	chr1	154458426	154458426	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggggcttacttactttagggCaatggagtacctgctgttcc	12	9	0	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:154458426C>A	ENST00000304760.2	-	5	1380	c.1294G>T	c.(1294-1296)Gcc>Tcc	p.A432S		NM_001010846.2	NP_001010846.1	Q5VZ18	SHE_HUMAN	Src homology 2 domain containing E	432	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.									breast(4)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	14	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TACTTTAGGGCAATGGAGTAC	0.488																																					p.A432S		Atlas-SNP	.											.	SHE	41	.	0			c.G1294T						.						116	97	103					1																	154458426		2203	4300	6503	SO:0001583	missense	126669	exon5			TTAGGGCAATGGA	AK074067	CCDS30877.1	1q21.3	2013-02-14			ENSG00000169291	ENSG00000169291		"SH2 domain containing"	27004	protein-coding gene	gene with protein product		610482				9315092	Standard	NM_001010846		Approved		uc001ffb.3	Q5VZ18	OTTHUMG00000036072	ENST00000304760.2:c.1294G>T	chr1.hg19:g.154458426C>A	ENSP00000307369:p.Ala432Ser	90.0	0.0		109.0	16.0	NM_001010846	Q8TEQ5	Missense_Mutation	SNP	ENST00000304760.2	hg19	CCDS30877.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.22|12.22	1.873660|1.873660	0.33069|0.33069	.|.	.|.	ENSG00000169291|ENSG00000169291	ENST00000304760|ENST00000486773;ENST00000555188	T|.	0.49139|.	0.79|.	5.41|5.41	5.41|5.41	0.78517|0.78517	SH2 motif (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.07279|0.07279	0.0184|0.0184	N|N	0.00201|0.00201	-1.865|-1.865	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|T	0.36744|0.36744	-0.9735|-0.9735	10|5	0.02654|.	T|.	1|.	-23.2344|-23.2344	17.9533|17.9533	0.89061|0.89061	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	432|.	Q5VZ18|.	SHE_HUMAN|.	S|F	432|32;129	ENSP00000307369:A432S|.	ENSP00000307369:A432S|.	A|C	-|-	1|2	0|0	SHE|SHE	152725050|152725050	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.943000|0.943000	0.58893|0.58893	3.378000|3.378000	0.52432|0.52432	2.826000|2.826000	0.97356|0.97356	0.561000|0.561000	0.74099|0.74099	GCC|TGC	.	.		0.488	SHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087910.2	NM_001010846		A	154458426	C	A	154458426	3	1	79	1	0	0	0	0	1	0	0	0	14291	710	25	3	201	3	SHE	1	154458426	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	1575227	154458426	94792195	13	10767										
NDUFS2	4720	hgsc.bcm.edu	37	chr1	161172205	161172205	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctgagggctttgtgcggcttCcggggcgtcgcggcccaggt	18	12	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:161172205C>A	ENST00000367993.3	+	2	478	c.30C>A	c.(28-30)ttC>ttA	p.F10L	NDUFS2_ENST00000476409.2_5'UTR|NDUFS2_ENST00000392179.4_Missense_Mutation_p.F10L	NM_004550.4	NP_004541.1	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)	10					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|quinone binding (GO:0048038)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	18	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Doxorubicin(DB00997)	TGTGCGGCTTCCGGGGCGTCG	0.657																																					p.F10L		Atlas-SNP	.											.	NDUFS2	33	.	0			c.C30A						.						18	20	20					1																	161172205		2201	4300	6501	SO:0001583	missense	4720	exon1			CGGCTTCCGGGGC	BC008868	CCDS1224.1, CCDS53404.1	1q23.3	2011-07-04	2002-08-29		ENSG00000158864	ENSG00000158864	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7708	protein-coding gene	gene with protein product	"complex I 49kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial"	602985	"NADH dehydrogenase (ubiquinone) Fe-S protein 2 (49kD) (NADH-coenzyme Q reductase)"			1832859, 9585441	Standard	NM_004550		Approved	CI-49	uc001fyw.3	O75306	OTTHUMG00000034344	ENST00000367993.3:c.30C>A	chr1.hg19:g.161172205C>A	ENSP00000356972:p.Phe10Leu	118.0	0.0		124.0	29.0	NM_001166159	D3DVG7|J3KPM7|Q5VTW0|Q969P3|Q9UEV3	Missense_Mutation	SNP	ENST00000367993.3	hg19	CCDS1224.1	.	.	.	.	.	.	.	.	.	.	C	6.814	0.519380	0.13005	.	.	ENSG00000158864	ENST00000367993;ENST00000392179	D;D	0.83591	-1.74;-1.74	5.56	-3.32	0.04973	.	0.080811	0.51477	N	0.000099	T	0.31670	0.0804	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36163	-0.9759	10	0.02654	T	1	.	6.1434	0.20273	0.1097:0.2064:0.5387:0.1452	.	10;10	Q53HG2;O75306	.;NDUS2_HUMAN	L	10	ENSP00000356972:F10L;ENSP00000376018:F10L	ENSP00000356972:F10L	F	+	3	2	NDUFS2	159438829	0.399000	0.25287	0.043000	0.18650	0.481000	0.33189	-1.076000	0.03420	-1.048000	0.03238	0.655000	0.94253	TTC	.	.		0.657	NDUFS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083015.1	NM_004550		A	161172205	C	A	161172205	3	1	79	1	0	0	0	0	1	0	0	0	10301	854	30	3	32	3	NDUFS2	1	161172205	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	6713779	161172205	88078416	14	10768										
XCL2	6846	hgsc.bcm.edu	37	chr1	168511286	168511286	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggtcttgattctgctaactgGcagtcgctgggtagtgaggc	15	8	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:168511286G>A	ENST00000367819.2	-	2	153	c.121C>T	c.(121-123)Cca>Tca	p.P41S		NM_003175.3	NP_003166.1	Q9UBD3	XCL2_HUMAN	chemokine (C motif) ligand 2	41					blood circulation (GO:0008015)|cell chemotaxis (GO:0060326)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			large_intestine(1)|lung(6)|ovary(1)	8	all_hematologic(923;0.215)					CTGCTAACTGGCAGTCGCTGG	0.488																																					p.P41S		Atlas-SNP	.											XCL2,colon,carcinoma,0,1	XCL2	18	.	0			c.C121T						.						138	115	123					1																	168511286		2203	4298	6501	SO:0001583	missense	6846	exon2			TAACTGGCAGTCG	BC070309	CCDS1273.1	1q24.2	2013-02-28	2002-08-22	2002-08-23	ENSG00000143185	ENSG00000143185		"Endogenous ligands"	10646	protein-coding gene	gene with protein product		604828	"small inducible cytokine subfamily C, member 2"	SCYC2		7875320	Standard	NM_003175		Approved	SCM-1b	uc001gfn.4	Q9UBD3	OTTHUMG00000034549	ENST00000367819.2:c.121C>T	chr1.hg19:g.168511286G>A	ENSP00000356793:p.Pro41Ser	61.0	0.0		66.0	14.0	NM_003175		Missense_Mutation	SNP	ENST00000367819.2	hg19	CCDS1273.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.668233	0.47677	.	.	ENSG00000143185	ENST00000367819	T	0.07216	3.21	2.49	2.49	0.30216	Chemokine interleukin-8-like domain (3);	0.431115	0.22250	N	0.062578	T	0.13415	0.0325	M	0.76574	2.34	0.27815	N	0.942019	D	0.76494	0.999	D	0.70487	0.969	T	0.01617	-1.1311	9	0.44086	T	0.13	-6.1507	8.4754	0.33009	0.0:0.0:1.0:0.0	.	41	Q9UBD3	XCL2_HUMAN	S	41	ENSP00000356793:P41S	ENSP00000356793:P41S	P	-	1	0	XCL2	166777910	0.964000	0.33143	0.521000	0.27850	0.218000	0.24690	3.906000	0.56340	1.381000	0.46364	0.195000	0.17529	CCA	.	.		0.488	XCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083613.1	NM_003175		A	168511286	G	A	168511286	3	1	79	1	0	0	0	0	1	0	0	0	17439	1203	42	3	231	3	XCL2	1	168511286	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	7339081	168511286	80739335	15	10769										
XCL1	6375	hgsc.bcm.edu	37	chr1	168549360	168549360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcctcactacccagcgactgCcggttagcagaatcaagacc	9	15	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:168549360C>T	ENST00000367818.3	+	2	286	c.121C>T	c.(121-123)Ccg>Tcg	p.P41S		NM_002995.2	NP_002986.1	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1	41					cell-cell signaling (GO:0007267)|cellular response to interleukin-4 (GO:0071353)|cellular response to transforming growth factor beta stimulus (GO:0071560)|immune response (GO:0006955)|mature natural killer cell chemotaxis (GO:0035782)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T cell cytokine production (GO:0002725)|negative regulation of T-helper 1 cell activation (GO:2000518)|negative regulation of T-helper 1 type immune response (GO:0002826)|negative regulation of transcription, DNA-templated (GO:0045892)|neutrophil chemotaxis (GO:0030593)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000566)|positive regulation of granzyme A production (GO:2000513)|positive regulation of granzyme B production (GO:0071663)|positive regulation of immunoglobulin production in mucosal tissue (GO:2000558)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 cell cytokine production (GO:2000556)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of thymocyte migration (GO:2000412)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of inflammatory response (GO:0050727)|release of sequestered calcium ion into cytosol (GO:0051209)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|protein homodimerization activity (GO:0042803)			kidney(2)|lung(7)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.208)					CCAGCGACTGCCGGTTAGCAG	0.478																																					p.P41S		Atlas-SNP	.											XCL1,colon,carcinoma,0,1	XCL1	16	.	0			c.C121T						.						155	146	149					1																	168549360		2203	4300	6503	SO:0001583	missense	6375	exon2			CGACTGCCGGTTA	D43768	CCDS1274.1	1q24.2	2014-01-30	2002-08-22	2002-08-23	ENSG00000143184	ENSG00000143184		"Endogenous ligands"	10645	protein-coding gene	gene with protein product		600250	"small inducible cytokine subfamily C, member 1 (lymphotactin)"	LTN, SCYC1		7602097, 7875320	Standard	NM_002995		Approved	LPTN, ATAC, SCM-1a, SCM-1, lymphotactin	uc001gfo.2	P47992	OTTHUMG00000034548	ENST00000367818.3:c.121C>T	chr1.hg19:g.168549360C>T	ENSP00000356792:p.Pro41Ser	268.0	0.0		345.0	25.0	NM_002995	Q52MA8	Missense_Mutation	SNP	ENST00000367818.3	hg19	CCDS1274.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.470263	0.26423	.	.	ENSG00000143184	ENST00000367818	T	0.07216	3.21	4.36	3.42	0.39159	Chemokine interleukin-8-like domain (3);	0.431115	0.22250	N	0.062578	T	0.14485	0.0350	M	0.73598	2.24	0.27815	N	0.942019	D	0.76494	0.999	D	0.70487	0.969	T	0.01884	-1.1254	9	0.52906	T	0.07	-6.1507	9.5622	0.39376	0.2095:0.7905:0.0:0.0	.	41	P47992	XCL1_HUMAN	S	41	ENSP00000356792:P41S	ENSP00000356792:P41S	P	+	1	0	XCL1	166815984	0.138000	0.22547	0.345000	0.25642	0.011000	0.07611	3.188000	0.50958	1.153000	0.42468	0.655000	0.94253	CCG	.	.		0.478	XCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083612.1	NM_002995		T	168549360	C	T	168549360	3	4	79	1	0	0	0	0	1	0	0	0	17438	739	26	3	127	3	XCL1	1	168549360	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	38074	168549360	80701261	16	10770										
DNM3	26052	hgsc.bcm.edu	37	chr1	172356293	172356293	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gttaaagatttcataaattcCgagctcctagcacagttgta	7	8	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:172356293C>A	ENST00000355305.5	+	19	2254	c.2097C>A	c.(2095-2097)tcC>tcA	p.S699S	DNM3_ENST00000358155.4_Silent_p.S693S|DNM3_ENST00000367731.1_Silent_p.S689S			Q9UQ16	DYN3_HUMAN	dynamin 3	699	GED. {ECO:0000255|PROSITE- ProRule:PRU00720}.				endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TCATAAATTCCGAGCTCCTAG	0.453																																					p.S693S		Atlas-SNP	.											DNM3,NS,carcinoma,0,1	DNM3	85	.	0			c.C2079A						.						86	85	85					1																	172356293		1873	4109	5982	SO:0001819	synonymous_variant	26052	exon19			AAATTCCGAGCTC	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.2097C>A	chr1.hg19:g.172356293C>A		114.0	0.0		122.0	33.0	NM_015569	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Silent	SNP	ENST00000355305.5	hg19																																																																																				.	.		0.453	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		A	172356293	C	A	172356293	2	1	79	1	0	0	0	0	0	0	0	1	4675	639	23	1		1	DNM3	1	172356293	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	3806933	172356293	76894328	17	10771										
NPL	80896	hgsc.bcm.edu	37	chr1	182797868	182797868	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttcccgtctaggttttggagTgtcacagaccaaagccatca	9	11	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:182797868T>A	ENST00000367553.1	+	12	832	c.788T>A	c.(787-789)gTg>gAg	p.V263E	NPL_ENST00000367552.2_Intron|NPL_ENST00000367555.1_Intron|NPL_ENST00000258317.2_Missense_Mutation_p.V263E|NPL_ENST00000367554.3_Missense_Mutation_p.V244E	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	263					carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)			breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						GGTTTTGGAGTGTCACAGACC	0.483																																					p.V263E		Atlas-SNP	.											.	NPL	55	.	0			c.T788A						.						78	77	78					1																	182797868		2203	4300	6503	SO:0001583	missense	80896	exon13			TTGGAGTGTCACA	AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"dihydrodipicolinate synthetase homolog 1 (E. coli)"	611412	"chromosome 1 open reading frame 13"	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.788T>A	chr1.hg19:g.182797868T>A	ENSP00000356524:p.Val263Glu	78.0	0.0		115.0	17.0	NM_030769	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Missense_Mutation	SNP	ENST00000367553.1	hg19	CCDS1350.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.588361	0.86851	.	.	ENSG00000135838	ENST00000445965;ENST00000367554;ENST00000367553;ENST00000258317	D;D;D	0.95821	-3.82;-3.82;-3.82	5.93	5.93	0.95920	Aldolase-type TIM barrel (1);	0.188069	0.45606	D	0.000341	D	0.96074	0.8721	L	0.50333	1.59	0.50813	D	0.999893	P;D	0.60575	0.906;0.988	P;P	0.58520	0.698;0.84	D	0.96424	0.9314	10	0.87932	D	0	-13.469	14.5964	0.68410	0.0:0.0:0.0:1.0	.	263;244	Q9BXD5;Q9BXD5-2	NPL_HUMAN;.	E	150;244;263;263	ENSP00000356525:V244E;ENSP00000356524:V263E;ENSP00000258317:V263E	ENSP00000258317:V263E	V	+	2	0	NPL	181064491	1.000000	0.71417	0.990000	0.47175	0.912000	0.54170	4.740000	0.62087	2.265000	0.75225	0.460000	0.39030	GTG	.	.		0.483	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769		A	182797868	T	A	182797868	3	1	79	1	0	0	0	0	1	0	0	0	10594	1696	59	4	830	4	NPL	1	182797868	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	10441575	182797868	66452753	18	10772										
ZNF281	23528	hgsc.bcm.edu	37	chr1	200377850	200377850	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgtctctccatatggtacttCtgaataaacttcatgctgca	6	10	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:200377850C>A	ENST00000294740.3	-	2	1108	c.984G>T	c.(982-984)caG>caT	p.Q328H	ZNF281_ENST00000367352.3_Missense_Mutation_p.Q292H|ZNF281_ENST00000367353.1_Missense_Mutation_p.Q328H	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	328					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						TATGGTACTTCTGAATAAACT	0.383																																					p.Q328H		Atlas-SNP	.											.	ZNF281	74	.	0			c.G984T						.						205	214	211					1																	200377850		2203	4300	6503	SO:0001583	missense	23528	exon2			GTACTTCTGAATA	AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"Zinc fingers, C2H2-type"	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.984G>T	chr1.hg19:g.200377850C>A	ENSP00000294740:p.Gln328His	65.0	0.0		90.0	18.0	NM_012482	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Missense_Mutation	SNP	ENST00000294740.3	hg19	CCDS1402.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.497085	0.64186	.	.	ENSG00000162702	ENST00000294740;ENST00000367353;ENST00000367352;ENST00000537759	T;T;T	0.60797	0.16;0.16;0.16	5.76	5.76	0.90799	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.46819	1.47	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.70037	-0.4982	10	0.62326	D	0.03	-3.2994	13.2115	0.59828	0.0:0.9277:0.0:0.0723	.	292;328	A6NF48;Q9Y2X9	.;ZN281_HUMAN	H	328;328;292;33	ENSP00000294740:Q328H;ENSP00000356322:Q328H;ENSP00000356321:Q292H	ENSP00000294740:Q328H	Q	-	3	2	ZNF281	198644473	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.706000	0.92434	0.655000	0.94253	CAG	.	.		0.383	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		A	200377850	C	A	200377850	3	1	79	1	0	0	0	0	1	0	0	0	17833	912	32	3	1707	3	ZNF281	1	200377850	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	17579982	200377850	48872771	19	10773										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201020120	201020120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tcagcatctcaccaggaaggCacagagcatgtagaagctga	11	10	2	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:201020120C>T	ENST00000362061.3	-	33	4331	c.4105G>A	c.(4105-4107)Gcc>Acc	p.A1369T	CACNA1S_ENST00000367338.3_Missense_Mutation_p.A1350T	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1369	Dihydropyridine binding. {ECO:0000250}.|Phenylalkylamine binding. {ECO:0000250}.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ACCAGGAAGGCACAGAGCATG	0.582																																					p.A1369T		Atlas-SNP	.											.	CACNA1S	249	.	0			c.G4105A						.						163	141	149					1																	201020120		2203	4300	6503	SO:0001583	missense	779	exon33			GGAAGGCACAGAG	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.4105G>A	chr1.hg19:g.201020120C>T	ENSP00000355192:p.Ala1369Thr	75.0	0.0		62.0	8.0	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	27.2	4.809796	0.90707	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.97505	-4.41;-4.41	4.43	4.43	0.53597	Ion transport (1);	0.104706	0.64402	D	0.000004	D	0.97682	0.9240	L	0.52126	1.63	0.80722	D	1	D	0.67145	0.996	D	0.74023	0.982	D	0.98936	1.0789	10	0.87932	D	0	.	17.4679	0.87638	0.0:1.0:0.0:0.0	.	1369	Q13698	CAC1S_HUMAN	T	1369;1350	ENSP00000355192:A1369T;ENSP00000356307:A1350T	ENSP00000355192:A1369T	A	-	1	0	CACNA1S	199286743	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	7.773000	0.85462	2.186000	0.69663	0.456000	0.33151	GCC	.	.		0.582	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		T	201020120	C	T	201020120	3	4	79	1	0	0	0	0	1	0	0	0	2549	710	25	3	1564	3	CACNA1S	1	201020120	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	642270	201020120	48230501	20	10774										
IGFN1	91156	hgsc.bcm.edu	37	chr1	201184917	201184917	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggccagtacagcgtgacactGaggagtgagggaggctctgt	17	8	1	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:201184917G>A	ENST00000335211.4	+	15	9376	c.9246G>A	c.(9244-9246)ctG>ctA	p.L3082L	IGFN1_ENST00000451870.2_Intron|IGFN1_ENST00000295591.8_Silent_p.L242L	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	625						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GCGTGACACTGAGGAGTGAGG	0.637																																					p.L3082L		Atlas-SNP	.											.	IGFN1	220	.	0			c.G9246A						.						30	32	31					1																	201184917		2203	4300	6503	SO:0001819	synonymous_variant	91156	exon15			GACACTGAGGAGT	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.9246G>A	chr1.hg19:g.201184917G>A		67.0	0.0		78.0	15.0	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	hg19	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	G	7.183	0.589965	0.13812	.	.	ENSG00000163395	ENST00000412892	.	.	.	4.83	4.83	0.62350	.	.	.	.	.	T	0.68705	0.3030	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67730	-0.5595	4	.	.	.	.	13.4953	0.61421	0.0:0.1559:0.8441:0.0	.	.	.	.	K	500	.	.	E	+	1	0	IGFN1	199451540	0.993000	0.37304	0.518000	0.27811	0.028000	0.11728	0.629000	0.24538	2.234000	0.73211	0.561000	0.74099	GAG	.	.		0.637	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		A	201184917	G	A	201184917	2	1	79	1	0	0	0	0	0	0	0	1	7599	1277	45	3		3	IGFN1	1	201184917	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	164797	201184917	48065704	21	10775										
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204210607	204210607	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgtccgagggggcacaacgcCaactgcagaaagacagagta	13	10	0	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:204210607C>A	ENST00000272203.3	-	17	2621	c.2305G>T	c.(2305-2307)Ggc>Tgc	p.G769C	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.G789C	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	769										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			GGCACAACGCCAACTGCAGAA	0.562																																					p.G769C		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.G2305T						.						28	25	26					1																	204210607		2203	4300	6503	SO:0001583	missense	22874	exon17			CAACGCCAACTGC	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2305G>T	chr1.hg19:g.204210607C>A	ENSP00000272203:p.Gly769Cys	34.0	0.0		36.0	15.0	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	hg19	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.463166	0.63513	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.29142	1.58;2.05	5.81	5.81	0.92471	.	0.109584	0.64402	D	0.000008	T	0.61337	0.2339	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.63994	-0.6511	10	0.87932	D	0	-39.6689	19.6713	0.95912	0.0:1.0:0.0:0.0	.	769	Q9Y2H5	PKHA6_HUMAN	C	769;789	ENSP00000272203:G769C;ENSP00000402046:G789C	ENSP00000272203:G769C	G	-	1	0	PLEKHA6	202477230	1.000000	0.71417	0.998000	0.56505	0.105000	0.19272	6.976000	0.76135	2.756000	0.94617	0.655000	0.94253	GGC	.	.		0.562	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		A	204210607	C	A	204210607	3	1	79	1	0	0	0	0	1	0	0	0	12069	594	21	3	865	3	PLEKHA6	1	204210607	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	3025690	204210607	45040014	22	10776										
USH2A	7399	hgsc.bcm.edu	37	chr1	216371684	216371684	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tcccgttctttctgagacccAggcagaagacacacttccag	8	14	2	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:216371684A>T	ENST00000307340.3	-	18	4440	c.4054T>A	c.(4054-4056)Tgg>Agg	p.W1352R	USH2A_ENST00000366943.2_Missense_Mutation_p.W1352R|RP5-1099E6.3_ENST00000420867.1_RNA|USH2A_ENST00000366942.3_Missense_Mutation_p.W1352R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1352	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCTGAGACCCAGGCAGAAGAC	0.398										HNSCC(13;0.011)																											p.W1352R		Atlas-SNP	.											.	USH2A	1168	.	0			c.T4054A						.						103	99	101					1																	216371684		2203	4300	6503	SO:0001583	missense	7399	exon18			AGACCCAGGCAGA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.4054T>A	chr1.hg19:g.216371684A>T	ENSP00000305941:p.Trp1352Arg	58.0	0.0		101.0	18.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.981811	0.74474	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.53423	0.62;0.62;0.62	5.3	5.3	0.74995	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.41001	U	0.000972	T	0.65249	0.2673	M	0.72353	2.195	0.58432	D	0.999999	D;D	0.89917	1.0;0.993	D;P	0.97110	1.0;0.879	T	0.62324	-0.6878	10	0.15066	T	0.55	.	15.2472	0.73513	1.0:0.0:0.0:0.0	.	1352;1352	O75445-2;O75445	.;USH2A_HUMAN	R	1352	ENSP00000305941:W1352R;ENSP00000355910:W1352R;ENSP00000355909:W1352R	ENSP00000305941:W1352R	W	-	1	0	USH2A	214438307	0.998000	0.40836	0.992000	0.48379	0.844000	0.47949	3.882000	0.56160	1.999000	0.58509	0.455000	0.32223	TGG	.	.		0.398	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216371684	A	T	216371684	3	4	79	1	0	0	0	0	1	0	0	0	17051	188	7	4	11788	4	USH2A	1	216371684	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	12161077	216371684	32878937	23	10777										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228503672	228503672	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tggctgctggacgacgaaccCgtgcacacctcggagaacgc	13	14	0	1	rs111746072		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:228503672C>G	ENST00000422127.1	+	50	13181	c.13137C>G	c.(13135-13137)ccC>ccG	p.P4379P	OBSCN_ENST00000366709.4_Silent_p.P1498P|OBSCN_ENST00000570156.2_Silent_p.P5336P|OBSCN_ENST00000366707.4_Silent_p.P2013P|OBSCN_ENST00000284548.11_Silent_p.P4379P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4379	Ig-like 45.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				ACGACGAACCCGTGCACACCT	0.662																																					p.P5336P		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C16008G						.						25	31	29					1																	228503672		2085	4181	6266	SO:0001819	synonymous_variant	84033	exon61			CGAACCCGTGCAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.13137C>G	chr1.hg19:g.228503672C>G		157.0	0.0		218.0	79.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	C|0.500;T|0.500		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228503672	C	G	228503672	2	3	79	1	0	0	0	0	0	0	0	1	10821	639	23	4		4	OBSCN	1	228503672	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	12131988	228503672	20746949	24	10778										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228547311	228547311	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cccccagagaagagaccatcAccactgtggtgaagagccca	10	14	1	4			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:228547311A>T	ENST00000422127.1	+	80	18705				OBSCN_ENST00000366709.4_Missense_Mutation_p.T3359S|OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000284548.11_Missense_Mutation_p.T6240S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGAGACCATCACCACTGTGGT	0.647																																					p.T6240S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A18718T						.						16	21	19					1																	228547311		2140	4246	6386	SO:0001627	intron_variant	84033	exon81			ACCATCACCACTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18662-2966A>T	chr1.hg19:g.228547311A>T		111.0	0.0		134.0	25.0	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.839921	0.91117	.	.	ENSG00000154358	ENST00000284548;ENST00000366709	T;T	0.58506	0.33;0.47	4.56	3.41	0.39046	.	.	.	.	.	T	0.64897	0.2640	M	0.76002	2.32	0.35152	D	0.769898	D	0.60575	0.988	P	0.57152	0.814	T	0.68880	-0.5292	9	0.10636	T	0.68	.	10.3416	0.43882	0.9214:0.0:0.0786:0.0	.	6240	Q5VST9-3	.	S	6240;3359	ENSP00000284548:T6240S;ENSP00000355670:T3359S	ENSP00000284548:T6240S	T	+	1	0	OBSCN	226613934	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	8.049000	0.89443	0.769000	0.33313	0.454000	0.30748	ACC	.	.		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228547311	A	T	228547311	1	4	79	0	1	0	0	0	0	0	0	0	10821	159	6	4		4	OBSCN	1	228547311	Intron	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	43639	228547311	20703310	25	10779										
HIST3H2A	92815	hgsc.bcm.edu	37	chr1	228645460	228645460	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggaactgcagccccgcgcgcGacgagcgcgacttagccttg	14	15	0	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:228645460G>A	ENST00000366695.2	-	1	100	c.59C>T	c.(58-60)tCg>tTg	p.S20L	HIST3H2BB_ENST00000369160.2_5'Flank	NM_033445.2	NP_254280.1	Q7L7L0	H2A3_HUMAN	histone cluster 3, H2a	20					nucleosome disassembly (GO:0006337)|UV-damage excision repair (GO:0070914)	extracellular vesicular exosome (GO:0070062)|nuclear nucleosome (GO:0000788)	DNA binding (GO:0003677)			endometrium(1)|lung(3)|ovary(1)	5		Prostate(94;0.183)				CCCCGCGCGCGACGAGCGCGA	0.667																																					p.S20L		Atlas-SNP	.											.	HIST3H2A	13	.	0			c.C59T						.						14	17	16					1																	228645460		2137	4221	6358	SO:0001583	missense	92815	exon1			GCGCGCGACGAGC	AY131974	CCDS1573.1	1q42.13	2011-01-27	2006-10-11		ENSG00000181218	ENSG00000181218		"Histones / Replication-dependent"	20507	protein-coding gene	gene with protein product		615015	"histone 3, H2a"			12408966	Standard	NM_033445		Approved	MGC3165	uc001hsy.3	Q7L7L0	OTTHUMG00000040046	ENST00000366695.2:c.59C>T	chr1.hg19:g.228645460G>A	ENSP00000355656:p.Ser20Leu	258.0	0.0		298.0	64.0	NM_033445	B2R4S4	Missense_Mutation	SNP	ENST00000366695.2	hg19	CCDS1573.1	.	.	.	.	.	.	.	.	.	.	.	14.05	2.419397	0.42918	.	.	ENSG00000181218	ENST00000366695	T	0.47528	0.84	4.07	4.07	0.47477	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.44285	D	0.000479	T	0.68833	0.3044	M	0.83118	2.625	0.49483	D	0.99979	D	0.65815	0.995	D	0.67900	0.954	T	0.74691	-0.3580	10	0.87932	D	0	.	14.5656	0.68173	0.0:0.0:1.0:0.0	.	20	Q7L7L0	H2A3_HUMAN	L	20	ENSP00000355656:S20L	ENSP00000355656:S20L	S	-	2	0	HIST3H2A	226712083	1.000000	0.71417	0.106000	0.21319	0.300000	0.27592	5.957000	0.70323	2.549000	0.85964	0.655000	0.94253	TCG	.	.		0.667	HIST3H2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096598.1	NM_033445		A	228645460	G	A	228645460	3	1	79	1	0	0	0	0	1	0	0	0	7191	1059	37	1	337	1	HIST3H2A	1	228645460	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	98149	228645460	20605161	26	10780										
C1orf198	84886	hgsc.bcm.edu	37	chr1	230979535	230979535	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctgccttgggaggacttgagGgcctgggagccctgggaagc	18	10	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:230979535G>T	ENST00000366663.5	-	3	632	c.492C>A	c.(490-492)gcC>gcA	p.A164A	C1orf198_ENST00000427697.2_5'UTR|C1orf198_ENST00000523410.1_Silent_p.A34A|C1orf198_ENST00000470540.1_Silent_p.A126A	NM_032800.2	NP_116189.1	Q9H425	CA198_HUMAN	chromosome 1 open reading frame 198	164						cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	17	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				AGGACTTGAGGGCCTGGGAGC	0.637																																					p.A164A		Atlas-SNP	.											.	C1orf198	29	.	0			c.C492A						.						84	96	92					1																	230979535		2203	4300	6503	SO:0001819	synonymous_variant	84886	exon3			CTTGAGGGCCTGG	BC066649	CCDS1587.1, CCDS44330.1, CCDS44331.1	1q42.2	2008-02-05			ENSG00000119280	ENSG00000119280			25900	protein-coding gene	gene with protein product							Standard	NM_032800		Approved	FLJ14525, MGC10710, FLJ16283, DKFZp667D152, FLJ38847	uc001hub.3	Q9H425	OTTHUMG00000037790	ENST00000366663.5:c.492C>A	chr1.hg19:g.230979535G>T		70.0	0.0		53.0	5.0	NM_032800	A8K8R8|B3KTW1|G5EA08	Silent	SNP	ENST00000366663.5	hg19	CCDS1587.1																																																																																			.	.		0.637	C1orf198-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092236.2	NM_032800		T	230979535	G	T	230979535	2	4	79	1	0	0	0	0	0	0	0	1	2028	1219	43	3		3	C1orf198	1	230979535	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	2334075	230979535	18271086	27	10781										
PLD5	200150	hgsc.bcm.edu	37	chr1	242263975	242263975	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agccctgacacctaccaataTaagctgctccatctgtcacc	5	16	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr1:242263975T>A	ENST00000536534.2	-	9	1590	c.1349A>T	c.(1348-1350)tAt>tTt	p.Y450F	PLD5_ENST00000442594.2_Missense_Mutation_p.Y358F|PLD5_ENST00000427495.1_Missense_Mutation_p.Y388F			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	450	PLD phosphodiesterase 2.					integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)	p.Y450C(1)|p.Y358C(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			CCTACCAATATAAGCTGCTCC	0.502																																					p.Y450F		Atlas-SNP	.											PLD5_ENST00000536534,NS,carcinoma,0,2	PLD5	216	.	2	Substitution - Missense(2)	endometrium(2)	c.A1349T						.						219	179	193					1																	242263975		2203	4300	6503	SO:0001583	missense	200150	exon10			CCAATATAAGCTG	AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.1349A>T	chr1.hg19:g.242263975T>A	ENSP00000440896:p.Tyr450Phe	64.0	0.0		63.0	16.0	NM_152666	A1KXV0|B7Z324|Q494U9|Q8NB22	Missense_Mutation	SNP	ENST00000536534.2	hg19	CCDS1621.2	.	.	.	.	.	.	.	.	.	.	T	18.03	3.531979	0.64972	.	.	ENSG00000180287	ENST00000427495;ENST00000442594;ENST00000536534	T;T;T	0.19938	2.11;2.11;2.11	5.34	5.34	0.76211	Phospholipase D/Transphosphatidylase (1);	0.000000	0.85682	D	0.000000	T	0.26774	0.0655	L	0.56396	1.775	0.58432	D	0.999995	P;P;P	0.45474	0.859;0.779;0.724	B;B;B	0.43889	0.435;0.232;0.34	T	0.02301	-1.1180	10	0.49607	T	0.09	-16.1727	13.8569	0.63534	0.0:0.0:0.0:1.0	.	358;450;388	Q8N7P1-2;Q8N7P1;Q8N7P1-4	.;PLD5_HUMAN;.	F	388;358;450	ENSP00000401285:Y388F;ENSP00000414188:Y358F;ENSP00000440896:Y450F	ENSP00000401285:Y388F	Y	-	2	0	PLD5	240330598	1.000000	0.71417	0.914000	0.36105	0.968000	0.65278	6.471000	0.73562	2.153000	0.67306	0.528000	0.53228	TAT	.	.		0.502	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		A	242263975	T	A	242263975	3	1	79	1	0	0	0	0	1	0	0	0	12058	1406	49	4	269	4	PLD5	1	242263975	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	11284440	242263975	6986646	28	10782										
FAM150B	285016	hgsc.bcm.edu	37	chr2	283165	283165	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cgggtaagaagcctggcgcaTcttttatagtctacggtgaa	12	8	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:283165T>G	ENST00000403610.4	-	5	739	c.399A>C	c.(397-399)agA>agC	p.R133S	FAM150B_ENST00000344414.5_Missense_Mutation_p.R41S|FAM150B_ENST00000401503.1_Missense_Mutation_p.R41S|FAM150B_ENST00000405290.1_Missense_Mutation_p.R41S	NM_001002919.2	NP_001002919.2	Q6UX46	F150B_HUMAN	family with sequence similarity 150, member B	133						extracellular region (GO:0005576)				breast(1)|kidney(2)	3	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.00091)|Epithelial(75;0.00656)|OV - Ovarian serous cystadenocarcinoma(76;0.00954)|GBM - Glioblastoma multiforme(21;0.128)		GCCTGGCGCATCTTTTATAGT	0.413																																					p.R133S		Atlas-SNP	.											.	FAM150B	12	.	0			c.A399C						.						57	56	56					2																	283165		1858	4098	5956	SO:0001583	missense	285016	exon5			GGCGCATCTTTTA		CCDS46218.1	2p25.3	2008-05-02			ENSG00000189292	ENSG00000189292			27683	protein-coding gene	gene with protein product							Standard	NM_001002919		Approved		uc002qwi.4	Q6UX46	OTTHUMG00000151366	ENST00000403610.4:c.399A>C	chr2.hg19:g.283165T>G	ENSP00000384604:p.Arg133Ser	123.0	0.0		83.0	18.0	NM_001002919	B5MC76	Missense_Mutation	SNP	ENST00000403610.4	hg19	CCDS46218.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.75|17.75	3.467005|3.467005	0.63625|0.63625	.|.	.|.	ENSG00000189292|ENSG00000189292	ENST00000401489|ENST00000436353;ENST00000403610;ENST00000401503;ENST00000405290;ENST00000344414;ENST00000452023	.|.	.|.	.|.	4.69|4.69	-3.15|-3.15	0.05233|0.05233	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.71995|0.71995	0.3406|0.3406	M|M	0.71036|0.71036	2.16|2.16	0.44852|0.44852	D|D	0.997865|0.997865	.|D	.|0.76494	.|0.999	.|D	.|0.83275	.|0.996	T|T	0.70880|0.70880	-0.4752|-0.4752	5|9	.|0.87932	.|D	.|0	.|.	10.4301|10.4301	0.44403|0.44403	0.0:0.5584:0.0:0.4416|0.0:0.5584:0.0:0.4416	.|.	.|133	.|Q6UX46	.|F150B_HUMAN	A|S	84|73;133;41;41;41;133	.|.	.|ENSP00000339565:R41S	D|R	-|-	2|3	0|2	FAM150B|FAM150B	273165|273165	1.000000|1.000000	0.71417|0.71417	0.071000|0.071000	0.20095|0.20095	0.712000|0.712000	0.41017|0.41017	1.400000|1.400000	0.34577|0.34577	-0.818000|-0.818000	0.04329|0.04329	0.533000|0.533000	0.62120|0.62120	GAT|AGA	.	.		0.413	FAM150B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322394.2	NM_001002919		G	283165	T	G	283165	3	3	79	1	0	0	0	0	1	0	0	0	5462	1432	50	5	67	5	FAM150B	2	283165	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10		283165	242916208	29	10783										
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55571513	55571513	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttaaaacttaccatttccatAtcatgaagtttagctttcag	4	8	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:55571513A>T	ENST00000436346.1	-	11	2020	c.1179T>A	c.(1177-1179)gaT>gaA	p.D393E	CCDC88A_ENST00000263630.8_Missense_Mutation_p.D393E|CCDC88A_ENST00000336838.6_Missense_Mutation_p.D393E|CCDC88A_ENST00000413716.2_Missense_Mutation_p.D393E|AC012358.8_ENST00000594078.1_RNA	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	393					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						CCATTTCCATATCATGAAGTT	0.373																																					p.D393E		Atlas-SNP	.											.	CCDC88A	336	.	0			c.T1179A						.						109	104	106					2																	55571513		2203	4297	6500	SO:0001583	missense	55704	exon11			TTCCATATCATGA	AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.1179T>A	chr2.hg19:g.55571513A>T	ENSP00000410608:p.Asp393Glu	80.0	0.0		73.0	17.0	NM_018084	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.63	3.177405	0.57692	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716	T;T;T;T	0.35236	1.32;1.32;1.32;1.32	5.87	3.28	0.37604	.	0.128273	0.34531	U	0.003887	T	0.21347	0.0514	N	0.25426	0.745	0.80722	D	1	B;B;B	0.25904	0.011;0.068;0.137	B;B;B	0.25884	0.03;0.064;0.054	T	0.06006	-1.0851	10	0.21540	T	0.41	-23.6018	6.2193	0.20673	0.7396:0.0:0.1425:0.1179	.	393;393;393	B7ZM78;Q3V6T2-2;Q3V6T2-3	.;.;.	E	393	ENSP00000338728:D393E;ENSP00000263630:D393E;ENSP00000410608:D393E;ENSP00000404431:D393E	ENSP00000263630:D393E	D	-	3	2	CCDC88A	55425017	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.298000	0.33412	0.400000	0.25396	0.477000	0.44152	GAT	.	.		0.373	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		T	55571513	A	T	55571513	3	4	79	1	0	0	0	0	1	0	0	0	2865	446	16	4	4524	4	CCDC88A	2	55571513	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	55288348	55571513	187627860	30	10784										
LRRTM4	80059	hgsc.bcm.edu	37	chr2	77746081	77746081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tatttccagacaatgtgatgGatattaatgatatccacgca	7	7	0	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:77746081G>A	ENST00000409093.1	-	3	1250	c.914C>T	c.(913-915)tCc>tTc	p.S305F	LRRTM4_ENST00000409282.1_Missense_Mutation_p.S306F|LRRTM4_ENST00000409884.1_Missense_Mutation_p.S305F|LRRTM4_ENST00000409911.1_Missense_Mutation_p.S306F|LRRTM4_ENST00000409088.3_Missense_Mutation_p.S305F			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	305					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		CAATGTGATGGATATTAATGA	0.353																																					p.S305F		Atlas-SNP	.											.	LRRTM4	334	.	0			c.C914T						.						45	40	42					2																	77746081		1857	4108	5965	SO:0001583	missense	80059	exon3			GTGATGGATATTA	AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.914C>T	chr2.hg19:g.77746081G>A	ENSP00000386357:p.Ser305Phe	78.0	0.0		76.0	19.0	NM_024993	Q4FZ98|Q6UXJ7	Missense_Mutation	SNP	ENST00000409093.1	hg19	CCDS46346.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.992139	0.54041	.	.	ENSG00000176204	ENST00000409911;ENST00000409884;ENST00000409093;ENST00000409088;ENST00000409282	T;T;T;T;T	0.04603	3.59;3.59;3.59;3.59;3.59	5.84	5.84	0.93424	.	0.178707	0.50627	D	0.000109	T	0.13157	0.0319	L	0.31926	0.97	0.58432	D	0.999995	D;P;D	0.55605	0.972;0.906;0.972	P;P;P	0.62435	0.839;0.751;0.902	T	0.01460	-1.1349	10	0.44086	T	0.13	.	18.6944	0.91594	0.0:0.0:1.0:0.0	.	306;305;305	Q4KMX1;Q86VH4-2;Q86VH4	.;.;LRRT4_HUMAN	F	306;305;305;305;306	ENSP00000387228:S306F;ENSP00000387297:S305F;ENSP00000386357:S305F;ENSP00000386236:S305F;ENSP00000386286:S306F	ENSP00000386236:S305F	S	-	2	0	LRRTM4	77599589	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.817000	0.75252	2.751000	0.94390	0.655000	0.94253	TCC	.	.		0.353	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		A	77746081	G	A	77746081	3	1	79	1	0	0	0	0	1	0	0	0	9051	1174	41	3	872	3	LRRTM4	2	77746081	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	22174568	77746081	165453292	31	10785										
GPAT2	150763	hgsc.bcm.edu	37	chr2	96690205	96690205	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctcgctcaggaagacgggcaGcagctcagcactcagttgtg	13	12	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:96690205G>A	ENST00000434632.1	-	16	2098	c.1639C>T	c.(1639-1641)Ctg>Ttg	p.L547L	FAHD2CP_ENST00000607780.1_RNA|GPAT2_ENST00000453542.1_Silent_p.L476L|GPAT2_ENST00000359548.4_Silent_p.L547L|GPAT2_ENST00000377137.3_Silent_p.L547L			Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2, mitochondrial	547					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerol-3-phosphate metabolic process (GO:0006072)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(5)|skin(3)	16						AAGACGGGCAGCAGCTCAGCA	0.642																																					p.L547L		Atlas-SNP	.											.	GPAT2	46	.	0			c.C1639T						.						51	57	55					2																	96690205		2165	4238	6403	SO:0001819	synonymous_variant	150763	exon15			CGGGCAGCAGCTC	BC042847	CCDS42714.1	2q11.2	2010-05-04			ENSG00000186281	ENSG00000186281			27168	protein-coding gene	gene with protein product	"cancer/testis antigen 123"					12477932	Standard	NM_207328		Approved	CT123	uc010yuf.1	Q6NUI2	OTTHUMG00000155208	ENST00000434632.1:c.1639C>T	chr2.hg19:g.96690205G>A		80.0	0.0		55.0	11.0	NM_207328	Q6P2E4|Q6ZNI3|Q6ZNI5|Q6ZWJ4	Silent	SNP	ENST00000434632.1	hg19	CCDS42714.1																																																																																			.	.		0.642	GPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338786.1	NM_207328		A	96690205	G	A	96690205	2	1	79	1	0	0	0	0	0	0	0	1	6597	962	34	3		3	GPAT2	2	96690205	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	18944124	96690205	146509168	32	10786										
SLC4A10	57282	hgsc.bcm.edu	37	chr2	162761399	162761399	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ccagttttggtgtttgaaaaGattttgtttaaattttgcaa	8	3	0	2	rs534495211		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:162761399G>T	ENST00000446997.1	+	14	1824	c.1731G>T	c.(1729-1731)aaG>aaT	p.K577N	SLC4A10_ENST00000375514.5_Missense_Mutation_p.K558N|SLC4A10_ENST00000415876.2_Missense_Mutation_p.K547N|SLC4A10_ENST00000272716.5_Missense_Mutation_p.K547N|SLC4A10_ENST00000421911.1_Missense_Mutation_p.K577N	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	577					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	TGTTTGAAAAGATTTTGTTTA	0.388																																					p.K577N		Atlas-SNP	.											SLC4A10_ENST00000446997,NS,carcinoma,0,2	SLC4A10	309	.	0			c.G1731T						.						159	150	153					2																	162761399		1900	4145	6045	SO:0001583	missense	57282	exon14			TGAAAAGATTTTG		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.1731G>T	chr2.hg19:g.162761399G>T	ENSP00000393066:p.Lys577Asn	132.0	0.0		120.0	30.0	NM_001178015	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	hg19	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.224603	0.79576	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	T;T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31;-1.31	5.56	4.69	0.59074	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87533	0.6201	M	0.77406	2.37	0.58432	D	0.999999	D;D;D	0.63046	0.97;0.97;0.992	P;P;D	0.64506	0.844;0.844;0.926	D	0.87864	0.2666	10	0.59425	D	0.04	.	10.409	0.44280	0.1484:0.0:0.8516:0.0	.	558;547;577	F8W675;Q6U841-2;Q6U841	.;.;S4A10_HUMAN	N	558;547;547;546;577;577;576	ENSP00000364664:K558N;ENSP00000395797:K547N;ENSP00000272716:K547N;ENSP00000393066:K577N;ENSP00000404486:K577N	ENSP00000272716:K547N	K	+	3	2	SLC4A10	162469645	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.562000	0.53777	1.350000	0.45770	0.557000	0.71058	AAG	.	.		0.388	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		T	162761399	G	T	162761399	3	4	79	1	0	0	0	0	1	0	0	0	14666	933	33	3	1870	3	SLC4A10	2	162761399	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	66071194	162761399	80437974	33	10787										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168103206	168103206	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cacacagagtcaaatgaaacActgacagctaagaaacaaga	7	9	1	5			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:168103206A>G	ENST00000409195.1	+	9	5393	c.5304A>G	c.(5302-5304)acA>acG	p.T1768T	XIRP2_ENST00000295237.9_Silent_p.T1768T|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Silent_p.T1546T|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1593					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CAAATGAAACACTGACAGCTA	0.403																																					p.T1768T		Atlas-SNP	.											.	XIRP2	914	.	0			c.A5304G						.						120	114	116					2																	168103206		1902	4113	6015	SO:0001819	synonymous_variant	129446	exon9			TGAAACACTGACA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5304A>G	chr2.hg19:g.168103206A>G		173.0	0.0		203.0	56.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.403	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168103206	A	G	168103206	2	3	79	1	0	0	0	0	0	0	0	1	17445	146	6	2		2	XIRP2	2	168103206	Silent	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	5341807	168103206	75096167	34	10788										
GPR155	151556	hgsc.bcm.edu	37	chr2	175309901	175309901	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ccaccataaacaactggaaaGattctgtaaagaaaggagaa	8	7	1	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:175309901G>A	ENST00000392552.2	-	13	2255	c.2017C>T	c.(2017-2019)Ctt>Ttt	p.L673F	GPR155_ENST00000459996.1_5'UTR|GPR155_ENST00000295500.4_Missense_Mutation_p.L673F|GPR155_ENST00000392551.2_Missense_Mutation_p.L673F	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	673					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.L673I(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						CAACTGGAAAGATTCTGTAAA	0.343																																					p.L673F		Atlas-SNP	.											GPR155,rectum,carcinoma,0,1	GPR155	76	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2017T						.						39	40	40					2																	175309901		2203	4300	6503	SO:0001583	missense	151556	exon14			TGGAAAGATTCTG	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.2017C>T	chr2.hg19:g.175309901G>A	ENSP00000376335:p.Leu673Phe	71.0	0.0		60.0	17.0	NM_001033045	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	ENST00000392552.2	hg19	CCDS2259.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.294451	0.60086	.	.	ENSG00000163328	ENST00000392552;ENST00000510236;ENST00000392551;ENST00000295500	T;T;T	0.61980	0.06;0.06;0.06	5.54	4.67	0.58626	.	0.116810	0.64402	D	0.000012	T	0.71787	0.3381	M	0.72118	2.19	0.51482	D	0.999929	D;P	0.59357	0.985;0.863	P;P	0.57244	0.816;0.594	T	0.74771	-0.3552	10	0.87932	D	0	-13.0178	10.023	0.42055	0.0724:0.1374:0.7902:0.0	.	153;673	F5H464;Q7Z3F1	.;GP155_HUMAN	F	673;153;673;673	ENSP00000376335:L673F;ENSP00000376334:L673F;ENSP00000295500:L673F	ENSP00000295500:L673F	L	-	1	0	GPR155	175018147	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	3.849000	0.55910	1.356000	0.45884	0.551000	0.68910	CTT	.	.		0.343	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		A	175309901	G	A	175309901	3	1	79	1	0	0	0	0	1	0	0	0	6668	942	33	3	611	3	GPR155	2	175309901	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	7206695	175309901	67889472	35	10789										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178879182	178879194	+	Splice_Site	DEL	TCGATCCTAAAAA	TCGATCCTAAAAA	-													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tcgatttcatcattgaatcgTcgatcctaaaaataagacaa					rs76865936		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	TCGATCCTAAAAA	TCGATCCTAAAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:178879182_178879194delTCGATCCTAAAAA	ENST00000286063.6	-	2	1230_1235	c.913_918delTTTTTAGGATCGA	c.(913-918)tttttadel	p.FL305fs	PDE11A_ENST00000358450.4_Splice_Site_p.FL55fs|AC011998.1_ENST00000457053.1_RNA	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	305	GAF 1.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)	p.D305Y(1)|p.D55Y(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	CATTGAATCGTCGATCCTAAAAATAAGACAAAG	0.413									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.305_307del		Atlas-INDEL	.											.	PDE11A	283	.	2	Substitution - Missense(2)	large_intestine(2)	c.913_919del						.																																			SO:0001630	splice_region_variant	50940	exon2	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	.	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.913-1TTTTTAGGATCGA>-	chr2.hg19:g.178879182_178879194delTCGATCCTAAAAA		48.0	0.0		55.0	19.0	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Frame_Shift_Del	DEL	ENST00000286063.6	hg19	CCDS33334.1																																																																																			.	.		0.413	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		Frame_Shift_Del	-	178879194	TCGATCCTAAAAA	-	178879182	8	5	79	1	0	1	0	1	0	0	1	0	11640	1654	58	0	1959	0	PDE11A	2	178879182	Splice_Site	DEL	TCGATCCTAAAAA	TCGA-CC-A8HT-01A-11D-A35Z-10	3569281	178879182	64320191	36	10790										
TTN	7273	hgsc.bcm.edu	37	chr2	179447182	179447182	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agagacttgagcccagttggGcctgcttgtttcacgtttgt	12	9	1	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:179447182G>T	ENST00000591111.1	-	264	61302	c.61078C>A	c.(61078-61080)Ccc>Acc	p.P20360T	TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P22001T|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P13128T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P13061T|TTN_ENST00000460472.2_Missense_Mutation_p.P12936T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P19433T|TTN-AS1_ENST00000591332.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20360	Fibronectin type-III 47. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCCAGTTGGGCCTGCTTGTT	0.463																																					p.P22001T		Atlas-SNP	.											.	TTN	18412	.	0			c.C66001A						.						78	72	74					2																	179447182		1911	4130	6041	SO:0001583	missense	7273	exon314			AGTTGGGCCTGCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.61078C>A	chr2.hg19:g.179447182G>T	ENSP00000465570:p.Pro20360Thr	158.0	0.0		148.0	28.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.37	2.217876	0.39201	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.86	4.0	0.46444	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.36608	0.0973	N	0.16201	0.385	0.38358	D	0.944526	P;P;P;P	0.36354	0.549;0.549;0.549;0.549	B;B;B;B	0.35182	0.197;0.197;0.197;0.197	T	0.41910	-0.9482	9	0.87932	D	0	.	13.1155	0.59297	0.0:0.1229:0.7491:0.1279	.	12936;13061;13128;20360	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	19433;12936;13128;13061;12934	ENSP00000343764:P19433T;ENSP00000434586:P12936T;ENSP00000340554:P13128T;ENSP00000352154:P13061T	ENSP00000340554:P13128T	P	-	1	0	TTN	179155428	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	4.098000	0.57748	0.748000	0.32831	0.655000	0.94253	CCC	.	.		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179447182	G	T	179447182	3	4	79	1	0	0	0	0	1	0	0	0	16750	1203	42	3	42174	3	TTN	2	179447182	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	568000	179447182	63752191	37	10791										
SLC39A10	57181	hgsc.bcm.edu	37	chr2	196544891	196544891	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcttcacagacagcatcgtgGaatgacagaattggagccaa	11	9	1	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:196544891G>T	ENST00000409086.3	+	2	400	c.125G>T	c.(124-126)gGa>gTa	p.G42V	SLC39A10_ENST00000359634.5_Missense_Mutation_p.G42V|SLC39A10_ENST00000541054.1_Intron	NM_001127257.1	NP_001120729.1	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter), member 10	42					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(16)|pancreas(1)|prostate(1)|skin(2)	34			OV - Ovarian serous cystadenocarcinoma(117;0.221)			CAGCATCGTGGAATGACAGAA	0.373																																					p.G42V		Atlas-SNP	.											.	SLC39A10	89	.	0			c.G125T						.						48	51	50					2																	196544891		2203	4300	6503	SO:0001583	missense	57181	exon2			ATCGTGGAATGAC		CCDS33353.1	2q33.1	2013-05-22			ENSG00000196950	ENSG00000196950		"Solute carriers"	20861	protein-coding gene	gene with protein product		608733	"solute carrier family 39 (metal ion transporter), member 10"			12659941	Standard	NM_020342		Approved	KIAA1265, FLJ90515, DKFZp564L2123	uc002utg.4	Q9ULF5	OTTHUMG00000154380	ENST00000409086.3:c.125G>T	chr2.hg19:g.196544891G>T	ENSP00000386766:p.Gly42Val	399.0	0.0		377.0	87.0	NM_020342	A8K5C6|B4DGU0|Q3MJA4|Q68CR5|Q6DKH6|Q9Y3Z1	Missense_Mutation	SNP	ENST00000409086.3	hg19	CCDS33353.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.292879	0.40594	.	.	ENSG00000196950	ENST00000458054;ENST00000409086;ENST00000359634;ENST00000418005	T;T;T;T	0.66460	0.81;-0.21;-0.21;0.83	4.54	4.54	0.55810	.	0.783507	0.11448	N	0.563053	T	0.77579	0.4151	L	0.51422	1.61	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.75274	-0.3375	10	0.54805	T	0.06	.	14.8192	0.70059	0.0:0.0:1.0:0.0	.	42	Q9ULF5	S39AA_HUMAN	V	42	ENSP00000389640:G42V;ENSP00000386766:G42V;ENSP00000352655:G42V;ENSP00000409272:G42V	ENSP00000352655:G42V	G	+	2	0	SLC39A10	196253136	1.000000	0.71417	0.392000	0.26245	0.986000	0.74619	4.577000	0.60922	2.324000	0.78689	0.650000	0.86243	GGA	.	.		0.373	SLC39A10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335186.1	XM_047707		T	196544891	G	T	196544891	3	4	79	1	0	0	0	0	1	0	0	0	14628	1174	41	3	127	3	SLC39A10	2	196544891	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	17097709	196544891	46654482	38	10792										
SLC39A10	57181	hgsc.bcm.edu	37	chr2	196545343	196545343	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	atcatcttgatcataacaacActcaccattttcataatgat	2	10	5	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:196545343A>T	ENST00000409086.3	+	2	852	c.577A>T	c.(577-579)Act>Tct	p.T193S	SLC39A10_ENST00000359634.5_Missense_Mutation_p.T193S|SLC39A10_ENST00000541054.1_Intron	NM_001127257.1	NP_001120729.1	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter), member 10	193	His-rich.				transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(16)|pancreas(1)|prostate(1)|skin(2)	34			OV - Ovarian serous cystadenocarcinoma(117;0.221)			TCATAACAACACTCACCATTT	0.408																																					p.T193S		Atlas-SNP	.											.	SLC39A10	89	.	0			c.A577T						.						115	100	105					2																	196545343		2203	4300	6503	SO:0001583	missense	57181	exon2			AACAACACTCACC		CCDS33353.1	2q33.1	2013-05-22			ENSG00000196950	ENSG00000196950		"Solute carriers"	20861	protein-coding gene	gene with protein product		608733	"solute carrier family 39 (metal ion transporter), member 10"			12659941	Standard	NM_020342		Approved	KIAA1265, FLJ90515, DKFZp564L2123	uc002utg.4	Q9ULF5	OTTHUMG00000154380	ENST00000409086.3:c.577A>T	chr2.hg19:g.196545343A>T	ENSP00000386766:p.Thr193Ser	276.0	0.0		296.0	71.0	NM_020342	A8K5C6|B4DGU0|Q3MJA4|Q68CR5|Q6DKH6|Q9Y3Z1	Missense_Mutation	SNP	ENST00000409086.3	hg19	CCDS33353.1	.	.	.	.	.	.	.	.	.	.	A	4.619	0.115116	0.08831	.	.	ENSG00000196950	ENST00000409086;ENST00000359634	T;T	0.64438	-0.1;-0.1	4.91	3.76	0.43208	.	1.458410	0.04213	N	0.332009	T	0.46833	0.1413	L	0.27053	0.805	0.20196	N	0.999922	B	0.14438	0.01	B	0.10450	0.005	T	0.34428	-0.9829	10	0.06891	T	0.86	.	6.6278	0.22839	0.7667:0.1547:0.0787:0.0	.	193	Q9ULF5	S39AA_HUMAN	S	193	ENSP00000386766:T193S;ENSP00000352655:T193S	ENSP00000352655:T193S	T	+	1	0	SLC39A10	196253588	0.989000	0.36119	0.545000	0.28153	0.352000	0.29268	3.293000	0.51779	0.900000	0.36469	0.533000	0.62120	ACT	.	.		0.408	SLC39A10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335186.1	XM_047707		T	196545343	A	T	196545343	3	4	79	1	0	0	0	0	1	0	0	0	14628	159	6	4	579	4	SLC39A10	2	196545343	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	452	196545343	46654030	39	10793										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207169971	207169971	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggcctctagaaatcctgtgcCatcatcccatgtagaaacta	7	12	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:207169971C>G	ENST00000374423.3	+	5	1105	c.719C>G	c.(718-720)cCa>cGa	p.P240R		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	240							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AATCCTGTGCCATCATCCCAT	0.378																																					p.P240R		Atlas-SNP	.											.	ZDBF2	531	.	0			c.C719G						.						37	37	37					2																	207169971		1844	4089	5933	SO:0001583	missense	57683	exon5			CTGTGCCATCATC	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.719C>G	chr2.hg19:g.207169971C>G	ENSP00000363545:p.Pro240Arg	247.0	0.0		248.0	65.0	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.773495	0.31411	.	.	ENSG00000204186	ENST00000374423	T	0.16597	2.33	5.11	1.97	0.26223	.	1.790210	0.03932	N	0.285394	T	0.13756	0.0333	N	0.22421	0.69	0.09310	N	1	P	0.45902	0.868	B	0.40329	0.326	T	0.27123	-1.0083	10	0.48119	T	0.1	.	7.5635	0.27866	0.0:0.575:0.0:0.425	.	240	Q9HCK1	ZDBF2_HUMAN	R	240	ENSP00000363545:P240R	ENSP00000363545:P240R	P	+	2	0	ZDBF2	206878216	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.070000	0.11523	0.078000	0.16900	-0.157000	0.13467	CCA	.	.		0.378	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		G	207169971	C	G	207169971	3	3	79	1	0	0	0	0	1	0	0	0	17614	594	21	4	729	4	ZDBF2	2	207169971	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	10624628	207169971	36029402	40	10794										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222308221	222308221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tcagacacttaccaactcctAtaactttttcaatcttaatg	2	11	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr2:222308221A>G	ENST00000281821.2	-	10	1921	c.1880T>C	c.(1879-1881)aTa>aCa	p.I627T	EPHA4_ENST00000409938.1_Missense_Mutation_p.I627T|EPHA4_ENST00000409854.1_Missense_Mutation_p.I627T|EPHA4_ENST00000392071.4_Missense_Mutation_p.I576T	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	627	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		ACCAACTCCTATAACTTTTTC	0.398																																					p.I627T		Atlas-SNP	.											.	EPHA4	263	.	0			c.T1880C						.						142	127	132					2																	222308221		2203	4300	6503	SO:0001583	missense	2043	exon10			ACTCCTATAACTT	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.1880T>C	chr2.hg19:g.222308221A>G	ENSP00000281821:p.Ile627Thr	159.0	0.0		147.0	29.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.706095	0.89018	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071	T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47	5.96	5.96	0.96718	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.89406	0.6706	H	0.96208	3.785	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.92601	0.6091	10	0.87932	D	0	.	16.4484	0.83959	1.0:0.0:0.0:0.0	.	627	P54764	EPHA4_HUMAN	T	627;627;627;576	ENSP00000281821:I627T;ENSP00000386276:I627T;ENSP00000386829:I627T;ENSP00000375923:I576T	ENSP00000281821:I627T	I	-	2	0	EPHA4	222016465	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.285000	0.76669	0.533000	0.62120	ATA	.	.		0.398	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			G	222308221	A	G	222308221	3	3	79	1	0	0	0	0	1	0	0	0	5171	449	16	2	1112	2	EPHA4	2	222308221	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	15138250	222308221	20891152	41	10795										
SETD5	55209	hgsc.bcm.edu	37	chr3	9485064	9485064	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctgccatcaccaaggatgctGaggtcaccatagcatttgat	9	11	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:9485064G>A	ENST00000406341.1	+	10	1340	c.1150G>A	c.(1150-1152)Gag>Aag	p.E384K	SETD5_ENST00000402198.1_Missense_Mutation_p.E384K|SETD5_ENST00000402466.1_Missense_Mutation_p.E286K|SETD5_ENST00000407969.1_Missense_Mutation_p.E403K|SETD5_ENST00000302463.6_Missense_Mutation_p.E286K			Q9C0A6	SETD5_HUMAN	SET domain containing 5	384	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.									NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		CAAGGATGCTGAGGTCACCAT	0.423																																					p.E384K		Atlas-SNP	.											.	SETD5	210	.	0			c.G1150A						.						62	62	62					3																	9485064		1953	4135	6088	SO:0001583	missense	55209	exon11			GATGCTGAGGTCA	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.1150G>A	chr3.hg19:g.9485064G>A	ENSP00000383939:p.Glu384Lys	56.0	0.0		74.0	25.0	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	hg19	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	G	37	6.132865	0.97310	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	D;D;D;D;D	0.94723	-3.5;-3.5;-3.5;-3.5;-3.5	6.03	6.03	0.97812	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.97782	0.9272	M	0.87328	2.875	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;1.0	D;D;D;D;D	0.97110	0.998;0.998;0.997;0.995;1.0	D	0.97818	1.0255	10	0.87932	D	0	-5.0038	20.5568	0.99304	0.0:0.0:1.0:0.0	.	53;286;286;384;403	B3KXG4;B3KRD6;Q9C0A6-3;Q9C0A6;E7EWN3	.;.;.;SETD5_HUMAN;.	K	384;286;384;403;286	ENSP00000385852:E384K;ENSP00000384429:E286K;ENSP00000383939:E384K;ENSP00000384114:E403K;ENSP00000302028:E286K	ENSP00000302028:E286K	E	+	1	0	SETD5	9460064	1.000000	0.71417	0.990000	0.47175	0.999000	0.98932	9.869000	0.99810	2.861000	0.98227	0.655000	0.94253	GAG	.	.		0.423	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		A	9485064	G	A	9485064	3	1	79	1	0	0	0	0	1	0	0	0	14149	1291	45	3	1184	3	SETD5	3	9485064	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10		9485064	188537366	42	10796										
SCN5A	6331	hgsc.bcm.edu	37	chr3	38616808	38616808	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cagcgctccactgctgagtaGgatcatgaagatgatgaatg	12	8	1	5			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:38616808G>A	ENST00000333535.4	-	20	3795	c.3646C>T	c.(3646-3648)Cta>Tta	p.L1216L	SCN5A_ENST00000425664.1_Silent_p.L1216L|SCN5A_ENST00000423572.2_Silent_p.L1215L|SCN5A_ENST00000414099.2_Silent_p.L1216L|SCN5A_ENST00000455624.2_Silent_p.L1215L|SCN5A_ENST00000443581.1_Silent_p.L1215L|SCN5A_ENST00000450102.2_Silent_p.L1162L|SCN5A_ENST00000451551.2_Silent_p.L1162L|SCN5A_ENST00000413689.1_Silent_p.L1216L|SCN5A_ENST00000449557.2_Silent_p.L1162L			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1216					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CTGCTGAGTAGGATCATGAAG	0.617																																					p.L1216L		Atlas-SNP	.											.	SCN5A	634	.	0			c.C3646T						.						46	48	47					3																	38616808		2203	4300	6503	SO:0001819	synonymous_variant	6331	exon20			TGAGTAGGATCAT	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.3646C>T	chr3.hg19:g.38616808G>A		98.0	0.0		87.0	23.0	NM_198056	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	hg19	CCDS46796.1																																																																																			.	.		0.617	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		A	38616808	G	A	38616808	2	1	79	1	0	0	0	0	0	0	0	1	13937	991	35	3		3	SCN5A	3	38616808	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	29131744	38616808	159405622	43	10797										
BSN	8927	hgsc.bcm.edu	37	chr3	49691918	49691918	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gctgagaacatctccctgtgCcggatctcctctgtccctgg	10	15	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:49691918C>T	ENST00000296452.4	+	5	5043	c.4929C>T	c.(4927-4929)tgC>tgT	p.C1643C		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1643					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		TCTCCCTGTGCCGGATCTCCT	0.647																																					p.C1643C		Atlas-SNP	.											.	BSN	272	.	0			c.C4929T						.						49	47	48					3																	49691918		2203	4300	6503	SO:0001819	synonymous_variant	8927	exon5			CCTGTGCCGGATC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.4929C>T	chr3.hg19:g.49691918C>T		56.0	0.0		42.0	11.0	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	hg19	CCDS2800.1																																																																																			.	.		0.647	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		T	49691918	C	T	49691918	2	4	79	1	0	0	0	0	0	0	0	1	1532	747	26	3		3	BSN	3	49691918	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	11075110	49691918	148330512	44	10798										
BSN	8927	hgsc.bcm.edu	37	chr3	49692087	49692087	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cgaggaagtatggtcttgccCtggatccaatcccaggacgg	13	11	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:49692087C>G	ENST00000296452.4	+	5	5212	c.5098C>G	c.(5098-5100)Ctg>Gtg	p.L1700V		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1700					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		TGGTCTTGCCCTGGATCCAAT	0.582																																					p.L1700V		Atlas-SNP	.											.	BSN	272	.	0			c.C5098G						.						111	103	106					3																	49692087		2203	4300	6503	SO:0001583	missense	8927	exon5			CTTGCCCTGGATC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.5098C>G	chr3.hg19:g.49692087C>G	ENSP00000296452:p.Leu1700Val	49.0	0.0		59.0	14.0	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	hg19	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	8.005	0.756301	0.15846	.	.	ENSG00000164061	ENST00000296452	T	0.18960	2.18	5.16	-2.04	0.07343	.	0.454750	0.21838	N	0.068378	T	0.11324	0.0276	L	0.43152	1.355	0.26432	N	0.975925	P	0.48407	0.91	B	0.39217	0.294	T	0.40979	-0.9534	10	0.12766	T	0.61	.	6.0504	0.19783	0.2033:0.2652:0.0:0.5315	.	1700	Q9UPA5	BSN_HUMAN	V	1700	ENSP00000296452:L1700V	ENSP00000296452:L1700V	L	+	1	2	BSN	49667091	0.000000	0.05858	0.951000	0.38953	0.792000	0.44763	-1.386000	0.02537	-0.305000	0.08831	-1.193000	0.01689	CTG	.	.		0.582	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		G	49692087	C	G	49692087	3	3	79	1	0	0	0	0	1	0	0	0	1532	680	24	4	5116	4	BSN	3	49692087	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	169	49692087	148330343	45	10799										
NEK4	6787	hgsc.bcm.edu	37	chr3	52786310	52786310	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggcaggtgacttcaagagacCagaggccctgggtttctcct	13	11	2	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:52786310C>A	ENST00000233027.5	-	7	1208	c.1006G>T	c.(1006-1008)Ggt>Tgt	p.G336C	NEK4_ENST00000383721.4_Missense_Mutation_p.G336C|NEK4_ENST00000535191.1_Missense_Mutation_p.G247C	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	336					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		TTCAAGAGACCAGAGGCCCTG	0.423																																					p.G336C		Atlas-SNP	.											.	NEK4	51	.	0			c.G1006T						.						92	101	98					3																	52786310		2203	4300	6503	SO:0001583	missense	6787	exon7			AGAGACCAGAGGC	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"serine/threonine protein kinase-2"	601959	"serine/threonine kinase 2", "NIMA (never in mitosis gene a)-related kinase 4"	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.1006G>T	chr3.hg19:g.52786310C>A	ENSP00000233027:p.Gly336Cys	131.0	0.0		125.0	30.0	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	hg19	CCDS2863.1	.	.	.	.	.	.	.	.	.	.	C	2.022	-0.424554	0.04734	.	.	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;T;T	0.73152	-0.63;-0.72;-0.64;-0.72	4.64	-0.731	0.11151	.	0.905827	0.09484	N	0.795977	T	0.54515	0.1863	L	0.45137	1.4	0.09310	N	0.999999	B;B;B	0.20368	0.044;0.001;0.001	B;B;B	0.16722	0.016;0.004;0.004	T	0.45891	-0.9230	10	0.42905	T	0.14	.	0.4339	0.00475	0.2258:0.3307:0.143:0.3005	.	247;336;336	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	C	336;247;336;247	ENSP00000233027:G336C;ENSP00000437703:G247C;ENSP00000373227:G336C;ENSP00000419666:G247C	ENSP00000233027:G336C	G	-	1	0	NEK4	52761350	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.001000	0.13038	0.153000	0.19213	-0.339000	0.08088	GGT	.	.		0.423	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157		A	52786310	C	A	52786310	3	1	79	1	0	0	0	0	1	0	0	0	10335	594	21	3	1559	3	NEK4	3	52786310	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	3094223	52786310	145236120	46	10800										
FEZF2	55079	hgsc.bcm.edu	37	chr3	62358201	62358201	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcacactggggcccccccgcCgccgccgccgccaccgccgc	12	25	0	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:62358201C>G	ENST00000283268.3	-	2	637	c.343G>C	c.(343-345)Ggc>Cgc	p.G115R	FEZF2_ENST00000475839.1_Missense_Mutation_p.G115R|FEZF2_ENST00000486811.1_Missense_Mutation_p.G115R	NM_018008.3	NP_060478.3	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2	115	Gly-rich.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cerebral cortex GABAergic interneuron migration (GO:0021853)|dendrite development (GO:0016358)|dentate gyrus development (GO:0021542)|forebrain anterior/posterior pattern specification (GO:0021797)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|lung(8)|skin(1)	20		Lung SC(41;0.0262)		BRCA - Breast invasive adenocarcinoma(55;0.000221)|KIRC - Kidney renal clear cell carcinoma(15;0.00834)|Kidney(15;0.00957)		GCCCCCccgccgccgccgccg	0.746																																					p.G115R	NSCLC(170;1772 2053 12525 15604 23984)	Atlas-SNP	.											.	FEZF2	46	.	0			c.G343C						.						1	2	2					3																	62358201		606	1706	2312	SO:0001583	missense	55079	exon2			CCCCGCCGCCGCC	AF064845	CCDS2897.1	3p21.1	2013-01-08	2006-08-15	2006-08-15	ENSG00000153266	ENSG00000153266		"Zinc fingers, C2H2-type"	13506	protein-coding gene	gene with protein product		607414	"zinc finger protein 312"	ZNF312			Standard	NM_018008		Approved	FLJ10142, FKSG36, TOF, FEZL, Zfp312	uc003dli.2	Q8TBJ5	OTTHUMG00000158705	ENST00000283268.3:c.343G>C	chr3.hg19:g.62358201C>G	ENSP00000283268:p.Gly115Arg	22.0	0.0		19.0	4.0	NM_018008	A8K349|Q9BZ91|Q9NWB9	Missense_Mutation	SNP	ENST00000283268.3	hg19	CCDS2897.1	.	.	.	.	.	.	.	.	.	.	C	9.951	1.220055	0.22373	.	.	ENSG00000153266	ENST00000486811;ENST00000283268;ENST00000475839	D;D;D	0.86627	-2.15;-2.15;-2.15	3.21	1.28	0.21552	.	0.250031	0.27966	N	0.017125	T	0.68531	0.3011	N	0.22421	0.69	0.22866	N	0.99864	P	0.43826	0.818	B	0.30495	0.116	T	0.61926	-0.6962	10	0.30078	T	0.28	-11.9517	5.1556	0.15032	0.0:0.7207:0.0:0.2793	.	115	Q8TBJ5	FEZF2_HUMAN	R	115	ENSP00000418589:G115R;ENSP00000283268:G115R;ENSP00000418804:G115R	ENSP00000283268:G115R	G	-	1	0	FEZF2	62333241	0.937000	0.31787	1.000000	0.80357	0.954000	0.61252	0.000000	0.12993	1.414000	0.47017	0.289000	0.19496	GGC	.	.		0.746	FEZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351813.1	NM_018008		G	62358201	C	G	62358201	3	3	79	1	0	0	0	0	1	0	0	0	5834	652	23	4	1052	4	FEZF2	3	62358201	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	9571891	62358201	135664229	47	10801										
MAGI1	9223	hgsc.bcm.edu	37	chr3	65365036	65365036	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tccacgtcgtagggctgcacCacggtgctgaccacgccgct	12	16	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:65365036C>T	ENST00000497477.2	-	17	2894	c.2895G>A	c.(2893-2895)gtG>gtA	p.V965V	MAGI1_ENST00000330909.8_Silent_p.V993V|MAGI1_ENST00000402939.2_Silent_p.V965V|MAGI1_ENST00000483466.1_Silent_p.V993V			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	993					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		AGGGCTGCACCACGGTGCTGA	0.697																																					p.V993V		Atlas-SNP	.											.	MAGI1	481	.	0			c.G2979A						.						36	31	32					3																	65365036		2202	4299	6501	SO:0001819	synonymous_variant	9223	exon18			CTGCACCACGGTG	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.2895G>A	chr3.hg19:g.65365036C>T		88.0	0.0		89.0	23.0	NM_015520	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	hg19		.	.	.	.	.	.	.	.	.	.	C	8.800	0.932657	0.18131	.	.	ENSG00000151276	ENST00000460329	.	.	.	5.33	-1.69	0.08186	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999993	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.0203	4.4422	0.11579	0.1144:0.4208:0.334:0.1307	.	.	.	.	X	874	.	.	W	-	2	0	MAGI1	65340076	0.250000	0.23951	0.051000	0.19133	0.713000	0.41058	0.020000	0.13466	-0.042000	0.13535	0.460000	0.39030	TGG	.	.		0.697	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		T	65365036	C	T	65365036	2	4	79	1	0	0	0	0	0	0	0	1	9199	581	21	3		3	MAGI1	3	65365036	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	3006835	65365036	132657394	48	10802										
EPHA6	285220	hgsc.bcm.edu	37	chr3	97251373	97251374	+	Missense_Mutation	DNP	GG	GG	CT													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	aaacatcattcgcctagaagGggttgtcaccaaaagtaagt					rs369130484		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:97251373_97251374GG>CT	ENST00000514100.1	+	8	790_791	c.548_549GG>CT	c.(547-549)gGG>gCT	p.G183A	EPHA6_ENST00000442602.2_Missense_Mutation_p.G157A|EPHA6_ENST00000389672.5_Missense_Mutation_p.G791A|EPHA6_ENST00000502694.1_Missense_Mutation_p.G183A	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	697	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						CGCCTAGAAGGGGTTGTCACCA	0.371																																					p.G791A|p.G791G		Atlas-SNP	.											.	EPHA6	439	.	0			c.G2372C|c.G2373T						.																																			SO:0001583	missense	285220	exon11			TAGAAGGGGTTGT|AGAAGGGGTTGTC	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	Exception_encountered	chr3.hg19:g.97251373_97251374delinsCT	ENSP00000421711:p.Gly183Ala	165.0	0.0		146.0|147.0	37.0	NM_001080448	D6RAL5	Missense_Mutation|Silent	SNP	ENST00000514100.1	hg19																																																																																				.	.		0.371	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448		CT	97251374	GG	CT	97251373	3	2	79	1	0	0	0	0	1	0	0	0	5173	1232	43	4	2482	4	EPHA6	3	97251373	Missense_Mutation	DNP	GG	TCGA-CC-A8HT-01A-11D-A35Z-10	31886337	97251373	100771057	49	10803										
OR5K2	402135	hgsc.bcm.edu	37	chr3	98216699	98216699	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	actgtcggcttcacacaccaAtgtacatctttctgggaaat	7	11	3	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:98216699A>T	ENST00000427338.1	+	1	252	c.175A>T	c.(175-177)Atg>Ttg	p.M59L		NM_001004737.1	NP_001004737.1	Q8NHB8	OR5K2_HUMAN	olfactory receptor, family 5, subfamily K, member 2	59						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCACACACCAATGTACATCTT	0.443																																					p.M59L		Atlas-SNP	.											.	OR5K2	56	.	0			c.A175T						.						228	234	232					3																	98216699		2203	4300	6503	SO:0001583	missense	402135	exon1			ACACCAATGTACA	AC021660	CCDS33804.1	3q11.2	2013-09-23			ENSG00000231861	ENSG00000231861		"GPCR / Class A : Olfactory receptors"	14774	protein-coding gene	gene with protein product							Standard	NM_001004737		Approved		uc011bgx.2	Q8NHB8	OTTHUMG00000160049	ENST00000427338.1:c.175A>T	chr3.hg19:g.98216699A>T	ENSP00000393889:p.Met59Leu	130.0	0.0		131.0	41.0	NM_001004737	B2RN70|Q6IF47	Missense_Mutation	SNP	ENST00000427338.1	hg19	CCDS33804.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.882331	0.33255	.	.	ENSG00000231861	ENST00000427338	T	0.08458	3.09	2.91	2.91	0.33838	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000076	T	0.17152	0.0412	M	0.92367	3.3	0.26165	N	0.979947	B	0.28636	0.218	B	0.28385	0.089	T	0.14783	-1.0460	10	0.87932	D	0	-19.3782	9.6296	0.39772	1.0:0.0:0.0:0.0	.	59	Q8NHB8	OR5K2_HUMAN	L	59	ENSP00000393889:M59L	ENSP00000393889:M59L	M	+	1	0	OR5K2	99699389	0.998000	0.40836	0.991000	0.47740	0.672000	0.39443	3.834000	0.55798	1.580000	0.49851	0.248000	0.18094	ATG	.	.		0.443	OR5K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359020.2			T	98216699	A	T	98216699	3	4	79	1	0	0	0	0	1	0	0	0	11176	101	4	4	177	4	OR5K2	3	98216699	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	965326	98216699	99805731	50	10804										
ABI3BP	25890	hgsc.bcm.edu	37	chr3	100513777	100513777	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cgaaatttacccagagtggtCtgtagttcctcttgactagg	10	9	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:100513777C>A	ENST00000284322.5	-	22	1987	c.1878G>T	c.(1876-1878)caG>caT	p.Q626H	ABI3BP_ENST00000383691.4_Missense_Mutation_p.Q580H|ABI3BP_ENST00000471714.1_Missense_Mutation_p.Q1303H	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	626	Pro-rich.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						CCAGAGTGGTCTGTAGTTCCT	0.378																																					p.Q626H		Atlas-SNP	.											.	ABI3BP	305	.	0			c.G1878T						.						52	49	50					3																	100513777		1805	4065	5870	SO:0001583	missense	25890	exon22			AGTGGTCTGTAGT	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"Fibronectin type III domain containing"	17265	protein-coding gene	gene with protein product	"target of Nesh-SH3"	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.1878G>T	chr3.hg19:g.100513777C>A	ENSP00000284322:p.Gln626His	298.0	0.0		264.0	71.0	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	hg19	CCDS46880.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	13.39|13.39|13.39	2.222393|2.222393|2.222393	0.39300|0.39300|0.39300	.|.|.	.|.|.	ENSG00000154175|ENSG00000154175|ENSG00000154175	ENST00000497395;ENST00000466947|ENST00000471714;ENST00000284322;ENST00000383692;ENST00000429331;ENST00000383691;ENST00000486770;ENST00000482765|ENST00000495591;ENST00000471901;ENST00000527943;ENST00000478235	.|T;T;T|.	.|0.59083|.	.|2.13;0.29;1.78|.	5.82|5.82|5.82	0.77|0.77|0.77	0.18497|0.18497|0.18497	.|.|.	.|0.803834|.	.|0.11767|.	.|N|.	.|0.531490|.	T|T|T	0.36524|0.36524|0.36524	0.0970|0.0970|0.0970	L|L|L	0.43152|0.43152|0.43152	1.355|1.355|1.355	0.09310|0.09310|0.09310	N|N|N	1|1|1	.|D;P;D;D|.	.|0.69078|.	.|0.997;0.77;0.997;0.994|.	.|P;B;P;P|.	.|0.62014|.	.|0.854;0.423;0.897;0.784|.	T|T|T	0.28170|0.28170|0.28170	-1.0052|-1.0052|-1.0052	5|10|5	.|0.46703|.	.|T|.	.|0.11|.	-1.2595|-1.2595|-1.2595	7.8465|7.8465|7.8465	0.29428|0.29428|0.29428	0.0:0.3522:0.0:0.6478|0.0:0.3522:0.0:0.6478|0.0:0.3522:0.0:0.6478	.|.|.	.|580;626;1303;310|.	.|B4DSV9;Q7Z7G0;D3YTG3;D3YTD6|.	.|.;TARSH_HUMAN;.;.|.	Y|H|I	42;184|1303;626;310;12;580;64;155|682;206;148;184	.|ENSP00000420524:Q1303H;ENSP00000284322:Q626H;ENSP00000373189:Q580H|.	.|ENSP00000284322:Q626H|.	D|Q|R	-|-|-	1|3|2	0|2|0	ABI3BP|ABI3BP|ABI3BP	101996467|101996467|101996467	0.684000|0.684000|0.684000	0.27642|0.27642|0.27642	0.041000|0.041000|0.041000	0.18516|0.18516|0.18516	0.577000|0.577000|0.577000	0.36160|0.36160|0.36160	-0.048000|-0.048000|-0.048000	0.11944|0.11944|0.11944	-0.086000|-0.086000|-0.086000	0.12550|0.12550|0.12550	-0.302000|-0.302000|-0.302000	0.09304|0.09304|0.09304	GAC|CAG|AGA	.	.		0.378	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			A	100513777	C	A	100513777	3	1	79	1	0	0	0	0	1	0	0	0	91	912	32	3	1405	3	ABI3BP	3	100513777	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	2297078	100513777	97508653	51	10805										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113378345	113378345	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcaggctggctaatagacaaTtgtacacagctttgcccagc	10	11	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:113378345T>C	ENST00000478658.1	-	5	2201	c.2184A>G	c.(2182-2184)caA>caG	p.Q728Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q728Q			Q68DE3	K2018_HUMAN	KIAA2018	728						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						TAATAGACAATTGTACACAGC	0.448																																					p.Q728Q		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A2184G						.						55	54	54					3																	113378345		1910	4129	6039	SO:0001819	synonymous_variant	205717	exon7			AGACAATTGTACA	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.2184A>G	chr3.hg19:g.113378345T>C		111.0	0.0		113.0	28.0	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.		0.448	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		C	113378345	T	C	113378345	2	2	79	1	0	0	0	0	0	0	0	1	8277	1490	52	2		2	KIAA2018	3	113378345	Silent	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	12864568	113378345	84644085	52	10806										
ACPP	55	hgsc.bcm.edu	37	chr3	132061418	132061418	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttttatagctaccttgggaaAactttcaggattacatggcc	8	8	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:132061418A>G	ENST00000336375.5	+	6	668	c.578A>G	c.(577-579)aAa>aGa	p.K193R	ACPP_ENST00000475741.1_Missense_Mutation_p.K160R|ACPP_ENST00000351273.7_Missense_Mutation_p.K193R	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	193					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						ACCTTGGGAAAACTTTCAGGA	0.358																																					p.K193R		Atlas-SNP	.											.	ACPP	118	.	0			c.A578G						.						123	130	128					3																	132061418		2203	4300	6503	SO:0001583	missense	55	exon6			TGGGAAAACTTTC		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.578A>G	chr3.hg19:g.132061418A>G	ENSP00000337471:p.Lys193Arg	82.0	0.0		67.0	18.0	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Missense_Mutation	SNP	ENST00000336375.5	hg19	CCDS3073.1	.	.	.	.	.	.	.	.	.	.	A	14.53	2.561473	0.45590	.	.	ENSG00000014257	ENST00000336375;ENST00000495911;ENST00000475741;ENST00000351273	T;T;T;T	0.23950	2.19;1.88;2.19;2.19	6.08	-0.583	0.11706	.	1.022660	0.07743	N	0.947279	T	0.28896	0.0717	L	0.40543	1.245	0.21604	N	0.999622	B;B;P	0.39920	0.176;0.146;0.695	B;B;B	0.43274	0.064;0.038;0.414	T	0.44498	-0.9324	10	0.45353	T	0.12	.	16.0565	0.80809	0.3:0.7:0.0:0.0	.	193;193;160	P15309;P15309-2;Q5FBY0	PPAP_HUMAN;.;.	R	193;164;160;193	ENSP00000337471:K193R;ENSP00000418366:K164R;ENSP00000417744:K160R;ENSP00000323036:K193R	ENSP00000337471:K193R	K	+	2	0	ACPP	133544108	0.048000	0.20356	0.799000	0.32177	0.959000	0.62525	0.113000	0.15499	-0.027000	0.13873	0.482000	0.46254	AAA	.	.		0.358	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099		G	132061418	A	G	132061418	3	3	79	1	0	0	0	0	1	0	0	0	167	14	1	2	600	2	ACPP	3	132061418	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	18683073	132061418	65961012	53	10807										
NCK1	4690	hgsc.bcm.edu	37	chr3	136664512	136664512	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgacccaggggaacgtctctAtgacctcaacatgcccgctt	9	14	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:136664512A>G	ENST00000481752.1	+	3	478	c.314A>G	c.(313-315)tAt>tGt	p.Y105C	NCK1_ENST00000288986.2_Missense_Mutation_p.Y105C|NCK1_ENST00000469404.1_Missense_Mutation_p.Y41C			P16333	NCK1_HUMAN	NCK adaptor protein 1	105					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of translation (GO:0006417)|response to other organism (GO:0051707)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|protein kinase inhibitor activity (GO:0004860)|receptor binding (GO:0005102)|receptor signaling complex scaffold activity (GO:0030159)|receptor tyrosine kinase binding (GO:0030971)			cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	13						GAACGTCTCTATGACCTCAAC	0.413																																					p.Y105C		Atlas-SNP	.											.	NCK1	26	.	0			c.A314G						.						125	126	126					3																	136664512		2203	4300	6503	SO:0001583	missense	4690	exon3			GTCTCTATGACCT	X17576	CCDS3092.1, CCDS54644.1	3q21	2013-02-14			ENSG00000158092	ENSG00000158092		"SH2 domain containing"	7664	protein-coding gene	gene with protein product		600508		NCK		7806213, 9737977	Standard	XM_005247498		Approved	NCKalpha	uc003erh.3	P16333	OTTHUMG00000159781	ENST00000481752.1:c.314A>G	chr3.hg19:g.136664512A>G	ENSP00000417273:p.Tyr105Cys	217.0	0.0		183.0	55.0	NM_006153	B7Z751|D3DNE3	Missense_Mutation	SNP	ENST00000481752.1	hg19	CCDS3092.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.41|19.41	3.821736|3.821736	0.71028|0.71028	.|.	.|.	ENSG00000158092|ENSG00000158092	ENST00000496489|ENST00000288986;ENST00000481752;ENST00000491539;ENST00000485096;ENST00000488930;ENST00000469404;ENST00000467911	.|T;T;T;T;T;T;T	.|0.69306	.|-0.32;-0.32;1.39;0.78;2.29;-0.39;2.29	6.16|6.16	6.16|6.16	0.99307|0.99307	.|Src homology-3 domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.76593|0.76593	0.4009|0.4009	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	.|D;D	.|0.62365	.|0.975;0.991	.|P;P	.|0.57776	.|0.67;0.827	T|T	0.76242|0.76242	-0.3031|-0.3031	5|10	.|0.40728	.|T	.|0.16	-11.1531|-11.1531	14.7581|14.7581	0.69583|0.69583	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|41;105	.|B7Z751;P16333	.|.;NCK1_HUMAN	V|C	93|105;105;105;105;105;41;41	.|ENSP00000288986:Y105C;ENSP00000417273:Y105C;ENSP00000419302:Y105C;ENSP00000419677:Y105C;ENSP00000417729:Y105C;ENSP00000419631:Y41C;ENSP00000418060:Y41C	.|ENSP00000288986:Y105C	M|Y	+|+	1|2	0|0	NCK1|NCK1	138147202|138147202	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	8.859000|8.859000	0.92264|0.92264	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	ATG|TAT	.	.		0.413	NCK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357307.1	NM_006153		G	136664512	A	G	136664512	3	3	79	1	0	0	0	0	1	0	0	0	10228	449	16	2	320	2	NCK1	3	136664512	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	4603094	136664512	61357918	54	10808										
ZBBX	79740	hgsc.bcm.edu	37	chr3	167083713	167083713	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttttgtgacatcatatatgaTtgattgaccaatttgcccac	6	8	1	4			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:167083713T>C	ENST00000392766.2	-	6	574	c.234A>G	c.(232-234)caA>caG	p.Q78Q	ZBBX_ENST00000392767.2_Silent_p.Q78Q|ZBBX_ENST00000307529.5_Silent_p.Q78Q|ZBBX_ENST00000455345.2_Silent_p.Q78Q|ZBBX_ENST00000392764.1_Silent_p.Q49Q|ZBBX_ENST00000469220.1_Intron	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	78						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						TCATATATGATTGATTGACCA	0.289																																					p.Q78Q		Atlas-SNP	.											.	ZBBX	299	.	0			c.A234G						.						117	109	112					3																	167083713		1824	4071	5895	SO:0001819	synonymous_variant	79740	exon6			ATATGATTGATTG	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.234A>G	chr3.hg19:g.167083713T>C		350.0	0.0		362.0	96.0	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	hg19	CCDS3199.2																																																																																			.	.		0.289	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		C	167083713	T	C	167083713	2	2	79	1	0	0	0	0	0	0	0	1	17531	1490	52	2		2	ZBBX	3	167083713	Silent	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	30419201	167083713	30938717	55	10809										
LRRC31	79782	hgsc.bcm.edu	37	chr3	169574626	169574626	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctgttccaagacaaatttagCtcttcaagttcaggaatcat	6	9	4	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:169574626C>T	ENST00000316428.5	-	4	579	c.522G>A	c.(520-522)gaG>gaA	p.E174E	LRRC31_ENST00000397805.2_5'UTR|LRRC31_ENST00000523069.1_Silent_p.E174E|LRRC31_ENST00000264676.5_Silent_p.E118E	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	174										cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			ACAAATTTAGCTCTTCAAGTT	0.393																																					p.Q174Q		Atlas-SNP	.											.	LRRC31	66	.	0			c.A522A						.						143	130	134					3																	169574626		1843	4096	5939	SO:0001819	synonymous_variant	79782	exon4			ATTTAGCTCTTCA	AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.522G>A	chr3.hg19:g.169574626C>T		78.0	0.0		55.0	12.0	NM_024727	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Silent	SNP	ENST00000316428.5	hg19	CCDS43167.1																																																																																			.	.		0.393	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727		T	169574626	C	T	169574626	2	4	79	1	0	0	0	0	0	0	0	1	8995	796	28	3		3	LRRC31	3	169574626	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	2490913	169574626	28447804	56	10810										
SLC7A14	57709	hgsc.bcm.edu	37	chr3	170198647	170198647	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cacatgtgttggtggctgggCcagaaaactcatccccctca	10	13	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:170198647C>A	ENST00000231706.5	-	7	1739	c.1424G>T	c.(1423-1425)gGc>gTc	p.G475V	CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	475					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			GGTGGCTGGGCCAGAAAACTC	0.502																																					p.G475V		Atlas-SNP	.											SLC7A14,colon,carcinoma,0,1	SLC7A14	110	.	0			c.G1424T						.						150	150	150					3																	170198647		2203	4300	6503	SO:0001583	missense	57709	exon7			GCTGGGCCAGAAA	BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"Solute carriers"	29326	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 142"	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.1424G>T	chr3.hg19:g.170198647C>A	ENSP00000231706:p.Gly475Val	107.0	1.0		82.0	30.0	NM_020949	B3KV33|Q9HCF9	Missense_Mutation	SNP	ENST00000231706.5	hg19	CCDS33892.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.526503	0.44969	.	.	ENSG00000013293	ENST00000231706	D	0.87103	-2.21	5.03	5.03	0.67393	.	0.105272	0.64402	D	0.000003	D	0.91260	0.7245	L	0.51422	1.61	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.89380	0.3681	10	0.27785	T	0.31	.	18.3552	0.90355	0.0:1.0:0.0:0.0	.	475	Q8TBB6	S7A14_HUMAN	V	475	ENSP00000231706:G475V	ENSP00000231706:G475V	G	-	2	0	SLC7A14	171681341	1.000000	0.71417	0.968000	0.41197	0.362000	0.29581	7.178000	0.77657	2.337000	0.79520	0.655000	0.94253	GGC	.	.		0.502	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		A	170198647	C	A	170198647	3	1	79	1	0	0	0	0	1	0	0	0	14711	739	26	3	899	3	SLC7A14	3	170198647	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	624021	170198647	27823783	57	10811										
CLCN2	1181	hgsc.bcm.edu	37	chr3	184073263	184073263	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tagctcctccaccaggccctGgcggacccacgtccgattgt	10	17	0	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:184073263G>T	ENST00000265593.4	-	12	1396	c.1225C>A	c.(1225-1227)Cag>Aag	p.Q409K	CLCN2_ENST00000344937.7_Missense_Mutation_p.Q409K|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000423355.2_Missense_Mutation_p.Q50K|CLCN2_ENST00000457512.1_Missense_Mutation_p.Q409K|CLCN2_ENST00000475279.1_5'UTR|CLCN2_ENST00000434054.2_Missense_Mutation_p.Q365K	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	409					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	ACCAGGCCCTGGCGGACCCAC	0.577																																					p.Q409K		Atlas-SNP	.											.	CLCN2	74	.	0			c.C1225A						.						130	116	121					3																	184073263		2203	4300	6503	SO:0001583	missense	1181	exon12			GGCCCTGGCGGAC	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"Ion channels / Chloride channels : Voltage-sensitive"	2020	protein-coding gene	gene with protein product		600570	"chloride channel 2"			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.1225C>A	chr3.hg19:g.184073263G>T	ENSP00000265593:p.Gln409Lys	114.0	0.0		99.0	4.0	NM_001171087	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	ENST00000265593.4	hg19	CCDS3263.1	.	.	.	.	.	.	.	.	.	.	g	21.1	4.099745	0.76983	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000423355;ENST00000434054;ENST00000457512	D;D;T;D;D	0.84660	-1.83;-1.78;-0.33;-1.88;-1.86	5.6	5.6	0.85130	Chloride channel, core (2);	0.053535	0.85682	D	0.000000	D	0.82893	0.5136	N	0.21324	0.655	0.58432	D	0.999999	B;P;P;P;P	0.50066	0.03;0.931;0.536;0.835;0.863	B;P;B;B;P	0.52454	0.038;0.699;0.42;0.295;0.524	T	0.78370	-0.2230	10	0.11485	T	0.65	-21.8536	19.2283	0.93825	0.0:0.0:1.0:0.0	.	409;365;409;409;409	B4DYE3;E9PBD9;E9PCD2;P51788-3;P51788	.;.;.;.;CLCN2_HUMAN	K	409;409;50;365;409	ENSP00000265593:Q409K;ENSP00000345056:Q409K;ENSP00000412226:Q50K;ENSP00000400425:Q365K;ENSP00000391928:Q409K	ENSP00000265593:Q409K	Q	-	1	0	CLCN2	185555957	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	7.876000	0.87215	2.653000	0.90120	0.563000	0.77884	CAG	.	.		0.577	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			T	184073263	G	T	184073263	3	4	79	1	0	0	0	0	1	0	0	0	3465	1357	47	3	1523	3	CLCN2	3	184073263	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	13874616	184073263	13949167	58	10812										
ACAP2	23527	hgsc.bcm.edu	37	chr3	195101743	195101743	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cttactgacacttactgtgtGaaaatttatcatttcttgaa	5	7	2	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr3:195101743G>T	ENST00000326793.6	-	4	510	c.280C>A	c.(280-282)Cac>Aac	p.H94N		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	94	BAR.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						CTTACTGTGTGAAAATTTATC	0.294																																					p.H94N		Atlas-SNP	.											.	ACAP2	72	.	0			c.C280A						.						81	81	81					3																	195101743		2203	4300	6503	SO:0001583	missense	23527	exon4			CTGTGTGAAAATT		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.280C>A	chr3.hg19:g.195101743G>T	ENSP00000324287:p.His94Asn	508.0	1.0		497.0	124.0	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	hg19	CCDS33924.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.417707	0.83449	.	.	ENSG00000114331	ENST00000326793;ENST00000439666	T;T	0.04603	3.59;3.59	5.42	5.42	0.78866	.	0.138359	0.64402	D	0.000003	T	0.23649	0.0572	M	0.79805	2.47	0.80722	D	1	D;D	0.61080	0.989;0.984	D;P	0.72982	0.979;0.889	T	0.00313	-1.1825	10	0.72032	D	0.01	.	16.7133	0.85391	0.0:0.0:1.0:0.0	.	50;94	C9J8L1;Q15057	.;ACAP2_HUMAN	N	94;50	ENSP00000324287:H94N;ENSP00000411336:H50N	ENSP00000324287:H94N	H	-	1	0	ACAP2	196583032	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.963000	0.70372	2.533000	0.85409	0.561000	0.74099	CAC	.	.		0.294	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287		T	195101743	G	T	195101743	3	4	79	1	0	0	0	0	1	0	0	0	119	1290	45	3	2136	3	ACAP2	3	195101743	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	11028480	195101743	2920687	59	10813										
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8229789	8229789	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cgctgcgcggccccctctacAccagcttggcccagctgtac	10	19	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:8229789A>G	ENST00000245105.3	+	12	2435	c.2368A>G	c.(2368-2370)Acc>Gcc	p.T790A	SH3TC1_ENST00000539824.1_Missense_Mutation_p.T714A	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	790										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						CCCCCTCTACACCAGCTTGGC	0.682																																					p.T790A	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.A2368G						.						31	30	30					4																	8229789		2202	4299	6501	SO:0001583	missense	54436	exon12			CTCTACACCAGCT	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"Tetratricopeptide (TTC) repeat domain containing"	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.2368A>G	chr4.hg19:g.8229789A>G	ENSP00000245105:p.Thr790Ala	141.0	0.0		112.0	35.0	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	hg19	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	a	0.016	-1.538051	0.00942	.	.	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.63255	-0.03;-0.03	4.14	-0.0128	0.13987	Tetratricopeptide-like helical (1);	1.034550	0.07626	N	0.927881	T	0.21186	0.0510	N	0.00419	-1.52	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.21621	-1.0240	10	0.13470	T	0.59	-8.0674	1.6741	0.02818	0.1797:0.2463:0.3797:0.1943	.	790	Q8TE82	S3TC1_HUMAN	A	528;790;714;619	ENSP00000245105:T790A;ENSP00000441045:T714A	ENSP00000245105:T790A	T	+	1	0	SH3TC1	8280689	0.101000	0.21875	0.328000	0.25416	0.030000	0.12068	0.397000	0.20883	0.215000	0.20761	-0.400000	0.06385	ACC	.	.		0.682	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		G	8229789	A	G	8229789	3	3	79	1	0	0	0	0	1	0	0	0	14276	159	6	2	2410	2	SH3TC1	4	8229789	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10		8229789	182924487	60	10814										
HTRA3	94031	hgsc.bcm.edu	37	chr4	8293260	8293260	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gggcctccgggactccgacaTggactacatccagacggatg	13	13	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:8293260T>A	ENST00000307358.2	+	4	1076	c.872T>A	c.(871-873)aTg>aAg	p.M291K	HTRA3_ENST00000382512.3_Missense_Mutation_p.M291K	NM_053044.3	NP_444272.1	P83110	HTRA3_HUMAN	HtrA serine peptidase 3	291	Serine protease.				negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|prostate(1)|urinary_tract(1)	18						GACTCCGACATGGACTACATC	0.637																																					p.M291K		Atlas-SNP	.											.	HTRA3	39	.	0			c.T872A						.						35	31	32					4																	8293260		2202	4299	6501	SO:0001583	missense	94031	exon4			CCGACATGGACTA	AY040094	CCDS3400.1, CCDS75105.1	4p16.1	2008-02-05			ENSG00000170801	ENSG00000170801			30406	protein-coding gene	gene with protein product	"pregnancy-related serine protease"	608785				12513693, 14500695	Standard	XM_005248040		Approved	Tasp, Prsp	uc003gla.3	P83110	OTTHUMG00000090561	ENST00000307358.2:c.872T>A	chr4.hg19:g.8293260T>A	ENSP00000303766:p.Met291Lys	115.0	0.0		96.0	30.0	NM_053044	Q7Z7A2	Missense_Mutation	SNP	ENST00000307358.2	hg19	CCDS3400.1	.	.	.	.	.	.	.	.	.	.	t	19.88	3.909966	0.72983	.	.	ENSG00000170801	ENST00000307358;ENST00000382512	D;D	0.88664	-2.41;-2.41	4.08	4.08	0.47627	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.092720	0.64402	D	0.000001	D	0.88735	0.6517	N	0.13198	0.31	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.995;0.996	D	0.90434	0.4426	10	0.87932	D	0	-54.1374	13.0698	0.59055	0.0:0.0:0.0:1.0	.	291;291	P83110;P83110-2	HTRA3_HUMAN;.	K	291	ENSP00000303766:M291K;ENSP00000371952:M291K	ENSP00000303766:M291K	M	+	2	0	HTRA3	8344160	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	5.720000	0.68470	1.497000	0.48584	0.373000	0.22412	ATG	.	.		0.637	HTRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092669.1	NM_053044		A	8293260	T	A	8293260	3	1	79	1	0	0	0	0	1	0	0	0	7464	1464	51	4	886	4	HTRA3	4	8293260	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	63471	8293260	182861016	61	10815										
KIT	3815	hgsc.bcm.edu	37	chr4	55598097	55598097	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggatgacgagttggccctagActtagaagacttgctgagct	13	8	0	5			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:55598097A>G	ENST00000288135.5	+	16	2391	c.2294A>G	c.(2293-2295)gAc>gGc	p.D765G		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	765	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTGGCCCTAGACTTAGAAGAC	0.458		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.D765G		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT	7396	.	0			c.A2294G						.						120	101	107					4																	55598097		2203	4299	6502	SO:0001583	missense	3815	exon16	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	CCCTAGACTTAGA	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2294A>G	chr4.hg19:g.55598097A>G	ENSP00000288135:p.Asp765Gly	95.0	0.0		130.0	22.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	18.64	3.667928	0.67814	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.89746	-2.56;-2.56	5.96	5.96	0.96718	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.084488	0.50627	D	0.000116	D	0.90195	0.6935	N	0.25485	0.75	0.80722	D	1	P;D	0.54772	0.929;0.968	P;P	0.61940	0.644;0.896	D	0.91544	0.5252	10	0.72032	D	0.01	.	16.4484	0.83959	1.0:0.0:0.0:0.0	.	761;765	P10721-2;P10721	.;KIT_HUMAN	G	765;761	ENSP00000288135:D765G;ENSP00000390987:D761G	ENSP00000288135:D765G	D	+	2	0	KIT	55292854	1.000000	0.71417	0.990000	0.47175	0.070000	0.16714	9.190000	0.94934	2.285000	0.76669	0.533000	0.62120	GAC	.	.		0.458	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55598097	A	G	55598097	3	3	79	1	0	0	0	0	1	0	0	0	8338	275	10	2	2356	2	KIT	4	55598097	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	47304837	55598097	135556179	62	10816										
CSN1S1	1446	hgsc.bcm.edu	37	chr4	70810724	70810724	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	acgtcatgctacagtggtggTaagttcatttaaattactac	8	7	2	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:70810724T>C	ENST00000246891.4	+	15	606		c.e15+2		CSN1S1_ENST00000507763.1_Splice_Site|CSN1S1_ENST00000505782.1_Splice_Site|CSN1S1_ENST00000444405.3_Splice_Site|CSN1S1_ENST00000507772.1_Splice_Site	NM_001890.1	NP_001881.1	P47710	CASA1_HUMAN	casein alpha s1							extracellular region (GO:0005576)|extracellular space (GO:0005615)	transporter activity (GO:0005215)			lung(5)|prostate(1)|upper_aerodigestive_tract(1)	7						ACAGTGGTGGTAAGTTCATTT	0.358																																					.		Atlas-SNP	.											.	CSN1S1	20	.	0			c.530+2T>C						.						110	103	105					4																	70810724		1856	4099	5955	SO:0001630	splice_region_variant	1446	exon14			TGGTGGTAAGTTC	X78416	CCDS47067.1, CCDS54769.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000126545	ENSG00000126545			2445	protein-coding gene	gene with protein product		115450	"casein, alpha"	CASA, CSN1		9050925, 7619062	Standard	NM_001890		Approved		uc003hep.1	P47710	OTTHUMG00000160843	ENST00000246891.4:c.555+2T>C	chr4.hg19:g.70810724T>C		111.0	0.0		110.0	33.0	NM_001025104	A1A510|A1A511|E9PB60|Q4PNR5	Splice_Site	SNP	ENST00000246891.4	hg19	CCDS47067.1																																																																																			.	.		0.358	CSN1S1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362629.1		Intron	C	70810724	T	C	70810724	5	2	79	1	0	0	0	0	0	0	1	0	3949	1652	57	2	613	2	CSN1S1	4	70810724	Splice_Site	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	15212627	70810724	120343552	63	10817										
GRSF1	2926	hgsc.bcm.edu	37	chr4	71698027	71698027	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	atacaactgcaaagtacctgCaaagaagtctacaatgtctt	6	9	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:71698027C>A	ENST00000254799.6	-	4	928	c.811G>T	c.(811-813)Gca>Tca	p.A271S	GRSF1_ENST00000502323.1_Missense_Mutation_p.A109S|GRSF1_ENST00000439371.1_Missense_Mutation_p.A109S|GRSF1_ENST00000545193.1_Missense_Mutation_p.A153S|GRSF1_ENST00000508091.1_Intron	NM_002092.3	NP_002083	Q12849	GRSF1_HUMAN	G-rich RNA sequence binding factor 1	271	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anterior/posterior pattern specification (GO:0009952)|morphogenesis of embryonic epithelium (GO:0016331)|mRNA polyadenylation (GO:0006378)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(2)	17		all_hematologic(202;0.21)	Lung(101;0.235)			AAAGTACCTGCAAAGAAGTCT	0.423																																					p.A271S		Atlas-SNP	.											.	GRSF1	35	.	0			c.G811T						.						123	120	121					4																	71698027		1900	4119	6019	SO:0001583	missense	2926	exon4			TACCTGCAAAGAA	BC040485	CCDS47069.1, CCDS47070.1	4q13	2013-07-16				ENSG00000132463		"RNA binding motif (RRM) containing"	4610	protein-coding gene	gene with protein product		604851				8036161	Standard	NM_001098477		Approved		uc010iia.1	Q12849		ENST00000254799.6:c.811G>T	chr4.hg19:g.71698027C>A	ENSP00000254799:p.Ala271Ser	109.0	0.0		102.0	22.0	NM_002092	B3KPW0|Q4W5S5|Q6ZST3|Q8IWD6|Q8NBD2	Missense_Mutation	SNP	ENST00000254799.6	hg19	CCDS47069.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.094|8.094	0.775119|0.775119	0.16051|0.16051	.|.	.|.	ENSG00000132463|ENSG00000132463	ENST00000254799;ENST00000439371;ENST00000540657;ENST00000499044;ENST00000502323;ENST00000545193|ENST00000514161	T;T;T;T;T|.	0.06528|.	3.29;3.29;3.29;3.29;3.29|.	5.93|5.93	5.93|5.93	0.95920|0.95920	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|.	0.053759|.	0.85682|.	D|.	0.000000|.	T|T	0.36386|0.36386	0.0965|0.0965	N|N	0.04387|0.04387	-0.21|-0.21	0.40915|0.40915	D|D	0.984266|0.984266	B;B|.	0.28026|.	0.016;0.198|.	B;B|.	0.34873|.	0.021;0.191|.	T|T	0.33854|0.33854	-0.9852|-0.9852	10|5	0.05959|.	T|.	0.93|.	.|.	14.5816|14.5816	0.68295|0.68295	0.265:0.735:0.0:0.0|0.265:0.735:0.0:0.0	.|.	184;271|.	B7Z5F9;Q12849|.	.;GRSF1_HUMAN|.	S|F	271;109;203;244;109;153|207	ENSP00000254799:A271S;ENSP00000389219:A109S;ENSP00000427354:A244S;ENSP00000425430:A109S;ENSP00000443380:A153S|.	ENSP00000254799:A271S|.	A|L	-|-	1|3	0|2	GRSF1|GRSF1	71916891|71916891	0.961000|0.961000	0.32948|0.32948	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.057000|1.057000	0.30492|0.30492	2.808000|2.808000	0.96608|0.96608	0.655000|0.655000	0.94253|0.94253	GCA|TTG	.	.		0.423	GRSF1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362642.1	NM_002092		A	71698027	C	A	71698027	3	1	79	1	0	0	0	0	1	0	0	0	6818	710	25	3	655	3	GRSF1	4	71698027	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	887303	71698027	119456249	64	10818										
ALB	213	hgsc.bcm.edu	37	chr4	74285989	74285989	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agggtaaaaaacttgttgctGcaagtcaagctgccttaggc	11	8	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:74285989G>T	ENST00000503124.1	+	12	1561	c.1354G>T	c.(1354-1356)Gca>Tca	p.A452S	ALB_ENST00000415165.2_Missense_Mutation_p.A410S|ALB_ENST00000509063.1_Intron|ALB_ENST00000295897.4_Missense_Mutation_p.A602S|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Missense_Mutation_p.A487S			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACTTGTTGCTGCAAGTCAAGC	0.274																																					p.A602S		Atlas-SNP	.											.	ALB	132	.	0			c.G1804T						.						88	87	87					4																	74285989		2201	4300	6501	SO:0001583	missense	213	exon14			GTTGCTGCAAGTC	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1354G>T	chr4.hg19:g.74285989G>T	ENSP00000421027:p.Ala452Ser	191.0	0.0		167.0	35.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.011|0.011	-1.732458|-1.732458	0.00687|0.00687	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000329326;ENST00000503124;ENST00000401494;ENST00000430202|ENST00000511370	T;T;T;T|.	0.58060|.	0.36;0.36;0.36;0.36|.	5.54|5.54	-11.1|-11.1	0.00147|0.00147	Serum albumin-like (1);|.	.|2.578920	.|0.00997	.|N	.|0.003611	T|T	0.14013|0.14013	0.0339|0.0339	N|N	0.04203|0.04203	-0.255|-0.255	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.06405|.	0.001;0.002;0.001;0.001|.	T|T	0.10245|0.10245	-1.0638|-1.0638	9|6	0.08381|.	T|.	0.77|.	17.2539|17.2539	8.6814|8.6814	0.34212|0.34212	0.3562:0.0:0.094:0.5498|0.3562:0.0:0.094:0.5498	.|.	487;410;452;602|.	B7WNR0;C9JKR2;D6RHD5;P02768|.	.;.;.;ALBU_HUMAN|.	S|F	602;410;389;452;487;611|446	ENSP00000295897:A602S;ENSP00000401820:A410S;ENSP00000421027:A452S;ENSP00000384695:A487S|.	ENSP00000295897:A602S|.	A|C	+|+	1|2	0|0	ALB|ALB	74504853|74504853	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.104000|0.104000	0.19210|0.19210	-4.042000|-4.042000	0.00307|0.00307	-3.470000|-3.470000	0.00157|0.00157	-0.806000|-0.806000	0.03193|0.03193	GCA|TGC	.	.		0.274	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		T	74285989	G	T	74285989	3	4	79	1	0	0	0	0	1	0	0	0	486	1319	46	3	1858	3	ALB	4	74285989	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	2587962	74285989	116868287	65	10819										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79387360	79387360	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tggtattttgccttccggacAggccgagtctgtcacattca	10	11	3	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:79387360A>C	ENST00000264895.6	+	50	7469		c.e50-1			NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1						cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CCTTCCGGACAGGCCGAGTCT	0.537																																					.		Atlas-SNP	.											.	FRAS1	779	.	0			c.7030-2A>C						.						56	56	56					4																	79387360		2122	4240	6362	SO:0001630	splice_region_variant	80144	exon50			CCGGACAGGCCGA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.7030-1A>C	chr4.hg19:g.79387360A>C		107.0	0.0		84.0	14.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Splice_Site	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.209385	0.79240	.	.	ENSG00000138759	ENST00000264895;ENST00000512123	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.954	0.79865	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FRAS1	79606384	1.000000	0.71417	0.996000	0.52242	0.794000	0.44872	8.987000	0.93497	2.235000	0.73313	0.477000	0.44152	.	.	.		0.537	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Intron	C	79387360	A	C	79387360	5	2	79	1	0	0	0	0	0	0	1	0	6050	202	7	5	7301	5	FRAS1	4	79387360	Splice_Site	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	5101371	79387360	111766916	66	10820										
PDLIM5	10611	hgsc.bcm.edu	37	chr4	95507590	95507590	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gaagccgataatacaaagaaGgcaaagtaagttctctatct	8	7	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:95507590G>A	ENST00000317968.4	+	7	1051	c.915G>A	c.(913-915)aaG>aaA	p.K305K	PDLIM5_ENST00000380180.3_Silent_p.K202K|PDLIM5_ENST00000542407.1_Silent_p.K183K|PDLIM5_ENST00000514743.1_Silent_p.K202K|PDLIM5_ENST00000437932.1_Silent_p.K196K|PDLIM5_ENST00000318007.5_Silent_p.K182K|PDLIM5_ENST00000508216.1_Silent_p.K202K|PDLIM5_ENST00000538141.1_Silent_p.K182K|PDLIM5_ENST00000450793.1_Silent_p.K202K|PDLIM5_ENST00000380176.3_3'UTR	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	305					regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		ATACAAAGAAGGCAAAGTAAG	0.284																																					p.K305K		Atlas-SNP	.											.	PDLIM5	76	.	0			c.G915A						.						120	131	127					4																	95507590		2203	4300	6503	SO:0001819	synonymous_variant	10611	exon7			AAAGAAGGCAAAG	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.915G>A	chr4.hg19:g.95507590G>A		70.0	0.0		80.0	14.0	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Silent	SNP	ENST00000317968.4	hg19	CCDS3641.1	.	.	.	.	.	.	.	.	.	.	G	7.740	0.701066	0.15172	.	.	ENSG00000163110	ENST00000513341	.	.	.	5.24	2.55	0.30701	.	.	.	.	.	T	0.59059	0.2166	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54234	-0.8324	4	.	.	.	.	10.0519	0.42221	0.2235:0.0:0.7765:0.0	.	.	.	.	K	164	.	.	R	+	2	0	PDLIM5	95726613	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	2.877000	0.48506	0.703000	0.31848	-0.140000	0.14226	AGG	.	.		0.284	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1			A	95507590	G	A	95507590	2	1	79	1	0	0	0	0	0	0	0	1	11692	991	35	3		3	PDLIM5	4	95507590	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	16120230	95507590	95646686	67	10821										
C4orf21	55345	hgsc.bcm.edu	37	chr4	113540196	113540196	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gaagaatgtataggtgaactCtgtgaggataaatacatggc	12	4	1	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:113540196C>T	ENST00000505019.1	-	6	1127	c.1002G>A	c.(1000-1002)caG>caA	p.Q334Q	C4orf21_ENST00000445203.2_Silent_p.Q303Q|C4orf21_ENST00000309071.5_Silent_p.Q334Q	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		334						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		TAGGTGAACTCTGTGAGGATA	0.383																																					p.Q334Q		Atlas-SNP	.											.	C4orf21	223	.	0			c.G1002A						.						78	83	81					4																	113540196		2201	4300	6501	SO:0001819	synonymous_variant	55345	exon6			TGAACTCTGTGAG																												ENST00000505019.1:c.1002G>A	chr4.hg19:g.113540196C>T		120.0	0.0		102.0	30.0	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Silent	SNP	ENST00000505019.1	hg19																																																																																				.	.		0.383	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1			T	113540196	C	T	113540196	2	4	79	1	0	0	0	0	0	0	0	1	2256	912	32	3		3	C4orf21	4	113540196	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	18032606	113540196	77614080	68	10822										
FAT4	79633	hgsc.bcm.edu	37	chr4	126238464	126238464	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggacccccttccaaatggacCctgagacgggacttatcacg	10	14	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:126238464C>T	ENST00000394329.3	+	1	911	c.898C>T	c.(898-900)Cct>Tct	p.P300S		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	300	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCAAATGGACCCTGAGACGGG	0.662											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P300S		Atlas-SNP	.											FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	.	0			c.C898T						.						23	28	26					4																	126238464		2004	4156	6160	SO:0001583	missense	79633	exon1			ATGGACCCTGAGA	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.898C>T	chr4.hg19:g.126238464C>T	ENSP00000377862:p.Pro300Ser	98.0	0.0	1548	86.0	14.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	14.32	2.498986	0.44455	.	.	ENSG00000196159	ENST00000394329	T	0.53423	0.62	5.02	4.15	0.48705	Cadherin (4);Cadherin-like (1);	0.000000	0.34362	U	0.004027	T	0.51160	0.1658	N	0.17278	0.47	0.80722	D	1	P	0.49358	0.923	D	0.65874	0.939	T	0.50676	-0.8800	10	0.34782	T	0.22	.	15.2765	0.73745	0.0:0.8592:0.1408:0.0	.	300	Q6V0I7	FAT4_HUMAN	S	300	ENSP00000377862:P300S	ENSP00000377862:P300S	P	+	1	0	FAT4	126457914	1.000000	0.71417	0.993000	0.49108	0.430000	0.31655	3.692000	0.54727	1.048000	0.40298	0.655000	0.94253	CCT	.	.		0.662	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126238464	C	T	126238464	3	4	79	1	0	0	0	0	1	0	0	0	5700	623	22	3	900	3	FAT4	4	126238464	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	12698268	126238464	64915812	69	10823										
C4orf45	152940	hgsc.bcm.edu	37	chr4	159836450	159836450	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gtcctcgaaagcactcatatGccaggcaaaagaagcgcgac	10	12	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:159836450G>T	ENST00000434826.2	-	4	502	c.418C>A	c.(418-420)Cat>Aat	p.H140N	C4orf45_ENST00000508011.1_5'UTR	NM_152543.2	NP_689756.2	Q96LM5	CD045_HUMAN	chromosome 4 open reading frame 45	140										large_intestine(2)|lung(3)	5						GCACTCATATGCCAGGCAAAA	0.438																																					p.H140N		Atlas-SNP	.											.	C4orf45	8	.	0			c.C418A						.						87	80	82					4																	159836450		1910	4132	6042	SO:0001583	missense	152940	exon4			TCATATGCCAGGC		CCDS47156.1	4q32.1	2012-03-02			ENSG00000164123	ENSG00000164123			26342	protein-coding gene	gene with protein product							Standard	NM_152543		Approved	FLJ25371	uc003iqf.1	Q96LM5	OTTHUMG00000161988	ENST00000434826.2:c.418C>A	chr4.hg19:g.159836450G>T	ENSP00000412215:p.His140Asn	97.0	0.0		148.0	32.0	NM_152543	A8MPU3|C9J0T8	Missense_Mutation	SNP	ENST00000434826.2	hg19	CCDS47156.1	.	.	.	.	.	.	.	.	.	.	G	0.624	-0.819843	0.02776	.	.	ENSG00000164123	ENST00000434826	T	0.11930	2.73	5.83	-1.44	0.08856	.	0.719586	0.12927	N	0.427699	T	0.07188	0.0182	N	0.16743	0.435	0.09310	N	0.999994	B	0.06786	0.001	B	0.06405	0.002	T	0.40646	-0.9552	9	.	.	.	-20.633	9.6433	0.39853	0.0789:0.0:0.2185:0.7026	.	140	Q96LM5	CD045_HUMAN	N	140	ENSP00000412215:H140N	.	H	-	1	0	C4orf45	160055900	0.959000	0.32827	0.184000	0.23157	0.008000	0.06430	0.268000	0.18571	-0.175000	0.10725	-0.137000	0.14449	CAT	.	.		0.438	C4orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366636.1	NM_152543		T	159836450	G	T	159836450	3	4	79	1	0	0	0	0	1	0	0	0	2275	1319	46	3	150	3	C4orf45	4	159836450	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	33597986	159836450	31317826	70	10824										
FAT1	2195	hgsc.bcm.edu	37	chr4	187628856	187628856	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	actgcggtatgtgagcattgAcagagtgagaatcgaagaaa	13	5	0	5			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr4:187628856A>G	ENST00000441802.2	-	2	2335	c.2126T>C	c.(2125-2127)gTc>gCc	p.V709A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	709					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GTGAGCATTGACAGAGTGAGA	0.458										HNSCC(5;0.00058)																											p.V709A	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T2126C						.						50	48	49					4																	187628856		1918	4136	6054	SO:0001583	missense	2195	exon2			GCATTGACAGAGT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.2126T>C	chr4.hg19:g.187628856A>G	ENSP00000406229:p.Val709Ala	91.0	0.0		64.0	15.0	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	10.12	1.264387	0.23136	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.71341	-0.56	5.4	5.4	0.78164	Cadherin (1);Cadherin-like (1);	0.424017	0.25714	N	0.028783	T	0.65260	0.2674	L	0.59436	1.845	0.43114	D	0.994826	B	0.30455	0.28	B	0.32980	0.156	T	0.61884	-0.6971	10	0.23891	T	0.37	.	9.9872	0.41849	0.9252:0.0:0.0748:0.0	.	709	Q14517	FAT1_HUMAN	A	709	ENSP00000406229:V709A	ENSP00000260147:V709A	V	-	2	0	FAT1	187865850	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	7.383000	0.79741	2.263000	0.75096	0.533000	0.62120	GTC	.	.		0.458	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187628856	A	G	187628856	3	3	79	1	0	0	0	0	1	0	0	0	5697	275	10	2	11744	2	FAT1	4	187628856	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	27792406	187628856	3525420	71	10825										
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1073787	1073787	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tccatgtgcttgtccaggtaCgtcccctccagcaccgagcc	9	17	0	0	rs564599238	byFrequency	TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr5:1073787C>T	ENST00000264930.5	-	17	2245	c.2202G>A	c.(2200-2202)acG>acA	p.T734T		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	734					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	TGTCCAGGTACGTCCCCTCCA	0.697													C|||	3	0.000599042	0	0	5008	,	,		15054	0		0	False		,,,				2504	0.0031				p.T734T		Atlas-SNP	.											.	SLC12A7	97	.	0			c.G2202A						.						57	61	60					5																	1073787		2201	4298	6499	SO:0001819	synonymous_variant	10723	exon17			CAGGTACGTCCCC	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2202G>A	chr5.hg19:g.1073787C>T		124.0	0.0		110.0	25.0	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	hg19	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	c	4.157	0.027531	0.08054	.	.	ENSG00000113504	ENST00000513223	.	.	.	4.04	0.916	0.19373	.	.	.	.	.	T	0.55114	0.1900	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46884	-0.9159	4	.	.	.	.	8.0386	0.30508	0.0:0.1417:0.4439:0.4144	.	.	.	.	I	92	.	.	V	-	1	0	SLC12A7	1126787	1.000000	0.71417	0.997000	0.53966	0.366000	0.29705	0.655000	0.24933	0.281000	0.22233	-1.468000	0.01013	GTA	.	.		0.697	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		T	1073787	C	T	1073787	2	4	79	1	0	0	0	0	0	0	0	1	14403	523	19	1		1	SLC12A7	5	1073787	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10		1073787	179841473	72	10826										
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5232631	5232631	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcctctgcaccaaccccaagTaagtatgccttgacctcctt	6	16	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr5:5232631T>C	ENST00000274181.7	+	12	1988		c.e12+2			NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16						branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						CAACCCCAAGTAAGTATGCCT	0.512																																					.		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.1850+2T>C						.						93	104	100					5																	5232631		2167	4278	6445	SO:0001630	splice_region_variant	170690	exon12			CCCAAGTAAGTAT	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.1850+2T>C	chr5.hg19:g.5232631T>C		33.0	0.0		27.0	11.0	NM_139056	C6G490|Q8IVE2	Splice_Site	SNP	ENST00000274181.7	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	T	12.37	1.919008	0.33908	.	.	ENSG00000145536	ENST00000274181;ENST00000536857	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0292	0.64604	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADAMTS16	5285631	1.000000	0.71417	0.916000	0.36221	0.031000	0.12232	7.653000	0.83643	1.959000	0.56917	0.402000	0.26972	.	.	.		0.512	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	Intron	C	5232631	T	C	5232631	5	2	79	1	0	0	0	0	0	0	1	0	261	1652	57	2	1898	2	ADAMTS16	5	5232631	Splice_Site	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	4158844	5232631	175682629	73	10827										
FBN2	2201	hgsc.bcm.edu	37	chr5	127680112	127680112	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cctccatgtctagagcaaagCcactattgcaacggcatttg	8	12	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr5:127680112C>A	ENST00000508053.1	-	31	4282	c.3308G>T	c.(3307-3309)gGc>gTc	p.G1103V	FBN2_ENST00000262464.4_Missense_Mutation_p.G1103V|FBN2_ENST00000508989.1_Missense_Mutation_p.G1070V			P35556	FBN2_HUMAN	fibrillin 2	1103	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TAGAGCAAAGCCACTATTGCA	0.418																																					p.G1103V		Atlas-SNP	.											.	FBN2	858	.	0			c.G3308T						.						148	143	144					5																	127680112		2203	4300	6503	SO:0001583	missense	2201	exon25			GCAAAGCCACTAT	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.3308G>T	chr5.hg19:g.127680112C>A	ENSP00000424571:p.Gly1103Val	177.0	0.0		127.0	35.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612793	0.46631	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.92965	-3.14;-3.14;-3.14	4.54	3.67	0.42095	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000005	D	0.97114	0.9057	H	0.95224	3.64	0.80722	D	1	D;B	0.89917	1.0;0.035	D;B	0.91635	0.999;0.061	D	0.98417	1.0575	10	0.87932	D	0	.	14.9775	0.71286	0.1442:0.8558:0.0:0.0	.	1070;1103	D6RJI3;P35556	.;FBN2_HUMAN	V	1103;1103;1070	ENSP00000262464:G1103V;ENSP00000424571:G1103V;ENSP00000425596:G1070V	ENSP00000262464:G1103V	G	-	2	0	FBN2	127708011	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	7.548000	0.82154	1.495000	0.48549	-0.324000	0.08512	GGC	.	.		0.418	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127680112	C	A	127680112	3	1	79	1	0	0	0	0	1	0	0	0	5711	739	26	3	5594	3	FBN2	5	127680112	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	122447481	127680112	53235148	74	10828										
SLC6A7	6534	hgsc.bcm.edu	37	chr5	149580667	149580667	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctcaggtggtgtatttcacgGccacgttcccctacctcatc	8	15	3	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr5:149580667G>T	ENST00000230671.2	+	6	1110	c.739G>T	c.(739-741)Gcc>Tcc	p.A247S	SLC6A7_ENST00000524041.1_Missense_Mutation_p.A247S	NM_014228.3	NP_055043.2	Q99884	SC6A7_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 7	247					proline transport (GO:0015824)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	GTATTTCACGGCCACGTTCCC	0.562																																					p.A247S		Atlas-SNP	.											.	SLC6A7	52	.	0			c.G739T						.						210	150	170					5																	149580667		2203	4300	6503	SO:0001583	missense	6534	exon6			TTCACGGCCACGT	S80071	CCDS4305.1	5q32	2013-07-19	2013-07-19		ENSG00000011083	ENSG00000011083		"Solute carriers"	11054	protein-coding gene	gene with protein product	"brain-specific L-proline transporter", "sodium-dependent proline transporter"	606205	"solute carrier family 6 (neurotransmitter transporter, L-proline), member 7"			7651355	Standard	NM_014228		Approved	PROT	uc003lrr.3	Q99884	OTTHUMG00000130046	ENST00000230671.2:c.739G>T	chr5.hg19:g.149580667G>T	ENSP00000230671:p.Ala247Ser	54.0	0.0		60.0	16.0	NM_014228	Q0VG81|Q52LU6	Missense_Mutation	SNP	ENST00000230671.2	hg19	CCDS4305.1	.	.	.	.	.	.	.	.	.	.	G	34	5.323535	0.95708	.	.	ENSG00000011083	ENST00000230671;ENST00000524041	T;T	0.76448	-1.02;-1.02	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.88377	0.6420	M	0.77616	2.38	0.80722	D	1	D	0.65815	0.995	D	0.70935	0.971	D	0.89715	0.3915	10	0.87932	D	0	.	18.8226	0.92103	0.0:0.0:1.0:0.0	.	247	Q99884	SC6A7_HUMAN	S	247	ENSP00000230671:A247S;ENSP00000428200:A247S	ENSP00000230671:A247S	A	+	1	0	SLC6A7	149560860	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.841000	0.99482	2.436000	0.82500	0.561000	0.74099	GCC	.	.		0.562	SLC6A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252325.1	NM_014228		T	149580667	G	T	149580667	3	4	79	1	0	0	0	0	1	0	0	0	14704	1203	42	3	761	3	SLC6A7	5	149580667	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	21900555	149580667	31334593	75	10829										
TIMD4	91937	hgsc.bcm.edu	37	chr5	156378589	156378589	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	acctgtggcttcctccggaaGggtgcttggggttagtgaaa	15	8	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr5:156378589G>T	ENST00000274532.2	-	3	669	c.613C>A	c.(613-615)Ctt>Att	p.L205I	TIMD4_ENST00000407087.3_Missense_Mutation_p.L205I	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	205	Thr-rich.					integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCCTCCGGAAGGGTGCTTGGG	0.537																																					p.L205I		Atlas-SNP	.											.	TIMD4	94	.	0			c.C613A						.						288	255	267					5																	156378589		2203	4300	6503	SO:0001583	missense	91937	exon3			CCGGAAGGGTGCT	BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850		"Immunoglobulin superfamily / V-set domain containing"	25132	protein-coding gene	gene with protein product		610096				12477932	Standard	NM_001146726		Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.613C>A	chr5.hg19:g.156378589G>T	ENSP00000274532:p.Leu205Ile	256.0	0.0		245.0	75.0	NM_138379	B5MCL9	Missense_Mutation	SNP	ENST00000274532.2	hg19	CCDS4332.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.933883	0.52866	.	.	ENSG00000145850	ENST00000274532;ENST00000407087	T;T	0.22336	1.96;2.07	4.7	0.642	0.17765	.	1.288300	0.05518	N	0.561561	T	0.15998	0.0385	L	0.29908	0.895	0.09310	N	1	P;P	0.41978	0.767;0.767	B;B	0.40940	0.344;0.344	T	0.19321	-1.0309	10	0.41790	T	0.15	-0.925	4.3172	0.10998	0.2465:0.0:0.5886:0.1649	.	205;205	B5MCL9;Q96H15	.;TIMD4_HUMAN	I	205	ENSP00000274532:L205I;ENSP00000385973:L205I	ENSP00000274532:L205I	L	-	1	0	TIMD4	156311167	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	0.363000	0.20301	-0.016000	0.14127	0.561000	0.74099	CTT	.	.		0.537	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379		T	156378589	G	T	156378589	3	4	79	1	0	0	0	0	1	0	0	0	15918	1000	35	3	551	3	TIMD4	5	156378589	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	6797922	156378589	24536671	76	10830										
C5orf40	408263	hgsc.bcm.edu	37	chr5	156770032	156770032	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agcccctgcaggtcttcctcCctctgaccaagatccggggc	10	17	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr5:156770032C>A	ENST00000312349.4	-	2	700	c.513G>T	c.(511-513)agG>agT	p.R171S	CYFIP2_ENST00000435847.2_Intron|CYFIP2_ENST00000521420.1_Intron|CYFIP2_ENST00000318218.6_Intron|CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000541131.1_Intron|CYFIP2_ENST00000442283.2_Intron|CYFIP2_ENST00000377576.3_Intron|CYFIP2_ENST00000347377.6_Intron	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9	171						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						GGTCTTCCTCCCTCTGACCAA	0.612											OREG0016977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R171S		Atlas-SNP	.											.	FNDC9	22	.	0			c.G513T						.						82	85	84					5																	156770032		2203	4300	6503	SO:0001583	missense	408263	exon2			TTCCTCCCTCTGA	BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"Fibronectin type III domain containing"	33547	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 40"	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248	ENST00000312349.4:c.513G>T	chr5.hg19:g.156770032C>A	ENSP00000310594:p.Arg171Ser	118.0	0.0	1781	116.0	28.0	NM_001001343	A8K0Y6	Missense_Mutation	SNP	ENST00000312349.4	hg19	CCDS4337.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.848354	0.32699	.	.	ENSG00000172568	ENST00000312349;ENST00000520782	T;T	0.63580	-0.05;-0.05	5.08	0.0721	0.14385	.	0.760320	0.12187	N	0.491536	T	0.39759	0.1090	N	0.14661	0.345	0.29734	N	0.83767	B	0.22414	0.069	B	0.21917	0.037	T	0.30592	-0.9973	10	0.22706	T	0.39	-6.3422	8.0343	0.30482	0.0:0.3929:0.0:0.6071	.	171	Q8TBE3	FNDC9_HUMAN	S	171	ENSP00000310594:R171S;ENSP00000429434:R171S	ENSP00000310594:R171S	R	-	3	2	FNDC9	156702610	0.890000	0.30428	0.683000	0.30040	0.908000	0.53690	-0.159000	0.10056	-0.070000	0.12908	0.491000	0.48974	AGG	.	.		0.612	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343		A	156770032	C	A	156770032	3	1	79	1	0	0	0	0	1	0	0	0	2301	622	22	3	165	3	C5orf40	5	156770032	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	391443	156770032	24145228	77	10831										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161116767	161116767	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gacaaacagtatctagtgagAcaattaaatctaacacaggt	7	7	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr5:161116767A>T	ENST00000274545.5	+	6	1088	c.655A>T	c.(655-657)Aca>Tca	p.T219S	RP11-348M17.2_ENST00000521984.1_RNA|GABRA6_ENST00000523217.1_Missense_Mutation_p.T209S			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	219					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	ATCTAGTGAGACAATTAAATC	0.363										TCGA Ovarian(5;0.080)																											p.T219S		Atlas-SNP	.											.	GABRA6	139	.	0			c.A655T						.						70	78	75					5																	161116767		2203	4299	6502	SO:0001583	missense	2559	exon6			AGTGAGACAATTA		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.655A>T	chr5.hg19:g.161116767A>T	ENSP00000274545:p.Thr219Ser	188.0	0.0		177.0	36.0	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	hg19	CCDS4356.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.98|17.98	3.520195|3.520195	0.64747|0.64747	.|.	.|.	ENSG00000145863|ENSG00000145863	ENST00000520000|ENST00000274545;ENST00000523217;ENST00000517823;ENST00000523691	.|T;T;T;T	.|0.79141	.|-1.24;-1.24;-1.24;-1.24	5.41|5.41	5.41|5.41	0.78517|0.78517	.|Neurotransmitter-gated ion-channel ligand-binding (3);	.|0.244270	.|0.44688	.|D	.|0.000437	D|D	0.82291|0.82291	0.5005|0.5005	L|L	0.48260|0.48260	1.515|1.515	0.41055|0.41055	D|D	0.985335|0.985335	.|P	.|0.43412	.|0.806	.|P	.|0.55667	.|0.781	D|D	0.83661|0.83661	0.0161|0.0161	5|10	.|0.56958	.|D	.|0.05	.|.	15.4372|15.4372	0.75155|0.75155	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|219	.|Q16445	.|GBRA6_HUMAN	S|S	158|219;209;166;139	.|ENSP00000274545:T219S;ENSP00000430527:T209S;ENSP00000430212:T166S;ENSP00000427989:T139S	.|ENSP00000274545:T219S	R|T	+|+	3|1	2|0	GABRA6|GABRA6	161049345|161049345	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	5.069000|5.069000	0.64370|0.64370	2.043000|2.043000	0.60533|0.60533	0.533000|0.533000	0.62120|0.62120	AGA|ACA	.	.		0.363	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			T	161116767	A	T	161116767	3	4	79	1	0	0	0	0	1	0	0	0	6173	275	10	4	677	4	GABRA6	5	161116767	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	4346735	161116767	19798493	78	10832										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169494671	169494671	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggaccctgctgtcatgggagGcttcgccaagtatgagaagg	15	9	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr5:169494671G>T	ENST00000256935.8	+	45	4705	c.4625G>T	c.(4624-4626)gGc>gTc	p.G1542V	DOCK2_ENST00000540750.1_Missense_Mutation_p.G603V|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Missense_Mutation_p.G1034V	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1542	DHR-2.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTCATGGGAGGCTTCGCCAAG	0.552																																					p.G1542V		Atlas-SNP	.											.	DOCK2	389	.	0			c.G4625T						.						144	137	139					5																	169494671		2203	4300	6503	SO:0001583	missense	1794	exon45			TGGGAGGCTTCGC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4625G>T	chr5.hg19:g.169494671G>T	ENSP00000256935:p.Gly1542Val	93.0	0.0		91.0	23.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.513180	0.64522	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.72835	-0.69;-0.69;-0.69	4.83	3.95	0.45737	Cytochrome c domain (1);	0.000000	0.85682	D	0.000000	D	0.87700	0.6243	H	0.94698	3.57	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90715	0.4630	10	0.87932	D	0	.	13.7225	0.62737	0.0762:0.0:0.9238:0.0	.	1034;98;1542	E7ERW7;B3KY14;Q92608	.;.;DOCK2_HUMAN	V	1542;1034;603	ENSP00000256935:G1542V;ENSP00000429283:G1034V;ENSP00000438827:G603V	ENSP00000256935:G1542V	G	+	2	0	DOCK2	169427249	1.000000	0.71417	0.998000	0.56505	0.543000	0.35085	9.809000	0.99208	1.147000	0.42369	0.563000	0.77884	GGC	.	.		0.552	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169494671	G	T	169494671	3	4	79	1	0	0	0	0	1	0	0	0	4689	1203	42	3	4803	3	DOCK2	5	169494671	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	8377904	169494671	11420589	79	10833										
CDHR2	54825	hgsc.bcm.edu	37	chr5	175995968	175995968	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctggctgctgcagacactctAcacattcaaagtcaccatct	6	14	4	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr5:175995968A>G	ENST00000510636.1	+	5	546	c.272A>G	c.(271-273)tAc>tGc	p.Y91C	CDHR2_ENST00000506348.1_Missense_Mutation_p.Y91C|CDHR2_ENST00000261944.5_Missense_Mutation_p.Y91C	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	91	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CAGACACTCTACACATTCAAA	0.637																																					p.Y91C		Atlas-SNP	.											.	CDHR2	152	.	0			c.A272G						.						69	64	66					5																	175995968		2203	4300	6503	SO:0001583	missense	54825	exon5			CACTCTACACATT	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.272A>G	chr5.hg19:g.175995968A>G	ENSP00000424565:p.Tyr91Cys	64.0	0.0		68.0	20.0	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	hg19	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	A	12.13	1.845260	0.32606	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.60797	0.16;0.16;0.16	3.97	-7.93	0.01156	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.40743	0.1129	L	0.43152	1.355	0.09310	N	1	P	0.48640	0.913	B	0.43103	0.408	T	0.37934	-0.9684	9	0.52906	T	0.07	-0.405	2.9253	0.05783	0.1617:0.441:0.0867:0.3106	.	91	Q9BYE9	CDHR2_HUMAN	C	91	ENSP00000424565:Y91C;ENSP00000261944:Y91C;ENSP00000421078:Y91C	ENSP00000261944:Y91C	Y	+	2	0	CDHR2	175928574	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.488000	0.02308	-1.484000	0.01856	0.454000	0.30748	TAC	.	.		0.637	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		G	175995968	A	G	175995968	3	3	79	1	0	0	0	0	1	0	0	0	3121	391	14	2	286	2	CDHR2	5	175995968	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	6501297	175995968	4919292	80	10834										
MDC1	9656	hgsc.bcm.edu	37	chr6	30672768	30672768	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	aggggtcttgccagaggatcTattttttcttcccctagtag	10	9	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr6:30672768T>C	ENST00000376406.3	-	10	4839	c.4192A>G	c.(4192-4194)Aga>Gga	p.R1398G	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Missense_Mutation_p.R1134G	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1398	Interaction with the PRKDC complex.|Pro-rich.				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						CCAGAGGATCTATTTTTTCTT	0.562								Other conserved DNA damage response genes																													p.R1398G		Atlas-SNP	.											.	MDC1	218	.	0			c.A4192G						.						92	100	97					6																	30672768		2203	4300	6503	SO:0001583	missense	9656	exon10			AGGATCTATTTTT	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.4192A>G	chr6.hg19:g.30672768T>C	ENSP00000365588:p.Arg1398Gly	120.0	0.0		106.0	5.0	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	hg19	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.151365	0.38021	.	.	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000422104	T;T	0.15603	2.41;2.41	2.8	2.8	0.32819	.	.	.	.	.	T	0.19087	0.0458	M	0.62723	1.935	0.09310	N	1	D;D	0.65815	0.995;0.982	D;P	0.64321	0.924;0.624	T	0.03534	-1.1027	9	0.59425	D	0.04	-3.3366	7.361	0.26745	0.0:0.0:0.0:1.0	.	1134;1398	Q14676-2;Q14676	.;MDC1_HUMAN	G	1398;1134;964	ENSP00000365588:R1398G;ENSP00000365587:R1134G	ENSP00000365587:R1134G	R	-	1	2	MDC1	30780747	0.243000	0.23878	0.026000	0.17262	0.023000	0.10783	3.434000	0.52841	1.300000	0.44818	0.248000	0.18094	AGA	.	.		0.562	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		C	30672768	T	C	30672768	3	2	79	1	0	0	0	0	1	0	0	0	9412	1530	53	2	2101	2	MDC1	6	30672768	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10		30672768	140442299	81	10835										
NCR3	259197	hgsc.bcm.edu	37	chr6	31557387	31557387	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agcccgaaggaggaggactgTaccagcccctagctgaggat	14	11	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr6:31557387T>C	ENST00000340027.5	-	3	675	c.412A>G	c.(412-414)Aca>Gca	p.T138A	NCR3_ENST00000376071.4_Missense_Mutation_p.T113A|NCR3_ENST00000376072.3_Missense_Mutation_p.T138A|NCR3_ENST00000491161.1_5'UTR|NCR3_ENST00000376073.4_Missense_Mutation_p.T138A	NM_147130.2	NP_667341.1	O14931	NCTR3_HUMAN	natural cytotoxicity triggering receptor 3	138					cell recognition (GO:0008037)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	integral component of plasma membrane (GO:0005887)		p.T138A(1)		cervix(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)	9						AGGAGGACTGTACCAGCCCCT	0.582																																					p.T138A		Atlas-SNP	.											NCR3,NS,carcinoma,0,1	NCR3	21	.	1	Substitution - Missense(1)	cervix(1)	c.A412G						.						57	55	56					6																	31557387		1510	2709	4219	SO:0001583	missense	259197	exon3			GGACTGTACCAGC	AB055881	CCDS34397.1, CCDS47401.1, CCDS47402.1	6p21.3	2013-01-11	2002-11-13	2002-11-15	ENSG00000204475	ENSG00000204475		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	19077	protein-coding gene	gene with protein product		611550	"lymphocyte antigen 117"	LY117		8824804, 11782277	Standard	NM_001145466		Approved	1C7, NKp30, CD337	uc003nuv.2	O14931	OTTHUMG00000031123	ENST00000340027.5:c.412A>G	chr6.hg19:g.31557387T>C	ENSP00000342156:p.Thr138Ala	60.0	0.0		92.0	41.0	NM_001145466	B0S8F2|B0S8F4|B0S8F5|O14930|O14932|O95667|O95668|O95669|Q5ST89|Q5ST90|Q5ST91|Q5ST92|Q5STA3	Missense_Mutation	SNP	ENST00000340027.5	hg19	CCDS34397.1	.	.	.	.	.	.	.	.	.	.	T	8.756	0.922368	0.17982	.	.	ENSG00000204475	ENST00000340027;ENST00000376073;ENST00000376072;ENST00000376071	T;T;T;T	0.41400	1.56;1.0;1.02;1.9	4.12	-1.46	0.08800	.	0.671525	0.12081	N	0.501286	T	0.10337	0.0253	L	0.34521	1.04	0.09310	N	1	B;B;B	0.20052	0.041;0.002;0.024	B;B;B	0.20184	0.028;0.004;0.012	T	0.29305	-1.0016	10	0.35671	T	0.21	-0.0271	3.9419	0.09331	0.0:0.2159:0.3773:0.4068	.	138;138;138	O14931-2;Q05D23;O14931	.;.;NCTR3_HUMAN	A	138;138;138;113	ENSP00000342156:T138A;ENSP00000365241:T138A;ENSP00000365240:T138A;ENSP00000365239:T113A	ENSP00000342156:T138A	T	-	1	0	NCR3	31665366	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.031000	0.03578	-0.028000	0.13850	-0.313000	0.08912	ACA	.	.		0.582	NCR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076210.2			C	31557387	T	C	31557387	3	2	79	1	0	0	0	0	1	0	0	0	10248	1638	57	2	324	2	NCR3	6	31557387	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	884619	31557387	139557680	82	10836										
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83846990	83846990	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tcactgtgaatccattaagtGacagactttccctcctaagt	6	11	1	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr6:83846990G>T	ENST00000349129.2	+	21	3489	c.3229G>T	c.(3229-3231)Gac>Tac	p.D1077Y	DOPEY1_ENST00000369739.3_Missense_Mutation_p.D1068Y|DOPEY1_ENST00000237163.5_Missense_Mutation_p.D1058Y	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	1077					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TCCATTAAGTGACAGACTTTC	0.398																																					p.D1077Y		Atlas-SNP	.											.	DOPEY1	190	.	0			c.G3229T						.						102	97	99					6																	83846990		2203	4299	6502	SO:0001583	missense	23033	exon21			TTAAGTGACAGAC	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.3229G>T	chr6.hg19:g.83846990G>T	ENSP00000195654:p.Asp1077Tyr	260.0	0.0		266.0	59.0	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	hg19	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910507	0.52439	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.27256	1.68;1.69	5.48	5.48	0.80851	.	0.092779	0.64402	D	0.000001	T	0.43010	0.1228	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	0.997;0.993;1.0	D;P;D	0.85130	0.942;0.888;0.997	T	0.34551	-0.9824	10	0.72032	D	0.01	.	19.3515	0.94389	0.0:0.0:1.0:0.0	.	968;1068;1077	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	Y	1077;1058;1058	ENSP00000195654:D1077Y;ENSP00000237163:D1058Y	ENSP00000237163:D1058Y	D	+	1	0	DOPEY1	83903709	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	9.471000	0.97696	2.567000	0.86603	0.460000	0.39030	GAC	.	.		0.398	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		T	83846990	G	T	83846990	3	4	79	1	0	0	0	0	1	0	0	0	4709	1290	45	3	3303	3	DOPEY1	6	83846990	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	52289603	83846990	87268077	83	10837										
BEND3	57673	hgsc.bcm.edu	37	chr6	107390740	107390740	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gctccttgctgagcaggcagTcggcaccgggcacctcgaag	14	14	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr6:107390740T>C	ENST00000369042.1	-	4	1845	c.1655A>G	c.(1654-1656)gAc>gGc	p.D552G	BEND3_ENST00000429433.2_Missense_Mutation_p.D552G			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	552	BEN 3. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						GAGCAGGCAGTCGGCACCGGG	0.647																																					p.D552G		Atlas-SNP	.											.	BEND3	70	.	0			c.A1655G						.						35	34	35					6																	107390740		2202	4300	6502	SO:0001583	missense	57673	exon5			AGGCAGTCGGCAC	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"BEN domain containing"	23040	protein-coding gene	gene with protein product			"KIAA1553"	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.1655A>G	chr6.hg19:g.107390740T>C	ENSP00000358038:p.Asp552Gly	49.0	0.0		35.0	10.0	NM_001080450	A2RRH2|Q9HCL9	Missense_Mutation	SNP	ENST00000369042.1	hg19	CCDS34507.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.462512	0.43736	.	.	ENSG00000178409	ENST00000369042;ENST00000429433	.	.	.	5.06	5.06	0.68205	BEN domain (1);	0.189333	0.47852	D	0.000203	T	0.31918	0.0812	N	0.22421	0.69	0.54753	D	0.999986	B	0.20780	0.048	B	0.23018	0.043	T	0.33085	-0.9882	9	0.66056	D	0.02	-4.0128	14.9624	0.71166	0.0:0.0:0.0:1.0	.	552	Q5T5X7	BEND3_HUMAN	G	552	.	ENSP00000358038:D552G	D	-	2	0	BEND3	107497433	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.477000	0.81069	2.121000	0.65114	0.459000	0.35465	GAC	.	.		0.647	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913		C	107390740	T	C	107390740	3	2	79	1	0	0	0	0	1	0	0	0	1399	1667	58	2	835	2	BEND3	6	107390740	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	23543750	107390740	63724327	84	10838										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152690719	152690719	+	Frame_Shift_Del	DEL	C	C	-													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctggataggctcagcacttaCttcaaagtccttcatttgga							TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr6:152690719delC	ENST00000367255.5	-	60	10139	c.9538delG	c.(9538-9540)gtafs	p.V3180fs	SYNE1_ENST00000341594.5_Frame_Shift_Del_p.V3219fs|SYNE1_ENST00000265368.4_Frame_Shift_Del_p.V3180fs|SYNE1_ENST00000448038.1_Frame_Shift_Del_p.V3187fs|SYNE1_ENST00000423061.1_Frame_Shift_Del_p.V3187fs	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3180					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCAGCACTTACTTCAAAGTCC	0.438										HNSCC(10;0.0054)																											p.V3187fs		Atlas-INDEL	.											.	SYNE1	3227	.	0			c.9560delT						.						96	90	92					6																	152690719		2203	4300	6503	SO:0001589	frameshift_variant	23345	exon60			.	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.9538delG	chr6.hg19:g.152690719delC	ENSP00000356224:p.Val3180fs	89.0	0.0		83.0	18.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Frame_Shift_Del	DEL	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.438	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		-	152690719	C	-	152690719	7	5	79	1	0	1	0	1	0	0	0	0	15460	565	20	0	17276	0	SYNE1	6	152690719	Frame_Shift_Del	DEL	C	TCGA-CC-A8HT-01A-11D-A35Z-10	45299979	152690719	18424348	85	10839										
SDK1	221935	hgsc.bcm.edu	37	chr7	4056922	4056922	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gtatgagatacaggtggcggCgtacaacggggccggtctgg	18	8	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:4056922C>G	ENST00000404826.2	+	17	2679	c.2540C>G	c.(2539-2541)gCg>gGg	p.A847G	SDK1_ENST00000389531.3_Missense_Mutation_p.A847G	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	847	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CAGGTGGCGGCGTACAACGGG	0.592																																					p.A847G		Atlas-SNP	.											.	SDK1	361	.	0			c.C2540G						.						79	69	73					7																	4056922		2203	4300	6503	SO:0001583	missense	221935	exon17			TGGCGGCGTACAA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.2540C>G	chr7.hg19:g.4056922C>G	ENSP00000385899:p.Ala847Gly	139.0	0.0		170.0	30.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.551867	0.86127	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.76060	-0.99;-0.99	6.07	6.07	0.98685	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.075397	0.51477	D	0.000087	D	0.88815	0.6539	M	0.88842	2.985	0.58432	D	0.999999	D;D	0.63880	0.986;0.993	D;P	0.65987	0.94;0.862	D	0.89511	0.3771	10	0.87932	D	0	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	847;847	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	G	847	ENSP00000385899:A847G;ENSP00000374182:A847G	ENSP00000374182:A847G	A	+	2	0	SDK1	4023448	1.000000	0.71417	0.268000	0.24571	0.517000	0.34286	7.726000	0.84824	2.884000	0.98904	0.655000	0.94253	GCG	.	.		0.592	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		G	4056922	C	G	4056922	3	3	79	1	0	0	0	0	1	0	0	0	13983	768	27	4	2606	4	SDK1	7	4056922	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10		4056922	155081741	86	10840										
PHF14	9678	hgsc.bcm.edu	37	chr7	11076165	11076165	+	Frame_Shift_Del	DEL	G	G	-													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cactcaccagcagtgcttcaGctattcgtaaacttatgcgg							TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:11076165delG	ENST00000403050.3	+	9	2175	c.1723delG	c.(1723-1725)gctfs	p.A575fs	PHF14_ENST00000445996.2_Frame_Shift_Del_p.A290fs	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	575					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		CAGTGCTTCAGCTATTCGTAA	0.483																																					p.S574fs		Atlas-INDEL	.											.	PHF14	90	.	0			c.1722delA						.						88	85	86					7																	11076165		1901	4132	6033	SO:0001589	frameshift_variant	9678	exon9			.	AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"Zinc fingers, PHD-type"	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.1723delG	chr7.hg19:g.11076165delG	ENSP00000385795:p.Ala575fs	197.0	0.0		252.0	54.0	NM_014660	A7MCZ3|B4DI82	Frame_Shift_Del	DEL	ENST00000403050.3	hg19	CCDS47542.1																																																																																			.	.		0.483	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		-	11076165	G	-	11076165	7	5	79	1	0	1	0	1	0	0	0	0	11834	971	34	0	1757	0	PHF14	7	11076165	Frame_Shift_Del	DEL	G	TCGA-CC-A8HT-01A-11D-A35Z-10	7019243	11076165	148062498	87	10841										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18801900	18801900	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tggaccccaggatactcctaGgtctgtacgggcctccactg	11	14	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:18801900G>T	ENST00000432645.2	+	14	2155	c.2155G>T	c.(2155-2157)Ggt>Tgt	p.G719C	HDAC9_ENST00000406451.4_Splice_Site_p.G719C|HDAC9_ENST00000401921.1_Splice_Site_p.G678C|HDAC9_ENST00000441542.2_Splice_Site_p.G722C	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	719	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	GATACTCCTAGGTCTGTACGG	0.498																																					p.G722C		Atlas-SNP	.											.	HDAC9	560	.	0			c.G2164T						.						49	49	49					7																	18801900		1969	4148	6117	SO:0001630	splice_region_variant	9734	exon14			CTCCTAGGTCTGT	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.2155+1G>T	chr7.hg19:g.18801900G>T		169.0	0.0		155.0	28.0	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	hg19	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.486952	0.84854	.	.	ENSG00000048052	ENST00000406451;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000341009	T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46	5.56	5.56	0.83823	Histone deacetylase domain (2);	0.000000	0.64402	D	0.000005	D	0.85919	0.5809	M	0.90082	3.085	0.80722	D	1	P;D;D;D;D;D	0.89917	0.943;1.0;1.0;1.0;1.0;1.0	B;D;D;D;D;D	0.81914	0.15;0.992;0.992;0.995;0.992;0.933	D	0.88023	0.2770	10	0.87932	D	0	-23.0363	19.9052	0.97004	0.0:0.0:1.0:0.0	.	719;678;722;719;719;697	Q9UKV0-4;Q9UKV0-6;Q9UKV0-7;Q9UKV0;Q9UKV0-5;Q8N879	.;.;.;HDAC9_HUMAN;.;.	C	719;678;719;722;631	ENSP00000384657:G719C;ENSP00000383912:G678C;ENSP00000410337:G719C;ENSP00000408617:G722C	ENSP00000339165:G631C	G	+	1	0	HDAC9	18768425	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.151000	0.89636	2.776000	0.95493	0.655000	0.94253	GGT	.	.		0.498	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		Missense_Mutation	T	18801900	G	T	18801900	5	4	79	1	0	0	0	0	0	0	1	0	7023	1014	35	3	2269	3	HDAC9	7	18801900	Splice_Site	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	7725735	18801900	140336763	88	10842										
ITGB8	3696	hgsc.bcm.edu	37	chr7	20406804	20406804	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agaagtgtctatccagctgcGtccaggtttggtcattttca	10	9	3	1	rs139414321		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:20406804G>T	ENST00000222573.4	+	3	1067	c.383G>T	c.(382-384)cGt>cTt	p.R128L	ITGB8_ENST00000537992.1_5'UTR	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	128					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						ATCCAGCTGCGTCCAGGTTTG	0.338																																					p.R128L		Atlas-SNP	.											.	ITGB8	159	.	0			c.G383T						.						85	86	85					7																	20406804		2203	4300	6503	SO:0001583	missense	3696	exon3			AGCTGCGTCCAGG		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.383G>T	chr7.hg19:g.20406804G>T	ENSP00000222573:p.Arg128Leu	55.0	0.0		78.0	28.0	NM_002214	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	hg19	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.878497	0.51801	.	.	ENSG00000105855	ENST00000222573	D	0.95069	-3.6	5.71	1.89	0.25635	Integrin beta subunit, N-terminal (2);	0.357573	0.27715	N	0.018157	D	0.92935	0.7752	M	0.83953	2.67	0.80722	D	1	P;B	0.37781	0.608;0.213	B;B	0.34652	0.187;0.154	D	0.89432	0.3717	10	0.87932	D	0	-9.7637	9.5068	0.39051	0.3515:0.0:0.6485:0.0	.	128;128	P26012;Q9BUG9	ITB8_HUMAN;.	L	128	ENSP00000222573:R128L	ENSP00000222573:R128L	R	+	2	0	ITGB8	20373329	0.999000	0.42202	0.987000	0.45799	0.992000	0.81027	1.353000	0.34045	0.068000	0.16574	0.655000	0.94253	CGT	.	G|1.000;A|0.000		0.338	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		T	20406804	G	T	20406804	3	4	79	1	0	0	0	0	1	0	0	0	7910	1145	40	1	393	1	ITGB8	7	20406804	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	1604904	20406804	138731859	89	10843										
HIBADH	11112	hgsc.bcm.edu	37	chr7	27570940	27570940	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gagctcatatttaggattttAgccagtagttttgggtcaag	11	5	2	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:27570940A>G	ENST00000265395.2	-	7	929	c.723T>C	c.(721-723)gcT>gcC	p.A241A		NM_152740.3	NP_689953.1	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase	241					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	3-hydroxyisobutyrate dehydrogenase activity (GO:0008442)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(4)|kidney(2)|lung(3)|ovary(2)|prostate(1)	12			GBM - Glioblastoma multiforme(3;0.0368)			TTAGGATTTTAGCCAGTAGTT	0.433																																					p.A241A		Atlas-SNP	.											.	HIBADH	28	.	0			c.T723C						.						102	88	93					7																	27570940		2203	4300	6503	SO:0001819	synonymous_variant	11112	exon7			GATTTTAGCCAGT	AF529362	CCDS5414.1	7p15	2009-06-12			ENSG00000106049	ENSG00000106049	1.1.1.31		4907	protein-coding gene	gene with protein product		608475					Standard	NM_152740		Approved	NS5ATP1	uc003szf.3	P31937	OTTHUMG00000097035	ENST00000265395.2:c.723T>C	chr7.hg19:g.27570940A>G		117.0	0.0		132.0	27.0	NM_152740	Q546Z2|Q9UDN3	Silent	SNP	ENST00000265395.2	hg19	CCDS5414.1	.	.	.	.	.	.	.	.	.	.	A	4.729	0.135482	0.09032	.	.	ENSG00000106049	ENST00000425715	.	.	.	6.17	1.05	0.20165	.	.	.	.	.	T	0.40297	0.1111	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23440	-1.0188	4	.	.	.	-13.8618	0.4451	0.00492	0.2993:0.2044:0.2975:0.1988	.	.	.	.	P	184	.	.	L	-	2	0	HIBADH	27537465	0.998000	0.40836	1.000000	0.80357	0.595000	0.36748	0.498000	0.22530	0.176000	0.19873	-1.303000	0.01326	CTA	.	.		0.433	HIBADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214132.1	NM_152740		G	27570940	A	G	27570940	2	3	79	1	0	0	0	0	0	0	0	1	7108	407	15	2		2	HIBADH	7	27570940	Silent	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	7164136	27570940	131567723	90	10844										
HIP1	3092	hgsc.bcm.edu	37	chr7	75183415	75183415	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	catgccccagtactcacagtCggcaggctcaggtggggctc	13	14	2	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:75183415C>A	ENST00000336926.6	-	21	2181	c.2155G>T	c.(2155-2157)Gac>Tac	p.D719Y	HIP1_ENST00000434438.2_Missense_Mutation_p.D719Y	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	719					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						TACTCACAGTCGGCAGGCTCA	0.612			T	PDGFRB	CMML																																p.D719Y		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.G2155T						.						39	37	38					7																	75183415		2203	4300	6503	SO:0001583	missense	3092	exon21			CACAGTCGGCAGG	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.2155G>T	chr7.hg19:g.75183415C>A	ENSP00000336747:p.Asp719Tyr	41.0	0.0		54.0	7.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	hg19	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	c	24.6	4.544608	0.86022	.	.	ENSG00000127946	ENST00000336926;ENST00000434438	T;T	0.25250	2.36;1.81	5.39	5.39	0.77823	.	0.144766	0.64402	D	0.000008	T	0.52948	0.1766	M	0.78456	2.415	0.80722	D	1	D;D	0.76494	0.999;0.979	D;P	0.68765	0.96;0.818	T	0.53627	-0.8412	10	0.59425	D	0.04	.	17.8977	0.88893	0.0:1.0:0.0:0.0	.	719;719	E7ES17;O00291	.;HIP1_HUMAN	Y	719	ENSP00000336747:D719Y;ENSP00000410300:D719Y	ENSP00000336747:D719Y	D	-	1	0	HIP1	75021351	1.000000	0.71417	0.989000	0.46669	0.850000	0.48378	6.603000	0.74145	2.810000	0.96702	0.650000	0.86243	GAC	.	.		0.612	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		A	75183415	C	A	75183415	3	1	79	1	0	0	0	0	1	0	0	0	7123	884	31	1	1002	1	HIP1	7	75183415	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	47612475	75183415	83955248	91	10845										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84636185	84636185	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttgcttgttgggatttaggtAtacattccagaaaggttgag	12	4	0	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:84636185A>G	ENST00000284136.6	-	16	1884	c.1841T>C	c.(1840-1842)aTa>aCa	p.I614T	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	614	Ig-like C2-type.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						GGATTTAGGTATACATTCCAG	0.383																																					p.I614T	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.T1841C						.						190	175	180					7																	84636185		2203	4300	6503	SO:0001583	missense	223117	exon16			TTAGGTATACATT	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1841T>C	chr7.hg19:g.84636185A>G	ENSP00000284136:p.Ile614Thr	110.0	0.0		110.0	21.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	hg19	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	A	8.047	0.765096	0.15914	.	.	ENSG00000153993	ENST00000284136	T	0.63096	-0.02	6.01	6.01	0.97437	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.173757	0.64402	D	0.000007	T	0.43277	0.1240	N	0.17312	0.475	0.80722	D	1	B	0.09022	0.002	B	0.12156	0.007	T	0.37454	-0.9705	10	0.09843	T	0.71	.	12.3054	0.54900	0.9328:0.0:0.0672:0.0	.	614	O95025	SEM3D_HUMAN	T	614	ENSP00000284136:I614T	ENSP00000284136:I614T	I	-	2	0	SEMA3D	84474121	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.112000	0.57845	2.307000	0.77673	0.528000	0.53228	ATA	.	.		0.383	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		G	84636185	A	G	84636185	3	3	79	1	0	0	0	0	1	0	0	0	14042	449	16	2	500	2	SEMA3D	7	84636185	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	9452770	84636185	74502478	92	10846										
PDK4	5166	hgsc.bcm.edu	37	chr7	95217044	95217044	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	acagagaatggttaccttaaTggtaaggtcttcttttccca	8	8	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:95217044T>A	ENST00000005178.5	-	8	1062	c.865A>T	c.(865-867)Att>Ttt	p.I289F		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	289	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			GTTACCTTAATGGTAAGGTCT	0.383																																					p.I289F		Atlas-SNP	.											.	PDK4	42	.	0			c.A865T						.						73	68	69					7																	95217044		2203	4300	6503	SO:0001583	missense	5166	exon8			CCTTAATGGTAAG	U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"pyruvate dehydrogenase kinase, isoenzyme 4"			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.865A>T	chr7.hg19:g.95217044T>A	ENSP00000005178:p.Ile289Phe	110.0	0.0		111.0	26.0	NM_002612		Missense_Mutation	SNP	ENST00000005178.5	hg19	CCDS5643.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.705964	0.48412	.	.	ENSG00000004799	ENST00000005178;ENST00000542888	T	0.61040	0.14	5.47	5.47	0.80525	Signal transduction histidine kinase, core (1);ATPase-like, ATP-binding domain (4);	0.000000	0.85682	D	0.000000	T	0.76198	0.3954	M	0.82923	2.615	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.79890	-0.1612	10	0.87932	D	0	.	11.8038	0.52143	0.0:0.0:0.1465:0.8535	.	289	Q16654	PDK4_HUMAN	F	289;253	ENSP00000005178:I289F	ENSP00000005178:I289F	I	-	1	0	PDK4	95054980	0.998000	0.40836	1.000000	0.80357	0.265000	0.26407	2.022000	0.41030	2.202000	0.70862	0.482000	0.46254	ATT	.	.		0.383	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612		A	95217044	T	A	95217044	3	1	79	1	0	0	0	0	1	0	0	0	11687	1464	51	4	386	4	PDK4	7	95217044	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	10580859	95217044	63921619	93	10847										
MUC17	140453	hgsc.bcm.edu	37	chr7	100683981	100683981	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	acctgctgaaggtaccagcaTgccaatctcaacttatagtg	8	11	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:100683981T>G	ENST00000306151.4	+	3	9348	c.9284T>G	c.(9283-9285)aTg>aGg	p.M3095R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3095	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GGTACCAGCATGCCAATCTCA	0.493																																					p.M3095R		Atlas-SNP	.											.	MUC17	804	.	0			c.T9284G						.						263	266	265					7																	100683981		2203	4300	6503	SO:0001583	missense	140453	exon3			CCAGCATGCCAAT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.9284T>G	chr7.hg19:g.100683981T>G	ENSP00000302716:p.Met3095Arg	59.0	0.0		75.0	24.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	t	3.822	-0.037642	0.07497	.	.	ENSG00000169876	ENST00000306151	T	0.01887	4.58	0.863	-1.73	0.08081	.	.	.	.	.	T	0.02156	0.0067	N	0.19112	0.55	0.09310	N	1	P	0.39520	0.676	P	0.49047	0.599	T	0.40194	-0.9576	9	0.15952	T	0.53	.	2.7502	0.05279	0.0:0.3099:0.2554:0.4347	.	3095	Q685J3	MUC17_HUMAN	R	3095	ENSP00000302716:M3095R	ENSP00000302716:M3095R	M	+	2	0	MUC17	100470701	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.060000	0.03475	-0.977000	0.03537	0.102000	0.15555	ATG	.	.		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100683981	T	G	100683981	3	3	79	1	0	0	0	0	1	0	0	0	9983	1464	51	5	9294	5	MUC17	7	100683981	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	5466937	100683981	58454682	94	10848										
DLD	1738	hgsc.bcm.edu	37	chr7	107556141	107556141	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agatggaaaaattgatgtttCgtaagtatacatcatttgtt	8	3	1	2	rs201652869		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:107556141C>T	ENST00000205402.5	+	9	1156	c.875C>T	c.(874-876)tCt>tTt	p.S292F	DLD_ENST00000440410.1_Splice_Site_p.S269F|DLD_ENST00000437604.2_Splice_Site_p.S244F|DLD_ENST00000537148.1_Splice_Site_p.S193F	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	292					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)	p.S292F(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	ATTGATGTTTCGTAAGTATAC	0.313																																					p.S292F		Atlas-SNP	.											DLD,rectum,carcinoma,0,1	DLD	72	.	1	Substitution - Missense(1)	large_intestine(1)	c.C875T						.	C	PHE/SER	0,4406		0,0,2203	48	49	49		875	3.5	1	7		49	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice	DLD	NM_000108.3	155	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	292/510	107556141	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	1738	exon9			ATGTTTCGTAAGT	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.875+1C>T	chr7.hg19:g.107556141C>T		94.0	1.0		107.0	22.0	NM_000108	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Missense_Mutation	SNP	ENST00000205402.5	hg19	CCDS5749.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.910567	0.72983	0.0	1.16E-4	ENSG00000091140	ENST00000205402;ENST00000417551;ENST00000537148;ENST00000440410;ENST00000437604;ENST00000539590	T;T;T;T;T	0.66460	-0.21;-0.21;0.34;-0.21;0.34	5.3	3.51	0.40186	Pyridine nucleotide-disulphide oxidoreductase, NAD-binding domain (1);Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.208574	0.49916	N	0.000138	T	0.76681	0.4021	M	0.82056	2.57	0.58432	D	0.999999	P;P;D	0.63880	0.879;0.513;0.993	P;B;P	0.55455	0.544;0.329;0.776	T	0.79240	-0.1885	10	0.72032	D	0.01	-1.8583	11.8398	0.52346	0.0:0.8586:0.0:0.1414	.	269;244;292	E9PEX6;B4DT69;P09622	.;.;DLDH_HUMAN	F	292;292;193;269;244;242	ENSP00000205402:S292F;ENSP00000390667:S292F;ENSP00000442399:S193F;ENSP00000417016:S269F;ENSP00000387542:S244F	ENSP00000205402:S292F	S	+	2	0	DLD	107343377	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.247000	0.51422	0.812000	0.34326	0.591000	0.81541	TCT	.	.		0.313	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108	Missense_Mutation	T	107556141	C	T	107556141	5	4	79	1	0	0	0	0	0	0	1	0	4553	898	31	1	909	1	DLD	7	107556141	Splice_Site	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	6872160	107556141	51582522	95	10849										
ST7	7982	hgsc.bcm.edu	37	chr7	116759650	116759653	+	Frame_Shift_Del	DEL	TTCA	TTCA	-													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tattttcgcaaatacggaacTtcattcattgaacaagtctc					rs368082187		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	TTCA	TTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:116759650_116759653delTTCA	ENST00000393446.2	+	3	573_576	c.270_273delTTCA	c.(268-273)acttcafs	p.TS90fs	ST7_ENST00000422922.1_Frame_Shift_Del_p.TS44fs|ST7_ENST00000465133.1_Frame_Shift_Del_p.TS47fs|ST7-AS2_ENST00000432541.1_RNA|ST7-AS2_ENST00000442719.1_RNA|ST7_ENST00000393447.4_Frame_Shift_Del_p.TS47fs|ST7_ENST00000432298.1_Frame_Shift_Del_p.TS44fs|ST7_ENST00000393443.1_Frame_Shift_Del_p.TS40fs|ST7-AS2_ENST00000434993.1_RNA|ST7_ENST00000487459.1_3'UTR|ST7_ENST00000393444.3_Frame_Shift_Del_p.TS47fs|ST7_ENST00000393449.1_Frame_Shift_Del_p.TS90fs|ST7_ENST00000265437.5_Frame_Shift_Del_p.TS90fs|ST7_ENST00000393451.3_Frame_Shift_Del_p.TS90fs|ST7_ENST00000323984.3_Frame_Shift_Del_p.TS90fs			Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		AATACGGAACTTCATTCATTGAAC	0.417																																					p.90_91del		Atlas-INDEL	.											.	ST7	64	.	0			c.269_272del						.																																			SO:0001589	frameshift_variant	7982	exon3			.	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000393446.2:c.270_273delTTCA	chr7.hg19:g.116759654_116759657delTTCA	ENSP00000377092:p.Thr90fs	80.0	0.0		92.0	19.0	NM_018412	A8K137|B4DRQ2	Frame_Shift_Del	DEL	ENST00000393446.2	hg19																																																																																				.	.		0.417	ST7-013	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000319687.1	NM_021908		-	116759653	TTCA	-	116759650	7	5	79	1	0	1	0	1	0	0	0	0	15244	1596	56	0	280	0	ST7	7	116759650	Frame_Shift_Del	DEL	TTCA	TCGA-CC-A8HT-01A-11D-A35Z-10	9203509	116759650	42379013	96	10850										
FAM3C	10447	hgsc.bcm.edu	37	chr7	121002990	121002990	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	atatttagtgtctaatacttCtcctgtttttcctaaaagag	5	7	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:121002990C>A	ENST00000359943.3	-	7	556	c.343G>T	c.(343-345)Gaa>Taa	p.E115*		NM_001040020.1|NM_014888.2	NP_001035109.1|NP_055703.1	Q92520	FAM3C_HUMAN	family with sequence similarity 3, member C	115					multicellular organismal development (GO:0007275)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	cytokine activity (GO:0005125)			kidney(1)|lung(8)	9	all_neural(327;0.117)					TCTAATACTTCTCCTGTTTTT	0.323																																					p.E115X		Atlas-SNP	.											.	FAM3C	29	.	0			c.G343T						.						143	126	132					7																	121002990		2203	4299	6502	SO:0001587	stop_gained	10447	exon7			ATACTTCTCCTGT	D87120	CCDS5782.1	7q22.1-q31.1	2014-08-14			ENSG00000196937	ENSG00000196937			18664	protein-coding gene	gene with protein product	"predicted osteoblast protein", "interleukin-like EMT inducer", "interleukin-like epithelial-mesenchymal transition inducer"	608618				12160727	Standard	NM_014888		Approved	GS3876, ILEI	uc010lkm.3	Q92520	OTTHUMG00000156979	ENST00000359943.3:c.343G>T	chr7.hg19:g.121002990C>A	ENSP00000353025:p.Glu115*	116.0	0.0		90.0	23.0	NM_014888	A6NDN2|A8K3R7	Nonsense_Mutation	SNP	ENST00000359943.3	hg19	CCDS5782.1	.	.	.	.	.	.	.	.	.	.	C	31	5.070424	0.93950	.	.	ENSG00000196937	ENST00000359943;ENST00000412653;ENST00000426156	.	.	.	5.51	4.61	0.57282	.	0.389466	0.33180	N	0.005183	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	-27.5175	16.4252	0.83812	0.0:0.8683:0.1317:0.0	.	.	.	.	X	115;115;85	.	ENSP00000353025:E115X	E	-	1	0	FAM3C	120790226	1.000000	0.71417	0.952000	0.39060	0.996000	0.88848	3.240000	0.51368	1.396000	0.46663	0.650000	0.86243	GAA	.	.		0.323	FAM3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346945.1	NM_001040020		A	121002990	C	A	121002990	4	1	79	1	0	0	0	0	0	1	0	0	5566	922	32	3	356	3	FAM3C	7	121002990	Nonsense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	4243340	121002990	38135673	97	10851										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142563351	142563351	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgcctggagggcttctaccgGgccagttccgacccaccaga	12	15	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:142563351G>C	ENST00000392957.2	+	8	1855	c.1068G>C	c.(1066-1068)cgG>cgC	p.R356R	EPHB6_ENST00000442129.1_Silent_p.R356R|EPHB6_ENST00000411471.2_Silent_p.R79R	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	356	Cys-rich.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)	p.R341R(1)		NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GCTTCTACCGGGCCAGTTCCG	0.647																																					p.R356R		Atlas-SNP	.											EPHB6,NS,carcinoma,+1,1	EPHB6	168	.	1	Substitution - coding silent(1)	pancreas(1)	c.G1068C						.						30	30	30					7																	142563351		2203	4300	6503	SO:0001819	synonymous_variant	2051	exon8			CTACCGGGCCAGT	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1068G>C	chr7.hg19:g.142563351G>C		64.0	0.0		41.0	6.0	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	hg19	CCDS5873.2																																																																																			.	.		0.647	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			C	142563351	G	C	142563351	2	2	79	1	0	0	0	0	0	0	0	1	5180	1219	43	4		4	EPHB6	7	142563351	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	21560361	142563351	16575312	98	10852										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142565796	142565796	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggagcagctgcagcaatacaGcagcccaggtggggatgagg	17	9	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr7:142565796G>A	ENST00000392957.2	+	13	2694	c.1907G>A	c.(1906-1908)aGc>aAc	p.S636N	EPHB6_ENST00000442129.1_Missense_Mutation_p.S636N|EPHB6_ENST00000411471.2_Missense_Mutation_p.S359N	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	636						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					CAGCAATACAGCAGCCCAGGT	0.627																																					p.S636N		Atlas-SNP	.											EPHB6,NS,malignant_melanoma,0,1	EPHB6	168	.	0			c.G1907A						.						39	38	38					7																	142565796		2202	4297	6499	SO:0001583	missense	2051	exon13			AATACAGCAGCCC	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1907G>A	chr7.hg19:g.142565796G>A	ENSP00000376684:p.Ser636Asn	284.0	0.0		259.0	68.0	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	hg19	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	G	9.226	1.034634	0.19590	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.10960	2.82;2.82;2.82	4.73	1.7	0.24286	.	0.514302	0.18045	N	0.153485	T	0.08088	0.0202	L	0.49350	1.555	0.29514	N	0.853981	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.23511	-1.0186	10	0.16896	T	0.51	.	4.0361	0.09730	0.0946:0.1328:0.5596:0.213	.	636;359	O15197;O15197-2	EPHB6_HUMAN;.	N	636;636;359	ENSP00000376684:S636N;ENSP00000410789:S636N;ENSP00000409061:S359N	ENSP00000376684:S636N	S	+	2	0	EPHB6	142275918	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	0.955000	0.29188	0.959000	0.37980	0.561000	0.74099	AGC	.	.		0.627	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			A	142565796	G	A	142565796	3	1	79	1	0	0	0	0	1	0	0	0	5180	971	34	3	1941	3	EPHB6	7	142565796	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	2445	142565796	16572867	99	10853										
GPR124	25960	hgsc.bcm.edu	37	chr8	37688996	37688996	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	caggcgagtgggagtgcaccGtgtccatggcccaaggcaac	15	12	0	0	rs372154008		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr8:37688996G>A	ENST00000412232.2	+	8	1001	c.988G>A	c.(988-990)Gtg>Atg	p.V330M	GPR124_ENST00000315215.7_Missense_Mutation_p.V330M	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	330	Ig-like.				central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			GGAGTGCACCGTGTCCATGGC	0.662																																					p.V330M		Atlas-SNP	.											.	GPR124	85	.	0			c.G988A						.	G	MET/VAL	0,4406		0,0,2203	145	103	117		988	5.2	1	8		117	1,8599	1.2+/-3.3	0,1,4299	no	missense	GPR124	NM_032777.9	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	330/1339	37688996	1,13005	2203	4300	6503	SO:0001583	missense	25960	exon8			TGCACCGTGTCCA	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.988G>A	chr8.hg19:g.37688996G>A	ENSP00000406367:p.Val330Met	84.0	0.0		62.0	22.0	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	G	20.7	4.038315	0.75617	0.0	1.16E-4	ENSG00000020181	ENST00000416514;ENST00000315215;ENST00000412232	T;T	0.54479	0.57;0.57	5.22	5.22	0.72569	Immunoglobulin subtype (1);Immunoglobulin-like (1);GPCR, family 2, extracellular hormone receptor domain (1);Immunoglobulin-like fold (1);	0.154508	0.41823	D	0.000810	T	0.58991	0.2161	M	0.62723	1.935	0.43214	D	0.995087	D;D	0.55385	0.963;0.971	P;P	0.51016	0.656;0.595	T	0.63251	-0.6679	10	0.66056	D	0.02	-16.9956	11.8794	0.52566	0.1269:0.0:0.8731:0.0	.	330;330	Q96PE1-2;Q96PE1	.;GP124_HUMAN	M	323;330;330	ENSP00000323508:V330M;ENSP00000406367:V330M	ENSP00000323508:V330M	V	+	1	0	GPR124	37808154	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	4.080000	0.57620	2.458000	0.83093	0.449000	0.29647	GTG	.	.		0.662	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			A	37688996	G	A	37688996	3	1	79	1	0	0	0	0	1	0	0	0	6646	1145	40	1	997	1	GPR124	8	37688996	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10		37688996	108675026	100	10854										
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48508432	48508432	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tctgaatacttacttttgtgAgaaagttgttgccaaagaag	9	5	1	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr8:48508432A>T	ENST00000297423.4	+	9	1541	c.1157A>T	c.(1156-1158)gAg>gTg	p.E386V	SPIDR_ENST00000541342.1_Missense_Mutation_p.E316V|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000518074.1_Missense_Mutation_p.E326V	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	386	Necessary for interaction with RAD51.				cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											TACTTTTGTGAGAAAGTTGTT	0.383																																					p.E386V		Atlas-SNP	.											.	KIAA0146	64	.	0			c.A1157T						.						98	91	93					8																	48508432		1821	4093	5914	SO:0001583	missense	23514	exon9			TTTGTGAGAAAGT	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"KIAA0146"	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.1157A>T	chr8.hg19:g.48508432A>T	ENSP00000297423:p.Glu386Val	173.0	0.0		187.0	46.0	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	hg19	CCDS43737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.27|16.27	3.075840|3.075840	0.55646|0.55646	.|.	.|.	ENSG00000164808|ENSG00000164808	ENST00000297423;ENST00000518074;ENST00000541342;ENST00000524006|ENST00000519401	.|.	.|.	.|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.243014|.	0.34291|.	N|.	0.004082|.	T|.	0.43100|.	0.1232|.	L|L	0.29908|0.29908	0.895|0.895	0.29979|0.29979	N|N	0.817881|0.817881	P;P;P;P|.	0.35982|.	0.531;0.531;0.531;0.531|.	B;B;B;B|.	0.32805|.	0.153;0.153;0.153;0.153|.	T|.	0.41716|.	-0.9493|.	9|.	0.87932|.	D|.	0|.	.|.	13.0538|13.0538	0.58969|0.58969	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	326;316;386;386|.	B4E0Y6;B4DFV2;B4DEV5;Q14159|.	.;.;.;K0146_HUMAN|.	V|X	386;326;316;75|68	.|.	ENSP00000297423:E386V|.	E|R	+|+	2|1	0|2	KIAA0146|KIAA0146	48670985|48670985	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.656000|0.656000	0.38851|0.38851	5.135000|5.135000	0.64777|0.64777	2.133000|2.133000	0.65898|0.65898	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.383	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		T	48508432	A	T	48508432	3	4	79	1	0	0	0	0	1	0	0	0	8166	304	11	4	1191	4	KIAA0146	8	48508432	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	10819436	48508432	97855590	101	10855										
TOX	9760	hgsc.bcm.edu	37	chr8	59764302	59764302	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcaggctggccccttggtctCatggctgccatctgaggatg	14	12	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr8:59764302C>A	ENST00000361421.1	-	4	694	c.474G>T	c.(472-474)atG>atT	p.M158I		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	158						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				CCCTTGGTCTCATGGCTGCCA	0.438																																					p.M158I	Pancreas(161;610 1969 17913 21374 22725)	Atlas-SNP	.											.	TOX	83	.	0			c.G474T						.						117	100	106					8																	59764302		2203	4300	6503	SO:0001583	missense	9760	exon4			TGGTCTCATGGCT		CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.474G>T	chr8.hg19:g.59764302C>A	ENSP00000354842:p.Met158Ile	62.0	0.0		75.0	16.0	NM_014729	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	hg19	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.691497	0.30052	.	.	ENSG00000198846	ENST00000361421	T	0.41065	1.01	5.82	4.04	0.47022	.	0.658299	0.17842	N	0.160180	T	0.37839	0.1018	L	0.54323	1.7	0.37032	D	0.896738	B	0.02656	0.0	B	0.01281	0.0	T	0.27123	-1.0083	9	.	.	.	.	12.4044	0.55430	0.0:0.8655:0.0:0.1345	.	158	O94900	TOX_HUMAN	I	158	ENSP00000354842:M158I	.	M	-	3	0	TOX	59926856	1.000000	0.71417	0.983000	0.44433	0.960000	0.62799	2.549000	0.45803	0.816000	0.34421	0.555000	0.69702	ATG	.	.		0.438	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		A	59764302	C	A	59764302	3	1	79	1	0	0	0	0	1	0	0	0	16392	826	29	3	1130	3	TOX	8	59764302	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	11255870	59764302	86599720	102	10856										
PREX2	80243	hgsc.bcm.edu	37	chr8	69011946	69011946	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gccctggctaaaagtgatgaGcattttgtacaaaactgtac	9	8	0	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr8:69011946G>T	ENST00000288368.4	+	23	2860	c.2583G>T	c.(2581-2583)gaG>gaT	p.E861D	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	861					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AAAGTGATGAGCATTTTGTAC	0.398																																					p.E861D		Atlas-SNP	.											.	PREX2	614	.	0			c.G2583T						.						158	138	145					8																	69011946		2203	4300	6503	SO:0001583	missense	80243	exon23			TGATGAGCATTTT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2583G>T	chr8.hg19:g.69011946G>T	ENSP00000288368:p.Glu861Asp	92.0	0.0		115.0	24.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	9.898	1.206102	0.22205	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.35973	1.28	5.66	-3.04	0.05412	.	0.275519	0.36268	N	0.002681	T	0.16214	0.0390	N	0.22421	0.69	0.45307	D	0.998305	B;B;B	0.09022	0.0;0.0;0.002	B;B;B	0.14578	0.002;0.001;0.011	T	0.03993	-1.0986	10	0.29301	T	0.29	.	3.0037	0.06021	0.3619:0.0728:0.3959:0.1694	.	861;861;861	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	D	861	ENSP00000288368:E861D	ENSP00000288368:E861D	E	+	3	2	PREX2	69174500	0.348000	0.24861	0.996000	0.52242	0.522000	0.34438	-0.219000	0.09228	-0.154000	0.11118	-1.740000	0.00687	GAG	.	.		0.398	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	69011946	G	T	69011946	3	4	79	1	0	0	0	0	1	0	0	0	12489	962	34	3	2673	3	PREX2	8	69011946	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	9247644	69011946	77352076	103	10857										
PMP2	5375	hgsc.bcm.edu	37	chr8	82356797	82356797	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctctttgccatcccatctctGcacttgattcagtgatcctc	5	15	3	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr8:82356797G>T	ENST00000256103.2	-	3	422	c.286C>A	c.(286-288)Cag>Aag	p.Q96K	PMP2_ENST00000519260.1_Missense_Mutation_p.A38E|RP11-157I4.4_ENST00000524085.2_RNA	NM_002677.3	NP_002668.1	P02689	MYP2_HUMAN	peripheral myelin protein 2	96					membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cholesterol binding (GO:0015485)|fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			Epithelial(68;0.186)			TCCCATCTCTGCACTTGATTC	0.403																																					p.Q96K		Atlas-SNP	.											PMP2,NS,carcinoma,0,1	PMP2	21	.	0			c.C286A						.						153	137	142					8																	82356797		2203	4300	6503	SO:0001583	missense	5375	exon3			ATCTCTGCACTTG	X62167	CCDS6229.1	8q21.3-q22.1	2013-03-01			ENSG00000147588	ENSG00000147588		"Fatty acid binding protein family"	9117	protein-coding gene	gene with protein product		170715				1720307, 8288226	Standard	NM_002677		Approved	MP2, FABP8, M-FABP	uc003ycb.1	P02689	OTTHUMG00000164600	ENST00000256103.2:c.286C>A	chr8.hg19:g.82356797G>T	ENSP00000256103:p.Gln96Lys	136.0	0.0		152.0	64.0	NM_002677	Q6FHL4	Missense_Mutation	SNP	ENST00000256103.2	hg19	CCDS6229.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.28|17.28	3.350624|3.350624	0.61183|0.61183	.|.	.|.	ENSG00000147588|ENSG00000147588	ENST00000519260|ENST00000256103	.|T	.|0.09163	.|3.01	5.89|5.89	5.89|5.89	0.94794|0.94794	.|Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.40619|0.40619	0.1124|0.1124	M|M	0.84846|0.84846	2.72|2.72	0.43982|0.43982	D|D	0.996674|0.996674	.|D	.|0.89917	.|1.0	.|D	.|0.71870	.|0.975	T|T	0.27157|0.27157	-1.0082|-1.0082	6|10	0.87932|0.72032	D|D	0|0.01	.|.	20.2508|20.2508	0.98407|0.98407	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|96	.|P02689	.|MYP2_HUMAN	E|K	38|96	.|ENSP00000256103:Q96K	ENSP00000429917:A38E|ENSP00000256103:Q96K	A|Q	-|-	2|1	0|0	PMP2|PMP2	82519352|82519352	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.885000|0.885000	0.51271|0.51271	7.984000|7.984000	0.88150|0.88150	2.788000|2.788000	0.95919|0.95919	0.585000|0.585000	0.79938|0.79938	GCA|CAG	.	.		0.403	PMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379365.1	NM_002677		T	82356797	G	T	82356797	3	4	79	1	0	0	0	0	1	0	0	0	12147	1328	46	3	120	3	PMP2	8	82356797	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	13344851	82356797	64007225	104	10858										
RAD54B	25788	hgsc.bcm.edu	37	chr8	95384520	95384520	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	aaaatgtttccattgcttcaGctgggacatagaaagaggtt	10	6	1	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr8:95384520G>C	ENST00000336148.5	-	15	2735	c.2611C>G	c.(2611-2613)Ctg>Gtg	p.L871V	RAD54B_ENST00000519348.1_5'UTR	NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	871					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			CATTGCTTCAGCTGGGACATA	0.353								Direct reversal of damage;Homologous recombination																													p.L871V		Atlas-SNP	.											.	RAD54B	88	.	0			c.C2611G						.						93	92	92					8																	95384520		2203	4300	6503	SO:0001583	missense	25788	exon15			GCTTCAGCTGGGA	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.2611C>G	chr8.hg19:g.95384520G>C	ENSP00000336606:p.Leu871Val	107.0	0.0		150.0	29.0	NM_012415	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	hg19	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.473171	0.63737	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	D	0.91237	-2.81	5.65	3.53	0.40419	.	0.000000	0.64402	D	0.000001	D	0.95059	0.8400	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94735	0.7913	10	0.72032	D	0.01	-5.5327	8.9996	0.36074	0.2644:0.0:0.7356:0.0	.	871	Q9Y620	RA54B_HUMAN	V	871;543	ENSP00000336606:L871V	ENSP00000336606:L871V	L	-	1	2	RAD54B	95453696	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.830000	0.27462	1.397000	0.46682	0.563000	0.77884	CTG	.	.		0.353	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		C	95384520	G	C	95384520	3	2	79	1	0	0	0	0	1	0	0	0	13007	962	34	4	125	4	RAD54B	8	95384520	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	13027723	95384520	50979502	105	10859										
RGS22	26166	hgsc.bcm.edu	37	chr8	101011556	101011556	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggcagccatacattttctagCctattttgcacatgcttctg	7	11	2	0	rs371559852		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr8:101011556C>G	ENST00000360863.6	-	19	3077	c.2883G>C	c.(2881-2883)agG>agC	p.R961S	RGS22_ENST00000523287.1_Missense_Mutation_p.R780S|RGS22_ENST00000519421.1_5'Flank|RGS22_ENST00000523437.1_Missense_Mutation_p.R949S	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	961	RGS 1. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			CATTTTCTAGCCTATTTTGCA	0.383																																					p.R961S		Atlas-SNP	.											.	RGS22	319	.	0			c.G2883C						.						86	83	84					8																	101011556		1859	4108	5967	SO:0001583	missense	26166	exon19			TTCTAGCCTATTT	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.2883G>C	chr8.hg19:g.101011556C>G	ENSP00000354109:p.Arg961Ser	107.0	0.0		118.0	27.0	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	hg19	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563471	0.45694	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437	T;T;T	0.21543	2.0;2.0;2.0	5.1	0.182	0.15077	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.135740	0.47455	D	0.000223	T	0.28632	0.0709	M	0.71581	2.175	0.26408	N	0.976315	P;P;D	0.55172	0.892;0.892;0.97	P;P;P	0.51657	0.575;0.575;0.676	T	0.14531	-1.0469	10	0.87932	D	0	.	6.3177	0.21200	0.0:0.5105:0.1194:0.3701	.	949;961;780	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	S	961;948;780;949	ENSP00000354109:R961S;ENSP00000429382:R780S;ENSP00000428212:R949S	ENSP00000354109:R961S	R	-	3	2	RGS22	101080732	1.000000	0.71417	0.763000	0.31416	0.853000	0.48598	1.006000	0.29847	-0.289000	0.09038	-0.140000	0.14226	AGG	.	.		0.383	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		G	101011556	C	G	101011556	3	3	79	1	0	0	0	0	1	0	0	0	13320	738	26	4	947	4	RGS22	8	101011556	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	5627036	101011556	45352466	106	10860										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110408332	110408332	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ataagtgggcgtttctttgaTcagacagatttccccgtcag	10	9	3	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr8:110408332T>C	ENST00000378402.5	+	11	992	c.888T>C	c.(886-888)gaT>gaC	p.D296D		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	296	IPT/TIG 3.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GTTTCTTTGATCAGACAGATT	0.403										HNSCC(38;0.096)																											p.D296D		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T888C						.						78	68	71					8																	110408332		1992	4187	6179	SO:0001819	synonymous_variant	93035	exon11			CTTTGATCAGACA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.888T>C	chr8.hg19:g.110408332T>C		70.0	0.0		90.0	14.0	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.		0.403	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110408332	T	C	110408332	2	2	79	1	0	0	0	0	0	0	0	1	11981	1432	50	2		2	PKHD1L1	8	110408332	Silent	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	9396776	110408332	35955690	107	10861										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116599386	116599386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	aggtcgcgccagatgggcggCctccacattgggactatccc	13	14	0	1	rs377704400		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr8:116599386C>T	ENST00000220888.5	-	4	2662	c.2503G>A	c.(2503-2505)Gcc>Acc	p.A835T	TRPS1_ENST00000519674.1_Missense_Mutation_p.A835T|TRPS1_ENST00000395715.3_Missense_Mutation_p.A848T|TRPS1_ENST00000519076.1_Missense_Mutation_p.A589T|TRPS1_ENST00000520276.1_Missense_Mutation_p.A839T			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	835					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			AGATGGGCGGCCTCCACATTG	0.617									Langer-Giedion syndrome																												p.A848T		Atlas-SNP	.											.	TRPS1	516	.	0			c.G2542A						.	C	THR/ALA	1,3749		0,1,1874	54	56	56		2542	5.8	1	8		56	0,8204		0,0,4102	no	missense	TRPS1	NM_014112.2	58	0,1,5976	TT,TC,CC		0.0,0.0267,0.0084	probably-damaging	848/1295	116599386	1,11953	1875	4102	5977	SO:0001583	missense	7227	exon5	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	GGGCGGCCTCCAC	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2503G>A	chr8.hg19:g.116599386C>T	ENSP00000220888:p.Ala835Thr	77.0	0.0		89.0	35.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	C	22.5	4.299244	0.81025	2.67E-4	0.0	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276;ENST00000519674	D;D;D;D;T	0.98474	-4.95;-4.92;-4.9;-4.92;0.87	5.76	5.76	0.90799	.	0.179181	0.47852	D	0.000218	D	0.97879	0.9303	L	0.29908	0.895	0.41908	D	0.990457	D;D;D	0.67145	0.996;0.993;0.996	P;P;P	0.60609	0.829;0.679;0.877	D	0.99453	1.0941	10	0.72032	D	0.01	.	19.9813	0.97326	0.0:1.0:0.0:0.0	.	839;835;848	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	T	848;835;589;839;835	ENSP00000379065:A848T;ENSP00000220888:A835T;ENSP00000428910:A589T;ENSP00000428680:A839T;ENSP00000429174:A835T	ENSP00000220888:A835T	A	-	1	0	TRPS1	116668561	1.000000	0.71417	0.999000	0.59377	0.654000	0.38779	5.359000	0.66074	2.726000	0.93360	0.655000	0.94253	GCC	.	.		0.617	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		T	116599386	C	T	116599386	3	4	79	1	0	0	0	0	1	0	0	0	16608	739	26	3	1354	3	TRPS1	8	116599386	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	6191054	116599386	29764636	108	10862										
LRRC14	9684	hgsc.bcm.edu	37	chr8	145746557	145746557	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tacccatcctgactcagtgcGccagtctccggtaccttggc	9	16	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr8:145746557G>A	ENST00000292524.1	+	4	1323	c.1177G>A	c.(1177-1179)Gcc>Acc	p.A393T	LRRC14_ENST00000529022.1_Missense_Mutation_p.A393T	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	393										endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GACTCAGTGCGCCAGTCTCCG	0.607																																					p.A393T		Atlas-SNP	.											LRRC14,NS,carcinoma,0,1	LRRC14	25	.	0			c.G1177A						.						77	67	70					8																	145746557		2203	4300	6503	SO:0001583	missense	9684	exon5			CAGTGCGCCAGTC	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179	ENST00000292524.1:c.1177G>A	chr8.hg19:g.145746557G>A	ENSP00000292524:p.Ala393Thr	59.0	0.0		58.0	20.0	NM_001272036	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.621997	0.00117	.	.	ENSG00000160959	ENST00000529022;ENST00000292524	T;T	0.09255	3.0;3.0	4.61	-3.77	0.04346	.	0.608394	0.17343	N	0.177692	T	0.02888	0.0086	N	0.02539	-0.55	0.09310	N	1	B	0.18013	0.025	B	0.12156	0.007	T	0.32508	-0.9904	10	0.32370	T	0.25	.	4.5321	0.12010	0.3629:0.0:0.3217:0.3154	.	393	Q15048	LRC14_HUMAN	T	393	ENSP00000434768:A393T;ENSP00000292524:A393T	ENSP00000292524:A393T	A	+	1	0	LRRC14	145717365	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.824000	0.04438	-1.100000	0.03030	-2.067000	0.00394	GCC	.	.		0.607	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		A	145746557	G	A	145746557	3	1	79	1	0	0	0	0	1	0	0	0	8977	1087	38	1	1187	1	LRRC14	8	145746557	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	29147171	145746557	617465	109	10863										
KANK1	23189	hgsc.bcm.edu	37	chr9	711564	711564	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctgcagcacatccgcgagcaGatggccattgctctgaaacg	11	13	1	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr9:711564G>T	ENST00000382303.1	+	7	1450	c.798G>T	c.(796-798)caG>caT	p.Q266H	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.Q266H|KANK1_ENST00000382293.3_Missense_Mutation_p.Q108H	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	266					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		TCCGCGAGCAGATGGCCATTG	0.597																																					p.Q266H		Atlas-SNP	.											.	KANK1	231	.	0			c.G798T						.						75	72	73					9																	711564		2203	4300	6503	SO:0001583	missense	23189	exon7			CGAGCAGATGGCC	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.798G>T	chr9.hg19:g.711564G>T	ENSP00000371740:p.Gln266His	66.0	0.0		70.0	11.0	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	hg19	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252651	0.59212	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.00966	5.49;5.49;5.49	5.82	3.67	0.42095	.	0.000000	0.53938	D	0.000055	T	0.05044	0.0135	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.05225	-1.0898	10	0.87932	D	0	-6.5511	9.3378	0.38060	0.2512:0.0:0.7488:0.0	.	266;266	Q5W0W1;Q14678	.;KANK1_HUMAN	H	266;266;266;108	ENSP00000371740:Q266H;ENSP00000371734:Q266H;ENSP00000371730:Q108H	ENSP00000346479:Q266H	Q	+	3	2	KANK1	701564	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.457000	0.45005	1.485000	0.48380	0.655000	0.94253	CAG	.	.		0.597	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		T	711564	G	T	711564	3	4	79	1	0	0	0	0	1	0	0	0	7985	933	33	3	804	3	KANK1	9	711564	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10		711564	140501867	110	10864										
KANK1	23189	hgsc.bcm.edu	37	chr9	713298	713298	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cagacactgctggctgagaaCtacagtgaactggcagaagc	12	10	0	4			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr9:713298C>A	ENST00000382303.1	+	7	3184	c.2532C>A	c.(2530-2532)aaC>aaA	p.N844K	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.N844K|KANK1_ENST00000382293.3_Missense_Mutation_p.N686K	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	844					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		TGGCTGAGAACTACAGTGAAC	0.532																																					p.N844K		Atlas-SNP	.											.	KANK1	231	.	0			c.C2532A						.						146	139	141					9																	713298		2203	4300	6503	SO:0001583	missense	23189	exon7			TGAGAACTACAGT	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.2532C>A	chr9.hg19:g.713298C>A	ENSP00000371740:p.Asn844Lys	115.0	0.0		113.0	27.0	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	hg19	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.347522	0.82022	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.16597	2.33;2.33;2.33	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000017	T	0.42040	0.1185	M	0.74258	2.255	0.80722	D	1	D;P	0.89917	1.0;0.853	D;B	0.87578	0.998;0.406	T	0.25257	-1.0137	10	0.72032	D	0.01	.	13.4043	0.60903	0.0:0.919:0.0:0.081	.	844;844	Q5W0W1;Q14678	.;KANK1_HUMAN	K	844;844;844;686	ENSP00000371740:N844K;ENSP00000371734:N844K;ENSP00000371730:N686K	ENSP00000346479:N844K	N	+	3	2	KANK1	703298	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.635000	0.46537	2.654000	0.90174	0.655000	0.94253	AAC	.	.		0.532	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		A	713298	C	A	713298	3	1	79	1	0	0	0	0	1	0	0	0	7985	564	20	3	2538	3	KANK1	9	713298	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	1734	713298	140500133	111	10865										
C9orf131	138724	hgsc.bcm.edu	37	chr9	35044802	35044802	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gccctctggcagtggatcccCtacacccagtaccccagcct	8	19	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr9:35044802C>T	ENST00000312292.5	+	2	2223	c.2176C>T	c.(2176-2178)Cta>Tta	p.L726L	C9orf131_ENST00000354479.5_Silent_p.L653L|C9orf131_ENST00000421362.2_Silent_p.L678L|FLJ00273_ENST00000595331.1_5'Flank	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	726										cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			AGTGGATCCCCTACACCCAGT	0.552																																					p.L726L		Atlas-SNP	.											.	C9orf131	71	.	0			c.C2176T						.						65	64	64					9																	35044802		2203	4300	6503	SO:0001819	synonymous_variant	138724	exon2			GATCCCCTACACC	BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.2176C>T	chr9.hg19:g.35044802C>T		61.0	0.0		67.0	11.0	NM_203299	A6NLE6|E9PB26|Q86XC6|Q9UF74	Silent	SNP	ENST00000312292.5	hg19	CCDS6572.2																																																																																			.	.		0.552	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299		T	35044802	C	T	35044802	2	4	79	1	0	0	0	0	0	0	0	1	2459	680	24	3		3	C9orf131	9	35044802	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	34331504	35044802	106168629	112	10866										
ALDOB	229	hgsc.bcm.edu	37	chr9	104187850	104187850	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gtcaccatgttgggctttagCagggtgccctccaggtaaac	12	11	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr9:104187850C>T	ENST00000374855.4	-	7	808	c.684G>A	c.(682-684)ctG>ctA	p.L228L	ALDOB_ENST00000468981.3_5'UTR	NM_000035.3	NP_000026.2	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	228					carbohydrate metabolic process (GO:0005975)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose catabolic process (GO:0006001)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|NADH oxidation (GO:0006116)|positive regulation of ATPase activity (GO:0032781)|small molecule metabolic process (GO:0044281)|vacuolar proton-transporting V-type ATPase complex assembly (GO:0070072)	centriolar satellite (GO:0034451)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)	ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)|fructose binding (GO:0070061)|fructose-1-phosphate aldolase activity (GO:0061609)|fructose-bisphosphate aldolase activity (GO:0004332)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(5)|prostate(2)|skin(4)|urinary_tract(1)	24		Acute lymphoblastic leukemia(62;0.0559)				TGGGCTTTAGCAGGGTGCCCT	0.527																																					p.L228L		Atlas-SNP	.											.	ALDOB	69	.	0			c.G684A						.						196	158	171					9																	104187850		2203	4300	6503	SO:0001819	synonymous_variant	229	exon7			CTTTAGCAGGGTG	X01098	CCDS6756.1	9q21.3-q22.2	2008-02-05			ENSG00000136872	ENSG00000136872	4.1.2.13		417	protein-coding gene	gene with protein product		612724					Standard	NM_000035		Approved		uc004bbk.2	P05062	OTTHUMG00000020378	ENST00000374855.4:c.684G>A	chr9.hg19:g.104187850C>T		90.0	0.0		70.0	12.0	NM_000035	Q13741|Q13742|Q5T7D6	Silent	SNP	ENST00000374855.4	hg19	CCDS6756.1																																																																																			.	.		0.527	ALDOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053434.2			T	104187850	C	T	104187850	2	4	79	1	0	0	0	0	0	0	0	1	508	697	25	3		3	ALDOB	9	104187850	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	69143048	104187850	37025581	113	10867										
INPP5E	56623	hgsc.bcm.edu	37	chr9	139333590	139333590	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tcctggctgcctcgaaaacgCctcctcctccagcccttgtc	7	19	0	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr9:139333590C>A	ENST00000371712.3	-	1	684	c.282G>T	c.(280-282)agG>agT	p.R94S	SEC16A_ENST00000467838.1_5'Flank	NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		CTCGAAAACGCCTCCTCCTCC	0.731																																					p.R94S		Atlas-SNP	.											.	INPP5E	18	.	0			c.G282T						.						5	5	5					9																	139333590		1958	3868	5826	SO:0001583	missense	56623	exon1			AAAACGCCTCCTC	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"Joubert syndrome 1"	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.282G>T	chr9.hg19:g.139333590C>A	ENSP00000360777:p.Arg94Ser	518.0	0.0		395.0	101.0	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371712.3	hg19	CCDS7000.1	.	.	.	.	.	.	.	.	.	.	C	15.77	2.931158	0.52866	.	.	ENSG00000148384	ENST00000371712	T	0.42900	0.96	3.98	1.92	0.25849	.	2.353540	0.02539	N	0.094378	T	0.59715	0.2214	L	0.55990	1.75	0.44373	D	0.997277	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.987	T	0.50215	-0.8854	10	0.87932	D	0	-30.922	6.157	0.20344	0.0:0.6564:0.1563:0.1873	.	94;94	Q9NRR6-2;Q9NRR6	.;INP5E_HUMAN	S	94	ENSP00000360777:R94S	ENSP00000360777:R94S	R	-	3	2	INPP5E	138453411	0.883000	0.30277	0.851000	0.33527	0.059000	0.15707	0.031000	0.13710	0.778000	0.33520	0.558000	0.71614	AGG	.	.		0.731	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892		A	139333590	C	A	139333590	3	1	79	1	0	0	0	0	1	0	0	0	7766	738	26	3	1692	3	INPP5E	9	139333590	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	35145740	139333590	1879841	114	10868										
C10orf18	54906	hgsc.bcm.edu	37	chr10	5791217	5791217	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgagaacttcacacggcctgAggaggcacccgagtttcagt	12	11	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr10:5791217A>C	ENST00000328090.5	+	15	6458	c.5833A>C	c.(5833-5835)Agg>Cgg	p.R1945R		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1945																	ACACGGCCTGAGGAGGCACCC	0.522																																					p.R1945R		Atlas-SNP	.											.	.	.	.	0			c.A5833C						.						40	42	41					10																	5791217		2051	4186	6237	SO:0001819	synonymous_variant	54906	exon15			GGCCTGAGGAGGC	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.5833A>C	chr10.hg19:g.5791217A>C		81.0	0.0		87.0	23.0	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Silent	SNP	ENST00000328090.5	hg19	CCDS41485.1																																																																																			.	.		0.522	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		C	5791217	A	C	5791217	2	2	79	1	0	0	0	0	0	0	0	1	1598	295	11	5		5	C10orf18	10	5791217	Silent	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10		5791217	129743530	115	10869										
FBXO18	84893	hgsc.bcm.edu	37	chr10	5945032	5945032	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gccattgactgccagcatttGgctcggagtcacttggctgt	12	11	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr10:5945032G>C	ENST00000362091.4	+	2	166	c.51G>C	c.(49-51)ttG>ttC	p.L17F	FBXO18_ENST00000379999.5_Missense_Mutation_p.L68F|FBXO18_ENST00000397269.3_5'UTR|FBXO18_ENST00000470089.1_Intron	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	17					DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						GCCAGCATTTGGCTCGGAGTC	0.478																																					p.L68F		Atlas-SNP	.											.	FBXO18	108	.	0			c.G204C						.						105	92	96					10																	5945032		2203	4300	6503	SO:0001583	missense	84893	exon3			GCATTTGGCTCGG	AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"F-boxes /  "other""	13620	protein-coding gene	gene with protein product		607222	"F-box only protein 18"			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.51G>C	chr10.hg19:g.5945032G>C	ENSP00000355415:p.Leu17Phe	119.0	0.0		96.0	29.0	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Missense_Mutation	SNP	ENST00000362091.4	hg19	CCDS7072.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.893268	0.52121	.	.	ENSG00000134452	ENST00000362091;ENST00000379999	.	.	.	5.42	2.29	0.28610	.	0.000000	0.64402	D	0.000004	T	0.66819	0.2828	L	0.58101	1.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.67284	-0.5709	9	0.87932	D	0	-13.0962	6.659	0.23004	0.1508:0.2834:0.5657:0.0	.	68;17	Q8NFZ0-2;Q8NFZ0	.;FBX18_HUMAN	F	17;68	.	ENSP00000355415:L17F	L	+	3	2	FBXO18	5985038	0.063000	0.20901	0.998000	0.56505	0.345000	0.29048	0.119000	0.15626	1.268000	0.44264	0.655000	0.94253	TTG	.	.		0.478	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807		C	5945032	G	C	5945032	3	2	79	1	0	0	0	0	1	0	0	0	5739	1339	47	4	219	4	FBXO18	10	5945032	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	153815	5945032	129589715	116	10870										
CUBN	8029	hgsc.bcm.edu	37	chr10	17113474	17113474	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	aacttccaatttcaaagacaGtgaagttgaggagaatgact	9	6	1	5			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr10:17113474G>A	ENST00000377833.4	-	19	2641	c.2576C>T	c.(2575-2577)aCt>aTt	p.T859I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	859	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTCAAAGACAGTGAAGTTGAG	0.398																																					p.T859I		Atlas-SNP	.											.	CUBN	515	.	0			c.C2576T						.						88	86	87					10																	17113474		2203	4300	6503	SO:0001583	missense	8029	exon19			AAGACAGTGAAGT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2576C>T	chr10.hg19:g.17113474G>A	ENSP00000367064:p.Thr859Ile	134.0	0.0		103.0	21.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	7.077	0.569519	0.13560	.	.	ENSG00000107611	ENST00000377833	T	0.18810	2.19	5.47	4.56	0.56223	CUB (5);	0.000000	0.41605	D	0.000858	T	0.14743	0.0356	L	0.41824	1.3	0.80722	D	1	P	0.35383	0.498	B	0.32677	0.15	T	0.03240	-1.1057	10	0.32370	T	0.25	.	7.1499	0.25604	0.1383:0.0:0.7177:0.144	.	859	O60494	CUBN_HUMAN	I	859	ENSP00000367064:T859I	ENSP00000367064:T859I	T	-	2	0	CUBN	17153480	0.994000	0.37717	0.986000	0.45419	0.500000	0.33767	2.635000	0.46537	2.576000	0.86940	0.502000	0.49764	ACT	.	.		0.398	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	17113474	G	A	17113474	3	1	79	1	0	0	0	0	1	0	0	0	4053	1029	36	3	8491	3	CUBN	10	17113474	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	11168442	17113474	118421273	117	10871										
NRP1	8829	hgsc.bcm.edu	37	chr10	33619799	33619799	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gctttcaatttttatagtatCgccacatttatctgcaatga	5	8	2	1	rs374276976		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr10:33619799C>T	ENST00000265371.4	-	3	610	c.85G>A	c.(85-87)Gat>Aat	p.D29N	NRP1_ENST00000374823.5_Missense_Mutation_p.D29N|NRP1_ENST00000432372.2_Missense_Mutation_p.D29N|NRP1_ENST00000395995.1_Missense_Mutation_p.D29N|NRP1_ENST00000374875.1_5'UTR|NRP1_ENST00000374821.5_Missense_Mutation_p.D29N|NRP1_ENST00000374867.2_Missense_Mutation_p.D29N|NRP1_ENST00000374816.3_Missense_Mutation_p.D29N|NRP1_ENST00000374822.4_Missense_Mutation_p.D29N			O14786	NRP1_HUMAN	neuropilin 1	29	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	TTTATAGTATCGCCACATTTA	0.373																																					p.D29N	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.G85A						.	C	ASN/ASP,ASN/ASP,ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	79	88	85		85,85,85	5.1	0.9	10		85	0,8598		0,0,4299	no	missense,missense,missense	NRP1	NM_001024628.2,NM_001024629.2,NM_003873.5	23,23,23	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	29/645,29/610,29/924	33619799	1,13003	2203	4299	6502	SO:0001583	missense	8829	exon2			TAGTATCGCCACA	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"CD molecules"	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.85G>A	chr10.hg19:g.33619799C>T	ENSP00000265371:p.Asp29Asn	117.0	0.0		148.0	28.0	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Missense_Mutation	SNP	ENST00000265371.4	hg19	CCDS7177.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.258284	0.59321	2.27E-4	0.0	ENSG00000099250	ENST00000265371;ENST00000374867;ENST00000395995;ENST00000374822;ENST00000374821;ENST00000374823;ENST00000374816	T;T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25;2.25	5.99	5.09	0.68999	CUB (5);	0.242175	0.47455	N	0.000234	T	0.17874	0.0429	L	0.28344	0.845	0.47659	D	0.999481	P;P;D;B;B;B;P;P	0.55800	0.808;0.95;0.973;0.316;0.002;0.002;0.808;0.808	B;P;P;B;B;B;B;B	0.46585	0.305;0.521;0.521;0.146;0.002;0.004;0.305;0.305	T	0.01444	-1.1353	10	0.72032	D	0.01	-5.9915	15.2411	0.73471	0.0:0.9331:0.0:0.0669	.	29;29;29;29;29;29;29;29	A8K9V7;E7EX60;Q5T7F0;Q5T7F1;O14786-2;Q68DN3;O14786;E9PEP6	.;.;.;.;.;.;NRP1_HUMAN;.	N	29	ENSP00000265371:D29N;ENSP00000364001:D29N;ENSP00000379317:D29N;ENSP00000363955:D29N;ENSP00000363954:D29N;ENSP00000363956:D29N;ENSP00000363949:D29N	ENSP00000265371:D29N	D	-	1	0	NRP1	33659805	1.000000	0.71417	0.944000	0.38274	0.999000	0.98932	5.731000	0.68554	1.540000	0.49301	0.655000	0.94253	GAT	.	.		0.373	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2			T	33619799	C	T	33619799	3	4	79	1	0	0	0	0	1	0	0	0	10669	884	31	1	2761	1	NRP1	10	33619799	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	16506325	33619799	101914948	118	10872										
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46999960	46999960	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctggaagcgcctgcagccctGcatgtgttcccagaggtaac	12	13	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr10:46999960G>T	ENST00000374317.1	+	3	1353	c.1080G>T	c.(1078-1080)ctG>ctT	p.L360L	GPRIN2_ENST00000374314.4_Silent_p.L360L	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	360										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						CTGCAGCCCTGCATGTGTTCC	0.667																																					p.L360L		Atlas-SNP	.											.	GPRIN2	94	.	0			c.G1080T						.						110	101	104					10																	46999960		2203	4300	6503	SO:0001819	synonymous_variant	9721	exon3			AGCCCTGCATGTG	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"KIAA0514"	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.1080G>T	chr10.hg19:g.46999960G>T		84.0	0.0		61.0	9.0	NM_014696	Q5SVF0	Silent	SNP	ENST00000374317.1	hg19	CCDS31192.1																																																																																			.	.		0.667	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		T	46999960	G	T	46999960	2	4	79	1	0	0	0	0	0	0	0	1	6739	1306	46	3		3	GPRIN2	10	46999960	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	13380161	46999960	88534787	119	10873										
RBP3	5949	hgsc.bcm.edu	37	chr10	48383926	48383926	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tccagcagaactggagggccTtcatcaaagaagtaggagca	12	9	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr10:48383926T>G	ENST00000224600.4	-	3	3419	c.3306A>C	c.(3304-3306)gaA>gaC	p.E1102D		NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	1102	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	CTGGAGGGCCTTCATCAAAGA	0.547																																					p.E1102D		Atlas-SNP	.											.	RBP3	152	.	0			c.A3306C						.						122	100	108					10																	48383926		2203	4300	6503	SO:0001583	missense	5949	exon3			AGGGCCTTCATCA	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.3306A>C	chr10.hg19:g.48383926T>G	ENSP00000224600:p.Glu1102Asp	136.0	0.0		78.0	26.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	hg19	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	T	12.60	1.987859	0.35036	.	.	ENSG00000107618	ENST00000224600	T	0.63913	-0.07	5.44	0.427	0.16489	Interphotoreceptor retinol-binding (2);	0.187424	0.48286	D	0.000189	T	0.65281	0.2676	L	0.55743	1.74	0.32204	N	0.577401	D	0.63880	0.993	P	0.57620	0.824	T	0.69465	-0.5138	10	0.66056	D	0.02	-18.6071	8.4746	0.33005	0.0:0.354:0.0:0.646	.	1102	P10745	RET3_HUMAN	D	1102	ENSP00000224600:E1102D	ENSP00000224600:E1102D	E	-	3	2	RBP3	48003932	0.994000	0.37717	0.461000	0.27105	0.421000	0.31385	0.163000	0.16520	-0.169000	0.10834	-0.379000	0.06801	GAA	.	.		0.547	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		G	48383926	T	G	48383926	3	3	79	1	0	0	0	0	1	0	0	0	13172	1606	56	5	445	5	RBP3	10	48383926	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	1383966	48383926	87150821	120	10874										
OBFC1	79991	hgsc.bcm.edu	37	chr10	105658711	105658711	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cctgtagatagtgggcagctCaagcatccttgcaatttgaa	10	9	1	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr10:105658711C>T	ENST00000224950.3	-	6	672	c.505G>A	c.(505-507)Gag>Aag	p.E169K	OBFC1_ENST00000466828.1_5'UTR|OBFC1_ENST00000369764.1_Missense_Mutation_p.E169K	NM_024928.4	NP_079204.2	Q9H668	STN1_HUMAN	oligonucleotide/oligosaccharide-binding fold containing 1	169					positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromosome, telomeric region (GO:0000784)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)|single-stranded telomeric DNA binding (GO:0043047)			large_intestine(3)|lung(7)|ovary(1)|pancreas(2)	13		Colorectal(252;0.178)		Epithelial(162;3.39e-10)|all cancers(201;1.32e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0151)		GTGGGCAGCTCAAGCATCCTT	0.418																																					p.E169K		Atlas-SNP	.											.	OBFC1	33	.	0			c.G505A						.						134	121	125					10																	105658711		2203	4300	6503	SO:0001583	missense	79991	exon6			GCAGCTCAAGCAT	BC017400	CCDS7552.1	10q25.1	2011-06-14				ENSG00000107960			26200	protein-coding gene	gene with protein product		613128				12477932	Standard	NM_024928		Approved	FLJ22559, bA541N10.2	uc001kxm.3	Q9H668		ENST00000224950.3:c.505G>A	chr10.hg19:g.105658711C>T	ENSP00000224950:p.Glu169Lys	132.0	0.0		79.0	23.0	NM_024928	D3DR99|Q5TCZ0	Missense_Mutation	SNP	ENST00000224950.3	hg19	CCDS7552.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507558	0.85282	.	.	ENSG00000107960	ENST00000224950;ENST00000369764	T;T	0.54071	0.59;0.59	5.79	5.79	0.91817	Nucleic acid-binding, OB-fold-like (1);Domain of unknown function DUF1879, CTS complex STN1 subunit (1);	0.095986	0.64402	D	0.000001	T	0.70168	0.3193	M	0.66506	2.035	0.53005	D	0.999964	D	0.76494	0.999	D	0.74674	0.984	T	0.69975	-0.4999	10	0.51188	T	0.08	-22.9178	15.531	0.75960	0.0:1.0:0.0:0.0	.	169	Q9H668	STN1_HUMAN	K	169	ENSP00000224950:E169K;ENSP00000358779:E169K	ENSP00000224950:E169K	E	-	1	0	OBFC1	105648701	0.998000	0.40836	0.999000	0.59377	0.995000	0.86356	3.464000	0.53057	2.734000	0.93682	0.555000	0.69702	GAG	.	.		0.418	OBFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050174.1	NM_024928		T	105658711	C	T	105658711	3	4	79	1	0	0	0	0	1	0	0	0	10816	835	29	3	621	3	OBFC1	10	105658711	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	57274785	105658711	29876036	121	10875										
ZRANB1	54764	hgsc.bcm.edu	37	chr10	126631222	126631222	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gtgatgttggtagagattggGatccttccagcaccgaagga	14	7	0	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr10:126631222G>T	ENST00000359653.4	+	1	531	c.160G>T	c.(160-162)Gat>Tat	p.D54Y	RP11-298J20.4_ENST00000508096.1_RNA|RP11-298J20.3_ENST00000449984.1_RNA	NM_017580.2	NP_060050.2	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1	54					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|positive regulation of Wnt signaling pathway (GO:0030177)|protein deubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0071947)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell morphogenesis (GO:0022604)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	23		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)		TAGAGATTGGGATCCTTCCAG	0.413																																					p.D54Y		Atlas-SNP	.											.	ZRANB1	60	.	0			c.G160T						.						155	143	147					10																	126631222		2203	4300	6503	SO:0001583	missense	54764	exon1			GATTGGGATCCTT	AJ252060	CCDS7642.1	10q26.12	2014-02-24			ENSG00000019995	ENSG00000019995		"Zinc fingers, RAN-binding domain containing", "OTU domain containing"	18224	protein-coding gene	gene with protein product		611749				11463333	Standard	NM_017580		Approved	TRABID	uc001lic.3	Q9UGI0	OTTHUMG00000019223	ENST00000359653.4:c.160G>T	chr10.hg19:g.126631222G>T	ENSP00000352676:p.Asp54Tyr	219.0	0.0		123.0	11.0	NM_017580	B4DZ98|D3DRF4|Q5SQP6|Q69YK3	Missense_Mutation	SNP	ENST00000359653.4	hg19	CCDS7642.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.310539	0.40895	.	.	ENSG00000019995	ENST00000359653	T	0.18502	2.21	5.81	4.91	0.64330	.	0.170149	0.50627	D	0.000113	T	0.12390	0.0301	N	0.22421	0.69	0.47994	D	0.999563	P	0.44090	0.826	B	0.38562	0.276	T	0.04811	-1.0925	10	0.46703	T	0.11	-29.6117	13.077	0.59093	0.0743:0.0:0.9257:0.0	.	54	Q9UGI0	ZRAN1_HUMAN	Y	54	ENSP00000352676:D54Y	ENSP00000352676:D54Y	D	+	1	0	ZRANB1	126621212	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.845000	0.69437	1.457000	0.47850	0.655000	0.94253	GAT	.	.		0.413	ZRANB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050898.1	NM_017580		T	126631222	G	T	126631222	3	4	79	1	0	0	0	0	1	0	0	0	18237	1174	41	3	162	3	ZRANB1	10	126631222	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	20972511	126631222	8903525	122	10876										
OR51A7	119687	hgsc.bcm.edu	37	chr11	4929380	4929380	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tcatcaccctggctgccatgCatcactttgccaagcacaaa	6	15	3	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr11:4929380C>T	ENST00000359350.4	+	1	781	c.781C>T	c.(781-783)Cat>Tat	p.H261Y	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGCTGCCATGCATCACTTTGC	0.488																																					p.H261Y		Atlas-SNP	.											.	OR51A7	86	.	0			c.C781T						.						222	214	216					11																	4929380		2201	4298	6499	SO:0001583	missense	119687	exon1			GCCATGCATCACT	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"GPCR / Class A : Olfactory receptors"	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.781C>T	chr11.hg19:g.4929380C>T	ENSP00000352305:p.His261Tyr	97.0	0.0		84.0	34.0	NM_001004749	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	hg19	CCDS31364.1	.	.	.	.	.	.	.	.	.	.	C	12.26	1.884265	0.33255	.	.	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.71934	-0.61	5.02	4.11	0.48088	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000164	T	0.69052	0.3068	M	0.61703	1.905	0.09310	N	1	B	0.20052	0.041	B	0.28991	0.097	T	0.64715	-0.6342	10	0.62326	D	0.03	.	12.2195	0.54425	0.0:0.9172:0.0:0.0828	.	261	Q8NH64	O51A7_HUMAN	Y	261;261;250	ENSP00000352305:H261Y	ENSP00000352305:H261Y	H	+	1	0	OR51A7	4885956	0.000000	0.05858	0.983000	0.44433	0.983000	0.72400	0.573000	0.23699	1.340000	0.45581	0.655000	0.94253	CAT	.	.		0.488	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749		T	4929380	C	T	4929380	3	4	79	1	0	0	0	0	1	0	0	0	11097	710	25	3	783	3	OR51A7	11	4929380	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10		4929380	130077136	123	10877										
SPRYD5	84767	hgsc.bcm.edu	37	chr11	55655563	55655563	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgaatatcagaagatgcctgCatttctccatgaagaagagc	9	8	2	6			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr11:55655563C>A	ENST00000449290.2	+	4	655	c.563C>A	c.(562-564)gCa>gAa	p.A188E	TRIM51_ENST00000244891.3_Missense_Mutation_p.A45E	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	188						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										AAGATGCCTGCATTTCTCCAT	0.403																																					p.A188E		Atlas-SNP	.											.	.	.	.	0			c.C563A						.						36	35	36					11																	55655563		2201	4293	6494	SO:0001583	missense	84767	exon4			TGCCTGCATTTCT	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19023	protein-coding gene	gene with protein product			"SPRY domain containing 5"	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.563C>A	chr11.hg19:g.55655563C>A	ENSP00000395086:p.Ala188Glu	379.0	0.0		397.0	112.0	NM_032681	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	hg19		.	.	.	.	.	.	.	.	.	.	.	0.006	-2.040004	0.00402	.	.	ENSG00000124900	ENST00000449290;ENST00000244891	T;T	0.04758	3.56;3.56	.	.	.	.	.	.	.	.	T	0.05547	0.0146	M	0.79475	2.455	0.09310	N	1	B	0.24618	0.107	B	0.28784	0.094	T	0.50857	-0.8778	7	0.02654	T	1	.	.	.	.	.	188	Q9BSJ1	SPRY5_HUMAN	E	188;45	ENSP00000395086:A188E;ENSP00000244891:A45E	ENSP00000244891:A45E	A	+	2	0	SPRYD5	55412139	0.010000	0.17322	0.002000	0.10522	0.601000	0.36947	-0.452000	0.06787	-0.673000	0.05259	0.152000	0.16155	GCA	.	.		0.403	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681		A	55655563	C	A	55655563	3	1	79	1	0	0	0	0	1	0	0	0	15126	710	25	3	573	3	SPRYD5	11	55655563	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	50726183	55655563	79350953	124	10878										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62288122	62288122	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggcatagagatcttcggtgcCttgaggtgtaagtcaggcat	14	7	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr11:62288122C>T	ENST00000378024.4	-	5	14041	c.13767G>A	c.(13765-13767)aaG>aaA	p.K4589K	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4589					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TCTTCGGTGCCTTGAGGTGTA	0.483																																					p.K4589K		Atlas-SNP	.											.	AHNAK	532	.	0			c.G13767A						.						102	102	102					11																	62288122		2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			CGGTGCCTTGAGG	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.13767G>A	chr11.hg19:g.62288122C>T		98.0	0.0		90.0	20.0	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.483	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62288122	C	T	62288122	2	4	79	1	0	0	0	0	0	0	0	1	414	680	24	3		3	AHNAK	11	62288122	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	6632559	62288122	72718394	125	10879										
TUT1	64852	hgsc.bcm.edu	37	chr11	62344401	62344401	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gctttctgggtgagctgggaCacagtgggcaacacaggagg	17	8	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr11:62344401C>A	ENST00000476907.1	-	7	2050	c.1359G>T	c.(1357-1359)gtG>gtT	p.V453V	MIR3654_ENST00000496634.2_Silent_p.V453V|EEF1G_ENST00000329251.4_5'Flank|EEF1G_ENST00000378019.3_5'Flank|EEF1G_ENST00000532986.1_5'Flank|TUT1_ENST00000308436.7_Silent_p.V491V			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	453					mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						TGAGCTGGGACACAGTGGGCA	0.522																																					p.V491V		Atlas-SNP	.											.	TUT1	122	.	0			c.G1473T						.						68	70	69					11																	62344401		2202	4299	6501	SO:0001819	synonymous_variant	64852	exon7			CTGGGACACAGTG	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"RNA binding motif (RRM) containing"	26184	protein-coding gene	gene with protein product	"RNA uridylyltransferase", "U6 TUTase", "TUTase 6"	610641	"RNA binding motif protein 21"	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.1359G>T	chr11.hg19:g.62344401C>A		157.0	0.0		137.0	35.0	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Silent	SNP	ENST00000476907.1	hg19																																																																																				.	.		0.522	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		A	62344401	C	A	62344401	2	1	79	1	0	0	0	0	0	0	0	1	16795	465	17	3		3	TUT1	11	62344401	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	56279	62344401	72662115	126	10880										
FLRT1	28992	hgsc.bcm.edu	37	chr11	63883778	63883778	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	accgccactgccaccaccacGcccactgccactgtcacggc	7	22	1	0	rs575714111		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr11:63883778G>A	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Silent_p.T13T	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						ccaccaccacgcccactgcca	0.672																																					p.T13T		Atlas-SNP	.											.	FLRT1	46	.	0			c.G39A						.						63	37	46					11																	63883778		2200	4297	6497	SO:0001627	intron_variant	23769	exon2			CACCACGCCCACT	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+34932C>T	chr11.hg19:g.63883778G>A		31.0	0.0		29.0	8.0	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	hg19	CCDS8056.1																																																																																			.	.		0.672	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		A	63883778	G	A	63883778	1	1	79	0	1	0	0	0	0	0	0	0	5946	1074	38	1		1	FLRT1	11	63883778	Intron	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	1539377	63883778	71122738	127	10881										
RPS6KA4	8986	hgsc.bcm.edu	37	chr11	64138858	64138858	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcggagcgccaccgcctcccGccggggctcccctgcaccag	13	21	0	0	rs111697527		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr11:64138858G>T	ENST00000334205.4	+	17	2290	c.2225G>T	c.(2224-2226)cGc>cTc	p.R742L	MIR1237_ENST00000408346.1_RNA|RPS6KA4_ENST00000528057.1_Missense_Mutation_p.R735L|RPS6KA4_ENST00000294261.4_Missense_Mutation_p.R494L	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	742	Required for nuclear targeting and association with MAPK14.				axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						ACCGCCTCCCGCCGGGGCTCC	0.726																																					p.R742L		Atlas-SNP	.											.	RPS6KA4	85	.	0			c.G2225T						.						15	19	18					11																	64138858		2025	4020	6045	SO:0001583	missense	8986	exon17			CCTCCCGCCGGGG	AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"ribosomal protein S6 kinase, 90kD, polypeptide 4"			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.2225G>T	chr11.hg19:g.64138858G>T	ENSP00000333896:p.Arg742Leu	169.0	0.0		126.0	22.0	NM_003942	A8K7Z8|O75585|Q53ES8	Missense_Mutation	SNP	ENST00000334205.4	hg19	CCDS8073.1	.	.	.	.	.	.	.	.	.	.	g	18.60	3.658420	0.67586	.	.	ENSG00000162302	ENST00000528057;ENST00000334205;ENST00000294261	T;T;T	0.68479	-0.33;-0.27;-0.32	4.72	4.72	0.59763	.	0.250878	0.32918	N	0.005482	T	0.61553	0.2356	L	0.58101	1.795	0.33638	D	0.606918	P;P;B;P	0.52170	0.773;0.918;0.026;0.951	B;B;B;B	0.38264	0.269;0.139;0.008;0.269	T	0.78104	-0.2334	10	0.87932	D	0	.	15.1434	0.72630	0.0:0.0:1.0:0.0	.	494;735;742;736	G3XAA9;E9PJN1;O75676;O75676-2	.;.;KS6A4_HUMAN;.	L	735;742;494	ENSP00000435580:R735L;ENSP00000333896:R742L;ENSP00000294261:R494L	ENSP00000294261:R494L	R	+	2	0	RPS6KA4	63895434	1.000000	0.71417	0.718000	0.30602	0.213000	0.24496	4.546000	0.60705	2.150000	0.67090	0.491000	0.48974	CGC	.	T|1.000;|0.000		0.726	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942		T	64138858	G	T	64138858	3	4	79	1	0	0	0	0	1	0	0	0	13668	1087	38	1	2291	1	RPS6KA4	11	64138858	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	255080	64138858	70867658	128	10882										
C11orf2	738	hgsc.bcm.edu	37	chr11	64863897	64863897	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ccgcggggcccgaccccctgGacccgactgatctgaacggg	14	17	1	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr11:64863897G>T	ENST00000279281.3	+	1	267	c.175G>T	c.(175-177)Gac>Tac	p.D59Y		NM_013265.2	NP_037397.2	Q9UID3	VPS51_HUMAN	vacuolar protein sorting 51 homolog (S. cerevisiae)	59					autophagy (GO:0006914)|lipid transport (GO:0006869)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											CGACCCCCTGGACCCGACTGA	0.701																																					p.D59Y		Atlas-SNP	.											.	.	.	.	0			c.G175T						.						5	7	7					11																	64863897		2031	4084	6115	SO:0001583	missense	738	exon1			CCCCTGGACCCGA	AF024631	CCDS8093.1	11q13.1	2012-07-19	2012-07-19	2012-07-19	ENSG00000149823	ENSG00000149823			1172	protein-coding gene	gene with protein product	"fat-free homolog (zebrafish)"	615738	"chromosome 11 open reading frame 3", "chromosome 11 open reading frame 2"	C11orf3, C11orf2		9286704, 20685960	Standard	NM_013265		Approved	ANG2, ANG3, FFR	uc001ocr.2	Q9UID3	OTTHUMG00000165600	ENST00000279281.3:c.175G>T	chr11.hg19:g.64863897G>T	ENSP00000279281:p.Asp59Tyr	155.0	0.0		141.0	44.0	NM_013265	Q6PJV5|Q7L8A6|Q8WZ35|Q96DF4|Q96GR3	Missense_Mutation	SNP	ENST00000279281.3	hg19	CCDS8093.1	.	.	.	.	.	.	.	.	.	.	G	34	5.378941	0.95945	.	.	ENSG00000149823	ENST00000528588;ENST00000530773;ENST00000279281;ENST00000529180	.	.	.	5.34	5.34	0.76211	.	0.052577	0.85682	D	0.000000	T	0.55097	0.1899	N	0.19112	0.55	0.80722	D	1	D	0.67145	0.996	P	0.61201	0.885	T	0.58702	-0.7590	9	0.66056	D	0.02	-16.66	14.3843	0.66934	0.0:0.0:1.0:0.0	.	59	Q9UID3	FFR_HUMAN	Y	89;59;59;59	.	ENSP00000279281:D59Y	D	+	1	0	C11orf2	64620473	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	8.553000	0.90686	2.773000	0.95371	0.655000	0.94253	GAC	.	.		0.701	VPS51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385217.1	NM_013265		T	64863897	G	T	64863897	3	4	79	1	0	0	0	0	1	0	0	0	1635	1174	41	3	177	3	C11orf2	11	64863897	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	725039	64863897	70142619	129	10883										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73760482	73760482	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	caacttttatctgcccctggCactctccactgaagtctgtg	7	14	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr11:73760482C>A	ENST00000334126.7	-	27	5487	c.5261G>T	c.(5260-5262)tGc>tTc	p.C1754F	C2CD3_ENST00000313663.7_Missense_Mutation_p.C1754F			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1754					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					CTGCCCCTGGCACTCTCCACT	0.512																																					p.C1754F		Atlas-SNP	.											.	C2CD3	288	.	0			c.G5261T						.						92	78	83					11																	73760482		2200	4293	6493	SO:0001583	missense	26005	exon27			CCCTGGCACTCTC	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.5261G>T	chr11.hg19:g.73760482C>A	ENSP00000334379:p.Cys1754Phe	99.0	0.0		90.0	28.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	26.4	4.729858	0.89390	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.40476	1.03;1.03;1.03	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	M	0.81802	2.56	0.58432	D	0.999998	D	0.71674	0.998	D	0.81914	0.995	T	0.72218	-0.4357	10	0.87932	D	0	-7.4595	19.1566	0.93514	0.0:1.0:0.0:0.0	.	1754	Q4AC94-1	.	F	1754;1754;1735;562	ENSP00000334379:C1754F;ENSP00000323339:C1754F;ENSP00000388750:C562F	ENSP00000323339:C1754F	C	-	2	0	C2CD3	73438130	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.796000	0.85898	2.632000	0.89209	0.655000	0.94253	TGC	.	.		0.512	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		A	73760482	C	A	73760482	3	1	79	1	0	0	0	0	1	0	0	0	2156	710	25	3	650	3	C2CD3	11	73760482	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	8896585	73760482	61246034	130	10884										
OR10G9	219870	hgsc.bcm.edu	37	chr11	123893761	123893761	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	acagcgttcatcctcacgggCcttccccatgccccagggct	9	18	2	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr11:123893761C>A	ENST00000375024.1	+	1	42	c.42C>A	c.(40-42)ggC>ggA	p.G14G		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		TCCTCACGGGCCTTCCCCATG	0.567																																					p.G14G		Atlas-SNP	.											.	OR10G9	80	.	0			c.C42A						.						183	177	179					11																	123893761		2201	4299	6500	SO:0001819	synonymous_variant	219870	exon1			CACGGGCCTTCCC	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"GPCR / Class A : Olfactory receptors"	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.42C>A	chr11.hg19:g.123893761C>A		215.0	0.0		220.0	46.0	NM_001001953		Silent	SNP	ENST00000375024.1	hg19	CCDS31703.1																																																																																			.	.		0.567	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953		A	123893761	C	A	123893761	2	1	79	1	0	0	0	0	0	0	0	1	10913	726	26	3		3	OR10G9	11	123893761	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	50133279	123893761	11112755	131	10885										
OR8A1	390275	hgsc.bcm.edu	37	chr11	124440061	124440061	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgacagagttcattctcaagGgtttaacgaagagagcagac	11	7	2	4			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr11:124440061G>C	ENST00000284287.3	+	1	169	c.97G>C	c.(97-99)Ggt>Cgt	p.G33R		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	33					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		CATTCTCAAGGGTTTAACGAA	0.522																																					p.G33R		Atlas-SNP	.											.	OR8A1	61	.	0			c.G97C						.						91	85	87					11																	124440061		2201	4299	6500	SO:0001583	missense	390275	exon1			CTCAAGGGTTTAA	BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"GPCR / Class A : Olfactory receptors"	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.97G>C	chr11.hg19:g.124440061G>C	ENSP00000284287:p.Gly33Arg	86.0	0.0		72.0	15.0	NM_001005194	Q6IEW7|Q96RC6	Missense_Mutation	SNP	ENST00000284287.3	hg19	CCDS31712.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.753271	0.49362	.	.	ENSG00000196119	ENST00000284287	T	0.00659	5.94	5.08	5.08	0.68730	.	0.000000	0.44902	D	0.000407	T	0.07279	0.0184	M	0.93016	3.37	0.58432	D	0.999993	D	0.89917	1.0	D	0.79784	0.993	T	0.01081	-1.1458	10	0.87932	D	0	.	18.2469	0.89989	0.0:0.0:1.0:0.0	.	33	Q8NGG7	OR8A1_HUMAN	R	33	ENSP00000284287:G33R	ENSP00000284287:G33R	G	+	1	0	OR8A1	123945271	0.999000	0.42202	0.152000	0.22495	0.007000	0.05969	3.710000	0.54860	2.636000	0.89361	0.585000	0.79938	GGT	.	.		0.522	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194		C	124440061	G	C	124440061	3	2	79	1	0	0	0	0	1	0	0	0	11234	1232	43	4	99	4	OR8A1	11	124440061	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	546300	124440061	10566455	132	10886										
PRMT8	56341	hgsc.bcm.edu	37	chr12	3701519	3701519	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agccaaatgccaaaaatgtgGtaagtgccgagggacataag	12	7	0	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:3701519G>A	ENST00000382622.3	+	9	1491		c.e9+1		PRMT8_ENST00000452611.2_Splice_Site|PRMT8_ENST00000261252.4_Splice_Site	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8						histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			CAAAAATGTGGTAAGTGCCGA	0.532																																					.		Atlas-SNP	.											.	PRMT8	97	.	0			c.1074+1G>A						.						65	66	66					12																	3701519		2203	4300	6503	SO:0001630	splice_region_variant	56341	exon9			AATGTGGTAAGTG	AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"Protein arginine methyltransferases"	5188	protein-coding gene	gene with protein product		610086	"HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)", "HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.1101+1G>A	chr12.hg19:g.3701519G>A		76.0	0.0		66.0	17.0	NM_001256536	B2RDP0|Q8TBJ8	Splice_Site	SNP	ENST00000382622.3	hg19	CCDS8521.2	.	.	.	.	.	.	.	.	.	.	G	26.8	4.773810	0.90108	.	.	ENSG00000111218	ENST00000452611;ENST00000382622	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6208	0.84929	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRMT8	3571780	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.797000	0.99108	2.509000	0.84616	0.655000	0.94253	.	.	.		0.532	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854	Intron	A	3701519	G	A	3701519	5	1	79	1	0	0	0	0	0	0	1	0	12554	1275	44	3	1136	3	PRMT8	12	3701519	Splice_Site	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10		3701519	130150376	133	10887										
PZP	5858	hgsc.bcm.edu	37	chr12	9349002	9349002	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gtttggatacaatgtttgtgAtttcactgatcctgtttgca	9	6	1	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:9349002A>T	ENST00000261336.2	-	10	1044	c.1016T>A	c.(1015-1017)aTc>aAc	p.I339N	PZP_ENST00000381997.2_Missense_Mutation_p.I208N	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	339					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						AATGTTTGTGATTTCACTGAT	0.343																																					p.I339N	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.T1016A						.						116	106	109					12																	9349002		2203	4300	6503	SO:0001583	missense	5858	exon10			TTTGTGATTTCAC	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.1016T>A	chr12.hg19:g.9349002A>T	ENSP00000261336:p.Ile339Asn	62.0	0.0		54.0	8.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	A	15.91	2.970919	0.53614	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.46451	1.08;0.87	3.12	3.12	0.35913	.	0.222679	0.29417	U	0.012220	T	0.66167	0.2762	M	0.90145	3.09	0.23304	N	0.997941	D;D	0.89917	1.0;0.992	D;P	0.85130	0.997;0.864	T	0.57458	-0.7808	10	0.87932	D	0	.	8.3273	0.32165	1.0:0.0:0.0:0.0	.	208;339	P20742-2;P20742	.;PZP_HUMAN	N	339;208	ENSP00000261336:I339N;ENSP00000371427:I208N	ENSP00000261336:I339N	I	-	2	0	PZP	9240269	0.975000	0.34042	0.898000	0.35279	0.230000	0.25150	4.747000	0.62141	1.408000	0.46895	0.254000	0.18369	ATC	.	.		0.343	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		T	9349002	A	T	9349002	3	4	79	1	0	0	0	0	1	0	0	0	12884	333	12	4	3540	4	PZP	12	9349002	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	5647483	9349002	124502893	134	10888										
PZP	5858	hgsc.bcm.edu	37	chr12	9356498	9356498	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gctcagaaggacacagccctTcttaggggcctcagtgtgga	13	11	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:9356498T>A	ENST00000261336.2	-	2	161	c.133A>T	c.(133-135)Aag>Tag	p.K45*	PZP_ENST00000381997.2_5'Flank	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	45					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						ACACAGCCCTTCTTAGGGGCC	0.512																																					p.K45X	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A133T						.						89	90	90					12																	9356498		2203	4300	6503	SO:0001587	stop_gained	5858	exon2			AGCCCTTCTTAGG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.133A>T	chr12.hg19:g.9356498T>A	ENSP00000261336:p.Lys45*	125.0	0.0		131.0	33.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Nonsense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	16.56	3.156838	0.57259	.	.	ENSG00000126838	ENST00000261336	.	.	.	2.22	2.22	0.28083	.	0.000000	0.46442	U	0.000292	.	.	.	.	.	.	0.42116	D	0.991408	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.4277	0.21778	0.0:0.0:0.0:1.0	.	.	.	.	X	45	.	ENSP00000261336:K45X	K	-	1	0	PZP	9247765	0.186000	0.23225	0.536000	0.28039	0.432000	0.31715	0.225000	0.17757	1.298000	0.44778	0.383000	0.25322	AAG	.	.		0.512	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		A	9356498	T	A	9356498	4	1	79	1	0	0	0	0	0	1	0	0	12884	1792	62	4	4455	4	PZP	12	9356498	Nonsense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	7496	9356498	124495397	135	10889										
ARID2	196528	hgsc.bcm.edu	37	chr12	46285641	46285641	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gatgtatatccagggcagtgTctttgggaaggttgtgagcc	15	6	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:46285641T>A	ENST00000334344.6	+	17	5173	c.5001T>A	c.(4999-5001)tgT>tgA	p.C1667*	ARID2_ENST00000422737.1_Nonsense_Mutation_p.C1518*|ARID2_ENST00000444670.1_Nonsense_Mutation_p.C1277*|ARID2_ENST00000457135.1_Nonsense_Mutation_p.C275*|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1667					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CAGGGCAGTGTCTTTGGGAAG	0.393			"N, S, F"		hepatocellular carcinoma																																p.C1667X		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	ARID2,NS,carcinoma,0,1	ARID2	311	.	0			c.T5001A						.						157	155	156					12																	46285641		2203	4300	6503	SO:0001587	stop_gained	196528	exon17			GCAGTGTCTTTGG		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.5001T>A	chr12.hg19:g.46285641T>A	ENSP00000335044:p.Cys1667*	154.0	0.0		90.0	29.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Nonsense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	T	46	12.312171	0.99656	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670;ENST00000457135	.	.	.	5.42	2.96	0.34315	.	0.143616	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.902	9.8049	0.40786	0.0:0.2087:0.0:0.7913	.	.	.	.	X	1667;784;784;1518;1277;275	.	ENSP00000335044:C1667X	C	+	3	2	ARID2	44571908	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.133000	0.31430	0.946000	0.37632	0.533000	0.62120	TGT	.	.		0.393	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46285641	T	A	46285641	4	1	79	1	0	0	0	0	0	1	0	0	915	1673	58	4	5067	4	ARID2	12	46285641	Nonsense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	36929143	46285641	87566254	136	10890										
ESPL1	9700	hgsc.bcm.edu	37	chr12	53684210	53684210	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cagcagctgtactgacaagcGagaatggtggacagggcggc	16	9	0	2	rs542853803		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:53684210G>A	ENST00000257934.4	+	24	5412	c.5321G>A	c.(5320-5322)cGa>cAa	p.R1774Q	ESPL1_ENST00000552462.1_Missense_Mutation_p.R1774Q	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1774					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						ACTGACAAGCGAGAATGGTGG	0.577																																					p.R1774Q	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.G5321A						.						117	106	110					12																	53684210		2203	4300	6503	SO:0001583	missense	9700	exon24			ACAAGCGAGAATG	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"separin", "separase", "separin, cysteine protease"	604143	"extra spindle poles like 1 (S. cerevisiae)"			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.5321G>A	chr12.hg19:g.53684210G>A	ENSP00000257934:p.Arg1774Gln	57.0	0.0		38.0	8.0	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	hg19	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	G	17.52	3.411292	0.62399	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.12255	2.7;2.7	5.4	3.5	0.40072	.	0.613068	0.16292	N	0.220879	T	0.09862	0.0242	N	0.26130	0.795	0.09310	N	1	D	0.54397	0.966	P	0.44921	0.464	T	0.16453	-1.0402	10	0.49607	T	0.09	.	4.3227	0.11025	0.2619:0.186:0.5521:0.0	.	1774	Q14674	ESPL1_HUMAN	Q	1774;1449;1774	ENSP00000257934:R1774Q;ENSP00000449831:R1774Q	ENSP00000257934:R1774Q	R	+	2	0	ESPL1	51970477	0.962000	0.33011	0.984000	0.44739	0.990000	0.78478	1.512000	0.35812	1.518000	0.48934	0.650000	0.86243	CGA	.	.		0.577	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		A	53684210	G	A	53684210	3	1	79	1	0	0	0	0	1	0	0	0	5255	1058	37	1	5411	1	ESPL1	12	53684210	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	7398569	53684210	80167685	137	10891										
PPM1H	57460	hgsc.bcm.edu	37	chr12	63061108	63061108	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttgaaagatcgtagattcttAcctgaaaaaaaacaagaata	6	5	1	5			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:63061108A>T	ENST00000228705.6	-	9	1547	c.1247T>A	c.(1246-1248)gTa>gAa	p.V416E	PPM1H_ENST00000551214.1_5'UTR	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	416	PP2C-like.						phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		GTAGATTCTTACCTGAAAAAA	0.393																																					p.V416E		Atlas-SNP	.											.	PPM1H	42	.	0			c.T1247A						.						60	57	58					12																	63061108		1870	4113	5983	SO:0001630	splice_region_variant	57460	exon9			ATTCTTACCTGAA	AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	18583	protein-coding gene	gene with protein product	"neurite extension-related protein phosphatase related to PP2C"		"ras homolog gene family, member C like 1", "protein phosphatase 1H (PP2C domain containing)"	ARHCL1			Standard	NM_020700		Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.1246-1T>A	chr12.hg19:g.63061108A>T		36.0	0.0		42.0	12.0	NM_020700	B1Q2A9|B2RXG4|Q6PI86	Missense_Mutation	SNP	ENST00000228705.6	hg19	CCDS44934.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.490987	0.84962	.	.	ENSG00000111110	ENST00000228705	T	0.21361	2.01	5.74	5.74	0.90152	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.64136	0.2571	H	0.98111	4.15	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.79029	-0.1970	9	.	.	.	1.2876	16.0274	0.80553	1.0:0.0:0.0:0.0	.	416	Q9ULR3	PPM1H_HUMAN	E	416	ENSP00000228705:V416E	.	V	-	2	0	PPM1H	61347375	1.000000	0.71417	0.999000	0.59377	0.825000	0.46686	8.826000	0.92034	2.185000	0.69588	0.528000	0.53228	GTA	.	.		0.393	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700	Missense_Mutation	T	63061108	A	T	63061108	5	4	79	1	0	0	0	0	0	0	1	0	12353	405	14	4	305	4	PPM1H	12	63061108	Splice_Site	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	9376898	63061108	70790787	138	10892										
TMEM19	55266	hgsc.bcm.edu	37	chr12	72083445	72083445	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttctgatcgtctctaatggcCttaaaaagaaaagtctagat	7	7	3	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:72083445C>A	ENST00000266673.5	+	2	799	c.205C>A	c.(205-207)Ctt>Att	p.L69I	TMEM19_ENST00000549735.1_Missense_Mutation_p.L69I|RP11-293I14.2_ENST00000548802.1_3'UTR	NM_018279.3	NP_060749.2	Q96HH6	TMM19_HUMAN	transmembrane protein 19	69						integral component of membrane (GO:0016021)				large_intestine(1)|lung(8)	9		Breast(359;0.0889)		GBM - Glioblastoma multiforme(134;0.044)		CTCTAATGGCCTTAAAAAGAA	0.363																																					p.L69I		Atlas-SNP	.											.	TMEM19	35	.	0			c.C205A						.						209	199	202					12																	72083445		2203	4300	6503	SO:0001583	missense	55266	exon2			AATGGCCTTAAAA	BC008596	CCDS9002.1	12q15	2004-03-04				ENSG00000139291			25605	protein-coding gene	gene with protein product						12477932	Standard	NM_018279		Approved	FLJ10936	uc001sws.3	Q96HH6	OTTHUMG00000169558	ENST00000266673.5:c.205C>A	chr12.hg19:g.72083445C>A	ENSP00000266673:p.Leu69Ile	133.0	0.0		103.0	40.0	NM_018279	B2RDL2|Q53FY3|Q9NV41	Missense_Mutation	SNP	ENST00000266673.5	hg19	CCDS9002.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.437668	0.25900	.	.	ENSG00000139291	ENST00000266673;ENST00000550524;ENST00000549735	.	.	.	5.35	2.95	0.34219	.	0.427456	0.26844	N	0.022214	T	0.25232	0.0613	N	0.25332	0.735	0.28958	N	0.890014	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.12941	-1.0528	9	0.35671	T	0.21	-9.4499	4.9133	0.13833	0.3086:0.0792:0.0:0.6122	.	69;69	Q96HH6;Q96HH6-2	TMM19_HUMAN;.	I	69	.	ENSP00000266673:L69I	L	+	1	0	TMEM19	70369712	0.882000	0.30256	1.000000	0.80357	0.932000	0.56968	0.820000	0.27323	0.315000	0.23110	-0.302000	0.09304	CTT	.	.		0.363	TMEM19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404801.1	NM_018279		A	72083445	C	A	72083445	3	1	79	1	0	0	0	0	1	0	0	0	16128	681	24	3	211	3	TMEM19	12	72083445	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	9022337	72083445	61768450	139	10893										
EEA1	8411	hgsc.bcm.edu	37	chr12	93213181	93213181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cataaagatcttctctttctTtttctagtaatgaaatattt	3	6	4	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:93213181T>C	ENST00000322349.8	-	14	1895	c.1631A>G	c.(1630-1632)aAa>aGa	p.K544R		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	544	Gln/Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TTCTCTTTCTTTTTCTAGTAA	0.353																																					p.K544R		Atlas-SNP	.											.	EEA1	104	.	0			c.A1631G						.						65	66	66					12																	93213181		2201	4298	6499	SO:0001583	missense	8411	exon14			CTTTCTTTTTCTA	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.1631A>G	chr12.hg19:g.93213181T>C	ENSP00000317955:p.Lys544Arg	122.0	0.0		110.0	24.0	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	hg19	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.289240	0.40494	.	.	ENSG00000102189	ENST00000322349	T	0.77229	-1.08	5.55	4.42	0.53409	.	0.107006	0.40222	N	0.001144	T	0.61160	0.2325	N	0.17082	0.46	0.32696	N	0.513536	B	0.15141	0.012	B	0.12156	0.007	T	0.63497	-0.6624	10	0.27785	T	0.31	.	10.8898	0.46990	0.0:0.0735:0.0:0.9265	.	544	Q15075	EEA1_HUMAN	R	544	ENSP00000317955:K544R	ENSP00000317955:K544R	K	-	2	0	EEA1	91737312	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.556000	0.53734	2.120000	0.65058	0.377000	0.23210	AAA	.	.		0.353	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		C	93213181	T	C	93213181	3	2	79	1	0	0	0	0	1	0	0	0	4923	1841	64	2	2668	2	EEA1	12	93213181	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	21129736	93213181	40638714	140	10894										
CCDC41	51134	hgsc.bcm.edu	37	chr12	94772626	94772626	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ccgcacctgtattctttgggCattttccacctgagcctcag	8	14	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:94772626C>T	ENST00000397809.5	-	7	1291	c.742G>A	c.(742-744)Gcc>Acc	p.A248T	CCDC41_ENST00000339839.5_Missense_Mutation_p.A248T|CCDC41_ENST00000549352.1_5'UTR|CCDC41_ENST00000397807.2_Missense_Mutation_p.A215T|CCDC41_ENST00000547575.1_Missense_Mutation_p.A248T	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		240					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						ATTCTTTGGGCATTTTCCACC	0.423																																					p.A248T		Atlas-SNP	.											.	CCDC41	59	.	0			c.G742A						.						131	129	130					12																	94772626		1882	4123	6005	SO:0001583	missense	51134	exon7			TTTGGGCATTTTC																												ENST00000397809.5:c.742G>A	chr12.hg19:g.94772626C>T	ENSP00000380911:p.Ala248Thr	96.0	0.0		125.0	26.0	NM_016122	A4FVB1|Q08AP1	Missense_Mutation	SNP	ENST00000397809.5	hg19	CCDS41820.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.557333	0.45590	.	.	ENSG00000173588	ENST00000339839;ENST00000397809;ENST00000397807;ENST00000547575	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	5.69	3.81	0.43845	.	.	.	.	.	T	0.11024	0.0269	N	0.08118	0	0.22591	N	0.99896	B;B;B	0.19200	0.034;0.034;0.034	B;B;B	0.21708	0.036;0.022;0.036	T	0.35549	-0.9784	9	0.15066	T	0.55	0.996	11.1071	0.48210	0.0:0.8436:0.0:0.1564	.	248;215;240	F8VYN8;Q9Y592-2;Q9Y592	.;.;CCD41_HUMAN	T	248;248;215;248	ENSP00000344655:A248T;ENSP00000380911:A248T;ENSP00000380909:A215T;ENSP00000448913:A248T	ENSP00000344655:A248T	A	-	1	0	CCDC41	93296757	1.000000	0.71417	0.947000	0.38551	0.810000	0.45777	3.957000	0.56730	0.703000	0.31848	0.585000	0.79938	GCC	.	.		0.423	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3			T	94772626	C	T	94772626	3	4	79	1	0	0	0	0	1	0	0	0	2815	710	25	3	1407	3	CCDC41	12	94772626	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	1559445	94772626	39079269	141	10895										
ACACB	32	hgsc.bcm.edu	37	chr12	109616910	109616910	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	caggtacagagtgagatcccAggctcgcccatctttctcat	9	13	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:109616910A>G	ENST00000338432.7	+	10	1574	c.1455A>G	c.(1453-1455)ccA>ccG	p.P485P	ACACB_ENST00000377848.3_Silent_p.P485P|ACACB_ENST00000543080.1_3'UTR|ACACB_ENST00000377854.5_Silent_p.P485P			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	485	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GTGAGATCCCAGGCTCGCCCA	0.542																																					p.P485P		Atlas-SNP	.											.	ACACB	330	.	0			c.A1455G						.						49	40	43					12																	109616910		2203	4300	6503	SO:0001819	synonymous_variant	32	exon9			GATCCCAGGCTCG	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.1455A>G	chr12.hg19:g.109616910A>G		82.0	0.0		52.0	11.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	hg19	CCDS31898.1																																																																																			.	.		0.542	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		G	109616910	A	G	109616910	2	3	79	1	0	0	0	0	0	0	0	1	107	175	7	2		2	ACACB	12	109616910	Silent	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	14844284	109616910	24234985	142	10896										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112926248	112926248	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tttgtccttctgcccgcagtGctggaattggccggacaggg	14	11	1	0	rs121918468		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:112926248G>T	ENST00000351677.2	+	12	1579	c.1381G>T	c.(1381-1383)Gct>Tct	p.A461S		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	465	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						TGCCCGCAGTGCTGGAATTGG	0.453			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																												p.A461S		Atlas-SNP	.		Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	PTPN11,NS,carcinoma,-1,1	PTPN11	623	.	0			c.G1381T	GRCh37	CM043335	PTPN11	M	rs121918468	.						122	110	114					12																	112926248		2203	4300	6503	SO:0001630	splice_region_variant	5781	exon12	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CGCAGTGCTGGAA	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1380-1G>T	chr12.hg19:g.112926248G>T		59.0	0.0		60.0	13.0	NM_002834	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	hg19	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.869259	0.91587	.	.	ENSG00000179295	ENST00000351677	D	0.99567	-6.18	5.05	5.05	0.67936	.	0.057274	0.64402	D	0.000001	D	0.99753	0.9901	H	0.94620	3.56	0.80722	D	1	D	0.57899	0.981	D	0.79784	0.993	D	0.97162	0.9838	10	0.87932	D	0	.	18.7696	0.91885	0.0:0.0:1.0:0.0	.	461	Q06124-2	.	S	461	ENSP00000340944:A461S	ENSP00000340944:A461S	A	+	1	0	PTPN11	111410631	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.237000	0.95368	2.508000	0.84585	0.650000	0.86243	GCT	.	.		0.453	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2		Missense_Mutation	T	112926248	G	T	112926248	5	4	79	1	0	0	0	0	0	0	1	0	12793	1333	46	3	1427	3	PTPN11	12	112926248	Splice_Site	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	3309338	112926248	20925647	143	10897										
CAMKK2	10645	hgsc.bcm.edu	37	chr12	121687622	121687622	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	caccacgatcctcgactcggGgttcttgtccagcatacggg	11	14	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:121687622G>A	ENST00000324774.5	-	13	2119	c.1291C>T	c.(1291-1293)Ccc>Tcc	p.P431S	CAMKK2_ENST00000402834.4_Missense_Mutation_p.P431S|CAMKK2_ENST00000412367.2_Missense_Mutation_p.P431S|CAMKK2_ENST00000392473.2_Missense_Mutation_p.P431S|CAMKK2_ENST00000337174.3_Missense_Mutation_p.P431S|CAMKK2_ENST00000392474.2_Missense_Mutation_p.P431S|CAMKK2_ENST00000404169.3_Missense_Mutation_p.P431S|CAMKK2_ENST00000446440.2_Missense_Mutation_p.P431S|CAMKK2_ENST00000347034.2_Missense_Mutation_p.P431S|CAMKK2_ENST00000538733.1_Missense_Mutation_p.P431S|CAMKK2_ENST00000545538.1_Missense_Mutation_p.P218S	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	431	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CTCGACTCGGGGTTCTTGTCC	0.617																																					p.P431S		Atlas-SNP	.											.	CAMKK2	87	.	0			c.C1291T						.						178	165	169					12																	121687622		2203	4300	6503	SO:0001583	missense	10645	exon13			ACTCGGGGTTCTT	AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.1291C>T	chr12.hg19:g.121687622G>A	ENSP00000312741:p.Pro431Ser	99.0	0.0		93.0	16.0	NM_153500	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Missense_Mutation	SNP	ENST00000324774.5	hg19	CCDS9216.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.708776	0.89018	.	.	ENSG00000110931	ENST00000392474;ENST00000347034;ENST00000538733;ENST00000337174;ENST00000324774;ENST00000545538;ENST00000412367;ENST00000404169;ENST00000360452;ENST00000446440;ENST00000392473	T;T;T;T;T;T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15;0.48;0.15;0.15;0.15;0.15	5.74	4.85	0.62838	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.75737	0.3890	M	0.76938	2.355	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.996;0.993;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.87578	0.993;0.997;0.993;0.935;0.944;0.998;0.997;0.993	T	0.79376	-0.1829	10	0.87932	D	0	-4.9585	13.8045	0.63223	0.0732:0.0:0.9268:0.0	.	431;431;431;218;431;431;431;431	Q96RR4-6;Q96RR4-2;Q96RR4-7;F5GZ00;Q96RR4-5;Q96RR4-4;Q96RR4;Q96RR4-3	.;.;.;.;.;.;KKCC2_HUMAN;.	S	431;431;431;431;431;218;431;431;414;431;431	ENSP00000376266:P431S;ENSP00000321230:P431S;ENSP00000445944:P431S;ENSP00000336634:P431S;ENSP00000312741:P431S;ENSP00000441352:P218S;ENSP00000388368:P431S;ENSP00000384600:P431S;ENSP00000388273:P431S;ENSP00000376265:P431S	ENSP00000312741:P431S	P	-	1	0	CAMKK2	120172005	1.000000	0.71417	0.994000	0.49952	0.906000	0.53458	9.209000	0.95087	1.438000	0.47492	0.561000	0.74099	CCC	.	.		0.617	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226		A	121687622	G	A	121687622	3	1	79	1	0	0	0	0	1	0	0	0	2609	1232	43	3	505	3	CAMKK2	12	121687622	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	8761374	121687622	12164273	144	10898										
KDM2B	84678	hgsc.bcm.edu	37	chr12	121947514	121947514	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgggtccatttggcagagacCtccgtggcgggagagccggt	17	10	0	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr12:121947514C>G	ENST00000377071.4	-	11	1575	c.1503G>C	c.(1501-1503)gaG>gaC	p.E501D	KDM2B_ENST00000538046.2_Missense_Mutation_p.E411D|KDM2B_ENST00000377069.4_Missense_Mutation_p.E470D|KDM2B_ENST00000536437.1_Missense_Mutation_p.E384D|KDM2B_ENST00000542973.1_5'Flank	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	501					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						TGGCAGAGACCTCCGTGGCGG	0.542																																					p.E501D		Atlas-SNP	.											.	KDM2B	218	.	0			c.G1503C						.						70	77	75					12																	121947514		1904	4108	6012	SO:0001583	missense	84678	exon11			AGAGACCTCCGTG	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.1503G>C	chr12.hg19:g.121947514C>G	ENSP00000366271:p.Glu501Asp	114.0	0.0		76.0	24.0	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	hg19	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	C	2.720	-0.266704	0.05754	.	.	ENSG00000089094	ENST00000397480;ENST00000377069;ENST00000377071;ENST00000536437;ENST00000397478;ENST00000261824;ENST00000446152	T;T;T;T	0.47177	2.42;1.83;0.85;0.86	5.14	3.27	0.37495	.	0.351880	0.24059	N	0.041933	T	0.24275	0.0588	N	0.15975	0.35	0.34767	D	0.733323	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.06405	0.002;0.001;0.002;0.001	T	0.20605	-1.0270	10	0.08179	T	0.78	-15.4273	7.9911	0.30242	0.0:0.5786:0.3001:0.1213	.	501;384;501;470	E7EML5;Q1RLM7;Q8NHM5;A8MRS1	.;.;KDM2B_HUMAN;.	D	501;470;501;384;501;501;464	ENSP00000366269:E470D;ENSP00000366271:E501D;ENSP00000445196:E384D;ENSP00000398279:E464D	ENSP00000261824:E501D	E	-	3	2	KDM2B	120431897	0.997000	0.39634	0.771000	0.31576	0.276000	0.26787	1.387000	0.34430	1.301000	0.44836	0.655000	0.94253	GAG	.	.		0.542	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		G	121947514	C	G	121947514	3	3	79	1	0	0	0	0	1	0	0	0	8134	680	24	4	2611	4	KDM2B	12	121947514	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	259892	121947514	11904381	145	10899										
FAM123A	219287	hgsc.bcm.edu	37	chr13	25744099	25744099	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcatagagatcatagagcgcGtccccgctgtagctatcccg	11	13	1	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr13:25744099G>T	ENST00000515384.1	-	1	2326	c.1659C>A	c.(1657-1659)gaC>gaA	p.D553E	AMER2-AS1_ENST00000413501.1_lincRNA|AMER2_ENST00000381853.3_Missense_Mutation_p.D434E|AMER2_ENST00000357816.2_Missense_Mutation_p.D434E			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	553					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)										CATAGAGCGCGTCCCCGCTGT	0.642																																					p.D553E		Atlas-SNP	.											.	.	.	.	0			c.C1659A						.						66	63	64					13																	25744099		2203	4300	6503	SO:0001583	missense	219287	exon1			GAGCGCGTCCCCG	AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"-"	26360	protein-coding gene	gene with protein product		614659	"family with sequence similarity 123A"	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1659C>A	chr13.hg19:g.25744099G>T	ENSP00000426528:p.Asp553Glu	52.0	0.0		46.0	13.0	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	hg19	CCDS53859.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.609889	0.46527	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.52295	0.67;0.67;0.67	5.57	-4.09	0.03951	.	0.000000	0.85682	D	0.000000	T	0.64394	0.2594	M	0.81497	2.545	0.34556	D	0.711819	D;D	0.89917	1.0;0.999	D;D	0.74674	0.984;0.956	T	0.73148	-0.4074	10	0.87932	D	0	-31.5622	14.5557	0.68100	0.749:0.0:0.251:0.0	.	553;434	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	E	434;434;553	ENSP00000350469:D434E;ENSP00000371277:D434E;ENSP00000426528:D553E	ENSP00000350469:D434E	D	-	3	2	FAM123A	24642099	0.847000	0.29606	0.003000	0.11579	0.400000	0.30750	0.183000	0.16919	-0.733000	0.04850	-0.367000	0.07326	GAC	.	.		0.642	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704		T	25744099	G	T	25744099	3	4	79	1	0	0	0	0	1	0	0	0	5427	1136	40	1	360	1	FAM123A	13	25744099	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10		25744099	89425779	146	10900										
FREM2	341640	hgsc.bcm.edu	37	chr13	39438522	39438522	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ccaacctcctggattatactGaagtgaagactcattatggt	8	9	1	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr13:39438522G>T	ENST00000280481.7	+	16	7978	c.7762G>T	c.(7762-7764)Gaa>Taa	p.E2588*		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2588					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GGATTATACTGAAGTGAAGAC	0.448																																					p.E2588X		Atlas-SNP	.											.	FREM2	385	.	0			c.G7762T						.						128	117	121					13																	39438522		2203	4300	6503	SO:0001587	stop_gained	341640	exon16			TATACTGAAGTGA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.7762G>T	chr13.hg19:g.39438522G>T	ENSP00000280481:p.Glu2588*	138.0	0.0		128.0	24.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Nonsense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	50	16.934631	0.99875	.	.	ENSG00000150893	ENST00000280481	.	.	.	5.81	4.95	0.65309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.1575	0.81676	0.0:0.0:0.8656:0.1344	.	.	.	.	X	2588	.	ENSP00000280481:E2588X	E	+	1	0	FREM2	38336522	1.000000	0.71417	0.584000	0.28653	0.951000	0.60555	9.837000	0.99465	1.424000	0.47217	0.650000	0.86243	GAA	.	.		0.448	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39438522	G	T	39438522	4	4	79	1	0	0	0	0	0	1	0	0	6053	1291	45	3	7824	3	FREM2	13	39438522	Nonsense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	13694423	39438522	75731356	147	10901										
KBTBD6	89890	hgsc.bcm.edu	37	chr13	41705442	41705442	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttatacacccagaggtctgtCctgggctgagcagctagata	11	10	1	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr13:41705442C>A	ENST00000379485.1	-	1	1440	c.1206G>T	c.(1204-1206)agG>agT	p.R402S	KBTBD6_ENST00000499385.2_Missense_Mutation_p.R336S	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	402										NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		AGAGGTCTGTCCTGGGCTGAG	0.512																																					p.R402S		Atlas-SNP	.											.	KBTBD6	83	.	0			c.G1206T						.						112	104	107					13																	41705442		2203	4300	6503	SO:0001583	missense	89890	exon1			GTCTGTCCTGGGC	AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"BTB/POZ domain containing"	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.1206G>T	chr13.hg19:g.41705442C>A	ENSP00000368799:p.Arg402Ser	128.0	0.0		99.0	28.0	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	hg19	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	c	7.762	0.705690	0.15172	.	.	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.63096	-0.02;-0.02	3.8	1.99	0.26369	Kelch-type beta propeller (1);	0.451876	0.23561	N	0.046849	T	0.40067	0.1102	L	0.28274	0.84	0.33816	D	0.628451	B;B	0.23058	0.079;0.017	B;B	0.23852	0.049;0.009	T	0.35400	-0.9790	10	0.08381	T	0.77	.	6.108	0.20084	0.1861:0.7088:0.0:0.1051	.	336;402	F5GZN7;Q86V97	.;KBTB6_HUMAN	S	402;336	ENSP00000368799:R402S;ENSP00000444326:R336S	ENSP00000368799:R402S	R	-	3	2	KBTBD6	40603442	1.000000	0.71417	0.998000	0.56505	0.656000	0.38851	0.987000	0.29603	0.372000	0.24591	-0.379000	0.06801	AGG	.	.		0.512	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		A	41705442	C	A	41705442	3	1	79	1	0	0	0	0	1	0	0	0	8006	854	30	3	822	3	KBTBD6	13	41705442	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	2266920	41705442	73464436	148	10902										
FRMD6	122786	hgsc.bcm.edu	37	chr14	52174893	52174893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttccgaagctcatcttaaatAtatcaaagaggctgtccgac	7	10	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr14:52174893A>G	ENST00000344768.5	+	7	852	c.656A>G	c.(655-657)tAt>tGt	p.Y219C	FRMD6_ENST00000395718.2_Missense_Mutation_p.Y211C|FRMD6_ENST00000356218.4_Missense_Mutation_p.Y211C|FRMD6_ENST00000554167.1_Missense_Mutation_p.Y142C			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	219	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					CATCTTAAATATATCAAAGAG	0.423																																					p.Y219C		Atlas-SNP	.											.	FRMD6	100	.	0			c.A656G						.						101	88	92					14																	52174893		2203	4300	6503	SO:0001583	missense	122786	exon7			TTAAATATATCAA	BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"expanded homolog"	614555	"chromosome 14 open reading frame 31"	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.656A>G	chr14.hg19:g.52174893A>G	ENSP00000343899:p.Tyr219Cys	121.0	0.0		69.0	22.0	NM_001267046	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Missense_Mutation	SNP	ENST00000344768.5	hg19	CCDS58318.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.225516	0.79576	.	.	ENSG00000139926	ENST00000356218;ENST00000395718;ENST00000344768;ENST00000554167;ENST00000557405	D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96	5.42	5.42	0.78866	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	D	0.000000	D	0.91257	0.7244	M	0.67397	2.05	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.79108	0.99;0.992;0.987	D	0.92255	0.5812	10	0.87932	D	0	.	15.4492	0.75259	1.0:0.0:0.0:0.0	.	142;219;211	G3V4T7;Q96NE9;Q96NE9-2	.;FRMD6_HUMAN;.	C	211;211;219;142;109	ENSP00000348550:Y211C;ENSP00000379068:Y211C;ENSP00000343899:Y219C;ENSP00000451977:Y142C;ENSP00000450667:Y109C	ENSP00000343899:Y219C	Y	+	2	0	FRMD6	51244643	1.000000	0.71417	0.964000	0.40570	0.710000	0.40934	7.513000	0.81739	2.063000	0.61619	0.482000	0.46254	TAT	.	.		0.423	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330		G	52174893	A	G	52174893	3	3	79	1	0	0	0	0	1	0	0	0	6062	449	16	2	654	2	FRMD6	14	52174893	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10		52174893	55174647	149	10903										
MAP3K9	4293	hgsc.bcm.edu	37	chr14	71216737	71216737	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cactccataagcgactgctaAgccatcaatgcctcgaaagg	8	13	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr14:71216737A>C	ENST00000554752.2	-	4	1062	c.1063T>G	c.(1063-1065)Tta>Gta	p.L355V	MAP3K9_ENST00000553414.1_Missense_Mutation_p.L49V|MAP3K9_ENST00000381250.4_Missense_Mutation_p.L355V|MAP3K9_ENST00000555993.2_Missense_Mutation_p.L355V|MAP3K9_ENST00000554146.1_Missense_Mutation_p.L92V	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	355	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		GCGACTGCTAAGCCATCAATG	0.488																																					p.L355V	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.T1063G						.						152	134	140					14																	71216737		2203	4300	6503	SO:0001583	missense	4293	exon4			CTGCTAAGCCATC	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.1063T>G	chr14.hg19:g.71216737A>C	ENSP00000451612:p.Leu355Val	213.0	0.0		126.0	43.0	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	ENST00000554752.2	hg19		.	.	.	.	.	.	.	.	.	.	A	15.61	2.884617	0.51908	.	.	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62	5.91	3.6	0.41247	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.80171	0.4574	N	0.13003	0.285	0.49130	D	0.99975	D;D;D;D	0.89917	0.997;1.0;1.0;1.0	D;D;D;D	0.87578	0.985;0.997;0.996;0.998	T	0.78295	-0.2259	10	0.48119	T	0.1	.	5.5105	0.16878	0.6442:0.0:0.3558:0.0	.	92;355;355;49	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	V	355;355;49;355;92;83	ENSP00000451612:L355V;ENSP00000451038:L49V;ENSP00000370649:L355V;ENSP00000451921:L92V	ENSP00000005198:L355V	L	-	1	2	MAP3K9	70286490	1.000000	0.71417	1.000000	0.80357	0.039000	0.13416	3.461000	0.53035	1.067000	0.40740	0.533000	0.62120	TTA	.	.		0.488	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			C	71216737	A	C	71216737	3	2	79	1	0	0	0	0	1	0	0	0	9266	69	3	5	2333	5	MAP3K9	14	71216737	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	19041844	71216737	36132803	150	10904										
VPS39	23339	hgsc.bcm.edu	37	chr15	42453011	42453011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	atggacgaccactccattggGgtatcttgcaaatgcactgc	10	11	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr15:42453011G>A	ENST00000348544.4	-	26	2601	c.2602C>T	c.(2602-2604)Ccc>Tcc	p.P868S	VPS39_ENST00000318006.5_Missense_Mutation_p.P857S			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	868					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		ACTCCATTGGGGTATCTTGCA	0.537																																					p.P857S		Atlas-SNP	.											.	VPS39	53	.	0			c.C2569T						.						127	113	117					15																	42453011		2203	4299	6502	SO:0001583	missense	23339	exon25			CATTGGGGTATCT	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.2602C>T	chr15.hg19:g.42453011G>A	ENSP00000335193:p.Pro868Ser	117.0	0.0		110.0	21.0	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Missense_Mutation	SNP	ENST00000348544.4	hg19	CCDS10083.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.786091	0.90282	.	.	ENSG00000166887	ENST00000318006;ENST00000348544	T;T	0.58506	0.33;0.34	6.04	6.04	0.98038	Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.78310	0.4263	M	0.81179	2.53	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.969	T	0.78989	-0.1986	10	0.62326	D	0.03	-19.4284	18.7597	0.91845	0.0:0.0:1.0:0.0	.	868;857	Q96JC1;Q96JC1-2	VPS39_HUMAN;.	S	857;868	ENSP00000326534:P857S;ENSP00000335193:P868S	ENSP00000326534:P857S	P	-	1	0	VPS39	40240303	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.920000	0.92779	2.873000	0.98535	0.561000	0.74099	CCC	.	.		0.537	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		A	42453011	G	A	42453011	3	1	79	1	0	0	0	0	1	0	0	0	17224	1232	43	3	62	3	VPS39	15	42453011	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10		42453011	60078381	151	10905										
SPATA8	145946	hgsc.bcm.edu	37	chr15	97326945	97326945	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgtctctaccaggaaattgcCccctcttttcagaggctgcc	8	14	3	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr15:97326945C>A	ENST00000328504.3	+	1	327	c.60C>A	c.(58-60)gcC>gcA	p.A20A	SPATA8_ENST00000558553.1_Intron|SPATA8-AS1_ENST00000558722.1_RNA|SPATA8-AS1_ENST00000560888.1_RNA	NM_173499.3	NP_775770.1	Q6RVD6	SPAT8_HUMAN	spermatogenesis associated 8	20										large_intestine(4)|lung(8)|ovary(1)|skin(3)	16	Melanoma(26;0.0142)|Lung NSC(78;0.041)|all_lung(78;0.0468)		OV - Ovarian serous cystadenocarcinoma(32;0.0718)			AGGAAATTGCCCCCTCTTTTC	0.557																																					p.A20A		Atlas-SNP	.											.	SPATA8	42	.	0			c.C60A						.						81	71	74					15																	97326945		2197	4298	6495	SO:0001819	synonymous_variant	145946	exon1			AATTGCCCCCTCT	AY489187	CCDS10376.1	15q26	2008-02-05			ENSG00000185594	ENSG00000185594			28676	protein-coding gene	gene with protein product		613948					Standard	NM_173499		Approved	MGC44294	uc002bue.3	Q6RVD6	OTTHUMG00000149847	ENST00000328504.3:c.60C>A	chr15.hg19:g.97326945C>A		99.0	0.0		80.0	22.0	NM_173499	Q2KJ07	Silent	SNP	ENST00000328504.3	hg19	CCDS10376.1																																																																																			.	.		0.557	SPATA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313533.1	NM_173499		A	97326945	C	A	97326945	2	1	79	1	0	0	0	0	0	0	0	1	15030	610	22	3		3	SPATA8	15	97326945	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	54873934	97326945	5204447	152	10906										
TSC2	7249	hgsc.bcm.edu	37	chr16	2137899	2137899	+	Frame_Shift_Del	DEL	G	G	-													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gtccacgtgatcgtcaccccGctggactacgagtgcaacct					rs35118875|rs137854382	byFrequency	TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr16:2137899delG	ENST00000219476.3	+	39	5655	c.5025delG	c.(5023-5025)ccgfs	p.P1675fs	TSC2_ENST00000568454.1_Frame_Shift_Del_p.P1619fs|TSC2_ENST00000382538.6_Frame_Shift_Del_p.P1560fs|MIR1225_ENST00000408729.1_RNA|TSC2_ENST00000439673.2_Frame_Shift_Del_p.P1572fs|TSC2_ENST00000353929.4_Frame_Shift_Del_p.P1632fs|TSC2_ENST00000350773.4_Frame_Shift_Del_p.P1652fs|TSC2_ENST00000401874.2_Frame_Shift_Del_p.P1608fs	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1675	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.		P -> L (in TSC2). {ECO:0000269|PubMed:10570911, ECO:0000269|PubMed:15024740, ECO:0000269|PubMed:9302281}.		acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				TCGTCACCCCGCTGGACTACG	0.632			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.P1675fs		Atlas-INDEL	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	TSC2,NS,other,0,1	TSC2	364	.	0			c.5024delC	GRCh37	CD982989	TSC2	D	rs35118875	.						66	49	55					16																	2137899		2194	4299	6493	SO:0001589	frameshift_variant	7249	exon39	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	.	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.5025delG	chr16.hg19:g.2137899delG	ENSP00000219476:p.Pro1675fs	171.0	0.0		102.0	45.0	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Frame_Shift_Del	DEL	ENST00000219476.3	hg19	CCDS10458.1																																																																																			.	.		0.632	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		-	2137899	G	-	2137899	7	5	79	1	0	1	0	1	0	0	0	0	16621	1074	38	0	5175	0	TSC2	16	2137899	Frame_Shift_Del	DEL	G	TCGA-CC-A8HT-01A-11D-A35Z-10		2137899	88216854	153	10907										
BBS2	583	hgsc.bcm.edu	37	chr16	56539942	56539942	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	atgaatgctcatggcatgatTtttcgactgaaaaagaattt	8	5	1	4			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr16:56539942T>C	ENST00000245157.5	-	7	1144	c.724A>G	c.(724-726)Aat>Gat	p.N242D	BBS2_ENST00000568104.1_Missense_Mutation_p.N242D|BBS2_ENST00000561951.1_5'UTR	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	242					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						ATGGCATGATTTTTCGACTGA	0.343									Bardet-Biedl syndrome																												p.N242D		Atlas-SNP	.											.	BBS2	67	.	0			c.A724G						.						79	80	79					16																	56539942		2198	4300	6498	SO:0001583	missense	583	exon7	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CATGATTTTTCGA	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.724A>G	chr16.hg19:g.56539942T>C	ENSP00000245157:p.Asn242Asp	105.0	0.0		68.0	25.0	NM_031885	Q96CM0|Q96SN9	Missense_Mutation	SNP	ENST00000245157.5	hg19	CCDS32451.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.618986	0.87460	.	.	ENSG00000125124	ENST00000245157	D	0.86230	-2.09	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.92984	0.7767	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71184	0.972;0.972	D	0.92872	0.6315	10	0.45353	T	0.12	-18.2174	15.9668	0.79979	0.0:0.0:0.0:1.0	.	242;242	A8K0N9;Q9BXC9	.;BBS2_HUMAN	D	242	ENSP00000245157:N242D	ENSP00000245157:N242D	N	-	1	0	BBS2	55097443	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	7.805000	0.86005	2.173000	0.68751	0.533000	0.62120	AAT	.	.		0.343	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		C	56539942	T	C	56539942	3	2	79	1	0	0	0	0	1	0	0	0	1338	1841	64	2	1485	2	BBS2	16	56539942	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	54402043	56539942	33814811	154	10908										
PSKH1	5681	hgsc.bcm.edu	37	chr16	67942761	67942761	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctaagagtgacgtgtacaagCacttcatcacagaggtggac	11	9	2	3	rs374100286		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr16:67942761C>T	ENST00000291041.5	+	2	279	c.109C>T	c.(109-111)Cac>Tac	p.H37Y		NM_006742.2	NP_006733.1	P11801	KPSH1_HUMAN	protein serine kinase H1	37						cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|large_intestine(1)|lung(7)|pancreas(1)	12		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0044)|Epithelial(162;0.0197)|all cancers(182;0.128)		CGTGTACAAGCACTTCATCAC	0.592																																					p.H37Y		Atlas-SNP	.											.	PSKH1	28	.	0			c.C109T						.						118	89	99					16																	67942761		2198	4300	6498	SO:0001583	missense	5681	exon2			TACAAGCACTTCA	M14504	CCDS10851.1	16q22.1	2008-02-05			ENSG00000159792	ENSG00000159792			9529	protein-coding gene	gene with protein product		177015				8268911	Standard	NM_006742		Approved		uc002euv.3	P11801	OTTHUMG00000137548	ENST00000291041.5:c.109C>T	chr16.hg19:g.67942761C>T	ENSP00000291041:p.His37Tyr	168.0	0.0		97.0	35.0	NM_006742	Q9NY19	Missense_Mutation	SNP	ENST00000291041.5	hg19	CCDS10851.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.660567	0.47572	.	.	ENSG00000159792	ENST00000291041	T	0.67698	-0.28	5.8	5.8	0.92144	.	0.097482	0.64402	D	0.000001	T	0.56877	0.2015	L	0.40543	1.245	0.40157	D	0.977011	B	0.32829	0.386	B	0.25759	0.063	T	0.61783	-0.6992	10	0.72032	D	0.01	-29.9324	14.4963	0.67691	0.1469:0.8531:0.0:0.0	.	37	P11801	KPSH1_HUMAN	Y	37	ENSP00000291041:H37Y	ENSP00000291041:H37Y	H	+	1	0	PSKH1	66500262	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.733000	0.55029	2.755000	0.94549	0.655000	0.94253	CAC	.	.		0.592	PSKH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268882.3	NM_006742		T	67942761	C	T	67942761	3	4	79	1	0	0	0	0	1	0	0	0	12676	710	25	3	111	3	PSKH1	16	67942761	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	11402819	67942761	22411992	155	10909										
SNAI3	333929	hgsc.bcm.edu	37	chr16	88747782	88747782	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggcatccgctcagccccaagCagtttttccggagccccgtg	11	16	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr16:88747782C>A	ENST00000332281.5	-	2	503	c.417G>T	c.(415-417)ctG>ctT	p.L139L	SNAI3-AS1_ENST00000563261.1_RNA	NM_178310.3	NP_840101.1	Q3KNW1	SNAI3_HUMAN	snail family zinc finger 3	139					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	copper ion binding (GO:0005507)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(1)|kidney(1)|lung(1)|ovary(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(80;0.048)		CAGCCCCAAGCAGTTTTTCCG	0.687																																					p.L139L	Colon(27;366 710 19748 23199 27567)	Atlas-SNP	.											.	SNAI3	23	.	0			c.G417T						.						38	49	46					16																	88747782		2198	4299	6497	SO:0001819	synonymous_variant	333929	exon2			CCCAAGCAGTTTT	BC041461	CCDS32505.1	16q24.3	2013-05-23	2013-05-23			ENSG00000185669		"Snail homologs", "Zinc fingers, C2H2-type"	18411	protein-coding gene	gene with protein product		612741	"zinc finger protein 293", "snail homolog 3 (Drosophila)"	ZNF293		12579345	Standard	NM_178310		Approved	SMUC, Zfp293	uc002flj.3	Q3KNW1		ENST00000332281.5:c.417G>T	chr16.hg19:g.88747782C>A		111.0	0.0		64.0	21.0	NM_178310	Q86SU5	Silent	SNP	ENST00000332281.5	hg19	CCDS32505.1																																																																																			.	.		0.687	SNAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422582.1			A	88747782	C	A	88747782	2	1	79	1	0	0	0	0	0	0	0	1	14843	697	25	3		3	SNAI3	16	88747782	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	20805021	88747782	1606971	156	10910										
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6386917	6386917	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	atgtggcccagggcagcaggGaaatgggctcgtgtgacctt	16	9	0	1	rs367702668		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:6386917G>A	ENST00000262483.8	-	6	594	c.507C>T	c.(505-507)ttC>ttT	p.F169F	PITPNM3_ENST00000421306.3_Silent_p.F133F	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	169					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		GGGCAGCAGGGAAATGGGCTC	0.597																																					p.F169F		Atlas-SNP	.											.	PITPNM3	91	.	0			c.C507T						.						152	101	118					17																	6386917		2203	4300	6503	SO:0001819	synonymous_variant	83394	exon6			AGCAGGGAAATGG	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.507C>T	chr17.hg19:g.6386917G>A		126.0	0.0		67.0	29.0	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	hg19	CCDS11076.1																																																																																			.	.		0.597	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		A	6386917	G	A	6386917	2	1	79	1	0	0	0	0	0	0	0	1	11961	1165	41	3		3	PITPNM3	17	6386917	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10		6386917	74808293	157	10911										
TP53	7157	hgsc.bcm.edu	37	chr17	7577570	7577570	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cccatgcaggaactgttacaCatgtagttgtagtggatggt	12	7	0	0	rs587782664		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:7577570C>A	ENST00000269305.4	-	7	900	c.711G>T	c.(709-711)atG>atT	p.M237I	TP53_ENST00000445888.2_Missense_Mutation_p.M237I|TP53_ENST00000455263.2_Missense_Mutation_p.M237I|TP53_ENST00000413465.2_Missense_Mutation_p.M237I|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.M237I|TP53_ENST00000420246.2_Missense_Mutation_p.M237I	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	237	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		M -> I (in LFS; germline mutation and in sporadic cancers; somatic mutation).|M -> K (in sporadic cancers; somatic mutation).|M -> L (in sporadic cancers; somatic mutation).|M -> R (in sporadic cancers; somatic mutation).|M -> T (in sporadic cancers; somatic mutation).|M -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.M237I(109)|p.0?(8)|p.?(5)|p.M144I(4)|p.M237_N239delMCN(4)|p.Y236_M237delYM(1)|p.H233fs*6(1)|p.M144_N146delMCN(1)|p.Y236_M243delYMCNSSCM(1)|p.C238fs*2(1)|p.V225fs*23(1)|p.M237_C238insX(1)|p.H233_C242del10(1)|p.M237fs*1(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AACTGTTACACATGTAGTTGT	0.567		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.M237I	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,0,1	TP53	33396	.	139	Substitution - Missense(113)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(3)|Insertion - Frameshift(1)|Insertion - In frame(1)	upper_aerodigestive_tract(23)|ovary(22)|lung(18)|breast(18)|central_nervous_system(11)|haematopoietic_and_lymphoid_tissue(9)|large_intestine(9)|stomach(6)|biliary_tract(5)|bone(5)|oesophagus(4)|urinary_tract(3)|pancreas(2)|thyroid(1)|testis(1)|soft_tissue(1)|liver(1)	c.G711T	GRCh37	CM011014	TP53	M		.						130	102	112					17																	7577570		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GTTACACATGTAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.711G>T	chr17.hg19:g.7577570C>A	ENSP00000269305:p.Met237Ile	88.0	0.0		51.0	22.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.282984	0.80692	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99793	-6.77;-6.77;-6.77;-6.77;-6.77;-6.77;-6.77;-6.77	4.09	3.12	0.35913	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99697	0.9885	M	0.86953	2.85	0.54753	D	0.999982	D;D;D;D;D;D	0.89917	1.0;0.975;0.999;1.0;0.998;1.0	D;P;D;D;D;D	0.91635	0.999;0.864;0.999;0.999;0.999;0.998	D	0.97922	1.0315	10	0.72032	D	0.01	-32.6033	10.0519	0.42221	0.0:0.8993:0.0:0.1007	.	237;237;144;237;237;237	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	I	237;237;237;237;237;237;226;144;105;144	ENSP00000410739:M237I;ENSP00000352610:M237I;ENSP00000269305:M237I;ENSP00000398846:M237I;ENSP00000391127:M237I;ENSP00000391478:M237I;ENSP00000425104:M105I;ENSP00000423862:M144I	ENSP00000269305:M237I	M	-	3	0	TP53	7518295	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.556000	0.82233	1.305000	0.44909	0.462000	0.41574	ATG	.	.		0.567	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577570	C	A	7577570	3	1	79	1	0	0	0	0	1	0	0	0	16396	478	17	3	579	3	TP53	17	7577570	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	1190653	7577570	73617640	158	10912										
PER1	5187	hgsc.bcm.edu	37	chr17	8046658	8046694	+	Frame_Shift_Del	DEL	CAGCAGCCCCCTCAGCACGGGGGAGCTCCTCCAGCTG	CAGCAGCCCCCTCAGCACGGGGGAGCTCCTCCAGCTG	-													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gctcccagggcctcctgcaaCagcagccccctcagcacggg					rs3027194|rs112474322|rs112185134|rs571320541|rs376885431	byFrequency	TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	CAGCAGCCCCCTCAGCACGGGGGAGCTCCTCCAGCTG	CAGCAGCCCCCTCAGCACGGGGGAGCTCCTCCAGCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:8046658_8046694delCAGCAGCCCCCTCAGCACGGGGGAGCTCCTCCAGCTG	ENST00000317276.4	-	19	3199_3235	c.2962_2998delCAGCTGGAGGAGCTCCCCCGTGCTGAGGGGGCTGCTG	c.(2962-3000)cagctggaggagctcccccgtgctgagggggctgctgttfs	p.QLEELPRAEGAAV988fs	PER1_ENST00000578089.1_5'Flank|PER1_ENST00000581082.1_Frame_Shift_Del_p.QLEELPRAEGAAV965fs	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	988	Pro-rich.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CCTCCTGCAACAGCAGCCCCCTCAGCACGGGGGAGCTCCTCCAGCTGCAGCAGATTG	0.671			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.988_1000del		Atlas-INDEL	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.2963_2999del						.																																			SO:0001589	frameshift_variant	5187	exon19			.	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"period (Drosophila) homolog 1", "period homolog 1 (Drosophila)"	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2962_2998delCAGCTGGAGGAGCTCCCCCGTGCTGAGGGGGCTGCTG	chr17.hg19:g.8046658_8046694delCAGCAGCCCCCTCAGCACGGGGGAGCTCCTCCAGCTG	ENSP00000314420:p.Gln988fs	117.0	0.0		88.0	19.0	NM_002616	B2RPA8|B4DI49|D3DTR3	Frame_Shift_Del	DEL	ENST00000317276.4	hg19	CCDS11131.1																																																																																			.	.		0.671	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			-	8046694	CAGCAGCCCCCTCAGCACGGGGGAGCTCCTCCAGCTG	-	8046658	7	5	79	1	0	1	0	1	0	0	0	0	11738	478	17	0	894	0	PER1	17	8046658	Frame_Shift_Del	DEL	CAGCAGCCCCCTCAGCACGGGGGAGCTCCTCCAGCTG	TCGA-CC-A8HT-01A-11D-A35Z-10	469088	8046658	73148552	159	10913										
PER1	5187	hgsc.bcm.edu	37	chr17	8049299	8049299	+	Frame_Shift_Del	DEL	C	C	-													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	actccgggggcttcttgtctCccacatggacgatggtggag							TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:8049299delC	ENST00000317276.4	-	17	2432	c.2195delG	c.(2194-2196)ggafs	p.G732fs	PER1_ENST00000354903.5_Frame_Shift_Del_p.G716fs|PER1_ENST00000578089.1_5'UTR|PER1_ENST00000581082.1_Frame_Shift_Del_p.G712fs	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	732	Required for phosphorylation by CSNK1E. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CTTCTTGTCTCCCACATGGAC	0.637			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.G732fs		Atlas-INDEL	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.2196delA						.						69	68	69					17																	8049299		2203	4300	6503	SO:0001589	frameshift_variant	5187	exon17			.	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"period (Drosophila) homolog 1", "period homolog 1 (Drosophila)"	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2195delG	chr17.hg19:g.8049299delC	ENSP00000314420:p.Gly732fs	64.0	0.0		50.0	17.0	NM_002616	B2RPA8|B4DI49|D3DTR3	Frame_Shift_Del	DEL	ENST00000317276.4	hg19	CCDS11131.1																																																																																			.	.		0.637	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			-	8049299	C	-	8049299	7	5	79	1	0	1	0	1	0	0	0	0	11738	855	30	0	1705	0	PER1	17	8049299	Frame_Shift_Del	DEL	C	TCGA-CC-A8HT-01A-11D-A35Z-10	2641	8049299	73145911	160	10914										
PER1	5187	hgsc.bcm.edu	37	chr17	8053380	8053380	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cgctctggcggcagtcgaagCttgagctctcgaagtgctgt	14	11	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:8053380C>G	ENST00000317276.4	-	4	675	c.438G>C	c.(436-438)aaG>aaC	p.K146N	PER1_ENST00000354903.5_Missense_Mutation_p.K130N|PER1_ENST00000581082.1_Missense_Mutation_p.K146N	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	146	Interaction with BTRC. {ECO:0000269|PubMed:15917222}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GCAGTCGAAGCTTGAGCTCTC	0.607			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.K146N		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.G438C						.						109	121	117					17																	8053380		2203	4300	6503	SO:0001583	missense	5187	exon4			TCGAAGCTTGAGC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"period (Drosophila) homolog 1", "period homolog 1 (Drosophila)"	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.438G>C	chr17.hg19:g.8053380C>G	ENSP00000314420:p.Lys146Asn	85.0	0.0		41.0	16.0	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	hg19	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972943	0.74246	.	.	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.61627	1.31;0.09	4.93	2.79	0.32731	.	0.000000	0.85682	D	0.000000	T	0.70202	0.3197	M	0.72894	2.215	0.46609	D	0.999126	D;D;D	0.89917	1.0;1.0;0.993	D;D;D	0.85130	0.996;0.997;0.977	T	0.71567	-0.4554	10	0.87932	D	0	-24.6327	7.9204	0.29843	0.0:0.7752:0.0:0.2248	.	146;130;146	Q6IN51;B4DI49;O15534	.;.;PER1_HUMAN	N	146;130	ENSP00000314420:K146N;ENSP00000346979:K130N	ENSP00000314420:K146N	K	-	3	2	PER1	7994105	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.430000	0.44766	1.283000	0.44513	0.563000	0.77884	AAG	.	.		0.607	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			G	8053380	C	G	8053380	3	3	79	1	0	0	0	0	1	0	0	0	11738	796	28	4	3514	4	PER1	17	8053380	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	4081	8053380	73141830	161	10915										
MYH13	8735	hgsc.bcm.edu	37	chr17	10227448	10227448	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cttccagattcctcttcttgGcaaccaattcagaattcatc	4	13	4	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:10227448G>T	ENST00000418404.3	-	22	2988	c.2825C>A	c.(2824-2826)gCc>gAc	p.A942D	MYH13_ENST00000252172.4_Missense_Mutation_p.A942D|RP11-401O9.3_ENST00000577743.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	942					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CCTCTTCTTGGCAACCAATTC	0.448																																					p.A942D		Atlas-SNP	.											.	MYH13	533	.	0			c.C2825A						.						139	143	142					17																	10227448		2163	4282	6445	SO:0001583	missense	8735	exon23			TTCTTGGCAACCA	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.2825C>A	chr17.hg19:g.10227448G>T	ENSP00000404570:p.Ala942Asp	103.0	0.0		65.0	19.0	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	hg19	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.306054	0.81247	.	.	ENSG00000006788	ENST00000252172;ENST00000418404	D	0.94138	-3.36	4.37	3.4	0.38934	.	.	.	.	.	D	0.95446	0.8521	M	0.83012	2.62	0.46478	D	0.999061	P;D	0.57899	0.955;0.981	P;P	0.56343	0.707;0.796	D	0.95440	0.8524	9	0.72032	D	0.01	.	12.2713	0.54708	0.0821:0.0:0.9179:0.0	.	568;942	B4DFX9;Q9UKX3	.;MYH13_HUMAN	D	942;568	ENSP00000252172:A942D	ENSP00000252172:A942D	A	-	2	0	MYH13	10168173	1.000000	0.71417	0.935000	0.37517	0.922000	0.55478	7.663000	0.83820	1.177000	0.42855	0.655000	0.94253	GCC	.	.		0.448	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		T	10227448	G	T	10227448	3	4	79	1	0	0	0	0	1	0	0	0	10041	1203	42	3	3067	3	MYH13	17	10227448	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	2174068	10227448	70967762	162	10916										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18036653	18036653	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	aggacagcatcttccgcatcCtggcctccatcctgcacctg	8	17	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:18036653C>T	ENST00000205890.5	+	12	4773	c.4435C>T	c.(4435-4437)Ctg>Ttg	p.L1479L		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1479	Myosin motor.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CTTCCGCATCCTGGCCTCCAT	0.607																																					p.L1479L		Atlas-SNP	.											.	MYO15A	268	.	0			c.C4435T						.						49	53	52					17																	18036653		2097	4219	6316	SO:0001819	synonymous_variant	51168	exon11			CGCATCCTGGCCT	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.4435C>T	chr17.hg19:g.18036653C>T		60.0	0.0		57.0	18.0	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	hg19	CCDS42271.1																																																																																			.	.		0.607	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		T	18036653	C	T	18036653	2	4	79	1	0	0	0	0	0	0	0	1	10072	680	24	3		3	MYO15A	17	18036653	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	7809205	18036653	63158557	163	10917										
GGNBP2	79893	hgsc.bcm.edu	37	chr17	34923515	34923515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tctacagaggttgttggatgGatgtatgggaactaatgtcg	14	4	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:34923515G>A	ENST00000304718.4	+	6	857	c.541G>A	c.(541-543)Gat>Aat	p.D181N		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	181					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		TTGTTGGATGGATGTATGGGA	0.348																																					p.D181N		Atlas-SNP	.											.	GGNBP2	72	.	0			c.G541A						.						148	140	143					17																	34923515		2203	4300	6503	SO:0001583	missense	79893	exon6			TGGATGGATGTAT	AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.541G>A	chr17.hg19:g.34923515G>A	ENSP00000307617:p.Asp181Asn	248.0	0.0		203.0	38.0	NM_024835	B2RPK7|Q96T90|Q9GZR8|Q9H767	Missense_Mutation	SNP	ENST00000304718.4	hg19	CCDS11314.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.936419	0.92458	.	.	ENSG00000005955	ENST00000304718	.	.	.	5.48	5.48	0.80851	.	0.098933	0.64402	D	0.000002	T	0.78941	0.4363	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.76575	0.988;0.974	T	0.80291	-0.1444	9	0.72032	D	0.01	-8.1271	19.4017	0.94632	0.0:0.0:1.0:0.0	.	181;181	Q9H3C7;Q9H3C7-3	GGNB2_HUMAN;.	N	181	.	ENSP00000307617:D181N	D	+	1	0	GGNBP2	31997628	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.092000	0.94157	2.577000	0.86979	0.558000	0.71614	GAT	.	.		0.348	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		A	34923515	G	A	34923515	3	1	79	1	0	0	0	0	1	0	0	0	6367	1174	41	3	559	3	GGNBP2	17	34923515	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	16886862	34923515	46271695	164	10918										
GGNBP2	79893	hgsc.bcm.edu	37	chr17	34945736	34945736	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tctttctacagcaatagagaAcaataccgacagcatctgaa	6	10	3	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:34945736A>T	ENST00000304718.4	+	14	2305	c.1989A>T	c.(1987-1989)gaA>gaT	p.E663D	DHRS11_ENST00000590554.1_5'Flank|DHRS11_ENST00000251312.5_5'Flank	NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	663					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		GCAATAGAGAACAATACCGAC	0.393																																					p.E663D		Atlas-SNP	.											.	GGNBP2	72	.	0			c.A1989T						.						139	154	149					17																	34945736		2203	4300	6503	SO:0001583	missense	79893	exon14			TAGAGAACAATAC	AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.1989A>T	chr17.hg19:g.34945736A>T	ENSP00000307617:p.Glu663Asp	113.0	0.0		132.0	24.0	NM_024835	B2RPK7|Q96T90|Q9GZR8|Q9H767	Missense_Mutation	SNP	ENST00000304718.4	hg19	CCDS11314.1	.	.	.	.	.	.	.	.	.	.	A	12.46	1.944414	0.34283	.	.	ENSG00000005955	ENST00000304718	.	.	.	5.85	5.85	0.93711	.	0.283334	0.39615	N	0.001317	T	0.41259	0.1151	N	0.14661	0.345	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.31696	-0.9934	9	0.59425	D	0.04	-15.9473	12.0645	0.53580	0.9315:0.0:0.0685:0.0	.	663	Q9H3C7	GGNB2_HUMAN	D	663	.	ENSP00000307617:E663D	E	+	3	2	GGNBP2	32019849	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.320000	0.59203	2.237000	0.73441	0.459000	0.35465	GAA	.	.		0.393	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		T	34945736	A	T	34945736	3	4	79	1	0	0	0	0	1	0	0	0	6367	40	2	4	2039	4	GGNBP2	17	34945736	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	22221	34945736	46249474	165	10919										
PLEKHM1	9842	hgsc.bcm.edu	37	chr17	43516880	43516880	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctcaaaggggaagatgatgtCgtggtgctggcagatctggc	16	7	2	3	rs200261737		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:43516880C>A	ENST00000430334.3	-	11	3155	c.3022G>T	c.(3022-3024)Gac>Tac	p.D1008Y	PLEKHM1_ENST00000580404.1_5'UTR|PLEKHM1_ENST00000421073.2_Missense_Mutation_p.D919Y	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	1008					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					AAGATGATGTCGTGGTGCTGG	0.602																																					p.D1008Y		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.G3022T						.						114	90	98					17																	43516880		2203	4300	6503	SO:0001583	missense	9842	exon11			TGATGTCGTGGTG	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"Pleckstrin homology (PH) domain containing"	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.3022G>T	chr17.hg19:g.43516880C>A	ENSP00000389913:p.Asp1008Tyr	56.0	0.0		54.0	12.0	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Missense_Mutation	SNP	ENST00000430334.3	hg19	CCDS32671.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.979830	0.92982	.	.	ENSG00000225190	ENST00000430334;ENST00000421073	T;T	0.68331	-0.32;-0.32	5.2	5.2	0.72013	Protein kinase C-like, phorbol ester/diacylglycerol binding (2);	0.100604	0.64402	D	0.000003	D	0.82889	0.5135	M	0.84082	2.675	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.987	D	0.85204	0.1017	10	0.87932	D	0	.	16.362	0.83271	0.0:1.0:0.0:0.0	.	919;1008	F8W648;Q9Y4G2	.;PKHM1_HUMAN	Y	1008;919	ENSP00000389913:D1008Y;ENSP00000414352:D919Y	ENSP00000414352:D919Y	D	-	1	0	PLEKHM1	40872663	1.000000	0.71417	0.997000	0.53966	0.920000	0.55202	4.727000	0.61993	2.720000	0.93068	0.556000	0.70494	GAC	.	C|0.999;T|0.001		0.602	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798		A	43516880	C	A	43516880	3	1	79	1	0	0	0	0	1	0	0	0	12089	884	31	1	156	1	PLEKHM1	17	43516880	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	8571144	43516880	37678330	166	10920										
TBC1D16	125058	hgsc.bcm.edu	37	chr17	77921558	77921558	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	aggacctcggccaagatgggCgccaccaggtccgacatccc	12	16	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:77921558C>T	ENST00000310924.2	-	9	1729	c.1614G>A	c.(1612-1614)gcG>gcA	p.A538A	TBC1D16_ENST00000340848.7_Silent_p.A176A|TBC1D16_ENST00000576768.1_Silent_p.A163A|TBC1D16_ENST00000570373.1_Silent_p.A177A|TBC1D16_ENST00000572862.1_Silent_p.A176A	NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	538	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)	p.A538A(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			CCAAGATGGGCGCCACCAGGT	0.602																																					p.A538A	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											TBC1D16,colon,carcinoma,0,1	TBC1D16	48	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1614A						.						116	87	97					17																	77921558		2203	4300	6503	SO:0001819	synonymous_variant	125058	exon9			GATGGGCGCCACC	AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.1614G>A	chr17.hg19:g.77921558C>T		148.0	0.0		127.0	36.0	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Silent	SNP	ENST00000310924.2	hg19	CCDS11766.1																																																																																			.	.		0.602	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020		T	77921558	C	T	77921558	2	4	79	1	0	0	0	0	0	0	0	1	15620	755	27	1		1	TBC1D16	17	77921558	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	34404678	77921558	3273652	167	10921										
METRNL	284207	hgsc.bcm.edu	37	chr17	81052084	81052084	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgcgcgtgagcagactctatCggcagaaaagcagggtcttc	13	10	2	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr17:81052084C>T	ENST00000320095.7	+	4	825	c.700C>T	c.(700-702)Cgg>Tgg	p.R234W	METRNL_ENST00000571940.1_3'UTR|METRNL_ENST00000571814.1_Missense_Mutation_p.R152W|METRNL_ENST00000570778.1_Missense_Mutation_p.R152W	NM_001004431.1	NP_001004431.1	Q641Q3	METRL_HUMAN	meteorin, glial cell differentiation regulator-like	234					brown fat cell differentiation (GO:0050873)|fat cell differentiation (GO:0045444)|negative regulation of inflammatory response (GO:0050728)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of energy homeostasis (GO:2000507)|response to cold (GO:0009409)|response to muscle activity (GO:0014850)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)		BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			CAGACTCTATCGGCAGAAAAG	0.672																																					p.R234W		Atlas-SNP	.											.	METRNL	29	.	0			c.C700T						.						54	56	56					17																	81052084		2202	4292	6494	SO:0001583	missense	284207	exon4			CTCTATCGGCAGA	AK093748	CCDS32779.1	17q25.3	2004-12-01				ENSG00000176845			27584	protein-coding gene	gene with protein product							Standard	NM_001004431		Approved		uc002kgh.3	Q641Q3		ENST00000320095.7:c.700C>T	chr17.hg19:g.81052084C>T	ENSP00000315731:p.Arg234Trp	212.0	0.0		155.0	44.0	NM_001004431	B3KSJ5|Q86VM0	Missense_Mutation	SNP	ENST00000320095.7	hg19	CCDS32779.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.878071	0.33162	.	.	ENSG00000176845	ENST00000320095	T	0.32515	1.45	5.12	3.02	0.34903	.	0.000000	0.85682	U	0.000000	T	0.32912	0.0845	L	0.58101	1.795	0.58432	D	0.999998	D	0.55800	0.973	P	0.46110	0.504	T	0.06006	-1.0851	9	.	.	.	-25.8411	11.285	0.49216	0.4709:0.5291:0.0:0.0	.	234	Q641Q3	METRL_HUMAN	W	234	ENSP00000315731:R234W	.	R	+	1	2	METRNL	78645504	0.291000	0.24352	0.911000	0.35937	0.372000	0.29890	0.020000	0.13466	0.599000	0.29845	0.561000	0.74099	CGG	.	.		0.672	METRNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438902.1	NM_001004431		T	81052084	C	T	81052084	3	4	79	1	0	0	0	0	1	0	0	0	9498	875	31	1	714	1	METRNL	17	81052084	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	3130526	81052084	143126	168	10922										
PTPRM	5797	hgsc.bcm.edu	37	chr18	8370961	8370961	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agttaccctaatagaaacagAactactggcagaatatgtga	8	7	0	4	rs551645103		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr18:8370961A>T	ENST00000332175.8	+	22	4126	c.3089A>T	c.(3088-3090)gAa>gTa	p.E1030V	PTPRM_ENST00000400060.4_Missense_Mutation_p.E1044V|PTPRM_ENST00000400053.4_Missense_Mutation_p.E968V|PTPRM_ENST00000580170.1_Missense_Mutation_p.E1043V|PTPRM_ENST00000444013.1_Missense_Mutation_p.E817V	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1030	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				ATAGAAACAGAACTACTGGCA	0.338													A|||	1	0.000199681	0	0	5008	,	,		20012	0.001		0	False		,,,				2504	0				p.E1043V		Atlas-SNP	.											.	PTPRM	185	.	0			c.A3128T						.						100	99	99					18																	8370961		2203	4300	6503	SO:0001583	missense	5797	exon24			AAACAGAACTACT	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3089A>T	chr18.hg19:g.8370961A>T	ENSP00000331418:p.Glu1030Val	107.0	0.0		98.0	29.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.315533	0.81469	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	5.56	5.56	0.83823	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.048422	0.85682	D	0.000000	D	0.86385	0.5920	L	0.60455	1.87	0.58432	D	0.999999	D;P;P	0.63046	0.992;0.956;0.952	D;P;P	0.63793	0.918;0.525;0.618	T	0.82780	-0.0288	10	0.02654	T	1	.	16.0068	0.80367	1.0:0.0:0.0:0.0	.	817;1043;1030	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	V	1030;1044;968;817	ENSP00000331418:E1030V;ENSP00000382933:E1044V;ENSP00000382927:E968V;ENSP00000387608:E817V	ENSP00000331418:E1030V	E	+	2	0	PTPRM	8360961	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.255000	0.95524	2.240000	0.73641	0.528000	0.53228	GAA	.	.		0.338	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	8370961	A	T	8370961	3	4	79	1	0	0	0	0	1	0	0	0	12821	246	9	4	3222	4	PTPRM	18	8370961	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10		8370961	69706287	169	10923										
TTC39C	125488	hgsc.bcm.edu	37	chr18	21660787	21660787	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cacctttgcatatccatggtGcccccaaacctgctcaaaat	5	15	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr18:21660787G>A	ENST00000317571.3	+	5	935	c.699G>A	c.(697-699)gtG>gtA	p.V233V	RP11-403A21.3_ENST00000578443.1_RNA|TTC39C_ENST00000304621.6_Silent_p.V172V	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	233										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						TATCCATGGTGCCCCCAAACC	0.483																																					p.V233V		Atlas-SNP	.											TTC39C_ENST00000317571,NS,neuroblastoma,0,2	TTC39C	83	.	0			c.G699A						.						103	99	100					18																	21660787		2203	4300	6503	SO:0001819	synonymous_variant	125488	exon5			CATGGTGCCCCCA	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"Tetratricopeptide (TTC) repeat domain containing"	26595	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 17"	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.699G>A	chr18.hg19:g.21660787G>A		95.0	0.0		106.0	34.0	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Silent	SNP	ENST00000317571.3	hg19	CCDS45839.1																																																																																			.	.		0.483	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211		A	21660787	G	A	21660787	2	1	79	1	0	0	0	0	0	0	0	1	16724	1306	46	3		3	TTC39C	18	21660787	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	13289826	21660787	56416461	170	10924										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22805355	22805355	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ctcggaagctccatttgttcCacagttgggtgtcttggttt	11	9	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr18:22805355C>A	ENST00000361524.3	-	4	2675	c.2527G>T	c.(2527-2529)Gga>Tga	p.G843*	ZNF521_ENST00000584787.1_Nonsense_Mutation_p.G623*|ZNF521_ENST00000538137.2_Nonsense_Mutation_p.G843*|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	843					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CCATTTGTTCCACAGTTGGGT	0.478			T	PAX5	ALL																																p.G843X		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.G2527T						.						183	175	178					18																	22805355		2203	4300	6503	SO:0001587	stop_gained	25925	exon4			TTGTTCCACAGTT	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2527G>T	chr18.hg19:g.22805355C>A	ENSP00000354794:p.Gly843*	127.0	0.0		114.0	26.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Nonsense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	37	6.138049	0.97315	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	.	.	.	5.93	5.93	0.95920	.	0.106321	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-23.3642	13.5312	0.61623	0.0:0.9294:0.0:0.0706	.	.	.	.	X	843;877;843	.	ENSP00000354794:G843X	G	-	1	0	ZNF521	21059353	0.994000	0.37717	0.900000	0.35374	0.082000	0.17680	4.675000	0.61619	2.826000	0.97356	0.655000	0.94253	GGA	.	.		0.478	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		A	22805355	C	A	22805355	4	1	79	1	0	0	0	0	0	1	0	0	17980	603	21	3	1428	3	ZNF521	18	22805355	Nonsense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	1144568	22805355	55271893	171	10925										
NOL4	8715	hgsc.bcm.edu	37	chr18	31709985	31709985	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tcatctacccctacgccatcCtggaaacaaaacaacaacaa	3	15	2	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr18:31709985C>A	ENST00000261592.5	-	2	562		c.e2-1		NOL4_ENST00000538587.1_Splice_Site|NOL4_ENST00000535475.1_Splice_Site|NOL4_ENST00000589544.1_Splice_Site|NOL4_ENST00000269185.4_Splice_Site	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4							nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						CTACGCCATCCTGGAAACAAA	0.343																																					.		Atlas-SNP	.											.	NOL4	139	.	0			c.265-1G>T						.						50	47	48					18																	31709985		2202	4299	6501	SO:0001630	splice_region_variant	8715	exon3			GCCATCCTGGAAA	AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.265-1G>T	chr18.hg19:g.31709985C>A		105.0	0.0		85.0	20.0	NM_001198546	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Splice_Site	SNP	ENST00000261592.5	hg19	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	C	23.0	4.359656	0.82353	.	.	ENSG00000101746	ENST00000261592;ENST00000538587	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.866	0.92292	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NOL4	29963983	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.772000	0.75001	2.710000	0.92621	0.585000	0.79938	.	.	.		0.343	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787	Intron	A	31709985	C	A	31709985	5	1	79	1	0	0	0	0	0	0	1	0	10533	695	24	3	1692	3	NOL4	18	31709985	Splice_Site	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	8904630	31709985	46367263	172	10926										
ST8SIA5	29906	hgsc.bcm.edu	37	chr18	44260286	44260293	+	Frame_Shift_Del	DEL	TGACCAGG	TGACCAGG	-													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gagccagtagcgcgacacgtTgaccaggtactgcggatgga					rs200781006		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	TGACCAGG	TGACCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr18:44260286_44260293delTGACCAGG	ENST00000315087.7	-	7	1503_1510	c.843_850delCCTGGTCA	c.(841-852)tacctggtcaacfs	p.YLVN281fs	ST8SIA5_ENST00000536490.1_Frame_Shift_Del_p.YLVN250fs|ST8SIA5_ENST00000538168.1_Frame_Shift_Del_p.YLVN317fs|ST8SIA5_ENST00000590497.1_5'UTR	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	281					carbohydrate metabolic process (GO:0005975)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)			kidney(1)|large_intestine(10)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	22						CGCGACACGTTGACCAGGTACTGCGGAT	0.615																																					p.282_284del		Atlas-INDEL	.											.	ST8SIA5	57	.	0			c.844_851del						.																																			SO:0001589	frameshift_variant	29906	exon7			.	U91641	CCDS11930.1	18q12.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000101638	ENSG00000101638		"Sialyltransferases"	17827	protein-coding gene	gene with protein product	"ST8Sia V"	607162	"sialyltransferase 8E (alpha-2, 8-polysialytransferase)"	SIAT8E		9199191	Standard	XM_005258250		Approved		uc002lcj.1	O15466	OTTHUMG00000132643	ENST00000315087.7:c.843_850delCCTGGTCA	chr18.hg19:g.44260286_44260293delTGACCAGG	ENSP00000321343:p.Tyr281fs	99.0	0.0		84.0	18.0	NM_013305	B7Z1K9|Q6IAW7	Frame_Shift_Del	DEL	ENST00000315087.7	hg19	CCDS11930.1																																																																																			.	.		0.615	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255892.1	NM_013305		-	44260293	TGACCAGG	-	44260286	7	5	79	1	0	1	0	1	0	0	0	0	15250	1812	63	0	284	0	ST8SIA5	18	44260286	Frame_Shift_Del	DEL	TGACCAGG	TCGA-CC-A8HT-01A-11D-A35Z-10	12550301	44260286	33816962	173	10927										
NFATC1	4772	hgsc.bcm.edu	37	chr18	77170794	77170794	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gacccctcgtgcctgagcccGgccagcagcctgtcctcccg	11	20	0	1	rs571313182		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr18:77170794G>T	ENST00000427363.2	+	2	519	c.519G>T	c.(517-519)ccG>ccT	p.P173P	NFATC1_ENST00000587635.1_Silent_p.P173P|NFATC1_ENST00000586434.1_Silent_p.P160P|NFATC1_ENST00000545796.1_Intron|NFATC1_ENST00000253506.5_Silent_p.P173P|NFATC1_ENST00000318065.5_Silent_p.P160P|NFATC1_ENST00000542384.1_Silent_p.P173P|NFATC1_ENST00000591814.1_Silent_p.P173P|NFATC1_ENST00000329101.4_Silent_p.P160P|NFATC1_ENST00000592223.1_Silent_p.P160P|NFATC1_ENST00000397790.2_Intron			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	173	Trans-activation domain A (TAD-A).				calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	GCCTGAGCCCGGCCAGCAGCC	0.662																																					p.P173P	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.G519T						.						40	43	42					18																	77170794		2203	4299	6502	SO:0001819	synonymous_variant	4772	exon2			GAGCCCGGCCAGC	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"Nuclear factor of activated T-cells"	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.519G>T	chr18.hg19:g.77170794G>T		58.0	0.0		42.0	14.0	NM_006162	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Silent	SNP	ENST00000427363.2	hg19																																																																																				.	.		0.662	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390		T	77170794	G	T	77170794	2	4	79	1	0	0	0	0	0	0	0	1	10370	1103	39	1		1	NFATC1	18	77170794	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	32910508	77170794	906454	174	10928										
EVI5L	115704	hgsc.bcm.edu	37	chr19	7923102	7923102	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agtgacacgggcgcaggaggCggaggagaactacgtcatca	16	9	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:7923102C>T	ENST00000270530.4	+	12	1422	c.1226C>T	c.(1225-1227)gCg>gTg	p.A409V	EVI5L_ENST00000600802.1_3'UTR|EVI5L_ENST00000538904.2_Missense_Mutation_p.A420V	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	409					negative regulation of cilium assembly (GO:1902018)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	12						GCGCAGGAGGCGGAGGAGAAC	0.701																																					p.A420V		Atlas-SNP	.											.	EVI5L	43	.	0			c.C1259T						.						30	20	23					19																	7923102		2171	4270	6441	SO:0001583	missense	115704	exon12			AGGAGGCGGAGGA	BC014111	CCDS12188.1, CCDS54209.1	19p13	2013-07-09				ENSG00000142459			30464	protein-coding gene	gene with protein product						23669355	Standard	NM_001159944		Approved		uc010xjz.2	Q96CN4		ENST00000270530.4:c.1226C>T	chr19.hg19:g.7923102C>T	ENSP00000270530:p.Ala409Val	186.0	0.0		148.0	35.0	NM_001159944	B9A6I9	Missense_Mutation	SNP	ENST00000270530.4	hg19	CCDS12188.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.098626	0.76870	.	.	ENSG00000142459	ENST00000270530;ENST00000538904	D;T	0.97186	-4.28;3.39	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.97312	0.9121	L	0.59436	1.845	0.58432	D	0.999991	D;D	0.89917	1.0;1.0	D;D	0.63033	0.91;0.91	D	0.95837	0.8863	10	0.18276	T	0.48	-21.4401	15.8352	0.78793	0.0:1.0:0.0:0.0	.	420;409	B9A6I9;Q96CN4	.;EVI5L_HUMAN	V	409;420	ENSP00000270530:A409V;ENSP00000445905:A420V	ENSP00000270530:A409V	A	+	2	0	EVI5L	7829102	1.000000	0.71417	0.959000	0.39883	0.764000	0.43329	7.526000	0.81920	2.607000	0.88179	0.498000	0.49722	GCG	.	.		0.701	EVI5L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461347.1	NM_145245		T	7923102	C	T	7923102	3	4	79	1	0	0	0	0	1	0	0	0	5292	768	27	1	1305	1	EVI5L	19	7923102	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10		7923102	51205881	175	10929										
MAP2K7	5609	hgsc.bcm.edu	37	chr19	7975602	7975602	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cggacgtcttcatcgccatgGagctcatgggcacctgcgct	12	14	3	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:7975602G>T	ENST00000397979.3	+	6	643	c.589G>T	c.(589-591)Gag>Tag	p.E197*	CTD-3193O13.13_ENST00000595655.1_RNA|MAP2K7_ENST00000545011.1_Nonsense_Mutation_p.E239*|MAP2K7_ENST00000397983.3_Nonsense_Mutation_p.E213*|MAP2K7_ENST00000397981.3_Nonsense_Mutation_p.E197*	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	197	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						CATCGCCATGGAGCTCATGGG	0.662																																					p.E197X		Atlas-SNP	.											.	MAP2K7	66	.	0			c.G589T						.						15	17	16					19																	7975602		2052	4178	6230	SO:0001587	stop_gained	5609	exon6			GCCATGGAGCTCA	AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.589G>T	chr19.hg19:g.7975602G>T	ENSP00000381066:p.Glu197*	105.0	0.0		108.0	22.0	NM_145185	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Nonsense_Mutation	SNP	ENST00000397979.3	hg19	CCDS42491.1	.	.	.	.	.	.	.	.	.	.	G	37	6.073297	0.97256	.	.	ENSG00000076984	ENST00000397981;ENST00000397983;ENST00000545011;ENST00000425613;ENST00000397979	.	.	.	4.75	4.75	0.60458	.	0.053841	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-6.3089	15.6565	0.77140	0.0:0.0:1.0:0.0	.	.	.	.	X	197;213;239;213;197	.	ENSP00000381066:E197X	E	+	1	0	MAP2K7	7881602	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.325000	0.96381	2.378000	0.81104	0.555000	0.69702	GAG	.	.		0.662	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1			T	7975602	G	T	7975602	4	4	79	1	0	0	0	0	0	1	0	0	9251	1175	41	3	611	3	MAP2K7	19	7975602	Nonsense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	52500	7975602	51153381	176	10930										
MUC16	94025	hgsc.bcm.edu	37	chr19	9058023	9058023	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ccaccgctgtgtttgaggaaGgatgaattttctctgtatct	10	8	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:9058023G>A	ENST00000397910.4	-	3	29626	c.29423C>T	c.(29422-29424)cCt>cTt	p.P9808L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9810	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTTTGAGGAAGGATGAATTTT	0.453																																					p.P9808L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C29423T						.						98	96	97					19																	9058023		1970	4154	6124	SO:0001583	missense	94025	exon3			GAGGAAGGATGAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29423C>T	chr19.hg19:g.9058023G>A	ENSP00000381008:p.Pro9808Leu	148.0	0.0		128.0	37.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	5.191	0.220872	0.09863	.	.	ENSG00000181143	ENST00000397910	T	0.26957	1.7	2.58	-2.55	0.06288	.	.	.	.	.	T	0.13756	0.0333	N	0.24115	0.695	.	.	.	B	0.16603	0.018	B	0.15484	0.013	T	0.25641	-1.0126	8	0.87932	D	0	.	3.4806	0.07601	0.4848:0.2136:0.3016:0.0	.	9808	B5ME49	.	L	9808	ENSP00000381008:P9808L	ENSP00000381008:P9808L	P	-	2	0	MUC16	8919023	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.831000	0.04405	-0.522000	0.06417	-0.259000	0.10710	CCT	.	.		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9058023	G	A	9058023	3	1	79	1	0	0	0	0	1	0	0	0	9982	1000	35	3	14428	3	MUC16	19	9058023	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	1082421	9058023	50070960	177	10931										
OR7G3	390883	hgsc.bcm.edu	37	chr19	9237267	9237267	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cagatggccacaaatcgatcAtaggccatcatgaccagaat	8	11	2	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:9237267A>G	ENST00000305444.2	-	1	359	c.360T>C	c.(358-360)taT>taC	p.Y120Y		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	120						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						CAAATCGATCATAGGCCATCA	0.478																																					p.Y120Y		Atlas-SNP	.											.	OR7G3	41	.	0			c.T360C						.						109	104	106					19																	9237267		2203	4300	6503	SO:0001819	synonymous_variant	390883	exon1			TCGATCATAGGCC		CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"GPCR / Class A : Olfactory receptors"	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.360T>C	chr19.hg19:g.9237267A>G		152.0	0.0		116.0	24.0	NM_001001958	Q6IFJ6|Q96R99	Silent	SNP	ENST00000305444.2	hg19	CCDS32899.1																																																																																			.	.		0.478	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1			G	9237267	A	G	9237267	2	3	79	1	0	0	0	0	0	0	0	1	11233	224	8	2		2	OR7G3	19	9237267	Silent	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	179244	9237267	49891716	178	10932										
RAVER1	125950	hgsc.bcm.edu	37	chr19	10439536	10439536	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agccgagtccttcttcatgtActcagcaaagccatagccct	7	14	3	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:10439536A>G	ENST00000293677.6	-	3	670	c.589T>C	c.(589-591)Tac>Cac	p.Y197H		NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1	180	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	18			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)			TTCTTCATGTACTCAGCAAAG	0.637																																					p.Y197H		Atlas-SNP	.											.	RAVER1	67	.	0			c.T589C						.						34	40	38					19																	10439536		2125	4240	6365	SO:0001583	missense	125950	exon3			TCATGTACTCAGC		CCDS45960.1	19p13.2	2013-02-12				ENSG00000161847		"RNA binding motif (RRM) containing"	30296	protein-coding gene	gene with protein product		609950				11853319, 11724819	Standard	NM_133452		Approved	KIAA1978	uc002moa.3	Q8IY67		ENST00000293677.6:c.589T>C	chr19.hg19:g.10439536A>G	ENSP00000293677:p.Tyr197His	137.0	0.0		108.0	28.0	NM_133452	A6NMU4|Q8IY60|Q8TF24	Missense_Mutation	SNP	ENST00000293677.6	hg19	CCDS45960.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.363784	0.82353	.	.	ENSG00000161847	ENST00000293677;ENST00000331131	T	0.21031	2.03	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.58963	0.2159	H	0.96518	3.835	0.49483	D	0.999792	D	0.89917	1.0	D	0.97110	1.0	T	0.72424	-0.4298	10	0.87932	D	0	-24.5206	12.8059	0.57614	1.0:0.0:0.0:0.0	.	197	E9PAU2	.	H	197;180	ENSP00000293677:Y197H	ENSP00000293677:Y197H	Y	-	1	0	RAVER1	10300536	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.849000	0.92178	1.911000	0.55334	0.528000	0.53228	TAC	.	.		0.637	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452		G	10439536	A	G	10439536	3	3	79	1	0	0	0	0	1	0	0	0	13109	391	14	2	1725	2	RAVER1	19	10439536	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	1202269	10439536	48689447	179	10933										
LOC55908	55908	hgsc.bcm.edu	37	chr19	11352206	11352206	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggagatggtggcacagcagcAtcggctgcgacagatccagg	16	10	0	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:11352206A>G	ENST00000252453.8	+	3	564	c.545A>G	c.(544-546)cAt>cGt	p.H182R	DOCK6_ENST00000294618.7_Intron|C19orf80_ENST00000591200.1_Missense_Mutation_p.H83R	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	182					cellular lipid metabolic process (GO:0044255)|glucose metabolic process (GO:0006006)|positive regulation of protein processing (GO:0010954)|regulation of lipoprotein metabolic process (GO:0050746)|triglyceride homeostasis (GO:0070328)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|breast(1)|endometrium(2)	4						GCACAGCAGCATCGGCTGCGA	0.662																																					p.H182R		Atlas-SNP	.											.	C19orf80	8	.	0			c.A545G						.						9	14	12					19																	11352206		2095	4099	6194	SO:0001583	missense	55908	exon3			AGCAGCATCGGCT		CCDS54220.1	19p13.2	2014-02-13			ENSG00000130173	ENSG00000130173			24933	protein-coding gene	gene with protein product	"lipasin", "betatrophin"					22809513, 23150577, 24262987	Standard	NM_018687		Approved	TD26, RIFL, ANGPTL8	uc021upg.1	Q6UXH0		ENST00000252453.8:c.545A>G	chr19.hg19:g.11352206A>G	ENSP00000252453:p.His182Arg	113.0	0.0		87.0	19.0	NM_018687	Q9NQZ1	Missense_Mutation	SNP	ENST00000252453.8	hg19	CCDS54220.1	.	.	.	.	.	.	.	.	.	.	A	7.988	0.752637	0.15778	.	.	ENSG00000130173	ENST00000397785;ENST00000252453	T	0.28895	1.59	4.07	3.05	0.35203	.	0.813446	0.10613	N	0.654272	T	0.20333	0.0489	L	0.38175	1.15	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.35325	-0.9793	10	0.11182	T	0.66	-8.8099	5.7922	0.18367	0.8772:0.0:0.1228:0.0	.	182	Q6UXH0	TD26_HUMAN	R	107;182	ENSP00000252453:H182R	ENSP00000252453:H182R	H	+	2	0	C19orf80	11213206	0.020000	0.18652	0.064000	0.19789	0.776000	0.43924	0.320000	0.19540	0.642000	0.30620	0.254000	0.18369	CAT	.	.		0.662	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687		G	11352206	A	G	11352206	3	3	79	1	0	0	0	0	1	0	0	0	8890	217	8	2	555	2	LOC55908	19	11352206	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	912670	11352206	47776777	180	10934										
ZNF442	79973	hgsc.bcm.edu	37	chr19	12461479	12461479	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttctttcatgtattcgaaggGaactggaaacactgaaggct	10	7	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:12461479G>A	ENST00000242804.4	-	6	1502	c.920C>T	c.(919-921)tCc>tTc	p.S307F	CTD-3105H18.13_ENST00000563695.2_lincRNA|ZNF442_ENST00000438182.1_Missense_Mutation_p.S238F	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TATTCGAAGGGAACTGGAAAC	0.413																																					p.S307F		Atlas-SNP	.											.	ZNF442	102	.	0			c.C920T						.						157	153	154					19																	12461479		2203	4300	6503	SO:0001583	missense	79973	exon6			CGAAGGGAACTGG	AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"Zinc fingers, C2H2-type", "-"	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.920C>T	chr19.hg19:g.12461479G>A	ENSP00000242804:p.Ser307Phe	78.0	0.0		98.0	25.0	NM_030824	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	hg19	CCDS12271.1	.	.	.	.	.	.	.	.	.	.	G	5.744	0.321792	0.10845	.	.	ENSG00000198342	ENST00000242804;ENST00000438182	T;T	0.07567	3.18;3.18	0.832	-1.66	0.08265	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07638	0.0192	M	0.61703	1.905	0.09310	N	1	B	0.14805	0.011	B	0.16289	0.015	T	0.42137	-0.9469	9	0.25106	T	0.35	.	2.4995	0.04630	0.2607:0.3136:0.4256:0.0	.	307	Q9H7R0	ZN442_HUMAN	F	307;238	ENSP00000242804:S307F;ENSP00000388634:S238F	ENSP00000242804:S307F	S	-	2	0	ZNF442	12322479	0.003000	0.15002	0.000000	0.03702	0.451000	0.32288	0.585000	0.23879	-0.832000	0.04251	0.313000	0.20887	TCC	.	.		0.413	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824		A	12461479	G	A	12461479	3	1	79	1	0	0	0	0	1	0	0	0	17930	1174	41	3	967	3	ZNF442	19	12461479	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	1109273	12461479	46667504	181	10935										
TECR	9524	hgsc.bcm.edu	37	chr19	14674897	14674897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tgactttacgtccagtcggcAtacagtggtgcagtaagtgg	13	8	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:14674897A>G	ENST00000215567.5	+	6	508	c.371A>G	c.(370-372)cAt>cGt	p.H124R	TECR_ENST00000436007.2_Missense_Mutation_p.H139R|TECR_ENST00000600083.1_5'UTR|TECR_ENST00000596073.1_5'UTR	NM_138501.5	NP_612510.1	Q9NZ01	TECR_HUMAN	trans-2,3-enoyl-CoA reductase	124					cellular lipid metabolic process (GO:0044255)|fatty acid elongation (GO:0030497)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|nucleus (GO:0005634)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|large_intestine(1)|ovary(1)	3						TCCAGTCGGCATACAGTGGTG	0.587																																					p.H124R		Atlas-SNP	.											.	TECR	22	.	0			c.A371G						.						133	138	136					19																	14674897		2203	4300	6503	SO:0001583	missense	9524	exon6			GTCGGCATACAGT	AK001416	CCDS12313.1	19p13.12	2014-05-27	2009-07-21	2009-07-21	ENSG00000099797	ENSG00000099797			4551	protein-coding gene	gene with protein product		610057	"glycoprotein, synaptic 2"	SC2, GPSN2		9653160, 12482854	Standard	NM_138501		Approved	TER, MRT14	uc002mza.3	Q9NZ01		ENST00000215567.5:c.371A>G	chr19.hg19:g.14674897A>G	ENSP00000215567:p.His124Arg	39.0	0.0		30.0	7.0	NM_138501	B2RD55|O75350|Q6IBB2|Q9BWK3|Q9Y6P0	Missense_Mutation	SNP	ENST00000215567.5	hg19	CCDS12313.1	.	.	.	.	.	.	.	.	.	.	A	19.00	3.741547	0.69304	.	.	ENSG00000099797	ENST00000215567;ENST00000436007	T;T	0.26373	1.75;1.74	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.31638	0.0803	M	0.73319	2.225	0.80722	D	1	P;P;P	0.49961	0.84;0.93;0.84	B;B;B	0.43809	0.432;0.432;0.432	T	0.11348	-1.0591	10	0.37606	T	0.19	-18.2031	12.6983	0.57016	1.0:0.0:0.0:0.0	.	124;139;124	B3KM97;B3KSQ1;Q9NZ01	.;.;TECR_HUMAN	R	124;139	ENSP00000215567:H124R;ENSP00000397206:H139R	ENSP00000215567:H124R	H	+	2	0	TECR	14535897	1.000000	0.71417	0.998000	0.56505	0.815000	0.46073	8.347000	0.90062	1.892000	0.54788	0.374000	0.22700	CAT	.	.		0.587	TECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466000.1	NM_138501		G	14674897	A	G	14674897	3	3	79	1	0	0	0	0	1	0	0	0	15760	217	8	2	393	2	TECR	19	14674897	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	2213418	14674897	44454086	182	10936										
ZNF93	81931	hgsc.bcm.edu	37	chr19	20044671	20044671	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	aatcctcaacacttactaaaCataagaaaattcatactgga	3	9	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:20044671C>T	ENST00000343769.5	+	4	935	c.907C>T	c.(907-909)Cat>Tat	p.H303Y	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						ACTTACTAAACATAAGAAAAT	0.368																																					p.H303Y		Atlas-SNP	.											.	ZNF93	81	.	0			c.C907T						.						33	36	35					19																	20044671		2199	4291	6490	SO:0001583	missense	81931	exon4			ACTAAACATAAGA	M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"Zinc fingers, C2H2-type", "-"	13169	protein-coding gene	gene with protein product		603975	"zinc finger protein 505", "zinc finger protein 93 (HTF34)"	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.907C>T	chr19.hg19:g.20044671C>T	ENSP00000342002:p.His303Tyr	64.0	0.0		50.0	9.0	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Missense_Mutation	SNP	ENST00000343769.5	hg19	CCDS32973.1	.	.	.	.	.	.	.	.	.	.	c	15.44	2.832924	0.50951	.	.	ENSG00000184635	ENST00000343769;ENST00000427325	D	0.86769	-2.17	0.85	0.85	0.18980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94427	0.8207	H	0.96175	3.78	0.26448	N	0.975667	D	0.89917	1.0	D	0.91635	0.999	D	0.85531	0.1209	9	0.87932	D	0	.	6.9971	0.24789	0.0:1.0:0.0:0.0	.	303	P35789	ZNF93_HUMAN	Y	303	ENSP00000342002:H303Y	ENSP00000342002:H303Y	H	+	1	0	ZNF93	19905671	0.959000	0.32827	0.488000	0.27440	0.486000	0.33341	2.741000	0.47426	0.192000	0.20272	0.195000	0.17529	CAT	.	.		0.368	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218		T	20044671	C	T	20044671	3	4	79	1	0	0	0	0	1	0	0	0	18217	478	17	3	921	3	ZNF93	19	20044671	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	5369774	20044671	39084312	183	10937										
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39330912	39330912	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gtagcgacttgggccccgacGgtgaccccccactggtggac	14	15	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:39330912G>A	ENST00000221419.5	-	8	1423	c.1057C>T	c.(1057-1059)Cgt>Tgt	p.R353C	AC104534.3_ENST00000594769.1_5'Flank|HNRNPL_ENST00000600873.1_Missense_Mutation_p.R220C	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	353	Pro-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			GGGCCCCGACGGTGACCCCCC	0.682																																					p.R353C		Atlas-SNP	.											.	HNRNPL	67	.	0			c.C1057T						.						6	7	7					19																	39330912		1846	3643	5489	SO:0001583	missense	3191	exon8			CCCGACGGTGACC	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1057C>T	chr19.hg19:g.39330912G>A	ENSP00000221419:p.Arg353Cys	127.0	0.0		129.0	8.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	hg19	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.173300	0.78452	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750	T	0.44881	0.91	5.09	5.09	0.68999	.	0.047994	0.85682	D	0.000000	T	0.45256	0.1333	L	0.36672	1.1	0.80722	D	1	D;D;D	0.76494	0.988;0.993;0.999	B;B;P	0.50490	0.353;0.348;0.642	T	0.41520	-0.9504	10	0.54805	T	0.06	.	17.4286	0.87533	0.0:0.0:1.0:0.0	.	353;220;336	P14866;A6NIT8;Q6NTA2	HNRPL_HUMAN;.;.	C	353;220;220	ENSP00000221419:R353C	ENSP00000221419:R353C	R	-	1	0	HNRNPL	44022752	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.187000	0.58344	2.652000	0.90054	0.555000	0.69702	CGT	.	.		0.682	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			A	39330912	G	A	39330912	3	1	79	1	0	0	0	0	1	0	0	0	7279	1116	39	1	736	1	HNRNPL	19	39330912	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	19286241	39330912	19798071	184	10938										
EGLN2	112398	hgsc.bcm.edu	37	chr19	41313170	41313170	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ccacgaggtgaagccagcctAtgccaccaggtatgacctgt	11	13	0	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:41313170A>G	ENST00000593726.1	+	3	2119	c.1091A>G	c.(1090-1092)tAt>tGt	p.Y364C	EGLN2_ENST00000303961.4_Missense_Mutation_p.Y364C|EGLN2_ENST00000594140.1_Missense_Mutation_p.Y82C|RAB4B-EGLN2_ENST00000594136.1_3'UTR|CTC-490E21.12_ENST00000601627.1_Intron|EGLN2_ENST00000406058.2_Missense_Mutation_p.Y364C			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	364	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	AAGCCAGCCTATGCCACCAGG	0.597											OREG0025478	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y364C		Atlas-SNP	.											.	EGLN2	31	.	0			c.A1091G						.						83	81	82					19																	41313170		2203	4300	6503	SO:0001583	missense	112398	exon4			CAGCCTATGCCAC	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"HIF prolyl hydroxylase 1"	606424	"EGL nine (C.elegans) homolog 2", "egl nine homolog 2 (C. elegans)"				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.1091A>G	chr19.hg19:g.41313170A>G	ENSP00000469686:p.Tyr364Cys	57.0	0.0	900	55.0	15.0	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Missense_Mutation	SNP	ENST00000593726.1	hg19	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	A	15.82	2.946141	0.53079	.	.	ENSG00000171570	ENST00000303961;ENST00000406058	T;T	0.58797	0.31;0.31	4.93	4.93	0.64822	Oxoglutarate/iron-dependent oxygenase (2);Prolyl 4-hydroxylase, alpha subunit (1);	0.187832	0.45606	D	0.000345	T	0.60170	0.2248	M	0.63208	1.945	0.46478	D	0.99906	P	0.48294	0.908	P	0.49252	0.604	T	0.62932	-0.6749	10	0.51188	T	0.08	-7.1554	9.161	0.37023	0.8374:0.0:0.0:0.1626	.	364	Q96KS0	EGLN2_HUMAN	C	364	ENSP00000307080:Y364C;ENSP00000385253:Y364C	ENSP00000307080:Y364C	Y	+	2	0	EGLN2	46005010	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.890000	0.48609	2.072000	0.62099	0.533000	0.62120	TAT	.	.		0.597	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1			G	41313170	A	G	41313170	3	3	79	1	0	0	0	0	1	0	0	0	4971	449	16	2	1101	2	EGLN2	19	41313170	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	1982258	41313170	17815813	185	10939										
LIPE	3991	hgsc.bcm.edu	37	chr19	42909571	42909571	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gacatcttctgggacttgcgCccacttaactccaggaagga	10	12	2	0	rs148306456	byFrequency	TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:42909571C>T	ENST00000244289.4	-	8	2784	c.2508G>A	c.(2506-2508)ggG>ggA	p.G836G	LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE_ENST00000602000.1_5'Flank|LIPE-AS1_ENST00000593491.2_RNA|LIPE-AS1_ENST00000597203.1_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	836					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				GGGACTTGCGCCCACTTAACT	0.622																																					p.G836G		Atlas-SNP	.											.	LIPE	83	.	0			c.G2508A						.						56	48	50					19																	42909571		2203	4300	6503	SO:0001819	synonymous_variant	3991	exon8			CTTGCGCCCACTT	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2508G>A	chr19.hg19:g.42909571C>T		89.0	0.0		84.0	13.0	NM_005357	Q3LRT2|Q6NSL7	Silent	SNP	ENST00000244289.4	hg19	CCDS12607.1																																																																																			.	C|1.000;A|0.000		0.622	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		T	42909571	C	T	42909571	2	4	79	1	0	0	0	0	0	0	0	1	8830	726	26	3		3	LIPE	19	42909571	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	1596401	42909571	16219412	186	10940										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51175305	51175305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttgccggagcatcaacccagGtcctggaggcaggaaagaag	14	10	1	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:51175305G>A	ENST00000293441.1	-	21	2662	c.2644C>T	c.(2644-2646)Cct>Tct	p.P882S	SHANK1_ENST00000391814.1_Missense_Mutation_p.P890S|SHANK1_ENST00000359082.3_Missense_Mutation_p.P873S|SHANK1_ENST00000391813.1_Missense_Mutation_p.P269S	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	882					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)	p.P882S(1)		breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		ATCAACCCAGGTCCTGGAGGC	0.577																																					p.P882S		Atlas-SNP	.											SHANK1,rectum,carcinoma,0,1	SHANK1	210	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2644T						.						107	91	97					19																	51175305		2203	4300	6503	SO:0001583	missense	50944	exon21			ACCCAGGTCCTGG	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.2644C>T	chr19.hg19:g.51175305G>A	ENSP00000293441:p.Pro882Ser	86.0	1.0		98.0	23.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	hg19	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.181707	0.57800	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	T;T;T;T	0.38722	1.24;1.64;1.22;1.12	3.87	3.87	0.44632	.	1.972760	0.04376	N	0.359926	T	0.43322	0.1242	L	0.47190	1.495	0.39149	D	0.962181	P;P	0.47253	0.507;0.892	B;B	0.44224	0.116;0.444	T	0.48833	-0.9000	10	0.08381	T	0.77	-2.5979	15.1098	0.72346	0.0:0.0:1.0:0.0	.	882;269	Q9Y566;Q9Y566-2	SHAN1_HUMAN;.	S	882;269;873;890	ENSP00000293441:P882S;ENSP00000375689:P269S;ENSP00000351984:P873S;ENSP00000375690:P890S	ENSP00000293441:P882S	P	-	1	0	SHANK1	55867117	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.752000	0.55172	2.161000	0.67846	0.491000	0.48974	CCT	.	.		0.577	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		A	51175305	G	A	51175305	3	1	79	1	0	0	0	0	1	0	0	0	14279	1261	44	3	3853	3	SHANK1	19	51175305	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	8265734	51175305	7953678	187	10941										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54313287	54313287	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcgtactcggtcaacagcctGgtcacgtcctggtctgggcc	13	14	3	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr19:54313287G>A	ENST00000324134.6	-	3	1794	c.1626C>T	c.(1624-1626)acC>acT	p.T542T	NLRP12_ENST00000354278.3_Silent_p.T542T|NLRP12_ENST00000391772.1_Silent_p.T542T|NLRP12_ENST00000345770.5_Silent_p.T542T|NLRP12_ENST00000535162.1_Silent_p.T542T|NLRP12_ENST00000351894.4_Silent_p.T542T|NLRP12_ENST00000391773.1_Silent_p.T542T|NLRP12_ENST00000391775.3_Silent_p.T542T	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	542					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		TCAACAGCCTGGTCACGTCCT	0.567																																					p.L542F		Atlas-SNP	.											.	NLRP12	236	.	0			c.G1626T						.						100	95	97					19																	54313287		2203	4300	6503	SO:0001819	synonymous_variant	91662	exon3			CAGCCTGGTCACG	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.1626C>T	chr19.hg19:g.54313287G>A		67.0	0.0		69.0	14.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	hg19	CCDS12864.1																																																																																			.	.		0.567	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		A	54313287	G	A	54313287	2	1	79	1	0	0	0	0	0	0	0	1	10483	1335	47	3		3	NLRP12	19	54313287	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	3137982	54313287	4815696	188	10942										
STK35	140901	hgsc.bcm.edu	37	chr20	2083558	2083558	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcgcccgcagaggtacacaaAgcccggagcggaaaaggcga	15	12	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr20:2083558A>C	ENST00000381482.3	+	2	710	c.439A>C	c.(439-441)Agc>Cgc	p.S147R	STK35_ENST00000400064.3_5'UTR|STK35_ENST00000246032.3_Missense_Mutation_p.S14R			Q8TDR2	STK35_HUMAN	serine/threonine kinase 35	147	Ala-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(2)|liver(2)|lung(6)|ovary(1)|prostate(2)	13						AGGTACACAAAGCCCGGAGCG	0.761																																					p.S147R		Atlas-SNP	.											.	STK35	31	.	0			c.A439C						.						4	5	5					20																	2083558		1805	3759	5564	SO:0001583	missense	140901	exon2			ACACAAAGCCCGG	AL359916	CCDS13024.1, CCDS13024.2	20p13	2008-07-02			ENSG00000125834	ENSG00000125834			16254	protein-coding gene	gene with protein product	"CLP-36 interacting kinase"	609370				11973348	Standard	NM_080836		Approved	bA550O8.2, CLIK1	uc002wfw.4	Q8TDR2	OTTHUMG00000031688	ENST00000381482.3:c.439A>C	chr20.hg19:g.2083558A>C	ENSP00000370891:p.Ser147Arg	11.0	0.0		13.0	7.0	NM_080836	B2RBM3|C7ENV8|Q2NKW6|Q5T3R1|Q5T3R2|Q96AB4|Q9BZ06	Missense_Mutation	SNP	ENST00000381482.3	hg19	CCDS13024.2	.	.	.	.	.	.	.	.	.	.	A	18.03	3.532569	0.64972	.	.	ENSG00000125834	ENST00000381482;ENST00000246032	T;T	0.70399	-0.25;-0.48	5.07	3.97	0.46021	.	0.213391	0.38381	N	0.001701	T	0.45458	0.1343	N	0.08118	0	0.80722	D	1	B	0.14438	0.01	B	0.10450	0.005	T	0.37033	-0.9723	10	0.25106	T	0.35	-3.087	6.9699	0.24642	0.8986:0.0:0.1014:0.0	.	147	Q8TDR2	STK35_HUMAN	R	147;14	ENSP00000370891:S147R;ENSP00000246032:S14R	ENSP00000246032:S14R	S	+	1	0	STK35	2031558	0.988000	0.35896	1.000000	0.80357	0.996000	0.88848	0.906000	0.28517	2.047000	0.60756	0.533000	0.62120	AGC	.	.		0.761	STK35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077574.3	NM_080836		C	2083558	A	C	2083558	3	2	79	1	0	0	0	0	1	0	0	0	15316	72	3	5	445	5	STK35	20	2083558	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10		2083558	60941962	189	10943										
CHD6	84181	hgsc.bcm.edu	37	chr20	40050513	40050513	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gttcagcccatgtttggcagTgccgatgagcaggtctcgat	13	10	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr20:40050513T>C	ENST00000373233.3	-	31	4939	c.4762A>G	c.(4762-4764)Act>Gct	p.T1588A		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1588					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				TGTTTGGCAGTGCCGATGAGC	0.562																																					p.T1588A		Atlas-SNP	.											.	CHD6	312	.	0			c.A4762G						.						111	76	88					20																	40050513		2203	4300	6503	SO:0001583	missense	84181	exon31			TGGCAGTGCCGAT	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.4762A>G	chr20.hg19:g.40050513T>C	ENSP00000362330:p.Thr1588Ala	95.0	0.0		84.0	23.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	T	5.145	0.212360	0.09757	.	.	ENSG00000124177	ENST00000373233	D	0.83591	-1.74	5.89	5.89	0.94794	.	0.090574	0.48767	D	0.000174	T	0.68339	0.2990	N	0.13168	0.305	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.64668	-0.6353	10	0.02654	T	1	-13.5213	16.3499	0.83199	0.0:0.0:0.0:1.0	.	1588	Q8TD26	CHD6_HUMAN	A	1588	ENSP00000362330:T1588A	ENSP00000362330:T1588A	T	-	1	0	CHD6	39483927	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	4.695000	0.61767	2.270000	0.75569	0.529000	0.55759	ACT	.	.		0.562	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			C	40050513	T	C	40050513	3	2	79	1	0	0	0	0	1	0	0	0	3331	1696	59	2	3413	2	CHD6	20	40050513	Missense_Mutation	SNP	T	TCGA-CC-A8HT-01A-11D-A35Z-10	37966955	40050513	22975007	190	10944										
SFRS6	6431	hgsc.bcm.edu	37	chr20	42088512	42088512	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ttgtagaaaatctttctagtCggtgcagttggcaagattta	10	5	2	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr20:42088512C>T	ENST00000244020.3	+	3	464	c.358C>T	c.(358-360)Cgg>Tgg	p.R120W		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	120	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						TCTTTCTAGTCGGTGCAGTTG	0.378																																					p.R120W		Atlas-SNP	.											.	SRSF6	37	.	0			c.C358T						.						132	124	127					20																	42088512		2203	4300	6503	SO:0001583	missense	6431	exon3			TCTAGTCGGTGCA	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10788	protein-coding gene	gene with protein product	"pre-mRNA splicing factor SRP55", "SR splicing factor 6"	601944	"splicing factor, arginine/serine-rich 6"	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.358C>T	chr20.hg19:g.42088512C>T	ENSP00000244020:p.Arg120Trp	135.0	0.0		94.0	26.0	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Missense_Mutation	SNP	ENST00000244020.3	hg19	CCDS13318.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.980437	0.53827	.	.	ENSG00000124193	ENST00000244020	T	0.16324	2.35	5.86	5.86	0.93980	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.046784	0.85682	D	0.000000	T	0.59432	0.2193	H	0.98276	4.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.74328	-0.3701	10	0.87932	D	0	.	13.871	0.63619	0.1528:0.8472:0.0:0.0	.	120;120	Q13247;A8K588	SRSF6_HUMAN;.	W	120	ENSP00000244020:R120W	ENSP00000244020:R120W	R	+	1	2	SRSF6	41521926	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	5.539000	0.67199	2.777000	0.95525	0.591000	0.81541	CGG	.	.		0.378	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275		T	42088512	C	T	42088512	3	4	79	1	0	0	0	0	1	0	0	0	14196	875	31	1	368	1	SFRS6	20	42088512	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	2037999	42088512	20937008	191	10945										
WISP2	8839	hgsc.bcm.edu	37	chr20	43355822	43355822	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ccctgctcgaccacctgtggGctgggcatggccacccgggt	14	16	0	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr20:43355822G>A	ENST00000372868.2	+	5	970	c.627G>A	c.(625-627)ggG>ggA	p.G209G	RP11-445H22.4_ENST00000427598.1_RNA|WISP2_ENST00000190983.4_Silent_p.G209G|WISP2_ENST00000372865.4_Missense_Mutation_p.G127D|RP11-445H22.4_ENST00000427303.1_RNA|WISP2_ENST00000471629.1_3'UTR|RP11-445H22.4_ENST00000445420.1_RNA			O76076	WISP2_HUMAN	WNT1 inducible signaling pathway protein 2	209	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				skin(1)	1		Myeloproliferative disorder(115;0.0122)				CCACCTGTGGGCTGGGCATGG	0.687																																					p.G209G		Atlas-SNP	.											.	WISP2	28	.	0			c.G627A						.						50	50	50					20																	43355822		2202	4298	6500	SO:0001819	synonymous_variant	8839	exon4			CTGTGGGCTGGGC	AF100780	CCDS13336.1	20q13.12	2007-05-14			ENSG00000064205	ENSG00000064205			12770	protein-coding gene	gene with protein product		603399				9843955	Standard	NM_003881		Approved	CT58, CTGF-L, CCN5	uc002xmp.3	O76076	OTTHUMG00000033071	ENST00000372868.2:c.627G>A	chr20.hg19:g.43355822G>A		81.0	0.0		60.0	14.0	NM_003881	B2R9N4|E1P612|Q6PEG3	Silent	SNP	ENST00000372868.2	hg19	CCDS13336.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.217237	0.39201	.	.	ENSG00000064205	ENST00000372865	T	0.70164	-0.46	4.05	2.04	0.26737	.	0.000000	0.85682	D	0.000000	T	0.78342	0.4268	.	.	.	0.80722	D	1	D	0.63880	0.993	P	0.58721	0.844	T	0.82096	-0.0626	9	0.87932	D	0	-22.4119	15.8618	0.79032	0.0:0.4864:0.5135:0.0	.	127	Q6PEG3	.	D	127	ENSP00000361956:G127D	ENSP00000361956:G127D	G	+	2	0	WISP2	42789236	0.165000	0.22948	0.999000	0.59377	0.645000	0.38454	0.615000	0.24329	0.354000	0.24105	0.561000	0.74099	GGC	.	.		0.687	WISP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127824.1	NM_003881		A	43355822	G	A	43355822	2	1	79	1	0	0	0	0	0	0	0	1	17388	1190	42	3		3	WISP2	20	43355822	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	1267310	43355822	19669698	192	10946										
SAMSN1	64092	hgsc.bcm.edu	37	chr21	15858279	15858279	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tcttatgtaccatgtcagacAgattttcagactccagatcc	6	11	3	4			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr21:15858279A>C	ENST00000400566.1	-	8	1157	c.1076T>G	c.(1075-1077)cTg>cGg	p.L359R	SAMSN1_ENST00000285670.2_Missense_Mutation_p.L427R|SAMSN1_ENST00000400564.1_Missense_Mutation_p.L191R	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	359					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		CATGTCAGACAGATTTTCAGA	0.383																																					p.L427R		Atlas-SNP	.											.	SAMSN1	112	.	0			c.T1280G						.						171	156	161					21																	15858279		1866	4116	5982	SO:0001583	missense	64092	exon9			TCAGACAGATTTT	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.1076T>G	chr21.hg19:g.15858279A>C	ENSP00000383411:p.Leu359Arg	84.0	0.0		67.0	14.0	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	hg19	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	A	16.38	3.107243	0.56291	.	.	ENSG00000155307	ENST00000285670;ENST00000400566;ENST00000400564	T;T	0.55588	0.51;0.63	6.08	6.08	0.98989	.	0.232716	0.36519	N	0.002542	T	0.73202	0.3557	M	0.75447	2.3	0.46298	D	0.998978	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.91635	0.974;0.999;0.942	T	0.75031	-0.3461	10	0.56958	D	0.05	-8.2454	16.6512	0.85203	1.0:0.0:0.0:0.0	.	191;427;359	Q9NSI8-2;F8WAA1;Q9NSI8	.;.;SAMN1_HUMAN	R	427;359;191	ENSP00000285670:L427R;ENSP00000383411:L359R	ENSP00000285670:L427R	L	-	2	0	SAMSN1	14780150	1.000000	0.71417	0.999000	0.59377	0.170000	0.22686	4.794000	0.62482	2.333000	0.79357	0.482000	0.46254	CTG	.	.		0.383	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			C	15858279	A	C	15858279	3	2	79	1	0	0	0	0	1	0	0	0	13845	188	7	5	49	5	SAMSN1	21	15858279	Missense_Mutation	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10		15858279	32271616	193	10947										
C21orf59	56683	hgsc.bcm.edu	37	chr21	33984425	33984425	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cgagccgcacctgagcagagGcgctgcaccttgagccgccc	13	17	0	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr21:33984425G>A	ENST00000290155.3	-	1	751	c.129C>T	c.(127-129)cgC>cgT	p.R43R	C21orf59_ENST00000540881.1_Silent_p.R43R|C21orf59_ENST00000382549.4_Silent_p.R43R|AP000275.65_ENST00000553001.1_Silent_p.R43R	NM_021254.2	NP_067077.1	P57076	CU059_HUMAN	chromosome 21 open reading frame 59	43						cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|prostate(1)|skin(1)	5						CTGAGCAGAGGCGCTGCACCT	0.677																																					p.R43R		Atlas-SNP	.											.	C21orf59	11	.	0			c.C129T						.						11	11	11					21																	33984425		2158	4242	6400	SO:0001819	synonymous_variant	56683	exon1			GCAGAGGCGCTGC	AF282851	CCDS13617.1	21q22.11	2014-02-03	2003-07-22		ENSG00000159079	ENSG00000159079			1301	protein-coding gene	gene with protein product		615494	"chromosome 21 open reading frame 48"	C21orf48		24094744	Standard	NM_021254		Approved	FLJ20467, FBB18, CILD26	uc002yqc.3	P57076	OTTHUMG00000179510	ENST00000290155.3:c.129C>T	chr21.hg19:g.33984425G>A		86.0	0.0		82.0	21.0	NM_021254	Q53FH0	Silent	SNP	ENST00000290155.3	hg19	CCDS13617.1	.	.	.	.	.	.	.	.	.	.	G	10.28	1.306556	0.23736	.	.	ENSG00000159079	ENST00000431216	.	.	.	4.85	2.96	0.34315	.	.	.	.	.	T	0.61813	0.2377	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57458	-0.7808	4	.	.	.	-27.2964	11.4906	0.50379	0.0755:0.5252:0.3993:0.0	.	.	.	.	V	11	.	.	A	-	2	0	C21orf59	32906296	0.010000	0.17322	0.991000	0.47740	0.852000	0.48524	-0.141000	0.10327	0.559000	0.29153	0.455000	0.32223	GCC	.	.		0.677	C21orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139431.1	NM_021254		A	33984425	G	A	33984425	2	1	79	1	0	0	0	0	0	0	0	1	2132	1190	42	3		3	C21orf59	21	33984425	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	18126146	33984425	14145470	194	10948										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37603416	37603416	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	accgagcagctctgtgcaacGctcttccagctgccaggtga	11	14	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr21:37603416G>A	ENST00000399151.3	+	14	2419	c.2334G>A	c.(2332-2334)acG>acA	p.T778T		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	778					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TCTGTGCAACGCTCTTCCAGC	0.587																																					p.T778T		Atlas-SNP	.											.	DOPEY2	184	.	0			c.G2334A						.						44	41	42					21																	37603416		2183	4275	6458	SO:0001819	synonymous_variant	9980	exon14			TGCAACGCTCTTC	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.2334G>A	chr21.hg19:g.37603416G>A		106.0	0.0		108.0	22.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	hg19	CCDS13643.1																																																																																			.	.		0.587	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		A	37603416	G	A	37603416	2	1	79	1	0	0	0	0	0	0	0	1	4710	1074	38	1		1	DOPEY2	21	37603416	Silent	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	3618991	37603416	10526479	195	10949										
KRTAP10-12	386685	hgsc.bcm.edu	37	chr21	46117302	46117302	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	agccgtgtatccagcccctgCtgccgagtgacctgtgagcc	12	15	0	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr21:46117302C>A	ENST00000400365.3	+	1	216	c.186C>A	c.(184-186)tgC>tgA	p.C62*	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	62	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						CCAGCCCCTGCTGCCGAGTGA	0.692																																					p.C62X		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.C186A						.						66	77	73					21																	46117302		2197	4295	6492	SO:0001587	stop_gained	386685	exon1			CCCCTGCTGCCGA	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"Keratin associated proteins"	20533	protein-coding gene	gene with protein product			"keratin associated protein 18-12"	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.186C>A	chr21.hg19:g.46117302C>A	ENSP00000383216:p.Cys62*	44.0	0.0		64.0	13.0	NM_198699	B2RPA3	Nonsense_Mutation	SNP	ENST00000400365.3	hg19	CCDS42967.1	.	.	.	.	.	.	.	.	.	.	N	11.13	1.548431	0.27652	.	.	ENSG00000189169	ENST00000400365	.	.	.	1.57	0.462	0.16695	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.8249	0.18548	0.0:0.6664:0.3336:0.0	.	.	.	.	X	62	.	ENSP00000383216:C62X	C	+	3	2	KRTAP10-12	44941730	0.002000	0.14202	0.354000	0.25760	0.198000	0.23893	1.114000	0.31196	-0.484000	0.06763	0.298000	0.19748	TGC	.	.		0.692	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		A	46117302	C	A	46117302	4	1	79	1	0	0	0	0	0	1	0	0	8517	805	28	3	188	3	KRTAP10-12	21	46117302	Nonsense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	8513886	46117302	2012593	196	10950										
MAPK1	5594	hgsc.bcm.edu	37	chr22	22221631	22221631	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ccacaccatgccgtaggcgcCctcgccgatgtacgagaggt	12	15	0	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr22:22221631C>A	ENST00000215832.6	-	1	288	c.100G>T	c.(100-102)Ggc>Tgc	p.G34C	MAPK1_ENST00000398822.3_Missense_Mutation_p.G34C|MAPK1_ENST00000544786.1_Missense_Mutation_p.G34C	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	34	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	CCGTAGGCGCCCTCGCCGATG	0.786																																					p.G34C		Atlas-SNP	.											.	MAPK1	38	.	0			c.G100T						.						10	8	9					22																	22221631		2015	4006	6021	SO:0001583	missense	5594	exon1			AGGCGCCCTCGCC	M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1			Standard	NM_138957		Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.100G>T	chr22.hg19:g.22221631C>A	ENSP00000215832:p.Gly34Cys	72.0	0.0		42.0	10.0	NM_002745	A8CZ64	Missense_Mutation	SNP	ENST00000215832.6	hg19	CCDS13795.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520411	0.85495	.	.	ENSG00000100030	ENST00000215832;ENST00000415911;ENST00000398822;ENST00000544786	D;D;D	0.96365	-3.99;-3.99;-3.99	4.71	3.67	0.42095	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98966	0.9648	H	0.99379	4.54	0.80722	D	1	D;D	0.65815	0.995;0.991	D;D	0.72982	0.979;0.978	D	0.98797	1.0738	10	0.87932	D	0	.	13.9758	0.64273	0.0:0.8469:0.1531:0.0	.	34;34	A8CZ64;P28482	.;MK01_HUMAN	C	34;22;34;34	ENSP00000215832:G34C;ENSP00000381803:G34C;ENSP00000440842:G34C	ENSP00000215832:G34C	G	-	1	0	MAPK1	20551631	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	4.140000	0.58031	1.173000	0.42796	0.467000	0.42956	GGC	.	.		0.786	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075396.2			A	22221631	C	A	22221631	3	1	79	1	0	0	0	0	1	0	0	0	9280	623	22	3	1014	3	MAPK1	22	22221631	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10		22221631	29082935	197	10951										
MCHR1	2847	hgsc.bcm.edu	37	chr22	41077826	41077826	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cgtgctctgtgagacgttccGcaaacgcttggtcctgtcgg	13	12	1	1	rs199697488		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr22:41077826G>A	ENST00000249016.4	+	2	1859	c.1163G>A	c.(1162-1164)cGc>cAc	p.R388H	MCHR1_ENST00000381433.2_Missense_Mutation_p.R262H|MCHR1_ENST00000498400.1_3'UTR	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	388					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|melanin-concentrating hormone receptor activity (GO:0030273)|neuropeptide receptor activity (GO:0008188)			endometrium(5)|large_intestine(7)|lung(6)|pancreas(1)|urinary_tract(1)	20						GAGACGTTCCGCAAACGCTTG	0.572																																					p.R388H		Atlas-SNP	.											MCHR1,caecum,carcinoma,0,3	MCHR1	45	.	0			c.G1163A						.						111	90	97					22																	41077826		2203	4300	6503	SO:0001583	missense	2847	exon2			CGTTCCGCAAACG		CCDS14004.1	22q13.3	2014-06-05	2006-02-15	2006-02-15	ENSG00000128285	ENSG00000128285		"GPCR / Class A : MCH receptors"	4479	protein-coding gene	gene with protein product		601751	"G protein-coupled receptor 24"	GPR24			Standard	XM_005261581		Approved	SLC1, MCH1R	uc003ayz.3	Q99705	OTTHUMG00000150256	ENST00000249016.4:c.1163G>A	chr22.hg19:g.41077826G>A	ENSP00000249016:p.Arg388His	51.0	0.0		53.0	16.0	NM_005297	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Missense_Mutation	SNP	ENST00000249016.4	hg19	CCDS14004.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.209252	0.79240	.	.	ENSG00000128285	ENST00000249016;ENST00000381433	T;T	0.58358	0.34;0.34	5.4	5.4	0.78164	.	0.101947	0.64402	D	0.000008	T	0.57286	0.2043	N	0.19112	0.55	0.41286	D	0.986946	D	0.76494	0.999	P	0.62184	0.899	T	0.62955	-0.6744	10	0.87932	D	0	.	17.0403	0.86487	0.0:0.0:1.0:0.0	.	388	Q99705	MCHR1_HUMAN	H	388;262	ENSP00000249016:R388H;ENSP00000370841:R262H	ENSP00000249016:R388H	R	+	2	0	MCHR1	39407772	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.226000	0.58606	2.698000	0.92095	0.655000	0.94253	CGC	.	.		0.572	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297		A	41077826	G	A	41077826	3	1	79	1	0	0	0	0	1	0	0	0	9391	1087	38	1	1169	1	MCHR1	22	41077826	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	18856195	41077826	10226740	198	10952										
EFCAB6	64800	hgsc.bcm.edu	37	chr22	43986003	43986003	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ggtaagagaacatccacattCttccagcacttcctgcatct	6	13	2	1			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr22:43986003C>G	ENST00000262726.7	-	24	3236	c.2983G>C	c.(2983-2985)Gaa>Caa	p.E995Q	EFCAB6_ENST00000396231.2_Missense_Mutation_p.E843Q	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	995	EF-hand 11. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				CATCCACATTCTTCCAGCACT	0.423																																					p.E995Q		Atlas-SNP	.											.	EFCAB6	177	.	0			c.G2983C						.						299	258	272					22																	43986003		2203	4300	6503	SO:0001583	missense	64800	exon24			CACATTCTTCCAG	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.2983G>C	chr22.hg19:g.43986003C>G	ENSP00000262726:p.Glu995Gln	142.0	0.0		130.0	33.0	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	hg19	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.684606	0.47991	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	D;D	0.82344	-1.6;-1.6	4.87	3.85	0.44370	EF-hand-like domain (1);	0.651897	0.14965	N	0.288132	D	0.87904	0.6295	M	0.66939	2.045	0.33808	D	0.627484	D;P	0.89917	1.0;0.454	D;B	0.74023	0.982;0.282	D	0.86390	0.1735	10	0.15499	T	0.54	-14.2413	11.4244	0.50001	0.0:0.9163:0.0:0.0837	.	843;995	Q5THR3-2;Q5THR3	.;EFCB6_HUMAN	Q	843;995	ENSP00000379533:E843Q;ENSP00000262726:E995Q	ENSP00000262726:E995Q	E	-	1	0	EFCAB6	42317336	0.038000	0.19896	0.006000	0.13384	0.234000	0.25298	1.499000	0.35671	1.199000	0.43173	0.555000	0.69702	GAA	.	.		0.423	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		G	43986003	C	G	43986003	3	3	79	1	0	0	0	0	1	0	0	0	4941	922	32	4	1558	4	EFCAB6	22	43986003	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	2908177	43986003	7318563	199	10953										
EFCAB6	64800	hgsc.bcm.edu	37	chr22	44168801	44168801	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	cacgtcctgaaactgttctcGtgtgagcggcatcaggaagt	12	10	2	2	rs372200947		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr22:44168801G>A	ENST00000262726.7	-	4	575	c.322C>T	c.(322-324)Cga>Tga	p.R108*	EFCAB6_ENST00000356087.4_Intron|EFCAB6_ENST00000396231.2_Intron|EFCAB6_ENST00000358439.4_Intron	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	108					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				AACTGTTCTCGTGTGAGCGGC	0.463													G|||	1	0.000199681	0	0.0014	5008	,	,		18475	0		0	False		,,,				2504	0				p.R108X		Atlas-SNP	.											.	EFCAB6	177	.	0			c.C322T						.	G	stop/ARG,	0,4406		0,0,2203	179	137	151		322,	-1.1	0	22		151	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,intron	EFCAB6	NM_022785.3,NM_198856.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	108/1502,	44168801	1,13005	2203	4300	6503	SO:0001587	stop_gained	64800	exon4			GTTCTCGTGTGAG	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.322C>T	chr22.hg19:g.44168801G>A	ENSP00000262726:p.Arg108*	121.0	0.0		88.0	27.0	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Nonsense_Mutation	SNP	ENST00000262726.7	hg19	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.050463	0.75960	0.0	1.16E-4	ENSG00000186976	ENST00000262726	.	.	.	4.28	-1.1	0.09872	.	0.520250	0.17345	N	0.177606	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-13.8913	11.8982	0.52667	0.0:0.0:0.6984:0.3016	.	.	.	.	X	108	.	ENSP00000262726:R108X	R	-	1	2	EFCAB6	42500134	0.000000	0.05858	0.001000	0.08648	0.474000	0.32979	0.115000	0.15540	-0.042000	0.13535	-0.457000	0.05445	CGA	.	.		0.463	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		A	44168801	G	A	44168801	4	1	79	1	0	0	0	0	0	1	0	0	4941	1153	40	1	4299	1	EFCAB6	22	44168801	Nonsense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	182798	44168801	7135765	200	10954										
LDOC1L	84247	hgsc.bcm.edu	37	chr22	44893314	44893314	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gcccgcagggtggaagcctcCcgcctcagcgccgagttggt	15	15	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr22:44893314C>A	ENST00000341255.3	-	2	632	c.123G>T	c.(121-123)cgG>cgT	p.R41R		NM_032287.2	NP_115663.2	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	41										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(3)|prostate(2)	11		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)		TGGAAGCCTCCCGCCTCAGCG	0.627																																					p.R41R		Atlas-SNP	.											.	LDOC1L	24	.	0			c.G123T						.						37	32	34					22																	44893314		2202	4300	6502	SO:0001819	synonymous_variant	84247	exon2			AGCCTCCCGCCTC	CR456439	CCDS33662.1	22q13.3	2006-09-06			ENSG00000188636	ENSG00000188636			13343	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_032287		Approved	dJ1033E15.2, DKFZp761O17121, Mart6, Mar6	uc003beu.1	Q6ICC9	OTTHUMG00000150465	ENST00000341255.3:c.123G>T	chr22.hg19:g.44893314C>A		70.0	0.0		72.0	11.0	NM_032287	Q6ZTR1	Silent	SNP	ENST00000341255.3	hg19	CCDS33662.1																																																																																			.	.		0.627	LDOC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318222.1	NM_032287		A	44893314	C	A	44893314	2	1	79	1	0	0	0	0	0	0	0	1	8719	610	22	3		3	LDOC1L	22	44893314	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	724513	44893314	6411252	201	10955										
ARSA	410	hgsc.bcm.edu	37	chr22	51065813	51065813	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	atgcccatccgaaccgggagCcggccggtcaggagggcggc	17	14	1	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chr22:51065813C>T	ENST00000547307.1	-	2	645	c.240G>A	c.(238-240)cgG>cgA	p.R80R	ARSA_ENST00000356098.5_Silent_p.R82R|ARSA_ENST00000547805.1_Silent_p.R80R|ARSA_ENST00000395621.3_Silent_p.R82R|ARSA_ENST00000395619.3_Silent_p.R82R|ARSA_ENST00000453344.2_5'UTR|ARSA_ENST00000216124.5_Silent_p.R82R			P15289	ARSA_HUMAN	arylsulfatase A	80					autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)			endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)|Suramin(DB04786)	GAACCGGGAGCCGGCCGGTCA	0.672																																					p.R82R		Atlas-SNP	.											.	ARSA	19	.	0			c.G246A						.						8	9	9					22																	51065813		2159	4231	6390	SO:0001819	synonymous_variant	410	exon3			CGGGAGCCGGCCG	X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"Arylsulfatase family"	713	protein-coding gene	gene with protein product	"metachromatic leucodystrophy"	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.240G>A	chr22.hg19:g.51065813C>T		79.0	0.0		87.0	19.0	NM_001085426	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Silent	SNP	ENST00000547307.1	hg19																																																																																				.	.		0.672	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487		T	51065813	C	T	51065813	2	4	79	1	0	0	0	0	0	0	0	1	987	726	26	3		3	ARSA	22	51065813	Silent	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	6172499	51065813	238753	202	10956										
ZRSR2	8233	hgsc.bcm.edu	37	chrX	15809111	15809111	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	aaacgaaagaaacgtcggcaGgaacttgctcgactgagaga	12	8	0	3			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chrX:15809111G>T	ENST00000307771.7	+	2	120	c.96G>T	c.(94-96)caG>caT	p.Q32H	ZRSR2_ENST00000468028.1_3'UTR|ZRSR2_ENST00000380308.3_Missense_Mutation_p.Q32H	NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	32					mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					AACGTCGGCAGGAACTTGCTC	0.483			"F, S, Mis"		"MDS, CLL"																																p.Q32H	NSCLC(197;1631 3042 5741 31152)	Atlas-SNP	.		Rec	yes		X	Xp22.1	8233	"zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"		L	.	ZRSR2	78	.	0			c.G96T						.						87	77	80					X																	15809111		2203	4300	6503	SO:0001583	missense	8233	exon2			TCGGCAGGAACTT	BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	23019	protein-coding gene	gene with protein product		300028	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 2", "U2 small nuclear RNA auxiliary factor 1-like 2"	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.96G>T	chrX.hg19:g.15809111G>T	ENSP00000303015:p.Gln32His	226.0	0.0		214.0	104.0	NM_005089	Q14D69	Missense_Mutation	SNP	ENST00000307771.7	hg19	CCDS14172.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.711698	0.48517	.	.	ENSG00000169249	ENST00000307771;ENST00000380308	D;T	0.85629	-2.01;4.96	5.02	4.15	0.48705	.	0.000000	0.85682	D	0.000000	D	0.91758	0.7393	M	0.86953	2.85	0.52099	D	0.99994	D	0.61697	0.99	D	0.70487	0.969	D	0.91573	0.5273	10	0.87932	D	0	.	8.8273	0.35063	0.1075:0.0:0.8925:0.0	.	32	Q15696	U2AFM_HUMAN	H	32	ENSP00000303015:Q32H;ENSP00000369664:Q32H	ENSP00000303015:Q32H	Q	+	3	2	ZRSR2	15719032	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.623000	0.37008	1.037000	0.40024	0.429000	0.28392	CAG	.	.		0.483	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089		T	15809111	G	T	15809111	3	4	79	1	0	0	0	0	1	0	0	0	18240	991	35	3	102	3	ZRSR2	23	15809111	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10		15809111	139461449	203	10957										
CTPS2	56474	hgsc.bcm.edu	37	chrX	16707658	16707658	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	tctctccttaaaatatttcaCaatgctttgttcctctaaaa	2	10	3	0			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chrX:16707658C>A	ENST00000443824.1	-	8	1530	c.787G>T	c.(787-789)Gtg>Ttg	p.V263L	CTPS2_ENST00000359276.4_Missense_Mutation_p.V263L|CTPS2_ENST00000380241.3_Missense_Mutation_p.V263L	NM_001144002.1	NP_001137474.1	Q9NRF8	PYRG2_HUMAN	CTP synthase 2	263					'de novo' CTP biosynthetic process (GO:0044210)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP synthase activity (GO:0003883)			breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Hepatocellular(33;0.0997)					AAATATTTCACAATGCTTTGT	0.398																																					p.V263L		Atlas-SNP	.											.	CTPS2	49	.	0			c.G787T						.						129	116	120					X																	16707658		2203	4300	6503	SO:0001583	missense	56474	exon8			ATTTCACAATGCT	AF086422	CCDS14175.1	Xp22	2012-05-02	2012-05-02		ENSG00000047230	ENSG00000047230	6.3.4.2		2520	protein-coding gene	gene with protein product		300380	"CTP synthase II"			10899599	Standard	NM_001144002		Approved		uc004cxm.3	Q9NRF8	OTTHUMG00000021193	ENST00000443824.1:c.787G>T	chrX.hg19:g.16707658C>A	ENSP00000401264:p.Val263Leu	283.0	0.0		247.0	123.0	NM_001144002	B3KWM2|Q9BRI0|Q9H809|Q9H8K9	Missense_Mutation	SNP	ENST00000443824.1	hg19	CCDS14175.1	.	.	.	.	.	.	.	.	.	.	c	0.044	-1.272067	0.01421	.	.	ENSG00000047230	ENST00000443824;ENST00000380241;ENST00000359276	T;T;T	0.40225	1.04;1.04;1.04	5.83	2.81	0.32909	CTP synthase, N-terminal (1);	0.326238	0.25951	N	0.027252	T	0.24967	0.0606	L	0.28344	0.845	0.09310	N	0.999999	B	0.10296	0.003	B	0.17979	0.02	T	0.27434	-1.0074	10	0.10636	T	0.68	-15.2566	8.0937	0.30816	0.0:0.4482:0.0:0.5518	.	263	Q9NRF8	PYRG2_HUMAN	L	263	ENSP00000401264:V263L;ENSP00000369590:V263L;ENSP00000352222:V263L	ENSP00000352222:V263L	V	-	1	0	CTPS2	16617579	0.778000	0.28640	0.001000	0.08648	0.203000	0.24098	1.484000	0.35508	0.118000	0.18165	0.597000	0.82753	GTG	.	.		0.398	CTPS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055906.1	NM_019857		A	16707658	C	A	16707658	3	1	79	1	0	0	0	0	1	0	0	0	4025	478	17	3	1017	3	CTPS2	23	16707658	Missense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	898547	16707658	138562902	204	10958										
TRO	7216	hgsc.bcm.edu	37	chrX	54949458	54949458	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gccatgagggtggcactataCagctgaagtcacccttgcag	12	11	1	2			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chrX:54949458C>T	ENST00000173898.7	+	3	605	c.493C>T	c.(493-495)Cag>Tag	p.Q165*	TRO_ENST00000375041.2_Intron|TRO_ENST00000319167.8_Nonsense_Mutation_p.Q165*|TRO_ENST00000399736.1_Intron|TRO_ENST00000375022.4_Nonsense_Mutation_p.Q165*|TRO_ENST00000484031.1_Intron|TRO_ENST00000420798.2_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	165					embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						TGGCACTATACAGCTGAAGTC	0.507																																					p.Q165X		Atlas-SNP	.											.	TRO	246	.	0			c.C493T						.						42	41	42					X																	54949458		2066	4204	6270	SO:0001587	stop_gained	7216	exon3			ACTATACAGCTGA	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.493C>T	chrX.hg19:g.54949458C>T	ENSP00000173898:p.Gln165*	136.0	0.0		106.0	58.0	NM_016157	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Nonsense_Mutation	SNP	ENST00000173898.7	hg19	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.300474	0.23650	.	.	ENSG00000067445	ENST00000411534;ENST00000430420;ENST00000442098;ENST00000173898;ENST00000319167;ENST00000375022;ENST00000440759;ENST00000449980;ENST00000416704;ENST00000427099	.	.	.	3.3	1.46	0.22682	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	3.1836	0.06593	0.2613:0.5906:0.0:0.148	.	.	.	.	X	121;121;165;165;165;165;165;121;165;121	.	ENSP00000173898:Q165X	Q	+	1	0	TRO	54966183	0.001000	0.12720	0.006000	0.13384	0.439000	0.31926	-0.026000	0.12392	0.237000	0.21200	0.506000	0.49869	CAG	.	.		0.507	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		T	54949458	C	T	54949458	4	4	79	1	0	0	0	0	0	1	0	0	16589	479	17	3	499	3	TRO	23	54949458	Nonsense_Mutation	SNP	C	TCGA-CC-A8HT-01A-11D-A35Z-10	38241800	54949458	100321102	205	10959										
PFKFB1	5207	hgsc.bcm.edu	37	chrX	54975557	54975558	+	Missense_Mutation	DNP	GC	GC	TA													0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gctcataggggacacccaggGcctcagctgtctggatggtc							TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chrX:54975557_54975558GC>TA	ENST00000375006.3	-	9	1013_1014	c.943_944GC>TA	c.(943-945)GCc>TAc	p.A315Y	PFKFB1_ENST00000374992.2_Intron|PFKFB1_ENST00000545676.1_Missense_Mutation_p.A250Y	NM_002625.2	NP_002616.2	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	315	Fructose-2,6-bisphosphatase.				carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|intracellular signal transduction (GO:0035556)|organ regeneration (GO:0031100)|positive regulation of glucokinase activity (GO:0033133)|response to cAMP (GO:0051591)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex (GO:0043540)|cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|fructose-6-phosphate binding (GO:0070095)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)	24						GACACCCAGGGCCTCAGCTGTC	0.564																																					p.A315D|p.A315S		Atlas-SNP	.											.	PFKFB1	64	.	0			c.C944A|c.G943T						.																																			SO:0001583	missense	5207	exon9			CCCAGGGCCTCAG|CCAGGGCCTCAGC		CCDS14364.1, CCDS65273.1	Xp11.21	2012-07-13			ENSG00000158571	ENSG00000158571	2.7.1.105, 3.1.3.46		8872	protein-coding gene	gene with protein product		311790		PFRX		9119406	Standard	NM_002625		Approved		uc004dty.2	P16118	OTTHUMG00000021643	ENST00000375006.3:c.943_944delinsTA	chrX.hg19:g.54975557_54975558delinsTA	ENSP00000364145:p.Ala315Tyr	118.0|119.0	0.0		114.0|112.0	70.0|69.0	NM_002625	B2RA88|B4DUN5|Q5JXS5|Q99951	Missense_Mutation	SNP	ENST00000375006.3	hg19	CCDS14364.1																																																																																			.	.		0.564	PFKFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056847.1			TA	54975558	GC	TA	54975557	3	4	79	1	0	0	0	0	1	0	0	0	11769	1203	42	3	495	3	PFKFB1	23	54975557	Missense_Mutation	DNP	GC	TCGA-CC-A8HT-01A-11D-A35Z-10	26099	54975557	100295003	206	10960										
NLGN3	54413	hgsc.bcm.edu	37	chrX	70375180	70375180	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	ccagttatggcaatgtcatcGtcatcaccctcaactatcgg	7	13	4	0	rs201424510		TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chrX:70375180G>C	ENST00000358741.3	+	5	997	c.694G>C	c.(694-696)Gtc>Ctc	p.V232L	NLGN3_ENST00000374051.3_Missense_Mutation_p.V212L|NLGN3_ENST00000476589.1_3'UTR|NLGN3_ENST00000536169.1_Missense_Mutation_p.V192L	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	232					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					CAATGTCATCGTCATCACCCT	0.537																																					p.V232L	Esophageal Squamous(103;760 1488 16849 22250 40351)	Atlas-SNP	.											.	NLGN3	159	.	0			c.G694C						.						300	196	231					X																	70375180		2203	4300	6503	SO:0001583	missense	54413	exon5			GTCATCGTCATCA	AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.694G>C	chrX.hg19:g.70375180G>C	ENSP00000351591:p.Val232Leu	72.0	0.0		73.0	31.0	NM_181303	B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Missense_Mutation	SNP	ENST00000358741.3	hg19	CCDS55441.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.613969	0.87359	.	.	ENSG00000196338	ENST00000536169;ENST00000542063;ENST00000374051;ENST00000395855;ENST00000358741	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	4.43	4.43	0.53597	Carboxylesterase, type B (1);	0.000000	0.85682	D	0.000000	T	0.78836	0.4346	L	0.60012	1.86	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;0.997	D;D;D;P	0.91635	0.953;0.999;0.982;0.86	T	0.80094	-0.1526	10	0.49607	T	0.09	.	16.4473	0.83942	0.0:0.0:1.0:0.0	.	192;192;232;212	D3DVV1;B7Z5Y1;Q9NZ94;Q9NZ94-2	.;.;NLGN3_HUMAN;.	L	192;95;212;192;232	ENSP00000445298:V192L;ENSP00000363163:V212L;ENSP00000379196:V192L;ENSP00000351591:V232L	ENSP00000351591:V232L	V	+	1	0	NLGN3	70291905	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.601000	0.98297	2.051000	0.60960	0.540000	0.68198	GTC	.	G|1.000;A|0.000		0.537	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977		C	70375180	G	C	70375180	3	2	79	1	0	0	0	0	1	0	0	0	10472	1145	40	4	708	4	NLGN3	23	70375180	Missense_Mutation	SNP	G	TCGA-CC-A8HT-01A-11D-A35Z-10	15399623	70375180	84895380	207	10961										
COL4A6	1288	hgsc.bcm.edu	37	chrX	107464563	107464563	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0289855072463768	6	1	0.589651304103954	0.497927767910006	0.612206272020499	0.168582375478927	0.751940625889747	0	gtagagccagtgaatccttgAggacctgttgggccttgaat	13	8	0	4			TCGA-CC-A8HT-01A-11D-A35Z-10	TCGA-CC-A8HT-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	278e9596-350e-4dc0-be6a-009ab7846250	c14f9d6e-16bb-499c-b83b-d97d1da50b37	g.chrX:107464563A>G	ENST00000372216.4	-	4	289	c.189T>C	c.(187-189)ccT>ccC	p.P63P	COL4A6_ENST00000334504.7_Silent_p.P62P|COL4A6_ENST00000538570.1_Silent_p.P62P|COL4A6_ENST00000545689.1_Silent_p.P62P|COL4A6_ENST00000394872.2_Silent_p.P62P	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	63	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						TGAATCCTTGAGGACCTGTTG	0.468									Alport syndrome with Diffuse Leiomyomatosis																												p.P63P	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.T189C						.						131	112	119					X																	107464563		2203	4300	6503	SO:0001819	synonymous_variant	1288	exon4	Familial Cancer Database		TCCTTGAGGACCT	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.189T>C	chrX.hg19:g.107464563A>G		102.0	0.0		82.0	46.0	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Silent	SNP	ENST00000372216.4	hg19	CCDS14541.1																																																																																			.	.		0.468	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			G	107464563	A	G	107464563	2	3	79	1	0	0	0	0	0	0	0	1	3697	291	11	2		2	COL4A6	23	107464563	Silent	SNP	A	TCGA-CC-A8HT-01A-11D-A35Z-10	37089383	107464563	47805997	208	10962										
UBR4	23352	hgsc.bcm.edu	37	chr1	19455517	19455517	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ccgccaacgtttcgtaattgAggcagggtctgcagtaatct	11	10	2	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:19455517A>C	ENST00000375254.3	-	61	8985	c.8958T>G	c.(8956-8958)ccT>ccG	p.P2986P	UBR4_ENST00000375217.2_Silent_p.P2979P|UBR4_ENST00000375226.2_Silent_p.P2962P|UBR4_ENST00000375267.2_Silent_p.P2986P	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2986					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TTCGTAATTGAGGCAGGGTCT	0.498																																					p.P2986P		Atlas-SNP	.											.	UBR4	415	.	0			c.T8958G						.						146	121	129					1																	19455517		2203	4300	6503	SO:0001819	synonymous_variant	23352	exon61			TAATTGAGGCAGG	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.8958T>G	chr1.hg19:g.19455517A>C		170.0	0.0		129.0	38.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.		0.498	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19455517	A	C	19455517	2	2	80	1	0	0	0	0	0	0	0	1	16919	291	11	5		5	UBR4	1	19455517	Silent	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10		19455517	229795104	1	10963										
TCEB3	6924	hgsc.bcm.edu	37	chr1	24080866	24080866	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	tctgcagcaatctttgaagtGggaggagtcccatactctgt	11	9	3	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:24080866G>A	ENST00000418390.2	+	7	2056	c.1785G>A	c.(1783-1785)gtG>gtA	p.V595V	TCEB3_ENST00000609199.1_Silent_p.V569V	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	595	Activation domain. {ECO:0000250}.|F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		TCTTTGAAGTGGGAGGAGTCC	0.463																																					p.V595V		Atlas-SNP	.											.	TCEB3	61	.	0			c.G1785A						.						167	151	156					1																	24080866		2203	4300	6503	SO:0001819	synonymous_variant	6924	exon7			TGAAGTGGGAGGA	L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.1785G>A	chr1.hg19:g.24080866G>A		98.0	0.0		105.0	34.0	NM_003198	B2R7Q8|Q8IXH1	Silent	SNP	ENST00000418390.2	hg19	CCDS239.2																																																																																			.	.		0.463	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198		A	24080866	G	A	24080866	2	1	80	1	0	0	0	0	0	0	0	1	15696	1335	47	3		3	TCEB3	1	24080866	Silent	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	4625349	24080866	225169755	2	10964										
FUCA1	2517	hgsc.bcm.edu	37	chr1	24181042	24181042	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ccccatcggtcatttactacCacctcatcctaaggagggaa	7	14	2	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:24181042C>A	ENST00000374479.3	-	5	784	c.777G>T	c.(775-777)gtG>gtT	p.V259V		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	259					fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		CATTTACTACCACCTCATCCT	0.413																																					p.V259V		Atlas-SNP	.											.	FUCA1	24	.	0			c.G777T						.						92	91	91					1																	24181042		2203	4300	6503	SO:0001819	synonymous_variant	2517	exon5			TACTACCACCTCA	BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.777G>T	chr1.hg19:g.24181042C>A		105.0	0.0		63.0	33.0	NM_000147	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Silent	SNP	ENST00000374479.3	hg19	CCDS244.2																																																																																			.	.		0.413	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147		A	24181042	C	A	24181042	2	1	80	1	0	0	0	0	0	0	0	1	6102	581	21	3		3	FUCA1	1	24181042	Silent	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	100176	24181042	225069579	3	10965										
LEPRE1	64175	hgsc.bcm.edu	37	chr1	43212987	43212987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ggtgaaccacagggcgatggCacagcgctgccccctggtga	15	13	0	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:43212987C>T	ENST00000296388.5	-	14	2062	c.2011G>A	c.(2011-2013)Gcc>Acc	p.A671T	LEPRE1_ENST00000236040.4_Missense_Mutation_p.A671T|LEPRE1_ENST00000397054.3_Missense_Mutation_p.A671T|LEPRE1_ENST00000462474.1_5'UTR			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	671	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	AGGGCGATGGCACAGCGCTGC	0.622											OREG0013422	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A671T		Atlas-SNP	.											.	LEPRE1	130	.	0			c.G2011A						.						58	59	59					1																	43212987		2203	4300	6503	SO:0001583	missense	64175	exon14			CGATGGCACAGCG	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 1", "growth suppressor 1"	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.2011G>A	chr1.hg19:g.43212987C>T	ENSP00000296388:p.Ala671Thr	84.0	0.0	914	72.0	32.0	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	hg19	CCDS472.2	.	.	.	.	.	.	.	.	.	.	C	35	5.522291	0.96431	.	.	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027	T;T;T	0.62105	0.05;0.05;0.05	5.36	5.36	0.76844	Oxoglutarate/iron-dependent oxygenase (2);Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	T	0.77916	0.4202	M	0.66560	2.04	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.79614	-0.1730	10	0.66056	D	0.02	-25.9617	16.6203	0.84928	0.0:1.0:0.0:0.0	.	671;536;671	Q32P28-3;B4DNM8;Q32P28	.;.;P3H1_HUMAN	T	671;671;671;536	ENSP00000380245:A671T;ENSP00000236040:A671T;ENSP00000296388:A671T	ENSP00000236040:A671T	A	-	1	0	LEPRE1	42985574	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.466000	0.80914	2.523000	0.85059	0.655000	0.94253	GCC	.	.		0.622	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356		T	43212987	C	T	43212987	3	4	80	1	0	0	0	0	1	0	0	0	8738	710	25	3	226	3	LEPRE1	1	43212987	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	19031945	43212987	206037634	4	10966										
CD101	9398	hgsc.bcm.edu	37	chr1	117559864	117559864	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	agacacagcccgagtttgtgGctggcatggggcaggatggc	17	9	0	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:117559864G>C	ENST00000256652.4	+	5	1439	c.1381G>C	c.(1381-1383)Gct>Cct	p.A461P	CD101_ENST00000369470.1_Missense_Mutation_p.A461P	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	461	Ig-like C2-type 4.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CGAGTTTGTGGCTGGCATGGG	0.582																																					p.A461P		Atlas-SNP	.											.	CD101	95	.	0			c.G1381C						.						78	70	73					1																	117559864		2203	4300	6503	SO:0001583	missense	9398	exon5			TTTGTGGCTGGCA	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.1381G>C	chr1.hg19:g.117559864G>C	ENSP00000256652:p.Ala461Pro	142.0	0.0		119.0	8.0	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	hg19	CCDS891.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.082095	0.76528	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.23950	1.88;1.88	4.72	4.72	0.59763	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.098836	0.44285	D	0.000474	T	0.40040	0.1101	M	0.72118	2.19	0.45076	D	0.998096	D	0.89917	1.0	D	0.74023	0.982	T	0.17930	-1.0353	10	0.54805	T	0.06	-19.4866	13.3731	0.60723	0.0:0.0:1.0:0.0	.	461	Q93033	IGSF2_HUMAN	P	461	ENSP00000256652:A461P;ENSP00000358482:A461P	ENSP00000256652:A461P	A	+	1	0	CD101	117361387	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.420000	0.44679	2.594000	0.87642	0.655000	0.94253	GCT	.	.		0.582	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		C	117559864	G	C	117559864	3	2	80	1	0	0	0	0	1	0	0	0	2964	1203	42	4	1399	4	CD101	1	117559864	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	74346877	117559864	131690757	5	10967										
PAQR6	79957	hgsc.bcm.edu	37	chr1	156214169	156214169	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	tgggtgcccagcactgcacaGatgtggaataactggtggct	14	9	0	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:156214169G>T	ENST00000292291.5	-	8	944	c.786C>A	c.(784-786)atC>atA	p.I262I	PAQR6_ENST00000368270.1_Silent_p.I238I|PAQR6_ENST00000492619.1_5'UTR|PAQR6_ENST00000335852.1_Missense_Mutation_p.S180Y|PAQR6_ENST00000540423.1_Silent_p.I259I|PAQR6_ENST00000356983.2_Missense_Mutation_p.S180Y	NM_001272104.1|NM_001272105.1|NM_198406.2	NP_001259033.1|NP_001259034.1|NP_940798.1	Q6TCH4	PAQR6_HUMAN	progestin and adipoQ receptor family member VI	262						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			lung(4)|ovary(1)	5	Hepatocellular(266;0.158)					GCACTGCACAGATGTGGAATA	0.622																																					p.S180Y	GBM(16;219 398 12385 32425 38531)	Atlas-SNP	.											.	PAQR6	23	.	0			c.C539A						.						8	8	8					1																	156214169		2177	4277	6454	SO:0001819	synonymous_variant	79957	exon7			TGCACAGATGTGG	AF455045	CCDS1135.1, CCDS1136.1, CCDS60301.1, CCDS72945.1, CCDS72946.1	1q23	2008-02-05			ENSG00000160781	ENSG00000160781			30132	protein-coding gene	gene with protein product		614579				12477932	Standard	NM_024897		Approved	FLJ22672	uc010phh.2	Q6TCH4	OTTHUMG00000017490	ENST00000292291.5:c.786C>A	chr1.hg19:g.156214169G>T		32.0	0.0		47.0	13.0	NM_024897	B7Z9R9|D3DVB4|D3DVB6|Q5TCK9|Q6PDU0|Q7Z4Q7|Q7Z4Q9|Q8N121|Q8N3M2|Q9H621	Missense_Mutation	SNP	ENST00000292291.5	hg19	CCDS1136.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.768777	0.49680	.	.	ENSG00000160781	ENST00000360733;ENST00000335852;ENST00000356983	T;T;T	0.38722	1.12;1.12;1.12	4.71	3.78	0.43462	.	.	.	.	.	T	0.35480	0.0933	.	.	.	0.80722	D	1	D;D;P	0.64830	0.994;0.994;0.617	P;P;B	0.51895	0.683;0.683;0.403	T	0.14117	-1.0484	8	0.39692	T	0.17	-7.3744	11.8718	0.52525	0.0:0.0:0.8239:0.1761	.	112;40;180	B4DJ42;Q7Z4Q8;Q6TCH4-2	.;.;.	Y	180	ENSP00000353961:S180Y;ENSP00000338330:S180Y;ENSP00000349474:S180Y	ENSP00000338330:S180Y	S	-	2	0	PAQR6	154480793	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.472000	0.35376	1.188000	0.43014	0.462000	0.41574	TCT	.	.		0.622	PAQR6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046297.2	NM_024897		T	156214169	G	T	156214169	2	4	80	1	0	0	0	0	0	0	0	1	11448	942	33	3		3	PAQR6	1	156214169	Silent	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	38654305	156214169	93036452	6	10968										
ATP1A2	477	hgsc.bcm.edu	37	chr1	160100081	160100081	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gacttggggagcgtgtgctgGgtgagaggccagaaacagga	19	6	0	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:160100081G>T	ENST00000361216.3	+	12	1740	c.1651G>T	c.(1651-1653)Gga>Tga	p.G551*	ATP1A2_ENST00000392233.3_Splice_Site_p.G551*	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	551					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			GCGTGTGCTGGGTGAGAGGCC	0.622																																					p.G551X		Atlas-SNP	.											.	ATP1A2	167	.	0			c.G1651T						.						46	48	47					1																	160100081		2203	4300	6503	SO:0001630	splice_region_variant	477	exon12			GTGCTGGGTGAGA	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.1651+1G>T	chr1.hg19:g.160100081G>T		79.0	0.0		87.0	22.0	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Nonsense_Mutation	SNP	ENST00000361216.3	hg19	CCDS1196.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.075725|8.075725	0.98640|0.98640	.|.	.|.	ENSG00000018625|ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000435866|ENST00000447527	.|.	.|.	.|.	4.61|4.61	4.61|4.61	0.57282|0.57282	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.64316	.|0.2587	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.65125	.|-0.6244	.|3	0.87932|.	D|.	0|.	.|.	16.564|16.564	0.84574|0.84574	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|C	551;551;254|261	.|.	ENSP00000354490:G551X|.	G|W	+|+	1|3	0|0	ATP1A2|ATP1A2	158366705|158366705	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	9.614000|9.614000	0.98353|0.98353	2.283000|2.283000	0.76528|0.76528	0.511000|0.511000	0.50034|0.50034	GGA|TGG	.	.		0.622	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	Nonsense_Mutation	T	160100081	G	T	160100081	5	4	80	1	0	0	0	0	0	0	1	0	1129	1246	43	3	1697	3	ATP1A2	1	160100081	Splice_Site	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	3885912	160100081	89150540	7	10969										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096907	167096907	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	agaaggagatgcagatggagCttagggagaagatgtctgag	17	3	1	6			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:167096907C>T	ENST00000361200.2	+	6	2705	c.2539C>T	c.(2539-2541)Ctt>Ttt	p.L847F	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.L847F|DUSP27_ENST00000443333.1_Missense_Mutation_p.L847F			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	847					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GCAGATGGAGCTTAGGGAGAA	0.493																																					p.L847F		Atlas-SNP	.											.	DUSP27	235	.	0			c.C2539T						.						71	65	67					1																	167096907		2203	4300	6503	SO:0001583	missense	92235	exon5			ATGGAGCTTAGGG	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2539C>T	chr1.hg19:g.167096907C>T	ENSP00000354483:p.Leu847Phe	157.0	0.0		150.0	14.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	C	9.713	1.157582	0.21454	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.04502	3.61;3.61;3.61	5.47	1.42	0.22433	.	0.084937	0.40302	N	0.001137	T	0.02455	0.0075	M	0.63428	1.95	0.36705	D	0.880344	P	0.50272	0.933	B	0.42386	0.386	T	0.46596	-0.9180	10	0.87932	D	0	-16.9947	5.0654	0.14580	0.3598:0.4207:0.0:0.2194	.	847	Q5VZP5	DUS27_HUMAN	F	847	ENSP00000354483:L847F;ENSP00000271385:L847F;ENSP00000404874:L847F	ENSP00000271385:L847F	L	+	1	0	DUSP27	165363531	0.916000	0.31088	0.910000	0.35882	0.126000	0.20510	1.871000	0.39539	0.258000	0.21686	-0.332000	0.08345	CTT	.	.		0.493	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		T	167096907	C	T	167096907	3	4	80	1	0	0	0	0	1	0	0	0	4826	797	28	3	2557	3	DUSP27	1	167096907	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	6996826	167096907	82153714	8	10970										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176759102	176759102	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gtgtgctcaactgtaaccagGaacgtgaaaaggtaaggaac	12	7	1	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:176759102G>A	ENST00000367662.3	+	18	6037	c.4873G>A	c.(4873-4875)Gaa>Aaa	p.E1625K		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1625	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CTGTAACCAGGAACGTGAAAA	0.428																																					p.E1625K		Atlas-SNP	.											.	PAPPA2	665	.	0			c.G4873A						.						162	154	156					1																	176759102		1938	4138	6076	SO:0001583	missense	60676	exon18			AACCAGGAACGTG	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.4873G>A	chr1.hg19:g.176759102G>A	ENSP00000356634:p.Glu1625Lys	115.0	0.0		111.0	31.0	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	hg19	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	7.706	0.694129	0.15039	.	.	ENSG00000116183	ENST00000367662	T	0.01548	4.78	5.64	4.68	0.58851	Complement control module (1);Sushi/SCR/CCP (2);	0.481828	0.20204	N	0.097028	T	0.01940	0.0061	L	0.34521	1.04	0.80722	D	1	B	0.25955	0.138	B	0.25987	0.065	T	0.61143	-0.7122	10	0.20519	T	0.43	-20.1431	12.1547	0.54070	0.0:0.2626:0.7374:0.0	.	1625	Q9BXP8	PAPP2_HUMAN	K	1625	ENSP00000356634:E1625K	ENSP00000356634:E1625K	E	+	1	0	PAPPA2	175025725	0.711000	0.27906	1.000000	0.80357	0.766000	0.43426	1.711000	0.37930	2.651000	0.90000	0.650000	0.86243	GAA	.	.		0.428	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176759102	G	A	176759102	3	1	80	1	0	0	0	0	1	0	0	0	11442	1175	41	3	4992	3	PAPPA2	1	176759102	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	9662195	176759102	72491519	9	10971										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179564900	179564900	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	tgagcatggaaaagacttccAagttaaatgtagtggagact	11	5	0	3	rs183977806		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:179564900A>T	ENST00000367614.1	+	4	1137	c.778A>T	c.(778-780)Aag>Tag	p.K260*	TDRD5_ENST00000294848.8_Nonsense_Mutation_p.K260*|TDRD5_ENST00000444136.1_Nonsense_Mutation_p.K260*	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	260					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						AAAGACTTCCAAGTTAAATGT	0.373																																					p.K260X		Atlas-SNP	.											.	TDRD5	149	.	0			c.A778T						.						83	84	84					1																	179564900		2203	4300	6503	SO:0001587	stop_gained	163589	exon4			ACTTCCAAGTTAA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.778A>T	chr1.hg19:g.179564900A>T	ENSP00000356586:p.Lys260*	318.0	0.0		353.0	107.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Nonsense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	A	40	7.969106	0.98588	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	.	.	.	5.48	3.15	0.36227	.	0.938732	0.08883	N	0.879808	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	13.2353	4.8045	0.13314	0.7141:0.0:0.2859:0.0	.	.	.	.	X	260	.	ENSP00000294848:K260X	K	+	1	0	TDRD5	177831523	0.017000	0.18338	0.003000	0.11579	0.905000	0.53344	2.520000	0.45554	0.925000	0.37094	0.477000	0.44152	AAG	.	A|1.000;G|0.000		0.373	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		T	179564900	A	T	179564900	4	4	80	1	0	0	0	0	0	1	0	0	15748	131	5	4	788	4	TDRD5	1	179564900	Nonsense_Mutation	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	2805798	179564900	69685721	10	10972										
FAM129A	116496	hgsc.bcm.edu	37	chr1	184764697	184764697	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gaacgtggctctccccattcGtatcttcttccatcactgga	7	14	4	0	rs201876014		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:184764697G>T	ENST00000367511.3	-	14	2394	c.2201C>A	c.(2200-2202)aCg>aAg	p.T734K	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	734	Glu-rich.				negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						CTCCCCATTCGTATCTTCTTC	0.522																																					p.T734K		Atlas-SNP	.											.	FAM129A	98	.	0			c.C2201A						.						115	120	118					1																	184764697		2203	4300	6503	SO:0001583	missense	116496	exon14			CCATTCGTATCTT	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"cell growth inhibiting protein 39"		"chromosome 1 open reading frame 24"	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.2201C>A	chr1.hg19:g.184764697G>T	ENSP00000356481:p.Thr734Lys	60.0	0.0		80.0	51.0	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	hg19	CCDS1364.1	.	.	.	.	.	.	.	.	.	.	g	16.75	3.209232	0.58343	.	.	ENSG00000135842	ENST00000367511	T	0.10668	2.85	5.44	1.31	0.21738	.	1.607640	0.03629	N	0.237594	T	0.08088	0.0202	L	0.32530	0.975	0.09310	N	1	B	0.16802	0.019	B	0.18561	0.022	T	0.34825	-0.9813	10	0.07030	T	0.85	-0.4004	4.771	0.13155	0.3444:0.0:0.5138:0.1417	.	734	Q9BZQ8	NIBAN_HUMAN	K	734	ENSP00000356481:T734K	ENSP00000356481:T734K	T	-	2	0	FAM129A	183031320	0.000000	0.05858	0.002000	0.10522	0.020000	0.10135	-1.236000	0.02925	0.247000	0.21414	-0.320000	0.08662	ACG	.	G|1.000;A|0.000		0.522	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			T	184764697	G	T	184764697	3	4	80	1	0	0	0	0	1	0	0	0	5441	1145	40	1	589	1	FAM129A	1	184764697	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	5199797	184764697	64485924	11	10973										
C1orf106	55765	hgsc.bcm.edu	37	chr1	200877890	200877890	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	tgccaaaacctcctccagagTctccagccccaccttctcgg	6	19	2	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:200877890T>G	ENST00000367342.4	+	7	1062	c.862T>G	c.(862-864)Tct>Gct	p.S288A	C1orf106_ENST00000413687.2_Missense_Mutation_p.S203A	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	288	Pro-rich.									endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						TCCTCCAGAGTCTCCAGCCCC	0.597																																					p.S302A		Atlas-SNP	.											.	C1orf106	59	.	0			c.T904G						.						84	99	94					1																	200877890		2203	4300	6503	SO:0001583	missense	55765	exon7			CCAGAGTCTCCAG	AK001763	CCDS44292.1	1q32.1	2011-02-15			ENSG00000163362	ENSG00000163362			25599	protein-coding gene	gene with protein product						14702039	Standard	NM_018265		Approved	FLJ10901	uc001gvo.4	Q3KP66	OTTHUMG00000035789	ENST00000367342.4:c.862T>G	chr1.hg19:g.200877890T>G	ENSP00000356311:p.Ser288Ala	284.0	0.0		365.0	45.0	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Missense_Mutation	SNP	ENST00000367342.4	hg19		.	.	.	.	.	.	.	.	.	.	T	15.37	2.814824	0.50527	.	.	ENSG00000163362	ENST00000367342;ENST00000413687	T;T	0.51325	0.71;0.77	4.88	1.02	0.19986	.	0.145914	0.47093	N	0.000254	T	0.36331	0.0963	M	0.62723	1.935	0.24058	N	0.996026	B	0.09022	0.002	B	0.08055	0.003	T	0.22417	-1.0217	10	0.22706	T	0.39	-11.4219	4.4203	0.11477	0.0:0.1799:0.3267:0.4934	.	288	Q3KP66	CA106_HUMAN	A	288;203	ENSP00000356311:S288A;ENSP00000392105:S203A	ENSP00000356311:S288A	S	+	1	0	C1orf106	199144513	0.984000	0.35163	0.938000	0.37757	0.806000	0.45545	0.277000	0.18734	-0.080000	0.12685	0.455000	0.32223	TCT	.	.		0.597	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265		G	200877890	T	G	200877890	3	3	80	1	0	0	0	0	1	0	0	0	1982	1667	58	5	888	5	C1orf106	1	200877890	Missense_Mutation	SNP	T	TCGA-CC-A8HU-01A-11D-A35Z-10	16113193	200877890	48372731	12	10974										
CR2	1380	hgsc.bcm.edu	37	chr1	207649761	207649761	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gccaacctgcccctcattgtAaaggtgctttgtctattttt	7	11	2	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:207649761A>G	ENST00000367058.3	+	14	2911	c.2722A>G	c.(2722-2724)Aaa>Gaa	p.K908E	CR2_ENST00000458541.2_Missense_Mutation_p.K881E|CR2_ENST00000367059.3_Intron|CR2_ENST00000367057.3_Missense_Mutation_p.K967E	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	908	Sushi 14. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CCCTCATTGTAAAGGTGCTTT	0.408																																					p.K967E		Atlas-SNP	.											.	CR2	164	.	0			c.A2899G						.						44	42	43					1																	207649761		2203	4300	6503	SO:0001583	missense	1380	exon15			CATTGTAAAGGTG	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.2722A>G	chr1.hg19:g.207649761A>G	ENSP00000356025:p.Lys908Glu	96.0	0.0		119.0	40.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	A	16.38	3.106877	0.56291	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000458541	T;T;T	0.47177	0.85;0.85;0.85	4.87	4.87	0.63330	Complement control module (2);Sushi/SCR/CCP (1);	.	.	.	.	T	0.31451	0.0797	L	0.35723	1.085	0.47374	D	0.999408	B;B	0.30727	0.059;0.292	B;B	0.27380	0.06;0.079	T	0.11299	-1.0593	9	0.02654	T	1	.	11.4381	0.50081	1.0:0.0:0.0:0.0	.	908;967	P20023;P20023-3	CR2_HUMAN;.	E	908;967;881	ENSP00000356025:K908E;ENSP00000356024:K967E;ENSP00000404222:K881E	ENSP00000356024:K967E	K	+	1	0	CR2	205716384	0.989000	0.36119	0.997000	0.53966	0.935000	0.57460	0.693000	0.25497	2.135000	0.66039	0.533000	0.62120	AAA	.	.		0.408	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		G	207649761	A	G	207649761	3	3	80	1	0	0	0	0	1	0	0	0	3844	363	13	2	2957	2	CR2	1	207649761	Missense_Mutation	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	6771871	207649761	41600860	13	10975										
ACTN2	88	hgsc.bcm.edu	37	chr1	236925852	236925852	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gcccgcctactcgggcccagGcagtgtgcctggtgcactgg	15	15	0	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:236925852G>A	ENST00000366578.4	+	21	2784	c.2618G>A	c.(2617-2619)gGc>gAc	p.G873D	ACTN2_ENST00000542672.1_Missense_Mutation_p.G873D|ACTN2_ENST00000546208.1_Missense_Mutation_p.G367D	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	873					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			TCGGGCCCAGGCAGTGTGCCT	0.597																																					p.G873D		Atlas-SNP	.											.	ACTN2	191	.	0			c.G2618A						.						58	52	54					1																	236925852		2203	4300	6503	SO:0001583	missense	88	exon21			GCCCAGGCAGTGT	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.2618G>A	chr1.hg19:g.236925852G>A	ENSP00000355537:p.Gly873Asp	131.0	0.0		174.0	102.0	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	hg19	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	G	6.323	0.427669	0.11987	.	.	ENSG00000077522	ENST00000542672;ENST00000366578;ENST00000546208;ENST00000545611	T;T;T	0.39787	1.06;1.06;1.06	5.43	5.43	0.79202	EF-hand, Ca insensitive (1);EF-hand-like domain (1);	0.099100	0.64402	D	0.000002	T	0.21841	0.0526	N	0.02751	-0.505	0.80722	D	1	B;B;B;B	0.18863	0.017;0.004;0.031;0.015	B;B;B;B	0.26969	0.075;0.02;0.075;0.03	T	0.17349	-1.0372	10	0.02654	T	1	.	19.6166	0.95636	0.0:0.0:1.0:0.0	.	658;873;643;873	B7Z4K1;B2RCS5;Q59FD9;P35609	.;.;.;ACTN2_HUMAN	D	873;873;367;642	ENSP00000443495:G873D;ENSP00000355537:G873D;ENSP00000438384:G367D	ENSP00000355537:G873D	G	+	2	0	ACTN2	234992475	0.999000	0.42202	0.951000	0.38953	0.338000	0.28826	2.856000	0.48341	2.721000	0.93114	0.655000	0.94253	GGC	.	.		0.597	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		A	236925852	G	A	236925852	3	1	80	1	0	0	0	0	1	0	0	0	205	1203	42	3	2700	3	ACTN2	1	236925852	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	29276091	236925852	12324769	14	10976										
EXO1	9156	hgsc.bcm.edu	37	chr1	242052844	242052844	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ccaactaactccagaagcggAagaggatatatttaacaaac	7	9	0	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:242052844A>G	ENST00000366548.3	+	16	3076	c.2483A>G	c.(2482-2484)gAa>gGa	p.E828G	EXO1_ENST00000518483.1_3'UTR|EXO1_ENST00000348581.5_Missense_Mutation_p.E828G	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	828	Interaction with MLH1.|Interaction with MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			CCAGAAGCGGAAGAGGATATA	0.403								Editing and processing nucleases																													p.E828G		Atlas-SNP	.											EXO1,NS,carcinoma,0,1	EXO1	103	.	0			c.A2483G						.						95	96	96					1																	242052844		2203	4300	6503	SO:0001583	missense	9156	exon16			AAGCGGAAGAGGA	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.2483A>G	chr1.hg19:g.242052844A>G	ENSP00000355506:p.Glu828Gly	148.0	1.0		152.0	47.0	NM_130398	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	hg19	CCDS1620.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677379	0.88445	.	.	ENSG00000174371	ENST00000366548;ENST00000348581	T;T	0.76186	-1.0;-1.0	5.53	5.53	0.82687	.	0.057931	0.64402	D	0.000002	D	0.83022	0.5164	M	0.67953	2.075	0.40806	D	0.983384	D;D	0.76494	0.999;0.991	D;P	0.64042	0.921;0.7	D	0.85452	0.1161	10	0.72032	D	0.01	-12.2096	13.1877	0.59691	1.0:0.0:0.0:0.0	.	827;828	A8K5H6;Q9UQ84	.;EXO1_HUMAN	G	828	ENSP00000355506:E828G;ENSP00000311873:E828G	ENSP00000311873:E828G	E	+	2	0	EXO1	240119467	1.000000	0.71417	0.995000	0.50966	0.949000	0.60115	3.768000	0.55295	2.088000	0.63022	0.533000	0.62120	GAA	.	.		0.403	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027		G	242052844	A	G	242052844	3	3	80	1	0	0	0	0	1	0	0	0	5302	246	9	2	2533	2	EXO1	1	242052844	Missense_Mutation	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	5126992	242052844	7197777	15	10977										
OR2G6	391211	hgsc.bcm.edu	37	chr1	248685216	248685216	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	taccatgaataagaaagacaAaaccatgagctacggtggct	9	8	0	4			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr1:248685216A>T	ENST00000343414.4	+	1	301	c.269A>T	c.(268-270)aAa>aTa	p.K90I		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	90						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AAGAAAGACAAAACCATGAGC	0.512																																					p.K90I		Atlas-SNP	.											OR2G6,colon,carcinoma,0,1	OR2G6	124	.	0			c.A269T						.						123	117	119					1																	248685216		2203	4300	6503	SO:0001583	missense	391211	exon1			AAGACAAAACCAT		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"GPCR / Class A : Olfactory receptors"	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.269A>T	chr1.hg19:g.248685216A>T	ENSP00000341291:p.Lys90Ile	153.0	0.0		167.0	48.0	NM_001013355	B2RP33	Missense_Mutation	SNP	ENST00000343414.4	hg19	CCDS31119.1	.	.	.	.	.	.	.	.	.	.	N	9.806	1.181975	0.21787	.	.	ENSG00000188558	ENST00000343414	T	0.38560	1.13	3.68	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	U	0.000268	T	0.69851	0.3157	H	0.97103	3.94	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64487	-0.6396	10	0.87932	D	0	.	3.8217	0.08837	0.6608:0.2231:0.1161:0.0	.	90	Q5TZ20	OR2G6_HUMAN	I	90	ENSP00000341291:K90I	ENSP00000341291:K90I	K	+	2	0	OR2G6	246751839	0.001000	0.12720	0.007000	0.13788	0.092000	0.18411	0.256000	0.18351	1.523000	0.49018	0.329000	0.21502	AAA	.	.		0.512	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842		T	248685216	A	T	248685216	3	4	80	1	0	0	0	0	1	0	0	0	11009	14	1	4	271	4	OR2G6	1	248685216	Missense_Mutation	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	6632372	248685216	565405	16	10978										
C2orf16	84226	hgsc.bcm.edu	37	chr2	27804119	27804119	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	tctgagagaacccgtcataaCccctcttggagaaaccatcg	8	13	3	3			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr2:27804119C>T	ENST00000408964.2	+	1	4731	c.4680C>T	c.(4678-4680)aaC>aaT	p.N1560N	ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000355467.4_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000379717.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1560	Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CCCGTCATAACCCCTCTTGGA	0.532																																					p.N1560N		Atlas-SNP	.											.	C2orf16	357	.	0			c.C4680T						.						118	118	118					2																	27804119		1895	4112	6007	SO:0001819	synonymous_variant	84226	exon1			TCATAACCCCTCT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4680C>T	chr2.hg19:g.27804119C>T		115.0	0.0		81.0	42.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	hg19	CCDS42666.1																																																																																			.	.		0.532	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		T	27804119	C	T	27804119	2	4	80	1	0	0	0	0	0	0	0	1	2159	506	18	3		3	C2orf16	2	27804119	Silent	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10		27804119	215395254	17	10979										
DHX57	90957	hgsc.bcm.edu	37	chr2	39046259	39046261	+	In_Frame_Del	DEL	CTT	CTT	-													0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ttccagctttttctggttagCttcttcttttttatcccagg							TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr2:39046259_39046261delCTT	ENST00000295373.6	-	18	3443_3445	c.3317_3319delAAG	c.(3316-3321)gaagct>gct	p.E1106del		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1106							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TTCTGGTTAGCTTCTTCTTTTTT	0.36																																					p.1106_1107del	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-Indel,Pindel	.											.	DHX57	127	.	0			c.3318_3320del						.																																			SO:0001651	inframe_deletion	90957	exon18			.	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3317_3319delAAG	chr2.hg19:g.39046265_39046267delCTT	ENSP00000295373:p.Glu1106del	191.0	0.0		137.0	52.0	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	In_Frame_Del	DEL	ENST00000295373.6	hg19	CCDS1800.1																																																																																			.	.		0.36	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		-	39046261	CTT	-	39046259	7	5	80	1	0	1	0	1	0	0	0	0	4515	797	28	0	869	0	DHX57	2	39046259	In_Frame_Del	DEL	CTT	TCGA-CC-A8HU-01A-11D-A35Z-10	11242140	39046259	204153114	18	10980										
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43937431	43937431	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	cttggaagcggcggtggtttGttcttaaaggtggtgaatta	15	4	1	1	rs183194066		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr2:43937431G>A	ENST00000282406.4	+	13	2286	c.2176G>A	c.(2176-2178)Gtt>Att	p.V726I		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	726	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GCGGTGGTTTGTTCTTAAAGG	0.353																																					p.V726I		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.G2176A						.						109	124	119					2																	43937431		2203	4299	6502	SO:0001583	missense	130271	exon13			TGGTTTGTTCTTA	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.2176G>A	chr2.hg19:g.43937431G>A	ENSP00000282406:p.Val726Ile	179.0	0.0		128.0	51.0	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.161086	0.78226	.	.	ENSG00000152527	ENST00000282406	T	0.18810	2.19	5.02	4.14	0.48551	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.065835	0.64402	N	0.000013	T	0.38108	0.1028	L	0.46157	1.445	0.58432	D	0.999998	D;D;D	0.89917	0.972;0.996;1.0	P;D;D	0.85130	0.836;0.987;0.997	T	0.08166	-1.0735	10	0.49607	T	0.09	-12.5885	13.0333	0.58856	0.0778:0.0:0.9222:0.0	.	726;163;726	Q8IVE3;Q8IVE3-2;Q8IVE3-3	PKHH2_HUMAN;.;.	I	726	ENSP00000282406:V726I	ENSP00000282406:V726I	V	+	1	0	PLEKHH2	43790935	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.412000	0.66392	1.098000	0.41479	0.563000	0.77884	GTT	.	.		0.353	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		A	43937431	G	A	43937431	3	1	80	1	0	0	0	0	1	0	0	0	12086	1377	48	3	2222	3	PLEKHH2	2	43937431	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	4891172	43937431	199261942	19	10981										
ANKRD36B	0	hgsc.bcm.edu	37	chr2	98160311	98160311	+	IGR	DEL	C	C	-													0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	atattcgaaacagaatctttCttgtcacttgtagcctgaat							TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr2:98160311delC								AC159540.1 (69262 upstream) : ANKRD36B (3716 downstream)																							CAGAATCTTTCTTGTCACTTG	0.318																																					p.K576fs		Atlas-INDEL	.											.	.	.	.	0			c.1726delA						.						1	1	1					2																	98160311		89	138	227	SO:0001628	intergenic_variant	57730	exon26			.																													chr2.hg19:g.98160311delC		78.0	0.0		44.0	11.0	NM_025190		Frame_Shift_Del	DEL		hg19																																																																																				.	.	0	0.318									-	98160311	C	-	98160311	6	5	80	0	1	1	0	1	0	0	0	0	666	912	32	0		0	ANKRD36B	2	98160311	IGR	DEL	C	TCGA-CC-A8HU-01A-11D-A35Z-10	54222880	98160311	145039062	20	10982										
IWS1	55677	hgsc.bcm.edu	37	chr2	128255759	128255759	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	atcagaatctgaatcttctgCttcttttacctgtgtttcac	5	10	6	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr2:128255759C>G	ENST00000295321.4	-	6	1781	c.1522G>C	c.(1522-1524)Gca>Cca	p.A508P	IWS1_ENST00000455721.2_Intron|AC010976.2_ENST00000599001.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	508	Glu-rich.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		GAATCTTCTGCTTCTTTTACC	0.313																																					p.A508P		Atlas-SNP	.											.	IWS1	61	.	0			c.G1522C						.						190	195	193					2																	128255759		2202	4299	6501	SO:0001583	missense	55677	exon6			CTTCTGCTTCTTT	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.1522G>C	chr2.hg19:g.128255759C>G	ENSP00000295321:p.Ala508Pro	199.0	0.0		126.0	54.0	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	hg19	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.404115	0.62288	.	.	ENSG00000163166	ENST00000295321;ENST00000433551	T	0.17691	2.26	5.69	5.69	0.88448	.	0.115899	0.56097	D	0.000021	T	0.17831	0.0428	L	0.56769	1.78	0.80722	D	1	P	0.45474	0.859	B	0.34038	0.174	T	0.03344	-1.1046	10	0.32370	T	0.25	-19.4506	17.9972	0.89187	0.0:1.0:0.0:0.0	.	508	Q96ST2	IWS1_HUMAN	P	508;461	ENSP00000295321:A508P	ENSP00000295321:A508P	A	-	1	0	IWS1	127972229	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.183000	0.58317	2.685000	0.91497	0.557000	0.71058	GCA	.	.		0.313	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		G	128255759	C	G	128255759	3	3	80	1	0	0	0	0	1	0	0	0	7940	797	28	4	973	4	IWS1	2	128255759	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	30095448	128255759	114943614	21	10983										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148684720	148684736	+	Frame_Shift_Del	DEL	ATGTGTAGGTGAAAGAA	ATGTGTAGGTGAAAGAA	-													0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gaagccaggttatcagctggAtgtgtaggtgaaagaattac							TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	ATGTGTAGGTGAAAGAA	ATGTGTAGGTGAAAGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr2:148684720_148684736delATGTGTAGGTGAAAGAA	ENST00000241416.7	+	11	2055_2071	c.1419_1435delATGTGTAGGTGAAAGAA	c.(1417-1437)ggatgtgtaggtgaaagaattfs	p.CVGERI474fs	ACVR2A_ENST00000495775.1_3'UTR|ACVR2A_ENST00000404590.1_Frame_Shift_Del_p.CVGERI474fs|ACVR2A_ENST00000535787.1_Frame_Shift_Del_p.CVGERI366fs	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	474	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TATCAGCTGGATGTGTAGGTGAAAGAATTACCCAGAT	0.41																																					p.473_478del		Atlas-Indel,Pindel	.											.	ACVR2A	125	.	0			c.1418_1434del						.																																			SO:0001589	frameshift_variant	92	exon11			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1419_1435delATGTGTAGGTGAAAGAA	chr2.hg19:g.148684720_148684736delATGTGTAGGTGAAAGAA	ENSP00000241416:p.Cys474fs	138.0	0.0		51.0	15.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Frame_Shift_Del	DEL	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.41	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		-	148684736	ATGTGTAGGTGAAAGAA	-	148684720	7	5	80	1	0	1	0	1	0	0	0	0	223	320	12	0	1461	0	ACVR2A	2	148684720	Frame_Shift_Del	DEL	ATGTGTAGGTGAAAGAA	TCGA-CC-A8HU-01A-11D-A35Z-10	20428961	148684720	94514653	22	10984										
PER2	8864	hgsc.bcm.edu	37	chr2	239184411	239184411	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ctgcttcacgctcctgagggCgtacttcaaggtggccagcg	13	13	2	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr2:239184411C>A	ENST00000254657.3	-	4	700	c.421G>T	c.(421-423)Gcc>Tcc	p.A141S	PER2_ENST00000355768.2_Missense_Mutation_p.A141S|PER2_ENST00000440245.1_Missense_Mutation_p.A141S|PER2_ENST00000254658.3_Missense_Mutation_p.A141S	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	141					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		CTCCTGAGGGCGTACTTCAAG	0.493																																					p.A141S		Atlas-SNP	.											.	PER2	85	.	0			c.G421T						.						237	223	228					2																	239184411		2203	4300	6503	SO:0001583	missense	8864	exon4			TGAGGGCGTACTT	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.421G>T	chr2.hg19:g.239184411C>A	ENSP00000254657:p.Ala141Ser	129.0	0.0		76.0	38.0	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	hg19	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.611819	0.66558	.	.	ENSG00000132326	ENST00000254657;ENST00000254658;ENST00000440245;ENST00000355768	T;T;T;T	0.62639	1.77;0.01;0.84;0.01	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.81173	0.4767	M	0.87038	2.855	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.995;1.0;0.999	D	0.85029	0.0916	10	0.72032	D	0.01	-34.1693	14.9485	0.71050	0.0:1.0:0.0:0.0	.	141;141;141;141	F5GYD5;B4DH14;O15055-2;O15055	.;.;.;PER2_HUMAN	S	141	ENSP00000254657:A141S;ENSP00000254658:A141S;ENSP00000397516:A141S;ENSP00000348013:A141S	ENSP00000254657:A141S	A	-	1	0	PER2	238849150	1.000000	0.71417	0.994000	0.49952	0.053000	0.15095	7.534000	0.82004	2.194000	0.70268	0.655000	0.94253	GCC	.	.		0.493	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		A	239184411	C	A	239184411	3	1	80	1	0	0	0	0	1	0	0	0	11739	768	27	1	3426	1	PER2	2	239184411	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	90499691	239184411	4014962	23	10985										
ITGB5	3693	hgsc.bcm.edu	37	chr3	124483275	124483275	+	Frame_Shift_Del	DEL	T	T	-													0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	tggatcgctcgctctgaaacTttgcaaactccctccggtcg							TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr3:124483275delT	ENST00000296181.4	-	14	2563	c.2267delA	c.(2266-2268)aagfs	p.K756fs	ITGB5_ENST00000461306.1_5'Flank	NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	756					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		GCTCTGAAACTTTGCAAACTC	0.557																																					p.K756fs		Atlas-Indel,Pindel	.											.	ITGB5	66	.	0			c.2268delG						.						63	59	60					3																	124483275		2203	4300	6503	SO:0001589	frameshift_variant	3693	exon14			.	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.2267delA	chr3.hg19:g.124483275delT	ENSP00000296181:p.Lys756fs	79.0	0.0		60.0	21.0	NM_002213	B0LPF8|B2RD70	Frame_Shift_Del	DEL	ENST00000296181.4	hg19	CCDS3030.1																																																																																			.	.		0.557	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		-	124483275	T	-	124483275	7	5	80	1	0	1	0	1	0	0	0	0	7907	1609	56	0	140	0	ITGB5	3	124483275	Frame_Shift_Del	DEL	T	TCGA-CC-A8HU-01A-11D-A35Z-10		124483275	73539155	24	10986										
KY	339855	hgsc.bcm.edu	37	chr3	134346635	134346635	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ccaggttgccggggtcttgtGtttccatttttatcaccttg	10	10	2	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr3:134346635G>T	ENST00000423778.2	-	5	424	c.363C>A	c.(361-363)aaC>aaA	p.N121K	KY_ENST00000503669.1_Missense_Mutation_p.N121K|KY_ENST00000508956.1_Missense_Mutation_p.N100K|KY_ENST00000508041.1_5'UTR	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	121					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGGGTCTTGTGTTTCCATTTT	0.423																																					p.N121K		Atlas-SNP	.											.	KY	92	.	0			c.C363A						.						136	133	134					3																	134346635		1916	4136	6052	SO:0001583	missense	339855	exon5			TCTTGTGTTTCCA	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.363C>A	chr3.hg19:g.134346635G>T	ENSP00000397598:p.Asn121Lys	125.0	0.0		91.0	32.0	NM_178554	B7Z1S4|Q6ZT15	Missense_Mutation	SNP	ENST00000423778.2	hg19	CCDS46920.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.386268	0.42308	.	.	ENSG00000174611	ENST00000508956;ENST00000423778;ENST00000503669;ENST00000310263	.	.	.	5.67	4.8	0.61643	.	0.138770	0.49916	D	0.000129	T	0.47563	0.1452	L	0.56769	1.78	0.32062	N	0.595599	B;B;B;B	0.17852	0.002;0.024;0.006;0.023	B;B;B;B	0.12837	0.002;0.005;0.003;0.008	T	0.52946	-0.8507	9	0.23891	T	0.37	-8.4855	12.4582	0.55716	0.078:0.0:0.922:0.0	.	100;121;121;82	Q8NBH2-3;B4DGA7;Q8NBH2-4;Q8NBH2-2	.;.;.;.	K	100;121;121;121	.	ENSP00000309520:N121K	N	-	3	2	KY	135829325	0.992000	0.36948	0.998000	0.56505	0.998000	0.95712	0.829000	0.27449	1.409000	0.46915	0.655000	0.94253	AAC	.	.		0.423	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554		T	134346635	G	T	134346635	3	4	80	1	0	0	0	0	1	0	0	0	8595	1368	48	3	1650	3	KY	3	134346635	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	9863360	134346635	63675795	25	10987										
BCHE	590	hgsc.bcm.edu	37	chr3	165503966	165503966	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gacttttggaaaaaatgatgTccagaatcgacattgttgag	10	5	0	3			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr3:165503966T>C	ENST00000264381.3	-	3	1817	c.1651A>G	c.(1651-1653)Aca>Gca	p.T551A	BCHE_ENST00000540653.1_Missense_Mutation_p.T13A	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	551					cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	AAAAATGATGTCCAGAATCGA	0.348																																					p.T551A		Atlas-SNP	.											.	BCHE	136	.	0			c.A1651G						.						135	121	126					3																	165503966		2203	4299	6502	SO:0001583	missense	590	exon3			ATGATGTCCAGAA	M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"cholinesterase 1", "cholinesterase (serum) 2"	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.1651A>G	chr3.hg19:g.165503966T>C	ENSP00000264381:p.Thr551Ala	94.0	0.0		87.0	45.0	NM_000055	A8K7P8	Missense_Mutation	SNP	ENST00000264381.3	hg19	CCDS3198.1	.	.	.	.	.	.	.	.	.	.	T	11.92	1.784020	0.31593	.	.	ENSG00000114200	ENST00000264381;ENST00000479451;ENST00000540653;ENST00000488954	D;D;T;D	0.95238	-3.65;-3.65;-1.03;-3.65	5.72	5.72	0.89469	Acetylcholinesterase, tetramerisation (1);	0.267280	0.40554	N	0.001070	D	0.91570	0.7337	L	0.39898	1.24	0.22531	N	0.999011	B	0.15141	0.012	B	0.10450	0.005	D	0.84208	0.0454	10	0.56958	D	0.05	.	15.1866	0.73006	0.0:0.0:0.0:1.0	.	551	P06276	CHLE_HUMAN	A	551;81;13;81	ENSP00000264381:T551A;ENSP00000418325:T81A;ENSP00000443583:T13A;ENSP00000418504:T81A	ENSP00000264381:T551A	T	-	1	0	BCHE	166986660	1.000000	0.71417	0.977000	0.42913	0.390000	0.30446	5.581000	0.67471	2.184000	0.69523	0.533000	0.62120	ACA	.	.		0.348	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350254.1			C	165503966	T	C	165503966	3	2	80	1	0	0	0	0	1	0	0	0	1358	1667	58	2	165	2	BCHE	3	165503966	Missense_Mutation	SNP	T	TCGA-CC-A8HU-01A-11D-A35Z-10	31157331	165503966	32518464	26	10988										
LRRC66	339977	hgsc.bcm.edu	37	chr4	52869443	52869443	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ggaattttgaatatcttgttGctctttaaacagagattctc	7	6	3	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr4:52869443G>T	ENST00000343457.3	-	2	618	c.612C>A	c.(610-612)agC>agA	p.S204R		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	204						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(8)|lung(34)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	58						ATATCTTGTTGCTCTTTAAAC	0.368																																					p.S204R		Atlas-SNP	.											.	LRRC66	128	.	0			c.C612A						.						140	130	133					4																	52869443		1833	4089	5922	SO:0001583	missense	339977	exon2			CTTGTTGCTCTTT	BC040414	CCDS43229.1	4q12	2008-08-08			ENSG00000188993	ENSG00000188993			34299	protein-coding gene	gene with protein product							Standard	XM_005265739		Approved		uc003gzi.3	Q68CR7	OTTHUMG00000160623	ENST00000343457.3:c.612C>A	chr4.hg19:g.52869443G>T	ENSP00000341944:p.Ser204Arg	109.0	0.0		80.0	5.0	NM_001024611		Missense_Mutation	SNP	ENST00000343457.3	hg19	CCDS43229.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.758293	0.31137	.	.	ENSG00000188993	ENST00000343457	T	0.57595	0.39	5.55	2.67	0.31697	.	0.552778	0.17941	N	0.156846	T	0.33731	0.0873	N	0.13098	0.295	0.28198	N	0.927468	P	0.41624	0.757	B	0.41036	0.346	T	0.18618	-1.0331	10	0.66056	D	0.02	-2.796	6.591	0.22646	0.1777:0.1542:0.6681:0.0	.	204	Q68CR7	LRC66_HUMAN	R	204	ENSP00000341944:S204R	ENSP00000341944:S204R	S	-	3	2	LRRC66	52564200	0.976000	0.34144	0.982000	0.44146	0.016000	0.09150	1.607000	0.36836	0.895000	0.36342	-0.175000	0.13238	AGC	.	.		0.368	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		T	52869443	G	T	52869443	3	4	80	1	0	0	0	0	1	0	0	0	9027	1310	46	3	2042	3	LRRC66	4	52869443	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10		52869443	138284833	27	10989										
EIF4E	1977	hgsc.bcm.edu	37	chr4	99823068	99823068	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	atatagtgttctgggttagcAacctcctgattagattccgt	9	8	1	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr4:99823068A>C	ENST00000450253.2	-	2	1608	c.84T>G	c.(82-84)gtT>gtG	p.V28V	EIF4E_ENST00000280892.6_Silent_p.V48V|EIF4E_ENST00000504432.1_Silent_p.V56V|EIF4E_ENST00000504472.1_5'UTR|EIF4E_ENST00000505992.1_Silent_p.V28V	NM_001968.3	NP_001959.1	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E	28					cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of mitotic cell cycle (GO:0045931)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|extracellular vesicular exosome (GO:0070062)|mRNA cap binding complex (GO:0005845)|RISC complex (GO:0016442)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)		CTGGGTTAGCAACCTCCTGAT	0.398																																					p.V48V		Atlas-SNP	.											.	EIF4E	18	.	0			c.T144G						.						165	161	162					4																	99823068		2203	4300	6503	SO:0001819	synonymous_variant	1977	exon2			GTTAGCAACCTCC	M15353	CCDS34031.1, CCDS47109.1, CCDS54779.1	4q21-q25	2008-02-05			ENSG00000151247	ENSG00000151247			3287	protein-coding gene	gene with protein product		133440		EIF4EL1, EIF4F		9330633, 1916814	Standard	NM_001968		Approved	EIF4E1	uc011cea.1	P06730	OTTHUMG00000161090	ENST00000450253.2:c.84T>G	chr4.hg19:g.99823068A>C		132.0	0.0		47.0	39.0	NM_001130678	B7Z6V1|D6RCQ6|Q96E95	Silent	SNP	ENST00000450253.2	hg19	CCDS34031.1	.	.	.	.	.	.	.	.	.	.	A	10.44	1.350923	0.24512	.	.	ENSG00000151247	ENST00000511644	.	.	.	5.85	4.68	0.58851	.	.	.	.	.	T	0.58221	0.2107	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55611	-0.8114	4	.	.	.	-21.5605	7.7084	0.28663	0.8069:0.0:0.0685:0.1246	.	.	.	.	G	25	.	.	C	-	1	0	EIF4E	100042091	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.373000	0.52394	1.144000	0.42321	-0.288000	0.09946	TGC	.	.		0.398	EIF4E-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363739.1	NM_001968		C	99823068	A	C	99823068	2	2	80	1	0	0	0	0	0	0	0	1	5030	117	5	5		5	EIF4E	4	99823068	Silent	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	46953625	99823068	91331208	28	10990										
PCDHB6	56130	hgsc.bcm.edu	37	chr5	140529886	140529886	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	aaaaggcaagtggctttcttCattttattgatgctttgggg	11	5	2	1	rs143226291		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr5:140529886C>T	ENST00000231136.1	+	1	48	c.48C>T	c.(46-48)ttC>ttT	p.F16F	PCDHB6_ENST00000543635.1_Intron	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	16					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGCTTTCTTCATTTTATTGA	0.418																																					p.F16F		Atlas-SNP	.											.	PCDHB6	161	.	0			c.C48T						.	C		0,4406		0,0,2203	170	169	169		48	-5.3	0	5	dbSNP_134	169	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PCDHB6	NM_018939.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		16/795	140529886	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	56130	exon1			TTTCTTCATTTTA	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.48C>T	chr5.hg19:g.140529886C>T		101.0	0.0		62.0	16.0	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	hg19	CCDS4248.1																																																																																			.	C|1.000;T|0.000		0.418	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		T	140529886	C	T	140529886	2	4	80	1	0	0	0	0	0	0	0	1	11555	825	29	3		3	PCDHB6	5	140529886	Silent	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10		140529886	40385374	29	10991										
N4BP3	23138	hgsc.bcm.edu	37	chr5	177548620	177548620	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	agcccaggctcaggacgcagAgctggtccggctgcgcgagg	17	13	1	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr5:177548620A>G	ENST00000274605.5	+	5	1612	c.1253A>G	c.(1252-1254)gAg>gGg	p.E418G		NM_015111.1	NP_055926.1	O15049	N4BP3_HUMAN	NEDD4 binding protein 3	418						cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)				breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGGACGCAGAGCTGGTCCGG	0.667																																					p.E418G		Atlas-SNP	.											.	N4BP3	25	.	0			c.A1253G						.						38	44	42					5																	177548620		2203	4299	6502	SO:0001583	missense	23138	exon5			ACGCAGAGCTGGT	AB002339	CCDS34307.1	5q35.3	2012-05-17				ENSG00000145911			29852	protein-coding gene	gene with protein product						9205841, 11717310	Standard	XM_006714834		Approved	LZTS4	uc003mik.1	O15049		ENST00000274605.5:c.1253A>G	chr5.hg19:g.177548620A>G	ENSP00000274605:p.Glu418Gly	104.0	0.0		84.0	39.0	NM_015111	B4DIL3|D3DWP3|Q6ZSQ6|Q7Z6I3	Missense_Mutation	SNP	ENST00000274605.5	hg19	CCDS34307.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.004504	0.54254	.	.	ENSG00000145911	ENST00000274605	T	0.45668	0.89	5.33	5.33	0.75918	.	0.103321	0.64402	D	0.000003	T	0.36524	0.0970	L	0.46157	1.445	0.37392	D	0.912475	B	0.31256	0.316	B	0.29077	0.098	T	0.45440	-0.9261	10	0.62326	D	0.03	-28.7585	11.6945	0.51536	1.0:0.0:0.0:0.0	.	418	O15049	N4BP3_HUMAN	G	418	ENSP00000274605:E418G	ENSP00000274605:E418G	E	+	2	0	N4BP3	177481226	1.000000	0.71417	1.000000	0.80357	0.287000	0.27160	6.069000	0.71209	2.026000	0.59711	0.459000	0.35465	GAG	.	.		0.667	N4BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373552.2	NM_015111		G	177548620	A	G	177548620	3	3	80	1	0	0	0	0	1	0	0	0	10122	304	11	2	1267	2	N4BP3	5	177548620	Missense_Mutation	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	37018734	177548620	3366640	30	10992										
KCNK17	89822	hgsc.bcm.edu	37	chr6	39271872	39271872	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	aggaggcccgagaggagggcGccagagcccgccagccaccg	17	15	0	2	rs374325536		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr6:39271872G>T	ENST00000373231.4	-	4	781	c.549C>A	c.(547-549)ggC>ggA	p.G183G	KCNK17_ENST00000453413.2_Silent_p.G183G	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	183					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						AGAGGAGGGCGCCAGAGCCCG	0.657																																					p.G183G		Atlas-SNP	.											.	KCNK17	61	.	0			c.C549A						.						42	46	45					6																	39271872		2202	4300	6502	SO:0001819	synonymous_variant	89822	exon4			GAGGGCGCCAGAG	AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.549C>A	chr6.hg19:g.39271872G>T		93.0	0.0		114.0	60.0	NM_001135111	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Silent	SNP	ENST00000373231.4	hg19	CCDS4842.1																																																																																			.	.		0.657	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460		T	39271872	G	T	39271872	2	4	80	1	0	0	0	0	0	0	0	1	8073	1074	38	1		1	KCNK17	6	39271872	Silent	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10		39271872	131843195	31	10993										
KIF6	221458	hgsc.bcm.edu	37	chr6	39607459	39607459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	cactgtaacgctctgcacccCctgtgatagtgaatgtcttc	8	13	2	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr6:39607459C>T	ENST00000287152.7	-	4	420	c.326G>A	c.(325-327)gGg>gAg	p.G109E	KIF6_ENST00000373216.3_Missense_Mutation_p.G109E|KIF6_ENST00000373215.3_Missense_Mutation_p.G109E|KIF6_ENST00000538893.1_Missense_Mutation_p.G109E	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	109	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						CTCTGCACCCCCTGTGATAGT	0.423																																					p.G109E		Atlas-SNP	.											.	KIF6	233	.	0			c.G326A						.						180	135	150					6																	39607459		2203	4300	6503	SO:0001583	missense	221458	exon4			GCACCCCCTGTGA	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.326G>A	chr6.hg19:g.39607459C>T	ENSP00000287152:p.Gly109Glu	117.0	0.0		103.0	60.0	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	hg19	CCDS4844.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.171911|5.171911	0.94807|0.94807	.|.	.|.	ENSG00000164627|ENSG00000164627	ENST00000287152;ENST00000373216;ENST00000373215;ENST00000538893|ENST00000458470	D;D;D;D|.	0.84800|.	-1.9;-1.9;-1.9;-1.9|.	5.67|5.67	5.67|5.67	0.87782|0.87782	Kinesin, motor domain (5);|.	.|.	.|.	.|.	.|.	D|D	0.90721|0.90721	0.7088|0.7088	H|H	0.98901|0.98901	4.365|4.365	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;0.999;1.0|.	D|D	0.93998|0.93998	0.7273|0.7273	9|5	0.87932|.	D|.	0|.	.|.	19.3678|19.3678	0.94471|0.94471	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	109;109;109|.	E7EUN7;F6VGH2;Q6ZMV9|.	.;.;KIF6_HUMAN|.	E|R	109|1	ENSP00000287152:G109E;ENSP00000362312:G109E;ENSP00000362311:G109E;ENSP00000441435:G109E|.	ENSP00000287152:G109E|.	G|G	-|-	2|1	0|0	KIF6|KIF6	39715437|39715437	1.000000|1.000000	0.71417|0.71417	0.821000|0.821000	0.32701|0.32701	0.965000|0.965000	0.64279|0.64279	7.696000|7.696000	0.84270|0.84270	2.687000|2.687000	0.91594|0.91594	0.655000|0.655000	0.94253|0.94253	GGG|GGG	.	.		0.423	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		T	39607459	C	T	39607459	3	4	80	1	0	0	0	0	1	0	0	0	8317	623	22	3	2198	3	KIF6	6	39607459	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	335587	39607459	131507608	32	10994										
BMPER	168667	hgsc.bcm.edu	37	chr7	33945272	33945272	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	tctggctgagcgttactgccGccgctcgcctgggattacgt	13	13	1	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr7:33945272G>T	ENST00000297161.2	+	2	421	c.47G>T	c.(46-48)cGc>cTc	p.R16L	BMPER_ENST00000426693.1_Missense_Mutation_p.R16L	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	16					blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						CGTTACTGCCGCCGCTCGCCT	0.657																																					p.R16L		Atlas-SNP	.											.	BMPER	131	.	0			c.G47T						.						46	43	44					7																	33945272		2203	4300	6503	SO:0001583	missense	168667	exon2			ACTGCCGCCGCTC		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"crossveinless-2"	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.47G>T	chr7.hg19:g.33945272G>T	ENSP00000297161:p.Arg16Leu	54.0	0.0		73.0	26.0	NM_133468	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	hg19	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.720401	0.48728	.	.	ENSG00000164619	ENST00000297161;ENST00000426693;ENST00000436222	T;T	0.18810	2.19;2.19	3.65	1.57	0.23409	.	0.821803	0.10575	N	0.658668	T	0.06781	0.0173	N	0.00926	-1.1	0.24705	N	0.993235	B	0.02656	0.0	B	0.01281	0.0	T	0.35699	-0.9778	10	0.26408	T	0.33	.	8.5787	0.33614	0.0:0.0:0.474:0.526	.	16	Q8N8U9	BMPER_HUMAN	L	16	ENSP00000297161:R16L;ENSP00000393950:R16L	ENSP00000297161:R16L	R	+	2	0	BMPER	33911797	0.994000	0.37717	0.969000	0.41365	0.692000	0.40212	0.898000	0.28404	0.822000	0.34565	0.557000	0.71058	CGC	.	.		0.657	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		T	33945272	G	T	33945272	3	4	80	1	0	0	0	0	1	0	0	0	1468	1087	38	1	49	1	BMPER	7	33945272	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10		33945272	125193391	33	10995										
SHFM1	7979	hgsc.bcm.edu	37	chr7	96324128	96324128	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	accgtaactgattagagaagTcatcctctacattgtcatca	6	10	4	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr7:96324128T>A	ENST00000248566.2	-	2	279	c.152A>T	c.(151-153)gAc>gTc	p.D51V	SHFM1_ENST00000413065.1_Missense_Mutation_p.D51V|SHFM1_ENST00000417009.1_Missense_Mutation_p.D51V|SHFM1_ENST00000444799.1_Missense_Mutation_p.D51V	NM_006304.1	NP_006295.1	P60896	DSS1_HUMAN	split hand/foot malformation (ectrodactyly) type 1	51	Asp/Glu-rich (highly acidic).				double-strand break repair via homologous recombination (GO:0000724)	proteasome complex (GO:0000502)				breast(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5	all_cancers(62;4.24e-09)|all_epithelial(64;5.59e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0353)|Lung NSC(181;0.0987)					ATTAGAGAAGTCATCCTCTAC	0.348								Homologous recombination																													p.D51V		Atlas-SNP	.											.	SHFM1	12	.	0			c.A152T						.						170	168	169					7																	96324128		2203	4300	6503	SO:0001583	missense	7979	exon2			GAGAAGTCATCCT	U41515	CCDS5646.1	7q21.3	2010-04-22			ENSG00000127922	ENSG00000127922			10845	protein-coding gene	gene with protein product	"deleted in split-hand/foot 1"	601285		SHFD1		1895319, 8733122	Standard	NM_006304		Approved	DSS1, Shfdg1, ECD, SEM1, SHSF1	uc003uoi.3	P60896	OTTHUMG00000150680	ENST00000248566.2:c.152A>T	chr7.hg19:g.96324128T>A	ENSP00000248566:p.Asp51Val	115.0	0.0		98.0	52.0	NM_006304	Q13437|Q61067	Missense_Mutation	SNP	ENST00000248566.2	hg19	CCDS5646.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.964468	0.53507	.	.	ENSG00000127922	ENST00000417009;ENST00000444799;ENST00000413065;ENST00000248566	T;T;T;T	0.59906	0.23;0.23;0.23;0.23	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.76241	0.3960	.	.	.	0.80722	D	1	D;D	0.89917	1.0;0.987	D;D	0.91635	0.999;0.942	T	0.80002	-0.1565	9	0.87932	D	0	.	15.1597	0.72775	0.0:0.0:0.0:1.0	.	51;51	F2Z309;P60896	.;DSS1_HUMAN	V	51	ENSP00000416322:D51V;ENSP00000390049:D51V;ENSP00000409481:D51V;ENSP00000248566:D51V	ENSP00000248566:D51V	D	-	2	0	SHFM1	96162064	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.815000	0.86186	2.202000	0.70862	0.528000	0.53228	GAC	.	.		0.348	SHFM1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319595.1	NM_006304		A	96324128	T	A	96324128	3	1	80	1	0	0	0	0	1	0	0	0	14293	1667	58	4	68	4	SHFM1	7	96324128	Missense_Mutation	SNP	T	TCGA-CC-A8HU-01A-11D-A35Z-10	62378856	96324128	62814535	34	10996										
LHFPL3	375612	hgsc.bcm.edu	37	chr7	103969251	103969251	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	cccggagccgccgccgctgcCgccgccgccgccgccgcgat	14	23	0	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr7:103969251C>T	ENST00000535008.1	+	1	148	c.24C>T	c.(22-24)gcC>gcT	p.A8A	LHFPL3_ENST00000543266.1_Silent_p.A8A|LHFPL3_ENST00000424859.1_5'UTR|LHFPL3_ENST00000401970.2_5'UTR			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	8						integral component of membrane (GO:0016021)		p.A8A(1)		kidney(1)|large_intestine(2)|lung(6)	9						ccgccgctgccgccgccgccg	0.721																																					p.A8A		Atlas-SNP	.											LHFPL3,NS,carcinoma,0,1	LHFPL3	24	.	1	Substitution - coding silent(1)	kidney(1)	c.C24T						.						11	14	13					7																	103969251		1949	4092	6041	SO:0001819	synonymous_variant	375612	exon1			CGCTGCCGCCGCC	AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416			6589	protein-coding gene	gene with protein product		609719	"lipoma HMGIC fusion partner-like 4"	LHFPL4		10329012	Standard	NM_199000		Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000535008.1:c.24C>T	chr7.hg19:g.103969251C>T		39.0	0.0		38.0	3.0	NM_199000	A1L383|A4D0Q5	Silent	SNP	ENST00000535008.1	hg19																																																																																				.	.		0.721	LHFPL3-201	KNOWN	basic	protein_coding	protein_coding		NM_199000		T	103969251	C	T	103969251	2	4	80	1	0	0	0	0	0	0	0	1	8775	639	23	1		1	LHFPL3	7	103969251	Silent	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	7645123	103969251	55169412	35	10997										
SND1	27044	hgsc.bcm.edu	37	chr7	127347629	127347629	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	aggtttgccaaagagcgcagGctgagaatatggagagacta	14	6	0	3			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr7:127347629G>T	ENST00000354725.3	+	9	1160	c.966G>T	c.(964-966)agG>agT	p.R322S		NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	322	TNase-like 2. {ECO:0000255|PROSITE- ProRule:PRU00272}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)			central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						AAGAGCGCAGGCTGAGAATAT	0.483																																					p.R322S		Atlas-SNP	.											.	SND1	104	.	0			c.G966T						.						130	116	121					7																	127347629		2203	4300	6503	SO:0001583	missense	27044	exon9			GCGCAGGCTGAGA		CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"Tudor domain containing"	30646	protein-coding gene	gene with protein product	"p100 EBNA2 co-activator", "Tudor-SN"	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.966G>T	chr7.hg19:g.127347629G>T	ENSP00000346762:p.Arg322Ser	93.0	0.0		110.0	17.0	NM_014390	Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	hg19	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.846359	0.71603	.	.	ENSG00000197157	ENST00000354725;ENST00000438400	T	0.34275	1.37	5.29	4.39	0.52855	Staphylococcal nuclease (SNase-like) (4);Staphylococcal nuclease (SNase-like), OB-fold (1);	0.186986	0.56097	D	0.000037	T	0.53270	0.1786	M	0.85710	2.77	0.49213	D	0.999761	B	0.27166	0.17	B	0.42593	0.392	T	0.60347	-0.7281	10	0.72032	D	0.01	-17.4254	12.4975	0.55937	0.0873:0.0:0.9127:0.0	.	322	Q7KZF4	SND1_HUMAN	S	322;312	ENSP00000346762:R322S	ENSP00000346762:R322S	R	+	3	2	SND1	127134865	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.106000	0.41835	2.621000	0.88768	0.557000	0.71058	AGG	.	.		0.483	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390		T	127347629	G	T	127347629	3	4	80	1	0	0	0	0	1	0	0	0	14859	1194	42	3	1000	3	SND1	7	127347629	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	23378378	127347629	31791034	36	10998										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131848926	131848926	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ttttgtagtcaatctgctggCggatgagcttgtcctcgctc	11	10	2	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr7:131848926C>T	ENST00000359827.3	-	24	5437	c.4475G>A	c.(4474-4476)cGc>cAc	p.R1492H	PLXNA4_ENST00000321063.4_Missense_Mutation_p.R1492H			Q9HCM2	PLXA4_HUMAN	plexin A4	1492					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						AATCTGCTGGCGGATGAGCTT	0.602																																					p.R1492H		Atlas-SNP	.											PLXNA4_ENST00000359827,NS,carcinoma,0,2	PLXNA4	873	.	0			c.G4475A						.						79	88	85					7																	131848926		2203	4300	6503	SO:0001583	missense	91584	exon24			TGCTGGCGGATGA	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.4475G>A	chr7.hg19:g.131848926C>T	ENSP00000352882:p.Arg1492His	94.0	0.0		98.0	23.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	35	5.484409	0.96323	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.15487	2.42;2.42	5.45	5.45	0.79879	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.51278	0.1665	M	0.88241	2.94	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.58645	-0.7600	10	0.59425	D	0.04	.	19.3079	0.94171	0.0:1.0:0.0:0.0	.	1492	Q9HCM2	PLXA4_HUMAN	H	1492	ENSP00000323194:R1492H;ENSP00000352882:R1492H	ENSP00000323194:R1492H	R	-	2	0	PLXNA4	131499466	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.550000	0.86006	0.655000	0.94253	CGC	.	.		0.602	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131848926	C	T	131848926	3	4	80	1	0	0	0	0	1	0	0	0	12131	768	27	1	1245	1	PLXNA4	7	131848926	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	4501297	131848926	27289737	37	10999										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2813254	2813254	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gatcgatggctctcacatccGcgtgtgccggggtttctggc	14	12	2	0	rs534317062		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr8:2813254G>C	ENST00000520002.1	-	65	10409	c.9854C>G	c.(9853-9855)gCg>gGg	p.A3285G	CSMD1_ENST00000400186.3_Missense_Mutation_p.A3108G|CSMD1_ENST00000537824.1_Missense_Mutation_p.A3284G|CSMD1_ENST00000602723.1_Missense_Mutation_p.A3108G|CSMD1_ENST00000602557.1_Missense_Mutation_p.A3285G|CSMD1_ENST00000542608.1_Missense_Mutation_p.A3107G			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3285	Sushi 28. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TCTCACATCCGCGTGTGCCGG	0.483																																					p.A3284G		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C9851G						.						132	130	131					8																	2813254		1965	4164	6129	SO:0001583	missense	64478	exon64			ACATCCGCGTGTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9854C>G	chr8.hg19:g.2813254G>C	ENSP00000430733:p.Ala3285Gly	144.0	0.0		50.0	41.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	G	1.772	-0.484170	0.04383	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T;T;T;T	0.35421	1.31;1.31;1.31;1.31	5.64	5.64	0.86602	Complement control module (2);Sushi/SCR/CCP (3);	0.088045	0.48767	D	0.000178	T	0.35038	0.0918	N	0.05158	-0.105	0.80722	D	1	D;P;B	0.76494	0.999;0.498;0.304	D;P;B	0.83275	0.996;0.624;0.429	T	0.22765	-1.0207	10	0.25751	T	0.34	.	10.7635	0.46279	0.1147:0.0:0.8853:0.0	.	3285;3285;3107	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	G	3108;3285;3146;3284;3107	ENSP00000383047:A3108G;ENSP00000430733:A3285G;ENSP00000441462:A3284G;ENSP00000446243:A3107G	ENSP00000320445:A3146G	A	-	2	0	CSMD1	2800661	0.922000	0.31269	0.156000	0.22583	0.011000	0.07611	3.114000	0.50383	2.656000	0.90262	0.460000	0.39030	GCG	.	.		0.483	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		C	2813254	G	C	2813254	3	2	80	1	0	0	0	0	1	0	0	0	3946	1087	38	4	871	4	CSMD1	8	2813254	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10		2813254	143550768	38	11000										
TMEM74	157753	hgsc.bcm.edu	37	chr8	109796520	109796520	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	accatagagttttgcagactCtttggaagaggcaaatctgt	10	7	2	3			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr8:109796520C>T	ENST00000297459.3	-	2	986	c.808G>A	c.(808-810)Gag>Aag	p.E270K	TMEM74_ENST00000518838.1_Intron	NM_153015.1	NP_694560.1	Q96NL1	TMM74_HUMAN	transmembrane protein 74	270					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)			TTTGCAGACTCTTTGGAAGAG	0.493																																					p.E270K		Atlas-SNP	.											.	TMEM74	70	.	0			c.G808A						.						87	84	85					8																	109796520		2203	4300	6503	SO:0001583	missense	157753	exon2			CAGACTCTTTGGA	AK055230	CCDS6310.1	8q23.1	2009-11-06				ENSG00000164841			26409	protein-coding gene	gene with protein product		613935				12477932	Standard	NM_153015		Approved	FLJ30668, NET36	uc003ymy.1	Q96NL1		ENST00000297459.3:c.808G>A	chr8.hg19:g.109796520C>T	ENSP00000297459:p.Glu270Lys	237.0	0.0		144.0	14.0	NM_153015		Missense_Mutation	SNP	ENST00000297459.3	hg19	CCDS6310.1	.	.	.	.	.	.	.	.	.	.	C	19.10	3.760950	0.69763	.	.	ENSG00000164841	ENST00000297459	.	.	.	5.93	5.93	0.95920	.	0.288210	0.39687	N	0.001298	T	0.56307	0.1976	L	0.51422	1.61	0.46678	D	0.999155	P	0.45531	0.86	B	0.41510	0.359	T	0.51545	-0.8692	9	0.25106	T	0.35	-15.4478	20.3404	0.98760	0.0:1.0:0.0:0.0	.	270	Q96NL1	TMM74_HUMAN	K	270	.	ENSP00000297459:E270K	E	-	1	0	TMEM74	109865696	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.879000	0.63100	2.812000	0.96745	0.637000	0.83480	GAG	.	.		0.493	TMEM74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380755.1	NM_153015		T	109796520	C	T	109796520	3	4	80	1	0	0	0	0	1	0	0	0	16217	922	32	3	113	3	TMEM74	8	109796520	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	106983266	109796520	36567502	39	11001										
C9orf172	389813	hgsc.bcm.edu	37	chr9	139739752	139739752	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gcttccggggcagctttgcaGccagtcccggcccaaccttc	11	17	0	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr9:139739752G>T	ENST00000436881.1	+	1	886	c.886G>T	c.(886-888)Gcc>Tcc	p.A296S		NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	296	Pro-rich.									endometrium(2)|large_intestine(1)|lung(6)	9						CAGCTTTGCAGCCAGTCCCGG	0.682																																					p.A296S		Atlas-SNP	.											.	C9orf172	23	.	0			c.G886T						.						16	17	17					9																	139739752		1885	4094	5979	SO:0001583	missense	389813	exon1			TTTGCAGCCAGTC		CCDS48059.1	9q34.3	2012-04-03			ENSG00000232434	ENSG00000232434			37284	protein-coding gene	gene with protein product							Standard	NM_001080482		Approved		uc011meh.2	C9J069		ENST00000436881.1:c.886G>T	chr9.hg19:g.139739752G>T	ENSP00000412388:p.Ala296Ser	99.0	0.0		51.0	47.0	NM_001080482		Missense_Mutation	SNP	ENST00000436881.1	hg19	CCDS48059.1	.	.	.	.	.	.	.	.	.	.	.	0.011	-1.706190	0.00719	.	.	ENSG00000232434	ENST00000436881	.	.	.	3.61	1.62	0.23740	.	.	.	.	.	T	0.17704	0.0425	N	0.19112	0.55	0.09310	N	1	B	0.17038	0.02	B	0.14023	0.01	T	0.31024	-0.9958	8	0.07030	T	0.85	.	5.5261	0.16959	0.3703:0.0:0.6297:0.0	.	296	C9J069	CI172_HUMAN	S	296	.	ENSP00000412388:A296S	A	+	1	0	C9orf172	138859573	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.322000	0.19576	0.592000	0.29728	0.442000	0.29010	GCC	.	.		0.682	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482		T	139739752	G	T	139739752	3	4	80	1	0	0	0	0	1	0	0	0	2473	971	34	3	888	3	C9orf172	9	139739752	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10		139739752	1473679	40	11002										
RBM17	84991	hgsc.bcm.edu	37	chr10	6154319	6154319	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	catcgtgggcgacgccacagAgaaaggtgtgtccccaggga	15	11	0	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr10:6154319A>G	ENST00000446108.1	+	8	1495	c.851A>G	c.(850-852)gAg>gGg	p.E284G	RBM17_ENST00000379888.4_Missense_Mutation_p.E284G	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17	284					alternative mRNA splicing, via spliceosome (GO:0000380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	19						GACGCCACAGAGAAAGGTGTG	0.597																																					p.E284G		Atlas-SNP	.											.	RBM17	45	.	0			c.A851G						.						40	33	36					10																	6154319		2203	4300	6503	SO:0001583	missense	84991	exon8			CCACAGAGAAAGG	AF083384	CCDS7077.1	10p15.1	2013-01-28			ENSG00000134453	ENSG00000134453		"RNA binding motif (RRM) containing", "G patch domain containing"	16944	protein-coding gene	gene with protein product	"splicing factor 45kDa"	606935				9731529	Standard	NM_032905		Approved	SPF45, MGC14439	uc001ijb.3	Q96I25	OTTHUMG00000017618	ENST00000446108.1:c.851A>G	chr10.hg19:g.6154319A>G	ENSP00000388638:p.Glu284Gly	111.0	0.0		192.0	76.0	NM_001145547	Q96GY6	Missense_Mutation	SNP	ENST00000446108.1	hg19	CCDS7077.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.17|16.17	3.046183|3.046183	0.55110|0.55110	.|.	.|.	ENSG00000134453|ENSG00000134453	ENST00000379888;ENST00000446108|ENST00000447032	.|.	.|.	.|.	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	0.046083|.	0.85682|.	D|.	0.000000|.	T|T	0.55847|0.55847	0.1946|0.1946	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	B|.	0.26002|.	0.139|.	B|.	0.21360|.	0.034|.	T|T	0.52548|0.52548	-0.8561|-0.8561	9|5	0.22109|.	T|.	0.4|.	-31.0153|-31.0153	15.7261|15.7261	0.77761|0.77761	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	284|.	Q96I25|.	SPF45_HUMAN|.	G|G	284|191	.|.	ENSP00000369218:E284G|.	E|R	+|+	2|1	0|2	RBM17|RBM17	6194325|6194325	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.337000|0.337000	0.28794|0.28794	9.036000|9.036000	0.93758|0.93758	2.119000|2.119000	0.64992|0.64992	0.379000|0.379000	0.24179|0.24179	GAG|AGA	.	.		0.597	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905		G	6154319	A	G	6154319	3	3	80	1	0	0	0	0	1	0	0	0	13134	304	11	2	877	2	RBM17	10	6154319	Missense_Mutation	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10		6154319	129380428	41	11003										
PTPLA	9200	hgsc.bcm.edu	37	chr10	17636234	17636234	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	tgatgccatggttataagaaGaaaataatagtagtcaaaag	9	3	1	3			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr10:17636234G>T	ENST00000361271.3	-	6	791	c.754C>A	c.(754-756)Ctt>Att	p.L252I		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	252					fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						GTTATAAGAAGAAAATAATAG	0.289																																					p.L252I		Atlas-SNP	.											PTPLA,NS,carcinoma,0,1	PTPLA	34	.	0			c.C754A						.						58	61	60					10																	17636234		2202	4295	6497	SO:0001583	missense	9200	exon6			TAAGAAGAAAATA	AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"cementum attachment protein"	610467	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.754C>A	chr10.hg19:g.17636234G>T	ENSP00000355308:p.Leu252Ile	357.0	0.0		487.0	160.0	NM_014241	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Missense_Mutation	SNP	ENST00000361271.3	hg19	CCDS7121.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.892142	0.91889	.	.	ENSG00000165996	ENST00000361271	T	0.36340	1.26	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.57154	0.2034	M	0.72353	2.195	0.80722	D	1	P	0.46859	0.885	P	0.55222	0.771	T	0.55667	-0.8105	10	0.59425	D	0.04	-21.2146	20.2406	0.98372	0.0:0.0:1.0:0.0	.	252	B0YJ81	HACD1_HUMAN	I	252	ENSP00000355308:L252I	ENSP00000355308:L252I	L	-	1	0	PTPLA	17676240	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.846000	0.99502	2.857000	0.98124	0.650000	0.86243	CTT	.	.		0.289	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241		T	17636234	G	T	17636234	3	4	80	1	0	0	0	0	1	0	0	0	12787	942	33	3	120	3	PTPLA	10	17636234	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	11481915	17636234	117898513	42	11004										
RHOBTB1	9886	hgsc.bcm.edu	37	chr10	62648855	62648855	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	cttgataccaaactggtcaaAcacgcttgtttcatagtatg	7	9	2	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr10:62648855A>G	ENST00000337910.5	-	6	908	c.571T>C	c.(571-573)Ttt>Ctt	p.F191L	RHOBTB1_ENST00000357917.4_Missense_Mutation_p.F191L	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	191	Rho-like.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					AACTGGTCAAACACGCTTGTT	0.463																																					p.F191L		Atlas-SNP	.											.	RHOBTB1	61	.	0			c.T571C						.						143	142	142					10																	62648855		2203	4300	6503	SO:0001583	missense	9886	exon6			GGTCAAACACGCT	AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"BTB/POZ domain containing"	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.571T>C	chr10.hg19:g.62648855A>G	ENSP00000338671:p.Phe191Leu	99.0	0.0		62.0	22.0	NM_014836		Missense_Mutation	SNP	ENST00000337910.5	hg19	CCDS7261.1	.	.	.	.	.	.	.	.	.	.	A	17.61	3.433077	0.62844	.	.	ENSG00000072422	ENST00000357917;ENST00000337910	T;T	0.75367	-0.93;-0.93	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.40196	0.1107	N	0.00339	-1.615	0.80722	D	1	B	0.15930	0.015	B	0.23419	0.046	T	0.55711	-0.8098	10	0.02654	T	1	.	16.1026	0.81194	1.0:0.0:0.0:0.0	.	191	O94844	RHBT1_HUMAN	L	191	ENSP00000350595:F191L;ENSP00000338671:F191L	ENSP00000338671:F191L	F	-	1	0	RHOBTB1	62318861	1.000000	0.71417	0.940000	0.37924	0.969000	0.65631	5.738000	0.68613	2.198000	0.70561	0.383000	0.25322	TTT	.	.		0.463	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			G	62648855	A	G	62648855	3	3	80	1	0	0	0	0	1	0	0	0	13348	43	2	2	1543	2	RHOBTB1	10	62648855	Missense_Mutation	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	45012621	62648855	72885892	43	11005										
PLCE1	51196	hgsc.bcm.edu	37	chr10	96066392	96066392	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ttttgcagttgtggaaaacaAtagttcagcggtaactgctc	10	7	1	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr10:96066392A>G	ENST00000371380.3	+	25	6066	c.5831A>G	c.(5830-5832)aAt>aGt	p.N1944S	PLCE1_ENST00000371385.3_Missense_Mutation_p.N1636S|PLCE1_ENST00000260766.3_Missense_Mutation_p.N1944S|PLCE1_ENST00000371375.1_Missense_Mutation_p.N1636S			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1944	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				GTGGAAAACAATAGTTCAGCG	0.393																																					p.N1944S		Atlas-SNP	.											.	PLCE1	543	.	0			c.A5831G						.						104	93	96					10																	96066392		1895	4140	6035	SO:0001583	missense	51196	exon26			AAAACAATAGTTC		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.5831A>G	chr10.hg19:g.96066392A>G	ENSP00000360431:p.Asn1944Ser	119.0	0.0		79.0	14.0	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	hg19	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	A	19.12	3.766322	0.69878	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.13538	2.58;2.58;2.58;2.58	5.43	5.43	0.79202	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.22627	0.0546	N	0.20845	0.615	0.41657	D	0.989164	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.87578	0.998;0.995;0.988	T	0.08006	-1.0743	10	0.27082	T	0.32	.	15.4603	0.75349	1.0:0.0:0.0:0.0	.	1928;1636;1944	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	S	1944;1944;1636;1636	ENSP00000260766:N1944S;ENSP00000360431:N1944S;ENSP00000360438:N1636S;ENSP00000360426:N1636S	ENSP00000260766:N1944S	N	+	2	0	PLCE1	96056382	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	6.237000	0.72345	2.197000	0.70478	0.533000	0.62120	AAT	.	.		0.393	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		G	96066392	A	G	96066392	3	3	80	1	0	0	0	0	1	0	0	0	12043	101	4	2	6215	2	PLCE1	10	96066392	Missense_Mutation	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	33417537	96066392	39468355	44	11006										
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26734192	26734192	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	agccatgaccacttaccgtcTgtacaatgtagatgaccgtg	9	11	1	3			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr11:26734192T>C	ENST00000396005.3	-	2	710	c.401A>G	c.(400-402)cAg>cGg	p.Q134R	SLC5A12_ENST00000280467.6_Missense_Mutation_p.Q134R	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	134					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						ACTTACCGTCTGTACAATGTA	0.423																																					p.Q134R		Atlas-SNP	.											SLC5A12_ENST00000280467,right_upper_lobe,carcinoma,0,2	SLC5A12	134	.	0			c.A401G						.						333	285	301					11																	26734192		2203	4299	6502	SO:0001583	missense	159963	exon2			ACCGTCTGTACAA	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.401A>G	chr11.hg19:g.26734192T>C	ENSP00000379326:p.Gln134Arg	114.0	0.0		79.0	37.0	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	hg19	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	T	27.0	4.787648	0.90367	.	.	ENSG00000148942	ENST00000396005;ENST00000280467	D;D	0.87650	-2.28;-2.28	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.92893	0.7739	M	0.77486	2.375	0.80722	D	1	D;D	0.71674	0.961;0.998	P;D	0.70487	0.823;0.969	D	0.93529	0.6868	10	0.59425	D	0.04	.	15.2167	0.73274	0.0:0.0:0.0:1.0	.	134;134	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	R	134	ENSP00000379326:Q134R;ENSP00000280467:Q134R	ENSP00000280467:Q134R	Q	-	2	0	SLC5A12	26690768	1.000000	0.71417	0.995000	0.50966	0.923000	0.55619	7.655000	0.83696	2.040000	0.60383	0.533000	0.62120	CAG	.	.		0.423	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		C	26734192	T	C	26734192	3	2	80	1	0	0	0	0	1	0	0	0	14679	1580	55	2	1511	2	SLC5A12	11	26734192	Missense_Mutation	SNP	T	TCGA-CC-A8HU-01A-11D-A35Z-10		26734192	108272324	45	11007										
GYLTL1B	120071	hgsc.bcm.edu	37	chr11	45949843	45949843	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	aaccctacgtggtggtgccaCgagactgtccccgctatgat	11	13	0	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr11:45949843C>T	ENST00000531526.1	+	13	1981	c.1870C>T	c.(1870-1872)Cga>Tga	p.R624*	GYLTL1B_ENST00000325468.5_Nonsense_Mutation_p.R624*|GYLTL1B_ENST00000529052.1_Nonsense_Mutation_p.R593*|GYLTL1B_ENST00000401752.1_Nonsense_Mutation_p.R624*|GYLTL1B_ENST00000536139.1_Nonsense_Mutation_p.R593*	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	624					muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		GGTGGTGCCACGAGACTGTCC	0.637																																					p.R624X		Atlas-SNP	.											.	GYLTL1B	45	.	0			c.C1870T						.						173	167	169					11																	45949843		2203	4299	6502	SO:0001587	stop_gained	120071	exon13			GTGCCACGAGACT		CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"Glycosyltransferase family 8 domain containing"	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.1870C>T	chr11.hg19:g.45949843C>T	ENSP00000432869:p.Arg624*	115.0	0.0		82.0	46.0	NM_152312	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Nonsense_Mutation	SNP	ENST00000531526.1	hg19	CCDS31473.1	.	.	.	.	.	.	.	.	.	.	C	38	6.657050	0.97739	.	.	ENSG00000165905	ENST00000529052;ENST00000531526;ENST00000401752;ENST00000325468;ENST00000536139	.	.	.	5.57	2.41	0.29592	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.2775	14.0692	0.64851	0.3941:0.6059:0.0:0.0	.	.	.	.	X	593;624;624;624;593	.	ENSP00000324570:R624X	R	+	1	2	GYLTL1B	45906419	0.323000	0.24643	0.170000	0.22879	0.747000	0.42532	0.938000	0.28965	0.656000	0.30886	0.561000	0.74099	CGA	.	.		0.637	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312		T	45949843	C	T	45949843	4	4	80	1	0	0	0	0	0	1	0	0	6916	528	19	1	1916	1	GYLTL1B	11	45949843	Nonsense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	19215651	45949843	89056673	46	11008										
KRTAP5-10	387273	hgsc.bcm.edu	37	chr11	71277043	71277043	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	caaggggggctgtggttcttGtggctgctcccagtgcaatt	15	9	1	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr11:71277043G>T	ENST00000398531.1	+	1	435	c.410G>T	c.(409-411)tGt>tTt	p.C137F	KRTAP5-10_ENST00000376536.4_Missense_Mutation_p.C89F	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	137	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						TGTGGTTCTTGTGGCTGCTCC	0.637																																					p.C137F		Atlas-SNP	.											.	KRTAP5-10	37	.	0			c.G410T						.						85	112	103					11																	71277043		2199	4292	6491	SO:0001583	missense	387273	exon1			GTTCTTGTGGCTG	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"Keratin associated proteins"	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.410G>T	chr11.hg19:g.71277043G>T	ENSP00000381542:p.Cys137Phe	184.0	0.0		70.0	39.0	NM_001012710	B9EHA4	Missense_Mutation	SNP	ENST00000398531.1	hg19	CCDS41684.1	.	.	.	.	.	.	.	.	.	.	.	3.585	-0.084715	0.07097	.	.	ENSG00000204572	ENST00000398531;ENST00000376536	T;T	0.01113	5.32;5.53	1.95	1.95	0.26073	.	.	.	.	.	T	0.01421	0.0046	L	0.56199	1.76	0.21527	N	0.999652	B	0.33549	0.417	B	0.30646	0.118	T	0.45352	-0.9267	9	0.72032	D	0.01	.	4.4788	0.11757	0.1965:0.0:0.8035:0.0	.	137	Q6L8G5	KR510_HUMAN	F	137;89	ENSP00000381542:C137F;ENSP00000365719:C89F	ENSP00000365719:C89F	C	+	2	0	KRTAP5-10	70954691	0.015000	0.18098	0.783000	0.31826	0.129000	0.20672	1.589000	0.36644	1.415000	0.47037	0.467000	0.42956	TGT	.	.		0.637	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2			T	71277043	G	T	71277043	3	4	80	1	0	0	0	0	1	0	0	0	8568	1377	48	3	412	3	KRTAP5-10	11	71277043	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	25327200	71277043	63729473	47	11009										
KLHL35	283212	hgsc.bcm.edu	37	chr11	75139638	75139638	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	cctttgcggtcgcaaccgccGatgaccacgatcacttcagc	9	16	2	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr11:75139638G>T	ENST00000539798.1	-	2	914	c.915C>A	c.(913-915)atC>atA	p.I305I	KLHL35_ENST00000376292.4_Silent_p.I85I	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	305										lung(2)|stomach(1)	3						CGCAACCGCCGATGACCACGA	0.627																																					p.I305I	Colon(77;683 1691 18820 23811)	Atlas-SNP	.											.	KLHL35	15	.	0			c.C915A						.						36	42	40					11																	75139638		2015	4139	6154	SO:0001819	synonymous_variant	283212	exon2			ACCGCCGATGACC		CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"Kelch-like", "BTB/POZ domain containing"	26597	protein-coding gene	gene with protein product			"kelch-like 35 (Drosophila)"				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.915C>A	chr11.hg19:g.75139638G>T		48.0	0.0		18.0	16.0	NM_001039548	A2RU06|F5H412|Q86XM7|Q8NBB1	Silent	SNP	ENST00000539798.1	hg19	CCDS44685.2																																																																																			.	.		0.627	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583		T	75139638	G	T	75139638	2	4	80	1	0	0	0	0	0	0	0	1	8397	1048	37	1		1	KLHL35	11	75139638	Silent	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	3862595	75139638	59866878	48	11010										
FAT3	120114	hgsc.bcm.edu	37	chr11	92532846	92532846	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	aaggcatcatatatatcattAtcgatggggacccttttaaa	7	7	2	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr11:92532846A>T	ENST00000298047.6	+	9	6684	c.6667A>T	c.(6667-6669)Atc>Ttc	p.I2223F	FAT3_ENST00000525166.1_Missense_Mutation_p.I2073F|FAT3_ENST00000409404.2_Missense_Mutation_p.I2223F			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2223	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ATATATCATTATCGATGGGGA	0.408										TCGA Ovarian(4;0.039)																											p.I2223F		Atlas-SNP	.											.	FAT3	1822	.	0			c.A6667T						.						49	47	48					11																	92532846		1923	4140	6063	SO:0001583	missense	120114	exon9			ATCATTATCGATG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.6667A>T	chr11.hg19:g.92532846A>T	ENSP00000298047:p.Ile2223Phe	63.0	0.0		35.0	26.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	A	11.26	1.586369	0.28268	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.53423	0.62;0.62;0.62	6.16	3.65	0.41850	.	.	.	.	.	T	0.45915	0.1366	M	0.71036	2.16	0.49798	D	0.999822	B	0.31383	0.321	B	0.38225	0.268	T	0.32798	-0.9893	9	0.27082	T	0.32	.	5.2285	0.15408	0.4837:0.0:0.5163:0.0	.	2223	Q8TDW7-3	.	F	2223;2223;2073	ENSP00000298047:I2223F;ENSP00000387040:I2223F;ENSP00000432586:I2073F	ENSP00000298047:I2223F	I	+	1	0	FAT3	92172494	0.997000	0.39634	0.785000	0.31869	0.862000	0.49288	3.510000	0.53393	1.016000	0.39470	0.528000	0.53228	ATC	.	.		0.408	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92532846	A	T	92532846	3	4	80	1	0	0	0	0	1	0	0	0	5699	449	16	4	6701	4	FAT3	11	92532846	Missense_Mutation	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	17393208	92532846	42473670	49	11011										
GUCY1A2	2977	hgsc.bcm.edu	37	chr11	106810453	106810453	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	atgctaattctgaggtccgcAggaacttgggaggttccctg	13	9	1	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr11:106810453A>T	ENST00000526355.2	-	4	1407	c.939T>A	c.(937-939)ccT>ccA	p.P313P	GUCY1A2_ENST00000347596.2_Silent_p.P313P|GUCY1A2_ENST00000282249.2_Silent_p.P313P	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	313					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	TGAGGTCCGCAGGAACTTGGG	0.438																																					p.P313P		Atlas-SNP	.											.	GUCY1A2	180	.	0			c.T939A						.						78	73	75					11																	106810453		2201	4298	6499	SO:0001819	synonymous_variant	2977	exon4			GTCCGCAGGAACT	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.939T>A	chr11.hg19:g.106810453A>T		129.0	0.0		61.0	49.0	NM_000855	A1L4C4|B7ZLT5	Silent	SNP	ENST00000526355.2	hg19	CCDS8335.1																																																																																			.	.		0.438	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			T	106810453	A	T	106810453	2	4	80	1	0	0	0	0	0	0	0	1	6902	175	7	4		4	GUCY1A2	11	106810453	Silent	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	14277607	106810453	28196063	50	11012										
ELMOD1	55531	hgsc.bcm.edu	37	chr11	107526740	107526740	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ggagctctaaaaacccatttCtacaatatcgccccagaagc	6	13	2	1	rs190625125		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr11:107526740C>G	ENST00000265840.7	+	11	1045	c.780C>G	c.(778-780)ttC>ttG	p.F260L	ELMOD1_ENST00000531234.1_Missense_Mutation_p.F254L|ELMOD1_ENST00000443271.2_Missense_Mutation_p.F252L	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	260	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)	cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)			endometrium(2)|large_intestine(5)|liver(2)|lung(7)|pancreas(2)|prostate(1)	19		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		AAACCCATTTCTACAATATCG	0.388																																					p.F260L		Atlas-SNP	.											ELMOD1,NS,carcinoma,0,1	ELMOD1	40	.	0			c.C780G						.						94	87	89					11																	107526740		1867	4090	5957	SO:0001583	missense	55531	exon11			CCATTTCTACAAT	AL359601	CCDS44723.1, CCDS44724.1	11q23.1	2012-10-15	2006-01-20		ENSG00000110675	ENSG00000110675			25334	protein-coding gene	gene with protein product		615456	"ELMO domain containing 1"			12477932	Standard	NM_018712		Approved	DKFZp547C176	uc010rvs.2	Q8N336	OTTHUMG00000166361	ENST00000265840.7:c.780C>G	chr11.hg19:g.107526740C>G	ENSP00000265840:p.Phe260Leu	81.0	0.0		28.0	25.0	NM_018712	B4E167|G5E9S5|Q9NPW3	Missense_Mutation	SNP	ENST00000265840.7	hg19	CCDS44723.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.914298	0.52546	.	.	ENSG00000110675	ENST00000531234;ENST00000265840;ENST00000443271	T;T;T	0.27557	1.66;1.66;1.66	6.16	6.16	0.99307	Engulfment/cell motility, ELMO (2);	0.071070	0.64402	D	0.000001	T	0.25827	0.0629	N	0.20766	0.605	0.53688	D	0.999977	B;B	0.20052	0.041;0.018	B;B	0.24269	0.052;0.024	T	0.04693	-1.0933	10	0.25106	T	0.35	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	260;252	Q8N336;G5E9S5	ELMD1_HUMAN;.	L	254;260;252	ENSP00000433232:F254L;ENSP00000265840:F260L;ENSP00000412257:F252L	ENSP00000265840:F260L	F	+	3	2	ELMOD1	107031950	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.215000	0.51169	2.937000	0.99478	0.650000	0.86243	TTC	.	C|1.000;T|0.000		0.388	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389406.1	NM_018712		G	107526740	C	G	107526740	3	3	80	1	0	0	0	0	1	0	0	0	5070	912	32	4	818	4	ELMOD1	11	107526740	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	716287	107526740	27479776	51	11013										
ABCG4	64137	hgsc.bcm.edu	37	chr11	119025505	119025505	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	agagatcctgacggcactggGcctgatgtcgtgctcccaca	12	13	0	3			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr11:119025505G>T	ENST00000449422.2	+	6	754	c.566G>T	c.(565-567)gGc>gTc	p.G189V	ABCG4_ENST00000531739.1_Missense_Mutation_p.G189V|ABCG4_ENST00000307417.3_Missense_Mutation_p.G189V	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	189	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		ACGGCACTGGGCCTGATGTCG	0.642																																					p.G189V		Atlas-SNP	.											.	ABCG4	77	.	0			c.G566T						.						98	92	94					11																	119025505		2200	4295	6495	SO:0001583	missense	64137	exon6			CACTGGGCCTGAT	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"ATP binding cassette transporters / subfamily G"	13884	protein-coding gene	gene with protein product	"putative ABC transporter", "ATP-binding cassette, subfamily G, member 4"	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.566G>T	chr11.hg19:g.119025505G>T	ENSP00000406874:p.Gly189Val	87.0	0.0		33.0	29.0	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.542891	0.86022	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739	D;D;D	0.95238	-3.65;-3.65;-3.65	5.11	4.13	0.48395	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.050273	0.85682	D	0.000000	D	0.98378	0.9461	H	0.99286	4.5	0.80722	D	1	D	0.67145	0.996	D	0.68765	0.96	D	0.98891	1.0773	10	0.87932	D	0	-19.0063	14.3175	0.66463	0.0:0.0:0.8509:0.1491	.	189	Q9H172	ABCG4_HUMAN	V	189	ENSP00000304111:G189V;ENSP00000406874:G189V;ENSP00000434318:G189V	ENSP00000304111:G189V	G	+	2	0	ABCG4	118530715	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.918000	0.87506	2.386000	0.81285	0.491000	0.48974	GGC	.	.		0.642	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		T	119025505	G	T	119025505	3	4	80	1	0	0	0	0	1	0	0	0	70	1203	42	3	584	3	ABCG4	11	119025505	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	11498765	119025505	15981011	52	11014										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133794761	133794761	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ctgggctcgctgatcagatcCtgcatgacggccagaacccg	12	14	1	4			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr11:133794761C>T	ENST00000321016.8	-	15	2303	c.2073G>A	c.(2071-2073)caG>caA	p.Q691Q	IGSF9B_ENST00000533871.2_Silent_p.Q691Q			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	691	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		TGATCAGATCCTGCATGACGG	0.587																																					p.Q691Q		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G2073A						.						113	123	119					11																	133794761		2089	4217	6306	SO:0001819	synonymous_variant	22997	exon15			CAGATCCTGCATG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.2073G>A	chr11.hg19:g.133794761C>T		46.0	0.0		15.0	13.0	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	hg19																																																																																				.	.		0.587	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		T	133794761	C	T	133794761	2	4	80	1	0	0	0	0	0	0	0	1	7615	680	24	3		3	IGSF9B	11	133794761	Silent	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	14769256	133794761	1211755	53	11015										
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94692459	94692459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ttagaagcatttggagtttaCccaacagcagagctccattt	8	9	0	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr12:94692459C>T	ENST00000258526.4	+	27	4375	c.4126C>T	c.(4126-4128)Ccc>Tcc	p.P1376S	PLXNC1_ENST00000547057.1_Missense_Mutation_p.P423S|PLXNC1_ENST00000545312.1_Missense_Mutation_p.P115S	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1376					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TTGGAGTTTACCCAACAGCAG	0.373																																					p.P1376S		Atlas-SNP	.											.	PLXNC1	135	.	0			c.C4126T						.						72	74	73					12																	94692459		2203	4300	6503	SO:0001583	missense	10154	exon27			AGTTTACCCAACA	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.4126C>T	chr12.hg19:g.94692459C>T	ENSP00000258526:p.Pro1376Ser	155.0	0.0		169.0	32.0	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.365118	0.41902	.	.	ENSG00000136040	ENST00000258526;ENST00000547057;ENST00000545312	T;T;T	0.15487	2.42;2.42;2.42	5.95	5.95	0.96441	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.051093	0.85682	D	0.000000	T	0.31606	0.0802	L	0.35288	1.05	0.80722	D	1	P;D	0.61697	0.573;0.99	P;D	0.71870	0.46;0.975	T	0.01205	-1.1419	10	0.16896	T	0.51	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	423;1376	B4DHQ7;O60486	.;PLXC1_HUMAN	S	1376;423;115	ENSP00000258526:P1376S;ENSP00000446720:P423S;ENSP00000439225:P115S	ENSP00000258526:P1376S	P	+	1	0	PLXNC1	93216590	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.991000	0.56973	2.824000	0.97209	0.655000	0.94253	CCC	.	.		0.373	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			T	94692459	C	T	94692459	3	4	80	1	0	0	0	0	1	0	0	0	12135	507	18	3	4232	3	PLXNC1	12	94692459	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10		94692459	39159436	54	11016										
N6AMT2	221143	hgsc.bcm.edu	37	chr13	21306081	21306081	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gaggatctgctattacgatgTcaaaactatgtgcagcaatt	9	7	2	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr13:21306081T>A	ENST00000382758.1	-	4	454	c.407A>T	c.(406-408)gAc>gTc	p.D136V	N6AMT2_ENST00000382754.4_Missense_Mutation_p.D136V			Q8WVE0	N6MT2_HUMAN	N-6 adenine-specific DNA methyltransferase 2 (putative)	136						extracellular vesicular exosome (GO:0070062)	methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(3)|lung(3)	7		all_cancers(29;5.91e-19)|all_epithelial(30;1.42e-15)|all_lung(29;5.9e-14)|Lung SC(185;0.0367)		all cancers(112;0.000234)|Epithelial(112;0.000471)|OV - Ovarian serous cystadenocarcinoma(117;0.0111)|Lung(94;0.0161)|LUSC - Lung squamous cell carcinoma(192;0.0431)		TATTACGATGTCAAAACTATG	0.413																																					p.D136V		Atlas-SNP	.											.	N6AMT2	26	.	0			c.A407T						.						133	125	128					13																	21306081		2203	4300	6503	SO:0001583	missense	221143	exon4			ACGATGTCAAAAC	AK055408	CCDS9293.1	13q12.11	2006-12-14			ENSG00000150456	ENSG00000150456			27351	protein-coding gene	gene with protein product						12477932	Standard	NM_174928		Approved		uc001uno.1	Q8WVE0	OTTHUMG00000016519	ENST00000382758.1:c.407A>T	chr13.hg19:g.21306081T>A	ENSP00000372206:p.Asp136Val	109.0	0.0		1065.0	43.0	NM_174928	B5G4V1	Missense_Mutation	SNP	ENST00000382758.1	hg19	CCDS9293.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.195870	0.58126	.	.	ENSG00000150456	ENST00000382758;ENST00000382754	T;T	0.35421	1.31;1.31	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.71426	0.3338	H	0.94264	3.515	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80369	-0.1411	10	0.87932	D	0	.	16.4484	0.83959	0.0:0.0:0.0:1.0	.	136	Q8WVE0	N6MT2_HUMAN	V	136	ENSP00000372206:D136V;ENSP00000372202:D136V	ENSP00000372202:D136V	D	-	2	0	N6AMT2	20204081	1.000000	0.71417	0.873000	0.34254	0.036000	0.12997	7.634000	0.83273	2.285000	0.76669	0.533000	0.62120	GAC	.	.		0.413	N6AMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044083.1	NM_174928		A	21306081	T	A	21306081	3	1	80	1	0	0	0	0	1	0	0	0	10124	1667	58	4	245	4	N6AMT2	13	21306081	Missense_Mutation	SNP	T	TCGA-CC-A8HU-01A-11D-A35Z-10		21306081	93863797	55	11017										
RB1	5925	hgsc.bcm.edu	37	chr13	48881475	48881475	+	Missense_Mutation	SNP	T	T	A													0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	attatgtcagaaattaaagaTaccagatcatgtcagagaga							TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr13:48881475T>A	ENST00000267163.4	+	2	335	c.197T>A	c.(196-198)aTa>aAa	p.I66K		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	66					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(3)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	AAATTAAAGATACCAGATCAT	0.318		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.I66K		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	18	Whole gene deletion(15)|Unknown(3)	bone(10)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|eye(1)|soft_tissue(1)|endometrium(1)|stomach(1)	c.T197A						.						134	137	136					13																	48881475		2203	4300	6503	SO:0001583	missense	5925	exon2	Familial Cancer Database		TAAAGATACCAGA	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.197T>A	chr13.hg19:g.48881475T>A	ENSP00000267163:p.Ile66Lys	195.0	0.0		54.0	41.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.831991	0.50845	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.92965	-3.14	4.83	4.83	0.62350	.	0.941668	0.09031	N	0.858753	D	0.85729	0.5764	N	0.14661	0.345	0.43657	D	0.996079	B	0.23735	0.09	B	0.21360	0.034	T	0.78486	-0.2185	10	0.72032	D	0.01	.	11.0932	0.48128	0.0:0.0:0.0:1.0	.	66	P06400	RB_HUMAN	K	45;66	ENSP00000267163:I66K	ENSP00000267163:I66K	I	+	2	0	RB1	47779476	1.000000	0.71417	0.973000	0.42090	0.981000	0.71138	3.717000	0.54911	1.923000	0.55706	0.528000	0.53228	ATA	.	.		0.318	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			A	48881475	T	A	48881475	3	1	80	1	0	0	0	0	1	0	0	0	13113	1406	49	4	203	4	RB1	13	48881475	Missense_Mutation	SNP	T	TCGA-CC-A8HU-01A-11D-A35Z-10	27575394	48881475	66288403	56	11018	46	2								
RB1	5925	hgsc.bcm.edu	37	chr13	48881477	48881477	+	Missense_Mutation	SNP	C	C	G													0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	tatgtcagaaattaaagataCcagatcatgtcagagagaga							TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr13:48881477C>G	ENST00000267163.4	+	2	337	c.199C>G	c.(199-201)Cca>Gca	p.P67A		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	67					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(3)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	ATTAAAGATACCAGATCATGT	0.318		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.P67A		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	18	Whole gene deletion(15)|Unknown(3)	bone(10)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|eye(1)|soft_tissue(1)|endometrium(1)|stomach(1)	c.C199G						.						135	138	137					13																	48881477		2203	4300	6503	SO:0001583	missense	5925	exon2	Familial Cancer Database		AAGATACCAGATC	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.199C>G	chr13.hg19:g.48881477C>G	ENSP00000267163:p.Pro67Ala	195.0	0.0		54.0	43.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.472402	0.26423	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.91407	-2.84	4.83	3.98	0.46160	.	0.121948	0.56097	D	0.000029	D	0.85111	0.5622	L	0.40543	1.245	0.39844	D	0.973156	B	0.02656	0.0	B	0.01281	0.0	T	0.80417	-0.1391	10	0.36615	T	0.2	.	10.7368	0.46130	0.1906:0.8094:0.0:0.0	.	67	P06400	RB_HUMAN	A	46;67	ENSP00000267163:P67A	ENSP00000267163:P67A	P	+	1	0	RB1	47779478	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	0.529000	0.23019	1.125000	0.41998	-0.188000	0.12872	CCA	.	.		0.318	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	48881477	C	G	48881477	3	3	80	1	0	0	0	0	1	0	0	0	13113	507	18	4	205	4	RB1	13	48881477	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	2	48881477	66288401	57	11019	46	2								
C13orf39	196541	hgsc.bcm.edu	37	chr13	103338746	103338746	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ttgaaggtttcccaggacatCaggcaaatctgttgctgtga	11	8	2	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr13:103338746C>T	ENST00000267273.6	-	4	435	c.430G>A	c.(430-432)Gat>Aat	p.D144N		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	144					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)			breast(1)|large_intestine(3)|lung(2)|skin(1)	7						CCCAGGACATCAGGCAAATCT	0.433																																					p.D144N		Atlas-SNP	.											.	METTL21C	23	.	0			c.G430A						.						58	57	57					13																	103338746		2203	4300	6503	SO:0001583	missense	196541	exon4			GGACATCAGGCAA		CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"chromosome 13 open reading frame 39"	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.430G>A	chr13.hg19:g.103338746C>T	ENSP00000267273:p.Asp144Asn	82.0	0.0		187.0	33.0	NM_001010977		Missense_Mutation	SNP	ENST00000267273.6	hg19	CCDS32003.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.463723	0.63513	.	.	ENSG00000139780	ENST00000267273	T	0.06849	3.25	5.68	5.68	0.88126	.	0.144740	0.64402	D	0.000010	T	0.09555	0.0235	L	0.41356	1.27	0.46521	D	0.999084	B	0.28419	0.211	B	0.30029	0.11	T	0.07139	-1.0788	10	0.54805	T	0.06	-0.9339	13.0479	0.58937	0.0:0.9266:0.0:0.0734	.	144	Q5VZV1	MT21C_HUMAN	N	144	ENSP00000267273:D144N	ENSP00000267273:D144N	D	-	1	0	METTL21C	102136747	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.744000	0.68664	2.691000	0.91804	0.650000	0.86243	GAT	.	.		0.433	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977		T	103338746	C	T	103338746	3	4	80	1	0	0	0	0	1	0	0	0	1734	826	29	3	368	3	C13orf39	13	103338746	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	54457269	103338746	11831132	58	11020										
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24884995	24884995	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	cctttccttctcctgctcccCttacacgccaacctatgccc	3	21	1	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr14:24884995C>T	ENST00000382554.3	+	9	4358	c.4040C>T	c.(4039-4041)cCt>cTt	p.P1347L		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1347					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						TCCTGCTCCCCTTACACGCCA	0.607																																					p.P1347L		Atlas-SNP	.											.	NYNRIN	120	.	0			c.C4040T						.						111	117	115					14																	24884995		2051	4185	6236	SO:0001583	missense	57523	exon9			GCTCCCCTTACAC	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.4040C>T	chr14.hg19:g.24884995C>T	ENSP00000371994:p.Pro1347Leu	82.0	0.0		49.0	24.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.901344	0.52227	.	.	ENSG00000205978	ENST00000382554	T	0.11385	2.78	4.93	4.05	0.47172	Ribonuclease H-like (1);	.	.	.	.	T	0.08044	0.0201	N	0.24115	0.695	0.28694	N	0.90444	B	0.09022	0.002	B	0.10450	0.005	T	0.13361	-1.0512	9	0.87932	D	0	.	7.2135	0.25947	0.0:0.8061:0.0:0.1939	.	1347	Q9P2P1	NYNRI_HUMAN	L	1347	ENSP00000371994:P1347L	ENSP00000371994:P1347L	P	+	2	0	NYNRIN	23954835	0.004000	0.15560	0.894000	0.35097	0.976000	0.68499	1.214000	0.32419	1.298000	0.44778	0.655000	0.94253	CCT	.	.		0.607	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			T	24884995	C	T	24884995	3	4	80	1	0	0	0	0	1	0	0	0	10805	681	24	3	4070	3	NYNRIN	14	24884995	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10		24884995	82464545	59	11021										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102467511	102467511	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ctggtgattgaactgaaatcCgaagcacttaaagaccgcca	9	10	0	4			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr14:102467511C>T	ENST00000360184.4	+	20	4379	c.4215C>T	c.(4213-4215)tcC>tcT	p.S1405S		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1405	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						AACTGAAATCCGAAGCACTTA	0.438																																					p.S1405S		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C4215T						.						217	224	222					14																	102467511		2203	4300	6503	SO:0001819	synonymous_variant	1778	exon20			GAAATCCGAAGCA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.4215C>T	chr14.hg19:g.102467511C>T		196.0	0.0		81.0	44.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	hg19	CCDS9966.1																																																																																			.	.		0.438	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102467511	C	T	102467511	2	4	80	1	0	0	0	0	0	0	0	1	4843	639	23	1		1	DYNC1H1	14	102467511	Silent	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	77582516	102467511	4882029	60	11022										
LRRC49	54839	hgsc.bcm.edu	37	chr15	71305223	71305225	+	In_Frame_Del	DEL	TCG	TCG	-													0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	tcttctgagttaccccagtaTcgtctgatttccattctggg					rs199883910|rs150157186	byFrequency	TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	TCG	TCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr15:71305223_71305225delTCG	ENST00000260382.5	+	14	1934_1936	c.1674_1676delTCG	c.(1672-1677)tatcgt>tat	p.R559del	LRRC49_ENST00000443425.2_In_Frame_Del_p.R515del|LRRC49_ENST00000436542.2_3'UTR|LRRC49_ENST00000560158.2_In_Frame_Del_p.R247del|LRRC49_ENST00000544974.2_In_Frame_Del_p.R549del|LRRC49_ENST00000560369.1_In_Frame_Del_p.R564del|LRRC49_ENST00000560691.1_In_Frame_Del_p.R265del	NM_001199017.1|NM_017691.3	NP_001185946.1|NP_060161.2	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49	559						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						TACCCCAGTATCGTCTGATTTCC	0.365																																					p.563_564del		Atlas-Indel,Pindel	.											.	LRRC49	73	.	0			c.1688_1690del						.																																			SO:0001651	inframe_deletion	54839	exon14			.		CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1	15q23	2005-08-09				ENSG00000137821			25965	protein-coding gene	gene with protein product						12477932	Standard	NM_001199017		Approved	FLJ20156	uc010ukf.2	Q8IUZ0		ENST00000260382.5:c.1674_1676delTCG	chr15.hg19:g.71305223_71305225delTCG	ENSP00000260382:p.Arg559del	88.0	0.0		63.0	29.0	NM_001199017	B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6	In_Frame_Del	DEL	ENST00000260382.5	hg19	CCDS32282.1																																																																																			.	.		0.365	LRRC49-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417209.3	NM_017691		-	71305225	TCG	-	71305223	7	5	80	1	0	1	0	1	0	0	0	0	9015	1442	50	0	1728	0	LRRC49	15	71305223	In_Frame_Del	DEL	TCG	TCGA-CC-A8HU-01A-11D-A35Z-10		71305223	31226169	61	11023										
ISL2	64843	hgsc.bcm.edu	37	chr15	76632778	76632778	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ctctcatgaaggagcagctgGtggagatgaccggcctgagc	15	10	1	4			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr15:76632778G>T	ENST00000290759.4	+	4	833	c.673G>T	c.(673-675)Gtg>Ttg	p.V225L	RP11-685G9.2_ENST00000559539.1_RNA	NM_145805.1	NP_665804.1	Q96A47	ISL2_HUMAN	ISL LIM homeobox 2	225					negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|peripheral nervous system neuron development (GO:0048935)|regulation of transcription, DNA-templated (GO:0006355)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord motor neuron cell fate specification (GO:0021520)|visceral motor neuron differentiation (GO:0021524)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6						GGAGCAGCTGGTGGAGATGAC	0.622																																					p.V225L	GBM(97;953 1391 16164 31496 36951)	Atlas-SNP	.											.	ISL2	20	.	0			c.G673T						.						36	40	39					15																	76632778		2197	4292	6489	SO:0001583	missense	64843	exon4			CAGCTGGTGGAGA	AK001022	CCDS10290.1	15q24.3	2012-03-09	2007-07-13		ENSG00000159556	ENSG00000159556		"Homeoboxes / LIM class"	18524	protein-coding gene	gene with protein product		609481	"ISL2 transcription factor, LIM/homeodomain, (islet-2)"				Standard	NM_145805		Approved	FLJ10160	uc002bbw.1	Q96A47	OTTHUMG00000143723	ENST00000290759.4:c.673G>T	chr15.hg19:g.76632778G>T	ENSP00000290759:p.Val225Leu	192.0	0.0		151.0	62.0	NM_145805	B3KM37	Missense_Mutation	SNP	ENST00000290759.4	hg19	CCDS10290.1	.	.	.	.	.	.	.	.	.	.	G	36	5.737768	0.96865	.	.	ENSG00000159556	ENST00000290759	D	0.96104	-3.91	5.19	5.19	0.71726	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.94165	0.8128	L	0.31420	0.93	0.80722	D	1	P	0.41848	0.763	P	0.48571	0.582	D	0.94964	0.8111	10	0.87932	D	0	.	16.5729	0.84629	0.0:0.0:1.0:0.0	.	225	Q96A47	ISL2_HUMAN	L	225	ENSP00000290759:V225L	ENSP00000290759:V225L	V	+	1	0	ISL2	74419833	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.716000	0.98752	2.584000	0.87258	0.555000	0.69702	GTG	.	.		0.622	ISL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289779.1			T	76632778	G	T	76632778	3	4	80	1	0	0	0	0	1	0	0	0	7866	1261	44	3	687	3	ISL2	15	76632778	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	5327555	76632778	25898614	62	11024										
MEFV	4210	hgsc.bcm.edu	37	chr16	3297138	3297138	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	cctgatctgcccaaccatctGgcccacgtcctccagtgagg	9	17	2	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr16:3297138G>T	ENST00000219596.1	-	5	1504	c.1465C>A	c.(1465-1467)Cag>Aag	p.Q489K	MEFV_ENST00000541159.1_Missense_Mutation_p.Q278K|MEFV_ENST00000339854.4_Missense_Mutation_p.Q309K|MEFV_ENST00000536379.1_Missense_Mutation_p.Q278K	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	489	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						CCAACCATCTGGCCCACGTCC	0.587																																					p.Q489K		Atlas-SNP	.											.	MEFV	170	.	0			c.C1465A						.						188	167	174					16																	3297138		2197	4300	6497	SO:0001583	missense	4210	exon5			CCATCTGGCCCAC	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1465C>A	chr16.hg19:g.3297138G>T	ENSP00000219596:p.Gln489Lys	111.0	0.0		100.0	4.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	hg19	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	G	2.758	-0.258602	0.05791	.	.	ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000541159;ENST00000536379;ENST00000534868	T;T;T;T	0.63580	-0.05;0.4;0.37;0.4	5.29	3.15	0.36227	.	0.741932	0.12025	N	0.506522	T	0.46678	0.1405	L	0.39566	1.225	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.31503	-0.9941	10	0.08837	T	0.75	-34.618	7.4954	0.27485	0.0:0.1469:0.5702:0.2829	.	489	O15553	MEFV_HUMAN	K	489;489;309;278;278;278	ENSP00000219596:Q489K;ENSP00000339639:Q309K;ENSP00000438711:Q278K;ENSP00000445079:Q278K	ENSP00000219596:Q489K	Q	-	1	0	MEFV	3237139	0.008000	0.16893	0.088000	0.20740	0.012000	0.07955	0.569000	0.23638	1.429000	0.47314	0.655000	0.94253	CAG	.	.		0.587	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		T	3297138	G	T	3297138	3	4	80	1	0	0	0	0	1	0	0	0	9468	1357	47	3	904	3	MEFV	16	3297138	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10		3297138	87057615	63	11025										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000420246.2_Missense_Mutation_p.R249S|TP53_ENST00000455263.2_Missense_Mutation_p.R249S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	115.0	1.0		47.0	36.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	80	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10		7577534	73617676	64	11026										
LSMD1	84316	hgsc.bcm.edu	37	chr17	7760598	7760598	+	Intron	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	agctcccggcagcccgcgggGcactcacacaaagcccagag	12	17	1	1	rs201706296		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr17:7760598G>C	ENST00000335155.5	-	2	81				CYB5D1_ENST00000570446.1_5'Flank|LSMD1_ENST00000575771.1_Intron|LSMD1_ENST00000575071.1_Intron|LSMD1_ENST00000575208.1_Intron|CYB5D1_ENST00000571846.1_5'Flank|CYB5D1_ENST00000332439.4_5'Flank|LSMD1_ENST00000576861.1_Intron|LSMD1_ENST00000570555.1_5'Flank|LSMD1_ENST00000576384.1_5'Flank|LSMD1_ENST00000333775.5_Missense_Mutation_p.C48W			Q9BRA0	LSMD1_HUMAN							negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|lung(2)|ovary(1)	4		all_cancers(10;0.11)|Prostate(122;0.219)				AGCCCGCGGGGCACTCACACA	0.692																																					p.C48W	GBM(66;626 1401 29924 42527)	Atlas-SNP	.											.	LSMD1	8	.	0			c.C144G						.						13	18	16					17																	7760598		2143	4212	6355	SO:0001627	intron_variant	84316	exon1			CGCGGGGCACTCA																												ENST00000335155.5:c.82-82C>G	chr17.hg19:g.7760598G>C		106.0	0.0		39.0	32.0	NM_032356	Q8N4M0	Missense_Mutation	SNP	ENST00000335155.5	hg19		.	.	.	.	.	.	.	.	.	.	G	5.519	0.280739	0.10458	.	.	ENSG00000183011	ENST00000333775	T	0.48522	0.81	4.83	3.5	0.40072	.	1.036590	0.07611	N	0.925311	T	0.39384	0.1076	.	.	.	0.80722	D	1	B	0.28584	0.216	B	0.34180	0.177	T	0.09292	-1.0681	8	.	.	.	.	7.6789	0.28502	0.1436:0.0:0.8564:0.0	.	48	Q9BRA0-2	.	W	48	ENSP00000332103:C48W	.	C	-	3	2	LSMD1	7701323	0.065000	0.20965	0.911000	0.35937	0.304000	0.27724	0.531000	0.23052	1.114000	0.41781	0.462000	0.41574	TGC	.	G|0.999;A|0.001		0.692	LSMD1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				C	7760598	G	C	7760598	1	2	80	0	1	0	0	0	0	0	0	0	9071	1195	42	4		4	LSMD1	17	7760598	Intron	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	183064	7760598	73434612	65	11027										
LIG3	3980	hgsc.bcm.edu	37	chr17	33319683	33319683	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	agctctgagcgtccaggcctCgctgatgacacctgtgcagc	12	14	1	3			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr17:33319683C>T	ENST00000378526.4	+	8	1560	c.1427C>T	c.(1426-1428)tCg>tTg	p.S476L	LIG3_ENST00000262327.5_Missense_Mutation_p.S476L	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	476					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	GTCCAGGCCTCGCTGATGACA	0.622								Other BER factors																													p.S476L		Atlas-SNP	.											.	LIG3	164	.	0			c.C1427T						.						55	48	50					17																	33319683		2203	4300	6503	SO:0001583	missense	3980	exon8			AGGCCTCGCTGAT		CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"ligase II, DNA, ATP-dependent"	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.1427C>T	chr17.hg19:g.33319683C>T	ENSP00000367787:p.Ser476Leu	84.0	0.0		61.0	22.0	NM_013975	Q16714|Q6NVK3	Missense_Mutation	SNP	ENST00000378526.4	hg19	CCDS11284.2	.	.	.	.	.	.	.	.	.	.	C	23.1	4.372567	0.82573	.	.	ENSG00000005156	ENST00000378526;ENST00000262327	T;T	0.19394	2.15;2.15	5.5	5.5	0.81552	DNA ligase, ATP-dependent, N-terminal (2);	0.059458	0.64402	D	0.000001	T	0.24586	0.0596	M	0.66939	2.045	0.50313	D	0.999865	P;P;P	0.38922	0.651;0.651;0.607	B;B;B	0.28991	0.068;0.068;0.097	T	0.08106	-1.0738	10	0.66056	D	0.02	-8.3791	18.5685	0.91126	0.0:1.0:0.0:0.0	.	476;476;476	E5KLB5;P49916;E5KLB6	.;DNLI3_HUMAN;.	L	476	ENSP00000367787:S476L;ENSP00000262327:S476L	ENSP00000262327:S476L	S	+	2	0	LIG3	30343796	1.000000	0.71417	0.047000	0.18901	0.957000	0.61999	7.461000	0.80834	2.861000	0.98227	0.655000	0.94253	TCG	.	.		0.622	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975		T	33319683	C	T	33319683	3	4	80	1	0	0	0	0	1	0	0	0	8791	893	31	1	1453	1	LIG3	17	33319683	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	25559085	33319683	47875527	66	11028										
KRTAP4-4	84616	hgsc.bcm.edu	37	chr17	39316584	39316584	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	acacagtagctggggcagcaGcaggtgggctggcagcacac	16	11	0	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr17:39316584G>A	ENST00000390661.3	-	1	399	c.360C>T	c.(358-360)tgC>tgT	p.C120C		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	120	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			TGGGGCAGCAGCAGGTGGGCT	0.662																																					p.C120C		Atlas-SNP	.											.	KRTAP4-4	21	.	0			c.C360T						.						39	46	44					17																	39316584		2201	4295	6496	SO:0001819	synonymous_variant	84616	exon1			GCAGCAGCAGGTG	AJ406936	CCDS11383.1	17q21.2	2013-06-25			ENSG00000171396	ENSG00000171396		"Keratin associated proteins"	16928	protein-coding gene	gene with protein product			"keratin associated protein 4-13"	KRTAP4-13		11279113	Standard	NM_032524		Approved	KAP4.4, KAP4.13	uc002hwc.3	Q9BYR3	OTTHUMG00000133428	ENST00000390661.3:c.360C>T	chr17.hg19:g.39316584G>A		105.0	0.0		93.0	44.0	NM_032524	Q9BYU7	Silent	SNP	ENST00000390661.3	hg19	CCDS11383.1																																																																																			.	.		0.662	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1			A	39316584	G	A	39316584	2	1	80	1	0	0	0	0	0	0	0	1	8562	963	34	3		3	KRTAP4-4	17	39316584	Silent	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	5996901	39316584	41878626	67	11029										
TRIM25	7706	hgsc.bcm.edu	37	chr17	54981814	54981814	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gccttcatttccgtgtattcTtgttgtagctgctccacctt	7	12	2	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr17:54981814T>G	ENST00000316881.4	-	3	778	c.729A>C	c.(727-729)caA>caC	p.Q243H	TRIM25_ENST00000537230.1_Missense_Mutation_p.Q243H	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	243	Interaction with influenza A virus NS1.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)|response to estrogen (GO:0043627)|response to vitamin D (GO:0033280)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Breast(9;6.15e-08)					CCGTGTATTCTTGTTGTAGCT	0.512																																					p.Q243H		Atlas-SNP	.											.	TRIM25	52	.	0			c.A729C						.						163	147	153					17																	54981814		2203	4300	6503	SO:0001583	missense	7706	exon3			GTATTCTTGTTGT	D21205	CCDS11591.1	17q23.1	2013-01-09	2011-01-25	2004-03-30				"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	12932	protein-coding gene	gene with protein product		600453	"zinc finger protein 147 (estrogen-responsive finger protein)", "tripartite motif-containing 25"	ZNF147		7789997	Standard	NM_005082		Approved	EFP, RNF147	uc002iut.3	Q14258		ENST00000316881.4:c.729A>C	chr17.hg19:g.54981814T>G	ENSP00000323889:p.Gln243His	76.0	0.0		92.0	32.0	NM_005082		Missense_Mutation	SNP	ENST00000316881.4	hg19	CCDS11591.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.935906	0.52972	.	.	ENSG00000121060	ENST00000316881;ENST00000537230	T;T	0.43688	0.94;0.94	5.76	-6.17	0.02091	.	0.527372	0.18118	N	0.151152	T	0.30293	0.0760	M	0.67953	2.075	0.20196	N	0.999922	B	0.14012	0.009	B	0.14023	0.01	T	0.29882	-0.9997	10	0.62326	D	0.03	.	3.9418	0.09331	0.1286:0.4421:0.2476:0.1817	.	243	Q14258	TRI25_HUMAN	H	243	ENSP00000323889:Q243H;ENSP00000445961:Q243H	ENSP00000323889:Q243H	Q	-	3	2	TRIM25	52336813	0.000000	0.05858	0.532000	0.27989	0.650000	0.38633	-0.873000	0.04214	-0.664000	0.05324	0.533000	0.62120	CAA	.	.		0.512	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082		G	54981814	T	G	54981814	3	3	80	1	0	0	0	0	1	0	0	0	16514	1606	56	5	1191	5	TRIM25	17	54981814	Missense_Mutation	SNP	T	TCGA-CC-A8HU-01A-11D-A35Z-10	15665230	54981814	26213396	68	11030										
TTYH2	94015	hgsc.bcm.edu	37	chr17	72218751	72218751	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gcagaccaagcagcaccactCctgctgcatcacctggacgg	10	16	1	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr17:72218751C>A	ENST00000269346.4	+	2	331	c.257C>A	c.(256-258)tCc>tAc	p.S86Y	TTYH2_ENST00000529107.1_Missense_Mutation_p.S65Y	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	86						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						CAGCACCACTCCTGCTGCATC	0.647																																					p.S86Y		Atlas-SNP	.											.	TTYH2	63	.	0			c.C257A						.						81	65	71					17																	72218751		2203	4300	6503	SO:0001583	missense	94015	exon2			ACCACTCCTGCTG		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"tweety (Drosophila) homolog 2", "tweety homolog 2 (Drosophila)"			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.257C>A	chr17.hg19:g.72218751C>A	ENSP00000269346:p.Ser86Tyr	39.0	0.0		82.0	20.0	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	hg19	CCDS32717.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.084635	0.76642	.	.	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.12984	2.63;2.63	5.05	5.05	0.67936	.	0.187469	0.47852	D	0.000204	T	0.38134	0.1029	M	0.78223	2.4	0.80722	D	1	D;D	0.60160	0.987;0.971	D;P	0.63703	0.917;0.905	T	0.20009	-1.0288	10	0.59425	D	0.04	-16.6	17.5539	0.87885	0.0:1.0:0.0:0.0	.	65;86	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	Y	86;65	ENSP00000269346:S86Y;ENSP00000433089:S65Y	ENSP00000269346:S86Y	S	+	2	0	TTYH2	69730346	0.999000	0.42202	0.670000	0.29842	0.776000	0.43924	5.467000	0.66737	2.493000	0.84123	0.655000	0.94253	TCC	.	.		0.647	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1			A	72218751	C	A	72218751	3	1	80	1	0	0	0	0	1	0	0	0	16755	855	30	3	263	3	TTYH2	17	72218751	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	17236937	72218751	8976459	69	11031										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76503830	76503830	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	catcatggtgcctgtccgcgGgtgcggctcgtgctggaatt	15	11	1	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr17:76503830G>T	ENST00000585328.1	-	28	4409	c.4285C>A	c.(4285-4287)Ccg>Acg	p.P1429T	DNAH17_ENST00000389840.5_Missense_Mutation_p.P1428T	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1428	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CCTGTCCGCGGGTGCGGCTCG	0.552																																					p.P1432T		Atlas-SNP	.											.	DNAH17	347	.	0			c.C4294A						.						23	24	24					17																	76503830		2038	4196	6234	SO:0001583	missense	8632	exon28			TCCGCGGGTGCGG	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.4285C>A	chr17.hg19:g.76503830G>T	ENSP00000465516:p.Pro1429Thr	31.0	0.0		27.0	18.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	G	4.132	0.022823	0.08006	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.59906	0.23	4.92	3.88	0.44766	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.33614	0.0869	N	0.11064	0.09	0.32192	N	0.579001	B	0.02656	0.0	B	0.11329	0.006	T	0.33369	-0.9871	9	0.15499	T	0.54	.	8.1441	0.31102	0.0784:0.0:0.654:0.2676	.	1428	Q9UFH2	DYH17_HUMAN	T	1429;1428	ENSP00000374490:P1428T	ENSP00000300671:P1429T	P	-	1	0	DNAH17	74015425	0.798000	0.28890	1.000000	0.80357	0.985000	0.73830	0.122000	0.15687	2.236000	0.73375	0.563000	0.77884	CCG	.	.		0.552	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		T	76503830	G	T	76503830	3	4	80	1	0	0	0	0	1	0	0	0	4603	1232	43	3	9310	3	DNAH17	17	76503830	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	4285079	76503830	4691380	70	11032										
C18orf10	25941	hgsc.bcm.edu	37	chr18	34385439	34385439	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ttttgagatgctgttaattgCcatgcttcccagtggaatga	10	7	0	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr18:34385439C>A	ENST00000334295.4	-	4	707	c.280G>T	c.(280-282)Gca>Tca	p.A94S	TPGS2_ENST00000587129.1_Missense_Mutation_p.A94S|TPGS2_ENST00000593035.1_Intron|TPGS2_ENST00000590842.1_Missense_Mutation_p.A94S|TPGS2_ENST00000589049.1_Missense_Mutation_p.A94S|TPGS2_ENST00000383056.3_Intron	NM_015476.2	NP_056291.2	Q68CL5	TPGS2_HUMAN	tubulin polyglutamylase complex subunit 2	94						cytoplasm (GO:0005737)|microtubule (GO:0005874)											CTGTTAATTGCCATGCTTCCC	0.453																																					p.A94S		Atlas-SNP	.											.	.	.	.	0			c.G280T						.						283	236	252					18																	34385439		2203	4300	6503	SO:0001583	missense	25941	exon4			TAATTGCCATGCT	BC015178	CCDS32817.1, CCDS62421.1, CCDS62422.1, CCDS62423.1, CCDS62424.1, CCDS74214.1, CCDS74215.1	18q12.2	2011-11-25	2011-11-25	2011-11-25	ENSG00000134779	ENSG00000134779			24561	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 10"	C18orf10		12477932	Standard	NM_015476		Approved	DKFZP586M1523, HsT3006	uc031rhw.1	Q68CL5		ENST00000334295.4:c.280G>T	chr18.hg19:g.34385439C>A	ENSP00000335144:p.Ala94Ser	156.0	0.0		97.0	43.0	NM_001271954	B4DIX2|K7EIJ9|Q4KN59|Q8WTU3|Q96BT9|Q9Y435	Missense_Mutation	SNP	ENST00000334295.4	hg19	CCDS32817.1	.	.	.	.	.	.	.	.	.	.	C	9.767	1.171608	0.21704	.	.	ENSG00000134779	ENST00000334295	T	0.28255	1.62	5.7	-0.0592	0.13794	Cell wall assembly/cell proliferation coordinating protein, KNR4-like (1);	0.796894	0.11948	N	0.513942	T	0.21590	0.0520	L	0.29908	0.895	0.23704	N	0.997061	B;B	0.30236	0.199;0.274	B;B	0.30179	0.076;0.112	T	0.18871	-1.0323	10	0.38643	T	0.18	0.2599	10.9003	0.47047	0.0:0.5243:0.0:0.4757	.	94;94	Q68CL5-3;Q68CL5	.;TPGS2_HUMAN	S	94	ENSP00000335144:A94S	ENSP00000335144:A94S	A	-	1	0	C18orf10	32639437	0.945000	0.32115	0.987000	0.45799	0.508000	0.34012	0.082000	0.14847	0.047000	0.15862	0.655000	0.94253	GCA	.	.		0.453	TPGS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440410.2	NM_015476		A	34385439	C	A	34385439	3	1	80	1	0	0	0	0	1	0	0	0	1897	739	26	3	638	3	C18orf10	18	34385439	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10		34385439	43691809	71	11033										
MADCAM1	8174	hgsc.bcm.edu	37	chr19	497839	497839	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	cgcggtcgccgcaggccagtCcctccaggtgaagcccctgc	13	18	0	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr19:497839C>G	ENST00000215637.3	+	2	105	c.59C>G	c.(58-60)tCc>tGc	p.S20C	MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Missense_Mutation_p.S20C|MADCAM1_ENST00000587541.1_Intron	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	20					aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAGGCCAGTCCCTCCAGGTG	0.801																																					p.S20C		Atlas-SNP	.											.	MADCAM1	29	.	0			c.C59G						.						1	2	2					19																	497839		973	2063	3036	SO:0001583	missense	8174	exon2			GCCAGTCCCTCCA	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6765	protein-coding gene	gene with protein product	"mucosal addressin cell adhesion molecule-1"	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.59C>G	chr19.hg19:g.497839C>G	ENSP00000215637:p.Ser20Cys	3.0	0.0		10.0	6.0	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	hg19	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.907375	0.33628	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637;ENST00000346144	T;T	0.19938	2.43;2.11	1.41	-0.0249	0.13937	.	93.576700	0.00166	U	0.000000	T	0.09335	0.0230	N	0.02011	-0.69	0.09310	N	0.999999	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.24941	-1.0146	10	0.46703	T	0.11	.	5.9779	0.19391	0.0:0.5957:0.4043:0.0	.	20;20	B2RPL9;Q13477	.;MADCA_HUMAN	C	20	ENSP00000215637:S20C;ENSP00000304247:S20C	ENSP00000215637:S20C	S	+	2	0	MADCAM1	448839	0.001000	0.12720	0.001000	0.08648	0.628000	0.37860	0.595000	0.24029	0.076000	0.16826	0.165000	0.16767	TCC	.	.		0.801	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760		G	497839	C	G	497839	3	3	80	1	0	0	0	0	1	0	0	0	9160	855	30	4	65	4	MADCAM1	19	497839	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10		497839	58631144	72	11034										
PRSSL1	400668	hgsc.bcm.edu	37	chr19	687062	687062	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	catcagtccaggcggcagctCctcaaagtcagacacgaagc	10	14	3	1	rs376121318		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr19:687062C>A	ENST00000329267.7	-	4	537	c.508G>T	c.(508-510)Gag>Tag	p.E170*		NM_214710.3	NP_999875	Q6UWY2	PRS57_HUMAN	protease, serine, 57	170	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|lung(5)	6						GGCGGCAGCTCCTCAAAGTCA	0.672																																					p.E170X		Atlas-SNP	.											.	PRSS57	18	.	0			c.G508T						.	C	stop/GLU	0,4406		0,0,2203	43	41	42		508	3.5	0.5	19		42	3,8597	3.0+/-9.4	0,3,4297	no	stop-gained	PRSS57	NM_214710.3		0,3,6500	AA,AC,CC		0.0349,0.0,0.0231		170/284	687062	3,13003	2203	4300	6503	SO:0001587	stop_gained	400668	exon4			GCAGCTCCTCAAA	AY358594	CCDS12041.1	19p13.3	2012-03-26	2011-03-07	2011-03-07		ENSG00000185198		"Serine peptidases / Serine peptidases"	31397	protein-coding gene	gene with protein product			"protease, serine-like 1"	PRSSL1		12975309	Standard	NM_214710		Approved	UNQ782	uc002lpl.1	Q6UWY2		ENST00000329267.7:c.508G>T	chr19.hg19:g.687062C>A	ENSP00000327386:p.Glu170*	256.0	1.0		148.0	59.0	NM_214710	B2RNW8	Nonsense_Mutation	SNP	ENST00000329267.7	hg19	CCDS12041.1	.	.	.	.	.	.	.	.	.	.	C	13.06	2.125780	0.37533	0.0	3.49E-4	ENSG00000185198	ENST00000329267	.	.	.	4.6	3.51	0.40186	.	0.702099	0.12310	N	0.480283	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	7.6261	0.28212	0.0:0.7436:0.1667:0.0897	.	.	.	.	X	170	.	ENSP00000327386:E170X	E	-	1	0	PRSS57	638062	0.146000	0.22672	0.527000	0.27925	0.043000	0.13939	1.382000	0.34374	2.107000	0.64212	0.462000	0.41574	GAG	.	.		0.672	PRSS57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452480.2	NM_214710		A	687062	C	A	687062	4	1	80	1	0	0	0	0	0	1	0	0	12648	864	30	3	351	3	PRSSL1	19	687062	Nonsense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	189223	687062	58441921	73	11035										
SYDE1	85360	hgsc.bcm.edu	37	chr19	15224669	15224669	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gtcaccggtgacttcgaagaCgacttcgatgcgcccttcaa	10	13	2	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr19:15224669C>T	ENST00000342784.2	+	8	2134	c.2103C>T	c.(2101-2103)gaC>gaT	p.D701D	SYDE1_ENST00000600440.1_Silent_p.D634D|SYDE1_ENST00000600252.1_Silent_p.D358D	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	701					activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)			endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						ACTTCGAAGACGACTTCGATG	0.597																																					p.D701D		Atlas-SNP	.											.	SYDE1	44	.	0			c.C2103T						.						134	143	140					19																	15224669		2203	4300	6503	SO:0001819	synonymous_variant	85360	exon8			CGAAGACGACTTC	BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.2103C>T	chr19.hg19:g.15224669C>T		113.0	0.0		81.0	17.0	NM_033025	Q7L2I8|Q8N6J2|Q9H8K4	Silent	SNP	ENST00000342784.2	hg19	CCDS12324.1																																																																																			.	.		0.597	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025		T	15224669	C	T	15224669	2	4	80	1	0	0	0	0	0	0	0	1	15450	535	19	1		1	SYDE1	19	15224669	Silent	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	14537607	15224669	43904314	74	11036										
RPS16	6217	hgsc.bcm.edu	37	chr19	39926515	39926515	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ccgaagacctgcacagactgCagcgggcccttggacggcat	13	14	0	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr19:39926515C>A	ENST00000251453.3	-	1	73	c.21G>T	c.(19-21)ctG>ctT	p.L7L	RPS16_ENST00000339471.4_Silent_p.L7L|RPS16_ENST00000601655.1_Silent_p.L7L|RPS16_ENST00000599539.1_Silent_p.L7L	NM_001020.4	NP_001011.1	P62249	RS16_HUMAN	ribosomal protein S16	7					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|large_intestine(2)|lung(2)|skin(2)	7	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;4.14e-26)|all cancers(26;2.68e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GCACAGACTGCAGCGGGCCCT	0.667																																					p.L7L		Atlas-SNP	.											.	RPS16	12	.	0			c.G21T						.						46	46	46					19																	39926515		2202	4300	6502	SO:0001819	synonymous_variant	6217	exon1			AGACTGCAGCGGG	M60854	CCDS12535.1	19q13.1	2011-04-05				ENSG00000105193		"S ribosomal proteins"	10396	protein-coding gene	gene with protein product	"40S ribosomal protein S16"	603675				2016298, 9582194	Standard	XM_005259137		Approved	S16	uc002olk.3	P62249		ENST00000251453.3:c.21G>T	chr19.hg19:g.39926515C>A		37.0	0.0		40.0	29.0	NM_001020	B2RDD5|P17008	Silent	SNP	ENST00000251453.3	hg19	CCDS12535.1																																																																																			.	.		0.667	RPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464511.1	NM_001020		A	39926515	C	A	39926515	2	1	80	1	0	0	0	0	0	0	0	1	13642	697	25	3		3	RPS16	19	39926515	Silent	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	24701846	39926515	19202468	75	11037										
GGTLC1	92086	hgsc.bcm.edu	37	chr20	23966368	23966368	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ggttgtgcagccggggctccTccacggcccacttcacgtca	12	16	2	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr20:23966368T>C	ENST00000335694.4	-	5	671	c.467A>G	c.(466-468)gAg>gGg	p.E156G	GGTLC1_ENST00000278765.4_Missense_Mutation_p.E156G|GGTLC1_ENST00000286890.4_Missense_Mutation_p.E156G	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	156					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						CCGGGGCTCCTCCACGGCCCA	0.607																																					p.E156G		Atlas-SNP	.											.	GGTLC1	37	.	0			c.A467G						.						75	78	77					20																	23966368		2203	4293	6496	SO:0001583	missense	92086	exon5			GGCTCCTCCACGG	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"Gamma-glutamyltransferases"	16437	protein-coding gene	gene with protein product		612338	"gamma-glutamyltransferase-like activity 4", "gamma-glutamyltransferase-like activity 3"	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.467A>G	chr20.hg19:g.23966368T>C	ENSP00000337587:p.Glu156Gly	52.0	0.0		63.0	41.0	NM_178311	D3DW43|Q08246	Missense_Mutation	SNP	ENST00000335694.4	hg19	CCDS13163.1	.	.	.	.	.	.	.	.	.	.	t	8.818	0.936846	0.18206	.	.	ENSG00000149435	ENST00000286890;ENST00000278765;ENST00000335694	T;T;T	0.07908	3.15;3.15;3.15	0.844	0.844	0.18943	.	0.406919	0.26082	N	0.026454	T	0.08626	0.0214	M	0.62016	1.91	0.30145	N	0.80361	B	0.15930	0.015	B	0.18263	0.021	T	0.09862	-1.0655	10	0.40728	T	0.16	-28.6386	5.802	0.18420	0.0:1.0E-4:0.0:0.9999	.	156	Q9BX51	GGTL1_HUMAN	G	156	ENSP00000286890:E156G;ENSP00000278765:E156G;ENSP00000337587:E156G	ENSP00000278765:E156G	E	-	2	0	GGTLC1	23914368	0.837000	0.29446	0.220000	0.23810	0.222000	0.24845	0.469000	0.22067	0.077000	0.16863	0.076000	0.15429	GAG	.	.		0.607	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2		C	23966368	T	C	23966368	3	2	80	1	0	0	0	0	1	0	0	0	6373	1551	54	2	218	2	GGTLC1	20	23966368	Missense_Mutation	SNP	T	TCGA-CC-A8HU-01A-11D-A35Z-10		23966368	39059152	76	11038										
POFUT1	23509	hgsc.bcm.edu	37	chr20	30818724	30818724	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gcacagcggcccccctcacgAtgactatgtgcctgcctgac	10	17	1	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr20:30818724A>G	ENST00000375749.3	+	6	900	c.838A>G	c.(838-840)Atg>Gtg	p.M280V	POFUT1_ENST00000539210.1_Missense_Mutation_p.M69V|POFUT1_ENST00000486717.1_3'UTR	NM_015352.1	NP_056167.1	Q9H488	OFUT1_HUMAN	protein O-fucosyltransferase 1	280					angiogenesis (GO:0001525)|embryo development (GO:0009790)|fucose metabolic process (GO:0006004)|heart development (GO:0007507)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|O-glycan processing (GO:0016266)|protein O-linked fucosylation (GO:0036066)|protein O-linked glycosylation (GO:0006493)|regulation of transcription, DNA-templated (GO:0006355)|somitogenesis (GO:0001756)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	6			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			CCCCCTCACGATGACTATGTG	0.617																																					p.M280V		Atlas-SNP	.											.	POFUT1	52	.	0			c.A838G						.						91	83	86					20																	30818724		2203	4300	6503	SO:0001583	missense	23509	exon6			CTCACGATGACTA	AF375884	CCDS13198.1, CCDS13199.1	20q11	2013-03-06			ENSG00000101346	ENSG00000101346	2.4.1.221	"Fucosyltransferases"	14988	protein-coding gene	gene with protein product	"peptide-O-fucosyltransferase", "GDP-fucose protein O-fucosyltransferase 1"	607491				9023546, 9525914	Standard	NM_015352		Approved	O-FUT, O-Fuc-T, KIAA0180, FUT12	uc002wxp.3	Q9H488	OTTHUMG00000133268	ENST00000375749.3:c.838A>G	chr20.hg19:g.30818724A>G	ENSP00000364902:p.Met280Val	104.0	0.0		120.0	5.0	NM_015352	A8K4R8|E1P5M4|Q14685|Q5W185|Q9BW76	Missense_Mutation	SNP	ENST00000375749.3	hg19	CCDS13198.1	.	.	.	.	.	.	.	.	.	.	A	9.094	1.002379	0.19121	.	.	ENSG00000101346	ENST00000375749;ENST00000539210	T;T	0.29142	1.58;1.58	5.19	1.25	0.21368	.	0.542116	0.21731	N	0.069973	T	0.21718	0.0523	L	0.60455	1.87	0.30163	N	0.801988	B	0.11235	0.004	B	0.18263	0.021	T	0.23119	-1.0197	10	0.11485	T	0.65	-11.5451	3.5038	0.07683	0.6309:0.1709:0.0739:0.1243	.	280	Q9H488	OFUT1_HUMAN	V	280;69	ENSP00000364902:M280V;ENSP00000446154:M69V	ENSP00000364902:M280V	M	+	1	0	POFUT1	30282385	0.991000	0.36638	0.995000	0.50966	0.835000	0.47333	0.488000	0.22371	0.254000	0.21573	0.477000	0.44152	ATG	.	.		0.617	POFUT1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078613.1	NM_015352		G	30818724	A	G	30818724	3	3	80	1	0	0	0	0	1	0	0	0	12192	333	12	2	907	2	POFUT1	20	30818724	Missense_Mutation	SNP	A	TCGA-CC-A8HU-01A-11D-A35Z-10	6852356	30818724	32206796	77	11039										
GNAS	2778	hgsc.bcm.edu	37	chr20	57429286	57429286	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	gctggggtcgacgacactccCgtcaacatggacagcccccc	11	17	1	0			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr20:57429286C>T	ENST00000306120.3	+	1	776	c.776C>T	c.(775-777)cCg>cTg	p.P259L	GNAS_ENST00000371100.4_Silent_p.P322P|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371102.4_Silent_p.P322P|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000371099.2_Silent_p.P322P			P63092	GNAS2_HUMAN	GNAS complex locus	0			E -> V (in AHO). {ECO:0000269|PubMed:12624854}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			ACGACACTCCCGTCAACATGG	0.642			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.P260L	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	GNAS_ENST00000371100,NS,carcinoma,0,1	GNAS	867	.	0			c.C779T						.						20	25	23					20																	57429286		1910	4105	6015	SO:0001583	missense	2778	exon1			CACTCCCGTCAAC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000306120.3:c.776C>T	chr20.hg19:g.57429286C>T	ENSP00000302237:p.Pro259Leu	115.0	0.0		194.0	103.0	NM_001077490	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000306120.3	hg19		.	.	.	.	.	.	.	.	.	.	C	13.02	2.111752	0.37242	.	.	ENSG00000087460	ENST00000306120	.	.	.	3.76	2.51	0.30379	.	9.224370	0.00166	N	0.000004	T	0.64159	0.2573	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52268	-0.8598	6	0.72032	D	0.01	.	7.2563	0.26179	0.0:0.7984:0.0:0.2016	.	.	.	.	L	259	.	ENSP00000302237:P259L	P	+	2	0	GNAS	56862681	0.551000	0.26497	1.000000	0.80357	0.896000	0.52359	0.590000	0.23954	0.780000	0.33566	0.462000	0.41574	CCG	.	.		0.642	GNAS-050	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000267987.1	NM_000516		T	57429286	C	T	57429286	3	4	80	1	0	0	0	0	1	0	0	0	6518	652	23	1	1710	1	GNAS	20	57429286	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	26610562	57429286	5596234	78	11040										
DIP2A	23181	hgsc.bcm.edu	37	chr21	47976001	47976001	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	actgggatattagcgggagtGaaggtaggtcctctgaaatc	14	6	1	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr21:47976001G>T	ENST00000417564.2	+	29	3516	c.3495G>T	c.(3493-3495)gtG>gtT	p.V1165V	DIP2A_ENST00000400274.1_Silent_p.V1161V|DIP2A_ENST00000427143.2_Silent_p.V1101V|DIP2A_ENST00000318711.7_Silent_p.V1166V			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1165					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TAGCGGGAGTGAAGGTAGGTC	0.493																																					p.V1165V		Atlas-SNP	.											.	DIP2A	332	.	0			c.G3495T						.						139	141	140					21																	47976001		1955	4137	6092	SO:0001819	synonymous_variant	23181	exon29			GGGAGTGAAGGTA	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.3495G>T	chr21.hg19:g.47976001G>T		109.0	0.0		71.0	18.0	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	hg19	CCDS46655.1																																																																																			.	.		0.493	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		T	47976001	G	T	47976001	2	4	80	1	0	0	0	0	0	0	0	1	4529	1277	45	3		3	DIP2A	21	47976001	Silent	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10		47976001	153894	79	11041										
POTEH	23784	hgsc.bcm.edu	37	chr22	16287880	16287880	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ggcattgaaccagcctcagcCaccatctgcttttaacagcc	7	15	2	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr22:16287880C>A	ENST00000343518.6	-	1	57	c.6G>T	c.(4-6)gtG>gtT	p.V2V		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	2										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						CAGCCTCAGCCACCATCTGCT	0.552																																					p.V2V		Atlas-SNP	.											.	POTEH	114	.	0			c.G6T						.						61	71	68					22																	16287880		1968	3794	5762	SO:0001819	synonymous_variant	23784	exon1			CTCAGCCACCATC	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	133	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 7"	608913	"actin, beta-like 1", "ANKRD26-like family C, member 3"	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.6G>T	chr22.hg19:g.16287880C>A		727.0	1.0		507.0	111.0	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Silent	SNP	ENST00000343518.6	hg19	CCDS46658.1																																																																																			.	.		0.552	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		A	16287880	C	A	16287880	2	1	80	1	0	0	0	0	0	0	0	1	12276	581	21	3		3	POTEH	22	16287880	Silent	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10		16287880	35016686	80	11042										
SREBF2	6721	hgsc.bcm.edu	37	chr22	42273342	42273342	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ctcctttaaccccctgacttCcctgctgcagtggggagggg	12	14	0	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chr22:42273342C>G	ENST00000361204.4	+	8	1662	c.1496C>G	c.(1495-1497)tCc>tGc	p.S499C		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	499					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						CCCCTGACTTCCCTGCTGCAG	0.617																																					p.S499C		Atlas-SNP	.											.	SREBF2	99	.	0			c.C1496G						.						107	104	105					22																	42273342		2203	4300	6503	SO:0001583	missense	6721	exon8			TGACTTCCCTGCT	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"Basic helix-loop-helix proteins"	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.1496C>G	chr22.hg19:g.42273342C>G	ENSP00000354476:p.Ser499Cys	101.0	0.0		73.0	42.0	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	hg19	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.307905	0.81247	.	.	ENSG00000198911	ENST00000361204;ENST00000444813;ENST00000457567	T	0.58506	0.33	6.06	3.99	0.46301	.	0.315300	0.39985	N	0.001216	T	0.65015	0.2651	M	0.72353	2.195	0.52099	D	0.999942	P	0.51147	0.942	P	0.50934	0.654	T	0.67848	-0.5564	10	0.59425	D	0.04	-3.0553	12.4248	0.55540	0.0:0.8657:0.0:0.1343	.	499	Q12772	SRBP2_HUMAN	C	499	ENSP00000354476:S499C	ENSP00000354476:S499C	S	+	2	0	SREBF2	40603288	0.594000	0.26849	0.215000	0.23724	0.985000	0.73830	3.991000	0.56973	0.901000	0.36495	0.643000	0.83706	TCC	.	.		0.617	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		G	42273342	C	G	42273342	3	3	80	1	0	0	0	0	1	0	0	0	15157	855	30	4	1526	4	SREBF2	22	42273342	Missense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	25985462	42273342	9031224	81	11043										
MSL3	10943	hgsc.bcm.edu	37	chrX	11790751	11790751	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ttaatgcagtgaaacttccaGaaatccttggaaagatgtcc	8	8	0	3			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chrX:11790751G>A	ENST00000312196.4	+	12	1498	c.1393G>A	c.(1393-1395)Gaa>Aaa	p.E465K	MSL3_ENST00000361672.2_Missense_Mutation_p.E316K|MSL3_ENST00000398527.2_Missense_Mutation_p.E453K|MSL3_ENST00000380693.3_Missense_Mutation_p.E299K	NM_078629.3	NP_523353.2	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3 homolog (Drosophila)	465	MRG. {ECO:0000255|PROSITE- ProRule:PRU00972}.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|multicellular organismal development (GO:0007275)|transcription from RNA polymerase II promoter (GO:0006366)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	19						GAAACTTCCAGAAATCCTTGG	0.358																																					p.E465K		Atlas-SNP	.											.	MSL3	88	.	0			c.G1393A						.						77	69	72					X																	11790751		2203	4300	6503	SO:0001583	missense	10943	exon12			CTTCCAGAAATCC	AF117065	CCDS14147.1, CCDS14148.1, CCDS14149.1, CCDS55369.1, CCDS65213.1	Xp22.3	2008-10-29	2008-10-29	2008-10-29	ENSG00000005302	ENSG00000005302			7370	protein-coding gene	gene with protein product		300609	"male-specific lethal-3 (Drosophila)-like 1", "male-specific lethal 3-like 1 (Drosophila)"	MSL3L1		10395802, 10908644	Standard	NM_078628		Approved		uc004cuw.3	Q8N5Y2	OTTHUMG00000021132	ENST00000312196.4:c.1393G>A	chrX.hg19:g.11790751G>A	ENSP00000312244:p.Glu465Lys	246.0	0.0		203.0	121.0	NM_078629	A6NCU2|A6NHW8|A8K165|B4DUV8|B7Z227|Q9UG70|Q9Y5Z8	Missense_Mutation	SNP	ENST00000312196.4	hg19	CCDS14147.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875542	0.91664	.	.	ENSG00000005302	ENST00000312196;ENST00000361672;ENST00000398527;ENST00000380693	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.40694	0.1127	M	0.89968	3.075	0.54753	D	0.999988	D;D;D;D	0.76494	0.999;0.997;0.996;0.999	D;D;D;D	0.81914	0.995;0.989;0.987;0.995	T	0.46789	-0.9166	10	0.32370	T	0.25	.	17.5611	0.87908	0.0:0.0:1.0:0.0	.	453;316;406;465	B4DUV8;B7Z227;Q8N5Y2-2;Q8N5Y2	.;.;.;MS3L1_HUMAN	K	465;316;453;299	ENSP00000312244:E465K;ENSP00000354562:E316K;ENSP00000381538:E453K;ENSP00000370069:E299K	ENSP00000312244:E465K	E	+	1	0	MSL3	11700672	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.649000	0.91067	2.074000	0.62210	0.600000	0.82982	GAA	.	.		0.358	MSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055757.1	NM_006800		A	11790751	G	A	11790751	3	1	80	1	0	0	0	0	1	0	0	0	9888	943	33	3	1519	3	MSL3	23	11790751	Missense_Mutation	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10		11790751	143479809	82	11044										
CXorf58	254158	hgsc.bcm.edu	37	chrX	23928463	23928463	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	acgtaaaggtattctgaaatCaggtacaagatccttacaaa	7	7	2	2			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chrX:23928463C>G	ENST00000379211.3	+	2	593	c.44C>G	c.(43-45)tCa>tGa	p.S15*	APOO_ENST00000379220.3_5'Flank|APOO_ENST00000379226.4_5'Flank	NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58	15										breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						ATTCTGAAATCAGGTACAAGA	0.358																																					p.S15X		Atlas-SNP	.											.	CXorf58	53	.	0			c.C44G						.						129	98	109					X																	23928463		2203	4300	6503	SO:0001587	stop_gained	254158	exon2			TGAAATCAGGTAC	AK058173	CCDS14209.1	Xp22.11	2012-11-28			ENSG00000165182	ENSG00000165182			26356	protein-coding gene	gene with protein product							Standard	NM_152761		Approved	FLJ25444	uc004daz.1	Q96LI9	OTTHUMG00000021258	ENST00000379211.3:c.44C>G	chrX.hg19:g.23928463C>G	ENSP00000368511:p.Ser15*	381.0	0.0		374.0	204.0	NM_152761		Nonsense_Mutation	SNP	ENST00000379211.3	hg19	CCDS14209.1	.	.	.	.	.	.	.	.	.	.	C	38	6.777893	0.97833	.	.	ENSG00000165182	ENST00000379211	.	.	.	3.52	1.74	0.24563	.	0.261790	0.20378	N	0.093510	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-3.7147	5.1842	0.15176	0.0:0.7194:0.0:0.2806	.	.	.	.	X	15	.	ENSP00000368511:S15X	S	+	2	0	CXorf58	23838384	0.760000	0.28428	0.037000	0.18230	0.003000	0.03518	0.933000	0.28897	0.334000	0.23590	-0.192000	0.12808	TCA	.	.		0.358	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761		G	23928463	C	G	23928463	4	3	80	1	0	0	0	0	0	1	0	0	4116	838	29	4	46	4	CXorf58	23	23928463	Nonsense_Mutation	SNP	C	TCGA-CC-A8HU-01A-11D-A35Z-10	12137712	23928463	131342097	83	11045										
MAGED1	9500	hgsc.bcm.edu	37	chrX	51638488	51638488	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	caaatgctgcctatgattttTcccaggcagcaaccactggt	8	12	0	1			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chrX:51638488T>C	ENST00000375722.1	+	3	637	c.385T>C	c.(385-387)Tcc>Ccc	p.S129P	MAGED1_ENST00000494718.1_3'UTR|MAGED1_ENST00000326587.7_Missense_Mutation_p.S129P|MAGED1_ENST00000375772.3_Missense_Mutation_p.S129P|MAGED1_ENST00000375695.2_Missense_Mutation_p.S185P			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1	129					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					CTATGATTTTTCCCAGGCAGC	0.512										Multiple Myeloma(10;0.10)																											p.S185P		Atlas-SNP	.											.	MAGED1	84	.	0			c.T553C						.						42	37	39					X																	51638488		2203	4297	6500	SO:0001583	missense	9500	exon4			GATTTTTCCCAGG	AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.385T>C	chrX.hg19:g.51638488T>C	ENSP00000364874:p.Ser129Pro	196.0	0.0		178.0	42.0	NM_001005333	Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Missense_Mutation	SNP	ENST00000375722.1	hg19	CCDS14337.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.877151	0.33162	.	.	ENSG00000179222	ENST00000375772;ENST00000375722;ENST00000326587;ENST00000375695	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	3.91	3.91	0.45181	.	0.000000	0.42821	D	0.000641	T	0.40743	0.1129	L	0.34521	1.04	0.31722	N	0.638211	P;B	0.37731	0.607;0.236	B;B	0.39419	0.299;0.081	T	0.52298	-0.8594	10	0.46703	T	0.11	.	8.3147	0.32093	0.0:0.0:0.0:1.0	.	185;129	Q9Y5V3-2;Q9Y5V3	.;MAGD1_HUMAN	P	129;129;129;185	ENSP00000364927:S129P;ENSP00000364874:S129P;ENSP00000325333:S129P;ENSP00000364847:S185P	ENSP00000325333:S129P	S	+	1	0	MAGED1	51655228	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.904000	0.48719	1.781000	0.52344	0.422000	0.28245	TCC	.	.		0.512	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056593.1	NM_001005332		C	51638488	T	C	51638488	3	2	80	1	0	0	0	0	1	0	0	0	9192	1783	62	2	563	2	MAGED1	23	51638488	Missense_Mutation	SNP	T	TCGA-CC-A8HU-01A-11D-A35Z-10	27710025	51638488	103632072	84	11046										
PHF8	23133	hgsc.bcm.edu	37	chrX	54013589	54013589	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ttcgcacggggcaatttccgGggaaattctagaaaacaatg	11	8	1	1	rs148356929		TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chrX:54013589G>A	ENST00000357988.5	-	16	2383	c.2025C>T	c.(2023-2025)ccC>ccT	p.P675P	PHF8_ENST00000338946.6_Silent_p.P538P|PHF8_ENST00000338154.6_Silent_p.P639P|PHF8_ENST00000322659.8_Silent_p.P639P	NM_001184896.1	NP_001171825.1	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	675					brain development (GO:0007420)|G1/S transition of mitotic cell cycle (GO:0000082)|histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of chromatin silencing at rDNA (GO:0061188)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	40						GCAATTTCCGGGGAAATTCTA	0.423																																					p.P675P		Atlas-SNP	.											.	PHF8	198	.	0			c.C2025T						.						70	61	64					X																	54013589		2203	4300	6503	SO:0001819	synonymous_variant	23133	exon16			TTTCCGGGGAAAT	AB029034	CCDS14355.1, CCDS55418.1, CCDS55419.1, CCDS55420.1	Xp11.22	2013-01-28			ENSG00000172943	ENSG00000172943		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	20672	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1F"	300560				10470851, 20023638, 20644565	Standard	NM_015107		Approved	ZNF422, KIAA1111, JHDM1F	uc004dsu.3	Q9UPP1	OTTHUMG00000021622	ENST00000357988.5:c.2025C>T	chrX.hg19:g.54013589G>A		173.0	0.0		153.0	86.0	NM_001184896	B3KMV4|B7Z911|Q5H9U5|Q5JPR9|Q5JPS0|Q5JPS2|Q5JPS3|Q5VUJ4|Q7Z6D4|Q9HAH2	Silent	SNP	ENST00000357988.5	hg19	CCDS55420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.574|9.574	1.121761|1.121761	0.20877|0.20877	.|.	.|.	ENSG00000172943|ENSG00000172943	ENST00000396282|ENST00000443302	T|T	0.31247|0.45668	1.5|0.89	5.08|5.08	0.976|0.976	0.19727|0.19727	.|.	0.594842|0.594842	0.18063|0.18063	N|N	0.152871|0.152871	T|T	0.39410|0.39410	0.1077|0.1077	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.07731|0.07731	-1.0757|-1.0757	7|7	0.45353|0.28530	T|T	0.12|0.3	-6.1382|-6.1382	7.6553|7.6553	0.28371|0.28371	0.4155:0.0:0.5845:0.0|0.4155:0.0:0.5845:0.0	.|.	.|.	.|.	.|.	L|S	543|403	ENSP00000379578:P543L|ENSP00000397129:P403S	ENSP00000379578:P543L|ENSP00000397129:P403S	P|P	-|-	2|1	0|0	PHF8|PHF8	54030314|54030314	0.951000|0.951000	0.32395|0.32395	0.991000|0.991000	0.47740|0.47740	0.986000|0.986000	0.74619|0.74619	-0.032000|-0.032000	0.12266|0.12266	-0.249000|-0.249000	0.09569|0.09569	-0.407000|-0.407000	0.06327|0.06327	CCC|CCG	.	G|1.000;C|0.000		0.423	PHF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056784.2	NM_015107		A	54013589	G	A	54013589	2	1	80	1	0	0	0	0	0	0	0	1	11849	1219	43	3		3	PHF8	23	54013589	Silent	SNP	G	TCGA-CC-A8HU-01A-11D-A35Z-10	2375101	54013589	101256971	85	11047										
AR	367	hgsc.bcm.edu	37	chrX	66765551	66765552	+	Missense_Mutation	DNP	CC	CC	AA													0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	taaagacatcctgagcgaggCcagcaccatgcaactccttc							TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chrX:66765551_66765552CC>AA	ENST00000374690.3	+	1	1087_1088	c.563_564CC>AA	c.(562-564)gCC>gAA	p.A188E	AR_ENST00000504326.1_Missense_Mutation_p.A188E|AR_ENST00000396044.3_Missense_Mutation_p.A188E|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	186	Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CTGAGCGAGGCCAGCACCATGC	0.624									Androgen Insensitivity Syndrome																												p.A188D|p.A188A		Atlas-SNP	.											.	AR	249	.	0			c.C563A|c.C564A						.																																			SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GCGAGGCCAGCAC|CGAGGCCAGCACC	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	Exception_encountered	chrX.hg19:g.66765551_66765552delinsAA	ENSP00000363822:p.Ala188Glu	156.0|157.0	0.0		172.0|170.0	58.0|57.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation|Silent	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.		0.624	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		AA	66765552	CC	AA	66765551	3	1	80	1	0	0	0	0	1	0	0	0	836	739	26	3	565	3	AR	23	66765551	Missense_Mutation	DNP	CC	TCGA-CC-A8HU-01A-11D-A35Z-10	12751962	66765551	88505009	86	11048										
TAF1	6872	hgsc.bcm.edu	37	chrX	70598216	70598216	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0697674418604651	6	1	1.51041666666667	2.01388888888889	1.34259259259259	0.619909502262444	1	0	ctgtggtatgatatgctgggTgtccctgaagatggcagtgg	16	6	0	3			TCGA-CC-A8HU-01A-11D-A35Z-10	TCGA-CC-A8HU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5d7d4f-5e5c-46e5-b7de-7cc07db0791d	bb86c7c8-28de-4fbb-830b-e0328aa71b1d	g.chrX:70598216T>A	ENST00000373790.4	+	7	1113	c.1062T>A	c.(1060-1062)ggT>ggA	p.G354G	TAF1_ENST00000423759.1_Silent_p.G375G|TAF1_ENST00000449580.1_Silent_p.G354G|TAF1_ENST00000276072.3_Silent_p.G375G	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	354	Protein kinase 1.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				ATATGCTGGGTGTCCCTGAAG	0.453																																					p.G375G		Atlas-SNP	.											.	TAF1	439	.	0			c.T1125A						.						197	161	174					X																	70598216		2203	4300	6503	SO:0001819	synonymous_variant	6872	exon7			GCTGGGTGTCCCT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.1062T>A	chrX.hg19:g.70598216T>A		258.0	0.0		227.0	56.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	hg19	CCDS35325.1																																																																																			.	.		0.453	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70598216	T	A	70598216	2	1	80	1	0	0	0	0	0	0	0	1	15528	1683	59	4		4	TAF1	23	70598216	Silent	SNP	T	TCGA-CC-A8HU-01A-11D-A35Z-10	3832665	70598216	84672344	87	11049										
ATAD3B	83858	hgsc.bcm.edu	37	chr1	1431055	1431055	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	atggagcctggccacggaccCctcctacccctgccttgccg	10	19	0	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:1431055C>T	ENST00000308647.7	+	16	1921	c.1805C>T	c.(1804-1806)cCc>cTc	p.P602L		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	602						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GCCACGGACCCCTCCTACCCC	0.672																																					p.P602L		Atlas-SNP	.											.	ATAD3B	68	.	0			c.C1805T						.						35	36	36					1																	1431055		2202	4298	6500	SO:0001583	missense	83858	exon16			CGGACCCCTCCTA	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"ATPases / AAA-type"	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1805C>T	chr1.hg19:g.1431055C>T	ENSP00000311766:p.Pro602Leu	108.0	0.0		48.0	24.0	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	hg19	CCDS30.1	.	.	.	.	.	.	.	.	.	.	c	8.226	0.803560	0.16467	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.94376	-3.41	1.2	0.203	0.15195	.	10.614000	0.03382	U	0.200496	D	0.91109	0.7201	N	0.08118	0	0.09310	N	0.999999	D;P	0.69078	0.997;0.588	D;B	0.68483	0.958;0.072	T	0.81904	-0.0719	10	0.87932	D	0	.	3.3576	0.07174	0.0:0.7016:0.0:0.2984	.	556;602	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	L	436;602	ENSP00000311766:P602L	ENSP00000311766:P602L	P	+	2	0	ATAD3B	1420918	0.000000	0.05858	0.002000	0.10522	0.025000	0.11179	-1.241000	0.02911	0.070000	0.16634	0.194000	0.17425	CCC	.	.		0.672	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		T	1431055	C	T	1431055	3	4	81	1	0	0	0	0	1	0	0	0	1074	623	22	3	1867	3	ATAD3B	1	1431055	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10		1431055	247819566	1	11050										
TAS1R1	80835	hgsc.bcm.edu	37	chr1	6631179	6631179	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gagctccaaggagaccttctCcactattcccctacggtgct	8	15	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:6631179C>T	ENST00000333172.6	+	2	595	c.402C>T	c.(400-402)ctC>ctT	p.L134L	TAS1R1_ENST00000328191.4_Silent_p.L134L|TAS1R1_ENST00000351136.3_Silent_p.L134L	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	134					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		GAGACCTTCTCCACTATTCCC	0.577																																					p.L134L		Atlas-SNP	.											.	TAS1R1	76	.	0			c.C402T						.						136	126	130					1																	6631179		2203	4300	6503	SO:0001819	synonymous_variant	80835	exon2			CCTTCTCCACTAT		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14448	protein-coding gene	gene with protein product		606225	"G protein-coupled receptor 70"	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.402C>T	chr1.hg19:g.6631179C>T		104.0	0.0		89.0	21.0	NM_177540	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Silent	SNP	ENST00000333172.6	hg19	CCDS81.1	.	.	.	.	.	.	.	.	.	.	C	3.842	-0.033535	0.07543	.	.	ENSG00000173662	ENST00000411823;ENST00000415267	.	.	.	5.08	3.18	0.36537	.	.	.	.	.	T	0.34571	0.0902	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.20207	-1.0282	4	.	.	.	.	7.4485	0.27225	0.0:0.5539:0.3546:0.0915	.	.	.	.	F	60	.	.	S	+	2	0	TAS1R1	6553766	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.281000	0.08456	0.499000	0.27970	0.650000	0.86243	TCC	.	.		0.577	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			T	6631179	C	T	6631179	2	4	81	1	0	0	0	0	0	0	0	1	15577	842	30	3		3	TAS1R1	1	6631179	Silent	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	5200124	6631179	242619442	2	11051										
TCEB3	6924	hgsc.bcm.edu	37	chr1	24070016	24070016	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ggcggcggagtcggcgctccAagttgtggagaagctgcagg	19	9	0	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:24070016A>G	ENST00000418390.2	+	1	372	c.101A>G	c.(100-102)cAa>cGa	p.Q34R	TCEB3_ENST00000609199.1_Missense_Mutation_p.Q8R	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	34	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		TCGGCGCTCCAAGTTGTGGAG	0.721																																					p.Q34R		Atlas-SNP	.											.	TCEB3	61	.	0			c.A101G						.						4	4	4					1																	24070016		1818	3531	5349	SO:0001583	missense	6924	exon1			CGCTCCAAGTTGT	L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.101A>G	chr1.hg19:g.24070016A>G	ENSP00000395574:p.Gln34Arg	48.0	0.0		27.0	15.0	NM_003198	B2R7Q8|Q8IXH1	Missense_Mutation	SNP	ENST00000418390.2	hg19	CCDS239.2	.	.	.	.	.	.	.	.	.	.	a	10.57	1.387508	0.25031	.	.	ENSG00000011007	ENST00000418390	T	0.06218	3.33	3.02	3.02	0.34903	Transcription factor IIS, N-terminal (3);Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type (1);	0.316661	0.22419	U	0.060314	T	0.03608	0.0103	N	0.16790	0.44	0.29693	N	0.840764	B	0.26672	0.156	B	0.18871	0.023	T	0.32295	-0.9912	10	0.09338	T	0.73	-12.4162	11.5142	0.50511	1.0:0.0:0.0:0.0	.	34	Q14241	ELOA1_HUMAN	R	34	ENSP00000395574:Q34R	ENSP00000395574:Q34R	Q	+	2	0	TCEB3	23942603	1.000000	0.71417	0.995000	0.50966	0.024000	0.10985	3.473000	0.53122	1.160000	0.42584	0.370000	0.22315	CAA	.	.		0.721	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198		G	24070016	A	G	24070016	3	3	81	1	0	0	0	0	1	0	0	0	15696	130	5	2	103	2	TCEB3	1	24070016	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	17438837	24070016	225180605	3	11052										
TEKT2	27285	hgsc.bcm.edu	37	chr1	36551578	36551578	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	atgagctgcataaagaggtgGaggtcatcgaggccaccaag	14	8	1	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:36551578G>A	ENST00000207457.3	+	4	551	c.424G>A	c.(424-426)Gag>Aag	p.E142K	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	142					cell projection organization (GO:0030030)|inner dynein arm assembly (GO:0036159)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)|skin(2)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TAAAGAGGTGGAGGTCATCGA	0.592																																					p.E142K		Atlas-SNP	.											.	TEKT2	32	.	0			c.G424A						.						86	62	70					1																	36551578		2202	4300	6502	SO:0001583	missense	27285	exon4			GAGGTGGAGGTCA	AB033823	CCDS401.1	1p34.3	2008-02-05			ENSG00000092850	ENSG00000092850			11725	protein-coding gene	gene with protein product		608953				12029069, 11751288	Standard	NM_014466		Approved	TEKTB1	uc001bzr.3	Q9UIF3	OTTHUMG00000007629	ENST00000207457.3:c.424G>A	chr1.hg19:g.36551578G>A	ENSP00000207457:p.Glu142Lys	231.0	1.0		161.0	79.0	NM_014466	A6NIS6|O60638	Missense_Mutation	SNP	ENST00000207457.3	hg19	CCDS401.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.513959	0.64522	.	.	ENSG00000092850	ENST00000207457	T	0.02787	4.16	5.51	5.51	0.81932	.	0.104490	0.64402	D	0.000006	T	0.06005	0.0156	M	0.83312	2.635	0.48511	D	0.999667	P	0.34977	0.478	B	0.31390	0.129	T	0.23119	-1.0197	10	0.26408	T	0.33	.	13.1696	0.59591	0.0821:0.0:0.9179:0.0	.	142	Q9UIF3	TEKT2_HUMAN	K	142	ENSP00000207457:E142K	ENSP00000207457:E142K	E	+	1	0	TEKT2	36324165	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.693000	0.61753	2.593000	0.87608	0.655000	0.94253	GAG	.	.		0.592	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466		A	36551578	G	A	36551578	3	1	81	1	0	0	0	0	1	0	0	0	15768	1175	41	3	434	3	TEKT2	1	36551578	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	12481562	36551578	212699043	4	11053										
MFSD2A	84879	hgsc.bcm.edu	37	chr1	40422841	40422841	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gggagccccctaccaggtgaCgggctgtgccctgggtttct	15	13	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:40422841C>T	ENST00000372809.5	+	2	319	c.176C>T	c.(175-177)aCg>aTg	p.T59M	MFSD2A_ENST00000372811.5_Missense_Mutation_p.T59M|MFSD2A_ENST00000420632.2_Intron	NM_001136493.1	NP_001129965.1	Q8NA29	NLS1_HUMAN	major facilitator superfamily domain containing 2A	59					establishment of blood-brain barrier (GO:0060856)|fatty acid transport (GO:0015908)|lipid transport across blood brain barrier (GO:1990379)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phospholipid transporter activity (GO:0005548)|symporter activity (GO:0015293)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						TACCAGGTGACGGGCTGTGCC	0.517																																					p.T59M		Atlas-SNP	.											.	MFSD2A	53	.	0			c.C176T						.						181	192	188					1																	40422841		2203	4300	6503	SO:0001583	missense	84879	exon2			AGGTGACGGGCTG	AK093223	CCDS446.1, CCDS44118.1, CCDS72762.1	1p34.2	2009-09-08	2009-09-08	2009-09-08	ENSG00000168389	ENSG00000168389			25897	protein-coding gene	gene with protein product		614397	"major facilitator superfamily domain containing 2"	MFSD2		18694395	Standard	XM_005271285		Approved	FLJ14490	uc001cev.3	Q8NA29	OTTHUMG00000009293	ENST00000372809.5:c.176C>T	chr1.hg19:g.40422841C>T	ENSP00000361895:p.Thr59Met	102.0	0.0		58.0	30.0	NM_032793	A8K675|Q6UWU5|Q96F59|Q9BRC8	Missense_Mutation	SNP	ENST00000372809.5	hg19	CCDS44118.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.029815	0.75504	.	.	ENSG00000168389	ENST00000372811;ENST00000434861;ENST00000372809	D;D;D	0.87103	-2.21;-2.21;-2.21	4.86	4.86	0.63082	Major facilitator superfamily domain, general substrate transporter (1);	0.093439	0.64402	D	0.000001	D	0.93080	0.7797	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.81914	0.995;0.977	D	0.91914	0.5542	10	0.27785	T	0.31	-13.4054	16.9853	0.86338	0.0:1.0:0.0:0.0	.	59;59	Q8NA29;Q8NA29-2	MFS2A_HUMAN;.	M	59;57;59	ENSP00000361898:T59M;ENSP00000407606:T57M;ENSP00000361895:T59M	ENSP00000361895:T59M	T	+	2	0	MFSD2A	40195428	1.000000	0.71417	0.944000	0.38274	0.904000	0.53231	7.258000	0.78371	2.250000	0.74265	0.462000	0.41574	ACG	.	.		0.517	MFSD2A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025756.1	NM_032793		T	40422841	C	T	40422841	3	4	81	1	0	0	0	0	1	0	0	0	9539	536	19	1	182	1	MFSD2A	1	40422841	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	3871263	40422841	208827780	5	11054										
EBNA1BP2	10969	hgsc.bcm.edu	37	chr1	43637224	43637224	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttctgaggtgctggcgcctcAgatccaccgatctccggtac	11	14	3	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:43637224A>C	ENST00000236051.2	-	3	390	c.249T>G	c.(247-249)tcT>tcG	p.S83S	EBNA1BP2_ENST00000472982.1_5'UTR|EBNA1BP2_ENST00000431635.2_Silent_p.S138S|WDR65_ENST00000372492.4_5'Flank|WDR65_ENST00000528956.1_5'Flank	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	83					ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)	16	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTGGCGCCTCAGATCCACCGA	0.498																																					p.S138S		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.T414G						.						164	160	161					1																	43637224		2203	4300	6503	SO:0001819	synonymous_variant	10969	exon4			CGCCTCAGATCCA	U86602	CCDS478.1, CCDS53308.1	1p35-p33	2011-02-10	2001-11-28		ENSG00000117395	ENSG00000117395			15531	protein-coding gene	gene with protein product		614443	"EBNA1-binding protein 2"			10074103, 11438656	Standard	NM_001159936		Approved	NOBP, EBP2, P40	uc010ojx.2	Q99848	OTTHUMG00000007284	ENST00000236051.2:c.249T>G	chr1.hg19:g.43637224A>C		140.0	0.0		121.0	71.0	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	hg19	CCDS478.1																																																																																			.	.		0.498	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1			C	43637224	A	C	43637224	2	2	81	1	0	0	0	0	0	0	0	1	4887	175	7	5		5	EBNA1BP2	1	43637224	Silent	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	3214383	43637224	205613397	6	11055										
FAM73A	374986	hgsc.bcm.edu	37	chr1	78245389	78245389	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tcagctgggaagctggcgtgGgcaggccagctgtacctggc	17	11	1	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:78245389G>C	ENST00000370791.3	+	1	81	c.49G>C	c.(49-51)Ggc>Cgc	p.G17R	RNA5SP21_ENST00000410917.1_RNA|FAM73A_ENST00000443751.2_Missense_Mutation_p.G17R	NM_001270384.1|NM_198549.3	NP_001257313.1|NP_940951.1	Q8NAN2	FA73A_HUMAN	family with sequence similarity 73, member A	17						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	19				Colorectal(170;0.226)		AGCTGGCGTGGGCAGGCCAGC	0.677																																					p.G17R		Atlas-SNP	.											.	FAM73A	56	.	0			c.G49C						.						7	7	7					1																	78245389		2178	4250	6428	SO:0001583	missense	374986	exon1			GGCGTGGGCAGGC		CCDS681.1, CCDS72809.1	1p31.1	2008-02-05			ENSG00000180488	ENSG00000180488			24741	protein-coding gene	gene with protein product							Standard	NM_001270384		Approved	FLJ35093	uc010ork.3	Q8NAN2	OTTHUMG00000009766	ENST00000370791.3:c.49G>C	chr1.hg19:g.78245389G>C	ENSP00000359827:p.Gly17Arg	84.0	0.0		59.0	26.0	NM_001270384	Q6MZG0	Missense_Mutation	SNP	ENST00000370791.3	hg19	CCDS681.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.363884	0.24684	.	.	ENSG00000180488	ENST00000370791;ENST00000443751	T;T	0.38401	1.76;1.14	1.59	0.584	0.17422	.	.	.	.	.	T	0.06096	0.0158	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.32052	-0.9921	9	0.87932	D	0	-5.6091	3.1193	0.06386	0.302:0.0:0.698:0.0	.	17;17;17	F8W7S1;B7ZLZ8;Q8NAN2	.;.;FA73A_HUMAN	R	17	ENSP00000359827:G17R;ENSP00000393675:G17R	ENSP00000359827:G17R	G	+	1	0	FAM73A	78017977	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-0.729000	0.04920	0.777000	0.33496	0.650000	0.86243	GGC	.	.		0.677	FAM73A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026931.1	NM_198549		C	78245389	G	C	78245389	3	2	81	1	0	0	0	0	1	0	0	0	5625	1232	43	4	51	4	FAM73A	1	78245389	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	34608165	78245389	171005232	7	11056										
CLCA1	1179	hgsc.bcm.edu	37	chr1	86965557	86965558	+	Missense_Mutation	DNP	CA	CA	AG													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ctgaaatcagaaatatccaaCattgcacgagtatctttgtt							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:86965557_86965558CA>AG	ENST00000234701.3	+	15	2925_2926	c.2574_2575CA>AG	c.(2572-2577)aaCAtt>aaAGtt	p.858_859NI>KV	CLCA1_ENST00000394711.1_Missense_Mutation_p.858_859NI>KV			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	858					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		AAATATCCAACATTGCACGAGT	0.386																																					p.N858K|p.I859V		Atlas-SNP	.											.	CLCA1	109	.	0			c.C2574A|c.A2575G						.																																			SO:0001583	missense	1179	exon14			ATCCAACATTGCA|TCCAACATTGCAC		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	Exception_encountered	chr1.hg19:g.86965557_86965558delinsAG	ENSP00000234701:p.N858_I859delinsKV	179.0|180.0	0.0		123.0|122.0	29.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	hg19	CCDS709.1																																																																																			.	.		0.386	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		AG	86965558	CA	AG	86965557	3	1	81	1	0	0	0	0	1	0	0	0	3459	477	17	3	2628	3	CLCA1	1	86965557	Missense_Mutation	DNP	CA	TCGA-CC-A8HV-01A-11D-A35Z-10	8720168	86965557	162285064	8	11057										
GPR61	83873	hgsc.bcm.edu	37	chr1	110085966	110085966	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gctctgccctctttgaccacGccctctttggggaggtggcc	12	15	3	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:110085966G>A	ENST00000527748.1	+	2	1005	c.322G>A	c.(322-324)Gcc>Acc	p.A108T	RP5-1160K1.8_ENST00000526411.1_RNA	NM_031936.4	NP_114142.3	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	108						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.A108T(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	23		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)		CTTTGACCACGCCCTCTTTGG	0.592																																					p.A108T		Atlas-SNP	.											GPR61,colon,carcinoma,0,1	GPR61	60	.	1	Substitution - Missense(1)	large_intestine(1)	c.G322A						.						94	88	90					1																	110085966		2203	4300	6503	SO:0001583	missense	83873	exon2			GACCACGCCCTCT	AF317652	CCDS801.1	1p13.3	2012-08-21			ENSG00000156097	ENSG00000156097		"GPCR / Class A : Orphans"	13300	protein-coding gene	gene with protein product		606916				11165367, 11690637	Standard	NM_031936		Approved	BALGR	uc001dxy.2	Q9BZJ8	OTTHUMG00000011633	ENST00000527748.1:c.322G>A	chr1.hg19:g.110085966G>A	ENSP00000432456:p.Ala108Thr	56.0	0.0		50.0	25.0	NM_031936	A8K1W2|Q6NWS0|Q8TDV4|Q96PR4	Missense_Mutation	SNP	ENST00000527748.1	hg19	CCDS801.1	.	.	.	.	.	.	.	.	.	.	G	7.585	0.669553	0.14776	.	.	ENSG00000156097	ENST00000527748;ENST00000286603	T	0.71698	-0.59	5.46	4.55	0.56014	GPCR, rhodopsin-like superfamily (1);	0.380223	0.22057	N	0.065238	T	0.37892	0.1020	L	0.34521	1.04	0.29396	N	0.86225	B	0.11235	0.004	B	0.06405	0.002	T	0.27872	-1.0061	10	0.54805	T	0.06	-2.2681	6.2484	0.20832	0.1602:0.2661:0.5737:0.0	.	108	Q9BZJ8	GPR61_HUMAN	T	108;236	ENSP00000432456:A108T	ENSP00000286603:A236T	A	+	1	0	GPR61	109887489	0.007000	0.16637	0.804000	0.32291	0.976000	0.68499	1.699000	0.37804	1.294000	0.44707	0.655000	0.94253	GCC	.	.		0.592	GPR61-005	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385575.1			A	110085966	G	A	110085966	3	1	81	1	0	0	0	0	1	0	0	0	6710	1087	38	1	324	1	GPR61	1	110085966	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	23120409	110085966	139164655	9	11058										
MAGI3	260425	hgsc.bcm.edu	37	chr1	114162434	114162434	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	agcagttaggacaggttgaaAttgggtcttcaaaaccaggt	12	6	2	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:114162434A>C	ENST00000307546.9	+	8	1228	c.1153A>C	c.(1153-1155)Att>Ctt	p.I385L	MAGI3_ENST00000369617.4_Missense_Mutation_p.I410L|MAGI3_ENST00000369615.1_Missense_Mutation_p.I385L|MAGI3_ENST00000369611.4_Missense_Mutation_p.I385L	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	410					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAGGTTGAAATTGGGTCTTC	0.348																																					p.I385L		Atlas-SNP	.											.	MAGI3	181	.	0			c.A1153C						.						104	110	108					1																	114162434		2203	4300	6503	SO:0001583	missense	260425	exon8			GTTGAAATTGGGT	AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.1153A>C	chr1.hg19:g.114162434A>C	ENSP00000304604:p.Ile385Leu	344.0	0.0		231.0	75.0	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Missense_Mutation	SNP	ENST00000307546.9	hg19	CCDS44196.1	.	.	.	.	.	.	.	.	.	.	A	9.647	1.140504	0.21205	.	.	ENSG00000081026	ENST00000369617;ENST00000307546;ENST00000369615;ENST00000369611	T;T;T;T	0.13420	2.69;2.59;2.72;2.72	4.77	2.41	0.29592	.	0.374402	0.29383	N	0.012320	T	0.01558	0.0050	N	0.14661	0.345	0.24123	N	0.995796	B;B;B	0.14805	0.011;0.001;0.0	B;B;B	0.15052	0.012;0.002;0.001	T	0.47100	-0.9143	10	0.08837	T	0.75	-20.8909	5.3451	0.16004	0.6104:0.0:0.3896:0.0	.	385;385;410	Q5TCQ9-4;Q5TCQ9-3;Q5TCQ9-2	.;.;.	L	410;385;385;385	ENSP00000358630:I410L;ENSP00000304604:I385L;ENSP00000358628:I385L;ENSP00000358624:I385L	ENSP00000304604:I385L	I	+	1	0	MAGI3	113963957	0.861000	0.29849	0.976000	0.42696	0.979000	0.70002	1.264000	0.33015	0.678000	0.31325	0.460000	0.39030	ATT	.	.		0.348	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		C	114162434	A	C	114162434	3	2	81	1	0	0	0	0	1	0	0	0	9201	101	4	5	1183	5	MAGI3	1	114162434	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	4076468	114162434	135088187	10	11059										
PTPN22	26191	hgsc.bcm.edu	37	chr1	114380834	114380834	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ggaaatgcctttgtctgccaTttcatggttgtgtcagcatt	10	8	3	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:114380834T>C	ENST00000359785.5	-	13	1323	c.1188A>G	c.(1186-1188)aaA>aaG	p.K396K	PTPN22_ENST00000420377.2_Silent_p.K396K|PTPN22_ENST00000528414.1_Silent_p.K341K|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000538253.1_Silent_p.K152K|PTPN22_ENST00000525799.1_Silent_p.K269K	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	396					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTGTCTGCCATTTCATGGTTG	0.393																																					p.K396K		Atlas-SNP	.											.	PTPN22	90	.	0			c.A1188G						.						93	93	93					1																	114380834		2203	4300	6503	SO:0001819	synonymous_variant	26191	exon13			CTGCCATTTCATG	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.1188A>G	chr1.hg19:g.114380834T>C		93.0	0.0		74.0	22.0	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Silent	SNP	ENST00000359785.5	hg19	CCDS863.1																																																																																			.	.		0.393	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		C	114380834	T	C	114380834	2	2	81	1	0	0	0	0	0	0	0	1	12802	1490	52	2		2	PTPN22	1	114380834	Silent	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	218400	114380834	134869787	11	11060										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158654957	158654957	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gatattgactttctccatgaTccacttccccagatcatctg	5	13	3	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:158654957T>C	ENST00000368147.4	-	2	385	c.205A>G	c.(205-207)Atc>Gtc	p.I69V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	69					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTCTCCATGATCCACTtcccc	0.448																																					p.I69V		Atlas-SNP	.											.	SPTA1	720	.	0			c.A205G						.						119	114	115					1																	158654957		1928	4145	6073	SO:0001583	missense	6708	exon2			CCATGATCCACTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.205A>G	chr1.hg19:g.158654957T>C	ENSP00000357129:p.Ile69Val	120.0	0.0		171.0	32.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268040	0.40095	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.39787	1.06;1.06	5.18	4.05	0.47172	.	0.249234	0.21012	N	0.081678	T	0.53222	0.1783	M	0.79693	2.465	0.49582	D	0.999806	B	0.28820	0.224	P	0.54270	0.747	T	0.58272	-0.7665	10	0.51188	T	0.08	.	10.0598	0.42268	0.0:0.0798:0.0:0.9202	.	69	P02549	SPTA1_HUMAN	V	69	ENSP00000357130:I69V;ENSP00000357129:I69V	ENSP00000357129:I69V	I	-	1	0	SPTA1	156921581	1.000000	0.71417	0.997000	0.53966	0.320000	0.28249	5.567000	0.67378	0.989000	0.38761	0.383000	0.25322	ATC	.	.		0.448	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158654957	T	C	158654957	3	2	81	1	0	0	0	0	1	0	0	0	15131	1435	50	2	7258	2	SPTA1	1	158654957	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	44274123	158654957	90595664	12	11061										
ATP1A4	480	hgsc.bcm.edu	37	chr1	160137138	160137138	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gcagtcttacagctctgtggCggagatgagagagaaaaacc	13	8	2	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:160137138C>A	ENST00000368081.4	+	10	1898	c.1427C>A	c.(1426-1428)gCg>gAg	p.A476E		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	476					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGCTCTGTGGCGGAGATGAGA	0.517																																					p.A476E		Atlas-SNP	.											.	ATP1A4	167	.	0			c.C1427A						.						109	108	108					1																	160137138		2203	4300	6503	SO:0001583	missense	480	exon10			CTGTGGCGGAGAT	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1427C>A	chr1.hg19:g.160137138C>A	ENSP00000357060:p.Ala476Glu	114.0	0.0		147.0	21.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	hg19	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	C	1.570	-0.534430	0.04082	.	.	ENSG00000132681	ENST00000368081	D	0.96136	-3.92	4.55	-1.99	0.07457	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.953858	0.08790	N	0.893388	T	0.72211	0.3432	N	0.02854	-0.475	0.20074	N	0.999937	B	0.09022	0.002	B	0.16289	0.015	T	0.67043	-0.5770	10	0.48119	T	0.1	.	2.703	0.05154	0.2161:0.4662:0.1928:0.1248	.	476	Q13733	AT1A4_HUMAN	E	476	ENSP00000357060:A476E	ENSP00000357060:A476E	A	+	2	0	ATP1A4	158403762	0.000000	0.05858	0.960000	0.40013	0.700000	0.40528	-0.398000	0.07259	0.008000	0.14787	0.591000	0.81541	GCG	.	.		0.517	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		A	160137138	C	A	160137138	3	1	81	1	0	0	0	0	1	0	0	0	1131	768	27	1	1465	1	ATP1A4	1	160137138	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	1482181	160137138	89113483	13	11062										
SELE	6401	hgsc.bcm.edu	37	chr1	169700980	169700980	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	caagaaccagacttactttgCtcacacttgagtccactgaa	6	12	1	4			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:169700980C>T	ENST00000333360.7	-	4	664	c.525G>A	c.(523-525)gaG>gaA	p.E175E	SELE_ENST00000367779.4_Silent_p.E175E|SELE_ENST00000367780.4_Silent_p.E175E|SELE_ENST00000367776.1_Silent_p.E175E|SELE_ENST00000367782.4_Silent_p.E175E|SELE_ENST00000367775.1_Silent_p.E175E|SELE_ENST00000367781.4_Silent_p.E175E|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367777.1_Silent_p.E175E|SELE_ENST00000367774.1_Silent_p.E175E	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	175	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	ACTTACTTTGCTCACACTTGA	0.493																																					p.E175E		Atlas-SNP	.											.	SELE	84	.	0			c.G525A						.						134	106	115					1																	169700980		2203	4300	6503	SO:0001819	synonymous_variant	6401	exon4			ACTTTGCTCACAC	M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"CD molecules"	10718	protein-coding gene	gene with protein product		131210	"endothelial adhesion molecule 1"	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.525G>A	chr1.hg19:g.169700980C>T		84.0	0.0		112.0	17.0	NM_000450	A2RRD6|P16111	Silent	SNP	ENST00000333360.7	hg19	CCDS1283.1																																																																																			.	.		0.493	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450		T	169700980	C	T	169700980	2	4	81	1	0	0	0	0	0	0	0	1	14028	796	28	3		3	SELE	1	169700980	Silent	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	9563842	169700980	79549641	14	11063										
CFH	3075	hgsc.bcm.edu	37	chr1	196654311	196654311	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tggtttttatcctgcaacccGgggaaatacagcaaaatgca	9	9	0	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:196654311G>T	ENST00000359637.2	+	6	778	c.716G>T	c.(715-717)cGg>cTg	p.R239L	CFH_ENST00000439155.2_Missense_Mutation_p.R303L|CFH_ENST00000367429.4_Missense_Mutation_p.R303L			P08603	CFAH_HUMAN	complement factor H	303	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						CCTGCAACCCGGGGAAATACA	0.398																																					p.R303L		Atlas-SNP	.											.	CFH	251	.	0			c.G908T	GRCh37	CM086802	CFH	M		.						121	111	114					1																	196654311		2203	4300	6503	SO:0001583	missense	3075	exon7			CAACCCGGGGAAA	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000359637.2:c.716G>T	chr1.hg19:g.196654311G>T	ENSP00000352658:p.Arg239Leu	280.0	1.0		305.0	219.0	NM_001014975	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000359637.2	hg19		.	.	.	.	.	.	.	.	.	.	g	14.06	2.421254	0.42918	.	.	ENSG00000000971	ENST00000367429;ENST00000439155;ENST00000391986;ENST00000359637	T;T;T	0.64991	-0.13;-0.13;-0.13	5.11	-5.86	0.02304	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.61788	0.2375	L	0.51422	1.61	0.09310	N	1	P;D;D;D	0.61080	0.788;0.989;0.965;0.976	P;P;P;P	0.58660	0.448;0.843;0.688;0.508	T	0.57590	-0.7785	9	0.27785	T	0.31	.	8.4014	0.32588	0.5061:0.1117:0.3823:0.0	.	239;303;303;303	Q5TFM2;P08603-2;P08603;F8WDX4	.;.;CFAH_HUMAN;.	L	303;303;303;239	ENSP00000356399:R303L;ENSP00000402656:R303L;ENSP00000352658:R239L	ENSP00000352658:R239L	R	+	2	0	CFH	194920934	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.875000	0.01634	-0.943000	0.03691	-1.329000	0.01275	CGG	.	.		0.398	CFH-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000087502.1	NM_000186		T	196654311	G	T	196654311	3	4	81	1	0	0	0	0	1	0	0	0	3285	1116	39	1	934	1	CFH	1	196654311	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	26953331	196654311	52596310	15	11064										
PTPRC	5788	hgsc.bcm.edu	37	chr1	198713253	198713253	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	agaaacagaagtgaatttgtCtgaattacatccatatctac	6	7	2	4			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:198713253C>T	ENST00000367376.2	+	26	2933	c.2762C>T	c.(2761-2763)tCt>tTt	p.S921F	PTPRC_ENST00000352140.3_Missense_Mutation_p.S873F|PTPRC_ENST00000594404.1_Missense_Mutation_p.S760F|PTPRC_ENST00000348564.6_Missense_Mutation_p.S762F|PTPRC_ENST00000442510.2_Missense_Mutation_p.S923F	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	921					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						GTGAATTTGTCTGAATTACAT	0.393																																					p.S923F		Atlas-SNP	.											.	PTPRC	229	.	0			c.C2768T						.						112	106	108					1																	198713253		2203	4299	6502	SO:0001583	missense	5788	exon26			ATTTGTCTGAATT	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.2762C>T	chr1.hg19:g.198713253C>T	ENSP00000356346:p.Ser921Phe	134.0	0.0		176.0	26.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	hg19		.	.	.	.	.	.	.	.	.	.	C	19.70	3.877091	0.72180	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000442510;ENST00000348564	T	0.14516	2.5	5.78	4.86	0.63082	.	0.139297	0.33553	N	0.004796	T	0.32882	0.0844	M	0.62723	1.935	0.48341	D	0.999637	D;D;D	0.60160	0.987;0.987;0.987	D;D;D	0.64595	0.91;0.927;0.927	T	0.01524	-1.1333	10	0.72032	D	0.01	.	15.2403	0.73465	0.0:0.9314:0.0:0.0686	.	762;873;921	B1ALS3;E9PC28;P08575	.;.;PTPRC_HUMAN	F	923;873;921;760	ENSP00000193532:S873F	ENSP00000306782:S760F	S	+	2	0	PTPRC	196979876	0.999000	0.42202	0.965000	0.40720	0.900000	0.52787	2.404000	0.44539	2.724000	0.93272	0.637000	0.83480	TCT	.	.		0.393	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198713253	C	T	198713253	3	4	81	1	0	0	0	0	1	0	0	0	12812	913	32	3	2871	3	PTPRC	1	198713253	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	2058942	198713253	50537368	16	11065										
TP53BP2	7159	hgsc.bcm.edu	37	chr1	223984262	223984262	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ctgggtgctgctgttgattcTgggcagcagcaattacaggc	14	9	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:223984262T>C	ENST00000343537.7	-	13	2270	c.1979A>G	c.(1978-1980)cAg>cGg	p.Q660R	TP53BP2_ENST00000391879.2_5'UTR|TP53BP2_ENST00000391878.2_Missense_Mutation_p.Q531R|TP53BP2_ENST00000498843.1_5'UTR	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	654					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		CTGTTGATTCTGGGCAGCAGC	0.418																																					p.Q660R		Atlas-SNP	.											.	TP53BP2	144	.	0			c.A1979G						.						66	73	71					1																	223984262		2195	4251	6446	SO:0001583	missense	7159	exon13			TGATTCTGGGCAG	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.1979A>G	chr1.hg19:g.223984262T>C	ENSP00000341957:p.Gln660Arg	34.0	0.0		50.0	8.0	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	hg19	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.527710	0.64860	.	.	ENSG00000143514	ENST00000391878;ENST00000343537	T;T	0.46819	0.86;1.03	5.92	5.92	0.95590	.	0.590783	0.18967	N	0.126239	T	0.41811	0.1175	L	0.47716	1.5	0.80722	D	1	P;P	0.42827	0.791;0.592	B;B	0.38378	0.272;0.238	T	0.35151	-0.9800	10	0.42905	T	0.14	.	12.8313	0.57748	0.0:0.0:0.136:0.864	.	660;654	B4DG66;Q13625	.;ASPP2_HUMAN	R	531;660	ENSP00000375750:Q531R;ENSP00000341957:Q660R	ENSP00000341957:Q660R	Q	-	2	0	TP53BP2	222050885	1.000000	0.71417	0.901000	0.35422	0.934000	0.57294	3.762000	0.55250	2.274000	0.75844	0.533000	0.62120	CAG	.	.		0.418	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		C	223984262	T	C	223984262	3	2	81	1	0	0	0	0	1	0	0	0	16399	1580	55	2	1449	2	TP53BP2	1	223984262	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	25271009	223984262	25266359	17	11066										
FBXO28	23219	hgsc.bcm.edu	37	chr1	224345243	224345243	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	acagcttcaagaccaggaccAgaaactgctagagcagaccc	9	13	1	4			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr1:224345243A>G	ENST00000366862.5	+	5	945	c.902A>G	c.(901-903)cAg>cGg	p.Q301R	FBXO28_ENST00000424254.2_3'UTR	NM_015176.3	NP_055991.1	Q9NVF7	FBX28_HUMAN	F-box protein 28	301										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(2)|skin(1)	10	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		GACCAGGACCAGAAACTGCTA	0.458																																					p.Q301R		Atlas-SNP	.											.	FBXO28	34	.	0			c.A902G						.						164	168	167					1																	224345243		2203	4300	6503	SO:0001583	missense	23219	exon5			AGGACCAGAAACT	AK001628	CCDS1539.1, CCDS44320.1	1q42.12	2011-08-12			ENSG00000143756	ENSG00000143756		"F-boxes /  "other""	29046	protein-coding gene	gene with protein product	"centromere protein 30"	609100				9455484	Standard	NM_015176		Approved	FLJ10766, KIAA0483, Fbx28, CENP-30	uc001hoh.3	Q9NVF7	OTTHUMG00000037495	ENST00000366862.5:c.902A>G	chr1.hg19:g.224345243A>G	ENSP00000355827:p.Gln301Arg	174.0	0.0		237.0	28.0	NM_015176	E9PEM8|O75070	Missense_Mutation	SNP	ENST00000366862.5	hg19	CCDS1539.1	.	.	.	.	.	.	.	.	.	.	A	11.87	1.767115	0.31320	.	.	ENSG00000143756	ENST00000366862	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.58495	0.2126	N	0.19112	0.55	0.80722	D	1	D	0.54601	0.967	D	0.65140	0.932	T	0.52434	-0.8576	9	0.07030	T	0.85	-14.222	16.8222	0.85835	1.0:0.0:0.0:0.0	.	301	Q9NVF7	FBX28_HUMAN	R	301	.	ENSP00000355827:Q301R	Q	+	2	0	FBXO28	222411866	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.707000	0.91367	2.371000	0.80710	0.533000	0.62120	CAG	.	.		0.458	FBXO28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091283.2	NM_015176		G	224345243	A	G	224345243	3	3	81	1	0	0	0	0	1	0	0	0	5746	188	7	2	920	2	FBXO28	1	224345243	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	360981	224345243	24905378	18	11067										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25467443	25467443	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gtttccgcacatgagcacctCacggcccccacagcagatgg	10	16	1	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:25467443C>G	ENST00000264709.3	-	14	1970	c.1633G>C	c.(1633-1635)Gag>Cag	p.E545Q	DNMT3A_ENST00000402667.1_Missense_Mutation_p.E322Q|DNMT3A_ENST00000380746.4_Missense_Mutation_p.E356Q|DNMT3A_ENST00000321117.5_Missense_Mutation_p.E545Q|DNMT3A_ENST00000474887.1_5'Flank	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	545	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATGAGCACCTCACGGCCCCCA	0.627			"Mis, F, N, S"		AML																																p.E545Q		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.G1633C						.						119	101	108					2																	25467443		2203	4300	6503	SO:0001583	missense	1788	exon14			GCACCTCACGGCC		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1633G>C	chr2.hg19:g.25467443C>G	ENSP00000264709:p.Glu545Gln	57.0	0.0		66.0	20.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	ENST00000264709.3	hg19	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417391	0.62622	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	5.65	5.65	0.86999	Zinc finger, FYVE/PHD-type (1);	0.100374	0.64402	D	0.000003	T	0.68568	0.3015	L	0.35542	1.07	0.80722	D	1	B;B	0.31227	0.314;0.008	B;B	0.21917	0.037;0.003	T	0.67745	-0.5591	10	0.46703	T	0.11	-11.8684	17.2343	0.86994	0.0:1.0:0.0:0.0	.	545;356	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	Q	356;545;545;322	ENSP00000370122:E356Q;ENSP00000324375:E545Q;ENSP00000264709:E545Q;ENSP00000384237:E322Q	ENSP00000264709:E545Q	E	-	1	0	DNMT3A	25320947	1.000000	0.71417	0.967000	0.41034	0.693000	0.40251	6.083000	0.71326	2.655000	0.90218	0.655000	0.94253	GAG	.	.		0.627	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		G	25467443	C	G	25467443	3	3	81	1	0	0	0	0	1	0	0	0	4678	835	29	4	1145	4	DNMT3A	2	25467443	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10		25467443	217731930	19	11068										
GALNT13	114805	hgsc.bcm.edu	37	chr2	155115572	155115572	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tggcctattttctattgacaGaaactactttgaagagatag	8	6	1	4			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:155115572G>T	ENST00000392825.3	+	8	1463	c.896G>T	c.(895-897)aGa>aTa	p.R299I	GALNT13_ENST00000409237.1_Missense_Mutation_p.R299I|GALNT13_ENST00000487047.1_3'UTR	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	299	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						TCTATTGACAGAAACTACTTT	0.333																																					p.R299I		Atlas-SNP	.											.	GALNT13	170	.	0			c.G896T						.						96	102	100					2																	155115572		2203	4300	6503	SO:0001583	missense	114805	exon8			TTGACAGAAACTA	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23242	protein-coding gene	gene with protein product	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13", "polypeptide GalNAc transferase 13"	608369	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.896G>T	chr2.hg19:g.155115572G>T	ENSP00000376570:p.Arg299Ile	146.0	0.0		143.0	29.0	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Missense_Mutation	SNP	ENST00000392825.3	hg19	CCDS2199.1	.	.	.	.	.	.	.	.	.	.	G	17.63	3.437693	0.62955	.	.	ENSG00000144278	ENST00000392825;ENST00000409237	T;T	0.69040	-0.37;-0.37	5.85	5.85	0.93711	Glycosyl transferase, family 2 (1);	0.047828	0.85682	D	0.000000	T	0.82056	0.4954	H	0.95780	3.72	0.80722	D	1	B;B;B;B	0.32160	0.358;0.06;0.143;0.06	B;B;B;B	0.40199	0.322;0.124;0.171;0.124	D	0.84451	0.0588	10	0.87932	D	0	.	19.1513	0.93491	0.0:0.0:1.0:0.0	.	299;299;299;299	Q8IUC8-2;B3KY85;Q08ER7;Q8IUC8	.;.;.;GLT13_HUMAN	I	299	ENSP00000376570:R299I;ENSP00000387239:R299I	ENSP00000376570:R299I	R	+	2	0	GALNT13	154823818	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.404000	0.66344	2.772000	0.95346	0.650000	0.86243	AGA	.	.		0.333	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917		T	155115572	G	T	155115572	3	4	81	1	0	0	0	0	1	0	0	0	6219	942	33	3	918	3	GALNT13	2	155115572	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	129648129	155115572	88083801	20	11069										
KCNJ3	3760	hgsc.bcm.edu	37	chr2	155711536	155711536	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	accatctaagctgcagaaaaTtactggaagagaagactttc	8	8	1	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:155711536T>A	ENST00000295101.2	+	3	1694	c.1217T>A	c.(1216-1218)aTt>aAt	p.I406N	KCNJ3_ENST00000544049.1_3'UTR|KCNJ3_ENST00000493505.1_3'UTR	NM_001260509.1|NM_002239.3	NP_001247438.1|NP_002230.1	P48549	KCNJ3_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 3	406					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to electrical stimulus (GO:0051602)|synaptic transmission (GO:0007268)	external side of plasma membrane (GO:0009897)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)			breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(30)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	54					Halothane(DB01159)	CTGCAGAAAATTACTGGAAGA	0.393																																					p.I406N		Atlas-SNP	.											.	KCNJ3	126	.	0			c.T1217A						.						87	96	93					2																	155711536		2203	4300	6503	SO:0001583	missense	3760	exon3			AGAAAATTACTGG	U50964	CCDS2200.1, CCDS58733.1	2q24.1	2011-07-05			ENSG00000162989	ENSG00000162989		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6264	protein-coding gene	gene with protein product		601534				8088798, 16382105	Standard	NM_002239		Approved	Kir3.1, GIRK1, KGA	uc002tyv.2	P48549	OTTHUMG00000131937	ENST00000295101.2:c.1217T>A	chr2.hg19:g.155711536T>A	ENSP00000295101:p.Ile406Asn	190.0	0.0		247.0	41.0	NM_002239	B4DEW7|Q8TBI0	Missense_Mutation	SNP	ENST00000295101.2	hg19	CCDS2200.1	.	.	.	.	.	.	.	.	.	.	T	16.33	3.092444	0.55968	.	.	ENSG00000162989	ENST00000295101	D	0.89939	-2.59	5.95	5.95	0.96441	.	0.355624	0.31976	N	0.006763	T	0.77896	0.4199	N	0.08118	0	0.80722	D	1	P	0.41748	0.761	B	0.38562	0.276	T	0.78140	-0.2320	10	0.15952	T	0.53	.	15.6134	0.76744	0.0:0.0:0.0:1.0	.	406	P48549	IRK3_HUMAN	N	406	ENSP00000295101:I406N	ENSP00000295101:I406N	I	+	2	0	KCNJ3	155419782	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.281000	0.76405	0.528000	0.53228	ATT	.	.		0.393	KCNJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254890.2	NM_002239		A	155711536	T	A	155711536	3	1	81	1	0	0	0	0	1	0	0	0	8061	1493	52	4	1227	4	KCNJ3	2	155711536	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	595964	155711536	87487837	21	11070										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166847916	166847917	+	Frame_Shift_Ins	INS	-	-	T													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ctgtcaattatcatgtcttcINSttttataagaagattagccc							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:166847916_166847917insT	ENST00000303395.4	-	26	5867_5868	c.5868_5869insA	c.(5866-5871)aaagaafs	p.E1957fs	SCN1A_ENST00000409050.1_Frame_Shift_Ins_p.E1929fs|SCN1A_ENST00000423058.2_Frame_Shift_Ins_p.E1957fs|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Frame_Shift_Ins_p.E1946fs			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1957			E -> G (in infantile spasms; dbSNP:rs121918802). {ECO:0000269|PubMed:14504318}.		adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATCATGTCTTCTTTTATAAGAA	0.386																																					p.E1957fs		Atlas-Indel,Pindel	.											.	SCN1A	641	.	0			c.5869_5870insA						.																																			SO:0001589	frameshift_variant	6323	exon28			.	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.5869dupA	chr2.hg19:g.166847920_166847920dupT	ENSP00000303540:p.Glu1957fs	107.0	0.0		134.0	17.0	NM_001202435	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Frame_Shift_Ins	INS	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.386	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166847917	-	T	166847916	7	5	81	1	0	1	1	0	0	0	0	0	13929	922	32	0	164	0	SCN1A	2	166847916	Frame_Shift_Ins	INS	-	TCGA-CC-A8HV-01A-11D-A35Z-10	11136380	166847916	76351457	22	11071										
KBTBD10	10324	hgsc.bcm.edu	37	chr2	170366494	170366494	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tttatctgaaattgatgaggCgaaaaaaaaggaggtagtgc	12	3	1	3	rs151212497		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:170366494C>T	ENST00000284669.1	+	1	283	c.206C>T	c.(205-207)gCg>gTg	p.A69V	BBS5_ENST00000554017.1_Intron|RP11-724O16.1_ENST00000513963.1_Intron	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	69	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)		p.A69V(1)									ATTGATGAGGCGAAAAAAAAG	0.388																																					p.A69V		Atlas-SNP	.											KBTBD10,rectum,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C206T						.	C	VAL/ALA	4,4402	8.1+/-20.4	0,4,2199	147	146	146		206	-8	0.3	2	dbSNP_134	146	0,8600		0,0,4300	no	missense	KBTBD10	NM_006063.2	64	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	benign	69/607	170366494	4,13002	2203	4300	6503	SO:0001583	missense	10324	exon1			ATGAGGCGAAAAA	AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"Kelch-like", "BTB/POZ domain containing"	16905	protein-coding gene	gene with protein product	"sarcomeric muscle protein"	607701	"kelch repeat and BTB (POZ) domain containing 10", "kelch-like 41 (Drosophila)"	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.206C>T	chr2.hg19:g.170366494C>T	ENSP00000284669:p.Ala69Val	153.0	0.0		132.0	33.0	NM_006063	Q53R42	Missense_Mutation	SNP	ENST00000284669.1	hg19	CCDS2234.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.133833	0.37630	9.08E-4	0.0	ENSG00000239474	ENST00000284669	T	0.71698	-0.59	5.17	-8.03	0.01114	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.336995	0.33980	N	0.004372	T	0.56108	0.1963	L	0.58810	1.83	0.20703	N	0.999863	B	0.27594	0.182	B	0.28916	0.096	T	0.42666	-0.9438	10	0.56958	D	0.05	.	7.0064	0.24838	0.405:0.4496:0.0599:0.0855	.	69	O60662	KBTBA_HUMAN	V	69	ENSP00000284669:A69V	ENSP00000284669:A69V	A	+	2	0	KBTBD10	170074740	1.000000	0.71417	0.315000	0.25238	0.898000	0.52572	3.337000	0.52120	-1.967000	0.01008	-0.291000	0.09656	GCG	.	C|1.000;T|0.000		0.388	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063		T	170366494	C	T	170366494	3	4	81	1	0	0	0	0	1	0	0	0	7999	768	27	1	208	1	KBTBD10	2	170366494	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	3518578	170366494	72832879	23	11072										
KLHL23	151230	hgsc.bcm.edu	37	chr2	170592146	170592146	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tagagccagttattaagtggActgctcatgatgtagaaaat	10	5	1	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:170592146A>G	ENST00000392647.2	+	2	866	c.622A>G	c.(622-624)Act>Gct	p.T208A	KLHL23_ENST00000272797.4_Missense_Mutation_p.T208A|KLHL23_ENST00000602521.1_Intron	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	208	BACK.									breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						TATTAAGTGGACTGCTCATGA	0.358																																					p.T208A		Atlas-SNP	.											.	KLHL23	52	.	0			c.A622G						.						47	50	49					2																	170592146		2203	4300	6503	SO:0001583	missense	151230	exon2			AAGTGGACTGCTC	BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160		"Kelch-like", "BTB/POZ domain containing"	27506	protein-coding gene	gene with protein product			"kelch-like 23 (Drosophila)"				Standard	NM_144711		Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000392647.2:c.622A>G	chr2.hg19:g.170592146A>G	ENSP00000376419:p.Thr208Ala	220.0	0.0		182.0	28.0	NM_144711	Q8N9B9|Q96FT8	Missense_Mutation	SNP	ENST00000392647.2	hg19	CCDS2236.1	.	.	.	.	.	.	.	.	.	.	A	10.22	1.289934	0.23478	.	.	ENSG00000213160	ENST00000272797;ENST00000392647;ENST00000437875	T;T;T	0.68181	-0.31;-0.31;-0.31	5.81	5.81	0.92471	BTB/Kelch-associated (2);	0.177917	0.47852	D	0.000206	T	0.55893	0.1949	L	0.40543	1.245	0.31123	N	0.708669	B	0.06786	0.001	B	0.06405	0.002	T	0.63998	-0.6510	9	0.87932	D	0	.	8.2201	0.31537	0.8481:0.0:0.1519:0.0	.	208	Q8NBE8	KLH23_HUMAN	A	208;208;29	ENSP00000272797:T208A;ENSP00000376419:T208A;ENSP00000394732:T29A	ENSP00000272797:T208A	T	+	1	0	KLHL23	170300392	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.977000	0.49297	2.210000	0.71456	0.533000	0.62120	ACT	.	.		0.358	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711		G	170592146	A	G	170592146	3	3	81	1	0	0	0	0	1	0	0	0	8387	275	10	2	624	2	KLHL23	2	170592146	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	225652	170592146	72607227	24	11073										
TTN	7273	hgsc.bcm.edu	37	chr2	179665283	179665283	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gggagctctggatttcggctCcatcccggtagaacttcacc	11	13	2	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:179665283C>T	ENST00000591111.1	-	4	646	c.422G>A	c.(421-423)gGa>gAa	p.G141E	TTN_ENST00000342992.6_Missense_Mutation_p.G141E|TTN_ENST00000360870.5_Missense_Mutation_p.G141E|TTN_ENST00000342175.6_Missense_Mutation_p.G141E|TTN_ENST00000359218.5_Missense_Mutation_p.G141E|TTN_ENST00000460472.2_Missense_Mutation_p.G141E|TTN_ENST00000589042.1_Missense_Mutation_p.G141E			Q8WZ42	TITIN_HUMAN	titin	32759	Ig-like 2.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GATTTCGGCTCCATCCCGGTA	0.507																																					p.G141E		Atlas-SNP	.											.	TTN	18412	.	0			c.G422A						.						143	129	134					2																	179665283		2203	4300	6503	SO:0001583	missense	7273	exon4			TCGGCTCCATCCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.422G>A	chr2.hg19:g.179665283C>T	ENSP00000465570:p.Gly141Glu	115.0	0.0		144.0	16.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.93	3.509613	0.64522	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92	5.95	5.95	0.96441	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.87386	0.6164	M	0.79123	2.44	0.46078	D	0.998859	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.81914	0.984;0.984;0.984;0.984;0.995	D	0.87571	0.2478	9	0.87932	D	0	.	20.3789	0.98926	0.0:1.0:0.0:0.0	.	141;141;141;141;141	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	E	141	ENSP00000343764:G141E;ENSP00000434586:G141E;ENSP00000340554:G141E;ENSP00000352154:G141E;ENSP00000354117:G141E	ENSP00000340554:G141E	G	-	2	0	TTN	179373528	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.826000	0.97356	0.563000	0.77884	GGA	.	.		0.507	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179665283	C	T	179665283	3	4	81	1	0	0	0	0	1	0	0	0	16750	855	30	3	111002	3	TTN	2	179665283	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	9073137	179665283	63534090	25	11074										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185802803	185802803	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttccttctgaaaccaatggtGaaactgagcatttagaaatg	8	7	1	4			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:185802803G>A	ENST00000302277.6	+	4	3274	c.2680G>A	c.(2680-2682)Gaa>Aaa	p.E894K		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	894							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						AACCAATGGTGAAACTGAGCA	0.403																																					p.E894K		Atlas-SNP	.											.	ZNF804A	322	.	0			c.G2680A						.						96	89	92					2																	185802803		2203	4300	6503	SO:0001583	missense	91752	exon4			AATGGTGAAACTG	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.2680G>A	chr2.hg19:g.185802803G>A	ENSP00000303252:p.Glu894Lys	110.0	0.0		106.0	16.0	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	G	4.377	0.069463	0.08436	.	.	ENSG00000170396	ENST00000302277	T	0.05925	3.37	5.57	1.42	0.22433	.	0.638690	0.14470	N	0.317606	T	0.03827	0.0108	N	0.17082	0.46	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.39482	-0.9612	10	0.41790	T	0.15	-3.0364	5.4331	0.16464	0.3234:0.2033:0.4733:0.0	.	894	Q7Z570	Z804A_HUMAN	K	894	ENSP00000303252:E894K	ENSP00000303252:E894K	E	+	1	0	ZNF804A	185511048	0.000000	0.05858	0.001000	0.08648	0.228000	0.25075	-0.376000	0.07465	0.694000	0.31654	0.591000	0.81541	GAA	.	.		0.403	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		A	185802803	G	A	185802803	3	1	81	1	0	0	0	0	1	0	0	0	18185	1291	45	3	2694	3	ZNF804A	2	185802803	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	6137520	185802803	57396570	26	11075										
XRCC5	7520	hgsc.bcm.edu	37	chr2	217006004	217006004	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttgaagacttgtttccaaccAccaaaatcccaaatcctcga	4	13	0	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:217006004A>G	ENST00000392133.3	+	15	1899	c.1438A>G	c.(1438-1440)Acc>Gcc	p.T480A	XRCC5_ENST00000392132.2_Missense_Mutation_p.T480A|XRCC5_ENST00000471649.1_3'UTR			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	480	Pro-rich.				brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to fatty acid (GO:0071398)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|hematopoietic stem cell differentiation (GO:0060218)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of type I interferon production (GO:0032481)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|kidney(3)|large_intestine(8)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		GTTTCCAACCACCAAAATCCC	0.383								Non-homologous end-joining																													p.T480A		Atlas-SNP	.											.	XRCC5	64	.	0			c.A1438G						.						134	133	133					2																	217006004		2203	4300	6503	SO:0001583	missense	7520	exon13			CCAACCACCAAAA	AF039597	CCDS2402.1	2q35	2008-07-31	2008-07-31		ENSG00000079246	ENSG00000079246			12833	protein-coding gene	gene with protein product	"Ku autoantigen, 80kDa"	194364	"X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)"			9636207, 9214634	Standard	NM_021141		Approved	KU80, KARP-1, Ku86, KUB2	uc002vfy.3	P13010	OTTHUMG00000133059	ENST00000392133.3:c.1438A>G	chr2.hg19:g.217006004A>G	ENSP00000375978:p.Thr480Ala	126.0	0.0		90.0	29.0	NM_021141	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Missense_Mutation	SNP	ENST00000392133.3	hg19	CCDS2402.1	.	.	.	.	.	.	.	.	.	.	A	9.588	1.125388	0.20959	.	.	ENSG00000079246	ENST00000392133;ENST00000392132	T;T	0.41758	0.99;0.99	5.56	-0.622	0.11560	Spen Paralogue and Orthologue SPOC, C-terminal-like (1);Ku70/Ku80 C-terminal arm (2);	0.627414	0.16965	N	0.192329	T	0.23094	0.0558	L	0.29908	0.895	0.21604	N	0.999625	B	0.02656	0.0	B	0.04013	0.001	T	0.22836	-1.0205	10	0.12766	T	0.61	.	6.5536	0.22448	0.5625:0.0:0.0723:0.3652	.	480	P13010	XRCC5_HUMAN	A	480	ENSP00000375978:T480A;ENSP00000375977:T480A	ENSP00000375977:T480A	T	+	1	0	XRCC5	216714249	0.985000	0.35326	0.977000	0.42913	0.803000	0.45373	1.445000	0.35079	0.054000	0.16065	-0.336000	0.08194	ACC	.	.		0.383	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141		G	217006004	A	G	217006004	3	3	81	1	0	0	0	0	1	0	0	0	17471	159	6	2	1488	2	XRCC5	2	217006004	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	31203201	217006004	26193369	27	11076										
DES	1674	hgsc.bcm.edu	37	chr2	220283471	220283471	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ggacttctcactggccgacgCggtgaaccaggagtttctga	13	11	2	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:220283471C>T	ENST00000373960.3	+	1	373	c.287C>T	c.(286-288)gCg>gTg	p.A96V		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	96	Head.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTGGCCGACGCGGTGAACCAG	0.677																																					p.A96V		Atlas-SNP	.											DES,NS,malignant_melanoma,0,1	DES	53	.	0			c.C287T						.						20	19	19					2																	220283471		2175	4263	6438	SO:0001583	missense	1674	exon1			CCGACGCGGTGAA	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"Intermediate filaments type III"	2770	protein-coding gene	gene with protein product	"intermediate filament protein"	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.287C>T	chr2.hg19:g.220283471C>T	ENSP00000363071:p.Ala96Val	339.0	0.0		262.0	51.0	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Missense_Mutation	SNP	ENST00000373960.3	hg19	CCDS33383.1	.	.	.	.	.	.	.	.	.	.	C	31	5.090082	0.94149	.	.	ENSG00000175084	ENST00000373960	D	0.86694	-2.16	4.55	4.55	0.56014	Intermediate filament head, DNA-binding domain (1);	0.000000	0.49305	D	0.000143	D	0.93969	0.8069	M	0.84511	2.7	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.94813	0.7980	10	0.62326	D	0.03	.	17.2901	0.87153	0.0:1.0:0.0:0.0	.	96	P17661	DESM_HUMAN	V	96	ENSP00000363071:A96V	ENSP00000363071:A96V	A	+	2	0	DES	219991715	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	7.593000	0.82686	2.254000	0.74563	0.561000	0.74099	GCG	.	.		0.677	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927		T	220283471	C	T	220283471	3	4	81	1	0	0	0	0	1	0	0	0	4451	768	27	1	289	1	DES	2	220283471	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	3277467	220283471	22915902	28	11077										
SPEG	10290	hgsc.bcm.edu	37	chr2	220348192	220348192	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gccaggagcccgcagctgggGctagccccaggcggggagag	19	13	0	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:220348192G>T	ENST00000312358.7	+	30	6139	c.6007G>T	c.(6007-6009)Gct>Tct	p.A2003S	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2003					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CGCAGCTGGGGCTAGCCCCAG	0.771																																					p.A2003S		Atlas-SNP	.											.	SPEG	272	.	0			c.G6007T						.						2	3	3					2																	220348192		1271	3082	4353	SO:0001583	missense	10290	exon30			GCTGGGGCTAGCC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.6007G>T	chr2.hg19:g.220348192G>T	ENSP00000311684:p.Ala2003Ser	37.0	0.0		30.0	20.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	0.767	-0.767292	0.02974	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.61980	0.06	4.06	-3.76	0.04359	.	1.079220	0.07387	N	0.888451	T	0.27063	0.0663	N	0.04508	-0.205	0.21762	N	0.999553	B	0.02656	0.0	B	0.01281	0.0	T	0.21245	-1.0251	10	0.06891	T	0.86	.	1.1771	0.01838	0.1367:0.2099:0.3213:0.3321	.	2003	Q15772	SPEG_HUMAN	S	2003	ENSP00000311684:A2003S	ENSP00000265327:A2003S	A	+	1	0	SPEG	220056436	0.003000	0.15002	0.013000	0.15412	0.264000	0.26372	-0.533000	0.06157	-0.585000	0.05905	-0.519000	0.04390	GCT	.	.		0.771	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220348192	G	T	220348192	3	4	81	1	0	0	0	0	1	0	0	0	15051	1203	42	3	6137	3	SPEG	2	220348192	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	64721	220348192	22851181	29	11078										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222294720	222294720	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tcttcaagctgttggggttgCggatgagtttgtccaacatg	13	7	2	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:222294720C>T	ENST00000281821.2	-	15	2689	c.2648G>A	c.(2647-2649)cGc>cAc	p.R883H	EPHA4_ENST00000409854.1_Missense_Mutation_p.R883H|EPHA4_ENST00000409938.1_Missense_Mutation_p.R883H|EPHA4_ENST00000392071.4_Missense_Mutation_p.R832H	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	883					adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GTTGGGGTTGCGGATGAGTTT	0.512																																					p.R883H		Atlas-SNP	.											.	EPHA4	263	.	0			c.G2648A						.						191	187	188					2																	222294720		2203	4300	6503	SO:0001583	missense	2043	exon15			GGGTTGCGGATGA	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.2648G>A	chr2.hg19:g.222294720C>T	ENSP00000281821:p.Arg883His	73.0	0.0		76.0	9.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.994878	0.93167	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	5.89	5.89	0.94794	Protein kinase-like domain (1);	0.097095	0.64402	D	0.000001	T	0.76737	0.4029	L	0.51422	1.61	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.76366	-0.2985	10	0.66056	D	0.02	.	20.3344	0.98733	0.0:1.0:0.0:0.0	.	883	P54764	EPHA4_HUMAN	H	883;883;883;832	ENSP00000281821:R883H;ENSP00000386276:R883H;ENSP00000386829:R883H;ENSP00000375923:R832H	ENSP00000281821:R883H	R	-	2	0	EPHA4	222002964	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.087000	0.71362	2.822000	0.97130	0.650000	0.86243	CGC	.	.		0.512	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222294720	C	T	222294720	3	4	81	1	0	0	0	0	1	0	0	0	5171	768	27	1	324	1	EPHA4	2	222294720	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	1946528	222294720	20904653	30	11079										
USP40	55230	hgsc.bcm.edu	37	chr2	234465583	234465583	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	acagacgatagatgaggtcaTgaccggaggtcccaactaaa	11	9	1	4			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr2:234465583T>C	ENST00000427112.2	-	4	499	c.464A>G	c.(463-465)cAt>cGt	p.H155R	USP40_ENST00000450966.1_Missense_Mutation_p.H167R|USP40_ENST00000251722.6_Missense_Mutation_p.H155R			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	155	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		GATGAGGTCATGACCGGAGGT	0.423																																					p.H167R		Atlas-SNP	.											.	USP40	174	.	0			c.A500G						.						101	94	96					2																	234465583		1858	4102	5960	SO:0001583	missense	55230	exon4			AGGTCATGACCGG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.464A>G	chr2.hg19:g.234465583T>C	ENSP00000387898:p.His155Arg	160.0	0.0		165.0	53.0	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	hg19	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.107667	0.77096	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112;ENST00000435959	T;T;T	0.30182	1.54;1.54;1.54	5.33	5.33	0.75918	.	0.093277	0.64402	D	0.000001	T	0.35941	0.0949	N	0.25789	0.76	0.46564	D	0.999104	D	0.53885	0.963	P	0.54026	0.74	T	0.18493	-1.0335	10	0.66056	D	0.02	.	15.312	0.74042	0.0:0.0:0.0:1.0	.	167	Q9NVE5-3	.	R	167;155;155;155	ENSP00000415434:H167R;ENSP00000251722:H155R;ENSP00000387898:H155R	ENSP00000251722:H155R	H	-	2	0	USP40	234130322	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.700000	0.68318	2.022000	0.59522	0.533000	0.62120	CAT	.	.		0.423	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		C	234465583	T	C	234465583	3	2	81	1	0	0	0	0	1	0	0	0	17087	1464	51	2	3355	2	USP40	2	234465583	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	12170863	234465583	8733790	31	11080										
ZNF197	10168	hgsc.bcm.edu	37	chr3	44674045	44674045	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ggcccaatccagagggccttGtactgggatgtgatgctgga	15	9	0	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr3:44674045G>A	ENST00000396058.1	+	4	890	c.723G>A	c.(721-723)ttG>ttA	p.L241L	RP11-944L7.4_ENST00000457331.1_RNA|ZNF197_ENST00000383745.2_Silent_p.L241L|ZNF197_ENST00000344387.4_Silent_p.L241L|ZNF197_ENST00000383744.4_Silent_p.L241L			O14709	ZN197_HUMAN	zinc finger protein 197	241	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		AGAGGGCCTTGTACTGGGATG	0.448																																					p.L241L		Atlas-SNP	.											.	ZNF197	81	.	0			c.G723A						.						230	208	216					3																	44674045		2203	4300	6503	SO:0001819	synonymous_variant	10168	exon5			GGCCTTGTACTGG	AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"Zinc fingers, C2H2-type", "-", "-", "-"	12988	protein-coding gene	gene with protein product			"zinc finger protein 166"	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.723G>A	chr3.hg19:g.44674045G>A		134.0	0.0		84.0	45.0	NM_001024855	B2RAH8|Q86VG0	Silent	SNP	ENST00000396058.1	hg19	CCDS2717.1																																																																																			.	.		0.448	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991		A	44674045	G	A	44674045	2	1	81	1	0	0	0	0	0	0	0	1	17774	1368	48	3		3	ZNF197	3	44674045	Silent	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10		44674045	153348385	32	11081										
PRSS42	339906	hgsc.bcm.edu	37	chr3	46871985	46871986	+	Splice_Site	INS	-	-	A													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gcggcccccagaatctccctINSagagaaagagaaagaaacga							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr3:46871985_46871986insA	ENST00000429665.1	-	5	792		c.e5-2		PRSS42_ENST00000447340.1_Splice_Site	NM_182702.1	NP_874361.1	Q7Z5A4	PRS42_HUMAN	protease, serine, 42						germ cell development (GO:0007281)|spermatogenesis (GO:0007283)	anchored component of plasma membrane (GO:0046658)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	8						AGAATCTCCCTAGAGAAAGAGA	0.5																																					.		Atlas-INDEL	.											.	PRSS42	17	.	0			c.793-2->T						.																																			SO:0001630	splice_region_variant	339906	exon6			.		CCDS46816.1	3p21.31	2010-05-07			ENSG00000178055	ENSG00000178055		"Serine peptidases / Serine peptidases"	30716	protein-coding gene	gene with protein product	"testis serine protease 2"					12838346	Standard	NM_182702		Approved	TESSP2	uc011bap.2	Q7Z5A4	OTTHUMG00000156496	ENST00000429665.1:c.793-2->T	chr3.hg19:g.46871986_46871986dupA		90.0	0.0		70.0	17.0	NM_182702		Splice_Site	INS	ENST00000429665.1	hg19	CCDS46816.1																																																																																			.	.		0.5	PRSS42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344347.1	NM_182702	Intron	A	46871986	-	A	46871985	8	5	81	1	0	1	1	0	0	0	1	0	12640	1536	53	0	93	0	PRSS42	3	46871985	Splice_Site	INS	-	TCGA-CC-A8HV-01A-11D-A35Z-10	2197940	46871985	151150445	33	11082										
SETD2	29072	hgsc.bcm.edu	37	chr3	47163348	47163348	+	Frame_Shift_Del	DEL	T	T	-													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cctacttctactattgtttcTttccctgcatgctttaaaaa							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr3:47163348delT	ENST00000409792.3	-	3	2820	c.2778delA	c.(2776-2778)aaafs	p.K926fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	926					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CTATTGTTTCTTTCCCTGCAT	0.413			"N, F, S, Mis"		clear cell renal carcinoma																																p.E927fs		Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.2779delG						.						115	119	117					3																	47163348		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.2778delA	chr3.hg19:g.47163348delT	ENSP00000386759:p.Lys926fs	114.0	0.0		102.0	45.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.		0.413	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47163348	T	-	47163348	7	5	81	1	0	1	0	1	0	0	0	0	14146	1606	56	0	4992	0	SETD2	3	47163348	Frame_Shift_Del	DEL	T	TCGA-CC-A8HV-01A-11D-A35Z-10	291363	47163348	150859082	34	11083										
HYAL3	8372	hgsc.bcm.edu	37	chr3	50330774	50330774	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aggacttccaatctccaaggCtgccgtctggccacaggtgt	11	13	2	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr3:50330774C>A	ENST00000336307.1	-	4	1429	c.1157G>T	c.(1156-1158)aGc>aTc	p.S386I	HYAL3_ENST00000359051.3_Missense_Mutation_p.S356I|HYAL3_ENST00000450982.1_Missense_Mutation_p.S356I|HYAL3_ENST00000415204.1_Missense_Mutation_p.S137I|IFRD2_ENST00000336089.4_5'Flank|IFRD2_ENST00000429673.2_5'Flank|HYAL3_ENST00000513170.1_Missense_Mutation_p.S107I|IFRD2_ENST00000484043.1_5'Flank|IFRD2_ENST00000417626.2_5'Flank|IFRD2_ENST00000436390.1_5'Flank	NM_001200029.1|NM_003549.3	NP_001186958.1|NP_003540.2	O43820	HYAL3_HUMAN	hyaluronoglucosaminidase 3	386	EGF-like.				carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|hyaluronan catabolic process (GO:0030214)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)|response to virus (GO:0009615)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|lysosome (GO:0005764)	hyaluronoglucuronidase activity (GO:0033906)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(5)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		ATCTCCAAGGCTGCCGTCTGG	0.632																																					p.S386I		Atlas-SNP	.											.	HYAL3	34	.	0			c.G1157T						.						41	46	44					3																	50330774		2203	4300	6503	SO:0001583	missense	8372	exon4			CCAAGGCTGCCGT	AF040710	CCDS2815.1, CCDS56259.1, CCDS56260.1, CCDS56257.1	3p21.3	2004-03-12			ENSG00000186792	ENSG00000186792			5322	protein-coding gene	gene with protein product		604038				10493834	Standard	NM_003549		Approved	LUCA-3, LUCA14, Minna14	uc021wyn.1	O43820	OTTHUMG00000156936	ENST00000336307.1:c.1157G>T	chr3.hg19:g.50330774C>A	ENSP00000337425:p.Ser386Ile	268.0	0.0		219.0	76.0	NM_001200029	O60540|Q8NFK2|Q8NFK3|Q8NFK4|Q96E56|Q9BRW9	Missense_Mutation	SNP	ENST00000336307.1	hg19	CCDS2815.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.830294	0.32329	.	.	ENSG00000186792	ENST00000359051;ENST00000336307;ENST00000415204;ENST00000513170;ENST00000450982	T;T;T;T	0.45668	1.87;2.23;0.89;1.87	5.44	0.14	0.14804	Epidermal growth factor-like (1);	0.538663	0.13889	U	0.355763	T	0.42988	0.1227	M	0.88310	2.945	0.38319	D	0.943462	B;B;B;B	0.12630	0.001;0.001;0.003;0.006	B;B;B;B	0.14023	0.005;0.003;0.005;0.01	T	0.38757	-0.9646	10	0.45353	T	0.12	-9.5212	3.4003	0.07321	0.123:0.4823:0.2383:0.1563	.	107;137;386;356	O43820-4;O43820-3;O43820;O43820-2	.;.;HYAL3_HUMAN;.	I	356;386;137;107;356	ENSP00000351946:S356I;ENSP00000337425:S386I;ENSP00000401092:S137I;ENSP00000391922:S356I	ENSP00000337425:S386I	S	-	2	0	HYAL3	50305778	0.002000	0.14202	0.998000	0.56505	0.586000	0.36452	-0.055000	0.11807	0.106000	0.17784	-0.140000	0.14226	AGC	.	.		0.632	HYAL3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000346664.1	NM_003549		A	50330774	C	A	50330774	3	1	81	1	0	0	0	0	1	0	0	0	7474	797	28	3	100	3	HYAL3	3	50330774	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	3167426	50330774	147691656	35	11084										
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	55052296	55052296	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tccagcattcgtctctgagcGcaccatcaaggagactacag	9	13	2	2	rs376433361		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr3:55052296G>A	ENST00000474759.1	+	35	2987	c.2939G>A	c.(2938-2940)cGc>cAc	p.R980H	CACNA2D3_ENST00000490478.1_Missense_Mutation_p.R886H|CACNA2D3_ENST00000288197.5_Missense_Mutation_p.R980H|CACNA2D3_ENST00000415676.2_Missense_Mutation_p.R980H|CACNA2D3_ENST00000478261.1_3'UTR	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	980						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	GTCTCTGAGCGCACCATCAAG	0.483																																					p.R980H		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.G2939A						.						86	84	85					3																	55052296		1946	4144	6090	SO:0001583	missense	55799	exon35			CTGAGCGCACCAT	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.2939G>A	chr3.hg19:g.55052296G>A	ENSP00000419101:p.Arg980His	125.0	0.0		116.0	41.0	NM_018398	B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	hg19	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.393397	0.83011	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.61362	0.2341	M	0.61703	1.905	0.46798	D	0.9992	D	0.61080	0.989	P	0.50708	0.648	T	0.63065	-0.6720	10	0.46703	T	0.11	.	17.3487	0.87316	0.0:0.0:1.0:0.0	.	980	Q8IZS8	CA2D3_HUMAN	H	980;980;980;886;886	ENSP00000389506:R980H;ENSP00000419101:R980H;ENSP00000288197:R980H;ENSP00000417279:R886H	ENSP00000288197:R980H	R	+	2	0	CACNA2D3	55027336	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.233000	0.95337	2.522000	0.85027	0.563000	0.77884	CGC	.	.		0.483	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			A	55052296	G	A	55052296	3	1	81	1	0	0	0	0	1	0	0	0	2552	1087	38	1	3077	1	CACNA2D3	3	55052296	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	4721522	55052296	142970134	36	11085										
DNAJB8	165721	hgsc.bcm.edu	37	chr3	128181523	128181523	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tggtgaccttgtggccattgAtcatctcggtggacgacatc	12	10	2	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr3:128181523A>C	ENST00000469083.1	-	2	3123	c.566T>G	c.(565-567)aTc>aGc	p.I189S	DNAJB8-AS1_ENST00000471626.1_RNA|DNAJB8_ENST00000319153.3_Missense_Mutation_p.I189S			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	189					chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		GTGGCCATTGATCATCTCGGT	0.627																																					p.I189S		Atlas-SNP	.											.	DNAJB8	34	.	0			c.T566G						.						134	112	120					3																	128181523		2203	4300	6503	SO:0001583	missense	165721	exon3			CCATTGATCATCT		CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"Heat shock proteins / DNAJ (HSP40)"	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.566T>G	chr3.hg19:g.128181523A>C	ENSP00000417418:p.Ile189Ser	110.0	0.0		81.0	38.0	NM_153330	B3KWV7	Missense_Mutation	SNP	ENST00000469083.1	hg19	CCDS3048.1	.	.	.	.	.	.	.	.	.	.	A	9.883	1.202088	0.22121	.	.	ENSG00000179407	ENST00000469083;ENST00000319153	T;T	0.46063	0.88;0.88	4.75	3.59	0.41128	.	0.518516	0.20427	N	0.092549	T	0.38639	0.1048	L	0.51422	1.61	0.38866	D	0.956598	B	0.32968	0.392	B	0.36666	0.23	T	0.32079	-0.9920	10	0.59425	D	0.04	.	9.1168	0.36762	0.9156:0.0:0.0844:0.0	.	189	Q8NHS0	DNJB8_HUMAN	S	189	ENSP00000417418:I189S;ENSP00000316053:I189S	ENSP00000316053:I189S	I	-	2	0	DNAJB8	129664213	1.000000	0.71417	0.415000	0.26534	0.022000	0.10575	4.136000	0.58004	0.668000	0.31126	-0.375000	0.07067	ATC	.	.		0.627	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330		C	128181523	A	C	128181523	3	2	81	1	0	0	0	0	1	0	0	0	4628	333	12	5	136	5	DNAJB8	3	128181523	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	73129227	128181523	69840907	37	11086										
ACPP	55	hgsc.bcm.edu	37	chr3	132071587	132071587	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gacactactgtgagtggcctAcagatggcgctagatgttta	12	8	0	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr3:132071587A>C	ENST00000336375.5	+	9	978	c.888A>C	c.(886-888)ctA>ctC	p.L296L	ACPP_ENST00000351273.7_Silent_p.L296L|ACPP_ENST00000475741.1_Silent_p.L263L	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	296					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						TGAGTGGCCTACAGATGGCGC	0.433																																					p.L296L		Atlas-SNP	.											.	ACPP	118	.	0			c.A888C						.						154	139	144					3																	132071587		2203	4300	6503	SO:0001819	synonymous_variant	55	exon9			TGGCCTACAGATG		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.888A>C	chr3.hg19:g.132071587A>C		62.0	0.0		63.0	19.0	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Silent	SNP	ENST00000336375.5	hg19	CCDS3073.1																																																																																			.	.		0.433	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099		C	132071587	A	C	132071587	2	2	81	1	0	0	0	0	0	0	0	1	167	378	14	5		5	ACPP	3	132071587	Silent	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	3890064	132071587	65950843	38	11087										
CEP70	80321	hgsc.bcm.edu	37	chr3	138289288	138289288	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cataatttgttccaagtcatTagctcgttgttcttgattgg	8	7	2	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr3:138289288T>C	ENST00000264982.3	-	6	603	c.337A>G	c.(337-339)Aat>Gat	p.N113D	CEP70_ENST00000484888.1_Missense_Mutation_p.N113D|CEP70_ENST00000489254.1_Intron|CEP70_ENST00000481834.1_Missense_Mutation_p.N113D|CEP70_ENST00000478673.1_5'UTR|CEP70_ENST00000464035.1_Missense_Mutation_p.N113D|CEP70_ENST00000542237.1_Missense_Mutation_p.N93D	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	113					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						TCCAAGTCATTAGCTCGTTGT	0.348																																					p.N113D		Atlas-SNP	.											.	CEP70	51	.	0			c.A337G						.						149	138	142					3																	138289288		2203	4299	6502	SO:0001583	missense	80321	exon6			AGTCATTAGCTCG	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.337A>G	chr3.hg19:g.138289288T>C	ENSP00000264982:p.Asn113Asp	164.0	0.0		147.0	67.0	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	hg19	CCDS3102.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.039049	0.55003	.	.	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000484888;ENST00000474781;ENST00000481834;ENST00000468900;ENST00000462419;ENST00000464035;ENST00000470159	T;T;T;T;T;T;T;T	0.46451	1.48;1.49;1.48;1.49;1.47;0.88;0.88;0.87	4.98	4.98	0.66077	.	0.365869	0.28067	N	0.016730	T	0.33323	0.0859	L	0.43152	1.355	0.26613	N	0.972796	P;B;P	0.48503	0.911;0.026;0.911	B;B;B	0.41510	0.359;0.027;0.359	T	0.19321	-1.0309	10	0.19590	T	0.45	-15.1773	10.9787	0.47482	0.0:0.0:0.0:1.0	.	93;113;113	F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;CEP70_HUMAN	D	113;93;113;95;113;92;93;113;113	ENSP00000264982:N113D;ENSP00000444128:N93D;ENSP00000419231:N113D;ENSP00000419833:N95D;ENSP00000417465:N113D;ENSP00000418131:N92D;ENSP00000417819:N93D;ENSP00000419743:N113D	ENSP00000264982:N113D	N	-	1	0	CEP70	139771978	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	2.003000	0.40844	2.093000	0.63338	0.528000	0.53228	AAT	.	.		0.348	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491		C	138289288	T	C	138289288	3	2	81	1	0	0	0	0	1	0	0	0	3261	1754	61	2	1508	2	CEP70	3	138289288	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	6217701	138289288	59733142	39	11088										
C3orf34	84984	hgsc.bcm.edu	37	chr3	196435517	196435517	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ctaatcccacatttcttggcAgtgcacatcattcccatgta	5	13	2	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr3:196435517A>T	ENST00000409690.3	-	2	446	c.24T>A	c.(22-24)acT>acA	p.T8T	RNU6-646P_ENST00000364571.1_RNA|CEP19_ENST00000399942.4_Intron	NM_032898.3	NP_116287.2	Q96LK0	CEP19_HUMAN	centrosomal protein 19kDa	4						centriole (GO:0005814)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	10						ATTTCTTGGCAGTGCACATCA	0.413																																					p.T8T		Atlas-SNP	.											.	CEP19	22	.	0			c.T24A						.						110	101	104					3																	196435517		1909	4136	6045	SO:0001819	synonymous_variant	84984	exon2			CTTGGCAGTGCAC	BC007827	CCDS43193.2	3q29	2014-02-20	2011-05-06	2011-05-06	ENSG00000174007	ENSG00000174007			28209	protein-coding gene	gene with protein product		615586	"chromosome 3 open reading frame 34"	C3orf34		21399614	Standard	XM_005269370		Approved	MGC14126	uc011btw.2	Q96LK0	OTTHUMG00000153933	ENST00000409690.3:c.24T>A	chr3.hg19:g.196435517A>T		88.0	0.0		59.0	13.0	NM_032898	B2RA74|Q96I48	Silent	SNP	ENST00000409690.3	hg19	CCDS43193.2																																																																																			.	.		0.413	CEP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333080.2	NM_032898		T	196435517	A	T	196435517	2	4	81	1	0	0	0	0	0	0	0	1	2226	175	7	4		4	C3orf34	3	196435517	Silent	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	58146229	196435517	1586913	40	11089										
SLBP	7884	hgsc.bcm.edu	37	chr4	1701359	1701359	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tagttgatctgcttctgtctCctcattaggacactttcatc	6	11	5	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr4:1701359C>G	ENST00000489418.1	-	5	777	c.411G>C	c.(409-411)agG>agC	p.R137S	SLBP_ENST00000318386.4_Missense_Mutation_p.R144S|SLBP_ENST00000488267.1_Missense_Mutation_p.R102S|SLBP_ENST00000429429.2_Missense_Mutation_p.R98S	NM_006527.2	NP_006518.1	Q14493	SLBP_HUMAN	stem-loop binding protein	137	RNA-binding.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA transport (GO:0051028)|nuclear cell cycle DNA replication (GO:0033260)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	histone pre-mRNA DCP binding (GO:0071208)|histone pre-mRNA stem-loop binding (GO:0071207)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|lung(2)	5		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.0055)			GCTTCTGTCTCCTCATTAGGA	0.403																																					p.R137S		Atlas-SNP	.											.	SLBP	12	.	0			c.G411C						.						159	146	150					4																	1701359		2203	4300	6503	SO:0001583	missense	7884	exon5			CTGTCTCCTCATT	Z71188	CCDS3350.1	4p16.3	2008-02-11	2008-02-11		ENSG00000163950	ENSG00000163950			10904	protein-coding gene	gene with protein product	"histone binding protein"	602422	"stem-loop (histone) binding protein"			9049306, 1338771	Standard	NM_006527		Approved	HBP	uc003gdi.1	Q14493	OTTHUMG00000089349	ENST00000489418.1:c.411G>C	chr4.hg19:g.1701359C>G	ENSP00000417686:p.Arg137Ser	78.0	0.0		32.0	27.0	NM_006527	B3KRJ5	Missense_Mutation	SNP	ENST00000489418.1	hg19	CCDS3350.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	21.7|21.7|21.7	4.191240|4.191240|4.191240	0.78902|0.78902|0.78902	.|.|.	.|.|.	ENSG00000163950|ENSG00000163950|ENSG00000163950	ENST00000480936|ENST00000483348|ENST00000429429;ENST00000489418;ENST00000460392;ENST00000318386;ENST00000488267	.|.|.	.|.|.	.|.|.	5.08|5.08|5.08	-2.32|-2.32|-2.32	0.06745|0.06745|0.06745	.|.|.	.|.|0.053107	.|.|0.64402	.|.|D	.|.|0.000001	T|T|T	0.66257|0.66257|0.66257	0.2771|0.2771|0.2771	M|M|M	0.67397|0.67397|0.67397	2.05|2.05|2.05	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;P;B;D	.|.|0.89917	.|.|1.0;0.987;0.476;0.087;0.993	.|.|D;P;B;B;P	.|.|0.70716	.|.|0.97;0.88;0.216;0.063;0.88	T|T|T	0.63646|0.63646|0.63646	-0.6590|-0.6590|-0.6590	5|5|9	.|.|0.52906	.|.|T	.|.|0.07	-13.5987|-13.5987|-13.5987	9.0891|9.0891|9.0891	0.36598|0.36598|0.36598	0.0:0.2302:0.113:0.6568|0.0:0.2302:0.113:0.6568|0.0:0.2302:0.113:0.6568	.|.|.	.|.|102;144;98;117;137	.|.|E7EUV9;F8W8D3;B3KRJ5;C9IY53;Q14493	.|.|.;.;.;.;SLBP_HUMAN	Q|A|S	145|92|98;137;117;144;102	.|.|.	.|.|ENSP00000316490:R144S	E|G|R	-|-|-	1|2|3	0|0|2	SLBP|SLBP|SLBP	1671157|1671157|1671157	0.288000|0.288000|0.288000	0.24324|0.24324|0.24324	0.977000|0.977000|0.977000	0.42913|0.42913|0.42913	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	-0.484000|-0.484000|-0.484000	0.06528|0.06528|0.06528	-0.597000|-0.597000|-0.597000	0.05813|0.05813|0.05813	0.644000|0.644000|0.644000	0.83932|0.83932|0.83932	GAG|GGA|AGG	.	.		0.403	SLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203176.1	NM_006527		G	1701359	C	G	1701359	3	3	81	1	0	0	0	0	1	0	0	0	14387	854	30	4	417	4	SLBP	4	1701359	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10		1701359	189452917	41	11090										
TBC1D19	55296	hgsc.bcm.edu	37	chr4	26661311	26661312	+	Nonsense_Mutation	DNP	AA	AA	GT													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	attcaagttccactgaaagtAaaagacatccctgaattggt							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr4:26661311_26661312AA>GT	ENST00000264866.4	+	8	851_852	c.573_574AA>GT	c.(571-576)gtAAaa>gtGTaa	p.K192*	TBC1D19_ENST00000515568.1_3'UTR|TBC1D19_ENST00000511789.1_Nonsense_Mutation_p.K127*	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	192							Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				CACTGAAAGTAAAAGACATCCC	0.287																																					p.V191V|p.K192X		Atlas-SNP	.											.	TBC1D19	53	.	0			c.A573G|c.A574T						.																																			SO:0001587	stop_gained	55296	exon8			GAAAGTAAAAGAC|AAAGTAAAAGACA	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	Exception_encountered	chr4.hg19:g.26661311_26661312delinsGT	ENSP00000264866:p.Lys192*	72.0|71.0	0.0		45.0	32.0|33.0	NM_018317	B9A6M0|Q9NUX1	Silent|Nonsense_Mutation	SNP	ENST00000264866.4	hg19	CCDS3439.1																																																																																			.	.		0.287	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317		GT	26661312	AA	GT	26661311	4	3	81	1	0	0	0	0	0	1	0	0	15622	349	13	2	603	2	TBC1D19	4	26661311	Nonsense_Mutation	DNP	AA	TCGA-CC-A8HV-01A-11D-A35Z-10	24959952	26661311	164492965	42	11091										
GABRB1	2560	hgsc.bcm.edu	37	chr4	47163294	47163294	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	actcaccatgtatttccagcAgtcttggaaagacaaaaggc	8	10	2	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr4:47163294A>C	ENST00000295454.3	+	4	561	c.269A>C	c.(268-270)cAg>cCg	p.Q90P	GABRB1_ENST00000538619.1_Missense_Mutation_p.Q20P	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	90					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TATTTCCAGCAGTCTTGGAAA	0.358																																					p.Q90P		Atlas-SNP	.											.	GABRB1	107	.	0			c.A269C						.						80	83	82					4																	47163294		2203	4298	6501	SO:0001583	missense	2560	exon4			TCCAGCAGTCTTG		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4081	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 1"	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.269A>C	chr4.hg19:g.47163294A>C	ENSP00000295454:p.Gln90Pro	63.0	0.0		71.0	39.0	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Missense_Mutation	SNP	ENST00000295454.3	hg19	CCDS3474.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.312877	0.81358	.	.	ENSG00000163288	ENST00000513567;ENST00000295454;ENST00000538619	T;T;T	0.79845	-1.31;-1.31;-1.31	5.01	5.01	0.66863	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.64402	D	0.000003	D	0.92870	0.7732	H	0.96833	3.89	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.97110	1.0;0.992	D	0.94968	0.8114	10	0.87932	D	0	-13.0383	14.0523	0.64745	1.0:0.0:0.0:0.0	.	20;90	F5GXV5;P18505	.;GBRB1_HUMAN	P	57;90;20	ENSP00000426753:Q57P;ENSP00000295454:Q90P;ENSP00000440330:Q20P	ENSP00000295454:Q90P	Q	+	2	0	GABRB1	46858051	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.139000	0.94554	2.109000	0.64355	0.528000	0.53228	CAG	.	.		0.358	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1			C	47163294	A	C	47163294	3	2	81	1	0	0	0	0	1	0	0	0	6174	188	7	5	283	5	GABRB1	4	47163294	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	20501983	47163294	143990982	43	11092										
REST	5978	hgsc.bcm.edu	37	chr4	57796730	57796730	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cagcaaagtggaggagaataAaaagcaaaatacttgcatga	10	5	0	2	rs541994823		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr4:57796730A>G	ENST00000309042.7	+	4	2020	c.1706A>G	c.(1705-1707)aAa>aGa	p.K569R		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	569	Lys-rich.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					GAGGAGAATAAAAAGCAAAAT	0.348																																					p.K569R		Atlas-SNP	.											.	REST	104	.	0			c.A1706G						.						18	20	19					4																	57796730		2183	4290	6473	SO:0001583	missense	5978	exon4			AGAATAAAAAGCA	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.1706A>G	chr4.hg19:g.57796730A>G	ENSP00000311816:p.Lys569Arg	453.0	0.0		242.0	167.0	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	hg19	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	A	17.96	3.516842	0.64634	.	.	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.41400	1.0	5.35	5.35	0.76521	.	0.631179	0.15334	N	0.267877	T	0.63189	0.2490	M	0.71581	2.175	0.46609	D	0.999121	D;D	0.69078	0.997;0.986	D;P	0.65443	0.935;0.722	T	0.64639	-0.6360	10	0.62326	D	0.03	-5.6695	15.008	0.71527	1.0:0.0:0.0:0.0	.	546;569	F8WAN5;Q13127	.;REST_HUMAN	R	569;546	ENSP00000311816:K569R	ENSP00000311816:K569R	K	+	2	0	REST	57491487	1.000000	0.71417	0.267000	0.24556	0.495000	0.33615	3.170000	0.50816	2.029000	0.59856	0.459000	0.35465	AAA	.	.		0.348	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		G	57796730	A	G	57796730	3	3	81	1	0	0	0	0	1	0	0	0	13249	14	1	2	1716	2	REST	4	57796730	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	10633436	57796730	133357546	44	11093										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87556432	87556432	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gcacgtgtcactagctgaggCcctggaggttcggggtggac	17	10	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr4:87556432C>A	ENST00000411767.2	+	2	86	c.23C>A	c.(22-24)gCc>gAc	p.A8D	PTPN13_ENST00000316707.6_Missense_Mutation_p.A8D|PTPN13_ENST00000502971.1_Missense_Mutation_p.A8D|PTPN13_ENST00000427191.2_Missense_Mutation_p.A8D|PTPN13_ENST00000511467.1_Missense_Mutation_p.A8D|PTPN13_ENST00000436978.1_Missense_Mutation_p.A8D			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	8	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CTAGCTGAGGCCCTGGAGGTT	0.428																																					p.A8D		Atlas-SNP	.											.	PTPN13	203	.	0			c.C23A						.						57	59	58					4																	87556432		1931	4133	6064	SO:0001583	missense	5783	exon2			CTGAGGCCCTGGA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.23C>A	chr4.hg19:g.87556432C>A	ENSP00000407249:p.Ala8Asp	92.0	0.0		60.0	45.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789033	0.90367	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000502971;ENST00000316707;ENST00000411767;ENST00000507902;ENST00000511467	T;T;T;T;T;T;T	0.33216	2.09;2.09;1.42;2.09;2.09;2.09;2.09	5.65	4.81	0.61882	KIND (2);	0.000000	0.50627	D	0.000105	T	0.55909	0.1950	M	0.75264	2.295	0.58432	D	0.999999	D;D;D;D	0.89917	0.998;1.0;1.0;1.0	D;D;D;D	0.97110	0.981;1.0;0.999;1.0	T	0.61476	-0.7055	10	0.87932	D	0	.	14.4557	0.67416	0.0:0.9284:0.0:0.0716	.	8;8;8;8	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	D	8	ENSP00000408368:A8D;ENSP00000394794:A8D;ENSP00000423531:A8D;ENSP00000322675:A8D;ENSP00000407249:A8D;ENSP00000422835:A8D;ENSP00000426626:A8D	ENSP00000322675:A8D	A	+	2	0	PTPN13	87775456	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.157000	0.77461	1.379000	0.46325	0.650000	0.86243	GCC	.	.		0.428	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87556432	C	A	87556432	3	1	81	1	0	0	0	0	1	0	0	0	12795	739	26	3	25	3	PTPN13	4	87556432	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	29759702	87556432	103597844	45	11094										
KIAA1712	80817	hgsc.bcm.edu	37	chr4	175225507	175225507	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tgatatcagtggcaggtttaTgacctcaggaaaggtatgca	12	6	2	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr4:175225507T>G	ENST00000503780.1	+	6	908	c.494T>G	c.(493-495)aTg>aGg	p.M165R	CEP44_ENST00000296519.4_Missense_Mutation_p.M165R|CEP44_ENST00000457424.2_Missense_Mutation_p.M165R|CEP44_ENST00000426172.1_Missense_Mutation_p.M165R	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	165						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)				endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						GGCAGGTTTATGACCTCAGGA	0.373																																					p.M165R		Atlas-SNP	.											.	CEP44	35	.	0			c.T494G						.						63	66	65					4																	175225507		2203	4300	6503	SO:0001583	missense	80817	exon6			GGTTTATGACCTC	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"KIAA1712"	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.494T>G	chr4.hg19:g.175225507T>G	ENSP00000423153:p.Met165Arg	206.0	0.0		142.0	96.0	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Missense_Mutation	SNP	ENST00000503780.1	hg19	CCDS34106.1	.	.	.	.	.	.	.	.	.	.	T	6.671	0.492391	0.12702	.	.	ENSG00000164118	ENST00000503780;ENST00000457424;ENST00000515299;ENST00000426172;ENST00000296519	T;T;T;T;T	0.47177	0.88;0.85;0.87;0.85;0.88	4.59	3.4	0.38934	.	0.577476	0.17031	N	0.189696	T	0.39358	0.1075	L	0.47716	1.5	0.22412	N	0.999124	B;B	0.24963	0.036;0.115	B;B	0.26310	0.051;0.068	T	0.36866	-0.9730	10	0.62326	D	0.03	.	7.3367	0.26613	0.0:0.104:0.0:0.896	.	165;165	Q9C0F1-2;Q9C0F1	.;CEP44_HUMAN	R	165	ENSP00000423153:M165R;ENSP00000389427:M165R;ENSP00000421128:M165R;ENSP00000408221:M165R;ENSP00000296519:M165R	ENSP00000296519:M165R	M	+	2	0	CEP44	175462082	0.994000	0.37717	0.875000	0.34327	0.003000	0.03518	3.892000	0.56235	0.853000	0.35312	0.379000	0.24179	ATG	.	.		0.373	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633		G	175225507	T	G	175225507	3	3	81	1	0	0	0	0	1	0	0	0	8262	1464	51	5	508	5	KIAA1712	4	175225507	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	87669075	175225507	15928769	46	11095										
SLC1A3	6507	hgsc.bcm.edu	37	chr5	36629587	36629587	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttaccctccgaccatacagaAtgagctaccgggaagtcaag	9	12	1	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:36629587A>G	ENST00000265113.4	+	3	693	c.217A>G	c.(217-219)Atg>Gtg	p.M73V	SLC1A3_ENST00000381918.3_Missense_Mutation_p.M73V	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	73					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACCATACAGAATGAGCTACCG	0.403																																					p.M73V		Atlas-SNP	.											.	SLC1A3	88	.	0			c.A217G						.						183	162	169					5																	36629587		2203	4300	6503	SO:0001583	missense	6507	exon3			TACAGAATGAGCT		CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"Solute carriers"	10941	protein-coding gene	gene with protein product	"glutamate transporter variant EAAT1ex9skip"	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.217A>G	chr5.hg19:g.36629587A>G	ENSP00000265113:p.Met73Val	102.0	0.0		96.0	18.0	NM_004172	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	hg19	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.696327	0.30052	.	.	ENSG00000079215	ENST00000265113;ENST00000513903;ENST00000505202;ENST00000513646;ENST00000381918	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	6.06	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.39064	0.1064	N	0.20881	0.62	0.44555	D	0.997511	B;B	0.21225	0.053;0.0	B;B	0.29524	0.103;0.007	T	0.29027	-1.0025	10	0.44086	T	0.13	-33.8452	9.2396	0.37489	0.7511:0.1273:0.0:0.1216	.	73;73	Q4JCQ8;P43003	.;EAA1_HUMAN	V	73	ENSP00000265113:M73V;ENSP00000427203:M73V;ENSP00000424986:M73V;ENSP00000420992:M73V;ENSP00000371343:M73V	ENSP00000265113:M73V	M	+	1	0	SLC1A3	36665344	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	1.488000	0.35551	2.324000	0.78689	0.533000	0.62120	ATG	.	.		0.403	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172		G	36629587	A	G	36629587	3	3	81	1	0	0	0	0	1	0	0	0	14448	101	4	2	240	2	SLC1A3	5	36629587	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10		36629587	144285673	47	11096										
DDX4	54514	hgsc.bcm.edu	37	chr5	55111225	55111225	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gtggtagtacaagaggaaacGtgtttgcatcagttgatacc	12	6	1	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:55111225G>A	ENST00000505374.1	+	21	2163	c.2071G>A	c.(2071-2073)Gtg>Atg	p.V691M	DDX4_ENST00000511853.1_Missense_Mutation_p.V542M|DDX4_ENST00000354991.5_Missense_Mutation_p.V657M|DDX4_ENST00000514278.2_Missense_Mutation_p.V671M|DDX4_ENST00000353507.5_Missense_Mutation_p.V657M	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	691					male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				AAGAGGAAACGTGTTTGCATC	0.363																																					p.V691M		Atlas-SNP	.											.	DDX4	194	.	0			c.G2071A						.						127	122	123					5																	55111225		2203	4300	6503	SO:0001583	missense	54514	exon21			GGAAACGTGTTTG	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.2071G>A	chr5.hg19:g.55111225G>A	ENSP00000424838:p.Val691Met	105.0	0.0		90.0	39.0	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Missense_Mutation	SNP	ENST00000505374.1	hg19	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	G	6.325	0.428110	0.11987	.	.	ENSG00000152670	ENST00000353507;ENST00000514278;ENST00000505374;ENST00000354991;ENST00000511853	T;T;T;T;T	0.22134	2.01;2.0;1.99;2.01;1.97	5.42	-1.16	0.09678	.	2.029550	0.02966	N	0.143808	T	0.21307	0.0513	L	0.49126	1.545	0.09310	N	1	B;B;B	0.20550	0.016;0.006;0.046	B;B;B	0.19391	0.011;0.025;0.014	T	0.27502	-1.0072	10	0.45353	T	0.12	-27.7346	6.8667	0.24098	0.5598:0.0:0.3163:0.1239	.	542;657;691	E9PCD8;Q9NQI0-2;Q9NQI0	.;.;DDX4_HUMAN	M	657;671;691;657;542	ENSP00000334167:V657M;ENSP00000425359:V671M;ENSP00000424838:V691M;ENSP00000347087:V657M;ENSP00000423123:V542M	ENSP00000334167:V657M	V	+	1	0	DDX4	55146982	0.000000	0.05858	0.013000	0.15412	0.384000	0.30261	-0.290000	0.08354	-0.634000	0.05538	-0.253000	0.11424	GTG	.	.		0.363	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		A	55111225	G	A	55111225	3	1	81	1	0	0	0	0	1	0	0	0	4362	1145	40	1	2190	1	DDX4	5	55111225	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	18481638	55111225	125804035	48	11097										
HTR1A	3350	hgsc.bcm.edu	37	chr5	63256758	63256758	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttgctctccacgcccagcctCcagttcctgctccccgactc	6	21	1	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:63256758C>G	ENST00000323865.3	-	1	1022	c.789G>C	c.(787-789)tgG>tgC	p.W263C	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	263					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	CGCCCAGCCTCCAGTTCCTGC	0.652																																					p.W263C		Atlas-SNP	.											.	HTR1A	128	.	0			c.G789C						.						57	54	55					5																	63256758		2203	4300	6503	SO:0001583	missense	3350	exon1			CAGCCTCCAGTTC	AF498978	CCDS34168.1	5q11.2-q13	2012-08-08	2012-02-03			ENSG00000178394		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5286	protein-coding gene	gene with protein product		109760	"5-hydroxytryptamine (serotonin) receptor 1A"	ADRB2RL1, ADRBRL1		2591972, 12969265	Standard	NM_000524		Approved	5-HT1A	uc011cqt.3	P08908		ENST00000323865.3:c.789G>C	chr5.hg19:g.63256758C>G	ENSP00000316244:p.Trp263Cys	58.0	0.0		54.0	18.0	NM_000524	Q6LAE7	Missense_Mutation	SNP	ENST00000323865.3	hg19	CCDS34168.1	.	.	.	.	.	.	.	.	.	.	C	7.251	0.603189	0.13939	.	.	ENSG00000178394	ENST00000323865	T	0.61859	0.07	5.17	4.3	0.51218	GPCR, rhodopsin-like superfamily (1);	0.122077	0.64402	N	0.000013	T	0.53045	0.1772	L	0.45228	1.405	0.80722	D	1	B	0.23650	0.089	B	0.29077	0.098	T	0.54221	-0.8326	10	0.54805	T	0.06	.	15.2	0.73130	0.0:0.8593:0.1407:0.0	.	263	P08908	5HT1A_HUMAN	C	263	ENSP00000316244:W263C	ENSP00000316244:W263C	W	-	3	0	HTR1A	63292514	1.000000	0.71417	0.992000	0.48379	0.505000	0.33919	3.875000	0.56108	1.385000	0.46445	0.655000	0.94253	TGG	.	.		0.652	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524		G	63256758	C	G	63256758	3	3	81	1	0	0	0	0	1	0	0	0	7445	856	30	4	482	4	HTR1A	5	63256758	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	8145533	63256758	117658502	49	11098										
ANKRD32	84250	hgsc.bcm.edu	37	chr5	94001708	94001708	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttgtatgaaaggagcatggtCtttagtagaagtccttatca	10	5	2	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:94001708C>G	ENST00000265140.5	+	12	1930	c.1511C>G	c.(1510-1512)tCt>tGt	p.S504C		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	504						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		GGAGCATGGTCTTTAGTAGAA	0.368																																					p.S504C		Atlas-SNP	.											.	ANKRD32	117	.	0			c.C1511G						.						176	141	151					5																	94001708		692	1591	2283	SO:0001583	missense	84250	exon12			CATGGTCTTTAGT	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"Ankyrin repeat domain containing"	25408	protein-coding gene	gene with protein product			"BRCT domain containing 1"	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.1511C>G	chr5.hg19:g.94001708C>G	ENSP00000265140:p.Ser504Cys	19.0	0.0		28.0	6.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Missense_Mutation	SNP	ENST00000265140.5	hg19	CCDS4071.2	.	.	.	.	.	.	.	.	.	.	C	17.82	3.483311	0.63962	.	.	ENSG00000133302	ENST00000265140	T	0.51817	0.69	5.21	4.34	0.51931	.	0.000000	0.42294	D	0.000728	T	0.47284	0.1437	L	0.43152	1.355	0.22771	N	0.998756	D	0.55172	0.97	P	0.47206	0.541	T	0.44605	-0.9317	10	0.66056	D	0.02	.	14.4281	0.67230	0.266:0.734:0.0:0.0	.	504	Q9BQI6	ANR32_HUMAN	C	504	ENSP00000265140:S504C	ENSP00000265140:S504C	S	+	2	0	ANKRD32	94027464	0.995000	0.38212	0.999000	0.59377	0.995000	0.86356	2.035000	0.41155	1.153000	0.42468	0.585000	0.79938	TCT	.	.		0.368	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290		G	94001708	C	G	94001708	3	3	81	1	0	0	0	0	1	0	0	0	660	913	32	4	1553	4	ANKRD32	5	94001708	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	30744950	94001708	86913552	50	11099										
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109106073	109106073	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tagatctgggatctgtcacaGatattttatgccacatgatg	9	7	3	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:109106073G>T	ENST00000261483.4	+	7	2079	c.1027G>T	c.(1027-1029)Gat>Tat	p.D343Y		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	343					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		ATCTGTCACAGATATTTTATG	0.363																																					p.D343Y		Atlas-SNP	.											.	MAN2A1	136	.	0			c.G1027T						.						102	99	100					5																	109106073		2202	4300	6502	SO:0001583	missense	4124	exon7			GTCACAGATATTT		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.1027G>T	chr5.hg19:g.109106073G>T	ENSP00000261483:p.Asp343Tyr	106.0	0.0		60.0	16.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035510	0.75617	.	.	ENSG00000112893	ENST00000261483	T	0.24908	1.83	5.75	4.87	0.63330	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.091298	0.64402	D	0.000001	T	0.58524	0.2128	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.68804	-0.5312	10	0.87932	D	0	-12.3213	16.1022	0.81184	0.0:0.0:0.865:0.135	.	343	Q16706	MA2A1_HUMAN	Y	343	ENSP00000261483:D343Y	ENSP00000261483:D343Y	D	+	1	0	MAN2A1	109133972	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.832000	0.99423	1.395000	0.46643	0.563000	0.77884	GAT	.	.		0.363	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			T	109106073	G	T	109106073	3	4	81	1	0	0	0	0	1	0	0	0	9223	942	33	3	1053	3	MAN2A1	5	109106073	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	15104365	109106073	71809187	51	11100										
PPIC	5480	hgsc.bcm.edu	37	chr5	122372304	122372304	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gcacgagaggtagcagcagcCgaggacccgggcccatggtg	17	12	0	1	rs375305758		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:122372304C>G	ENST00000306442.4	-	1	132	c.17G>C	c.(16-18)cGg>cCg	p.R6P	RP11-359P5.1_ENST00000506859.1_RNA	NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)	6					protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	TAGCAGCAGCCGAGGACCCGG	0.711																																					p.R6P	Ovarian(99;690 1502 20765 45543 49568)	Atlas-SNP	.											.	PPIC	18	.	0			c.G17C						.						18	20	20					5																	122372304		2175	4259	6434	SO:0001583	missense	5480	exon1			AGCAGCCGAGGAC	S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.17G>C	chr5.hg19:g.122372304C>G	ENSP00000303057:p.Arg6Pro	166.0	0.0		126.0	28.0	NM_000943	A4LBB5	Missense_Mutation	SNP	ENST00000306442.4	hg19	CCDS4133.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.254484	0.22965	.	.	ENSG00000168938	ENST00000306442	T	0.24908	1.83	3.94	1.8	0.24995	.	0.297905	0.28754	U	0.014259	T	0.11665	0.0284	N	0.08118	0	0.09310	N	1	P;B	0.49862	0.929;0.165	B;B	0.40134	0.32;0.053	T	0.13845	-1.0494	10	0.72032	D	0.01	.	8.4358	0.32786	0.163:0.738:0.0:0.099	.	6;6	B4E200;P45877	.;PPIC_HUMAN	P	6	ENSP00000303057:R6P	ENSP00000303057:R6P	R	-	2	0	PPIC	122400203	0.992000	0.36948	0.457000	0.27056	0.033000	0.12548	0.897000	0.28390	0.637000	0.30526	-0.373000	0.07131	CGG	.	.		0.711	PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250898.2	NM_000943		G	122372304	C	G	122372304	3	3	81	1	0	0	0	0	1	0	0	0	12332	652	23	4	641	4	PPIC	5	122372304	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	13266231	122372304	58542956	52	11101										
PKD2L2	27039	hgsc.bcm.edu	37	chr5	137257348	137257348	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tgcacaatttcgaattgttcTtggagattttaattttgctg	8	5	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:137257348T>C	ENST00000508883.1	+	9	1378	c.1352T>C	c.(1351-1353)cTt>cCt	p.L451P	PKD2L2_ENST00000350250.4_Missense_Mutation_p.L417P|PKD2L2_ENST00000508638.1_Intron|PKD2L2_ENST00000290431.5_Missense_Mutation_p.L451P|PKD2L2_ENST00000502810.1_Missense_Mutation_p.L429P			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	451					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CGAATTGTTCTTGGAGATTTT	0.338																																					p.L451P		Atlas-SNP	.											.	PKD2L2	68	.	0			c.T1352C						.						139	126	130					5																	137257348		1797	4070	5867	SO:0001583	missense	27039	exon9			TTGTTCTTGGAGA	AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"Voltage-gated ion channels / Transient receptor potential cation channels"	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.1352T>C	chr5.hg19:g.137257348T>C	ENSP00000424725:p.Leu451Pro	75.0	0.0		57.0	28.0	NM_014386	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	hg19		.	.	.	.	.	.	.	.	.	.	T	23.9	4.467755	0.84533	.	.	ENSG00000078795	ENST00000350250;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	5.89	5.89	0.94794	Polycystin cation channel, PKD1/PKD2 (1);	0.000000	0.64402	D	0.000019	D	0.86251	0.5888	M	0.86502	2.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.88592	0.3144	10	0.87932	D	0	-22.6061	15.9724	0.80031	0.0:0.0:0.0:1.0	.	451;451	Q9NZM6;Q9NZM6-5	PK2L2_HUMAN;.	P	417;429;451;451	ENSP00000344177:L417P;ENSP00000425513:L429P;ENSP00000424725:L451P;ENSP00000290431:L451P	ENSP00000290431:L451P	L	+	2	0	PKD2L2	137285247	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.161000	0.77505	2.257000	0.74773	0.460000	0.39030	CTT	.	.		0.338	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		C	137257348	T	C	137257348	3	2	81	1	0	0	0	0	1	0	0	0	11977	1609	56	2	1386	2	PKD2L2	5	137257348	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	14885044	137257348	43657912	53	11102										
PCDHB15	56121	hgsc.bcm.edu	37	chr5	140626364	140626364	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttctacaggctggtaacagaAggggcgctggacagagagac	15	8	1	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:140626364A>T	ENST00000231173.3	+	1	1218	c.1218A>T	c.(1216-1218)gaA>gaT	p.E406D		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	406	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGTAACAGAAGGGGCGCTGG	0.473																																					p.E406D		Atlas-SNP	.											.	PCDHB15	138	.	0			c.A1218T						.						69	69	69					5																	140626364		2203	4300	6503	SO:0001583	missense	56121	exon1			AACAGAAGGGGCG	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1218A>T	chr5.hg19:g.140626364A>T	ENSP00000231173:p.Glu406Asp	138.0	0.0		99.0	26.0	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	hg19	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	A	6.166	0.398783	0.11696	.	.	ENSG00000113248	ENST00000231173	T	0.52295	0.67	4.56	-9.13	0.00704	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.19685	0.0473	N	0.12746	0.255	0.09310	N	1	B	0.06786	0.001	B	0.17979	0.02	T	0.13469	-1.0508	9	0.26408	T	0.33	.	3.0603	0.06197	0.1924:0.3566:0.0747:0.3763	.	406	Q9Y5E8	PCDBF_HUMAN	D	406	ENSP00000231173:E406D	ENSP00000231173:E406D	E	+	3	2	PCDHB15	140606548	0.000000	0.05858	0.004000	0.12327	0.719000	0.41307	-7.724000	0.00031	-1.243000	0.02519	0.402000	0.26972	GAA	.	.		0.473	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		T	140626364	A	T	140626364	3	4	81	1	0	0	0	0	1	0	0	0	11549	69	3	4	1220	4	PCDHB15	5	140626364	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	3369016	140626364	40288896	54	11103										
PCDHGB5	56102	hgsc.bcm.edu	37	chr5	140778726	140778726	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gacaatagcccagaagttacAttccattctctacttgaaat	5	10	1	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:140778726A>G	ENST00000576222.1	+	1	2546				PCDHGA2_ENST00000394576.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAAGTTACATTCCATTCTC	0.403																																					p.T344T		Atlas-SNP	.											.	.	.	.	0			c.A1032G						.						91	90	91					5																	140778726		1884	4122	6006	SO:0001627	intron_variant	56101	exon1			AGTTACATTCCAT	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+26350A>G	chr5.hg19:g.140778726A>G		156.0	0.0		97.0	19.0	NM_018925	A7E229|Q9Y5C7	Silent	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.		0.403	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		G	140778726	A	G	140778726	1	3	81	0	1	0	0	0	0	0	0	0	11575	204	8	2		2	PCDHGB5	5	140778726	Intron	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	152362	140778726	40136534	55	11104										
PCDH1	5097	hgsc.bcm.edu	37	chr5	141243510	141243510	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gcgtgggggcttgccgcggtCactgaccttcaccaccaggc	14	15	2	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:141243510C>T	ENST00000394536.3	-	3	2525	c.2386G>A	c.(2386-2388)Gac>Aac	p.D796N	PCDH1_ENST00000503492.1_Intron|PCDH1_ENST00000456271.1_Missense_Mutation_p.D784N|PCDH1_ENST00000536585.1_Missense_Mutation_p.D774N|PCDH1_ENST00000287008.3_Missense_Mutation_p.D796N|PCDH1_ENST00000511044.1_5'UTR	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	796	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		TTGCCGCGGTCACTGACCTTC	0.602																																					p.D796N	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.G2386A						.						45	44	44					5																	141243510		2203	4300	6503	SO:0001583	missense	5097	exon3			CGCGGTCACTGAC	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"Cadherins / Protocadherins : Non-clustered"	8655	protein-coding gene	gene with protein product		603626	"protocadherin 1 (cadherin-like 1)"			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.2386G>A	chr5.hg19:g.141243510C>T	ENSP00000378043:p.Asp796Asn	67.0	0.0		47.0	9.0	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000394536.3	hg19	CCDS43375.1	.	.	.	.	.	.	.	.	.	.	c	21.0	4.088431	0.76756	.	.	ENSG00000156453	ENST00000287008;ENST00000394536;ENST00000456271;ENST00000357517;ENST00000536585	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.23	5.23	0.72850	Cadherin (4);Cadherin-like (1);	0.000000	0.52532	D	0.000070	D	0.83339	0.5233	M	0.91717	3.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.87276	0.2289	10	0.87932	D	0	.	16.2953	0.82767	0.0:1.0:0.0:0.0	.	796;796	Q08174;Q08174-2	PCDH1_HUMAN;.	N	796;796;784;807;774	ENSP00000287008:D796N;ENSP00000378043:D796N;ENSP00000403497:D784N;ENSP00000350122:D807N;ENSP00000438825:D774N	ENSP00000287008:D796N	D	-	1	0	PCDH1	141223694	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.783000	0.85696	2.445000	0.82738	0.457000	0.33378	GAC	.	.		0.602	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420		T	141243510	C	T	141243510	3	4	81	1	0	0	0	0	1	0	0	0	11515	826	29	3	1423	3	PCDH1	5	141243510	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	464784	141243510	39671750	56	11105										
NSD1	64324	hgsc.bcm.edu	37	chr5	176721807	176721807	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	atcaggtcacaccacaggctGatgagaagatgccagtgttg	12	9	2	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr5:176721807G>A	ENST00000439151.2	+	23	7483	c.7438G>A	c.(7438-7440)Gat>Aat	p.D2480N	NSD1_ENST00000354179.4_Missense_Mutation_p.D2211N|NSD1_ENST00000347982.4_Missense_Mutation_p.D2211N|NSD1_ENST00000361032.4_Missense_Mutation_p.D2377N	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2480					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		ACCACAGGCTGATGAGAAGAT	0.517			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.D2480N		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G7438A						.						98	95	96					5																	176721807		2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	CAGGCTGATGAGA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.7438G>A	chr5.hg19:g.176721807G>A	ENSP00000395929:p.Asp2480Asn	40.0	0.0		25.0	13.0	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.370078	0.42003	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93426	-3.12;-3.12;-3.12;-3.22	4.78	3.82	0.43975	.	0.608791	0.15551	N	0.256422	D	0.84506	0.5487	N	0.19112	0.55	0.09310	N	1	P;P	0.37276	0.589;0.454	B;B	0.35770	0.21;0.104	T	0.76822	-0.2817	10	0.72032	D	0.01	.	2.4014	0.04402	0.1016:0.163:0.4564:0.279	.	2211;2480	Q96L73-2;Q96L73	.;NSD1_HUMAN	N	2211;2480;2211;2377	ENSP00000346111:D2211N;ENSP00000395929:D2480N;ENSP00000343209:D2211N;ENSP00000354310:D2377N	ENSP00000343209:D2211N	D	+	1	0	NSD1	176654413	0.409000	0.25368	0.997000	0.53966	0.889000	0.51656	3.031000	0.49728	2.502000	0.84385	0.462000	0.41574	GAT	.	.		0.517	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		A	176721807	G	A	176721807	3	1	81	1	0	0	0	0	1	0	0	0	10678	1290	45	3	7524	3	NSD1	5	176721807	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	35478297	176721807	4193453	57	11106										
LY6G5B	58496	hgsc.bcm.edu	37	chr6	31640030	31640030	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gacttttggttcttccccagGctggactcttgacacctcac	8	14	3	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr6:31640030G>T	ENST00000375864.4	+	3	1361	c.577G>T	c.(577-579)Gct>Tct	p.A193S	LY6G5B_ENST00000409525.1_Missense_Mutation_p.A138S|CSNK2B-LY6G5B-1181_ENST00000375880.2_3'UTR	NM_021221.2	NP_067044.2	Q8NDX9	LY65B_HUMAN	lymphocyte antigen 6 complex, locus G5B	193						extracellular region (GO:0005576)				lung(4)	4						TCTTCCCCAGGCTGGACTCTT	0.512																																					p.A193S		Atlas-SNP	.											.	LY6G5B	8	.	0			c.G577T						.						151	149	150					6																	31640030		1511	2709	4220	SO:0001583	missense	58496	exon3			CCCCAGGCTGGAC	AF129756	CCDS34400.1	6p21.3	2008-08-01	2002-07-29	2002-08-01	ENSG00000240053	ENSG00000240053			13931	protein-coding gene	gene with protein product		610433	"chromosome 6 open reading frame 19"	C6orf19		8812450, 12079290, 17008713	Standard	NM_021221		Approved	G5b		Q8NDX9	OTTHUMG00000031227	ENST00000375864.4:c.577G>T	chr6.hg19:g.31640030G>T	ENSP00000365024:p.Ala193Ser	107.0	0.0		40.0	8.0	NM_021221	B0UXB2|B0UZ65|B0UZP8|B7ZCA3|Q5SQ62|Q5SST3|Q9UKT0|Q9UMQ0	Missense_Mutation	SNP	ENST00000375864.4	hg19	CCDS34400.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.369035	0.24771	.	.	ENSG00000240053	ENST00000409691;ENST00000375864;ENST00000409525	T;T	0.27557	1.66;1.67	3.93	1.16	0.20824	.	.	.	.	.	T	0.07548	0.0190	N	0.24115	0.695	.	.	.	B	0.28760	0.221	B	0.27887	0.084	T	0.18366	-1.0339	8	0.66056	D	0.02	9.0E-4	6.6738	0.23083	0.188:0.1502:0.6617:0.0	.	193	Q8NDX9	LY65B_HUMAN	S	190;193;138	ENSP00000365024:A193S;ENSP00000386365:A138S	ENSP00000365024:A193S	A	+	1	0	LY6G5B	31748009	0.000000	0.05858	0.000000	0.03702	0.187000	0.23431	-0.140000	0.10342	-0.104000	0.12154	-3.714000	0.00023	GCT	.	.		0.512	LY6G5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000124389.4			T	31640030	G	T	31640030	3	4	81	1	0	0	0	0	1	0	0	0	9101	1203	42	3	587	3	LY6G5B	6	31640030	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10		31640030	139475037	58	11107										
KHDC1L	100129128	hgsc.bcm.edu	37	chr6	73933531	73933531	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aggtcatcattggtcaggggCtggcttcggacacgctctag	14	10	4	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr6:73933531C>T	ENST00000370388.3	-	3	370	c.327G>A	c.(325-327)caG>caA	p.Q109Q	RP11-257K9.8_ENST00000423730.3_3'UTR|KHDC1L_ENST00000471312.1_5'Flank	NM_001126063.2	NP_001119535.1	Q5JSQ8	KHDCL_HUMAN	KH homology domain containing 1-like	109										breast(1)|endometrium(1)|kidney(1)|lung(3)|skin(1)	7						TGGTCAGGGGCTGGCTTCGGA	0.567																																					p.Q109Q		Atlas-SNP	.											.	KHDC1L	22	.	0			c.G327A						.						90	93	92					6																	73933531		692	1591	2283	SO:0001819	synonymous_variant	100129128	exon3			CAGGGGCTGGCTT	BC004267	CCDS47450.1	6q13	2014-05-15			ENSG00000256980	ENSG00000256980			37274	protein-coding gene	gene with protein product							Standard	NM_001126063		Approved	RP11-257K9.7	uc003pgm.4	Q5JSQ8	OTTHUMG00000132474	ENST00000370388.3:c.327G>A	chr6.hg19:g.73933531C>T		70.0	0.0		64.0	26.0	NM_001126063	E1P535	Silent	SNP	ENST00000370388.3	hg19	CCDS47450.1																																																																																			.	.		0.567	KHDC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255640.1	NM_001126063		T	73933531	C	T	73933531	2	4	81	1	0	0	0	0	0	0	0	1	8154	796	28	3		3	KHDC1L	6	73933531	Silent	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	42293501	73933531	97181536	59	11108										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75866062	75866062	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	atgtggtctgtggctgaagtCgctttaacactgtcgaagtg	13	7	1	1	rs577784031		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr6:75866062C>A	ENST00000322507.8	-	15	3470	c.3161G>T	c.(3160-3162)cGa>cTa	p.R1054L	COL12A1_ENST00000483888.2_Missense_Mutation_p.R1054L|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Missense_Mutation_p.R1054L	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1054	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TGGCTGAAGTCGCTTTAACAC	0.473																																					p.R1054L		Atlas-SNP	.											.	COL12A1	385	.	0			c.G3161T						.						188	176	180					6																	75866062		1952	4152	6104	SO:0001583	missense	1303	exon15			TGAAGTCGCTTTA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.3161G>T	chr6.hg19:g.75866062C>A	ENSP00000325146:p.Arg1054Leu	168.0	0.0		147.0	59.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891332	0.72524	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.54479	0.57;0.57;0.57	5.46	5.46	0.80206	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.172689	0.42053	D	0.000772	T	0.61813	0.2377	L	0.57536	1.79	0.50813	D	0.999896	D	0.61080	0.989	D	0.63283	0.913	T	0.59600	-0.7424	10	0.42905	T	0.14	.	19.2969	0.94126	0.0:1.0:0.0:0.0	.	1054	Q99715	COCA1_HUMAN	L	1054	ENSP00000325146:R1054L;ENSP00000412864:R1054L;ENSP00000421216:R1054L	ENSP00000325146:R1054L	R	-	2	0	COL12A1	75922782	1.000000	0.71417	0.991000	0.47740	0.412000	0.31113	7.487000	0.81328	2.543000	0.85770	0.591000	0.81541	CGA	.	.		0.473	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75866062	C	A	75866062	3	1	81	1	0	0	0	0	1	0	0	0	3671	884	31	1	6238	1	COL12A1	6	75866062	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	1932531	75866062	95249005	60	11109										
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90572457	90572457	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tctcaaagtgacaaaaaactAgaaagacaaagtgaaagatc	7	6	1	5	rs9444715	byFrequency	TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr6:90572457A>G	ENST00000551025.1	+	0	2466									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		ACAAAAAACTAGAAAGACAAA	0.343													A|||	12	0.00239617	0.0091	0	5008	,	,		21629	0		0	False		,,,				2504	0				p.L343L	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.A1029G						.	A	,,	15,3601		0,15,1793	60	60	60		1029,1029,1029	0.5	1	6	dbSNP_119	60	0,8132		0,0,4066	no	coding-synonymous,coding-synonymous,coding-synonymous	CASP8AP2	NM_001137667.1,NM_001137668.1,NM_012115.3	,,	0,15,5859	GG,GA,AA		0.0,0.4148,0.1277	,,	343/1967,343/1967,343/1967	90572457	15,11733	1808	4066	5874			9994	exon7			AAAACTAGAAAGA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90572457A>G		134.0	0.0		69.0	20.0	NM_001137667		Silent	SNP	ENST00000551025.1	hg19																																																																																				.	A|1.000;|0.000		0.343	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		G	90572457	A	G	90572457	1	3	81	0	1	0	0	0	0	0	0	0	2680	407	15	2		2	CASP8AP2	6	90572457	RNA	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	14706395	90572457	80542610	61	11110										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101075734	101075735	+	Frame_Shift_Ins	INS	-	-	AG													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tacctgcttaatattgagccINSaatcagcaaggtctctggca							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr6:101075734_101075735insAG	ENST00000369162.2	-	28	4848_4849	c.4504_4505insCT	c.(4504-4506)tggfs	p.W1502fs		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1502	Helicase ATP-binding 2. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		AATATTGAGCCAATCAGCAAGG	0.317																																					p.W1502fs		Atlas-INDEL	.											.	ASCC3	205	.	0			c.4505_4506insCT						.																																			SO:0001589	frameshift_variant	10973	exon28			.	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.4504_4505insCT	chr6.hg19:g.101075734_101075735insAG	ENSP00000358159:p.Trp1502fs	74.0	0.0		73.0	11.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Frame_Shift_Ins	INS	ENST00000369162.2	hg19	CCDS5046.1																																																																																			.	.		0.317	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		AG	101075735	-	AG	101075734	7	5	81	1	0	1	1	0	0	0	0	0	1033	595	21	0	2163	0	ASCC3	6	101075734	Frame_Shift_Ins	INS	-	TCGA-CC-A8HV-01A-11D-A35Z-10	10503277	101075734	70039333	62	11111	47	3								
ASCC3	10973	hgsc.bcm.edu	37	chr6	101075740	101075740	+	Missense_Mutation	SNP	G	G	T													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gcttaatattgagccaatcaGcaaggtctctggcattagct							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr6:101075740G>T	ENST00000369162.2	-	28	4843	c.4499C>A	c.(4498-4500)gCt>gAt	p.A1500D		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1500	Helicase ATP-binding 2. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GAGCCAATCAGCAAGGTCTCT	0.333																																					p.A1500D		Atlas-SNP	.											.	ASCC3	205	.	0			c.C4499A						.						101	95	97					6																	101075740		2203	4300	6503	SO:0001583	missense	10973	exon28			CAATCAGCAAGGT	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.4499C>A	chr6.hg19:g.101075740G>T	ENSP00000358159:p.Ala1500Asp	74.0	0.0		73.0	11.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.858958	0.91433	.	.	ENSG00000112249	ENST00000369162	T	0.38887	1.11	6.07	6.07	0.98685	DEAD-like helicase (2);	0.000000	0.85682	D	0.000000	T	0.79805	0.4509	H	0.99074	4.42	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87385	0.2359	10	0.87932	D	0	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	1500	Q8N3C0	HELC1_HUMAN	D	1500	ENSP00000358159:A1500D	ENSP00000358159:A1500D	A	-	2	0	ASCC3	101182461	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.885000	0.99019	0.655000	0.94253	GCT	.	.		0.333	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		T	101075740	G	T	101075740	3	4	81	1	0	0	0	0	1	0	0	0	1033	971	34	3	2169	3	ASCC3	6	101075740	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	6	101075740	70039327	63	11112	47	3								
ASCC3	10973	hgsc.bcm.edu	37	chr6	101075744	101075744	+	Missense_Mutation	SNP	G	G	A													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aatattgagccaatcagcaaGgtctctggcattagctaatg							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr6:101075744G>A	ENST00000369162.2	-	28	4839	c.4495C>T	c.(4495-4497)Ctt>Ttt	p.L1499F		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1499	Helicase ATP-binding 2. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		CAATCAGCAAGGTCTCTGGCA	0.328																																					p.L1499F		Atlas-SNP	.											.	ASCC3	205	.	0			c.C4495T						.						105	99	101					6																	101075744		2203	4300	6503	SO:0001583	missense	10973	exon28			CAGCAAGGTCTCT	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.4495C>T	chr6.hg19:g.101075744G>A	ENSP00000358159:p.Leu1499Phe	78.0	0.0		77.0	11.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.776571	0.90195	.	.	ENSG00000112249	ENST00000369162	T	0.40756	1.02	6.07	6.07	0.98685	DEAD-like helicase (2);	0.000000	0.85682	D	0.000000	T	0.62708	0.2450	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.61292	-0.7092	10	0.56958	D	0.05	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	1499	Q8N3C0	HELC1_HUMAN	F	1499	ENSP00000358159:L1499F	ENSP00000358159:L1499F	L	-	1	0	ASCC3	101182465	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.993000	0.88291	2.885000	0.99019	0.655000	0.94253	CTT	.	.		0.328	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		A	101075744	G	A	101075744	3	1	81	1	0	0	0	0	1	0	0	0	1033	1000	35	3	2173	3	ASCC3	6	101075744	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	4	101075744	70039323	64	11113	47	3								
POPDC3	64208	hgsc.bcm.edu	37	chr6	105609574	105609574	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tatgtcagctgcacagacatCtacccaagcccagacagcag	8	14	2	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr6:105609574C>A	ENST00000254765.3	-	2	489	c.211G>T	c.(211-213)Gat>Tat	p.D71Y	BVES-AS1_ENST00000580511.1_RNA|POPDC3_ENST00000474760.1_Intron|BVES-AS1_ENST00000369122.3_RNA|BVES-AS1_ENST00000580854.1_RNA|BVES-AS1_ENST00000369120.2_RNA	NM_022361.4	NP_071756.2	Q9HBV1	POPD3_HUMAN	popeye domain containing 3	71					regulation of membrane potential (GO:0042391)	integral component of membrane (GO:0016021)				NS(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(3)|urinary_tract(1)	26		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)				GCACAGACATCTACCCAAGCC	0.438																																					p.D71Y		Atlas-SNP	.											.	POPDC3	47	.	0			c.G211T						.						109	122	118					6																	105609574		2203	4300	6503	SO:0001583	missense	64208	exon2			AGACATCTACCCA	BC022323	CCDS5052.1	6q21	2003-06-12			ENSG00000132429	ENSG00000132429			17649	protein-coding gene	gene with protein product		605824				10882522	Standard	NM_022361		Approved	POP3, MGC22671, bA355M14.1	uc003prb.3	Q9HBV1	OTTHUMG00000015293	ENST00000254765.3:c.211G>T	chr6.hg19:g.105609574C>A	ENSP00000254765:p.Asp71Tyr	209.0	0.0		173.0	69.0	NM_022361	B2RA98|Q5T3Y8|Q8TBW6	Missense_Mutation	SNP	ENST00000254765.3	hg19	CCDS5052.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.874310	0.51695	.	.	ENSG00000132429	ENST00000254765	T	0.54279	0.58	5.72	4.85	0.62838	.	0.142736	0.64402	D	0.000011	T	0.34774	0.0909	L	0.57536	1.79	0.80722	D	1	B	0.32338	0.365	B	0.40101	0.319	T	0.46775	-0.9167	10	0.02654	T	1	-33.8669	16.9001	0.86110	0.0:0.8719:0.1281:0.0	.	71	Q9HBV1	POPD3_HUMAN	Y	71	ENSP00000254765:D71Y	ENSP00000254765:D71Y	D	-	1	0	POPDC3	105716267	0.999000	0.42202	0.997000	0.53966	0.996000	0.88848	4.070000	0.57548	1.420000	0.47138	0.655000	0.94253	GAT	.	.		0.438	POPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041651.1	NM_022361		A	105609574	C	A	105609574	3	1	81	1	0	0	0	0	1	0	0	0	12265	913	32	3	676	3	POPDC3	6	105609574	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	4533830	105609574	65505493	65	11114										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136597048	136597048	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aggacggtgagaatcactcgCtatcattttgatcctaagtg	10	8	2	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr6:136597048C>T	ENST00000531224.1	-	5	1867	c.1615G>A	c.(1615-1617)Gcg>Acg	p.A539T	BCLAF1_ENST00000527759.1_Missense_Mutation_p.A537T|BCLAF1_ENST00000530767.1_Missense_Mutation_p.A366T|BCLAF1_ENST00000353331.4_Missense_Mutation_p.A537T|BCLAF1_ENST00000527536.1_Missense_Mutation_p.A539T|BCLAF1_ENST00000392348.2_Missense_Mutation_p.A537T	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	539					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.A539T(1)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		GAATCACTCGCTATCATTTTG	0.423																																					p.A539T	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											BCLAF1_ENST00000531224,NS,carcinoma,0,1	BCLAF1	203	.	1	Substitution - Missense(1)	breast(1)	c.G1615A						.						210	210	210					6																	136597048		2203	4300	6503	SO:0001583	missense	9774	exon5			CACTCGCTATCAT	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.1615G>A	chr6.hg19:g.136597048C>T	ENSP00000435210:p.Ala539Thr	80.0	0.0		60.0	15.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.012753	0.75161	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T;T	0.14022	2.93;2.93;2.92;2.54;2.93;2.93;2.73	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000006	T	0.12732	0.0309	N	0.08118	0	0.80722	D	1	D;D;D;D	0.67145	0.971;0.964;0.971;0.996	P;P;P;D	0.73708	0.882;0.841;0.882;0.981	T	0.41413	-0.9510	10	0.32370	T	0.25	-4.6349	19.7634	0.96333	0.0:1.0:0.0:0.0	.	537;537;539;366	Q9NYF8-2;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;BCLF1_HUMAN;.	T	539;537;539;366;537;537;539	ENSP00000435210:A539T;ENSP00000229446:A537T;ENSP00000435441:A539T;ENSP00000436501:A366T;ENSP00000434826:A537T;ENSP00000376159:A537T;ENSP00000431734:A539T	ENSP00000229446:A537T	A	-	1	0	BCLAF1	136638741	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.497000	0.53295	2.747000	0.94245	0.460000	0.39030	GCG	.	.		0.423	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		T	136597048	C	T	136597048	3	4	81	1	0	0	0	0	1	0	0	0	1383	797	28	3	1183	3	BCLAF1	6	136597048	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	30987474	136597048	34518019	66	11115										
ZNF735	0	hgsc.bcm.edu	37	chr7	63673536	63673536	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	agtggcaatgcctggatcatGctcagcagaatttatataga	10	7	2	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr7:63673536G>T								GUSBP6 (62437 upstream) : ZNF679 (15315 downstream)																							CCTGGATCATGCTCAGCAGAA	0.398																																					p.A36S		Atlas-SNP	.											.	.	.	.	0			c.G106T						.						60	55	57					7																	63673536		692	1591	2283	SO:0001628	intergenic_variant	730291	exon2			GATCATGCTCAGC																													chr7.hg19:g.63673536G>T		375.0	0.0		354.0	145.0	NM_001159524		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.398									T	63673536	G	T	63673536	1	4	81	0	1	0	0	0	0	0	0	0	18139	1319	46	3		3	ZNF735	7	63673536	IGR	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10		63673536	95465127	67	11116										
OR6B1	135946	hgsc.bcm.edu	37	chr7	143701669	143701669	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tctcctgcacagacatgtccAtaactgagttggtagacttt	8	10	1	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr7:143701669A>G	ENST00000408922.2	+	1	648	c.580A>G	c.(580-582)Ata>Gta	p.I194V		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	194						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|large_intestine(3)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	27	Melanoma(164;0.0783)					AGACATGTCCATAACTGAGTT	0.458																																					p.I194V		Atlas-SNP	.											.	OR6B1	60	.	0			c.A580G						.						168	161	163					7																	143701669		2017	4212	6229	SO:0001583	missense	135946	exon1			ATGTCCATAACTG		CCDS43667.1	7q33-q35	2012-08-09			ENSG00000221813	ENSG00000221813		"GPCR / Class A : Olfactory receptors"	8354	protein-coding gene	gene with protein product							Standard	NM_001005281		Approved	OR7-3	uc003wdt.1	O95007	OTTHUMG00000157765	ENST00000408922.2:c.580A>G	chr7.hg19:g.143701669A>G	ENSP00000386151:p.Ile194Val	96.0	0.0		84.0	31.0	NM_001005281	A4D2G2|B9EH47|Q6IFP6|Q96R38	Missense_Mutation	SNP	ENST00000408922.2	hg19	CCDS43667.1	.	.	.	.	.	.	.	.	.	.	A	3.494	-0.103184	0.06967	.	.	ENSG00000221813	ENST00000408922	T	0.00130	8.69	5.17	-0.187	0.13268	GPCR, rhodopsin-like superfamily (1);	0.595840	0.13617	N	0.374669	T	0.00039	0.0001	N	0.03000	-0.44	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22661	-1.0210	10	0.02654	T	1	.	5.4014	0.16299	0.4889:0.3466:0.1645:0.0	.	194	O95007	OR6B1_HUMAN	V	194	ENSP00000386151:I194V	ENSP00000386151:I194V	I	+	1	0	OR6B1	143332602	0.000000	0.05858	0.219000	0.23793	0.986000	0.74619	-1.328000	0.02680	-0.182000	0.10602	0.533000	0.62120	ATA	.	.		0.458	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1			G	143701669	A	G	143701669	3	3	81	1	0	0	0	0	1	0	0	0	11196	217	8	2	582	2	OR6B1	7	143701669	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	80028133	143701669	15436994	68	11117										
SSPO	23145	hgsc.bcm.edu	37	chr7	149493599	149493599	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gtggagctgctgggctgcgaGccaggtacaggttgcgcagg	19	9	0	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr7:149493599G>A	ENST00000378016.2	+	0	6675							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGGGCTGCGAGCCAGGTACAG	0.677																																					p.E2225E		Atlas-SNP	.											.	.	.	.	0			c.G6675A						.						59	71	67					7																	149493599		2149	4233	6382			23145	exon44			CTGCGAGCCAGGT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149493599G>A		61.0	0.0		61.0	28.0	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.677	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149493599	G	A	149493599	1	1	81	0	1	0	0	0	0	0	0	0	15204	962	34	3		3	SSPO	7	149493599	RNA	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	5791930	149493599	9645064	69	11118										
SGK223	157285	hgsc.bcm.edu	37	chr8	8185368	8185368	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	agtggagctcctttttctggCcgcccatgaagaggtcctca	11	12	2	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr8:8185368C>A	ENST00000520004.1	-	5	3188	c.2924G>T	c.(2923-2925)gGc>gTc	p.G975V	SGK223_ENST00000330777.4_Missense_Mutation_p.G975V			Q86YV5	SG223_HUMAN		977							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CTTTTTCTGGCCGCCCATGAA	0.537																																					p.G975V	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G2924T						.						66	68	68					8																	8185368		1935	4143	6078	SO:0001583	missense	0	exon4			TTCTGGCCGCCCA																												ENST00000520004.1:c.2924G>T	chr8.hg19:g.8185368C>A	ENSP00000428054:p.Gly975Val	102.0	0.0		45.0	31.0	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	hg19	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.964055	0.34659	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.27557	1.66;1.66	4.73	4.73	0.59995	.	0.473238	0.21636	N	0.071408	T	0.27063	0.0663	L	0.50333	1.59	0.58432	D	0.999997	B	0.29988	0.264	B	0.26693	0.072	T	0.05131	-1.0904	10	0.44086	T	0.13	.	10.5646	0.45165	0.0:0.901:0.0:0.099	.	975	Q86YV5	SG223_HUMAN	V	975	ENSP00000330930:G975V;ENSP00000428054:G975V	ENSP00000330930:G975V	G	-	2	0	AC068353.1	8222778	0.570000	0.26651	1.000000	0.80357	0.990000	0.78478	1.436000	0.34980	2.623000	0.88846	0.563000	0.77884	GGC	.	.		0.537	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			A	8185368	C	A	8185368	3	1	81	1	0	0	0	0	1	0	0	0	14225	739	26	3	1292	3	SGK223	8	8185368	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10		8185368	138178654	70	11119										
RAB11FIP1	80223	hgsc.bcm.edu	37	chr8	37756665	37756665	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gcccaggaacttgtcgaggcCgagcagcgcgcggtgcagca	16	13	0	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr8:37756665C>A	ENST00000330843.4	-	1	307	c.295G>T	c.(295-297)Ggc>Tgc	p.G99C	RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000287263.4_Missense_Mutation_p.G99C	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	99	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TTGTCGAGGCCGAGCAGCGCG	0.741																																					p.G99C		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.G295T						.						4	5	5					8																	37756665		1986	4010	5996	SO:0001583	missense	80223	exon1			CGAGGCCGAGCAG	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.295G>T	chr8.hg19:g.37756665C>A	ENSP00000331342:p.Gly99Cys	30.0	0.0		16.0	5.0	NM_025151	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	hg19	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	C	36	5.682575	0.96774	.	.	ENSG00000156675	ENST00000287263;ENST00000330843;ENST00000343853	T;T	0.72282	-0.64;-0.64	5.07	5.07	0.68467	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000008	D	0.90130	0.6916	H	0.97465	4.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.93784	0.7086	10	0.87932	D	0	-14.8866	18.0698	0.89403	0.0:1.0:0.0:0.0	.	99;99	Q6WKZ4-3;Q6WKZ4	.;RFIP1_HUMAN	C	99	ENSP00000287263:G99C;ENSP00000331342:G99C	ENSP00000287263:G99C	G	-	1	0	RAB11FIP1	37875823	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.630000	0.83225	2.354000	0.79902	0.655000	0.94253	GGC	.	.		0.741	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		A	37756665	C	A	37756665	3	1	81	1	0	0	0	0	1	0	0	0	12908	652	23	1	3580	1	RAB11FIP1	8	37756665	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	29571297	37756665	108607357	71	11120										
TRIM55	84675	hgsc.bcm.edu	37	chr8	67049364	67049364	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tggcatcgccatcctcgtggGcagcaacgatcgagtccagg	13	13	0	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr8:67049364G>T	ENST00000315962.4	+	4	915	c.542G>T	c.(541-543)gGc>gTc	p.G181V	TRIM55_ENST00000350034.4_Missense_Mutation_p.G181V|TRIM55_ENST00000276573.7_Missense_Mutation_p.G181V|TRIM55_ENST00000353317.5_Missense_Mutation_p.G181V	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	181					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			ATCCTCGTGGGCAGCAACGAT	0.527																																					p.G181V		Atlas-SNP	.											.	TRIM55	91	.	0			c.G542T						.						106	88	94					8																	67049364		2203	4300	6503	SO:0001583	missense	84675	exon4			TCGTGGGCAGCAA	AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	14215	protein-coding gene	gene with protein product		606469	"ring finger protein 29", "tripartite motif-containing 55"	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.542G>T	chr8.hg19:g.67049364G>T	ENSP00000323913:p.Gly181Val	79.0	0.0		44.0	11.0	NM_184086	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	hg19	CCDS6184.1	.	.	.	.	.	.	.	.	.	.	G	19.78	3.891933	0.72524	.	.	ENSG00000147573	ENST00000315962;ENST00000353317;ENST00000276573;ENST00000350034	T;T;T;T	0.38722	1.48;1.52;1.47;1.12	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.61763	0.2373	M	0.75264	2.295	0.80722	D	1	P;P;P;P	0.50528	0.936;0.864;0.892;0.864	P;P;P;P	0.55545	0.511;0.646;0.778;0.713	T	0.64765	-0.6330	10	0.66056	D	0.02	.	19.5251	0.95201	0.0:0.0:1.0:0.0	.	181;181;181;181	Q9BYV6-4;Q9BYV6-2;Q9BYV6;Q9BYV6-3	.;.;TRI55_HUMAN;.	V	181	ENSP00000323913:G181V;ENSP00000297348:G181V;ENSP00000276573:G181V;ENSP00000332302:G181V	ENSP00000276573:G181V	G	+	2	0	TRIM55	67211918	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	5.508000	0.67006	2.678000	0.91216	0.655000	0.94253	GGC	.	.		0.527	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		T	67049364	G	T	67049364	3	4	81	1	0	0	0	0	1	0	0	0	16544	1203	42	3	556	3	TRIM55	8	67049364	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	29292699	67049364	79314658	72	11121										
TP53INP1	94241	hgsc.bcm.edu	37	chr8	95952161	95952161	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	accagggcaggagttatgcaCagcatagacagacatgctgg	13	9	0	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr8:95952161C>A	ENST00000342697.4	-	3	807	c.400G>T	c.(400-402)Gtg>Ttg	p.V134L	TP53INP1_ENST00000448464.2_Missense_Mutation_p.V134L|TP53INP1_ENST00000378776.4_Missense_Mutation_p.V134L|NDUFAF6_ENST00000396113.1_Intron	NM_033285.3	NP_150601.1	Q96A56	T53I1_HUMAN	tumor protein p53 inducible nuclear protein 1	134					apoptotic process (GO:0006915)|autophagic cell death (GO:0048102)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to hydroperoxide (GO:0071447)|cellular response to methyl methanesulfonate (GO:0072703)|cellular response to UV (GO:0034644)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription, DNA-templated (GO:0045893)|response to heat (GO:0009408)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	antioxidant activity (GO:0016209)			kidney(2)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	9	Breast(36;8.75e-07)					GAGTTATGCACAGCATAGACA	0.468																																					p.V134L		Atlas-SNP	.											.	TP53INP1	22	.	0			c.G400T						.						151	126	134					8																	95952161		2203	4300	6503	SO:0001583	missense	94241	exon3			TATGCACAGCATA	AF409115	CCDS6265.1, CCDS47899.1	8q22	2004-03-11				ENSG00000164938			18022	protein-coding gene	gene with protein product		606185				11511362, 12438758	Standard	NM_033285		Approved	DKFZp434M1317, FLJ22139, P53DINP1, SIP, TP53INP1A, TP53INP1B, Teap	uc003yhg.3	Q96A56		ENST00000342697.4:c.400G>T	chr8.hg19:g.95952161C>A	ENSP00000344215:p.Val134Leu	97.0	0.0		103.0	9.0	NM_001135733	B2RCE5|Q969R9	Missense_Mutation	SNP	ENST00000342697.4	hg19	CCDS6265.1	.	.	.	.	.	.	.	.	.	.	C	18.88	3.717622	0.68844	.	.	ENSG00000164938	ENST00000448464;ENST00000342697;ENST00000378776	T;T;T	0.45276	0.9;0.9;0.9	5.45	3.59	0.41128	.	0.309813	0.34223	N	0.004157	T	0.59362	0.2188	M	0.61703	1.905	0.43073	D	0.994718	B;D	0.89917	0.003;1.0	B;D	0.80764	0.009;0.994	T	0.60586	-0.7234	10	0.49607	T	0.09	-10.0776	13.0286	0.58829	0.1292:0.7467:0.1241:0.0	.	134;134	Q96A56-2;Q96A56	.;T53I1_HUMAN	L	134	ENSP00000390063:V134L;ENSP00000344215:V134L;ENSP00000368052:V134L	ENSP00000344215:V134L	V	-	1	0	TP53INP1	96021337	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.094000	0.41719	0.888000	0.36160	0.655000	0.94253	GTG	.	.		0.468	TP53INP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379818.1			A	95952161	C	A	95952161	3	1	81	1	0	0	0	0	1	0	0	0	16403	478	17	3	356	3	TP53INP1	8	95952161	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	28902797	95952161	50411861	73	11122										
HAS2	3037	hgsc.bcm.edu	37	chr8	122627072	122627072	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttcgtgagatgcctgtcatcAccaaagctacattggttgcc	9	11	2	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr8:122627072A>G	ENST00000303924.4	-	4	1473	c.936T>C	c.(934-936)ggT>ggC	p.G312G		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	312					atrioventricular canal development (GO:0036302)|bone morphogenesis (GO:0060349)|cellular response to fluid shear stress (GO:0071498)|cellular response to interleukin-1 (GO:0071347)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|endocardial cushion to mesenchymal transition (GO:0090500)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|hyaluronan biosynthetic process (GO:0030213)|kidney development (GO:0001822)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	hyaluronan synthase activity (GO:0050501)		HAS2/PLAG1(10)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			GCCTGTCATCACCAAAGCTAC	0.443																																					p.G312G		Atlas-SNP	.											.	HAS2	87	.	0			c.T936C						.						159	151	154					8																	122627072		2203	4300	6503	SO:0001819	synonymous_variant	3037	exon4			GTCATCACCAAAG	U54804	CCDS6335.1	8q24.12	2013-02-22			ENSG00000170961	ENSG00000170961	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4819	protein-coding gene	gene with protein product		601636				9169154	Standard	NM_005328		Approved		uc003yph.2	Q92819	OTTHUMG00000164953	ENST00000303924.4:c.936T>C	chr8.hg19:g.122627072A>G		80.0	0.0		79.0	10.0	NM_005328	Q32MM3	Silent	SNP	ENST00000303924.4	hg19	CCDS6335.1																																																																																			.	.		0.443	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328		G	122627072	A	G	122627072	2	3	81	1	0	0	0	0	0	0	0	1	6971	146	6	2		2	HAS2	8	122627072	Silent	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	26674911	122627072	23736950	74	11123										
ZHX1	11244	hgsc.bcm.edu	37	chr8	124267098	124267098	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ataacagttatggtctgaggTacagtatgcactgttccatt	9	7	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr8:124267098T>A	ENST00000522655.1	-	3	1629	c.1089A>T	c.(1087-1089)gtA>gtT	p.V363V	ZHX1_ENST00000522595.1_5'Flank|ZHX1_ENST00000395571.3_Silent_p.V363V|ZHX1_ENST00000297857.2_Silent_p.V363V|ZHX1-C8ORF76_ENST00000357082.4_Intron			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	363	Required for dimerization.|Required for interaction with NFYA.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			TGGTCTGAGGTACAGTATGCA	0.428																																					p.V363V		Atlas-SNP	.											.	ZHX1	89	.	0			c.A1089T						.						227	187	200					8																	124267098		2203	4300	6503	SO:0001819	synonymous_variant	11244	exon3			CTGAGGTACAGTA	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	12871	protein-coding gene	gene with protein product		604764	"zinc-fingers and homeoboxes 1"			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.1089A>T	chr8.hg19:g.124267098T>A		142.0	0.0		225.0	24.0	NM_007222	Q8IWD8	Silent	SNP	ENST00000522655.1	hg19	CCDS6342.1	.	.	.	.	.	.	.	.	.	.	T	5.142	0.211822	0.09757	.	.	ENSG00000165156	ENST00000520474	.	.	.	5.27	2.8	0.32819	.	.	.	.	.	T	0.43722	0.1260	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29640	-1.0005	4	.	.	.	-16.5914	1.4834	0.02441	0.282:0.081:0.2926:0.3443	.	.	.	.	F	48	.	.	Y	-	2	0	ZHX1	124336279	0.998000	0.40836	1.000000	0.80357	0.986000	0.74619	0.438000	0.21559	0.413000	0.25759	0.454000	0.30748	TAC	.	.		0.428	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1			A	124267098	T	A	124267098	2	1	81	1	0	0	0	0	0	0	0	1	17690	1625	57	4		4	ZHX1	8	124267098	Silent	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	1640026	124267098	22096924	75	11124										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5922128	5922129	+	Frame_Shift_Del	DEL	CA	CA	-													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ggtctgtacttttacaactcCagtgttcccacctcgtgtcc							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr9:5922128_5922129delCA	ENST00000399933.3	-	8	3866_3867	c.3867_3868delTG	c.(3865-3870)actggafs	p.G1290fs	KIAA2026_ENST00000381461.2_Frame_Shift_Del_p.G1260fs	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1290										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TTTACAACTCCAGTGTTCCCAC	0.426																																					p.1290_1290del		Atlas-Indel,Pindel	.											.	KIAA2026	231	.	0			c.3868_3869del						.																																			SO:0001589	frameshift_variant	158358	exon8			.	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.3867_3868delTG	chr9.hg19:g.5922128_5922129delCA	ENSP00000382815:p.Gly1290fs	150.0	0.0		173.0	54.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Frame_Shift_Del	DEL	ENST00000399933.3	hg19																																																																																				.	.		0.426	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		-	5922129	CA	-	5922128	7	5	81	1	0	1	0	1	0	0	0	0	8279	603	21	0	2447	0	KIAA2026	9	5922128	Frame_Shift_Del	DEL	CA	TCGA-CC-A8HV-01A-11D-A35Z-10		5922128	135291303	76	11125										
CNTLN	54875	hgsc.bcm.edu	37	chr9	17340879	17340879	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aaaaacgcaaggaacggctaCagatgttacagaccaactac	8	10	0	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr9:17340879C>G	ENST00000380647.3	+	11	1783	c.1699C>G	c.(1699-1701)Cag>Gag	p.Q567E	CNTLN_ENST00000425824.1_Missense_Mutation_p.Q567E|CNTLN_ENST00000262360.5_Missense_Mutation_p.Q567E			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	567					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		GGAACGGCTACAGATGTTACA	0.388																																					p.Q567E		Atlas-SNP	.											.	CNTLN	128	.	0			c.C1699G						.						89	85	86					9																	17340879		1911	4129	6040	SO:0001583	missense	54875	exon11			CGGCTACAGATGT	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.1699C>G	chr9.hg19:g.17340879C>G	ENSP00000370021:p.Gln567Glu	368.0	0.0		393.0	16.0	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	hg19	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	C	18.03	3.532147	0.64972	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.10960	2.82;2.82;2.82	5.4	5.4	0.78164	.	.	.	.	.	T	0.24890	0.0604	M	0.63428	1.95	0.33236	D	0.556564	D;D;D	0.67145	0.996;0.991;0.991	P;P;P	0.59056	0.851;0.789;0.789	T	0.14727	-1.0462	9	0.08381	T	0.77	.	19.1457	0.93467	0.0:1.0:0.0:0.0	.	567;567;567	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	E	567	ENSP00000370021:Q567E;ENSP00000392798:Q567E;ENSP00000262360:Q567E	ENSP00000262360:Q567E	Q	+	1	0	CNTLN	17330879	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.442000	0.59988	2.518000	0.84900	0.591000	0.81541	CAG	.	.		0.388	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		G	17340879	C	G	17340879	3	3	81	1	0	0	0	0	1	0	0	0	3641	479	17	4	1771	4	CNTLN	9	17340879	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	11418751	17340879	123872552	77	11126										
IFNA5	3442	hgsc.bcm.edu	37	chr9	21305082	21305082	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tcctcctgaggaaatccaaaGtcatgtctgtccttcaggca	8	12	3	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr9:21305082G>C	ENST00000259555.4	-	1	230	c.174C>G	c.(172-174)gaC>gaG	p.D58E		NM_002169.2	NP_002160.1	P01569	IFNA5_HUMAN	interferon, alpha 5	58					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	7				Lung(24;2.34e-24)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		GAAATCCAAAGTCATGTCTGT	0.483																																					p.D58E		Atlas-SNP	.											.	IFNA5	21	.	0			c.C174G						.						144	137	139					9																	21305082		2203	4300	6503	SO:0001583	missense	3442	exon1			TCCAAAGTCATGT		CCDS6502.1	9p22	2010-08-24			ENSG00000147873	ENSG00000147873		"Interferons"	5426	protein-coding gene	gene with protein product		147565				1385305	Standard	NM_002169		Approved	IFN-alphaG	uc011lnh.2	P01569	OTTHUMG00000019664	ENST00000259555.4:c.174C>G	chr9.hg19:g.21305082G>C	ENSP00000259555:p.Asp58Glu	114.0	0.0		92.0	23.0	NM_002169	Q52LX3	Missense_Mutation	SNP	ENST00000259555.4	hg19	CCDS6502.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.489528	0.44249	.	.	ENSG00000147873	ENST00000259555	T	0.04862	3.54	4.16	4.16	0.48862	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.785759	0.11871	N	0.521452	T	0.24084	0.0583	H	0.95328	3.655	0.26721	N	0.97077	B	0.20164	0.042	B	0.34452	0.183	T	0.14035	-1.0487	10	0.72032	D	0.01	.	13.7771	0.63059	0.0:0.0:1.0:0.0	.	58	P01569	IFNA5_HUMAN	E	58	ENSP00000259555:D58E	ENSP00000259555:D58E	D	-	3	2	IFNA5	21295082	0.966000	0.33281	0.109000	0.21407	0.007000	0.05969	2.275000	0.43399	2.052000	0.61016	0.537000	0.68136	GAC	.	.		0.483	IFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051893.1	NM_002169		C	21305082	G	C	21305082	3	2	81	1	0	0	0	0	1	0	0	0	7549	1020	36	4	399	4	IFNA5	9	21305082	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	3964203	21305082	119908349	78	11127										
HSDL2	84263	hgsc.bcm.edu	37	chr9	115171195	115171195	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttttgaaaacaggaattgatAttctggtaaataatgccagt	8	4	1	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr9:115171195A>G	ENST00000398805.3	+	4	516	c.289A>G	c.(289-291)Att>Gtt	p.I97V	HSDL2_ENST00000262542.7_5'UTR|HSDL2_ENST00000398803.1_Intron|HSDL2_ENST00000488101.1_3'UTR|HSDL2_ENST00000539114.1_5'UTR	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	97						membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|cervix(2)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	13						AGGAATTGATATTCTGGTAAA	0.358																																					p.I97V		Atlas-SNP	.											.	HSDL2	24	.	0			c.A289G						.						94	84	87					9																	115171195		1858	4103	5961	SO:0001583	missense	84263	exon4			ATTGATATTCTGG	AY093428	CCDS43864.1, CCDS56582.1	9q32	2011-09-14			ENSG00000119471	ENSG00000119471		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18572	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 13C, member 1"		"chromosome 9 open reading frame 99"	C9orf99		12834046, 19027726	Standard	NM_032303		Approved	SDR13C1	uc004bga.2	Q6YN16	OTTHUMG00000020504	ENST00000398805.3:c.289A>G	chr9.hg19:g.115171195A>G	ENSP00000381785:p.Ile97Val	71.0	0.0		58.0	21.0	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	hg19	CCDS43864.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.337394	0.41398	.	.	ENSG00000119471	ENST00000398805	D	0.86865	-2.18	6.17	1.21	0.21127	NAD(P)-binding domain (1);	0.265476	0.41712	N	0.000835	T	0.76593	0.4009	N	0.21282	0.65	0.80722	D	1	B	0.12013	0.005	B	0.19946	0.027	T	0.64609	-0.6367	10	0.32370	T	0.25	.	10.3627	0.44003	0.6855:0.0:0.3145:0.0	.	97	Q6YN16	HSDL2_HUMAN	V	97	ENSP00000381785:I97V	ENSP00000381785:I97V	I	+	1	0	HSDL2	114211016	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.681000	0.37618	0.207000	0.20607	0.533000	0.62120	ATT	.	.		0.358	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303		G	115171195	A	G	115171195	3	3	81	1	0	0	0	0	1	0	0	0	7403	449	16	2	303	2	HSDL2	9	115171195	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	93866113	115171195	26042236	79	11128										
PPP2R4	5524	hgsc.bcm.edu	37	chr9	131891300	131891300	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tcgctcttctcaacacgctgGacaggtggattgatgagact	11	10	2	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr9:131891300G>C	ENST00000337738.1	+	5	625	c.358G>C	c.(358-360)Gac>Cac	p.D120H	PPP2R4_ENST00000393370.2_Missense_Mutation_p.D85H|PPP2R4_ENST00000357197.4_Missense_Mutation_p.D56H|PPP2R4_ENST00000348141.5_Missense_Mutation_p.D91H|PPP2R4_ENST00000347048.4_Intron|PPP2R4_ENST00000358994.4_Missense_Mutation_p.D85H|PPP2R4_ENST00000355007.3_Intron|PPP2R4_ENST00000452489.2_Missense_Mutation_p.D120H	NM_178001.2	NP_821068.1	Q15257	PTPA_HUMAN	protein phosphatase 2A activator, regulatory subunit 4	120					ATP catabolic process (GO:0006200)|mitotic spindle organization in nucleus (GO:0030472)|negative regulation of phosphoprotein phosphatase activity (GO:0032515)|negative regulation of protein dephosphorylation (GO:0035308)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein dephosphorylation (GO:0035307)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of phosphoprotein phosphatase activity (GO:0043666)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	ATP binding (GO:0005524)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein tyrosine phosphatase activator activity (GO:0008160)|receptor binding (GO:0005102)			breast(3)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12		Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		CAACACGCTGGACAGGTGGAT	0.547																																					p.D120H	Colon(158;2158 2504 4450 20433)	Atlas-SNP	.											.	PPP2R4	32	.	0			c.G358C						.						95	80	86					9																	131891300		2203	4300	6503	SO:0001583	missense	5524	exon5			ACGCTGGACAGGT	X73478	CCDS6920.1, CCDS65156.1, CCDS75917.1	9q34	2010-06-18	2007-01-22		ENSG00000119383	ENSG00000119383		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9308	protein-coding gene	gene with protein product	"phosphotyrosyl phosphatase activator", "PP2A phosphatase activator"	600756	"protein phosphatase 2A, regulatory subunit B' (PR 53)"			8530035	Standard	NM_021131		Approved	PTPA, PR53	uc004bxm.2	Q15257	OTTHUMG00000020774	ENST00000337738.1:c.358G>C	chr9.hg19:g.131891300G>C	ENSP00000337448:p.Asp120His	126.0	0.0		93.0	35.0	NM_178001	A2A347|A9IZU4|B4DXM4|Q15258|Q53GZ3|Q5TZQ2|Q9BUK1|Q9NNZ7|Q9NNZ8|Q9NNZ9	Missense_Mutation	SNP	ENST00000337738.1	hg19		.	.	.	.	.	.	.	.	.	.	G	22.0	4.231536	0.79688	.	.	ENSG00000119383	ENST00000358994;ENST00000455292;ENST00000393370;ENST00000337738;ENST00000348141;ENST00000452489;ENST00000357197;ENST00000445241;ENST00000414331;ENST00000417728;ENST00000453358;ENST00000417504;ENST00000440346	T;T;T;T;T;T;T;T;T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.48;1.43;1.43;1.43	5.08	5.08	0.68730	.	0.046675	0.85682	D	0.000000	T	0.47432	0.1445	M	0.69463	2.115	0.80722	D	1	P;P;B;D	0.57899	0.951;0.831;0.11;0.981	P;P;B;P	0.58873	0.847;0.516;0.098;0.785	T	0.47598	-0.9105	10	0.72032	D	0.01	-32.6307	11.3487	0.49575	0.0829:0.0:0.9171:0.0	.	56;120;120;85	Q15257-3;B4DZF8;Q15257;Q15257-2	.;.;PTPA_HUMAN;.	H	85;120;85;120;91;120;56;120;48;50;50;108;50	ENSP00000351885:D85H;ENSP00000395499:D120H;ENSP00000377036:D85H;ENSP00000337448:D120H;ENSP00000335200:D91H;ENSP00000394338:D120H;ENSP00000349726:D56H;ENSP00000406997:D120H;ENSP00000399069:D48H;ENSP00000403542:D50H;ENSP00000393092:D50H;ENSP00000400314:D108H;ENSP00000393796:D50H	ENSP00000337448:D120H	D	+	1	0	PPP2R4	130931121	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	7.964000	0.87933	2.507000	0.84556	0.655000	0.94253	GAC	.	.		0.547	PPP2R4-201	KNOWN	basic	protein_coding	protein_coding		NM_021131		C	131891300	G	C	131891300	3	2	81	1	0	0	0	0	1	0	0	0	12403	1174	41	4	376	4	PPP2R4	9	131891300	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	16720105	131891300	9322131	80	11129										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7679256	7679256	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gcacctccagggatgcgatgCccgcgctctccaggatattc	11	15	1	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr10:7679256C>G	ENST00000256861.6	-	5	665	c.587G>C	c.(586-588)gGc>gCc	p.G196A	ITIH5_ENST00000397145.2_Missense_Mutation_p.G196A|ITIH5_ENST00000397146.2_Missense_Mutation_p.G196A|ITIH5_ENST00000446830.2_5'UTR|ITIH5_ENST00000434980.1_5'UTR	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	196					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						GGATGCGATGCCCGCGCTCTC	0.662																																					p.G196A		Atlas-SNP	.											.	ITIH5	343	.	0			c.G587C						.						72	73	73					10																	7679256		2203	4300	6503	SO:0001583	missense	80760	exon5			GCGATGCCCGCGC			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.587G>C	chr10.hg19:g.7679256C>G	ENSP00000256861:p.Gly196Ala	32.0	0.0		40.0	9.0	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	C	13.53	2.264026	0.39995	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000397145	T;T;T	0.03124	4.55;4.04;4.04	5.88	5.88	0.94601	.	0.143885	0.64402	D	0.000007	T	0.21227	0.0511	.	.	.	0.42283	D	0.992109	D;P	0.76494	0.999;0.78	D;B	0.77004	0.989;0.18	T	0.00042	-1.2230	9	0.72032	D	0.01	-40.7125	20.2092	0.98286	0.0:1.0:0.0:0.0	.	196;196	G5E9D8;Q86UX2	.;ITIH5_HUMAN	A	196	ENSP00000256861:G196A;ENSP00000380333:G196A;ENSP00000380332:G196A	ENSP00000256861:G196A	G	-	2	0	ITIH5	7719262	1.000000	0.71417	0.339000	0.25562	0.013000	0.08279	3.717000	0.54911	2.776000	0.95493	0.655000	0.94253	GGC	.	.		0.662	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		G	7679256	C	G	7679256	3	3	81	1	0	0	0	0	1	0	0	0	7916	739	26	4	2418	4	ITIH5	10	7679256	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10		7679256	127855491	81	11130										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72432599	72432599	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gctgtcctacctgctgccttTgcactgtgcgctctgcgccg	11	16	1	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr10:72432599T>G	ENST00000373207.1	+	1	41	c.41T>G	c.(40-42)tTg>tGg	p.L14W	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.L14W	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	14					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CTGCTGCCTTTGCACTGTGCG	0.761																																					p.L14W		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.T41G						.						3	3	3					10																	72432599		1817	3587	5404	SO:0001583	missense	140766	exon1			TGCCTTTGCACTG	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.41T>G	chr10.hg19:g.72432599T>G	ENSP00000362303:p.Leu14Trp	88.0	0.0		67.0	5.0	NM_080722	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	hg19	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.819137	0.32145	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.63255	-0.03;-0.01	3.68	2.5	0.30297	.	1.110620	0.07131	N	0.845627	T	0.43433	0.1247	N	0.12182	0.205	0.22112	N	0.999351	B;B	0.12630	0.006;0.006	B;B	0.08055	0.003;0.003	T	0.32241	-0.9914	10	0.46703	T	0.11	.	6.8519	0.24020	0.0:0.0:0.2536:0.7464	.	14;14	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	W	14	ENSP00000362304:L14W;ENSP00000362303:L14W	ENSP00000362303:L14W	L	+	2	0	ADAMTS14	72102605	0.095000	0.21747	0.997000	0.53966	0.292000	0.27327	1.539000	0.36104	0.540000	0.28808	0.379000	0.24179	TTG	.	.		0.761	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		G	72432599	T	G	72432599	3	3	81	1	0	0	0	0	1	0	0	0	259	1821	63	5	43	5	ADAMTS14	10	72432599	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	64753343	72432599	63102148	82	11131										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88259625	88259625	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttcatcatcttcgctttcacTgagatcatcaaagccaaaat	4	11	6	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr10:88259625T>G	ENST00000298767.5	-	3	1847	c.1375A>C	c.(1375-1377)Agt>Cgt	p.S459R		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	459	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						TCGCTTTCACTGAGATCATCA	0.388																																					p.S459R		Atlas-SNP	.											.	WAPAL	81	.	0			c.A1375C						.						122	114	116					10																	88259625		2203	4300	6503	SO:0001583	missense	23063	exon3			TTTCACTGAGATC	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.1375A>C	chr10.hg19:g.88259625T>G	ENSP00000298767:p.Ser459Arg	129.0	0.0		109.0	18.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.000294	0.74818	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.56275	0.47	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.69305	0.3096	L	0.59436	1.845	0.80722	D	1	D;D;D	0.89917	0.998;0.998;1.0	D;D;D	0.85130	0.991;0.991;0.997	T	0.72074	-0.4400	10	0.66056	D	0.02	.	15.4971	0.75662	0.0:0.0:0.0:1.0	.	459;459;502	B2RTX8;Q7Z5K2;Q7Z5K2-2	.;WAPL_HUMAN;.	R	544;459;544	ENSP00000298767:S459R	ENSP00000298767:S459R	S	-	1	0	WAPAL	88249605	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.068000	0.61886	0.533000	0.62120	AGT	.	.		0.388	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		G	88259625	T	G	88259625	3	3	81	1	0	0	0	0	1	0	0	0	17263	1580	55	5	2265	5	WAPAL	10	88259625	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	15827026	88259625	47275122	83	11132										
SIRT3	23410	hgsc.bcm.edu	37	chr11	219012	219012	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cggggaactgagctccgcacGgcctcggtcaagctggcaaa	14	13	1	1	rs376721867		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr11:219012G>A	ENST00000382743.4	-	6	1101	c.999C>T	c.(997-999)gcC>gcT	p.A333A	SIRT3_ENST00000529382.1_Silent_p.A191A|SIRT3_ENST00000532956.1_Silent_p.A279A|SIRT3_ENST00000525319.1_Silent_p.A252A|SIRT3_ENST00000524564.1_Silent_p.A269A	NM_001017524.2|NM_012239.5	NP_001017524.1|NP_036371.1	Q9NTG7	SIR3_HUMAN	sirtuin 3	333	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				aerobic respiration (GO:0009060)|peptidyl-lysine deacetylation (GO:0034983)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)	membrane (GO:0016020)|mitochondrion (GO:0005739)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|zinc ion binding (GO:0008270)			endometrium(1)|lung(5)|urinary_tract(1)	7		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		AGCTCCGCACGGCCTCGGTCA	0.612																																					p.A333A		Atlas-SNP	.											.	SIRT3	28	.	0			c.C999T						.	G	,	0,4406		0,0,2203	45	42	43		573,999	-10.1	0	11		43	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	SIRT3	NM_001017524.2,NM_012239.5	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	191/258,333/400	219012	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23410	exon6			CCGCACGGCCTCG	AF083108	CCDS7691.1, CCDS53590.1	11p15.5	2010-06-25	2010-06-25		ENSG00000142082	ENSG00000142082			14931	protein-coding gene	gene with protein product		604481	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 3", "sirtuin (silent mating type information regulation 2 homolog) 3 (S. cerevisiae)"			10381378, 18215119	Standard	NM_012239		Approved	SIR2L3	uc001lok.4	Q9NTG7	OTTHUMG00000119074	ENST00000382743.4:c.999C>T	chr11.hg19:g.219012G>A		113.0	0.0		84.0	32.0	NM_012239	B7Z5U6|Q9Y6E8	Silent	SNP	ENST00000382743.4	hg19	CCDS7691.1																																																																																			.	.		0.612	SIRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239288.3			A	219012	G	A	219012	2	1	81	1	0	0	0	0	0	0	0	1	14354	1103	39	1		1	SIRT3	11	219012	Silent	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10		219012	134787504	84	11133										
OR51V1	283111	hgsc.bcm.edu	37	chr11	5221636	5221636	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ggaatccaagctgatctctcGaatgatcccccacaggatcc	8	14	1	2	rs558002486		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr11:5221636G>A	ENST00000321255.1	-	1	294	c.295C>T	c.(295-297)Cga>Tga	p.R99*		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	99					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGATCTCTCGAATGATCCCC	0.537													G|||	1	0.000199681	0	0	5008	,	,		19423	0		0	False		,,,				2504	0.001				p.R99X		Atlas-SNP	.											.	OR51V1	77	.	0			c.C295T						.						70	63	65					11																	5221636		2201	4298	6499	SO:0001587	stop_gained	283111	exon1			TCTCTCGAATGAT	BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"GPCR / Class A : Olfactory receptors"	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.295C>T	chr11.hg19:g.5221636G>A	ENSP00000321729:p.Arg99*	118.0	0.0		103.0	37.0	NM_001004760		Nonsense_Mutation	SNP	ENST00000321255.1	hg19	CCDS31375.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.760934	0.31137	.	.	ENSG00000176742	ENST00000321255	.	.	.	5.48	-5.71	0.02413	.	1.102880	0.07131	N	0.845508	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.698	0.17867	0.0621:0.2469:0.1743:0.5166	.	.	.	.	X	99	.	ENSP00000321729:R99X	R	-	1	2	OR51V1	5178212	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	-0.800000	0.04555	-0.777000	0.04572	-0.127000	0.14921	CGA	.	.		0.537	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760		A	5221636	G	A	5221636	4	1	81	1	0	0	0	0	0	1	0	0	11116	1066	37	1	673	1	OR51V1	11	5221636	Nonsense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	5002624	5221636	129784880	85	11134										
ZNF215	7762	hgsc.bcm.edu	37	chr11	6977365	6977365	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tgaatgttatcaatgtgggaAagccttctgccgaagttcat	10	7	3	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr11:6977365A>G	ENST00000278319.5	+	7	1745	c.1157A>G	c.(1156-1158)aAa>aGa	p.K386R	ZNF215_ENST00000414517.2_Missense_Mutation_p.K386R|ZNF215_ENST00000529903.1_Intron	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	386					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		CAATGTGGGAAAGCCTTCTGC	0.388																																					p.K386R		Atlas-SNP	.											.	ZNF215	72	.	0			c.A1157G						.						73	71	72					11																	6977365		2201	4296	6497	SO:0001583	missense	7762	exon7			GTGGGAAAGCCTT	AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"Zinc fingers, C2H2-type", "-", "-", "-"	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.1157A>G	chr11.hg19:g.6977365A>G	ENSP00000278319:p.Lys386Arg	78.0	0.0		71.0	18.0	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	hg19	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	A	10.87	1.471824	0.26423	.	.	ENSG00000149054	ENST00000278319;ENST00000414517	T;T	0.20738	2.05;2.05	4.85	1.09	0.20402	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.48286	D	0.000189	T	0.17365	0.0417	M	0.62016	1.91	0.80722	D	1	B	0.28208	0.203	B	0.32583	0.148	T	0.07829	-1.0752	9	.	.	.	-4.3472	1.2929	0.02064	0.4446:0.1598:0.0869:0.3087	.	386	Q9UL58	ZN215_HUMAN	R	386	ENSP00000278319:K386R;ENSP00000393202:K386R	.	K	+	2	0	ZNF215	6933941	1.000000	0.71417	0.830000	0.32933	0.356000	0.29392	3.202000	0.51067	0.080000	0.16959	-0.333000	0.08304	AAA	.	.		0.388	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1			G	6977365	A	G	6977365	3	3	81	1	0	0	0	0	1	0	0	0	17786	14	1	2	1175	2	ZNF215	11	6977365	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	1755729	6977365	128029151	86	11135										
PLEKHA7	144100	hgsc.bcm.edu	37	chr11	16863174	16863174	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttcatgtcctcctgggtgtcGgcactgaagtagtaggtcct	12	10	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr11:16863174G>A	ENST00000355661.3	-	9	802	c.792C>T	c.(790-792)gcC>gcT	p.A264A	PLEKHA7_ENST00000532079.1_Intron|RN7SKP90_ENST00000363013.1_RNA|PLEKHA7_ENST00000448080.2_Silent_p.A264A|PLEKHA7_ENST00000531066.1_Silent_p.A264A			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	264	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						CCTGGGTGTCGGCACTGAAGT	0.582																																					p.A264A		Atlas-SNP	.											.	PLEKHA7	120	.	0			c.C792T						.						126	104	111					11																	16863174		2200	4294	6494	SO:0001819	synonymous_variant	144100	exon9			GGTGTCGGCACTG	BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"Pleckstrin homology (PH) domain containing"	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.792C>T	chr11.hg19:g.16863174G>A		68.0	0.0		73.0	30.0	NM_175058	B4DK33|B4DWC3|Q86VZ7	Silent	SNP	ENST00000355661.3	hg19	CCDS31434.1																																																																																			.	.		0.582	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058		A	16863174	G	A	16863174	2	1	81	1	0	0	0	0	0	0	0	1	12070	1103	39	1		1	PLEKHA7	11	16863174	Silent	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	9885809	16863174	118143342	87	11136										
ACCS	84680	hgsc.bcm.edu	37	chr11	44089305	44089305	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ctccagaaaactggaccagaAgctgccagagctccgtggag	12	12	0	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr11:44089305A>T	ENST00000263776.8	+	2	562	c.128A>T	c.(127-129)aAg>aTg	p.K43M	ACCS_ENST00000432284.2_Missense_Mutation_p.K43M|ACCS_ENST00000533208.1_3'UTR	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	43					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						CTGGACCAGAAGCTGCCAGAG	0.552																																					p.K43M	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											.	ACCS	64	.	0			c.A128T						.						91	91	91					11																	44089305		2203	4300	6503	SO:0001583	missense	84680	exon2			ACCAGAAGCTGCC	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.128A>T	chr11.hg19:g.44089305A>T	ENSP00000263776:p.Lys43Met	112.0	0.0		81.0	23.0	NM_032592	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	hg19	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	A	14.57	2.575550	0.45902	.	.	ENSG00000110455	ENST00000524990;ENST00000263776;ENST00000432284;ENST00000533404	T;T;T;T	0.62788	0.9;0.0;0.9;0.52	4.66	3.51	0.40186	.	0.438298	0.21208	N	0.078344	T	0.71256	0.3318	M	0.65975	2.015	0.18873	N	0.999984	D;P	0.76494	0.999;0.901	D;P	0.63192	0.912;0.541	T	0.60647	-0.7222	10	0.45353	T	0.12	-23.1932	8.4274	0.32737	0.8032:0.1968:0.0:0.0	.	43;43	B4E219;Q96QU6	.;1A1L1_HUMAN	M	43	ENSP00000434156:K43M;ENSP00000263776:K43M;ENSP00000391775:K43M;ENSP00000435919:K43M	ENSP00000263776:K43M	K	+	2	0	ACCS	44045881	0.985000	0.35326	0.590000	0.28732	0.643000	0.38383	2.502000	0.45398	0.794000	0.33899	0.496000	0.49642	AAG	.	.		0.552	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		T	44089305	A	T	44089305	3	4	81	1	0	0	0	0	1	0	0	0	133	72	3	4	130	4	ACCS	11	44089305	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10	27226131	44089305	90917211	88	11137										
LPXN	9404	hgsc.bcm.edu	37	chr11	58318615	58318615	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gccaaggtcctgcaattcctGctccagacccccaagcattg	8	16	0	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr11:58318615G>A	ENST00000395074.2	-	5	497	c.409C>T	c.(409-411)Cag>Tag	p.Q137*	LPXN_ENST00000528954.1_Nonsense_Mutation_p.Q142*|LPXN_ENST00000528489.1_Nonsense_Mutation_p.Q117*	NM_004811.2	NP_004802.1	O60711	LPXN_HUMAN	leupaxin	137					cell adhesion (GO:0007155)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell adhesion (GO:0007162)|protein complex assembly (GO:0006461)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|podosome (GO:0002102)	transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				TGCAATTCCTGCTCCAGACCC	0.552																																					p.Q142X		Atlas-SNP	.											.	LPXN	55	.	0			c.C424T						.						110	91	97					11																	58318615		2201	4295	6496	SO:0001587	stop_gained	9404	exon5			ATTCCTGCTCCAG	AF062075	CCDS7969.1, CCDS53635.1	11q12.1	2013-09-20			ENSG00000110031	ENSG00000110031			14061	protein-coding gene	gene with protein product		605390				9565592	Standard	NM_004811		Approved	LDPL	uc001nmw.3	O60711	OTTHUMG00000167466	ENST00000395074.2:c.409C>T	chr11.hg19:g.58318615G>A	ENSP00000378512:p.Gln137*	84.0	0.0		98.0	21.0	NM_001143995	B2R8B4|B4DV71|Q53FW6|Q6FI07	Nonsense_Mutation	SNP	ENST00000395074.2	hg19	CCDS7969.1	.	.	.	.	.	.	.	.	.	.	G	35	5.595418	0.96602	.	.	ENSG00000110031	ENST00000528954;ENST00000395074	.	.	.	5.7	5.7	0.88788	.	0.203947	0.45606	D	0.000352	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	12.0042	0.53248	0.0797:0.0:0.9203:0.0	.	.	.	.	X	142;137	.	ENSP00000378512:Q137X	Q	-	1	0	LPXN	58075191	1.000000	0.71417	1.000000	0.80357	0.659000	0.38960	5.941000	0.70195	2.683000	0.91414	0.655000	0.94253	CAG	.	.		0.552	LPXN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394709.1	NM_004811		A	58318615	G	A	58318615	4	1	81	1	0	0	0	0	0	1	0	0	8938	1328	46	3	771	3	LPXN	11	58318615	Nonsense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	14229310	58318615	76687901	89	11138										
ZP1	22917	hgsc.bcm.edu	37	chr11	60641131	60641131	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cctttcaagggcgacagctaCagaacccaaatggtagcctt	9	12	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr11:60641131C>A	ENST00000278853.5	+	9	1455	c.1455C>A	c.(1453-1455)taC>taA	p.Y485*		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	485	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						GCGACAGCTACAGAACCCAAA	0.587																																					p.Y485X		Atlas-SNP	.											.	ZP1	69	.	0			c.C1455A						.						143	146	145					11																	60641131		2203	4299	6502	SO:0001587	stop_gained	22917	exon9			CAGCTACAGAACC	BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"Zona pellucida glycoproteins"	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.1455C>A	chr11.hg19:g.60641131C>A	ENSP00000278853:p.Tyr485*	105.0	0.0		91.0	36.0	NM_207341		Nonsense_Mutation	SNP	ENST00000278853.5	hg19	CCDS31572.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.991325	0.74703	.	.	ENSG00000149506	ENST00000278853;ENST00000544498	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.4487	13.2789	0.60202	0.0:0.9218:0.0:0.0782	.	.	.	.	X	485;192	.	ENSP00000278853:Y485X	Y	+	3	2	ZP1	60397707	0.993000	0.37304	1.000000	0.80357	0.177000	0.22998	1.030000	0.30153	2.477000	0.83638	0.313000	0.20887	TAC	.	.		0.587	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341		A	60641131	C	A	60641131	4	1	81	1	0	0	0	0	0	1	0	0	18230	489	17	3	1489	3	ZP1	11	60641131	Nonsense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	2322516	60641131	74365385	90	11139										
ANO1	55107	hgsc.bcm.edu	37	chr11	69949238	69949238	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	acgtgctgtgcagagaggccGagtttctgaaactgaagatg	14	7	1	4			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr11:69949238G>T	ENST00000355303.5	+	3	813	c.508G>T	c.(508-510)Gag>Tag	p.E170*	ANO1_ENST00000530676.1_Nonsense_Mutation_p.E54*|ANO1_ENST00000398543.2_Nonsense_Mutation_p.E54*|ANO1_ENST00000538023.1_Nonsense_Mutation_p.E170*|ANO1_ENST00000316296.5_Nonsense_Mutation_p.E142*	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	170					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	CAGAGAGGCCGAGTTTCTGAA	0.532																																					p.E170X		Atlas-SNP	.											.	ANO1	156	.	0			c.G508T						.						77	84	82					11																	69949238		2031	4169	6200	SO:0001587	stop_gained	55107	exon3			GAGGCCGAGTTTC	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	21625	protein-coding gene	gene with protein product		610108	"oral cancer overexpressed 2", "transmembrane protein 16A"	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.508G>T	chr11.hg19:g.69949238G>T	ENSP00000347454:p.Glu170*	173.0	0.0		142.0	30.0	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Nonsense_Mutation	SNP	ENST00000355303.5	hg19	CCDS44663.1	.	.	.	.	.	.	.	.	.	.	G	32	5.119449	0.94385	.	.	ENSG00000131620	ENST00000355303;ENST00000538023;ENST00000398543;ENST00000316296;ENST00000530676	.	.	.	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9172	0.88955	0.0:0.0:1.0:0.0	.	.	.	.	X	170;170;54;142;54	.	.	E	+	1	0	ANO1	69626886	1.000000	0.71417	0.793000	0.32043	0.258000	0.26162	8.978000	0.93450	2.474000	0.83562	0.650000	0.86243	GAG	.	.		0.532	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043		T	69949238	G	T	69949238	4	4	81	1	0	0	0	0	0	1	0	0	695	1059	37	1	518	1	ANO1	11	69949238	Nonsense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	9308107	69949238	65057278	91	11140										
PRDM10	56980	hgsc.bcm.edu	37	chr11	129827684	129827684	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tgtacaccagcgtgtgctctGgaccatccactgatgtgtag	11	11	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr11:129827684G>A	ENST00000360871.3	-	3	422	c.191C>T	c.(190-192)cCa>cTa	p.P64L	PRDM10_ENST00000358825.5_Missense_Mutation_p.P64L|PRDM10_ENST00000528746.1_Missense_Mutation_p.P64L	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	64					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		CGTGTGCTCTGGACCATCCAC	0.502																																					p.P64L		Atlas-SNP	.											.	PRDM10	120	.	0			c.C191T						.						188	165	172					11																	129827684		2201	4297	6498	SO:0001583	missense	56980	exon3			TGCTCTGGACCAT	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"Zinc fingers, C2H2-type"	13995	protein-coding gene	gene with protein product	"PRDM zinc finger transcription factor", "PR-domain family member 7", "tristanin"					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.191C>T	chr11.hg19:g.129827684G>A	ENSP00000354118:p.Pro64Leu	75.0	0.0		38.0	29.0	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	hg19	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.612566	0.66672	.	.	ENSG00000170325	ENST00000358825;ENST00000360871;ENST00000528746;ENST00000527581;ENST00000531431	T;T;T;T;T	0.46819	1.13;1.13;2.9;0.9;0.86	5.75	4.84	0.62591	.	0.198064	0.44688	D	0.000424	T	0.33789	0.0875	N	0.19112	0.55	0.80722	D	1	B;B;B	0.28128	0.002;0.001;0.201	B;B;B	0.19148	0.004;0.003;0.024	T	0.18524	-1.0334	10	0.72032	D	0.01	-24.742	14.7624	0.69614	0.0693:0.0:0.9307:0.0	.	64;64;64	Q9NQV6-4;G3XAE5;Q9NQV6	.;.;PRD10_HUMAN	L	64	ENSP00000351686:P64L;ENSP00000354118:P64L;ENSP00000431262:P64L;ENSP00000432093:P64L;ENSP00000436681:P64L	ENSP00000351686:P64L	P	-	2	0	PRDM10	129332894	1.000000	0.71417	0.574000	0.28523	0.991000	0.79684	7.526000	0.81920	1.447000	0.47661	0.650000	0.86243	CCA	.	.		0.502	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		A	129827684	G	A	129827684	3	1	81	1	0	0	0	0	1	0	0	0	12463	1348	47	3	3407	3	PRDM10	11	129827684	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	59878446	129827684	5178832	92	11141										
OS9	10956	hgsc.bcm.edu	37	chr12	58087962	58087962	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aagatggcggcggaaacgctGctgtccagtttgttaggact	14	8	0	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr12:58087962G>T	ENST00000315970.7	+	1	59	c.18G>T	c.(16-18)ctG>ctT	p.L6L	OS9_ENST00000552285.1_Silent_p.L6L|OS9_ENST00000435406.2_Silent_p.L6L|OS9_ENST00000389142.5_Silent_p.L6L|OS9_ENST00000413095.2_Silent_p.L6L|OS9_ENST00000551035.1_Silent_p.L6L|RP11-571M6.7_ENST00000549477.1_RNA|OS9_ENST00000439210.2_Silent_p.L6L|OS9_ENST00000389146.6_Silent_p.L6L|OS9_ENST00000257966.8_Silent_p.L6L	NM_001017958.2|NM_006812.3	NP_001017958.1|NP_006803.1	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum lectin	6					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein retention in ER lumen (GO:0006621)|protein targeting (GO:0006605)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum lumen (GO:0005788)|Hrd1p ubiquitin ligase complex (GO:0000836)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	21	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			CGGAAACGCTGCTGTCCAGTT	0.592																																					p.L6L		Atlas-SNP	.											.	OS9	55	.	0			c.G18T						.						139	138	138					12																	58087962		2203	4300	6503	SO:0001819	synonymous_variant	10956	exon1			AACGCTGCTGTCC	AB002806	CCDS31843.1, CCDS31844.1, CCDS31845.1, CCDS31846.1, CCDS58246.1, CCDS58247.1, CCDS58248.1, CCDS58249.1	12q13	2009-08-26	2009-08-26						16994	protein-coding gene	gene with protein product	"endoplasmic reticulum lectin 2", "erlectin 2"	609677				8634085, 9498564, 19346256, 18264092	Standard	NM_006812		Approved	OS-9, ERLEC2	uc001spj.3	Q13438	OTTHUMG00000170284	ENST00000315970.7:c.18G>T	chr12.hg19:g.58087962G>T		128.0	0.0		95.0	35.0	NM_001261423	A6NDD1|A6NFR7|A6NLB2|A8K5Q9|B4DE28|B4DPX1|B4E1I6|E7ENT8|E7EW91|F8VUH2|G3XA88|O00579|Q6IBL2|Q8IZ58|Q9BW99	Silent	SNP	ENST00000315970.7	hg19	CCDS31843.1																																																																																			.	.		0.592	OS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408344.1	NM_006812		T	58087962	G	T	58087962	2	4	81	1	0	0	0	0	0	0	0	1	11281	1306	46	3		3	OS9	12	58087962	Silent	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10		58087962	75763933	93	11142										
IRAK3	11213	hgsc.bcm.edu	37	chr12	66638955	66638955	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ctagataagaaagtgcctccCtgccctcggaatttctctgc	8	13	1	2	rs367771929		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr12:66638955C>G	ENST00000261233.4	+	11	1648	c.1227C>G	c.(1225-1227)ccC>ccG	p.P409P	IRAK3_ENST00000457197.2_Silent_p.P348P	NM_007199.2	NP_009130.2			interleukin-1 receptor-associated kinase 3											breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(28;0.0203)		AAGTGCCTCCCTGCCCTCGGA	0.478																																					p.P409P		Atlas-SNP	.											.	IRAK3	75	.	0			c.C1227G						.						79	81	80					12																	66638955		2203	4300	6503	SO:0001819	synonymous_variant	11213	exon11			GCCTCCCTGCCCT	AF113136	CCDS8975.1, CCDS44937.1	12q13.13	2008-05-02			ENSG00000090376	ENSG00000090376			17020	protein-coding gene	gene with protein product		604459				10383454	Standard	NM_001142523		Approved	IRAK-M	uc001sth.3	Q9Y616	OTTHUMG00000169002	ENST00000261233.4:c.1227C>G	chr12.hg19:g.66638955C>G		144.0	0.0		88.0	18.0	NM_007199		Silent	SNP	ENST00000261233.4	hg19	CCDS8975.1																																																																																			.	.		0.478	IRAK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401908.1			G	66638955	C	G	66638955	2	3	81	1	0	0	0	0	0	0	0	1	7833	668	24	4		4	IRAK3	12	66638955	Silent	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	8550993	66638955	67212940	94	11143										
LUM	4060	hgsc.bcm.edu	37	chr12	91502117	91502117	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gatgttgctgatcttattgtTgtctaagtagagagttagaa	11	3	2	3	rs375444776		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr12:91502117T>A	ENST00000266718.4	-	2	1094	c.640A>T	c.(640-642)Aac>Tac	p.N214Y	LUM_ENST00000548071.1_Intron	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	214					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						ATCTTATTGTTGTCTAAGTAG	0.413																																					p.N214Y		Atlas-SNP	.											.	LUM	65	.	0			c.A640T						.						157	150	152					12																	91502117		2203	4300	6503	SO:0001583	missense	4060	exon2			TATTGTTGTCTAA	BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6724	protein-coding gene	gene with protein product	"lumican proteoglycan"	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.640A>T	chr12.hg19:g.91502117T>A	ENSP00000266718:p.Asn214Tyr	110.0	0.0		77.0	40.0	NM_002345	B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	hg19	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	T	11.33	1.606668	0.28623	.	.	ENSG00000139329	ENST00000266718	T	0.59906	0.23	5.84	4.66	0.58398	.	0.144445	0.64402	D	0.000013	T	0.52354	0.1729	L	0.55017	1.72	0.54753	D	0.999986	B	0.12013	0.005	B	0.15870	0.014	T	0.45644	-0.9247	10	0.34782	T	0.22	-15.0475	12.9935	0.58634	0.0:0.0:0.135:0.865	.	214	P51884	LUM_HUMAN	Y	214	ENSP00000266718:N214Y	ENSP00000266718:N214Y	N	-	1	0	LUM	90026248	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.384000	0.44362	1.002000	0.39104	0.455000	0.32223	AAC	.	.		0.413	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345		A	91502117	T	A	91502117	3	1	81	1	0	0	0	0	1	0	0	0	9094	1812	63	4	384	4	LUM	12	91502117	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	24863162	91502117	42349778	95	11144										
ATP2A2	488	hgsc.bcm.edu	37	chr12	110765661	110765661	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cagccattcctgaaggtctgCctgcagtcatcaccacctgc	8	16	3	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr12:110765661C>T	ENST00000539276.2	+	8	1043	c.934C>T	c.(934-936)Cct>Tct	p.P312S	ATP2A2_ENST00000395494.2_Missense_Mutation_p.P285S|ATP2A2_ENST00000308664.6_Missense_Mutation_p.P312S			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	312					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						TGAAGGTCTGCCTGCAGTCAT	0.512																																					p.P312S		Atlas-SNP	.											.	ATP2A2	78	.	0			c.C934T						.						66	63	64					12																	110765661		2203	4300	6503	SO:0001583	missense	488	exon8			GGTCTGCCTGCAG		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.934C>T	chr12.hg19:g.110765661C>T	ENSP00000440045:p.Pro312Ser	91.0	0.0		117.0	18.0	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Missense_Mutation	SNP	ENST00000539276.2	hg19	CCDS9144.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.400539|5.400539	0.96030|0.96030	.|.	.|.	ENSG00000174437|ENSG00000174437	ENST00000548169|ENST00000308664;ENST00000395494;ENST00000539276	.|D;D;D	.|0.92495	.|-3.05;-3.05;-3.05	5.48|5.48	5.48|5.48	0.80851|0.80851	.|ATPase, P-type, ATPase-associated domain (1);	.|0.046197	.|0.85682	.|D	.|0.000000	D|D	0.96700|0.96700	0.8923|0.8923	M|M	0.88775|0.88775	2.98|2.98	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.64830	.|0.986;0.986;0.994	.|D;P;D	.|0.67725	.|0.953;0.884;0.929	D|D	0.96980|0.96980	0.9714|0.9714	5|10	.|0.87932	.|D	.|0	.|.	19.7748|19.7748	0.96388|0.96388	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|285;312;312	.|P16615-4;P16615-2;P16615	.|.;.;AT2A2_HUMAN	V|S	202|312;285;312	.|ENSP00000311186:P312S;ENSP00000378872:P285S;ENSP00000440045:P312S	.|ENSP00000311186:P312S	A|P	+|+	2|1	0|0	ATP2A2|ATP2A2	109250044|109250044	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.760000|7.760000	0.85248|0.85248	2.741000|2.741000	0.93983|0.93983	0.585000|0.585000	0.79938|0.79938	GCC|CCT	.	.		0.512	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		T	110765661	C	T	110765661	3	4	81	1	0	0	0	0	1	0	0	0	1137	739	26	3	964	3	ATP2A2	12	110765661	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	19263544	110765661	23086234	96	11145										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112681775	112681775	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aaaaacaggctgcctgacagCgtgagatatcacttttgttt	9	8	1	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr12:112681775C>T	ENST00000430131.2	-	29	4431	c.3286G>A	c.(3286-3288)Gct>Act	p.A1096T	HECTD4_ENST00000550722.1_Missense_Mutation_p.A1372T|HECTD4_ENST00000377560.5_Missense_Mutation_p.A1346T			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1096					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TGCCTGACAGCGTGAGATATC	0.393																																					p.A1384T		Atlas-SNP	.											.	.	.	.	0			c.G4150A						.						74	74	74					12																	112681775		1901	4126	6027	SO:0001583	missense	283450	exon30			TGACAGCGTGAGA	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.3286G>A	chr12.hg19:g.112681775C>T	ENSP00000404379:p.Ala1096Thr	208.0	0.0		251.0	49.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	C	20.2	3.953806	0.73902	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.44881	0.91;0.91;0.91	5.85	5.85	0.93711	.	.	.	.	.	T	0.24275	0.0588	N	0.08118	0	0.46823	D	0.999212	P	0.39782	0.688	B	0.25884	0.064	T	0.21042	-1.0257	9	0.72032	D	0.01	.	20.1649	0.98147	0.0:1.0:0.0:0.0	.	1096	Q9Y4D8	K0614_HUMAN	T	1346;1096;1372	ENSP00000366783:A1346T;ENSP00000404379:A1096T;ENSP00000449784:A1372T	ENSP00000366783:A1346T	A	-	1	0	C12orf51	111166158	0.965000	0.33210	0.999000	0.59377	0.971000	0.66376	2.094000	0.41719	2.753000	0.94483	0.655000	0.94253	GCT	.	.		0.393	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112681775	C	T	112681775	3	4	81	1	0	0	0	0	1	0	0	0	1698	768	27	1	8892	1	C12orf51	12	112681775	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	1916114	112681775	21170120	97	11146										
TBX3	6926	hgsc.bcm.edu	37	chr12	115109713	115109713	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	taaccaaccgctggatgctcTgcagttcgctggtggccgcc	12	14	1	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr12:115109713T>A	ENST00000257566.3	-	8	2554	c.2165A>T	c.(2164-2166)cAg>cTg	p.Q722L	TBX3_ENST00000349155.2_Missense_Mutation_p.Q702L	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	722					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		CTGGATGCTCTGCAGTTCGCT	0.627																																					p.Q722L		Atlas-SNP	.											.	TBX3	106	.	0			c.A2165T						.						18	15	16					12																	115109713		2201	4289	6490	SO:0001583	missense	6926	exon8			ATGCTCTGCAGTT	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.2165A>T	chr12.hg19:g.115109713T>A	ENSP00000257566:p.Gln722Leu	108.0	0.0		92.0	16.0	NM_016569	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	hg19	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.785247	0.90282	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.93307	-3.2;-3.05	4.92	4.92	0.64577	.	1.865220	0.02247	N	0.066317	D	0.97219	0.9091	M	0.78637	2.42	0.80722	D	1	D;D	0.76494	0.999;0.967	D;D	0.91635	0.999;0.932	D	0.88306	0.2953	10	0.72032	D	0.01	.	13.7499	0.62901	0.0:0.0:0.0:1.0	.	702;722	O15119-2;O15119	.;TBX3_HUMAN	L	702;722;579	ENSP00000257567:Q702L;ENSP00000257566:Q722L	ENSP00000257566:Q722L	Q	-	2	0	TBX3	113594096	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.451000	0.80668	1.851000	0.53745	0.460000	0.39030	CAG	.	.		0.627	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		A	115109713	T	A	115109713	3	1	81	1	0	0	0	0	1	0	0	0	15674	1580	55	4	70	4	TBX3	12	115109713	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	2427938	115109713	18742182	98	11147										
VSIG10	54621	hgsc.bcm.edu	37	chr12	118506330	118506330	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tcccctactgcagcatcttcCtcctcctcctcctcctcctc	2	23	1	0	rs67582641|rs72125532	byFrequency	TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr12:118506330C>A	ENST00000359236.5	-	8	1695	c.1419G>T	c.(1417-1419)gaG>gaT	p.E473D		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	473	Glu-rich.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						CAGCAtcttcctcctcctcct	0.488																																					p.E473D		Atlas-SNP	.											.	VSIG10	41	.	0			c.G1419T						.						116	118	118					12																	118506330		2078	4210	6288	SO:0001583	missense	54621	exon8			ATCTTCCTCCTCC		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1419G>T	chr12.hg19:g.118506330C>A	ENSP00000352172:p.Glu473Asp	32.0	0.0		59.0	6.0	NM_019086	Q9NWQ7	Missense_Mutation	SNP	ENST00000359236.5	hg19	CCDS44992.1	.	.	.	.	.	.	.	.	.	.	C	0.055	-1.239784	0.01493	.	.	ENSG00000176834	ENST00000359236	T	0.54479	0.57	4.75	-4.46	0.03536	.	2.032290	0.02720	N	0.113904	T	0.44603	0.1301	M	0.63428	1.95	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.14783	-1.0460	10	0.14656	T	0.56	.	6.5058	0.22194	0.1399:0.2336:0.0:0.6265	.	473	Q8N0Z9	VSI10_HUMAN	D	473	ENSP00000352172:E473D	ENSP00000352172:E473D	E	-	3	2	VSIG10	116990713	0.012000	0.17670	0.009000	0.14445	0.089000	0.18198	-0.503000	0.06383	-0.757000	0.04697	-1.453000	0.01033	GAG	.	.		0.488	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086		A	118506330	C	A	118506330	3	1	81	1	0	0	0	0	1	0	0	0	17238	680	24	3	211	3	VSIG10	12	118506330	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	3396617	118506330	15345565	99	11148										
DACH1	1602	hgsc.bcm.edu	37	chr13	72063270	72063270	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cttgcggttggtgtagaaagCggggtctcatctgcatgtga	15	7	2	2	rs370706409		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr13:72063270C>T	ENST00000359684.2	-	8	1742	c.1743G>A	c.(1741-1743)ccG>ccA	p.P581P	DACH1_ENST00000354591.4_Silent_p.P327P|DACH1_ENST00000305425.4_Silent_p.P529P|DACH1_ENST00000313174.7_Silent_p.P381P			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	581					cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		GTGTAGAAAGCGGGGTCTCAT	0.443																																					p.P529P		Atlas-SNP	.											.	DACH1	123	.	0			c.G1587A						.	C	,,	1,3789		0,1,1894	194	191	192		981,1587,1143	4.2	1	13		192	1,8261		0,1,4130	no	coding-synonymous,coding-synonymous,coding-synonymous	DACH1	NM_004392.5,NM_080759.4,NM_080760.4	,,	0,2,6024	TT,TC,CC		0.0121,0.0264,0.0166	,,	327/507,529/709,381/561	72063270	2,12050	1895	4131	6026	SO:0001819	synonymous_variant	1602	exon7			AGAAAGCGGGGTC	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.1743G>A	chr13.hg19:g.72063270C>T		71.0	0.0		31.0	18.0	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Silent	SNP	ENST00000359684.2	hg19																																																																																				.	.		0.443	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		T	72063270	C	T	72063270	2	4	81	1	0	0	0	0	0	0	0	1	4222	755	27	1		1	DACH1	13	72063270	Silent	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10		72063270	43106608	100	11149										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77700507	77700507	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aacattccaattgggataccTctaaggttagggcagcttct	9	9	2	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr13:77700507T>A	ENST00000544440.2	-	53	7733	c.7716A>T	c.(7714-7716)agA>agT	p.R2572S	MYCBP2_ENST00000482517.1_5'UTR|MYCBP2_ENST00000357337.6_Missense_Mutation_p.R2572S|MYCBP2_ENST00000360084.5_Missense_Mutation_p.R35S|MYCBP2_ENST00000407578.2_Missense_Mutation_p.R2610S					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TTGGGATACCTCTAAGGTTAG	0.438																																					p.R2610S		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A7830T						.						200	167	178					13																	77700507		2203	4300	6503	SO:0001583	missense	23077	exon53			GATACCTCTAAGG	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.7716A>T	chr13.hg19:g.77700507T>A	ENSP00000444596:p.Arg2572Ser	131.0	0.0		51.0	31.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.09	3.024165	0.54683	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440;ENST00000360084	T;T;T;T	0.51071	1.48;1.47;1.48;0.72	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.59851	0.2224	L	0.40543	1.245	0.54753	D	0.999982	D;D	0.61080	0.989;0.967	D;P	0.72625	0.978;0.879	T	0.63418	-0.6642	10	0.72032	D	0.01	.	14.696	0.69121	0.0:0.0:0.0:1.0	.	2572;2572	O75592-2;O75592	.;MYCB2_HUMAN	S	2572;2610;2572;35	ENSP00000349892:R2572S;ENSP00000384288:R2610S;ENSP00000444596:R2572S;ENSP00000353197:R35S	ENSP00000349892:R2572S	R	-	3	2	MYCBP2	76598508	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.611000	0.61162	1.873000	0.54277	0.460000	0.39030	AGA	.	.		0.438	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		A	77700507	T	A	77700507	3	1	81	1	0	0	0	0	1	0	0	0	10027	1548	54	4	6330	4	MYCBP2	13	77700507	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	5637237	77700507	37469371	101	11150										
ADPRHL1	113622	hgsc.bcm.edu	37	chr13	114083321	114083321	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttctgccagaggcaccgcccGcagcatgtctctcccccact	8	19	2	1	rs375108772		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr13:114083321G>A	ENST00000375418.3	-	4	678	c.592C>T	c.(592-594)Cgg>Tgg	p.R198W	ADPRHL1_ENST00000356501.4_Missense_Mutation_p.R116W	NM_138430.3	NP_612439.2	Q8NDY3	ARHL1_HUMAN	ADP-ribosylhydrolase like 1	198					protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	11	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.0195)|GBM - Glioblastoma multiforme(44;0.116)			GGCACCGCCCGCAGCATGTCT	0.662																																					p.R198W		Atlas-SNP	.											ADPRHL1,NS,carcinoma,0,1	ADPRHL1	30	.	0			c.C592T						.	G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	52	47	49		592,346	-4.4	0	13		49	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ADPRHL1	NM_138430.3,NM_199162.1	101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	198/355,116/273	114083321	1,13005	2203	4300	6503	SO:0001583	missense	113622	exon4			CCGCCCGCAGCAT	AJ313429	CCDS9535.1, CCDS9536.1	13q34	2003-06-19			ENSG00000153531	ENSG00000153531			21303	protein-coding gene	gene with protein product		610620				12070318	Standard	NM_138430		Approved	ARH2	uc001vtq.1	Q8NDY3	OTTHUMG00000017386	ENST00000375418.3:c.592C>T	chr13.hg19:g.114083321G>A	ENSP00000364567:p.Arg198Trp	62.0	0.0		23.0	14.0	NM_138430	Q5JUG2|Q96GD1	Missense_Mutation	SNP	ENST00000375418.3	hg19	CCDS9535.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.553440	0.45487	0.0	1.16E-4	ENSG00000153531	ENST00000356501;ENST00000375418;ENST00000413169	T;T;T	0.31769	1.48;1.48;1.48	5.26	-4.37	0.03633	.	0.382789	0.29884	N	0.010960	T	0.36054	0.0953	L	0.51422	1.61	0.23138	N	0.998234	D	0.67145	0.996	P	0.51101	0.659	T	0.50474	-0.8824	10	0.72032	D	0.01	-13.3827	18.9624	0.92681	0.0:0.0:0.6911:0.3089	.	198	Q8NDY3	ARHL1_HUMAN	W	116;198;116	ENSP00000348894:R116W;ENSP00000364567:R198W;ENSP00000416213:R116W	ENSP00000348894:R116W	R	-	1	2	ADPRHL1	113131322	1.000000	0.71417	0.001000	0.08648	0.004000	0.04260	1.838000	0.39211	-1.079000	0.03113	-0.475000	0.04921	CGG	.	.		0.662	ADPRHL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045915.2	NM_138430		A	114083321	G	A	114083321	3	1	81	1	0	0	0	0	1	0	0	0	332	1086	38	1	488	1	ADPRHL1	13	114083321	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	36382814	114083321	1086557	102	11151										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86087999	86087999	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cgctgcgacaggaactttgtCtactgtaatgagcgaagctt	11	9	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr14:86087999C>A	ENST00000330753.4	+	2	908	c.141C>A	c.(139-141)gtC>gtA	p.V47V	FLRT2_ENST00000554746.1_Silent_p.V47V	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	47	LRRNT.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		GGAACTTTGTCTACTGTAATG	0.502																																					p.V47V		Atlas-SNP	.											.	FLRT2	168	.	0			c.C141A						.						131	121	125					14																	86087999		2203	4300	6503	SO:0001819	synonymous_variant	23768	exon2			CTTTGTCTACTGT	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.141C>A	chr14.hg19:g.86087999C>A		78.0	0.0		42.0	27.0	NM_013231	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	hg19	CCDS9877.1																																																																																			.	.		0.502	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			A	86087999	C	A	86087999	2	1	81	1	0	0	0	0	0	0	0	1	5947	900	32	3		3	FLRT2	14	86087999	Silent	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10		86087999	21261541	103	11152										
CHGA	1113	hgsc.bcm.edu	37	chr14	93399004	93399004	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gggcaggaggaggaggaggaCaaccgggacagttccatgaa	18	7	0	1	rs200576557		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr14:93399004C>A	ENST00000216492.5	+	7	1378	c.1098C>A	c.(1096-1098)gaC>gaA	p.D366E	CHGA_ENST00000334654.4_Missense_Mutation_p.D215E	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)	366					regulation of blood pressure (GO:0008217)	extracellular region (GO:0005576)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)				cervix(1)|large_intestine(1)|lung(3)|skin(3)	8		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		AGGAGGAGGACAACCGGGACA	0.677																																					p.D366E	Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)	Atlas-SNP	.											.	CHGA	32	.	0			c.C1098A						.						24	19	21					14																	93399004		2199	4295	6494	SO:0001583	missense	1113	exon7			GGAGGACAACCGG		CCDS9906.1	14q32	2012-10-02			ENSG00000100604	ENSG00000100604			1929	protein-coding gene	gene with protein product	"vasostatin", "pancreastatin", "parastatin"	118910				3403545	Standard	NM_001275		Approved		uc001ybc.4	P10645		ENST00000216492.5:c.1098C>A	chr14.hg19:g.93399004C>A	ENSP00000216492:p.Asp366Glu	77.0	0.0		28.0	18.0	NM_001275	B2R9E9|Q53FA8|Q6NR84|Q96E84|Q96GL7|Q9BQB5	Missense_Mutation	SNP	ENST00000216492.5	hg19	CCDS9906.1	.	.	.	.	.	.	.	.	.	.	C	0.463	-0.887995	0.02511	.	.	ENSG00000100604	ENST00000216492;ENST00000334654	T;T	0.01560	4.77;4.77	4.66	-9.32	0.00643	.	1.158180	0.06445	N	0.726621	T	0.00875	0.0029	N	0.10809	0.05	0.18873	N	0.999985	B;B	0.27625	0.183;0.001	B;B	0.24974	0.057;0.003	T	0.45891	-0.9230	10	0.21014	T	0.42	-0.0084	3.94	0.09323	0.2863:0.114:0.4446:0.155	.	215;366	G5E968;P10645	.;CMGA_HUMAN	E	366;215	ENSP00000216492:D366E;ENSP00000334023:D215E	ENSP00000216492:D366E	D	+	3	2	CHGA	92468757	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-2.121000	0.01322	-2.554000	0.00477	-0.233000	0.12211	GAC	.	.		0.677	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	NM_001275		A	93399004	C	A	93399004	3	1	81	1	0	0	0	0	1	0	0	0	3340	477	17	3	1124	3	CHGA	14	93399004	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	7311005	93399004	13950536	104	11153										
KIF26A	26153	hgsc.bcm.edu	37	chr14	104641670	104641670	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cggagctgcaggagcggctgGaatgcatggacggcaacgag	18	9	0	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr14:104641670G>A	ENST00000423312.2	+	12	2545	c.2545G>A	c.(2545-2547)Gaa>Aaa	p.E849K	KIF26A_ENST00000315264.7_Missense_Mutation_p.E710K	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	849					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		GGAGCGGCTGGAATGCATGGA	0.711																																					p.E849K		Atlas-SNP	.											.	KIF26A	84	.	0			c.G2545A						.						14	17	16					14																	104641670		1993	4140	6133	SO:0001583	missense	26153	exon12			CGGCTGGAATGCA	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"Kinesins"	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.2545G>A	chr14.hg19:g.104641670G>A	ENSP00000388241:p.Glu849Lys	114.0	0.0		38.0	29.0	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	hg19	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.532825	0.64972	.	.	ENSG00000066735	ENST00000423312;ENST00000315264	T;T	0.81163	-1.46;-1.46	3.9	3.9	0.45041	.	.	.	.	.	T	0.81039	0.4740	M	0.64404	1.975	0.80722	D	1	P	0.50443	0.935	P	0.45829	0.494	D	0.83552	0.0102	9	0.49607	T	0.09	.	16.2557	0.82516	0.0:0.0:1.0:0.0	.	849	Q9ULI4	KI26A_HUMAN	K	849;710	ENSP00000388241:E849K;ENSP00000325452:E710K	ENSP00000325452:E710K	E	+	1	0	KIF26A	103711423	1.000000	0.71417	0.860000	0.33809	0.269000	0.26545	7.578000	0.82498	1.894000	0.54839	0.462000	0.41574	GAA	.	.		0.711	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			A	104641670	G	A	104641670	3	1	81	1	0	0	0	0	1	0	0	0	8303	1175	41	3	2591	3	KIF26A	14	104641670	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	11242666	104641670	2707870	105	11154										
APBA2	321	hgsc.bcm.edu	37	chr15	29406112	29406112	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tgagagggggcattgctgagCgagggggcgtccgtgtgggc	22	7	0	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr15:29406112C>T	ENST00000558402.1	+	15	2670	c.2071C>T	c.(2071-2073)Cga>Tga	p.R691*	APBA2_ENST00000411764.1_Nonsense_Mutation_p.R679*|APBA2_ENST00000561069.1_Nonsense_Mutation_p.R691*|APBA2_ENST00000558330.1_Nonsense_Mutation_p.R679*|APBA2_ENST00000558259.1_Nonsense_Mutation_p.R691*			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	691	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CATTGCTGAGCGAGGGGGCGT	0.632																																					p.R691X		Atlas-SNP	.											.	APBA2	132	.	0			c.C2071T						.						82	71	75					15																	29406112		2203	4300	6503	SO:0001587	stop_gained	321	exon13			GCTGAGCGAGGGG	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.2071C>T	chr15.hg19:g.29406112C>T	ENSP00000453293:p.Arg691*	47.0	0.0		20.0	8.0	NM_005503	E9PGI4|O60571|Q5XKC0	Nonsense_Mutation	SNP	ENST00000558402.1	hg19	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	C	40	8.022872	0.98616	.	.	ENSG00000034053	ENST00000411764;ENST00000219865	.	.	.	4.55	4.55	0.56014	.	0.087637	0.41097	D	0.000944	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4989	0.44794	0.3159:0.6841:0.0:0.0	.	.	.	.	X	679;691	.	ENSP00000219865:R691X	R	+	1	2	APBA2	27193404	1.000000	0.71417	0.999000	0.59377	0.935000	0.57460	1.077000	0.30741	2.068000	0.61886	0.462000	0.41574	CGA	.	.		0.632	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		T	29406112	C	T	29406112	4	4	81	1	0	0	0	0	0	1	0	0	757	760	27	1	2113	1	APBA2	15	29406112	Nonsense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10		29406112	73125280	106	11155										
GJD2	57369	hgsc.bcm.edu	37	chr15	35045139	35045139	+	Frame_Shift_Del	DEL	A	A	-													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gagtcagctccttaacctctAaacaatctggctctgtctcc							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr15:35045139delA	ENST00000290374.4	-	2	982	c.506delT	c.(505-507)ttafs	p.L169fs	RP11-814P5.1_ENST00000558707.1_RNA|RP11-814P5.1_ENST00000503496.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	169					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		CTTAACCTCTAAACAATCTGG	0.483																																					p.L169fs		Atlas-Indel,Pindel	.											.	GJD2	49	.	0			c.507delA						.						182	188	186					15																	35045139		2201	4298	6499	SO:0001589	frameshift_variant	57369	exon2			.	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"Ion channels / Gap junction proteins (connexins)"	19154	protein-coding gene	gene with protein product	"connexin 36"	607058	"gap junction protein, alpha 9, 36kDa"	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.506delT	chr15.hg19:g.35045139delA	ENSP00000290374:p.Leu169fs	142.0	0.0		84.0	27.0	NM_020660	Q2M241|Q9P2R0	Frame_Shift_Del	DEL	ENST00000290374.4	hg19	CCDS10040.1																																																																																			.	.		0.483	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2			-	35045139	A	-	35045139	7	5	81	1	0	1	0	1	0	0	0	0	6425	372	13	0	463	0	GJD2	15	35045139	Frame_Shift_Del	DEL	A	TCGA-CC-A8HV-01A-11D-A35Z-10	5639027	35045139	67486253	107	11156										
MGA	23269	hgsc.bcm.edu	37	chr15	42058313	42058313	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tcctcatgaagttcctgataGcaagccatctgaccatctga	7	12	3	4			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr15:42058313G>T	ENST00000570161.1	+	23	8033	c.8033G>T	c.(8032-8034)aGc>aTc	p.S2678I	MGA_ENST00000566586.1_Missense_Mutation_p.S2469I|MGA_ENST00000389936.4_Missense_Mutation_p.S2639I|MGA_ENST00000219905.7_Missense_Mutation_p.S2678I|MGA_ENST00000545763.1_Missense_Mutation_p.S2469I			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GTTCCTGATAGCAAGCCATCT	0.433																																					p.S2678I		Atlas-SNP	.											.	MGA	264	.	0			c.G8033T						.						79	75	77					15																	42058313		1905	4128	6033	SO:0001583	missense	23269	exon24			CTGATAGCAAGCC	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.8033G>T	chr15.hg19:g.42058313G>T	ENSP00000457035:p.Ser2678Ile	310.0	0.0		166.0	65.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.250318	0.39797	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.84873	-1.91;-1.89;-1.91	5.38	3.44	0.39384	.	1.228810	0.05850	N	0.620973	T	0.77552	0.4147	N	0.08118	0	0.19775	N	0.999957	B;B	0.27791	0.189;0.167	B;B	0.35607	0.206;0.063	T	0.69105	-0.5233	10	0.87932	D	0	.	11.1122	0.48239	0.075:0.1384:0.7866:0.0	.	2469;2678	F5H7K2;E7ENI0	.;.	I	2678;2639;2469	ENSP00000219905:S2678I;ENSP00000374586:S2639I;ENSP00000442467:S2469I	ENSP00000219905:S2678I	S	+	2	0	MGA	39845605	0.998000	0.40836	0.998000	0.56505	0.961000	0.63080	1.967000	0.40491	1.516000	0.48900	-0.122000	0.15005	AGC	.	.		0.433	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	42058313	G	T	42058313	3	4	81	1	0	0	0	0	1	0	0	0	9549	971	34	3	8123	3	MGA	15	42058313	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	7013174	42058313	60473079	108	11157										
PML	5371	hgsc.bcm.edu	37	chr15	74328285	74328285	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cccaggcgcccgtcaagcagGcctctgagagtgctaccctt	11	16	2	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr15:74328285G>T	ENST00000268058.3	+	7	1806				PML_ENST00000569965.1_Intron|PML_ENST00000395135.3_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000354026.6_Missense_Mutation_p.G780V|PML_ENST00000268059.6_Missense_Mutation_p.G828V|PML_ENST00000563500.1_3'UTR|PML_ENST00000565898.1_Intron|PML_ENST00000564428.1_Intron|PML_ENST00000435786.2_3'UTR|PML_ENST00000436891.3_3'UTR|PML_ENST00000359928.4_Intron	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CGTCAAGCAGGCCTCTGAGAG	0.622			T	"RARA, PAX5"	"APL, ALL"																																p.G828V		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.G2483T						.						136	163	154					15																	74328285		2198	4297	6495	SO:0001627	intron_variant	5371	exon8			AAGCAGGCCTCTG	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+1414G>T	chr15.hg19:g.74328285G>T		51.0	0.0		40.0	11.0	NM_033239	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Missense_Mutation	SNP	ENST00000268058.3	hg19	CCDS10255.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.239891	0.39598	.	.	ENSG00000140464	ENST00000268059;ENST00000354026	.	.	.	3.59	-0.651	0.11454	.	.	.	.	.	T	0.15176	0.0366	N	0.08118	0	0.09310	N	1	P;P	0.43701	0.815;0.815	B;B	0.42522	0.39;0.39	T	0.13710	-1.0499	8	0.87932	D	0	.	4.3844	0.11309	0.2161:0.3631:0.4208:0.0	.	780;828	P29590-13;P29590-8	.;.	V	828;780	.	ENSP00000268059:G828V	G	+	2	0	PML	72115338	0.000000	0.05858	0.001000	0.08648	0.040000	0.13550	0.338000	0.19858	-0.097000	0.12307	0.456000	0.33151	GGC	.	.		0.622	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		T	74328285	G	T	74328285	1	4	81	0	1	0	0	0	0	0	0	0	12144	1203	42	3		3	PML	15	74328285	Intron	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	32269972	74328285	28203107	109	11158										
PSTPIP1	9051	hgsc.bcm.edu	37	chr15	77310799	77310799	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aatgcccttttttttgcaggGcccaggcggaggagcggtac	14	10	0	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr15:77310799G>T	ENST00000558012.1	+	3	628	c.139G>T	c.(139-141)Gcc>Tcc	p.A47S	PSTPIP1_ENST00000559295.1_Splice_Site_p.A47S|PSTPIP1_ENST00000379595.3_Splice_Site_p.A47S|PSTPIP1_ENST00000267939.5_Splice_Site_p.A46S	NM_003978.3	NP_003969.2	O43586	PPIP1_HUMAN	proline-serine-threonine phosphatase interacting protein 1	47	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				cell adhesion (GO:0007155)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|signal transduction (GO:0007165)	actomyosin contractile ring (GO:0005826)|cell projection (GO:0042995)|cleavage furrow (GO:0032154)|cytosol (GO:0005829)|membrane (GO:0016020)|stress fiber (GO:0001725)				breast(1)|endometrium(3)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						TTTTTGCAGGGCCCAGGCGGA	0.577																																					p.A47S		Atlas-SNP	.											.	PSTPIP1	50	.	0			c.G139T						.						28	33	31					15																	77310799		1971	4125	6096	SO:0001630	splice_region_variant	9051	exon3			TGCAGGGCCCAGG	U94778	CCDS45312.1	15q24.3	2014-09-17			ENSG00000140368	ENSG00000140368			9580	protein-coding gene	gene with protein product	"CD2 cytoplasmic tail-binding protein", "CD2 antigen-binding protein 1", "PEST phosphatase-interacting protein 1"	606347				9857189	Standard	NM_003978		Approved	PSTPIP, CD2BP1L, CD2BP1, CD2BP1S, H-PIP, PAPAS	uc002bcf.2	O43586	OTTHUMG00000172594	ENST00000558012.1:c.138-1G>T	chr15.hg19:g.77310799G>T		80.0	0.0		29.0	9.0	NM_003978	B5BU74|B5BUK4|O43585|O95657	Missense_Mutation	SNP	ENST00000558012.1	hg19	CCDS45312.1	.	.	.	.	.	.	.	.	.	.	G	18.48	3.632312	0.67015	.	.	ENSG00000140368	ENST00000379595;ENST00000267939	T;T	0.19669	2.13;2.13	3.81	3.81	0.43845	Fps/Fes/Fer/CIP4 homology (3);Prismane-like (1);	0.198845	0.42420	D	0.000716	T	0.43389	0.1245	M	0.69463	2.115	0.51767	D	0.999932	P;D;D;D	0.69078	0.859;0.997;0.996;0.994	P;D;P;D	0.70487	0.623;0.969;0.883;0.934	T	0.46638	-0.9177	10	0.72032	D	0.01	-10.2682	14.9929	0.71401	0.0:0.0:1.0:0.0	.	47;46;47;47	O43586-2;C9K004;B4E1Z9;O43586	.;.;.;PPIP1_HUMAN	S	47;46	ENSP00000368914:A47S;ENSP00000267939:A46S	ENSP00000267939:A46S	A	+	1	0	PSTPIP1	75097854	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	5.122000	0.64697	2.136000	0.66102	0.591000	0.81541	GCC	.	.		0.577	PSTPIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419373.2	NM_003978	Missense_Mutation	T	77310799	G	T	77310799	5	4	81	1	0	0	0	0	0	0	1	0	12733	1217	42	3	149	3	PSTPIP1	15	77310799	Splice_Site	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	2982514	77310799	25220593	110	11159										
ALPK3	57538	hgsc.bcm.edu	37	chr15	85399661	85399661	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	accacggctcctaccatgtcGgccagcagcagctctgatgt	10	15	1	1	rs549394061		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr15:85399661G>A	ENST00000258888.5	+	6	2465	c.2298G>A	c.(2296-2298)tcG>tcA	p.S766S		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	766	Poly-Ser.				heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CTACCATGTCGGCCAGCAGCA	0.498																																					p.S766S		Atlas-SNP	.											.	ALPK3	289	.	0			c.G2298A						.						123	115	118					15																	85399661		2203	4299	6502	SO:0001819	synonymous_variant	57538	exon6			CATGTCGGCCAGC	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.2298G>A	chr15.hg19:g.85399661G>A		133.0	0.0		74.0	19.0	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	hg19	CCDS10333.1																																																																																			.	.		0.498	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		A	85399661	G	A	85399661	2	1	81	1	0	0	0	0	0	0	0	1	546	1103	39	1		1	ALPK3	15	85399661	Silent	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	8088862	85399661	17131731	111	11160										
BLM	641	hgsc.bcm.edu	37	chr15	91326134	91326134	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aggtggcatttgattgcctaGaatggatcagaaagcaccac	11	8	1	3	rs201770808		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr15:91326134G>C	ENST00000355112.3	+	13	2756	c.2638G>C	c.(2638-2640)Gaa>Caa	p.E880Q	BLM_ENST00000560509.1_Missense_Mutation_p.E880Q|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	880	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TGATTGCCTAGAATGGATCAG	0.348			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.E880Q		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	.	BLM	122	.	0			c.G2638C						.	G	GLN/GLU	0,4396		0,0,2198	71	59	63		2638	4.6	1	15		63	2,8594	2.2+/-6.3	0,2,4296	yes	missense	BLM	NM_000057.2	29	0,2,6494	CC,CG,GG		0.0233,0.0,0.0154	benign	880/1418	91326134	2,12990	2198	4298	6496	SO:0001583	missense	641	exon13	Familial Cancer Database		TGCCTAGAATGGA	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"Bloom syndrome"			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.2638G>C	chr15.hg19:g.91326134G>C	ENSP00000347232:p.Glu880Gln	288.0	0.0		175.0	7.0	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	hg19	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.614372	0.46631	0.0	2.33E-4	ENSG00000197299	ENST00000355112;ENST00000536925;ENST00000543977	T	0.48201	0.82	5.54	4.56	0.56223	Helicase, C-terminal (1);	0.366671	0.31438	N	0.007656	T	0.34803	0.0910	L	0.31476	0.935	0.44956	D	0.99797	B;B;B	0.29571	0.167;0.249;0.167	B;B;B	0.29176	0.099;0.082;0.099	T	0.11397	-1.0589	10	0.25751	T	0.34	-11.2439	12.8729	0.57975	0.0:0.0:0.8365:0.1635	.	880;505;880	B2RAN0;B7ZKN7;P54132	.;.;BLM_HUMAN	Q	880;533;67	ENSP00000347232:E880Q	ENSP00000347232:E880Q	E	+	1	0	BLM	89127138	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.586000	0.46119	2.603000	0.88011	0.655000	0.94253	GAA	.	.		0.348	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			C	91326134	G	C	91326134	3	2	81	1	0	0	0	0	1	0	0	0	1445	943	33	4	2684	4	BLM	15	91326134	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	5926473	91326134	11205258	112	11161										
PIGQ	9091	hgsc.bcm.edu	37	chr16	633537	633537	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ccctgcatctgggggattgaAgcagtcgctgacccccgtcc	12	15	1	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr16:633537A>C	ENST00000026218.5	+	10	2274	c.2186A>C	c.(2185-2187)aAg>aCg	p.K729T	PIGQ_ENST00000321878.5_3'UTR	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	729					C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				GGGGGATTGAAGCAGTCGCTG	0.642																																					p.K729T		Atlas-SNP	.											.	PIGQ	43	.	0			c.A2186C						.						40	40	40					16																	633537		2200	4300	6500	SO:0001583	missense	9091	exon10			GATTGAAGCAGTC	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"Phosphatidylinositol glycan anchor biosynthesis"	14135	protein-coding gene	gene with protein product		605754	"phosphatidylinositol glycan, class Q"			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.2186A>C	chr16.hg19:g.633537A>C	ENSP00000026218:p.Lys729Thr	78.0	0.0		35.0	26.0	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	hg19	CCDS10411.1	.	.	.	.	.	.	.	.	.	.	A	8.297	0.819046	0.16607	.	.	ENSG00000007541	ENST00000026218	T	0.22945	1.93	3.3	-2.21	0.06973	.	.	.	.	.	T	0.09642	0.0237	N	0.08118	0	0.09310	N	1	B;B	0.28713	0.22;0.002	B;B	0.27076	0.076;0.003	T	0.34329	-0.9833	8	.	.	.	.	4.0361	0.09730	0.3543:0.2199:0.4257:0.0	.	299;729	B3KRR7;Q9BRB3	.;PIGQ_HUMAN	T	729	ENSP00000026218:K729T	.	K	+	2	0	PIGQ	573538	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.847000	0.01675	-0.197000	0.10350	0.369000	0.22263	AAG	.	.		0.642	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204		C	633537	A	C	633537	3	2	81	1	0	0	0	0	1	0	0	0	11905	72	3	5	2286	5	PIGQ	16	633537	Missense_Mutation	SNP	A	TCGA-CC-A8HV-01A-11D-A35Z-10		633537	89721216	113	11162										
TRAF7	84231	hgsc.bcm.edu	37	chr16	2218152	2218152	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cccttgcctactccccgcggGacgaggaggacagcatggta	13	14	0	0	rs547586265		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr16:2218152G>T	ENST00000326181.6	+	4	346	c.214G>T	c.(214-216)Gac>Tac	p.D72Y		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	72					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						CTCCCCGCGGGACGAGGAGGA	0.667																																					p.D72Y		Atlas-SNP	.											.	TRAF7	158	.	0			c.G214T						.						82	62	69					16																	2218152		2198	4300	6498	SO:0001583	missense	84231	exon4			CCGCGGGACGAGG	AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"RING-type (C3HC4) zinc fingers", "WD repeat domain containing"	20456	protein-coding gene	gene with protein product		606692	"ring finger and WD repeat domain 1", "TNF receptor-associated factor 7"	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.214G>T	chr16.hg19:g.2218152G>T	ENSP00000318944:p.Asp72Tyr	64.0	0.0		24.0	16.0	NM_032271	Q9H073	Missense_Mutation	SNP	ENST00000326181.6	hg19	CCDS10461.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.726518	0.48833	.	.	ENSG00000131653	ENST00000326181	T	0.32988	1.43	4.8	4.8	0.61643	.	0.048962	0.85682	D	0.000000	T	0.36468	0.0968	N	0.24115	0.695	0.80722	D	1	D	0.67145	0.996	P	0.57548	0.823	T	0.25502	-1.0130	10	0.72032	D	0.01	-22.9954	15.3698	0.74554	0.0:0.0:1.0:0.0	.	72	Q6Q0C0	TRAF7_HUMAN	Y	72	ENSP00000318944:D72Y	ENSP00000318944:D72Y	D	+	1	0	TRAF7	2158153	1.000000	0.71417	0.639000	0.29394	0.101000	0.19017	8.497000	0.90488	2.368000	0.80403	0.561000	0.74099	GAC	.	.		0.667	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271		T	2218152	G	T	2218152	3	4	81	1	0	0	0	0	1	0	0	0	16461	1174	41	3	224	3	TRAF7	16	2218152	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	1584615	2218152	88136601	114	11163										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21156684	21156684	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gtgcagccaaggtccatgacGtgcgttgcatcaagggcggg	16	10	1	1	rs138032546		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr16:21156684G>C	ENST00000261383.3	-	3	265	c.266C>G	c.(265-267)aCg>aGg	p.T89R	DNAH3_ENST00000575491.1_5'UTR|DNAH3_ENST00000415178.1_Missense_Mutation_p.T89R	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	89	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GGTCCATGACGTGCGTTGCAT	0.527																																					p.T89R		Atlas-SNP	.											.	DNAH3	1142	.	0			c.C266G						.						168	129	142					16																	21156684		2201	4300	6501	SO:0001583	missense	55567	exon3			CATGACGTGCGTT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.266C>G	chr16.hg19:g.21156684G>C	ENSP00000261383:p.Thr89Arg	115.0	0.0		57.0	39.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.485799	0.26686	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.22539	1.95;2.14	5.8	4.84	0.62591	.	0.199508	0.35555	N	0.003135	T	0.11922	0.0290	N	0.22421	0.69	0.26371	N	0.976883	B;P	0.37141	0.2;0.584	B;B	0.35899	0.069;0.213	T	0.18147	-1.0346	10	0.12103	T	0.63	.	9.3454	0.38104	0.1627:0.0:0.8373:0.0	.	89;60	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	R	89;89;60	ENSP00000261383:T89R;ENSP00000394245:T89R	ENSP00000261383:T89R	T	-	2	0	DNAH3	21064185	0.006000	0.16342	0.978000	0.43139	0.749000	0.42624	0.956000	0.29202	2.750000	0.94351	0.650000	0.86243	ACG	.	G|1.000;A|0.000		0.527	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		C	21156684	G	C	21156684	3	2	81	1	0	0	0	0	1	0	0	0	4605	1145	40	4	12323	4	DNAH3	16	21156684	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	18938532	21156684	69198069	115	11164										
CBFB	865	hgsc.bcm.edu	37	chr16	67100668	67100668	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ctccaaagactggatggtatGggctgtctggagtttgatga	14	6	1	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr16:67100668G>A	ENST00000290858.6	+	4	627	c.366G>A	c.(364-366)atG>atA	p.M122I	CBFB_ENST00000412916.2_Missense_Mutation_p.M122I|CBFB_ENST00000561924.2_Missense_Mutation_p.M22I	NM_001755.2|NM_022845.2	NP_001746.1|NP_074036.1	Q13951	PEBB_HUMAN	core-binding factor, beta subunit	122					cell maturation (GO:0048469)|definitive hemopoiesis (GO:0060216)|lymphocyte differentiation (GO:0030098)|myeloid cell differentiation (GO:0030099)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|large_intestine(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)		TGGATGGTATGGGCTGTCTGG	0.478			T	MYH11	AML																																p.M122I		Atlas-SNP	.		Dom	yes		16	16q22	865	"core-binding factor, beta subunit"		L	.	CBFB	52	.	0			c.G366A						.						145	124	131					16																	67100668		2200	4300	6500	SO:0001583	missense	865	exon4			TGGTATGGGCTGT	BC018509	CCDS10827.1, CCDS45508.1	16q22.1	2008-02-05			ENSG00000067955	ENSG00000067955			1539	protein-coding gene	gene with protein product		121360				8351518, 7587111	Standard	NM_001755		Approved	PEBP2B	uc002erb.3	Q13951	OTTHUMG00000137520	ENST00000290858.6:c.366G>A	chr16.hg19:g.67100668G>A	ENSP00000290858:p.Met122Ile	138.0	0.0		84.0	32.0	NM_022845	A8K347|Q13124|Q9HCT2	Missense_Mutation	SNP	ENST00000290858.6	hg19	CCDS10827.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.375083	0.61735	.	.	ENSG00000067955	ENST00000290858;ENST00000412916	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.66877	0.2834	L	0.27053	0.805	0.80722	D	1	B;B	0.28820	0.187;0.224	P;P	0.51055	0.526;0.657	T	0.59085	-0.7520	9	0.15499	T	0.54	-12.5189	18.1601	0.89705	0.0:0.0:1.0:0.0	.	122;122	Q13951-2;Q13951	.;PEBB_HUMAN	I	122	.	ENSP00000290858:M122I	M	+	3	0	CBFB	65658169	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.578000	0.98200	2.648000	0.89879	0.561000	0.74099	ATG	.	.		0.478	CBFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268843.2	NM_001755		A	67100668	G	A	67100668	3	1	81	1	0	0	0	0	1	0	0	0	2701	1348	47	3	380	3	CBFB	16	67100668	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	45943984	67100668	23254085	116	11165										
FHOD1	29109	hgsc.bcm.edu	37	chr16	67265130	67265130	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gcagggatttctgaatagagGtcagaggactcaggccgggt	16	7	3	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr16:67265130G>A	ENST00000258201.4	-	17	2875	c.2628C>T	c.(2626-2628)gaC>gaT	p.D876D		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	876	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		CTGAATAGAGGTCAGAGGACT	0.592																																					p.D876D		Atlas-SNP	.											.	FHOD1	86	.	0			c.C2628T						.						69	60	63					16																	67265130		2198	4300	6498	SO:0001819	synonymous_variant	29109	exon17			ATAGAGGTCAGAG	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.2628C>T	chr16.hg19:g.67265130G>A		141.0	0.0		62.0	48.0	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Silent	SNP	ENST00000258201.4	hg19	CCDS10834.1																																																																																			.	.		0.592	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2			A	67265130	G	A	67265130	2	1	81	1	0	0	0	0	0	0	0	1	5890	1252	44	3		3	FHOD1	16	67265130	Silent	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	164462	67265130	23089623	117	11166										
DPH1	1801	hgsc.bcm.edu	37	chr17	1945139	1945139	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	agggacgagaaggtggcgccGctggctccttgacgcgctcc	16	13	0	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr17:1945139G>A	ENST00000263083.6	+	12	1365	c.1320G>A	c.(1318-1320)ccG>ccA	p.P440P	OVCA2_ENST00000572195.1_5'Flank|RP11-667K14.3_ENST00000572790.1_lincRNA|DPH1_ENST00000570477.1_Silent_p.P360P|RP11-667K14.4_ENST00000572404.1_RNA	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	440					cell proliferation (GO:0008283)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	17						AGGTGGCGCCGCTGGCTCCTT	0.692											OREG0024078	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P440P		Atlas-SNP	.											.	DPH1	32	.	0			c.G1320A						.						10	14	13					17																	1945139		2056	4170	6226	SO:0001819	synonymous_variant	1801	exon12			GGCGCCGCTGGCT	S81752	CCDS42228.1	17p13.3	2013-05-02	2013-05-02	2005-06-03	ENSG00000108963	ENSG00000108963			3003	protein-coding gene	gene with protein product	"ovarian tumor suppressor candidate 1"	603527	"diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (S. cerevisiae)", "DPH-like 1 (S. cerevisiae)", "DPH1 homolog (S. cerevisiae)"	DPH2L, DPH2L1		8603384, 15485916, 22869748	Standard	NM_001383		Approved	OVCA1	uc002fts.3	Q9BZG8	OTTHUMG00000177724	ENST00000263083.6:c.1320G>A	chr17.hg19:g.1945139G>A		60.0	0.0	599	50.0	39.0	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Silent	SNP	ENST00000263083.6	hg19	CCDS42228.1																																																																																			.	.		0.692	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383		A	1945139	G	A	1945139	2	1	81	1	0	0	0	0	0	0	0	1	4721	1074	38	1		1	DPH1	17	1945139	Silent	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10		1945139	79250071	118	11167										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000420246.2_Missense_Mutation_p.R249S|TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000359597.4_Missense_Mutation_p.R249S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	120.0	0.0		70.0	50.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	81	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	5632395	7577534	73617676	119	11168										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26965006	26965006	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ataagatacgagacagacatTgggcacaggtatctgatgct	11	7	1	4			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr17:26965006T>G	ENST00000528896.2	-	14	1693	c.1619A>C	c.(1618-1620)cAa>cCa	p.Q540P	RP11-192H23.7_ENST00000577814.1_RNA|KIAA0100_ENST00000389003.3_Missense_Mutation_p.Q397P|KIAA0100_ENST00000544884.1_Missense_Mutation_p.Q397P	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	540						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					AGACAGACATTGGGCACAGGT	0.488																																					p.Q540P		Atlas-SNP	.											.	KIAA0100	175	.	0			c.A1619C						.						87	77	81					17																	26965006		2203	4300	6503	SO:0001583	missense	9703	exon14			AGACATTGGGCAC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.1619A>C	chr17.hg19:g.26965006T>G	ENSP00000436773:p.Gln540Pro	79.0	0.0		56.0	12.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.016149	0.35606	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.23950	1.88;1.88	5.95	5.95	0.96441	FMP27, N-terminal (1);	0.372867	0.30401	N	0.009714	T	0.18759	0.0450	N	0.14661	0.345	0.32272	N	0.568716	P	0.35821	0.523	B	0.35727	0.209	T	0.15435	-1.0437	10	0.46703	T	0.11	.	16.4101	0.83708	0.0:0.0:0.0:1.0	.	540	Q14667	K0100_HUMAN	P	540;540;540;397	ENSP00000436773:Q540P;ENSP00000446443:Q397P	ENSP00000005905:Q540P	Q	-	2	0	KIAA0100	23989133	1.000000	0.71417	0.717000	0.30585	0.508000	0.34012	5.345000	0.65987	2.280000	0.76307	0.460000	0.39030	CAA	.	.		0.488	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		G	26965006	T	G	26965006	3	3	81	1	0	0	0	0	1	0	0	0	8163	1812	63	5	5192	5	KIAA0100	17	26965006	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	19387472	26965006	54230204	120	11169										
IKZF3	22806	hgsc.bcm.edu	37	chr17	37947672	37947681	+	Frame_Shift_Del	DEL	AATGTGTCCT	AATGTGTCCT	-													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tcatttctctcacttaccagAatgtgtcctaagatgccccg							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	AATGTGTCCT	AATGTGTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr17:37947672_37947681delAATGTGTCCT	ENST00000346872.3	-	5	641_650	c.580_589delAGGACACATT	c.(580-591)aggacacattctfs	p.RTHS194fs	IKZF3_ENST00000377944.3_Intron|IKZF3_ENST00000467757.1_Intron|IKZF3_ENST00000350532.3_Frame_Shift_Del_p.RTHS194fs|IKZF3_ENST00000351680.3_Frame_Shift_Del_p.RTHS194fs|IKZF3_ENST00000346243.3_Frame_Shift_Del_p.RTHS194fs|IKZF3_ENST00000377945.3_Intron|IKZF3_ENST00000377958.2_Frame_Shift_Del_p.RTHS107fs|IKZF3_ENST00000535189.1_Frame_Shift_Del_p.RTHS160fs|IKZF3_ENST00000377952.2_Intron|IKZF3_ENST00000439016.2_Intron|IKZF3_ENST00000394189.2_Intron|IKZF3_ENST00000439167.2_Frame_Shift_Del_p.RTHS160fs	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	194					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CACTTACCAGAATGTGTCCTAAGATGCCCC	0.462																																					p.194_197del		Atlas-Indel,Pindel	.											.	IKZF3	79	.	0			c.581_590del						.																																			SO:0001589	frameshift_variant	22806	exon5			.	AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13178	protein-coding gene	gene with protein product		606221	"zinc finger protein, subfamily 1A, 3 (Aiolos)"	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.580_589delAGGACACATT	chr17.hg19:g.37947672_37947681delAATGTGTCCT	ENSP00000344544:p.Arg194fs	78.0	0.0		89.0	11.0	NM_183229	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Frame_Shift_Del	DEL	ENST00000346872.3	hg19	CCDS11346.1																																																																																			.	.		0.462	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		-	37947681	AATGTGTCCT	-	37947672	7	5	81	1	0	1	0	1	0	0	0	0	7625	246	9	0	956	0	IKZF3	17	37947672	Frame_Shift_Del	DEL	AATGTGTCCT	TCGA-CC-A8HV-01A-11D-A35Z-10	10982666	37947672	43247538	121	11170										
KCNH4	23415	hgsc.bcm.edu	37	chr17	40330149	40330149	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tcatgcctccctggccccggCggccaaagtggccggtcagt	13	16	2	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr17:40330149C>A	ENST00000264661.3	-	4	886	c.554G>T	c.(553-555)cGc>cTc	p.R185L	KCNH4_ENST00000607371.1_Missense_Mutation_p.R185L	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	185					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|urinary_tract(1)	32		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CTGGCCCCGGCGGCCAAAGTG	0.592																																					p.R185L	NSCLC(117;707 1703 2300 21308 31858)	Atlas-SNP	.											.	KCNH4	105	.	0			c.G554T						.						72	80	78					17																	40330149		2203	4300	6503	SO:0001583	missense	23415	exon4			CCCCGGCGGCCAA	AB022698	CCDS11420.1	17q21	2012-07-05				ENSG00000089558		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6253	protein-coding gene	gene with protein product		604528				10455180, 16382104	Standard	NM_012285		Approved	Kv12.3, elk1	uc002hzb.2	Q9UQ05		ENST00000264661.3:c.554G>T	chr17.hg19:g.40330149C>A	ENSP00000264661:p.Arg185Leu	112.0	0.0		74.0	27.0	NM_012285		Missense_Mutation	SNP	ENST00000264661.3	hg19	CCDS11420.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.002981	0.54254	.	.	ENSG00000089558	ENST00000264661	D	0.98807	-5.15	4.86	4.86	0.63082	.	0.000000	0.41500	D	0.000865	D	0.97663	0.9234	M	0.68593	2.085	0.31562	N	0.657439	B	0.21606	0.058	B	0.23419	0.046	D	0.98342	1.0539	10	0.62326	D	0.03	.	17.1648	0.86812	0.0:1.0:0.0:0.0	.	185	Q9UQ05	KCNH4_HUMAN	L	185	ENSP00000264661:R185L	ENSP00000264661:R185L	R	-	2	0	KCNH4	37583675	0.649000	0.27322	0.999000	0.59377	0.747000	0.42532	1.560000	0.36331	2.520000	0.84964	0.467000	0.42956	CGC	.	.		0.592	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285		A	40330149	C	A	40330149	3	1	81	1	0	0	0	0	1	0	0	0	8043	768	27	1	2551	1	KCNH4	17	40330149	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	2382477	40330149	40865061	122	11171										
NPEPPS	9520	hgsc.bcm.edu	37	chr17	45669377	45669377	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	atttgatgctatatcatataGcaaaggtgcatctgtcatcc	7	8	3	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr17:45669377G>T	ENST00000322157.4	+	11	1553	c.1316G>T	c.(1315-1317)aGc>aTc	p.S439I	NPEPPS_ENST00000544660.1_Missense_Mutation_p.S359I|NPEPPS_ENST00000525037.1_3'UTR|NPEPPS_ENST00000530173.1_Missense_Mutation_p.S435I	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	439					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						ATATCATATAGCAAAGGTGCA	0.393																																					p.S439I		Atlas-SNP	.											.	NPEPPS	59	.	0			c.G1316T						.						149	88	108					17																	45669377		1980	4121	6101	SO:0001583	missense	9520	exon11			CATATAGCAAAGG	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"puromycin-sensitive aminopeptidase", "metalloproteinase MP100"	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1316G>T	chr17.hg19:g.45669377G>T	ENSP00000320324:p.Ser439Ile	498.0	0.0		548.0	28.0	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Missense_Mutation	SNP	ENST00000322157.4	hg19	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.121816	0.77436	.	.	ENSG00000141279	ENST00000530173;ENST00000322157;ENST00000539572;ENST00000544660;ENST00000527964;ENST00000527360	T;T;T;T;T	0.03004	4.08;4.08;4.08;4.08;4.08	5.51	5.51	0.81932	Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.20981	0.0505	M	0.84219	2.685	0.80722	D	1	D;D;P	0.55605	0.972;0.966;0.935	D;P;P	0.65233	0.933;0.796;0.733	T	0.00203	-1.1924	10	0.62326	D	0.03	.	19.4176	0.94708	0.0:0.0:1.0:0.0	.	439;435;439	A6NEC2;E9PLK3;P55786	PSAL_HUMAN;.;PSA_HUMAN	I	435;439;426;359;122;136	ENSP00000433287:S435I;ENSP00000320324:S439I;ENSP00000442461:S359I;ENSP00000435639:S122I;ENSP00000435966:S136I	ENSP00000320324:S439I	S	+	2	0	NPEPPS	43024376	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.626000	0.98410	2.596000	0.87737	0.650000	0.86243	AGC	.	.		0.393	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310		T	45669377	G	T	45669377	3	4	81	1	0	0	0	0	1	0	0	0	10584	971	34	3	1358	3	NPEPPS	17	45669377	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	5339228	45669377	35525833	123	11172										
AATK	9625	hgsc.bcm.edu	37	chr17	79096446	79096446	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ccgcccagcatgggccccgcCgcaccgggcccgggccccac	13	23	0	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr17:79096446C>T	ENST00000326724.4	-	11	1314	c.1290G>A	c.(1288-1290)gcG>gcA	p.A430A	MIR657_ENST00000385003.1_RNA|AATK_ENST00000572339.1_5'Flank|AATK_ENST00000417379.1_Silent_p.A327A	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	430					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			Tgggccccgccgcaccgggcc	0.761																																					p.A430A		Atlas-SNP	.											.	AATK	102	.	0			c.G1290A						.						1	1	1					17																	79096446		874	2043	2917	SO:0001819	synonymous_variant	9625	exon11			CCCCGCCGCACCG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.1290G>A	chr17.hg19:g.79096446C>T		19.0	0.0		16.0	9.0	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	hg19	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	c	0.897	-0.723410	0.03158	.	.	ENSG00000181409	ENST00000417379	.	.	.	2.95	-3.48	0.04739	.	.	.	.	.	T	0.20455	0.0492	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30357	-0.9981	4	.	.	.	.	3.8175	0.08821	0.0:0.2904:0.382:0.3276	.	.	.	.	Q	383	.	.	R	-	2	0	AATK	76711041	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.897000	0.01603	-0.394000	0.07727	-0.461000	0.05368	CGG	.	.		0.761	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		T	79096446	C	T	79096446	2	4	81	1	0	0	0	0	0	0	0	1	26	639	23	1		1	AATK	17	79096446	Silent	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	33427069	79096446	2098764	124	11173										
RAB3D	9545	hgsc.bcm.edu	37	chr19	11446411	11446411	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	caggaagcccatggctccccGgtagtaggccgtggtgatgg	16	11	0	1	rs200767418	byFrequency	TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr19:11446411G>C	ENST00000222120.3	-	3	537	c.277C>G	c.(277-279)Cgg>Ggg	p.R93G	RAB3D_ENST00000589655.1_Missense_Mutation_p.R93G	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	93					exocytosis (GO:0006887)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)|zymogen granule (GO:0042588)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|ovary(2)	14						ATGGCTCCCCGGTAGTAGGCC	0.587																																					p.R93G		Atlas-SNP	.											.	RAB3D	24	.	0			c.C277G						.						171	151	158					19																	11446411		2203	4300	6503	SO:0001583	missense	9545	exon3			CTCCCCGGTAGTA	AF081353	CCDS12257.1	19p13.2	2012-10-02			ENSG00000105514	ENSG00000105514		"RAB, member RAS oncogene"	9779	protein-coding gene	gene with protein product	"Rab3D upregulated with myeloid differentiation", "glioblastoma overexpressed"	604350		GOV		10023084, 10072586	Standard	NM_004283		Approved	RAB16, D2-2, RAD3D	uc002mqx.3	O95716	OTTHUMG00000180835	ENST00000222120.3:c.277C>G	chr19.hg19:g.11446411G>C	ENSP00000222120:p.Arg93Gly	109.0	0.0		96.0	12.0	NM_004283		Missense_Mutation	SNP	ENST00000222120.3	hg19	CCDS12257.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.474598	0.63737	.	.	ENSG00000105514	ENST00000222120	D	0.82081	-1.57	4.64	3.52	0.40303	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.92848	0.7725	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93809	0.7108	10	0.87932	D	0	.	12.0923	0.53733	0.0:0.0:0.7754:0.2246	.	93	O95716	RAB3D_HUMAN	G	93	ENSP00000222120:R93G	ENSP00000222120:R93G	R	-	1	2	RAB3D	11307411	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	2.071000	0.41500	2.584000	0.87258	0.462000	0.41574	CGG	.	.		0.587	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1	NM_004283		C	11446411	G	C	11446411	3	2	81	1	0	0	0	0	1	0	0	0	12949	1115	39	4	394	4	RAB3D	19	11446411	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10		11446411	47682572	125	11174										
GTPBP3	84705	hgsc.bcm.edu	37	chr19	17452488	17452488	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gagatcctggacatcatcttCcaggacttctgtgtgggcaa	11	10	3	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr19:17452488C>T	ENST00000324894.8	+	9	1523	c.1455C>T	c.(1453-1455)ttC>ttT	p.F485F	GTPBP3_ENST00000358792.7_Silent_p.F517F|GTPBP3_ENST00000600625.1_Silent_p.F464F|GTPBP3_ENST00000361619.5_Silent_p.F507F|GTPBP3_ENST00000598038.1_3'UTR	NM_032620.3|NM_133644.3	NP_116009.2|NP_598399.2	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial)	485					tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	18						ACATCATCTTCCAGGACTTCT	0.642																																					p.F517F		Atlas-SNP	.											.	GTPBP3	40	.	0			c.C1551T						.						56	63	60					19																	17452488		2202	4300	6502	SO:0001819	synonymous_variant	84705	exon8			CATCTTCCAGGAC	AF360742	CCDS32950.1, CCDS32951.1, CCDS56088.1, CCDS59364.1	19p13.2	2008-02-05				ENSG00000130299			14880	protein-coding gene	gene with protein product		608536				1290633	Standard	NM_001128855		Approved	MSS1, THDF1, GTPBG3, MTGP1, FLJ14700	uc010xpo.2	Q969Y2		ENST00000324894.8:c.1455C>T	chr19.hg19:g.17452488C>T		202.0	0.0		178.0	15.0	NM_133644	A6NFH1|A6NIG5|A6NKR4|A8K7B4|B7Z4V8|Q8TCY6|Q8WUW9|Q969G4|Q9BX61	Silent	SNP	ENST00000324894.8	hg19	CCDS32951.1																																																																																			.	.		0.642	GTPBP3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463624.1	NM_032620		T	17452488	C	T	17452488	2	4	81	1	0	0	0	0	0	0	0	1	6890	854	30	3		3	GTPBP3	19	17452488	Silent	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	6006077	17452488	41676495	126	11175										
COMP	1311	hgsc.bcm.edu	37	chr19	18896509	18896509	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gagcaccacccagttggggtCaatctgcgcgtcaccctccg	11	16	3	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr19:18896509C>T	ENST00000222271.2	-	14	1686	c.1642G>A	c.(1642-1644)Gac>Aac	p.D548N	COMP_ENST00000425807.1_Missense_Mutation_p.D495N|COMP_ENST00000542601.2_Missense_Mutation_p.D515N	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	548	Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CAGTTGGGGTCAATCTGCGCG	0.627																																					p.D548N		Atlas-SNP	.											.	COMP	62	.	0			c.G1642A						.						55	52	53					19																	18896509		2203	4300	6503	SO:0001583	missense	1311	exon14			TGGGGTCAATCTG	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"thrombospondin-5"	600310	"cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1642G>A	chr19.hg19:g.18896509C>T	ENSP00000222271:p.Asp548Asn	72.0	0.0		61.0	23.0	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	ENST00000222271.2	hg19	CCDS12385.1	.	.	.	.	.	.	.	.	.	.	C	36	5.934338	0.97122	.	.	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.95622	-3.76;-3.76;-3.76	4.61	4.61	0.57282	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.85682	U	0.000000	D	0.98021	0.9348	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.989;0.999	D	0.99260	1.0890	10	0.87932	D	0	-30.656	15.9659	0.79970	0.0:1.0:0.0:0.0	.	495;548	B4DKJ3;P49747	.;COMP_HUMAN	N	515;548;495;535	ENSP00000439156:D515N;ENSP00000222271:D548N;ENSP00000403792:D495N	ENSP00000222271:D548N	D	-	1	0	COMP	18757509	1.000000	0.71417	0.990000	0.47175	0.977000	0.68977	7.676000	0.84012	2.106000	0.64143	0.491000	0.48974	GAC	.	.		0.627	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095		T	18896509	C	T	18896509	3	4	81	1	0	0	0	0	1	0	0	0	3726	826	29	3	655	3	COMP	19	18896509	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	1444021	18896509	40232474	127	11176										
ZFP82	284406	hgsc.bcm.edu	37	chr19	36884088	36884088	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tttcaccagtatgaattctgTgatggagaataagatgataa	9	4	2	5			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr19:36884088T>C	ENST00000392161.3	-	5	1396	c.1154A>G	c.(1153-1155)cAc>cGc	p.H385R	ZFP82_ENST00000392171.1_Missense_Mutation_p.H385R	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ATGAATTCTGTGATGGAGAAT	0.383																																					p.H385R		Atlas-SNP	.											.	ZFP82	71	.	0			c.A1154G						.						114	113	113					19																	36884088		2203	4300	6503	SO:0001583	missense	284406	exon5			ATTCTGTGATGGA	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"Zinc fingers, C2H2-type", "-"	28682	protein-coding gene	gene with protein product			"zinc finger protein 545", "zinc finger protein 82 homolog (mouse)", "zinc finger protein 82"	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.1154A>G	chr19.hg19:g.36884088T>C	ENSP00000431265:p.His385Arg	120.0	0.0		75.0	23.0	NM_133466	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	hg19	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	T	10.51	1.371076	0.24771	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.33865	1.39;1.39	4.53	4.53	0.55603	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43747	D	0.000524	T	0.25082	0.0609	N	0.10782	0.045	0.26717	N	0.970861	B	0.32467	0.372	B	0.42959	0.403	T	0.14868	-1.0457	10	0.52906	T	0.07	.	6.6697	0.23062	0.0:0.1048:0.0:0.8952	.	385	Q8N141	ZFP82_HUMAN	R	385	ENSP00000431265:H385R;ENSP00000446080:H385R	ENSP00000431265:H385R	H	-	2	0	ZFP82	41575928	0.016000	0.18221	1.000000	0.80357	0.993000	0.82548	0.139000	0.16036	1.905000	0.55150	0.482000	0.46254	CAC	.	.		0.383	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		C	36884088	T	C	36884088	3	2	81	1	0	0	0	0	1	0	0	0	17668	1696	59	2	448	2	ZFP82	19	36884088	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	17987579	36884088	22244895	128	11177										
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47593287	47593287	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cagctctttggtgaagtcgtCatagtcctccttgcccatgt	9	12	2	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr19:47593287C>T	ENST00000253048.5	-	5	689	c.652G>A	c.(652-654)Gac>Aac	p.D218N	ZC3H4_ENST00000594019.1_5'UTR	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	218							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		GTGAAGTCGTCATAGTCCTCC	0.577																																					p.D218N		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G652A						.						134	137	136					19																	47593287		2159	4249	6408	SO:0001583	missense	23211	exon5			AGTCGTCATAGTC	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"Zinc fingers, CCCH-type domain containing"	17808	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 7"	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.652G>A	chr19.hg19:g.47593287C>T	ENSP00000253048:p.Asp218Asn	92.0	0.0		81.0	31.0	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	hg19	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.317685	0.60524	.	.	ENSG00000130749	ENST00000253048	T	0.26373	1.74	5.74	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.30198	0.0757	L	0.55481	1.735	0.80722	D	1	P	0.41393	0.748	B	0.41374	0.355	T	0.11991	-1.0565	10	0.87932	D	0	.	15.5167	0.75830	0.0:0.8497:0.1503:0.0	.	218	Q9UPT8	ZC3H4_HUMAN	N	218	ENSP00000253048:D218N	ENSP00000253048:D218N	D	-	1	0	ZC3H4	52285127	1.000000	0.71417	0.932000	0.37286	0.349000	0.29174	7.363000	0.79516	1.409000	0.46915	-0.211000	0.12701	GAC	.	.		0.577	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			T	47593287	C	T	47593287	3	4	81	1	0	0	0	0	1	0	0	0	17585	826	29	3	3303	3	ZC3H4	19	47593287	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	10709199	47593287	11535696	129	11178										
C19orf76	199800	hgsc.bcm.edu	37	chr19	50193723	50193723	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ccagcccctgaaaccgtcttCcccagtccctccccgggctg	8	21	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr19:50193723C>A	ENST00000420022.3	+	2	1609	c.435C>A	c.(433-435)ttC>ttA	p.F145L	CPT1C_ENST00000354199.5_5'Flank|CPT1C_ENST00000392518.4_5'Flank|CPT1C_ENST00000598293.1_5'Flank|CPT1C_ENST00000405931.2_5'Flank|CTB-33G10.6_ENST00000596472.1_RNA|CPT1C_ENST00000323446.5_5'Flank	NM_001101340.1	NP_001094810.1	C9JUS6	ADM5_HUMAN	adrenomedullin 5 (putative)	145						extracellular region (GO:0005576)											AAACCGTCTTCCCCAGTCCCT	0.577																																					p.F145L		Atlas-SNP	.											.	.	.	.	0			c.C435A						.						32	36	35					19																	50193723		1349	2764	4113	SO:0001583	missense	199800	exon2			CGTCTTCCCCAGT	BC032764	CCDS46146.1	19q13.33	2012-12-07	2012-12-07	2012-10-29	ENSG00000224420	ENSG00000224420			27293	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 76", "adrenomedullin 5 homolog (pig)"	C19orf76		18434369	Standard	NM_001101340		Approved	AM5	uc002pph.2	C9JUS6		ENST00000420022.3:c.435C>A	chr19.hg19:g.50193723C>A	ENSP00000393631:p.Phe145Leu	141.0	0.0		100.0	55.0	NM_001101340		Missense_Mutation	SNP	ENST00000420022.3	hg19	CCDS46146.1	.	.	.	.	.	.	.	.	.	.	C	8.587	0.883609	0.17467	.	.	ENSG00000224420	ENST00000420022	.	.	.	1.84	-2.15	0.07102	.	.	.	.	.	T	0.16257	0.0391	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.20042	-1.0287	8	0.87932	D	0	.	4.8657	0.13607	0.2194:0.3721:0.4085:0.0	.	145	C9JUS6	ADM5_HUMAN	L	145	.	ENSP00000393631:F145L	F	+	3	2	C19orf76	54885535	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.812000	0.04496	-0.435000	0.07264	0.561000	0.74099	TTC	.	.		0.577	ADM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465777.1	NM_001101340		A	50193723	C	A	50193723	3	1	81	1	0	0	0	0	1	0	0	0	1952	854	30	3	441	3	C19orf76	19	50193723	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	2600436	50193723	8935260	130	11179										
MYH14	79784	hgsc.bcm.edu	37	chr19	50753873	50753873	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gtagcccaggagcagggcggCcaccccaagttccagcggcc	14	16	0	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr19:50753873C>T	ENST00000596571.1	+	13	1734	c.1734C>T	c.(1732-1734)ggC>ggT	p.G578G	MYH14_ENST00000440075.2_Silent_p.G586G|MYH14_ENST00000598205.1_Silent_p.G586G|MYH14_ENST00000262269.8_Silent_p.G586G|MYH14_ENST00000376970.2_Silent_p.G578G|MYH14_ENST00000601313.1_Silent_p.G586G|MYH14_ENST00000425460.1_Silent_p.G586G			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	578	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		AGCAGGGCGGCCACCCCAAGT	0.662																																					p.G586G		Atlas-SNP	.											.	MYH14	261	.	0			c.C1758T						.						32	40	37					19																	50753873		2169	4266	6435	SO:0001819	synonymous_variant	79784	exon15			GGGCGGCCACCCC	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.1734C>T	chr19.hg19:g.50753873C>T		244.0	0.0		191.0	41.0	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	hg19	CCDS59411.1																																																																																			.	.		0.662	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50753873	C	T	50753873	2	4	81	1	0	0	0	0	0	0	0	1	10042	726	26	3		3	MYH14	19	50753873	Silent	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	560150	50753873	8375110	131	11180										
ZNF816A	125893	hgsc.bcm.edu	37	chr19	53454379	53454379	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gcatatttcctgtatttgtgTgaatgaagaatggaggaaat	11	3	0	3			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr19:53454379T>C	ENST00000357666.4	-	5	949	c.649A>G	c.(649-651)Aca>Gca	p.T217A	ZNF816_ENST00000434371.2_Intron|ZNF321P_ENST00000391777.3_Intron|ZNF816_ENST00000444460.2_Missense_Mutation_p.T217A	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	217					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						TGTATTTGTGTGAATGAAGAA	0.373																																					p.T217A		Atlas-SNP	.											.	ZNF816	73	.	0			c.A649G						.						73	79	77					19																	53454379		2203	4300	6503	SO:0001583	missense	125893	exon4			TTTGTGTGAATGA	BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"Zinc fingers, C2H2-type", "-"	26995	protein-coding gene	gene with protein product			"zinc finger protein 816A"	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.649A>G	chr19.hg19:g.53454379T>C	ENSP00000350295:p.Thr217Ala	87.0	0.0		66.0	13.0	NM_001202457	A8K7H5|Q3KR39|Q659B3	Missense_Mutation	SNP	ENST00000357666.4	hg19	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	-	1.148	-0.647601	0.03506	.	.	ENSG00000180257	ENST00000357666;ENST00000444460	T;T	0.15256	2.44;2.44	0.852	-0.54	0.11861	.	.	.	.	.	T	0.11153	0.0272	N	0.25485	0.75	0.20926	N	0.999829	P	0.48694	0.914	P	0.46825	0.528	T	0.17471	-1.0368	9	0.17369	T	0.5	.	2.7723	0.05338	0.4181:0.0:0.0:0.5819	.	217	Q0VGE8	ZN816_HUMAN	A	217	ENSP00000350295:T217A;ENSP00000403266:T217A	ENSP00000350295:T217A	T	-	1	0	ZNF816	58146191	0.000000	0.05858	0.012000	0.15200	0.166000	0.22503	-0.618000	0.05578	-0.242000	0.09667	0.163000	0.16589	ACA	.	.		0.373	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		C	53454379	T	C	53454379	3	2	81	1	0	0	0	0	1	0	0	0	18192	1696	59	2	1310	2	ZNF816A	19	53454379	Missense_Mutation	SNP	T	TCGA-CC-A8HV-01A-11D-A35Z-10	2700506	53454379	5674604	132	11181										
PPP1R12C	54776	hgsc.bcm.edu	37	chr19	55610211	55610211	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	tacttcctcatcggccaggtCacagggacgctgcccctggg	12	15	2	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr19:55610211C>T	ENST00000263433.3	-	6	907	c.892G>A	c.(892-894)Gac>Aac	p.D298N	PPP1R12C_ENST00000435544.2_Missense_Mutation_p.D224N|PPP1R12C_ENST00000376393.2_Missense_Mutation_p.D298N	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		TCGGCCAGGTCACAGGGACGC	0.652																																					p.D298N		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.G892A						.						77	60	65					19																	55610211		2203	4300	6503	SO:0001583	missense	54776	exon6			CCAGGTCACAGGG	AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14947	protein-coding gene	gene with protein product	"myosin-binding subunit 85"	613245	"leukocyte receptor cluster (LRC) member 3", "protein phosphatase 1, regulatory (inhibitor) subunit 12C"	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.892G>A	chr19.hg19:g.55610211C>T	ENSP00000263433:p.Asp298Asn	178.0	0.0		128.0	22.0	NM_017607		Missense_Mutation	SNP	ENST00000263433.3	hg19	CCDS12916.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.959503	0.92791	.	.	ENSG00000125503	ENST00000263433;ENST00000376393;ENST00000435544	T;T;T	0.57107	0.42;0.42;0.42	5.03	5.03	0.67393	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.72285	0.3441	M	0.74467	2.265	0.80722	D	1	D;D;D	0.76494	0.984;0.999;0.999	D;D;D	0.80764	0.96;0.994;0.985	T	0.75725	-0.3217	10	0.72032	D	0.01	.	16.2252	0.82286	0.0:1.0:0.0:0.0	.	224;298;298	B4DME2;Q9BZL4-3;Q9BZL4	.;.;PP12C_HUMAN	N	298;298;224	ENSP00000263433:D298N;ENSP00000365573:D298N;ENSP00000387833:D224N	ENSP00000263433:D298N	D	-	1	0	PPP1R12C	60302023	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	6.839000	0.75364	2.506000	0.84524	0.563000	0.77884	GAC	.	.		0.652	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607		T	55610211	C	T	55610211	3	4	81	1	0	0	0	0	1	0	0	0	12368	826	29	3	1524	3	PPP1R12C	19	55610211	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	2155832	55610211	3518772	133	11182										
GGT7	2686	hgsc.bcm.edu	37	chr20	33460489	33460489	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aaaggcgtcctcgtccttgcGgcccctcagcggggccgcgg	15	16	1	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr20:33460489G>A	ENST00000336431.5	-	1	174	c.130C>T	c.(130-132)Cgc>Tgc	p.R44C	ACSS2_ENST00000336325.4_5'Flank	NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	44					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						TCGTCCTTGCGGCCCCTCAGC	0.711																																					p.R44C		Atlas-SNP	.											.	GGT7	41	.	0			c.C130T						.						6	9	8					20																	33460489		2140	4211	6351	SO:0001583	missense	2686	exon1			CCTTGCGGCCCCT	AL049709	CCDS13242.2	20q11.22	2008-11-24	2008-03-10	2008-03-10	ENSG00000131067	ENSG00000131067		"Gamma-glutamyltransferases"	4259	protein-coding gene	gene with protein product		612342	"gamma-glutamyltransferase-like 3"	GGTL5, GGTL3		8104871, 18357469	Standard	NM_178026		Approved	D20S101, dJ18C9.2	uc002xay.3	Q9UJ14	OTTHUMG00000032314	ENST00000336431.5:c.130C>T	chr20.hg19:g.33460489G>A	ENSP00000338964:p.Arg44Cys	245.0	0.0		231.0	100.0	NM_178026	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Missense_Mutation	SNP	ENST00000336431.5	hg19	CCDS13242.2	.	.	.	.	.	.	.	.	.	.	G	19.68	3.873395	0.72180	.	.	ENSG00000131067	ENST00000336431;ENST00000427420	T;T	0.49720	3.18;0.77	3.35	3.35	0.38373	.	0.469748	0.21700	N	0.070438	T	0.44052	0.1275	L	0.44542	1.39	0.80722	D	1	D;D;D	0.71674	0.998;0.975;0.975	P;B;B	0.47744	0.556;0.432;0.249	T	0.47711	-0.9096	10	0.87932	D	0	-6.0296	9.8145	0.40844	0.0977:0.0:0.9023:0.0	.	44;44;44	Q9UJ14-5;A4FU32;Q9UJ14	.;.;GGT7_HUMAN	C	44	ENSP00000338964:R44C;ENSP00000394993:R44C	ENSP00000338964:R44C	R	-	1	0	GGT7	32924150	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.784000	0.62411	2.202000	0.70862	0.313000	0.20887	CGC	.	.		0.711	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2	NM_178026		A	33460489	G	A	33460489	3	1	81	1	0	0	0	0	1	0	0	0	6372	1116	39	1	1918	1	GGT7	20	33460489	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10		33460489	29565031	134	11183										
C20orf4	25980	hgsc.bcm.edu	37	chr20	34828015	34828015	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aaggaagtaggccctcgtatGggtttcttccttagcctgca	11	10	1	0	rs147662826		TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr20:34828015G>T	ENST00000373932.3	+	2	571	c.225G>T	c.(223-225)atG>atT	p.M75I	AAR2_ENST00000320849.4_Missense_Mutation_p.M75I|AAR2_ENST00000397286.3_Missense_Mutation_p.M75I	NM_015511.3	NP_056326.2	Q9Y312	AAR2_HUMAN	AAR2 splicing factor homolog (S. cerevisiae)	75																	GCCCTCGTATGGGTTTCTTCC	0.602																																					p.M75I		Atlas-SNP	.											.	.	.	.	0			c.G225T						.						69	67	68					20																	34828015		2203	4300	6503	SO:0001583	missense	25980	exon2			TCGTATGGGTTTC		CCDS13273.1	20q11.23	2012-07-20	2012-07-20	2012-07-20	ENSG00000131043	ENSG00000131043			15886	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 4"	C20orf4			Standard	NM_015511		Approved	bA234K24.2	uc002xfc.3	Q9Y312	OTTHUMG00000032380	ENST00000373932.3:c.225G>T	chr20.hg19:g.34828015G>T	ENSP00000363043:p.Met75Ile	152.0	0.0		128.0	48.0	NM_001271874	E1P5S7|Q9H4F9|Q9P1P3|Q9UFK9	Missense_Mutation	SNP	ENST00000373932.3	hg19	CCDS13273.1	.	.	.	.	.	.	.	.	.	.	G	4.095	0.015638	0.07959	.	.	ENSG00000131043	ENST00000397286;ENST00000320849;ENST00000373932	T;T;T	0.40225	1.04;1.04;1.04	5.03	3.1	0.35709	.	0.222035	0.53938	N	0.000045	T	0.19087	0.0458	N	0.05487	-0.04	0.30156	N	0.802655	B;B	0.17268	0.021;0.004	B;B	0.13407	0.009;0.005	T	0.12319	-1.0552	10	0.22109	T	0.4	.	6.4086	0.21678	0.1634:0.1503:0.6862:0.0	.	75;75	A2A2Q9;Q9Y312	.;CT004_HUMAN	I	75	ENSP00000380455:M75I;ENSP00000313674:M75I;ENSP00000363043:M75I	ENSP00000313674:M75I	M	+	3	0	C20orf4	34291429	0.982000	0.34865	0.994000	0.49952	0.622000	0.37654	0.120000	0.15647	0.834000	0.34852	-0.140000	0.14226	ATG	.	G|1.000;C|0.000		0.602	AAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079001.2	NM_015511		T	34828015	G	T	34828015	3	4	81	1	0	0	0	0	1	0	0	0	2113	1348	47	3	227	3	C20orf4	20	34828015	Missense_Mutation	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	1367526	34828015	28197505	135	11184										
CDH22	64405	hgsc.bcm.edu	37	chr20	44806803	44806803	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cctgctcctgccggttgaagCccacgtgctgcgtgtgcact	12	15	0	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr20:44806803C>A	ENST00000372262.3	-	10	2097	c.1697G>T	c.(1696-1698)gGc>gTc	p.G566V	CDH22_ENST00000537909.1_Missense_Mutation_p.G566V	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	566	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				CCGGTTGAAGCCCACGTGCTG	0.637																																					p.G566V		Atlas-SNP	.											.	CDH22	112	.	0			c.G1697T						.						72	55	60					20																	44806803		2203	4300	6503	SO:0001583	missense	64405	exon11			TTGAAGCCCACGT	AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"Cadherins / Major cadherins"	13251	protein-coding gene	gene with protein product		609920	"cadherin-like 22"	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.1697G>T	chr20.hg19:g.44806803C>A	ENSP00000361336:p.Gly566Val	94.0	0.0		70.0	28.0	NM_021248	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	hg19	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.819249	0.71028	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.58506	0.33;0.33	4.36	4.36	0.52297	Cadherin (4);Cadherin-like (1);	0.128938	0.51477	D	0.000083	T	0.63426	0.2510	M	0.74546	2.27	0.80722	D	1	P	0.49559	0.925	P	0.48524	0.58	T	0.68648	-0.5353	10	0.59425	D	0.04	.	11.6329	0.51187	0.0:0.8198:0.1802:0.0	.	566	Q9UJ99	CAD22_HUMAN	V	566	ENSP00000361336:G566V;ENSP00000437790:G566V	ENSP00000361336:G566V	G	-	2	0	CDH22	44240210	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.795000	0.55499	2.263000	0.75096	0.650000	0.86243	GGC	.	.		0.637	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		A	44806803	C	A	44806803	3	1	81	1	0	0	0	0	1	0	0	0	3109	739	26	3	797	3	CDH22	20	44806803	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	9978788	44806803	18218717	136	11185										
ZMYND8	23613	hgsc.bcm.edu	37	chr20	45905296	45905296	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aagttgagcttgaccttctcCtgcttgtctatcttggcagt	9	10	3	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr20:45905296C>T	ENST00000311275.7	-	11	1435	c.1182G>A	c.(1180-1182)caG>caA	p.Q394Q	ZMYND8_ENST00000540497.1_Silent_p.Q389Q|ZMYND8_ENST00000461685.1_Silent_p.Q414Q|ZMYND8_ENST00000396281.4_Silent_p.Q394Q|ZMYND8_ENST00000446994.2_Silent_p.Q331Q|ZMYND8_ENST00000471951.2_Silent_p.Q414Q|ZMYND8_ENST00000360911.3_Silent_p.Q389Q|ZMYND8_ENST00000262975.4_Silent_p.Q394Q|ZMYND8_ENST00000536340.1_Silent_p.Q421Q|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000372023.3_Silent_p.Q389Q|ZMYND8_ENST00000352431.2_Silent_p.Q414Q|ZMYND8_ENST00000355972.4_Silent_p.Q394Q|ZMYND8_ENST00000458360.2_Silent_p.Q389Q	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	394					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			TGACCTTCTCCTGCTTGTCTA	0.557																																					p.Q414Q		Atlas-SNP	.											.	ZMYND8	166	.	0			c.G1242A						.						165	145	151					20																	45905296		2203	4300	6503	SO:0001819	synonymous_variant	23613	exon11			CTTCTCCTGCTTG	U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"Zinc fingers, MYND-type", "Zinc fingers, PHD-type"	9397	protein-coding gene	gene with protein product		615713	"protein kinase C binding protein 1"	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.1182G>A	chr20.hg19:g.45905296C>T		161.0	0.0		170.0	44.0	NM_183047	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Silent	SNP	ENST00000311275.7	hg19		.	.	.	.	.	.	.	.	.	.	C	8.519	0.868267	0.17250	.	.	ENSG00000101040	ENST00000467200	.	.	.	5.63	3.36	0.38483	.	.	.	.	.	T	0.59088	0.2168	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56025	-0.8047	4	.	.	.	-22.1805	9.2138	0.37335	0.0:0.7434:0.0:0.2566	.	.	.	.	R	321	.	.	G	-	1	0	ZMYND8	45338703	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.736000	0.26130	1.379000	0.46325	0.655000	0.94253	GGA	.	.		0.557	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047		T	45905296	C	T	45905296	2	4	81	1	0	0	0	0	0	0	0	1	17726	680	24	3		3	ZMYND8	20	45905296	Silent	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	1098493	45905296	17120224	137	11186										
KCNJ15	3772	hgsc.bcm.edu	37	chr21	39671702	39671702	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	aaaatcgccagacccaaaaaGcgggctgagaccatcaagtt	9	11	1	2			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr21:39671702G>A	ENST00000328656.4	+	4	822	c.519G>A	c.(517-519)aaG>aaA	p.K173K	KCNJ15_ENST00000398930.1_Silent_p.K173K|KCNJ15_ENST00000398938.2_Silent_p.K173K|KCNJ15_ENST00000398932.1_Silent_p.K173K|KCNJ15_ENST00000398934.1_Silent_p.K173K	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	173					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	GACCCAAAAAGCGGGCTGAGA	0.507																																					p.M173I		Atlas-SNP	.											.	KCNJ15	43	.	0			c.G519A						.						62	60	61					21																	39671702		2203	4300	6503	SO:0001819	synonymous_variant	3772	exon3			CAAAAAGCGGGCT	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.519G>A	chr21.hg19:g.39671702G>A		54.0	0.0		33.0	20.0	NM_170737	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	hg19	CCDS13656.1																																																																																			.	.		0.507	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		A	39671702	G	A	39671702	2	1	81	1	0	0	0	0	0	0	0	1	8058	962	34	3		3	KCNJ15	21	39671702	Silent	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10		39671702	8458193	138	11187										
DGCR14	8220	hgsc.bcm.edu	37	chr22	19126677	19126677	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gacccgcctgctcacctgggCattgagggcggctgcctgct	14	15	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chr22:19126677C>T	ENST00000252137.6	-	6	860	c.817G>A	c.(817-819)Gcc>Acc	p.A273T		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	273					mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					CTCACCTGGGCATTGAGGGCG	0.647																																					p.A273T		Atlas-SNP	.											.	DGCR14	43	.	0			c.G817A						.						28	28	28					22																	19126677		2203	4298	6501	SO:0001583	missense	8220	exon6			CCTGGGCATTGAG	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"DiGeorge syndrome critical region gene 13"	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.817G>A	chr22.hg19:g.19126677C>T	ENSP00000252137:p.Ala273Thr	40.0	0.0		29.0	15.0	NM_022719	Q49AH7|Q9BTZ4	Missense_Mutation	SNP	ENST00000252137.6	hg19	CCDS13756.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.589071	0.86851	.	.	ENSG00000100056	ENST00000252137	T	0.46063	0.88	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.61924	0.2386	M	0.64260	1.97	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58853	-0.7563	10	0.30854	T	0.27	-17.3583	17.7639	0.88471	0.0:1.0:0.0:0.0	.	273	Q96DF8	DGC14_HUMAN	T	273	ENSP00000252137:A273T	ENSP00000252137:A273T	A	-	1	0	DGCR14	17506677	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.683000	0.68189	2.284000	0.76573	0.563000	0.77884	GCC	.	.		0.647	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2			T	19126677	C	T	19126677	3	4	81	1	0	0	0	0	1	0	0	0	4462	710	25	3	633	3	DGCR14	22	19126677	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10		19126677	32177889	139	11188										
MAGEB6	158809	hgsc.bcm.edu	37	chrX	26212737	26212737	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttgaaagaaatggattccagCggcgagtcctacacccttgt	10	10	0	2	rs143373947	byFrequency	TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chrX:26212737C>G	ENST00000379034.1	+	2	923	c.774C>G	c.(772-774)agC>agG	p.S258R		NM_173523.2	NP_775794.2	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	258	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.S258R(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(18)|ovary(3)|prostate(2)	33						TGGATTCCAGCGGCGAGTCCT	0.537																																					p.S258R		Atlas-SNP	.											.	MAGEB6	91	.	1	Substitution - Missense(1)	lung(1)	c.C774G						.						76	64	68					X																	26212737		2202	4300	6502	SO:0001583	missense	158809	exon2			TTCCAGCGGCGAG	AF320514	CCDS14217.1	Xp22.12	2009-03-17			ENSG00000176746	ENSG00000176746			23796	protein-coding gene	gene with protein product	"cancer/testis antigen family 3, member 4"	300467				10861452	Standard	NM_173523		Approved	FLJ40242, MAGE-B6, MAGEB6A, CT3.4	uc004dbr.3	Q8N7X4	OTTHUMG00000021285	ENST00000379034.1:c.774C>G	chrX.hg19:g.26212737C>G	ENSP00000368320:p.Ser258Arg	152.0	0.0		58.0	29.0	NM_173523	Q6GS19|Q9H219	Missense_Mutation	SNP	ENST00000379034.1	hg19	CCDS14217.1	.	.	.	.	.	.	.	.	.	.	C	1.741	-0.491709	0.04322	.	.	ENSG00000176746	ENST00000379034	T	0.04360	3.64	3.1	-5.37	0.02681	.	0.334596	0.28760	U	0.014226	T	0.03263	0.0095	N	0.20881	0.62	0.09310	N	1	P	0.39181	0.663	B	0.43018	0.405	T	0.21381	-1.0247	10	0.40728	T	0.16	.	6.1106	0.20097	0.1447:0.1932:0.0:0.6621	.	258	Q8N7X4	MAGB6_HUMAN	R	258	ENSP00000368320:S258R	ENSP00000368320:S258R	S	+	3	2	MAGEB6	26122658	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.360000	0.01084	-1.784000	0.01272	-1.119000	0.02030	AGC	.	C|0.997;T|0.003		0.537	MAGEB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056123.1	NM_173523		G	26212737	C	G	26212737	3	3	81	1	0	0	0	0	1	0	0	0	9188	767	27	4	776	4	MAGEB6	23	26212737	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10		26212737	129057823	140	11189										
WNK3	65267	hgsc.bcm.edu	37	chrX	54275438	54275438	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gagcaagtttcttaatttttCatccagagttttaattcggt	7	6	2	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chrX:54275438C>A	ENST00000375159.2	-	16	3342	c.3343G>T	c.(3343-3345)Gaa>Taa	p.E1115*	WNK3_ENST00000354646.2_Nonsense_Mutation_p.E1115*|WNK3_ENST00000375169.3_Nonsense_Mutation_p.E1115*			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1115					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						CTTAATTTTTCATCCAGAGTT	0.438																																					p.E1115X		Atlas-SNP	.											.	WNK3	218	.	0			c.G3343T						.						102	99	100					X																	54275438		2203	4300	6503	SO:0001587	stop_gained	65267	exon17			ATTTTTCATCCAG	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.3343G>T	chrX.hg19:g.54275438C>A	ENSP00000364301:p.Glu1115*	161.0	0.0		109.0	25.0	NM_001002838	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Nonsense_Mutation	SNP	ENST00000375159.2	hg19	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	C	42	9.367798	0.99150	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	.	.	.	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-16.631	16.4428	0.83907	0.0:1.0:0.0:0.0	.	.	.	.	X	1115	.	ENSP00000346667:E1115X	E	-	1	0	WNK3	54292163	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.367000	0.66127	2.138000	0.66242	0.544000	0.68410	GAA	.	.		0.438	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		A	54275438	C	A	54275438	4	1	81	1	0	0	0	0	0	1	0	0	17394	835	29	3	2091	3	WNK3	23	54275438	Nonsense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	28062701	54275438	100995122	141	11190										
FGD1	2245	hgsc.bcm.edu	37	chrX	54475585	54475585	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ccaacactcacatgcccgcaGgccttgcagtggtgcctgcg	11	16	1	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chrX:54475585G>A	ENST00000375135.3	-	15	2998	c.2265C>T	c.(2263-2265)gcC>gcT	p.A755A		NM_004463.2	NP_004454.2	P98174	FGD1_HUMAN	FYVE, RhoGEF and PH domain containing 1	755					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						CATGCCCGCAGGCCTTGCAGT	0.622																																					p.A755A		Atlas-SNP	.											.	FGD1	99	.	0			c.C2265T						.						76	70	72					X																	54475585		2203	4300	6503	SO:0001819	synonymous_variant	2245	exon15			CCCGCAGGCCTTG	U11690	CCDS14359.1	Xp11.21	2013-01-10	2008-08-01		ENSG00000102302	ENSG00000102302		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	3663	protein-coding gene	gene with protein product		300546	"faciogenital dysplasia (Aarskog-Scott syndrome)"	FGDY			Standard	NM_004463		Approved	ZFYVE3	uc004dtg.3	P98174	OTTHUMG00000021627	ENST00000375135.3:c.2265C>T	chrX.hg19:g.54475585G>A		103.0	0.0		80.0	25.0	NM_004463	Q5H999|Q8N4D9	Silent	SNP	ENST00000375135.3	hg19	CCDS14359.1																																																																																			.	.		0.622	FGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056801.1	NM_004463		A	54475585	G	A	54475585	2	1	81	1	0	0	0	0	0	0	0	1	5840	987	35	3		3	FGD1	23	54475585	Silent	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	200147	54475585	100794975	142	11191										
DGAT2L6	347516	hgsc.bcm.edu	37	chrX	69419697	69419697	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	cttgggtacgaaactggaccCtatggaagtatttccgaaat	10	8	0	0			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chrX:69419697C>A	ENST00000333026.3	+	3	332	c.232C>A	c.(232-234)Cta>Ata	p.L78I		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	78					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(1)	12						AAACTGGACCCTATGGAAGTA	0.557																																					p.L78I		Atlas-SNP	.											.	DGAT2L6	40	.	0			c.C232A						.						93	73	80					X																	69419697		2203	4300	6503	SO:0001583	missense	347516	exon3			TGGACCCTATGGA	AK129500	CCDS14397.1	Xq13.1	2008-02-05			ENSG00000184210	ENSG00000184210			23250	protein-coding gene	gene with protein product		300926				15671038	Standard	NM_198512		Approved	DC3, FLJ25989	uc004dxx.1	Q6ZPD8	OTTHUMG00000021774	ENST00000333026.3:c.232C>A	chrX.hg19:g.69419697C>A	ENSP00000328036:p.Leu78Ile	139.0	0.0		88.0	18.0	NM_198512	Q6IEE2	Missense_Mutation	SNP	ENST00000333026.3	hg19	CCDS14397.1	.	.	.	.	.	.	.	.	.	.	C	8.678	0.904479	0.17760	.	.	ENSG00000184210	ENST00000333026	T	0.11821	2.74	4.86	0.871	0.19107	.	0.443686	0.20940	N	0.082922	T	0.05456	0.0144	N	0.05608	-0.01	0.29275	N	0.87044	B	0.17465	0.022	B	0.25987	0.065	T	0.44513	-0.9323	10	0.02654	T	1	-12.5692	8.6207	0.33859	0.5688:0.2939:0.1373:0.0	.	78	Q6ZPD8	DG2L6_HUMAN	I	78	ENSP00000328036:L78I	ENSP00000328036:L78I	L	+	1	2	DGAT2L6	69336422	0.930000	0.31532	0.908000	0.35775	0.694000	0.40290	1.451000	0.35145	-0.069000	0.12931	0.600000	0.82982	CTA	.	.		0.557	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057067.1	NM_198512		A	69419697	C	A	69419697	3	1	81	1	0	0	0	0	1	0	0	0	4461	680	24	3	242	3	DGAT2L6	23	69419697	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	14944112	69419697	85850863	143	11192										
P2RY10	27334	hgsc.bcm.edu	37	chrX	78216995	78216996	+	Missense_Mutation	DNP	CC	CC	AA													0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ggcagttctgtgacccgctcCcgcctcatgagcaaggagag							TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chrX:78216995_78216996CC>AA	ENST00000171757.2	+	4	1258_1259	c.978_979CC>AA	c.(976-981)tcCCgc>tcAAgc	p.R327S	P2RY10_ENST00000544091.1_Missense_Mutation_p.R327S	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	327						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)	p.S326S(1)		breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2)	42						TGACCCGCTCCCGCCTCATGAG	0.426																																					p.S326S|p.R327S		Atlas-SNP	.											.	P2RY10	99	.	1	Substitution - coding silent(1)	lung(1)	c.C978A|c.C979A						.																																			SO:0001583	missense	27334	exon2			CCGCTCCCGCCTC|CGCTCCCGCCTCA	AF000545	CCDS14442.1	Xq21.1	2012-08-23			ENSG00000078589	ENSG00000078589		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	19906	protein-coding gene	gene with protein product		300529				11004484, 9755289	Standard	NM_014499		Approved	P2Y10	uc004edf.3	O00398	OTTHUMG00000021896	Exception_encountered	chrX.hg19:g.78216995_78216996delinsAA	ENSP00000171757:p.Arg327Ser	250.0|251.0	0.0		195.0|196.0	89.0	NM_198333	D3DTE5|Q4VBN7|Q86V16	Silent|Missense_Mutation	SNP	ENST00000171757.2	hg19	CCDS14442.1																																																																																			.	.		0.426	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1			AA	78216996	CC	AA	78216995	3	1	81	1	0	0	0	0	1	0	0	0	11356	610	22	3	980	3	P2RY10	23	78216995	Missense_Mutation	DNP	CC	TCGA-CC-A8HV-01A-11D-A35Z-10	8797298	78216995	77053565	144	11193										
RNF128	79589	hgsc.bcm.edu	37	chrX	105970236	105970236	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ttcctgctggccctgagtccGcaggcacccggttcccgggg	14	16	0	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chrX:105970236G>A	ENST00000255499.2	+	1	343	c.93G>A	c.(91-93)ccG>ccA	p.P31P	RNF128_ENST00000324342.3_Intron	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase	31					negative regulation of cytokine biosynthetic process (GO:0042036)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						CCCTGAGTCCGCAGGCACCCG	0.706																																					p.P31P		Atlas-SNP	.											.	RNF128	74	.	0			c.G93A						.						12	11	11					X																	105970236		2188	4267	6455	SO:0001819	synonymous_variant	79589	exon1			GAGTCCGCAGGCA	AK027169	CCDS14520.1, CCDS14521.1	Xq22.3	2013-01-09	2012-02-23		ENSG00000133135	ENSG00000133135		"RING-type (C3HC4) zinc fingers"	21153	protein-coding gene	gene with protein product		300439	"ring finger protein 128"				Standard	NM_024539		Approved	FLJ23516, GRAIL	uc004eml.3	Q8TEB7	OTTHUMG00000022151	ENST00000255499.2:c.93G>A	chrX.hg19:g.105970236G>A		277.0	0.0		216.0	58.0	NM_194463	A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Silent	SNP	ENST00000255499.2	hg19	CCDS14521.1																																																																																			.	.		0.706	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539		A	105970236	G	A	105970236	2	1	81	1	0	0	0	0	0	0	0	1	13451	1074	38	1		1	RNF128	23	105970236	Silent	SNP	G	TCGA-CC-A8HV-01A-11D-A35Z-10	27753241	105970236	49300324	145	11194										
MAGEA11	4110	hgsc.bcm.edu	37	chrX	148798034	148798034	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	gtccttgtcacctccctcaaCctctcttatgatggcataca	5	15	3	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chrX:148798034C>G	ENST00000355220.5	+	5	990	c.888C>G	c.(886-888)aaC>aaG	p.N296K	MAGEA11_ENST00000333104.4_Missense_Mutation_p.N267K	NM_005366.4	NP_005357.2	P43364	MAGAB_HUMAN	melanoma antigen family A, 11	296	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	9	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					CCTCCCTCAACCTCTCTTATG	0.493																																					p.N296K		Atlas-SNP	.											.	MAGEA11	86	.	0			c.C888G						.						137	125	129					X																	148798034		2203	4300	6503	SO:0001583	missense	4110	exon5			CCTCAACCTCTCT		CCDS48180.1	Xq28	2009-03-13			ENSG00000185247	ENSG00000185247			6798	protein-coding gene	gene with protein product	"MAGE-11 antigen", "melanoma-associated antigen 11", "cancer/testis antigen family 1, member 11"	300344		MAGE11		8575766	Standard	NM_001011544		Approved	MAGE-11, MAGEA-11, MGC10511, CT1.11	uc004fdq.3	P43364	OTTHUMG00000022633	ENST00000355220.5:c.888C>G	chrX.hg19:g.148798034C>G	ENSP00000347358:p.Asn296Lys	332.0	0.0		211.0	40.0	NM_005366	Q5ETU4|Q6ZRZ5	Missense_Mutation	SNP	ENST00000355220.5	hg19	CCDS48180.1	.	.	.	.	.	.	.	.	.	.	N	4.673	0.125040	0.08931	.	.	ENSG00000185247	ENST00000412632;ENST00000333104;ENST00000355220	T;T;T	0.04275	3.66;3.66;3.66	0.762	0.762	0.18454	.	.	.	.	.	T	0.03520	0.0101	N	0.17082	0.46	0.09310	N	1	B;B	0.19817	0.004;0.039	B;B	0.25759	0.038;0.063	T	0.42799	-0.9430	8	0.51188	T	0.08	.	.	.	.	.	267;296	G5E962;P43364	.;MAGAB_HUMAN	K	267;267;296	ENSP00000391496:N267K;ENSP00000328177:N267K;ENSP00000347358:N296K	ENSP00000328177:N267K	N	+	3	2	MAGEA11	148576371	0.023000	0.18921	0.007000	0.13788	0.003000	0.03518	-0.148000	0.10219	0.635000	0.30488	0.377000	0.23210	AAC	.	.		0.493	MAGEA11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058725.4	NM_005366		G	148798034	C	G	148798034	3	3	81	1	0	0	0	0	1	0	0	0	9174	506	18	4	915	4	MAGEA11	23	148798034	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	42827798	148798034	6472526	146	11195										
TREX2	11219	hgsc.bcm.edu	37	chrX	152710779	152710779	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	10	1	1.19120489690722	1.34536082474227	1.13544636981794	0.245077461269365	0.896214637779148	0	ccgggttctccagggaggagCggtggacagcaaagagggac	18	9	1	1			TCGA-CC-A8HV-01A-11D-A35Z-10	TCGA-CC-A8HV-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0093c24-2b98-43fb-87bc-090fedcba21d	34604e11-7a84-4463-a0db-b90bf2ee82a5	g.chrX:152710779C>G	ENST00000334497.2	-	11	1380	c.239G>C	c.(238-240)cGc>cCc	p.R80P	TREX2_ENST00000330912.2_Missense_Mutation_p.R37P|TREX2_ENST00000393862.2_Missense_Mutation_p.R37P|TREX2_ENST00000414588.1_Missense_Mutation_p.R79P|TREX2_ENST00000370232.1_Missense_Mutation_p.R80P|TREX2_ENST00000370231.2_Missense_Mutation_p.R37P|TREX2_ENST00000338525.2_Missense_Mutation_p.R37P|TREX2_ENST00000402951.1_Missense_Mutation_p.R80P|HAUS7_ENST00000484394.1_5'Flank			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	80					DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)	nucleus (GO:0005634)	3'-5'-exodeoxyribonuclease activity (GO:0008296)|exodeoxyribonuclease III activity (GO:0008853)|magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)			endometrium(4)|large_intestine(2)|lung(3)|ovary(2)	11	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGGAGGAGCGGTGGACAGC	0.657								Editing and processing nucleases																													p.R37P		Atlas-SNP	.											.	TREX2	36	.	0			c.G110C						.						41	42	41					X																	152710779		2202	4299	6501	SO:0001583	missense	11219	exon2			GAGGAGCGGTGGA	AF151107	CCDS35437.1	Xq28	2012-05-08			ENSG00000183479	ENSG00000183479			12270	protein-coding gene	gene with protein product		300370				10391904	Standard	NM_080701		Approved		uc011myp.2	Q9BQ50	OTTHUMG00000159319	ENST00000334497.2:c.239G>C	chrX.hg19:g.152710779C>G	ENSP00000334993:p.Arg80Pro	323.0	1.0		200.0	93.0	NM_080701	Q45F08|Q9UN77	Missense_Mutation	SNP	ENST00000334497.2	hg19		.	.	.	.	.	.	.	.	.	.	C	14.47	2.545058	0.45280	.	.	ENSG00000183479	ENST00000393862;ENST00000330912;ENST00000338525;ENST00000334497;ENST00000370232;ENST00000402951;ENST00000414588;ENST00000370231	T;T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92	5.04	4.18	0.49190	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.572588	0.14640	U	0.307244	T	0.38852	0.1056	L	0.45137	1.4	0.32453	N	0.545107	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.48175	-0.9058	10	0.72032	D	0.01	0.6256	5.8999	0.18960	0.1883:0.7104:0.0:0.1013	.	79;80	Q06S70;Q9BQ50	.;TREX2_HUMAN	P	37;37;37;80;80;80;79;37	ENSP00000377442:R37P;ENSP00000333441:R37P;ENSP00000345218:R37P;ENSP00000334993:R80P;ENSP00000359252:R80P;ENSP00000386078:R80P;ENSP00000401692:R79P;ENSP00000359251:R37P	ENSP00000333441:R37P	R	-	2	0	TREX2	152363973	0.994000	0.37717	0.959000	0.39883	0.346000	0.29079	2.519000	0.45546	0.913000	0.36797	0.529000	0.55759	CGC	.	.		0.657	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701		G	152710779	C	G	152710779	3	3	81	1	0	0	0	0	1	0	0	0	16492	768	27	4	603	4	TREX2	23	152710779	Missense_Mutation	SNP	C	TCGA-CC-A8HV-01A-11D-A35Z-10	3912745	152710779	2559781	147	11196										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27097796	27097796	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	attccaagaagtcccagcccAagatccagcctccctctcct	5	18	1	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr1:27097796A>T	ENST00000324856.7	+	12	3756	c.3385A>T	c.(3385-3387)Aag>Tag	p.K1129*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.K746*|ARID1A_ENST00000540690.1_5'Flank|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.K1129*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1129					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GTCCCAGCCCAAGATCCAGCC	0.542			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.K1129X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.A3385T						.						50	47	48					1																	27097796		2203	4300	6503	SO:0001587	stop_gained	8289	exon12			CAGCCCAAGATCC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3385A>T	chr1.hg19:g.27097796A>T	ENSP00000320485:p.Lys1129*	121.0	0.0		78.0	27.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	43|43	9.927584|9.927584	0.99298|0.99298	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152|ENST00000430799	.|.	.|.	.|.	5.34|5.34	5.34|5.34	0.76211|0.76211	.|.	0.095193|.	0.85682|.	D|.	0.000000|.	.|T	.|0.71517	.|0.3349	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70880	.|-0.4752	.|4	0.02654|.	T|.	1|.	-13.2016|-13.2016	15.4712|15.4712	0.75441|0.75441	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	1129;1129;746|26	.|.	ENSP00000320485:K1129X|.	K|Q	+|+	1|2	0|0	ARID1A|ARID1A	26970383|26970383	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.065000|9.065000	0.93941|0.93941	2.246000|2.246000	0.74042|0.74042	0.482000|0.482000	0.46254|0.46254	AAG|CAA	.	.		0.542	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27097796	A	T	27097796	4	4	82	1	0	0	0	0	0	1	0	0	913	131	5	4	3431	4	ARID1A	1	27097796	Nonsense_Mutation	SNP	A	TCGA-CC-A9FS-01A-11D-A36X-10		27097796	222152825	1	11197										
C1orf177	163747	hgsc.bcm.edu	37	chr1	55279596	55279596	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	acttccccgaaacccgaaaaCccctacagagaggatttact	6	14	0	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr1:55279596C>T	ENST00000371273.3	+	7	887	c.872C>T	c.(871-873)aCc>aTc	p.T291I	C1orf177_ENST00000358193.3_Missense_Mutation_p.T291I	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	291										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						AACCCGAAAACCCCTACAGAG	0.512																																					p.T291I		Atlas-SNP	.											.	C1orf177	36	.	0			c.C872T						.						82	88	86					1																	55279596		2203	4300	6503	SO:0001583	missense	163747	exon7			CGAAAACCCCTAC	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.872C>T	chr1.hg19:g.55279596C>T	ENSP00000360320:p.Thr291Ile	222.0	0.0		186.0	79.0	NM_001110533	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	hg19	CCDS44153.1	.	.	.	.	.	.	.	.	.	.	C	0.319	-0.962807	0.02249	.	.	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.23552	1.9;1.9	4.98	0.634	0.17718	.	0.909170	0.09438	N	0.802222	T	0.15998	0.0385	L	0.38531	1.155	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.33548	-0.9864	10	0.21540	T	0.41	-1.4365	2.9818	0.05955	0.2034:0.4693:0.0:0.3273	.	291;291	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	I	291	ENSP00000350924:T291I;ENSP00000360320:T291I	ENSP00000350924:T291I	T	+	2	0	C1orf177	55052184	0.000000	0.05858	0.001000	0.08648	0.105000	0.19272	-0.041000	0.12084	0.262000	0.21774	-0.254000	0.11334	ACC	.	.		0.512	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607		T	55279596	C	T	55279596	3	4	82	1	0	0	0	0	1	0	0	0	2019	507	18	3	898	3	C1orf177	1	55279596	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	28181800	55279596	193971025	2	11198										
CLCA4	22802	hgsc.bcm.edu	37	chr1	87045742	87045742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ggaggccaactccaaggaaaGctttgcatttaaaccagaaa	9	9	0	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr1:87045742G>A	ENST00000370563.3	+	14	2516	c.2474G>A	c.(2473-2475)aGc>aAc	p.S825N	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	825					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		TCCAAGGAAAGCTTTGCATTT	0.338																																					p.S825N		Atlas-SNP	.											.	CLCA4	131	.	0			c.G2474A						.						67	59	62					1																	87045742		1824	4088	5912	SO:0001583	missense	22802	exon14			AGGAAAGCTTTGC	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"chloride channel, calcium activated, family member 4", "chloride channel regulator 4"			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2474G>A	chr1.hg19:g.87045742G>A	ENSP00000359594:p.Ser825Asn	205.0	0.0		166.0	64.0	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Missense_Mutation	SNP	ENST00000370563.3	hg19	CCDS41355.1	.	.	.	.	.	.	.	.	.	.	G	9.037	0.988681	0.18966	.	.	ENSG00000016602	ENST00000370563	T	0.02974	4.09	5.82	-7.28	0.01456	.	0.634996	0.16267	N	0.221984	T	0.00356	0.0011	N	0.10809	0.05	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.47381	-0.9122	10	0.20519	T	0.43	-0.0211	1.7568	0.02983	0.3695:0.2778:0.0774:0.2753	.	377;825	Q9NXP1;Q14CN2	.;CLCA4_HUMAN	N	825	ENSP00000359594:S825N	ENSP00000359594:S825N	S	+	2	0	CLCA4	86818330	0.000000	0.05858	0.310000	0.25168	0.905000	0.53344	-1.428000	0.02439	-0.669000	0.05289	-1.239000	0.01543	AGC	.	.		0.338	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128		A	87045742	G	A	87045742	3	1	82	1	0	0	0	0	1	0	0	0	3461	971	34	3	2528	3	CLCA4	1	87045742	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	31766146	87045742	162204879	3	11199										
DCAF6	55827	hgsc.bcm.edu	37	chr1	167971753	167971753	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cagttaagcgtttgagacttCgtggtgattggtcagatact	12	6	1	3			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr1:167971753C>T	ENST00000312263.6	+	8	1141	c.937C>T	c.(937-939)Cgt>Tgt	p.R313C	DCAF6_ENST00000367843.3_Missense_Mutation_p.R313C|DCAF6_ENST00000432587.2_Missense_Mutation_p.R282C|DCAF6_ENST00000367840.3_Missense_Mutation_p.R313C	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	313					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						TTTGAGACTTCGTGGTGATTG	0.403																																					p.R313C		Atlas-SNP	.											.	DCAF6	99	.	0			c.C937T						.						154	153	153					1																	167971753		2203	4300	6503	SO:0001583	missense	55827	exon8			AGACTTCGTGGTG	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.937C>T	chr1.hg19:g.167971753C>T	ENSP00000311949:p.Arg313Cys	131.0	0.0		145.0	97.0	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	hg19	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.174368	0.78452	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	D;T;D;D	0.88664	-2.28;-0.62;-2.26;-2.41	5.56	5.56	0.83823	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.92718	0.7685	M	0.74647	2.275	0.47245	D	0.999362	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79784	0.993;0.989;0.915;0.958	D	0.91966	0.5583	9	0.45353	T	0.12	.	14.6209	0.68584	0.1799:0.8201:0.0:0.0	.	282;313;313;313	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	C	313;282;313;313	ENSP00000356817:R313C;ENSP00000396238:R282C;ENSP00000311949:R313C;ENSP00000356814:R313C	ENSP00000311949:R313C	R	+	1	0	DCAF6	166238377	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.470000	0.45119	2.787000	0.95880	0.650000	0.86243	CGT	.	.		0.403	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		T	167971753	C	T	167971753	3	4	82	1	0	0	0	0	1	0	0	0	4276	884	31	1	967	1	DCAF6	1	167971753	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	80926011	167971753	81278868	4	11200										
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180885825	180885825	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aagccgaatggacacttcctGaccatgacagaggtccgctg	11	12	0	3			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr1:180885825G>T	ENST00000367588.4	+	2	641	c.586G>T	c.(586-588)Gac>Tac	p.D196Y		NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	196										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						GACACTTCCTGACCATGACAG	0.637																																					p.D196Y		Atlas-SNP	.											.	KIAA1614	75	.	0			c.G586T						.						67	72	70					1																	180885825		1903	4101	6004	SO:0001583	missense	57710	exon2			CTTCCTGACCATG	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.586G>T	chr1.hg19:g.180885825G>T	ENSP00000356560:p.Asp196Tyr	100.0	0.0		103.0	11.0	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	hg19	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	G	16.29	3.081693	0.55753	.	.	ENSG00000135835	ENST00000367588	T	0.07444	3.19	4.39	4.39	0.52855	.	1.097620	0.07136	N	0.846383	T	0.19167	0.0460	N	0.24115	0.695	0.28439	N	0.916919	D	0.89917	1.0	D	0.70016	0.967	T	0.19257	-1.0311	9	0.72032	D	0.01	-8.1746	14.0028	0.64444	0.0:0.0:1.0:0.0	.	196	Q5VZ46	K1614_HUMAN	Y	196	ENSP00000356560:D196Y	ENSP00000356560:D196Y	D	+	1	0	KIAA1614	179152448	0.078000	0.21339	0.027000	0.17364	0.001000	0.01503	2.036000	0.41165	2.268000	0.75426	0.563000	0.77884	GAC	.	.		0.637	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		T	180885825	G	T	180885825	3	4	82	1	0	0	0	0	1	0	0	0	8257	1290	45	3	592	3	KIAA1614	1	180885825	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	12914072	180885825	68364796	5	11201										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201012432	201012432	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gaaaacacatggctgttgctAtggttgctgttgccataggc	12	8	0	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr1:201012432A>G	ENST00000362061.3	-	40	5251	c.5025T>C	c.(5023-5025)caT>caC	p.H1675H	CACNA1S_ENST00000367338.3_Silent_p.H1656H|RP11-168O16.2_ENST00000415359.1_RNA	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1675					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GGCTGTTGCTATGGTTGCTGT	0.547											OREG0014067	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H1675H		Atlas-SNP	.											.	CACNA1S	249	.	0			c.T5025C						.						232	206	215					1																	201012432		2203	4300	6503	SO:0001819	synonymous_variant	779	exon40			GTTGCTATGGTTG	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.5025T>C	chr1.hg19:g.201012432A>G		115.0	0.0	2118	86.0	62.0	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	hg19	CCDS1407.1																																																																																			.	.		0.547	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		G	201012432	A	G	201012432	2	3	82	1	0	0	0	0	0	0	0	1	2549	446	16	2		2	CACNA1S	1	201012432	Silent	SNP	A	TCGA-CC-A9FS-01A-11D-A36X-10	20126607	201012432	48238189	6	11202										
TPO	7173	hgsc.bcm.edu	37	chr2	1481013	1481013	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gggttgacctcgttcctggaCgcgtccaccgtgtatggcag	14	12	0	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr2:1481013C>A	ENST00000345913.4	+	8	1066	c.975C>A	c.(973-975)gaC>gaA	p.D325E	TPO_ENST00000337415.3_Missense_Mutation_p.D325E|TPO_ENST00000346956.3_Missense_Mutation_p.D325E|TPO_ENST00000329066.4_Missense_Mutation_p.D325E|TPO_ENST00000349624.3_Intron|TPO_ENST00000497517.2_Intron|TPO_ENST00000382201.3_Missense_Mutation_p.D325E|TPO_ENST00000382198.1_Intron	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	325					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CGTTCCTGGACGCGTCCACCG	0.697																																					p.D325E		Atlas-SNP	.											TPO,colon,carcinoma,0,1	TPO	224	.	0			c.C975A						.						20	18	19					2																	1481013		2201	4290	6491	SO:0001583	missense	7173	exon8			CCTGGACGCGTCC		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.975C>A	chr2.hg19:g.1481013C>A	ENSP00000318820:p.Asp325Glu	1079.0	1.0		1074.0	395.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	C	18.71	3.682715	0.68157	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000536482;ENST00000329066;ENST00000382201;ENST00000422464	D;D;D;D;D;D	0.91945	-2.94;-2.94;-2.94;-2.94;-2.94;-2.94	4.99	0.445	0.16597	.	0.000000	0.85682	D	0.000000	D	0.96765	0.8944	H	0.98068	4.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.992;0.995;0.995	D	0.94537	0.7741	10	0.87932	D	0	-48.4892	7.413	0.27027	0.0:0.2715:0.0:0.7285	.	325;325;325	P07202-4;P07202-2;P07202	.;.;PERT_HUMAN	E	325;325;325;9;325;325;254	ENSP00000337263:D325E;ENSP00000318820:D325E;ENSP00000263886:D325E;ENSP00000329869:D325E;ENSP00000371636:D325E;ENSP00000405788:D254E	ENSP00000329869:D325E	D	+	3	2	TPO	1460020	0.994000	0.37717	0.986000	0.45419	0.757000	0.42996	0.295000	0.19065	0.152000	0.19188	0.460000	0.39030	GAC	.	.		0.697	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		A	1481013	C	A	1481013	3	1	82	1	0	0	0	0	1	0	0	0	16425	535	19	1	1001	1	TPO	2	1481013	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10		1481013	241718360	7	11203										
KLF11	8462	hgsc.bcm.edu	37	chr2	10192629	10192629	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tggtgagcatgccagcctctGcctgaaaggtccattaggac	12	11	1	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr2:10192629G>A	ENST00000305883.1	+	4	1696	c.1534G>A	c.(1534-1536)Gcc>Acc	p.A512T	KLF11_ENST00000535335.1_Missense_Mutation_p.A495T|KLF11_ENST00000540845.1_Missense_Mutation_p.A495T|RP11-254F7.3_ENST00000607181.1_RNA	NM_003597.4	NP_003588.1	O14901	KLF11_HUMAN	Kruppel-like factor 11	512					apoptotic process (GO:0006915)|cellular response to peptide (GO:1901653)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)		GCCAGCCTCTGCCTGAAAGGT	0.532																																					p.A512T	Melanoma(56;431 1507 23687 50789)	Atlas-SNP	.											.	KLF11	45	.	0			c.G1534A						.						22	23	23					2																	10192629		2202	4297	6499	SO:0001583	missense	8462	exon4			GCCTCTGCCTGAA	AF028008	CCDS1668.1, CCDS54333.1	2p25	2013-01-08	2004-11-29	2004-12-01	ENSG00000172059	ENSG00000172059		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11811	protein-coding gene	gene with protein product		603301	"TGFB inducible early growth response 2"	TIEG2		9748269, 11087666	Standard	NM_001177716		Approved	Tieg3, MODY7	uc002raf.1	O14901	OTTHUMG00000119004	ENST00000305883.1:c.1534G>A	chr2.hg19:g.10192629G>A	ENSP00000307023:p.Ala512Thr	99.0	0.0		79.0	42.0	NM_003597	B4DZE7|Q9EPF4	Missense_Mutation	SNP	ENST00000305883.1	hg19	CCDS1668.1	.	.	.	.	.	.	.	.	.	.	G	9.865	1.197419	0.22037	.	.	ENSG00000172059	ENST00000305883;ENST00000540845;ENST00000535335	T;T;T	0.14893	2.48;2.47;2.47	6.08	-0.256	0.12984	.	1.091710	0.06805	N	0.789414	T	0.10723	0.0262	N	0.19112	0.55	0.09310	N	1	B	0.17852	0.024	B	0.12156	0.007	T	0.36696	-0.9737	10	0.49607	T	0.09	.	5.3178	0.15864	0.1876:0.0:0.4756:0.3369	.	512	O14901	KLF11_HUMAN	T	512;495;495	ENSP00000307023:A512T;ENSP00000444690:A495T;ENSP00000442722:A495T	ENSP00000307023:A512T	A	+	1	0	KLF11	10110080	0.003000	0.15002	0.002000	0.10522	0.034000	0.12701	0.498000	0.22530	-0.084000	0.12595	-0.216000	0.12614	GCC	.	.		0.532	KLF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000239202.3	NM_003597		A	10192629	G	A	10192629	3	1	82	1	0	0	0	0	1	0	0	0	8348	1319	46	3	1548	3	KLF11	2	10192629	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	8711616	10192629	233006744	8	11204										
LOXL3	84695	hgsc.bcm.edu	37	chr2	74763931	74763931	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	caccactgcagggcccccccCagggcacctggcggtgtcat	12	18	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr2:74763931C>A	ENST00000264094.3	-	5	888	c.817G>T	c.(817-819)Ggg>Tgg	p.G273W	LOXL3_ENST00000409986.1_Intron|LOXL3_ENST00000409549.1_Missense_Mutation_p.G273W|LOXL3_ENST00000484369.1_5'Flank|LOXL3_ENST00000409249.1_Missense_Mutation_p.G273W|LOXL3_ENST00000393937.2_Intron	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	273	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						GGGCCCCCCCCAGGGCACCTG	0.647																																					p.G273W		Atlas-SNP	.											.	LOXL3	73	.	0			c.G817T						.						66	72	70					2																	74763931		2203	4300	6503	SO:0001583	missense	84695	exon5			CCCCCCCAGGGCA	AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.817G>T	chr2.hg19:g.74763931C>A	ENSP00000264094:p.Gly273Trp	115.0	0.0		122.0	49.0	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Missense_Mutation	SNP	ENST00000264094.3	hg19	CCDS1953.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.057719	0.76074	.	.	ENSG00000115318	ENST00000264094;ENST00000409249;ENST00000409549;ENST00000413469	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	4.63	4.63	0.57726	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.122525	0.53938	D	0.000041	T	0.61048	0.2316	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.973;0.996	T	0.64676	-0.6351	10	0.59425	D	0.04	.	15.3571	0.74434	0.0:1.0:0.0:0.0	.	273;273	E7END4;P58215	.;LOXL3_HUMAN	W	273	ENSP00000264094:G273W;ENSP00000387103:G273W;ENSP00000386696:G273W;ENSP00000398260:G273W	ENSP00000264094:G273W	G	-	1	0	LOXL3	74617439	0.060000	0.20803	1.000000	0.80357	0.969000	0.65631	2.467000	0.45093	2.573000	0.86826	0.563000	0.77884	GGG	.	.		0.647	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		A	74763931	C	A	74763931	3	1	82	1	0	0	0	0	1	0	0	0	8910	594	21	3	1484	3	LOXL3	2	74763931	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	64571302	74763931	168435442	9	11205										
NMS	129521	hgsc.bcm.edu	37	chr2	101096961	101096961	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gcctcatttccttgcagggcTcggggactgctgcagtggac	14	12	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr2:101096961T>C	ENST00000376865.1	+	7	347	c.340T>C	c.(340-342)Tcg>Ccg	p.S114P		NM_001011717.1	NP_001011717.1	Q5H8A3	NMS_HUMAN	neuromedin S	114					neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				breast(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)	14						CTTGCAGGGCTCGGGGACTGC	0.542																																					p.S114P		Atlas-SNP	.											.	NMS	26	.	0			c.T340C						.						121	114	117					2																	101096961		2203	4300	6503	SO:0001583	missense	129521	exon7			CAGGGCTCGGGGA	AB164464	CCDS33259.1	2q11.2	2013-02-26			ENSG00000204640	ENSG00000204640		"Endogenous ligands"	32203	protein-coding gene	gene with protein product	"prepro-NMS"					15635449	Standard	NM_001011717		Approved		uc002tan.1	Q5H8A3	OTTHUMG00000153142	ENST00000376865.1:c.340T>C	chr2.hg19:g.101096961T>C	ENSP00000366061:p.Ser114Pro	112.0	0.0		111.0	33.0	NM_001011717		Missense_Mutation	SNP	ENST00000376865.1	hg19	CCDS33259.1	.	.	.	.	.	.	.	.	.	.	T	7.473	0.647070	0.14516	.	.	ENSG00000204640	ENST00000376865	T	0.26223	1.75	3.53	-1.95	0.07548	.	0.603497	0.14808	N	0.297227	T	0.18467	0.0443	L	0.60455	1.87	0.09310	N	1	B	0.14805	0.011	B	0.11329	0.006	T	0.31166	-0.9953	10	0.72032	D	0.01	-0.1112	0.6718	0.00860	0.3494:0.1062:0.1802:0.3642	.	114	Q5H8A3	NMS_HUMAN	P	114	ENSP00000366061:S114P	ENSP00000366061:S114P	S	+	1	0	NMS	100463393	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.077000	0.11394	-0.353000	0.08224	-0.336000	0.08194	TCG	.	.		0.542	NMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329737.1	NM_001011717		C	101096961	T	C	101096961	3	2	82	1	0	0	0	0	1	0	0	0	10511	1551	54	2	366	2	NMS	2	101096961	Missense_Mutation	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10	26333030	101096961	142102412	10	11206										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167162425	167162425	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aagtatatattccagtaaaaGtgtacctaaacacaagattc	5	7	0	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr2:167162425G>T	ENST00000409435.1	-	4	472	c.473C>A	c.(472-474)aCt>aAt	p.T158N	SCN9A_ENST00000303354.6_Missense_Mutation_p.T159N|SCN9A_ENST00000409672.1_Missense_Mutation_p.T158N|SCN9A_ENST00000375387.4_Missense_Mutation_p.T159N			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	158					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCCAGTAAAAGTGTACCTAAA	0.358																																					p.T158N		Atlas-SNP	.											.	SCN9A	296	.	0			c.C473A						.						65	66	66					2																	167162425		1835	4090	5925	SO:0001583	missense	6335	exon5			GTAAAAGTGTACC	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.473C>A	chr2.hg19:g.167162425G>T	ENSP00000386330:p.Thr158Asn	241.0	0.0		269.0	79.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	g	33	5.251713	0.95336	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435;ENST00000454569;ENST00000452182	D;D;D;D;D;D	0.98633	-5.04;-5.04;-5.04;-5.04;-5.04;-5.04	5.85	5.85	0.93711	Ion transport (1);	0.000000	0.64402	D	0.000003	D	0.99396	0.9787	M	0.92970	3.365	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.87578	0.981;0.998;0.985	D	0.98869	1.0765	10	0.87932	D	0	.	20.168	0.98156	0.0:0.0:1.0:0.0	.	158;158;159	E7EUN6;Q15858;E9PF08	.;SCN9A_HUMAN;.	N	158;159;159;158;23;23	ENSP00000386306:T158N;ENSP00000364536:T159N;ENSP00000304748:T159N;ENSP00000386330:T158N;ENSP00000413212:T23N;ENSP00000393141:T23N	ENSP00000304748:T159N	T	-	2	0	SCN9A	166870671	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.001000	0.88508	2.761000	0.94854	0.650000	0.86243	ACT	.	.		0.358	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167162425	G	T	167162425	3	4	82	1	0	0	0	0	1	0	0	0	13940	1029	36	3	5552	3	SCN9A	2	167162425	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	66065464	167162425	76036948	11	11207										
XIRP2	129446	hgsc.bcm.edu	37	chr2	167760305	167760305	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aggattccctgagcagtcggCgcaggattgaacgcttttcc	12	11	0	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr2:167760305C>A	ENST00000409728.1	+	2	402	c.313C>A	c.(313-315)Cgc>Agc	p.R105S	XIRP2_ENST00000295237.9_Missense_Mutation_p.R105S|XIRP2_ENST00000420519.1_Missense_Mutation_p.R105S|XIRP2_ENST00000409043.1_Missense_Mutation_p.R105S|XIRP2_ENST00000409195.1_Missense_Mutation_p.R105S|XIRP2_ENST00000409756.2_Missense_Mutation_p.R105S	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.R105C(2)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GAGCAGTCGGCGCAGGATTGA	0.512																																					p.R105S		Atlas-SNP	.											XIRP2_ENST00000409728,NS,carcinoma,-1,2	XIRP2	914	.	2	Substitution - Missense(2)	large_intestine(2)	c.C313A						.						114	116	115					2																	167760305		2024	4159	6183	SO:0001583	missense	129446	exon2			AGTCGGCGCAGGA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.313C>A	chr2.hg19:g.167760305C>A	ENSP00000386619:p.Arg105Ser	233.0	0.0		207.0	82.0	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	hg19	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.678518	0.29783	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409195;ENST00000409756;ENST00000420519;ENST00000295237	D;D;T;D;D;T	0.82711	-1.63;-1.64;3.74;-1.63;-1.64;3.74	5.12	4.23	0.50019	.	.	.	.	.	D	0.88603	0.6481	.	.	.	0.29262	N	0.871235	D;D	0.76494	0.999;0.999	D;D	0.70935	0.961;0.971	T	0.82135	-0.0607	8	0.62326	D	0.03	-2.224	8.5532	0.33465	0.0:0.8965:0.0:0.1035	.	105;105	A4UGR9-4;A4UGR9-6	.;.	S	105	ENSP00000386454:R105S;ENSP00000386619:R105S;ENSP00000386840:R105S;ENSP00000386724:R105S;ENSP00000415541:R105S;ENSP00000295237:R105S	ENSP00000295237:R105S	R	+	1	0	XIRP2	167468551	0.964000	0.33143	0.939000	0.37840	0.218000	0.24690	1.551000	0.36233	2.390000	0.81377	0.655000	0.94253	CGC	.	.		0.512	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		A	167760305	C	A	167760305	3	1	82	1	0	0	0	0	1	0	0	0	17445	768	27	1	315	1	XIRP2	2	167760305	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	597880	167760305	75439068	12	11208										
TTN	7273	hgsc.bcm.edu	37	chr2	179600418	179600418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cccatctttgctccacgtaaCtgtgacttttctgtcttcat	5	13	4	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr2:179600418C>T	ENST00000591111.1	-	48	14028	c.13804G>A	c.(13804-13806)Gtt>Att	p.V4602I	TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V4919I|TTN_ENST00000342992.6_Missense_Mutation_p.V3675I|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	12354	Ig-like 26.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCCACGTAACTGTGACTTTT	0.408																																					p.V4919I		Atlas-SNP	.											.	TTN	18412	.	0			c.G14755A						.						96	91	92					2																	179600418		1873	4104	5977	SO:0001583	missense	7273	exon50			ACGTAACTGTGAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.13804G>A	chr2.hg19:g.179600418C>T	ENSP00000465570:p.Val4602Ile	101.0	0.0		86.0	37.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.62	1.400690	0.25291	.	.	ENSG00000155657	ENST00000342992	T	0.72282	-0.64	5.77	1.32	0.21799	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.58750	0.2144	L	0.35593	1.075	0.80722	D	1	B	0.06786	0.001	B	0.14023	0.01	T	0.55398	-0.8147	9	0.87932	D	0	.	11.4275	0.50020	0.0:0.7402:0.0:0.2598	.	4602	Q8WZ42	TITIN_HUMAN	I	3675	ENSP00000343764:V3675I	ENSP00000343764:V3675I	V	-	1	0	TTN	179308663	0.160000	0.22878	0.411000	0.26484	0.959000	0.62525	0.441000	0.21611	0.268000	0.21939	0.655000	0.94253	GTT	.	.		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179600418	C	T	179600418	3	4	82	1	0	0	0	0	1	0	0	0	16750	565	20	3	90026	3	TTN	2	179600418	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	11840113	179600418	63598955	13	11209										
GPR1	2825	hgsc.bcm.edu	37	chr2	207041060	207041060	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aacttcttactaattaggacAtaaaggatggggttcaagca	9	6	2	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr2:207041060A>G	ENST00000407325.2	-	3	1274	c.912T>C	c.(910-912)taT>taC	p.Y304Y	GPR1_ENST00000437420.1_Silent_p.Y304Y	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	304					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		TAATTAGGACATAAAGGATGG	0.488																																					p.Y304Y		Atlas-SNP	.											.	GPR1	38	.	0			c.T912C						.						105	103	104					2																	207041060		2203	4300	6503	SO:0001819	synonymous_variant	2825	exon3			TAGGACATAAAGG		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"GPCR / Class A : Orphans"	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.912T>C	chr2.hg19:g.207041060A>G		134.0	0.0		132.0	49.0	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Silent	SNP	ENST00000407325.2	hg19	CCDS2368.1																																																																																			.	.		0.488	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199		G	207041060	A	G	207041060	2	3	82	1	0	0	0	0	0	0	0	1	6629	224	8	2		2	GPR1	2	207041060	Silent	SNP	A	TCGA-CC-A9FS-01A-11D-A36X-10	27440642	207041060	36158313	14	11210										
FN1	2335	hgsc.bcm.edu	37	chr2	216248812	216248813	+	Frame_Shift_Ins	INS	-	-	A													0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cggccagtgacagcatacacINSagtgatggtataatcaactc					rs200252728		TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr2:216248812_216248813insA	ENST00000359671.1	-	29	4816_4817	c.4551_4552insT	c.(4549-4554)actgtgfs	p.V1518fs	FN1_ENST00000356005.4_Frame_Shift_Ins_p.V1518fs|FN1_ENST00000354785.4_Frame_Shift_Ins_p.V1609fs|FN1_ENST00000323926.6_Frame_Shift_Ins_p.V1609fs|FN1_ENST00000432072.2_Frame_Shift_Ins_p.V1609fs|FN1_ENST00000490833.1_5'Flank|FN1_ENST00000336916.4_Frame_Shift_Ins_p.V1518fs|FN1_ENST00000346544.3_Frame_Shift_Ins_p.V1518fs|FN1_ENST00000357009.2_Frame_Shift_Ins_p.V1518fs|FN1_ENST00000421182.1_Frame_Shift_Ins_p.V1518fs|FN1_ENST00000345488.5_Frame_Shift_Ins_p.V1518fs|FN1_ENST00000357867.4_Frame_Shift_Ins_p.V1518fs|FN1_ENST00000446046.1_Frame_Shift_Ins_p.V1518fs|FN1_ENST00000443816.1_Frame_Shift_Ins_p.V1518fs			P02751	FINC_HUMAN	fibronectin 1	1518	Cell-attachment.|Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	ACAGCATACACAGTGATGGTAT	0.51																																					p.V1609fs		Atlas-Indel,Pindel	.											.	FN1	521	.	0			c.4825_4826insT						.																																			SO:0001589	frameshift_variant	2335	exon30			.		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.4552dupT	chr2.hg19:g.216248813_216248813dupA	ENSP00000352696:p.Val1518fs	110.0	0.0		118.0	34.0	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Frame_Shift_Ins	INS	ENST00000359671.1	hg19																																																																																				.	.		0.51	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		A	216248813	-	A	216248812	7	5	82	1	0	1	1	0	0	0	0	0	5970	478	17	0	2676	0	FN1	2	216248812	Frame_Shift_Ins	INS	-	TCGA-CC-A9FS-01A-11D-A36X-10	9207752	216248812	26950561	15	11211										
IL17RE	132014	hgsc.bcm.edu	37	chr3	9957185	9957185	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	agcggcgccgaccttcgcccGgtcagcggccccgacccccg	13	21	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr3:9957185G>A	ENST00000383814.3	+	16	1803	c.1698G>A	c.(1696-1698)ccG>ccA	p.P566P	IL17RC_ENST00000413608.1_5'Flank|IL17RE_ENST00000421412.1_Silent_p.P599P|IL17RC_ENST00000416074.2_5'Flank|IL17RE_ENST00000295980.3_Silent_p.P566P|IL17RC_ENST00000295981.3_5'Flank|IL17RC_ENST00000383812.4_5'Flank|IL17RE_ENST00000454190.2_3'UTR|IL17RC_ENST00000403601.3_5'Flank|IL17RC_ENST00000455057.1_5'Flank	NM_153480.1	NP_705613.1	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E	566	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(11)|skin(1)	21				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		ACCTTCGCCCGGTCAGCGgcc	0.781																																					p.P606P		Atlas-SNP	.											.	IL17RE	62	.	0			c.G1818A						.						1	1	1					3																	9957185		734	1589	2323	SO:0001819	synonymous_variant	132014	exon17			TCGCCCGGTCAGC	AF458069	CCDS2589.1, CCDS54552.1	3p25.3	2008-02-05			ENSG00000163701	ENSG00000163701		"Interleukins and interleukin receptors"	18439	protein-coding gene	gene with protein product		614995					Standard	NM_153480		Approved	FLJ23658	uc003btu.3	Q8NFR9	OTTHUMG00000128649	ENST00000383814.3:c.1698G>A	chr3.hg19:g.9957185G>A		0.0	0.0		5.0	4.0	NM_153483	B2RB34|B2RNR1|B9EH65|Q6P532|Q8N8H7|Q8N8H8|Q8TEC2	Silent	SNP	ENST00000383814.3	hg19	CCDS2589.1																																																																																			.	.		0.781	IL17RE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250529.1	NM_153480		A	9957185	G	A	9957185	2	1	82	1	0	0	0	0	0	0	0	1	7652	1103	39	1		1	IL17RE	3	9957185	Silent	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10		9957185	188065245	16	11212										
TATDN2	9797	hgsc.bcm.edu	37	chr3	10291105	10291105	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gaggttatcctggggctcatCccgccgcagaaataactcct	10	13	1	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr3:10291105C>T	ENST00000287652.4	+	2	1272	c.221C>T	c.(220-222)tCc>tTc	p.S74F	TATDN2_ENST00000448281.2_Missense_Mutation_p.S74F|RP11-438J1.1_ENST00000450534.1_Missense_Mutation_p.S17F	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	74					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						TGGGGCTCATCCCGCCGCAGA	0.637																																					p.S74F		Atlas-SNP	.											.	TATDN2	59	.	0			c.C221T						.						66	82	77					3																	10291105		2201	4297	6498	SO:0001583	missense	9797	exon2			GCTCATCCCGCCG	D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.221C>T	chr3.hg19:g.10291105C>T	ENSP00000287652:p.Ser74Phe	233.0	0.0		227.0	91.0	NM_014760	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	hg19	CCDS33698.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.045281	0.55110	.	.	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.26067	1.76;1.76	4.16	2.32	0.28847	.	.	.	.	.	T	0.23289	0.0563	L	0.54323	1.7	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.21280	-1.0250	9	0.52906	T	0.07	-4.1582	6.9762	0.24677	0.0:0.7834:0.0:0.2166	.	74	Q93075	TATD2_HUMAN	F	74	ENSP00000287652:S74F;ENSP00000408736:S74F	ENSP00000287652:S74F	S	+	2	0	TATDN2	10266105	0.000000	0.05858	0.058000	0.19502	0.834000	0.47266	0.218000	0.17622	0.484000	0.27630	0.563000	0.77884	TCC	.	.		0.637	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		T	10291105	C	T	10291105	3	4	82	1	0	0	0	0	1	0	0	0	15607	855	30	3	223	3	TATDN2	3	10291105	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	333920	10291105	187731325	17	11213										
CLEC3B	7123	hgsc.bcm.edu	37	chr3	45077310	45077310	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	caccgcgcaacccgatggcgGcaagaccgagaactgcgcgg	14	15	0	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr3:45077310G>T	ENST00000296130.4	+	3	683	c.503G>T	c.(502-504)gGc>gTc	p.G168V	RNU5B-3P_ENST00000516601.1_RNA|CLEC3B_ENST00000428034.1_Missense_Mutation_p.G126V|CLEC3B_ENST00000490386.1_3'UTR	NM_003278.2	NP_003269.2	P05452	TETN_HUMAN	C-type lectin domain family 3, member B	168	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				bone mineralization (GO:0030282)|cellular response to organic substance (GO:0071310)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ossification (GO:0001503)|positive regulation of plasminogen activation (GO:0010756)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)|kringle domain binding (GO:0036143)			endometrium(1)|lung(3)	4				BRCA - Breast invasive adenocarcinoma(193;0.00863)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)	Tenecteplase(DB00031)	CCCGATGGCGGCAAGACCGAG	0.652																																					p.G168V	GBM(139;1487 3263 30871)	Atlas-SNP	.											.	CLEC3B	15	.	0			c.G503T						.						39	41	40					3																	45077310		2202	4296	6498	SO:0001583	missense	7123	exon3			ATGGCGGCAAGAC		CCDS2726.1	3p22-p21.3	2010-04-27	2005-02-09	2005-02-09	ENSG00000163815	ENSG00000163815		"C-type lectin domain containing"	11891	protein-coding gene	gene with protein product		187520	"tetranectin (plasminogen binding protein)"	TNA			Standard	NM_003278		Approved	TN	uc003cok.4	P05452	OTTHUMG00000133087	ENST00000296130.4:c.503G>T	chr3.hg19:g.45077310G>T	ENSP00000296130:p.Gly168Val	183.0	0.0		149.0	49.0	NM_003278	Q6FGX6	Missense_Mutation	SNP	ENST00000296130.4	hg19	CCDS2726.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.576324	0.45902	.	.	ENSG00000163815	ENST00000296130;ENST00000428034	T;T	0.19938	2.11;2.11	4.38	3.49	0.39957	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.055195	0.64402	D	0.000001	T	0.51822	0.1697	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.61907	-0.6966	10	0.59425	D	0.04	-23.3689	14.4498	0.67376	0.0:0.1488:0.8512:0.0	.	168	P05452	TETN_HUMAN	V	168;126	ENSP00000296130:G168V;ENSP00000396013:G126V	ENSP00000296130:G168V	G	+	2	0	CLEC3B	45052314	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	6.108000	0.71522	0.939000	0.37446	-0.305000	0.09177	GGC	.	.		0.652	CLEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256745.1	NM_003278		T	45077310	G	T	45077310	3	4	82	1	0	0	0	0	1	0	0	0	3513	1203	42	3	513	3	CLEC3B	3	45077310	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	34786205	45077310	152945120	18	11214										
RBM15B	29890	hgsc.bcm.edu	37	chr3	51430282	51430282	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ttgggtggaccagaccgcagGctccgcgtggattttgccaa	14	11	0	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr3:51430282G>T	ENST00000323686.4	+	1	1552	c.1452G>T	c.(1450-1452)agG>agT	p.R484S		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	484	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CAGACCGCAGGCTCCGCGTGG	0.562																																					p.R484S		Atlas-SNP	.											.	RBM15B	47	.	0			c.G1452T						.						55	59	57					3																	51430282		2203	4300	6503	SO:0001583	missense	29890	exon1			CCGCAGGCTCCGC	AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"RNA binding motif (RRM) containing"	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.1452G>T	chr3.hg19:g.51430282G>T	ENSP00000313890:p.Arg484Ser	56.0	0.0		45.0	11.0	NM_013286	A4QPG7|Q6QE19|Q9BV96	Missense_Mutation	SNP	ENST00000323686.4	hg19	CCDS33764.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.464469	0.63513	.	.	ENSG00000179837	ENST00000323686;ENST00000541145	T	0.06142	3.34	5.55	3.78	0.43462	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	.	.	.	.	T	0.15825	0.0381	L	0.47716	1.5	0.58432	D	0.999999	D	0.65815	0.995	D	0.67548	0.952	T	0.00305	-1.1831	9	0.66056	D	0.02	-25.1014	10.2649	0.43449	0.2665:0.0:0.7335:0.0	.	484	Q8NDT2	RB15B_HUMAN	S	484;157	ENSP00000313890:R484S	ENSP00000313890:R484S	R	+	3	2	RBM15B	51405322	0.996000	0.38824	1.000000	0.80357	0.996000	0.88848	0.287000	0.18920	0.721000	0.32231	-0.136000	0.14681	AGG	.	.		0.562	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286		T	51430282	G	T	51430282	3	4	82	1	0	0	0	0	1	0	0	0	13132	1194	42	3	1454	3	RBM15B	3	51430282	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	6352972	51430282	146592148	19	11215										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89156962	89156962	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ttctcgacagcttcggggaaCtgattccgcagccttccaat	9	13	1	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr3:89156962C>A	ENST00000336596.2	+	1	289	c.64C>A	c.(64-66)Ctg>Atg	p.L22M	EPHA3_ENST00000452448.2_Missense_Mutation_p.L22M|EPHA3_ENST00000494014.1_Missense_Mutation_p.L22M	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	22					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CTTCGGGGAACTGATTCCGCA	0.587										TSP Lung(6;0.00050)																											p.L22M		Atlas-SNP	.											.	EPHA3	501	.	0			c.C64A						.						145	113	124					3																	89156962		2203	4300	6503	SO:0001583	missense	2042	exon1			GGGGAACTGATTC	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.64C>A	chr3.hg19:g.89156962C>A	ENSP00000337451:p.Leu22Met	82.0	0.0		66.0	26.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.981746	0.34942	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.73047	-0.69;2.76;-0.71	5.46	1.49	0.22878	.	0.193191	0.35646	N	0.003062	T	0.52869	0.1761	N	0.24115	0.695	0.34559	D	0.712159	B;P	0.40794	0.38;0.729	B;B	0.41946	0.135;0.371	T	0.56153	-0.8026	9	.	.	.	.	6.8658	0.24093	0.1203:0.5811:0.2326:0.066	.	22;22	P29320;P29320-2	EPHA3_HUMAN;.	M	22	ENSP00000337451:L22M;ENSP00000399926:L22M;ENSP00000419190:L22M	.	L	+	1	2	EPHA3	89239652	1.000000	0.71417	0.992000	0.48379	0.155000	0.21991	1.126000	0.31344	0.245000	0.21373	-0.467000	0.05162	CTG	.	.		0.587	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		A	89156962	C	A	89156962	3	1	82	1	0	0	0	0	1	0	0	0	5170	564	20	3	66	3	EPHA3	3	89156962	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	37726680	89156962	108865468	20	11216										
ILDR1	286676	hgsc.bcm.edu	37	chr3	121724154	121724154	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cacgggctcattctgcccccGccgctgggccactatgcgaa	11	17	2	0	rs200029008		TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr3:121724154G>A	ENST00000344209.5	-	3	442	c.316C>T	c.(316-318)Cgg>Tgg	p.R106W	ILDR1_ENST00000273691.3_Missense_Mutation_p.R106W|ILDR1_ENST00000393631.1_Missense_Mutation_p.R106W|ILDR1_ENST00000462014.1_Missense_Mutation_p.R118W|ILDR1_ENST00000460554.1_5'UTR	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	106	Ig-like V-type.				positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		TTCTGCCCCCGCCGCTGGGCC	0.627																																					p.R106W		Atlas-SNP	.											.	ILDR1	120	.	0			c.C316T						.						44	44	44					3																	121724154		2203	4300	6503	SO:0001583	missense	286676	exon3			GCCCCCGCCGCTG	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"deafness, autosomal recessive 42"	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.316C>T	chr3.hg19:g.121724154G>A	ENSP00000345667:p.Arg106Trp	115.0	0.0		105.0	37.0	NM_175924	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	hg19	CCDS56271.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.975973	0.74360	.	.	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000393631;ENST00000462014	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.63	4.74	0.60224	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.097924	0.64402	D	0.000002	T	0.68274	0.2983	L	0.57536	1.79	0.54753	D	0.999989	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.987;0.994;0.994	T	0.71490	-0.4577	10	0.72032	D	0.01	-33.643	13.8564	0.63529	0.0:0.0:0.846:0.154	.	106;106;106;118	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	W	106;106;106;118	ENSP00000273691:R106W;ENSP00000345667:R106W;ENSP00000377251:R106W;ENSP00000419414:R118W	ENSP00000273691:R106W	R	-	1	2	ILDR1	123206844	0.866000	0.29940	0.950000	0.38849	0.814000	0.46013	1.920000	0.40025	1.464000	0.47987	0.563000	0.77884	CGG	.	G|0.999;A|0.001		0.627	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924		A	121724154	G	A	121724154	3	1	82	1	0	0	0	0	1	0	0	0	7718	1086	38	1	1212	1	ILDR1	3	121724154	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	32567192	121724154	76298276	21	11217										
ATR	545	hgsc.bcm.edu	37	chr3	142279231	142279231	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	attcaagggaaatctgaaggGattcagctttctgtttcagt	10	6	5	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr3:142279231G>C	ENST00000350721.4	-	6	1536	c.1415C>G	c.(1414-1416)tCc>tGc	p.S472C	ATR_ENST00000383101.3_Intron	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	472					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						AATCTGAAGGGATTCAGCTTT	0.353								Other conserved DNA damage response genes																													p.S472C		Atlas-SNP	.											.	ATR	285	.	0			c.C1415G						.						172	173	173					3																	142279231		2203	4300	6503	SO:0001583	missense	545	exon6			TGAAGGGATTCAG	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.1415C>G	chr3.hg19:g.142279231G>C	ENSP00000343741:p.Ser472Cys	204.0	0.0		136.0	54.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.085421	0.55861	.	.	ENSG00000175054	ENST00000350721	T	0.03772	3.81	5.71	2.82	0.32997	Armadillo-type fold (1);	0.509864	0.21286	N	0.077064	T	0.04227	0.0117	L	0.34521	1.04	0.80722	D	1	P	0.44344	0.833	B	0.39185	0.293	T	0.49133	-0.8971	10	0.87932	D	0	0.4881	7.2793	0.26302	0.1511:0.0:0.7124:0.1365	.	472	Q13535	ATR_HUMAN	C	472	ENSP00000343741:S472C	ENSP00000343741:S472C	S	-	2	0	ATR	143761921	1.000000	0.71417	0.817000	0.32601	0.998000	0.95712	3.156000	0.50708	0.287000	0.22375	0.585000	0.79938	TCC	.	.		0.353	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		C	142279231	G	C	142279231	3	2	82	1	0	0	0	0	1	0	0	0	1204	1174	41	4	6687	4	ATR	3	142279231	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	20555077	142279231	55743199	22	11218										
SGEF	26084	hgsc.bcm.edu	37	chr3	153943788	153943788	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aacgatgtgctcattatcacCaagaagaagaggtaagtctt	9	7	3	3			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr3:153943788C>T	ENST00000356448.4	+	11	2363	c.2079C>T	c.(2077-2079)acC>acT	p.T693T	ARHGEF26_ENST00000465817.1_Intron|ARHGEF26_ENST00000465093.1_Silent_p.T693T|ARHGEF26_ENST00000483068.1_3'UTR	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	693	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						TCATTATCACCAAGAAGAAGA	0.388																																					p.T693T	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.C2079T						.						82	72	75					3																	153943788		1884	4109	5993	SO:0001819	synonymous_variant	26084	exon11			TATCACCAAGAAG	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.2079C>T	chr3.hg19:g.153943788C>T		132.0	0.0		101.0	30.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Silent	SNP	ENST00000356448.4	hg19	CCDS46938.1																																																																																			.	.		0.388	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		T	153943788	C	T	153943788	2	4	82	1	0	0	0	0	0	0	0	1	14220	581	21	3		3	SGEF	3	153943788	Silent	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	11664557	153943788	44078642	23	11219										
OPA1	4976	hgsc.bcm.edu	37	chr3	193384162	193384162	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gcaaatactttaaggcaacaActtacaaatactgaaggtaa	6	7	0	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr3:193384162A>G	ENST00000392438.3	+	26	2925	c.2691A>G	c.(2689-2691)caA>caG	p.Q897Q	OPA1_ENST00000361510.2_Silent_p.Q952Q|OPA1_ENST00000361150.2_Silent_p.Q898Q|OPA1_ENST00000361908.3_Silent_p.Q934Q|OPA1_ENST00000361828.2_Silent_p.Q915Q|OPA1_ENST00000361715.2_Silent_p.Q916Q	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	897					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		TAAGGCAACAACTTACAAATA	0.343																																					p.Q952Q		Atlas-SNP	.											.	OPA1	79	.	0			c.A2856G						.						125	116	119					3																	193384162		2203	4300	6503	SO:0001819	synonymous_variant	4976	exon28			GCAACAACTTACA	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.2691A>G	chr3.hg19:g.193384162A>G		143.0	0.0		114.0	45.0	NM_130837	D3DNW4	Silent	SNP	ENST00000392438.3	hg19	CCDS43186.1																																																																																			.	.		0.343	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		G	193384162	A	G	193384162	2	3	82	1	0	0	0	0	0	0	0	1	10880	40	2	2		2	OPA1	3	193384162	Silent	SNP	A	TCGA-CC-A9FS-01A-11D-A36X-10	39440374	193384162	4638268	24	11220										
ZNF732	654254	hgsc.bcm.edu	37	chr4	265712	265712	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ggacctattaaagactttgcCacattcctgacatttgtaga	7	9	0	3			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr4:265712C>G	ENST00000419098.1	-	4	944	c.934G>C	c.(934-936)Ggc>Cgc	p.G312R		NM_001137608.1	NP_001131080.1	B4DXR9	ZN732_HUMAN	zinc finger protein 732	312					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)	3						AAGACTTTGCCACATTCCTGA	0.383																																					p.G311R		Atlas-SNP	.											.	ZNF732	117	.	0			c.G931C						.						70	66	67					4																	265712		692	1591	2283	SO:0001583	missense	654254	exon3			CTTTGCCACATTC	AK302099	CCDS46990.1	4p16.3	2014-02-12	2009-07-22		ENSG00000186777	ENSG00000186777		"Zinc fingers, C2H2-type", "-"	37138	protein-coding gene	gene with protein product							Standard	NM_001137608		Approved	FLJ59067	uc011buu.1	B4DXR9	OTTHUMG00000159883	ENST00000419098.1:c.934G>C	chr4.hg19:g.265712C>G	ENSP00000415774:p.Gly312Arg	98.0	0.0		74.0	26.0	NM_001137608		Missense_Mutation	SNP	ENST00000419098.1	hg19	CCDS46990.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.163831	0.38217	.	.	ENSG00000186777	ENST00000419098	T	0.01484	4.84	0.977	0.977	0.19733	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08447	0.0210	M	0.80746	2.51	0.31811	N	0.627117	D	0.89917	1.0	D	0.91635	0.999	T	0.04454	-1.0950	9	0.72032	D	0.01	.	7.3306	0.26580	0.0:1.0:0.0:0.0	.	312	B4DXR9	ZN732_HUMAN	R	312	ENSP00000415774:G312R	ENSP00000415774:G312R	G	-	1	0	ZNF732	255712	1.000000	0.71417	0.102000	0.21198	0.094000	0.18550	3.564000	0.53791	0.399000	0.25367	0.400000	0.26472	GGC	.	.		0.383	ZNF732-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357937.2	NM_001137608		G	265712	C	G	265712	3	3	82	1	0	0	0	0	1	0	0	0	18138	594	21	4	827	4	ZNF732	4	265712	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10		265712	190888564	25	11221										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13605490	13605490	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	atctgacaactttctctcaaGcctggtggaagtggagtctt	10	9	4	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr4:13605490G>A	ENST00000040738.5	-	10	3169	c.3034C>T	c.(3034-3036)Ctt>Ttt	p.L1012F		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1012	Lys-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)										TTTCTCTCAAGCCTGGTGGAA	0.383																																					p.L1012F		Atlas-SNP	.											.	.	.	.	0			c.C3034T						.						234	251	245					4																	13605490		2202	4300	6502	SO:0001583	missense	259282	exon10			TCTCAAGCCTGGT	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.3034C>T	chr4.hg19:g.13605490G>A	ENSP00000040738:p.Leu1012Phe	92.0	0.0		89.0	8.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	11.46	1.646714	0.29246	.	.	ENSG00000038219	ENST00000040738	T	0.13538	2.58	5.1	4.19	0.49359	.	0.168276	0.28706	N	0.014407	T	0.26376	0.0644	L	0.53249	1.67	0.23120	N	0.998265	D	0.58268	0.982	P	0.55824	0.785	T	0.02365	-1.1170	10	0.52906	T	0.07	-3.9775	15.3079	0.74008	0.0:0.1404:0.8596:0.0	.	1012	Q8NFC6	BOD1L_HUMAN	F	1012	ENSP00000040738:L1012F	ENSP00000040738:L1012F	L	-	1	0	BOD1L	13214588	0.981000	0.34729	0.110000	0.21437	0.195000	0.23768	1.541000	0.36126	2.534000	0.85438	0.555000	0.69702	CTT	.	.		0.383	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13605490	G	A	13605490	3	1	82	1	0	0	0	0	1	0	0	0	1483	971	34	3	6189	3	BOD1L	4	13605490	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	13339778	13605490	177548786	26	11222										
OCIAD2	132299	hgsc.bcm.edu	37	chr4	48894859	48894859	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	atggaatttactctggcataCtcctatgtatgatacctttc	6	9	1	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr4:48894859C>T	ENST00000508632.1	-	6	545	c.313G>A	c.(313-315)Gta>Ata	p.V105I	OCIAD2_ENST00000508069.2_5'UTR|OCIAD2_ENST00000273860.4_Intron	NM_001014446.1	NP_001014446.1	Q56VL3	OCAD2_HUMAN	OCIA domain containing 2	105	OCIA.					endosome (GO:0005768)|mitochondrial inner membrane (GO:0005743)				kidney(1)|lung(3)|skin(1)|urinary_tract(1)	6						CTCTGGCATACTCCTATGTAT	0.413																																					p.V105I		Atlas-SNP	.											.	OCIAD2	16	.	0			c.G313A						.						136	141	139					4																	48894859		2203	4300	6503	SO:0001583	missense	132299	exon6			GGCATACTCCTAT	BC032808	CCDS3485.1, CCDS33981.1	4p12	2013-10-11			ENSG00000145247	ENSG00000145247			28685	protein-coding gene	gene with protein product						17054434	Standard	NM_001286774		Approved	MGC45416	uc003gyt.3	Q56VL3	OTTHUMG00000128626	ENST00000508632.1:c.313G>A	chr4.hg19:g.48894859C>T	ENSP00000423014:p.Val105Ile	452.0	0.0		408.0	167.0	NM_001014446	B4DPE7|Q8N544	Missense_Mutation	SNP	ENST00000508632.1	hg19	CCDS33981.1	.	.	.	.	.	.	.	.	.	.	C	10.90	1.481291	0.26598	.	.	ENSG00000145247	ENST00000508632	T	0.43688	0.94	4.76	4.76	0.60689	.	0.326941	0.27659	N	0.018388	T	0.27278	0.0669	N	0.14661	0.345	0.80722	D	1	B	0.26935	0.164	B	0.31191	0.125	T	0.07481	-1.0770	9	.	.	.	-3.3541	13.4643	0.61245	0.0:1.0:0.0:0.0	.	105	Q56VL3	OCAD2_HUMAN	I	105	ENSP00000423014:V105I	.	V	-	1	0	OCIAD2	48589616	0.637000	0.27216	0.103000	0.21229	0.426000	0.31534	1.028000	0.30128	2.649000	0.89929	0.650000	0.86243	GTA	.	.		0.413	OCIAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361984.5	NM_152398		T	48894859	C	T	48894859	3	4	82	1	0	0	0	0	1	0	0	0	10827	565	20	3	159	3	OCIAD2	4	48894859	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	35289369	48894859	142259417	27	11223										
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119952156	119952156	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ctcagcttgggggcagaggcTtgtaatttcatgcaaagctc	12	9	2	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr4:119952156T>A	ENST00000429713.2	+	4	2408	c.2226T>A	c.(2224-2226)gcT>gcA	p.A742A	SYNPO2_ENST00000434046.2_Silent_p.A742A|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Silent_p.A742A	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	742						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GGGCAGAGGCTTGTAATTTCA	0.517																																					p.A742A		Atlas-SNP	.											.	SYNPO2	353	.	0			c.T2226A						.						74	82	80					4																	119952156		2203	4300	6503	SO:0001819	synonymous_variant	171024	exon4			AGAGGCTTGTAAT	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.2226T>A	chr4.hg19:g.119952156T>A		143.0	0.0		93.0	47.0	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Silent	SNP	ENST00000429713.2	hg19	CCDS47129.1	.	.	.	.	.	.	.	.	.	.	T	7.638	0.680352	0.14907	.	.	ENSG00000172403	ENST00000504178	.	.	.	5.41	-3.3	0.05003	.	.	.	.	.	T	0.47544	0.1451	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41142	-0.9525	4	.	.	.	-16.7542	5.0415	0.14462	0.2268:0.363:0.0:0.4102	.	.	.	.	M	694	.	.	L	+	1	2	SYNPO2	120171604	0.967000	0.33354	0.827000	0.32855	0.882000	0.50991	0.015000	0.13355	-0.551000	0.06175	-0.290000	0.09829	TTG	.	.		0.517	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			A	119952156	T	A	119952156	2	1	82	1	0	0	0	0	0	0	0	1	15472	1596	56	4		4	SYNPO2	4	119952156	Silent	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10	71057297	119952156	71202120	28	11224										
GYPE	2996	hgsc.bcm.edu	37	chr4	144801586	144801586	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tttgtctgtgatgagatgtaActctttgtgactgaagaaga	11	4	2	6			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr4:144801586A>G	ENST00000358615.4	-	2	165	c.114T>C	c.(112-114)agT>agC	p.S38S	GYPE_ENST00000437468.2_Silent_p.S38S	NM_198682.2	NP_941391.2	P15421	GLPE_HUMAN	glycophorin E (MNS blood group)	38						integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_hematologic(180;0.158)					ATGAGATGTAACTCTTTGTGA	0.373																																					p.S38S		Atlas-SNP	.											.	GYPE	21	.	0			c.T114C						.						169	183	178					4																	144801586		2203	4298	6501	SO:0001819	synonymous_variant	2996	exon2			GATGTAACTCTTT		CCDS47138.1	4q31.21	2010-01-19	2010-01-19		ENSG00000197465	ENSG00000197465		"Blood group antigens"	4705	protein-coding gene	gene with protein product		138590	"glycophorin E"				Standard	NM_198682		Approved	GPE, MNS	uc003ijj.3	P15421	OTTHUMG00000161402	ENST00000358615.4:c.114T>C	chr4.hg19:g.144801586A>G		525.0	0.0		330.0	32.0	NM_198682	D3DNZ5	Silent	SNP	ENST00000358615.4	hg19	CCDS47138.1																																																																																			.	.		0.373	GYPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364780.1	NM_002102		G	144801586	A	G	144801586	2	3	82	1	0	0	0	0	0	0	0	1	6920	40	2	2		2	GYPE	4	144801586	Silent	SNP	A	TCGA-CC-A9FS-01A-11D-A36X-10	24849430	144801586	46352690	29	11225										
RASA1	5921	hgsc.bcm.edu	37	chr5	86564557	86564577	+	In_Frame_Del	DEL	GGTGCTGCTGCTGGCGTGGCC	GGTGCTGCTGCTGGCGTGGCC	-													0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gtactgctgctggcgtagctGgtgctgctgctggcgtggcc					rs115606026|rs111840875	byFrequency	TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	GGTGCTGCTGCTGGCGTGGCC	GGTGCTGCTGCTGGCGTGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr5:86564557_86564577delGGTGCTGCTGCTGGCGTGGCC	ENST00000274376.6	+	1	853_873	c.289_309delGGTGCTGCTGCTGGCGTGGCC	c.(289-309)ggtgctgctgctggcgtggccdel	p.GAAAGVA97del	RASA1_ENST00000456692.2_5'Flank|RASA1_ENST00000506290.1_5'Flank|RASA1_ENST00000512763.1_5'Flank	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	97					blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.A99_A106delAAGVAGAA(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		tggcgtagctggtgctgctgctggcgtggccggtgctgctg	0.652																																					p.96_103del		Atlas-Indel,Pindel	.											.	RASA1	213	.	1	Deletion - In frame(1)	large_intestine(1)	c.288_308del						.																																			SO:0001651	inframe_deletion	5921	exon1			.		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.289_309delGGTGCTGCTGCTGGCGTGGCC	chr5.hg19:g.86564557_86564577delGGTGCTGCTGCTGGCGTGGCC	ENSP00000274376:p.Gly97_Ala103del	89.0	0.0		89.0	21.0	NM_002890	B2R6W3|Q9UDI1	In_Frame_Del	DEL	ENST00000274376.6	hg19	CCDS34200.1																																																																																			.	.		0.652	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		-	86564577	GGTGCTGCTGCTGGCGTGGCC	-	86564557	7	5	82	1	0	1	0	1	0	0	0	0	13075	1348	47	0	291	0	RASA1	5	86564557	In_Frame_Del	DEL	GGTGCTGCTGCTGGCGTGGCC	TCGA-CC-A9FS-01A-11D-A36X-10		86564557	94350703	30	11226										
PCDHGA2	56113	hgsc.bcm.edu	37	chr5	140720901	140720901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ccaggagagctgtgagaaaaAggattttttatcagcgcctc	11	8	1	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr5:140720901A>G	ENST00000394576.2	+	1	2363	c.2363A>G	c.(2362-2364)aAg>aGg	p.K788R	PCDHGA3_ENST00000253812.6_5'Flank|PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	788					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTGAGAAAAAGGATTTTTTA	0.478																																					p.K788R		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.A2363G						.						89	96	93					5																	140720901		2203	4300	6503	SO:0001583	missense	56113	exon1			AGAAAAAGGATTT	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"Cadherins / Protocadherins : Clustered"	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.2363A>G	chr5.hg19:g.140720901A>G	ENSP00000378077:p.Lys788Arg	336.0	0.0		281.0	26.0	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	hg19	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	9.307	1.054594	0.19907	.	.	ENSG00000081853	ENST00000394576	T	0.49432	0.78	4.56	0.736	0.18307	.	0.394621	0.17653	U	0.166607	T	0.34890	0.0913	L	0.54323	1.7	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.13407	0.008;0.009	T	0.28839	-1.0031	10	0.46703	T	0.11	.	1.6275	0.02726	0.4657:0.2548:0.1554:0.124	.	788;788	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	R	788	ENSP00000378077:K788R	ENSP00000378077:K788R	K	+	2	0	PCDHGA2	140701085	0.362000	0.24980	0.886000	0.34754	0.831000	0.47069	0.002000	0.13061	0.043000	0.15746	0.402000	0.26972	AAG	.	.		0.478	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		G	140720901	A	G	140720901	3	3	82	1	0	0	0	0	1	0	0	0	11563	72	3	2	2365	2	PCDHGA2	5	140720901	Missense_Mutation	SNP	A	TCGA-CC-A9FS-01A-11D-A36X-10	54156344	140720901	40194359	31	11227										
FAT2	2196	hgsc.bcm.edu	37	chr5	150886785	150886785	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tgggaagggaccgcagctggCgggagtctggggggcacact	20	9	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr5:150886785C>T	ENST00000261800.5	-	22	12459	c.12447G>A	c.(12445-12447)ccG>ccA	p.P4149P	CTC-251D13.1_ENST00000606930.1_RNA	NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	4149					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCGCAGCTGGCGGGAGTCTGG	0.562																																					p.P4149P		Atlas-SNP	.											.	FAT2	465	.	0			c.G12447A						.						91	97	95					5																	150886785		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon22			AGCTGGCGGGAGT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.12447G>A	chr5.hg19:g.150886785C>T		89.0	0.0		71.0	28.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	0.043	-1.276884	0.01410	.	.	ENSG00000086570	ENST00000520200	.	.	.	4.75	-9.49	0.00587	.	.	.	.	.	T	0.47002	0.1422	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56001	-0.8051	4	.	.	.	.	8.7785	0.34776	0.0:0.3505:0.2423:0.4072	.	.	.	.	T	922	.	.	A	-	1	0	FAT2	150866978	0.006000	0.16342	0.295000	0.24960	0.009000	0.06853	-2.669000	0.00845	-1.938000	0.01046	-1.740000	0.00687	GCC	.	.		0.562	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150886785	C	T	150886785	2	4	82	1	0	0	0	0	0	0	0	1	5698	755	27	1		1	FAT2	5	150886785	Silent	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	10165884	150886785	30028475	32	11228										
FAM50B	26240	hgsc.bcm.edu	37	chr6	3850894	3850894	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ctcagcgacgccaccatggaGaaggacgagtcgcacgcggg	15	13	1	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr6:3850894G>A	ENST00000380274.1	+	1	1275	c.849G>A	c.(847-849)gaG>gaA	p.E283E	FAM50B_ENST00000380272.3_Silent_p.E283E			Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	283						nucleus (GO:0005634)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(3)|urinary_tract(3)	17	Ovarian(93;0.0925)	all_hematologic(90;0.108)				CCACCATGGAGAAGGACGAGT	0.637																																					p.E283E		Atlas-SNP	.											.	FAM50B	44	.	0			c.G849A						.						73	60	65					6																	3850894		2203	4300	6503	SO:0001819	synonymous_variant	26240	exon2			CATGGAGAAGGAC	Y18504	CCDS4487.1	6p25.2	2008-05-15			ENSG00000145945	ENSG00000145945			18789	protein-coding gene	gene with protein product		614686				10534398	Standard	NM_012135		Approved	D6S2654E, X5L	uc003mvu.3	Q9Y247	OTTHUMG00000014147	ENST00000380274.1:c.849G>A	chr6.hg19:g.3850894G>A		128.0	0.0		90.0	20.0	NM_012135	Q5T2L6	Silent	SNP	ENST00000380274.1	hg19	CCDS4487.1																																																																																			.	.		0.637	FAM50B-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039693.1	NM_012135		A	3850894	G	A	3850894	2	1	82	1	0	0	0	0	0	0	0	1	5586	933	33	3		3	FAM50B	6	3850894	Silent	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10		3850894	167264173	33	11229										
HIST1H3H	8357	hgsc.bcm.edu	37	chr6	27777979	27777979	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	caagaagccccatcgctatcGgcctggtacagtggctctcc	10	15	1	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr6:27777979G>A	ENST00000369163.2	+	1	138	c.128G>A	c.(127-129)cGg>cAg	p.R43Q	HIST1H2BL_ENST00000377401.2_5'Flank	NM_003536.2	NP_003527.1	P68431	H31_HUMAN	histone cluster 1, H3h	43					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			haematopoietic_and_lymphoid_tissue(1)|lung(4)|ovary(2)|upper_aerodigestive_tract(3)	10						CATCGCTATCGGCCTGGTACA	0.647																																					p.R43Q		Atlas-SNP	.											.	HIST1H3H	25	.	0			c.G128A						.						46	48	47					6																	27777979		2203	4300	6503	SO:0001583	missense	8357	exon1			GCTATCGGCCTGG	Z83735	CCDS4627.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000203813	ENSG00000278828		"Histones / Replication-dependent"	4775	protein-coding gene	gene with protein product		602818	"H3 histone family, member K", "histone 1, H3h"	H3FK		9439656, 12408966	Standard	NM_003536		Approved	H3/k, H3F1K	uc003njm.3	P68431	OTTHUMG00000014483	ENST00000369163.2:c.128G>A	chr6.hg19:g.27777979G>A	ENSP00000358160:p.Arg43Gln	138.0	0.0		121.0	48.0	NM_003536	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000369163.2	hg19	CCDS4627.1	.	.	.	.	.	.	.	.	.	.	.	15.73	2.918896	0.52546	.	.	ENSG00000203813	ENST00000369163	T	0.49432	0.78	4.33	4.33	0.51752	.	.	.	.	.	T	0.55986	0.1955	.	.	.	0.35348	D	0.787116	.	.	.	.	.	.	T	0.64101	-0.6486	6	0.87932	D	0	.	16.683	0.85297	0.0:0.0:1.0:0.0	.	.	.	.	Q	43	ENSP00000358160:R43Q	ENSP00000358160:R43Q	R	+	2	0	HIST1H3H	27885958	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	7.483000	0.81158	2.329000	0.79093	0.655000	0.94253	CGG	.	.		0.647	HIST1H3H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040151.1	NM_003536		A	27777979	G	A	27777979	3	1	82	1	0	0	0	0	1	0	0	0	7171	1116	39	1	130	1	HIST1H3H	6	27777979	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	23927085	27777979	143337088	34	11230										
CFB	629	hgsc.bcm.edu	37	chr6	31915209	31915209	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tgaagacagcgtcacctaccActgcagccgggggcttaccc	11	15	1	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr6:31915209A>C	ENST00000425368.2	+	4	1082	c.569A>C	c.(568-570)cAc>cCc	p.H190P	CFB_ENST00000477310.1_Missense_Mutation_p.H541P|CFB_ENST00000556679.1_Missense_Mutation_p.H692P|CFB_ENST00000456570.1_Missense_Mutation_p.H692P	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	190	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						GTCACCTACCACTGCAGCCGG	0.632																																					p.H190P		Atlas-SNP	.											.	CFB	33	.	0			c.A569C						.						112	112	112					6																	31915209		1510	2707	4217	SO:0001583	missense	629	exon4			CCTACCACTGCAG	L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"Complement system"	1037	protein-coding gene	gene with protein product		138470	"B-factor, properdin"	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.569A>C	chr6.hg19:g.31915209A>C	ENSP00000416561:p.His190Pro	88.0	0.0		77.0	32.0	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	hg19	CCDS4729.1	.	.	.	.	.	.	.	.	.	.	A	16.58	3.164165	0.57476	.	.	ENSG00000243649;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000556679;ENST00000425368;ENST00000456570;ENST00000477310	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	4.93	3.74	0.42951	Complement control module (2);Sushi/SCR/CCP (3);	0.631464	0.14107	N	0.340986	T	0.48677	0.1513	M	0.72118	2.19	0.29267	N	0.870918	P;B;P	0.44734	0.805;0.324;0.842	P;B;B	0.48189	0.57;0.397;0.377	T	0.44590	-0.9318	10	0.38643	T	0.18	-7.7263	5.545	0.17059	0.646:0.1806:0.0:0.1734	.	692;190;190	B4E1Z4;P00751;P00751-2	.;CFAB_HUMAN;.	P	692;190;692;541	ENSP00000451848:H692P;ENSP00000416561:H190P;ENSP00000410815:H692P;ENSP00000418996:H541P	ENSP00000416561:H190P	H	+	2	0	CFB;XXbac-BPG116M5.17	32023188	0.185000	0.23213	0.998000	0.56505	0.817000	0.46193	0.972000	0.29409	0.876000	0.35872	0.533000	0.62120	CAC	.	.		0.632	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		C	31915209	A	C	31915209	3	2	82	1	0	0	0	0	1	0	0	0	3280	159	6	5	583	5	CFB	6	31915209	Missense_Mutation	SNP	A	TCGA-CC-A9FS-01A-11D-A36X-10	4137230	31915209	139199858	35	11231										
KLHDC3	116138	hgsc.bcm.edu	37	chr6	42988468	42988468	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cccatcgtctcctcccatggGtaggaggaagtttctgccac	10	14	2	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr6:42988468G>T	ENST00000326974.4	+	11	1341	c.1146G>T	c.(1144-1146)ggG>ggT	p.G382G	RRP36_ENST00000244496.5_5'Flank|KLHDC3_ENST00000244670.8_Silent_p.G248G|KLHDC3_ENST00000332245.8_Silent_p.G323G	NM_057161.3	NP_476502.1	Q9BQ90	KLDC3_HUMAN	kelch domain containing 3	382					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|reciprocal meiotic recombination (GO:0007131)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)	chromatin binding (GO:0003682)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CCTCCCATGGGTAGGAGGAAG	0.567																																					p.G382G		Atlas-SNP	.											.	KLHDC3	23	.	0			c.G1146T						.						129	107	114					6																	42988468		2203	4300	6503	SO:0001819	synonymous_variant	116138	exon11			CCATGGGTAGGAG	AB055925	CCDS4880.1	6p21.1	2003-06-12			ENSG00000124702	ENSG00000124702			20704	protein-coding gene	gene with protein product		611248				12444059, 12606021	Standard	NM_057161		Approved	PEAS, hPeas, dJ20C7.3	uc003otl.3	Q9BQ90	OTTHUMG00000014714	ENST00000326974.4:c.1146G>T	chr6.hg19:g.42988468G>T		88.0	0.0		74.0	25.0	NM_057161	A8K2W9	Silent	SNP	ENST00000326974.4	hg19	CCDS4880.1																																																																																			.	.		0.567	KLHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040570.1	NM_057161		T	42988468	G	T	42988468	2	4	82	1	0	0	0	0	0	0	0	1	8366	1248	44	3		3	KLHDC3	6	42988468	Silent	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	11073259	42988468	128126599	36	11232										
MACC1	346389	hgsc.bcm.edu	37	chr7	20198211	20198211	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	taccattctttcactttggaCtgaccaatagcttttacctt	4	11	2	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr7:20198211C>T	ENST00000400331.5	-	5	2081	c.1773G>A	c.(1771-1773)caG>caA	p.Q591Q	MACC1_ENST00000332878.4_Silent_p.Q591Q|MACC1_ENST00000589011.1_Silent_p.Q591Q	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	591	SH3.				positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						TCACTTTGGACTGACCAATAG	0.403																																					p.Q591Q		Atlas-SNP	.											.	MACC1	99	.	0			c.G1773A						.						169	166	167					7																	20198211		2203	4300	6503	SO:0001819	synonymous_variant	346389	exon5			TTTGGACTGACCA		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.1773G>A	chr7.hg19:g.20198211C>T		105.0	0.0		91.0	13.0	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Silent	SNP	ENST00000400331.5	hg19	CCDS5369.1																																																																																			.	.		0.403	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		T	20198211	C	T	20198211	2	4	82	1	0	0	0	0	0	0	0	1	9152	564	20	3		3	MACC1	7	20198211	Silent	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10		20198211	138940452	37	11233										
HOXA13	3209	hgsc.bcm.edu	37	chr7	27239233	27239233	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tctgcgccgctgccgagcagGggctgcattgcttggcggcc	16	14	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr7:27239233G>C	ENST00000222753.4	-	1	492	c.464C>G	c.(463-465)cCc>cGc	p.P155R	HOTTIP_ENST00000421733.1_RNA|HOTTIP_ENST00000472494.1_RNA|HOTTIP_ENST00000521028.2_RNA|HOTTIP_ENST00000605136.1_RNA	NM_000522.4	NP_000513.2	P31271	HXA13_HUMAN	homeobox A13	155					artery morphogenesis (GO:0048844)|branching involved in prostate gland morphogenesis (GO:0060442)|embryonic forelimb morphogenesis (GO:0035115)|endothelial cell fate specification (GO:0060847)|endothelial cell morphogenesis (GO:0001886)|inner ear development (GO:0048839)|male genitalia development (GO:0030539)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of BMP signaling pathway (GO:0030510)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|ventricular septum development (GO:0003281)	intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	6						TGCCGAGCAGGGGCTGCATTG	0.801			T	NUP98	AML																																p.P155R		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3209	homeo box A13		L	.	HOXA13	25	.	0			c.C464G						.						1	1	1					7																	27239233		986	2182	3168	SO:0001583	missense	3209	exon1			GAGCAGGGGCTGC		CCDS5412.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106031	ENSG00000106031		"Homeoboxes / ANTP class : HOXL subclass"	5102	protein-coding gene	gene with protein product		142959	"homeo box A13"	HOX1J, HOX1		1973146, 1358459	Standard	NM_000522		Approved		uc003szb.1	P31271	OTTHUMG00000023438	ENST00000222753.4:c.464C>G	chr7.hg19:g.27239233G>C	ENSP00000222753:p.Pro155Arg	250.0	0.0		247.0	101.0	NM_000522	A4D188|O43371	Missense_Mutation	SNP	ENST00000222753.4	hg19	CCDS5412.1	.	.	.	.	.	.	.	.	.	.	g	15.85	2.956238	0.53293	.	.	ENSG00000106031	ENST00000222753	T	0.63913	-0.07	3.33	3.33	0.38152	.	0.063753	0.64402	U	0.000005	T	0.68604	0.3019	M	0.77313	2.365	0.46149	D	0.99889	D	0.55172	0.97	P	0.47864	0.559	T	0.76558	-0.2915	10	0.62326	D	0.03	.	15.0423	0.71799	0.0:0.0:1.0:0.0	.	155	P31271	HXA13_HUMAN	R	155	ENSP00000222753:P155R	ENSP00000222753:P155R	P	-	2	0	HOXA13	27205758	1.000000	0.71417	0.986000	0.45419	0.816000	0.46133	5.279000	0.65597	1.584000	0.49913	0.450000	0.29827	CCC	.	.		0.801	HOXA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358752.3			C	27239233	G	C	27239233	3	2	82	1	0	0	0	0	1	0	0	0	7300	1232	43	4	710	4	HOXA13	7	27239233	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	7041022	27239233	131899430	38	11234										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48313700	48313700	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gtacttactacagtctttgaAaaagagaagaaacctaaatt	6	6	1	3			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr7:48313700A>T	ENST00000435803.1	+	17	4461	c.4437A>T	c.(4435-4437)gaA>gaT	p.E1479D		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1479					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CAGTCTTTGAAAAAGAGAAGA	0.289																																					p.E1479D		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A4437T						.						23	24	23					7																	48313700		1798	4036	5834	SO:0001583	missense	154664	exon17			CTTTGAAAAAGAG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4437A>T	chr7.hg19:g.48313700A>T	ENSP00000411096:p.Glu1479Asp	273.0	0.0		239.0	98.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	11.65	1.701108	0.30142	.	.	ENSG00000179869	ENST00000435803	D	0.91407	-2.84	5.44	2.99	0.34606	.	0.265429	0.26478	N	0.024147	D	0.85066	0.5612	L	0.55481	1.735	0.80722	D	1	B	0.15719	0.014	B	0.15484	0.013	T	0.74822	-0.3534	9	.	.	.	.	5.7675	0.18235	0.7725:0.0:0.0795:0.1479	.	1479	Q86UQ4	ABCAD_HUMAN	D	1479	ENSP00000411096:E1479D	.	E	+	3	2	ABCA13	48284246	0.895000	0.30542	0.979000	0.43373	0.480000	0.33159	0.098000	0.15189	0.411000	0.25702	-0.376000	0.06991	GAA	.	.		0.289	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48313700	A	T	48313700	3	4	82	1	0	0	0	0	1	0	0	0	31	11	1	4	4332	4	ABCA13	7	48313700	Missense_Mutation	SNP	A	TCGA-CC-A9FS-01A-11D-A36X-10	21074467	48313700	110824963	39	11235										
MUC17	140453	hgsc.bcm.edu	37	chr7	100677098	100677098	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ccagcatgccaatctcaactCctagtgaaggaagtccttta	7	12	1	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr7:100677098C>A	ENST00000306151.4	+	3	2465	c.2401C>A	c.(2401-2403)Cct>Act	p.P801T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	801	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AATCTCAACTCCTAGTGAAGG	0.468																																					p.P801T		Atlas-SNP	.											.	MUC17	804	.	0			c.C2401A						.						280	286	284					7																	100677098		2203	4300	6503	SO:0001583	missense	140453	exon3			TCAACTCCTAGTG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.2401C>A	chr7.hg19:g.100677098C>A	ENSP00000302716:p.Pro801Thr	84.0	0.0		82.0	7.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	0.483	-0.878777	0.02550	.	.	ENSG00000169876	ENST00000306151	T	0.03212	4.01	1.08	-2.17	0.07059	.	.	.	.	.	T	0.01976	0.0062	L	0.27053	0.805	0.09310	N	1	B	0.20459	0.045	B	0.13407	0.009	T	0.48525	-0.9028	9	0.07325	T	0.83	.	2.4611	0.04541	0.4826:0.3166:0.0:0.2008	.	801	Q685J3	MUC17_HUMAN	T	801	ENSP00000302716:P801T	ENSP00000302716:P801T	P	+	1	0	MUC17	100463818	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-4.807000	0.00183	-0.613000	0.05694	0.134000	0.15878	CCT	.	.		0.468	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100677098	C	A	100677098	3	1	82	1	0	0	0	0	1	0	0	0	9983	855	30	3	2411	3	MUC17	7	100677098	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	52363398	100677098	58461565	40	11236										
CADPS2	93664	hgsc.bcm.edu	37	chr7	122033326	122033326	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aagattaagaggcagacttgGaacttttggaagagctacat	11	5	0	4			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr7:122033326G>T	ENST00000449022.2	-	22	2951	c.2932C>A	c.(2932-2934)Cca>Aca	p.P978T	RP5-1101C3.1_ENST00000593910.1_RNA|CADPS2_ENST00000313070.7_Intron|RP5-1101C3.1_ENST00000591140.1_RNA|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000334010.7_Missense_Mutation_p.P976T	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	978	Interaction with DRD2.|MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						GGCAGACTTGGAACTTTTGGA	0.428																																					p.P982T		Atlas-SNP	.											.	CADPS2	116	.	0			c.C2944A						.						109	106	107					7																	122033326		1945	4146	6091	SO:0001583	missense	93664	exon22			GACTTGGAACTTT		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.2932C>A	chr7.hg19:g.122033326G>T	ENSP00000398481:p.Pro978Thr	222.0	0.0		209.0	11.0	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	hg19	CCDS55158.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.83|13.83	2.354333|2.354333	0.41700|0.41700	.|.	.|.	ENSG00000081803|ENSG00000081803	ENST00000462699|ENST00000360097;ENST00000334010;ENST00000420900;ENST00000449022	.|T;T	.|0.28069	.|1.63;1.63	5.63|5.63	2.59|2.59	0.31030|0.31030	.|Munc13 homology 1 (1);	.|0.123889	.|0.56097	.|D	.|0.000038	T|T	0.26774|0.26774	0.0655|0.0655	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|B;B	.|0.26081	.|0.043;0.141	.|B;B	.|0.31016	.|0.077;0.123	T|T	0.04635|0.04635	-1.0937|-1.0937	5|10	.|0.15066	.|T	.|0.55	-4.3754|-4.3754	17.9093|17.9093	0.88929|0.88929	0.0:0.4547:0.5453:0.0|0.0:0.4547:0.5453:0.0	.|.	.|982;978	.|B7ZM57;Q86UW7	.|.;CAPS2_HUMAN	L|T	171|151;976;983;978	.|ENSP00000333940:P976T;ENSP00000398481:P978T	.|ENSP00000333940:P976T	F|P	-|-	3|1	2|0	CADPS2|CADPS2	121820562|121820562	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.459000|4.459000	0.60102|0.60102	0.799000|0.799000	0.34018|0.34018	0.655000|0.655000	0.94253|0.94253	TTC|CCA	.	.		0.428	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		T	122033326	G	T	122033326	3	4	82	1	0	0	0	0	1	0	0	0	2573	1174	41	3	1013	3	CADPS2	7	122033326	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	21356228	122033326	37105337	41	11237										
TAS2R38	5726	hgsc.bcm.edu	37	chr7	141673088	141673088	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gagatcttcctggagacccaGcttgccaagcagatcaggaa	11	11	2	3			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr7:141673088G>A	ENST00000547270.1	-	1	485	c.402C>T	c.(400-402)agC>agT	p.S134S		NM_176817.4	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	134					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			NS(2)|breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)|stomach(1)	21	Melanoma(164;0.0171)					TGGAGACCCAGCTTGCCAAGC	0.517																																					p.S134S		Atlas-SNP	.											.	TAS2R38	51	.	0			c.C402T						.						46	43	44					7																	141673088		2203	4300	6503	SO:0001819	synonymous_variant	5726	exon1			GACCCAGCTTGCC	AF494231	CCDS34765.1	7q34	2012-10-03	2003-05-29	2003-05-30	ENSG00000257138	ENSG00000257138		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	9584	protein-coding gene	gene with protein product		607751	"phenylthiocarbamide tasting"	PTC		12624758, 12584440	Standard	NM_176817		Approved	T2R61	uc003vwx.1	P59533	OTTHUMG00000158374	ENST00000547270.1:c.402C>T	chr7.hg19:g.141673088G>A		137.0	0.0		120.0	37.0	NM_176817	A4D1U6|P59552|Q2M3E8|Q645W3|Q86UK3	Silent	SNP	ENST00000547270.1	hg19	CCDS34765.1																																																																																			.	.		0.517	TAS2R38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350810.2	NM_176817		A	141673088	G	A	141673088	2	1	82	1	0	0	0	0	0	0	0	1	15590	962	34	3		3	TAS2R38	7	141673088	Silent	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	19639762	141673088	17465575	42	11238										
PRSS55	203074	hgsc.bcm.edu	37	chr8	10396245	10396245	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cccagagccaggcagccccaGatcctggctcctgctctgtc	10	18	1	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr8:10396245G>A	ENST00000328655.3	+	5	1041	c.1001G>A	c.(1000-1002)aGa>aAa	p.R334K	PRSS55_ENST00000522210.1_Intron|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	334						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						GGCAGCCCCAGATCCTGGCTC	0.522																																					p.R334K		Atlas-SNP	.											.	PRSS55	67	.	0			c.G1001A						.						98	110	106					8																	10396245		2203	4300	6503	SO:0001583	missense	203074	exon5			GCCCCAGATCCTG	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.1001G>A	chr8.hg19:g.10396245G>A	ENSP00000333003:p.Arg334Lys	123.0	0.0		94.0	15.0	NM_198464	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	hg19	CCDS5976.1	.	.	.	.	.	.	.	.	.	.	G	9.479	1.097580	0.20552	.	.	ENSG00000184647	ENST00000328655	D	0.87809	-2.3	3.29	-1.36	0.09085	.	0.596206	0.12735	N	0.443488	T	0.72598	0.3480	L	0.27053	0.805	0.09310	N	1	B	0.15141	0.012	B	0.06405	0.002	T	0.54629	-0.8265	10	0.14656	T	0.56	.	4.8992	0.13766	0.228:0.4323:0.3397:0.0	.	334	Q6UWB4	PRS55_HUMAN	K	334	ENSP00000333003:R334K	ENSP00000333003:R334K	R	+	2	0	PRSS55	10433655	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.142000	0.10311	-0.291000	0.09012	-0.150000	0.13652	AGA	.	.		0.522	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		A	10396245	G	A	10396245	3	1	82	1	0	0	0	0	1	0	0	0	12646	942	33	3	1019	3	PRSS55	8	10396245	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10		10396245	135967777	43	11239										
XKR4	114786	hgsc.bcm.edu	37	chr8	56436289	56436289	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aggctccccagattgcagacGcatttgccattccagcgctg	10	14	0	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr8:56436289G>T	ENST00000327381.6	+	3	1556	c.1456G>T	c.(1456-1458)Gca>Tca	p.A486S	RP11-628E19.2_ENST00000522918.1_RNA	NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	486						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GATTGCAGACGCATTTGCCAT	0.463																																					p.A486S		Atlas-SNP	.											XKR4,NS,carcinoma,0,1	XKR4	104	.	0			c.G1456T						.						108	97	101					8																	56436289		2203	4300	6503	SO:0001583	missense	114786	exon3			GCAGACGCATTTG	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 4"				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.1456G>T	chr8.hg19:g.56436289G>T	ENSP00000328326:p.Ala486Ser	83.0	1.0		195.0	19.0	NM_052898	Q96PZ8	Missense_Mutation	SNP	ENST00000327381.6	hg19	CCDS34893.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.301318	0.40694	.	.	ENSG00000206579	ENST00000327381;ENST00000543752	T	0.62639	0.01	5.85	4.97	0.65823	.	0.047732	0.85682	D	0.000000	T	0.61173	0.2326	N	0.16130	0.375	0.58432	D	0.999999	D	0.69078	0.997	D	0.65233	0.933	T	0.59316	-0.7477	10	0.21540	T	0.41	-8.849	14.5127	0.67800	0.0696:0.0:0.9304:0.0	.	486	Q5GH76	XKR4_HUMAN	S	486	ENSP00000328326:A486S	ENSP00000328326:A486S	A	+	1	0	XKR4	56598843	1.000000	0.71417	0.412000	0.26496	0.744000	0.42396	9.869000	0.99810	1.477000	0.48234	0.655000	0.94253	GCA	.	.		0.463	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		T	56436289	G	T	56436289	3	4	82	1	0	0	0	0	1	0	0	0	17448	1087	38	1	1466	1	XKR4	8	56436289	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	46040044	56436289	89927733	44	11240										
TEK	7010	hgsc.bcm.edu	37	chr9	27228299	27228299	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aaacagaatgttagaggagcGaaaggtaagtattaaagtca	11	3	1	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr9:27228299G>A	ENST00000380036.4	+	22	3738	c.3296G>A	c.(3295-3297)cGa>cAa	p.R1099Q	TEK_ENST00000406359.4_Missense_Mutation_p.R1056Q|TEK_ENST00000519097.1_Missense_Mutation_p.R951Q	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	1099					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	TTAGAGGAGCGAAAGGTAAGT	0.408																																					p.R1099Q		Atlas-SNP	.											.	TEK	250	.	0			c.G3296A						.						88	89	89					9																	27228299		2203	4300	6503	SO:0001583	missense	7010	exon22			AGGAGCGAAAGGT	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.3296G>A	chr9.hg19:g.27228299G>A	ENSP00000369375:p.Arg1099Gln	53.0	0.0		52.0	21.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	G	35	5.491223	0.96339	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359	T;T;T	0.69175	-0.38;-0.38;-0.38	5.81	5.81	0.92471	Protein kinase-like domain (1);	0.000000	0.42053	D	0.000766	T	0.72890	0.3517	L	0.27053	0.805	0.58432	D	0.999996	D;D;D	0.89917	0.995;1.0;0.995	P;D;P	0.63703	0.823;0.917;0.823	T	0.74780	-0.3549	10	0.62326	D	0.03	.	19.6728	0.95916	0.0:0.0:1.0:0.0	.	951;1132;1099	E7EWI2;Q59HG2;Q02763	.;.;TIE2_HUMAN	Q	951;1099;1056	ENSP00000430686:R951Q;ENSP00000369375:R1099Q;ENSP00000383977:R1056Q	ENSP00000369375:R1099Q	R	+	2	0	TEK	27218299	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	8.794000	0.91867	2.760000	0.94817	0.643000	0.83706	CGA	.	.		0.408	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			A	27228299	G	A	27228299	3	1	82	1	0	0	0	0	1	0	0	0	15766	1058	37	1	3382	1	TEK	9	27228299	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10		27228299	113985132	45	11241										
FANCC	2176	hgsc.bcm.edu	37	chr9	97869519	97869519	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ctgctgcttctggacattgcCaggaggtggcccagcacggc	14	13	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr9:97869519C>T	ENST00000289081.3	-	14	1616	c.1362G>A	c.(1360-1362)ctG>ctA	p.L454L	FANCC_ENST00000375305.1_Silent_p.L454L	NM_000136.2	NP_000127.2	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C	454					DNA repair (GO:0006281)|germ cell development (GO:0007281)|myeloid cell homeostasis (GO:0002262)|nucleotide-excision repair (GO:0006289)|protein complex assembly (GO:0006461)|removal of superoxide radicals (GO:0019430)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				kidney(1)|skin(1)|upper_aerodigestive_tract(1)	3		Acute lymphoblastic leukemia(62;0.138)				TGGACATTGCCAGGAGGTGGC	0.557			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.L454L		Atlas-SNP	.	yes	Rec		Fanconi anaemia C	9	9q22.3	2176	"Fanconi anemia, complementation group C"		L	.	FANCC	53	.	0			c.G1362A						.						113	93	100					9																	97869519		2203	4300	6503	SO:0001819	synonymous_variant	2176	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CATTGCCAGGAGG	BC006303	CCDS35071.1, CCDS75861.1	9q22.3	2014-09-17			ENSG00000158169	ENSG00000158169		"Fanconi anemia, complementation groups"	3584	protein-coding gene	gene with protein product		613899		FACC		1303234	Standard	NM_001243743		Approved	FAC, FA3	uc004avh.3	Q00597	OTTHUMG00000020279	ENST00000289081.3:c.1362G>A	chr9.hg19:g.97869519C>T		74.0	0.0		62.0	26.0	NM_001243743	B1ALR8	Silent	SNP	ENST00000289081.3	hg19	CCDS35071.1																																																																																			.	.		0.557	FANCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053219.1	NM_000136		T	97869519	C	T	97869519	2	4	82	1	0	0	0	0	0	0	0	1	5672	581	21	3		3	FANCC	9	97869519	Silent	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	70641220	97869519	43343912	46	11242										
GSN	2934	hgsc.bcm.edu	37	chr9	124062174	124062174	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ccccgcgcccgcgctgctttGcgcgctgtccctggcgctgt	13	19	0	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr9:124062174G>T	ENST00000373818.4	+	1	104	c.35G>T	c.(34-36)tGc>tTc	p.C12F	GSN_ENST00000412819.1_Intron|GSN_ENST00000436847.1_Intron|GSN_ENST00000545652.1_Intron|GSN_ENST00000449733.1_Intron|GSN_ENST00000341272.2_Intron|GSN_ENST00000373808.2_Intron|GSN_ENST00000373823.3_Intron|GSN_ENST00000394353.2_Intron	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	12					actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						GCGCTGCTTTGCGCGCTGTCC	0.796																																					p.C12F		Atlas-SNP	.											.	GSN	81	.	0			c.G35T						.						1	1	1					9																	124062174		770	1465	2235	SO:0001583	missense	2934	exon1			TGCTTTGCGCGCT	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"amyloidosis, Finnish type"	137350	"gelsolin (amyloidosis, Finnish type)"			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.35G>T	chr9.hg19:g.124062174G>T	ENSP00000362924:p.Cys12Phe	47.0	0.0		61.0	29.0	NM_000177	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Missense_Mutation	SNP	ENST00000373818.4	hg19	CCDS6828.1	.	.	.	.	.	.	.	.	.	.	G	9.327	1.059600	0.19987	.	.	ENSG00000148180	ENST00000373818	T	0.14893	2.47	5.63	2.44	0.29823	.	327.001000	0.00166	U	0.000000	T	0.10252	0.0251	N	0.08118	0	0.22684	N	0.998858	B	0.12630	0.006	B	0.15052	0.012	T	0.21042	-1.0257	10	0.32370	T	0.25	-1.0659	5.1963	0.15239	0.0853:0.1347:0.6255:0.1546	.	12	P06396	GELS_HUMAN	F	12	ENSP00000362924:C12F	ENSP00000362924:C12F	C	+	2	0	GSN	123101995	0.016000	0.18221	0.524000	0.27887	0.119000	0.20118	0.902000	0.28459	0.714000	0.32081	0.563000	0.77884	TGC	.	.		0.796	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177		T	124062174	G	T	124062174	3	4	82	1	0	0	0	0	1	0	0	0	6834	1319	46	3	37	3	GSN	9	124062174	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	26192655	124062174	17151257	47	11243										
FUT7	2529	hgsc.bcm.edu	37	chr9	139925311	139925311	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ggcaaagaagcgttggtatcGgctctcattcatgccagtga	12	9	2	2	rs201121157		TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr9:139925311G>T	ENST00000314412.6	-	2	1898	c.880C>A	c.(880-882)Cga>Aga	p.R294R	ABCA2_ENST00000265662.5_5'Flank|ABCA2_ENST00000492260.1_5'Flank|C9orf139_ENST00000314330.2_Intron|ABCA2_ENST00000341511.6_5'Flank|ABCA2_ENST00000371605.3_5'Flank	NM_004479.3	NP_004470.1	Q11130	FUT7_HUMAN	fucosyltransferase 7 (alpha (1,3) fucosyltransferase)	294					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|leukocyte migration involved in immune response (GO:0002522)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			NS(1)|endometrium(1)|lung(4)|ovary(1)|skin(1)	8	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		CGTTGGTATCGGCTCTCATTC	0.602																																					p.R294R		Atlas-SNP	.											.	FUT7	24	.	0			c.C880A						.						50	48	49					9																	139925311		2198	4296	6494	SO:0001819	synonymous_variant	2529	exon2			GGTATCGGCTCTC	X78031, AB012668	CCDS7022.1	9q34.3	2013-02-26			ENSG00000180549	ENSG00000180549		"Fucosyltransferases"	4018	protein-coding gene	gene with protein product		602030				8207002, 8182079	Standard	NM_004479		Approved		uc004ckq.2	Q11130	OTTHUMG00000020964	ENST00000314412.6:c.880C>A	chr9.hg19:g.139925311G>T		80.0	0.0		79.0	33.0	NM_004479	B2R7U7|Q6DK54	Silent	SNP	ENST00000314412.6	hg19	CCDS7022.1																																																																																			.	G|0.999;A|0.001		0.602	FUT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055220.1	NM_004479		T	139925311	G	T	139925311	2	4	82	1	0	0	0	0	0	0	0	1	6117	1124	39	1		1	FUT7	9	139925311	Silent	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	15863137	139925311	1288120	48	11244										
ST8SIA6	338596	hgsc.bcm.edu	37	chr10	17401546	17401546	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	attcttctgcttgccgtttcCatggacaactctgtatatct	6	11	4	0	rs193920832		TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr10:17401546C>T	ENST00000377602.4	-	4	418	c.344G>A	c.(343-345)tGg>tAg	p.W115*		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	115					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						TTGCCGTTTCCATGGACAACT	0.269																																					p.W115X		Atlas-SNP	.											ST8SIA6,NS,adenoma,0,1	ST8SIA6	85	.	0			c.G344A						.						55	54	54					10																	17401546		2202	4298	6500	SO:0001587	stop_gained	338596	exon4			CGTTTCCATGGAC		CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.344G>A	chr10.hg19:g.17401546C>T	ENSP00000366827:p.Trp115*	367.0	0.0		381.0	140.0	NM_001004470	B0YJ97|B9EH72|Q5VZH4	Nonsense_Mutation	SNP	ENST00000377602.4	hg19	CCDS31158.1	.	.	.	.	.	.	.	.	.	.	C	33	5.272950	0.95429	.	.	ENSG00000148488	ENST00000377602	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.029	14.2478	0.65999	0.0:1.0:0.0:0.0	.	.	.	.	X	115	.	ENSP00000366827:W115X	W	-	2	0	ST8SIA6	17441552	1.000000	0.71417	0.997000	0.53966	0.970000	0.65996	4.018000	0.57174	2.753000	0.94483	0.555000	0.69702	TGG	.	.		0.269	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		T	17401546	C	T	17401546	4	4	82	1	0	0	0	0	0	1	0	0	15251	595	21	3	872	3	ST8SIA6	10	17401546	Nonsense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10		17401546	118133201	49	11245										
PRKG1	5592	hgsc.bcm.edu	37	chr10	53227585	53227585	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ttacaactgtacccggacagCgaccgtcaagagtaagacta	9	11	1	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr10:53227585C>T	ENST00000401604.2	+	3	730	c.536C>T	c.(535-537)gCg>gTg	p.A179V	PRKG1_ENST00000373980.4_Missense_Mutation_p.A194V|PRKG1_ENST00000373985.1_Missense_Mutation_p.A167V			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	179	cGMP-binding, high affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		ACCCGGACAGCGACCGTCAAG	0.373																																					p.A194V		Atlas-SNP	.											.	PRKG1	167	.	0			c.C581T						.						126	117	120					10																	53227585		2203	4300	6503	SO:0001583	missense	5592	exon3			GGACAGCGACCGT		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.536C>T	chr10.hg19:g.53227585C>T	ENSP00000384200:p.Ala179Val	161.0	0.0		123.0	49.0	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	hg19	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	C	32	5.193151	0.94960	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	D;D;D;D	0.94092	-3.35;-3.35;-3.35;-3.35	5.79	5.79	0.91817	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.065506	0.64402	D	0.000012	D	0.97907	0.9312	H	0.96398	3.815	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.998	D	0.98753	1.0721	10	0.72032	D	0.01	-7.9069	17.5173	0.87777	0.0:1.0:0.0:0.0	.	179;194;179	B4DT93;Q13976-2;Q13976	.;.;KGP1_HUMAN	V	179;167;194;52	ENSP00000384200:A179V;ENSP00000363097:A167V;ENSP00000363092:A194V;ENSP00000363087:A52V	ENSP00000363087:A52V	A	+	2	0	PRKG1	52897591	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.481000	0.81124	2.727000	0.93392	0.563000	0.77884	GCG	.	.		0.373	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	53227585	C	T	53227585	3	4	82	1	0	0	0	0	1	0	0	0	12534	768	27	1	861	1	PRKG1	10	53227585	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	35826039	53227585	82307162	50	11246										
C10orf96	374355	hgsc.bcm.edu	37	chr10	118100283	118100283	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aaaatccttcttcttacagcTtttgaaagctcatgaaaatg	5	8	3	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr10:118100283T>G	ENST00000333254.3	+	4	454	c.203T>G	c.(202-204)cTt>cGt	p.L68R	CCDC172_ENST00000497093.1_3'UTR	NM_198515.2	NP_940917.1	P0C7W6	CC172_HUMAN	coiled-coil domain containing 172	68																	TTCTTACAGCTTTTGAAAGCT	0.308																																					p.L68R		Atlas-SNP	.											.	.	.	.	0			c.T203G						.						43	46	45					10																	118100283		2202	4283	6485	SO:0001583	missense	374355	exon4			TACAGCTTTTGAA	BC044830	CCDS31291.1	10q26.11-q26.12	2012-05-31	2012-05-31	2012-05-31	ENSG00000182645	ENSG00000182645			30524	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 96"	C10orf96		12477932	Standard	NM_198515		Approved	MGC35062	uc001lck.3	P0C7W6	OTTHUMG00000019098	ENST00000333254.3:c.203T>G	chr10.hg19:g.118100283T>G	ENSP00000329860:p.Leu68Arg	234.0	0.0		229.0	89.0	NM_198515		Missense_Mutation	SNP	ENST00000333254.3	hg19	CCDS31291.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.142367	0.57044	.	.	ENSG00000182645	ENST00000333254;ENST00000423072	.	.	.	5.95	5.95	0.96441	.	0.275088	0.31010	N	0.008423	T	0.77798	0.4184	M	0.74881	2.28	0.39685	D	0.97095	D	0.76494	0.999	D	0.66497	0.944	T	0.81609	-0.0855	9	0.87932	D	0	-3.0916	14.9826	0.71321	0.0:0.0:0.0:1.0	.	68	P0C7W6	CJ096_HUMAN	R	68	.	ENSP00000329860:L68R	L	+	2	0	C10orf96	118090273	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	3.939000	0.56591	2.276000	0.75962	0.528000	0.53228	CTT	.	.		0.308	CCDC172-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050516.2	NM_198515		G	118100283	T	G	118100283	3	3	82	1	0	0	0	0	1	0	0	0	1629	1609	56	5	213	5	C10orf96	10	118100283	Missense_Mutation	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10	64872698	118100283	17434464	51	11247										
OR52B4	143496	hgsc.bcm.edu	37	chr11	4389145	4389145	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tacctcagtgggtagcatatGgcaatatagtggtcaaaggc	12	7	2	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr11:4389145G>T	ENST00000408920.2	-	1	471	c.381C>A	c.(379-381)gcC>gcA	p.A127A		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	127					cognition (GO:0050890)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGTAGCATATGGCAATATAGT	0.443																																					p.A127A		Atlas-SNP	.											.	OR52B4	56	.	0			c.C381A						.						103	102	103					11																	4389145		2079	4228	6307	SO:0001819	synonymous_variant	143496	exon1			GCATATGGCAATA	AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"GPCR / Class A : Olfactory receptors"	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.381C>A	chr11.hg19:g.4389145G>T		176.0	0.0		155.0	57.0	NM_001005161	A6NP68|Q6IFK6	Silent	SNP	ENST00000408920.2	hg19	CCDS41609.1																																																																																			.	.		0.443	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3	NM_001005161		T	4389145	G	T	4389145	2	4	82	1	0	0	0	0	0	0	0	1	11121	1335	47	3		3	OR52B4	11	4389145	Silent	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10		4389145	130617371	52	11248										
OR56A3	390083	hgsc.bcm.edu	37	chr11	5968754	5968754	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tctggctggaggcctctctgCaccagcccctgtactacctg	10	16	2	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr11:5968754C>T	ENST00000329564.6	+	1	185	c.178C>T	c.(178-180)Cac>Tac	p.H60Y	AC025016.1_ENST00000528915.1_lincRNA	NM_001003443.2	NP_001003443.2	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A, member 3	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(27)|stomach(1)|upper_aerodigestive_tract(1)	41		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCCTCTCTGCACCAGCCCCT	0.612																																					p.H60Y		Atlas-SNP	.											.	OR56A3	81	.	0			c.C178T						.						121	121	121					11																	5968754		2201	4296	6497	SO:0001583	missense	390083	exon1			TCTCTGCACCAGC		CCDS41614.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184478	ENSG00000184478		"GPCR / Class A : Olfactory receptors"	14786	protein-coding gene	gene with protein product				OR56A6, OR56A3P			Standard	NM_001003443		Approved		uc010qzt.2	Q8NH54	OTTHUMG00000165373	ENST00000329564.6:c.178C>T	chr11.hg19:g.5968754C>T	ENSP00000331572:p.His60Tyr	110.0	0.0		136.0	42.0	NM_001003443	A6NN77|Q6IFF7	Missense_Mutation	SNP	ENST00000329564.6	hg19	CCDS41614.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.437551	0.62955	.	.	ENSG00000184478	ENST00000329564	T	0.15952	2.38	5.12	5.12	0.69794	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000007	T	0.33294	0.0858	M	0.93106	3.38	0.42313	D	0.992222	B	0.31859	0.343	B	0.33620	0.167	T	0.39461	-0.9613	10	0.87932	D	0	-16.0956	14.0107	0.64495	0.0:1.0:0.0:0.0	.	60	Q8NH54	O56A3_HUMAN	Y	60	ENSP00000331572:H60Y	ENSP00000331572:H60Y	H	+	1	0	OR56A3	5925330	1.000000	0.71417	0.996000	0.52242	0.977000	0.68977	6.697000	0.74603	2.683000	0.91414	0.644000	0.83932	CAC	.	.		0.612	OR56A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383753.1	NM_001003443		T	5968754	C	T	5968754	3	4	82	1	0	0	0	0	1	0	0	0	11143	710	25	3	180	3	OR56A3	11	5968754	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	1579609	5968754	129037762	53	11249										
OR8H1	219469	hgsc.bcm.edu	37	chr11	56058116	56058116	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tagggcccagtgacaagagcGcaacacagccttttggacat	11	11	0	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr11:56058116G>T	ENST00000313022.2	-	1	450	c.423C>A	c.(421-423)tgC>tgA	p.C141*		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	141						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					TGACAAGAGCGCAACACAGCC	0.448																																					p.C141X		Atlas-SNP	.											.	OR8H1	89	.	0			c.C423A						.						88	84	85					11																	56058116		2201	4296	6497	SO:0001587	stop_gained	219469	exon1			AAGAGCGCAACAC	AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"GPCR / Class A : Olfactory receptors"	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.423C>A	chr11.hg19:g.56058116G>T	ENSP00000323595:p.Cys141*	125.0	0.0		129.0	53.0	NM_001005199	B2RNI7|Q6IFC5	Nonsense_Mutation	SNP	ENST00000313022.2	hg19	CCDS31526.1	.	.	.	.	.	.	.	.	.	.	G	9.125	1.010073	0.19277	.	.	ENSG00000181693	ENST00000313022;ENST00000395186	.	.	.	3.82	-7.64	0.01286	.	1.117080	0.06604	N	0.754428	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	2.2253	0.03982	0.4301:0.2063:0.2595:0.1041	.	.	.	.	X	141;137	.	ENSP00000323595:C141X	C	-	3	2	OR8H1	55814692	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.597000	0.00111	-1.403000	0.02053	-0.410000	0.06199	TGC	.	.		0.448	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199		T	56058116	G	T	56058116	4	4	82	1	0	0	0	0	0	1	0	0	11246	1079	38	1	514	1	OR8H1	11	56058116	Nonsense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	50089362	56058116	78948400	54	11250										
OSBP	5007	hgsc.bcm.edu	37	chr11	59361132	59361132	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ttgctggtgattttgatttcCtgacgcaatgtccagccatt	9	9	0	3			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr11:59361132C>G	ENST00000263847.1	-	9	2102	c.1623G>C	c.(1621-1623)caG>caC	p.Q541H	MIR3162_ENST00000581818.1_RNA	NM_002556.2	NP_002547.1	P22059	OSBP1_HUMAN	oxysterol binding protein	541					lipid transport (GO:0006869)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	oxysterol binding (GO:0008142)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		TTTTGATTTCCTGACGCAATG	0.458																																					p.Q541H		Atlas-SNP	.											.	OSBP	57	.	0			c.G1623C						.						146	127	133					11																	59361132		2201	4295	6496	SO:0001583	missense	5007	exon9			GATTTCCTGACGC	AF185696	CCDS7974.1	11q12-q13	2013-01-10			ENSG00000110048	ENSG00000110048		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	8503	protein-coding gene	gene with protein product		167040					Standard	NM_002556		Approved	OSBP1	uc001noc.1	P22059	OTTHUMG00000167422	ENST00000263847.1:c.1623G>C	chr11.hg19:g.59361132C>G	ENSP00000263847:p.Gln541His	104.0	0.0		88.0	7.0	NM_002556	Q6P524	Missense_Mutation	SNP	ENST00000263847.1	hg19	CCDS7974.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.391314	0.83011	.	.	ENSG00000110048	ENST00000263847;ENST00000378235	T	0.30714	1.52	6.06	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.60117	0.2244	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.67421	-0.5675	10	0.72032	D	0.01	-25.3475	14.5961	0.68407	0.0:0.9289:0.0:0.0711	.	541	P22059	OSBP1_HUMAN	H	541;141	ENSP00000263847:Q541H	ENSP00000263847:Q541H	Q	-	3	2	OSBP	59117708	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.105000	0.41825	1.575000	0.49775	0.655000	0.94253	CAG	.	.		0.458	OSBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394555.1			G	59361132	C	G	59361132	3	3	82	1	0	0	0	0	1	0	0	0	11282	680	24	4	824	4	OSBP	11	59361132	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	3303016	59361132	75645384	55	11251										
STARD10	10809	hgsc.bcm.edu	37	chr11	72470359	72470359	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cgttgctgtcccatttcttgCggtactcaatgtcgtgtagg	11	10	2	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr11:72470359C>A	ENST00000334805.6	-	3	1194	c.275G>T	c.(274-276)cGc>cTc	p.R92L	STARD10_ENST00000538437.1_5'UTR|STARD10_ENST00000538536.1_Missense_Mutation_p.R46L|ARAP1_ENST00000359373.5_Intron|STARD10_ENST00000545082.1_Missense_Mutation_p.R63L|STARD10_ENST00000543304.1_Missense_Mutation_p.R92L	NM_006645.2	NP_006636.2	Q9Y365	PCTL_HUMAN	StAR-related lipid transfer (START) domain containing 10	92	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				bile acid secretion (GO:0032782)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)	cytosol (GO:0005829)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|microvillus (GO:0005902)	lipid binding (GO:0008289)			endometrium(4)|large_intestine(1)|lung(2)|prostate(1)	8			BRCA - Breast invasive adenocarcinoma(5;7.08e-07)			CCATTTCTTGCGGTACTCAAT	0.527																																					p.R92L		Atlas-SNP	.											.	STARD10	25	.	0			c.G275T						.						150	155	153					11																	72470359		2182	4270	6452	SO:0001583	missense	10809	exon3			TTCTTGCGGTACT	AF039696	CCDS41688.1	11q13	2011-09-12	2007-08-16	2003-02-07		ENSG00000214530		"StAR-related lipid transfer (START) domain containing"	10666	protein-coding gene	gene with protein product			"serologically defined colon cancer antigen 28", "START domain containing 10"	SDCCAG28		9610721	Standard	NM_006645		Approved	NY-CO-28, CGI-52, PCTP2	uc001otb.3	Q9Y365		ENST00000334805.6:c.275G>T	chr11.hg19:g.72470359C>A	ENSP00000335247:p.Arg92Leu	174.0	0.0		153.0	64.0	NM_006645	O60532	Missense_Mutation	SNP	ENST00000334805.6	hg19	CCDS41688.1	.	.	.	.	.	.	.	.	.	.	C	34	5.313575	0.95655	.	.	ENSG00000214530	ENST00000543304;ENST00000334805;ENST00000538536;ENST00000545082;ENST00000544767;ENST00000537947;ENST00000536728;ENST00000542989;ENST00000546314;ENST00000539138;ENST00000535054	T;T;T;T;T;T;T;T;T;D;T	0.86230	1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;-2.09;0.65	5.61	4.69	0.59074	Lipid-binding START (3);START-like domain (1);	0.158692	0.41396	U	0.000894	D	0.93828	0.8026	M	0.92970	3.365	0.45607	D	0.998549	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.993	D	0.93907	0.7193	10	0.87932	D	0	-8.17	8.4866	0.33076	0.0:0.7626:0.1535:0.0839	.	46;92	F5GY11;Q9Y365	.;PCTL_HUMAN	L	92;92;46;63;23;92;23;92;92;63;46	ENSP00000438792:R92L;ENSP00000335247:R92L;ENSP00000440016:R46L;ENSP00000443548:R63L;ENSP00000438357:R23L;ENSP00000445657:R92L;ENSP00000442414:R23L;ENSP00000443597:R92L;ENSP00000445886:R92L;ENSP00000441589:R63L;ENSP00000440924:R46L	ENSP00000335247:R92L	R	-	2	0	STARD10	72148007	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.653000	0.90120	0.655000	0.94253	CGC	.	.		0.527	STARD10-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397254.1			A	72470359	C	A	72470359	3	1	82	1	0	0	0	0	1	0	0	0	15270	768	27	1	620	1	STARD10	11	72470359	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	13109227	72470359	62536157	56	11252										
FAT3	120114	hgsc.bcm.edu	37	chr11	92616466	92616466	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cagcccggcggggcgtggtcGtgtgcagtgtggcccccaac	17	14	0	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr11:92616466G>A	ENST00000298047.6	+	23	12861	c.12844G>A	c.(12844-12846)Gtg>Atg	p.V4282M	FAT3_ENST00000525166.1_Missense_Mutation_p.V4132M|FAT3_ENST00000409404.2_Missense_Mutation_p.V4282M|FAT3_ENST00000533797.1_Missense_Mutation_p.V617M|FAT3_ENST00000489716.1_3'UTR			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4282					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGGCGTGGTCGTGTGCAGTGT	0.657										TCGA Ovarian(4;0.039)																											p.V4282M		Atlas-SNP	.											.	FAT3	1822	.	0			c.G12844A						.						31	38	36					11																	92616466		2098	4197	6295	SO:0001583	missense	120114	exon23			GTGGTCGTGTGCA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12844G>A	chr11.hg19:g.92616466G>A	ENSP00000298047:p.Val4282Met	92.0	0.0		72.0	14.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	33	5.201275	0.94997	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;D	0.90261	-1.04;-1.32;-1.05;-2.64	5.85	5.85	0.93711	.	.	.	.	.	D	0.95736	0.8613	M	0.81497	2.545	0.80722	D	1	D;B	0.89917	1.0;0.382	D;B	0.91635	0.999;0.019	D	0.95204	0.8319	9	0.56958	D	0.05	.	20.161	0.98133	0.0:0.0:1.0:0.0	.	4282;4282	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	M	4282;4282;4132;617	ENSP00000298047:V4282M;ENSP00000387040:V4282M;ENSP00000432586:V4132M;ENSP00000436399:V617M	ENSP00000298047:V4282M	V	+	1	0	FAT3	92256114	1.000000	0.71417	0.992000	0.48379	0.990000	0.78478	9.746000	0.98859	2.770000	0.95276	0.655000	0.94253	GTG	.	.		0.657	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92616466	G	A	92616466	3	1	82	1	0	0	0	0	1	0	0	0	5699	1145	40	1	12934	1	FAT3	11	92616466	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	20146107	92616466	42390050	57	11253										
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101833467	101833467	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aaaatgaaatacaacatccaTgagagaaatggtgtgagatt	9	4	0	4			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr11:101833467T>C	ENST00000263468.8	+	6	1971	c.1701T>C	c.(1699-1701)caT>caC	p.H567H	KIAA1377_ENST00000537689.1_Silent_p.H368H	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	567										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		ACAACATCCATGAGAGAAATG	0.279																																					p.H567H		Atlas-SNP	.											.	KIAA1377	111	.	0			c.T1701C						.						36	40	39					11																	101833467		2189	4276	6465	SO:0001819	synonymous_variant	57562	exon6			CATCCATGAGAGA	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.1701T>C	chr11.hg19:g.101833467T>C		302.0	0.0		275.0	24.0	NM_020802	Q4G0U6	Silent	SNP	ENST00000263468.8	hg19	CCDS31658.1																																																																																			.	.		0.279	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		C	101833467	T	C	101833467	2	2	82	1	0	0	0	0	0	0	0	1	8236	1461	51	2		2	KIAA1377	11	101833467	Silent	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10	9217001	101833467	33173049	58	11254										
ACAT1	38	hgsc.bcm.edu	37	chr11	108018101	108018101	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aggaggtgcttctgccatgcTaattcagaagctgtagacaa	11	8	2	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr11:108018101T>G	ENST00000265838.4	+	12	1359	c.1268T>G	c.(1267-1269)cTa>cGa	p.L423R		NM_000019.3	NP_000010.1	P24752	THIL_HUMAN	acetyl-CoA acetyltransferase 1	423					adipose tissue development (GO:0060612)|brain development (GO:0007420)|branched-chain amino acid catabolic process (GO:0009083)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular nitrogen compound metabolic process (GO:0034641)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|metanephric proximal convoluted tubule development (GO:0072229)|protein homooligomerization (GO:0051260)|response to hormone (GO:0009725)|response to organic cyclic compound (GO:0014070)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acetyl-CoA C-acetyltransferase activity (GO:0003985)|coenzyme binding (GO:0050662)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|prostate(2)	10		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	TCTGCCATGCTAATTCAGAAG	0.468																																					p.L423R		Atlas-SNP	.											.	ACAT1	35	.	0			c.T1268G						.						138	123	128					11																	108018101		2201	4298	6499	SO:0001583	missense	38	exon12			CCATGCTAATTCA	D90228	CCDS8339.1	11q22.3	2010-04-30	2010-04-30		ENSG00000075239	ENSG00000075239	2.3.1.9		93	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	607809	"acetyl-Coenzyme A acetyltransferase 1"	ACAT		1979337	Standard	NM_000019		Approved	THIL	uc001pjy.3	P24752	OTTHUMG00000166381	ENST00000265838.4:c.1268T>G	chr11.hg19:g.108018101T>G	ENSP00000265838:p.Leu423Arg	59.0	0.0		63.0	24.0	NM_000019	B2R6H1|G3XAB4|Q96FG8	Missense_Mutation	SNP	ENST00000265838.4	hg19	CCDS8339.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.612583	0.87258	.	.	ENSG00000075239	ENST00000265838	D	0.93547	-3.24	5.87	5.87	0.94306	Thiolase-like, subgroup (1);Thiolase-like (1);Thiolase, C-terminal (1);	0.146323	0.47455	D	0.000236	D	0.97021	0.9027	M	0.89214	3.015	0.80722	D	1	D	0.69078	0.997	D	0.68039	0.955	D	0.97707	1.0188	10	0.87932	D	0	-5.2666	16.2806	0.82678	0.0:0.0:0.0:1.0	.	423	P24752	THIL_HUMAN	R	423	ENSP00000265838:L423R	ENSP00000265838:L423R	L	+	2	0	ACAT1	107523311	1.000000	0.71417	0.739000	0.30968	0.895000	0.52256	7.753000	0.85153	2.248000	0.74166	0.533000	0.62120	CTA	.	.		0.468	ACAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389474.1	NM_000019		G	108018101	T	G	108018101	3	3	82	1	0	0	0	0	1	0	0	0	121	1522	53	5	1314	5	ACAT1	11	108018101	Missense_Mutation	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10	6184634	108018101	26988415	59	11255										
OR8G2	0	hgsc.bcm.edu	37	chr11	124096063	124096063	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	agtgcatttaacatcctgacGcctgccttaaccatccttgc	6	14	0	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr11:124096063G>A								OR10D3 (39111 upstream) : OR8G1 (24359 downstream)																							ACATCCTGACGCCTGCCTTAA	0.483																																					p.T222T		Atlas-SNP	.											.	.	.	.	0			c.G666A						.						140	148	145					11																	124096063		2126	4262	6388	SO:0001628	intergenic_variant	26492	exon1			CCTGACGCCTGCC																													chr11.hg19:g.124096063G>A		122.0	0.0		121.0	46.0	NM_001007249		Silent	SNP		hg19																																																																																				.	.	0	0.483									A	124096063	G	A	124096063	1	1	82	0	1	0	0	0	0	0	0	0	11244	1074	38	1		1	OR8G2	11	124096063	IGR	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	16077962	124096063	10910453	60	11256										
CDKN1B	1027	hgsc.bcm.edu	37	chr12	12871119	12871119	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tcagcgggagccgcccggcgGcgcctttaattggggctccg	16	14	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr12:12871119G>T	ENST00000228872.4	+	1	1062	c.346G>T	c.(346-348)Gcg>Tcg	p.A116S	CDKN1B_ENST00000396340.1_Missense_Mutation_p.A116S|CDKN1B_ENST00000477087.1_Intron	NM_004064.3	NP_004055.1	P46527	CDN1B_HUMAN	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	116					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|cellular response to antibiotic (GO:0071236)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular component movement (GO:0051271)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of kinase activity (GO:0033673)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|potassium ion transport (GO:0006813)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein phosphatase binding (GO:0019903)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)			breast(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(5)	13		Prostate(47;0.0322)|all_epithelial(100;0.159)		BRCA - Breast invasive adenocarcinoma(232;0.0336)		CCGCCCGGCGGCGCCTTTAAT	0.652																																					p.A116S		Atlas-SNP	.											.	CDKN1B	48	.	0			c.G346T						.						20	27	25					12																	12871119		2201	4296	6497	SO:0001583	missense	1027	exon1			CCGGCGGCGCCTT	AF480891	CCDS8653.1	12p13.1-p12	2008-08-04			ENSG00000111276	ENSG00000111276			1785	protein-coding gene	gene with protein product		600778				8033212	Standard	NM_004064		Approved	KIP1, P27KIP1	uc001rat.2	P46527	OTTHUMG00000149914	ENST00000228872.4:c.346G>T	chr12.hg19:g.12871119G>T	ENSP00000228872:p.Ala116Ser	1050.0	2.0		973.0	365.0	NM_004064	Q16307|Q5U0H2|Q9BUS6	Missense_Mutation	SNP	ENST00000228872.4	hg19	CCDS8653.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.934669	0.34189	.	.	ENSG00000111276	ENST00000228872;ENST00000535674;ENST00000396340	T;T	0.59364	0.27;0.27	5.51	4.6	0.57074	.	0.857520	0.10244	N	0.698043	T	0.40297	0.1111	N	0.14661	0.345	0.20489	N	0.999896	B	0.13145	0.007	B	0.09377	0.004	T	0.09751	-1.0660	10	0.09084	T	0.74	-22.8831	14.2207	0.65826	0.0:0.1492:0.8507:0.0	.	116	P46527	CDN1B_HUMAN	S	116;65;116	ENSP00000228872:A116S;ENSP00000379629:A116S	ENSP00000228872:A116S	A	+	1	0	CDKN1B	12762386	0.439000	0.25610	0.943000	0.38184	0.831000	0.47069	1.249000	0.32839	1.290000	0.44636	0.650000	0.86243	GCG	.	.		0.652	CDKN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313878.2	NM_004064		T	12871119	G	T	12871119	3	4	82	1	0	0	0	0	1	0	0	0	3161	1203	42	3	348	3	CDKN1B	12	12871119	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10		12871119	120980776	61	11257										
MON2	23041	hgsc.bcm.edu	37	chr12	62946910	62946910	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tttctacaattggtgcgcatGgaactttattacagcattca	7	8	2	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr12:62946910G>T	ENST00000393632.2	+	24	3557	c.3166G>T	c.(3166-3168)Gga>Tga	p.G1056*	MON2_ENST00000393630.3_Nonsense_Mutation_p.G1057*|MON2_ENST00000393629.2_Nonsense_Mutation_p.G1056*|MON2_ENST00000280379.6_Nonsense_Mutation_p.G1057*|MON2_ENST00000552738.1_Nonsense_Mutation_p.G1033*|MON2_ENST00000546600.1_Nonsense_Mutation_p.G1056*|MON2_ENST00000552115.1_Nonsense_Mutation_p.G1056*	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1056					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TGGTGCGCATGGAACTTTATT	0.393																																					p.G1056X		Atlas-SNP	.											.	MON2	160	.	0			c.G3166T						.						218	210	213					12																	62946910		2203	4300	6503	SO:0001587	stop_gained	23041	exon24			GCGCATGGAACTT		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.3166G>T	chr12.hg19:g.62946910G>T	ENSP00000377252:p.Gly1056*	174.0	0.0		179.0	59.0	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Nonsense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	G	39	7.821282	0.98507	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629;ENST00000552115	.	.	.	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.6111	17.9971	0.89187	0.0:0.0:1.0:0.0	.	.	.	.	X	1056;1057;1057;1056;1033;1056;1056	.	.	G	+	1	0	MON2	61233177	1.000000	0.71417	1.000000	0.80357	0.032000	0.12392	9.420000	0.97426	2.322000	0.78497	0.650000	0.86243	GGA	.	.		0.393	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		T	62946910	G	T	62946910	4	4	82	1	0	0	0	0	0	1	0	0	9709	1349	47	3	3260	3	MON2	12	62946910	Nonsense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	50075791	62946910	70904985	62	11258										
CPSF6	11052	hgsc.bcm.edu	37	chr12	69652698	69652698	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cttacactagctcctcctccGcatcttcctggaccacctcc	4	20	1	0	rs559355987		TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr12:69652698G>T	ENST00000435070.2	+	6	1133	c.1023G>T	c.(1021-1023)ccG>ccT	p.P341P	CPSF6_ENST00000456847.3_Silent_p.P268P|CPSF6_ENST00000551516.1_Intron|CPSF6_ENST00000266679.8_Silent_p.P378P	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa	341	Pro-rich.				mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P341P(2)		endometrium(1)|large_intestine(7)|lung(8)	16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			CTCCTCCTCCGCATCTTCCTG	0.612																																					p.P341P		Atlas-SNP	.											CPSF6_ENST00000435070,caecum,carcinoma,0,2	CPSF6	96	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1023T						.						127	123	124					12																	69652698		2203	4300	6503	SO:0001819	synonymous_variant	11052	exon6			TCCTCCGCATCTT	X67336	CCDS8988.1, CCDS73494.1	12q15	2013-06-18	2002-08-29			ENSG00000111605		"RNA binding motif (RRM) containing"	13871	protein-coding gene	gene with protein product	"cleavage factor Im complex 68 kDa subunit"	604979	"cleavage and polyadenylation specific factor 6, 68kD subunit"			9659921, 17267687	Standard	NM_007007		Approved	CFIM, HPBRII-4, HPBRII-7, CFIM68	uc001sut.4	Q16630		ENST00000435070.2:c.1023G>T	chr12.hg19:g.69652698G>T		87.0	0.0		76.0	33.0	NM_007007	A8K7K9|Q53ES1|Q9BSJ7|Q9BW18	Silent	SNP	ENST00000435070.2	hg19	CCDS8988.1																																																																																			.	.		0.612	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	NM_007007		T	69652698	G	T	69652698	2	4	82	1	0	0	0	0	0	0	0	1	3831	1074	38	1		1	CPSF6	12	69652698	Silent	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	6705788	69652698	64199197	63	11259										
DHX37	57647	hgsc.bcm.edu	37	chr12	125434543	125434543	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aggcagtacctggcccacgtCttcagcatggtgccggggct	14	13	2	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr12:125434543C>A	ENST00000308736.2	-	25	3377	c.3279G>T	c.(3277-3279)aaG>aaT	p.K1093N	DHX37_ENST00000544745.1_Missense_Mutation_p.K880N	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	1093							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		TGGCCCACGTCTTCAGCATGG	0.662																																					p.K1093N		Atlas-SNP	.											.	DHX37	114	.	0			c.G3279T						.						33	30	31					12																	125434543		2202	4300	6502	SO:0001583	missense	57647	exon25			CCACGTCTTCAGC	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.3279G>T	chr12.hg19:g.125434543C>A	ENSP00000311135:p.Lys1093Asn	133.0	0.0		91.0	28.0	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	hg19	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.839171	0.71373	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.03580	3.95;3.88	5.64	4.66	0.58398	.	0.096235	0.64402	D	0.000001	T	0.19846	0.0477	M	0.86740	2.835	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.00548	-1.1677	10	0.87932	D	0	-43.9874	10.9941	0.47565	0.0:0.7891:0.0:0.2109	.	880;1093	F5H3Y4;Q8IY37	.;DHX37_HUMAN	N	1093;880	ENSP00000311135:K1093N;ENSP00000439009:K880N	ENSP00000311135:K1093N	K	-	3	2	DHX37	124000496	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	1.165000	0.31822	1.225000	0.43566	0.555000	0.69702	AAG	.	.		0.662	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		A	125434543	C	A	125434543	3	1	82	1	0	0	0	0	1	0	0	0	4512	912	32	3	206	3	DHX37	12	125434543	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	55781845	125434543	8417352	64	11260										
PRTG	283659	hgsc.bcm.edu	37	chr15	55965587	55965587	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	acctttcacgcttgtagcttTgggcgtcctatgtgaagtcc	10	11	1	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr15:55965587T>C	ENST00000389286.4	-	10	1881	c.1834A>G	c.(1834-1836)Aaa>Gaa	p.K612E		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		CTTGTAGCTTTGGGCGTCCTA	0.408																																					p.K612E		Atlas-SNP	.											.	PRTG	110	.	0			c.A1834G						.						59	57	58					15																	55965587		1863	4104	5967	SO:0001583	missense	283659	exon10			TAGCTTTGGGCGT	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.1834A>G	chr15.hg19:g.55965587T>C	ENSP00000373937:p.Lys612Glu	104.0	0.0		100.0	17.0	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	hg19	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	T	17.22	3.333334	0.60853	.	.	ENSG00000166450	ENST00000389286	T	0.50813	0.73	4.67	4.67	0.58626	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.50120	0.1597	L	0.31207	0.915	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.44528	-0.9322	10	0.02654	T	1	-19.1474	13.6104	0.62074	0.0:0.0:0.0:1.0	.	612	Q2VWP7	PRTG_HUMAN	E	612	ENSP00000373937:K612E	ENSP00000373937:K612E	K	-	1	0	PRTG	53752879	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	7.707000	0.84623	1.871000	0.54225	0.528000	0.53228	AAA	.	.		0.408	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		C	55965587	T	C	55965587	3	2	82	1	0	0	0	0	1	0	0	0	12650	1821	63	2	1662	2	PRTG	15	55965587	Missense_Mutation	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10		55965587	46565805	65	11261										
IGDCC3	9543	hgsc.bcm.edu	37	chr15	65624285	65624285	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	caccacacacatacctgttgTtattcttgagcctgacgtgg	8	12	1	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr15:65624285T>C	ENST00000327987.4	-	7	1393	c.1142A>G	c.(1141-1143)aAc>aGc	p.N381S	IGDCC3_ENST00000559231.1_5'UTR	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	381	Ig-like C2-type 4.				neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						ATACCTGTTGTTATTCTTGAG	0.602																																					p.N381S		Atlas-SNP	.											.	IGDCC3	82	.	0			c.A1142G						.						100	89	93					15																	65624285		2201	4299	6500	SO:0001583	missense	9543	exon7			CTGTTGTTATTCT	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9700	protein-coding gene	gene with protein product		604184	"putative neuronal cell adhesion molecule"	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.1142A>G	chr15.hg19:g.65624285T>C	ENSP00000332773:p.Asn381Ser	26.0	0.0		15.0	7.0	NM_004884	O95215	Missense_Mutation	SNP	ENST00000327987.4	hg19	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	T	9.712	1.157428	0.21454	.	.	ENSG00000174498	ENST00000327987;ENST00000443278	T	0.37915	1.17	4.53	3.4	0.38934	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.049418	0.85682	D	0.000000	T	0.33789	0.0875	L	0.39326	1.205	0.51482	D	0.999928	B	0.30361	0.277	B	0.41510	0.359	T	0.10291	-1.0636	10	0.25106	T	0.35	-15.1154	9.66	0.39950	0.0:0.0831:0.0:0.9169	.	381	Q8IVU1	IGDC3_HUMAN	S	381;244	ENSP00000332773:N381S	ENSP00000332773:N381S	N	-	2	0	IGDCC3	63411338	1.000000	0.71417	0.998000	0.56505	0.246000	0.25737	5.115000	0.64655	1.790000	0.52503	0.533000	0.62120	AAC	.	.		0.602	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884		C	65624285	T	C	65624285	3	2	82	1	0	0	0	0	1	0	0	0	7577	1725	60	2	1334	2	IGDCC3	15	65624285	Missense_Mutation	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10	9658698	65624285	36907107	66	11262										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75981258	75981258	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gcaccctccaccccacctgcCccctgcttctgcagctcccc	5	25	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr15:75981258C>A	ENST00000308508.5	-	3	2240	c.2148G>T	c.(2146-2148)ggG>ggT	p.G716G		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	716	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.|Interaction with COL6A2. {ECO:0000250}.			QGA -> HST (in Ref. 1; CAA65529). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCCCACCTGCCCCCTGCTTCT	0.672																																					p.G716G		Atlas-SNP	.											.	CSPG4	175	.	0			c.G2148T						.						51	52	52					15																	75981258		2197	4292	6489	SO:0001819	synonymous_variant	1464	exon3			ACCTGCCCCCTGC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.2148G>T	chr15.hg19:g.75981258C>A		60.0	0.0		58.0	6.0	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	hg19	CCDS10284.1																																																																																			.	.		0.672	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		A	75981258	C	A	75981258	2	1	82	1	0	0	0	0	0	0	0	1	3962	610	22	3		3	CSPG4	15	75981258	Silent	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	10356973	75981258	26550134	67	11263										
AXIN1	8312	hgsc.bcm.edu	37	chr16	347107	347107	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ccttttccccctcaatgatcCactgcatgattttctggttc	5	14	2	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr16:347107C>T	ENST00000262320.3	-	7	2275	c.1904G>A	c.(1903-1905)tGg>tAg	p.W635*	AXIN1_ENST00000354866.3_Nonsense_Mutation_p.W635*|AXIN1_ENST00000481769.1_5'Flank	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	635	Interaction with PPP2CA.|Interaction with RNF111.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CTCAATGATCCACTGCATGAT	0.622																																					p.W635X		Atlas-SNP	.											.	AXIN1	290	.	0			c.G1904A						.						231	210	217					16																	347107		2203	4300	6503	SO:0001587	stop_gained	8312	exon7			ATGATCCACTGCA	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1904G>A	chr16.hg19:g.347107C>T	ENSP00000262320:p.Trp635*	36.0	0.0		18.0	9.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Nonsense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	C	42	9.594752	0.99214	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.3868	18.2287	0.89927	0.0:1.0:0.0:0.0	.	.	.	.	X	635	.	ENSP00000262320:W635X	W	-	2	0	AXIN1	287108	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.153000	0.77428	2.317000	0.78254	0.478000	0.44815	TGG	.	.		0.622	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			T	347107	C	T	347107	4	4	82	1	0	0	0	0	0	1	0	0	1236	595	21	3	704	3	AXIN1	16	347107	Nonsense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10		347107	90007646	68	11264										
TSC2	7249	hgsc.bcm.edu	37	chr16	2108810	2108810	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ttttgtgggcatggctctctGgggagcccaccggctctatt	13	11	2	0	rs397515106|rs137854012|rs45517140		TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr16:2108810G>A	ENST00000219476.3	+	10	1541	c.911G>A	c.(910-912)tGg>tAg	p.W304*	TSC2_ENST00000350773.4_Nonsense_Mutation_p.W304*|TSC2_ENST00000568454.1_Nonsense_Mutation_p.W315*|TSC2_ENST00000382538.6_Nonsense_Mutation_p.W255*|TSC2_ENST00000439673.2_Nonsense_Mutation_p.W267*|TSC2_ENST00000401874.2_Nonsense_Mutation_p.W304*|TSC2_ENST00000353929.4_Nonsense_Mutation_p.W304*	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	304	Required for interaction with TSC1.		W -> WGMALW (in TSC2).		acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				ATGGCTCTCTGGGGAGCCCAC	0.562			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.W304X		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.G911A	GRCh37	CM090987	TSC2	M	rs45517140	.						64	56	59					16																	2108810		2195	4297	6492	SO:0001587	stop_gained	7249	exon10	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CTCTCTGGGGAGC	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.911G>A	chr16.hg19:g.2108810G>A	ENSP00000219476:p.Trp304*	44.0	0.0		31.0	13.0	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Nonsense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	.	38	7.067979	0.98040	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	.	.	.	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.1893	18.9169	0.92508	0.0:0.0:1.0:0.0	rs45517140	.	.	.	X	304;304;304;267;255;304	.	ENSP00000219476:W304X	W	+	2	0	TSC2	2048811	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.406000	0.97321	2.541000	0.85698	0.655000	0.94253	TGG	.	.		0.562	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		A	2108810	G	A	2108810	4	1	82	1	0	0	0	0	0	1	0	0	16621	1357	47	3	945	3	TSC2	16	2108810	Nonsense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	1761703	2108810	88245943	69	11265										
ZP2	7783	hgsc.bcm.edu	37	chr16	21212847	21212847	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gaatctcactagagggtactCgttttccccataaggttgtt	9	9	1	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr16:21212847C>A	ENST00000574002.1	-	15	2019	c.1537G>T	c.(1537-1539)Gag>Tag	p.E513*	ZP2_ENST00000574091.1_Nonsense_Mutation_p.E504*|ZP2_ENST00000219593.4_Nonsense_Mutation_p.E513*|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	513	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		AGAGGGTACTCGTTTTCCCCA	0.433																																					p.E513X		Atlas-SNP	.											.	ZP2	92	.	0			c.G1537T						.						195	179	185					16																	21212847		2200	4300	6500	SO:0001587	stop_gained	7783	exon14			GGTACTCGTTTTC	M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"Zona pellucida glycoproteins"	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.1537G>T	chr16.hg19:g.21212847C>A	ENSP00000460971:p.Glu513*	199.0	0.0		127.0	66.0	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Nonsense_Mutation	SNP	ENST00000574002.1	hg19	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.316130	0.60524	.	.	ENSG00000103310	ENST00000219593	.	.	.	5.1	4.06	0.47325	.	0.171032	0.40469	N	0.001088	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-16.3183	11.9133	0.52751	0.0:0.628:0.372:0.0	.	.	.	.	X	513	.	ENSP00000219593:E513X	E	-	1	0	ZP2	21120348	0.997000	0.39634	0.170000	0.22879	0.124000	0.20399	3.431000	0.52814	2.530000	0.85305	0.591000	0.81541	GAG	.	.		0.433	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			A	21212847	C	A	21212847	4	1	82	1	0	0	0	0	0	1	0	0	18231	893	31	1	724	1	ZP2	16	21212847	Nonsense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	19104037	21212847	69141906	70	11266										
SETD6	79918	hgsc.bcm.edu	37	chr16	58552349	58552349	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	acctagtgtacgagcgctggGatttcctatgcaaactggag	12	9	0	0	rs11865588	byFrequency	TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr16:58552349G>T	ENST00000219315.4	+	7	1068	c.1018G>T	c.(1018-1020)Gat>Tat	p.D340Y	SETD6_ENST00000310682.2_Missense_Mutation_p.D316Y|SETD6_ENST00000394266.4_Missense_Mutation_p.D271Y|SETD6_ENST00000418480.1_3'UTR			Q8TBK2	SETD6_HUMAN	SET domain containing 6	340			D -> N (in dbSNP:rs11865588).		negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						CGAGCGCTGGGATTTCCTATG	0.488																																					p.D340Y		Atlas-SNP	.											.	SETD6	27	.	0			c.G1018T						.						119	115	116					16																	58552349		2198	4300	6498	SO:0001583	missense	79918	exon7			CGCTGGGATTTCC	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.1018G>T	chr16.hg19:g.58552349G>T	ENSP00000219315:p.Asp340Tyr	174.0	0.0		93.0	52.0	NM_001160305	A8K380|B5ME38|Q9H787	Missense_Mutation	SNP	ENST00000219315.4	hg19	CCDS54013.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.894081	0.52121	.	.	ENSG00000103037	ENST00000310682;ENST00000394266;ENST00000219315;ENST00000447443	T;T;T;T	0.23950	2.18;2.18;2.18;1.88	5.73	2.77	0.32553	Rubisco LS methyltransferase, substrate-binding domain (2);	0.156119	0.56097	D	0.000029	T	0.44623	0.1302	M	0.67953	2.075	0.53688	D	0.999979	D;D	0.69078	0.997;0.997	D;P	0.68943	0.961;0.837	T	0.32052	-0.9921	10	0.72032	D	0.01	-2.4539	10.4577	0.44561	0.209:0.0:0.791:0.0	.	340;316	Q8TBK2;Q8TBK2-2	SETD6_HUMAN;.	Y	316;271;340;102	ENSP00000310082:D316Y;ENSP00000377809:D271Y;ENSP00000219315:D340Y;ENSP00000396437:D102Y	ENSP00000219315:D340Y	D	+	1	0	SETD6	57109850	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	3.090000	0.50191	0.372000	0.24591	-0.742000	0.03525	GAT	.	G|0.995;A|0.005		0.488	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860		T	58552349	G	T	58552349	3	4	82	1	0	0	0	0	1	0	0	0	14150	1174	41	3	1044	3	SETD6	16	58552349	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	37339502	58552349	31802404	71	11267										
PDPR	55066	hgsc.bcm.edu	37	chr16	70176519	70176519	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ttggtttgacatcgtggagtCtgaagtcaagtgctgtaagg	14	5	2	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr16:70176519C>G	ENST00000288050.4	+	13	2492	c.1535C>G	c.(1534-1536)tCt>tGt	p.S512C	PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000568530.1_Missense_Mutation_p.S512C|PDPR_ENST00000398122.3_Missense_Mutation_p.S412C	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	512					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		ATCGTGGAGTCTGAAGTCAAG	0.418																																					p.S512C		Atlas-SNP	.											.	PDPR	66	.	0			c.C1535G						.						80	88	85					16																	70176519		1903	4132	6035	SO:0001583	missense	55066	exon13			TGGAGTCTGAAGT		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1535C>G	chr16.hg19:g.70176519C>G	ENSP00000288050:p.Ser512Cys	94.0	0.0		49.0	30.0	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	hg19	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.252198	0.80135	.	.	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055	D;D	0.83837	-1.77;-1.77	4.99	4.99	0.66335	.	0.166576	0.53938	D	0.000047	D	0.85062	0.5611	L	0.47190	1.495	0.80722	D	1	D;P	0.63880	0.993;0.863	P;B	0.52856	0.711;0.353	D	0.86783	0.1980	10	0.66056	D	0.02	.	17.6204	0.88079	0.0:1.0:0.0:0.0	.	240;512	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	C	512;412;240	ENSP00000288050:S512C;ENSP00000381190:S412C	ENSP00000205055:S240C	S	+	2	0	PDPR	68734020	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.770000	0.68873	2.478000	0.83669	0.555000	0.69702	TCT	.	.		0.418	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990		G	70176519	C	G	70176519	3	3	82	1	0	0	0	0	1	0	0	0	11698	913	32	4	1577	4	PDPR	16	70176519	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	11624170	70176519	20178234	72	11268										
ADAT1	23536	hgsc.bcm.edu	37	chr16	75654670	75654670	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cccatagtgttcatagcataGctgagcaatctcatccgcgg	9	12	2	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr16:75654670G>T	ENST00000307921.3	-	3	173	c.28C>A	c.(28-30)Cta>Ata	p.L10I		NM_012091.3	NP_036223.2	Q9BUB4	ADAT1_HUMAN	adenosine deaminase, tRNA-specific 1	10					tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|RNA binding (GO:0003723)|tRNA-specific adenosine deaminase activity (GO:0008251)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)	19						TCATAGCATAGCTGAGCAATC	0.502																																					p.L10I		Atlas-SNP	.											.	ADAT1	45	.	0			c.C28A						.						93	86	88					16																	75654670		2198	4300	6498	SO:0001583	missense	23536	exon3			AGCATAGCTGAGC	AF125188	CCDS10922.1	16q23	2008-02-05			ENSG00000065457	ENSG00000065457			228	protein-coding gene	gene with protein product		604230				10430867	Standard	NM_012091		Approved		uc002feo.2	Q9BUB4	OTTHUMG00000137611	ENST00000307921.3:c.28C>A	chr16.hg19:g.75654670G>T	ENSP00000310015:p.Leu10Ile	54.0	0.0		34.0	21.0	NM_012091	Q9NVB7|Q9UNG3	Missense_Mutation	SNP	ENST00000307921.3	hg19	CCDS10922.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.710275	0.48517	.	.	ENSG00000065457	ENST00000307921	T	0.17213	2.29	5.5	4.55	0.56014	Adenosine deaminase/editase (1);	0.000000	0.53938	D	0.000050	T	0.36220	0.0959	M	0.67953	2.075	0.51767	D	0.999938	D	0.89917	1.0	D	0.91635	0.999	T	0.06285	-1.0835	10	0.44086	T	0.13	-10.2188	9.2865	0.37760	0.1639:0.0:0.8361:0.0	.	10	Q9BUB4	ADAT1_HUMAN	I	10	ENSP00000310015:L10I	ENSP00000310015:L10I	L	-	1	2	ADAT1	74212171	0.853000	0.29707	0.181000	0.23098	0.198000	0.23893	1.270000	0.33086	1.342000	0.45619	0.491000	0.48974	CTA	.	.		0.502	ADAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269027.1	NM_012091		T	75654670	G	T	75654670	3	4	82	1	0	0	0	0	1	0	0	0	284	962	34	3	1516	3	ADAT1	16	75654670	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	5478151	75654670	14700083	73	11269										
CCT6B	10693	hgsc.bcm.edu	37	chr17	33281459	33281459	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	acatacctctgttaagacatCagccagttcagcatgaactt	6	11	3	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr17:33281459C>T	ENST00000314144.5	-	4	611	c.496G>A	c.(496-498)Gat>Aat	p.D166N	CCT6B_ENST00000421975.3_Missense_Mutation_p.D166N|CCT6B_ENST00000436961.3_Missense_Mutation_p.D121N	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	166					chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				GTTAAGACATCAGCCAGTTCA	0.313																																					p.D166N		Atlas-SNP	.											.	CCT6B	63	.	0			c.G496A						.						141	125	131					17																	33281459		2202	4299	6501	SO:0001583	missense	10693	exon4			AGACATCAGCCAG	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"Heat Shock Proteins / Chaperonins"	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.496G>A	chr17.hg19:g.33281459C>T	ENSP00000327191:p.Asp166Asn	104.0	0.0		86.0	30.0	NM_006584	B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	hg19	CCDS32617.1	.	.	.	.	.	.	.	.	.	.	C	12.16	1.854491	0.32791	.	.	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.79653	-1.29;-1.29;-1.29	5.15	3.16	0.36331	.	0.085387	0.85682	N	0.000000	T	0.76877	0.4049	M	0.64676	1.99	0.58432	D	0.999999	B;B;B	0.20550	0.046;0.044;0.022	B;B;B	0.28991	0.097;0.072;0.047	T	0.72947	-0.4137	10	0.52906	T	0.07	-8.033	8.4249	0.32723	0.154:0.7642:0.0:0.0818	.	121;166;166	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	N	166;166;121	ENSP00000398044:D166N;ENSP00000327191:D166N;ENSP00000400917:D121N	ENSP00000327191:D166N	D	-	1	0	CCT6B	30305572	1.000000	0.71417	0.996000	0.52242	0.488000	0.33401	3.506000	0.53364	0.871000	0.35750	0.650000	0.86243	GAT	.	.		0.313	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584		T	33281459	C	T	33281459	3	4	82	1	0	0	0	0	1	0	0	0	2960	826	29	3	1140	3	CCT6B	17	33281459	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10		33281459	47913751	74	11270										
KRT13	3860	hgsc.bcm.edu	37	chr17	39659673	39659673	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gtcggcctccacgctctggcGcagggccagctcattctcat	11	16	3	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr17:39659673G>A	ENST00000246635.3	-	3	647	c.601C>T	c.(601-603)Cgc>Tgc	p.R201C	KRT13_ENST00000336861.3_Missense_Mutation_p.R201C|KRT13_ENST00000587544.1_Missense_Mutation_p.R201C|AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000587118.1_5'Flank	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	201	Coil 1B.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				ACGCTCTGGCGCAGGGCCAGC	0.483																																					p.R201C		Atlas-SNP	.											.	KRT13	72	.	0			c.C601T						.						62	62	62					17																	39659673		2203	4300	6503	SO:0001583	missense	3860	exon3			TCTGGCGCAGGGC		CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"-", "Intermediate filaments type I, keratins (acidic)"	6415	protein-coding gene	gene with protein product	"keratin, type I cytoskeletal 13", "cytokeratin 13"	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.601C>T	chr17.hg19:g.39659673G>A	ENSP00000246635:p.Arg201Cys	87.0	0.0		65.0	25.0	NM_002274	Q53G54|Q6AZK5|Q8N240	Missense_Mutation	SNP	ENST00000246635.3	hg19	CCDS11396.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.669876	0.88348	.	.	ENSG00000171401	ENST00000246635;ENST00000336861;ENST00000157775	D;D	0.91792	-2.91;-2.91	4.4	4.4	0.53042	Filament (1);	0.000000	0.46145	D	0.000309	D	0.93986	0.8074	M	0.82132	2.575	0.80722	D	1	P;P;P;P	0.49559	0.925;0.896;0.873;0.896	P;P;B;P	0.49192	0.602;0.478;0.346;0.478	D	0.94975	0.8120	10	0.66056	D	0.02	.	17.5315	0.87816	0.0:0.0:1.0:0.0	.	189;201;201;201	P13646-2;A1A4E9;P13646-3;P13646	.;.;.;K1C13_HUMAN	C	201;201;189	ENSP00000246635:R201C;ENSP00000336604:R201C	ENSP00000157775:R189C	R	-	1	0	KRT13	36913199	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	5.441000	0.66569	2.444000	0.82710	0.561000	0.74099	CGC	.	.		0.483	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		A	39659673	G	A	39659673	3	1	82	1	0	0	0	0	1	0	0	0	8459	1087	38	1	799	1	KRT13	17	39659673	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	6378214	39659673	41535537	75	11271										
RSAD1	55316	hgsc.bcm.edu	37	chr17	48561893	48561893	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tgctggagcggggcctactgCagctggatcacaggtgtgtt	16	9	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr17:48561893C>T	ENST00000258955.2	+	8	1283	c.1198C>T	c.(1198-1200)Cag>Tag	p.Q400*		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	400					porphyrin-containing compound biosynthetic process (GO:0006779)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|coproporphyrinogen oxidase activity (GO:0004109)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GGGCCTACTGCAGCTGGATCA	0.627																																					p.Q400X		Atlas-SNP	.											.	RSAD1	36	.	0			c.C1198T						.						45	47	46					17																	48561893		2203	4300	6503	SO:0001587	stop_gained	55316	exon8			CTACTGCAGCTGG	AK002026	CCDS11569.1	17q21.33	2004-11-08			ENSG00000136444	ENSG00000136444			25634	protein-coding gene	gene with protein product						12477932	Standard	NM_018346		Approved	FLJ11164	uc002iqw.1	Q9HA92	OTTHUMG00000162126	ENST00000258955.2:c.1198C>T	chr17.hg19:g.48561893C>T	ENSP00000258955:p.Gln400*	30.0	0.0		44.0	18.0	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Nonsense_Mutation	SNP	ENST00000258955.2	hg19	CCDS11569.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.698350	0.88830	.	.	ENSG00000136444	ENST00000258955	.	.	.	5.76	4.74	0.60224	.	0.239366	0.37437	N	0.002087	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-10.2354	8.6469	0.34011	0.243:0.6175:0.1395:0.0	.	.	.	.	X	400	.	ENSP00000258955:Q400X	Q	+	1	0	RSAD1	45916892	1.000000	0.71417	1.000000	0.80357	0.357000	0.29423	1.053000	0.30442	2.709000	0.92574	0.655000	0.94253	CAG	.	.		0.627	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346		T	48561893	C	T	48561893	4	4	82	1	0	0	0	0	0	1	0	0	13709	711	25	3	1228	3	RSAD1	17	48561893	Nonsense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	8902220	48561893	32633317	76	11272										
APPBP2	10513	hgsc.bcm.edu	37	chr17	58533692	58533692	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	aagaagccaaaagaagatgaTcttcaggtaggatgtgggta	13	4	2	4			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr17:58533692T>C	ENST00000083182.3	-	10	1399	c.1112A>G	c.(1111-1113)gAt>gGt	p.D371G		NM_001282476.1|NM_006380.2	NP_001269405.1|NP_006371.2	Q92624	APBP2_HUMAN	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	371					intracellular protein transport (GO:0006886)|intracellular transport (GO:0046907)|metabolic process (GO:0008152)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	microtubule motor activity (GO:0003777)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(17)|pancreas(1)|urinary_tract(1)	25	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			AAGAAGATGATCTTCAGGTAG	0.328																																					p.D371G		Atlas-SNP	.											.	APPBP2	48	.	0			c.A1112G						.						120	111	114					17																	58533692		2203	4297	6500	SO:0001583	missense	10513	exon10			AGATGATCTTCAG	AF017782	CCDS32699.1	17q23.2	2012-09-20	2001-11-28		ENSG00000062725	ENSG00000062725			622	protein-coding gene	gene with protein product	"protein interacting with APP tail 1"	605324	"amyloid beta precursor protein (cytoplasmic tail)-binding protein 2"			9843960	Standard	NM_006380		Approved	KIAA0228, Hs.84084, PAT1	uc002iys.1	Q92624		ENST00000083182.3:c.1112A>G	chr17.hg19:g.58533692T>C	ENSP00000083182:p.Asp371Gly	103.0	0.0		107.0	47.0	NM_006380	A8K862|O95095|Q8WVC9	Missense_Mutation	SNP	ENST00000083182.3	hg19	CCDS32699.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.379225	0.61735	.	.	ENSG00000062725	ENST00000083182	D	0.85013	-1.93	5.42	5.42	0.78866	Tetratricopeptide-like helical (1);	0.044306	0.85682	D	0.000000	D	0.87943	0.6305	L	0.39898	1.24	0.80722	D	1	P	0.49447	0.924	P	0.59424	0.857	D	0.88812	0.3292	10	0.59425	D	0.04	-18.3692	15.4629	0.75373	0.0:0.0:0.0:1.0	.	371	Q92624	APBP2_HUMAN	G	371	ENSP00000083182:D371G	ENSP00000083182:D371G	D	-	2	0	APPBP2	55888474	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.302000	0.78861	2.049000	0.60858	0.477000	0.44152	GAT	.	.		0.328	APPBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449465.1	NM_006380		C	58533692	T	C	58533692	3	2	82	1	0	0	0	0	1	0	0	0	816	1435	50	2	661	2	APPBP2	17	58533692	Missense_Mutation	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10	9971799	58533692	22661518	77	11273										
AXIN2	8313	hgsc.bcm.edu	37	chr17	63553964	63553964	+	Frame_Shift_Del	DEL	C	C	-													0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ttccgtggacctcacactcgCcgtggccctcagagttttgc							TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr17:63553964delC	ENST00000375702.5	-	1	883	c.775delG	c.(775-777)gcgfs	p.A259fs	AXIN2_ENST00000307078.5_Frame_Shift_Del_p.A259fs|CTD-2535L24.2_ENST00000577662.1_3'UTR			Q9Y2T1	AXIN2_HUMAN	axin 2	259					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						CTCACACTCGCCGTGGCCCTC	0.527									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																												p.A259fs		Atlas-Indel,Pindel	.											.	AXIN2	92	.	0			c.776delC						.						79	75	76					17																	63553964		2203	4300	6503	SO:0001589	frameshift_variant	8313	exon2	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	.	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"conductin", "axil"	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.775delG	chr17.hg19:g.63553964delC	ENSP00000364854:p.Ala259fs	96.0	0.0		81.0	28.0	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Frame_Shift_Del	DEL	ENST00000375702.5	hg19																																																																																				.	.		0.527	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		-	63553964	C	-	63553964	7	5	82	1	0	1	0	1	0	0	0	0	1237	739	26	0	1796	0	AXIN2	17	63553964	Frame_Shift_Del	DEL	C	TCGA-CC-A9FS-01A-11D-A36X-10	5020272	63553964	17641246	78	11274										
TRIM65	201292	hgsc.bcm.edu	37	chr17	73888160	73888160	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cctcttccaagaggaggccaCacagccggcttagcaactgc	10	15	1	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr17:73888160C>T	ENST00000269383.3	-	4	916	c.851G>A	c.(850-852)tGt>tAt	p.C284Y		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	284						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			GAGGAGGCCACACAGCCGGCT	0.652																																					p.C284Y		Atlas-SNP	.											.	TRIM65	23	.	0			c.G851A						.						17	18	18					17																	73888160		2120	4131	6251	SO:0001583	missense	201292	exon4			AGGCCACACAGCC	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	27316	protein-coding gene	gene with protein product			"tripartite motif-containing 65"			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.851G>A	chr17.hg19:g.73888160C>T	ENSP00000269383:p.Cys284Tyr	110.0	0.0		102.0	38.0	NM_001256124	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	hg19	CCDS11732.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.948|8.948	0.967543|0.967543	0.18659|0.18659	.|.	.|.	ENSG00000141569|ENSG00000141569	ENST00000269383|ENST00000543309	T|.	0.56941|.	0.43|.	3.89|3.89	0.707|0.707	0.18139|0.18139	.|.	0.706641|.	0.12949|.	N|.	0.425964|.	T|T	0.20901|0.20901	0.0503|0.0503	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	0.999999|0.999999	B|.	0.17852|.	0.024|.	B|.	0.12837|.	0.008|.	T|T	0.22382|0.22382	-1.0218|-1.0218	10|5	0.02654|.	T|.	1|.	.|.	3.2377|3.2377	0.06770|0.06770	0.0:0.4709:0.2109:0.3182|0.0:0.4709:0.2109:0.3182	.|.	284|.	Q6PJ69|.	TRI65_HUMAN|.	Y|M	284|158	ENSP00000269383:C284Y|.	ENSP00000269383:C284Y|.	C|V	-|-	2|1	0|0	TRIM65|TRIM65	71399755|71399755	0.000000|0.000000	0.05858|0.05858	0.871000|0.871000	0.34182|0.34182	0.966000|0.966000	0.64601|0.64601	-0.428000|-0.428000	0.06991|0.06991	0.418000|0.418000	0.25898|0.25898	0.456000|0.456000	0.33151|0.33151	TGT|GTG	.	.		0.652	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547		T	73888160	C	T	73888160	3	4	82	1	0	0	0	0	1	0	0	0	16554	478	17	3	714	3	TRIM65	17	73888160	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	10334196	73888160	7307050	79	11275										
EIF4A3	9775	hgsc.bcm.edu	37	chr17	78110084	78110084	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	agttaatgatgagggacaccTgagggacatccaaccccctg	11	11	0	3			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr17:78110084T>A	ENST00000269349.3	-	10	1255	c.1034A>T	c.(1033-1035)cAg>cTg	p.Q345L		NM_014740.3	NP_055555.1	P38919	IF4A3_HUMAN	eukaryotic translation initiation factor 4A3	345	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cytokine-mediated signaling pathway (GO:0019221)|embryonic cranial skeleton morphogenesis (GO:0048701)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|mRNA binding (GO:0003729)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)			GAGGGACACCTGAGGGACATC	0.428																																					p.Q345L		Atlas-SNP	.											.	EIF4A3	35	.	0			c.A1034T						.						107	104	105					17																	78110084		2203	4300	6503	SO:0001583	missense	9775	exon10			GACACCTGAGGGA	BC004386	CCDS11767.1	17q25.3	2010-02-10	2010-02-10	2006-11-27		ENSG00000141543		"DEAD-boxes"	18683	protein-coding gene	gene with protein product		608546	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 48", "eukaryotic translation initiation factor 4A, isoform 3"	DDX48		10623621, 14730019	Standard	NM_014740		Approved	KIAA0111, EIF4AIII	uc002jxs.3	P38919		ENST00000269349.3:c.1034A>T	chr17.hg19:g.78110084T>A	ENSP00000269349:p.Gln345Leu	272.0	0.0		194.0	53.0	NM_014740	Q15033|Q6IBQ2|Q96A18	Missense_Mutation	SNP	ENST00000269349.3	hg19	CCDS11767.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.459734	0.84317	.	.	ENSG00000141543	ENST00000269349	T	0.04809	3.55	4.03	4.03	0.46877	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.11836	0.0288	L	0.55743	1.74	0.80722	D	1	P	0.50156	0.932	P	0.55055	0.767	T	0.00819	-1.1553	10	0.87932	D	0	-27.5873	10.9528	0.47341	0.0:0.0:0.0:1.0	.	345	P38919	IF4A3_HUMAN	L	345	ENSP00000269349:Q345L	ENSP00000269349:Q345L	Q	-	2	0	EIF4A3	75724679	1.000000	0.71417	0.990000	0.47175	0.898000	0.52572	7.315000	0.78998	1.714000	0.51371	0.459000	0.35465	CAG	.	.		0.428	EIF4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437446.1	NM_014740		A	78110084	T	A	78110084	3	1	82	1	0	0	0	0	1	0	0	0	5028	1580	55	4	213	4	EIF4A3	17	78110084	Missense_Mutation	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10	4221924	78110084	3085126	80	11276										
DOK6	220164	hgsc.bcm.edu	37	chr18	67365697	67365697	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ggatatttatggtgaatgcaCaatgcagatcactcatgaaa	9	6	2	3			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr18:67365697C>T	ENST00000382713.5	+	5	657	c.467C>T	c.(466-468)aCa>aTa	p.T156I	DOK6_ENST00000584435.1_3'UTR	NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	156	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.									central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	20		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				GGTGAATGCACAATGCAGATC	0.438																																					p.T156I		Atlas-SNP	.											.	DOK6	56	.	0			c.C467T						.						131	112	118					18																	67365697		2203	4300	6503	SO:0001583	missense	220164	exon5			AATGCACAATGCA	AK057795	CCDS32841.1	18q22.2	2013-01-10	2005-01-18	2005-01-18		ENSG00000206052		"Pleckstrin homology (PH) domain containing"	28301	protein-coding gene	gene with protein product		611402	"docking protein 5-like"	DOK5L		15286081	Standard	NM_152721		Approved	MGC20785, HsT3226	uc002lkl.3	Q6PKX4		ENST00000382713.5:c.467C>T	chr18.hg19:g.67365697C>T	ENSP00000372160:p.Thr156Ile	113.0	0.0		111.0	32.0	NM_152721	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Missense_Mutation	SNP	ENST00000382713.5	hg19	CCDS32841.1	.	.	.	.	.	.	.	.	.	.	C	16.24	3.066350	0.55539	.	.	ENSG00000206052	ENST00000382713	D	0.82526	-1.62	5.72	5.72	0.89469	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (3);	0.105872	0.64402	D	0.000005	T	0.73644	0.3613	N	0.11818	0.18	0.80722	D	1	B	0.26318	0.146	B	0.32928	0.155	T	0.68191	-0.5474	10	0.22109	T	0.4	.	18.8571	0.92257	0.0:1.0:0.0:0.0	.	156	Q6PKX4	DOK6_HUMAN	I	156	ENSP00000372160:T156I	ENSP00000372160:T156I	T	+	2	0	DOK6	65516677	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.706000	0.84615	2.709000	0.92574	0.591000	0.81541	ACA	.	.		0.438	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721		T	67365697	C	T	67365697	3	4	82	1	0	0	0	0	1	0	0	0	4703	478	17	3	485	3	DOK6	18	67365697	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10		67365697	10711551	81	11277										
SCAMP4	113178	hgsc.bcm.edu	37	chr19	1924197	1924197	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ggcggaacccaccgtcgaggGaggcccagtacaacaacttc	12	14	0	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr19:1924197G>C	ENST00000316097.8	+	7	871	c.604G>C	c.(604-606)Gag>Cag	p.E202Q	SCAMP4_ENST00000409472.1_Missense_Mutation_p.E168Q	NM_079834.2	NP_524558.1	Q969E2	SCAM4_HUMAN	secretory carrier membrane protein 4	202					protein transport (GO:0015031)	integral component of membrane (GO:0016021)							Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCGTCGAGGGAGGCCCAGTA	0.642																																					p.E202Q		Atlas-SNP	.											.	SCAMP4	7	.	0			c.G604C						.						38	48	45					19																	1924197		2008	4169	6177	SO:0001583	missense	113178	exon7			TCGAGGGAGGCCC	AK091166	CCDS45903.1	19p13.3	2013-02-21			ENSG00000227500	ENSG00000227500		"Secretory carrier membrane proteins"	30385	protein-coding gene	gene with protein product		613764					Standard	NM_079834		Approved	FLJ33847	uc002luj.4	Q969E2	OTTHUMG00000154590	ENST00000316097.8:c.604G>C	chr19.hg19:g.1924197G>C	ENSP00000316007:p.Glu202Gln	89.0	0.0		122.0	69.0	NM_079834	Q8N2N1|Q8NAV0	Missense_Mutation	SNP	ENST00000316097.8	hg19	CCDS45903.1	.	.	.	.	.	.	.	.	.	.	g	10.64	1.407442	0.25378	.	.	ENSG00000227500	ENST00000316097;ENST00000409472	T;T	0.32753	2.23;1.44	4.97	4.97	0.65823	.	.	.	.	.	T	0.24392	0.0591	L	0.31294	0.92	0.50313	D	0.999869	P;B	0.38535	0.635;0.361	B;B	0.37888	0.26;0.057	T	0.03325	-1.1048	9	0.15952	T	0.53	-16.849	17.2084	0.86924	0.0:0.0:1.0:0.0	.	168;202	Q969E2-2;Q969E2	.;SCAM4_HUMAN	Q	202;168	ENSP00000316007:E202Q;ENSP00000386865:E168Q	ENSP00000316007:E202Q	E	+	1	0	SCAMP4	1875197	1.000000	0.71417	0.989000	0.46669	0.230000	0.25150	3.534000	0.53568	2.301000	0.77427	0.462000	0.41574	GAG	.	.		0.642	SCAMP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336210.3	NM_079834		C	1924197	G	C	1924197	3	2	82	1	0	0	0	0	1	0	0	0	13888	1175	41	4	626	4	SCAMP4	19	1924197	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10		1924197	57204786	82	11278										
NFIC	4782	hgsc.bcm.edu	37	chr19	3366645	3366645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cgcgcccgggatgtattcgtCcccgctctgcctcacccagg	11	18	2	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr19:3366645C>T	ENST00000443272.2	+	1	62	c.11C>T	c.(10-12)tCc>tTc	p.S4F	NFIC_ENST00000341919.3_Missense_Mutation_p.S4F|NFIC_ENST00000586919.1_Intron|NFIC_ENST00000589123.1_Intron|NFIC_ENST00000395111.3_Intron|NFIC_ENST00000590282.1_Missense_Mutation_p.S4F|NFIC_ENST00000346156.5_Intron	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	4					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		ATGTATTCGTCCCCGCTCTGC	0.741																																					p.S4F		Atlas-SNP	.											.	NFIC	36	.	0			c.C11T						.						8	12	11					19																	3366645		1929	3957	5886	SO:0001583	missense	4782	exon1			ATTCGTCCCCGCT	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.11C>T	chr19.hg19:g.3366645C>T	ENSP00000396843:p.Ser4Phe	104.0	0.0		133.0	31.0	NM_001245004	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	hg19	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	c	15.52	2.858640	0.51376	.	.	ENSG00000141905	ENST00000341919;ENST00000343825;ENST00000269778	T	0.52057	0.68	2.37	2.37	0.29283	CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	.	.	.	.	T	0.29652	0.0740	N	0.03608	-0.345	0.80722	D	1	B;B;D	0.53885	0.378;0.378;0.963	B;B;P	0.49085	0.287;0.266;0.6	T	0.21690	-1.0238	9	0.87932	D	0	.	8.2664	0.31817	0.0:1.0:0.0:0.0	.	4;4;4	B7Z4U5;P08651;P08651-5	.;NFIC_HUMAN;.	F	4	ENSP00000342194:S4F	ENSP00000269778:S4F	S	+	2	0	NFIC	3317645	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.373000	0.34272	1.331000	0.45412	0.387000	0.25754	TCC	.	.		0.741	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597		T	3366645	C	T	3366645	3	4	82	1	0	0	0	0	1	0	0	0	10381	855	30	3	20	3	NFIC	19	3366645	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	1442448	3366645	55762338	83	11279										
DPP9	91039	hgsc.bcm.edu	37	chr19	4695441	4695441	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	accacatacggctggacattCctggggacagctctggcaga	12	12	1	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr19:4695441C>A	ENST00000598800.1	-	13	1720	c.1215G>T	c.(1213-1215)agG>agT	p.R405S	DPP9_ENST00000262960.9_Missense_Mutation_p.R434S|DPP9_ENST00000597849.1_Missense_Mutation_p.R434S|DPP9_ENST00000594671.1_Missense_Mutation_p.R405S			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	405						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		GCTGGACATTCCTGGGGACAG	0.637																																					p.R434S		Atlas-SNP	.											.	DPP9	59	.	0			c.G1302T						.						18	21	20					19																	4695441		2051	4192	6243	SO:0001583	missense	91039	exon12			GACATTCCTGGGG	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"dipeptidylpeptidase 9"				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.1215G>T	chr19.hg19:g.4695441C>A	ENSP00000469603:p.Arg405Ser	161.0	0.0		232.0	60.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Missense_Mutation	SNP	ENST00000598800.1	hg19		.	.	.	.	.	.	.	.	.	.	C	0.019	-1.465164	0.01053	.	.	ENSG00000142002	ENST00000357909;ENST00000381797;ENST00000262960	T	0.28454	1.61	3.91	1.58	0.23477	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	1.390610	0.04174	N	0.325322	T	0.13586	0.0329	N	0.04297	-0.235	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.0;0.004	T	0.24584	-1.0156	10	0.13853	T	0.58	-5.6602	4.1753	0.10349	0.2314:0.6015:0.0:0.1671	.	405;434	Q86TI2;Q1ZZB8	DPP9_HUMAN;.	S	513;375;434	ENSP00000262960:R434S	ENSP00000262960:R434S	R	-	3	2	DPP9	4646441	0.000000	0.05858	0.007000	0.13788	0.262000	0.26303	0.129000	0.15830	0.830000	0.34757	0.561000	0.74099	AGG	.	.		0.637	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2			A	4695441	C	A	4695441	3	1	82	1	0	0	0	0	1	0	0	0	4735	854	30	3	1420	3	DPP9	19	4695441	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	1328796	4695441	54433542	84	11280										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10112250	10112250	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	atattctgctgcccggaagtCagggcccatggtggaatcat	12	10	3	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr19:10112250C>T	ENST00000264828.3	-	8	1145	c.1060G>A	c.(1060-1062)Gac>Aac	p.D354N		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	354	Nonhelical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			GCCCGGAAGTCAGGGCCCATG	0.552											OREG0025228	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D354N		Atlas-SNP	.											.	COL5A3	243	.	0			c.G1060A						.						99	95	97					19																	10112250		2203	4300	6503	SO:0001583	missense	50509	exon8			GGAAGTCAGGGCC	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.1060G>A	chr19.hg19:g.10112250C>T	ENSP00000264828:p.Asp354Asn	98.0	0.0	662	132.0	43.0	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.240366	0.22711	.	.	ENSG00000080573	ENST00000264828	D	0.89050	-2.46	4.74	-9.45	0.00600	.	1.251440	0.05709	U	0.595565	T	0.70780	0.3263	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.58730	-0.7585	10	0.17832	T	0.49	.	7.6719	0.28463	0.0:0.1421:0.3559:0.502	.	354	P25940	CO5A3_HUMAN	N	354	ENSP00000264828:D354N	ENSP00000264828:D354N	D	-	1	0	COL5A3	9973250	0.000000	0.05858	0.004000	0.12327	0.840000	0.47671	-2.598000	0.00894	-1.636000	0.01533	0.462000	0.41574	GAC	.	.		0.552	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		T	10112250	C	T	10112250	3	4	82	1	0	0	0	0	1	0	0	0	3700	826	29	3	4417	3	COL5A3	19	10112250	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	5416809	10112250	49016733	85	11281										
PPAN	56342	hgsc.bcm.edu	37	chr19	10218693	10218693	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cgccggcaccgcatgcacgaGcagcagtttgcccacccacc	10	19	0	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr19:10218693G>A	ENST00000253107.7	+	5	502	c.396G>A	c.(394-396)gaG>gaA	p.E132E	PPAN_ENST00000556468.1_Silent_p.E132E|PPAN-P2RY11_ENST00000428358.1_Silent_p.E132E|PPAN-P2RY11_ENST00000393796.4_Silent_p.E132E|PPAN_ENST00000393793.1_Silent_p.E79E|SNORD105B_ENST00000458770.1_RNA|SNORD105_ENST00000386910.1_RNA	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	132	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|liver(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			GCATGCACGAGCAGCAGTTTG	0.597																																					p.E132E		Atlas-SNP	.											.	PPAN	43	.	0			c.G396A						.						140	103	116					19																	10218693		2203	4300	6503	SO:0001819	synonymous_variant	56342	exon5			GCACGAGCAGCAG	BC033202	CCDS12225.1	19p13.2	2008-02-05	2001-11-28		ENSG00000130810	ENSG00000130810			9227	protein-coding gene	gene with protein product		607793	"peter pan (Drosophila) homolog"			10873382	Standard	NM_020230		Approved	SSF1, SSF2, SSF, BXDC3		Q9NQ55	OTTHUMG00000156826	ENST00000253107.7:c.396G>A	chr19.hg19:g.10218693G>A		79.0	0.0		123.0	23.0	NM_020230	C9J3F9|Q9BW97|Q9H170	Silent	SNP	ENST00000253107.7	hg19	CCDS12225.1																																																																																			.	.		0.597	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230		A	10218693	G	A	10218693	2	1	82	1	0	0	0	0	0	0	0	1	12297	962	34	3		3	PPAN	19	10218693	Silent	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	106443	10218693	48910290	86	11282										
TNPO2	30000	hgsc.bcm.edu	37	chr19	12822419	12822419	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tcatcccattcaccaagatgGggatcaacctgcacagagag	9	12	3	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr19:12822419G>C	ENST00000592287.1	-	10	1007	c.899C>G	c.(898-900)cCc>cGc	p.P300R	TNPO2_ENST00000425528.1_Missense_Mutation_p.P300R|TNPO2_ENST00000441499.1_Missense_Mutation_p.P300R|TNPO2_ENST00000589956.1_Intron|TNPO2_ENST00000588216.1_Missense_Mutation_p.P300R|TNPO2_ENST00000356861.5_Missense_Mutation_p.P300R|TNPO2_ENST00000450764.2_Missense_Mutation_p.P300R	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	300					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CACCAAGATGGGGATCAACCT	0.592																																					p.P300R		Atlas-SNP	.											.	TNPO2	108	.	0			c.C899G						.						58	56	57					19																	12822419		2008	4170	6178	SO:0001583	missense	30000	exon10			AAGATGGGGATCA	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"Importins"	19998	protein-coding gene	gene with protein product	"importin 3", "karyopherin beta 2b"	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.899C>G	chr19.hg19:g.12822419G>C	ENSP00000468434:p.Pro300Arg	63.0	0.0		73.0	39.0	NM_013433	O14655|Q6IN77	Missense_Mutation	SNP	ENST00000592287.1	hg19	CCDS45991.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.847485	0.71603	.	.	ENSG00000105576	ENST00000536114;ENST00000425528;ENST00000441499;ENST00000450764;ENST00000356861;ENST00000420511;ENST00000546320	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	4.98	4.98	0.66077	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.87220	0.6123	H	0.95574	3.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.987;0.993	D	0.91173	0.4970	10	0.87932	D	0	-25.4138	17.3752	0.87390	0.0:0.0:1.0:0.0	.	464;300	Q4LE60;O14787	.;TNPO2_HUMAN	R	464;300;300;300;300;300;300	ENSP00000407182:P300R;ENSP00000389648:P300R;ENSP00000397379:P300R;ENSP00000349321:P300R	ENSP00000349321:P300R	P	-	2	0	TNPO2	12683419	1.000000	0.71417	0.998000	0.56505	0.630000	0.37929	9.036000	0.93758	2.474000	0.83562	0.561000	0.74099	CCC	.	.		0.592	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433		C	12822419	G	C	12822419	3	2	82	1	0	0	0	0	1	0	0	0	16351	1232	43	4	1854	4	TNPO2	19	12822419	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	2603726	12822419	46306564	87	11283										
EPHX3	79852	hgsc.bcm.edu	37	chr19	15343002	15343002	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	cgcgacggcgccagcagcgcGgtcaccaccagctccggcat	13	18	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr19:15343002G>T	ENST00000221730.3	-	1	241	c.21C>A	c.(19-21)acC>acA	p.T7T	EPHX3_ENST00000435261.1_Silent_p.T7T|EPHX3_ENST00000602233.1_Silent_p.T7T	NM_024794.2	NP_079070.1	Q9H6B9	EPHX3_HUMAN	epoxide hydrolase 3	7						extracellular region (GO:0005576)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(1)	7						CCAGCAGCGCGGTCACCACCA	0.741																																					p.T7T		Atlas-SNP	.											.	EPHX3	22	.	0			c.C21A						.						6	7	7					19																	15343002		1786	3463	5249	SO:0001819	synonymous_variant	79852	exon2			CAGCGCGGTCACC	AK026061	CCDS12327.1	19p13.13	2011-10-05	2009-04-06	2009-04-06	ENSG00000105131	ENSG00000105131		"Abhydrolase domain containing"	23760	protein-coding gene	gene with protein product			"abhydrolase domain containing 9"	ABHD9			Standard	NM_024794		Approved	FLJ22408	uc002nap.3	Q9H6B9		ENST00000221730.3:c.21C>A	chr19.hg19:g.15343002G>T		22.0	0.0		30.0	18.0	NM_001142886	A3KMR3	Silent	SNP	ENST00000221730.3	hg19	CCDS12327.1																																																																																			.	.		0.741	EPHX3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465797.1	NM_024794		T	15343002	G	T	15343002	2	4	82	1	0	0	0	0	0	0	0	1	5183	1103	39	1		1	EPHX3	19	15343002	Silent	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	2520583	15343002	43785981	88	11284										
SARS2	54938	hgsc.bcm.edu	37	chr19	39412662	39412662	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	acaaggagagaaagctggccTgggaatgggaggaacgtagg	18	5	0	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr19:39412662T>A	ENST00000221431.6	-	3	553				SARS2_ENST00000594171.1_Intron|CTC-360G5.8_ENST00000599996.1_Intron|SARS2_ENST00000448145.2_Intron|SARS2_ENST00000600042.1_Silent_p.P150P|SARS2_ENST00000430193.3_Intron	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial						gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			aaagctggcctgggaatggga	0.483																																					p.P150P		Atlas-SNP	.											.	SARS2	33	.	0			c.A450T						.						81	80	81					19																	39412662		692	1591	2283	SO:0001627	intron_variant	54938	exon4			CTGGCCTGGGAAT	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"Aminoacyl tRNA synthetases / Class II"	17697	protein-coding gene	gene with protein product	"serine tRNA ligase 2, mitochondrial"	612804	"serine-tRNA ligase, mitochondrial", "seryl-tRNA synthetase 2"	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.393+215A>T	chr19.hg19:g.39412662T>A		166.0	0.0		199.0	81.0	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	hg19	CCDS33017.1																																																																																			.	.		0.483	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827		A	39412662	T	A	39412662	1	1	82	0	1	0	0	0	0	0	0	0	13860	1567	55	4		4	SARS2	19	39412662	Intron	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10	24069660	39412662	19716321	89	11285										
FCAR	2204	hgsc.bcm.edu	37	chr19	55401023	55401023	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ttgtgtctccagactccatcCaccaagattacacgacgcag	7	14	1	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr19:55401023C>G	ENST00000355524.3	+	5	668	c.658C>G	c.(658-660)Cac>Gac	p.H220D	FCAR_ENST00000345937.4_Missense_Mutation_p.H124D|FCAR_ENST00000353758.4_Missense_Mutation_p.H111D|CTB-61M7.2_ENST00000594721.1_lincRNA|FCAR_ENST00000359272.4_Missense_Mutation_p.H208D|FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000391723.3_Missense_Mutation_p.P183R|FCAR_ENST00000391724.3_Missense_Mutation_p.H186D|FCAR_ENST00000391726.3_Missense_Mutation_p.H112D|FCAR_ENST00000391725.3_Missense_Mutation_p.H198D	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	220					immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		AGACTCCATCCACCAAGATTA	0.517																																					p.H220D		Atlas-SNP	.											.	FCAR	110	.	0			c.C658G						.						322	319	320					19																	55401023		2203	4300	6503	SO:0001583	missense	2204	exon5			TCCATCCACCAAG	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.658C>G	chr19.hg19:g.55401023C>G	ENSP00000347714:p.His220Asp	54.0	0.0		53.0	24.0	NM_002000	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Missense_Mutation	SNP	ENST00000355524.3	hg19	CCDS12907.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.009|0.009	-1.858717|-1.858717	0.00558|0.00558	.|.	.|.	ENSG00000186431|ENSG00000186431	ENST00000391726;ENST00000355524;ENST00000391725;ENST00000345937;ENST00000353758;ENST00000359272;ENST00000391724|ENST00000391723	T;T;T;T;T;T;T|T	0.11277|0.00551	4.14;6.96;2.79;5.15;6.72;6.88;2.79|6.65	3.86|3.86	-7.72|-7.72	0.01250|0.01250	.|.	.|.	.|.	.|.	.|.	T|T	0.00468|0.00468	0.0015|0.0015	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B;B;B;B;B;B;B|B	0.10296|0.02656	0.0;0.001;0.0;0.001;0.003;0.0;0.002|0.0	B;B;B;B;B;B;B|B	0.09377|0.01281	0.0;0.003;0.0;0.0;0.004;0.0;0.001|0.0	T|T	0.36672|0.36672	-0.9738|-0.9738	8|8	0.10377|0.66056	T|D	0.69|0.02	.|.	14.192|14.192	0.65644|0.65644	0.1341:0.7877:0.0782:0.0|0.1341:0.7877:0.0782:0.0	.|.	111;186;112;208;198;124;220|183	Q92592;Q92593;Q92587;Q9UEK0;Q53X39;P24071-3;P24071|Q92588	.;.;.;.;.;.;FCAR_HUMAN|.	D|R	112;220;198;124;111;208;186|183	ENSP00000375606:H112D;ENSP00000347714:H220D;ENSP00000375605:H198D;ENSP00000338257:H124D;ENSP00000338058:H111D;ENSP00000352218:H208D;ENSP00000375604:H186D|ENSP00000375603:P183R	ENSP00000338257:H124D|ENSP00000375603:P183R	H|P	+|+	1|2	0|0	FCAR|FCAR	60092835|60092835	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-1.114000|-1.114000	0.03293|0.03293	-2.658000|-2.658000	0.00420|0.00420	-1.772000|-1.772000	0.00662|0.00662	CAC|CCA	.	.		0.517	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000		G	55401023	C	G	55401023	3	3	82	1	0	0	0	0	1	0	0	0	5781	594	21	4	747	4	FCAR	19	55401023	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	15988361	55401023	3727960	90	11286										
XRN2	22803	hgsc.bcm.edu	37	chr20	21312420	21312420	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	gtttagcccagcctaaccatGacccaaatactcatcattgt	5	13	2	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr20:21312420G>T	ENST00000377191.3	+	8	759	c.664G>T	c.(664-666)Gac>Tac	p.D222Y	XRN2_ENST00000430571.2_Missense_Mutation_p.D146Y|XRN2_ENST00000539513.1_Missense_Mutation_p.D168Y	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	222					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D222Y(1)		endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						GCCTAACCATGACCCAAATAC	0.343																																					p.D222Y		Atlas-SNP	.											XRN2,colon,carcinoma,0,1	XRN2	90	.	1	Substitution - Missense(1)	large_intestine(1)	c.G664T						.						227	199	209					20																	21312420		2203	4300	6503	SO:0001583	missense	22803	exon8			AACCATGACCCAA	AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.664G>T	chr20.hg19:g.21312420G>T	ENSP00000366396:p.Asp222Tyr	170.0	0.0		111.0	48.0	NM_012255	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Missense_Mutation	SNP	ENST00000377191.3	hg19	CCDS13144.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.421264	0.83559	.	.	ENSG00000088930	ENST00000377191;ENST00000430571;ENST00000539513	T;T;T	0.37411	1.22;1.2;1.21	5.18	5.18	0.71444	Putative 5-3 exonuclease (1);	0.000000	0.85682	D	0.000000	T	0.74419	0.3714	H	0.97051	3.93	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84052	0.0370	10	0.87932	D	0	-18.0977	19.0515	0.93049	0.0:0.0:1.0:0.0	.	222	Q9H0D6	XRN2_HUMAN	Y	222;146;168	ENSP00000366396:D222Y;ENSP00000413548:D146Y;ENSP00000441113:D168Y	ENSP00000366396:D222Y	D	+	1	0	XRN2	21260420	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.247000	0.95444	2.556000	0.86216	0.655000	0.94253	GAC	.	.		0.343	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255		T	21312420	G	T	21312420	3	4	82	1	0	0	0	0	1	0	0	0	17475	1290	45	3	694	3	XRN2	20	21312420	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10		21312420	41713100	91	11287										
C20orf134	170487	hgsc.bcm.edu	37	chr20	32256018	32256018	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	accaggagtgtggctccaggCtgctgtacgatgtgttcaac	13	10	1	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr20:32256018C>A	ENST00000330271.4	+	1	1715	c.715C>A	c.(715-717)Ctg>Atg	p.L239M	NECAB3_ENST00000375238.4_Intron|NECAB3_ENST00000246190.6_Intron	NM_001024675.1	NP_001019846.1	Q5JWF8	ACL10_HUMAN	actin-like 10	239																	TGGCTCCAGGCTGCTGTACGA	0.612											OREG0025871	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L239M		Atlas-SNP	.											.	.	.	.	0			c.C715A						.						28	32	31					20																	32256018		2198	4293	6491	SO:0001583	missense	170487	exon1			TCCAGGCTGCTGT	AL121906	CCDS33463.1	20q11.22	2011-11-24	2011-11-24	2011-11-24	ENSG00000182584	ENSG00000182584			16127	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 134"	C20orf134			Standard	NM_001024675		Approved		uc002wzt.3	Q5JWF8	OTTHUMG00000032262	ENST00000330271.4:c.715C>A	chr20.hg19:g.32256018C>A	ENSP00000329647:p.Leu239Met	95.0	0.0	831	89.0	5.0	NM_001024675	B9EH76	Missense_Mutation	SNP	ENST00000330271.4	hg19	CCDS33463.1	.	.	.	.	.	.	.	.	.	.	c	14.90	2.673478	0.47781	.	.	ENSG00000182584	ENST00000330271	D	0.94862	-3.54	4.59	3.65	0.41850	.	0.540185	0.13903	N	0.354816	D	0.95252	0.8460	L	0.49350	1.555	0.28769	N	0.900475	D	0.76494	0.999	D	0.72338	0.977	D	0.89202	0.3558	10	0.87932	D	0	-11.191	6.9532	0.24556	0.0:0.798:0.0:0.202	.	239	Q5JWF8	CT134_HUMAN	M	239	ENSP00000329647:L239M	ENSP00000329647:L239M	L	+	1	2	C20orf134	31719679	0.355000	0.24921	0.987000	0.45799	0.810000	0.45777	0.626000	0.24492	1.165000	0.42670	-0.389000	0.06534	CTG	.	.		0.612	ACTL10-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078713.1			A	32256018	C	A	32256018	3	1	82	1	0	0	0	0	1	0	0	0	2089	796	28	3	717	3	C20orf134	20	32256018	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	10943598	32256018	30769502	92	11288										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39791106	39791106	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tctcagtatatcagccaaggAcctgaagaacatgctgtccc	8	12	2	2			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr20:39791106A>T	ENST00000373271.1	+	5	932	c.527A>T	c.(526-528)gAc>gTc	p.D176V	PLCG1_ENST00000244007.3_Missense_Mutation_p.D176V|PLCG1_ENST00000373272.2_Missense_Mutation_p.D176V	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	176	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				TCAGCCAAGGACCTGAAGAAC	0.582																																					p.D176V		Atlas-SNP	.											.	PLCG1	111	.	0			c.A527T						.						104	87	93					20																	39791106		2203	4300	6503	SO:0001583	missense	5335	exon5			CCAAGGACCTGAA	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.527A>T	chr20.hg19:g.39791106A>T	ENSP00000362368:p.Asp176Val	102.0	0.0		104.0	30.0	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	hg19	CCDS13314.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935902	0.73442	.	.	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.43688	0.94;0.94;0.94	4.96	4.96	0.65561	EF-hand-like domain (1);	0.051911	0.85682	D	0.000000	T	0.62344	0.2420	M	0.73217	2.22	0.80722	D	1	D;D	0.71674	0.998;0.996	D;D	0.69479	0.964;0.943	T	0.67284	-0.5709	10	0.87932	D	0	.	14.2961	0.66314	1.0:0.0:0.0:0.0	.	176;176	P19174;A2A284	PLCG1_HUMAN;.	V	176	ENSP00000244007:D176V;ENSP00000362368:D176V;ENSP00000362369:D176V	ENSP00000244007:D176V	D	+	2	0	PLCG1	39224520	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.339000	0.96797	1.869000	0.54173	0.379000	0.24179	GAC	.	.		0.582	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		T	39791106	A	T	39791106	3	4	82	1	0	0	0	0	1	0	0	0	12044	275	10	4	545	4	PLCG1	20	39791106	Missense_Mutation	SNP	A	TCGA-CC-A9FS-01A-11D-A36X-10	7535088	39791106	23234414	93	11289										
CLIC6	54102	hgsc.bcm.edu	37	chr21	36042758	36042758	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	agggcagacgctggcgaggaCagggtaggggatgggccaca	20	8	0	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr21:36042758C>T	ENST00000360731.3	+	1	1071	c.1071C>T	c.(1069-1071)gaC>gaT	p.D357D	CLIC6_ENST00000349499.2_Silent_p.D357D			Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6	357						chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19						CTGGCGAGGACAGGGTAGGGG	0.721																																					p.D357D		Atlas-SNP	.											.	CLIC6	49	.	0			c.C1071T						.						5	8	7					21																	36042758		1825	3569	5394	SO:0001819	synonymous_variant	54102	exon1			CGAGGACAGGGTA	AF426169	CCDS13638.1	21q22.12	2012-09-26			ENSG00000159212	ENSG00000159212		"Ion channels / Chloride channels : Intracellular"	2065	protein-coding gene	gene with protein product		615321		CLIC1L		10830953	Standard	NM_053277		Approved	CLIC5	uc002yuf.1	Q96NY7	OTTHUMG00000086237	ENST00000360731.3:c.1071C>T	chr21.hg19:g.36042758C>T		165.0	0.0		163.0	12.0	NM_053277	A8K0U8|Q8IX31	Silent	SNP	ENST00000360731.3	hg19																																																																																				.	.		0.721	CLIC6-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000194156.1			T	36042758	C	T	36042758	2	4	82	1	0	0	0	0	0	0	0	1	3532	477	17	3		3	CLIC6	21	36042758	Silent	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10		36042758	12087137	94	11290										
MMP11	4320	hgsc.bcm.edu	37	chr22	24123543	24123543	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ccactggcagggactgcccaGccctgtggacgctgccttcg	13	16	0	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr22:24123543G>A	ENST00000215743.3	+	6	1074	c.1022G>A	c.(1021-1023)aGc>aAc	p.S341N		NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	341					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	GGACTGCCCAGCCCTGTGGAC	0.632																																					p.S341N		Atlas-SNP	.											.	MMP11	53	.	0			c.G1022A						.						26	26	26					22																	24123543		2202	4300	6502	SO:0001583	missense	4320	exon6			TGCCCAGCCCTGT		CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"matrix metalloproteinase 11 (stromelysin 3)"	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.1022G>A	chr22.hg19:g.24123543G>A	ENSP00000215743:p.Ser341Asn	55.0	0.0		38.0	14.0	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Missense_Mutation	SNP	ENST00000215743.3	hg19	CCDS13816.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.624648	0.28889	.	.	ENSG00000099953	ENST00000215743	T	0.02812	4.15	4.73	-1.76	0.08006	Hemopexin/matrixin, conserved site (1);Hemopexin/matrixin (2);	0.699813	0.16349	N	0.218319	T	0.01320	0.0043	N	0.12611	0.24	0.09310	N	1	B	0.15930	0.015	B	0.16289	0.015	T	0.46512	-0.9186	10	0.21540	T	0.41	.	1.9291	0.03323	0.2282:0.2443:0.4026:0.1248	.	341	P24347	MMP11_HUMAN	N	341	ENSP00000215743:S341N	ENSP00000215743:S341N	S	+	2	0	MMP11	22453543	0.005000	0.15991	0.967000	0.41034	0.947000	0.59692	1.403000	0.34612	0.028000	0.15324	0.650000	0.86243	AGC	.	.		0.632	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940		A	24123543	G	A	24123543	3	1	82	1	0	0	0	0	1	0	0	0	9659	971	34	3	1044	3	MMP11	22	24123543	Missense_Mutation	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10		24123543	27181023	95	11291										
THOC5	8563	hgsc.bcm.edu	37	chr22	29913067	29913067	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tagagattggtgtccccagcCagtcccgcatccacaatgtc	9	14	0	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr22:29913067C>G	ENST00000490103.1	-	17	1754	c.1632G>C	c.(1630-1632)ctG>ctC	p.L544L	CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Silent_p.L544L|THOC5_ENST00000397872.1_Silent_p.L544L|THOC5_ENST00000397873.2_Silent_p.L544L	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	544					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TGTCCCCAGCCAGTCCCGCAT	0.532																																					p.L544L		Atlas-SNP	.											.	THOC5	58	.	0			c.G1632C						.						150	138	142					22																	29913067		2203	4300	6503	SO:0001819	synonymous_variant	8563	exon18			CCCAGCCAGTCCC	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"THO complex subunits"	19074	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 79"	612733	"chromosome 22 open reading frame 19"	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1632G>C	chr22.hg19:g.29913067C>G		151.0	0.0		99.0	39.0	NM_001002878	O60839|Q9UPZ5	Silent	SNP	ENST00000490103.1	hg19	CCDS13859.1																																																																																			.	.		0.532	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678		G	29913067	C	G	29913067	2	3	82	1	0	0	0	0	0	0	0	1	15883	581	21	4		4	THOC5	22	29913067	Silent	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	5789524	29913067	21391499	96	11292										
ASCC2	84164	hgsc.bcm.edu	37	chr22	30202839	30202839	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ttcaggatgatgtggaaaatCtccattagcttcttcctgga	9	8	3	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr22:30202839C>A	ENST00000397771.2	-	11	1140	c.963G>T	c.(961-963)gaG>gaT	p.E321D	ASCC2_ENST00000478812.1_5'UTR|ASCC2_ENST00000307790.3_Missense_Mutation_p.E321D|ASCC2_ENST00000542393.1_Missense_Mutation_p.E245D			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			TGTGGAAAATCTCCATTAGCT	0.512																																					p.E321D		Atlas-SNP	.											.	ASCC2	53	.	0			c.G963T						.						99	91	94					22																	30202839		2203	4300	6503	SO:0001583	missense	84164	exon10			GAAAATCTCCATT	AY013289	CCDS13869.1, CCDS56226.1	22q12.1	2004-07-27			ENSG00000100325	ENSG00000100325			24103	protein-coding gene	gene with protein product	"ASC 1 complex subunit P100"	614216				12077347, 9847074	Standard	NM_032204		Approved	ASC1p100, FLJ21588, DKFZp586O0223	uc003agr.3	Q9H1I8	OTTHUMG00000067658	ENST00000397771.2:c.963G>T	chr22.hg19:g.30202839C>A	ENSP00000380877:p.Glu321Asp	98.0	0.0		73.0	13.0	NM_032204	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	Missense_Mutation	SNP	ENST00000397771.2	hg19	CCDS13869.1	.	.	.	.	.	.	.	.	.	.	C	17.87	3.494911	0.64186	.	.	ENSG00000100325	ENST00000307790;ENST00000397771;ENST00000542393	T;T;T	0.08896	3.04;3.04;3.05	5.52	2.19	0.27852	.	0.049714	0.85682	N	0.000000	T	0.15392	0.0371	L	0.59436	1.845	0.52099	D	0.99994	P;D	0.63046	0.849;0.992	P;P	0.60173	0.555;0.87	T	0.14337	-1.0476	10	0.17369	T	0.5	-19.4826	7.746	0.28869	0.1241:0.6788:0.0:0.1971	.	245;321	F5H6J9;Q9H1I8	.;ASCC2_HUMAN	D	321;321;245	ENSP00000305502:E321D;ENSP00000380877:E321D;ENSP00000437570:E245D	ENSP00000305502:E321D	E	-	3	2	ASCC2	28532839	0.998000	0.40836	0.998000	0.56505	0.755000	0.42902	0.595000	0.24029	0.778000	0.33520	0.655000	0.94253	GAG	.	.		0.512	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322127.1	NM_032204		A	30202839	C	A	30202839	3	1	82	1	0	0	0	0	1	0	0	0	1032	912	32	3	1354	3	ASCC2	22	30202839	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	289772	30202839	21101727	97	11293										
DDX17	10521	hgsc.bcm.edu	37	chr22	38890032	38890032	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	ggtgctatactcacccatctCtgcgcatccttcgagtcaga	8	14	3	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr22:38890032C>A	ENST00000396821.3	-	9	1418	c.1319G>T	c.(1318-1320)aGa>aTa	p.R440I	DDX17_ENST00000432525.1_5'UTR|DDX17_ENST00000381633.3_Missense_Mutation_p.R361I	NM_001098504.1|NM_006386.4	NP_001091974|NP_006377.2	Q92841	DDX17_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 17	440	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of skeletal muscle cell differentiation (GO:2001014)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA helicase activity (GO:0003724)|RNA-dependent ATPase activity (GO:0008186)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	25	Melanoma(58;0.0286)					TCACCCATCTCTGCGCATCCT	0.348																																					p.R440I	Ovarian(55;1085 1454 6392 21425)	Atlas-SNP	.											.	DDX17	73	.	0			c.G1319T						.						180	154	162					22																	38890032		2203	4300	6503	SO:0001583	missense	10521	exon9			CCATCTCTGCGCA	U59321	CCDS33646.1, CCDS46706.1	22q13.1	2012-02-23	2012-02-23		ENSG00000100201	ENSG00000100201		"DEAD-boxes"	2740	protein-coding gene	gene with protein product		608469	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 17"			8871553, 17226766	Standard	NM_006386		Approved	P72	uc003avy.4	Q92841	OTTHUMG00000151136	ENST00000396821.3:c.1319G>T	chr22.hg19:g.38890032C>A	ENSP00000380033:p.Arg440Ile	106.0	0.0		107.0	36.0	NM_006386	B1AHM0|Q69YT1|Q6ICD6	Missense_Mutation	SNP	ENST00000396821.3	hg19	CCDS46706.1	.	.	.	.	.	.	.	.	.	.	C	35	5.567063	0.96540	.	.	ENSG00000100201	ENST00000396821;ENST00000381633;ENST00000403230;ENST00000404499	T;T;T	0.75477	-0.94;-0.94;-0.94	5.8	5.8	0.92144	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	L	0.49513	1.565	0.80722	D	1	D;P;P	0.89917	1.0;0.93;0.914	D;P;P	0.81914	0.995;0.793;0.689	D	0.84632	0.0690	10	0.87932	D	0	-15.7527	20.0693	0.97712	0.0:1.0:0.0:0.0	.	361;442;440	Q92841;Q59F66;Q92841-4	DDX17_HUMAN;.;.	I	440;361;440;442	ENSP00000380033:R440I;ENSP00000371046:R361I;ENSP00000385536:R440I	ENSP00000371046:R361I	R	-	2	0	DDX17	37219978	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	3.110000	0.50352	2.758000	0.94735	0.563000	0.77884	AGA	.	.		0.348	DDX17-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321476.2	NM_030881		A	38890032	C	A	38890032	3	1	82	1	0	0	0	0	1	0	0	0	4346	913	32	3	896	3	DDX17	22	38890032	Missense_Mutation	SNP	C	TCGA-CC-A9FS-01A-11D-A36X-10	8687193	38890032	12414534	98	11294										
ARSA	410	hgsc.bcm.edu	37	chr22	51066154	51066154	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	atgttgggcggacgggcaacGgccaggccagcagccagggc	18	12	0	0			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chr22:51066154G>A	ENST00000547307.1	-	1	453	c.48C>T	c.(46-48)gcC>gcT	p.A16A	ARSA_ENST00000395619.3_Silent_p.A18A|ARSA_ENST00000547805.1_Silent_p.A16A|ARSA_ENST00000216124.5_Silent_p.A18A|ARSA_ENST00000453344.2_Intron|ARSA_ENST00000395621.3_Silent_p.A18A|ARSA_ENST00000356098.5_Silent_p.A18A			P15289	ARSA_HUMAN	arylsulfatase A	16					autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)			endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)|Suramin(DB04786)	GACGGGCAACGGCCAGGCCAG	0.672																																					p.A18A		Atlas-SNP	.											.	ARSA	19	.	0			c.C54T						.						18	17	18					22																	51066154		2160	4215	6375	SO:0001819	synonymous_variant	410	exon2			GGCAACGGCCAGG	X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"Arylsulfatase family"	713	protein-coding gene	gene with protein product	"metachromatic leucodystrophy"	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.48C>T	chr22.hg19:g.51066154G>A		569.0	0.0		523.0	205.0	NM_001085426	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Silent	SNP	ENST00000547307.1	hg19																																																																																				.	.		0.672	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487		A	51066154	G	A	51066154	2	1	82	1	0	0	0	0	0	0	0	1	987	1103	39	1		1	ARSA	22	51066154	Silent	SNP	G	TCGA-CC-A9FS-01A-11D-A36X-10	12176122	51066154	238412	99	11295										
ZNF157	7712	hgsc.bcm.edu	37	chrX	47272152	47272152	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	taatgaatgtgggaaatcttTtggcaggaagtcacaactca	10	6	3	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chrX:47272152T>A	ENST00000377073.3	+	4	766	c.680T>A	c.(679-681)tTt>tAt	p.F227Y		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	227					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						GGGAAATCTTTTGGCAGGAAG	0.433																																					p.F227Y		Atlas-SNP	.											.	ZNF157	46	.	0			c.T680A						.						73	65	68					X																	47272152		2203	4300	6503	SO:0001583	missense	7712	exon4			AATCTTTTGGCAG	U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"Zinc fingers, C2H2-type", "-"	12942	protein-coding gene	gene with protein product		300024	"zinc finger protein 157 (HZF22)"			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.680T>A	chrX.hg19:g.47272152T>A	ENSP00000366273:p.Phe227Tyr	156.0	1.0		162.0	125.0	NM_003446	Q96LE9	Missense_Mutation	SNP	ENST00000377073.3	hg19	CCDS14278.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.420480	0.62622	.	.	ENSG00000147117	ENST00000377073	T	0.40476	1.03	3.09	1.87	0.25490	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40694	0.1127	M	0.66439	2.03	0.25599	N	0.986619	P	0.40578	0.722	B	0.40659	0.336	T	0.32455	-0.9906	9	0.72032	D	0.01	.	6.2526	0.20854	0.2259:0.0:0.0:0.7741	.	227	P51786	ZN157_HUMAN	Y	227	ENSP00000366273:F227Y	ENSP00000366273:F227Y	F	+	2	0	ZNF157	47157096	1.000000	0.71417	0.985000	0.45067	0.989000	0.77384	7.316000	0.79007	0.403000	0.25479	0.486000	0.48141	TTT	.	.		0.433	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446		A	47272152	T	A	47272152	3	1	82	1	0	0	0	0	1	0	0	0	17752	1841	64	4	694	4	ZNF157	23	47272152	Missense_Mutation	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10		47272152	107998408	100	11296										
THOC2	57187	hgsc.bcm.edu	37	chrX	122761595	122761595	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0495049504950495	5	1	0.958132045088567	0.979423868312757	0.952952952952953	0.303405572755418	1	0	tggactttaagtttattgacTtctcgttcatagctggtgtg	10	6	2	1			TCGA-CC-A9FS-01A-11D-A36X-10	TCGA-CC-A9FS-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	353e3047-6c29-4edb-8adb-f19e6d570a0f	c0bdfb14-d7ae-4bb0-a5bf-5c16a0c65e29	g.chrX:122761595T>G	ENST00000245838.8	-	23	2737	c.2706A>C	c.(2704-2706)gaA>gaC	p.E902D	THOC2_ENST00000491737.1_Missense_Mutation_p.E787D|THOC2_ENST00000355725.4_Missense_Mutation_p.E902D	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	902					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						GTTTATTGACTTCTCGTTCAT	0.378																																					p.E902D		Atlas-SNP	.											.	THOC2	310	.	0			c.A2706C						.						176	148	157					X																	122761595		1923	4132	6055	SO:0001583	missense	57187	exon23			ATTGACTTCTCGT	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.2706A>C	chrX.hg19:g.122761595T>G	ENSP00000245838:p.Glu902Asp	114.0	0.0		155.0	18.0	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	hg19	CCDS43988.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.198695	0.79015	.	.	ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737;ENST00000408933	T;T;T	0.38887	1.11;1.11;1.11	5.73	4.56	0.56223	THO complex, subunitTHOC2, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.70316	0.3210	M	0.93150	3.385	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.987	T	0.76958	-0.2766	10	0.66056	D	0.02	-21.9946	10.4534	0.44535	0.0:0.0768:0.0:0.9232	.	827;902	B4DKZ6;Q8NI27	.;THOC2_HUMAN	D	902;902;787;827	ENSP00000245838:E902D;ENSP00000347959:E902D;ENSP00000419795:E787D	ENSP00000245838:E902D	E	-	3	2	THOC2	122589276	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.755000	0.47540	2.036000	0.60181	0.486000	0.48141	GAA	.	.		0.378	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			G	122761595	T	G	122761595	3	3	82	1	0	0	0	0	1	0	0	0	15880	1606	56	5	2139	5	THOC2	23	122761595	Missense_Mutation	SNP	T	TCGA-CC-A9FS-01A-11D-A36X-10	75489443	122761595	32508965	101	11297										
TCEB3	6924	hgsc.bcm.edu	37	chr1	24078287	24078287	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ttgaggagacagatatggagGatgaattcgagcagccaacc	13	7	0	4			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr1:24078287G>A	ENST00000418390.2	+	4	1541	c.1270G>A	c.(1270-1272)Gat>Aat	p.D424N	TCEB3_ENST00000609199.1_Missense_Mutation_p.D398N	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	424					gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		AGATATGGAGGATGAATTCGA	0.448											OREG0013232	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D424N		Atlas-SNP	.											.	TCEB3	61	.	0			c.G1270A						.						116	132	127					1																	24078287		2203	4300	6503	SO:0001583	missense	6924	exon4			ATGGAGGATGAAT	L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.1270G>A	chr1.hg19:g.24078287G>A	ENSP00000395574:p.Asp424Asn	173.0	0.0	768	95.0	83.0	NM_003198	B2R7Q8|Q8IXH1	Missense_Mutation	SNP	ENST00000418390.2	hg19	CCDS239.2	.	.	.	.	.	.	.	.	.	.	G	22.2	4.254306	0.80135	.	.	ENSG00000011007	ENST00000418390	T	0.12879	2.64	5.72	5.72	0.89469	.	0.078764	0.53938	D	0.000052	T	0.30665	0.0772	M	0.61703	1.905	0.80722	D	1	D	0.64830	0.994	P	0.55055	0.767	T	0.00256	-1.1873	10	0.38643	T	0.18	-18.9194	19.8965	0.96963	0.0:0.0:1.0:0.0	.	424	Q14241	ELOA1_HUMAN	N	424	ENSP00000395574:D424N	ENSP00000395574:D424N	D	+	1	0	TCEB3	23950874	1.000000	0.71417	0.975000	0.42487	0.223000	0.24884	7.782000	0.85680	2.717000	0.92951	0.655000	0.94253	GAT	.	.		0.448	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198		A	24078287	G	A	24078287	3	1	83	1	0	0	0	0	1	0	0	0	15696	1174	41	3	1284	3	TCEB3	1	24078287	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10		24078287	225172334	1	11298										
PDZK1IP1	10158	hgsc.bcm.edu	37	chr1	47649702	47649702	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	cacattctcataggcattctCatgctcactggacctgaaag	7	12	3	1	rs559430062		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr1:47649702C>A	ENST00000294338.2	-	4	408	c.286G>T	c.(286-288)Gag>Tag	p.E96*	PDZK1IP1_ENST00000491793.1_5'UTR|PDZK1IP1_ENST00000371885.1_Nonsense_Mutation_p.E96*	NM_005764.3	NP_005755.1	Q13113	PDZ1I_HUMAN	PDZK1 interacting protein 1	96						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|prostate(1)	3						TAGGCATTCTCATGCTCACTG	0.567																																					p.E96X		Atlas-SNP	.											.	PDZK1IP1	9	.	0			c.G286T						.						181	122	142					1																	47649702		2202	4298	6500	SO:0001587	stop_gained	10158	exon4			CATTCTCATGCTC	U21049	CCDS546.1	1p33	2008-02-05			ENSG00000162366	ENSG00000162366			16887	protein-coding gene	gene with protein product		607178				9815914, 8701988, 12754212, 12837682	Standard	NM_005764		Approved	DD96, MAP17, SPAP	uc001cqw.3	Q13113	OTTHUMG00000007852	ENST00000294338.2:c.286G>T	chr1.hg19:g.47649702C>A	ENSP00000294338:p.Glu96*	61.0	0.0		65.0	24.0	NM_005764	Q6ICT9|Q96EI1	Nonsense_Mutation	SNP	ENST00000294338.2	hg19	CCDS546.1	.	.	.	.	.	.	.	.	.	.	c	20.1	3.939024	0.73557	.	.	ENSG00000162366	ENST00000294338;ENST00000371885	.	.	.	4.64	-1.28	0.09318	.	1.101510	0.07068	N	0.834946	.	.	.	.	.	.	0.51482	D	0.999928	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-0.9702	5.1918	0.15214	0.0:0.4866:0.161:0.3523	.	.	.	.	X	96	.	ENSP00000294338:E96X	E	-	1	0	PDZK1IP1	47422289	0.000000	0.05858	0.347000	0.25668	0.963000	0.63663	-0.298000	0.08265	-0.115000	0.11915	0.556000	0.70494	GAG	.	.		0.567	PDZK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021655.1	NM_005764		A	47649702	C	A	47649702	4	1	83	1	0	0	0	0	0	1	0	0	11717	835	29	3	62	3	PDZK1IP1	1	47649702	Nonsense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	23571415	47649702	201600919	2	11299										
DMRTA2	63950	hgsc.bcm.edu	37	chr1	50885040	50885040	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	gcgtccgctgccgtggacccGagcctccgcccagccctggc	13	20	0	0			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr1:50885040G>T	ENST00000404795.3	-	3	1318	c.926C>A	c.(925-927)tCg>tAg	p.S309*	DMRTA2_ENST00000418121.1_Nonsense_Mutation_p.S309*	NM_032110.2	NP_115486.1	Q96SC8	DMTA2_HUMAN	DMRT-like family A2	309	Gly-rich.				cerebral cortex regionalization (GO:0021796)|dopaminergic neuron differentiation (GO:0071542)|neuron fate specification (GO:0048665)|positive regulation of neuroblast proliferation (GO:0002052)|skeletal muscle cell differentiation (GO:0035914)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(4)|pancreas(1)	6						CCGTGGACCCGAGCCTCCGCC	0.706																																					p.S309X	Colon(196;1651 2045 3292 36497 38236)|Esophageal Squamous(2;257 258 11567 27043 43804)	Atlas-SNP	.											.	DMRTA2	17	.	0			c.C926A						.						29	32	31					1																	50885040		1753	3782	5535	SO:0001587	stop_gained	63950	exon3			GGACCCGAGCCTC	AJ301580	CCDS44141.1	1p33	2008-08-04			ENSG00000142700	ENSG00000142700			13908	protein-coding gene	gene with protein product		614804				11863363	Standard	NM_032110		Approved		uc010onb.2	Q96SC8	OTTHUMG00000007884	ENST00000404795.3:c.926C>A	chr1.hg19:g.50885040G>T	ENSP00000383909:p.Ser309*	18.0	0.0		32.0	13.0	NM_032110	Q5TFQ3	Nonsense_Mutation	SNP	ENST00000404795.3	hg19	CCDS44141.1	.	.	.	.	.	.	.	.	.	.	G	37	6.116258	0.97296	.	.	ENSG00000142700	ENST00000404795;ENST00000418121	.	.	.	3.8	3.8	0.43715	.	0.678034	0.14119	N	0.340156	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.3709	14.946	0.71032	0.0:0.0:1.0:0.0	.	.	.	.	X	309	.	ENSP00000383909:S309X	S	-	2	0	DMRTA2	50657627	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.607000	0.82883	2.107000	0.64212	0.462000	0.41574	TCG	.	.		0.706	DMRTA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351074.1	NM_032110		T	50885040	G	T	50885040	4	4	83	1	0	0	0	0	0	1	0	0	4591	1059	37	1	706	1	DMRTA2	1	50885040	Nonsense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	3235338	50885040	198365581	3	11300										
DEPDC1	55635	hgsc.bcm.edu	37	chr1	68947881	68947881	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ttgtgctgccttgtccaacaTttggtttcatgataatttca	7	8	2	1			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr1:68947881T>A	ENST00000456315.2	-	8	1724	c.1610A>T	c.(1609-1611)aAt>aTt	p.N537I	DEPDC1_ENST00000370966.5_Intron|RP4-694A7.2_ENST00000425820.1_RNA	NM_001114120.1	NP_001107592.1	Q5TB30	DEP1A_HUMAN	DEP domain containing 1	537					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)		TTGTCCAACATTTGGTTTCAT	0.378																																					p.N537I		Atlas-SNP	.											.	DEPDC1	102	.	0			c.A1610T						.						236	215	222					1																	68947881		1568	3582	5150	SO:0001583	missense	55635	exon8			CCAACATTTGGTT	AK000361	CCDS644.1, CCDS44159.1	1p31.2	2008-08-19			ENSG00000024526	ENSG00000024526			22949	protein-coding gene	gene with protein product		612002					Standard	NM_001114120		Approved	DEP.8, FLJ20354, SDP35, DEPDC1A	uc001dem.4	Q5TB30	OTTHUMG00000009212	ENST00000456315.2:c.1610A>T	chr1.hg19:g.68947881T>A	ENSP00000412292:p.Asn537Ile	78.0	0.0		145.0	63.0	NM_001114120	A8QXE0|A8QXE1|Q05DU3|Q5TB28|Q9H9I3|Q9NX21|Q9NXZ0	Missense_Mutation	SNP	ENST00000456315.2	hg19	CCDS44159.1	.	.	.	.	.	.	.	.	.	.	T	9.976	1.226690	0.22542	.	.	ENSG00000024526	ENST00000456315	T	0.10382	2.88	5.61	1.79	0.24919	Rho GTPase activation protein (1);	0.424789	0.25823	N	0.028064	T	0.01905	0.0060	N	0.24115	0.695	0.22918	N	0.998567	B	0.20671	0.047	B	0.19148	0.024	T	0.41858	-0.9485	10	0.87932	D	0	-2.4203	2.7912	0.05388	0.1021:0.1329:0.283:0.482	.	537	Q5TB30	DEP1A_HUMAN	I	537	ENSP00000412292:N537I	ENSP00000412292:N537I	N	-	2	0	DEPDC1	68720469	0.022000	0.18835	0.903000	0.35520	0.876000	0.50452	0.349000	0.20055	0.363000	0.24346	0.528000	0.53228	AAT	.	.		0.378	DEPDC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025514.2	NM_017779		A	68947881	T	A	68947881	3	1	83	1	0	0	0	0	1	0	0	0	4441	1493	52	4	845	4	DEPDC1	1	68947881	Missense_Mutation	SNP	T	TCGA-CC-A9FU-01A-11D-A36X-10	18062841	68947881	180302740	4	11301										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190068224	190068228	+	Frame_Shift_Del	DEL	AGAGA	AGAGA	-													0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	gaggccgttctcattgcagtAgagaaaagactggatgcgag							TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	AGAGA	AGAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr1:190068224_190068228delAGAGA	ENST00000367462.3	-	8	1452_1456	c.1221_1225delTCTCT	c.(1219-1227)tttctctacfs	p.FLY407fs	BRINP3_ENST00000534846.1_Frame_Shift_Del_p.FLY305fs	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	407					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											TCATTGCAGTAGAGAAAAGACTGGA	0.478																																					p.408_409del		Atlas-Indel,Pindel	.											.	FAM5C	343	.	0			c.1222_1226del						.																																			SO:0001589	frameshift_variant	339479	exon8			.	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1221_1225delTCTCT	chr1.hg19:g.190068224_190068228delAGAGA	ENSP00000356432:p.Phe407fs	175.0	0.0		298.0	66.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Frame_Shift_Del	DEL	ENST00000367462.3	hg19	CCDS1373.1																																																																																			.	.		0.478	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		-	190068228	AGAGA	-	190068224	7	5	83	1	0	1	0	1	0	0	0	0	5602	420	15	0	1079	0	FAM5C	1	190068224	Frame_Shift_Del	DEL	AGAGA	TCGA-CC-A9FU-01A-11D-A36X-10	121120343	190068224	59182397	5	11302										
SOX13	9580	hgsc.bcm.edu	37	chr1	204095155	204095155	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	gagaggagggtgagggcacaGatgacaggcactcggtggct	19	7	0	4			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr1:204095155G>A	ENST00000367204.1	+	14	1871	c.1762G>A	c.(1762-1764)Gat>Aat	p.D588N		NM_005686.2	NP_005677.2	Q9UN79	SOX13_HUMAN	SRY (sex determining region Y)-box 13	588					anatomical structure morphogenesis (GO:0009653)|regulation of gamma-delta T cell differentiation (GO:0045586)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	13	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			TGAGGGCACAGATGACAGGCA	0.612																																					p.D588N		Atlas-SNP	.											.	SOX13	38	.	0			c.G1762A						.						115	135	128					1																	204095155		2176	4263	6439	SO:0001583	missense	9580	exon14			GGCACAGATGACA		CCDS44299.1	1q32	2008-07-18			ENSG00000143842	ENSG00000143842		"SRY (sex determining region Y)-boxes"	11192	protein-coding gene	gene with protein product	"islet cell antibody 12", "SRY-related HMG-box gene 13", "type 1 diabetes autoantigen", "SRY-box 13"	604748				10198172	Standard	NM_005686		Approved	Sox-13, ICA12, MGC117216	uc001ham.3	Q9UN79	OTTHUMG00000036050	ENST00000367204.1:c.1762G>A	chr1.hg19:g.204095155G>A	ENSP00000356172:p.Asp588Asn	135.0	0.0		210.0	68.0	NM_005686	B4E2B0|O95275|O95826|Q3KQV7|Q5SXX1|Q9UHW7	Missense_Mutation	SNP	ENST00000367204.1	hg19	CCDS44299.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.307400	0.40795	.	.	ENSG00000143842	ENST00000367204	T	0.41400	1.0	4.58	4.58	0.56647	.	0.204892	0.33591	N	0.004743	T	0.34513	0.0900	L	0.40543	1.245	0.35814	D	0.824099	B;B;B	0.20780	0.048;0.048;0.048	B;B;B	0.20767	0.031;0.016;0.031	T	0.32745	-0.9895	10	0.18710	T	0.47	.	15.6929	0.77469	0.0:0.0:1.0:0.0	.	455;455;588	B4DX26;B4E3N9;Q9UN79	.;.;SOX13_HUMAN	N	588	ENSP00000356172:D588N	ENSP00000356172:D588N	D	+	1	0	SOX13	202361778	1.000000	0.71417	0.476000	0.27291	0.520000	0.34377	7.160000	0.77495	2.540000	0.85666	0.561000	0.74099	GAT	.	.		0.612	SOX13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087881.2	NM_005686		A	204095155	G	A	204095155	3	1	83	1	0	0	0	0	1	0	0	0	14959	942	33	3	1812	3	SOX13	1	204095155	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	14026931	204095155	45155466	6	11303										
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204198158	204198158	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ggtgtctcgtaggcatgcccGccaggctcctctgcccgcag	13	16	2	0			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr1:204198158G>A	ENST00000272203.3	-	19	2974	c.2658C>T	c.(2656-2658)ggC>ggT	p.G886G	PLEKHA6_ENST00000414478.1_Silent_p.G906G	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	886										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			AGGCATGCCCGCCAGGCTCCT	0.607																																					p.G886G		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.C2658T						.						57	60	59					1																	204198158		2203	4300	6503	SO:0001819	synonymous_variant	22874	exon19			ATGCCCGCCAGGC	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2658C>T	chr1.hg19:g.204198158G>A		75.0	0.0		128.0	43.0	NM_014935	A7MD51|Q5VTI6	Silent	SNP	ENST00000272203.3	hg19	CCDS1444.1																																																																																			.	.		0.607	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		A	204198158	G	A	204198158	2	1	83	1	0	0	0	0	0	0	0	1	12069	1074	38	1		1	PLEKHA6	1	204198158	Silent	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	103003	204198158	45052463	7	11304										
FMN2	56776	hgsc.bcm.edu	37	chr1	240256986	240256986	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ggccgccaaggcgtctggggCccccgcggctgcggatggct	18	15	1	0			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr1:240256986C>T	ENST00000319653.9	+	1	1807	c.1577C>T	c.(1576-1578)gCc>gTc	p.A526V		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	526					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GCGTCTGGGGCCCCCGCGGCT	0.726																																					p.A526V		Atlas-SNP	.											.	FMN2	451	.	0			c.C1577T						.						3	5	4					1																	240256986		1754	3651	5405	SO:0001583	missense	56776	exon1			CTGGGGCCCCCGC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1577C>T	chr1.hg19:g.240256986C>T	ENSP00000318884:p.Ala526Val	15.0	0.0		40.0	10.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	C	8.049	0.765619	0.15914	.	.	ENSG00000155816	ENST00000319653	T	0.79554	-1.28	4.14	2.07	0.26955	.	0.615335	0.14123	N	0.339901	T	0.59851	0.2224	N	0.11560	0.145	0.09310	N	0.999999	B	0.02656	0.0	B	0.06405	0.002	T	0.47598	-0.9105	10	0.32370	T	0.25	.	6.2136	0.20644	0.0:0.6034:0.0:0.3966	.	526	Q9NZ56	FMN2_HUMAN	V	526	ENSP00000318884:A526V	ENSP00000318884:A526V	A	+	2	0	FMN2	238323609	0.725000	0.28048	0.134000	0.22075	0.456000	0.32438	1.163000	0.31798	0.942000	0.37525	0.563000	0.77884	GCC	.	.		0.726	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240256986	C	T	240256986	3	4	83	1	0	0	0	0	1	0	0	0	5958	739	26	3	1579	3	FMN2	1	240256986	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	36058828	240256986	8993635	8	11305										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32724628	32724628	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ctgcaggggtgctttccagaCaggccaaggacctctcgatg	13	12	1	1			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr2:32724628C>T	ENST00000421745.2	+	46	8617	c.8483C>T	c.(8482-8484)aCa>aTa	p.T2828I		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2828					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					GCTTTCCAGACAGGCCAAGGA	0.418																																					p.T2828I	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C8483T						.						44	40	41					2																	32724628		2203	4300	6503	SO:0001583	missense	57448	exon46			TCCAGACAGGCCA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.8483C>T	chr2.hg19:g.32724628C>T	ENSP00000393596:p.Thr2828Ile	42.0	0.0		67.0	31.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220619	0.58560	.	.	ENSG00000115760	ENST00000421745	T	0.74315	-0.83	4.99	4.99	0.66335	.	0.063541	0.64402	D	0.000005	T	0.61085	0.2319	N	0.14661	0.345	0.58432	D	0.999996	P	0.44578	0.838	B	0.38803	0.282	T	0.68777	-0.5319	10	0.56958	D	0.05	.	18.6543	0.91445	0.0:1.0:0.0:0.0	.	2828	Q9NR09	BIRC6_HUMAN	I	2828	ENSP00000393596:T2828I	ENSP00000393596:T2828I	T	+	2	0	BIRC6	32578132	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.055000	0.71103	2.465000	0.83290	0.563000	0.77884	ACA	.	.		0.418	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32724628	C	T	32724628	3	4	83	1	0	0	0	0	1	0	0	0	1438	478	17	3	8665	3	BIRC6	2	32724628	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10		32724628	210474745	9	11306										
CYTIP	9595	hgsc.bcm.edu	37	chr2	158300471	158300471	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	agtaagagctatacgctggcCcagcgcagaagtccgccaaa	11	12	0	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr2:158300471C>T	ENST00000264192.3	-	1	183	c.62G>A	c.(61-63)gGg>gAg	p.G21E	AC019201.1_ENST00000401235.1_RNA|CYTIP_ENST00000540637.1_Intron|CYTIP_ENST00000497432.1_Intron	NM_004288.4	NP_004279.3	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein	21					regulation of cell adhesion (GO:0030155)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	15						ATACGCTGGCCCAGCGCAGAA	0.507																																					p.G21E		Atlas-SNP	.											.	CYTIP	45	.	0			c.G62A						.						163	150	154					2																	158300471		2203	4300	6503	SO:0001583	missense	9595	exon1			GCTGGCCCAGCGC	L06633	CCDS2204.1	2q11.2	2011-09-08	2008-08-14	2008-08-19	ENSG00000115165	ENSG00000115165			9506	protein-coding gene	gene with protein product	"cytohesin binding protein HE", "cytohesin binder and regulator"	604448	"pleckstrin homology, Sec7 and coiled-coil domains, binding protein"	PSCDBP		18926288, 10343115, 11867758, 20530790, 21562043	Standard	NM_004288		Approved	B3-1, HE, CYBR, CASP, CYTHIP	uc002tzj.1	O60759	OTTHUMG00000154551	ENST00000264192.3:c.62G>A	chr2.hg19:g.158300471C>T	ENSP00000264192:p.Gly21Glu	69.0	0.0		74.0	35.0	NM_004288	B4DWH9|Q15630|Q8NE32	Missense_Mutation	SNP	ENST00000264192.3	hg19	CCDS2204.1	.	.	.	.	.	.	.	.	.	.	C	7.768	0.706801	0.15239	.	.	ENSG00000115165	ENST00000264192	T	0.17370	2.28	5.72	3.9	0.45041	.	0.209202	0.39615	N	0.001318	T	0.11707	0.0285	L	0.27053	0.805	0.26543	N	0.974059	P	0.45986	0.87	B	0.41571	0.36	T	0.09796	-1.0658	10	0.52906	T	0.07	-2.5154	6.7546	0.23505	0.1755:0.7338:0.0:0.0907	.	21	O60759	CYTIP_HUMAN	E	21	ENSP00000264192:G21E	ENSP00000264192:G21E	G	-	2	0	CYTIP	158008717	0.041000	0.20044	0.004000	0.12327	0.005000	0.04900	2.954000	0.49113	0.735000	0.32537	0.655000	0.94253	GGG	.	.		0.507	CYTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254926.1	NM_004288		T	158300471	C	T	158300471	3	4	83	1	0	0	0	0	1	0	0	0	4209	623	22	3	1049	3	CYTIP	2	158300471	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	125575843	158300471	84898902	10	11307										
RBM45	129831	hgsc.bcm.edu	37	chr2	178985043	178985043	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	caatcttggctgaacctaaaAataaagcatctgaatcctct	5	10	3	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr2:178985043A>T	ENST00000286070.5	+	4	672	c.580A>T	c.(580-582)Aat>Tat	p.N194Y		NM_152945.2	NP_694453.2	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	194	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			TGAACCTAAAAATAAAGCATC	0.333																																					p.N194Y		Atlas-SNP	.											.	RBM45	49	.	0			c.A580T						.						68	72	71					2																	178985043		2203	4300	6503	SO:0001583	missense	129831	exon4			CCTAAAAATAAAG	AF526533	CCDS33335.1	2q31.2	2013-02-12			ENSG00000155636	ENSG00000155636		"RNA binding motif (RRM) containing"	24468	protein-coding gene	gene with protein product	"developmentally regulated RNA binding protein 1"	608888				12220514	Standard	XM_005246287		Approved	DRB1, FLJ44612	uc002ulv.3	Q8IUH3	OTTHUMG00000154202	ENST00000286070.5:c.580A>T	chr2.hg19:g.178985043A>T	ENSP00000286070:p.Asn194Tyr	133.0	0.0		177.0	64.0	NM_152945	Q6NYL0|Q8NFC9	Missense_Mutation	SNP	ENST00000286070.5	hg19	CCDS33335.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.575069	0.86542	.	.	ENSG00000155636	ENST00000286070	T	0.05786	3.39	6.16	6.16	0.99307	.	0.088341	0.85682	D	0.000000	T	0.16257	0.0391	L	0.39245	1.2	0.80722	D	1	D	0.65815	0.995	P	0.61201	0.885	T	0.00303	-1.1833	10	0.51188	T	0.08	-26.1567	15.9872	0.80168	1.0:0.0:0.0:0.0	.	194	Q8IUH3-3	.	Y	194	ENSP00000286070:N194Y	ENSP00000286070:N194Y	N	+	1	0	RBM45	178693289	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.028000	0.70889	2.367000	0.80283	0.528000	0.53228	AAT	.	.		0.333	RBM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334375.2	NM_152945		T	178985043	A	T	178985043	3	4	83	1	0	0	0	0	1	0	0	0	13154	14	1	4	594	4	RBM45	2	178985043	Missense_Mutation	SNP	A	TCGA-CC-A9FU-01A-11D-A36X-10	20684572	178985043	64214330	11	11308										
TTN	7273	hgsc.bcm.edu	37	chr2	179451970	179451970	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	gattggttacatggaagcttGttttcttaacttctggggta	11	5	2	0			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr2:179451970G>A	ENST00000591111.1	-	257	59269	c.59045C>T	c.(59044-59046)aCa>aTa	p.T19682I	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T18755I|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T21323I|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T12450I|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T12383I|TTN_ENST00000460472.2_Missense_Mutation_p.T12258I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19682	Fibronectin type-III 42. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGGAAGCTTGTTTTCTTAAC	0.473																																					p.T21323I		Atlas-SNP	.											.	TTN	18412	.	0			c.C63968T						.						136	135	135					2																	179451970		1927	4137	6064	SO:0001583	missense	7273	exon307			AAGCTTGTTTTCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.59045C>T	chr2.hg19:g.179451970G>A	ENSP00000465570:p.Thr19682Ile	111.0	0.0		134.0	64.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	21.2	4.120260	0.77323	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	5.98	5.11	0.69529	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.68274	0.2983	M	0.81614	2.55	0.53005	D	0.999967	D;D;D;D	0.60160	0.987;0.987;0.987;0.987	P;P;P;P	0.54889	0.763;0.763;0.763;0.763	T	0.74717	-0.3571	9	0.87932	D	0	.	15.2241	0.73336	0.067:0.0:0.933:0.0	.	12258;12383;12450;19682	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	18755;12258;12450;12383;12256	ENSP00000343764:T18755I;ENSP00000434586:T12258I;ENSP00000340554:T12450I;ENSP00000352154:T12383I	ENSP00000340554:T12450I	T	-	2	0	TTN	179160216	1.000000	0.71417	0.986000	0.45419	0.873000	0.50193	6.633000	0.74286	1.536000	0.49237	0.650000	0.86243	ACA	.	.		0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179451970	G	A	179451970	3	1	83	1	0	0	0	0	1	0	0	0	16750	1377	48	3	44235	3	TTN	2	179451970	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	466927	179451970	63747403	12	11309										
ADAM23	8745	hgsc.bcm.edu	37	chr2	207437863	207437863	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	agccacgagggtatgaatgcCgggatgctgtgaacgagtgt	16	7	0	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr2:207437863C>T	ENST00000264377.3	+	18	2009	c.1681C>T	c.(1681-1683)Cgg>Tgg	p.R561W	ADAM23_ENST00000374416.1_Missense_Mutation_p.R561W|ADAM23_ENST00000374415.3_Missense_Mutation_p.R561W	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	561	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		GTATGAATGCCGGGATGCTGT	0.373																																					p.R561W	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											.	ADAM23	239	.	0			c.C1681T						.						243	219	227					2																	207437863		2203	4300	6503	SO:0001583	missense	8745	exon18			GAATGCCGGGATG	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"ADAM metallopeptidase domain containing"	202	protein-coding gene	gene with protein product		603710	"a disintegrin and metalloproteinase domain 23"			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.1681C>T	chr2.hg19:g.207437863C>T	ENSP00000264377:p.Arg561Trp	94.0	0.0		113.0	46.0	NM_003812	A2RU59	Missense_Mutation	SNP	ENST00000264377.3	hg19	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.983609	0.93044	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	T;T;T	0.19532	2.14;2.14;2.14	5.99	5.99	0.97316	Blood coagulation inhibitor, Disintegrin (5);	0.118923	0.37857	N	0.001915	T	0.64114	0.2569	H	0.96996	3.92	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75755	-0.3206	10	0.87932	D	0	.	19.3086	0.94175	0.0:1.0:0.0:0.0	.	561	O75077	ADA23_HUMAN	W	561;561;455;561	ENSP00000264377:R561W;ENSP00000363537:R561W;ENSP00000363536:R561W	ENSP00000264377:R561W	R	+	1	2	ADAM23	207146108	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.794000	0.62482	2.857000	0.98124	0.650000	0.86243	CGG	.	.		0.373	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812		T	207437863	C	T	207437863	3	4	83	1	0	0	0	0	1	0	0	0	245	643	23	1	1751	1	ADAM23	2	207437863	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	27985893	207437863	35761510	13	11310										
SETD2	29072	hgsc.bcm.edu	37	chr3	47129617	47129617	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	gttcacctgtatgagttccaGacaggtaagtttctgctcca	9	10	2	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr3:47129617G>C	ENST00000409792.3	-	10	5305	c.5263C>G	c.(5263-5265)Ctg>Gtg	p.L1755V	snoU13_ENST00000516129.1_RNA	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1755					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		ATGAGTTCCAGACAGGTAAGT	0.378			"N, F, S, Mis"		clear cell renal carcinoma																																p.L1755V		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.C5263G						.						122	127	125					3																	47129617		2203	4300	6503	SO:0001583	missense	29072	exon10			GTTCCAGACAGGT	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5263C>G	chr3.hg19:g.47129617G>C	ENSP00000386759:p.Leu1755Val	55.0	0.0		81.0	22.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643554	0.67244	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.95035	-3.59	4.46	4.46	0.54185	.	0.000000	0.46758	D	0.000268	D	0.97155	0.9070	M	0.80183	2.485	0.58432	D	0.999993	D;D	0.69078	0.997;0.997	D;D	0.78314	0.991;0.991	D	0.97599	1.0122	10	0.62326	D	0.03	.	17.6746	0.88227	0.0:0.0:1.0:0.0	.	1755;1755	F2Z317;Q9BYW2	.;SETD2_HUMAN	V	1755	ENSP00000386759:L1755V	ENSP00000386759:L1755V	L	-	1	2	SETD2	47104621	1.000000	0.71417	0.995000	0.50966	0.969000	0.65631	6.041000	0.70988	2.464000	0.83262	0.650000	0.86243	CTG	.	.		0.378	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		C	47129617	G	C	47129617	3	2	83	1	0	0	0	0	1	0	0	0	14146	933	33	4	2479	4	SETD2	3	47129617	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10		47129617	150892813	14	11311										
C3orf64	285203	hgsc.bcm.edu	37	chr3	69028841	69028841	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ttcaaatacagcagcccagtCtggaaggaaaagtaaatggg	11	7	2	0			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr3:69028841C>T	ENST00000383701.3	-	16	2054	c.1312G>A	c.(1312-1314)Gac>Aac	p.D438N	EOGT_ENST00000295571.5_Missense_Mutation_p.D354N|EOGT_ENST00000540764.1_Missense_Mutation_p.D337N|EOGT_ENST00000540955.1_Missense_Mutation_p.D162N	NM_001278689.1	NP_001265618.1	Q5NDL2	EOGT_HUMAN	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	438					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)	protein N-acetylglucosaminyltransferase activity (GO:0016262)										GCAGCCCAGTCTGGAAGGAAA	0.408																																					p.D354N		Atlas-SNP	.											.	.	.	.	0			c.G1060A						.						175	164	167					3																	69028841		2203	4300	6503	SO:0001583	missense	285203	exon13			CCCAGTCTGGAAG	AK091089	CCDS2908.1, CCDS63684.1	3p14.1	2013-10-11	2012-05-21	2012-05-21	ENSG00000163378	ENSG00000163378	2.4.1.255		28526	protein-coding gene	gene with protein product	"AER61 glycosyltransferase"	614789	"chromosome 3 open reading frame 64"	C3orf64		22310717	Standard	NM_001278689		Approved	AER61, FLJ33770	uc003dnk.3	Q5NDL2	OTTHUMG00000156279	ENST00000383701.3:c.1312G>A	chr3.hg19:g.69028841C>T	ENSP00000373206:p.Asp438Asn	108.0	0.0		110.0	70.0	NM_173654	A8K2U1|B4DFH5|L7X1M5|Q6MZY0|Q6P985|Q6ZTV0	Missense_Mutation	SNP	ENST00000383701.3	hg19		.	.	.	.	.	.	.	.	.	.	C	29.6	5.016922	0.93404	.	.	ENSG00000163378	ENST00000383701;ENST00000295571;ENST00000540955;ENST00000540764	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.76169	0.3950	L	0.58428	1.81	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	T	0.68496	-0.5393	9	0.17832	T	0.49	.	19.9987	0.97401	0.0:1.0:0.0:0.0	.	438;354	Q5NDL2;Q5NDL2-3	AER61_HUMAN;.	N	438;354;162;337	.	ENSP00000295571:D354N	D	-	1	0	C3orf64	69111531	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.481000	0.81124	2.738000	0.93877	0.591000	0.81541	GAC	.	.		0.408	EOGT-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000343722.1	NM_173654		T	69028841	C	T	69028841	3	4	83	1	0	0	0	0	1	0	0	0	2242	913	32	3	283	3	C3orf64	3	69028841	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	21899224	69028841	128993589	15	11312										
RG9MTD1	54931	hgsc.bcm.edu	37	chr3	101284816	101284816	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	tctcaagagtttatcaacagActaaagaaggcaaagactta	7	7	2	4			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr3:101284816A>G	ENST00000309922.6	+	2	1345	c.1191A>G	c.(1189-1191)agA>agG	p.R397R		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	397					mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										TTATCAACAGACTAAAGAAGG	0.368																																					p.R397R		Atlas-SNP	.											.	.	.	.	0			c.A1191G						.						39	37	38					3																	101284816		1807	4089	5896	SO:0001819	synonymous_variant	54931	exon2			CAACAGACTAAAG	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 1"	615423	"RNA (guanine-9-) methyltransferase domain containing 1"	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.1191A>G	chr3.hg19:g.101284816A>G		189.0	0.0		170.0	8.0	NM_017819	Q9NRG5|Q9NX54|Q9Y596	Silent	SNP	ENST00000309922.6	hg19	CCDS43122.1																																																																																			.	.		0.368	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819		G	101284816	A	G	101284816	2	3	83	1	0	0	0	0	0	0	0	1	13286	272	10	2		2	RG9MTD1	3	101284816	Silent	SNP	A	TCGA-CC-A9FU-01A-11D-A36X-10	32255975	101284816	96737614	16	11313										
CCDC39	339829	hgsc.bcm.edu	37	chr3	180334069	180334069	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ttttttaaccctccgcttacCttgctgatagtgaagtatgt	7	9	0	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr3:180334069C>T	ENST00000442201.2	-	19	2788	c.2669G>A	c.(2668-2670)aGg>aAg	p.R890K	TTC14_ENST00000382584.4_Intron|CCDC39_ENST00000273654.4_3'UTR	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	890	Ser-rich.				axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CTCCGCTTACCTTGCTGATAG	0.453																																					p.R890K		Atlas-SNP	.											.	CCDC39	242	.	0			c.G2669A						.						124	112	115					3																	180334069		1912	4122	6034	SO:0001630	splice_region_variant	339829	exon19			GCTTACCTTGCTG	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.2669+1G>A	chr3.hg19:g.180334069C>T		91.0	0.0		91.0	41.0	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	hg19	CCDS46964.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.63|13.63	2.293590|2.293590	0.40594|0.40594	.|.	.|.	ENSG00000145075|ENSG00000145075	ENST00000473854|ENST00000489868;ENST00000442201	.|.	.|.	.|.	4.99|4.99	4.12|4.12	0.48240|0.48240	.|.	.|.	.|.	.|.	.|.	T|T	0.54208|0.54208	0.1844|0.1844	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	.|B	.|0.15930	.|0.015	.|B	.|0.14023	.|0.01	T|T	0.49163|0.49163	-0.8968|-0.8968	5|7	.|.	.|.	.|.	.|.	12.3535|12.3535	0.55161|0.55161	0.0:0.9171:0.0:0.0829|0.0:0.9171:0.0:0.0829	.|.	.|890	.|Q9UFE4	.|CCD39_HUMAN	S|K	74|62;890	.|.	.|.	G|R	-|-	1|2	0|0	CCDC39|CCDC39	181816763|181816763	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.096000|0.096000	0.18686|0.18686	1.440000|1.440000	0.35024|0.35024	1.245000|1.245000	0.43885|0.43885	0.455000|0.455000	0.32223|0.32223	GGT|AGA;AGG	.	.		0.453	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	Missense_Mutation	T	180334069	C	T	180334069	5	4	83	1	0	0	0	0	0	0	1	0	2813	695	24	3	164	3	CCDC39	3	180334069	Splice_Site	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	79049253	180334069	17688361	17	11314										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46043146	46043146	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	gatcctgttctgcagtcttcAaagcaacagaagaagctggc	10	10	3	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr4:46043146A>C	ENST00000295452.4	-	9	1424	c.1257T>G	c.(1255-1257)ttT>ttG	p.F419L		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	419					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGCAGTCTTCAAAGCAACAGA	0.423																																					p.F419L		Atlas-SNP	.											.	GABRG1	172	.	0			c.T1257G						.						123	124	124					4																	46043146		2203	4300	6503	SO:0001583	missense	2565	exon9			GTCTTCAAAGCAA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.1257T>G	chr4.hg19:g.46043146A>C	ENSP00000295452:p.Phe419Leu	146.0	0.0		198.0	8.0	NM_173536	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	A	14.07	2.427180	0.43122	.	.	ENSG00000163285	ENST00000295452	D	0.82526	-1.62	5.49	0.104	0.14531	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.000000	0.85682	D	0.000000	T	0.69178	0.3082	L	0.48642	1.525	0.49213	D	0.999761	P	0.38582	0.638	B	0.32677	0.15	T	0.61642	-0.7021	10	0.10636	T	0.68	.	9.1931	0.37211	0.7105:0.0:0.2895:0.0	.	419	Q8N1C3	GBRG1_HUMAN	L	419	ENSP00000295452:F419L	ENSP00000295452:F419L	F	-	3	2	GABRG1	45737903	0.988000	0.35896	0.999000	0.59377	0.998000	0.95712	0.349000	0.20055	0.032000	0.15435	0.477000	0.44152	TTT	.	.		0.423	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		C	46043146	A	C	46043146	3	2	83	1	0	0	0	0	1	0	0	0	6179	127	5	5	144	5	GABRG1	4	46043146	Missense_Mutation	SNP	A	TCGA-CC-A9FU-01A-11D-A36X-10		46043146	145111130	18	11315										
DSPP	1834	hgsc.bcm.edu	37	chr4	88536956	88536973	+	In_Frame_Del	DEL	AGCAGTGACAGCAGTGAC	AGCAGTGACAGCAGTGAC	-													0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	atagcagtgacagcagcgatAgcagtgacagcagtgacagc					rs200486992|rs368829445|rs199560438|rs546297122|rs373171676		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	AGCAGTGACAGCAGTGAC	AGCAGTGACAGCAGTGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr4:88536956_88536973delAGCAGTGACAGCAGTGAC	ENST00000282478.7	+	4	3175_3192	c.3142_3159delAGCAGTGACAGCAGTGAC	c.(3142-3159)agcagtgacagcagtgacdel	p.SSDSSD1048del	DSPP_ENST00000399271.1_In_Frame_Del_p.SSDSSD1048del|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1048	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		cagcagcgatagcagtgacagcagtgacagcagcaata	0.518																																					p.1047_1053del		Pindel	.											.	DSPP	174	.	0			c.3141_3158del						.																																			SO:0001651	inframe_deletion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3142_3159delAGCAGTGACAGCAGTGAC	chr4.hg19:g.88536956_88536973delAGCAGTGACAGCAGTGAC	ENSP00000282478:p.Ser1048_Asp1053del	204.0	0.0		172.0	10.0	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.518	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		-	88536973	AGCAGTGACAGCAGTGAC	-	88536956	7	5	83	1	0	1	0	1	0	0	0	0	4784	420	15	0	3156	0	DSPP	4	88536956	In_Frame_Del	DEL	AGCAGTGACAGCAGTGAC	TCGA-CC-A9FU-01A-11D-A36X-10	42493810	88536956	102617320	19	11316										
IMPG1	3617	hgsc.bcm.edu	37	chr6	76712648	76712648	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	aacttaccaggtagaccatgCtctgctccgtccactgtctc	7	15	2	1			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr6:76712648C>A	ENST00000369950.3	-	12	1467	c.1278G>T	c.(1276-1278)gaG>gaT	p.E426D	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				GTAGACCATGCTCTGCTCCGT	0.443																																					p.E426D	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.G1278T						.						129	111	117					6																	76712648		2203	4300	6503	SO:0001583	missense	3617	exon12			ACCATGCTCTGCT	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.1278G>T	chr6.hg19:g.76712648C>A	ENSP00000358966:p.Glu426Asp	105.0	0.0		143.0	63.0	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	hg19	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	C	4.958	0.177989	0.09443	.	.	ENSG00000112706	ENST00000369950	T	0.20200	2.09	5.14	0.391	0.16282	.	1.183520	0.05997	N	0.647093	T	0.01800	0.0057	N	0.08118	0	0.09310	N	1	P	0.38335	0.627	B	0.29598	0.104	T	0.31024	-0.9958	10	0.13108	T	0.6	.	2.3811	0.04354	0.3833:0.2743:0.0:0.3424	.	426	Q17R60	IMPG1_HUMAN	D	426	ENSP00000358966:E426D	ENSP00000358966:E426D	E	-	3	2	IMPG1	76769368	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.043000	0.13971	-0.180000	0.10637	-0.309000	0.09137	GAG	.	.		0.443	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76712648	C	A	76712648	3	1	83	1	0	0	0	0	1	0	0	0	7737	796	28	3	1139	3	IMPG1	6	76712648	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10		76712648	94402419	20	11317										
SASH1	23328	hgsc.bcm.edu	37	chr6	148846451	148846451	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	cctgcagttttggaggatttGacttgacgaatcgctctctg	11	9	1	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr6:148846451G>C	ENST00000367467.3	+	11	1709	c.1234G>C	c.(1234-1236)Gac>Cac	p.D412H	AL033378.1_ENST00000411390.2_RNA	NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	412					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		TGGAGGATTTGACTTGACGAA	0.473																																					p.D412H		Atlas-SNP	.											.	SASH1	123	.	0			c.G1234C						.						225	206	213					6																	148846451		2203	4300	6503	SO:0001583	missense	23328	exon11			GGATTTGACTTGA	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1234G>C	chr6.hg19:g.148846451G>C	ENSP00000356437:p.Asp412His	57.0	0.0		65.0	22.0	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	hg19	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	G	31	5.065409	0.93898	.	.	ENSG00000111961	ENST00000367467;ENST00000535767	T	0.49432	0.78	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.65749	0.2721	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.67213	-0.5727	10	0.87932	D	0	-33.0619	20.0442	0.97604	0.0:0.0:1.0:0.0	.	393;412	Q6P4R9;O94885	.;SASH1_HUMAN	H	412;173	ENSP00000356437:D412H	ENSP00000356437:D412H	D	+	1	0	SASH1	148888144	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.420000	0.97426	2.814000	0.96858	0.655000	0.94253	GAC	.	.		0.473	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		C	148846451	G	C	148846451	3	2	83	1	0	0	0	0	1	0	0	0	13863	1290	45	4	1276	4	SASH1	6	148846451	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	72133803	148846451	22268616	21	11318										
LPA	4018	hgsc.bcm.edu	37	chr6	160953610	160953611	+	Frame_Shift_Ins	INS	-	-	A													0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	tgctcagcacaaatatacttINSatagtgattgcacacttcat							TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr6:160953610_160953611insA	ENST00000316300.5	-	38	5957_5958	c.5913_5914insT	c.(5911-5916)tataagfs	p.K1972fs	LPA_ENST00000447678.1_Frame_Shift_Ins_p.K1972fs			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4480	Kringle 18. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	CAAATATACTTATAGTGATTGC	0.426																																					p.K1972_Y1973delinsX		Atlas-Indel,Pindel	.											.	LPA	237	.	0			c.5914_5915insT						.																																			SO:0001589	frameshift_variant	4018	exon39			.	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.5914dupT	chr6.hg19:g.160953611_160953611dupA	ENSP00000321334:p.Lys1972fs	32.0	0.0		46.0	18.0	NM_005577	Q5VTD7|Q9UD88	Frame_Shift_Ins	INS	ENST00000316300.5	hg19	CCDS43523.1																																																																																			.	.		0.426	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		A	160953611	-	A	160953610	7	5	83	1	0	1	1	0	0	0	0	0	8912	1763	61	0	216	0	LPA	6	160953610	Frame_Shift_Ins	INS	-	TCGA-CC-A9FU-01A-11D-A36X-10	12107159	160953610	10161457	22	11319										
ZNF703	80139	hgsc.bcm.edu	37	chr8	37554679	37554679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	acagctggacgccaagaagaGccccttggcgctgctggctc	13	14	0	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr8:37554679G>A	ENST00000331569.4	+	2	489	c.260G>A	c.(259-261)aGc>aAc	p.S87N		NM_025069.1	NP_079345.1	Q9H7S9	ZN703_HUMAN	zinc finger protein 703	87					adherens junction assembly (GO:0034333)|cellular response to estradiol stimulus (GO:0071392)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)		FGFR1/ZNF703(2)	breast(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)	7			BRCA - Breast invasive adenocarcinoma(5;7.93e-25)|LUSC - Lung squamous cell carcinoma(8;1.05e-09)			GCCAAGAAGAGCCCCTTGGCG	0.711																																					p.S87N		Atlas-SNP	.											.	ZNF703	16	.	0			c.G260A						.						14	16	15					8																	37554679		2091	4052	6143	SO:0001583	missense	80139	exon2			AGAAGAGCCCCTT	AK024361	CCDS6094.1	8p12	2008-05-02				ENSG00000183779			25883	protein-coding gene	gene with protein product						15897872	Standard	NM_025069		Approved	FLJ14299, ZNF503L	uc003xjy.1	Q9H7S9		ENST00000331569.4:c.260G>A	chr8.hg19:g.37554679G>A	ENSP00000332325:p.Ser87Asn	79.0	0.0		32.0	21.0	NM_025069	Q5XG76	Missense_Mutation	SNP	ENST00000331569.4	hg19	CCDS6094.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.933487	0.52866	.	.	ENSG00000183779	ENST00000331569;ENST00000397235	T	0.73897	-0.79	3.87	1.95	0.26073	.	0.050532	0.85682	D	0.000000	D	0.83746	0.5321	M	0.77103	2.36	0.54753	D	0.999984	D	0.63046	0.992	D	0.75020	0.985	D	0.83429	0.0037	10	0.87932	D	0	-2.3712	10.8896	0.46988	0.0:0.0:0.6588:0.3412	.	87	Q9H7S9	ZN703_HUMAN	N	87	ENSP00000332325:S87N	ENSP00000332325:S87N	S	+	2	0	ZNF703	37673837	1.000000	0.71417	0.296000	0.24974	0.834000	0.47266	8.833000	0.92089	0.269000	0.21961	0.313000	0.20887	AGC	.	.		0.711	ZNF703-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376683.2	NM_025069		A	37554679	G	A	37554679	3	1	83	1	0	0	0	0	1	0	0	0	18121	971	34	3	266	3	ZNF703	8	37554679	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10		37554679	108809343	23	11320										
UBR5	51366	hgsc.bcm.edu	37	chr8	103335715	103335715	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	tgataaagaggattatttctCaagcatacctagcaaacaaa	6	7	1	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr8:103335715C>G	ENST00000520539.1	-	14	2214	c.1608G>C	c.(1606-1608)ttG>ttC	p.L536F	UBR5_ENST00000521922.1_Missense_Mutation_p.L530F|UBR5_ENST00000220959.4_Missense_Mutation_p.L536F	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	536					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			GATTATTTCTCAAGCATACCT	0.303																																					p.L536F	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											UBR5,NS,carcinoma,0,1	UBR5	285	.	0			c.G1608C						.						55	49	51					8																	103335715		2203	4300	6503	SO:0001583	missense	51366	exon14			ATTTCTCAAGCAT	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.1608G>C	chr8.hg19:g.103335715C>G	ENSP00000429084:p.Leu536Phe	97.0	0.0		136.0	30.0	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	hg19	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.005084	0.54254	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	T;T;T	0.53206	0.63;0.63;0.63	5.78	2.06	0.26882	.	0.000000	0.64402	D	0.000001	T	0.42743	0.1216	L	0.33485	1.01	0.51012	D	0.999907	D;D	0.54207	0.965;0.965	P;P	0.51016	0.656;0.656	T	0.13683	-1.0500	10	0.40728	T	0.16	.	9.2968	0.37819	0.0:0.2115:0.0:0.7885	.	530;536	E7EMW7;O95071	.;UBR5_HUMAN	F	536;536;530	ENSP00000429084:L536F;ENSP00000220959:L536F;ENSP00000427819:L530F	ENSP00000220959:L536F	L	-	3	2	UBR5	103404891	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	1.588000	0.36633	0.110000	0.17919	-0.469000	0.05056	TTG	.	.		0.303	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		G	103335715	C	G	103335715	3	3	83	1	0	0	0	0	1	0	0	0	16920	825	29	4	6975	4	UBR5	8	103335715	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	65781036	103335715	43028307	24	11321										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113697726	113697726	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ctattactagtaagatgggaAggcacctcagccccagtaaa	9	10	1	1			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr8:113697726A>T	ENST00000297405.5	-	15	2635	c.2391T>A	c.(2389-2391)ccT>ccA	p.P797P	CSMD3_ENST00000343508.3_Silent_p.P757P|CSMD3_ENST00000352409.3_Silent_p.P797P|CSMD3_ENST00000455883.2_Silent_p.P693P	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	797	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TAAGATGGGAAGGCACCTCAG	0.438										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.P797P		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T2391A						.						94	93	93					8																	113697726		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon15			ATGGGAAGGCACC	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2391T>A	chr8.hg19:g.113697726A>T		106.0	0.0		112.0	107.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.438	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113697726	A	T	113697726	2	4	83	1	0	0	0	0	0	0	0	1	3948	59	3	4		4	CSMD3	8	113697726	Silent	SNP	A	TCGA-CC-A9FU-01A-11D-A36X-10	10362011	113697726	32666296	25	11322										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116426936	116426936	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ttcctttcccttcagatacgGatgaactatttcctggatct	6	11	2	2	rs78385846		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr8:116426936G>T	ENST00000220888.5	-	6	3320	c.3161C>A	c.(3160-3162)tCc>tAc	p.S1054Y	TRPS1_ENST00000395715.3_Missense_Mutation_p.S1067Y|TRPS1_ENST00000519076.1_Missense_Mutation_p.S808Y|TRPS1_ENST00000520276.1_Missense_Mutation_p.S1058Y			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	1054	Mediates interaction with RNF4. {ECO:0000250}.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			TTCAGATACGGATGAACTATT	0.438									Langer-Giedion syndrome																												p.S1067Y		Atlas-SNP	.											.	TRPS1	516	.	0			c.C3200A						.						183	175	177					8																	116426936		1894	4111	6005	SO:0001583	missense	7227	exon7	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	GATACGGATGAAC	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.3161C>A	chr8.hg19:g.116426936G>T	ENSP00000220888:p.Ser1054Tyr	106.0	0.0		141.0	128.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	G	12.30	1.895856	0.33442	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276	D;D;D;D	0.98649	-5.05;-5.03;-5.0;-5.03	5.72	5.72	0.89469	.	0.130143	0.53938	D	0.000041	D	0.98058	0.9360	N	0.19112	0.55	0.80722	D	1	D;D;D	0.64830	0.994;0.99;0.994	P;P;P	0.62560	0.904;0.804;0.904	D	0.99903	1.1170	10	0.87932	D	0	.	19.865	0.96801	0.0:0.0:1.0:0.0	.	1058;1054;1067	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	Y	1067;1054;808;1058	ENSP00000379065:S1067Y;ENSP00000220888:S1054Y;ENSP00000428910:S808Y;ENSP00000428680:S1058Y	ENSP00000220888:S1054Y	S	-	2	0	TRPS1	116496112	1.000000	0.71417	0.935000	0.37517	0.522000	0.34438	5.456000	0.66665	2.685000	0.91497	0.655000	0.94253	TCC	.	.		0.438	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		T	116426936	G	T	116426936	3	4	83	1	0	0	0	0	1	0	0	0	16608	1174	41	3	688	3	TRPS1	8	116426936	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	2729210	116426936	29937086	26	11323										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113170455	113170455	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	tctccacaaagggtggtagtAtttcccaccaattcaaagcc	7	12	2	0			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr9:113170455A>G	ENST00000401783.2	-	38	7761	c.7425T>C	c.(7423-7425)aaT>aaC	p.N2475N	SVEP1_ENST00000374469.1_Silent_p.N2452N|SVEP1_ENST00000297826.5_Silent_p.N401N	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2475	Sushi 18. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GGGTGGTAGTATTTCCCACCA	0.458																																					p.N2475N		Atlas-SNP	.											.	SVEP1	326	.	0			c.T7425C						.						58	58	58					9																	113170455		1918	4134	6052	SO:0001819	synonymous_variant	79987	exon38			GGTAGTATTTCCC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.7425T>C	chr9.hg19:g.113170455A>G		77.0	0.0		67.0	54.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.		0.458	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	113170455	A	G	113170455	2	3	83	1	0	0	0	0	0	0	0	1	15435	446	16	2		2	SVEP1	9	113170455	Silent	SNP	A	TCGA-CC-A9FU-01A-11D-A36X-10		113170455	28042976	27	11324										
TNC	3371	hgsc.bcm.edu	37	chr9	117849523	117849523	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	agtgctgaagttgccccgacCgctacagaagggcctggtgt	14	11	0	2	rs368041702		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr9:117849523C>T	ENST00000350763.4	-	3	898	c.487G>A	c.(487-489)Ggt>Agt	p.G163S	TNC_ENST00000346706.3_Missense_Mutation_p.G163S|TNC_ENST00000341037.4_Missense_Mutation_p.G163S|TNC_ENST00000535648.1_Missense_Mutation_p.G163S|TNC_ENST00000537320.1_Missense_Mutation_p.G163S|TNC_ENST00000423613.2_Missense_Mutation_p.G163S|TNC_ENST00000542877.1_Missense_Mutation_p.G163S|TNC_ENST00000340094.3_Missense_Mutation_p.G163S|TNC_ENST00000345230.3_Missense_Mutation_p.G163S	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	163					bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TTGCCCCGACCGCTACAGAAG	0.557																																					p.G163S		Atlas-SNP	.											.	TNC	282	.	0			c.G487A						.						57	55	56					9																	117849523		2203	4300	6503	SO:0001583	missense	3371	exon3			CCCGACCGCTACA		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.487G>A	chr9.hg19:g.117849523C>T	ENSP00000265131:p.Gly163Ser	132.0	0.0		162.0	75.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676073	0.88445	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44	5.43	5.43	0.79202	.	0.098992	0.64402	D	0.000001	T	0.57475	0.2056	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.54309	-0.8313	10	0.40728	T	0.16	.	18.5715	0.91137	0.0:1.0:0.0:0.0	.	163;163	E9PC84;P24821	.;TENA_HUMAN	S	163	ENSP00000344400:G163S;ENSP00000438152:G163S;ENSP00000344555:G163S;ENSP00000345861:G163S;ENSP00000265131:G163S;ENSP00000339553:G163S;ENSP00000411406:G163S;ENSP00000443478:G163S;ENSP00000442242:G163S	ENSP00000344400:G163S	G	-	1	0	TNC	116889344	1.000000	0.71417	0.775000	0.31657	0.871000	0.50021	7.776000	0.85560	2.702000	0.92279	0.467000	0.42956	GGT	.	.		0.557	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117849523	C	T	117849523	3	4	83	1	0	0	0	0	1	0	0	0	16285	652	23	1	6222	1	TNC	9	117849523	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	4679068	117849523	23363908	28	11325										
LCN15	389812	hgsc.bcm.edu	37	chr9	139656673	139656673	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	catgaccatcatgtccttggGgagccccagggtcgggtaga	14	11	1	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr9:139656673G>T	ENST00000316144.5	-	5	511	c.487C>A	c.(487-489)Ccc>Acc	p.P163T	LCN15_ENST00000482511.1_5'UTR	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15	163					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						ATGTCCTTGGGGAGCCCCAGG	0.652																																					p.P163T		Atlas-SNP	.											.	LCN15	11	.	0			c.C487A						.						18	19	18					9																	139656673		2192	4295	6487	SO:0001583	missense	389812	exon5			CCTTGGGGAGCCC		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"Lipocalins"	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943	ENST00000316144.5:c.487C>A	chr9.hg19:g.139656673G>T	ENSP00000313833:p.Pro163Thr	154.0	0.0		186.0	77.0	NM_203347		Missense_Mutation	SNP	ENST00000316144.5	hg19	CCDS7006.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.417072	0.00188	.	.	ENSG00000177984	ENST00000316144	T	0.08193	3.12	4.0	-3.89	0.04193	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	2.044890	0.02605	N	0.101526	T	0.03783	0.0107	N	0.16098	0.37	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32666	-0.9898	10	0.10111	T	0.7	.	1.1132	0.01708	0.2622:0.1244:0.3835:0.23	.	163	Q6UWW0	LCN15_HUMAN	T	163	ENSP00000313833:P163T	ENSP00000313833:P163T	P	-	1	0	LCN15	138776494	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.421000	0.07053	-0.829000	0.04268	-1.736000	0.00690	CCC	.	.		0.652	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347		T	139656673	G	T	139656673	3	4	83	1	0	0	0	0	1	0	0	0	8692	1232	43	3	75	3	LCN15	9	139656673	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	21807150	139656673	1556758	29	11326										
VTI1A	143187	hgsc.bcm.edu	37	chr10	114220309	114220309	+	Missense_Mutation	SNP	G	G	T													0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	agaaacagatggttgcaaatGtggagaaacagcttgaagaa							TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr10:114220309G>T	ENST00000393077.2	+	2	237	c.121G>T	c.(121-123)Gtg>Ttg	p.V41L	VTI1A_ENST00000432306.1_Missense_Mutation_p.V41L	NM_145206.2	NP_660207.2	Q96AJ9	VTI1A_HUMAN	vesicle transport through interaction with t-SNAREs 1A	41					intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021)	SNAP receptor activity (GO:0005484)		VTI1A/TCF7L2(8)	breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		GGTTGCAAATGTGGAGAAACA	0.318			T	TCF7L2	colorectal																																p.V41L		Atlas-SNP	.		Dom	yes		10	10q25.2	143187	vesicle transport through interaction with t-SNAREs homolog 1A		E	.	VTI1A	15	.	0			c.G121T						.						92	92	92					10																	114220309		2203	4300	6503	SO:0001583	missense	143187	exon2			GCAAATGTGGAGA	BC017052	CCDS7575.2	10q25.2	2012-12-10	2012-12-10		ENSG00000151532	ENSG00000151532			17792	protein-coding gene	gene with protein product		614316	"vesicle transport through interaction with t-SNAREs homolog 1A (yeast)"			9446565	Standard	NM_145206		Approved	MVti1, Vti1a, Vti1-rp2	uc001kzz.3	Q96AJ9	OTTHUMG00000019063	ENST00000393077.2:c.121G>T	chr10.hg19:g.114220309G>T	ENSP00000376792:p.Val41Leu	528.0	1.0		471.0	132.0	NM_145206	A2A307|B4E137|Q5W0D7	Missense_Mutation	SNP	ENST00000393077.2	hg19	CCDS7575.2	.	.	.	.	.	.	.	.	.	.	G	22.0	4.227189	0.79576	.	.	ENSG00000151532	ENST00000393077;ENST00000432306	.	.	.	5.11	5.11	0.69529	t-SNARE (1);Vesicle transport v-SNARE, N-terminal (1);	0.062472	0.64402	D	0.000006	T	0.68860	0.3047	M	0.64997	1.995	0.47949	D	0.999558	B;B	0.22414	0.069;0.031	B;B	0.35353	0.159;0.201	T	0.64145	-0.6476	9	0.19147	T	0.46	-41.2954	18.1206	0.89569	0.0:0.0:1.0:0.0	.	41;41	Q5W0D7;Q96AJ9	.;VTI1A_HUMAN	L	41	.	ENSP00000376792:V41L	V	+	1	0	VTI1A	114210299	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.033000	0.76504	2.383000	0.81215	0.655000	0.94253	GTG	.	.		0.318	VTI1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050397.2			T	114220309	G	T	114220309	3	4	83	1	0	0	0	0	1	0	0	0	17250	1377	48	3	127	3	VTI1A	10	114220309	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10		114220309	21314438	30	11327	48	2								
VTI1A	143187	hgsc.bcm.edu	37	chr10	114220314	114220315	+	Nonsense_Mutation	DNP	GA	GA	TT													0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	cagatggttgcaaatgtggaGaaacagcttgaagaagcgaa							TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr10:114220314_114220315GA>TT	ENST00000393077.2	+	2	242_243	c.126_127GA>TT	c.(124-129)gaGAaa>gaTTaa	p.42_43EK>D*	VTI1A_ENST00000432306.1_Nonsense_Mutation_p.42_43EK>D*	NM_145206.2	NP_660207.2	Q96AJ9	VTI1A_HUMAN	vesicle transport through interaction with t-SNAREs 1A	42					intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021)	SNAP receptor activity (GO:0005484)		VTI1A/TCF7L2(8)	breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		CAAATGTGGAGAAACAGCTTGA	0.322			T	TCF7L2	colorectal																																p.E42D|p.K43X		Atlas-SNP	.		Dom	yes		10	10q25.2	143187	vesicle transport through interaction with t-SNAREs homolog 1A		E	.	VTI1A	15	.	0			c.G126T|c.A127T						.																																			SO:0001587	stop_gained	143187	exon2			TGTGGAGAAACAG|GTGGAGAAACAGC	BC017052	CCDS7575.2	10q25.2	2012-12-10	2012-12-10		ENSG00000151532	ENSG00000151532			17792	protein-coding gene	gene with protein product		614316	"vesicle transport through interaction with t-SNAREs homolog 1A (yeast)"			9446565	Standard	NM_145206		Approved	MVti1, Vti1a, Vti1-rp2	uc001kzz.3	Q96AJ9	OTTHUMG00000019063	Exception_encountered	chr10.hg19:g.114220314_114220315delinsTT	ENSP00000376792:p.E42_K43delinsD*	538.0|536.0	1.0		454.0|451.0	111.0|112.0	NM_145206	A2A307|B4E137|Q5W0D7	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000393077.2	hg19	CCDS7575.2																																																																																			.	.		0.322	VTI1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050397.2			TT	114220315	GA	TT	114220314	4	4	83	1	0	0	0	0	0	1	0	0	17250	933	33	3	132	3	VTI1A	10	114220314	Nonsense_Mutation	DNP	GA	TCGA-CC-A9FU-01A-11D-A36X-10	5	114220314	21314433	31	11328	48	2								
SFXN4	119559	hgsc.bcm.edu	37	chr10	120916266	120916266	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	atctggacaaactgagggatTacctagaaaagaagagagaa	11	5	1	5			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr10:120916266T>A	ENST00000355697.2	-	10	559	c.540A>T	c.(538-540)gtA>gtT	p.V180V	SFXN4_ENST00000461438.1_5'UTR|SFXN4_ENST00000330036.6_Silent_p.V171V	NM_213649.1	NP_998814.1	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	180					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	11		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		ACTGAGGGATTACCTAGAAAA	0.468																																					p.V180V		Atlas-SNP	.											.	SFXN4	24	.	0			c.A540T						.						40	36	38					10																	120916266		2203	4300	6503	SO:0001819	synonymous_variant	119559	exon10			AGGGATTACCTAG		CCDS7610.1	10q26.11	2006-03-13			ENSG00000183605	ENSG00000183605		"Sideroflexins"	16088	protein-coding gene	gene with protein product		615564				14756423	Standard	NM_213649		Approved		uc001leb.3	Q6P4A7	OTTHUMG00000019147	ENST00000355697.2:c.540A>T	chr10.hg19:g.120916266T>A		53.0	0.0		60.0	24.0	NM_213649	Q6WSU4|Q86TD9	Silent	SNP	ENST00000355697.2	hg19	CCDS7610.1																																																																																			.	.		0.468	SFXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050642.3	XM_058406		A	120916266	T	A	120916266	2	1	83	1	0	0	0	0	0	0	0	1	14212	1741	61	4		4	SFXN4	10	120916266	Silent	SNP	T	TCGA-CC-A9FU-01A-11D-A36X-10	6695952	120916266	14618481	32	11329										
OR10A3	26496	hgsc.bcm.edu	37	chr11	7960486	7960486	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	gtgaaggcatagatttcaaaTaagaaggtgtctgcacacac	10	7	2	3			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr11:7960486T>A	ENST00000360759.3	-	1	655	c.582A>T	c.(580-582)ttA>ttT	p.L194F		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	194					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L194L(1)		endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGATTTCAAATAAGAAGGTGT	0.413																																					p.L194F		Atlas-SNP	.											OR10A3,NS,carcinoma,0,1	OR10A3	54	.	1	Substitution - coding silent(1)	endometrium(1)	c.A582T						.						91	86	88					11																	7960486		2201	4296	6497	SO:0001583	missense	26496	exon1			TTCAAATAAGAAG	BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"GPCR / Class A : Olfactory receptors"	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.582A>T	chr11.hg19:g.7960486T>A	ENSP00000353988:p.Leu194Phe	173.0	0.0		175.0	47.0	NM_001003745	B9EH39|Q6IF58|Q96R11	Missense_Mutation	SNP	ENST00000360759.3	hg19	CCDS31421.1	.	.	.	.	.	.	.	.	.	.	T	3.041	-0.197404	0.06259	.	.	ENSG00000170683	ENST00000360759	T	0.00237	8.47	4.81	1.81	0.25067	GPCR, rhodopsin-like superfamily (1);	0.247095	0.20217	U	0.096794	T	0.00144	0.0004	L	0.41356	1.27	0.09310	N	1	B	0.14012	0.009	B	0.21708	0.036	T	0.25572	-1.0128	10	0.33940	T	0.23	.	5.22	0.15364	0.1452:0.6246:0.1419:0.0883	.	194	P58181	O10A3_HUMAN	F	194	ENSP00000353988:L194F	ENSP00000353988:L194F	L	-	3	2	OR10A3	7917062	0.000000	0.05858	0.554000	0.28268	0.168000	0.22595	-2.055000	0.01397	0.285000	0.22329	-1.049000	0.02347	TTA	.	.		0.413	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745		A	7960486	T	A	7960486	3	1	83	1	0	0	0	0	1	0	0	0	10900	1403	49	4	365	4	OR10A3	11	7960486	Missense_Mutation	SNP	T	TCGA-CC-A9FU-01A-11D-A36X-10		7960486	127046030	33	11330										
OR4A16	81327	hgsc.bcm.edu	37	chr11	55111591	55111591	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ctctggtgtgaaaagttaagTatagttagaaaaagagtatc	10	3	1	3			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr11:55111591T>C	ENST00000314721.2	+	1	965	c.915T>C	c.(913-915)agT>agC	p.S305S		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	305						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						AAAAGTTAAGTATAGTTAGAA	0.323																																					p.S305S		Atlas-SNP	.											.	OR4A16	120	.	0			c.T915C						.						35	35	35					11																	55111591		2201	4295	6496	SO:0001819	synonymous_variant	81327	exon1			GTTAAGTATAGTT	AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"GPCR / Class A : Olfactory receptors"	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.915T>C	chr11.hg19:g.55111591T>C		40.0	0.0		24.0	8.0	NM_001005274	Q6IFL3	Silent	SNP	ENST00000314721.2	hg19	CCDS31499.1																																																																																			.	.		0.323	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		C	55111591	T	C	55111591	2	2	83	1	0	0	0	0	0	0	0	1	11050	1635	57	2		2	OR4A16	11	55111591	Silent	SNP	T	TCGA-CC-A9FU-01A-11D-A36X-10	47151105	55111591	79894925	34	11331										
C12orf57	113246	hgsc.bcm.edu	37	chr12	7053299	7053299	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	cgccctatggcgtccgcctcGacccaaccggcggccttgag	12	18	0	1	rs144652065		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr12:7053299G>T	ENST00000229281.5	+	1	114	c.15G>T	c.(13-15)tcG>tcT	p.S5S	U47924.31_ENST00000607421.1_RNA|C12orf57_ENST00000544681.1_Silent_p.S5S|PTPN6_ENST00000447931.2_5'Flank|RNU7-1_ENST00000458811.1_RNA|C12orf57_ENST00000542222.1_Intron|PTPN6_ENST00000399448.1_5'Flank|C12orf57_ENST00000540506.2_5'UTR|C12orf57_ENST00000537087.1_Silent_p.S5S	NM_138425.2	NP_612434.1	Q99622	C10_HUMAN	chromosome 12 open reading frame 57	5						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)	2						CGTCCGCCTCGACCCAACCGG	0.587											OREG0021642	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S5S		Atlas-SNP	.											.	C12orf57	10	.	0			c.G15T						.						90	95	94					12																	7053299		2203	4300	6503	SO:0001819	synonymous_variant	113246	exon1			CGCCTCGACCCAA	U47924	CCDS8571.1	12p13.31	2012-05-30			ENSG00000111678	ENSG00000111678			29521	protein-coding gene	gene with protein product		615140				9445485	Standard	NM_138425		Approved	GRCC10, C10	uc009zfj.2	Q99622	OTTHUMG00000169017	ENST00000229281.5:c.15G>T	chr12.hg19:g.7053299G>T		84.0	0.0	638	83.0	4.0	NM_138425	B2R4Q6	Silent	SNP	ENST00000229281.5	hg19	CCDS8571.1																																																																																			.	G|1.000;A|0.000		0.587	C12orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401959.1	NM_138425		T	7053299	G	T	7053299	2	4	83	1	0	0	0	0	0	0	0	1	1703	1045	37	1		1	C12orf57	12	7053299	Silent	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10		7053299	126798596	35	11332										
SOX5	6660	hgsc.bcm.edu	37	chr12	23793762	23793762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ttacctgcagttggagtgggCctaagcctggtgttgctgcg	15	9	0	0			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr12:23793762C>T	ENST00000451604.2	-	8	1102	c.1001G>A	c.(1000-1002)gGc>gAc	p.G334D	RP11-437F6.1_ENST00000546118.1_RNA|SOX5_ENST00000309359.1_Missense_Mutation_p.G321D|SOX5_ENST00000545921.1_Missense_Mutation_p.G324D|SOX5_ENST00000381381.2_Missense_Mutation_p.G321D|SOX5_ENST00000541536.1_Missense_Mutation_p.G321D|SOX5_ENST00000537393.1_Missense_Mutation_p.G299D|SOX5_ENST00000546136.1_Missense_Mutation_p.G321D			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	334					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						TTGGAGTGGGCCTAAGCCTGG	0.453																																					p.G334D		Atlas-SNP	.											.	SOX5	134	.	0			c.G1001A						.						120	117	118					12																	23793762		2203	4300	6503	SO:0001583	missense	6660	exon8			AGTGGGCCTAAGC	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"SRY (sex determining region Y)-boxes"	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.1001G>A	chr12.hg19:g.23793762C>T	ENSP00000398273:p.Gly334Asp	54.0	0.0		53.0	28.0	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	hg19	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	C	14.50	2.554304	0.45487	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921	D;D;D;D;D;D;D	0.97256	-4.29;-4.29;-4.28;-4.29;-4.31;-4.28;-4.29	5.81	5.81	0.92471	.	0.164822	0.52532	D	0.000068	D	0.95001	0.8382	L	0.54323	1.7	0.58432	D	0.999998	B;P;P	0.43477	0.438;0.49;0.808	B;B;B	0.39706	0.197;0.125;0.307	D	0.93602	0.6931	10	0.19147	T	0.46	.	15.5471	0.76112	0.0:0.8627:0.1373:0.0	.	299;321;334	F5H0I3;P35711-4;P35711	.;.;SOX5_HUMAN	D	321;321;321;334;286;299;321;324	ENSP00000437487:G321D;ENSP00000308927:G321D;ENSP00000370788:G321D;ENSP00000398273:G334D;ENSP00000439832:G299D;ENSP00000441973:G321D;ENSP00000443520:G324D	ENSP00000308927:G321D	G	-	2	0	SOX5	23685029	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.115000	0.71566	2.736000	0.93811	0.655000	0.94253	GGC	.	.		0.453	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		T	23793762	C	T	23793762	3	4	83	1	0	0	0	0	1	0	0	0	14969	739	26	3	1332	3	SOX5	12	23793762	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	16740463	23793762	110058133	36	11333										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26640009	26640009	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	atacttctttacctctcattCgtggaccagatgtcatcaat	5	11	4	1			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr12:26640009C>A	ENST00000381340.3	-	40	5962	c.5546G>T	c.(5545-5547)cGa>cTa	p.R1849L		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1849					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	ACCTCTCATTCGTGGACCAGA	0.368																																					p.R1849L		Atlas-SNP	.											.	ITPR2	270	.	0			c.G5546T						.						198	181	186					12																	26640009		1875	4114	5989	SO:0001583	missense	3709	exon40			CTCATTCGTGGAC	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.5546G>T	chr12.hg19:g.26640009C>A	ENSP00000370744:p.Arg1849Leu	91.0	0.0		102.0	53.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.585441	0.46110	.	.	ENSG00000123104	ENST00000381340	D	0.89415	-2.51	4.94	4.94	0.65067	.	0.628906	0.15732	N	0.247382	D	0.82595	0.5071	L	0.41492	1.28	0.28954	N	0.890259	B	0.19817	0.039	B	0.17433	0.018	T	0.70167	-0.4946	10	0.21540	T	0.41	.	9.711	0.40245	0.0:0.8756:0.0:0.1244	.	1849	Q14571	ITPR2_HUMAN	L	1849	ENSP00000370744:R1849L	ENSP00000370744:R1849L	R	-	2	0	ITPR2	26531276	0.942000	0.31987	0.040000	0.18447	0.994000	0.84299	2.202000	0.42743	2.745000	0.94114	0.650000	0.86243	CGA	.	.		0.368	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26640009	C	A	26640009	3	1	83	1	0	0	0	0	1	0	0	0	7930	884	31	1	2631	1	ITPR2	12	26640009	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	2846247	26640009	107211886	37	11334										
LRIG3	121227	hgsc.bcm.edu	37	chr12	59266374	59266374	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ctatgtgtccaagtcataagActgaaaatttggagtcctgt	9	7	1	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr12:59266374A>T	ENST00000320743.3	-	19	3626	c.3340T>A	c.(3340-3342)Tct>Act	p.S1114T	LRIG3_ENST00000379141.4_Missense_Mutation_p.S1054T	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	1114					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			AAGTCATAAGACTGAAAATTT	0.338			T	ROS1	NSCLC																																p.S1114T		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.T3340A						.						62	70	67					12																	59266374		2203	4300	6503	SO:0001583	missense	121227	exon19			CATAAGACTGAAA	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.3340T>A	chr12.hg19:g.59266374A>T	ENSP00000326759:p.Ser1114Thr	56.0	0.0		55.0	36.0	NM_153377	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	hg19	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	A	9.814	1.184035	0.21870	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.61859	0.12;0.07	5.79	3.33	0.38152	.	0.216295	0.23635	N	0.046098	T	0.36220	0.0959	N	0.19112	0.55	0.23739	N	0.996972	B;B	0.10296	0.003;0.002	B;B	0.09377	0.004;0.002	T	0.13629	-1.0502	9	.	.	.	.	6.9043	0.24301	0.7928:0.0:0.0735:0.1338	.	1054;1114	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	T	1054;1114	ENSP00000368436:S1054T;ENSP00000326759:S1114T	.	S	-	1	0	LRIG3	57552641	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	3.317000	0.51968	1.032000	0.39892	0.460000	0.39030	TCT	.	.		0.338	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		T	59266374	A	T	59266374	3	4	83	1	0	0	0	0	1	0	0	0	8955	275	10	4	23	4	LRIG3	12	59266374	Missense_Mutation	SNP	A	TCGA-CC-A9FU-01A-11D-A36X-10	32626365	59266374	74585521	38	11335										
MYF5	4617	hgsc.bcm.edu	37	chr12	81112793	81112793	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ttcacagcctgcaactccagGggcttctagttccaggctta	9	13	2	0			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr12:81112793G>C	ENST00000228644.3	+	3	883	c.731G>C	c.(730-732)gGg>gCg	p.G244A		NM_005593.2	NP_005584.2	P13349	MYF5_HUMAN	myogenic factor 5	244					camera-type eye development (GO:0043010)|cartilage condensation (GO:0001502)|embryonic skeletal system morphogenesis (GO:0048704)|extracellular matrix organization (GO:0030198)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle tissue morphogenesis (GO:0060415)|ossification (GO:0001503)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)	protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(8)|lung(15)|ovary(2)|pancreas(1)	30						GCAACTCCAGGGGCTTCTAGT	0.507																																					p.G244A		Atlas-SNP	.											.	MYF5	78	.	0			c.G731C						.						81	80	80					12																	81112793		2203	4300	6503	SO:0001583	missense	4617	exon3			CTCCAGGGGCTTC		CCDS9020.1	12q21	2013-05-21			ENSG00000111049	ENSG00000111049		"Basic helix-loop-helix proteins"	7565	protein-coding gene	gene with protein product		159990				8978788, 12105204	Standard	NM_005593		Approved	bHLHc2	uc001szg.2	P13349	OTTHUMG00000170166	ENST00000228644.3:c.731G>C	chr12.hg19:g.81112793G>C	ENSP00000228644:p.Gly244Ala	67.0	0.0		56.0	33.0	NM_005593	Q6ISR9	Missense_Mutation	SNP	ENST00000228644.3	hg19	CCDS9020.1	.	.	.	.	.	.	.	.	.	.	G	10.28	1.306859	0.23821	.	.	ENSG00000111049	ENST00000228644	D	0.98362	-4.89	6.06	6.06	0.98353	.	0.140827	0.64402	D	0.000012	D	0.94255	0.8155	L	0.38175	1.15	0.38266	D	0.942013	P	0.37525	0.598	B	0.34824	0.19	D	0.92106	0.5692	10	0.06099	T	0.92	-7.413	9.4003	0.38428	0.1507:0.0:0.8493:0.0	.	244	P13349	MYF5_HUMAN	A	244	ENSP00000228644:G244A	ENSP00000228644:G244A	G	+	2	0	MYF5	79636924	1.000000	0.71417	0.981000	0.43875	0.968000	0.65278	3.953000	0.56699	2.882000	0.98803	0.655000	0.94253	GGG	.	.		0.507	MYF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407757.1	NM_005593		C	81112793	G	C	81112793	3	2	83	1	0	0	0	0	1	0	0	0	10036	1232	43	4	741	4	MYF5	12	81112793	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	21846419	81112793	52739102	39	11336										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124341720	124341720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ctgggctggactgccctcgcGtccgctaccctgacttcaac	10	17	1	1	rs557513283		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr12:124341720G>A	ENST00000409039.3	+	36	6227	c.6202G>A	c.(6202-6204)Gtc>Atc	p.V2068I		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2068					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V2068I(1)|p.V660I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CTGCCCTCGCGTCCGCTACCC	0.532													G|||	1	0.000199681	0	0	5008	,	,		13626	0		0	False		,,,				2504	0.001				p.V2068I		Atlas-SNP	.											DNAH10_same_name,NS,carcinoma,0,2	DNAH10	888	.	2	Substitution - Missense(2)	breast(2)	c.G6202A						.						135	138	137					12																	124341720		2078	4205	6283	SO:0001583	missense	196385	exon36			CCTCGCGTCCGCT	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.6202G>A	chr12.hg19:g.124341720G>A	ENSP00000386770:p.Val2068Ile	104.0	0.0		105.0	32.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	12.26	1.883920	0.33255	.	.	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.75	5.75	0.90469	.	0.000000	0.64402	U	0.000007	T	0.33789	0.0875	L	0.50919	1.6	0.80722	D	1	D	0.65815	0.995	P	0.52159	0.691	T	0.00555	-1.1673	10	0.33940	T	0.23	.	19.9522	0.97203	0.0:0.0:1.0:0.0	.	2068	Q8IVF4	DYH10_HUMAN	I	2068	ENSP00000386770:V2068I	ENSP00000386770:V2068I	V	+	1	0	DNAH10	122907673	1.000000	0.71417	0.763000	0.31416	0.165000	0.22458	9.725000	0.98778	2.725000	0.93324	0.655000	0.94253	GTC	.	.		0.532	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124341720	G	A	124341720	3	1	83	1	0	0	0	0	1	0	0	0	4600	1145	40	1	6344	1	DNAH10	12	124341720	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	43228927	124341720	9510175	40	11337										
FLT1	2321	hgsc.bcm.edu	37	chr13	28959141	28959141	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ccactgtgtgatcactgaggTttcgcaggaggtatggtgct	14	8	1	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr13:28959141T>A	ENST00000282397.4	-	14	2248	c.1997A>T	c.(1996-1998)aAc>aTc	p.N666I	FLT1_ENST00000541932.1_Missense_Mutation_p.N666I	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	666	Ig-like C2-type 7.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATCACTGAGGTTTCGCAGGAG	0.438																																					p.N666I		Atlas-SNP	.											.	FLT1	393	.	0			c.A1997T						.						206	185	192					13																	28959141		2203	4300	6503	SO:0001583	missense	2321	exon14			CTGAGGTTTCGCA	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1997A>T	chr13.hg19:g.28959141T>A	ENSP00000282397:p.Asn666Ile	119.0	0.0		68.0	59.0	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	hg19	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.419333	0.83559	.	.	ENSG00000102755	ENST00000282397;ENST00000541932	T;T	0.65364	-0.15;2.65	5.59	5.59	0.84812	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.158216	0.53938	D	0.000043	T	0.72070	0.3415	L	0.43646	1.37	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.71414	0.973;0.966	T	0.74774	-0.3551	10	0.72032	D	0.01	.	14.3433	0.66643	0.0:0.0:0.0:1.0	.	666;666	P17948-3;P17948	.;VGFR1_HUMAN	I	666	ENSP00000282397:N666I;ENSP00000437631:N666I	ENSP00000282397:N666I	N	-	2	0	FLT1	27857141	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	4.956000	0.63645	2.125000	0.65367	0.460000	0.39030	AAC	.	.		0.438	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			A	28959141	T	A	28959141	3	1	83	1	0	0	0	0	1	0	0	0	5949	1725	60	4	2177	4	FLT1	13	28959141	Missense_Mutation	SNP	T	TCGA-CC-A9FU-01A-11D-A36X-10		28959141	86210737	41	11338										
OR4N2	390429	hgsc.bcm.edu	37	chr14	20296476	20296476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	tcctgtcatttatacccttcGcaaccaggaagtgaaagctt	7	11	1	1			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr14:20296476G>A	ENST00000315947.1	+	1	869	c.869G>A	c.(868-870)cGc>cAc	p.R290H	OR4N2_ENST00000568211.1_3'UTR	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TATACCCTTCGCAACCAGGAA	0.403																																					p.R290H		Atlas-SNP	.											OR4N2,NS,carcinoma,+1,2	OR4N2	125	.	0			c.G869A						.						47	50	49					14																	20296476		2203	4296	6499	SO:0001583	missense	390429	exon1			CCCTTCGCAACCA		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"GPCR / Class A : Olfactory receptors"	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.869G>A	chr14.hg19:g.20296476G>A	ENSP00000319601:p.Arg290His	93.0	1.0		99.0	4.0	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	hg19	CCDS32022.1	.	.	.	.	.	.	.	.	.	.	.	7.943	0.743201	0.15642	.	.	ENSG00000176294	ENST00000315947	T	0.41065	1.01	4.57	2.73	0.32206	.	0.000000	0.39909	N	0.001237	T	0.49372	0.1553	M	0.93462	3.42	0.19945	N	0.999941	B	0.32302	0.363	B	0.27715	0.082	T	0.53844	-0.8381	10	0.87932	D	0	-6.4057	8.7854	0.34818	0.1889:0.0:0.8111:0.0	.	290	Q8NGD1	OR4N2_HUMAN	H	290	ENSP00000319601:R290H	ENSP00000319601:R290H	R	+	2	0	OR4N2	19366316	0.173000	0.23056	0.675000	0.29917	0.112000	0.19704	2.979000	0.49313	0.651000	0.30788	0.591000	0.81541	CGC	.	.		0.403	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2			A	20296476	G	A	20296476	3	1	83	1	0	0	0	0	1	0	0	0	11086	1087	38	1	871	1	OR4N2	14	20296476	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10		20296476	87053064	42	11339										
C14orf166	51637	hgsc.bcm.edu	37	chr14	52458049	52458049	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ttgcagatgaaacagaatttAgaaacttcatcgtttggctt	8	6	1	4			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr14:52458049A>G	ENST00000261700.3	+	2	241	c.76A>G	c.(76-78)Aga>Gga	p.R26G	C14orf166_ENST00000556760.1_Missense_Mutation_p.R26G	NM_016039.2	NP_057123.1	Q9Y224	CN166_HUMAN	chromosome 14 open reading frame 166	26					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA transport (GO:0050658)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II core binding (GO:0000993)			endometrium(1)|large_intestine(3)|lung(2)	6	Breast(41;0.0639)|all_epithelial(31;0.101)					AACAGAATTTAGAAACTTCAT	0.358																																					p.R26G		Atlas-SNP	.											.	C14orf166	23	.	0			c.A76G						.						62	64	64					14																	52458049		2203	4300	6503	SO:0001583	missense	51637	exon2			GAATTTAGAAACT	AF151857	CCDS9705.1	14q22.1	2014-05-29			ENSG00000087302	ENSG00000087302			23169	protein-coding gene	gene with protein product	"RLL motif containing 1"	610858				10810093, 24608264	Standard	NM_016039		Approved	CGI-99, RLLM1, CLE, CLE7, LCRP369	uc010aod.3	Q9Y224	OTTHUMG00000152332	ENST00000261700.3:c.76A>G	chr14.hg19:g.52458049A>G	ENSP00000261700:p.Arg26Gly	277.0	0.0		278.0	166.0	NM_016039		Missense_Mutation	SNP	ENST00000261700.3	hg19	CCDS9705.1	.	.	.	.	.	.	.	.	.	.	A	18.34	3.602070	0.66445	.	.	ENSG00000087302	ENST00000261700;ENST00000556760	.	.	.	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.79598	0.4473	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.82273	-0.0539	9	0.62326	D	0.03	0.0063	10.4046	0.44249	0.7024:0.2976:0.0:0.0	.	26	Q9Y224	CN166_HUMAN	G	26	.	ENSP00000261700:R26G	R	+	1	2	C14orf166	51527799	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.541000	0.60670	1.967000	0.57214	0.397000	0.26171	AGA	.	.		0.358	C14orf166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276887.1	NM_016039		G	52458049	A	G	52458049	3	3	83	1	0	0	0	0	1	0	0	0	1758	412	15	2	82	2	C14orf166	14	52458049	Missense_Mutation	SNP	A	TCGA-CC-A9FU-01A-11D-A36X-10	32161573	52458049	54891491	43	11340										
ZSCAN29	146050	hgsc.bcm.edu	37	chr15	43661977	43661977	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	cgcacctccggccttagccaCcgacagcaaagttcccagag	9	17	0	1			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr15:43661977C>A	ENST00000396976.2	-	1	269	c.135G>T	c.(133-135)cgG>cgT	p.R45R	ZSCAN29_ENST00000396972.1_Silent_p.R45R|ZSCAN29_ENST00000563508.1_5'Flank|ZSCAN29_ENST00000568898.1_Silent_p.R44R|ZSCAN29_ENST00000562072.1_Silent_p.R44R|TUBGCP4_ENST00000570081.1_Intron|TUBGCP4_ENST00000564079.1_5'Flank|TUBGCP4_ENST00000260383.7_5'Flank	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	45	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		GCCTTAGCCACCGACAGCAAA	0.562																																					p.R45R		Atlas-SNP	.											ZSCAN29,NS,carcinoma,0,1	ZSCAN29	57	.	0			c.G135T						.						68	68	68					15																	43661977		2201	4299	6500	SO:0001819	synonymous_variant	146050	exon1			TAGCCACCGACAG	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"-", "Zinc fingers, C2H2-type"	26673	protein-coding gene	gene with protein product			"zinc finger protein 690"	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.135G>T	chr15.hg19:g.43661977C>A		66.0	0.0		65.0	21.0	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Silent	SNP	ENST00000396976.2	hg19	CCDS10095.2																																																																																			.	.		0.562	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455		A	43661977	C	A	43661977	2	1	83	1	0	0	0	0	0	0	0	1	18251	494	18	3		3	ZSCAN29	15	43661977	Silent	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10		43661977	58869415	44	11341										
AXIN1	8312	hgsc.bcm.edu	37	chr16	360070	360070	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	tgtatggggggatcccatccCtgtccaggagaaagaggcag	15	9	0	2			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr16:360070C>A	ENST00000262320.3	-	4	1391		c.e4-1		AXIN1_ENST00000481769.1_Splice_Site|AXIN1_ENST00000354866.3_Splice_Site	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1						activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GATCCCATCCCTGTCCAGGAG	0.627																																					.		Atlas-SNP	.											.	AXIN1	290	.	0			c.1020-1G>T						.						50	34	39					16																	360070		2201	4300	6501	SO:0001630	splice_region_variant	8312	exon5			CCATCCCTGTCCA	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1020-1G>T	chr16.hg19:g.360070C>A		85.0	0.0		56.0	46.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Splice_Site	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150069	0.37923	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9963	0.89185	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AXIN1	300071	1.000000	0.71417	0.995000	0.50966	0.058000	0.15608	7.310000	0.78947	2.257000	0.74773	0.456000	0.33151	.	.	.		0.627	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		Intron	A	360070	C	A	360070	5	1	83	1	0	0	0	0	0	0	1	0	1236	695	24	3	1601	3	AXIN1	16	360070	Splice_Site	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10		360070	89994683	45	11342										
MAP2K3	5606	hgsc.bcm.edu	37	chr17	21203869	21203869	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ccttcaagaactttgaggtgGaggctgatgacttggtgacc	13	8	1	5			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr17:21203869G>C	ENST00000342679.4	+	4	427	c.178G>C	c.(178-180)Gag>Cag	p.E60Q	MAP2K3_ENST00000316920.6_Missense_Mutation_p.E31Q|MAP2K3_ENST00000361818.5_Missense_Mutation_p.E31Q	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	60					activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CTTTGAGGTGGAGGCTGATGA	0.577																																					p.E60Q		Atlas-SNP	.											.	MAP2K3	135	.	0			c.G178C						.						56	50	52					17																	21203869		2201	4300	6501	SO:0001583	missense	5606	exon4			GAGGTGGAGGCTG	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"Mitogen-activated protein kinase cascade / Kinase kinases"	6843	protein-coding gene	gene with protein product	"MAPK/ERK kinase 3", "MAP kinase kinase 3", "dual specificity mitogen activated protein kinase kinase 3"	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.178G>C	chr17.hg19:g.21203869G>C	ENSP00000345083:p.Glu60Gln	117.0	0.0		120.0	31.0	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	hg19	CCDS11217.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.560567	0.45590	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000526076;ENST00000316920	T;T;D	0.89050	1.1;1.1;-2.46	5.47	5.47	0.80525	Protein kinase-like domain (1);	0.149655	0.42420	D	0.000711	T	0.79581	0.4470	N	0.25485	0.75	0.43408	D	0.995542	B	0.33413	0.411	B	0.24701	0.055	T	0.76820	-0.2818	10	0.20519	T	0.43	-48.034	12.6439	0.56723	0.0755:0.0:0.9245:0.0	.	60	P46734	MP2K3_HUMAN	Q	60;31;31;31;64	ENSP00000345083:E60Q;ENSP00000355081:E31Q;ENSP00000434068:E31Q	ENSP00000319139:E64Q	E	+	1	0	MAP2K3	21144462	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.909000	0.56363	2.582000	0.87167	0.655000	0.94253	GAG	.	.		0.577	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109		C	21203869	G	C	21203869	3	2	83	1	0	0	0	0	1	0	0	0	9247	1175	41	4	192	4	MAP2K3	17	21203869	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10		21203869	59991341	46	11343										
PIGS	94005	hgsc.bcm.edu	37	chr17	26885512	26885512	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	acccagccgggactccactgGgttgatgacatgggggaggc	16	11	0	2	rs201018217		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr17:26885512G>A	ENST00000308360.7	-	8	1291	c.916C>T	c.(916-918)Cca>Tca	p.P306S	PIGS_ENST00000543734.1_Missense_Mutation_p.P245S|PIGS_ENST00000395346.2_Missense_Mutation_p.P298S|PIGS_ENST00000465444.1_5'Flank	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	306					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					GACTCCACTGGGTTGATGACA	0.557																																					p.P306S		Atlas-SNP	.											.	PIGS	42	.	0			c.C916T						.						58	53	55					17																	26885512		2203	4300	6503	SO:0001583	missense	94005	exon8			CCACTGGGTTGAT		CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"Phosphatidylinositol glycan anchor biosynthesis"	14937	protein-coding gene	gene with protein product	"GPI transamidase subunit"	610271	"phosphatidylinositol glycan, class S"				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.916C>T	chr17.hg19:g.26885512G>A	ENSP00000309430:p.Pro306Ser	85.0	0.0		72.0	47.0	NM_033198	Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	hg19	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.793003	0.70452	.	.	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.37915	1.17;1.17;1.17	5.64	5.64	0.86602	.	0.097154	0.64402	N	0.000001	T	0.32041	0.0816	N	0.21617	0.685	0.80722	D	1	B;B	0.23854	0.092;0.075	B;B	0.38106	0.265;0.173	T	0.06625	-1.0816	10	0.02654	T	1	-4.9301	19.6862	0.95979	0.0:0.0:1.0:0.0	.	306;298	Q96S52;Q96S52-2	PIGS_HUMAN;.	S	298;306;245	ENSP00000378755:P298S;ENSP00000309430:P306S;ENSP00000438447:P245S	ENSP00000309430:P306S	P	-	1	0	PIGS	23909639	1.000000	0.71417	0.996000	0.52242	0.975000	0.68041	9.209000	0.95087	2.657000	0.90304	0.491000	0.48974	CCA	.	G|0.999;C|0.001		0.557	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198		A	26885512	G	A	26885512	3	1	83	1	0	0	0	0	1	0	0	0	11907	1232	43	3	771	3	PIGS	17	26885512	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	5681643	26885512	54309698	47	11344										
MEOX1	4222	hgsc.bcm.edu	37	chr17	41738601	41738601	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ctgagttgggcctgcgccggGcgtctgagacagggaagtgc	18	10	1	2	rs183202008		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr17:41738601G>A	ENST00000318579.4	-	1	721	c.302C>T	c.(301-303)gCc>gTc	p.A101V	MEOX1_ENST00000549132.1_Missense_Mutation_p.P72S|MEOX1_ENST00000329168.3_Missense_Mutation_p.A101V|MEOX1_ENST00000393661.2_5'UTR	NM_001040002.1|NM_004527.3	NP_001035091.1|NP_004518.1	P50221	MEOX1_HUMAN	mesenchyme homeobox 1	101					multicellular organismal development (GO:0007275)|somite specification (GO:0001757)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)		CCTGCGCCGGGCGTCTGAGAC	0.667																																					p.A101V		Atlas-SNP	.											.	MEOX1	29	.	0			c.C302T						.						47	55	53					17																	41738601		2203	4300	6503	SO:0001583	missense	4222	exon1			CGCCGGGCGTCTG		CCDS11466.1, CCDS11467.1, CCDS42343.1	17q21.31	2014-07-15	2005-12-22					"Homeoboxes / ANTP class : HOXL subclass"	7013	protein-coding gene	gene with protein product		600147	"mesenchyme homeo box 1"			7987315	Standard	NM_013999		Approved	MOX1	uc002idz.3	P50221	OTTHUMG00000170513	ENST00000318579.4:c.302C>T	chr17.hg19:g.41738601G>A	ENSP00000321684:p.Ala101Val	125.0	0.0		89.0	21.0	NM_004527	A8K524|A8MWF9|Q15069	Missense_Mutation	SNP	ENST00000318579.4	hg19	CCDS11466.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.43|12.43	1.936433|1.936433	0.34189|0.34189	.|.	.|.	ENSG00000005102|ENSG00000005102	ENST00000318579;ENST00000329168|ENST00000549132	D;T|.	0.91407|.	-2.84;0.59|.	4.92|4.92	3.94|3.94	0.45596|0.45596	.|.	0.292544|.	0.38663|.	N|.	0.001605|.	T|T	0.59783|0.59783	0.2219|0.2219	L|L	0.53249|0.53249	1.67|1.67	0.33764|0.33764	D|D	0.622209|0.622209	P;P|.	0.42692|.	0.787;0.745|.	P;B|.	0.44359|.	0.447;0.164|.	T|T	0.72959|0.72959	-0.4133|-0.4133	10|6	0.51188|0.87932	T|D	0.08|0	-26.9951|-26.9951	13.1299|13.1299	0.59375|0.59375	0.0:0.3068:0.6932:0.0|0.0:0.3068:0.6932:0.0	.|.	101;101|.	Q15069;P50221|.	.;MEOX1_HUMAN|.	V|S	101|72	ENSP00000321684:A101V;ENSP00000328678:A101V|.	ENSP00000321684:A101V|ENSP00000449049:P72S	A|P	-|-	2|1	0|0	MEOX1|MEOX1	39094127|39094127	0.998000|0.998000	0.40836|0.40836	0.996000|0.996000	0.52242|0.52242	0.392000|0.392000	0.30506|0.30506	3.059000|3.059000	0.49947|0.49947	1.277000|1.277000	0.44412|0.44412	0.655000|0.655000	0.94253|0.94253	GCC|CCC	.	G|0.999;T|0.001		0.667	MEOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409452.1			A	41738601	G	A	41738601	3	1	83	1	0	0	0	0	1	0	0	0	9482	1203	42	3	474	3	MEOX1	17	41738601	Missense_Mutation	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	14853089	41738601	39456609	48	11345										
REXO1	57455	hgsc.bcm.edu	37	chr19	1827911	1827912	+	Frame_Shift_Ins	INS	-	-	CTCAT													0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ttacctgggaccgtggcggcINSctcatcttctgagtctgaga							TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr19:1827911_1827912insCTCAT	ENST00000170168.4	-	2	970_971	c.876_877insATGAG	c.(874-879)gaggccfs	p.A293fs	REXO1_ENST00000587524.1_De_novo_Start_OutOfFrame	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	293						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCGTGGCGGCCTCATCTTCTG	0.653																																					p.A293fs		Atlas-Indel,Pindel	.											.	REXO1	55	.	0			c.877_878insATGAG						.																																			SO:0001589	frameshift_variant	57455	exon2			.	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"elongin A binding protein 1"	609614	"transcription elongation factor B polypeptide 3 binding protein 1"	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.872_876dupATGAG	chr19.hg19:g.1827912_1827916dupCTCAT	ENSP00000170168:p.Ala293fs	63.0	0.0		62.0	46.0	NM_020695	Q9ULT2	Frame_Shift_Ins	INS	ENST00000170168.4	hg19	CCDS32866.1																																																																																			.	.		0.653	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		CTCAT	1827912	-	CTCAT	1827911	7	5	83	1	0	1	1	0	0	0	0	0	13256	739	26	0	2848	0	REXO1	19	1827911	Frame_Shift_Ins	INS	-	TCGA-CC-A9FU-01A-11D-A36X-10		1827911	57301072	49	11346										
PNMAL2	57469	hgsc.bcm.edu	37	chr19	46997793	46997793	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	tgcgagtcgctctccgaagtGtcgctgtccaccggctcctc	11	16	1	0			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr19:46997793G>A	ENST00000377655.2	-	1	734				AC011484.1_ENST00000377652.3_5'UTR|PNMAL2_ENST00000599531.1_Silent_p.D310D|PNMAL2_ENST00000594749.1_Intron			Q9ULN7	PNML2_HUMAN	paraneoplastic Ma antigen family-like 2											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)	8		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		TCTCCGAAGTGTCGCTGTCCA	0.577																																					p.D310D		Atlas-SNP	.											.	PNMAL2	44	.	0			c.C930T						.						65	70	68					19																	46997793		2203	4298	6501	SO:0001627	intron_variant	57469	exon1			CGAAGTGTCGCTG	AB033009	CCDS59400.1	19q13.32	2014-02-12	2012-02-09		ENSG00000204851	ENSG00000204851		"Paraneoplastic Ma antigens"	29206	protein-coding gene	gene with protein product			"PNMA-like 2"			10574461	Standard	NM_020709		Approved	KIAA1183	uc002pes.2	Q9ULN7		ENST00000377655.2:c.734+195C>T	chr19.hg19:g.46997793G>A		88.0	0.0		154.0	14.0	NM_020709	C9JGD5|M0R374|Q08E79|Q0D2F9|Q6ZVD1	Silent	SNP	ENST00000377655.2	hg19																																																																																				.	.		0.577	PNMAL2-201	KNOWN	basic	protein_coding	protein_coding		NM_020709		A	46997793	G	A	46997793	1	1	83	0	1	0	0	0	0	0	0	0	12167	1368	48	3		3	PNMAL2	19	46997793	Intron	SNP	G	TCGA-CC-A9FU-01A-11D-A36X-10	45169882	46997793	12131190	50	11347										
TTYH1	57348	hgsc.bcm.edu	37	chr19	54930426	54930426	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ccccgggtccaagatcccctCgcccgggggaggctgcgtca	14	17	1	1			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr19:54930426C>G	ENST00000376530.3	+	2	354	c.251C>G	c.(250-252)tCg>tGg	p.S84W	TTYH1_ENST00000376531.3_Missense_Mutation_p.S84W|TTYH1_ENST00000391739.3_Missense_Mutation_p.S133W|TTYH1_ENST00000301194.4_Missense_Mutation_p.S84W	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1	84					cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)			endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		AAGATCCCCTCGCCCGGGGGA	0.706																																					p.S84W		Atlas-SNP	.											.	TTYH1	78	.	0			c.C251G						.						24	30	28					19																	54930426		2199	4290	6489	SO:0001583	missense	57348	exon2			TCCCCTCGCCCGG	AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"tweety (Drosophila) homolog 1", "tweety homolog 1 (Drosophila)"			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.251C>G	chr19.hg19:g.54930426C>G	ENSP00000365713:p.Ser84Trp	36.0	0.0		75.0	64.0	NM_020659	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Missense_Mutation	SNP	ENST00000376530.3	hg19	CCDS12893.1	.	.	.	.	.	.	.	.	.	.	C	9.920	1.211808	0.22289	.	.	ENSG00000167614	ENST00000444661;ENST00000423529;ENST00000301194;ENST00000376530;ENST00000445095;ENST00000391739;ENST00000376531	T;T;T;T;T;T	0.48522	0.81;2.82;2.82;1.4;2.11;2.63	3.51	-0.352	0.12598	.	0.547787	0.17616	N	0.167901	T	0.45994	0.1370	N	0.24115	0.695	0.09310	N	1	D;P;D;P	0.71674	0.998;0.941;0.983;0.924	D;P;P;P	0.67382	0.951;0.609;0.609;0.555	T	0.33059	-0.9883	10	0.66056	D	0.02	-11.3325	6.662	0.23018	0.5082:0.3255:0.1664:0.0	.	133;84;84;84	B7Z1H9;Q9H313-2;Q9H313-3;Q9H313	.;.;.;TTYH1_HUMAN	W	56;80;84;84;133;133;84	ENSP00000391282:S80W;ENSP00000301194:S84W;ENSP00000365713:S84W;ENSP00000393592:S133W;ENSP00000375619:S133W;ENSP00000365714:S84W	ENSP00000301194:S84W	S	+	2	0	TTYH1	59622238	0.000000	0.05858	0.006000	0.13384	0.047000	0.14425	0.142000	0.16096	-0.050000	0.13356	0.561000	0.74099	TCG	.	.		0.706	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1			G	54930426	C	G	54930426	3	3	83	1	0	0	0	0	1	0	0	0	16754	893	31	4	257	4	TTYH1	19	54930426	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10	7932633	54930426	4198557	51	11348										
BRSK1	84446	hgsc.bcm.edu	37	chr19	55815479	55815480	+	Splice_Site	INS	-	-	TAA													0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	ccctctaagcagcccaagggINStaaggccaggtccccagtgg							TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr19:55815479_55815480insTAA	ENST00000309383.1	+	13	1624		c.e13+1		BRSK1_ENST00000326848.7_Splice_Site|BRSK1_ENST00000590333.1_Splice_Site|BRSK1_ENST00000588584.1_Splice_Site	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1						axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		CAGCCCAAGGGTAAGGCCAGGT	0.49																																					.		Atlas-Indel,Pindel	.											.	BRSK1	192	.	0			c.1347+1->TAA						.																																			SO:0001630	splice_region_variant	84446	exon13			.	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1347+1->TAA	chr19.hg19:g.55815480_55815482dupTAA		53.0	0.0		86.0	17.0	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Splice_Site	INS	ENST00000309383.1	hg19	CCDS12921.1																																																																																			.	.		0.49	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	Intron	TAA	55815480	-	TAA	55815479	8	5	83	1	0	1	1	0	0	0	1	0	1525	1275	44	0	1398	0	BRSK1	19	55815479	Splice_Site	INS	-	TCGA-CC-A9FU-01A-11D-A36X-10	885053	55815479	3313504	52	11349										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32595765	32595765	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	aaaagattccaaggcggcccAtggccactttcgttggtcga	11	11	0	1			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr21:32595765A>T	ENST00000286827.3	-	9	2423	c.1952T>A	c.(1951-1953)aTg>aAg	p.M651K	TIAM1_ENST00000541036.1_Missense_Mutation_p.M651K|TIAM1_ENST00000469412.1_5'UTR	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	651					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						AAGGCGGCCCATGGCCACTTT	0.478																																					p.M651K		Atlas-SNP	.											.	TIAM1	522	.	0			c.T1952A						.						85	89	88					21																	32595765		2203	4300	6503	SO:0001583	missense	7074	exon9			CGGCCCATGGCCA		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.1952T>A	chr21.hg19:g.32595765A>T	ENSP00000286827:p.Met651Lys	92.0	0.0		96.0	4.0	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	hg19	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.731586	0.89390	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.47869	0.86;0.83	4.5	4.5	0.54988	.	0.000000	0.85682	D	0.000000	T	0.53142	0.1778	L	0.51422	1.61	0.80722	D	1	P;P;D;P	0.58620	0.942;0.905;0.983;0.905	P;B;P;P	0.51615	0.675;0.298;0.628;0.475	T	0.59375	-0.7466	10	0.87932	D	0	.	14.2703	0.66147	1.0:0.0:0.0:0.0	.	651;651;492;651	F5GZ53;B7ZLR6;E9PD83;Q13009	.;.;.;TIAM1_HUMAN	K	651;492;651	ENSP00000286827:M651K;ENSP00000441570:M651K	ENSP00000286827:M651K	M	-	2	0	TIAM1	31517636	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.015000	0.93640	2.020000	0.59435	0.533000	0.62120	ATG	.	.		0.478	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32595765	A	T	32595765	3	4	83	1	0	0	0	0	1	0	0	0	15905	217	8	4	2907	4	TIAM1	21	32595765	Missense_Mutation	SNP	A	TCGA-CC-A9FU-01A-11D-A36X-10		32595765	15534130	53	11350										
DGCR14	8220	hgsc.bcm.edu	37	chr22	19124915	19124915	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0943396226415094	5	1	1.59304511278195	3.82330827067669	0.849624060150376	1	1	0	agggtgtgttctcaacctccCcccaggtcatcatcggggac	11	14	3	0			TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	g.chr22:19124915C>A	ENST00000252137.6	-	8	999	c.956G>T	c.(955-957)gGg>gTg	p.G319V		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	319					mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					CTCAACCTCCCCCCAGGTCAT	0.597																																					p.G319V		Atlas-SNP	.											.	DGCR14	43	.	0			c.G956T						.						200	172	182					22																	19124915		2203	4300	6503	SO:0001583	missense	8220	exon8			ACCTCCCCCCAGG	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"DiGeorge syndrome critical region gene 13"	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.956G>T	chr22.hg19:g.19124915C>A	ENSP00000252137:p.Gly319Val	88.0	0.0		82.0	35.0	NM_022719	Q49AH7|Q9BTZ4	Missense_Mutation	SNP	ENST00000252137.6	hg19	CCDS13756.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.172109	0.78452	.	.	ENSG00000100056	ENST00000252137	T	0.59638	0.25	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.80681	0.4669	M	0.90814	3.15	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85501	0.1191	10	0.87932	D	0	-36.6444	17.2171	0.86947	0.0:1.0:0.0:0.0	.	319	Q96DF8	DGC14_HUMAN	V	319	ENSP00000252137:G319V	ENSP00000252137:G319V	G	-	2	0	DGCR14	17504915	1.000000	0.71417	0.999000	0.59377	0.694000	0.40290	7.000000	0.76290	2.394000	0.81467	0.484000	0.47621	GGG	.	.		0.597	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2			A	19124915	C	A	19124915	3	1	83	1	0	0	0	0	1	0	0	0	4462	623	22	3	486	3	DGCR14	22	19124915	Missense_Mutation	SNP	C	TCGA-CC-A9FU-01A-11D-A36X-10		19124915	32179651	54	11351										
CCDC76	54482	hgsc.bcm.edu	37	chr1	100602441	100602441	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	atctcttaatttattaggaaGaagatgctcggaaaagaatc	8	5	1	3			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr1:100602441G>A	ENST00000370141.2	+	2	157	c.151G>A	c.(151-153)Gaa>Aaa	p.E51K	TRMT13_ENST00000370143.1_Missense_Mutation_p.E51K|TRMT13_ENST00000370139.1_Missense_Mutation_p.E20K	NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)	51					tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										TTATTAGGAAGAAGATGCTCG	0.323																																					p.E51K		Atlas-SNP	.											.	.	.	.	0			c.G151A						.						52	59	57					1																	100602441		2201	4298	6499	SO:0001583	missense	54482	exon2			TAGGAAGAAGATG	BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"coiled-coil domain containing 76"	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.151G>A	chr1.hg19:g.100602441G>A	ENSP00000359160:p.Glu51Lys	123.0	0.0		190.0	12.0	NM_019083	Q5VVL0|Q9NW65	Missense_Mutation	SNP	ENST00000370141.2	hg19	CCDS765.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669791	0.47677	.	.	ENSG00000122435	ENST00000370143;ENST00000370141;ENST00000370139	T;T;T	0.43688	0.97;0.98;0.94	5.59	5.59	0.84812	.	0.150529	0.64402	D	0.000017	T	0.13157	0.0319	N	0.20766	0.605	0.52501	D	0.999951	B;B	0.31485	0.068;0.325	B;B	0.27796	0.014;0.083	T	0.06481	-1.0824	10	0.11182	T	0.66	-23.1678	14.7734	0.69696	0.0:0.1443:0.8557:0.0	.	51;51	B4DQS9;Q9NUP7	.;TRM13_HUMAN	K	51;51;20	ENSP00000359162:E51K;ENSP00000359160:E51K;ENSP00000359158:E20K	ENSP00000359158:E20K	E	+	1	0	CCDC76	100375029	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.204000	0.72143	2.611000	0.88343	0.650000	0.86243	GAA	.	.		0.323	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083		A	100602441	G	A	100602441	3	1	84	1	0	0	0	0	1	0	0	0	2852	943	33	3	157	3	CCDC76	1	100602441	Missense_Mutation	SNP	G	TCGA-CC-A9FV-01A-11D-A36X-10		100602441	148648180	1	11352										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228527773	228527773	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	tgcaggctgagtcggtggtcGtcagcacggccatccaggag	16	11	1	1			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr1:228527773G>A	ENST00000422127.1	+	70	17430	c.17386G>A	c.(17386-17388)Gtc>Atc	p.V5796I	OBSCN_ENST00000366707.4_Missense_Mutation_p.V3430I|OBSCN_ENST00000570156.2_Missense_Mutation_p.V6753I|OBSCN_ENST00000284548.11_Missense_Mutation_p.V5796I|OBSCN_ENST00000366709.4_Missense_Mutation_p.V2915I	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5796	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTCGGTGGTCGTCAGCACGGC	0.602																																					p.V6753I		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G20257A						.						68	80	76					1																	228527773		2098	4202	6300	SO:0001583	missense	84033	exon81			GTGGTCGTCAGCA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.17386G>A	chr1.hg19:g.228527773G>A	ENSP00000409493:p.Val5796Ile	61.0	0.0		89.0	4.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.74|19.74	3.884428|3.884428	0.72410|0.72410	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.|T;T;T;T	.|0.62941	.|-0.01;-0.01;-0.01;-0.01	4.98|4.98	4.06|4.06	0.47325|0.47325	.|Dbl homology (DH) domain (4);	.|0.251783	.|0.33477	.|N	.|0.004879	T|T	0.56659|0.56659	0.2000|0.2000	L|L	0.31420|0.31420	0.93|0.93	0.28547|0.28547	N|N	0.911833|0.911833	.|D;D	.|0.59357	.|0.985;0.963	.|P;B	.|0.47786	.|0.557;0.281	T|T	0.58381|0.58381	-0.7646|-0.7646	5|10	.|0.87932	.|D	.|0	.|.	13.9957|13.9957	0.64397|0.64397	0.0:0.2891:0.7109:0.0|0.0:0.2891:0.7109:0.0	.|.	.|5796;5796	.|Q5VST9;Q5VST9-3	.|OBSCN_HUMAN;.	H|I	412|5796;5796;3430;2915	.|ENSP00000284548:V5796I;ENSP00000409493:V5796I;ENSP00000355668:V3430I;ENSP00000355670:V2915I	.|ENSP00000284548:V5796I	R|V	+|+	2|1	0|0	OBSCN|OBSCN	226594396|226594396	1.000000|1.000000	0.71417|0.71417	0.941000|0.941000	0.38009|0.38009	0.367000|0.367000	0.29736|0.29736	3.951000|3.951000	0.56684|0.56684	1.315000|1.315000	0.45114|0.45114	-0.502000|-0.502000	0.04539|0.04539	CGT|GTC	.	.		0.602	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228527773	G	A	228527773	3	1	84	1	0	0	0	0	1	0	0	0	10821	1145	40	1	17660	1	OBSCN	1	228527773	Missense_Mutation	SNP	G	TCGA-CC-A9FV-01A-11D-A36X-10	127925332	228527773	20722848	2	11353										
FSHR	2492	hgsc.bcm.edu	37	chr2	49295430	49295430	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	gcttggtgaggacaaacctcCtgcaaagagagtagaaataa	11	7	0	3			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr2:49295430C>T	ENST00000406846.2	-	2	272		c.e2-1		FSHR_ENST00000304421.4_Splice_Site|FSHR_ENST00000346173.3_Splice_Site	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor						female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	GACAAACCTCCTGCAAAGAGA	0.383									Gonadal Dysgenesis, 46 XX																												.		Atlas-SNP	.											FSHR,NS,carcinoma,0,1	FSHR	164	.	0			c.153-1G>A						.						100	99	99					2																	49295430		2203	4299	6502	SO:0001630	splice_region_variant	2492	exon3	Familial Cancer Database		AACCTCCTGCAAA		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.153-1G>A	chr2.hg19:g.49295430C>T		50.0	0.0		74.0	11.0	NM_181446	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Splice_Site	SNP	ENST00000406846.2	hg19	CCDS1843.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.591742	0.66219	.	.	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000454032	.	.	.	4.86	4.86	0.63082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3532	0.60613	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FSHR	49148934	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.722000	0.54948	2.521000	0.84997	0.462000	0.41574	.	.	.		0.383	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2		Intron	T	49295430	C	T	49295430	5	4	84	1	0	0	0	0	0	0	1	0	6081	695	24	3	1971	3	FSHR	2	49295430	Splice_Site	SNP	C	TCGA-CC-A9FV-01A-11D-A36X-10		49295430	193903943	3	11354										
HK2	3099	hgsc.bcm.edu	37	chr2	75109363	75109363	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	tgccagcagaacagcctggaCgaggtaacagcaccttcctg	11	13	0	1	rs200225889		TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr2:75109363C>T	ENST00000290573.2	+	12	2436	c.1836C>T	c.(1834-1836)gaC>gaT	p.D612D	HK2_ENST00000409174.1_Silent_p.D584D	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	612	Catalytic.|Hexokinase type-1 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						ACAGCCTGGACGAGGTAACAG	0.547																																					p.D612D		Atlas-SNP	.											HK2,NS,carcinoma,0,1	HK2	85	.	0			c.C1836T						.	C		0,4406		0,0,2203	78	76	77		1836	-9	0.3	2		77	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	HK2	NM_000189.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		612/918	75109363	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3099	exon12			CCTGGACGAGGTA		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.1836C>T	chr2.hg19:g.75109363C>T		104.0	0.0		132.0	13.0	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	hg19	CCDS1956.1																																																																																			.	C|0.999;T|0.001		0.547	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189		T	75109363	C	T	75109363	2	4	84	1	0	0	0	0	0	0	0	1	7200	535	19	1		1	HK2	2	75109363	Silent	SNP	C	TCGA-CC-A9FV-01A-11D-A36X-10	25813933	75109363	168090010	4	11355										
NDUFB3	4709	hgsc.bcm.edu	37	chr2	201943675	201943675	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	cagattatagacaatggaagAtagaagggacaccattagaa	10	5	0	5			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr2:201943675A>G	ENST00000237889.4	+	2	393	c.70A>G	c.(70-72)Ata>Gta	p.I24V	RNU6-1206P_ENST00000516339.1_RNA|NDUFB3_ENST00000433898.1_Missense_Mutation_p.I24V|NDUFB3_ENST00000454214.1_Missense_Mutation_p.I24V	NM_001257102.1|NM_002491.2	NP_001244031.1|NP_002482.1	O43676	NDUB3_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3, 12kDa	24					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			large_intestine(1)|lung(1)|urinary_tract(1)	3						ACAATGGAAGATAGAAGGGAC	0.403																																					p.I24V		Atlas-SNP	.											.	NDUFB3	5	.	0			c.A70G						.						77	76	76					2																	201943675		2203	4300	6503	SO:0001583	missense	4709	exon3			TGGAAGATAGAAG	AF047183	CCDS2336.1	2q33.1	2011-07-04	2002-08-29		ENSG00000119013	ENSG00000119013		"Mitochondrial respiratory chain complex / Complex I"	7698	protein-coding gene	gene with protein product	"complex I B12 subunit"	603839	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3 (12kD, B12)"			9425316, 11474204	Standard	NM_002491		Approved	B12	uc002uwx.4	O43676	OTTHUMG00000132820	ENST00000237889.4:c.70A>G	chr2.hg19:g.201943675A>G	ENSP00000237889:p.Ile24Val	225.0	0.0		290.0	24.0	NM_001257102	Q6IB80	Missense_Mutation	SNP	ENST00000237889.4	hg19	CCDS2336.1	.	.	.	.	.	.	.	.	.	.	A	11.81	1.748465	0.30955	.	.	ENSG00000119013	ENST00000450023;ENST00000237889;ENST00000433898;ENST00000454214	T;T;T;T	0.75821	-0.97;-0.88;-0.88;-0.88	5.11	5.11	0.69529	.	0.214597	0.46758	N	0.000280	T	0.50326	0.1609	.	.	.	0.38465	D	0.947323	P	0.44006	0.824	B	0.34418	0.182	T	0.60182	-0.7313	9	0.05721	T	0.95	-0.9102	14.1733	0.65525	1.0:0.0:0.0:0.0	.	24	O43676	NDUB3_HUMAN	V	24	ENSP00000401834:I24V;ENSP00000237889:I24V;ENSP00000410600:I24V;ENSP00000407336:I24V	ENSP00000237889:I24V	I	+	1	0	NDUFB3	201651920	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.887000	0.48586	2.049000	0.60858	0.533000	0.62120	ATA	.	.		0.403	NDUFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256277.1	NM_002491		G	201943675	A	G	201943675	3	3	84	1	0	0	0	0	1	0	0	0	10291	333	12	2	72	2	NDUFB3	2	201943675	Missense_Mutation	SNP	A	TCGA-CC-A9FV-01A-11D-A36X-10	126834312	201943675	41255698	5	11356										
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25849364	25849364	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	tcaaccgagacttcagaaacGttgcgaacgtttccttcaaa	7	11	3	2	rs371579636		TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr4:25849364G>T	ENST00000399878.3	-	2	407	c.285C>A	c.(283-285)aaC>aaA	p.N95K	SEL1L3_ENST00000513364.1_Intron|SEL1L3_ENST00000264868.5_Missense_Mutation_p.N60K|SEL1L3_ENST00000502949.1_5'UTR	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	95						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						CTTCAGAAACGTTGCGAACGT	0.433																																					p.N95K		Atlas-SNP	.											.	SEL1L3	62	.	0			c.C285A						.						92	84	86					4																	25849364		1851	4112	5963	SO:0001583	missense	23231	exon2			AGAAACGTTGCGA	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.285C>A	chr4.hg19:g.25849364G>T	ENSP00000382767:p.Asn95Lys	148.0	0.0		176.0	30.0	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032919	0.54790	.	.	ENSG00000091490	ENST00000399878;ENST00000264868	T;T	0.16073	2.37;2.41	5.25	-3.42	0.04825	.	0.062148	0.64402	D	0.000005	T	0.28499	0.0705	L	0.50333	1.59	0.80722	D	1	D	0.76494	0.999	D	0.66847	0.947	T	0.01839	-1.1263	10	0.72032	D	0.01	-22.1871	12.9132	0.58190	0.7017:0.0:0.2983:0.0	.	95	Q68CR1	SE1L3_HUMAN	K	95;60	ENSP00000382767:N95K;ENSP00000264868:N60K	ENSP00000264868:N60K	N	-	3	2	SEL1L3	25458462	0.048000	0.20356	0.325000	0.25375	0.894000	0.52154	-0.648000	0.05391	-0.595000	0.05828	-0.274000	0.10170	AAC	.	.		0.433	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		T	25849364	G	T	25849364	3	4	84	1	0	0	0	0	1	0	0	0	14027	1136	40	1	3205	1	SEL1L3	4	25849364	Missense_Mutation	SNP	G	TCGA-CC-A9FV-01A-11D-A36X-10		25849364	165304912	6	11357										
GZMA	3001	hgsc.bcm.edu	37	chr5	54404222	54404222	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	ggtggaagagactcgtgcaaTgtaagtaaaataagatccca	11	6	0	2			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr5:54404222T>C	ENST00000274306.6	+	4	662	c.627T>C	c.(625-627)aaT>aaC	p.N209N		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	209	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				ACTCGTGCAATGTAAGTAAAA	0.393																																					p.N209N		Atlas-SNP	.											.	GZMA	60	.	0			c.T627C						.						67	69	68					5																	54404222		2203	4300	6503	SO:0001630	splice_region_variant	3001	exon4			GTGCAATGTAAGT		CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"CTL tryptase", "Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.627+1T>C	chr5.hg19:g.54404222T>C		106.0	0.0		143.0	20.0	NM_006144	A4PHN1|Q6IB36	Silent	SNP	ENST00000274306.6	hg19	CCDS3965.1																																																																																			.	.		0.393	GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144	Silent	C	54404222	T	C	54404222	5	2	84	1	0	0	0	0	0	0	1	0	6924	1478	51	2	641	2	GZMA	5	54404222	Splice_Site	SNP	T	TCGA-CC-A9FV-01A-11D-A36X-10		54404222	126511038	7	11358										
C6orf62	81688	hgsc.bcm.edu	37	chr6	24718778	24718778	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	tttaaattaccttctccttgAatacaaaggcaatatacatc	3	9	1	1			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr6:24718778A>C	ENST00000378119.4	-	1	2286	c.119T>G	c.(118-120)tTc>tGc	p.F40C	C6orf62_ENST00000378102.3_Intron|C6orf62_ENST00000540769.1_Intron	NM_030939.4	NP_112201.1	Q9GZU0	CF062_HUMAN	chromosome 6 open reading frame 62	40						intracellular (GO:0005622)				endometrium(2)|kidney(3)|large_intestine(2)|lung(3)	10						CTTCTCCTTGAATACAAAGGC	0.313																																					p.F40C		Atlas-SNP	.											.	C6orf62	18	.	0			c.T119G						.						72	73	73					6																	24718778		2203	4300	6503	SO:0001583	missense	81688	exon1			TCCTTGAATACAA	AL136632	CCDS4559.1	6p22.1	2011-12-13			ENSG00000112308	ENSG00000112308			20998	protein-coding gene	gene with protein product	"HBV X-transactivated protein 12"					11230166	Standard	NM_030939		Approved	FLJ12619, DKFZP564G182, XTP12	uc003nel.3	Q9GZU0	OTTHUMG00000014361	ENST00000378119.4:c.119T>G	chr6.hg19:g.24718778A>C	ENSP00000367359:p.Phe40Cys	109.0	0.0		127.0	16.0	NM_030939	Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2	Missense_Mutation	SNP	ENST00000378119.4	hg19	CCDS4559.1	.	.	.	.	.	.	.	.	.	.	A	19.05	3.752550	0.69533	.	.	ENSG00000112308	ENST00000378119	T	0.41400	1.0	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.42585	0.1209	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.51733	-0.8668	10	0.87932	D	0	-9.8903	15.9584	0.79906	1.0:0.0:0.0:0.0	.	40	Q9GZU0	CF062_HUMAN	C	40	ENSP00000367359:F40C	ENSP00000367359:F40C	F	-	2	0	C6orf62	24826757	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.678000	0.91211	2.165000	0.68154	0.528000	0.53228	TTC	.	.		0.313	C6orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040017.1	NM_030939		C	24718778	A	C	24718778	3	2	84	1	0	0	0	0	1	0	0	0	2370	246	9	5	590	5	C6orf62	6	24718778	Missense_Mutation	SNP	A	TCGA-CC-A9FV-01A-11D-A36X-10		24718778	146396289	8	11359										
TIGD3	220359	hgsc.bcm.edu	37	chr11	65124527	65124527	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	gaggagataggcactgaagaCgagaagggggacagagaggg	20	4	0	5			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr11:65124527C>T	ENST00000309880.5	+	2	1455	c.1248C>T	c.(1246-1248)gaC>gaT	p.D416D		NM_145719.2	NP_663771.1	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	416						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(3)|large_intestine(1)|lung(9)|prostate(2)|skin(2)	17						GCACTGAAGACGAGAAGGGGG	0.607																																					p.D416D		Atlas-SNP	.											.	TIGD3	32	.	0			c.C1248T						.						106	100	102					11																	65124527		2201	4297	6498	SO:0001819	synonymous_variant	220359	exon2			TGAAGACGAGAAG		CCDS8101.1	11q13.1	2008-07-21				ENSG00000173825			18334	protein-coding gene	gene with protein product							Standard	NM_145719		Approved		uc001odo.4	Q6B0B8		ENST00000309880.5:c.1248C>T	chr11.hg19:g.65124527C>T		87.0	0.0		111.0	9.0	NM_145719		Silent	SNP	ENST00000309880.5	hg19	CCDS8101.1																																																																																			.	.		0.607	TIGD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387310.1	NM_145719		T	65124527	C	T	65124527	2	4	84	1	0	0	0	0	0	0	0	1	15912	535	19	1		1	TIGD3	11	65124527	Silent	SNP	C	TCGA-CC-A9FV-01A-11D-A36X-10		65124527	69881989	9	11360										
DDX47	51202	hgsc.bcm.edu	37	chr12	12974309	12974309	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	agcagtttgaagccctggggTcctctattggagtgcagagt	14	8	1	2			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr12:12974309T>G	ENST00000358007.3	+	3	371	c.349T>G	c.(349-351)Tcc>Gcc	p.S117A	DDX47_ENST00000352940.4_Missense_Mutation_p.S117A	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	117	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		AGCCCTGGGGTCCTCTATTGG	0.532																																					p.S117A		Atlas-SNP	.											.	DDX47	37	.	0			c.T349G						.						110	110	110					12																	12974309		2203	4300	6503	SO:0001583	missense	51202	exon3			CTGGGGTCCTCTA	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"DEAD-boxes"	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.349T>G	chr12.hg19:g.12974309T>G	ENSP00000350698:p.Ser117Ala	63.0	0.0		101.0	18.0	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	hg19	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	T	15.91	2.973325	0.53614	.	.	ENSG00000213782	ENST00000352940;ENST00000358007	T;T	0.15256	2.44;2.44	5.6	5.6	0.85130	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.08492	0.0211	N	0.02275	-0.615	0.80722	D	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.12156	0.004;0.004;0.003;0.007	T	0.29243	-1.0018	10	0.30854	T	0.27	-14.6871	15.7878	0.78322	0.0:0.0:0.0:1.0	.	117;117;117;117	B4DYP6;Q9H4E3;G5E955;Q9H0S4	.;.;.;DDX47_HUMAN	A	117	ENSP00000319578:S117A;ENSP00000350698:S117A	ENSP00000319578:S117A	S	+	1	0	DDX47	12865576	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.506000	0.81665	2.135000	0.66039	0.454000	0.30748	TCC	.	.		0.532	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355		G	12974309	T	G	12974309	3	3	84	1	0	0	0	0	1	0	0	0	4367	1667	58	5	359	5	DDX47	12	12974309	Missense_Mutation	SNP	T	TCGA-CC-A9FV-01A-11D-A36X-10		12974309	120877586	10	11361										
MTA1	9112	hgsc.bcm.edu	37	chr14	105929876	105929876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	gagcaagttaaagcaagtttAtattcccaactagtaagtgt	8	6	0	0			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr14:105929876A>G	ENST00000331320.7	+	12	1278	c.1064A>G	c.(1063-1065)tAt>tGt	p.Y355C	MTA1_ENST00000435036.2_5'UTR|MTA1_ENST00000406191.1_Missense_Mutation_p.Y355C|MTA1_ENST00000405646.1_Missense_Mutation_p.Y338C	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	355					circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		AAGCAAGTTTATATTCCCAAC	0.582																																					p.Y355C		Atlas-SNP	.											.	MTA1	61	.	0			c.A1064G						.						64	66	66					14																	105929876		2203	4300	6503	SO:0001583	missense	9112	exon12			AAGTTTATATTCC	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"GATA zinc finger domain containing"	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.1064A>G	chr14.hg19:g.105929876A>G	ENSP00000333633:p.Tyr355Cys	99.0	0.0		115.0	12.0	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.145321	0.77888	.	.	ENSG00000182979	ENST00000414153;ENST00000331320;ENST00000406191;ENST00000405646;ENST00000434050	T;T;T;T	0.36699	1.26;1.25;1.25;1.24	4.11	4.11	0.48088	.	0.000000	0.85682	D	0.000000	T	0.60340	0.2261	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.984	T	0.66333	-0.5950	10	0.87932	D	0	-8.3006	12.2357	0.54514	1.0:0.0:0.0:0.0	.	147;355	Q59FW1;Q13330	.;MTA1_HUMAN	C	264;355;355;338;147	ENSP00000333633:Y355C;ENSP00000385702:Y355C;ENSP00000384180:Y338C;ENSP00000394106:Y147C	ENSP00000333633:Y355C	Y	+	2	0	MTA1	105000921	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.181000	0.94874	1.632000	0.50472	0.460000	0.39030	TAT	.	.		0.582	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			G	105929876	A	G	105929876	3	3	84	1	0	0	0	0	1	0	0	0	9917	449	16	2	1110	2	MTA1	14	105929876	Missense_Mutation	SNP	A	TCGA-CC-A9FV-01A-11D-A36X-10		105929876	1419664	11	11362										
SMARCD2	6603	hgsc.bcm.edu	37	chr17	61911595	61911595	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	ctgcagctggttgtgcttgaTgtaaagccacagggcctgca	13	10	0	1			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr17:61911595T>C	ENST00000448276.2	-	8	1280	c.1015A>G	c.(1015-1017)Atc>Gtc	p.I339V	SMARCD2_ENST00000323347.10_Missense_Mutation_p.I291V|SMARCD2_ENST00000225742.9_Missense_Mutation_p.I264V	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	339	SWIB.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						TTGTGCTTGATGTAAAGCCAC	0.597											OREG0024642	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I339V		Atlas-SNP	.											.	SMARCD2	29	.	0			c.A1015G						.						34	35	34					17																	61911595		2083	4196	6279	SO:0001583	missense	6603	exon8			GCTTGATGTAAAG	U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60B", "Swp73-like protein", "chromatin remodeling complex BAF60B subunit", "SWI/SNF complex 60 kDa subunit B"	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.1015A>G	chr17.hg19:g.61911595T>C	ENSP00000392617:p.Ile339Val	102.0	0.0	1057	119.0	21.0	NM_001098426	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Missense_Mutation	SNP	ENST00000448276.2	hg19	CCDS45756.1	.	.	.	.	.	.	.	.	.	.	.	5.438	0.266022	0.10294	.	.	ENSG00000108604	ENST00000448276;ENST00000225742;ENST00000450364;ENST00000323347	T;T	0.56941	0.43;0.46	5.55	4.48	0.54585	SWIB/MDM2 domain (2);	0.000000	0.85682	D	0.000000	T	0.49457	0.1558	L	0.54863	1.705	0.80722	D	1	B;B;B	0.27286	0.007;0.04;0.174	B;B;B	0.36092	0.003;0.036;0.217	T	0.40156	-0.9578	10	0.25751	T	0.34	-8.4759	9.6059	0.39632	0.0:0.0816:0.0:0.9184	.	291;302;339	Q92925-3;B9EGA3;Q92925	.;.;SMRD2_HUMAN	V	339;281;302;291	ENSP00000392617:I339V;ENSP00000318451:I291V	ENSP00000225742:I281V	I	-	1	0	SMARCD2	59265327	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	4.987000	0.63857	1.130000	0.42092	-0.250000	0.11733	ATC	.	.		0.597	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426		C	61911595	T	C	61911595	3	2	84	1	0	0	0	0	1	0	0	0	14793	1464	51	2	604	2	SMARCD2	17	61911595	Missense_Mutation	SNP	T	TCGA-CC-A9FV-01A-11D-A36X-10		61911595	19283615	12	11363										
RNF213	57674	hgsc.bcm.edu	37	chr17	78363961	78363961	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	ttgaaactaaagaacccccaAacccaaaccgaggagcgctt	7	13	0	2			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr17:78363961A>C	ENST00000582970.1	+	67	15578	c.15435A>C	c.(15433-15435)caA>caC	p.Q5145H	RNF213_ENST00000508628.2_Missense_Mutation_p.Q5194H|RNF213_ENST00000427003.3_3'UTR|CTD-2047H16.4_ENST00000573394.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.Q3218H	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	5145					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AGAACCCCCAAACCCAAACCG	0.507																																					p.Q5145H		Atlas-SNP	.											.	RNF213	766	.	0			c.A15435C						.						78	89	85					17																	78363961		2202	4300	6502	SO:0001583	missense	57674	exon67			CCCCCAAACCCAA	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.15435A>C	chr17.hg19:g.78363961A>C	ENSP00000464087:p.Gln5145His	122.0	0.0		158.0	23.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	A	6.357	0.433998	0.12045	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301;ENST00000427003	T	0.23348	1.91	.	.	.	.	.	.	.	.	T	0.14356	0.0347	N	0.25144	0.715	0.09310	N	1	P;P	0.39940	0.696;0.676	B;B	0.36030	0.056;0.216	T	0.15009	-1.0452	7	0.72032	D	0.01	.	.	.	.	.	5145;3218	D6RI12;Q63HN8	.;RN213_HUMAN	H	5145;5194;3218;495	ENSP00000338218:Q3218H	ENSP00000338218:Q3218H	Q	+	3	2	RNF213	75978556	0.012000	0.17670	0.002000	0.10522	0.072000	0.16883	-0.267000	0.08619	0.077000	0.16863	0.076000	0.15429	CAA	.	.		0.507	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		C	78363961	A	C	78363961	3	2	84	1	0	0	0	0	1	0	0	0	13492	11	1	5	16016	5	RNF213	17	78363961	Missense_Mutation	SNP	A	TCGA-CC-A9FV-01A-11D-A36X-10	16452366	78363961	2831249	13	11364										
FANCB	2187	hgsc.bcm.edu	37	chrX	14862009	14862009	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	1	1	1.36315789473684	NA	1.36315789473684	1	1	0	tgccatattatcaattaggaAattctcacttcctgatttta	4	8	2	1			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chrX:14862009A>T	ENST00000324138.3	-	9	2413	c.2260T>A	c.(2260-2262)Ttc>Atc	p.F754I	FANCB_ENST00000398334.1_Missense_Mutation_p.F754I	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	754					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					TCAATTAGGAAATTCTCACTT	0.343								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.F754I		Atlas-SNP	.											.	FANCB	78	.	0			c.T2260A						.						75	73	74					X																	14862009		2203	4299	6502	SO:0001583	missense	2187	exon9	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TTAGGAAATTCTC	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"Fanconi anemia, complementation groups"	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.2260T>A	chrX.hg19:g.14862009A>T	ENSP00000326819:p.Phe754Ile	29.0	0.0		44.0	6.0	NM_152633	B2RMZ4|Q7Z2U2|Q86XG1	Missense_Mutation	SNP	ENST00000324138.3	hg19	CCDS14161.1	.	.	.	.	.	.	.	.	.	.	A	1.827	-0.470744	0.04445	.	.	ENSG00000181544	ENST00000324138;ENST00000398334;ENST00000452869	.	.	.	5.6	1.66	0.24008	.	0.756841	0.13152	N	0.409779	T	0.24005	0.0581	L	0.31926	0.97	0.09310	N	1	B	0.17268	0.021	B	0.16722	0.016	T	0.27226	-1.0080	9	0.12430	T	0.62	-0.7611	1.9414	0.03347	0.5002:0.19:0.0784:0.2314	.	754	Q8NB91	FANCB_HUMAN	I	754	.	ENSP00000326819:F754I	F	-	1	0	FANCB	14771930	0.000000	0.05858	0.031000	0.17742	0.138000	0.21146	-0.110000	0.10824	-0.063000	0.13065	0.481000	0.45027	TTC	.	.		0.343	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633		T	14862009	A	T	14862009	3	4	84	1	0	0	0	0	1	0	0	0	5671	14	1	4	323	4	FANCB	23	14862009	Missense_Mutation	SNP	A	TCGA-CC-A9FV-01A-11D-A36X-10		14862009	140408551	14	11365										
UBR4	23352	hgsc.bcm.edu	37	chr1	19490752	19490752	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acttcatcatcttaccatctGctcagccaatccacagcagc	4	16	5	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:19490752G>A	ENST00000375254.3	-	33	4722	c.4695C>T	c.(4693-4695)agC>agT	p.S1565S	UBR4_ENST00000375226.2_Silent_p.S1565S|UBR4_ENST00000375267.2_Silent_p.S1565S|UBR4_ENST00000375217.2_Silent_p.S1565S	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1565					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CTTACCATCTGCTCAGCCAAT	0.443																																					p.S1565S		Atlas-SNP	.											.	UBR4	415	.	0			c.C4695T						.						71	60	64					1																	19490752		2203	4300	6503	SO:0001819	synonymous_variant	23352	exon33			CCATCTGCTCAGC	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.4695C>T	chr1.hg19:g.19490752G>A		295.0	0.0		204.0	137.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.		0.443	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19490752	G	A	19490752	2	1	85	1	0	0	0	0	0	0	0	1	16919	1310	46	3		3	UBR4	1	19490752	Silent	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10		19490752	229759869	1	11366										
C1orf128	57095	hgsc.bcm.edu	37	chr1	24113847	24113847	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ggtccatcaggttaccccacAgacacactttatttcctaag	6	13	1	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:24113847A>T	ENST00000246151.4	+	6	728	c.617A>T	c.(616-618)cAg>cTg	p.Q206L	PITHD1_ENST00000374524.1_Missense_Mutation_p.Q93L	NM_020362.4	NP_065095.2	Q9GZP4	PITH1_HUMAN	PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1	206						nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	6						GTTACCCCACAGACACACTTT	0.527																																					p.Q206L		Atlas-SNP	.											.	PITHD1	20	.	0			c.A617T						.						89	81	83					1																	24113847		2203	4300	6503	SO:0001583	missense	57095	exon6			CCCCACAGACACA		CCDS240.1	1p36.11	2011-02-21	2011-02-21	2011-02-21	ENSG00000057757	ENSG00000057757			25022	protein-coding gene	gene with protein product	"TXNL1 C-terminal like"		"chromosome 1 open reading frame 128"	C1orf128		12477932	Standard	NM_020362		Approved	HT014, TXNL1CL	uc001bhq.3	Q9GZP4	OTTHUMG00000002960	ENST00000246151.4:c.617A>T	chr1.hg19:g.24113847A>T	ENSP00000246151:p.Gln206Leu	81.0	0.0		53.0	36.0	NM_020362	B2R7J4|Q5QPN6|Q5QPN7|Q9NRI8	Missense_Mutation	SNP	ENST00000246151.4	hg19	CCDS240.1	.	.	.	.	.	.	.	.	.	.	A	17.91	3.504636	0.64410	.	.	ENSG00000057757	ENST00000246151;ENST00000374524	.	.	.	5.75	5.75	0.90469	.	0.231700	0.46145	D	0.000304	T	0.52885	0.1762	L	0.32530	0.975	0.80722	D	1	B	0.20887	0.049	B	0.19666	0.026	T	0.46871	-0.9160	9	0.30078	T	0.28	-8.957	16.0591	0.80826	1.0:0.0:0.0:0.0	.	206	Q9GZP4	PITH1_HUMAN	L	206;93	.	ENSP00000246151:Q206L	Q	+	2	0	PITHD1	23986434	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.126000	0.94411	2.185000	0.69588	0.533000	0.62120	CAG	.	.		0.527	PITHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008243.1	NM_020362		T	24113847	A	T	24113847	3	4	85	1	0	0	0	0	1	0	0	0	1997	188	7	4	639	4	C1orf128	1	24113847	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	4623095	24113847	225136774	2	11367										
GRIK3	2899	hgsc.bcm.edu	37	chr1	37291402	37291403	+	Frame_Shift_Ins	INS	-	-	G													0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tcgaacatgggtgatggtcaINSggggggccacggccagatct							TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:37291402_37291403insG	ENST00000373091.3	-	11	1571_1572	c.1555_1556insC	c.(1555-1557)ctgfs	p.L519fs	GRIK3_ENST00000373093.4_Frame_Shift_Ins_p.L519fs	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	519					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				GGTGATGGTCAGGGGGGCCACG	0.54																																					p.L519fs		Atlas-Indel,Pindel	.											.	GRIK3	195	.	0			c.1556_1557insC						.																																			SO:0001589	frameshift_variant	2899	exon11			.	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.1556dupC	chr1.hg19:g.37291408_37291408dupG	ENSP00000362183:p.Leu519fs	106.0	0.0		57.0	18.0	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Frame_Shift_Ins	INS	ENST00000373091.3	hg19	CCDS416.1																																																																																			.	.		0.54	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		G	37291403	-	G	37291402	7	5	85	1	0	1	1	0	0	0	0	0	6784	188	7	0	1227	0	GRIK3	1	37291402	Frame_Shift_Ins	INS	-	TCGA-CC-A9FW-01A-11D-A36X-10	13177555	37291402	211959219	3	11368										
RLF	6018	hgsc.bcm.edu	37	chr1	40701785	40701785	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cttttgatcctgagttttggGactggaaaactttaaaacga	9	6	0	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:40701785G>T	ENST00000372771.4	+	8	1438	c.1411G>T	c.(1411-1413)Gac>Tac	p.D471Y		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	471					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			TGAGTTTTGGGACTGGAAAAC	0.393																																					p.D471Y		Atlas-SNP	.											.	RLF	152	.	0			c.G1411T						.						67	73	71					1																	40701785		2203	4300	6503	SO:0001583	missense	6018	exon8			TTTTGGGACTGGA		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.1411G>T	chr1.hg19:g.40701785G>T	ENSP00000361857:p.Asp471Tyr	109.0	0.0		81.0	56.0	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	hg19	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.545078	0.65198	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.39056	1.1	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.68054	0.2959	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.67620	-0.5624	10	0.66056	D	0.02	-14.5446	20.6593	0.99626	0.0:0.0:1.0:0.0	.	164;471	F5H2M5;Q13129	.;RLF_HUMAN	Y	471;164	ENSP00000361857:D471Y	ENSP00000361857:D471Y	D	+	1	0	RLF	40474372	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.885000	0.99019	0.655000	0.94253	GAC	.	.		0.393	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		T	40701785	G	T	40701785	3	4	85	1	0	0	0	0	1	0	0	0	13404	1174	41	3	1441	3	RLF	1	40701785	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	3410383	40701785	208548836	4	11369										
KIAA0467	81888	hgsc.bcm.edu	37	chr1	43916134	43916134	+	IGR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acacagcctgtttcaccctcTggacccgcctcctctgaggg	9	17	3	1	rs75906384		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:43916134T>G	ENST00000372425.4	-	0	1115				SZT2_ENST00000562955.1_Missense_Mutation_p.W3371G|SZT2-AS1_ENST00000396885.2_RNA|SZT2_ENST00000372442.1_Missense_Mutation_p.W2529G			Q5T013	HYI_HUMAN	hydroxypyruvate isomerase (putative)								hydroxypyruvate isomerase activity (GO:0008903)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	6	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTTCACCCTCTGGACCCGCCT	0.597																																					p.W3371G		Atlas-SNP	.											.	SZT2	383	.	0			c.T10111G						.						141	137	138					1																	43916134		2203	4300	6503	SO:0001628	intergenic_variant	23334	exon71			ACCCTCTGGACCC		CCDS488.1, CCDS488.2, CCDS53309.1, CCDS72771.1	1p34.2	2010-06-24	2010-06-24		ENSG00000178922	ENSG00000178922	5.3.1.22		26948	protein-coding gene	gene with protein product			"hydroxypyruvate isomerase homolog (E. coli)"			10561547	Standard	NM_031207		Approved	HT036	uc001cjo.3	Q5T013	OTTHUMG00000007502		chr1.hg19:g.43916134T>G		114.0	0.0		65.0	39.0	NM_015284	D3DPX4|D3DPX5|Q5Q9A2|Q7Z778|Q96S83|Q9BZR3|Q9BZR4	Missense_Mutation	SNP	ENST00000372425.4	hg19	CCDS53309.1	.	.	.	.	.	.	.	.	.	.	T	18.36	3.607180	0.66558	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.76154	0.3948	L	0.54323	1.7	0.39212	D	0.963345	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	T	0.79572	-0.1748	9	0.87932	D	0	.	16.3817	0.83467	0.0:0.0:0.0:1.0	.	3428;3371	Q5T011;Q5T011-5	SZT2_HUMAN;.	G	2529	.	ENSP00000361519:W2529G	W	+	1	0	SZT2	43688721	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.556000	0.82233	2.276000	0.75962	0.454000	0.30748	TGG	.	.		0.597	HYI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031207		G	43916134	T	G	43916134	1	3	85	0	1	0	0	0	0	0	0	0	8187	1580	55	5		5	KIAA0467	1	43916134	IGR	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	3214349	43916134	205334487	5	11370										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86426957	86426957	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	caccaatttttccaatatttCcttgatctcctacttctccc	1	15	2	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:86426957C>A	ENST00000370571.2	-	24	2903	c.2537G>T	c.(2536-2538)gGa>gTa	p.G846V	COL24A1_ENST00000436319.1_Missense_Mutation_p.G846V	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	846	Collagen-like 5.			GYAGEPGPEGLKGEVGDQGNIG -> ITVFATLYSFLTGRS RRSRKYW (in Ref. 5; BAD92923). {ECO:0000305}.	extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TCCAATATTTCCTTGATCTCC	0.279																																					p.G846V		Atlas-SNP	.											.	COL24A1	202	.	0			c.G2537T						.						98	95	96					1																	86426957		1800	4057	5857	SO:0001583	missense	255631	exon24			ATATTTCCTTGAT	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.2537G>T	chr1.hg19:g.86426957C>A	ENSP00000359603:p.Gly846Val	210.0	0.0		176.0	121.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	hg19	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.442699	0.43326	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.99488	-6.0;-6.0	4.74	4.74	0.60224	.	.	.	.	.	D	0.99775	0.9907	H	0.98664	4.295	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96912	0.9668	9	0.87932	D	0	.	15.6133	0.76744	0.0:1.0:0.0:0.0	.	846	Q17RW2	COOA1_HUMAN	V	846	ENSP00000359603:G846V;ENSP00000392531:G846V	ENSP00000359603:G846V	G	-	2	0	COL24A1	86199545	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.791000	0.62460	2.349000	0.79799	0.655000	0.94253	GGA	.	.		0.279	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		A	86426957	C	A	86426957	3	1	85	1	0	0	0	0	1	0	0	0	3685	855	30	3	2755	3	COL24A1	1	86426957	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	42510823	86426957	162823664	6	11371										
ADAM30	11085	hgsc.bcm.edu	37	chr1	120436833	120436833	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	aagtggtttcctatcacttgCcggaaaaacacaaaaaccac	6	11	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:120436833C>A	ENST00000369400.1	-	1	2285	c.2127G>T	c.(2125-2127)cgG>cgT	p.R709R		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	709					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		CTATCACTTGCCGGAAAAACA	0.393																																					p.R709R		Atlas-SNP	.											.	ADAM30	88	.	0			c.G2127T						.						96	102	100					1																	120436833		2203	4300	6503	SO:0001819	synonymous_variant	11085	exon1			CACTTGCCGGAAA	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.2127G>T	chr1.hg19:g.120436833C>A		144.0	0.0		94.0	61.0	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Silent	SNP	ENST00000369400.1	hg19	CCDS907.1																																																																																			.	.		0.393	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		A	120436833	C	A	120436833	2	1	85	1	0	0	0	0	0	0	0	1	248	726	26	3		3	ADAM30	1	120436833	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	34009876	120436833	128813788	7	11372										
SPRR2G	6706	hgsc.bcm.edu	37	chr1	153122523	153122523	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tggacatggctctgggcactTtggcgtggggcacacaggag	17	9	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:153122523T>A	ENST00000368748.4	-	2	102	c.64A>T	c.(64-66)Aag>Tag	p.K22*		NM_001014291.3	NP_001014313.1	Q9BYE4	SPR2G_HUMAN	small proline-rich protein 2G	22	3 X 9 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				endometrium(1)|lung(1)|skin(1)	3	all_lung(78;1.78e-30)|Lung NSC(65;7.29e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TCTGGGCACTTTGGCGTGGGG	0.577																																					p.K22X		Atlas-SNP	.											.	SPRR2G	20	.	0			c.A64T						.						130	102	112					1																	153122523		2203	4298	6501	SO:0001587	stop_gained	6706	exon2			GGCACTTTGGCGT	AF333957	CCDS30868.1	1q21-q22	2008-02-05			ENSG00000159516	ENSG00000159516			11267	protein-coding gene	gene with protein product						8325635, 11279051	Standard	NM_001014291		Approved		uc009wod.2	Q9BYE4	OTTHUMG00000014399	ENST00000368748.4:c.64A>T	chr1.hg19:g.153122523T>A	ENSP00000357737:p.Lys22*	33.0	0.0		59.0	10.0	NM_001014291		Nonsense_Mutation	SNP	ENST00000368748.4	hg19	CCDS30868.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.303983	0.60305	.	.	ENSG00000159516	ENST00000368748	.	.	.	5.89	3.47	0.39725	.	.	.	.	.	.	.	.	.	.	.	0.39099	D	0.96124	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-20.1786	5.4686	0.16658	0.0:0.0878:0.1754:0.7368	.	.	.	.	X	22	.	ENSP00000357737:K22X	K	-	1	0	SPRR2G	151389147	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.502000	0.22594	1.059000	0.40554	0.496000	0.49642	AAG	.	.		0.577	SPRR2G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040057.1			A	153122523	T	A	153122523	4	1	85	1	0	0	0	0	0	1	0	0	15117	1850	64	4	161	4	SPRR2G	1	153122523	Nonsense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	32685690	153122523	96128098	8	11373										
UBAP2L	9898	hgsc.bcm.edu	37	chr1	154226519	154226519	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cacacagactcggcggtaccCcagctccatctcttcatcac	6	18	3	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:154226519C>T	ENST00000361546.2	+	14	1850	c.1808C>T	c.(1807-1809)cCc>cTc	p.P603L	UBAP2L_ENST00000343815.6_Missense_Mutation_p.P603L|UBAP2L_ENST00000271877.7_Missense_Mutation_p.P614L|UBAP2L_ENST00000428931.1_Missense_Mutation_p.P603L|AL590431.1_ENST00000517008.1_RNA			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	603					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CGGCGGTACCCCAGCTCCATC	0.493																																					p.P603L		Atlas-SNP	.											.	UBAP2L	197	.	0			c.C1808T						.						68	64	65					1																	154226519		2203	4300	6503	SO:0001583	missense	9898	exon15			GGTACCCCAGCTC	BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.1808C>T	chr1.hg19:g.154226519C>T	ENSP00000355343:p.Pro603Leu	102.0	0.0		131.0	24.0	NM_001127320	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	hg19	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.740597	0.69304	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000456955;ENST00000433006;ENST00000271877;ENST00000361546	T;T;T;T	0.12774	2.65;2.66;2.69;2.66	5.05	5.05	0.67936	.	0.115656	0.64402	D	0.000012	T	0.20536	0.0494	L	0.36672	1.1	0.80722	D	1	D;D;D;D;D	0.89917	0.998;1.0;0.999;0.999;0.998	D;D;D;D;D	0.87578	0.981;0.998;0.991;0.991;0.981	T	0.01036	-1.1473	10	0.48119	T	0.1	-7.3634	17.5691	0.87930	0.0:1.0:0.0:0.0	.	517;614;596;603;603	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	L	603;603;99;99;614;603	ENSP00000345308:P603L;ENSP00000389445:P603L;ENSP00000271877:P614L;ENSP00000355343:P603L	ENSP00000271877:P614L	P	+	2	0	UBAP2L	152493143	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.164000	0.71885	2.623000	0.88846	0.655000	0.94253	CCC	.	.		0.493	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		T	154226519	C	T	154226519	3	4	85	1	0	0	0	0	1	0	0	0	16853	623	22	3	1862	3	UBAP2L	1	154226519	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	1103996	154226519	95024102	9	11374										
C1orf53	388722	hgsc.bcm.edu	37	chr1	197872017	197872017	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ccgcggcggagcgacagatcGcggagctgcacgctgccgcc	16	16	0	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:197872017G>A	ENST00000367393.3	+	1	241	c.238G>A	c.(238-240)Gcg>Acg	p.A80T		NM_001024594.2	NP_001019765.1	Q5VUE5	CA053_HUMAN	chromosome 1 open reading frame 53	80										endometrium(1)|lung(1)	2						GCGACAGATCGCGGAGCTGCA	0.776																																					p.A80T		Atlas-SNP	.											.	C1orf53	18	.	0			c.G238A						.						5	7	6					1																	197872017		1761	3867	5628	SO:0001583	missense	388722	exon1			CAGATCGCGGAGC	BC038214	CCDS44290.1	1q31.3	2011-01-26			ENSG00000203724	ENSG00000203724			30003	protein-coding gene	gene with protein product						15897902	Standard	NM_001024594		Approved		uc001guh.3	Q5VUE5	OTTHUMG00000035659	ENST00000367393.3:c.238G>A	chr1.hg19:g.197872017G>A	ENSP00000356363:p.Ala80Thr	48.0	0.0		63.0	17.0	NM_001024594	A1L4N2|Q5VUE4	Missense_Mutation	SNP	ENST00000367393.3	hg19	CCDS44290.1	.	.	.	.	.	.	.	.	.	.	G	7.343	0.621283	0.14193	.	.	ENSG00000203724	ENST00000367393	.	.	.	3.34	1.17	0.20885	.	0.739003	0.11375	U	0.570463	T	0.25195	0.0612	L	0.52573	1.65	0.09310	N	1	D	0.56746	0.977	B	0.36666	0.23	T	0.14476	-1.0471	9	0.29301	T	0.29	-20.5471	7.543	0.27751	0.0:0.0:0.5386:0.4614	.	80	Q5VUE5	CA053_HUMAN	T	80	.	ENSP00000356363:A80T	A	+	1	0	C1orf53	196138640	0.196000	0.23350	0.076000	0.20297	0.027000	0.11550	0.205000	0.17356	0.723000	0.32274	0.313000	0.20887	GCG	.	.		0.776	C1orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086555.1	NM_001024594		A	197872017	G	A	197872017	3	1	85	1	0	0	0	0	1	0	0	0	2047	1087	38	1	240	1	C1orf53	1	197872017	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	43645498	197872017	51378604	10	11375										
RNPEP	6051	hgsc.bcm.edu	37	chr1	201970854	201970854	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tctggacttctacttggaatAtttccctgagcttaagaaaa	7	8	2	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:201970854A>G	ENST00000295640.4	+	8	1428	c.1385A>G	c.(1384-1386)tAt>tGt	p.Y462C	RNPEP_ENST00000471105.1_3'UTR|RP11-465N4.4_ENST00000415582.1_RNA|RNPEP_ENST00000367286.3_Missense_Mutation_p.Y423C|RP11-465N4.4_ENST00000419190.1_RNA	NM_020216.3	NP_064601.3	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase (aminopeptidase B)	462					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|large_intestine(4)|lung(6)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		TACTTGGAATATTTCCCTGAG	0.428																																					p.Y462C	GBM(19;39 479 7473 13131 19462)	Atlas-SNP	.											.	RNPEP	39	.	0			c.A1385G						.						127	129	128					1																	201970854		2203	4300	6503	SO:0001583	missense	6051	exon8			TGGAATATTTCCC	BC001064	CCDS1418.1	1q32	2008-02-05			ENSG00000176393	ENSG00000176393	3.4.11.6		10078	protein-coding gene	gene with protein product		602675				9533033, 10467730	Standard	NM_020216		Approved		uc001gxd.3	Q9H4A4	OTTHUMG00000035866	ENST00000295640.4:c.1385A>G	chr1.hg19:g.201970854A>G	ENSP00000295640:p.Tyr462Cys	114.0	0.0		121.0	52.0	NM_020216	Q9BVM9|Q9H1D4|Q9NPT7	Missense_Mutation	SNP	ENST00000295640.4	hg19	CCDS1418.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.772289	0.49680	.	.	ENSG00000176393	ENST00000295640;ENST00000367286;ENST00000447312	T;T;T	0.05081	3.5;3.5;3.5	5.71	3.39	0.38822	.	0.078022	0.52532	D	0.000065	T	0.19167	0.0460	M	0.84948	2.725	0.51767	D	0.999932	P;P	0.44478	0.836;0.584	P;P	0.53954	0.738;0.548	T	0.00165	-1.1967	10	0.72032	D	0.01	-7.3823	7.6867	0.28544	0.7853:0.1411:0.0736:0.0	.	470;462	Q7RU04;Q9H4A4	.;AMPB_HUMAN	C	462;423;331	ENSP00000295640:Y462C;ENSP00000356255:Y423C;ENSP00000389602:Y331C	ENSP00000295640:Y462C	Y	+	2	0	RNPEP	200237477	1.000000	0.71417	0.636000	0.29352	0.457000	0.32468	3.401000	0.52601	0.431000	0.26258	0.459000	0.35465	TAT	.	.		0.428	RNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087345.1	NM_020216		G	201970854	A	G	201970854	3	3	85	1	0	0	0	0	1	0	0	0	13524	449	16	2	1415	2	RNPEP	1	201970854	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	4098837	201970854	47279767	11	11376										
WNT3A	89780	hgsc.bcm.edu	37	chr1	228238391	228238391	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gcctttgtccacgccattgcCtcagccggtgtggcctttgc	11	15	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr1:228238391C>A	ENST00000284523.1	+	3	426	c.348C>A	c.(346-348)gcC>gcA	p.A116A	WNT3A_ENST00000366753.2_Silent_p.A116A	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	116					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				ACGCCATTGCCTCAGCCGGTG	0.627																																					p.A116A		Atlas-SNP	.											.	WNT3A	40	.	0			c.C348A						.						107	82	91					1																	228238391		2203	4300	6503	SO:0001819	synonymous_variant	89780	exon3			CATTGCCTCAGCC	AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"Wingless-type MMTV integration sites", "Endogenous ligands"	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.348C>A	chr1.hg19:g.228238391C>A		89.0	0.0		109.0	54.0	NM_033131	Q3SY79|Q3SY80|Q969P2	Silent	SNP	ENST00000284523.1	hg19	CCDS1564.1																																																																																			.	.		0.627	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131		A	228238391	C	A	228238391	2	1	85	1	0	0	0	0	0	0	0	1	17404	668	24	3		3	WNT3A	1	228238391	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	26267537	228238391	21012230	12	11377										
KCNK3	3777	hgsc.bcm.edu	37	chr2	26951035	26951035	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	agcgcgacgccgagcaccgcGcgctgctcacgcgcaacggg	15	17	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:26951035G>A	ENST00000302909.3	+	2	909	c.784G>A	c.(784-786)Gcg>Acg	p.A262T		NM_002246.2	NP_002237.1	O14649	KCNK3_HUMAN	potassium channel, subfamily K, member 3	262					brain development (GO:0007420)|cellular response to hypoxia (GO:0071456)|cellular response to zinc ion (GO:0071294)|cochlea development (GO:0090102)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)|open rectifier potassium channel activity (GO:0005252)|potassium channel activity (GO:0005267)|potassium ion leak channel activity (GO:0022841)|S100 protein binding (GO:0044548)			endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Doxapram(DB00561)|Halothane(DB01159)	CGAGCACCGCGCGCTGCTCAC	0.731																																					p.A262T	GBM(80;1457 1631 27100 45946)	Atlas-SNP	.											.	KCNK3	43	.	0			c.G784A						.						24	19	21					2																	26951035		2191	4281	6472	SO:0001583	missense	3777	exon2			CACCGCGCGCTGC	AF006823	CCDS1727.1	2p23	2012-03-07			ENSG00000171303	ENSG00000171303		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6278	protein-coding gene	gene with protein product		603220				9312005, 9721223, 16382106	Standard	NM_002246		Approved	K2p3.1, TASK, TASK-1	uc002rhn.2	O14649	OTTHUMG00000125530	ENST00000302909.3:c.784G>A	chr2.hg19:g.26951035G>A	ENSP00000306275:p.Ala262Thr	38.0	0.0		66.0	23.0	NM_002246	Q53SU2	Missense_Mutation	SNP	ENST00000302909.3	hg19	CCDS1727.1	.	.	.	.	.	.	.	.	.	.	G	18.34	3.603441	0.66445	.	.	ENSG00000171303	ENST00000538762;ENST00000302909	T	0.25414	1.8	4.76	4.76	0.60689	.	0.333064	0.31177	N	0.008103	T	0.23611	0.0571	L	0.47716	1.5	0.53005	D	0.999962	B	0.27765	0.188	B	0.21360	0.034	T	0.04255	-1.0965	10	0.52906	T	0.07	.	13.6164	0.62110	0.0:0.0:1.0:0.0	.	262	O14649	KCNK3_HUMAN	T	139;262	ENSP00000306275:A262T	ENSP00000306275:A262T	A	+	1	0	KCNK3	26804539	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.561000	0.98142	2.329000	0.79093	0.511000	0.50034	GCG	.	.		0.731	KCNK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246861.2	NM_002246		A	26951035	G	A	26951035	3	1	85	1	0	0	0	0	1	0	0	0	8076	1087	38	1	790	1	KCNK3	2	26951035	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10		26951035	216248338	13	11378										
UCN	7349	hgsc.bcm.edu	37	chr2	27530547	27530547	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ccgctcgcctgccgtcccgaGtcccaatcggccgggccccg	12	21	0	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:27530547G>T	ENST00000296099.2	-	2	515	c.217C>A	c.(217-219)Ctc>Atc	p.L73I		NM_003353.2	NP_003344.1	P55089	UCN1_HUMAN	urocortin	73					activation of protein kinase A activity (GO:0034199)|aerobic respiration (GO:0009060)|associative learning (GO:0008306)|drinking behavior (GO:0042756)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric emptying (GO:0035483)|inflammatory response (GO:0006954)|negative regulation of apoptotic process (GO:0043066)|negative regulation of appetite (GO:0032099)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell size (GO:0045792)|negative regulation of feeding behavior (GO:2000252)|negative regulation of gastric acid secretion (GO:0060455)|negative regulation of gene expression (GO:0010629)|negative regulation of hormone secretion (GO:0046888)|negative regulation of necrotic cell death (GO:0060547)|negative regulation of neuron death (GO:1901215)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|pancreatic juice secretion (GO:0030157)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cardiac muscle contraction (GO:0060452)|positive regulation of cell growth (GO:0030307)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of corticotropin secretion (GO:0051461)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of translation (GO:0045727)|positive regulation of vascular permeability (GO:0043117)|positive regulation of vasodilation (GO:0045909)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|response to pain (GO:0048265)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|perikaryon (GO:0043204)|varicosity (GO:0043196)	histone deacetylase inhibitor activity (GO:0046811)|neuropeptide hormone activity (GO:0005184)			lung(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCGTCCCGAGTCCCAATcgg	0.746																																					p.L73I		Atlas-SNP	.											.	UCN	4	.	0			c.C217A						.						5	7	6					2																	27530547		1998	3938	5936	SO:0001583	missense	7349	exon2			TCCCGAGTCCCAA	AF038633	CCDS1747.1	2p23-p21	2013-02-28			ENSG00000163794	ENSG00000163794		"Endogenous ligands"	12516	protein-coding gene	gene with protein product	"prepro-urocortin"	600945				9628819, 861256	Standard	NM_003353		Approved	UROC, UI	uc002rjp.1	P55089	OTTHUMG00000097068	ENST00000296099.2:c.217C>A	chr2.hg19:g.27530547G>T	ENSP00000296099:p.Leu73Ile	1005.0	0.0		1009.0	233.0	NM_003353	Q6FG64	Missense_Mutation	SNP	ENST00000296099.2	hg19	CCDS1747.1	.	.	.	.	.	.	.	.	.	.	G	7.962	0.747188	0.15710	.	.	ENSG00000163794	ENST00000296099	.	.	.	4.89	-8.27	0.01017	.	1.314350	0.05352	N	0.532015	T	0.14098	0.0341	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.18335	-1.0340	9	0.34782	T	0.22	-4.0E-4	3.7812	0.08682	0.1527:0.3541:0.3763:0.1168	.	73	P55089	UCN1_HUMAN	I	73	.	ENSP00000296099:L73I	L	-	1	0	UCN	27384051	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.258000	0.01179	-1.006000	0.03412	-0.367000	0.07326	CTC	.	.		0.746	UCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214184.2	NM_003353		T	27530547	G	T	27530547	3	4	85	1	0	0	0	0	1	0	0	0	16942	1029	36	3	161	3	UCN	2	27530547	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	579512	27530547	215668826	14	11379										
GGCX	2677	hgsc.bcm.edu	37	chr2	85779044	85779059	+	Frame_Shift_Del	DEL	GGATGTGCGCTGAAAG	GGATGTGCGCTGAAAG	-													0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	atcaagagtggttgcacccaGgatgtgcgctgaaagggtga					rs146811957|rs41290033|rs146758153|rs372161185	byFrequency	TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	GGATGTGCGCTGAAAG	GGATGTGCGCTGAAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:85779044_85779059delGGATGTGCGCTGAAAG	ENST00000233838.4	-	11	1565_1580	c.1485_1500delCTTTCAGCGCACATCC	c.(1483-1500)ccctttcagcgcacatccfs	p.PFQRTS495fs	GGCX_ENST00000430215.3_Frame_Shift_Del_p.PFQRTS438fs|GGCX_ENST00000473665.1_5'Flank	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	495					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	GTTGCACCCAGGATGTGCGCTGAAAGGGTGACCAAG	0.528											OREG0014747	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.496_501del		Atlas-Indel,Pindel	.											.	GGCX	44	.	0			c.1486_1501del						.																																			SO:0001589	frameshift_variant	2677	exon11			.		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"vitamin K-dependent gamma-carboxylase"	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.1485_1500delCTTTCAGCGCACATCC	chr2.hg19:g.85779044_85779059delGGATGTGCGCTGAAAG	ENSP00000233838:p.Pro495fs	99.0	0.0	1239	76.0	22.0	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Frame_Shift_Del	DEL	ENST00000233838.4	hg19	CCDS1978.1																																																																																			.	.		0.528	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		-	85779059	GGATGTGCGCTGAAAG	-	85779044	7	5	85	1	0	1	0	1	0	0	0	0	6364	987	35	0	796	0	GGCX	2	85779044	Frame_Shift_Del	DEL	GGATGTGCGCTGAAAG	TCGA-CC-A9FW-01A-11D-A36X-10	58248497	85779044	157420329	15	11380										
PLEKHB2	55041	hgsc.bcm.edu	37	chr2	131890529	131890529	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	catccgtggtttcctcacctCcaccatacacggcctatgct	6	17	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:131890529C>T	ENST00000403716.1	+	6	948	c.388C>T	c.(388-390)Cca>Tca	p.P130S	PLEKHB2_ENST00000409612.1_Missense_Mutation_p.P130S|PLEKHB2_ENST00000538982.1_Missense_Mutation_p.P82S|PLEKHB2_ENST00000404460.1_Missense_Mutation_p.P130S|PLEKHB2_ENST00000438882.2_Missense_Mutation_p.P130S|PLEKHB2_ENST00000234115.6_Missense_Mutation_p.P130S|PLEKHB2_ENST00000303908.3_Missense_Mutation_p.P130S|PLEKHB2_ENST00000409158.1_Missense_Mutation_p.P130S|PLEKHB2_ENST00000409279.1_Missense_Mutation_p.P130S|PLEKHB2_ENST00000439822.2_Intron	NM_001100623.1|NM_001267062.1|NM_001267063.1|NM_001267064.1|NM_001267065.1|NM_001267066.1|NM_017958.2	NP_001094093.1|NP_001253991.1|NP_001253992.1|NP_001253993.1|NP_001253994.1|NP_001253995.1|NP_060428.2	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	130						endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		TTCCTCACCTCCACCATACAC	0.602																																					p.P130S		Atlas-SNP	.											.	PLEKHB2	47	.	0			c.C388T						.						126	107	114					2																	131890529		2203	4300	6503	SO:0001583	missense	55041	exon6			TCACCTCCACCAT		CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"Pleckstrin homology (PH) domain containing"	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000403716.1:c.388C>T	chr2.hg19:g.131890529C>T	ENSP00000385892:p.Pro130Ser	181.0	0.0		229.0	128.0	NM_001267062	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Missense_Mutation	SNP	ENST00000403716.1	hg19	CCDS46413.1	.	.	.	.	.	.	.	.	.	.	C	13.74	2.327906	0.41197	.	.	ENSG00000115762	ENST00000409158;ENST00000403716;ENST00000234115;ENST00000438882;ENST00000538982;ENST00000404460;ENST00000409612;ENST00000409279;ENST00000303908	.	.	.	4.81	4.81	0.61882	.	0.000000	0.85682	U	0.000000	T	0.77558	0.4148	M	0.74258	2.255	0.58432	D	0.999996	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.993;1.0;1.0	D;D;D;D;D;D	0.87578	0.992;0.996;0.998;0.979;0.996;0.996	T	0.78826	-0.2051	9	0.51188	T	0.08	-2.571	13.7255	0.62756	0.0:1.0:0.0:0.0	.	130;130;130;130;130;130	B4DF08;Q53FF1;Q96CS7-3;B7WPA5;Q96CS7;B8ZZN1	.;.;.;.;PKHB2_HUMAN;.	S	130;130;130;130;82;130;130;130;130	.	ENSP00000234115:P130S	P	+	1	0	PLEKHB2	131606999	0.998000	0.40836	0.941000	0.38009	0.037000	0.13140	4.001000	0.57046	2.383000	0.81215	0.491000	0.48974	CCA	.	.		0.602	PLEKHB2-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331304.2	NM_017958		T	131890529	C	T	131890529	3	4	85	1	0	0	0	0	1	0	0	0	12074	855	30	3	406	3	PLEKHB2	2	131890529	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	46111485	131890529	111308844	16	11381										
R3HDM1	23518	hgsc.bcm.edu	37	chr2	136389287	136389287	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	agtcttcatactttgtttcaGggacagaatgatgctgctga	10	7	3	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:136389287G>A	ENST00000264160.4	+	8	867		c.e8-1		R3HDM1_ENST00000410054.1_Splice_Site|R3HDM1_ENST00000409606.1_Splice_Site|R3HDM1_ENST00000409478.1_Splice_Site|R3HDM1_ENST00000329971.3_Splice_Site	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1								poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		CTTTGTTTCAGGGACAGAATG	0.323																																					.		Atlas-SNP	.											.	R3HDM1	84	.	0			c.498-1G>A						.						90	91	91					2																	136389287		2202	4300	6502	SO:0001630	splice_region_variant	23518	exon8			GTTTCAGGGACAG	D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing"	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.498-1G>A	chr2.hg19:g.136389287G>A		105.0	0.0		110.0	28.0	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Splice_Site	SNP	ENST00000264160.4	hg19	CCDS2177.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.635123	0.87760	.	.	ENSG00000048991	ENST00000422577;ENST00000409478;ENST00000264160;ENST00000329971;ENST00000410054;ENST00000436436;ENST00000409606;ENST00000456040	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9405	0.97159	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	R3HDM1	136105757	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.716000	0.92895	0.650000	0.86243	.	.	.		0.323	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361	Intron	A	136389287	G	A	136389287	5	1	85	1	0	0	0	0	0	0	1	0	12902	1014	35	3	519	3	R3HDM1	2	136389287	Splice_Site	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	4498758	136389287	106810086	17	11382										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209188869	209188869	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tgatttatcttacttaggaaAgggaattcttgaagaattat	8	3	2	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:209188869A>G	ENST00000264380.4	+	18	2352	c.2194A>G	c.(2194-2196)Agg>Ggg	p.R732G		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	732					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TACTTAGGAAAGGGAATTCTT	0.383																																					p.R732G		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.A2194G						.						127	127	127					2																	209188869		2203	4300	6503	SO:0001583	missense	200576	exon18			TAGGAAAGGGAAT	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.2194A>G	chr2.hg19:g.209188869A>G	ENSP00000264380:p.Arg732Gly	95.0	0.0		145.0	36.0	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	hg19	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.209709	0.79240	.	.	ENSG00000115020	ENST00000264380;ENST00000392200;ENST00000452564	T;T	0.79845	-1.31;-1.31	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.88833	0.6544	M	0.73598	2.24	0.80722	D	1	D;D	0.69078	0.997;0.994	P;D	0.75020	0.908;0.985	D	0.89613	0.3843	10	0.59425	D	0.04	-18.1534	14.6334	0.68673	1.0:0.0:0.0:0.0	.	732;676	Q9Y2I7;E9PDH4	FYV1_HUMAN;.	G	732;308;676	ENSP00000264380:R732G;ENSP00000405736:R676G	ENSP00000264380:R732G	R	+	1	2	PIKFYVE	208897114	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	6.905000	0.75714	2.196000	0.70406	0.374000	0.22700	AGG	.	.		0.383	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		G	209188869	A	G	209188869	3	3	85	1	0	0	0	0	1	0	0	0	11933	63	3	2	2271	2	PIKFYVE	2	209188869	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	72799582	209188869	34010504	18	11383										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212537964	212537964	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tccacacagatggagccattCtcaaactcccgaaattcact	5	14	2	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:212537964C>T	ENST00000342788.4	-	14	1951	c.1641G>A	c.(1639-1641)gaG>gaA	p.E547E	ERBB4_ENST00000402597.1_Silent_p.E547E|ERBB4_ENST00000436443.1_Silent_p.E547E	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	547	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	TGGAGCCATTCTCAAACTCCC	0.473										TSP Lung(8;0.080)																											p.E547E		Atlas-SNP	.											.	ERBB4	480	.	0			c.G1641A						.						117	93	102					2																	212537964		2203	4300	6503	SO:0001819	synonymous_variant	2066	exon14			GCCATTCTCAAAC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1641G>A	chr2.hg19:g.212537964C>T		70.0	0.0		74.0	17.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	hg19	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	7.196	0.592517	0.13875	.	.	ENSG00000178568	ENST00000260943	.	.	.	5.33	3.49	0.39957	.	.	.	.	.	T	0.47544	0.1451	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40098	-0.9581	4	.	.	.	.	4.1158	0.10081	0.0:0.3795:0.3409:0.2796	.	.	.	.	K	547	.	.	R	-	2	0	ERBB4	212246209	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.455000	0.35190	1.203000	0.43233	0.557000	0.71058	AGA	.	.		0.473	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212537964	C	T	212537964	2	4	85	1	0	0	0	0	0	0	0	1	5211	912	32	3		3	ERBB4	2	212537964	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	3349095	212537964	30661409	19	11384										
TUBA4A	7277	hgsc.bcm.edu	37	chr2	220115164	220115164	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gccatatcctcacgggcctcGgagaactcaccctcctccat	7	18	2	1	rs199590938		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:220115164G>A	ENST00000248437.4	-	4	1430	c.1257C>T	c.(1255-1257)tcC>tcT	p.S419S	TUBA4B_ENST00000490341.1_RNA|TUBA4A_ENST00000392088.2_Silent_p.S404S|TUBA4A_ENST00000498660.1_5'Flank	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	419					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	CACGGGCCTCGGAGAACTCAC	0.582																																					p.S419S		Atlas-SNP	.											.	TUBA4A	96	.	0			c.C1257T						.						122	117	119					2																	220115164		2203	4300	6503	SO:0001819	synonymous_variant	7277	exon4			GGCCTCGGAGAAC	AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"Tubulins"	12407	protein-coding gene	gene with protein product		191110	"tubulin, alpha 1 (testis specific)", "tubulin, alpha 1"	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.1257C>T	chr2.hg19:g.220115164G>A		201.0	0.0		186.0	98.0	NM_006000	A8MUB1|B3KNQ6|P05215	Silent	SNP	ENST00000248437.4	hg19	CCDS2438.1																																																																																			.	G|0.999;A|0.001		0.582	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000		A	220115164	G	A	220115164	2	1	85	1	0	0	0	0	0	0	0	1	16764	1103	39	1		1	TUBA4A	2	220115164	Silent	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	7577200	220115164	23084209	20	11385										
CHPF	79586	hgsc.bcm.edu	37	chr2	220404725	220404725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acgccgctccagctctgccaCgtgggccttgacaggtgcga	13	15	1	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:220404725C>T	ENST00000243776.6	-	4	1956	c.1708G>A	c.(1708-1710)Gtg>Atg	p.V570M	CHPF_ENST00000535926.1_Missense_Mutation_p.V408M	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	570	Ala-rich.				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		AGCTCTGCCACGTGGGCCTTG	0.657																																					p.V570M		Atlas-SNP	.											.	CHPF	56	.	0			c.G1708A						.						27	32	30					2																	220404725		2202	4297	6499	SO:0001583	missense	79586	exon4			CTGCCACGTGGGC	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24291	protein-coding gene	gene with protein product	"chondroitin sulfate synthase 2"	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1708G>A	chr2.hg19:g.220404725C>T	ENSP00000243776:p.Val570Met	129.0	0.0		132.0	70.0	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Missense_Mutation	SNP	ENST00000243776.6	hg19	CCDS2443.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.456932	0.63401	.	.	ENSG00000123989	ENST00000243776;ENST00000535926	T;T	0.15603	2.41;2.41	4.62	4.62	0.57501	.	0.073067	0.56097	D	0.000023	T	0.15132	0.0365	N	0.08118	0	0.40918	D	0.984286	D	0.63880	0.993	D	0.63793	0.918	T	0.11867	-1.0570	10	0.23302	T	0.38	-30.4285	5.7428	0.18104	0.0:0.7648:0.0:0.2352	.	570	Q8IZ52	CHSS2_HUMAN	M	570;408	ENSP00000243776:V570M;ENSP00000445571:V408M	ENSP00000243776:V570M	V	-	1	0	CHPF	220112969	0.993000	0.37304	0.994000	0.49952	0.998000	0.95712	2.546000	0.45778	2.563000	0.86464	0.561000	0.74099	GTG	.	.		0.657	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536		T	220404725	C	T	220404725	3	4	85	1	0	0	0	0	1	0	0	0	3370	536	19	1	623	1	CHPF	2	220404725	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	289561	220404725	22794648	21	11386										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220502422	220502422	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cccaccgagggcccccccagCccgaggaaccagcccaatac	9	21	0	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:220502422C>A	ENST00000358055.3	+	17	3167	c.2655C>A	c.(2653-2655)agC>agA	p.S885R	SLC4A3_ENST00000373762.3_Missense_Mutation_p.S912R|SLC4A3_ENST00000317151.3_Missense_Mutation_p.S885R|SLC4A3_ENST00000273063.6_Missense_Mutation_p.S912R|SLC4A3_ENST00000373760.2_Missense_Mutation_p.S885R			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	885	Membrane (anion exchange).			SPR -> GPE (in Ref. 2; AAB05850). {ECO:0000305}.	bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCCCCCCAGCCCGAGGAACC	0.647																																					p.S912R		Atlas-SNP	.											.	SLC4A3	144	.	0			c.C2736A						.						60	49	53					2																	220502422		2203	4300	6503	SO:0001583	missense	6508	exon17			CCCCAGCCCGAGG		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2655C>A	chr2.hg19:g.220502422C>A	ENSP00000350756:p.Ser885Arg	178.0	0.0		183.0	56.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	hg19	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	C	8.527	0.870061	0.17322	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000356251;ENST00000317151	T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18	4.54	1.5	0.22942	Bicarbonate transporter, C-terminal (1);	0.516257	0.16127	N	0.228373	T	0.54351	0.1853	N	0.15975	0.35	0.24045	N	0.996068	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.002;0.0	T	0.31166	-0.9953	10	0.18710	T	0.47	.	4.8304	0.13437	0.1264:0.6074:0.1121:0.154	.	589;885;912	P48751-2;P48751;P48751-3	.;B3A3_HUMAN;.	R	885;885;912;912;145;885	ENSP00000350756:S885R;ENSP00000362865:S885R;ENSP00000273063:S912R;ENSP00000362867:S912R;ENSP00000314006:S885R	ENSP00000273063:S912R	S	+	3	2	SLC4A3	220210666	0.403000	0.25319	0.981000	0.43875	0.138000	0.21146	0.079000	0.14782	0.640000	0.30582	-0.270000	0.10280	AGC	.	.		0.647	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		A	220502422	C	A	220502422	3	1	85	1	0	0	0	0	1	0	0	0	14670	738	26	3	2798	3	SLC4A3	2	220502422	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	97697	220502422	22696951	22	11387										
SLC16A14	151473	hgsc.bcm.edu	37	chr2	230924025	230924025	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gtgtctttttgtctttggggCcatcttcaaaatcataccca	7	10	5	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr2:230924025C>T	ENST00000295190.4	-	2	502	c.44G>A	c.(43-45)gGc>gAc	p.G15D	RNY4P19_ENST00000362530.1_RNA	NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	15						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		GTCTTTGGGGCCATCTTCAAA	0.393																																					p.G15D		Atlas-SNP	.											.	SLC16A14	75	.	0			c.G44A						.						78	73	75					2																	230924025		2203	4300	6503	SO:0001583	missense	151473	exon2			TTGGGGCCATCTT	BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053		"Solute carriers"	26417	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 14"		"solute carrier family 16 (monocarboxylic acid transporters), member 14"				Standard	NM_152527		Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.44G>A	chr2.hg19:g.230924025C>T	ENSP00000295190:p.Gly15Asp	150.0	0.0		147.0	78.0	NM_152527	A8KA08|Q53R92|Q96NI7	Missense_Mutation	SNP	ENST00000295190.4	hg19	CCDS2473.1	.	.	.	.	.	.	.	.	.	.	C	0.039	-1.292404	0.01375	.	.	ENSG00000163053	ENST00000295190;ENST00000457406;ENST00000412034;ENST00000425822;ENST00000436869	T;T;T	0.08102	3.13;3.13;3.14	5.5	-1.05	0.10036	Major facilitator superfamily domain, general substrate transporter (1);	0.479994	0.19173	N	0.120896	T	0.02304	0.0071	N	0.02539	-0.55	0.20975	N	0.999813	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46652	-0.9176	10	0.10902	T	0.67	.	6.0552	0.19807	0.1193:0.3494:0.0:0.5313	.	15;15	E7EMG7;Q7RTX9	.;MOT14_HUMAN	D	15	ENSP00000295190:G15D;ENSP00000400352:G15D;ENSP00000395775:G15D	ENSP00000295190:G15D	G	-	2	0	SLC16A14	230632269	0.983000	0.35010	0.996000	0.52242	0.323000	0.28346	0.275000	0.18698	-0.064000	0.13043	-1.004000	0.02495	GGC	.	.		0.393	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256918.2	NM_152527		T	230924025	C	T	230924025	3	4	85	1	0	0	0	0	1	0	0	0	14422	739	26	3	1504	3	SLC16A14	2	230924025	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	10421603	230924025	12275348	23	11388										
TMEM40	55287	hgsc.bcm.edu	37	chr3	12791298	12791298	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tctgtggacttgactgttgtCctgaggctgggaggaggatg	17	6	1	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:12791298C>A	ENST00000314124.7	-	2	390	c.34G>T	c.(34-36)Gac>Tac	p.D12Y	TMEM40_ENST00000435218.2_Missense_Mutation_p.D12Y|TMEM40_ENST00000431022.2_Missense_Mutation_p.D28Y|TMEM40_ENST00000435575.1_Missense_Mutation_p.D12Y|TMEM40_ENST00000264728.8_Missense_Mutation_p.D12Y	NM_001284406.1|NM_018306.2	NP_001271335.1|NP_060776.2	Q8WWA1	TMM40_HUMAN	transmembrane protein 40	12						integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(5)|urinary_tract(1)	10						TGACTGTTGTCCTGAGGCTGG	0.433																																					p.D12Y		Atlas-SNP	.											.	TMEM40	22	.	0			c.G34T						.						204	174	184					3																	12791298		2203	4300	6503	SO:0001583	missense	55287	exon2			TGTTGTCCTGAGG	BC020658	CCDS2613.1, CCDS68347.1, CCDS68348.1	3p25.2	2005-01-10			ENSG00000088726	ENSG00000088726			25620	protein-coding gene	gene with protein product						12477932	Standard	NM_018306		Approved	FLJ11036	uc003bxg.1	Q8WWA1	OTTHUMG00000129801	ENST00000314124.7:c.34G>T	chr3.hg19:g.12791298C>A	ENSP00000322837:p.Asp12Tyr	171.0	0.0		198.0	31.0	NM_018306	C9JID5|Q8NAL4|Q9NUZ4	Missense_Mutation	SNP	ENST00000314124.7	hg19	CCDS2613.1	.	.	.	.	.	.	.	.	.	.	C	11.22	1.573435	0.28092	.	.	ENSG00000088726	ENST00000314124;ENST00000435575;ENST00000435218;ENST00000264728;ENST00000431022	.	.	.	3.81	2.92	0.33932	.	0.320112	0.22782	N	0.055701	T	0.51568	0.1682	L	0.59436	1.845	0.09310	N	1	D;D;D;D	0.65815	0.995;0.992;0.969;0.995	P;P;P;P	0.60415	0.874;0.757;0.824;0.874	T	0.36744	-0.9735	9	0.87932	D	0	-16.4868	7.795	0.29141	0.0:0.8844:0.0:0.1156	.	28;12;12;12	B4DXI0;C9JID5;Q8WWA1-2;Q8WWA1	.;.;.;TMM40_HUMAN	Y	12;12;12;12;28	.	ENSP00000264728:D12Y	D	-	1	0	TMEM40	12766298	0.024000	0.19004	0.024000	0.17045	0.412000	0.31113	1.427000	0.34881	1.152000	0.42452	0.655000	0.94253	GAC	.	.		0.433	TMEM40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252029.2	NM_018306		A	12791298	C	A	12791298	3	1	85	1	0	0	0	0	1	0	0	0	16178	855	30	3	711	3	TMEM40	3	12791298	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10		12791298	185231132	24	11389										
TTC21A	199223	hgsc.bcm.edu	37	chr3	39166927	39166927	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gagcttcacttctccagcatGcaaggcatccctcttggctc	8	15	3	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:39166927G>T	ENST00000431162.2	+	11	1454	c.1320G>T	c.(1318-1320)atG>atT	p.M440I	TTC21A_ENST00000440121.1_Missense_Mutation_p.M391I|TTC21A_ENST00000301819.6_Missense_Mutation_p.M440I			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	440										NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TCTCCAGCATGCAAGGCATCC	0.532											OREG0015487	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M440I		Atlas-SNP	.											.	TTC21A	96	.	0			c.G1320T						.						99	97	97					3																	39166927		2050	4201	6251	SO:0001583	missense	199223	exon11			CAGCATGCAAGGC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"Tetratricopeptide (TTC) repeat domain containing"	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.1320G>T	chr3.hg19:g.39166927G>T	ENSP00000398211:p.Met440Ile	74.0	0.0	883	52.0	21.0	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	hg19	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.397832	0.42512	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.59638	0.25;0.25;0.36	5.73	4.84	0.62591	.	0.259217	0.39544	N	0.001328	T	0.49184	0.1542	L	0.39898	1.24	0.38087	D	0.936836	B;B;B	0.24920	0.017;0.114;0.07	B;B;B	0.20955	0.008;0.032;0.014	T	0.49293	-0.8955	10	0.36615	T	0.2	-14.3663	14.9106	0.70755	0.0:0.0:0.8554:0.1446	.	391;440;440	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	I	440;422;440;391	ENSP00000301819:M440I;ENSP00000398211:M440I;ENSP00000410882:M391I	ENSP00000301819:M440I	M	+	3	0	TTC21A	39141931	1.000000	0.71417	0.999000	0.59377	0.936000	0.57629	1.673000	0.37534	1.388000	0.46506	0.609000	0.83330	ATG	.	.		0.532	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		T	39166927	G	T	39166927	3	4	85	1	0	0	0	0	1	0	0	0	16702	1319	46	3	1362	3	TTC21A	3	39166927	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	26375629	39166927	158855503	25	11390										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266104	41266104	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acagtcttacctggactctgGaatccattctggtgccacta	8	12	3	0	rs28931589|rs121913416		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:41266104G>T	ENST00000349496.5	+	3	381	c.101G>T	c.(100-102)gGa>gTa	p.G34V	CTNNB1_ENST00000453024.1_Missense_Mutation_p.G27V|CTNNB1_ENST00000405570.1_Missense_Mutation_p.G34V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.G34V|CTNNB1_ENST00000396185.3_Missense_Mutation_p.G34V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	34			G -> E (in PTR). {ECO:0000269|PubMed:10192393}.|G -> R (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|G -> V (in hepatoblastoma; dbSNP:rs28931589). {ECO:0000269|PubMed:9927029}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.G34E(73)|p.G34V(72)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTGGACTCTGGAATCCATTCT	0.488	G34E(AGS_STOMACH)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.G34V	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,161	CTNNB1	4904	.	276	Substitution - Missense(145)|Deletion - In frame(105)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(146)|endometrium(30)|large_intestine(27)|stomach(21)|central_nervous_system(20)|skin(8)|pancreas(8)|ovary(6)|small_intestine(2)|lung(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|pituitary(1)|prostate(1)|bone(1)	c.G101T						.						93	78	83					3																	41266104		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACTCTGGAATCCA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.101G>T	chr3.hg19:g.41266104G>T	ENSP00000344456:p.Gly34Val	142.0	0.0		122.0	44.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.450603	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-31.2232	19.9596	0.97236	0.0:0.0:1.0:0.0	rs28931589	34	P35222	CTNB1_HUMAN	V	27;34;34;34;34;27;34;34;34	ENSP00000400508:G27V;ENSP00000385604:G34V;ENSP00000412219:G34V;ENSP00000379486:G34V;ENSP00000344456:G34V;ENSP00000411226:G27V;ENSP00000379488:G34V;ENSP00000409302:G34V;ENSP00000401599:G34V	ENSP00000344456:G34V	G	+	2	0	CTNNB1	41241108	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GGA	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266104	G	T	41266104	3	4	85	1	0	0	0	0	1	0	0	0	4018	1174	41	3	107	3	CTNNB1	3	41266104	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	2099177	41266104	156756326	26	11391										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49161060	49161060	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ctcagtggcctccccaatttCacgcctgcaatgatggagag	10	13	2	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:49161060C>A	ENST00000418109.1	-	26	3966	c.3802G>T	c.(3802-3804)Gaa>Taa	p.E1268*	LAMB2_ENST00000464891.1_5'Flank|USP19_ENST00000488993.1_5'Flank|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank|LAMB2_ENST00000305544.4_Nonsense_Mutation_p.E1268*|USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398888.2_5'Flank|USP19_ENST00000434032.2_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1268	Domain II.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TCCCCAATTTCACGCCTGCAA	0.562																																					p.E1268X		Atlas-SNP	.											.	LAMB2	156	.	0			c.G3802T						.						101	99	99					3																	49161060		2203	4300	6503	SO:0001587	stop_gained	3913	exon25			CAATTTCACGCCT		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.3802G>T	chr3.hg19:g.49161060C>A	ENSP00000388325:p.Glu1268*	78.0	0.0		43.0	14.0	NM_002292	Q16321	Nonsense_Mutation	SNP	ENST00000418109.1	hg19	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	C	39	7.671004	0.98425	.	.	ENSG00000172037	ENST00000418109;ENST00000305544;ENST00000395387	.	.	.	5.83	4.95	0.65309	.	0.363722	0.31709	N	0.007192	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	9.5476	0.39291	0.0:0.6553:0.2727:0.072	.	.	.	.	X	1268;1268;35	.	ENSP00000307156:E1268X	E	-	1	0	LAMB2	49136064	0.152000	0.22762	1.000000	0.80357	0.453000	0.32348	0.386000	0.20702	1.434000	0.47414	0.655000	0.94253	GAA	.	.		0.562	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		A	49161060	C	A	49161060	4	1	85	1	0	0	0	0	0	1	0	0	8620	835	29	3	1626	3	LAMB2	3	49161060	Nonsense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	7894956	49161060	148861370	27	11392										
BSN	8927	hgsc.bcm.edu	37	chr3	49700524	49700524	+	Frame_Shift_Del	DEL	C	C	-													0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gccatgcctcagccaaggaaCaccggcacggtgaccacggg							TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:49700524delC	ENST00000296452.4	+	7	11047	c.10933delC	c.(10933-10935)cacfs	p.H3645fs		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3645					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		AGCCAAGGAACACCGGCACGG	0.677																																					p.E3644fs		Atlas-Indel,Pindel	.											.	BSN	272	.	0			c.10932delA						.						25	25	25					3																	49700524		2202	4299	6501	SO:0001589	frameshift_variant	8927	exon7			.	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.10933delC	chr3.hg19:g.49700524delC	ENSP00000296452:p.His3645fs	41.0	0.0		34.0	13.0	NM_003458	O43161|Q7LGH3	Frame_Shift_Del	DEL	ENST00000296452.4	hg19	CCDS2800.1																																																																																			.	.		0.677	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		-	49700524	C	-	49700524	7	5	85	1	0	1	0	1	0	0	0	0	1532	478	17	0	10959	0	BSN	3	49700524	Frame_Shift_Del	DEL	C	TCGA-CC-A9FW-01A-11D-A36X-10	539464	49700524	148321906	28	11393										
IFRD2	7866	hgsc.bcm.edu	37	chr3	50328069	50328069	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ggcctcactggctgcctcatCgtcactggaacccgagtcag	11	15	4	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:50328069C>G	ENST00000429673.2	-	2	291	c.292G>C	c.(292-294)Gat>Cat	p.D98H	IFRD2_ENST00000336089.4_Missense_Mutation_p.D200H|IFRD2_ENST00000436390.1_Missense_Mutation_p.D34H|IFRD2_ENST00000417626.2_Missense_Mutation_p.D34H|IFRD2_ENST00000484043.1_5'UTR			Q12894	IFRD2_HUMAN	interferon-related developmental regulator 2	98						nucleus (GO:0005634)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCTGCCTCATCGTCACTGGAA	0.607																																					p.D98H		Atlas-SNP	.											.	IFRD2	34	.	0			c.G292C						.						38	44	42					3																	50328069		2184	4283	6467	SO:0001583	missense	7866	exon2			CCTCATCGTCACT	U09585		3p21.3	2008-07-18			ENSG00000214706	ENSG00000214706			5457	protein-coding gene	gene with protein product	"interferon-related protein"	602725				9050919	Standard	NM_006764		Approved	SKMc15, SM15, IFNRP	uc011bdp.2	Q12894	OTTHUMG00000156935	ENST00000429673.2:c.292G>C	chr3.hg19:g.50328069C>G	ENSP00000398971:p.Asp98His	79.0	0.0		51.0	12.0	NM_006764	Q9BVB4|Q9UJ88	Missense_Mutation	SNP	ENST00000429673.2	hg19	CCDS46831.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.355933	0.41700	.	.	ENSG00000214706	ENST00000417626;ENST00000436390;ENST00000336089;ENST00000429673	T;T;T;T	0.52983	0.72;0.72;0.64;0.68	5.09	5.09	0.68999	Interferon-related developmental regulator, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70579	0.3240	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	T	0.75531	-0.3285	10	0.87932	D	0	-19.5283	15.9842	0.80138	0.0:1.0:0.0:0.0	.	98;200	Q12894;Q9UJ88	IFRD2_HUMAN;.	H	34;34;200;98	ENSP00000402849:D34H;ENSP00000392316:D34H;ENSP00000336936:D200H;ENSP00000398971:D98H	ENSP00000336936:D200H	D	-	1	0	IFRD2	50303073	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.676000	0.61627	2.344000	0.79699	0.655000	0.94253	GAT	.	.		0.607	IFRD2-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006764		G	50328069	C	G	50328069	3	3	85	1	0	0	0	0	1	0	0	0	7563	884	31	4	1272	4	IFRD2	3	50328069	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	627545	50328069	147694361	29	11394										
TLR9	54106	hgsc.bcm.edu	37	chr3	52255747	52255747	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gcagggcatcctcatctcgcCcactttgccgcccccgccag	9	20	2	0	rs148303873	byFrequency	TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:52255747C>A	ENST00000360658.2	-	2	3218	c.2585G>T	c.(2584-2586)gGg>gTg	p.G862V	TLR9_ENST00000494383.1_Missense_Mutation_p.W1015C|TLR9_ENST00000597542.1_Missense_Mutation_p.G886V	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	862					defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	CTCATCTCGCCCACTTTGCCG	0.642																																					p.G862V		Atlas-SNP	.											.	TLR9	72	.	0			c.G2585T						.						64	64	64					3																	52255747		2203	4300	6503	SO:0001583	missense	54106	exon2			TCTCGCCCACTTT	AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"CD molecules"	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.2585G>T	chr3.hg19:g.52255747C>A	ENSP00000353874:p.Gly862Val	141.0	0.0		65.0	27.0	NM_017442	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	hg19	CCDS2848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.016|0.016	-1.533658|-1.533658	0.00951|0.00951	.|.	.|.	ENSG00000239732|ENSG00000173366	ENST00000360658|ENST00000494383	T|.	0.02606|.	4.23|.	1.03|1.03	1.03|1.03	0.20045|0.20045	.|.	.|.	.|.	.|.	.|.	T|T	0.19287|0.19287	0.0463|0.0463	N|N	0.14661|0.14661	0.345|0.345	0.20764|0.20764	N|N	0.999855|0.999855	B;P|.	0.37233|.	0.209;0.588|.	B;B|.	0.21708|.	0.011;0.036|.	T|T	0.26087|0.26087	-1.0113|-1.0113	9|5	0.49607|.	T|.	0.09|.	.|.	5.6834|5.6834	0.17788|0.17788	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	959;862|.	B4E0A1;Q9NR96|.	.;TLR9_HUMAN|.	V|C	862|1015	ENSP00000353874:G862V|.	ENSP00000353874:G862V|.	G|W	-|-	2|3	0|0	TLR9|RP11-330H6.5	52230787|52230787	0.000000|0.000000	0.05858|0.05858	0.007000|0.007000	0.13788|0.13788	0.008000|0.008000	0.06430|0.06430	-1.722000|-1.722000	0.01868|0.01868	0.308000|0.308000	0.22923|0.22923	0.313000|0.313000	0.20887|0.20887	GGG|TGG	.	C|0.998;T|0.002		0.642	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1			A	52255747	C	A	52255747	3	1	85	1	0	0	0	0	1	0	0	0	15973	623	22	3	517	3	TLR9	3	52255747	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	1927678	52255747	145766683	30	11395										
FLNB	2317	hgsc.bcm.edu	37	chr3	58121724	58121724	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	aggaccaagaaggaaaacccAaaagagccattgtccatgac	9	10	0	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:58121724A>C	ENST00000295956.4	+	28	4855	c.4690A>C	c.(4690-4692)Aaa>Caa	p.K1564Q	FLNB_ENST00000358537.3_Missense_Mutation_p.K1564Q|FLNB_ENST00000357272.4_Missense_Mutation_p.K1564Q|FLNB_ENST00000348383.5_Missense_Mutation_p.K1564Q|FLNB_ENST00000419752.2_Missense_Mutation_p.K1395Q|FLNB_ENST00000429972.2_Missense_Mutation_p.K1564Q|FLNB_ENST00000490882.1_Missense_Mutation_p.K1595Q|FLNB_ENST00000493452.1_Missense_Mutation_p.K1395Q	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1564					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		AGGAAAACCCAAAAGAGCCAT	0.433																																					p.K1595Q		Atlas-SNP	.											.	FLNB	430	.	0			c.A4783C						.						76	68	71					3																	58121724		2203	4300	6503	SO:0001583	missense	2317	exon29			AAACCCAAAAGAG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.4690A>C	chr3.hg19:g.58121724A>C	ENSP00000295956:p.Lys1564Gln	191.0	0.0		151.0	43.0	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.105480	0.77096	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.84442	-1.85;-1.85;-1.85;-1.85;-1.85;-1.85;-1.85;-1.85	6.1	4.93	0.64822	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.082859	0.85682	N	0.000000	D	0.88235	0.6382	L	0.42529	1.33	0.48087	D	0.999589	D;B;P;P;D;D	0.60575	0.975;0.035;0.926;0.722;0.988;0.988	P;B;P;P;D;D	0.64877	0.757;0.391;0.848;0.449;0.93;0.93	D	0.87978	0.2741	10	0.52906	T	0.07	.	13.3249	0.60454	0.8637:0.1363:0.0:0.0	.	1564;1595;1395;1395;1564;1564	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	Q	1564;1595;1564;1564;1564;1564;1395;1395	ENSP00000295956:K1564Q;ENSP00000420213:K1595Q;ENSP00000351339:K1564Q;ENSP00000415599:K1564Q;ENSP00000232447:K1564Q;ENSP00000349819:K1564Q;ENSP00000418510:K1395Q;ENSP00000414532:K1395Q	ENSP00000295956:K1564Q	K	+	1	0	FLNB	58096764	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.034000	0.70933	1.108000	0.41662	0.528000	0.53228	AAA	.	.		0.433	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		C	58121724	A	C	58121724	3	2	85	1	0	0	0	0	1	0	0	0	5942	131	5	5	4897	5	FLNB	3	58121724	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	5865977	58121724	139900706	31	11396										
ARL13B	200894	hgsc.bcm.edu	37	chr3	93762021	93762021	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ttggactagtagaaaattatAaggaggcattaacacagcag	10	5	0	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:93762021A>T	ENST00000394222.3	+	7	1236	c.961A>T	c.(961-963)Aag>Tag	p.K321*	ARL13B_ENST00000471138.1_Nonsense_Mutation_p.K321*|ARL13B_ENST00000535334.1_Nonsense_Mutation_p.K218*|ARL13B_ENST00000303097.7_Nonsense_Mutation_p.K214*|ARL13B_ENST00000539730.1_Nonsense_Mutation_p.K42*	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	321					cilium assembly (GO:0042384)|dorsal/ventral pattern formation (GO:0009953)|formation of radial glial scaffolds (GO:0021943)|heart looping (GO:0001947)|interneuron migration from the subpallium to the cortex (GO:0021830)|left/right axis specification (GO:0070986)|neural tube patterning (GO:0021532)|nonmotile primary cilium assembly (GO:0035058)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|intracellular (GO:0005622)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(2)	10						AGAAAATTATAAGGAGGCATT	0.343																																					p.K321X		Atlas-SNP	.											.	ARL13B	52	.	0			c.A961T						.						78	79	78					3																	93762021		2203	4300	6503	SO:0001587	stop_gained	200894	exon7			AATTATAAGGAGG	AL713789	CCDS2924.1, CCDS2925.1, CCDS54615.1	3q11	2014-05-09	2005-11-18	2005-11-18	ENSG00000169379	ENSG00000169379		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	25419	protein-coding gene	gene with protein product		608922	"ADP-ribosylation factor-like 2-like 1"	ARL2L1		15314642, 18674751	Standard	NR_033427		Approved	DKFZp761H079, JBTS8	uc003drf.3	Q3SXY8	OTTHUMG00000159012	ENST00000394222.3:c.961A>T	chr3.hg19:g.93762021A>T	ENSP00000377769:p.Lys321*	691.0	0.0		448.0	142.0	NM_182896	D3DN29|G3V1S8|Q504W8|Q8TCL5	Nonsense_Mutation	SNP	ENST00000394222.3	hg19	CCDS2925.1	.	.	.	.	.	.	.	.	.	.	A	37	6.139759	0.97320	.	.	ENSG00000169379	ENST00000535334;ENST00000303097;ENST00000394222;ENST00000471138;ENST00000539730	.	.	.	5.33	1.57	0.23409	.	0.599838	0.18355	N	0.143756	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.3737	5.6445	0.17582	0.712:0.1445:0.1436:0.0	.	.	.	.	X	218;214;321;321;42	.	ENSP00000306225:K214X	K	+	1	0	ARL13B	95244711	0.994000	0.37717	0.869000	0.34112	0.827000	0.46813	2.545000	0.45769	0.098000	0.17522	0.533000	0.62120	AAG	.	.		0.343	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896		T	93762021	A	T	93762021	4	4	85	1	0	0	0	0	0	1	0	0	929	363	13	4	987	4	ARL13B	3	93762021	Nonsense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	35640297	93762021	104260409	32	11397										
POPDC2	64091	hgsc.bcm.edu	37	chr3	119378986	119378986	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tcctcacgcaggcggtatacCaggtgtgccagctggagcag	14	12	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:119378986C>T	ENST00000264231.3	-	1	451	c.285G>A	c.(283-285)ctG>ctA	p.L95L	POPDC2_ENST00000538678.1_Silent_p.L95L|POPDC2_ENST00000468801.1_Silent_p.L95L|POPDC2_ENST00000493094.1_Silent_p.L95L|POPDC2_ENST00000474523.1_Intron	NM_022135.2	NP_071418.2	Q9HBU9	POPD2_HUMAN	popeye domain containing 2	95					regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sinoatrial node cell development (GO:0060931)	integral component of membrane (GO:0016021)	cAMP binding (GO:0030552)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.242)		GGCGGTATACCAGGTGTGCCA	0.597																																					p.L95L		Atlas-SNP	.											.	POPDC2	36	.	0			c.G285A						.						130	113	119					3																	119378986		2203	4300	6503	SO:0001819	synonymous_variant	64091	exon1			GTATACCAGGTGT	AF204173	CCDS2992.1	3q13.33	2004-01-15			ENSG00000121577	ENSG00000121577			17648	protein-coding gene	gene with protein product		605823				10882522	Standard	NM_022135		Approved	POP2	uc031sbc.1	Q9HBU9	OTTHUMG00000159438	ENST00000264231.3:c.285G>A	chr3.hg19:g.119378986C>T		106.0	0.0		87.0	22.0	NM_022135	Q86UE7	Silent	SNP	ENST00000264231.3	hg19	CCDS2992.1																																																																																			.	.		0.597	POPDC2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355378.1	NM_022135		T	119378986	C	T	119378986	2	4	85	1	0	0	0	0	0	0	0	1	12264	581	21	3		3	POPDC2	3	119378986	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	25616965	119378986	78643444	33	11398										
RAB43	339122	hgsc.bcm.edu	37	chr3	128813830	128813830	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cgaggaatccccaactcaccGatcagcagctgcacaatgtt	8	14	2	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:128813830G>C	ENST00000315150.5	-	2	687	c.387C>G	c.(385-387)atC>atG	p.I129M	ISY1-RAB43_ENST00000418265.1_3'UTR|RAB43_ENST00000393308.1_Splice_Site_p.I129M|RAB43_ENST00000393305.1_Splice_Site_p.I129M|RAB43_ENST00000476465.1_Splice_Site_p.I129M|RAB43_ENST00000393307.1_Splice_Site_p.I129M|RAB43_ENST00000393304.1_Splice_Site_p.I129M	NM_001204888.1|NM_198490.2	NP_001191817.1|NP_940892.1	Q86YS6	RAB43_HUMAN	RAB43, member RAS oncogene family	129					Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|phagosome maturation (GO:0090382)|protein transport (GO:0015031)|retrograde transport, plasma membrane to Golgi (GO:0035526)|small GTPase mediated signal transduction (GO:0007264)|virion assembly (GO:0019068)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(2)|liver(1)|lung(2)|skin(1)	6						CCAACTCACCGATCAGCAGCT	0.537																																					p.I129M		Atlas-SNP	.											.	RAB43	13	.	0			c.C387G						.						146	114	125					3																	128813830		2203	4300	6503	SO:0001630	splice_region_variant	339122	exon3			CTCACCGATCAGC	AY166852	CCDS33850.1, CCDS56275.1	3q21.3	2010-03-30			ENSG00000172780	ENSG00000172780		"RAB, member RAS oncogene"	19983	protein-coding gene	gene with protein product						15018353	Standard	NM_198490		Approved	RAB41, RAB11B, ISY1	uc021xdp.1	Q86YS6	OTTHUMG00000137364	ENST00000315150.5:c.388+1C>G	chr3.hg19:g.128813830G>C		54.0	0.0		32.0	10.0	NM_001204886	A8K4P9|E9PBQ0	Missense_Mutation	SNP	ENST00000315150.5	hg19	CCDS33850.1	.	.	.	.	.	.	.	.	.	.	G	9.496	1.101877	0.20632	.	.	ENSG00000172780	ENST00000315150;ENST00000393304;ENST00000393308;ENST00000393307;ENST00000393305;ENST00000476465	T;T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45;4.93	4.59	-6.45	0.01914	Small GTP-binding protein domain (1);	.	.	.	.	D	0.87943	0.6305	M	0.84511	2.7	0.80722	D	1	P;P	0.48764	0.723;0.915	D;D	0.63597	0.915;0.916	D	0.89033	0.3443	9	0.72032	D	0.01	.	15.3967	0.74801	0.6546:0.0:0.3454:0.0	.	129;129	E9PBQ0;Q86YS6	.;RAB43_HUMAN	M	129	ENSP00000319781:I129M;ENSP00000376981:I129M;ENSP00000376985:I129M;ENSP00000376984:I129M;ENSP00000376982:I129M;ENSP00000427632:I129M	ENSP00000319781:I129M	I	-	3	3	RAB43	130296520	0.000000	0.05858	0.602000	0.28890	0.243000	0.25628	-2.462000	0.00997	-1.910000	0.01083	-1.583000	0.00853	ATC	.	.		0.537	RAB43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267849.1	XM_290714	Missense_Mutation	C	128813830	G	C	128813830	5	2	85	1	0	0	0	0	0	0	1	0	12960	1072	37	4	259	4	RAB43	3	128813830	Splice_Site	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	9434844	128813830	69208600	34	11399										
BDH1	622	hgsc.bcm.edu	37	chr3	197238829	197238829	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gtcatgatctgcattcgcagCcaccagtagtagtccatggg	11	11	2	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr3:197238829C>A	ENST00000392378.2	-	7	1279	c.969G>T	c.(967-969)tgG>tgT	p.W323C	BDH1_ENST00000392379.1_Missense_Mutation_p.W323C|BDH1_ENST00000441275.1_Missense_Mutation_p.W236C|BDH1_ENST00000358186.2_Missense_Mutation_p.W323C	NM_004051.4	NP_004042.1	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1	323					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|response to cadmium ion (GO:0046686)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to growth hormone (GO:0060416)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|phospholipid binding (GO:0005543)			endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)		GCATTCGCAGCCACCAGTAGT	0.602																																					p.W323C		Atlas-SNP	.											.	BDH1	24	.	0			c.G969T						.						133	124	127					3																	197238829		2203	4300	6503	SO:0001583	missense	622	exon7			TCGCAGCCACCAG	M93107	CCDS3328.1	3q29	2011-09-14	2005-11-15	2005-11-15	ENSG00000161267	ENSG00000161267	1.1.1.30	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	1027	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 9C, member 1"	603063	"3-hydroxybutyrate dehydrogenase (heart, mitochondrial)"	BDH		1639787, 19027726	Standard	XM_005269352		Approved	SDR9C1	uc003fxs.3	Q02338	OTTHUMG00000155478	ENST00000392378.2:c.969G>T	chr3.hg19:g.197238829C>A	ENSP00000376183:p.Trp323Cys	119.0	0.0		92.0	29.0	NM_004051	D3DXC0|Q96ET1|Q9BRZ4	Missense_Mutation	SNP	ENST00000392378.2	hg19	CCDS3328.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.528445	0.85706	.	.	ENSG00000161267	ENST00000392378;ENST00000358186;ENST00000392379;ENST00000441275	D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15	5.85	5.85	0.93711	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.96632	0.8901	M	0.83774	2.66	0.80722	D	1	D	0.71674	0.998	D	0.64144	0.922	D	0.96505	0.9374	10	0.66056	D	0.02	.	18.0364	0.89305	0.0:1.0:0.0:0.0	.	323	Q02338	BDH_HUMAN	C	323;323;323;236	ENSP00000376183:W323C;ENSP00000350914:W323C;ENSP00000376184:W323C;ENSP00000411014:W236C	ENSP00000350914:W323C	W	-	3	0	BDH1	198723226	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	TGG	.	.		0.602	BDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340267.1	NM_004051		A	197238829	C	A	197238829	3	1	85	1	0	0	0	0	1	0	0	0	1390	740	26	3	66	3	BDH1	3	197238829	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	68424999	197238829	783601	35	11400										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6052342	6052342	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gacagaacagctggagagcgCtgctgtggttctcggggaag	17	8	1	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr4:6052342C>A	ENST00000409021.3	-	14	2320	c.1871G>T	c.(1870-1872)aGc>aTc	p.S624I	JAKMIP1_ENST00000409371.3_Missense_Mutation_p.S439I	NM_001099433.1	NP_001092903.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	0	Mediates interaction with TYK2 and GABBR1.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CTGGAGAGCGCTGCTGTGGTT	0.562																																					p.S624I		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.G1871T						.						85	93	91					4																	6052342		2034	4164	6198	SO:0001583	missense	152789	exon14			AGAGCGCTGCTGT	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000409021.3:c.1871G>T	chr4.hg19:g.6052342C>A	ENSP00000386711:p.Ser624Ile	116.0	0.0		91.0	64.0	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000409021.3	hg19	CCDS47005.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.457624	0.84317	.	.	ENSG00000152969	ENST00000409021;ENST00000409371	T;T	0.51325	1.15;0.71	5.1	5.1	0.69264	.	.	.	.	.	T	0.59891	0.2227	.	.	.	0.80722	D	1	P;D	0.54964	0.693;0.969	P;P	0.52424	0.588;0.698	T	0.63431	-0.6639	8	0.52906	T	0.07	.	17.5397	0.87843	0.0:1.0:0.0:0.0	.	439;624	Q96N16-5;Q96N16-2	.;.	I	624;439	ENSP00000386711:S624I;ENSP00000387042:S439I	ENSP00000386711:S624I	S	-	2	0	JAKMIP1	6103243	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.374000	0.73132	2.375000	0.81037	0.555000	0.69702	AGC	.	.		0.562	JAKMIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329747.1	NM_144720		A	6052342	C	A	6052342	3	1	85	1	0	0	0	0	1	0	0	0	7949	797	28	3	656	3	JAKMIP1	4	6052342	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10		6052342	185101934	36	11401										
TLL1	7092	hgsc.bcm.edu	37	chr4	167020562	167020562	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gaacggggctctcgacttgaAttatccttccagacatttga	9	10	1	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr4:167020562A>T	ENST00000061240.2	+	20	3437	c.2790A>T	c.(2788-2790)gaA>gaT	p.E930D	TLL1_ENST00000507499.1_Missense_Mutation_p.E953D	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	930	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		CTCGACTTGAATTATCCTTCC	0.463																																					p.E930D		Atlas-SNP	.											.	TLL1	194	.	0			c.A2790T						.						206	196	199					4																	167020562		2203	4300	6503	SO:0001583	missense	7092	exon20			ACTTGAATTATCC	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2790A>T	chr4.hg19:g.167020562A>T	ENSP00000061240:p.Glu930Asp	228.0	1.0		193.0	127.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	hg19	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	A	14.58	2.578925	0.46006	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	T;T	0.18960	2.18;2.18	5.76	-4.91	0.03085	CUB (5);	0.000000	0.85682	U	0.000000	T	0.47507	0.1449	M	0.91196	3.185	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.83275	0.996;0.992	T	0.59220	-0.7495	10	0.36615	T	0.2	.	15.0015	0.71476	0.6781:0.0:0.3219:0.0	.	953;930	E9PD25;O43897	.;TLL1_HUMAN	D	930;953	ENSP00000061240:E930D;ENSP00000426082:E953D	ENSP00000061240:E930D	E	+	3	2	TLL1	167240012	0.988000	0.35896	0.245000	0.24217	0.000000	0.00434	0.319000	0.19522	-0.830000	0.04262	-1.782000	0.00648	GAA	.	.		0.463	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			T	167020562	A	T	167020562	3	4	85	1	0	0	0	0	1	0	0	0	15960	98	4	4	2868	4	TLL1	4	167020562	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	160968220	167020562	24133714	37	11402										
SLC9A3	6550	hgsc.bcm.edu	37	chr5	484645	484645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	agggactcacgcgaggatggCcgacagcgacagcatctcgg	15	12	2	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr5:484645C>T	ENST00000264938.3	-	5	931	c.922G>A	c.(922-924)Gcc>Acc	p.A308T	SLC9A3_ENST00000514375.1_Missense_Mutation_p.A308T	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	308					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			GCGAGGATGGCCGACAGCGAC	0.642																																					p.A308T		Atlas-SNP	.											.	SLC9A3	89	.	0			c.G922A						.						143	107	119					5																	484645		2201	4300	6501	SO:0001583	missense	6550	exon5			GGATGGCCGACAG		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.922G>A	chr5.hg19:g.484645C>T	ENSP00000264938:p.Ala308Thr	131.0	0.0		152.0	72.0	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	hg19	CCDS3855.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.026719	0.54683	.	.	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.16897	2.31;2.31	4.31	-0.023	0.13945	Cation/H+ exchanger (1);	0.389797	0.27807	N	0.017780	T	0.35970	0.0950	M	0.81497	2.545	0.25061	N	0.991064	D;P	0.55605	0.972;0.698	P;P	0.57679	0.825;0.451	T	0.36432	-0.9748	10	0.72032	D	0.01	.	14.1259	0.65219	0.6891:0.3109:0.0:0.0	.	308;308	E9PF67;P48764	.;SL9A3_HUMAN	T	308	ENSP00000264938:A308T;ENSP00000422983:A308T	ENSP00000264938:A308T	A	-	1	0	SLC9A3	537645	0.710000	0.27896	0.126000	0.21872	0.391000	0.30476	1.401000	0.34589	-0.433000	0.07286	0.561000	0.74099	GCC	.	.		0.642	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		T	484645	C	T	484645	3	4	85	1	0	0	0	0	1	0	0	0	14728	739	26	3	1634	3	SLC9A3	5	484645	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10		484645	180430615	38	11403										
MYO10	4651	hgsc.bcm.edu	37	chr5	16701801	16701801	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tcctgctgctccttcatgcgCtgcaggtcctcgatttcttt	8	14	2	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr5:16701801C>T	ENST00000513610.1	-	25	3157	c.2703G>A	c.(2701-2703)caG>caA	p.Q901Q	MYO10_ENST00000505695.1_Silent_p.Q240Q|MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000274203.9_Silent_p.Q258Q|MYO10_ENST00000427430.2_Silent_p.Q258Q|MYO10_ENST00000515803.1_Silent_p.Q240Q	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	901	Mediates antiparallel dimerization.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CCTTCATGCGCTGCAGGTCCT	0.587																																					p.Q901Q		Atlas-SNP	.											.	MYO10	198	.	0			c.G2703A						.						42	46	44					5																	16701801		2117	4252	6369	SO:0001819	synonymous_variant	4651	exon25			CATGCGCTGCAGG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2703G>A	chr5.hg19:g.16701801C>T		62.0	0.0		66.0	17.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.587	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16701801	C	T	16701801	2	4	85	1	0	0	0	0	0	0	0	1	10071	796	28	3		3	MYO10	5	16701801	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	16217156	16701801	164213459	39	11404										
CAST	831	hgsc.bcm.edu	37	chr5	96100971	96100971	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cttggataaactctctgacaGtctaggacaaaggcagcctg	10	10	2	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr5:96100971G>A	ENST00000341926.3	+	24	1892	c.1730G>A	c.(1729-1731)aGt>aAt	p.S577N	CAST_ENST00000359176.4_Missense_Mutation_p.S641N|CAST_ENST00000509903.1_Missense_Mutation_p.S542N|CAST_ENST00000395813.1_Missense_Mutation_p.S660N|CAST_ENST00000348386.3_3'UTR|CAST_ENST00000508608.1_Missense_Mutation_p.S623N|CAST_ENST00000338252.3_Missense_Mutation_p.S564N|CAST_ENST00000325674.7_Missense_Mutation_p.S625N|CAST_ENST00000395812.2_Missense_Mutation_p.S619N|CAST_ENST00000508579.1_Missense_Mutation_p.S292N|CAST_ENST00000511049.1_Missense_Mutation_p.S562N|CAST_ENST00000309190.5_Missense_Mutation_p.S555N|CAST_ENST00000510756.1_Missense_Mutation_p.S638N|ERAP1_ENST00000296754.3_Intron|CAST_ENST00000515663.1_Missense_Mutation_p.S300N|CAST_ENST00000511782.1_Missense_Mutation_p.S563N|CAST_ENST00000504465.1_Missense_Mutation_p.S505N|CAST_ENST00000508830.1_Missense_Mutation_p.S660N			P20810	ICAL_HUMAN	calpastatin	577					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		CTCTCTGACAGTCTAGGACAA	0.353																																					p.S619N		Atlas-SNP	.											.	CAST	58	.	0			c.G1856A						.						134	135	135					5																	96100971		2203	4300	6503	SO:0001583	missense	831	exon24			CTGACAGTCTAGG	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.1730G>A	chr5.hg19:g.96100971G>A	ENSP00000339914:p.Ser577Asn	208.0	0.0		288.0	103.0	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Missense_Mutation	SNP	ENST00000341926.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.38|19.38	3.817343|3.817343	0.70912|0.70912	.|.	.|.	ENSG00000153113|ENSG00000153113	ENST00000338252;ENST00000508830;ENST00000395813;ENST00000359176;ENST00000325674;ENST00000395812;ENST00000510756;ENST00000508608;ENST00000341926;ENST00000511049;ENST00000309190;ENST00000510156;ENST00000504465;ENST00000509903;ENST00000511782;ENST00000508579;ENST00000515663|ENST00000437034	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.30182|.	1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54|.	5.8|5.8	4.89|4.89	0.63831|0.63831	.|.	0.231496|.	0.42682|.	D|.	0.000667|.	T|T	0.80037|0.80037	0.4550|0.4550	M|M	0.88105|0.88105	2.93|2.93	0.80722|0.80722	D|D	1|1	P;P;D;D;D;P;D;P;P;D;P;D;P;P;D;P|.	0.76494|.	0.88;0.837;0.999;0.996;0.999;0.929;0.961;0.855;0.915;0.999;0.855;0.998;0.944;0.804;0.999;0.855|.	P;P;D;D;D;P;P;P;P;D;P;D;P;P;D;P|.	0.91635|.	0.745;0.692;0.979;0.93;0.979;0.889;0.889;0.69;0.628;0.999;0.697;0.998;0.842;0.566;0.998;0.69|.	T|T	0.82859|0.82859	-0.0249|-0.0249	10|5	0.54805|.	T|.	0.06|.	-9.419|-9.419	14.674|14.674	0.68964|0.68964	0.0:0.245:0.755:0.0|0.0:0.245:0.755:0.0	.|.	505;623;300;328;299;562;542;555;536;577;625;619;641;638;660;564|.	E9PDE4;B7Z468;E7EQA0;Q86YM9;E7EPY6;E7EVY3;E9PCH5;G5E946;P20810-4;P20810;P20810-5;G5E9D3;P20810-7;E7ESM9;P20810-6;P20810-2|.	.;.;.;.;.;.;.;.;.;ICAL_HUMAN;.;.;.;.;.;.|.	N|I	564;660;660;641;625;619;638;623;577;562;555;577;505;542;563;292;300|329	ENSP00000343421:S564N;ENSP00000425721:S660N;ENSP00000379158:S660N;ENSP00000352098:S641N;ENSP00000320319:S625N;ENSP00000379157:S619N;ENSP00000422176:S638N;ENSP00000422677:S623N;ENSP00000339914:S577N;ENSP00000421130:S562N;ENSP00000312523:S555N;ENSP00000422325:S577N;ENSP00000425670:S505N;ENSP00000426946:S542N;ENSP00000423638:S563N;ENSP00000425787:S292N;ENSP00000422929:S300N|.	ENSP00000312523:S555N|.	S|V	+|+	2|1	0|0	CAST|CAST	96126727|96126727	0.989000|0.989000	0.36119|0.36119	1.000000|1.000000	0.80357|0.80357	0.888000|0.888000	0.51559|0.51559	2.257000|2.257000	0.43240|0.43240	2.735000|2.735000	0.93741|0.93741	0.655000|0.655000	0.94253|0.94253	AGT|GTC	.	.		0.353	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062		A	96100971	G	A	96100971	3	1	85	1	0	0	0	0	1	0	0	0	2686	1029	36	3	2205	3	CAST	5	96100971	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	79399170	96100971	84814289	40	11405										
TSLP	85480	hgsc.bcm.edu	37	chr5	110409265	110409265	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	aatcccaccgccggctgcgcGtcgctcgccaaagaaatgtt	10	15	0	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr5:110409265G>T	ENST00000344895.3	+	3	472	c.273G>T	c.(271-273)gcG>gcT	p.A91A	TSLP_ENST00000420978.2_Silent_p.A91A|TSLP_ENST00000379706.4_5'UTR	NM_033035.4	NP_149024.1	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin	91						extracellular space (GO:0005615)				breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)		CCGGCTGCGCGTCGCTCGCCA	0.522																																					p.A91A		Atlas-SNP	.											.	TSLP	22	.	0			c.G273T						.						144	153	150					5																	110409265		2202	4300	6502	SO:0001819	synonymous_variant	85480	exon3			CTGCGCGTCGCTC	BC040592	CCDS4101.1	5q22.1	2007-08-24			ENSG00000145777	ENSG00000145777			30743	protein-coding gene	gene with protein product		607003				11418668, 11480573	Standard	NM_033035		Approved		uc003kpb.2	Q969D9	OTTHUMG00000128791	ENST00000344895.3:c.273G>T	chr5.hg19:g.110409265G>T		213.0	0.0		287.0	122.0	NM_033035	Q8IW99	Silent	SNP	ENST00000344895.3	hg19	CCDS4101.1																																																																																			.	.		0.522	TSLP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250717.1	NM_033035		T	110409265	G	T	110409265	2	4	85	1	0	0	0	0	0	0	0	1	16643	1132	40	1		1	TSLP	5	110409265	Silent	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	14308294	110409265	70505995	41	11406										
PCDHGA9	56107	hgsc.bcm.edu	37	chr5	140782595	140782595	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tcctggggatgctatgggagGccagggccagtcagattcgc	16	10	1	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr5:140782595G>T	ENST00000573521.1	+	1	76	c.76G>T	c.(76-78)Gcc>Tcc	p.A26S	PCDHGA5_ENST00000518069.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	26					homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTATGGGAGGCCAGGGCCAG	0.562																																					p.A26S		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.G76T						.						48	55	53					5																	140782595		2074	4241	6315	SO:0001583	missense	56107	exon1			TGGGAGGCCAGGG	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.76G>T	chr5.hg19:g.140782595G>T	ENSP00000460274:p.Ala26Ser	92.0	0.0		148.0	52.0	NM_032089	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	hg19	CCDS58981.1																																																																																			.	.		0.562	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921		T	140782595	G	T	140782595	3	4	85	1	0	0	0	0	1	0	0	0	11570	1203	42	3	78	3	PCDHGA9	5	140782595	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	30373330	140782595	40132665	42	11407										
FCHSD1	89848	hgsc.bcm.edu	37	chr5	141021270	141021270	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ccaaggcaagggcccttaccGgcctgagtcgaggtgccatc	13	14	0	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr5:141021270G>A	ENST00000435817.2	-	19	2056	c.2006C>T	c.(2005-2007)cCg>cTg	p.P669L	FCHSD1_ENST00000523856.1_5'UTR|FCHSD1_ENST00000522126.1_3'UTR|FCHSD1_ENST00000522783.1_3'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	669	Pro-rich.								FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCCCTTACCGGCCTGAGTCG	0.502																																					p.P669L		Atlas-SNP	.											.	FCHSD1	51	.	0			c.C2006T						.						75	78	77					5																	141021270		1908	4138	6046	SO:0001630	splice_region_variant	89848	exon19			CTTACCGGCCTGA	AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.2007+1C>T	chr5.hg19:g.141021270G>A		107.0	0.0		132.0	55.0	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	hg19	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.164558	0.57476	.	.	ENSG00000197948	ENST00000435817	T	0.33865	1.39	5.2	5.2	0.72013	.	0.074967	0.53938	D	0.000052	T	0.48295	0.1492	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.31052	-0.9957	10	0.42905	T	0.14	0.012	14.4281	0.67230	0.0:0.0:1.0:0.0	.	349;669	Q86WN1-2;Q86WN1	.;FCSD1_HUMAN	L	669	ENSP00000399259:P669L	ENSP00000399259:P669L	P	-	2	0	FCHSD1	141001454	1.000000	0.71417	1.000000	0.80357	0.706000	0.40770	2.978000	0.49305	2.861000	0.98227	0.655000	0.94253	CCG	.	.		0.502	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	Missense_Mutation	A	141021270	G	A	141021270	5	1	85	1	0	0	0	0	0	0	1	0	5797	1130	39	1	74	1	FCHSD1	5	141021270	Splice_Site	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	238675	141021270	39893990	43	11408										
DPYSL3	1809	hgsc.bcm.edu	37	chr5	146777290	146777290	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acgggctgcagggtatgaagCggccagccccctgggtcacg	16	13	1	1	rs377459296		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr5:146777290C>A	ENST00000398514.3	-	12	1771	c.1400G>T	c.(1399-1401)cGc>cTc	p.R467L	DPYSL3_ENST00000343218.5_Missense_Mutation_p.R581L|DPYSL3_ENST00000534907.1_Missense_Mutation_p.R93L	NM_001387.2	NP_001378.1	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	467					actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cell migration (GO:0030336)|negative regulation of neuron projection development (GO:0010977)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron projection development (GO:0010976)|protein homooligomerization (GO:0051260)|pyrimidine nucleobase catabolic process (GO:0006208)|response to axon injury (GO:0048678)	cell body (GO:0044297)|cytosol (GO:0005829)|extracellular space (GO:0005615)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|lamellipodium (GO:0030027)	chondroitin sulfate binding (GO:0035374)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)|SH3 domain binding (GO:0017124)			breast(2)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGTATGAAGCGGCCAGCCCC	0.567																																					p.R581L		Atlas-SNP	.											.	DPYSL3	58	.	0			c.G1742T						.						80	86	84					5																	146777290		2040	4184	6224	SO:0001583	missense	1809	exon12			ATGAAGCGGCCAG	D78014	CCDS43381.1, CCDS56387.1	5q32	2008-02-05							3015	protein-coding gene	gene with protein product		601168				8973361, 9115293	Standard	NM_001197294		Approved	DRP-3, ULIP, CRMP4	uc003loo.3	Q14195		ENST00000398514.3:c.1400G>T	chr5.hg19:g.146777290C>A	ENSP00000381526:p.Arg467Leu	44.0	0.0		45.0	23.0	NM_001197294	B3SXQ8|Q93012	Missense_Mutation	SNP	ENST00000398514.3	hg19	CCDS43381.1	.	.	.	.	.	.	.	.	.	.	C	35	5.532479	0.96446	.	.	ENSG00000113657	ENST00000398514;ENST00000343218;ENST00000534907	T;T;T	0.76839	-1.05;-1.05;-1.05	6.03	6.03	0.97812	Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.90943	0.7153	M	0.93808	3.46	0.80722	D	1	D;D	0.69078	0.997;0.994	P;P	0.61533	0.89;0.663	D	0.92247	0.5805	10	0.87932	D	0	-15.4814	20.5753	0.99366	0.0:1.0:0.0:0.0	.	581;467	B3SXQ8;Q14195	.;DPYL3_HUMAN	L	467;581;93	ENSP00000381526:R467L;ENSP00000343690:R581L;ENSP00000441819:R93L	ENSP00000343690:R581L	R	-	2	0	DPYSL3	146757483	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	6.046000	0.71029	2.868000	0.98415	0.557000	0.71058	CGC	.	.		0.567	DPYSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373421.2	NM_001387		A	146777290	C	A	146777290	3	1	85	1	0	0	0	0	1	0	0	0	4750	768	27	1	324	1	DPYSL3	5	146777290	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	5756020	146777290	34137970	44	11409										
ALDH5A1	7915	hgsc.bcm.edu	37	chr6	24495386	24495386	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gctgggcgcctggcgggcctCtctgcggcgctgctgcgcac	17	16	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr6:24495386C>T	ENST00000357578.3	+	1	307	c.162C>T	c.(160-162)ctC>ctT	p.L54L	GPLD1_ENST00000474784.1_5'UTR|ALDH5A1_ENST00000491546.1_Silent_p.L54L|ALDH5A1_ENST00000546278.1_Intron|ALDH5A1_ENST00000348925.2_Silent_p.L54L	NM_001080.3	NP_001071.1	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5 family, member A1	54					acetate metabolic process (GO:0006083)|central nervous system development (GO:0007417)|galactosylceramide metabolic process (GO:0006681)|gamma-aminobutyric acid catabolic process (GO:0009450)|glucose metabolic process (GO:0006006)|glucosylceramide metabolic process (GO:0006678)|glutamate metabolic process (GO:0006536)|glutamine metabolic process (GO:0006541)|glutathione metabolic process (GO:0006749)|glycerophospholipid metabolic process (GO:0006650)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|respiratory electron transport chain (GO:0022904)|short-chain fatty acid metabolic process (GO:0046459)|succinate metabolic process (GO:0006105)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	protein homodimerization activity (GO:0042803)|succinate-semialdehyde dehydrogenase (NAD+) activity (GO:0004777)|succinate-semialdehyde dehydrogenase [NAD(P)+] activity (GO:0009013)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|skin(2)|urinary_tract(1)	20					Chlormerodrin(DB00534)|Succinic acid(DB00139)|Valproic Acid(DB00313)	TGGCGGGCCTCTCTGCGGCGC	0.816																																					p.L54L		Atlas-SNP	.											.	ALDH5A1	42	.	0			c.C162T						.						1	1	1					6																	24495386		249	517	766	SO:0001819	synonymous_variant	7915	exon1			GGGCCTCTCTGCG	L34820	CCDS4555.1, CCDS4556.1	6p22	2013-06-03	2008-07-31		ENSG00000112294	ENSG00000112294	1.2.1.24	"Aldehyde dehydrogenases"	408	protein-coding gene	gene with protein product	"succinate-semialdehyde dehydrogenase"	610045				7814412, 9059628	Standard	NM_001080		Approved	SSADH, SSDH	uc003nef.3	P51649	OTTHUMG00000014356	ENST00000357578.3:c.162C>T	chr6.hg19:g.24495386C>T		51.0	0.0		82.0	31.0	NM_001080	B2RD26|G5E949|Q546H9|Q8N3W6	Silent	SNP	ENST00000357578.3	hg19	CCDS4555.1																																																																																			.	.		0.816	ALDH5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040007.2			T	24495386	C	T	24495386	2	4	85	1	0	0	0	0	0	0	0	1	502	900	32	3		3	ALDH5A1	6	24495386	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10		24495386	146619681	45	11410										
HIST1H2BC	8347	hgsc.bcm.edu	37	chr6	26123951	26123951	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	taacgaaagaattcatgatgCccatggccttggaagagatg	11	7	1	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr6:26123951C>A	ENST00000314332.5	-	1	187	c.182G>T	c.(181-183)gGc>gTc	p.G61V	HIST1H2AC_ENST00000602637.1_5'Flank|HIST1H2BC_ENST00000396984.1_Missense_Mutation_p.G61V|HIST1H2AC_ENST00000377791.2_5'Flank			P62807	H2B1C_HUMAN	histone cluster 1, H2bc	61					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.G61D(1)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	16						ATTCATGATGCCCATGGCCTT	0.552																																					p.G61V		Atlas-SNP	.											HIST1H2BC,tonsil,lymphoid_neoplasm,0,1	HIST1H2BC	35	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G182T						.						173	161	165					6																	26123951		2203	4300	6503	SO:0001583	missense	8347	exon1			ATGATGCCCATGG	Z80783	CCDS4584.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000180596	ENSG00000180596		"Histones / Replication-dependent"	4757	protein-coding gene	gene with protein product		602847	"H2B histone family, member L", "histone 1, H2bc"	H2BFL		9119399, 12408966	Standard	NM_003526		Approved	H2B/l, H2B.1	uc003ngl.3	P62807	OTTHUMG00000014425	ENST00000314332.5:c.182G>T	chr6.hg19:g.26123951C>A	ENSP00000321744:p.Gly61Val	104.0	0.0		98.0	49.0	NM_003526	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000314332.5	hg19	CCDS4584.1	.	.	.	.	.	.	.	.	.	.	.	19.20	3.781435	0.70222	.	.	ENSG00000180596	ENST00000314332;ENST00000396984	T;T	0.21543	2.0;2.0	5.61	5.61	0.85477	Histone-fold (2);Histone core (1);	.	.	.	.	T	0.38374	0.1038	.	.	.	0.58432	D	0.999999	P	0.49783	0.928	P	0.59703	0.862	T	0.10200	-1.0640	8	0.66056	D	0.02	.	18.9929	0.92801	0.0:1.0:0.0:0.0	.	61	P62807	H2B1C_HUMAN	V	61	ENSP00000321744:G61V;ENSP00000380180:G61V	ENSP00000321744:G61V	G	-	2	0	HIST1H2BC	26231930	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	5.828000	0.69307	2.799000	0.96334	0.650000	0.86243	GGC	.	.		0.552	HIST1H2BC-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468022.1	NM_003526		A	26123951	C	A	26123951	3	1	85	1	0	0	0	0	1	0	0	0	7151	739	26	3	202	3	HIST1H2BC	6	26123951	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	1628565	26123951	144991116	46	11411										
HIST1H2AK	8330	hgsc.bcm.edu	37	chr6	27805803	27805803	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	atattgggcaggacaccaccCtgggcgatggtcactttacc	11	12	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr6:27805803C>A	ENST00000330180.2	-	1	314	c.315G>T	c.(313-315)caG>caT	p.Q105H	HIST1H2BN_ENST00000606613.1_5'Flank|HIST1H2BN_ENST00000396980.3_5'Flank	NM_003510.2	NP_003501.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ak	105						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(2)|endometrium(2)|kidney(1)|lung(3)|upper_aerodigestive_tract(2)	10						GGACACCACCCTGGGCGATGG	0.587																																					p.Q105H		Atlas-SNP	.											.	HIST1H2AK	28	.	0			c.G315T						.						112	111	112					6																	27805803		2203	4300	6503	SO:0001583	missense	8330	exon1			ACCACCCTGGGCG	Z83739	CCDS4632.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000184348	ENSG00000275221		"Histones / Replication-dependent"	4726	protein-coding gene	gene with protein product		602788	"H2A histone family, member D", "histone 1, H2ak"	H2AFD		9439656, 12408966	Standard	NM_003510		Approved	H2A/d	uc003njs.3	P0C0S8	OTTHUMG00000016382	ENST00000330180.2:c.315G>T	chr6.hg19:g.27805803C>A	ENSP00000330307:p.Gln105His	133.0	0.0		164.0	75.0	NM_003510	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000330180.2	hg19	CCDS4632.1	.	.	.	.	.	.	.	.	.	.	.	13.85	2.359331	0.41801	.	.	ENSG00000184348	ENST00000330180	T	0.43688	0.94	4.28	4.28	0.50868	.	0.000000	0.30168	U	0.010251	T	0.51686	0.1689	.	.	.	0.44000	D	0.996701	.	.	.	.	.	.	T	0.57207	-0.7851	7	0.62326	D	0.03	.	16.5671	0.84601	0.0:1.0:0.0:0.0	.	.	.	.	H	105	ENSP00000330307:Q105H	ENSP00000330307:Q105H	Q	-	3	2	HIST1H2AK	27913782	1.000000	0.71417	1.000000	0.80357	0.094000	0.18550	3.823000	0.55715	2.295000	0.77249	0.555000	0.69702	CAG	.	.		0.587	HIST1H2AK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043814.1	NM_003510		A	27805803	C	A	27805803	3	1	85	1	0	0	0	0	1	0	0	0	7146	680	24	3	81	3	HIST1H2AK	6	27805803	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	1681852	27805803	143309264	47	11412										
ZSCAN23	222696	hgsc.bcm.edu	37	chr6	28402493	28402493	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ggctttgccacaaacactgcActggtagcgcttctccccag	9	15	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr6:28402493A>G	ENST00000289788.4	-	4	1064	c.919T>C	c.(919-921)Tgc>Cgc	p.C307R	ZSCAN23_ENST00000486481.1_5'Flank	NM_001012455.1	NP_001012458.1	Q3MJ62	ZSC23_HUMAN	zinc finger and SCAN domain containing 23	307					transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|prostate(1)|stomach(2)	4						CAAACACTGCACTGGTAGCGC	0.532																																					p.C307R		Atlas-SNP	.											.	ZSCAN23	18	.	0			c.T919C						.						71	63	66					6																	28402493		692	1591	2283	SO:0001583	missense	222696	exon4			CACTGCACTGGTA	AK092117	CCDS47393.1	6p21.33	2013-01-08	2007-02-20	2007-02-20	ENSG00000187987	ENSG00000187987		"-", "Zinc fingers, C2H2-type"	21193	protein-coding gene	gene with protein product			"zinc finger protein 453", "zinc finger protein 390"	ZNF453, ZNF390			Standard	NM_001012455		Approved	dJ29K1.3.1	uc003nli.4	Q3MJ62	OTTHUMG00000016346	ENST00000289788.4:c.919T>C	chr6.hg19:g.28402493A>G	ENSP00000289788:p.Cys307Arg	61.0	0.0		90.0	20.0	NM_001012455	Q96KV9	Missense_Mutation	SNP	ENST00000289788.4	hg19	CCDS47393.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.085953	0.76642	.	.	ENSG00000187987	ENST00000289788	D	0.85258	-1.96	4.32	4.32	0.51571	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43747	D	0.000528	D	0.93609	0.7959	H	0.96916	3.905	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	D	0.94922	0.8074	10	0.87932	D	0	.	11.4771	0.50304	1.0:0.0:0.0:0.0	.	307	Q3MJ62	ZSC23_HUMAN	R	307	ENSP00000289788:C307R	ENSP00000289788:C307R	C	-	1	0	ZSCAN23	28510472	1.000000	0.71417	0.956000	0.39512	0.976000	0.68499	8.593000	0.90832	1.801000	0.52704	0.528000	0.53228	TGC	.	.		0.532	ZSCAN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043751.2	XM_167147		G	28402493	A	G	28402493	3	3	85	1	0	0	0	0	1	0	0	0	18250	159	6	2	254	2	ZSCAN23	6	28402493	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	596690	28402493	142712574	48	11413										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51907825	51907825	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acagactacattggtctggtTtgagaaaataactttgcaac	8	7	1	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr6:51907825T>C	ENST00000371117.3	-	27	3204	c.2929A>G	c.(2929-2931)Aac>Gac	p.N977D	PKHD1_ENST00000340994.4_Missense_Mutation_p.N977D	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	977	IPT/TIG 4.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TTGGTCTGGTTTGAGAAAATA	0.448																																					p.N977D		Atlas-SNP	.											.	PKHD1	927	.	0			c.A2929G						.						112	106	108					6																	51907825		2203	4300	6503	SO:0001583	missense	5314	exon27			TCTGGTTTGAGAA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.2929A>G	chr6.hg19:g.51907825T>C	ENSP00000360158:p.Asn977Asp	94.0	0.0		116.0	27.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	17.53	3.412681	0.62511	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.78707	-1.2;-1.2	5.98	5.98	0.97165	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.73345	0.3575	M	0.74881	2.28	0.33698	D	0.614125	B;P	0.48162	0.084;0.906	B;P	0.50754	0.1;0.649	T	0.73585	-0.3936	10	0.12103	T	0.63	.	13.9016	0.63806	0.0:0.0:0.0:1.0	.	977;977	P08F94-2;P08F94	.;PKHD1_HUMAN	D	977	ENSP00000360158:N977D;ENSP00000341097:N977D	ENSP00000341097:N977D	N	-	1	0	PKHD1	52015784	0.998000	0.40836	1.000000	0.80357	0.860000	0.49131	3.350000	0.52224	2.307000	0.77673	0.529000	0.55759	AAC	.	.		0.448	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		C	51907825	T	C	51907825	3	2	85	1	0	0	0	0	1	0	0	0	11980	1841	64	2	9498	2	PKHD1	6	51907825	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	23505332	51907825	119207242	49	11414										
REV3L	5980	hgsc.bcm.edu	37	chr6	111680114	111680114	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gcagtggagtgtcagatgagAtgcagtagaacagagcacag	15	6	1	4			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr6:111680114A>T	ENST00000358835.3	-	18	7437	c.6983T>A	c.(6982-6984)aTc>aAc	p.I2328N	REV3L_ENST00000368805.1_Missense_Mutation_p.I2328N|REV3L_ENST00000435970.1_Missense_Mutation_p.I2250N|REV3L_ENST00000368802.3_Missense_Mutation_p.I2328N|REV3L-IT1_ENST00000411895.1_RNA			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2328					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		GTCAGATGAGATGCAGTAGAA	0.418								DNA polymerases (catalytic subunits)																													p.I2328N		Atlas-SNP	.											.	REV3L	386	.	0			c.T6983A						.						162	150	154					6																	111680114		2203	4300	6503	SO:0001583	missense	5980	exon17			GATGAGATGCAGT	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.6983T>A	chr6.hg19:g.111680114A>T	ENSP00000351697:p.Ile2328Asn	115.0	0.0		124.0	65.0	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	A	25.6	4.653588	0.88056	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	T;T;T;T	0.11277	2.79;2.79;2.79;2.79	5.65	5.65	0.86999	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.253058	0.33772	N	0.004563	T	0.19208	0.0461	L	0.55834	1.745	0.50313	D	0.999863	D	0.55385	0.971	D	0.65323	0.934	T	0.00482	-1.1713	10	0.87932	D	0	.	15.883	0.79216	1.0:0.0:0.0:0.0	.	2328	O60673	DPOLZ_HUMAN	N	2328;2328;2328;2250;401	ENSP00000357792:I2328N;ENSP00000357795:I2328N;ENSP00000351697:I2328N;ENSP00000402003:I2250N	ENSP00000351697:I2328N	I	-	2	0	REV3L	111786807	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.721000	0.91446	2.150000	0.67090	0.455000	0.32223	ATC	.	.		0.418	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		T	111680114	A	T	111680114	3	4	85	1	0	0	0	0	1	0	0	0	13255	333	12	4	2473	4	REV3L	6	111680114	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	59772289	111680114	59434953	50	11415										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48428794	48428794	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	accgccctgctggggacaaaCggtgccgggaaaaccactat	12	13	0	0	rs374031988		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr7:48428794C>T	ENST00000435803.1	+	37	11655	c.11631C>T	c.(11629-11631)aaC>aaT	p.N3877N		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3877	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.N3822N(1)|p.N3877N(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TGGGGACAAACGGTGCCGGGA	0.493																																					p.N3877N		Atlas-SNP	.											ABCA13_ENST00000435803,caecum,carcinoma,0,2	ABCA13	1192	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C11631T						.	C		0,3780		0,0,1890	48	50	49		11631	-8.5	0	7		49	1,8251		0,1,4125	no	coding-synonymous	ABCA13	NM_152701.3		0,1,6015	TT,TC,CC		0.0121,0.0,0.0083		3877/5059	48428794	1,12031	1890	4126	6016	SO:0001819	synonymous_variant	154664	exon37			GACAAACGGTGCC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11631C>T	chr7.hg19:g.48428794C>T		150.0	0.0		172.0	59.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.493	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48428794	C	T	48428794	2	4	85	1	0	0	0	0	0	0	0	1	31	535	19	1		1	ABCA13	7	48428794	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10		48428794	110709869	51	11416										
EZH2	2146	hgsc.bcm.edu	37	chr7	148515060	148515060	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cctgcttccctatcactgtcTgtatcctttgattccagcac	5	15	2	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr7:148515060T>A	ENST00000460911.1	-	10	1222	c.1134A>T	c.(1132-1134)acA>acT	p.T378T	EZH2_ENST00000476773.1_Silent_p.T369T|EZH2_ENST00000541220.1_Silent_p.T369T|EZH2_ENST00000350995.2_Silent_p.T339T|EZH2_ENST00000478654.1_Silent_p.T369T|EZH2_ENST00000483967.1_Silent_p.T369T|EZH2_ENST00000320356.2_Silent_p.T383T			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	378	Interaction with CDYL.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			TATCACTGTCTGTATCCTTTG	0.507			Mis		DLBCL																																p.T383T		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	.	EZH2	823	.	0			c.A1149T						.						173	141	152					7																	148515060		2203	4300	6503	SO:0001819	synonymous_variant	2146	exon10			ACTGTCTGTATCC		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"Chromatin-modifying enzymes / K-methyltransferases"	3527	protein-coding gene	gene with protein product		601573	"enhancer of zeste (Drosophila) homolog 2", "enhancer of zeste homolog 2 (Drosophila)"			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.1134A>T	chr7.hg19:g.148515060T>A		95.0	0.0		139.0	58.0	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Silent	SNP	ENST00000460911.1	hg19	CCDS56516.1																																																																																			.	.		0.507	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		A	148515060	T	A	148515060	2	1	85	1	0	0	0	0	0	0	0	1	5336	1567	55	4		4	EZH2	7	148515060	Silent	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	100086266	148515060	10623603	52	11417										
TMEM176B	28959	hgsc.bcm.edu	37	chr7	150488705	150488705	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tagcctcttctctgatccttCctcattctggaaaaaaaaga	5	11	4	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr7:150488705C>A	ENST00000447204.2	-	7	1099	c.727G>T	c.(727-729)Gaa>Taa	p.E243*	TMEM176B_ENST00000434545.1_Nonsense_Mutation_p.E243*|TMEM176B_ENST00000450753.2_Nonsense_Mutation_p.E206*|TMEM176B_ENST00000492607.1_Nonsense_Mutation_p.E243*|TMEM176B_ENST00000429904.2_Nonsense_Mutation_p.E243*|TMEM176B_ENST00000326442.5_Nonsense_Mutation_p.E243*	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	243					cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCTGATCCTTCCTCATTCTGG	0.488																																					p.E243X		Atlas-SNP	.											.	TMEM176B	36	.	0			c.G727T						.						40	45	43					7																	150488705		2203	4300	6503	SO:0001587	stop_gained	28959	exon7			ATCCTTCCTCATT	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.727G>T	chr7.hg19:g.150488705C>A	ENSP00000410269:p.Glu243*	51.0	0.0		43.0	14.0	NM_014020	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Nonsense_Mutation	SNP	ENST00000447204.2	hg19	CCDS5908.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.327588	0.60743	.	.	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000450753;ENST00000528038	.	.	.	3.8	2.91	0.33838	.	0.964414	0.08446	N	0.944640	.	.	.	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-4.3687	7.2132	0.25945	0.0:0.8769:0.0:0.1231	.	.	.	.	X	243;243;243;243;243;206;243	.	ENSP00000318409:E243X	E	-	1	0	TMEM176B	150119638	0.017000	0.18338	0.006000	0.13384	0.019000	0.09904	0.273000	0.18662	0.950000	0.37743	0.557000	0.71058	GAA	.	.		0.488	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020		A	150488705	C	A	150488705	4	1	85	1	0	0	0	0	0	1	0	0	16108	864	30	3	89	3	TMEM176B	7	150488705	Nonsense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	1973645	150488705	8649958	53	11418										
ADAM32	203102	hgsc.bcm.edu	37	chr8	39022641	39022641	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acagttggtgaggcagatgaAttattgcaaaaatttttaga	10	3	0	4			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr8:39022641A>C	ENST00000379907.4	+	9	886	c.759A>C	c.(757-759)gaA>gaC	p.E253D	ADAM32_ENST00000437682.2_Missense_Mutation_p.E260D|ADAM32_ENST00000519315.1_Missense_Mutation_p.E253D	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	253	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			AGGCAGATGAATTATTGCAAA	0.303																																					p.E253D		Atlas-SNP	.											.	ADAM32	70	.	0			c.A759C						.						109	102	104					8																	39022641		1802	4076	5878	SO:0001583	missense	203102	exon9			AGATGAATTATTG	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"ADAM metallopeptidase domain containing"	15479	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 32"			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.759A>C	chr8.hg19:g.39022641A>C	ENSP00000369238:p.Glu253Asp	66.0	0.0		50.0	31.0	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	hg19	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	A	13.83	2.352992	0.41700	.	.	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907;ENST00000399826	T;T;T	0.63580	-0.05;-0.05;-0.05	5.09	2.63	0.31362	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.240568	0.21441	N	0.074483	T	0.44414	0.1292	N	0.05510	-0.035	0.23950	N	0.996379	B;B;B	0.28880	0.226;0.226;0.176	B;B;B	0.43386	0.262;0.418;0.267	T	0.41484	-0.9506	10	0.21540	T	0.41	.	4.5445	0.12074	0.7374:0.0:0.0929:0.1697	.	260;253;253	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	D	260;253;253;254	ENSP00000405978:E260D;ENSP00000429422:E253D;ENSP00000369238:E253D	ENSP00000369238:E253D	E	+	3	2	ADAM32	39141798	0.121000	0.22262	0.678000	0.29963	0.709000	0.40893	0.013000	0.13310	0.332000	0.23536	-0.379000	0.06801	GAA	.	.		0.303	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		C	39022641	A	C	39022641	3	2	85	1	0	0	0	0	1	0	0	0	249	98	4	5	793	5	ADAM32	8	39022641	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10		39022641	107341381	54	11419			1	13		2	2	15	N	T_A	5.833783e-05
ADAM32	203102	hgsc.bcm.edu	37	chr8	39022655	39022655	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	agatgaattattgcaaaaatTtttagaatggaaacaatctt	6	3	1	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr8:39022655T>C	ENST00000379907.4	+	9	900	c.773T>C	c.(772-774)tTt>tCt	p.F258S	ADAM32_ENST00000437682.2_Missense_Mutation_p.F265S|ADAM32_ENST00000519315.1_Missense_Mutation_p.F258S	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	258	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			TTGCAAAAATTTTTAGAATGG	0.303																																					p.F258S		Atlas-SNP	.											.	ADAM32	70	.	0			c.T773C						.						94	88	90					8																	39022655		1794	4070	5864	SO:0001583	missense	203102	exon9			AAAAATTTTTAGA	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"ADAM metallopeptidase domain containing"	15479	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 32"			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.773T>C	chr8.hg19:g.39022655T>C	ENSP00000369238:p.Phe258Ser	57.0	0.0		51.0	32.0	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	hg19	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.627337	0.66901	.	.	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907;ENST00000399826	T;T;T	0.73575	-0.76;-0.76;-0.76	5.09	5.09	0.68999	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.34291	N	0.004082	D	0.89347	0.6689	H	0.95574	3.69	0.39990	D	0.975028	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.92086	0.5676	10	0.87932	D	0	.	11.5338	0.50626	0.0:0.0:0.0:1.0	.	265;258;258	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	S	265;258;258;259	ENSP00000405978:F265S;ENSP00000429422:F258S;ENSP00000369238:F258S	ENSP00000369238:F258S	F	+	2	0	ADAM32	39141812	1.000000	0.71417	0.920000	0.36463	0.818000	0.46254	4.155000	0.58131	2.041000	0.60428	0.459000	0.35465	TTT	.	.		0.303	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		C	39022655	T	C	39022655	3	2	85	1	0	0	0	0	1	0	0	0	249	1841	64	2	807	2	ADAM32	8	39022655	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	14	39022655	107341367	55	11420			1	13		2	2	15	N	T_A	5.833783e-05
NUDCD1	84955	hgsc.bcm.edu	37	chr8	110305580	110305580	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acttttgttttaccttgattTttcttactgatagtgaccca	5	8	1	3	rs150705202	byFrequency	TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr8:110305580T>G	ENST00000239690.4	-	4	1007	c.633A>C	c.(631-633)aaA>aaC	p.K211N	NUDCD1_ENST00000427660.2_Missense_Mutation_p.K182N	NM_032869.3	NP_116258.2			NudC domain containing 1											breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(2)|skin(1)	25	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)			TACCTTGATTTTTCTTACTGA	0.358																																					p.K211N		Atlas-SNP	.											.	NUDCD1	58	.	0			c.A633C						.						92	97	95					8																	110305580		2203	4300	6503	SO:0001583	missense	84955	exon4			TTGATTTTTCTTA	AF283302	CCDS6312.1, CCDS47910.1	8q23	2005-02-07			ENSG00000120526	ENSG00000120526			24306	protein-coding gene	gene with protein product		606109				11416219	Standard	NM_032869		Approved	CML66, FLJ14991	uc003ynb.4	Q96RS6	OTTHUMG00000164931	ENST00000239690.4:c.633A>C	chr8.hg19:g.110305580T>G	ENSP00000239690:p.Lys211Asn	57.0	0.0		101.0	16.0	NM_032869		Missense_Mutation	SNP	ENST00000239690.4	hg19	CCDS6312.1	.	.	.	.	.	.	.	.	.	.	T	10.85	1.467557	0.26335	.	.	ENSG00000120526	ENST00000239690;ENST00000427660	T;T	0.18338	2.22;2.22	5.93	4.79	0.61399	.	0.263954	0.43579	D	0.000543	T	0.17408	0.0418	L	0.57536	1.79	0.31128	N	0.708077	B;B;B	0.22346	0.05;0.068;0.005	B;B;B	0.25884	0.064;0.019;0.005	T	0.12502	-1.0545	10	0.22706	T	0.39	-7.7157	9.3449	0.38102	0.0:0.1502:0.0:0.8498	.	124;211;182	Q96RS6-3;Q96RS6;Q96RS6-2	.;NUDC1_HUMAN;.	N	211;182	ENSP00000239690:K211N;ENSP00000410707:K182N	ENSP00000239690:K211N	K	-	3	2	NUDCD1	110374756	0.996000	0.38824	1.000000	0.80357	0.990000	0.78478	1.164000	0.31810	1.094000	0.41399	0.533000	0.62120	AAA	.	T|1.000;C|0.000		0.358	NUDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380996.1	NM_032869		G	110305580	T	G	110305580	3	3	85	1	0	0	0	0	1	0	0	0	10731	1838	64	5	1146	5	NUDCD1	8	110305580	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	71282925	110305580	36058442	56	11421										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110520397	110520397	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	agtgctttgggatggaatatGcaatgatggttattgaaagt	13	2	0	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr8:110520397G>T	ENST00000378402.5	+	70	11403	c.11299G>T	c.(11299-11301)Gca>Tca	p.A3767S		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3767					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GATGGAATATGCAATGATGGT	0.383										HNSCC(38;0.096)																											p.A3767S		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G11299T						.						179	175	176					8																	110520397		1863	4103	5966	SO:0001583	missense	93035	exon70			GAATATGCAATGA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.11299G>T	chr8.hg19:g.110520397G>T	ENSP00000367655:p.Ala3767Ser	89.0	0.0		121.0	5.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.586805	0.28268	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.85955	-2.05;-1.9	6.17	6.17	0.99709	.	0.190262	0.47093	D	0.000250	T	0.79759	0.4501	L	0.43152	1.355	0.25558	N	0.987014	B	0.29716	0.255	B	0.26969	0.075	T	0.64080	-0.6491	10	0.09843	T	0.71	.	18.3732	0.90420	0.0:0.0:1.0:0.0	.	3767	Q86WI1	PKHL1_HUMAN	S	3767;695	ENSP00000367655:A3767S;ENSP00000437376:A695S	ENSP00000367655:A3767S	A	+	1	0	PKHD1L1	110589573	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.373000	0.44266	2.941000	0.99782	0.655000	0.94253	GCA	.	.		0.383	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110520397	G	T	110520397	3	4	85	1	0	0	0	0	1	0	0	0	11981	1319	46	3	11577	3	PKHD1L1	8	110520397	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	214817	110520397	35843625	57	11422										
WDR67	93594	hgsc.bcm.edu	37	chr8	124089437	124089437	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ggcttttgatggcacaggcgActgcttaattgctggggacc	14	9	0	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr8:124089437A>C	ENST00000287380.1	+	2	254	c.164A>C	c.(163-165)gAc>gCc	p.D55A	TBC1D31_ENST00000378080.2_5'UTR|TBC1D31_ENST00000521676.1_5'UTR|TBC1D31_ENST00000327098.5_Missense_Mutation_p.D55A|TBC1D31_ENST00000309336.3_Missense_Mutation_p.D55A|TBC1D31_ENST00000522420.1_5'UTR	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	55						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										GGCACAGGCGACTGCTTAATT	0.358																																					p.D55A		Atlas-SNP	.											.	WDR67	97	.	0			c.A164C						.						137	130	132					8																	124089437		2203	4300	6503	SO:0001583	missense	93594	exon2			CAGGCGACTGCTT	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"WD repeat domain containing"	30888	protein-coding gene	gene with protein product			"WD repeat domain 67"	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.164A>C	chr8.hg19:g.124089437A>C	ENSP00000287380:p.Asp55Ala	62.0	0.0		79.0	36.0	NM_001145088	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Missense_Mutation	SNP	ENST00000287380.1	hg19	CCDS6338.1	.	.	.	.	.	.	.	.	.	.	A	15.96	2.985612	0.53934	.	.	ENSG00000156787	ENST00000287380;ENST00000309336;ENST00000327098;ENST00000522276	T;T;T;T	0.71579	-0.25;1.51;1.51;-0.58	5.53	5.53	0.82687	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.78298	0.4261	M	0.62723	1.935	0.80722	D	1	B;D;P	0.55800	0.087;0.973;0.842	B;P;B	0.55055	0.05;0.767;0.324	T	0.79422	-0.1810	10	0.49607	T	0.09	-27.8003	15.6607	0.77186	1.0:0.0:0.0:0.0	.	55;55;55	B7ZL19;Q96DN5;Q3KRB0	.;WDR67_HUMAN;.	A	55;55;55;45	ENSP00000287380:D55A;ENSP00000308358:D55A;ENSP00000312701:D55A;ENSP00000428891:D45A	ENSP00000287380:D55A	D	+	2	0	WDR67	124158618	1.000000	0.71417	0.218000	0.23776	0.715000	0.41141	8.384000	0.90160	2.106000	0.64143	0.528000	0.53228	GAC	.	.		0.358	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647		C	124089437	A	C	124089437	3	2	85	1	0	0	0	0	1	0	0	0	17333	275	10	5	170	5	WDR67	8	124089437	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	13569040	124089437	22274585	58	11423										
TG	7038	hgsc.bcm.edu	37	chr8	134147018	134147018	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	taagcctccaggaaccaggcTctaagacctacagcaagtga	9	12	1	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr8:134147018T>A	ENST00000220616.4	+	48	8327	c.8287T>A	c.(8287-8289)Tct>Act	p.S2763T	TG_ENST00000377869.1_Missense_Mutation_p.S2706T|TG_ENST00000542445.1_Missense_Mutation_p.S1133T|TG_ENST00000519543.1_Missense_Mutation_p.S896T	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2763					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GGAACCAGGCTCTAAGACCTA	0.532																																					p.S2763T		Atlas-SNP	.											.	TG	416	.	0			c.T8287A						.						90	77	81					8																	134147018		2203	4300	6503	SO:0001583	missense	7038	exon48			CCAGGCTCTAAGA	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.8287T>A	chr8.hg19:g.134147018T>A	ENSP00000220616:p.Ser2763Thr	61.0	0.0		76.0	26.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.61|14.61	2.586793|2.586793	0.46110|0.46110	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000519178|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000535932;ENST00000542445;ENST00000519543;ENST00000521107	.|T;T;T;T;T	.|0.68025	.|-0.08;-0.08;-0.29;-0.3;0.88	4.16|4.16	-2.6|-2.6	0.06190|0.06190	.|.	.|1.631640	.|0.03633	.|N	.|0.238144	T|T	0.49745|0.49745	0.1575|0.1575	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	.|P;P;P	.|0.45827	.|0.651;0.867;0.651	.|B;B;B	.|0.39027	.|0.15;0.288;0.15	T|T	0.49652|0.49652	-0.8917|-0.8917	5|10	.|0.52906	.|T	.|0.07	.|.	5.5132|5.5132	0.16892|0.16892	0.0:0.5016:0.1797:0.3186|0.0:0.5016:0.1797:0.3186	.|.	.|896;1133;2763	.|E7EVM0;F5GWW5;P01266	.|.;.;THYG_HUMAN	H|T	1218|2706;1569;2763;882;1133;896;167	.|ENSP00000367100:S2706T;ENSP00000220616:S2763T;ENSP00000441693:S1133T;ENSP00000430430:S896T;ENSP00000430161:S167T	.|ENSP00000220616:S2763T	L|S	+|+	2|1	0|0	TG|TG	134216200|134216200	0.031000|0.031000	0.19500|0.19500	0.203000|0.203000	0.23512|0.23512	0.449000|0.449000	0.32228|0.32228	-0.081000|-0.081000	0.11321|0.11321	-0.325000|-0.325000	0.08577|0.08577	0.172000|0.172000	0.16884|0.16884	CTC|TCT	.	.		0.532	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	134147018	T	A	134147018	3	1	85	1	0	0	0	0	1	0	0	0	15828	1551	54	4	8477	4	TG	8	134147018	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	10057581	134147018	12217004	59	11424										
WNK2	65268	hgsc.bcm.edu	37	chr9	96024181	96024181	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gccaccggctgcggtcctctCgccgcctctgccggaagtgc	13	18	2	0	rs370654793		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr9:96024181C>T	ENST00000297954.4	+	12	3152	c.3152C>T	c.(3151-3153)tCg>tTg	p.S1051L	WNK2_ENST00000349097.3_Missense_Mutation_p.S663L|WNK2_ENST00000395477.2_Missense_Mutation_p.S1051L|WNK2_ENST00000427277.2_Missense_Mutation_p.S663L|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000356055.3_5'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1051					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						GCGGTCCTCTCGCCGCCTCTG	0.697																																					p.S1051L		Atlas-SNP	.											.	WNK2	277	.	0			c.C3152T						.	C	LEU/SER	0,4404		0,0,2202	38	35	36		3152	5.2	1	9		36	1,8593	1.2+/-3.3	0,1,4296	no	missense	WNK2	NM_006648.3	145	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1051/2218	96024181	1,12997	2202	4297	6499	SO:0001583	missense	65268	exon12			TCCTCTCGCCGCC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.3152C>T	chr9.hg19:g.96024181C>T	ENSP00000297954:p.Ser1051Leu	42.0	0.0		32.0	7.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.04|15.04	2.714816|2.714816	0.48622|0.48622	0.0|0.0	1.16E-4|1.16E-4	ENSG00000165238|ENSG00000165238	ENST00000432730|ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277	.|T;T;T;T	.|0.72615	.|-0.64;-0.67;-0.03;-0.02	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	.|0.307026	.|0.30890	.|N	.|0.008662	T|T	0.77432|0.77432	0.4129|0.4129	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|0.999;1.0;1.0;0.999	.|D;D;D;D	.|0.81914	.|0.99;0.991;0.995;0.978	T|T	0.79332|0.79332	-0.1847|-0.1847	5|10	.|0.59425	.|D	.|0.04	.|.	16.4324|16.4324	0.83853|0.83853	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1051;654;1051;1051	.|Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1	.|.;.;.;WNK2_HUMAN	C|L	1047|1051;1051;663;663	.|ENSP00000297954:S1051L;ENSP00000378860:S1051L;ENSP00000297876:S663L;ENSP00000411181:S663L	.|ENSP00000297954:S1051L	R|S	+|+	1|2	0|0	WNK2|WNK2	95064002|95064002	0.975000|0.975000	0.34042|0.34042	0.992000|0.992000	0.48379|0.48379	0.517000|0.517000	0.34286|0.34286	4.459000|4.459000	0.60102|0.60102	2.405000|2.405000	0.81733|0.81733	0.313000|0.313000	0.20887|0.20887	CGC|TCG	.	.		0.697	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		T	96024181	C	T	96024181	3	4	85	1	0	0	0	0	1	0	0	0	17393	893	31	1	3198	1	WNK2	9	96024181	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10		96024181	45189250	60	11425										
SETX	23064	hgsc.bcm.edu	37	chr9	135202688	135202688	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	caaagggcaagcatcatcagTtgctggagacccatgttttg	11	9	2	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr9:135202688T>G	ENST00000224140.5	-	10	4479	c.4297A>C	c.(4297-4299)Act>Cct	p.T1433P	SETX_ENST00000393220.1_Missense_Mutation_p.T1433P|SETX_ENST00000372169.2_Missense_Mutation_p.T1433P	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1433					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GCATCATCAGTTGCTGGAGAC	0.418																																					p.T1433P		Atlas-SNP	.											.	SETX	234	.	0			c.A4297C						.						234	207	216					9																	135202688		2203	4300	6503	SO:0001583	missense	23064	exon10			CATCAGTTGCTGG	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.4297A>C	chr9.hg19:g.135202688T>G	ENSP00000224140:p.Thr1433Pro	100.0	0.0		85.0	58.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	0.263	-0.997949	0.02145	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.86694	-2.06;-2.16;-1.77	5.43	-9.64	0.00541	.	1.135150	0.06451	N	0.727751	T	0.71204	0.3312	N	0.25144	0.715	0.09310	N	1	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.09377	0.004;0.001;0.004	T	0.54944	-0.8217	10	0.33940	T	0.23	.	4.668	0.12675	0.1478:0.3876:0.3252:0.1394	.	1433;1433;1433	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	P	1433	ENSP00000224140:T1433P;ENSP00000361242:T1433P;ENSP00000376913:T1433P	ENSP00000224140:T1433P	T	-	1	0	SETX	134192509	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.767000	0.01795	-1.407000	0.02043	0.533000	0.62120	ACT	.	.		0.418	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		G	135202688	T	G	135202688	3	3	85	1	0	0	0	0	1	0	0	0	14156	1725	60	5	3804	5	SETX	9	135202688	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	39178507	135202688	6010743	61	11426										
PARG	119016	hgsc.bcm.edu	37	chr10	51370883	51370883	+	5'UTR	DEL	C	C	-													0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tggcgctgcctctgtgctgtCccgcctgccctgggacgcag							TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr10:51370883delC	ENST00000602930.1	-	0	438				RP11-592B15.3_ENST00000432221.2_RNA|TIMM23B_ENST00000451577.2_5'Flank|TIMM23B_ENST00000478381.1_5'Flank	NM_001276343.1	NP_001263272.1	Q5SRD3	AGAP8_HUMAN							regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(2)|ovary(2)	6						TCTGTGCTGTCCCGCCTGCCC	0.632																																					p.G63fs		Pindel	.											.	PARG	46	.	0			c.189delA						.						2	1	2					10																	51370883		225	461	686	SO:0001623	5_prime_UTR_variant	8505	exon1			.																												ENST00000602930.1:c.-112G>-	chr10.hg19:g.51370883delC		165.0	0.0		189.0	29.0	NM_003631		Frame_Shift_Del	DEL	ENST00000602930.1	hg19																																																																																				.	.		0.632	AGAP8-006	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000467541.1			-	51370883	C	-	51370883	6	5	85	0	1	1	0	1	0	0	0	0	11457	855	30	0		0	PARG	10	51370883	5'UTR	DEL	C	TCGA-CC-A9FW-01A-11D-A36X-10		51370883	84163864	62	11427										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55955617	55955617	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tcaatgtgtagaccggcaaaGgcaggaagaggatgaccatt	13	7	1	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr10:55955617G>A	ENST00000320301.6	-	11	1525	c.1131C>T	c.(1129-1131)gcC>gcT	p.A377A	PCDH15_ENST00000395432.2_Silent_p.A340A|PCDH15_ENST00000373957.3_Silent_p.A355A|PCDH15_ENST00000395446.1_Silent_p.A377A|PCDH15_ENST00000395430.1_Silent_p.A377A|PCDH15_ENST00000373955.1_Silent_p.A377A|PCDH15_ENST00000373965.2_Silent_p.A377A|PCDH15_ENST00000395438.1_Silent_p.A377A|PCDH15_ENST00000414778.1_Silent_p.A382A|PCDH15_ENST00000395433.1_Silent_p.A355A|PCDH15_ENST00000409834.1_5'UTR|PCDH15_ENST00000361849.3_Silent_p.A377A|PCDH15_ENST00000395440.1_Silent_p.A377A|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395445.1_Silent_p.A377A|PCDH15_ENST00000437009.1_Silent_p.A377A	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	377	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GACCGGCAAAGGCAGGAAGAG	0.373										HNSCC(58;0.16)																											p.A382A		Atlas-SNP	.											.	PCDH15	1715	.	0			c.C1146T						.						121	116	118					10																	55955617		2203	4300	6503	SO:0001819	synonymous_variant	65217	exon12			GGCAAAGGCAGGA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1131C>T	chr10.hg19:g.55955617G>A		92.0	0.0		103.0	32.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.		0.373	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55955617	G	A	55955617	2	1	85	1	0	0	0	0	0	0	0	1	11520	987	35	3		3	PCDH15	10	55955617	Silent	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	4584734	55955617	79579130	63	11428										
SLC16A9	220963	hgsc.bcm.edu	37	chr10	61413702	61413702	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acttgaagtcagccagtatcCctaaaagcagtttaccaact	6	11	1	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr10:61413702C>T	ENST00000395348.3	-	5	1718	c.1082G>A	c.(1081-1083)gGg>gAg	p.G361E	SLC16A9_ENST00000395347.1_Missense_Mutation_p.G361E	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	361					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						AGCCAGTATCCCTAAAAGCAG	0.383																																					p.G361E		Atlas-SNP	.											.	SLC16A9	58	.	0			c.G1082A						.						108	102	104					10																	61413702		2203	4300	6503	SO:0001583	missense	220963	exon5			AGTATCCCTAAAA	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.1082G>A	chr10.hg19:g.61413702C>T	ENSP00000378757:p.Gly361Glu	60.0	0.0		73.0	31.0	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	hg19	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197422	0.79015	.	.	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.70749	-0.51;-0.51	4.93	4.93	0.64822	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.86924	0.6050	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89792	0.3969	10	0.87932	D	0	.	18.134	0.89612	0.0:1.0:0.0:0.0	.	361	Q7RTY1	MOT9_HUMAN	E	361	ENSP00000378757:G361E;ENSP00000378756:G361E	ENSP00000378756:G361E	G	-	2	0	SLC16A9	61083708	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.487000	0.81328	2.265000	0.75225	0.591000	0.81541	GGG	.	.		0.383	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		T	61413702	C	T	61413702	3	4	85	1	0	0	0	0	1	0	0	0	14430	623	22	3	455	3	SLC16A9	10	61413702	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	5458085	61413702	74121045	64	11429										
TET1	80312	hgsc.bcm.edu	37	chr10	70406241	70406241	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gagatatcctgaatcagcagAggaaaaggtgaaggttgaac	13	5	1	5			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr10:70406241A>T	ENST00000373644.4	+	4	3964	c.3755A>T	c.(3754-3756)gAg>gTg	p.E1252V		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1252					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GAATCAGCAGAGGAAAAGGTG	0.398																																					p.E1252V		Atlas-SNP	.											.	TET1	255	.	0			c.A3755T						.						75	72	73					10																	70406241		2203	4300	6503	SO:0001583	missense	80312	exon4			CAGCAGAGGAAAA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.3755A>T	chr10.hg19:g.70406241A>T	ENSP00000362748:p.Glu1252Val	140.0	0.0		178.0	83.0	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	A	8.572	0.880217	0.17467	.	.	ENSG00000138336	ENST00000373644	T	0.07444	3.19	5.25	4.04	0.47022	.	2.332980	0.01849	N	0.035799	T	0.06917	0.0176	N	0.08118	0	0.25671	N	0.985892	B	0.22276	0.067	B	0.18263	0.021	T	0.16719	-1.0393	10	0.59425	D	0.04	.	10.5843	0.45273	0.8388:0.1612:0.0:0.0	.	1252	Q8NFU7	TET1_HUMAN	V	1252	ENSP00000362748:E1252V	ENSP00000362748:E1252V	E	+	2	0	TET1	70076247	1.000000	0.71417	0.857000	0.33713	0.115000	0.19883	3.261000	0.51530	1.975000	0.57531	0.460000	0.39030	GAG	.	.		0.398	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		T	70406241	A	T	70406241	3	4	85	1	0	0	0	0	1	0	0	0	15784	304	11	4	3765	4	TET1	10	70406241	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	8992539	70406241	65128506	65	11430										
OPALIN	93377	hgsc.bcm.edu	37	chr10	98105735	98105735	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tgggcacaagccaccacaatCccctccttctttccatttct	4	17	2	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr10:98105735C>G	ENST00000371172.3	-	6	794	c.389G>C	c.(388-390)gGa>gCa	p.G130A	OPALIN_ENST00000393870.2_Missense_Mutation_p.G119A|OPALIN_ENST00000393871.1_Missense_Mutation_p.G107A|OPALIN_ENST00000419479.1_Missense_Mutation_p.G120A|OPALIN_ENST00000536387.1_Missense_Mutation_p.G120A	NM_001284326.1|NM_001284327.1|NM_033207.3	NP_001271255.1|NP_001271256.1|NP_149984.1	Q96PE5	OPALI_HUMAN	oligodendrocytic myelin paranodal and inner loop protein	130						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(5)|prostate(2)	9						CCACCACAATCCCCTCCTTCT	0.522																																					p.G130A		Atlas-SNP	.											.	OPALIN	31	.	0			c.G389C						.						156	135	142					10																	98105735		2203	4300	6503	SO:0001583	missense	93377	exon6			CACAATCCCCTCC	AF367761	CCDS7448.1, CCDS41556.1, CCDS44466.1, CCDS60602.1, CCDS73172.1, CCDS73173.1	10q23-q24	2010-11-23	2008-05-01	2008-05-01	ENSG00000197430	ENSG00000197430			20707	protein-coding gene	gene with protein product			"transmembrane protein 10"	TMEM10		11814680, 17442045	Standard	NM_001284324		Approved	TMP10, HTMP10	uc001kmj.3	Q96PE5	OTTHUMG00000018831	ENST00000371172.3:c.389G>C	chr10.hg19:g.98105735C>G	ENSP00000360214:p.Gly130Ala	36.0	0.0		86.0	19.0	NM_033207	A8MX69|A8MYG4|B4DK96|B4DKH0|Q5W102	Missense_Mutation	SNP	ENST00000371172.3	hg19	CCDS7448.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.604345	0.46423	.	.	ENSG00000197430	ENST00000371172;ENST00000393871;ENST00000419479;ENST00000393870;ENST00000536387	.	.	.	4.12	2.17	0.27698	.	0.474665	0.18221	N	0.147886	T	0.50017	0.1591	L	0.34521	1.04	0.09310	N	1	D;D;B	0.76494	0.999;0.999;0.015	D;D;B	0.87578	0.998;0.998;0.018	T	0.37549	-0.9701	9	0.87932	D	0	-12.9564	10.3513	0.43937	0.0:0.611:0.389:0.0	.	107;130;120	A8MYG4;Q96PE5;B4DK96	.;OPALI_HUMAN;.	A	130;107;120;119;120	.	ENSP00000360214:G130A	G	-	2	0	OPALIN	98095725	0.002000	0.14202	0.055000	0.19348	0.836000	0.47400	0.621000	0.24418	0.459000	0.27016	0.650000	0.86243	GGA	.	.		0.522	OPALIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049606.1	NM_033207		G	98105735	C	G	98105735	3	3	85	1	0	0	0	0	1	0	0	0	10882	855	30	4	40	4	OPALIN	10	98105735	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	27699494	98105735	37429012	66	11431										
FGF8	2253	hgsc.bcm.edu	37	chr10	103535640	103535640	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	actcacaggcagctcagcgcGgagcgggggctgcccatggc	16	14	2	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr10:103535640G>A	ENST00000344255.3	-	1	17	c.18C>T	c.(16-18)tcC>tcT	p.S6S	FGF8_ENST00000347978.2_Silent_p.S6S|FGF8_ENST00000320185.2_Silent_p.S6S|FGF8_ENST00000485728.1_5'UTR|FGF8_ENST00000346714.3_Silent_p.S6S			P55075	FGF8_HUMAN	fibroblast growth factor 8 (androgen-induced)	6					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in mesendoderm migration (GO:0090134)|cell proliferation in forebrain (GO:0021846)|corticotropin hormone secreting cell differentiation (GO:0060128)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral axon guidance (GO:0033563)|embryonic hindlimb morphogenesis (GO:0035116)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain morphogenesis (GO:0048853)|forebrain neuron development (GO:0021884)|gastrulation (GO:0007369)|gonad development (GO:0008406)|heart looping (GO:0001947)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lung morphogenesis (GO:0060425)|male genitalia development (GO:0030539)|MAPK cascade (GO:0000165)|mesodermal cell migration (GO:0008078)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|midbrain-hindbrain boundary development (GO:0030917)|motor neuron axon guidance (GO:0008045)|negative regulation of cardiac muscle tissue development (GO:0055026)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate morphogenesis (GO:0001839)|neuroepithelial cell differentiation (GO:0060563)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|pallium development (GO:0021543)|patterning of blood vessels (GO:0001569)|pharyngeal system development (GO:0060037)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitosis (GO:0045840)|positive regulation of organ growth (GO:0046622)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)|signal transduction involved in regulation of gene expression (GO:0023019)|subpallium development (GO:0021544)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(2)	5		Colorectal(252;0.122)		Epithelial(162;3.94e-09)|all cancers(201;2.13e-07)		AGCTCAGCGCGGAGCGGGGGC	0.811																																					p.S6S		Atlas-SNP	.											.	FGF8	23	.	0			c.C18T						.						1	1	1					10																	103535640		210	476	686	SO:0001819	synonymous_variant	2253	exon1			CAGCGCGGAGCGG	D38752	CCDS7515.1, CCDS7516.1, CCDS7517.1, CCDS7518.1, CCDS73185.1	10q25-q26	2014-01-30			ENSG00000107831	ENSG00000107831		"Endogenous ligands"	3686	protein-coding gene	gene with protein product		600483				8595889	Standard	NM_033164		Approved	AIGF	uc001ktq.2	P55075	OTTHUMG00000018940	ENST00000344255.3:c.18C>T	chr10.hg19:g.103535640G>A		198.0	0.0		250.0	52.0	NM_033164	A1A514|Q14915|Q15766	Silent	SNP	ENST00000344255.3	hg19	CCDS7517.1																																																																																			.	.		0.811	FGF8-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049999.1	NM_006119, NM_033165		A	103535640	G	A	103535640	2	1	85	1	0	0	0	0	0	0	0	1	5866	1103	39	1		1	FGF8	10	103535640	Silent	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	5429905	103535640	31999107	67	11432										
FANK1	92565	hgsc.bcm.edu	37	chr10	127685132	127685132	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tcccaagccgtgttaaggttGatgttcccaataagtttggc	10	9	0	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr10:127685132G>T	ENST00000368693.1	+	5	516	c.412G>T	c.(412-414)Gat>Tat	p.D138Y	FANK1_ENST00000368695.1_Missense_Mutation_p.D132Y			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	138						cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				TGTTAAGGTTGATGTTCCCAA	0.458																																					p.D138Y		Atlas-SNP	.											.	FANK1	46	.	0			c.G412T						.						250	237	241					10																	127685132		2203	4300	6503	SO:0001583	missense	92565	exon5			AAGGTTGATGTTC	BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	23527	protein-coding gene	gene with protein product		611640	"fibronectin type 3 and ankyrin repeat domains 1"			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.412G>T	chr10.hg19:g.127685132G>T	ENSP00000357682:p.Asp138Tyr	85.0	0.0		58.0	38.0	NM_145235	Q6UXY9|Q6X7T6	Missense_Mutation	SNP	ENST00000368693.1	hg19	CCDS31309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.50|15.50	2.851790|2.851790	0.51270|0.51270	.|.	.|.	ENSG00000203780|ENSG00000203780	ENST00000368695;ENST00000368693;ENST00000368691;ENST00000368692|ENST00000456942	T;T;T|.	0.56103|.	0.48;0.48;0.48|.	5.02|5.02	5.02|5.02	0.67125|0.67125	Ankyrin repeat-containing domain (4);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.68054|0.68054	0.2959|0.2959	M|M	0.77486|0.77486	2.375|2.375	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.76071|.	0.964;0.964;0.987|.	T|T	0.68868|0.68868	-0.5295|-0.5295	10|5	0.87932|.	D|.	0|.	-33.5661|-33.5661	8.9647|8.9647	0.35869|0.35869	0.0816:0.1519:0.7665:0.0|0.0816:0.1519:0.7665:0.0	.|.	164;138;138|.	Q8TC84-3;Q8TC84-2;Q8TC84|.	.;.;FANK1_HUMAN|.	Y|F	132;138;138;164|32	ENSP00000357684:D132Y;ENSP00000357682:D138Y;ENSP00000357680:D138Y|.	ENSP00000357680:D138Y|.	D|L	+|+	1|3	0|2	FANK1|FANK1	127675122|127675122	0.999000|0.999000	0.42202|0.42202	0.950000|0.950000	0.38849|0.38849	0.707000|0.707000	0.40811|0.40811	3.310000|3.310000	0.51911|0.51911	2.628000|2.628000	0.89032|0.89032	0.650000|0.650000	0.86243|0.86243	GAT|TTG	.	.		0.458	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145235		T	127685132	G	T	127685132	3	4	85	1	0	0	0	0	1	0	0	0	5680	1290	45	3	430	3	FANK1	10	127685132	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	24149492	127685132	7849615	68	11433										
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643054	1643055	+	Frame_Shift_Ins	INS	-	-	C													0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	aacccccacaggagacacagINSccccccttggaacccccaca							TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:1643054_1643055insC	ENST00000399682.1	-	1	313_314	c.269_270insG	c.(268-270)ggcfs	p.G90fs		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AGGAGACACAGCCCCCCTTGGA	0.668																																					p.G90fs		Atlas-INDEL	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	.	0			c.270_271insG						.																																			SO:0001589	frameshift_variant	387267	exon1			.	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"Keratin associated proteins"	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.270dupG	chr11.hg19:g.1643060_1643060dupC	ENSP00000382590:p.Gly90fs	269.0	0.0		267.0	22.0	NM_001012709		Frame_Shift_Ins	INS	ENST00000399682.1	hg19																																																																																				.	.		0.668	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		C	1643055	-	C	1643054	7	5	85	1	0	1	1	0	0	0	0	0	8572	958	34	0	420	0	KRTAP5-4	11	1643054	Frame_Shift_Ins	INS	-	TCGA-CC-A9FW-01A-11D-A36X-10		1643054	133363462	69	11434										
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26743147	26743147	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tcccccaaccaggaactctcGggaagttgccttttttctct	7	14	2	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:26743147G>A	ENST00000396005.3	-	1	424	c.115C>T	c.(115-117)Cga>Tga	p.R39*	SLC5A12_ENST00000280467.6_Nonsense_Mutation_p.R39*	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	39					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						AGGAACTCTCGGGAAGTTGCC	0.502																																					p.R39X		Atlas-SNP	.											.	SLC5A12	134	.	0			c.C115T						.						72	74	73					11																	26743147		2203	4299	6502	SO:0001587	stop_gained	159963	exon1			ACTCTCGGGAAGT	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.115C>T	chr11.hg19:g.26743147G>A	ENSP00000379326:p.Arg39*	211.0	0.0		257.0	16.0	NM_178498	Q86UC7	Nonsense_Mutation	SNP	ENST00000396005.3	hg19	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	G	38	6.792305	0.97841	.	.	ENSG00000148942	ENST00000396005;ENST00000280467	.	.	.	5.59	-1.02	0.10135	.	0.130324	0.48767	D	0.000172	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	7.7191	0.28721	0.0:0.2948:0.2871:0.4181	.	.	.	.	X	39	.	ENSP00000280467:R39X	R	-	1	2	SLC5A12	26699723	0.012000	0.17670	0.014000	0.15608	0.981000	0.71138	1.284000	0.33249	-0.416000	0.07473	0.585000	0.79938	CGA	.	.		0.502	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		A	26743147	G	A	26743147	4	1	85	1	0	0	0	0	0	1	0	0	14679	1124	39	1	1801	1	SLC5A12	11	26743147	Nonsense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	25100093	26743147	108263369	70	11435										
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563231	55563231	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tatgtactttttccttagtcAcctctcttttgttgattttt	4	8	2	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:55563231A>G	ENST00000335605.1	+	1	200	c.200A>G	c.(199-201)cAc>cGc	p.H67R		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	67						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				TTCCTTAGTCACCTCTCTTTT	0.383																																					p.H67R		Atlas-SNP	.											.	OR5D14	116	.	0			c.A200G						.						220	198	206					11																	55563231		2200	4296	6496	SO:0001583	missense	219436	exon1			TTAGTCACCTCTC	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.200A>G	chr11.hg19:g.55563231A>G	ENSP00000334456:p.His67Arg	51.0	0.0		71.0	18.0	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	hg19	CCDS31508.1	.	.	.	.	.	.	.	.	.	.	a	3.513	-0.099367	0.07010	.	.	ENSG00000186113	ENST00000335605	T	0.12465	2.68	5.08	2.62	0.31277	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47455	D	0.000233	T	0.19446	0.0467	M	0.89414	3.03	0.09310	N	1	B	0.24533	0.105	B	0.20767	0.031	T	0.24835	-1.0149	10	0.72032	D	0.01	-12.2834	5.8009	0.18414	0.7686:0.0:0.0831:0.1483	.	67	Q8NGL3	OR5DE_HUMAN	R	67	ENSP00000334456:H67R	ENSP00000334456:H67R	H	+	2	0	OR5D14	55319807	0.003000	0.15002	0.234000	0.24042	0.016000	0.09150	2.096000	0.41738	0.792000	0.33850	-0.263000	0.10527	CAC	.	.		0.383	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		G	55563231	A	G	55563231	3	3	85	1	0	0	0	0	1	0	0	0	11164	159	6	2	202	2	OR5D14	11	55563231	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	28820084	55563231	79443285	71	11436										
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563576	55563576	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	aatcaaccacttcttttgtgAgtatactgctctcatctctg	5	11	4	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:55563576A>G	ENST00000335605.1	+	1	545	c.545A>G	c.(544-546)gAg>gGg	p.E182G		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				TTCTTTTGTGAGTATACTGCT	0.468																																					p.E182G		Atlas-SNP	.											.	OR5D14	116	.	0			c.A545G						.						219	217	218					11																	55563576		2200	4296	6496	SO:0001583	missense	219436	exon1			TTTGTGAGTATAC	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.545A>G	chr11.hg19:g.55563576A>G	ENSP00000334456:p.Glu182Gly	85.0	0.0		80.0	14.0	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	hg19	CCDS31508.1	.	.	.	.	.	.	.	.	.	.	a	13.33	2.205426	0.39003	.	.	ENSG00000186113	ENST00000335605	T	0.00227	8.5	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000276	T	0.00845	0.0028	H	0.95816	3.725	0.38932	D	0.957962	D	0.67145	0.996	D	0.70016	0.967	T	0.52472	-0.8571	10	0.87932	D	0	-17.3985	13.7086	0.62654	1.0:0.0:0.0:0.0	.	182	Q8NGL3	OR5DE_HUMAN	G	182	ENSP00000334456:E182G	ENSP00000334456:E182G	E	+	2	0	OR5D14	55320152	1.000000	0.71417	0.839000	0.33178	0.004000	0.04260	4.390000	0.59646	1.916000	0.55485	0.523000	0.50628	GAG	.	.		0.468	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		G	55563576	A	G	55563576	3	3	85	1	0	0	0	0	1	0	0	0	11164	304	11	2	547	2	OR5D14	11	55563576	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	345	55563576	79442940	72	11437										
OR5W2	390148	hgsc.bcm.edu	37	chr11	55681236	55681236	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cacaagggtgtaaaacaatgAggtcattttatcttgatcta	8	6	3	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:55681236A>T	ENST00000344514.1	-	1	822	c.823T>A	c.(823-825)Tca>Aca	p.S275T		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TAAAACAATGAGGTCATTTTA	0.408																																					p.S275T	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.T823A						.						64	71	69					11																	55681236		2201	4296	6497	SO:0001583	missense	390148	exon1			ACAATGAGGTCAT	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"GPCR / Class A : Olfactory receptors"	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.823T>A	chr11.hg19:g.55681236A>T	ENSP00000342448:p.Ser275Thr	186.0	0.0		209.0	47.0	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	hg19	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	A	11.84	1.759001	0.31137	.	.	ENSG00000187612	ENST00000344514	T	0.00235	8.48	5.01	3.87	0.44632	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34268	N	0.004119	T	0.00468	0.0015	M	0.74389	2.26	0.09310	N	1	D	0.71674	0.998	D	0.75484	0.986	T	0.43163	-0.9408	10	0.56958	D	0.05	.	8.9155	0.35579	0.91:0.0:0.09:0.0	.	275	Q8NH69	OR5W2_HUMAN	T	275	ENSP00000342448:S275T	ENSP00000342448:S275T	S	-	1	0	OR5W2	55437812	0.537000	0.26386	0.023000	0.16930	0.375000	0.29983	1.313000	0.33585	0.748000	0.32831	0.448000	0.29417	TCA	.	.		0.408	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		T	55681236	A	T	55681236	3	4	85	1	0	0	0	0	1	0	0	0	11194	304	11	4	111	4	OR5W2	11	55681236	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	117660	55681236	79325280	73	11438										
OR8J3	81168	hgsc.bcm.edu	37	chr11	55904552	55904552	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	aatattgaaataagatactaGaactgtaatcatggaaaaaa	6	3	1	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:55904552G>T	ENST00000301529.1	-	1	642	c.643C>A	c.(643-645)Cta>Ata	p.L215I		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					TAAGATACTAGAACTGTAATC	0.363																																					p.L215I		Atlas-SNP	.											OR8J3,NS,carcinoma,0,1	OR8J3	112	.	0			c.C643A						.						94	96	95					11																	55904552		2201	4296	6497	SO:0001583	missense	81168	exon1			ATACTAGAACTGT		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"GPCR / Class A : Olfactory receptors"	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.643C>A	chr11.hg19:g.55904552G>T	ENSP00000301529:p.Leu215Ile	54.0	1.0		44.0	10.0	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	hg19	CCDS31520.1	.	.	.	.	.	.	.	.	.	.	G	7.010	0.556557	0.13436	.	.	ENSG00000167822	ENST00000301529	T	0.00235	8.48	3.27	-2.52	0.06346	GPCR, rhodopsin-like superfamily (1);	0.982347	0.08299	N	0.967222	T	0.00144	0.0004	L	0.28556	0.865	0.09310	N	1	B	0.17465	0.022	B	0.26969	0.075	T	0.12578	-1.0542	10	0.44086	T	0.13	.	2.663	0.05032	0.0958:0.2364:0.1955:0.4722	.	215	Q8NGG0	OR8J3_HUMAN	I	215	ENSP00000301529:L215I	ENSP00000301529:L215I	L	-	1	2	OR8J3	55661128	0.000000	0.05858	0.048000	0.18961	0.728000	0.41692	-2.323000	0.01117	-0.912000	0.03837	0.297000	0.19635	CTA	.	.		0.363	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064		T	55904552	G	T	55904552	3	4	85	1	0	0	0	0	1	0	0	0	11251	933	33	3	306	3	OR8J3	11	55904552	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	223316	55904552	79101964	74	11439										
SLC22A25	387601	hgsc.bcm.edu	37	chr11	62984853	62984853	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gaggatgcactggtctcgaaTgacaaaagccaggcttccca	11	11	1	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:62984853T>C	ENST00000306494.6	-	4	762	c.763A>G	c.(763-765)Att>Gtt	p.I255V	SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000525620.1_Intron|SLC22A25_ENST00000403374.2_Missense_Mutation_p.I89V	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						TGGTCTCGAATGACAAAAGCC	0.443																																					p.I255V		Atlas-SNP	.											.	SLC22A25	87	.	0			c.A763G						.						144	130	134					11																	62984853		2201	4298	6499	SO:0001583	missense	387601	exon4			CTCGAATGACAAA	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"Solute carriers"	32935	protein-coding gene	gene with protein product		610792	"MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.763A>G	chr11.hg19:g.62984853T>C	ENSP00000307443:p.Ile255Val	97.0	0.0		117.0	28.0	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	hg19	CCDS31592.1	.	.	.	.	.	.	.	.	.	.	T	7.578	0.668168	0.14710	.	.	ENSG00000196600	ENST00000306494;ENST00000403374	T;T	0.60171	0.26;0.21	3.49	-4.23	0.03789	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.279859	0.34178	N	0.004181	T	0.42966	0.1226	L	0.51914	1.62	0.09310	N	1	B;B	0.28026	0.047;0.198	B;B	0.31016	0.123;0.123	T	0.30995	-0.9959	10	0.25751	T	0.34	.	8.3022	0.32021	0.6482:0.0:0.0:0.3518	.	253;255	A4IF29;Q6T423	.;S22AP_HUMAN	V	255;89	ENSP00000307443:I255V;ENSP00000384208:I89V	ENSP00000307443:I255V	I	-	1	0	SLC22A25	62741429	0.014000	0.17966	0.000000	0.03702	0.012000	0.07955	-0.099000	0.11007	-1.369000	0.02147	0.432000	0.28606	ATT	.	.		0.443	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352		C	62984853	T	C	62984853	3	2	85	1	0	0	0	0	1	0	0	0	14469	1464	51	2	904	2	SLC22A25	11	62984853	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	7080301	62984853	72021663	75	11440										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78369713	78369713	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	aggcaaacttgacccccttgCcaaagactgagccgctggat	10	13	0	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:78369713C>T	ENST00000278550.7	-	34	8162	c.7700G>A	c.(7699-7701)gGc>gAc	p.G2567D		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2567					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										GACCCCCTTGCCAAAGACTGA	0.537																																					p.G2567D		Atlas-SNP	.											.	.	.	.	0			c.G7700A						.						46	48	47					11																	78369713		2031	4182	6213	SO:0001583	missense	26011	exon34			CCCTTGCCAAAGA	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.7700G>A	chr11.hg19:g.78369713C>T	ENSP00000278550:p.Gly2567Asp	67.0	0.0		84.0	41.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599009	0.87055	.	.	ENSG00000149256	ENST00000278550	D	0.91631	-2.88	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.96002	0.8698	M	0.74467	2.265	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94941	0.8091	9	.	.	.	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	2567	Q6N022	TEN4_HUMAN	D	2567	ENSP00000278550:G2567D	.	G	-	2	0	ODZ4	78047361	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.609000	0.82925	2.941000	0.99782	0.655000	0.94253	GGC	.	.		0.537	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78369713	C	T	78369713	3	4	85	1	0	0	0	0	1	0	0	0	10846	739	26	3	613	3	ODZ4	11	78369713	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	15384860	78369713	56636803	76	11441										
GPR83	10888	hgsc.bcm.edu	37	chr11	94113805	94113805	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gccacagtttcttggccacaCgagcgtaggccacagagatg	12	12	1	1	rs139287789		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:94113805C>T	ENST00000243673.2	-	4	953	c.782G>A	c.(781-783)cGt>cAt	p.R261H	GPR83_ENST00000539203.2_Missense_Mutation_p.R219H	NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83	261					response to glucocorticoid (GO:0051384)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CTTGGCCACACGAGCGTAGGC	0.527																																					p.R261H		Atlas-SNP	.											.	GPR83	47	.	0			c.G782A						.	C	HIS/ARG	0,4402		0,0,2201	72	64	67		782	4.4	0.4	11	dbSNP_134	67	1,8595	1.2+/-3.3	0,1,4297	no	missense	GPR83	NM_016540.3	29	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	benign	261/424	94113805	1,12997	2201	4298	6499	SO:0001583	missense	10888	exon4			GCCACACGAGCGT	AF236081	CCDS8297.1	11q21	2012-08-21	2003-07-30	2003-08-01	ENSG00000123901	ENSG00000123901		"GPCR / Class A : Orphans"	4523	protein-coding gene	gene with protein product		605569	"G protein-coupled receptor 72"	GPR72		10760605, 11060465	Standard	NM_016540		Approved		uc001pet.2	Q9NYM4	OTTHUMG00000167779	ENST00000243673.2:c.782G>A	chr11.hg19:g.94113805C>T	ENSP00000243673:p.Arg261His	78.0	0.0		102.0	30.0	NM_016540	B0M0K5|Q6NWR4|Q9P1Y8	Missense_Mutation	SNP	ENST00000243673.2	hg19	CCDS8297.1	.	.	.	.	.	.	.	.	.	.	C	9.499	1.102782	0.20632	0.0	1.16E-4	ENSG00000123901	ENST00000243673;ENST00000539203	T;T	0.39056	1.1;1.1	5.41	4.44	0.53790	GPCR, rhodopsin-like superfamily (1);	0.258283	0.36703	N	0.002441	T	0.27524	0.0676	L	0.33093	0.98	0.23411	N	0.997737	B	0.18461	0.028	B	0.15870	0.014	T	0.09930	-1.0652	10	0.15499	T	0.54	.	8.617	0.33838	0.1509:0.586:0.2631:0.0	.	261	Q9NYM4	GPR83_HUMAN	H	261;219	ENSP00000243673:R261H;ENSP00000441550:R219H	ENSP00000243673:R261H	R	-	2	0	GPR83	93753453	0.995000	0.38212	0.363000	0.25875	0.982000	0.71751	2.604000	0.46274	2.535000	0.85469	0.655000	0.94253	CGT	.	C|1.000;T|0.000		0.527	GPR83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396232.1	NM_016540		T	94113805	C	T	94113805	3	4	85	1	0	0	0	0	1	0	0	0	6721	536	19	1	493	1	GPR83	11	94113805	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	15744092	94113805	40892711	77	11442										
MTMR2	8898	hgsc.bcm.edu	37	chr11	95595469	95595469	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ttgaaatataacctataattCgtgacagtcagagttcctcg	7	8	1	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:95595469C>A	ENST00000346299.5	-	4	664	c.324G>T	c.(322-324)acG>acT	p.T108T	MTMR2_ENST00000484818.1_5'UTR|MTMR2_ENST00000393223.3_Silent_p.T36T|MTMR2_ENST00000409459.1_Silent_p.T36T|MTMR2_ENST00000352297.7_Silent_p.T36T	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	108	GRAM.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ACCTATAATTCGTGACAGTCA	0.358																																					p.T108T		Atlas-SNP	.											.	MTMR2	79	.	0			c.G324T	GRCh37	CD013478	MTMR2	D		.						74	73	73					11																	95595469		2201	4298	6499	SO:0001819	synonymous_variant	8898	exon4			ATAATTCGTGACA	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.324G>T	chr11.hg19:g.95595469C>A		77.0	0.0		60.0	7.0	NM_016156	A6NN98|Q9UPS9	Silent	SNP	ENST00000346299.5	hg19	CCDS8305.1																																																																																			.	.		0.358	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156		A	95595469	C	A	95595469	2	1	85	1	0	0	0	0	0	0	0	1	9953	871	31	1		1	MTMR2	11	95595469	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	1481664	95595469	39411047	78	11443										
CHEK1	1111	hgsc.bcm.edu	37	chr11	125513708	125513708	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ggcaaaaaggccccgagtcaCttcaggtggtgtgtcagagt	14	9	3	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr11:125513708C>T	ENST00000534070.1	+	9	1091	c.836C>T	c.(835-837)aCt>aTt	p.T279I	CHEK1_ENST00000427383.2_Missense_Mutation_p.T295I|CHEK1_ENST00000544373.1_Missense_Mutation_p.T279I|CHEK1_ENST00000532449.1_3'UTR|CHEK1_ENST00000524737.1_Missense_Mutation_p.T279I|CHEK1_ENST00000428830.2_Missense_Mutation_p.T279I|CHEK1_ENST00000278916.3_Missense_Mutation_p.T279I|CHEK1_ENST00000438015.1_Missense_Mutation_p.T279I	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	279					cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		CCCCGAGTCACTTCAGGTGGT	0.393								Other conserved DNA damage response genes																													p.T279I		Atlas-SNP	.											.	CHEK1	44	.	0			c.C836T						.						85	85	85					11																	125513708		2201	4299	6500	SO:0001583	missense	1111	exon9			GAGTCACTTCAGG	AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"CHK1 (checkpoint, S.pombe) homolog", "CHK1 checkpoint homolog (S. pombe)"			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.836C>T	chr11.hg19:g.125513708C>T	ENSP00000435371:p.Thr279Ile	54.0	0.0		45.0	9.0	NM_001244846	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Missense_Mutation	SNP	ENST00000534070.1	hg19	CCDS8459.1	.	.	.	.	.	.	.	.	.	.	C	12.16	1.855337	0.32791	.	.	ENSG00000149554	ENST00000438015;ENST00000427383;ENST00000428830;ENST00000544373;ENST00000534070;ENST00000524737;ENST00000278916	T;T;T;T;T;T;T	0.72835	-0.69;-0.36;-0.69;-0.68;-0.69;-0.69;-0.68	5.26	4.34	0.51931	Protein kinase-like domain (1);	0.643479	0.16320	N	0.219599	T	0.49184	0.1542	N	0.04959	-0.14	0.41567	D	0.988666	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.0	T	0.38929	-0.9638	10	0.21014	T	0.42	-2.7108	13.4504	0.61167	0.0:0.8423:0.1577:0.0	.	279;295;279;279	F5H7S4;E7EPP6;B5BTY6;O14757	.;.;.;CHK1_HUMAN	I	279;295;279;279;279;279;279	ENSP00000388648:T279I;ENSP00000391090:T295I;ENSP00000412504:T279I;ENSP00000442317:T279I;ENSP00000435371:T279I;ENSP00000432890:T279I;ENSP00000278916:T279I	ENSP00000278916:T279I	T	+	2	0	CHEK1	125018918	0.979000	0.34478	0.990000	0.47175	0.976000	0.68499	2.468000	0.45102	1.356000	0.45884	0.655000	0.94253	ACT	.	.		0.393	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274		T	125513708	C	T	125513708	3	4	85	1	0	0	0	0	1	0	0	0	3336	565	20	3	866	3	CHEK1	11	125513708	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	29918239	125513708	9492808	79	11444										
TSPAN9	10867	hgsc.bcm.edu	37	chr12	3390913	3390913	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tccccagggctgctatgaaaAggtgaagatgtggttcgatg	14	7	0	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr12:3390913A>C	ENST00000011898.5	+	8	739	c.578A>C	c.(577-579)aAg>aCg	p.K193T	TSPAN9_ENST00000537971.1_Missense_Mutation_p.K193T|TSPAN9_ENST00000407263.1_Missense_Mutation_p.K193T	NM_006675.4	NP_006666.1	O75954	TSN9_HUMAN	tetraspanin 9	193						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)				endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			TGCTATGAAAAGGTGAAGATG	0.622																																					p.K193T		Atlas-SNP	.											.	TSPAN9	20	.	0			c.A578C						.						128	101	110					12																	3390913		2203	4300	6503	SO:0001583	missense	10867	exon8			ATGAAAAGGTGAA	AF089749	CCDS8520.1	12p13.33-p13.32	2013-02-14			ENSG00000011105	ENSG00000011105		"Tetraspanins"	21640	protein-coding gene	gene with protein product		613137				10719184, 11739647	Standard	NM_006675		Approved	NET-5	uc021qtd.1	O75954	OTTHUMG00000150333	ENST00000011898.5:c.578A>C	chr12.hg19:g.3390913A>C	ENSP00000011898:p.Lys193Thr	86.0	0.0		103.0	22.0	NM_006675	D3DUQ7|Q53FV2|Q6FGJ8	Missense_Mutation	SNP	ENST00000011898.5	hg19	CCDS8520.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.462408	0.63513	.	.	ENSG00000011105	ENST00000537971;ENST00000011898;ENST00000407263	D;D;D	0.88664	-2.41;-2.41;-2.41	4.42	4.42	0.53409	Tetraspanin, EC2 domain (1);	0.000000	0.85682	D	0.000000	D	0.85894	0.5803	L	0.41573	1.285	0.80722	D	1	B	0.27732	0.187	B	0.38880	0.284	T	0.81611	-0.0854	10	0.26408	T	0.33	.	11.6265	0.51149	1.0:0.0:0.0:0.0	.	193	O75954	TSN9_HUMAN	T	193	ENSP00000444799:K193T;ENSP00000011898:K193T;ENSP00000384488:K193T	ENSP00000011898:K193T	K	+	2	0	TSPAN9	3261174	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.525000	0.53502	1.640000	0.50565	0.459000	0.35465	AAG	.	.		0.622	TSPAN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317606.2	NM_006675		C	3390913	A	C	3390913	3	2	85	1	0	0	0	0	1	0	0	0	16669	72	3	5	600	5	TSPAN9	12	3390913	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10		3390913	130460982	80	11445										
ACRBP	84519	hgsc.bcm.edu	37	chr12	6756045	6756045	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tgggttgcacggagacggcaGgtagtctctgccttccaggt	15	10	1	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr12:6756045G>A	ENST00000229243.2	-	2	270	c.177C>T	c.(175-177)acC>acT	p.T59T	ACRBP_ENST00000414226.2_Silent_p.T59T|ACRBP_ENST00000536350.1_Silent_p.T59T	NM_032489.2	NP_115878.2			acrosin binding protein											NS(1)|breast(1)|central_nervous_system(1)|large_intestine(8)|lung(5)|ovary(1)	17						GGAGACGGCAGGTAGTCTCTG	0.587																																					p.T59T		Atlas-SNP	.											.	ACRBP	52	.	0			c.C177T						.						98	91	93					12																	6756045		2203	4300	6503	SO:0001819	synonymous_variant	84519	exon2			ACGGCAGGTAGTC	AB051833	CCDS8554.1	12p13.31	2009-03-12			ENSG00000111644	ENSG00000111644			17195	protein-coding gene	gene with protein product	"proacrosin binding protein sp32", "cancer/testis antigen 23"	608352				11248070	Standard	NM_032489		Approved	SP32, OY-TES-1, CT23	uc001qpu.1	Q8NEB7	OTTHUMG00000168715	ENST00000229243.2:c.177C>T	chr12.hg19:g.6756045G>A		86.0	0.0		119.0	54.0	NM_032489		Silent	SNP	ENST00000229243.2	hg19	CCDS8554.1																																																																																			.	.		0.587	ACRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400703.1	NM_032489		A	6756045	G	A	6756045	2	1	85	1	0	0	0	0	0	0	0	1	170	987	35	3		3	ACRBP	12	6756045	Silent	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	3365132	6756045	127095850	81	11446										
CNOT2	4848	hgsc.bcm.edu	37	chr12	70726591	70726591	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gaatcaggcatttggaatgaAtaactccttatcaagtaaca	7	7	2	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr12:70726591A>G	ENST00000418359.3	+	8	1065	c.614A>G	c.(613-615)aAt>aGt	p.N205S	CNOT2_ENST00000229195.3_Missense_Mutation_p.N205S|CNOT2_ENST00000551483.1_5'Flank|CNOT2_ENST00000548230.1_3'UTR	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	205					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription corepressor binding (GO:0001226)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(2)|urinary_tract(1)	20	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			TTTGGAATGAATAACTCCTTA	0.313																																					p.N205S		Atlas-SNP	.											.	CNOT2	53	.	0			c.A614G						.						127	133	131					12																	70726591		2203	4298	6501	SO:0001583	missense	4848	exon8			GAATGAATAACTC	AF180473	CCDS31857.1	12q15	2008-05-14				ENSG00000111596			7878	protein-coding gene	gene with protein product		604909		NOT2		10637334	Standard	NM_014515		Approved	CDC36, NOT2H	uc001svv.3	Q9NZN8		ENST00000418359.3:c.614A>G	chr12.hg19:g.70726591A>G	ENSP00000412091:p.Asn205Ser	59.0	0.0		87.0	45.0	NM_001199302	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Missense_Mutation	SNP	ENST00000418359.3	hg19	CCDS31857.1	.	.	.	.	.	.	.	.	.	.	A	14.70	2.614160	0.46631	.	.	ENSG00000111596	ENST00000552231;ENST00000229195;ENST00000418359;ENST00000552915;ENST00000550641;ENST00000548159;ENST00000551043;ENST00000551873;ENST00000550194;ENST00000550155	T;T;T;T;T;T;T;T;T;T	0.73047	-0.71;-0.71;-0.71;-0.71;-0.71;-0.71;-0.71;-0.71;-0.71;-0.71	5.68	5.68	0.88126	.	0.081932	0.85682	D	0.000000	T	0.60586	0.2280	L	0.44542	1.39	0.48571	D	0.999679	B	0.20887	0.049	B	0.14023	0.01	T	0.56637	-0.7946	10	0.09590	T	0.72	-7.1856	14.5043	0.67743	1.0:0.0:0.0:0.0	.	205	Q9NZN8	CNOT2_HUMAN	S	205;205;205;144;185;196;205;120;197;15	ENSP00000450318:N205S;ENSP00000229195:N205S;ENSP00000412091:N205S;ENSP00000447497:N144S;ENSP00000448024:N185S;ENSP00000449659:N196S;ENSP00000449260:N205S;ENSP00000450090:N120S;ENSP00000449446:N197S;ENSP00000448499:N15S	ENSP00000229195:N205S	N	+	2	0	CNOT2	69012858	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.044000	0.57361	2.164000	0.68074	0.477000	0.44152	AAT	.	.		0.313	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404260.1			G	70726591	A	G	70726591	3	3	85	1	0	0	0	0	1	0	0	0	3621	101	4	2	636	2	CNOT2	12	70726591	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	63970546	70726591	63125304	82	11447										
RAB21	23011	hgsc.bcm.edu	37	chr12	72164380	72164380	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tgctttctttaggatacggcAggtcaagagagattccatgc	11	8	2	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr12:72164380A>T	ENST00000261263.3	+	3	484	c.228A>T	c.(226-228)gcA>gcT	p.A76A		NM_014999.2	NP_055814.1	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	76					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(4)|prostate(1)	6						AGGATACGGCAGGTCAAGAGA	0.338																																					p.A76A		Atlas-SNP	.											.	RAB21	17	.	0			c.A228T						.						72	77	75					12																	72164380		2203	4300	6503	SO:0001819	synonymous_variant	23011	exon3			TACGGCAGGTCAA	AF091035	CCDS9003.1	12q21.1	2014-09-04			ENSG00000080371	ENSG00000080371		"RAB, member RAS oncogene"	18263	protein-coding gene	gene with protein product		612398				10887961, 11697911, 16754960	Standard	NM_014999		Approved	KIAA0118	uc001swt.3	Q9UL25	OTTHUMG00000169572	ENST00000261263.3:c.228A>T	chr12.hg19:g.72164380A>T		67.0	0.0		95.0	37.0	NM_014999	Q14466|Q569H3	Silent	SNP	ENST00000261263.3	hg19	CCDS9003.1																																																																																			.	.		0.338	RAB21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404855.1			T	72164380	A	T	72164380	2	4	85	1	0	0	0	0	0	0	0	1	12923	175	7	4		4	RAB21	12	72164380	Silent	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	1437789	72164380	61687515	83	11448										
APPL2	55198	hgsc.bcm.edu	37	chr12	105591692	105591692	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ttcccgccttgggtgaagaaAtaaagcctctcccaggtggt	11	11	1	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr12:105591692A>G	ENST00000258530.3	-	11	1128	c.903T>C	c.(901-903)taT>taC	p.Y301Y	APPL2_ENST00000549573.1_Intron|APPL2_ENST00000551662.1_Silent_p.Y307Y|APPL2_ENST00000539978.2_Silent_p.Y258Y	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GGGTGAAGAAATAAAGCCTCT	0.542																																					p.Y307Y		Atlas-SNP	.											.	APPL2	69	.	0			c.T921C						.						84	85	85					12																	105591692		2203	4300	6503	SO:0001819	synonymous_variant	55198	exon11			GAAGAAATAAAGC	AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"Pleckstrin homology (PH) domain containing"	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.903T>C	chr12.hg19:g.105591692A>G		140.0	0.0		166.0	63.0	NM_001251904	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Silent	SNP	ENST00000258530.3	hg19	CCDS9101.1																																																																																			.	.		0.542	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406238.3	NM_018171		G	105591692	A	G	105591692	2	3	85	1	0	0	0	0	0	0	0	1	818	108	4	2		2	APPL2	12	105591692	Silent	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	33427312	105591692	28260203	84	11449										
EFHA1	221154	hgsc.bcm.edu	37	chr13	22084242	22084242	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gttctttcactattgcttccTattaaaaaaatcacaataat	2	8	3	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr13:22084242T>G	ENST00000382374.4	-	8	729		c.e8-2			NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2						mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										TATTGCTTCCtattaaaaaaa	0.259																																					.		Atlas-SNP	.											.	EFHA1	33	.	0			c.664-2A>C						.						35	38	37					13																	22084242		2183	4279	6462	SO:0001630	splice_region_variant	221154	exon9			GCTTCCTATTAAA	AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"EF-hand domain containing"	31830	protein-coding gene	gene with protein product		610632	"EF hand domain family A1", "EF-hand domain family, member A1"	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.664-2A>C	chr13.hg19:g.22084242T>G		256.0	0.0		190.0	66.0	NM_152726	Q8N0T6|Q8NAX8	Splice_Site	SNP	ENST00000382374.4	hg19	CCDS9297.1																																																																																			.	.		0.259	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726	Intron	G	22084242	T	G	22084242	5	3	85	1	0	0	0	0	0	0	1	0	4945	1536	53	5	662	5	EFHA1	13	22084242	Splice_Site	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10		22084242	93085636	85	11450										
PDS5B	23047	hgsc.bcm.edu	37	chr13	33241961	33241961	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tgaagaggacagctcaagctAttgagccatatattaccaat	8	8	1	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr13:33241961A>G	ENST00000315596.10	+	7	871	c.685A>G	c.(685-687)Att>Gtt	p.I229V		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	229					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		AGCTCAAGCTATTGAGCCATA	0.303																																					p.I229V		Atlas-SNP	.											.	PDS5B	141	.	0			c.A685G						.						53	50	51					13																	33241961		1823	4065	5888	SO:0001583	missense	23047	exon7			CAAGCTATTGAGC	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"androgen-induced proliferation inhibitor"	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.685A>G	chr13.hg19:g.33241961A>G	ENSP00000313851:p.Ile229Val	346.0	0.0		225.0	163.0	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	hg19	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.524974	0.85600	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	4.63	4.63	0.57726	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72104	0.3419	M	0.66939	2.045	0.80722	D	1	P;P	0.50369	0.934;0.816	P;B	0.55871	0.786;0.384	T	0.73585	-0.3936	9	0.44086	T	0.13	-0.6757	14.4151	0.67145	1.0:0.0:0.0:0.0	.	229;229	Q9NTI5;Q9NTI5-3	PDS5B_HUMAN;.	V	229	.	ENSP00000313851:I229V	I	+	1	0	PDS5B	32139961	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.178000	0.94855	1.854000	0.53819	0.529000	0.55759	ATT	.	.		0.303	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		G	33241961	A	G	33241961	3	3	85	1	0	0	0	0	1	0	0	0	11701	449	16	2	707	2	PDS5B	13	33241961	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	11157719	33241961	81927917	86	11451										
NHLRC3	387921	hgsc.bcm.edu	37	chr13	39621235	39621235	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	atttgataaagacactggggAgtggttaggagcatggaata	14	3	0	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr13:39621235A>T	ENST00000379600.3	+	6	1059	c.737A>T	c.(736-738)gAg>gTg	p.E246V	NHLRC3_ENST00000379599.2_Missense_Mutation_p.E179V|NHLRC3_ENST00000470258.1_Missense_Mutation_p.E49V	NM_001012754.3	NP_001012772.1	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3	246						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|skin(2)	11		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		GACACTGGGGAGTGGTTAGGA	0.363																																					p.E246V		Atlas-SNP	.											.	NHLRC3	35	.	0			c.A737T						.						149	151	150					13																	39621235		2203	4300	6503	SO:0001583	missense	387921	exon6			CTGGGGAGTGGTT		CCDS31961.1, CCDS31962.1	13q13.3	2007-12-18			ENSG00000188811	ENSG00000188811			33751	protein-coding gene	gene with protein product							Standard	NM_001017370		Approved		uc001uxc.4	Q5JS37	OTTHUMG00000016765	ENST00000379600.3:c.737A>T	chr13.hg19:g.39621235A>T	ENSP00000368920:p.Glu246Val	85.0	0.0		69.0	54.0	NM_001012754	B2RTZ2|B4DTL0|Q69YI9	Missense_Mutation	SNP	ENST00000379600.3	hg19	CCDS31961.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703164	0.68501	.	.	ENSG00000188811	ENST00000470258;ENST00000379600;ENST00000379599	D;D;D	0.90504	-2.68;-2.68;-2.68	5.68	4.48	0.54585	Six-bladed beta-propeller, TolB-like (1);	0.222920	0.45606	D	0.000342	D	0.88713	0.6511	L	0.55481	1.735	0.45015	D	0.998035	P;P	0.48089	0.883;0.905	B;P	0.45119	0.368;0.47	D	0.86539	0.1827	9	.	.	.	-16.8343	11.6371	0.51211	0.8668:0.0:0.0:0.1331	.	179;246	B4DTL0;Q5JS37	.;NHLC3_HUMAN	V	49;246;179	ENSP00000418127:E49V;ENSP00000368920:E246V;ENSP00000368919:E179V	.	E	+	2	0	NHLRC3	38519235	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.899000	0.75682	1.052000	0.40392	0.460000	0.39030	GAG	.	.		0.363	NHLRC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044616.2	NM_001012754		T	39621235	A	T	39621235	3	4	85	1	0	0	0	0	1	0	0	0	10416	304	11	4	759	4	NHLRC3	13	39621235	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	6379274	39621235	75548643	87	11452										
KTN1	3895	hgsc.bcm.edu	37	chr14	56079290	56079290	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gaagtctaaaaatggaagcgGtattgtaatctatttaatct	8	4	3	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr14:56079290G>A	ENST00000395314.3	+	2	591		c.e2+1		KTN1_ENST00000395308.1_Splice_Site|KTN1_ENST00000438792.2_Splice_Site|KTN1_ENST00000395309.3_Splice_Site|KTN1_ENST00000413890.2_Splice_Site|KTN1_ENST00000416613.1_Splice_Site|KTN1_ENST00000395311.1_Splice_Site	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)						microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AATGGAAGCGGTATTGTAATC	0.368			T	RET	papillary thryoid																																.		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.523+1G>A						.						40	47	45					14																	56079290		2203	4299	6502	SO:0001630	splice_region_variant	3895	exon2			GAAGCGGTATTGT		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.523+1G>A	chr14.hg19:g.56079290G>A		155.0	0.0		176.0	98.0	NM_001079521	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Splice_Site	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.740146	0.49045	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2704	0.98474	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KTN1	55149043	1.000000	0.71417	1.000000	0.80357	0.539000	0.34962	7.215000	0.77966	2.793000	0.96121	0.591000	0.81541	.	.	.		0.368	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		Intron	A	56079290	G	A	56079290	5	1	85	1	0	0	0	0	0	0	1	0	8594	1275	44	3	526	3	KTN1	14	56079290	Splice_Site	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10		56079290	51270250	88	11453										
RYR3	6263	hgsc.bcm.edu	37	chr15	34065806	34065806	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ttgggacgggaaagaacattTatgttgaaaggtaattagtg	13	2	0	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr15:34065806T>C	ENST00000389232.4	+	64	9197	c.9127T>C	c.(9127-9129)Tat>Cat	p.Y3043H	RYR3_ENST00000415757.3_Missense_Mutation_p.Y3043H	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3043					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AAAGAACATTTATGTTGAAAG	0.373																																					p.Y3043H		Atlas-SNP	.											.	RYR3	760	.	0			c.T9127C						.						98	86	90					15																	34065806		1915	4129	6044	SO:0001583	missense	6263	exon64			AACATTTATGTTG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.9127T>C	chr15.hg19:g.34065806T>C	ENSP00000373884:p.Tyr3043His	46.0	0.0		51.0	18.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.053465	0.75960	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.96802	-4.12;-4.13	6.17	6.17	0.99709	.	0.144186	0.48286	D	0.000182	D	0.96510	0.8861	L	0.33753	1.03	0.58432	D	0.999996	D;D	0.76494	0.986;0.999	P;D	0.68483	0.742;0.958	D	0.96017	0.9006	10	0.33940	T	0.23	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	3043;3043	Q15413-2;Q15413	.;RYR3_HUMAN	H	3043	ENSP00000373884:Y3043H;ENSP00000399610:Y3043H	ENSP00000354735:Y3043H	Y	+	1	0	RYR3	31853098	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.841000	0.86834	2.371000	0.80710	0.533000	0.62120	TAT	.	.		0.373	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			C	34065806	T	C	34065806	3	2	85	1	0	0	0	0	1	0	0	0	13785	1754	61	2	9381	2	RYR3	15	34065806	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10		34065806	68465586	89	11454										
CASC5	57082	hgsc.bcm.edu	37	chr15	40914304	40914304	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tcttcagatgaatgtgaagaAattaccaaaagtcgtaatga	8	5	2	5			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr15:40914304A>C	ENST00000346991.5	+	11	2310	c.1920A>C	c.(1918-1920)gaA>gaC	p.E640D	CASC5_ENST00000399668.2_Missense_Mutation_p.E614D|CASC5_ENST00000527044.1_3'UTR			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	640	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		AATGTGAAGAAATTACCAAAA	0.408																																					p.E640D		Atlas-SNP	.											.	CASC5	269	.	0			c.A1920C						.						60	57	58					15																	40914304		1884	4108	5992	SO:0001583	missense	57082	exon11			TGAAGAAATTACC	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1920A>C	chr15.hg19:g.40914304A>C	ENSP00000335463:p.Glu640Asp	107.0	0.0		80.0	29.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	hg19	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	A	0.081	-1.183850	0.01620	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.18502	2.21;2.21	3.92	2.75	0.32379	.	1.862450	0.02677	N	0.109237	T	0.20577	0.0495	L	0.51422	1.61	0.09310	N	1	B;B;B	0.27932	0.115;0.053;0.194	B;B;B	0.26864	0.064;0.031;0.074	T	0.28586	-1.0039	10	0.52906	T	0.07	.	8.3673	0.32393	0.6868:0.0:0.0:0.3132	.	614;640;614	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	D	640;614;614	ENSP00000335463:E640D;ENSP00000382576:E614D	ENSP00000260369:E614D	E	+	3	2	CASC5	38701596	0.907000	0.30839	0.007000	0.13788	0.016000	0.09150	1.120000	0.31271	0.532000	0.28657	0.455000	0.32223	GAA	.	.		0.408	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		C	40914304	A	C	40914304	3	2	85	1	0	0	0	0	1	0	0	0	2665	11	1	5	1958	5	CASC5	15	40914304	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	6848498	40914304	61617088	90	11455										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54305560	54305560	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	caatgccagttagacgcaacAgaaagagttcaagcagcctt	9	10	1	3	rs201347376		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr15:54305560A>C	ENST00000260323.11	+	1	460	c.460A>C	c.(460-462)Aga>Cga	p.R154R	UNC13C_ENST00000545554.1_Silent_p.R154R|UNC13C_ENST00000537900.1_Silent_p.R154R	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	154					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TAGACGCAACAGAAAGAGTTC	0.458																																					p.R154R		Atlas-SNP	.											.	UNC13C	674	.	0			c.A460C						.						88	89	89					15																	54305560		2022	4183	6205	SO:0001819	synonymous_variant	440279	exon1			CGCAACAGAAAGA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.460A>C	chr15.hg19:g.54305560A>C		120.0	0.0		107.0	33.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.458	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		C	54305560	A	C	54305560	2	2	85	1	0	0	0	0	0	0	0	1	17001	180	7	5		5	UNC13C	15	54305560	Silent	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	13391256	54305560	48225832	91	11456										
MYO1E	4643	hgsc.bcm.edu	37	chr15	59445837	59445837	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ggaaatccaggctctctggcGtctgtgacactcggtctgaa	12	11	3	2	rs546147455		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr15:59445837G>A	ENST00000288235.4	-	26	3431	c.3032C>T	c.(3031-3033)aCg>aTg	p.T1011M	AC092757.1_ENST00000408169.1_RNA	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	1011					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		GCTCTCTGGCGTCTGTGACAC	0.582													G|||	1	0.000199681	8e-04	0	5008	,	,		18279	0		0	False		,,,				2504	0				p.T1011M		Atlas-SNP	.											.	MYO1E	99	.	0			c.C3032T						.						89	87	87					15																	59445837		2191	4291	6482	SO:0001583	missense	4643	exon26			TCTGGCGTCTGTG	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.3032C>T	chr15.hg19:g.59445837G>A	ENSP00000288235:p.Thr1011Met	95.0	0.0		79.0	24.0	NM_004998	Q14778	Missense_Mutation	SNP	ENST00000288235.4	hg19	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	G	10.25	1.298887	0.23650	.	.	ENSG00000157483	ENST00000288235	D	0.87029	-2.2	5.54	2.4	0.29515	.	0.860605	0.10774	N	0.635629	T	0.78978	0.4369	L	0.34521	1.04	0.20975	N	0.999817	B	0.12013	0.005	B	0.08055	0.003	T	0.66352	-0.5945	10	0.45353	T	0.12	.	6.3791	0.21523	0.172:0.0:0.5869:0.2411	.	1011	Q12965	MYO1E_HUMAN	M	1011	ENSP00000288235:T1011M	ENSP00000288235:T1011M	T	-	2	0	MYO1E	57233129	0.022000	0.18835	0.049000	0.19019	0.325000	0.28411	0.935000	0.28924	0.711000	0.32018	0.655000	0.94253	ACG	.	.		0.582	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		A	59445837	G	A	59445837	3	1	85	1	0	0	0	0	1	0	0	0	10081	1145	40	1	306	1	MYO1E	15	59445837	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	5140277	59445837	43085555	92	11457										
LMAN1L	79748	hgsc.bcm.edu	37	chr15	75113449	75113449	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tgacctggaggagacgctggGcagacaccgccggatcctgc	15	13	0	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr15:75113449G>C	ENST00000309664.5	+	9	1080	c.941G>C	c.(940-942)gGc>gCc	p.G314A	LMAN1L_ENST00000379709.3_Missense_Mutation_p.G302A|RP11-414J4.2_ENST00000564823.1_RNA	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	314						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GAGACGCTGGGCAGACACCGC	0.627																																					p.G314A		Atlas-SNP	.											.	LMAN1L	43	.	0			c.G941C						.						17	19	18					15																	75113449		2187	4276	6463	SO:0001583	missense	79748	exon9			CGCTGGGCAGACA	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.941G>C	chr15.hg19:g.75113449G>C	ENSP00000310431:p.Gly314Ala	348.0	0.0		229.0	86.0	NM_021819	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	hg19	CCDS10270.1	.	.	.	.	.	.	.	.	.	.	G	4.582	0.108145	0.08780	.	.	ENSG00000140506	ENST00000309664;ENST00000379709	T;T	0.37915	1.21;1.17	5.43	-0.965	0.10323	.	1.447880	0.03887	N	0.277976	T	0.30885	0.0779	L	0.39898	1.24	0.09310	N	0.999999	B;B	0.27068	0.167;0.104	B;B	0.28011	0.085;0.039	T	0.29458	-1.0011	10	0.33141	T	0.24	.	8.6091	0.33791	0.5407:0.0:0.4593:0.0	.	302;314	Q9HAT1-3;Q9HAT1	.;LMA1L_HUMAN	A	314;302	ENSP00000310431:G314A;ENSP00000369031:G302A	ENSP00000310431:G314A	G	+	2	0	LMAN1L	72900502	0.015000	0.18098	0.002000	0.10522	0.001000	0.01503	0.243000	0.18106	-0.123000	0.11745	-0.812000	0.03155	GGC	.	.		0.627	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4			C	75113449	G	C	75113449	3	2	85	1	0	0	0	0	1	0	0	0	8846	1203	42	4	975	4	LMAN1L	15	75113449	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	15667612	75113449	27417943	93	11458										
IREB2	3658	hgsc.bcm.edu	37	chr15	78732183	78732183	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acattaaatgacagttcacaTaagaagttcttcgatgtatc	6	7	2	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr15:78732183T>G	ENST00000258886.8	+	2	215	c.66T>G	c.(64-66)caT>caG	p.H22Q	IREB2_ENST00000560440.1_Missense_Mutation_p.H22Q	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	22					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		ACAGTTCACATAAGAAGTTCT	0.299																																					p.H22Q	NSCLC(200;764 2208 35157 49871 50830)	Atlas-SNP	.											.	IREB2	106	.	0			c.T66G						.						137	116	123					15																	78732183		2196	4293	6489	SO:0001583	missense	3658	exon2			TTCACATAAGAAG	M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.66T>G	chr15.hg19:g.78732183T>G	ENSP00000258886:p.His22Gln	55.0	0.0		27.0	7.0	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	hg19	CCDS10302.1	.	.	.	.	.	.	.	.	.	.	T	7.383	0.629125	0.14257	.	.	ENSG00000136381	ENST00000258886	T	0.16073	2.37	4.72	-0.922	0.10468	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (1);	2.372550	0.01391	N	0.013258	T	0.04363	0.0120	N	0.00729	-1.24	0.18873	N	0.999988	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26710	-1.0095	10	0.13108	T	0.6	.	1.8901	0.03246	0.1539:0.0956:0.3396:0.4109	.	22;22	P48200;Q8WVK6	IREB2_HUMAN;.	Q	22	ENSP00000258886:H22Q	ENSP00000258886:H22Q	H	+	3	2	IREB2	76519238	0.747000	0.28283	0.892000	0.35008	0.971000	0.66376	-0.223000	0.09177	-0.096000	0.12329	0.383000	0.25322	CAT	.	.		0.299	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		G	78732183	T	G	78732183	3	3	85	1	0	0	0	0	1	0	0	0	7835	1403	49	5	72	5	IREB2	15	78732183	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	3618734	78732183	23799209	94	11459										
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84639291	84639291	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	aaagcaggtgtgtcaaaggcTggcagccaaaggtcggcgca	15	9	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr15:84639291T>A	ENST00000286744.5	+	20	2770	c.2546T>A	c.(2545-2547)cTg>cAg	p.L849Q	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.L849Q|ADAMTSL3_ENST00000567716.1_3'UTR	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	849	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			TGTCAAAGGCTGGCAGCCAAA	0.517																																					p.L849Q		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.T2546A						.						176	157	164					15																	84639291		2203	4300	6503	SO:0001583	missense	57188	exon20			AAAGGCTGGCAGC	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2546T>A	chr15.hg19:g.84639291T>A	ENSP00000286744:p.Leu849Gln	74.0	0.0		80.0	17.0	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	hg19	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.033030	0.35893	.	.	ENSG00000156218	ENST00000286744	T	0.50277	0.75	4.39	4.39	0.52855	.	0.502098	0.15040	N	0.283925	T	0.50548	0.1622	L	0.32530	0.975	0.35576	D	0.805862	B;D	0.58268	0.415;0.982	B;P	0.60473	0.142;0.875	T	0.51710	-0.8671	10	0.22109	T	0.4	.	10.5206	0.44916	0.0:0.0:0.1619:0.838	.	849;849	P82987-2;P82987	.;ATL3_HUMAN	Q	849	ENSP00000286744:L849Q	ENSP00000286744:L849Q	L	+	2	0	ADAMTSL3	82430295	1.000000	0.71417	0.997000	0.53966	0.698000	0.40448	3.475000	0.53136	1.830000	0.53286	0.528000	0.53228	CTG	.	.		0.517	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		A	84639291	T	A	84639291	3	1	85	1	0	0	0	0	1	0	0	0	276	1580	55	4	2620	4	ADAMTSL3	15	84639291	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	5907108	84639291	17892101	95	11460										
CDH8	1006	hgsc.bcm.edu	37	chr16	61689556	61689556	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cactatcactgattatgattGgtaaaagatagacttcttgc	7	7	2	4			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr16:61689556G>T	ENST00000577390.1	-	11	2678	c.1724C>A	c.(1723-1725)cCa>cAa	p.P575Q	CDH8_ENST00000299345.6_Missense_Mutation_p.P575Q|CDH8_ENST00000577730.1_Missense_Mutation_p.P575Q	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	575	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		GATTATGATTGGTAAAAGATA	0.413																																					p.P575Q		Atlas-SNP	.											.	CDH8	273	.	0			c.C1724A						.						141	129	133					16																	61689556		2203	4300	6503	SO:0001583	missense	1006	exon11			ATGATTGGTAAAA	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1724C>A	chr16.hg19:g.61689556G>T	ENSP00000462701:p.Pro575Gln	145.0	0.0		136.0	90.0	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	hg19	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.941676	0.92526	.	.	ENSG00000150394	ENST00000299345	T	0.49720	0.77	5.65	5.65	0.86999	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.72179	0.3428	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.75326	-0.3357	10	0.87932	D	0	.	18.7203	0.91691	0.0:0.0:1.0:0.0	.	575	P55286	CADH8_HUMAN	Q	575	ENSP00000299345:P575Q	ENSP00000299345:P575Q	P	-	2	0	CDH8	60247057	1.000000	0.71417	0.959000	0.39883	0.968000	0.65278	9.414000	0.97362	2.668000	0.90789	0.655000	0.94253	CCA	.	.		0.413	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		T	61689556	G	T	61689556	3	4	85	1	0	0	0	0	1	0	0	0	3118	1348	47	3	683	3	CDH8	16	61689556	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10		61689556	28665197	96	11461										
CDH13	1012	hgsc.bcm.edu	37	chr16	83636063	83636063	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tgcttgtgctttgtagactcTggaaaatcccaagtatgaac	9	8	1	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr16:83636063T>C	ENST00000566620.1	+	8	1255	c.965T>C	c.(964-966)cTg>cCg	p.L322P	CDH13_ENST00000428848.3_Missense_Mutation_p.L283P|CDH13_ENST00000268613.10_Missense_Mutation_p.L369P	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	322	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		TTGTAGACTCTGGAAAATCCC	0.473																																					p.L369P		Atlas-SNP	.											.	CDH13	97	.	0			c.T1106C						.						249	249	249					16																	83636063		1954	4164	6118	SO:0001583	missense	1012	exon9			AGACTCTGGAAAA	U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"Cadherins / Major cadherins"	1753	protein-coding gene	gene with protein product	"T-cadherin", "H-cadherin (heart)"	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.965T>C	chr16.hg19:g.83636063T>C	ENSP00000454435:p.Leu322Pro	91.0	0.0		76.0	28.0	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	hg19	CCDS58486.1	.	.	.	.	.	.	.	.	.	.	T	16.84	3.234272	0.58886	.	.	ENSG00000140945	ENST00000268613;ENST00000428848;ENST00000536143;ENST00000538855;ENST00000540531	T	0.51325	0.71	6.02	6.02	0.97574	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.45478	0.1344	L	0.48174	1.505	0.80722	D	1	B;B;B	0.22541	0.027;0.003;0.071	B;B;B	0.24848	0.04;0.025;0.056	T	0.36648	-0.9739	9	0.56958	D	0.05	.	15.3796	0.74645	0.0:0.0:0.0:1.0	.	283;369;322	B7Z590;B7Z9B1;P55290	.;.;CAD13_HUMAN	P	369;322;283;24;12	ENSP00000268613:L369P	ENSP00000268613:L369P	L	+	2	0	CDH13	82193564	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.225000	0.72271	2.311000	0.77944	0.533000	0.62120	CTG	.	.		0.473	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		C	83636063	T	C	83636063	3	2	85	1	0	0	0	0	1	0	0	0	3101	1580	55	2	995	2	CDH13	16	83636063	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	21946507	83636063	6718690	97	11462										
ADAD2	161931	hgsc.bcm.edu	37	chr16	84229176	84229176	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tgctggccacacaggggggcCccaagggcaaggagcagtcc	16	13	0	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr16:84229176C>T	ENST00000315906.5	+	6	977	c.925C>T	c.(925-927)Ccc>Tcc	p.P309S	RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.P391S|RP11-486L19.2_ENST00000536986.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	309	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						ACAGGGGGGCCCCAAGGGCAA	0.652																																					p.P391S		Atlas-SNP	.											.	ADAD2	46	.	0			c.C1171T						.						23	29	27					16																	84229176		2200	4297	6497	SO:0001583	missense	161931	exon7			GGGGGCCCCAAGG	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.925C>T	chr16.hg19:g.84229176C>T	ENSP00000325153:p.Pro309Ser	101.0	0.0		83.0	63.0	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	hg19	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	C	6.164	0.398482	0.11696	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	D;D	0.92858	-3.12;-3.12	5.22	-0.288	0.12855	Adenosine deaminase/editase (2);	0.433630	0.24226	N	0.040396	D	0.88731	0.6516	L	0.48642	1.525	0.19945	N	0.99994	B;B	0.25048	0.117;0.096	B;B	0.37198	0.243;0.169	T	0.79902	-0.1607	10	0.48119	T	0.1	-5.9549	8.4731	0.32997	0.0:0.5012:0.3528:0.146	.	309;391	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	S	309;391	ENSP00000325153:P309S;ENSP00000268624:P391S	ENSP00000268624:P391S	P	+	1	0	ADAD2	82786677	0.720000	0.27996	0.000000	0.03702	0.001000	0.01503	1.172000	0.31908	-0.457000	0.07033	-0.810000	0.03169	CCC	.	.		0.652	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		T	84229176	C	T	84229176	3	4	85	1	0	0	0	0	1	0	0	0	232	623	22	3	1197	3	ADAD2	16	84229176	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	593113	84229176	6125577	98	11463										
PMP22	5376	hgsc.bcm.edu	37	chr17	15134247	15134247	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gggcgcctcattcgcgtttcCgcaagatcacatagatgaca	10	12	2	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr17:15134247C>T	ENST00000395938.2	-	5	664	c.470G>A	c.(469-471)cGg>cAg	p.R157Q	PMP22_ENST00000494511.1_Silent_p.A97A|PMP22_ENST00000312280.3_Missense_Mutation_p.R157Q|PMP22_ENST00000395936.1_3'UTR	NM_001281455.1|NM_153321.1	NP_001268384.1|NP_696996.1	Q01453	PMP22_HUMAN	peripheral myelin protein 22	157			R -> G (in dbSNP:rs28936682). {ECO:0000269|PubMed:10632107}.|R -> W (in DSS; dbSNP:rs28936682). {ECO:0000269|PubMed:10211478}.		cell death (GO:0008219)|peripheral nervous system development (GO:0007422)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8				UCEC - Uterine corpus endometrioid carcinoma (92;0.0884)|BRCA - Breast invasive adenocarcinoma(8;4.92e-06)		TTCGCGTTTCCGCAAGATCAC	0.542																																					p.R157Q		Atlas-SNP	.											.	PMP22	18	.	0			c.G470A						.						83	79	80					17																	15134247		2203	4300	6503	SO:0001583	missense	5376	exon4			CGTTTCCGCAAGA	D11428	CCDS11168.1	17p12	2014-09-17			ENSG00000109099	ENSG00000109099			9118	protein-coding gene	gene with protein product		601097				8482547, 1497668	Standard	NM_001281456		Approved	HNPP, GAS-3, Sp110	uc002goj.3	Q01453	OTTHUMG00000058960	ENST00000395938.2:c.470G>A	chr17.hg19:g.15134247C>T	ENSP00000379269:p.Arg157Gln	94.0	0.0		123.0	49.0	NM_153322	Q8WV01	Missense_Mutation	SNP	ENST00000395938.2	hg19	CCDS11168.1	.	.	.	.	.	.	.	.	.	.	C	33	5.254022	0.95336	.	.	ENSG00000109099	ENST00000395938;ENST00000312280;ENST00000426385	D;D	0.96856	-4.15;-4.15	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.98298	0.9436	M	0.86864	2.845	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.99222	1.0879	10	0.87932	D	0	-46.1731	18.1907	0.89806	0.0:1.0:0.0:0.0	.	157	Q01453	PMP22_HUMAN	Q	157;157;146	ENSP00000379269:R157Q;ENSP00000308937:R157Q	ENSP00000308937:R157Q	R	-	2	0	PMP22	15074972	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.507000	0.81676	2.630000	0.89119	0.563000	0.77884	CGG	.	.		0.542	PMP22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130378.1	NM_000304		T	15134247	C	T	15134247	3	4	85	1	0	0	0	0	1	0	0	0	12148	652	23	1	16	1	PMP22	17	15134247	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10		15134247	66060963	99	11464										
TBC1D26	353149	hgsc.bcm.edu	37	chr17	15638739	15638739	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cattactaagtatgagcaggTacaagttgggccgctccctc	10	11	0	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr17:15638739T>A	ENST00000437605.2	+	3	325		c.e3+2		ZNF286A_ENST00000413242.2_Intron|AC005324.6_ENST00000434017.1_RNA|ZNF286A_ENST00000593105.1_Splice_Site|TBC1D26_ENST00000579428.1_Splice_Site	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26								Rab GTPase activator activity (GO:0005097)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		TATGAGCAGGTACAAGTTGGG	0.582																																					.		Atlas-SNP	.											.	TBC1D26	16	.	0			c.75+2T>A						.						75	77	76					17																	15638739		1889	4102	5991	SO:0001630	splice_region_variant	353149	exon3			AGCAGGTACAAGT		CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.75+2T>A	chr17.hg19:g.15638739T>A		243.0	0.0		226.0	82.0	NM_178571	A8K929|Q4G172	Splice_Site	SNP	ENST00000437605.2	hg19	CCDS42265.1	.	.	.	.	.	.	.	.	.	.	.	2.413	-0.334811	0.05278	.	.	ENSG00000214946	ENST00000437605	.	.	.	0.632	-0.951	0.10369	.	.	.	.	.	.	.	.	.	.	.	0.21861	N	0.999507	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	-1	.	.	.	+	.	.	TBC1D26	15579464	0.148000	0.22702	0.019000	0.16419	0.051000	0.14879	1.007000	0.29860	-0.400000	0.07656	0.378000	0.23410	.	.	.		0.582	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571	Intron	A	15638739	T	A	15638739	5	1	85	1	0	0	0	0	0	0	1	0	15631	1652	57	4	79	4	TBC1D26	17	15638739	Splice_Site	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	504492	15638739	65556471	100	11465										
TMEM98	26022	hgsc.bcm.edu	37	chr17	31258571	31258571	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	agactgtggtgattgttgccAtaggtgtgctggccaccatc	13	9	0	2	rs142287076		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr17:31258571A>G	ENST00000579849.1	+	3	456	c.25A>G	c.(25-27)Ata>Gta	p.I9V	TMEM98_ENST00000394642.3_Missense_Mutation_p.I9V|TMEM98_ENST00000578289.1_Missense_Mutation_p.I9V	NM_015544.2	NP_056359.2	Q9Y2Y6	TMM98_HUMAN	transmembrane protein 98	9						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(2)|large_intestine(1)	3		Ovarian(249;0.182)|Breast(31;0.244)	BRCA - Breast invasive adenocarcinoma(9;0.0769)			GATTGTTGCCATAGGTGTGCT	0.567																																					p.I9V		Atlas-SNP	.											.	TMEM98	23	.	0			c.A25G						.	A	VAL/ILE,VAL/ILE	2,4404	4.2+/-10.8	0,2,2201	142	114	124		25,25	4.9	1	17	dbSNP_134	124	0,8600		0,0,4300	no	missense,missense	TMEM98	NM_001033504.1,NM_015544.2	29,29	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	benign,benign	9/227,9/227	31258571	2,13004	2203	4300	6503	SO:0001583	missense	26022	exon2			GTTGCCATAGGTG	CR605381	CCDS11274.1	17q11.2	2005-12-16			ENSG00000006042	ENSG00000006042			24529	protein-coding gene	gene with protein product		615949				11230166	Standard	NM_001301746		Approved	DKFZP564K1964	uc002hhr.3	Q9Y2Y6	OTTHUMG00000132882	ENST00000579849.1:c.25A>G	chr17.hg19:g.31258571A>G	ENSP00000463245:p.Ile9Val	44.0	0.0		61.0	20.0	NM_001033504	E1P631|Q9UFK2	Missense_Mutation	SNP	ENST00000579849.1	hg19	CCDS11274.1	.	.	.	.	.	.	.	.	.	.	A	14.70	2.613331	0.46631	4.54E-4	0.0	ENSG00000006042	ENST00000394642;ENST00000261713;ENST00000395149;ENST00000439138	T;T;T;T	0.47177	0.85;0.86;0.86;0.86	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.31949	0.0813	L	0.29908	0.895	0.53005	D	0.999962	B	0.29862	0.259	B	0.19666	0.026	T	0.11348	-1.0591	10	0.17369	T	0.5	-10.05	12.5519	0.56231	1.0:0.0:0.0:0.0	.	9	Q9Y2Y6	TMM98_HUMAN	V	9	ENSP00000378138:I9V;ENSP00000261713:I9V;ENSP00000398446:I9V;ENSP00000406394:I9V	ENSP00000261713:I9V	I	+	1	0	TMEM98	28282684	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.376000	0.90138	2.055000	0.61198	0.529000	0.55759	ATA	.	A|1.000;G|0.000		0.567	TMEM98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256372.2	NM_015544		G	31258571	A	G	31258571	3	3	85	1	0	0	0	0	1	0	0	0	16240	217	8	2	27	2	TMEM98	17	31258571	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	15619832	31258571	49936639	101	11466										
SLFN11	91607	hgsc.bcm.edu	37	chr17	33679831	33679831	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gggatgttaaatgaaggattActtctaattacttgcatttc	8	5	1	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr17:33679831A>G	ENST00000394566.1	-	7	2522	c.2250T>C	c.(2248-2250)agT>agC	p.S750S	SLFN11_ENST00000308377.4_Silent_p.S750S	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	750					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATGAAGGATTACTTCTAATTA	0.423																																					p.S750S		Atlas-SNP	.											.	SLFN11	112	.	0			c.T2250C						.						98	91	93					17																	33679831		2203	4300	6503	SO:0001819	synonymous_variant	91607	exon5			AGGATTACTTCTA	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.2250T>C	chr17.hg19:g.33679831A>G		68.0	0.0		112.0	49.0	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Silent	SNP	ENST00000394566.1	hg19	CCDS11294.1																																																																																			.	.		0.423	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		G	33679831	A	G	33679831	2	3	85	1	0	0	0	0	0	0	0	1	14748	388	14	2		2	SLFN11	17	33679831	Silent	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10	2421260	33679831	47515379	102	11467										
C17orf46	124783	hgsc.bcm.edu	37	chr17	43332844	43332845	+	Frame_Shift_Ins	INS	-	-	GGTGGCGGGAGATCTGAGGACAGGAGGGGGCTTGGTGCCT													0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ttagctctgtcaggtcaatgINSggtggcgggagatctgagga							TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr17:43332844_43332845insGGTGGCGGGAGATCTGAGGACAGGAGGGGGCTTGGTGCCT	ENST00000331780.4	-	4	799_800	c.704_705insAGGCACCAAGCCCCCTCCTGTCCTCAGATCTCCCGCCACC	c.(703-705)cccfs	p.-235fs	MAP3K14-AS1_ENST00000588504.1_RNA|MAP3K14-AS1_ENST00000590100.1_RNA|MAP3K14-AS1_ENST00000592422.1_RNA|MAP3K14-AS1_ENST00000585346.1_RNA|MAP3K14-AS1_ENST00000591263.1_RNA|SPATA32_ENST00000543122.1_Frame_Shift_Ins_p.-214fs|MAP3K14-AS1_ENST00000588160.1_RNA|MAP3K14-AS1_ENST00000588698.1_RNA	NM_152343.2	NP_689556.2	Q96LK8	SPT32_HUMAN	spermatogenesis associated 32						spermatogenesis (GO:0007283)	perinuclear region of cytoplasm (GO:0048471)											TCAGGTCAATGGGTGGCGGGAG	0.589																																					p.P235fs		Pindel	.											.	.	.	.	0			c.705_706insAGGCACCAAGCCCCCTCCTGTCCTCAGATCTCCCGCCACC						.																																			SO:0001589	frameshift_variant	124783	exon4			.	AK058143	CCDS32669.1	17q21.31	2013-10-11	2012-10-08	2012-10-08	ENSG00000184361	ENSG00000184361			26349	protein-coding gene	gene with protein product	"acrosome expressed 2"		"chromosome 17 open reading frame 46", "testis expressed 34"	C17orf46, TEX34		18621766	Standard	NM_152343		Approved	FLJ25414, AEP2, VAD1.2	uc002iis.1	Q96LK8	OTTHUMG00000180363	ENST00000331780.4:c.665_704dupAGGCACCAAGCCCCCTCCTGTCCTCAGATCTCCCGCCACC	chr17.hg19:g.43332844_43332845insGGTGGCGGGAGATCTGAGGACAGGAGGGGGCTTGGTGCCT	ENSP00000331532:p.Pro235fs	95.0	0.0		114.0	11.0	NM_152343	Q7Z4U1|Q8N6V6	Frame_Shift_Ins	INS	ENST00000331780.4	hg19	CCDS32669.1																																																																																			.	.		0.589	SPATA32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450946.1	NM_152343		GGTGGCGGGAGATCTGAGGACAGGAGGGGGCTTGGTGCCT	43332845	-	GGTGGCGGGAGATCTGAGGACAGGAGGGGGCTTGGTGCCT	43332844	7	5	85	1	0	1	1	0	0	0	0	0	1859	1335	47	0	457	0	C17orf46	17	43332844	Frame_Shift_Ins	INS	-	TCGA-CC-A9FW-01A-11D-A36X-10	9653013	43332844	37862366	103	11468										
SFRS1	6426	hgsc.bcm.edu	37	chr17	56082903	56082903	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tacggcttcgagatcgagatCttccataacttggacttctg	9	10	2	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr17:56082903C>T	ENST00000258962.4	-	4	819	c.611G>A	c.(610-612)aGa>aAa	p.R204K	SRSF1_ENST00000584773.1_Missense_Mutation_p.R204K|RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000582730.2_3'UTR|SRSF1_ENST00000581497.1_5'Flank|SRSF1_ENST00000585096.1_Intron	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	204	Arg/Ser-rich (RS domain).|Interacts with SAFB1.				cardiac muscle contraction (GO:0060048)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA 3'-end processing (GO:0031124)|mRNA 5'-splice site recognition (GO:0000395)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGATCGAGATCTTCCATAACT	0.483																																					p.R204K		Atlas-SNP	.											.	SRSF1	41	.	0			c.G611A						.						140	134	136					17																	56082903		2203	4300	6503	SO:0001583	missense	6426	exon4			CGAGATCTTCCAT		CCDS11600.1, CCDS58580.1	17q22	2013-02-12	2010-06-22	2010-06-22	ENSG00000136450	ENSG00000136450		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10780	protein-coding gene	gene with protein product	"splicing factor 2", "pre-mRNA-splicing factor SF2, P33 subunit", "alternate splicing factor", "SR splicing factor 1"	600812	"splicing factor, arginine/serine-rich 1"	SFRS1		8530103, 20516191	Standard	NM_006924		Approved	ASF, SF2, SRp30a, SF2p33, MGC5228	uc002ivi.3	Q07955		ENST00000258962.4:c.611G>A	chr17.hg19:g.56082903C>T	ENSP00000258962:p.Arg204Lys	143.0	0.0		142.0	24.0	NM_006924	B2R6Z7|D3DTZ3|Q13809	Missense_Mutation	SNP	ENST00000258962.4	hg19	CCDS11600.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.151069	0.38021	.	.	ENSG00000136450	ENST00000258962	T	0.15487	2.42	5.65	5.65	0.86999	Nucleotide-binding, alpha-beta plait (1);	3.278820	0.01640	N	0.023995	T	0.27731	0.0682	L	0.39245	1.2	0.80722	D	1	B	0.22746	0.074	B	0.36719	0.231	T	0.50294	-0.8845	10	0.08381	T	0.77	.	20.1057	0.97893	0.0:1.0:0.0:0.0	.	204	Q07955	SRSF1_HUMAN	K	204	ENSP00000258962:R204K	ENSP00000258962:R204K	R	-	2	0	SRSF1	53437902	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.339000	0.79282	2.827000	0.97445	0.650000	0.86243	AGA	.	.		0.483	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924		T	56082903	C	T	56082903	3	4	85	1	0	0	0	0	1	0	0	0	14180	913	32	3	139	3	SFRS1	17	56082903	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	12750059	56082903	25112307	104	11469										
CELF4	56853	hgsc.bcm.edu	37	chr18	34855176	34855176	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cgtcctcggactgttgcttgTtgagcatgcccacgaagagt	12	11	0	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr18:34855176T>C	ENST00000591282.1	-	4	478	c.479A>G	c.(478-480)aAc>aGc	p.N160S	CELF4_ENST00000334919.5_Missense_Mutation_p.N150S|CELF4_ENST00000412753.1_Missense_Mutation_p.N160S|RP11-797E24.3_ENST00000588766.1_RNA|CELF4_ENST00000588597.1_Missense_Mutation_p.N149S|CELF4_ENST00000603232.1_Missense_Mutation_p.N160S|CELF4_ENST00000420428.2_Missense_Mutation_p.N160S|CELF4_ENST00000601019.1_Missense_Mutation_p.N159S|RP11-797E24.3_ENST00000586610.1_RNA|CELF4_ENST00000361795.5_Missense_Mutation_p.N159S|CELF4_ENST00000591287.1_Missense_Mutation_p.N159S			Q9BZC1	CELF4_HUMAN	CUGBP, Elav-like family member 4	160	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.|Sufficient for RNA-binding and MSE- dependent splicing activity.				alternative mRNA splicing, via spliceosome (GO:0000380)|embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA splice site selection (GO:0006376)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of translation (GO:0017148)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	44						CTGTTGCTTGTTGAGCATGCC	0.607																																					p.N160S		Atlas-SNP	.											.	CELF4	90	.	0			c.A479G						.						63	65	64					18																	34855176		2203	4300	6503	SO:0001583	missense	56853	exon4			TGCTTGTTGAGCA	AF248651	CCDS32818.1, CCDS45857.1, CCDS45858.1	18q12	2013-02-12	2010-02-19	2010-02-19				"RNA binding motif (RRM) containing"	14015	protein-coding gene	gene with protein product		612679	"Bruno (Drosophila) -like 4, RNA binding protein", "bruno-like 4, RNA binding protein (Drosophila)"	BRUNOL4		10893231	Standard	NM_020180		Approved		uc002lae.2	Q9BZC1		ENST00000591282.1:c.479A>G	chr18.hg19:g.34855176T>C	ENSP00000464794:p.Asn160Ser	181.0	0.0		154.0	127.0	NM_001025087	Q59EN7|Q86XB9|Q8N2M6|Q9BQ96|Q9NR84|Q9NR85	Missense_Mutation	SNP	ENST00000591282.1	hg19	CCDS32818.1	.	.	.	.	.	.	.	.	.	.	T	7.522	0.656849	0.14580	.	.	ENSG00000101489	ENST00000361795;ENST00000412753;ENST00000420428;ENST00000334919;ENST00000361683	T;T	0.05025	3.51;3.51	4.38	4.38	0.52667	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.02727	0.0082	N	0.00972	-1.085	0.49130	D	0.999752	B;P;B;B;B	0.36183	0.063;0.542;0.226;0.028;0.036	B;B;B;B;B	0.42959	0.053;0.403;0.08;0.053;0.06	T	0.48625	-0.9019	10	0.02654	T	1	-12.1704	14.0379	0.64656	0.0:0.0:0.0:1.0	.	159;149;150;159;160	Q9BZC1-3;B4DHA8;Q9BZC1-5;Q9BZC1-2;Q9BZC1	.;.;.;.;CELF4_HUMAN	S	160;160;159;150;43	ENSP00000406823:N160S;ENSP00000335631:N150S	ENSP00000335631:N150S	N	-	2	0	CELF4	33109174	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.031000	0.41117	1.960000	0.56953	0.533000	0.62120	AAC	.	.		0.607	CELF4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440892.1	NM_020180		C	34855176	T	C	34855176	3	2	85	1	0	0	0	0	1	0	0	0	3220	1725	60	2	1017	2	CELF4	18	34855176	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10		34855176	43222072	105	11470										
DENND1C	79958	hgsc.bcm.edu	37	chr19	6475892	6475892	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ggcagcgtggggatcagcacGtgctcccagcgcatggggta	17	11	1	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr19:6475892G>A	ENST00000381480.2	-	11	847	c.735C>T	c.(733-735)caC>caT	p.H245H	DENND1C_ENST00000591030.1_5'Flank|DENND1C_ENST00000543576.1_Silent_p.H201H	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	245	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						GGATCAGCACGTGCTCCCAGC	0.721																																					p.H245H		Atlas-SNP	.											.	DENND1C	93	.	0			c.C735T						.						9	11	10					19																	6475892		2142	4233	6375	SO:0001819	synonymous_variant	79958	exon11			CAGCACGTGCTCC	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.735C>T	chr19.hg19:g.6475892G>A		89.0	0.0		67.0	30.0	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Silent	SNP	ENST00000381480.2	hg19	CCDS45938.1																																																																																			.	.		0.721	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		A	6475892	G	A	6475892	2	1	85	1	0	0	0	0	0	0	0	1	4430	1136	40	1		1	DENND1C	19	6475892	Silent	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10		6475892	52653091	106	11471										
ARMC6	93436	hgsc.bcm.edu	37	chr19	19162935	19162935	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tccgtgtgccctttggccatGcccacaaccatgccaagatg	9	15	0	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr19:19162935G>A	ENST00000535612.1	+	5	1216	c.784G>A	c.(784-786)Gcc>Acc	p.A262T	ARMC6_ENST00000269932.6_Missense_Mutation_p.A237T|ARMC6_ENST00000392335.2_Missense_Mutation_p.A237T|ARMC6_ENST00000392336.3_Missense_Mutation_p.A262T|ARMC6_ENST00000546344.1_Missense_Mutation_p.A169T	NM_001199196.1	NP_001186125.1	Q6NXE6	ARMC6_HUMAN	armadillo repeat containing 6	262					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(5)|ovary(1)|prostate(1)	14			OV - Ovarian serous cystadenocarcinoma(5;5.66e-06)|Epithelial(12;0.000391)			CTTTGGCCATGCCCACAACCA	0.582																																					p.A262T		Atlas-SNP	.											.	ARMC6	56	.	0			c.G784A						.						76	46	56					19																	19162935		2203	4300	6503	SO:0001583	missense	93436	exon5			GGCCATGCCCACA	BX648486	CCDS32965.1, CCDS56089.1	19p13	2013-02-14				ENSG00000105676		"Armadillo repeat containing"	25049	protein-coding gene	gene with protein product						12477932	Standard	NM_033415		Approved	MGC19595	uc002nlc.3	Q6NXE6		ENST00000535612.1:c.784G>A	chr19.hg19:g.19162935G>A	ENSP00000444156:p.Ala262Thr	40.0	0.0		37.0	18.0	NM_001199196	B4DI98|O94999|Q9BTH5	Missense_Mutation	SNP	ENST00000535612.1	hg19	CCDS56089.1	.	.	.	.	.	.	.	.	.	.	G	32	5.121373	0.94385	.	.	ENSG00000105676	ENST00000392335;ENST00000535612;ENST00000537263;ENST00000269932;ENST00000546344;ENST00000541898;ENST00000545190;ENST00000379532;ENST00000392336	T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.70701	0.3254	M	0.78344	2.41	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.70561	-0.4838	10	0.45353	T	0.12	-31.8184	18.5631	0.91108	0.0:0.0:1.0:0.0	.	262	Q6NXE6	ARMC6_HUMAN	T	237;262;237;237;169;237;173;173;262	ENSP00000376147:A237T;ENSP00000444156:A262T;ENSP00000441948:A237T;ENSP00000269932:A237T;ENSP00000444341:A169T;ENSP00000446037:A237T;ENSP00000376148:A262T	ENSP00000269932:A237T	A	+	1	0	ARMC6	19023935	1.000000	0.71417	0.871000	0.34182	0.678000	0.39670	7.687000	0.84139	2.637000	0.89404	0.555000	0.69702	GCC	.	.		0.582	ARMC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403226.1	NM_033415		A	19162935	G	A	19162935	3	1	85	1	0	0	0	0	1	0	0	0	955	1319	46	3	719	3	ARMC6	19	19162935	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	12687043	19162935	39966048	107	11472										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42880376	42880376	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	tctcctgcttcttcctcttcCtctcactctgtgtgctcctc	4	18	5	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr19:42880376C>G	ENST00000251268.6	+	42	7987	c.7987C>G	c.(7987-7989)Ctc>Gtc	p.L2663V	MEGF8_ENST00000334370.4_Missense_Mutation_p.L2596V|MEGF8_ENST00000378073.4_Missense_Mutation_p.L257V	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2663					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				cttcctcttcctctCACTCTG	0.612																																					p.L2663V		Atlas-SNP	.											.	MEGF8	358	.	0			c.C7987G						.						26	24	25					19																	42880376		2195	4296	6491	SO:0001583	missense	1954	exon42			CTCTTCCTCTCAC	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.7987C>G	chr19.hg19:g.42880376C>G	ENSP00000251268:p.Leu2663Val	108.0	0.0		93.0	22.0	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	C	17.39	3.378110	0.61735	.	.	ENSG00000105429	ENST00000334370;ENST00000251268;ENST00000378073	T;T;T	0.53206	0.95;0.94;0.63	4.14	4.14	0.48551	.	0.000000	0.51477	D	0.000098	T	0.67998	0.2953	M	0.75085	2.285	0.80722	D	1	D;D;D	0.67145	0.988;0.993;0.996	D;D;D	0.80764	0.992;0.987;0.994	T	0.73493	-0.3965	10	0.87932	D	0	-17.9535	15.741	0.77894	0.0:1.0:0.0:0.0	.	257;2663;2596	F5GZG7;Q7Z7M0;Q7Z7M0-2	.;MEGF8_HUMAN;.	V	2596;2663;257	ENSP00000334219:L2596V;ENSP00000251268:L2663V;ENSP00000367313:L257V	ENSP00000251268:L2663V	L	+	1	0	MEGF8	47572216	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	2.683000	0.46943	2.326000	0.78906	0.462000	0.41574	CTC	.	.		0.612	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		G	42880376	C	G	42880376	3	3	85	1	0	0	0	0	1	0	0	0	9472	681	24	4	7948	4	MEGF8	19	42880376	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	23717441	42880376	16248607	108	11473										
NSFL1C	55968	hgsc.bcm.edu	37	chr20	1447368	1447368	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ccgccgcgcggcgctacctgCaagtcccagccggccgactc	12	20	0	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr20:1447368C>T	ENST00000216879.4	-	1	969	c.102G>A	c.(100-102)ttG>ttA	p.L34L	NSFL1C_ENST00000381658.4_5'UTR|NSFL1C_ENST00000353088.2_Silent_p.L34L|NSFL1C_ENST00000350991.4_Silent_p.L34L|NSFL1C_ENST00000476071.1_Silent_p.L34L	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)	34						chromosome (GO:0005694)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	16						GCGCTACCTGCAAGTCCCAGC	0.741																																					p.L34L		Atlas-SNP	.											.	NSFL1C	38	.	0			c.G102A						.						5	7	6					20																	1447368		1943	3904	5847	SO:0001819	synonymous_variant	55968	exon1			TACCTGCAAGTCC	AF112211	CCDS13015.1, CCDS13016.1, CCDS56175.1	20p13	2011-06-28			ENSG00000088833	ENSG00000088833		"UBX domain containing"	15912	protein-coding gene	gene with protein product	"SHP1 homolog (S. cerevisiae)", "UBX domain protein 2C"	606610				11042152	Standard	NM_016143		Approved	dJ776F14.1, p47, UBXD10, UBX1, UBXN2C	uc002wfc.3	Q9UNZ2	OTTHUMG00000031665	ENST00000216879.4:c.102G>A	chr20.hg19:g.1447368C>T		101.0	0.0		155.0	75.0	NM_016143	A2A2L1|B2RD74|Q5JXA4|Q5JXA5|Q7Z533|Q9H102|Q9NVL9|Q9UI06	Silent	SNP	ENST00000216879.4	hg19	CCDS13015.1																																																																																			.	.		0.741	NSFL1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077525.2	NM_016143		T	1447368	C	T	1447368	2	4	85	1	0	0	0	0	0	0	0	1	10681	709	25	3		3	NSFL1C	20	1447368	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10		1447368	61578152	109	11474										
THBD	7056	hgsc.bcm.edu	37	chr20	23029882	23029882	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gtggcagctgcaggccgatcCagaggcgccggcggccaacg	17	14	0	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr20:23029882C>T	ENST00000377103.2	-	1	496	c.260G>A	c.(259-261)tGg>tAg	p.W87*		NM_000361.2	NP_000352.1	P07204	TRBM_HUMAN	thrombomodulin	87	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood coagulation (GO:0007596)|female pregnancy (GO:0007565)|leukocyte migration (GO:0050900)|negative regulation of blood coagulation (GO:0030195)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|response to cAMP (GO:0051591)|response to lipopolysaccharide (GO:0032496)|response to X-ray (GO:0010165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|large_intestine(3)|ovary(1)|skin(1)	7	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)				Drotrecogin alfa(DB00055)|Ibuprofen(DB01050)	CAGGCCGATCCAGAGGCGCCG	0.682																																					p.W87X		Atlas-SNP	.											.	THBD	26	.	0			c.G260A						.						4	3	4					20																	23029882		1859	3652	5511	SO:0001587	stop_gained	7056	exon1			CCGATCCAGAGGC		CCDS13148.1	20p11.21	2014-09-17			ENSG00000178726	ENSG00000178726		"CD molecules"	11784	protein-coding gene	gene with protein product		188040					Standard	NM_000361		Approved	CD141	uc002wss.3	P07204	OTTHUMG00000032053	ENST00000377103.2:c.260G>A	chr20.hg19:g.23029882C>T	ENSP00000366307:p.Trp87*	138.0	0.0		199.0	39.0	NM_000361	Q8IV29|Q9UC32	Nonsense_Mutation	SNP	ENST00000377103.2	hg19	CCDS13148.1	.	.	.	.	.	.	.	.	.	.	C	38	6.957767	0.97964	.	.	ENSG00000178726	ENST00000377103	.	.	.	5.82	4.87	0.63330	.	0.000000	0.64402	U	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.6675	15.3253	0.74157	0.1408:0.8592:0.0:0.0	.	.	.	.	X	87	.	ENSP00000366307:W87X	W	-	2	0	THBD	22977882	1.000000	0.71417	1.000000	0.80357	0.537000	0.34900	3.931000	0.56529	1.446000	0.47643	0.549000	0.68633	TGG	.	.		0.682	THBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078307.2			T	23029882	C	T	23029882	4	4	85	1	0	0	0	0	0	1	0	0	15867	595	21	3	1471	3	THBD	20	23029882	Nonsense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	21582514	23029882	39995638	110	11475										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31016225	31016225	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	agctacagagcttcctcacaGgtaaggaagaggtagagcct	12	9	1	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr20:31016225G>A	ENST00000375687.4	+	6	895	c.471G>A	c.(469-471)caG>caA	p.Q157Q	ASXL1_ENST00000306058.5_Splice_Site_p.Q152Q|ASXL1_ENST00000470145.1_3'UTR|ASXL1_ENST00000542461.1_3'UTR	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	157					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CTTCCTCACAGGTAAGGAAGA	0.483			"F, N, Mis"		"MDS, CMML"																																p.Q157Q		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.G471A						.						106	99	102					20																	31016225		2203	4300	6503	SO:0001630	splice_region_variant	171023	exon5			CTCACAGGTAAGG	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.471+1G>A	chr20.hg19:g.31016225G>A		116.0	0.0		159.0	13.0	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	hg19	CCDS13201.1																																																																																			.	.		0.483	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	Silent	A	31016225	G	A	31016225	5	1	85	1	0	0	0	0	0	0	1	0	1066	1014	35	3	499	3	ASXL1	20	31016225	Splice_Site	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	7986343	31016225	32009295	111	11476										
B4GALT5	9334	hgsc.bcm.edu	37	chr20	48252994	48252994	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ttgacttcctcagcagagcaTacctgtttagggagggaaca	11	9	1	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr20:48252994T>A	ENST00000371711.4	-	9	1209	c.1022A>T	c.(1021-1023)tAt>tTt	p.Y341F		NM_004776.3	NP_004767.1	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5	341					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)			CAGCAGAGCATACCTGTTTAG	0.517																																					p.Y341F		Atlas-SNP	.											.	B4GALT5	40	.	0			c.A1022T						.						148	128	135					20																	48252994		2203	4300	6503	SO:0001583	missense	9334	exon9			AGAGCATACCTGT	AB004550	CCDS13420.1	20q13.1-q13.2	2013-02-19			ENSG00000158470	ENSG00000158470		"Beta 4-glycosyltransferases"	928	protein-coding gene	gene with protein product	"beta4-GalT IV"	604016				9597550, 9435216	Standard	NM_004776		Approved	beta4GalT-V	uc002xuu.4	O43286	OTTHUMG00000033086	ENST00000371711.4:c.1022A>T	chr20.hg19:g.48252994T>A	ENSP00000360776:p.Tyr341Phe	117.0	0.0		130.0	47.0	NM_004776	E1P625|Q2M394|Q9UJQ8	Missense_Mutation	SNP	ENST00000371711.4	hg19	CCDS13420.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.075870	0.36662	.	.	ENSG00000158470	ENST00000371711	T	0.34472	1.36	5.43	5.43	0.79202	.	0.109041	0.64402	D	0.000004	T	0.29588	0.0738	L	0.42581	1.335	0.80722	D	1	B	0.20052	0.041	B	0.20184	0.028	T	0.10636	-1.0621	10	0.06494	T	0.89	-21.5454	15.4778	0.75497	0.0:0.0:0.0:1.0	.	341	O43286	B4GT5_HUMAN	F	341	ENSP00000360776:Y341F	ENSP00000360776:Y341F	Y	-	2	0	B4GALT5	47686401	1.000000	0.71417	0.983000	0.44433	0.947000	0.59692	7.841000	0.86834	2.050000	0.60909	0.460000	0.39030	TAT	.	.		0.517	B4GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080543.3	NM_004776		A	48252994	T	A	48252994	3	1	85	1	0	0	0	0	1	0	0	0	1274	1406	49	4	148	4	B4GALT5	20	48252994	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	17236769	48252994	14772526	112	11477										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57769575	57769575	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	agccacagcacccgcagtccCcacagcacccaaaacccctt	5	21	0	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr20:57769575C>T	ENST00000371030.2	+	1	3501	c.3501C>T	c.(3499-3501)ccC>ccT	p.P1167P		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1167							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CCCGCAGTCCCCACAGCACCC	0.667																																					p.P1167P		Atlas-SNP	.											.	ZNF831	287	.	0			c.C3501T						.						48	55	53					20																	57769575		2066	4173	6239	SO:0001819	synonymous_variant	128611	exon1			CAGTCCCCACAGC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.3501C>T	chr20.hg19:g.57769575C>T		98.0	0.0		119.0	36.0	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	hg19	CCDS42894.1																																																																																			.	.		0.667	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57769575	C	T	57769575	2	4	85	1	0	0	0	0	0	0	0	1	18200	610	22	3		3	ZNF831	20	57769575	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	9516581	57769575	5255945	113	11478										
C20orf151	140893	hgsc.bcm.edu	37	chr20	60987760	60987760	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gggtgcagatgcactcaggcCcctccccggtcgtgctcgta	13	15	1	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr20:60987760C>T	ENST00000252998.1	-	13	1952	c.1796G>A	c.(1795-1797)gGg>gAg	p.G599E		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	599						extracellular space (GO:0005615)											GCACTCAGGCCCCTCCCCGGT	0.697																																					p.G599E		Atlas-SNP	.											.	.	.	.	0			c.G1796A						.						61	60	60					20																	60987760		2202	4300	6502	SO:0001583	missense	140893	exon13			TCAGGCCCCTCCC	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"hypothetical protein LOC140893"		"chromosome 20 open reading frame 151"	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.1796G>A	chr20.hg19:g.60987760C>T	ENSP00000252998:p.Gly599Glu	27.0	0.0		43.0	18.0	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	hg19	CCDS13498.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.417755	0.25552	.	.	ENSG00000130701	ENST00000252998	T	0.19669	2.13	3.52	0.643	0.17770	.	0.808221	0.10407	N	0.678451	T	0.14184	0.0343	L	0.50333	1.59	0.09310	N	1	B	0.28900	0.227	B	0.22152	0.038	T	0.34625	-0.9821	10	0.10377	T	0.69	-18.1535	4.869	0.13622	0.0:0.5739:0.0:0.4261	.	599	Q8NC74	CT151_HUMAN	E	599	ENSP00000252998:G599E	ENSP00000252998:G599E	G	-	2	0	C20orf151	60421155	0.000000	0.05858	0.001000	0.08648	0.051000	0.14879	0.230000	0.17852	0.274000	0.22072	0.491000	0.48974	GGG	.	.		0.697	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833		T	60987760	C	T	60987760	3	4	85	1	0	0	0	0	1	0	0	0	2093	623	22	3	206	3	C20orf151	20	60987760	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	3218185	60987760	2037760	114	11479										
CLDN17	26285	hgsc.bcm.edu	37	chr21	31538490	31538490	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ctatgtggatggctgggttgTagaaatctctgatgattata	12	4	1	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr21:31538490T>C	ENST00000286808.3	-	1	481	c.446A>G	c.(445-447)tAc>tGc	p.Y149C		NM_012131.2	NP_036263.1	P56750	CLD17_HUMAN	claudin 17	149					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	23						GGCTGGGTTGTAGAAATCTCT	0.522																																					p.Y149C		Atlas-SNP	.											.	CLDN17	61	.	0			c.A446G						.						78	76	76					21																	31538490		2203	4300	6503	SO:0001583	missense	26285	exon1			GGGTTGTAGAAAT	AJ250712	CCDS13586.1	21q22.1	2008-07-31			ENSG00000156282	ENSG00000156282		"Claudins"	2038	protein-coding gene	gene with protein product						12736707	Standard	NM_012131		Approved	MGC126552, MGC126554	uc011acv.2	P56750	OTTHUMG00000081873	ENST00000286808.3:c.446A>G	chr21.hg19:g.31538490T>C	ENSP00000286808:p.Tyr149Cys	74.0	0.0		55.0	35.0	NM_012131	Q3MJB5|Q6UY37	Missense_Mutation	SNP	ENST00000286808.3	hg19	CCDS13586.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.465356	0.63513	.	.	ENSG00000156282	ENST00000286808	D	0.89196	-2.48	4.54	4.54	0.55810	.	0.064498	0.64402	D	0.000005	D	0.96122	0.8736	H	0.95850	3.73	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97306	0.9934	10	0.87932	D	0	.	14.5833	0.68308	0.0:0.0:0.0:1.0	.	149	P56750	CLD17_HUMAN	C	149	ENSP00000286808:Y149C	ENSP00000286808:Y149C	Y	-	2	0	CLDN17	30460361	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	6.010000	0.70753	2.266000	0.75297	0.533000	0.62120	TAC	.	.		0.522	CLDN17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182261.1	NM_012131		C	31538490	T	C	31538490	3	2	85	1	0	0	0	0	1	0	0	0	3480	1638	57	2	232	2	CLDN17	21	31538490	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10		31538490	16591405	115	11480										
TRAPPC10	7109	hgsc.bcm.edu	37	chr21	45507598	45507598	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	agaacagtcttctgaggccgCgctccggattcagtcctccg	11	14	3	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr21:45507598C>T	ENST00000291574.4	+	17	2733	c.2558C>T	c.(2557-2559)gCg>gTg	p.A853V		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	853					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						TCTGAGGCCGCGCTCCGGATT	0.517																																					p.A853V		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.C2558T						.						75	72	73					21																	45507598		2203	4300	6503	SO:0001583	missense	7109	exon17			AGGCCGCGCTCCG	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"Trafficking protein particle complex"	11868	protein-coding gene	gene with protein product	"trafficking protein particle complex subunit 130", "TRAPP 130 kDa subunit"	602103	"transmembrane protein 1"	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.2558C>T	chr21.hg19:g.45507598C>T	ENSP00000291574:p.Ala853Val	45.0	0.0		22.0	12.0	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	hg19	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	C	6.958	0.546617	0.13312	.	.	ENSG00000160218	ENST00000291574	T	0.21932	1.98	5.33	-3.33	0.04958	.	1.301150	0.05013	N	0.471366	T	0.09862	0.0242	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31558	-0.9939	10	0.27082	T	0.32	.	6.6749	0.23087	0.0:0.4266:0.1157:0.4577	.	853	P48553	TPC10_HUMAN	V	853	ENSP00000291574:A853V	ENSP00000291574:A853V	A	+	2	0	TRAPPC10	44332026	0.000000	0.05858	0.000000	0.03702	0.070000	0.16714	0.027000	0.13621	-1.165000	0.02786	-0.140000	0.14226	GCG	.	.		0.517	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		T	45507598	C	T	45507598	3	4	85	1	0	0	0	0	1	0	0	0	16472	768	27	1	2624	1	TRAPPC10	21	45507598	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	13969108	45507598	2622297	116	11481										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46875463	46875472	+	Frame_Shift_Del	DEL	GGCTGCCACA	GGCTGCCACA	-													0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cgatggctccctacccctgtGgctgccacatcctgctgctg							TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	GGCTGCCACA	GGCTGCCACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr21:46875463_46875472delGGCTGCCACA	ENST00000359759.4	+	1	40_49	c.19_28delGGCTGCCACA	c.(19-30)ggctgccacatcfs	p.GCHI7fs	COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_Frame_Shift_Del_p.GCHI7fs			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	7					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)	p.G7S(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CTACCCCTGTGGCTGCCACATCCTGCTGCT	0.667																																					p.6_9del		Atlas-Indel,Pindel	.											.	COL18A1	129	.	1	Substitution - Missense(1)	lung(1)	c.18_27del						.																																			SO:0001589	frameshift_variant	80781	exon1			.		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.19_28delGGCTGCCACA	chr21.hg19:g.46875463_46875472delGGCTGCCACA	ENSP00000352798:p.Gly7fs	73.0	0.0		43.0	29.0	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Frame_Shift_Del	DEL	ENST00000359759.4	hg19																																																																																				.	.		0.667	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			-	46875472	GGCTGCCACA	-	46875463	7	5	85	1	0	1	0	1	0	0	0	0	3677	1348	47	0	135	0	COL18A1	21	46875463	Frame_Shift_Del	DEL	GGCTGCCACA	TCGA-CC-A9FW-01A-11D-A36X-10	1367865	46875463	1254432	117	11482										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46888580	46888597	+	In_Frame_Del	DEL	CGTGGACTGTGAGGAGTT	CGTGGACTGTGAGGAGTT	-													0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ggtggctttgtggccctctaCgtggactgtgaggagttcca							TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	CGTGGACTGTGAGGAGTT	CGTGGACTGTGAGGAGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr21:46888580_46888597delCGTGGACTGTGAGGAGTT	ENST00000359759.4	+	2	1797_1814	c.1776_1793delCGTGGACTGTGAGGAGTT	c.(1774-1794)tacgtggactgtgaggagttc>tac	p.VDCEEF593del	COL18A1_ENST00000400337.2_In_Frame_Del_p.VDCEEF178del|COL18A1_ENST00000355480.5_In_Frame_Del_p.VDCEEF358del			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	593	Laminin G-like.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		TGGCCCTCTACGTGGACTGTGAGGAGTTCCAGAGAATG	0.67																																					p.357_363del		Atlas-Indel,Pindel	.											.	COL18A1	129	.	0			c.1070_1087del						.																																			SO:0001651	inframe_deletion	80781	exon2			.		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.1776_1793delCGTGGACTGTGAGGAGTT	chr21.hg19:g.46888580_46888597delCGTGGACTGTGAGGAGTT	ENSP00000352798:p.Val593_Phe598del	59.0	0.0		30.0	12.0	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	In_Frame_Del	DEL	ENST00000359759.4	hg19																																																																																				.	.		0.67	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			-	46888597	CGTGGACTGTGAGGAGTT	-	46888580	7	5	85	1	0	1	0	1	0	0	0	0	3677	547	19	0	1896	0	COL18A1	21	46888580	In_Frame_Del	DEL	CGTGGACTGTGAGGAGTT	TCGA-CC-A9FW-01A-11D-A36X-10	13117	46888580	1241315	118	11483										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47666731	47666731	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	aagcagcagcatgagcccacTggctcccaggaggtccttct	11	14	1	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr21:47666731T>A	ENST00000397708.1	-	22	4614	c.4360A>T	c.(4360-4362)Agt>Tgt	p.S1454C	MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000455567.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.S1454C|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1454					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					ATGAGCCCACTGGCTCCCAGG	0.577																																					p.S1454C		Atlas-SNP	.											.	MCM3AP	146	.	0			c.A4360T						.						121	117	119					21																	47666731		2203	4300	6503	SO:0001583	missense	8888	exon21			GCCCACTGGCTCC	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.4360A>T	chr21.hg19:g.47666731T>A	ENSP00000380820:p.Ser1454Cys	157.0	0.0		123.0	87.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.584902	0.65992	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.05382	3.45;3.45	5.68	5.68	0.88126	.	0.128488	0.64402	D	0.000001	T	0.25975	0.0633	M	0.73598	2.24	0.44345	D	0.997232	D	0.89917	1.0	D	0.76071	0.987	T	0.00688	-1.1609	10	0.87932	D	0	-19.436	15.9289	0.79644	0.0:0.0:0.0:1.0	.	1454	O60318	MCM3A_HUMAN	C	1454	ENSP00000380820:S1454C;ENSP00000291688:S1454C	ENSP00000291688:S1454C	S	-	1	0	MCM3AP	46491159	1.000000	0.71417	1.000000	0.80357	0.495000	0.33615	3.192000	0.50989	2.173000	0.68751	0.528000	0.53228	AGT	.	.		0.577	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		A	47666731	T	A	47666731	3	1	85	1	0	0	0	0	1	0	0	0	9397	1580	55	4	1614	4	MCM3AP	21	47666731	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	778151	47666731	463164	119	11484										
C22orf29	79680	hgsc.bcm.edu	37	chr22	19839277	19839277	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cttgagatcctggcagaagaGctcgtaatcgtcaggcaggg	14	9	1	3	rs144116940		TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr22:19839277G>A	ENST00000405640.1	-	2	1176	c.508C>T	c.(508-510)Ctc>Ttc	p.L170F	GNB1L_ENST00000405009.1_Intron|C22orf29_ENST00000328554.4_Missense_Mutation_p.L170F|C22orf29_ENST00000484072.1_Intron|GNB1L_ENST00000403325.1_Intron|GNB1L_ENST00000460402.1_Intron|GNB1L_ENST00000329517.6_Intron|C22orf29_ENST00000407472.1_Missense_Mutation_p.L170F			Q7L3V2	BOP_HUMAN	chromosome 22 open reading frame 29	170					mitochondrial outer membrane permeabilization (GO:0097345)|regulation of mitochondrial membrane potential (GO:0051881)	mitochondrion (GO:0005739)				NS(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	7	Colorectal(54;0.0993)					TGGCAGAAGAGCTCGTAATCG	0.612																																					p.L170F		Atlas-SNP	.											.	C22orf29	23	.	0			c.C508T						.	G	PHE/LEU,	0,4406		0,0,2203	69	69	69		508,	1.5	0.2	22	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	GNB1L,C22orf29	NM_024627.5,NM_053004.2	22,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,	170/365,	19839277	1,13005	2203	4300	6503	SO:0001583	missense	79680	exon3			AGAAGAGCTCGTA	BX640998	CCDS13769.1	22q11.21	2006-07-05			ENSG00000215012	ENSG00000215012			26112	protein-coding gene	gene with protein product						12477932	Standard	NM_024627		Approved	FLJ21125	uc002zqh.3	Q7L3V2	OTTHUMG00000030314	ENST00000405640.1:c.508C>T	chr22.hg19:g.19839277G>A	ENSP00000384924:p.Leu170Phe	69.0	0.0		92.0	32.0	NM_024627	A8K5E7|D3DX21|Q6MZM8|Q6N000|Q9H7A0	Missense_Mutation	SNP	ENST00000405640.1	hg19	CCDS13769.1	.	.	.	.	.	.	.	.	.	.	G	8.506	0.865382	0.17250	0.0	1.16E-4	ENSG00000215012	ENST00000407472;ENST00000328554;ENST00000405640	T;T;T	0.30981	1.51;1.51;1.51	3.68	1.5	0.22942	.	0.305062	0.16490	U	0.212122	T	0.17280	0.0415	N	0.22421	0.69	0.09310	N	0.999997	B	0.27498	0.18	B	0.26310	0.068	T	0.16158	-1.0412	10	0.56958	D	0.05	.	4.2931	0.10888	0.1192:0.0:0.6561:0.2247	.	170	Q7L3V2	CV029_HUMAN	F	170	ENSP00000386111:L170F;ENSP00000330596:L170F;ENSP00000384924:L170F	ENSP00000330596:L170F	L	-	1	0	C22orf29	18219277	0.001000	0.12720	0.236000	0.24074	0.248000	0.25809	0.126000	0.15769	0.498000	0.27948	0.655000	0.94253	CTC	.	G|1.000;A|0.000		0.612	C22orf29-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317290.2	NM_024627		A	19839277	G	A	19839277	3	1	85	1	0	0	0	0	1	0	0	0	2143	971	34	3	590	3	C22orf29	22	19839277	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10		19839277	31465289	120	11485										
SUSD2	56241	hgsc.bcm.edu	37	chr22	24583203	24583203	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ggtggctgccggggacagggTctccatcatgctggcatcag	16	11	3	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr22:24583203T>C	ENST00000358321.3	+	11	1937	c.1676T>C	c.(1675-1677)gTc>gCc	p.V559A		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	559	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						GGGGACAGGGTCTCCATCATG	0.652																																					p.V559A		Atlas-SNP	.											.	SUSD2	68	.	0			c.T1676C						.						97	85	89					22																	24583203		2203	4300	6503	SO:0001583	missense	56241	exon11			ACAGGGTCTCCAT	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.1676T>C	chr22.hg19:g.24583203T>C	ENSP00000351075:p.Val559Ala	44.0	0.0		43.0	23.0	NM_019601	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	hg19	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.083533	0.36758	.	.	ENSG00000099994	ENST00000358321	T	0.58652	0.32	4.5	3.44	0.39384	von Willebrand factor, type D domain (3);	0.062758	0.64402	D	0.000007	T	0.49047	0.1534	L	0.51422	1.61	0.45076	D	0.998095	B	0.14805	0.011	B	0.19946	0.027	T	0.41645	-0.9497	10	0.44086	T	0.13	-16.9332	8.6327	0.33928	0.0:0.0954:0.0:0.9046	.	559	Q9UGT4	SUSD2_HUMAN	A	559	ENSP00000351075:V559A	ENSP00000351075:V559A	V	+	2	0	SUSD2	22913203	0.995000	0.38212	0.019000	0.16419	0.476000	0.33039	0.903000	0.28475	0.668000	0.31126	0.369000	0.22263	GTC	.	.		0.652	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		C	24583203	T	C	24583203	3	2	85	1	0	0	0	0	1	0	0	0	15423	1667	58	2	1718	2	SUSD2	22	24583203	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10	4743926	24583203	26721363	121	11486										
MN1	4330	hgsc.bcm.edu	37	chr22	28195917	28195917	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gagccgctggaggacggcagGccgtggaaggaggcggctcg	21	10	0	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr22:28195917G>C	ENST00000302326.4	-	1	1569	c.615C>G	c.(613-615)ggC>ggG	p.G205G		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	205					intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						AGGACGGCAGGCCGTGGAAGG	0.672			T	ETV6	"AML, meningioma"																																p.G205G		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	.	MN1	122	.	0			c.C615G						.						15	18	17					22																	28195917		1996	4161	6157	SO:0001819	synonymous_variant	4330	exon1			CGGCAGGCCGTGG	X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"probable tumor suppressor protein MN1"	156100	"meningioma chromosome region"	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.615C>G	chr22.hg19:g.28195917G>C		74.0	0.0		112.0	6.0	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	hg19	CCDS42998.1																																																																																			.	.		0.672	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		C	28195917	G	C	28195917	2	2	85	1	0	0	0	0	0	0	0	1	9682	1190	42	4		4	MN1	22	28195917	Silent	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	3612714	28195917	23108649	122	11487										
SEPT3	55964	hgsc.bcm.edu	37	chr22	42387581	42387581	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ttctcctcgcctctaggttcGcaaggagcttgaagtaaatg	10	10	2	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr22:42387581G>A	ENST00000396426.3	+	7	929	c.674G>A	c.(673-675)cGc>cAc	p.R225H	SEPT3_ENST00000396425.3_Missense_Mutation_p.R225H|SEPT3_ENST00000291236.11_Missense_Mutation_p.R161H|SEPT3_ENST00000406029.1_Missense_Mutation_p.R161H|SEPT3_ENST00000328414.8_3'UTR	NM_145733.2	NP_663786.2	Q9UH03	SEPT3_HUMAN	septin 3	225	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cell junction (GO:0030054)|septin complex (GO:0031105)|synapse (GO:0045202)	GTP binding (GO:0005525)			breast(1)|kidney(3)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17						CTCTAGGTTCGCAAGGAGCTT	0.493																																					p.R225H		Atlas-SNP	.											.	SEPT3	53	.	0			c.G674A						.						106	99	101					22																	42387581		2203	4300	6503	SO:0001583	missense	55964	exon7			AGGTTCGCAAGGA	AF285107	CCDS14026.2, CCDS14027.2	22q13.2	2013-01-21			ENSG00000100167	ENSG00000100167		"Septins"	10750	protein-coding gene	gene with protein product		608314		SEP3			Standard	NM_019106		Approved		uc003bbr.4	Q9UH03	OTTHUMG00000030494	ENST00000396426.3:c.674G>A	chr22.hg19:g.42387581G>A	ENSP00000379704:p.Arg225His	100.0	0.0		93.0	49.0	NM_019106	B1AHR0|Q2NKJ7|Q59GF7|Q6IBZ6|Q8N3P3|Q9HD35	Missense_Mutation	SNP	ENST00000396426.3	hg19	CCDS14026.2	.	.	.	.	.	.	.	.	.	.	G	28.3	4.904679	0.92035	.	.	ENSG00000100167	ENST00000396426;ENST00000406029;ENST00000396425;ENST00000291236	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	5.38	5.38	0.77491	.	0.049025	0.85682	D	0.000000	T	0.59595	0.2205	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.69078	0.994;0.997;0.997;0.997	P;D;P;P	0.68765	0.71;0.96;0.775;0.899	T	0.57528	-0.7796	10	0.46703	T	0.11	.	19.5313	0.95230	0.0:0.0:1.0:0.0	.	161;161;225;225	B7Z686;B1AHR1;Q9UH03-2;Q9UH03	.;.;.;SEPT3_HUMAN	H	225;161;225;161	ENSP00000379704:R225H;ENSP00000383956:R161H;ENSP00000379703:R225H;ENSP00000291236:R161H	ENSP00000291236:R161H	R	+	2	0	SEPT3	40717527	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.950000	0.87804	2.694000	0.91930	0.655000	0.94253	CGC	.	.		0.493	SEPT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322051.1	NM_145734		A	42387581	G	A	42387581	3	1	85	1	0	0	0	0	1	0	0	0	14080	1087	38	1	700	1	SEPT3	22	42387581	Missense_Mutation	SNP	G	TCGA-CC-A9FW-01A-11D-A36X-10	14191664	42387581	8916985	123	11488										
CRELD2	79174	hgsc.bcm.edu	37	chr22	50316312	50316312	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ctgaccaacagagactgcggCgagtgtgaagtgggctgggt	17	8	0	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chr22:50316312C>T	ENST00000328268.4	+	6	719	c.645C>T	c.(643-645)ggC>ggT	p.G215G	CRELD2_ENST00000403427.3_Silent_p.G215G|CRELD2_ENST00000407217.3_Silent_p.G215G|CRELD2_ENST00000404488.3_Silent_p.G264G|CRELD2_ENST00000444954.1_3'UTR	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	215						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		GAGACTGCGGCGAGTGTGAAG	0.677																																					p.G264G		Atlas-SNP	.											.	CRELD2	57	.	0			c.C792T						.						45	33	37					22																	50316312		2185	4283	6468	SO:0001819	synonymous_variant	79174	exon7			CTGCGGCGAGTGT	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.645C>T	chr22.hg19:g.50316312C>T		82.0	0.0		56.0	11.0	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Silent	SNP	ENST00000328268.4	hg19	CCDS14082.1																																																																																			.	.		0.677	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324		T	50316312	C	T	50316312	2	4	85	1	0	0	0	0	0	0	0	1	3869	755	27	1		1	CRELD2	22	50316312	Silent	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	7928731	50316312	988254	124	11489										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12736481	12736481	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	cacctgcgaccatccttccaAgcttcctgaggctgatgaga	9	14	0	3			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chrX:12736481A>G	ENST00000380682.1	+	16	4042	c.3536A>G	c.(3535-3537)aAg>aGg	p.K1179R		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	1179					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						CATCCTTCCAAGCTTCCTGAG	0.547																																					p.K1179R		Atlas-SNP	.											.	FRMPD4	214	.	0			c.A3536G						.						140	125	130					X																	12736481		2203	4300	6503	SO:0001583	missense	9758	exon16			CTTCCAAGCTTCC	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.3536A>G	chrX.hg19:g.12736481A>G	ENSP00000370057:p.Lys1179Arg	81.0	0.0		92.0	75.0	NM_014728	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	hg19	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.004015	0.54254	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.07327	3.2	5.5	5.5	0.81552	.	0.173518	0.50627	D	0.000120	T	0.13841	0.0335	M	0.67953	2.075	0.39915	D	0.974071	P;P	0.43857	0.819;0.819	B;B	0.41374	0.355;0.355	T	0.01767	-1.1278	10	0.62326	D	0.03	-14.0447	14.6325	0.68666	1.0:0.0:0.0:0.0	.	1171;1179	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	R	1179;1170;1168	ENSP00000370057:K1179R	ENSP00000304583:K1168R	K	+	2	0	FRMPD4	12646402	1.000000	0.71417	0.988000	0.46212	0.936000	0.57629	7.020000	0.76419	1.836000	0.53414	0.486000	0.48141	AAG	.	.		0.547	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		G	12736481	A	G	12736481	3	3	85	1	0	0	0	0	1	0	0	0	6067	72	3	2	3598	2	FRMPD4	23	12736481	Missense_Mutation	SNP	A	TCGA-CC-A9FW-01A-11D-A36X-10		12736481	142534079	125	11490										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20179839	20179839	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	acctattcgtgccaatatttCctctggtgtatcatcaggac	7	11	3	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chrX:20179839C>A	ENST00000379565.3	-	20	2089	c.1882G>T	c.(1882-1884)Gaa>Taa	p.E628*	RPS6KA3_ENST00000544447.1_Nonsense_Mutation_p.E600*|RPS6KA3_ENST00000379548.4_Nonsense_Mutation_p.E598*|RPS6KA3_ENST00000540702.1_Nonsense_Mutation_p.E599*|RPS6KA3_ENST00000479809.1_5'UTR	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	628	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	GCCAATATTTCCTCTGGTGTA	0.323																																					p.E628X		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.G1882T						.						142	111	122					X																	20179839		2203	4300	6503	SO:0001587	stop_gained	6197	exon20			ATATTTCCTCTGG	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1882G>T	chrX.hg19:g.20179839C>A	ENSP00000368884:p.Glu628*	27.0	0.0		35.0	28.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Nonsense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	C	39	7.594497	0.98378	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	18.8899	0.92395	0.0:1.0:0.0:0.0	.	.	.	.	X	628;600;598;599	.	ENSP00000368865:E598X	E	-	1	0	RPS6KA3	20089760	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.487000	0.81328	2.409000	0.81822	0.513000	0.50165	GAA	.	.		0.323	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		A	20179839	C	A	20179839	4	1	85	1	0	0	0	0	0	1	0	0	13667	864	30	3	352	3	RPS6KA3	23	20179839	Nonsense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	7443358	20179839	135090721	126	11491										
DACH2	117154	hgsc.bcm.edu	37	chrX	85403711	85403711	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	ttccgggccgaacccctgtaCtcgactcccagagagccccc	9	19	0	1			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chrX:85403711C>A	ENST00000373125.4	+	1	87	c.87C>A	c.(85-87)taC>taA	p.Y29*	DACH2_ENST00000373131.1_Nonsense_Mutation_p.Y29*	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	29					development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						AACCCCTGTACTCGACTCCCA	0.592																																					p.Y29X		Atlas-SNP	.											.	DACH2	263	.	0			c.C87A						.						25	24	24					X																	85403711		2203	4300	6503	SO:0001587	stop_gained	117154	exon1			CCTGTACTCGACT	AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.87C>A	chrX.hg19:g.85403711C>A	ENSP00000362217:p.Tyr29*	114.0	0.0		152.0	129.0	NM_001139514	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Nonsense_Mutation	SNP	ENST00000373125.4	hg19	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.353874	0.82243	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125	.	.	.	4.64	1.03	0.20045	.	0.000000	0.46145	D	0.000315	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.8598	0.13577	0.0:0.5164:0.1445:0.3391	.	.	.	.	X	29	.	ENSP00000345134:Y29X	Y	+	3	2	DACH2	85290367	0.990000	0.36364	0.679000	0.29978	0.027000	0.11550	0.572000	0.23684	0.159000	0.19401	0.538000	0.68166	TAC	.	.		0.592	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		A	85403711	C	A	85403711	4	1	85	1	0	0	0	0	0	1	0	0	4223	576	20	3	89	3	DACH2	23	85403711	Nonsense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	65223872	85403711	69866849	127	11492										
NAP1L3	4675	hgsc.bcm.edu	37	chrX	92928252	92928252	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	gctagccatctcctcttcggCaaccccatgggcgacaggtt	10	15	2	0			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chrX:92928252C>A	ENST00000373079.3	-	1	315	c.52G>T	c.(52-54)Gcc>Tcc	p.A18S	NAP1L3_ENST00000475430.2_Missense_Mutation_p.A11S|FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000332647.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	18					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						TCCTCTTCGGCAACCCCATGG	0.547																																					p.A18S		Atlas-SNP	.											.	NAP1L3	81	.	0			c.G52T						.						55	51	52					X																	92928252		2203	4300	6503	SO:0001583	missense	4675	exon1			CTTCGGCAACCCC		CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.52G>T	chrX.hg19:g.92928252C>A	ENSP00000362171:p.Ala18Ser	76.0	0.0		99.0	83.0	NM_004538	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	hg19	CCDS14465.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.946511	0.34377	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.34859	1.34	3.65	2.79	0.32731	.	0.309642	0.30329	N	0.009880	T	0.18299	0.0439	N	0.19112	0.55	0.21553	N	0.999646	P	0.37061	0.58	B	0.32090	0.14	T	0.12268	-1.0554	10	0.20519	T	0.43	.	8.6193	0.33851	0.0:0.8802:0.0:0.1198	.	18	Q99457	NP1L3_HUMAN	S	18;11	ENSP00000362171:A18S	ENSP00000362171:A18S	A	-	1	0	NAP1L3	92814908	0.987000	0.35691	0.312000	0.25196	0.538000	0.34931	1.533000	0.36040	0.922000	0.37019	0.529000	0.55759	GCC	.	.		0.547	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538		A	92928252	C	A	92928252	3	1	85	1	0	0	0	0	1	0	0	0	10167	710	25	3	1472	3	NAP1L3	23	92928252	Missense_Mutation	SNP	C	TCGA-CC-A9FW-01A-11D-A36X-10	7524541	92928252	62342308	128	11493										
KDM5D	8284	hgsc.bcm.edu	37	chrY	21871366	21871366	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	3	1	0.486674174174174	0	0.556199056199056	0.181818181818182	0.751940625889747	0	aggcagaaatgagccttttcTtcccagcgctctgcaatggt	10	11	2	2			TCGA-CC-A9FW-01A-11D-A36X-10	TCGA-CC-A9FW-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8da84d1c-a7dd-4e0f-82e8-abbcd33c5261	ffe29f46-9b5c-47f4-98bf-390f2183b420	g.chrY:21871366T>A	ENST00000317961.4	-	20	3184	c.2913A>T	c.(2911-2913)gaA>gaT	p.E971D	KDM5D_ENST00000541639.1_Missense_Mutation_p.E1002D|KDM5D_ENST00000382806.2_Missense_Mutation_p.E914D	NM_004653.4	NP_004644.2	Q9BY66	KDM5D_HUMAN	lysine (K)-specific demethylase 5D	971					histone H3-K4 demethylation (GO:0034720)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(9)|lung(6)|skin(1)	17					Vitamin C(DB00126)	GAGCCTTTTCTTCCCAGCGCT	0.527																																					p.E1002D		Atlas-SNP	.											.	KDM5D	40	.	0			c.A3006T						.						34	34	34					Y																	21871366		582	1915	2497	SO:0001583	missense	8284	exon21			CTTTTCTTCCCAG	U52191	CCDS14794.1, CCDS55554.1, CCDS55555.1	Yq11	2013-01-28	2009-04-06	2009-04-06	ENSG00000012817	ENSG00000012817		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11115	protein-coding gene	gene with protein product		426000	"Jumonji, AT rich interactive domain 1D (RBP2-like)", "Smcy homolog, Y-linked (mouse)", "jumonji, AT rich interactive domain 1D"	HYA, HY, SMCY, JARID1D		795123, 8841177	Standard	NM_001146705		Approved	KIAA0234	uc011naz.2	Q9BY66	OTTHUMG00000036508	ENST00000317961.4:c.2913A>T	chrY.hg19:g.21871366T>A	ENSP00000322408:p.Glu971Asp	36.0	0.0		70.0	30.0	NM_001146705	A2RU19|A6H8V7|B7ZLX1|Q92509|Q92809|Q9HCU1	Missense_Mutation	SNP	ENST00000317961.4	hg19	CCDS14794.1																																																																																			.	.		0.527	KDM5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088790.1	NM_004653		A	21871366	T	A	21871366	3	1	85	1	0	0	0	0	1	0	0	0	8145	1606	56	4	1738	4	KDM5D	24	21871366	Missense_Mutation	SNP	T	TCGA-CC-A9FW-01A-11D-A36X-10		21871366	37502200	129	11494										
SLC2A5	6518	hgsc.bcm.edu	37	chr1	9097670	9097670	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gttccgaagtgacaggtggaAgctctttcagttcctccttt	10	10	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:9097670A>G	ENST00000377424.4	-	12	1660	c.1481T>C	c.(1480-1482)cTt>cCt	p.L494P	SLC2A5_ENST00000535586.1_Missense_Mutation_p.L379P|SLC2A5_ENST00000536305.1_Missense_Mutation_p.L435P	NM_003039.2	NP_003030.1	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated glucose/fructose transporter), member 5	494					carbohydrate metabolic process (GO:0005975)|cellular response to fructose stimulus (GO:0071332)|fructose transport (GO:0015755)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fructose transmembrane transporter activity (GO:0005353)|glucose transmembrane transporter activity (GO:0005355)			endometrium(6)|kidney(15)|large_intestine(6)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|urinary_tract(1)	36	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		GACAGGTGGAAGCTCTTTCAG	0.498																																					p.L494P		Atlas-SNP	.											.	SLC2A5	77	.	0			c.T1481C						.						119	125	123					1																	9097670		2203	4300	6503	SO:0001583	missense	6518	exon12			GGTGGAAGCTCTT	BC001820	CCDS99.1, CCDS44054.1	1p36.2	2013-05-22			ENSG00000142583	ENSG00000142583		"Solute carriers"	11010	protein-coding gene	gene with protein product		138230		GLUT5		9691177	Standard	NM_003039		Approved		uc001apo.3	P22732	OTTHUMG00000001771	ENST00000377424.4:c.1481T>C	chr1.hg19:g.9097670A>G	ENSP00000366641:p.Leu494Pro	148.0	0.0		140.0	14.0	NM_003039	Q14770|Q5T977|Q8IVB3	Missense_Mutation	SNP	ENST00000377424.4	hg19	CCDS99.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.816434	0.50527	.	.	ENSG00000142583	ENST00000377424;ENST00000456780;ENST00000536305;ENST00000535586	T;D;T	0.81739	-1.27;-1.53;-1.17	5.71	3.34	0.38264	.	1.362620	0.04509	N	0.382496	T	0.64962	0.2646	N	0.08118	0	0.25367	N	0.988734	B;B;B	0.15473	0.004;0.013;0.004	B;B;B	0.12156	0.007;0.007;0.007	T	0.53634	-0.8411	10	0.31617	T	0.26	.	6.8386	0.23951	0.7704:0.1503:0.0793:0.0	.	450;435;494	B4DG19;B4DU31;P22732	.;.;GTR5_HUMAN	P	494;477;435;379	ENSP00000366641:L494P;ENSP00000440688:L435P;ENSP00000442744:L379P	ENSP00000366641:L494P	L	-	2	0	SLC2A5	9020257	0.004000	0.15560	0.001000	0.08648	0.009000	0.06853	1.870000	0.39529	0.965000	0.38133	-0.313000	0.08912	CTT	.	.		0.498	SLC2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004932.1	NM_003039		G	9097670	A	G	9097670	3	3	86	1	0	0	0	0	1	0	0	0	14563	72	3	2	28	2	SLC2A5	1	9097670	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10		9097670	240152951	1	11495										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11562021	11562021	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ccccacgaggtgctcaaggaTctgccgctgggctcctactc	11	16	2	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:11562021T>G	ENST00000294484.6	+	2	1110	c.972T>G	c.(970-972)gaT>gaG	p.D324E	PTCHD2_ENST00000389575.3_Missense_Mutation_p.D324E	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	324					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		TGCTCAAGGATCTGCCGCTGG	0.607																																					p.D324E		Atlas-SNP	.											.	PTCHD2	193	.	0			c.T972G						.						37	40	39					1																	11562021		1958	4145	6103	SO:0001583	missense	57540	exon2			CAAGGATCTGCCG	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.972T>G	chr1.hg19:g.11562021T>G	ENSP00000294484:p.Asp324Glu	97.0	0.0		84.0	11.0	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	hg19	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.765394	0.69878	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	T;T	0.49139	0.79;0.79	5.42	1.99	0.26369	.	0.053624	0.64402	D	0.000001	T	0.49029	0.1533	L	0.27053	0.805	0.37011	D	0.895714	D	0.89917	1.0	D	0.80764	0.994	T	0.49670	-0.8915	10	0.40728	T	0.16	-43.3451	7.6093	0.28120	0.1202:0.6579:0.0:0.2219	.	324	Q9P2K9	PTHD2_HUMAN	E	324	ENSP00000294484:D324E;ENSP00000374226:D324E	ENSP00000294484:D324E	D	+	3	2	PTCHD2	11484608	0.997000	0.39634	1.000000	0.80357	0.980000	0.70556	0.497000	0.22514	0.259000	0.21709	-0.119000	0.15052	GAT	.	.		0.607	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		G	11562021	T	G	11562021	3	3	86	1	0	0	0	0	1	0	0	0	12745	1432	50	5	974	5	PTCHD2	1	11562021	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	2464351	11562021	237688600	2	11496										
TMEM53	79639	hgsc.bcm.edu	37	chr1	45120780	45120780	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	atctcataatcaaagagcagCtcgagcagcttctgggccaa	9	11	3	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:45120780C>A	ENST00000372237.3	-	3	448	c.285G>T	c.(283-285)gaG>gaT	p.E95D	TMEM53_ENST00000372235.3_Missense_Mutation_p.E65D|TMEM53_ENST00000476724.1_5'UTR|TMEM53_ENST00000372244.3_Intron|TMEM53_ENST00000372242.3_Missense_Mutation_p.E95D|TMEM53_ENST00000372243.3_Intron	NM_024587.2	NP_078863.2	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	95						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(3)|ovary(2)|urinary_tract(1)	10	Acute lymphoblastic leukemia(166;0.155)					CAAAGAGCAGCTCGAGCAGCT	0.547											OREG0013446	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E95D		Atlas-SNP	.											.	TMEM53	40	.	0			c.G285T						.						56	61	59					1																	45120780		2203	4300	6503	SO:0001583	missense	79639	exon3			GAGCAGCTCGAGC		CCDS511.1, CCDS72773.1	1p34.1	2008-02-26			ENSG00000126106	ENSG00000126106			26186	protein-coding gene	gene with protein product						12958361	Standard	XR_425151		Approved	FLJ22353, NET4	uc001cmc.3	Q6P2H8	OTTHUMG00000007833	ENST00000372237.3:c.285G>T	chr1.hg19:g.45120780C>A	ENSP00000361311:p.Glu95Asp	107.0	0.0	929	67.0	56.0	NM_024587	B4DKG0|Q5JPH2|Q6IA07|Q9H6E2	Missense_Mutation	SNP	ENST00000372237.3	hg19	CCDS511.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.203085	0.79127	.	.	ENSG00000126106	ENST00000372242;ENST00000372237;ENST00000372235;ENST00000420706	.	.	.	5.67	3.79	0.43588	.	0.000000	0.85682	D	0.000000	T	0.68751	0.3035	L	0.57536	1.79	0.58432	D	0.999996	D	0.89917	1.0	D	0.83275	0.996	T	0.65224	-0.6220	9	0.21540	T	0.41	.	12.6523	0.56768	0.0:0.8639:0.0:0.1361	.	95	Q6P2H8	TMM53_HUMAN	D	95;95;65;64	.	ENSP00000361309:E65D	E	-	3	2	TMEM53	44893367	1.000000	0.71417	0.995000	0.50966	0.969000	0.65631	3.999000	0.57031	1.413000	0.46997	0.563000	0.77884	GAG	.	.		0.547	TMEM53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021599.1	NM_024587		A	45120780	C	A	45120780	3	1	86	1	0	0	0	0	1	0	0	0	16194	796	28	3	552	3	TMEM53	1	45120780	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	33558759	45120780	204129841	3	11497										
VAV3	10451	hgsc.bcm.edu	37	chr1	108315394	108315394	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ctgccttcattaagtcctcaTagacttctccaccttcatct	3	15	5	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:108315394T>G	ENST00000370056.4	-	5	792	c.518A>C	c.(517-519)tAt>tCt	p.Y173S	VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000527011.1_Missense_Mutation_p.Y173S|VAV3_ENST00000371846.4_Missense_Mutation_p.Y108S	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	173					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TAAGTCCTCATAGACTTCTCC	0.368																																					p.Y173S		Atlas-SNP	.											.	VAV3	176	.	0			c.A518C						.						180	167	172					1																	108315394		2203	4300	6503	SO:0001583	missense	10451	exon5			TCCTCATAGACTT	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.518A>C	chr1.hg19:g.108315394T>G	ENSP00000359073:p.Tyr173Ser	185.0	0.0		179.0	16.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.4|25.4	4.630967|4.630967	0.87660|0.87660	.|.	.|.	ENSG00000134215|ENSG00000134215	ENST00000490388|ENST00000370056;ENST00000527011;ENST00000371846	.|T;T;T	.|0.36878	.|1.23;1.23;1.23	5.92|5.92	5.92|5.92	0.95590|0.95590	.|Dbl homology (DH) domain (1);Calponin homology domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.56906|0.56906	0.2017|0.2017	M|M	0.85041|0.85041	2.73|2.73	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|0.999;1.0;0.997	.|D;D;D	.|0.97110	.|0.995;1.0;0.957	T|T	0.61633|0.61633	-0.7023|-0.7023	5|10	.|0.45353	.|T	.|0.12	.|.	15.3456|15.3456	0.74334|0.74334	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|173;173;173	.|B7ZLR1;E9PQ97;Q9UKW4	.|.;.;VAV3_HUMAN	L|S	168|173;173;108	.|ENSP00000359073:Y173S;ENSP00000432540:Y173S;ENSP00000360912:Y108S	.|ENSP00000359073:Y173S	M|Y	-|-	1|2	0|0	VAV3|VAV3	108116917|108116917	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.977000|0.977000	0.68977|0.68977	6.722000|6.722000	0.74735|0.74735	2.266000|2.266000	0.75297|0.75297	0.533000|0.533000	0.62120|0.62120	ATG|TAT	.	.		0.368	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		G	108315394	T	G	108315394	3	3	86	1	0	0	0	0	1	0	0	0	17148	1406	49	5	2142	5	VAV3	1	108315394	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	63194614	108315394	140935227	4	11498										
GDAP2	54834	hgsc.bcm.edu	37	chr1	118454654	118454654	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	catcctctaaaggataaccaCgttttgcagaattgatgaca	7	9	1	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:118454654C>T	ENST00000369443.5	-	5	770	c.521G>A	c.(520-522)cGt>cAt	p.R174H	GDAP2_ENST00000369442.3_Missense_Mutation_p.R174H	NM_017686.3	NP_060156.1	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated protein 2	174	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				response to retinoic acid (GO:0032526)	lysosomal membrane (GO:0005765)				kidney(2)|large_intestine(3)|lung(9)|ovary(2)	16		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		AGGATAACCACGTTTTGCAGA	0.353																																					p.R174H		Atlas-SNP	.											GDAP2,colon,carcinoma,0,1	GDAP2	37	.	0			c.G521A						.						112	104	107					1																	118454654		2203	4300	6503	SO:0001583	missense	54834	exon5			TAACCACGTTTTG	AK000149	CCDS897.1, CCDS44201.1	1q11	2011-10-20			ENSG00000196505	ENSG00000196505			18010	protein-coding gene	gene with protein product						1021725	Standard	NM_017686		Approved	FLJ20142, dJ776P7.1, MACROD3	uc001ehf.3	Q9NXN4	OTTHUMG00000012199	ENST00000369443.5:c.521G>A	chr1.hg19:g.118454654C>T	ENSP00000358451:p.Arg174His	433.0	0.0		355.0	274.0	NM_017686	Q96DZ0	Missense_Mutation	SNP	ENST00000369443.5	hg19	CCDS897.1	.	.	.	.	.	.	.	.	.	.	C	35	5.545744	0.96488	.	.	ENSG00000196505	ENST00000369443;ENST00000369442	T;T	0.22336	1.96;1.96	5.23	5.23	0.72850	Appr-1-p processing (2);	0.000000	0.85682	D	0.000000	T	0.38108	0.1028	L	0.61387	1.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.04440	-1.0951	10	0.48119	T	0.1	-9.6423	19.0551	0.93059	0.0:1.0:0.0:0.0	.	174;174	Q9NXN4-2;Q9NXN4	.;GDAP2_HUMAN	H	174	ENSP00000358451:R174H;ENSP00000358450:R174H	ENSP00000358450:R174H	R	-	2	0	GDAP2	118256177	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.174000	0.77620	2.729000	0.93468	0.650000	0.86243	CGT	.	.		0.353	GDAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033732.2	NM_017686		T	118454654	C	T	118454654	3	4	86	1	0	0	0	0	1	0	0	0	6317	536	19	1	1057	1	GDAP2	1	118454654	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	10139260	118454654	130795967	5	11499										
TMEM79	84283	hgsc.bcm.edu	37	chr1	156255314	156255314	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ggctggcgggacattgaaccAgagccccctgagtcagaacc	13	13	1	4	rs553983602		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:156255314A>T	ENST00000405535.2	+	2	468	c.297A>T	c.(295-297)ccA>ccT	p.P99P	TMEM79_ENST00000357501.2_Intron|SMG5_ENST00000368267.5_5'Flank|SMG5_ENST00000361813.5_5'Flank|TMEM79_ENST00000495881.1_3'UTR|TMEM79_ENST00000295694.5_Silent_p.P99P	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	99					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					ACATTGAACCAGAGCCCCCTG	0.622																																					p.P99P		Atlas-SNP	.											.	TMEM79	43	.	0			c.A297T						.						49	55	53					1																	156255314		2203	4300	6503	SO:0001819	synonymous_variant	84283	exon2			TGAACCAGAGCCC	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"mattrin"	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.297A>T	chr1.hg19:g.156255314A>T		78.0	0.0		192.0	53.0	NM_032323	B2RE22|D3DVB8	Silent	SNP	ENST00000405535.2	hg19	CCDS1138.1																																																																																			.	.		0.622	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		T	156255314	A	T	156255314	2	4	86	1	0	0	0	0	0	0	0	1	16218	175	7	4		4	TMEM79	1	156255314	Silent	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	37800660	156255314	92995307	6	11500										
KIRREL	55243	hgsc.bcm.edu	37	chr1	158059385	158059385	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ccatcgtgcctcgaatcggaGtggctgagcgggaggtgccg	17	11	0	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:158059385G>A	ENST00000359209.6	+	9	1205	c.1138G>A	c.(1138-1140)Gtg>Atg	p.V380M	KIRREL_ENST00000368173.3_Missense_Mutation_p.V396M|KIRREL_ENST00000360089.4_Missense_Mutation_p.V216M|KIRREL_ENST00000368172.1_Missense_Mutation_p.V194M|KIRREL_ENST00000392272.2_Missense_Mutation_p.V277M|KIRREL_ENST00000416935.2_Missense_Mutation_p.V280M			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	380	Ig-like C2-type 4.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					TCGAATCGGAGTGGCTGAGCG	0.622																																					p.V380M		Atlas-SNP	.											.	KIRREL	346	.	0			c.G1138A						.						56	59	58					1																	158059385		2203	4300	6503	SO:0001583	missense	55243	exon9			ATCGGAGTGGCTG	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15734	protein-coding gene	gene with protein product	"nephrin-like protein 1"	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.1138G>A	chr1.hg19:g.158059385G>A	ENSP00000352138:p.Val380Met	85.0	0.0		174.0	47.0	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Missense_Mutation	SNP	ENST00000359209.6	hg19	CCDS1172.2	.	.	.	.	.	.	.	.	.	.	G	27.0	4.792257	0.90453	.	.	ENSG00000183853	ENST00000360089;ENST00000368173;ENST00000392272;ENST00000359209;ENST00000416935;ENST00000368172	T;T;T;T;T;T	0.12569	2.67;2.67;2.67;2.67;2.67;2.67	4.71	4.71	0.59529	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.441677	0.16510	N	0.211273	T	0.16171	0.0389	L	0.28344	0.845	0.80722	D	1	P;D;D;D	0.71674	0.742;0.998;0.997;0.997	P;D;D;D	0.70227	0.644;0.968;0.964;0.964	T	0.03139	-1.1068	10	0.51188	T	0.08	-11.7061	15.1859	0.73002	0.0:0.0:1.0:0.0	.	280;216;194;380	B4DN67;Q5W0F9;Q5W0G0;Q96J84	.;.;.;KIRR1_HUMAN	M	216;396;277;380;280;194	ENSP00000353202:V216M;ENSP00000357155:V396M;ENSP00000376098:V277M;ENSP00000352138:V380M;ENSP00000389674:V280M;ENSP00000357154:V194M	ENSP00000352138:V380M	V	+	1	0	KIRREL	156326009	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.135000	0.94478	2.434000	0.82447	0.460000	0.39030	GTG	.	.		0.622	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240		A	158059385	G	A	158059385	3	1	86	1	0	0	0	0	1	0	0	0	8333	1029	36	3	1172	3	KIRREL	1	158059385	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	1804071	158059385	91191236	7	11501										
DNM3	26052	hgsc.bcm.edu	37	chr1	172100413	172100413	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	actgcggaaagcttgtcctgGtataaagatgatgaggtaag	13	5	0	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:172100413G>C	ENST00000355305.5	+	15	1831	c.1674G>C	c.(1672-1674)tgG>tgC	p.W558C	DNM3_ENST00000520906.1_Missense_Mutation_p.W548C|DNM3_ENST00000367731.1_Missense_Mutation_p.W548C|DNM3_ENST00000367733.2_Missense_Mutation_p.W548C|DNM3_ENST00000358155.4_Missense_Mutation_p.W548C			Q9UQ16	DYN3_HUMAN	dynamin 3	558	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						GCTTGTCCTGGTATAAAGATG	0.393																																					p.W548C		Atlas-SNP	.											.	DNM3	85	.	0			c.G1644C						.						88	85	86					1																	172100413		1952	4177	6129	SO:0001583	missense	26052	exon14			GTCCTGGTATAAA	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.1674G>C	chr1.hg19:g.172100413G>C	ENSP00000347457:p.Trp558Cys	132.0	0.0		231.0	80.0	NM_001136127	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	hg19		.	.	.	.	.	.	.	.	.	.	G	18.28	3.589394	0.66105	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000367733;ENST00000355305;ENST00000367731;ENST00000520906;ENST00000523513	D;D;D;D;D;D	0.96265	-3.96;-3.96;-3.96;-3.96;-3.96;-3.96	5.85	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.98169	0.9395	M	0.90082	3.085	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.994;0.997;0.977	D	0.99160	1.0861	10	0.72032	D	0.01	.	15.4223	0.75022	0.0:0.0:0.8599:0.1401	.	548;548;548;548	E5RHK8;Q9UQ16-2;Q9UQ16-3;Q6P2G1	.;.;.;.	C	558;548;548;558;548;548;438	ENSP00000350876:W548C;ENSP00000356707:W548C;ENSP00000347457:W558C;ENSP00000356705:W548C;ENSP00000429701:W548C;ENSP00000429416:W438C	ENSP00000347457:W558C	W	+	3	0	DNM3	170367036	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	9.813000	0.99286	1.458000	0.47871	-0.321000	0.08615	TGG	.	.		0.393	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		C	172100413	G	C	172100413	3	2	86	1	0	0	0	0	1	0	0	0	4675	1270	44	4	1698	4	DNM3	1	172100413	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	14041028	172100413	77150208	8	11502										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183085929	183085929	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cctggattttttaatctggaAtcatctaatcctcggggttg	9	8	3	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:183085929A>G	ENST00000258341.4	+	8	1712	c.1455A>G	c.(1453-1455)gaA>gaG	p.E485E		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	485	Laminin EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TTAATCTGGAATCATCTAATC	0.383																																					p.E485E		Atlas-SNP	.											.	LAMC1	176	.	0			c.A1455G						.						114	111	112					1																	183085929		2203	4300	6503	SO:0001819	synonymous_variant	3915	exon8			TCTGGAATCATCT	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.1455A>G	chr1.hg19:g.183085929A>G		293.0	0.0		572.0	150.0	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	hg19	CCDS1351.1																																																																																			.	.		0.383	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		G	183085929	A	G	183085929	2	3	86	1	0	0	0	0	0	0	0	1	8623	98	4	2		2	LAMC1	1	183085929	Silent	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	10985516	183085929	66164692	9	11503										
PTGS2	5743	hgsc.bcm.edu	37	chr1	186648333	186648333	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ttattcttgtcaaaaattccGctgcaagaagacgaagaaag	8	7	2	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:186648333G>A	ENST00000367468.5	-	3	306	c.170C>T	c.(169-171)cCg>cTg	p.P57L	PTGS2_ENST00000490885.2_5'UTR|RP5-973M2.2_ENST00000608917.1_lincRNA	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	57					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	CAAAAATTCCGCTGCAAGAAG	0.388																																					p.P57L		Atlas-SNP	.											.	PTGS2	144	.	0			c.C170T						.						82	82	82					1																	186648333		2203	4300	6503	SO:0001630	splice_region_variant	5743	exon3			AATTCCGCTGCAA	D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.170-1C>T	chr1.hg19:g.186648333G>A		291.0	0.0		581.0	35.0	NM_000963	A8K802|Q16876	Missense_Mutation	SNP	ENST00000367468.5	hg19	CCDS1371.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327597	0.81690	.	.	ENSG00000073756	ENST00000367468	T	0.73469	-0.75	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.85309	0.5667	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.64144	0.922	D	0.86531	0.1822	10	0.87932	D	0	.	19.5047	0.95110	0.0:0.0:1.0:0.0	.	57	P35354	PGH2_HUMAN	L	57	ENSP00000356438:P57L	ENSP00000356438:P57L	P	-	2	0	PTGS2	184914956	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	9.617000	0.98361	2.585000	0.87301	0.655000	0.94253	CCG	.	.		0.388	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963	Missense_Mutation	A	186648333	G	A	186648333	5	1	86	1	0	0	0	0	0	0	1	0	12769	1101	38	1	1676	1	PTGS2	1	186648333	Splice_Site	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	3562404	186648333	62602288	10	11504										
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186948491	186948491	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	agaaagaaatcgctgactttGatatttttgatgacccagaa	8	6	0	7			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:186948491G>T	ENST00000367466.3	+	17	2157	c.2005G>T	c.(2005-2007)Gat>Tat	p.D669Y	PLA2G4A_ENST00000442353.2_Missense_Mutation_p.D609Y	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	669	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	CGCTGACTTTGATATTTTTGA	0.338																																					p.D669Y		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.G2005T						.						108	105	106					1																	186948491		2203	4300	6503	SO:0001583	missense	5321	exon17			GACTTTGATATTT	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.2005G>T	chr1.hg19:g.186948491G>T	ENSP00000356436:p.Asp669Tyr	401.0	1.0		603.0	205.0	NM_024420	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	hg19	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.619506	0.87460	.	.	ENSG00000116711	ENST00000367466;ENST00000442353	T;T	0.13196	2.61;2.61	5.6	5.6	0.85130	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.089358	0.85682	D	0.000000	T	0.41488	0.1161	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79108	0.992;0.992	T	0.26326	-1.0106	10	0.72032	D	0.01	-13.8788	18.5987	0.91239	0.0:0.0:1.0:0.0	.	609;669	E7EU42;P47712	.;PA24A_HUMAN	Y	669;609	ENSP00000356436:D669Y;ENSP00000406892:D609Y	ENSP00000356436:D669Y	D	+	1	0	PLA2G4A	185215114	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.338000	0.96553	2.625000	0.88918	0.563000	0.77884	GAT	.	.		0.338	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		T	186948491	G	T	186948491	3	4	86	1	0	0	0	0	1	0	0	0	12010	1290	45	3	2067	3	PLA2G4A	1	186948491	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	300158	186948491	62302130	11	11505										
ARL8A	127829	hgsc.bcm.edu	37	chr1	202104642	202104642	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cggaaggtctcgcttgttacCcaggactaagacctacggag	12	11	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:202104642C>G	ENST00000272217.2	-	5	553	c.385G>C	c.(385-387)Ggt>Cgt	p.G129R	ARL8A_ENST00000486225.1_5'UTR	NM_001256129.1|NM_138795.3	NP_001243058.1|NP_620150.1	Q96BM9	ARL8A_HUMAN	ADP-ribosylation factor-like 8A	129					chromosome segregation (GO:0007059)|GTP catabolic process (GO:0006184)|mitotic nuclear division (GO:0007067)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|midbody (GO:0030496)|spindle midzone (GO:0051233)	alpha-tubulin binding (GO:0043014)|beta-tubulin binding (GO:0048487)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(2)|ovary(2)|skin(1)	6						CGCTTGTTACCCAGGACTAAG	0.552											OREG0012976	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G129R		Atlas-SNP	.											.	ARL8A	14	.	0			c.G385C						.						132	132	132					1																	202104642		2203	4300	6503	SO:0001583	missense	127829	exon5			TGTTACCCAGGAC	BC015408	CCDS1421.1, CCDS73004.1	1q32.1	2014-05-09	2005-11-03	2005-11-03	ENSG00000143862	ENSG00000143862		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	25192	protein-coding gene	gene with protein product			"ADP-ribosylation factor-like 10B"	ARL10B		8889548	Standard	NM_001256129		Approved	FLJ45195, Gie2	uc001gxk.2	Q96BM9	OTTHUMG00000035923	ENST00000272217.2:c.385G>C	chr1.hg19:g.202104642C>G	ENSP00000272217:p.Gly129Arg	114.0	0.0	2126	155.0	40.0	NM_138795	B3KXD0	Missense_Mutation	SNP	ENST00000272217.2	hg19	CCDS1421.1	.	.	.	.	.	.	.	.	.	.	C	31	5.092006	0.94149	.	.	ENSG00000143862	ENST00000272217	D	0.84070	-1.8	5.06	5.06	0.68205	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95040	0.8394	H	0.98629	4.285	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97249	0.9896	10	0.87932	D	0	-36.1721	18.4214	0.90591	0.0:1.0:0.0:0.0	.	129	Q96BM9	ARL8A_HUMAN	R	129	ENSP00000272217:G129R	ENSP00000272217:G129R	G	-	1	0	ARL8A	200371265	1.000000	0.71417	0.997000	0.53966	0.883000	0.51084	7.606000	0.82863	2.334000	0.79466	0.305000	0.20034	GGT	.	.		0.552	ARL8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087493.1	NM_138795		G	202104642	C	G	202104642	3	3	86	1	0	0	0	0	1	0	0	0	946	623	22	4	187	4	ARL8A	1	202104642	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	15156151	202104642	47145979	12	11506										
RYR2	6262	hgsc.bcm.edu	37	chr1	237905615	237905615	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gagttgtcatgatgaggaagAtgacgatggtgaagaggaag	17	2	1	6			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:237905615A>T	ENST00000366574.2	+	80	11428	c.11111A>T	c.(11110-11112)gAt>gTt	p.D3704V	RYR2_ENST00000542537.1_Missense_Mutation_p.D3688V|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Missense_Mutation_p.D3702V	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3704					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GATGAGGAAGATGACGATGGT	0.318																																					p.D3704V		Atlas-SNP	.											.	RYR2	1273	.	0			c.A11111T						.						201	204	203					1																	237905615		1868	4091	5959	SO:0001583	missense	6262	exon80			AGGAAGATGACGA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.11111A>T	chr1.hg19:g.237905615A>T	ENSP00000355533:p.Asp3704Val	219.0	0.0		364.0	70.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.071034	0.36566	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.96913	-4.17;-4.12;-4.16	5.89	4.76	0.60689	.	0.077328	0.49916	D	0.000133	D	0.93871	0.8039	L	0.32530	0.975	0.80722	D	1	D;B	0.53462	0.96;0.346	P;B	0.47744	0.556;0.047	D	0.93001	0.6423	10	0.72032	D	0.01	-14.9408	9.9481	0.41623	0.9235:0.0:0.0765:0.0	.	659;3704	B4DGV4;Q92736	.;RYR2_HUMAN	V	3704;3702;3688;659	ENSP00000355533:D3704V;ENSP00000353174:D3702V;ENSP00000443798:D3688V	ENSP00000353174:D3702V	D	+	2	0	RYR2	235972238	1.000000	0.71417	0.997000	0.53966	0.287000	0.27160	6.112000	0.71547	1.052000	0.40392	0.477000	0.44152	GAT	.	.		0.318	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237905615	A	T	237905615	3	4	86	1	0	0	0	0	1	0	0	0	13784	333	12	4	11429	4	RYR2	1	237905615	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	35800973	237905615	11345006	13	11507										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247024552	247024553	+	Frame_Shift_Ins	INS	-	-	T													0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gtttccactggaactgcacaINSttttttaggtgtagtaaata							TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:247024552_247024553insT	ENST00000391829.2	-	29	3903_3904	c.3780_3781insA	c.(3778-3783)aaatgtfs	p.C1261fs	AHCTF1_ENST00000366508.1_Frame_Shift_Ins_p.C1296fs|AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000326225.3_Frame_Shift_Ins_p.C1270fs			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1261	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GGAACTGCACATTTTTTAGGTG	0.361																																					p.C1270fs	Colon(145;197 1800 4745 15099 26333)	Atlas-Indel,Pindel	.											.	AHCTF1	187	.	0			c.3808_3809insA						.																																			SO:0001589	frameshift_variant	25909	exon29			.		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.3781dupA	chr1.hg19:g.247024558_247024558dupT	ENSP00000375705:p.Cys1261fs	424.0	0.0		904.0	217.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Frame_Shift_Ins	INS	ENST00000391829.2	hg19																																																																																				.	.		0.361	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		T	247024553	-	T	247024552	7	5	86	1	0	1	1	0	0	0	0	0	408	217	8	0	3051	0	AHCTF1	1	247024552	Frame_Shift_Ins	INS	-	TCGA-DD-A113-01A-11D-A12Z-10	9118937	247024552	2226069	14	11508										
PGBD2	267002	hgsc.bcm.edu	37	chr1	249211815	249211815	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cttcaggagcgtggttttctGccatatcacatattttttga	8	8	3	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr1:249211815G>A	ENST00000329291.5	+	3	1179	c.1032G>A	c.(1030-1032)ctG>ctA	p.L344L	PGBD2_ENST00000539153.1_Silent_p.L341L|PGBD2_ENST00000355360.4_Silent_p.L93L	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	344										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GTGGTTTTCTGCCATATCACA	0.443																																					p.L344L		Atlas-SNP	.											.	PGBD2	103	.	0			c.G1032A						.						121	125	124					1																	249211815		2203	4300	6503	SO:0001819	synonymous_variant	267002	exon3			TTTTCTGCCATAT	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.1032G>A	chr1.hg19:g.249211815G>A		169.0	0.0		386.0	89.0	NM_170725	B3KVR8|Q6MZF8	Silent	SNP	ENST00000329291.5	hg19	CCDS31128.1																																																																																			.	.		0.443	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1			A	249211815	G	A	249211815	2	1	86	1	0	0	0	0	0	0	0	1	11790	1306	46	3		3	PGBD2	1	249211815	Silent	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	2187263	249211815	38806	15	11509										
APOB	338	hgsc.bcm.edu	37	chr2	21228862	21228862	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	catctgatcttctggttcttAgtgttagcattcagggccac	9	10	5	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr2:21228862A>C	ENST00000233242.1	-	26	11005	c.10878T>G	c.(10876-10878)acT>acG	p.T3626T		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3626					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTGGTTCTTAGTGTTAGCAT	0.488																																					p.T3626T		Atlas-SNP	.											.	APOB	761	.	0			c.T10878G						.						60	57	58					2																	21228862		2203	4300	6503	SO:0001819	synonymous_variant	338	exon26			GTTCTTAGTGTTA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10878T>G	chr2.hg19:g.21228862A>C		273.0	0.0		350.0	115.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.488	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21228862	A	C	21228862	2	2	86	1	0	0	0	0	0	0	0	1	785	407	15	5		5	APOB	2	21228862	Silent	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10		21228862	221970511	16	11510										
KIAA1310	55683	hgsc.bcm.edu	37	chr2	97285440	97285440	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ccaagcgggcaagccggtcaGactgcagggctttgaggatc	15	11	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr2:97285440G>C	ENST00000431828.1	-	4	522	c.446C>G	c.(445-447)tCt>tGt	p.S149C	KANSL3_ENST00000435669.1_Missense_Mutation_p.S62C|KANSL3_ENST00000441706.2_Missense_Mutation_p.S62C|KANSL3_ENST00000599854.1_Missense_Mutation_p.S62C|KANSL3_ENST00000487070.1_Intron|KANSL3_ENST00000440133.1_Intron			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	149					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											AAGCCGGTCAGACTGCAGGGC	0.542																																					p.S149C		Atlas-SNP	.											.	.	.	.	0			c.C446G						.						33	35	34					2																	97285440		1938	4138	6076	SO:0001583	missense	55683	exon4			CGGTCAGACTGCA	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.446C>G	chr2.hg19:g.97285440G>C	ENSP00000396749:p.Ser149Cys	229.0	0.0		302.0	158.0	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	hg19	CCDS46361.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.127703	0.77549	.	.	ENSG00000114982	ENST00000354204;ENST00000447759;ENST00000431828;ENST00000441706;ENST00000452268;ENST00000435669	T	0.49139	0.79	5.49	3.64	0.41730	.	0.055620	0.64402	D	0.000001	T	0.57403	0.2051	L	0.42245	1.32	0.38769	D	0.954504	B;D;B	0.76494	0.0;0.999;0.0	B;D;B	0.63192	0.0;0.912;0.0	T	0.61964	-0.6954	10	0.62326	D	0.03	.	13.8808	0.63682	0.0:0.292:0.708:0.0	.	149;62;37	Q9P2N6-3;Q9P2N6-5;Q9P2N6-6	.;.;.	C	62;37;149;62;62;62	ENSP00000396749:S149C	ENSP00000346144:S62C	S	-	2	0	KIAA1310	96649167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.320000	0.65841	0.635000	0.30488	0.655000	0.94253	TCT	.	.		0.542	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		C	97285440	G	C	97285440	3	2	86	1	0	0	0	0	1	0	0	0	8231	942	33	4	2262	4	KIAA1310	2	97285440	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	76056578	97285440	145913933	17	11511										
MERTK	10461	hgsc.bcm.edu	37	chr2	112786337	112786337	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gggagagacttgttaggaatGgggtctcctggtcccattcg	15	8	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr2:112786337G>C	ENST00000295408.4	+	19	3153	c.2896G>C	c.(2896-2898)Ggg>Cgg	p.G966R	MERTK_ENST00000409780.1_Missense_Mutation_p.G790R|MERTK_ENST00000421804.2_Missense_Mutation_p.G966R			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	966					apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						TGTTAGGAATGGGGTCTCCTG	0.532																																					p.G966R		Atlas-SNP	.											.	MERTK	112	.	0			c.G2896C						.						47	43	44					2																	112786337		2203	4300	6503	SO:0001583	missense	10461	exon19			AGGAATGGGGTCT	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7027	protein-coding gene	gene with protein product		604705	"c-mer proto-oncogene tyrosine kinase"			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.2896G>C	chr2.hg19:g.112786337G>C	ENSP00000295408:p.Gly966Arg	68.0	0.0		80.0	28.0	NM_006343	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	hg19	CCDS2094.1	.	.	.	.	.	.	.	.	.	.	G	4.785	0.146018	0.09134	.	.	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000409780	T;T;T	0.76186	-1.0;-1.0;-0.93	5.58	2.78	0.32641	.	0.000000	0.34067	U	0.004283	T	0.63651	0.2529	L	0.55103	1.725	0.09310	N	0.999996	B	0.22541	0.071	B	0.19666	0.026	T	0.55655	-0.8107	10	0.48119	T	0.1	-11.8275	3.6891	0.08339	0.1107:0.2531:0.5065:0.1297	.	966	Q12866	MERTK_HUMAN	R	966;966;790	ENSP00000295408:G966R;ENSP00000389152:G966R;ENSP00000387277:G790R	ENSP00000295408:G966R	G	+	1	0	MERTK	112502808	0.490000	0.26012	0.040000	0.18447	0.188000	0.23474	1.066000	0.30604	0.290000	0.22444	0.655000	0.94253	GGG	.	.		0.532	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			C	112786337	G	C	112786337	3	2	86	1	0	0	0	0	1	0	0	0	9488	1348	47	4	2970	4	MERTK	2	112786337	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	15500897	112786337	130413036	18	11512										
FMNL2	114793	hgsc.bcm.edu	37	chr2	153496548	153496548	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	actcctagagcaagaagctcTgatggagcagcaggatccaa	11	10	1	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr2:153496548T>A	ENST00000475377.2	+	11	1348	c.1148T>A	c.(1147-1149)cTg>cAg	p.L383Q	FMNL2_ENST00000288670.9_Missense_Mutation_p.L1008Q			Q96PY5	FMNL2_HUMAN	formin-like 2	1008	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						CAAGAAGCTCTGATGGAGCAG	0.488																																					p.L1008Q		Atlas-SNP	.											.	FMNL2	75	.	0			c.T3023A						.						37	35	35					2																	153496548		1925	4088	6013	SO:0001583	missense	114793	exon24			AAGCTCTGATGGA	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000475377.2:c.1148T>A	chr2.hg19:g.153496548T>A	ENSP00000418959:p.Leu383Gln	342.0	0.0		491.0	246.0	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000475377.2	hg19		.	.	.	.	.	.	.	.	.	.	T	10.94	1.491974	0.26774	.	.	ENSG00000157827	ENST00000288670;ENST00000421344;ENST00000475377	T;T	0.77229	-1.08;2.19	5.08	5.08	0.68730	Actin-binding FH2/DRF autoregulatory (1);	.	.	.	.	T	0.58581	0.2132	N	0.08118	0	0.37242	D	0.906156	B;B;B	0.28512	0.214;0.006;0.009	B;B;B	0.26517	0.07;0.01;0.054	T	0.60469	-0.7257	9	0.13853	T	0.58	.	15.1392	0.72599	0.0:0.0:0.0:1.0	.	1008;489;1008	Q96PY5;Q6ZN96;Q96PY5-3	FMNL2_HUMAN;.;.	Q	1008;489;383	ENSP00000288670:L1008Q;ENSP00000418959:L383Q	ENSP00000288670:L1008Q	L	+	2	0	FMNL2	153204794	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	4.350000	0.59392	2.044000	0.60594	0.455000	0.32223	CTG	.	.		0.488	FMNL2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333583.3	NM_052905		A	153496548	T	A	153496548	3	1	86	1	0	0	0	0	1	0	0	0	5960	1580	55	4	3117	4	FMNL2	2	153496548	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	40710211	153496548	89702825	19	11513										
SCN3A	6328	hgsc.bcm.edu	37	chr2	165948928	165948928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tcatgtatttgccctggtcaTccgtttccaccatcatggtg	8	12	3	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr2:165948928T>C	ENST00000360093.3	-	27	5134	c.4643A>G	c.(4642-4644)gAt>gGt	p.D1548G	SCN3A_ENST00000283254.7_Missense_Mutation_p.D1548G|AC013463.2_ENST00000431341.1_RNA|SCN3A_ENST00000465043.1_5'UTR|SCN3A_ENST00000409101.3_Missense_Mutation_p.D1499G|SCN3A_ENST00000540861.1_Missense_Mutation_p.D31G	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1548					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GCCCTGGTCATCCGTTTCCAC	0.448																																					p.D1548G		Atlas-SNP	.											.	SCN3A	544	.	0			c.A4643G						.						178	135	149					2																	165948928		2203	4300	6503	SO:0001583	missense	6328	exon27			TGGTCATCCGTTT	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.4643A>G	chr2.hg19:g.165948928T>C	ENSP00000353206:p.Asp1548Gly	368.0	0.0		413.0	204.0	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	hg19		.	.	.	.	.	.	.	.	.	.	T	27.1	4.797628	0.90538	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000540861	D;D;D;D	0.97378	-4.36;-4.36;-4.36;-4.36	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.98836	0.9607	M	0.93550	3.43	0.80722	D	1	D;D;D	0.71674	0.998;0.983;0.988	D;P;P	0.81914	0.995;0.822;0.688	D	0.99690	1.1001	10	0.72032	D	0.01	.	16.4053	0.83662	0.0:0.0:0.0:1.0	.	1499;1499;1548	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	G	1548;1548;1499;31	ENSP00000353206:D1548G;ENSP00000283254:D1548G;ENSP00000386726:D1499G;ENSP00000439920:D31G	ENSP00000283254:D1548G	D	-	2	0	SCN3A	165657174	1.000000	0.71417	0.986000	0.45419	0.903000	0.53119	7.997000	0.88414	2.333000	0.79357	0.482000	0.46254	GAT	.	.		0.448	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		C	165948928	T	C	165948928	3	2	86	1	0	0	0	0	1	0	0	0	13933	1435	50	2	1367	2	SCN3A	2	165948928	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	12452380	165948928	77250445	20	11514										
TTN	7273	hgsc.bcm.edu	37	chr2	179510675	179510675	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tggaatattttctccttcacAtcttccttaggtggagcagg	9	9	3	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr2:179510675A>T	ENST00000591111.1	-	167	35681	c.35457T>A	c.(35455-35457)gaT>gaA	p.D11819E	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D10892E|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.D13460E|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000431752.1_RNA|RP11-171I2.3_ENST00000605021.1_lincRNA			Q8WZ42	TITIN_HUMAN	titin	11819	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTCCTTCACATCTTCCTTAG	0.408																																					p.D13460E		Atlas-SNP	.											.	TTN	18412	.	0			c.T40380A						.						105	98	100					2																	179510675		1830	4079	5909	SO:0001583	missense	7273	exon217			CTTCACATCTTCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.35457T>A	chr2.hg19:g.179510675A>T	ENSP00000465570:p.Asp11819Glu	437.0	0.0		604.0	30.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.758|3.758	-0.050228|-0.050228	0.07407|0.07407	.|.	.|.	ENSG00000155657|ENSG00000155657	ENST00000426232|ENST00000342992;ENST00000429997;ENST00000446966;ENST00000434777	.|T	.|0.68025	.|-0.3	5.39|5.39	-5.56|-5.56	0.02529|0.02529	.|Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.|.	.|.	.|.	.|.	T|T	0.39036|0.39036	0.1063|0.1063	N|N	0.14661|0.14661	0.345|0.345	0.38293|0.38293	D|D	0.942765|0.942765	.|B;B	.|0.17667	.|0.0;0.023	.|B;B	.|0.14578	.|0.001;0.011	T|T	0.10706|0.10706	-1.0618|-1.0618	5|9	.|0.87932	.|D	.|0	.|.	2.3534|2.3534	0.04290|0.04290	0.414:0.0947:0.3252:0.1661|0.414:0.0947:0.3252:0.1661	.|.	.|11819;299	.|Q8WZ42;A2TKE4	.|TITIN_HUMAN;.	S|E	167|10892;299;299;119	.|ENSP00000343764:D10892E	.|ENSP00000343764:D10892E	C|D	-|-	1|3	0|2	TTN|TTN	179218920|179218920	0.001000|0.001000	0.12720|0.12720	0.939000|0.939000	0.37840|0.37840	0.707000|0.707000	0.40811|0.40811	-0.805000|-0.805000	0.04530|0.04530	-0.478000|-0.478000	0.06823|0.06823	-0.376000|-0.376000	0.06991|0.06991	TGT|GAT	.	.		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179510675	A	T	179510675	3	4	86	1	0	0	0	0	1	0	0	0	16750	214	8	4	67897	4	TTN	2	179510675	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	13561747	179510675	63688698	21	11515										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196674472	196674472	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	atgaaaacagtactgaccgcCcgctcatgcagcagtagatt	9	11	1	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr2:196674472C>T	ENST00000312428.6	-	52	9985	c.9885G>A	c.(9883-9885)cgG>cgA	p.R3295R		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3295					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TACTGACCGCCCGCTCATGCA	0.323																																					p.R3295R		Atlas-SNP	.											.	DNAH7	512	.	0			c.G9885A						.						67	61	63					2																	196674472		1836	4077	5913	SO:0001819	synonymous_variant	56171	exon52			GACCGCCCGCTCA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.9885G>A	chr2.hg19:g.196674472C>T		283.0	0.0		515.0	160.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.323	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196674472	C	T	196674472	2	4	86	1	0	0	0	0	0	0	0	1	4608	610	22	3		3	DNAH7	2	196674472	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	17163797	196674472	46524901	22	11516										
BZW1	9689	hgsc.bcm.edu	37	chr2	201677965	201677965	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ataatcaaaagcagcaaaagCcaacgctatcaggccagcgt	8	11	2	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr2:201677965C>T	ENST00000409600.1	+	2	480	c.25C>T	c.(25-27)Cca>Tca	p.P9S	BZW1_ENST00000452790.2_Missense_Mutation_p.P41S|BZW1_ENST00000409226.1_Missense_Mutation_p.P13S|AC007163.6_ENST00000447972.3_RNA	NM_001207067.1|NM_014670.3	NP_001193996.1|NP_055485.2	Q7L1Q6	BZW1_HUMAN	basic leucine zipper and W2 domains 1	9					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(1)|kidney(2)|large_intestine(1)|lung(2)	6						GCAGCAAAAGCCAACGCTATC	0.338																																					p.P41S		Atlas-SNP	.											.	BZW1	49	.	0			c.C121T						.						83	78	80					2																	201677965		1844	4081	5925	SO:0001583	missense	9689	exon2			CAAAAGCCAACGC	D13630	CCDS56154.1, CCDS56155.1, CCDS56156.1	2q33	2010-04-09			ENSG00000082153	ENSG00000082153			18380	protein-coding gene	gene with protein product						10964520, 11524015	Standard	NM_001207067		Approved	BZAP45, KIAA0005	uc021vus.1	Q7L1Q6	OTTHUMG00000154560	ENST00000409600.1:c.25C>T	chr2.hg19:g.201677965C>T	ENSP00000386474:p.Pro9Ser	98.0	0.0		117.0	62.0	NM_001207068	B4DLZ8|B4DWF7|Q14281|Q15394|Q9BUY0	Missense_Mutation	SNP	ENST00000409600.1	hg19	CCDS56156.1	.	.	.	.	.	.	.	.	.	.	C	32	5.140318	0.94560	.	.	ENSG00000082153	ENST00000450637;ENST00000452206;ENST00000410110;ENST00000409600;ENST00000409226;ENST00000452790;ENST00000447069;ENST00000419090	T;T;T;D;D;D;T;T	0.94330	-1.03;-1.14;-1.42;-3.17;-3.24;-3.4;-1.11;-1.07	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	D	0.97213	0.9089	M	0.88310	2.945	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.98027	1.0374	10	0.72032	D	0.01	-13.5255	18.166	0.89727	0.0:1.0:0.0:0.0	.	13;41;9	B4DWF7;B4DLZ8;Q7L1Q6	.;.;BZW1_HUMAN	S	9;9;9;9;13;41;13;9	ENSP00000412072:P9S;ENSP00000390766:P9S;ENSP00000387086:P9S;ENSP00000386474:P9S;ENSP00000386837:P13S;ENSP00000394316:P41S;ENSP00000393587:P13S;ENSP00000407268:P9S	ENSP00000386837:P13S	P	+	1	0	BZW1	201386210	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.580000	0.82523	2.360000	0.80028	0.555000	0.69702	CCA	.	.		0.338	BZW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335975.1	NM_014670		T	201677965	C	T	201677965	3	4	86	1	0	0	0	0	1	0	0	0	1580	739	26	3	27	3	BZW1	2	201677965	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	5003493	201677965	41521408	23	11517										
COPS8	10920	hgsc.bcm.edu	37	chr2	237998516	237998516	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ttattgcaggcaaattctgaActtgggggaatttggtcagt	12	5	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr2:237998516A>G	ENST00000354371.2	+	4	863	c.210A>G	c.(208-210)gaA>gaG	p.E70E	COPS8_ENST00000409629.1_Silent_p.E70E|COPS8_ENST00000392008.2_Silent_p.E21E|COPS8_ENST00000409334.1_Silent_p.E70E	NM_006710.4	NP_006701.1	Q99627	CSN8_HUMAN	COP9 signalosome subunit 8	70	PCI.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|cullin deneddylation (GO:0010388)|negative regulation of cell proliferation (GO:0008285)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4		Breast(86;0.000162)|Renal(207;0.00339)|all_hematologic(139;0.0123)|Ovarian(221;0.0694)|Acute lymphoblastic leukemia(138;0.0775)|all_lung(227;0.169)|all_neural(83;0.211)		Epithelial(121;7.41e-23)|OV - Ovarian serous cystadenocarcinoma(60;5.42e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000175)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.0258)		CAAATTCTGAACTTGGGGGAA	0.403																																					p.E70E		Atlas-SNP	.											.	COPS8	14	.	0			c.A210G						.						63	65	64					2																	237998516		2203	4300	6503	SO:0001819	synonymous_variant	10920	exon4			TTCTGAACTTGGG		CCDS2517.1, CCDS42835.1	2q37.3	2013-03-14	2013-03-14		ENSG00000198612	ENSG00000198612			24335	protein-coding gene	gene with protein product			"COP9 constitutive photomorphogenic homolog subunit 8 (Arabidopsis)"			7634324, 12732143	Standard	NM_006710		Approved	COP9, CSN8, MGC1297, SGN8	uc002vwh.3	Q99627	OTTHUMG00000133297	ENST00000354371.2:c.210A>G	chr2.hg19:g.237998516A>G		157.0	0.0		79.0	42.0	NM_006710	A8K1H6|Q53QS9	Silent	SNP	ENST00000354371.2	hg19	CCDS2517.1																																																																																			.	.		0.403	COPS8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257082.3	NM_006710		G	237998516	A	G	237998516	2	3	86	1	0	0	0	0	0	0	0	1	3742	40	2	2		2	COPS8	2	237998516	Silent	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	36320551	237998516	5200857	24	11518										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4726834	4726834	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	agcagcaacagcgtctgctcCggaacatgggcgcgcacgcc	13	15	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr3:4726834C>T	ENST00000443694.2	+	27	3601	c.3601C>T	c.(3601-3603)Cgg>Tgg	p.R1201W	ITPR1_ENST00000357086.4_Missense_Mutation_p.R1207W|ITPR1_ENST00000456211.2_Missense_Mutation_p.R1192W|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.R1216W|ITPR1_ENST00000302640.8_Missense_Mutation_p.R1201W|ITPR1_ENST00000423119.2_Missense_Mutation_p.R1207W			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1216					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	GCGTCTGCTCCGGAACATGGG	0.542																																					p.R1207W		Atlas-SNP	.											.	ITPR1	659	.	0			c.C3619T						.						41	40	40					3																	4726834		2079	4222	6301	SO:0001583	missense	3708	exon30			CTGCTCCGGAACA	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.3601C>T	chr3.hg19:g.4726834C>T	ENSP00000401671:p.Arg1201Trp	90.0	0.0		70.0	30.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.003942	0.54254	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.97553	-4.43;-4.43;-4.43;-4.43;-4.43;-4.43	5.25	1.08	0.20341	Intracellular calcium-release channel (1);	0.049033	0.85682	N	0.000000	D	0.97785	0.9273	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.975	D	0.96915	0.9670	10	0.87932	D	0	.	10.0029	0.41940	0.5879:0.3431:0.0:0.069	.	1216;1207	Q14643;G5E9P1	ITPR1_HUMAN;.	W	1216;1201;1216;1207;1207;1192;1201	ENSP00000306253:R1201W;ENSP00000346595:R1216W;ENSP00000405934:R1207W;ENSP00000349597:R1207W;ENSP00000397885:R1192W;ENSP00000401671:R1201W	ENSP00000306253:R1201W	R	+	1	2	ITPR1	4701834	0.832000	0.29368	0.996000	0.52242	0.486000	0.33341	1.274000	0.33132	0.164000	0.19529	-0.293000	0.09583	CGG	.	.		0.542	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4726834	C	T	4726834	3	4	86	1	0	0	0	0	1	0	0	0	7929	643	23	1	3756	1	ITPR1	3	4726834	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10		4726834	193295596	25	11519										
MTMR14	64419	hgsc.bcm.edu	37	chr3	9703950	9703950	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cttctcttgcctgtgtgttaGgtttgagagtaccgtacagg	12	8	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr3:9703950G>A	ENST00000296003.4	+	3	430		c.e3-1		MTMR14_ENST00000351233.5_Splice_Site|MTMR14_ENST00000420925.1_Intron|MTMR14_ENST00000353332.5_Splice_Site	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14						phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(2)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	21	Medulloblastoma(99;0.227)					CTGTGTGTTAGGTTTGAGAGT	0.493																																					.		Atlas-SNP	.											.	MTMR14	43	.	0			c.309-1G>A						.						102	103	103					3																	9703950		2029	4192	6221	SO:0001630	splice_region_variant	64419	exon3			GTGTTAGGTTTGA	BC001674	CCDS43043.1, CCDS43044.1, CCDS43045.1	3p26	2011-06-09	2006-12-18	2006-12-18	ENSG00000163719	ENSG00000163719		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	26190	protein-coding gene	gene with protein product	"egg-derived tyrosine phosphatase homolog (Drosophila)"	611089	"chromosome 3 open reading frame 29"	C3orf29		15186772	Standard	NM_022485		Approved	FLJ22405, FLJ90311, hJumpy, hEDTP	uc003brz.3	Q8NCE2	OTTHUMG00000155111	ENST00000296003.4:c.309-1G>A	chr3.hg19:g.9703950G>A		204.0	0.0		188.0	39.0	NM_001077525	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Splice_Site	SNP	ENST00000296003.4	hg19	CCDS43043.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.013365	0.75161	.	.	ENSG00000163719	ENST00000353332;ENST00000296003;ENST00000351233;ENST00000419048	.	.	.	6.01	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0845	0.86608	0.0:0.1269:0.8731:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MTMR14	9678950	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	9.160000	0.94734	1.547000	0.49401	0.650000	0.86243	.	.	.		0.493	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485	Intron	A	9703950	G	A	9703950	5	1	86	1	0	0	0	0	0	0	1	0	9951	1014	35	3	318	3	MTMR14	3	9703950	Splice_Site	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	4977116	9703950	188318480	26	11520										
C3orf63	23272	hgsc.bcm.edu	37	chr3	56681065	56681065	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	taaactctcgtttacctgaaCcaaaacctcgcttaaaaaat	3	11	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr3:56681065C>T	ENST00000493960.2	-	14	1710	c.1700G>A	c.(1699-1701)gGt>gAt	p.G567D	FAM208A_ENST00000355628.5_Missense_Mutation_p.G567D|FAM208A_ENST00000431842.2_Missense_Mutation_p.G171D	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	567							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						TTTACCTGAACCAAAACCTCG	0.303																																					p.G567D		Atlas-SNP	.											.	FAM208A	113	.	0			c.G1700A						.						41	45	43					3																	56681065		2196	4294	6490	SO:0001583	missense	23272	exon14			CCTGAACCAAAAC	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 63"	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1700G>A	chr3.hg19:g.56681065C>T	ENSP00000417509:p.Gly567Asp	194.0	0.0		189.0	93.0	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.858711	0.32791	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.11821	2.74;2.92;2.93	5.38	5.38	0.77491	.	0.093149	0.47093	D	0.000251	T	0.20941	0.0504	L	0.29908	0.895	0.35335	D	0.785953	D;D;D	0.89917	0.98;0.986;1.0	P;P;D	0.73708	0.844;0.504;0.981	T	0.09465	-1.0673	10	0.23302	T	0.38	-14.328	9.453	0.38739	0.1427:0.7842:0.0:0.0731	.	567;567;171	Q9UK61-3;Q9UK61-4;Q9UK61-2	.;.;.	D	171;567;567	ENSP00000399410:G171D;ENSP00000417509:G567D;ENSP00000347845:G567D	ENSP00000347845:G567D	G	-	2	0	C3orf63	56656105	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.164000	0.64954	2.793000	0.96121	0.655000	0.94253	GGT	.	.		0.303	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		T	56681065	C	T	56681065	3	4	86	1	0	0	0	0	1	0	0	0	2241	507	18	3	3416	3	C3orf63	3	56681065	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	46977115	56681065	141341365	27	11521										
ADCY5	111	hgsc.bcm.edu	37	chr3	123166600	123166600	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	caggtagggcagctggagcgGgggccgcgccgcgtggaagg	22	10	0	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr3:123166600G>T	ENST00000462833.1	-	1	2005	c.793C>A	c.(793-795)Ccg>Acg	p.P265T		NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	265					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.P265T(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		AGCTGGAGCGGGGGCCGCGCC	0.672																																					p.P265T		Atlas-SNP	.											ADCY5,NS,carcinoma,0,1	ADCY5	169	.	1	Substitution - Missense(1)	lung(1)	c.C793A						.						22	25	24					3																	123166600		2198	4292	6490	SO:0001583	missense	111	exon1			GGAGCGGGGGCCG	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.793C>A	chr3.hg19:g.123166600G>T	ENSP00000419361:p.Pro265Thr	50.0	0.0		66.0	17.0	NM_183357	B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	hg19	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	G	6.211	0.407100	0.11754	.	.	ENSG00000173175	ENST00000462833	T	0.76186	-1.0	4.91	4.0	0.46444	.	0.688433	0.13366	N	0.393306	T	0.65770	0.2723	L	0.44542	1.39	0.47737	D	0.999503	B	0.02656	0.0	B	0.06405	0.002	T	0.55736	-0.8094	10	0.17832	T	0.49	.	12.5467	0.56203	0.0:0.0:0.8331:0.1669	.	265	O95622	ADCY5_HUMAN	T	265	ENSP00000419361:P265T	ENSP00000419361:P265T	P	-	1	0	ADCY5	124649290	0.994000	0.37717	0.948000	0.38648	0.967000	0.64934	2.196000	0.42686	1.005000	0.39183	0.505000	0.49811	CCG	.	.		0.672	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		T	123166600	G	T	123166600	3	4	86	1	0	0	0	0	1	0	0	0	297	1232	43	3	3076	3	ADCY5	3	123166600	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	66485535	123166600	74855830	28	11522										
RNF13	11342	hgsc.bcm.edu	37	chr3	149589886	149589886	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tccaccagtaaaagacaattCatctggcactttcatcgtgt	6	11	3	1	rs138683130		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr3:149589886C>T	ENST00000344229.3	+	5	968	c.266C>T	c.(265-267)tCa>tTa	p.S89L	RNF13_ENST00000392894.3_Missense_Mutation_p.S89L|RNF13_ENST00000361785.6_5'UTR	NM_007282.4	NP_009213.1	O43567	RNF13_HUMAN	ring finger protein 13	89	PA.				protein autoubiquitination (GO:0051865)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	11		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			AAAGACAATTCATCTGGCACT	0.313																																					p.S89L		Atlas-SNP	.											.	RNF13	57	.	0			c.C266T						.	C	LEU/SER,LEU/SER	0,4406		0,0,2203	85	83	84		266,266	5.3	1	3	dbSNP_134	84	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RNF13	NM_007282.4,NM_183381.2	145,145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	89/382,89/382	149589886	1,13005	2203	4300	6503	SO:0001583	missense	11342	exon5			ACAATTCATCTGG	AF037204	CCDS3146.1	3q25.1	2013-01-09			ENSG00000082996	ENSG00000082996		"RING-type (C3HC4) zinc fingers"	10057	protein-coding gene	gene with protein product		609247					Standard	NM_183381		Approved	RZF	uc003exp.4	O43567	OTTHUMG00000150338	ENST00000344229.3:c.266C>T	chr3.hg19:g.149589886C>T	ENSP00000341361:p.Ser89Leu	263.0	0.0		221.0	36.0	NM_007282	A6NC87|B3KR12|Q05D66|Q6IBJ9	Missense_Mutation	SNP	ENST00000344229.3	hg19	CCDS3146.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.707979	0.48412	0.0	1.16E-4	ENSG00000082996	ENST00000392894;ENST00000344229;ENST00000543506;ENST00000468648;ENST00000459632;ENST00000466795;ENST00000482539;ENST00000490631	T;T;T;T;T;T;T	0.51325	3.3;3.3;2.44;3.3;3.3;0.71;3.3	5.28	5.28	0.74379	Protease-associated domain, PA (1);	5.674880	0.00166	N	0.000002	T	0.48077	0.1480	L	0.41492	1.28	0.80722	D	1	B	0.12013	0.005	B	0.15052	0.012	T	0.04635	-1.0937	10	0.24483	T	0.36	-15.648	15.9549	0.79880	0.0:1.0:0.0:0.0	.	89	O43567	RNF13_HUMAN	L	89	ENSP00000376628:S89L;ENSP00000341361:S89L;ENSP00000420067:S89L;ENSP00000419069:S89L;ENSP00000417655:S89L;ENSP00000420691:S89L;ENSP00000417294:S89L	ENSP00000341361:S89L	S	+	2	0	RNF13	151072576	0.966000	0.33281	0.996000	0.52242	0.928000	0.56348	2.120000	0.41968	2.756000	0.94617	0.655000	0.94253	TCA	.	C|1.000;T|0.000		0.313	RNF13-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356876.1	NM_183384		T	149589886	C	T	149589886	3	4	86	1	0	0	0	0	1	0	0	0	13452	838	29	3	276	3	RNF13	3	149589886	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	26423286	149589886	48432544	29	11523										
MCF2L2	23101	hgsc.bcm.edu	37	chr3	183056602	183056602	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gcttaccggcactttcgtttTaaactcatttcgatagtatt	6	9	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr3:183056602T>G	ENST00000328913.3	-	5	769	c.472A>C	c.(472-474)Aaa>Caa	p.K158Q	MCF2L2_ENST00000414362.2_Missense_Mutation_p.K158Q|MCF2L2_ENST00000473233.1_Missense_Mutation_p.K158Q|MCF2L2_ENST00000447025.2_Missense_Mutation_p.K158Q	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	158	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			ACTTTCGTTTTAAACTCATTT	0.418																																					p.K158Q		Atlas-SNP	.											.	MCF2L2	164	.	0			c.A472C						.						117	105	109					3																	183056602		2203	4300	6503	SO:0001583	missense	23101	exon5			TCGTTTTAAACTC	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.472A>C	chr3.hg19:g.183056602T>G	ENSP00000328118:p.Lys158Gln	151.0	0.0		147.0	51.0	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	hg19	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.667007	0.47677	.	.	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000414362	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	4.81	4.81	0.61882	Cellular retinaldehyde-binding/triple function, C-terminal (3);	0.112777	0.64402	D	0.000016	T	0.75027	0.3794	M	0.76574	2.34	0.36373	D	0.861417	P;P;P	0.52577	0.938;0.552;0.954	P;P;P	0.58331	0.837;0.661;0.759	T	0.82870	-0.0243	10	0.66056	D	0.02	.	14.0518	0.64742	0.0:0.0:0.0:1.0	.	158;158;158	Q86YR7-3;Q86YR7-2;Q86YR7	.;.;MF2L2_HUMAN	Q	158	ENSP00000328118:K158Q;ENSP00000420070:K158Q;ENSP00000388190:K158Q;ENSP00000414131:K158Q	ENSP00000328118:K158Q	K	-	1	0	MCF2L2	184539296	1.000000	0.71417	0.986000	0.45419	0.028000	0.11728	4.406000	0.59748	1.814000	0.52955	0.533000	0.62120	AAA	.	.		0.418	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		G	183056602	T	G	183056602	3	3	86	1	0	0	0	0	1	0	0	0	9389	1763	61	5	2976	5	MCF2L2	3	183056602	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	33466716	183056602	14965828	30	11524										
LEPREL1	55214	hgsc.bcm.edu	37	chr3	189700835	189700835	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aaaagtgcacagctacttacCttctcttaggtctcgatcta	6	11	3	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr3:189700835C>T	ENST00000319332.5	-	8	1521	c.1324G>A	c.(1324-1326)Ggt>Agt	p.G442S	LEPREL1_ENST00000427335.2_Splice_Site_p.G261S	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1	442					collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5)	41	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	AGCTACTTACCTTCTCTTAGG	0.473																																					p.G442S		Atlas-SNP	.											.	LEPREL1	95	.	0			c.G1324A						.						174	166	169					3																	189700835		2203	4300	6503	SO:0001630	splice_region_variant	55214	exon8			ACTTACCTTCTCT		CCDS3294.1, CCDS46981.1	3q29	2014-01-28			ENSG00000090530	ENSG00000090530	1.14.11.7		19317	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 2"	610341				15063763, 21885030	Standard	NM_018192		Approved	FLJ10718, MLAT4, P3H2	uc011bsk.2	Q8IVL5	OTTHUMG00000156312	ENST00000319332.5:c.1324+1G>A	chr3.hg19:g.189700835C>T		396.0	0.0		365.0	21.0	NM_018192	B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Missense_Mutation	SNP	ENST00000319332.5	hg19	CCDS3294.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.782428	0.70222	.	.	ENSG00000090530	ENST00000319332;ENST00000427335	T;T	0.36520	1.25;1.6	5.25	5.25	0.73442	.	0.311844	0.34110	N	0.004249	T	0.48295	0.1492	L	0.44542	1.39	0.80722	D	1	D	0.56035	0.974	P	0.58013	0.831	T	0.26985	-1.0087	9	.	.	.	-13.1508	17.7955	0.88568	0.0:1.0:0.0:0.0	.	442	Q8IVL5	P3H2_HUMAN	S	442;261	ENSP00000316881:G442S;ENSP00000408947:G261S	.	G	-	1	0	LEPREL1	191183529	1.000000	0.71417	0.998000	0.56505	0.427000	0.31564	4.636000	0.61339	2.622000	0.88805	0.637000	0.83480	GGT	.	.		0.473	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1	NM_018192	Missense_Mutation	T	189700835	C	T	189700835	5	4	86	1	0	0	0	0	0	0	1	0	8739	695	24	3	834	3	LEPREL1	3	189700835	Splice_Site	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	6644233	189700835	8321595	31	11525										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	193028474	193028474	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cttgatttctgcccaggagaCattcttgcaaaaactgttcc	7	11	2	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr3:193028474C>A	ENST00000342358.4	-	21	2595	c.2478G>T	c.(2476-2478)atG>atT	p.M826I	ATP13A5-AS1_ENST00000414634.1_RNA|ATP13A5_ENST00000495496.1_5'UTR	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	826						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		GCCCAGGAGACATTCTTGCAA	0.343																																					p.M826I		Atlas-SNP	.											.	ATP13A5	171	.	0			c.G2478T						.						107	99	102					3																	193028474		2203	4300	6503	SO:0001583	missense	344905	exon21			AGGAGACATTCTT	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.2478G>T	chr3.hg19:g.193028474C>A	ENSP00000341942:p.Met826Ile	154.0	0.0		167.0	10.0	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	hg19	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.916650	0.92249	.	.	ENSG00000187527	ENST00000342358	T	0.64991	-0.13	5.56	5.56	0.83823	HAD-like domain (2);	0.056781	0.64402	D	0.000001	T	0.77751	0.4177	M	0.85373	2.75	0.52501	D	0.99995	P	0.52316	0.952	P	0.54664	0.758	T	0.80750	-0.1243	10	0.62326	D	0.03	-30.5217	17.3696	0.87372	0.0:1.0:0.0:0.0	.	826	Q4VNC0	AT135_HUMAN	I	826	ENSP00000341942:M826I	ENSP00000341942:M826I	M	-	3	0	ATP13A5	194511168	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.414000	0.73318	2.778000	0.95560	0.655000	0.94253	ATG	.	.		0.343	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		A	193028474	C	A	193028474	3	1	86	1	0	0	0	0	1	0	0	0	1127	478	17	3	1216	3	ATP13A5	3	193028474	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	3327639	193028474	4993956	32	11526										
HTT	3064	hgsc.bcm.edu	37	chr4	3230361	3230361	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ggtgtccatacactccgtgtGgctggggaacagcatcacac	12	12	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr4:3230361G>T	ENST00000355072.5	+	58	8013	c.7868G>T	c.(7867-7869)tGg>tTg	p.W2623L		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2623					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CACTCCGTGTGGCTGGGGAAC	0.647																																					p.W2623L		Atlas-SNP	.											.	HTT	221	.	0			c.G7868T						.						48	55	53					4																	3230361		2077	4185	6262	SO:0001583	missense	3064	exon58			CCGTGTGGCTGGG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.7868G>T	chr4.hg19:g.3230361G>T	ENSP00000347184:p.Trp2623Leu	57.0	0.0		80.0	38.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	19.78	3.890780	0.72524	.	.	ENSG00000197386	ENST00000355072	T	0.62232	0.04	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.60637	0.2284	L	0.56769	1.78	0.80722	D	1	P	0.36990	0.577	B	0.33568	0.166	T	0.67337	-0.5696	10	0.72032	D	0.01	.	18.7031	0.91627	0.0:0.0:1.0:0.0	.	2623	P42858	HD_HUMAN	L	2623	ENSP00000347184:W2623L	ENSP00000347184:W2623L	W	+	2	0	HTT	3200159	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	9.118000	0.94355	2.511000	0.84671	0.563000	0.77884	TGG	.	.		0.647	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3230361	G	T	3230361	3	4	86	1	0	0	0	0	1	0	0	0	7466	1357	47	3	8098	3	HTT	4	3230361	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10		3230361	187923915	33	11527										
PDS5A	23244	hgsc.bcm.edu	37	chr4	39878616	39878616	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	agaaaaaatgtactcacgatCgtatctggggaaggtctgtt	11	6	3	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr4:39878616C>T	ENST00000303538.8	-	19	2689	c.2150G>A	c.(2149-2151)cGa>cAa	p.R717Q		NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						TACTCACGATCGTATCTGGGG	0.378																																					p.R717Q		Atlas-SNP	.											.	PDS5A	114	.	0			c.G2150A						.						138	122	127					4																	39878616		1836	4086	5922	SO:0001583	missense	23244	exon19			CACGATCGTATCT	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.2150G>A	chr4.hg19:g.39878616C>T	ENSP00000303427:p.Arg717Gln	302.0	0.0		437.0	30.0	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.603618	0.66445	.	.	ENSG00000121892	ENST00000303538	T	0.64438	-0.1	5.04	5.04	0.67666	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67942	0.2947	L	0.47716	1.5	0.80722	D	1	D	0.61697	0.99	P	0.53450	0.726	T	0.66571	-0.5890	9	.	.	.	.	18.7568	0.91836	0.0:1.0:0.0:0.0	.	717	Q29RF7	PDS5A_HUMAN	Q	717	ENSP00000303427:R717Q	.	R	-	2	0	PDS5A	39555011	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	4.912000	0.63335	2.501000	0.84356	0.591000	0.81541	CGA	.	.		0.378	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		T	39878616	C	T	39878616	3	4	86	1	0	0	0	0	1	0	0	0	11700	884	31	1	1923	1	PDS5A	4	39878616	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	36648255	39878616	151275660	34	11528										
MUC7	4589	hgsc.bcm.edu	37	chr4	71346650	71346650	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ccgttcattagaaagtcctaTaaatgtctgcacaaacgctg	7	10	2	1	rs147746777		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr4:71346650T>A	ENST00000304887.5	+	3	379	c.189T>A	c.(187-189)taT>taA	p.Y63*	MUC7_ENST00000514512.1_3'UTR|MUC7_ENST00000456088.1_Nonsense_Mutation_p.Y63*|MUC7_ENST00000413702.1_Nonsense_Mutation_p.Y63*	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	63					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			GAAAGTCCTATAAATGTCTGC	0.448																																					p.Y63X		Atlas-SNP	.											.	MUC7	91	.	0			c.T189A						.						170	165	167					4																	71346650		2203	4300	6503	SO:0001587	stop_gained	4589	exon4			GTCCTATAAATGT	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"Mucins"	7518	protein-coding gene	gene with protein product		158375	"mucin 7, salivary"			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.189T>A	chr4.hg19:g.71346650T>A	ENSP00000302021:p.Tyr63*	214.0	0.0		273.0	12.0	NM_001145007	Q9UCD7|Q9UCD8	Nonsense_Mutation	SNP	ENST00000304887.5	hg19	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.640851	0.47153	.	.	ENSG00000171195	ENST00000413702;ENST00000505411;ENST00000456088;ENST00000304887	.	.	.	2.8	-3.52	0.04682	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.2724	1.2396	0.01960	0.1666:0.3649:0.2001:0.2684	.	.	.	.	X	63	.	ENSP00000302021:Y63X	Y	+	3	2	MUC7	71381239	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.849000	0.04322	-0.686000	0.05170	-0.256000	0.11100	TAT	.	T|1.000;C|0.000		0.448	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		A	71346650	T	A	71346650	4	1	86	1	0	0	0	0	0	1	0	0	9990	1413	49	4	195	4	MUC7	4	71346650	Nonsense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	31468034	71346650	119807626	35	11529										
TNIP3	79931	hgsc.bcm.edu	37	chr4	122078361	122078361	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tctcccgcgtgctgaggaatCtttccgcggcgtccagtttc	11	14	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr4:122078361C>A	ENST00000509841.1	-	7	560	c.482G>T	c.(481-483)aGa>aTa	p.R161I	TNIP3_ENST00000454328.1_Missense_Mutation_p.R84I|TNIP3_ENST00000507879.1_Missense_Mutation_p.R154I|TNIP3_ENST00000057513.3_Missense_Mutation_p.R84I	NM_001244764.1	NP_001231693.1			TNFAIP3 interacting protein 3											NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2)	24						GCTGAGGAATCTTTCCGCGGC	0.587																																					p.R161I		Atlas-SNP	.											.	TNIP3	58	.	0			c.G482T						.						212	232	225					4																	122078361		2203	4300	6503	SO:0001583	missense	79931	exon7			AGGAATCTTTCCG	AJ320534	CCDS3718.1, CCDS58925.1, CCDS58926.1	4q27	2008-02-05			ENSG00000050730	ENSG00000050730			19315	protein-coding gene	gene with protein product		608019				11345586	Standard	NM_024873		Approved	LIND, FLJ21162, ABIN-3	uc021xrj.1	Q96KP6	OTTHUMG00000132969	ENST00000509841.1:c.482G>T	chr4.hg19:g.122078361C>A	ENSP00000426613:p.Arg161Ile	335.0	1.0		364.0	132.0	NM_001244764		Missense_Mutation	SNP	ENST00000509841.1	hg19	CCDS58926.1	.	.	.	.	.	.	.	.	.	.	C	13.06	2.124248	0.37533	.	.	ENSG00000050730	ENST00000057513;ENST00000454328;ENST00000507879;ENST00000509841	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	4.16	2.35	0.29111	.	0.464644	0.23038	N	0.052657	T	0.70605	0.3243	M	0.68952	2.095	0.09310	N	1	D;D;B	0.71674	0.998;0.994;0.114	D;P;B	0.72075	0.976;0.808;0.032	T	0.57774	-0.7753	10	0.48119	T	0.1	-0.2459	5.0205	0.14358	0.0:0.6637:0.2172:0.1191	.	154;84;84	B4DVF5;A5HU65;Q96KP6	.;.;TNIP3_HUMAN	I	84;84;154;161	ENSP00000057513:R84I;ENSP00000411817:R84I;ENSP00000427106:R154I;ENSP00000426613:R161I	ENSP00000057513:R84I	R	-	2	0	TNIP3	122297811	0.000000	0.05858	0.001000	0.08648	0.128000	0.20619	0.228000	0.17814	0.658000	0.30925	0.484000	0.47621	AGA	.	.		0.587	TNIP3-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364000.4	NM_024873		A	122078361	C	A	122078361	3	1	86	1	0	0	0	0	1	0	0	0	16331	913	32	3	758	3	TNIP3	4	122078361	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	50731711	122078361	69075915	36	11530										
ADCY2	108	hgsc.bcm.edu	37	chr5	7773143	7773143	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	atcatgatggtggccttggtGggctacaacaccatcctact	10	11	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr5:7773143G>A	ENST00000338316.4	+	18	2402	c.2313G>A	c.(2311-2313)gtG>gtA	p.V771V	ADCY2_ENST00000537121.1_Silent_p.V591V	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	771					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						TGGCCTTGGTGGGCTACAACA	0.517																																					p.V771V		Atlas-SNP	.											ADCY2,NS,carcinoma,+2,1	ADCY2	337	.	0			c.G2313A						.						225	193	204					5																	7773143		2203	4300	6503	SO:0001819	synonymous_variant	108	exon18			CTTGGTGGGCTAC	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2313G>A	chr5.hg19:g.7773143G>A		382.0	0.0		412.0	186.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	hg19	CCDS3872.2																																																																																			.	.		0.517	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7773143	G	A	7773143	2	1	86	1	0	0	0	0	0	0	0	1	294	1335	47	3		3	ADCY2	5	7773143	Silent	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10		7773143	173142117	37	11531										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38406944	38406944	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ctttaggttaaaccacttccTgctaccaaaggagggaataa	8	9	0	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr5:38406944T>A	ENST00000354891.3	+	8	1189	c.843T>A	c.(841-843)ccT>ccA	p.P281P	EGFLAM_ENST00000397202.2_Intron|EGFLAM_ENST00000322350.5_Silent_p.P281P|EGFLAM_ENST00000336740.6_Silent_p.P47P	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	281					extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					AACCACTTCCTGCTACCAAAG	0.418																																					p.P281P	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.T843A						.						89	85	86					5																	38406944		2203	4300	6503	SO:0001819	synonymous_variant	133584	exon8			ACTTCCTGCTACC	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.843T>A	chr5.hg19:g.38406944T>A		319.0	0.0		338.0	21.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	hg19	CCDS56363.1																																																																																			.	.		0.418	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		A	38406944	T	A	38406944	2	1	86	1	0	0	0	0	0	0	0	1	4968	1567	55	4		4	EGFLAM	5	38406944	Silent	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	30633801	38406944	142508316	38	11532										
C5orf28	64417	hgsc.bcm.edu	37	chr5	43446540	43446540	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gatataaataacatccagggAagaaagcaccatgagtcttt	8	7	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr5:43446540A>C	ENST00000500337.2	-	5	763	c.432T>G	c.(430-432)ctT>ctG	p.L144L	C5orf28_ENST00000537319.1_Silent_p.L13L|C5orf28_ENST00000511525.1_5'UTR|C5orf28_ENST00000397080.3_Silent_p.L144L|C5orf28_ENST00000510130.1_Silent_p.L42L|C5orf28_ENST00000512085.1_Silent_p.L144L			Q0VDI3	CE028_HUMAN	chromosome 5 open reading frame 28	144						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(5)	9	Lung NSC(6;2.07e-05)					ACATCCAGGGAAGAAAGCACC	0.423																																					p.L144L		Atlas-SNP	.											.	C5orf28	25	.	0			c.T432G						.						110	102	105					5																	43446540		2203	4300	6503	SO:0001819	synonymous_variant	64417	exon3			CCAGGGAAGAAAG	AK025310	CCDS3945.1	5p12	2011-01-25			ENSG00000151881	ENSG00000151881			26139	protein-coding gene	gene with protein product						12477932	Standard	NM_022483		Approved	FLJ21657	uc003jny.3	Q0VDI3	OTTHUMG00000131150	ENST00000500337.2:c.432T>G	chr5.hg19:g.43446540A>C		195.0	0.0		214.0	13.0	NM_022483	B2RDA6|Q9H6Z2	Silent	SNP	ENST00000500337.2	hg19	CCDS3945.1																																																																																			.	.		0.423	C5orf28-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368003.1	NM_022483		C	43446540	A	C	43446540	2	2	86	1	0	0	0	0	0	0	0	1	2291	233	9	5		5	C5orf28	5	43446540	Silent	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	5039596	43446540	137468720	39	11533										
MSH3	4437	hgsc.bcm.edu	37	chr5	80021280	80021280	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tttttctttcagtgtgcaggAtgacagaattcgagtcgaaa	10	6	2	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr5:80021280A>G	ENST00000265081.6	+	9	1429	c.1349A>G	c.(1348-1350)gAt>gGt	p.D450G	MSH3_ENST00000512258.1_3'UTR	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	450					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		AGTGTGCAGGATGACAGAATT	0.348								Mismatch excision repair (MMR)																													p.D450G	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.A1349G						.						110	104	106					5																	80021280		2203	4300	6503	SO:0001583	missense	4437	exon9			TGCAGGATGACAG	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.1349A>G	chr5.hg19:g.80021280A>G	ENSP00000265081:p.Asp450Gly	317.0	0.0		388.0	16.0	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	hg19	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	A	7.372	0.627023	0.14257	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.88201	-2.35	5.25	5.25	0.73442	DNA mismatch repair protein MutS, connector (2);	1.874300	0.03171	N	0.170725	D	0.91499	0.7316	N	0.20845	0.615	0.44330	D	0.997217	D	0.89917	1.0	D	0.81914	0.995	T	0.80627	-0.1298	9	.	.	.	-21.3145	14.4164	0.67153	1.0:0.0:0.0:0.0	.	450	P20585	MSH3_HUMAN	G	450;441	ENSP00000265081:D450G	.	D	+	2	0	MSH3	80057036	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	5.514000	0.67043	2.111000	0.64477	0.472000	0.43445	GAT	.	.		0.348	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		G	80021280	A	G	80021280	3	3	86	1	0	0	0	0	1	0	0	0	9880	333	12	2	1383	2	MSH3	5	80021280	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	36574740	80021280	100893980	40	11534										
GPR98	84059	hgsc.bcm.edu	37	chr5	89933635	89933635	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ttaattcaaaagcagtgaccCcggatgatataggccccttt	8	10	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr5:89933635C>A	ENST00000405460.2	+	11	2206	c.2110C>A	c.(2110-2112)Ccg>Acg	p.P704T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	704	Calx-beta 5. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGCAGTGACCCCGGATGATAT	0.423																																					p.P704T		Atlas-SNP	.											.	GPR98	605	.	0			c.C2110A						.						69	64	66					5																	89933635		1824	4080	5904	SO:0001583	missense	84059	exon11			GTGACCCCGGATG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.2110C>A	chr5.hg19:g.89933635C>A	ENSP00000384582:p.Pro704Thr	106.0	0.0		144.0	12.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.061|2.061	-0.415274|-0.415274	0.04766|0.04766	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000504142|ENST00000405460;ENST00000296619;ENST00000399043	.|T	.|0.26957	.|1.7	5.46|5.46	-3.43|-3.43	0.04810|0.04810	.|.	1.763740|1.763740	0.02465|0.02465	N|N	0.086918|0.086918	T|T	0.13415|0.13415	0.0325|0.0325	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.09377	.|0.004	T|T	0.10567|0.10567	-1.0624|-1.0624	6|10	.|0.14252	.|T	.|0.57	.|.	1.6629|1.6629	0.02796|0.02796	0.2717:0.1765:0.3587:0.1931|0.2717:0.1765:0.3587:0.1931	.|.	.|704	.|Q8WXG9	.|GPR98_HUMAN	H|T	292|704	.|ENSP00000384582:P704T	.|ENSP00000296619:P704T	P|P	+|+	2|1	0|0	GPR98|GPR98	89969391|89969391	0.000000|0.000000	0.05858|0.05858	0.539000|0.539000	0.28077|0.28077	0.744000|0.744000	0.42396|0.42396	-0.617000|-0.617000	0.05584|0.05584	-0.761000|-0.761000	0.04670|0.04670	-0.156000|-0.156000	0.13503|0.13503	CCC|CCG	.	.		0.423	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	89933635	C	A	89933635	3	1	86	1	0	0	0	0	1	0	0	0	6730	623	22	3	2152	3	GPR98	5	89933635	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	9912355	89933635	90981625	41	11535										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139915024	139915024	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	caagtttttccggcataccaGgaacaagggttttcctgcaa	9	10	0	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr5:139915024G>A	ENST00000360839.2	+	30	7082	c.6928G>A	c.(6928-6930)Gga>Aga	p.G2310R	ANKHD1_ENST00000544120.1_Intron|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.G2310R|ANKHD1_ENST00000297183.6_Missense_Mutation_p.G2310R	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	2310						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCATACCAGGAACAAGGGT	0.502																																					p.G2310R		Atlas-SNP	.											.	ANKHD1	233	.	0			c.G6928A						.						104	101	102					5																	139915024		2203	4300	6503	SO:0001583	missense	54882	exon30			ATACCAGGAACAA	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.6928G>A	chr5.hg19:g.139915024G>A	ENSP00000354085:p.Gly2310Arg	252.0	0.0		288.0	115.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.8|28.8	4.952477|4.952477	0.92660|0.92660	.|.	.|.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996;ENSG00000254996|ENSG00000131503	ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000433049;ENST00000532219;ENST00000437495|ENST00000435794	T;T;T;T;T;T|.	0.74106|.	-0.76;-0.81;1.29;1.29;-0.81;0.27|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.058131|.	0.64402|.	D|.	0.000002|.	T|T	0.70527|0.70527	0.3234|0.3234	L|L	0.52573|0.52573	1.65|1.65	0.42584|0.42584	D|D	0.99322|0.99322	D;D;D|.	0.71674|.	0.994;0.982;0.998|.	P;P;D|.	0.78314|.	0.865;0.785;0.991|.	T|T	0.67047|0.67047	-0.5769|-0.5769	10|5	0.72032|.	D|.	0.01|.	.|.	19.0911|19.0911	0.93227|0.93227	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	2310;2310;2310|.	E9PF56;Q8IWZ2;Q8IWZ3|.	.;.;ANKH1_HUMAN|.	R|K	2310;2310;2310;966;832;2310;321|800	ENSP00000354085:G2310R;ENSP00000297183:G2310R;ENSP00000393204:G966R;ENSP00000390034:G832R;ENSP00000432016:G2310R;ENSP00000396882:G321R|.	ENSP00000396882:G321R|.	G|R	+|+	1|2	0|0	ANKHD1-EIF4EBP3;ANKHD1|ANKHD1	139895208|139895208	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.179000|8.179000	0.89692|0.89692	2.746000|2.746000	0.94184|0.94184	0.563000|0.563000	0.77884|0.77884	GGA|AGG	.	.		0.502	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		A	139915024	G	A	139915024	3	1	86	1	0	0	0	0	1	0	0	0	628	1001	35	3	7152	3	ANKHD1	5	139915024	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	49981389	139915024	41000236	42	11536										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167643791	167643791	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aggtattgcagtagacaagaAtgggctcatgtactttgtcg	12	6	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr5:167643791A>G	ENST00000518659.1	+	22	4136	c.4097A>G	c.(4096-4098)aAt>aGt	p.N1366S	TENM2_ENST00000545108.1_Missense_Mutation_p.N1365S|TENM2_ENST00000520394.1_Missense_Mutation_p.N1127S|TENM2_ENST00000403607.2_Missense_Mutation_p.N1190S|TENM2_ENST00000519204.1_Missense_Mutation_p.N1245S	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1366					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										GTAGACAAGAATGGGCTCATG	0.527																																					p.N1357S		Atlas-SNP	.											.	.	.	.	0			c.A4070G						.						91	91	91					5																	167643791		2035	4193	6228	SO:0001583	missense	57451	exon22			ACAAGAATGGGCT	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.4097A>G	chr5.hg19:g.167643791A>G	ENSP00000429430:p.Asn1366Ser	219.0	0.0		267.0	98.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.06	3.014983	0.54468	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90324	-2.65;-2.65;-2.65;-2.65;-2.65	5.42	5.42	0.78866	Six-bladed beta-propeller, TolB-like (1);	0.088409	0.85682	D	0.000000	D	0.86744	0.6006	L	0.35288	1.05	0.38826	D	0.955746	B;B;B	0.20164	0.014;0.008;0.042	B;B;B	0.28465	0.031;0.014;0.09	D	0.83624	0.0141	10	0.33141	T	0.24	.	15.4962	0.75653	1.0:0.0:0.0:0.0	.	1365;1366;1127	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	S	1366;1365;1245;1127;1190	ENSP00000429430:N1366S;ENSP00000438635:N1365S;ENSP00000428964:N1245S;ENSP00000427874:N1127S;ENSP00000384905:N1190S	ENSP00000384905:N1190S	N	+	2	0	ODZ2	167576369	1.000000	0.71417	0.969000	0.41365	0.992000	0.81027	9.339000	0.96797	2.058000	0.61347	0.533000	0.62120	AAT	.	.		0.527	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		G	167643791	A	G	167643791	3	3	86	1	0	0	0	0	1	0	0	0	10844	101	4	2	4156	2	ODZ2	5	167643791	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	27728767	167643791	13271469	43	11537										
HIST1H2BB	3018	hgsc.bcm.edu	37	chr6	26043596	26043596	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gcagcagcaggcgcacagccGtctgaatctccctggaggtg	14	13	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr6:26043596G>A	ENST00000357905.2	-	1	289	c.290C>T	c.(289-291)aCg>aTg	p.T97M	HIST1H3C_ENST00000540144.1_5'Flank	NM_021062.2	NP_066406.1	P33778	H2B1B_HUMAN	histone cluster 1, H2bb	97					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7						GCGCACAGCCGTCTGAATCTC	0.557																																					p.T97M		Atlas-SNP	.											HIST1H2BB,NS,carcinoma,+1,1	HIST1H2BB	20	.	0			c.C290T						.						60	61	60					6																	26043596		2203	4300	6503	SO:0001583	missense	3018	exon1			ACAGCCGTCTGAA	AF531285	CCDS4575.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196226			"Histones / Replication-dependent"	4751	protein-coding gene	gene with protein product		602803	"H2B histone family, member F", "histone 1, H2bb"	H2BFF		8227173, 12408966	Standard	NM_021062		Approved	H2B/f	uc003nfu.3	P33778	OTTHUMG00000014421	ENST00000357905.2:c.290C>T	chr6.hg19:g.26043596G>A	ENSP00000350580:p.Thr97Met	160.0	1.0		175.0	12.0	NM_021062	Q4KN36	Missense_Mutation	SNP	ENST00000357905.2	hg19	CCDS4575.1	.	.	.	.	.	.	.	.	.	.	g	19.17	3.776577	0.70107	.	.	ENSG00000196226	ENST00000357905	T	0.45276	0.9	5.08	5.08	0.68730	Histone-fold (2);Histone core (1);	0.000000	0.64402	U	0.000015	T	0.70116	0.3187	M	0.93763	3.455	0.50171	D	0.999851	D	0.89917	1.0	D	0.85130	0.997	T	0.79210	-0.1897	10	0.87932	D	0	.	17.8155	0.88632	0.0:0.0:1.0:0.0	.	97	P33778	H2B1B_HUMAN	M	97	ENSP00000350580:T97M	ENSP00000350580:T97M	T	-	2	0	HIST1H2BB	26151575	1.000000	0.71417	0.998000	0.56505	0.909000	0.53808	9.789000	0.99068	2.498000	0.84270	0.467000	0.42956	ACG	.	.		0.557	HIST1H2BB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040083.1	NM_021062		A	26043596	G	A	26043596	3	1	86	1	0	0	0	0	1	0	0	0	7150	1145	40	1	94	1	HIST1H2BB	6	26043596	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10		26043596	145071471	44	11538										
TNXB	7148	hgsc.bcm.edu	37	chr6	32010105	32010105	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	agtcctcccagtccctccagAagtctgtctgtccatccatg	7	16	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr6:32010105A>C	ENST00000375244.3	-	41	12446	c.12245T>G	c.(12244-12246)tTc>tGc	p.F4082C	TNXB_ENST00000451343.1_Missense_Mutation_p.F511C|TNXB_ENST00000375247.2_Missense_Mutation_p.F4080C			P22105	TENX_HUMAN	tenascin XB	4127	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GTCCCTCCAGAAGTCTGTCTG	0.612																																					p.F4080C		Atlas-SNP	.											.	TNXB	553	.	0			c.T12239G						.																																			SO:0001583	missense	7148	exon41			CTCCAGAAGTCTG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.12245T>G	chr6.hg19:g.32010105A>C	ENSP00000364393:p.Phe4082Cys	1140.0	2.0		1240.0	314.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	a	19.73	3.881496	0.72294	.	.	ENSG00000168477	ENST00000375244;ENST00000451343;ENST00000375247	D;D;D	0.99418	-5.87;-5.87;-5.87	4.8	4.8	0.61643	.	0.000000	0.51477	D	0.000087	D	0.99746	0.9899	H	0.98426	4.23	0.52501	D	0.99995	D	0.89917	1.0	D	0.85130	0.997	D	0.97106	0.9801	10	0.87932	D	0	.	13.5365	0.61650	1.0:0.0:0.0:0.0	.	4080	P22105-3	.	C	4082;511;4080	ENSP00000364393:F4082C;ENSP00000407685:F511C;ENSP00000364396:F4080C	ENSP00000364393:F4082C	F	-	2	0	TNXB	32118084	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.560000	0.73950	2.046000	0.60703	0.525000	0.51046	TTC	.	.		0.612	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		C	32010105	A	C	32010105	3	2	86	1	0	0	0	0	1	0	0	0	16361	246	9	5	2490	5	TNXB	6	32010105	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	5966509	32010105	139104962	45	11539										
FRS3	10817	hgsc.bcm.edu	37	chr6	41738507	41738507	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cgggcagggtgggtggtgggCatgggggcttgggggctcga	25	6	0	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr6:41738507C>A	ENST00000373018.3	-	7	1580	c.1329G>T	c.(1327-1329)atG>atT	p.M443I	FRS3_ENST00000259748.2_Missense_Mutation_p.M443I	NM_006653.3	NP_006644.1	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3	443					fibroblast growth factor receptor signaling pathway (GO:0008543)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GGGTGGTGGGCATGGGGGCTT	0.637																																					p.M443I		Atlas-SNP	.											.	FRS3	53	.	0			c.G1329T						.						49	57	55					6																	41738507		2203	4300	6503	SO:0001583	missense	10817	exon7			GGTGGGCATGGGG	AF036718	CCDS4860.1	6p21.1	2010-08-05			ENSG00000137218	ENSG00000137218			16970	protein-coding gene	gene with protein product		607744				8761293, 9660748	Standard	NM_006653		Approved	SNT-2, FRS2beta, FRS2B	uc003orc.1	O43559	OTTHUMG00000014686	ENST00000373018.3:c.1329G>T	chr6.hg19:g.41738507C>A	ENSP00000362109:p.Met443Ile	72.0	0.0		59.0	22.0	NM_006653	Q5T3D5	Missense_Mutation	SNP	ENST00000373018.3	hg19	CCDS4860.1	.	.	.	.	.	.	.	.	.	.	C	7.680	0.688906	0.14973	.	.	ENSG00000137218	ENST00000373018;ENST00000259748	T;T	0.20738	2.05;2.05	5.33	4.45	0.53987	.	2.877110	0.00714	N	0.000856	T	0.03564	0.0102	N	0.02539	-0.55	0.19945	N	0.999943	B	0.02656	0.0	B	0.01281	0.0	T	0.37033	-0.9723	10	0.23302	T	0.38	-0.3259	12.6261	0.56630	0.4229:0.5771:0.0:0.0	.	443	O43559	FRS3_HUMAN	I	443	ENSP00000362109:M443I;ENSP00000259748:M443I	ENSP00000259748:M443I	M	-	3	0	FRS3	41846485	0.357000	0.24938	0.536000	0.28039	0.933000	0.57130	1.030000	0.30153	1.230000	0.43646	0.655000	0.94253	ATG	.	.		0.637	FRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040532.2	NM_006653		A	41738507	C	A	41738507	3	1	86	1	0	0	0	0	1	0	0	0	6070	710	25	3	153	3	FRS3	6	41738507	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	9728402	41738507	129376560	46	11540										
C6orf57	135154	hgsc.bcm.edu	37	chr6	71298368	71298368	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aagaaaaaggtggacccaggGgcccagaacctacccgatat	11	11	0	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr6:71298368G>C	ENST00000370474.3	+	3	292	c.268G>C	c.(268-270)Ggc>Cgc	p.G90R		NM_145267.2	NP_660310.2	Q5VUM1	SDHF4_HUMAN	chromosome 6 open reading frame 57	90					innate immune response (GO:0045087)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)				kidney(1)|lung(1)|skin(1)	3						TGGACCCAGGGGCCCAGAACC	0.393																																					p.G90R		Atlas-SNP	.											.	C6orf57	13	.	0			c.G268C						.						79	87	84					6																	71298368		2203	4300	6503	SO:0001583	missense	135154	exon3			CCCAGGGGCCCAG	BC018085	CCDS4972.1	6q12	2011-12-13			ENSG00000154079	ENSG00000154079			20957	protein-coding gene	gene with protein product							Standard	NM_145267		Approved		uc003pfq.1	Q5VUM1	OTTHUMG00000014992	ENST00000370474.3:c.268G>C	chr6.hg19:g.71298368G>C	ENSP00000359505:p.Gly90Arg	262.0	0.0		281.0	120.0	NM_145267	E1P532	Missense_Mutation	SNP	ENST00000370474.3	hg19	CCDS4972.1	.	.	.	.	.	.	.	.	.	.	G	33	5.269293	0.95429	.	.	ENSG00000154079	ENST00000370474	T	0.57907	0.37	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.72112	0.3420	M	0.80422	2.495	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74093	-0.3776	10	0.87932	D	0	-20.4851	19.3381	0.94329	0.0:0.0:1.0:0.0	.	90	Q5VUM1	CF057_HUMAN	R	90	ENSP00000359505:G90R	ENSP00000359505:G90R	G	+	1	0	C6orf57	71355089	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.894000	0.92506	2.854000	0.98071	0.655000	0.94253	GGC	.	.		0.393	C6orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041140.1	NM_145267		C	71298368	G	C	71298368	3	2	86	1	0	0	0	0	1	0	0	0	2368	1232	43	4	278	4	C6orf57	6	71298368	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	29559861	71298368	99816699	47	11541										
C6orf150	115004	hgsc.bcm.edu	37	chr6	74161889	74161889	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	agctctctgcatggcctttcCgtgccaaggctgcatggctg	12	13	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr6:74161889C>T	ENST00000370315.3	-	1	110	c.16G>A	c.(16-18)Gga>Aga	p.G6R	MB21D1_ENST00000370318.1_Missense_Mutation_p.G6R	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	6					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						ATGGCCTTTCCGTGCCAAGGC	0.627																																					p.G6R		Atlas-SNP	.											.	MB21D1	33	.	0			c.G16A						.						10	11	11					6																	74161889		2161	4236	6397	SO:0001583	missense	115004	exon1			CCTTTCCGTGCCA	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"chromosome 6 open reading frame 150"	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.16G>A	chr6.hg19:g.74161889C>T	ENSP00000359339:p.Gly6Arg	69.0	0.0		110.0	25.0	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Missense_Mutation	SNP	ENST00000370315.3	hg19	CCDS4978.1	.	.	.	.	.	.	.	.	.	.	C	6.306	0.424561	0.11928	.	.	ENSG00000164430	ENST00000370318;ENST00000370315;ENST00000296913	T;T	0.56941	0.43;0.6	3.59	-3.7	0.04437	.	1.610930	0.04166	N	0.324014	T	0.07548	0.0190	N	0.19112	0.55	0.09310	N	1	P	0.34826	0.471	B	0.20184	0.028	T	0.04090	-1.0978	10	0.10111	T	0.7	-0.2984	0.895	0.01262	0.148:0.2687:0.2908:0.2925	.	6	Q8N884	M21D1_HUMAN	R	6	ENSP00000359342:G6R;ENSP00000359339:G6R	ENSP00000296913:G6R	G	-	1	0	MB21D1	74218610	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-0.790000	0.04604	-1.092000	0.03062	0.313000	0.20887	GGA	.	.		0.627	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441		T	74161889	C	T	74161889	3	4	86	1	0	0	0	0	1	0	0	0	2339	661	23	1	1572	1	C6orf150	6	74161889	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	2863521	74161889	96953178	48	11542										
MYO6	4646	hgsc.bcm.edu	37	chr6	76599823	76599823	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gaaagaatatgatgcactggTtaaaagctcagaggaactcc	10	7	1	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr6:76599823T>G	ENST00000369977.3	+	26	2847	c.2708T>G	c.(2707-2709)gTt>gGt	p.V903G	MYO6_ENST00000369975.1_Missense_Mutation_p.V903G|MYO6_ENST00000369981.3_Missense_Mutation_p.V903G|MYO6_ENST00000369985.4_Missense_Mutation_p.V903G	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	903					actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		GATGCACTGGTTAAAAGCTCA	0.368																																					p.V903G		Atlas-SNP	.											.	MYO6	124	.	0			c.T2708G						.						85	91	89					6																	76599823		2203	4300	6503	SO:0001583	missense	4646	exon26			CACTGGTTAAAAG	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.2708T>G	chr6.hg19:g.76599823T>G	ENSP00000358994:p.Val903Gly	273.0	0.0		325.0	123.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	hg19	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	T	19.31	3.803091	0.70682	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	T;D;T;T	0.89617	2.24;-2.54;1.64;2.24	5.84	5.84	0.93424	.	0.061435	0.64402	D	0.000004	D	0.91352	0.7272	L	0.55990	1.75	0.80722	D	1	D;D	0.89917	1.0;0.994	D;P	0.76575	0.988;0.731	D	0.90986	0.4831	10	0.41790	T	0.15	.	16.216	0.82217	0.0:0.0:0.0:1.0	.	903;903	Q9UM54-2;Q9UM54-1	.;.	G	903	ENSP00000358998:V903G;ENSP00000359002:V903G;ENSP00000358994:V903G;ENSP00000358992:V903G	ENSP00000358992:V903G	V	+	2	0	MYO6	76656543	1.000000	0.71417	0.984000	0.44739	0.528000	0.34623	6.970000	0.76099	2.228000	0.72767	0.482000	0.46254	GTT	.	.		0.368	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		G	76599823	T	G	76599823	3	3	86	1	0	0	0	0	1	0	0	0	10090	1725	60	5	2806	5	MYO6	6	76599823	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	2437934	76599823	94515244	49	11543										
UBE2J1	51465	hgsc.bcm.edu	37	chr6	90053437	90053437	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	atggtaatgatctgttggatCtttcaattctgccgcttctt	8	8	5	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr6:90053437C>A	ENST00000435041.2	-	2	348	c.70G>T	c.(70-72)Gat>Tat	p.D24Y		NM_016021.2	NP_057105.2	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1	24					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(11)|stomach(1)	18		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)		TCTGTTGGATCTTTCAATTCT	0.279																																					p.D24Y		Atlas-SNP	.											.	UBE2J1	28	.	0			c.G70T						.						58	58	58					6																	90053437		2203	4299	6502	SO:0001583	missense	51465	exon2			TTGGATCTTTCAA	AJ245898	CCDS5021.1	6q15	2014-01-28	2012-06-08		ENSG00000198833	ENSG00000198833		"Ubiquitin-conjugating enzymes E2"	17598	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)"			10708578	Standard	NM_016021		Approved	HSPC153, CGI-76, NCUBE1, UBC6	uc003pnc.3	Q9Y385	OTTHUMG00000016337	ENST00000435041.2:c.70G>T	chr6.hg19:g.90053437C>A	ENSP00000451261:p.Asp24Tyr	96.0	0.0		82.0	64.0	NM_016021	A8K3F9|Q53F25|Q5W0N4|Q9BZ32|Q9NQL3|Q9NY66|Q9P011|Q9P0S0|Q9UF10	Missense_Mutation	SNP	ENST00000435041.2	hg19	CCDS5021.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.406487	0.83230	.	.	ENSG00000198833	ENST00000435041;ENST00000536477	T	0.50277	0.75	5.4	5.4	0.78164	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.041477	0.85682	D	0.000000	T	0.71533	0.3351	M	0.90019	3.08	0.80722	D	1	D	0.64830	0.994	D	0.68943	0.961	T	0.77466	-0.2577	10	0.87932	D	0	.	19.5511	0.95322	0.0:1.0:0.0:0.0	.	24	Q9Y385	UB2J1_HUMAN	Y	24;9	ENSP00000451261:D24Y	ENSP00000354684:D24Y	D	-	1	0	UBE2J1	90110156	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.423000	0.73361	2.704000	0.92352	0.650000	0.86243	GAT	.	.		0.279	UBE2J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043742.2	NM_016021		A	90053437	C	A	90053437	3	1	86	1	0	0	0	0	1	0	0	0	16875	913	32	3	914	3	UBE2J1	6	90053437	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	13453614	90053437	81061630	50	11544										
RNF217	154214	hgsc.bcm.edu	37	chr6	125402633	125402633	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ggttttgggattggcactagGggccatagcggttgtaatcg	16	6	0	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr6:125402633G>T	ENST00000521654.2	+	5	1535	c.1535G>T	c.(1534-1536)gGg>gTg	p.G512V	RNF217_ENST00000275184.6_Missense_Mutation_p.G156V|RNF217_ENST00000560949.1_Missense_Mutation_p.G277V|RNF217_ENST00000359704.2_Missense_Mutation_p.G220V|RNF217_ENST00000368414.2_Missense_Mutation_p.G74V			Q8TC41	RN217_HUMAN	ring finger protein 217	512					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0162)		TTGGCACTAGGGGCCATAGCG	0.363																																					p.G220V		Atlas-SNP	.											.	RNF217	64	.	0			c.G659T						.						100	100	100					6																	125402633		2203	4300	6503	SO:0001583	missense	154214	exon7			CACTAGGGGCCAT	BC026087	CCDS5129.1, CCDS69191.1	6q22.33	2014-07-15	2007-08-20	2007-08-20	ENSG00000146373	ENSG00000146373		"RING-type (C3HC4) zinc fingers"	21487	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 172", "IBR domain containing 1"	C6orf172, IBRDC1			Standard	NM_001286398		Approved	MGC26996, dJ84N20.1	uc003pzs.3	Q8TC41	OTTHUMG00000015504	ENST00000521654.2:c.1535G>T	chr6.hg19:g.125402633G>T	ENSP00000428698:p.Gly512Val	303.0	0.0		325.0	30.0	NM_152553	H7C5V4|Q5TCA4|Q9BX48	Missense_Mutation	SNP	ENST00000521654.2	hg19		.	.	.	.	.	.	.	.	.	.	G	24.9	4.577046	0.86645	.	.	ENSG00000146373	ENST00000521654;ENST00000368414;ENST00000359704;ENST00000275184	T;T	0.46063	0.88;0.88	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.57917	0.2086	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;0.994	D;P	0.91635	0.999;0.792	T	0.50048	-0.8873	10	0.37606	T	0.19	.	19.3694	0.94479	0.0:0.0:1.0:0.0	.	220;277	Q8TC41;F2Z2M4	RN217_HUMAN;.	V	277;74;220;156	ENSP00000352734:G220V;ENSP00000275184:G156V	ENSP00000275184:G156V	G	+	2	0	RNF217	125444332	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.577000	0.74027	2.821000	0.97095	0.650000	0.86243	GGG	.	.		0.363	RNF217-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000042063.3	NM_152553		T	125402633	G	T	125402633	3	4	86	1	0	0	0	0	1	0	0	0	13496	1232	43	3	677	3	RNF217	6	125402633	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	35349196	125402633	45712434	51	11545										
UTRN	7402	hgsc.bcm.edu	37	chr6	144765510	144765510	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tattgtggcaggaattattgGaagaacaggtatgaaactgt	12	3	0	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr6:144765510G>T	ENST00000367545.3	+	13	1606	c.1606G>T	c.(1606-1608)Gaa>Taa	p.E536*		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	536	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GGAATTATTGGAAGAACAGGT	0.373																																					p.E536X		Atlas-SNP	.											.	UTRN	327	.	0			c.G1606T						.						65	64	64					6																	144765510		2203	4300	6503	SO:0001587	stop_gained	7402	exon13			TTATTGGAAGAAC	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.1606G>T	chr6.hg19:g.144765510G>T	ENSP00000356515:p.Glu536*	51.0	0.0		42.0	29.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Nonsense_Mutation	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	G	39	7.624871	0.98396	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	.	.	.	5.44	5.44	0.79542	.	0.000000	0.53938	D	0.000058	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	.	19.6212	0.95656	0.0:0.0:1.0:0.0	.	.	.	.	X	536	.	ENSP00000356499:E536X	E	+	1	0	UTRN	144807203	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.338000	0.59316	2.723000	0.93209	0.655000	0.94253	GAA	.	.		0.373	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144765510	G	T	144765510	4	4	86	1	0	0	0	0	0	1	0	0	17118	1175	41	3	1656	3	UTRN	6	144765510	Nonsense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	19362877	144765510	26349557	52	11546										
RAB32	10981	hgsc.bcm.edu	37	chr6	146865246	146865246	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tctggtgcgcctgcagctgtGggacatcgcgggtaagcgcg	17	11	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr6:146865246G>A	ENST00000367495.3	+	1	418	c.239G>A	c.(238-240)tGg>tAg	p.W80*		NM_006834.3	NP_006825.1	Q13637	RAB32_HUMAN	RAB32, member RAS oncogene family	80					antigen processing and presentation (GO:0019882)|endosome to melanosome transport (GO:0035646)|GTP catabolic process (GO:0006184)|melanosome organization (GO:0032438)|phagosome maturation (GO:0090382)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	early endosome (GO:0005769)|melanosome (GO:0042470)|membrane (GO:0016020)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)	AP-1 adaptor complex binding (GO:0035650)|AP-3 adaptor complex binding (GO:0035651)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	8		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.68e-09)|GBM - Glioblastoma multiforme(68;0.00608)		CTGCAGCTGTGGGACATCGCG	0.632																																					p.W80X		Atlas-SNP	.											.	RAB32	16	.	0			c.G239A						.						29	27	28					6																	146865246		2203	4300	6503	SO:0001587	stop_gained	10981	exon1			AGCTGTGGGACAT	U71127	CCDS5210.1	6q24.2	2010-08-20			ENSG00000118508	ENSG00000118508		"RAB, member RAS oncogene", "A-kinase anchor proteins"	9772	protein-coding gene	gene with protein product		612906					Standard	NM_006834		Approved		uc003qln.1	Q13637	OTTHUMG00000015755	ENST00000367495.3:c.239G>A	chr6.hg19:g.146865246G>A	ENSP00000356465:p.Trp80*	136.0	0.0		133.0	17.0	NM_006834		Nonsense_Mutation	SNP	ENST00000367495.3	hg19	CCDS5210.1	.	.	.	.	.	.	.	.	.	.	G	40	8.156051	0.98680	.	.	ENSG00000118508	ENST00000367495	.	.	.	4.54	4.54	0.55810	.	0.435444	0.28431	N	0.015362	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.071	17.2973	0.87173	0.0:0.0:1.0:0.0	.	.	.	.	X	80	.	ENSP00000356465:W80X	W	+	2	0	RAB32	146906939	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.441000	0.97557	2.057000	0.61298	0.557000	0.71058	TGG	.	.		0.632	RAB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042579.1	NM_006834		A	146865246	G	A	146865246	4	1	86	1	0	0	0	0	0	1	0	0	12936	1357	47	3	241	3	RAB32	6	146865246	Nonsense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	2099736	146865246	24249821	53	11547										
USP42	84132	hgsc.bcm.edu	37	chr7	6189266	6189266	+	Frame_Shift_Del	DEL	C	C	-													0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gaaagacacgccaagcagttCcatgtcgagtcctaacggga							TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr7:6189266delC	ENST00000306177.5	+	13	1597	c.1439delC	c.(1438-1440)tccfs	p.S480fs		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	480					cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		CCAAGCAGTTCCATGTCGAGT	0.488																																					p.S480fs		Atlas-Indel,Pindel	.											USP42_ENST00000306177,colon,carcinoma,0,2	USP42	138	.	0			c.1438delT						.						127	122	123					7																	6189266		1970	4147	6117	SO:0001589	frameshift_variant	84132	exon13			.	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"Ubiquitin-specific peptidases"	20068	protein-coding gene	gene with protein product			"ubiquitin specific protease 42"			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.1439delC	chr7.hg19:g.6189266delC	ENSP00000301962:p.Ser480fs	206.0	0.0		278.0	57.0	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Frame_Shift_Del	DEL	ENST00000306177.5	hg19	CCDS47535.1																																																																																			.	.		0.488	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526		-	6189266	C	-	6189266	7	5	86	1	0	1	0	1	0	0	0	0	17088	855	30	0	1485	0	USP42	7	6189266	Frame_Shift_Del	DEL	C	TCGA-DD-A113-01A-11D-A12Z-10		6189266	152949397	54	11548										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7571014	7571014	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tttatctacaagggttggatCactcaacagtaaagtgggtt	10	6	3	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr7:7571014C>T	ENST00000399429.3	-	3	786	c.646G>A	c.(646-648)Gat>Aat	p.D216N		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	216	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		AGGGTTGGATCACTCAACAGT	0.363																																					p.D216N		Atlas-SNP	.											.	COL28A1	113	.	0			c.G646A						.						78	71	73					7																	7571014		1841	4087	5928	SO:0001583	missense	340267	exon3			TTGGATCACTCAA	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.646G>A	chr7.hg19:g.7571014C>T	ENSP00000382356:p.Asp216Asn	124.0	0.0		148.0	50.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	hg19	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	C	14.80	2.643034	0.47153	.	.	ENSG00000215018	ENST00000399429;ENST00000399419;ENST00000448652	T	0.56776	0.44	3.88	3.88	0.44766	von Willebrand factor, type A (2);	0.000000	0.64402	U	0.000002	T	0.65407	0.2688	L	0.54323	1.7	0.47308	D	0.999389	D	0.69078	0.997	D	0.64321	0.924	T	0.68326	-0.5438	10	0.51188	T	0.08	-4.4813	16.016	0.80441	0.0:1.0:0.0:0.0	.	216	Q2UY09	COSA1_HUMAN	N	216	ENSP00000382356:D216N	ENSP00000382347:D216N	D	-	1	0	COL28A1	7537539	1.000000	0.71417	0.341000	0.25589	0.051000	0.14879	3.488000	0.53229	2.183000	0.69458	0.655000	0.94253	GAT	.	.		0.363	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		T	7571014	C	T	7571014	3	4	86	1	0	0	0	0	1	0	0	0	3688	826	29	3	2863	3	COL28A1	7	7571014	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	1381748	7571014	151567649	55	11549										
SNX13	23161	hgsc.bcm.edu	37	chr7	17833732	17833732	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tgtttatatttctgcatctgCtttgaccgtgaatgcagttt	8	7	2	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr7:17833732C>T	ENST00000428135.3	-	26	3009	c.2811G>A	c.(2809-2811)aaG>aaA	p.K937K	SNX13_ENST00000496855.1_5'UTR|SNX13_ENST00000409389.1_3'UTR	NM_015132.4	NP_055947.1	Q9Y5W8	SNX13_HUMAN	sorting nexin 13	948					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					TCTGCATCTGCTTTGACCGTG	0.383																																					p.K937K		Atlas-SNP	.											.	SNX13	113	.	0			c.G2811A						.						109	102	104					7																	17833732		1848	4089	5937	SO:0001819	synonymous_variant	23161	exon26			CATCTGCTTTGAC	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"Sorting nexins"	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000428135.3:c.2811G>A	chr7.hg19:g.17833732C>T		463.0	0.0		707.0	37.0	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Silent	SNP	ENST00000428135.3	hg19	CCDS47551.1																																																																																			.	.		0.383	SNX13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327607.2	NM_015132		T	17833732	C	T	17833732	2	4	86	1	0	0	0	0	0	0	0	1	14899	796	28	3		3	SNX13	7	17833732	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	10262718	17833732	141304931	56	11550										
POM121L12	285877	hgsc.bcm.edu	37	chr7	53104219	53104219	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	agtagggtctccttcgccctCgaggtcacccagtctgctgg	12	14	3	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr7:53104219C>T	ENST00000408890.4	+	1	871	c.855C>T	c.(853-855)ctC>ctT	p.L285L		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	285										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CCTTCGCCCTCGAGGTCACCC	0.622																																					p.L285L		Atlas-SNP	.											.	POM121L12	146	.	0			c.C855T						.						42	47	45					7																	53104219		1995	4171	6166	SO:0001819	synonymous_variant	285877	exon1			CGCCCTCGAGGTC		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.855C>T	chr7.hg19:g.53104219C>T		80.0	0.0		142.0	80.0	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	hg19	CCDS43584.1																																																																																			.	.		0.622	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		T	53104219	C	T	53104219	2	4	86	1	0	0	0	0	0	0	0	1	12250	871	31	1		1	POM121L12	7	53104219	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	35270487	53104219	106034444	57	11551										
CDK14	5218	hgsc.bcm.edu	37	chr7	90355912	90355912	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aaagatgtctacacggaactGccagggaatggactcagtga	12	8	2	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr7:90355912G>T	ENST00000380050.3	+	3	286	c.155G>T	c.(154-156)tGc>tTc	p.C52F	CDK14_ENST00000496279.1_3'UTR|CDK14_ENST00000436577.2_5'UTR|CDK14_ENST00000265741.3_Missense_Mutation_p.C34F|CDK14_ENST00000406263.1_Missense_Mutation_p.C6F			O94921	CDK14_HUMAN	cyclin-dependent kinase 14	52					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						ACACGGAACTGCCAGGGAATG	0.388																																					p.C34F	GBM(83;1228 1256 8311 16577 31299)	Atlas-SNP	.											.	CDK14	153	.	0			c.G101T						.						88	80	83					7																	90355912		2203	4300	6503	SO:0001583	missense	5218	exon2			GGAACTGCCAGGG		CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"Cyclin-dependent kinases"	8883	protein-coding gene	gene with protein product		610679	"PFTAIRE protein kinase 1"	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.155G>T	chr7.hg19:g.90355912G>T	ENSP00000369390:p.Cys52Phe	180.0	0.0		194.0	11.0	NM_012395	A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Missense_Mutation	SNP	ENST00000380050.3	hg19		.	.	.	.	.	.	.	.	.	.	G	12.12	1.842206	0.32513	.	.	ENSG00000058091	ENST00000449528;ENST00000446224;ENST00000430760;ENST00000456689;ENST00000380050;ENST00000446790;ENST00000265741;ENST00000406263	T;T;T;T;T;T;T	0.70282	1.97;1.97;1.97;1.97;-0.46;-0.47;-0.45	5.72	4.84	0.62591	.	0.112528	0.64402	D	0.000008	T	0.54481	0.1861	L	0.27053	0.805	0.80722	D	1	B;B	0.25667	0.131;0.08	B;B	0.19148	0.024;0.016	T	0.50432	-0.8829	10	0.09338	T	0.73	-9.1952	14.4616	0.67453	0.0703:0.0:0.9297:0.0	.	34;52	O94921-2;O94921	.;CDK14_HUMAN	F	6;6;6;6;52;6;34;6	ENSP00000393616:C6F;ENSP00000410770:C6F;ENSP00000394570:C6F;ENSP00000406848:C6F;ENSP00000369390:C52F;ENSP00000265741:C34F;ENSP00000385034:C6F	ENSP00000265741:C34F	C	+	2	0	CDK14	90193848	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.075000	0.76798	1.427000	0.47276	0.563000	0.77884	TGC	.	.		0.388	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5	NM_012395		T	90355912	G	T	90355912	3	4	86	1	0	0	0	0	1	0	0	0	3132	1319	46	3	107	3	CDK14	7	90355912	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	37251693	90355912	68782751	58	11552										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113518905	113518905	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cttagcaattattgctttttCtctagcagacatgctttctg	6	9	2	1	rs4304271		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr7:113518905C>G	ENST00000284601.3	-	4	2310	c.2242G>C	c.(2242-2244)Gaa>Caa	p.E748Q		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	748			E -> K (in dbSNP:rs4304271).		glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						ATTGCTTTTTCTCTAGCAGAC	0.423																																					p.E748Q		Atlas-SNP	.											PPP1R3A,caecum,carcinoma,0,1	PPP1R3A	317	.	0			c.G2242C						.						126	116	119					7																	113518905		2203	4300	6503	SO:0001583	missense	5506	exon4			CTTTTTCTCTAGC	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.2242G>C	chr7.hg19:g.113518905C>G	ENSP00000284601:p.Glu748Gln	121.0	0.0		143.0	48.0	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	hg19	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.708574	0.68615	.	.	ENSG00000154415	ENST00000284601	T	0.23147	1.92	5.9	5.9	0.94986	.	0.266734	0.32328	N	0.006248	T	0.50188	0.1601	M	0.67953	2.075	0.34365	D	0.691406	D	0.76494	0.999	P	0.62491	0.903	T	0.59096	-0.7518	10	0.72032	D	0.01	-2.4646	20.2626	0.98452	0.0:1.0:0.0:0.0	.	748	Q16821	PPR3A_HUMAN	Q	748	ENSP00000284601:E748Q	ENSP00000284601:E748Q	E	-	1	0	PPP1R3A	113306141	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	5.114000	0.64648	2.802000	0.96397	0.650000	0.86243	GAA	.	C|1.000;|0.000		0.423	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		G	113518905	C	G	113518905	3	3	86	1	0	0	0	0	1	0	0	0	12383	922	32	4	1130	4	PPP1R3A	7	113518905	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	23162993	113518905	45619758	59	11553										
MDFIC	29969	hgsc.bcm.edu	37	chr7	114655974	114655974	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tgtatggaatgctgtggaatTtgttttccttcataaatatt	8	4	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr7:114655974T>C	ENST00000393486.1	+	5	1316	c.726T>C	c.(724-726)atT>atC	p.I242I	MDFIC_ENST00000257724.3_Silent_p.I351I	NM_001166345.1|NM_199072.4	NP_001159817.1|NP_951038.1			MyoD family inhibitor domain containing											breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						GCTGTGGAATTTGTTTTCCTT	0.373																																					p.I351I		Atlas-SNP	.											.	MDFIC	30	.	0			c.T1053C						.						231	209	216					7																	114655974		2203	4300	6503	SO:0001819	synonymous_variant	29969	exon5			TGGAATTTGTTTT	AF054589	CCDS34737.1, CCDS55155.1	7q31.1-q31.2	2006-01-11			ENSG00000135272	ENSG00000135272			28870	protein-coding gene	gene with protein product		614511				10671520	Standard	NM_199072		Approved	HIC	uc003vhf.3	Q9P1T7	OTTHUMG00000023647	ENST00000393486.1:c.726T>C	chr7.hg19:g.114655974T>C		225.0	0.0		267.0	106.0	NM_199072		Silent	SNP	ENST00000393486.1	hg19	CCDS55155.1																																																																																			.	.		0.373	MDFIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059968.4	NM_199072		C	114655974	T	C	114655974	2	2	86	1	0	0	0	0	0	0	0	1	9414	1829	64	2		2	MDFIC	7	114655974	Silent	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	1137069	114655974	44482689	60	11554										
MKRN1	23608	hgsc.bcm.edu	37	chr7	140156621	140156621	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	catgtccttgctgcgctgcaCggcaaatgagagctccatgt	11	12	0	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr7:140156621C>A	ENST00000255977.2	-	5	1041	c.817G>T	c.(817-819)Gtg>Ttg	p.V273L	MKRN1_ENST00000480552.1_Silent_p.P56P|MKRN1_ENST00000474576.1_Missense_Mutation_p.V209L|MKRN1_ENST00000443720.2_Missense_Mutation_p.V273L|MKRN1_ENST00000437223.2_Missense_Mutation_p.V7L	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	273					protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					CTGCGCTGCACGGCAAATGAG	0.532																																					p.V273L		Atlas-SNP	.											.	MKRN1	35	.	0			c.G817T						.						73	58	63					7																	140156621		2203	4300	6503	SO:0001583	missense	23608	exon5			GCTGCACGGCAAA	AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606		"RING-type (C3HC4) zinc fingers"	7112	protein-coding gene	gene with protein product		607754				10843807	Standard	NM_013446		Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.817G>T	chr7.hg19:g.140156621C>A	ENSP00000255977:p.Val273Leu	103.0	0.0		129.0	45.0	NM_013446	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Missense_Mutation	SNP	ENST00000255977.2	hg19	CCDS5860.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.593459	0.46214	.	.	ENSG00000133606	ENST00000255977;ENST00000539898;ENST00000437223;ENST00000474576;ENST00000443720	T;T;T;T	0.65916	0.98;1.46;0.98;-0.18	5.11	4.23	0.50019	Zinc finger, RING/FYVE/PHD-type (1);	0.163809	0.53938	D	0.000041	T	0.58352	0.2116	L	0.47016	1.485	0.48632	D	0.999682	P	0.43094	0.799	B	0.44163	0.443	T	0.56294	-0.8003	10	0.29301	T	0.29	.	13.6921	0.62553	0.0:0.9261:0.0:0.0739	.	273	Q9UHC7	MKRN1_HUMAN	L	273;209;7;209;273	ENSP00000255977:V273L;ENSP00000439823:V7L;ENSP00000417863:V209L;ENSP00000416369:V273L	ENSP00000255977:V273L	V	-	1	0	MKRN1	139803090	1.000000	0.71417	0.716000	0.30569	0.997000	0.91878	4.435000	0.59941	1.392000	0.46585	0.655000	0.94253	GTG	.	.		0.532	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446		A	140156621	C	A	140156621	3	1	86	1	0	0	0	0	1	0	0	0	9615	536	19	1	651	1	MKRN1	7	140156621	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	25500647	140156621	18982042	61	11555										
KEL	3792	hgsc.bcm.edu	37	chr7	142639989	142639989	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gcgatggctagccccccaacGtctgcagcattctctaagaa	9	14	2	1	rs367661434		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr7:142639989G>A	ENST00000355265.2	-	17	2388	c.1914C>T	c.(1912-1914)gaC>gaT	p.D638D		NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	638					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					GCCCCCCAACGTCTGCAGCAT	0.502																																					p.D638D		Atlas-SNP	.											.	KEL	128	.	0			c.C1914T						.	G		0,4406		0,0,2203	103	95	98		1914	-1.9	0	7		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KEL	NM_000420.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		638/733	142639989	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3792	exon17			CCCAACGTCTGCA	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"CD molecules", "Blood group antigens"	6308	protein-coding gene	gene with protein product		613883	"Kell blood group", "Kell blood group, metalloendopeptidase"			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1914C>T	chr7.hg19:g.142639989G>A		121.0	0.0		147.0	8.0	NM_000420	B2RBV4|Q96RS8|Q99885	Silent	SNP	ENST00000355265.2	hg19	CCDS34766.1																																																																																			.	.		0.502	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		A	142639989	G	A	142639989	2	1	86	1	0	0	0	0	0	0	0	1	8151	1136	40	1		1	KEL	7	142639989	Silent	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	2483368	142639989	16498674	62	11556										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53569525	53569525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	agtcttctaacactatttctCgtgactgcttcagttcttta	5	10	5	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr8:53569525C>T	ENST00000025008.5	-	15	3387	c.2864G>A	c.(2863-2865)cGa>cAa	p.R955Q	RB1CC1_ENST00000539297.1_Missense_Mutation_p.R955Q|RB1CC1_ENST00000435644.2_Missense_Mutation_p.R955Q|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	955					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				CACTATTTCTCGTGACTGCTT	0.363																																					p.R955Q	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.G2864A						.						80	81	81					8																	53569525		2203	4300	6503	SO:0001583	missense	9821	exon15			ATTTCTCGTGACT	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.2864G>A	chr8.hg19:g.53569525C>T	ENSP00000025008:p.Arg955Gln	359.0	0.0		356.0	16.0	NM_001083617	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	hg19	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	C	8.990	0.977503	0.18812	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.03982	3.74;3.74;3.74	5.39	2.6	0.31112	.	0.123631	0.53938	D	0.000059	T	0.07279	0.0184	L	0.34521	1.04	0.28551	N	0.911606	D;D	0.69078	0.997;0.996	P;P	0.53549	0.729;0.54	T	0.12837	-1.0532	10	0.41790	T	0.15	-6.0497	8.9166	0.35585	0.0:0.7411:0.1233:0.1356	.	955;955	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	Q	955	ENSP00000025008:R955Q;ENSP00000396067:R955Q;ENSP00000445960:R955Q	ENSP00000025008:R955Q	R	-	2	0	RB1CC1	53732078	0.955000	0.32602	0.001000	0.08648	0.053000	0.15095	2.037000	0.41174	0.335000	0.23614	-0.182000	0.12963	CGA	.	.		0.363	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		T	53569525	C	T	53569525	3	4	86	1	0	0	0	0	1	0	0	0	13114	884	31	1	1960	1	RB1CC1	8	53569525	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10		53569525	92794497	63	11557										
XKR9	389668	hgsc.bcm.edu	37	chr8	71646369	71646369	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ttatctttacattttttaatAttaagggacagaataccaag	5	5	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr8:71646369A>G	ENST00000408926.3	+	5	1366	c.832A>G	c.(832-834)Att>Gtt	p.I278V	XKR9_ENST00000520273.1_Intron|XKR9_ENST00000520030.1_Missense_Mutation_p.I278V	NM_001011720.1	NP_001011720.1	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related family, member 9	278						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)			ATTTTTTAATATTAAGGGACA	0.348																																					p.I278V		Atlas-SNP	.											.	XKR9	43	.	0			c.A832G						.						76	75	75					8																	71646369		2203	4298	6501	SO:0001583	missense	389668	exon5			TTTAATATTAAGG	AY534247	CCDS34905.1	8q13.3	2006-01-12	2006-01-12			ENSG00000221947			20937	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 9"				Standard	NM_001287258		Approved		uc003xyq.3	Q5GH70		ENST00000408926.3:c.832A>G	chr8.hg19:g.71646369A>G	ENSP00000386141:p.Ile278Val	544.0	0.0		895.0	44.0	NM_001011720	B2RNS9|B9EH74	Missense_Mutation	SNP	ENST00000408926.3	hg19	CCDS34905.1	.	.	.	.	.	.	.	.	.	.	A	5.564	0.288872	0.10513	.	.	ENSG00000221947	ENST00000408926;ENST00000520030	T;T	0.56275	0.47;0.47	4.99	-0.673	0.11373	.	0.380726	0.29565	N	0.011793	T	0.20210	0.0486	N	0.02985	-0.445	0.38921	D	0.957737	B	0.09022	0.002	B	0.12156	0.007	T	0.38178	-0.9673	10	0.02654	T	1	-10.3735	10.2591	0.43416	0.592:0.0:0.408:0.0	.	278	Q5GH70	XKR9_HUMAN	V	278	ENSP00000386141:I278V;ENSP00000431088:I278V	ENSP00000386141:I278V	I	+	1	0	XKR9	71808923	0.993000	0.37304	0.999000	0.59377	0.982000	0.71751	0.215000	0.17562	0.006000	0.14734	0.460000	0.39030	ATT	.	.		0.348	XKR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378752.1	NM_001011720		G	71646369	A	G	71646369	3	3	86	1	0	0	0	0	1	0	0	0	17453	449	16	2	842	2	XKR9	8	71646369	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	18076844	71646369	74717653	64	11558										
RDH10	157506	hgsc.bcm.edu	37	chr8	74209535	74209535	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tacctgacggctgaaagagtCcgcaaggaggttggcgaagt	15	8	0	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr8:74209535C>T	ENST00000240285.5	+	2	1074	c.396C>T	c.(394-396)gtC>gtT	p.V132V	RDH10_ENST00000519380.1_5'UTR|RPL7_ENST00000396466.1_5'Flank|RPL7_ENST00000396465.1_5'Flank|RP11-434I12.2_ENST00000520894.1_RNA	NM_172037.4	NP_742034.1	Q8IZV5	RDH10_HUMAN	retinol dehydrogenase 10 (all-trans)	132					bud elongation involved in lung branching (GO:0060449)|ear development (GO:0043583)|embryonic camera-type eye development (GO:0031076)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|gonad development (GO:0008406)|in utero embryonic development (GO:0001701)|metanephros development (GO:0001656)|neural crest cell development (GO:0014032)|nose development (GO:0043584)|phototransduction, visible light (GO:0007603)|primary lung bud formation (GO:0060431)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)	11	Breast(64;0.0954)		Epithelial(68;0.0105)|all cancers(69;0.0465)|BRCA - Breast invasive adenocarcinoma(89;0.0608)			CTGAAAGAGTCCGCAAGGAGG	0.512																																					p.V132V		Atlas-SNP	.											.	RDH10	31	.	0			c.C396T						.						213	169	184					8																	74209535		2203	4300	6503	SO:0001819	synonymous_variant	157506	exon2			AAGAGTCCGCAAG	AF456765	CCDS6213.1	8q21.11	2011-09-20			ENSG00000121039	ENSG00000121039	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	19975	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 16C, member 4"	607599				12407145, 19027726	Standard	NM_172037		Approved	SDR16C4	uc003xzi.3	Q8IZV5	OTTHUMG00000164492	ENST00000240285.5:c.396C>T	chr8.hg19:g.74209535C>T		252.0	0.0		445.0	19.0	NM_172037		Silent	SNP	ENST00000240285.5	hg19	CCDS6213.1																																																																																			.	.		0.512	RDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378982.1			T	74209535	C	T	74209535	2	4	86	1	0	0	0	0	0	0	0	1	13204	842	30	3		3	RDH10	8	74209535	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	2563166	74209535	72154487	65	11559										
INTS8	55656	hgsc.bcm.edu	37	chr8	95839952	95839952	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ttcctgtcttttcttcagggCaattaggacaattgttcaaa	7	8	4	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr8:95839952C>A	ENST00000523731.1	+	4	582	c.449C>A	c.(448-450)gCa>gAa	p.A150E	INTS8_ENST00000447247.1_Missense_Mutation_p.A150E	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	150					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					TTCTTCAGGGCAATTAGGACA	0.353																																					p.A150E		Atlas-SNP	.											.	INTS8	92	.	0			c.C449A						.						109	113	112					8																	95839952		2203	4300	6503	SO:0001583	missense	55656	exon4			TCAGGGCAATTAG	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.449C>A	chr8.hg19:g.95839952C>A	ENSP00000430338:p.Ala150Glu	173.0	0.0		271.0	11.0	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Missense_Mutation	SNP	ENST00000523731.1	hg19	CCDS34925.1	.	.	.	.	.	.	.	.	.	.	C	32	5.168172	0.94768	.	.	ENSG00000164941	ENST00000522171;ENST00000519457;ENST00000519053;ENST00000523731;ENST00000447247	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.78329	0.4266	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.76501	-0.2936	9	0.54805	T	0.06	-0.7547	20.5948	0.99439	0.0:1.0:0.0:0.0	.	150;150	Q75QN2;Q75QN2-2	INT8_HUMAN;.	E	109;103;41;150;150	.	ENSP00000343274:A150E	A	+	2	0	INTS8	95909128	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.346000	0.79347	2.873000	0.98535	0.563000	0.77884	GCA	.	.		0.353	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		A	95839952	C	A	95839952	3	1	86	1	0	0	0	0	1	0	0	0	7793	710	25	3	463	3	INTS8	8	95839952	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	21630417	95839952	50524070	66	11560										
ADCY8	114	hgsc.bcm.edu	37	chr8	131793001	131793001	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ataggtctcctctgggacttGgatccggccactaacccccg	10	15	2	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr8:131793001G>A	ENST00000286355.5	-	18	5483	c.3391C>T	c.(3391-3393)Caa>Taa	p.Q1131*	ADCY8_ENST00000377928.3_Nonsense_Mutation_p.Q1000*	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	1131					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TCTGGGACTTGGATCCGGCCA	0.522										HNSCC(32;0.087)																											p.Q1131X		Atlas-SNP	.											.	ADCY8	291	.	0			c.C3391T						.						134	134	134					8																	131793001		2203	4300	6503	SO:0001587	stop_gained	114	exon18			GGACTTGGATCCG	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.3391C>T	chr8.hg19:g.131793001G>A	ENSP00000286355:p.Gln1131*	93.0	0.0		127.0	35.0	NM_001115		Nonsense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	55	23.590000	0.99956	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.0195	0.92908	0.0:0.0:1.0:0.0	.	.	.	.	X	1131;1000	.	ENSP00000286355:Q1131X	Q	-	1	0	ADCY8	131862183	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.746000	0.94184	0.655000	0.94253	CAA	.	.		0.522	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	131793001	G	A	131793001	4	1	86	1	0	0	0	0	0	1	0	0	300	1357	47	3	368	3	ADCY8	8	131793001	Nonsense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	35953049	131793001	14571021	67	11561										
KCNV2	169522	hgsc.bcm.edu	37	chr9	2718691	2718691	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gcttcttcacgctcgagtacCtgctgcgcctagcctccacg	9	17	2	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr9:2718691C>T	ENST00000382082.3	+	1	1190	c.952C>T	c.(952-954)Ctg>Ttg	p.L318L		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	318					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		GCTCGAGTACCTGCTGCGCCT	0.682																																					p.L318L		Atlas-SNP	.											.	KCNV2	72	.	0			c.C952T						.						44	49	47					9																	2718691		2203	4299	6502	SO:0001819	synonymous_variant	169522	exon1			GAGTACCTGCTGC	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.952C>T	chr9.hg19:g.2718691C>T		113.0	0.0		97.0	9.0	NM_133497	Q5T6X0	Silent	SNP	ENST00000382082.3	hg19	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	C	4.290	0.052959	0.08291	.	.	ENSG00000168263	ENST00000423608	.	.	.	5.22	3.4	0.38934	.	.	.	.	.	T	0.55033	0.1895	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47861	-0.9084	4	.	.	.	.	6.4921	0.22121	0.1286:0.6578:0.0:0.2137	.	.	.	.	L	268	.	.	P	+	2	0	KCNV2	2708691	1.000000	0.71417	1.000000	0.80357	0.656000	0.38851	1.001000	0.29783	0.610000	0.30035	-0.253000	0.11424	CCT	.	.		0.682	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		T	2718691	C	T	2718691	2	4	86	1	0	0	0	0	0	0	0	1	8104	680	24	3		3	KCNV2	9	2718691	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10		2718691	138494740	68	11562										
NFIB	4781	hgsc.bcm.edu	37	chr9	14307000	14307000	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gctcctaccttgctcctgcaCgtagtatgccaaaaacaaat	6	13	0	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr9:14307000C>T	ENST00000380959.3	-	2	1023	c.550G>A	c.(550-552)Gtg>Atg	p.V184M	NFIB_ENST00000397575.3_Missense_Mutation_p.V184M|NFIB_ENST00000380953.1_Missense_Mutation_p.V184M|NFIB_ENST00000380934.4_Missense_Mutation_p.V210M|NFIB_ENST00000397579.2_Missense_Mutation_p.V184M|NFIB_ENST00000380921.3_Missense_Mutation_p.V184M|NFIB_ENST00000397581.2_Missense_Mutation_p.V184M	NM_005596.3	NP_005587.2	O00712	NFIB_HUMAN	nuclear factor I/B	184					anterior commissure morphogenesis (GO:0021960)|chondrocyte differentiation (GO:0002062)|Clara cell differentiation (GO:0060486)|commissural neuron axon guidance (GO:0071679)|DNA replication (GO:0006260)|glial cell differentiation (GO:0010001)|hindbrain development (GO:0030902)|lung ciliated cell differentiation (GO:0061141)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000795)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|principal sensory nucleus of trigeminal nerve development (GO:0021740)|transcription from RNA polymerase II promoter (GO:0006366)|Type I pneumocyte differentiation (GO:0060509)|Type II pneumocyte differentiation (GO:0060510)	cerebellar mossy fiber (GO:0044300)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		TGCTCCTGCACGTAGTATGCC	0.458			T	"MYB, HGMA2"	"adenoid cystic carcinoma, lipoma"																																p.V210M	Esophageal Squamous(132;921 1730 14828 40753 46471)	Atlas-SNP	.		Dom	yes		9	9p24.1	4781	nuclear factor I/B		E	.	NFIB	91	.	0			c.G628A						.						131	119	123					9																	14307000		2203	4300	6503	SO:0001583	missense	4781	exon2			CCTGCACGTAGTA	U07810	CCDS6474.1, CCDS55291.1, CCDS55292.1, CCDS65007.1	9p24.1	2008-02-05			ENSG00000147862	ENSG00000147862			7785	protein-coding gene	gene with protein product		600728				7590749	Standard	NM_001190737		Approved	NFI-RED, NFIB2, NFIB3	uc003zlf.3	O00712	OTTHUMG00000021027	ENST00000380959.3:c.550G>A	chr9.hg19:g.14307000C>T	ENSP00000370346:p.Val184Met	160.0	0.0		157.0	83.0	NM_001190738	G3V1P1|H7BYE8|O00166|Q12858|Q5VW29|Q63HM5|Q6ZNF9|Q96J45	Missense_Mutation	SNP	ENST00000380959.3	hg19	CCDS6474.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.662716	0.67700	.	.	ENSG00000147862	ENST00000380934;ENST00000380959;ENST00000380953;ENST00000397575;ENST00000397581;ENST00000397579;ENST00000380921	T;T;T;T;T;T	0.55588	0.57;0.59;0.55;0.51;0.52;0.59	5.53	5.53	0.82687	CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.67813	0.2933	L	0.49126	1.545	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;P;D	0.70935	0.971;0.902;0.971	T	0.63337	-0.6660	10	0.33940	T	0.23	-3.4196	19.4694	0.94956	0.0:1.0:0.0:0.0	.	184;184;184	Q5VW27;Q5VW29;O00712	.;.;NFIB_HUMAN	M	210;184;184;184;184;184;184	ENSP00000370321:V210M;ENSP00000370346:V184M;ENSP00000370340:V184M;ENSP00000380705:V184M;ENSP00000380711:V184M;ENSP00000380709:V184M	ENSP00000370308:V184M	V	-	1	0	NFIB	14297000	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.790000	0.85794	2.587000	0.87381	0.591000	0.81541	GTG	.	.		0.458	NFIB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055468.1	NM_005596		T	14307000	C	T	14307000	3	4	86	1	0	0	0	0	1	0	0	0	10380	536	19	1	744	1	NFIB	9	14307000	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	11588309	14307000	126906431	69	11563										
SH3GL2	6456	hgsc.bcm.edu	37	chr9	17787406	17787406	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cttggtgaggtcggggaggcCatgcgggaactgtcggaggt	20	7	0	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr9:17787406C>A	ENST00000380607.4	+	5	480	c.360C>A	c.(358-360)gcC>gcA	p.A120A	SH3GL2_ENST00000537391.1_Silent_p.A73A	NM_003026.2	NP_003017.1	Q99962	SH3G2_HUMAN	SH3-domain GRB2-like 2	120	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.|Binds and tubulates liposomes. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of receptor internalization (GO:0002090)|signal transduction (GO:0007165)|synaptic vesicle endocytosis (GO:0048488)	clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)		TCGGGGAGGCCATGCGGGAAC	0.463																																					p.A120A		Atlas-SNP	.											.	SH3GL2	60	.	0			c.C360A						.						121	117	118					9																	17787406		2203	4300	6503	SO:0001819	synonymous_variant	6456	exon5			GGAGGCCATGCGG	X99657	CCDS6483.1	9p22	2008-02-05			ENSG00000107295	ENSG00000107295			10831	protein-coding gene	gene with protein product		604465				9169142	Standard	XM_005251549		Approved	SH3P4, SH3D2A, CNSA2, EEN-B1	uc003zna.3	Q99962	OTTHUMG00000019601	ENST00000380607.4:c.360C>A	chr9.hg19:g.17787406C>A		95.0	0.0		49.0	9.0	NM_003026	B2R618|Q9NQK5	Silent	SNP	ENST00000380607.4	hg19	CCDS6483.1																																																																																			.	.		0.463	SH3GL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051796.1	NM_003026		A	17787406	C	A	17787406	2	1	86	1	0	0	0	0	0	0	0	1	14266	581	21	3		3	SH3GL2	9	17787406	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	3480406	17787406	123426025	70	11564										
TEK	7010	hgsc.bcm.edu	37	chr9	27228230	27228230	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tctaatgagacaatgctggcGggagaagccttatgagaggc	14	7	1	3	rs536255448		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr9:27228230G>T	ENST00000380036.4	+	22	3669	c.3227G>T	c.(3226-3228)cGg>cTg	p.R1076L	TEK_ENST00000519097.1_Missense_Mutation_p.R928L|TEK_ENST00000406359.4_Missense_Mutation_p.R1033L	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	1076	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CAATGCTGGCGGGAGAAGCCT	0.433																																					p.R1076L		Atlas-SNP	.											.	TEK	250	.	0			c.G3227T						.						130	129	129					9																	27228230		2203	4300	6503	SO:0001583	missense	7010	exon22			GCTGGCGGGAGAA	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.3227G>T	chr9.hg19:g.27228230G>T	ENSP00000369375:p.Arg1076Leu	105.0	0.0		99.0	27.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	G	30	5.054881	0.93793	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359	D;D;D	0.82803	-1.65;-1.65;-1.65	5.81	5.81	0.92471	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.45867	D	0.000337	D	0.86083	0.5848	N	0.20304	0.555	0.58432	D	0.999999	D;P;D	0.69078	0.997;0.942;0.997	D;P;D	0.78314	0.991;0.635;0.991	D	0.87827	0.2642	10	0.87932	D	0	.	19.6728	0.95916	0.0:0.0:1.0:0.0	.	928;1109;1076	E7EWI2;Q59HG2;Q02763	.;.;TIE2_HUMAN	L	928;1076;1033	ENSP00000430686:R928L;ENSP00000369375:R1076L;ENSP00000383977:R1033L	ENSP00000369375:R1076L	R	+	2	0	TEK	27218230	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.797000	0.69087	2.760000	0.94817	0.643000	0.83706	CGG	.	.		0.433	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			T	27228230	G	T	27228230	3	4	86	1	0	0	0	0	1	0	0	0	15766	1116	39	1	3313	1	TEK	9	27228230	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	9440824	27228230	113985201	71	11565										
ZCCHC6	79670	hgsc.bcm.edu	37	chr9	88934568	88934568	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	acgagcctgatcttctataaTtgttggagaaaaatcctctg	8	8	3	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr9:88934568T>A	ENST00000375963.3	-	15	3218	c.3046A>T	c.(3046-3048)Att>Ttt	p.I1016F	ZCCHC6_ENST00000375957.1_5'Flank|ZCCHC6_ENST00000375961.2_Missense_Mutation_p.I1016F|ZCCHC6_ENST00000277141.6_Missense_Mutation_p.I305F|ZCCHC6_ENST00000375960.2_Intron	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	1016					RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						TCTTCTATAATTGTTGGAGAA	0.279																																					p.I1016F		Atlas-SNP	.											.	ZCCHC6	105	.	0			c.A3046T						.						44	45	45					9																	88934568		2202	4298	6500	SO:0001583	missense	79670	exon15			CTATAATTGTTGG	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.3046A>T	chr9.hg19:g.88934568T>A	ENSP00000365130:p.Ile1016Phe	87.0	0.0		90.0	19.0	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	hg19	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	T	11.11	1.542120	0.27563	.	.	ENSG00000083223	ENST00000277141;ENST00000375961;ENST00000375963	T;T;T	0.42513	0.97;0.97;0.97	4.95	-2.8	0.05823	.	0.686043	0.15557	N	0.256148	T	0.25644	0.0624	N	0.16656	0.425	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.15464	-1.0436	10	0.52906	T	0.07	-0.6012	13.7231	0.62740	0.0:0.574:0.0:0.426	.	1016	Q5VYS8	TUT7_HUMAN	F	305;1016;1016	ENSP00000277141:I305F;ENSP00000365128:I1016F;ENSP00000365130:I1016F	ENSP00000277141:I305F	I	-	1	0	ZCCHC6	88124388	0.001000	0.12720	0.076000	0.20297	0.965000	0.64279	0.122000	0.15687	-0.607000	0.05738	0.528000	0.53228	ATT	.	.		0.279	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		A	88934568	T	A	88934568	3	1	86	1	0	0	0	0	1	0	0	0	17607	1493	52	4	1493	4	ZCCHC6	9	88934568	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	61706338	88934568	52278863	72	11566										
WDR31	114987	hgsc.bcm.edu	37	chr9	116082738	116082738	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ctgaatgtgctgctttgcagGaaacatatgagctacctgca	10	9	0	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr9:116082738G>C	ENST00000374193.4	-	9	925	c.679C>G	c.(679-681)Cct>Gct	p.P227A	WDR31_ENST00000374195.3_Missense_Mutation_p.P102A|WDR31_ENST00000461942.1_5'UTR|WDR31_ENST00000341761.4_Missense_Mutation_p.P226A	NM_001012361.2|NM_145241.3	NP_001012361.1|NP_660284.1	Q8NA23	WDR31_HUMAN	WD repeat domain 31	227										NS(1)|large_intestine(1)|lung(2)|prostate(2)	6						TGCTTTGCAGGAAACATATGA	0.478																																					p.P227A		Atlas-SNP	.											WDR31,NS,malignant_melanoma,0,1	WDR31	23	.	0			c.C679G						.						104	91	95					9																	116082738		2203	4300	6503	SO:0001583	missense	114987	exon9			TTGCAGGAAACAT	BC012352	CCDS6792.1, CCDS35110.1	9q33.1	2013-01-09			ENSG00000148225	ENSG00000148225		"WD repeat domain containing"	21421	protein-coding gene	gene with protein product	"similar to spermatid WD-repeat protein"						Standard	NM_145241		Approved	FLJ35921	uc004bhb.3	Q8NA23	OTTHUMG00000020525	ENST00000374193.4:c.679C>G	chr9.hg19:g.116082738G>C	ENSP00000363308:p.Pro227Ala	142.0	0.0		121.0	61.0	NM_001012361	Q5W0T9|Q96EG8	Missense_Mutation	SNP	ENST00000374193.4	hg19	CCDS35110.1	.	.	.	.	.	.	.	.	.	.	G	17.37	3.373672	0.61624	.	.	ENSG00000148225	ENST00000374193;ENST00000374195;ENST00000341761	T;T;T	0.06608	3.28;3.28;3.28	5.86	5.86	0.93980	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.059559	0.64402	D	0.000002	T	0.08626	0.0214	L	0.55990	1.75	0.80722	D	1	P;P	0.41450	0.635;0.75	B;B	0.39152	0.153;0.292	T	0.34650	-0.9820	10	0.13108	T	0.6	-14.2162	16.2869	0.82725	0.0:0.1321:0.8679:0.0	.	227;226	Q8NA23;Q8NA23-2	WDR31_HUMAN;.	A	227;102;226	ENSP00000363308:P227A;ENSP00000363310:P102A;ENSP00000345027:P226A	ENSP00000345027:P226A	P	-	1	0	WDR31	115122559	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	6.877000	0.75562	2.771000	0.95319	0.563000	0.77884	CCT	.	.		0.478	WDR31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053734.2	NM_145241		C	116082738	G	C	116082738	3	2	86	1	0	0	0	0	1	0	0	0	17301	1174	41	4	436	4	WDR31	9	116082738	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	27148170	116082738	25130693	73	11567										
LYZL1	84569	hgsc.bcm.edu	37	chr10	29599920	29599920	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gcttccctctcatcctcaggCaaggctggaagaaacattgt	9	12	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr10:29599920C>A	ENST00000375500.3	+	5	574	c.517C>A	c.(517-519)Caa>Aaa	p.Q173K		NM_032517.4	NP_115906.3	Q6UWQ5	LYZL1_HUMAN	lysozyme-like 1	127					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			central_nervous_system(1)|cervix(2)|large_intestine(2)|lung(5)|skin(1)	11		Breast(68;0.203)				CATCCTCAGGCAAGGCTGGAA	0.493																																					p.Q173K		Atlas-SNP	.											.	LYZL1	25	.	0			c.C517A						.						151	144	147					10																	29599920		2203	4300	6503	SO:0001630	splice_region_variant	84569	exon5			CTCAGGCAAGGCT		CCDS31174.1	10p12.1	2004-08-02			ENSG00000120563	ENSG00000120563	3.2.1.1		30502	protein-coding gene	gene with protein product						12477932	Standard	XM_005252627		Approved	MGC33408, LYC2	uc001iul.3	Q6UWQ5	OTTHUMG00000017880	ENST00000375500.3:c.516-1C>A	chr10.hg19:g.29599920C>A		159.0	0.0		195.0	104.0	NM_032517	Q5T921|Q8WW16	Missense_Mutation	SNP	ENST00000375500.3	hg19	CCDS31174.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.509264	0.27036	.	.	ENSG00000120563	ENST00000375500	T	0.68025	-0.3	4.95	3.97	0.46021	.	0.427338	0.23387	N	0.048730	T	0.40423	0.1116	N	0.05306	-0.075	0.35034	D	0.759021	B	0.16802	0.019	B	0.24541	0.054	T	0.44498	-0.9324	10	0.16420	T	0.52	-31.3683	7.7752	0.29033	0.1811:0.6437:0.1752:0.0	.	173	Q6UWQ5-2	.	K	173	ENSP00000364650:Q173K	ENSP00000364650:Q173K	Q	+	1	0	LYZL1	29639926	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	1.059000	0.30517	2.673000	0.90976	0.650000	0.86243	CAA	.	.		0.493	LYZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047381.1	NM_032517	Missense_Mutation	A	29599920	C	A	29599920	5	1	86	1	0	0	0	0	0	0	1	0	9140	724	25	3	535	3	LYZL1	10	29599920	Splice_Site	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10		29599920	105934827	74	11568										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49661391	49661391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ctacctgtggccgcagaatgTtaggtccaaaaacggttgcc	11	11	0	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr10:49661391T>C	ENST00000249601.4	-	8	1240	c.944A>G	c.(943-945)aAc>aGc	p.N315S	ARHGAP22_ENST00000417247.2_Missense_Mutation_p.N225S|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.N321S|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.N331S|ARHGAP22_ENST00000477708.2_5'Flank|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.N206S|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.N156S	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	315	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCGCAGAATGTTAGGTCCAAA	0.517																																					p.N331S		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.A992G						.						155	131	139					10																	49661391		2202	4300	6502	SO:0001583	missense	58504	exon8			AGAATGTTAGGTC	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.944A>G	chr10.hg19:g.49661391T>C	ENSP00000249601:p.Asn315Ser	244.0	0.0		282.0	17.0	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	hg19	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.878238	0.91664	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T	0.41400	2.78;1.0;2.78;2.78;2.78;1.0	5.37	5.37	0.77165	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.59074	0.2167	L	0.52823	1.66	0.80722	D	1	P;D;D;D;P	0.71674	0.944;0.998;0.998;0.998;0.931	D;D;D;D;P	0.76071	0.968;0.98;0.987;0.98;0.881	T	0.58769	-0.7578	10	0.45353	T	0.12	.	14.5586	0.68120	0.0:0.0:0.0:1.0	.	321;315;331;315;225	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3	.;.;.;RHG22_HUMAN;.	S	315;206;156;225;321;331	ENSP00000249601:N315S;ENSP00000363287:N206S;ENSP00000363285:N156S;ENSP00000410054:N225S;ENSP00000416701:N321S;ENSP00000412461:N331S	ENSP00000249601:N315S	N	-	2	0	ARHGAP22	49331397	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	7.871000	0.87180	2.036000	0.60181	0.519000	0.50382	AAC	.	.		0.517	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		C	49661391	T	C	49661391	3	2	86	1	0	0	0	0	1	0	0	0	872	1725	60	2	1164	2	ARHGAP22	10	49661391	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	20061471	49661391	85873356	75	11569										
TCTN3	26123	hgsc.bcm.edu	37	chr10	97447351	97447351	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ccccttccccaggctcacccTgtaaaaagatggtggtgatt	9	13	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr10:97447351T>A	ENST00000371217.5	-	4	648	c.625A>T	c.(625-627)Agg>Tgg	p.R209W	TCTN3_ENST00000430368.2_Intron|TCTN3_ENST00000265993.9_Missense_Mutation_p.R227W|TCTN3_ENST00000371209.5_Missense_Mutation_p.R209W			Q6NUS6	TECT3_HUMAN	tectonic family member 3	209					apoptotic process (GO:0006915)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(3)|endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		AGGCTCACCCTGTAAAAAGAT	0.478																																					p.R209W		Atlas-SNP	.											.	TCTN3	66	.	0			c.A625T						.						90	86	88					10																	97447351		2203	4300	6503	SO:0001583	missense	26123	exon4			TCACCCTGTAAAA	AK098295	CCDS31258.2, CCDS44461.1	10q24.1	2014-01-28	2007-08-20	2007-08-20	ENSG00000119977	ENSG00000119977		"Tectonic proteins"	24519	protein-coding gene	gene with protein product		613847	"chromosome 10 open reading frame 61"	C10orf61		12975309	Standard	NM_015631		Approved	DKFZP564D116, TECT3, JBTS18	uc001klb.4	Q6NUS6	OTTHUMG00000018814	ENST00000371217.5:c.625A>T	chr10.hg19:g.97447351T>A	ENSP00000360261:p.Arg209Trp	141.0	0.0		208.0	117.0	NM_015631	A6NIC8|B0QZ90|B4DR81|Q6P7P3|Q6UW27|Q6ZQQ0|Q8N7K1|Q8NBQ0|Q96GF7|Q9Y3U1	Missense_Mutation	SNP	ENST00000371217.5	hg19	CCDS31258.2	.	.	.	.	.	.	.	.	.	.	T	17.61	3.431269	0.62844	.	.	ENSG00000119977	ENST00000265993;ENST00000371217;ENST00000343162;ENST00000371209	D;D	0.83673	-1.75;-1.75	5.72	5.72	0.89469	Domain of unknown function DUF1619 (1);	0.327980	0.33438	N	0.004920	D	0.89280	0.6670	M	0.70275	2.135	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.994	D;D;P	0.66979	0.948;0.936;0.898	D	0.90179	0.4241	10	0.72032	D	0.01	-3.1243	12.3905	0.55356	0.0:0.0:0.0:1.0	.	209;209;58	Q6NUS6-2;Q6NUS6;Q6NUS6-3	.;TECT3_HUMAN;.	W	209;227;58;209	ENSP00000265993:R209W;ENSP00000360253:R209W	ENSP00000265993:R209W	R	-	1	2	TCTN3	97437341	0.998000	0.40836	0.915000	0.36163	0.226000	0.24999	2.432000	0.44784	2.169000	0.68431	0.482000	0.46254	AGG	.	.		0.478	TCTN3-009	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000471858.1	NM_015631		A	97447351	T	A	97447351	3	1	86	1	0	0	0	0	1	0	0	0	15739	1579	55	4	1242	4	TCTN3	10	97447351	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	47785960	97447351	38087396	76	11570										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117607492	117607492	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tcatcaggtgcccctcccccTgggcagtcaggtatgataaa	10	13	3	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr10:117607492T>A	ENST00000355044.3	+	28	4134	c.4008T>A	c.(4006-4008)ccT>ccA	p.P1336P	ATRNL1_ENST00000423111.2_Silent_p.P387P|ATRNL1_ENST00000303745.7_Silent_p.P129P	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1336					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CCCCTCCCCCTGGGCAGTCAG	0.468																																					p.P1336P		Atlas-SNP	.											.	ATRNL1	219	.	0			c.T4008A						.						97	87	90					10																	117607492		2203	4300	6503	SO:0001819	synonymous_variant	26033	exon28			TCCCCCTGGGCAG	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.4008T>A	chr10.hg19:g.117607492T>A		207.0	0.0		229.0	70.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	hg19	CCDS7592.1																																																																																			.	.		0.468	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		A	117607492	T	A	117607492	2	1	86	1	0	0	0	0	0	0	0	1	1207	1567	55	4		4	ATRNL1	10	117607492	Silent	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	20160141	117607492	17927255	77	11571										
DUSP8	1850	hgsc.bcm.edu	37	chr11	1586842	1586842	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gtacctggctgcgtgcagccGgctggatgagctccgcaatg	15	12	0	1	rs571594390		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr11:1586842G>A	ENST00000397374.3	-	2	342	c.215C>T	c.(214-216)cCg>cTg	p.P72L	DUSP8_ENST00000331588.4_Missense_Mutation_p.P72L	NM_004420.2	NP_004411.2	Q13202	DUS8_HUMAN	dual specificity phosphatase 8	72	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|lung(2)|prostate(1)|urinary_tract(1)	5		all_epithelial(84;0.000134)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000621)|Lung(200;0.0687)|LUSC - Lung squamous cell carcinoma(625;0.0825)		GCGTGCAGCCGGCTGGATGAG	0.657													G|||	1	0.000199681	0	0	5008	,	,		14272	0		0.001	False		,,,				2504	0				p.P72L		Atlas-SNP	.											.	DUSP8	22	.	0			c.C215T						.						34	27	30					11																	1586842		2197	4295	6492	SO:0001583	missense	1850	exon2			GCAGCCGGCTGGA		CCDS7724.1	11p15.5	2011-06-09			ENSG00000184545	ENSG00000184545		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3074	protein-coding gene	gene with protein product	"serine/threonine specific protein phosphatase", "H1 phosphatase, vaccinia virus homolog"	602038	"chromosome 11 open reading frame 81"	C11orf81		7561881, 9192849	Standard	NM_004420		Approved	HVH-5, HB5, FLJ42958	uc001lts.2	Q13202	OTTHUMG00000133348	ENST00000397374.3:c.215C>T	chr11.hg19:g.1586842G>A	ENSP00000380530:p.Pro72Leu	126.0	0.0		108.0	23.0	NM_004420	Q86SS8	Missense_Mutation	SNP	ENST00000397374.3	hg19	CCDS7724.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.657585	0.47467	.	.	ENSG00000184545	ENST00000397374;ENST00000331588	T;T	0.47528	0.84;0.84	3.23	3.23	0.37069	Rhodanese-like (5);	0.183457	0.35262	N	0.003337	T	0.59500	0.2198	L	0.59436	1.845	0.80722	D	1	D	0.65815	0.995	P	0.62649	0.905	T	0.58983	-0.7539	10	0.34782	T	0.22	.	13.8674	0.63596	0.0:0.0:1.0:0.0	.	72	Q13202	DUS8_HUMAN	L	72	ENSP00000380530:P72L;ENSP00000329539:P72L	ENSP00000329539:P72L	P	-	2	0	DUSP8	1543418	1.000000	0.71417	0.913000	0.36048	0.148000	0.21650	4.402000	0.59722	2.113000	0.64589	0.561000	0.74099	CCG	.	.		0.657	DUSP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257178.3	NM_004420		A	1586842	G	A	1586842	3	1	86	1	0	0	0	0	1	0	0	0	4833	1116	39	1	1686	1	DUSP8	11	1586842	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10		1586842	133419674	78	11572										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6566486	6566486	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aagctgcagggtccccttccTctgcatccagatctccctaa	7	16	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr11:6566486T>A	ENST00000527990.2	+	19	4317	c.4317T>A	c.(4315-4317)ccT>ccA	p.P1439P	DNHD1_ENST00000254579.6_Silent_p.P1439P			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1439					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GTCCCCTTCCTCTGCATCCAG	0.607																																					p.P1439P		Atlas-SNP	.											.	DNHD1	198	.	0			c.T4317A						.						97	102	101					11																	6566486		692	1591	2283	SO:0001819	synonymous_variant	144132	exon21			CCTTCCTCTGCAT	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.4317T>A	chr11.hg19:g.6566486T>A		77.0	0.0		53.0	12.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	hg19	CCDS44532.1																																																																																			.	.		0.607	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6566486	T	A	6566486	2	1	86	1	0	0	0	0	0	0	0	1	4670	1538	54	4		4	DNHD1	11	6566486	Silent	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	4979644	6566486	128440030	79	11573										
RAG1	5896	hgsc.bcm.edu	37	chr11	36597714	36597714	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ctgaaattattgagagggatGgctccattggggcatgggca	15	6	0	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr11:36597714G>T	ENST00000299440.5	+	2	2972	c.2860G>T	c.(2860-2862)Ggc>Tgc	p.G954C		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	954					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				TGAGAGGGATGGCTCCATTGG	0.443									Familial Hemophagocytic Lymphohistiocytosis																												p.G954C	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.G2860T						.						82	88	86					11																	36597714		2202	4298	6500	SO:0001583	missense	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AGGGATGGCTCCA	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.2860G>T	chr11.hg19:g.36597714G>T	ENSP00000299440:p.Gly954Cys	117.0	0.0		114.0	45.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	hg19	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.819164	0.71028	.	.	ENSG00000166349	ENST00000299440	D	0.86366	-2.11	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.92492	0.7616	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90999	0.4841	9	.	.	.	.	20.1028	0.97881	0.0:0.0:1.0:0.0	.	954	P15918	RAG1_HUMAN	C	954	ENSP00000299440:G954C	.	G	+	1	0	RAG1	36554290	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.420000	0.97426	2.827000	0.97445	0.644000	0.83932	GGC	.	.		0.443	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		T	36597714	G	T	36597714	3	4	86	1	0	0	0	0	1	0	0	0	13018	1348	47	3	2862	3	RAG1	11	36597714	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	30031228	36597714	98408802	80	11574										
OR8K1	390157	hgsc.bcm.edu	37	chr11	56113637	56113637	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ggactcttcctcatcatataTctggtcacagtgataggcaa	8	10	5	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr11:56113637T>C	ENST00000279783.2	+	1	217	c.123T>C	c.(121-123)taT>taC	p.Y41Y		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					TCATCATATATCTGGTCACAG	0.463										HNSCC(65;0.19)																											p.Y41Y		Atlas-SNP	.											.	OR8K1	93	.	0			c.T123C						.						145	129	134					11																	56113637		2201	4296	6497	SO:0001819	synonymous_variant	390157	exon1			CATATATCTGGTC	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.123T>C	chr11.hg19:g.56113637T>C		374.0	0.0		343.0	21.0	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Silent	SNP	ENST00000279783.2	hg19	CCDS31528.1																																																																																			.	.		0.463	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		C	56113637	T	C	56113637	2	2	86	1	0	0	0	0	0	0	0	1	11252	1442	50	2		2	OR8K1	11	56113637	Silent	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	19515923	56113637	78892879	81	11575										
SMTNL1	219537	hgsc.bcm.edu	37	chr11	57317551	57317551	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ggaactgtaccgcagccttgTgcagaaaggactggtgaaga	14	8	0	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr11:57317551T>G	ENST00000399154.2	+	8	1340	c.1340T>G	c.(1339-1341)gTg>gGg	p.V447G	SMTNL1_ENST00000527972.1_Missense_Mutation_p.V484G|SMTNL1_ENST00000457912.1_Missense_Mutation_p.V502G			A8MU46	SMTL1_HUMAN	smoothelin-like 1	447	Calmodulin-binding. {ECO:0000250}.				negative regulation of vasodilation (GO:0045908)|positive regulation of vasoconstriction (GO:0045907)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	8						CGCAGCCTTGTGCAGAAAGGA	0.602																																					p.V484G		Atlas-SNP	.											.	SMTNL1	68	.	0			c.T1451G						.						54	54	54					11																	57317551		2098	4223	6321	SO:0001583	missense	219537	exon7			GCCTTGTGCAGAA	BX116227		11q12.1	2006-02-02				ENSG00000214872			32394	protein-coding gene	gene with protein product	"calponin homology-associated smooth muscle protein"	613664				15327999	Standard	NM_001105565		Approved	CHASM	uc021qjh.1	A8MU46		ENST00000399154.2:c.1340T>G	chr11.hg19:g.57317551T>G	ENSP00000382108:p.Val447Gly	137.0	0.0		120.0	53.0	NM_001105565		Missense_Mutation	SNP	ENST00000399154.2	hg19		.	.	.	.	.	.	.	.	.	.	T	21.9	4.213952	0.79352	.	.	ENSG00000214872	ENST00000457912;ENST00000527972;ENST00000399154	D;D;D	0.94138	-3.34;-3.32;-3.36	4.89	4.89	0.63831	.	.	.	.	.	D	0.95404	0.8508	L	0.60455	1.87	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.95000	0.8142	9	0.45353	T	0.12	-20.1687	13.6324	0.62202	0.0:0.0:0.0:1.0	.	502	C9J621	.	G	502;484;447	ENSP00000406485:V502G;ENSP00000432651:V484G;ENSP00000382108:V447G	ENSP00000382108:V447G	V	+	2	0	SMTNL1	57074127	1.000000	0.71417	0.994000	0.49952	0.885000	0.51271	3.229000	0.51278	2.062000	0.61559	0.459000	0.35465	GTG	.	.		0.602	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203		G	57317551	T	G	57317551	3	3	86	1	0	0	0	0	1	0	0	0	14830	1696	59	5	1535	5	SMTNL1	11	57317551	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	1203914	57317551	77688965	82	11576										
MS4A6A	64231	hgsc.bcm.edu	37	chr11	59947427	59947427	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aataccatcatgccacacaaGatctggatagtctgtgggaa	9	9	3	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr11:59947427G>T	ENST00000530839.1	-	4	651	c.159C>A	c.(157-159)atC>atA	p.I53I	MS4A6A_ENST00000529906.1_5'UTR|MS4A6A_ENST00000529054.1_Silent_p.I81I|MS4A6A_ENST00000420732.2_Silent_p.I53I|MS4A6A_ENST00000412309.2_Silent_p.I81I|MS4A6A_ENST00000528851.1_Silent_p.I53I|MS4A6A_ENST00000533023.1_Intron|MS4A6A_ENST00000532169.1_Silent_p.I53I|MS4A6A_ENST00000323961.3_Silent_p.I53I|MS4A6A_ENST00000426738.2_Intron	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	53						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGCCACACAAGATCTGGATAG	0.438																																					p.I81I		Atlas-SNP	.											MS4A6A_ENST00000529054,NS,carcinoma,0,2	MS4A6A	85	.	0			c.C243A						.						92	85	88					11																	59947427		2201	4295	6496	SO:0001819	synonymous_variant	64231	exon4			ACACAAGATCTGG	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.159C>A	chr11.hg19:g.59947427G>T		158.0	0.0		163.0	86.0	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Silent	SNP	ENST00000530839.1	hg19	CCDS7981.1																																																																																			.	.		0.438	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1			T	59947427	G	T	59947427	2	4	86	1	0	0	0	0	0	0	0	1	9873	932	33	3		3	MS4A6A	11	59947427	Silent	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	2629876	59947427	75059089	83	11577										
FAT3	120114	hgsc.bcm.edu	37	chr11	92565042	92565042	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gggactacctggtgacggtgCctgaggacacctcccctggc	14	14	0	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr11:92565042C>T	ENST00000298047.6	+	13	9753	c.9736C>T	c.(9736-9738)Cct>Tct	p.P3246S	FAT3_ENST00000525166.1_Missense_Mutation_p.P3096S|FAT3_ENST00000409404.2_Missense_Mutation_p.P3246S			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3246	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGTGACGGTGCCTGAGGACAC	0.527										TCGA Ovarian(4;0.039)																											p.P3246S		Atlas-SNP	.											.	FAT3	1822	.	0			c.C9736T						.						71	73	72					11																	92565042		1978	4168	6146	SO:0001583	missense	120114	exon13			ACGGTGCCTGAGG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.9736C>T	chr11.hg19:g.92565042C>T	ENSP00000298047:p.Pro3246Ser	129.0	0.0		76.0	21.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	C	11.30	1.597153	0.28445	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.01629	4.72;4.72;4.72	5.04	5.04	0.67666	.	.	.	.	.	T	0.02929	0.0087	N	0.25485	0.75	0.80722	D	1	D	0.52996	0.957	P	0.54590	0.756	T	0.62955	-0.6744	9	0.07325	T	0.83	.	14.3827	0.66921	0.0:0.8523:0.1477:0.0	.	3246	Q8TDW7-3	.	S	3246;3246;3096	ENSP00000298047:P3246S;ENSP00000387040:P3246S;ENSP00000432586:P3096S	ENSP00000298047:P3246S	P	+	1	0	FAT3	92204690	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	2.531000	0.45650	2.488000	0.83962	0.655000	0.94253	CCT	.	.		0.527	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92565042	C	T	92565042	3	4	86	1	0	0	0	0	1	0	0	0	5699	739	26	3	9786	3	FAT3	11	92565042	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	32617615	92565042	42441474	84	11578										
PANX1	24145	hgsc.bcm.edu	37	chr11	93911635	93911635	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tatttgctcagacttgaagtTtatcatggaagaacttgaca	8	6	2	4			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr11:93911635T>C	ENST00000227638.3	+	3	807	c.422T>C	c.(421-423)tTt>tCt	p.F141S	PANX1_ENST00000436171.2_Missense_Mutation_p.F141S	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	141					calcium ion transport (GO:0006816)|cation transport (GO:0006812)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|protein hexamerization (GO:0034214)|response to ATP (GO:0033198)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	bleb (GO:0032059)|endoplasmic reticulum (GO:0005783)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium channel activity (GO:0005262)|gap junction hemi-channel activity (GO:0055077)|leak channel activity (GO:0022840)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Probenecid(DB01032)	GACTTGAAGTTTATCATGGAA	0.498																																					p.F141S		Atlas-SNP	.											.	PANX1	38	.	0			c.T422C						.						115	99	105					11																	93911635		2201	4298	6499	SO:0001583	missense	24145	exon3			TGAAGTTTATCAT	AF093239	CCDS8296.1	11q14-q21	2011-12-02			ENSG00000110218	ENSG00000110218		"Ion channels / Pannexins"	8599	protein-coding gene	gene with protein product	"innexin"	608420				14597722	Standard	NM_015368		Approved	MRS1, UNQ2529, PX1	uc001per.3	Q96RD7	OTTHUMG00000167757	ENST00000227638.3:c.422T>C	chr11.hg19:g.93911635T>C	ENSP00000227638:p.Phe141Ser	272.0	0.0		234.0	13.0	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Missense_Mutation	SNP	ENST00000227638.3	hg19	CCDS8296.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.886232	0.91814	.	.	ENSG00000110218	ENST00000227638;ENST00000436171	T;T	0.26518	1.73;1.73	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.56558	0.1993	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.64145	-0.6476	10	0.56958	D	0.05	-28.1811	15.0086	0.71533	0.0:0.0:0.0:1.0	.	141;141	Q96RD7;Q96RD7-2	PANX1_HUMAN;.	S	141	ENSP00000227638:F141S;ENSP00000411461:F141S	ENSP00000227638:F141S	F	+	2	0	PANX1	93551283	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.538000	0.82048	1.945000	0.56424	0.460000	0.39030	TTT	.	.		0.498	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368		C	93911635	T	C	93911635	3	2	86	1	0	0	0	0	1	0	0	0	11429	1841	64	2	432	2	PANX1	11	93911635	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	1346593	93911635	41094881	85	11579										
CEP164	22897	hgsc.bcm.edu	37	chr11	117222658	117222658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	taagaagaagaaaaaaaaaaAggaaaagaaagacaagaagg	10	1	0	6			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr11:117222658A>G	ENST00000278935.3	+	5	494	c.347A>G	c.(346-348)aAg>aGg	p.K116R		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	116	Interaction with ATRIP.|Lys-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		aaaaaaaaaaaggaaaagaaa	0.502																																					p.K116R		Atlas-SNP	.											CEP164,caecum,carcinoma,0,1	CEP164	121	.	0			c.A347G						.						33	34	34					11																	117222658		2201	4296	6497	SO:0001583	missense	22897	exon4			AAAAAAAGGAAAA	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.347A>G	chr11.hg19:g.117222658A>G	ENSP00000278935:p.Lys116Arg	71.0	0.0		74.0	6.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	hg19	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744661	0.49151	.	.	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000533570;ENST00000529538	T;T;T;T	0.76060	-0.34;-0.03;-0.29;-0.99	5.95	4.82	0.62117	.	0.243999	0.29172	N	0.012934	T	0.80221	0.4583	M	0.62723	1.935	0.34770	D	0.733632	D;P;B;D	0.56521	0.959;0.482;0.023;0.976	P;B;B;P	0.56960	0.65;0.11;0.01;0.81	D	0.85776	0.1358	10	0.62326	D	0.03	-27.2573	11.2799	0.49188	0.9276:0.0:0.0724:0.0	.	116;70;116;116	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	R	70;116;70;70;116;116	ENSP00000436034:K70R;ENSP00000278935:K116R;ENSP00000435759:K70R;ENSP00000431302:K116R	ENSP00000278935:K116R	K	+	2	0	CEP164	116727868	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.713000	0.91408	1.068000	0.40764	0.533000	0.62120	AAG	.	.		0.502	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		G	117222658	A	G	117222658	3	3	86	1	0	0	0	0	1	0	0	0	3251	72	3	2	357	2	CEP164	11	117222658	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	23311023	117222658	17783858	86	11580										
CLEC1B	51266	hgsc.bcm.edu	37	chr12	10150973	10150973	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gccaccaggaggaggatgcaGagccaactgtaggcatataa	13	9	0	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr12:10150973G>T	ENST00000298527.6	-	2	250	c.71C>A	c.(70-72)tCt>tAt	p.S24Y	CLEC1B_ENST00000428126.2_Intron|CLEC1B_ENST00000348658.4_Intron	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	24			S -> P (in dbSNP:rs2273986). {ECO:0000269|PubMed:12975309}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						GGAGGATGCAGAGCCAACTGT	0.562																																					p.S24Y		Atlas-SNP	.											.	CLEC1B	39	.	0			c.C71A						.						87	94	91					12																	10150973		2104	4214	6318	SO:0001583	missense	51266	exon2			GATGCAGAGCCAA	AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"C-type lectin domain containing"	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.71C>A	chr12.hg19:g.10150973G>T	ENSP00000298527:p.Ser24Tyr	238.0	0.0		244.0	11.0	NM_016509	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	hg19	CCDS41752.1	.	.	.	.	.	.	.	.	.	.	G	8.645	0.896920	0.17686	.	.	ENSG00000165682	ENST00000298527	T	0.01505	4.82	4.37	3.47	0.39725	.	0.126684	0.36101	N	0.002786	T	0.01976	0.0062	L	0.34521	1.04	0.19945	N	0.999948	B	0.20550	0.046	B	0.22601	0.04	T	0.41945	-0.9480	10	0.72032	D	0.01	.	9.6983	0.40171	0.0:0.0:0.7925:0.2075	.	24	Q9P126	CLC1B_HUMAN	Y	24	ENSP00000298527:S24Y	ENSP00000298527:S24Y	S	-	2	0	CLEC1B	10042240	0.005000	0.15991	0.003000	0.11579	0.001000	0.01503	1.506000	0.35747	0.809000	0.34255	-0.856000	0.03024	TCT	.	.		0.562	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509		T	10150973	G	T	10150973	3	4	86	1	0	0	0	0	1	0	0	0	3508	942	33	3	638	3	CLEC1B	12	10150973	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10		10150973	123700922	87	11581										
ABCD2	225	hgsc.bcm.edu	37	chr12	39973407	39973407	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	caggacatctttccagtccaTaacagcatcccatccttaag	5	14	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr12:39973407T>A	ENST00000308666.3	-	8	1942	c.1807A>T	c.(1807-1809)Atg>Ttg	p.M603L		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	603	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						TTCCAGTCCATAACAGCATCC	0.328																																					p.M603L		Atlas-SNP	.											.	ABCD2	127	.	0			c.A1807T						.						158	150	152					12																	39973407		2203	4300	6503	SO:0001583	missense	225	exon8			AGTCCATAACAGC	U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.1807A>T	chr12.hg19:g.39973407T>A	ENSP00000310688:p.Met603Leu	24.0	0.0		64.0	36.0	NM_005164	B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	hg19	CCDS8734.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.803390	0.31869	.	.	ENSG00000173208	ENST00000308666	D	0.99840	-7.08	5.23	1.41	0.22369	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.369037	0.28895	N	0.013793	D	0.96904	0.8989	N	0.01015	-1.05	0.27788	N	0.942933	B	0.02656	0.0	B	0.09377	0.004	D	0.98220	1.0477	9	.	.	.	-11.4561	7.9315	0.29905	0.1275:0.0:0.2665:0.606	.	603	Q9UBJ2	ABCD2_HUMAN	L	603	ENSP00000310688:M603L	.	M	-	1	0	ABCD2	38259674	1.000000	0.71417	0.981000	0.43875	0.994000	0.84299	2.561000	0.45905	0.004000	0.14682	0.472000	0.43445	ATG	.	.		0.328	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164		A	39973407	T	A	39973407	3	1	86	1	0	0	0	0	1	0	0	0	61	1406	49	4	427	4	ABCD2	12	39973407	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	29822434	39973407	93878488	88	11582										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40745384	40745384	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tgaattagtctgtctgacgaGacgcattttattacctaaaa	7	7	2	3	rs371284884		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr12:40745384G>A	ENST00000298910.7	+	44	6483	c.6425G>A	c.(6424-6426)aGa>aAa	p.R2142K		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2142					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TGTCTGACGAGACGCATTTTA	0.398																																					p.R2142K		Atlas-SNP	.											.	LRRK2	763	.	0			c.G6425A						.	G	LYS/ARG	1,4405		0,1,2202	66	64	65		6425	4.2	0.9	12		65	0,8600		0,0,4300	no	missense	LRRK2	NM_198578.3	26	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	2142/2528	40745384	1,13005	2203	4300	6503	SO:0001583	missense	120892	exon44			TGACGAGACGCAT	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.6425G>A	chr12.hg19:g.40745384G>A	ENSP00000298910:p.Arg2142Lys	195.0	0.0		179.0	10.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	18.41	3.617000	0.66672	2.27E-4	0.0	ENSG00000188906	ENST00000298910	T	0.71934	-0.61	6.06	4.24	0.50183	.	0.123348	0.64402	N	0.000001	T	0.62816	0.2459	L	0.58101	1.795	0.39344	D	0.965639	P;P	0.40681	0.528;0.727	B;B	0.33568	0.166;0.166	T	0.63332	-0.6661	10	0.37606	T	0.19	.	12.5172	0.56038	0.1337:0.0:0.8663:0.0	.	2142;2142	Q17RV3;Q5S007	.;LRRK2_HUMAN	K	2142	ENSP00000298910:R2142K	ENSP00000298910:R2142K	R	+	2	0	LRRK2	39031651	1.000000	0.71417	0.939000	0.37840	0.428000	0.31595	5.232000	0.65332	0.896000	0.36366	0.655000	0.94253	AGA	.	.		0.398	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		A	40745384	G	A	40745384	3	1	86	1	0	0	0	0	1	0	0	0	9042	942	33	3	6599	3	LRRK2	12	40745384	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	771977	40745384	93106511	89	11583										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43769288	43769288	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tcttcccttctactcccattAaaaggacattgatatggatt	5	10	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr12:43769288A>T	ENST00000389420.3	-	36	5339	c.5340T>A	c.(5338-5340)ttT>ttA	p.F1780L		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1780	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TACTCCCATTAAAAGGACATT	0.368																																					p.F1780L		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T5340A						.						147	147	147					12																	43769288		2203	4300	6503	SO:0001583	missense	80070	exon36			CCCATTAAAAGGA	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.5340T>A	chr12.hg19:g.43769288A>T	ENSP00000374071:p.Phe1780Leu	269.0	0.0		314.0	16.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744687	0.49151	.	.	ENSG00000173157	ENST00000389420	T	0.16597	2.33	4.8	-0.635	0.11512	Peptidase M12B, GON-ADAMTSs (2);	0.000000	0.51477	D	0.000084	T	0.27594	0.0678	M	0.75264	2.295	0.80722	D	1	D	0.56035	0.974	P	0.54664	0.758	T	0.06752	-1.0809	10	0.25751	T	0.34	.	10.3787	0.44099	0.5499:0.0:0.4501:0.0	.	1780	P59510	ATS20_HUMAN	L	1780	ENSP00000374071:F1780L	ENSP00000374071:F1780L	F	-	3	2	ADAMTS20	42055555	0.998000	0.40836	0.997000	0.53966	0.398000	0.30690	0.460000	0.21924	-0.163000	0.10946	0.377000	0.23210	TTT	.	.		0.368	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43769288	A	T	43769288	3	4	86	1	0	0	0	0	1	0	0	0	266	359	13	4	407	4	ADAMTS20	12	43769288	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	3023904	43769288	90082607	90	11584										
LRP1	4035	hgsc.bcm.edu	37	chr12	57599015	57599015	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ctgcggggacggctctgacgAggaggactgcagcatcggtg	18	10	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr12:57599015A>G	ENST00000243077.3	+	73	11784	c.11318A>G	c.(11317-11319)gAg>gGg	p.E3773G		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3773	LDL-receptor class A 31. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GGCTCTGACGAGGAGGACTGC	0.657																																					p.E3773G		Atlas-SNP	.											.	LRP1	428	.	0			c.A11318G						.						66	64	65					12																	57599015		2203	4300	6503	SO:0001583	missense	4035	exon73			CTGACGAGGAGGA	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.11318A>G	chr12.hg19:g.57599015A>G	ENSP00000243077:p.Glu3773Gly	69.0	0.0		75.0	19.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494334	0.64186	.	.	ENSG00000123384	ENST00000243077	D	0.97959	-4.63	4.55	3.41	0.39046	Low-density lipoprotein (LDL) receptor class A, conserved site (1);Growth factor, receptor (1);	0.148881	0.42053	D	0.000777	D	0.98207	0.9407	H	0.96805	3.885	0.80722	D	1	P	0.47484	0.896	P	0.46510	0.519	D	0.97606	1.0126	10	0.72032	D	0.01	.	9.4051	0.38457	0.9134:0.0:0.0866:0.0	.	3773	Q07954	LRP1_HUMAN	G	3773	ENSP00000243077:E3773G	ENSP00000243077:E3773G	E	+	2	0	LRP1	55885282	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.276000	0.78559	0.900000	0.36469	0.533000	0.62120	GAG	.	.		0.657	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		G	57599015	A	G	57599015	3	3	86	1	0	0	0	0	1	0	0	0	8960	304	11	2	11608	2	LRP1	12	57599015	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	13829727	57599015	76252880	91	11585										
NOS1	4842	hgsc.bcm.edu	37	chr12	117696859	117696859	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tctcagggggatctccattgCcaaaggtgctggtgaccaca	12	11	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr12:117696859C>A	ENST00000338101.4	-	14	2448	c.2444G>T	c.(2443-2445)gGc>gTc	p.G815V	NOS1_ENST00000317775.6_Missense_Mutation_p.G815V|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		ATCTCCATTGCCAAAGGTGCT	0.502																																					p.G815V	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.G2444T						.						110	108	109					12																	117696859		2030	4203	6233	SO:0001583	missense	4842	exon15			CCATTGCCAAAGG		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2444G>T	chr12.hg19:g.117696859C>A	ENSP00000337459:p.Gly815Val	140.0	0.0		161.0	39.0	NM_000620		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.757750	0.89843	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.73789	-0.78;-0.78	4.95	4.95	0.65309	Flavodoxin/nitric oxide synthase (2);	0.000000	0.85682	D	0.000000	D	0.91646	0.7360	H	0.97918	4.105	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94580	0.7778	10	0.72032	D	0.01	-28.7058	17.9604	0.89083	0.0:1.0:0.0:0.0	.	815	P29475	NOS1_HUMAN	V	710;815;815;815	ENSP00000320758:G815V;ENSP00000337459:G815V	ENSP00000320758:G815V	G	-	2	0	NOS1	116181242	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.555000	0.82223	2.560000	0.86352	0.655000	0.94253	GGC	.	.		0.502	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			A	117696859	C	A	117696859	3	1	86	1	0	0	0	0	1	0	0	0	10550	739	26	3	1920	3	NOS1	12	117696859	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	60097844	117696859	16155036	92	11586										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124399402	124399402	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	atggctgtttcttccagatgGggatcccagggccttccccc	11	14	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr12:124399402G>T	ENST00000409039.3	+	61	10249	c.10224G>T	c.(10222-10224)tgG>tgT	p.W3408C		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3408	AAA 5. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CTTCCAGATGGGGATCCCAGG	0.562																																					p.W3408C		Atlas-SNP	.											.	DNAH10	888	.	0			c.G10224T						.						25	30	28					12																	124399402		1909	4123	6032	SO:0001583	missense	196385	exon61			CAGATGGGGATCC	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.10224G>T	chr12.hg19:g.124399402G>T	ENSP00000386770:p.Trp3408Cys	95.0	0.0		130.0	21.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	20.5	3.998006	0.74818	.	.	ENSG00000197653	ENST00000409039	T	0.35048	1.33	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.78227	0.4250	H	0.99425	4.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88959	0.3392	10	0.87932	D	0	.	18.093	0.89480	0.0:0.0:1.0:0.0	.	3408	Q8IVF4	DYH10_HUMAN	C	3408	ENSP00000386770:W3408C	ENSP00000386770:W3408C	W	+	3	0	DNAH10	122965355	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	9.739000	0.98837	2.242000	0.73789	0.555000	0.69702	TGG	.	.		0.562	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124399402	G	T	124399402	3	4	86	1	0	0	0	0	1	0	0	0	4600	1241	43	3	10466	3	DNAH10	12	124399402	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	6702543	124399402	9452493	93	11587										
PDX1	3651	hgsc.bcm.edu	37	chr13	28498525	28498525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gccgcgccgggtggagctggCtgtcatgttgaacttgaccg	16	11	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr13:28498525C>T	ENST00000381033.4	+	2	658	c.539C>T	c.(538-540)gCt>gTt	p.A180V	PDX1-AS1_ENST00000499662.2_RNA	NM_000209.3	NP_000200.1	O00330	ODPX_HUMAN	pancreatic and duodenal homeobox 1	0					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)					all_cancers(110;0.175)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155)	Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0402)|all cancers(112;0.0404)|OV - Ovarian serous cystadenocarcinoma(117;0.197)		GTGGAGCTGGCTGTCATGTTG	0.582																																					p.A180V		Atlas-SNP	.											.	PDX1	7	.	0			c.C539T						.						56	60	59					13																	28498525		2203	4300	6503	SO:0001583	missense	3651	exon2			AGCTGGCTGTCAT	AF035260	CCDS9327.1	13q12.1	2012-03-09	2006-12-01	2006-12-01	ENSG00000139515	ENSG00000139515		"Homeoboxes / ANTP class : HOXL subclass"	6107	protein-coding gene	gene with protein product	"somatostatin transcription factor 1"	600733	"insulin promoter factor 1, homeodomain transcription factor"	IPF1		7590740	Standard	NM_000209		Approved	IDX-1, STF-1, PDX-1, MODY4	uc001urt.2	P52945	OTTHUMG00000016638	ENST00000381033.4:c.539C>T	chr13.hg19:g.28498525C>T	ENSP00000370421:p.Ala180Val	104.0	0.0		82.0	66.0	NM_000209	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000381033.4	hg19	CCDS9327.1	.	.	.	.	.	.	.	.	.	.	C	33	5.230002	0.95173	.	.	ENSG00000139515	ENST00000381033	D	0.98362	-4.89	4.86	4.86	0.63082	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99306	0.9757	H	0.95151	3.63	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98776	1.0730	10	0.87932	D	0	.	18.338	0.90295	0.0:1.0:0.0:0.0	.	180	P52945	PDX1_HUMAN	V	180	ENSP00000370421:A180V	ENSP00000370421:A180V	A	+	2	0	PDX1	27396525	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.743000	0.85020	2.382000	0.81193	0.555000	0.69702	GCT	.	.		0.582	PDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044310.2	NM_000209		T	28498525	C	T	28498525	3	4	86	1	0	0	0	0	1	0	0	0	11704	797	28	3	545	3	PDX1	13	28498525	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10		28498525	86671353	94	11588										
RB1	5925	hgsc.bcm.edu	37	chr13	48881512	48881512	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gagagagcttggttaacttgGgagaaagtttcatctgtgga	14	4	2	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr13:48881512G>A	ENST00000267163.4	+	2	372	c.234G>A	c.(232-234)tgG>tgA	p.W78*		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	78					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.W78*(3)|p.?(3)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	GGTTAACTTGGGAGAAAGTTT	0.323		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.W78X		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	RB1_ENST00000267163,colon,carcinoma,+1,2	RB1	1068	.	21	Whole gene deletion(15)|Substitution - Nonsense(3)|Unknown(3)	bone(11)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|eye(1)|soft_tissue(1)|endometrium(1)|lung(1)|skin(1)|stomach(1)	c.G234A						.						136	138	137					13																	48881512		2203	4299	6502	SO:0001587	stop_gained	5925	exon2	Familial Cancer Database		AACTTGGGAGAAA	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.234G>A	chr13.hg19:g.48881512G>A	ENSP00000267163:p.Trp78*	247.0	0.0		235.0	173.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Nonsense_Mutation	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	37	5.989199	0.97179	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	4.86	4.86	0.63082	.	0.135639	0.53938	D	0.000048	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.2922	13.8493	0.63487	0.0:0.0:1.0:0.0	.	.	.	.	X	57;78	.	ENSP00000267163:W78X	W	+	3	0	RB1	47779513	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.967000	0.49216	2.401000	0.81631	0.650000	0.86243	TGG	.	.		0.323	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			A	48881512	G	A	48881512	4	1	86	1	0	0	0	0	0	1	0	0	13113	1241	43	3	240	3	RB1	13	48881512	Nonsense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	20382987	48881512	66288366	95	11589										
DCT	1638	hgsc.bcm.edu	37	chr13	95131263	95131263	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ttttcttggccacagctcacGgtcatcctggtttcgtagga	10	11	3	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr13:95131263G>A	ENST00000377028.5	-	1	660	c.247C>T	c.(247-249)Cgt>Tgt	p.R83C	DCT_ENST00000446125.1_Missense_Mutation_p.R83C	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	83					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		CACAGCTCACGGTCATCCTGG	0.607																																					p.R83C		Atlas-SNP	.											DCT_ENST00000446125,colon,carcinoma,0,2	DCT	186	.	0			c.C247T						.						101	87	91					13																	95131263		2203	4300	6503	SO:0001583	missense	1638	exon1			GCTCACGGTCATC	D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.247C>T	chr13.hg19:g.95131263G>A	ENSP00000366227:p.Arg83Cys	100.0	0.0		101.0	48.0	NM_001129889	Q09GT4	Missense_Mutation	SNP	ENST00000377028.5	hg19	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.287558	0.80803	.	.	ENSG00000080166	ENST00000377028;ENST00000446125	D;D	0.86956	-2.19;-2.19	5.32	5.32	0.75619	Uncharacterised domain, di-copper centre (1);	0.000000	0.85682	D	0.000000	D	0.95793	0.8631	H	0.95504	3.68	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.96961	0.9701	10	0.87932	D	0	-15.1729	19.0	0.92829	0.0:0.0:1.0:0.0	.	83;83	Q09GT4;P40126	.;TYRP2_HUMAN	C	83	ENSP00000366227:R83C;ENSP00000392762:R83C	ENSP00000366227:R83C	R	-	1	0	DCT	93929264	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	3.887000	0.56197	2.482000	0.83794	0.650000	0.86243	CGT	.	.		0.607	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			A	95131263	G	A	95131263	3	1	86	1	0	0	0	0	1	0	0	0	4306	1116	39	1	1451	1	DCT	13	95131263	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	46249751	95131263	20038615	96	11590										
FOXG1	2290	hgsc.bcm.edu	37	chr14	29237217	29237217	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tgcttcgtgaaggtgccgcgCcactacgacgacccgggcaa	13	14	0	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr14:29237217C>A	ENST00000313071.4	+	1	931	c.732C>A	c.(730-732)cgC>cgA	p.R244R	RP11-966I7.1_ENST00000546560.1_RNA|RP11-966I7.1_ENST00000551395.1_RNA|FOXG1_ENST00000382535.3_Silent_p.R244R|RP11-966I7.1_ENST00000549487.1_RNA	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	244			R -> C (in RTTCV; the mutant protein extensively, although not fully, localizes in nuclear speckles, while the wild-type is more widely dispersed throughout the nucleus). {ECO:0000269|PubMed:21280142}.		aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		AGGTGCCGCGCCACTACGACG	0.617																																					p.R244R		Atlas-SNP	.											.	FOXG1	92	.	0			c.C732A						.						47	48	47					14																	29237217		2203	4300	6503	SO:0001819	synonymous_variant	2290	exon1			GCCGCGCCACTAC		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.732C>A	chr14.hg19:g.29237217C>A		126.0	0.0		91.0	23.0	NM_005249	A6NFY2|P55315|Q14488|Q86XT7	Silent	SNP	ENST00000313071.4	hg19	CCDS9636.1																																																																																			.	.		0.617	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			A	29237217	C	A	29237217	2	1	86	1	0	0	0	0	0	0	0	1	6015	726	26	3		3	FOXG1	14	29237217	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10		29237217	78112323	97	11591										
MLH3	27030	hgsc.bcm.edu	37	chr14	75513372	75513372	+	Frame_Shift_Del	DEL	C	C	-													0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cactgggagagtcaagacttCctatctgttgttctgaggct							TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr14:75513372delC	ENST00000556740.1	-	1	3022	c.2987delG	c.(2986-2988)ggafs	p.G996fs	MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000355774.2_Frame_Shift_Del_p.G996fs|MLH3_ENST00000556257.1_Frame_Shift_Del_p.G996fs|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000238662.7_Frame_Shift_Del_p.G996fs|MLH3_ENST00000555671.1_5'UTR			Q9UHC1	MLH3_HUMAN	mutL homolog 3	996					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GTCAAGACTTCCTATCTGTTG	0.388								Mismatch excision repair (MMR)																													p.G996fs		Atlas-Indel,Pindel	.											.	MLH3	200	.	0			c.2988delA						.						111	117	115					14																	75513372		2203	4300	6503	SO:0001589	frameshift_variant	27030	exon2			.	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.2987delG	chr14.hg19:g.75513372delC	ENSP00000452316:p.Gly996fs	335.0	0.0		265.0	62.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Frame_Shift_Del	DEL	ENST00000556740.1	hg19	CCDS32123.1																																																																																			.	.		0.388	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		-	75513372	C	-	75513372	7	5	86	1	0	1	0	1	0	0	0	0	9627	855	30	0	1422	0	MLH3	14	75513372	Frame_Shift_Del	DEL	C	TCGA-DD-A113-01A-11D-A12Z-10	46276155	75513372	31836168	98	11592										
C14orf49	161176	hgsc.bcm.edu	37	chr14	95918595	95918595	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cccagatacctctgatactcCtggatggtagcgatgacact	9	12	1	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr14:95918595C>T	ENST00000334258.5	-	6	1277	c.1263G>A	c.(1261-1263)caG>caA	p.Q421Q	SYNE3_ENST00000553340.1_Silent_p.Q421Q|SYNE3_ENST00000557275.1_Silent_p.Q421Q|SYNE3_ENST00000554873.1_Silent_p.Q178Q	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	421					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						TCTGATACTCCTGGATGGTAG	0.582											OREG0022900	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q421Q		Atlas-SNP	.											.	SYNE3	130	.	0			c.G1263A						.						119	100	106					14																	95918595		2203	4300	6503	SO:0001819	synonymous_variant	161176	exon6			ATACTCCTGGATG	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.1263G>A	chr14.hg19:g.95918595C>T		118.0	0.0	1316	112.0	29.0	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	hg19	CCDS9935.1																																																																																			.	.		0.582	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		T	95918595	C	T	95918595	2	4	86	1	0	0	0	0	0	0	0	1	1778	680	24	3		3	C14orf49	14	95918595	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	20405223	95918595	11430945	99	11593										
INF2	64423	hgsc.bcm.edu	37	chr14	105174811	105174811	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cgtccctgagcagccccgacGccgaggctgtggagcccgac	14	17	0	1	rs530285485		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr14:105174811G>A	ENST00000392634.4	+	9	1886	c.1774G>A	c.(1774-1776)Gcc>Acc	p.A592T	INF2_ENST00000330634.7_Missense_Mutation_p.A592T	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	592	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CAGCCCCGACGCCGAGGCTGT	0.682											OREG0022959	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0	0.0014	5008	,	,		15905	0		0	False		,,,				2504	0				p.A592T		Atlas-SNP	.											.	INF2	148	.	0			c.G1774A						.						35	41	39					14																	105174811		1936	4130	6066	SO:0001583	missense	64423	exon9			CCCGACGCCGAGG	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"inverted formin 2"	610982	"chromosome 14 open reading frame 151", "chromosome 14 open reading frame 173"	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.1774G>A	chr14.hg19:g.105174811G>A	ENSP00000376410:p.Ala592Thr	84.0	0.0	1387	85.0	15.0	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	hg19	CCDS9989.2	.	.	.	.	.	.	.	.	.	.	G	2.400	-0.337744	0.05278	.	.	ENSG00000203485	ENST00000330634;ENST00000392634	T;T	0.17054	2.3;2.3	4.04	-7.77	0.01227	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.650666	0.15095	N	0.280854	T	0.05456	0.0144	N	0.20685	0.6	0.09310	N	1	B;B	0.12013	0.004;0.005	B;B	0.08055	0.001;0.003	T	0.34403	-0.9830	10	0.12766	T	0.61	.	1.837	0.03142	0.2573:0.2406:0.3818:0.1203	.	592;592	Q27J81-2;Q27J81	.;INF2_HUMAN	T	592	ENSP00000376406:A592T;ENSP00000376410:A592T	ENSP00000252527:A60T	A	+	1	0	INF2	104245856	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.152000	0.10159	-1.360000	0.02172	0.561000	0.74099	GCC	.	.		0.682	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		A	105174811	G	A	105174811	3	1	86	1	0	0	0	0	1	0	0	0	7743	1087	38	1	1808	1	INF2	14	105174811	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	9256216	105174811	2174729	100	11594										
BTBD6	90135	hgsc.bcm.edu	37	chr14	105716439	105716439	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ctagaggagtttgccaacggCgctgcccagtcagacatcct	11	13	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr14:105716439C>T	ENST00000392554.3	+	4	1185	c.888C>T	c.(886-888)ggC>ggT	p.G296G	BRF1_ENST00000440513.3_Intron|BTBD6_ENST00000463376.2_Silent_p.G221G|BRF1_ENST00000551787.1_5'Flank|BTBD6_ENST00000536364.1_Silent_p.G296G|BRF1_ENST00000392557.4_5'Flank|BRF1_ENST00000379937.2_Intron|BRF1_ENST00000546474.1_Intron|BTBD6_ENST00000327471.3_Silent_p.G221G|BRF1_ENST00000379932.4_5'Flank|BRF1_ENST00000446501.2_5'Flank|BRF1_ENST00000327359.3_Intron			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	296						cytoplasm (GO:0005737)				endometrium(1)|lung(3)	4		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391)	Epithelial(152;0.18)		TTGCCAACGGCGCTGCCCAGT	0.587																																					p.G296G		Atlas-SNP	.											.	BTBD6	24	.	0			c.C888T						.						66	73	71					14																	105716439		2203	4300	6503	SO:0001819	synonymous_variant	90135	exon5			CAACGGCGCTGCC	AF353674	CCDS10002.1, CCDS10002.2	14q32.33	2013-01-08			ENSG00000184887	ENSG00000184887		"BTB/POZ domain containing"	19897	protein-coding gene	gene with protein product							Standard	NM_033271		Approved	BDPL	uc010tyq.2	Q96KE9	OTTHUMG00000029887	ENST00000392554.3:c.888C>T	chr14.hg19:g.105716439C>T		48.0	0.0		41.0	25.0	NM_033271	Q8IVQ7|Q9BR94	Silent	SNP	ENST00000392554.3	hg19	CCDS10002.2																																																																																			.	.		0.587	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4			T	105716439	C	T	105716439	2	4	86	1	0	0	0	0	0	0	0	1	1547	755	27	1		1	BTBD6	14	105716439	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	541628	105716439	1633101	101	11595										
AQR	9716	hgsc.bcm.edu	37	chr15	35212596	35212596	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tttttaggaagagttggcaaCaagcagaggtatgatgccac	12	6	0	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr15:35212596C>A	ENST00000156471.5	-	14	1383	c.1158G>T	c.(1156-1158)ttG>ttT	p.L386F		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	386					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		GAGTTGGCAACAAGCAGAGGT	0.333																																					p.L386F		Atlas-SNP	.											.	AQR	139	.	0			c.G1158T						.						79	76	77					15																	35212596		1829	4088	5917	SO:0001583	missense	9716	exon14			TGGCAACAAGCAG	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.1158G>T	chr15.hg19:g.35212596C>A	ENSP00000156471:p.Leu386Phe	76.0	0.0		69.0	33.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	hg19	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.261543	0.59431	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.94793	-3.52	5.16	3.09	0.35607	.	0.068279	0.56097	D	0.000024	D	0.94262	0.8157	M	0.68317	2.08	0.48341	D	0.999631	D	0.63046	0.992	P	0.57911	0.829	D	0.92124	0.5706	10	0.44086	T	0.13	-10.9319	3.6009	0.08024	0.1526:0.5579:0.1594:0.13	.	386	O60306	AQR_HUMAN	F	386	ENSP00000156471:L386F	ENSP00000156471:L386F	L	-	3	2	AQR	32999888	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	0.734000	0.26101	1.368000	0.46115	0.563000	0.77884	TTG	.	.		0.333	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		A	35212596	C	A	35212596	3	1	86	1	0	0	0	0	1	0	0	0	835	477	17	3	3387	3	AQR	15	35212596	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10		35212596	67318796	102	11596										
FSIP1	161835	hgsc.bcm.edu	37	chr15	39909936	39909936	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	acatgttcgccaagcctcacCtgctattgtattctctggag	8	12	2	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr15:39909936C>T	ENST00000350221.3	-	11	1908	c.1699G>A	c.(1699-1701)Gat>Aat	p.D567N		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	567										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		CAAGCCTCACCTGCTATTGTA	0.388																																					p.D567N		Atlas-SNP	.											.	FSIP1	53	.	0			c.G1699A						.						83	79	80					15																	39909936		2200	4297	6497	SO:0001630	splice_region_variant	161835	exon11			CCTCACCTGCTAT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1699+1G>A	chr15.hg19:g.39909936C>T		126.0	0.0		101.0	54.0	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	hg19	CCDS10050.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.718952	0.30503	.	.	ENSG00000150667	ENST00000350221	T	0.15256	2.44	4.84	4.84	0.62591	.	0.202066	0.31909	N	0.006878	T	0.21841	0.0526	N	0.19112	0.55	0.39441	D	0.967248	D	0.67145	0.996	P	0.56916	0.809	T	0.02852	-1.1102	9	.	.	.	-5.2151	16.6331	0.85039	0.0:1.0:0.0:0.0	.	567	Q8NA03	FSIP1_HUMAN	N	567	ENSP00000280236:D567N	.	D	-	1	0	FSIP1	37697228	1.000000	0.71417	0.991000	0.47740	0.074000	0.17049	4.302000	0.59092	2.669000	0.90835	0.591000	0.81541	GAT	.	.		0.388	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	Missense_Mutation	T	39909936	C	T	39909936	5	4	86	1	0	0	0	0	0	0	1	0	6082	695	24	3	54	3	FSIP1	15	39909936	Splice_Site	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	4697340	39909936	62621456	103	11597										
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42115228	42115228	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	agcagccgagaggcaatggtGccaatccccctggagcaccc	12	15	0	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr15:42115228G>A	ENST00000456763.2	+	29	3620	c.3424G>A	c.(3424-3426)Gcc>Acc	p.A1142T	MAPKBP1_ENST00000260357.7_Missense_Mutation_p.A975T|RP11-23P13.4_ENST00000512295.1_RNA|MAPKBP1_ENST00000514566.1_Intron|RP11-23P13.4_ENST00000510176.1_RNA|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.A1019T|MAPKBP1_ENST00000457542.2_Missense_Mutation_p.A1136T	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	1142										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		AGGCAATGGTGCCAATCCCCC	0.647																																					p.A1142T		Atlas-SNP	.											.	MAPKBP1	120	.	0			c.G3424A						.						58	50	53					15																	42115228		2203	4300	6503	SO:0001583	missense	23005	exon29			AATGGTGCCAATC	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.3424G>A	chr15.hg19:g.42115228G>A	ENSP00000393099:p.Ala1142Thr	60.0	0.0		61.0	31.0	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	hg19	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	.	16.59	3.165632	0.57476	.	.	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000260357;ENST00000456763	T;T;T;T	0.40476	1.2;1.37;1.03;1.25	5.22	4.31	0.51392	.	0.828534	0.11372	N	0.570812	T	0.29850	0.0746	N	0.24115	0.695	0.19300	N	0.99998	B;B;B;B;P	0.43352	0.035;0.129;0.197;0.323;0.804	B;B;B;B;B	0.42282	0.013;0.046;0.036;0.114;0.382	T	0.03945	-1.0990	10	0.15066	T	0.55	-12.0694	9.6994	0.40178	0.0933:0.0:0.9067:0.0	.	975;1019;975;1142;1136	F8WC21;O60336-3;B4DYK7;O60336;O60336-6	.;.;.;MABP1_HUMAN;.	T	1136;1019;975;1142	ENSP00000397570:A1136T;ENSP00000221214:A1019T;ENSP00000260357:A975T;ENSP00000393099:A1142T	ENSP00000221214:A1019T	A	+	1	0	MAPKBP1	39902520	0.081000	0.21417	0.661000	0.29709	0.865000	0.49528	1.427000	0.34881	1.435000	0.47434	0.561000	0.74099	GCC	.	.		0.647	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		A	42115228	G	A	42115228	3	1	86	1	0	0	0	0	1	0	0	0	9301	1319	46	3	3534	3	MAPKBP1	15	42115228	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	2205292	42115228	60416164	104	11598										
AGBL1	123624	hgsc.bcm.edu	37	chr15	86810275	86810275	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ttcttctccaaatttgagtcAggaaatcttcgcaaagccat	6	10	4	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr15:86810275A>G	ENST00000441037.2	+	12	1763	c.1668A>G	c.(1666-1668)tcA>tcG	p.S556S	AGBL1_ENST00000421325.2_Silent_p.S556S|AGBL1_ENST00000389298.3_Silent_p.S287S	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	556					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						AATTTGAGTCAGGAAATCTTC	0.423																																					p.S556S		Atlas-SNP	.											.	AGBL1	151	.	0			c.A1668G						.						88	79	82					15																	86810275		1907	4120	6027	SO:0001819	synonymous_variant	123624	exon12			TGAGTCAGGAAAT	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.1668A>G	chr15.hg19:g.86810275A>G		290.0	0.0		260.0	144.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	hg19	CCDS58398.1																																																																																			.	.		0.423	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		G	86810275	A	G	86810275	2	3	86	1	0	0	0	0	0	0	0	1	375	175	7	2		2	AGBL1	15	86810275	Silent	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	44695047	86810275	15721117	105	11599										
RHBDL1	9028	hgsc.bcm.edu	37	chr16	726998	726998	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tgttcctgtgttacggggccCgcctcaacaagtgggtgctg	14	11	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr16:726998C>T	ENST00000219551.2	+	3	676	c.649C>T	c.(649-651)Cgc>Tgc	p.R217C	LA16c-313D11.9_ENST00000571933.1_RNA|RHBDL1_ENST00000352681.3_Missense_Mutation_p.R152C|LA16c-313D11.9_ENST00000567091.1_RNA			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	217					signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(1)|lung(4)|urinary_tract(3)	9		Hepatocellular(780;0.0218)				TTACGGGGCCCGCCTCAACAA	0.682																																					p.R217C		Atlas-SNP	.											.	RHBDL1	14	.	0			c.C649T						.						63	67	66					16																	726998		2201	4298	6499	SO:0001583	missense	9028	exon3			GGGGCCCGCCTCA	Y17108	CCDS61779.1	16p13.3	2008-02-05	2001-11-28	2003-04-11	ENSG00000103269	ENSG00000103269			10007	protein-coding gene	gene with protein product		603264	"rhomboid (veinlet, Drosophila)-like"	RHBDL		9662444	Standard	NM_001278720		Approved	RRP	uc002cis.1	O75783	OTTHUMG00000121141	ENST00000219551.2:c.649C>T	chr16.hg19:g.726998C>T	ENSP00000219551:p.Arg217Cys	73.0	0.0		71.0	12.0	NM_003961	A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Missense_Mutation	SNP	ENST00000219551.2	hg19	CCDS10418.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.859017	0.32884	.	.	ENSG00000103269	ENST00000352681;ENST00000450775;ENST00000219551	T;T	0.33216	1.46;1.42	3.99	3.99	0.46301	.	0.143249	0.42964	D	0.000631	T	0.22399	0.0540	N	0.08118	0	0.46981	D	0.999279	D;D;D	0.61080	0.989;0.977;0.958	P;B;P	0.50617	0.54;0.439;0.646	T	0.05099	-1.0906	10	0.56958	D	0.05	-18.8892	10.2818	0.43543	0.1975:0.8025:0.0:0.0	.	152;217;152	B4DFK3;O75783;O75783-2	.;RHBL1_HUMAN;.	C	152;152;217	ENSP00000344206:R152C;ENSP00000219551:R217C	ENSP00000219551:R217C	R	+	1	0	RHBDL1	666999	0.811000	0.29063	0.683000	0.30040	0.029000	0.11900	1.737000	0.38197	2.062000	0.61559	0.557000	0.71058	CGC	.	.		0.682	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1	NM_003961		T	726998	C	T	726998	3	4	86	1	0	0	0	0	1	0	0	0	13336	652	23	1	659	1	RHBDL1	16	726998	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10		726998	89627755	106	11600										
MYH11	4629	hgsc.bcm.edu	37	chr16	15931795	15931795	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cctgagaagtaccgctccctCaggttgtgtagcacggaggc	13	12	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr16:15931795C>T	ENST00000300036.5	-	2	424	c.315G>A	c.(313-315)ctG>ctA	p.L105L	MYH11_ENST00000576790.2_Silent_p.L105L|MYH11_ENST00000452625.2_Silent_p.L105L|MYH11_ENST00000396324.3_Silent_p.L105L	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	105	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						ACCGCTCCCTCAGGTTGTGTA	0.517			T	CBFB	AML																																p.L105L		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.G315A						.						164	140	148					16																	15931795		2197	4300	6497	SO:0001819	synonymous_variant	4629	exon2			CTCCCTCAGGTTG	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.315G>A	chr16.hg19:g.15931795C>T		192.0	0.0		224.0	102.0	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	hg19	CCDS10565.1																																																																																			.	.		0.517	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15931795	C	T	15931795	2	4	86	1	0	0	0	0	0	0	0	1	10040	813	29	3		3	MYH11	16	15931795	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	15204797	15931795	74422958	107	11601										
DOC2A	8448	hgsc.bcm.edu	37	chr16	30018188	30018188	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gatgcctaccagcagtccccGgcgccgcgagctgtagctga	13	15	0	1	rs370463371		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr16:30018188G>T	ENST00000350119.4	-	8	986	c.796C>A	c.(796-798)Cgg>Agg	p.R266R	DOC2A_ENST00000564944.1_Silent_p.R266R|DOC2A_ENST00000564979.1_Silent_p.R266R	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	266	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Interaction with UNC13D.				nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						AGCAGTCCCCGGCGCCGCGAG	0.662																																					p.R266R		Atlas-SNP	.											.	DOC2A	40	.	0			c.C796A						.						30	34	33					16																	30018188		2197	4300	6497	SO:0001819	synonymous_variant	8448	exon8			GTCCCCGGCGCCG	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"Synaptotagmins"	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.796C>A	chr16.hg19:g.30018188G>T		51.0	0.0		68.0	8.0	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Silent	SNP	ENST00000350119.4	hg19	CCDS10666.1																																																																																			.	.		0.662	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586		T	30018188	G	T	30018188	2	4	86	1	0	0	0	0	0	0	0	1	4685	1115	39	1		1	DOC2A	16	30018188	Silent	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	14086393	30018188	60336565	108	11602										
FBXL19	54620	hgsc.bcm.edu	37	chr16	30958514	30958514	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cgggccccctggccccttccGctgccctgaggagaagctgc	13	18	0	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr16:30958514G>A	ENST00000380310.2	+	11	2206	c.2048G>A	c.(2047-2049)cGc>cAc	p.R683H	ORAI3_ENST00000318663.4_5'Flank|ORAI3_ENST00000562699.1_5'Flank|FBXL19_ENST00000471231.2_Missense_Mutation_p.R371H|ORAI3_ENST00000566237.1_5'Flank|AC135048.13_ENST00000566056.1_RNA|FBXL19_ENST00000562319.1_Missense_Mutation_p.R663H|FBXL19_ENST00000565690.1_Missense_Mutation_p.R547H|FBXL19_ENST00000338343.4_Missense_Mutation_p.R663H	NM_001099784.2	NP_001093254.2	Q6PCT2	FXL19_HUMAN	F-box and leucine-rich repeat protein 19	683					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)	SCF ubiquitin ligase complex (GO:0019005)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						GGCCCCTTCCGCTGCCCTGAG	0.697																																					p.R683H		Atlas-SNP	.											.	FBXL19	74	.	0			c.G2048A						.						10	13	12					16																	30958514		1861	4071	5932	SO:0001583	missense	54620	exon11			CCTTCCGCTGCCC	AK127701	CCDS45465.1, CCDS73873.1	16p11.2	2014-02-20			ENSG00000099364	ENSG00000099364		"F-boxes / Leucine-rich repeats"	25300	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1C"	609085					Standard	NM_001099784		Approved	DKFZp434K0410, Fbl19, JHDM1C, CXXC11	uc002eab.2	Q6PCT2	OTTHUMG00000132403	ENST00000380310.2:c.2048G>A	chr16.hg19:g.30958514G>A	ENSP00000369666:p.Arg683His	14.0	0.0		24.0	9.0	NM_001099784	A8MT10|Q8N789|Q9NT14	Missense_Mutation	SNP	ENST00000380310.2	hg19	CCDS45465.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.534276	0.45073	.	.	ENSG00000099364	ENST00000338343;ENST00000380310	T;T	0.24723	1.84;2.17	5.16	5.16	0.70880	.	0.259655	0.26499	N	0.024036	T	0.23330	0.0564	N	0.08118	0	0.38690	D	0.952749	D;D	0.71674	0.998;0.985	P;P	0.61070	0.883;0.619	T	0.10451	-1.0629	10	0.18276	T	0.48	-14.6679	11.0036	0.47620	0.0877:0.0:0.9123:0.0	.	683;640	Q6PCT2;Q6PCT2-2	FXL19_HUMAN;.	H	663;683	ENSP00000339712:R663H;ENSP00000369666:R683H	ENSP00000339712:R663H	R	+	2	0	FBXL19	30866015	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.387000	0.44389	2.398000	0.81561	0.555000	0.69702	CGC	.	.		0.697	FBXL19-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_019085		A	30958514	G	A	30958514	3	1	86	1	0	0	0	0	1	0	0	0	5723	1087	38	1	2090	1	FBXL19	16	30958514	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	940326	30958514	59396239	109	11603										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31426269	31426269	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cccctccccccagaacctgcGtcctgtgctggccgtgggct	11	19	0	1	rs200483957		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr16:31426269G>A	ENST00000389202.2	+	18	2289	c.2240G>A	c.(2239-2241)cGt>cAt	p.R747H		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	747					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CAGAACCTGCGTCCTGTGCTG	0.547																																					p.R747H		Atlas-SNP	.											.	ITGAD	154	.	0			c.G2240A						.	G	HIS/ARG	0,4394		0,0,2197	115	103	107		2240	3	0.5	16		107	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ITGAD	NM_005353.2	29	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	benign	747/1162	31426269	1,12993	2197	4300	6497	SO:0001583	missense	3681	exon18			ACCTGCGTCCTGT	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.2240G>A	chr16.hg19:g.31426269G>A	ENSP00000373854:p.Arg747His	92.0	0.0		110.0	50.0	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	G	8.869	0.948792	0.18356	0.0	1.16E-4	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.46819	0.86	5.03	3.04	0.35103	Integrin alpha-2 (1);	.	.	.	.	T	0.46151	0.1378	M	0.80422	2.495	0.20764	N	0.999857	B;B	0.34226	0.443;0.443	B;B	0.27715	0.082;0.082	T	0.41197	-0.9522	9	0.56958	D	0.05	.	8.1469	0.31117	0.1879:0.0:0.8121:0.0	.	763;747	Q59H14;Q13349	.;ITAD_HUMAN	H	763;747	ENSP00000373854:R747H	ENSP00000373854:R747H	R	+	2	0	ITGAD	31333770	0.000000	0.05858	0.542000	0.28115	0.127000	0.20565	-0.442000	0.06871	0.524000	0.28502	0.195000	0.17529	CGT	.	.		0.547	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		A	31426269	G	A	31426269	3	1	86	1	0	0	0	0	1	0	0	0	7893	1145	40	1	2310	1	ITGAD	16	31426269	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	467755	31426269	58928484	110	11604										
SLC6A4	6532	hgsc.bcm.edu	37	chr17	28530206	28530206	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gtacctctttaaatgtccctGgagtgatgatcaaccgataa	8	9	2	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr17:28530206G>A	ENST00000401766.2	-	13	2314	c.1802C>T	c.(1801-1803)cCa>cTa	p.P601L	RP11-354P11.4_ENST00000581633.1_RNA|SLC6A4_ENST00000261707.3_Missense_Mutation_p.P601L			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	601					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	AAATGTCCCTGGAGTGATGAT	0.373																																					p.P601L		Atlas-SNP	.											.	SLC6A4	60	.	0			c.C1802T						.						145	137	139					17																	28530206		2203	4300	6503	SO:0001583	missense	6532	exon14			GTCCCTGGAGTGA	L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"Solute carriers"	11050	protein-coding gene	gene with protein product	"serotonin transporter 1"	182138	"solute carrier family 6 (neurotransmitter transporter, serotonin), member 4", "5-hydroxytryptamine (serotonin) transporter", "obsessive-compulsive disorder 1"	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.1802C>T	chr17.hg19:g.28530206G>A	ENSP00000385822:p.Pro601Leu	135.0	0.0		196.0	13.0	NM_001045	Q5EE02	Missense_Mutation	SNP	ENST00000401766.2	hg19	CCDS11256.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.355819	0.82243	.	.	ENSG00000108576	ENST00000394821;ENST00000401766;ENST00000261707	T;T	0.74421	-0.84;-0.84	6.17	6.17	0.99709	.	0.098249	0.64402	D	0.000001	T	0.69369	0.3103	N	0.08118	0	0.58432	D	0.999999	P	0.45011	0.848	P	0.50352	0.638	T	0.74487	-0.3649	10	0.66056	D	0.02	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	601	P31645	SC6A4_HUMAN	L	643;601;601	ENSP00000385822:P601L;ENSP00000261707:P601L	ENSP00000261707:P601L	P	-	2	0	SLC6A4	25554332	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.151000	0.64875	2.941000	0.99782	0.655000	0.94253	CCA	.	.		0.373	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045		A	28530206	G	A	28530206	3	1	86	1	0	0	0	0	1	0	0	0	14701	1348	47	3	98	3	SLC6A4	17	28530206	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10		28530206	52665004	111	11605										
AP2B1	163	hgsc.bcm.edu	37	chr17	33925274	33925274	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	atatttgaactaaaagctgaActcaacaatgaaaagaaaga	6	5	1	5			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr17:33925274A>T	ENST00000262325.7	+	3	616	c.63A>T	c.(61-63)gaA>gaT	p.E21D	AP2B1_ENST00000589344.1_Missense_Mutation_p.E21D|AP2B1_ENST00000592545.1_Missense_Mutation_p.E21D|AP2B1_ENST00000538556.1_5'UTR|AP2B1_ENST00000537622.2_Missense_Mutation_p.E21D|AP2B1_ENST00000312678.8_Missense_Mutation_p.E21D	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	21					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		TAAAAGCTGAACTCAACAATG	0.403																																					p.E21D		Atlas-SNP	.											.	AP2B1	70	.	0			c.A63T						.						94	88	90					17																	33925274		2203	4300	6503	SO:0001583	missense	163	exon3			AGCTGAACTCAAC	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.63A>T	chr17.hg19:g.33925274A>T	ENSP00000262325:p.Glu21Asp	138.0	0.0		180.0	77.0	NM_001282	A6NJP3|P21851|Q7Z451|Q96J19	Missense_Mutation	SNP	ENST00000262325.7	hg19	CCDS32622.1	.	.	.	.	.	.	.	.	.	.	A	14.98	2.696408	0.48202	.	.	ENSG00000006125	ENST00000262325;ENST00000312678;ENST00000537622	T;T;T	0.25085	1.82;1.82;1.82	5.01	-3.25	0.05079	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.23766	0.0575	L	0.46947	1.48	0.80722	D	1	B;B;B	0.19331	0.035;0.015;0.0	B;B;B	0.33690	0.168;0.063;0.009	T	0.09530	-1.0670	10	0.44086	T	0.13	-9.3327	13.0692	0.59050	0.4582:0.0:0.5418:0.0	.	21;21;21	B4DWG4;P63010;P63010-2	.;AP2B1_HUMAN;.	D	21	ENSP00000262325:E21D;ENSP00000314414:E21D;ENSP00000437413:E21D	ENSP00000262325:E21D	E	+	3	2	AP2B1	30949387	0.997000	0.39634	1.000000	0.80357	0.902000	0.53008	0.438000	0.21559	-0.516000	0.06470	-1.409000	0.01127	GAA	.	.		0.403	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1			T	33925274	A	T	33925274	3	4	86	1	0	0	0	0	1	0	0	0	741	40	2	4	69	4	AP2B1	17	33925274	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	5395068	33925274	47269936	112	11606										
TUBG1	7283	hgsc.bcm.edu	37	chr17	40766524	40766524	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cccaccccaggtccacaagaGcttgcagaggatccgggaac	11	15	0	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr17:40766524G>A	ENST00000251413.3	+	10	1069	c.1007G>A	c.(1006-1008)aGc>aAc	p.S336N		NM_001070.4	NP_001061.2	P23258	TBG1_HUMAN	tubulin, gamma 1	336					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic spindle organization (GO:0000212)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	apical part of cell (GO:0045177)|cell leading edge (GO:0031252)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|nonmotile primary cilium (GO:0031513)|pericentriolar material (GO:0000242)|polar microtubule (GO:0005827)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Vinblastine(DB00570)	GTCCACAAGAGCTTGCAGAGG	0.652																																					p.S336N	Colon(20;114 698 11420 22864)	Atlas-SNP	.											.	TUBG1	25	.	0			c.G1007A						.						43	46	45					17																	40766524		2203	4300	6503	SO:0001583	missense	7283	exon10			ACAAGAGCTTGCA	BC000619	CCDS11433.1	17q21.31	2010-03-15	2000-01-20		ENSG00000131462	ENSG00000131462		"Tubulins"	12417	protein-coding gene	gene with protein product		191135	"tubulin, gamma polypeptide"	TUBG		1904010	Standard	NM_001070		Approved	TUBGCP1	uc002ian.3	P23258		ENST00000251413.3:c.1007G>A	chr17.hg19:g.40766524G>A	ENSP00000251413:p.Ser336Asn	158.0	0.0		182.0	17.0	NM_001070	Q53X79|Q9BW59	Missense_Mutation	SNP	ENST00000251413.3	hg19	CCDS11433.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.217680	0.79352	.	.	ENSG00000131462	ENST00000251413	D	0.84660	-1.88	4.06	4.06	0.47325	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94765	0.8310	H	0.96398	3.815	0.80722	D	1	D	0.71674	0.998	D	0.87578	0.998	D	0.96683	0.9505	10	0.87932	D	0	-24.4152	16.4351	0.83872	0.0:0.0:1.0:0.0	.	336	P23258	TBG1_HUMAN	N	336	ENSP00000251413:S336N	ENSP00000251413:S336N	S	+	2	0	TUBG1	38020050	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.630000	0.83225	2.104000	0.64026	0.563000	0.77884	AGC	.	.		0.652	TUBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450548.1	NM_001070		A	40766524	G	A	40766524	3	1	86	1	0	0	0	0	1	0	0	0	16779	971	34	3	1045	3	TUBG1	17	40766524	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	6841250	40766524	40428686	113	11607										
SPOP	8405	hgsc.bcm.edu	37	chr17	47677798	47677798	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aagggcactgtgctgaagccAgagagcggtatgcctcagcc	14	11	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr17:47677798A>T	ENST00000393328.2	-	11	1432	c.1067T>A	c.(1066-1068)cTg>cAg	p.L356Q	SPOP_ENST00000393331.3_Missense_Mutation_p.L356Q|SPOP_ENST00000347630.2_Missense_Mutation_p.L356Q|SPOP_ENST00000503676.1_Missense_Mutation_p.L356Q|SPOP_ENST00000504102.1_Missense_Mutation_p.L356Q	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	356					glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						TGCTGAAGCCAGAGAGCGGTA	0.522										Prostate(2;0.17)																											p.L356Q		Atlas-SNP	.											.	SPOP	91	.	0			c.T1067A						.						150	150	150					17																	47677798		2203	4300	6503	SO:0001583	missense	8405	exon10			GAAGCCAGAGAGC	AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"BTB/POZ domain containing"	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.1067T>A	chr17.hg19:g.47677798A>T	ENSP00000377001:p.Leu356Gln	103.0	0.0		146.0	69.0	NM_001007228	B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	hg19	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.199968	0.79015	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503536;ENST00000503676;ENST00000513872	T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.87767	0.6260	M	0.93763	3.455	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	D	0.90838	0.4721	10	0.87932	D	0	-6.5284	15.6986	0.77521	1.0:0.0:0.0:0.0	.	356	O43791	SPOP_HUMAN	Q	356;356;356;356;240;356;309	ENSP00000377001:L356Q;ENSP00000377004:L356Q;ENSP00000240327:L356Q;ENSP00000425905:L356Q;ENSP00000420908:L356Q	ENSP00000240327:L356Q	L	-	2	0	SPOP	45032797	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.959000	0.93110	2.371000	0.80710	0.533000	0.62120	CTG	.	.		0.522	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563		T	47677798	A	T	47677798	3	4	86	1	0	0	0	0	1	0	0	0	15099	188	7	4	61	4	SPOP	17	47677798	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	6911274	47677798	33517412	114	11608										
SLC16A6	9120	hgsc.bcm.edu	37	chr17	66270184	66270184	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ctaccagacggtgtccgaaaCgattgctcaggactgtggcg	13	11	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr17:66270184C>T	ENST00000327268.4	-	4	424	c.260G>A	c.(259-261)cGt>cAt	p.R87H	SLC16A6_ENST00000580666.1_Missense_Mutation_p.R87H|ARSG_ENST00000448504.2_Intron	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	87					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	GTGTCCGAAACGATTGCTCAG	0.542																																					p.R87H		Atlas-SNP	.											.	SLC16A6	56	.	0			c.G260A						.						81	70	74					17																	66270184		2203	4300	6503	SO:0001583	missense	9120	exon4			CCGAAACGATTGC	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"Solute carriers"	10927	protein-coding gene	gene with protein product		603880	"solute carrier family 16 (monocarboxylic acid transporters), member 6", "solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.260G>A	chr17.hg19:g.66270184C>T	ENSP00000319991:p.Arg87His	50.0	0.0		57.0	20.0	NM_001174166	Q6P1X3	Missense_Mutation	SNP	ENST00000327268.4	hg19	CCDS11675.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.174901	0.78564	.	.	ENSG00000108932	ENST00000327268	T	0.65549	-0.16	5.8	4.84	0.62591	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.114238	0.64402	D	0.000007	T	0.62356	0.2421	M	0.73319	2.225	0.58432	D	0.999999	P	0.50617	0.937	B	0.43754	0.43	T	0.62469	-0.6848	10	0.25106	T	0.35	.	13.6225	0.62144	0.0:0.9266:0.0:0.0734	.	87	O15403	MOT7_HUMAN	H	87	ENSP00000319991:R87H	ENSP00000319991:R87H	R	-	2	0	SLC16A6	63781779	1.000000	0.71417	0.004000	0.12327	0.609000	0.37215	4.440000	0.59975	1.453000	0.47775	0.655000	0.94253	CGT	.	.		0.542	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694		T	66270184	C	T	66270184	3	4	86	1	0	0	0	0	1	0	0	0	14427	536	19	1	1327	1	SLC16A6	17	66270184	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	18592386	66270184	14925026	115	11609										
FBF1	85302	hgsc.bcm.edu	37	chr17	73915917	73915917	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ctctccggagccgctcctccCgttgctggtacgatgtttct	10	15	2	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr17:73915917C>A	ENST00000586717.1	-	19	2201	c.1928G>T	c.(1927-1929)cGg>cTg	p.R643L	FBF1_ENST00000389570.4_Missense_Mutation_p.R643L|FBF1_ENST00000319129.5_Missense_Mutation_p.R642L			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	643					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						CCGCTCCTCCCGTTGCTGGTA	0.617																																					p.R642L		Atlas-SNP	.											.	FBF1	48	.	0			c.G1925T						.						92	92	92					17																	73915917		2029	4188	6217	SO:0001583	missense	85302	exon19			TCCTCCCGTTGCT	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.1928G>T	chr17.hg19:g.73915917C>A	ENSP00000465132:p.Arg643Leu	110.0	0.0		137.0	51.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	C	19.17	3.775097	0.70107	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.21191	2.02;2.02	5.15	4.18	0.49190	.	.	.	.	.	T	0.44746	0.1308	M	0.75264	2.295	0.43965	D	0.996644	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.98;1.0;0.999	T	0.35201	-0.9798	9	0.36615	T	0.2	-27.4853	13.2587	0.60093	0.0:0.9225:0.0:0.0775	.	657;643;642	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	L	643;643;642;656	ENSP00000374221:R643L;ENSP00000324292:R642L	ENSP00000324292:R642L	R	-	2	0	FBF1	71427512	0.996000	0.38824	0.995000	0.50966	0.321000	0.28281	5.135000	0.64777	1.184000	0.42957	-0.136000	0.14681	CGG	.	.		0.617	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		A	73915917	C	A	73915917	3	1	86	1	0	0	0	0	1	0	0	0	5703	652	23	1	1520	1	FBF1	17	73915917	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	7645733	73915917	7279293	116	11610										
TMC6	11322	hgsc.bcm.edu	37	chr17	76120679	76120679	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gggtgggaaggcgacctgagGgcccatgatgaaggccacca	17	10	0	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr17:76120679G>T	ENST00000590602.1	-	8	976	c.817C>A	c.(817-819)Cct>Act	p.P273T	TMC6_ENST00000591436.1_5'Flank|TMC6_ENST00000322914.3_Missense_Mutation_p.P273T|TMC6_ENST00000589553.1_Missense_Mutation_p.P46T|TMC6_ENST00000392467.3_Missense_Mutation_p.P273T|TMC6_ENST00000592076.1_5'Flank|TMC6_ENST00000322933.4_5'UTR|TMC6_ENST00000306591.7_Missense_Mutation_p.P273T			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	273					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GCGACCTGAGGGCCCATGATG	0.662																																					p.P273T		Atlas-SNP	.											.	TMC6	42	.	0			c.C817A						.						17	19	18					17																	76120679		2182	4237	6419	SO:0001583	missense	11322	exon8			CCTGAGGGCCCAT	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"epidermodysplasia verruciformis 1"	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.817C>A	chr17.hg19:g.76120679G>T	ENSP00000465261:p.Pro273Thr	41.0	0.0		60.0	22.0	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	hg19	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	G	9.668	1.146041	0.21288	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000306591	T;T;T	0.62232	0.04;0.04;0.04	3.64	1.5	0.22942	.	0.614231	0.15341	N	0.267532	T	0.74313	0.3700	M	0.84156	2.68	0.53005	D	0.999961	B;D;D;B;D	0.71674	0.358;0.985;0.985;0.081;0.998	B;P;P;B;D	0.65010	0.08;0.795;0.733;0.015;0.931	T	0.71738	-0.4502	10	0.52906	T	0.07	-9.6633	6.3986	0.21626	0.0:0.3705:0.4436:0.1859	.	110;273;46;273;273	B4E003;Q7Z403-2;Q7Z403-4;B3KTU5;Q7Z403	.;.;.;.;TMC6_HUMAN	T	273	ENSP00000313408:P273T;ENSP00000376260:P273T;ENSP00000306405:P273T	ENSP00000306405:P273T	P	-	1	0	TMC6	73632274	0.927000	0.31430	0.515000	0.27774	0.007000	0.05969	1.360000	0.34125	0.493000	0.27837	-0.502000	0.04539	CCT	.	.		0.662	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			T	76120679	G	T	76120679	3	4	86	1	0	0	0	0	1	0	0	0	16004	1232	43	3	1652	3	TMC6	17	76120679	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	2204762	76120679	5074531	117	11611										
FASN	2194	hgsc.bcm.edu	37	chr17	80047248	80047248	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cctcagctgctccacgaactCaaacaccggggcctggacat	9	16	2	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr17:80047248C>A	ENST00000306749.2	-	13	2196	c.1978G>T	c.(1978-1980)Gag>Tag	p.E660*		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	660	Acyl and malonyl transferases. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	TCCACGAACTCAAACACCGGG	0.642																																					p.E660X	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G1978T						.						54	54	54					17																	80047248		2202	4299	6501	SO:0001587	stop_gained	2194	exon13			CGAACTCAAACAC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.1978G>T	chr17.hg19:g.80047248C>A	ENSP00000304592:p.Glu660*	74.0	0.0		120.0	19.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Nonsense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	38	6.758981	0.97817	.	.	ENSG00000169710	ENST00000306749	.	.	.	4.4	-2.35	0.06684	.	0.628162	0.14977	N	0.287497	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	-8.453	6.412	0.21696	0.0:0.3849:0.1295:0.4856	.	.	.	.	X	660	.	ENSP00000304592:E660X	E	-	1	0	FASN	77640537	0.001000	0.12720	0.003000	0.11579	0.003000	0.03518	-0.179000	0.09768	-0.244000	0.09639	0.462000	0.41574	GAG	.	.		0.642	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80047248	C	A	80047248	4	1	86	1	0	0	0	0	0	1	0	0	5691	835	29	3	5681	3	FASN	17	80047248	Nonsense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	3926569	80047248	1147962	118	11612										
ZNF397OS	100101467	hgsc.bcm.edu	37	chr18	32843982	32843982	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cttcctctccattctctggcCgatgctctcgcagccaagct	7	17	3	0	rs368624179		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr18:32843982C>T	ENST00000420878.3	-	3	790	c.335G>A	c.(334-336)cGg>cAg	p.R112Q	ZSCAN30_ENST00000333206.5_Missense_Mutation_p.R112Q|ZSCAN30_ENST00000589178.1_Missense_Mutation_p.R112Q|ZSCAN30_ENST00000601405.1_Intron|ZNF397_ENST00000589420.1_Intron|ZSCAN30_ENST00000592278.1_Missense_Mutation_p.R112Q|ZSCAN30_ENST00000383091.2_Missense_Mutation_p.R112Q	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	112	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(3)|urinary_tract(1)	9						ATTCTCTGGCCGATGCTCTCG	0.527																																					p.R112Q		Atlas-SNP	.											.	ZSCAN30	34	.	0			c.G335A						.	C	GLN/ARG,GLN/ARG	0,3136		0,0,1568	58	56	57		335,335	-2.5	0	18		57	1,7163		0,1,3581	no	missense,missense	ZSCAN30	NM_001112734.2,NM_001166012.1	43,43	0,1,5149	TT,TC,CC		0.014,0.0,0.0097	benign,benign	112/495,112/495	32843982	1,10299	1568	3582	5150	SO:0001583	missense	100101467	exon3			TCTGGCCGATGCT	AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"-", "Zinc fingers, C2H2-type"	33517	protein-coding gene	gene with protein product			"zinc finger protein 397 opposite strand", "ZNF397 opposite strand"	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.335G>A	chr18.hg19:g.32843982C>T	ENSP00000392371:p.Arg112Gln	223.0	0.0		352.0	17.0	NM_001166012	B4E0N0|Q6ZNB3|Q96PN3	Missense_Mutation	SNP	ENST00000420878.3	hg19	CCDS42427.1	.	.	.	.	.	.	.	.	.	.	C	7.519	0.656308	0.14580	0.0	1.4E-4	ENSG00000186814	ENST00000420878;ENST00000333206;ENST00000360932;ENST00000383091	T;T;T	0.05855	3.38;3.38;3.38	4.6	-2.48	0.06423	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.04679	0.0127	L	0.31120	0.905	0.09310	N	1	B;B	0.18166	0.026;0.001	B;B	0.13407	0.009;0.005	T	0.42632	-0.9440	9	0.24483	T	0.36	.	9.7917	0.40710	0.0:0.3334:0.0:0.6666	.	112;112	C9JCM2;Q86W11	.;ZSC30_HUMAN	Q	112;112;69;112	ENSP00000392371:R112Q;ENSP00000329738:R112Q;ENSP00000372569:R112Q	ENSP00000329738:R112Q	R	-	2	0	ZSCAN30	31097980	0.000000	0.05858	0.000000	0.03702	0.915000	0.54546	-1.800000	0.01744	-0.685000	0.05177	-0.143000	0.13931	CGG	.	.		0.527	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734		T	32843982	C	T	32843982	3	4	86	1	0	0	0	0	1	0	0	0	17899	652	23	1	1161	1	ZNF397OS	18	32843982	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10		32843982	45233266	119	11613										
MYO5B	4645	hgsc.bcm.edu	37	chr18	47500944	47500944	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tccatctgactgtgctccacCcctagcagtcggcagaagtt	9	14	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr18:47500944C>T	ENST00000285039.7	-	10	1397	c.1098G>A	c.(1096-1098)ggG>ggA	p.G366G		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	366	Myosin motor.				endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TGTGCTCCACCCCTAGCAGTC	0.587																																					p.G366G		Atlas-SNP	.											.	MYO5B	178	.	0			c.G1098A						.						142	140	141					18																	47500944		2129	4252	6381	SO:0001819	synonymous_variant	4645	exon10			CTCCACCCCTAGC	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.1098G>A	chr18.hg19:g.47500944C>T		105.0	0.0		133.0	52.0	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	hg19	CCDS42436.1																																																																																			.	.		0.587	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			T	47500944	C	T	47500944	2	4	86	1	0	0	0	0	0	0	0	1	10088	610	22	3		3	MYO5B	18	47500944	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	14656962	47500944	30576304	120	11614										
SH3GL1	6455	hgsc.bcm.edu	37	chr19	4361758	4361758	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gtcgttctcgggctcgaagtCgtacagcgccttgcagctcg	13	13	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr19:4361758C>G	ENST00000269886.3	-	10	1124	c.946G>C	c.(946-948)Gac>Cac	p.D316H	SH3GL1_ENST00000598564.1_Missense_Mutation_p.D252H|SH3GL1_ENST00000417295.2_Missense_Mutation_p.D268H|AC007292.6_ENST00000594444.1_RNA	NM_003025.3	NP_003016.1	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	316	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.			D -> G (in Ref. 5; BAG61213). {ECO:0000305}.	central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|endosome (GO:0005768)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|endometrium(2)|kidney(16)|large_intestine(3)|lung(2)|ovary(2)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		GGCTCGAAGTCGTACAGCGCC	0.677			T	MLL	AL																																p.D316H	NSCLC(94;1152 2133 30346 33362)	Atlas-SNP	.		Dom	yes		19	19p13.3	6455	SH3-domain GRB2-like 1 (EEN)		L	.	SH3GL1	52	.	0			c.G946C						.						72	57	62					19																	4361758		2203	4300	6503	SO:0001583	missense	6455	exon10			CGAAGTCGTACAG		CCDS32874.1, CCDS56076.1, CCDS59335.1	19p13.3	2008-07-22							10830	protein-coding gene	gene with protein product	"extra 11-19 leukemia fusion", "fusion partner of MLL", "SH3-containing Grb-2-like 1 protein", "SH3-containing protein EEN", "SH3 domain GRB2-like 1"	601768				9169142	Standard	NM_003025		Approved	SH3P8, SH3D2B, CNSA1, EEN, MGC111371	uc002maj.3	Q99961		ENST00000269886.3:c.946G>C	chr19.hg19:g.4361758C>G	ENSP00000269886:p.Asp316His	54.0	0.0		50.0	42.0	NM_003025	B4DRA1|E7EVZ4|M0QZV5|Q99668	Missense_Mutation	SNP	ENST00000269886.3	hg19	CCDS32874.1	.	.	.	.	.	.	.	.	.	.	.	23.1	4.373428	0.82573	.	.	ENSG00000141985	ENST00000269886;ENST00000417295	T;T	0.67698	-0.28;-0.28	3.9	3.9	0.45041	Src homology-3 domain (5);	0.000000	0.85682	D	0.000000	D	0.86468	0.5940	H	0.95645	3.7	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.91635	0.999;0.988;0.988	D	0.90934	0.4792	10	0.87932	D	0	-1.3315	15.0282	0.71684	0.0:1.0:0.0:0.0	.	268;316;316	E7EVZ4;Q6FGM0;Q99961	.;.;SH3G1_HUMAN	H	316;268	ENSP00000269886:D316H;ENSP00000404568:D268H	ENSP00000269886:D316H	D	-	1	0	SH3GL1	4312758	1.000000	0.71417	0.959000	0.39883	0.736000	0.42039	7.486000	0.81215	1.998000	0.58463	0.511000	0.50034	GAC	.	.		0.677	SH3GL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458302.1	NM_003025		G	4361758	C	G	4361758	3	3	86	1	0	0	0	0	1	0	0	0	14265	884	31	4	164	4	SH3GL1	19	4361758	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10		4361758	54767225	121	11615										
MUC16	94025	hgsc.bcm.edu	37	chr19	9074278	9074278	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	agctccagtaggacctgtttGggtggtgatggtcactcctg	14	9	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr19:9074278G>A	ENST00000397910.4	-	3	13371	c.13168C>T	c.(13168-13170)Caa>Taa	p.Q4390*		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4392	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGACCTGTTTGGGTGGTGATG	0.458																																					p.Q4390X		Atlas-SNP	.											.	MUC16	4315	.	0			c.C13168T						.						135	131	132					19																	9074278		2040	4183	6223	SO:0001587	stop_gained	94025	exon3			CTGTTTGGGTGGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.13168C>T	chr19.hg19:g.9074278G>A	ENSP00000381008:p.Gln4390*	529.0	0.0		395.0	36.0	NM_024690	Q6ZQW5|Q96RK2	Nonsense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	54	22.026602	0.99945	.	.	ENSG00000181143	ENST00000397910	.	.	.	1.58	0.443	0.16587	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	5.605	0.17374	0.0:0.3505:0.6495:0.0	.	.	.	.	X	4390	.	ENSP00000381008:Q4390X	Q	-	1	0	MUC16	8935278	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	0.087000	0.14958	0.199000	0.20427	0.305000	0.20034	CAA	.	.		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9074278	G	A	9074278	4	1	86	1	0	0	0	0	0	1	0	0	9982	1357	47	3	30683	3	MUC16	19	9074278	Nonsense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	4712520	9074278	50054705	122	11616										
OR7E24	26648	hgsc.bcm.edu	37	chr19	9362317	9362317	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ctaatttcttctgtgaccctTctcaactcctccaccttagg	4	15	3	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr19:9362317T>C	ENST00000456448.1	+	1	712	c.598T>C	c.(598-600)Tct>Cct	p.S200P		NM_001079935.1	NP_001073404.1	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E, member 24	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)	16						CTGTGACCCTTCTCAACTCCT	0.413																																					p.S200P		Atlas-SNP	.											.	OR7E24	48	.	0			c.T598C						.						69	72	71					19																	9362317		1945	4144	6089	SO:0001583	missense	26648	exon1			GACCCTTCTCAAC	Y10529	CCDS45955.1	19p13.2	2012-08-09	2004-03-04	2004-03-05		ENSG00000237521		"GPCR / Class A : Olfactory receptors"	8396	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily E, member 24 pseudogene"	OR7E24P		9268701	Standard	NM_001079935		Approved	OR19-8, HSHT2, OR7E24Q	uc002mlb.1	Q6IFN5		ENST00000456448.1:c.598T>C	chr19.hg19:g.9362317T>C	ENSP00000387523:p.Ser200Pro	307.0	0.0		271.0	18.0	NM_001079935	B9EJD9|Q9UPJ1	Missense_Mutation	SNP	ENST00000456448.1	hg19	CCDS45955.1	.	.	.	.	.	.	.	.	.	.	t	7.759	0.705086	0.15172	.	.	ENSG00000237521	ENST00000456448	T	0.00026	8.94	2.21	-4.42	0.03579	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00109	0.0003	N	0.13043	0.29	0.09310	N	1	D	0.71674	0.998	D	0.74674	0.984	T	0.44742	-0.9308	9	0.30854	T	0.27	.	0.6522	0.00828	0.2432:0.2341:0.3333:0.1894	.	200	Q6IFN5	O7E24_HUMAN	P	200	ENSP00000387523:S200P	ENSP00000387523:S200P	S	+	1	0	OR7E24	9223317	0.000000	0.05858	0.002000	0.10522	0.012000	0.07955	-3.223000	0.00551	-1.444000	0.01950	0.358000	0.22013	TCT	.	.		0.413	OR7E24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449006.1			C	9362317	T	C	9362317	3	2	86	1	0	0	0	0	1	0	0	0	11230	1783	62	2	600	2	OR7E24	19	9362317	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	288039	9362317	49766666	123	11617										
ZNF69	7620	hgsc.bcm.edu	37	chr19	12014498	12014498	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gtgatgctggaaactttcagGaacctgacctctgtaggtaa	11	8	2	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr19:12014498G>C	ENST00000429654.2	+	2	314	c.174G>C	c.(172-174)agG>agC	p.R58S	ZNF69_ENST00000340180.5_Missense_Mutation_p.R44S			Q9UC07	ZNF69_HUMAN	zinc finger protein 69	58	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|skin(2)	4				Lung(535;0.011)		AAACTTTCAGGAACCTGACCT	0.443																																					p.R44S		Atlas-SNP	.											.	ZNF69	27	.	0			c.G132C						.						145	141	142					19																	12014498		2203	4300	6503	SO:0001583	missense	7620	exon2			TTTCAGGAACCTG	X60076	CCDS32914.1	19p13.2	2013-01-08	2006-05-12		ENSG00000198429	ENSG00000198429		"Zinc fingers, C2H2-type", "-"	13138	protein-coding gene	gene with protein product		194543	"zinc finger protein 69 (Cos5)"			1639391	Standard	NM_021915		Approved	Cos5	uc002mst.4	Q9UC07	OTTHUMG00000156526	ENST00000429654.2:c.174G>C	chr19.hg19:g.12014498G>C	ENSP00000402985:p.Arg58Ser	385.0	0.0		679.0	386.0	NM_021915	Q86VA7	Missense_Mutation	SNP	ENST00000429654.2	hg19		.	.	.	.	.	.	.	.	.	.	g	8.952	0.968472	0.18659	.	.	ENSG00000198429	ENST00000429654;ENST00000445911;ENST00000340180	T;T;T	0.01629	4.72;4.72;4.72	1.04	-1.38	0.09027	.	.	.	.	.	T	0.03477	0.0100	L	0.53671	1.685	0.19300	N	0.99997	B	0.31026	0.304	B	0.43658	0.426	T	0.45071	-0.9286	9	0.72032	D	0.01	.	5.24	0.15467	0.3966:0.0:0.6034:0.0	.	44	C9JR48	.	S	58;44;44	ENSP00000402985:R58S;ENSP00000388784:R44S;ENSP00000345333:R44S	ENSP00000345333:R44S	R	+	3	2	ZNF69	11875498	0.001000	0.12720	0.034000	0.17996	0.362000	0.29581	0.353000	0.20130	-0.409000	0.07553	0.398000	0.26397	AGG	.	.		0.443	ZNF69-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000344082.1	NM_021915		C	12014498	G	C	12014498	3	2	86	1	0	0	0	0	1	0	0	0	18110	1165	41	4	138	4	ZNF69	19	12014498	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	2652181	12014498	47114485	124	11618										
ZNF253	56242	hgsc.bcm.edu	37	chr19	20003387	20003387	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aactctaactacacataagaGaattcatactggagagaaac	6	8	2	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr19:20003387G>A	ENST00000589717.1	+	4	1423	c.1331G>A	c.(1330-1332)aGa>aAa	p.R444K	AC011477.1_ENST00000578823.1_RNA|ZNF253_ENST00000355650.4_Missense_Mutation_p.R368K|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	444					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACACATAAGAGAATTCATACT	0.358																																					p.R444K		Atlas-SNP	.											ZNF492,NS,carcinoma,0,2	ZNF253	99	.	0			c.G1331A						.						43	47	46					19																	20003387		2132	4271	6403	SO:0001583	missense	56242	exon4			ATAAGAGAATTCA	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"Zinc fingers, C2H2-type", "-"	13497	protein-coding gene	gene with protein product		606954	"zinc finger protein 411"	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.1331G>A	chr19.hg19:g.20003387G>A	ENSP00000468720:p.Arg444Lys	122.0	0.0		233.0	15.0	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Missense_Mutation	SNP	ENST00000589717.1	hg19	CCDS42532.1	.	.	.	.	.	.	.	.	.	.	g	2.517	-0.311623	0.05422	.	.	ENSG00000256771	ENST00000355650	.	.	.	0.876	-1.75	0.08031	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17195	0.0413	N	0.13003	0.285	0.25324	N	0.98909	B	0.06786	0.001	B	0.11329	0.006	T	0.27226	-1.0080	7	.	.	.	.	5.676	0.17749	0.0:0.0:0.686:0.314	.	444	O75346	ZN253_HUMAN	K	444	.	.	R	+	2	0	ZNF253	19864387	0.000000	0.05858	0.018000	0.16275	0.018000	0.09664	0.158000	0.16422	-0.892000	0.03935	-0.901000	0.02856	AGA	.	.		0.358	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047		A	20003387	G	A	20003387	3	1	86	1	0	0	0	0	1	0	0	0	17812	942	33	3	1345	3	ZNF253	19	20003387	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	7988889	20003387	39125596	125	11619										
ZNF253	56242	hgsc.bcm.edu	37	chr19	20003414	20003414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tactggagagaaaccttacaAatgtgaagaatgtggcaaag	11	5	0	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr19:20003414A>G	ENST00000589717.1	+	4	1450	c.1358A>G	c.(1357-1359)aAa>aGa	p.K453R	AC011477.1_ENST00000578823.1_RNA|ZNF253_ENST00000355650.4_Missense_Mutation_p.K377R|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	453					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AAACCTTACAAATGTGAAGAA	0.363																																					p.K453R		Atlas-SNP	.											.	ZNF253	99	.	0			c.A1358G						.						47	53	51					19																	20003414		2115	4267	6382	SO:0001583	missense	56242	exon4			CTTACAAATGTGA	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"Zinc fingers, C2H2-type", "-"	13497	protein-coding gene	gene with protein product		606954	"zinc finger protein 411"	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.1358A>G	chr19.hg19:g.20003414A>G	ENSP00000468720:p.Lys453Arg	150.0	0.0		316.0	28.0	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Missense_Mutation	SNP	ENST00000589717.1	hg19	CCDS42532.1	.	.	.	.	.	.	.	.	.	.	a	6.633	0.485302	0.12641	.	.	ENSG00000256771	ENST00000355650	.	.	.	0.876	0.876	0.19138	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31670	0.0804	M	0.65498	2.005	0.18873	N	0.999982	P	0.42078	0.77	B	0.40199	0.322	T	0.20174	-1.0283	7	.	.	.	.	2.9089	0.05730	0.5963:0.0:0.0:0.4036	.	453	O75346	ZN253_HUMAN	R	453	.	.	K	+	2	0	ZNF253	19864414	0.000000	0.05858	0.056000	0.19401	0.056000	0.15407	-1.607000	0.02070	0.251000	0.21505	0.248000	0.18094	AAA	.	.		0.363	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047		G	20003414	A	G	20003414	3	3	86	1	0	0	0	0	1	0	0	0	17812	14	1	2	1372	2	ZNF253	19	20003414	Missense_Mutation	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	27	20003414	39125569	126	11620										
ATP4A	495	hgsc.bcm.edu	37	chr19	36047867	36047867	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	catcagggacggtggcccggGgtgggtcaatcatggataca	16	9	3	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr19:36047867G>A	ENST00000262623.3	-	12	1845	c.1817C>T	c.(1816-1818)cCc>cTc	p.P606L		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	606					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	GGTGGCCCGGGGTGGGTCAAT	0.592																																					p.P606L		Atlas-SNP	.											.	ATP4A	123	.	0			c.C1817T						.						67	63	64					19																	36047867		2203	4300	6503	SO:0001583	missense	495	exon12			GCCCGGGGTGGGT		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.1817C>T	chr19.hg19:g.36047867G>A	ENSP00000262623:p.Pro606Leu	84.0	0.0		126.0	10.0	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.973527	0.92919	.	.	ENSG00000105675	ENST00000262623	D	0.95272	-3.66	4.93	4.93	0.64822	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.64402	D	0.000005	D	0.96990	0.9017	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97432	1.0016	10	0.87932	D	0	.	15.671	0.77274	0.0:0.0:1.0:0.0	.	606	P20648	ATP4A_HUMAN	L	606	ENSP00000262623:P606L	ENSP00000262623:P606L	P	-	2	0	ATP4A	40739707	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	9.623000	0.98386	2.562000	0.86427	0.591000	0.81541	CCC	.	.		0.592	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		A	36047867	G	A	36047867	3	1	86	1	0	0	0	0	1	0	0	0	1145	1232	43	3	1334	3	ATP4A	19	36047867	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	16044453	36047867	23081116	127	11621										
NFKBIB	4793	hgsc.bcm.edu	37	chr19	39395721	39395721	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tttcttctaggcttctcggcCggcactgagtacatggacct	10	12	3	1	rs142337920		TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr19:39395721C>A	ENST00000313582.5	+	2	280	c.246C>A	c.(244-246)gcC>gcA	p.A82A	NFKBIB_ENST00000392079.3_Silent_p.A50A|NFKBIB_ENST00000572515.1_Silent_p.A82A	NM_002503.4	NP_002494.2	Q15653	IKBB_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta	82					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|signal transduction (GO:0007165)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	8	all_cancers(60;4.39e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			GCTTCTCGGCCGGCACTGAGT	0.577																																					p.A82A	Pancreas(165;1492 2005 6979 7739 34483)	Atlas-SNP	.											.	NFKBIB	23	.	0			c.C246A						.						168	163	165					19																	39395721		2203	4300	6503	SO:0001819	synonymous_variant	4793	exon2			CTCGGCCGGCACT	L40407	CCDS12524.1, CCDS74362.1	19q13.1	2013-01-10				ENSG00000104825		"Ankyrin repeat domain containing"	7798	protein-coding gene	gene with protein product		604495				9763672	Standard	NM_002503		Approved	IKBB, TRIP9	uc002ojw.3	Q15653		ENST00000313582.5:c.246C>A	chr19.hg19:g.39395721C>A		214.0	0.0		326.0	130.0	NM_002503	A8K3F4|Q96BJ7	Silent	SNP	ENST00000313582.5	hg19	CCDS12524.1																																																																																			.	C|1.000;T|0.000		0.577	NFKBIB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438155.1	NM_002503		A	39395721	C	A	39395721	2	1	86	1	0	0	0	0	0	0	0	1	10387	639	23	1		1	NFKBIB	19	39395721	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	3347854	39395721	19733262	128	11622										
ZNF578	147660	hgsc.bcm.edu	37	chr19	53008031	53008031	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	actacaggaacctggaggctGtgggtgaggaaaatgtccct	14	8	0	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr19:53008031G>A	ENST00000421239.2	+	5	431	c.187G>A	c.(187-189)Gtg>Atg	p.V63M		NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	63	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		CCTGGAGGCTGTGGGTGAGGA	0.488																																					p.V63M		Atlas-SNP	.											.	.	.	.	0			c.G187A						.						80	89	86					19																	53008031		2203	4297	6500	SO:0001583	missense	147660	exon5			GAGGCTGTGGGTG	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.187G>A	chr19.hg19:g.53008031G>A	ENSP00000459216:p.Val63Met	89.0	0.0		101.0	47.0	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	hg19	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	8.400	0.841750	0.16963	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.29	-2.57	0.06248	.	.	.	.	.	T	0.39963	0.1098	L	0.49350	1.555	0.09310	N	1	D	0.58620	0.983	P	0.57776	0.827	T	0.26189	-1.0110	7	.	.	.	.	4.2396	0.10642	0.0:0.3577:0.3802:0.2621	.	63	G3V4F6	.	M	63	.	.	V	+	1	0	ZNF578	57699843	0.000000	0.05858	0.084000	0.20598	0.426000	0.31534	-1.278000	0.02809	-1.233000	0.02551	0.194000	0.17425	GTG	.	.		0.488	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		A	53008031	G	A	53008031	3	1	86	1	0	0	0	0	1	0	0	0	18025	1377	48	3	193	3	ZNF578	19	53008031	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	13612310	53008031	6120952	129	11623										
PAK7	57144	hgsc.bcm.edu	37	chr20	9525047	9525047	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aaggtagcctagaaatcaccTcaggggccatccagtaggga	12	10	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr20:9525047T>A	ENST00000378429.3	-	9	2384	c.1838A>T	c.(1837-1839)gAg>gTg	p.E613V	PAK7_ENST00000378423.1_Missense_Mutation_p.E613V|PAK7_ENST00000353224.5_Missense_Mutation_p.E613V	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	613	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			AGAAATCACCTCAGGGGCCAT	0.502																																					p.E613V		Atlas-SNP	.											.	PAK7	194	.	0			c.A1838T						.						123	112	116					20																	9525047		2203	4300	6503	SO:0001583	missense	57144	exon8			ATCACCTCAGGGG	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1838A>T	chr20.hg19:g.9525047T>A	ENSP00000367686:p.Glu613Val	134.0	0.0		64.0	42.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	T	33	5.210553	0.95069	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423	D;D;D	0.82167	-1.58;-1.58;-1.58	5.97	5.97	0.96955	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95310	0.8478	H	0.99249	4.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97385	0.9985	9	.	.	.	.	16.4608	0.84044	0.0:0.0:0.0:1.0	.	613	Q9P286	PAK7_HUMAN	V	613	ENSP00000367686:E613V;ENSP00000322957:E613V;ENSP00000367679:E613V	.	E	-	2	0	PAK7	9473047	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	7.988000	0.88194	2.288000	0.76882	0.533000	0.62120	GAG	.	.		0.502	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			A	9525047	T	A	9525047	3	1	86	1	0	0	0	0	1	0	0	0	11414	1551	54	4	333	4	PAK7	20	9525047	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10		9525047	53500473	130	11624										
FOXS1	2307	hgsc.bcm.edu	37	chr20	30432421	30432421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ccccaatgggtagccggagcCtccctggacagggaagccac	13	15	0	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr20:30432421C>T	ENST00000375978.3	-	1	999	c.925G>A	c.(925-927)Ggc>Agc	p.G309S		NM_004118.3	NP_004109.1	O43638	FOXS1_HUMAN	forkhead box S1	309					blood vessel development (GO:0001568)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|positive regulation of multicellular organism growth (GO:0040018)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	9						TAGCCGGAGCCTCCCTGGACA	0.647																																					p.G309S		Atlas-SNP	.											FOXS1,right_upper_lobe,carcinoma,0,1	FOXS1	29	.	0			c.G925A						.						37	38	38					20																	30432421		2203	4300	6503	SO:0001583	missense	2307	exon1			CGGAGCCTCCCTG	AF042831	CCDS13192.1	20q11.1-q11.2	2008-04-10	2008-04-10	2008-04-10	ENSG00000179772	ENSG00000179772		"Forkhead boxes"	3735	protein-coding gene	gene with protein product		602939	"forkhead (Drosophila)-like 18", "forkhead-like 18 (Drosophila)"	FKHL18		9325056, 17062144	Standard	NM_004118		Approved	FREAC10	uc002wwt.1	O43638	OTTHUMG00000032183	ENST00000375978.3:c.925G>A	chr20.hg19:g.30432421C>T	ENSP00000365145:p.Gly309Ser	138.0	1.0		235.0	12.0	NM_004118	Q96D28	Missense_Mutation	SNP	ENST00000375978.3	hg19	CCDS13192.1	.	.	.	.	.	.	.	.	.	.	C	8.173	0.792063	0.16258	.	.	ENSG00000179772	ENST00000375978	D	0.96992	-4.2	4.54	2.55	0.30701	.	0.273747	0.25692	N	0.028923	D	0.90249	0.6951	N	0.19112	0.55	0.09310	N	0.999999	B	0.10296	0.003	B	0.08055	0.003	T	0.81920	-0.0712	10	0.46703	T	0.11	.	6.9371	0.24472	0.0:0.6996:0.0:0.3004	.	309	O43638	FOXS1_HUMAN	S	309	ENSP00000365145:G309S	ENSP00000365145:G309S	G	-	1	0	FOXS1	29896082	0.000000	0.05858	0.750000	0.31169	0.337000	0.28794	-0.023000	0.12456	0.497000	0.27926	0.462000	0.41574	GGC	.	.		0.647	FOXS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078560.2	NM_004118		T	30432421	C	T	30432421	3	4	86	1	0	0	0	0	1	0	0	0	6043	681	24	3	71	3	FOXS1	20	30432421	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	20907374	30432421	32593099	131	11625										
CHD6	84181	hgsc.bcm.edu	37	chr20	40049753	40049753	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	ataaatcaattaattgctgaTctgatgacaggtttcttttg	7	5	3	3	rs140430642	byFrequency	TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr20:40049753T>A	ENST00000373233.3	-	31	5699	c.5522A>T	c.(5521-5523)gAt>gTt	p.D1841V		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1841					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				TAATTGCTGATCTGATGACAG	0.383																																					p.D1841V		Atlas-SNP	.											.	CHD6	312	.	0			c.A5522T						.						104	116	112					20																	40049753		2201	4300	6501	SO:0001583	missense	84181	exon31			TGCTGATCTGATG	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.5522A>T	chr20.hg19:g.40049753T>A	ENSP00000362330:p.Asp1841Val	116.0	0.0		89.0	54.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.521344	0.44866	.	.	ENSG00000124177	ENST00000373233	D	0.87103	-2.21	5.82	5.82	0.92795	.	0.317824	0.27060	N	0.021139	T	0.81009	0.4734	L	0.27053	0.805	0.80722	D	1	B	0.27559	0.181	B	0.24974	0.057	T	0.79502	-0.1777	10	0.72032	D	0.01	-6.9308	14.755	0.69557	0.0:0.0:0.0:1.0	.	1841	Q8TD26	CHD6_HUMAN	V	1841	ENSP00000362330:D1841V	ENSP00000362330:D1841V	D	-	2	0	CHD6	39483167	1.000000	0.71417	0.733000	0.30861	0.996000	0.88848	3.292000	0.51772	2.222000	0.72286	0.533000	0.62120	GAT	.	T|1.000;C|0.000		0.383	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40049753	T	A	40049753	3	1	86	1	0	0	0	0	1	0	0	0	3331	1435	50	4	2653	4	CHD6	20	40049753	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	9617332	40049753	22975767	132	11626										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58467323	58467323	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	atatttaggatgattttgttGctgattgtgtttcttgcaaa	9	3	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr20:58467323G>A	ENST00000357552.3	-	24	2311	c.2086C>T	c.(2086-2088)Caa>Taa	p.Q696*	SYCP2_ENST00000371001.2_Nonsense_Mutation_p.Q696*			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	696					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			TGATTTTGTTGCTGATTGTGT	0.343																																					p.Q696X		Atlas-SNP	.											.	SYCP2	204	.	0			c.C2086T						.						173	178	177					20																	58467323		2203	4300	6503	SO:0001587	stop_gained	10388	exon23			TTTGTTGCTGATT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.2086C>T	chr20.hg19:g.58467323G>A	ENSP00000350162:p.Gln696*	502.0	1.0		687.0	327.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Nonsense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.039507	0.93630	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	.	.	.	4.89	2.44	0.29823	.	0.919223	0.09243	N	0.828993	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	-6.7525	4.1694	0.10322	0.1611:0.2497:0.5892:0.0	.	.	.	.	X	696	.	ENSP00000350162:Q696X	Q	-	1	0	SYCP2	57900718	0.021000	0.18746	0.006000	0.13384	0.163000	0.22366	1.341000	0.33907	1.149000	0.42402	0.591000	0.81541	CAA	.	.		0.343	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		A	58467323	G	A	58467323	4	1	86	1	0	0	0	0	0	1	0	0	15447	1328	46	3	2594	3	SYCP2	20	58467323	Nonsense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	18417570	58467323	4558197	133	11627										
UCKL1	54963	hgsc.bcm.edu	37	chr20	62577849	62577849	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tgcgtgccgtgttcattgtaCcagggcggccgcccggcggt	16	13	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr20:62577849C>T	ENST00000354216.6	-	2	303	c.261G>A	c.(259-261)tgG>tgA	p.W87*	UCKL1_ENST00000492660.1_5'UTR|UCKL1_ENST00000369892.3_Nonsense_Mutation_p.W87*|UCKL1_ENST00000369908.5_Nonsense_Mutation_p.W72*|UCKL1_ENST00000358711.3_Nonsense_Mutation_p.W87*	NM_017859.3	NP_060329.2	Q9NWZ5	UCKL1_HUMAN	uridine-cytidine kinase 1-like 1	87					CTP salvage (GO:0044211)|UMP salvage (GO:0044206)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|uridine kinase activity (GO:0004849)			endometrium(3)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	8	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GTTCATTGTACCAGGGCGGCC	0.682																																					p.W87X		Atlas-SNP	.											.	UCKL1	28	.	0			c.G261A						.						55	50	52					20																	62577849		2201	4294	6495	SO:0001587	stop_gained	54963	exon2			ATTGTACCAGGGC	AK000524	CCDS13547.1, CCDS54479.1	20q13.33	2012-09-20	2004-07-13	2004-07-13	ENSG00000198276	ENSG00000198276			15938	protein-coding gene	gene with protein product		610866	"uridine kinase-like 1"	URKL1			Standard	NM_017859		Approved	FLJ20517	uc010gkn.3	Q9NWZ5	OTTHUMG00000033003	ENST00000354216.6:c.261G>A	chr20.hg19:g.62577849C>T	ENSP00000346155:p.Trp87*	91.0	0.0		128.0	20.0	NM_017859	B7Z8N2|Q5JWV0|Q70AQ5|Q8N524|Q9H3Z2	Nonsense_Mutation	SNP	ENST00000354216.6	hg19	CCDS13547.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372231	0.61624	.	.	ENSG00000198276	ENST00000354216;ENST00000369892;ENST00000358711;ENST00000369908;ENST00000418992	.	.	.	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.984	15.4917	0.75611	0.0:1.0:0.0:0.0	.	.	.	.	X	87;87;87;72;72	.	ENSP00000346155:W87X	W	-	3	0	UCKL1	62048293	1.000000	0.71417	1.000000	0.80357	0.013000	0.08279	7.328000	0.79160	2.063000	0.61619	0.313000	0.20887	TGG	.	.		0.682	UCKL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080236.1	NM_017859		T	62577849	C	T	62577849	4	4	86	1	0	0	0	0	0	1	0	0	16940	508	18	3	1441	3	UCKL1	20	62577849	Nonsense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	4110526	62577849	447671	134	11628										
NCAM2	4685	hgsc.bcm.edu	37	chr21	22664428	22664428	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tttgctttctttccagatcgGttcgctatgttagcaaacaa	7	9	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr21:22664428G>A	ENST00000400546.1	+	5	735	c.486G>A	c.(484-486)cgG>cgA	p.R162R	NCAM2_ENST00000535285.1_Silent_p.R187R|NCAM2_ENST00000486367.1_3'UTR|NCAM2_ENST00000284894.7_Silent_p.R20R	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	162	Ig-like C2-type 2.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		TTCCAGATCGGTTCGCTATGT	0.398																																					p.R162R		Atlas-SNP	.											.	NCAM2	220	.	0			c.G486A						.						124	114	117					21																	22664428		1848	4101	5949	SO:0001819	synonymous_variant	4685	exon5			AGATCGGTTCGCT		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.486G>A	chr21.hg19:g.22664428G>A		352.0	0.0		489.0	37.0	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Silent	SNP	ENST00000400546.1	hg19	CCDS42910.1																																																																																			.	.		0.398	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		A	22664428	G	A	22664428	2	1	86	1	0	0	0	0	0	0	0	1	10212	1248	44	3		3	NCAM2	21	22664428	Silent	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10		22664428	25465467	135	11629										
RNF160	26046	hgsc.bcm.edu	37	chr21	30354673	30354673	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gtatcaggtgtttcttttatAagatgatcctgcagcaccta	8	8	2	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr21:30354673A>G	ENST00000361371.5	-	5	673	c.594T>C	c.(592-594)ctT>ctC	p.L198L	LTN1_ENST00000389195.2_Silent_p.L244L|LTN1_ENST00000389194.2_Silent_p.L244L			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	198					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						TTTCTTTTATAAGATGATCCT	0.378																																					p.L244L		Atlas-SNP	.											.	LTN1	141	.	0			c.T732C						.						81	80	81					21																	30354673		2203	4300	6503	SO:0001819	synonymous_variant	26046	exon5			TTTTATAAGATGA	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"RING-type (C3HC4) zinc fingers"	13082	protein-coding gene	gene with protein product	"listerin"	613083	"chromosome 21 open reading frame 98", "zinc finger protein 294", "ring finger protein 160"	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.594T>C	chr21.hg19:g.30354673A>G		101.0	0.0		182.0	87.0	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Silent	SNP	ENST00000361371.5	hg19																																																																																				.	.		0.378	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		G	30354673	A	G	30354673	2	3	86	1	0	0	0	0	0	0	0	1	13470	349	13	2		2	RNF160	21	30354673	Silent	SNP	A	TCGA-DD-A113-01A-11D-A12Z-10	7690245	30354673	17775222	136	11630										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34067440	34067440	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	cattaaacctggtcccagctCgttcacagcttaatcttgaa	6	12	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr21:34067440C>T	ENST00000322229.7	-	4	631	c.632G>A	c.(631-633)cGa>cAa	p.R211Q	SYNJ1_ENST00000382491.3_Missense_Mutation_p.R211Q|SYNJ1_ENST00000357345.3_Missense_Mutation_p.R211Q|SYNJ1_ENST00000382499.2_Missense_Mutation_p.R250Q|SYNJ1_ENST00000433931.2_Missense_Mutation_p.R250Q			O43426	SYNJ1_HUMAN	synaptojanin 1	211	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						GGTCCCAGCTCGTTCACAGCT	0.383																																					p.R250Q		Atlas-SNP	.											.	SYNJ1	253	.	0			c.G749A						.						148	131	137					21																	34067440		2203	4300	6503	SO:0001583	missense	8867	exon5			CCAGCTCGTTCAC	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.632G>A	chr21.hg19:g.34067440C>T	ENSP00000322234:p.Arg211Gln	174.0	0.0		312.0	105.0	NM_203446	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	hg19	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	C	36	5.691462	0.96793	.	.	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229;ENST00000429236	T;T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04;0.04	4.96	4.96	0.65561	Synaptojanin, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.84884	0.5571	M	0.93150	3.385	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;1.0;0.999;0.996	D	0.89107	0.3493	10	0.87932	D	0	.	18.6311	0.91360	0.0:1.0:0.0:0.0	.	211;250;211;211;211	B9EGN3;C9JFZ1;O43426-2;O43426;O43426-4	.;.;.;SYNJ1_HUMAN;.	Q	211;211;250;250;211;211	ENSP00000371931:R211Q;ENSP00000349903:R211Q;ENSP00000371939:R250Q;ENSP00000409667:R250Q;ENSP00000322234:R211Q;ENSP00000413649:R211Q	ENSP00000322234:R211Q	R	-	2	0	SYNJ1	32989311	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.214000	0.77958	2.486000	0.83907	0.558000	0.71614	CGA	.	.		0.383	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	34067440	C	T	34067440	3	4	86	1	0	0	0	0	1	0	0	0	15467	884	31	1	4235	1	SYNJ1	21	34067440	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	3712767	34067440	14062455	137	11631										
SLC25A17	10478	hgsc.bcm.edu	37	chr22	41173261	41173261	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tttctttaaaagctgccgttTtaaaccttcataaaacatga	4	8	2	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr22:41173261T>C	ENST00000435456.2	-	6	701	c.568A>G	c.(568-570)Aaa>Gaa	p.K190E	SLC25A17_ENST00000542412.1_Missense_Mutation_p.K117E|SLC25A17_ENST00000402844.3_Missense_Mutation_p.K108E|SLC25A17_ENST00000544408.1_Missense_Mutation_p.K153E|SLC25A17_ENST00000491545.1_5'UTR	NM_006358.2	NP_006349.1	O43808	PM34_HUMAN	solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kDa), member 17	190					ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|cellular lipid metabolic process (GO:0044255)|coenzyme A transmembrane transport (GO:0035349)|FAD transmembrane transport (GO:0035350)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|fatty acid transport (GO:0015908)|NAD transport (GO:0043132)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)	integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|chaperone binding (GO:0051087)|coenzyme A transmembrane transporter activity (GO:0015228)|FAD transmembrane transporter activity (GO:0015230)|FMN transmembrane transporter activity (GO:0044610)|NAD transporter activity (GO:0051724)			central_nervous_system(1)|large_intestine(4)|lung(2)|skin(1)	8						AGCTGCCGTTTTAAACCTTCA	0.388																																					p.K190E		Atlas-SNP	.											.	SLC25A17	25	.	0			c.A568G						.						65	60	61					22																	41173261		2203	4300	6503	SO:0001583	missense	10478	exon6			GCCGTTTTAAACC	Y12860	CCDS14005.1, CCDS74868.1	22q13.2	2013-05-22	2002-08-29		ENSG00000100372	ENSG00000100372		"Solute carriers"	10987	protein-coding gene	gene with protein product	"peroxisomal membrane protein (34kD)"	606795	"solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kD), member 17"			9874197	Standard	NM_006358		Approved	PMP34	uc003azc.3	O43808	OTTHUMG00000151139	ENST00000435456.2:c.568A>G	chr22.hg19:g.41173261T>C	ENSP00000390722:p.Lys190Glu	262.0	0.0		195.0	73.0	NM_006358	A8KA59|Q5TFL0|Q9UGW8|Q9UGY7	Missense_Mutation	SNP	ENST00000435456.2	hg19	CCDS14005.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.858739	0.91433	.	.	ENSG00000100372	ENST00000435456;ENST00000402844;ENST00000544408;ENST00000542412	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73	5.86	4.81	0.61882	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.91898	0.7435	M	0.90542	3.125	0.80722	D	1	D;D;D	0.71674	0.994;0.998;0.998	D;D;D	0.73380	0.919;0.967;0.98	D	0.92770	0.6231	10	0.87932	D	0	-25.5221	12.5436	0.56186	0.1249:0.0:0.0:0.8751	.	117;153;190	F5GYD1;B4DU97;O43808	.;.;PM34_HUMAN	E	190;108;153;117	ENSP00000390722:K190E;ENSP00000385303:K108E;ENSP00000438355:K153E;ENSP00000446471:K117E	ENSP00000385303:K108E	K	-	1	0	SLC25A17	39503207	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.742000	0.85008	1.110000	0.41699	0.528000	0.53228	AAA	.	.		0.388	SLC25A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321487.1	NM_006358		C	41173261	T	C	41173261	3	2	86	1	0	0	0	0	1	0	0	0	14494	1850	64	2	371	2	SLC25A17	22	41173261	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10		41173261	10131305	138	11632										
EFCAB6	64800	hgsc.bcm.edu	37	chr22	44112732	44112732	+	Frame_Shift_Del	DEL	A	A	-													0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	taggaaaacatcttacttgtAgacaaaagttcctctcaatt							TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr22:44112732delA	ENST00000262726.7	-	9	1131	c.878delT	c.(877-879)ctafs	p.L293fs	EFCAB6_ENST00000356087.4_Frame_Shift_Del_p.L187fs|EFCAB6_ENST00000358439.4_Frame_Shift_Del_p.L187fs|EFCAB6_ENST00000396231.2_Frame_Shift_Del_p.L141fs	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	293					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				TCTTACTTGTAGACAAAAGTT	0.343																																					p.L293fs		Atlas-Indel,Pindel	.											.	EFCAB6	177	.	0			c.879delA						.						119	112	114					22																	44112732		2202	4300	6502	SO:0001589	frameshift_variant	64800	exon9			.	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.878delT	chr22.hg19:g.44112732delA	ENSP00000262726:p.Leu293fs	428.0	0.0		295.0	117.0	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Frame_Shift_Del	DEL	ENST00000262726.7	hg19	CCDS14049.1																																																																																			.	.		0.343	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		-	44112732	A	-	44112732	7	5	86	1	0	1	0	1	0	0	0	0	4941	420	15	0	3723	0	EFCAB6	22	44112732	Frame_Shift_Del	DEL	A	TCGA-DD-A113-01A-11D-A12Z-10	2939471	44112732	7191834	139	11633										
SAPS2	9701	hgsc.bcm.edu	37	chr22	50876004	50876004	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	agtttggcttcaatgatgagGagtttgccgaccaggacgac	13	8	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chr22:50876004G>C	ENST00000216061.5	+	17	2123	c.1753G>C	c.(1753-1755)Gag>Cag	p.E585Q	PPP6R2_ENST00000359139.3_Missense_Mutation_p.E558Q|PPP6R2_ENST00000395744.3_Missense_Mutation_p.E558Q|PPP6R2_ENST00000395741.3_Missense_Mutation_p.E559Q			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	585						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						CAATGATGAGGAGTTTGCCGA	0.597																																					p.E585Q		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G1753C						.						128	105	113					22																	50876004		2203	4300	6503	SO:0001583	missense	9701	exon16			GATGAGGAGTTTG	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	19253	protein-coding gene	gene with protein product		610877	"KIAA0685", "SAPS domain family, member 2"	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.1753G>C	chr22.hg19:g.50876004G>C	ENSP00000216061:p.Glu585Gln	90.0	0.0		86.0	33.0	NM_001242898	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	hg19		.	.	.	.	.	.	.	.	.	.	G	27.7	4.850992	0.91277	.	.	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.42131	0.98;0.98;0.98;1.1	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.64713	0.2623	M	0.73319	2.225	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;0.999	D;D;D;D;D;D	0.91635	0.992;0.999;0.998;0.991;0.999;0.991	T	0.68977	-0.5267	10	0.72032	D	0.01	-30.6513	16.869	0.86036	0.0:0.0:1.0:0.0	.	117;585;585;559;558;558	F2Z3M7;O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;.;PP6R2_HUMAN;.;.;.	Q	558;559;558;585	ENSP00000352051:E558Q;ENSP00000379090:E559Q;ENSP00000379093:E558Q;ENSP00000216061:E585Q	ENSP00000216061:E585Q	E	+	1	0	PPP6R2	49222870	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	7.770000	0.85390	2.280000	0.76307	0.462000	0.41574	GAG	.	.		0.597	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		C	50876004	G	C	50876004	3	2	86	1	0	0	0	0	1	0	0	0	13852	1175	41	4	1722	4	SAPS2	22	50876004	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	6763272	50876004	428562	140	11634										
CNKSR2	22866	hgsc.bcm.edu	37	chrX	21550127	21550127	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gatactgtcttatattgctaTgaatatgaaaaaggaagatc	8	4	1	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chrX:21550127T>C	ENST00000379510.3	+	11	1281	c.1245T>C	c.(1243-1245)taT>taC	p.Y415Y	CNKSR2_ENST00000279451.4_Silent_p.Y415Y|CNKSR2_ENST00000425654.2_Silent_p.Y415Y|CNKSR2_ENST00000485012.1_3'UTR|CNKSR2_ENST00000543067.1_Silent_p.Y366Y	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	415	DUF1170.				regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						TATATTGCTATGAATATGAAA	0.338																																					p.Y415Y		Atlas-SNP	.											.	CNKSR2	158	.	0			c.T1245C						.						93	89	90					X																	21550127		2202	4299	6501	SO:0001819	synonymous_variant	22866	exon11			TTGCTATGAATAT	AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.1245T>C	chrX.hg19:g.21550127T>C		354.0	0.0		345.0	66.0	NM_001168647	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Silent	SNP	ENST00000379510.3	hg19	CCDS14198.1																																																																																			.	.		0.338	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927		C	21550127	T	C	21550127	2	2	86	1	0	0	0	0	0	0	0	1	3609	1471	51	2		2	CNKSR2	23	21550127	Silent	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10		21550127	133720433	141	11635										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34962850	34962850	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gcagtgcaagtttacaagtaCaaagaagacgtcacagatgc	10	8	1	3			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chrX:34962850C>T	ENST00000329357.5	+	1	1938	c.1902C>T	c.(1900-1902)taC>taT	p.Y634Y		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	634										breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						TTTACAAGTACAAAGAAGACG	0.383																																					p.Y634Y		Atlas-SNP	.											.	FAM47B	209	.	0			c.C1902T						.						122	109	113					X																	34962850		2202	4300	6502	SO:0001819	synonymous_variant	170062	exon1			CAAGTACAAAGAA	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.1902C>T	chrX.hg19:g.34962850C>T		244.0	0.0		212.0	15.0	NM_152631	Q5JQN5|Q6PIG3	Silent	SNP	ENST00000329357.5	hg19	CCDS14236.1																																																																																			.	.		0.383	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		T	34962850	C	T	34962850	2	4	86	1	0	0	0	0	0	0	0	1	5578	489	17	3		3	FAM47B	23	34962850	Silent	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	13412723	34962850	120307710	142	11636										
NOX1	27035	hgsc.bcm.edu	37	chrX	100105359	100105359	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	tctgcaattccaaaactttgGatgggtgcataacaacctgt	8	9	1	0			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chrX:100105359G>A	ENST00000372966.3	-	9	1119	c.914C>T	c.(913-915)tCc>tTc	p.S305F	NOX1_ENST00000372960.4_Missense_Mutation_p.S268F|NOX1_ENST00000217885.5_Missense_Mutation_p.S305F|NOX1_ENST00000372964.1_Intron	NM_007052.4|NM_013955.2	NP_008983.2|NP_039249.1	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1	305	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|cellular response to hyperoxia (GO:0071455)|cellular stress response to acidic pH (GO:1990451)|extracellular matrix organization (GO:0030198)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|intracellular pH elevation (GO:0051454)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of JNK cascade (GO:0046330)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation vascular endothelial growth factor production (GO:0010575)|proton transport (GO:0015992)|regulation of blood pressure (GO:0008217)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|respiratory burst (GO:0045730)|signal transduction (GO:0007165)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|invadopodium membrane (GO:0071438)|NADPH oxidase complex (GO:0043020)	metal ion binding (GO:0046872)|NADP binding (GO:0050661)|Rac GTPase binding (GO:0048365)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated proton channel activity (GO:0030171)			cervix(1)|lung(3)|ovary(1)|skin(2)	7						CAAAACTTTGGATGGGTGCAT	0.448																																					p.S305F		Atlas-SNP	.											.	NOX1	79	.	0			c.C914T						.						32	28	30					X																	100105359		2202	4297	6499	SO:0001583	missense	27035	exon9			ACTTTGGATGGGT	AF127763	CCDS14474.1, CCDS14475.1, CCDS65298.1	Xq22	2008-08-01			ENSG00000007952	ENSG00000007952			7889	protein-coding gene	gene with protein product	"mitogenic oxidase (pyridine nucleotide-dependent superoxide-generating)", "NADPH oxidase homolog-1", "NADPH oxidase 1 variant NOH-1L"	300225				10485709, 10615049	Standard	NM_007052		Approved	NOH1, NOH-1, MOX1, GP91-2	uc004egj.3	Q9Y5S8	OTTHUMG00000022007	ENST00000372966.3:c.914C>T	chrX.hg19:g.100105359G>A	ENSP00000362057:p.Ser305Phe	248.0	0.0		183.0	103.0	NM_013955	A8K836|O95691|Q2PP02	Missense_Mutation	SNP	ENST00000372966.3	hg19	CCDS14474.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.853958	0.32791	.	.	ENSG00000007952	ENST00000372966;ENST00000217885;ENST00000372960	T;T;T	0.15256	2.44;2.44;2.44	3.87	3.87	0.44632	Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.141960	0.47852	D	0.000210	T	0.30008	0.0751	M	0.90705	3.14	0.58432	D	0.999994	P;B;B	0.42871	0.792;0.188;0.18	B;B;B	0.41619	0.361;0.162;0.25	T	0.36744	-0.9735	10	0.36615	T	0.2	-6.1232	13.7359	0.62817	0.0:0.0:1.0:0.0	.	268;305;305	A6NGA6;Q9Y5S8-3;Q9Y5S8	.;.;NOX1_HUMAN	F	305;305;268	ENSP00000362057:S305F;ENSP00000217885:S305F;ENSP00000362051:S268F	ENSP00000217885:S305F	S	-	2	0	NOX1	99992015	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.678000	0.61641	1.767000	0.52121	0.422000	0.28245	TCC	.	.		0.448	NOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057495.1	NM_007052		A	100105359	G	A	100105359	3	1	86	1	0	0	0	0	1	0	0	0	10565	1174	41	3	800	3	NOX1	23	100105359	Missense_Mutation	SNP	G	TCGA-DD-A113-01A-11D-A12Z-10	65142509	100105359	55165201	143	11637										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107834827	107834827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	accaggccctccaggcccccCaggatctccaggtgataaag	10	16	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chrX:107834827C>T	ENST00000361603.2	+	21	1620	c.1376C>T	c.(1375-1377)cCa>cTa	p.P459L	COL4A5_ENST00000328300.6_Missense_Mutation_p.P459L	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	459	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						CCAGGCCCCCCAGGATCTCCA	0.393									Alport syndrome with Diffuse Leiomyomatosis																												p.P459L		Atlas-SNP	.											.	COL4A5	262	.	0			c.C1376T	GRCh37	CD961912	COL4A5	D	rs104886113	.						101	105	104					X																	107834827		2203	4300	6503	SO:0001583	missense	1287	exon21	Familial Cancer Database		GCCCCCCAGGATC	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.1376C>T	chrX.hg19:g.107834827C>T	ENSP00000354505:p.Pro459Leu	735.0	0.0		566.0	150.0	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	hg19	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	c	9.965	1.223813	0.22457	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.96685	-4.09;-4.09	5.36	4.47	0.54385	.	0.122857	0.56097	D	0.000032	D	0.96728	0.8932	M	0.87617	2.895	0.80722	D	1	D;P;D	0.54047	0.964;0.954;0.964	P;P;P	0.48454	0.563;0.578;0.563	D	0.95576	0.8642	10	0.51188	T	0.08	.	11.4258	0.50009	0.3268:0.6732:0.0:0.0	.	459;67;459	E7EVY4;Q49AM6;P29400	.;.;CO4A5_HUMAN	L	459	ENSP00000331902:P459L;ENSP00000354505:P459L	ENSP00000331902:P459L	P	+	2	0	COL4A5	107721483	0.998000	0.40836	0.030000	0.17652	0.003000	0.03518	2.341000	0.43983	0.977000	0.38444	0.540000	0.68198	CCA	.	.		0.393	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			T	107834827	C	T	107834827	3	4	86	1	0	0	0	0	1	0	0	0	3696	594	21	3	1458	3	COL4A5	23	107834827	Missense_Mutation	SNP	C	TCGA-DD-A113-01A-11D-A12Z-10	7729468	107834827	47435733	144	11638										
PAK3	5063	hgsc.bcm.edu	37	chrX	110439120	110439120	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aaccaggtgatccatagagaTataaagagtgacaatattct	8	6	1	4			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chrX:110439120T>C	ENST00000372010.1	+	16	1648	c.1206T>C	c.(1204-1206)gaT>gaC	p.D402D	PAK3_ENST00000262836.4_Silent_p.D402D|PAK3_ENST00000518291.1_Silent_p.D423D|PAK3_ENST00000446737.1_Silent_p.D387D|PAK3_ENST00000417227.1_Silent_p.D408D|PAK3_ENST00000360648.4_Silent_p.D423D|PAK3_ENST00000425146.1_Silent_p.D387D|PAK3_ENST00000519681.1_Silent_p.D408D|PAK3_ENST00000372007.5_Silent_p.D387D			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	402	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						TCCATAGAGATATAAAGAGTG	0.338										TSP Lung(19;0.15)																											p.D423D		Atlas-SNP	.											.	PAK3	179	.	0			c.T1269C						.						128	125	126					X																	110439120		2203	4300	6503	SO:0001819	synonymous_variant	5063	exon13			TAGAGATATAAAG	AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.1206T>C	chrX.hg19:g.110439120T>C		528.0	0.0		460.0	239.0	NM_001128168	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Silent	SNP	ENST00000372010.1	hg19	CCDS48153.1																																																																																			.	.		0.338	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		C	110439120	T	C	110439120	2	2	86	1	0	0	0	0	0	0	0	1	11411	1403	49	2		2	PAK3	23	110439120	Silent	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	2604293	110439120	44831440	145	11639										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117752664	117752664	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	aagaatcttttgataaaacaTgcatttgacacaagatacca	5	7	1	4			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chrX:117752664T>G	ENST00000276202.7	+	31	3507	c.3444T>G	c.(3442-3444)caT>caG	p.H1148Q	DOCK11_ENST00000276204.6_Missense_Mutation_p.H1148Q	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1148					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TGATAAAACATGCATTTGACA	0.358																																					p.H1148Q		Atlas-SNP	.											.	DOCK11	185	.	0			c.T3444G						.						70	61	64					X																	117752664		2203	4299	6502	SO:0001583	missense	139818	exon31			AAAACATGCATTT	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.3444T>G	chrX.hg19:g.117752664T>G	ENSP00000276202:p.His1148Gln	377.0	0.0		365.0	35.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	hg19	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.444422	0.63178	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	D;D	0.96885	-4.16;-4.16	5.68	0.724	0.18236	.	0.000000	0.85682	D	0.000000	D	0.98172	0.9396	H	0.94183	3.505	0.52501	D	0.999958	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.97216	0.9874	10	0.87932	D	0	-31.3629	9.0274	0.36239	0.0:0.2886:0.0:0.7114	.	1148;1148	A6NIW2;Q5JSL3	.;DOC11_HUMAN	Q	1148	ENSP00000276204:H1148Q;ENSP00000276202:H1148Q	ENSP00000276202:H1148Q	H	+	3	2	DOCK11	117636692	0.997000	0.39634	0.999000	0.59377	0.983000	0.72400	0.320000	0.19540	0.049000	0.15920	-0.435000	0.05868	CAT	.	.		0.358	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		G	117752664	T	G	117752664	3	3	86	1	0	0	0	0	1	0	0	0	4688	1461	51	5	3566	5	DOCK11	23	117752664	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	7313544	117752664	37517896	146	11640										
GABRA3	2556	hgsc.bcm.edu	37	chrX	151393310	151393310	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	catgggacactcagcatgaaTtgttaacctaaaagaaaggc	9	8	1	2			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chrX:151393310T>C	ENST00000370314.4	-	6	797	c.559A>G	c.(559-561)Att>Gtt	p.I187V	GABRA3_ENST00000535043.1_Missense_Mutation_p.I187V	NM_000808.3	NP_000799.1	P34903	GBRA3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 3	187					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(6)	37	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	TCAGCATGAATTGTTAACCTA	0.388																																					p.I187V	NSCLC(142;2578 2613 10251 16743)	Atlas-SNP	.											.	GABRA3	97	.	0			c.A559G						.						112	105	108					X																	151393310		2203	4300	6503	SO:0001583	missense	2556	exon6			CATGAATTGTTAA		CCDS14706.1	Xq28	2012-06-22			ENSG00000011677	ENSG00000011677		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4077	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 3"	305660					Standard	NM_000808		Approved		uc010ntk.1	P34903	OTTHUMG00000024183	ENST00000370314.4:c.559A>G	chrX.hg19:g.151393310T>C	ENSP00000359337:p.Ile187Val	854.0	0.0		702.0	199.0	NM_000808	Q8TAF9	Missense_Mutation	SNP	ENST00000370314.4	hg19	CCDS14706.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.601978	0.46423	.	.	ENSG00000011677	ENST00000370314;ENST00000370311;ENST00000535043	T;T;T	0.77750	-1.12;-1.12;-1.12	5.46	5.46	0.80206	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.78610	0.4310	N	0.20685	0.6	0.58432	D	0.999994	P	0.47604	0.898	D	0.68192	0.956	T	0.77284	-0.2645	10	0.31617	T	0.26	.	12.3594	0.55194	0.0:0.0:0.0:1.0	.	187	P34903	GBRA3_HUMAN	V	187	ENSP00000359337:I187V;ENSP00000359334:I187V;ENSP00000443527:I187V	ENSP00000359334:I187V	I	-	1	0	GABRA3	151143966	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.826000	0.48104	1.824000	0.53156	0.441000	0.28932	ATT	.	.		0.388	GABRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060921.1	NM_000808		C	151393310	T	C	151393310	3	2	86	1	0	0	0	0	1	0	0	0	6170	1493	52	2	939	2	GABRA3	23	151393310	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	33640646	151393310	3877250	147	11641										
ATP6AP1	537	hgsc.bcm.edu	37	chrX	153657461	153657461	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	0.740576813249572	1.43883495145631	0.620187479075996	0.378260869565217	1	0	gcgacttgcagctctctaccTacttagatcccgccctggag	9	15	1	1			TCGA-DD-A113-01A-11D-A12Z-10	TCGA-DD-A113-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6c53601-c4c7-429b-9fac-cf9d3db20ab1	59993464-9550-4996-b7c9-ca8629febad1	g.chrX:153657461T>A	ENST00000369762.2	+	2	290	c.229T>A	c.(229-231)Tac>Aac	p.Y77N		NM_001183.4	NP_001174.2	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1	77					ATP hydrolysis coupled proton transport (GO:0015991)|establishment of organelle localization (GO:0051656)|pH reduction (GO:0045851)|positive regulation of bone resorption (GO:0045780)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoclast development (GO:2001206)|proton transport (GO:0015992)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuole (GO:0005773)	ATP binding (GO:0005524)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(5)	14	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCTCTCTACCTACTTAGATCC	0.642																																					p.Y77N		Atlas-SNP	.											.	ATP6AP1	46	.	0			c.T229A						.						103	91	95					X																	153657461		2203	4300	6503	SO:0001583	missense	537	exon2			TCTACCTACTTAG	D16469	CCDS35451.1	Xq28	2010-03-10	2003-08-28	2003-08-29	ENSG00000071553	ENSG00000071553			868	protein-coding gene	gene with protein product		300197	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1"	ATP6S1, ATP6IP1		8733135, 8281148	Standard	NM_001183		Approved	ORF, XAP-3, VATPS1, 16A, Ac45, XAP3, CF2	uc004flf.1	Q15904	OTTHUMG00000033291	ENST00000369762.2:c.229T>A	chrX.hg19:g.153657461T>A	ENSP00000358777:p.Tyr77Asn	268.0	0.0		197.0	33.0	NM_001183	A6ZKI4|Q8NBT4|Q9H0C7	Missense_Mutation	SNP	ENST00000369762.2	hg19	CCDS35451.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.517895	0.85495	.	.	ENSG00000071553	ENST00000369762;ENST00000422890;ENST00000449556	.	.	.	4.74	4.74	0.60224	.	0.187498	0.48286	D	0.000196	T	0.71995	0.3406	M	0.72894	2.215	0.42659	D	0.993473	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.74160	-0.3755	9	0.56958	D	0.05	-16.6308	9.7389	0.40406	0.0:0.0:0.0:1.0	.	37;77	B3KR70;Q15904	.;VAS1_HUMAN	N	77	.	ENSP00000358777:Y77N	Y	+	1	0	ATP6AP1	153310655	1.000000	0.71417	0.965000	0.40720	0.845000	0.48019	3.303000	0.51858	1.560000	0.49568	0.430000	0.28490	TAC	.	.		0.642	ATP6AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081639.4	NM_001183		A	153657461	T	A	153657461	3	1	86	1	0	0	0	0	1	0	0	0	1165	1522	53	4	235	4	ATP6AP1	23	153657461	Missense_Mutation	SNP	T	TCGA-DD-A113-01A-11D-A12Z-10	2264151	153657461	1613099	148	11642										
ESPN	83715	hgsc.bcm.edu	37	chr1	6520166	6520166	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	caagctggcgccctggcagcGacaggtcatcctgaagaagg	14	12	1	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:6520166G>T	ENST00000377828.1	+	13	2693	c.2525G>T	c.(2524-2526)cGa>cTa	p.R842L	ESPN_ENST00000461727.1_Missense_Mutation_p.R276L|ESPN_ENST00000416731.1_Missense_Mutation_p.R276L	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	842					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		CCCTGGCAGCGACAGGTCATC	0.657																																					p.R842L		Atlas-SNP	.											.	ESPN	32	.	0			c.G2525T						.						46	47	47					1																	6520166		2203	4300	6503	SO:0001583	missense	83715	exon13			GGCAGCGACAGGT	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"Ankyrin repeat domain containing"	13281	protein-coding gene	gene with protein product		606351	"deafness, autosomal recessive 36"	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.2525G>T	chr1.hg19:g.6520166G>T	ENSP00000367059:p.Arg842Leu	164.0	0.0		203.0	38.0	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	hg19	CCDS70.1	.	.	.	.	.	.	.	.	.	.	g	26.2	4.712101	0.89112	.	.	ENSG00000187017	ENST00000377828;ENST00000416731	D;D	0.87887	-2.31;-2.31	4.32	4.32	0.51571	.	0.470861	0.18767	N	0.131731	D	0.90631	0.7062	M	0.67953	2.075	0.32685	N	0.514916	D;D	0.57571	0.98;0.98	P;P	0.56343	0.736;0.796	D	0.93084	0.6494	10	0.72032	D	0.01	-6.5359	14.3356	0.66586	0.0:0.0:1.0:0.0	.	276;842	B1AK53-2;B1AK53	.;ESPN_HUMAN	L	842;276	ENSP00000367059:R842L;ENSP00000399239:R276L	ENSP00000367059:R842L	R	+	2	0	ESPN	6442753	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.036000	0.70948	1.945000	0.56424	0.450000	0.29827	CGA	.	.		0.657	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		T	6520166	G	T	6520166	3	4	87	1	0	0	0	0	1	0	0	0	5256	1058	37	1	2575	1	ESPN	1	6520166	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10		6520166	242730455	1	11643										
MAST2	23139	hgsc.bcm.edu	37	chr1	46485312	46485312	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gaagtggcttttgtgatgcaGctggtgaaaaagctgatgat	14	4	0	4			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:46485312G>A	ENST00000361297.2	+	11	1516	c.1233G>A	c.(1231-1233)caG>caA	p.Q411Q	MAST2_ENST00000372009.2_Silent_p.Q341Q	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					TTGTGATGCAGCTGGTGAAAA	0.507																																					p.Q411Q		Atlas-SNP	.											.	MAST2	136	.	0			c.G1233A						.						88	87	87					1																	46485312		1976	4170	6146	SO:0001819	synonymous_variant	23139	exon11			GATGCAGCTGGTG	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.1233G>A	chr1.hg19:g.46485312G>A		188.0	0.0		157.0	26.0	NM_015112		Silent	SNP	ENST00000361297.2	hg19	CCDS41326.1																																																																																			.	.		0.507	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		A	46485312	G	A	46485312	2	1	87	1	0	0	0	0	0	0	0	1	9334	962	34	3		3	MAST2	1	46485312	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	39965146	46485312	202765309	2	11644										
C1orf173	127254	hgsc.bcm.edu	37	chr1	75037157	75037157	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ctctgctgctggcacttcctCcccactccgtgctaattcct	6	18	1	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:75037157C>A	ENST00000326665.5	-	14	4455	c.4237G>T	c.(4237-4239)Gag>Tag	p.E1413*	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1413	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						GGCACTTCCTCCCCACTCCGT	0.552																																					p.E1413X		Atlas-SNP	.											.	C1orf173	380	.	0			c.G4237T						.						99	99	99					1																	75037157		2203	4300	6503	SO:0001587	stop_gained	127254	exon14			CTTCCTCCCCACT																												ENST00000326665.5:c.4237G>T	chr1.hg19:g.75037157C>A	ENSP00000322609:p.Glu1413*	358.0	0.0		299.0	41.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Nonsense_Mutation	SNP	ENST00000326665.5	hg19	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	42	9.519403	0.99193	.	.	ENSG00000178965	ENST00000326665	.	.	.	4.58	3.64	0.41730	.	.	.	.	.	.	.	.	.	.	.	0.25645	N	0.986154	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-1.463	12.1663	0.54131	0.0:0.8257:0.1743:0.0	.	.	.	.	X	1413	.	ENSP00000322609:E1413X	E	-	1	0	C1orf173	74809745	0.087000	0.21565	0.027000	0.17364	0.032000	0.12392	2.336000	0.43938	0.888000	0.36160	0.561000	0.74099	GAG	.	.		0.552	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75037157	C	A	75037157	4	1	87	1	0	0	0	0	0	1	0	0	2016	864	30	3	359	3	C1orf173	1	75037157	Nonsense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	28551845	75037157	174213464	3	11645										
NEXN	91624	hgsc.bcm.edu	37	chr1	78407772	78407772	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	atttactcacaaagtgaataTgaaagctagatttgaacaaa	6	5	1	4			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:78407772T>A	ENST00000334785.7	+	12	1722	c.1538T>A	c.(1537-1539)aTg>aAg	p.M513K	FUBP1_ENST00000489495.1_5'Flank|NEXN_ENST00000457030.1_Missense_Mutation_p.M499K|NEXN_ENST00000330010.8_Missense_Mutation_p.M449K|NEXN_ENST00000480732.2_3'UTR	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		AAAGTGAATATGAAAGCTAGA	0.388																																					p.M513K		Atlas-SNP	.											.	NEXN	77	.	0			c.T1538A						.						56	50	52					1																	78407772		1847	4095	5942	SO:0001583	missense	91624	exon12			TGAATATGAAAGC	AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"Immunoglobulin superfamily / I-set domain containing"	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.1538T>A	chr1.hg19:g.78407772T>A	ENSP00000333938:p.Met513Lys	339.0	0.0		299.0	43.0	NM_144573		Missense_Mutation	SNP	ENST00000334785.7	hg19	CCDS41351.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.1|26.1	4.706696|4.706696	0.89018|0.89018	.|.	.|.	ENSG00000162614|ENSG00000162614	ENST00000457030;ENST00000330010;ENST00000334785|ENST00000342754	T;T;T|.	0.60797|.	0.24;0.16;0.24|.	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	0.255168|.	0.29145|.	N|.	0.013004|.	T|.	0.67468|.	0.2896|.	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.999;0.995;0.992;0.999|.	D;D;D;D|.	0.79784|.	0.993;0.988;0.972;0.993|.	T|.	0.68614|.	-0.5362|.	10|.	0.07030|.	T|.	0.85|.	-17.1734|-17.1734	15.9818|15.9818	0.80116|0.80116	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	449;499;513;449|.	D3DQ79;Q0ZGT2-2;Q0ZGT2;B4DPZ7|.	.;.;NEXN_HUMAN;.|.	K|R	499;449;513|413	ENSP00000388048:M499K;ENSP00000327363:M449K;ENSP00000333938:M513K|.	ENSP00000327363:M449K|.	M|X	+|+	2|1	0|0	NEXN|NEXN	78180360|78180360	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	8.022000|8.022000	0.88759|0.88759	2.172000|2.172000	0.68678|0.68678	0.477000|0.477000	0.44152|0.44152	ATG|TGA	.	.		0.388	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573		A	78407772	T	A	78407772	3	1	87	1	0	0	0	0	1	0	0	0	10364	1464	51	4	1580	4	NEXN	1	78407772	Missense_Mutation	SNP	T	TCGA-DD-A114-01A-11D-A12Z-10	3370615	78407772	170842849	4	11646										
S100A7A	338324	hgsc.bcm.edu	37	chr1	153390678	153390678	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	acgatgatgaaggagaacttCcccaatttcctcagtgcctg	9	11	1	3			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:153390678C>A	ENST00000368729.4	+	2	177	c.120C>A	c.(118-120)ttC>ttA	p.F40L	S100A7A_ENST00000329256.2_Missense_Mutation_p.F40L|S100A7A_ENST00000368728.2_Missense_Mutation_p.F40L	NM_176823.3	NP_789793.1	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7A	40	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein self-association (GO:0043621)	p.F40F(1)		cervix(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	12	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGAGAACTTCCCCAATTTCC	0.488																																					p.F40L		Atlas-SNP	.											S100A7A,NS,carcinoma,0,1	S100A7A	24	.	1	Substitution - coding silent(1)	lung(1)	c.C120A						.						183	159	167					1																	153390678		2203	4300	6503	SO:0001583	missense	338324	exon2			GAACTTCCCCAAT	AY189118	CCDS30872.1	1q22	2013-01-10	2006-09-11	2006-09-11	ENSG00000184330	ENSG00000184330		"S100 calcium binding proteins", "EF-hand domain containing"	21657	protein-coding gene	gene with protein product			"S100 calcium binding protein A15", "S100 calcium binding protein A7-like 1"	S100A15, S100A7L1		11230159	Standard	NM_176823		Approved	S100A7f	uc001fbt.1	Q86SG5	OTTHUMG00000013122	ENST00000368729.4:c.120C>A	chr1.hg19:g.153390678C>A	ENSP00000357718:p.Phe40Leu	312.0	1.0		446.0	163.0	NM_176823	D3DV38|Q5SY69	Missense_Mutation	SNP	ENST00000368729.4	hg19	CCDS30872.1	.	.	.	.	.	.	.	.	.	.	.	17.41	3.382061	0.61845	.	.	ENSG00000184330	ENST00000368729;ENST00000368728;ENST00000329256	T;T;T	0.04360	3.64;3.64;3.64	2.42	1.46	0.22682	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	.	.	.	.	T	0.01627	0.0052	N	0.11364	0.135	0.24705	N	0.993231	D	0.89917	1.0	D	0.91635	0.999	T	0.28138	-1.0053	9	0.02654	T	1	.	5.5578	0.17125	0.0:0.8329:0.0:0.1671	.	40	Q86SG5	S1A7A_HUMAN	L	40	ENSP00000357718:F40L;ENSP00000357717:F40L;ENSP00000329008:F40L	ENSP00000329008:F40L	F	+	3	2	S100A7A	151657302	0.107000	0.21998	0.917000	0.36280	0.436000	0.31835	0.132000	0.15891	0.534000	0.28695	0.585000	0.79938	TTC	.	.		0.488	S100A7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036786.2	NM_176823		A	153390678	C	A	153390678	3	1	87	1	0	0	0	0	1	0	0	0	13799	854	30	3	122	3	S100A7A	1	153390678	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	74982906	153390678	95859943	5	11647										
IVNS1ABP	10625	hgsc.bcm.edu	37	chr1	185274712	185274712	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	atcactgccaaacacctcagCctgtccatctagtaggttcc	6	15	3	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:185274712C>A	ENST00000367498.3	-	8	1343	c.721G>T	c.(721-723)Gct>Tct	p.A241S	IVNS1ABP_ENST00000392007.3_Missense_Mutation_p.A23S|IVNS1ABP_ENST00000459929.1_5'UTR	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	241	Sufficient for AHR interaction and signaling.				negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)				breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						AACACCTCAGCCTGTCCATCT	0.453																																					p.A241S		Atlas-SNP	.											.	IVNS1ABP	80	.	0			c.G721T						.						191	157	168					1																	185274712		2203	4300	6503	SO:0001583	missense	10625	exon8			CCTCAGCCTGTCC	AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.721G>T	chr1.hg19:g.185274712C>A	ENSP00000356468:p.Ala241Ser	259.0	0.0		297.0	107.0	NM_006469	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	hg19	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	C	8.607	0.888224	0.17540	.	.	ENSG00000116679	ENST00000367498;ENST00000392007	T;T	0.75704	-0.96;-0.56	5.57	5.57	0.84162	.	0.147379	0.64402	D	0.000009	T	0.54532	0.1864	N	0.14661	0.345	0.46260	D	0.998957	B;B	0.14438	0.01;0.01	B;B	0.15052	0.012;0.005	T	0.51537	-0.8693	10	0.07325	T	0.83	.	12.8374	0.57782	0.0:0.9256:0.0:0.0744	.	23;241	A8MVR0;Q9Y6Y0	.;NS1BP_HUMAN	S	241;23	ENSP00000356468:A241S;ENSP00000375864:A23S	ENSP00000356468:A241S	A	-	1	0	IVNS1ABP	183541335	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.597000	0.54031	2.614000	0.88457	0.557000	0.71058	GCT	.	.		0.453	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		A	185274712	C	A	185274712	3	1	87	1	0	0	0	0	1	0	0	0	7939	739	26	3	1239	3	IVNS1ABP	1	185274712	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	31884034	185274712	63975909	6	11648										
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458244	248458244	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gatgagaccataggaggacaGgatgagggaaaaggggacca	17	5	0	2	rs369151985		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:248458244G>T	ENST00000317996.1	-	1	636	c.637C>A	c.(637-639)Ctg>Atg	p.L213M		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			TAGGAGGACAGGATGAGGGAA	0.542																																					p.L213M		Atlas-SNP	.											OR2T12,NS,carcinoma,0,1	OR2T12	113	.	0			c.C637A						.						80	68	72					1																	248458244		2203	4297	6500	SO:0001583	missense	127064	exon1			AGGACAGGATGAG	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.637C>A	chr1.hg19:g.248458244G>T	ENSP00000324583:p.Leu213Met	1449.0	2.0		1594.0	243.0	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	hg19	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	g	11.34	1.610495	0.28712	.	.	ENSG00000177201	ENST00000317996	T	0.00269	8.37	1.55	-2.43	0.06522	GPCR, rhodopsin-like superfamily (1);	0.000000	0.29280	U	0.012616	T	0.00271	0.0008	L	0.51914	1.62	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.54964	-0.8214	10	0.41790	T	0.15	.	1.1523	0.01788	0.1468:0.1493:0.2893:0.4146	.	213	Q8NG77	O2T12_HUMAN	M	213	ENSP00000324583:L213M	ENSP00000324583:L213M	L	-	1	2	OR2T12	246524867	0.000000	0.05858	0.002000	0.10522	0.305000	0.27757	-2.179000	0.01259	-0.207000	0.10187	0.175000	0.17021	CTG	.	.		0.542	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		T	248458244	G	T	248458244	3	4	87	1	0	0	0	0	1	0	0	0	11028	991	35	3	328	3	OR2T12	1	248458244	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	63183532	248458244	792377	7	11649										
EGR4	1961	hgsc.bcm.edu	37	chr2	73518960	73518960	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cgcgtgctgcatttgccgccGcggcgccccttgcgtcgcgc	14	18	0	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr2:73518960G>A	ENST00000545030.1	-	2	1469	c.1395C>T	c.(1393-1395)cgC>cgT	p.R465R	EGR4_ENST00000436467.2_Silent_p.R362R	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	465					cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						ATTTGCCGCCGCGGCGCCCCT	0.731																																					p.R465R		Atlas-SNP	.											.	EGR4	52	.	0			c.C1395T						.						7	8	8					2																	73518960		2130	4139	6269	SO:0001819	synonymous_variant	1961	exon2			GCCGCCGCGGCGC		CCDS1925.2	2p13	2013-01-08			ENSG00000135625	ENSG00000135625		"Zinc fingers, C2H2-type"	3241	protein-coding gene	gene with protein product		128992				1584812	Standard	NM_001965		Approved	NGFI-C, PAT133	uc010yrj.2	Q05215	OTTHUMG00000129774	ENST00000545030.1:c.1395C>T	chr2.hg19:g.73518960G>A		2.0	0.0		11.0	7.0	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Silent	SNP	ENST00000545030.1	hg19	CCDS1925.2																																																																																			.	.		0.731	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965		A	73518960	G	A	73518960	2	1	87	1	0	0	0	0	0	0	0	1	4976	1074	38	1		1	EGR4	2	73518960	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10		73518960	169680413	8	11650										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73677972	73677972	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	agaagcctggtagtttctacCaacaggtcttgccacatagt	9	10	2	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr2:73677972C>T	ENST00000264448.6	+	8	4426	c.4315C>T	c.(4315-4317)Caa>Taa	p.Q1439*	ALMS1_ENST00000377715.1_Nonsense_Mutation_p.Q1439*|ALMS1_ENST00000409009.1_Nonsense_Mutation_p.Q1397*	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1439	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TAGTTTCTACCAACAGGTCTT	0.498																																					p.Q1439X		Atlas-SNP	.											.	ALMS1	384	.	0			c.C4315T						.						123	123	123					2																	73677972		1869	4109	5978	SO:0001587	stop_gained	7840	exon8			TTCTACCAACAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.4315C>T	chr2.hg19:g.73677972C>T	ENSP00000264448:p.Gln1439*	304.0	0.0		246.0	23.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Nonsense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	41	8.732772	0.98933	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	.	.	.	4.29	3.41	0.39046	.	1.331870	0.05417	N	0.543610	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	9.7911	0.40706	0.2048:0.7952:0.0:0.0	.	.	.	.	X	1397;1439;1439	.	ENSP00000264448:Q1439X	Q	+	1	0	ALMS1	73531480	0.001000	0.12720	0.004000	0.12327	0.001000	0.01503	0.974000	0.29436	1.382000	0.46385	-0.230000	0.12252	CAA	.	.		0.498	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73677972	C	T	73677972	4	4	87	1	0	0	0	0	0	1	0	0	535	595	21	3	4345	3	ALMS1	2	73677972	Nonsense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	159012	73677972	169521401	9	11651										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73800105	73800105	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	aaagcaaggtgctttctcatCatcgagctgggaggtctaat	11	8	3	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr2:73800105C>T	ENST00000264448.6	+	16	11209	c.11098C>T	c.(11098-11100)Cat>Tat	p.H3700Y	ALMS1_ENST00000409009.1_Missense_Mutation_p.H3658Y	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3700					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GCTTTCTCATCATCGAGCTGG	0.333																																					p.H3700Y		Atlas-SNP	.											.	ALMS1	384	.	0			c.C11098T						.						44	44	44					2																	73800105		1818	4065	5883	SO:0001583	missense	7840	exon16			TCTCATCATCGAG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.11098C>T	chr2.hg19:g.73800105C>T	ENSP00000264448:p.His3700Tyr	138.0	0.0		153.0	18.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	7.166	0.586628	0.13749	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.08193	3.12;3.12	4.89	2.0	0.26442	.	0.000000	0.47455	D	0.000234	T	0.12774	0.0310	L	0.38175	1.15	0.09310	N	0.999999	D;P;P	0.64830	0.994;0.578;0.578	P;B;B	0.62184	0.899;0.264;0.264	T	0.05321	-1.0892	10	0.66056	D	0.02	.	4.4163	0.11457	0.1781:0.6328:0.0:0.1891	.	3700;3658;3700	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	Y	3658;3700	ENSP00000386627:H3658Y;ENSP00000264448:H3700Y	ENSP00000264448:H3700Y	H	+	1	0	ALMS1	73653613	0.000000	0.05858	0.016000	0.15963	0.006000	0.05464	0.222000	0.17699	0.642000	0.30620	0.609000	0.83330	CAT	.	.		0.333	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73800105	C	T	73800105	3	4	87	1	0	0	0	0	1	0	0	0	535	826	29	3	11160	3	ALMS1	2	73800105	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	122133	73800105	169399268	10	11652										
MYO7B	4648	hgsc.bcm.edu	37	chr2	128335798	128335798	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tcctccagttctccgactccGagagctgggacgtcatcaag	10	14	3	1	rs549327895		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr2:128335798G>T	ENST00000409816.2	+	8	972	c.940G>T	c.(940-942)Gag>Tag	p.E314*	MYO7B_ENST00000428314.1_Nonsense_Mutation_p.E314*|MYO7B_ENST00000389524.4_Nonsense_Mutation_p.E314*			Q6PIF6	MYO7B_HUMAN	myosin VIIB	314	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CTCCGACTCCGAGAGCTGGGA	0.607																																					p.E314X		Atlas-SNP	.											.	MYO7B	359	.	0			c.G940T						.						55	60	58					2																	128335798		2101	4219	6320	SO:0001587	stop_gained	4648	exon9			GACTCCGAGAGCT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.940G>T	chr2.hg19:g.128335798G>T	ENSP00000386461:p.Glu314*	140.0	0.0		171.0	24.0	NM_001080527	Q14786|Q8TEE1	Nonsense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	G	32	5.107329	0.94292	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	.	.	.	4.25	4.25	0.50352	.	0.060140	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	17.1863	0.86868	0.0:0.0:1.0:0.0	.	.	.	.	X	314	.	ENSP00000374175:E314X	E	+	1	0	MYO7B	128052268	1.000000	0.71417	0.935000	0.37517	0.289000	0.27227	7.682000	0.84083	2.365000	0.80145	0.563000	0.77884	GAG	.	.		0.607	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		T	128335798	G	T	128335798	4	4	87	1	0	0	0	0	0	1	0	0	10092	1059	37	1	970	1	MYO7B	2	128335798	Nonsense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	54535693	128335798	114863575	11	11653										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171260816	171260816	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gaatatgaggacaaccgcccGctcttggacatgttcctcca	9	13	1	1	rs201316029		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr2:171260816G>T	ENST00000408978.4	+	20	2480	c.2337G>T	c.(2335-2337)ccG>ccT	p.P779P	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Silent_p.P779P|MYO3B_ENST00000334231.6_Silent_p.P788P	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	779	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						ACAACCGCCCGCTCTTGGACA	0.502																																					p.P779P		Atlas-SNP	.											.	MYO3B	320	.	0			c.G2337T						.						124	119	120					2																	171260816		1909	4115	6024	SO:0001819	synonymous_variant	140469	exon20			CCGCCCGCTCTTG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2337G>T	chr2.hg19:g.171260816G>T		225.0	0.0		210.0	41.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	hg19	CCDS42773.1																																																																																			.	G|0.999;A|0.001		0.502	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			T	171260816	G	T	171260816	2	4	87	1	0	0	0	0	0	0	0	1	10086	1074	38	1		1	MYO3B	2	171260816	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	42925018	171260816	71938557	12	11654										
USP19	10869	hgsc.bcm.edu	37	chr3	49151699	49151699	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	caccggcagataaagaaacgGgtcaaaagtgatggagacct	12	8	1	4			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr3:49151699G>C	ENST00000398888.2	-	15	2320	c.2002C>G	c.(2002-2004)Ccg>Gcg	p.P668A	USP19_ENST00000453664.1_Missense_Mutation_p.P759A|USP19_ENST00000488993.1_5'Flank|USP19_ENST00000434032.2_Missense_Mutation_p.P769A|USP19_ENST00000398898.2_Missense_Mutation_p.P708A|USP19_ENST00000398896.1_Missense_Mutation_p.P476A|USP19_ENST00000417901.1_Missense_Mutation_p.P771A|USP19_ENST00000398892.3_Missense_Mutation_p.P708A	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	668	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TAAAGAAACGGGTCAAAAGTG	0.537																																					p.P771A		Atlas-SNP	.											.	USP19	158	.	0			c.C2311G						.						71	77	75					3																	49151699		1977	4166	6143	SO:0001583	missense	10869	exon16			GAAACGGGTCAAA	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"Zinc fingers, MYND-type", "Ubiquitin-specific peptidases"	12617	protein-coding gene	gene with protein product		614471	"ubiquitin specific protease 19"			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.2002C>G	chr3.hg19:g.49151699G>C	ENSP00000381863:p.Pro668Ala	132.0	0.0		200.0	39.0	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	hg19	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	G	32	5.149690	0.94645	.	.	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36;1.36	6.17	6.17	0.99709	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.64538	0.2607	M	0.75150	2.29	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.83275	0.996;0.996;0.983;0.992;0.994	T	0.63897	-0.6533	10	0.87932	D	0	-16.0913	20.8794	0.99867	0.0:0.0:1.0:0.0	.	769;759;668;708;476	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	A	476;708;771;759;708;668;769	ENSP00000381870:P476A;ENSP00000381872:P708A;ENSP00000395260:P771A;ENSP00000400090:P759A;ENSP00000381867:P708A;ENSP00000381863:P668A;ENSP00000401197:P769A	ENSP00000381863:P668A	P	-	1	0	USP19	49126703	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.896000	0.87350	2.941000	0.99782	0.655000	0.94253	CCG	.	.		0.537	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		C	49151699	G	C	49151699	3	2	87	1	0	0	0	0	1	0	0	0	17065	1232	43	4	2002	4	USP19	3	49151699	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10		49151699	148870731	13	11655										
STAB1	23166	hgsc.bcm.edu	37	chr3	52546358	52546358	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tttctcactcccaccccaggCcacctgccgggcagtggggg	12	17	1	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr3:52546358C>T	ENST00000321725.6	+	27	2961	c.2885C>T	c.(2884-2886)gCc>gTc	p.A962V		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	962	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CCACCCCAGGCCACCTGCCGG	0.657																																					p.A962V		Atlas-SNP	.											.	STAB1	178	.	0			c.C2885T						.						62	69	67					3																	52546358		2203	4299	6502	SO:0001630	splice_region_variant	23166	exon27			CCCAGGCCACCTG	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.2884-1C>T	chr3.hg19:g.52546358C>T		75.0	0.0		68.0	9.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.924544	0.73213	.	.	ENSG00000010327	ENST00000321725	D	0.97710	-4.5	5.57	5.57	0.84162	EGF domain, merozoite surface protein 1-like (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.98112	0.9377	L	0.60012	1.86	0.58432	D	0.999992	D	0.69078	0.997	D	0.68765	0.96	D	0.98740	1.0716	10	0.87932	D	0	.	15.0541	0.71897	0.0:1.0:0.0:0.0	.	962	Q9NY15	STAB1_HUMAN	V	962	ENSP00000312946:A962V	ENSP00000312946:A962V	A	+	2	0	STAB1	52521398	1.000000	0.71417	1.000000	0.80357	0.158000	0.22134	3.154000	0.50693	2.633000	0.89246	0.563000	0.77884	GCC	.	.		0.657	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	Missense_Mutation	T	52546358	C	T	52546358	5	4	87	1	0	0	0	0	0	0	1	0	15252	753	26	3	2991	3	STAB1	3	52546358	Splice_Site	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	3394659	52546358	145476072	14	11656										
MECOM	2122	hgsc.bcm.edu	37	chr3	168819859	168819859	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgcagttacctgcaggtataGcgctcctttcccttccgcag	9	14	0	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr3:168819859G>A	ENST00000464456.1	-	9	3369	c.2169C>T	c.(2167-2169)cgC>cgT	p.R723R	MECOM_ENST00000472280.1_Silent_p.R733R|MECOM_ENST00000468789.1_Silent_p.R732R|MECOM_ENST00000460814.1_Silent_p.R723R|MECOM_ENST00000392736.3_Silent_p.R732R|MECOM_ENST00000494292.1_Silent_p.R911R|MECOM_ENST00000433243.2_Silent_p.R733R|MECOM_ENST00000264674.3_Silent_p.R797R	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						TGCAGGTATAGCGCTCCTTTC	0.488																																					p.R920R		Atlas-SNP	.											.	MECOM	216	.	0			c.C2760T						.						66	63	64					3																	168819859		2203	4300	6503	SO:0001819	synonymous_variant	2122	exon11			GGTATAGCGCTCC	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2169C>T	chr3.hg19:g.168819859G>A		172.0	0.0		153.0	24.0	NM_004991	Q13466|Q6FH90	Silent	SNP	ENST00000464456.1	hg19	CCDS54669.1																																																																																			.	.		0.488	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		A	168819859	G	A	168819859	2	1	87	1	0	0	0	0	0	0	0	1	9431	958	34	3		3	MECOM	3	168819859	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	116273501	168819859	29202571	15	11657										
PPBP	5473	hgsc.bcm.edu	37	chr4	74853684	74853684	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ggcctctacctttgcctttcGccaagtttctcttagtttgt	7	12	2	0	rs201755460		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr4:74853684G>T	ENST00000296028.3	-	1	230	c.137C>A	c.(136-138)gCg>gAg	p.A46E		NM_002704.3	NP_002695.1	P02775	CXCL7_HUMAN	pro-platelet basic protein (chemokine (C-X-C motif) ligand 7)	46					blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|defense response to bacterium (GO:0042742)|glucose transport (GO:0015758)|immune response (GO:0006955)|leukocyte migration involved in inflammatory response (GO:0002523)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell division (GO:0051781)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|platelet alpha granule lumen (GO:0031093)	glucose transmembrane transporter activity (GO:0005355)			breast(1)|central_nervous_system(1)|lung(1)|ovary(2)|skin(2)|stomach(1)|urinary_tract(2)	10	Breast(15;0.00136)		all cancers(17;0.00273)|Lung(101;0.196)			TTTGCCTTTCGCCAAGTTTCT	0.532																																					p.A46E		Atlas-SNP	.											.	PPBP	27	.	0			c.C137A						.						136	127	130					4																	74853684		2203	4300	6503	SO:0001583	missense	5473	exon1			CCTTTCGCCAAGT	M54995	CCDS3563.1	4q12-q13	2013-02-25	2002-08-22		ENSG00000163736	ENSG00000163736		"Endogenous ligands"	9240	protein-coding gene	gene with protein product	"platelet basic protein", "beta-thromboglobulin", "connective tissue-activating peptide III", "neutrophil-activating peptide-2"	121010		THBGB1		1826003	Standard	NM_002704		Approved	SCYB7, TGB, NAP-2-L1, LA-PF4, MDGF, LDGF, Beta-TG, CTAP3, CXCL7, PBP, b-TG1, TGB1, CTAPIII, NAP-2	uc003hhj.3	P02775	OTTHUMG00000130008	ENST00000296028.3:c.137C>A	chr4.hg19:g.74853684G>T	ENSP00000296028:p.Ala46Glu	291.0	0.0		229.0	51.0	NM_002704	B2R5F3|Q6IBJ8	Missense_Mutation	SNP	ENST00000296028.3	hg19	CCDS3563.1	.	.	.	.	.	.	.	.	.	.	G	2.782	-0.253372	0.05829	.	.	ENSG00000163736	ENST00000296028	T	0.44482	0.92	2.23	-1.96	0.07525	Chemokine interleukin-8-like domain (1);	5.599220	0.01243	U	0.008678	T	0.14270	0.0345	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05801	-1.0863	10	0.27082	T	0.32	.	0.3377	0.00328	0.1992:0.3118:0.2055:0.2835	.	46	P02775	CXCL7_HUMAN	E	46	ENSP00000296028:A46E	ENSP00000296028:A46E	A	-	2	0	PPBP	75072548	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.482000	0.02320	-0.618000	0.05656	-1.398000	0.01145	GCG	.	.		0.532	PPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252281.2	NM_002704		T	74853684	G	T	74853684	3	4	87	1	0	0	0	0	1	0	0	0	12312	1087	38	1	261	1	PPBP	4	74853684	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10		74853684	116300592	16	11658										
GFM2	84340	hgsc.bcm.edu	37	chr5	74047313	74047313	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgtcactgtgtctccatcatCaacatctagccaggaaaaag	7	11	5	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr5:74047313C>T	ENST00000296805.3	-	6	767	c.310G>A	c.(310-312)Gat>Aat	p.D104N	GFM2_ENST00000509430.1_Missense_Mutation_p.D104N|GFM2_ENST00000427854.2_Missense_Mutation_p.D104N|GFM2_ENST00000345239.2_Missense_Mutation_p.D104N	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		TCTCCATCATCAACATCTAGC	0.383																																					p.D104N		Atlas-SNP	.											.	GFM2	38	.	0			c.G310A						.						172	163	166					5																	74047313		2203	4300	6503	SO:0001583	missense	84340	exon6			CATCATCAACATC	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.310G>A	chr5.hg19:g.74047313C>T	ENSP00000296805:p.Asp104Asn	168.0	0.0		188.0	24.0	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.024543	0.93518	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430;ENST00000427854;ENST00000506778	T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85	5.84	4.98	0.66077	Small GTP-binding protein domain (1);Protein synthesis factor, GTP-binding (1);	0.088118	0.85682	D	0.000000	D	0.88306	0.6401	M	0.89601	3.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.77557	0.982;0.99;0.99;0.99	D	0.90761	0.4665	10	0.87932	D	0	-20.5045	14.9609	0.71156	0.0:0.9316:0.0:0.0684	.	104;104;104;104	Q969S9-3;Q969S9-5;Q969S9-2;Q969S9	.;.;.;RRF2M_HUMAN	N	104;104;104;104;104;29	ENSP00000296805:D104N;ENSP00000296804:D104N;ENSP00000427004:D104N;ENSP00000405808:D104N;ENSP00000424877:D29N	ENSP00000296805:D104N	D	-	1	0	GFM2	74083069	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.691000	0.84191	1.474000	0.48178	0.650000	0.86243	GAT	.	.		0.383	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		T	74047313	C	T	74047313	3	4	87	1	0	0	0	0	1	0	0	0	6350	826	29	3	2125	3	GFM2	5	74047313	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10		74047313	106867947	17	11659										
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140250371	140250371	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ctggacgagaacgacaacgcGccggcactgctggcgactca	13	14	1	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr5:140250371G>A	ENST00000398640.2	+	1	1683	c.1683G>A	c.(1681-1683)gcG>gcA	p.A561A	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	561	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGACAACGCGCCGGCACTGC	0.682																																					p.A561A		Atlas-SNP	.											.	PCDHA11	209	.	0			c.G1683A						.						86	95	92					5																	140250371		2203	4299	6502	SO:0001819	synonymous_variant	56138	exon1			CAACGCGCCGGCA	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1683G>A	chr5.hg19:g.140250371G>A		105.0	0.0		104.0	16.0	NM_018902	B2RN58|O75279	Silent	SNP	ENST00000398640.2	hg19	CCDS47284.1																																																																																			.	.		0.682	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		A	140250371	G	A	140250371	2	1	87	1	0	0	0	0	0	0	0	1	11530	1074	38	1		1	PCDHA11	5	140250371	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	66203058	140250371	40664889	18	11660										
PPARGC1B	133522	hgsc.bcm.edu	37	chr5	149213132	149213132	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgcagatgagccgctggtccCctcggagccccaaggtgctc	13	15	0	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr5:149213132C>T	ENST00000309241.5	+	5	1528	c.1496C>T	c.(1495-1497)cCc>cTc	p.P499L	PPARGC1B_ENST00000394320.3_Missense_Mutation_p.P499L|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.P460L|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.P435L	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	499					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCGCTGGTCCCCTCGGAGCCC	0.667																																					p.P499L		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.C1496T						.						27	30	29					5																	149213132		2196	4298	6494	SO:0001583	missense	133522	exon5			TGGTCCCCTCGGA	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"RNA binding motif (RRM) containing"	30022	protein-coding gene	gene with protein product		608886	"peroxisome proliferative activated receptor, gamma, coactivator 1, beta"			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.1496C>T	chr5.hg19:g.149213132C>T	ENSP00000312649:p.Pro499Leu	89.0	0.0		102.0	21.0	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	hg19	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977948	0.53720	.	.	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.08370	3.1;3.1;3.1;3.1	4.96	4.03	0.46877	.	0.745481	0.12560	N	0.458285	T	0.25121	0.0610	L	0.59436	1.845	0.20196	N	0.99993	D;D;D;D;D	0.76494	0.996;0.997;0.996;0.993;0.999	P;D;P;P;D	0.76575	0.9;0.913;0.9;0.796;0.988	T	0.02632	-1.1131	10	0.87932	D	0	-7.8559	13.1038	0.59235	0.0:0.8394:0.1606:0.0	.	478;478;460;499;499	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	L	460;499;499;435	ENSP00000353638:P460L;ENSP00000377855:P499L;ENSP00000312649:P499L;ENSP00000384403:P435L	ENSP00000312649:P499L	P	+	2	0	PPARGC1B	149193325	0.000000	0.05858	0.550000	0.28217	0.644000	0.38419	0.539000	0.23175	2.289000	0.77006	0.561000	0.74099	CCC	.	.		0.667	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		T	149213132	C	T	149213132	3	4	87	1	0	0	0	0	1	0	0	0	12310	623	22	3	1521	3	PPARGC1B	5	149213132	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	8962761	149213132	31702128	19	11661										
CYFIP2	408263	hgsc.bcm.edu	37	chr5	156768087	156768087	+	IGR	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gcttctactagttttgtgcgGactgccattcctttcaccca	7	13	2	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr5:156768087G>T	ENST00000312349.4	-	0	2125				CYFIP2_ENST00000377576.3_Silent_p.R865R|CYFIP2_ENST00000435847.2_Silent_p.R564R|CYFIP2_ENST00000541131.1_Silent_p.R790R|CYFIP2_ENST00000347377.6_Silent_p.R865R|CYFIP2_ENST00000522463.1_Silent_p.R669R|CYFIP2_ENST00000442283.2_Silent_p.R150R|CYFIP2_ENST00000318218.6_Silent_p.R890R|CYFIP2_ENST00000521420.1_Silent_p.R839R	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						GTTTTGTGCGGACTGCCATTC	0.473																																					p.R865R		Atlas-SNP	.											.	CYFIP2	354	.	0			c.G2595T						.						125	120	122					5																	156768087		1916	4132	6048	SO:0001628	intergenic_variant	26999	exon23			TGTGCGGACTGCC	BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"Fibronectin type III domain containing"	33547	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 40"	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248		chr5.hg19:g.156768087G>T		245.0	0.0		251.0	42.0	NM_001037332	A8K0Y6	Silent	SNP	ENST00000312349.4	hg19	CCDS4337.1																																																																																			.	.		0.473	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343		T	156768087	G	T	156768087	1	4	87	0	1	0	0	0	0	0	0	0	4140	1161	41	3		3	CYFIP2	5	156768087	IGR	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	7554955	156768087	24147173	20	11662										
CUL7	9820	hgsc.bcm.edu	37	chr6	43012996	43012996	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gtgcaggaggctcctgcggtCctctgccatgtcctggctcc	13	15	1	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr6:43012996C>T	ENST00000265348.3	-	15	3092	c.3007G>A	c.(3007-3009)Gac>Aac	p.D1003N	CUL7_ENST00000535468.1_Missense_Mutation_p.D1087N|CUL7_ENST00000478630.1_5'Flank			Q14999	CUL7_HUMAN	cullin 7	1003					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CTCCTGCGGTCCTCTGCCATG	0.582																																					p.D1087N		Atlas-SNP	.											.	CUL7	133	.	0			c.G3259A						.						89	84	86					6																	43012996		2203	4300	6503	SO:0001583	missense	9820	exon15			TGCGGTCCTCTGC	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"KIAA0076"	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.3007G>A	chr6.hg19:g.43012996C>T	ENSP00000265348:p.Asp1003Asn	112.0	0.0		125.0	9.0	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	hg19	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.570692	0.65765	.	.	ENSG00000044090	ENST00000265348;ENST00000535468	D;D	0.83163	-1.66;-1.69	4.98	4.07	0.47477	.	0.150464	0.64402	N	0.000016	T	0.75199	0.3817	M	0.66939	2.045	0.80722	D	1	B;B;B	0.26258	0.145;0.124;0.129	B;B;B	0.37387	0.13;0.248;0.248	T	0.75861	-0.3168	10	0.59425	D	0.04	-16.9653	8.5871	0.33664	0.0:0.8162:0.0:0.1838	.	1087;1087;1003	F5H0L1;B4DYZ0;Q14999	.;.;CUL7_HUMAN	N	1003;1087	ENSP00000265348:D1003N;ENSP00000438788:D1087N	ENSP00000265348:D1003N	D	-	1	0	CUL7	43120974	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.877000	0.63086	1.018000	0.39521	0.563000	0.77884	GAC	.	.		0.582	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780		T	43012996	C	T	43012996	3	4	87	1	0	0	0	0	1	0	0	0	4062	855	30	3	2137	3	CUL7	6	43012996	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10		43012996	128102071	21	11663										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18633535	18633535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tccttgtcttttctagggctGcccaccacacatcattggat	7	13	3	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr7:18633535G>A	ENST00000432645.2	+	5	538	c.538G>A	c.(538-540)Gcc>Acc	p.A180T	HDAC9_ENST00000406451.4_Missense_Mutation_p.A180T|HDAC9_ENST00000524023.1_Missense_Mutation_p.A147T|HDAC9_ENST00000456174.2_Missense_Mutation_p.A152T|HDAC9_ENST00000441542.2_Missense_Mutation_p.A183T|HDAC9_ENST00000401921.1_Missense_Mutation_p.A183T|HDAC9_ENST00000428307.2_Missense_Mutation_p.A180T|HDAC9_ENST00000417496.2_Missense_Mutation_p.A222T|HDAC9_ENST00000405010.3_Missense_Mutation_p.A180T|HDAC9_ENST00000406072.1_Missense_Mutation_p.A211T	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	180	Interaction with MAPK10. {ECO:0000250}.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	TTCTAGGGCTGCCCACCACAC	0.448																																					p.A222T		Atlas-SNP	.											.	HDAC9	560	.	0			c.G664A						.						196	189	192					7																	18633535		1978	4147	6125	SO:0001583	missense	9734	exon8			AGGGCTGCCCACC	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.538G>A	chr7.hg19:g.18633535G>A	ENSP00000410337:p.Ala180Thr	216.0	0.0		146.0	23.0	NM_001204144	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	hg19	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.547390	0.45383	.	.	ENSG00000048052	ENST00000417496;ENST00000262069;ENST00000405010;ENST00000406451;ENST00000428307;ENST00000406072;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000456174;ENST00000524023;ENST00000341009	T;T;T;T;T;T;T;T;T;T	0.57752	0.96;0.98;0.38;0.99;0.97;0.39;0.38;0.38;0.98;0.94	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000008	T	0.62816	0.2459	L	0.31120	0.905	0.53005	D	0.999968	P;P;D;B;D;P;D;D;P;D;D;P;D	0.69078	0.851;0.954;0.975;0.02;0.958;0.851;0.975;0.975;0.533;0.997;0.975;0.946;0.958	B;P;P;B;B;B;P;P;B;D;P;P;B	0.77004	0.297;0.541;0.591;0.021;0.441;0.297;0.591;0.591;0.123;0.989;0.591;0.592;0.386	T	0.51834	-0.8655	10	0.17832	T	0.49	-13.9477	20.8794	0.99867	0.0:0.0:1.0:0.0	.	147;152;180;211;222;183;183;183;180;152;180;180;202	E7EX34;C9JS87;Q9UKV0-4;B5MCF1;B7Z917;Q68D71;Q9UKV0-6;Q9UKV0-7;Q9UKV0;B7Z928;Q9UKV0-5;Q9UKV0-3;Q8N879	.;.;.;.;.;.;.;.;HDAC9_HUMAN;.;.;.;.	T	222;225;180;180;180;211;183;180;183;152;147;180	ENSP00000401669:A222T;ENSP00000384382:A180T;ENSP00000384657:A180T;ENSP00000395655:A180T;ENSP00000384017:A211T;ENSP00000383912:A183T;ENSP00000410337:A180T;ENSP00000408617:A183T;ENSP00000388568:A152T;ENSP00000430036:A147T	ENSP00000262069:A225T	A	+	1	0	HDAC9	18600060	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.018000	0.64054	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.448	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			A	18633535	G	A	18633535	3	1	87	1	0	0	0	0	1	0	0	0	7023	1319	46	3	565	3	HDAC9	7	18633535	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10		18633535	140505128	22	11664										
ZP3	7784	hgsc.bcm.edu	37	chr7	76062261	76062261	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	caggcagggcaatgtgagcaGccaggccatcctgcccacct	12	15	0	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr7:76062261G>T	ENST00000394857.3	+	3	507	c.449G>T	c.(448-450)aGc>aTc	p.S150I	ZP3_ENST00000336517.4_Missense_Mutation_p.S99I|ZP3_ENST00000416245.1_5'UTR	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	150	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						AATGTGAGCAGCCAGGCCATC	0.582																																					p.S150I		Atlas-SNP	.											.	ZP3	32	.	0			c.G449T						.						89	74	79					7																	76062261		2203	4300	6503	SO:0001583	missense	7784	exon3			TGAGCAGCCAGGC	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"Zona pellucida glycoproteins"	13189	protein-coding gene	gene with protein product		182889	"zona pellucida glycoprotein 3A (sperm receptor)"	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.449G>T	chr7.hg19:g.76062261G>T	ENSP00000378326:p.Ser150Ile	95.0	0.0		103.0	19.0	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	hg19	CCDS47618.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382218	0.82792	.	.	ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121	D;D	0.82619	-1.63;-1.63	5.4	5.4	0.78164	Zona pellucida sperm-binding protein (3);	0.000000	0.85682	D	0.000000	D	0.92247	0.7541	M	0.91920	3.255	0.80722	D	1	D;P	0.62365	0.991;0.563	D;B	0.63381	0.914;0.345	D	0.93608	0.6936	10	0.66056	D	0.02	-41.2133	16.6568	0.85230	0.0:0.0:1.0:0.0	.	99;150	P21754-3;P21754	.;ZP3_HUMAN	I	99;150;150	ENSP00000337310:S99I;ENSP00000378326:S150I	ENSP00000337310:S99I	S	+	2	0	ZP3	75900197	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.459000	0.80802	2.536000	0.85505	0.561000	0.74099	AGC	.	.		0.582	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1			T	76062261	G	T	76062261	3	4	87	1	0	0	0	0	1	0	0	0	18232	971	34	3	459	3	ZP3	7	76062261	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	57428726	76062261	83076402	23	11665										
PCLO	27445	hgsc.bcm.edu	37	chr7	82435139	82435139	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ctgcaggccggtgattgggaGgctttgctgcatggtgtggg	19	7	0	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr7:82435139G>A	ENST00000333891.9	-	21	15135	c.14798C>T	c.(14797-14799)cCt>cTt	p.P4933L		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GTGATTGGGAGGCTTTGCTGC	0.483																																					p.P4933L		Atlas-SNP	.											.	PCLO	1506	.	0			c.C14798T						.						39	41	41					7																	82435139		2022	4177	6199	SO:0001583	missense	27445	exon21			TTGGGAGGCTTTG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14798C>T	chr7.hg19:g.82435139G>A	ENSP00000334319:p.Pro4933Leu	216.0	0.0		187.0	17.0	NM_033026		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.790558	0.50102	.	.	ENSG00000186472	ENST00000333891	T	0.16073	2.37	5.69	5.69	0.88448	.	.	.	.	.	T	0.22627	0.0546	N	0.08118	0	0.80722	D	1	D	0.63046	0.992	P	0.59357	0.856	T	0.23797	-1.0178	9	0.87932	D	0	.	19.8069	0.96534	0.0:0.0:1.0:0.0	.	4933	Q9Y6V0-5	.	L	4933	ENSP00000334319:P4933L	ENSP00000334319:P4933L	P	-	2	0	PCLO	82273075	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	7.159000	0.77483	2.668000	0.90789	0.557000	0.71058	CCT	.	.		0.483	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82435139	G	A	82435139	3	1	87	1	0	0	0	0	1	0	0	0	11592	1000	35	3	650	3	PCLO	7	82435139	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	6372878	82435139	76703524	24	11666										
EXOC4	60412	hgsc.bcm.edu	37	chr7	133314872	133314872	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ctggagccagaaacattaccGtcatattccacccattacta	5	13	1	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr7:133314872G>T	ENST00000253861.4	+	10	1521	c.1492G>T	c.(1492-1494)Gtc>Ttc	p.V498F	EXOC4_ENST00000545148.1_Missense_Mutation_p.V108F|EXOC4_ENST00000539845.1_Missense_Mutation_p.V397F|EXOC4_ENST00000460346.1_3'UTR	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	498					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				AAACATTACCGTCATATTCCA	0.368																																					p.V498F		Atlas-SNP	.											.	EXOC4	118	.	0			c.G1492T						.						123	118	120					7																	133314872		2203	4300	6503	SO:0001583	missense	60412	exon10			ATTACCGTCATAT	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"SEC8-like 1 (S. cerevisiae)"	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.1492G>T	chr7.hg19:g.133314872G>T	ENSP00000253861:p.Val498Phe	184.0	0.0		140.0	21.0	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	hg19	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.706842	0.30232	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148	.	.	.	6.03	4.24	0.50183	.	0.140692	0.47852	D	0.000209	T	0.44477	0.1295	L	0.48642	1.525	0.80722	D	1	B;P;P	0.44877	0.01;0.845;0.664	B;P;B	0.44921	0.017;0.464;0.195	T	0.26503	-1.0101	9	0.15066	T	0.55	.	7.4852	0.27427	0.3458:0.0:0.6542:0.0	.	30;108;498	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	F	498;117;397;108	.	ENSP00000253861:V498F	V	+	1	0	EXOC4	132965412	1.000000	0.71417	0.860000	0.33809	0.866000	0.49608	4.254000	0.58798	0.893000	0.36288	0.655000	0.94253	GTC	.	.		0.368	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		T	133314872	G	T	133314872	3	4	87	1	0	0	0	0	1	0	0	0	5308	1145	40	1	1539	1	EXOC4	7	133314872	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	50879733	133314872	25823791	25	11667										
EBF2	64641	hgsc.bcm.edu	37	chr8	25898461	25898461	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gtagaagagctcaccgttgcTgtagaggagctgtaacttgt	13	7	1	3			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr8:25898461T>G	ENST00000520164.1	-	3	883	c.346A>C	c.(346-348)Agc>Cgc	p.S116R	EBF2_ENST00000408929.3_5'UTR	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	116					adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		TCACCGTTGCTGTAGAGGAGC	0.582																																					p.S116R	Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)	Atlas-SNP	.											.	EBF2	138	.	0			c.A346C						.						135	140	138					8																	25898461		2030	4202	6232	SO:0001583	missense	64641	exon3			CGTTGCTGTAGAG	AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.346A>C	chr8.hg19:g.25898461T>G	ENSP00000430241:p.Ser116Arg	562.0	0.0		647.0	62.0	NM_022659	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Missense_Mutation	SNP	ENST00000520164.1	hg19	CCDS43726.1	.	.	.	.	.	.	.	.	.	.	T	31	5.092377	0.94149	.	.	ENSG00000221818	ENST00000520164	T	0.49139	0.79	5.59	5.59	0.84812	.	0.000000	0.85682	U	0.000000	T	0.54382	0.1855	M	0.78049	2.395	0.80722	D	1	D	0.53312	0.959	P	0.44597	0.454	T	0.60622	-0.7227	10	0.44086	T	0.13	-4.0617	15.7811	0.78260	0.0:0.0:0.0:1.0	.	116	Q9HAK2	COE2_HUMAN	R	116	ENSP00000430241:S116R	ENSP00000430241:S116R	S	-	1	0	EBF2	25954378	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.040000	0.89188	2.123000	0.65237	0.533000	0.62120	AGC	.	.		0.582	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659		G	25898461	T	G	25898461	3	3	87	1	0	0	0	0	1	0	0	0	4883	1580	55	5	1437	5	EBF2	8	25898461	Missense_Mutation	SNP	T	TCGA-DD-A114-01A-11D-A12Z-10		25898461	120465561	26	11668										
STK3	6788	hgsc.bcm.edu	37	chr8	99560362	99560362	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ctccacactagtcttcaccaTggtgtgggaatccagctcat	8	13	3	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr8:99560362T>A	ENST00000419617.2	-	9	1116	c.976A>T	c.(976-978)Atg>Ttg	p.M326L	STK3_ENST00000523601.1_Missense_Mutation_p.M354L	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	326					apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		GTCTTCACCATGGTGTGGGAA	0.463																																					p.M354L		Atlas-SNP	.											.	STK3	47	.	0			c.A1060T						.						57	54	55					8																	99560362		1937	4146	6083	SO:0001583	missense	6788	exon11			TCACCATGGTGTG	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"serine/threonine kinase 3 (Ste20, yeast homolog)"			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.976A>T	chr8.hg19:g.99560362T>A	ENSP00000390500:p.Met326Leu	188.0	0.0		152.0	34.0	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Missense_Mutation	SNP	ENST00000419617.2	hg19	CCDS47900.1	.	.	.	.	.	.	.	.	.	.	T	18.55	3.648917	0.67358	.	.	ENSG00000104375	ENST00000419617;ENST00000523601;ENST00000518165	T;T;T	0.71222	-0.55;-0.54;0.27	5.74	5.74	0.90152	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.72827	0.3509	L	0.49455	1.56	0.80722	D	1	B;B;B	0.27068	0.167;0.011;0.026	B;B;B	0.41332	0.354;0.02;0.02	T	0.68349	-0.5432	10	0.27082	T	0.32	.	16.0502	0.80755	0.0:0.0:0.0:1.0	.	215;326;354	E5RFQ9;Q13188;B3KYA7	.;STK3_HUMAN;.	L	326;354;215	ENSP00000390500:M326L;ENSP00000429744:M354L;ENSP00000428014:M215L	ENSP00000390500:M326L	M	-	1	0	STK3	99629538	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.625000	0.83145	2.197000	0.70478	0.528000	0.53228	ATG	.	.		0.463	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281		A	99560362	T	A	99560362	3	1	87	1	0	0	0	0	1	0	0	0	15310	1464	51	4	511	4	STK3	8	99560362	Missense_Mutation	SNP	T	TCGA-DD-A114-01A-11D-A12Z-10	73661901	99560362	46803660	27	11669										
GRHL2	79977	hgsc.bcm.edu	37	chr8	102611376	102611376	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgggacgtgaatgaagaggcGaaggtgagtgacattgattc	16	4	0	6	rs267601683		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr8:102611376G>A	ENST00000251808.3	+	8	1433	c.1095G>A	c.(1093-1095)gcG>gcA	p.A365A	GRHL2_ENST00000395927.1_Silent_p.A349A	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	365					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			ATGAAGAGGCGAAGGTGAGTG	0.378																																					p.A365A		Atlas-SNP	.											GRHL2,colon,carcinoma,0,1	GRHL2	68	.	0			c.G1095A						.						99	91	94					8																	102611376		2203	4300	6503	SO:0001819	synonymous_variant	79977	exon8			AGAGGCGAAGGTG	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"deafness, autosomal dominant 28", "transcription factor CP2-like 3"	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.1095G>A	chr8.hg19:g.102611376G>A		304.0	0.0		298.0	60.0	NM_024915	A1L303|Q6NT03|Q9H8B8	Silent	SNP	ENST00000251808.3	hg19	CCDS34931.1																																																																																			.	.		0.378	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915		A	102611376	G	A	102611376	2	1	87	1	0	0	0	0	0	0	0	1	6773	1045	37	1		1	GRHL2	8	102611376	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	3051014	102611376	43752646	28	11670										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139838990	139838990	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ccggaaggttgtgacaaaggCgtactcatcaggtaaacctt	11	9	2	1	rs372910376		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr8:139838990C>A	ENST00000303045.6	-	6	1326	c.880G>T	c.(880-882)Gcc>Tcc	p.A294S	COL22A1_ENST00000435777.1_Missense_Mutation_p.A294S	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	294	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GTGACAAAGGCGTACTCATCA	0.532										HNSCC(7;0.00092)																											p.A294S		Atlas-SNP	.											.	COL22A1	390	.	0			c.G880T						.						117	95	103					8																	139838990		2203	4300	6503	SO:0001583	missense	169044	exon6			CAAAGGCGTACTC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.880G>T	chr8.hg19:g.139838990C>A	ENSP00000303153:p.Ala294Ser	121.0	0.0		138.0	35.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.633641	0.87660	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	T;T	0.13778	2.56;2.56	5.21	5.21	0.72293	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.46758	U	0.000264	T	0.27559	0.0677	L	0.33485	1.01	0.58432	D	0.999997	D	0.89917	1.0	D	0.81914	0.995	T	0.01182	-1.1426	9	.	.	.	.	17.8006	0.88586	0.0:1.0:0.0:0.0	.	294	Q8NFW1	COMA1_HUMAN	S	294	ENSP00000303153:A294S;ENSP00000387655:A294S	.	A	-	1	0	COL22A1	139908172	1.000000	0.71417	0.999000	0.59377	0.827000	0.46813	4.718000	0.61930	2.452000	0.82932	0.644000	0.83932	GCC	.	.		0.532	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139838990	C	A	139838990	3	1	87	1	0	0	0	0	1	0	0	0	3683	768	27	1	4240	1	COL22A1	8	139838990	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	37227614	139838990	6525032	29	11671										
PFKP	5214	hgsc.bcm.edu	37	chr10	3146084	3146084	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgaccatcggcacggactccGccctgcacaggatcatcgag	11	15	1	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr10:3146084G>A	ENST00000381125.4	+	5	644	c.568G>A	c.(568-570)Gcc>Acc	p.A190T	PFKP_ENST00000421751.1_3'UTR|PFKP_ENST00000381075.2_Missense_Mutation_p.A182T	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	190	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		CACGGACTCCGCCCTGCACAG	0.637																																					p.A190T		Atlas-SNP	.											.	PFKP	182	.	0			c.G568A						.						103	77	86					10																	3146084		2203	4300	6503	SO:0001583	missense	5214	exon5			GACTCCGCCCTGC	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"Phosphofructokinase, platelet type"	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.568G>A	chr10.hg19:g.3146084G>A	ENSP00000370517:p.Ala190Thr	60.0	0.0		72.0	17.0	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Missense_Mutation	SNP	ENST00000381125.4	hg19	CCDS7059.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.819537	0.71028	.	.	ENSG00000067057	ENST00000381125;ENST00000397834;ENST00000381075;ENST00000421751;ENST00000407806	D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61	4.64	4.64	0.57946	Phosphofructokinase domain (2);	0.000000	0.85682	D	0.000000	D	0.96917	0.8993	H	0.98507	4.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98797	1.0738	10	0.72032	D	0.01	.	17.8892	0.88866	0.0:0.0:1.0:0.0	.	182;190	Q5VSR7;Q01813	.;K6PP_HUMAN	T	190;179;182;152;152	ENSP00000370517:A190T;ENSP00000370465:A182T;ENSP00000410590:A152T;ENSP00000385880:A152T	ENSP00000370465:A182T	A	+	1	0	PFKP	3136084	1.000000	0.71417	0.051000	0.19133	0.004000	0.04260	9.498000	0.97972	2.293000	0.77203	0.650000	0.86243	GCC	.	.		0.637	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627		A	3146084	G	A	3146084	3	1	87	1	0	0	0	0	1	0	0	0	11775	1087	38	1	586	1	PFKP	10	3146084	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10		3146084	132388663	30	11672										
LCOR	84458	hgsc.bcm.edu	37	chr10	98715171	98715171	+	Frame_Shift_Del	DEL	G	G	-													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tcgaggaatggatctttcttGggagtctcgcactggtgatc							TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr10:98715171delG	ENST00000371097.4	+	8	1340	c.794delG	c.(793-795)tggfs	p.W265fs	LCOR_ENST00000371103.3_Frame_Shift_Del_p.W265fs|LCOR_ENST00000540664.1_Frame_Shift_Del_p.W265fs|LCOR_ENST00000356016.3_Frame_Shift_Del_p.W265fs|LCOR_ENST00000498444.1_Intron			Q96JN0	LCOR_HUMAN	ligand dependent nuclear receptor corepressor	265					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|urinary_tract(1)	13		Colorectal(252;0.162)		Epithelial(162;4.43e-09)|all cancers(201;2.96e-07)		GATCTTTCTTGGGAGTCTCGC	0.408																																					p.W265fs		Atlas-Indel,Pindel	.											.	LCOR	32	.	0			c.793delT						.						82	85	84					10																	98715171		2203	4300	6503	SO:0001589	frameshift_variant	84458	exon8			.		CCDS7451.1, CCDS53561.1	10q24	2006-06-28			ENSG00000196233	ENSG00000196233			29503	protein-coding gene	gene with protein product		607698				12535528, 15193453	Standard	NM_001170765		Approved	MLR2, FLJ38026, KIAA1795		Q96JN0	OTTHUMG00000018841	ENST00000371097.4:c.794delG	chr10.hg19:g.98715171delG	ENSP00000360138:p.Trp265fs	157.0	0.0		138.0	23.0	NM_001170766	D3DR47|Q5VW16|Q7Z723|Q86T32|Q86T33|Q8N3L6	Frame_Shift_Del	DEL	ENST00000371097.4	hg19	CCDS7451.1																																																																																			.	.		0.408	LCOR-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049628.2			-	98715171	G	-	98715171	7	5	87	1	0	1	0	1	0	0	0	0	8698	1357	47	0	804	0	LCOR	10	98715171	Frame_Shift_Del	DEL	G	TCGA-DD-A114-01A-11D-A12Z-10	95569087	98715171	36819576	31	11673										
OR52R1	119695	hgsc.bcm.edu	37	chr11	4825512	4825512	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	acagcatacgtggcacagaaCggaaaggcaatccacaactg	10	11	0	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:4825512C>A	ENST00000356069.2	-	1	98	c.99G>T	c.(97-99)ccG>ccT	p.P33P	MMP26_ENST00000477339.1_Intron|OR52R1_ENST00000380382.1_Silent_p.P112P|MMP26_ENST00000380390.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCACAGAACGGAAAGGCAA	0.512																																					p.P33P		Atlas-SNP	.											OR52R1,NS,malignant_melanoma,-1,4	OR52R1	81	.	0			c.G99T						.						94	84	87					11																	4825512		2201	4298	6499	SO:0001819	synonymous_variant	119695	exon1			ACAGAACGGAAAG	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"GPCR / Class A : Olfactory receptors"	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.99G>T	chr11.hg19:g.4825512C>A		148.0	1.0		132.0	20.0	NM_001005177	Q6IFI0	Silent	SNP	ENST00000356069.2	hg19	CCDS31360.2																																																																																			.	.		0.512	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177		A	4825512	C	A	4825512	2	1	87	1	0	0	0	0	0	0	0	1	11140	523	19	1		1	OR52R1	11	4825512	Silent	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10		4825512	130181004	32	11674										
ANO5	203859	hgsc.bcm.edu	37	chr11	22297638	22297659	+	Splice_Site	DEL	TGCATTTACTTCCACTTTTCAG	TGCATTTACTTCCACTTTTCAG	-													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgcatttacttccacttttcAggtacagagattacagatat					rs367604910		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	TGCATTTACTTCCACTTTTCAG	TGCATTTACTTCCACTTTTCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:22297638_22297659delTGCATTTACTTCCACTTTTCAG	ENST00000324559.8	+	21	2731_2751	c.2414_2434delTGCATTTACTTCCACTTTTCAG	c.(2413-2436)atgcatttacttccacttttcagc>agc	p.MHLLPLF805fs	ANO5_ENST00000532043.1_3'UTR	NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	805					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCCACTTTTCAGGTACAGAGATTACAGATATCCTCCTGATGA	0.324																																					.		Pindel	.											.	ANO5	162	.	0			.						.																																			SO:0001630	splice_region_variant	203859	.			.	AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.2415-1TGCATTTACTTCCACTTTTCAG>-	chr11.hg19:g.22297638_22297659delTGCATTTACTTCCACTTTTCAG		156.0	0.0		236.0	10.0	.		Splice_Site	DEL	ENST00000324559.8	hg19	CCDS31444.1																																																																																			.	.		0.324	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599	Frame_Shift_Del	-	22297659	TGCATTTACTTCCACTTTTCAG	-	22297638	8	5	87	1	0	1	0	1	0	0	1	0	700	202	7	0	2495	0	ANO5	11	22297638	Splice_Site	DEL	TGCATTTACTTCCACTTTTCAG	TCGA-DD-A114-01A-11D-A12Z-10	17472126	22297638	112708878	33	11675	49	2								
ANO5	203859	hgsc.bcm.edu	37	chr11	22297639	22297639	+	Splice_Site	DEL	G	G	-													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gcatttacttccacttttcaGgtacagagattacagatatc							TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:22297639delG	ENST00000324559.8	+	21	2731		c.e21-1		ANO5_ENST00000532043.1_Splice_Site	NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CCACTTTTCAGGTACAGAGAT	0.323																																					.		Atlas-Indel,Pindel	.											.	ANO5	162	.	0			c.2412-2G>-						.						70	67	68					11																	22297639		2203	4298	6501	SO:0001630	splice_region_variant	203859	exon21			.	AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.2415-1G>-	chr11.hg19:g.22297639delG		199.0	0.0		286.0	31.0	NM_001142649		Splice_Site	DEL	ENST00000324559.8	hg19	CCDS31444.1																																																																																			.	.		0.323	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599	Intron	-	22297639	G	-	22297639	8	5	87	1	0	1	0	1	0	0	1	0	700	1014	35	0	2496	0	ANO5	11	22297639	Splice_Site	DEL	G	TCGA-DD-A114-01A-11D-A12Z-10	1	22297639	112708877	34	11676	49	2								
LRRC4C	57689	hgsc.bcm.edu	37	chr11	40137653	40137653	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	aacctcacgcaggtttttccGaacacaaatcaccttgctga	6	13	2	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:40137653G>T	ENST00000278198.2	-	2	2153	c.190C>A	c.(190-192)Cgg>Agg	p.R64R	LRRC4C_ENST00000527150.1_Silent_p.R64R|LRRC4C_ENST00000528697.1_Silent_p.R64R|LRRC4C_ENST00000530763.1_Silent_p.R64R			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	64	LRRNT.				regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				AGGTTTTTCCGAACACAAATC	0.532																																					p.R64R		Atlas-SNP	.											.	LRRC4C	190	.	0			c.C190A						.						86	74	78					11																	40137653		2203	4300	6503	SO:0001819	synonymous_variant	57689	exon7			TTTTCCGAACACA	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.190C>A	chr11.hg19:g.40137653G>T		157.0	0.0		155.0	20.0	NM_001258419	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	hg19	CCDS31464.1																																																																																			.	.		0.532	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		T	40137653	G	T	40137653	2	4	87	1	0	0	0	0	0	0	0	1	9017	1057	37	1		1	LRRC4C	11	40137653	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	17840014	40137653	94868863	35	11677										
OR4A15	81328	hgsc.bcm.edu	37	chr11	55135486	55135486	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	atgtgactgaatttatcctcTtagggctcacacagaaccct	7	11	2	3			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:55135486T>C	ENST00000314706.3	+	1	127	c.127T>C	c.(127-129)Tta>Cta	p.L43L		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	43						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						ATTTATCCTCTTAGGGCTCAC	0.408																																					p.L43L		Atlas-SNP	.											.	OR4A15	161	.	0			c.T127C						.						66	63	64					11																	55135486		2201	4296	6497	SO:0001819	synonymous_variant	81328	exon1			ATCCTCTTAGGGC	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"GPCR / Class A : Olfactory receptors"	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.127T>C	chr11.hg19:g.55135486T>C		262.0	0.0		220.0	35.0	NM_001005275	Q6IFL4|Q96R65	Silent	SNP	ENST00000314706.3	hg19	CCDS31500.1																																																																																			.	.		0.408	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		C	55135486	T	C	55135486	2	2	87	1	0	0	0	0	0	0	0	1	11049	1606	56	2		2	OR4A15	11	55135486	Silent	SNP	T	TCGA-DD-A114-01A-11D-A12Z-10	14997833	55135486	79871030	36	11678										
OR5T2	219464	hgsc.bcm.edu	37	chr11	55999981	55999981	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tttgtgtgagtgtcagaataAgaaatagcaaggagaggagg	15	2	1	4			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:55999981A>C	ENST00000313264.4	-	1	756	c.681T>G	c.(679-681)tcT>tcG	p.S227S		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	227						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TGTCAGAATAAGAAATAGCAA	0.423																																					p.S227S		Atlas-SNP	.											OR5T2,NS,carcinoma,0,4	OR5T2	107	.	0			c.T681G						.						140	130	133					11																	55999981		2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			AGAATAAGAAATA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.681T>G	chr11.hg19:g.55999981A>C		655.0	1.0		658.0	95.0	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	hg19	CCDS31523.1																																																																																			.	.		0.423	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		C	55999981	A	C	55999981	2	2	87	1	0	0	0	0	0	0	0	1	11191	59	3	5		5	OR5T2	11	55999981	Silent	SNP	A	TCGA-DD-A114-01A-11D-A12Z-10	864495	55999981	79006535	37	11679										
TRIM49	57093	hgsc.bcm.edu	37	chr11	89537604	89537604	+	Frame_Shift_Del	DEL	C	C	-													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gcacagggggcagatgagttCcccctgaaagacctgtaaga							TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:89537604delC	ENST00000329758.1	-	3	362	c.34delG	c.(34-36)gaafs	p.E12fs	TRIM49_ENST00000532501.2_Frame_Shift_Del_p.E12fs	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	12						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(14)|prostate(1)|skin(2)|stomach(1)	27		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CAGATGAGTTCCCCCTGAAAG	0.463																																					p.E12fs		Atlas-INDEL	.											.	TRIM49	45	.	0			c.35delA						.						14	15	15					11																	89537604		2155	4245	6400	SO:0001589	frameshift_variant	57093	exon3			.	AB037682	CCDS8287.1	11p11.12-q12	2012-05-21	2011-01-25	2004-11-17	ENSG00000168930	ENSG00000168930		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	13431	protein-coding gene	gene with protein product		606124	"ring finger protein 18", "tripartite motif-containing 49"	RNF18		11018261	Standard	NM_020358		Approved	TRIM49A	uc001pdb.3	P0CI25		ENST00000329758.1:c.34delG	chr11.hg19:g.89537604delC	ENSP00000327604:p.Glu12fs	435.0	0.0		392.0	36.0	NM_020358	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Frame_Shift_Del	DEL	ENST00000329758.1	hg19	CCDS8287.1																																																																																			.	.		0.463	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358		-	89537604	C	-	89537604	7	5	87	1	0	1	0	1	0	0	0	0	16539	864	30	0	1348	0	TRIM49	11	89537604	Frame_Shift_Del	DEL	C	TCGA-DD-A114-01A-11D-A12Z-10	33537623	89537604	45468912	38	11680										
FAM55D	54827	hgsc.bcm.edu	37	chr11	114453455	114453455	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cccgccatattgcttcctgcGtcccaagtggtccctcacct	7	18	1	0	rs111330181		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:114453455G>A	ENST00000375478.3	-	3	565	c.385C>T	c.(385-387)Cgc>Tgc	p.R129C	NXPE4_ENST00000424261.2_Intron	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	129						extracellular vesicular exosome (GO:0070062)											TGCTTCCTGCGTCCCAAGTGG	0.587													G|||	1	0.000199681	8e-04	0	5008	,	,		22557	0		0	False		,,,				2504	0				p.R129C		Atlas-SNP	.											FAM55D,right_upper_lobe,carcinoma,0,2	.	.	.	0			c.C385T						.	G	CYS/ARG,	0,4390		0,0,2195	109	110	110		385,	3.1	0	11	dbSNP_132	110	3,8581		0,3,4289	yes	missense,intron	FAM55D	NM_001077639.1,NM_017678.2	180,	0,3,6484	AA,AG,GG		0.0349,0.0,0.0231	benign,	129/545,	114453455	3,12971	2195	4292	6487	SO:0001583	missense	54827	exon3			TCCTGCGTCCCAA	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 33", "family with sequence similarity 55, member D"	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.385C>T	chr11.hg19:g.114453455G>A	ENSP00000364627:p.Arg129Cys	456.0	0.0		443.0	59.0	NM_001077639	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	hg19	CCDS41718.1	.	.	.	.	.	.	.	.	.	.	G	3.731	-0.055544	0.07362	0.0	3.49E-4	ENSG00000137634	ENST00000375478	T	0.14516	2.5	5.01	3.12	0.35913	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	1.043540	0.07504	N	0.907792	T	0.23249	0.0562	M	0.89840	3.065	0.09310	N	1	B	0.29481	0.245	B	0.27715	0.082	T	0.35076	-0.9803	10	0.54805	T	0.06	.	4.665	0.12660	0.1645:0.0:0.5301:0.3054	.	129	Q6UWF7	FA55D_HUMAN	C	129	ENSP00000364627:R129C	ENSP00000364627:R129C	R	-	1	0	FAM55D	113958665	0.005000	0.15991	0.007000	0.13788	0.003000	0.03518	1.457000	0.35212	0.607000	0.29982	-0.229000	0.12294	CGC	.	A|1.000;|0.000		0.587	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678		A	114453455	G	A	114453455	3	1	87	1	0	0	0	0	1	0	0	0	5595	1145	40	1	1265	1	FAM55D	11	114453455	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	24915851	114453455	20553061	39	11681										
SLC37A4	51399	hgsc.bcm.edu	37	chr11	118896705	118896705	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	agtcactggtcactgttaccCggaagaggtacatggacact	11	10	2	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:118896705C>A	ENST00000533632.1	+	0	1759				SLC37A4_ENST00000330775.7_Missense_Mutation_p.R318L|SLC37A4_ENST00000538950.1_Missense_Mutation_p.R246L|SLC37A4_ENST00000525102.1_5'UTR|SLC37A4_ENST00000545985.1_Missense_Mutation_p.R319L|SLC37A4_ENST00000357590.5_Missense_Mutation_p.R319L	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4						dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)				NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		CACTGTTACCCGGAAGAGGTA	0.567																																					p.R319L		Atlas-SNP	.											.	SLC37A4	19	.	0			c.G956T						.						54	59	58					11																	118896705		2081	4220	6301	SO:0001628	intergenic_variant	2542	exon8			GTTACCCGGAAGA	AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"Trafficking protein particle complex"	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296			chr11.hg19:g.118896705C>A		140.0	0.0		134.0	14.0	NM_001467	A8K3A5|B4DME1	Missense_Mutation	SNP	ENST00000533632.1	hg19	CCDS8407.1																																																																																			.	.		0.567	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146		A	118896705	C	A	118896705	1	1	87	0	1	0	0	0	0	0	0	0	14615	652	23	1		1	SLC37A4	11	118896705	IGR	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	4443250	118896705	16109811	40	11682										
ZNF202	7753	hgsc.bcm.edu	37	chr11	123598880	123598880	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	acagtcttcttccaagacatAttctccatagaactctttct	3	12	5	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:123598880A>G	ENST00000529691.1	-	5	1012	c.793T>C	c.(793-795)Tat>Cat	p.Y265H	ZNF202_ENST00000336139.4_Missense_Mutation_p.Y265H|ZNF202_ENST00000530393.1_Missense_Mutation_p.Y265H			O95125	ZN202_HUMAN	zinc finger protein 202	265	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		TCCAAGACATATTCTCCATAG	0.443																																					p.Y265H		Atlas-SNP	.											.	ZNF202	72	.	0			c.T793C						.						118	107	111					11																	123598880		2202	4299	6501	SO:0001583	missense	7753	exon7			AGACATATTCTCC	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"Zinc fingers, C2H2-type", "-", "-", "-"	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.793T>C	chr11.hg19:g.123598880A>G	ENSP00000433881:p.Tyr265His	227.0	0.0		238.0	13.0	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	hg19	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	A	18.39	3.613970	0.66672	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691	T;T;T	0.01767	4.65;4.65;4.65	4.58	4.58	0.56647	Krueppel-associated box (4);	0.000000	0.43579	D	0.000543	T	0.06600	0.0169	L	0.60455	1.87	0.35864	D	0.827721	D	0.76494	0.999	D	0.77004	0.989	T	0.46527	-0.9185	10	0.27082	T	0.32	-21.7355	10.2596	0.43419	1.0:0.0:0.0:0.0	.	265	O95125	ZN202_HUMAN	H	265	ENSP00000337724:Y265H;ENSP00000432504:Y265H;ENSP00000433881:Y265H	ENSP00000337724:Y265H	Y	-	1	0	ZNF202	123104090	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.524000	0.60552	1.929000	0.55896	0.459000	0.35465	TAT	.	.		0.443	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		G	123598880	A	G	123598880	3	3	87	1	0	0	0	0	1	0	0	0	17778	449	16	2	1165	2	ZNF202	11	123598880	Missense_Mutation	SNP	A	TCGA-DD-A114-01A-11D-A12Z-10	4702175	123598880	11407636	41	11683										
ZNF202	7753	hgsc.bcm.edu	37	chr11	123600353	123600353	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cagggtctggagctcctcttCctggtgtggacgctgctctg	14	12	3	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:123600353C>A	ENST00000529691.1	-	3	802	c.583G>T	c.(583-585)Gaa>Taa	p.E195*	ZNF202_ENST00000336139.4_Nonsense_Mutation_p.E195*|ZNF202_ENST00000530393.1_Nonsense_Mutation_p.E195*			O95125	ZN202_HUMAN	zinc finger protein 202	195					lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		AGCTCCTCTTCCTGGTGTGGA	0.617																																					p.E195X		Atlas-SNP	.											.	ZNF202	72	.	0			c.G583T						.						49	43	45					11																	123600353		2202	4299	6501	SO:0001587	stop_gained	7753	exon5			CCTCTTCCTGGTG	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"Zinc fingers, C2H2-type", "-", "-", "-"	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.583G>T	chr11.hg19:g.123600353C>A	ENSP00000433881:p.Glu195*	140.0	0.0		123.0	10.0	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Nonsense_Mutation	SNP	ENST00000529691.1	hg19	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.930758	0.92389	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691	.	.	.	5.32	4.4	0.53042	.	0.143577	0.32093	N	0.006590	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-10.0485	8.9155	0.35579	0.0:0.9009:0.0:0.0991	.	.	.	.	X	195	.	ENSP00000337724:E195X	E	-	1	0	ZNF202	123105563	0.088000	0.21588	0.069000	0.20011	0.518000	0.34316	3.040000	0.49799	2.482000	0.83794	0.557000	0.71058	GAA	.	.		0.617	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		A	123600353	C	A	123600353	4	1	87	1	0	0	0	0	0	1	0	0	17778	864	30	3	1383	3	ZNF202	11	123600353	Nonsense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	1473	123600353	11406163	42	11684										
OVCH1	341350	hgsc.bcm.edu	37	chr12	29617463	29617463	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cactgatgcttccccatccgGtcacagcacagatctccgag	8	16	2	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:29617463G>T	ENST00000318184.5	-	18	2101	c.2102C>A	c.(2101-2103)aCc>aAc	p.T701N	OVCH1-AS1_ENST00000549411.1_Intron|OVCH1-AS1_ENST00000551108.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	701	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TCCCCATCCGGTCACAGCACA	0.438																																					p.T701N		Atlas-SNP	.											.	OVCH1	195	.	0			c.C2102A						.						60	59	59					12																	29617463		1924	4131	6055	SO:0001583	missense	341350	exon18			CATCCGGTCACAG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.2102C>A	chr12.hg19:g.29617463G>T	ENSP00000326708:p.Thr701Asn	148.0	0.0		142.0	20.0	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	hg19		.	.	.	.	.	.	.	.	.	.	G	15.85	2.955964	0.53293	.	.	ENSG00000187950	ENST00000318184	D	0.89552	-2.53	2.97	1.13	0.20643	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.92080	0.7490	M	0.78285	2.405	0.27105	N	0.962511	D	0.71674	0.998	D	0.63113	0.911	D	0.83443	0.0044	9	0.72032	D	0.01	.	6.8944	0.24247	0.2445:0.0:0.7555:0.0	.	701	Q7RTY7	OVCH1_HUMAN	N	701	ENSP00000326708:T701N	ENSP00000326708:T701N	T	-	2	0	OVCH1	29508730	1.000000	0.71417	0.048000	0.18961	0.993000	0.82548	4.138000	0.58017	0.301000	0.22738	0.655000	0.94253	ACC	.	.		0.438	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		T	29617463	G	T	29617463	3	4	87	1	0	0	0	0	1	0	0	0	11332	1261	44	3	1346	3	OVCH1	12	29617463	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10		29617463	104234432	43	11685										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32137832	32137832	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ataaaatgacagcatcttatGaacaagcttctcaggaaacc	6	9	2	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:32137832G>T	ENST00000312561.4	+	4	4357	c.3943G>T	c.(3943-3945)Gaa>Taa	p.E1315*	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1315																	AGCATCTTATGAACAAGCTTC	0.338																																					p.E1315X		Atlas-SNP	.											.	.	.	.	0			c.G3943T						.						82	85	84					12																	32137832		2203	4300	6503	SO:0001587	stop_gained	55196	exon4			TCTTATGAACAAG	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3943G>T	chr12.hg19:g.32137832G>T	ENSP00000310338:p.Glu1315*	118.0	0.0		153.0	20.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Nonsense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	G	43	10.299438	0.99378	.	.	ENSG00000174718	ENST00000312561	.	.	.	3.99	1.03	0.20045	.	0.844950	0.10220	N	0.701071	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7252	0.23353	0.4378:0.0:0.5622:0.0	.	.	.	.	X	1315	.	.	E	+	1	0	C12orf35	32029099	0.279000	0.24239	0.001000	0.08648	0.145000	0.21501	1.027000	0.30115	0.148000	0.19059	-0.253000	0.11424	GAA	.	.		0.338	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		T	32137832	G	T	32137832	4	4	87	1	0	0	0	0	0	1	0	0	1684	1291	45	3	3945	3	C12orf35	12	32137832	Nonsense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	2520369	32137832	101714063	44	11686										
KIF21A	55605	hgsc.bcm.edu	37	chr12	39726715	39726715	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ctgtttccatttgttgccggCgttggtaaggcctggactct	12	10	1	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:39726715C>G	ENST00000361418.5	-	19	2697	c.2682G>C	c.(2680-2682)acG>acC	p.T894T	KIF21A_ENST00000395670.3_Silent_p.T894T|KIF21A_ENST00000361961.3_Silent_p.T881T|KIF21A_ENST00000544797.2_Silent_p.T881T|KIF21A_ENST00000541463.2_Silent_p.T858T			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	894					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				TTGTTGCCGGCGTTGGTAAGG	0.458																																					p.T894T		Atlas-SNP	.											.	KIF21A	238	.	0			c.G2682C						.						70	72	71					12																	39726715		2203	4300	6503	SO:0001819	synonymous_variant	55605	exon19			TGCCGGCGTTGGT	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.2682G>C	chr12.hg19:g.39726715C>G		177.0	0.0		187.0	37.0	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Silent	SNP	ENST00000361418.5	hg19	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	C	0.021	-1.426334	0.01117	.	.	ENSG00000139116	ENST00000552961	.	.	.	5.58	-11.2	0.00127	.	.	.	.	.	T	0.24236	0.0587	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.17561	-1.0365	4	.	.	.	.	9.0399	0.36311	0.1905:0.0738:0.0656:0.6701	.	.	.	.	P	242	.	.	R	-	2	0	KIF21A	38012982	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-1.244000	0.02902	-2.383000	0.00592	-0.484000	0.04775	CGC	.	.		0.458	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		G	39726715	C	G	39726715	2	3	87	1	0	0	0	0	0	0	0	1	8297	755	27	4		4	KIF21A	12	39726715	Silent	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	7588883	39726715	94125180	45	11687										
MLL2	8085	hgsc.bcm.edu	37	chr12	49443882	49443882	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gggtagacctccataggggtCacaggggccagctcctcggg	16	12	1	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:49443882C>A	ENST00000301067.7	-	11	3488	c.3489G>T	c.(3487-3489)gtG>gtT	p.V1163V		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1163	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CCATAGGGGTCACAGGGGCCA	0.627																																					p.V1163V		Atlas-SNP	.											.	MLL2	1173	.	0			c.G3489T						.						53	58	56					12																	49443882		1942	4129	6071	SO:0001819	synonymous_variant	8085	exon11			AGGGGTCACAGGG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.3489G>T	chr12.hg19:g.49443882C>A		124.0	0.0		157.0	23.0	NM_003482	O14687	Silent	SNP	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.627	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49443882	C	A	49443882	2	1	87	1	0	0	0	0	0	0	0	1	9630	813	29	3		3	MLL2	12	49443882	Silent	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	9717167	49443882	84408013	46	11688										
BCDIN3D	144233	hgsc.bcm.edu	37	chr12	50236856	50236856	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	acactccctccatccagttcCgtgggcaccgccattagcct	7	18	0	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:50236856C>A	ENST00000333924.4	-	1	56	c.15G>T	c.(13-15)acG>acT	p.T5T	BCDIN3D-AS1_ENST00000549124.1_RNA|BCDIN3D-AS1_ENST00000548872.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	5					miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						CATCCAGTTCCGTGGGCACCG	0.642																																					p.T5T		Atlas-SNP	.											.	BCDIN3D	20	.	0			c.G15T						.						40	38	39					12																	50236856		2202	4299	6501	SO:0001819	synonymous_variant	144233	exon1			CAGTTCCGTGGGC		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.15G>T	chr12.hg19:g.50236856C>A		55.0	0.0		88.0	16.0	NM_181708	A8K829	Silent	SNP	ENST00000333924.4	hg19	CCDS8790.1																																																																																			.	.		0.642	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708		A	50236856	C	A	50236856	2	1	87	1	0	0	0	0	0	0	0	1	1357	639	23	1		1	BCDIN3D	12	50236856	Silent	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	792974	50236856	83615039	47	11689										
ALDH1L2	160428	hgsc.bcm.edu	37	chr12	105464456	105464456	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgggaatgaactgagtgcagAaagggagcacatttagctct	13	6	1	3			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:105464456A>G	ENST00000258494.9	-	3	460	c.320T>C	c.(319-321)tTc>tCc	p.F107S	ALDH1L2_ENST00000424857.2_Missense_Mutation_p.F107S|RP11-61E11.1_ENST00000547750.1_RNA	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	107	GART.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						CTGAGTGCAGAAAGGGAGCAC	0.498																																					p.F107S		Atlas-SNP	.											.	ALDH1L2	71	.	0			c.T320C						.						168	137	147					12																	105464456		2203	4300	6503	SO:0001583	missense	160428	exon3			GTGCAGAAAGGGA	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.320T>C	chr12.hg19:g.105464456A>G	ENSP00000258494:p.Phe107Ser	307.0	0.0		335.0	62.0	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	hg19	CCDS31891.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.683030	0.88542	.	.	ENSG00000136010	ENST00000258494;ENST00000424857	T;T	0.75367	-0.93;-0.93	5.27	5.27	0.74061	Formyl transferase, N-terminal (3);	0.047094	0.85682	D	0.000000	T	0.80607	0.4655	L	0.45470	1.425	0.80722	D	1	D	0.59767	0.986	D	0.72075	0.976	T	0.81924	-0.0710	10	0.72032	D	0.01	.	10.6981	0.45911	0.8576:0.0:0.0:0.1424	.	107	Q3SY69	AL1L2_HUMAN	S	107	ENSP00000258494:F107S;ENSP00000389608:F107S	ENSP00000258494:F107S	F	-	2	0	ALDH1L2	103988586	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.217000	0.77982	2.133000	0.65898	0.533000	0.62120	TTC	.	.		0.498	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		G	105464456	A	G	105464456	3	3	87	1	0	0	0	0	1	0	0	0	495	246	9	2	2535	2	ALDH1L2	12	105464456	Missense_Mutation	SNP	A	TCGA-DD-A114-01A-11D-A12Z-10	55227600	105464456	28387439	48	11690										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124387605	124387605	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cagaggtcatgcccatcctgGaggccgccaagctggaactg	13	13	1	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:124387605G>A	ENST00000409039.3	+	56	9431	c.9406G>A	c.(9406-9408)Gag>Aag	p.E3136K		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3136	Stalk. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCCCATCCTGGAGGCCGCCAA	0.572																																					p.E3136K		Atlas-SNP	.											.	DNAH10	888	.	0			c.G9406A						.						51	62	59					12																	124387605		2104	4226	6330	SO:0001583	missense	196385	exon56			ATCCTGGAGGCCG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.9406G>A	chr12.hg19:g.124387605G>A	ENSP00000386770:p.Glu3136Lys	112.0	0.0		96.0	19.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	22.6	4.311572	0.81358	.	.	ENSG00000197653	ENST00000409039	T	0.74002	-0.8	5.65	5.65	0.86999	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.85682	D	0.000000	D	0.88764	0.6525	M	0.89287	3.02	0.58432	D	0.999997	D	0.76494	0.999	D	0.75020	0.985	D	0.89316	0.3636	10	0.52906	T	0.07	.	19.7205	0.96142	0.0:0.0:1.0:0.0	.	3136	Q8IVF4	DYH10_HUMAN	K	3136	ENSP00000386770:E3136K	ENSP00000386770:E3136K	E	+	1	0	DNAH10	122953558	1.000000	0.71417	1.000000	0.80357	0.545000	0.35147	6.589000	0.74080	2.671000	0.90904	0.462000	0.41574	GAG	.	.		0.572	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124387605	G	A	124387605	3	1	87	1	0	0	0	0	1	0	0	0	4600	1175	41	3	9628	3	DNAH10	12	124387605	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	18923149	124387605	9464290	49	11691										
SACS	26278	hgsc.bcm.edu	37	chr13	23904756	23904756	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tctgtccggctgaaggggggCatttttctttgttctgttgc	13	8	3	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr13:23904756C>A	ENST00000382292.3	-	9	13532	c.13259G>T	c.(13258-13260)tGc>tTc	p.C4420F	SACS_ENST00000402364.1_Missense_Mutation_p.C3670F|SACS_ENST00000382298.3_Missense_Mutation_p.C4420F			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4420					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGAAGGGGGGCATTTTTCTTT	0.433																																					p.C4420F		Atlas-SNP	.											.	SACS	871	.	0			c.G13259T						.						81	85	84					13																	23904756		2203	4299	6502	SO:0001583	missense	26278	exon10			GGGGGGCATTTTT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.13259G>T	chr13.hg19:g.23904756C>A	ENSP00000371729:p.Cys4420Phe	129.0	0.0		151.0	35.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	0.058	-1.231456	0.01505	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.86956	-2.04;-2.19;-2.04	5.85	5.85	0.93711	.	0.485149	0.26746	N	0.022708	T	0.71796	0.3382	N	0.02011	-0.69	0.24750	N	0.992988	B	0.02656	0.0	B	0.01281	0.0	T	0.63791	-0.6557	10	0.49607	T	0.09	.	14.9345	0.70944	0.143:0.857:0.0:0.0	.	4420	Q9NZJ4	SACS_HUMAN	F	4420;3670;4420	ENSP00000371729:C4420F;ENSP00000385844:C3670F;ENSP00000371735:C4420F	ENSP00000371729:C4420F	C	-	2	0	SACS	22802756	0.984000	0.35163	0.565000	0.28409	0.072000	0.16883	2.273000	0.43381	2.767000	0.95098	0.563000	0.77884	TGC	.	.		0.433	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23904756	C	A	23904756	3	1	87	1	0	0	0	0	1	0	0	0	13819	710	25	3	484	3	SACS	13	23904756	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10		23904756	91265122	50	11692										
RB1	5925	hgsc.bcm.edu	37	chr13	49030478	49030479	+	Frame_Shift_Ins	INS	-	-	A													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cctctctttcactgttttatINSaaaaaaggttagtagatgat							TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr13:49030478_49030479insA	ENST00000267163.4	+	19	2091_2092	c.1953_1954insA	c.(1954-1956)aaafs	p.K652fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	652	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.V654fs*4(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CACTGTTTTATAAAAAAGGTTA	0.401		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.Y651fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	26	Whole gene deletion(15)|Unknown(10)|Deletion - Frameshift(1)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|soft_tissue(2)|adrenal_gland(1)|eye(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	c.1953_1954insA						.																																			SO:0001589	frameshift_variant	5925	exon19	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1959dupA	chr13.hg19:g.49030484_49030484dupA	ENSP00000267163:p.Lys652fs	126.0	0.0		103.0	19.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Ins	INS	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.401	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			A	49030479	-	A	49030478	7	5	87	1	0	1	1	0	0	0	0	0	13113	1413	49	0	2027	0	RB1	13	49030478	Frame_Shift_Ins	INS	-	TCGA-DD-A114-01A-11D-A12Z-10	25125722	49030478	66139400	51	11693										
COMMD6	170622	hgsc.bcm.edu	37	chr13	76111799	76111799	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gcggggcggccgctcacccaCctggttggtgacctgaaacg	15	14	1	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr13:76111799C>A	ENST00000377615.3	-	3	219		c.e3+1		COMMD6_ENST00000460675.1_Intron|COMMD6_ENST00000377619.5_5'Flank|COMMD6_ENST00000406936.3_Splice_Site|COMMD6_ENST00000355801.4_Splice_Site			Q7Z4G1	COMD6_HUMAN	COMM domain containing 6						negative regulation of NF-kappaB transcription factor activity (GO:0032088)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			breast(1)|lung(1)|urinary_tract(1)	3		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)		CGCTCACCCACCTGGTTGGTG	0.627																																					.		Atlas-SNP	.											.	COMMD6	4	.	0			c.54+1G>T						.						60	56	57					13																	76111799		2203	4300	6503	SO:0001630	splice_region_variant	170622	exon3			CACCCACCTGGTT	AY542161	CCDS9451.1, CCDS9452.1	13q22	2004-02-18			ENSG00000188243	ENSG00000188243			24015	protein-coding gene	gene with protein product		612377				15799966	Standard	NM_203497		Approved	Acrg	uc001vjn.1	Q7Z4G1	OTTHUMG00000017089	ENST00000377615.3:c.54+1G>T	chr13.hg19:g.76111799C>A		63.0	0.0		78.0	13.0	NM_203497	A6NF28|B7ZLN0|Q5TBK4	Splice_Site	SNP	ENST00000377615.3	hg19	CCDS9451.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.898710	0.72639	.	.	ENSG00000188243	ENST00000406936;ENST00000377615;ENST00000355801	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5719	0.61851	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COMMD6	75009800	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.273000	0.51623	2.563000	0.86464	0.655000	0.94253	.	.	.		0.627	COMMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045288.4	XM_085023	Intron	A	76111799	C	A	76111799	5	1	87	1	0	0	0	0	0	0	1	0	3722	521	18	3	257	3	COMMD6	13	76111799	Splice_Site	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	27081321	76111799	39058079	52	11694										
SLITRK6	84189	hgsc.bcm.edu	37	chr13	86370026	86370026	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	agatccaatattcggccaatGtgttcgagaaaaccaacata	7	9	0	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr13:86370026G>T	ENST00000400286.2	-	2	1216	c.618C>A	c.(616-618)caC>caA	p.H206Q		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	206					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		TTCGGCCAATGTGTTCGAGAA	0.408																																					p.H206Q		Atlas-SNP	.											.	SLITRK6	150	.	0			c.C618A						.						104	93	96					13																	86370026		1879	4104	5983	SO:0001583	missense	84189	exon2			GCCAATGTGTTCG	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.618C>A	chr13.hg19:g.86370026G>T	ENSP00000383143:p.His206Gln	120.0	0.0		131.0	24.0	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	hg19	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872355	0.51695	.	.	ENSG00000184564	ENST00000400286	T	0.51817	0.69	5.96	3.31	0.37934	.	0.000000	0.85682	D	0.000000	T	0.55768	0.1941	L	0.39467	1.215	0.49798	D	0.999829	D	0.76494	0.999	D	0.85130	0.997	T	0.52704	-0.8540	10	0.45353	T	0.12	-15.3126	9.8979	0.41329	0.2205:0.0:0.7795:0.0	.	206	Q9H5Y7	SLIK6_HUMAN	Q	206	ENSP00000383143:H206Q	ENSP00000383143:H206Q	H	-	3	2	SLITRK6	85268027	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.524000	0.35942	0.870000	0.35726	0.655000	0.94253	CAC	.	.		0.408	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		T	86370026	G	T	86370026	3	4	87	1	0	0	0	0	1	0	0	0	14762	1368	48	3	1911	3	SLITRK6	13	86370026	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	10258227	86370026	28799852	53	11695										
MYH6	4624	hgsc.bcm.edu	37	chr14	23859463	23859463	+	Frame_Shift_Del	DEL	C	C	-													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cagcgtggcctcctccaggtCccgccgcatcttctggaact							TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr14:23859463delC	ENST00000356287.3	-	25	3564	c.3535delG	c.(3535-3537)gacfs	p.D1179fs	MIR208A_ENST00000362287.1_RNA|MYH6_ENST00000405093.3_Frame_Shift_Del_p.D1179fs			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1179					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TCCTCCAGGTCCCGCCGCATC	0.682																																					p.D1179fs		Atlas-INDEL	.											.	MYH6	274	.	0			c.3536delA						.						6	7	7					14																	23859463		1974	3882	5856	SO:0001589	frameshift_variant	4624	exon26			.	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.3535delG	chr14.hg19:g.23859463delC	ENSP00000348634:p.Asp1179fs	183.0	0.0		329.0	21.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Frame_Shift_Del	DEL	ENST00000356287.3	hg19	CCDS9600.1																																																																																			.	.		0.682	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			-	23859463	C	-	23859463	7	5	87	1	0	1	0	1	0	0	0	0	10047	855	30	0	2340	0	MYH6	14	23859463	Frame_Shift_Del	DEL	C	TCGA-DD-A114-01A-11D-A12Z-10		23859463	83490077	54	11696										
MYH7	4625	hgsc.bcm.edu	37	chr14	23889251	23889251	+	Frame_Shift_Del	DEL	C	C	-													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cagcgtggcctcctccaggtCccgccgcatcttctggaact							TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr14:23889251delC	ENST00000355349.3	-	27	3691	c.3529delG	c.(3529-3531)gacfs	p.D1177fs	MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1177					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCCTCCAGGTCCCGCCGCATC	0.682																																					p.D1177fs		Atlas-INDEL	.											.	MYH7	349	.	0			c.3530delA						.						6	7	7					14																	23889251		1994	3915	5909	SO:0001589	frameshift_variant	4625	exon27			.	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.3529delG	chr14.hg19:g.23889251delC	ENSP00000347507:p.Asp1177fs	187.0	0.0		326.0	34.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Frame_Shift_Del	DEL	ENST00000355349.3	hg19	CCDS9601.1																																																																																			.	.		0.682	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		-	23889251	C	-	23889251	7	5	87	1	0	1	0	1	0	0	0	0	10048	855	30	0	2334	0	MYH7	14	23889251	Frame_Shift_Del	DEL	C	TCGA-DD-A114-01A-11D-A12Z-10	29788	23889251	83460289	55	11697										
SYT16	83851	hgsc.bcm.edu	37	chr14	62551067	62551067	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ctgtggaaatgatcaaaggcAgccatttccgaaacctcgct	9	11	1	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr14:62551067A>T	ENST00000430451.2	+	5	1785	c.1588A>T	c.(1588-1590)Agc>Tgc	p.S530C		NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	530	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GATCAAAGGCAGCCATTTCCG	0.552																																					p.S530C		Atlas-SNP	.											.	SYT16	144	.	0			c.A1588T						.						59	58	59					14																	62551067		1961	4143	6104	SO:0001583	missense	83851	exon5			AAAGGCAGCCATT	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1588A>T	chr14.hg19:g.62551067A>T	ENSP00000394700:p.Ser530Cys	80.0	0.0		113.0	22.0	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	hg19	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631373	0.87660	.	.	ENSG00000139973	ENST00000430451	T	0.69806	-0.43	5.44	5.44	0.79542	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.84042	0.5385	M	0.88842	2.985	0.80722	D	1	D	0.62365	0.991	D	0.70487	0.969	D	0.87170	0.2220	10	0.72032	D	0.01	-7.4393	15.6783	0.77344	1.0:0.0:0.0:0.0	.	530	Q17RD7	SYT16_HUMAN	C	530	ENSP00000394700:S530C	ENSP00000394700:S530C	S	+	1	0	SYT16	61620820	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.752000	0.91632	2.284000	0.76573	0.523000	0.50628	AGC	.	.		0.552	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		T	62551067	A	T	62551067	3	4	87	1	0	0	0	0	1	0	0	0	15487	188	7	4	1606	4	SYT16	14	62551067	Missense_Mutation	SNP	A	TCGA-DD-A114-01A-11D-A12Z-10	38661816	62551067	44798473	56	11698										
SLC24A4	123041	hgsc.bcm.edu	37	chr14	92949118	92949118	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgcagcaagccccgctgggaGaagttcttcatggtcacctt	11	12	3	1	rs563681958		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr14:92949118G>T	ENST00000532405.1	+	13	1576	c.1350G>T	c.(1348-1350)gaG>gaT	p.E450D	SLC24A4_ENST00000298877.1_Missense_Mutation_p.E433D|SLC24A4_ENST00000351924.5_Missense_Mutation_p.E414D|SLC24A4_ENST00000393265.2_Missense_Mutation_p.E386D|SLC24A4_ENST00000531433.1_Missense_Mutation_p.E431D			Q8NFF2	NCKX4_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	450					amelogenesis (GO:0097186)|cellular calcium ion homeostasis (GO:0006874)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|sensory perception of smell (GO:0007608)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(20)|ovary(2)|skin(1)	36		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		CCCGCTGGGAGAAGTTCTTCA	0.602																																					p.E450D	NSCLC(10;315 435 10383 28450 38798)	Atlas-SNP	.											.	SLC24A4	112	.	0			c.G1350T						.						117	96	103					14																	92949118		2203	4300	6503	SO:0001583	missense	123041	exon13			CTGGGAGAAGTTC	AF520704	CCDS9903.1, CCDS45155.1, CCDS45156.1, CCDS9903.2, CCDS45155.2	14q32.12	2013-05-22			ENSG00000140090	ENSG00000140090		"Solute carriers"	10978	protein-coding gene	gene with protein product		609840					Standard	NM_153646		Approved	NCKX4	uc001yak.3	Q8NFF2	OTTHUMG00000167589	ENST00000532405.1:c.1350G>T	chr14.hg19:g.92949118G>T	ENSP00000431840:p.Glu450Asp	146.0	0.0		135.0	20.0	NM_153646	B4DHE7|B9ZVY2|Q8N8U6|Q8NCX1|Q8NFF0|Q8NFF1	Missense_Mutation	SNP	ENST00000532405.1	hg19	CCDS9903.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.5|28.5	4.922728|4.922728	0.92319|0.92319	.|.	.|.	ENSG00000140090|ENSG00000140090	ENST00000393265;ENST00000531433;ENST00000532405;ENST00000298877;ENST00000351924;ENST00000318079|ENST00000525557	T;T;T;T;T|.	0.79845|.	0.44;-0.02;0.44;0.44;-1.31|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.71896|.	0.3394|.	M|M	0.84683|0.84683	2.71|2.71	0.58432|0.58432	D|D	0.999996|0.999996	P;P;B|.	0.39903|.	0.694;0.529;0.246|.	P;B;B|.	0.45406|.	0.479;0.331;0.331|.	T|.	0.68488|.	-0.5395|.	10|.	0.46703|0.08179	T|T	0.11|0.78	.|.	13.1576|13.1576	0.59527|0.59527	0.0728:0.0:0.9272:0.0|0.0728:0.0:0.9272:0.0	.|.	431;386;450|.	Q8NFF2-3;Q8NFF2-2;Q8NFF2|.	.;.;NCKX4_HUMAN|.	D|X	386;431;450;433;414;302|316	ENSP00000376948:E386D;ENSP00000433302:E431D;ENSP00000431840:E450D;ENSP00000298877:E433D;ENSP00000337789:E414D|.	ENSP00000298877:E433D|ENSP00000432464:E316X	E|E	+|+	3|1	2|0	SLC24A4|SLC24A4	92018871|92018871	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.479000|6.479000	0.73600|0.73600	2.716000|2.716000	0.92895|0.92895	0.561000|0.561000	0.74099|0.74099	GAG|GAA	.	.		0.602	SLC24A4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395240.1	NM_153646		T	92949118	G	T	92949118	3	4	87	1	0	0	0	0	1	0	0	0	14483	933	33	3	1349	3	SLC24A4	14	92949118	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	30398051	92949118	14400422	57	11699										
CDC42BPB	9578	hgsc.bcm.edu	37	chr14	103430853	103430853	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	aagtacctttccaaggtgagGttggcgtccttgaccttcct	10	11	0	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr14:103430853G>T	ENST00000361246.2	-	19	3000	c.2712C>A	c.(2710-2712)aaC>aaA	p.N904K		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		CCAAGGTGAGGTTGGCGTCCT	0.652																																					p.N904K		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.C2712A						.						72	65	67					14																	103430853		2203	4300	6503	SO:0001583	missense	9578	exon19			GGTGAGGTTGGCG	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"CDC42-binding protein kinase beta (DMPK-like)"			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.2712C>A	chr14.hg19:g.103430853G>T	ENSP00000355237:p.Asn904Lys	58.0	0.0		60.0	13.0	NM_006035		Missense_Mutation	SNP	ENST00000361246.2	hg19	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	G	6.114	0.389289	0.11581	.	.	ENSG00000198752	ENST00000361246;ENST00000541396	T	0.39056	1.1	5.51	-7.37	0.01412	Myotonic dystrophy protein kinase, coiled coil (2);	0.047074	0.85682	D	0.000000	T	0.39145	0.1067	M	0.71581	2.175	0.39011	D	0.959553	B;B	0.17465	0.022;0.022	B;B	0.35353	0.201;0.143	T	0.22312	-1.0220	10	0.30078	T	0.28	.	11.6997	0.51564	0.3722:0.0764:0.5514:0.0	.	904;904	A9JR72;Q9Y5S2	.;MRCKB_HUMAN	K	904;41	ENSP00000355237:N904K	ENSP00000355237:N904K	N	-	3	2	CDC42BPB	102500606	0.996000	0.38824	0.000000	0.03702	0.141000	0.21300	0.383000	0.20651	-1.475000	0.01876	-0.253000	0.11424	AAC	.	.		0.652	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		T	103430853	G	T	103430853	3	4	87	1	0	0	0	0	1	0	0	0	3075	1252	44	3	2499	3	CDC42BPB	14	103430853	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	10481735	103430853	3918687	58	11700										
TSC2	7249	hgsc.bcm.edu	37	chr16	2098719	2098719	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ccaggtctgcagagggtaaaCagacggagtttatcatcacc	11	10	3	2	rs137854105		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr16:2098719C>T	ENST00000219476.3	+	2	733	c.103C>T	c.(103-105)Cag>Tag	p.Q35*	TSC2_ENST00000353929.4_Nonsense_Mutation_p.Q35*|TSC2_ENST00000382538.6_Intron|TSC2_ENST00000439673.2_Nonsense_Mutation_p.Q35*|TSC2_ENST00000568454.1_Nonsense_Mutation_p.Q46*|NTHL1_ENST00000219066.1_5'Flank|TSC2_ENST00000401874.2_Nonsense_Mutation_p.Q35*|TSC2_ENST00000350773.4_Nonsense_Mutation_p.Q35*	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	35	Required for interaction with TSC1.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				AGAGGGTAAACAGACGGAGTT	0.493			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.Q35X		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.C103T						.						172	145	154					16																	2098719		2198	4299	6497	SO:0001587	stop_gained	7249	exon2	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GGTAAACAGACGG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.103C>T	chr16.hg19:g.2098719C>T	ENSP00000219476:p.Gln35*	227.0	0.0		264.0	59.0	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Nonsense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.768370	0.90020	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000350773;ENST00000445113	.	.	.	5.16	5.16	0.70880	.	0.211530	0.41294	D	0.000910	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-20.3627	18.6588	0.91465	0.0:1.0:0.0:0.0	.	.	.	.	X	35;35;35;35;35;46	.	ENSP00000219476:Q35X	Q	+	1	0	TSC2	2038720	1.000000	0.71417	0.921000	0.36526	0.909000	0.53808	5.108000	0.64609	2.403000	0.81681	0.563000	0.77884	CAG	.	.		0.493	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		T	2098719	C	T	2098719	4	4	87	1	0	0	0	0	0	1	0	0	16621	479	17	3	105	3	TSC2	16	2098719	Nonsense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10		2098719	88256034	59	11701										
DPEP2	64174	hgsc.bcm.edu	37	chr16	68027109	68027109	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gggaccctcgaggccggaggGctgcatgttgtgcagggccg	19	11	0	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr16:68027109G>T	ENST00000572888.1	-	1	657	c.7C>A	c.(7-9)Ccc>Acc	p.P3T	DPEP2_ENST00000412757.2_Missense_Mutation_p.P3T|DPEP2_ENST00000393847.1_Missense_Mutation_p.P3T			Q9H4A9	DPEP2_HUMAN	dipeptidase 2	3					arachidonic acid metabolic process (GO:0019369)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		AGGCCGGAGGGCTGCATGTTG	0.687											OREG0023893	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P3T		Atlas-SNP	.											.	DPEP2	43	.	0			c.C7A						.						12	12	12					16																	68027109		2164	4269	6433	SO:0001583	missense	64174	exon2			CGGAGGGCTGCAT	AJ295149	CCDS10857.1	16q22.1	2011-07-22			ENSG00000167261	ENSG00000167261	3.4.13.19		23028	protein-coding gene	gene with protein product		609925					Standard	NM_022355		Approved		uc002eve.4	Q9H4A9	OTTHUMG00000137542	ENST00000572888.1:c.7C>A	chr16.hg19:g.68027109G>T	ENSP00000458977:p.Pro3Thr	47.0	0.0	1104	68.0	17.0	NM_022355	B2RCF8|Q6UX92|Q8TC95	Missense_Mutation	SNP	ENST00000572888.1	hg19	CCDS10857.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.617733	0.46736	.	.	ENSG00000167261	ENST00000393847;ENST00000412757;ENST00000322384;ENST00000268795	T;T	0.23147	1.92;1.92	3.64	0.504	0.16946	.	2.002900	0.02667	N	0.108176	T	0.25082	0.0609	L	0.50333	1.59	0.09310	N	0.999995	B;B	0.24258	0.1;0.01	B;B	0.23018	0.043;0.006	T	0.28681	-1.0036	10	0.72032	D	0.01	-1.9434	4.2288	0.10592	0.1131:0.0:0.4785:0.4084	.	3;3	B4DNP7;Q9H4A9	.;DPEP2_HUMAN	T	3	ENSP00000377430:P3T;ENSP00000412549:P3T	ENSP00000268795:P3T	P	-	1	0	DPEP2	66584610	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	0.611000	0.24268	0.153000	0.19213	-0.314000	0.08810	CCC	.	.		0.687	DPEP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437026.1	NM_022355		T	68027109	G	T	68027109	3	4	87	1	0	0	0	0	1	0	0	0	4716	1203	42	3	1493	3	DPEP2	16	68027109	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	65928390	68027109	22327644	60	11702										
PLCG2	5336	hgsc.bcm.edu	37	chr16	81927388	81927388	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ctgcctgcgcatgggctgtcGctgcattgaacgtgagtagc	14	11	0	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr16:81927388G>T	ENST00000359376.3	+	12	1275	c.1061G>T	c.(1060-1062)cGc>cTc	p.R354L		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	354	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						ATGGGCTGTCGCTGCATTGAA	0.542																																					p.R354L		Atlas-SNP	.											.	PLCG2	276	.	0			c.G1061T						.						63	65	64					16																	81927388		2182	4293	6475	SO:0001583	missense	5336	exon12			GCTGTCGCTGCAT		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1061G>T	chr16.hg19:g.81927388G>T	ENSP00000352336:p.Arg354Leu	90.0	0.0		74.0	13.0	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	hg19	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.825445	0.90955	.	.	ENSG00000197943	ENST00000359376	T	0.81415	-1.49	3.71	3.71	0.42584	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.000000	0.85682	D	0.000000	D	0.94463	0.8218	H	0.99650	4.68	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.913	D	0.97373	0.9977	10	0.87932	D	0	.	16.357	0.83239	0.0:0.0:1.0:0.0	.	221;354	B4E3H3;P16885	.;PLCG2_HUMAN	L	354	ENSP00000352336:R354L	ENSP00000352336:R354L	R	+	2	0	PLCG2	80484889	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.618000	0.98365	2.034000	0.60081	0.467000	0.42956	CGC	.	.		0.542	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			T	81927388	G	T	81927388	3	4	87	1	0	0	0	0	1	0	0	0	12045	1087	38	1	1103	1	PLCG2	16	81927388	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	13900279	81927388	8427365	61	11703										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000420246.2_Missense_Mutation_p.R249S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	202.0	2.0		172.0	34.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	87	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10		7577534	73617676	62	11704										
PHF12	57649	hgsc.bcm.edu	37	chr17	27251239	27251239	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tctgtccaacaagtcagtgtCactgctgggggatgtagtcc	12	10	3	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:27251239C>A	ENST00000332830.4	-	4	1213	c.403G>T	c.(403-405)Gac>Tac	p.D135Y	RP11-20B24.5_ENST00000580782.1_RNA|PHF12_ENST00000268756.3_Missense_Mutation_p.D135Y|PHF12_ENST00000582655.1_5'UTR|PHF12_ENST00000577226.1_Missense_Mutation_p.D135Y|RP11-20B24.5_ENST00000582631.1_RNA	NM_001033561.1	NP_001028733.1			PHD finger protein 12											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			AAGTCAGTGTCACTGCTGGGG	0.537																																					p.D135Y		Atlas-SNP	.											.	PHF12	69	.	0			c.G403T						.						153	123	133					17																	27251239		2203	4300	6503	SO:0001583	missense	57649	exon4			CAGTGTCACTGCT	AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"Zinc fingers, PHD-type"	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.403G>T	chr17.hg19:g.27251239C>A	ENSP00000329933:p.Asp135Tyr	172.0	0.0		212.0	48.0	NM_020889		Missense_Mutation	SNP	ENST00000332830.4	hg19	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667068	0.88251	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.94828	-3.5;-3.53;-3.53	5.58	5.58	0.84498	.	0.095435	0.64402	D	0.000001	D	0.95937	0.8677	L	0.44542	1.39	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.976;0.999	D;D;P;D	0.70935	0.936;0.971;0.656;0.936	D	0.96325	0.9239	10	0.72032	D	0.01	-7.893	18.1066	0.89521	0.0:1.0:0.0:0.0	.	117;135;135;135	B4DFE2;Q96QT6-2;Q2TAK2;Q96QT6	.;.;.;PHF12_HUMAN	Y	135	ENSP00000329933:D135Y;ENSP00000368157:D135Y;ENSP00000268756:D135Y	ENSP00000268756:D135Y	D	-	1	0	PHF12	24275365	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.252000	0.78309	2.609000	0.88269	0.655000	0.94253	GAC	.	.		0.537	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889		A	27251239	C	A	27251239	3	1	87	1	0	0	0	0	1	0	0	0	11832	826	29	3	2685	3	PHF12	17	27251239	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	19673705	27251239	53943971	63	11705										
MSL1	339287	hgsc.bcm.edu	37	chr17	38289863	38289868	+	In_Frame_Del	DEL	CAGGAA	CAGGAA	-													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgtataaaaagaaaggaattCaggaatctgagcctgaggtt							TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	CAGGAA	CAGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:38289863_38289868delCAGGAA	ENST00000398532.4	+	7	1948_1953	c.1633_1638delCAGGAA	c.(1633-1638)caggaadel	p.QE545del	MSL1_ENST00000578648.1_In_Frame_Del_p.QE529del|MSL1_ENST00000579565.1_In_Frame_Del_p.QE282del	NM_001012241.1	NP_001012241.1	Q68DK7	MSL1_HUMAN	male-specific lethal 1 homolog (Drosophila)	545					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(2)	7						GAAAGGAATTCAGGAATCTGAGCCTG	0.413																																					p.281_283del		Atlas-Indel,Pindel	.											.	MSL1	21	.	0			c.843_848del						.																																			SO:0001651	inframe_deletion	339287	exon8			.		CCDS45670.1	17q21.1	2011-03-21			ENSG00000188895	ENSG00000188895			27905	protein-coding gene	gene with protein product		614801				16227571, 16543150	Standard	NM_001012241		Approved	hMSL1, MSL-1, DKFZp686P24239	uc002hua.4	Q68DK7		ENST00000398532.4:c.1633_1638delCAGGAA	chr17.hg19:g.38289863_38289868delCAGGAA	ENSP00000381543:p.Gln545_Glu546del	125.0	0.0		103.0	17.0	NM_001012241	Q0VF46|Q69Z03	In_Frame_Del	DEL	ENST00000398532.4	hg19																																																																																				.	.		0.413	MSL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000447409.2	NM_001012241		-	38289868	CAGGAA	-	38289863	7	5	87	1	0	1	0	1	0	0	0	0	9886	827	29	0	866	0	MSL1	17	38289863	In_Frame_Del	DEL	CAGGAA	TCGA-DD-A114-01A-11D-A12Z-10	11038624	38289863	42905347	64	11706										
KRT33B	3884	hgsc.bcm.edu	37	chr17	39522752	39522752	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ttctgcttgagggacagcagCtcctccttcagggactccat	10	13	2	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:39522752C>A	ENST00000251646.3	-	3	607	c.558G>T	c.(556-558)gaG>gaT	p.E186D		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	186	Coil 1B.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				GGGACAGCAGCTCCTCCTTCA	0.562																																					p.E186D		Atlas-SNP	.											.	KRT33B	46	.	0			c.G558T						.						72	70	71					17																	39522752		2191	4300	6491	SO:0001583	missense	3884	exon3			CAGCAGCTCCTCC	X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"-", "Intermediate filaments type I, keratins (acidic)"	6451	protein-coding gene	gene with protein product	"hard keratin type I 3II"	602762	"keratin, hair, acidic, 3B"	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.558G>T	chr17.hg19:g.39522752C>A	ENSP00000251646:p.Glu186Asp	128.0	0.0		95.0	19.0	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	hg19	CCDS11389.1	.	.	.	.	.	.	.	.	.	.	c	16.08	3.022491	0.54683	.	.	ENSG00000131738	ENST00000251646	D	0.92249	-3.0	4.51	3.53	0.40419	Filament (1);	0.000000	0.64402	D	0.000004	D	0.92371	0.7579	M	0.76328	2.33	0.28712	N	0.903508	P	0.36125	0.538	B	0.43838	0.433	D	0.87459	0.2406	10	0.49607	T	0.09	.	11.4448	0.50116	0.0:0.8395:0.0:0.1605	.	186	Q14525	KT33B_HUMAN	D	186	ENSP00000251646:E186D	ENSP00000251646:E186D	E	-	3	2	KRT33B	36776278	0.998000	0.40836	0.997000	0.53966	0.912000	0.54170	0.636000	0.24644	0.654000	0.30846	-1.134000	0.01955	GAG	.	.		0.562	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279		A	39522752	C	A	39522752	3	1	87	1	0	0	0	0	1	0	0	0	8479	796	28	3	676	3	KRT33B	17	39522752	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	1232889	39522752	41672458	65	11707										
GOSR2	9570	hgsc.bcm.edu	37	chr17	45017921	45017921	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	aaggctgtcctgtcccccagGcacccaaggatcctgccaga	10	16	0	1	rs147434599		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:45017921G>T	ENST00000393456.2	+	0	847				RP11-156P1.2_ENST00000571841.1_Intron|GOSR2_ENST00000439730.2_Intron|GOSR2_ENST00000225567.4_Splice_Site_p.G195V	NM_004287.3	NP_004278.2	O14653	GOSR2_HUMAN	golgi SNAP receptor complex member 2						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|skin(1)	7			BRCA - Breast invasive adenocarcinoma(9;0.102)			TGTCCCCCAGGCACCCAAGGA	0.577																																					p.G195V		Atlas-SNP	.											.	GOSR2	38	.	0			c.G584T						.						135	128	130					17																	45017921		2203	4300	6503	SO:0001628	intergenic_variant	9570	exon7			CCCCAGGCACCCA	AF007548	CCDS11507.1, CCDS42355.1, CCDS45719.1	17q21	2006-02-10				ENSG00000108433			4431	protein-coding gene	gene with protein product		604027				9349823, 10198168	Standard	XM_005257843		Approved	GS27, Bos1	uc002ikz.3	O14653			chr17.hg19:g.45017921G>T		31.0	0.0		56.0	17.0	NM_054022	D3DXJ5|D3DXJ6|Q8N4B8|Q96DA5|Q9BZZ4	Missense_Mutation	SNP	ENST00000393456.2	hg19	CCDS42355.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.994802	0.35226	.	.	ENSG00000108433	ENST00000225567	D	0.82255	-1.59	4.15	1.12	0.20585	.	0.236625	0.42964	D	0.000630	D	0.84170	0.5413	L	0.56340	1.77	0.09310	N	0.999999	D	0.63880	0.993	P	0.62740	0.906	T	0.73251	-0.4042	9	.	.	.	.	6.0972	0.20027	0.3186:0.0:0.6814:0.0	.	195	O14653-2	.	V	195	ENSP00000225567:G195V	.	G	+	2	0	GOSR2	42372920	0.001000	0.12720	0.005000	0.12908	0.008000	0.06430	0.157000	0.16402	0.314000	0.23086	-0.258000	0.10820	GGC	.	G|0.999;C|0.001		0.577	GOSR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440438.1			T	45017921	G	T	45017921	1	4	87	0	1	0	0	0	0	0	0	0	6586	1217	42	3		3	GOSR2	17	45017921	IGR	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	5495169	45017921	36177289	66	11708										
MTMR4	9110	hgsc.bcm.edu	37	chr17	56582859	56582859	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ggatccggcatctggctacaCacagcccggaggtactgaaa	12	12	1	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:56582859C>A	ENST00000323456.5	-	11	1201	c.1077G>T	c.(1075-1077)gtG>gtT	p.V359V	MTMR4_ENST00000579925.1_Silent_p.V359V	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	359	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCTGGCTACACACAGCCCGGA	0.493																																					p.V359V		Atlas-SNP	.											.	MTMR4	91	.	0			c.G1077T						.						123	104	110					17																	56582859		2203	4300	6503	SO:0001819	synonymous_variant	9110	exon11			GCTACACACAGCC	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.1077G>T	chr17.hg19:g.56582859C>A		121.0	0.0		152.0	26.0	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Silent	SNP	ENST00000323456.5	hg19	CCDS11608.1																																																																																			.	.		0.493	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687		A	56582859	C	A	56582859	2	1	87	1	0	0	0	0	0	0	0	1	9955	465	17	3		3	MTMR4	17	56582859	Silent	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	11564938	56582859	24612351	67	11709										
KIAA1328	57536	hgsc.bcm.edu	37	chr18	34647292	34647292	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	agaatcatgcagttattgtcGgctttcttgggcatctctgg	11	8	3	1	rs531868906		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr18:34647292G>C	ENST00000280020.5	+	7	1038	c.1016G>C	c.(1015-1017)cGg>cCg	p.R339P	KIAA1328_ENST00000435985.2_Missense_Mutation_p.R55P|KIAA1328_ENST00000591619.1_Missense_Mutation_p.R335P|KIAA1328_ENST00000543923.1_Missense_Mutation_p.R231P|KIAA1328_ENST00000586501.1_Missense_Mutation_p.R55P|KIAA1328_ENST00000586135.1_Missense_Mutation_p.R55P	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	339										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		AGTTATTGTCGGCTTTCTTGG	0.463																																					p.R339P		Atlas-SNP	.											KIAA1328,NS,carcinoma,+1,1	KIAA1328	39	.	0			c.G1016C						.						94	89	91					18																	34647292		2050	4208	6258	SO:0001583	missense	57536	exon7			ATTGTCGGCTTTC	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.1016G>C	chr18.hg19:g.34647292G>C	ENSP00000280020:p.Arg339Pro	538.0	0.0		435.0	68.0	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Missense_Mutation	SNP	ENST00000280020.5	hg19	CCDS45855.1	.	.	.	.	.	.	.	.	.	.	G	8.834	0.940660	0.18281	.	.	ENSG00000150477	ENST00000543923;ENST00000280020;ENST00000383055;ENST00000435985	T;T;T	0.50277	0.75;0.75;0.75	6.17	3.25	0.37280	.	0.649434	0.16451	N	0.213853	T	0.35219	0.0924	L	0.34521	1.04	0.25823	N	0.98426	P;B;B;P	0.34757	0.467;0.195;0.195;0.467	B;B;B;B	0.38880	0.197;0.128;0.263;0.284	T	0.14172	-1.0482	10	0.28530	T	0.3	.	6.6411	0.22909	0.1392:0.0:0.6337:0.2272	.	55;339;55;339	Q86T90-4;A8K8C3;Q86T90-3;Q86T90	.;.;.;K1328_HUMAN	P	231;339;339;55	ENSP00000441359:R231P;ENSP00000280020:R339P;ENSP00000390515:R55P	ENSP00000280020:R339P	R	+	2	0	KIAA1328	32901290	0.731000	0.28111	1.000000	0.80357	0.601000	0.36947	0.710000	0.25748	1.635000	0.50512	0.655000	0.94253	CGG	.	.		0.463	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776		C	34647292	G	C	34647292	3	2	87	1	0	0	0	0	1	0	0	0	8234	1116	39	4	1042	4	KIAA1328	18	34647292	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10		34647292	43429956	68	11710										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43460188	43460188	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tcagaagctgctccgcggagCctgccagcagggacaggaag	15	12	1	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr18:43460188C>A	ENST00000282041.5	-	32	5553	c.5519G>T	c.(5518-5520)aGc>aTc	p.S1840I	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1840					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CTCCGCGGAGCCTGCCAGCAG	0.547											OREG0024951	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1840I		Atlas-SNP	.											EPG5,NS,carcinoma,0,1	EPG5	199	.	0			c.G5519T						.						10	11	11					18																	43460188		1805	3991	5796	SO:0001630	splice_region_variant	57724	exon32			GCGGAGCCTGCCA	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.5519-1G>T	chr18.hg19:g.43460188C>A		53.0	0.0	916	63.0	12.0	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	C	18.25	3.583360	0.65992	.	.	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.11712	2.75	5.8	5.8	0.92144	.	.	.	.	.	T	0.31670	0.0804	L	0.59436	1.845	0.80722	D	1	D	0.71674	0.998	D	0.66979	0.948	T	0.00402	-1.1762	9	0.72032	D	0.01	.	20.0466	0.97609	0.0:1.0:0.0:0.0	.	1840	Q9HCE0	EPG5_HUMAN	I	1840;715	ENSP00000282041:S1840I	ENSP00000282041:S1840I	S	-	2	0	EPG5	41714186	1.000000	0.71417	0.995000	0.50966	0.009000	0.06853	7.048000	0.76606	2.729000	0.93468	0.563000	0.77884	AGC	.	.		0.547	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	Missense_Mutation	A	43460188	C	A	43460188	5	1	87	1	0	0	0	0	0	0	1	0	8258	753	26	3	2272	3	KIAA1632	18	43460188	Splice_Site	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	8812896	43460188	34617060	69	11711										
MC4R	4160	hgsc.bcm.edu	37	chr18	58039123	58039123	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	aatgttatggtactggagagCatagaagatagtaaagtacc	11	4	0	3			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr18:58039123C>A	ENST00000299766.3	-	1	878	c.460G>T	c.(460-462)Gct>Tct	p.A154S		NM_005912.2	NP_005903.2	P32245	MC4R_HUMAN	melanocortin 4 receptor	154					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|diet induced thermogenesis (GO:0002024)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|insulin secretion (GO:0030073)|negative regulation of feeding behavior (GO:2000252)|positive regulation of bone resorption (GO:0045780)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of grooming behavior (GO:2000821)|response to insulin (GO:0032868)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(73;0.0946)				TACTGGAGAGCATAGAAGATA	0.418																																					p.A154S		Atlas-SNP	.											.	MC4R	49	.	0			c.G460T						.						93	83	86					18																	58039123		2203	4300	6503	SO:0001583	missense	4160	exon1			GGAGAGCATAGAA	AY236539	CCDS11976.1	18q22	2012-08-10			ENSG00000166603	ENSG00000166603		"GPCR / Class A : Melanocortin receptors"	6932	protein-coding gene	gene with protein product		155541				7949735, 9763669	Standard	NM_005912		Approved		uc002lie.1	P32245	OTTHUMG00000132766	ENST00000299766.3:c.460G>T	chr18.hg19:g.58039123C>A	ENSP00000299766:p.Ala154Ser	121.0	0.0		99.0	14.0	NM_005912	B2RAC3|Q16317|Q3MIJ6	Missense_Mutation	SNP	ENST00000299766.3	hg19	CCDS11976.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.823342	0.90873	.	.	ENSG00000166603	ENST00000299766	T	0.37584	1.19	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67524	0.2902	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.72956	-0.4134	10	0.87932	D	0	.	17.6572	0.88181	0.0:1.0:0.0:0.0	.	154	P32245	MC4R_HUMAN	S	154	ENSP00000299766:A154S	ENSP00000299766:A154S	A	-	1	0	MC4R	56190103	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.818000	0.86416	2.773000	0.95371	0.655000	0.94253	GCT	.	.		0.418	MC4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256139.1	NM_005912		A	58039123	C	A	58039123	3	1	87	1	0	0	0	0	1	0	0	0	9375	710	25	3	542	3	MC4R	18	58039123	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	14578935	58039123	20038125	70	11712										
SERPINB4	6318	hgsc.bcm.edu	37	chr18	61308143	61308143	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ccacccaggagttaatcttcTttcgactttcttctggagca	7	12	4	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr18:61308143T>C	ENST00000341074.5	-	5	549	c.434A>G	c.(433-435)aAg>aGg	p.K145R	SERPINB4_ENST00000356424.6_Missense_Mutation_p.K145R	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	145					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						GTTAATCTTCTTTCGACTTTC	0.408																																					p.K145R		Atlas-SNP	.											.	SERPINB4	89	.	0			c.A434G						.						121	109	113					18																	61308143		2203	4300	6503	SO:0001583	missense	6318	exon5			ATCTTCTTTCGAC	X89015	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073		"Serine (or cysteine) peptidase inhibitors"	10570	protein-coding gene	gene with protein product	"squamous cell carcinoma antigen 2"	600518	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"	SCCA2		7724531, 14630915, 24172014	Standard	NM_175041		Approved	PI11, LEUPIN, SCCA-2, SCCA1		P48594	OTTHUMG00000060405	ENST00000341074.5:c.434A>G	chr18.hg19:g.61308143T>C	ENSP00000343445:p.Lys145Arg	512.0	0.0		463.0	77.0	NM_002974	A8K847	Missense_Mutation	SNP	ENST00000341074.5	hg19	CCDS11986.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.26|13.26	2.183101|2.183101	0.38511|0.38511	.|.	.|.	ENSG00000206073|ENSG00000206073	ENST00000341074;ENST00000356424;ENST00000436264|ENST00000413673	D;D;D|.	0.84944|.	-1.92;-1.92;-1.92|.	4.28|4.28	1.78|1.78	0.24846|0.24846	Serpin domain (3);|.	0.582093|.	0.14232|.	N|.	0.332645|.	T|T	0.54919|0.54919	0.1888|0.1888	M|M	0.78049|0.78049	2.395|2.395	0.09310|0.09310	N|N	1|1	B;P|.	0.49862|.	0.379;0.929|.	P;P|.	0.59825|.	0.496;0.864|.	T|T	0.46857|0.46857	-0.9161|-0.9161	10|5	0.62326|.	D|.	0.03|.	.|.	7.7402|7.7402	0.28837|0.28837	0.0:0.3425:0.0:0.6575|0.0:0.3425:0.0:0.6575	.|.	145;145|.	P48594;Q9BYF7|.	SPB4_HUMAN;.|.	R|G	145;145;102|147	ENSP00000343445:K145R;ENSP00000348795:K145R;ENSP00000399796:K102R|.	ENSP00000343445:K145R|.	K|R	-|-	2|1	0|2	SERPINB4|SERPINB4	59459123|59459123	0.000000|0.000000	0.05858|0.05858	0.760000|0.760000	0.31359|0.31359	0.539000|0.539000	0.34962|0.34962	0.618000|0.618000	0.24373|0.24373	0.683000|0.683000	0.31428|0.31428	0.491000|0.491000	0.48974|0.48974	AAG|AGA	.	.		0.408	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2	NM_175041		C	61308143	T	C	61308143	3	2	87	1	0	0	0	0	1	0	0	0	14118	1609	56	2	754	2	SERPINB4	18	61308143	Missense_Mutation	SNP	T	TCGA-DD-A114-01A-11D-A12Z-10	3269020	61308143	16769105	71	11713										
ZNF407	55628	hgsc.bcm.edu	37	chr18	72775861	72775861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgctcacccaggtggtccatCcctcagcagccatggcctct	9	17	3	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr18:72775861C>T	ENST00000299687.5	+	8	6184	c.6184C>T	c.(6184-6186)Ccc>Tcc	p.P2062S		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2062					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GGTGGTCCATCCCTCAGCAGC	0.682																																					p.P2062S		Atlas-SNP	.											.	ZNF407	231	.	0			c.C6184T						.						38	44	42					18																	72775861		2085	4211	6296	SO:0001583	missense	55628	exon8			GTCCATCCCTCAG	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.6184C>T	chr18.hg19:g.72775861C>T	ENSP00000299687:p.Pro2062Ser	74.0	0.0		94.0	9.0	NM_017757	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	C	3.939	-0.014518	0.07681	.	.	ENSG00000215421	ENST00000299687	T	0.32988	1.43	4.42	3.53	0.40419	.	.	.	.	.	T	0.33933	0.0880	L	0.43757	1.38	0.58432	D	0.999997	P	0.50066	0.931	P	0.47673	0.554	T	0.32587	-0.9901	9	0.87932	D	0	.	14.3761	0.66879	0.0:0.8512:0.1487:0.0	.	2062	Q9C0G0	ZN407_HUMAN	S	2062	ENSP00000299687:P2062S	ENSP00000299687:P2062S	P	+	1	0	ZNF407	70904849	0.866000	0.29940	0.025000	0.17156	0.007000	0.05969	1.312000	0.33574	2.025000	0.59659	0.462000	0.41574	CCC	.	.		0.682	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72775861	C	T	72775861	3	4	87	1	0	0	0	0	1	0	0	0	17902	855	30	3	6344	3	ZNF407	18	72775861	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	11467718	72775861	5301387	72	11714										
OR7D4	125958	hgsc.bcm.edu	37	chr19	9324917	9324917	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	agcagtgccgtggccacataCaagacaatgttattgaggag	12	8	0	2	rs377419980		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:9324917C>T	ENST00000308682.2	-	1	625	c.597G>A	c.(595-597)ttG>ttA	p.L199L		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L199L(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						TGGCCACATACAAGACAATGT	0.522																																					p.L199L		Atlas-SNP	.											OR7D4,NS,carcinoma,0,1	OR7D4	66	.	1	Substitution - coding silent(1)	lung(1)	c.G597A						.						106	99	102					19																	9324917		2203	4300	6503	SO:0001819	synonymous_variant	125958	exon1			CACATACAAGACA		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"GPCR / Class A : Olfactory receptors"	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.597G>A	chr19.hg19:g.9324917C>T		146.0	0.0		186.0	33.0	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Silent	SNP	ENST00000308682.2	hg19	CCDS32901.1																																																																																			.	.		0.522	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1			T	9324917	C	T	9324917	2	4	87	1	0	0	0	0	0	0	0	1	11229	477	17	3		3	OR7D4	19	9324917	Silent	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10		9324917	49804066	73	11715										
LDLR	3949	hgsc.bcm.edu	37	chr19	11213382	11213382	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ggacttcagctgtgggggccGtgtcaaccgctgcattcctc	13	13	2	0	rs146675823		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:11213382G>T	ENST00000558518.1	+	3	420	c.233G>T	c.(232-234)cGt>cTt	p.R78L	LDLR_ENST00000557933.1_Missense_Mutation_p.R78L|LDLR_ENST00000455727.2_Missense_Mutation_p.R78L|LDLR_ENST00000545707.1_Missense_Mutation_p.R78L|LDLR_ENST00000535915.1_Intron|LDLR_ENST00000558013.1_Missense_Mutation_p.R78L	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	78	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.		R -> C (in FH).		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	TGTGGGGGCCGTGTCAACCGC	0.567													G|||	1	0.000199681	0	0	5008	,	,		19169	0		0	False		,,,				2504	0.001				p.R78L	GBM(18;201 575 7820 21545)	Atlas-SNP	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.G233T						.						172	151	159					19																	11213382		2203	4300	6503	SO:0001583	missense	3949	exon3			GGGGCCGTGTCAA	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"Low density lipoprotein receptors"	6547	protein-coding gene	gene with protein product	"familial hypercholesterolemia"	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.233G>T	chr19.hg19:g.11213382G>T	ENSP00000454071:p.Arg78Leu	230.0	0.0		230.0	44.0	NM_001195800	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	hg19	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805102	0.70682	.	.	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000455727	D;D	0.91407	-2.84;-2.84	5.65	1.11	0.20524	.	0.118981	0.35677	N	0.003043	D	0.92961	0.7760	M	0.79614	2.46	0.43745	D	0.996243	B;B;P;D	0.76494	0.038;0.0;0.895;0.999	B;B;P;D	0.77557	0.033;0.006;0.793;0.99	D	0.88835	0.3308	10	0.22109	T	0.4	.	7.6124	0.28137	0.1636:0.0:0.7106:0.1258	.	78;78;90;78	B4DR00;B4DJZ8;Q59FQ1;P01130	.;.;.;LDLR_HUMAN	L	78	ENSP00000437639:R78L;ENSP00000397829:R78L	ENSP00000252444:R78L	R	+	2	0	LDLR	11074382	0.463000	0.25799	0.124000	0.21820	0.944000	0.59088	1.497000	0.35649	0.054000	0.16065	0.591000	0.81541	CGT	.	G|1.000;A|0.000		0.567	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2			T	11213382	G	T	11213382	3	4	87	1	0	0	0	0	1	0	0	0	8713	1145	40	1	243	1	LDLR	19	11213382	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	1888465	11213382	47915601	74	11716										
RASAL3	64926	hgsc.bcm.edu	37	chr19	15563967	15563968	+	Frame_Shift_Ins	INS	-	-	G													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ctggtttcggtcttgcggctINSggtccatttggcgctgccag							TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:15563967_15563968insG	ENST00000343625.7	-	15	2705_2706	c.2620_2621insC	c.(2620-2622)cagfs	p.Q874fs		NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	874					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						GTCTTGCGGCTGGTCCATTTGG	0.693																																					p.Q874fs		Atlas-INDEL	.											.	RASAL3	49	.	0			c.2621_2622insC						.																																			SO:0001589	frameshift_variant	64926	exon15			.		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.2621dupC	chr19.hg19:g.15563969_15563969dupG	ENSP00000341905:p.Gln874fs	52.0	0.0		125.0	10.0	NM_022904	Q8N2T9|Q9H735	Frame_Shift_Ins	INS	ENST00000343625.7	hg19	CCDS46006.1																																																																																			.	.		0.693	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904		G	15563968	-	G	15563967	7	5	87	1	0	1	1	0	0	0	0	0	13080	1580	55	0	430	0	RASAL3	19	15563967	Frame_Shift_Ins	INS	-	TCGA-DD-A114-01A-11D-A12Z-10	4350585	15563967	43565016	75	11717										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935048	30935048	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	aaggggcgtgggcgtgtgcgCgaggagaaccgcctgctgca	19	10	0	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:30935048C>T	ENST00000355537.3	+	2	726	c.579C>T	c.(577-579)cgC>cgT	p.R193R		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	193					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GGCGTGTGCGCGAGGAGAACC	0.692																																					p.R193R		Atlas-SNP	.											ZNF536,right_upper_lobe,carcinoma,0,1	ZNF536	424	.	0			c.C579T						.						17	13	15					19																	30935048		2193	4290	6483	SO:0001819	synonymous_variant	9745	exon2			TGTGCGCGAGGAG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.579C>T	chr19.hg19:g.30935048C>T		32.0	0.0		50.0	12.0	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.		0.692	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30935048	C	T	30935048	2	4	87	1	0	0	0	0	0	0	0	1	17989	755	27	1		1	ZNF536	19	30935048	Silent	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	15371081	30935048	28193935	76	11718										
RYR1	6261	hgsc.bcm.edu	37	chr19	38974064	38974064	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cccaaccacttcctgcaggtGgagacgaggcgtgccggcga	14	14	0	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:38974064G>A	ENST00000359596.3	+	33	4842	c.4842G>A	c.(4840-4842)gtG>gtA	p.V1614V	RYR1_ENST00000360985.3_Silent_p.V1614V|RYR1_ENST00000355481.4_Silent_p.V1614V			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1614	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TCCTGCAGGTGGAGACGAGGC	0.697																																					p.V1614V		Atlas-SNP	.											.	RYR1	708	.	0			c.G4842A						.						13	14	13					19																	38974064		2193	4284	6477	SO:0001819	synonymous_variant	6261	exon33			GCAGGTGGAGACG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.4842G>A	chr19.hg19:g.38974064G>A		91.0	0.0		76.0	13.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.697	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38974064	G	A	38974064	2	1	87	1	0	0	0	0	0	0	0	1	13783	1335	47	3		3	RYR1	19	38974064	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	8039016	38974064	20154919	77	11719										
CEACAM4	1089	hgsc.bcm.edu	37	chr19	42132051	42132051	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cgtagggtgtaggatcctgcGtcctccagggtgatgttttg	15	8	0	1	rs199959927		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:42132051G>T	ENST00000221954.2	-	2	458	c.348C>A	c.(346-348)gaC>gaA	p.D116E	CEACAM4_ENST00000600925.1_Missense_Mutation_p.D116E	NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	116	Ig-like V-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						AGGATCCTGCGTCCTCCAGGG	0.522																																					p.D116E		Atlas-SNP	.											.	CEACAM4	42	.	0			c.C348A						.						197	170	179					19																	42132051		2203	4300	6503	SO:0001583	missense	1089	exon2			TCCTGCGTCCTCC	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"Immunoglobulin superfamily / V-set domain containing"	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.348C>A	chr19.hg19:g.42132051G>T	ENSP00000221954:p.Asp116Glu	540.0	0.0		590.0	108.0	NM_001817	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	hg19	CCDS33033.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.399384	0.42512	.	.	ENSG00000105352	ENST00000221954	D	0.87729	-2.29	1.82	1.82	0.25136	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.94056	0.8095	H	0.95679	3.705	0.09310	N	1	D;D	0.76494	0.999;0.976	D;P	0.69142	0.962;0.821	D	0.84347	0.0530	9	0.87932	D	0	.	7.103	0.25348	0.0:0.0:1.0:0.0	.	116;116	E7EMX3;O75871	.;CEAM4_HUMAN	E	116	ENSP00000221954:D116E	ENSP00000221954:D116E	D	-	3	2	CEACAM4	46823891	0.018000	0.18449	0.007000	0.13788	0.010000	0.07245	0.956000	0.29202	1.319000	0.45190	0.313000	0.20887	GAC	.	G|0.999;A|0.001		0.522	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817		T	42132051	G	T	42132051	3	4	87	1	0	0	0	0	1	0	0	0	3196	1136	40	1	410	1	CEACAM4	19	42132051	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	3157987	42132051	16996932	78	11720										
C19orf61	56006	hgsc.bcm.edu	37	chr19	44238560	44238560	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cctaggtgggggtagtactcGgtgccttcatcggagcccga	15	11	1	0	rs368481505		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:44238560G>T	ENST00000270066.6	-	10	1425	c.1083C>A	c.(1081-1083)acC>acA	p.T361T	SMG9_ENST00000601170.1_Silent_p.T361T	NM_019108.2	NP_061981.2	Q9H0W8	SMG9_HUMAN	SMG9 nonsense mediated mRNA decay factor	361					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|intracellular (GO:0005622)	identical protein binding (GO:0042802)			kidney(1)|large_intestine(5)|liver(1)|lung(7)|pancreas(1)|prostate(2)|urinary_tract(2)	19						GGTAGTACTCGGTGCCTTCAT	0.612																																					p.T361T		Atlas-SNP	.											.	SMG9	39	.	0			c.C1083A						.						33	28	30					19																	44238560		2188	4284	6472	SO:0001819	synonymous_variant	56006	exon10			GTACTCGGTGCCT	BC008869	CCDS33043.2	19q13.31	2013-07-02	2013-07-02	2011-06-21	ENSG00000105771	ENSG00000105771			25763	protein-coding gene	gene with protein product		613176	"chromosome 19 open reading frame 61", "smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C19orf61		11230166, 19417104	Standard	NM_019108		Approved	FLJ12886	uc002oxj.2	Q9H0W8	OTTHUMG00000150337	ENST00000270066.6:c.1083C>A	chr19.hg19:g.44238560G>T		76.0	0.0		101.0	5.0	NM_019108	O60429|Q9H9A9	Silent	SNP	ENST00000270066.6	hg19	CCDS33043.2																																																																																			.	.		0.612	SMG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317668.1	NM_019108		T	44238560	G	T	44238560	2	4	87	1	0	0	0	0	0	0	0	1	1945	1103	39	1		1	C19orf61	19	44238560	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	2106509	44238560	14890423	79	11721										
RSPH6A	81492	hgsc.bcm.edu	37	chr19	46318184	46318184	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tcacagatgggtactccatgCcacccagccgggcttcctca	9	16	2	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:46318184C>A	ENST00000221538.3	-	1	393	c.251G>T	c.(250-252)gGc>gTc	p.G84V	RSPH6A_ENST00000597055.1_Missense_Mutation_p.G84V|SYMPK_ENST00000598155.1_5'Flank	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	84						intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						GTACTCCATGCCACCCAGCCG	0.607																																					p.G84V		Atlas-SNP	.											.	RSPH6A	70	.	0			c.G251T						.						51	46	47					19																	46318184		2203	4300	6503	SO:0001583	missense	81492	exon1			TCCATGCCACCCA	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"radial spokehead-like 1"	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.251G>T	chr19.hg19:g.46318184C>A	ENSP00000221538:p.Gly84Val	77.0	0.0		112.0	11.0	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	hg19	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	C	11.32	1.603976	0.28534	.	.	ENSG00000104941	ENST00000221538	T	0.15372	2.43	4.11	-5.72	0.02406	.	3.303470	0.00984	N	0.003424	T	0.09992	0.0245	L	0.29908	0.895	0.09310	N	1	B	0.26002	0.139	B	0.22386	0.039	T	0.18461	-1.0336	10	0.33141	T	0.24	-6.806	1.5802	0.02633	0.1887:0.2035:0.3962:0.2117	.	84	Q9H0K4	RSH6A_HUMAN	V	84	ENSP00000221538:G84V	ENSP00000221538:G84V	G	-	2	0	RSPH6A	51010024	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.057000	0.01395	-0.630000	0.05567	-0.310000	0.09108	GGC	.	.		0.607	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			A	46318184	C	A	46318184	3	1	87	1	0	0	0	0	1	0	0	0	13722	739	26	3	1926	3	RSPH6A	19	46318184	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	2079624	46318184	12810799	80	11722										
CCDC155	147872	hgsc.bcm.edu	37	chr19	49920647	49920647	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	gtcactcgacatccactgatCccagctcctgtcctgggcct	8	17	1	1	rs182291239	byFrequency	TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:49920647C>A	ENST00000447857.3	+	20	1774	c.1569C>A	c.(1567-1569)atC>atA	p.I523I		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	523						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						ATCCACTGATCCCAGCTCCTG	0.642																																					p.I523I		Atlas-SNP	.											.	CCDC155	46	.	0			c.C1569A						.						54	61	59					19																	49920647		2133	4220	6353	SO:0001819	synonymous_variant	147872	exon20			ACTGATCCCAGCT		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.1569C>A	chr19.hg19:g.49920647C>A		104.0	0.0		137.0	30.0	NM_144688	Q96MC3	Silent	SNP	ENST00000447857.3	hg19	CCDS46140.1																																																																																			.	C|1.000;T|0.000		0.642	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688		A	49920647	C	A	49920647	2	1	87	1	0	0	0	0	0	0	0	1	2790	845	30	3		3	CCDC155	19	49920647	Silent	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	3602463	49920647	9208336	81	11723										
VN1R2	317701	hgsc.bcm.edu	37	chr19	53761860	53761860	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tatttctacactctcttgtcTctgcacacggagagaaaccc	6	13	3	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:53761860T>G	ENST00000341702.3	+	1	316	c.232T>G	c.(232-234)Tct>Gct	p.S78A		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	78					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		ctctcttgtctctgcacacgg	0.468																																					p.S78A		Atlas-SNP	.											.	VN1R2	71	.	0			c.T232G						.						36	35	36					19																	53761860		2190	4283	6473	SO:0001583	missense	317701	exon1			CTTGTCTCTGCAC	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.232T>G	chr19.hg19:g.53761860T>G	ENSP00000351244:p.Ser78Ala	90.0	0.0		135.0	26.0	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	hg19	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	T	4.435	0.080571	0.08533	.	.	ENSG00000196131	ENST00000341702	T	0.08984	3.03	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.04003	0.0112	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.40515	-0.9559	8	0.49607	T	0.09	.	.	.	.	.	78	Q8NFZ6	VN1R2_HUMAN	A	78	ENSP00000351244:S78A	ENSP00000351244:S78A	S	+	1	0	VN1R2	58453672	0.004000	0.15560	0.021000	0.16686	0.021000	0.10359	1.432000	0.34936	0.115000	0.18071	0.113000	0.15668	TCT	.	.		0.468	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		G	53761860	T	G	53761860	3	3	87	1	0	0	0	0	1	0	0	0	17194	1551	54	5	234	5	VN1R2	19	53761860	Missense_Mutation	SNP	T	TCGA-DD-A114-01A-11D-A12Z-10	3841213	53761860	5367123	82	11724										
ZNF154	7710	hgsc.bcm.edu	37	chr19	58216279	58216279	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tcacggtacaggcatctttgAgcctcatcaaggagacccca	9	13	4	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:58216279A>T	ENST00000512439.2	-	2	298	c.102T>A	c.(100-102)gcT>gcA	p.A34A	AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF551_ENST00000596085.1_Intron|ZNF154_ENST00000426889.1_Silent_p.A34A			Q13106	ZN154_HUMAN	zinc finger protein 154	34	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GGCATCTTTGAGCCTCATCAA	0.502																																					p.A34A		Atlas-SNP	.											.	ZNF154	34	.	0			c.T102A						.						181	171	175					19																	58216279		2203	4300	6503	SO:0001819	synonymous_variant	7710	exon2			TCTTTGAGCCTCA	U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"Zinc fingers, C2H2-type", "-"	12939	protein-coding gene	gene with protein product		604085	"zinc finger protein 154 (pHZ-92)"			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.102T>A	chr19.hg19:g.58216279A>T		314.0	0.0		266.0	30.0	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Silent	SNP	ENST00000512439.2	hg19	CCDS42639.1																																																																																			.	.		0.502	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2			T	58216279	A	T	58216279	2	4	87	1	0	0	0	0	0	0	0	1	17750	291	11	4		4	ZNF154	19	58216279	Silent	SNP	A	TCGA-DD-A114-01A-11D-A12Z-10	4454419	58216279	912704	83	11725										
ZNF324B	388569	hgsc.bcm.edu	37	chr19	58967236	58967236	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	agcaccagcgcatccacagcGgcgagacgccctacgcgtgc	12	17	0	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:58967236G>T	ENST00000336614.4	+	4	1032	c.925G>T	c.(925-927)Ggc>Tgc	p.G309C	ZNF324B_ENST00000391696.1_Missense_Mutation_p.G299C|ZNF324B_ENST00000545523.1_Missense_Mutation_p.G309C	NM_207395.2	NP_997278.2	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	309					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CATCCACAGCGGCGAGACGCC	0.692																																					p.G309C		Atlas-SNP	.											.	ZNF324B	58	.	0			c.G925T						.						19	18	18					19																	58967236		2116	4167	6283	SO:0001583	missense	388569	exon4			CACAGCGGCGAGA	AK127750	CCDS33138.1	19q13.43	2013-01-08				ENSG00000249471		"Zinc fingers, C2H2-type", "-"	33107	protein-coding gene	gene with protein product							Standard	NM_207395		Approved	FLJ45850	uc002qsv.1	Q6AW86		ENST00000336614.4:c.925G>T	chr19.hg19:g.58967236G>T	ENSP00000337473:p.Gly309Cys	185.0	0.0		158.0	23.0	NM_207395	B2RTZ6|Q6ZMX8|Q6ZS42	Missense_Mutation	SNP	ENST00000336614.4	hg19	CCDS33138.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877387	0.51801	.	.	ENSG00000249471	ENST00000336614;ENST00000545523;ENST00000391696	T;T;T	0.01629	4.72;4.72;4.72	3.22	2.14	0.27477	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42682	D	0.000665	T	0.09291	0.0229	M	0.83118	2.625	0.09310	N	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.01786	-1.1274	10	0.87932	D	0	.	9.6711	0.40013	0.0:0.0:0.7916:0.2084	.	309;299	Q6AW86;C9JTQ8	Z324B_HUMAN;.	C	309;309;299	ENSP00000337473:G309C;ENSP00000438930:G309C;ENSP00000375578:G299C	ENSP00000337473:G309C	G	+	1	0	ZNF324B	63659048	0.432000	0.25554	0.086000	0.20670	0.944000	0.59088	1.881000	0.39638	0.649000	0.30751	0.591000	0.81541	GGC	.	.		0.692	ZNF324B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467038.1	NM_207395		T	58967236	G	T	58967236	3	4	87	1	0	0	0	0	1	0	0	0	17860	1116	39	1	935	1	ZNF324B	19	58967236	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	750957	58967236	161747	84	11726										
RBCK1	10616	hgsc.bcm.edu	37	chr20	400070	400071	+	Frame_Shift_Ins	INS	-	-	C													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	agcccggggtcccccaggaaINScccggacgggggcagccaga							TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr20:400070_400071insC	ENST00000356286.5	+	5	1245_1246	c.540_541insC	c.(541-543)cccfs	p.P181fs	RBCK1_ENST00000382181.2_Frame_Shift_Ins_p.NP64fs|RBCK1_ENST00000353660.3_Frame_Shift_Ins_p.P139fs	NM_031229.2	NP_112506.2	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing 1	181	Interaction with IRF3.|Interaction with TAB2.				negative regulation of necroptotic process (GO:0060546)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(4)	5		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)				TCCCCCAGGAACCCGGACGGGG	0.678																																					p.E180fs		Atlas-INDEL	.											.	RBCK1	38	.	0			c.540_541insC						.																																			SO:0001589	frameshift_variant	10616	exon5			.	U67322	CCDS12998.1, CCDS13000.2	20p13	2014-09-17	2006-06-28	2006-06-28	ENSG00000125826	ENSG00000125826		"RING-type (C3HC4) zinc fingers", "Zinc fingers, RAN-binding domain containing"	15864	protein-coding gene	gene with protein product	"heme-oxidized IRP2 ubiquitin ligase 1"	610924	"chromosome 20 open reading frame 18"	C20orf18			Standard	NM_031229		Approved	RBCK2, XAP4, RNF54, ZRANB4, UBCE7IP3, HOIL1	uc002wdp.4	Q9BYM8	OTTHUMG00000031634	ENST00000356286.5:c.543dupC	chr20.hg19:g.400073_400073dupC	ENSP00000348632:p.Pro181fs	140.0	0.0		156.0	13.0	NM_031229	O95623|Q86SL2|Q96BS3|Q9BYM9	Frame_Shift_Ins	INS	ENST00000356286.5	hg19	CCDS13000.2																																																																																			.	.		0.678	RBCK1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077461.3	NM_031229		C	400071	-	C	400070	7	5	87	1	0	1	1	0	0	0	0	0	13122	40	2	0	577	0	RBCK1	20	400070	Frame_Shift_Ins	INS	-	TCGA-DD-A114-01A-11D-A12Z-10		400070	62625450	85	11727										
GNRH2	2797	hgsc.bcm.edu	37	chr20	3025397	3025397	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cccaagtgatgccctggctcCcctggacgacagcatgccct	10	17	0	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr20:3025397C>T	ENST00000245983.2	+	3	278	c.227C>T	c.(226-228)cCc>cTc	p.P76L	MRPS26_ENST00000380325.3_5'Flank|GNRH2_ENST00000380347.2_Missense_Mutation_p.P69L|GNRH2_ENST00000359100.2_Missense_Mutation_p.P69L|GNRH2_ENST00000380346.2_Missense_Mutation_p.P68L|GNRH2_ENST00000359987.1_Missense_Mutation_p.P68L	NM_001501.1	NP_001492.1	O43555	GON2_HUMAN	gonadotropin-releasing hormone 2	76					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			ovary(1)|upper_aerodigestive_tract(1)	2						GCCCTGGCTCCCCTGGACGAC	0.642																																					p.P76L		Atlas-SNP	.											.	GNRH2	15	.	0			c.C227T						.						36	34	35					20																	3025397		2201	4300	6501	SO:0001583	missense	2797	exon3			TGGCTCCCCTGGA	AF036329	CCDS13040.1, CCDS13041.1, CCDS13042.1	20p13	2013-02-26			ENSG00000125787	ENSG00000125787		"Endogenous ligands"	4420	protein-coding gene	gene with protein product		602352				9419371, 12447356	Standard	NM_178331		Approved		uc002whr.1	O43555	OTTHUMG00000031723	ENST00000245983.2:c.227C>T	chr20.hg19:g.3025397C>T	ENSP00000245983:p.Pro76Leu	96.0	0.0		110.0	12.0	NM_001501	Q14C68|Q14C69|Q9BYN9|Q9BYP0	Missense_Mutation	SNP	ENST00000245983.2	hg19	CCDS13040.1	.	.	.	.	.	.	.	.	.	.	C	3.326	-0.137718	0.06711	.	.	ENSG00000125787	ENST00000245983;ENST00000359100;ENST00000359987;ENST00000380347;ENST00000380346	T;T;T;T;T	0.52295	0.77;0.75;0.67;0.75;0.67	4.38	-5.1	0.02911	.	1.743350	0.03660	N	0.242458	T	0.24967	0.0606	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.002	T	0.06917	-1.0800	10	0.32370	T	0.25	.	2.5	0.04631	0.111:0.331:0.325:0.2331	.	76;68;69	O43555;O43555-2;O43555-3	GON2_HUMAN;.;.	L	76;69;68;69;68	ENSP00000245983:P76L;ENSP00000352003:P69L;ENSP00000353077:P68L;ENSP00000369705:P69L;ENSP00000369704:P68L	ENSP00000245983:P76L	P	+	2	0	GNRH2	2973397	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.227000	0.02950	-1.051000	0.03226	-1.966000	0.00469	CCC	.	.		0.642	GNRH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077694.2	NM_001501		T	3025397	C	T	3025397	3	4	87	1	0	0	0	0	1	0	0	0	6556	623	22	3	233	3	GNRH2	20	3025397	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	2625327	3025397	60000123	86	11728										
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37154091	37154091	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgtaaatccaacagaattgcGaagatcctccattaatatcc	5	10	0	2			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr20:37154091G>C	ENST00000262879.6	+	12	2116	c.1832G>C	c.(1831-1833)cGa>cCa	p.R611P	RALGAPB_ENST00000397038.1_Missense_Mutation_p.R389P|RALGAPB_ENST00000397040.1_Missense_Mutation_p.R611P|RALGAPB_ENST00000397042.3_Missense_Mutation_p.R611P			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	611					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.R611P(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						ACAGAATTGCGAAGATCCTCC	0.328																																					p.R611P		Atlas-SNP	.											RALGAPB,NS,carcinoma,0,1	RALGAPB	134	.	1	Substitution - Missense(1)	lung(1)	c.G1832C						.						133	136	135					20																	37154091		2203	4300	6503	SO:0001583	missense	57148	exon12			AATTGCGAAGATC	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"KIAA1219"	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.1832G>C	chr20.hg19:g.37154091G>C	ENSP00000262879:p.Arg611Pro	711.0	0.0		607.0	105.0	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	hg19	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	G	32	5.164602	0.94727	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000397038;ENST00000397040;ENST00000438490	T;T	0.73363	-0.74;-0.74	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.86138	0.5861	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;0.998	D;D;D;D	0.87578	0.998;0.991;0.997;0.991	D	0.86502	0.1804	10	0.87932	D	0	.	20.0308	0.97536	0.0:0.0:1.0:0.0	.	439;611;611;611	A2A2F0;Q86X10-4;A2A2E9;Q86X10	.;.;.;RLGPB_HUMAN	P	611;611;611;389;611;439	ENSP00000262879:R611P;ENSP00000380233:R611P	ENSP00000262879:R611P	R	+	2	0	RALGAPB	36587505	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.476000	0.97823	2.732000	0.93576	0.585000	0.79938	CGA	.	.		0.328	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		C	37154091	G	C	37154091	3	2	87	1	0	0	0	0	1	0	0	0	13030	1058	37	4	1874	4	RALGAPB	20	37154091	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	34128694	37154091	25871429	87	11729										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46279951	46279951	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgactgcttcccccagcatgGatgggcttttggcaggaccc	12	13	0	1	rs376291640		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr20:46279951G>T	ENST00000371998.3	+	20	4068	c.3877G>T	c.(3877-3879)Gat>Tat	p.D1293Y	NCOA3_ENST00000371997.3_Missense_Mutation_p.D1284Y|NCOA3_ENST00000341724.6_Missense_Mutation_p.D1219Y|NCOA3_ENST00000372004.3_Missense_Mutation_p.D1289Y			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1293	Acetyltransferase.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CCCCAGCATGGATGGGCTTTT	0.522																																					p.D1293Y		Atlas-SNP	.											.	NCOA3	156	.	0			c.G3877T						.						111	104	106					20																	46279951		2203	4300	6503	SO:0001583	missense	8202	exon20			AGCATGGATGGGC	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3877G>T	chr20.hg19:g.46279951G>T	ENSP00000361066:p.Asp1293Tyr	139.0	0.0		133.0	22.0	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	hg19	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.877183	0.91664	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.26810	1.71;4.51;4.51;1.71	6.17	6.17	0.99709	Domain of unknown function DUF1518 (1);	0.000000	0.85682	D	0.000000	T	0.52533	0.1740	M	0.64997	1.995	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.996;1.0;0.996;0.996;0.993;0.996	T	0.40059	-0.9583	10	0.56958	D	0.05	-28.1929	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1293;1284;1296;1288;1289;1293	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	Y	1289;1219;1289;1293;1284	ENSP00000342123:D1219Y;ENSP00000361073:D1289Y;ENSP00000361066:D1293Y;ENSP00000361065:D1284Y	ENSP00000345671:D1289Y	D	+	1	0	NCOA3	45713358	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	GAT	.	.		0.522	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		T	46279951	G	T	46279951	3	4	87	1	0	0	0	0	1	0	0	0	10239	1174	41	3	3977	3	NCOA3	20	46279951	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	9125860	46279951	16745569	88	11730										
ZGPAT	84619	hgsc.bcm.edu	37	chr20	62340061	62340061	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cgccagctgcagggggacctGaaggagctcatcgagctcac	14	13	2	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr20:62340061G>T	ENST00000328969.5	+	2	256	c.129G>T	c.(127-129)ctG>ctT	p.L43L	ARFRP1_ENST00000607873.1_5'Flank|ARFRP1_ENST00000324228.2_5'Flank|ZGPAT_ENST00000369967.3_Silent_p.L43L|ARFRP1_ENST00000609142.1_5'Flank|ZGPAT_ENST00000448100.2_Silent_p.L43L|ZGPAT_ENST00000357119.4_Silent_p.L43L|ARFRP1_ENST00000440854.1_5'Flank|ARFRP1_ENST00000359715.5_5'Flank|ZGPAT_ENST00000355969.6_Silent_p.L43L|RP4-583P15.15_ENST00000490623.2_5'Flank	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	43					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					AGGGGGACCTGAAGGAGCTCA	0.672																																					p.L43L		Atlas-SNP	.											.	ZGPAT	57	.	0			c.G129T						.						38	41	40					20																	62340061		2203	4297	6500	SO:0001819	synonymous_variant	84619	exon2			GGACCTGAAGGAG	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"Zinc fingers, CCCH-type domain containing", "G patch domain containing"	15948	protein-coding gene	gene with protein product			"KIAA1847"	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.129G>T	chr20.hg19:g.62340061G>T		63.0	0.0		59.0	11.0	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Silent	SNP	ENST00000328969.5	hg19	CCDS13534.1																																																																																			.	.		0.672	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		T	62340061	G	T	62340061	2	4	87	1	0	0	0	0	0	0	0	1	17689	1277	45	3		3	ZGPAT	20	62340061	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	16060110	62340061	685459	89	11731										
KRTAP19-4	337971	hgsc.bcm.edu	37	chr21	31869199	31869199	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	atttggttaaattgaatgatCttcttatgacctctgatatc	6	6	3	4			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr21:31869199C>A	ENST00000334058.2	-	1	252	c.230G>T	c.(229-231)aGa>aTa	p.R77I		NM_181610.1	NP_853641.1	Q3LI73	KR194_HUMAN	keratin associated protein 19-4	77						intermediate filament (GO:0005882)				central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						ATTGAATGATCTTCTTATGAC	0.373																																					p.R77I		Atlas-SNP	.											.	KRTAP19-4	22	.	0			c.G230T						.						175	173	174					21																	31869199		2203	4300	6503	SO:0001583	missense	337971	exon1			AATGATCTTCTTA	AP001708	CCDS33534.1	21q22.1	2011-02-10			ENSG00000186967	ENSG00000186967		"Keratin associated proteins"	18939	protein-coding gene	gene with protein product						12359730	Standard	NM_181610		Approved	KAP19.4	uc011acz.2	Q3LI73	OTTHUMG00000057767	ENST00000334058.2:c.230G>T	chr21.hg19:g.31869199C>A	ENSP00000335567:p.Arg77Ile	250.0	0.0		239.0	32.0	NM_181610	Q17RT4|Q17RT6	Missense_Mutation	SNP	ENST00000334058.2	hg19	CCDS33534.1	.	.	.	.	.	.	.	.	.	.	C	6.342	0.431173	0.12045	.	.	ENSG00000186967	ENST00000334058	T	0.21361	2.01	3.72	-0.509	0.11977	.	.	.	.	.	T	0.16342	0.0393	.	.	.	0.09310	N	1	P	0.52316	0.952	B	0.41571	0.36	T	0.15809	-1.0424	8	0.87932	D	0	.	6.3611	0.21429	0.0:0.4322:0.0:0.5678	.	77	Q3LI73	KR194_HUMAN	I	77	ENSP00000335567:R77I	ENSP00000335567:R77I	R	-	2	0	KRTAP19-4	30791070	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.249000	0.08842	-0.100000	0.12241	0.543000	0.68304	AGA	.	.		0.373	KRTAP19-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128219.2			A	31869199	C	A	31869199	3	1	87	1	0	0	0	0	1	0	0	0	8540	913	32	3	27	3	KRTAP19-4	21	31869199	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10		31869199	16260696	90	11732										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885571	29885572	+	In_Frame_Ins	INS	-	-	CCCCTGAGAAGGCCAAGT													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	aacgaaggaggaagcaaagtINScccctgagaaggccaagtcc							TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr22:29885571_29885572insCCCCTGAGAAGGCCAAGT	ENST00000310624.6	+	4	1975_1976	c.1942_1943insCCCCTGAGAAGGCCAAGT	c.(1942-1944)tcc>tCCCCTGAGAAGGCCAAGTcc	p.648_648S>SPEKAKS		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	654	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GGAAGCAAAGTCCCCTGAGAAG	0.569																																					p.S648delinsSPEKAKS		Atlas-INDEL	.											.	NEFH	178	.	0			c.1942_1943insCCCCTGAGAAGGCCAAGT						.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1943_1960dupCCCCTGAGAAGGCCAAGT	chr22.hg19:g.29885571_29885572insCCCCTGAGAAGGCCAAGT	Exception_encountered	189.0	0.0		170.0	33.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		CCCCTGAGAAGGCCAAGT	29885572	-	CCCCTGAGAAGGCCAAGT	29885571	7	5	87	1	0	1	1	0	0	0	0	0	10323	1667	58	0	1956	0	NEFH	22	29885571	In_Frame_Ins	INS	-	TCGA-DD-A114-01A-11D-A12Z-10		29885571	21418995	91	11733										
PLA2G3	50487	hgsc.bcm.edu	37	chr22	31534717	31534717	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tcggatgccatagttgtactGcaagggtgagatgttctgtg	14	6	1	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr22:31534717G>T	ENST00000215885.3	-	2	835	c.583C>A	c.(583-585)Cag>Aag	p.Q195K		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	195	Phospholipase A2-like.				acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						TAGTTGTACTGCAAGGGTGAG	0.597																																					p.Q195K		Atlas-SNP	.											.	PLA2G3	85	.	0			c.C583A						.						309	240	263					22																	31534717		2203	4300	6503	SO:0001583	missense	50487	exon2			TGTACTGCAAGGG	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.583C>A	chr22.hg19:g.31534717G>T	ENSP00000215885:p.Gln195Lys	593.0	1.0		544.0	95.0	NM_015715	O95768	Missense_Mutation	SNP	ENST00000215885.3	hg19	CCDS13889.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.491740	0.64074	.	.	ENSG00000100078	ENST00000215885	T	0.29142	1.58	5.41	4.35	0.52113	Phospholipase A2 (3);	0.370207	0.28871	N	0.013866	T	0.34366	0.0895	L	0.55990	1.75	0.32021	N	0.60077	P	0.47677	0.899	P	0.45610	0.487	T	0.49000	-0.8984	10	0.56958	D	0.05	-17.6393	12.855	0.57880	0.0:0.2879:0.7121:0.0	.	195	Q9NZ20	PA2G3_HUMAN	K	195	ENSP00000215885:Q195K	ENSP00000215885:Q195K	Q	-	1	0	PLA2G3	29864717	1.000000	0.71417	0.998000	0.56505	0.870000	0.49936	1.665000	0.37449	2.546000	0.85860	0.561000	0.74099	CAG	.	.		0.597	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715		T	31534717	G	T	31534717	3	4	87	1	0	0	0	0	1	0	0	0	12009	1328	46	3	970	3	PLA2G3	22	31534717	Missense_Mutation	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	1649146	31534717	19769849	92	11734										
GRAP2	9402	hgsc.bcm.edu	37	chr22	40343142	40343142	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgccaagtttgatttcactgCttcaggtgaggatgaactga	11	7	2	4			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr22:40343142C>A	ENST00000344138.4	+	2	295	c.32C>A	c.(31-33)gCt>gAt	p.A11D	GRAP2_ENST00000399090.2_Intron|GRAP2_ENST00000544756.1_5'UTR|GRAP2_ENST00000407075.3_Missense_Mutation_p.A11D|GRAP2_ENST00000478445.1_Intron|GRAP2_ENST00000543252.1_Missense_Mutation_p.A11D|GRAP2_ENST00000540310.1_Intron	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	11	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						GATTTCACTGCTTCAGGTGAG	0.502																																					p.A11D		Atlas-SNP	.											.	GRAP2	29	.	0			c.C32A						.						192	172	179					22																	40343142		2203	4300	6503	SO:0001583	missense	9402	exon2			TCACTGCTTCAGG	AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"SH2 domain containing"	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.32C>A	chr22.hg19:g.40343142C>A	ENSP00000339186:p.Ala11Asp	338.0	0.0		263.0	68.0	NM_004810	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	hg19	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.802409	0.90538	.	.	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000420971;ENST00000407075	T;T;T;T	0.58940	1.11;0.3;0.3;1.11	5.65	5.65	0.86999	Src homology-3 domain (4);	0.148621	0.64402	D	0.000011	D	0.83339	0.5233	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.87997	0.2753	10	0.87932	D	0	-29.0893	16.6526	0.85220	0.0:1.0:0.0:0.0	.	11;11	Q6FI14;O75791	.;GRAP2_HUMAN	D	11	ENSP00000339186:A11D;ENSP00000446350:A11D;ENSP00000396355:A11D;ENSP00000385607:A11D	ENSP00000339186:A11D	A	+	2	0	GRAP2	38673088	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.883000	0.63128	2.660000	0.90430	0.557000	0.71058	GCT	.	.		0.502	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810		A	40343142	C	A	40343142	3	1	87	1	0	0	0	0	1	0	0	0	6763	797	28	3	34	3	GRAP2	22	40343142	Missense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	8808425	40343142	10961424	93	11735										
CRELD2	79174	hgsc.bcm.edu	37	chr22	50315943	50315980	+	Intron	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	cgattcttacgcccctcagcAgtcaggaccggcctctccga					rs377640443|rs562885075|rs542695980|rs113299196|rs7410276|rs12160965|rs386822607|rs386822606|rs564615833|rs368043307|rs71805922|rs386822608|rs73891177	byFrequency	TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr22:50315943_50315980delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	ENST00000328268.4	+	6	666				CRELD2_ENST00000403427.3_Intron|CRELD2_ENST00000404488.3_Splice_Site_p.PQQSGPASPILTR198fs|CRELD2_ENST00000407217.3_Intron|CRELD2_ENST00000444954.1_Intron	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2							endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		GCCCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCGCCTTGCTGTCTGTCTCT	0.618																																					p.198_207del		Atlas-INDEL	.											.	CRELD2	57	.	0			c.593_620del						.																																			SO:0001627	intron_variant	79174	exon6			.	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.593-280CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG>-	chr22.hg19:g.50315943_50315980delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG		27.0	0.0		74.0	49.0	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Frame_Shift_Del	DEL	ENST00000328268.4	hg19	CCDS14082.1																																																																																			.	.		0.618	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324		-	50315980	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-	50315943	6	5	87	0	1	1	0	1	0	0	0	0	3869	202	7	0		0	CRELD2	22	50315943	Intron	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	TCGA-DD-A114-01A-11D-A12Z-10	9972801	50315943	988623	94	11736										
TLR8	51311	hgsc.bcm.edu	37	chrX	12939183	12939183	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	actacatataaatgataataTgttaaagttttttaactgga	5	3	0	1			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chrX:12939183T>C	ENST00000218032.6	+	2	2111	c.2024T>C	c.(2023-2025)aTg>aCg	p.M675T	TLR8_ENST00000311912.5_Missense_Mutation_p.M693T	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	675					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	AATGATAATATGTTAAAGTTT	0.378																																					p.M675T		Atlas-SNP	.											.	TLR8	134	.	0			c.T2024C						.						49	50	50					X																	12939183		2202	4295	6497	SO:0001583	missense	51311	exon2			ATAATATGTTAAA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2024T>C	chrX.hg19:g.12939183T>C	ENSP00000218032:p.Met675Thr	87.0	0.0		134.0	47.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.492083	0.00159	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.56275	0.47;0.47	5.82	-11.6	0.00059	.	3.369210	0.00904	N	0.002384	T	0.35393	0.0930	L	0.39397	1.21	0.09310	N	1	B;B	0.12630	0.002;0.006	B;B	0.04013	0.001;0.001	T	0.14282	-1.0478	10	0.22706	T	0.39	.	6.4243	0.21760	0.4747:0.1082:0.3411:0.076	.	675;693	Q9NR97;D1CS70	TLR8_HUMAN;.	T	675;693	ENSP00000218032:M675T;ENSP00000312082:M693T	ENSP00000218032:M675T	M	+	2	0	TLR8	12849104	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-1.880000	0.01627	-4.010000	0.00082	-0.396000	0.06452	ATG	.	.		0.378	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		C	12939183	T	C	12939183	3	2	87	1	0	0	0	0	1	0	0	0	15972	1464	51	2	2030	2	TLR8	23	12939183	Missense_Mutation	SNP	T	TCGA-DD-A114-01A-11D-A12Z-10		12939183	142331377	95	11737										
TRO	7216	hgsc.bcm.edu	37	chrX	54955568	54955598	+	Frame_Shift_Del	DEL	GTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	GTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	-													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tgcacacagcaccagcactaGtttcagcagtgaagccagca					rs369090033		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	GTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	GTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chrX:54955568_54955598delGTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	ENST00000173898.7	+	12	2523_2553	c.2411_2441delGTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	c.(2410-2442)agtttcagcagtgaagccagcattagctttggtfs	p.SFSSEASISFG804fs	TRO_ENST00000375022.4_Intron|TRO_ENST00000375041.2_Frame_Shift_Del_p.SFSSEASISFG407fs|TRO_ENST00000399736.1_Intron|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000420798.2_Frame_Shift_Del_p.SFSSEASISFG335fs|TRO_ENST00000319167.8_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	804	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						ACCAGCACTAGTTTCAGCAGTGAAGCCAGCATTAGCTTTGGTGGCATGCCT	0.528																																					p.804_814del		Atlas-Indel,Pindel	.											.	TRO	246	.	0			c.2410_2440del						.																																			SO:0001589	frameshift_variant	7216	exon12			.	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.2411_2441delGTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	chrX.hg19:g.54955568_54955598delGTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	ENSP00000173898:p.Ser804fs	134.0	0.0		133.0	28.0	NM_001039705	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Frame_Shift_Del	DEL	ENST00000173898.7	hg19	CCDS43959.1																																																																																			.	.		0.528	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		-	54955598	GTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	-	54955568	7	5	87	1	0	1	0	1	0	0	0	0	16589	1029	36	0	2453	0	TRO	23	54955568	Frame_Shift_Del	DEL	GTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	TCGA-DD-A114-01A-11D-A12Z-10	42016385	54955568	100314992	96	11738										
SPIN4	139886	hgsc.bcm.edu	37	chrX	62570624	62570624	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	ggcttgcgccgttgcttcctGtgggtgtgccttttcttcat	12	11	2	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chrX:62570624G>A	ENST00000335144.3	-	1	594	c.75C>T	c.(73-75)caC>caT	p.H25H	SPIN4_ENST00000374884.2_Silent_p.H7H|SPIN4-AS1_ENST00000451979.1_RNA	NM_001012968.2	NP_001012986.2	Q56A73	SPIN4_HUMAN	spindlin family, member 4	25					gamete generation (GO:0007276)					endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	11						GTTGCTTCCTGTGGGTGTGCC	0.582																																					p.H25H		Atlas-SNP	.											.	SPIN4	29	.	0			c.C75T						.						64	63	63					X																	62570624		2067	4173	6240	SO:0001819	synonymous_variant	139886	exon1			CTTCCTGTGGGTG	AK126931	CCDS43964.1	Xq11.1	2008-02-05			ENSG00000186767	ENSG00000186767			27040	protein-coding gene	gene with protein product						12477932	Standard	NM_001012968		Approved	FLJ44984	uc004dvf.3	Q56A73	OTTHUMG00000021696	ENST00000335144.3:c.75C>T	chrX.hg19:g.62570624G>A		89.0	0.0		84.0	44.0	NM_001012968	B3KX90|Q5JUL2	Silent	SNP	ENST00000335144.3	hg19	CCDS43964.1																																																																																			.	.		0.582	SPIN4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001012968		A	62570624	G	A	62570624	2	1	87	1	0	0	0	0	0	0	0	1	15071	1368	48	3		3	SPIN4	23	62570624	Silent	SNP	G	TCGA-DD-A114-01A-11D-A12Z-10	7615056	62570624	92699936	97	11739										
MED12	9968	hgsc.bcm.edu	37	chrX	70361159	70361160	+	In_Frame_Ins	INS	-	-	CCAGCAGCAACA													0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	caacagcaacaacagcaacaINSccagcagcaacagcagcaac					rs79912241		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chrX:70361159_70361160insCCAGCAGCAACA	ENST00000374080.3	+	43	6379_6380	c.6347_6348insCCAGCAGCAACA	c.(6346-6351)caccag>caCCAGCAGCAACAccag	p.2116_2117HQ>HQQQHQ	MED12_ENST00000333646.6_In_Frame_Ins_p.2119_2120HQ>HQQQHQ|MED12_ENST00000374102.1_In_Frame_Ins_p.2115_2116HQ>HQQQHQ|AL590764.1_ENST00000579622.1_RNA			Q93074	MED12_HUMAN	mediator complex subunit 12	2116	Gln-rich.				androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					caacagcaacaccagcagcaac	0.594			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.H2116delinsHQQQH		Atlas-INDEL	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.6347_6348insCCAGCAGCAACA						.																																			SO:0001652	inframe_insertion	9968	exon43			.	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.6348_6359dupCCAGCAGCAACA	chrX.hg19:g.70361159_70361160insCCAGCAGCAACA	ENSP00000363193:p.Gln2113_His2116dup	138.0	0.0		243.0	94.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	In_Frame_Ins	INS	ENST00000374080.3	hg19	CCDS43970.1																																																																																			.	.		0.594	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		CCAGCAGCAACA	70361160	-	CCAGCAGCAACA	70361159	7	5	87	1	0	1	1	0	0	0	0	0	9437	159	6	0	6517	0	MED12	23	70361159	In_Frame_Ins	INS	-	TCGA-DD-A114-01A-11D-A12Z-10	7790535	70361159	84909401	98	11740										
MAGEE2	139599	hgsc.bcm.edu	37	chrX	75004287	75004287	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	2	1	0.591478696741855	0	0.690058479532164	0.466666666666667	1	0	tcaacttttagcagcaagtcCcaaatggaggcctctcttgc	8	12	2	0			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chrX:75004287C>T	ENST00000373359.2	-	1	792	c.600G>A	c.(598-600)tgG>tgA	p.W200*		NM_138703.4	NP_619648.1	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	200	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.									autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GCAGCAAGTCCCAAATGGAGG	0.512																																					p.W200X		Atlas-SNP	.											.	MAGEE2	94	.	0			c.G600A						.						67	61	63					X																	75004287		2203	4300	6503	SO:0001587	stop_gained	139599	exon1			CAAGTCCCAAATG	AF490509	CCDS14431.1	Xq13	2008-02-05			ENSG00000186675	ENSG00000186675			24935	protein-coding gene	gene with protein product		300760				11454705	Standard	NM_138703		Approved	HCA3	uc004ecj.2	Q8TD90	OTTHUMG00000021870	ENST00000373359.2:c.600G>A	chrX.hg19:g.75004287C>T	ENSP00000362457:p.Trp200*	69.0	0.0		110.0	26.0	NM_138703	Q5JSI5	Nonsense_Mutation	SNP	ENST00000373359.2	hg19	CCDS14431.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.263087	0.39995	.	.	ENSG00000186675	ENST00000373359	.	.	.	3.1	2.21	0.28008	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1813	0.25774	0.0:0.7278:0.2722:0.0	.	.	.	.	X	200	.	ENSP00000362457:W200X	W	-	3	0	MAGEE2	74921012	1.000000	0.71417	0.289000	0.24876	0.026000	0.11368	1.172000	0.31908	0.664000	0.31047	0.422000	0.28245	TGG	.	.		0.512	MAGEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057288.1	NM_138703		T	75004287	C	T	75004287	4	4	87	1	0	0	0	0	0	1	0	0	9195	624	22	3	975	3	MAGEE2	23	75004287	Nonsense_Mutation	SNP	C	TCGA-DD-A114-01A-11D-A12Z-10	4643128	75004287	80266273	99	11741										
TNFRSF25	8718	hgsc.bcm.edu	37	chr1	6522204	6522204	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	aggaggtgctagaagggtgtGggcgctgtccaagggtgaca	19	6	0	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr1:6522204G>A	ENST00000356876.3	-	9	862	c.775C>T	c.(775-777)Cac>Tac	p.H259Y	TNFRSF25_ENST00000377782.3_Missense_Mutation_p.H268Y|TNFRSF25_ENST00000351748.3_Missense_Mutation_p.H76Y|TNFRSF25_ENST00000351959.5_Missense_Mutation_p.H222Y|TNFRSF25_ENST00000461703.2_5'Flank|TNFRSF25_ENST00000348333.3_Missense_Mutation_p.H214Y	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	259					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|central_nervous_system(2)|endometrium(1)|lung(4)|prostate(1)|stomach(1)	10	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		AGAAGGGTGTGGGCGCTGTCC	0.637																																					p.H268Y		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.C802T						.						128	132	130					1																	6522204		2203	4300	6503	SO:0001583	missense	8718	exon9			GGGTGTGGGCGCT	U72763	CCDS71.1, CCDS72.1, CCDS73.1, CCDS74.1, CCDS75.1	1p36.2	2008-02-05	2002-12-20	2002-12-20	ENSG00000215788	ENSG00000215788		"Tumor necrosis factor receptor superfamily"	11910	protein-coding gene	gene with protein product		603366	"tumor necrosis factor receptor superfamily, member 12 (translocating chain-association membrane protein)"	TNFRSF12		9052839, 8934525	Standard	NM_003790		Approved	DR3, TRAMP, WSL-1, LARD, WSL-LR, DDR3, TR3, APO-3	uc001anh.3	Q93038	OTTHUMG00000000831	ENST00000356876.3:c.775C>T	chr1.hg19:g.6522204G>A	ENSP00000349341:p.His259Tyr	146.0	0.0		102.0	35.0	NM_148965	B1ALX2|B1ALX3|B7ZLL7|O00275|O00276|O00277|O00278|O00279|O00280|O14865|O14866|P78507|P78515|Q17RU4|Q92983|Q93036|Q93037|Q99722|Q99830|Q99831|Q9BY86|Q9UME0|Q9UME1|Q9UME5	Missense_Mutation	SNP	ENST00000356876.3	hg19	CCDS71.1	.	.	.	.	.	.	.	.	.	.	G	3.260	-0.151332	0.06585	.	.	ENSG00000215788	ENST00000356876;ENST00000377782;ENST00000351959;ENST00000351748;ENST00000348333	D;D;D;T;D	0.92965	-2.96;-3.14;-3.05;2.5;-2.01	4.89	1.93	0.25924	.	688.334000	0.00447	U	0.000093	D	0.93609	0.7959	M	0.64997	1.995	0.09310	N	1	D;D;D;P;D;D	0.67145	0.996;0.969;0.986;0.947;0.975;0.962	P;P;P;P;P;P	0.53450	0.726;0.656;0.656;0.454;0.726;0.67	T	0.79960	-0.1583	10	0.56958	D	0.05	0.8416	7.6734	0.28471	0.2917:0.0:0.7083:0.0	.	268;214;222;259;260;76	Q93038-11;Q93038-9;Q93038-10;Q93038;Q93038-2;Q93038-8	.;.;.;TNR25_HUMAN;.;.	Y	259;268;222;76;214	ENSP00000349341:H259Y;ENSP00000367013:H268Y;ENSP00000337713:H222Y;ENSP00000326762:H76Y;ENSP00000314451:H214Y	ENSP00000314451:H214Y	H	-	1	0	TNFRSF25	6444791	0.116000	0.22171	0.003000	0.11579	0.075000	0.17131	0.987000	0.29603	0.563000	0.29222	0.655000	0.94253	CAC	.	.		0.637	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965		A	6522204	G	A	6522204	3	1	88	1	0	0	0	0	1	0	0	0	16311	1348	47	3	486	3	TNFRSF25	1	6522204	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10		6522204	242728417	1	11742										
SF3A3	10946	hgsc.bcm.edu	37	chr1	38453345	38453345	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tggcattgagctcctcctttCgtaatctgcaatttcaggaa	8	10	2	1	rs372195588		TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr1:38453345C>T	ENST00000373019.4	-	4	1158	c.203G>A	c.(202-204)cGa>cAa	p.R68Q	SF3A3_ENST00000489537.1_5'UTR|SF3A3_ENST00000448721.2_Intron	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	68					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CTCCTCCTTTCGTAATCTGCA	0.423																																					p.R68Q		Atlas-SNP	.											.	SF3A3	37	.	0			c.G203A						.	C	GLN/ARG	0,4406		0,0,2203	104	105	105		203	5.6	1	1		105	1,8599	1.2+/-3.3	0,1,4299	no	missense	SF3A3	NM_006802.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	68/502	38453345	1,13005	2203	4300	6503	SO:0001583	missense	10946	exon4			TCCTTTCGTAATC	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"splicing factor 3a, subunit 3, 60kD"			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.203G>A	chr1.hg19:g.38453345C>T	ENSP00000362110:p.Arg68Gln	220.0	0.0		131.0	54.0	NM_006802	D3DPT5|Q15460|Q5VT87	Missense_Mutation	SNP	ENST00000373019.4	hg19	CCDS428.1	.	.	.	.	.	.	.	.	.	.	C	36	5.708777	0.96821	0.0	1.16E-4	ENSG00000183431	ENST00000373019	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.86351	0.5912	M	0.92604	3.325	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.88495	0.3078	9	0.56958	D	0.05	-7.9523	19.6316	0.95708	0.0:1.0:0.0:0.0	.	68	Q12874	SF3A3_HUMAN	Q	68	.	ENSP00000362110:R68Q	R	-	2	0	SF3A3	38225932	1.000000	0.71417	0.995000	0.50966	0.936000	0.57629	7.684000	0.84104	2.642000	0.89623	0.557000	0.71058	CGA	.	.		0.423	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802		T	38453345	C	T	38453345	3	4	88	1	0	0	0	0	1	0	0	0	14163	884	31	1	1358	1	SF3A3	1	38453345	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	31931141	38453345	210797276	2	11743										
SMAP2	64744	hgsc.bcm.edu	37	chr1	40839819	40839819	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ggcaagtcggtgaaggacgtGgatcggtaccaggctgtcct	16	9	0	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr1:40839819G>A								COL9A2 (56853 upstream) : SMAP2 (22687 downstream)																							TGAAGGACGTGGATCGGTACC	0.652																																					p.V9V		Atlas-SNP	.											.	SMAP2	48	.	0			c.G27A						.						66	57	60					1																	40839819		2203	4300	6503	SO:0001628	intergenic_variant	64744	exon1			GGACGTGGATCGG																													chr1.hg19:g.40839819G>A		198.0	0.0		124.0	47.0	NM_022733		Silent	SNP		hg19																																																																																				.	.	0	0.652									A	40839819	G	A	40839819	1	1	88	0	1	0	0	0	0	0	0	0	14782	1335	47	3		3	SMAP2	1	40839819	IGR	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	2386474	40839819	208410802	3	11744										
MKNK1	8569	hgsc.bcm.edu	37	chr1	47028365	47028365	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ccggtcccagccacagtcggCcccgcagtgacccacgaagg	12	18	0	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr1:47028365C>T	ENST00000371946.4	-	11	1082	c.919G>A	c.(919-921)Gcc>Acc	p.A307T	MKNK1-AS1_ENST00000602433.1_RNA|MKNK1_ENST00000371944.4_Missense_Mutation_p.A171T|MKNK1_ENST00000428112.2_Missense_Mutation_p.A266T|MKNK1_ENST00000371945.4_Missense_Mutation_p.A266T|MKNK1_ENST00000341183.5_Missense_Mutation_p.A266T	NM_003684.5	NP_003675.2	Q9BUB5	MKNK1_HUMAN	MAP kinase interacting serine/threonine kinase 1	307	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast growth factor receptor signaling pathway (GO:0008543)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|response to salt stress (GO:0009651)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	13	Acute lymphoblastic leukemia(166;0.155)					CCACAGTCGGCCCCGCAGTGA	0.657																																					p.A307T		Atlas-SNP	.											.	MKNK1	36	.	0			c.G919A						.						28	25	26					1																	47028365		2200	4286	6486	SO:0001583	missense	8569	exon11			AGTCGGCCCCGCA	AB000409	CCDS538.1, CCDS30705.1, CCDS44134.1	1p33	2008-02-05			ENSG00000079277	ENSG00000079277			7110	protein-coding gene	gene with protein product		606724				9155018	Standard	NM_003684		Approved	MNK1	uc001cqb.4	Q9BUB5	OTTHUMG00000007983	ENST00000371946.4:c.919G>A	chr1.hg19:g.47028365C>T	ENSP00000361014:p.Ala307Thr	77.0	0.0		59.0	11.0	NM_003684	D3DQ20|D3DQ21|O00312|Q5TC06|Q5TC07|Q6V0N6	Missense_Mutation	SNP	ENST00000371946.4	hg19	CCDS538.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.807832	0.31961	.	.	ENSG00000079277	ENST00000371946;ENST00000371945;ENST00000371944;ENST00000341183;ENST00000428112	T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1	5.42	1.26	0.21427	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.356802	0.34986	N	0.003538	T	0.09949	0.0244	N	0.12611	0.24	0.80722	D	1	B;B;B;B;B;B	0.10296	0.003;0.003;0.0;0.0;0.0;0.002	B;B;B;B;B;B	0.14023	0.01;0.01;0.004;0.002;0.003;0.006	T	0.17961	-1.0352	10	0.25751	T	0.34	.	8.0312	0.30465	0.0:0.5842:0.0:0.4158	.	171;171;266;266;266;307	B4DQK5;Q7Z319;A8K341;Q9BUB5-3;Q9BUB5-2;Q9BUB5	.;.;.;.;.;MKNK1_HUMAN	T	307;266;171;266;266	ENSP00000361014:A307T;ENSP00000361013:A266T;ENSP00000361012:A171T;ENSP00000339573:A266T;ENSP00000411135:A266T	ENSP00000339573:A266T	A	-	1	0	MKNK1	46800952	1.000000	0.71417	0.929000	0.37066	0.564000	0.35744	1.333000	0.33816	0.424000	0.26061	0.563000	0.77884	GCC	.	.		0.657	MKNK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021897.2	NM_003684		T	47028365	C	T	47028365	3	4	88	1	0	0	0	0	1	0	0	0	9613	739	26	3	494	3	MKNK1	1	47028365	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	6188546	47028365	202222256	4	11745										
MTF2	22823	hgsc.bcm.edu	37	chr1	93599749	93599749	+	Frame_Shift_Del	DEL	A	A	-													0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gtctagcatttccaggcattAtgggtagatattttacattc							TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr1:93599749delA	ENST00000370298.4	+	14	1710	c.1421delA	c.(1420-1422)tatfs	p.Y474fs	MTF2_ENST00000545708.1_Frame_Shift_Del_p.Y372fs|MTF2_ENST00000471953.1_3'UTR|MTF2_ENST00000540243.1_Frame_Shift_Del_p.Y372fs|MTF2_ENST00000370303.4_Frame_Shift_Del_p.Y417fs	NM_001164392.1|NM_007358.3	NP_001157864.1|NP_031384	Q9Y483	MTF2_HUMAN	metal response element binding transcription factor 2	474					chromatin modification (GO:0016568)|negative regulation of histone H3-K27 methylation (GO:0061086)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|segment specification (GO:0007379)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)		TCCAGGCATTATGGGTAGATA	0.338																																					p.Y474fs		Atlas-Indel,Pindel	.											.	MTF2	51	.	0			c.1420delT						.						64	68	66					1																	93599749		2201	4299	6500	SO:0001589	frameshift_variant	22823	exon14			.	AJ010014	CCDS742.1, CCDS53340.1, CCDS53341.1	1p22.1	2013-01-28			ENSG00000143033	ENSG00000143033		"Tudor domain containing", "Zinc fingers, PHD-type"	29535	protein-coding gene	gene with protein product	"polycomb-like 2", "tudor domain containing 19A"	609882				15563832	Standard	NM_007358		Approved	M96, PCL2, TDRD19A	uc009wdj.3	Q9Y483	OTTHUMG00000010161	ENST00000370298.4:c.1421delA	chr1.hg19:g.93599749delA	ENSP00000359321:p.Tyr474fs	183.0	0.0		121.0	50.0	NM_007358	A6NGQ9|A8K2Q3|B1AKT5|B1AKT6|Q9UES9|Q9UP40	Frame_Shift_Del	DEL	ENST00000370298.4	hg19	CCDS742.1																																																																																			.	.		0.338	MTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028075.3	NM_007358		-	93599749	A	-	93599749	7	5	88	1	0	1	0	1	0	0	0	0	9932	449	16	0	1475	0	MTF2	1	93599749	Frame_Shift_Del	DEL	A	TCGA-DD-A115-01A-11D-A12Z-10	46571384	93599749	155650872	5	11746										
ZBTB7B	51043	hgsc.bcm.edu	37	chr1	154988092	154988092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tgacctgatggcctacctaaGctccctgcaccaggacaacc	8	16	0	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr1:154988092G>A	ENST00000368426.3	+	3	1093	c.956G>A	c.(955-957)aGc>aAc	p.S319N	ZBTB7B_ENST00000292176.2_Missense_Mutation_p.S319N|ZBTB7B_ENST00000535420.1_Missense_Mutation_p.S319N|ZBTB7B_ENST00000417934.2_Missense_Mutation_p.S353N	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	319					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCCTACCTAAGCTCCCTGCAC	0.657																																					p.S353N		Atlas-SNP	.											.	ZBTB7B	69	.	0			c.G1058A						.						44	43	43					1																	154988092		2203	4300	6503	SO:0001583	missense	51043	exon4			ACCTAAGCTCCCT	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	18668	protein-coding gene	gene with protein product	"zinc finger and BTB domain containing 15"	607646	"zinc finger protein 67 homolog (mouse)"	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.956G>A	chr1.hg19:g.154988092G>A	ENSP00000357411:p.Ser319Asn	91.0	0.0		93.0	16.0	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	hg19	CCDS1081.1	.	.	.	.	.	.	.	.	.	.	g	14.18	2.459273	0.43634	.	.	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.10477	2.89;2.89;2.87;2.89	4.08	4.08	0.47627	.	0.187911	0.30969	N	0.008506	T	0.02119	0.0066	N	0.14661	0.345	0.28989	N	0.888149	B;B;B	0.21225	0.053;0.053;0.053	B;B;B	0.17722	0.019;0.01;0.019	T	0.38286	-0.9668	10	0.44086	T	0.13	.	7.6015	0.28079	0.115:0.0:0.885:0.0	.	319;319;353	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	N	319;319;353;319	ENSP00000438647:S319N;ENSP00000357411:S319N;ENSP00000406286:S353N;ENSP00000292176:S319N	ENSP00000292176:S319N	S	+	2	0	ZBTB7B	153254716	0.953000	0.32496	0.988000	0.46212	0.972000	0.66771	2.260000	0.43267	2.109000	0.64355	0.462000	0.41574	AGC	.	.		0.657	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872		A	154988092	G	A	154988092	3	1	88	1	0	0	0	0	1	0	0	0	17569	971	34	3	958	3	ZBTB7B	1	154988092	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	61388343	154988092	94262529	6	11747										
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161017651	161017651	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	agacccttctgcaccttcagAtgggagctccaggcagctaa	10	13	2	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr1:161017651A>T	ENST00000368013.3	-	12	3480	c.3160T>A	c.(3160-3162)Tct>Act	p.S1054T	USF1_ENST00000435396.1_5'Flank|USF1_ENST00000368020.1_5'Flank|USF1_ENST00000368021.3_5'Flank|ARHGAP30_ENST00000368015.1_Missense_Mutation_p.S877T|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.S843T	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	1054					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GCACCTTCAGATGGGAGCTCC	0.592																																					p.S1054T		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.T3160A						.						76	76	76					1																	161017651		2203	4300	6503	SO:0001583	missense	257106	exon12			CTTCAGATGGGAG	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"Rho GTPase activating proteins"	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.3160T>A	chr1.hg19:g.161017651A>T	ENSP00000356992:p.Ser1054Thr	114.0	0.0		79.0	35.0	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	hg19	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	A	1.347	-0.592555	0.03799	.	.	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368015	T;T;T	0.30182	3.07;3.07;1.54	3.89	-3.82	0.04281	.	1.419890	0.04833	N	0.439041	T	0.07999	0.0200	L	0.36672	1.1	0.09310	N	1	B;B	0.18610	0.01;0.029	B;B	0.12156	0.007;0.006	T	0.33523	-0.9865	10	0.49607	T	0.09	.	6.4205	0.21740	0.5708:0.1497:0.2795:0.0	.	1054;843	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	T	843;1054;877	ENSP00000356995:S843T;ENSP00000356992:S1054T;ENSP00000356994:S877T	ENSP00000356992:S1054T	S	-	1	0	ARHGAP30	159284275	0.012000	0.17670	0.018000	0.16275	0.020000	0.10135	-0.680000	0.05197	-1.463000	0.01904	-1.815000	0.00603	TCT	.	.		0.592	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		T	161017651	A	T	161017651	3	4	88	1	0	0	0	0	1	0	0	0	879	333	12	4	149	4	ARHGAP30	1	161017651	Missense_Mutation	SNP	A	TCGA-DD-A115-01A-11D-A12Z-10	6029559	161017651	88232970	7	11748										
OR2B11	127623	hgsc.bcm.edu	37	chr1	247615107	247615108	+	Missense_Mutation	DNP	GG	GG	TT													0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gaagatgtacatggggctgtGgagttgaggatccacccggg							TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr1:247615107_247615108GG>TT	ENST00000318749.6	-	1	200_201	c.177_178CC>AA	c.(175-180)ctCCac>ctAAac	p.H60N		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			ATGGGGCTGTGGAGTTGAGGAT	0.579																																					p.H60N|p.L59L		Atlas-SNP	.											.	OR2B11	102	.	0			c.C178A|c.C177A						.																																			SO:0001583	missense	127623	exon1			GGCTGTGGAGTTG|GCTGTGGAGTTGA		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"GPCR / Class A : Olfactory receptors"	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.177_178delinsTT	chr1.hg19:g.247615107_247615108delinsTT	ENSP00000325682:p.His60Asn	124.0	0.0		88.0|87.0	34.0|32.0	NM_001004492	B2RP03	Missense_Mutation|Silent	SNP	ENST00000318749.6	hg19	CCDS31090.1																																																																																			.	.		0.579	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492		TT	247615108	GG	TT	247615107	3	4	88	1	0	0	0	0	1	0	0	0	10997	1348	47	3	778	3	OR2B11	1	247615107	Missense_Mutation	DNP	GG	TCGA-DD-A115-01A-11D-A12Z-10	86597456	247615107	1635514	8	11749										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1946920	1946920	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tcatcccctggctcatcattGtcctcggagtactcctcccc	6	18	3	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr2:1946920G>A	ENST00000399161.2	-	9	1086	c.339C>T	c.(337-339)gaC>gaT	p.D113D	MYT1L_ENST00000428368.2_Silent_p.D113D	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	113	Asp/Glu-rich.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GCTCATCATTGTCCTCGGAGT	0.587																																					p.D113D		Atlas-SNP	.											.	MYT1L	241	.	0			c.C339T						.						112	111	111					2																	1946920		2091	4109	6200	SO:0001819	synonymous_variant	23040	exon9			ATCATTGTCCTCG	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.339C>T	chr2.hg19:g.1946920G>A		555.0	0.0		509.0	26.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	hg19																																																																																				.	.		0.587	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1946920	G	A	1946920	2	1	88	1	0	0	0	0	0	0	0	1	10116	1368	48	3		3	MYT1L	2	1946920	Silent	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10		1946920	241252453	9	11750										
KLRAQ1	129285	hgsc.bcm.edu	37	chr2	48718183	48718183	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tccttcttcagcaacaatttGgactacttcattgcttcact	4	12	4	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr2:48718183G>A	ENST00000294952.8	+	15	1630	c.1473G>A	c.(1471-1473)ttG>ttA	p.L491L	PPP1R21_ENST00000449090.2_Silent_p.L491L|PPP1R21_ENST00000281394.4_Silent_p.L491L	NM_001135629.2	NP_001129101.1	Q6ZMI0	PPR21_HUMAN	protein phosphatase 1, regulatory subunit 21	491						membrane (GO:0016020)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(4)|lung(9)	15						GCAACAATTTGGACTACTTCA	0.343																																					p.L491L		Atlas-SNP	.											.	PPP1R21	47	.	0			c.G1473A						.						135	128	130					2																	48718183		2203	4300	6503	SO:0001819	synonymous_variant	129285	exon15			CAATTTGGACTAC	AY134855	CCDS1839.1, CCDS46278.1, CCDS54358.1	2p16.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000162869	ENSG00000162869		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30595	protein-coding gene	gene with protein product			"coiled-coil domain containing 128", "KLRAQ motif containing 1"	CCDC128, KLRAQ1		12477932	Standard	NM_001135629		Approved	FLJ16566	uc002rwm.3	Q6ZMI0	OTTHUMG00000129167	ENST00000294952.8:c.1473G>A	chr2.hg19:g.48718183G>A		218.0	0.0		134.0	9.0	NM_152994	B7ZKY5|B7ZKY7|E1B6W7|Q2TA78|Q6ZMI6|Q8IW83|Q8J029|Q96ES8	Silent	SNP	ENST00000294952.8	hg19	CCDS46278.1																																																																																			.	.		0.343	PPP1R21-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251238.4	NM_152994		A	48718183	G	A	48718183	2	1	88	1	0	0	0	0	0	0	0	1	8422	1339	47	3		3	KLRAQ1	2	48718183	Silent	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	46771263	48718183	194481190	10	11751										
PCBP1	5093	hgsc.bcm.edu	37	chr2	70315174	70315174	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	cagcaggcccccggtcacccTgaggctggtggtgccggcca	15	16	1	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr2:70315174T>A	ENST00000303577.5	+	1	590	c.299T>A	c.(298-300)cTg>cAg	p.L100Q	PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000439670.2_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000596573.1_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	100	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.L100P(1)|p.L100Q(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						CCGGTCACCCTGAGGCTGGTG	0.602																																					p.L100Q	Colon(85;1146 1307 3484 18706 25380)	Atlas-SNP	.											PCBP1,rectum,carcinoma,0,6	PCBP1	28	.	2	Substitution - Missense(2)	large_intestine(2)	c.T299A						.						59	73	68					2																	70315174		2201	4300	6501	SO:0001583	missense	5093	exon1			TCACCCTGAGGCT		CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.299T>A	chr2.hg19:g.70315174T>A	ENSP00000305556:p.Leu100Gln	57.0	0.0		30.0	10.0	NM_006196	Q13157|Q14975	Missense_Mutation	SNP	ENST00000303577.5	hg19	CCDS1898.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.551119	0.65311	.	.	ENSG00000169564	ENST00000303577	T	0.30714	1.52	4.16	4.16	0.48862	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.168590	0.40469	U	0.001094	T	0.60573	0.2279	M	0.91459	3.21	0.54753	D	0.999986	D	0.71674	0.998	D	0.70487	0.969	T	0.69781	-0.5052	10	0.87932	D	0	.	11.8577	0.52449	0.0:0.0:0.0:1.0	.	100	Q15365	PCBP1_HUMAN	Q	100	ENSP00000305556:L100Q	ENSP00000305556:L100Q	L	+	2	0	PCBP1	70168678	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	5.884000	0.69729	2.120000	0.65058	0.477000	0.44152	CTG	.	.		0.602	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		A	70315174	T	A	70315174	3	1	88	1	0	0	0	0	1	0	0	0	11509	1580	55	4	301	4	PCBP1	2	70315174	Missense_Mutation	SNP	T	TCGA-DD-A115-01A-11D-A12Z-10	21596991	70315174	172884199	11	11752										
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71043634	71043634	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gagtttaaagcatttgtgttCtgcaaattttcctttagtcc	7	7	1	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr2:71043634C>G	ENST00000272367.2	-	4	955	c.879G>C	c.(877-879)caG>caC	p.Q293H	CLEC4F_ENST00000426626.1_Missense_Mutation_p.Q293H	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	293					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						CATTTGTGTTCTGCAAATTTT	0.408																																					p.Q293H	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.G879C						.						91	96	94					2																	71043634		2203	4299	6502	SO:0001583	missense	165530	exon4			TGTGTTCTGCAAA	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.879G>C	chr2.hg19:g.71043634C>G	ENSP00000272367:p.Gln293His	428.0	0.0		297.0	19.0	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	hg19	CCDS1910.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.082720	0.55861	.	.	ENSG00000152672	ENST00000272367;ENST00000426626	T;T	0.79554	-1.28;-1.28	4.19	-0.85	0.10720	.	0.178344	0.27223	N	0.020352	D	0.83751	0.5322	M	0.61703	1.905	0.09310	N	1	D;D	0.71674	0.998;0.998	D;D	0.68192	0.956;0.956	T	0.74847	-0.3525	10	0.87932	D	0	.	7.336	0.26609	0.0:0.4908:0.0:0.5092	.	293;293	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	H	293	ENSP00000272367:Q293H;ENSP00000390581:Q293H	ENSP00000272367:Q293H	Q	-	3	2	CLEC4F	70897142	0.000000	0.05858	0.001000	0.08648	0.652000	0.38707	-0.120000	0.10660	-0.237000	0.09739	0.313000	0.20887	CAG	.	.		0.408	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		G	71043634	C	G	71043634	3	3	88	1	0	0	0	0	1	0	0	0	3518	912	32	4	906	4	CLEC4F	2	71043634	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	728460	71043634	172155739	12	11753										
TEX261	113419	hgsc.bcm.edu	37	chr2	71215838	71215838	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ttggtgaaataattggagacGacatcatctgtggagataca	11	5	2	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr2:71215838G>A	ENST00000272438.4	-	6	670	c.483C>T	c.(481-483)gtC>gtT	p.V161V	AC007040.11_ENST00000606025.1_Intron|TEX261_ENST00000466731.1_5'UTR	NM_144582.2	NP_653183.2	Q6UWH6	TX261_HUMAN	testis expressed 261	161						integral component of membrane (GO:0016021)				NS(1)|breast(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	8						AATTGGAGACGACATCATCTG	0.512																																					p.V161V		Atlas-SNP	.											.	TEX261	11	.	0			c.C483T						.						99	92	94					2																	71215838		2203	4300	6503	SO:0001819	synonymous_variant	113419	exon6			GGAGACGACATCA	AL832385	CCDS1914.1	2p13.3	2013-09-24	2007-03-13		ENSG00000144043	ENSG00000144043			30712	protein-coding gene	gene with protein product			"testis expressed sequence 261"			9464256	Standard	NM_144582		Approved	MGC32043, TEG-261	uc002shn.3	Q6UWH6	OTTHUMG00000129708	ENST00000272438.4:c.483C>T	chr2.hg19:g.71215838G>A		101.0	0.0		68.0	27.0	NM_144582	A1A587|D6W5G9|Q8WUJ5	Silent	SNP	ENST00000272438.4	hg19	CCDS1914.1																																																																																			.	.		0.512	TEX261-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251916.1	NM_144582		A	71215838	G	A	71215838	2	1	88	1	0	0	0	0	0	0	0	1	15797	1045	37	1		1	TEX261	2	71215838	Silent	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	172204	71215838	171983535	13	11754										
NPAS2	4862	hgsc.bcm.edu	37	chr2	101580593	101580593	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gtgccactaggaaaggaggtTtgcttcattgccaccgttcg	12	10	1	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr2:101580593T>C	ENST00000335681.5	+	8	957	c.672T>C	c.(670-672)gtT>gtC	p.V224V	NPAS2_ENST00000542504.1_Silent_p.V289V|NPAS2_ENST00000486017.1_3'UTR	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	224					cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GAAAGGAGGTTTGCTTCATTG	0.502																																					p.V224V		Atlas-SNP	.											.	NPAS2	88	.	0			c.T672C						.						129	120	123					2																	101580593		2203	4300	6503	SO:0001819	synonymous_variant	4862	exon8			GGAGGTTTGCTTC	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"Basic helix-loop-helix proteins"	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.672T>C	chr2.hg19:g.101580593T>C		138.0	0.0		88.0	31.0	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Silent	SNP	ENST00000335681.5	hg19	CCDS2048.1																																																																																			.	.		0.502	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3			C	101580593	T	C	101580593	2	2	88	1	0	0	0	0	0	0	0	1	10572	1828	64	2		2	NPAS2	2	101580593	Silent	SNP	T	TCGA-DD-A115-01A-11D-A12Z-10	30364755	101580593	141618780	14	11755										
CACNB4	785	hgsc.bcm.edu	37	chr2	152732958	152732958	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	accctccgtgaaaacgtcctCttttttgttcttgctggatc	7	12	2	1	rs376364352		TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr2:152732958C>G	ENST00000539935.1	-	5	570	c.503G>C	c.(502-504)aGa>aCa	p.R168T	CACNB4_ENST00000397327.2_Missense_Mutation_p.R121T|CACNB4_ENST00000360283.6_Missense_Mutation_p.R134T|CACNB4_ENST00000201943.5_Missense_Mutation_p.R168T|CACNB4_ENST00000534999.1_Missense_Mutation_p.R134T|CACNB4_ENST00000427385.1_Missense_Mutation_p.R150T	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	168					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AAAACGTCCTCTTTTTTGTTC	0.418																																					p.R168T		Atlas-SNP	.											.	CACNB4	108	.	0			c.G503C						.	C	THR/ARG,THR/ARG,THR/ARG,THR/ARG	1,3793		0,1,1896	139	131	134		503,449,401,503	5.6	1	2		134	0,8242		0,0,4121	no	missense,missense,missense,missense	CACNB4	NM_000726.3,NM_001005746.2,NM_001005747.2,NM_001145798.1	71,71,71,71	0,1,6017	GG,GC,CC		0.0,0.0264,0.0083	benign,benign,benign,benign	168/521,150/503,134/487,168/459	152732958	1,12035	1897	4121	6018	SO:0001583	missense	785	exon5			CGTCCTCTTTTTT	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"Calcium channel subunits"	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.503G>C	chr2.hg19:g.152732958C>G	ENSP00000438949:p.Arg168Thr	279.0	0.0		63.0	28.0	NM_001145798	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Missense_Mutation	SNP	ENST00000539935.1	hg19	CCDS46426.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.731069	0.48939	2.64E-4	0.0	ENSG00000182389	ENST00000539935;ENST00000360283;ENST00000543269;ENST00000439467;ENST00000534999;ENST00000397327;ENST00000427385;ENST00000201943;ENST00000339254	D;D;D;D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57;-1.57;-1.57	5.63	5.63	0.86233	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	T	0.76343	0.3974	L	0.28115	0.83	0.58432	D	0.999999	P;B;P;B;P	0.38922	0.651;0.129;0.561;0.418;0.554	B;B;B;B;B	0.39419	0.212;0.071;0.157;0.157;0.299	T	0.72228	-0.4354	10	0.15952	T	0.53	-17.4098	20.0499	0.97621	0.0:1.0:0.0:0.0	.	168;134;168;150;134	A7BJ74;E7DBM8;O00305;B4DG40;O00305-2	.;.;CACB4_HUMAN;.;.	T	168;134;125;163;134;121;150;168;168	ENSP00000438949:R168T;ENSP00000353425:R134T;ENSP00000390161:R163T;ENSP00000443893:R134T;ENSP00000380490:R121T;ENSP00000410978:R150T;ENSP00000201943:R168T	ENSP00000201943:R168T	R	-	2	0	CACNB4	152441204	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.847000	0.69451	2.798000	0.96311	0.655000	0.94253	AGA	.	.		0.418	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3		G	152732958	C	G	152732958	3	3	88	1	0	0	0	0	1	0	0	0	2557	913	32	4	1099	4	CACNB4	2	152732958	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	51152365	152732958	90466415	15	11756										
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172691267	172691267	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ttcaacatctttccttgtgcCagctagagtgctatatatct	6	10	3	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr2:172691267C>A	ENST00000422440.2	-	7	758	c.721G>T	c.(721-723)Ggc>Tgc	p.G241C	SLC25A12_ENST00000392592.4_Missense_Mutation_p.G134C	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	241					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	TTCCTTGTGCCAGCTAGAGTG	0.363																																					p.G241C		Atlas-SNP	.											.	SLC25A12	59	.	0			c.G721T						.						132	124	127					2																	172691267		2203	4300	6503	SO:0001583	missense	8604	exon7			TTGTGCCAGCTAG	Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"Solute carriers", "EF-hand domain containing"	10982	protein-coding gene	gene with protein product		603667	"solute carrier family 25 (mitochondrial carrier, Aralar), member 12"			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.721G>T	chr2.hg19:g.172691267C>A	ENSP00000388658:p.Gly241Cys	112.0	0.0		47.0	8.0	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	hg19	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817550	0.90790	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	T;T	0.80214	-1.35;-1.19	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.89577	0.6755	M	0.81682	2.555	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.61800	0.894;0.894	D	0.90304	0.4332	10	0.72032	D	0.01	-10.0474	19.7609	0.96316	0.0:1.0:0.0:0.0	.	134;241	B3KR64;O75746	.;CMC1_HUMAN	C	241;134	ENSP00000388658:G241C;ENSP00000376371:G134C	ENSP00000376371:G134C	G	-	1	0	SLC25A12	172399513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.729000	0.84864	2.741000	0.93983	0.563000	0.77884	GGC	.	.		0.363	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		A	172691267	C	A	172691267	3	1	88	1	0	0	0	0	1	0	0	0	14489	594	21	3	1363	3	SLC25A12	2	172691267	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	19958309	172691267	70508106	16	11757										
ALS2	57679	hgsc.bcm.edu	37	chr2	202633600	202633600	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tgattttaccttctcttcttTgagtccatcggtcagtggga	9	9	3	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr2:202633600T>G	ENST00000264276.6	-	2	381	c.9A>C	c.(7-9)tcA>tcC	p.S3S	ALS2_ENST00000467448.1_Silent_p.S3S|ALS2_ENST00000496244.1_5'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	3					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TTCTCTTCTTTGAGTCCATCG	0.368																																					p.S3S		Atlas-SNP	.											.	ALS2	172	.	0			c.A9C						.						137	129	131					2																	202633600		1862	4102	5964	SO:0001819	synonymous_variant	57679	exon2			CTTCTTTGAGTCC	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.9A>C	chr2.hg19:g.202633600T>G		140.0	0.0		72.0	22.0	NM_001135745	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Silent	SNP	ENST00000264276.6	hg19	CCDS42800.1																																																																																			.	.		0.368	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		G	202633600	T	G	202633600	2	3	88	1	0	0	0	0	0	0	0	1	550	1799	63	5		5	ALS2	2	202633600	Silent	SNP	T	TCGA-DD-A115-01A-11D-A12Z-10	29942333	202633600	40565773	17	11758										
FARP2	9855	hgsc.bcm.edu	37	chr2	242343251	242343251	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ctctctgcacagcctaaatgCgatggccaggtattactgac	9	12	1	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr2:242343251C>T	ENST00000264042.3	+	3	362	c.192C>T	c.(190-192)tgC>tgT	p.C64C	FARP2_ENST00000373287.4_Silent_p.C64C|FARP2_ENST00000545004.1_Silent_p.C64C	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	64	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.C64C(2)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		AGCCTAAATGCGATGGCCAGG	0.413																																					p.C64C		Atlas-SNP	.											FARP2,caecum,carcinoma,0,2	FARP2	92	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C192T						.						109	102	104					2																	242343251		2203	4300	6503	SO:0001819	synonymous_variant	9855	exon3			TAAATGCGATGGC	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.192C>T	chr2.hg19:g.242343251C>T		192.0	0.0		100.0	20.0	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Silent	SNP	ENST00000264042.3	hg19	CCDS33424.1																																																																																			.	.		0.413	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			T	242343251	C	T	242343251	2	4	88	1	0	0	0	0	0	0	0	1	5685	776	27	1		1	FARP2	2	242343251	Silent	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	39709651	242343251	856122	18	11759										
TIMP4	7079	hgsc.bcm.edu	37	chr3	12195189	12195189	+	Frame_Shift_Del	DEL	G	G	-													0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ttaggggccgagatggtacaGggtactgtgtagcaggtggt							TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr3:12195189delG	ENST00000287814.4	-	5	1011	c.501delC	c.(499-501)cccfs	p.P167fs	SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4	167					central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						AGATGGTACAGGGTACTGTGT	0.488																																					p.C168fs	Melanoma(199;1446 2144 30617 38794 51714)	Atlas-INDEL	.											.	TIMP4	21	.	0			c.502delT						.						134	124	127					3																	12195189		2203	4300	6503	SO:0001589	frameshift_variant	7079	exon5			.	U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"tissue inhibitor of metalloproteinase 4"			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763	ENST00000287814.4:c.501delC	chr3.hg19:g.12195189delG	ENSP00000287814:p.Pro167fs	201.0	0.0		102.0	23.0	NM_003256	B2R7K6	Frame_Shift_Del	DEL	ENST00000287814.4	hg19	CCDS2608.1																																																																																			.	.		0.488	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256		-	12195189	G	-	12195189	7	5	88	1	0	1	0	1	0	0	0	0	15935	987	35	0	177	0	TIMP4	3	12195189	Frame_Shift_Del	DEL	G	TCGA-DD-A115-01A-11D-A12Z-10		12195189	185827241	19	11760										
TRIM71	131405	hgsc.bcm.edu	37	chr3	32915309	32915309	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tgtaccctctcttgtccccaGgtgctgcacctgtactgtga	9	14	1	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr3:32915309G>A	ENST00000383763.5	+	2	915		c.e2-1			NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase						fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CTTGTCCCCAGGTGCTGCACC	0.592																																					.		Atlas-SNP	.											.	TRIM71	73	.	0			c.853-1G>A						.						301	312	308					3																	32915309		2116	4231	6347	SO:0001630	splice_region_variant	131405	exon2			TCCCCAGGTGCTG		CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32669	protein-coding gene	gene with protein product			"tripartite motif-containing 71", "tripartite motif containing 71"				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.853-1G>A	chr3.hg19:g.32915309G>A		299.0	0.0		199.0	32.0	NM_001039111		Splice_Site	SNP	ENST00000383763.5	hg19	CCDS43060.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.606327	0.87157	.	.	ENSG00000206557	ENST00000383763	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3848	0.90463	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TRIM71	32890313	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	9.751000	0.98889	2.769000	0.95229	0.655000	0.94253	.	.	.		0.592	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111	Intron	A	32915309	G	A	32915309	5	1	88	1	0	0	0	0	0	0	1	0	16559	1014	35	3	858	3	TRIM71	3	32915309	Splice_Site	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	20720120	32915309	165107121	20	11761										
RG9MTD1	54931	hgsc.bcm.edu	37	chr3	101283884	101283884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	caacaatctcaagcagtaagGatgaagatcctctagctgcc	8	11	2	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr3:101283884G>A	ENST00000309922.6	+	2	413	c.259G>A	c.(259-261)Gat>Aat	p.D87N		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	87					mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										AAGCAGTAAGGATGAAGATCC	0.438																																					p.D87N		Atlas-SNP	.											.	.	.	.	0			c.G259A						.						117	108	111					3																	101283884		1907	4127	6034	SO:0001583	missense	54931	exon2			AGTAAGGATGAAG	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 1"	615423	"RNA (guanine-9-) methyltransferase domain containing 1"	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.259G>A	chr3.hg19:g.101283884G>A	ENSP00000312356:p.Asp87Asn	193.0	0.0		118.0	44.0	NM_017819	Q9NRG5|Q9NX54|Q9Y596	Missense_Mutation	SNP	ENST00000309922.6	hg19	CCDS43122.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.673703	0.29693	.	.	ENSG00000174173	ENST00000309922;ENST00000495642	T;T	0.54866	0.55;0.55	5.45	5.45	0.79879	.	0.854822	0.10779	N	0.635072	T	0.54598	0.1868	L	0.57536	1.79	0.32643	N	0.520404	B	0.27559	0.181	B	0.20767	0.031	T	0.57768	-0.7754	10	0.39692	T	0.17	-2.6616	20.1745	0.98175	0.0:0.0:1.0:0.0	.	87	Q7L0Y3	MRRP1_HUMAN	N	87	ENSP00000312356:D87N;ENSP00000419389:D87N	ENSP00000312356:D87N	D	+	1	0	RG9MTD1	102766574	1.000000	0.71417	0.943000	0.38184	0.644000	0.38419	3.148000	0.50647	2.941000	0.99782	0.655000	0.94253	GAT	.	.		0.438	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819		A	101283884	G	A	101283884	3	1	88	1	0	0	0	0	1	0	0	0	13286	1174	41	3	261	3	RG9MTD1	3	101283884	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	68368575	101283884	96738546	21	11762										
CEP97	79598	hgsc.bcm.edu	37	chr3	101481359	101481360	+	Frame_Shift_Ins	INS	-	-	A													0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	aaagagatgaagaacgtattINSaaaaaatttgtacaagaaga							TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr3:101481359_101481360insA	ENST00000341893.3	+	10	2600_2601	c.1848_1849insA	c.(1849-1851)aaafs	p.K617fs	CEP97_ENST00000494050.1_Frame_Shift_Ins_p.K558fs|CEP97_ENST00000327230.4_Frame_Shift_Ins_p.K617fs			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	617	CCP110-binding.				cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						AAGAACGTATTAAAAAATTTGT	0.337																																					p.I616fs		Atlas-Indel,Pindel	.											.	CEP97	122	.	0			c.1848_1849insA						.																																			SO:0001589	frameshift_variant	79598	exon10			.	AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504			26244	protein-coding gene	gene with protein product		615864	"leucine-rich repeats and IQ motif containing 2"	LRRIQ2		17719545, 18068367	Standard	NM_024548		Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.1854dupA	chr3.hg19:g.101481365_101481365dupA	ENSP00000342510:p.Lys617fs	511.0	0.0		282.0	52.0	NM_024548	B5MDY8|Q8NA71|Q9H5T9	Frame_Shift_Ins	INS	ENST00000341893.3	hg19	CCDS2944.1																																																																																			.	.		0.337	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548		A	101481360	-	A	101481359	7	5	88	1	0	1	1	0	0	0	0	0	3265	1742	61	0	1886	0	CEP97	3	101481359	Frame_Shift_Ins	INS	-	TCGA-DD-A115-01A-11D-A12Z-10	197475	101481359	96541071	22	11763										
GTF2E1	2960	hgsc.bcm.edu	37	chr3	120469757	120469757	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gaattgagaccgatgagagaGattcgaccaaccgggcttcc	12	10	0	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr3:120469757G>A	ENST00000283875.5	+	2	451	c.358G>A	c.(358-360)Gat>Aat	p.D120N		NM_005513.2	NP_005504.2	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1, alpha 56kDa	120					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)	22				GBM - Glioblastoma multiforme(114;0.159)		CGATGAGAGAGATTCGACCAA	0.403																																					p.D120N		Atlas-SNP	.											.	GTF2E1	52	.	0			c.G358A						.						81	82	82					3																	120469757		2203	4300	6503	SO:0001583	missense	2960	exon2			GAGAGAGATTCGA	S67859	CCDS3002.1	3q21-q24	2010-03-23	2002-08-29		ENSG00000153767	ENSG00000153767		"General transcription factors"	4650	protein-coding gene	gene with protein product		189962	"general transcription factor IIE, polypeptide 1 (alpha subunit, 56kD)"			1454543, 8162052	Standard	NM_005513		Approved	TFIIE-A, FE	uc003edz.4	P29083	OTTHUMG00000159667	ENST00000283875.5:c.358G>A	chr3.hg19:g.120469757G>A	ENSP00000283875:p.Asp120Asn	155.0	0.0		116.0	61.0	NM_005513	Q16103	Missense_Mutation	SNP	ENST00000283875.5	hg19	CCDS3002.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.973662	0.53720	.	.	ENSG00000153767	ENST00000283875;ENST00000492959	T	0.47528	0.84	6.06	5.18	0.71444	Zinc finger, RING/FYVE/PHD-type (1);TFIIEalpha/SarR/Rpc3 HTH domain (1);	0.042733	0.85682	N	0.000000	T	0.49115	0.1538	M	0.68593	2.085	0.80722	D	1	B;B	0.16166	0.002;0.016	B;B	0.29077	0.047;0.098	T	0.43130	-0.9410	9	.	.	.	-8.7497	13.5627	0.61799	0.075:0.0:0.925:0.0	.	120;120	P29083;Q53F88	T2EA_HUMAN;.	N	120	ENSP00000283875:D120N	.	D	+	1	0	GTF2E1	121952447	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	7.905000	0.87416	1.547000	0.49401	0.655000	0.94253	GAT	.	.		0.403	GTF2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356770.1	NM_005513		A	120469757	G	A	120469757	3	1	88	1	0	0	0	0	1	0	0	0	6865	942	33	3	360	3	GTF2E1	3	120469757	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	18988398	120469757	77552673	23	11764										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129275500	129275500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	cgtacttataaatctctgccAtggccacattggtgttgaac	8	10	1	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr3:129275500A>G	ENST00000324093.4	-	35	5799	c.5621T>C	c.(5620-5622)aTg>aCg	p.M1874T	PLXND1_ENST00000393239.1_3'UTR|PLXND1_ENST00000504689.1_Missense_Mutation_p.M30T	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1874					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						AATCTCTGCCATGGCCACATT	0.552																																					p.M1874T	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.T5621C						.						158	142	147					3																	129275500		2203	4300	6503	SO:0001583	missense	23129	exon35			TCTGCCATGGCCA	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.5621T>C	chr3.hg19:g.129275500A>G	ENSP00000317128:p.Met1874Thr	179.0	0.0		148.0	55.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.636703	0.47049	.	.	ENSG00000004399	ENST00000324093;ENST00000504689	T;T	0.11930	2.73;2.73	5.11	3.96	0.45880	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.103102	0.64402	D	0.000004	T	0.09905	0.0243	N	0.14661	0.345	0.80722	D	1	B;P	0.38677	0.017;0.642	B;B	0.39971	0.018;0.315	T	0.14559	-1.0468	10	0.87932	D	0	.	10.902	0.47058	0.9258:0.0:0.0742:0.0	.	470;1874	B4DRU3;Q9Y4D7	.;PLXD1_HUMAN	T	1874;30	ENSP00000317128:M1874T;ENSP00000426162:M30T	ENSP00000317128:M1874T	M	-	2	0	PLXND1	130758190	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	5.168000	0.64978	0.786000	0.33708	-0.609000	0.04063	ATG	.	.		0.552	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		G	129275500	A	G	129275500	3	3	88	1	0	0	0	0	1	0	0	0	12136	217	8	2	164	2	PLXND1	3	129275500	Missense_Mutation	SNP	A	TCGA-DD-A115-01A-11D-A12Z-10	8805743	129275500	68746930	24	11765										
NAAA	27163	hgsc.bcm.edu	37	chr4	76861223	76861223	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ggttcatgaagtcacacatgCcgcggatctcgccggtgaag	13	11	3	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr4:76861223C>A	ENST00000286733.4	-	2	403	c.302G>T	c.(301-303)gGc>gTc	p.G101V	NAAA_ENST00000507187.2_Missense_Mutation_p.G101V|NAAA_ENST00000399497.3_Missense_Mutation_p.G101V|NAAA_ENST00000507956.1_Missense_Mutation_p.G101V|NAAA_ENST00000505594.1_5'UTR	NM_014435.3	NP_055250.2	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase	101					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	11						GTCACACATGCCGCGGATCTC	0.622																																					p.G101V		Atlas-SNP	.											.	NAAA	26	.	0			c.G302T						.						52	60	57					4																	76861223		2029	4183	6212	SO:0001583	missense	27163	exon2			CACATGCCGCGGA	M92449	CCDS43239.1	4q21.1	2011-09-23	2008-04-24	2008-04-24	ENSG00000138744	ENSG00000138744	3.5.1.-		736	protein-coding gene	gene with protein product		607469	"N-acylsphingosine amidohydrolase (acid ceramidase)-like"	ASAHL		10610717, 1446826	Standard	NM_001042402		Approved		uc003hjb.3	Q02083	OTTHUMG00000160855	ENST00000286733.4:c.302G>T	chr4.hg19:g.76861223C>A	ENSP00000286733:p.Gly101Val	121.0	0.0		57.0	22.0	NM_014435	Q5KTF2|Q96EY2|Q9BRA8	Missense_Mutation	SNP	ENST00000286733.4	hg19	CCDS43239.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.262281	0.80358	.	.	ENSG00000138744	ENST00000399497;ENST00000286733;ENST00000507956;ENST00000399490;ENST00000507187	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.1	5.1	0.69264	.	0.055581	0.64402	D	0.000001	T	0.77130	0.4085	M	0.73217	2.22	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.79784	0.993;0.985	T	0.79249	-0.1881	10	0.87932	D	0	-19.6079	13.8776	0.63662	0.0:1.0:0.0:0.0	.	101;101	D6R9S9;Q02083	.;NAAA_HUMAN	V	101	ENSP00000382420:G101V;ENSP00000286733:G101V;ENSP00000427641:G101V;ENSP00000423142:G101V	ENSP00000286733:G101V	G	-	2	0	NAAA	77080247	0.937000	0.31787	0.992000	0.48379	0.693000	0.40251	5.302000	0.65733	2.655000	0.90218	0.585000	0.79938	GGC	.	.		0.622	NAAA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362843.4			A	76861223	C	A	76861223	3	1	88	1	0	0	0	0	1	0	0	0	10136	739	26	3	820	3	NAAA	4	76861223	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10		76861223	114293053	25	11766										
STBD1	100631383	hgsc.bcm.edu	37	chr4	77230589	77230589	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gcagctacatgttttgcagaGaagttgccttctagcaacct	9	10	1	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr4:77230589G>T	ENST00000237642.6	+	2	1257	c.513G>T	c.(511-513)gaG>gaT	p.E171D	FAM47E_ENST00000515604.1_3'UTR|FAM47E-STBD1_ENST00000539752.1_Missense_Mutation_p.E22D	NM_003943.4	NP_003934.1			FAM47E-STBD1 readthrough																		GTTTTGCAGAGAAGTTGCCTT	0.443																																					p.E171D		Atlas-SNP	.											.	STBD1	22	.	0			c.G513T						.						52	54	54					4																	77230589		2203	4300	6503	SO:0001583	missense	8987	exon2			TGCAGAGAAGTTG		CCDS58908.1	4q21.1	2013-04-23			ENSG00000118804	ENSG00000118804			44667	other	readthrough							Standard	NM_001242939		Approved				OTTHUMG00000160966	ENST00000237642.6:c.513G>T	chr4.hg19:g.77230589G>T	ENSP00000237642:p.Glu171Asp	146.0	0.0		109.0	42.0	NM_003943		Missense_Mutation	SNP	ENST00000237642.6	hg19	CCDS3578.1	.	.	.	.	.	.	.	.	.	.	G	2.139	-0.397246	0.04899	.	.	ENSG00000118804	ENST00000539752;ENST00000237642	.	.	.	4.73	-1.64	0.08318	.	0.933364	0.08922	N	0.874297	T	0.23926	0.0579	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.21930	-1.0231	9	0.30078	T	0.28	-0.6048	1.7559	0.02982	0.3423:0.1295:0.3961:0.132	.	171	O95210	STBD1_HUMAN	D	22;171	.	ENSP00000237642:E171D	E	+	3	2	STBD1	77449613	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-0.073000	0.11468	-0.250000	0.09555	-0.165000	0.13383	GAG	.	.		0.443	FAM47E-STBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252415.2			T	77230589	G	T	77230589	3	4	88	1	0	0	0	0	1	0	0	0	15289	933	33	3	519	3	STBD1	4	77230589	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	369366	77230589	113923687	26	11767										
ANXA3	306	hgsc.bcm.edu	37	chr4	79503384	79503384	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ggccactttgagcatctcatGgtggccctagtgactccacc	10	14	1	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr4:79503384G>A	ENST00000264908.6	+	5	631	c.252G>A	c.(250-252)atG>atA	p.M84I	ANXA3_ENST00000512884.1_Missense_Mutation_p.M45I|ANXA3_ENST00000503570.2_Missense_Mutation_p.M45I	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	84					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						AGCATCTCATGGTGGCCCTAG	0.453																																					p.M84I	GBM(2;126 157 27790 28920 42492)	Atlas-SNP	.											.	ANXA3	35	.	0			c.G252A						.						87	84	85					4																	79503384		2203	4300	6503	SO:0001583	missense	306	exon5			TCTCATGGTGGCC	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"Annexins"	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.252G>A	chr4.hg19:g.79503384G>A	ENSP00000264908:p.Met84Ile	304.0	0.0		157.0	62.0	NM_005139	B2R9W6|Q6LET2	Missense_Mutation	SNP	ENST00000264908.6	hg19	CCDS3584.1	.	.	.	.	.	.	.	.	.	.	G	8.570	0.879933	0.17467	.	.	ENSG00000138772	ENST00000264908;ENST00000512884;ENST00000503570;ENST00000512373;ENST00000514171;ENST00000508214	T;T;T;T;T;T	0.03181	4.02;4.02;4.02;4.02;4.02;4.02	5.16	5.16	0.70880	Annexin repeat, conserved site (1);	0.146214	0.64402	D	0.000009	T	0.03220	0.0094	N	0.16066	0.365	0.51233	D	0.999914	B	0.27117	0.168	B	0.34346	0.18	T	0.32268	-0.9913	10	0.02654	T	1	.	17.5603	0.87905	0.0:0.0:1.0:0.0	.	84	P12429	ANXA3_HUMAN	I	84;45;45;84;84;84	ENSP00000264908:M84I;ENSP00000423068:M45I;ENSP00000421015:M45I;ENSP00000424584:M84I;ENSP00000421512:M84I;ENSP00000422281:M84I	ENSP00000264908:M84I	M	+	3	0	ANXA3	79722408	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	1.792000	0.38754	2.674000	0.91012	0.591000	0.81541	ATG	.	.		0.453	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139		A	79503384	G	A	79503384	3	1	88	1	0	0	0	0	1	0	0	0	719	1348	47	3	266	3	ANXA3	4	79503384	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	2272795	79503384	111650892	27	11768										
GHR	2690	hgsc.bcm.edu	37	chr5	42713546	42713546	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ttcagatttctactttccatGgctcttaattattatctttg	4	8	4	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr5:42713546G>A	ENST00000230882.4	+	8	990	c.800G>A	c.(799-801)tGg>tAg	p.W267*	GHR_ENST00000537449.1_Nonsense_Mutation_p.W80*|GHR_ENST00000357703.3_Nonsense_Mutation_p.W245*	NM_000163.4|NM_001242399.2|NM_001242400.2|NM_001242401.3|NM_001242402.2|NM_001242403.2|NM_001242404.2|NM_001242405.2|NM_001242406.2	NP_000154.1|NP_001229328.1|NP_001229329.1|NP_001229330.1|NP_001229331.1|NP_001229332.1|NP_001229333.1|NP_001229334.1|NP_001229335.1	P10912	GHR_HUMAN	growth hormone receptor	267					2-oxoglutarate metabolic process (GO:0006103)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPK activity (GO:0000187)|allantoin metabolic process (GO:0000255)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|endocytosis (GO:0006897)|fatty acid metabolic process (GO:0006631)|growth hormone receptor signaling pathway (GO:0060396)|insulin-like growth factor receptor signaling pathway (GO:0048009)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|multicellular organismal metabolic process (GO:0044236)|oxaloacetate metabolic process (GO:0006107)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|receptor internalization (GO:0031623)|regulation of multicellular organism growth (GO:0040014)|response to cycloheximide (GO:0046898)|response to estradiol (GO:0032355)|succinate metabolic process (GO:0006105)|taurine metabolic process (GO:0019530)|valine metabolic process (GO:0006573)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|growth hormone receptor complex (GO:0070195)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine receptor activity (GO:0004896)|growth factor binding (GO:0019838)|peptide hormone binding (GO:0017046)|proline-rich region binding (GO:0070064)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			NS(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	TACTTTCCATGGCTCTTAATT	0.328																																					p.W274X		Atlas-SNP	.											.	GHR	94	.	0			c.G821A						.						181	186	184					5																	42713546		2202	4295	6497	SO:0001587	stop_gained	2690	exon8			TTCCATGGCTCTT		CCDS3940.1, CCDS56364.1, CCDS75239.1, CCDS75240.1	5p14-p12	2013-03-25			ENSG00000112964	ENSG00000112964		"Fibronectin type III domain containing"	4263	protein-coding gene	gene with protein product	"growth hormone binding protein"	600946					Standard	NM_001242460		Approved	GHBP	uc003jmt.3	P10912	OTTHUMG00000094791	ENST00000230882.4:c.800G>A	chr5.hg19:g.42713546G>A	ENSP00000230882:p.Trp267*	425.0	0.0		158.0	49.0	NM_001242399	Q9HCX2	Nonsense_Mutation	SNP	ENST00000230882.4	hg19	CCDS3940.1	.	.	.	.	.	.	.	.	.	.	G	39	7.446990	0.98289	.	.	ENSG00000112964	ENST00000230882;ENST00000357703;ENST00000356276;ENST00000537449	.	.	.	5.43	5.43	0.79202	.	0.224065	0.39341	N	0.001389	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-5.871	17.4237	0.87521	0.0:0.0:1.0:0.0	.	.	.	.	X	267;245;267;80	.	ENSP00000230882:W267X	W	+	2	0	GHR	42749303	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.594000	0.61041	2.550000	0.86006	0.591000	0.81541	TGG	.	.		0.328	GHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211605.2	NM_000163		A	42713546	G	A	42713546	4	1	88	1	0	0	0	0	0	1	0	0	6379	1357	47	3	826	3	GHR	5	42713546	Nonsense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10		42713546	138201714	28	11769										
RGNEF	64283	hgsc.bcm.edu	37	chr5	73168941	73168941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	caccgtggataaaattttccCctgtttagatgagttgcttg	9	8	0	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr5:73168941C>T	ENST00000426542.2	+	21	2704	c.2684C>T	c.(2683-2685)cCc>cTc	p.P895L	ARHGEF28_ENST00000545377.1_Missense_Mutation_p.P895L|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.P895L|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.P582L|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.P895L|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.P895L|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.P895L			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	895	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										AAAATTTTCCCCTGTTTAGAT	0.468																																					p.P895L		Atlas-SNP	.											.	.	.	.	0			c.C2684T						.						58	58	58					5																	73168941		1937	4140	6077	SO:0001583	missense	64283	exon22			TTTTCCCCTGTTT		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2684C>T	chr5.hg19:g.73168941C>T	ENSP00000412175:p.Pro895Leu	172.0	0.0		158.0	50.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.970568	0.92919	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	5.24	5.24	0.73138	Dbl homology (DH) domain (5);	.	.	.	.	D	0.84401	0.5464	M	0.85041	2.73	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;0.999	D;D;D;D	0.97110	1.0;0.99;0.99;0.986	D	0.86711	0.1936	9	0.87932	D	0	.	19.1848	0.93639	0.0:1.0:0.0:0.0	.	582;895;895;895	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	L	895;895;895;895;895;895;582	ENSP00000296794:P895L;ENSP00000441913:P895L;ENSP00000441436:P895L;ENSP00000287898:P895L;ENSP00000411459:P895L;ENSP00000412175:P895L;ENSP00000296799:P582L	ENSP00000287898:P895L	P	+	2	0	RP11-428C6.1	73204697	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.729000	0.84864	2.610000	0.88304	0.650000	0.86243	CCC	.	.		0.468	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			T	73168941	C	T	73168941	3	4	88	1	0	0	0	0	1	0	0	0	13298	623	22	3	2766	3	RGNEF	5	73168941	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	30455395	73168941	107746319	29	11770										
PSD2	84249	hgsc.bcm.edu	37	chr5	139193051	139193051	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gcgacagctgcgtcagcttcGaggcccccctcacacccctc	9	20	2	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr5:139193051G>T	ENST00000274710.3	+	3	734	c.529G>T	c.(529-531)Gag>Tag	p.E177*		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	177					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTCAGCTTCGAGGCCCCCCT	0.662																																					p.E177X		Atlas-SNP	.											.	PSD2	88	.	0			c.G529T						.						37	41	39					5																	139193051		2203	4300	6503	SO:0001587	stop_gained	84249	exon3			AGCTTCGAGGCCC	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.529G>T	chr5.hg19:g.139193051G>T	ENSP00000274710:p.Glu177*	144.0	0.0		97.0	51.0	NM_032289	D3DQD3|Q8N3J8	Nonsense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	G	38	7.037932	0.98021	.	.	ENSG00000146005	ENST00000274710	.	.	.	3.99	3.99	0.46301	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.7866	0.69808	0.0:0.0:1.0:0.0	.	.	.	.	X	177	.	ENSP00000274710:E177X	E	+	1	0	PSD2	139173235	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.484000	0.90445	2.214000	0.71695	0.462000	0.41574	GAG	.	.		0.662	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139193051	G	T	139193051	4	4	88	1	0	0	0	0	0	1	0	0	12659	1059	37	1	535	1	PSD2	5	139193051	Nonsense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	66024110	139193051	41722209	30	11771										
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140249239	140249239	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tttttctttagattcaccaaCaaatggtaagcagattaaaa	5	6	2	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr5:140249239C>T	ENST00000398640.2	+	1	551	c.551C>T	c.(550-552)aCa>aTa	p.T184I	PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	184	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.T184I(2)		breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATTCACCAACAAATGGTAAG	0.383																																					p.T184I		Atlas-SNP	.											PCDHA11_ENST00000398640,NS,carcinoma,0,2	PCDHA11	209	.	2	Substitution - Missense(2)	lung(2)	c.C551T						.						68	75	73					5																	140249239		2000	4181	6181	SO:0001583	missense	56138	exon1			CACCAACAAATGG	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.551C>T	chr5.hg19:g.140249239C>T	ENSP00000381636:p.Thr184Ile	58.0	0.0		58.0	9.0	NM_018902	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	hg19	CCDS47284.1	.	.	.	.	.	.	.	.	.	.	C	0.427	-0.905228	0.02453	.	.	ENSG00000249158	ENST00000398640	T	0.58060	0.36	5.71	0.824	0.18818	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.44265	0.1285	M	0.66297	2.02	0.09310	N	1	B;B	0.17852	0.024;0.017	B;B	0.21151	0.019;0.033	T	0.44298	-0.9337	9	0.44086	T	0.13	.	1.251	0.01982	0.202:0.3351:0.2615:0.2014	.	184;184	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	I	184	ENSP00000381636:T184I	ENSP00000381636:T184I	T	+	2	0	PCDHA11	140229423	0.000000	0.05858	0.029000	0.17559	0.175000	0.22909	-3.644000	0.00405	-0.129000	0.11620	-0.122000	0.15005	ACA	.	.		0.383	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		T	140249239	C	T	140249239	3	4	88	1	0	0	0	0	1	0	0	0	11530	478	17	3	553	3	PCDHA11	5	140249239	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	1056188	140249239	40666021	31	11772										
ODZ2	57451	hgsc.bcm.edu	37	chr5	166711893	166711893	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ttgaccagaggacgctgtggCaaagagtgtcgctacacaag	13	9	0	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr5:166711893C>T	ENST00000518659.1	+	1	90	c.51C>T	c.(49-51)ggC>ggT	p.G17G	CTB-180C19.1_ENST00000521697.1_RNA|TENM2_ENST00000545108.1_Silent_p.G17G	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	17	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										GACGCTGTGGCAAAGAGTGTC	0.527																																					p.G17G		Atlas-SNP	.											.	.	.	.	0			c.C51T						.						66	63	64					5																	166711893		692	1591	2283	SO:0001819	synonymous_variant	57451	exon1			CTGTGGCAAAGAG	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.51C>T	chr5.hg19:g.166711893C>T		85.0	0.0		72.0	22.0	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	hg19																																																																																				.	.		0.527	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	166711893	C	T	166711893	2	4	88	1	0	0	0	0	0	0	0	1	10844	697	25	3		3	ODZ2	5	166711893	Silent	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	26462654	166711893	14203367	32	11773										
SYCP2L	221711	hgsc.bcm.edu	37	chr6	10894136	10894136	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	cggatgcattccatgataaaGgatttcagaaaataaaagaa	8	5	1	3	rs529185874		TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr6:10894136G>T	ENST00000283141.6	+	3	411	c.115G>T	c.(115-117)Gga>Tga	p.G39*	SYCP2L_ENST00000543878.1_5'UTR|RP11-637O19.3_ENST00000480294.1_3'UTR	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	39						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			CCATGATAAAGGATTTCAGAA	0.294																																					p.G39X		Atlas-SNP	.											.	SYCP2L	101	.	0			c.G115T						.						34	33	33					6																	10894136		1798	4060	5858	SO:0001587	stop_gained	221711	exon3			GATAAAGGATTTC	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 177"	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.115G>T	chr6.hg19:g.10894136G>T	ENSP00000283141:p.Gly39*	285.0	0.0		173.0	70.0	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Nonsense_Mutation	SNP	ENST00000283141.6	hg19	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.585750	0.86748	.	.	ENSG00000153157	ENST00000283141	.	.	.	5.66	1.91	0.25777	.	0.456218	0.21304	N	0.076756	.	.	.	.	.	.	0.24096	N	0.995895	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.7238	6.7655	0.23564	0.2148:0.1279:0.6572:0.0	.	.	.	.	X	39	.	ENSP00000283141:G39X	G	+	1	0	SYCP2L	11002122	1.000000	0.71417	0.053000	0.19242	0.184000	0.23303	2.359000	0.44142	0.063000	0.16370	-0.878000	0.02970	GGA	.	.		0.294	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		T	10894136	G	T	10894136	4	4	88	1	0	0	0	0	0	1	0	0	15448	1001	35	3	125	3	SYCP2L	6	10894136	Nonsense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10		10894136	160220931	33	11774										
OR2H2	7932	hgsc.bcm.edu	37	chr6	29556102	29556102	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tacgtggctgtctgccagccCctccactatgccaccatcat	7	17	2	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr6:29556102C>A	ENST00000383640.2	+	1	420	c.381C>A	c.(379-381)ccC>ccA	p.P127P	GABBR1_ENST00000355973.3_Intron	NM_007160.3	NP_009091.3	O95918	OR2H2_HUMAN	olfactory receptor, family 2, subfamily H, member 2	127					defense response (GO:0006952)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|mating (GO:0007618)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	14						TCTGCCAGCCCCTCCACTATG	0.577																																					p.P127P		Atlas-SNP	.											.	OR2H2	29	.	0			c.C381A						.						124	128	126					6																	29556102		1509	2709	4218	SO:0001819	synonymous_variant	7932	exon1			CCAGCCCCTCCAC		CCDS34365.1	6p22.2-p21.31	2012-08-09				ENSG00000204657		"GPCR / Class A : Olfactory receptors"	8253	protein-coding gene	gene with protein product		600578					Standard	XM_005249407		Approved	hs6M1-12	uc003nmr.1	O95918		ENST00000383640.2:c.381C>A	chr6.hg19:g.29556102C>A		180.0	0.0		122.0	40.0	NM_007160	Q15062|Q2M1Y3|Q5STL8|Q5SUK1|Q6IFN7|Q6NTB7|Q96R14	Silent	SNP	ENST00000383640.2	hg19	CCDS34365.1																																																																																			.	.		0.577	OR2H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076057.2			A	29556102	C	A	29556102	2	1	88	1	0	0	0	0	0	0	0	1	11011	610	22	3		3	OR2H2	6	29556102	Silent	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	18661966	29556102	141558965	34	11775										
FRS3	10817	hgsc.bcm.edu	37	chr6	41738386	41738386	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	caggtcggtgctgttgtgccGggttttcctggcggtgccat	16	10	0	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr6:41738386G>C	ENST00000373018.3	-	7	1701	c.1450C>G	c.(1450-1452)Cgg>Ggg	p.R484G	FRS3_ENST00000259748.2_Missense_Mutation_p.R484G	NM_006653.3	NP_006644.1	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3	484					fibroblast growth factor receptor signaling pathway (GO:0008543)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CTGTTGTGCCGGGTTTTCCTG	0.602																																					p.R484G		Atlas-SNP	.											.	FRS3	53	.	0			c.C1450G						.						109	100	103					6																	41738386		2203	4300	6503	SO:0001583	missense	10817	exon7			TGTGCCGGGTTTT	AF036718	CCDS4860.1	6p21.1	2010-08-05			ENSG00000137218	ENSG00000137218			16970	protein-coding gene	gene with protein product		607744				8761293, 9660748	Standard	NM_006653		Approved	SNT-2, FRS2beta, FRS2B	uc003orc.1	O43559	OTTHUMG00000014686	ENST00000373018.3:c.1450C>G	chr6.hg19:g.41738386G>C	ENSP00000362109:p.Arg484Gly	151.0	0.0		82.0	29.0	NM_006653	Q5T3D5	Missense_Mutation	SNP	ENST00000373018.3	hg19	CCDS4860.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.494080	0.64186	.	.	ENSG00000137218	ENST00000373018;ENST00000259748	T;T	0.62639	0.01;0.01	5.8	4.0	0.46444	.	0.000000	0.85682	D	0.000000	T	0.71643	0.3364	M	0.73598	2.24	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.76767	-0.2838	10	0.87932	D	0	-31.9543	13.9088	0.63853	0.0:0.0:0.6035:0.3965	.	484	O43559	FRS3_HUMAN	G	484	ENSP00000362109:R484G;ENSP00000259748:R484G	ENSP00000259748:R484G	R	-	1	2	FRS3	41846364	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	2.681000	0.46926	0.776000	0.33473	0.655000	0.94253	CGG	.	.		0.602	FRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040532.2	NM_006653		C	41738386	G	C	41738386	3	2	88	1	0	0	0	0	1	0	0	0	6070	1115	39	4	32	4	FRS3	6	41738386	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	12182284	41738386	129376681	35	11776										
PLA2G7	7941	hgsc.bcm.edu	37	chr6	46672428	46672428	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ccactgatcaaaatctttatGaagtcctataaaatataaag	4	7	2	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr6:46672428G>C	ENST00000274793.7	-	12	1391	c.1195C>G	c.(1195-1197)Cat>Gat	p.H399D	PLA2G7_ENST00000537365.1_Missense_Mutation_p.H399D	NM_005084.3	NP_005075.3	Q13093	PAFA_HUMAN	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	399					cellular protein metabolic process (GO:0044267)|lipid catabolic process (GO:0016042)|lipid oxidation (GO:0034440)|low-density lipoprotein particle remodeling (GO:0034374)|plasma lipoprotein particle oxidation (GO:0034441)|positive regulation of inflammatory response (GO:0050729)|positive regulation of monocyte chemotaxis (GO:0090026)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|low-density lipoprotein particle (GO:0034362)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|skin(1)|soft_tissue(1)	14			Lung(136;0.192)			AAATCTTTATGAAGTCCTATA	0.338																																					p.H399D		Atlas-SNP	.											.	PLA2G7	49	.	0			c.C1195G						.						72	67	69					6																	46672428		2202	4298	6500	SO:0001583	missense	7941	exon12			CTTTATGAAGTCC	U20157	CCDS4917.1	6p21.2-p12	2008-09-19			ENSG00000146070	ENSG00000146070	3.1.1.4		9040	protein-coding gene	gene with protein product		601690				7700381, 8624782	Standard	NM_005084		Approved	PAFAH, LDL-PLA2	uc021zae.1	Q13093	OTTHUMG00000014789	ENST00000274793.7:c.1195C>G	chr6.hg19:g.46672428G>C	ENSP00000274793:p.His399Asp	385.0	0.0		275.0	144.0	NM_005084	A5HTT5|Q15692|Q5VTT1|Q8IVA2	Missense_Mutation	SNP	ENST00000274793.7	hg19	CCDS4917.1	.	.	.	.	.	.	.	.	.	.	G	9.263	1.043790	0.19748	.	.	ENSG00000146070	ENST00000274793;ENST00000537365	T;T	0.39406	1.08;1.08	5.5	2.48	0.30137	.	0.960419	0.08735	N	0.901426	T	0.09598	0.0236	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31447	-0.9943	10	0.13853	T	0.58	.	9.9133	0.41419	0.0:0.1357:0.5908:0.2735	.	399	Q13093	PAFA_HUMAN	D	399	ENSP00000274793:H399D;ENSP00000445666:H399D	ENSP00000274793:H399D	H	-	1	0	PLA2G7	46780387	0.995000	0.38212	0.982000	0.44146	0.966000	0.64601	0.383000	0.20651	0.254000	0.21573	0.561000	0.74099	CAT	.	.		0.338	PLA2G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040802.1			C	46672428	G	C	46672428	3	2	88	1	0	0	0	0	1	0	0	0	12018	1290	45	4	134	4	PLA2G7	6	46672428	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	4934042	46672428	124442639	36	11777										
PGK2	5232	hgsc.bcm.edu	37	chr6	49753721	49753721	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tagactggcaccgcctccagTgctgacatggctgactttat	10	12	0	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr6:49753721T>A	ENST00000304801.3	-	1	1332	c.1180A>T	c.(1180-1182)Act>Tct	p.T394S		NM_138733.4	NP_620061.2	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	394					glycolytic process (GO:0006096)|phosphorylation (GO:0016310)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	ATP binding (GO:0005524)|phosphoglycerate kinase activity (GO:0004618)			autonomic_ganglia(1)|endometrium(3)|large_intestine(12)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	47	Lung NSC(77;0.0402)					CCGCCTCCAGTGCTGACATGG	0.483																																					p.T394S		Atlas-SNP	.											.	PGK2	87	.	0			c.A1180T						.						114	110	112					6																	49753721		2203	4300	6503	SO:0001583	missense	5232	exon1			CTCCAGTGCTGAC	K03019	CCDS4930.1	6p12.3	2012-09-20		2002-04-19	ENSG00000170950	ENSG00000170950			8898	protein-coding gene	gene with protein product		172270				3839763, 3453121	Standard	NM_138733		Approved	PGKPS, PGK-2	uc003ozu.3	P07205	OTTHUMG00000014824	ENST00000304801.3:c.1180A>T	chr6.hg19:g.49753721T>A	ENSP00000305995:p.Thr394Ser	153.0	0.0		109.0	54.0	NM_138733	B2R6Y8|Q9H107	Missense_Mutation	SNP	ENST00000304801.3	hg19	CCDS4930.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.388149	0.82902	.	.	ENSG00000170950	ENST00000304801	D	0.94330	-3.4	4.19	4.19	0.49359	Phosphoglycerate kinase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96337	0.8805	M	0.92691	3.335	0.58432	D	0.999997	P	0.51537	0.946	P	0.61275	0.886	D	0.96806	0.9593	10	0.72032	D	0.01	-20.2441	11.8373	0.52333	0.0:0.0:0.0:1.0	.	394	P07205	PGK2_HUMAN	S	394	ENSP00000305995:T394S	ENSP00000305995:T394S	T	-	1	0	PGK2	49861680	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.565000	0.67365	2.115000	0.64714	0.477000	0.44152	ACT	.	.		0.483	PGK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040872.1			A	49753721	T	A	49753721	3	1	88	1	0	0	0	0	1	0	0	0	11800	1696	59	4	77	4	PGK2	6	49753721	Missense_Mutation	SNP	T	TCGA-DD-A115-01A-11D-A12Z-10	3081293	49753721	121361346	37	11778										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48311639	48311639	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tctgccactgatgctcagaaActcttggaatttggcaacga	9	10	3	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr7:48311639A>G	ENST00000435803.1	+	17	2400	c.2376A>G	c.(2374-2376)aaA>aaG	p.K792K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	792					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATGCTCAGAAACTCTTGGAAT	0.383																																					p.K792K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A2376G						.						41	41	41					7																	48311639		1835	4093	5928	SO:0001819	synonymous_variant	154664	exon17			TCAGAAACTCTTG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.2376A>G	chr7.hg19:g.48311639A>G		159.0	0.0		81.0	11.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.383	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48311639	A	G	48311639	2	3	88	1	0	0	0	0	0	0	0	1	31	40	2	2		2	ABCA13	7	48311639	Silent	SNP	A	TCGA-DD-A115-01A-11D-A12Z-10		48311639	110827024	38	11779										
TAS2R39	259285	hgsc.bcm.edu	37	chr7	142881187	142881187	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ctcctctgatcatgttcatcCtgacagccaccctgctgatc	6	16	3	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr7:142881187C>A	ENST00000446620.1	+	1	676	c.676C>A	c.(676-678)Ctg>Atg	p.L226M		NM_176881.2	NP_795362.2	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	226					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	Melanoma(164;0.059)					CATGTTCATCCTGACAGCCAC	0.507																																					p.L226M		Atlas-SNP	.											.	TAS2R39	42	.	0			c.C676A						.						135	124	128					7																	142881187		1989	4154	6143	SO:0001583	missense	259285	exon1			TTCATCCTGACAG	AF494230	CCDS47729.1	7q34	2012-08-22			ENSG00000236398	ENSG00000236398		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18886	protein-coding gene	gene with protein product						12379855	Standard	NM_176881		Approved		uc011ksw.2	P59534	OTTHUMG00000152636	ENST00000446620.1:c.676C>A	chr7.hg19:g.142881187C>A	ENSP00000405095:p.Leu226Met	260.0	0.0		181.0	12.0	NM_176881	A4FUI7|Q3ZCN6|Q645W4	Missense_Mutation	SNP	ENST00000446620.1	hg19	CCDS47729.1	.	.	.	.	.	.	.	.	.	.	C	8.827	0.938867	0.18281	.	.	ENSG00000236398	ENST00000446620	T	0.39592	1.07	4.45	-0.668	0.11392	.	.	.	.	.	T	0.24470	0.0593	L	0.28504	0.86	0.09310	N	1	B	0.31256	0.316	B	0.30646	0.118	T	0.18999	-1.0319	9	0.24483	T	0.36	.	4.097	0.09995	0.1009:0.1888:0.4806:0.2297	.	226	P59534	T2R39_HUMAN	M	226	ENSP00000405095:L226M	ENSP00000405095:L226M	L	+	1	2	TAS2R39	142591309	0.000000	0.05858	0.025000	0.17156	0.934000	0.57294	-1.823000	0.01710	-0.248000	0.09583	-0.143000	0.13931	CTG	.	.		0.507	TAS2R39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327090.2	NM_176881		A	142881187	C	A	142881187	3	1	88	1	0	0	0	0	1	0	0	0	15591	680	24	3	678	3	TAS2R39	7	142881187	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	94569548	142881187	16257476	39	11780										
SLC10A5	347051	hgsc.bcm.edu	37	chr8	82606130	82606130	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tttacaaacaggaagaggcaGcgtacaaactttagcaaagg	10	7	0	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr8:82606130G>A	ENST00000518568.1	-	1	2279	c.1078C>T	c.(1078-1080)Ctg>Ttg	p.L360L		NM_001010893.2	NP_001010893.1	Q5PT55	NTCP5_HUMAN	solute carrier family 10, member 5	360						integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)	p.L360L(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)	15						GGAAGAGGCAGCGTACAAACT	0.408																																					p.L360L		Atlas-SNP	.											SLC10A5,NS,carcinoma,0,1	SLC10A5	35	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1078T						.						76	73	74					8																	82606130		2203	4300	6503	SO:0001819	synonymous_variant	347051	exon1			GAGGCAGCGTACA		CCDS34915.1	8q21.13	2013-07-18	2013-07-18		ENSG00000253598	ENSG00000253598		"Solute carriers"	22981	protein-coding gene	gene with protein product							Standard	NM_001010893		Approved		uc011lfs.2	Q5PT55	OTTHUMG00000164683	ENST00000518568.1:c.1078C>T	chr8.hg19:g.82606130G>A		130.0	0.0		47.0	13.0	NM_001010893	B2RN26	Silent	SNP	ENST00000518568.1	hg19	CCDS34915.1																																																																																			.	.		0.408	SLC10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379736.1	XM_294493		A	82606130	G	A	82606130	2	1	88	1	0	0	0	0	0	0	0	1	14392	962	34	3		3	SLC10A5	8	82606130	Silent	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10		82606130	63757892	40	11781										
YWHAZ	7534	hgsc.bcm.edu	37	chr8	101960838	101960838	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tctcaccagtacatcattgcAgatatctcttagctccgtct	5	13	4	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr8:101960838A>T	ENST00000395957.2	-	3	621	c.280T>A	c.(280-282)Tgc>Agc	p.C94S	YWHAZ_ENST00000353245.3_Missense_Mutation_p.C94S|YWHAZ_ENST00000395948.2_Missense_Mutation_p.C17S|YWHAZ_ENST00000395951.3_Missense_Mutation_p.C94S|YWHAZ_ENST00000395958.2_Missense_Mutation_p.C94S|YWHAZ_ENST00000522542.1_5'Flank|YWHAZ_ENST00000457309.1_Missense_Mutation_p.C94S|YWHAZ_ENST00000521309.1_Intron|YWHAZ_ENST00000419477.2_Missense_Mutation_p.C94S|YWHAZ_ENST00000395956.3_Missense_Mutation_p.C94S|YWHAZ_ENST00000395953.2_Missense_Mutation_p.C94S			P63104	1433Z_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta	94					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|gene expression (GO:0010467)|histamine secretion by mast cell (GO:0002553)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|platelet activation (GO:0030168)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting to mitochondrion (GO:0006626)|response to drug (GO:0042493)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mast cell granule (GO:0042629)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			large_intestine(1)|lung(2)	3	all_cancers(14;7.43e-06)|all_epithelial(15;2.77e-08)|Lung NSC(17;6.08e-05)|all_lung(17;0.000197)		Epithelial(11;2.79e-11)|all cancers(13;5.45e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.75e-05)			ACATCATTGCAGATATCTCTT	0.393																																					p.C94S		Atlas-SNP	.											.	YWHAZ	23	.	0			c.T280A						.						297	311	306					8																	101960838		2203	4300	6503	SO:0001583	missense	7534	exon2			CATTGCAGATATC	U28964	CCDS6290.1	8q22.3	2013-12-03	2013-12-03		ENSG00000164924	ENSG00000164924			12855	protein-coding gene	gene with protein product	"14-3-3 zeta", "14-3-3 delta"	601288	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, delta polypeptide", "tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide"	YWHAD		8617504, 7890696	Standard	NM_003406		Approved	KCIP-1, 14-3-3-zeta	uc010mbr.2	P63104	OTTHUMG00000134291	ENST00000395957.2:c.280T>A	chr8.hg19:g.101960838A>T	ENSP00000379287:p.Cys94Ser	286.0	0.0		158.0	12.0	NM_145690	A8K1N0|B7Z465|P29213|P29312|Q32P43|Q5XJ08|Q6GPI2|Q6IN74|Q6NUR9|Q6P3U9|Q86V33	Missense_Mutation	SNP	ENST00000395957.2	hg19	CCDS6290.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.881205	0.91740	.	.	ENSG00000164924	ENST00000395957;ENST00000457309;ENST00000395958;ENST00000395956;ENST00000353245;ENST00000517797;ENST00000395953;ENST00000395948;ENST00000395951;ENST00000419477;ENST00000521607;ENST00000521328;ENST00000418997	T;T;T;T;T;T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	5.68	5.68	0.88126	14-3-3 domain (4);	0.144262	0.49305	D	0.000147	D	0.83422	0.5251	M	0.91406	3.205	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.87247	0.2270	10	0.72032	D	0.01	.	15.9332	0.79683	1.0:0.0:0.0:0.0	.	94;94	D0PNI1;P63104	.;1433Z_HUMAN	S	94;94;94;94;94;17;94;17;94;94;94;94;94	ENSP00000379287:C94S;ENSP00000398599:C94S;ENSP00000379288:C94S;ENSP00000379286:C94S;ENSP00000309503:C94S;ENSP00000379283:C94S;ENSP00000379278:C17S;ENSP00000379281:C94S;ENSP00000395114:C94S;ENSP00000430058:C94S;ENSP00000429041:C94S;ENSP00000416551:C94S	ENSP00000309503:C94S	C	-	1	0	YWHAZ	102030014	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.287000	0.95975	2.172000	0.68678	0.533000	0.62120	TGC	.	.		0.393	YWHAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259017.2	NM_145690		T	101960838	A	T	101960838	3	4	88	1	0	0	0	0	1	0	0	0	17521	188	7	4	477	4	YWHAZ	8	101960838	Missense_Mutation	SNP	A	TCGA-DD-A115-01A-11D-A12Z-10	19354708	101960838	44403184	41	11782										
LINGO2	158038	hgsc.bcm.edu	37	chr9	27949442	27949442	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	cttcttttcacggattttggGttttttgcaggtaaagtaaa	9	5	2	0	rs199551773		TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr9:27949442G>T	ENST00000379992.2	-	6	1677	c.1228C>A	c.(1228-1230)Ccc>Acc	p.P410T	LINGO2_ENST00000308675.3_Missense_Mutation_p.P410T	NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	410	Ig-like C2-type.					integral component of membrane (GO:0016021)		p.P410T(2)		autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		CGGATTTTGGGTTTTTTGCAG	0.488																																					p.P410T		Atlas-SNP	.											LINGO2_ENST00000379992,NS,carcinoma,0,2	LINGO2	244	.	2	Substitution - Missense(2)	prostate(2)	c.C1228A						.						97	93	94					9																	27949442		2203	4300	6503	SO:0001583	missense	158038	exon7			TTTTGGGTTTTTT	AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482		"Immunoglobulin superfamily / I-set domain containing"	21207	protein-coding gene	gene with protein product		609793	"leucine rich repeat neuronal 6C"	LRRN6C		14686891	Standard	NM_152570		Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.1228C>A	chr9.hg19:g.27949442G>T	ENSP00000369328:p.Pro410Thr	192.0	0.0		108.0	16.0	NM_001258282	A8K4K7|B2RPM5|Q6ZMD0	Missense_Mutation	SNP	ENST00000379992.2	hg19	CCDS6524.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400240	0.62177	.	.	ENSG00000174482	ENST00000379992;ENST00000308675	D;D	0.99789	-6.75;-6.75	6.16	6.16	0.99307	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.93550	3.43	0.80722	D	1	D	0.69078	0.997	D	0.69479	0.964	D	0.97341	0.9957	9	.	.	.	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	410	Q7L985	LIGO2_HUMAN	T	410	ENSP00000369328:P410T;ENSP00000310126:P410T	.	P	-	1	0	LINGO2	27939442	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.837000	0.99465	2.937000	0.99478	0.650000	0.86243	CCC	.	G|0.999;A|0.001		0.488	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051978.2	NM_152570		T	27949442	G	T	27949442	3	4	88	1	0	0	0	0	1	0	0	0	8824	1261	44	3	596	3	LINGO2	9	27949442	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10		27949442	113263989	42	11783										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27352965	27352965	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ttcttttccgtctgcagcccCagctaaaggatcaacatact	6	13	3	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr10:27352965C>A	ENST00000376087.4	-	12	1480	c.1315G>T	c.(1315-1317)Ggg>Tgg	p.G439W	ANKRD26_ENST00000436985.2_Missense_Mutation_p.G488W	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	439					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TCTGCAGCCCCAGCTAAAGGA	0.308																																					p.G439W		Atlas-SNP	.											.	ANKRD26	179	.	0			c.G1315T						.						92	82	85					10																	27352965		1791	4063	5854	SO:0001583	missense	22852	exon12			CAGCCCCAGCTAA	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.1315G>T	chr10.hg19:g.27352965C>A	ENSP00000365255:p.Gly439Trp	211.0	0.0		122.0	45.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	hg19	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	C	12.74	2.028967	0.35797	.	.	ENSG00000107890	ENST00000376087;ENST00000436985	T;T	0.35973	1.37;1.28	4.16	3.23	0.37069	.	.	.	.	.	T	0.56156	0.1966	M	0.71036	2.16	0.27959	N	0.936847	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.74674	0.984;0.964;0.976	T	0.48210	-0.9055	9	0.66056	D	0.02	.	10.4564	0.44553	0.0:0.8008:0.1992:0.0	.	439;439;488	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	W	439;488	ENSP00000365255:G439W;ENSP00000405112:G488W	ENSP00000365255:G439W	G	-	1	0	ANKRD26	27392971	0.526000	0.26298	0.034000	0.17996	0.001000	0.01503	1.865000	0.39479	1.022000	0.39626	-0.305000	0.09177	GGG	.	.		0.308	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			A	27352965	C	A	27352965	3	1	88	1	0	0	0	0	1	0	0	0	654	594	21	3	3909	3	ANKRD26	10	27352965	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10		27352965	108181782	43	11784										
STOX1	219736	hgsc.bcm.edu	37	chr10	70652470	70652470	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	atctaattccttactaccgcTaactccagtcataaacgttt	3	12	2	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr10:70652470T>C	ENST00000298596.6	+	4	3031	c.2948T>C	c.(2947-2949)cTa>cCa	p.L983P	STOX1_ENST00000399165.4_3'UTR|STOX1_ENST00000421961.2_Missense_Mutation_p.L873P|STOX1_ENST00000399169.4_Missense_Mutation_p.L983P|STOX1_ENST00000399162.2_3'UTR	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	983						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						TTACTACCGCTAACTCCAGTC	0.333																																					p.L983P		Atlas-SNP	.											.	STOX1	75	.	0			c.T2948C						.						111	115	113					10																	70652470		1984	4191	6175	SO:0001583	missense	219736	exon4			TACCGCTAACTCC	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"chromosome 10 open reading frame 24"	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.2948T>C	chr10.hg19:g.70652470T>C	ENSP00000298596:p.Leu983Pro	303.0	0.0		180.0	77.0	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	hg19	CCDS41535.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.712971	0.48517	.	.	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000421961	D;D;T	0.84146	-1.81;-1.81;-1.48	5.83	5.83	0.93111	.	0.171834	0.38837	N	0.001547	D	0.91683	0.7371	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.92517	0.6021	10	0.87932	D	0	.	15.8862	0.79251	0.0:0.0:0.0:1.0	.	983	Q6ZVD7	STOX1_HUMAN	P	983;983;873	ENSP00000382121:L983P;ENSP00000298596:L983P;ENSP00000394509:L873P	ENSP00000298596:L983P	L	+	2	0	STOX1	70322476	1.000000	0.71417	0.998000	0.56505	0.013000	0.08279	5.045000	0.64220	2.236000	0.73375	0.533000	0.62120	CTA	.	.		0.333	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		C	70652470	T	C	70652470	3	2	88	1	0	0	0	0	1	0	0	0	15334	1522	53	2	2962	2	STOX1	10	70652470	Missense_Mutation	SNP	T	TCGA-DD-A115-01A-11D-A12Z-10	43299505	70652470	64882277	44	11785										
C10orf93	54777	hgsc.bcm.edu	37	chr10	134751175	134751175	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ttgcagataacactccagaaGttccctggataatagaaaca	7	9	0	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr10:134751175G>T	ENST00000368586.5	-	6	641	c.541C>A	c.(541-543)Ctt>Att	p.L181I	TTC40_ENST00000368585.3_Missense_Mutation_p.L181I|TTC40_ENST00000368582.2_Missense_Mutation_p.L181I	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CACTCCAGAAGTTCCCTGGAT	0.448																																					p.L181I		Atlas-SNP	.											.	TTC40	100	.	0			c.C541A						.						95	102	100					10																	134751175		2203	4300	6503	SO:0001583	missense	54777	exon6			CCAGAAGTTCCCT																												ENST00000368586.5:c.541C>A	chr10.hg19:g.134751175G>T	ENSP00000357575:p.Leu181Ile	98.0	0.0		44.0	30.0	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	hg19	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.510690	0.64522	.	.	ENSG00000171811	ENST00000368586;ENST00000368582;ENST00000368585	D;D;D	0.82619	-1.63;-1.63;-1.63	4.74	4.74	0.60224	.	0.204737	0.30556	N	0.009374	D	0.90215	0.6941	M	0.80183	2.485	0.29567	N	0.850207	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.991	D	0.86489	0.1796	10	0.87932	D	0	.	11.2452	0.48993	0.091:0.0:0.909:0.0	.	181;181	Q5SR76-2;Q5SR76-1	.;.	I	181	ENSP00000357575:L181I;ENSP00000357571:L181I;ENSP00000357574:L181I	ENSP00000357571:L181I	L	-	1	0	C10orf93	134601165	1.000000	0.71417	0.991000	0.47740	0.753000	0.42808	2.650000	0.46665	2.336000	0.79503	0.650000	0.86243	CTT	.	.		0.448	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3			T	134751175	G	T	134751175	3	4	88	1	0	0	0	0	1	0	0	0	1627	1029	36	3	692	3	C10orf93	10	134751175	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	64098705	134751175	783572	45	11786										
OR51E2	81285	hgsc.bcm.edu	37	chr11	4703712	4703712	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	aaagggcaaggatcttaggcAtggtggatgtggataaggcc	16	5	1	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr11:4703712A>T	ENST00000396950.3	-	2	469	c.230T>A	c.(229-231)aTg>aAg	p.M77K		NM_030774.3	NP_110401.1	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E, member 2	77					cellular response to fatty acid (GO:0071398)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|positive regulation of blood pressure (GO:0045777)|positive regulation of renin secretion into blood stream (GO:1900135)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|signaling receptor activity (GO:0038023)|steroid hormone receptor activity (GO:0003707)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(3)	23		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)		GATCTTAGGCATGGTGGATGT	0.502																																					p.M77K		Atlas-SNP	.											.	OR51E2	77	.	0			c.T230A						.						101	85	90					11																	4703712		2201	4298	6499	SO:0001583	missense	81285	exon2			TTAGGCATGGTGG	AY033942	CCDS7751.1	11p15	2012-08-09			ENSG00000167332	ENSG00000167332		"GPCR / Class A : Olfactory receptors"	15195	protein-coding gene	gene with protein product		611268				11118034	Standard	NM_030774		Approved	PSGR	uc001lzk.2	Q9H255	OTTHUMG00000133362	ENST00000396950.3:c.230T>A	chr11.hg19:g.4703712A>T	ENSP00000380153:p.Met77Lys	94.0	0.0		34.0	15.0	NM_030774	B2RA63|Q6IF94	Missense_Mutation	SNP	ENST00000396950.3	hg19	CCDS7751.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.945756	0.73672	.	.	ENSG00000167332	ENST00000396950;ENST00000532598	T;T	0.03035	4.07;4.07	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000027	T	0.15869	0.0382	M	0.82193	2.58	0.42787	D	0.993881	D	0.55172	0.97	P	0.57324	0.818	T	0.00411	-1.1756	10	0.87932	D	0	.	13.681	0.62484	1.0:0.0:0.0:0.0	.	77	Q9H255	O51E2_HUMAN	K	77	ENSP00000380153:M77K;ENSP00000432644:M77K	ENSP00000380153:M77K	M	-	2	0	OR51E2	4660288	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.718000	0.68455	2.112000	0.64535	0.533000	0.62120	ATG	.	.		0.502	OR51E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257198.1	NM_030774		T	4703712	A	T	4703712	3	4	88	1	0	0	0	0	1	0	0	0	11104	217	8	4	736	4	OR51E2	11	4703712	Missense_Mutation	SNP	A	TCGA-DD-A115-01A-11D-A12Z-10		4703712	130302804	46	11787										
OR51A4	401666	hgsc.bcm.edu	37	chr11	4968139	4968139	+	Frame_Shift_Del	DEL	A	A	-													0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gacatagccaacatggaaagAaaatagtacatgggctcatg							TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr11:4968139delA	ENST00000380373.2	-	1	217	c.192delT	c.(190-192)tttfs	p.F64fs	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACATGGAAAGAAAATAGTACA	0.418																																					p.L65fs		Atlas-Indel,Pindel	.											OR51A4,NS,carcinoma,0,1	OR51A4	73	.	0			c.193delC						.						163	147	153					11																	4968139		2198	4298	6496	SO:0001589	frameshift_variant	401666	exon1			.	AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497		"GPCR / Class A : Olfactory receptors"	14795	protein-coding gene	gene with protein product							Standard	NM_001005329		Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.192delT	chr11.hg19:g.4968139delA	ENSP00000369731:p.Phe64fs	1224.0	0.0		591.0	135.0	NM_001005329		Frame_Shift_Del	DEL	ENST00000380373.2	hg19	CCDS31367.1																																																																																			.	.		0.418	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329		-	4968139	A	-	4968139	7	5	88	1	0	1	0	1	0	0	0	0	11096	243	9	0	751	0	OR51A4	11	4968139	Frame_Shift_Del	DEL	A	TCGA-DD-A115-01A-11D-A12Z-10	264427	4968139	130038377	47	11788										
DPP3	10072	hgsc.bcm.edu	37	chr11	66249912	66249912	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	agctgcgccaacatgccctgGctgaaggccttaccgaggag	13	13	0	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr11:66249912G>T	ENST00000360510.2	+	2	306	c.241G>T	c.(241-243)Gct>Tct	p.A81S	CTD-3074O7.5_ENST00000527092.1_RNA|DPP3_ENST00000453114.1_Missense_Mutation_p.A81S|CTD-3074O7.5_ENST00000525142.1_RNA|DPP3_ENST00000530165.1_Missense_Mutation_p.A81S|CTD-3074O7.5_ENST00000533502.1_RNA|DPP3_ENST00000541961.1_Missense_Mutation_p.A81S|DPP3_ENST00000531863.1_Missense_Mutation_p.A101S|DPP3_ENST00000532677.1_Missense_Mutation_p.A100S|CTD-3074O7.5_ENST00000527274.2_RNA			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	81					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						ACATGCCCTGGCTGAAGGCCT	0.592																																					p.A81S		Atlas-SNP	.											.	DPP3	61	.	0			c.G241T						.						41	43	42					11																	66249912		2200	4295	6495	SO:0001583	missense	10072	exon2			GCCCTGGCTGAAG	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"dipeptidylpeptidase III", "dipeptidylpeptidase 3"			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.241G>T	chr11.hg19:g.66249912G>T	ENSP00000353701:p.Ala81Ser	36.0	0.0		44.0	9.0	NM_001256670	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Missense_Mutation	SNP	ENST00000360510.2	hg19	CCDS8141.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.494377	0.26774	.	.	ENSG00000254986	ENST00000531863;ENST00000532677;ENST00000360510;ENST00000453114;ENST00000541961;ENST00000526515;ENST00000530165;ENST00000347422;ENST00000531314;ENST00000531354	T;T;T;T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	5.71	3.59	0.41128	.	0.553031	0.19477	N	0.113320	T	0.22399	0.0540	N	0.17278	0.47	0.29919	N	0.82289	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.03384	-1.1042	10	0.38643	T	0.18	.	4.3711	0.11247	0.1748:0.2096:0.6156:0.0	.	100;81	G3V1D3;Q9NY33	.;DPP3_HUMAN	S	101;100;81;81;81;81;81;81;81;81	ENSP00000432782:A101S;ENSP00000435284:A100S;ENSP00000353701:A81S;ENSP00000389943:A81S;ENSP00000440502:A81S;ENSP00000431606:A81S;ENSP00000436941:A81S;ENSP00000436820:A81S;ENSP00000432618:A81S	ENSP00000309957:A81S	A	+	1	0	DPP3	66006488	0.999000	0.42202	1.000000	0.80357	0.978000	0.69477	1.588000	0.36633	2.691000	0.91804	0.563000	0.77884	GCT	.	.		0.592	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2			T	66249912	G	T	66249912	3	4	88	1	0	0	0	0	1	0	0	0	4730	1203	42	3	243	3	DPP3	11	66249912	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	61281773	66249912	68756604	48	11789										
GPR152	390212	hgsc.bcm.edu	37	chr11	67219120	67219121	+	Frame_Shift_Ins	INS	-	-	G													0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ctggagtgtggggttcacctINSgaggctgggccacaggatcc							TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr11:67219120_67219121insG	ENST00000312457.2	-	1	1079_1080	c.1075_1076insC	c.(1075-1077)cagfs	p.Q359fs	CABP4_ENST00000438189.2_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	359						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			GGGGTTCACCTGAGGCTGGGCC	0.634																																					p.Q359fs	Pancreas(102;800 1581 2723 7382 33622)	Atlas-INDEL	.											.	GPR152	41	.	0			c.1076_1077insC						.																																			SO:0001589	frameshift_variant	390212	exon1			.	AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"GPCR / Class A : Orphans"	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.1076dupC	chr11.hg19:g.67219121_67219121dupG	ENSP00000310255:p.Gln359fs	205.0	0.0		181.0	12.0	NM_206997	Q0VD88|Q86SM0	Frame_Shift_Ins	INS	ENST00000312457.2	hg19	CCDS8165.1																																																																																			.	.		0.634	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1			G	67219121	-	G	67219120	7	5	88	1	0	1	1	0	0	0	0	0	6666	1580	55	0	340	0	GPR152	11	67219120	Frame_Shift_Ins	INS	-	TCGA-DD-A115-01A-11D-A12Z-10	969208	67219120	67787396	49	11790										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76858899	76858899	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	caagcctatgcaccccacgtCggtccacggcgtggaggaca	12	15	0	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr11:76858899C>G	ENST00000409709.3	+	4	460	c.188C>G	c.(187-189)tCg>tGg	p.S63W	MYO7A_ENST00000409619.2_Missense_Mutation_p.S52W|MYO7A_ENST00000458637.2_Missense_Mutation_p.S63W|MYO7A_ENST00000409893.1_Missense_Mutation_p.S63W	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	63					actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CACCCCACGTCGGTCCACGGC	0.637																																					p.S63W		Atlas-SNP	.											.	MYO7A	164	.	0			c.C188G						.						32	37	35					11																	76858899		2102	4217	6319	SO:0001583	missense	4647	exon4			CCACGTCGGTCCA	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.188C>G	chr11.hg19:g.76858899C>G	ENSP00000386331:p.Ser63Trp	69.0	0.0		54.0	24.0	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	C	33	5.195496	0.94960	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67	4.86	4.86	0.63082	Myosin head, motor domain (1);	0.000000	0.64402	D	0.000001	D	0.86855	0.6033	M	0.88377	2.95	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.89341	0.3654	10	0.72032	D	0.01	.	18.1904	0.89805	0.0:1.0:0.0:0.0	.	63;63;63	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	W	63;63;63;52;62;62;62;62	ENSP00000386331:S63W;ENSP00000386689:S63W;ENSP00000392185:S63W;ENSP00000386635:S52W	ENSP00000345075:S62W	S	+	2	0	MYO7A	76536547	1.000000	0.71417	0.969000	0.41365	0.986000	0.74619	4.730000	0.62015	2.523000	0.85059	0.455000	0.32223	TCG	.	.		0.637	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		G	76858899	C	G	76858899	3	3	88	1	0	0	0	0	1	0	0	0	10091	893	31	4	198	4	MYO7A	11	76858899	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	9639779	76858899	58147617	50	11791										
ATM	472	hgsc.bcm.edu	37	chr11	108172499	108172499	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tggcctatctacagccttttAgaacatcaagaaaaaaggtc	7	9	2	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr11:108172499A>G	ENST00000452508.2	+	36	5491	c.5302A>G	c.(5302-5304)Aga>Gga	p.R1768G	ATM_ENST00000278616.4_Missense_Mutation_p.R1768G			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1768					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	ACAGCCTTTTAGAACATCAAG	0.353			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.R1768G		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.A5302G						.						85	88	87					11																	108172499		2201	4298	6499	SO:0001583	missense	472	exon35	Familial Cancer Database	AT, Louis-Bar syndrome	CCTTTTAGAACAT	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5302A>G	chr11.hg19:g.108172499A>G	ENSP00000388058:p.Arg1768Gly	180.0	0.0		113.0	15.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.196148	0.58126	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	D;D	0.83506	-1.73;-1.73	4.8	2.41	0.29592	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88043	0.6331	M	0.73598	2.24	0.40800	D	0.983336	D	0.69078	0.997	P	0.61003	0.882	D	0.87215	0.2250	10	0.52906	T	0.07	.	12.038	0.53435	0.6669:0.3331:0.0:0.0	.	1768	Q13315	ATM_HUMAN	G	1768	ENSP00000278616:R1768G;ENSP00000388058:R1768G	ENSP00000278616:R1768G	R	+	1	2	ATM	107677709	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.034000	0.49751	0.274000	0.22072	0.377000	0.23210	AGA	.	.		0.353	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108172499	A	G	108172499	3	3	88	1	0	0	0	0	1	0	0	0	1109	412	15	2	5436	2	ATM	11	108172499	Missense_Mutation	SNP	A	TCGA-DD-A115-01A-11D-A12Z-10	31313600	108172499	26834017	51	11792										
SLC2A3	6515	hgsc.bcm.edu	37	chr12	8086448	8086448	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ccagtgttgtagccaaattgGaaagagccgattgtagcaac	11	8	0	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr12:8086448G>T	ENST00000075120.7	-	2	306	c.66C>A	c.(64-66)ttC>ttA	p.F22L		NM_006931.2	NP_008862.1	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 3	22					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(14)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				Kidney(36;0.0866)		AGCCAAATTGGAAAGAGCCGA	0.443											OREG0021656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F22L	Colon(96;424 1461 14416 20933 23688)	Atlas-SNP	.											.	SLC2A3	83	.	0			c.C66A						.						97	94	95					12																	8086448		2203	4300	6503	SO:0001583	missense	6515	exon2			AAATTGGAAAGAG	M20681	CCDS8586.1	12p13.3	2013-05-22			ENSG00000059804	ENSG00000059804		"Solute carriers"	11007	protein-coding gene	gene with protein product		138170		GLUT3			Standard	NM_006931		Approved		uc001qtr.3	P11169	OTTHUMG00000133685	ENST00000075120.7:c.66C>A	chr12.hg19:g.8086448G>T	ENSP00000075120:p.Phe22Leu	211.0	0.0	646	143.0	47.0	NM_006931	B2R606|D3DUU6|Q6I9U2|Q9UG15	Missense_Mutation	SNP	ENST00000075120.7	hg19	CCDS8586.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870476	0.72065	.	.	ENSG00000059804	ENST00000075120	D	0.82167	-1.58	4.23	3.33	0.38152	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.062472	0.64402	D	0.000003	T	0.60689	0.2288	N	0.05534	-0.03	0.45216	D	0.998223	B	0.10296	0.003	B	0.20184	0.028	T	0.53989	-0.8360	10	0.12430	T	0.62	.	5.4377	0.16490	0.1094:0.2076:0.6829:0.0	.	22	P11169	GTR3_HUMAN	L	22	ENSP00000075120:F22L	ENSP00000075120:F22L	F	-	3	2	SLC2A3	7977715	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	1.215000	0.32431	2.370000	0.80446	0.543000	0.68304	TTC	.	.		0.443	SLC2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257914.1	NM_006931		T	8086448	G	T	8086448	3	4	88	1	0	0	0	0	1	0	0	0	14560	1165	41	3	1460	3	SLC2A3	12	8086448	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10		8086448	125765447	52	11793										
CNPY2	10330	hgsc.bcm.edu	37	chr12	56708752	56708752	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tccaccagagccctgcatgcTggtggaagaggagagaatga	14	9	0	4			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr12:56708752T>C	ENST00000273308.4	-	3	629		c.e3-2		RP11-977G19.11_ENST00000549860.1_RNA|RP11-977G19.10_ENST00000549318.1_Splice_Site|CNPY2_ENST00000551720.1_Splice_Site|RP11-977G19.11_ENST00000549565.1_RNA|PAN2_ENST00000549090.1_5'Flank	NM_014255.5	NP_055070.1	Q9Y2B0	CNPY2_HUMAN	canopy FGF signaling regulator 2						negative regulation of gene expression (GO:0010629)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of low-density lipoprotein particle clearance (GO:0010988)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)				large_intestine(2)|lung(2)	4						CCCTGCATGCTGGTGGAAGAG	0.537																																					.		Atlas-SNP	.											.	CNPY2	16	.	0			c.89-2A>G						.						71	66	68					12																	56708752		2203	4300	6503	SO:0001630	splice_region_variant	10330	exon4			GCATGCTGGTGGA	AB015631	CCDS8914.1	12q15	2013-07-23	2013-07-23	2007-10-22		ENSG00000257727			13529	protein-coding gene	gene with protein product		605861	"transmembrane protein 4", "canopy 2 homolog (zebrafish)"	TMEM4		10072769, 15905959	Standard	NM_001190991		Approved	HP10390, ZSIG9, Cnpy2	uc001sku.2	Q9Y2B0	OTTHUMG00000170330	ENST00000273308.4:c.89-2A>G	chr12.hg19:g.56708752T>C		129.0	0.0		82.0	32.0	NM_014255	B2R7B9|Q9UHE9	Splice_Site	SNP	ENST00000273308.4	hg19	CCDS8914.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937588	0.52972	.	.	ENSG00000144785;ENSG00000144785;ENSG00000144785;ENSG00000257727;ENSG00000257727	ENST00000549318;ENST00000547423;ENST00000548360;ENST00000273308;ENST00000551475	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9233	0.70856	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RP11-977G19.10;CNPY2	54995019	1.000000	0.71417	0.999000	0.59377	0.575000	0.36095	7.848000	0.86902	2.231000	0.72958	0.533000	0.62120	.	.	.		0.537	CNPY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408546.1	NM_014255	Intron	C	56708752	T	C	56708752	5	2	88	1	0	0	0	0	0	0	1	0	3630	1594	55	2	477	2	CNPY2	12	56708752	Splice_Site	SNP	T	TCGA-DD-A115-01A-11D-A12Z-10	48622304	56708752	77143143	53	11794										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70960239	70960239	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tcggccttcagtctgggcttCcttgctaaagaggcctccac	10	14	2	1	rs374292920		TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr12:70960239C>G	ENST00000261266.5	-	13	3255	c.3226G>C	c.(3226-3228)Gaa>Caa	p.E1076Q	PTPRB_ENST00000550358.1_Missense_Mutation_p.E1206Q|PTPRB_ENST00000451516.2_Missense_Mutation_p.E986Q|PTPRB_ENST00000551525.1_Missense_Mutation_p.E1293Q|PTPRB_ENST00000334414.6_Missense_Mutation_p.E1294Q|PTPRB_ENST00000550857.1_Missense_Mutation_p.E986Q|PTPRB_ENST00000538708.1_Intron	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1076	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			GTCTGGGCTTCCTTGCTAAAG	0.453																																					p.E1294Q		Atlas-SNP	.											.	PTPRB	676	.	0			c.G3880C						.						162	152	155					12																	70960239		2012	4159	6171	SO:0001583	missense	5787	exon15			GGGCTTCCTTGCT	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.3226G>C	chr12.hg19:g.70960239C>G	ENSP00000261266:p.Glu1076Gln	543.0	0.0		349.0	142.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	C	8.361	0.833091	0.16820	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T	0.04406	3.63;3.63;3.63;3.63;3.63;3.63;3.63	5.37	3.05	0.35203	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.649807	0.15086	N	0.281376	T	0.03011	0.0089	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B	0.19445	0.016;0.036;0.027;0.021;0.011;0.033	B;B;B;B;B;B	0.25405	0.02;0.06;0.015;0.034;0.021;0.059	T	0.45906	-0.9229	10	0.17369	T	0.5	.	7.7889	0.29108	0.0:0.5497:0.3184:0.1319	.	986;1173;1293;1294;1076;1206	P23467-2;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;PTPRB_HUMAN;.	Q	1294;986;1206;986;1076;1293;1173	ENSP00000334928:E1294Q;ENSP00000393028:E986Q;ENSP00000448058:E1206Q;ENSP00000447302:E986Q;ENSP00000261266:E1076Q;ENSP00000448349:E1293Q;ENSP00000446982:E1173Q	ENSP00000261266:E1076Q	E	-	1	0	PTPRB	69246506	0.219000	0.23619	0.990000	0.47175	0.708000	0.40852	1.169000	0.31871	2.515000	0.84797	0.655000	0.94253	GAA	.	.		0.453	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			G	70960239	C	G	70960239	3	3	88	1	0	0	0	0	1	0	0	0	12811	864	30	4	2847	4	PTPRB	12	70960239	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	14251487	70960239	62891656	54	11795										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120602144	120602144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gcccagatgccctcaccttgTgagaactgaggacagtcttc	10	13	2	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr12:120602144T>C	ENST00000300648.6	-	18	1856	c.1844A>G	c.(1843-1845)cAc>cGc	p.H615R		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	615					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCTCACCTTGTGAGAACTGAG	0.582																																					p.H615R		Atlas-SNP	.											.	GCN1L1	207	.	0			c.A1844G						.						101	105	104					12																	120602144		1968	4141	6109	SO:0001583	missense	10985	exon18			ACCTTGTGAGAAC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.1844A>G	chr12.hg19:g.120602144T>C	ENSP00000300648:p.His615Arg	96.0	0.0		85.0	32.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.017799	0.35606	.	.	ENSG00000089154	ENST00000300648	T	0.04551	3.6	5.83	5.83	0.93111	Armadillo-like helical (1);Domain of unknown function DUF3554 (1);Armadillo-type fold (1);	0.048650	0.85682	D	0.000000	T	0.08582	0.0213	M	0.69823	2.125	0.80722	D	1	B	0.30973	0.302	B	0.30855	0.121	T	0.21827	-1.0234	10	0.14656	T	0.56	.	16.2009	0.82078	0.0:0.0:0.0:1.0	.	615	Q92616	GCN1L_HUMAN	R	615	ENSP00000300648:H615R	ENSP00000300648:H615R	H	-	2	0	GCN1L1	119086527	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.403000	0.79983	2.235000	0.73313	0.533000	0.62120	CAC	.	.		0.582	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			C	120602144	T	C	120602144	3	2	88	1	0	0	0	0	1	0	0	0	6307	1696	59	2	6335	2	GCN1L1	12	120602144	Missense_Mutation	SNP	T	TCGA-DD-A115-01A-11D-A12Z-10	49641905	120602144	13249751	55	11796										
RNF10	9921	hgsc.bcm.edu	37	chr12	121013648	121013648	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	acagcgacggggagagtgatAattcagaccgtgttcctgtg	14	8	1	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr12:121013648A>T	ENST00000325954.4	+	16	2715	c.2254A>T	c.(2254-2256)Aat>Tat	p.N752Y	RNF10_ENST00000413266.2_Missense_Mutation_p.N757Y|RNF10_ENST00000542701.1_3'UTR	NM_014868.4	NP_055683.3	Q8N5U6	RNF10_HUMAN	ring finger protein 10	752					negative regulation of Schwann cell proliferation (GO:0010626)|positive regulation of myelination (GO:0031643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autoubiquitination (GO:0051865)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	27	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGAGAGTGATAATTCAGACCG	0.443																																					p.N752Y		Atlas-SNP	.											.	RNF10	75	.	0			c.A2254T						.						178	183	181					12																	121013648		2203	4300	6503	SO:0001583	missense	9921	exon16			AGTGATAATTCAG	AB027196	CCDS9201.1	12q23-q24	2013-01-09			ENSG00000022840	ENSG00000022840		"RING-type (C3HC4) zinc fingers"	10055	protein-coding gene	gene with protein product							Standard	NM_014868		Approved	KIAA0262, RIE2	uc001typ.4	Q8N5U6	OTTHUMG00000168999	ENST00000325954.4:c.2254A>T	chr12.hg19:g.121013648A>T	ENSP00000322242:p.Asn752Tyr	187.0	0.0		115.0	13.0	NM_014868	Q92550|Q9NPP8|Q9ULW4	Missense_Mutation	SNP	ENST00000325954.4	hg19	CCDS9201.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.027270	0.35797	.	.	ENSG00000022840	ENST00000325954;ENST00000458409;ENST00000413266;ENST00000538254	D;D	0.89681	-2.55;-2.54	5.39	5.39	0.77823	.	0.338826	0.36200	N	0.002732	D	0.89663	0.6780	L	0.40543	1.245	0.40164	D	0.977097	D;D	0.61080	0.989;0.976	P;P	0.59546	0.859;0.556	D	0.90106	0.4188	10	0.54805	T	0.06	.	10.6496	0.45640	0.8572:0.0:0.0:0.1428	.	757;752	Q8N5U6-2;Q8N5U6	.;RNF10_HUMAN	Y	752;752;757;87	ENSP00000322242:N752Y;ENSP00000415682:N757Y	ENSP00000322242:N752Y	N	+	1	0	RNF10	119498031	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.487000	0.60293	2.054000	0.61138	0.533000	0.62120	AAT	.	.		0.443	RNF10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401898.4			T	121013648	A	T	121013648	3	4	88	1	0	0	0	0	1	0	0	0	13437	362	13	4	2316	4	RNF10	12	121013648	Missense_Mutation	SNP	A	TCGA-DD-A115-01A-11D-A12Z-10	411504	121013648	12838247	56	11797										
MLXIP	22877	hgsc.bcm.edu	37	chr12	122623457	122623457	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tgacgaatacgtgaaaacccGgaccttgcagaattggaagt	11	8	0	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr12:122623457G>A	ENST00000319080.7	+	15	2612	c.2480G>A	c.(2479-2481)cGg>cAg	p.R827Q	MLXIP_ENST00000538698.1_Missense_Mutation_p.R434Q					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		GTGAAAACCCGGACCTTGCAG	0.532																																					p.R827Q	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.G2480A						.						78	80	80					12																	122623457		1885	4099	5984	SO:0001583	missense	22877	exon15			AAACCCGGACCTT	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"Basic helix-loop-helix proteins"	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.2480G>A	chr12.hg19:g.122623457G>A	ENSP00000312834:p.Arg827Gln	389.0	0.0		210.0	12.0	NM_014938		Missense_Mutation	SNP	ENST00000319080.7	hg19		.	.	.	.	.	.	.	.	.	.	G	25.7	4.664907	0.88251	.	.	ENSG00000175727	ENST00000319080;ENST00000538698;ENST00000366272	T;T;T	0.53206	2.27;1.52;0.63	5.45	5.45	0.79879	.	0.241216	0.42420	D	0.000710	T	0.35770	0.0943	.	.	.	0.80722	D	1	D	0.53312	0.959	B	0.35607	0.206	T	0.26643	-1.0097	9	0.39692	T	0.17	-28.5222	14.5441	0.68015	0.0721:0.0:0.9279:0.0	.	827	Q9HAP2	MLXIP_HUMAN	Q	827;434;298	ENSP00000312834:R827Q;ENSP00000440769:R434Q;ENSP00000445891:R298Q	ENSP00000312834:R827Q	R	+	2	0	MLXIP	121189410	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	4.772000	0.62324	2.549000	0.85964	0.655000	0.94253	CGG	.	.		0.532	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938		A	122623457	G	A	122623457	3	1	88	1	0	0	0	0	1	0	0	0	9645	1116	39	1	2538	1	MLXIP	12	122623457	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	1609809	122623457	11228438	57	11798										
DHRS4L1	728635	hgsc.bcm.edu	37	chr14	24517998	24517998	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ctgcctagcacctggacttaTcaagactagcttcagcagga	9	12	2	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr14:24517998T>C	ENST00000558293.1	+	0	646					NR_102693.1																						CCTGGACTTATCAAGACTAGC	0.522																																					p.I218T		Atlas-SNP	.											.	.	.	.	0			c.T653C						.						141	137	139					14																	24517998		2203	4298	6501			728635	exon8			GACTTATCAAGAC																													chr14.hg19:g.24517998T>C		818.0	2.0		502.0	180.0	NM_001082488		Missense_Mutation	SNP	ENST00000558293.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.56	1.384474	0.25031	.	.	ENSG00000225766	ENST00000397065	.	.	.	4.67	4.67	0.58626	NAD(P)-binding domain (1);	.	.	.	.	T	0.70360	0.3215	L	0.60455	1.87	0.50813	D	0.999890	D	0.89917	1.0	D	0.97110	1.0	T	0.76694	-0.2865	7	0.46703	T	0.11	.	12.0988	0.53772	0.0:0.0:0.0:1.0	.	218	P0CG22	DR4L1_HUMAN	T	218	.	ENSP00000380255:I218T	I	+	2	0	AL136295.1	23587838	1.000000	0.71417	1.000000	0.80357	0.068000	0.16541	6.335000	0.72949	1.958000	0.56883	0.329000	0.21502	ATC	.	.		0.522	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1			C	24517998	T	C	24517998	1	2	88	0	1	0	0	0	0	0	0	0	4495	1435	50	2		2	DHRS4L1	14	24517998	RNA	SNP	T	TCGA-DD-A115-01A-11D-A12Z-10		24517998	82831542	58	11799										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102466376	102466376	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gctctcaccatatatgagggGaagtttggtaggctgaagga	14	6	1	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr14:102466376G>A	ENST00000360184.4	+	17	4019	c.3855G>A	c.(3853-3855)ggG>ggA	p.G1285G		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1285	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TATATGAGGGGAAGTTTGGTA	0.532																																					p.G1285G		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.G3855A						.						103	94	97					14																	102466376		2203	4300	6503	SO:0001819	synonymous_variant	1778	exon17			TGAGGGGAAGTTT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.3855G>A	chr14.hg19:g.102466376G>A		116.0	0.0		65.0	25.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	hg19	CCDS9966.1																																																																																			.	.		0.532	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		A	102466376	G	A	102466376	2	1	88	1	0	0	0	0	0	0	0	1	4843	1161	41	3		3	DYNC1H1	14	102466376	Silent	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	77948378	102466376	4883164	59	11800										
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40268641	40268641	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	aacaagttggacggctgctgCtacgcagtgaagcgcatccc	12	12	0	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr15:40268641C>T	ENST00000263791.5	+	12	1888	c.1845C>T	c.(1843-1845)tgC>tgT	p.C615C	EIF2AK4_ENST00000382727.2_Silent_p.C615C	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	615	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		ACGGCTGCTGCTACGCAGTGA	0.622																																					p.C615C		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.C1845T						.						32	34	34					15																	40268641		2090	4211	6301	SO:0001819	synonymous_variant	440275	exon12			CTGCTGCTACGCA	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.1845C>T	chr15.hg19:g.40268641C>T		87.0	0.0		62.0	34.0	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Silent	SNP	ENST00000263791.5	hg19	CCDS42016.1																																																																																			.	.		0.622	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			T	40268641	C	T	40268641	2	4	88	1	0	0	0	0	0	0	0	1	5001	805	28	3		3	EIF2AK4	15	40268641	Silent	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10		40268641	62262751	60	11801										
HERC1	8925	hgsc.bcm.edu	37	chr15	63991120	63991120	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	actcaaaggaataggaggagTtgcataaccagtctctgcta	10	8	2	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr15:63991120T>C	ENST00000443617.2	-	26	4799	c.4712A>G	c.(4711-4713)aAc>aGc	p.N1571S	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1571					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						ATAGGAGGAGTTGCATAACCA	0.413																																					p.N1571S		Atlas-SNP	.											.	HERC1	624	.	0			c.A4712G						.						145	139	141					15																	63991120		1857	4106	5963	SO:0001583	missense	8925	exon26			GAGGAGTTGCATA	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.4712A>G	chr15.hg19:g.63991120T>C	ENSP00000390158:p.Asn1571Ser	158.0	0.0		93.0	17.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	4.091	0.014801	0.07959	.	.	ENSG00000103657	ENST00000443617;ENST00000425434	T	0.21543	2.0	5.54	1.4	0.22301	.	0.368782	0.24154	N	0.041047	T	0.05456	0.0144	N	0.02539	-0.55	0.27402	N	0.954825	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39057	-0.9632	10	0.06625	T	0.88	.	4.6136	0.12415	0.0:0.314:0.3802:0.3058	.	555;1571	B4DKS2;Q15751	.;HERC1_HUMAN	S	1571;555	ENSP00000390158:N1571S	ENSP00000389613:N555S	N	-	2	0	HERC1	61778173	1.000000	0.71417	0.996000	0.52242	0.985000	0.73830	1.607000	0.36836	0.933000	0.37291	0.482000	0.46254	AAC	.	.		0.413	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		C	63991120	T	C	63991120	3	2	88	1	0	0	0	0	1	0	0	0	7066	1725	60	2	10085	2	HERC1	15	63991120	Missense_Mutation	SNP	T	TCGA-DD-A115-01A-11D-A12Z-10	23722479	63991120	38540272	61	11802										
SCAPER	49855	hgsc.bcm.edu	37	chr15	77134131	77134131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tacatagatttcatctactgCtcggcgaagattatcaaaaa	6	8	3	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr15:77134131C>T	ENST00000563290.1	-	5	432	c.337G>A	c.(337-339)Gca>Aca	p.A113T	SCAPER_ENST00000538941.2_5'UTR|SCAPER_ENST00000324767.7_Missense_Mutation_p.A113T			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	113						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						TCATCTACTGCTCGGCGAAGA	0.393																																					p.A113T		Atlas-SNP	.											.	SCAPER	160	.	0			c.G337A						.						132	118	123					15																	77134131		1837	4078	5915	SO:0001583	missense	49855	exon4			CTACTGCTCGGCG	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.337G>A	chr15.hg19:g.77134131C>T	ENSP00000454973:p.Ala113Thr	271.0	0.0		151.0	87.0	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	hg19	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	C	36	5.657937	0.96734	.	.	ENSG00000140386	ENST00000324767;ENST00000303521	T	0.54866	0.55	5.14	5.14	0.70334	.	0.115428	0.64402	D	0.000016	T	0.68952	0.3057	L	0.49640	1.575	0.58432	D	0.999999	D;P	0.89917	1.0;0.935	D;P	0.91635	0.999;0.847	T	0.71337	-0.4623	10	0.66056	D	0.02	.	18.6068	0.91270	0.0:1.0:0.0:0.0	.	113;128	Q6NSF1;Q9BY12-2	.;.	T	113;129	ENSP00000326924:A113T	ENSP00000303560:A129T	A	-	1	0	SCAPER	74921186	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.487000	0.81328	2.412000	0.81896	0.655000	0.94253	GCA	.	.		0.393	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		T	77134131	C	T	77134131	3	4	88	1	0	0	0	0	1	0	0	0	13893	797	28	3	4015	3	SCAPER	15	77134131	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	13143011	77134131	25397261	62	11803										
ABCC6	368	hgsc.bcm.edu	37	chr16	16244451	16244451	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ttaccgggcacagtccatcaCggagcgcaggcggtgggcaa	15	12	1	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr16:16244451C>A	ENST00000205557.7	-	30	4416	c.4387G>T	c.(4387-4389)Gtg>Ttg	p.V1463L		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1463	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CAGTCCATCACGGAGCGCAGG	0.682																																					p.V1463L		Atlas-SNP	.											.	ABCC6	110	.	0			c.G4387T						.						36	30	32					16																	16244451		2197	4298	6495	SO:0001583	missense	368	exon30			CCATCACGGAGCG	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.4387G>T	chr16.hg19:g.16244451C>A	ENSP00000205557:p.Val1463Leu	89.0	0.0		57.0	24.0	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	hg19	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.673134	0.29693	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	T	0.70164	-0.46	4.38	4.38	0.52667	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.187888	0.25086	U	0.033253	T	0.42832	0.1220	N	0.16903	0.455	0.80722	D	1	P;P	0.42961	0.795;0.795	B;B	0.35073	0.195;0.195	T	0.47407	-0.9120	10	0.62326	D	0.03	.	5.1143	0.14825	0.0:0.6404:0.1828:0.1768	.	1463;1463	O95255;A8Y988	MRP6_HUMAN;.	L	1463;401	ENSP00000205557:V1463L	ENSP00000205557:V1463L	V	-	1	0	ABCC6	16151952	0.905000	0.30787	0.868000	0.34077	0.300000	0.27592	1.567000	0.36407	2.164000	0.68074	0.561000	0.74099	GTG	.	.		0.682	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			A	16244451	C	A	16244451	3	1	88	1	0	0	0	0	1	0	0	0	57	536	19	1	132	1	ABCC6	16	16244451	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10		16244451	74110302	63	11804										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27517278	27517278	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tgtcaccactgttgctgtccGcacagtgggagacaaaggac	12	11	1	1	rs140459536		TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr16:27517278G>T	ENST00000356183.4	-	10	1727	c.1712C>A	c.(1711-1713)gCg>gAg	p.A571E	GTF3C1_ENST00000561623.1_Missense_Mutation_p.A571E	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	571					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						GTTGCTGTCCGCACAGTGGGA	0.567																																					p.A571E		Atlas-SNP	.											.	GTF3C1	210	.	0			c.C1712A						.						139	115	123					16																	27517278		2197	4300	6497	SO:0001583	missense	2975	exon10			CTGTCCGCACAGT	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.1712C>A	chr16.hg19:g.27517278G>T	ENSP00000348510:p.Ala571Glu	148.0	0.0		105.0	41.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	G	0.498	-0.872140	0.02570	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.22539	1.95	5.39	2.83	0.33086	.	1.419090	0.03886	N	0.277842	T	0.12050	0.0293	N	0.19112	0.55	0.09310	N	1	B;B	0.18610	0.001;0.029	B;B	0.12156	0.0;0.007	T	0.28427	-1.0044	10	0.02654	T	1	-4.6393	5.1223	0.14867	0.7147:0.0:0.2853:0.0	.	571;571	Q12789;Q12789-3	TF3C1_HUMAN;.	E	571;569	ENSP00000348510:A571E	ENSP00000348510:A571E	A	-	2	0	GTF3C1	27424779	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	0.574000	0.23714	0.984000	0.38629	-0.302000	0.09304	GCG	.	G|1.000;A|0.000		0.567	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		T	27517278	G	T	27517278	3	4	88	1	0	0	0	0	1	0	0	0	6881	1087	38	1	4729	1	GTF3C1	16	27517278	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	11272827	27517278	62837475	64	11805										
AP1G1	164	hgsc.bcm.edu	37	chr16	71823203	71823204	+	Missense_Mutation	DNP	GC	GC	AA													0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tgtccaaagtgagcagggtaGcccagcatgtgcatatacag							TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr16:71823203_71823204GC>AA	ENST00000299980.4	-	2	620_621	c.179_180GC>TT	c.(178-180)gGC>gTT	p.G60V	AP1G1_ENST00000433195.2_Missense_Mutation_p.G83V|AP1G1_ENST00000569748.1_Missense_Mutation_p.G60V|AP1G1_ENST00000393512.3_Missense_Mutation_p.G60V|AP1G1_ENST00000423132.2_Missense_Mutation_p.G60V|AP1G1_ENST00000570297.1_5'Flank	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	60					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				GAGCAGGGTAGCCCAGCATGTG	0.45																																					p.G60G|p.G60V		Atlas-SNP	.											.	AP1G1	83	.	0			c.C180T|c.G179T						.																																			SO:0001583	missense	164	exon2			AGGGTAGCCCAGC|GGGTAGCCCAGCA	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.179_180delinsAA	chr16.hg19:g.71823203_71823204delinsAA	ENSP00000299980:p.Gly60Val	169.0|172.0	0.0		111.0|113.0	52.0|51.0	NM_001030007	O75709|O75842|Q9UG09|Q9Y3U4	Silent|Missense_Mutation	SNP	ENST00000299980.4	hg19	CCDS32480.1																																																																																			.	.		0.45	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			AA	71823204	GC	AA	71823203	3	1	88	1	0	0	0	0	1	0	0	0	732	958	34	3	2389	3	AP1G1	16	71823203	Missense_Mutation	DNP	GC	TCGA-DD-A115-01A-11D-A12Z-10	44305925	71823203	18531550	65	11806										
TBC1D26	353149	hgsc.bcm.edu	37	chr17	15642100	15642100	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	atccagctagatgtcagccaCaccctgcagaaacacatgat	7	13	1	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr17:15642100C>T	ENST00000437605.2	+	8	703	c.453C>T	c.(451-453)caC>caT	p.H151H	ZNF286A_ENST00000413242.2_3'UTR|TBC1D26_ENST00000579428.1_Silent_p.H151H|AC005324.6_ENST00000580194.1_RNA|AC005324.6_ENST00000434017.1_RNA|AC005324.6_ENST00000433873.1_RNA	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	151	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		ATGTCAGCCACACCCTGCAGA	0.537																																					p.H151H		Atlas-SNP	.											.	TBC1D26	16	.	0			c.C453T						.						108	99	102					17																	15642100		2154	4235	6389	SO:0001819	synonymous_variant	353149	exon8			CAGCCACACCCTG		CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.453C>T	chr17.hg19:g.15642100C>T		585.0	2.0		222.0	94.0	NM_178571	A8K929|Q4G172	Silent	SNP	ENST00000437605.2	hg19	CCDS42265.1																																																																																			.	.		0.537	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571		T	15642100	C	T	15642100	2	4	88	1	0	0	0	0	0	0	0	1	15631	477	17	3		3	TBC1D26	17	15642100	Silent	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10		15642100	65553110	66	11807										
MPO	4353	hgsc.bcm.edu	37	chr17	56355395	56355395	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ggcgtccacgaaggaagtgaGcgcgttgatctggttgcgga	17	8	1	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr17:56355395G>A	ENST00000225275.3	-	7	1173	c.997C>T	c.(997-999)Ctc>Ttc	p.L333F	MPO_ENST00000578493.1_5'UTR|MPO_ENST00000340482.3_Missense_Mutation_p.L365F	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	333					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	AAGGAAGTGAGCGCGTTGATC	0.637																																					p.L333F		Atlas-SNP	.											.	MPO	114	.	0			c.C997T						.						114	98	103					17																	56355395		2203	4300	6503	SO:0001583	missense	4353	exon7			AAGTGAGCGCGTT		CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.997C>T	chr17.hg19:g.56355395G>A	ENSP00000225275:p.Leu333Phe	61.0	0.0		54.0	23.0	NM_000250	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	hg19	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.187934	0.78789	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.70164	-0.46;-0.46	5.32	4.35	0.52113	.	0.060693	0.64402	D	0.000003	D	0.84338	0.5450	M	0.92555	3.32	0.58432	D	0.999994	D	0.89917	1.0	D	0.80764	0.994	D	0.87509	0.2438	10	0.87932	D	0	-37.0231	12.4835	0.55859	0.0802:0.0:0.9198:0.0	.	333	P05164	PERM_HUMAN	F	365;333	ENSP00000344419:L365F;ENSP00000225275:L333F	ENSP00000225275:L333F	L	-	1	0	MPO	53710394	1.000000	0.71417	0.996000	0.52242	0.909000	0.53808	3.253000	0.51469	2.518000	0.84900	0.561000	0.74099	CTC	.	.		0.637	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			A	56355395	G	A	56355395	3	1	88	1	0	0	0	0	1	0	0	0	9741	971	34	3	1264	3	MPO	17	56355395	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	40713295	56355395	24839815	67	11808										
RPS6KB1	6198	hgsc.bcm.edu	37	chr17	58013587	58013587	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	tctttaaagctgctgaaaagAaatgctgcttctcgtctggg	10	8	3	2			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr17:58013587A>T	ENST00000225577.4	+	11	1011	c.990A>T	c.(988-990)agA>agT	p.R330S	RPS6KB1_ENST00000393021.3_Missense_Mutation_p.R277S|RPS6KB1_ENST00000443572.2_Missense_Mutation_p.R307S|RPS6KB1_ENST00000406116.3_Missense_Mutation_p.R330S	NM_001272042.1|NM_001272044.1|NM_001272060.1|NM_003161.2	NP_001258971.1|NP_001258973.1|NP_001258989.1|NP_003152.1	P23443	KS6B1_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 1	330	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				aging (GO:0007568)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell development (GO:0007281)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue growth (GO:0048633)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of glucose import (GO:0046324)|response to drug (GO:0042493)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to ethanol (GO:0045471)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to leucine (GO:0043201)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to testosterone (GO:0033574)|response to toxic substance (GO:0009636)|response to tumor necrosis factor (GO:0034612)|response to wounding (GO:0009611)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	all_cancers(5;1.63e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.57e-12)|all cancers(12;6.41e-11)			TGCTGAAAAGAAATGCTGCTT	0.408																																					p.R330S		Atlas-SNP	.											.	RPS6KB1	43	.	0			c.A990T						.						110	110	110					17																	58013587		2203	4300	6503	SO:0001583	missense	6198	exon11			GAAAAGAAATGCT	M60724	CCDS11621.1, CCDS62271.1, CCDS62272.1, CCDS62273.1	17q23.1	2011-04-05	2002-08-29		ENSG00000108443	ENSG00000108443			10436	protein-coding gene	gene with protein product		608938	"ribosomal protein S6 kinase, 70kD, polypeptide 1"	STK14A		1922062	Standard	NM_003161		Approved	S6K1, p70(S6K)-alpha, PS6K	uc002ixy.4	P23443	OTTHUMG00000150642	ENST00000225577.4:c.990A>T	chr17.hg19:g.58013587A>T	ENSP00000225577:p.Arg330Ser	302.0	1.0		257.0	155.0	NM_001272043	B2R779|B4DLT4|B4DTG1|E7ESB8|F6UYM1|Q7Z721	Missense_Mutation	SNP	ENST00000225577.4	hg19	CCDS11621.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716500	0.89205	.	.	ENSG00000108443	ENST00000443572;ENST00000406116;ENST00000225577;ENST00000393021	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.55	3.35	0.38373	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.62648	0.2445	L	0.33710	1.025	0.80722	D	1	D;D;D	0.89917	1.0;0.996;0.999	D;D;D	0.78314	0.991;0.978;0.987	T	0.63849	-0.6544	10	0.87932	D	0	.	9.3291	0.38010	0.8551:0.0:0.1449:0.0	.	307;330;330	F6UYM1;Q7Z721;P23443	.;.;KS6B1_HUMAN	S	307;330;330;277	ENSP00000441993:R307S;ENSP00000384335:R330S;ENSP00000225577:R330S;ENSP00000376744:R277S	ENSP00000225577:R330S	R	+	3	2	RPS6KB1	55368369	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.090000	0.57693	0.941000	0.37499	0.524000	0.50904	AGA	.	.		0.408	RPS6KB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319324.1	NM_003161		T	58013587	A	T	58013587	3	4	88	1	0	0	0	0	1	0	0	0	13671	243	9	4	1032	4	RPS6KB1	17	58013587	Missense_Mutation	SNP	A	TCGA-DD-A115-01A-11D-A12Z-10	1658192	58013587	23181623	68	11809										
MRC2	9902	hgsc.bcm.edu	37	chr17	60743465	60743465	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ccccctgcagaggtctacacCatccagggaaactcccacgg	9	17	1	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr17:60743465C>T	ENST00000303375.5	+	3	933	c.531C>T	c.(529-531)acC>acT	p.T177T		NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	177					collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						AGGTCTACACCATCCAGGGAA	0.617																																					p.T177T		Atlas-SNP	.											.	MRC2	126	.	0			c.C531T						.						58	43	49					17																	60743465		2199	4294	6493	SO:0001819	synonymous_variant	9902	exon3			CTACACCATCCAG	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.531C>T	chr17.hg19:g.60743465C>T		76.0	0.0		50.0	33.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	hg19	CCDS11634.1																																																																																			.	.		0.617	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			T	60743465	C	T	60743465	2	4	88	1	0	0	0	0	0	0	0	1	9767	581	21	3		3	MRC2	17	60743465	Silent	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	2729878	60743465	20451745	69	11810										
MAP2K6	5608	hgsc.bcm.edu	37	chr17	67521065	67521065	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gaaagaataaacccagagctCaaccagaagggatacagtgt	10	8	1	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr17:67521065C>T	ENST00000590474.1	+	9	974	c.687C>T	c.(685-687)ctC>ctT	p.L229L	MAP2K6_ENST00000589647.1_Silent_p.L173L	NM_002758.3	NP_002749.2	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6	229	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|cardiac muscle contraction (GO:0060048)|cell cycle arrest (GO:0007050)|cellular response to sorbitol (GO:0072709)|DNA damage induced protein phosphorylation (GO:0006975)|innate immune response (GO:0045087)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to ischemia (GO:0002931)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	20	Breast(10;6.05e-10)					ACCCAGAGCTCAACCAGAAGG	0.438																																					p.L229L		Atlas-SNP	.											.	MAP2K6	41	.	0			c.C687T						.						105	94	98					17																	67521065		2203	4300	6503	SO:0001819	synonymous_variant	5608	exon9			AGAGCTCAACCAG	U39064	CCDS11686.1	17q	2011-06-09						"Mitogen-activated protein kinase cascade / Kinase kinases"	6846	protein-coding gene	gene with protein product	"protein kinase, mitogen-activated, kinase 6 (MAP kinase kinase 6)"	601254		PRKMK6		8621675	Standard	XM_005257515		Approved	MEK6, MKK6, SAPKK3, MAPKK6	uc002jij.3	P52564		ENST00000590474.1:c.687C>T	chr17.hg19:g.67521065C>T		150.0	0.0		150.0	86.0	NM_002758		Silent	SNP	ENST00000590474.1	hg19	CCDS11686.1																																																																																			.	.		0.438	MAP2K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450689.1	NM_002758		T	67521065	C	T	67521065	2	4	88	1	0	0	0	0	0	0	0	1	9250	813	29	3		3	MAP2K6	17	67521065	Silent	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	6777600	67521065	13674145	70	11811										
GAA	2548	hgsc.bcm.edu	37	chr17	78091993	78091993	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	cgtgtccttccctttccaggGccctggcctcacaaccacag	8	18	1	0			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr17:78091993G>T	ENST00000302262.3	+	18	2702	c.2483G>T	c.(2482-2484)gGc>gTc	p.G828V	GAA_ENST00000390015.3_Splice_Site_p.G828V	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	828					cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	CCTTTCCAGGGCCCTGGCCTC	0.667																																					p.G828V		Atlas-SNP	.											.	GAA	66	.	0			c.G2483T						.						44	46	45					17																	78091993		2203	4300	6503	SO:0001630	splice_region_variant	2548	exon19			TCCAGGGCCCTGG		CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"Pompe disease", "glycogen storage disease type II"	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.2482-1G>T	chr17.hg19:g.78091993G>T		72.0	0.0		70.0	27.0	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Missense_Mutation	SNP	ENST00000302262.3	hg19	CCDS32760.1	.	.	.	.	.	.	.	.	.	.	G	9.396	1.076732	0.20227	.	.	ENSG00000171298	ENST00000302262;ENST00000390015	D;D	0.89810	-2.57;-2.57	5.51	1.96	0.26148	.	0.464777	0.24020	N	0.042294	T	0.78635	0.4314	L	0.37850	1.14	0.58432	D	0.999996	B	0.09022	0.002	B	0.09377	0.004	T	0.69888	-0.5023	10	0.34782	T	0.22	-33.8352	2.0092	0.03484	0.1276:0.3792:0.2986:0.1945	.	828	P10253	LYAG_HUMAN	V	828	ENSP00000305692:G828V;ENSP00000374665:G828V	ENSP00000305692:G828V	G	+	2	0	GAA	75706588	0.950000	0.32346	0.985000	0.45067	0.615000	0.37417	1.871000	0.39539	1.267000	0.44247	0.655000	0.94253	GGC	.	.		0.667	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		Missense_Mutation	T	78091993	G	T	78091993	5	4	88	1	0	0	0	0	0	0	1	0	6155	1217	42	3	2549	3	GAA	17	78091993	Splice_Site	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	10570928	78091993	3103217	71	11812										
RAB40B	10966	hgsc.bcm.edu	37	chr17	80615904	80615904	+	Frame_Shift_Del	DEL	G	G	-													0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	aggccgttggccatcgagaaGgacttgaggtggcttcttaa							TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr17:80615904delG	ENST00000571995.1	-	6	803	c.672delC	c.(670-672)tccfs	p.S224fs	RAB40B_ENST00000571880.1_5'Flank|RAB40B_ENST00000269347.6_Frame_Shift_Del_p.S45fs|RAB40B_ENST00000538809.2_3'UTR	NM_006822.2	NP_006813.1	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family	224	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(2)	10	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			CCATCGAGAAGGACTTGAGGT	0.617																																					p.F225fs		Atlas-Indel,Pindel	.											.	RAB40B	24	.	0			c.673delT						.						159	143	149					17																	80615904		2203	4300	6503	SO:0001589	frameshift_variant	10966	exon6			.	U05227	CCDS11816.1	17q25.3	2014-08-12			ENSG00000141542	ENSG00000141542		"RAB, member RAS oncogene"	18284	protein-coding gene	gene with protein product						11697911	Standard	NM_006822		Approved	SEC4L, RAR	uc002kft.3	Q12829	OTTHUMG00000177806	ENST00000571995.1:c.672delC	chr17.hg19:g.80615904delG	ENSP00000461785:p.Ser224fs	190.0	0.0		164.0	23.0	NM_006822	Q8WVG3	Frame_Shift_Del	DEL	ENST00000571995.1	hg19	CCDS11816.1																																																																																			.	.		0.617	RAB40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439007.1			-	80615904	G	-	80615904	7	5	88	1	0	1	0	1	0	0	0	0	12956	987	35	0	168	0	RAB40B	17	80615904	Frame_Shift_Del	DEL	G	TCGA-DD-A115-01A-11D-A12Z-10	2523911	80615904	579306	72	11813										
FUT3	2525	hgsc.bcm.edu	37	chr19	5844841	5844841	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ttgtggcttggctgcacccaGgggatccatgggtcagagta	15	9	1	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr19:5844841G>A	ENST00000303225.6	-	3	644	c.10C>T	c.(10-12)Ctg>Ttg	p.L4L	FUT3_ENST00000458379.2_Silent_p.L4L|FUT3_ENST00000589918.1_Silent_p.L4L|AC024592.9_ENST00000589276.1_RNA|FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000589620.1_Silent_p.L4L	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	4					cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						GCTGCACCCAGGGGATCCATG	0.572																																					p.L4L	Esophageal Squamous(82;745 1728 24593 44831)	Atlas-SNP	.											.	FUT3	30	.	0			c.C10T						.						23	22	22					19																	5844841		2203	4300	6503	SO:0001819	synonymous_variant	2525	exon3			CACCCAGGGGATC		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"CD molecules", "Blood group antigens", "Fucosyltransferases"	4014	protein-coding gene	gene with protein product		111100	"fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.10C>T	chr19.hg19:g.5844841G>A		173.0	0.0		102.0	13.0	NM_001097640	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Silent	SNP	ENST00000303225.6	hg19	CCDS12153.1																																																																																			.	.		0.572	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149		A	5844841	G	A	5844841	2	1	88	1	0	0	0	0	0	0	0	1	6113	991	35	3		3	FUT3	19	5844841	Silent	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10		5844841	53284142	73	11814										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17038989	17038989	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	actggacctctggtggcctcGggagggtccaggccacaatg	15	12	1	0	rs200032712		TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr19:17038989G>A	ENST00000443236.1	-	25	3372	c.3341C>T	c.(3340-3342)cCg>cTg	p.P1114L		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1067						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						TGGTGGCCTCGGGAGGGTCCA	0.582																																					p.P1114L		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C3341T						.						44	49	47					19																	17038989		1933	4133	6066	SO:0001583	missense	27151	exon25			GGCCTCGGGAGGG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.3341C>T	chr19.hg19:g.17038989G>A	ENSP00000402505:p.Pro1114Leu	46.0	0.0		59.0	23.0	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	hg19	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.094|8.094	0.775190|0.775190	0.16051|0.16051	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	3.02|3.02	-0.754|-0.754	0.11065|0.11065	Farnesoic acid O-methyl transferase (1);|.	0.630912|.	0.14270|.	N|.	0.330240|.	T|.	0.46483|.	0.1395|.	M|M	0.81682|0.81682	2.555|2.555	0.09310|0.09310	N|N	0.999994|0.999994	D|.	0.53151|.	0.958|.	B|.	0.43680|.	0.427|.	T|.	0.45498|.	-0.9257|.	9|.	0.33141|.	T|.	0.24|.	.|.	2.7214|2.7214	0.05202|0.05202	0.0941:0.1586:0.4216:0.3257|0.0941:0.1586:0.4216:0.3257	.|.	1067|.	Q8IZJ3|.	CPMD8_HUMAN|.	L|X	1114|1125	.|.	ENSP00000291440:P1114L|.	P|R	-|-	2|1	0|2	CPAMD8|CPAMD8	16899989|16899989	1.000000|1.000000	0.71417|0.71417	0.026000|0.026000	0.17262|0.17262	0.000000|0.000000	0.00434|0.00434	1.685000|1.685000	0.37659|0.37659	-0.498000|-0.498000	0.06632|0.06632	-1.802000|-1.802000	0.00618|0.00618	CCG|CGA	.	G|0.999;A|0.001		0.582	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		A	17038989	G	A	17038989	3	1	88	1	0	0	0	0	1	0	0	0	3797	1116	39	1	2529	1	CPAMD8	19	17038989	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	11194148	17038989	42089994	74	11815										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52001391	52001391	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ctcgaggcagctccagcaccCcaaggttcgaggactgtgag	13	13	0	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr19:52001391C>A	ENST00000291707.3	-	5	1341	c.1286G>T	c.(1285-1287)gGg>gTg	p.G429V	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.G311V	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	429	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CTCCAGCACCCCAAGGTTCGA	0.617																																					p.G429V		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.G1286T						.						50	49	49					19																	52001391		2203	4300	6503	SO:0001583	missense	89858	exon5			AGCACCCCAAGGT	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1286G>T	chr19.hg19:g.52001391C>A	ENSP00000291707:p.Gly429Val	86.0	0.0		66.0	17.0	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	hg19	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	9.204	1.029301	0.19512	.	.	ENSG00000254521	ENST00000291707	T	0.15718	2.4	1.39	-2.77	0.05877	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.198493	0.24779	U	0.035667	T	0.41673	0.1169	H	0.95402	3.665	0.09310	N	0.999998	D;D	0.69078	0.997;0.99	D;D	0.76071	0.987;0.929	T	0.33394	-0.9870	10	0.72032	D	0.01	.	2.2019	0.03926	0.2445:0.4208:0.0:0.3347	.	429;311	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	V	429	ENSP00000291707:G429V	ENSP00000291707:G429V	G	-	2	0	SIGLEC12	56693203	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.240000	0.18042	-0.859000	0.04105	-0.784000	0.03344	GGG	.	.		0.617	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		A	52001391	C	A	52001391	3	1	88	1	0	0	0	0	1	0	0	0	14323	623	22	3	517	3	SIGLEC12	19	52001391	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	34962402	52001391	7127592	75	11816										
ZNF432	9668	hgsc.bcm.edu	37	chr19	52538685	52538685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ctgcagatgatcatcaacttCgttgttttctaggaaagaag	9	7	3	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr19:52538685C>T	ENST00000594154.1	-	5	459	c.247G>A	c.(247-249)Gaa>Aaa	p.E83K	ZNF432_ENST00000221315.5_Missense_Mutation_p.E83K			O94892	ZN432_HUMAN	zinc finger protein 432	83					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	29		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)		TCATCAACTTCGTTGTTTTCT	0.343																																					p.E83K		Atlas-SNP	.											.	ZNF432	172	.	0			c.G247A						.						58	56	57					19																	52538685		2202	4300	6502	SO:0001583	missense	9668	exon5			CAACTTCGTTGTT	AB018341	CCDS12848.1	19q13.41	2013-01-08				ENSG00000256087		"Zinc fingers, C2H2-type", "-"	20810	protein-coding gene	gene with protein product						9872452	Standard	NM_014650		Approved	KIAA0798	uc002pyk.3	O94892		ENST00000594154.1:c.247G>A	chr19.hg19:g.52538685C>T	ENSP00000470488:p.Glu83Lys	246.0	0.0		163.0	61.0	NM_014650		Missense_Mutation	SNP	ENST00000594154.1	hg19	CCDS12848.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.015319	0.00042	.	.	ENSG00000256087	ENST00000221315	T	0.05258	3.47	3.32	1.14	0.20703	.	.	.	.	.	T	0.02156	0.0067	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46638	-0.9177	9	0.02654	T	1	.	4.1709	0.10329	0.0:0.2106:0.1774:0.612	.	83	O94892	ZN432_HUMAN	K	83	ENSP00000221315:E83K	ENSP00000221315:E83K	E	-	1	0	ZNF432	57230497	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.266000	0.18534	-0.095000	0.12351	-0.332000	0.08345	GAA	.	.		0.343	ZNF432-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462410.1	NM_014650		T	52538685	C	T	52538685	3	4	88	1	0	0	0	0	1	0	0	0	17921	893	31	1	1715	1	ZNF432	19	52538685	Missense_Mutation	SNP	C	TCGA-DD-A115-01A-11D-A12Z-10	537294	52538685	6590298	76	11817										
SIRPD	128646	hgsc.bcm.edu	37	chr20	1532400	1532400	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gatagctcttccttttatgaActtcacgcagtaataggtgc	8	9	2	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr20:1532400A>G	ENST00000381623.3	-	2	1547	c.358T>C	c.(358-360)Ttc>Ctc	p.F120L	SIRPD_ENST00000381621.1_Missense_Mutation_p.F120L			Q9H106	SIRPD_HUMAN	signal-regulatory protein delta	120	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)	15						CCTTTTATGAACTTCACGCAG	0.488																																					p.F120L		Atlas-SNP	.											.	SIRPD	34	.	0			c.T358C						.						149	143	145					20																	1532400		2203	4300	6503	SO:0001583	missense	128646	exon2			TTATGAACTTCAC	AL049634	CCDS13018.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000125900	ENSG00000125900		"Signal-regulatory proteins", "Immunoglobulin superfamily / V-set domain containing"	16248	protein-coding gene	gene with protein product			"protein tyrosine phosphatase, non-receptor type substrate 1-like 2"	PTPNS1L2		16339511	Standard	NM_178460		Approved	dJ576H24.4	uc002wfi.3	Q9H106	OTTHUMG00000031674	ENST00000381623.3:c.358T>C	chr20.hg19:g.1532400A>G	ENSP00000371036:p.Phe120Leu	137.0	0.0		79.0	24.0	NM_178460	B3KS88|Q5TFQ6	Missense_Mutation	SNP	ENST00000381623.3	hg19	CCDS13018.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.272461	0.40194	.	.	ENSG00000125900	ENST00000381623;ENST00000381621	T;T	0.64991	-0.13;-0.13	4.02	1.74	0.24563	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.680568	0.12147	N	0.495245	T	0.44973	0.1319	L	0.33753	1.03	0.24203	N	0.995501	P	0.34587	0.458	B	0.29077	0.098	T	0.32188	-0.9916	10	0.59425	D	0.04	.	5.698	0.17867	0.7725:0.0:0.2275:0.0	.	120	Q9H106	SIRPD_HUMAN	L	120	ENSP00000371036:F120L;ENSP00000371034:F120L	ENSP00000371034:F120L	F	-	1	0	SIRPD	1480400	1.000000	0.71417	0.776000	0.31678	0.180000	0.23129	2.564000	0.45931	0.235000	0.21160	-0.394000	0.06481	TTC	.	.		0.488	SIRPD-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077552.1	NM_178460		G	1532400	A	G	1532400	3	3	88	1	0	0	0	0	1	0	0	0	14350	43	2	2	247	2	SIRPD	20	1532400	Missense_Mutation	SNP	A	TCGA-DD-A115-01A-11D-A12Z-10		1532400	61493120	77	11818										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9401994	9401994	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	aaaattggcacctacgtagaGgtggatatgtatgggttgcc	13	6	0	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr20:9401994G>T	ENST00000378493.1	+	23	2184	c.2169G>T	c.(2167-2169)gaG>gaT	p.E723D	PLCB4_ENST00000414679.2_Missense_Mutation_p.E735D|PLCB4_ENST00000378473.3_Missense_Mutation_p.E735D|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378501.2_Missense_Mutation_p.E723D|PLCB4_ENST00000278655.4_Missense_Mutation_p.E723D|PLCB4_ENST00000334005.3_Missense_Mutation_p.E723D			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	723	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						CCTACGTAGAGGTGGATATGT	0.418																																					p.E735D		Atlas-SNP	.											.	PLCB4	204	.	0			c.G2205T						.						116	106	109					20																	9401994		2203	4300	6503	SO:0001583	missense	5332	exon26			CGTAGAGGTGGAT		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.2169G>T	chr20.hg19:g.9401994G>T	ENSP00000367754:p.Glu723Asp	168.0	0.0		116.0	48.0	NM_001172646	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	hg19	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.605140	0.66445	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	5.68	2.21	0.28008	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.86301	0.5900	H	0.94658	3.565	0.80722	D	1	D;P;D;D	0.89917	1.0;0.913;0.962;0.983	D;P;D;P	0.91635	0.999;0.549;0.957;0.826	D	0.85773	0.1356	10	0.87932	D	0	.	9.7585	0.40517	0.7336:0.0:0.2664:0.0	.	735;570;723;723	E2QRH8;Q15147-2;Q15147;Q15147-4	.;.;PLCB4_HUMAN;.	D	723;735;723;723;723;571	ENSP00000334105:E723D;ENSP00000367734:E735D;ENSP00000278655:E723D;ENSP00000367754:E723D;ENSP00000367762:E723D;ENSP00000390616:E571D	ENSP00000278655:E723D	E	+	3	2	PLCB4	9349994	1.000000	0.71417	0.998000	0.56505	0.926000	0.56050	1.150000	0.31639	0.119000	0.18210	-0.483000	0.04790	GAG	.	.		0.418	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			T	9401994	G	T	9401994	3	4	88	1	0	0	0	0	1	0	0	0	12039	991	35	3	2299	3	PLCB4	20	9401994	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10	7869594	9401994	53623526	78	11819										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50346419	50346419	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	acttctgattgttgatgacaTtccgaggatacctctggtct	9	9	3	3			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr20:50346419T>A	ENST00000338821.5	-	2	431	c.167A>T	c.(166-168)aAt>aTt	p.N56I	ATP9A_ENST00000477492.1_5'UTR|ATP9A_ENST00000311637.5_Missense_Mutation_p.N41I|ATP9A_ENST00000402822.1_Missense_Mutation_p.N56I	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	56					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GTTGATGACATTCCGAGGATA	0.547																																					p.N56I		Atlas-SNP	.											.	ATP9A	135	.	0			c.A167T						.						155	133	140					20																	50346419		2203	4300	6503	SO:0001583	missense	10079	exon2			ATGACATTCCGAG	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.167A>T	chr20.hg19:g.50346419T>A	ENSP00000342481:p.Asn56Ile	140.0	0.0		74.0	23.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	hg19	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.980823	0.92982	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	D;D;D	0.98762	-5.12;-5.12;-5.12	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.98855	0.9613	M	0.85041	2.73	0.33794	D	0.625851	B;P	0.49862	0.054;0.929	B;P	0.54815	0.055;0.761	D	0.99978	1.2344	10	0.87932	D	0	-20.706	15.4675	0.75412	0.0:0.0:0.0:1.0	.	56;56	O75110-2;O75110	.;ATP9A_HUMAN	I	41;56;56	ENSP00000309086:N41I;ENSP00000342481:N56I;ENSP00000385875:N56I	ENSP00000309086:N41I	N	-	2	0	ATP9A	49779826	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.461000	0.80834	2.107000	0.64212	0.460000	0.39030	AAT	.	.		0.547	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		A	50346419	T	A	50346419	3	1	88	1	0	0	0	0	1	0	0	0	1198	1493	52	4	3084	4	ATP9A	20	50346419	Missense_Mutation	SNP	T	TCGA-DD-A115-01A-11D-A12Z-10	40944425	50346419	12679101	79	11820										
KCNJ6	3763	hgsc.bcm.edu	37	chr21	39086700	39086700	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	gatatccgtctggttcaacgGgatgaactccccctccgagg	11	13	2	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr21:39086700G>A	ENST00000609713.1	-	3	1349	c.760C>T	c.(760-762)Ccg>Tcg	p.P254S	KCNJ6_ENST00000288309.6_Missense_Mutation_p.P254S|KCNJ6-IT1_ENST00000435001.1_RNA	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	254					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	TGGTTCAACGGGATGAACTCC	0.502																																					p.P254S	Pancreas(48;379 1118 2936 19024 28214)	Atlas-SNP	.											.	KCNJ6	58	.	0			c.C760T						.						108	109	109					21																	39086700		1909	4143	6052	SO:0001583	missense	3763	exon3			TCAACGGGATGAA	U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.760C>T	chr21.hg19:g.39086700G>A	ENSP00000477437:p.Pro254Ser	321.0	0.0		179.0	33.0	NM_002240	Q3MJ74|Q53WW6	Missense_Mutation	SNP	ENST00000609713.1	hg19	CCDS42927.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.585385	0.86748	.	.	ENSG00000157542	ENST00000400482;ENST00000288309	D;D	0.91996	-2.95;-2.95	6.17	6.17	0.99709	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.96839	0.8968	M	0.86420	2.815	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95956	0.8958	10	0.52906	T	0.07	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	254	P48051	IRK6_HUMAN	S	254	ENSP00000383330:P254S;ENSP00000288309:P254S	ENSP00000288309:P254S	P	-	1	0	KCNJ6	38008570	1.000000	0.71417	0.993000	0.49108	0.883000	0.51084	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	CCG	.	.		0.502	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194828.2	NM_002240		A	39086700	G	A	39086700	3	1	88	1	0	0	0	0	1	0	0	0	8064	1232	43	3	519	3	KCNJ6	21	39086700	Missense_Mutation	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10		39086700	9043195	80	11821										
EWSR1	2130	hgsc.bcm.edu	37	chr22	29694814	29694814	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	ttccctccaagaggaccccgGggttcccgagggaacccctc	11	17	0	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr22:29694814G>A	ENST00000397938.2	+	14	1828	c.1509G>A	c.(1507-1509)cgG>cgA	p.R503R	EWSR1_ENST00000332050.6_Silent_p.R430R|EWSR1_ENST00000414183.2_Silent_p.R508R|EWSR1_ENST00000331029.7_Silent_p.R465R|EWSR1_ENST00000332035.6_Silent_p.R447R|EWSR1_ENST00000406548.1_Silent_p.R502R	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1	503	Arg/Gly/Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GAGGACCCCGGGGTTCCCGAG	0.607			T	"FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"	"Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"																																p.R508R		Atlas-SNP	.		Dom	yes		22	22q12	2130	Ewing sarcoma breakpoint region 1 (EWS)		"L, M"	.	EWSR1	104	.	0			c.G1524A						.						56	65	62					22																	29694814		2203	4300	6503	SO:0001819	synonymous_variant	2130	exon15			ACCCCGGGGTTCC		CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944		"RNA binding motif (RRM) containing"	3508	protein-coding gene	gene with protein product		133450	"Ewing sarcoma breakpoint region 1"			1522903	Standard	NM_005243		Approved	EWS	uc003aev.3	Q01844	OTTHUMG00000151107	ENST00000397938.2:c.1509G>A	chr22.hg19:g.29694814G>A		73.0	0.0		61.0	23.0	NM_013986	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	Silent	SNP	ENST00000397938.2	hg19	CCDS13851.1	.	.	.	.	.	.	.	.	.	.	G	4.311	0.056969	0.08339	.	.	ENSG00000182944	ENST00000360091	.	.	.	5.52	-1.92	0.07618	.	.	.	.	.	T	0.38558	0.1045	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28138	-1.0053	4	.	.	.	.	0.704	0.00913	0.3743:0.1243:0.2641:0.2373	.	.	.	.	R	159	.	.	G	+	1	0	EWSR1	28024814	0.897000	0.30589	0.828000	0.32881	0.332000	0.28634	-0.043000	0.12043	-0.501000	0.06605	-0.379000	0.06801	GGG	.	.		0.607	EWSR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321345.1	NM_005243		A	29694814	G	A	29694814	2	1	88	1	0	0	0	0	0	0	0	1	5298	1219	43	3		3	EWSR1	22	29694814	Silent	SNP	G	TCGA-DD-A115-01A-11D-A12Z-10		29694814	21609752	81	11822										
SEC14L3	266629	hgsc.bcm.edu	37	chr22	30857663	30857664	+	Frame_Shift_Ins	INS	-	-	C													0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	acgtacatggacttggggatINSctccccgccatagttaatct							TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chr22:30857663_30857664insC	ENST00000215812.4	-	10	879_880	c.789_790insG	c.(787-792)gagatcfs	p.I264fs	SEC14L3_ENST00000403066.1_Frame_Shift_Ins_p.I205fs|SEC14L3_ENST00000402286.1_Frame_Shift_Ins_p.I187fs|SEC14L3_ENST00000540910.1_Frame_Shift_Ins_p.I187fs|SEC14L3_ENST00000539629.1_Frame_Shift_Ins_p.I205fs|SEC14L3_ENST00000415957.2_Frame_Shift_Ins_p.I205fs|SEC14L3_ENST00000401751.1_Frame_Shift_Ins_p.I205fs	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	264						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	GACTTGGGGATCTCCCCGCCAT	0.54																																					p.I264fs	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-INDEL	.											.	SEC14L3	46	.	0			c.790_791insG						.																																			SO:0001589	frameshift_variant	266629	exon10			.	AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.790dupG	chr22.hg19:g.30857664_30857664dupC	ENSP00000215812:p.Ile264fs	129.0	0.0		93.0	11.0	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Frame_Shift_Ins	INS	ENST00000215812.4	hg19	CCDS13877.1																																																																																			.	.		0.54	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975		C	30857664	-	C	30857663	7	5	88	1	0	1	1	0	0	0	0	0	13998	1435	50	0	424	0	SEC14L3	22	30857663	Frame_Shift_Ins	INS	-	TCGA-DD-A115-01A-11D-A12Z-10	1162849	30857663	20446903	82	11823										
TAF1	6872	hgsc.bcm.edu	37	chrX	70680629	70680629	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0602409638554217	5	1	1.00535317926622	3.71980676328502	0.479975066230326	1	1	0	agacggtggggaggcttcccAtggtttggaggatagcaaca	16	7	0	1			TCGA-DD-A115-01A-11D-A12Z-10	TCGA-DD-A115-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29d6950d-f63e-48ca-afb5-cdd95aa16f0e	97ef9891-4c64-4f64-b1be-59895971138d	g.chrX:70680629A>G	ENST00000373790.4	+	37	5423	c.5372A>G	c.(5371-5373)cAt>cGt	p.H1791R	TAF1_ENST00000461764.1_3'UTR|TAF1_ENST00000276072.3_Missense_Mutation_p.H1812R|TAF1_ENST00000449580.1_Missense_Mutation_p.H1825R|TAF1_ENST00000423759.1_Missense_Mutation_p.H1814R	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1791	Asp/Glu-rich (acidic tail).|Protein kinase 2.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GAGGCTTCCCATGGTTTGGAG	0.507																																					p.H1812R		Atlas-SNP	.											.	TAF1	439	.	0			c.A5435G						.						117	81	93					X																	70680629		2201	4299	6500	SO:0001583	missense	6872	exon37			CTTCCCATGGTTT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.5372A>G	chrX.hg19:g.70680629A>G	ENSP00000362895:p.His1791Arg	146.0	0.0		90.0	67.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.11|10.11	1.259763|1.259763	0.23051|0.23051	.|.	.|.	ENSG00000147133|ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000395779;ENST00000276072|ENST00000437147	T;T;T;T|.	0.08370|.	3.1;3.14;3.16;3.1|.	4.76|4.76	-0.271|-0.271	0.12922|0.12922	.|.	0.662303|.	0.16392|.	N|.	0.216437|.	T|T	0.22704|0.22704	0.0548|0.0548	N|N	0.19112|0.19112	0.55|0.55	0.20873|0.20873	N|N	0.999833|0.999833	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.001;0.0;0.001|.	T|T	0.29701|0.29701	-1.0003|-1.0003	10|5	0.11485|.	T|.	0.65|.	.|.	8.3625|8.3625	0.32367|0.32367	0.6661:0.0:0.3339:0.0|0.6661:0.0:0.3339:0.0	.|.	481;1825;1791;1812|.	A5CVC9;P21675-4;P21675;P21675-2|.	.;.;TAF1_HUMAN;.|.	R|V	1791;1825;1814;533;1812|480	ENSP00000362895:H1791R;ENSP00000389000:H1825R;ENSP00000406549:H1814R;ENSP00000276072:H1812R|.	ENSP00000276072:H1812R|.	H|M	+|+	2|1	0|0	TAF1|TAF1	70597354|70597354	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.997000|0.997000	0.91878|0.91878	1.978000|1.978000	0.40598|0.40598	-0.324000|-0.324000	0.08589|0.08589	0.430000|0.430000	0.28490|0.28490	CAT|ATG	.	.		0.507	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		G	70680629	A	G	70680629	3	3	88	1	0	0	0	0	1	0	0	0	15528	217	8	2	5581	2	TAF1	23	70680629	Missense_Mutation	SNP	A	TCGA-DD-A115-01A-11D-A12Z-10		70680629	84589931	83	11824										
EIF2C4	192670	hgsc.bcm.edu	37	chr1	36291032	36291032	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	agctttggctgggcacttgaAtgaagtcccagatgactcag	12	9	1	4			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:36291032A>G	ENST00000373210.3	+	4	670	c.425A>G	c.(424-426)aAt>aGt	p.N142S		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	142					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										GGGCACTTGAATGAAGTCCCA	0.443																																					p.N142S		Atlas-SNP	.											.	.	.	.	0			c.A425G						.						168	157	161					1																	36291032		2203	4300	6503	SO:0001583	missense	192670	exon4			ACTTGAATGAAGT	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"Argonaute/PIWI family"	18424	protein-coding gene	gene with protein product	"argonaute 4"	607356	"eukaryotic translation initiation factor 2C, 4"	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.425A>G	chr1.hg19:g.36291032A>G	ENSP00000362306:p.Asn142Ser	123.0	0.0		264.0	143.0	NM_017629	A7MD27	Missense_Mutation	SNP	ENST00000373210.3	hg19	CCDS397.1	.	.	.	.	.	.	.	.	.	.	A	5.505	0.278206	0.10403	.	.	ENSG00000134698	ENST00000373210	T	0.08984	3.03	5.57	1.47	0.22746	Argonaute/Dicer protein, PAZ (1);	0.126247	0.64402	N	0.000001	T	0.03305	0.0096	N	0.05351	-0.065	0.42460	D	0.992783	B	0.02656	0.0	B	0.06405	0.002	T	0.44802	-0.9304	10	0.06625	T	0.88	-8.6246	9.0857	0.36579	0.771:0.0:0.229:0.0	.	142	Q9HCK5	AGO4_HUMAN	S	142	ENSP00000362306:N142S	ENSP00000362306:N142S	N	+	2	0	EIF2C4	36063619	0.994000	0.37717	0.999000	0.59377	0.992000	0.81027	0.670000	0.25157	-0.013000	0.14199	0.533000	0.62120	AAT	.	.		0.443	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629		G	36291032	A	G	36291032	3	3	89	1	0	0	0	0	1	0	0	0	5010	101	4	2	439	2	EIF2C4	1	36291032	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10		36291032	212959589	1	11825										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109795619	109795619	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tgaggtctttcagctggacaTcttctccggggagctgacag	13	10	4	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:109795619T>C	ENST00000271332.3	+	1	2979	c.2918T>C	c.(2917-2919)aTc>aCc	p.I973T		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	973	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CAGCTGGACATCTTCTCCGGG	0.597																																					p.I973T	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.T2918C						.						113	102	105					1																	109795619		2203	4300	6503	SO:0001583	missense	1952	exon1			TGGACATCTTCTC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.2918T>C	chr1.hg19:g.109795619T>C	ENSP00000271332:p.Ile973Thr	37.0	0.0		95.0	42.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	N	9.247	1.039869	0.19669	.	.	ENSG00000143126	ENST00000271332	T	0.44482	0.92	4.92	4.92	0.64577	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.22044	0.0531	N	0.03000	-0.44	0.43448	D	0.995637	D	0.56521	0.976	D	0.65140	0.932	T	0.21314	-1.0249	9	0.12766	T	0.61	.	14.7889	0.69824	0.0:0.0:0.0:1.0	.	973	Q9HCU4	CELR2_HUMAN	T	973	ENSP00000271332:I973T	ENSP00000271332:I973T	I	+	2	0	CELSR2	109597142	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.982000	0.70532	2.095000	0.63458	0.529000	0.55759	ATC	.	.		0.597	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		C	109795619	T	C	109795619	3	2	89	1	0	0	0	0	1	0	0	0	3224	1435	50	2	2920	2	CELSR2	1	109795619	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	73504587	109795619	139455002	2	11826										
ZNF687	57592	hgsc.bcm.edu	37	chr1	151260007	151260007	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	agaacgccagtactgccatgCtgatggcagccagtgtggct	13	11	0	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:151260007C>T	ENST00000368879.2	+	2	1338	c.1240C>T	c.(1240-1242)Ctg>Ttg	p.L414L		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TACTGCCATGCTGATGGCAGC	0.597																																					p.L414L		Atlas-SNP	.											.	ZNF687	94	.	0			c.C1240T						.						45	42	43					1																	151260007		2203	4300	6503	SO:0001819	synonymous_variant	57592	exon2			GCCATGCTGATGG		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.1240C>T	chr1.hg19:g.151260007C>T		19.0	0.0		71.0	26.0	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Silent	SNP	ENST00000368879.2	hg19																																																																																				.	.		0.597	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		T	151260007	C	T	151260007	2	4	89	1	0	0	0	0	0	0	0	1	18107	796	28	3		3	ZNF687	1	151260007	Silent	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	41464388	151260007	97990614	3	11827										
CGN	57530	hgsc.bcm.edu	37	chr1	151499552	151499552	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gcaggcccgagctagtgctgGagatactcgccaggttgagg	16	10	0	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:151499552G>T	ENST00000271636.7	+	10	1998	c.1865G>T	c.(1864-1866)gGa>gTa	p.G622V	SNORA44_ENST00000517031.1_RNA	NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	616	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCTAGTGCTGGAGATACTCGC	0.542																																					p.G622V		Atlas-SNP	.											.	CGN	106	.	0			c.G1865T						.						117	107	111					1																	151499552		2203	4300	6503	SO:0001583	missense	57530	exon10			GTGCTGGAGATAC	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.1865G>T	chr1.hg19:g.151499552G>T	ENSP00000271636:p.Gly622Val	83.0	0.0		228.0	79.0	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	hg19	CCDS999.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.309784	0.23821	.	.	ENSG00000143375	ENST00000271636	T	0.62364	0.03	5.54	3.27	0.37495	.	0.748757	0.13601	N	0.375871	T	0.24431	0.0592	N	0.25647	0.755	0.27275	N	0.958263	B	0.10296	0.003	B	0.09377	0.004	T	0.07986	-1.0744	10	0.31617	T	0.26	-1.8441	5.9002	0.18962	0.1227:0.4023:0.4749:0.0	.	616	Q9P2M7	CING_HUMAN	V	622	ENSP00000271636:G622V	ENSP00000271636:G622V	G	+	2	0	CGN	149766176	0.766000	0.28496	0.614000	0.29051	0.983000	0.72400	0.482000	0.22276	1.457000	0.47850	0.650000	0.86243	GGA	.	.		0.542	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		T	151499552	G	T	151499552	3	4	89	1	0	0	0	0	1	0	0	0	3305	1174	41	3	1899	3	CGN	1	151499552	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	239545	151499552	97751069	4	11828										
DCST2	127579	hgsc.bcm.edu	37	chr1	155003099	155003099	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aactcaaactcctgacgcacCcggttgagcaactgaatcac	7	14	2	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:155003099C>A	ENST00000368424.3	-	6	886	c.828G>T	c.(826-828)cgG>cgT	p.R276R	DCST2_ENST00000295536.5_Silent_p.R276R	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	276						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CCTGACGCACCCGGTTGAGCA	0.617																																					p.R276R		Atlas-SNP	.											.	DCST2	80	.	0			c.G828T						.						66	47	54					1																	155003099		2203	4300	6503	SO:0001819	synonymous_variant	127579	exon6			ACGCACCCGGTTG	AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.828G>T	chr1.hg19:g.155003099C>A		67.0	0.0		253.0	94.0	NM_144622	Q2M2R2|Q8N810|Q96M03	Silent	SNP	ENST00000368424.3	hg19	CCDS1082.2																																																																																			.	.		0.617	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622		A	155003099	C	A	155003099	2	1	89	1	0	0	0	0	0	0	0	1	4305	610	22	3		3	DCST2	1	155003099	Silent	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	3503547	155003099	94247522	5	11829										
SMG5	23381	hgsc.bcm.edu	37	chr1	156220788	156220788	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ctaggatcttatagagagtcCtggggatggggggcagaggg	19	5	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:156220788C>A	ENST00000361813.5	-	21	2973		c.e21-1		PAQR6_ENST00000368270.1_5'Flank|PAQR6_ENST00000335852.1_5'Flank|PAQR6_ENST00000540423.1_5'Flank|PAQR6_ENST00000356983.2_5'Flank|PAQR6_ENST00000292291.5_5'Flank|SMG5_ENST00000368267.5_Intron|PAQR6_ENST00000492619.1_5'Flank	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor						gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	48	Hepatocellular(266;0.158)					ATAGAGAGTCCTGGGGATGGG	0.612																																					.		Atlas-SNP	.											.	SMG5	98	.	0			c.2829-1G>T						.						46	51	49					1																	156220788		2203	4300	6503	SO:0001630	splice_region_variant	23381	exon22			AGAGTCCTGGGGA	AB029012	CCDS1137.1	1q21	2013-07-02	2013-07-02		ENSG00000198952	ENSG00000198952			24644	protein-coding gene	gene with protein product	"EST1 telomerase component homolog B (S. cerevisiae)"	610962	"smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)"			12676087, 12699629	Standard	NM_015327		Approved	KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B	uc001foc.4	Q9UPR3	OTTHUMG00000017491	ENST00000361813.5:c.2829-1G>T	chr1.hg19:g.156220788C>A		22.0	0.0		58.0	31.0	NM_015327	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Splice_Site	SNP	ENST00000361813.5	hg19	CCDS1137.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.437754	0.62955	.	.	ENSG00000198952	ENST00000361813;ENST00000420555	.	.	.	4.19	4.19	0.49359	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.641	0.77001	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SMG5	154487412	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	7.028000	0.76470	2.359000	0.80004	0.655000	0.94253	.	.	.		0.612	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327	Intron	A	156220788	C	A	156220788	5	1	89	1	0	0	0	0	0	0	1	0	14811	695	24	3	230	3	SMG5	1	156220788	Splice_Site	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	1217689	156220788	93029833	6	11830										
FMO1	2326	hgsc.bcm.edu	37	chr1	171251160	171251160	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	taaatgatgagctcccaggaCgcatcatcactgggaaagtg	11	9	2	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:171251160C>T	ENST00000354841.4	+	6	1002	c.871C>T	c.(871-873)Cgc>Tgc	p.R291C	FMO1_ENST00000367750.3_Missense_Mutation_p.R291C|FMO1_ENST00000469112.1_3'UTR|FMO1_ENST00000402921.2_Missense_Mutation_p.R228C	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	291					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.R291C(2)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	GCTCCCAGGACGCATCATCAC	0.418																																					p.R291C		Atlas-SNP	.											FMO1,colon,carcinoma,0,2	FMO1	79	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C871T						.						75	69	71					1																	171251160		2203	4300	6503	SO:0001583	missense	2326	exon7			CCAGGACGCATCA	M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.871C>T	chr1.hg19:g.171251160C>T	ENSP00000346901:p.Arg291Cys	39.0	0.0		37.0	7.0	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Missense_Mutation	SNP	ENST00000354841.4	hg19	CCDS1294.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.348608	0.24426	.	.	ENSG00000010932	ENST00000367750;ENST00000402921;ENST00000354841	T;T;T	0.55413	0.52;0.52;0.52	5.81	-0.52	0.11935	.	0.108962	0.64402	N	0.000005	T	0.29126	0.0724	L	0.56769	1.78	0.19775	N	0.999951	B;B;B	0.33857	0.429;0.178;0.113	B;B;B	0.39738	0.14;0.308;0.099	T	0.35773	-0.9775	10	0.29301	T	0.29	-6.6858	10.3213	0.43767	0.0:0.4836:0.0:0.5164	.	228;291;291	B7Z3P4;B2RCG5;Q01740	.;.;FMO1_HUMAN	C	291;228;291	ENSP00000356724:R291C;ENSP00000385543:R228C;ENSP00000346901:R291C	ENSP00000346901:R291C	R	+	1	0	FMO1	169517784	0.000000	0.05858	0.933000	0.37362	0.769000	0.43574	-0.086000	0.11233	-0.118000	0.11851	0.555000	0.69702	CGC	.	.		0.418	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021		T	171251160	C	T	171251160	3	4	89	1	0	0	0	0	1	0	0	0	5962	536	19	1	893	1	FMO1	1	171251160	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	15030372	171251160	77999461	7	11831										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181548355	181548355	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tcgagcatgcttcatgaacaAttcaggtagggtcgttcttt	10	8	3	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:181548355A>T	ENST00000367573.2	+	5	764	c.764A>T	c.(763-765)aAt>aTt	p.N255I	CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000357570.5_Missense_Mutation_p.N206I|CACNA1E_ENST00000367570.1_Missense_Mutation_p.N255I|CACNA1E_ENST00000526775.1_Missense_Mutation_p.N255I|CACNA1E_ENST00000360108.3_Missense_Mutation_p.N255I|CACNA1E_ENST00000358338.5_Missense_Mutation_p.N206I	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	255					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TTCATGAACAATTCAGGTAGG	0.453																																					p.N255I		Atlas-SNP	.											.	CACNA1E	778	.	0			c.A764T						.						303	277	285					1																	181548355		1934	4151	6085	SO:0001583	missense	777	exon5			TGAACAATTCAGG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.764A>T	chr1.hg19:g.181548355A>T	ENSP00000356545:p.Asn255Ile	113.0	0.0		545.0	189.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.570357	0.45798	.	.	ENSG00000198216	ENST00000524607;ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.97430	-4.38;-4.0;-3.99;-4.01;-3.99;-3.99;-4.0	4.88	4.88	0.63580	.	11.845600	0.00166	N	0.000006	D	0.95370	0.8497	L	0.33245	0.995	0.80722	D	1	B;B	0.14012	0.009;0.009	B;B	0.15484	0.013;0.013	T	0.72626	-0.4236	10	0.33141	T	0.24	.	14.4515	0.67389	1.0:0.0:0.0:0.0	.	255;255	Q15878-2;Q15878-3	.;.	I	255;255;255;206;206;255;255	ENSP00000432038:N255I;ENSP00000356542:N255I;ENSP00000434814:N255I;ENSP00000350183:N206I;ENSP00000351101:N206I;ENSP00000353222:N255I;ENSP00000356545:N255I	ENSP00000350183:N206I	N	+	2	0	CACNA1E	179814978	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.016000	0.49607	1.951000	0.56629	0.459000	0.35465	AAT	.	.		0.453	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181548355	A	T	181548355	3	4	89	1	0	0	0	0	1	0	0	0	2544	101	4	4	782	4	CACNA1E	1	181548355	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	10297195	181548355	67702266	8	11832										
PIGR	5284	hgsc.bcm.edu	37	chr1	207110487	207110487	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggataggcgagccttcctgcAgctgaccatccgaatgggct	13	12	0	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:207110487A>G	ENST00000356495.4	-	4	1181	c.998T>C	c.(997-999)cTg>cCg	p.L333P		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	333	Ig-like V-type 3.				detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GCCTTCCTGCAGCTGACCATC	0.597																																					p.L333P		Atlas-SNP	.											.	PIGR	98	.	0			c.T998C						.						70	60	63					1																	207110487		2203	4300	6503	SO:0001583	missense	5284	exon4			TCCTGCAGCTGAC		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.998T>C	chr1.hg19:g.207110487A>G	ENSP00000348888:p.Leu333Pro	53.0	0.0		112.0	30.0	NM_002644	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	hg19	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	A	4.224	0.040357	0.08148	.	.	ENSG00000162896	ENST00000356495	T	0.15372	2.43	5.52	0.96	0.19631	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.793165	0.11491	N	0.558714	T	0.04452	0.0122	N	0.00972	-1.085	0.09310	N	0.999999	B	0.06786	0.001	B	0.04013	0.001	T	0.38542	-0.9656	10	0.30078	T	0.28	-33.0436	2.8831	0.05654	0.3868:0.0:0.4222:0.191	.	333	P01833	PIGR_HUMAN	P	333	ENSP00000348888:L333P	ENSP00000348888:L333P	L	-	2	0	PIGR	205177110	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.286000	0.08399	0.179000	0.19938	0.528000	0.53228	CTG	.	.		0.597	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		G	207110487	A	G	207110487	3	3	89	1	0	0	0	0	1	0	0	0	11906	188	7	2	1328	2	PIGR	1	207110487	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	25562132	207110487	42140134	9	11833										
INTS7	25896	hgsc.bcm.edu	37	chr1	212184718	212184718	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ctaaatgaagaatacataccTtgaatcatttcactgatttt	4	7	2	4			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:212184718T>C	ENST00000366994.3	-	5	659	c.555A>G	c.(553-555)caA>caG	p.Q185Q	INTS7_ENST00000366992.3_Splice_Site_p.Q185Q|INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000440600.2_Splice_Site_p.Q136Q|INTS7_ENST00000366993.3_Splice_Site_p.Q185Q	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	185					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		AATACATACCTTGAATCATTT	0.274																																					p.Q185Q		Atlas-SNP	.											.	INTS7	68	.	0			c.A555G						.						46	47	47					1																	212184718		2201	4296	6497	SO:0001630	splice_region_variant	25896	exon5			CATACCTTGAATC	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.556+1A>G	chr1.hg19:g.212184718T>C		153.0	0.0		559.0	39.0	NM_015434	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Silent	SNP	ENST00000366994.3	hg19	CCDS1501.1																																																																																			.	.		0.274	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434	Silent	C	212184718	T	C	212184718	5	2	89	1	0	0	0	0	0	0	1	0	7792	1623	56	2	2397	2	INTS7	1	212184718	Splice_Site	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	5074231	212184718	37065903	10	11834										
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220356254	220356254	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gcagttctttttcatcaagcCttagtaacagagccaagtcc	7	11	3	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr1:220356254C>G	ENST00000358951.2	-	20	2134	c.2018G>C	c.(2017-2019)aGg>aCg	p.R673T		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	673					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		TTCATCAAGCCTTAGTAACAG	0.363																																					p.R673T		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.G2018C						.						67	65	66					1																	220356254		2203	4300	6503	SO:0001583	missense	25782	exon20			TCAAGCCTTAGTA	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.2018G>C	chr1.hg19:g.220356254C>G	ENSP00000351832:p.Arg673Thr	103.0	0.0		373.0	116.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	hg19	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.901431	0.33535	.	.	ENSG00000118873	ENST00000358951	T	0.31247	1.5	5.67	2.81	0.32909	.	0.256963	0.43747	D	0.000536	T	0.22975	0.0555	L	0.40543	1.245	0.32568	N	0.530193	B	0.30361	0.277	B	0.29942	0.109	T	0.23762	-1.0179	10	0.21014	T	0.42	.	10.9519	0.47334	0.0:0.7976:0.0:0.2024	.	673	Q9H2M9	RBGPR_HUMAN	T	673	ENSP00000351832:R673T	ENSP00000351832:R673T	R	-	2	0	RAB3GAP2	218422877	0.372000	0.25064	0.997000	0.53966	0.990000	0.78478	1.597000	0.36729	0.346000	0.23899	-0.225000	0.12378	AGG	.	.		0.363	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		G	220356254	C	G	220356254	3	3	89	1	0	0	0	0	1	0	0	0	12951	681	24	4	2227	4	RAB3GAP2	1	220356254	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	8171536	220356254	28894367	11	11835										
HS1BP3	64342	hgsc.bcm.edu	37	chr2	20818851	20818852	+	Frame_Shift_Ins	INS	-	-	C													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tgctcctgcggcttctgctgINScccagccacagcttcagccg							TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr2:20818851_20818852insC	ENST00000304031.3	-	7	1099_1100	c.1074_1075insG	c.(1072-1077)gggcagfs	p.Q359fs		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	359							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCTTCTGCTGCCCAGCCACAG	0.619																																					p.Q359fs		Atlas-INDEL	.											.	HS1BP3	33	.	0			c.1075_1076insG						.																																			SO:0001589	frameshift_variant	64342	exon7			.		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.1075dupG	chr2.hg19:g.20818854_20818854dupC	ENSP00000305193:p.Gln359fs	35.0	0.0		137.0	10.0	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Frame_Shift_Ins	INS	ENST00000304031.3	hg19	CCDS1700.1																																																																																			.	.		0.619	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460		C	20818852	-	C	20818851	7	5	89	1	0	1	1	0	0	0	0	0	7370	1328	46	0	107	0	HS1BP3	2	20818851	Frame_Shift_Ins	INS	-	TCGA-DD-A116-01A-11D-A12Z-10		20818851	222380522	12	11836										
ANAPC1	64682	hgsc.bcm.edu	37	chr2	112537964	112537965	+	Splice_Site	INS	-	-	A													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tgctgagattgtttctggctINSaaaaaaacaaacaaccacaa							TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr2:112537964_112537965insA	ENST00000341068.3	-	44	5975		c.e44-2			NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						TGTTTCTGGCTAAAAAAACAAA	0.366																																					.		Atlas-INDEL	.											.	ANAPC1	116	.	0			c.5203-2->T						.																																			SO:0001630	splice_region_variant	64682	exon45			.	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"Anaphase promoting complex subunits"	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.5203-2->T	chr2.hg19:g.112537971_112537971dupA		151.0	0.0		801.0	144.0	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Splice_Site	INS	ENST00000341068.3	hg19	CCDS2093.1																																																																																			.	.		0.366	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	Intron	A	112537965	-	A	112537964	8	5	89	1	0	1	1	0	0	0	1	0	598	1536	53	0	653	0	ANAPC1	2	112537964	Splice_Site	INS	-	TCGA-DD-A116-01A-11D-A12Z-10	91719113	112537964	130661409	13	11837										
SCTR	6344	hgsc.bcm.edu	37	chr2	120197740	120197741	+	Frame_Shift_Ins	INS	-	-	G													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tggctctgctccaagtggctINSggccttggtgctgttgctga							TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr2:120197740_120197741insG	ENST00000019103.5	-	13	1542_1543	c.1275_1276insC	c.(1273-1278)gccagcfs	p.S426fs		NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor	426					digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	TCCAAGTGGCTGGCCTTGGTGC	0.629																																					p.S426fs		Atlas-INDEL	.											.	SCTR	45	.	0			c.1276_1277insC						.																																			SO:0001589	frameshift_variant	6344	exon13			.		CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"GPCR / Class B : Glucagon receptors"	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407	ENST00000019103.5:c.1276dupC	chr2.hg19:g.120197742_120197742dupG	ENSP00000019103:p.Ser426fs	42.0	0.0		131.0	10.0	NM_002980	Q12961|Q13213|Q53T00	Frame_Shift_Ins	INS	ENST00000019103.5	hg19	CCDS2127.1																																																																																			.	.		0.629	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			G	120197741	-	G	120197740	7	5	89	1	0	1	1	0	0	0	0	0	13958	1580	55	0	50	0	SCTR	2	120197740	Frame_Shift_Ins	INS	-	TCGA-DD-A116-01A-11D-A12Z-10	7659776	120197740	123001633	14	11838										
BIN1	274	hgsc.bcm.edu	37	chr2	127821169	127821169	+	Frame_Shift_Del	DEL	T	T	-													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tgctcatctccttgtggaagTtttcctccaggcccgcgatg							TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr2:127821169delT	ENST00000316724.5	-	9	1163	c.752delA	c.(751-753)aacfs	p.N251fs	BIN1_ENST00000376113.2_Frame_Shift_Del_p.N220fs|BIN1_ENST00000409400.1_Frame_Shift_Del_p.N220fs|BIN1_ENST00000348750.4_Frame_Shift_Del_p.N220fs|BIN1_ENST00000346226.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000466111.1_5'UTR|BIN1_ENST00000393040.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000357970.3_Frame_Shift_Del_p.N251fs|BIN1_ENST00000352848.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000259238.4_Frame_Shift_Del_p.N220fs|BIN1_ENST00000351659.3_Frame_Shift_Del_p.N251fs|BIN1_ENST00000393041.3_Frame_Shift_Del_p.N220fs	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	251	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CTTGTGGAAGTTTTCCTCCAG	0.632																																					p.N251fs		Atlas-Indel,Pindel	.											.	BIN1	85	.	0			c.753delC						.						94	70	78					2																	127821169		2203	4300	6503	SO:0001589	frameshift_variant	274	exon9			.	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"amphiphysin II"	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.752delA	chr2.hg19:g.127821169delT	ENSP00000316779:p.Asn251fs	54.0	0.0		150.0	52.0	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Frame_Shift_Del	DEL	ENST00000316724.5	hg19	CCDS2138.1																																																																																			.	.		0.632	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		-	127821169	T	-	127821169	7	5	89	1	0	1	0	1	0	0	0	0	1432	1725	60	0	1122	0	BIN1	2	127821169	Frame_Shift_Del	DEL	T	TCGA-DD-A116-01A-11D-A12Z-10	7623429	127821169	115378204	15	11839										
ACVR1	90	hgsc.bcm.edu	37	chr2	158637001	158637001	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggtagacgtggaagccatcgTtgatgctcagtgaggaaaag	15	6	1	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr2:158637001T>C	ENST00000263640.3	-	4	608	c.179A>G	c.(178-180)aAc>aGc	p.N60S	ACVR1_ENST00000409283.2_Missense_Mutation_p.N60S|ACVR1_ENST00000434821.1_Missense_Mutation_p.N60S|ACVR1_ENST00000410057.2_Missense_Mutation_p.N60S|ACVR1_ENST00000487456.1_5'UTR	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	60					activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	GAAGCCATCGTTGATGCTCAG	0.547																																					p.N60S		Atlas-SNP	.											.	ACVR1	52	.	0			c.A179G						.						117	115	116					2																	158637001		2203	4300	6503	SO:0001583	missense	90	exon4			CCATCGTTGATGC		CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.179A>G	chr2.hg19:g.158637001T>C	ENSP00000263640:p.Asn60Ser	43.0	0.0		163.0	61.0	NM_001105		Missense_Mutation	SNP	ENST00000263640.3	hg19	CCDS2206.1	.	.	.	.	.	.	.	.	.	.	T	12.73	2.024122	0.35701	.	.	ENSG00000115170	ENST00000263640;ENST00000409283;ENST00000434821;ENST00000410057;ENST00000412025;ENST00000440523;ENST00000539637;ENST00000424669	D;D;D;D;D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88	5.26	5.26	0.73747	TGF-beta receptor/activin receptor, type I/II (1);	0.044226	0.85682	D	0.000000	T	0.82029	0.4948	N	0.05230	-0.09	0.45366	D	0.998355	B	0.06786	0.001	B	0.14023	0.01	T	0.77230	-0.2664	10	0.13108	T	0.6	.	14.8539	0.70319	0.0:0.0:0.0:1.0	.	60	Q04771	ACVR1_HUMAN	S	60	ENSP00000263640:N60S;ENSP00000387273:N60S;ENSP00000405004:N60S;ENSP00000387127:N60S;ENSP00000403006:N60S;ENSP00000401189:N60S;ENSP00000440091:N60S;ENSP00000400767:N60S	ENSP00000263640:N60S	N	-	2	0	ACVR1	158345247	1.000000	0.71417	0.935000	0.37517	0.984000	0.73092	4.833000	0.62766	1.990000	0.58119	0.533000	0.62120	AAC	.	.		0.547	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105		C	158637001	T	C	158637001	3	2	89	1	0	0	0	0	1	0	0	0	220	1725	60	2	1382	2	ACVR1	2	158637001	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	30815832	158637001	84562372	16	11840										
HECW2	57520	hgsc.bcm.edu	37	chr2	197084796	197084796	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tgtgttgtttctccaatcacTtaggtctatttcagctgtgc	8	9	4	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr2:197084796T>C	ENST00000260983.3	-	26	4557	c.4375A>G	c.(4375-4377)Agt>Ggt	p.S1459G	HECW2_ENST00000409111.1_Missense_Mutation_p.S1103G	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1459	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						CTCCAATCACTTAGGTCTATT	0.393																																					p.S1459G		Atlas-SNP	.											.	HECW2	239	.	0			c.A4375G						.						130	127	128					2																	197084796		2203	4300	6503	SO:0001583	missense	57520	exon26			AATCACTTAGGTC	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.4375A>G	chr2.hg19:g.197084796T>C	ENSP00000260983:p.Ser1459Gly	56.0	0.0		120.0	38.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.121861	0.37436	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	T;T	0.42513	0.97;0.97	5.25	5.25	0.73442	HECT (4);	0.203518	0.53938	D	0.000053	T	0.36303	0.0962	L	0.37800	1.135	0.28399	N	0.918746	B	0.12013	0.005	B	0.10450	0.005	T	0.33445	-0.9868	10	0.56958	D	0.05	.	15.3174	0.74092	0.0:0.0:0.0:1.0	.	1459	Q9P2P5	HECW2_HUMAN	G	1103;1459	ENSP00000386775:S1103G;ENSP00000260983:S1459G	ENSP00000260983:S1459G	S	-	1	0	HECW2	196793041	0.897000	0.30589	0.989000	0.46669	0.991000	0.79684	1.394000	0.34509	2.199000	0.70637	0.533000	0.62120	AGT	.	.		0.393	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		C	197084796	T	C	197084796	3	2	89	1	0	0	0	0	1	0	0	0	7052	1609	56	2	359	2	HECW2	2	197084796	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	38447795	197084796	46114577	17	11841										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9027370	9027370	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ctgggcgccagccaggcgggCggacagggctggcttgaagg	20	11	0	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr3:9027370C>T	ENST00000383836.3	-	22	3560	c.3133G>A	c.(3133-3135)Gcc>Acc	p.A1045T	SRGAP3_ENST00000360413.3_Missense_Mutation_p.A1021T	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	1045					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GCCAGGCGGGCGGACAGGGCT	0.726			T	RAF1	pilocytic astrocytoma																																p.A1045T		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.G3133A						.						16	20	19					3																	9027370		2172	4264	6436	SO:0001583	missense	9901	exon22			GGCGGGCGGACAG	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.3133G>A	chr3.hg19:g.9027370C>T	ENSP00000373347:p.Ala1045Thr	2.0	0.0		31.0	16.0	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.055039	0.55325	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.24908	1.83;2.24	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.21590	0.0520	N	0.17082	0.46	0.80722	D	1	D;D	0.56746	0.977;0.961	P;B	0.45195	0.473;0.281	T	0.02505	-1.1149	10	0.38643	T	0.18	.	18.1454	0.89653	0.0:1.0:0.0:0.0	.	1021;1045	O43295-2;O43295	.;SRGP2_HUMAN	T	1045;1021	ENSP00000373347:A1045T;ENSP00000353587:A1021T	ENSP00000353587:A1021T	A	-	1	0	SRGAP3	9002370	1.000000	0.71417	0.991000	0.47740	0.985000	0.73830	5.825000	0.69286	2.369000	0.80426	0.591000	0.81541	GCC	.	.		0.726	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			T	9027370	C	T	9027370	3	4	89	1	0	0	0	0	1	0	0	0	15162	768	27	1	170	1	SRGAP3	3	9027370	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10		9027370	188995060	18	11842										
ZFYVE20	64145	hgsc.bcm.edu	37	chr3	15115343	15115343	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tgcttcagctcccgcagattCtctgtcagcacctctacctc	6	17	4	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr3:15115343C>A	ENST00000253699.3	-	14	2914	c.2301G>T	c.(2299-2301)gaG>gaT	p.E767D	ZFYVE20_ENST00000476527.2_Missense_Mutation_p.E767D	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	767	Necessary for the interaction with EHD1.|Necessary for the interaction with RAB5A.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						CCCGCAGATTCTCTGTCAGCA	0.592																																					p.E767D		Atlas-SNP	.											.	ZFYVE20	61	.	0			c.G2301T						.						69	64	66					3																	15115343		2203	4300	6503	SO:0001583	missense	64145	exon14			CAGATTCTCTGTC	AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"Zinc fingers, FYVE domain containing"	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.2301G>T	chr3.hg19:g.15115343C>A	ENSP00000253699:p.Glu767Asp	50.0	0.0		143.0	56.0	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Missense_Mutation	SNP	ENST00000253699.3	hg19	CCDS2623.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.539092	0.45176	.	.	ENSG00000131381	ENST00000253699;ENST00000476527	T;T	0.47177	0.85;0.85	5.49	2.74	0.32292	.	0.151633	0.56097	D	0.000025	T	0.45577	0.1349	L	0.38838	1.175	0.80722	D	1	P	0.50819	0.939	P	0.51453	0.67	T	0.41822	-0.9487	10	0.72032	D	0.01	-15.3114	9.4222	0.38559	0.0:0.7149:0.0:0.2851	.	767	Q9H1K0	RBNS5_HUMAN	D	767	ENSP00000253699:E767D;ENSP00000422551:E767D	ENSP00000253699:E767D	E	-	3	2	ZFYVE20	15090347	0.999000	0.42202	0.997000	0.53966	0.956000	0.61745	0.732000	0.26072	0.685000	0.31468	-0.216000	0.12614	GAG	.	.		0.592	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		A	15115343	C	A	15115343	3	1	89	1	0	0	0	0	1	0	0	0	17681	912	32	3	57	3	ZFYVE20	3	15115343	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	6087973	15115343	182907087	19	11843										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266100	41266100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	agcaacagtcttacctggacTctggaatccattctggtgcc	9	12	3	0	rs121913416		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr3:41266100T>C	ENST00000349496.5	+	3	377	c.97T>C	c.(97-99)Tct>Cct	p.S33P	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.S33P(47)|p.S33A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.W25_D32del(4)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.D32_S33insS(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.S33T(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TTACCTGGACTCTGGAATCCA	0.488		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	212	Deletion - In frame(115)|Substitution - Missense(70)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Insertion - In frame(1)	liver(130)|large_intestine(20)|endometrium(14)|stomach(10)|pituitary(9)|pancreas(9)|central_nervous_system(8)|adrenal_gland(2)|small_intestine(2)|biliary_tract(2)|skin(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|breast(1)	c.T97C						.						93	77	82					3																	41266100		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTGGACTCTGGAA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.97T>C	chr3.hg19:g.41266100T>C	ENSP00000344456:p.Ser33Pro	91.0	1.0		223.0	71.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.395782	0.83011	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70281	0.3206	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74509	-0.3642	10	0.87932	D	0	-10.7796	16.0677	0.80897	0.0:0.0:0.0:1.0	.	33	P35222	CTNB1_HUMAN	P	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26P;ENSP00000385604:S33P;ENSP00000412219:S33P;ENSP00000379486:S33P;ENSP00000344456:S33P;ENSP00000411226:S26P;ENSP00000379488:S33P;ENSP00000409302:S33P;ENSP00000401599:S33P	ENSP00000344456:S33P	S	+	1	0	CTNNB1	41241104	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266100	T	C	41266100	3	2	89	1	0	0	0	0	1	0	0	0	4018	1551	54	2	103	2	CTNNB1	3	41266100	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	26150757	41266100	156756330	20	11844										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52588770	52588770	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gatgcccgggaggccaggcaCacctggcggaagatggtggg	19	10	0	1	rs143564112	byFrequency	TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr3:52588770C>A	ENST00000296302.7	-	27	4580	c.4579G>T	c.(4579-4581)Gtg>Ttg	p.V1527L	SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409057.1_Missense_Mutation_p.V1472L|PBRM1_ENST00000356770.4_Missense_Mutation_p.V1440L|RNU6-856P_ENST00000516959.1_RNA|PBRM1_ENST00000337303.4_Intron|PBRM1_ENST00000409114.3_Intron|PBRM1_ENST00000394830.3_Missense_Mutation_p.V1420L|PBRM1_ENST00000409767.1_Intron|PBRM1_ENST00000410007.1_Missense_Mutation_p.V1447L			Q86U86	PB1_HUMAN	polybromo 1	1527	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AGGCCAGGCACACCTGGCGGA	0.557			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.V1420L		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	PBRM1_ENST00000356770,NS,lymphoid_neoplasm,0,1	PBRM1	1252	.	0			c.G4258T						.						45	44	45					3																	52588770		2203	4300	6503	SO:0001583	missense	55193	exon27			CAGGCACACCTGG	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4579G>T	chr3.hg19:g.52588770C>A	ENSP00000296302:p.Val1527Leu	69.0	0.0		229.0	83.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	C	13.52	2.262476	0.39995	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000409057;ENST00000410007	T;T;T;T;T	0.33216	1.42;1.42;1.46;1.43;1.42	5.62	3.58	0.41010	.	0.353225	0.30850	N	0.008759	T	0.13884	0.0336	N	0.08118	0	0.80722	D	1	B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001	B;B;B;B;B	0.17722	0.005;0.003;0.005;0.001;0.019	T	0.06516	-1.0822	10	0.49607	T	0.09	-7.5268	4.2397	0.10642	0.0:0.6107:0.0:0.3893	.	1447;1420;1472;1527;1440	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86;Q86U86-3	.;.;.;PB1_HUMAN;.	L	1440;1420;1527;1472;1447	ENSP00000349213:V1440L;ENSP00000378307:V1420L;ENSP00000296302:V1527L;ENSP00000386593:V1472L;ENSP00000386529:V1447L	ENSP00000296302:V1527L	V	-	1	0	PBRM1	52563810	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.917000	0.56424	1.348000	0.45733	0.563000	0.77884	GTG	.	C|0.999;T|0.001		0.557	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		A	52588770	C	A	52588770	3	1	89	1	0	0	0	0	1	0	0	0	11500	478	17	3	506	3	PBRM1	3	52588770	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	11322670	52588770	145433660	21	11845										
RETNLB	84666	hgsc.bcm.edu	37	chr3	108474715	108474716	+	Frame_Shift_Ins	INS	-	-	C													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gctgaacatcccacgaaccaINScagccatagccacaagcaca							TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr3:108474715_108474716insC	ENST00000295755.6	-	3	443_444	c.245_246insG	c.(244-246)tgtfs	p.C82fs	RETNLB_ENST00000482939.1_Intron	NM_032579.2	NP_115968.1	Q9BQ08	RETNB_HUMAN	resistin like beta	82					cell proliferation (GO:0008283)	extracellular region (GO:0005576)				endometrium(1)|kidney(3)|lung(10)|prostate(1)|skin(1)	16						CCCACGAACCACAGCCATAGCC	0.579																																					p.C82fs		Atlas-INDEL	.											.	RETNLB	38	.	0			c.246_247insG						.																																			SO:0001589	frameshift_variant	84666	exon3			.	AF290873	CCDS2953.1	3q13.1	2008-02-05			ENSG00000163515	ENSG00000163515			20388	protein-coding gene	gene with protein product		605645				10921885, 12574343	Standard	NM_032579		Approved	HXCP2, FIZZ2, RELMb	uc003dxh.2	Q9BQ08	OTTHUMG00000159393	ENST00000295755.6:c.246dupG	chr3.hg19:g.108474716_108474716dupC	ENSP00000295755:p.Cys82fs	57.0	0.0		375.0	30.0	NM_032579	Q14D27	Frame_Shift_Ins	INS	ENST00000295755.6	hg19	CCDS2953.1																																																																																			.	.		0.579	RETNLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355093.1			C	108474716	-	C	108474715	7	5	89	1	0	1	1	0	0	0	0	0	13252	157	6	0	93	0	RETNLB	3	108474715	Frame_Shift_Ins	INS	-	TCGA-DD-A116-01A-11D-A12Z-10	55885945	108474715	89547715	22	11846										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130286897	130286897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tttttcctatgcagcttgcaAagagatgaaagctgacatca	8	8	1	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr3:130286897A>G	ENST00000358511.6	+	5	1881	c.1850A>G	c.(1849-1851)aAa>aGa	p.K617R	COL6A6_ENST00000453409.2_Missense_Mutation_p.K617R	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	617	Nonhelical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GCAGCTTGCAAAGAGATGAAA	0.343																																					p.K617R		Atlas-SNP	.											.	COL6A6	497	.	0			c.A1850G						.						50	48	49					3																	130286897		1828	4101	5929	SO:0001583	missense	131873	exon5			CTTGCAAAGAGAT	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1850A>G	chr3.hg19:g.130286897A>G	ENSP00000351310:p.Lys617Arg	50.0	0.0		121.0	45.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	A	8.783	0.928789	0.18131	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.78246	-1.16;-1.16	5.32	0.312	0.15837	.	0.095602	0.45867	N	0.000322	T	0.57417	0.2052	N	0.20304	0.555	0.25997	N	0.982165	B	0.18310	0.027	B	0.15052	0.012	T	0.38866	-0.9641	10	0.19147	T	0.46	.	8.7651	0.34698	0.6943:0.0:0.3057:0.0	.	617	A6NMZ7	CO6A6_HUMAN	R	617	ENSP00000351310:K617R;ENSP00000399236:K617R	ENSP00000351310:K617R	K	+	2	0	COL6A6	131769587	1.000000	0.71417	0.985000	0.45067	0.538000	0.34931	3.306000	0.51881	-0.161000	0.10983	-0.250000	0.11733	AAA	.	.		0.343	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		G	130286897	A	G	130286897	3	3	89	1	0	0	0	0	1	0	0	0	3705	14	1	2	1868	2	COL6A6	3	130286897	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	21812182	130286897	67735533	23	11847										
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184049265	184049265	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ccttttccattgcagaaggtGgagtataccctgggagagga	13	8	0	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr3:184049265G>A	ENST00000346169.2	+	30	4537	c.4266G>A	c.(4264-4266)gtG>gtA	p.V1422V	EIF4G1_ENST00000411531.1_Silent_p.V1383V|EIF4G1_ENST00000441154.1_Silent_p.V1259V|EIF4G1_ENST00000352767.3_Silent_p.V1429V|EIF4G1_ENST00000414031.1_Silent_p.V1382V|EIF4G1_ENST00000382330.3_Silent_p.V1429V|EIF4G1_ENST00000424196.1_Silent_p.V1429V|EIF4G1_ENST00000342981.4_Silent_p.V1423V|EIF4G1_ENST00000319274.6_Silent_p.V1422V|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000350481.5_Silent_p.V1258V|EIF4G1_ENST00000392537.2_Silent_p.V1335V|EIF4G1_ENST00000434061.2_Silent_p.V1227V|EIF4G1_ENST00000427845.1_Silent_p.V1336V|EIF4G1_ENST00000435046.2_Silent_p.V1226V	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1422					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGCAGAAGGTGGAGTATACCC	0.557																																					p.V1429V		Atlas-SNP	.											.	EIF4G1	151	.	0			c.G4287A						.						103	120	114					3																	184049265		2203	4300	6503	SO:0001819	synonymous_variant	1981	exon31			GAAGGTGGAGTAT	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.4266G>A	chr3.hg19:g.184049265G>A		28.0	0.0		68.0	28.0	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	hg19	CCDS3259.1																																																																																			.	.		0.557	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		A	184049265	G	A	184049265	2	1	89	1	0	0	0	0	0	0	0	1	5038	1335	47	3		3	EIF4G1	3	184049265	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	53762368	184049265	13973165	24	11848										
ZDHHC19	131540	hgsc.bcm.edu	37	chr3	195935366	195935366	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	cacagggacaggacaagcagCatgaagaagcggaagttgcg	15	8	0	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr3:195935366C>T	ENST00000296326.3	-	4	553	c.474G>A	c.(472-474)atG>atA	p.M158I	ZDHHC19_ENST00000488508.1_5'UTR	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	158						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		GGACAAGCAGCATGAAGAAGC	0.597																																					p.M158I		Atlas-SNP	.											.	ZDHHC19	25	.	0			c.G474A						.						126	146	139					3																	195935366		2192	4282	6474	SO:0001583	missense	131540	exon4			AAGCAGCATGAAG	BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958		"Zinc fingers, DHHC-type"	20713	protein-coding gene	gene with protein product							Standard	XR_246038		Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.474G>A	chr3.hg19:g.195935366C>T	ENSP00000296326:p.Met158Ile	81.0	0.0		269.0	91.0	NM_001039617	A8MSY6|B3KVI1	Missense_Mutation	SNP	ENST00000296326.3	hg19	CCDS43190.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485295	0.63962	.	.	ENSG00000163958	ENST00000296326	T	0.20881	2.04	5.61	4.68	0.58851	Zinc finger, DHHC-type, palmitoyltransferase (2);	0.368313	0.26635	N	0.023291	T	0.11324	0.0276	N	0.11845	0.185	0.31438	N	0.672257	P	0.35656	0.514	B	0.31016	0.123	T	0.06427	-1.0827	10	0.48119	T	0.1	-23.8633	11.6545	0.51309	0.0:0.8214:0.1786:0.0	.	158	Q8WVZ1	ZDH19_HUMAN	I	158	ENSP00000296326:M158I	ENSP00000296326:M158I	M	-	3	0	ZDHHC19	197419763	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.782000	0.47758	2.638000	0.89438	0.561000	0.74099	ATG	.	.		0.597	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341533.1	NM_144637		T	195935366	C	T	195935366	3	4	89	1	0	0	0	0	1	0	0	0	17624	710	25	3	471	3	ZDHHC19	3	195935366	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	11886101	195935366	2087064	25	11849										
BDH1	622	hgsc.bcm.edu	37	chr3	197238766	197238766	+	Nonstop_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	agaggccacagcgagactctTcagcggatgtagatcatgtc	12	10	3	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr3:197238766T>G	ENST00000392378.2	-	7	1342	c.1032A>C	c.(1030-1032)tgA>tgC	p.*344C	BDH1_ENST00000441275.1_Nonstop_Mutation_p.*257C|BDH1_ENST00000392379.1_Nonstop_Mutation_p.*344C|BDH1_ENST00000358186.2_Nonstop_Mutation_p.*344C	NM_004051.4	NP_004042.1	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1	0					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|response to cadmium ion (GO:0046686)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to growth hormone (GO:0060416)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|phospholipid binding (GO:0005543)			endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)		GCGAGACTCTTCAGCGGATGT	0.552																																					p.X344C		Atlas-SNP	.											.	BDH1	24	.	0			c.A1032C						.						62	61	62					3																	197238766		2203	4300	6503	SO:0001578	stop_lost	622	exon7			GACTCTTCAGCGG	M93107	CCDS3328.1	3q29	2011-09-14	2005-11-15	2005-11-15	ENSG00000161267	ENSG00000161267	1.1.1.30	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	1027	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 9C, member 1"	603063	"3-hydroxybutyrate dehydrogenase (heart, mitochondrial)"	BDH		1639787, 19027726	Standard	XM_005269352		Approved	SDR9C1	uc003fxs.3	Q02338	OTTHUMG00000155478	ENST00000392378.2:c.1032A>C	chr3.hg19:g.197238766T>G	ENSP00000376183:p.*344Trpext*26	60.0	0.0		153.0	51.0	NM_004051	D3DXC0|Q96ET1|Q9BRZ4	Missense_Mutation	SNP	ENST00000392378.2	hg19	CCDS3328.1	.	.	.	.	.	.	.	.	.	.	T	8.121	0.780841	0.16120	.	.	ENSG00000161267	ENST00000392378;ENST00000358186;ENST00000392379;ENST00000441275	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.6685	0.28445	0.0:0.0917:0.0:0.9083	.	.	.	.	C	344;344;344;257	.	.	X	-	3	0	BDH1	198723163	0.996000	0.38824	0.840000	0.33206	0.024000	0.10985	3.278000	0.51662	2.281000	0.76405	0.533000	0.62120	TGA	.	.		0.552	BDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340267.1	NM_004051		G	197238766	T	G	197238766	4	3	89	1	0	0	0	0	0	0	0	0	1390	1796	62	5	3	5	BDH1	3	197238766	Nonstop_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	1303400	197238766	783664	26	11850										
ARAP2	116984	hgsc.bcm.edu	37	chr4	36216083	36216083	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ttcagttgaggtagcaacatTtcttctttcacggaaatagc	8	8	4	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr4:36216083T>A	ENST00000303965.4	-	3	1414	c.925A>T	c.(925-927)Aat>Tat	p.N309Y		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	309					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						GTAGCAACATTTCTTCTTTCA	0.284																																					p.N309Y		Atlas-SNP	.											.	ARAP2	210	.	0			c.A925T						.						83	85	84					4																	36216083		2202	4300	6502	SO:0001583	missense	116984	exon3			CAACATTTCTTCT	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.925A>T	chr4.hg19:g.36216083T>A	ENSP00000302895:p.Asn309Tyr	120.0	0.0		397.0	281.0	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	hg19	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.572079	0.45798	.	.	ENSG00000047365	ENST00000303965	T	0.08720	3.06	5.34	5.34	0.76211	.	0.388395	0.24527	N	0.037743	T	0.10551	0.0258	L	0.53249	1.67	0.25641	N	0.986201	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.10337	-1.0634	10	0.51188	T	0.08	.	11.7098	0.51618	0.0:0.0:0.0:1.0	.	239;309	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	Y	309	ENSP00000302895:N309Y	ENSP00000302895:N309Y	N	-	1	0	ARAP2	35892478	0.932000	0.31603	0.989000	0.46669	0.996000	0.88848	1.326000	0.33735	1.997000	0.58415	0.533000	0.62120	AAT	.	.		0.284	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		A	36216083	T	A	36216083	3	1	89	1	0	0	0	0	1	0	0	0	839	1841	64	4	4313	4	ARAP2	4	36216083	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10		36216083	154938193	27	11851										
TRAM1L1	133022	hgsc.bcm.edu	37	chr4	118006517	118006517	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aattcctggctgagaacgggGgggttcttggtgctcttctt	14	8	3	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr4:118006517G>A	ENST00000310754.4	-	1	219	c.33C>T	c.(31-33)ccC>ccT	p.P11P		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	11					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22						TGAGAACGGGGGGGTTCTTGG	0.627																																					p.P11P		Atlas-SNP	.											.	TRAM1L1	55	.	0			c.C33T						.						50	49	49					4																	118006517		2203	4300	6503	SO:0001819	synonymous_variant	133022	exon1			AACGGGGGGGTTC	AK074617	CCDS3707.1	4q26	2008-02-05			ENSG00000174599	ENSG00000174599			28371	protein-coding gene	gene with protein product						12477932	Standard	NM_152402		Approved	MGC26568	uc003ibv.4	Q8N609	OTTHUMG00000132956	ENST00000310754.4:c.33C>T	chr4.hg19:g.118006517G>A		40.0	0.0		63.0	45.0	NM_152402	Q8N2L7	Silent	SNP	ENST00000310754.4	hg19	CCDS3707.1																																																																																			.	.		0.627	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402		A	118006517	G	A	118006517	2	1	89	1	0	0	0	0	0	0	0	1	16467	1219	43	3		3	TRAM1L1	4	118006517	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	81790434	118006517	73147759	28	11852										
QRFPR	84109	hgsc.bcm.edu	37	chr4	122250816	122250816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggaaaatccaataatttgcaCgatagcaaaaatcatcttga	6	7	2	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr4:122250816C>T	ENST00000394427.2	-	6	1360	c.949G>A	c.(949-951)Gtg>Atg	p.V317M	Y_RNA_ENST00000384419.1_RNA|QRFPR_ENST00000334383.5_3'UTR	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	317					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						ATAATTTGCACGATAGCAAAA	0.279																																					p.V317M		Atlas-SNP	.											.	QRFPR	65	.	0			c.G949A						.						35	36	36					4																	122250816		2202	4298	6500	SO:0001583	missense	84109	exon6			TTTGCACGATAGC	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"GPCR / Class A : RF amide peptide receptors"	15565	protein-coding gene	gene with protein product		606925	"G protein-coupled receptor 103"	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.949G>A	chr4.hg19:g.122250816C>T	ENSP00000377948:p.Val317Met	63.0	0.0		108.0	64.0	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	hg19	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.471314	0.84533	.	.	ENSG00000186867	ENST00000394427	T	0.72505	-0.66	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.83211	0.5205	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.82896	-0.0230	10	0.48119	T	0.1	.	19.3074	0.94169	0.0:1.0:0.0:0.0	.	317	Q96P65	QRFPR_HUMAN	M	317	ENSP00000377948:V317M	ENSP00000377948:V317M	V	-	1	0	QRFPR	122470266	1.000000	0.71417	0.943000	0.38184	0.946000	0.59487	5.898000	0.69838	2.569000	0.86673	0.491000	0.48974	GTG	.	.		0.279	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		T	122250816	C	T	122250816	3	4	89	1	0	0	0	0	1	0	0	0	12893	536	19	1	350	1	QRFPR	4	122250816	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	4244299	122250816	68903460	29	11853										
ADAD1	132612	hgsc.bcm.edu	37	chr4	123301311	123301311	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aacctgccagttcaaccagcGacaaagacgataactacacc	6	14	1	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr4:123301311G>A	ENST00000296513.2	+	3	272	c.87G>A	c.(85-87)gcG>gcA	p.A29A	ADAD1_ENST00000388724.2_Silent_p.A29A|ADAD1_ENST00000388725.2_Silent_p.A11A	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	29					multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						TTCAACCAGCGACAAAGACGA	0.483																																					p.A29A		Atlas-SNP	.											.	ADAD1	94	.	0			c.G87A						.						100	84	89					4																	123301311		2203	4300	6503	SO:0001819	synonymous_variant	132612	exon3			ACCAGCGACAAAG	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.87G>A	chr4.hg19:g.123301311G>A		65.0	0.0		130.0	87.0	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Silent	SNP	ENST00000296513.2	hg19	CCDS34058.1																																																																																			.	.		0.483	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		A	123301311	G	A	123301311	2	1	89	1	0	0	0	0	0	0	0	1	231	1045	37	1		1	ADAD1	4	123301311	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	1050495	123301311	67852965	30	11854										
SLC9A3	6550	hgsc.bcm.edu	37	chr5	474998	474998	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gggaggcccgggagcgttacAtgtgtgtggactcggggagg	21	7	0	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr5:474998A>T	ENST00000264938.3	-	16	2510	c.2501T>A	c.(2500-2502)aTg>aAg	p.M834K	CTD-2228K2.7_ENST00000606319.1_RNA|CTD-2228K2.5_ENST00000510714.1_5'Flank|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.5_ENST00000342584.3_5'Flank|CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA|SLC9A3_ENST00000514375.1_Splice_Site_p.M825K|CTD-2228K2.5_ENST00000510604.1_5'Flank	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	834					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			GGAGCGTTACATGTGTGTGGA	0.711																																					p.M834K		Atlas-SNP	.											.	SLC9A3	89	.	0			c.T2501A						.						7	8	8					5																	474998		2153	4209	6362	SO:0001630	splice_region_variant	6550	exon16			CGTTACATGTGTG		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.2501+1T>A	chr5.hg19:g.474998A>T		23.0	0.0		68.0	20.0	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	hg19	CCDS3855.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.527702	0.44969	.	.	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.56941	0.84;0.43	4.81	4.81	0.61882	.	0.922181	0.08928	N	0.873468	T	0.50463	0.1617	L	0.60455	1.87	0.42249	D	0.99196	P;P	0.49185	0.704;0.92	B;B	0.38106	0.104;0.265	T	0.51616	-0.8683	9	.	.	.	.	14.0272	0.64592	1.0:0.0:0.0:0.0	.	825;834	E9PF67;P48764	.;SL9A3_HUMAN	K	834;825	ENSP00000264938:M834K;ENSP00000422983:M825K	.	M	-	2	0	SLC9A3	527998	1.000000	0.71417	1.000000	0.80357	0.197000	0.23852	7.450000	0.80656	1.810000	0.52873	0.379000	0.24179	ATG	.	.		0.711	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	Missense_Mutation	T	474998	A	T	474998	5	4	89	1	0	0	0	0	0	0	1	0	14728	231	8	4	11	4	SLC9A3	5	474998	Splice_Site	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10		474998	180440262	31	11855										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13770967	13770967	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gtgggtagaacgtcggaatcTctgaaaataatcaacacact	9	8	2	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr5:13770967T>C	ENST00000265104.4	-	56	9600	c.9496A>G	c.(9496-9498)Aga>Gga	p.R3166G	DNAH5_ENST00000504001.3_5'UTR	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3166	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CGTCGGAATCTCTGAAAATAA	0.468									Kartagener syndrome																												p.R3166G		Atlas-SNP	.											.	DNAH5	868	.	0			c.A9496G						.						137	132	134					5																	13770967		2203	4300	6503	SO:0001583	missense	1767	exon56	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGAATCTCTGAAA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.9496A>G	chr5.hg19:g.13770967T>C	ENSP00000265104:p.Arg3166Gly	66.0	0.0		272.0	77.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	19.49	3.838286	0.71373	.	.	ENSG00000039139	ENST00000265104	T	0.41400	1.0	5.71	4.51	0.55191	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.85682	D	0.000000	T	0.70465	0.3227	M	0.92649	3.33	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.76650	-0.2881	10	0.87932	D	0	.	12.0222	0.53350	0.0:0.0:0.2733:0.7267	.	3166	Q8TE73	DYH5_HUMAN	G	3166	ENSP00000265104:R3166G	ENSP00000265104:R3166G	R	-	1	2	DNAH5	13823967	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.820000	0.48057	0.933000	0.37291	0.533000	0.62120	AGA	.	.		0.468	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13770967	T	C	13770967	3	2	89	1	0	0	0	0	1	0	0	0	4606	1559	54	2	4474	2	DNAH5	5	13770967	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	13295969	13770967	167144293	32	11856										
AMACR	23600	hgsc.bcm.edu	37	chr5	34005875	34005875	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	acatacctgacaaagccaaaTagttgatatcgtggccagct	8	10	0	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr5:34005875T>C	ENST00000335606.6	-	2	465	c.377A>G	c.(376-378)tAt>tGt	p.Y126C	AMACR_ENST00000382072.2_Missense_Mutation_p.Y126C|AMACR_ENST00000426255.2_Missense_Mutation_p.Y126C|AMACR_ENST00000502637.1_Missense_Mutation_p.Y126C|RP11-1084J3.4_ENST00000382079.3_Silent_p.L273L|AMACR_ENST00000382068.3_Missense_Mutation_p.Y126C|AMACR_ENST00000382085.3_Missense_Mutation_p.Y126C|AMACR_ENST00000512079.1_Missense_Mutation_p.Y126C|AMACR_ENST00000514195.1_5'UTR|AMACR_ENST00000441713.2_Missense_Mutation_p.Y126C	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	126					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						CAAAGCCAAATAGTTGATATC	0.388																																					p.Y126C		Atlas-SNP	.											.	AMACR	38	.	0			c.A377G						.						47	50	49					5																	34005875		2203	4300	6503	SO:0001583	missense	23600	exon2			GCCAAATAGTTGA	AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.377A>G	chr5.hg19:g.34005875T>C	ENSP00000334424:p.Tyr126Cys	27.0	0.0		61.0	16.0	NM_014324	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	hg19	CCDS3902.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.545157	0.65198	.	.	ENSG00000242110	ENST00000335606;ENST00000382072;ENST00000382085;ENST00000502637;ENST00000441713	T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52	5.46	-0.439	0.12264	CoA-transferase family III domain (2);	0.166117	0.56097	D	0.000034	T	0.76702	0.4024	H	0.95294	3.65	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.998;0.998;0.996;0.998;0.998;0.998	T	0.80171	-0.1493	10	0.87932	D	0	-7.7514	11.1724	0.48579	0.4662:0.0:0.0:0.5338	.	126;126;126;126;126;126	B3KMU8;Q6VRU4;F8W9N1;D6RB81;Q9UHK6-4;Q9UHK6	.;.;.;.;.;AMACR_HUMAN	C	126	ENSP00000334424:Y126C;ENSP00000371504:Y126C;ENSP00000371517:Y126C;ENSP00000424351:Y126C;ENSP00000403800:Y126C	ENSP00000334424:Y126C	Y	-	2	0	AMACR	34041632	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	1.441000	0.35035	0.071000	0.16664	0.533000	0.62120	TAT	.	.		0.388	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324		C	34005875	T	C	34005875	3	2	89	1	0	0	0	0	1	0	0	0	562	1406	49	2	1117	2	AMACR	5	34005875	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	20234908	34005875	146909385	33	11857										
ERCC8	1161	hgsc.bcm.edu	37	chr5	60217888	60217888	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tttaaatacatacctgccaaTggaacacactgctttacatg	5	10	0	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr5:60217888T>C	ENST00000265038.5	-	3	310	c.268A>G	c.(268-270)Att>Gtt	p.I90V	ERCC8_ENST00000543101.1_5'UTR|ERCC8_ENST00000426742.2_Missense_Mutation_p.I32V|AC104113.3_ENST00000457499.1_RNA	NM_000082.3	NP_000073.1	Q13216	ERCC8_HUMAN	excision repair cross-complementation group 8	90					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|positive regulation of DNA repair (GO:0045739)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|transcription-coupled nucleotide-excision repair (GO:0006283)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|protein complex (GO:0043234)	protein complex binding (GO:0032403)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)				TACCTGCCAATGGAACACACT	0.328																																					p.I90V		Atlas-SNP	.											.	ERCC8	31	.	0			c.A268G						.						84	80	82					5																	60217888		2203	4299	6502	SO:0001583	missense	1161	exon3			TGCCAATGGAACA	U28413	CCDS3978.1	5q12.1	2014-09-17	2014-03-07		ENSG00000049167	ENSG00000049167		"WD repeat domain containing"	3439	protein-coding gene	gene with protein product		609412	"Cockayne syndrome 1 (classical)", "excision repair cross-complementing rodent repair deficiency, complementation group 8"	CKN1		8596535	Standard	NM_000082		Approved	CSA	uc003jsm.3	Q13216	OTTHUMG00000097741	ENST00000265038.5:c.268A>G	chr5.hg19:g.60217888T>C	ENSP00000265038:p.Ile90Val	36.0	0.0		59.0	24.0	NM_000082	B2RB64|Q6FHX5|Q96GB9	Missense_Mutation	SNP	ENST00000265038.5	hg19	CCDS3978.1	.	.	.	.	.	.	.	.	.	.	T	2.841	-0.240564	0.05944	.	.	ENSG00000049167	ENST00000426742;ENST00000265038;ENST00000536596;ENST00000439176	T;T;T	0.70516	-0.49;-0.17;-0.09	5.16	-3.51	0.04696	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.288635	0.38217	N	0.001777	T	0.36853	0.0982	N	0.02665	-0.54	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45673	-0.9245	10	0.02654	T	1	-27.2961	15.792	0.78372	0.0:0.7793:0.0:0.2207	.	90;90	Q13216-2;Q13216	.;ERCC8_HUMAN	V	32;90;89;32	ENSP00000400110:I32V;ENSP00000265038:I90V;ENSP00000408344:I32V	ENSP00000265038:I90V	I	-	1	0	ERCC8	60253645	0.131000	0.22433	0.943000	0.38184	0.960000	0.62799	0.130000	0.15850	-0.568000	0.06038	-0.280000	0.10049	ATT	.	.		0.328	ERCC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214971.2	NM_000082		C	60217888	T	C	60217888	3	2	89	1	0	0	0	0	1	0	0	0	5221	1464	51	2	962	2	ERCC8	5	60217888	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	26212013	60217888	120697372	34	11858										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72144245	72144245	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	agtatgagtggaaacctgacGagcaagggcttcagcaaatc	12	8	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr5:72144245G>T	ENST00000337273.5	+	2	475	c.49G>T	c.(49-51)Gag>Tag	p.E17*	TNPO1_ENST00000506351.2_Nonsense_Mutation_p.E9*|TNPO1_ENST00000513944.1_3'UTR|TNPO1_ENST00000523768.1_Nonsense_Mutation_p.E17*|TNPO1_ENST00000454282.1_Nonsense_Mutation_p.E17*|TNPO1_ENST00000447967.2_Nonsense_Mutation_p.E9*	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	17					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		GAAACCTGACGAGCAAGGGCT	0.547																																					p.E17X		Atlas-SNP	.											.	TNPO1	90	.	0			c.G49T						.						98	88	91					5																	72144245		2203	4300	6503	SO:0001587	stop_gained	3842	exon2			CCTGACGAGCAAG	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.49G>T	chr5.hg19:g.72144245G>T	ENSP00000336712:p.Glu17*	43.0	0.0		99.0	21.0	NM_002270	B4DVC6|Q92957|Q92975	Nonsense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	G	33	5.259065	0.95368	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000447967;ENST00000523768;ENST00000506351	.	.	.	3.06	2.17	0.27698	.	0.112278	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-6.9146	10.1847	0.42991	0.1036:0.0:0.8964:0.0	.	.	.	.	X	17;17;9;17;9	.	ENSP00000336712:E17X	E	+	1	0	TNPO1	72180001	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	6.695000	0.74593	0.607000	0.29982	0.305000	0.20034	GAG	.	.		0.547	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		T	72144245	G	T	72144245	4	4	89	1	0	0	0	0	0	1	0	0	16350	1059	37	1	55	1	TNPO1	5	72144245	Nonsense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	11926357	72144245	108771015	35	11859										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141033643	141033643	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gatggctgggaaggacttccCaggcctgcagtggtctctcc	14	12	1	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr5:141033643C>A	ENST00000239440.4	-	33	4574	c.4509G>T	c.(4507-4509)ctG>ctT	p.L1503L	ARAP3_ENST00000512390.1_5'UTR|FCHSD1_ENST00000522783.1_5'Flank|FCHSD1_ENST00000519800.1_5'Flank|ARAP3_ENST00000513878.1_Silent_p.L1152L|FCHSD1_ENST00000435817.2_5'Flank|ARAP3_ENST00000508305.1_Silent_p.L1334L|FCHSD1_ENST00000522126.1_5'Flank	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1503	Pro-rich.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						AAGGACTTCCCAGGCCTGCAG	0.627																																					p.L1503L		Atlas-SNP	.											.	ARAP3	139	.	0			c.G4509T						.						41	49	46					5																	141033643		2203	4300	6503	SO:0001819	synonymous_variant	64411	exon33			ACTTCCCAGGCCT	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.4509G>T	chr5.hg19:g.141033643C>A		61.0	0.0		208.0	86.0	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	hg19	CCDS4266.1																																																																																			.	.		0.627	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		A	141033643	C	A	141033643	2	1	89	1	0	0	0	0	0	0	0	1	840	581	21	3		3	ARAP3	5	141033643	Silent	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	68889398	141033643	39881617	36	11860										
WWC1	23286	hgsc.bcm.edu	37	chr5	167891765	167891765	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	caagtcgctgcgctccgagcGtctgatccgtacctcgctgg	12	15	1	1	rs139653620		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr5:167891765G>A	ENST00000265293.4	+	21	3450	c.2948G>A	c.(2947-2949)cGt>cAt	p.R983H	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Missense_Mutation_p.R989H	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	983	Interaction with PRKCZ.|Interaction with histone H3.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)	p.R983H(1)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		CGCTCCGAGCGTCTGATCCGT	0.602																																					p.R989H		Atlas-SNP	.											WWC1,colon,carcinoma,0,2	WWC1	98	.	1	Substitution - Missense(1)	ovary(1)	c.G2966A						.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	54	53	53		2966,2966,2948	4.1	1	5	dbSNP_134	53	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	WWC1	NM_001161661.1,NM_001161662.1,NM_015238.2	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	989/1120,989/1119,983/1114	167891765	1,13005	2203	4300	6503	SO:0001583	missense	23286	exon21			CCGAGCGTCTGAT	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2948G>A	chr5.hg19:g.167891765G>A	ENSP00000265293:p.Arg983His	39.0	0.0		194.0	53.0	NM_001161662	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	hg19	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.760611	0.31137	0.0	1.16E-4	ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000524038	T;T;T	0.42131	0.98;0.98;0.98	4.99	4.12	0.48240	.	0.129675	0.56097	D	0.000032	T	0.30947	0.0781	L	0.33485	1.01	0.50632	D	0.999882	B;B	0.21821	0.061;0.01	B;B	0.16722	0.016;0.005	T	0.05971	-1.0853	10	0.18276	T	0.48	.	13.4327	0.61064	0.076:0.0:0.924:0.0	.	989;983	Q8IX03-2;Q8IX03	.;KIBRA_HUMAN	H	983;989;315	ENSP00000265293:R983H;ENSP00000427772:R989H;ENSP00000428084:R315H	ENSP00000265293:R983H	R	+	2	0	WWC1	167824343	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	5.504000	0.66968	1.106000	0.41623	0.442000	0.29010	CGT	.	G|1.000;A|0.000		0.602	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		A	167891765	G	A	167891765	3	1	89	1	0	0	0	0	1	0	0	0	17426	1145	40	1	3048	1	WWC1	5	167891765	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	26858122	167891765	13023495	37	11861										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169141427	169141427	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gctacaggagaatttagaaaAgttgaagattgtggatggag	14	2	0	4			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr5:169141427A>T	ENST00000256935.8	+	19	1987	c.1907A>T	c.(1906-1908)aAg>aTg	p.K636M	DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000520908.1_Missense_Mutation_p.K128M	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	636					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AATTTAGAAAAGTTGAAGATT	0.438																																					p.K636M		Atlas-SNP	.											.	DOCK2	389	.	0			c.A1907T						.						165	169	168					5																	169141427		2203	4300	6503	SO:0001583	missense	1794	exon19			TAGAAAAGTTGAA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.1907A>T	chr5.hg19:g.169141427A>T	ENSP00000256935:p.Lys636Met	100.0	0.0		385.0	103.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.603877	0.87157	.	.	ENSG00000134516	ENST00000256935;ENST00000520908	T;T	0.22134	1.97;1.97	5.64	5.64	0.86602	.	0.043687	0.85682	D	0.000000	T	0.47488	0.1448	M	0.80746	2.51	0.80722	D	1	D;D;D	0.76494	0.999;0.975;0.998	D;P;P	0.64687	0.928;0.701;0.818	T	0.48525	-0.9028	10	0.46703	T	0.11	.	15.8502	0.78924	1.0:0.0:0.0:0.0	.	128;636;636	E7ERW7;E5RFJ0;Q92608	.;.;DOCK2_HUMAN	M	636;128	ENSP00000256935:K636M;ENSP00000429283:K128M	ENSP00000256935:K636M	K	+	2	0	DOCK2	169074005	1.000000	0.71417	0.960000	0.40013	0.964000	0.63967	9.310000	0.96267	2.144000	0.66660	0.528000	0.53228	AAG	.	.		0.438	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169141427	A	T	169141427	3	4	89	1	0	0	0	0	1	0	0	0	4689	72	3	4	1981	4	DOCK2	5	169141427	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	1249662	169141427	11773833	38	11862										
FLT4	2324	hgsc.bcm.edu	37	chr5	180047636	180047636	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	atgttacagaagatgaggagGaggaggacccagaagaagac	15	5	0	6			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr5:180047636G>C	ENST00000261937.6	-	16	2457	c.2379C>G	c.(2377-2379)ctC>ctG	p.L793L	FLT4_ENST00000502649.1_Silent_p.L793L|FLT4_ENST00000424276.2_5'Flank|FLT4_ENST00000393347.3_Silent_p.L793L	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	793					blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGATGAGGAGGAGGAGGACCC	0.597																																					p.L793L	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C2379G						.						107	110	109					5																	180047636		2202	4300	6502	SO:0001819	synonymous_variant	2324	exon16			GAGGAGGAGGAGG	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.2379C>G	chr5.hg19:g.180047636G>C		47.0	0.0		172.0	64.0	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	hg19	CCDS4457.1																																																																																			.	.		0.597	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			C	180047636	G	C	180047636	2	2	89	1	0	0	0	0	0	0	0	1	5952	1161	41	4		4	FLT4	5	180047636	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	10906209	180047636	867624	39	11863										
DSP	1832	hgsc.bcm.edu	37	chr6	7585392	7585392	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aaaacctggagaaaatctccAttacagaaggtatagagcgg	10	7	1	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr6:7585392A>G	ENST00000379802.3	+	24	8238	c.7897A>G	c.(7897-7899)Att>Gtt	p.I2633V	DSP_ENST00000418664.2_Missense_Mutation_p.I2034V	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2633	4.5 X 38 AA tandem repeats (Domain C).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GAAAATCTCCATTACAGAAGG	0.522																																					p.I2633V		Atlas-SNP	.											.	DSP	306	.	0			c.A7897G						.						66	72	70					6																	7585392		2203	4300	6503	SO:0001583	missense	1832	exon24			ATCTCCATTACAG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.7897A>G	chr6.hg19:g.7585392A>G	ENSP00000369129:p.Ile2633Val	34.0	0.0		88.0	28.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	A	8.934	0.964183	0.18583	.	.	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.70282	-0.47;-0.47	5.8	4.64	0.57946	.	0.000000	0.64402	D	0.000006	T	0.39809	0.1092	L	0.28274	0.84	0.25457	N	0.987954	B;D	0.53745	0.24;0.962	B;P	0.45449	0.087;0.481	T	0.35500	-0.9786	10	0.13108	T	0.6	.	12.0016	0.53235	0.9326:0.0:0.0674:0.0	.	2081;2633	Q4LE79;P15924	.;DESP_HUMAN	V	2633;2034	ENSP00000369129:I2633V;ENSP00000396591:I2034V	ENSP00000369129:I2633V	I	+	1	0	DSP	7530391	0.959000	0.32827	0.449000	0.26957	0.979000	0.70002	2.309000	0.43699	1.025000	0.39708	-0.270000	0.10280	ATT	.	.		0.522	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		G	7585392	A	G	7585392	3	3	89	1	0	0	0	0	1	0	0	0	4783	217	8	2	7991	2	DSP	6	7585392	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10		7585392	163529675	40	11864										
NEU1	4758	hgsc.bcm.edu	37	chr6	31830507	31830507	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	agaagcccagaatccgcggcCcccagcgtctgtccgggagc	13	16	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr6:31830507C>A	ENST00000375631.4	-	1	176	c.47G>T	c.(46-48)gGg>gTg	p.G16V		NM_000434.3	NP_000425.1	Q99519	NEUR1_HUMAN	sialidase 1 (lysosomal sialidase)	16					glycosphingolipid metabolic process (GO:0006687)|lipid catabolic process (GO:0016042)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	10					Oseltamivir(DB00198)	AATCCGCGGCCCCCAGCGTCT	0.662																																					p.G16V		Atlas-SNP	.											.	NEU1	21	.	0			c.G47T						.						58	46	50					6																	31830507		1511	2709	4220	SO:0001583	missense	4758	exon1			CGCGGCCCCCAGC	AF040958	CCDS4723.1	6p21	2012-10-02			ENSG00000204386	ENSG00000204386	3.2.1.18		7758	protein-coding gene	gene with protein product		608272		NEU		9054950	Standard	NM_000434		Approved		uc003nxq.4	Q99519	OTTHUMG00000031284	ENST00000375631.4:c.47G>T	chr6.hg19:g.31830507C>A	ENSP00000364782:p.Gly16Val	32.0	0.0		105.0	32.0	NM_000434		Missense_Mutation	SNP	ENST00000375631.4	hg19	CCDS4723.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.796757	0.31777	.	.	ENSG00000204386	ENST00000375631	D	0.89343	-2.5	5.07	-0.41	0.12374	.	1.438730	0.04638	N	0.404912	T	0.64316	0.2587	L	0.36672	1.1	0.09310	N	0.999999	B;B	0.20671	0.005;0.047	B;B	0.17098	0.015;0.017	T	0.52480	-0.8570	10	0.12766	T	0.61	-9.4339	4.4117	0.11436	0.0:0.3306:0.3631:0.3063	.	16;16	E9PIF4;Q99519	.;NEUR1_HUMAN	V	16	ENSP00000364782:G16V	ENSP00000364782:G16V	G	-	2	0	NEU1	31938486	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-1.760000	0.01806	0.020000	0.15106	-0.229000	0.12294	GGG	.	.		0.662	NEU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076616.2			A	31830507	C	A	31830507	3	1	89	1	0	0	0	0	1	0	0	0	10350	623	22	3	1224	3	NEU1	6	31830507	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	24245115	31830507	139284560	41	11865										
FOXP4	116113	hgsc.bcm.edu	37	chr6	41533560	41533561	+	Frame_Shift_Ins	INS	-	-	C													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tctggtcagaatggcgtgggINScagcctctctgggcaagccg							TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr6:41533560_41533561insC	ENST00000307972.4	+	1	74_75	c.62_63insC	c.(61-66)ggcagcfs	p.S22fs	FOXP4_ENST00000373057.3_Frame_Shift_Ins_p.S22fs|FOXP4_ENST00000409208.1_Frame_Shift_Ins_p.S22fs|FOXP4_ENST00000373063.3_Frame_Shift_Ins_p.S22fs|FOXP4_ENST00000373060.1_Frame_Shift_Ins_p.S22fs			Q8IVH2	FOXP4_HUMAN	forkhead box P4	22					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					AATGGCGTGGGCAGCCTCTCTG	0.619																																					p.G21fs		Atlas-INDEL	.											.	FOXP4	83	.	0			c.62_63insC						.																																			SO:0001589	frameshift_variant	116113	exon2			.	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"Forkhead boxes"	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.63dupC	chr6.hg19:g.41533561_41533561dupC	ENSP00000309823:p.Ser22fs	46.0	0.0		179.0	12.0	NM_001012427	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Frame_Shift_Ins	INS	ENST00000307972.4	hg19	CCDS34447.1																																																																																			.	.		0.619	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		C	41533561	-	C	41533560	7	5	89	1	0	1	1	0	0	0	0	0	6037	1203	42	0	64	0	FOXP4	6	41533560	Frame_Shift_Ins	INS	-	TCGA-DD-A116-01A-11D-A12Z-10	9703053	41533560	129581507	42	11866										
GPR110	266977	hgsc.bcm.edu	37	chr6	46976681	46976681	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gttattgttactgttctcacCtggaatgcattgagtaaagc	9	7	1	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr6:46976681C>G	ENST00000371253.2	-	11	2705	c.2490G>C	c.(2488-2490)caG>caC	p.Q830H	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Splice_Site_p.Q633H	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	830					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						CTGTTCTCACCTGGAATGCAT	0.443																																					p.Q830H		Atlas-SNP	.											.	GPR110	102	.	0			c.G2490C						.						50	55	54					6																	46976681		2203	4300	6503	SO:0001630	splice_region_variant	266977	exon11			TCTCACCTGGAAT	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.2490+1G>C	chr6.hg19:g.46976681C>G		81.0	0.0		171.0	60.0	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	hg19	CCDS34471.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.412312	0.83340	.	.	ENSG00000153292	ENST00000371253;ENST00000283297	T;T	0.60424	0.19;0.19	5.9	5.9	0.94986	GPCR, family 2-like (1);	0.000000	0.56097	D	0.000025	T	0.80347	0.4606	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82837	-0.0260	9	.	.	.	-16.5137	20.2789	0.98501	0.0:1.0:0.0:0.0	.	830	Q5T601	GP110_HUMAN	H	830;633	ENSP00000360299:Q830H;ENSP00000283297:Q633H	.	Q	-	3	2	GPR110	47084640	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.852000	0.69488	2.788000	0.95919	0.650000	0.86243	CAG	.	.		0.443	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	Missense_Mutation	G	46976681	C	G	46976681	5	3	89	1	0	0	0	0	0	0	1	0	6635	695	24	4	262	4	GPR110	6	46976681	Splice_Site	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	5443121	46976681	124138386	43	11867										
C6orf165	154313	hgsc.bcm.edu	37	chr6	88128113	88128113	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tataatatacgacaatatgaGgtcttccttcagatcatttt	5	7	3	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr6:88128113G>T	ENST00000507897.1	+	7	902	c.819G>T	c.(817-819)gaG>gaT	p.E273D	C6ORF165_ENST00000369562.4_Missense_Mutation_p.E273D			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	273										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		GACAATATGAGGTCTTCCTTC	0.403																																					p.E273D		Atlas-SNP	.											.	C6orf165	116	.	0			c.G819T						.						98	105	103					6																	88128113		2203	4300	6503	SO:0001583	missense	154313	exon7			ATATGAGGTCTTC	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.819G>T	chr6.hg19:g.88128113G>T	ENSP00000426769:p.Glu273Asp	71.0	0.0		173.0	71.0	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	hg19	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.161388	0.78226	.	.	ENSG00000213204	ENST00000369562	T	0.35973	1.28	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.56934	0.2019	M	0.80183	2.485	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.989	T	0.58346	-0.7652	10	0.46703	T	0.11	.	18.607	0.91270	0.0:0.0:1.0:0.0	.	273;273	Q8IYR0;E1P509	CF165_HUMAN;.	D	273	ENSP00000358575:E273D	ENSP00000358575:E273D	E	+	3	2	C6orf165	88184832	0.991000	0.36638	0.996000	0.52242	0.815000	0.46073	1.652000	0.37313	2.575000	0.86900	0.591000	0.81541	GAG	.	.		0.403	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		T	88128113	G	T	88128113	3	4	89	1	0	0	0	0	1	0	0	0	2343	991	35	3	841	3	C6orf165	6	88128113	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	41151432	88128113	82986954	44	11868										
MYO1G	64005	hgsc.bcm.edu	37	chr7	45002481	45002481	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gtcggagacgcgaacctccaGggtgcggccctccctgcggc	15	16	0	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr7:45002481G>T	ENST00000258787.7	-	22	3050	c.2914C>A	c.(2914-2916)Ctg>Atg	p.L972M	RP4-647J21.1_ENST00000568457.1_RNA	NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	972	Myosin tail. {ECO:0000255}.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						CGAACCTCCAGGGTGCGGCCC	0.726																																					p.L972M		Atlas-SNP	.											.	MYO1G	86	.	0			c.C2914A						.						6	7	7					7																	45002481		2066	4115	6181	SO:0001583	missense	64005	exon22			CCTCCAGGGTGCG	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"Myosins / Myosin superfamily : Class I"	13880	protein-coding gene	gene with protein product	"minor histocompatibility antigen HA-2"	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.2914C>A	chr7.hg19:g.45002481G>T	ENSP00000258787:p.Leu972Met	8.0	0.0		47.0	18.0	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	hg19	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.600210	0.66332	.	.	ENSG00000136286	ENST00000258787	T	0.55413	0.52	4.38	3.5	0.40072	Myosin tail 2 (1);	0.000000	0.29133	U	0.013044	T	0.70894	0.3276	M	0.84326	2.69	0.38994	D	0.959207	D	0.67145	0.996	D	0.72982	0.979	T	0.75036	-0.3459	10	0.72032	D	0.01	.	9.9067	0.41381	0.099:0.0:0.901:0.0	.	972	B0I1T2	MYO1G_HUMAN	M	972	ENSP00000258787:L972M	ENSP00000258787:L972M	L	-	1	2	MYO1G	44969006	0.995000	0.38212	0.774000	0.31636	0.851000	0.48451	2.742000	0.47434	0.968000	0.38212	-0.263000	0.10527	CTG	.	.		0.726	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2			T	45002481	G	T	45002481	3	4	89	1	0	0	0	0	1	0	0	0	10083	991	35	3	146	3	MYO1G	7	45002481	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10		45002481	114136182	45	11869										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83037733	83037733	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gtgcggatatgggccagtcgCcccatgctgcggaagatcgc	15	12	0	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr7:83037733C>T	ENST00000307792.3	-	6	1088	c.621G>A	c.(619-621)ggG>ggA	p.G207G	SEMA3E_ENST00000427262.1_Silent_p.G147G	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	207	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				GGGCCAGTCGCCCCATGCTGC	0.468																																					p.G207G		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G621A						.						67	62	64					7																	83037733		2203	4300	6503	SO:0001819	synonymous_variant	9723	exon6			CAGTCGCCCCATG	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.621G>A	chr7.hg19:g.83037733C>T		69.0	0.0		214.0	71.0	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	hg19	CCDS34674.1																																																																																			.	.		0.468	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		T	83037733	C	T	83037733	2	4	89	1	0	0	0	0	0	0	0	1	14043	726	26	3		3	SEMA3E	7	83037733	Silent	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	38035252	83037733	76100930	46	11870										
STEAP2	261729	hgsc.bcm.edu	37	chr7	89854615	89854615	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tctgaattttttcctcatgtGgtagatgtcactcatcatga	7	8	5	3	rs145786195		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr7:89854615G>A	ENST00000287908.3	+	2	612	c.219G>A	c.(217-219)gtG>gtA	p.V73V	STEAP2_ENST00000394629.2_Silent_p.V73V|STEAP2_ENST00000394622.2_Silent_p.V73V|STEAP2_ENST00000394626.1_Silent_p.V73V|STEAP2_ENST00000402625.2_Silent_p.V73V|STEAP2_ENST00000394632.1_Silent_p.V73V|STEAP2_ENST00000394621.2_Silent_p.V73V	NM_001244944.1|NM_152999.3	NP_001231873.1|NP_694544.2	Q8NFT2	STEA2_HUMAN	STEAP family member 2, metalloreductase	73					copper ion import (GO:0015677)|endocytosis (GO:0006897)|ferric iron import into cell (GO:0097461)|Golgi to plasma membrane transport (GO:0006893)|iron ion homeostasis (GO:0055072)|regulated secretory pathway (GO:0045055)|response to hormone (GO:0009725)	cytosol (GO:0005829)|early endosome (GO:0005769)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15	all_hematologic(106;0.112)					TTCCTCATGTGGTAGATGTCA	0.378																																					p.V73V		Atlas-SNP	.											.	STEAP2	78	.	0			c.G219A						.						184	165	171					7																	89854615		2203	4300	6503	SO:0001819	synonymous_variant	261729	exon3			TCATGTGGTAGAT	AF455138	CCDS5615.1, CCDS43612.1, CCDS59064.1	7q21.13	2011-09-30	2011-09-30		ENSG00000157214	ENSG00000157214			17885	protein-coding gene	gene with protein product		605094	"prostate cancer associated protein 1", "six transmembrane epithelial antigen of the prostate 2"	PCANAP1		10613842, 12095985	Standard	NM_001040665		Approved	IPCA-1, STAMP1, STMP	uc003ujz.3	Q8NFT2	OTTHUMG00000023341	ENST00000287908.3:c.219G>A	chr7.hg19:g.89854615G>A		93.0	0.0		160.0	51.0	NM_001244946	A4D1F1|G5E9C6|Q6UXN6|Q6YPB1|Q8IUE7	Silent	SNP	ENST00000287908.3	hg19	CCDS5615.1																																																																																			.	G|1.000;T|0.000		0.378	STEAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059662.4	NM_152999		A	89854615	G	A	89854615	2	1	89	1	0	0	0	0	0	0	0	1	15293	1335	47	3		3	STEAP2	7	89854615	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	6816882	89854615	69284048	47	11871										
HYAL4	23553	hgsc.bcm.edu	37	chr7	123517143	123517143	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggctgctctggggtttccccTtctcctggttcactaatgac	10	13	3	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr7:123517143T>A	ENST00000223026.4	+	5	2018	c.1380T>A	c.(1378-1380)ccT>ccA	p.P460P	HYAL4_ENST00000476325.1_Silent_p.P460P	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	460					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						GGGTTTCCCCTTCTCCTGGTT	0.428																																					p.P460P		Atlas-SNP	.											.	HYAL4	65	.	0			c.T1380A						.						108	110	109					7																	123517143		2203	4300	6503	SO:0001819	synonymous_variant	23553	exon5			TTCCCCTTCTCCT	AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"hyaluronidase 4"	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	ENST00000223026.4:c.1380T>A	chr7.hg19:g.123517143T>A		106.0	0.0		302.0	112.0	NM_012269	D0VXG1|Q9UL99|Q9Y6T9	Silent	SNP	ENST00000223026.4	hg19	CCDS5789.1																																																																																			.	.		0.428	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1	NM_012269		A	123517143	T	A	123517143	2	1	89	1	0	0	0	0	0	0	0	1	7475	1596	56	4		4	HYAL4	7	123517143	Silent	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	33662528	123517143	35621520	48	11872										
MCPH1	79648	hgsc.bcm.edu	37	chr8	6296583	6296583	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	atggagaagagattacaagaGatgaaggagaaaagggaaaa	14	1	0	5			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr8:6296583G>A	ENST00000344683.5	+	6	622	c.546G>A	c.(544-546)gaG>gaA	p.E182E	MCPH1_ENST00000522905.1_Intron|MCPH1_ENST00000519480.1_Silent_p.E182E	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	182					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		GATTACAAGAGATGAAGGAGA	0.338																																					p.E182E	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.G546A						.						86	79	81					8																	6296583		1871	4104	5975	SO:0001819	synonymous_variant	79648	exon6			ACAAGAGATGAAG	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.546G>A	chr8.hg19:g.6296583G>A		36.0	0.0		95.0	29.0	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	hg19	CCDS43689.1																																																																																			.	.		0.338	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		A	6296583	G	A	6296583	2	1	89	1	0	0	0	0	0	0	0	1	9407	933	33	3		3	MCPH1	8	6296583	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10		6296583	140067439	49	11873										
HGSNAT	138050	hgsc.bcm.edu	37	chr8	43033222	43033222	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ctagattctttttaggtttgTatttattatgggatcttcca	7	5	2	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr8:43033222T>A	ENST00000458501.2	+	10	941	c.941T>A	c.(940-942)gTa>gAa	p.V314E	HGSNAT_ENST00000297798.7_5'Flank|HGSNAT_ENST00000521576.1_5'Flank|HGSNAT_ENST00000379644.4_Missense_Mutation_p.V286E			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	314					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			TTTAGGTTTGTATTTATTATG	0.333																																					p.V286E		Atlas-SNP	.											.	HGSNAT	85	.	0			c.T857A						.						115	116	116					8																	43033222		1792	4062	5854	SO:0001583	missense	138050	exon10			GGTTTGTATTTAT		CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"transmembrane protein 76"	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.941T>A	chr8.hg19:g.43033222T>A	ENSP00000389524:p.Val314Glu	114.0	0.0		197.0	110.0	NM_152419	B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	hg19		.	.	.	.	.	.	.	.	.	.	T	22.2	4.255759	0.80135	.	.	ENSG00000165102	ENST00000458501;ENST00000379644;ENST00000522082	D;D;D	0.91068	-2.78;-2.78;-1.89	5.68	5.68	0.88126	.	0.144593	0.46442	D	0.000287	D	0.95204	0.8445	M	0.85373	2.75	0.80722	D	1	D	0.63880	0.993	D	0.65573	0.936	D	0.95751	0.8792	10	0.87932	D	0	-10.7461	13.9256	0.63961	0.0:0.0:0.0:1.0	.	314	Q68CP4	HGNAT_HUMAN	E	314;286;33	ENSP00000389524:V314E;ENSP00000368965:V286E;ENSP00000430151:V33E	ENSP00000368965:V286E	V	+	2	0	HGSNAT	43152379	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	6.332000	0.72934	2.179000	0.69175	0.529000	0.55759	GTA	.	.		0.333	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038		A	43033222	T	A	43033222	3	1	89	1	0	0	0	0	1	0	0	0	7097	1638	57	4	895	4	HGSNAT	8	43033222	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	36736639	43033222	103330800	50	11874										
PREX2	80243	hgsc.bcm.edu	37	chr8	68939468	68939468	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tcaccccagaactgcatgctGcttggaggacggaagaacac	11	12	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr8:68939468G>T	ENST00000288368.4	+	5	730	c.453G>T	c.(451-453)ctG>ctT	p.L151L	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	151	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						ACTGCATGCTGCTTGGAGGAC	0.348																																					p.L151L		Atlas-SNP	.											.	PREX2	614	.	0			c.G453T						.						126	120	122					8																	68939468		2203	4300	6503	SO:0001819	synonymous_variant	80243	exon5			CATGCTGCTTGGA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.453G>T	chr8.hg19:g.68939468G>T		71.0	0.0		200.0	45.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	hg19	CCDS6201.1																																																																																			.	.		0.348	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	68939468	G	T	68939468	2	4	89	1	0	0	0	0	0	0	0	1	12489	1306	46	3		3	PREX2	8	68939468	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	25906246	68939468	77424554	51	11875										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72966074	72966074	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gtacccgcccatggacgcatGatgcaaagctgtccagccat	10	14	0	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr8:72966074G>C	ENST00000262209.4	-	13	1765	c.1558C>G	c.(1558-1560)Cat>Gat	p.H520D	RP11-383H13.1_ENST00000457356.4_3'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	520					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	ATGGACGCATGATGCAAAGCT	0.478																																					p.H520D		Atlas-SNP	.											.	TRPA1	256	.	0			c.C1558G						.						66	55	59					8																	72966074		2203	4300	6503	SO:0001583	missense	8989	exon13			ACGCATGATGCAA	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1558C>G	chr8.hg19:g.72966074G>C	ENSP00000262209:p.His520Asp	49.0	0.0		151.0	24.0	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.163430	0.57476	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.71461	-0.57;-0.57	5.35	4.47	0.54385	Ankyrin repeat-containing domain (4);	0.096049	0.64402	D	0.000001	T	0.80696	0.4672	M	0.73962	2.25	0.44227	D	0.997069	D	0.89917	1.0	D	0.77004	0.989	T	0.79006	-0.1979	10	0.36615	T	0.2	-17.8704	8.8632	0.35269	0.0745:0.0:0.7752:0.1503	.	520	O75762	TRPA1_HUMAN	D	372;520	ENSP00000428151:H372D;ENSP00000262209:H520D	ENSP00000262209:H520D	H	-	1	0	TRPA1	73128628	1.000000	0.71417	0.993000	0.49108	0.586000	0.36452	5.693000	0.68264	1.231000	0.43661	0.561000	0.74099	CAT	.	.		0.478	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		C	72966074	G	C	72966074	3	2	89	1	0	0	0	0	1	0	0	0	16592	1290	45	4	1861	4	TRPA1	8	72966074	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	4026606	72966074	73397948	52	11876										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77767241	77767241	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggccttagaaagccacattcGctctcggcactggaatgaag	11	11	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr8:77767241G>T	ENST00000521891.2	+	10	8532	c.8084G>T	c.(8083-8085)cGc>cTc	p.R2695L	ZFHX4_ENST00000050961.6_Missense_Mutation_p.R2650L|ZFHX4_ENST00000518282.1_Missense_Mutation_p.R2669L|ZFHX4_ENST00000455469.2_Missense_Mutation_p.R2650L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2650					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AGCCACATTCGCTCTCGGCAC	0.527										HNSCC(33;0.089)																											p.R2695L		Atlas-SNP	.											ZFHX4,NS,carcinoma,0,1	ZFHX4	878	.	0			c.G8084T						.						55	55	55					8																	77767241		1952	4139	6091	SO:0001583	missense	79776	exon10			ACATTCGCTCTCG		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.8084G>T	chr8.hg19:g.77767241G>T	ENSP00000430497:p.Arg2695Leu	36.0	0.0		175.0	36.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	12.47	1.947965	0.34377	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.45361	U	0.000364	T	0.50188	0.1601	L	0.47716	1.5	0.80722	D	1	D;P;D	0.57571	0.965;0.956;0.98	D;D;D	0.69307	0.963;0.939;0.961	T	0.46162	-0.9211	10	0.59425	D	0.04	.	18.8803	0.92353	0.0:0.0:1.0:0.0	.	2650;2650;2695	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	L	2695;2679;2650;2650;2669	ENSP00000430497:R2695L;ENSP00000399605:R2650L;ENSP00000050961:R2650L;ENSP00000430848:R2669L	ENSP00000050961:R2650L	R	+	2	0	ZFHX4	77929796	1.000000	0.71417	1.000000	0.80357	0.035000	0.12851	9.657000	0.98554	2.695000	0.91970	0.555000	0.69702	CGC	.	.		0.527	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77767241	G	T	77767241	3	4	89	1	0	0	0	0	1	0	0	0	17650	1087	38	1	8118	1	ZFHX4	8	77767241	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	4801167	77767241	68596781	53	11877										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113988234	113988234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aacttgcactcgctgttcctCggaaagtctatggatggtga	11	9	1	1	rs557572936		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr8:113988234C>T	ENST00000297405.5	-	7	1418	c.1174G>A	c.(1174-1176)Gag>Aag	p.E392K	CSMD3_ENST00000343508.3_Missense_Mutation_p.E352K|CSMD3_ENST00000455883.2_Intron|CSMD3_ENST00000352409.3_Missense_Mutation_p.E392K	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	392						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E392K(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CGCTGTTCCTCGGAAAGTCTA	0.502										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			C|||	1	0.000199681	0	0	5008	,	,		17209	0.001		0	False		,,,				2504	0				p.E392K		Atlas-SNP	.											CSMD3_ENST00000343508,caecum,carcinoma,+1,3	CSMD3	2325	.	1	Substitution - Missense(1)	ovary(1)	c.G1174A						.						203	178	186					8																	113988234		2203	4300	6503	SO:0001583	missense	114788	exon7			GTTCCTCGGAAAG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1174G>A	chr8.hg19:g.113988234C>T	ENSP00000297405:p.Glu392Lys	101.0	0.0		404.0	85.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.919931	0.73098	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000352409	T;T;T	0.18338	2.22;2.22;2.22	6.17	6.17	0.99709	.	0.177149	0.36268	N	0.002692	T	0.26846	0.0657	N	0.22421	0.69	0.36807	D	0.885667	D;D	0.65815	0.992;0.995	D;D	0.70716	0.935;0.97	T	0.01753	-1.1281	10	0.05959	T	0.93	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	392;352	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	K	352;392;392	ENSP00000345799:E352K;ENSP00000297405:E392K;ENSP00000343124:E392K	ENSP00000297405:E392K	E	-	1	0	CSMD3	114057410	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.685000	0.54678	2.941000	0.99782	0.655000	0.94253	GAG	.	.		0.502	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113988234	C	T	113988234	3	4	89	1	0	0	0	0	1	0	0	0	3948	893	31	1	10209	1	CSMD3	8	113988234	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	36220993	113988234	32375788	54	11878										
ZHX1	11244	hgsc.bcm.edu	37	chr8	124267557	124267557	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tctggtttgatttcattctcTttctcttcaggaacgtcctc	6	11	5	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr8:124267557T>C	ENST00000522655.1	-	3	1170	c.630A>G	c.(628-630)aaA>aaG	p.K210K	ZHX1_ENST00000297857.2_Silent_p.K210K|ZHX1_ENST00000522595.1_5'Flank|ZHX1_ENST00000395571.3_Silent_p.K210K|ZHX1-C8ORF76_ENST00000357082.4_Intron			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	210					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			TTTCATTCTCTTTCTCTTCAG	0.338																																					p.K210K		Atlas-SNP	.											.	ZHX1	89	.	0			c.A630G						.						97	101	100					8																	124267557		2203	4300	6503	SO:0001819	synonymous_variant	11244	exon3			ATTCTCTTTCTCT	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	12871	protein-coding gene	gene with protein product		604764	"zinc-fingers and homeoboxes 1"			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.630A>G	chr8.hg19:g.124267557T>C		109.0	0.0		608.0	126.0	NM_007222	Q8IWD8	Silent	SNP	ENST00000522655.1	hg19	CCDS6342.1																																																																																			.	.		0.338	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1			C	124267557	T	C	124267557	2	2	89	1	0	0	0	0	0	0	0	1	17690	1606	56	2		2	ZHX1	8	124267557	Silent	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	10279323	124267557	22096465	55	11879										
SLC45A4	57210	hgsc.bcm.edu	37	chr8	142231707	142231707	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ccgttaaggaaaagtgcaacGccaaagaggacgccaacgca	11	11	0	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr8:142231707G>A	ENST00000024061.3	-	2	553	c.246C>T	c.(244-246)ggC>ggT	p.G82G	SLC45A4_ENST00000517878.1_Silent_p.G133G|SLC45A4_ENST00000433583.2_Silent_p.G75G|SLC45A4_ENST00000519067.1_Silent_p.G82G	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			AAAGTGCAACGCCAAAGAGGA	0.622																																					p.G82G		Atlas-SNP	.											.	SLC45A4	71	.	0			c.C246T						.						71	78	76					8																	142231707		2203	4300	6503	SO:0001819	synonymous_variant	57210	exon2			TGCAACGCCAAAG	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"Solute carriers"	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.246C>T	chr8.hg19:g.142231707G>A		27.0	0.0		157.0	39.0	NM_001080431	Q6ZRI2|Q9ULU3	Silent	SNP	ENST00000024061.3	hg19	CCDS34948.1																																																																																			.	.		0.622	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325		A	142231707	G	A	142231707	2	1	89	1	0	0	0	0	0	0	0	1	14658	1074	38	1		1	SLC45A4	8	142231707	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	17964150	142231707	4132315	56	11880										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144945358	144945358	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	taggggtcagtgtagccagtGacagcgcgctcagccgacag	15	11	2	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr8:144945358G>T	ENST00000525985.1	-	2	2135	c.2064C>A	c.(2062-2064)gtC>gtA	p.V688V				P58107	EPIPL_HUMAN	epiplakin 1	688						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGTAGCCAGTGACAGCGCGCT	0.627																																					p.V688V		Atlas-SNP	.											.	EPPK1	199	.	0			c.C2064A						.						46	51	49					8																	144945358		2188	4281	6469	SO:0001819	synonymous_variant	83481	exon1			GCCAGTGACAGCG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.2064C>A	chr8.hg19:g.144945358G>T		37.0	0.0		209.0	40.0	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	hg19																																																																																				.	.		0.627	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144945358	G	T	144945358	2	4	89	1	0	0	0	0	0	0	0	1	5192	1277	45	3		3	EPPK1	8	144945358	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	2713651	144945358	1418664	57	11881										
ARID3C	138715	hgsc.bcm.edu	37	chr9	34623647	34623647	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	attgctgtctatggcggcctGgagctcccctggggagctga	15	11	1	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr9:34623647G>T	ENST00000378909.2	-	4	732	c.640C>A	c.(640-642)Cag>Aag	p.Q214K		NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	214					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		ATGGCGGCCTGGAGCTCCCCT	0.677																																					p.Q214K		Atlas-SNP	.											.	ARID3C	33	.	0			c.C640A						.						11	12	12					9																	34623647		2161	4249	6410	SO:0001583	missense	138715	exon4			CGGCCTGGAGCTC		CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"-"	21209	protein-coding gene	gene with protein product			"AT rich interactive domain 3C (BRIGHT- like)"				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.640C>A	chr9.hg19:g.34623647G>T	ENSP00000368189:p.Gln214Lys	19.0	0.0		32.0	17.0	NM_001017363		Missense_Mutation	SNP	ENST00000378909.2	hg19	CCDS35006.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.875305	0.72180	.	.	ENSG00000205143	ENST00000378909	T	0.64438	-0.1	5.01	5.01	0.66863	ARID/BRIGHT DNA-binding domain (2);	0.000000	0.47455	D	0.000225	T	0.64204	0.2577	M	0.78049	2.395	0.58432	D	0.999998	B	0.24576	0.106	B	0.28991	0.097	T	0.62144	-0.6916	10	0.12103	T	0.63	-13.6509	17.3336	0.87274	0.0:0.0:1.0:0.0	.	214	A6NKF2	ARI3C_HUMAN	K	214	ENSP00000368189:Q214K	ENSP00000368189:Q214K	Q	-	1	0	ARID3C	34613647	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.342000	0.97044	2.341000	0.79615	0.549000	0.68633	CAG	.	.		0.677	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061		T	34623647	G	T	34623647	3	4	89	1	0	0	0	0	1	0	0	0	918	1357	47	3	613	3	ARID3C	9	34623647	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10		34623647	106589784	58	11882										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77400791	77400791	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aaaactagactgtactcaccAtttttgcaatcatggtcaca	5	10	3	1	rs142068228		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr9:77400791A>G	ENST00000360774.1	-	21	3155	c.2918T>C	c.(2917-2919)aTg>aCg	p.M973T	TRPM6_ENST00000451710.3_Splice_Site_p.M973T|TRPM6_ENST00000449912.2_Splice_Site_p.M968T|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Splice_Site_p.M973T|TRPM6_ENST00000361255.3_Splice_Site_p.M968T|TRPM6_ENST00000376872.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	973					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TGTACTCACCATTTTTGCAAT	0.423																																					p.M973T		Atlas-SNP	.											.	TRPM6	377	.	0			c.T2918C						.	A	THR/MET,THR/MET,THR/MET	0,4406		0,0,2203	139	140	140		2903,2903,2918	5.4	1	9	dbSNP_134	140	2,8598	2.2+/-6.3	0,2,4298	yes	missense-near-splice,missense-near-splice,missense-near-splice	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	81,81,81	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging	968/2018,968/2018,973/2023	77400791	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	140803	exon21			CTCACCATTTTTG	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.2919+1T>C	chr9.hg19:g.77400791A>G		48.0	0.0		99.0	58.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	A	19.47	3.834164	0.71373	0.0	2.33E-4	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94;-0.94	5.39	5.39	0.77823	Ion transport (1);	0.068830	0.85682	D	0.000000	D	0.87414	0.6171	M	0.94063	3.49	0.80722	D	1	D;B;P	0.54397	0.966;0.45;0.8	P;P;P	0.55871	0.786;0.555;0.691	D	0.90845	0.4726	10	0.87932	D	0	.	15.5669	0.76300	1.0:0.0:0.0:0.0	.	636;973;968	F5H7D1;Q9BX84;Q9BX84-3	.;TRPM6_HUMAN;.	T	973;973;968;968;973;636;636	ENSP00000354006:M973T;ENSP00000407341:M973T;ENSP00000396672:M968T;ENSP00000354962:M968T;ENSP00000366060:M973T	ENSP00000309693:M636T	M	-	2	0	TRPM6	76590611	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.078000	0.94023	2.264000	0.75181	0.448000	0.29417	ATG	.	A|1.000;G|0.000		0.423	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	Missense_Mutation	G	77400791	A	G	77400791	5	3	89	1	0	0	0	0	0	0	1	0	16605	231	8	2	3226	2	TRPM6	9	77400791	Splice_Site	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	42777144	77400791	63812640	59	11883										
FAM75C1	441452	hgsc.bcm.edu	37	chr9	90535228	90535228	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tctctggtccagacccgccaGgtgaggtgggcaaaagaaca	13	11	1	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr9:90535228G>A	ENST00000602681.1	+	0	1132							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AGACCCGCCAGGTGAGGTGGG	0.597																																					p.G136S		Atlas-SNP	.											.	.	.	.	0			c.G406A						.						56	69	65					9																	90535228		692	1590	2282			441452	exon4			CCGCCAGGTGAGG	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"family with sequence similarity 75, member C1"	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		chr9.hg19:g.90535228G>A		123.0	0.0		348.0	187.0	NM_001145124		Missense_Mutation	SNP	ENST00000602681.1	hg19																																																																																				.	.		0.597	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124		A	90535228	G	A	90535228	1	1	89	0	1	0	0	0	0	0	0	0	5631	1000	35	3		3	FAM75C1	9	90535228	RNA	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	13134437	90535228	50678203	60	11884										
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134497245	134497245	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ctcctgcacggagtccacccCactgaaggagtcgctgaagc	11	15	0	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr9:134497245C>T	ENST00000372189.3	-	11	1915	c.1792G>A	c.(1792-1794)Ggg>Agg	p.G598R	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.G616R|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.G615R	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	598					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		GAGTCCACCCCACTGAAGGAG	0.602																																					p.G616R		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G1846A						.						50	59	56					9																	134497245		2046	4183	6229	SO:0001583	missense	2889	exon11			CCACCCCACTGAA	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1792G>A	chr9.hg19:g.134497245C>T	ENSP00000361263:p.Gly598Arg	58.0	0.0		140.0	80.0	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	hg19	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	C	7.333	0.619357	0.14129	.	.	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000398415;ENST00000437236;ENST00000372191;ENST00000357686;ENST00000431470;ENST00000545785	T;T;T	0.23950	1.88;1.89;1.89	4.84	-1.21	0.09524	.	1.978000	0.02142	N	0.057242	T	0.19167	0.0460	N	0.22421	0.69	0.19300	N	0.999979	P;B;P;B;P;B;B;B	0.45474	0.773;0.145;0.773;0.041;0.859;0.134;0.041;0.068	B;B;B;B;B;B;B;B	0.42422	0.219;0.101;0.3;0.043;0.387;0.043;0.043;0.094	T	0.26292	-1.0107	10	0.15499	T	0.54	.	9.5338	0.39209	0.0:0.3305:0.0:0.6695	.	12;293;56;578;559;615;598;616	E7ERR9;E9PDT1;Q5JUE7;C9JL20;Q13905-2;Q68DL3;Q13905;Q13905-3	.;.;.;.;.;.;RPGF1_HUMAN;.	R	598;615;492;598;616;578;524;12;12;293;615;12;12	ENSP00000361269:G615R;ENSP00000361263:G598R;ENSP00000361264:G616R	ENSP00000266110:G598R	G	-	1	0	RAPGEF1	133487066	0.990000	0.36364	0.002000	0.10522	0.004000	0.04260	1.045000	0.30341	-0.284000	0.09102	-0.258000	0.10820	GGG	.	.		0.602	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		T	134497245	C	T	134497245	3	4	89	1	0	0	0	0	1	0	0	0	13058	594	21	3	1497	3	RAPGEF1	9	134497245	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	43962017	134497245	6716186	61	11885										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140901281	140901281	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	atcgaatcgcaaggcggcgtCagcaaaggcatgttctcgtc	12	11	2	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr9:140901281C>G	ENST00000371372.1	+	16	2182	c.2037C>G	c.(2035-2037)gtC>gtG	p.V679V	CACNA1B_ENST00000371357.1_Silent_p.V680V|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000277551.2_Silent_p.V679V|CACNA1B_ENST00000371363.1_Silent_p.V679V|CACNA1B_ENST00000371355.4_Silent_p.V680V	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	679					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	AAGGCGGCGTCAGCAAAGGCA	0.562																																					p.V679V		Atlas-SNP	.											.	CACNA1B	266	.	0			c.C2037G						.						156	156	156					9																	140901281		2140	4257	6397	SO:0001819	synonymous_variant	774	exon16			CGGCGTCAGCAAA	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.2037C>G	chr9.hg19:g.140901281C>G		92.0	0.0		210.0	143.0	NM_001243812	B1AQK5	Silent	SNP	ENST00000371372.1	hg19	CCDS59522.1																																																																																			.	.		0.562	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		G	140901281	C	G	140901281	2	3	89	1	0	0	0	0	0	0	0	1	2541	813	29	4		4	CACNA1B	9	140901281	Silent	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	6404036	140901281	312150	62	11886										
VIM	7431	hgsc.bcm.edu	37	chr10	17277863	17277863	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aggatttctctgcctcttccAaacttttcctccctgaacct	4	15	2	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr10:17277863A>T	ENST00000224237.5	+	7	1393	c.1248A>T	c.(1246-1248)ccA>ccT	p.P416P	VIM_ENST00000544301.1_Silent_p.P416P|RP11-124N14.3_ENST00000456355.1_RNA			P08670	VIME_HUMAN	vimentin	416	Tail.				apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGCCTCTTCCAAACTTTTCCT	0.363																																					p.P416P		Atlas-SNP	.											.	VIM	71	.	0			c.A1248T						.						147	128	135					10																	17277863		2203	4300	6503	SO:0001819	synonymous_variant	7431	exon8			TCTTCCAAACTTT	M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.1248A>T	chr10.hg19:g.17277863A>T		114.0	0.0		391.0	151.0	NM_003380	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Silent	SNP	ENST00000224237.5	hg19	CCDS7120.1	.	.	.	.	.	.	.	.	.	.	A	11.12	1.545864	0.27652	.	.	ENSG00000026025	ENST00000545533	.	.	.	5.49	-3.86	0.04230	.	.	.	.	.	T	0.59018	0.2163	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62388	-0.6865	5	0.41790	T	0.15	.	11.3631	0.49655	0.3546:0.5813:0.0641:0.0	.	.	.	.	L	403	.	ENSP00000439432:Q403L	Q	+	2	0	VIM	17317869	0.326000	0.24669	0.973000	0.42090	0.998000	0.95712	-0.124000	0.10595	-0.403000	0.07622	0.523000	0.50628	CAA	.	.		0.363	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		T	17277863	A	T	17277863	2	4	89	1	0	0	0	0	0	0	0	1	17181	117	5	4		4	VIM	10	17277863	Silent	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10		17277863	118256884	63	11887										
OR13A1	79290	hgsc.bcm.edu	37	chr10	45799377	45799377	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	cggcgcagagcagccacacgGctgtggccagcccgctgcag	15	16	0	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr10:45799377G>T	ENST00000553795.1	-	4	802	c.494C>A	c.(493-495)gCc>gAc	p.A165D	OR13A1_ENST00000374401.2_Missense_Mutation_p.A165D|OR13A1_ENST00000536058.1_Missense_Mutation_p.A165D	NM_001004297.2	NP_001004297.2	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A, member 1	165						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)|urinary_tract(1)	19						CAGCCACACGGCTGTGGCCAG	0.597																																					p.A165D		Atlas-SNP	.											.	OR13A1	49	.	0			c.C494A						.						32	34	34					10																	45799377		2181	4259	6440	SO:0001583	missense	79290	exon4			CACACGGCTGTGG	AB065728	CCDS31188.1	10q11.21	2012-10-03			ENSG00000256574	ENSG00000256574		"GPCR / Class A : Olfactory receptors"	14772	protein-coding gene	gene with protein product							Standard	NM_001004297		Approved		uc001jcc.1	Q8NGR1	OTTHUMG00000018080	ENST00000553795.1:c.494C>A	chr10.hg19:g.45799377G>T	ENSP00000451950:p.Ala165Asp	4.0	0.0		30.0	18.0	NM_001004297	Q2M3M4|Q5VV57|Q6IFH5|Q6ZMN6	Missense_Mutation	SNP	ENST00000553795.1	hg19	CCDS31188.1	.	.	.	.	.	.	.	.	.	.	g	10.84	1.464242	0.26335	.	.	ENSG00000256574	ENST00000553795;ENST00000536058;ENST00000374401	T;T;T	0.40476	1.03;1.03;1.03	5.63	1.15	0.20763	GPCR, rhodopsin-like superfamily (1);	0.450530	0.18721	N	0.133006	T	0.51652	0.1687	M	0.86343	2.81	0.09310	N	1	B	0.27951	0.195	B	0.39027	0.288	T	0.54262	-0.8320	10	0.59425	D	0.04	0.0029	8.9152	0.35576	0.252:0.3573:0.3907:0.0	.	165	Q8NGR1	O13A1_HUMAN	D	165	ENSP00000451950:A165D;ENSP00000438657:A165D;ENSP00000363522:A165D	ENSP00000311379:A165D	A	-	2	0	OR13A1	45119383	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-0.288000	0.08377	0.704000	0.31869	-0.171000	0.13296	GCC	.	.		0.597	OR13A1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047779.2	NM_001004297		T	45799377	G	T	45799377	3	4	89	1	0	0	0	0	1	0	0	0	10942	1203	42	3	496	3	OR13A1	10	45799377	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	28521514	45799377	89735370	64	11888										
LRRC18	474354	hgsc.bcm.edu	37	chr10	50122143	50122143	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aaaagtgattttgatgcaatTcctggccaccttgagggtga	11	7	0	4			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr10:50122143T>C	ENST00000374160.3	-	1	134	c.58A>G	c.(58-60)Aat>Gat	p.N20D	WDFY4_ENST00000325239.5_Intron|RP11-523O18.7_ENST00000430438.1_RNA|LRRC18_ENST00000298124.3_Missense_Mutation_p.N20D|WDFY4_ENST00000413659.2_Intron	NM_001006939.3	NP_001006940.3	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	20						cytoplasm (GO:0005737)				NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						TTGATGCAATTCCTGGCCACC	0.448																																					p.N20D		Atlas-SNP	.											.	LRRC18	52	.	0			c.A58G						.						74	68	70					10																	50122143		2203	4300	6503	SO:0001583	missense	474354	exon1			TGCAATTCCTGGC	AY358137	CCDS31197.1	10q11.23	2011-02-10			ENSG00000165383	ENSG00000165383			23199	protein-coding gene	gene with protein product							Standard	NM_001006939		Approved	UNQ933, MGC34773, UNQ9338, VKGE9338	uc001jhd.3	Q8N456	OTTHUMG00000018182	ENST00000374160.3:c.58A>G	chr10.hg19:g.50122143T>C	ENSP00000363275:p.Asn20Asp	37.0	0.0		53.0	21.0	NM_001006939	Q6UY02	Missense_Mutation	SNP	ENST00000374160.3	hg19	CCDS31197.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.057109	0.76074	.	.	ENSG00000165383	ENST00000374160;ENST00000298124	T;T	0.59083	0.47;0.29	6.06	6.06	0.98353	.	0.101514	0.64402	D	0.000001	T	0.60573	0.2279	M	0.76002	2.32	0.50632	D	0.999882	P	0.47106	0.89	B	0.40901	0.343	T	0.64757	-0.6332	9	.	.	.	.	16.6245	0.84952	0.0:0.0:0.0:1.0	.	20	Q8N456	LRC18_HUMAN	D	20	ENSP00000363275:N20D;ENSP00000298124:N20D	.	N	-	1	0	LRRC18	49792149	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.105000	0.57797	2.323000	0.78572	0.528000	0.53228	AAT	.	.		0.448	LRRC18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047964.1	NM_001006939		C	50122143	T	C	50122143	3	2	89	1	0	0	0	0	1	0	0	0	8983	1783	62	2	735	2	LRRC18	10	50122143	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	4322766	50122143	85412604	65	11889										
SMC3	9126	hgsc.bcm.edu	37	chr10	112343665	112343665	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aaaagcagaaagaactggcaGaaacagaacccaaattcaac	7	9	1	4			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr10:112343665G>A	ENST00000361804.4	+	12	1162	c.1036G>A	c.(1036-1038)Gaa>Aaa	p.E346K		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	346					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		AGAACTGGCAGAAACAGAACC	0.338																																					p.E346K		Atlas-SNP	.											.	SMC3	103	.	0			c.G1036A						.						90	97	94					10																	112343665		2203	4300	6503	SO:0001583	missense	9126	exon12			CTGGCAGAAACAG	AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.1036G>A	chr10.hg19:g.112343665G>A	ENSP00000354720:p.Glu346Lys	89.0	0.0		311.0	101.0	NM_005445	A8K156|O60464|Q5T482	Missense_Mutation	SNP	ENST00000361804.4	hg19	CCDS31285.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.321619	0.60634	.	.	ENSG00000108055	ENST00000361804	T	0.78246	-1.16	5.52	5.52	0.82312	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.61813	0.2377	N	0.05554	-0.025	0.80722	D	1	B	0.23128	0.08	B	0.24269	0.052	T	0.57906	-0.7730	10	0.17369	T	0.5	.	18.4459	0.90683	0.0:0.0:1.0:0.0	.	346	Q9UQE7	SMC3_HUMAN	K	346	ENSP00000354720:E346K	ENSP00000354720:E346K	E	+	1	0	SMC3	112333655	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.916000	0.92745	2.589000	0.87451	0.650000	0.86243	GAA	.	.		0.338	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		A	112343665	G	A	112343665	3	1	89	1	0	0	0	0	1	0	0	0	14799	943	33	3	1082	3	SMC3	10	112343665	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	62221522	112343665	23191082	66	11890										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117228753	117228753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aggaatacagagatagttttTcctatgaaaaatttaacttt	6	4	0	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr10:117228753T>C	ENST00000355044.3	+	24	3694	c.3568T>C	c.(3568-3570)Tcc>Ccc	p.S1190P	ATRNL1_ENST00000303745.7_Intron|ATRNL1_ENST00000423111.2_Missense_Mutation_p.S241P	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1190					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		AGATAGTTTTTCCTATGAAAA	0.289																																					p.S1190P		Atlas-SNP	.											.	ATRNL1	219	.	0			c.T3568C						.						36	40	39					10																	117228753		2191	4264	6455	SO:0001583	missense	26033	exon24			AGTTTTTCCTATG	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3568T>C	chr10.hg19:g.117228753T>C	ENSP00000347152:p.Ser1190Pro	71.0	0.0		84.0	39.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.031252	0.75504	.	.	ENSG00000107518	ENST00000355044;ENST00000423111	T;T	0.63580	-0.05;-0.05	5.73	5.73	0.89815	.	0.049260	0.85682	D	0.000000	T	0.73024	0.3534	L	0.47016	1.485	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.986	T	0.70403	-0.4881	10	0.31617	T	0.26	-11.7768	16.0287	0.80560	0.0:0.0:0.0:1.0	.	241;1190	B4DH41;Q5VV63	.;ATRN1_HUMAN	P	1190;241	ENSP00000347152:S1190P;ENSP00000409624:S241P	ENSP00000347152:S1190P	S	+	1	0	ATRNL1	117218743	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.990000	0.88215	2.194000	0.70268	0.477000	0.44152	TCC	.	.		0.289	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		C	117228753	T	C	117228753	3	2	89	1	0	0	0	0	1	0	0	0	1207	1783	62	2	3662	2	ATRNL1	10	117228753	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	4885088	117228753	18305994	67	11891										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135025348	135025348	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gtaagaggctctcagaggacGgcatctccaggaaggtgggg	17	8	2	2	rs201175312		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr10:135025348G>T	ENST00000304613.3	+	23	4243	c.4222G>T	c.(4222-4224)Ggc>Tgc	p.G1408C	KNDC1_ENST00000368572.2_Missense_Mutation_p.G1410C			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1408					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CTCAGAGGACGGCATCTCCAG	0.642																																					p.G1408C		Atlas-SNP	.											.	KNDC1	155	.	0			c.G4222T						.						44	40	42					10																	135025348		2203	4299	6502	SO:0001583	missense	85442	exon23			GAGGACGGCATCT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.4222G>T	chr10.hg19:g.135025348G>T	ENSP00000304437:p.Gly1408Cys	11.0	0.0		36.0	21.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	12.48	1.950229	0.34377	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.13196	2.61;2.61	3.34	1.4	0.22301	Ras guanine nucleotide exchange factor, domain (1);	1.090190	0.07095	U	0.839449	T	0.07683	0.0193	N	0.24115	0.695	0.27204	N	0.9601	P	0.35844	0.524	B	0.25140	0.058	T	0.31194	-0.9952	10	0.45353	T	0.12	-13.6231	4.7291	0.12955	0.4066:0.0:0.5934:0.0	.	1408	Q76NI1	VKIND_HUMAN	C	1408;1410	ENSP00000304437:G1408C;ENSP00000357561:G1410C	ENSP00000304437:G1408C	G	+	1	0	KNDC1	134875338	0.030000	0.19436	0.985000	0.45067	0.442000	0.32017	0.212000	0.17497	0.702000	0.31825	0.282000	0.19409	GGC	.	G|0.999;A|0.001		0.642	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		T	135025348	G	T	135025348	3	4	89	1	0	0	0	0	1	0	0	0	8435	1116	39	1	4312	1	KNDC1	10	135025348	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	17796595	135025348	509399	68	11892										
CDHR5	53841	hgsc.bcm.edu	37	chr11	618896	618896	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gtgggaggtgctggttcccaCaccggggggcatcggctgag	19	10	0	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:618896C>T	ENST00000358353.3	-	14	1985	c.1663G>A	c.(1663-1665)Gtg>Atg	p.V555M	IRF7_ENST00000397574.2_5'Flank|IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000330243.5_5'Flank|CDHR5_ENST00000349570.7_Intron|IRF7_ENST00000397570.1_5'Flank|CDHR5_ENST00000397542.2_Missense_Mutation_p.V555M			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	555	4 X 31 AA approximate tandem repeats.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						CTGGTTCCCACACCGGGGGGC	0.657																																					p.V555M		Atlas-SNP	.											.	CDHR5	77	.	0			c.G1663A						.						90	101	97					11																	618896		2203	4300	6503	SO:0001583	missense	53841	exon13			TTCCCACACCGGG	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.1663G>A	chr11.hg19:g.618896C>T	ENSP00000351118:p.Val555Met	87.0	0.0		357.0	18.0	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Missense_Mutation	SNP	ENST00000358353.3	hg19	CCDS7707.1	.	.	.	.	.	.	.	.	.	.	C	8.682	0.905305	0.17760	.	.	ENSG00000099834	ENST00000397542;ENST00000358353	T;T	0.41758	0.99;0.99	3.08	-6.17	0.02091	.	.	.	.	.	T	0.27798	0.0684	N	0.19112	0.55	0.09310	N	1	B;D	0.55605	0.0;0.972	B;P	0.52217	0.002;0.693	T	0.28522	-1.0041	9	0.36615	T	0.2	.	1.1832	0.01849	0.2273:0.2114:0.3349:0.2264	.	549;555	Q9HBB8-4;Q9HBB8	.;CDHR5_HUMAN	M	555	ENSP00000380676:V555M;ENSP00000351118:V555M	ENSP00000351118:V555M	V	-	1	0	CDHR5	608896	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.946000	0.00680	-3.993000	0.00083	-0.994000	0.02522	GTG	.	.		0.657	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		T	618896	C	T	618896	3	4	89	1	0	0	0	0	1	0	0	0	3124	478	17	3	886	3	CDHR5	11	618896	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10		618896	134387620	69	11893										
USP47	55031	hgsc.bcm.edu	37	chr11	11927068	11927068	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ccattggtcatccgaccttaTgggtccagccaagcatttgc	9	13	1	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:11927068T>C	ENST00000399455.2	+	9	1122	c.1002T>C	c.(1000-1002)taT>taC	p.Y334Y	USP47_ENST00000527733.1_Silent_p.Y314Y|USP47_ENST00000539466.1_5'UTR|USP47_ENST00000339865.5_Silent_p.Y246Y	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	334	USP.				base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		TCCGACCTTATGGGTCCAGCC	0.448																																					p.Y246Y		Atlas-SNP	.											.	USP47	91	.	0			c.T738C						.						168	172	171					11																	11927068		2040	4204	6244	SO:0001819	synonymous_variant	55031	exon7			ACCTTATGGGTCC	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.1002T>C	chr11.hg19:g.11927068T>C		86.0	0.0		230.0	89.0	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Silent	SNP	ENST00000399455.2	hg19																																																																																				.	.		0.448	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		C	11927068	T	C	11927068	2	2	89	1	0	0	0	0	0	0	0	1	17093	1471	51	2		2	USP47	11	11927068	Silent	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	11308172	11927068	123079448	70	11894										
C11orf84	144097	hgsc.bcm.edu	37	chr11	63585307	63585307	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggagaagaccccaccgcctaGacccagcccgctagaggcag	12	16	0	4			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:63585307G>C	ENST00000294244.4	+	2	457	c.158G>C	c.(157-159)aGa>aCa	p.R53T		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	53										endometrium(3)|kidney(1)|lung(3)|skin(1)	8						CCACCGCCTAGACCCAGCCCG	0.617																																					p.R53T		Atlas-SNP	.											.	C11orf84	33	.	0			c.G158C						.						37	32	34					11																	63585307		2200	4296	6496	SO:0001583	missense	144097	exon2			CGCCTAGACCCAG	BC007540	CCDS31594.1	11q13.1	2014-02-10			ENSG00000168005	ENSG00000168005			25115	protein-coding gene	gene with protein product						12477932	Standard	NM_138471		Approved		uc001nxt.3	Q9BUA3	OTTHUMG00000167746	ENST00000294244.4:c.158G>C	chr11.hg19:g.63585307G>C	ENSP00000294244:p.Arg53Thr	38.0	0.0		87.0	24.0	NM_138471	Q68CV7|Q6PHS2|Q96IH0	Missense_Mutation	SNP	ENST00000294244.4	hg19	CCDS31594.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.423625	0.62733	.	.	ENSG00000168005	ENST00000294244	T	0.47177	0.85	5.48	4.58	0.56647	.	0.655189	0.14298	N	0.328492	T	0.40094	0.1103	L	0.51422	1.61	0.09310	N	1	P	0.36535	0.557	B	0.31101	0.124	T	0.37911	-0.9685	10	0.87932	D	0	-16.7214	10.21	0.43134	0.0915:0.0:0.9085:0.0	.	53	Q9BUA3	CK084_HUMAN	T	53	ENSP00000294244:R53T	ENSP00000294244:R53T	R	+	2	0	C11orf84	63341883	0.427000	0.25514	0.294000	0.24946	0.278000	0.26855	3.006000	0.49529	1.330000	0.45394	0.561000	0.74099	AGA	.	.		0.617	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471		C	63585307	G	C	63585307	3	2	89	1	0	0	0	0	1	0	0	0	1669	942	33	4	164	4	C11orf84	11	63585307	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	51658239	63585307	71421209	71	11895										
MAP4K2	5871	hgsc.bcm.edu	37	chr11	64564456	64564456	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	cttggggcaaacacttacatGcaccttgggagttgggggga	15	8	0	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:64564456G>T	ENST00000294066.2	-	20	1496	c.1405C>A	c.(1405-1407)Cat>Aat	p.H469N	MAP4K2_ENST00000377350.3_Missense_Mutation_p.H461N	NM_004579.3	NP_004570.2	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase kinase 2	469					activation of JUN kinase activity (GO:0007257)|immune response (GO:0006955)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|positive regulation of JNK cascade (GO:0046330)|protein phosphorylation (GO:0006468)|vesicle targeting (GO:0006903)	Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(1)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(2)	8						ACACTTACATGCACCTTGGGA	0.652																																					p.H469N		Atlas-SNP	.											.	MAP4K2	83	.	0			c.C1405A						.						75	71	72					11																	64564456		2201	4297	6498	SO:0001583	missense	5871	exon20			TTACATGCACCTT	BC047865	CCDS8082.1	11q13.1	2011-06-09			ENSG00000168067	ENSG00000168067		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6864	protein-coding gene	gene with protein product		603166		RAB8IP		7515885	Standard	NM_004579		Approved	GCK, BL44	uc001obh.3	Q12851	OTTHUMG00000045328	ENST00000294066.2:c.1405C>A	chr11.hg19:g.64564456G>T	ENSP00000294066:p.His469Asn	53.0	0.0		130.0	57.0	NM_004579	Q86VU3	Missense_Mutation	SNP	ENST00000294066.2	hg19	CCDS8082.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278474	0.59758	.	.	ENSG00000168067	ENST00000294066;ENST00000377350	T;T	0.70516	-0.49;-0.49	4.51	4.51	0.55191	.	0.610916	0.16303	N	0.220371	T	0.62600	0.2441	L	0.46157	1.445	0.40163	D	0.977082	D;D	0.53885	0.963;0.963	B;B	0.41036	0.346;0.346	T	0.62163	-0.6912	10	0.25106	T	0.35	.	13.1403	0.59430	0.0:0.0:1.0:0.0	.	461;469	Q86VU3;Q12851	.;M4K2_HUMAN	N	469;461	ENSP00000294066:H469N;ENSP00000366567:H461N	ENSP00000294066:H469N	H	-	1	0	MAP4K2	64321032	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.092000	0.64511	2.247000	0.74100	0.558000	0.71614	CAT	.	.		0.652	MAP4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105239.1	NM_004579		T	64564456	G	T	64564456	3	4	89	1	0	0	0	0	1	0	0	0	9269	1319	46	3	1109	3	MAP4K2	11	64564456	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	979149	64564456	70442060	72	11896										
LTBP3	4054	hgsc.bcm.edu	37	chr11	65315205	65315205	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ccacgtgcaggcggtagccgCggttgcagtggcaattgtag	16	10	0	0	rs150534522		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:65315205C>G	ENST00000301873.5	-	13	2202	c.1934G>C	c.(1933-1935)cGc>cCc	p.R645P	LTBP3_ENST00000529189.1_5'Flank|LTBP3_ENST00000532932.1_Missense_Mutation_p.R75P|LTBP3_ENST00000536982.1_Missense_Mutation_p.R271P|LTBP3_ENST00000322147.4_Missense_Mutation_p.R645P	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	645	Cys-rich.|EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						GCGGTAGCCGCGGTTGCAGTG	0.711																																					p.R645P		Atlas-SNP	.											LTBP3,colon,carcinoma,0,1	LTBP3	55	.	0			c.G1934C						.						9	11	10					11																	65315205		2165	4255	6420	SO:0001583	missense	4054	exon13			TAGCCGCGGTTGC	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.1934G>C	chr11.hg19:g.65315205C>G	ENSP00000301873:p.Arg645Pro	8.0	1.0		62.0	13.0	NM_001130144	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	hg19	CCDS44647.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.804536	0.31869	.	.	ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000532932;ENST00000536982;ENST00000530866	D;D;D;D;D	0.91945	-2.94;-2.94;-2.94;-2.94;-2.94	4.39	4.39	0.52855	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.344897	0.30999	N	0.008453	D	0.84051	0.5387	N	0.01076	-1.035	0.30505	N	0.77	D;B;B;P;B;B	0.67145	0.996;0.013;0.005;0.8;0.004;0.114	P;B;B;B;B;B	0.62491	0.903;0.011;0.003;0.301;0.007;0.135	T	0.79176	-0.1911	10	0.18710	T	0.47	.	9.6673	0.39992	0.2078:0.7922:0.0:0.0	.	556;271;528;645;645;75	E9PKW1;F5GWC4;B9EG76;Q9NS15;Q9NS15-2;E9PJR2	.;.;.;LTBP3_HUMAN;.;.	P	645;645;75;271;556	ENSP00000326647:R645P;ENSP00000301873:R645P;ENSP00000435530:R75P;ENSP00000441912:R271P;ENSP00000435276:R556P	ENSP00000301873:R645P	R	-	2	0	LTBP3	65071781	0.006000	0.16342	1.000000	0.80357	0.802000	0.45316	-0.053000	0.11846	2.272000	0.75746	0.313000	0.20887	CGC	.	.		0.711	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070		G	65315205	C	G	65315205	3	3	89	1	0	0	0	0	1	0	0	0	9084	768	27	4	2041	4	LTBP3	11	65315205	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	750749	65315205	69691311	73	11897										
LTBP3	4054	hgsc.bcm.edu	37	chr11	65320914	65320914	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	acactgcagctggggacactTgtggcacttgctctggcccc	12	14	1	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:65320914T>G	ENST00000301873.5	-	4	1220	c.952A>C	c.(952-954)Aag>Cag	p.K318Q	LTBP3_ENST00000536982.1_Intron|LTBP3_ENST00000322147.4_Missense_Mutation_p.K318Q	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	318	TB 1.				bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						TGGGGACACTTGTGGCACTTG	0.667																																					p.K318Q		Atlas-SNP	.											.	LTBP3	55	.	0			c.A952C						.						28	30	29					11																	65320914		2194	4291	6485	SO:0001583	missense	4054	exon4			GACACTTGTGGCA	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.952A>C	chr11.hg19:g.65320914T>G	ENSP00000301873:p.Lys318Gln	48.0	0.0		160.0	66.0	NM_001130144	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	hg19	CCDS44647.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.756048	0.69648	.	.	ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000530866;ENST00000530426	D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11	4.8	4.8	0.61643	Matrix fibril-associated (3);TGF-beta binding (1);	0.059831	0.64402	D	0.000005	D	0.91613	0.7350	L	0.28115	0.83	0.80722	D	1	D;P;D;P	0.76494	0.999;0.775;0.999;0.778	D;B;D;B	0.87578	0.998;0.306;0.998;0.262	D	0.88261	0.2923	10	0.13853	T	0.58	.	12.3307	0.55038	0.0:0.0:0.0:1.0	.	229;201;318;318	E9PKW1;B9EG76;Q9NS15;Q9NS15-2	.;.;LTBP3_HUMAN;.	Q	318;318;229;39	ENSP00000326647:K318Q;ENSP00000301873:K318Q;ENSP00000435276:K229Q;ENSP00000432476:K39Q	ENSP00000301873:K318Q	K	-	1	0	LTBP3	65077490	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.182000	0.50910	2.022000	0.59522	0.413000	0.27773	AAG	.	.		0.667	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070		G	65320914	T	G	65320914	3	3	89	1	0	0	0	0	1	0	0	0	9084	1821	63	5	3059	5	LTBP3	11	65320914	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	5709	65320914	69685602	74	11898										
TBX10	347853	hgsc.bcm.edu	37	chr11	67399113	67399113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	caggccccaggcacaccacaGtgggggacaggagccccagc	14	16	0	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:67399113G>A	ENST00000335385.3	-	8	1208	c.1121C>T	c.(1120-1122)aCt>aTt	p.T374I	NUDT8_ENST00000376693.2_5'Flank|NUDT8_ENST00000301490.4_5'Flank	NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	374					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						GCACACCACAGTGGGGGACAG	0.667																																					p.T374I		Atlas-SNP	.											.	TBX10	25	.	0			c.C1121T						.						14	14	14					11																	67399113		2195	4282	6477	SO:0001583	missense	347853	exon8			ACCACAGTGGGGG	AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"T-boxes"	11593	protein-coding gene	gene with protein product		604648	"T-box 7"	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.1121C>T	chr11.hg19:g.67399113G>A	ENSP00000335191:p.Thr374Ile	12.0	0.0		44.0	18.0	NM_005995	Q14D64|Q86XS3	Missense_Mutation	SNP	ENST00000335385.3	hg19	CCDS31621.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.693808	0.30052	.	.	ENSG00000167800	ENST00000335385	D	0.86865	-2.18	3.58	2.63	0.31362	.	1.123250	0.07046	N	0.831045	T	0.79209	0.4407	N	0.24115	0.695	0.09310	N	1	P	0.45348	0.856	B	0.40477	0.33	T	0.70876	-0.4753	10	0.87932	D	0	.	7.4119	0.27021	0.1367:0.0:0.8633:0.0	.	374	O75333	TBX10_HUMAN	I	374	ENSP00000335191:T374I	ENSP00000335191:T374I	T	-	2	0	TBX10	67155689	0.010000	0.17322	0.027000	0.17364	0.005000	0.04900	1.897000	0.39799	1.719000	0.51432	0.561000	0.74099	ACT	.	.		0.667	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995		A	67399113	G	A	67399113	3	1	89	1	0	0	0	0	1	0	0	0	15666	1029	36	3	40	3	TBX10	11	67399113	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	2078199	67399113	67607403	75	11899										
NUMA1	4926	hgsc.bcm.edu	37	chr11	71726211	71726220	+	Frame_Shift_Del	DEL	CCTGATGGGC	CCTGATGGGC	-													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ccgcaggacttcagtctcagCctgatgggcctccccaagct					rs3750912	byFrequency	TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	CCTGATGGGC	CCTGATGGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:71726211_71726220delCCTGATGGGC	ENST00000393695.3	-	15	2660_2669	c.2329_2338delGCCCATCAGG	c.(2329-2340)gcccatcaggctfs	p.AHQA777fs	RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Frame_Shift_Del_p.AHQA777fs|NUMA1_ENST00000351960.6_Intron	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						TCAGTCTCAGCCTGATGGGCCTCCCCAAGC	0.619			T	RARA	APL																																p.777_780del		Atlas-INDEL	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.2330_2339del						.																																			SO:0001589	frameshift_variant	4926	exon15			.	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.2329_2338delGCCCATCAGG	chr11.hg19:g.71726211_71726220delCCTGATGGGC	ENSP00000377298:p.Ala777fs	23.0	0.0		67.0	10.0	NM_006185		Frame_Shift_Del	DEL	ENST00000393695.3	hg19	CCDS31633.1																																																																																			.	.		0.619	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			-	71726220	CCTGATGGGC	-	71726211	7	5	89	1	0	1	0	1	0	0	0	0	10759	739	26	0	4061	0	NUMA1	11	71726211	Frame_Shift_Del	DEL	CCTGATGGGC	TCGA-DD-A116-01A-11D-A12Z-10	4327098	71726211	63280305	76	11900										
SYTL2	54843	hgsc.bcm.edu	37	chr11	85436897	85436897	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gttttttgaggccatgtcctAttttcagaaacacttggttc	8	8	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:85436897A>G	ENST00000528231.1	-	7	1737				SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000354566.3_Silent_p.N201N|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000359152.5_Silent_p.N725N|SYTL2_ENST00000525423.1_Silent_p.N201N|SYTL2_ENST00000527523.1_Intron	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		GCCATGTCCTATTTTCAGAAA	0.403																																					p.N201N		Atlas-SNP	.											.	SYTL2	231	.	0			c.T603C						.						137	126	130					11																	85436897		2203	4299	6502	SO:0001627	intron_variant	54843	exon1			TGTCCTATTTTCA	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2041T>C	chr11.hg19:g.85436897A>G		134.0	0.0		451.0	158.0	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	hg19	CCDS53688.1																																																																																			.	.		0.403	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		G	85436897	A	G	85436897	1	3	89	0	1	0	0	0	0	0	0	0	15498	446	16	2		2	SYTL2	11	85436897	Intron	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	13710686	85436897	49569619	77	11901										
SESN3	143686	hgsc.bcm.edu	37	chr11	94918494	94918494	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	atcacaaacgcagaaattgtTgactgatattagcctgaatc	7	8	1	4			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:94918494T>C	ENST00000536441.1	-	5	1024	c.688A>G	c.(688-690)Aac>Gac	p.N230D	SESN3_ENST00000416495.2_Missense_Mutation_p.N230D|RP11-712B9.2_ENST00000534864.1_RNA|SESN3_ENST00000393234.1_Missense_Mutation_p.N230D|SESN3_ENST00000278499.2_Missense_Mutation_p.N91D|RP11-712B9.2_ENST00000534891.1_RNA	NM_001271594.1|NM_144665.2	NP_001258523.1|NP_653266.2	P58005	SESN3_HUMAN	sestrin 3	230					glucose homeostasis (GO:0042593)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)|response to insulin (GO:0032868)	nucleus (GO:0005634)				endometrium(5)|large_intestine(6)|lung(3)|skin(1)|stomach(1)	16		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.234)		CAGAAATTGTTGACTGATATT	0.388																																					p.N230D		Atlas-SNP	.											.	SESN3	51	.	0			c.A688G						.						185	185	185					11																	94918494		2201	4298	6499	SO:0001583	missense	143686	exon5			AATTGTTGACTGA	AK096300	CCDS8303.1, CCDS60938.1	11q21	2005-09-18			ENSG00000149212	ENSG00000149212			23060	protein-coding gene	gene with protein product		607768				12607115	Standard	NM_144665		Approved	SEST3, MGC29667	uc001pfj.4	P58005	OTTHUMG00000167829	ENST00000536441.1:c.688A>G	chr11.hg19:g.94918494T>C	ENSP00000441927:p.Asn230Asp	95.0	0.0		134.0	47.0	NM_144665	B7Z7P9|Q96AD1	Missense_Mutation	SNP	ENST00000536441.1	hg19	CCDS8303.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.856634	0.51376	.	.	ENSG00000149212	ENST00000536441;ENST00000278499;ENST00000393234;ENST00000416495	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	5.68	5.68	0.88126	.	0.211356	0.47852	D	0.000206	T	0.16938	0.0407	L	0.36672	1.1	0.45415	D	0.998397	B;B;B	0.29301	0.011;0.241;0.011	B;B;B	0.26969	0.025;0.075;0.046	T	0.05099	-1.0906	10	0.10111	T	0.7	0.0614	15.9249	0.79609	0.0:0.0:0.0:1.0	.	91;230;230	B7Z7P9;P58005-3;P58005	.;.;SESN3_HUMAN	D	230;91;230;230	ENSP00000441927:N230D;ENSP00000278499:N91D;ENSP00000376926:N230D;ENSP00000407008:N230D	ENSP00000278499:N91D	N	-	1	0	SESN3	94558142	1.000000	0.71417	0.889000	0.34880	0.986000	0.74619	7.256000	0.78350	2.170000	0.68504	0.459000	0.35465	AAC	.	.		0.388	SESN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396475.3	NM_144665		C	94918494	T	C	94918494	3	2	89	1	0	0	0	0	1	0	0	0	14141	1812	63	2	814	2	SESN3	11	94918494	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	9481597	94918494	40088022	78	11902										
NCAM1	4684	hgsc.bcm.edu	37	chr11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ccctcccagccagcagattaCaatgctgccaaactaaggat					rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000532002.1_RNA|RP11-629G13.1_ENST00000500537.2_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		0.0	0.0		37.0	37.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		-	112832363	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	112832332	6	5	89	0	1	1	0	1	0	0	0	0	10211	493	17	0		0	NCAM1	11	112832332	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	TCGA-DD-A116-01A-11D-A12Z-10	17913838	112832332	22174184	79	11903										
ERC1	23085	hgsc.bcm.edu	37	chr12	1517402	1517402	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	atcaaacaaatcacaagcccTccccagaccaggtaagatgg	7	13	2	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:1517402T>A	ENST00000397203.2	+	17	3419	c.3013T>A	c.(3013-3015)Tcc>Acc	p.S1005T	ERC1_ENST00000589028.1_Missense_Mutation_p.S1005T|ERC1_ENST00000355446.5_Missense_Mutation_p.S1005T|ERC1_ENST00000360905.4_Missense_Mutation_p.S1005T|ERC1_ENST00000546231.2_Missense_Mutation_p.S1009T|ERC1_ENST00000543086.3_Missense_Mutation_p.S977T			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	1005					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			TCACAAGCCCTCCCCAGACCA	0.388																																					p.S1005T		Atlas-SNP	.											.	ERC1	95	.	0			c.T3013A						.						82	70	74					12																	1517402		2203	4300	6503	SO:0001583	missense	23085	exon17			AAGCCCTCCCCAG	AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"RAB6 interacting protein 2"	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.3013T>A	chr12.hg19:g.1517402T>A	ENSP00000380386:p.Ser1005Thr	17.0	0.0		63.0	18.0	NM_178040	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	hg19	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.870894	0.91587	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000299183;ENST00000543086;ENST00000542302;ENST00000545948;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394;ENST00000538971	T;T;T;T;T;T;T	0.34859	1.39;1.59;1.56;1.4;1.65;1.59;1.34	5.93	5.93	0.95920	.	0.062950	0.64402	D	0.000003	T	0.48390	0.1497	L	0.29908	0.895	0.58432	D	0.999999	P;D;D;D	0.61697	0.913;0.99;0.99;0.987	P;D;D;P	0.72982	0.716;0.979;0.979;0.857	T	0.38650	-0.9651	10	0.35671	T	0.21	-8.2394	16.3798	0.83452	0.0:0.0:0.0:1.0	.	713;981;977;1005	F5H327;Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;.;RB6I2_HUMAN	T	937;1005;981;937;709;977;981;709;1005;1005;1005;981;713	ENSP00000340054:S937T;ENSP00000380386:S1005T;ENSP00000438546:S977T;ENSP00000442976:S709T;ENSP00000347621:S1005T;ENSP00000354158:S1005T;ENSP00000410064:S981T	ENSP00000299183:S709T	S	+	1	0	ERC1	1387663	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.342000	0.79310	2.271000	0.75665	0.533000	0.62120	TCC	.	.		0.388	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		A	1517402	T	A	1517402	3	1	89	1	0	0	0	0	1	0	0	0	5212	1551	54	4	3075	4	ERC1	12	1517402	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10		1517402	132334493	80	11904										
C1S	716	hgsc.bcm.edu	37	chr12	7177505	7177505	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gtgcggctgaaagacccagtGaaaatgggacccaccgtctc	12	12	1	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:7177505G>A	ENST00000406697.1	+	15	2245	c.1617G>A	c.(1615-1617)gtG>gtA	p.V539V	C1S_ENST00000328916.3_Silent_p.V539V|C1S_ENST00000402681.3_Silent_p.V372V|C1S_ENST00000495061.1_3'UTR|C1S_ENST00000360817.5_Silent_p.V539V			P09871	C1S_HUMAN	complement component 1, s subcomponent	539	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	AAGACCCAGTGAAAATGGGAC	0.537																																					p.V539V	GBM(156;750 1943 12971 24779 31015)	Atlas-SNP	.											.	C1S	93	.	0			c.G1617A						.						60	58	59					12																	7177505		2203	4300	6503	SO:0001819	synonymous_variant	716	exon12			CCCAGTGAAAATG		CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"Complement system"	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.1617G>A	chr12.hg19:g.7177505G>A		35.0	0.0		86.0	33.0	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Silent	SNP	ENST00000406697.1	hg19	CCDS31735.1																																																																																			.	.		0.537	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734		A	7177505	G	A	7177505	2	1	89	1	0	0	0	0	0	0	0	1	1976	1277	45	3		3	C1S	12	7177505	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	5660103	7177505	126674390	81	11905										
PRB4	5545	hgsc.bcm.edu	37	chr12	11461456	11461456	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ttcctggatgaggtgggggaCcttgggactggttacctcct	15	9	0	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:11461456C>A	ENST00000535904.1	-	3	494	c.461G>T	c.(460-462)gGt>gTt	p.G154V	PRB4_ENST00000445719.2_Intron|PRB4_ENST00000279575.1_Missense_Mutation_p.G154V			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	175	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.		Missing (in allele M and allele S).	Missing (in Ref. 7; CAA30542). {ECO:0000305}.		extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						AGGTGGGGGACCTTGGGACTG	0.607										HNSCC(22;0.051)																											p.G154V		Atlas-SNP	.											.	PRB4	59	.	0			c.G461T						.						193	211	205					12																	11461456		2203	4300	6503	SO:0001583	missense	5545	exon3			GGGGGACCTTGGG		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.461G>T	chr12.hg19:g.11461456C>A	ENSP00000442834:p.Gly154Val	144.0	0.0		499.0	173.0	NM_002723	A1L439|O00600|P02813|P10161|P10162|P81489	Missense_Mutation	SNP	ENST00000535904.1	hg19	CCDS8641.1	.	.	.	.	.	.	.	.	.	.	.	4.941	0.174747	0.09391	.	.	ENSG00000230657	ENST00000279575;ENST00000535904	T;T	0.06068	3.35;3.35	0.903	-1.68	0.08212	.	.	.	.	.	T	0.09686	0.0238	M	0.75615	2.305	0.09310	N	1	D	0.58268	0.982	P	0.47673	0.554	T	0.13683	-1.0500	9	0.38643	T	0.18	.	3.7245	0.08469	0.0:0.46:0.0:0.54	.	154	E9PAL0	.	V	154	ENSP00000279575:G154V;ENSP00000442834:G154V	ENSP00000279575:G154V	G	-	2	0	PRB4	11352723	0.011000	0.17503	0.000000	0.03702	0.001000	0.01503	-0.528000	0.06193	-0.563000	0.06078	-0.362000	0.07510	GGT	.	.		0.607	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723		A	11461456	C	A	11461456	3	1	89	1	0	0	0	0	1	0	0	0	12457	507	18	3	286	3	PRB4	12	11461456	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	4283951	11461456	122390439	82	11906										
SLC2A13	114134	hgsc.bcm.edu	37	chr12	40499574	40499574	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	caggctgctcaggctccgcaGcgtgtactccacattctcgc	10	16	2	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:40499574G>C	ENST00000280871.4	-	1	87	c.37C>G	c.(37-39)Ctg>Gtg	p.L13V	SLC2A13_ENST00000380858.1_Missense_Mutation_p.L13V	NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	13					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				AGGCTCCGCAGCGTGTACTCC	0.751										HNSCC(50;0.14)																											p.L13V		Atlas-SNP	.											.	SLC2A13	91	.	0			c.C37G						.						1	1	1					12																	40499574		964	1903	2867	SO:0001583	missense	114134	exon1			TCCGCAGCGTGTA	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.37C>G	chr12.hg19:g.40499574G>C	ENSP00000280871:p.Leu13Val	9.0	0.0		56.0	22.0	NM_052885	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	hg19	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	G	16.18	3.051601	0.55218	.	.	ENSG00000151229	ENST00000280871;ENST00000380858	D;D	0.83163	-1.68;-1.69	4.0	2.06	0.26882	.	2.181300	0.03396	U	0.202639	T	0.72011	0.3408	N	0.14661	0.345	0.37298	D	0.908574	B;B	0.26744	0.158;0.158	B;B	0.22601	0.04;0.04	T	0.60125	-0.7324	10	0.56958	D	0.05	-1.066	8.0877	0.30782	0.0878:0.0:0.7579:0.1544	.	13;13	Q96QE2;E9PE47	MYCT_HUMAN;.	V	13	ENSP00000280871:L13V;ENSP00000370239:L13V	ENSP00000280871:L13V	L	-	1	2	SLC2A13	38785841	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.534000	0.60622	0.639000	0.30564	0.462000	0.41574	CTG	.	.		0.751	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			C	40499574	G	C	40499574	3	2	89	1	0	0	0	0	1	0	0	0	14557	962	34	4	1949	4	SLC2A13	12	40499574	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	29038118	40499574	93352321	83	11907										
GXYLT1	283464	hgsc.bcm.edu	37	chr12	42512967	42512967	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tcaacaggctgtattttcagActgtacctaataggaaagaa	8	7	2	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:42512967A>T	ENST00000398675.3	-	3	553	c.321T>A	c.(319-321)agT>agA	p.S107R	GXYLT1_ENST00000280876.6_Missense_Mutation_p.S76R	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	107					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						GTATTTTCAGACTGTACCTAA	0.363																																					p.S107R		Atlas-SNP	.											.	GXYLT1	47	.	0			c.T321A						.						84	77	79					12																	42512967		1887	4120	6007	SO:0001583	missense	283464	exon3			TTTCAGACTGTAC	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"Glycosyltransferase family 8 domain containing"	27482	protein-coding gene	gene with protein product		613321	"glycosyltransferase 8 domain containing 3"	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.321T>A	chr12.hg19:g.42512967A>T	ENSP00000381666:p.Ser107Arg	80.0	0.0		300.0	21.0	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Missense_Mutation	SNP	ENST00000398675.3	hg19	CCDS41772.1	.	.	.	.	.	.	.	.	.	.	A	3.804	-0.041095	0.07452	.	.	ENSG00000151233	ENST00000398675;ENST00000280876	.	.	.	5.73	-0.0214	0.13951	.	13.484300	0.00166	N	0.000000	T	0.17238	0.0414	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.16217	-1.0410	9	0.16420	T	0.52	0.0014	6.6682	0.23054	0.6919:0.0:0.1958:0.1123	.	76;107	Q4G148-2;Q4G148	.;GXLT1_HUMAN	R	107;76	.	ENSP00000280876:S76R	S	-	3	2	GXYLT1	40799234	0.001000	0.12720	0.003000	0.11579	0.400000	0.30750	0.574000	0.23714	0.117000	0.18138	0.482000	0.46254	AGT	.	.		0.363	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597		T	42512967	A	T	42512967	3	4	89	1	0	0	0	0	1	0	0	0	6912	272	10	4	1025	4	GXYLT1	12	42512967	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	2013393	42512967	91338928	84	11908										
ACVRL1	94	hgsc.bcm.edu	37	chr12	52307800	52307800	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ccacagggagtggctcagggCtccccttcctggtgcagagg	15	13	1	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:52307800C>T	ENST00000388922.4	+	5	851	c.568C>T	c.(568-570)Ctc>Ttc	p.L190F	ACVRL1_ENST00000419526.2_Intron|ACVRL1_ENST00000550683.1_Missense_Mutation_p.L204F	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	190	GS. {ECO:0000255|PROSITE- ProRule:PRU00585}.				activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	TGGCTCAGGGCTCCCCTTCCT	0.647																																					p.L190F		Atlas-SNP	.											.	ACVRL1	60	.	0			c.C568T						.						67	53	58					12																	52307800		2203	4300	6503	SO:0001583	missense	94	exon5			TCAGGGCTCCCCT	L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567			175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2		8397373, 8640225	Standard	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	ENST00000388922.4:c.568C>T	chr12.hg19:g.52307800C>T	ENSP00000373574:p.Leu190Phe	44.0	0.0		172.0	72.0	NM_000020	A6NGA8	Missense_Mutation	SNP	ENST00000388922.4	hg19	CCDS31804.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.661461	0.88154	.	.	ENSG00000139567	ENST00000388922;ENST00000267008;ENST00000550683	D;D	0.96459	-4.02;-4.02	5.18	5.18	0.71444	Protein kinase-like domain (1);TGF beta receptor, GS motif (3);	0.000000	0.40222	N	0.001159	D	0.97551	0.9198	L	0.60957	1.885	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98221	1.0478	10	0.87932	D	0	.	17.6209	0.88080	0.0:1.0:0.0:0.0	.	190	P37023	ACVL1_HUMAN	F	190;190;204	ENSP00000373574:L190F;ENSP00000447884:L204F	ENSP00000267008:L190F	L	+	1	0	ACVRL1	50594067	0.998000	0.40836	0.990000	0.47175	0.994000	0.84299	3.935000	0.56560	2.662000	0.90505	0.655000	0.94253	CTC	.	.		0.647	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2			T	52307800	C	T	52307800	3	4	89	1	0	0	0	0	1	0	0	0	225	797	28	3	582	3	ACVRL1	12	52307800	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	9794833	52307800	81544095	85	11909										
KRT75	9119	hgsc.bcm.edu	37	chr12	52826871	52826871	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	catgttcctcagttcagcttCaagcctgcccctctcggtgg	9	15	4	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:52826871C>A	ENST00000252245.5	-	2	884	c.664G>T	c.(664-666)Gaa>Taa	p.E222*		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	222	Coil 1B.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		AGTTCAGCTTCAAGCCTGCCC	0.537																																					p.E222X		Atlas-SNP	.											.	KRT75	75	.	0			c.G664T						.						119	108	111					12																	52826871		2203	4300	6503	SO:0001587	stop_gained	9119	exon2			CAGCTTCAAGCCT	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"-", "Intermediate filaments type II, keratins (basic)"	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.664G>T	chr12.hg19:g.52826871C>A	ENSP00000252245:p.Glu222*	53.0	0.0		192.0	83.0	NM_004693	B4DQU4|Q9NSA9	Nonsense_Mutation	SNP	ENST00000252245.5	hg19	CCDS8827.1	.	.	.	.	.	.	.	.	.	.	C	38	7.121599	0.98077	.	.	ENSG00000170454	ENST00000252245	.	.	.	5.77	5.77	0.91146	.	0.111882	0.38897	N	0.001521	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	16.252	0.82491	0.0:0.8675:0.1325:0.0	.	.	.	.	X	222	.	ENSP00000252245:E222X	E	-	1	0	KRT75	51113138	0.246000	0.23909	0.482000	0.27366	0.854000	0.48673	2.126000	0.42026	2.723000	0.93209	0.655000	0.94253	GAA	.	.		0.537	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693		A	52826871	C	A	52826871	4	1	89	1	0	0	0	0	0	1	0	0	8497	835	29	3	1023	3	KRT75	12	52826871	Nonsense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	519071	52826871	81025024	86	11910										
PAWR	5074	hgsc.bcm.edu	37	chr12	80083895	80083895	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	agcggcgtcgctgctgccccCtcccgggggggccgggcccg	18	18	0	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:80083895C>A	ENST00000328827.4	-	2	502	c.130G>T	c.(130-132)Ggg>Tgg	p.G44W	PAWR_ENST00000547571.1_5'Flank|RP11-530C5.1_ENST00000551995.1_lincRNA	NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator	44					actin filament bundle assembly (GO:0051017)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|interleukin-2 biosynthetic process (GO:0042094)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|positive regulation of apoptotic process (GO:0043065)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)|leucine zipper domain binding (GO:0043522)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						CTGCTGCCCCCTcccgggggg	0.756																																					p.G44W		Atlas-SNP	.											.	PAWR	14	.	0			c.G130T						.						1	1	1					12																	80083895		921	2291	3212	SO:0001583	missense	5074	exon2			TGCCCCCTCCCGG	U63809	CCDS31863.1	12q21.2	2013-03-07			ENSG00000177425	ENSG00000177425			8614	protein-coding gene	gene with protein product	"prostate apoptosis response-4"	601936				8943350, 9790775	Standard	NM_002583		Approved	par-4, PAR4	uc001syx.3	Q96IZ0	OTTHUMG00000170080	ENST00000328827.4:c.130G>T	chr12.hg19:g.80083895C>A	ENSP00000328088:p.Gly44Trp	15.0	0.0		22.0	6.0	NM_002583	O75796|Q6FHY9|Q8N700	Missense_Mutation	SNP	ENST00000328827.4	hg19	CCDS31863.1	.	.	.	.	.	.	.	.	.	.	C	8.981	0.975325	0.18736	.	.	ENSG00000177425	ENST00000328827;ENST00000548426;ENST00000552637	T;T;T	0.57907	2.71;0.38;0.37	2.45	0.216	0.15258	.	0.652385	0.14023	N	0.346688	T	0.50565	0.1623	L	0.34521	1.04	0.09310	N	1	D	0.61697	0.99	P	0.59171	0.853	T	0.39440	-0.9614	9	.	.	.	-6.6033	6.6153	0.22773	0.2117:0.5993:0.189:0.0	.	44	Q96IZ0	PAWR_HUMAN	W	44	ENSP00000328088:G44W;ENSP00000447454:G44W;ENSP00000449928:G44W	.	G	-	1	0	PAWR	78608026	0.155000	0.22806	0.013000	0.15412	0.391000	0.30476	1.772000	0.38552	-0.112000	0.11979	0.313000	0.20887	GGG	.	.		0.756	PAWR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407175.1	NM_002583		A	80083895	C	A	80083895	3	1	89	1	0	0	0	0	1	0	0	0	11486	681	24	3	916	3	PAWR	12	80083895	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	27257024	80083895	53768000	87	11911										
GIT2	9815	hgsc.bcm.edu	37	chr12	110385195	110385195	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gccccgggcagacggacgtcTctttaaggaagagtggttgg	16	9	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:110385195T>C	ENST00000355312.3	-	15	1506	c.1507A>G	c.(1507-1509)Aga>Gga	p.R503G	GIT2_ENST00000356259.4_Intron|GIT2_ENST00000354574.4_Missense_Mutation_p.R455G|GIT2_ENST00000547815.1_3'UTR|GIT2_ENST00000457474.2_Missense_Mutation_p.R455G|GIT2_ENST00000338373.5_Intron|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000361006.5_Missense_Mutation_p.R503G|GIT2_ENST00000551209.1_Missense_Mutation_p.R452G|GIT2_ENST00000553118.1_Intron|GIT2_ENST00000360185.4_Missense_Mutation_p.R453G|GIT2_ENST00000343646.5_Missense_Mutation_p.R423G	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	503					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						GACGGACGTCTCTTTAAGGAA	0.522																																					p.R503G		Atlas-SNP	.											.	GIT2	81	.	0			c.A1507G						.						122	109	113					12																	110385195		2203	4300	6503	SO:0001583	missense	9815	exon15			GACGTCTCTTTAA	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4273	protein-coding gene	gene with protein product		608564	"G protein-coupled receptor kinase interactor 2"			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.1507A>G	chr12.hg19:g.110385195T>C	ENSP00000347464:p.Arg503Gly	88.0	0.0		282.0	98.0	NM_001135214	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Missense_Mutation	SNP	ENST00000355312.3	hg19	CCDS9138.1	.	.	.	.	.	.	.	.	.	.	T	10.77	1.444315	0.25987	.	.	ENSG00000139436	ENST00000355312;ENST00000360185;ENST00000354574;ENST00000343646;ENST00000457474;ENST00000361006;ENST00000551209;ENST00000542273	T;T;T;T;T;T;T	0.78126	-0.66;-0.74;-1.15;-0.85;-1.12;-0.66;-0.77	5.97	3.04	0.35103	.	0.000000	0.85682	D	0.000000	T	0.70736	0.3258	L	0.48642	1.525	0.80722	D	1	B;B;B;B;B	0.10296	0.003;0.003;0.0;0.002;0.0	B;B;B;B;B	0.10450	0.005;0.005;0.001;0.001;0.003	T	0.62320	-0.6879	10	0.31617	T	0.26	.	14.1029	0.65068	0.0:0.0:0.4562:0.5438	.	455;455;503;441;503	Q14161-10;F8WAK2;Q14161;B4E027;Q14161-5	.;.;GIT2_HUMAN;.;.	G	503;453;455;423;455;503;452;441	ENSP00000347464:R503G;ENSP00000353312:R453G;ENSP00000346585:R455G;ENSP00000340938:R423G;ENSP00000391813:R455G;ENSP00000354282:R503G;ENSP00000448832:R452G	ENSP00000340938:R423G	R	-	1	2	GIT2	108869578	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.150000	0.42254	0.361000	0.24292	-0.460000	0.05396	AGA	.	.		0.522	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169		C	110385195	T	C	110385195	3	2	89	1	0	0	0	0	1	0	0	0	6405	1559	54	2	796	2	GIT2	12	110385195	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	30301300	110385195	23466700	88	11912										
PPP1CC	5501	hgsc.bcm.edu	37	chr12	111162541	111162541	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aaacagtctgtgaaagttttCcatagtttaatgttgtatct	7	5	2	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:111162541C>T	ENST00000335007.5	-	4	637	c.447G>A	c.(445-447)tgG>tgA	p.W149*	PPP1CC_ENST00000340766.5_Nonsense_Mutation_p.W149*|PPP1CC_ENST00000546933.1_Nonsense_Mutation_p.W158*|PPP1CC_ENST00000550991.1_Nonsense_Mutation_p.W149*|PPP1CC_ENST00000551676.1_Nonsense_Mutation_p.W149*	NM_002710.3	NP_002701.1	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma isozyme	149					cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|mitotic cell cycle (GO:0000278)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|large_intestine(2)|lung(3)	6						TGAAAGTTTTCCATAGTTTAA	0.368																																					p.W149X		Atlas-SNP	.											.	PPP1CC	22	.	0			c.G447A						.						154	135	142					12																	111162541		2203	4300	6503	SO:0001587	stop_gained	5501	exon4			AGTTTTCCATAGT		CCDS9150.1, CCDS58279.1	12q24.1-q24.2	2013-01-17	2010-03-05		ENSG00000186298	ENSG00000186298	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9283	protein-coding gene	gene with protein product		176914	"protein phosphatase 1, catalytic subunit, gamma isoform"				Standard	NM_002710		Approved	PP1C, PP1gamma	uc021rdx.1	P36873	OTTHUMG00000169531	ENST00000335007.5:c.447G>A	chr12.hg19:g.111162541C>T	ENSP00000335084:p.Trp149*	99.0	0.0		362.0	40.0	NM_002710		Nonsense_Mutation	SNP	ENST00000335007.5	hg19	CCDS9150.1	.	.	.	.	.	.	.	.	.	.	C	38	7.122684	0.98077	.	.	ENSG00000186298	ENST00000335007;ENST00000340766;ENST00000546933;ENST00000550991;ENST00000551676	.	.	.	5.86	5.86	0.93980	.	0.052633	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.3039	20.5632	0.99335	0.0:1.0:0.0:0.0	.	.	.	.	X	149;149;158;149;149	.	ENSP00000335084:W149X	W	-	3	0	PPP1CC	109646924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.937000	0.99478	0.650000	0.86243	TGG	.	.		0.368	PPP1CC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404659.1			T	111162541	C	T	111162541	4	4	89	1	0	0	0	0	0	1	0	0	12363	856	30	3	540	3	PPP1CC	12	111162541	Nonsense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	777346	111162541	22689354	89	11913										
NOS1	4842	hgsc.bcm.edu	37	chr12	117696926	117696926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	cacaatgtcatattcttccaTggacatcacctaggtgggca	8	11	3	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr12:117696926T>C	ENST00000338101.4	-	14	2381	c.2377A>G	c.(2377-2379)Atg>Gtg	p.M793V	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.M793V			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		TATTCTTCCATGGACATCACC	0.522																																					p.M793V	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.A2377G						.						105	102	103					12																	117696926		2006	4167	6173	SO:0001583	missense	4842	exon15			CTTCCATGGACAT		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2377A>G	chr12.hg19:g.117696926T>C	ENSP00000337459:p.Met793Val	43.0	0.0		156.0	58.0	NM_000620		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.230172	0.79688	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.73047	-0.71;-0.71	4.95	4.95	0.65309	Flavodoxin/nitric oxide synthase (2);	0.000000	0.85682	D	0.000000	D	0.85071	0.5613	M	0.85462	2.755	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.87639	0.2521	10	0.72032	D	0.01	-36.9725	14.4302	0.67243	0.0:0.0:0.0:1.0	.	793	P29475	NOS1_HUMAN	V	688;793;793;793	ENSP00000320758:M793V;ENSP00000337459:M793V	ENSP00000320758:M793V	M	-	1	0	NOS1	116181309	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.939000	0.70179	2.070000	0.61991	0.533000	0.62120	ATG	.	.		0.522	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			C	117696926	T	C	117696926	3	2	89	1	0	0	0	0	1	0	0	0	10550	1464	51	2	1987	2	NOS1	12	117696926	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	6534385	117696926	16154969	90	11914										
FREM2	341640	hgsc.bcm.edu	37	chr13	39265478	39265478	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tattaatggcaacagatttaGattcagaagacaaatctttg	7	5	2	4			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr13:39265478G>C	ENST00000280481.7	+	1	4213	c.3997G>C	c.(3997-3999)Gat>Cat	p.D1333H		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1333					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D1333Y(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AACAGATTTAGATTCAGAAGA	0.353																																					p.D1333H		Atlas-SNP	.											FREM2,rectum,carcinoma,0,1	FREM2	385	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3997C						.						76	80	79					13																	39265478		2203	4300	6503	SO:0001583	missense	341640	exon1			GATTTAGATTCAG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.3997G>C	chr13.hg19:g.39265478G>C	ENSP00000280481:p.Asp1333His	64.0	0.0		73.0	42.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.781469	0.70222	.	.	ENSG00000150893	ENST00000280481	T	0.74106	-0.81	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.92047	0.7480	H	0.97611	4.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93768	0.7072	10	0.87932	D	0	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	1333	Q5SZK8	FREM2_HUMAN	H	1333	ENSP00000280481:D1333H	ENSP00000280481:D1333H	D	+	1	0	FREM2	38163478	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.864000	0.99589	2.894000	0.99253	0.655000	0.94253	GAT	.	.		0.353	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39265478	G	C	39265478	3	2	89	1	0	0	0	0	1	0	0	0	6053	942	33	4	3999	4	FREM2	13	39265478	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10		39265478	75904400	91	11915										
POTEG	404785	hgsc.bcm.edu	37	chr14	19553573	19553573	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ctggagaccacgacgattctGctatgaagacactcaggagc	11	11	2	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr14:19553573G>T	ENST00000409832.3	+	1	209	c.157G>T	c.(157-159)Gct>Tct	p.A53S		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	53										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						CGACGATTCTGCTATGAAGAC	0.607																																					p.A53S		Atlas-SNP	.											.	POTEG	118	.	0			c.G157T						.						104	143	130					14																	19553573		2198	4286	6484	SO:0001583	missense	404785	exon1			GATTCTGCTATGA		CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33896	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 4"	608916	"ANKRD26-like family C, member 2"	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.157G>T	chr14.hg19:g.19553573G>T	ENSP00000386971:p.Ala53Ser	173.0	0.0		1087.0	131.0	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	hg19	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	g	4.687	0.127650	0.08981	.	.	ENSG00000222036	ENST00000409832	T	0.27720	1.65	.	.	.	.	.	.	.	.	T	0.19446	0.0467	L	0.40543	1.245	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.33954	-0.9848	7	0.11794	T	0.64	.	.	.	.	.	53	Q6S5H5	POTEG_HUMAN	S	53	ENSP00000386971:A53S	ENSP00000386971:A53S	A	+	1	0	POTEG	18623573	0.000000	0.05858	0.005000	0.12908	0.005000	0.04900	-0.334000	0.07883	0.162000	0.19483	0.165000	0.16767	GCT	.	.		0.607	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356		T	19553573	G	T	19553573	3	4	89	1	0	0	0	0	1	0	0	0	12275	1319	46	3	159	3	POTEG	14	19553573	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10		19553573	87795967	92	11916										
CCNB1IP1	57820	hgsc.bcm.edu	37	chr14	20779825	20779826	+	Frame_Shift_Ins	INS	-	-	A													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggtgctgtgggagaacccgcINSaaaaaatggtctgaactgaa							TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr14:20779825_20779826insA	ENST00000398169.3	-	7	1333_1334	c.717_718insT	c.(715-720)tttgcgfs	p.A240fs	CCNB1IP1_ENST00000358932.4_Frame_Shift_Ins_p.A240fs|CCNB1IP1_ENST00000353689.4_Frame_Shift_Ins_p.A240fs|CCNB1IP1_ENST00000398163.2_Frame_Shift_Ins_p.A240fs|CCNB1IP1_ENST00000437553.2_Frame_Shift_Ins_p.A240fs|CCNB1IP1_ENST00000398160.2_Frame_Shift_Ins_p.A240fs			Q9NPC3	CIP1_HUMAN	cyclin B1 interacting protein 1, E3 ubiquitin protein ligase	240					blastocyst formation (GO:0001825)|chiasma assembly (GO:0051026)|protein ubiquitination (GO:0016567)|reciprocal meiotic recombination (GO:0007131)|spermatid development (GO:0007286)	synaptonemal complex (GO:0000795)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		HMGA2/CCNB1IP1(2)	breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	9	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;8.86e-07)|all cancers(55;4.98e-06)	GBM - Glioblastoma multiforme(265;0.0164)		GGAGAACCCGCAAAAAATGGTC	0.45			T	HMGA2	leiomyoma																																p.A240fs		Atlas-Indel,Pindel	.		Dom	yes		14	14q11.2	57820	"cyclin B1 interacting protein 1, E3 ubiquitin protein ligase"		M	.	CCNB1IP1	29	.	0			c.718_719insT						.																																			SO:0001589	frameshift_variant	57820	exon7			.	AF216381	CCDS9547.1	14q11.2	2014-02-04	2011-01-31	2004-01-14	ENSG00000100814	ENSG00000100814			19437	protein-coding gene	gene with protein product	"human enhancer of invasion 10"	608249	"chromosome 14 open reading frame 18", "cyclin B1 interacting protein 1"	C14orf18		12612082, 21779533	Standard	NM_021178		Approved	HEI10	uc001vwy.4	Q9NPC3	OTTHUMG00000029509	ENST00000398169.3:c.718dupT	chr14.hg19:g.20779831_20779831dupA	ENSP00000381235:p.Ala240fs	90.0	0.0		291.0	83.0	NM_021178		Frame_Shift_Ins	INS	ENST00000398169.3	hg19	CCDS9547.1																																																																																			.	.		0.45	CCNB1IP1-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073538.3	NM_021178, NM_182849, NM_182851, NM_182852		A	20779826	-	A	20779825	7	5	89	1	0	1	1	0	0	0	0	0	2914	710	25	0	119	0	CCNB1IP1	14	20779825	Frame_Shift_Ins	INS	-	TCGA-DD-A116-01A-11D-A12Z-10	1226252	20779825	86569715	93	11917										
TEP1	7011	hgsc.bcm.edu	37	chr14	20872028	20872028	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gggcaccagcttattcttatCtccctcagccaggctctgtc	8	15	4	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr14:20872028C>A	ENST00000262715.5	-	6	1088	c.1048G>T	c.(1048-1050)Gat>Tat	p.D350Y	TEP1_ENST00000556935.1_Intron	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	350	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TTATTCTTATCTCCCTCAGCC	0.517																																					p.D350Y		Atlas-SNP	.											.	TEP1	224	.	0			c.G1048T						.						82	81	81					14																	20872028		2203	4300	6503	SO:0001583	missense	7011	exon6			TCTTATCTCCCTC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.1048G>T	chr14.hg19:g.20872028C>A	ENSP00000262715:p.Asp350Tyr	22.0	0.0		56.0	26.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	C	15.52	2.857644	0.51376	.	.	ENSG00000129566	ENST00000262715;ENST00000359243	T	0.19250	2.16	5.69	2.87	0.33458	TROVE (2);	1.146690	0.06270	N	0.695529	T	0.19886	0.0478	L	0.29908	0.895	0.09310	N	1	P	0.52577	0.954	B	0.42282	0.382	T	0.33317	-0.9873	10	0.62326	D	0.03	0.1176	11.4947	0.50402	0.0:0.5666:0.349:0.0844	.	350	Q99973	TEP1_HUMAN	Y	350	ENSP00000262715:D350Y	ENSP00000262715:D350Y	D	-	1	0	TEP1	19941868	0.000000	0.05858	0.001000	0.08648	0.696000	0.40369	0.342000	0.19926	0.329000	0.23460	0.655000	0.94253	GAT	.	.		0.517	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		A	20872028	C	A	20872028	3	1	89	1	0	0	0	0	1	0	0	0	15774	913	32	3	7035	3	TEP1	14	20872028	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	92203	20872028	86477512	94	11918										
MYH6	4624	hgsc.bcm.edu	37	chr14	23866803	23866803	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gagccctttttcttgcctccTttgcttttaccactgtcccc	5	16	1	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr14:23866803T>A	ENST00000356287.3	-	15	1940	c.1911A>T	c.(1909-1911)aaA>aaT	p.K637N	MYH6_ENST00000405093.3_Missense_Mutation_p.K637N			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	637	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TCTTGCCTCCTTTGCTTTTAC	0.572																																					p.K637N		Atlas-SNP	.											.	MYH6	274	.	0			c.A1911T						.						94	89	91					14																	23866803		2203	4300	6503	SO:0001583	missense	4624	exon16			GCCTCCTTTGCTT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.1911A>T	chr14.hg19:g.23866803T>A	ENSP00000348634:p.Lys637Asn	37.0	0.0		89.0	23.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	.	17.79	3.475098	0.63737	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.88201	-2.35;-2.35	4.27	4.27	0.50696	Myosin head, motor domain (2);	.	.	.	.	D	0.92270	0.7548	M	0.74881	2.28	0.50813	D	0.999891	P	0.44986	0.847	P	0.59056	0.851	D	0.92455	0.5973	9	0.72032	D	0.01	.	9.2762	0.37700	0.0:0.0893:0.0:0.9107	.	637	P13533	MYH6_HUMAN	N	637	ENSP00000386041:K637N;ENSP00000348634:K637N	ENSP00000348634:K637N	K	-	3	2	MYH6	22936643	0.988000	0.35896	1.000000	0.80357	0.917000	0.54804	0.286000	0.18902	1.933000	0.56026	0.533000	0.62120	AAA	.	.		0.572	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23866803	T	A	23866803	3	1	89	1	0	0	0	0	1	0	0	0	10047	1606	56	4	4004	4	MYH6	14	23866803	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	2994775	23866803	83482737	95	11919										
MYH7	4625	hgsc.bcm.edu	37	chr14	23883217	23883217	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ccccagcagggtcactcaccGcctcctcggcctggcgcttg	11	19	2	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr14:23883217G>A	ENST00000355349.3	-	38	5816	c.5654C>T	c.(5653-5655)gCg>gTg	p.A1885V	CTD-2201G16.1_ENST00000557368.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1885					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		GTCACTCACCGCCTCCTCGGC	0.637																																					p.A1885V		Atlas-SNP	.											.	MYH7	349	.	0			c.C5654T						.						78	75	76					14																	23883217		2203	4300	6503	SO:0001630	splice_region_variant	4625	exon38			CTCACCGCCTCCT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.5655+1C>T	chr14.hg19:g.23883217G>A		58.0	0.0		121.0	51.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	G	34	5.299435	0.95574	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	T	0.80393	-1.37	5.07	5.07	0.68467	Myosin tail (1);	.	.	.	.	D	0.88437	0.6436	M	0.83312	2.635	0.80722	D	1	D	0.52996	0.957	P	0.55577	0.779	D	0.89529	0.3784	9	0.56958	D	0.05	.	18.2298	0.89931	0.0:0.0:1.0:0.0	.	1885	P12883	MYH7_HUMAN	V	1885;1890	ENSP00000347507:A1885V	ENSP00000347507:A1885V	A	-	2	0	MYH7	22953057	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	9.444000	0.97578	2.653000	0.90120	0.561000	0.74099	GCG	.	.		0.637	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	Missense_Mutation	A	23883217	G	A	23883217	5	1	89	1	0	0	0	0	0	0	1	0	10048	1101	38	1	165	1	MYH7	14	23883217	Splice_Site	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	16414	23883217	83466323	96	11920										
C14orf39	317761	hgsc.bcm.edu	37	chr14	60921835	60921835	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggattccttttctgtttgaaCttcaggtactgcatttctat	7	8	3	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr14:60921835C>G	ENST00000321731.3	-	16	1546	c.1387G>C	c.(1387-1389)Gtt>Ctt	p.V463L		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	463					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TCTGTTTGAACTTCAGGTACT	0.299																																					p.V463L		Atlas-SNP	.											.	C14orf39	79	.	0			c.G1387C						.						58	63	61					14																	60921835		2201	4291	6492	SO:0001583	missense	317761	exon16			TTTGAACTTCAGG	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1387G>C	chr14.hg19:g.60921835C>G	ENSP00000324920:p.Val463Leu	104.0	0.0		252.0	89.0	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	hg19	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.656197	0.29425	.	.	ENSG00000179008	ENST00000321731	T	0.22336	1.96	5.84	-0.985	0.10256	.	1.016140	0.07853	N	0.965033	T	0.10981	0.0268	N	0.22421	0.69	0.09310	N	1	B	0.19817	0.039	B	0.18871	0.023	T	0.36915	-0.9728	9	.	.	.	2.2271	1.9519	0.03368	0.1248:0.452:0.1214:0.3018	.	463	Q8N1H7	S6OS1_HUMAN	L	463	ENSP00000324920:V463L	.	V	-	1	0	C14orf39	59991588	0.008000	0.16893	0.247000	0.24249	0.990000	0.78478	-0.400000	0.07241	-0.152000	0.11156	0.561000	0.74099	GTT	.	.		0.299	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		G	60921835	C	G	60921835	3	3	89	1	0	0	0	0	1	0	0	0	1774	565	20	4	388	4	C14orf39	14	60921835	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	37038618	60921835	46427705	97	11921										
ADCK1	57143	hgsc.bcm.edu	37	chr14	78353552	78353552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	cgtgaaggtccagcacccaaAggtgcgggctcagagctcga	14	12	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr14:78353552A>G	ENST00000238561.5	+	5	641	c.542A>G	c.(541-543)aAg>aGg	p.K181R	ADCK1_ENST00000341211.5_Missense_Mutation_p.K113R	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	188	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		CAGCACCCAAAGGTGCGGGCT	0.617																																					p.K181R		Atlas-SNP	.											.	ADCK1	81	.	0			c.A542G						.						75	70	72					14																	78353552		2203	4300	6503	SO:0001583	missense	57143	exon5			ACCCAAAGGTGCG	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.542A>G	chr14.hg19:g.78353552A>G	ENSP00000238561:p.Lys181Arg	23.0	0.0		50.0	22.0	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Missense_Mutation	SNP	ENST00000238561.5	hg19	CCDS9869.1	.	.	.	.	.	.	.	.	.	.	A	16.82	3.228732	0.58777	.	.	ENSG00000063761	ENST00000238561;ENST00000557501;ENST00000341211	T;T;T	0.55052	0.54;0.54;0.54	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.39145	0.1067	N	0.11651	0.15	0.80722	D	1	B;B	0.23937	0.028;0.094	B;B	0.30401	0.115;0.039	T	0.26395	-1.0104	10	0.37606	T	0.19	0.0012	16.3797	0.83452	1.0:0.0:0.0:0.0	.	113;181	Q9UIE6;Q86TW2-2	.;.	R	181;181;113	ENSP00000238561:K181R;ENSP00000451549:K181R;ENSP00000339663:K113R	ENSP00000238561:K181R	K	+	2	0	ADCK1	77423305	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.300000	0.96151	2.271000	0.75665	0.533000	0.62120	AAG	.	.		0.617	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421		G	78353552	A	G	78353552	3	3	89	1	0	0	0	0	1	0	0	0	288	72	3	2	556	2	ADCK1	14	78353552	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	17431717	78353552	28995988	98	11922										
ACTC1	70	hgsc.bcm.edu	37	chr15	35084616	35084616	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	cacacacactcaccagtggtGacaaaggagtagccacgctc	9	14	1	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr15:35084616G>A	ENST00000290378.4	-	4	1264	c.609C>T	c.(607-609)gtC>gtT	p.V203V	RP11-814P5.1_ENST00000558707.1_RNA|ACTC1_ENST00000557860.1_5'UTR|RP11-814P5.1_ENST00000503496.1_RNA	NM_005159.4	NP_005150.1	P68032	ACTC_HUMAN	actin, alpha, cardiac muscle 1	203					actin filament-based movement (GO:0030048)|actin-myosin filament sliding (GO:0033275)|actomyosin structure organization (GO:0031032)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|heart contraction (GO:0060047)|muscle filament sliding (GO:0030049)|negative regulation of apoptotic process (GO:0043066)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|skeletal muscle thin filament assembly (GO:0030240)	actin filament (GO:0005884)|actomyosin, actin portion (GO:0042643)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|I band (GO:0031674)|membrane (GO:0016020)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|myosin binding (GO:0017022)			central_nervous_system(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	31		all_lung(180;2.3e-08)		all cancers(64;5.83e-19)|GBM - Glioblastoma multiforme(113;1.98e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		CACCAGTGGTGACAAAGGAGT	0.537																																					p.V203V		Atlas-SNP	.											.	ACTC1	75	.	0			c.C609T						.						104	93	96					15																	35084616		2201	4298	6499	SO:0001819	synonymous_variant	70	exon4			AGTGGTGACAAAG	BC009978	CCDS10041.1	15q14	2014-09-17	2006-08-24	2006-08-24	ENSG00000159251	ENSG00000159251			143	protein-coding gene	gene with protein product		102540	"actin, alpha, cardiac muscle"	ACTC		1639426	Standard	NM_005159		Approved	CMD1R	uc001ziu.1	P68032	OTTHUMG00000129675	ENST00000290378.4:c.609C>T	chr15.hg19:g.35084616G>A		66.0	0.0		164.0	54.0	NM_005159	P04270	Silent	SNP	ENST00000290378.4	hg19	CCDS10041.1																																																																																			.	.		0.537	ACTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251876.3	NM_005159		A	35084616	G	A	35084616	2	1	89	1	0	0	0	0	0	0	0	1	195	1277	45	3		3	ACTC1	15	35084616	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10		35084616	67446776	99	11923										
BAHD1	22893	hgsc.bcm.edu	37	chr15	40757537	40757537	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	acctgtctccctttgagcccTtgcagaatgaagtgtttgca	9	11	1	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr15:40757537T>A	ENST00000416165.1	+	6	2127	c.2056T>A	c.(2056-2058)Ttg>Atg	p.L686M	RP11-64K12.8_ENST00000559730.1_RNA|BAHD1_ENST00000560846.1_Intron|BAHD1_ENST00000561234.1_Missense_Mutation_p.L685M	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	686	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		CTTTGAGCCCTTGCAGAATGA	0.537																																					p.L686M		Atlas-SNP	.											.	BAHD1	68	.	0			c.T2056A						.						166	124	138					15																	40757537		2203	4300	6503	SO:0001583	missense	22893	exon6			GAGCCCTTGCAGA	AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.2056T>A	chr15.hg19:g.40757537T>A	ENSP00000396976:p.Leu686Met	70.0	0.0		182.0	69.0	NM_014952	Q8NDF7|Q9Y2F4	Missense_Mutation	SNP	ENST00000416165.1	hg19	CCDS10058.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.518522	0.64634	.	.	ENSG00000140320	ENST00000416165	T	0.19669	2.13	5.75	5.75	0.90469	Bromo adjacent homology (BAH) domain (3);	0.177862	0.39407	N	0.001364	T	0.35068	0.0919	L	0.50333	1.59	0.80722	D	1	D;D	0.61697	0.99;0.987	P;P	0.62298	0.9;0.838	T	0.03493	-1.1031	10	0.36615	T	0.2	-6.7082	11.1463	0.48432	0.0:0.0:0.1535:0.8465	.	686;685	Q8TBE0;Q8TBE0-2	BAHD1_HUMAN;.	M	686	ENSP00000396976:L686M	ENSP00000396976:L686M	L	+	1	2	BAHD1	38544829	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	2.232000	0.43018	2.191000	0.70037	0.533000	0.62120	TTG	.	.		0.537	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		A	40757537	T	A	40757537	3	1	89	1	0	0	0	0	1	0	0	0	1297	1606	56	4	2074	4	BAHD1	15	40757537	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	5672921	40757537	61773855	100	11924										
LEO1	123169	hgsc.bcm.edu	37	chr15	52251010	52251010	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aaattcatcttcataatactGaggatcaaaaggtctacaaa	5	7	5	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr15:52251010G>T	ENST00000299601.5	-	6	1234	c.1174C>A	c.(1174-1176)Cag>Aag	p.Q392K	LEO1_ENST00000315141.5_Intron	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	392					endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		TCATAATACTGAGGATCAAAA	0.269																																					p.Q392K	Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)	Atlas-SNP	.											.	LEO1	46	.	0			c.C1174A						.						77	76	76					15																	52251010		2194	4288	6482	SO:0001583	missense	123169	exon6			AATACTGAGGATC	AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.1174C>A	chr15.hg19:g.52251010G>T	ENSP00000299601:p.Gln392Lys	101.0	0.0		280.0	101.0	NM_138792	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	hg19	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.433155	0.62844	.	.	ENSG00000166477	ENST00000299601;ENST00000538386	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.42966	0.1226	N	0.13168	0.305	0.80722	D	1	B	0.27910	0.193	B	0.27715	0.082	T	0.28522	-1.0041	9	0.18710	T	0.47	.	19.1406	0.93445	0.0:0.0:1.0:0.0	.	392	Q8WVC0	LEO1_HUMAN	K	392;370	.	ENSP00000299601:Q392K	Q	-	1	0	LEO1	50038302	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	9.602000	0.98312	2.619000	0.88677	0.557000	0.71058	CAG	.	.		0.269	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792		T	52251010	G	T	52251010	3	4	89	1	0	0	0	0	1	0	0	0	8735	1299	45	3	854	3	LEO1	15	52251010	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	11493473	52251010	50280382	101	11925										
RFX7	64864	hgsc.bcm.edu	37	chr15	56387675	56387675	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ttttatatctggagatgatgAtggggttgtttgctgttcca	12	4	1	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr15:56387675A>C	ENST00000559447.2	-	9	2231	c.1960T>G	c.(1960-1962)Tca>Gca	p.S654A	RFX7_ENST00000317318.6_Missense_Mutation_p.S751A|RFX7_ENST00000422057.1_Missense_Mutation_p.S654A|RFX7_ENST00000423270.1_Missense_Mutation_p.S751A			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	654					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GGAGATGATGATGGGGTTGTT	0.403																																					p.S751A		Atlas-SNP	.											.	RFX7	170	.	0			c.T2251G						.						95	86	89					15																	56387675		1888	4107	5995	SO:0001583	missense	64864	exon9			ATGATGATGGGGT			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.1960T>G	chr15.hg19:g.56387675A>C	ENSP00000453281:p.Ser654Ala	57.0	0.0		81.0	37.0	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	hg19		.	.	.	.	.	.	.	.	.	.	A	3.862	-0.029663	0.07589	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	T;T;T	0.55052	0.54;0.54;0.54	5.17	4.04	0.47022	.	0.378699	0.21995	N	0.066098	T	0.24044	0.0582	N	0.04508	-0.205	0.25871	N	0.983707	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.12192	-1.0557	10	0.14656	T	0.56	-6.2777	5.8648	0.18768	0.6162:0.294:0.0897:0.0	.	654;654	Q2KHR2;C9JU50	RFX7_HUMAN;.	A	654;751;751	ENSP00000387504:S654A;ENSP00000313299:S751A;ENSP00000397644:S751A	ENSP00000313299:S751A	S	-	1	0	RFX7	54174967	0.990000	0.36364	0.957000	0.39632	0.466000	0.32739	1.646000	0.37249	2.064000	0.61679	0.482000	0.46254	TCA	.	.		0.403	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		C	56387675	A	C	56387675	3	2	89	1	0	0	0	0	1	0	0	0	13283	333	12	5	2135	5	RFX7	15	56387675	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	4136665	56387675	46143717	102	11926										
BTBD12	84464	hgsc.bcm.edu	37	chr16	3651153	3651153	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gggcactcagggatctgaggCacagaaggtcttagtgtctt	14	8	4	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr16:3651153C>A	ENST00000294008.3	-	5	1630	c.990G>T	c.(988-990)gtG>gtT	p.V330V		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	330	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GGATCTGAGGCACAGAAGGTC	0.488								Direct reversal of damage																													p.V330V		Atlas-SNP	.											.	SLX4	173	.	0			c.G990T						.						110	103	105					16																	3651153		2197	4300	6497	SO:0001819	synonymous_variant	84464	exon5			CTGAGGCACAGAA	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.990G>T	chr16.hg19:g.3651153C>A		58.0	0.0		166.0	58.0	NM_032444	Q69YT8|Q8TF15|Q96JP1	Silent	SNP	ENST00000294008.3	hg19	CCDS10506.2																																																																																			.	.		0.488	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		A	3651153	C	A	3651153	2	1	89	1	0	0	0	0	0	0	0	1	1542	697	25	3		3	BTBD12	16	3651153	Silent	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10		3651153	86703600	103	11927										
ADAT1	23536	hgsc.bcm.edu	37	chr16	75637056	75637056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tgatctgaagagttccacttTgctgatttgggatctgtttg	11	6	2	4			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr16:75637056T>C	ENST00000307921.3	-	10	1448	c.1303A>G	c.(1303-1305)Aaa>Gaa	p.K435E	RP11-77K12.8_ENST00000564489.1_RNA|ADAT1_ENST00000568478.1_5'Flank	NM_012091.3	NP_036223.2	Q9BUB4	ADAT1_HUMAN	adenosine deaminase, tRNA-specific 1	435	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|RNA binding (GO:0003723)|tRNA-specific adenosine deaminase activity (GO:0008251)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)	19						AGTTCCACTTTGCTGATTTGG	0.423																																					p.K435E		Atlas-SNP	.											.	ADAT1	45	.	0			c.A1303G						.						258	244	249					16																	75637056		2198	4300	6498	SO:0001583	missense	23536	exon10			CCACTTTGCTGAT	AF125188	CCDS10922.1	16q23	2008-02-05			ENSG00000065457	ENSG00000065457			228	protein-coding gene	gene with protein product		604230				10430867	Standard	NM_012091		Approved		uc002feo.2	Q9BUB4	OTTHUMG00000137611	ENST00000307921.3:c.1303A>G	chr16.hg19:g.75637056T>C	ENSP00000310015:p.Lys435Glu	55.0	0.0		90.0	49.0	NM_012091	Q9NVB7|Q9UNG3	Missense_Mutation	SNP	ENST00000307921.3	hg19	CCDS10922.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.389856	0.82902	.	.	ENSG00000065457	ENST00000307921;ENST00000542252	D	0.96651	-4.08	5.5	5.5	0.81552	Adenosine deaminase/editase (3);	0.134749	0.64402	D	0.000003	D	0.98548	0.9515	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99585	1.0974	10	0.87932	D	0	-4.5079	13.2857	0.60241	0.0:0.0:0.0:1.0	.	435	Q9BUB4	ADAT1_HUMAN	E	435;406	ENSP00000310015:K435E	ENSP00000310015:K435E	K	-	1	0	ADAT1	74194557	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.303000	0.65738	2.206000	0.71126	0.528000	0.53228	AAA	.	.		0.423	ADAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269027.1	NM_012091		C	75637056	T	C	75637056	3	2	89	1	0	0	0	0	1	0	0	0	284	1821	63	2	213	2	ADAT1	16	75637056	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	71985903	75637056	14717697	104	11928										
ALOX15B	247	hgsc.bcm.edu	37	chr17	7951723	7951723	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gaggcccctgggcacctatcCggatgagcacttcacagagg	13	13	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr17:7951723C>T	ENST00000380183.4	+	14	2010	c.1871C>T	c.(1870-1872)cCg>cTg	p.P624L	ALOX15B_ENST00000572022.1_Missense_Mutation_p.P612L|ALOX15B_ENST00000380173.2_Missense_Mutation_p.P595L|ALOX15B_ENST00000573359.1_Missense_Mutation_p.P550L	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	624	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						GGCACCTATCCGGATGAGCAC	0.657																																					p.P624L		Atlas-SNP	.											.	ALOX15B	66	.	0			c.C1871T						.						43	48	46					17																	7951723		2203	4300	6503	SO:0001583	missense	247	exon14			CCTATCCGGATGA	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"Arachidonate lipoxygenases"	434	protein-coding gene	gene with protein product		603697	"arachidonate 15-lipoxygenase, second type"			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1871C>T	chr17.hg19:g.7951723C>T	ENSP00000369530:p.Pro624Leu	19.0	0.0		35.0	20.0	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	hg19	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.664341	0.67700	.	.	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	T;T	0.76316	-1.01;-1.01	3.89	3.89	0.44902	Lipoxygenase, C-terminal (3);	0.394849	0.28499	N	0.015135	D	0.86957	0.6058	M	0.73598	2.24	0.53005	D	0.999962	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.81914	0.934;0.984;0.984;0.995	D	0.88962	0.3394	10	0.87932	D	0	-19.5832	15.1338	0.72545	0.0:1.0:0.0:0.0	.	612;550;595;624	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	L	595;550;624	ENSP00000369520:P595L;ENSP00000369530:P624L	ENSP00000344337:P550L	P	+	2	0	ALOX15B	7892448	0.989000	0.36119	0.953000	0.39169	0.915000	0.54546	3.257000	0.51500	2.163000	0.67991	0.561000	0.74099	CCG	.	.		0.657	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2			T	7951723	C	T	7951723	3	4	89	1	0	0	0	0	1	0	0	0	539	652	23	1	1925	1	ALOX15B	17	7951723	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10		7951723	73243487	105	11929										
MAP2K4	6416	hgsc.bcm.edu	37	chr17	12016635	12016636	+	Frame_Shift_Del	DEL	TA	TA	-													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	agtggacagcttgtggactcTattgccaagacaagagatgc							TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr17:12016635_12016636delTA	ENST00000353533.5	+	7	834_835	c.771_772delTA	c.(769-774)tctattfs	p.I258fs	MAP2K4_ENST00000415385.3_Frame_Shift_Del_p.I269fs|MAP2K4_ENST00000581941.1_3'UTR	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	258	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TTGTGGACTCTATTGCCAAGAC	0.45			"D, Mis, N"		"pancreatic, breast, colorectal"																																p.257_257del		Atlas-Indel,Pindel	.		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	MAP2K4,NS,carcinoma,0,1	MAP2K4	176	.	11	Whole gene deletion(10)|Unknown(1)	ovary(4)|breast(4)|biliary_tract(1)|large_intestine(1)|pancreas(1)	c.770_771del						.																																			SO:0001589	frameshift_variant	6416	exon7			.	L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.771_772delTA	chr17.hg19:g.12016635_12016636delTA	ENSP00000262445:p.Ile258fs	50.0	0.0		71.0	37.0	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Frame_Shift_Del	DEL	ENST00000353533.5	hg19	CCDS11162.1																																																																																			.	.		0.45	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			-	12016636	TA	-	12016635	7	5	89	1	0	1	0	1	0	0	0	0	9248	1509	53	0	797	0	MAP2K4	17	12016635	Frame_Shift_Del	DEL	TA	TCGA-DD-A116-01A-11D-A12Z-10	4064912	12016635	69178575	106	11930										
FAM18B2	201158	hgsc.bcm.edu	37	chr17	15406424	15406424	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	atgtctacctgatgaaacttCctcgagggatggcccgggca	12	11	1	2	rs17850827		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr17:15406424C>A	ENST00000225576.3	-	6	680	c.585G>T	c.(583-585)agG>agT	p.R195S	TVP23C_ENST00000519970.1_Missense_Mutation_p.R152S|TVP23C-CDRT4_ENST00000522212.2_Intron	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)	195				R -> S (in Ref. 4; AAH11952). {ECO:0000305}.		integral component of membrane (GO:0016021)											GATGAAACTTCCTCGAGGGAT	0.562																																					p.R195S		Atlas-SNP	.											.	.	.	.	0			c.G585T						.						32	32	32					17																	15406424		2203	4300	6503	SO:0001583	missense	201158	exon6			AAACTTCCTCGAG	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"family with sequence similarity 18, member B2"	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.585G>T	chr17.hg19:g.15406424C>A	ENSP00000225576:p.Arg195Ser	29.0	0.0		64.0	41.0	NM_145301	Q3LIC7	Missense_Mutation	SNP	ENST00000225576.3	hg19	CCDS11170.1	.	.	.	.	.	.	.	.	.	.	C	10.91	1.482814	0.26598	.	.	ENSG00000259024;ENSG00000175106;ENSG00000175106	ENST00000557349;ENST00000519970;ENST00000225576	T	0.22336	1.96	1.71	1.71	0.24356	.	1.414060	0.04645	N	0.406015	T	0.10252	0.0251	N	0.11789	0.175	0.09310	N	1	B;B	0.33494	0.414;0.006	B;B	0.17979	0.02;0.003	T	0.18999	-1.0319	10	0.22706	T	0.39	.	6.893	0.24241	0.0:1.0:0.0:0.0	rs17850827	152;195	B4E0Q0;Q96ET8	.;F18B2_HUMAN	S	152;152;195	ENSP00000225576:R195S	ENSP00000225576:R195S	R	-	3	2	RP11-726O12.1;FAM18B2	15347149	0.005000	0.15991	0.020000	0.16555	0.035000	0.12851	-0.028000	0.12350	1.283000	0.44513	0.460000	0.39030	AGG	.	C|1.000;|0.000		0.562	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301		A	15406424	C	A	15406424	3	1	89	1	0	0	0	0	1	0	0	0	5525	854	30	3	249	3	FAM18B2	17	15406424	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	3389789	15406424	65788786	107	11931										
FOXN1	8456	hgsc.bcm.edu	37	chr17	26851109	26851109	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aggctcccctgccccacagaGtgtaagtacccggcatctgg	11	15	1	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr17:26851109G>T	ENST00000226247.2	+	1	151	c.122G>T	c.(121-123)aGt>aTt	p.S41I	FOXN1_ENST00000579795.1_Splice_Site_p.S41I	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	41					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					GCCCCACAGAGTGTAAGTACC	0.682																																					p.S41I		Atlas-SNP	.											.	FOXN1	51	.	0			c.G122T						.						10	10	10					17																	26851109		2192	4284	6476	SO:0001630	splice_region_variant	8456	exon1			CACAGAGTGTAAG	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"Forkhead boxes"	12765	protein-coding gene	gene with protein product		600838	"winged-helix nude", "Rowett nude"	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.123+1G>T	chr17.hg19:g.26851109G>T		37.0	0.0		78.0	34.0	NM_003593	B2R9Q7|O15352	Missense_Mutation	SNP	ENST00000226247.2	hg19	CCDS11232.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.268947	0.40095	.	.	ENSG00000109101	ENST00000226247	D	0.93133	-3.17	5.03	0.129	0.14739	.	0.431911	0.24229	N	0.040373	D	0.85080	0.5615	N	0.19112	0.55	0.24096	N	0.99589	B	0.29085	0.232	B	0.28709	0.093	T	0.76250	-0.3028	10	0.66056	D	0.02	.	7.9671	0.30104	0.3666:0.0:0.6334:0.0	.	41	O15353	FOXN1_HUMAN	I	41	ENSP00000226247:S41I	ENSP00000226247:S41I	S	+	2	0	FOXN1	23875236	0.037000	0.19845	0.969000	0.41365	0.619000	0.37552	-0.171000	0.09883	-0.133000	0.11537	0.561000	0.74099	AGT	.	.		0.682	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1		Missense_Mutation	T	26851109	G	T	26851109	5	4	89	1	0	0	0	0	0	0	1	0	6027	1043	36	3	124	3	FOXN1	17	26851109	Splice_Site	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	11444685	26851109	54344101	108	11932										
CDC27	996	hgsc.bcm.edu	37	chr17	45234594	45234729	+	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	cactagaatataagacacttAcaattgtgtcctggggtgtt					rs149474782|rs113608268|rs370849730|rs78395997|rs76624491|rs370261409|rs75353677|rs368304141|rs376818791|rs372212798|rs375653477|rs374472811|rs76359747|rs147617501|rs374614181|rs78108688|rs142987740|rs143453365|rs75990396|rs144985864|rs367644695|rs202182614|rs139751753|rs11570485|rs372926889|rs140171160|rs368750026|rs201098929|rs199899451|rs75175938|rs200340309|rs537990668	byFrequency	TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr17:45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	ENST00000066544.3	-	6	590_724	c.497_631delAGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG	c.(496-633)cagttcttacggaaacaccccaggacacaattgtaagtgtcttatattctagtgttcaaaatattatgaaaactacaaagaatgatctgaactaaataatatattgtgaatgacttggtagaaattttctgtttcaga>cga	p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	CDC27_ENST00000446365.2_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF105fs|CDC27_ENST00000527547.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000531206.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.T167T(7)|p.T171T(3)|p.V201I(2)|p.E199E(2)|p.T200T(2)|p.L173S(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACTGTCTCAGGCTGTCTGTGAGATAAACTATGATTAGGTACTTGTGTTGTGCAAGAGTTGGGCAGACAGTTGCTAAAGTTCTGTAAAGATGTGAATTTAAATGTTTGGTCAGGATC	0.342																																					p.201_211del		Pindel	.											.	CDC27	337	.	17	Substitution - coding silent(14)|Substitution - Missense(3)	large_intestine(6)|prostate(6)|kidney(4)|NS(1)	c.601_631del						.																																			SO:0001630	splice_region_variant	996	exon6			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.631-104AGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG>-	chr17.hg19:g.45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT		0.0	0.0		19.0	19.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.342	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Frame_Shift_Del	-	45234729	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	45234594	8	5	89	1	0	1	0	1	0	0	1	0	3068	405	14	0	1916	0	CDC27	17	45234594	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	TCGA-DD-A116-01A-11D-A12Z-10	18383485	45234594	35960616	109	11933										
MRPL10	124995	hgsc.bcm.edu	37	chr17	45906024	45906024	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	catagcggacagtctggaggGtaggcagccggcctgggagg	19	9	1	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr17:45906024G>A	ENST00000351111.2	-	2	70	c.65C>T	c.(64-66)aCc>aTc	p.T22I	MRPL10_ENST00000290208.7_Missense_Mutation_p.T32I|MRPL10_ENST00000414011.1_Missense_Mutation_p.T32I|LRRC46_ENST00000269025.4_5'Flank	NM_145255.3	NP_660298.2	Q7Z7H8	RM10_HUMAN	mitochondrial ribosomal protein L10	22					ribosome biogenesis (GO:0042254)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|large_intestine(1)|lung(3)|ovary(1)	8						AGTCTGGAGGGTAGGCAGCCG	0.552																																					p.T32I		Atlas-SNP	.											.	MRPL10	24	.	0			c.C95T						.						44	38	40					17																	45906024		2203	4300	6503	SO:0001583	missense	124995	exon3			TGGAGGGTAGGCA	AB051618	CCDS11516.1, CCDS11517.1	17q21.3	2012-09-13			ENSG00000159111	ENSG00000159111		"Mitochondrial ribosomal proteins / large subunits"	14055	protein-coding gene	gene with protein product	"39S ribosomal protein L10, mitochondrial"	611825				11551941	Standard	NM_148887		Approved	RPML8, MRP-L8, L10MT, MRP-L10, MRPL8, MGC17973	uc002ily.3	Q7Z7H8	OTTHUMG00000156302	ENST00000351111.2:c.65C>T	chr17.hg19:g.45906024G>A	ENSP00000324100:p.Thr22Ile	15.0	0.0		39.0	16.0	NM_148887	A6NGJ4|Q96B80|Q96Q55	Missense_Mutation	SNP	ENST00000351111.2	hg19	CCDS11516.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710597	0.30322	.	.	ENSG00000159111	ENST00000351111;ENST00000290208;ENST00000414011	T;T;T	0.48201	0.82;2.27;2.27	5.32	3.34	0.38264	.	0.295182	0.35555	N	0.003131	T	0.45617	0.1351	M	0.70595	2.14	0.28737	N	0.902192	B;B	0.31910	0.138;0.346	B;B	0.30943	0.086;0.122	T	0.46345	-0.9198	10	0.52906	T	0.07	-7.2633	10.8403	0.46710	0.1561:0.0:0.8439:0.0	.	22;32	Q7Z7H8;A6NGJ4	RM10_HUMAN;.	I	22;32;32	ENSP00000324100:T22I;ENSP00000290208:T32I;ENSP00000395870:T32I	ENSP00000290208:T32I	T	-	2	0	MRPL10	43261023	1.000000	0.71417	0.926000	0.36857	0.691000	0.40173	3.770000	0.55310	0.645000	0.30675	0.561000	0.74099	ACC	.	.		0.552	MRPL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343764.1	NM_145255		A	45906024	G	A	45906024	3	1	89	1	0	0	0	0	1	0	0	0	9784	1261	44	3	736	3	MRPL10	17	45906024	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	671430	45906024	35289186	110	11934										
SPHK1	8877	hgsc.bcm.edu	37	chr17	74383503	74383503	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tggtcgccttccgcttggagCccaaggatgggaaaggtgtg	16	9	0	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr17:74383503C>G	ENST00000545180.1	+	8	1800	c.991C>G	c.(991-993)Ccc>Gcc	p.P331A	SPHK1_ENST00000590959.1_Missense_Mutation_p.P345A|SPHK1_ENST00000392496.3_Missense_Mutation_p.P331A|SPHK1_ENST00000323374.4_Missense_Mutation_p.P417A|SPHK1_ENST00000592299.1_Missense_Mutation_p.P331A			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	331					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	CCGCTTGGAGCCCAAGGATGG	0.577																																					p.P417A	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.C1249G						.						78	78	78					17																	74383503		2202	4300	6502	SO:0001583	missense	8877	exon6			TTGGAGCCCAAGG	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.991C>G	chr17.hg19:g.74383503C>G	ENSP00000440970:p.Pro331Ala	51.0	0.0		187.0	56.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	hg19	CCDS45785.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.814537	0.50527	.	.	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.13538	2.58;2.58;2.58	5.08	4.11	0.48088	.	2.948360	0.02167	N	0.059323	T	0.47507	0.1449	M	0.85462	2.755	0.52501	D	0.999959	D;D;D	0.67145	0.993;0.987;0.996	P;P;D	0.70716	0.899;0.844;0.97	T	0.00468	-1.1721	10	0.72032	D	0.01	-12.5451	13.3258	0.60459	0.0:0.9235:0.0:0.0765	.	417;345;331	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	A	331;417;331;330	ENSP00000440970:P331A;ENSP00000313681:P417A;ENSP00000376285:P331A	ENSP00000313681:P417A	P	+	1	0	SPHK1	71895098	1.000000	0.71417	0.865000	0.33974	0.086000	0.17979	5.617000	0.67716	1.135000	0.42183	0.456000	0.33151	CCC	.	.		0.577	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		G	74383503	C	G	74383503	3	3	89	1	0	0	0	0	1	0	0	0	15061	739	26	4	1313	4	SPHK1	17	74383503	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	28477479	74383503	6811707	111	11935										
USP36	57602	hgsc.bcm.edu	37	chr17	76802273	76802273	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggccaagtggaggcaacgacGgggtgagaggttttcatggg	19	6	1	1	rs372776119		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr17:76802273G>A	ENST00000542802.3	-	15	2624	c.2181C>T	c.(2179-2181)ccC>ccT	p.P727P	USP36_ENST00000449938.2_Silent_p.P427P|USP36_ENST00000588467.1_5'Flank|USP36_ENST00000312010.6_Silent_p.P727P			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	727					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			AGGCAACGACGGGGTGAGAGG	0.632																																					p.P727P		Atlas-SNP	.											.	USP36	243	.	0			c.C2181T						.	G		1,4405	2.1+/-5.4	0,1,2202	89	82	85		2181	2	0.5	17		85	0,8600		0,0,4300	no	coding-synonymous	USP36	NM_025090.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		727/1124	76802273	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57602	exon15			AACGACGGGGTGA	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"Ubiquitin-specific peptidases"	20062	protein-coding gene	gene with protein product		612543	"ubiquitin specific protease 36"			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.2181C>T	chr17.hg19:g.76802273G>A		34.0	0.0		141.0	69.0	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Silent	SNP	ENST00000542802.3	hg19	CCDS32755.1																																																																																			.	.		0.632	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090		A	76802273	G	A	76802273	2	1	89	1	0	0	0	0	0	0	0	1	17082	1103	39	1		1	USP36	17	76802273	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	2418770	76802273	4392937	112	11936										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5433469	5433469	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggtttaaaaagatgcataccTtagcatgatgtaaatctacc	7	7	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr18:5433469T>A	ENST00000341928.2	-	8	1251	c.911A>T	c.(910-912)aAg>aTg	p.K304M	EPB41L3_ENST00000400111.3_Splice_Site_p.K304M|EPB41L3_ENST00000342933.3_Splice_Site_p.K304M|EPB41L3_ENST00000540638.2_Splice_Site_p.K304M|EPB41L3_ENST00000544123.1_Splice_Site_p.K304M|EPB41L3_ENST00000542652.2_5'UTR	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	304	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GATGCATACCTTAGCATGATG	0.318																																					p.K304M		Atlas-SNP	.											.	EPB41L3	222	.	0			c.A911T						.						146	139	142					18																	5433469		2203	4299	6502	SO:0001630	splice_region_variant	23136	exon8			CATACCTTAGCAT	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.912+1A>T	chr18.hg19:g.5433469T>A		42.0	0.0		85.0	27.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.293987	0.81025	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	D;D;D;D	0.84873	-1.91;-1.91;-1.91;-1.91	5.9	5.9	0.94986	FERM domain (1);Pleckstrin homology-type (1);	0.042501	0.85682	D	0.000000	D	0.93936	0.8059	M	0.91818	3.245	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.998;0.999;0.999;0.992	D;D;P;D;P	0.81914	0.994;0.951;0.9;0.995;0.8	D	0.95079	0.8211	10	0.87932	D	0	.	16.3076	0.82855	0.0:0.0:0.0:1.0	.	304;304;195;304;304	F5GX05;Q9Y2J2-3;A8K968;Q9Y2J2-2;Q9Y2J2	.;.;.;.;E41L3_HUMAN	M	304;195;304;195;304;304	ENSP00000343158:K304M;ENSP00000441174:K304M;ENSP00000341138:K304M;ENSP00000382981:K304M	ENSP00000343158:K304M	K	-	2	0	EPB41L3	5423469	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	5.139000	0.64801	2.252000	0.74401	0.533000	0.62120	AAG	.	.		0.318	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	Missense_Mutation	A	5433469	T	A	5433469	5	1	89	1	0	0	0	0	0	0	1	0	5156	1623	56	4	2412	4	EPB41L3	18	5433469	Splice_Site	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10		5433469	72643779	113	11937										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9256402	9256402	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	aaatagcttactcaaactaaAatctgaagcagataagccta	5	8	2	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr18:9256402A>T	ENST00000262126.4	+	9	3377	c.3137A>T	c.(3136-3138)aAa>aTa	p.K1046I	ANKRD12_ENST00000383440.2_Missense_Mutation_p.K1023I|ANKRD12_ENST00000400020.3_Missense_Mutation_p.K1023I|RP11-888D10.4_ENST00000609701.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1046						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CTCAAACTAAAATCTGAAGCA	0.303																																					p.K1046I		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A3137T						.						63	67	66					18																	9256402		2200	4295	6495	SO:0001583	missense	23253	exon9			AACTAAAATCTGA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.3137A>T	chr18.hg19:g.9256402A>T	ENSP00000262126:p.Lys1046Ile	122.0	0.0		239.0	64.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	18.66	3.672580	0.67928	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.46451	0.87;0.87	5.17	5.17	0.71159	.	0.100908	0.64402	D	0.000002	T	0.61286	0.2335	M	0.63428	1.95	0.44462	D	0.997395	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.65047	-0.6263	10	0.87932	D	0	-1.3383	13.5699	0.61841	1.0:0.0:0.0:0.0	.	1023;1046	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	I	1023;1046	ENSP00000372932:K1023I;ENSP00000262126:K1046I	ENSP00000262126:K1046I	K	+	2	0	ANKRD12	9246402	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.162000	0.77515	1.953000	0.56701	0.528000	0.53228	AAA	.	.		0.303	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		T	9256402	A	T	9256402	3	4	89	1	0	0	0	0	1	0	0	0	640	14	1	4	3167	4	ANKRD12	18	9256402	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	3822933	9256402	68820846	114	11938										
NPC1	4864	hgsc.bcm.edu	37	chr18	21125036	21125036	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tgtcactttcacgatttagtTcatcttcaatacttcgttca	4	10	6	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr18:21125036T>C	ENST00000269228.5	-	12	2389	c.1835A>G	c.(1834-1836)gAa>gGa	p.E612G	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Missense_Mutation_p.E294G	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	612			E -> D (in NPC1). {ECO:0000269|PubMed:11349231}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					ACGATTTAGTTCATCTTCAAT	0.358																																					p.E612G		Atlas-SNP	.											.	NPC1	114	.	0			c.A1835G						.						113	102	106					18																	21125036		2203	4300	6503	SO:0001583	missense	4864	exon12			TTTAGTTCATCTT	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.1835A>G	chr18.hg19:g.21125036T>C	ENSP00000269228:p.Glu612Gly	89.0	0.0		334.0	115.0	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	hg19	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.819773	0.90873	.	.	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.92199	-2.99;-2.99	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.95348	0.8490	M	0.87547	2.89	0.58432	D	0.999999	P;P	0.46395	0.877;0.747	P;P	0.52627	0.704;0.533	D	0.95455	0.8538	10	0.54805	T	0.06	-27.9068	16.422	0.83766	0.0:0.0:0.0:1.0	.	623;612	Q59GR1;O15118	.;NPC1_HUMAN	G	612;294;457	ENSP00000269228:E612G;ENSP00000408606:E294G	ENSP00000269228:E612G	E	-	2	0	NPC1	19379034	1.000000	0.71417	0.930000	0.37139	0.868000	0.49771	7.830000	0.86741	2.270000	0.75569	0.533000	0.62120	GAA	.	.		0.358	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		C	21125036	T	C	21125036	3	2	89	1	0	0	0	0	1	0	0	0	10579	1783	62	2	2057	2	NPC1	18	21125036	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	11868634	21125036	56952212	115	11939										
SYT4	6860	hgsc.bcm.edu	37	chr18	40850324	40850324	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tgctaaccatcacagagcacGtgccacttggcaatttgtct	8	12	2	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr18:40850324G>A	ENST00000255224.3	-	4	1628	c.1260C>T	c.(1258-1260)caC>caT	p.H420H	SYT4_ENST00000590752.1_Silent_p.H402H|SYT4_ENST00000586678.1_5'UTR	NM_020783.3	NP_065834.1	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	420					exocytosis (GO:0006887)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of vesicle fusion (GO:0031339)|neurotransmitter secretion (GO:0007269)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44						CACAGAGCACGTGCCACTTGG	0.458																																					p.H420H	NSCLC(85;81 1419 2855 22820 35912)	Atlas-SNP	.											.	SYT4	162	.	0			c.C1260T						.						187	193	191					18																	40850324		2203	4300	6503	SO:0001819	synonymous_variant	6860	exon4			GAGCACGTGCCAC	BC036538	CCDS11922.1	18q12.3	2013-01-21			ENSG00000132872	ENSG00000132872		"Synaptotagmins"	11512	protein-coding gene	gene with protein product		600103				8058779	Standard	NM_020783		Approved	KIAA1342, HsT1192	uc002law.3	Q9H2B2	OTTHUMG00000132610	ENST00000255224.3:c.1260C>T	chr18.hg19:g.40850324G>A		79.0	0.0		172.0	10.0	NM_020783	B4DEU3|Q9P2K4	Silent	SNP	ENST00000255224.3	hg19	CCDS11922.1																																																																																			.	.		0.458	SYT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255851.2	NM_020783		A	40850324	G	A	40850324	2	1	89	1	0	0	0	0	0	0	0	1	15491	1136	40	1		1	SYT4	18	40850324	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	19725288	40850324	37226924	116	11940										
CDH7	1005	hgsc.bcm.edu	37	chr18	63430104	63430104	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gttgggcaaagtggagttctGccattttctgcagctaatag	12	7	2	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr18:63430104G>T	ENST00000397968.2	+	2	452	c.26G>T	c.(25-27)tGc>tTc	p.C9F	CDH7_ENST00000323011.3_Missense_Mutation_p.C9F|CDH7_ENST00000536984.2_Missense_Mutation_p.C9F	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	9					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				GTGGAGTTCTGCCATTTTCTG	0.408																																					p.C9F		Atlas-SNP	.											.	CDH7	362	.	0			c.G26T						.						114	112	113					18																	63430104		2203	4300	6503	SO:0001583	missense	1005	exon2			AGTTCTGCCATTT	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.26G>T	chr18.hg19:g.63430104G>T	ENSP00000381058:p.Cys9Phe	54.0	0.0		94.0	31.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	hg19	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.399009	0.25291	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.54279	0.58;0.6;0.58	5.83	4.96	0.65561	.	0.073160	0.64402	D	0.000013	T	0.47985	0.1475	L	0.58101	1.795	0.42167	D	0.991626	P;P	0.50943	0.723;0.94	B;B	0.41571	0.173;0.36	T	0.47873	-0.9083	10	0.12766	T	0.61	.	15.2241	0.73336	0.0672:0.0:0.9328:0.0	.	9;9	F5H5X9;Q9ULB5	.;CADH7_HUMAN	F	9	ENSP00000319166:C9F;ENSP00000443030:C9F;ENSP00000381058:C9F	ENSP00000319166:C9F	C	+	2	0	CDH7	61581084	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.450000	0.60041	1.487000	0.48415	-0.127000	0.14921	TGC	.	.		0.408	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		T	63430104	G	T	63430104	3	4	89	1	0	0	0	0	1	0	0	0	3117	1319	46	3	28	3	CDH7	18	63430104	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	22579780	63430104	14647144	117	11941										
FZR1	51343	hgsc.bcm.edu	37	chr19	3527733	3527733	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggacgacttctacctcaatcTggtggactggtcgtccctca	10	13	4	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:3527733T>G	ENST00000395095.3	+	6	575	c.575T>G	c.(574-576)cTg>cGg	p.L192R	FZR1_ENST00000313639.8_Intron|FZR1_ENST00000441788.2_Missense_Mutation_p.L192R	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	192					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		TACCTCAATCTGGTGGACTGG	0.632																																					p.L192R		Atlas-SNP	.											.	FZR1	42	.	0			c.T575G						.						135	110	119					19																	3527733		2202	4298	6500	SO:0001583	missense	51343	exon6			TCAATCTGGTGGA	AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"WD repeat domain containing"	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.575T>G	chr19.hg19:g.3527733T>G	ENSP00000378529:p.Leu192Arg	50.0	0.0		160.0	47.0	NM_001136198	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Missense_Mutation	SNP	ENST00000395095.3	hg19	CCDS45916.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.646422	0.87958	.	.	ENSG00000105325	ENST00000441788;ENST00000395095	T;T	0.28895	1.59;1.59	5.14	5.14	0.70334	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.65186	0.2667	M	0.93638	3.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.75434	-0.3319	10	0.87932	D	0	-23.8474	13.811	0.63264	0.0:0.0:0.0:1.0	.	192;192	Q9UM11;Q9UM11-2	FZR_HUMAN;.	R	192	ENSP00000410369:L192R;ENSP00000378529:L192R	ENSP00000378529:L192R	L	+	2	0	FZR1	3478733	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.798000	0.85924	1.943000	0.56356	0.533000	0.62120	CTG	.	.		0.632	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		G	3527733	T	G	3527733	3	3	89	1	0	0	0	0	1	0	0	0	6146	1580	55	5	597	5	FZR1	19	3527733	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10		3527733	55601250	118	11942										
C19orf10	56005	hgsc.bcm.edu	37	chr19	4658077	4658077	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ttggacagctcagctttgaaTgccccgggcctgtgagccac	12	13	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:4658077T>A	ENST00000262947.3	-	6	497	c.462A>T	c.(460-462)gcA>gcT	p.A154A	AC005339.2_ENST00000598070.1_RNA	NM_019107.3	NP_061980.1	Q969H8	CS010_HUMAN	chromosome 19 open reading frame 10	154					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.015)		CAGCTTTGAATGCCCCGGGCC	0.572																																					p.A154A		Atlas-SNP	.											.	C19orf10	9	.	0			c.A462T						.						50	45	47					19																	4658077		2202	4299	6501	SO:0001819	synonymous_variant	56005	exon6			TTTGAATGCCCCG	AF282264	CCDS12133.1	19p13.3	2013-11-27	2003-06-25	2003-06-27	ENSG00000074842	ENSG00000074842			16948	protein-coding gene	gene with protein product		606746	"interleukin 27 working designation"	IL27, IL27w		17362502, 21128247	Standard	NM_019107		Approved	R33729_1, IL25, SF20, IL-25, IL-27	uc002may.3	Q969H8		ENST00000262947.3:c.462A>T	chr19.hg19:g.4658077T>A		23.0	0.0		38.0	11.0	NM_019107	D6W628|O75256|O75272|Q9BTK7|Q9NP69	Silent	SNP	ENST00000262947.3	hg19	CCDS12133.1																																																																																			.	.		0.572	C19orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458937.1	NM_019107		A	4658077	T	A	4658077	2	1	89	1	0	0	0	0	0	0	0	1	1910	1451	51	4		4	C19orf10	19	4658077	Silent	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	1130344	4658077	54470906	119	11943										
ZNF414	84330	hgsc.bcm.edu	37	chr19	8576572	8576572	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	cggccaggaaggggcgcaggCgcggggggcttaggccaaag	21	10	0	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:8576572C>A	ENST00000255616.8	-	5	904	c.803G>T	c.(802-804)cGc>cTc	p.R268L	ZNF414_ENST00000393927.4_Missense_Mutation_p.R268L	NM_032370.2	NP_115746.2	Q96IQ9	ZN414_HUMAN	zinc finger protein 414	268					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(2)	2						GGGGCGCAGGCGCGGGGGGCT	0.721																																					p.R268L		Atlas-SNP	.											.	ZNF414	25	.	0			c.G803T						.						4	6	5					19																	8576572		1937	3866	5803	SO:0001583	missense	84330	exon5			CGCAGGCGCGGGG	AK074191	CCDS12205.1, CCDS54211.1	19p13.2	2008-02-05				ENSG00000133250		"Zinc fingers, C2H2-type"	20630	protein-coding gene	gene with protein product							Standard	NM_032370		Approved	MGC15716, Zfp414	uc002mke.4	Q96IQ9		ENST00000255616.8:c.803G>T	chr19.hg19:g.8576572C>A	ENSP00000255616:p.Arg268Leu	11.0	0.0		34.0	19.0	NM_032370	A8MY94	Missense_Mutation	SNP	ENST00000255616.8	hg19	CCDS12205.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.936398	0.73442	.	.	ENSG00000133250	ENST00000393927;ENST00000255616	T;T	0.15372	2.43;2.43	4.52	4.52	0.55395	.	0.315541	0.29684	N	0.011468	T	0.30634	0.0771	L	0.34521	1.04	0.47037	D	0.999291	D;D	0.67145	0.996;0.996	D;D	0.76575	0.988;0.988	T	0.04664	-1.0935	10	0.87932	D	0	-15.5975	14.3255	0.66518	0.0:1.0:0.0:0.0	.	268;268	Q96IQ9;A8MY94	ZN414_HUMAN;.	L	268	ENSP00000377504:R268L;ENSP00000255616:R268L	ENSP00000255616:R268L	R	-	2	0	ZNF414	8482572	1.000000	0.71417	0.998000	0.56505	0.343000	0.28985	3.404000	0.52623	2.234000	0.73211	0.491000	0.48974	CGC	.	.		0.721	ZNF414-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460199.2	NM_032370		A	8576572	C	A	8576572	3	1	89	1	0	0	0	0	1	0	0	0	17906	768	27	1	399	1	ZNF414	19	8576572	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	3918495	8576572	50552411	120	11944										
MUC16	94025	hgsc.bcm.edu	37	chr19	8961997	8961998	+	Frame_Shift_Ins	INS	-	-	A													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tgactcccaggagtcctgccINSaagccgatgaggatgacagc					rs369723028		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:8961997_8961998insA	ENST00000397910.4	-	83	43582_43583	c.43379_43380insT	c.(43378-43380)ttgfs	p.L14460fs	MUC16_ENST00000380951.5_Frame_Shift_Ins_p.L1101fs	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	22105	SEA 16. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGAGTCCTGCCAAGCCGATGAG	0.559																																					p.L14460fs		Atlas-INDEL	.											.	MUC16	4315	.	0			c.43380_43381insT						.																																			SO:0001589	frameshift_variant	94025	exon83			.	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.43380dupT	chr19.hg19:g.8961999_8961999dupA	ENSP00000381008:p.Leu14460fs	37.0	0.0		112.0	10.0	NM_024690	Q6ZQW5|Q96RK2	Frame_Shift_Ins	INS	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.559	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	8961998	-	A	8961997	7	5	89	1	0	1	1	0	0	0	0	0	9982	593	21	0	151	0	MUC16	19	8961997	Frame_Shift_Ins	INS	-	TCGA-DD-A116-01A-11D-A12Z-10	385425	8961997	50166986	121	11945										
MUC16	94025	hgsc.bcm.edu	37	chr19	9002558	9002558	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gcccagctcagtgatgccgtGggtcagctggctcagcttcc	13	14	3	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:9002558G>T	ENST00000397910.4	-	51	40461	c.40258C>A	c.(40258-40260)Cac>Aac	p.H13420N	MUC16_ENST00000380951.5_Missense_Mutation_p.H61N	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13422	SEA 9. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGATGCCGTGGGTCAGCTGG	0.587																																					p.H13420N		Atlas-SNP	.											.	MUC16	4315	.	0			c.C40258A						.						187	170	175					19																	9002558		2150	4250	6400	SO:0001583	missense	94025	exon51			TGCCGTGGGTCAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.40258C>A	chr19.hg19:g.9002558G>T	ENSP00000381008:p.His13420Asn	99.0	0.0		363.0	117.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	6.688	0.495604	0.12762	.	.	ENSG00000181143	ENST00000397910;ENST00000380951	T;T	0.35605	1.3;1.3	2.75	1.69	0.24217	SEA (1);	.	.	.	.	T	0.43964	0.1271	L	0.46157	1.445	.	.	.	B;P	0.46859	0.003;0.885	B;P	0.60236	0.005;0.871	T	0.51568	-0.8689	8	0.37606	T	0.19	-0.5084	7.0787	0.25219	0.0:0.0:0.7305:0.2695	.	21065;13420	Q8WXI7;B5ME49	MUC16_HUMAN;.	N	13420;61	ENSP00000381008:H13420N;ENSP00000370338:H61N	ENSP00000370338:H61N	H	-	1	0	MUC16	8863558	0.001000	0.12720	0.250000	0.24296	0.003000	0.03518	0.235000	0.17948	0.737000	0.32582	-0.656000	0.03901	CAC	.	.		0.587	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9002558	G	T	9002558	3	4	89	1	0	0	0	0	1	0	0	0	9982	1348	47	3	3401	3	MUC16	19	9002558	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	40561	9002558	50126425	122	11946										
MUC16	94025	hgsc.bcm.edu	37	chr19	9087113	9087113	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ttgatctttgagtgactgtgTcacgtgagtaggactcatcg	12	7	3	4			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:9087113T>C	ENST00000397910.4	-	1	4905	c.4702A>G	c.(4702-4704)Aca>Gca	p.T1568A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1568	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGTGACTGTGTCACGTGAGTA	0.507																																					p.T1568A		Atlas-SNP	.											.	MUC16	4315	.	0			c.A4702G						.						407	391	396					19																	9087113		2089	4216	6305	SO:0001583	missense	94025	exon1			ACTGTGTCACGTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4702A>G	chr19.hg19:g.9087113T>C	ENSP00000381008:p.Thr1568Ala	139.0	0.0		406.0	153.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	0.138	-1.105758	0.01828	.	.	ENSG00000181143	ENST00000397910	T	0.02301	4.35	0.235	-0.47	0.12131	.	.	.	.	.	T	0.01254	0.0041	N	0.08118	0	.	.	.	B	0.06786	0.001	B	0.04013	0.001	T	0.46190	-0.9209	7	0.87932	D	0	.	.	.	.	.	1568	B5ME49	.	A	1568	ENSP00000381008:T1568A	ENSP00000381008:T1568A	T	-	1	0	MUC16	8948113	0.000000	0.05858	0.025000	0.17156	0.028000	0.11728	0.254000	0.18314	-0.867000	0.04063	-0.908000	0.02827	ACA	.	.		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9087113	T	C	9087113	3	2	89	1	0	0	0	0	1	0	0	0	9982	1667	58	2	39157	2	MUC16	19	9087113	Missense_Mutation	SNP	T	TCGA-DD-A116-01A-11D-A12Z-10	84555	9087113	50041870	123	11947										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363952	22363953	+	Missense_Mutation	DNP	AC	AC	TA													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ggtttctctccagtatgaatActcttataataagtaagggt					rs537289839|rs570225845	byFrequency	TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:22363952_22363953AC>TA	ENST00000397121.2	-	3	883_884	c.566_567GT>TA	c.(565-567)aGT>aTA	p.S189I		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	189				TLTYYKSI -> NLMEHKRV (in Ref. 2; BAC05174). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				CAGTATGAATACTCTTATAATA	0.342																																					p.S189R|p.S189I		Atlas-SNP	.											.	ZNF676	146	.	0			c.T567A|c.G566T						.																																			SO:0001583	missense	163223	exon3			ATGAATACTCTTA|TGAATACTCTTAT	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.566_567delinsTA	chr19.hg19:g.22363952_22363953delinsTA	ENSP00000380310:p.Ser189Ile	60.0	0.0		98.0|100.0	31.0|27.0	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	hg19	CCDS42539.1																																																																																			.	.		0.342	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		TA	22363953	AC	TA	22363952	3	4	89	1	0	0	0	0	1	0	0	0	18098	388	14	4	1203	4	ZNF676	19	22363952	Missense_Mutation	DNP	AC	TCGA-DD-A116-01A-11D-A12Z-10	13276839	22363952	36765031	124	11948	50	2								
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363957	22363958	+	Frame_Shift_Del	DEL	TA	TA	-													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ctctccagtatgaatactctTataataagtaagggttgagg					rs386807906		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:22363957_22363958delTA	ENST00000397121.2	-	3	878_879	c.561_562delTA	c.(559-564)tataagfs	p.YK187fs		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	187				TLTYYKSI -> NLMEHKRV (in Ref. 2; BAC05174). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TGAATACTCTTATAATAAGTAA	0.347																																					p.188_188del		Atlas-INDEL	.											.	ZNF676	146	.	0			c.562_563del						.																																			SO:0001589	frameshift_variant	163223	exon3			.	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.561_562delTA	chr19.hg19:g.22363959_22363960delTA	ENSP00000380310:p.Tyr187fs	60.0	0.0		110.0	30.0	NM_001001411	A8MVX5	Frame_Shift_Del	DEL	ENST00000397121.2	hg19	CCDS42539.1																																																																																			.	.		0.347	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		-	22363958	TA	-	22363957	7	5	89	1	0	1	0	1	0	0	0	0	18098	1763	61	0	1208	0	ZNF676	19	22363957	Frame_Shift_Del	DEL	TA	TCGA-DD-A116-01A-11D-A12Z-10	5	22363957	36765026	125	11949	50	2								
ZNF790	388536	hgsc.bcm.edu	37	chr19	37309866	37309869	+	Frame_Shift_Del	DEL	AAGA	AAGA	-													0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	cgattaaactctgagccatgAagaaaggtctttccacattc					rs199677584		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	AAGA	AAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:37309866_37309869delAAGA	ENST00000356725.4	-	5	1497_1500	c.1377_1380delTCTT	c.(1375-1380)tttcttfs	p.FL459fs	CTD-2162K18.5_ENST00000587278.1_RNA|CTD-2162K18.5_ENST00000588906.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	459					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CTGAGCCATGAAGAAAGGTCTTTC	0.377																																					p.460_461del		Atlas-Indel,Pindel	.											.	ZNF790	89	.	0			c.1378_1381del						.																																			SO:0001589	frameshift_variant	388536	exon5			.	BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.1377_1380delTCTT	chr19.hg19:g.37309866_37309869delAAGA	ENSP00000349161:p.Phe459fs	68.0	0.0		174.0	51.0	NM_206894		Frame_Shift_Del	DEL	ENST00000356725.4	hg19	CCDS12496.1																																																																																			.	.		0.377	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		-	37309869	AAGA	-	37309866	7	5	89	1	0	1	0	1	0	0	0	0	18177	233	9	0	534	0	ZNF790	19	37309866	Frame_Shift_Del	DEL	AAGA	TCGA-DD-A116-01A-11D-A12Z-10	14945909	37309866	21819117	126	11950										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40424311	40424311	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	ttgcgaactccacagcgtcaGgagccagagccccgtcaggc	12	15	2	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:40424311G>C	ENST00000221347.6	-	4	1899	c.1892C>G	c.(1891-1893)cCt>cGt	p.P631R		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	631	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CACAGCGTCAGGAGCCAGAGC	0.612																																					p.P631R		Atlas-SNP	.											.	FCGBP	416	.	0			c.C1892G						.						147	157	154					19																	40424311		2203	4300	6503	SO:0001583	missense	8857	exon4			GCGTCAGGAGCCA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.1892C>G	chr19.hg19:g.40424311G>C	ENSP00000221347:p.Pro631Arg	44.0	0.0		104.0	40.0	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.273349	0.23221	.	.	ENSG00000090920	ENST00000221347	T	0.18338	2.22	5.21	4.15	0.48705	von Willebrand factor, type D domain (1);	0.835797	0.10227	N	0.700215	T	0.30727	0.0774	L	0.52206	1.635	0.09310	N	1	D	0.63046	0.992	P	0.58520	0.84	T	0.18147	-1.0346	10	0.18710	T	0.47	.	13.821	0.63320	0.0:0.0:0.8454:0.1546	.	631	Q9Y6R7	FCGBP_HUMAN	R	631	ENSP00000221347:P631R	ENSP00000221347:P631R	P	-	2	0	FCGBP	45116151	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	0.779000	0.26746	1.159000	0.42565	0.561000	0.74099	CCT	.	.		0.612	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		C	40424311	G	C	40424311	3	2	89	1	0	0	0	0	1	0	0	0	5786	1000	35	4	14457	4	FCGBP	19	40424311	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	3114445	40424311	18704672	127	11951										
PHLDB3	653583	hgsc.bcm.edu	37	chr19	43983597	43983597	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gcttcctccaggtcttgatgCggccgcccatcttcaccagg	10	16	3	1	rs200179651		TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:43983597C>A	ENST00000292140.5	-	14	1994	c.1634G>T	c.(1633-1635)cGc>cTc	p.R545L		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	545	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GGTCTTGATGCGGCCGCCCAT	0.652																																					p.R545L		Atlas-SNP	.											.	PHLDB3	30	.	0			c.G1634T						.						15	18	17					19																	43983597		2039	4169	6208	SO:0001583	missense	653583	exon14			TTGATGCGGCCGC		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"Pleckstrin homology (PH) domain containing"	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1634G>T	chr19.hg19:g.43983597C>A	ENSP00000292140:p.Arg545Leu	39.0	0.0		165.0	63.0	NM_198850	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	hg19	CCDS12621.2	.	.	.	.	.	.	.	.	.	.	C	15.59	2.877146	0.51801	.	.	ENSG00000176531	ENST00000292140	T	0.74002	-0.8	4.59	3.56	0.40772	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.64402	D	0.000002	T	0.80330	0.4603	L	0.46157	1.445	0.50313	D	0.999866	D;D	0.76494	0.997;0.999	D;D	0.75484	0.949;0.986	T	0.81239	-0.1023	10	0.72032	D	0.01	.	11.179	0.48616	0.0:0.9062:0.0:0.0938	.	215;545	B2RXH3;Q6NSJ2	.;PHLB3_HUMAN	L	545	ENSP00000292140:R545L	ENSP00000292140:R545L	R	-	2	0	PHLDB3	48675437	0.996000	0.38824	0.899000	0.35326	0.222000	0.24845	2.367000	0.44213	1.260000	0.44134	-0.236000	0.12185	CGC	.	.		0.652	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2			A	43983597	C	A	43983597	3	1	89	1	0	0	0	0	1	0	0	0	11862	768	27	1	300	1	PHLDB3	19	43983597	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	3559286	43983597	15145386	128	11952										
LILRB1	10859	hgsc.bcm.edu	37	chr19	55148212	55148212	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tctgaagccccccaggatgtGacctacgcccagctgcacag	10	16	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:55148212G>A	ENST00000396331.1	+	16	2193	c.1836G>A	c.(1834-1836)gtG>gtA	p.V612V	LILRB1_ENST00000396321.2_Silent_p.V612V|LILRB1_ENST00000448689.1_3'UTR|LILRB1_ENST00000396317.1_Silent_p.V596V|LILRB1_ENST00000324602.7_Silent_p.V614V|AC009892.10_ENST00000456337.1_Intron|LILRB1_ENST00000427581.2_Silent_p.V663V|LILRB1_ENST00000396327.3_Silent_p.V613V|LILRB1_ENST00000434867.2_Silent_p.V612V|LILRB1_ENST00000418536.2_Silent_p.V596V|LILRB1_ENST00000396332.4_Silent_p.V613V|LILRB1_ENST00000396315.1_Silent_p.V614V|LILRB1_ENST00000462628.1_3'UTR	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	612					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CCCAGGATGTGACCTACGCCC	0.657										HNSCC(37;0.09)																											p.V614V		Atlas-SNP	.											.	LILRB1	140	.	0			c.G1842A						.						73	66	68					19																	55148212		2203	4300	6503	SO:0001819	synonymous_variant	10859	exon15			GGATGTGACCTAC	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1836G>A	chr19.hg19:g.55148212G>A		119.0	0.0		385.0	105.0	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	hg19	CCDS42617.1																																																																																			.	.		0.657	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			A	55148212	G	A	55148212	2	1	89	1	0	0	0	0	0	0	0	1	8799	1277	45	3		3	LILRB1	19	55148212	Silent	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	11164615	55148212	3980771	129	11953										
ZNF606	80095	hgsc.bcm.edu	37	chr19	58489830	58489830	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	acaaaatgctttttcacaatGattacatttgtagggctttt	6	6	1	1			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr19:58489830G>A	ENST00000341164.4	-	7	2838	c.2218C>T	c.(2218-2220)Cat>Tat	p.H740Y	ZNF606_ENST00000536132.1_Missense_Mutation_p.H650Y	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	740					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		TTTTCACAATGATTACATTTG	0.358																																					p.H740Y		Atlas-SNP	.											.	ZNF606	155	.	0			c.C2218T						.						129	136	134					19																	58489830		2203	4300	6503	SO:0001583	missense	80095	exon7			CACAATGATTACA	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"Zinc fingers, C2H2-type", "-"	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.2218C>T	chr19.hg19:g.58489830G>A	ENSP00000343617:p.His740Tyr	100.0	0.0		269.0	11.0	NM_025027	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	hg19	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	G	6.692	0.496343	0.12762	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.07216	3.21;3.21	4.55	4.55	0.56014	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.148462	0.31577	N	0.007412	T	0.08802	0.0218	N	0.12637	0.245	0.09310	N	1	D	0.53619	0.961	P	0.51701	0.677	T	0.12967	-1.0527	10	0.87932	D	0	.	11.5434	0.50679	0.0:0.2978:0.7022:0.0	.	740	Q8WXB4	ZN606_HUMAN	Y	740;650	ENSP00000343617:H740Y;ENSP00000445624:H650Y	ENSP00000343617:H740Y	H	-	1	0	ZNF606	63181642	0.000000	0.05858	0.976000	0.42696	0.987000	0.75469	-0.365000	0.07573	2.492000	0.84095	0.650000	0.86243	CAT	.	.		0.358	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		A	58489830	G	A	58489830	3	1	89	1	0	0	0	0	1	0	0	0	18047	1290	45	3	164	3	ZNF606	19	58489830	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	3341618	58489830	639153	130	11954										
SMOX	54498	hgsc.bcm.edu	37	chr20	4163387	4163387	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tctacccgcctgagcgctacGgccatgtgctgagcggctgg	14	14	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr20:4163387G>T	ENST00000305958.4	+	5	1486	c.1261G>T	c.(1261-1263)Ggc>Tgc	p.G421C	SMOX_ENST00000278795.3_Missense_Mutation_p.G368C|SMOX_ENST00000379460.2_Missense_Mutation_p.G421C|SMOX_ENST00000339123.6_Missense_Mutation_p.G368C|SMOX_ENST00000346595.2_Intron	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	421					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	TGAGCGCTACGGCCATGTGCT	0.622																																					p.G421C		Atlas-SNP	.											.	SMOX	119	.	0			c.G1261T						.						90	81	84					20																	4163387		2203	4300	6503	SO:0001583	missense	54498	exon5			CGCTACGGCCATG	AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"chromosome 20 open reading frame 16"	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.1261G>T	chr20.hg19:g.4163387G>T	ENSP00000307252:p.Gly421Cys	62.0	0.0		165.0	67.0	NM_175839	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Missense_Mutation	SNP	ENST00000305958.4	hg19	CCDS13075.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.883111	0.51908	.	.	ENSG00000088826	ENST00000339123;ENST00000305958;ENST00000278795;ENST00000379460;ENST00000457205	D;D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15;-3.15	5.5	4.55	0.56014	Amine oxidase (1);	0.092562	0.85682	D	0.000000	D	0.95284	0.8470	L	0.60957	1.885	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;1.0;1.0;0.981;0.998	D	0.94976	0.8121	10	0.56958	D	0.05	-21.4086	11.8162	0.52211	0.0847:0.0:0.9153:0.0	.	345;421;421;368;368	B4DE63;Q9NWM0-6;Q9NWM0;Q9NWM0-2;Q9NWM0-4	.;.;SMOX_HUMAN;.;.	C	368;421;368;421;278	ENSP00000344595:G368C;ENSP00000307252:G421C;ENSP00000278795:G368C;ENSP00000368773:G421C;ENSP00000407269:G278C	ENSP00000278795:G368C	G	+	1	0	SMOX	4111387	1.000000	0.71417	0.946000	0.38457	0.433000	0.31745	9.863000	0.99569	1.340000	0.45581	0.650000	0.86243	GGC	.	.		0.622	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842		T	4163387	G	T	4163387	3	4	89	1	0	0	0	0	1	0	0	0	14818	1116	39	1	1275	1	SMOX	20	4163387	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10		4163387	58862133	131	11955										
ZFP64	55734	hgsc.bcm.edu	37	chr20	50769740	50769740	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gtgcacgcggctgtgcttccGgagggtggctttgctgtcac	16	11	1	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr20:50769740G>A	ENST00000216923.4	-	6	1340	c.991C>T	c.(991-993)Cgg>Tgg	p.R331W	ZFP64_ENST00000477786.1_Intron|ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000346617.4_Missense_Mutation_p.R277W|ZFP64_ENST00000371515.4_Missense_Mutation_p.R329W	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	331					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CTGTGCTTCCGGAGGGTGGCT	0.582																																					p.R331W		Atlas-SNP	.											.	ZFP64	240	.	0			c.C991T						.						114	105	108					20																	50769740		2203	4300	6503	SO:0001583	missense	55734	exon6			GCTTCCGGAGGGT	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.991C>T	chr20.hg19:g.50769740G>A	ENSP00000216923:p.Arg331Trp	78.0	0.0		244.0	101.0	NM_018197	Q9NTS7|Q9NVH4	Missense_Mutation	SNP	ENST00000216923.4	hg19	CCDS13440.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.886396	0.91814	.	.	ENSG00000020256	ENST00000216923;ENST00000346617;ENST00000371515;ENST00000546083;ENST00000371516	T;T;T	0.16196	2.36;2.36;2.36	5.79	5.79	0.91817	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000042	T	0.51500	0.1678	M	0.88906	2.99	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.99;0.993;0.994	T	0.55792	-0.8085	10	0.54805	T	0.06	-27.0779	20.0381	0.97570	0.0:0.0:1.0:0.0	.	277;329;331	Q9NPA5-2;Q5JWM1;Q9NPA5	.;.;ZF64A_HUMAN	W	331;277;329;173;484	ENSP00000216923:R331W;ENSP00000344615:R277W;ENSP00000360570:R329W	ENSP00000216923:R331W	R	-	1	2	ZFP64	50203147	1.000000	0.71417	0.928000	0.36995	0.996000	0.88848	7.639000	0.83342	2.740000	0.93945	0.609000	0.83330	CGG	.	.		0.582	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197		A	50769740	G	A	50769740	3	1	89	1	0	0	0	0	1	0	0	0	17667	1115	39	1	2249	1	ZFP64	20	50769740	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	46606353	50769740	12255780	132	11956										
KRTAP13-2	337959	hgsc.bcm.edu	37	chr21	31744410	31744410	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gctggcaggtgctgggagagCagaggtcagtgctgtagacc	18	8	1	3			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr21:31744410C>A	ENST00000399889.2	-	1	147	c.122G>T	c.(121-123)tGc>tTc	p.C41F		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	41						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						GCTGGGAGAGCAGAGGTCAGT	0.597																																					p.C41F		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.G122T						.						86	82	83					21																	31744410		2203	4300	6503	SO:0001583	missense	337959	exon1			GGAGAGCAGAGGT	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"Keratin associated proteins"	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.122G>T	chr21.hg19:g.31744410C>A	ENSP00000382777:p.Cys41Phe	79.0	0.0		225.0	76.0	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	hg19	CCDS13589.1	.	.	.	.	.	.	.	.	.	.	C	13.25	2.181048	0.38511	.	.	ENSG00000182816	ENST00000399889	T	0.04454	3.62	4.51	2.16	0.27623	.	1.394900	0.05165	N	0.498547	T	0.16428	0.0395	M	0.72118	2.19	0.09310	N	1	P	0.48911	0.917	P	0.56700	0.804	T	0.14117	-1.0484	10	0.72032	D	0.01	.	7.6607	0.28402	0.0:0.816:0.0:0.184	.	41	Q52LG2	KR132_HUMAN	F	41	ENSP00000382777:C41F	ENSP00000382777:C41F	C	-	2	0	KRTAP13-2	30666281	0.000000	0.05858	0.001000	0.08648	0.979000	0.70002	-0.339000	0.07832	0.305000	0.22832	0.655000	0.94253	TGC	.	.		0.597	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1			A	31744410	C	A	31744410	3	1	89	1	0	0	0	0	1	0	0	0	8532	710	25	3	409	3	KRTAP13-2	21	31744410	Missense_Mutation	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10		31744410	16385485	133	11957										
RRP1B	23076	hgsc.bcm.edu	37	chr21	45094517	45094517	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	caaaaattgcctttctttagCtgattcgtctggtcctgagg	9	9	2	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr21:45094517C>A	ENST00000340648.4	+	5	475	c.358C>A	c.(358-360)Ctg>Atg	p.L120M		NM_015056.2	NP_055871.1	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1B	120					negative regulation of phosphatase activity (GO:0010923)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome, small subunit precursor (GO:0030688)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(1)	21				STAD - Stomach adenocarcinoma(101;0.178)		CTTTCTTTAGCTGATTCGTCT	0.353																																					p.L120M		Atlas-SNP	.											.	RRP1B	51	.	0			c.C358A						.						78	71	73					21																	45094517		2203	4300	6503	SO:0001630	splice_region_variant	23076	exon5			CTTTAGCTGATTC	AK124620	CCDS33577.1	21q22.3	2014-06-13	2013-07-02	2007-03-26	ENSG00000160208	ENSG00000160208			23818	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 136"	610654	"KIAA0179", "ribosomal RNA processing 1 homolog B (S. cerevisiae)"	KIAA0179			Standard	NM_015056		Approved	Nnp1, RRP1, PPP1R136	uc002zdk.3	Q14684	OTTHUMG00000086872	ENST00000340648.4:c.358-1C>A	chr21.hg19:g.45094517C>A		60.0	0.0		175.0	56.0	NM_015056	Q8TBZ4	Missense_Mutation	SNP	ENST00000340648.4	hg19	CCDS33577.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.083221	0.36758	.	.	ENSG00000160208	ENST00000340648	T	0.64991	-0.13	5.53	3.33	0.38152	.	0.069267	0.56097	D	0.000021	D	0.82426	0.5034	H	0.96604	3.85	0.53005	D	0.999964	D	0.89917	1.0	D	0.97110	1.0	T	0.82973	-0.0191	9	.	.	.	-9.1608	5.382	0.16196	0.0:0.6875:0.0:0.3124	.	120	Q14684	RRP1B_HUMAN	M	120	ENSP00000339145:L120M	.	L	+	1	2	RRP1B	43918945	1.000000	0.71417	0.993000	0.49108	0.114000	0.19823	1.046000	0.30354	1.466000	0.48025	0.650000	0.86243	CTG	.	.		0.353	RRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195651.1	NM_015056	Missense_Mutation	A	45094517	C	A	45094517	5	1	89	1	0	0	0	0	0	0	1	0	13703	811	28	3	376	3	RRP1B	21	45094517	Splice_Site	SNP	C	TCGA-DD-A116-01A-11D-A12Z-10	13350107	45094517	3035378	134	11958										
HIRA	7290	hgsc.bcm.edu	37	chr22	19376069	19376069	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	accaccagcggccgtttcagAcatgtgagctggaaggaaag	13	10	1	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr22:19376069A>G	ENST00000263208.5	-	10	1201	c.945T>C	c.(943-945)tgT>tgC	p.C315C	HIRA_ENST00000340170.4_Silent_p.C315C|HIRA_ENST00000541063.1_Silent_p.C271C|HIRA_ENST00000546308.1_Silent_p.C271C	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	315					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					GCCGTTTCAGACATGTGAGCT	0.423																																					p.C315C		Atlas-SNP	.											.	HIRA	100	.	0			c.T945C						.						65	63	64					22																	19376069		2203	4300	6503	SO:0001819	synonymous_variant	7290	exon10			TTTCAGACATGTG	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"WD repeat domain containing"	4916	protein-coding gene	gene with protein product	"DiGeorge critical region gene 1"	600237	"HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)", "HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.945T>C	chr22.hg19:g.19376069A>G		41.0	0.0		100.0	41.0	NM_003325	Q05BU9|Q8IXN2	Silent	SNP	ENST00000263208.5	hg19	CCDS13759.1																																																																																			.	.		0.423	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		G	19376069	A	G	19376069	2	3	89	1	0	0	0	0	0	0	0	1	7129	273	10	2		2	HIRA	22	19376069	Silent	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10		19376069	31928497	135	11959										
HMGXB4	10042	hgsc.bcm.edu	37	chr22	35661228	35661228	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	agtcccacagtgctaaccttGatctttcagggcttgaacct	8	12	2	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chr22:35661228G>A	ENST00000216106.5	+	5	975	c.847G>A	c.(847-849)Gat>Aat	p.D283N	HMGXB4_ENST00000444518.2_Missense_Mutation_p.D174N	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	283					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGCTAACCTTGATCTTTCAGG	0.502																																					p.D283N		Atlas-SNP	.											.	HMGXB4	52	.	0			c.G847A						.						80	77	78					22																	35661228		2203	4300	6503	SO:0001583	missense	10042	exon5			AACCTTGATCTTT	AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"High mobility group / Non-canonical"	5003	protein-coding gene	gene with protein product		604702	"high-mobility group protein 2-like 1"	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.847G>A	chr22.hg19:g.35661228G>A	ENSP00000216106:p.Asp283Asn	72.0	0.0		228.0	72.0	NM_001003681	O75672|O75673|Q9UMT5	Missense_Mutation	SNP	ENST00000216106.5	hg19	CCDS33641.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.020395	0.54576	.	.	ENSG00000100281	ENST00000420166;ENST00000444518;ENST00000455359;ENST00000216106	T;T;T;T	0.47869	0.83;2.18;0.83;2.18	5.71	5.71	0.89125	.	0.230253	0.44688	D	0.000430	T	0.35068	0.0919	N	0.14661	0.345	0.37220	D	0.905208	B	0.30482	0.281	B	0.27796	0.083	T	0.40213	-0.9575	10	0.72032	D	0.01	-10.556	18.4046	0.90529	0.0:0.0:1.0:0.0	.	283	Q9UGU5	HMGX4_HUMAN	N	174;174;174;283	ENSP00000401658:D174N;ENSP00000398302:D174N;ENSP00000415500:D174N;ENSP00000216106:D283N	ENSP00000216106:D283N	D	+	1	0	HMGXB4	33991228	0.998000	0.40836	0.266000	0.24541	0.927000	0.56198	4.208000	0.58486	2.861000	0.98227	0.650000	0.86243	GAT	.	.		0.502	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487		A	35661228	G	A	35661228	3	1	89	1	0	0	0	0	1	0	0	0	7248	1290	45	3	861	3	HMGXB4	22	35661228	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	16285159	35661228	15643338	136	11960										
SHROOM2	357	hgsc.bcm.edu	37	chrX	9863964	9863964	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	gggttgggaggtggcacccaGgaaggacccctcgctggcac	17	12	0	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chrX:9863964G>T	ENST00000380913.3	+	4	2106	c.2016G>T	c.(2014-2016)caG>caT	p.Q672H		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	672					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				GTGGCACCCAGGAAGGACCCC	0.672																																					p.Q672H		Atlas-SNP	.											.	SHROOM2	139	.	0			c.G2016T						.						9	8	8					X																	9863964		2136	4196	6332	SO:0001583	missense	357	exon4			CACCCAGGAAGGA	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"apical protein, Xenopus laevis-like", "apical protein-like (Xenopus laevis)"	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.2016G>T	chrX.hg19:g.9863964G>T	ENSP00000370299:p.Gln672His	9.0	0.0		33.0	22.0	NM_001649	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	hg19	CCDS14135.1	.	.	.	.	.	.	.	.	.	.	G	2.372	-0.344160	0.05208	.	.	ENSG00000146950	ENST00000380913	T	0.44083	0.93	4.52	-4.05	0.03998	Apx/shroom, ASD1 (1);	7.240040	0.00644	N	0.000523	T	0.36744	0.0978	L	0.38175	1.15	0.49915	D	0.999837	P	0.48694	0.914	P	0.48334	0.574	T	0.34650	-0.9820	10	0.59425	D	0.04	-3.1131	2.1711	0.03849	0.2795:0.1136:0.3817:0.2253	.	672	Q13796	SHRM2_HUMAN	H	672	ENSP00000370299:Q672H	ENSP00000370299:Q672H	Q	+	3	2	SHROOM2	9823964	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-2.504000	0.00964	-1.275000	0.02417	-0.340000	0.08031	CAG	.	.		0.672	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649		T	9863964	G	T	9863964	3	4	89	1	0	0	0	0	1	0	0	0	14309	991	35	3	2030	3	SHROOM2	23	9863964	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10		9863964	145406596	137	11961										
TGIF2LX	90316	hgsc.bcm.edu	37	chrX	89177754	89177754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	tcctgctgctagtcgatgcaGcagtacaaagggctgccgag	13	11	0	0			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chrX:89177754G>A	ENST00000561129.2	+	1	800	c.670G>A	c.(670-672)Gca>Aca	p.A224T	TGIF2LX_ENST00000283891.5_Missense_Mutation_p.A224T			Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	224					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(29)|ovary(1)|skin(3)|urinary_tract(1)	40						AGTCGATGCAGCAGTACAAAG	0.498																																					p.A224T		Atlas-SNP	.											.	TGIF2LX	84	.	0			c.G670A						.						44	47	46					X																	89177754		2198	4293	6491	SO:0001583	missense	90316	exon2			GATGCAGCAGTAC	AF497480	CCDS14459.1	Xq21.31	2014-05-14	2007-02-07		ENSG00000153779	ENSG00000153779		"Homeoboxes / TALE class"	18570	protein-coding gene	gene with protein product		300411	"TGFB-induced factor 2-like, X-linked"				Standard	NM_138960		Approved		uc004efe.3	Q8IUE1	OTTHUMG00000021954	ENST00000561129.2:c.670G>A	chrX.hg19:g.89177754G>A	ENSP00000453704:p.Ala224Thr	78.0	0.0		275.0	216.0	NM_138960	Q5JRM9|Q8TD48	Missense_Mutation	SNP	ENST00000561129.2	hg19	CCDS14459.1	.	.	.	.	.	.	.	.	.	.	G	11.15	1.553979	0.27739	.	.	ENSG00000153779	ENST00000283891	T	0.76060	-0.99	3.11	2.24	0.28232	.	0.671285	0.12355	N	0.476210	D	0.84051	0.5387	M	0.83483	2.645	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.70029	-0.4984	9	.	.	.	-20.3271	5.5631	0.17154	0.1575:0.0:0.8425:0.0	.	224	Q8IUE1	TF2LX_HUMAN	T	224	ENSP00000355119:A224T	.	A	+	1	0	TGIF2LX	89064410	0.990000	0.36364	0.011000	0.14972	0.004000	0.04260	4.421000	0.59848	0.723000	0.32274	0.415000	0.27848	GCA	.	.		0.498	TGIF2LX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417911.2	NM_138960		A	89177754	G	A	89177754	3	1	89	1	0	0	0	0	1	0	0	0	15842	971	34	3	672	3	TGIF2LX	23	89177754	Missense_Mutation	SNP	G	TCGA-DD-A116-01A-11D-A12Z-10	79313790	89177754	66092806	138	11962										
PLP1	5354	hgsc.bcm.edu	37	chrX	103041518	103041518	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0797101449275362	11	1	1.74021164021164	2.37301587301587	1.51010101010101	0.45779368380326	1	0	agatctttggcgactacaagAccaccatctgcggcaagggc	11	12	2	2			TCGA-DD-A116-01A-11D-A12Z-10	TCGA-DD-A116-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62bed857-df38-4647-9db4-b95bca893cfb	3e8275bd-f6e8-43cc-956f-83a6c36c0b09	g.chrX:103041518A>G	ENST00000303958.2	+	3	462	c.316A>G	c.(316-318)Acc>Gcc	p.T106A	PLP1_ENST00000418604.1_Missense_Mutation_p.T106A|PLP1_ENST00000361621.2_Missense_Mutation_p.T106A	NM_000533.3	NP_000524.3	P60201	MYPR_HUMAN	proteolipid protein 1	106					astrocyte development (GO:0014002)|axon development (GO:0061564)|axon ensheathment (GO:0008366)|cell death (GO:0008219)|cell maturation (GO:0048469)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|long-chain fatty acid biosynthetic process (GO:0042759)|positive regulation of gene expression (GO:0010628)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	structural constituent of myelin sheath (GO:0019911)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	17						CGACTACAAGACCACCATCTG	0.587																																					p.T106A		Atlas-SNP	.											.	PLP1	37	.	0			c.A316G						.						119	106	110					X																	103041518		2203	4300	6503	SO:0001583	missense	5354	exon4			TACAAGACCACCA	M27110	CCDS14513.1, CCDS14514.1	Xq22	2013-05-14	2008-07-28		ENSG00000123560	ENSG00000123560			9086	protein-coding gene	gene with protein product	"Pelizaeus-Merzbacher disease"	300401	"spastic paraplegia 2, uncomplicated"	SPG2, PLP			Standard	NM_001128834		Approved	GPM6C	uc004elk.3	P60201	OTTHUMG00000022111	ENST00000303958.2:c.316A>G	chrX.hg19:g.103041518A>G	ENSP00000305152:p.Thr106Ala	86.0	0.0		169.0	131.0	NM_001128834	P04400|P06905|Q502Y1|Q6FHZ6	Missense_Mutation	SNP	ENST00000303958.2	hg19	CCDS14513.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.564697	0.45694	.	.	ENSG00000123560	ENST00000434483;ENST00000429977;ENST00000455268;ENST00000422393;ENST00000418604;ENST00000443502;ENST00000303958;ENST00000361621	D;D;D;D;D;D;D;D	0.99259	-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64	5.78	5.78	0.91487	.	0.183995	0.64402	D	0.000018	D	0.97284	0.9112	N	0.19112	0.55	0.41067	D	0.985429	B;B;B;B;P	0.35192	0.022;0.003;0.003;0.003;0.489	B;B;B;B;B	0.39465	0.012;0.006;0.008;0.006;0.3	D	0.97617	1.0133	10	0.42905	T	0.14	-4.5431	12.8049	0.57607	1.0:0.0:0.0:0.0	.	51;106;106;106;106	B4DI30;A8K9L3;B1B1G6;P60201;P60201-2	.;.;.;MYPR_HUMAN;.	A	106	ENSP00000403335:T106A;ENSP00000399913:T106A;ENSP00000409802:T106A;ENSP00000413931:T106A;ENSP00000405750:T106A;ENSP00000391853:T106A;ENSP00000305152:T106A;ENSP00000354860:T106A	ENSP00000305152:T106A	T	+	1	0	PLP1	102928174	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.159000	0.77483	1.931000	0.55961	0.486000	0.48141	ACC	.	.		0.587	PLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057743.2			G	103041518	A	G	103041518	3	3	89	1	0	0	0	0	1	0	0	0	12113	275	10	2	326	2	PLP1	23	103041518	Missense_Mutation	SNP	A	TCGA-DD-A116-01A-11D-A12Z-10	13863764	103041518	52229042	139	11963										
THRAP3	9967	hgsc.bcm.edu	37	chr1	36757042	36757042	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tccatagcaacaaaaaggaaCaggagtttcgttccattttc	7	9	0	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr1:36757042C>T	ENST00000354618.5	+	6	2037	c.1813C>T	c.(1813-1815)Cag>Tag	p.Q605*	THRAP3_ENST00000466743.1_3'UTR|THRAP3_ENST00000469141.2_Nonsense_Mutation_p.Q605*	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	605	Required for mRNA decay activity.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CAAAAAGGAACAGGAGTTTCG	0.458			T	USP6	aneurysmal bone cysts																																p.Q605X	Pancreas(129;785 1795 20938 23278 32581)	Atlas-SNP	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	THRAP3	93	.	0			c.C1813T						.						114	104	107					1																	36757042		2203	4300	6503	SO:0001587	stop_gained	9967	exon6			AAGGAACAGGAGT	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.1813C>T	chr1.hg19:g.36757042C>T	ENSP00000346634:p.Gln605*	267.0	0.0		213.0	67.0	NM_005119	D3DPS5|Q5VTK6	Nonsense_Mutation	SNP	ENST00000354618.5	hg19	CCDS405.1	.	.	.	.	.	.	.	.	.	.	C	41	9.154439	0.99084	.	.	ENSG00000054118	ENST00000354618;ENST00000469141	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-17.844	19.0579	0.93074	0.0:1.0:0.0:0.0	.	.	.	.	X	605	.	ENSP00000346634:Q605X	Q	+	1	0	THRAP3	36529629	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.734000	0.68580	2.827000	0.97445	0.650000	0.86243	CAG	.	.		0.458	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		T	36757042	C	T	36757042	4	4	90	1	0	0	0	0	0	1	0	0	15889	479	17	3	1827	3	THRAP3	1	36757042	Nonsense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10		36757042	212493579	1	11964										
NASP	4678	hgsc.bcm.edu	37	chr1	46083194	46083194	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aagaaagccaaacaagagccGgaggtgaacggaggcagtgg	16	7	0	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr1:46083194G>A	ENST00000350030.3	+	14	2304	c.2217G>A	c.(2215-2217)ccG>ccA	p.P739P	NASP_ENST00000351223.3_Silent_p.P400P|NASP_ENST00000537798.1_Silent_p.P675P|NASP_ENST00000372052.4_Silent_p.P373P|NASP_ENST00000530073.1_3'UTR|NASP_ENST00000402363.3_Silent_p.P741P	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	739					blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					AACAAGAGCCGGAGGTGAACG	0.493																																					p.P739P		Atlas-SNP	.											.	NASP	77	.	0			c.G2217A						.						102	89	94					1																	46083194		2203	4300	6503	SO:0001819	synonymous_variant	4678	exon14			AGAGCCGGAGGTG	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"Tetratricopeptide (TTC) repeat domain containing"	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.2217G>A	chr1.hg19:g.46083194G>A		47.0	0.0		35.0	12.0	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Silent	SNP	ENST00000350030.3	hg19	CCDS524.1	.	.	.	.	.	.	.	.	.	.	G	9.102	1.004302	0.19199	.	.	ENSG00000132780	ENST00000531612	.	.	.	4.56	0.242	0.15498	.	.	.	.	.	T	0.51075	0.1653	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.39702	-0.9601	4	.	.	.	-3.0E-4	5.2561	0.15548	0.3982:0.0:0.4699:0.1319	.	.	.	.	Q	239	.	.	R	+	2	0	NASP	45855781	0.095000	0.21747	0.995000	0.50966	0.984000	0.73092	-0.075000	0.11431	0.245000	0.21373	0.563000	0.77884	CGG	.	.		0.493	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		A	46083194	G	A	46083194	2	1	90	1	0	0	0	0	0	0	0	1	10181	1103	39	1		1	NASP	1	46083194	Silent	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	9326152	46083194	203167427	2	11965										
BEND5	79656	hgsc.bcm.edu	37	chr1	49242456	49242456	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tcgcgcacgcacgacacgggCagcgcgtagcagacgttgtc	14	14	0	1	rs548809089	byFrequency	TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr1:49242456C>T	ENST00000371833.3	-	1	134	c.48G>A	c.(46-48)ctG>ctA	p.L16L	AGBL4_ENST00000371839.1_Intron|AGBL4_ENST00000371838.1_Intron	NM_024603.2	NP_078879.2	Q7L4P6	BEND5_HUMAN	BEN domain containing 5	16						Golgi apparatus (GO:0005794)				large_intestine(5)|lung(2)|skin(1)	8						ACGACACGGGCAGCGCGTAGC	0.716													C|||	3	0.000599042	0	0	5008	,	,		6062	0		0.003	False		,,,				2504	0				p.L16L		Atlas-SNP	.											.	BEND5	93	.	0			c.G48A						.						6	9	8					1																	49242456		654	1557	2211	SO:0001819	synonymous_variant	79656	exon1			CACGGGCAGCGCG	BC007932	CCDS552.2	1p33	2012-11-22	2008-10-03	2008-10-03	ENSG00000162373	ENSG00000162373		"BEN domain containing"	25668	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 165"	C1orf165		12477932	Standard	NM_024603		Approved	FLJ11588	uc001crx.4	Q7L4P6	OTTHUMG00000008153	ENST00000371833.3:c.48G>A	chr1.hg19:g.49242456C>T		40.0	0.0		61.0	22.0	NM_024603	D3DQ27|Q96A62|Q9HAI3	Silent	SNP	ENST00000371833.3	hg19	CCDS552.2																																																																																			.	.		0.716	BEND5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022323.1	NM_024603		T	49242456	C	T	49242456	2	4	90	1	0	0	0	0	0	0	0	1	1401	697	25	3		3	BEND5	1	49242456	Silent	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	3159262	49242456	200008165	3	11966										
FLG	2312	hgsc.bcm.edu	37	chr1	152281525	152281525	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	catctcttgactgctcccaaGcagatccaagatggtttctg	8	12	2	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr1:152281525G>A	ENST00000368799.1	-	3	5872	c.5837C>T	c.(5836-5838)gCt>gTt	p.A1946V	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1946	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.A1946V(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCTCCCAAGCAGATCCAAG	0.562									Ichthyosis																												p.A1946V		Atlas-SNP	.											FLG,colon,carcinoma,0,1	FLG	900	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5837T						.						250	237	242					1																	152281525		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCCCAAGCAGATC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5837C>T	chr1.hg19:g.152281525G>A	ENSP00000357789:p.Ala1946Val	683.0	0.0		734.0	151.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	3.101	-0.184746	0.06340	.	.	ENSG00000143631	ENST00000368799	T	0.01787	4.64	2.54	-2.28	0.06826	.	.	.	.	.	T	0.00468	0.0015	L	0.41824	1.3	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.46762	-0.9168	9	0.31617	T	0.26	-4.2776	0.552	0.00664	0.2588:0.1884:0.3614:0.1915	.	1946	P20930	FILA_HUMAN	V	1946	ENSP00000357789:A1946V	ENSP00000357789:A1946V	A	-	2	0	FLG	150548149	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.608000	0.02068	-0.570000	0.06022	-1.754000	0.00674	GCT	.	.		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152281525	G	A	152281525	3	1	90	1	0	0	0	0	1	0	0	0	5930	971	34	3	6352	3	FLG	1	152281525	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	103039069	152281525	96969096	4	11967										
CD1D	912	hgsc.bcm.edu	37	chr1	158151319	158151319	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gcagctggacgcgcaccgacGgcttggcgtggctgggggag	20	11	0	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr1:158151319G>A	ENST00000368171.3	+	3	635	c.136G>A	c.(136-138)Ggc>Agc	p.G46S		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	46					antigen processing and presentation, endogenous lipid antigen via MHC class Ib (GO:0048006)|detection of bacterium (GO:0016045)|heterotypic cell-cell adhesion (GO:0034113)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of T cell proliferation (GO:0042102)|T cell selection (GO:0045058)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	beta-2-microglobulin binding (GO:0030881)|cell adhesion molecule binding (GO:0050839)|exogenous lipid antigen binding (GO:0030884)|histone binding (GO:0042393)|lipid antigen binding (GO:0030882)|receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(1)|prostate(3)|urinary_tract(2)	30	all_hematologic(112;0.0378)					GCGCACCGACGGCTTGGCGTG	0.637																																					p.G46S		Atlas-SNP	.											.	CD1D	60	.	0			c.G136A						.						114	127	123					1																	158151319		2203	4300	6503	SO:0001583	missense	912	exon3			ACCGACGGCTTGG	BC027926	CCDS1173.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158473	ENSG00000158473		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1637	protein-coding gene	gene with protein product		188410	"CD1D antigen, d polypeptide", "CD1d antigen"			2463622	Standard	NM_001766		Approved		uc001frr.3	P15813	OTTHUMG00000022436	ENST00000368171.3:c.136G>A	chr1.hg19:g.158151319G>A	ENSP00000357153:p.Gly46Ser	66.0	0.0		104.0	17.0	NM_001766	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Missense_Mutation	SNP	ENST00000368171.3	hg19	CCDS1173.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.257100	0.59321	.	.	ENSG00000158473	ENST00000368171	T	0.14640	2.49	4.44	-1.63	0.08345	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.991118	0.08194	N	0.983361	T	0.03783	0.0107	L	0.41710	1.295	0.09310	N	1	P	0.49559	0.925	B	0.42282	0.382	T	0.37502	-0.9703	10	0.31617	T	0.26	-0.5456	7.4421	0.27190	0.0938:0.0:0.2371:0.6691	.	46	P15813	CD1D_HUMAN	S	46	ENSP00000357153:G46S	ENSP00000357153:G46S	G	+	1	0	CD1D	156417943	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.232000	0.17891	-0.412000	0.07519	0.655000	0.94253	GGC	.	.		0.637	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766		A	158151319	G	A	158151319	3	1	90	1	0	0	0	0	1	0	0	0	2979	1116	39	1	142	1	CD1D	1	158151319	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	5869794	158151319	91099302	5	11968										
OR10X1	128367	hgsc.bcm.edu	37	chr1	158549059	158549059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cagtgttataatgaattctgTgtggttactgtctatacaag	9	5	2	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr1:158549059T>C	ENST00000368150.1	-	1	630	c.631A>G	c.(631-633)Aca>Gca	p.T211A		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					ATGAATTCTGTGTGGTTACTG	0.428																																					p.T211A		Atlas-SNP	.											.	OR10X1	96	.	0			c.A631G						.						96	96	96					1																	158549059		2203	4300	6503	SO:0001583	missense	128367	exon1			ATTCTGTGTGGTT	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"GPCR / Class A : Olfactory receptors"	14995	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily X, member 1"	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.631A>G	chr1.hg19:g.158549059T>C	ENSP00000357132:p.Thr211Ala	159.0	0.0		235.0	39.0	NM_001004477	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	hg19	CCDS30900.1	.	.	.	.	.	.	.	.	.	.	T	6.748	0.506903	0.12883	.	.	ENSG00000186400	ENST00000368150	T	0.00069	8.77	4.8	3.65	0.41850	GPCR, rhodopsin-like superfamily (1);	0.128800	0.35466	N	0.003199	T	0.00039	0.0001	N	0.16790	0.44	0.09310	N	1	P	0.43857	0.819	B	0.43838	0.433	T	0.00001	-1.2759	10	0.62326	D	0.03	.	4.874	0.13648	0.1654:0.0883:0.0:0.7463	.	211	Q8NGY0	O10X1_HUMAN	A	211	ENSP00000357132:T211A	ENSP00000357132:T211A	T	-	1	0	OR10X1	156815683	0.000000	0.05858	0.364000	0.25888	0.018000	0.09664	-0.008000	0.12788	0.809000	0.34255	0.460000	0.39030	ACA	.	.		0.428	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477		C	158549059	T	C	158549059	3	2	90	1	0	0	0	0	1	0	0	0	10931	1696	59	2	344	2	OR10X1	1	158549059	Missense_Mutation	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	397740	158549059	90701562	6	11969										
IGSF9	57549	hgsc.bcm.edu	37	chr1	159912756	159912756	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ctgaggagaactcttacccaCgtaatcagggtcaattcggg	11	10	3	2	rs113355407		TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr1:159912756C>A	ENST00000368094.1	-	3	441	c.244G>T	c.(244-246)Gtg>Ttg	p.V82L	IGSF9_ENST00000361509.3_Missense_Mutation_p.V82L	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	82	Ig-like 1.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.V82M(1)		central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			CTCTTACCCACGTAATCAGGG	0.572																																					p.V82L		Atlas-SNP	.											IGSF9,colon,carcinoma,+1,1	IGSF9	123	.	1	Substitution - Missense(1)	ovary(1)	c.G244T						.						51	53	52					1																	159912756		2203	4300	6503	SO:0001583	missense	57549	exon3			TACCCACGTAATC	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.244G>T	chr1.hg19:g.159912756C>A	ENSP00000357073:p.Val82Leu	93.0	0.0		98.0	20.0	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	hg19	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.673316	0.29693	.	.	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.27104	1.69;1.69	4.66	3.67	0.42095	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.34603	N	0.003831	T	0.05135	0.0137	N	0.12182	0.205	0.29140	N	0.879086	B;B	0.19331	0.003;0.035	B;B	0.20577	0.002;0.03	T	0.31586	-0.9938	9	.	.	.	.	10.8919	0.47000	0.0:0.6766:0.3233:0.0	.	82;82	Q9P2J2;C9JI81	TUTLA_HUMAN;.	L	82	ENSP00000355049:V82L;ENSP00000357073:V82L	.	V	-	1	0	IGSF9	158179380	0.011000	0.17503	1.000000	0.80357	0.975000	0.68041	1.071000	0.30666	2.290000	0.77057	0.557000	0.71058	GTG	.	C|0.500;T|0.500		0.572	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		A	159912756	C	A	159912756	3	1	90	1	0	0	0	0	1	0	0	0	7614	536	19	1	3371	1	IGSF9	1	159912756	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	1363697	159912756	89337865	7	11970										
MIA3	375056	hgsc.bcm.edu	37	chr1	222802656	222802656	+	Frame_Shift_Del	DEL	G	G	-													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tttcatcacaaggcaatgcaGggcacagaggtaggacagac							TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr1:222802656delG	ENST00000344922.5	+	4	2119	c.2094delG	c.(2092-2094)cagfs	p.Q698fs	MIA3_ENST00000470521.1_3'UTR|MIA3_ENST00000344507.1_Intron|MIA3_ENST00000344441.6_Frame_Shift_Del_p.Q698fs	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	698					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		AGGCAATGCAGGGCACAGAGG	0.468																																					p.Q698fs		Atlas-Indel,Pindel	.											.	MIA3	167	.	0			c.2093delA						.						91	93	92					1																	222802656		1992	4177	6169	SO:0001589	frameshift_variant	375056	exon4			.		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.2094delG	chr1.hg19:g.222802656delG	ENSP00000340900:p.Gln698fs	146.0	0.0		152.0	27.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Frame_Shift_Del	DEL	ENST00000344922.5	hg19	CCDS41470.1																																																																																			.	.		0.468	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		-	222802656	G	-	222802656	7	5	90	1	0	1	0	1	0	0	0	0	9574	991	35	0	2108	0	MIA3	1	222802656	Frame_Shift_Del	DEL	G	TCGA-DD-A118-01A-11D-A12Z-10	62889900	222802656	26447965	8	11971										
C1orf65	164127	hgsc.bcm.edu	37	chr1	223567608	223567609	+	Missense_Mutation	DNP	TG	TG	CT													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gcagattgtggccctggtgcTgacccgtctcaagaaggccc							TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr1:223567608_223567609TG>CT	ENST00000366875.3	+	1	894_895	c.791_792TG>CT	c.(790-792)cTG>cCT	p.L264P		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		264										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		GCCCTGGTGCTGACCCGTCTCA	0.624																																					p.L264P|p.L264L		Atlas-SNP	.											.	C1orf65	71	.	0			c.T791C|c.G792T						.																																			SO:0001583	missense	164127	exon1			TGGTGCTGACCCG|GGTGCTGACCCGT																												Exception_encountered	chr1.hg19:g.223567608_223567609delinsCT	ENSP00000355840:p.Leu264Pro	142.0|141.0	0.0		182.0|183.0	26.0|27.0	NM_152610	Q8N746|Q8NA93	Missense_Mutation|Silent	SNP	ENST00000366875.3	hg19	CCDS1537.1																																																																																			.	.		0.624	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			CT	223567609	TG	CT	223567608	3	2	90	1	0	0	0	0	1	0	0	0	2057	1580	55	2	793	2	C1orf65	1	223567608	Missense_Mutation	DNP	TG	TCGA-DD-A118-01A-11D-A12Z-10	764952	223567608	25683013	9	11972										
LBR	3930	hgsc.bcm.edu	37	chr1	225609820	225609820	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aacttccacttccctccttgCttccttaatgtcggcctggt	6	15	0	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr1:225609820C>A	ENST00000338179.2	-	3	450	c.325G>T	c.(325-327)Gca>Tca	p.A109S	LBR_ENST00000487054.1_5'Flank|LBR_ENST00000272163.4_Missense_Mutation_p.A109S	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	109					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		TCCCTCCTTGCTTCCTTAATG	0.493																																					p.A109S		Atlas-SNP	.											.	LBR	54	.	0			c.G325T						.						93	90	91					1																	225609820		2203	4300	6503	SO:0001583	missense	3930	exon3			TCCTTGCTTCCTT	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"Tudor domain containing"	6518	protein-coding gene	gene with protein product	"tudor domain containing 18"	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.325G>T	chr1.hg19:g.225609820C>A	ENSP00000339883:p.Ala109Ser	69.0	0.0		76.0	16.0	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	hg19	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	C	6.172	0.400008	0.11696	.	.	ENSG00000143815	ENST00000272163;ENST00000338179;ENST00000425080	D;D;T	0.96685	-4.09;-4.09;0.63	5.1	-0.241	0.13043	.	0.982188	0.08369	N	0.956357	D	0.89918	0.6854	L	0.29908	0.895	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.77667	-0.2502	10	0.08599	T	0.76	-12.4429	3.909	0.09194	0.1489:0.3148:0.0:0.5364	.	109;109	C9JXK0;Q14739	.;LBR_HUMAN	S	109	ENSP00000272163:A109S;ENSP00000339883:A109S;ENSP00000388059:A109S	ENSP00000272163:A109S	A	-	1	0	LBR	223676443	0.000000	0.05858	0.009000	0.14445	0.946000	0.59487	0.026000	0.13599	-0.116000	0.11893	0.655000	0.94253	GCA	.	.		0.493	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		A	225609820	C	A	225609820	3	1	90	1	0	0	0	0	1	0	0	0	8661	797	28	3	1570	3	LBR	1	225609820	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	2042212	225609820	23640801	10	11973										
KLF11	8462	hgsc.bcm.edu	37	chr2	10188154	10188154	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ctcagcactaacttggtgtcCtgtcagccctgcttgcacaa	8	14	2	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr2:10188154C>T	ENST00000305883.1	+	3	852	c.690C>T	c.(688-690)tcC>tcT	p.S230S	KLF11_ENST00000540845.1_Silent_p.S213S|KLF11_ENST00000535335.1_Silent_p.S213S	NM_003597.4	NP_003588.1	O14901	KLF11_HUMAN	Kruppel-like factor 11	230					apoptotic process (GO:0006915)|cellular response to peptide (GO:1901653)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)		ACTTGGTGTCCTGTCAGCCCT	0.527																																					p.S230S	Melanoma(56;431 1507 23687 50789)	Atlas-SNP	.											.	KLF11	45	.	0			c.C690T						.						101	95	97					2																	10188154		2203	4300	6503	SO:0001819	synonymous_variant	8462	exon3			GGTGTCCTGTCAG	AF028008	CCDS1668.1, CCDS54333.1	2p25	2013-01-08	2004-11-29	2004-12-01	ENSG00000172059	ENSG00000172059		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11811	protein-coding gene	gene with protein product		603301	"TGFB inducible early growth response 2"	TIEG2		9748269, 11087666	Standard	NM_001177716		Approved	Tieg3, MODY7	uc002raf.1	O14901	OTTHUMG00000119004	ENST00000305883.1:c.690C>T	chr2.hg19:g.10188154C>T		58.0	0.0		62.0	20.0	NM_003597	B4DZE7|Q9EPF4	Silent	SNP	ENST00000305883.1	hg19	CCDS1668.1																																																																																			.	.		0.527	KLF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000239202.3	NM_003597		T	10188154	C	T	10188154	2	4	90	1	0	0	0	0	0	0	0	1	8348	668	24	3		3	KLF11	2	10188154	Silent	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10		10188154	233011219	11	11974										
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40656071	40656071	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	taatcagacccagcatttgcTgtgccatcctctgttctgaa	7	12	3	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr2:40656071T>A	ENST00000403092.1	-	2	1383	c.1350A>T	c.(1348-1350)acA>acT	p.T450T	SLC8A1_ENST00000542024.1_Silent_p.T450T|SLC8A1_ENST00000405269.1_Silent_p.T450T|SLC8A1_ENST00000406785.2_Silent_p.T450T|SLC8A1_ENST00000408028.2_Silent_p.T450T|SLC8A1_ENST00000542756.1_Silent_p.T450T|SLC8A1_ENST00000405901.3_Silent_p.T450T|SLC8A1_ENST00000402441.1_Silent_p.T450T|SLC8A1_ENST00000332839.4_Silent_p.T450T|SLC8A1_ENST00000406391.2_Silent_p.T450T			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	450	Calx-beta 1.				blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	CAGCATTTGCTGTGCCATCCT	0.443																																					p.T450T		Atlas-SNP	.											.	SLC8A1	221	.	0			c.A1350T						.						85	76	79					2																	40656071		2203	4300	6503	SO:0001819	synonymous_variant	6546	exon1			ATTTGCTGTGCCA		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.1350A>T	chr2.hg19:g.40656071T>A		83.0	0.0		70.0	10.0	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Silent	SNP	ENST00000403092.1	hg19	CCDS1806.1																																																																																			.	.		0.443	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		A	40656071	T	A	40656071	2	1	90	1	0	0	0	0	0	0	0	1	14721	1567	55	4		4	SLC8A1	2	40656071	Silent	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	30467917	40656071	202543302	12	11975										
IMMT	10989	hgsc.bcm.edu	37	chr2	86408465	86408465	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tctgcggcatggtcgcaatgGacggaggacaaacttcccac	12	12	1	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr2:86408465G>C	ENST00000410111.3	-	2	463	c.76C>G	c.(76-78)Cca>Gca	p.P26A	IMMT_ENST00000409051.2_Missense_Mutation_p.P26A|IMMT_ENST00000449247.2_Missense_Mutation_p.P26A|IMMT_ENST00000442664.2_Missense_Mutation_p.P26A|IMMT_ENST00000254636.5_5'UTR	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	26					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GGTCGCAATGGACGGAGGACA	0.448																																					p.P26A		Atlas-SNP	.											.	IMMT	65	.	0			c.C76G						.						73	71	72					2																	86408465		1926	4130	6056	SO:0001583	missense	10989	exon2			GCAATGGACGGAG	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.76C>G	chr2.hg19:g.86408465G>C	ENSP00000387262:p.Pro26Ala	90.0	0.0		84.0	18.0	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	hg19	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.988149	0.74589	.	.	ENSG00000132305	ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715	T;T;T;T	0.35236	1.34;1.35;1.35;1.32	5.55	4.68	0.58851	.	0.283448	0.38778	N	0.001572	T	0.46852	0.1414	L	0.34521	1.04	0.49582	D	0.999804	P;D;P;D;D;D;P;D;P	0.89917	0.944;0.999;0.908;1.0;1.0;0.97;0.944;0.97;0.908	P;D;P;D;D;P;P;P;P	0.91635	0.837;0.998;0.692;0.997;0.999;0.837;0.837;0.837;0.692	T	0.29088	-1.0023	10	0.23891	T	0.37	-14.0586	13.9895	0.64357	0.0735:0.0:0.9265:0.0	.	26;26;26;26;26;26;26;26;26	F5GZ32;B9A067;B4DKR1;Q05DN3;B4E2B5;F8W9I1;Q16891-2;Q16891-3;Q16891	.;.;.;.;.;.;.;.;IMMT_HUMAN	A	26	ENSP00000396899:P26A;ENSP00000387262:P26A;ENSP00000407788:P26A;ENSP00000387227:P26A	ENSP00000366526:P26A	P	-	1	0	IMMT	86261976	1.000000	0.71417	0.974000	0.42286	0.799000	0.45148	5.915000	0.69973	1.359000	0.45940	0.655000	0.94253	CCA	.	.		0.448	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		C	86408465	G	C	86408465	3	2	90	1	0	0	0	0	1	0	0	0	7727	1174	41	4	2256	4	IMMT	2	86408465	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	45752394	86408465	156790908	13	11976										
TBC1D8	11138	hgsc.bcm.edu	37	chr2	101666978	101666979	+	Missense_Mutation	DNP	CC	CC	GA													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	catgaccttaaacacctcatCcaggttcaggaacatggaga							TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr2:101666978_101666979CC>GA	ENST00000376840.4	-	5	710_711	c.711_712GG>TC	c.(709-714)ctGGat>ctTCat	p.D238H	TBC1D8_ENST00000409318.1_Missense_Mutation_p.D253H			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	238					blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						AACACCTCATCCAGGTTCAGGA	0.515																																					p.D238H|p.L237L		Atlas-SNP	.											.	TBC1D8	169	.	0			c.G712C|c.G711T						.																																			SO:0001583	missense	11138	exon5			CCTCATCCAGGTT|CTCATCCAGGTTC	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"BUB2-like protein 1", "vascular Rab-GAP/TBC-containing protein"					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.711_712delinsGA	chr2.hg19:g.101666978_101666979delinsGA	ENSP00000366036:p.Asp238His	160.0|163.0	0.0		146.0|147.0	55.0|56.0	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Missense_Mutation|Silent	SNP	ENST00000376840.4	hg19	CCDS46375.1																																																																																			.	.		0.515	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063		GA	101666979	CC	GA	101666978	3	3	90	1	0	0	0	0	1	0	0	0	15640	855	30	4	2774	4	TBC1D8	2	101666978	Missense_Mutation	DNP	CC	TCGA-DD-A118-01A-11D-A12Z-10	15258513	101666978	141532395	14	11977										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141598619	141598619	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	agctaatccagtataaattaCgtgacacccaatccactgct	5	12	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr2:141598619C>T	ENST00000389484.3	-	30	5953	c.4982G>A	c.(4981-4983)cGt>cAt	p.R1661H		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1661					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GTATAAATTACGTGACACCCA	0.373										TSP Lung(27;0.18)																											p.R1661H	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G4982A						.						135	125	129					2																	141598619		2203	4300	6503	SO:0001583	missense	53353	exon30			AAATTACGTGACA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4982G>A	chr2.hg19:g.141598619C>T	ENSP00000374135:p.Arg1661His	193.0	0.0		170.0	45.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.463445	0.84425	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91740	-2.9	5.44	5.44	0.79542	Six-bladed beta-propeller, TolB-like (1);	0.066897	0.56097	U	0.000027	D	0.93969	0.8069	M	0.64260	1.97	0.48341	D	0.999635	D	0.67145	0.996	P	0.53689	0.732	D	0.94199	0.7448	10	0.62326	D	0.03	.	19.2577	0.93952	0.0:1.0:0.0:0.0	.	1661	Q9NZR2	LRP1B_HUMAN	H	1661;1599	ENSP00000374135:R1661H	ENSP00000374135:R1661H	R	-	2	0	LRP1B	141315089	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.978000	0.56881	2.563000	0.86464	0.460000	0.39030	CGT	.	.		0.373	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141598619	C	T	141598619	3	4	90	1	0	0	0	0	1	0	0	0	8964	536	19	1	9065	1	LRP1B	2	141598619	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	39931641	141598619	101600754	15	11978										
TTN	7273	hgsc.bcm.edu	37	chr2	179440745	179440745	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccatgtcacttcaggagcagGacgacctttaattggcacaa	9	11	2	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr2:179440745G>C	ENST00000591111.1	-	276	65415	c.65191C>G	c.(65191-65193)Cct>Gct	p.P21731A	TTN-AS1_ENST00000590807.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P14432A|TTN_ENST00000460472.2_Missense_Mutation_p.P14307A|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591332.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P20804A|TTN_ENST00000589042.1_Missense_Mutation_p.P23372A|TTN_ENST00000342175.6_Missense_Mutation_p.P14499A			Q8WZ42	TITIN_HUMAN	titin	21731	Ig-like 114.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAGGAGCAGGACGACCTTTA	0.418																																					p.P23372A		Atlas-SNP	.											.	TTN	18412	.	0			c.C70114G						.						143	145	144					2																	179440745		1920	4118	6038	SO:0001583	missense	7273	exon326			GAGCAGGACGACC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.65191C>G	chr2.hg19:g.179440745G>C	ENSP00000465570:p.Pro21731Ala	68.0	0.0		56.0	13.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.62	2.292531	0.40594	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81	5.61	5.61	0.85477	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.90356	0.6982	M	0.93638	3.44	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	D	0.92310	0.5857	9	0.87932	D	0	.	19.635	0.95728	0.0:0.0:1.0:0.0	.	14307;14432;14499;21731	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	20804;14307;14499;14432;14305	ENSP00000343764:P20804A;ENSP00000434586:P14307A;ENSP00000340554:P14499A;ENSP00000352154:P14432A	ENSP00000340554:P14499A	P	-	1	0	TTN	179148991	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.869000	0.99810	2.656000	0.90262	0.655000	0.94253	CCT	.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179440745	G	C	179440745	3	2	90	1	0	0	0	0	1	0	0	0	16750	1174	41	4	38013	4	TTN	2	179440745	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	37842126	179440745	63758628	16	11979										
BSN	8927	hgsc.bcm.edu	37	chr3	49688366	49688366	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aaaagaagacccgagtccccActaaagctgagcccatgccg	9	14	0	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr3:49688366A>G	ENST00000296452.4	+	4	1954	c.1840A>G	c.(1840-1842)Act>Gct	p.T614A		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	614					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CCGAGTCCCCACTAAAGCTGA	0.622																																					p.T614A		Atlas-SNP	.											.	BSN	272	.	0			c.A1840G						.						108	125	119					3																	49688366		2203	4300	6503	SO:0001583	missense	8927	exon4			GTCCCCACTAAAG	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.1840A>G	chr3.hg19:g.49688366A>G	ENSP00000296452:p.Thr614Ala	95.0	0.0		53.0	15.0	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	hg19	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	A	5.094	0.202992	0.09704	.	.	ENSG00000164061	ENST00000296452	T	0.16457	2.34	5.34	1.77	0.24775	.	0.781774	0.12420	N	0.470499	T	0.03348	0.0097	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42224	-0.9464	10	0.02654	T	1	.	6.606	0.22726	0.1366:0.0:0.732:0.1315	.	614	Q9UPA5	BSN_HUMAN	A	614	ENSP00000296452:T614A	ENSP00000296452:T614A	T	+	1	0	BSN	49663370	0.003000	0.15002	0.004000	0.12327	0.522000	0.34438	0.538000	0.23160	0.055000	0.16094	-0.290000	0.09829	ACT	.	.		0.622	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		G	49688366	A	G	49688366	3	3	90	1	0	0	0	0	1	0	0	0	1532	159	6	2	1854	2	BSN	3	49688366	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10		49688366	148334064	17	11980										
BAP1	8314	hgsc.bcm.edu	37	chr3	52440295	52440295	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cagagcctctagtactgtctGacggttcaccttcagcacat	8	13	4	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr3:52440295G>A	ENST00000460680.1	-	9	1228	c.757C>T	c.(757-759)Cag>Tag	p.Q253*	BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q235*	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q253*(2)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		AGTACTGTCTGACGGTTCACC	0.602			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.Q253X	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	BAP1,colon,carcinoma,0,3	BAP1	371	.	2	Substitution - Nonsense(2)	eye(1)|kidney(1)	c.C757T						.						128	96	107					3																	52440295		2203	4300	6503	SO:0001587	stop_gained	8314	exon9			CTGTCTGACGGTT	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.757C>T	chr3.hg19:g.52440295G>A	ENSP00000417132:p.Gln253*	156.0	1.0		110.0	65.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Nonsense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	40	8.384367	0.98786	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-9.1034	20.3731	0.98895	0.0:0.0:1.0:0.0	.	.	.	.	X	253;235	.	ENSP00000296288:Q235X	Q	-	1	0	BAP1	52415335	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.819000	0.86621	2.829000	0.97493	0.650000	0.86243	CAG	.	.		0.602	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52440295	G	A	52440295	4	1	90	1	0	0	0	0	0	1	0	0	1311	1299	45	3	1468	3	BAP1	3	52440295	Nonsense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	2751929	52440295	145582135	18	11981										
ITIH3	3699	hgsc.bcm.edu	37	chr3	52835121	52835121	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tggagaaccatgggtttgccCggcgcatttatgaggactct	13	9	1	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr3:52835121C>T	ENST00000449956.2	+	11	1348	c.1342C>T	c.(1342-1344)Cgg>Tgg	p.R448W	ITIH3_ENST00000416872.2_Missense_Mutation_p.R448W	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	448	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		TGGGTTTGCCCGGCGCATTTA	0.517																																					p.R448W		Atlas-SNP	.											.	ITIH3	132	.	0			c.C1342T						.						68	71	70					3																	52835121		1947	4128	6075	SO:0001583	missense	3699	exon11			TTTGCCCGGCGCA		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.1342C>T	chr3.hg19:g.52835121C>T	ENSP00000415769:p.Arg448Trp	79.0	0.0		60.0	26.0	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	hg19	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.388894	0.82902	.	.	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	D;D	0.83591	-1.74;-1.74	5.33	4.46	0.54185	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.92254	0.7543	M	0.91140	3.18	0.50039	D	0.999849	P;D	0.89917	0.589;1.0	B;D	0.91635	0.156;0.999	D	0.93459	0.6809	10	0.66056	D	0.02	-14.4835	13.0138	0.58745	0.0:0.9216:0.0:0.0784	.	448;448	E7ET33;Q06033	.;ITIH3_HUMAN	W	448;436;443;448;448	ENSP00000413922:R448W;ENSP00000415769:R448W	ENSP00000273291:R443W	R	+	1	2	ITIH3	52810161	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	4.160000	0.58164	1.493000	0.48517	-0.136000	0.14681	CGG	.	.		0.517	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		T	52835121	C	T	52835121	3	4	90	1	0	0	0	0	1	0	0	0	7914	643	23	1	1384	1	ITIH3	3	52835121	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	394826	52835121	145187309	19	11982										
CD47	961	hgsc.bcm.edu	37	chr3	107799113	107799113	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gtgcctccatattagtaacaAagcatggaatgacgacagtg	10	8	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr3:107799113A>C	ENST00000361309.5	-	2	230	c.125T>G	c.(124-126)tTt>tGt	p.F42C	CD47_ENST00000355354.7_Missense_Mutation_p.F42C	NM_001777.3	NP_001768.1	Q08722	CD47_HUMAN	CD47 molecule	42	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|opsonization (GO:0008228)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of inflammatory response (GO:0050729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T cell activation (GO:0050870)|response to bacterium (GO:0009617)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(3;0.0191)|Epithelial(53;0.118)			ATTAGTAACAAAGCATGGAAT	0.343																																					p.F42C		Atlas-SNP	.											.	CD47	37	.	0			c.T125G						.						132	115	120					3																	107799113		1848	4085	5933	SO:0001583	missense	961	exon2			GTAACAAAGCATG		CCDS43125.1, CCDS43126.1	3q13.1-q13.2	2013-01-11	2006-03-28		ENSG00000196776	ENSG00000196776		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1682	protein-coding gene	gene with protein product	"antigen identified by monoclonal antibody 1D8", "antigenic surface determinant protein OA3", "integrin associated protein", "Rh-related antigen", "leukocyte surface antigen CD47", "CD47 glycoprotein"	601028	"CD47 antigen (Rh-related antigen, integrin-associated signal transducer)"	MER6		8294396, 2277087	Standard	XM_005247908		Approved	IAP, OA3	uc003dwt.1	Q08722	OTTHUMG00000044216	ENST00000361309.5:c.125T>G	chr3.hg19:g.107799113A>C	ENSP00000355361:p.Phe42Cys	181.0	0.0		152.0	40.0	NM_198793	A8K198|D3DN59|Q53Y71|Q96A60	Missense_Mutation	SNP	ENST00000361309.5	hg19	CCDS43126.1	.	.	.	.	.	.	.	.	.	.	A	8.461	0.855309	0.17106	.	.	ENSG00000196776	ENST00000355354;ENST00000361309	T;T	0.02656	4.21;4.21	6.04	0.876	0.19138	Immunoglobulin-like (1);CD47 immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.480890	0.03663	N	0.242905	T	0.03348	0.0097	L	0.44542	1.39	0.09310	N	1	B;B;B;B	0.21225	0.043;0.043;0.053;0.053	B;B;B;B	0.13407	0.005;0.005;0.009;0.009	T	0.45411	-0.9263	10	0.46703	T	0.11	.	1.852	0.03171	0.3905:0.2733:0.0731:0.2631	.	42;42;42;42	Q08722-2;Q08722-3;E9PB22;Q08722	.;.;.;CD47_HUMAN	C	42	ENSP00000347512:F42C;ENSP00000355361:F42C	ENSP00000347512:F42C	F	-	2	0	CD47	109281803	0.000000	0.05858	0.002000	0.10522	0.021000	0.10359	0.641000	0.24720	0.129000	0.18514	-0.488000	0.04728	TTT	.	.		0.343	CD47-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000102793.1	NM_001777		C	107799113	A	C	107799113	3	2	90	1	0	0	0	0	1	0	0	0	3021	14	1	5	890	5	CD47	3	107799113	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	54963992	107799113	90223317	20	11983										
CHCHD6	84303	hgsc.bcm.edu	37	chr3	126445955	126445955	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ggtgaaccgcatgaaggagcCcagctctccaccccctgctc	10	17	1	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr3:126445955C>T	ENST00000290913.3	+	2	215	c.122C>T	c.(121-123)cCc>cTc	p.P41L	CHCHD6_ENST00000508789.1_Missense_Mutation_p.P41L	NM_032343.2	NP_115719.1	Q9BRQ6	MIC25_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 6	41					cellular response to DNA damage stimulus (GO:0006974)|cristae formation (GO:0042407)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(3)|lung(3)	8						ATGAAGGAGCCCAGCTCTCCA	0.507																																					p.P41L		Atlas-SNP	.											.	CHCHD6	18	.	0			c.C122T						.						132	128	130					3																	126445955		2203	4300	6503	SO:0001583	missense	84303	exon2			AGGAGCCCAGCTC	BC006123	CCDS3041.1	3q21.3	2012-04-17			ENSG00000159685	ENSG00000159685		"Coiled-coil-helix-coiled-coil-helix domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	28184	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 23", "coiled-coil-helix cristae morphology 1"	615634				17624330, 22228767	Standard	NM_032343		Approved	MGC13016, PPP1R23, CHCM1	uc003ejf.2	Q9BRQ6	OTTHUMG00000159601	ENST00000290913.3:c.122C>T	chr3.hg19:g.126445955C>T	ENSP00000290913:p.Pro41Leu	222.0	0.0		205.0	51.0	NM_032343	D6R9U0|D6RIB4|H8Y0Y7	Missense_Mutation	SNP	ENST00000290913.3	hg19	CCDS3041.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.869381	0.32977	.	.	ENSG00000159685	ENST00000290913;ENST00000508789	T;T	0.50001	0.76;0.76	4.25	3.35	0.38373	.	0.425221	0.25639	N	0.029295	T	0.42765	0.1217	M	0.64404	1.975	0.09310	N	1	P;B	0.38677	0.642;0.376	B;B	0.38106	0.265;0.173	T	0.25152	-1.0140	10	0.30854	T	0.27	-1.019	9.5581	0.39351	0.0:0.7739:0.2261:0.0	.	41;41	D6R9U0;Q9BRQ6	.;CHCH6_HUMAN	L	41	ENSP00000290913:P41L;ENSP00000422912:P41L	ENSP00000290913:P41L	P	+	2	0	CHCHD6	127928645	0.007000	0.16637	0.014000	0.15608	0.047000	0.14425	1.825000	0.39081	0.950000	0.37743	0.591000	0.81541	CCC	.	.		0.507	CHCHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356432.1	NM_032343		T	126445955	C	T	126445955	3	4	90	1	0	0	0	0	1	0	0	0	3322	623	22	3	128	3	CHCHD6	3	126445955	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	18646842	126445955	71576475	21	11984										
ZCCHC4	29063	hgsc.bcm.edu	37	chr4	25351159	25351159	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ttttacaggaagataaaggcGaaggaatcattatggtgacg	12	4	1	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr4:25351159G>T	ENST00000302874.4	+	7	829	c.805G>T	c.(805-807)Gaa>Taa	p.E269*	ZCCHC4_ENST00000505451.1_3'UTR	NM_024936.2	NP_079212.2	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	269							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)	9		Breast(46;0.0503)				AGATAAAGGCGAAGGAATCAT	0.403																																					p.E269X		Atlas-SNP	.											.	ZCCHC4	34	.	0			c.G805T						.						209	198	201					4																	25351159		1881	4106	5987	SO:0001587	stop_gained	29063	exon7			AAAGGCGAAGGAA	AF161537	CCDS43218.1	4p15.31	2014-02-18			ENSG00000168228	ENSG00000168228		"Zinc fingers, CCHC domain containing"	22917	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 4"	611792				11042152	Standard	NM_024936		Approved	HSPC052, FLJ23024, ZGRF4	uc003grl.4	Q9H5U6	OTTHUMG00000160563	ENST00000302874.4:c.805G>T	chr4.hg19:g.25351159G>T	ENSP00000303468:p.Glu269*	228.0	0.0		321.0	41.0	NM_024936	B2RXF6|B4DRD8|B7ZW20|Q5IW78|Q96AN7	Nonsense_Mutation	SNP	ENST00000302874.4	hg19	CCDS43218.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.7|21.7	4.183110|4.183110	0.78677|0.78677	.|.	.|.	ENSG00000168228|ENSG00000168228	ENST00000302874|ENST00000505412	.|.	.|.	.|.	5.4|5.4	2.38|2.38	0.29361|0.29361	.|.	0.873879|.	0.10271|.	N|.	0.694758|.	.|T	.|0.31918	.|0.0812	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.34254	.|-0.9836	.|3	0.08179|.	T|.	0.78|.	-18.5719|-18.5719	3.8923|3.8923	0.09123|0.09123	0.2244:0.0:0.5893:0.1863|0.2244:0.0:0.5893:0.1863	.|.	.|.	.|.	.|.	X|L	269|133	.|.	ENSP00000303468:E269X|.	E|R	+|+	1|2	0|0	ZCCHC4|ZCCHC4	24960257|24960257	1.000000|1.000000	0.71417|0.71417	0.980000|0.980000	0.43619|0.43619	0.996000|0.996000	0.88848|0.88848	1.230000|1.230000	0.32612|0.32612	0.558000|0.558000	0.29135|0.29135	0.655000|0.655000	0.94253|0.94253	GAA|CGA	.	.		0.403	ZCCHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361151.1			T	25351159	G	T	25351159	4	4	90	1	0	0	0	0	0	1	0	0	17605	1059	37	1	831	1	ZCCHC4	4	25351159	Nonsense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10		25351159	165803117	22	11985										
NMU	10874	hgsc.bcm.edu	37	chr4	56475318	56475318	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gtagcattcccataatcataAagcaaagctcctccagtgcg	7	12	1	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr4:56475318A>C	ENST00000264218.3	-	4	353	c.248T>G	c.(247-249)tTt>tGt	p.F83C	NMU_ENST00000507338.1_Missense_Mutation_p.F83C|NMU_ENST00000505262.1_Missense_Mutation_p.F83C|NMU_ENST00000511469.1_Missense_Mutation_p.F67C|NMU_ENST00000515325.1_5'UTR	NM_006681.2	NP_006672.1	P48645	NMU_HUMAN	neuromedin U	83					digestion (GO:0007586)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of hormone secretion (GO:0046887)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic transmission (GO:0050806)|regulation of smooth muscle contraction (GO:0006940)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|terminal bouton (GO:0043195)	receptor binding (GO:0005102)			lung(3)|ovary(1)|urinary_tract(1)	5	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)		CATAATCATAAAGCAAAGCTC	0.358																																					p.F83C		Atlas-SNP	.											.	NMU	17	.	0			c.T248G						.						116	115	115					4																	56475318		2203	4300	6503	SO:0001583	missense	10874	exon4			ATCATAAAGCAAA	X76029	CCDS3501.1, CCDS75125.1	4q12	2013-02-26			ENSG00000109255	ENSG00000109255		"Endogenous ligands"	7859	protein-coding gene	gene with protein product	"prepro-NMU"	605103				7619205	Standard	XM_005265713		Approved		uc003hbc.3	P48645	OTTHUMG00000102161	ENST00000264218.3:c.248T>G	chr4.hg19:g.56475318A>C	ENSP00000264218:p.Phe83Cys	131.0	0.0		194.0	33.0	NM_006681		Missense_Mutation	SNP	ENST00000264218.3	hg19	CCDS3501.1	.	.	.	.	.	.	.	.	.	.	A	12.54	1.968839	0.34754	.	.	ENSG00000109255	ENST00000511469;ENST00000264218;ENST00000505262;ENST00000541393;ENST00000507338	T;T;T;T	0.55588	0.51;0.51;1.35;0.51	5.51	-0.0158	0.13974	.	0.597682	0.17095	N	0.187215	T	0.43875	0.1267	L	0.52573	1.65	0.09310	N	1	D	0.59357	0.985	P	0.46796	0.527	T	0.35674	-0.9779	10	0.56958	D	0.05	-12.8858	3.17	0.06549	0.6336:0.1195:0.1228:0.124	.	83	P48645	NMU_HUMAN	C	67;83;83;83;83	ENSP00000422399:F67C;ENSP00000264218:F83C;ENSP00000424246:F83C;ENSP00000422870:F83C	ENSP00000264218:F83C	F	-	2	0	NMU	56170075	0.055000	0.20627	0.004000	0.12327	0.420000	0.31355	1.456000	0.35201	0.161000	0.19458	0.533000	0.62120	TTT	.	.		0.358	NMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220006.2			C	56475318	A	C	56475318	3	2	90	1	0	0	0	0	1	0	0	0	10514	14	1	5	300	5	NMU	4	56475318	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	31124159	56475318	134678958	23	11986										
ENAM	10117	hgsc.bcm.edu	37	chr4	71508293	71508293	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cagtttatcacaaagcttacCctcctacttcaagaggcaat	5	12	2	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr4:71508293C>G	ENST00000396073.3	+	9	1431	c.1150C>G	c.(1150-1152)Cct>Gct	p.P384A	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	384					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CAAAGCTTACCCTCCTACTTC	0.443																																					p.P384A		Atlas-SNP	.											.	ENAM	140	.	0			c.C1150G						.						118	124	122					4																	71508293		2203	4300	6503	SO:0001583	missense	10117	exon9			GCTTACCCTCCTA	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1150C>G	chr4.hg19:g.71508293C>G	ENSP00000379383:p.Pro384Ala	239.0	0.0		305.0	53.0	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	hg19	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	C	0.643	-0.812528	0.02798	.	.	ENSG00000132464	ENST00000396073	T	0.29655	1.56	5.93	1.24	0.21308	.	0.829650	0.10838	N	0.628532	T	0.09555	0.0235	N	0.02181	-0.65	0.09310	N	1	B	0.06786	0.001	B	0.13407	0.009	T	0.30179	-0.9987	10	0.25106	T	0.35	0.4012	1.1226	0.01728	0.2366:0.3887:0.1927:0.182	.	384	Q9NRM1	ENAM_HUMAN	A	384	ENSP00000379383:P384A	ENSP00000379383:P384A	P	+	1	0	ENAM	71727157	0.000000	0.05858	0.003000	0.11579	0.070000	0.16714	-0.132000	0.10467	-0.081000	0.12662	0.655000	0.94253	CCT	.	.		0.443	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		G	71508293	C	G	71508293	3	3	90	1	0	0	0	0	1	0	0	0	5114	623	22	4	1180	4	ENAM	4	71508293	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	15032975	71508293	119645983	24	11987										
ALB	213	hgsc.bcm.edu	37	chr4	74285229	74285286	+	Frame_Shift_Del	DEL	TTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTAT	TTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTAT	-													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tccattcaaactcagtgcacTtgttgagctcgtgaaacaca					rs57636959|rs962004|rs78284052|rs267600249|rs77645174|rs61579038|rs11538208|rs11538206|rs72552712|rs371123711|rs80345158	byFrequency	TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	TTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTAT	TTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr4:74285229_74285286delTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTAT	ENST00000503124.1	+	11	1415_1472	c.1208_1265delTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTAT	c.(1207-1266)cttgttgagctcgtgaaacacaagcccaaggcaacaaaagagcaactgaaagctgttatgfs	p.LVELVKHKPKATKEQLKAVM403fs	ALB_ENST00000401494.3_Frame_Shift_Del_p.LVELVKHKPKATKEQLKAVM438fs|ALB_ENST00000415165.2_Frame_Shift_Del_p.LVELVKHKPKATKEQLKAVM361fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000295897.4_Frame_Shift_Del_p.LVELVKHKPKATKEQLKAVM553fs|ALB_ENST00000509063.1_Frame_Shift_Del_p.LVELVKHKPKATKEQLKAVM553fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.L568L(1)|p.E566Q(1)|p.D573fs*6(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTCAGTGCACTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTATGGATGATTTC	0.395																																					p.553_572del		Pindel	.											.	ALB	132	.	3	Substitution - Missense(1)|Deletion - Frameshift(1)|Substitution - coding silent(1)	urinary_tract(1)|liver(1)|endometrium(1)	c.1657_1714del	GRCh37	CM870081|CM900416|CM973673	ALB	M	rs77645174|rs78284052|rs80345158	.																																			SO:0001589	frameshift_variant	213	exon13			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1208_1265delTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTAT	chr4.hg19:g.74285229_74285286delTTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTAT	ENSP00000421027:p.Leu403fs	75.0	0.0		62.0	12.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.395	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74285286	TTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTAT	-	74285229	7	5	90	1	0	1	0	1	0	0	0	0	486	1609	56	0	1708	0	ALB	4	74285229	Frame_Shift_Del	DEL	TTGTTGAGCTCGTGAAACACAAGCCCAAGGCAACAAAAGAGCAACTGAAAGCTGTTAT	TCGA-DD-A118-01A-11D-A12Z-10	2776936	74285229	116869047	25	11988										
EPGN	255324	hgsc.bcm.edu	37	chr4	75174267	75174267	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ggaaatggctttgggagttcCaatatcagtctatcttttat	9	6	3	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr4:75174267C>T	ENST00000413830.1	+	1	78	c.17C>T	c.(16-18)cCa>cTa	p.P6L	EPGN_ENST00000502358.1_Missense_Mutation_p.P6L|EPGN_ENST00000503098.1_Missense_Mutation_p.P6L|EPGN_ENST00000332112.4_Missense_Mutation_p.P6L|EPGN_ENST00000505212.1_Missense_Mutation_p.P6L|EPGN_ENST00000514968.1_Missense_Mutation_p.P6L|EPGN_ENST00000509145.1_Missense_Mutation_p.P6L	NM_001270989.1	NP_001257918.1	Q6UW88	EPGN_HUMAN	epithelial mitogen	6					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|MAP kinase kinase activity (GO:0004708)	p.P6>?(1)		breast(3)|liver(1)|lung(1)|skin(1)	6			Lung(101;0.196)			TTGGGAGTTCCAATATCAGTC	0.333																																					p.P6L		Atlas-SNP	.											.	EPGN	14	.	1	Complex(1)	skin(1)	c.C17T						.						171	175	173					4																	75174267		2203	4300	6503	SO:0001583	missense	255324	exon1			GAGTTCCAATATC		CCDS59475.1, CCDS59476.1, CCDS59477.1, CCDS59478.1, CCDS59479.1	4q13.3	2012-12-07	2012-12-07						17470	protein-coding gene	gene with protein product			"epithelial mitogen homolog (mouse)"				Standard	NM_001270989		Approved	epigen, EPG, PRO9904, ALGV3072	uc003hic.2	Q6UW88		ENST00000413830.1:c.17C>T	chr4.hg19:g.75174267C>T	ENSP00000411898:p.Pro6Leu	391.0	0.0		343.0	43.0	NM_001270993	A1BMM3|A1BMM4|A1BMM5|A1BMM6|A1BMM7|A1BMM8|A8K090	Missense_Mutation	SNP	ENST00000413830.1	hg19	CCDS59478.1	.	.	.	.	.	.	.	.	.	.	C	9.887	1.203093	0.22121	.	.	ENSG00000182585	ENST00000413830;ENST00000332112;ENST00000514968;ENST00000503098;ENST00000502358;ENST00000509145;ENST00000505212	T;T	0.22539	1.98;1.95	5.37	4.52	0.55395	.	0.481200	0.18618	N	0.135964	T	0.19685	0.0473	L	0.48362	1.52	0.09310	N	1	B;B;B;B;B;B;B	0.19073	0.019;0.002;0.021;0.01;0.033;0.008;0.006	B;B;B;B;B;B;B	0.19946	0.012;0.009;0.021;0.009;0.027;0.01;0.015	T	0.13045	-1.0524	10	0.33940	T	0.23	-1.3249	10.7778	0.46361	0.0:0.9103:0.0:0.0897	.	6;6;6;6;6;6;6	Q6UW88-7;Q6UW88;Q6UW88-3;Q6UW88-5;Q6UW88-4;Q6UW88-6;Q6UW88-2	.;EPGN_HUMAN;.;.;.;.;.	L	6	ENSP00000411898:P6L;ENSP00000330375:P6L	ENSP00000330375:P6L	P	+	2	0	EPGN	75393131	0.003000	0.15002	0.015000	0.15790	0.986000	0.74619	1.635000	0.37134	1.380000	0.46344	0.462000	0.41574	CCA	.	.		0.333	EPGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362738.1	NM_001013442		T	75174267	C	T	75174267	3	4	90	1	0	0	0	0	1	0	0	0	5166	594	21	3	19	3	EPGN	4	75174267	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	889038	75174267	115980009	26	11989										
NPY5R	4889	hgsc.bcm.edu	37	chr4	164271533	164271533	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tgggatgactataaaagcagTgtagatgacttacagtattt	10	4	0	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr4:164271533T>G	ENST00000515560.1	+	4	1630	c.108T>G	c.(106-108)agT>agG	p.S36R	NPY5R_ENST00000338566.3_Missense_Mutation_p.S36R|NPY5R_ENST00000506953.1_Missense_Mutation_p.S36R			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	36					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				ATAAAAGCAGTGTAGATGACT	0.388																																					p.S36R	Melanoma(139;1287 1774 9781 19750 25599)	Atlas-SNP	.											.	NPY5R	101	.	0			c.T108G						.						99	95	96					4																	164271533		2203	4300	6503	SO:0001583	missense	4889	exon4			AAGCAGTGTAGAT	BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"GPCR / Class A : Neuropeptide receptors : Y"	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.108T>G	chr4.hg19:g.164271533T>G	ENSP00000423917:p.Ser36Arg	335.0	0.0		374.0	89.0	NM_006174	Q6GTR7|Q92916	Missense_Mutation	SNP	ENST00000515560.1	hg19	CCDS3804.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.563312	0.27915	.	.	ENSG00000164129	ENST00000338566;ENST00000515560;ENST00000506953	T;T;T	0.37235	1.21;1.21;1.21	5.35	0.222	0.15288	.	0.356841	0.23442	N	0.048125	T	0.25344	0.0616	L	0.32530	0.975	0.46061	D	0.998848	B	0.13594	0.008	B	0.15870	0.014	T	0.06338	-1.0832	10	0.52906	T	0.07	.	10.306	0.43680	0.0:0.446:0.0:0.554	.	36	Q15761	NPY5R_HUMAN	R	36	ENSP00000339377:S36R;ENSP00000423917:S36R;ENSP00000423474:S36R	ENSP00000339377:S36R	S	+	3	2	NPY5R	164490983	0.982000	0.34865	0.995000	0.50966	0.967000	0.64934	-0.013000	0.12678	-0.100000	0.12241	-0.274000	0.10170	AGT	.	.		0.388	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174		G	164271533	T	G	164271533	3	3	90	1	0	0	0	0	1	0	0	0	10619	1693	59	5	110	5	NPY5R	4	164271533	Missense_Mutation	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	89097266	164271533	26882743	27	11990										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55272094	55272094	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ggcttgcactagccaagtctGcaacgtcaacatcttgcgcg	10	13	3	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr5:55272094G>A	ENST00000381298.2	-	3	325	c.13C>T	c.(13-15)Cag>Tag	p.Q5*	IL6ST_ENST00000381286.3_Nonsense_Mutation_p.Q5*|IL6ST_ENST00000577363.1_5'UTR|IL6ST_ENST00000381294.3_Nonsense_Mutation_p.Q5*|IL6ST_ENST00000536319.1_Nonsense_Mutation_p.Q5*|IL6ST_ENST00000336909.5_Nonsense_Mutation_p.Q5*|IL6ST_ENST00000522633.2_Nonsense_Mutation_p.Q5*|IL6ST_ENST00000381287.4_Nonsense_Mutation_p.Q5*|IL6ST_ENST00000502326.3_Nonsense_Mutation_p.Q5*|IL6ST_ENST00000381293.2_Nonsense_Mutation_p.Q5*|IL6ST_ENST00000396816.1_Nonsense_Mutation_p.Q5*	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	5					ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				AGCCAAGTCTGCAACGTCAAC	0.338			O		hepatocellular ca																																p.Q5X		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.C13T						.						78	70	72					5																	55272094		2203	4300	6503	SO:0001587	stop_gained	3572	exon3			AAGTCTGCAACGT	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.13C>T	chr5.hg19:g.55272094G>A	ENSP00000370698:p.Gln5*	299.0	0.0		336.0	89.0	NM_175767	A0N0L4|Q5FC04|Q9UQ41	Nonsense_Mutation	SNP	ENST00000381298.2	hg19	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.222041	0.39300	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294;ENST00000381287;ENST00000536319;ENST00000381293;ENST00000381286;ENST00000522633;ENST00000542298	.	.	.	4.7	-4.85	0.03142	.	2.036040	0.02176	N	0.060126	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.4118	0.21696	0.1612:0.0:0.2807:0.558	.	.	.	.	X	5	.	ENSP00000338799:Q5X	Q	-	1	0	IL6ST	55307851	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-0.257000	0.08745	-0.787000	0.04510	0.585000	0.79938	CAG	.	.		0.338	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		A	55272094	G	A	55272094	4	1	90	1	0	0	0	0	0	1	0	0	7712	1328	46	3	2803	3	IL6ST	5	55272094	Nonsense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10		55272094	125643166	28	11991										
BHMT2	23743	hgsc.bcm.edu	37	chr5	78376532	78376532	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ggaagatgtaaatgctgctgCctgtgacctcgccagggaag	14	9	0	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr5:78376532C>T	ENST00000255192.3	+	4	347	c.281C>T	c.(280-282)gCc>gTc	p.A94V	DMGDH_ENST00000520388.1_Intron|BHMT2_ENST00000521567.1_Intron	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	94	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)	AATGCTGCTGCCTGTGACCTC	0.453																																					p.A94V		Atlas-SNP	.											.	BHMT2	44	.	0			c.C281T						.						123	126	125					5																	78376532		2203	4300	6503	SO:0001583	missense	23743	exon4			CTGCTGCCTGTGA		CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.281C>T	chr5.hg19:g.78376532C>T	ENSP00000255192:p.Ala94Val	209.0	0.0		249.0	18.0	NM_017614	B7Z516|Q9NXX7	Missense_Mutation	SNP	ENST00000255192.3	hg19	CCDS4045.1	.	.	.	.	.	.	.	.	.	.	C	35	5.571337	0.96553	.	.	ENSG00000132840	ENST00000255192;ENST00000518666	T;T	0.52754	0.65;0.65	6.16	6.16	0.99307	Homocysteine S-methyltransferase (4);	0.000000	0.85682	D	0.000000	T	0.69106	0.3074	M	0.92923	3.36	0.80722	D	1	D	0.55605	0.972	P	0.48654	0.585	T	0.76801	-0.2825	10	0.72032	D	0.01	-19.1782	20.8598	0.99761	0.0:1.0:0.0:0.0	.	94	Q9H2M3	BHMT2_HUMAN	V	94;34	ENSP00000255192:A94V;ENSP00000428640:A34V	ENSP00000255192:A94V	A	+	2	0	BHMT2	78412288	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	2.937000	0.99478	0.650000	0.86243	GCC	.	.		0.453	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614		T	78376532	C	T	78376532	3	4	90	1	0	0	0	0	1	0	0	0	1426	739	26	3	295	3	BHMT2	5	78376532	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	23104438	78376532	102538728	29	11992										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140216086	140216086	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ctgatcatcgccatctgcgcGgtgtccagtctgttggtgct	12	12	3	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr5:140216086G>T	ENST00000525929.1	+	1	2118	c.2118G>T	c.(2116-2118)gcG>gcT	p.A706A	PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000378125.3_Silent_p.A706A|PCDHA5_ENST00000529619.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	706					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCATCTGCGCGGTGTCCAGTC	0.617																																					p.A706A	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.G2118T						.						120	101	107					5																	140216086		2203	4300	6503	SO:0001819	synonymous_variant	56141	exon1			CTGCGCGGTGTCC	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.2118G>T	chr5.hg19:g.140216086G>T		364.0	0.0		490.0	280.0	NM_031852	O75282	Silent	SNP	ENST00000525929.1	hg19	CCDS54918.1																																																																																			.	.		0.617	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		T	140216086	G	T	140216086	2	4	90	1	0	0	0	0	0	0	0	1	11538	1103	39	1		1	PCDHA7	5	140216086	Silent	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	61839554	140216086	40699174	30	11993										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222188	140222188	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	atgagttggtggtaaccgcgCgggacgggggctcgccttcg	18	10	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr5:140222188C>T	ENST00000531613.1	+	1	1282	c.1282C>T	c.(1282-1284)Cgg>Tgg	p.R428W	PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.R428W|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	428	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTAACCGCGCGGGACGGGGG	0.632																																					p.R428W		Atlas-SNP	.											.	PCDHA8	366	.	0			c.C1282T						.						77	72	74					5																	140222188		2194	4262	6456	SO:0001583	missense	56140	exon1			ACCGCGCGGGACG	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1282C>T	chr5.hg19:g.140222188C>T	ENSP00000434655:p.Arg428Trp	322.0	0.0		339.0	58.0	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	hg19	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	C	6.302	0.423734	0.11928	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.01804	4.63;4.63	3.72	0.308	0.15815	Cadherin (5);Cadherin-like (1);	0.000000	0.33732	U	0.004611	T	0.01320	0.0043	N	0.17922	0.545	0.09310	N	1	P;P	0.39665	0.682;0.631	B;B	0.35931	0.214;0.136	T	0.51116	-0.8746	10	0.66056	D	0.02	.	8.5805	0.33626	0.4619:0.4082:0.1299:0.0	.	428;428	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	W	428	ENSP00000434655:R428W;ENSP00000367363:R428W	ENSP00000367363:R428W	R	+	1	2	PCDHA8	140202372	0.000000	0.05858	0.004000	0.12327	0.117000	0.20001	-1.572000	0.02136	0.144000	0.18951	0.306000	0.20318	CGG	.	.		0.632	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		T	140222188	C	T	140222188	3	4	90	1	0	0	0	0	1	0	0	0	11539	759	27	1	1284	1	PCDHA8	5	140222188	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	6102	140222188	40693072	31	11994										
FAT2	2196	hgsc.bcm.edu	37	chr5	150932949	150932949	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccactgtctgttgccttgatCtgaaaggaggccaacaccaa	9	12	2	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr5:150932949C>G	ENST00000261800.5	-	5	3958		c.e5-1			NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2						epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTGCCTTGATCTGAAAGGAGG	0.587																																					.		Atlas-SNP	.											.	FAT2	465	.	0			c.3946-1G>C						.						56	43	47					5																	150932949		2203	4300	6503	SO:0001630	splice_region_variant	2196	exon6			CTTGATCTGAAAG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3946-1G>C	chr5.hg19:g.150932949C>G		85.0	0.0		99.0	17.0	NM_001447	O75091|Q9NSR7	Splice_Site	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.321669	0.81580	.	.	ENSG00000086570	ENST00000261800	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3976	0.90504	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAT2	150913142	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.382000	0.79729	2.583000	0.87209	0.561000	0.74099	.	.	.		0.587	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	Intron	G	150932949	C	G	150932949	5	3	90	1	0	0	0	0	0	0	1	0	5698	927	32	4	9180	4	FAT2	5	150932949	Splice_Site	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	10710761	150932949	29982311	32	11995										
HIST1H4B	8366	hgsc.bcm.edu	37	chr6	26027241	26027241	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	acatccatggcagtgacagtCttgcgcttggcgtgctccgt	12	12	1	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr6:26027241C>A	ENST00000377364.3	-	1	239	c.240G>T	c.(238-240)aaG>aaT	p.K80N		NM_003544.2	NP_003535.1	P62805	H4_HUMAN	histone cluster 1, H4b	80					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			large_intestine(4)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	13						CAGTGACAGTCTTGCGCTTGG	0.537											OREG0017238	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K80N		Atlas-SNP	.											HIST1H4B,NS,carcinoma,0,1	HIST1H4B	27	.	0			c.G240T						.						113	97	102					6																	26027241		2203	4300	6503	SO:0001583	missense	8366	exon1			GACAGTCTTGCGC	X67081	CCDS4572.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124529	ENSG00000278705		"Histones / Replication-dependent"	4789	protein-coding gene	gene with protein product		602829	"H4 histone family, member I", "histone 1, H4b"	H4FI		9119399, 12408966	Standard	NM_003544		Approved	H4/I	uc003nfr.3	P62805	OTTHUMG00000014417	ENST00000377364.3:c.240G>T	chr6.hg19:g.26027241C>A	ENSP00000366581:p.Lys80Asn	168.0	1.0	783	198.0	30.0	NM_003544	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377364.3	hg19	CCDS4572.1	.	.	.	.	.	.	.	.	.	.	c	17.22	3.334950	0.60853	.	.	ENSG00000124529	ENST00000377364	T	0.71222	-0.55	4.65	1.88	0.25563	.	0.000000	0.56097	U	0.000032	T	0.65678	0.2714	.	.	.	0.36216	D	0.851672	.	.	.	.	.	.	T	0.69064	-0.5244	7	0.87932	D	0	.	9.135	0.36868	0.0:0.7522:0.0:0.2478	.	.	.	.	N	80	ENSP00000366581:K80N	ENSP00000366581:K80N	K	-	3	2	HIST1H4B	26135220	1.000000	0.71417	0.998000	0.56505	0.141000	0.21300	2.448000	0.44926	0.642000	0.30620	0.563000	0.77884	AAG	.	.		0.537	HIST1H4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040079.2	NM_003544		A	26027241	C	A	26027241	3	1	90	1	0	0	0	0	1	0	0	0	7175	912	32	3	75	3	HIST1H4B	6	26027241	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10		26027241	145087826	33	11996										
HIST1H4E	8367	hgsc.bcm.edu	37	chr6	26204899	26204899	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ggtcgcggcaaaggcggaaaGggactgggtaaaggaggcgc	20	7	0	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr6:26204899G>C	ENST00000360441.4	+	1	42	c.27G>C	c.(25-27)aaG>aaC	p.K9N		NM_003545.3	NP_003536.1	P62805	H4_HUMAN	histone cluster 1, H4e	9					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	18		all_hematologic(11;0.196)				AAGGCGGAAAGGGACTGGGTA	0.542																																					p.K9N		Atlas-SNP	.											.	HIST1H4E	22	.	0			c.G27C						.						78	81	80					6																	26204899		2203	4300	6503	SO:0001583	missense	8367	exon1			CGGAAAGGGACTG	Z80787	CCDS4593.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198518	ENSG00000276966		"Histones / Replication-dependent"	4790	protein-coding gene	gene with protein product		602830	"H4 histone family, member J", "histone 1, H4e"	H4FJ		9119399, 12408966	Standard	NM_003545		Approved	H4/j	uc003ngy.3	P62805	OTTHUMG00000014441	ENST00000360441.4:c.27G>C	chr6.hg19:g.26204899G>C	ENSP00000353624:p.Lys9Asn	139.0	0.0		159.0	35.0	NM_003545	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000360441.4	hg19	CCDS4593.1	.	.	.	.	.	.	.	.	.	.	.	5.613	0.297818	0.10622	.	.	ENSG00000198518	ENST00000360441	.	.	.	2.2	-4.41	0.03590	.	0.000000	0.85682	U	0.000000	T	0.57770	0.2076	.	.	.	0.46279	D	0.998965	.	.	.	.	.	.	T	0.66744	-0.5846	6	0.87932	D	0	.	12.694	0.56992	0.1659:0.0:0.8341:0.0	.	.	.	.	N	9	.	ENSP00000353624:K9N	K	+	3	2	HIST1H4E	26312878	0.196000	0.23350	0.001000	0.08648	0.001000	0.01503	-0.473000	0.06615	-1.637000	0.01531	-1.063000	0.02288	AAG	.	.		0.542	HIST1H4E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040104.1	NM_003545		C	26204899	G	C	26204899	3	2	90	1	0	0	0	0	1	0	0	0	7178	991	35	4	29	4	HIST1H4E	6	26204899	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	177658	26204899	144910168	34	11997										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32181471	32181471	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cagtgggcactcaccagacaCacagtagtcagtgctggttt	11	11	2	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr6:32181471C>A	ENST00000375023.3	-	14	2452	c.2314G>T	c.(2314-2316)Gtg>Ttg	p.V772L	NOTCH4_ENST00000465528.1_5'UTR	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	772	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TCACCAGACACACAGTAGTCA	0.527																																					p.V772L		Atlas-SNP	.											.	NOTCH4	201	.	0			c.G2314T						.						115	107	110					6																	32181471		1509	2708	4217	SO:0001583	missense	4855	exon14			CAGACACACAGTA		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.2314G>T	chr6.hg19:g.32181471C>A	ENSP00000364163:p.Val772Leu	87.0	0.0		115.0	20.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	C	5.248	0.231209	0.09969	.	.	ENSG00000204301	ENST00000375023	T	0.61274	0.12	3.88	3.0	0.34707	EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	1.143020	0.06809	N	0.790025	T	0.17109	0.0411	N	0.02802	-0.49	0.53688	D	0.999977	B	0.10296	0.003	B	0.13407	0.009	T	0.42849	-0.9427	10	0.87932	D	0	.	4.9258	0.13892	0.0:0.6603:0.221:0.1188	.	772	Q99466	NOTC4_HUMAN	L	772	ENSP00000364163:V772L	ENSP00000364163:V772L	V	-	1	0	NOTCH4	32289449	0.000000	0.05858	0.895000	0.35142	0.005000	0.04900	-0.327000	0.07955	2.169000	0.68431	0.561000	0.74099	GTG	.	.		0.527	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32181471	C	A	32181471	3	1	90	1	0	0	0	0	1	0	0	0	10560	478	17	3	3765	3	NOTCH4	6	32181471	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	5976572	32181471	138933596	35	11998										
DST	667	hgsc.bcm.edu	37	chr6	56417839	56417846	+	Frame_Shift_Del	DEL	TCAGTGAC	TCAGTGAC	-													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gaccatgtccaccttctggaTcagtgacttattctcatctg							TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	TCAGTGAC	TCAGTGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr6:56417839_56417846delTCAGTGAC	ENST00000361203.3	-	57	15118_15125	c.15111_15118delGTCACTGA	c.(15109-15120)aagtcactgatcfs	p.KSLI5037fs	DST_ENST00000244364.6_Frame_Shift_Del_p.KSLI2625fs|DST_ENST00000421834.2_Frame_Shift_Del_p.KSLI2951fs|DST_ENST00000312431.6_3'UTR|DST_ENST00000370788.2_Frame_Shift_Del_p.KSLI2951fs|DST_ENST00000370769.4_Frame_Shift_Del_p.KSLI5039fs|DST_ENST00000370754.5_Frame_Shift_Del_p.KSLI5217fs|DST_ENST00000446842.2_Frame_Shift_Del_p.KSLI4713fs			Q03001	DYST_HUMAN	dystonin	5037					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ACCTTCTGGATCAGTGACTTATTCTCAT	0.385																																					p.2626_2628del		Atlas-INDEL	.											.	DST	1427	.	0			c.7876_7883del						.																																			SO:0001589	frameshift_variant	667	exon42			.	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.15111_15118delGTCACTGA	chr6.hg19:g.56417839_56417846delTCAGTGAC	ENSP00000354508:p.Lys5037fs	101.0	0.0		128.0	11.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Frame_Shift_Del	DEL	ENST00000361203.3	hg19																																																																																				.	.		0.385	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		-	56417846	TCAGTGAC	-	56417839	7	5	90	1	0	1	0	1	0	0	0	0	4785	1435	50	0	7805	0	DST	6	56417839	Frame_Shift_Del	DEL	TCAGTGAC	TCGA-DD-A118-01A-11D-A12Z-10	24236368	56417839	114697228	36	11999										
EYS	346007	hgsc.bcm.edu	37	chr6	65303132	65303132	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gtgtggaaatgggatctgttCtttgaaagatgggagttaaa	14	2	2	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr6:65303132C>A	ENST00000370621.3	-	25	4281	c.3755G>T	c.(3754-3756)aGa>aTa	p.R1252I	EYS_ENST00000370616.2_Missense_Mutation_p.R1252I|EYS_ENST00000503581.1_Missense_Mutation_p.R1252I			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1252					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GGGATCTGTTCTTTGAAAGAT	0.388																																					p.R1252I		Atlas-SNP	.											.	EYS	527	.	0			c.G3755T						.						139	123	128					6																	65303132		692	1591	2283	SO:0001583	missense	346007	exon25			TCTGTTCTTTGAA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.3755G>T	chr6.hg19:g.65303132C>A	ENSP00000359655:p.Arg1252Ile	258.0	0.0		320.0	49.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	C	11.04	1.521155	0.27211	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.82081	-1.57;-1.56;-1.56	4.73	3.85	0.44370	.	.	.	.	.	T	0.67543	0.2904	N	0.19112	0.55	0.45150	D	0.998168	P;P	0.48016	0.904;0.845	P;B	0.48921	0.595;0.311	T	0.68565	-0.5375	9	0.33940	T	0.23	.	13.167	0.59577	0.0:0.8396:0.1604:0.0	.	1252;1252	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	I	1252	ENSP00000424243:R1252I;ENSP00000359655:R1252I;ENSP00000359650:R1252I	ENSP00000359650:R1252I	R	-	2	0	EYS	65359853	0.429000	0.25530	0.035000	0.18076	0.184000	0.23303	0.948000	0.29096	0.969000	0.38237	-0.175000	0.13238	AGA	.	.		0.388	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	65303132	C	A	65303132	3	1	90	1	0	0	0	0	1	0	0	0	5334	913	32	3	5600	3	EYS	6	65303132	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	8885293	65303132	105811935	37	12000										
MDN1	23195	hgsc.bcm.edu	37	chr6	90371908	90371908	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tgctggcttttatctttgttTgaattgccactatccaagtt	7	8	1	1	rs549598677	byFrequency	TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr6:90371908T>C	ENST00000369393.3	-	87	14578	c.14463A>G	c.(14461-14463)tcA>tcG	p.S4821S	MDN1_ENST00000428876.1_Silent_p.S4821S			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4821					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TATCTTTGTTTGAATTGCCAC	0.358																																					p.S4821S		Atlas-SNP	.											.	MDN1	478	.	0			c.A14463G						.						237	214	222					6																	90371908		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon87			TTTGTTTGAATTG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14463A>G	chr6.hg19:g.90371908T>C		735.0	0.0		565.0	146.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.358	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90371908	T	C	90371908	2	2	90	1	0	0	0	0	0	0	0	1	9424	1799	63	2		2	MDN1	6	90371908	Silent	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	25068776	90371908	80743159	38	12001										
GPR63	81491	hgsc.bcm.edu	37	chr6	97246895	97246895	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aaatcacataagcctggtagCctggattggttgtgtaccca	10	9	1	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr6:97246895C>A	ENST00000229955.3	-	2	1058	c.713G>T	c.(712-714)gGc>gTc	p.G238V	GPR63_ENST00000417980.1_Missense_Mutation_p.G238V	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		AGCCTGGTAGCCTGGATTGGT	0.463																																					p.G238V		Atlas-SNP	.											.	GPR63	60	.	0			c.G713T						.						78	83	81					6																	97246895		2203	4300	6503	SO:0001583	missense	81491	exon2			TGGTAGCCTGGAT	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.713G>T	chr6.hg19:g.97246895C>A	ENSP00000229955:p.Gly238Val	149.0	0.0		71.0	21.0	NM_030784	Q9UJH3	Missense_Mutation	SNP	ENST00000229955.3	hg19	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.444645	0.63178	.	.	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	T;T;T	0.35236	1.32;1.32;1.32	5.2	5.2	0.72013	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.31009	0.0783	N	0.25825	0.765	0.80722	D	1	B	0.34061	0.436	P	0.47118	0.538	T	0.25641	-1.0126	10	0.52906	T	0.07	-3.6581	19.0987	0.93265	0.0:1.0:0.0:0.0	.	238	Q9BZJ6	GPR63_HUMAN	V	262;238;238;238	ENSP00000393170:G238V;ENSP00000229955:G238V;ENSP00000358273:G238V	ENSP00000229955:G238V	G	-	2	0	GPR63	97353616	1.000000	0.71417	0.286000	0.24833	0.974000	0.67602	4.588000	0.60999	2.595000	0.87683	0.650000	0.86243	GGC	.	.		0.463	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			A	97246895	C	A	97246895	3	1	90	1	0	0	0	0	1	0	0	0	6712	739	26	3	550	3	GPR63	6	97246895	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	6874987	97246895	73868172	39	12002										
AKAP12	9590	hgsc.bcm.edu	37	chr6	151670985	151670985	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ctgacctcagtcctgatgagAaggtgctgtccaaacccccc	9	15	1	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr6:151670985A>T	ENST00000253332.1	+	3	1648	c.1459A>T	c.(1459-1461)Aag>Tag	p.K487*	AKAP12_ENST00000402676.2_Nonsense_Mutation_p.K487*|AKAP12_ENST00000359755.5_Nonsense_Mutation_p.K382*|snoU13_ENST00000458767.1_RNA|AKAP12_ENST00000354675.6_Nonsense_Mutation_p.K389*			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	487	Involved in PKC-binding. {ECO:0000305}.				G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		TCCTGATGAGAAGGTGCTGTC	0.527																																					p.K487X	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.A1459T						.						97	100	99					6																	151670985		2203	4300	6503	SO:0001587	stop_gained	9590	exon4			GATGAGAAGGTGC	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.1459A>T	chr6.hg19:g.151670985A>T	ENSP00000253332:p.Lys487*	60.0	0.0		50.0	29.0	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Nonsense_Mutation	SNP	ENST00000253332.1	hg19	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.211119	0.79240	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	.	.	.	4.97	2.35	0.29111	.	0.166543	0.28583	N	0.014832	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.811	0.23805	0.6029:0.2184:0.0:0.1787	.	.	.	.	X	487;487;389;382	.	ENSP00000253332:K487X	K	+	1	0	AKAP12	151712678	0.027000	0.19231	0.002000	0.10522	0.008000	0.06430	1.256000	0.32921	0.818000	0.34468	0.533000	0.62120	AAG	.	.		0.527	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			T	151670985	A	T	151670985	4	4	90	1	0	0	0	0	0	1	0	0	448	247	9	4	1498	4	AKAP12	6	151670985	Nonsense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	54424090	151670985	19444082	40	12003										
GTF2IRD1	9569	hgsc.bcm.edu	37	chr7	73944105	73944105	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	acatggtccccgtgccctacCggaagattgcctgtgacccg	11	15	0	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr7:73944105C>T	ENST00000265755.3	+	9	1525	c.1132C>T	c.(1132-1134)Cgg>Tgg	p.R378W	GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.R378W|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.R378W|GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.R410W|GTF2IRD1_ENST00000489094.1_3'UTR	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	378				R -> Q (in Ref. 5; AAF21796). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R378W(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CGTGCCCTACCGGAAGATTGC	0.607																																					p.R410W		Atlas-SNP	.											GTF2IRD1,rectum,carcinoma,0,3	GTF2IRD1	91	.	1	Substitution - Missense(1)	ovary(1)	c.C1228T						.						69	59	62					7																	73944105		2203	4300	6503	SO:0001583	missense	9569	exon9			CCCTACCGGAAGA	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"binding factor for early enhancer"	604318	"GTF2I repeat domain-containing 1"	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1132C>T	chr7.hg19:g.73944105C>T	ENSP00000265755:p.Arg378Trp	91.0	0.0		121.0	27.0	NM_001199207	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	hg19	CCDS5571.1	.	.	.	.	.	.	.	.	.	.	c	19.69	3.873889	0.72180	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	4.46	-2.05	0.07321	.	0.000000	0.85682	D	0.000000	T	0.46927	0.1418	N	0.19112	0.55	0.52501	D	0.999952	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.993;0.957;0.996;0.974	T	0.52245	-0.8601	10	0.87932	D	0	-25.9307	17.2233	0.86963	0.259:0.7409:0.0:0.0	.	410;378;378;378	Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.;.;GT2D1_HUMAN;.	W	378;410;378;378	ENSP00000265755:R378W;ENSP00000397566:R410W;ENSP00000408477:R378W;ENSP00000418383:R378W	ENSP00000265755:R378W	R	+	1	2	GTF2IRD1	73582041	1.000000	0.71417	0.996000	0.52242	0.862000	0.49288	2.453000	0.44970	-0.142000	0.11354	-0.535000	0.04281	CGG	.	.		0.607	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328		T	73944105	C	T	73944105	3	4	90	1	0	0	0	0	1	0	0	0	6877	643	23	1	1162	1	GTF2IRD1	7	73944105	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10		73944105	85194558	41	12004										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88964869	88964869	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cgacagattggactcttactCaatagagaaaatgtattact	7	7	2	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr7:88964869C>A	ENST00000333190.4	+	4	3182	c.2573C>A	c.(2572-2574)tCa>tAa	p.S858*		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	858							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GACTCTTACTCAATAGAGAAA	0.403										HNSCC(36;0.09)																											p.S858X		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C2573A						.						59	59	59					7																	88964869		2203	4300	6503	SO:0001587	stop_gained	219578	exon4			CTTACTCAATAGA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2573C>A	chr7.hg19:g.88964869C>A	ENSP00000329638:p.Ser858*	130.0	0.0		152.0	21.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Nonsense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	C	39	7.614829	0.98390	.	.	ENSG00000182348	ENST00000333190	.	.	.	5.19	3.21	0.36854	.	0.790576	0.11417	N	0.566226	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.0219	11.4841	0.50344	0.0:0.8285:0.0:0.1715	.	.	.	.	X	858	.	ENSP00000329638:S858X	S	+	2	0	ZNF804B	88802805	0.899000	0.30636	0.011000	0.14972	0.052000	0.14988	2.925000	0.48884	1.402000	0.46780	0.655000	0.94253	TCA	.	.		0.403	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		A	88964869	C	A	88964869	4	1	90	1	0	0	0	0	0	1	0	0	18186	838	29	3	2587	3	ZNF804B	7	88964869	Nonsense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	15020764	88964869	70173794	42	12005										
ATXN7L1	222255	hgsc.bcm.edu	37	chr7	105278897	105278897	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccctagcagagaatcctgtgCcggcccggattggcttggaa	13	12	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr7:105278897C>T	ENST00000419735.3	-	7	1150	c.1105G>A	c.(1105-1107)Gca>Aca	p.A369T	ATXN7L1_ENST00000472910.1_5'UTR|ATXN7L1_ENST00000477775.1_Missense_Mutation_p.A245T	NM_020725.1	NP_065776.1	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1	369	Ser-rich.									endometrium(1)|large_intestine(4)|lung(5)	10						GAATCCTGTGCCGGCCCGGAT	0.507																																					p.A369T		Atlas-SNP	.											.	ATXN7L1	56	.	0			c.G1105A						.						97	90	92					7																	105278897		692	1591	2283	SO:0001583	missense	222255	exon7			CCTGTGCCGGCCC	AB033044	CCDS34727.1, CCDS47682.1, CCDS47683.1	7q22.1	2007-11-13			ENSG00000146776	ENSG00000146776			22210	protein-coding gene	gene with protein product			"ataxin 7-like 4"	ATXN7L4		15115762	Standard	NM_152749		Approved	KIAA1218, MGC33190	uc003vde.2	Q9ULK2	OTTHUMG00000157521	ENST00000419735.3:c.1105G>A	chr7.hg19:g.105278897C>T	ENSP00000410759:p.Ala369Thr	288.0	1.0		350.0	125.0	NM_020725	A4D0Q2|B4DTS1|Q8N2T0	Missense_Mutation	SNP	ENST00000419735.3	hg19	CCDS47682.1	.	.	.	.	.	.	.	.	.	.	C	11.59	1.684422	0.29872	.	.	ENSG00000146776	ENST00000419735;ENST00000477775;ENST00000472195	T;T;T	0.14640	2.5;2.49;2.49	5.38	2.54	0.30619	.	1.125900	0.06660	N	0.764276	T	0.14960	0.0361	L	0.47716	1.5	0.28395	N	0.918924	P;B;B	0.43788	0.817;0.015;0.0	B;B;B	0.41764	0.366;0.008;0.0	T	0.24368	-1.0162	10	0.32370	T	0.25	.	7.6182	0.28171	0.1256:0.6872:0.1209:0.0663	.	153;245;369	A4D0Q3;Q9ULK2-3;Q9ULK2	.;.;AT7L1_HUMAN	T	369;245;245	ENSP00000410759:A369T;ENSP00000418476:A245T;ENSP00000419566:A245T	ENSP00000410759:A369T	A	-	1	0	ATXN7L1	105066133	0.002000	0.14202	0.000000	0.03702	0.859000	0.49053	1.600000	0.36762	0.319000	0.23209	0.655000	0.94253	GCA	.	.		0.507	ATXN7L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349037.2			T	105278897	C	T	105278897	3	4	90	1	0	0	0	0	1	0	0	0	1216	739	26	3	1507	3	ATXN7L1	7	105278897	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	16314028	105278897	53859766	43	12006										
ASB10	136371	hgsc.bcm.edu	37	chr7	150883617	150883617	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aggcctcgtgcagggcggtgCggcccccaggggcactgtct	17	14	1	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr7:150883617C>T	ENST00000420175.2	-	2	470	c.446G>A	c.(445-447)cGc>cAc	p.R149H	ASB10_ENST00000275838.1_Missense_Mutation_p.R149H|ASB10_ENST00000434669.1_Missense_Mutation_p.R194H|ASB10_ENST00000377867.3_Missense_Mutation_p.R134H|ASB10_ENST00000422024.1_Missense_Mutation_p.R194H			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	149					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGGGCGGTGCGGCCCCCAGG	0.677																																					p.R149H		Atlas-SNP	.											.	ASB10	99	.	0			c.G446A						.						19	19	19					7																	150883617		2196	4294	6490	SO:0001583	missense	136371	exon2			GCGGTGCGGCCCC	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"Ankyrin repeat domain containing"	17185	protein-coding gene	gene with protein product		615054	"ankyrin repeat and SOCS box-containing 10", "glaucoma 1, open angle, F (adult-onset)"	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.446G>A	chr7.hg19:g.150883617C>T	ENSP00000391137:p.Arg149His	58.0	0.0		59.0	10.0	NM_001142459	A0AVH0|Q6ZUL6	Missense_Mutation	SNP	ENST00000420175.2	hg19	CCDS47750.2	.	.	.	.	.	.	.	.	.	.	C	15.00	2.703764	0.48412	.	.	ENSG00000146926	ENST00000275838;ENST00000377867;ENST00000422024;ENST00000434669;ENST00000420175	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.15	5.15	0.70609	Ankyrin repeat-containing domain (4);	0.732986	0.13677	N	0.370464	T	0.50854	0.1640	L	0.44542	1.39	0.27720	N	0.945146	B;B;B	0.29270	0.027;0.24;0.081	B;B;B	0.25291	0.01;0.059;0.019	T	0.38457	-0.9660	10	0.15952	T	0.53	-6.5102	11.0942	0.48134	0.0:0.9057:0.0:0.0943	.	134;149;194	Q8WXI3-3;Q8WXI3;D5MNW9	.;ASB10_HUMAN;.	H	149;134;194;194;149	ENSP00000275838:R149H;ENSP00000367098:R134H;ENSP00000401369:R194H;ENSP00000398247:R194H;ENSP00000391137:R149H	ENSP00000275838:R149H	R	-	2	0	ASB10	150514550	0.996000	0.38824	1.000000	0.80357	0.989000	0.77384	0.339000	0.19875	2.397000	0.81536	0.491000	0.48974	CGC	.	.		0.677	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871		T	150883617	C	T	150883617	3	4	90	1	0	0	0	0	1	0	0	0	1014	768	27	1	973	1	ASB10	7	150883617	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	45604720	150883617	8255046	44	12007										
ACTR3B	57180	hgsc.bcm.edu	37	chr7	152549222	152549222	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gtcttgtagaatgtcgtactCtcaggaggctccaccatgtt	10	10	2	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr7:152549222C>G	ENST00000256001.8	+	10	1097	c.963C>G	c.(961-963)ctC>ctG	p.L321L	ACTR3B_ENST00000397282.2_Silent_p.L233L|ACTR3B_ENST00000537264.1_Silent_p.L233L|ACTR3B_ENST00000377776.3_Intron	NM_020445.5	NP_065178.1	Q9P1U1	ARP3B_HUMAN	ARP3 actin-related protein 3 homolog B (yeast)	321						cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	13		all_hematologic(28;0.0592)|Prostate(32;0.191)	OV - Ovarian serous cystadenocarcinoma(82;0.0287)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0434)		ATGTCGTACTCTCAGGAGGCT	0.577																																					p.L321L		Atlas-SNP	.											.	ACTR3B	50	.	0			c.C963G						.						119	103	109					7																	152549222		2203	4300	6503	SO:0001819	synonymous_variant	57180	exon10			CGTACTCTCAGGA		CCDS5934.1, CCDS34782.1	7q36.1	2010-07-20			ENSG00000133627	ENSG00000133627			17256	protein-coding gene	gene with protein product						10806390	Standard	NM_001040135		Approved	ARP11, ARP3beta	uc003wle.2	Q9P1U1	OTTHUMG00000151463	ENST00000256001.8:c.963C>G	chr7.hg19:g.152549222C>G		217.0	0.0		225.0	62.0	NM_020445	A8MTG1|B4DFW4|Q7Z526|Q96BT2	Silent	SNP	ENST00000256001.8	hg19	CCDS5934.1																																																																																			.	.		0.577	ACTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322803.1	NM_020445		G	152549222	C	G	152549222	2	3	90	1	0	0	0	0	0	0	0	1	213	900	32	4		4	ACTR3B	7	152549222	Silent	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	1665605	152549222	6589441	45	12008										
RBM33	155435	hgsc.bcm.edu	37	chr7	155556582	155556582	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gcctccggaagtgggaccacAgcctgcccgcaaggtgacgc	14	15	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr7:155556582A>T	ENST00000401878.3	+	15	3254	c.3056A>T	c.(3055-3057)cAg>cTg	p.Q1019L	RBM33_ENST00000341148.3_5'UTR	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	1019							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		GTGGGACCACAGCCTGCCCGC	0.662																																					p.Q1019L		Atlas-SNP	.											.	RBM33	157	.	0			c.A3056T						.						14	17	16					7																	155556582		2012	4177	6189	SO:0001583	missense	155435	exon15			GACCACAGCCTGC	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"RNA binding motif (RRM) containing"	27223	protein-coding gene	gene with protein product			"proline rich 8"	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.3056A>T	chr7.hg19:g.155556582A>T	ENSP00000384160:p.Gln1019Leu	101.0	0.0		106.0	26.0	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Missense_Mutation	SNP	ENST00000401878.3	hg19	CCDS5941.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.62|18.62	3.662602|3.662602	0.67700|0.67700	.|.	.|.	ENSG00000184863|ENSG00000184863	ENST00000401878|ENST00000392761	T|.	0.49720|.	0.77|.	5.91|5.91	3.46|3.46	0.39613|0.39613	.|.	0.192886|.	0.24886|.	U|.	0.034812|.	T|T	0.57858|0.57858	0.2082|0.2082	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	B;D|.	0.67145|.	0.001;0.996|.	B;D|.	0.62955|.	0.004;0.909|.	T|T	0.50874|0.50874	-0.8776|-0.8776	10|5	0.29301|.	T|.	0.29|.	.|.	8.2904|8.2904	0.31954|0.31954	0.7294:0.1386:0.0:0.1319|0.7294:0.1386:0.0:0.1319	.|.	737;1019|.	B4DVQ2;Q96EV2|.	.;RBM33_HUMAN|.	L|C	1019|792	ENSP00000384160:Q1019L|.	ENSP00000384160:Q1019L|.	Q|S	+|+	2|1	0|0	RBM33|RBM33	155249343|155249343	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.697000|0.697000	0.40408|0.40408	1.709000|1.709000	0.37909|0.37909	0.441000|0.441000	0.26529|0.26529	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.662	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		T	155556582	A	T	155556582	3	4	90	1	0	0	0	0	1	0	0	0	13145	188	7	4	3114	4	RBM33	7	155556582	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	3007360	155556582	3582081	46	12009										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77765482	77765482	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tggacgcactctctgcagacCtcacccaactttgccagcag	8	16	2	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr8:77765482C>T	ENST00000521891.2	+	10	6773	c.6325C>T	c.(6325-6327)Ctc>Ttc	p.L2109F	ZFHX4_ENST00000518282.1_Missense_Mutation_p.L2083F|ZFHX4_ENST00000050961.6_Missense_Mutation_p.L2064F|ZFHX4_ENST00000455469.2_Missense_Mutation_p.L2064F	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2064					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CTCTGCAGACCTCACCCAACT	0.522										HNSCC(33;0.089)																											p.L2109F		Atlas-SNP	.											.	ZFHX4	878	.	0			c.C6325T						.						33	35	34					8																	77765482		2064	4206	6270	SO:0001583	missense	79776	exon10			GCAGACCTCACCC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6325C>T	chr8.hg19:g.77765482C>T	ENSP00000430497:p.Leu2109Phe	135.0	0.0		158.0	37.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	14.29	2.491534	0.44249	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.55588	0.51;0.57;0.54;0.53	3.54	2.64	0.31445	.	0.182351	0.26317	U	0.025071	T	0.59487	0.2197	L	0.36672	1.1	0.54753	D	0.999987	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.87578	0.986;0.998;0.994	T	0.56786	-0.7921	10	0.42905	T	0.14	.	11.1432	0.48415	0.1861:0.8138:0.0:0.0	.	2064;2064;2109	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	F	2109;2093;2064;2064;2083	ENSP00000430497:L2109F;ENSP00000399605:L2064F;ENSP00000050961:L2064F;ENSP00000430848:L2083F	ENSP00000050961:L2064F	L	+	1	0	ZFHX4	77928037	1.000000	0.71417	0.891000	0.34965	0.899000	0.52679	4.720000	0.61944	0.820000	0.34516	0.455000	0.32223	CTC	.	.		0.522	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77765482	C	T	77765482	3	4	90	1	0	0	0	0	1	0	0	0	17650	681	24	3	6359	3	ZFHX4	8	77765482	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10		77765482	68598540	47	12010										
ABCA2	20	hgsc.bcm.edu	37	chr9	139907265	139907266	+	Frame_Shift_Ins	INS	-	-	G													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tgaccacccgcatctggggcINSgggtgcccgcccacactgct							TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr9:139907265_139907266insG	ENST00000371605.3	-	30	5123_5124	c.4976_4977insC	c.(4975-4977)ccgfs	p.P1659fs	ABCA2_ENST00000341511.6_Frame_Shift_Ins_p.P1660fs|ABCA2_ENST00000265662.5_Frame_Shift_Ins_p.P1660fs			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1659					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GCATCTGGGGCGGGTGCCCGCC	0.688																																					p.P1690fs		Atlas-INDEL	.											.	ABCA2	113	.	0			c.5070_5071insC						.																																			SO:0001589	frameshift_variant	20	exon31			.	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.4977dupC	chr9.hg19:g.139907268_139907268dupG	ENSP00000360666:p.Pro1659fs	95.0	0.0		100.0	14.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Frame_Shift_Ins	INS	ENST00000371605.3	hg19																																																																																				.	.		0.688	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		G	139907266	-	G	139907265	7	5	90	1	0	1	1	0	0	0	0	0	32	755	27	0	2406	0	ABCA2	9	139907265	Frame_Shift_Ins	INS	-	TCGA-DD-A118-01A-11D-A12Z-10		139907265	1306166	48	12011										
RPP30	10556	hgsc.bcm.edu	37	chr10	92638835	92638835	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cctagagagcaacttcttcaAgggcccggctctatgatgtt	10	11	3	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr10:92638835A>G	ENST00000371703.3	+	5	557	c.286A>G	c.(286-288)Agg>Ggg	p.R96G	RPP30_ENST00000413330.1_Missense_Mutation_p.R96G|Y_RNA_ENST00000410373.1_RNA	NM_006413.4	NP_006404.1	P78346	RPP30_HUMAN	ribonuclease P/MRP 30kDa subunit	96					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ribonuclease P activity (GO:0004526)			central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)	8						AACTTCTTCAAGGGCCCGGCT	0.323																																					p.R96G		Atlas-SNP	.											.	RPP30	45	.	0			c.A286G						.						94	98	97					10																	92638835		2203	4298	6501	SO:0001583	missense	10556	exon5			TCTTCAAGGGCCC	BC006991	CCDS7411.1, CCDS44458.1	10q23.32-q23.33	2012-05-21			ENSG00000148688	ENSG00000148688			17688	protein-coding gene	gene with protein product		606115				9037013, 9308968	Standard	NM_006413		Approved	TSG15	uc001khd.2	P78346	OTTHUMG00000018733	ENST00000371703.3:c.286A>G	chr10.hg19:g.92638835A>G	ENSP00000360768:p.Arg96Gly	129.0	0.0		81.0	21.0	NM_006413	B2R799|E9PB02	Missense_Mutation	SNP	ENST00000371703.3	hg19	CCDS7411.1	.	.	.	.	.	.	.	.	.	.	A	9.820	1.185527	0.21870	.	.	ENSG00000148688	ENST00000371703;ENST00000413330;ENST00000371705;ENST00000277882;ENST00000414836	T;T;T	0.43688	0.95;0.94;0.94	5.64	4.54	0.55810	Polymerase/histidinol phosphatase-like (1);	0.331224	0.36374	N	0.002637	T	0.24160	0.0585	L	0.27053	0.805	0.28451	N	0.91634	B;B;B	0.33318	0.007;0.086;0.408	B;B;B	0.28305	0.015;0.056;0.088	T	0.09952	-1.0651	10	0.23302	T	0.38	-13.7417	7.1899	0.25821	0.6981:0.1784:0.0:0.1234	.	96;96;96	B4DJR3;P78346;E9PB02	.;RPP30_HUMAN;.	G	96;96;96;118;50	ENSP00000360768:R96G;ENSP00000389182:R96G;ENSP00000277882:R118G	ENSP00000277882:R118G	R	+	1	2	RPP30	92628815	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.303000	0.33470	2.152000	0.67230	0.528000	0.53228	AGG	.	.		0.323	RPP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049347.1	NM_006413		G	92638835	A	G	92638835	3	3	90	1	0	0	0	0	1	0	0	0	13627	63	3	2	304	2	RPP30	10	92638835	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10		92638835	42895912	49	12012										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124329720	124329720	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gcccttggatccaactgtagCagaaggtaaggtctattatg	11	8	1	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr10:124329720C>T	ENST00000338354.3	+	3	240	c.134C>T	c.(133-135)gCa>gTa	p.A45V	DMBT1_ENST00000359586.6_Missense_Mutation_p.A45V|DMBT1_ENST00000344338.3_Missense_Mutation_p.A45V|DMBT1_ENST00000368909.3_Missense_Mutation_p.A45V|DMBT1_ENST00000330163.4_Missense_Mutation_p.A45V|DMBT1_ENST00000368956.2_Missense_Mutation_p.A45V|DMBT1_ENST00000368955.3_Missense_Mutation_p.A45V			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	45					defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCAACTGTAGCAGAAGGTAAG	0.532																																					p.A45V	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.C134T						.						118	118	118					10																	124329720		1873	4107	5980	SO:0001583	missense	1755	exon3			CTGTAGCAGAAGG		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.134C>T	chr10.hg19:g.124329720C>T	ENSP00000342210:p.Ala45Val	173.0	0.0		175.0	47.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	C	7.673	0.687306	0.14973	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.25912	1.85;1.83;1.77;1.85;1.83;1.77;1.8	1.52	-2.51	0.06365	.	.	.	.	.	T	0.17916	0.0430	N	0.14661	0.345	0.09310	N	1	P;P;B;D;P	0.58620	0.73;0.813;0.0;0.983;0.801	B;B;B;P;B	0.56042	0.194;0.219;0.0;0.79;0.36	T	0.09596	-1.0667	9	0.23891	T	0.37	.	2.0989	0.03675	0.2501:0.3872:0.0:0.3628	.	45;45;45;45;45	F8WEF7;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	V	45	ENSP00000342210:A45V;ENSP00000343175:A45V;ENSP00000327747:A45V;ENSP00000357905:A45V;ENSP00000357951:A45V;ENSP00000357952:A45V;ENSP00000352593:A45V	ENSP00000331522:A45V	A	+	2	0	DMBT1	124319710	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	-1.454000	0.02381	-0.671000	0.05274	-1.206000	0.01644	GCA	.	.		0.532	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		T	124329720	C	T	124329720	3	4	90	1	0	0	0	0	1	0	0	0	4579	710	25	3	144	3	DMBT1	10	124329720	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	31690885	124329720	11205027	50	12013										
OR52M1	119772	hgsc.bcm.edu	37	chr11	4567048	4567048	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tgagcatcggctttctggtgTtgatcctggactcagtggct	13	9	2	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr11:4567048T>C	ENST00000360213.1	+	1	628	c.628T>C	c.(628-630)Ttg>Ctg	p.L210L		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	210						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTTTCTGGTGTTGATCCTGGA	0.522																																					p.L210L		Atlas-SNP	.											.	OR52M1	53	.	0			c.T628C						.						259	244	249					11																	4567048		2201	4298	6499	SO:0001819	synonymous_variant	119772	exon1			CTGGTGTTGATCC	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"GPCR / Class A : Olfactory receptors"	15225	protein-coding gene	gene with protein product			"olfactory receptor, family 52, subfamily M, member 1 pseudogene"	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.628T>C	chr11.hg19:g.4567048T>C		324.0	0.0		374.0	78.0	NM_001004137		Silent	SNP	ENST00000360213.1	hg19	CCDS31353.1																																																																																			.	.		0.522	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137		C	4567048	T	C	4567048	2	2	90	1	0	0	0	0	0	0	0	1	11135	1722	60	2		2	OR52M1	11	4567048	Silent	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10		4567048	130439468	51	12014										
SLC17A6	57084	hgsc.bcm.edu	37	chr11	22398984	22398984	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ggcagtatgtcttcctgatcGctgccctagtccactatggt	10	12	1	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr11:22398984G>A	ENST00000263160.3	+	12	1884	c.1447G>A	c.(1447-1449)Gct>Act	p.A483T		NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	483					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						CTTCCTGATCGCTGCCCTAGT	0.458																																					p.A483T		Atlas-SNP	.											.	SLC17A6	135	.	0			c.G1447A						.						87	81	83					11																	22398984		2203	4300	6503	SO:0001583	missense	57084	exon12			CTGATCGCTGCCC	AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"Solute carriers"	16703	protein-coding gene	gene with protein product	"vesicular glutamate transporter 2", "differentiation-associated Na-dependent inorganic phosphate cotransporter"	607563	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.1447G>A	chr11.hg19:g.22398984G>A	ENSP00000263160:p.Ala483Thr	342.0	0.0		319.0	62.0	NM_020346	A6NKS2	Missense_Mutation	SNP	ENST00000263160.3	hg19	CCDS7856.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.503201	0.85176	.	.	ENSG00000091664	ENST00000263160;ENST00000546171	T	0.54675	0.56	5.98	5.98	0.97165	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.63474	0.2514	L	0.38649	1.16	0.80722	D	1	D	0.76494	0.999	P	0.62184	0.899	T	0.57768	-0.7754	10	0.37606	T	0.19	.	20.4434	0.99119	0.0:0.0:1.0:0.0	.	483	Q9P2U8	VGLU2_HUMAN	T	483;371	ENSP00000263160:A483T	ENSP00000263160:A483T	A	+	1	0	SLC17A6	22355560	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	9.869000	0.99810	2.838000	0.97847	0.655000	0.94253	GCT	.	.		0.458	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		A	22398984	G	A	22398984	3	1	90	1	0	0	0	0	1	0	0	0	14436	1087	38	1	1493	1	SLC17A6	11	22398984	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	17831936	22398984	112607532	52	12015										
ACCS	84680	hgsc.bcm.edu	37	chr11	44089261	44089262	+	Frame_Shift_Ins	INS	-	-	G													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aggacctgggcagtagccatINSggggaagatctggaaggaga							TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr11:44089261_44089262insG	ENST00000263776.8	+	2	518_519	c.84_85insG	c.(85-87)gggfs	p.G29fs	ACCS_ENST00000533208.1_3'UTR|ACCS_ENST00000432284.2_Frame_Shift_Ins_p.G29fs	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	29					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						GCAGTAGCCATGGGGAAGATCT	0.55																																					p.H28fs	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-Indel,Pindel	.											.	ACCS	64	.	0			c.84_85insG						.																																			SO:0001589	frameshift_variant	84680	exon2			.	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.88dupG	chr11.hg19:g.44089265_44089265dupG	ENSP00000263776:p.Gly29fs	165.0	0.0		143.0	16.0	NM_032592	B4E219|Q8WUL4|Q96LX5	Frame_Shift_Ins	INS	ENST00000263776.8	hg19	CCDS7907.1																																																																																			.	.		0.55	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		G	44089262	-	G	44089261	7	5	90	1	0	1	1	0	0	0	0	0	133	1461	51	0	86	0	ACCS	11	44089261	Frame_Shift_Ins	INS	-	TCGA-DD-A118-01A-11D-A12Z-10	21690277	44089261	90917255	53	12016										
ZDHHC5	25921	hgsc.bcm.edu	37	chr11	57466174	57466174	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tttcacttcgatccactatcCagtggctcacgctcctccag	6	16	2	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr11:57466174C>T	ENST00000287169.3	+	11	2628	c.1266C>T	c.(1264-1266)tcC>tcT	p.S422S	ZDHHC5_ENST00000527985.1_Silent_p.S369S	NM_015457.2	NP_056272.2	Q9C0B5	ZDHC5_HUMAN	zinc finger, DHHC-type containing 5	422					protein palmitoylation (GO:0018345)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(3)|lung(5)|skin(1)	18						ATCCACTATCCAGTGGCTCAC	0.577																																					p.S422S		Atlas-SNP	.											.	ZDHHC5	49	.	0			c.C1266T						.						86	76	79					11																	57466174		2201	4296	6497	SO:0001819	synonymous_variant	25921	exon11			ACTATCCAGTGGC	AB051535	CCDS7965.1	11q13.1	2008-05-02			ENSG00000156599	ENSG00000156599		"Zinc fingers, DHHC-type"	18472	protein-coding gene	gene with protein product		614586				11214970	Standard	NM_015457		Approved	KIAA1748, ZNF375	uc001nkx.1	Q9C0B5	OTTHUMG00000167198	ENST00000287169.3:c.1266C>T	chr11.hg19:g.57466174C>T		111.0	0.0		117.0	19.0	NM_015457	Q2TGF0|Q6ZMF0|Q8TAK8|Q9H923|Q9UFI7	Silent	SNP	ENST00000287169.3	hg19	CCDS7965.1																																																																																			.	.		0.577	ZDHHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393694.1	NM_015457		T	57466174	C	T	57466174	2	4	90	1	0	0	0	0	0	0	0	1	17633	581	21	3		3	ZDHHC5	11	57466174	Silent	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	13376913	57466174	77540342	54	12017										
LTBP3	4054	hgsc.bcm.edu	37	chr11	65315205	65315205	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccacgtgcaggcggtagccgCggttgcagtggcaattgtag	16	10	0	0	rs150534522		TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr11:65315205C>G	ENST00000301873.5	-	13	2202	c.1934G>C	c.(1933-1935)cGc>cCc	p.R645P	LTBP3_ENST00000536982.1_Missense_Mutation_p.R271P|LTBP3_ENST00000532932.1_Missense_Mutation_p.R75P|LTBP3_ENST00000322147.4_Missense_Mutation_p.R645P|LTBP3_ENST00000529189.1_5'Flank	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	645	Cys-rich.|EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						GCGGTAGCCGCGGTTGCAGTG	0.711																																					p.R645P		Atlas-SNP	.											LTBP3,colon,carcinoma,0,1	LTBP3	55	.	0			c.G1934C						.						9	11	10					11																	65315205		2165	4255	6420	SO:0001583	missense	4054	exon13			TAGCCGCGGTTGC	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.1934G>C	chr11.hg19:g.65315205C>G	ENSP00000301873:p.Arg645Pro	30.0	2.0		54.0	8.0	NM_001130144	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	hg19	CCDS44647.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.804536	0.31869	.	.	ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000532932;ENST00000536982;ENST00000530866	D;D;D;D;D	0.91945	-2.94;-2.94;-2.94;-2.94;-2.94	4.39	4.39	0.52855	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.344897	0.30999	N	0.008453	D	0.84051	0.5387	N	0.01076	-1.035	0.30505	N	0.77	D;B;B;P;B;B	0.67145	0.996;0.013;0.005;0.8;0.004;0.114	P;B;B;B;B;B	0.62491	0.903;0.011;0.003;0.301;0.007;0.135	T	0.79176	-0.1911	10	0.18710	T	0.47	.	9.6673	0.39992	0.2078:0.7922:0.0:0.0	.	556;271;528;645;645;75	E9PKW1;F5GWC4;B9EG76;Q9NS15;Q9NS15-2;E9PJR2	.;.;.;LTBP3_HUMAN;.;.	P	645;645;75;271;556	ENSP00000326647:R645P;ENSP00000301873:R645P;ENSP00000435530:R75P;ENSP00000441912:R271P;ENSP00000435276:R556P	ENSP00000301873:R645P	R	-	2	0	LTBP3	65071781	0.006000	0.16342	1.000000	0.80357	0.802000	0.45316	-0.053000	0.11846	2.272000	0.75746	0.313000	0.20887	CGC	.	.		0.711	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070		G	65315205	C	G	65315205	3	3	90	1	0	0	0	0	1	0	0	0	9084	768	27	4	2041	4	LTBP3	11	65315205	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	7849031	65315205	69691311	55	12018										
LRRC32	2615	hgsc.bcm.edu	37	chr11	76371941	76371941	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ggctgggaggccgtctgaaaGgcctcgatgctgttgcagct	16	10	1	1	rs180783243		TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr11:76371941G>T	ENST00000407242.2	-	3	938	c.696C>A	c.(694-696)gcC>gcA	p.A232A	AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000260061.5_Silent_p.A232A|LRRC32_ENST00000404995.1_Silent_p.A232A|LRRC32_ENST00000464145.1_Intron	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	232					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cytokine secretion (GO:0050710)|positive regulation of gene expression (GO:0010628)	integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						CCGTCTGAAAGGCCTCGATGC	0.617																																					p.A232A		Atlas-SNP	.											.	LRRC32	74	.	0			c.C696A						.						44	47	46					11																	76371941		2200	4292	6492	SO:0001819	synonymous_variant	2615	exon3			CTGAAAGGCCTCG	Z24680	CCDS8245.1	11q13.5-q14	2008-02-05	2005-02-25	2005-02-25	ENSG00000137507	ENSG00000137507			4161	protein-coding gene	gene with protein product		137207	"glycoprotein A repetitions predominant"	D11S833E, GARP		8180135, 1543912	Standard	NM_005512		Approved		uc001oxq.4	Q14392	OTTHUMG00000133687	ENST00000407242.2:c.696C>A	chr11.hg19:g.76371941G>T		85.0	0.0		80.0	20.0	NM_005512	Q86V06	Silent	SNP	ENST00000407242.2	hg19	CCDS8245.1																																																																																			.	G|0.999;C|0.001		0.617	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512		T	76371941	G	T	76371941	2	4	90	1	0	0	0	0	0	0	0	1	8996	987	35	3		3	LRRC32	11	76371941	Silent	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	11056736	76371941	58634575	56	12019										
ATM	472	hgsc.bcm.edu	37	chr11	108218075	108218075	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aaatgagcagtcagcagaacTtgtacatatagatctaggta	9	6	2	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr11:108218075T>A	ENST00000452508.2	+	60	8843	c.8654T>A	c.(8653-8655)cTt>cAt	p.L2885H	ATM_ENST00000525178.1_3'UTR|C11orf65_ENST00000526725.1_Intron|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.L2885H			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2885	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TCAGCAGAACTTGTACATATA	0.308			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.L2885H		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.T8654A						.						94	99	97					11																	108218075		2201	4295	6496	SO:0001583	missense	472	exon59	Familial Cancer Database	AT, Louis-Bar syndrome	CAGAACTTGTACA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.8654T>A	chr11.hg19:g.108218075T>A	ENSP00000388058:p.Leu2885His	247.0	0.0		257.0	125.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.347909	0.82022	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	D;D	0.83992	-1.79;-1.79	5.52	5.52	0.82312	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.93074	0.7795	M	0.92367	3.3	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94664	0.7851	10	0.87932	D	0	.	15.6511	0.77095	0.0:0.0:0.0:1.0	.	2885	Q13315	ATM_HUMAN	H	2885	ENSP00000278616:L2885H;ENSP00000388058:L2885H	ENSP00000278616:L2885H	L	+	2	0	ATM	107723285	1.000000	0.71417	0.997000	0.53966	0.967000	0.64934	7.461000	0.80834	2.090000	0.63153	0.454000	0.30748	CTT	.	.		0.308	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108218075	T	A	108218075	3	1	90	1	0	0	0	0	1	0	0	0	1109	1609	56	4	8884	4	ATM	11	108218075	Missense_Mutation	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	31846134	108218075	26788441	57	12020										
KRT1	3848	hgsc.bcm.edu	37	chr12	53073845	53073846	+	Frame_Shift_Ins	INS	-	-	C													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	caccaccaccaaagccaccaINSccaccataaccaccaccaaa							TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr12:53073845_53073846insC	ENST00000252244.3	-	1	345_346	c.287_288insG	c.(286-288)ggtfs	p.G96fs		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	96	Gly/Phe/Ser-rich.|Head.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						caaagccaccaccaccataacc	0.55																																					p.G96fs		Atlas-INDEL	.											.	KRT1	110	.	0			c.288_289insG						.																																			SO:0001589	frameshift_variant	3848	exon1			.	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.288dupG	chr12.hg19:g.53073847_53073847dupC	ENSP00000252244:p.Gly96fs	540.0	0.0		584.0	38.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Frame_Shift_Ins	INS	ENST00000252244.3	hg19	CCDS8836.1																																																																																			.	.		0.55	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		C	53073846	-	C	53073845	7	5	90	1	0	1	1	0	0	0	0	0	8456	146	6	0	1682	0	KRT1	12	53073845	Frame_Shift_Ins	INS	-	TCGA-DD-A118-01A-11D-A12Z-10		53073845	80778050	58	12021										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56487230	56487230	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gcgtatctatataagtgccaAtaggcagctctgctaccacc	8	12	2	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr12:56487230A>G	ENST00000267101.3	+	12	1816	c.1376A>G	c.(1375-1377)aAt>aGt	p.N459S	ERBB3_ENST00000415288.2_Missense_Mutation_p.N400S|ERBB3_ENST00000450146.2_Intron|ERBB3_ENST00000553131.1_5'Flank	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	459					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			ATAAGTGCCAATAGGCAGCTC	0.512																																					p.N459S		Atlas-SNP	.											.	ERBB3	350	.	0			c.A1376G						.						93	94	94					12																	56487230		2203	4300	6503	SO:0001583	missense	2065	exon12			GTGCCAATAGGCA	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.1376A>G	chr12.hg19:g.56487230A>G	ENSP00000267101:p.Asn459Ser	142.0	0.0		94.0	24.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.773507	0.90108	.	.	ENSG00000065361	ENST00000267101;ENST00000415288	D;D	0.91631	-2.88;-2.88	5.16	5.16	0.70880	EGF receptor, L domain (1);	0.000000	0.64402	D	0.000002	D	0.96926	0.8996	M	0.93375	3.41	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.97855	1.0277	10	0.87932	D	0	.	14.1129	0.65134	1.0:0.0:0.0:0.0	.	459;459	B4DGQ7;P21860	.;ERBB3_HUMAN	S	459;400	ENSP00000267101:N459S;ENSP00000408340:N400S	ENSP00000267101:N459S	N	+	2	0	ERBB3	54773497	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	8.331000	0.90022	2.162000	0.67917	0.533000	0.62120	AAT	.	.		0.512	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			G	56487230	A	G	56487230	3	3	90	1	0	0	0	0	1	0	0	0	5210	101	4	2	1553	2	ERBB3	12	56487230	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	3413385	56487230	77364665	59	12022										
ZDHHC17	23390	hgsc.bcm.edu	37	chr12	77203532	77203532	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gttgtgcaactaatgaaataTggtgcagatccttcattaat	8	6	1	2	rs376206630		TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr12:77203532T>C	ENST00000426126.2	+	5	1087	c.438T>C	c.(436-438)taT>taC	p.Y146Y	ZDHHC17_ENST00000359019.4_Silent_p.Y96Y|ZDHHC17_ENST00000334822.5_Silent_p.Y146Y	NM_015336.2	NP_056151.2	Q8IUH5	ZDH17_HUMAN	zinc finger, DHHC-type containing 17	146					lipoprotein transport (GO:0042953)|magnesium ion transport (GO:0015693)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein palmitoylation (GO:0018345)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(3)|liver(2)|lung(14)	23						TAATGAAATATGGTGCAGATC	0.368																																					p.Y146Y		Atlas-SNP	.											.	ZDHHC17	45	.	0			c.T438C						.	T		0,3742		0,0,1871	97	89	92		438	5.5	1	12		92	1,8217		0,1,4108	no	coding-synonymous	ZDHHC17	NM_015336.2		0,1,5979	CC,CT,TT		0.0122,0.0,0.0084		146/633	77203532	1,11959	1871	4109	5980	SO:0001819	synonymous_variant	23390	exon5			GAAATATGGTGCA	AB023163	CCDS44946.1	12q21.2	2013-01-10				ENSG00000186908		"Zinc fingers, DHHC-type", "Ankyrin repeat domain containing"	18412	protein-coding gene	gene with protein product		607799				9700202, 18794299	Standard	NM_015336		Approved	HIP14, HYPH, KIAA0946	uc001syk.1	Q8IUH5	OTTHUMG00000169917	ENST00000426126.2:c.438T>C	chr12.hg19:g.77203532T>C		71.0	0.0		90.0	26.0	NM_015336	B4DR39|O75407|Q7Z2I0|Q86W89|Q86YK0|Q9P088|Q9UPZ8	Silent	SNP	ENST00000426126.2	hg19	CCDS44946.1																																																																																			.	.		0.368	ZDHHC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406555.1	NM_015336		C	77203532	T	C	77203532	2	2	90	1	0	0	0	0	0	0	0	1	17622	1471	51	2		2	ZDHHC17	12	77203532	Silent	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	20716302	77203532	56648363	60	12023										
DUSP6	1848	hgsc.bcm.edu	37	chr12	89743032	89743032	+	Nonstop_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aggaggggtgtggggtctttCacgtagattgcagagagtcc	17	6	2	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr12:89743032C>A	ENST00000279488.7	-	3	2376	c.1145G>T	c.(1144-1146)tGa>tTa	p.*382L	DUSP6_ENST00000547140.1_5'Flank|DUSP6_ENST00000547291.1_Nonstop_Mutation_p.*257L|DUSP6_ENST00000308385.6_Nonstop_Mutation_p.*236L	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6	0					cell differentiation (GO:0030154)|dorsal/ventral pattern formation (GO:0009953)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|regulation of endodermal cell fate specification (GO:0042663)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of heart growth (GO:0060420)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			large_intestine(5)|lung(8)|skin(2)|urinary_tract(1)	16						TGGGGTCTTTCACGTAGATTG	0.542																																					p.X382L	Colon(132;3456 5224)	Atlas-SNP	.											.	DUSP6	30	.	0			c.G1145T						.						115	114	114					12																	89743032		2203	4300	6503	SO:0001578	stop_lost	1848	exon3			GTCTTTCACGTAG	BC037236	CCDS9033.1, CCDS9034.1	12q22-q23	2011-06-09				ENSG00000139318		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3072	protein-coding gene	gene with protein product		602748				8626780, 9205128	Standard	NM_001946		Approved	MKP-3, PYST1	uc001tay.3	Q16828		ENST00000279488.7:c.1145G>T	chr12.hg19:g.89743032C>A		83.0	0.0		80.0	20.0	NM_001946	O75109|Q53Y75|Q9BSH6	Missense_Mutation	SNP	ENST00000279488.7	hg19	CCDS9033.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.720300	0.68959	.	.	ENSG00000139318	ENST00000279488;ENST00000308385;ENST00000547291	.	.	.	5.98	5.98	0.97165	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4581	0.99154	0.0:1.0:0.0:0.0	.	.	.	.	L	382;236;257	.	.	X	-	2	2	DUSP6	88267163	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.745000	0.85046	2.835000	0.97688	0.650000	0.86243	TGA	.	.		0.542	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	NM_001946, NM_022652		A	89743032	C	A	89743032	4	1	90	1	0	0	0	0	0	0	0	0	4831	837	29	3	4	3	DUSP6	12	89743032	Nonstop_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	12539500	89743032	44108863	61	12024										
OAS1	4938	hgsc.bcm.edu	37	chr12	113344971	113344971	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tcatctgtgggttcctgaagGaaaggtgcttccgaggtagc	14	8	2	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr12:113344971G>T	ENST00000202917.5	+	1	390	c.127G>T	c.(127-129)Gaa>Taa	p.E43*	RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000553185.1_Nonsense_Mutation_p.E43*|OAS1_ENST00000452357.2_Nonsense_Mutation_p.E43*|OAS1_ENST00000551241.1_Nonsense_Mutation_p.E43*|OAS1_ENST00000445409.2_Nonsense_Mutation_p.E43*	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	43	Interaction with dsRNA.				cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						GTTCCTGAAGGAAAGGTGCTT	0.522																																					p.E43X		Atlas-SNP	.											.	OAS1	128	.	0			c.G127T						.						233	198	210					12																	113344971		2203	4300	6503	SO:0001587	stop_gained	4938	exon1			CTGAAGGAAAGGT	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"2',5'-oligoadenylate synthetase 1 (40-46 kD)"	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.127G>T	chr12.hg19:g.113344971G>T	ENSP00000202917:p.Glu43*	332.0	0.0		305.0	92.0	NM_001032409	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Nonsense_Mutation	SNP	ENST00000202917.5	hg19	CCDS41838.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.679336	0.88542	.	.	ENSG00000089127	ENST00000202917;ENST00000445409;ENST00000452357;ENST00000550883;ENST00000549820;ENST00000551241;ENST00000377508;ENST00000553185;ENST00000550689	.	.	.	5.26	5.26	0.73747	.	0.116612	0.38720	N	0.001581	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-46.8389	14.245	0.65983	0.0:0.0:1.0:0.0	.	.	.	.	X	43;43;43;43;43;43;43;43;39	.	ENSP00000202917:E43X	E	+	1	0	OAS1	111829354	0.992000	0.36948	0.996000	0.52242	0.424000	0.31475	1.935000	0.40173	2.746000	0.94184	0.655000	0.94253	GAA	.	.		0.522	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2			T	113344971	G	T	113344971	4	4	90	1	0	0	0	0	0	1	0	0	10808	1175	41	3	129	3	OAS1	12	113344971	Nonsense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	23601939	113344971	20506924	62	12025										
PIWIL1	9271	hgsc.bcm.edu	37	chr12	130830386	130830386	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	catgatcttggtgtgaatacAaggcagaacctagaccatgt	10	8	1	4			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr12:130830386A>G	ENST00000245255.3	+	4	551	c.279A>G	c.(277-279)acA>acG	p.T93T		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	93					gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		GTGTGAATACAAGGCAGAACC	0.378																																					p.T93T		Atlas-SNP	.											.	PIWIL1	157	.	0			c.A279G						.						138	130	133					12																	130830386		2203	4300	6503	SO:0001819	synonymous_variant	9271	exon4			GAATACAAGGCAG	AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.279A>G	chr12.hg19:g.130830386A>G		153.0	0.0		161.0	28.0	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Silent	SNP	ENST00000245255.3	hg19	CCDS9268.1																																																																																			.	.		0.378	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			G	130830386	A	G	130830386	2	3	90	1	0	0	0	0	0	0	0	1	11966	117	5	2		2	PIWIL1	12	130830386	Silent	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	17485415	130830386	3021509	63	12026										
POLE	5426	hgsc.bcm.edu	37	chr12	133240672	133240672	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tggtcgtcttgaagacaaaaTtttctgggaagctgttgggc	13	6	2	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr12:133240672T>G	ENST00000320574.5	-	23	2667	c.2624A>C	c.(2623-2625)aAt>aCt	p.N875T	POLE_ENST00000535270.1_Missense_Mutation_p.N848T	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	875					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GAAGACAAAATTTTCTGGGAA	0.522								DNA polymerases (catalytic subunits)																													p.N875T		Atlas-SNP	.											.	POLE	416	.	0			c.A2624C						.						193	191	192					12																	133240672		2203	4300	6503	SO:0001583	missense	5426	exon23			ACAAAATTTTCTG		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.2624A>C	chr12.hg19:g.133240672T>G	ENSP00000322570:p.Asn875Thr	244.0	0.0		214.0	59.0	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	hg19	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.661486	0.67700	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577	T;T;T;T	0.14893	4.08;4.08;4.09;2.47	5.57	5.57	0.84162	DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.000000	0.85682	D	0.000000	T	0.35335	0.0928	M	0.70787	2.145	0.80722	D	1	D;P	0.53312	0.959;0.887	P;P	0.54346	0.749;0.733	T	0.12372	-1.0550	10	0.72032	D	0.01	.	15.7723	0.78180	0.0:0.0:0.0:1.0	.	848;875	F5H1D6;Q07864	.;DPOE1_HUMAN	T	875;886;848;655;810	ENSP00000322570:N875T;ENSP00000406383:N886T;ENSP00000445753:N848T;ENSP00000442519:N655T	ENSP00000322570:N875T	N	-	2	0	POLE	131750745	1.000000	0.71417	1.000000	0.80357	0.193000	0.23685	7.990000	0.88215	2.133000	0.65898	0.519000	0.50382	AAT	.	.		0.522	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		G	133240672	T	G	133240672	3	3	90	1	0	0	0	0	1	0	0	0	12205	1493	52	5	4344	5	POLE	12	133240672	Missense_Mutation	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	2410286	133240672	611223	64	12027										
REC8	79711	hgsc.bcm.edu	37	chr14	24646590	24646590	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccacctccagctcctgcagaGtaagggcaagaactcctaga	9	14	0	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr14:24646590G>T	ENST00000354464.6	-	0	3646				REC8_ENST00000559919.1_Splice_Site|REC8_ENST00000311457.3_Splice_Site	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4						DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CTCCTGCAGAGTAAGGGCAAG	0.547																																					.		Atlas-SNP	.											.	REC8	47	.	0			c.734+1G>T						.						86	88	87					14																	24646590		1941	4134	6075	SO:0001628	intergenic_variant	9985	exon10			TGCAGAGTAAGGG	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"Importins"	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801		chr14.hg19:g.24646590G>T		249.0	0.0		220.0	51.0	NM_005132	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Splice_Site	SNP	ENST00000354464.6	hg19	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.841284	0.51057	.	.	ENSG00000100918	ENST00000311457;ENST00000447460	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7542	0.62926	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	REC8	23716430	0.999000	0.42202	0.957000	0.39632	0.245000	0.25701	4.453000	0.60061	2.630000	0.89119	0.561000	0.74099	.	.	.		0.547	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		T	24646590	G	T	24646590	1	4	90	0	1	0	0	0	0	0	0	0	13214	1043	36	3		3	REC8	14	24646590	IGR	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10		24646590	82702950	65	12028										
NFATC4	4776	hgsc.bcm.edu	37	chr14	24845640	24845640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cccatgaagaccctgcttgcGaaactccttacctatcagaa	6	14	1	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr14:24845640G>A	ENST00000250373.4	+	9	2338	c.2197G>A	c.(2197-2199)Gaa>Aaa	p.E733K	NFATC4_ENST00000553469.1_Missense_Mutation_p.E765K|NFATC4_ENST00000555167.1_Missense_Mutation_p.E268K|NFATC4_ENST00000556759.1_Missense_Mutation_p.E268K|NFATC4_ENST00000424781.2_Missense_Mutation_p.E746K|NFATC4_ENST00000557451.1_Missense_Mutation_p.E663K|NFATC4_ENST00000554050.1_Missense_Mutation_p.E733K|NFATC4_ENST00000554966.1_Missense_Mutation_p.E746K|NFATC4_ENST00000553879.1_Missense_Mutation_p.E663K|NFATC4_ENST00000539237.2_Missense_Mutation_p.E765K|NFATC4_ENST00000554344.1_Missense_Mutation_p.E663K|NFATC4_ENST00000554473.1_Missense_Mutation_p.E268K|NFATC4_ENST00000554591.1_Missense_Mutation_p.E796K|NFATC4_ENST00000555453.1_Missense_Mutation_p.E721K|NFATC4_ENST00000422617.3_Missense_Mutation_p.E721K|NFATC4_ENST00000553708.1_Missense_Mutation_p.E733K|NFATC4_ENST00000555393.1_Missense_Mutation_p.E21K|NFATC4_ENST00000556169.1_Missense_Mutation_p.E721K|NFATC4_ENST00000557767.1_Missense_Mutation_p.E21K|NFATC4_ENST00000555590.1_Missense_Mutation_p.E746K|NFATC4_ENST00000413692.2_Missense_Mutation_p.E796K|NFATC4_ENST00000554661.1_Missense_Mutation_p.E663K|NFATC4_ENST00000556279.1_Missense_Mutation_p.E765K|NFATC4_ENST00000555802.1_Missense_Mutation_p.E21K	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	733	Pro-rich.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		CCCTGCTTGCGAAACTCCTTA	0.617																																					p.E796K		Atlas-SNP	.											.	NFATC4	115	.	0			c.G2386A						.						59	63	62					14																	24845640		2203	4300	6503	SO:0001583	missense	4776	exon10			GCTTGCGAAACTC	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"Nuclear factor of activated T-cells"	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.2197G>A	chr14.hg19:g.24845640G>A	ENSP00000250373:p.Glu733Lys	147.0	0.0		108.0	23.0	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Missense_Mutation	SNP	ENST00000250373.4	hg19	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.021647	0.35701	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000250373;ENST00000553708;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453;ENST00000554473;ENST00000556759;ENST00000555167;ENST00000557767;ENST00000555393;ENST00000555802	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.56776	3.26;3.26;3.28;3.27;3.27;3.27;3.28;3.27;3.28;3.29;3.27;2.96;2.96;2.96;2.95;2.95;2.95;2.96;1.55;1.53;1.52;0.44;0.47	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000017	T	0.32406	0.0828	N	0.19112	0.55	0.27737	N	0.944606	B;B;B;B;B;B;B;B;B;B;B;B;B	0.33198	0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.279	B;B;B;B;B;B;B;B;B;B;B;B;B	0.26770	0.03;0.044;0.044;0.044;0.044;0.044;0.044;0.044;0.073;0.073;0.073;0.044;0.02	T	0.13335	-1.0513	10	0.09590	T	0.72	-5.1132	13.9397	0.64048	0.0:0.0:1.0:0.0	.	721;721;765;765;746;746;746;796;796;721;765;796;733	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-5;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	K	796;796;746;746;746;765;765;765;733;733;733;663;663;663;721;663;721;721;268;268;268;21;21;21	ENSP00000388910:E796K;ENSP00000452039:E796K;ENSP00000451224:E746K;ENSP00000450644:E746K;ENSP00000388668:E746K;ENSP00000439350:E765K;ENSP00000452270:E765K;ENSP00000451502:E765K;ENSP00000451151:E733K;ENSP00000250373:E733K;ENSP00000450590:E733K;ENSP00000452349:E663K;ENSP00000450469:E663K;ENSP00000450733:E663K;ENSP00000451454:E721K;ENSP00000451284:E663K;ENSP00000396788:E721K;ENSP00000450686:E721K;ENSP00000450810:E268K;ENSP00000451183:E268K;ENSP00000451395:E268K;ENSP00000451801:E21K;ENSP00000451590:E21K	ENSP00000250373:E733K	E	+	1	0	NFATC4	23915480	0.813000	0.29090	0.997000	0.53966	0.918000	0.54935	2.738000	0.47401	2.667000	0.90743	0.561000	0.74099	GAA	.	.		0.617	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554		A	24845640	G	A	24845640	3	1	90	1	0	0	0	0	1	0	0	0	10374	1059	37	1	2424	1	NFATC4	14	24845640	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	199050	24845640	82503900	66	12029										
C14orf39	317761	hgsc.bcm.edu	37	chr14	60945061	60945061	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ataaacagtaaattggtcctGcatataatcttcatgtttac	5	7	2	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr14:60945061G>C	ENST00000321731.3	-	5	439	c.280C>G	c.(280-282)Cag>Gag	p.Q94E		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	94					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		AATTGGTCCTGCATATAATCT	0.279																																					p.Q94E		Atlas-SNP	.											.	C14orf39	79	.	0			c.C280G						.						76	75	76					14																	60945061		2201	4295	6496	SO:0001583	missense	317761	exon5			GGTCCTGCATATA	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.280C>G	chr14.hg19:g.60945061G>C	ENSP00000324920:p.Gln94Glu	311.0	0.0		252.0	63.0	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	hg19	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	G	5.630	0.300924	0.10678	.	.	ENSG00000179008	ENST00000321731;ENST00000555476	T;T	0.44083	1.84;0.93	5.56	-1.51	0.08664	.	0.607073	0.16633	N	0.205985	T	0.40719	0.1128	M	0.62723	1.935	0.20821	N	0.999844	B	0.20052	0.041	B	0.20384	0.029	T	0.41484	-0.9506	10	0.49607	T	0.09	0.432	16.3264	0.82983	0.0:0.0:0.307:0.693	.	94	Q8N1H7	S6OS1_HUMAN	E	94;65	ENSP00000324920:Q94E;ENSP00000451665:Q65E	ENSP00000324920:Q94E	Q	-	1	0	C14orf39	60014814	0.997000	0.39634	0.154000	0.22540	0.030000	0.12068	0.487000	0.22356	-0.494000	0.06669	0.650000	0.86243	CAG	.	.		0.279	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		C	60945061	G	C	60945061	3	2	90	1	0	0	0	0	1	0	0	0	1774	1328	46	4	1539	4	C14orf39	14	60945061	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	36099421	60945061	46404479	67	12030										
BNIP2	663	hgsc.bcm.edu	37	chr15	59972472	59972472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ctggtccagttatagctagtAtatctgcttcaatactatca	6	9	3	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr15:59972472A>G	ENST00000607373.1	-	3	288	c.86T>C	c.(85-87)aTa>aCa	p.I29T	BNIP2_ENST00000267859.3_Missense_Mutation_p.I150T|BNIP2_ENST00000415213.2_Missense_Mutation_p.I91T	NM_004330.2	NP_004321.2	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 2	29					apoptotic process (GO:0006915)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|positive regulation of GTPase activity (GO:0043547)|positive regulation of muscle cell differentiation (GO:0051149)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)			NS(1)|large_intestine(2)|lung(5)|ovary(1)	9						TATAGCTAGTATATCTGCTTC	0.328																																					p.I150T	Ovarian(174;1936 1978 6671 8240 38212)	Atlas-SNP	.											BNIP2,caecum,carcinoma,0,1	BNIP2	27	.	0			c.T449C						.						61	57	59					15																	59972472		2188	4290	6478	SO:0001583	missense	663	exon3			GCTAGTATATCTG	U15173	CCDS10174.2	15q21.3	2008-07-18	2002-08-29		ENSG00000140299	ENSG00000140299			1083	protein-coding gene	gene with protein product		603292	"BCL2/adenovirus E1B 19kD-interacting protein 2"			7954800	Standard	NM_004330		Approved	Nip2, BNIP-2	uc010uhc.2	Q12982	OTTHUMG00000132727	ENST00000607373.1:c.86T>C	chr15.hg19:g.59972472A>G	ENSP00000475320:p.Ile29Thr	56.0	0.0		49.0	28.0	NM_004330	B4DS94	Missense_Mutation	SNP	ENST00000607373.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.080	0.999026	0.19121	.	.	ENSG00000140299	ENST00000267859;ENST00000415213	T;T	0.38887	1.11;1.11	5.54	-1.04	0.10068	.	0.483859	0.24991	N	0.033995	T	0.14227	0.0344	N	0.03115	-0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.21008	-1.0258	9	.	.	.	-3.1838	5.3354	0.15955	0.589:0.0:0.2908:0.1202	.	29;91	Q12982;Q12982-2	BNIP2_HUMAN;.	T	150;91	ENSP00000267859:I150T;ENSP00000412767:I91T	.	I	-	2	0	BNIP2	57759764	0.008000	0.16893	0.547000	0.28179	0.893000	0.52053	1.171000	0.31896	-0.171000	0.10797	0.460000	0.39030	ATA	.	.		0.328	BNIP2-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470740.1	NM_004330		G	59972472	A	G	59972472	3	3	90	1	0	0	0	0	1	0	0	0	1477	449	16	2	890	2	BNIP2	15	59972472	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10		59972472	42558920	68	12031										
PDE8A	5151	hgsc.bcm.edu	37	chr15	85660890	85660890	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aggcctttgatttatcttggTctcaaaatgtttgctcgctt	8	8	2	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr15:85660890T>A	ENST00000310298.4	+	18	1806	c.1554T>A	c.(1552-1554)ggT>ggA	p.G518G	PDE8A_ENST00000394553.1_Silent_p.G518G|PDE8A_ENST00000557957.1_Silent_p.G446G|PDE8A_ENST00000339708.5_Silent_p.G472G			O60658	PDE8A_HUMAN	phosphodiesterase 8A	518					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	TTTATCTTGGTCTCAAAATGT	0.393																																					p.G518G		Atlas-SNP	.											.	PDE8A	50	.	0			c.T1554A						.						244	218	227					15																	85660890		2203	4299	6502	SO:0001819	synonymous_variant	5151	exon17			TCTTGGTCTCAAA	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"Phosphodiesterases"	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.1554T>A	chr15.hg19:g.85660890T>A		343.0	0.0		406.0	92.0	NM_002605	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Silent	SNP	ENST00000310298.4	hg19	CCDS10336.1																																																																																			.	.		0.393	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		A	85660890	T	A	85660890	2	1	90	1	0	0	0	0	0	0	0	1	11662	1654	58	4		4	PDE8A	15	85660890	Silent	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	25688418	85660890	16870502	69	12032										
RHOT2	89941	hgsc.bcm.edu	37	chr16	723073	723074	+	Frame_Shift_Ins	INS	-	-	C													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gtgccgttctcctgtgctggINScccagccgagcccagcacca					rs200594328		TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr16:723073_723074insC	ENST00000315082.4	+	18	1787_1788	c.1673_1674insC	c.(1672-1677)ggcccafs	p.GP558fs	RHBDL1_ENST00000352681.3_5'Flank	NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	558	Miro 2.				cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				TCCTGTGCTGGCCCAGCCGAGC	0.678																																					p.G558fs		Atlas-INDEL	.											.	RHOT2	35	.	0			c.1673_1674insC						.																																			SO:0001589	frameshift_variant	89941	exon18			.	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"EF-hand domain containing"	21169	protein-coding gene	gene with protein product	"mitochondrial Rho (MIRO) GTPase 2"	613889	"chromosome 16 open reading frame 39", "ras homolog gene family, member T2"	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.1676dupC	chr16.hg19:g.723076_723076dupC	ENSP00000321971:p.Gly558fs	130.0	0.0		116.0	11.0	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Frame_Shift_Ins	INS	ENST00000315082.4	hg19	CCDS10417.1																																																																																			.	.		0.678	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769		C	723074	-	C	723073	7	5	90	1	0	1	1	0	0	0	0	0	13359	1203	42	0	1743	0	RHOT2	16	723073	Frame_Shift_Ins	INS	-	TCGA-DD-A118-01A-11D-A12Z-10		723073	89631680	70	12033										
CCDC135	84229	hgsc.bcm.edu	37	chr16	57734093	57734093	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccctccggcccacactgatgCcctaccccgagctctacaac	6	21	1	1	rs376601948		TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr16:57734093C>A	ENST00000360716.3	+	5	636	c.415C>A	c.(415-417)Ccc>Acc	p.P139T	CCDC135_ENST00000336825.8_Missense_Mutation_p.P139T|RP11-405F3.4_ENST00000563062.1_RNA|CCDC135_ENST00000394337.4_Missense_Mutation_p.P139T			Q8IY82	CC135_HUMAN		139					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						CACACTGATGCCCTACCCCGA	0.577																																					p.P139T		Atlas-SNP	.											.	CCDC135	97	.	0			c.C415A						.						150	139	143					16																	57734093		2198	4300	6498	SO:0001583	missense	84229	exon4			CTGATGCCCTACC																												ENST00000360716.3:c.415C>A	chr16.hg19:g.57734093C>A	ENSP00000353942:p.Pro139Thr	119.0	0.0		104.0	17.0	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	hg19	CCDS10787.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.725091	0.68959	.	.	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	D;D;D	0.81908	-1.55;-1.55;-1.55	5.39	4.44	0.53790	.	0.386968	0.29715	N	0.011392	D	0.90923	0.7147	M	0.85041	2.73	0.37232	D	0.905732	D;D	0.76494	0.999;0.999	D;D	0.71656	0.974;0.931	D	0.93255	0.6638	10	0.66056	D	0.02	-27.6046	12.9337	0.58301	0.0:0.9222:0.0:0.0778	.	139;139	Q8IY82-2;Q8IY82	.;CC135_HUMAN	T	139	ENSP00000377869:P139T;ENSP00000338938:P139T;ENSP00000353942:P139T	ENSP00000338938:P139T	P	+	1	0	CCDC135	56291594	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.861000	0.39438	1.275000	0.44379	0.453000	0.30009	CCC	.	.		0.577	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2			A	57734093	C	A	57734093	3	1	90	1	0	0	0	0	1	0	0	0	2771	739	26	3	425	3	CCDC135	16	57734093	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	57011020	57734093	32620660	71	12034										
MMP15	4324	hgsc.bcm.edu	37	chr16	58079051	58079051	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	agccaggcccccgatggcccGacgtggcccggccgcccttc	13	20	0	0	rs372389085		TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr16:58079051G>A	ENST00000219271.3	+	10	2496	c.1711G>A	c.(1711-1713)Gac>Aac	p.D571N		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	571					cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	CCGATGGCCCGACGTGGCCCG	0.726																																					p.D571N		Atlas-SNP	.											.	MMP15	58	.	0			c.G1711A						.						11	13	12					16																	58079051		2193	4287	6480	SO:0001583	missense	4324	exon10			TGGCCCGACGTGG	Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"matrix metalloproteinase 15 (membrane-inserted)"			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.1711G>A	chr16.hg19:g.58079051G>A	ENSP00000219271:p.Asp571Asn	28.0	0.0		70.0	32.0	NM_002428	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	hg19	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.033833	0.75504	.	.	ENSG00000102996	ENST00000219271	T	0.16597	2.33	4.65	3.68	0.42216	.	0.107611	0.64402	D	0.000009	T	0.08492	0.0211	N	0.08118	0	0.58432	D	0.999999	P	0.45827	0.867	B	0.38880	0.284	T	0.29088	-1.0023	10	0.32370	T	0.25	.	12.3011	0.54874	0.0:0.1851:0.8149:0.0	.	571	P51511	MMP15_HUMAN	N	571	ENSP00000219271:D571N	ENSP00000219271:D571N	D	+	1	0	MMP15	56636552	1.000000	0.71417	0.961000	0.40146	0.466000	0.32739	6.250000	0.72435	1.163000	0.42636	0.555000	0.69702	GAC	.	.		0.726	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		A	58079051	G	A	58079051	3	1	90	1	0	0	0	0	1	0	0	0	9663	1058	37	1	1749	1	MMP15	16	58079051	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	344958	58079051	32275702	72	12035										
VAT1L	57687	hgsc.bcm.edu	37	chr16	77896666	77896666	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gtcaagctgtggctcagctgTgttccactgtccccaacgtg	11	13	2	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr16:77896666T>A	ENST00000302536.2	+	4	754	c.601T>A	c.(601-603)Tgt>Agt	p.C201S	VAT1L_ENST00000563850.1_3'UTR	NM_020927.1	NP_065978.1	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport 1-like	201							oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(10)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24						GGCTCAGCTGTGTTCCACTGT	0.488																																					p.C201S		Atlas-SNP	.											.	VAT1L	68	.	0			c.T601A						.						182	151	162					16																	77896666		2198	4300	6498	SO:0001583	missense	57687	exon4			CAGCTGTGTTCCA	AB046796	CCDS32492.1	16q23.1	2014-09-09	2013-08-23		ENSG00000171724	ENSG00000171724			29315	protein-coding gene	gene with protein product			"vesicle amine transport protein 1 homolog (T. californica)-like"			10997877	Standard	NM_020927		Approved	KIAA1576	uc002ffg.1	Q9HCJ6	OTTHUMG00000176845	ENST00000302536.2:c.601T>A	chr16.hg19:g.77896666T>A	ENSP00000303129:p.Cys201Ser	133.0	0.0		137.0	39.0	NM_020927	Q8IYW8	Missense_Mutation	SNP	ENST00000302536.2	hg19	CCDS32492.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.054490	0.75960	.	.	ENSG00000171724	ENST00000302536	T	0.29142	1.58	5.93	5.93	0.95920	Alcohol dehydrogenase, C-terminal (1);Quinone oxidoreductase/zeta-crystallin, conserved site (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.31104	0.0786	L	0.48986	1.54	0.80722	D	1	P	0.39831	0.69	B	0.36666	0.23	T	0.06826	-1.0805	10	0.51188	T	0.08	-11.2408	16.0558	0.80805	0.0:0.0:0.0:1.0	.	201	Q9HCJ6	VAT1L_HUMAN	S	201	ENSP00000303129:C201S	ENSP00000303129:C201S	C	+	1	0	VAT1L	76454167	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	2.281000	0.76405	0.533000	0.62120	TGT	.	.		0.488	VAT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434010.1	NM_020927		A	77896666	T	A	77896666	3	1	90	1	0	0	0	0	1	0	0	0	17145	1696	59	4	615	4	VAT1L	16	77896666	Missense_Mutation	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	19817615	77896666	12458087	73	12036										
B9D1	27077	hgsc.bcm.edu	37	chr17	19261177	19261177	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gtaggggttggtgcttttaaAggtgacatcaatggggaagt	16	3	1	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr17:19261177A>T	ENST00000261499.4	-	3	363	c.220T>A	c.(220-222)Ttt>Att	p.F74I	B9D1_ENST00000461069.2_Missense_Mutation_p.F74I|B9D1_ENST00000477478.2_Silent_p.P49P|B9D1_ENST00000395616.3_Missense_Mutation_p.F74I|B9D1_ENST00000395615.1_Missense_Mutation_p.F74I|B9D1_ENST00000575403.1_Silent_p.P49P|B9D1_ENST00000268841.6_Missense_Mutation_p.F74I	NM_015681.3	NP_056496.1	Q9UPM9	B9D1_HUMAN	B9 protein domain 1	74	B9. {ECO:0000255|PROSITE- ProRule:PRU00713}.				camera-type eye development (GO:0043010)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|in utero embryonic development (GO:0001701)|neuroepithelial cell differentiation (GO:0060563)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)|vasculature development (GO:0001944)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)	hedgehog receptor activity (GO:0008158)			large_intestine(3)|urinary_tract(1)	4	all_cancers(12;2.04e-05)|all_epithelial(12;0.000806)|Hepatocellular(7;0.00345)|Breast(13;0.143)					GTGCTTTTAAAGGTGACATCA	0.572																																					p.F74I		Atlas-SNP	.											.	B9D1	8	.	0			c.T220A						.						162	129	141					17																	19261177		2203	4300	6503	SO:0001583	missense	27077	exon3			TTTTAAAGGTGAC	BC002944	CCDS11205.1, CCDS58528.1	17p11.2	2014-09-17			ENSG00000108641	ENSG00000108641			24123	protein-coding gene	gene with protein product	"endothelial precursor protein B9"	614144				21493627	Standard	NM_015681		Approved	B9, EPPB9, MKS9	uc010vyr.2	Q9UPM9	OTTHUMG00000059586	ENST00000261499.4:c.220T>A	chr17.hg19:g.19261177A>T	ENSP00000261499:p.Phe74Ile	83.0	0.0		60.0	24.0	NM_015681	Q9BU22	Missense_Mutation	SNP	ENST00000261499.4	hg19	CCDS11205.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.896219	0.91962	.	.	ENSG00000108641	ENST00000395615;ENST00000261499;ENST00000395616;ENST00000268841;ENST00000440841	T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.86356	0.5913	M	0.91920	3.255	0.80722	D	1	D	0.69078	0.997	D	0.72075	0.976	D	0.88966	0.3397	10	0.62326	D	0.03	.	13.3104	0.60376	1.0:0.0:0.0:0.0	.	74	Q9UPM9	B9D1_HUMAN	I	74;74;74;74;65	ENSP00000378977:F74I;ENSP00000261499:F74I;ENSP00000378978:F74I;ENSP00000268841:F74I;ENSP00000410835:F65I	ENSP00000261499:F74I	F	-	1	0	B9D1	19201770	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.893000	0.75649	2.019000	0.59389	0.533000	0.62120	TTT	.	.		0.572	B9D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132494.1	NM_015681		T	19261177	A	T	19261177	3	4	90	1	0	0	0	0	1	0	0	0	1277	72	3	4	414	4	B9D1	17	19261177	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10		19261177	61934033	74	12037										
NOS2	4843	hgsc.bcm.edu	37	chr17	26088234	26088234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gagccatgtgctgcagacgcCgtggtgcaggggaccctggc	17	12	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr17:26088234C>T	ENST00000313735.6	-	23	3057	c.2824G>A	c.(2824-2826)Ggc>Agc	p.G942S		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	942	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	CTGCAGACGCCGTGGTGCAGG	0.627																																					p.G942S		Atlas-SNP	.											.	NOS2	113	.	0			c.G2824A						.						55	47	50					17																	26088234		2203	4299	6502	SO:0001583	missense	4843	exon23			AGACGCCGTGGTG	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"nitric oxide synthase 2A (inducible, hepatocytes)"	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2824G>A	chr17.hg19:g.26088234C>T	ENSP00000327251:p.Gly942Ser	182.0	0.0		133.0	38.0	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	hg19	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	C	34	5.349011	0.95807	.	.	ENSG00000007171	ENST00000313735;ENST00000379105	D	0.88818	-2.43	4.76	4.76	0.60689	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);Ferredoxin reductase-type FAD-binding domain (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.000000	0.85682	D	0.000000	D	0.96738	0.8935	H	0.98133	4.155	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.98534	1.0629	10	0.87932	D	0	.	16.8272	0.85934	0.0:1.0:0.0:0.0	.	942	P35228	NOS2_HUMAN	S	942;903	ENSP00000327251:G942S	ENSP00000327251:G942S	G	-	1	0	NOS2	23112361	1.000000	0.71417	0.977000	0.42913	0.957000	0.61999	7.764000	0.85297	2.225000	0.72522	0.456000	0.33151	GGC	.	.		0.627	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		T	26088234	C	T	26088234	3	4	90	1	0	0	0	0	1	0	0	0	10552	652	23	1	657	1	NOS2	17	26088234	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	6827057	26088234	55106976	75	12038										
NFE2L1	4779	hgsc.bcm.edu	37	chr17	46128958	46128959	+	Frame_Shift_Ins	INS	-	-	C													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ggaggatttgggggctgtagINScccccccagtcagtggagac							TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr17:46128958_46128959insC	ENST00000362042.3	+	2	1094_1095	c.478_479insC	c.(478-480)gccfs	p.A160fs	NFE2L1_ENST00000585291.1_Frame_Shift_Ins_p.A160fs|NFE2L1_ENST00000357480.5_Frame_Shift_Ins_p.A160fs|NFE2L1_ENST00000361665.3_Frame_Shift_Ins_p.A160fs	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	160	Asp/Glu-rich (acidic).				anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)	p.V163fs*14(1)		cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGGGGCTGTAGCCCCCCCAGTC	0.589																																					p.A160fs		Atlas-Indel,Pindel	.											.,1	NFE2L1	60	.	1	Insertion - Frameshift(1)	kidney(1)	c.478_479insC						.																																			SO:0001589	frameshift_variant	4779	exon2			.	AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"basic leucine zipper proteins"	7781	protein-coding gene	gene with protein product		163260	"nuclear factor (erythroid-derived 2)-like 1"	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.485dupC	chr17.hg19:g.46128965_46128965dupC	ENSP00000354855:p.Ala160fs	65.0	0.0		63.0	19.0	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Frame_Shift_Ins	INS	ENST00000362042.3	hg19	CCDS11524.1																																																																																			.	.		0.589	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204		C	46128959	-	C	46128958	7	5	90	1	0	1	1	0	0	0	0	0	10376	971	34	0	480	0	NFE2L1	17	46128958	Frame_Shift_Ins	INS	-	TCGA-DD-A118-01A-11D-A12Z-10	20040724	46128958	35066252	76	12039										
GH1	2688	hgsc.bcm.edu	37	chr17	61995228	61995228	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aagacactcctgaggaactgCacgggctccagccacgactg	11	14	0	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr17:61995228C>T	ENST00000323322.5	-	4	390	c.348G>A	c.(346-348)gtG>gtA	p.V116V	GH1_ENST00000458650.2_Silent_p.V101V|GH1_ENST00000351388.4_Silent_p.V76V|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000342364.4_Intron	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	116					bone maturation (GO:0070977)|glucose transport (GO:0015758)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|growth hormone receptor binding (GO:0005131)|metal ion binding (GO:0046872)|prolactin receptor binding (GO:0005148)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	19						TGAGGAACTGCACGGGCTCCA	0.612																																					p.V116V		Atlas-SNP	.											.	GH1	39	.	0			c.G348A						.						58	60	59					17																	61995228		2203	4300	6503	SO:0001819	synonymous_variant	2688	exon4			GAACTGCACGGGC	M13438	CCDS11653.1, CCDS11654.1, CCDS45760.1	17q22-q24	2014-01-30				ENSG00000259384		"Endogenous ligands"	4261	protein-coding gene	gene with protein product	"pituitary growth hormone", "somatotropin"	139250				6306568	Standard	XM_005257218		Approved	GH-N, GHN, GH, hGH-N	uc002jdj.3	P01241		ENST00000323322.5:c.348G>A	chr17.hg19:g.61995228C>T		111.0	0.0		99.0	28.0	NM_000515	A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Silent	SNP	ENST00000323322.5	hg19	CCDS11653.1																																																																																			.	.		0.612	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515		T	61995228	C	T	61995228	2	4	90	1	0	0	0	0	0	0	0	1	6375	697	25	3		3	GH1	17	61995228	Silent	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	15866270	61995228	19199982	77	12040										
GPR142	350383	hgsc.bcm.edu	37	chr17	72368126	72368126	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cacggttgaccgctacactgCcctgtgccaccccctgcacc	8	20	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr17:72368126C>T	ENST00000335666.4	+	4	824	c.776C>T	c.(775-777)gCc>gTc	p.A259V		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	259						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						CGCTACACTGCCCTGTGCCAC	0.682																																					p.A259V		Atlas-SNP	.											.	GPR142	74	.	0			c.C776T						.						69	52	58					17																	72368126		2202	4300	6502	SO:0001583	missense	350383	exon4			ACACTGCCCTGTG	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"GPCR / Class A : Orphans"	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.776C>T	chr17.hg19:g.72368126C>T	ENSP00000335158:p.Ala259Val	76.0	0.0		61.0	13.0	NM_181790	A4CYJ8|Q86SL3	Missense_Mutation	SNP	ENST00000335666.4	hg19	CCDS11698.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.267772	0.59540	.	.	ENSG00000257008	ENST00000335666	T	0.52057	0.68	4.99	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.053906	0.64402	D	0.000001	T	0.69287	0.3094	M	0.80183	2.485	0.39780	D	0.972283	P;D	0.71674	0.911;0.998	P;D	0.71870	0.78;0.975	T	0.77275	-0.2648	10	0.87932	D	0	-22.7095	15.6433	0.77025	0.1379:0.8621:0.0:0.0	.	259;1221	Q7Z601;Q8NGB0	GP142_HUMAN;.	V	259	ENSP00000335158:A259V	ENSP00000335158:A259V	A	+	2	0	GPR142	69879721	1.000000	0.71417	0.995000	0.50966	0.018000	0.09664	5.650000	0.67944	1.430000	0.47334	-0.147000	0.13772	GCC	.	.		0.682	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790		T	72368126	C	T	72368126	3	4	90	1	0	0	0	0	1	0	0	0	6658	739	26	3	790	3	GPR142	17	72368126	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	10372898	72368126	8827084	78	12041										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34261446	34261446	+	Frame_Shift_Del	DEL	A	A	-													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	atccttcaggcagcaccaagAgtcactggcagcagagagag					rs201006691		TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr18:34261446delA	ENST00000359247.4	+	12	1358	c.1358delA	c.(1357-1359)gagfs	p.E453fs	FHOD3_ENST00000591635.1_Intron|FHOD3_ENST00000257209.4_Frame_Shift_Del_p.E453fs|FHOD3_ENST00000590592.1_Frame_Shift_Del_p.E628fs|FHOD3_ENST00000445677.1_Frame_Shift_Del_p.E415fs	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	453					actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CAGCACCAAGAGTCACTGGCA	0.473																																					p.E453fs		Atlas-Indel,Pindel	.											.	FHOD3	210	.	0			c.1357delG						.						103	106	105					18																	34261446		2203	4300	6503	SO:0001589	frameshift_variant	80206	exon12			.	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.1358delA	chr18.hg19:g.34261446delA	ENSP00000352186:p.Glu453fs	364.0	0.0		249.0	139.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Frame_Shift_Del	DEL	ENST00000359247.4	hg19																																																																																				.	.		0.473	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		-	34261446	A	-	34261446	7	5	90	1	0	1	0	1	0	0	0	0	5891	304	11	0	1404	0	FHOD3	18	34261446	Frame_Shift_Del	DEL	A	TCGA-DD-A118-01A-11D-A12Z-10		34261446	43815802	79	12042										
SBNO2	22904	hgsc.bcm.edu	37	chr19	1109390	1109390	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aactggccgcggttctgctcCgccagcaggcagctgggctt	14	14	1	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr19:1109390C>T	ENST00000361757.3	-	29	3486	c.3249G>A	c.(3247-3249)gcG>gcA	p.A1083A	SBNO2_ENST00000587024.1_Silent_p.A1073A|SBNO2_ENST00000438103.2_Silent_p.A1026A	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	1083					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTTCTGCTCCGCCAGCAGGC	0.726																																					p.A1083A		Atlas-SNP	.											.	SBNO2	112	.	0			c.G3249A						.						6	9	8					19																	1109390		1888	4040	5928	SO:0001819	synonymous_variant	22904	exon29			CTGCTCCGCCAGC	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.3249G>A	chr19.hg19:g.1109390C>T		12.0	0.0		27.0	13.0	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	hg19	CCDS45894.1																																																																																			.	.		0.726	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		T	1109390	C	T	1109390	2	4	90	1	0	0	0	0	0	0	0	1	13878	639	23	1		1	SBNO2	19	1109390	Silent	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10		1109390	58019593	80	12043										
GNA15	2769	hgsc.bcm.edu	37	chr19	3162793	3162793	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cccacactgtttccccaggcCctaagcaggatgctgaggca	10	15	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr19:3162793C>T	ENST00000262958.3	+	7	1159	c.901C>T	c.(901-903)Cct>Tct	p.P301S		NM_002068.2	NP_002059.2	P30679	GNA15_HUMAN	guanine nucleotide binding protein (G protein), alpha 15 (Gq class)	301					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.P301S(1)		large_intestine(5)|lung(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)		TTCCCCAGGCCCTAAGCAGGA	0.632											OREG0025150	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P301S		Atlas-SNP	.											GNA15,NS,malignant_melanoma,0,1	GNA15	40	.	1	Substitution - Missense(1)	skin(1)	c.C901T						.						52	40	44					19																	3162793		2203	4300	6503	SO:0001583	missense	2769	exon7			CCAGGCCCTAAGC		CCDS12104.1	19p13.3	2008-07-16				ENSG00000060558			4383	protein-coding gene	gene with protein product		139314				1302014	Standard	NM_002068		Approved	GNA16	uc002lxf.2	P30679		ENST00000262958.3:c.901C>T	chr19.hg19:g.3162793C>T	ENSP00000262958:p.Pro301Ser	54.0	0.0	609	42.0	11.0	NM_002068	E9KL40|E9KL47|O75247|Q53XK2	Missense_Mutation	SNP	ENST00000262958.3	hg19	CCDS12104.1	.	.	.	.	.	.	.	.	.	.	c	16.25	3.069436	0.55539	.	.	ENSG00000060558	ENST00000262958	D	0.88124	-2.34	4.42	4.42	0.53409	.	0.333185	0.24583	U	0.037298	D	0.88962	0.6580	L	0.41632	1.29	0.42246	D	0.991955	D	0.61080	0.989	D	0.63703	0.917	D	0.87432	0.2389	10	0.30078	T	0.28	.	14.5094	0.67774	0.0:1.0:0.0:0.0	.	301	P30679	GNA15_HUMAN	S	301	ENSP00000262958:P301S	ENSP00000262958:P301S	P	+	1	0	GNA15	3113793	0.997000	0.39634	0.971000	0.41717	0.293000	0.27360	3.588000	0.53964	1.991000	0.58162	0.561000	0.74099	CCT	.	.		0.632	GNA15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452320.2	NM_002068		T	3162793	C	T	3162793	3	4	90	1	0	0	0	0	1	0	0	0	6511	623	22	3	927	3	GNA15	19	3162793	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	2053403	3162793	55966190	81	12044										
ARHGEF18	23370	hgsc.bcm.edu	37	chr19	7516109	7516109	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ctggttacacaacgcataacCaaatacccagtgctggtgga	9	11	0	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr19:7516109C>T	ENST00000359920.6	+	6	1501	c.1248C>T	c.(1246-1248)acC>acT	p.T416T	CTD-2207O23.3_ENST00000593531.1_Missense_Mutation_p.P374L|ARHGEF18_ENST00000319670.9_Silent_p.T258T	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	416	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				AACGCATAACCAAATACCCAG	0.572																																					p.T416T		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.C1248T						.						112	85	94					19																	7516109		2203	4300	6503	SO:0001819	synonymous_variant	23370	exon6			CATAACCAAATAC	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	17090	protein-coding gene	gene with protein product	"Rho-specific guanine nucleotide exchange factor p114"		"rho/rac guanine nucleotide exchange factor (GEF) 18"			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.1248C>T	chr19.hg19:g.7516109C>T		107.0	0.0		130.0	25.0	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Silent	SNP	ENST00000359920.6	hg19	CCDS45946.1																																																																																			.	.		0.572	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		T	7516109	C	T	7516109	2	4	90	1	0	0	0	0	0	0	0	1	901	581	21	3		3	ARHGEF18	19	7516109	Silent	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	4353316	7516109	51612874	82	12045										
MUC16	94025	hgsc.bcm.edu	37	chr19	9087246	9087246	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccagttctgcccaaactcctGattcctaggtgctgatccaa	7	14	1	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr19:9087246G>T	ENST00000397910.4	-	1	4772	c.4569C>A	c.(4567-4569)atC>atA	p.I1523I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1523	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCAAACTCCTGATTCCTAGGT	0.468																																					p.I1523I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C4569A						.						285	266	272					19																	9087246		1998	4160	6158	SO:0001819	synonymous_variant	94025	exon1			ACTCCTGATTCCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4569C>A	chr19.hg19:g.9087246G>T		210.0	0.0		298.0	54.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9087246	G	T	9087246	2	4	90	1	0	0	0	0	0	0	0	1	9982	1280	45	3		3	MUC16	19	9087246	Silent	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	1571137	9087246	50041737	83	12046										
DNASE2	1777	hgsc.bcm.edu	37	chr19	12987092	12987092	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tgccagatatccgagcagttAgagggcaggatgcctacagt	13	9	0	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr19:12987092A>C	ENST00000222219.3	-	6	887	c.795T>G	c.(793-795)tcT>tcG	p.S265S	DNASE2_ENST00000538460.1_Silent_p.S210S	NM_001375.2	NP_001366.1	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal	265					apoptotic DNA fragmentation (GO:0006309)|DNA metabolic process (GO:0006259)|erythrocyte differentiation (GO:0030218)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)|DNA binding (GO:0003677)			breast(1)|large_intestine(1)|lung(4)|ovary(1)	7						CCGAGCAGTTAGAGGGCAGGA	0.552																																					p.S265S		Atlas-SNP	.											.	DNASE2	23	.	0			c.T795G						.						68	63	65					19																	12987092		2203	4300	6503	SO:0001819	synonymous_variant	1777	exon6			GCAGTTAGAGGGC	AF045937	CCDS12284.1	19p13.2	2012-10-02			ENSG00000105612	ENSG00000105612	3.1.22.1		2960	protein-coding gene	gene with protein product		126350		DNL, DNL2		1586130	Standard	NM_001375		Approved		uc002mvn.1	O00115		ENST00000222219.3:c.795T>G	chr19.hg19:g.12987092A>C		121.0	0.0		135.0	21.0	NM_001375	B2RD06|B7Z4K6|O43910	Silent	SNP	ENST00000222219.3	hg19	CCDS12284.1																																																																																			.	.		0.552	DNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451790.1			C	12987092	A	C	12987092	2	2	90	1	0	0	0	0	0	0	0	1	4666	407	15	5		5	DNASE2	19	12987092	Silent	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	3899846	12987092	46141891	84	12047										
DNASE2	1777	hgsc.bcm.edu	37	chr19	12991796	12991796	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cccccttcacctggctggtgTtgctccggtacagcggctgc	12	16	1	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr19:12991796T>C	ENST00000222219.3	-	2	349	c.257A>G	c.(256-258)aAc>aGc	p.N86S	DNASE2_ENST00000538460.1_Missense_Mutation_p.N86S|CTD-2265O21.7_ENST00000592400.1_RNA	NM_001375.2	NP_001366.1	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal	86					apoptotic DNA fragmentation (GO:0006309)|DNA metabolic process (GO:0006259)|erythrocyte differentiation (GO:0030218)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)|DNA binding (GO:0003677)			breast(1)|large_intestine(1)|lung(4)|ovary(1)	7						CTGGCTGGTGTTGCTCCGGTA	0.672																																					p.N86S		Atlas-SNP	.											.	DNASE2	23	.	0			c.A257G						.						35	36	35					19																	12991796		2203	4300	6503	SO:0001583	missense	1777	exon2			CTGGTGTTGCTCC	AF045937	CCDS12284.1	19p13.2	2012-10-02			ENSG00000105612	ENSG00000105612	3.1.22.1		2960	protein-coding gene	gene with protein product		126350		DNL, DNL2		1586130	Standard	NM_001375		Approved		uc002mvn.1	O00115		ENST00000222219.3:c.257A>G	chr19.hg19:g.12991796T>C	ENSP00000222219:p.Asn86Ser	91.0	0.0		82.0	16.0	NM_001375	B2RD06|B7Z4K6|O43910	Missense_Mutation	SNP	ENST00000222219.3	hg19	CCDS12284.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.148669	0.57151	.	.	ENSG00000105612	ENST00000222219;ENST00000538460	T;T	0.14516	2.5;2.5	5.37	3.27	0.37495	.	0.233910	0.43747	D	0.000532	T	0.22003	0.0530	M	0.65320	2	0.09310	N	1	D;B	0.61697	0.99;0.274	P;B	0.60173	0.87;0.18	T	0.11494	-1.0585	10	0.36615	T	0.2	.	1.9604	0.03385	0.164:0.0879:0.1712:0.577	.	86;86	B7Z4K6;O00115	.;DNS2A_HUMAN	S	86	ENSP00000222219:N86S;ENSP00000445988:N86S	ENSP00000222219:N86S	N	-	2	0	DNASE2	12852796	0.649000	0.27322	0.054000	0.19295	0.102000	0.19082	3.575000	0.53870	0.866000	0.35629	0.459000	0.35465	AAC	.	.		0.672	DNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451790.1			C	12991796	T	C	12991796	3	2	90	1	0	0	0	0	1	0	0	0	4666	1725	60	2	845	2	DNASE2	19	12991796	Missense_Mutation	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	4704	12991796	46137187	85	12048										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22155549	22155549	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tttcttatgataactaagggTtgaggaccacttataggctt	9	6	1	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr19:22155549T>C	ENST00000397126.4	-	4	2435	c.2287A>G	c.(2287-2289)Acc>Gcc	p.T763A	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	763					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TAACTAAGGGTTGAGGACCAC	0.353																																					p.T763A		Atlas-SNP	.											.	ZNF208	817	.	0			c.A2287G						.						28	30	30					19																	22155549		1937	4150	6087	SO:0001583	missense	7757	exon4			TAAGGGTTGAGGA	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2287A>G	chr19.hg19:g.22155549T>C	ENSP00000380315:p.Thr763Ala	47.0	0.0		46.0	16.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	0.014	-1.605183	0.00842	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.35048	1.33	2.28	-4.55	0.03441	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31918	0.0812	.	.	.	0.09310	N	1	D	0.61080	0.989	D	0.64877	0.93	T	0.13176	-1.0519	8	0.09843	T	0.71	.	0.423	0.00459	0.3996:0.1744:0.1393:0.2867	.	663	O43345	ZN208_HUMAN	A	763;663	ENSP00000380315:T763A	ENSP00000380315:T763A	T	-	1	0	ZNF208	21947389	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-7.399000	0.00037	-2.102000	0.00845	0.232000	0.17820	ACC	.	.		0.353	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		C	22155549	T	C	22155549	3	2	90	1	0	0	0	0	1	0	0	0	17781	1725	60	2	1559	2	ZNF208	19	22155549	Missense_Mutation	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	9163753	22155549	36973434	86	12049										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22156821	22156821	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ttctttacatttgtagggctTctctccagcatgaattgcct	7	10	2	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr19:22156821T>C	ENST00000397126.4	-	4	1163	c.1015A>G	c.(1015-1017)Aag>Gag	p.K339E	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTGTAGGGCTTCTCTCCAGCA	0.388																																					p.K339E		Atlas-SNP	.											.	ZNF208	817	.	0			c.A1015G						.						51	53	52					19																	22156821		2052	4204	6256	SO:0001583	missense	7757	exon4			AGGGCTTCTCTCC	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1015A>G	chr19.hg19:g.22156821T>C	ENSP00000380315:p.Lys339Glu	96.0	0.0		131.0	24.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.178930	0.57692	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.27104	1.69	2.69	2.69	0.31865	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28764	0.0713	.	.	.	0.27764	N	0.943723	D	0.54601	0.967	P	0.47346	0.544	T	0.10847	-1.0612	8	0.72032	D	0.01	.	9.5425	0.39260	0.0:0.0:0.0:1.0	.	339	O43345	ZN208_HUMAN	E	339	ENSP00000380315:K339E	ENSP00000380315:K339E	K	-	1	0	ZNF208	21948661	0.004000	0.15560	0.001000	0.08648	0.005000	0.04900	1.251000	0.32862	0.860000	0.35481	0.260000	0.18958	AAG	.	.		0.388	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		C	22156821	T	C	22156821	3	2	90	1	0	0	0	0	1	0	0	0	17781	1792	62	2	2831	2	ZNF208	19	22156821	Missense_Mutation	SNP	T	TCGA-DD-A118-01A-11D-A12Z-10	1272	22156821	36972162	87	12050										
ZNF540	163255	hgsc.bcm.edu	37	chr19	38102620	38102620	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gtcaaaagaaaatcgtctctAaaaaaatgtcaactgataga	6	6	3	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr19:38102620A>G	ENST00000592533.1	+	5	771	c.439A>G	c.(439-441)Aaa>Gaa	p.K147E	ZNF540_ENST00000316433.4_Missense_Mutation_p.K147E|ZNF540_ENST00000586792.1_3'UTR|ZNF540_ENST00000589117.1_Missense_Mutation_p.K115E|ZNF540_ENST00000343599.5_Missense_Mutation_p.K147E	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	147					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AATCGTCTCTAAAAAAATGTC	0.368																																					p.K147E		Atlas-SNP	.											.,3	ZNF540	75	.	0			c.A439G						.						91	98	96					19																	38102620		2203	4299	6502	SO:0001583	missense	163255	exon5			GTCTCTAAAAAAA	AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"Zinc fingers, C2H2-type", "-"	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.439A>G	chr19.hg19:g.38102620A>G	ENSP00000466274:p.Lys147Glu	168.0	0.0		183.0	73.0	NM_152606	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Missense_Mutation	SNP	ENST00000592533.1	hg19	CCDS12506.1	.	.	.	.	.	.	.	.	.	.	A	0.015	-1.568645	0.00895	.	.	ENSG00000171817	ENST00000316433;ENST00000343599	T	0.08634	3.07	1.85	-2.13	0.07144	.	.	.	.	.	T	0.04318	0.0119	N	0.26130	0.795	0.09310	N	1	B;B	0.20459	0.045;0.027	B;B	0.08055	0.003;0.001	T	0.47100	-0.9143	9	0.07030	T	0.85	.	6.5073	0.22202	0.5598:0.0:0.4402:0.0	.	115;147	Q8NDQ6-2;Q8NDQ6	.;ZN540_HUMAN	E	147;115	ENSP00000324598:K147E	ENSP00000324598:K147E	K	+	1	0	ZNF540	42794460	0.000000	0.05858	0.000000	0.03702	0.147000	0.21601	-0.941000	0.03925	-0.581000	0.05937	0.172000	0.16884	AAA	.	.		0.368	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606		G	38102620	A	G	38102620	3	3	90	1	0	0	0	0	1	0	0	0	17990	363	13	2	453	2	ZNF540	19	38102620	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	15945799	38102620	21026363	88	12051										
SYMPK	8189	hgsc.bcm.edu	37	chr19	46319169	46319169	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gcctcggtcagccccgagtcGtcatccatgctgatgaagat	11	13	2	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr19:46319169G>A	ENST00000245934.7	-	26	3871	c.3627C>T	c.(3625-3627)gaC>gaT	p.D1209D	RSPH6A_ENST00000221538.3_5'Flank|RSPH6A_ENST00000597055.1_5'Flank|SYMPK_ENST00000598155.1_5'UTR	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	1209					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		GCCCCGAGTCGTCATCCATGC	0.672																																					p.D1209D		Atlas-SNP	.											.	SYMPK	104	.	0			c.C3627T						.						17	18	17					19																	46319169		2187	4274	6461	SO:0001819	synonymous_variant	8189	exon26			CGAGTCGTCATCC	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.3627C>T	chr19.hg19:g.46319169G>A		104.0	0.0		113.0	17.0	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	hg19	CCDS12676.2																																																																																			.	.		0.672	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		A	46319169	G	A	46319169	2	1	90	1	0	0	0	0	0	0	0	1	15454	1136	40	1		1	SYMPK	19	46319169	Silent	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	8216549	46319169	12809814	89	12052										
NFS1	9054	hgsc.bcm.edu	37	chr20	34286442	34286442	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	acatccatatagagaggtcgCagcactggccccacctccgg	10	15	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr20:34286442C>T	ENST00000374092.4	-	2	238	c.168G>A	c.(166-168)ctG>ctA	p.L56L	NFS1_ENST00000540053.1_5'UTR|ROMO1_ENST00000397416.1_5'Flank|ROMO1_ENST00000374072.1_5'Flank|NFS1_ENST00000397425.1_5'UTR|ROMO1_ENST00000374078.1_5'Flank|NFS1_ENST00000541387.1_Silent_p.L56L|NFS1_ENST00000374085.1_5'UTR|NFS1_ENST00000306750.3_Silent_p.L56L|ROMO1_ENST00000374077.3_5'Flank|ROMO1_ENST00000336695.4_5'Flank	NM_021100.4	NP_066923.3	Q9Y697	NFS1_HUMAN	NFS1 cysteine desulfurase	56					cysteine metabolic process (GO:0006534)|iron incorporation into metallo-sulfur cluster (GO:0018283)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|protein complex assembly (GO:0006461)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine desulfurase activity (GO:0031071)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	18	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)	AGAGAGGTCGCAGCACTGGCC	0.532																																					p.L56L		Atlas-SNP	.											.	NFS1	43	.	0			c.G168A						.						52	57	56					20																	34286442		2203	4300	6503	SO:0001819	synonymous_variant	9054	exon2			AGGTCGCAGCACT	AF097025	CCDS13262.1, CCDS56185.1	20q11.22	2013-08-06	2013-08-06		ENSG00000244005	ENSG00000244005	2.8.1.7		15910	protein-coding gene	gene with protein product		603485	"nitrogen fixation 1 (S. cerevisiae, homolog)", "NFS1 nitrogen fixation 1 homolog (S. cerevisiae)"			9885568, 16847322	Standard	NM_021100		Approved	NifS, IscS	uc002xdw.2	Q9Y697	OTTHUMG00000032361	ENST00000374092.4:c.168G>A	chr20.hg19:g.34286442C>T		260.0	0.0		337.0	51.0	NM_021100	B3KMA5|B4DXK9|E1P5R8|F5GYK5|Q6P0L8|Q9NTZ5|Q9Y481	Silent	SNP	ENST00000374092.4	hg19	CCDS13262.1																																																																																			.	.		0.532	NFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078936.4	NM_021100		T	34286442	C	T	34286442	2	4	90	1	0	0	0	0	0	0	0	1	10394	697	25	3		3	NFS1	20	34286442	Silent	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10		34286442	28739078	90	12053										
GNAS	2778	hgsc.bcm.edu	37	chr20	57484420	57484420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ttcaggacctgcttcgctgcCgtgtcctgacttctggaatc	10	13	2	1	rs11554273		TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr20:57484420C>T	ENST00000371085.3	+	8	1025	c.601C>T	c.(601-603)Cgt>Tgt	p.R201C	GNAS_ENST00000306090.10_Missense_Mutation_p.R187C|GNAS_ENST00000265620.7_Missense_Mutation_p.R186C|GNAS_ENST00000354359.7_Missense_Mutation_p.R202C|GNAS_ENST00000371102.4_Missense_Mutation_p.R830C|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371100.4_Missense_Mutation_p.R844C|GNAS_ENST00000371095.3_Missense_Mutation_p.R187C|GNAS_ENST00000313949.7_3'UTR	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	201			R -> C (in MAS and somatotrophinoma; dbSNP:rs11554273). {ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> G (in MAS). {ECO:0000269|PubMed:10571700}.|R -> H (in MAS, somatotrophinoma and AIMAH1). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:1594625, ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> L (in non-MAS endocrine tumors). {ECO:0000269|PubMed:7751320}.|R -> S (in AIMAH1, pituitary tumor and polyostotic fibrous dysplasia). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:8766942, ECO:0000269|PubMed:9267696}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R201C(228)|p.R844C(9)|p.R201S(5)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCTTCGCTGCCGTGTCCTGAC	0.428			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.R844C	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	GNAS_ENST00000371100,NS,adenocarcinoma,0,338	GNAS	867	.	242	Substitution - Missense(242)	pituitary(141)|pancreas(35)|large_intestine(14)|ovary(12)|thyroid(10)|adrenal_gland(7)|biliary_tract(6)|parathyroid(5)|liver(3)|kidney(3)|testis(2)|upper_aerodigestive_tract(2)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)	c.C2530T						.						80	78	79					20																	57484420		2203	4300	6503	SO:0001583	missense	2778	exon8			CGCTGCCGTGTCC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.601C>T	chr20.hg19:g.57484420C>T	ENSP00000360126:p.Arg201Cys	163.0	0.0		213.0	35.0	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371085.3	hg19	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215896	0.79352	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99466	-5.95;-5.95;-5.95;-5.95;-5.95;-2.99;-5.95	5.53	4.53	0.55603	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99775	0.9907	H	0.99732	4.735	0.80722	D	1	D;D;D;D	0.89917	0.999;0.983;0.979;1.0	D;P;P;D	0.97110	0.939;0.845;0.643;1.0	D	0.96814	0.9599	10	0.87932	D	0	.	13.0593	0.58997	0.2437:0.7563:0.0:0.0	rs11554273	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	C	844;830;187;201;202;186;187	ENSP00000360141:R844C;ENSP00000360143:R830C;ENSP00000360136:R187C;ENSP00000360126:R201C;ENSP00000346328:R202C;ENSP00000265620:R186C;ENSP00000304472:R187C	ENSP00000265620:R186C	R	+	1	0	GNAS	56917815	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	4.055000	0.57441	2.596000	0.87737	0.563000	0.77884	CGT	.	C|1.000		0.428	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516		T	57484420	C	T	57484420	3	4	90	1	0	0	0	0	1	0	0	0	6518	652	23	1	3448	1	GNAS	20	57484420	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	23197978	57484420	5541100	91	12054										
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26695027	26695027	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tggacctgcactcaggtgggGtggcccactttcactgccac	12	14	2	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr22:26695027G>A	ENST00000248933.6	+	5	1335	c.1240G>A	c.(1240-1242)Gtg>Atg	p.V414M	SEZ6L_ENST00000360929.3_Missense_Mutation_p.V414M|SEZ6L_ENST00000529632.2_Missense_Mutation_p.V414M|SEZ6L_ENST00000403121.1_Missense_Mutation_p.V187M|SEZ6L_ENST00000404234.3_Missense_Mutation_p.V414M|SEZ6L_ENST00000402979.1_Missense_Mutation_p.V187M|SEZ6L_ENST00000343706.4_Missense_Mutation_p.V414M			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	414	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						CTCAGGTGGGGTGGCCCACTT	0.602																																					p.V414M		Atlas-SNP	.											.	SEZ6L	174	.	0			c.G1240A						.						59	50	53					22																	26695027		2203	4300	6503	SO:0001583	missense	23544	exon5			GGTGGGGTGGCCC	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1240G>A	chr22.hg19:g.26695027G>A	ENSP00000248933:p.Val414Met	95.0	0.0		142.0	25.0	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	hg19	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.687116	0.48097	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24;-0.24;-0.24	4.55	0.988	0.19796	Complement control module (2);Sushi/SCR/CCP (3);	0.755278	0.11315	N	0.576686	T	0.67487	0.2898	L	0.57536	1.79	0.50467	D	0.999872	P;P;P;P;P;P;P	0.50272	0.707;0.922;0.906;0.933;0.887;0.922;0.87	P;P;P;P;P;P;P	0.53224	0.626;0.721;0.564;0.689;0.594;0.721;0.721	T	0.65001	-0.6274	10	0.51188	T	0.08	.	4.2935	0.10890	0.2834:0.3834:0.3332:0.0	.	414;414;187;414;414;414;414	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	M	414;414;414;414;414;187;187	ENSP00000384772:V414M;ENSP00000437037:V414M;ENSP00000354185:V414M;ENSP00000248933:V414M;ENSP00000342661:V414M;ENSP00000384838:V187M;ENSP00000384733:V187M	ENSP00000248933:V414M	V	+	1	0	SEZ6L	25025027	0.004000	0.15560	0.999000	0.59377	0.827000	0.46813	0.581000	0.23819	0.508000	0.28173	-0.258000	0.10820	GTG	.	.		0.602	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26695027	G	A	26695027	3	1	90	1	0	0	0	0	1	0	0	0	14158	1261	44	3	1258	3	SEZ6L	22	26695027	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10		26695027	24609539	92	12055										
MTMR3	8897	hgsc.bcm.edu	37	chr22	30415674	30415674	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccaccagagtgccggggggtGccgagctttctgttgcagcc	15	13	1	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr22:30415674G>A	ENST00000401950.2	+	17	2368	c.2026G>A	c.(2026-2028)Gcc>Acc	p.A676T	CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000351488.3_Missense_Mutation_p.A676T|MTMR3_ENST00000323630.5_Missense_Mutation_p.A540T|MTMR3_ENST00000333027.3_Missense_Mutation_p.A676T|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000406629.1_Missense_Mutation_p.A676T	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	676					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			GCCGGGGGGTGCCGAGCTTTC	0.632																																					p.A676T		Atlas-SNP	.											.	MTMR3	106	.	0			c.G2026A						.						52	62	59					22																	30415674		2203	4300	6503	SO:0001583	missense	8897	exon17			GGGGGTGCCGAGC	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.2026G>A	chr22.hg19:g.30415674G>A	ENSP00000384651:p.Ala676Thr	71.0	0.0		70.0	18.0	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	hg19	CCDS13870.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.410194	0.83340	.	.	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000323630;ENST00000351488;ENST00000406629	D;D;D;D;D	0.94931	-3.34;-3.32;-3.56;-3.37;-3.32	5.8	5.8	0.92144	.	2.069360	0.01706	N	0.027425	D	0.93628	0.7965	L	0.27053	0.805	0.80722	D	1	D;D;D	0.54397	0.957;0.966;0.957	P;P;P	0.50490	0.642;0.524;0.642	T	0.80339	-0.1424	10	0.02654	T	1	.	19.0512	0.93046	0.0:0.0:1.0:0.0	.	676;676;676	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	T	676;676;540;676;676	ENSP00000384651:A676T;ENSP00000331649:A676T;ENSP00000318070:A540T;ENSP00000307271:A676T;ENSP00000384077:A676T	ENSP00000318070:A540T	A	+	1	0	MTMR3	28745674	1.000000	0.71417	0.211000	0.23655	0.573000	0.36030	7.463000	0.80869	2.735000	0.93741	0.655000	0.94253	GCC	.	.		0.632	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		A	30415674	G	A	30415674	3	1	90	1	0	0	0	0	1	0	0	0	9954	1319	46	3	2084	3	MTMR3	22	30415674	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	3720647	30415674	20888892	93	12056										
LARGE	9215	hgsc.bcm.edu	37	chr22	33670547	33670547	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ggaacggaacttggtaatgtCgaagctgggggcatgaggca	17	6	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chr22:33670547C>T	ENST00000354992.2	-	16	2708	c.2137G>A	c.(2137-2139)Gac>Aac	p.D713N	LARGE_ENST00000452586.2_Missense_Mutation_p.D512N|LARGE_ENST00000397394.2_Missense_Mutation_p.D713N|LARGE_ENST00000337431.2_Missense_Mutation_p.D661N|LARGE_ENST00000437602.2_Missense_Mutation_p.D664N|LARGE_ENST00000402320.1_Missense_Mutation_p.D661N	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	713					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				TTGGTAATGTCGAAGCTGGGG	0.527											OREG0026497	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D713N	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											.	LARGE	98	.	0			c.G2137A						.						155	127	137					22																	33670547		2203	4300	6503	SO:0001583	missense	9215	exon16			TAATGTCGAAGCT	AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"Glycosyltransferase family 8 domain containing"	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.2137G>A	chr22.hg19:g.33670547C>T	ENSP00000347088:p.Asp713Asn	148.0	0.0	841	187.0	41.0	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	ENST00000354992.2	hg19	CCDS13912.1	.	.	.	.	.	.	.	.	.	.	C	36	5.686561	0.96784	.	.	ENSG00000133424	ENST00000354992;ENST00000337431;ENST00000397394;ENST00000402320;ENST00000452586;ENST00000437602	T;T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97;1.97	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	M	0.88775	2.98	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.87578	0.998;0.913;0.981;0.998	T	0.60120	-0.7325	10	0.62326	D	0.03	0.0016	20.8598	0.99761	0.0:1.0:0.0:0.0	.	664;512;661;713	B7Z2I9;E9PH73;O95461-2;O95461	.;.;.;LARGE_HUMAN	N	713;661;713;661;512;664	ENSP00000347088:D713N;ENSP00000336636:D661N;ENSP00000380549:D713N;ENSP00000385223:D661N;ENSP00000407917:D512N;ENSP00000388544:D664N	ENSP00000336636:D661N	D	-	1	0	LARGE	32000547	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.348000	0.79366	2.937000	0.99478	0.650000	0.86243	GAC	.	.		0.527	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		T	33670547	C	T	33670547	3	4	90	1	0	0	0	0	1	0	0	0	8636	884	31	1	137	1	LARGE	22	33670547	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	3254873	33670547	17634019	94	12057										
ZBED1	9189	hgsc.bcm.edu	37	chrX	2407376	2407376	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gaaacatgtcgatctcgggcGtctcctggtaggtcttggaa	13	9	3	0			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:2407376G>A	ENST00000381223.4	-	2	1588	c.1385C>T	c.(1384-1386)aCg>aTg	p.T462M	DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381218.3_Missense_Mutation_p.T462M|ZBED1_ENST00000515319.1_5'Flank|ZBED1_ENST00000381222.2_Missense_Mutation_p.T462M	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	462					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)			endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GATCTCGGGCGTCTCCTGGTA	0.592																																					p.T462M		Atlas-SNP	.											.	ZBED1	64	.	0			c.C1385T						.	G	MET/THR,MET/THR,MET/THR,	0,4406		0,0,2203	181	169	173		1385,1385,1385,	2.2	0.1	X		173	1,8591		0,1,4295	no	missense,missense,missense,intron	ZBED1,DHRSX	NM_001171135.1,NM_001171136.1,NM_004729.3,NM_145177.2	81,81,81,	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,	462/695,462/695,462/695,	2407376	1,12997	2203	4296	6499	SO:0001583	missense	9189	exon2			TCGGGCGTCTCCT	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"Pseudoautosomal regions / PAR1", "Zinc fingers, BED-type"	447	protein-coding gene	gene with protein product		300178	"Ac-like transposable element"	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.1385C>T	chrX.hg19:g.2407376G>A	ENSP00000370621:p.Thr462Met	319.0	0.0		387.0	84.0	NM_001171135	Q96BY4	Missense_Mutation	SNP	ENST00000381223.4	hg19	CCDS14118.1	.	.	.	.	.	.	.	.	.	.	G	5.159	0.215005	0.09810	0.0	1.16E-4	ENSG00000214717	ENST00000381223;ENST00000381222;ENST00000381218	T;T;T	0.22539	1.95;1.95;1.95	3.06	2.18	0.27775	Ribonuclease H-like (1);	0.646554	0.12663	N	0.449481	T	0.12475	0.0303	.	.	.	0.09310	N	1	P	0.37708	0.606	B	0.28465	0.09	T	0.13150	-1.0520	9	0.34782	T	0.22	.	9.2617	0.37616	0.1168:0.0:0.8832:0.0	.	462	O96006	ZBED1_HUMAN	M	462	ENSP00000370621:T462M;ENSP00000370620:T462M;ENSP00000370616:T462M	ENSP00000370616:T462M	T	-	2	0	ZBED1	2417376	1.000000	0.71417	0.050000	0.19076	0.049000	0.14656	6.158000	0.71851	0.207000	0.20607	0.519000	0.50382	ACG	.	G|0.999;A|0.001		0.592	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729		A	2407376	G	A	2407376	3	1	90	1	0	0	0	0	1	0	0	0	17532	1145	40	1	703	1	ZBED1	23	2407376	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10		2407376	152863184	95	12058										
ARSD	414	hgsc.bcm.edu	37	chrX	2835844	2835844	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	taagatgcgatggttgcttaCctttcaatataggaaacagc	9	7	1	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:2835844C>T	ENST00000381154.1	-	5	939		c.e5+1		ARSD_ENST00000217890.6_Splice_Site	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D						cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGGTTGCTTACCTTTCAATAT	0.493																																					.		Atlas-SNP	.											.	ARSD	47	.	0			c.863+1G>A						.						43	36	39					X																	2835844		2203	4300	6503	SO:0001630	splice_region_variant	414	exon6			TGCTTACCTTTCA	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"Arylsulfatase family"	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.863+1G>A	chrX.hg19:g.2835844C>T		110.0	0.0		143.0	37.0	NM_001669	Q9UHJ8	Splice_Site	SNP	ENST00000381154.1	hg19	CCDS35196.1	.	.	.	.	.	.	.	.	.	.	C	8.965	0.971620	0.18736	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	.	.	.	3.12	3.12	0.35913	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8669	0.63594	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ARSD	2845844	1.000000	0.71417	0.052000	0.19188	0.089000	0.18198	6.317000	0.72862	1.215000	0.43411	0.281000	0.19383	.	.	.		0.493	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		Intron	T	2835844	C	T	2835844	5	4	90	1	0	0	0	0	0	0	1	0	989	521	18	3	1094	3	ARSD	23	2835844	Splice_Site	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	428468	2835844	152434716	96	12059										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5811323	5811323	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	cgtttggtttcaatgaggacAgttgtgtcctcaggccctgt	12	9	2	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:5811323A>G	ENST00000381095.3	-	6	2613	c.1986T>C	c.(1984-1986)acT>acC	p.T662T	NLGN4X_ENST00000538097.1_Silent_p.T662T|NLGN4X_ENST00000275857.6_Silent_p.T662T|NLGN4X_ENST00000381093.2_Silent_p.T682T|NLGN4X_ENST00000381092.1_Silent_p.T662T	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	662					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						CAATGAGGACAGTTGTGTCCT	0.522																																					p.T662T		Atlas-SNP	.											.	NLGN4X	191	.	0			c.T1986C						.						221	200	207					X																	5811323		2203	4300	6503	SO:0001819	synonymous_variant	57502	exon6			GAGGACAGTTGTG	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1986T>C	chrX.hg19:g.5811323A>G		739.0	1.0		897.0	334.0	NM_181332	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	hg19	CCDS14126.1																																																																																			.	.		0.522	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		G	5811323	A	G	5811323	2	3	90	1	0	0	0	0	0	0	0	1	10473	175	7	2		2	NLGN4X	23	5811323	Silent	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	2975479	5811323	149459237	97	12060										
RAB9A	9367	hgsc.bcm.edu	37	chrX	13727290	13727290	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	agaagaagcccaagcttggtGcagggacaacggcgactatc	13	10	0	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:13727290G>A	ENST00000464506.1	+	3	704	c.425G>A	c.(424-426)tGc>tAc	p.C142Y	RAB9A_ENST00000243325.5_3'UTR	NM_001195328.1|NM_004251.4	NP_001182257.1|NP_004242.1	P51151	RAB9A_HUMAN	RAB9A, member RAS oncogene family	142					GTP catabolic process (GO:0006184)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7						CAAGCTTGGTGCAGGGACAAC	0.478																																					p.C142Y		Atlas-SNP	.											.	RAB9A	17	.	0			c.G425A						.						102	102	102					X																	13727290		2203	4300	6503	SO:0001583	missense	9367	exon3			CTTGGTGCAGGGA	U44103	CCDS14156.1	Xp22.2	2010-04-19	2007-01-15	2007-01-15	ENSG00000123595	ENSG00000123595		"RAB, member RAS oncogene"	9792	protein-coding gene	gene with protein product		300284	"RAB9, member RAS oncogene family"	RAB9		9126495	Standard	NM_004251		Approved		uc010neh.3	P51151	OTTHUMG00000021156	ENST00000464506.1:c.425G>A	chrX.hg19:g.13727290G>A	ENSP00000420127:p.Cys142Tyr	83.0	0.0		102.0	20.0	NM_004251	A8K390|Q6ICN1	Missense_Mutation	SNP	ENST00000464506.1	hg19	CCDS14156.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.736739	0.69304	.	.	ENSG00000123595	ENST00000464506	T	0.76709	-1.04	5.51	4.61	0.57282	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.88187	0.6369	M	0.82433	2.59	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.89168	0.3535	9	.	.	.	-6.3705	15.4544	0.75302	0.0:0.1349:0.8651:0.0	.	142	P51151	RAB9A_HUMAN	Y	142	ENSP00000420127:C142Y	.	C	+	2	0	RAB9A	13637211	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.212000	0.95126	2.296000	0.77279	0.594000	0.82650	TGC	.	.		0.478	RAB9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055802.1	NM_004251		A	13727290	G	A	13727290	3	1	90	1	0	0	0	0	1	0	0	0	12973	1319	46	3	427	3	RAB9A	23	13727290	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	7915967	13727290	141543270	98	12061										
SH3KBP1	30011	hgsc.bcm.edu	37	chrX	19560246	19560247	+	Frame_Shift_Ins	INS	-	-	G													0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccgctgaggacagaggggctINSggcccaccgccacctgctgc							TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:19560246_19560247insG	ENST00000397821.3	-	16	1978_1979	c.1688_1689insC	c.(1687-1689)ccafs	p.P563fs	SH3KBP1_ENST00000379698.4_Frame_Shift_Ins_p.P526fs|SH3KBP1_ENST00000379716.1_Frame_Shift_Ins_p.P325fs|SH3KBP1_ENST00000541422.1_Frame_Shift_Ins_p.P302fs	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	563					apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						ACAGAGGGGCTGGCCCACCGCC	0.653																																					p.P563fs		Atlas-INDEL	.											.	SH3KBP1	96	.	0			c.1689_1690insC						.																																			SO:0001589	frameshift_variant	30011	exon16			.	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.1689dupC	chrX.hg19:g.19560248_19560248dupG	ENSP00000380921:p.Pro563fs	147.0	0.0		193.0	15.0	NM_031892	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Frame_Shift_Ins	INS	ENST00000397821.3	hg19	CCDS14193.1																																																																																			.	.		0.653	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892		G	19560247	-	G	19560246	7	5	90	1	0	1	1	0	0	0	0	0	14270	1567	55	0	320	0	SH3KBP1	23	19560246	Frame_Shift_Ins	INS	-	TCGA-DD-A118-01A-11D-A12Z-10	5832956	19560246	135710314	99	12062										
EFHC2	80258	hgsc.bcm.edu	37	chrX	44091923	44091923	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	agaacatcccaccagcaattCctataaaaaatagaaaagtt	4	9	0	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:44091923C>T	ENST00000420999.1	-	10	1507	c.1424G>A	c.(1423-1425)gGa>gAa	p.G475E		NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	475	DM10 3. {ECO:0000255|PROSITE- ProRule:PRU00665}.						calcium ion binding (GO:0005509)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						ACCAGCAATTCCTATAAAAAA	0.388																																					p.G475E		Atlas-SNP	.											.	EFHC2	81	.	0			c.G1424A						.						25	21	22					X																	44091923		1829	4061	5890	SO:0001630	splice_region_variant	80258	exon10			GCAATTCCTATAA	AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"EF-hand domain containing"	26233	protein-coding gene	gene with protein product		300817	"mental retardation, X-linked 74"	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.1424-1G>A	chrX.hg19:g.44091923C>T		98.0	0.0		154.0	66.0	NM_025184	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Missense_Mutation	SNP	ENST00000420999.1	hg19	CCDS55405.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.970907	0.74246	.	.	ENSG00000183690	ENST00000333807;ENST00000420999	D;D	0.94457	-3.43;-3.43	5.85	4.98	0.66077	Uncharacterised domain DM10 (2);	0.000000	0.85682	D	0.000000	D	0.98267	0.9426	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99164	1.0862	10	0.87932	D	0	.	16.045	0.80714	0.0:0.8693:0.1307:0.0	.	475	Q5JST6	EFHC2_HUMAN	E	475;503	ENSP00000333823:G475E;ENSP00000404232:G503E	ENSP00000333823:G475E	G	-	2	0	EFHC2	43976867	1.000000	0.71417	0.347000	0.25668	0.027000	0.11550	6.917000	0.75782	1.213000	0.43380	0.600000	0.82982	GGA	.	.		0.388	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184	Missense_Mutation	T	44091923	C	T	44091923	5	4	90	1	0	0	0	0	0	0	1	0	4949	869	30	3	849	3	EFHC2	23	44091923	Splice_Site	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	24531677	44091923	111178637	100	12063										
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53279675	53279675	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gctctcaaggctctcgttatCtccaccatcagagttctcgc	7	15	5	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:53279675C>T	ENST00000375368.5	-	4	2253	c.2053G>A	c.(2053-2055)Gat>Aat	p.D685N	IQSEC2_ENST00000375365.2_Missense_Mutation_p.D490N|IQSEC2_ENST00000396435.3_Missense_Mutation_p.D695N			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	685					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						CTCTCGTTATCTCCACCATCA	0.622																																					p.D695N		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G2083A						.						76	58	64					X																	53279675		2203	4300	6503	SO:0001583	missense	23096	exon5			CGTTATCTCCACC	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.2053G>A	chrX.hg19:g.53279675C>T	ENSP00000364517:p.Asp685Asn	175.0	0.0		214.0	49.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	c	24.3	4.510902	0.85389	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	T;T;T	0.51071	2.04;2.03;0.72	5.23	5.23	0.72850	.	0.782783	0.12603	N	0.454541	T	0.65923	0.2738	L	0.52905	1.665	0.80722	D	1	D;D	0.89917	1.0;0.971	D;P	0.71870	0.975;0.776	T	0.64964	-0.6283	10	0.66056	D	0.02	.	16.614	0.84902	0.0:1.0:0.0:0.0	.	695;490	Q5JU85-2;Q5JU85-3	.;.	N	695;685;490	ENSP00000379712:D695N;ENSP00000364517:D685N;ENSP00000364514:D490N	ENSP00000364514:D490N	D	-	1	0	IQSEC2	53296400	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.572000	0.82409	2.181000	0.69327	0.597000	0.82753	GAT	.	.		0.622	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		T	53279675	C	T	53279675	3	4	90	1	0	0	0	0	1	0	0	0	7827	913	32	3	2427	3	IQSEC2	23	53279675	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	9187752	53279675	101990885	101	12064										
MSN	4478	hgsc.bcm.edu	37	chrX	64957171	64957171	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	aggccttgctgcaggcctccCgggaccagaaaaagactcag	12	13	1	2			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:64957171C>T	ENST00000360270.5	+	10	1394	c.1222C>T	c.(1222-1224)Cgg>Tgg	p.R408W		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	408					cellular component movement (GO:0006928)|establishment of endothelial barrier (GO:0061028)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|regulation of lymphocyte migration (GO:2000401)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|uropod (GO:0001931)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|structural constituent of cytoskeleton (GO:0005200)		MSN/ALK(6)	breast(4)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	43						GCAGGCCTCCCGGGACCAGAA	0.542			T	ALK	ALCL																																p.R408W		Atlas-SNP	.		Dom	yes		X	Xq11.2-q12	4478	moesin		L	.	MSN	89	.	0			c.C1222T						.						26	25	26					X																	64957171		2203	4300	6503	SO:0001583	missense	4478	exon10			GCCTCCCGGGACC	M69066	CCDS14382.1	Xq11.1	2010-10-20			ENSG00000147065	ENSG00000147065			7373	protein-coding gene	gene with protein product		309845				1924289, 7628534	Standard	XM_005262269		Approved		uc004dwf.3	P26038	OTTHUMG00000021723	ENST00000360270.5:c.1222C>T	chrX.hg19:g.64957171C>T	ENSP00000353408:p.Arg408Trp	275.0	0.0		324.0	46.0	NM_002444		Missense_Mutation	SNP	ENST00000360270.5	hg19	CCDS14382.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.307067	0.60305	.	.	ENSG00000147065	ENST00000360270	D	0.86366	-2.11	4.97	3.12	0.35913	Ezrin/radixin/moesin, C-terminal (1);	0.475980	0.25132	N	0.032895	D	0.88020	0.6325	L	0.44542	1.39	0.23820	N	0.996756	P	0.37573	0.6	P	0.51453	0.67	T	0.81217	-0.1033	10	0.87932	D	0	.	11.7058	0.51597	0.3168:0.6832:0.0:0.0	.	408	P26038	MOES_HUMAN	W	408	ENSP00000353408:R408W	ENSP00000353408:R408W	R	+	1	2	MSN	64873896	0.954000	0.32549	0.135000	0.22099	0.968000	0.65278	1.925000	0.40074	0.450000	0.26774	0.594000	0.82650	CGG	.	.		0.542	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444		T	64957171	C	T	64957171	3	4	90	1	0	0	0	0	1	0	0	0	9894	643	23	1	1260	1	MSN	23	64957171	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	11677496	64957171	90313389	102	12065										
CSTF2	1478	hgsc.bcm.edu	37	chrX	100078295	100078295	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gattaggccttggcactggtGcccctgtcattgagtcacct	11	12	2	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:100078295G>T	ENST00000372972.2	+	4	338	c.322G>T	c.(322-324)Gcc>Tcc	p.A108S	CSTF2_ENST00000415585.2_Missense_Mutation_p.A108S|SNORA9_ENST00000365361.1_RNA	NM_001325.2	NP_001316.1	P33240	CSTF2_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa	108	Interactions with CSTF3 and SYMPK.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cleavage body (GO:0071920)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	13						TGGCACTGGTGCCCCTGTCAT	0.458																																					p.A108S		Atlas-SNP	.											.	CSTF2	47	.	0			c.G322T						.						112	92	99					X																	100078295		2203	4300	6503	SO:0001583	missense	1478	exon4			ACTGGTGCCCCTG	BC017712	CCDS14473.1	Xq22.1	2013-02-12	2002-08-29		ENSG00000101811	ENSG00000101811		"RNA binding motif (RRM) containing"	2484	protein-coding gene	gene with protein product		300907	"cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kD"			1741396	Standard	XM_006724622		Approved		uc004egh.3	P33240	OTTHUMG00000022709	ENST00000372972.2:c.322G>T	chrX.hg19:g.100078295G>T	ENSP00000362063:p.Ala108Ser	123.0	0.0		163.0	25.0	NM_001325	Q5H951|Q6LA74|Q8N502	Missense_Mutation	SNP	ENST00000372972.2	hg19	CCDS14473.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.927118	0.52759	.	.	ENSG00000101811	ENST00000415585;ENST00000372972;ENST00000458320;ENST00000413437	T;T;T	0.16597	2.53;2.54;2.33	5.44	5.44	0.79542	.	0.094221	0.64402	D	0.000001	T	0.17152	0.0412	N	0.21282	0.65	0.58432	D	0.999998	B;B;B	0.17465	0.006;0.022;0.006	B;B;B	0.32022	0.027;0.139;0.027	T	0.07868	-1.0750	10	0.33141	T	0.24	-8.8036	18.4238	0.90602	0.0:0.0:1.0:0.0	.	108;108;108	E7EWR4;P33240-2;P33240	.;.;CSTF2_HUMAN	S	108;108;108;99	ENSP00000387996:A108S;ENSP00000362063:A108S;ENSP00000415705:A99S	ENSP00000362063:A108S	A	+	1	0	CSTF2	99964951	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.015000	0.70791	2.292000	0.77174	0.544000	0.68410	GCC	.	.		0.458	CSTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058926.1	NM_001325		T	100078295	G	T	100078295	3	4	90	1	0	0	0	0	1	0	0	0	3986	1319	46	3	336	3	CSTF2	23	100078295	Missense_Mutation	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	35121124	100078295	55192265	103	12066										
BHLHB9	80823	hgsc.bcm.edu	37	chrX	102005369	102005369	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	actgcagccagagacatgatCaatatgaaggcattggcagc	11	9	1	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:102005369C>A	ENST00000372735.1	+	4	2031	c.1446C>A	c.(1444-1446)atC>atA	p.I482I	BHLHB9_ENST00000448867.1_Silent_p.I482I|BHLHB9_ENST00000447531.1_Silent_p.I482I|BHLHB9_ENST00000457056.1_Silent_p.I482I|BHLHB9_ENST00000361229.4_Silent_p.I482I			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	482					learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GAGACATGATCAATATGAAGG	0.363																																					p.I482I		Atlas-SNP	.											.	BHLHB9	60	.	0			c.C1446A						.						119	118	119					X																	102005369		2203	4300	6503	SO:0001819	synonymous_variant	80823	exon2			CATGATCAATATG	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"Basic helix-loop-helix proteins", "Armadillo repeat containing"	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.1446C>A	chrX.hg19:g.102005369C>A		452.0	1.0		566.0	231.0	NM_001142530	Q9C0G2	Silent	SNP	ENST00000372735.1	hg19	CCDS14502.1																																																																																			.	.		0.363	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639		A	102005369	C	A	102005369	2	1	90	1	0	0	0	0	0	0	0	1	1420	816	29	3		3	BHLHB9	23	102005369	Silent	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	1927074	102005369	53265191	104	12067										
TCEAL4	79921	hgsc.bcm.edu	37	chrX	102842040	102842040	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ggagtataaagaggccatacAtgatatgaatttcagcaatg	10	5	1	3			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:102842040A>T	ENST00000472745.1	+	3	989	c.437A>T	c.(436-438)cAt>cTt	p.H146L	TCEAL4_ENST00000372629.4_Missense_Mutation_p.H289L|TCEAL4_ENST00000468024.1_Missense_Mutation_p.H146L|TCEAL4_ENST00000415568.2_Missense_Mutation_p.H146L|TCEAL4_ENST00000472484.1_Missense_Mutation_p.H146L|TCEAL4_ENST00000494801.1_Missense_Mutation_p.H146L			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|skin(2)	6						GAGGCCATACATGATATGAAT	0.428																																					p.H146L		Atlas-SNP	.											.	TCEAL4	18	.	0			c.A437T						.						122	124	123					X																	102842040		2203	4300	6503	SO:0001583	missense	79921	exon3			CCATACATGATAT	AF314542	CCDS14510.2, CCDS76004.1	Xq22.2	2014-03-21			ENSG00000133142	ENSG00000133142			26121	protein-coding gene	gene with protein product						14702039, 16221301	Standard	XM_005262192		Approved	FLJ21174, WEX7	uc004ekn.3	Q96EI5	OTTHUMG00000022103	ENST00000472745.1:c.437A>T	chrX.hg19:g.102842040A>T	ENSP00000424314:p.His146Leu	185.0	0.0		227.0	90.0	NM_001006935	Q8WY12|Q9H2H1|Q9H775	Missense_Mutation	SNP	ENST00000472745.1	hg19	CCDS14510.2	.	.	.	.	.	.	.	.	.	.	A	13.49	2.252635	0.39797	.	.	ENSG00000133142	ENST00000372629;ENST00000468024;ENST00000472484;ENST00000415568;ENST00000414064;ENST00000472745;ENST00000494801	T;T;T;T;T;T	0.10763	2.84;2.84;2.84;2.84;2.84;2.84	3.99	2.78	0.32641	.	0.000000	0.48767	D	0.000166	T	0.25005	0.0607	M	0.65975	2.015	0.09310	N	1	D	0.76494	0.999	D	0.72338	0.977	T	0.02498	-1.1150	10	0.62326	D	0.03	.	6.6592	0.23004	0.759:0.241:0.0:0.0	.	146	Q96EI5	TCAL4_HUMAN	L	289;146;146;146;117;146;146	ENSP00000361712:H289L;ENSP00000421857:H146L;ENSP00000421156:H146L;ENSP00000415564:H146L;ENSP00000424314:H146L;ENSP00000427494:H146L	ENSP00000361712:H289L	H	+	2	0	TCEAL4	102728696	0.918000	0.31147	0.011000	0.14972	0.699000	0.40488	1.903000	0.39858	0.682000	0.31407	0.352000	0.21897	CAT	.	.		0.428	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863		T	102842040	A	T	102842040	3	4	90	1	0	0	0	0	1	0	0	0	15688	217	8	4	439	4	TCEAL4	23	102842040	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	836671	102842040	52428520	105	12068										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117788710	117788710	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	agccaagtcctatgcaagcaCcccagagctcaggaaaacct	8	14	1	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:117788710C>T	ENST00000276202.7	+	43	4904	c.4841C>T	c.(4840-4842)aCc>aTc	p.T1614I	DOCK11_ENST00000276204.6_Missense_Mutation_p.T1614I	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1614	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TATGCAAGCACCCCAGAGCTC	0.433																																					p.T1614I		Atlas-SNP	.											.	DOCK11	185	.	0			c.C4841T						.						98	90	92					X																	117788710		2203	4300	6503	SO:0001583	missense	139818	exon43			CAAGCACCCCAGA	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.4841C>T	chrX.hg19:g.117788710C>T	ENSP00000276202:p.Thr1614Ile	240.0	0.0		267.0	99.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	hg19	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308485	0.81247	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.18960	2.18;2.18	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.52725	0.1752	M	0.84433	2.695	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.87578	0.998;0.99	T	0.62267	-0.6890	10	0.87932	D	0	-15.9869	17.5152	0.87771	0.0:1.0:0.0:0.0	.	1614;1614	A6NIW2;Q5JSL3	.;DOC11_HUMAN	I	1614	ENSP00000276204:T1614I;ENSP00000276202:T1614I	ENSP00000276202:T1614I	T	+	2	0	DOCK11	117672738	1.000000	0.71417	0.977000	0.42913	0.982000	0.71751	7.480000	0.81109	2.062000	0.61559	0.600000	0.82982	ACC	.	.		0.433	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		T	117788710	C	T	117788710	3	4	90	1	0	0	0	0	1	0	0	0	4688	507	18	3	5011	3	DOCK11	23	117788710	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	14946670	117788710	37481850	106	12069										
GRIA3	2892	hgsc.bcm.edu	37	chrX	122538727	122538727	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gtgcaagggatccagagactAaaatatggaacggcatggtt	13	6	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:122538727A>G	ENST00000371251.1	+	10	1514	c.1462A>G	c.(1462-1464)Aaa>Gaa	p.K488E	GRIA3_ENST00000264357.5_Missense_Mutation_p.K488E|GRIA3_ENST00000371256.5_Missense_Mutation_p.K488E|GRIA3_ENST00000541091.1_Missense_Mutation_p.K472E|GRIA3_ENST00000542149.1_Missense_Mutation_p.K488E			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	488					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	TCCAGAGACTAAAATATGGAA	0.393																																					p.K488E		Atlas-SNP	.											.	GRIA3	386	.	0			c.A1462G						.						213	187	196					X																	122538727		2203	4300	6503	SO:0001583	missense	2892	exon10			GAGACTAAAATAT	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.1462A>G	chrX.hg19:g.122538727A>G	ENSP00000360297:p.Lys488Glu	461.0	0.0		529.0	102.0	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	hg19	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	A	18.07	3.541857	0.65198	.	.	ENSG00000125675	ENST00000264357;ENST00000542149;ENST00000371256;ENST00000371251;ENST00000541091	T;T;T;T;T	0.76709	1.13;1.13;1.13;1.13;-1.04	5.4	5.4	0.78164	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.89536	0.6743	M	0.90198	3.095	0.80722	D	1	P;D;D	0.63046	0.948;0.992;0.99	P;D;D	0.76071	0.719;0.987;0.979	D	0.90987	0.4832	10	0.54805	T	0.06	.	13.7182	0.62710	1.0:0.0:0.0:0.0	.	472;488;488	B7Z4C0;P42263;P42263-2	.;GRIA3_HUMAN;.	E	488;488;488;488;472	ENSP00000264357:K488E;ENSP00000446146:K488E;ENSP00000360302:K488E;ENSP00000360297:K488E;ENSP00000446440:K472E	ENSP00000264357:K488E	K	+	1	0	GRIA3	122366408	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.287000	0.95975	1.904000	0.55121	0.412000	0.27726	AAA	.	.		0.393	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		G	122538727	A	G	122538727	3	3	90	1	0	0	0	0	1	0	0	0	6778	363	13	2	1500	2	GRIA3	23	122538727	Missense_Mutation	SNP	A	TCGA-DD-A118-01A-11D-A12Z-10	4750017	122538727	32731833	107	12070										
ZNF449	203523	hgsc.bcm.edu	37	chrX	134494230	134494230	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	gctctccagggtcccattttGcaaaaagactatgtacagtt	8	10	1	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:134494230G>A	ENST00000339249.4	+	5	926	c.786G>A	c.(784-786)ttG>ttA	p.L262L		NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	262					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GTCCCATTTTGCAAAAAGACT	0.393																																					p.L262L		Atlas-SNP	.											.	ZNF449	68	.	0			c.G786A						.						59	62	61					X																	134494230		2184	4255	6439	SO:0001819	synonymous_variant	203523	exon5			CATTTTGCAAAAA	AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"-", "Zinc fingers, C2H2-type"	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.786G>A	chrX.hg19:g.134494230G>A		439.0	0.0		476.0	71.0	NM_152695	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Silent	SNP	ENST00000339249.4	hg19	CCDS14649.1																																																																																			.	.		0.393	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695		A	134494230	G	A	134494230	2	1	90	1	0	0	0	0	0	0	0	1	17935	1310	46	3		3	ZNF449	23	134494230	Silent	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	11955503	134494230	20776330	108	12071										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151806785	151806785	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	tcctctgctgtgcccgaagtCgtcctgaacctcttcaactg	8	15	3	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:151806785C>T	ENST00000370306.2	+	1	149	c.129C>T	c.(127-129)gtC>gtT	p.V43V		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	43					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGCCCGAAGTCGTCCTGAACC	0.627																																					p.V43V		Atlas-SNP	.											.	GABRQ	131	.	0			c.C129T						.						95	76	83					X																	151806785		2203	4300	6503	SO:0001819	synonymous_variant	55879	exon1			CGAAGTCGTCCTG	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.129C>T	chrX.hg19:g.151806785C>T		188.0	0.0		254.0	48.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Silent	SNP	ENST00000370306.2	hg19	CCDS14707.1																																																																																			.	.		0.627	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		T	151806785	C	T	151806785	2	4	90	1	0	0	0	0	0	0	0	1	6183	871	31	1		1	GABRQ	23	151806785	Silent	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	17312555	151806785	3463775	109	12072										
TREX2	11219	hgsc.bcm.edu	37	chrX	152710779	152710779	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccgggttctccagggaggagCggtggacagcaaagagggac	18	9	1	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:152710779C>T	ENST00000334497.2	-	11	1380	c.239G>A	c.(238-240)cGc>cAc	p.R80H	TREX2_ENST00000370232.1_Missense_Mutation_p.R80H|TREX2_ENST00000330912.2_Missense_Mutation_p.R37H|TREX2_ENST00000370231.2_Missense_Mutation_p.R37H|TREX2_ENST00000393862.2_Missense_Mutation_p.R37H|HAUS7_ENST00000484394.1_5'Flank|TREX2_ENST00000402951.1_Missense_Mutation_p.R80H|TREX2_ENST00000338525.2_Missense_Mutation_p.R37H|TREX2_ENST00000414588.1_Missense_Mutation_p.R79H			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	80					DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)	nucleus (GO:0005634)	3'-5'-exodeoxyribonuclease activity (GO:0008296)|exodeoxyribonuclease III activity (GO:0008853)|magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)			endometrium(4)|large_intestine(2)|lung(3)|ovary(2)	11	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGGAGGAGCGGTGGACAGC	0.657								Editing and processing nucleases																													p.R37H		Atlas-SNP	.											.	TREX2	36	.	0			c.G110A						.						41	42	41					X																	152710779		2202	4299	6501	SO:0001583	missense	11219	exon2			GAGGAGCGGTGGA	AF151107	CCDS35437.1	Xq28	2012-05-08			ENSG00000183479	ENSG00000183479			12270	protein-coding gene	gene with protein product		300370				10391904	Standard	NM_080701		Approved		uc011myp.2	Q9BQ50	OTTHUMG00000159319	ENST00000334497.2:c.239G>A	chrX.hg19:g.152710779C>T	ENSP00000334993:p.Arg80His	115.0	0.0		177.0	56.0	NM_080701	Q45F08|Q9UN77	Missense_Mutation	SNP	ENST00000334497.2	hg19		.	.	.	.	.	.	.	.	.	.	C	15.78	2.933924	0.52866	.	.	ENSG00000183479	ENST00000393862;ENST00000330912;ENST00000338525;ENST00000334497;ENST00000370232;ENST00000402951;ENST00000414588;ENST00000370231	T;T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92	5.04	4.18	0.49190	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.572588	0.14640	U	0.307244	T	0.41949	0.1181	L	0.55990	1.75	0.30388	N	0.78124	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.40572	-0.9556	10	0.72032	D	0.01	0.6256	5.8999	0.18960	0.1883:0.7104:0.0:0.1013	.	79;80	Q06S70;Q9BQ50	.;TREX2_HUMAN	H	37;37;37;80;80;80;79;37	ENSP00000377442:R37H;ENSP00000333441:R37H;ENSP00000345218:R37H;ENSP00000334993:R80H;ENSP00000359252:R80H;ENSP00000386078:R80H;ENSP00000401692:R79H;ENSP00000359251:R37H	ENSP00000333441:R37H	R	-	2	0	TREX2	152363973	0.994000	0.37717	0.959000	0.39883	0.346000	0.29079	2.519000	0.45546	0.913000	0.36797	0.529000	0.55759	CGC	.	.		0.657	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701		T	152710779	C	T	152710779	3	4	90	1	0	0	0	0	1	0	0	0	16492	768	27	1	603	1	TREX2	23	152710779	Missense_Mutation	SNP	C	TCGA-DD-A118-01A-11D-A12Z-10	903994	152710779	2559781	110	12073										
ARHGAP4	393	hgsc.bcm.edu	37	chrX	153185069	153185069	+	Intron	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.036036036036036	4	1	0.649726110772976	2.15221774193548	0.382616487455197	1	1	0	ccccaccatggagggtgcacGagaaacccagcttggagcca	12	14	0	1			TCGA-DD-A118-01A-11D-A12Z-10	TCGA-DD-A118-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	48d84dbb-ab16-4a9d-8a01-2700d8c457d6	c8499913-0f62-4b43-a7d4-49fb5e292768	g.chrX:153185069G>T	ENST00000350060.5	-	6	723				ARHGAP4_ENST00000370016.1_Intron|ARHGAP4_ENST00000370028.3_Silent_p.L251L|ARHGAP4_ENST00000393721.1_Intron|ARHGAP4_ENST00000537206.1_Intron	NM_001666.4	NP_001657.3	P98171	RHG04_HUMAN	Rho GTPase activating protein 4						apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|negative regulation of axon extension (GO:0030517)|negative regulation of fibroblast migration (GO:0010764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)	Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GAGGGTGCACGAGAAACCCAG	0.597																																					p.L251L		Atlas-SNP	.											.	ARHGAP4	103	.	0			c.C753A						.						38	40	40					X																	153185069		692	1591	2283	SO:0001627	intron_variant	393	exon6			GTGCACGAGAAAC	X78817	CCDS14736.1, CCDS55540.1	Xq28	2010-02-09			ENSG00000089820	ENSG00000089820		"Rho GTPase activating proteins"	674	protein-coding gene	gene with protein product	"Rho-GAP hematopoietic protein C1"	300023				8570618	Standard	NM_001666		Approved	KIAA0131, C1, p115, RhoGAP4, SrGAP4	uc004fjk.2	P98171	OTTHUMG00000024226	ENST00000350060.5:c.682-332C>A	chrX.hg19:g.153185069G>T		140.0	0.0		201.0	29.0	NM_001164741	Q14144|Q86UY3	Silent	SNP	ENST00000350060.5	hg19	CCDS14736.1	.	.	.	.	.	.	.	.	.	.	g	0.290	-0.980845	0.02197	.	.	ENSG00000089820	ENST00000418750	.	.	.	0.803	-1.61	0.08399	.	.	.	.	.	T	0.16685	0.0401	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.13899	-1.0492	3	.	.	.	.	.	.	.	.	.	.	.	S	99	.	.	R	-	1	0	ARHGAP4	152838263	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.064000	0.00622	-2.769000	0.00366	-2.634000	0.00153	CGT	.	.		0.597	ARHGAP4-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061119.1	NM_001666		T	153185069	G	T	153185069	1	4	90	0	1	0	0	0	0	0	0	0	885	1045	37	1		1	ARHGAP4	23	153185069	Intron	SNP	G	TCGA-DD-A118-01A-11D-A12Z-10	474290	153185069	2085491	111	12074										
PLEKHN1	84069	hgsc.bcm.edu	37	chr1	909218	909218	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggctctccctgcagttcctCagtgccatgcagagtgcacg	11	14	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:909218C>T	ENST00000379409.2	+	13	1626	c.1596C>T	c.(1594-1596)ctC>ctT	p.L532L	PLEKHN1_ENST00000379410.3_Silent_p.L480L|PLEKHN1_ENST00000379407.3_Silent_p.L445L			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	532										central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		TGCAGTTCCTCAGTGCCATGC	0.682																																					p.L480L		Atlas-SNP	.											.	PLEKHN1	49	.	0			c.C1440T						.						23	28	27					1																	909218		2195	4294	6489	SO:0001819	synonymous_variant	84069	exon14			GTTCCTCAGTGCC	AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"Pleckstrin homology (PH) domain containing"	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.1596C>T	chr1.hg19:g.909218C>T		89.0	0.0		72.0	4.0	NM_032129	Q494U2|Q5SV98|Q9H0M7	Silent	SNP	ENST00000379409.2	hg19																																																																																				.	.		0.682	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129		T	909218	C	T	909218	2	4	91	1	0	0	0	0	0	0	0	1	12092	813	29	3		3	PLEKHN1	1	909218	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10		909218	248341403	1	12075										
FAM132A	388581	hgsc.bcm.edu	37	chr1	1178923	1178923	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcctcgcaggaaggcaccttGggcagcaggctgtgaggggc	18	11	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:1178923G>A	ENST00000330388.2	-	5	572	c.541C>T	c.(541-543)Caa>Taa	p.Q181*		NM_001014980.2	NP_001014980.1	Q5T7M4	ADIPL_HUMAN	family with sequence similarity 132, member A	181	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of glucose import (GO:0046324)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|lung(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AAGGCACCTTGGGCAGCAGGC	0.711																																					p.Q181X		Atlas-SNP	.											.	FAM132A	12	.	0			c.C541T						.						16	14	15					1																	1178923		2086	4136	6222	SO:0001587	stop_gained	388581	exon5			CACCTTGGGCAGC	BC089443	CCDS30554.1	1p36.33	2012-03-26	2007-03-27	2007-03-27	ENSG00000184163	ENSG00000184163			32308	protein-coding gene	gene with protein product	"adipolin", "adipose-derived insulin-sensitizing factor"		"C1q domain containing 2"	C1QDC2		21849507	Standard	NM_001014980		Approved	MGC105127, C1QTNF12, CTRP12	uc001adl.2	Q5T7M4	OTTHUMG00000001412	ENST00000330388.2:c.541C>T	chr1.hg19:g.1178923G>A	ENSP00000329137:p.Gln181*	38.0	0.0		43.0	4.0	NM_001014980	Q5EBL5	Nonsense_Mutation	SNP	ENST00000330388.2	hg19	CCDS30554.1	.	.	.	.	.	.	.	.	.	.	g	14.87	2.665457	0.47677	.	.	ENSG00000184163	ENST00000330388	.	.	.	3.98	2.98	0.34508	.	0.065332	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-12.7246	8.4044	0.32605	0.0:0.0:0.7665:0.2335	.	.	.	.	X	181	.	ENSP00000329137:Q181X	Q	-	1	0	FAM132A	1168786	1.000000	0.71417	0.979000	0.43373	0.044000	0.14063	1.729000	0.38115	2.252000	0.74401	0.544000	0.68410	CAA	.	.		0.711	FAM132A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004080.4	XM_371208		A	1178923	G	A	1178923	4	1	91	1	0	0	0	0	0	1	0	0	5447	1357	47	3	383	3	FAM132A	1	1178923	Nonsense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	269705	1178923	248071698	2	12076										
CASZ1	54897	hgsc.bcm.edu	37	chr1	10699170	10699170	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcgtcctcgtcgtcgtcctcGtcgtcgtcgtcctcgtcgtc	10	17	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:10699170G>C	ENST00000377022.3	-	21	5426	c.5109C>G	c.(5107-5109)gaC>gaG	p.D1703E	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1703	Asp-rich.|Glu-rich.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		cgtcgtcctcgtcgtcgtcgt	0.731																																					p.D1703E		Atlas-SNP	.											.	CASZ1	150	.	0			c.C5109G						.						6	6	6					1																	10699170		1787	3642	5429	SO:0001583	missense	54897	exon21			GTCCTCGTCGTCG	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.5109C>G	chr1.hg19:g.10699170G>C	ENSP00000366221:p.Asp1703Glu	24.0	0.0		39.0	6.0	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	hg19	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.462549	0.43736	.	.	ENSG00000130940	ENST00000377022	T	0.15952	2.38	2.95	-0.672	0.11377	.	0.130452	0.25302	U	0.031647	T	0.05868	0.0153	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.39078	-0.9631	10	0.21014	T	0.42	-5.0237	3.1393	0.06450	0.1027:0.344:0.3949:0.1584	.	1703	Q86V15	CASZ1_HUMAN	E	1703	ENSP00000366221:D1703E	ENSP00000366221:D1703E	D	-	3	2	CASZ1	10621757	0.995000	0.38212	0.909000	0.35828	0.536000	0.34869	0.566000	0.23593	-0.514000	0.06488	0.195000	0.17529	GAC	.	.		0.731	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		C	10699170	G	C	10699170	3	2	91	1	0	0	0	0	1	0	0	0	2687	1136	40	4	174	4	CASZ1	1	10699170	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	9520247	10699170	238551451	3	12077										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11574569	11574569	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgctgccctggtctacatccTcacctcctgctcaggtaggg	10	15	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:11574569T>C	ENST00000294484.6	+	4	1577	c.1439T>C	c.(1438-1440)cTc>cCc	p.L480P	PTCHD2_ENST00000389575.3_Missense_Mutation_p.L480P	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	480	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GTCTACATCCTCACCTCCTGC	0.577																																					p.L480P		Atlas-SNP	.											.	PTCHD2	193	.	0			c.T1439C						.						110	109	109					1																	11574569		2085	4212	6297	SO:0001583	missense	57540	exon4			ACATCCTCACCTC	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.1439T>C	chr1.hg19:g.11574569T>C	ENSP00000294484:p.Leu480Pro	131.0	0.0		84.0	4.0	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	hg19	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.240377	0.79912	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	D;D	0.96491	-4.03;-4.03	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.97238	0.9097	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97812	1.0251	10	0.66056	D	0.02	-39.7503	14.2637	0.66102	0.0:0.0:0.0:1.0	.	480	Q9P2K9	PTHD2_HUMAN	P	480	ENSP00000294484:L480P;ENSP00000374226:L480P	ENSP00000294484:L480P	L	+	2	0	PTCHD2	11497156	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.628000	0.83189	2.017000	0.59298	0.533000	0.62120	CTC	.	.		0.577	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		C	11574569	T	C	11574569	3	2	91	1	0	0	0	0	1	0	0	0	12745	1551	54	2	1449	2	PTCHD2	1	11574569	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	875399	11574569	237676052	4	12078										
SPEN	23013	hgsc.bcm.edu	37	chr1	16254866	16254866	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagaacgtgaaagatttgagTctgaccgggacagagaccat	13	7	1	6			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:16254866T>C	ENST00000375759.3	+	11	2335	c.2131T>C	c.(2131-2133)Tct>Cct	p.S711P		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	711	Arg-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		AAGATTTGAGTCTGACCGGGA	0.483																																					p.S711P		Atlas-SNP	.											.	SPEN	374	.	0			c.T2131C						.						107	107	107					1																	16254866		2203	4300	6503	SO:0001583	missense	23013	exon11			TTTGAGTCTGACC		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.2131T>C	chr1.hg19:g.16254866T>C	ENSP00000364912:p.Ser711Pro	130.0	0.0		113.0	5.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	T	7.257	0.604477	0.14002	.	.	ENSG00000065526	ENST00000375759	T	0.09630	2.96	4.84	2.55	0.30701	.	.	.	.	.	T	0.06962	0.0177	N	0.24115	0.695	0.20074	N	0.999937	B	0.16166	0.016	B	0.10450	0.005	T	0.35968	-0.9767	9	0.62326	D	0.03	-7.7306	3.4928	0.07644	0.2694:0.1582:0.0:0.5724	.	711	Q96T58	MINT_HUMAN	P	711	ENSP00000364912:S711P	ENSP00000364912:S711P	S	+	1	0	SPEN	16127453	0.009000	0.17119	0.768000	0.31515	0.871000	0.50021	0.067000	0.14510	0.367000	0.24454	0.460000	0.39030	TCT	.	.		0.483	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		C	16254866	T	C	16254866	3	2	91	1	0	0	0	0	1	0	0	0	15053	1667	58	2	2173	2	SPEN	1	16254866	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4680297	16254866	232995755	5	12079										
SPEN	23013	hgsc.bcm.edu	37	chr1	16255354	16255354	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atagcgaaaaaccgcctggaActcatgccttgcgtggtttt	10	10	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:16255354A>G	ENST00000375759.3	+	11	2823	c.2619A>G	c.(2617-2619)gaA>gaG	p.E873E		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	873					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		ACCGCCTGGAACTCATGCCTT	0.453																																					p.E873E		Atlas-SNP	.											.	SPEN	374	.	0			c.A2619G						.						94	98	97					1																	16255354		2203	4300	6503	SO:0001819	synonymous_variant	23013	exon11			CCTGGAACTCATG		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.2619A>G	chr1.hg19:g.16255354A>G		104.0	0.0		91.0	4.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	hg19	CCDS164.1																																																																																			.	.		0.453	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16255354	A	G	16255354	2	3	91	1	0	0	0	0	0	0	0	1	15053	40	2	2		2	SPEN	1	16255354	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	488	16255354	232995267	6	12080										
PADI2	11240	hgsc.bcm.edu	37	chr1	17402249	17402249	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agccagtctgagtagagctcCacgggcgcctgcacctgctg	13	14	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:17402249C>T	ENST00000375486.4	-	12	1443	c.1380G>A	c.(1378-1380)gtG>gtA	p.V460V	PADI2_ENST00000466151.1_5'UTR|PADI2_ENST00000444885.2_Silent_p.V344V	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	460					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	AGTAGAGCTCCACGGGCGCCT	0.602											OREG0013145	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V460V		Atlas-SNP	.											.	PADI2	72	.	0			c.G1380A						.						97	95	95					1																	17402249		2203	4300	6503	SO:0001819	synonymous_variant	11240	exon12			GAGCTCCACGGGC	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"Peptidyl arginine deiminases"	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.1380G>A	chr1.hg19:g.17402249C>T		132.0	0.0	717	101.0	5.0	NM_007365	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	hg19	CCDS177.1																																																																																			.	.		0.602	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			T	17402249	C	T	17402249	2	4	91	1	0	0	0	0	0	0	0	1	11387	581	21	3		3	PADI2	1	17402249	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1146895	17402249	231848372	7	12081										
KLHDC7A	127707	hgsc.bcm.edu	37	chr1	18809370	18809370	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcgcacacggccacggtgcGtgccaaggaaatcttcgtca	13	13	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:18809370G>A	ENST00000400664.1	+	1	1947	c.1895G>A	c.(1894-1896)cGt>cAt	p.R632H		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	632						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GCCACGGTGCGTGCCAAGGAA	0.706																																					p.R632H		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G1895A						.						21	23	22					1																	18809370		2202	4297	6499	SO:0001583	missense	127707	exon1			CGGTGCGTGCCAA	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.1895G>A	chr1.hg19:g.18809370G>A	ENSP00000383505:p.Arg632His	47.0	0.0		26.0	13.0	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	hg19	CCDS185.2	.	.	.	.	.	.	.	.	.	.	G	11.64	1.699241	0.30142	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.65178	-0.14	4.85	4.85	0.62838	Kelch-type beta propeller (1);	0.182827	0.47852	D	0.000206	T	0.38134	0.1029	N	0.14661	0.345	0.21220	N	0.999751	P;P	0.35348	0.496;0.496	B;B	0.14578	0.008;0.011	T	0.41448	-0.9508	10	0.59425	D	0.04	.	10.2342	0.43273	0.0923:0.0:0.9077:0.0	.	569;632	A7E2V3;Q5VTJ3	.;KLD7A_HUMAN	H	632;569	ENSP00000383505:R632H	ENSP00000383505:R632H	R	+	2	0	KLHDC7A	18681957	1.000000	0.71417	0.105000	0.21289	0.145000	0.21501	7.932000	0.87634	2.233000	0.73108	0.561000	0.74099	CGT	.	.		0.706	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375		A	18809370	G	A	18809370	3	1	91	1	0	0	0	0	1	0	0	0	8369	1145	40	1	1897	1	KLHDC7A	1	18809370	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	1407121	18809370	230441251	8	12082										
ALDH4A1	8659	hgsc.bcm.edu	37	chr1	19212052	19212052	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcaggaagatctgggcccggTctgcaataggcttcaggtcc	13	11	4	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:19212052T>C	ENST00000375341.3	-	5	625	c.368A>G	c.(367-369)gAc>gGc	p.D123G	ALDH4A1_ENST00000454547.1_5'UTR|ALDH4A1_ENST00000538839.1_Missense_Mutation_p.D123G|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000538309.1_Missense_Mutation_p.D63G|ALDH4A1_ENST00000290597.5_Missense_Mutation_p.D123G|MIR4695_ENST00000577305.1_RNA	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	123					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGGCCCGGTCTGCAATAGG	0.622																																					p.D123G		Atlas-SNP	.											.	ALDH4A1	72	.	0			c.A368G						.						42	38	39					1																	19212052		2203	4300	6503	SO:0001583	missense	8659	exon5			GCCCGGTCTGCAA	U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"Aldehyde dehydrogenases"	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.368A>G	chr1.hg19:g.19212052T>C	ENSP00000364490:p.Asp123Gly	64.0	0.0		50.0	4.0	NM_003748	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	hg19	CCDS188.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.599861	0.87055	.	.	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309;ENST00000375335;ENST00000454547;ENST00000375334;ENST00000432718	T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04	5.41	5.41	0.78517	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.049262	0.85682	D	0.000000	D	0.84147	0.5408	M	0.73372	2.23	0.80722	D	1	P	0.51933	0.949	P	0.55508	0.777	D	0.86015	0.1503	10	0.66056	D	0.02	-44.778	14.2726	0.66159	0.0:0.0:0.0:1.0	.	123	P30038	AL4A1_HUMAN	G	123;123;123;63;107;21;63;107	ENSP00000290597:D123G;ENSP00000364490:D123G;ENSP00000446071:D123G;ENSP00000442988:D63G;ENSP00000393209:D107G	ENSP00000290597:D123G	D	-	2	0	ALDH4A1	19084639	1.000000	0.71417	0.998000	0.56505	0.900000	0.52787	5.678000	0.68153	2.063000	0.61619	0.459000	0.35465	GAC	.	.		0.622	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1			C	19212052	T	C	19212052	3	2	91	1	0	0	0	0	1	0	0	0	501	1667	58	2	1367	2	ALDH4A1	1	19212052	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	402682	19212052	230038569	9	12083										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22181466	22181466	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtgtcgcgatgtctgtgcgcTctgaccgggcctgccgtggg	17	12	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:22181466T>C	ENST00000374695.3	-	48	6087	c.6008A>G	c.(6007-6009)gAg>gGg	p.E2003G	HSPG2_ENST00000430507.1_5'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2003	Ig-like C2-type 5.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GTCTGTGCGCTCTGACCGGGC	0.662																																					p.E2003G		Atlas-SNP	.											.	HSPG2	311	.	0			c.A6008G						.						70	68	69					1																	22181466		2203	4300	6503	SO:0001583	missense	3339	exon48			GTGCGCTCTGACC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6008A>G	chr1.hg19:g.22181466T>C	ENSP00000363827:p.Glu2003Gly	161.0	0.0		139.0	6.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.049436	0.36181	.	.	ENSG00000142798	ENST00000374695	T	0.68331	-0.32	5.45	5.45	0.79879	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37530	N	0.002046	T	0.51787	0.1695	N	0.17082	0.46	0.44247	D	0.997098	B	0.28128	0.201	B	0.28385	0.089	T	0.53613	-0.8414	10	0.49607	T	0.09	.	13.4719	0.61287	0.0:0.0:0.0:1.0	.	2003	P98160	PGBM_HUMAN	G	2003	ENSP00000363827:E2003G	ENSP00000363827:E2003G	E	-	2	0	HSPG2	22054053	1.000000	0.71417	0.993000	0.49108	0.042000	0.13812	6.862000	0.75484	2.080000	0.62538	0.402000	0.26972	GAG	.	.		0.662	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		C	22181466	T	C	22181466	3	2	91	1	0	0	0	0	1	0	0	0	7439	1551	54	2	7367	2	HSPG2	1	22181466	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2969414	22181466	227069155	10	12084										
EPHA8	2046	hgsc.bcm.edu	37	chr1	22927919	22927919	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cggtaccgagaccacttcgcTgcgggcggatactcctctct	11	15	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:22927919T>C	ENST00000166244.3	+	16	2928	c.2856T>C	c.(2854-2856)gcT>gcC	p.A952A		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	952	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.A952A(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ACCACTTCGCTGCGGGCGGAT	0.701																																					p.A952A		Atlas-SNP	.											EPHA8,NS,carcinoma,0,1	EPHA8	221	.	1	Substitution - coding silent(1)	endometrium(1)	c.T2856C						.						40	46	44					1																	22927919		2203	4296	6499	SO:0001819	synonymous_variant	2046	exon16			CTTCGCTGCGGGC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.2856T>C	chr1.hg19:g.22927919T>C		42.0	0.0		36.0	4.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.		0.701	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		C	22927919	T	C	22927919	2	2	91	1	0	0	0	0	0	0	0	1	5175	1567	55	2		2	EPHA8	1	22927919	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	746453	22927919	226322702	11	12085										
RPL11	6135	hgsc.bcm.edu	37	chr1	24022368	24022368	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gccaaacacagaatcagcaaAgaggaggccatgcgctggtt	12	10	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:24022368A>G	ENST00000374550.3	+	5	522	c.477A>G	c.(475-477)aaA>aaG	p.K159K	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	159					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		GAATCAGCAAAGAGGAGGCCA	0.517																																					p.K159K		Atlas-SNP	.											.	RPL11	21	.	0			c.A477G						.						69	57	61					1																	24022368		2201	4299	6500	SO:0001819	synonymous_variant	6135	exon5			CAGCAAAGAGGAG	L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"L ribosomal proteins"	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.477A>G	chr1.hg19:g.24022368A>G		119.0	0.0		74.0	4.0	NM_000975	P25121|P39026|Q8TDH2|Q9Y674	Silent	SNP	ENST00000374550.3	hg19	CCDS238.1																																																																																			.	.		0.517	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975		G	24022368	A	G	24022368	2	3	91	1	0	0	0	0	0	0	0	1	13572	69	3	2		2	RPL11	1	24022368	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1094449	24022368	225228253	12	12086										
MYOM3	127294	hgsc.bcm.edu	37	chr1	24406666	24406666	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggcccgcacctcggatgccCgtacatcgtacggggggcct	14	15	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:24406666C>A	ENST00000374434.3	-	20	2588	c.2426G>T	c.(2425-2427)cGg>cTg	p.R809L	MYOM3_ENST00000329601.7_Missense_Mutation_p.R809L|MYOM3_ENST00000475306.1_5'Flank|RP11-293P20.2_ENST00000439239.2_RNA|RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000330966.7_Missense_Mutation_p.R810L	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	809	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		CTCGGATGCCCGTACATCGTA	0.612																																					p.R809L		Atlas-SNP	.											MYOM3,colon,carcinoma,0,1	MYOM3	131	.	0			c.G2426T						.						38	44	42					1																	24406666		2017	4170	6187	SO:0001583	missense	127294	exon20			GATGCCCGTACAT	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	26679	protein-coding gene	gene with protein product			"myomesin family, member 3"			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.2426G>T	chr1.hg19:g.24406666C>A	ENSP00000363557:p.Arg809Leu	65.0	0.0		49.0	3.0	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	hg19	CCDS41281.1	.	.	.	.	.	.	.	.	.	.	C	7.750	0.703214	0.15172	.	.	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.58652	0.32;0.32;0.32	5.38	2.17	0.27698	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.496761	0.22113	N	0.064454	T	0.53400	0.1794	M	0.65677	2.01	0.09310	N	1	B;P	0.36354	0.148;0.549	B;B	0.37304	0.246;0.217	T	0.43523	-0.9386	10	0.41790	T	0.15	.	9.8516	0.41059	0.0:0.691:0.0:0.309	.	809;809	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	L	809;810;809	ENSP00000363557:R809L;ENSP00000332670:R810L;ENSP00000328415:R809L	ENSP00000328415:R809L	R	-	2	0	MYOM3	24279253	0.002000	0.14202	0.034000	0.17996	0.003000	0.03518	0.052000	0.14163	0.130000	0.18549	0.563000	0.77884	CGG	.	.		0.612	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372		A	24406666	C	A	24406666	3	1	91	1	0	0	0	0	1	0	0	0	10102	652	23	1	1959	1	MYOM3	1	24406666	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	384298	24406666	224843955	13	12087										
IL22RA1	58985	hgsc.bcm.edu	37	chr1	24460747	24460747	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctctaagtggtagaacaggTcatggaagatgtcttccagg	13	7	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:24460747T>C	ENST00000270800.1	-	4	523	c.485A>G	c.(484-486)gAc>gGc	p.D162G		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	162	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		GTAGAACAGGTCATGGAAGAT	0.532																																					p.D162G		Atlas-SNP	.											.	IL22RA1	62	.	0			c.A485G						.						113	93	100					1																	24460747		2203	4300	6503	SO:0001583	missense	58985	exon4			AACAGGTCATGGA	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"Interleukins and interleukin receptors"	13700	protein-coding gene	gene with protein product		605457	"interleukin 22 receptor"	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.485A>G	chr1.hg19:g.24460747T>C	ENSP00000270800:p.Asp162Gly	147.0	0.0		85.0	4.0	NM_021258	A8K839|B2R9Y9|Q9HB22	Missense_Mutation	SNP	ENST00000270800.1	hg19	CCDS247.1	.	.	.	.	.	.	.	.	.	.	T	16.90	3.250320	0.59212	.	.	ENSG00000142677	ENST00000270800	T	0.46063	0.88	4.98	4.98	0.66077	Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	0.758712	0.12574	N	0.457035	T	0.49983	0.1589	L	0.32530	0.975	0.22581	N	0.998965	D;P	0.60575	0.988;0.875	D;P	0.63381	0.914;0.79	T	0.36744	-0.9735	10	0.45353	T	0.12	-2.7042	11.0682	0.47987	0.0:0.0:0.0:1.0	.	54;162	B4E2V9;Q8N6P7	.;I22R1_HUMAN	G	162	ENSP00000270800:D162G	ENSP00000270800:D162G	D	-	2	0	IL22RA1	24333334	0.960000	0.32886	0.066000	0.19879	0.854000	0.48673	3.640000	0.54350	1.875000	0.54330	0.459000	0.35465	GAC	.	.		0.532	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1			C	24460747	T	C	24460747	3	2	91	1	0	0	0	0	1	0	0	0	7682	1667	58	2	1255	2	IL22RA1	1	24460747	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	54081	24460747	224789874	14	12088										
IL22RA1	58985	hgsc.bcm.edu	37	chr1	24463631	24463631	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccaactcactgtgctgcagAgagctgaacctgtcagtcat	9	12	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:24463631A>G	ENST00000270800.1	-	3	383	c.345T>C	c.(343-345)tcT>tcC	p.S115S		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	115	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		TGTGCTGCAGAGAGCTGAACC	0.627																																					p.S115S		Atlas-SNP	.											.	IL22RA1	62	.	0			c.T345C						.						48	45	46					1																	24463631		2203	4300	6503	SO:0001819	synonymous_variant	58985	exon3			CTGCAGAGAGCTG	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"Interleukins and interleukin receptors"	13700	protein-coding gene	gene with protein product		605457	"interleukin 22 receptor"	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.345T>C	chr1.hg19:g.24463631A>G		61.0	0.0		49.0	4.0	NM_021258	A8K839|B2R9Y9|Q9HB22	Silent	SNP	ENST00000270800.1	hg19	CCDS247.1																																																																																			.	.		0.627	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1			G	24463631	A	G	24463631	2	3	91	1	0	0	0	0	0	0	0	1	7682	291	11	2		2	IL22RA1	1	24463631	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2884	24463631	224786990	15	12089										
C1orf135	79000	hgsc.bcm.edu	37	chr1	26162302	26162302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatctgactttctgtatgagAtgaaacactcttctggtcac	8	9	5	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:26162302A>G	ENST00000374298.3	-	3	310	c.256T>C	c.(256-258)Tct>Cct	p.S86P	AUNIP_ENST00000481602.1_Intron|AUNIP_ENST00000538789.1_Missense_Mutation_p.S86P	NM_024037.1	NP_076942.1	Q9H7T9	AUNIP_HUMAN	aurora kinase A and ninein interacting protein	86					spindle organization (GO:0007051)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)											TCTGTATGAGATGAAACACTC	0.418																																					p.S86P		Atlas-SNP	.											.	AUNIP	1	.	0			c.T256C						.						147	139	142					1																	26162302		2203	4300	6503	SO:0001583	missense	79000	exon3			TATGAGATGAAAC		CCDS266.1, CCDS72731.1	1p36.11	2012-08-07	2012-08-07	2012-08-07	ENSG00000127423	ENSG00000127423			28363	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 135"	C1orf135		20596670	Standard	NM_001287490		Approved	MGC2603, AIBp	uc001bkw.1	Q9H7T9	OTTHUMG00000007372	ENST00000374298.3:c.256T>C	chr1.hg19:g.26162302A>G	ENSP00000363416:p.Ser86Pro	139.0	0.0		96.0	4.0	NM_024037	C9EI59|Q53F70	Missense_Mutation	SNP	ENST00000374298.3	hg19	CCDS266.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.480097	0.44044	.	.	ENSG00000127423	ENST00000538789;ENST00000374298	T;T	0.60797	0.16;0.16	5.14	2.73	0.32206	.	0.276343	0.26331	N	0.024992	T	0.38799	0.1054	N	0.24115	0.695	0.09310	N	1	B	0.31227	0.314	B	0.34418	0.182	T	0.32161	-0.9917	10	0.72032	D	0.01	-7.3133	3.2163	0.06700	0.6823:0.0:0.1113:0.2065	.	86	Q9H7T9	CA135_HUMAN	P	86	ENSP00000443647:S86P;ENSP00000363416:S86P	ENSP00000363416:S86P	S	-	1	0	C1orf135	26034889	0.064000	0.20934	0.070000	0.20053	0.942000	0.58702	0.159000	0.16442	0.937000	0.37394	0.477000	0.44152	TCT	.	.		0.418	AUNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019309.2	NM_024037		G	26162302	A	G	26162302	3	3	91	1	0	0	0	0	1	0	0	0	2001	333	12	2	821	2	C1orf135	1	26162302	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1698671	26162302	223088319	16	12090										
NUDC	10726	hgsc.bcm.edu	37	chr1	27269479	27269479	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagcgatcattgatggggagCtctacaatgaagtgaaggtg	14	6	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:27269479C>A	ENST00000321265.5	+	6	787	c.664C>A	c.(664-666)Ctc>Atc	p.L222I		NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	222	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.				cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)				cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)		TGATGGGGAGCTCTACAATGA	0.587																																					p.L222I		Atlas-SNP	.											.	NUDC	15	.	0			c.C664A						.						99	100	99					1																	27269479		2203	4300	6503	SO:0001583	missense	10726	exon6			GGGGAGCTCTACA		CCDS292.1	1p35-p34	2013-08-06	2013-08-06		ENSG00000090273	ENSG00000090273			8045	protein-coding gene	gene with protein product		610325	"nuclear distribution gene C homolog (A. nidulans)", "nuclear distribution C homolog (A. nidulans)"				Standard	NM_006600		Approved	NudC	uc001bng.2	Q9Y266	OTTHUMG00000004226	ENST00000321265.5:c.664C>A	chr1.hg19:g.27269479C>A	ENSP00000319664:p.Leu222Ile	110.0	0.0		72.0	4.0	NM_006600	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Missense_Mutation	SNP	ENST00000321265.5	hg19	CCDS292.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.435768	0.83885	.	.	ENSG00000090273	ENST00000321265	T	0.53857	0.6	5.24	5.24	0.73138	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	0.000000	0.85682	D	0.000000	T	0.81307	0.4795	H	0.97440	4.005	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.79784	0.993;0.975	D	0.87208	0.2245	9	.	.	.	0.1555	13.2132	0.59836	0.0:0.9235:0.0:0.0765	.	173;222	Q9H2R7;Q9Y266	.;NUDC_HUMAN	I	222	ENSP00000319664:L222I	.	L	+	1	0	NUDC	27142066	0.969000	0.33509	0.994000	0.49952	0.743000	0.42351	2.330000	0.43885	2.473000	0.83533	0.449000	0.29647	CTC	.	.		0.587	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012172.2			A	27269479	C	A	27269479	3	1	91	1	0	0	0	0	1	0	0	0	10730	797	28	3	686	3	NUDC	1	27269479	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1107177	27269479	221981142	17	12091										
FCN3	8547	hgsc.bcm.edu	37	chr1	27697419	27697419	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctgctctgtaggaggaccaAgagcggaagaaatccacaga	12	10	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:27697419A>G	ENST00000270879.4	-	6	443	c.438T>C	c.(436-438)tcT>tcC	p.S146S	FCN3_ENST00000354982.2_Silent_p.S135S	NM_003665.2	NP_003656.2	O75636	FCN3_HUMAN	ficolin (collagen/fibrinogen domain containing) 3	146	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	7		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		AGGAGGACCAAGAGCGGAAGA	0.562																																					p.S146S		Atlas-SNP	.											.	FCN3	30	.	0			c.T438C						.						57	63	61					1																	27697419		2203	4300	6503	SO:0001819	synonymous_variant	8547	exon6			GGACCAAGAGCGG	D88587	CCDS300.1, CCDS301.1	1p36.11	2014-09-17	2013-09-12		ENSG00000142748	ENSG00000142748		"Fibrinogen C domain containing"	3625	protein-coding gene	gene with protein product	"Hakata antigen"	604973	"ficolin (collagen/fibrinogen domain-containing) 3 (Hakata antigen)"			9694814, 10330454	Standard	NM_003665		Approved	FCNH, HAKA1	uc001boa.3	O75636	OTTHUMG00000005722	ENST00000270879.4:c.438T>C	chr1.hg19:g.27697419A>G		118.0	0.0		95.0	5.0	NM_003665	Q6IBJ5|Q8WW86	Silent	SNP	ENST00000270879.4	hg19	CCDS300.1																																																																																			.	.		0.562	FCN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000015667.1			G	27697419	A	G	27697419	2	3	91	1	0	0	0	0	0	0	0	1	5801	59	3	2		2	FCN3	1	27697419	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	427940	27697419	221553202	18	12092										
OPRD1	4985	hgsc.bcm.edu	37	chr1	29185650	29185650	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atatgttcaccagcatcttcAcgctcaccatgatgagtgtt	7	11	4	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:29185650A>G	ENST00000234961.2	+	2	654	c.412A>G	c.(412-414)Acg>Gcg	p.T138A		NM_000911.3	NP_000902.3	P41143	OPRD_HUMAN	opioid receptor, delta 1	138					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adult locomotory behavior (GO:0008344)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|negative regulation of gene expression (GO:0010629)|negative regulation of protein oligomerization (GO:0032460)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein import into nucleus, translocation (GO:0000060)|regulation of calcium ion transport (GO:0051924)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of sensory perception of pain (GO:0051930)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	enkephalin receptor activity (GO:0038046)|opioid receptor activity (GO:0004985)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CAGCATCTTCACGCTCACCAT	0.567																																					p.T138A		Atlas-SNP	.											.	OPRD1	36	.	0			c.A412G						.						167	135	146					1																	29185650		2203	4300	6503	SO:0001583	missense	4985	exon2			ATCTTCACGCTCA	U10504	CCDS329.1	1p36.1-p34.3	2012-08-08			ENSG00000116329	ENSG00000116329		"GPCR / Class A : Opioid receptors"	8153	protein-coding gene	gene with protein product		165195				8415697	Standard	NM_000911		Approved		uc001brf.1	P41143	OTTHUMG00000003646	ENST00000234961.2:c.412A>G	chr1.hg19:g.29185650A>G	ENSP00000234961:p.Thr138Ala	115.0	0.0		89.0	4.0	NM_000911	B5B0B8	Missense_Mutation	SNP	ENST00000234961.2	hg19	CCDS329.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.207697	0.79240	.	.	ENSG00000116329	ENST00000234961;ENST00000536280	T	0.39229	1.09	4.57	4.57	0.56435	GPCR, rhodopsin-like superfamily (1);	0.059839	0.64402	D	0.000003	T	0.69106	0.3074	H	0.94306	3.52	0.58432	D	0.999999	P	0.51653	0.947	P	0.62740	0.906	T	0.74234	-0.3731	10	0.33141	T	0.24	.	11.9375	0.52882	1.0:0.0:0.0:0.0	.	138	P41143	OPRD_HUMAN	A	138	ENSP00000234961:T138A	ENSP00000234961:T138A	T	+	1	0	OPRD1	29058237	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.139000	0.94554	1.924000	0.55735	0.379000	0.24179	ACG	.	.		0.567	OPRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010330.1	NM_000911		G	29185650	A	G	29185650	3	3	91	1	0	0	0	0	1	0	0	0	10893	159	6	2	418	2	OPRD1	1	29185650	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1488231	29185650	220064971	19	12093										
HDAC1	3065	hgsc.bcm.edu	37	chr1	32797350	32797350	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgcaggcgattcctgaggacGccatccctgaggagagtggc	15	11	0	3	rs375198135		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:32797350G>A	ENST00000373548.3	+	11	1246	c.1162G>A	c.(1162-1164)Gcc>Acc	p.A388T	HDAC1_ENST00000490081.1_3'UTR|HDAC1_ENST00000373541.2_Missense_Mutation_p.A195T	NM_004964.2	NP_004955.2	Q13547	HDAC1_HUMAN	histone deacetylase 1	388					ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|mitotic cell cycle (GO:0000278)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deacetylation (GO:0006476)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	18		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)	TCCTGAGGACGCCATCCCTGA	0.572																																					p.A388T		Atlas-SNP	.											HDAC1,NS,carcinoma,0,1	HDAC1	43	.	0			c.G1162A						.	G	THR/ALA	0,4406		0,0,2203	99	93	95		1162	4.5	1	1		95	1,8599	1.2+/-3.3	0,1,4299	no	missense	HDAC1	NM_004964.2	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	388/483	32797350	1,13005	2203	4300	6503	SO:0001583	missense	3065	exon11			GAGGACGCCATCC	D50405	CCDS360.1	1p34	2008-02-05			ENSG00000116478	ENSG00000116478			4852	protein-coding gene	gene with protein product		601241		RPD3L1		8602529	Standard	NM_004964		Approved	HD1, GON-10	uc001bvb.1	Q13547	OTTHUMG00000007529	ENST00000373548.3:c.1162G>A	chr1.hg19:g.32797350G>A	ENSP00000362649:p.Ala388Thr	87.0	0.0		70.0	4.0	NM_004964	Q92534	Missense_Mutation	SNP	ENST00000373548.3	hg19	CCDS360.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.851677	0.51270	0.0	1.16E-4	ENSG00000116478	ENST00000373548;ENST00000373541	T;T	0.74421	-0.84;-0.52	4.52	4.52	0.55395	.	0.101865	0.64402	D	0.000002	T	0.68632	0.3022	L	0.53249	1.67	0.52501	D	0.999952	B	0.13594	0.008	B	0.15870	0.014	T	0.65187	-0.6229	10	0.34782	T	0.22	-5.5647	13.1543	0.59508	0.0:0.0:0.8398:0.1602	.	388	Q13547	HDAC1_HUMAN	T	388;195	ENSP00000362649:A388T;ENSP00000362642:A195T	ENSP00000362642:A195T	A	+	1	0	HDAC1	32569937	1.000000	0.71417	0.984000	0.44739	0.966000	0.64601	5.501000	0.66950	2.447000	0.82792	0.563000	0.77884	GCC	.	.		0.572	HDAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019815.3	NM_004964		A	32797350	G	A	32797350	3	1	91	1	0	0	0	0	1	0	0	0	7013	1087	38	1	1204	1	HDAC1	1	32797350	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3611700	32797350	216453271	20	12094										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35884071	35884071	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gactgttggcaagaggaaacGaaatgaagatgatgaggttc	14	4	0	5			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:35884071G>T	ENST00000314607.6	+	29	4417	c.4337G>T	c.(4336-4338)cGa>cTa	p.R1446L	ZMYM4_ENST00000373297.2_Missense_Mutation_p.R1357L	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	1446					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R1446Q(2)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AAGAGGAAACGAAATGAAGAT	0.393																																					p.R1446L		Atlas-SNP	.											ZMYM4,rectum,carcinoma,0,2	ZMYM4	143	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4337T						.						121	113	116					1																	35884071		2203	4300	6503	SO:0001583	missense	9202	exon29			GGAAACGAAATGA	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.4337G>T	chr1.hg19:g.35884071G>T	ENSP00000322915:p.Arg1446Leu	123.0	0.0		97.0	4.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	hg19	CCDS389.1	.	.	.	.	.	.	.	.	.	.	G	33	5.283802	0.95489	.	.	ENSG00000146463	ENST00000314607;ENST00000373297	T;T	0.25250	1.81;1.84	5.84	5.84	0.93424	.	0.315320	0.33959	N	0.004389	T	0.41419	0.1158	L	0.55481	1.735	0.54753	D	0.999982	B	0.30114	0.269	B	0.43658	0.426	T	0.25187	-1.0139	10	0.72032	D	0.01	-7.1968	20.1381	0.98040	0.0:0.0:1.0:0.0	.	1446	Q5VZL5	ZMYM4_HUMAN	L	1446;1357	ENSP00000322915:R1446L;ENSP00000362394:R1357L	ENSP00000322915:R1446L	R	+	2	0	ZMYM4	35656658	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.650000	0.67944	2.763000	0.94921	0.650000	0.86243	CGA	.	.		0.393	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		T	35884071	G	T	35884071	3	4	91	1	0	0	0	0	1	0	0	0	17717	1058	37	1	4451	1	ZMYM4	1	35884071	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3086721	35884071	213366550	21	12095										
KIAA0319L	79932	hgsc.bcm.edu	37	chr1	35972224	35972224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catgcttacctctgcagagcCactggtagtcagaccaccta	8	14	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:35972224C>T	ENST00000325722.3	-	3	889	c.655G>A	c.(655-657)Ggc>Agc	p.G219S		NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	219						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCTGCAGAGCCACTGGTAGTC	0.443																																					p.G219S		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.G655A						.						157	145	149					1																	35972224		2203	4300	6503	SO:0001583	missense	79932	exon3			CAGAGCCACTGGT	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.655G>A	chr1.hg19:g.35972224C>T	ENSP00000318406:p.Gly219Ser	184.0	0.0		123.0	5.0	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	hg19	CCDS390.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.631|7.631	0.678785|0.678785	0.14841|0.14841	.|.	.|.	ENSG00000142687|ENSG00000142687	ENST00000325722;ENST00000426982;ENST00000440579;ENST00000373258;ENST00000469892|ENST00000431916	T;T;T;T;T|.	0.41400|.	3.36;3.36;2.83;1.57;1.0|.	5.55|5.55	2.49|2.49	0.30216|0.30216	.|.	0.891435|.	0.09683|.	N|.	0.769400|.	T|.	0.18551|.	0.0445|.	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	N|N	1|1	B;B;B|.	0.19583|.	0.037;0.022;0.0|.	B;B;B|.	0.15052|.	0.012;0.008;0.001|.	T|.	0.17289|.	-1.0374|.	10|.	0.02654|.	T|.	1|.	-0.8278|-0.8278	5.0196|5.0196	0.14354|0.14354	0.0:0.6431:0.1729:0.184|0.0:0.6431:0.1729:0.184	.|.	219;219;219|.	B4DYG9;B1AN14;Q8IZA0|.	.;.;K319L_HUMAN|.	S|X	219|82	ENSP00000318406:G219S;ENSP00000395883:G219S;ENSP00000407576:G219S;ENSP00000362355:G219S;ENSP00000419396:G219S|.	ENSP00000318406:G219S|.	G|W	-|-	1|2	0|0	KIAA0319L|KIAA0319L	35744811|35744811	0.076000|0.076000	0.21285|0.21285	0.031000|0.031000	0.17742|0.17742	0.770000|0.770000	0.43624|0.43624	1.052000|1.052000	0.30429|0.30429	1.464000|1.464000	0.47987|0.47987	0.655000|0.655000	0.94253|0.94253	GGC|TGG	.	.		0.443	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874		T	35972224	C	T	35972224	3	4	91	1	0	0	0	0	1	0	0	0	8178	594	21	3	2570	3	KIAA0319L	1	35972224	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	88153	35972224	213278397	22	12096										
RHBDL2	54933	hgsc.bcm.edu	37	chr1	39381373	39381373	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccacacagcatagtaaataaAcactgccagctgatggaggg	10	10	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:39381373A>G	ENST00000289248.2	-	3	1264	c.256T>C	c.(256-258)Ttt>Ctt	p.F86L	RHBDL2_ENST00000372985.3_Missense_Mutation_p.F166L|RHBDL2_ENST00000540558.1_Missense_Mutation_p.F86L|RP5-864K19.4_ENST00000433671.2_RNA|RHBDL2_ENST00000538156.1_Missense_Mutation_p.F153L|RHBDL2_ENST00000372990.1_Missense_Mutation_p.F86L			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			TAGTAAATAAACACTGCCAGC	0.502																																					p.F86L		Atlas-SNP	.											.	RHBDL2	28	.	0			c.T256C						.						105	94	98					1																	39381373		2203	4300	6503	SO:0001583	missense	54933	exon3			AAATAAACACTGC	AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315			16083	protein-coding gene	gene with protein product		608962	"rhomboid (veinlet, Drosophila)-like 2"				Standard	NM_017821		Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.256T>C	chr1.hg19:g.39381373A>G	ENSP00000289248:p.Phe86Leu	134.0	0.0		84.0	5.0	NM_017821	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	Missense_Mutation	SNP	ENST00000289248.2	hg19	CCDS30680.1	.	.	.	.	.	.	.	.	.	.	A	35	5.514409	0.96402	.	.	ENSG00000158315	ENST00000372990;ENST00000289248;ENST00000538156;ENST00000372985;ENST00000540558	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.33933	0.0880	M	0.80332	2.49	0.80722	D	1	D;D;D	0.62365	0.988;0.991;0.991	P;P;P	0.57204	0.755;0.815;0.696	T	0.14615	-1.0466	10	0.54805	T	0.06	-21.9011	14.3335	0.66574	1.0:0.0:0.0:0.0	.	166;153;86	B7Z1Y9;B3KUN4;Q9NX52	.;.;RHBL2_HUMAN	L	86;86;153;166;86	ENSP00000362081:F86L;ENSP00000289248:F86L;ENSP00000439227:F153L;ENSP00000362076:F166L;ENSP00000441097:F86L	ENSP00000289248:F86L	F	-	1	0	RHBDL2	39153960	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	8.543000	0.90651	2.026000	0.59711	0.450000	0.29827	TTT	.	.		0.502	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001216.1	NM_017821		G	39381373	A	G	39381373	3	3	91	1	0	0	0	0	1	0	0	0	13337	43	2	2	679	2	RHBDL2	1	39381373	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3409149	39381373	209869248	23	12097										
BMP8A	353500	hgsc.bcm.edu	37	chr1	39991422	39991422	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gacagcagcaacaacgtcatCctgcgcaagcaccgcaacat	8	15	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:39991422C>A	ENST00000331593.5	+	7	1507	c.1161C>A	c.(1159-1161)atC>atA	p.I387I	RP11-69E11.4_ENST00000431553.1_RNA|RP11-69E11.4_ENST00000417869.1_RNA|RP11-69E11.4_ENST00000441741.1_RNA|RP11-69E11.4_ENST00000331856.2_RNA|RP11-69E11.4_ENST00000450157.1_RNA|RP11-69E11.4_ENST00000458207.1_RNA|RP11-69E11.4_ENST00000440190.1_RNA	NM_181809.3	NP_861525.2	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8a	387					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|diet induced thermogenesis (GO:0002024)|growth (GO:0040007)|negative regulation of insulin secretion (GO:0046676)|ossification (GO:0001503)|regulation of energy homeostasis (GO:2000505)	extracellular space (GO:0005615)				kidney(1)|large_intestine(2)|lung(1)|skin(1)	5	Lung NSC(20;2.08e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;9.69e-19)|Epithelial(16;9.34e-17)|all cancers(16;1.73e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACAACGTCATCCTGCGCAAGC	0.617																																					p.I387I		Atlas-SNP	.											.	BMP8A	24	.	0			c.C1161A						.						172	136	148					1																	39991422		2203	4300	6503	SO:0001819	synonymous_variant	353500	exon7			CGTCATCCTGCGC	AY303954	CCDS437.1	1p35-p32	2014-01-30			ENSG00000183682	ENSG00000183682		"Bone morphogenetic proteins", "Endogenous ligands"	21650	protein-coding gene	gene with protein product							Standard	NM_181809		Approved		uc001cdi.3	Q7Z5Y6	OTTHUMG00000008394	ENST00000331593.5:c.1161C>A	chr1.hg19:g.39991422C>A		99.0	0.0		85.0	5.0	NM_181809	Q5T3A5	Silent	SNP	ENST00000331593.5	hg19	CCDS437.1																																																																																			.	.		0.617	BMP8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023079.1	NM_181809		A	39991422	C	A	39991422	2	1	91	1	0	0	0	0	0	0	0	1	1466	845	30	3		3	BMP8A	1	39991422	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	610049	39991422	209259199	24	12098										
ZNF642	339559	hgsc.bcm.edu	37	chr1	40961674	40961674	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaagccttcagctataactcTtcacttagtcgacatcatga	5	11	4	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:40961674T>C	ENST00000372706.1	+	6	2530	c.1524T>C	c.(1522-1524)tcT>tcC	p.S508S	ZFP69_ENST00000372705.3_Silent_p.S508S|RP11-656D10.3_ENST00000450713.1_RNA			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	508					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										GCTATAACTCTTCACTTAGTC	0.378																																					p.S508S		Atlas-SNP	.											.	.	.	.	0			c.T1524C						.						62	64	63					1																	40961674		2203	4300	6503	SO:0001819	synonymous_variant	339559	exon6			TAACTCTTCACTT	AK122618	CCDS30686.1	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187815	ENSG00000187815		"Zinc fingers, C2H2-type", "-", "-", "-"	24708	protein-coding gene	gene with protein product	"ZFP69 zinc finger protein A"		"zinc finger protein 642"	ZNF642			Standard	XM_005270808		Approved	ZKSCAN23A, FLJ16030, ZFP69A, ZSCAN54A	uc001cfo.3	Q49AA0	OTTHUMG00000007303	ENST00000372706.1:c.1524T>C	chr1.hg19:g.40961674T>C		123.0	0.0		96.0	4.0	NM_198494	Q5SWM5|Q6ZWK8	Silent	SNP	ENST00000372706.1	hg19	CCDS30686.1																																																																																			.	.		0.378	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494		C	40961674	T	C	40961674	2	2	91	1	0	0	0	0	0	0	0	1	18073	1596	56	2		2	ZNF642	1	40961674	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	970252	40961674	208288947	25	12099										
SCMH1	22955	hgsc.bcm.edu	37	chr1	41579042	41579042	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggagtcgaagcggcaccagtAgtcaaaggcccctcgccacc	12	15	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:41579042A>G	ENST00000326197.7	-	7	927	c.628T>C	c.(628-630)Tac>Cac	p.Y210H	SCMH1_ENST00000397171.2_Missense_Mutation_p.Y149H|SCMH1_ENST00000361191.5_Missense_Mutation_p.Y149H|SCMH1_ENST00000372595.1_Missense_Mutation_p.Y149H|SCMH1_ENST00000402904.2_Missense_Mutation_p.Y210H|SCMH1_ENST00000361705.3_Missense_Mutation_p.Y163H|SCMH1_ENST00000397174.2_Missense_Mutation_p.Y190H|SCMH1_ENST00000456518.2_Intron|SCMH1_ENST00000372597.1_Missense_Mutation_p.Y163H|SCMH1_ENST00000372596.1_Missense_Mutation_p.Y149H|SCMH1_ENST00000337495.5_Missense_Mutation_p.Y220H					sex comb on midleg homolog 1 (Drosophila)											breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				CGGCACCAGTAGTCAAAGGCC	0.572																																					p.Y220H		Atlas-SNP	.											.	SCMH1	120	.	0			c.T658C						.						111	107	109					1																	41579042		2203	4300	6503	SO:0001583	missense	22955	exon8			ACCAGTAGTCAAA	AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"Sterile alpha motif (SAM) domain containing"	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.628T>C	chr1.hg19:g.41579042A>G	ENSP00000318094:p.Tyr210His	88.0	0.0		54.0	4.0	NM_001172219		Missense_Mutation	SNP	ENST00000326197.7	hg19	CCDS30688.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.913512	0.92178	.	.	ENSG00000010803	ENST00000361705;ENST00000402904;ENST00000397174;ENST00000397171;ENST00000361191;ENST00000372597;ENST00000372596;ENST00000337495;ENST00000372595;ENST00000326197	T;T;T;T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.62684	0.2448	M	0.88377	2.95	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;0.999;0.998	T	0.69953	-0.5005	10	0.72032	D	0.01	.	15.1834	0.72978	1.0:0.0:0.0:0.0	.	220;163;210	Q96GD3-2;Q96GD3-4;Q96GD3	.;.;SCMH1_HUMAN	H	163;210;190;149;149;163;149;220;149;210	ENSP00000354996:Y163H;ENSP00000386079:Y210H;ENSP00000380359:Y190H;ENSP00000380356:Y149H;ENSP00000354656:Y149H;ENSP00000361678:Y163H;ENSP00000361677:Y149H;ENSP00000337352:Y220H;ENSP00000361676:Y149H;ENSP00000318094:Y210H	ENSP00000318094:Y210H	Y	-	1	0	SCMH1	41351629	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.505000	0.81655	2.266000	0.75297	0.455000	0.32223	TAC	.	.		0.572	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1			G	41579042	A	G	41579042	3	3	91	1	0	0	0	0	1	0	0	0	13923	420	15	2	1390	2	SCMH1	1	41579042	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	617368	41579042	207671579	26	12100										
PPIH	10465	hgsc.bcm.edu	37	chr1	43133074	43133074	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctacctgtggtgatctcgcAgtgtggggagatgtagtcca	15	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:43133074A>G	ENST00000304979.3	+	9	540	c.518A>G	c.(517-519)cAg>cGg	p.Q173R	PPIH_ENST00000372550.1_Missense_Mutation_p.Q130R|PPIH_ENST00000455203.2_Missense_Mutation_p.Q130R	NM_006347.3	NP_006338.1	O43447	PPIH_HUMAN	peptidylprolyl isomerase H (cyclophilin H)	173	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)|U4/U6 x U5 tri-snRNP complex (GO:0046540)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|ribonucleoprotein complex binding (GO:0043021)			endometrium(1)|large_intestine(1)|lung(2)	4	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)			L-Proline(DB00172)	GTGATCTCGCAGTGTGGGGAG	0.478																																					p.Q173R	NSCLC(73;23 1942 10718 46854)	Atlas-SNP	.											.	PPIH	15	.	0			c.A518G						.						175	156	163					1																	43133074		2203	4300	6503	SO:0001583	missense	10465	exon9			TCTCGCAGTGTGG	AF016371	CCDS469.1	1p34.1	2012-06-07	2006-01-12		ENSG00000171960	ENSG00000171960			14651	protein-coding gene	gene with protein product	"USA-CyP SnuCyp-20", "cyclophilin H", "U-snRNP-associated cyclophilin SunCyp-20", "small nuclear ribonucleoprotein particle-specific cyclophilin H", "rotamase H", "peptidyl-prolyl cis-trans isomerase H", "PPIase h"	606095	"peptidyl prolyl isomerase H (cyclophilin H)"			9404889, 9570313	Standard	NM_006347		Approved	USA-CYP, CYP-20, SnuCyp-20, CYPH, MGC5016	uc001chq.3	O43447	OTTHUMG00000007520	ENST00000304979.3:c.518A>G	chr1.hg19:g.43133074A>G	ENSP00000306614:p.Gln173Arg	86.0	0.0		82.0	4.0	NM_006347	A6NNE7	Missense_Mutation	SNP	ENST00000304979.3	hg19	CCDS469.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.500232	0.64298	.	.	ENSG00000171960	ENST00000304979;ENST00000372550;ENST00000455203	T;T;T	0.40225	1.04;1.36;1.36	5.6	5.6	0.85130	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.167023	0.53938	D	0.000053	T	0.22627	0.0546	N	0.02539	-0.55	0.80722	D	1	B;B	0.17852	0.011;0.024	B;B	0.23150	0.02;0.044	T	0.11397	-1.0589	10	0.87932	D	0	.	13.7456	0.62872	1.0:0.0:0.0:0.0	.	130;173	A6NNE7;O43447	.;PPIH_HUMAN	R	173;130;130	ENSP00000306614:Q173R;ENSP00000361630:Q130R;ENSP00000416361:Q130R	ENSP00000306614:Q173R	Q	+	2	0	PPIH	42905661	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.896000	0.87350	2.125000	0.65367	0.533000	0.62120	CAG	.	.		0.478	PPIH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019778.1	NM_006347		G	43133074	A	G	43133074	3	3	91	1	0	0	0	0	1	0	0	0	12337	188	7	2	552	2	PPIH	1	43133074	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1554032	43133074	206117547	27	12101										
LEPRE1	64175	hgsc.bcm.edu	37	chr1	43224582	43224582	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggaggaagtcttcaaagggcTtctctcgacttgggtgggaa	15	7	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:43224582T>C	ENST00000296388.5	-	4	932	c.881A>G	c.(880-882)aAg>aGg	p.K294R	LEPRE1_ENST00000397054.3_Missense_Mutation_p.K294R|LEPRE1_ENST00000236040.4_Missense_Mutation_p.K294R			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	294					bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TTCAAAGGGCTTCTCTCGACT	0.443																																					p.K294R		Atlas-SNP	.											.	LEPRE1	130	.	0			c.A881G						.						110	99	103					1																	43224582		2203	4300	6503	SO:0001583	missense	64175	exon4			AAGGGCTTCTCTC	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 1", "growth suppressor 1"	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.881A>G	chr1.hg19:g.43224582T>C	ENSP00000296388:p.Lys294Arg	102.0	0.0		70.0	4.0	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	hg19	CCDS472.2	.	.	.	.	.	.	.	.	.	.	T	19.54	3.847584	0.71603	.	.	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027	T;T;T	0.37058	1.22;1.22;1.22	5.9	5.9	0.94986	.	0.141622	0.64402	D	0.000007	T	0.42268	0.1195	L	0.45137	1.4	0.38896	D	0.95721	D;P;P	0.57899	0.981;0.872;0.932	P;B;P	0.54629	0.757;0.34;0.49	T	0.24154	-1.0168	10	0.13470	T	0.59	-44.1592	14.2838	0.66232	0.0:0.0:0.0:1.0	.	294;159;294	Q32P28-3;B4DNM8;Q32P28	.;.;P3H1_HUMAN	R	294;294;294;159	ENSP00000380245:K294R;ENSP00000236040:K294R;ENSP00000296388:K294R	ENSP00000236040:K294R	K	-	2	0	LEPRE1	42997169	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.952000	0.40343	2.248000	0.74166	0.460000	0.39030	AAG	.	.		0.443	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356		C	43224582	T	C	43224582	3	2	91	1	0	0	0	0	1	0	0	0	8738	1609	56	2	1396	2	LEPRE1	1	43224582	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	91508	43224582	206026039	28	12102										
CCDC24	149473	hgsc.bcm.edu	37	chr1	44461509	44461509	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aggcatctgtggggccttctTgtgtctctcccaaccacagg	11	13	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:44461509T>C	ENST00000372318.3	+	8	853	c.682T>C	c.(682-684)Tgt>Cgt	p.C228R	SLC6A9_ENST00000372306.3_Intron|CCDC24_ENST00000479055.1_3'UTR|SLC6A9_ENST00000372307.3_Intron	NM_152499.1	NP_689712.1	Q8N4L8	CCD24_HUMAN	coiled-coil domain containing 24	228										endometrium(3)|large_intestine(2)|lung(3)|stomach(1)	9	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				GGGGCCTTCTTGTGTCTCTCC	0.537																																					p.C228R		Atlas-SNP	.											.	CCDC24	22	.	0			c.T682C						.						113	114	114					1																	44461509		2203	4300	6503	SO:0001583	missense	149473	exon8			CCTTCTTGTGTCT		CCDS507.1	1p34.1	2008-02-05			ENSG00000159214	ENSG00000159214			28688	protein-coding gene	gene with protein product						12477932	Standard	NM_152499		Approved	MGC45441	uc001clj.3	Q8N4L8	OTTHUMG00000008299	ENST00000372318.3:c.682T>C	chr1.hg19:g.44461509T>C	ENSP00000361392:p.Cys228Arg	116.0	0.0		86.0	4.0	NM_152499	Q6RWT2	Missense_Mutation	SNP	ENST00000372318.3	hg19	CCDS507.1	.	.	.	.	.	.	.	.	.	.	T	9.357	1.067077	0.20067	.	.	ENSG00000159214	ENST00000372318	.	.	.	5.03	1.11	0.20524	.	1.266720	0.05585	N	0.573587	T	0.34890	0.0913	L	0.54323	1.7	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.10450	0.001;0.005	T	0.22312	-1.0220	9	0.23302	T	0.38	-11.2091	3.2879	0.06939	0.1736:0.2214:0.0:0.605	.	192;228	Q8N4L8-2;Q8N4L8	.;CCD24_HUMAN	R	228	.	ENSP00000361392:C228R	C	+	1	0	CCDC24	44234096	0.000000	0.05858	0.001000	0.08648	0.790000	0.44656	-1.005000	0.03674	0.337000	0.23665	0.421000	0.28195	TGT	.	.		0.537	CCDC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022865.1	NM_152499		C	44461509	T	C	44461509	3	2	91	1	0	0	0	0	1	0	0	0	2801	1812	63	2	708	2	CCDC24	1	44461509	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1236927	44461509	204789112	29	12103										
HECTD3	79654	hgsc.bcm.edu	37	chr1	45469234	45469234	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccgcatagcggagcttctccTcgcataccttggcactgtgg	11	14	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:45469234T>C	ENST00000372172.4	-	21	2587	c.2516A>G	c.(2515-2517)gAg>gGg	p.E839G	HECTD3_ENST00000486132.1_5'UTR|HECTD3_ENST00000372168.3_Missense_Mutation_p.E449G	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	839	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					GAGCTTCTCCTCGCATACCTT	0.612																																					p.E839G		Atlas-SNP	.											.	HECTD3	158	.	0			c.A2516G						.						84	88	87					1																	45469234		2133	4248	6381	SO:0001583	missense	79654	exon21			TTCTCCTCGCATA	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.2516A>G	chr1.hg19:g.45469234T>C	ENSP00000361245:p.Glu839Gly	146.0	0.0		109.0	5.0	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Missense_Mutation	SNP	ENST00000372172.4	hg19	CCDS41318.1	.	.	.	.	.	.	.	.	.	.	.	19.18	3.777538	0.70107	.	.	ENSG00000126107	ENST00000372172;ENST00000372168	T;T	0.59083	0.29;0.29	5.72	4.59	0.56863	HECT (4);	0.100986	0.64402	D	0.000001	T	0.70954	0.3283	M	0.85859	2.78	0.80722	D	1	B;D	0.56287	0.022;0.975	B;P	0.54060	0.048;0.741	T	0.74372	-0.3687	10	0.56958	D	0.05	.	11.5447	0.50685	0.0:0.0699:0.0:0.9301	.	839;449	Q5T447;Q5T447-2	HECD3_HUMAN;.	G	839;449	ENSP00000361245:E839G;ENSP00000361241:E449G	ENSP00000361241:E449G	E	-	2	0	HECTD3	45241821	1.000000	0.71417	0.998000	0.56505	0.508000	0.34012	7.654000	0.83653	0.994000	0.38892	0.375000	0.23000	GAG	.	.		0.612	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		C	45469234	T	C	45469234	3	2	91	1	0	0	0	0	1	0	0	0	7050	1551	54	2	73	2	HECTD3	1	45469234	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1007725	45469234	203781387	30	12104										
CCDC17	149483	hgsc.bcm.edu	37	chr1	46086573	46086573	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aatccctgcgcaccacactcAcctgaggaatcccattcagc	6	17	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:46086573A>G	ENST00000528266.1	-	11	1747		c.e11+1		CCDC17_ENST00000343901.2_Splice_Site|CCDC17_ENST00000421127.2_Splice_Site|CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000464739.1_5'Flank			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17											kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					CACCACACTCACCTGAGGAAT	0.592																																					.		Atlas-SNP	.											.	CCDC17	54	.	0			c.1599+2T>C						.						55	47	50					1																	46086573		2203	4300	6503	SO:0001630	splice_region_variant	149483	exon12			ACACTCACCTGAG		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.1599+1T>C	chr1.hg19:g.46086573A>G		118.0	0.0		88.0	4.0	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Splice_Site	SNP	ENST00000528266.1	hg19	CCDS44131.2	.	.	.	.	.	.	.	.	.	.	A	22.5	4.299858	0.81136	.	.	ENSG00000159588	ENST00000421127;ENST00000343901;ENST00000528266	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3473	0.74350	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CCDC17	45859160	1.000000	0.71417	0.995000	0.50966	0.936000	0.57629	6.287000	0.72671	2.263000	0.75096	0.533000	0.62120	.	.	.		0.592	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	Intron	G	46086573	A	G	46086573	5	3	91	1	0	0	0	0	0	0	1	0	2795	173	6	2	279	2	CCDC17	1	46086573	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	617339	46086573	203164048	31	12105										
CMPK1	51727	hgsc.bcm.edu	37	chr1	47840605	47840605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtattgaacgatgtcttgagAggggaaagagtagtggtagg	17	2	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:47840605A>G	ENST00000371873.5	+	4	645	c.496A>G	c.(496-498)Agg>Ggg	p.R166G	CMPK1_ENST00000450808.2_Missense_Mutation_p.R117G	NM_001136140.1|NM_016308.2	NP_001129612.1|NP_057392.1			cytidine monophosphate (UMP-CMP) kinase 1, cytosolic											endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|stomach(2)	8						ATGTCTTGAGAGGGGAAAGAG	0.363																																					p.R166G		Atlas-SNP	.											.	CMPK1	13	.	0			c.A496G						.						81	79	80					1																	47840605		2203	4300	6503	SO:0001583	missense	51727	exon4			CTTGAGAGGGGAA	AF070416	CCDS549.1, CCDS44135.1	1p34.1-p33	2008-02-05	2008-01-25	2008-01-25	ENSG00000162368	ENSG00000162368	2.7.4.14		18170	protein-coding gene	gene with protein product	"UMP-CMP kinase", "Cytidine monophosphate kinase"	191710	"cytidylate kinase"	CMPK		10462544	Standard	NM_016308		Approved	UMP-CMPK	uc001cri.3	P30085	OTTHUMG00000007849	ENST00000371873.5:c.496A>G	chr1.hg19:g.47840605A>G	ENSP00000360939:p.Arg166Gly	135.0	0.0		91.0	4.0	NM_016308		Missense_Mutation	SNP	ENST00000371873.5	hg19	CCDS549.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.588893	0.66105	.	.	ENSG00000162368	ENST00000371873;ENST00000450808	T;T	0.80566	-1.39;-0.55	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.89051	0.6605	M	0.78344	2.41	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.90008	0.4119	10	0.72032	D	0.01	-22.1585	12.4682	0.55771	0.8606:0.1394:0.0:0.0	.	117;166	E9PGI8;B2R6S5	.;.	G	166;117	ENSP00000360939:R166G;ENSP00000398192:R117G	ENSP00000360939:R166G	R	+	1	2	CMPK1	47613192	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.809000	0.47971	2.323000	0.78572	0.528000	0.53228	AGG	.	.		0.363	CMPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021646.2	NM_016308		G	47840605	A	G	47840605	3	3	91	1	0	0	0	0	1	0	0	0	3582	295	11	2	510	2	CMPK1	1	47840605	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1754032	47840605	201410016	32	12106										
FAF1	11124	hgsc.bcm.edu	37	chr1	50941209	50941209	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggaagctacaaaatcaaagAcaatctggagcttgttgctg	10	7	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:50941209A>G	ENST00000396153.2	-	18	2247	c.1796T>C	c.(1795-1797)gTc>gCc	p.V599A	FAF1_ENST00000545823.1_Missense_Mutation_p.V357A|FAF1_ENST00000371778.4_Missense_Mutation_p.V599A	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	599	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.				apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		AAAATCAAAGACAATCTGGAG	0.498																																					p.V599A		Atlas-SNP	.											.	FAF1	64	.	0			c.T1796C						.						98	100	99					1																	50941209		2203	4300	6503	SO:0001583	missense	11124	exon18			TCAAAGACAATCT	AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"UBX domain containing"	3578	protein-coding gene	gene with protein product	"TNFRSF6-associated factor 1", "UBX domain protein 3A"	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.1796T>C	chr1.hg19:g.50941209A>G	ENSP00000379457:p.Val599Ala	115.0	0.0		97.0	4.0	NM_007051	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Missense_Mutation	SNP	ENST00000396153.2	hg19	CCDS554.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.877865	0.91664	.	.	ENSG00000185104	ENST00000396153;ENST00000371778;ENST00000545823;ENST00000371780;ENST00000543607	.	.	.	5.51	5.51	0.81932	UBX (3);	0.124659	0.53938	D	0.000057	T	0.69531	0.3121	M	0.75085	2.285	0.52099	D	0.999944	P;P	0.38280	0.583;0.625	B;B	0.43701	0.428;0.185	T	0.74097	-0.3775	9	0.87932	D	0	-3.8747	15.6291	0.76888	1.0:0.0:0.0:0.0	.	357;599	B4DEJ6;Q9UNN5	.;FAF1_HUMAN	A	599;599;357;439;447	.	ENSP00000360843:V599A	V	-	2	0	FAF1	50713797	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.890000	0.92477	2.083000	0.62718	0.533000	0.62120	GTC	.	.		0.498	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051		G	50941209	A	G	50941209	3	3	91	1	0	0	0	0	1	0	0	0	5374	275	10	2	164	2	FAF1	1	50941209	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3100604	50941209	198309412	33	12107										
CYB5RL	606495	hgsc.bcm.edu	37	chr1	54640392	54640392	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacagaccagtgcgaatggcTttctccgacagcagctgacc	10	14	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:54640392T>C	ENST00000534324.1	-	6	847	c.848A>G	c.(847-849)aAg>aGg	p.K283R	CYB5RL_ENST00000537208.1_Missense_Mutation_p.K215R|CYB5RL_ENST00000401046.3_Missense_Mutation_p.K135R|CYB5RL_ENST00000542737.1_Missense_Mutation_p.K283R|RP11-446E24.4_ENST00000311841.7_Intron|CYB5RL_ENST00000287899.8_Missense_Mutation_p.K215R|RP11-446E24.4_ENST00000525949.1_5'Flank|AL357673.1_ENST00000536061.1_5'Flank|CYB5RL_ENST00000419823.2_Missense_Mutation_p.K283R			Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like	283							cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|urinary_tract(1)	8						TGCGAATGGCTTTCTCCGACA	0.542																																					p.K283R		Atlas-SNP	.											.	CYB5RL	17	.	0			c.A848G						.						42	44	43					1																	54640392		1948	4167	6115	SO:0001583	missense	606495	exon8			AATGGCTTTCTCC		CCDS44151.1	1p32.3	2011-04-08			ENSG00000215883	ENSG00000215883			32220	protein-coding gene	gene with protein product						12477932	Standard	NM_001031672		Approved	LOC606495	uc009vzo.3	Q6IPT4	OTTHUMG00000008082	ENST00000534324.1:c.848A>G	chr1.hg19:g.54640392T>C	ENSP00000434343:p.Lys283Arg	62.0	0.0		41.0	4.0	NM_001031672	B7ZBS4|Q8NF25	Missense_Mutation	SNP	ENST00000534324.1	hg19	CCDS44151.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.707564	0.30322	.	.	ENSG00000215883	ENST00000419823;ENST00000401046;ENST00000534324;ENST00000287899;ENST00000542737;ENST00000537208	D;D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.15;-2.18;-2.15	5.14	2.79	0.32731	Oxidoreductase FAD/NAD(P)-binding (1);	0.176073	0.26446	N	0.024325	T	0.80204	0.4580	L	0.39397	1.21	0.32899	D	0.512984	B;B	0.15141	0.012;0.003	B;B	0.17433	0.018;0.006	T	0.76440	-0.2958	10	0.49607	T	0.09	-24.5527	8.26	0.31779	0.0:0.1568:0.0:0.8432	.	283;135	Q6IPT4;Q6IPT4-3	NB5R5_HUMAN;.	R	283;135;283;215;283;215	ENSP00000409075:K283R;ENSP00000383825:K135R;ENSP00000434343:K283R;ENSP00000287899:K215R;ENSP00000438151:K283R;ENSP00000443797:K215R	ENSP00000287899:K215R	K	-	2	0	CYB5RL	54412980	1.000000	0.71417	1.000000	0.80357	0.633000	0.38033	0.780000	0.26760	0.411000	0.25702	0.454000	0.30748	AAG	.	.		0.542	CYB5RL-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388318.1	NM_001031672		C	54640392	T	C	54640392	3	2	91	1	0	0	0	0	1	0	0	0	4132	1609	56	2	103	2	CYB5RL	1	54640392	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3699183	54640392	194610229	34	12108										
C1orf175	374977	hgsc.bcm.edu	37	chr1	55139780	55139780	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggagattggctgtgaggctcTggacggcatcatcatcctct	13	10	4	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:55139780T>C	ENST00000421030.2	+	10	2177	c.1892T>C	c.(1891-1893)cTg>cCg	p.L631P	MROH7_ENST00000454855.2_Missense_Mutation_p.L149P|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.L631P|MROH7_ENST00000409996.1_Missense_Mutation_p.L199P|MROH7_ENST00000545244.1_Missense_Mutation_p.L199P|MROH7_ENST00000395690.2_Missense_Mutation_p.L631P|MROH7_ENST00000339553.5_Missense_Mutation_p.L631P	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	631						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											TGTGAGGCTCTGGACGGCATC	0.527																																					p.L631P		Atlas-SNP	.											.	.	.	.	0			c.T1892C						.						119	125	123					1																	55139780		1964	4169	6133	SO:0001583	missense	374977	exon10			AGGCTCTGGACGG	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.1892T>C	chr1.hg19:g.55139780T>C	ENSP00000396622:p.Leu631Pro	172.0	0.0		147.0	6.0	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	hg19	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	T	15.76	2.927839	0.52759	.	.	ENSG00000184313	ENST00000421030;ENST00000545244;ENST00000414867;ENST00000339553;ENST00000409996;ENST00000454855;ENST00000395690	T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01	4.73	4.73	0.59995	.	0.172732	0.27008	N	0.021392	T	0.55689	0.1936	M	0.66939	2.045	0.80722	D	1	D;D;D	0.55385	0.971;0.958;0.958	P;P;P	0.58454	0.839;0.804;0.66	T	0.59123	-0.7513	10	0.62326	D	0.03	-10.9028	10.763	0.46277	0.0:0.0:0.0:1.0	.	631;631;199	F8W8P2;Q68CQ1;F5H7R4	.;HEAT8_HUMAN;.	P	631;199;660;631;199;149;631	ENSP00000396622:L631P;ENSP00000442333:L199P;ENSP00000343211:L631P;ENSP00000387048:L199P;ENSP00000401130:L149P;ENSP00000379044:L631P	ENSP00000343211:L631P	L	+	2	0	HEATR8	54912368	1.000000	0.71417	0.998000	0.56505	0.763000	0.43281	3.667000	0.54547	1.809000	0.52856	0.450000	0.29827	CTG	.	.		0.527	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		C	55139780	T	C	55139780	3	2	91	1	0	0	0	0	1	0	0	0	2018	1580	55	2	1922	2	C1orf175	1	55139780	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	499388	55139780	194110841	35	12109										
BSND	7809	hgsc.bcm.edu	37	chr1	55473990	55473990	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccaatgcatctccacatgacAgggaggaagcttgttcccca	9	13	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:55473990A>G	ENST00000371265.4	+	4	906	c.652A>G	c.(652-654)Agg>Ggg	p.R218G		NM_057176.2	NP_476517.1	Q8WZ55	BSND_HUMAN	barttin CLCNK-type chloride channel accessory beta subunit	218					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride channel activity (GO:0005254)|chloride channel regulator activity (GO:0017081)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17						TCCACATGACAGGGAGGAAGC	0.607																																					p.R218G	Ovarian(191;1657 2078 22894 42033 48899)	Atlas-SNP	.											.	BSND	36	.	0			c.A652G						.						47	47	47					1																	55473990		2203	4300	6503	SO:0001583	missense	7809	exon4			CATGACAGGGAGG	AY034632	CCDS602.1	1p32.3	2014-06-17	2014-06-17		ENSG00000162399	ENSG00000162399			16512	protein-coding gene	gene with protein product		606412	"deafness, autosomal recessive 73", "Bartter syndrome, infantile, with sensorineural deafness (Barttin)"	DFNB73		11687798, 11734858, 19646679	Standard	NM_057176		Approved	BART	uc001cye.3	Q8WZ55	OTTHUMG00000008112	ENST00000371265.4:c.652A>G	chr1.hg19:g.55473990A>G	ENSP00000360312:p.Arg218Gly	99.0	0.0		90.0	4.0	NM_057176	Q6NT28	Missense_Mutation	SNP	ENST00000371265.4	hg19	CCDS602.1	.	.	.	.	.	.	.	.	.	.	A	7.719	0.696747	0.15106	.	.	ENSG00000162399	ENST00000371265	T	0.63096	-0.02	4.74	-1.15	0.09709	.	1.224520	0.05600	N	0.576207	T	0.33323	0.0859	N	0.02736	-0.51	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20140	-1.0284	10	0.09338	T	0.73	-2.6923	8.9829	0.35977	0.6993:0.0:0.3007:0.0	.	218	Q8WZ55	BSND_HUMAN	G	218	ENSP00000360312:R218G	ENSP00000360312:R218G	R	+	1	2	BSND	55246578	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.089000	0.11180	-0.067000	0.12976	-1.223000	0.01593	AGG	.	.		0.607	BSND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022213.4	NM_057176		G	55473990	A	G	55473990	3	3	91	1	0	0	0	0	1	0	0	0	1533	179	7	2	666	2	BSND	1	55473990	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	334210	55473990	193776631	36	12110										
KANK4	163782	hgsc.bcm.edu	37	chr1	62739084	62739084	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aggagctcctggatcttcttCacatactgcccaatagtggc	9	12	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:62739084C>A	ENST00000371153.4	-	3	2070	c.1692G>T	c.(1690-1692)gtG>gtT	p.V564V	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	564						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						GGATCTTCTTCACATACTGCC	0.622																																					p.V564V		Atlas-SNP	.											.	KANK4	135	.	0			c.G1692T						.						57	53	54					1																	62739084		2203	4300	6503	SO:0001819	synonymous_variant	163782	exon3			CTTCTTCACATAC	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	27263	protein-coding gene	gene with protein product		614612	"ankyrin repeat domain 38"	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.1692G>T	chr1.hg19:g.62739084C>A		251.0	0.0		151.0	22.0	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Silent	SNP	ENST00000371153.4	hg19	CCDS620.1																																																																																			.	.		0.622	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		A	62739084	C	A	62739084	2	1	91	1	0	0	0	0	0	0	0	1	7988	813	29	3		3	KANK4	1	62739084	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	7265094	62739084	186511537	37	12111										
USP1	7398	hgsc.bcm.edu	37	chr1	62910512	62910512	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catgccaactcctaaaaaaaGaagaagtaaaaaatgtggca	7	7	0	2	rs372316949	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:62910512G>A	ENST00000339950.4	+	6	1476	c.661G>A	c.(661-663)Gaa>Aaa	p.E221K	USP1_ENST00000371146.1_Missense_Mutation_p.E221K	NM_003368.4	NP_003359.3	O94782	UBP1_HUMAN	ubiquitin specific peptidase 1	221	USP.				DNA repair (GO:0006281)|monoubiquitinated protein deubiquitination (GO:0035520)|protein deubiquitination (GO:0016579)|regulation of DNA repair (GO:0006282)|response to UV (GO:0009411)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	19		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		CCTAAAAAAAGAAGAAGTAAA	0.353																																					p.E221K	Ovarian(122;1846 2315 3982 19504)	Atlas-SNP	.											.	USP1	51	.	0			c.G661A						.						69	76	74					1																	62910512		2202	4299	6501	SO:0001583	missense	7398	exon6			AAAAAAGAAGAAG		CCDS621.1	1p31.3	2008-05-14	2005-08-08		ENSG00000162607	ENSG00000162607		"Ubiquitin-specific peptidases"	12607	protein-coding gene	gene with protein product		603478	"ubiquitin specific protease 1"			12838346	Standard	NM_003368		Approved		uc001dak.2	O94782	OTTHUMG00000008972	ENST00000339950.4:c.661G>A	chr1.hg19:g.62910512G>A	ENSP00000343526:p.Glu221Lys	171.0	0.0		125.0	13.0	NM_001017415	A0PJ95|D3DQ57|Q05BX7|Q59H66|Q9UFR0|Q9UNJ3	Missense_Mutation	SNP	ENST00000339950.4	hg19	CCDS621.1	.	.	.	.	.	.	.	.	.	.	G	32	5.177196	0.94846	.	.	ENSG00000162607	ENST00000371146;ENST00000339950	T;T	0.20463	2.07;2.07	5.43	5.43	0.79202	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.048213	0.85682	D	0.000000	T	0.31702	0.0805	N	0.17379	0.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.06092	-1.0846	10	0.23891	T	0.37	-17.8517	19.4366	0.94798	0.0:0.0:1.0:0.0	.	221	O94782	UBP1_HUMAN	K	221	ENSP00000360188:E221K;ENSP00000343526:E221K	ENSP00000343526:E221K	E	+	1	0	USP1	62683100	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.068000	0.93961	2.815000	0.96918	0.650000	0.86243	GAA	.	.		0.353	USP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024881.1	NM_001017415		A	62910512	G	A	62910512	3	1	91	1	0	0	0	0	1	0	0	0	17055	943	33	3	679	3	USP1	1	62910512	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	171428	62910512	186340109	38	12112										
DOCK7	85440	hgsc.bcm.edu	37	chr1	62995054	62995054	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggtcagagtaccgcgggtcTgagtcgtgactggagagtaa	17	7	2	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:62995054T>G	ENST00000340370.5	-	29	3599	c.3582A>C	c.(3580-3582)tcA>tcC	p.S1194S	DOCK7_ENST00000251157.5_Silent_p.S1225S	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1225					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						ACCGCGGGTCTGAGTCGTGAC	0.403																																					p.S1225S		Atlas-SNP	.											.	DOCK7	184	.	0			c.A3675C						.						109	103	105					1																	62995054		2203	4300	6503	SO:0001819	synonymous_variant	85440	exon30			CGGGTCTGAGTCG		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.3582A>C	chr1.hg19:g.62995054T>G		161.0	0.0		119.0	12.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	hg19	CCDS30734.1																																																																																			.	.		0.403	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		G	62995054	T	G	62995054	2	3	91	1	0	0	0	0	0	0	0	1	4694	1567	55	5		5	DOCK7	1	62995054	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	84542	62995054	186255567	39	12113										
JAK1	3716	hgsc.bcm.edu	37	chr1	65307245	65307245	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agccagctccttacatgatgGtgtcactggcctgcaccggc	11	14	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:65307245G>A	ENST00000342505.4	-	18	2691	c.2443C>T	c.(2443-2445)Cca>Tca	p.P815S	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	815	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TTACATGATGGTGTCACTGGC	0.493			Mis		ALL																																p.P815S		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.C2443T						.						121	115	117					1																	65307245		1967	4155	6122	SO:0001583	missense	3716	exon18			ATGATGGTGTCAC	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2443C>T	chr1.hg19:g.65307245G>A	ENSP00000343204:p.Pro815Ser	177.0	0.0		147.0	45.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519567	0.85495	.	.	ENSG00000162434	ENST00000342505	D	0.86230	-2.09	4.61	4.61	0.57282	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.93177	0.7827	M	0.83953	2.67	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	D	0.93553	0.6888	9	0.62326	D	0.03	-2.2034	17.9931	0.89175	0.0:0.0:1.0:0.0	.	815	P23458	JAK1_HUMAN	S	815	ENSP00000343204:P815S	ENSP00000343204:P815S	P	-	1	0	JAK1	65079833	1.000000	0.71417	0.698000	0.30274	0.738000	0.42128	9.146000	0.94640	2.550000	0.86006	0.557000	0.71058	CCA	.	.		0.493	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		A	65307245	G	A	65307245	3	1	91	1	0	0	0	0	1	0	0	0	7946	1261	44	3	1053	3	JAK1	1	65307245	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	2312191	65307245	183943376	40	12114										
JAK1	3716	hgsc.bcm.edu	37	chr1	65335078	65335078	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggacagccatccctagacacTcgttctcaatatcatgtcca	6	14	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:65335078T>C	ENST00000342505.4	-	6	811	c.563A>G	c.(562-564)gAg>gGg	p.E188G		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	188	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CCCTAGACACTCGTTCTCAAT	0.512			Mis		ALL																																p.E188G		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A563G						.						145	139	141					1																	65335078		2023	4191	6214	SO:0001583	missense	3716	exon6			AGACACTCGTTCT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.563A>G	chr1.hg19:g.65335078T>C	ENSP00000343204:p.Glu188Gly	149.0	0.0		87.0	4.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.726912	0.89390	.	.	ENSG00000162434	ENST00000342505	T	0.72615	-0.67	5.33	5.33	0.75918	FERM central domain (1);Band 4.1 domain (1);FERM domain (1);	.	.	.	.	D	0.82829	0.5122	M	0.85859	2.78	0.58432	D	0.999998	D	0.76494	0.999	D	0.80764	0.994	D	0.86274	0.1663	9	0.87932	D	0	.	15.6084	0.76692	0.0:0.0:0.0:1.0	.	188	P23458	JAK1_HUMAN	G	188	ENSP00000343204:E188G	ENSP00000343204:E188G	E	-	2	0	JAK1	65107666	1.000000	0.71417	0.999000	0.59377	0.767000	0.43475	7.676000	0.84012	2.152000	0.67230	0.533000	0.62120	GAG	.	.		0.512	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		C	65335078	T	C	65335078	3	2	91	1	0	0	0	0	1	0	0	0	7946	1551	54	2	2981	2	JAK1	1	65335078	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	27833	65335078	183915543	41	12115										
C1orf173	127254	hgsc.bcm.edu	37	chr1	75037860	75037860	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcttcactcagtctttccccTcctccttctttcctcagagc	4	18	5	1	rs10539747	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:75037860T>C	ENST00000326665.5	-	14	3752	c.3534A>G	c.(3532-3534)ggA>ggG	p.G1178G	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1178	Glu-rich.							p.G1178G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						GTCTTTCCCCTCCTCCTTCTT	0.493																																					p.G1178G		Atlas-SNP	.											C1orf173,NS,carcinoma,0,1	C1orf173	380	.	1	Substitution - coding silent(1)	lung(1)	c.A3534G						.						124	117	120					1																	75037860		2203	4297	6500	SO:0001819	synonymous_variant	127254	exon14			TTCCCCTCCTCCT																												ENST00000326665.5:c.3534A>G	chr1.hg19:g.75037860T>C		199.0	0.0		146.0	6.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	hg19	CCDS30755.1																																																																																			.	.		0.493	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			C	75037860	T	C	75037860	2	2	91	1	0	0	0	0	0	0	0	1	2016	1538	54	2		2	C1orf173	1	75037860	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9702782	75037860	174212761	42	12116										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79385900	79385900	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgtattgatcccaacaagaaAaacaagttcagcaagaaata	6	7	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:79385900A>G	ENST00000370742.3	-	10	1492	c.1429T>C	c.(1429-1431)Ttt>Ctt	p.F477L		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	477					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		CCAACAAGAAAAACAAGTTCA	0.328																																					p.F477L		Atlas-SNP	.											.	ELTD1	143	.	0			c.T1429C						.						87	82	83					1																	79385900		1823	4069	5892	SO:0001583	missense	64123	exon10			CAAGAAAAACAAG	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1429T>C	chr1.hg19:g.79385900A>G	ENSP00000359778:p.Phe477Leu	91.0	0.0		75.0	4.0	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631991	0.87660	.	.	ENSG00000162618	ENST00000370742	T	0.44482	0.92	5.01	5.01	0.66863	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.55433	0.1920	M	0.74467	2.265	0.80722	D	1	D	0.71674	0.998	D	0.73380	0.98	T	0.58951	-0.7545	9	.	.	.	.	15.0178	0.71600	1.0:0.0:0.0:0.0	.	477	Q9HBW9	ELTD1_HUMAN	L	477	ENSP00000359778:F477L	.	F	-	1	0	ELTD1	79158488	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.255000	0.95524	2.002000	0.58637	0.533000	0.62120	TTT	.	.		0.328	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		G	79385900	A	G	79385900	3	3	91	1	0	0	0	0	1	0	0	0	5086	14	1	2	667	2	ELTD1	1	79385900	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4348040	79385900	169864721	43	12117										
ALG14	199857	hgsc.bcm.edu	37	chr1	95448692	95448692	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctttcagagccggccactgAacaatgaagtaatctgagag	10	9	3	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:95448692A>G	ENST00000370205.5	-	4	637	c.591T>C	c.(589-591)gtT>gtC	p.V197V		NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	197					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	6		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		CCGGCCACTGAACAATGAAGT	0.403																																					p.V197V		Atlas-SNP	.											.	ALG14	13	.	0			c.T591C						.						108	100	103					1																	95448692		2203	4300	6503	SO:0001819	synonymous_variant	199857	exon4			CCACTGAACAATG		CCDS752.1	1p21.3	2013-02-21	2013-02-21		ENSG00000172339	ENSG00000172339			28287	protein-coding gene	gene with protein product		612866	"asparagine-linked glycosylation 14 homolog (yeast)", "asparagine-linked glycosylation 14 homolog (S. cerevisiae)"			15615718	Standard	NM_144988		Approved	MGC19780	uc001dra.2	Q96F25	OTTHUMG00000010781	ENST00000370205.5:c.591T>C	chr1.hg19:g.95448692A>G		162.0	0.0		100.0	4.0	NM_144988	A8K030	Silent	SNP	ENST00000370205.5	hg19	CCDS752.1																																																																																			.	.		0.403	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029699.2	NM_144988		G	95448692	A	G	95448692	2	3	91	1	0	0	0	0	0	0	0	1	516	233	9	2		2	ALG14	1	95448692	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	16062792	95448692	153801929	44	12118										
AKNAD1	254268	hgsc.bcm.edu	37	chr1	109394791	109394791	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagttggtcagtgagttctgGggtttgttcttttggccaag	15	5	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:109394791G>A	ENST00000370001.3	-	2	764	c.496C>T	c.(496-498)Cca>Tca	p.P166S	AKNAD1_ENST00000357393.4_Intron|AKNAD1_ENST00000369994.1_Missense_Mutation_p.P166S|AKNAD1_ENST00000369995.3_Missense_Mutation_p.P166S	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	166						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						GTGAGTTCTGGGGTTTGTTCT	0.408																																					p.P166S		Atlas-SNP	.											.	AKNAD1	83	.	0			c.C496T						.						59	61	60					1																	109394791		2203	4299	6502	SO:0001583	missense	254268	exon2			GTTCTGGGGTTTG	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 62"	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.496C>T	chr1.hg19:g.109394791G>A	ENSP00000359018:p.Pro166Ser	412.0	0.0		294.0	14.0	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	hg19	CCDS791.2	.	.	.	.	.	.	.	.	.	.	G	6.761	0.509331	0.12883	.	.	ENSG00000162641	ENST00000370001;ENST00000369994;ENST00000369995	T;T;T	0.07800	3.18;3.18;3.16	5.77	-2.1	0.07210	.	0.664334	0.14926	N	0.290352	T	0.01454	0.0047	L	0.29908	0.895	0.09310	N	0.999993	B	0.20052	0.041	B	0.14578	0.011	T	0.45234	-0.9275	10	0.30854	T	0.27	0.1785	5.138	0.14945	0.4742:0.0:0.3244:0.2014	.	166	Q5T1N1	AKND1_HUMAN	S	166	ENSP00000359018:P166S;ENSP00000359011:P166S;ENSP00000359012:P166S	ENSP00000359011:P166S	P	-	1	0	AKNAD1	109196314	0.000000	0.05858	0.834000	0.33040	0.604000	0.37047	-0.130000	0.10498	-0.199000	0.10317	-0.302000	0.09304	CCA	.	.		0.408	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763		A	109394791	G	A	109394791	3	1	91	1	0	0	0	0	1	0	0	0	464	1232	43	3	2074	3	AKNAD1	1	109394791	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	13946099	109394791	139855830	45	12119										
KIAA1324	57535	hgsc.bcm.edu	37	chr1	109716107	109716107	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggtttttaggtggagctaaaTcgaggcaataatgtcctcta	11	6	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:109716107T>C	ENST00000369939.3	+	6	891	c.708T>C	c.(706-708)aaT>aaC	p.N236N	KIAA1324_ENST00000529753.1_Silent_p.N236N	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	236					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		TGGAGCTAAATCGAGGCAATA	0.438																																					p.N236N		Atlas-SNP	.											.	KIAA1324	77	.	0			c.T708C						.						186	167	174					1																	109716107		2203	4300	6503	SO:0001819	synonymous_variant	57535	exon6			GCTAAATCGAGGC	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"estrogen induced gene 121"	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.708T>C	chr1.hg19:g.109716107T>C		107.0	0.0		91.0	4.0	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	hg19	CCDS794.1																																																																																			.	.		0.438	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775		C	109716107	T	C	109716107	2	2	91	1	0	0	0	0	0	0	0	1	8232	1432	50	2		2	KIAA1324	1	109716107	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	321316	109716107	139534514	46	12120										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109805547	109805547	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctgcaggtggacagccggcAcatagacatggctgacttca	12	12	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:109805547A>G	ENST00000271332.3	+	7	4725	c.4664A>G	c.(4663-4665)cAc>cGc	p.H1555R		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1555	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GACAGCCGGCACATAGACATG	0.652																																					p.H1555R	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.A4664G						.						46	44	45					1																	109805547		2203	4300	6503	SO:0001583	missense	1952	exon7			GCCGGCACATAGA	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.4664A>G	chr1.hg19:g.109805547A>G	ENSP00000271332:p.His1555Arg	111.0	0.0		94.0	4.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	A	8.398	0.841304	0.16891	.	.	ENSG00000143126	ENST00000271332	T	0.79352	-1.26	4.74	2.48	0.30137	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	T	0.29491	0.0735	N	0.03324	-0.35	0.40419	D	0.97982	B	0.02656	0.0	B	0.01281	0.0	T	0.14420	-1.0473	9	0.18276	T	0.48	.	4.8587	0.13571	0.5012:0.2806:0.2182:0.0	.	1555	Q9HCU4	CELR2_HUMAN	R	1555	ENSP00000271332:H1555R	ENSP00000271332:H1555R	H	+	2	0	CELSR2	109607070	0.000000	0.05858	0.948000	0.38648	0.953000	0.61014	0.364000	0.20325	0.962000	0.38057	0.459000	0.35465	CAC	.	.		0.652	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		G	109805547	A	G	109805547	3	3	91	1	0	0	0	0	1	0	0	0	3224	159	6	2	4690	2	CELSR2	1	109805547	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	89440	109805547	139445074	47	12121										
RSBN1	54665	hgsc.bcm.edu	37	chr1	114309729	114309729	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ataagttattacctgggaaaCtggaggttcatgaagatcta	10	5	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:114309729C>T	ENST00000261441.5	-	6	1990	c.1927G>A	c.(1927-1929)Gtt>Att	p.V643I	RSBN1_ENST00000369581.2_5'UTR	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	643						nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACCTGGGAAACTGGAGGTTCA	0.333																																					p.V643I		Atlas-SNP	.											.	RSBN1	71	.	0			c.G1927A						.						81	78	79					1																	114309729		2203	4300	6503	SO:0001583	missense	54665	exon6			GGGAAACTGGAGG	AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.1927G>A	chr1.hg19:g.114309729C>T	ENSP00000261441:p.Val643Ile	137.0	0.0		90.0	4.0	NM_018364	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Missense_Mutation	SNP	ENST00000261441.5	hg19	CCDS862.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.934912	0.52866	.	.	ENSG00000081019	ENST00000261441	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.38825	0.1055	L	0.28274	0.84	0.58432	D	0.999999	P	0.45715	0.865	B	0.44278	0.445	T	0.15065	-1.0450	9	0.17832	T	0.49	-10.0189	20.2566	0.98424	0.0:1.0:0.0:0.0	.	643	Q5VWQ0	RSBN1_HUMAN	I	643	.	ENSP00000261441:V643I	V	-	1	0	RSBN1	114111252	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.875000	0.56108	2.793000	0.96121	0.561000	0.74099	GTT	.	.		0.333	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364		T	114309729	C	T	114309729	3	4	91	1	0	0	0	0	1	0	0	0	13711	565	20	3	489	3	RSBN1	1	114309729	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	4504182	114309729	134940892	48	12122										
CD101	9398	hgsc.bcm.edu	37	chr1	117552527	117552527	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagaaaggaccactgtttagAgctgaaggttacccagtcag	11	9	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:117552527A>G	ENST00000256652.4	+	2	157	c.99A>G	c.(97-99)agA>agG	p.R33R	CD101_ENST00000369470.1_Silent_p.R33R	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	33	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CACTGTTTAGAGCTGAAGGTT	0.468																																					p.R33R		Atlas-SNP	.											.	CD101	95	.	0			c.A99G						.						95	90	91					1																	117552527		2203	4300	6503	SO:0001819	synonymous_variant	9398	exon2			GTTTAGAGCTGAA	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.99A>G	chr1.hg19:g.117552527A>G		113.0	0.0		84.0	4.0	NM_001256109	Q15856	Silent	SNP	ENST00000256652.4	hg19	CCDS891.1																																																																																			.	.		0.468	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		G	117552527	A	G	117552527	2	3	91	1	0	0	0	0	0	0	0	1	2964	301	11	2		2	CD101	1	117552527	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3242798	117552527	131698094	49	12123										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118727720	118727720	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaactgtgcagctatgagcgAgggttcccatatcttagaac	11	9	1	2	rs139383446	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:118727720A>G	ENST00000336338.5	-	1	126	c.61T>C	c.(61-63)Tcg>Ccg	p.S21P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	21						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GCTATGAGCGAGGGTTCCCAT	0.577																																					p.S21P		Atlas-SNP	.											.	SPAG17	263	.	0			c.T61C						.						204	195	198					1																	118727720		2203	4300	6503	SO:0001583	missense	200162	exon1			TGAGCGAGGGTTC		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.61T>C	chr1.hg19:g.118727720A>G	ENSP00000337804:p.Ser21Pro	152.0	0.0		97.0	4.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.824982	0.71143	.	.	ENSG00000155761	ENST00000336338	T	0.20463	2.07	4.99	3.83	0.44106	.	0.699229	0.12534	N	0.460503	T	0.14657	0.0354	L	0.40543	1.245	0.20975	N	0.999813	D	0.58268	0.982	P	0.54924	0.764	T	0.07770	-1.0755	10	0.56958	D	0.05	.	8.8277	0.35065	0.8103:0.1897:0.0:0.0	.	21	Q6Q759	SPG17_HUMAN	P	21	ENSP00000337804:S21P	ENSP00000337804:S21P	S	-	1	0	SPAG17	118529243	0.041000	0.20044	0.713000	0.30519	0.951000	0.60555	0.253000	0.18296	0.991000	0.38814	0.454000	0.30748	TCG	.	A|0.999;C|0.001		0.577	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		G	118727720	A	G	118727720	3	3	91	1	0	0	0	0	1	0	0	0	14994	304	11	2	6802	2	SPAG17	1	118727720	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1175193	118727720	130522901	50	12124										
HMGCS2	3158	hgsc.bcm.edu	37	chr1	120295968	120295968	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctaaaccagagccataagagAaggcaccaatcctggagcca	9	12	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:120295968A>G	ENST00000369406.3	-	7	1278	c.1229T>C	c.(1228-1230)tTc>tCc	p.F410S	HMGCS2_ENST00000544913.2_Missense_Mutation_p.F368S|HMGCS2_ENST00000476640.1_5'Flank	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	410					cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		GCCATAAGAGAAGGCACCAAT	0.478																																					p.F410S		Atlas-SNP	.											.	HMGCS2	58	.	0			c.T1229C						.						66	66	66					1																	120295968		2203	4300	6503	SO:0001583	missense	3158	exon7			TAAGAGAAGGCAC	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.1229T>C	chr1.hg19:g.120295968A>G	ENSP00000358414:p.Phe410Ser	144.0	0.0		97.0	4.0	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Missense_Mutation	SNP	ENST00000369406.3	hg19	CCDS905.1	.	.	.	.	.	.	.	.	.	.	A	19.40	3.821288	0.71028	.	.	ENSG00000134240	ENST00000369406;ENST00000544913	D;D	0.84298	-1.83;-1.83	5.39	4.24	0.50183	Hydroxymethylglutaryl-coenzyme A synthase C-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.080767	0.53938	D	0.000050	D	0.91205	0.7229	M	0.89534	3.04	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92212	0.5777	10	0.87932	D	0	-28.5483	10.7945	0.46453	0.8577:0.0:0.0:0.1423	.	368;410	B7Z8R3;P54868	.;HMCS2_HUMAN	S	410;368	ENSP00000358414:F410S;ENSP00000439495:F368S	ENSP00000358414:F410S	F	-	2	0	HMGCS2	120097491	1.000000	0.71417	1.000000	0.80357	0.674000	0.39518	6.684000	0.74538	0.945000	0.37605	0.379000	0.24179	TTC	.	.		0.478	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518		G	120295968	A	G	120295968	3	3	91	1	0	0	0	0	1	0	0	0	7242	246	9	2	309	2	HMGCS2	1	120295968	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1568248	120295968	128954653	51	12125										
TDRKH	11022	hgsc.bcm.edu	37	chr1	151751633	151751633	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atttttataagtcttgatagTagtaatgtcccttctgattc	6	6	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:151751633T>C	ENST00000368822.1	-	5	1140	c.507A>G	c.(505-507)ctA>ctG	p.L169L	TDRKH_ENST00000368823.1_Silent_p.L165L|TDRKH_ENST00000368827.6_Silent_p.L169L|TDRKH_ENST00000368825.3_Silent_p.L124L|TDRKH_ENST00000440583.2_5'UTR|TDRKH_ENST00000368824.3_Silent_p.L169L|TDRKH_ENST00000484421.1_5'UTR|TDRKH_ENST00000458431.2_Silent_p.L169L			Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing	169	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	mitochondrion (GO:0005739)|pi-body (GO:0071546)|piP-body (GO:0071547)	RNA binding (GO:0003723)			breast(5)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GTCTTGATAGTAGTAATGTCC	0.413																																					p.L169L		Atlas-SNP	.											.	TDRKH	45	.	0			c.A507G						.						187	175	178					1																	151751633		1878	4108	5986	SO:0001819	synonymous_variant	11022	exon5			TGATAGTAGTAAT	AF227192	CCDS41394.1, CCDS41395.1	1q21	2013-01-23	2003-11-07		ENSG00000182134	ENSG00000182134		"Tudor domain containing"	11713	protein-coding gene	gene with protein product		609501	"tudor and KH domain containing"			10767542	Standard	NM_001083964		Approved	TDRD2	uc001eza.4	Q9Y2W6	OTTHUMG00000013062	ENST00000368822.1:c.507A>G	chr1.hg19:g.151751633T>C		399.0	0.0		506.0	76.0	NM_001083965	D3DV24|Q5SZR3|Q5SZR5|Q8N582|Q9NYV5	Silent	SNP	ENST00000368822.1	hg19	CCDS41394.1																																																																																			.	.		0.413	TDRKH-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000036648.2	NM_006862		C	151751633	T	C	151751633	2	2	91	1	0	0	0	0	0	0	0	1	15752	1625	57	2		2	TDRKH	1	151751633	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	31455665	151751633	97498988	52	12126										
UBE2Q1	55585	hgsc.bcm.edu	37	chr1	154524627	154524627	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctttctctttgaggatctggAgatcgttgtgcaaagcgctg	12	8	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:154524627A>G	ENST00000292211.4	-	8	987	c.908T>C	c.(907-909)cTc>cCc	p.L303P	UBE2Q1_ENST00000497453.1_5'Flank|UBE2Q1-AS1_ENST00000441613.1_RNA	NM_017582.6	NP_060052.3	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q family member 1	303					embryo implantation (GO:0007566)|fertilization (GO:0009566)|mating behavior (GO:0007617)|prolactin secretion (GO:0070459)|protein ubiquitination (GO:0016567)|reproductive system development (GO:0061458)|suckling behavior (GO:0001967)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			GAGGATCTGGAGATCGTTGTG	0.493																																					p.L303P		Atlas-SNP	.											.	UBE2Q1	35	.	0			c.T908C						.						91	98	96					1																	154524627		2203	4300	6503	SO:0001583	missense	55585	exon8			ATCTGGAGATCGT	AJ243666	CCDS1069.1	1q22	2008-05-02	2008-05-02	2005-08-05	ENSG00000160714	ENSG00000160714		"Ubiquitin-conjugating enzymes E2"	15698	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2Q (putative)"	UBE2Q			Standard	NM_017582		Approved	PRO3094, NICE-5	uc001fff.1	Q7Z7E8	OTTHUMG00000037265	ENST00000292211.4:c.908T>C	chr1.hg19:g.154524627A>G	ENSP00000292211:p.Leu303Pro	104.0	0.0		150.0	6.0	NM_017582	B4DF92|Q3B841|Q5I0X2|Q6IS04|Q6P7P2|Q96MV4|Q9BVX5|Q9UGL6	Missense_Mutation	SNP	ENST00000292211.4	hg19	CCDS1069.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.518519	0.85495	.	.	ENSG00000160714	ENST00000292211	.	.	.	5.02	5.02	0.67125	Ubiquitin-conjugating enzyme, E2 (1);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.64402	D	0.000001	T	0.76535	0.4001	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81417	-0.0942	9	0.87932	D	0	-9.7885	13.7173	0.62705	1.0:0.0:0.0:0.0	.	303	Q7Z7E8	UB2Q1_HUMAN	P	303	.	ENSP00000292211:L303P	L	-	2	0	UBE2Q1	152791251	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.669000	0.91163	2.121000	0.65114	0.459000	0.35465	CTC	.	.		0.493	UBE2Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090704.1	NM_017582		G	154524627	A	G	154524627	3	3	91	1	0	0	0	0	1	0	0	0	16884	304	11	2	384	2	UBE2Q1	1	154524627	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2772994	154524627	94725994	53	12127										
GPATCH4	54865	hgsc.bcm.edu	37	chr1	156565051	156565051	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctggttccaccacctaaaaGtttcctcacctctatcttct	3	16	4	0	rs75463812		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:156565051G>C	ENST00000438976.2	-	8	1112	c.1082C>G	c.(1081-1083)aCt>aGt	p.T361S	GPATCH4_ENST00000368232.4_Missense_Mutation_p.T356S|GPATCH4_ENST00000497287.1_5'Flank			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	356							poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(3)|stomach(1)	17	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCACCTAAAAGTTTCCTCACC	0.507																																					p.T361S		Atlas-SNP	.											.	GPATCH4	34	.	0			c.C1082G						.						191	191	191					1																	156565051		2203	4300	6503	SO:0001583	missense	54865	exon8			CTAAAAGTTTCCT	BC056904	CCDS1146.1, CCDS44245.1	1q22	2013-01-28		2006-12-13	ENSG00000160818	ENSG00000160818		"G patch domain containing"	25982	protein-coding gene	gene with protein product				GPATC4		12477932	Standard	NM_015590		Approved	FLJ20249, DKFZP434F1735	uc001fpl.3	Q5T3I0	OTTHUMG00000033203	ENST00000438976.2:c.1082C>G	chr1.hg19:g.156565051G>C	ENSP00000396441:p.Thr361Ser	543.0	0.0		692.0	29.0	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Missense_Mutation	SNP	ENST00000438976.2	hg19	CCDS44245.1	.	.	.	.	.	.	.	.	.	.	G	8.543	0.873684	0.17322	.	.	ENSG00000160818	ENST00000368232;ENST00000368229;ENST00000438976	.	.	.	3.86	1.91	0.25777	.	0.922459	0.08880	N	0.880267	T	0.12178	0.0296	L	0.29908	0.895	0.09310	N	0.999997	B;B	0.22003	0.063;0.063	B;B	0.19666	0.026;0.026	T	0.33394	-0.9870	9	0.25106	T	0.35	-9.1235	8.1478	0.31121	0.0929:0.1607:0.7465:0.0	.	361;356	E9PAV9;Q5T3I0	.;GPTC4_HUMAN	S	356;356;361	.	ENSP00000357212:T356S	T	-	2	0	GPATCH4	154831675	0.003000	0.15002	0.000000	0.03702	0.036000	0.12997	1.263000	0.33004	0.555000	0.29079	0.557000	0.71058	ACT	.	C|1.000;|0.000		0.507	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725		C	156565051	G	C	156565051	3	2	91	1	0	0	0	0	1	0	0	0	6601	1029	36	4	49	4	GPATCH4	1	156565051	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	2040424	156565051	92685570	54	12128										
CASQ1	844	hgsc.bcm.edu	37	chr1	160160793	160160793	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gacaaggcctcacaaagacaAtttgagatggaggagctgat	12	7	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:160160793A>G	ENST00000368078.3	+	1	448	c.252A>G	c.(250-252)caA>caG	p.Q84Q	CASQ1_ENST00000368079.3_Silent_p.Q78Q			P31415	CASQ1_HUMAN	calsequestrin 1 (fast-twitch, skeletal muscle)	84					endoplasmic reticulum organization (GO:0007029)|ion transmembrane transport (GO:0034220)|protein polymerization (GO:0051258)|regulation of sequestering of calcium ion (GO:0051282)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to heat (GO:0009408)|response to organic substance (GO:0010033)|sarcomere organization (GO:0045214)|skeletal muscle tissue development (GO:0007519)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna lumen (GO:0014804)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	21	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CACAAAGACAATTTGAGATGG	0.522																																					p.Q84Q		Atlas-SNP	.											.	CASQ1	55	.	0			c.A252G						.						73	71	72					1																	160160793		2203	4300	6503	SO:0001819	synonymous_variant	844	exon1			AAGACAATTTGAG	S73775	CCDS1198.1, CCDS1198.2	1q21	2011-10-19			ENSG00000143318	ENSG00000143318		"Protein disulfide isomerases"	1512	protein-coding gene	gene with protein product	"calsequestrin 1, fast-twitch, skeletal muscle", "calmitine"	114250		CASQ		8406504, 2321095	Standard	NM_001231		Approved	PDIB1	uc010pja.2	P31415	OTTHUMG00000031607	ENST00000368078.3:c.252A>G	chr1.hg19:g.160160793A>G		88.0	0.0		109.0	5.0	NM_001231	B1AKZ2|B2R863|Q8TBW7	Silent	SNP	ENST00000368078.3	hg19	CCDS1198.2	.	.	.	.	.	.	.	.	.	.	A	8.410	0.843930	0.16963	.	.	ENSG00000143318	ENST00000441151	.	.	.	4.21	-4.72	0.03269	.	.	.	.	.	T	0.56411	0.1983	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68827	-0.5306	5	0.59425	D	0.04	.	13.1934	0.59723	0.3557:0.0:0.6443:0.0	.	.	.	.	S	34	.	ENSP00000387681:N34S	N	+	2	0	CASQ1	158427417	0.104000	0.21937	0.776000	0.31678	0.994000	0.84299	-0.497000	0.06428	-0.923000	0.03785	0.369000	0.22263	AAT	.	.		0.522	CASQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077412.1	NM_001231		G	160160793	A	G	160160793	2	3	91	1	0	0	0	0	0	0	0	1	2682	98	4	2		2	CASQ1	1	160160793	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3595742	160160793	89089828	55	12129										
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161019075	161019075	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggccaagacaaactgtgccTcatccagagacaggtcatcc	10	13	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:161019075T>C	ENST00000368013.3	-	12	2056	c.1736A>G	c.(1735-1737)gAg>gGg	p.E579G	ARHGAP30_ENST00000368016.3_Missense_Mutation_p.E579G|ARHGAP30_ENST00000368015.1_Missense_Mutation_p.E402G	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	579					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			AAACTGTGCCTCATCCAGAGA	0.592																																					p.E579G		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.A1736G						.						88	95	92					1																	161019075		2203	4300	6503	SO:0001583	missense	257106	exon12			TGTGCCTCATCCA	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"Rho GTPase activating proteins"	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.1736A>G	chr1.hg19:g.161019075T>C	ENSP00000356992:p.Glu579Gly	68.0	0.0		108.0	5.0	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	hg19	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.645527	0.67358	.	.	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.39997	2.65;2.55;1.05	5.18	5.18	0.71444	.	0.259165	0.27451	N	0.019310	T	0.42585	0.1209	M	0.65975	2.015	0.34804	D	0.737002	P;D	0.55605	0.877;0.972	B;P	0.53912	0.417;0.737	T	0.48854	-0.8998	10	0.44086	T	0.13	.	12.9925	0.58627	0.0:0.0:0.0:1.0	.	579;579	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	G	579;579;431;402	ENSP00000356995:E579G;ENSP00000356992:E579G;ENSP00000356994:E402G	ENSP00000356992:E579G	E	-	2	0	ARHGAP30	159285699	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	3.796000	0.55507	1.961000	0.56991	0.454000	0.30748	GAG	.	.		0.592	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		C	161019075	T	C	161019075	3	2	91	1	0	0	0	0	1	0	0	0	879	1551	54	2	1573	2	ARHGAP30	1	161019075	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	858282	161019075	88231546	56	12130										
NOS1AP	9722	hgsc.bcm.edu	37	chr1	162335312	162335312	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccagcacatctccctgctggTcaagcaggtgcaagagctgg	12	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:162335312T>C	ENST00000361897.5	+	9	1460	c.1058T>C	c.(1057-1059)gTc>gCc	p.V353A	NOS1AP_ENST00000530878.1_Missense_Mutation_p.V348A|RP11-565P22.6_ENST00000431696.1_Missense_Mutation_p.V39A|NOS1AP_ENST00000493151.1_Missense_Mutation_p.V58A	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	353					regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			TCCCTGCTGGTCAAGCAGGTG	0.607																																					p.V353A		Atlas-SNP	.											.	NOS1AP	139	.	0			c.T1058C						.						59	52	54					1																	162335312		2203	4300	6503	SO:0001583	missense	9722	exon9			TGCTGGTCAAGCA	AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"C-terminal PDZ domain ligand of neuronal nitric oxide synthase"	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.1058T>C	chr1.hg19:g.162335312T>C	ENSP00000355133:p.Val353Ala	68.0	0.0		85.0	4.0	NM_014697	B7ZLF5|O43564|Q3T551|Q5VU95	Missense_Mutation	SNP	ENST00000361897.5	hg19	CCDS1237.1	.	.	.	.	.	.	.	.	.	.	T	32	5.189634	0.94923	.	.	ENSG00000198929;ENSG00000198929;ENSG00000198929;ENSG00000198929;ENSG00000254706	ENST00000530878;ENST00000361897;ENST00000464284;ENST00000493151;ENST00000431696	D;D	0.84442	-1.85;-1.85	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.89455	0.6720	M	0.66297	2.02	.	.	.	D;D;D	0.76494	0.999;0.991;0.991	D;P;P	0.80764	0.994;0.639;0.787	D	0.90663	0.4592	9	0.59425	D	0.04	.	14.766	0.69640	0.0:0.0:0.0:1.0	.	58;348;353	Q3T551;B7ZLF5;O75052	.;.;CAPON_HUMAN	A	348;353;9;58;39	ENSP00000431586:V348A;ENSP00000355133:V353A	ENSP00000355133:V353A	V	+	2	0	NOS1AP;RP11-565P22.6	160601936	1.000000	0.71417	0.996000	0.52242	0.999000	0.98932	7.522000	0.81844	2.162000	0.67917	0.533000	0.62120	GTC	.	.		0.607	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697		C	162335312	T	C	162335312	3	2	91	1	0	0	0	0	1	0	0	0	10551	1667	58	2	1146	2	NOS1AP	1	162335312	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1316237	162335312	86915309	57	12131										
F5	2153	hgsc.bcm.edu	37	chr1	169510014	169510014	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtgtcactgatgtctggagaGagagtcacctggctgaggtc	15	8	3	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:169510014G>A	ENST00000367797.3	-	13	4515	c.4314C>T	c.(4312-4314)ctC>ctT	p.L1438L	F5_ENST00000367796.3_Silent_p.L1443L	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1438	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TGTCTGGAGAGAGAGTCACCT	0.507																																					p.L1438L		Atlas-SNP	.											.	F5	301	.	0			c.C4314T						.						70	74	73					1																	169510014		2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			TGGAGAGAGAGTC	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.4314C>T	chr1.hg19:g.169510014G>A		161.0	0.0		215.0	9.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	hg19	CCDS1281.1																																																																																			.	.		0.507	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169510014	G	A	169510014	2	1	91	1	0	0	0	0	0	0	0	1	5350	929	33	3		3	F5	1	169510014	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	7174702	169510014	79740607	58	12132										
TNR	7143	hgsc.bcm.edu	37	chr1	175375825	175375825	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caatgagcatgttcttcagaAccactgtttccccatctgcc	6	14	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:175375825A>G	ENST00000367674.2	-	3	734	c.26T>C	c.(25-27)gTt>gCt	p.V9A	TNR_ENST00000263525.2_Missense_Mutation_p.V9A			Q92752	TENR_HUMAN	tenascin R	9					associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					GTTCTTCAGAACCACTGTTTC	0.537																																					p.V9A		Atlas-SNP	.											.	TNR	399	.	0			c.T26C						.						141	129	133					1																	175375825		2203	4300	6503	SO:0001583	missense	7143	exon3			TTCAGAACCACTG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.26T>C	chr1.hg19:g.175375825A>G	ENSP00000356646:p.Val9Ala	122.0	0.0		171.0	7.0	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	A	6.929	0.541114	0.13250	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.26223	1.75;1.75	5.56	3.25	0.37280	.	0.617832	0.16137	N	0.227903	T	0.12305	0.0299	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.0	B;B	0.09377	0.004;0.0	T	0.31916	-0.9926	10	0.12430	T	0.62	.	7.2581	0.26187	0.7401:0.0:0.2599:0.0	.	9;9	B4DIX8;Q92752	.;TENR_HUMAN	A	9	ENSP00000356646:V9A;ENSP00000263525:V9A	ENSP00000263525:V9A	V	-	2	0	TNR	173642448	0.271000	0.24162	0.526000	0.27913	0.990000	0.78478	1.234000	0.32660	0.927000	0.37143	0.459000	0.35465	GTT	.	.		0.537	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		G	175375825	A	G	175375825	3	3	91	1	0	0	0	0	1	0	0	0	16353	43	2	2	4134	2	TNR	1	175375825	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	5865811	175375825	73874796	59	12133										
NFASC	23114	hgsc.bcm.edu	37	chr1	204937944	204937944	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agcccaacaccagacatcgcAtggtacaagaaaggtgggga	12	10	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:204937944A>G	ENST00000401399.1	+	9	1036	c.837A>G	c.(835-837)gcA>gcG	p.A279A	NFASC_ENST00000367172.4_Silent_p.A279A|NFASC_ENST00000339876.6_Silent_p.A279A|NFASC_ENST00000367170.4_Silent_p.A279A|NFASC_ENST00000404076.1_Silent_p.A273A|NFASC_ENST00000367171.4_Silent_p.A279A|NFASC_ENST00000404907.1_Silent_p.A290A|NFASC_ENST00000360049.4_Silent_p.A290A|NFASC_ENST00000513543.1_Silent_p.A290A|NFASC_ENST00000367169.4_Silent_p.A279A|NFASC_ENST00000539706.1_Silent_p.A290A|NFASC_ENST00000403080.1_Silent_p.A279A|NFASC_ENST00000338515.6_Silent_p.A279A|NFASC_ENST00000338586.6_Silent_p.A279A			O94856	NFASC_HUMAN	neurofascin	279	Ig-like C2-type 3.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CAGACATCGCATGGTACAAGA	0.512																																					p.A290A		Atlas-SNP	.											.	NFASC	396	.	0			c.A870G						.						69	62	64					1																	204937944		2203	4300	6503	SO:0001819	synonymous_variant	23114	exon10			CATCGCATGGTAC	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.837A>G	chr1.hg19:g.204937944A>G		87.0	0.0		100.0	4.0	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	hg19	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	A	9.552	1.116264	0.20795	.	.	ENSG00000163531	ENST00000367173	.	.	.	5.5	-11.0	0.00169	.	.	.	.	.	T	0.60366	0.2263	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.77448	-0.2584	4	.	.	.	.	16.347	0.83138	0.1114:0.3135:0.5751:0.0	.	.	.	.	R	249	.	.	H	+	2	0	NFASC	203204567	0.002000	0.14202	0.061000	0.19648	0.995000	0.86356	-1.564000	0.02152	-3.633000	0.00129	-0.297000	0.09499	CAT	.	.		0.512	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		G	204937944	A	G	204937944	2	3	91	1	0	0	0	0	0	0	0	1	10368	204	8	2		2	NFASC	1	204937944	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	29562119	204937944	44312677	60	12134										
LAMB3	3914	hgsc.bcm.edu	37	chr1	209788716	209788716	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggtccgctgagcgcagcatgAtggcctggctgccccgcagc	15	15	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:209788716A>G	ENST00000356082.4	-	23	3553	c.3419T>C	c.(3418-3420)aTc>aCc	p.I1140T	LAMB3_ENST00000391911.1_Missense_Mutation_p.I1140T|LAMB3_ENST00000367030.3_Missense_Mutation_p.I1140T	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	1140	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GCGCAGCATGATGGCCTGGCT	0.592																																					p.I1140T		Atlas-SNP	.											.	LAMB3	136	.	0			c.T3419C						.						101	84	90					1																	209788716		2203	4300	6503	SO:0001583	missense	3914	exon23			AGCATGATGGCCT	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.3419T>C	chr1.hg19:g.209788716A>G	ENSP00000348384:p.Ile1140Thr	75.0	0.0		98.0	4.0	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	hg19	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.147286	0.77888	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.36699	1.24;1.24;1.24	5.42	5.42	0.78866	.	0.222334	0.37715	N	0.001961	T	0.40222	0.1108	L	0.32530	0.975	0.32949	D	0.519421	D	0.57257	0.979	P	0.52554	0.702	T	0.56068	-0.8040	10	0.72032	D	0.01	.	13.6932	0.62559	1.0:0.0:0.0:0.0	.	1140	Q13751	LAMB3_HUMAN	T	1140	ENSP00000375778:I1140T;ENSP00000348384:I1140T;ENSP00000355997:I1140T	ENSP00000348384:I1140T	I	-	2	0	LAMB3	207855339	0.998000	0.40836	0.954000	0.39281	0.860000	0.49131	4.485000	0.60279	2.062000	0.61559	0.374000	0.22700	ATC	.	.		0.592	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		G	209788716	A	G	209788716	3	3	91	1	0	0	0	0	1	0	0	0	8621	333	12	2	103	2	LAMB3	1	209788716	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4850772	209788716	39461905	61	12135										
LAMB3	3914	hgsc.bcm.edu	37	chr1	209799289	209799289	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cactggtcacagcggggcccGgtcaagccagggcggcagag	17	13	2	1	rs376183751		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:209799289G>A	ENST00000356082.4	-	14	1814	c.1680C>T	c.(1678-1680)acC>acT	p.T560T	LAMB3_ENST00000391911.1_Silent_p.T560T|LAMB3_ENST00000367030.3_Silent_p.T560T|MIR4260_ENST00000583107.1_RNA	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	560	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		AGCGGGGCCCGGTCAAGCCAG	0.647																																					p.T560T		Atlas-SNP	.											LAMB3,bladder,carcinoma,0,1	LAMB3	136	.	0			c.C1680T						.	G	,,	1,4405		0,1,2202	25	28	27		1680,1680,1680	-10	0	1		27	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	,,	560/1173,560/1173,560/1173	209799289	1,13001	2203	4298	6501	SO:0001819	synonymous_variant	3914	exon14			GGGCCCGGTCAAG	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.1680C>T	chr1.hg19:g.209799289G>A		30.0	0.0		77.0	4.0	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	hg19	CCDS1487.1																																																																																			.	.		0.647	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		A	209799289	G	A	209799289	2	1	91	1	0	0	0	0	0	0	0	1	8621	1103	39	1		1	LAMB3	1	209799289	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	10573	209799289	39451332	62	12136										
RPS6KC1	26750	hgsc.bcm.edu	37	chr1	213415488	213415488	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcagatttttgaggaccttgAtaaaaaattagcactagcct	7	7	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:213415488A>G	ENST00000366960.3	+	11	2819	c.2669A>G	c.(2668-2670)gAt>gGt	p.D890G	RPS6KC1_ENST00000366959.3_Missense_Mutation_p.D878G|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543354.1_Missense_Mutation_p.D593G|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.D678G	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	890	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GAGGACCTTGATAAAAAATTA	0.428																																					p.D890G		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.A2669G						.						86	91	89					1																	213415488		2203	4300	6503	SO:0001583	missense	26750	exon11			ACCTTGATAAAAA	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.2669A>G	chr1.hg19:g.213415488A>G	ENSP00000355927:p.Asp890Gly	132.0	0.0		124.0	5.0	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	hg19	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	A	17.06	3.291679	0.59976	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	5.91	4.78	0.61160	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047787	0.85682	N	0.000000	T	0.69557	0.3124	L	0.35723	1.085	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.69691	-0.5077	10	0.51188	T	0.08	-47.1616	12.0664	0.53590	0.933:0.0:0.067:0.0	.	678;890;878	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	G	678;890;878;593	ENSP00000442306:D678G;ENSP00000355927:D890G;ENSP00000355926:D878G;ENSP00000439282:D593G	ENSP00000355926:D878G	D	+	2	0	RPS6KC1	211482111	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.495000	0.90481	1.049000	0.40321	0.533000	0.62120	GAT	.	.		0.428	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		G	213415488	A	G	213415488	3	3	91	1	0	0	0	0	1	0	0	0	13673	333	12	2	2711	2	RPS6KC1	1	213415488	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3616199	213415488	35835133	63	12137										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232650005	232650005	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtctgggatgctgcagatgCcccagtggttatgtttttcc	12	9	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:232650005C>A	ENST00000366630.1	-	2	1439	c.1081G>T	c.(1081-1083)Gca>Tca	p.A361S	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.A361S			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	361					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GCTGCAGATGCCCCAGTGGTT	0.488																																					p.A361S		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G1081T						.						101	103	103					1																	232650005		1952	4136	6088	SO:0001583	missense	57568	exon1			CAGATGCCCCAGT	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.1081G>T	chr1.hg19:g.232650005C>A	ENSP00000355589:p.Ala361Ser	61.0	0.0		70.0	48.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.694733	0.88830	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	D;D	0.91577	-2.87;-2.87	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.95472	0.8529	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95411	0.8498	10	0.72032	D	0.01	-26.4199	19.3561	0.94414	0.0:1.0:0.0:0.0	.	361	Q9P2F8	SI1L2_HUMAN	S	361	ENSP00000355589:A361S;ENSP00000262861:A361S	ENSP00000262861:A361S	A	-	1	0	SIPA1L2	230716628	1.000000	0.71417	0.938000	0.37757	0.992000	0.81027	7.651000	0.83577	2.810000	0.96702	0.650000	0.86243	GCA	.	.		0.488	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232650005	C	A	232650005	3	1	91	1	0	0	0	0	1	0	0	0	14345	739	26	3	4171	3	SIPA1L2	1	232650005	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	19234517	232650005	16600616	64	12138										
SH3BP5L	80851	hgsc.bcm.edu	37	chr1	249106273	249106273	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaagccaccgtgcgcaggctCagcagactcagggtatcggt	14	12	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:249106273C>G	ENST00000366472.5	-	7	2237	c.1008G>C	c.(1006-1008)ctG>ctC	p.L336L	SH3BP5L_ENST00000411742.2_Silent_p.L304L|SH3BP5L_ENST00000475978.1_5'UTR	NM_030645.1	NP_085148.1	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	336										endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TGCGCAGGCTCAGCAGACTCA	0.692																																					p.L336L		Atlas-SNP	.											.	SH3BP5L	47	.	0			c.G1008C						.						21	27	25					1																	249106273		2198	4296	6494	SO:0001819	synonymous_variant	80851	exon7			CAGGCTCAGCAGA	AB051507	CCDS31126.1	1q44	2008-02-05			ENSG00000175137	ENSG00000175137			29360	protein-coding gene	gene with protein product							Standard	NM_030645		Approved	KIAA1720	uc001iew.1	Q7L8J4	OTTHUMG00000040389	ENST00000366472.5:c.1008G>C	chr1.hg19:g.249106273C>G		63.0	0.0		83.0	12.0	NM_030645	B4DQ94|Q96FI5|Q9BQH8|Q9C0E3	Silent	SNP	ENST00000366472.5	hg19	CCDS31126.1																																																																																			.	.		0.692	SH3BP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097140.1	NM_030645		G	249106273	C	G	249106273	2	3	91	1	0	0	0	0	0	0	0	1	14263	813	29	4		4	SH3BP5L	1	249106273	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	16456268	249106273	144348	65	12139										
PXDN	7837	hgsc.bcm.edu	37	chr2	1664712	1664712	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggtgttccgggccacacacTcatagcgacctgcgtctgca	11	14	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:1664712T>C	ENST00000252804.4	-	14	1828	c.1778A>G	c.(1777-1779)gAg>gGg	p.E593G		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	593	Ig-like C2-type 4.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GGCCACACACTCATAGCGACC	0.537																																					p.E593G		Atlas-SNP	.											.	PXDN	255	.	0			c.A1778G						.						97	102	100					2																	1664712		2055	4191	6246	SO:0001583	missense	7837	exon14			ACACACTCATAGC	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1778A>G	chr2.hg19:g.1664712T>C	ENSP00000252804:p.Glu593Gly	78.0	0.0		75.0	4.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	hg19	CCDS46221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.65|17.65	3.442826|3.442826	0.63067|0.63067	.|.	.|.	ENSG00000130508|ENSG00000130508	ENST00000252804|ENST00000433670	T|.	0.77620|.	-1.11|.	5.05|5.05	5.05|5.05	0.67936|0.67936	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.063286|.	0.64402|.	N|.	0.000007|.	T|T	0.53110|0.53110	0.1776|0.1776	N|N	0.25380|0.25380	0.74|0.74	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.997|.	D;D|.	0.79108|.	0.991;0.992|.	T|T	0.50162|0.50162	-0.8860|-0.8860	10|5	0.87932|.	D|.	0|.	-46.6424|-46.6424	15.0638|15.0638	0.71977|0.71977	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	593;593|.	Q92626-2;Q92626|.	.;PXDN_HUMAN|.	G|G	593|589	ENSP00000252804:E593G|.	ENSP00000252804:E593G|.	E|S	-|-	2|1	0|0	PXDN|PXDN	1643719|1643719	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.027000|0.027000	0.11550|0.11550	7.908000|7.908000	0.87438|0.87438	2.028000|2.028000	0.59812|0.59812	0.482000|0.482000	0.46254|0.46254	GAG|AGT	.	.		0.537	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		C	1664712	T	C	1664712	3	2	91	1	0	0	0	0	1	0	0	0	12862	1551	54	2	2701	2	PXDN	2	1664712	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10		1664712	241534661	66	12140										
ASAP2	8853	hgsc.bcm.edu	37	chr2	9531316	9531316	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgctgccccctcttcgcgtgAcatctaccagtacgtttttt	7	15	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:9531316A>G	ENST00000281419.3	+	23	2849	c.2509A>G	c.(2509-2511)Aca>Gca	p.T837A	ASAP2_ENST00000491413.1_Intron|ASAP2_ENST00000315273.4_Intron	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	837	Pro-rich.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						TCTTCGCGTGACATCTACCAG	0.572																																					p.T837A		Atlas-SNP	.											.	ASAP2	91	.	0			c.A2509G						.						154	157	156					2																	9531316		2203	4300	6503	SO:0001583	missense	8853	exon23			CGCGTGACATCTA	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2509A>G	chr2.hg19:g.9531316A>G	ENSP00000281419:p.Thr837Ala	113.0	0.0		99.0	4.0	NM_003887	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	hg19	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.222354	0.58560	.	.	ENSG00000151693	ENST00000281419	T	0.56941	0.43	4.36	3.2	0.36748	.	0.646852	0.13487	N	0.384258	T	0.29389	0.0732	N	0.08118	0	0.80722	D	1	P	0.36027	0.533	B	0.34536	0.185	T	0.03060	-1.1077	10	0.21014	T	0.42	.	9.8219	0.40887	0.918:0.0:0.082:0.0	.	837	O43150	ASAP2_HUMAN	A	837	ENSP00000281419:T837A	ENSP00000281419:T837A	T	+	1	0	ASAP2	9448767	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.921000	0.56454	0.838000	0.34948	0.254000	0.18369	ACA	.	.		0.572	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		G	9531316	A	G	9531316	3	3	91	1	0	0	0	0	1	0	0	0	1011	275	10	2	2599	2	ASAP2	2	9531316	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	7866604	9531316	233668057	67	12141										
KLF11	8462	hgsc.bcm.edu	37	chr2	10188645	10188645	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttttcccgaaggaggaactAtgtatgcagcttcccaggtt	10	10	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:10188645A>G	ENST00000305883.1	+	3	1343	c.1181A>G	c.(1180-1182)tAt>tGt	p.Y394C	KLF11_ENST00000540845.1_Missense_Mutation_p.Y377C|KLF11_ENST00000535335.1_Missense_Mutation_p.Y377C	NM_003597.4	NP_003588.1	O14901	KLF11_HUMAN	Kruppel-like factor 11	394					apoptotic process (GO:0006915)|cellular response to peptide (GO:1901653)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)		AGGAGGAACTATGTATGCAGC	0.552											OREG0014425	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y394C	Melanoma(56;431 1507 23687 50789)	Atlas-SNP	.											.	KLF11	45	.	0			c.A1181G						.						93	93	93					2																	10188645		2203	4300	6503	SO:0001583	missense	8462	exon3			GGAACTATGTATG	AF028008	CCDS1668.1, CCDS54333.1	2p25	2013-01-08	2004-11-29	2004-12-01	ENSG00000172059	ENSG00000172059		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11811	protein-coding gene	gene with protein product		603301	"TGFB inducible early growth response 2"	TIEG2		9748269, 11087666	Standard	NM_001177716		Approved	Tieg3, MODY7	uc002raf.1	O14901	OTTHUMG00000119004	ENST00000305883.1:c.1181A>G	chr2.hg19:g.10188645A>G	ENSP00000307023:p.Tyr394Cys	81.0	0.0	662	78.0	4.0	NM_003597	B4DZE7|Q9EPF4	Missense_Mutation	SNP	ENST00000305883.1	hg19	CCDS1668.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.492158	0.64074	.	.	ENSG00000172059	ENST00000305883;ENST00000540845;ENST00000535335	T;T;T	0.18960	2.18;2.18;2.18	5.51	5.51	0.81932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.51550	0.1681	M	0.85197	2.74	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.57573	-0.7788	9	.	.	.	.	15.6141	0.76750	1.0:0.0:0.0:0.0	.	394	O14901	KLF11_HUMAN	C	394;377;377	ENSP00000307023:Y394C;ENSP00000444690:Y377C;ENSP00000442722:Y377C	.	Y	+	2	0	KLF11	10106096	1.000000	0.71417	0.529000	0.27951	0.495000	0.33615	9.291000	0.96070	2.094000	0.63399	0.172000	0.16884	TAT	.	.		0.552	KLF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000239202.3	NM_003597		G	10188645	A	G	10188645	3	3	91	1	0	0	0	0	1	0	0	0	8348	449	16	2	1191	2	KLF11	2	10188645	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	657329	10188645	233010728	68	12142										
PDIA6	10130	hgsc.bcm.edu	37	chr2	10925108	10925108	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctctcaacgatggtagggaaAgccccgcctcctacaggtgc	11	14	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:10925108A>G	ENST00000272227.3	-	12	1353	c.1206T>C	c.(1204-1206)gcT>gcC	p.A402A	PDIA6_ENST00000404371.2_Silent_p.A454A|PDIA6_ENST00000381611.4_Silent_p.A407A|ATP6V1C2_ENST00000381661.3_3'UTR|PDIA6_ENST00000540494.1_Silent_p.A399A|PDIA6_ENST00000404824.2_Silent_p.A450A	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	402					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		TGGTAGGGAAAGCCCCGCCTC	0.572																																					p.A402A	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											.	PDIA6	31	.	0			c.T1206C						.						34	30	31					2																	10925108		2201	4296	6497	SO:0001819	synonymous_variant	10130	exon12			AGGGAAAGCCCCG	BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"Protein disulfide isomerases"	30168	protein-coding gene	gene with protein product	"protein disulfide isomerase-related protein"	611099	"thioredoxin domain containing 7 (protein disulfide isomerase)", "protein disulfide isomerase-associated 6"	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000272227.3:c.1206T>C	chr2.hg19:g.10925108A>G		88.0	0.0		79.0	4.0	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	hg19	CCDS1675.1																																																																																			.	.		0.572	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742		G	10925108	A	G	10925108	2	3	91	1	0	0	0	0	0	0	0	1	11681	59	3	2		2	PDIA6	2	10925108	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	736463	10925108	232274265	69	12143										
GREB1	9687	hgsc.bcm.edu	37	chr2	11772120	11772120	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taatctgtaccacgcaatggAcggtgccagccatttgcacg	10	12	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:11772120A>G	ENST00000381486.2	+	27	4997	c.4697A>G	c.(4696-4698)gAc>gGc	p.D1566G	GREB1_ENST00000234142.5_Missense_Mutation_p.D1566G|GREB1_ENST00000396123.1_Missense_Mutation_p.D564G	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1566						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CACGCAATGGACGGTGCCAGC	0.478																																					p.D1566G	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.A4697G						.						97	96	97					2																	11772120		1984	4149	6133	SO:0001583	missense	9687	exon27			CAATGGACGGTGC		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.4697A>G	chr2.hg19:g.11772120A>G	ENSP00000370896:p.Asp1566Gly	187.0	0.0		146.0	6.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	A	19.59	3.855327	0.71719	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.50001	0.76;0.76;0.76	5.48	5.48	0.80851	.	0.046725	0.85682	D	0.000000	T	0.49253	0.1546	M	0.61703	1.905	0.80722	D	1	P	0.36110	0.537	B	0.36959	0.237	T	0.53920	-0.8370	10	0.59425	D	0.04	-30.0742	15.552	0.76161	1.0:0.0:0.0:0.0	.	1566	Q4ZG55	GREB1_HUMAN	G	1566;1566;564	ENSP00000370896:D1566G;ENSP00000234142:D1566G;ENSP00000379429:D564G	ENSP00000234142:D1566G	D	+	2	0	GREB1	11689571	1.000000	0.71417	0.919000	0.36401	0.442000	0.32017	8.837000	0.92110	2.079000	0.62486	0.455000	0.32223	GAC	.	.		0.478	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		G	11772120	A	G	11772120	3	3	91	1	0	0	0	0	1	0	0	0	6769	275	10	2	4907	2	GREB1	2	11772120	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	847012	11772120	231427253	70	12144										
DDX1	1653	hgsc.bcm.edu	37	chr2	15746378	15746378	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatggttacattgtcaaatcAcagcactcaggtattatacc	7	9	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:15746378A>G	ENST00000381341.2	+	13	1196	c.807A>G	c.(805-807)tcA>tcG	p.S269S	DDX1_ENST00000233084.3_Silent_p.S269S			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	269	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Necessary for interaction with HNRNPK.|Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		TTGTCAAATCACAGCACTCAG	0.393																																					p.S269S		Atlas-SNP	.											.	DDX1	70	.	0			c.A807G						.						64	59	61					2																	15746378		2203	4300	6503	SO:0001819	synonymous_variant	1653	exon12			CAAATCACAGCAC	X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"DEAD-boxes"	2734	protein-coding gene	gene with protein product		601257	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.807A>G	chr2.hg19:g.15746378A>G		158.0	0.0		149.0	6.0	NM_004939	B4DME8|B4DPN6	Silent	SNP	ENST00000381341.2	hg19	CCDS1686.1																																																																																			.	.		0.393	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939		G	15746378	A	G	15746378	2	3	91	1	0	0	0	0	0	0	0	1	4343	146	6	2		2	DDX1	2	15746378	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3974258	15746378	227452995	71	12145										
SMC6	79677	hgsc.bcm.edu	37	chr2	17922879	17922879	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agaagggaaaaaacacttacTtccattgttgccaacaacaa	6	9	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:17922879T>C	ENST00000448223.2	-	4	507	c.238A>G	c.(238-240)Agt>Ggt	p.S80G	SMC6_ENST00000402989.1_Splice_Site_p.S80G|SMC6_ENST00000351948.4_Splice_Site_p.S80G|SMC6_ENST00000381272.4_Splice_Site_p.S80G	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	80					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AAACACTTACTTCCATTGTTG	0.323																																					p.S80G		Atlas-SNP	.											.	SMC6	102	.	0			c.A238G						.						127	127	127					2																	17922879		2203	4300	6503	SO:0001630	splice_region_variant	79677	exon4			ACTTACTTCCATT	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.238+1A>G	chr2.hg19:g.17922879T>C		79.0	0.0		60.0	4.0	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	T	33	5.246391	0.95305	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.79845	-1.31;-1.31;1.99;-1.31;1.99	5.89	5.89	0.94794	RecF/RecN/SMC (1);	0.114600	0.85682	D	0.000000	D	0.88858	0.6551	M	0.75615	2.305	0.80722	D	1	P;D;P	0.58268	0.939;0.982;0.883	P;D;P	0.70227	0.783;0.968;0.835	D	0.88900	0.3352	9	.	.	.	.	15.2952	0.73898	0.0:0.0:0.0:1.0	.	80;80;80	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	G	80	ENSP00000404092:S80G;ENSP00000323439:S80G;ENSP00000370672:S80G;ENSP00000384539:S80G;ENSP00000408644:S80G	.	S	-	1	0	SMC6	17786360	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.622000	0.83099	2.246000	0.74042	0.533000	0.62120	AGT	.	.		0.323	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624	Missense_Mutation	C	17922879	T	C	17922879	5	2	91	1	0	0	0	0	0	0	1	0	14802	1623	56	2	3137	2	SMC6	2	17922879	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2176501	17922879	225276494	72	12146										
ASXL2	55252	hgsc.bcm.edu	37	chr2	25965337	25965337	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcagaggaagaacagtagaaCtgaaaagctcggggctgcta	14	7	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:25965337C>G	ENST00000435504.4	-	13	4162	c.3869G>C	c.(3868-3870)aGt>aCt	p.S1290T	ASXL2_ENST00000336112.4_Missense_Mutation_p.S1262T|ASXL2_ENST00000272341.4_Missense_Mutation_p.S773T|ASXL2_ENST00000404843.1_Missense_Mutation_p.S773T			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	1290					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACAGTAGAACTGAAAAGCTC	0.542																																					p.S1290T		Atlas-SNP	.											.	ASXL2	217	.	0			c.G3869C						.						38	40	39					2																	25965337		1944	4128	6072	SO:0001583	missense	55252	exon12			GTAGAACTGAAAA			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.3869G>C	chr2.hg19:g.25965337C>G	ENSP00000391447:p.Ser1290Thr	187.0	0.0		138.0	10.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	hg19		.	.	.	.	.	.	.	.	.	.	T	11.82	1.752668	0.31046	.	.	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	T;T;T;T	0.18960	2.2;2.2;2.18;2.18	4.79	-9.57	0.00562	.	1.174300	0.05956	N	0.639799	T	0.13628	0.0330	N	0.19112	0.55	0.09310	N	1	P;B	0.46220	0.874;0.094	B;B	0.44163	0.443;0.026	T	0.30650	-0.9971	10	0.20046	T	0.44	1.5602	14.0348	0.64638	0.0778:0.7438:0.0785:0.1	.	773;1290	Q76L83-2;Q76L83	.;ASXL2_HUMAN	T	1290;1262;773;773	ENSP00000391447:S1290T;ENSP00000337250:S1262T;ENSP00000383920:S773T;ENSP00000272341:S773T	ENSP00000272341:S773T	S	-	2	0	ASXL2	25818841	0.000000	0.05858	0.000000	0.03702	0.935000	0.57460	-2.133000	0.01308	-3.216000	0.00213	-0.254000	0.11334	AGT	.	.		0.542	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		G	25965337	C	G	25965337	3	3	91	1	0	0	0	0	1	0	0	0	1067	565	20	4	442	4	ASXL2	2	25965337	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	8042458	25965337	217234036	73	12147										
CGREF1	10669	hgsc.bcm.edu	37	chr2	27325406	27325406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctactcacccgagctgctccTggcctggctggaaggggttg	14	13	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:27325406T>C	ENST00000260595.5	-	3	426	c.134A>G	c.(133-135)cAg>cGg	p.Q45R	CGREF1_ENST00000404694.3_Missense_Mutation_p.Q167R|CGREF1_ENST00000402550.1_Missense_Mutation_p.Q45R|CGREF1_ENST00000452318.2_5'UTR|CGREF1_ENST00000312734.4_Missense_Mutation_p.Q45R|CGREF1_ENST00000402394.1_Missense_Mutation_p.Q45R|CGREF1_ENST00000405600.1_Missense_Mutation_p.Q45R			Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	45					cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGCTGCTCCTGGCCTGGCTG	0.642																																					p.Q45R		Atlas-SNP	.											.	CGREF1	31	.	0			c.A134G						.						52	57	56					2																	27325406		2203	4300	6503	SO:0001583	missense	10669	exon3			TGCTCCTGGCCTG	BC034764	CCDS33162.1, CCDS33162.2, CCDS54339.1	2p23.3	2013-01-10			ENSG00000138028	ENSG00000138028		"EF-hand domain containing"	16962	protein-coding gene	gene with protein product		606137				8968090	Standard	NM_006569		Approved	CGR11	uc002riq.3	Q99674	OTTHUMG00000152009	ENST00000260595.5:c.134A>G	chr2.hg19:g.27325406T>C	ENSP00000260595:p.Gln45Arg	68.0	0.0		74.0	4.0	NM_001166239	A6NHV7|B4DXY8|B5MCB7|B5MCC9|B5MCP5|E7EU99|Q8N4B7	Missense_Mutation	SNP	ENST00000260595.5	hg19		.	.	.	.	.	.	.	.	.	.	T	2.145	-0.395939	0.04899	.	.	ENSG00000138028	ENST00000402550;ENST00000402394;ENST00000405600;ENST00000389521;ENST00000312734;ENST00000404694;ENST00000260595	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.27	-10.5	0.00291	.	1.639240	0.03276	N	0.185498	T	0.15435	0.0372	N	0.24115	0.695	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.07102	-1.0790	10	0.14252	T	0.57	-15.0524	8.452	0.32877	0.0771:0.1376:0.5791:0.2063	.	167;45;45	B5MCC9;B5MCP5;Q99674	.;.;CGRE1_HUMAN	R	45;45;45;45;45;167;45	ENSP00000385452:Q45R;ENSP00000386113:Q45R;ENSP00000324025:Q45R;ENSP00000385574:Q167R;ENSP00000260595:Q45R	ENSP00000260595:Q45R	Q	-	2	0	CGREF1	27178910	0.001000	0.12720	0.001000	0.08648	0.021000	0.10359	-0.448000	0.06820	-2.171000	0.00775	-3.722000	0.00023	CAG	.	.		0.642	CGREF1-201	KNOWN	basic	protein_coding	protein_coding		NM_006569		C	27325406	T	C	27325406	3	2	91	1	0	0	0	0	1	0	0	0	3307	1580	55	2	1030	2	CGREF1	2	27325406	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1360069	27325406	215873967	74	12148										
CAD	790	hgsc.bcm.edu	37	chr2	27458485	27458485	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccagtctcggcacagctgacTtctacactgagcatggcgtc	10	14	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:27458485T>C	ENST00000403525.1	+	24	4006	c.3862T>C	c.(3862-3864)Ttc>Ctc	p.F1288L	CAD_ENST00000264705.4_Missense_Mutation_p.F1351L			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACAGCTGACTTCTACACTGA	0.542																																					p.F1351L		Atlas-SNP	.											.	CAD	199	.	0			c.T4051C						.						61	59	60					2																	27458485		2203	4300	6503	SO:0001583	missense	790	exon25			GCTGACTTCTACA	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.3862T>C	chr2.hg19:g.27458485T>C	ENSP00000384510:p.Phe1288Leu	107.0	0.0		112.0	6.0	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.	.	.	.	.	.	.	.	.	.	T	34	5.361358	0.95877	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	T;T	0.81078	-1.45;-1.45	4.82	4.82	0.62117	Methylglyoxal synthase-like domain (4);	0.043580	0.85682	D	0.000000	D	0.89577	0.6755	M	0.82517	2.595	0.80722	D	1	D;D	0.69078	0.968;0.997	P;D	0.77004	0.885;0.989	D	0.91146	0.4949	10	0.87932	D	0	-2.118	13.529	0.61611	0.0:0.0:0.0:1.0	.	1288;1351	F8VPD4;P27708	.;PYR1_HUMAN	L	1351;1288	ENSP00000264705:F1351L;ENSP00000384510:F1288L	ENSP00000264705:F1351L	F	+	1	0	CAD	27311989	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.268000	0.78473	1.941000	0.56285	0.459000	0.35465	TTC	.	.		0.542	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			C	27458485	T	C	27458485	3	2	91	1	0	0	0	0	1	0	0	0	2567	1609	56	2	4149	2	CAD	2	27458485	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	133079	27458485	215740888	75	12149										
C2orf16	84226	hgsc.bcm.edu	37	chr2	27802654	27802654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctccctcaagccaaattatcTttcccaggccaagactgact	5	15	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:27802654T>C	ENST00000408964.2	+	1	3266	c.3215T>C	c.(3214-3216)cTt>cCt	p.L1072P	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1072						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CCAAATTATCTTTCCCAGGCC	0.443																																					p.L1072P		Atlas-SNP	.											.	C2orf16	357	.	0			c.T3215C						.						121	121	121					2																	27802654		1913	4135	6048	SO:0001583	missense	84226	exon1			ATTATCTTTCCCA	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3215T>C	chr2.hg19:g.27802654T>C	ENSP00000386190:p.Leu1072Pro	142.0	0.0		108.0	5.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	hg19	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	T	8.403	0.842421	0.16963	.	.	ENSG00000221843	ENST00000408964	T	0.15139	2.45	5.12	1.46	0.22682	.	.	.	.	.	T	0.12390	0.0301	L	0.29908	0.895	0.09310	N	0.999994	B	0.19073	0.033	B	0.22601	0.04	T	0.29305	-1.0016	9	0.87932	D	0	.	6.168	0.20400	0.0:0.3087:0.0:0.6912	.	1072	Q68DN1	CB016_HUMAN	P	1072	ENSP00000386190:L1072P	ENSP00000386190:L1072P	L	+	2	0	C2orf16	27656158	0.003000	0.15002	0.006000	0.13384	0.010000	0.07245	1.089000	0.30890	0.290000	0.22444	0.260000	0.18958	CTT	.	.		0.443	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		C	27802654	T	C	27802654	3	2	91	1	0	0	0	0	1	0	0	0	2159	1609	56	2	3217	2	C2orf16	2	27802654	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	344169	27802654	215396719	76	12150										
C2orf16	84226	hgsc.bcm.edu	37	chr2	27803186	27803186	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtagaaaagacaaaaactagAgcacctgggcactatgaatt	9	7	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:27803186A>G	ENST00000408964.2	+	1	3798	c.3747A>G	c.(3745-3747)agA>agG	p.R1249R	RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000416005.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000355467.4_5'Flank|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1249						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CAAAAACTAGAGCACCTGGGC	0.473																																					p.R1249R		Atlas-SNP	.											.	C2orf16	357	.	0			c.A3747G						.						109	108	108					2																	27803186		1867	4116	5983	SO:0001819	synonymous_variant	84226	exon1			AACTAGAGCACCT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3747A>G	chr2.hg19:g.27803186A>G		161.0	0.0		116.0	5.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	hg19	CCDS42666.1																																																																																			.	.		0.473	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		G	27803186	A	G	27803186	2	3	91	1	0	0	0	0	0	0	0	1	2159	301	11	2		2	C2orf16	2	27803186	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	532	27803186	215396187	77	12151										
CCDC121	79635	hgsc.bcm.edu	37	chr2	27851424	27851424	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttattcgttcggtgctcaaaGggtctcggtgctgcccagca	12	11	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:27851424G>A	ENST00000324364.3	-	1	63				GPN1_ENST00000503738.1_5'Flank|CCDC121_ENST00000394775.3_Silent_p.P69P|GPN1_ENST00000458167.2_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|GPN1_ENST00000610189.1_5'Flank|GPN1_ENST00000407583.3_5'Flank|GPN1_ENST00000424214.1_5'Flank|GPN1_ENST00000515877.1_5'UTR|GPN1_ENST00000264718.3_5'Flank|ZNF512_ENST00000556601.1_Intron	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121											breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					GGTGCTCAAAGGGTCTCGGTG	0.582																																					p.P69P		Atlas-SNP	.											.	CCDC121	43	.	0			c.C207T						.						41	39	40					2																	27851424		692	1591	2283	SO:0001627	intron_variant	79635	exon1			CTCAAAGGGTCTC	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427	ENST00000324364.3:c.117+392C>T	chr2.hg19:g.27851424G>A		153.0	0.0		123.0	5.0	NM_001142683	B3KW66|J3KQZ8|Q9H8G6	Silent	SNP	ENST00000324364.3	hg19	CCDS1759.1																																																																																			.	.		0.582	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584		A	27851424	G	A	27851424	1	1	91	0	1	0	0	0	0	0	0	0	2759	987	35	3		3	CCDC121	2	27851424	Intron	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	48238	27851424	215347949	78	12152										
RBKS	64080	hgsc.bcm.edu	37	chr2	28004570	28004570	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgactgctgcaatgaaattgGatctgttgagcatgtcttcc	10	8	2	3	rs200310841		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:28004570G>T	ENST00000302188.3	-	8	1633	c.881C>A	c.(880-882)tCc>tAc	p.S294Y	AC110084.1_ENST00000601759.1_Intron	NM_022128.1	NP_071411.1	Q9H477	RBSK_HUMAN	ribokinase	294					D-ribose catabolic process (GO:0019303)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ribokinase activity (GO:0004747)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(172;0.155)					AATGAAATTGGATCTGTTGAG	0.458																																					p.S294Y		Atlas-SNP	.											.	RBKS	23	.	0			c.C881A						.						132	129	130					2																	28004570		2203	4300	6503	SO:0001583	missense	64080	exon8			AAATTGGATCTGT	BC017425	CCDS1762.1	2p23.3	2008-02-05			ENSG00000171174	ENSG00000171174	2.7.1.15		30325	protein-coding gene	gene with protein product		611132				8382990	Standard	NM_022128		Approved	DKFZp686G13268, RBSK	uc002rlo.1	Q9H477	OTTHUMG00000097833	ENST00000302188.3:c.881C>A	chr2.hg19:g.28004570G>T	ENSP00000306817:p.Ser294Tyr	146.0	0.0		83.0	4.0	NM_022128	A9UK04|B4DV96	Missense_Mutation	SNP	ENST00000302188.3	hg19	CCDS1762.1	.	.	.	.	.	.	.	.	.	.	G	19.49	3.837587	0.71373	.	.	ENSG00000171174	ENST00000302188	T	0.77877	-1.13	5.66	5.66	0.87406	Carbohydrate/purine kinase (1);	0.158108	0.56097	D	0.000025	D	0.87497	0.6192	M	0.75615	2.305	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.88509	0.3088	10	0.87932	D	0	-8.4338	16.4964	0.84246	0.0:0.197:0.803:0.0	.	294	Q9H477	RBSK_HUMAN	Y	294	ENSP00000306817:S294Y	ENSP00000306817:S294Y	S	-	2	0	RBKS	27858074	1.000000	0.71417	0.999000	0.59377	0.730000	0.41778	5.343000	0.65976	2.656000	0.90262	0.655000	0.94253	TCC	.	.		0.458	RBKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215118.1	NM_022128		T	28004570	G	T	28004570	3	4	91	1	0	0	0	0	1	0	0	0	13123	1174	41	3	91	3	RBKS	2	28004570	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	153146	28004570	215194803	79	12153										
XDH	7498	hgsc.bcm.edu	37	chr2	31604573	31604573	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cggagatggggctggcagtgAtgatgttccctccaacggac	15	10	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:31604573A>G	ENST00000379416.3	-	12	1106	c.1058T>C	c.(1057-1059)aTc>aCc	p.I353T	XDH_ENST00000491727.1_5'Flank	NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	353	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GCTGGCAGTGATGATGTTCCC	0.587																																					p.I353T	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.T1058C						.						93	86	88					2																	31604573		2203	4300	6503	SO:0001583	missense	7498	exon12			GCAGTGATGATGT	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.1058T>C	chr2.hg19:g.31604573A>G	ENSP00000368727:p.Ile353Thr	105.0	0.0		92.0	4.0	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	hg19	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.433643	0.62955	.	.	ENSG00000158125	ENST00000379416	T	0.22134	1.97	5.96	5.96	0.96718	FAD-binding, type 2 (2);CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2 (1);Xanthine dehydrogenase, small subunit (1);Molybdopterin dehydrogenase, FAD-binding (1);	0.039194	0.85682	D	0.000000	T	0.31295	0.0792	M	0.76170	2.325	0.58432	D	0.999998	B	0.22983	0.078	B	0.30029	0.11	T	0.06162	-1.0842	10	0.56958	D	0.05	.	15.2697	0.73689	1.0:0.0:0.0:0.0	.	353	P47989	XDH_HUMAN	T	353	ENSP00000368727:I353T	ENSP00000368727:I353T	I	-	2	0	XDH	31458077	1.000000	0.71417	0.986000	0.45419	0.910000	0.53928	8.632000	0.90995	2.282000	0.76494	0.450000	0.29827	ATC	.	.		0.587	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		G	31604573	A	G	31604573	3	3	91	1	0	0	0	0	1	0	0	0	17441	333	12	2	3043	2	XDH	2	31604573	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3600003	31604573	211594800	80	12154										
SLC30A6	55676	hgsc.bcm.edu	37	chr2	32399138	32399138	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttttattttcacagtcctggAagatactgctctttggtgta	8	7	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:32399138A>G	ENST00000282587.5	+	3	134	c.97A>G	c.(97-99)Aag>Gag	p.K33E	SLC30A6_ENST00000406369.1_Intron|SLC30A6_ENST00000357055.3_5'UTR|SLC30A6_ENST00000379343.2_Missense_Mutation_p.K33E|SLC30A6_ENST00000435660.1_Missense_Mutation_p.K33E|SLC30A6_ENST00000538303.1_Missense_Mutation_p.K4E	NM_017964.3	NP_060434.2	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter), member 6	33					cellular protein metabolic process (GO:0044267)|Golgi to endosome transport (GO:0006895)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(4)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					ACAGTCCTGGAAGATACTGCT	0.348																																					p.K33E		Atlas-SNP	.											.	SLC30A6	37	.	0			c.A97G						.						198	187	191					2																	32399138		2203	4300	6503	SO:0001583	missense	55676	exon3			TCCTGGAAGATAC	AK055663	CCDS1780.1, CCDS54341.1, CCDS54342.1, CCDS54343.1	2p22.3	2013-05-22			ENSG00000152683	ENSG00000152683		"Solute carriers"	19305	protein-coding gene	gene with protein product		611148					Standard	NM_017964		Approved	FLJ31101, ZNT6	uc002rof.2	Q6NXT4	OTTHUMG00000128456	ENST00000282587.5:c.97A>G	chr2.hg19:g.32399138A>G	ENSP00000282587:p.Lys33Glu	367.0	0.0		271.0	103.0	NM_001193513	A5YM45|B7Z901|Q8N5C9|Q96NC3	Missense_Mutation	SNP	ENST00000282587.5	hg19	CCDS1780.1	.	.	.	.	.	.	.	.	.	.	A	16.75	3.210719	0.58343	.	.	ENSG00000152683	ENST00000379343;ENST00000440718;ENST00000282587;ENST00000435660;ENST00000538303	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.09	5.09	0.68999	.	0.105147	0.64402	D	0.000005	T	0.49915	0.1585	L	0.27053	0.805	0.80722	D	1	B;B;B;B	0.24882	0.007;0.113;0.036;0.017	B;B;B;B	0.22601	0.011;0.04;0.037;0.011	T	0.49570	-0.8926	10	0.49607	T	0.09	-4.316	13.8575	0.63537	1.0:0.0:0.0:0.0	.	4;33;33;33	B7Z901;Q6NXT4-3;Q6NXT4-2;Q6NXT4	.;.;.;ZNT6_HUMAN	E	33;4;33;33;4	ENSP00000393946:K4E;ENSP00000282587:K33E;ENSP00000399005:K33E;ENSP00000440678:K4E	ENSP00000282587:K33E	K	+	1	0	SLC30A6	32252642	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.237000	0.78164	1.909000	0.55274	0.460000	0.39030	AAG	.	.		0.348	SLC30A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250254.2			G	32399138	A	G	32399138	3	3	91	1	0	0	0	0	1	0	0	0	14574	247	9	2	107	2	SLC30A6	2	32399138	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	794565	32399138	210800235	81	12155										
STRN	6801	hgsc.bcm.edu	37	chr2	37094974	37094974	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tacttatgggctctgaatgtAtagataggttctacatcaag	9	6	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:37094974A>T	ENST00000263918.4	-	12	1538	c.1530T>A	c.(1528-1530)taT>taA	p.Y510*	STRN_ENST00000379213.2_Nonsense_Mutation_p.Y461*|RNU6-577P_ENST00000516947.1_RNA	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	510					dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)	p.Y510*(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				CTCTGAATGTATAGATAGGTT	0.299																																					p.Y510X		Atlas-SNP	.											STRN,extremity,malignant_melanoma,0,1	STRN	71	.	1	Substitution - Nonsense(1)	skin(1)	c.T1530A						.						102	107	105					2																	37094974		2203	4292	6495	SO:0001587	stop_gained	6801	exon12			GAATGTATAGATA	AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"WD repeat domain containing"	11424	protein-coding gene	gene with protein product		614765	"striatin, calmodulin-binding protein"			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.1530T>A	chr2.hg19:g.37094974A>T	ENSP00000263918:p.Tyr510*	91.0	0.0		65.0	3.0	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Nonsense_Mutation	SNP	ENST00000263918.4	hg19	CCDS1784.1	.	.	.	.	.	.	.	.	.	.	A	37	6.265639	0.97426	.	.	ENSG00000115808	ENST00000263918;ENST00000538092;ENST00000379213	.	.	.	5.29	1.53	0.23141	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.7655	8.3881	0.32512	0.7046:0.0:0.2954:0.0	.	.	.	.	X	510;485;461	.	ENSP00000263918:Y510X	Y	-	3	2	STRN	36948478	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	2.401000	0.44513	0.020000	0.15106	-0.250000	0.11733	TAT	.	.		0.299	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1			T	37094974	A	T	37094974	4	4	91	1	0	0	0	0	0	1	0	0	15344	456	16	4	840	4	STRN	2	37094974	Nonsense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4695836	37094974	206104399	82	12156										
NRXN1	9378	hgsc.bcm.edu	37	chr2	51254792	51254792	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccccgccgctgttgggcggcTcatcgtccagcttcacctcg	11	18	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:51254792T>C	ENST00000406316.2	-	2	2096	c.620A>G	c.(619-621)gAg>gGg	p.E207G	NRXN1_ENST00000405472.3_Missense_Mutation_p.E207G|NRXN1_ENST00000401669.2_Missense_Mutation_p.E207G|NRXN1_ENST00000406859.3_Missense_Mutation_p.E207G|NRXN1_ENST00000405581.1_Missense_Mutation_p.E207G|NRXN1_ENST00000402717.3_Missense_Mutation_p.E207G|NRXN1_ENST00000404971.1_Missense_Mutation_p.E207G	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	207	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GTTGGGCGGCTCATCGTCCAG	0.697																																					p.E207G		Atlas-SNP	.											.	NRXN1	1118	.	0			c.A620G						.						18	23	21					2																	51254792		2050	4175	6225	SO:0001583	missense	9378	exon2			GGCGGCTCATCGT	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.620A>G	chr2.hg19:g.51254792T>C	ENSP00000384311:p.Glu207Gly	119.0	0.0		114.0	5.0	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.976948	0.74360	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859;ENST00000405581	T;T;T;T;T;T;T	0.71461	0.12;0.11;-0.57;-0.46;-0.17;-0.03;3.32	5.5	5.5	0.81552	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.835445	0.09637	U	0.775557	D	0.82783	0.5112	M	0.65975	2.015	0.42561	D	0.993145	B;D;B	0.67145	0.0;0.996;0.001	B;D;B	0.66497	0.002;0.944;0.002	T	0.76515	-0.2931	10	0.36615	T	0.2	.	15.6222	0.76816	0.0:0.0:0.0:1.0	.	207;207;207	Q9ULB1-3;F8WB18;Q9ULB1	.;.;NRX1A_HUMAN	G	207	ENSP00000385142:E207G;ENSP00000384311:E207G;ENSP00000434015:E207G;ENSP00000385017:E207G;ENSP00000385434:E207G;ENSP00000385681:E207G;ENSP00000385310:E207G	ENSP00000385017:E207G	E	-	2	0	NRXN1	51108296	0.995000	0.38212	1.000000	0.80357	0.895000	0.52256	4.129000	0.57957	2.087000	0.62958	0.460000	0.39030	GAG	.	.		0.697	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			C	51254792	T	C	51254792	3	2	91	1	0	0	0	0	1	0	0	0	10674	1551	54	2	4378	2	NRXN1	2	51254792	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	14159818	51254792	191944581	83	12157										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54753654	54753654	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtcgacgactgggacaatgaGaacagctctgcgcggctttt	13	10	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:54753654G>T	ENST00000356805.4	+	2	380	c.99G>T	c.(97-99)gaG>gaT	p.E33D	AC092839.3_ENST00000433475.1_RNA	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	33	Actin-binding.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GGGACAATGAGAACAGCTCTG	0.537																																					p.E33D		Atlas-SNP	.											.	SPTBN1	378	.	0			c.G99T						.						147	132	137					2																	54753654		2203	4300	6503	SO:0001583	missense	6711	exon2			CAATGAGAACAGC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.99G>T	chr2.hg19:g.54753654G>T	ENSP00000349259:p.Glu33Asp	103.0	0.0		95.0	4.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	G	5.135	0.210554	0.09757	.	.	ENSG00000115306	ENST00000356805;ENST00000389980	T;T	0.60040	0.22;0.22	5.77	2.5	0.30297	Calponin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.22666	0.0547	N	0.01410	-0.885	0.80722	D	1	B	0.13594	0.008	B	0.15052	0.012	T	0.31024	-0.9958	10	0.02654	T	1	.	10.8349	0.46681	0.1992:0.1114:0.6894:0.0	.	33	Q01082	SPTB2_HUMAN	D	33	ENSP00000349259:E33D;ENSP00000374630:E33D	ENSP00000349259:E33D	E	+	3	2	SPTBN1	54607158	1.000000	0.71417	0.988000	0.46212	0.961000	0.63080	2.133000	0.42093	0.340000	0.23745	-0.813000	0.03139	GAG	.	.		0.537	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54753654	G	T	54753654	3	4	91	1	0	0	0	0	1	0	0	0	15134	933	33	3	101	3	SPTBN1	2	54753654	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3498862	54753654	188445719	84	12158										
EHBP1	23301	hgsc.bcm.edu	37	chr2	63086387	63086387	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atccatttgatgatcctgatGctgcagaattaaatccattt	6	8	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:63086387G>A	ENST00000263991.5	+	9	1305	c.823G>A	c.(823-825)Gct>Act	p.A275T	EHBP1_ENST00000405015.3_Missense_Mutation_p.A240T|EHBP1_ENST00000431489.1_Missense_Mutation_p.A240T|EHBP1_ENST00000354487.3_Missense_Mutation_p.A240T|EHBP1_ENST00000405289.1_Missense_Mutation_p.A240T|AC007098.1_ENST00000452397.1_RNA	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	275						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TGATCCTGATGCTGCAGAATT	0.353																																					p.A275T		Atlas-SNP	.											.	EHBP1	127	.	0			c.G823A						.						123	119	121					2																	63086387		2203	4300	6503	SO:0001583	missense	23301	exon9			CCTGATGCTGCAG	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.823G>A	chr2.hg19:g.63086387G>A	ENSP00000263991:p.Ala275Thr	128.0	0.0		80.0	4.0	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	hg19	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	G	8.982	0.975558	0.18736	.	.	ENSG00000115504	ENST00000405015;ENST00000405482;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T;T	0.72835	-0.69;0.99;-0.69;-0.69;-0.69;-0.69	4.88	4.0	0.46444	.	0.255372	0.32002	N	0.006723	T	0.49047	0.1534	N	0.14661	0.345	0.19300	N	0.999977	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.24977	-1.0145	10	0.14656	T	0.56	.	9.9057	0.41375	0.2194:0.0:0.7806:0.0	.	240;240;275	Q8NDI1-2;Q8NDI1-3;Q8NDI1	.;.;EHBP1_HUMAN	T	240;240;240;275;240;240	ENSP00000384143:A240T;ENSP00000384829:A240T;ENSP00000403783:A240T;ENSP00000263991:A275T;ENSP00000346482:A240T;ENSP00000385524:A240T	ENSP00000263991:A275T	A	+	1	0	EHBP1	62939891	1.000000	0.71417	0.992000	0.48379	0.719000	0.41307	2.158000	0.42329	1.061000	0.40601	0.591000	0.81541	GCT	.	.		0.353	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		A	63086387	G	A	63086387	3	1	91	1	0	0	0	0	1	0	0	0	4977	1319	46	3	853	3	EHBP1	2	63086387	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	8332733	63086387	180112986	85	12159										
SERTAD2	9792	hgsc.bcm.edu	37	chr2	64863856	64863856	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggctctgtcaggggcctgtgGttatagagtttcataaggga	15	6	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:64863856G>A	ENST00000313349.3	-	2	447	c.150C>T	c.(148-150)aaC>aaT	p.N50N	SERTAD2_ENST00000476805.2_5'UTR	NM_014755.2	NP_055570.1	Q14140	SRTD2_HUMAN	SERTA domain containing 2	50	SERTA. {ECO:0000255|PROSITE- ProRule:PRU00396}.				negative regulation of cell growth (GO:0030308)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|skin(1)	12						GGGGCCTGTGGTTATAGAGTT	0.493																																					p.N50N		Atlas-SNP	.											.	SERTAD2	32	.	0			c.C150T						.						136	141	139					2																	64863856		2203	4300	6503	SO:0001819	synonymous_variant	9792	exon2			CCTGTGGTTATAG	D50917	CCDS33210.1	2p15	2007-05-01			ENSG00000179833	ENSG00000179833			30784	protein-coding gene	gene with protein product	"transcriptional regulator interacting with the PHS-bromodomain 2"					8590280, 11331592	Standard	NM_014755		Approved	TRIP-Br2, KIAA0127, Sei-2	uc002sde.2	Q14140	OTTHUMG00000152678	ENST00000313349.3:c.150C>T	chr2.hg19:g.64863856G>A		237.0	0.0		220.0	21.0	NM_014755	Q53TS2	Silent	SNP	ENST00000313349.3	hg19	CCDS33210.1																																																																																			.	.		0.493	SERTAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327322.2	NM_014755		A	64863856	G	A	64863856	2	1	91	1	0	0	0	0	0	0	0	1	14136	1252	44	3		3	SERTAD2	2	64863856	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	1777469	64863856	178335517	86	12160										
AAK1	22848	hgsc.bcm.edu	37	chr2	69741753	69741753	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtggccagctgttgctgttgCtgttgttgttgctgctgctg	15	8	0	0	rs66931661|rs3832159	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:69741753C>T	ENST00000409085.4	-	13	2002	c.1626G>A	c.(1624-1626)caG>caA	p.Q542Q	AAK1_ENST00000406297.3_Silent_p.Q542Q|RN7SL604P_ENST00000492589.2_RNA|AAK1_ENST00000409068.1_Silent_p.Q542Q	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	542	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						gttgctgttgctgttgttgtt	0.552																																					p.Q542Q		Atlas-SNP	.											.	AAK1	121	.	0			c.G1626A						.						33	35	34					2																	69741753		2192	4296	6488	SO:0001819	synonymous_variant	22848	exon13			CTGTTGCTGTTGT	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1626G>A	chr2.hg19:g.69741753C>T		147.0	0.0		134.0	14.0	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	hg19	CCDS1893.2																																																																																			.	.		0.552	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911		T	69741753	C	T	69741753	2	4	91	1	0	0	0	0	0	0	0	1	16	796	28	3		3	AAK1	2	69741753	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	4877897	69741753	173457620	87	12161										
VAX2	25806	hgsc.bcm.edu	37	chr2	71148294	71148294	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctggaccggcccaagcggaCacgtacatccttcactgccg	10	17	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:71148294C>T	ENST00000234392.2	+	2	346	c.314C>T	c.(313-315)aCa>aTa	p.T105I		NM_012476.2	NP_036608.1	Q9UIW0	VAX2_HUMAN	ventral anterior homeobox 2	105					axonogenesis (GO:0007409)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic eye morphogenesis (GO:0048048)|forebrain development (GO:0030900)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	7						CCCAAGCGGACACGTACATCC	0.612																																					p.T105I		Atlas-SNP	.											.	VAX2	27	.	0			c.C314T						.						49	45	46					2																	71148294		2203	4300	6503	SO:0001583	missense	25806	exon2			AGCGGACACGTAC	Y17791	CCDS1911.1	2p13.3	2011-06-20			ENSG00000116035	ENSG00000116035		"Homeoboxes / ANTP class : NKL subclass"	12661	protein-coding gene	gene with protein product		604295				10485894	Standard	NM_012476		Approved	DRES93	uc002shh.3	Q9UIW0	OTTHUMG00000129714	ENST00000234392.2:c.314C>T	chr2.hg19:g.71148294C>T	ENSP00000234392:p.Thr105Ile	144.0	0.0		95.0	4.0	NM_012476	Q53Y33	Missense_Mutation	SNP	ENST00000234392.2	hg19	CCDS1911.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.769813	0.69992	.	.	ENSG00000116035	ENST00000234392	D	0.96396	-4.0	5.43	4.55	0.56014	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.90796	0.7110	N	0.05199	-0.095	0.80722	D	1	P	0.36647	0.563	B	0.37989	0.262	D	0.91278	0.5049	10	0.72032	D	0.01	-21.0553	14.1912	0.65639	0.0:0.8496:0.1504:0.0	.	105	Q9UIW0	VAX2_HUMAN	I	105	ENSP00000234392:T105I	ENSP00000234392:T105I	T	+	2	0	VAX2	71001802	1.000000	0.71417	0.987000	0.45799	0.790000	0.44656	5.724000	0.68500	1.283000	0.44513	0.655000	0.94253	ACA	.	.		0.612	VAX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251923.1			T	71148294	C	T	71148294	3	4	91	1	0	0	0	0	1	0	0	0	17150	478	17	3	320	3	VAX2	2	71148294	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1406541	71148294	172051079	88	12162										
KDM3A	55818	hgsc.bcm.edu	37	chr2	86705806	86705806	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcaaactgcccttgttcaaAcaggcaattcaaactctttt	6	11	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:86705806A>G	ENST00000409556.1	+	16	2629	c.2264A>G	c.(2263-2265)aAc>aGc	p.N755S	KDM3A_ENST00000312912.5_Missense_Mutation_p.N755S|KDM3A_ENST00000409064.1_Missense_Mutation_p.N755S|KDM3A_ENST00000542128.1_Missense_Mutation_p.N703S			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	755					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						CCTTGTTCAAACAGGCAATTC	0.383																																					p.N755S	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.A2264G						.						111	100	104					2																	86705806		2203	4300	6503	SO:0001583	missense	55818	exon15			GTTCAAACAGGCA	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"Chromatin-modifying enzymes / K-demethylases"	20815	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 2A"	611512	"jumonji domain containing 1", "jumonji domain containing 1A"	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.2264A>G	chr2.hg19:g.86705806A>G	ENSP00000386660:p.Asn755Ser	132.0	0.0		87.0	4.0	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	hg19	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	A	12.00	1.805795	0.31961	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	5.73	3.29	0.37713	.	0.132172	0.51477	D	0.000096	T	0.41282	0.1152	L	0.28192	0.835	0.37720	D	0.92488	B;B	0.25312	0.123;0.017	B;B	0.29862	0.108;0.013	T	0.30416	-0.9979	10	0.23891	T	0.37	.	8.1164	0.30946	0.7946:0.1344:0.071:0.0	.	703;755	F5H070;Q9Y4C1	.;KDM3A_HUMAN	S	755;755;755;755;703	ENSP00000386660:N755S;ENSP00000323659:N755S;ENSP00000386516:N755S;ENSP00000438324:N703S	ENSP00000323659:N755S	N	+	2	0	KDM3A	86559317	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.339000	0.52135	0.971000	0.38288	0.533000	0.62120	AAC	.	.		0.383	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		G	86705806	A	G	86705806	3	3	91	1	0	0	0	0	1	0	0	0	8135	43	2	2	2318	2	KDM3A	2	86705806	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	15557512	86705806	156493567	89	12163										
PROM2	150696	hgsc.bcm.edu	37	chr2	95940507	95940507	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctcgagttcgtgcgccaggActcctggactccctctatgg	11	15	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:95940507A>G	ENST00000317620.9	+	1	307	c.174A>G	c.(172-174)ggA>ggG	p.G58G	PROM2_ENST00000542147.1_Silent_p.G58G|PROM2_ENST00000403131.2_Silent_p.G58G|PROM2_ENST00000317668.4_Silent_p.G58G|PROM2_ENST00000463580.1_3'UTR	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	58					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						GTGCGCCAGGACTCCTGGACT	0.662																																					p.G58G		Atlas-SNP	.											.	PROM2	78	.	0			c.A174G						.						82	91	88					2																	95940507		2203	4300	6503	SO:0001819	synonymous_variant	150696	exon1			GCCAGGACTCCTG	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.174A>G	chr2.hg19:g.95940507A>G		99.0	0.0		78.0	4.0	NM_001165977	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Silent	SNP	ENST00000317620.9	hg19	CCDS2012.1																																																																																			.	.		0.662	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707		G	95940507	A	G	95940507	2	3	91	1	0	0	0	0	0	0	0	1	12568	262	10	2		2	PROM2	2	95940507	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	9234701	95940507	147258866	90	12164										
SNRNP200	23020	hgsc.bcm.edu	37	chr2	96965077	96965077	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctgaacttacattagccgagAgggtgcagcgcacgacagcc	12	12	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:96965077A>G	ENST00000323853.5	-	6	796	c.719T>C	c.(718-720)cTc>cCc	p.L240P	SNRNP200_ENST00000349783.5_Missense_Mutation_p.L240P	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	240					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						ATTAGCCGAGAGGGTGCAGCG	0.493																																					p.L240P		Atlas-SNP	.											.	SNRNP200	195	.	0			c.T719C						.						256	230	239					2																	96965077		2203	4300	6503	SO:0001583	missense	23020	exon6			GCCGAGAGGGTGC	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.719T>C	chr2.hg19:g.96965077A>G	ENSP00000317123:p.Leu240Pro	119.0	0.0		100.0	5.0	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	hg19	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.440609	0.43326	.	.	ENSG00000144028	ENST00000323853;ENST00000349783	T;T	0.49720	0.77;0.77	5.07	5.07	0.68467	.	0.066905	0.64402	D	0.000016	T	0.48874	0.1524	M	0.74647	2.275	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.46638	-0.9177	10	0.35671	T	0.21	-14.5291	13.9456	0.64082	1.0:0.0:0.0:0.0	.	240	O75643	U520_HUMAN	P	240	ENSP00000317123:L240P;ENSP00000326937:L240P	ENSP00000317123:L240P	L	-	2	0	SNRNP200	96328804	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	8.641000	0.91032	2.125000	0.65367	0.454000	0.30748	CTC	.	.		0.493	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		G	96965077	A	G	96965077	3	3	91	1	0	0	0	0	1	0	0	0	14867	304	11	2	5851	2	SNRNP200	2	96965077	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1024570	96965077	146234296	91	12165										
ARID5A	10865	hgsc.bcm.edu	37	chr2	97216921	97216921	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caggaacagcacagaacagcAgggcctggcctctgggtctt	13	12	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:97216921A>G	ENST00000357485.3	+	7	734	c.656A>G	c.(655-657)cAg>cGg	p.Q219R	ARID5A_ENST00000454558.2_Missense_Mutation_p.Q151R	NM_212481.1	NP_997646.1	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A (MRF1-like)	219					chondrocyte differentiation (GO:0002062)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(2)	14						ACAGAACAGCAGGGCCTGGCC	0.587																																					p.Q219R		Atlas-SNP	.											.	ARID5A	31	.	0			c.A656G						.						59	66	64					2																	97216921		2203	4300	6503	SO:0001583	missense	10865	exon7			AACAGCAGGGCCT	M62324	CCDS33251.1	2p11.1	2013-02-07			ENSG00000196843	ENSG00000196843		"-"	17361	protein-coding gene	gene with protein product	"modulator recognition factor 1"	611583				8649988	Standard	NM_212481		Approved	MRF-1, RP11-363D14	uc002swe.3	Q03989	OTTHUMG00000155229	ENST00000357485.3:c.656A>G	chr2.hg19:g.97216921A>G	ENSP00000350078:p.Gln219Arg	122.0	0.0		93.0	4.0	NM_212481	Q6NX37	Missense_Mutation	SNP	ENST00000357485.3	hg19	CCDS33251.1	.	.	.	.	.	.	.	.	.	.	A	2.975	-0.211513	0.06140	.	.	ENSG00000196843	ENST00000357485;ENST00000359765;ENST00000454558	T	0.63580	-0.05	4.63	-3.23	0.05109	.	0.544000	0.13830	N	0.359795	T	0.21631	0.0521	N	0.02011	-0.69	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.23084	-1.0198	10	0.09843	T	0.71	-0.0151	0.5205	0.00611	0.2832:0.3139:0.1421:0.2608	.	219;151;219	A6NM59;C9J1Q0;Q03989	.;.;ARI5A_HUMAN	R	219;219;151	ENSP00000350078:Q219R	ENSP00000350078:Q219R	Q	+	2	0	ARID5A	96580648	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	0.185000	0.16958	-0.496000	0.06650	-0.527000	0.04329	CAG	.	.		0.587	ARID5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338888.2	NM_212481		G	97216921	A	G	97216921	3	3	91	1	0	0	0	0	1	0	0	0	921	188	7	2	682	2	ARID5A	2	97216921	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	251844	97216921	145982452	92	12166										
CLASP1	23332	hgsc.bcm.edu	37	chr2	122205082	122205082	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatttggtactaactgtagaAgctttagtgataaaggagga	12	3	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:122205082A>G	ENST00000263710.4	-	19	2132	c.1743T>C	c.(1741-1743)gcT>gcC	p.A581A	CLASP1_ENST00000541377.1_Splice_Site_p.A581A|CLASP1_ENST00000409078.3_Splice_Site_p.A581A|CLASP1_ENST00000541859.1_Splice_Site_p.A350A|CLASP1_ENST00000455322.2_Splice_Site_p.A581A|CLASP1_ENST00000397587.3_Splice_Site_p.A581A|CLASP1_ENST00000545861.1_Splice_Site_p.A349A	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	581	Ser-rich.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					TAACTGTAGAAGCTTTAGTGA	0.383																																					p.A581A		Atlas-SNP	.											.	CLASP1	135	.	0			c.T1743C						.						33	33	33					2																	122205082		1838	4024	5862	SO:0001630	splice_region_variant	23332	exon19			TGTAGAAGCTTTA	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"multiple asters 1"	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.1742-1T>C	chr2.hg19:g.122205082A>G		109.0	0.0		83.0	4.0	NM_001207051	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Silent	SNP	ENST00000263710.4	hg19																																																																																				.	.		0.383	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282	Silent	G	122205082	A	G	122205082	5	3	91	1	0	0	0	0	0	0	1	0	3456	86	3	2	3013	2	CLASP1	2	122205082	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	24988161	122205082	120994291	93	12167										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125367485	125367485	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgggacctctccaggtgtacTgcaatatcactggtaagggt	12	9	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:125367485T>C	ENST00000431078.1	+	12	2225	c.1861T>C	c.(1861-1863)Tgc>Cgc	p.C621R		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	621	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CCAGGTGTACTGCAATATCAC	0.532																																					p.C621R		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.T1861C						.						64	64	64					2																	125367485		1877	4113	5990	SO:0001583	missense	129684	exon12			GTGTACTGCAATA	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.1861T>C	chr2.hg19:g.125367485T>C	ENSP00000399013:p.Cys621Arg	71.0	0.0		42.0	4.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	T	18.38	3.612381	0.66672	.	.	ENSG00000155052	ENST00000431078	T	0.39997	1.05	5.66	5.66	0.87406	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2);	0.000000	0.56097	D	0.000039	T	0.74741	0.3756	H	0.95114	3.625	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.82914	-0.0221	10	0.87932	D	0	.	15.0047	0.71501	0.0:0.0:0.0:1.0	.	621	Q8WYK1	CNTP5_HUMAN	R	621	ENSP00000399013:C621R	ENSP00000399013:C621R	C	+	1	0	CNTNAP5	125083955	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	7.264000	0.78432	2.279000	0.76181	0.533000	0.62120	TGC	.	.		0.532	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			C	125367485	T	C	125367485	3	2	91	1	0	0	0	0	1	0	0	0	3652	1580	55	2	1907	2	CNTNAP5	2	125367485	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3162403	125367485	117831888	94	12168										
GPR148	344561	hgsc.bcm.edu	37	chr2	131486858	131486858	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctgggggacctcagggtgcCcagctccatgctgtactggc	14	14	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:131486858C>T	ENST00000309926.4	+	1	216	c.134C>T	c.(133-135)cCc>cTc	p.P45L		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	45				CMPQAASNTSLGLGDLRVPSSMLYWLFLPSSLLAAA -> S S (in Ref. 2; AAP34196). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					CTCAGGGTGCCCAGCTCCATG	0.622																																					p.P45L		Atlas-SNP	.											.	GPR148	54	.	0			c.C134T						.						78	70	73					2																	131486858		2203	4300	6503	SO:0001583	missense	344561	exon1			GGGTGCCCAGCTC	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"GPCR / Class A : Orphans"	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.134C>T	chr2.hg19:g.131486858C>T	ENSP00000308908:p.Pro45Leu	103.0	0.0		93.0	4.0	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	hg19	CCDS2163.1	.	.	.	.	.	.	.	.	.	.	.	11.74	1.730211	0.30684	.	.	ENSG00000173302	ENST00000309926	T	0.35605	1.3	2.55	2.55	0.30701	.	0.939982	0.08667	U	0.911494	T	0.21631	0.0521	N	0.08118	0	0.09310	N	1	D	0.60160	0.987	P	0.46362	0.514	T	0.01767	-1.1278	10	0.08381	T	0.77	-11.1141	11.2415	0.48972	0.0:1.0:0.0:0.0	.	45	Q8TDV2	GP148_HUMAN	L	45	ENSP00000308908:P45L	ENSP00000308908:P45L	P	+	2	0	GPR148	131203328	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	0.641000	0.24720	1.379000	0.46325	0.462000	0.41574	CCC	.	.		0.622	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092		T	131486858	C	T	131486858	3	4	91	1	0	0	0	0	1	0	0	0	6661	623	22	3	136	3	GPR148	2	131486858	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	6119373	131486858	111712515	95	12169										
THSD7B	80731	hgsc.bcm.edu	37	chr2	138373887	138373887	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gttccagtacaatctaacagGtacagttaaaatctatgacc	6	9	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:138373887G>A	ENST00000409968.1	+	18	3743		c.e18+1		THSD7B_ENST00000413152.2_Splice_Site|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000272643.3_Splice_Site			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B							integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		AATCTAACAGGTACAGTTAAA	0.413																																					.		Atlas-SNP	.											.	THSD7B	506	.	0			c.3477+1G>A						.						171	177	175					2																	138373887		2018	4178	6196	SO:0001630	splice_region_variant	80731	exon17			TAACAGGTACAGT			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.3565+1G>A	chr2.hg19:g.138373887G>A		103.0	0.0		98.0	4.0	NM_001080427		Splice_Site	SNP	ENST00000409968.1	hg19		.	.	.	.	.	.	.	.	.	.	G	24.2	4.505367	0.85282	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.6547	0.88174	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	THSD7B	138090357	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	8.389000	0.90172	2.703000	0.92315	0.650000	0.86243	.	.	.		0.413	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9	Intron	A	138373887	G	A	138373887	5	1	91	1	0	0	0	0	0	0	1	0	15895	1275	44	3	3544	3	THSD7B	2	138373887	Splice_Site	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	6887029	138373887	104825486	96	12170										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141707824	141707824	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttctttagtacaattgatcTgggcttcatcactgaagtcc	7	10	4	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:141707824T>C	ENST00000389484.3	-	20	4087	c.3116A>G	c.(3115-3117)cAg>cGg	p.Q1039R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1039	LDL-receptor class A 7. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACAATTGATCTGGGCTTCATC	0.373										TSP Lung(27;0.18)																											p.Q1039R	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A3116G						.						50	41	44					2																	141707824		2203	4300	6503	SO:0001583	missense	53353	exon20			TTGATCTGGGCTT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3116A>G	chr2.hg19:g.141707824T>C	ENSP00000374135:p.Gln1039Arg	133.0	0.0		124.0	5.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	7.997	0.754496	0.15778	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.95205	-2.25;-3.64	5.53	4.31	0.51392	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.301645	0.30244	U	0.010063	D	0.88869	0.6554	L	0.38175	1.15	0.09310	N	1	B;B	0.15719	0.001;0.014	B;B	0.15052	0.006;0.012	T	0.74902	-0.3506	10	0.19147	T	0.46	.	8.2266	0.31572	0.0:0.0714:0.1343:0.7943	.	222;1039	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	R	1039;977;184	ENSP00000374135:Q1039R;ENSP00000413239:Q184R	ENSP00000374135:Q1039R	Q	-	2	0	LRP1B	141424294	0.990000	0.36364	0.230000	0.23976	0.808000	0.45660	1.950000	0.40323	2.112000	0.64535	0.460000	0.39030	CAG	.	.		0.373	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141707824	T	C	141707824	3	2	91	1	0	0	0	0	1	0	0	0	8964	1580	55	2	10971	2	LRP1B	2	141707824	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3333937	141707824	101491549	97	12171										
ZEB2	9839	hgsc.bcm.edu	37	chr2	145162558	145162558	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gttttcttttggcaaagtatTcctcaaaatctgatgtgcaa	7	7	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:145162558T>C	ENST00000558170.2	-	5	1621	c.437A>G	c.(436-438)gAa>gGa	p.E146G	ZEB2_ENST00000539609.3_Missense_Mutation_p.E122G|ZEB2_ENST00000409487.3_Missense_Mutation_p.E146G|ZEB2_ENST00000303660.4_Missense_Mutation_p.E146G	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	146					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		GGCAAAGTATTCCTCAAAATC	0.453																																					p.E146G	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											.	ZEB2	218	.	0			c.A437G						.						91	81	84					2																	145162558		2203	4300	6503	SO:0001583	missense	9839	exon5			AAGTATTCCTCAA	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.437A>G	chr2.hg19:g.145162558T>C	ENSP00000454157:p.Glu146Gly	95.0	0.0		95.0	4.0	NM_014795	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	hg19	CCDS2186.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.93|15.93	2.979008|2.979008	0.53827|0.53827	.|.	.|.	ENSG00000169554|ENSG00000169554	ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861|ENST00000431672;ENST00000440875	D;T;T;T;T|.	0.81579|.	-1.51;-1.05;-1.05;-1.05;-1.05|.	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.143203|.	0.64402|.	D|.	0.000005|.	T|T	0.59783|0.59783	0.2219|0.2219	L|L	0.36672|0.36672	1.1|1.1	0.58432|0.58432	D|D	0.999998|0.999998	P;B;B;B|.	0.43352|.	0.804;0.435;0.231;0.231|.	B;B;B;B|.	0.37144|.	0.242;0.078;0.054;0.054|.	T|T	0.55503|0.55503	-0.8131|-0.8131	10|5	0.66056|.	D|.	0.02|.	-12.5066|-12.5066	16.5655|16.5655	0.84588|0.84588	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	122;11;145;146|.	F5H814;Q53TD9;A0JP08;O60315|.	.;.;.;ZEB2_HUMAN|.	G|D	141;122;146;146;146;146|112;133	ENSP00000443792:E122G;ENSP00000302501:E146G;ENSP00000386854:E146G;ENSP00000395496:E146G;ENSP00000376601:E146G|.	ENSP00000302501:E146G|.	E|N	-|-	2|1	0|0	ZEB2|ZEB2	144879028|144879028	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	8.040000|8.040000	0.89188|0.89188	2.302000|2.302000	0.77476|0.77476	0.533000|0.533000	0.62120|0.62120	GAA|AAT	.	.		0.453	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		C	145162558	T	C	145162558	3	2	91	1	0	0	0	0	1	0	0	0	17639	1783	62	2	3231	2	ZEB2	2	145162558	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3454734	145162558	98036815	98	12172										
RIF1	55183	hgsc.bcm.edu	37	chr2	152316610	152316610	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacaaacaaagaataaaaaaGaaaatatgaaaccagcagcc	5	8	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:152316610G>A	ENST00000243326.5	+	25	3535	c.3052G>A	c.(3052-3054)Gaa>Aaa	p.E1018K	RIF1_ENST00000428287.2_Missense_Mutation_p.E1018K|RIF1_ENST00000444746.2_Missense_Mutation_p.E1018K|RIF1_ENST00000430328.2_Missense_Mutation_p.E1018K|RIF1_ENST00000453091.2_Missense_Mutation_p.E1018K			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		GAATAAAAAAGAAAATATGAA	0.269																																					p.E1018K		Atlas-SNP	.											.	RIF1	244	.	0			c.G3052A						.						24	27	26					2																	152316610		2177	4275	6452	SO:0001583	missense	55183	exon26			AAAAAAGAAAATA	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.3052G>A	chr2.hg19:g.152316610G>A	ENSP00000243326:p.Glu1018Lys	137.0	0.0		186.0	21.0	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	hg19	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.431952	0.25813	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.78	4.89	0.63831	.	0.723385	0.13884	N	0.356121	T	0.17831	0.0428	N	0.17474	0.49	0.80722	D	1	B;B	0.12630	0.004;0.006	B;B	0.17098	0.004;0.017	T	0.03306	-1.1050	10	0.07644	T	0.81	-6.1798	10.7453	0.46177	0.1529:0.0:0.8471:0.0	.	1018;1018	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	K	1018	ENSP00000390181:E1018K;ENSP00000414615:E1018K;ENSP00000415691:E1018K;ENSP00000243326:E1018K;ENSP00000416123:E1018K	ENSP00000243326:E1018K	E	+	1	0	RIF1	152024856	1.000000	0.71417	0.658000	0.29665	0.302000	0.27658	2.337000	0.43947	1.416000	0.47057	0.555000	0.69702	GAA	.	.		0.269	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			A	152316610	G	A	152316610	3	1	91	1	0	0	0	0	1	0	0	0	13374	943	33	3	3150	3	RIF1	2	152316610	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	7154052	152316610	90882763	99	12173										
ACVR1	90	hgsc.bcm.edu	37	chr2	158636913	158636913	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccttggcagcactccacggcTtggccaggggacggcggggt	17	13	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:158636913T>C	ENST00000263640.3	-	4	696	c.267A>G	c.(265-267)caA>caG	p.Q89Q	ACVR1_ENST00000409283.2_Silent_p.Q89Q|ACVR1_ENST00000487456.1_5'UTR|ACVR1_ENST00000410057.2_Silent_p.Q89Q|ACVR1_ENST00000434821.1_Silent_p.Q89Q	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	89					activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	ACTCCACGGCTTGGCCAGGGG	0.547																																					p.Q89Q		Atlas-SNP	.											.	ACVR1	52	.	0			c.A267G						.						64	67	66					2																	158636913		2203	4300	6503	SO:0001819	synonymous_variant	90	exon4			CACGGCTTGGCCA		CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.267A>G	chr2.hg19:g.158636913T>C		102.0	0.0		86.0	4.0	NM_001105		Silent	SNP	ENST00000263640.3	hg19	CCDS2206.1																																																																																			.	.		0.547	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105		C	158636913	T	C	158636913	2	2	91	1	0	0	0	0	0	0	0	1	220	1606	56	2		2	ACVR1	2	158636913	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	6320303	158636913	84562460	100	12174										
FIGN	55137	hgsc.bcm.edu	37	chr2	164467712	164467712	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagctatgcaaaggagacggAtgaggtgaaggaagtgcagg	18	4	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:164467712A>G	ENST00000333129.3	-	3	944	c.630T>C	c.(628-630)caT>caC	p.H210H	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	210	Pro-rich.				mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						AAGGAGACGGATGAGGTGAAG	0.542																																					p.H210H		Atlas-SNP	.											.	FIGN	106	.	0			c.T630C						.						73	81	79					2																	164467712		2059	4203	6262	SO:0001819	synonymous_variant	55137	exon3			AGACGGATGAGGT	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"ATPases / AAA-type"	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.630T>C	chr2.hg19:g.164467712A>G		198.0	0.0		167.0	7.0	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Silent	SNP	ENST00000333129.3	hg19	CCDS2221.2																																																																																			.	.		0.542	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		G	164467712	A	G	164467712	2	3	91	1	0	0	0	0	0	0	0	1	5899	330	12	2		2	FIGN	2	164467712	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	5830799	164467712	78731661	101	12175										
SP3	6670	hgsc.bcm.edu	37	chr2	174820457	174820457	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggtacaaacgtaatatttccTggcagaccaagaggcacatt	9	9	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:174820457T>C	ENST00000310015.6	-	4	1313	c.783A>G	c.(781-783)ccA>ccG	p.P261P	SP3_ENST00000418194.2_Silent_p.P193P|SP3_ENST00000455789.2_Silent_p.P208P|SP3_ENST00000483084.1_5'Flank	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	261					B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			TAATATTTCCTGGCAGACCAA	0.468																																					p.P261P		Atlas-SNP	.											.	SP3	82	.	0			c.A783G						.						90	88	89					2																	174820457		2203	4300	6503	SO:0001819	synonymous_variant	6670	exon4			ATTTCCTGGCAGA	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.783A>G	chr2.hg19:g.174820457T>C		90.0	0.0		71.0	4.0	NM_003111	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Silent	SNP	ENST00000310015.6	hg19	CCDS2254.1	.	.	.	.	.	.	.	.	.	.	T	4.001	-0.002544	0.07819	.	.	ENSG00000172845	ENST00000416195	.	.	.	5.95	4.8	0.61643	.	.	.	.	.	T	0.57770	0.2076	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55192	-0.8179	4	.	.	.	.	7.0973	0.25317	0.1308:0.0688:0.0:0.8004	.	.	.	.	R	218	.	.	Q	-	2	0	SP3	174528703	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.068000	0.41471	1.079000	0.41038	-0.371000	0.07208	CAG	.	.		0.468	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111		C	174820457	T	C	174820457	2	2	91	1	0	0	0	0	0	0	0	1	14980	1567	55	2		2	SP3	2	174820457	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	10352745	174820457	68378916	102	12176										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178494173	178494173	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggctaccataacactggcagGggaggatgaggcagttgagg	17	7	0	2	rs397723704|rs3830637	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:178494173G>A	ENST00000286063.6	-	20	3081	c.2764C>T	c.(2764-2766)Cct>Tct	p.P922S	PDE11A_ENST00000450799.2_Missense_Mutation_p.P113S|PDE11A_ENST00000409504.1_Missense_Mutation_p.P564S|PDE11A_ENST00000449286.2_Missense_Mutation_p.P564S|PDE11A_ENST00000358450.4_Missense_Mutation_p.P672S|PDE11A_ENST00000389683.3_Missense_Mutation_p.P478S	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	922					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	ACACTGGCAGGGGAGGATGAG	0.502									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.P922S		Atlas-SNP	.											.	PDE11A	283	.	0			c.C2764T						.						236	179	198					2																	178494173		2203	4300	6503	SO:0001583	missense	50940	exon20	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	TGGCAGGGGAGGA	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2764C>T	chr2.hg19:g.178494173G>A	ENSP00000286063:p.Pro922Ser	268.0	0.0		254.0	13.0	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	hg19	CCDS33334.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.28|11.28	1.592474|1.592474	0.28357|0.28357	.|.	.|.	ENSG00000128655|ENSG00000128655	ENST00000436700|ENST00000286063;ENST00000358450;ENST00000450799;ENST00000409504;ENST00000389683;ENST00000449286	.|T;T;T;T;T;T	.|0.70749	.|-0.17;0.06;-0.1;-0.06;-0.51;-0.06	5.62|5.62	-0.681|-0.681	0.11342|0.11342	.|.	3.486060|3.486060	0.00890|0.00890	N|N	0.002221|0.002221	T|T	0.49915|0.49915	0.1585|0.1585	N|N	0.14661|0.14661	0.345|0.345	0.20196|0.20196	N|N	0.99993|0.99993	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.28235|0.28235	-1.0050|-1.0050	6|10	.|0.36615	.|T	.|0.2	.|.	0.627|0.627	0.00788|0.00788	0.3361:0.1255:0.2887:0.2497|0.3361:0.1255:0.2887:0.2497	.|.	.|672;922	.|Q9HCR9-2;Q9HCR9	.|.;PDE11_HUMAN	L|S	124|922;672;113;564;478;564	.|ENSP00000286063:P922S;ENSP00000351232:P672S;ENSP00000387964:P113S;ENSP00000386539:P564S;ENSP00000374333:P478S;ENSP00000390599:P564S	.|ENSP00000286063:P922S	P|P	-|-	2|1	0|0	PDE11A|PDE11A	178202419|178202419	0.452000|0.452000	0.25713|0.25713	0.002000|0.002000	0.10522|0.10522	0.053000|0.053000	0.15095|0.15095	0.290000|0.290000	0.18975|0.18975	-0.018000|-0.018000	0.14079|0.14079	-0.293000|-0.293000	0.09583|0.09583	CCC|CCT	.	.		0.502	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			A	178494173	G	A	178494173	3	1	91	1	0	0	0	0	1	0	0	0	11640	1232	43	3	41	3	PDE11A	2	178494173	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3673716	178494173	64705200	103	12177										
TTN	7273	hgsc.bcm.edu	37	chr2	179667053	179667053	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catccctaaaccagctcaccTcaggaactggaaaacctgaa	6	14	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:179667053T>C	ENST00000591111.1	-	3	331	c.107A>G	c.(106-108)gAg>gGg	p.E36G	TTN_ENST00000342175.6_Missense_Mutation_p.E36G|TTN_ENST00000360870.5_Missense_Mutation_p.E36G|TTN_ENST00000589042.1_Missense_Mutation_p.E36G|TTN_ENST00000342992.6_Missense_Mutation_p.E36G|TTN_ENST00000460472.2_Missense_Mutation_p.E36G|TTN_ENST00000359218.5_Missense_Mutation_p.E36G			Q8WZ42	TITIN_HUMAN	titin	32647	Ig-like 1.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCAGCTCACCTCAGGAACTGG	0.527																																					p.E36G		Atlas-SNP	.											.	TTN	18412	.	0			c.A107G						.						68	57	61					2																	179667053		2203	4300	6503	SO:0001583	missense	7273	exon3			CTCACCTCAGGAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.107A>G	chr2.hg19:g.179667053T>C	ENSP00000465570:p.Glu36Gly	146.0	0.0		120.0	5.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.85	2.955924	0.53293	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870;ENST00000412264	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	5.74	5.74	0.90152	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.83727	0.5317	M	0.84433	2.695	0.44142	D	0.996938	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.87578	0.997;0.997;0.997;0.997;0.998	D	0.86523	0.1817	9	0.87932	D	0	.	16.0351	0.80621	0.0:0.0:0.0:1.0	.	36;36;36;36;36	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	G	36;36;36;36;36;36;51	ENSP00000343764:E36G;ENSP00000434586:E36G;ENSP00000340554:E36G;ENSP00000352154:E36G;ENSP00000354117:E36G	ENSP00000340554:E36G	E	-	2	0	TTN	179375298	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.846000	0.86887	2.186000	0.69663	0.533000	0.62120	GAG	.	.		0.527	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179667053	T	C	179667053	3	2	91	1	0	0	0	0	1	0	0	0	16750	1551	54	2	111321	2	TTN	2	179667053	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1172880	179667053	63532320	104	12178										
RFTN2	130132	hgsc.bcm.edu	37	chr2	198480674	198480674	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcagccagagtgtgcagcagAgggccataatctgttttgat	12	8	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:198480674A>G	ENST00000295049.4	-	7	1616	c.1080T>C	c.(1078-1080)ccT>ccC	p.P360P		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	360					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						TGTGCAGCAGAGGGCCATAAT	0.428																																					p.P360P		Atlas-SNP	.											.	RFTN2	68	.	0			c.T1080C						.						90	73	79					2																	198480674		2198	4287	6485	SO:0001819	synonymous_variant	130132	exon7			CAGCAGAGGGCCA	AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 11"	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.1080T>C	chr2.hg19:g.198480674A>G		108.0	0.0		98.0	4.0	NM_144629	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Silent	SNP	ENST00000295049.4	hg19	CCDS2323.1																																																																																			.	.		0.428	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629		G	198480674	A	G	198480674	2	3	91	1	0	0	0	0	0	0	0	1	13274	291	11	2		2	RFTN2	2	198480674	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	18813621	198480674	44718699	105	12179										
FASTKD2	22868	hgsc.bcm.edu	37	chr2	207652780	207652780	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgccgcgggagctgccatcgTcacatacaaatgcaaaggtg	12	11	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:207652780T>C	ENST00000236980.6	+	9	2062	c.1714T>C	c.(1714-1716)Tca>Cca	p.S572P	FASTKD2_ENST00000403094.3_Missense_Mutation_p.S572P|FASTKD2_ENST00000402774.3_Missense_Mutation_p.S572P	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	572					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		GCTGCCATCGTCACATACAAA	0.488																																					p.S572P		Atlas-SNP	.											.	FASTKD2	49	.	0			c.T1714C						.						69	65	67					2																	207652780		2203	4300	6503	SO:0001583	missense	22868	exon9			CCATCGTCACATA	BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"KIAA0971"	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.1714T>C	chr2.hg19:g.207652780T>C	ENSP00000236980:p.Ser572Pro	95.0	0.0		66.0	4.0	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	hg19	CCDS2371.1	.	.	.	.	.	.	.	.	.	.	t	10.54	1.379882	0.24944	.	.	ENSG00000118246	ENST00000236980;ENST00000402774;ENST00000403094	T;T;T	0.49720	0.77;0.77;0.77	5.44	-2.93	0.05598	FAST kinase-like protein, subdomain 2 (1);	0.775465	0.12555	N	0.458720	T	0.33381	0.0861	L	0.47716	1.5	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.14023	0.004;0.01	T	0.21759	-1.0236	10	0.27785	T	0.31	-1.8665	6.5505	0.22431	0.0:0.3775:0.1415:0.481	.	572;572	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	P	572	ENSP00000236980:S572P;ENSP00000385990:S572P;ENSP00000384929:S572P	ENSP00000236980:S572P	S	+	1	0	FASTKD2	207361025	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.607000	0.02070	-0.686000	0.05170	-0.261000	0.10672	TCA	.	.		0.488	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		C	207652780	T	C	207652780	3	2	91	1	0	0	0	0	1	0	0	0	5694	1667	58	2	1744	2	FASTKD2	2	207652780	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9172106	207652780	35546593	106	12180										
MAP2	4133	hgsc.bcm.edu	37	chr2	210558428	210558428	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aagcagttacagattcagccAtgacctctaaaacactggag	8	10	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:210558428A>G	ENST00000360351.4	+	7	2040	c.1534A>G	c.(1534-1536)Atg>Gtg	p.M512V	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.M508V|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	512					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AGATTCAGCCATGACCTCTAA	0.418																																					p.M512V	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.A1534G						.						78	78	78					2																	210558428		2203	4300	6503	SO:0001583	missense	4133	exon7			TCAGCCATGACCT		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.1534A>G	chr2.hg19:g.210558428A>G	ENSP00000353508:p.Met512Val	107.0	0.0		76.0	4.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	hg19	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	A	0.057	-1.233648	0.01505	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.20463	2.07;2.07	5.62	-4.44	0.03557	MAP2/Tau projection (1);	0.750110	0.12834	N	0.435344	T	0.14056	0.0340	L	0.44542	1.39	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.31420	-0.9944	10	0.21014	T	0.42	-0.5443	10.0179	0.42024	0.1806:0.3516:0.4678:0.0	.	508;512	P11137-3;P11137	.;MAP2_HUMAN	V	512;508	ENSP00000353508:M512V;ENSP00000392164:M508V	ENSP00000353508:M512V	M	+	1	0	MAP2	210266673	0.000000	0.05858	0.000000	0.03702	0.344000	0.29017	-0.549000	0.06041	-0.828000	0.04273	-0.280000	0.10049	ATG	.	.		0.418	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		G	210558428	A	G	210558428	3	3	91	1	0	0	0	0	1	0	0	0	9244	217	8	2	1548	2	MAP2	2	210558428	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2905648	210558428	32640945	107	12181										
RQCD1	9125	hgsc.bcm.edu	37	chr2	219447748	219447748	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccaccttgacagcacaccagTctaacagagtttgcaatgct	7	13	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:219447748T>C	ENST00000273064.6	+	3	634	c.259T>C	c.(259-261)Tct>Cct	p.S87P	RQCD1_ENST00000295701.5_Missense_Mutation_p.S87P|RQCD1_ENST00000509807.2_Missense_Mutation_p.S87P|RQCD1_ENST00000542068.1_Missense_Mutation_p.S87P	NM_005444.2	NP_005435.1	Q92600	RCD1_HUMAN	RCD1 required for cell differentiation1 homolog (S. pombe)	87					cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)	15		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000192)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCACACCAGTCTAACAGAGT	0.388																																					p.S87P		Atlas-SNP	.											.	RQCD1	32	.	0			c.T259C						.						149	132	138					2																	219447748		2203	4300	6503	SO:0001583	missense	9125	exon3			CACCAGTCTAACA	D87957	CCDS33379.1, CCDS63123.1	2q35	2010-04-23	2001-11-28		ENSG00000144580	ENSG00000144580			10445	protein-coding gene	gene with protein product	"cancer/testis antigen 129"	612054	"rcd1 (required for cell differentiation, S.pombe) homolog 1"			9447985	Standard	NM_001271634		Approved	RCD1, RCD1+, CNOT9, CT129	uc010zki.3	Q92600	OTTHUMG00000154750	ENST00000273064.6:c.259T>C	chr2.hg19:g.219447748T>C	ENSP00000273064:p.Ser87Pro	130.0	0.0		95.0	4.0	NM_001271634	B2RPI0|B5MDQ4|B7Z1E5|Q96IX4	Missense_Mutation	SNP	ENST00000273064.6	hg19	CCDS33379.1	.	.	.	.	.	.	.	.	.	.	T	32	5.105907	0.94292	.	.	ENSG00000144580	ENST00000273064;ENST00000509807;ENST00000542068;ENST00000295701	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	6.08	6.08	0.98989	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77961	0.4209	H	0.94658	3.565	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.993;0.993	D	0.84395	0.0557	10	0.87932	D	0	0.3815	16.6438	0.85155	0.0:0.0:0.0:1.0	.	87;87;87	B7Z1E5;Q92600;B5MDQ4	.;RCD1_HUMAN;.	P	87	ENSP00000273064:S87P;ENSP00000441357:S87P;ENSP00000443687:S87P;ENSP00000295701:S87P	ENSP00000273064:S87P	S	+	1	0	RQCD1	219155992	1.000000	0.71417	0.929000	0.37066	0.986000	0.74619	8.040000	0.89188	2.333000	0.79357	0.533000	0.62120	TCT	.	.		0.388	RQCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336920.1	NM_005444		C	219447748	T	C	219447748	3	2	91	1	0	0	0	0	1	0	0	0	13685	1667	58	2	269	2	RQCD1	2	219447748	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	8889320	219447748	23751625	108	12182										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220432976	220432976	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgggagttgggtactttacaTtccagcacggcaatcccgtg	12	11	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:220432976T>C	ENST00000404537.1	-	2	1139	c.1083A>G	c.(1081-1083)gaA>gaG	p.E361E	OBSL1_ENST00000491370.1_5'Flank|OBSL1_ENST00000289656.3_5'UTR|OBSL1_ENST00000265318.4_Silent_p.E361E|OBSL1_ENST00000603926.1_Silent_p.E361E|OBSL1_ENST00000373873.4_Silent_p.E361E|OBSL1_ENST00000373876.1_Silent_p.E361E	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	361	Ig-like 4.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GTACTTTACATTCCAGCACGG	0.647											OREG0003988	type=REGULATORY REGION|Gene=OBSL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.E361E		Atlas-SNP	.											OBSL1_ENST00000404537,NS,carcinoma,0,1	OBSL1	120	.	0			c.A1083G						.						26	31	29					2																	220432976		1969	4138	6107	SO:0001819	synonymous_variant	23363	exon2			TTTACATTCCAGC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.1083A>G	chr2.hg19:g.220432976T>C		88.0	1.0	2266	40.0	2.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	hg19	CCDS46520.1																																																																																			.	.		0.647	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			C	220432976	T	C	220432976	2	2	91	1	0	0	0	0	0	0	0	1	10822	1490	52	2		2	OBSL1	2	220432976	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	985228	220432976	22766397	109	12183										
STK11IP	114790	hgsc.bcm.edu	37	chr2	220470738	220470738	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atacaacctgctggaaggacAccgggagctgtcaccactgt	11	12	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:220470738A>G	ENST00000456909.1	+	9	896	c.806A>G	c.(805-807)cAc>cGc	p.H269R	STK11IP_ENST00000459692.1_3'UTR|STK11IP_ENST00000295641.10_Missense_Mutation_p.H280R			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	280					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGGAAGGACACCGGGAGCTG	0.602											OREG0003992	type=REGULATORY REGION|Gene=STK11IP|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.H280R		Atlas-SNP	.											.	STK11IP	152	.	0			c.A839G						.						24	30	28					2																	220470738		2157	4270	6427	SO:0001583	missense	114790	exon9			AAGGACACCGGGA	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"LKB1 interacting protein"	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.806A>G	chr2.hg19:g.220470738A>G	ENSP00000389383:p.His269Arg	172.0	0.0	2267	116.0	5.0	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	hg19		.	.	.	.	.	.	.	.	.	.	A	19.14	3.769271	0.69992	.	.	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.21361	2.01;2.01	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.49932	0.1586	M	0.85197	2.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.993;0.999;0.997	T	0.56481	-0.7972	10	0.59425	D	0.04	-19.893	13.5291	0.61611	1.0:0.0:0.0:0.0	.	280;280;280;280	B4DUE4;B4DII2;Q8N1F8-2;Q8N1F8	.;.;.;S11IP_HUMAN	R	269;280;280	ENSP00000389383:H269R;ENSP00000295641:H280R	ENSP00000295641:H280R	H	+	2	0	STK11IP	220178982	1.000000	0.71417	1.000000	0.80357	0.485000	0.33311	7.325000	0.79124	2.061000	0.61500	0.533000	0.62120	CAC	.	.		0.602	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		G	220470738	A	G	220470738	3	3	91	1	0	0	0	0	1	0	0	0	15303	159	6	2	873	2	STK11IP	2	220470738	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	37762	220470738	22728635	110	12184										
COL4A3	1285	hgsc.bcm.edu	37	chr2	228162401	228162401	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctttgcaggagccaaaggaGacaggggagccccaggtttt	14	9	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:228162401G>T	ENST00000396578.3	+	42	3739	c.3577G>T	c.(3577-3579)Gac>Tac	p.D1193Y	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000439598.2_RNA|COL4A3_ENST00000468753.1_3'UTR|AC097662.2_ENST00000396588.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	1193	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		AGCCAAAGGAGACAGGGGAGC	0.507																																					p.D1193Y		Atlas-SNP	.											.	COL4A3	293	.	0			c.G3577T						.						15	17	16					2																	228162401		1830	4078	5908	SO:0001583	missense	1285	exon42			AAAGGAGACAGGG		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.3577G>T	chr2.hg19:g.228162401G>T	ENSP00000379823:p.Asp1193Tyr	144.0	0.0		95.0	4.0	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	hg19	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	G	8.583	0.882715	0.17467	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.96334	-3.98	5.54	1.06	0.20224	.	0.309908	0.27581	N	0.018735	D	0.93864	0.8037	M	0.76170	2.325	0.44702	D	0.997699	B;B;B;B	0.17667	0.009;0.009;0.023;0.015	B;B;B;B	0.19946	0.016;0.016;0.016;0.027	D	0.88052	0.2788	10	0.42905	T	0.14	.	5.9189	0.19070	0.3025:0.0:0.5647:0.1328	.	1193;1193;1193;1193	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	Y	1193	ENSP00000379823:D1193Y	ENSP00000323334:D1193Y	D	+	1	0	COL4A3	227870645	0.922000	0.31269	0.999000	0.59377	0.186000	0.23388	1.560000	0.36331	0.281000	0.22233	0.462000	0.41574	GAC	.	.		0.507	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		T	228162401	G	T	228162401	3	4	91	1	0	0	0	0	1	0	0	0	3693	942	33	3	3743	3	COL4A3	2	228162401	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	7691663	228162401	15036972	111	12185										
HTR2B	3357	hgsc.bcm.edu	37	chr2	231973880	231973880	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttcatccctttggaaaactGtagacacagtcaaccatgtt	6	10	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:231973880G>A	ENST00000258400.3	-	4	1309	c.797C>T	c.(796-798)aCa>aTa	p.T266I	PSMD1_ENST00000373635.4_Intron|PSMD1_ENST00000308696.6_Intron|PSMD1_ENST00000409643.1_Intron	NM_000867.4	NP_000858.3	P41595	5HT2B_HUMAN	5-hydroxytryptamine (serotonin) receptor 2B, G protein-coupled	266					activation of phospholipase C activity (GO:0007202)|behavior (GO:0007610)|calcium-mediated signaling (GO:0019722)|cardiac muscle hypertrophy (GO:0003300)|cellular calcium ion homeostasis (GO:0006874)|cellular response to temperature stimulus (GO:0071502)|cGMP biosynthetic process (GO:0006182)|embryonic morphogenesis (GO:0048598)|ERK1 and ERK2 cascade (GO:0070371)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|heart morphogenesis (GO:0003007)|intestine smooth muscle contraction (GO:0014827)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell death (GO:0060548)|neural crest cell differentiation (GO:0014033)|neural crest cell migration (GO:0001755)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphorylation (GO:0016310)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	drug binding (GO:0008144)|G-protein alpha-subunit binding (GO:0001965)|Ras GTPase activator activity (GO:0005099)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	11		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;4.48e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0141)	Amoxapine(DB00543)|Apomorphine(DB00714)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Dihydroergotamine(DB00320)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Lisuride(DB00589)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Ropinirole(DB00268)|Triflupromazine(DB00508)|Yohimbine(DB01392)	TTGGAAAACTGTAGACACAGT	0.458																																					p.T266I	Ovarian(155;1331 1891 12853 14038 34991)	Atlas-SNP	.											.	HTR2B	33	.	0			c.C797T						.						167	148	154					2																	231973880		2203	4300	6503	SO:0001583	missense	3357	exon4			AAAACTGTAGACA		CCDS2483.1	2q36.3-q37.1	2012-08-08	2012-02-03		ENSG00000135914	ENSG00000135914		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5294	protein-coding gene	gene with protein product		601122	"5-hydroxytryptamine (serotonin) receptor 2B"			8143856	Standard	NM_000867		Approved	5-HT(2B), 5-HT2B	uc002vro.3	P41595	OTTHUMG00000133222	ENST00000258400.3:c.797C>T	chr2.hg19:g.231973880G>A	ENSP00000258400:p.Thr266Ile	248.0	0.0		147.0	57.0	NM_000867	B2R9D5|Q53TI1|Q62221|Q6P523	Missense_Mutation	SNP	ENST00000258400.3	hg19	CCDS2483.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.664060	0.67700	.	.	ENSG00000135914	ENST00000258400	T	0.61742	0.08	5.61	5.61	0.85477	GPCR, rhodopsin-like superfamily (1);	0.049844	0.85682	D	0.000000	T	0.73434	0.3586	M	0.63428	1.95	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.68483	0.958;0.917	T	0.68895	-0.5288	10	0.30854	T	0.27	.	19.6415	0.95760	0.0:0.0:1.0:0.0	.	81;266	B3VRC5;P41595	.;5HT2B_HUMAN	I	266	ENSP00000258400:T266I	ENSP00000258400:T266I	T	-	2	0	HTR2B	231682124	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	9.869000	0.99810	2.638000	0.89438	0.650000	0.86243	ACA	.	.		0.458	HTR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256957.2	NM_000867		A	231973880	G	A	231973880	3	1	91	1	0	0	0	0	1	0	0	0	7451	1377	48	3	652	3	HTR2B	2	231973880	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3811479	231973880	11225493	112	12186										
NCL	4691	hgsc.bcm.edu	37	chr2	232325390	232325390	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atttaagtaccttcctcctcCtcttcttcctcctcctcatc	1	18	3	0	rs371798454		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:232325390C>T	ENST00000322723.4	-	4	1041	c.801G>A	c.(799-801)gaG>gaA	p.E267E	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	267	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CTTCCTCCTCCTCTTCTTCCT	0.413																																					p.E267E		Atlas-SNP	.											.	NCL	80	.	0			c.G801A						.	C		1,4405	2.1+/-5.4	0,1,2202	239	208	219		801	-3.1	0.5	2		219	0,8600		0,0,4300	no	coding-synonymous	NCL	NM_005381.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		267/711	232325390	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4691	exon4			CTCCTCCTCTTCT		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.801G>A	chr2.hg19:g.232325390C>T		318.0	0.0		208.0	17.0	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	hg19	CCDS33397.1																																																																																			.	.		0.413	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		T	232325390	C	T	232325390	2	4	91	1	0	0	0	0	0	0	0	1	10235	680	24	3		3	NCL	2	232325390	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	351510	232325390	10873983	113	12187										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234854669	234854669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtatatctctgagcgcactaTtcaaggtcagtggttaggag	12	7	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:234854669T>C	ENST00000324695.4	+	7	909	c.869T>C	c.(868-870)aTt>aCt	p.I290T	TRPM8_ENST00000433712.2_5'UTR|AC005538.5_ENST00000455991.1_RNA	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	290					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.I290N(1)		breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	GAGCGCACTATTCAAGGTCAG	0.473																																					p.I290T		Atlas-SNP	.											TRPM8,NS,carcinoma,0,1	TRPM8	146	.	1	Substitution - Missense(1)	lung(1)	c.T869C						.						71	62	65					2																	234854669		2203	4300	6503	SO:0001583	missense	79054	exon7			GCACTATTCAAGG	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.869T>C	chr2.hg19:g.234854669T>C	ENSP00000323926:p.Ile290Thr	95.0	0.0		77.0	4.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	hg19	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	T	6.697	0.497211	0.12762	.	.	ENSG00000144481	ENST00000324695	T	0.37058	1.22	5.75	4.65	0.58169	.	0.419814	0.24438	N	0.038539	T	0.25269	0.0614	L	0.33339	1.005	0.48830	D	0.999716	B	0.02656	0.0	B	0.06405	0.002	T	0.06716	-1.0811	10	0.41790	T	0.15	-8.8753	6.4808	0.22061	0.0:0.0859:0.2025:0.7117	.	290	Q7Z2W7	TRPM8_HUMAN	T	290	ENSP00000323926:I290T	ENSP00000323926:I290T	I	+	2	0	TRPM8	234519408	0.995000	0.38212	0.936000	0.37596	0.814000	0.46013	2.049000	0.41288	1.091000	0.41335	0.533000	0.62120	ATT	.	.		0.473	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		C	234854669	T	C	234854669	3	2	91	1	0	0	0	0	1	0	0	0	16607	1493	52	2	891	2	TRPM8	2	234854669	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2529279	234854669	8344704	114	12188										
CXCR7	57007	hgsc.bcm.edu	37	chr2	237489664	237489664	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acacctactacctgaagaccGtcacgtctgcgtccaacaat	6	15	2	2	rs143561143	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:237489664G>T	ENST00000272928.3	+	2	866	c.556G>T	c.(556-558)Gtc>Ttc	p.V186F		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	186					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)	p.V186F(1)|p.V186I(1)									CCTGAAGACCGTCACGTCTGC	0.587																																					p.V186F		Atlas-SNP	.											CXCR7_ENST00000272928,caecum,carcinoma,0,2	CXCR7	72	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G556T						.						148	132	138					2																	237489664		2203	4300	6503	SO:0001583	missense	57007	exon2			AAGACCGTCACGT	BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"CD molecules", "GPCR / Class A : Chemokine receptors : Atypical"	23692	protein-coding gene	gene with protein product		610376	"chemokine orphan receptor 1", "chemokine (C-X-C motif) receptor 7"	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.556G>T	chr2.hg19:g.237489664G>T	ENSP00000272928:p.Val186Phe	85.0	0.0		89.0	4.0	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	hg19	CCDS2516.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579509	0.65878	.	.	ENSG00000144476	ENST00000447924;ENST00000272928	T;T	0.37752	1.18;1.18	5.7	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	0.207947	0.39687	N	0.001293	T	0.40979	0.1139	L	0.45352	1.415	0.43372	D	0.995466	D	0.60160	0.987	P	0.62089	0.898	T	0.21143	-1.0254	10	0.11182	T	0.66	.	10.2608	0.43425	0.3193:0.0:0.6806:0.0	.	186	P25106	CXCR7_HUMAN	F	186	ENSP00000405945:V186F;ENSP00000272928:V186F	ENSP00000272928:V186F	V	+	1	0	CXCR7	237154403	0.999000	0.42202	0.961000	0.40146	0.988000	0.76386	2.813000	0.48002	0.773000	0.33404	-0.137000	0.14449	GTC	.	G|0.999;A|0.001		0.587	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		T	237489664	G	T	237489664	3	4	91	1	0	0	0	0	1	0	0	0	4098	1145	40	1	558	1	CXCR7	2	237489664	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	2634995	237489664	5709709	115	12189										
SEPT2	4735	hgsc.bcm.edu	37	chr2	242287583	242287583	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aggacatgaataaagaccagAtcttgctggaaaaagaagct	10	6	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:242287583A>G	ENST00000391973.2	+	11	1489	c.961A>G	c.(961-963)Atc>Gtc	p.I321V	SEPT2_ENST00000360051.3_Missense_Mutation_p.I321V|SEPT2_ENST00000401990.1_Missense_Mutation_p.I331V|SEPT2_ENST00000402092.2_Missense_Mutation_p.I321V|SEPT2_ENST00000407971.1_Missense_Mutation_p.I281V|SEPT2_ENST00000391971.2_Missense_Mutation_p.I321V	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	321					cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		TAAAGACCAGATCTTGCTGGA	0.383																																					p.I321V		Atlas-SNP	.											.	SEPT2	33	.	0			c.A961G						.						170	172	171					2																	242287583		2203	4300	6503	SO:0001583	missense	4735	exon12			GACCAGATCTTGC	D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"Septins"	7729	protein-coding gene	gene with protein product		601506	"neural precursor cell expressed, developmentally down-regulated 5"	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.961A>G	chr2.hg19:g.242287583A>G	ENSP00000375834:p.Ile321Val	160.0	0.0		100.0	4.0	NM_001008491	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Missense_Mutation	SNP	ENST00000391973.2	hg19	CCDS2548.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.433859	0.62955	.	.	ENSG00000168385	ENST00000391973;ENST00000360051;ENST00000391971;ENST00000401990;ENST00000407971;ENST00000402092;ENST00000391972;ENST00000421717	T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.73;0.73;0.72;0.94	6.07	6.07	0.98685	.	0.099286	0.64402	D	0.000003	T	0.47801	0.1465	M	0.71036	2.16	0.80722	D	1	B;B;B	0.27192	0.171;0.103;0.124	B;B;B	0.31869	0.137;0.023;0.075	T	0.48305	-0.9047	10	0.02654	T	1	.	16.6288	0.85011	1.0:0.0:0.0:0.0	.	356;281;321	Q15019-2;B5MCX3;Q15019	.;.;SEPT2_HUMAN	V	321;321;321;331;281;321;356;148	ENSP00000375834:I321V;ENSP00000353157:I321V;ENSP00000375832:I321V;ENSP00000385109:I331V;ENSP00000384525:I281V;ENSP00000385172:I321V;ENSP00000408296:I148V	ENSP00000353157:I321V	I	+	1	0	SEPT2	241936256	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.414000	0.90238	2.326000	0.78906	0.533000	0.62120	ATC	.	.		0.383	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155		G	242287583	A	G	242287583	3	3	91	1	0	0	0	0	1	0	0	0	14079	333	12	2	999	2	SEPT2	2	242287583	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4797919	242287583	911790	116	12190										
C3orf32	51066	hgsc.bcm.edu	37	chr3	8669446	8669446	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgcttggctttgcgcttggcTccgcagcaggatgggcaccg	15	12	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:8669446T>C	ENST00000317371.4	-	15	1771	c.546A>G	c.(544-546)ggA>ggG	p.G182G	SSUH2_ENST00000544814.1_Silent_p.G204G|SSUH2_ENST00000341795.3_Silent_p.G182G|SSUH2_ENST00000415132.1_Silent_p.G182G			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	182	Cys-rich.					cytoplasm (GO:0005737)											TGCGCTTGGCTCCGCAGCAGG	0.662																																					p.G204G		Atlas-SNP	.											.	.	.	.	0			c.A612G						.						59	55	56					3																	8669446		2203	4300	6503	SO:0001819	synonymous_variant	51066	exon8			CTTGGCTCCGCAG	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 32"	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.546A>G	chr3.hg19:g.8669446T>C		138.0	0.0		132.0	7.0	NM_001256748	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Silent	SNP	ENST00000317371.4	hg19	CCDS2568.1																																																																																			.	.		0.662	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931		C	8669446	T	C	8669446	2	2	91	1	0	0	0	0	0	0	0	1	2224	1538	54	2		2	C3orf32	3	8669446	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10		8669446	189352984	117	12191										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9146431	9146431	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgatgacattgttcatgaagAtgtcattgagggtggcatgg	14	5	2	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:9146431A>G	ENST00000383836.3	-	3	783	c.356T>C	c.(355-357)aTc>aCc	p.I119T	SRGAP3_ENST00000433332.3_5'UTR|SRGAP3_ENST00000360413.3_Missense_Mutation_p.I119T	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	119	F-BAR domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GTTCATGAAGATGTCATTGAG	0.542			T	RAF1	pilocytic astrocytoma																																p.I119T		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.T356C						.						151	137	142					3																	9146431		2203	4300	6503	SO:0001583	missense	9901	exon3			ATGAAGATGTCAT	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.356T>C	chr3.hg19:g.9146431A>G	ENSP00000373347:p.Ile119Thr	110.0	0.0		99.0	4.0	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.644603	0.87859	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.12984	2.63;2.63	5.69	5.69	0.88448	Fps/Fes/Fer/CIP4 homology (1);	0.000000	0.85682	D	0.000000	T	0.32823	0.0842	M	0.70903	2.155	0.80722	D	1	D;B;P	0.57571	0.98;0.403;0.458	P;B;B	0.58130	0.833;0.221;0.328	T	0.03166	-1.1065	10	0.56958	D	0.05	.	15.6084	0.76692	1.0:0.0:0.0:0.0	.	119;119;119	C7TPG7;O43295-2;O43295	.;.;SRGP2_HUMAN	T	119	ENSP00000373347:I119T;ENSP00000353587:I119T	ENSP00000353587:I119T	I	-	2	0	SRGAP3	9121431	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.224000	0.95209	2.157000	0.67596	0.528000	0.53228	ATC	.	.		0.542	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			G	9146431	A	G	9146431	3	3	91	1	0	0	0	0	1	0	0	0	15162	333	12	2	3058	2	SRGAP3	3	9146431	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	476985	9146431	188875999	118	12192										
CAND2	23066	hgsc.bcm.edu	37	chr3	12854590	12854590	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aggcttttgaggccttcttgAggaagtatgtatggtggggt	16	4	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:12854590A>G	ENST00000456430.2	+	6	900	c.859A>G	c.(859-861)Agg>Ggg	p.R287G	CAND2_ENST00000295989.5_Missense_Mutation_p.R194G	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	287					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GGCCTTCTTGAGGAAGTATGT	0.577																																					p.R287G	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.A859G						.						26	28	27					3																	12854590		1907	4128	6035	SO:0001583	missense	23066	exon6			TTCTTGAGGAAGT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.859A>G	chr3.hg19:g.12854590A>G	ENSP00000387641:p.Arg287Gly	116.0	0.0		90.0	4.0	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	A	14.46	2.542060	0.45280	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.32515	1.45;1.45	4.34	3.14	0.36123	Armadillo-like helical (1);Armadillo-type fold (1);	0.060935	0.64402	D	0.000005	T	0.42200	0.1192	L	0.49699	1.58	0.80722	D	1	P;D	0.57899	0.791;0.981	B;D	0.69142	0.231;0.962	T	0.12889	-1.0530	10	0.21014	T	0.42	-10.4408	9.068	0.36475	0.8141:0.1858:0.0:0.0	.	287;194	O75155;O75155-2	CAND2_HUMAN;.	G	194;287	ENSP00000295989:R194G;ENSP00000387641:R287G	ENSP00000295989:R194G	R	+	1	2	CAND2	12829590	1.000000	0.71417	0.998000	0.56505	0.904000	0.53231	3.319000	0.51983	0.494000	0.27859	0.379000	0.24179	AGG	.	.		0.577	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		G	12854590	A	G	12854590	3	3	91	1	0	0	0	0	1	0	0	0	2618	295	11	2	881	2	CAND2	3	12854590	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3708159	12854590	185167840	119	12193										
TOP2B	7155	hgsc.bcm.edu	37	chr3	25654010	25654010	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aagaggtatgtcataccttcTtcttcttcagcaactttttg	6	9	5	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:25654010T>C	ENST00000264331.4	-	28	3781	c.3782A>G	c.(3781-3783)aAg>aGg	p.K1261R	TOP2B_ENST00000475717.1_5'Flank|TOP2B_ENST00000540199.1_Missense_Mutation_p.K113R|TOP2B_ENST00000542520.1_Missense_Mutation_p.K113R|TOP2B_ENST00000435706.2_Missense_Mutation_p.K1256R	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1261					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	TCATACCTTCTTCTTCTTCAG	0.338																																					p.K1256R		Atlas-SNP	.											.	TOP2B	98	.	0			c.A3767G						.						131	126	127					3																	25654010		1848	4077	5925	SO:0001583	missense	7155	exon28			ACCTTCTTCTTCT	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.3782A>G	chr3.hg19:g.25654010T>C	ENSP00000264331:p.Lys1261Arg	90.0	0.0		102.0	5.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	hg19		.	.	.	.	.	.	.	.	.	.	T	13.86	2.361890	0.41801	.	.	ENSG00000077097	ENST00000542520;ENST00000435706;ENST00000264331;ENST00000540199	T;T;T;T	0.54071	0.59;0.82;0.82;0.59	6.16	5.01	0.66863	.	0.040493	0.85682	N	0.000000	T	0.47432	0.1445	L	0.48642	1.525	0.58432	D	0.999991	B;B	0.32010	0.001;0.351	B;B	0.36567	0.001;0.228	T	0.32955	-0.9887	10	0.21540	T	0.41	-12.2423	12.3261	0.55011	0.0:0.0654:0.0:0.9346	.	1261;1256	Q02880;Q02880-2	TOP2B_HUMAN;.	R	113;1256;1261;113	ENSP00000446023:K113R;ENSP00000396704:K1256R;ENSP00000264331:K1261R;ENSP00000437352:K113R	ENSP00000264331:K1261R	K	-	2	0	TOP2B	25629014	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.755000	0.62198	1.155000	0.42497	0.528000	0.53228	AAG	.	.		0.338	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				C	25654010	T	C	25654010	3	2	91	1	0	0	0	0	1	0	0	0	16381	1609	56	2	1134	2	TOP2B	3	25654010	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	12799420	25654010	172368420	120	12194										
LRRC3B	116135	hgsc.bcm.edu	37	chr3	26751506	26751506	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcaaaggagtagctgaaaccTtgcagactctggacttgtcc	10	10	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:26751506T>C	ENST00000396641.2	+	2	935	c.343T>C	c.(343-345)Ttg>Ctg	p.L115L	LRRC3B_ENST00000456208.2_Silent_p.L115L|LRRC3B_ENST00000417744.1_Silent_p.L115L|AC114877.3_ENST00000446601.1_lincRNA	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	115						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						AGCTGAAACCTTGCAGACTCT	0.453																																					p.L115L		Atlas-SNP	.											.	LRRC3B	51	.	0			c.T343C						.						64	60	61					3																	26751506		2203	4300	6503	SO:0001819	synonymous_variant	116135	exon2			GAAACCTTGCAGA	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.343T>C	chr3.hg19:g.26751506T>C		76.0	0.0		81.0	4.0	NM_052953	Q5M8T0	Silent	SNP	ENST00000396641.2	hg19	CCDS2644.1																																																																																			.	.		0.453	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953		C	26751506	T	C	26751506	2	2	91	1	0	0	0	0	0	0	0	1	9005	1606	56	2		2	LRRC3B	3	26751506	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1097496	26751506	171270924	121	12195										
LRRC3B	116135	hgsc.bcm.edu	37	chr3	26751740	26751740	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcaatgctgccaacgacgctGacctttgtaacctccctaaa	6	14	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:26751740G>T	ENST00000396641.2	+	2	1169	c.577G>T	c.(577-579)Gac>Tac	p.D193Y	LRRC3B_ENST00000456208.2_Missense_Mutation_p.D193Y|LRRC3B_ENST00000417744.1_Missense_Mutation_p.D193Y|AC114877.3_ENST00000446601.1_lincRNA	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	193	LRRCT.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						CAACGACGCTGACCTTTGTAA	0.468																																					p.D193Y		Atlas-SNP	.											.	LRRC3B	51	.	0			c.G577T						.						78	71	73					3																	26751740		2203	4300	6503	SO:0001583	missense	116135	exon2			GACGCTGACCTTT	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.577G>T	chr3.hg19:g.26751740G>T	ENSP00000379880:p.Asp193Tyr	197.0	0.0		146.0	10.0	NM_052953	Q5M8T0	Missense_Mutation	SNP	ENST00000396641.2	hg19	CCDS2644.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.666595	0.67814	.	.	ENSG00000179796	ENST00000396641;ENST00000417744;ENST00000456208	T;T;T	0.61742	0.08;0.08;0.08	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.70561	0.3238	L	0.41824	1.3	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	T	0.70103	-0.4964	10	0.72032	D	0.01	-18.9203	19.8676	0.96824	0.0:0.0:1.0:0.0	.	193	Q96PB8	LRC3B_HUMAN	Y	193	ENSP00000379880:D193Y;ENSP00000406370:D193Y;ENSP00000394940:D193Y	ENSP00000379880:D193Y	D	+	1	0	LRRC3B	26726744	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.062000	0.89475	2.941000	0.99782	0.655000	0.94253	GAC	.	.		0.468	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953		T	26751740	G	T	26751740	3	4	91	1	0	0	0	0	1	0	0	0	9005	1290	45	3	579	3	LRRC3B	3	26751740	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	234	26751740	171270690	122	12196										
ZNF860	344787	hgsc.bcm.edu	37	chr3	32030625	32030625	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaaaaggagccaggcatggcTcttcctcagggacacttgac	12	11	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:32030625T>C	ENST00000360311.4	+	2	603	c.54T>C	c.(52-54)gcT>gcC	p.A18A		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	18					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						CAGGCATGGCTCTTCCTCAGG	0.493																																					p.A18A		Atlas-SNP	.											.	ZNF860	96	.	0			c.T54C						.						47	42	44					3																	32030625		692	1591	2283	SO:0001819	synonymous_variant	344787	exon2			CATGGCTCTTCCT	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"Zinc fingers, C2H2-type", "-"	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.54T>C	chr3.hg19:g.32030625T>C		206.0	0.0		124.0	5.0	NM_001137674	B4DFA4	Silent	SNP	ENST00000360311.4	hg19	CCDS46784.1																																																																																			.	.		0.493	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1			C	32030625	T	C	32030625	2	2	91	1	0	0	0	0	0	0	0	1	18209	1538	54	2		2	ZNF860	3	32030625	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	5278885	32030625	165991805	123	12197										
ZNF860	344787	hgsc.bcm.edu	37	chr3	32032133	32032133	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgtggcaaggtttttaatcAacaagcaacccttgcacgtc	8	10	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:32032133A>G	ENST00000360311.4	+	2	2111	c.1562A>G	c.(1561-1563)cAa>cGa	p.Q521R		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	521					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						GTTTTTAATCAACAAGCAACC	0.403																																					p.Q521R		Atlas-SNP	.											.	ZNF860	96	.	0			c.A1562G						.						40	35	37					3																	32032133		692	1591	2283	SO:0001583	missense	344787	exon2			TTAATCAACAAGC	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"Zinc fingers, C2H2-type", "-"	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1562A>G	chr3.hg19:g.32032133A>G	ENSP00000373274:p.Gln521Arg	141.0	0.0		107.0	5.0	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	hg19	CCDS46784.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.965020	0.00049	.	.	ENSG00000197385	ENST00000360311	T	0.14893	2.47	0.309	-0.618	0.11576	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05273	0.0140	N	0.02658	-0.545	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40739	-0.9547	8	.	.	.	.	4.8639	0.13598	0.7388:0.0:0.2612:0.0	.	521	A6NHJ4	ZN860_HUMAN	R	521	ENSP00000373274:Q521R	.	Q	+	2	0	ZNF860	32007137	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.656000	0.05342	-1.377000	0.02123	-1.381000	0.01174	CAA	.	.		0.403	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1			G	32032133	A	G	32032133	3	3	91	1	0	0	0	0	1	0	0	0	18209	130	5	2	1564	2	ZNF860	3	32032133	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1508	32032133	165990297	124	12198										
XYLB	9942	hgsc.bcm.edu	37	chr3	38442465	38442465	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tagctgctaccccaagcccgGgagcttctcaggtgagagac	12	13	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:38442465G>A	ENST00000207870.3	+	18	1612	c.1522G>A	c.(1522-1524)Gga>Aga	p.G508R	XYLB_ENST00000542835.1_Missense_Mutation_p.G371R|XYLB_ENST00000472721.1_3'UTR	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	508					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		CCCAAGCCCGGGAGCTTCTCA	0.488																																					p.G508R		Atlas-SNP	.											.	XYLB	50	.	0			c.G1522A						.						119	113	115					3																	38442465		2203	4300	6503	SO:0001583	missense	9942	exon18			AGCCCGGGAGCTT	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"xylulokinase (H. influenzae) homolog"			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.1522G>A	chr3.hg19:g.38442465G>A	ENSP00000207870:p.Gly508Arg	134.0	0.0		98.0	4.0	NM_005108	B2RAW4|B4DDT2|B9EH64	Missense_Mutation	SNP	ENST00000207870.3	hg19	CCDS2678.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.824271	0.50739	.	.	ENSG00000093217	ENST00000207870;ENST00000542835	T;T	0.43294	0.95;0.95	5.5	5.5	0.81552	.	0.301489	0.30979	N	0.008498	T	0.37705	0.1013	L	0.46157	1.445	0.45676	D	0.998592	B;B	0.15719	0.006;0.014	B;B	0.17722	0.013;0.019	T	0.08027	-1.0742	10	0.27082	T	0.32	.	14.7704	0.69671	0.0:0.0:1.0:0.0	.	371;508	B4DDT2;O75191	.;XYLB_HUMAN	R	508;371	ENSP00000207870:G508R;ENSP00000443659:G371R	ENSP00000207870:G508R	G	+	1	0	XYLB	38417469	1.000000	0.71417	0.931000	0.37212	0.815000	0.46073	4.629000	0.61290	2.861000	0.98227	0.655000	0.94253	GGA	.	.		0.488	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108		A	38442465	G	A	38442465	3	1	91	1	0	0	0	0	1	0	0	0	17477	1233	43	3	1592	3	XYLB	3	38442465	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	6410332	38442465	159579965	125	12199										
EXOG	9941	hgsc.bcm.edu	37	chr3	38539163	38539164	+	Missense_Mutation	DNP	AA	AA	TT													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaacaatttggattccctttAactggaacagaggcaaggtg							TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:38539163_38539164AA>TT	ENST00000287675.5	+	2	303_304	c.207_208AA>TT	c.(205-210)ttAAct>ttTTct	p.69_70LT>FS	EXOG_ENST00000358249.2_5'UTR|EXOG_ENST00000422077.2_Intron	NM_005107.3	NP_005098.2	Q9Y2C4	EXOG_HUMAN	endo/exonuclease (5'-3'), endonuclease G-like	69					DNA catabolic process, endonucleolytic (GO:0000737)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			central_nervous_system(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	17						GATTCCCTTTAACTGGAACAGA	0.401																																					p.L69F|p.T70S		Atlas-SNP	.											.	EXOG	29	.	0			c.A207T|c.A208T						.																																			SO:0001583	missense	9941	exon2			CCCTTTAACTGGA|CCTTTAACTGGAA	AB020523	CCDS2680.1, CCDS46795.1	3p21.3	2010-05-07	2009-01-08	2009-01-08	ENSG00000157036	ENSG00000157036	3.1.30.-		3347	protein-coding gene	gene with protein product		604051	"endonuclease G-like 1", "endonuclease G-like 2"	ENDOGL1, ENDOGL2		10231028, 18187503	Standard	NM_005107		Approved	ENGL-a, ENGL, ENGL-b	uc003cih.2	Q9Y2C4	OTTHUMG00000131295	Exception_encountered	chr3.hg19:g.38539163_38539164delinsTT	ENSP00000287675:p.L69_T70delinsFS	115.0|117.0	0.0		81.0	5.0|4.0	NM_005107	A8K242|B4DVG2|Q3SXM9|Q9Y2C8	Missense_Mutation	SNP	ENST00000287675.5	hg19	CCDS2680.1																																																																																			.	.		0.401	EXOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254063.2	NM_005107		TT	38539164	AA	TT	38539163	3	4	91	1	0	0	0	0	1	0	0	0	5314	359	13	4	213	4	EXOG	3	38539163	Missense_Mutation	DNP	AA	TCGA-DD-A119-01A-11D-A12Z-10	96698	38539163	159483267	126	12200										
RPSA	3921	hgsc.bcm.edu	37	chr3	39453157	39453157	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagggagctcactcagtgggTttgatgtggtggatgctggc	17	7	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:39453157T>C	ENST00000301821.6	+	5	625	c.516T>C	c.(514-516)ggT>ggC	p.G172G	RPSA_ENST00000478027.1_3'UTR|RPSA_ENST00000443003.1_Silent_p.G177G|SNORA62_ENST00000365493.1_RNA	NM_001012321.1|NM_002295.4	NP_001012321.1|NP_002286.2			ribosomal protein SA											endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064)		ACTCAGTGGGTTTGATGTGGT	0.512																																					p.G172G		Atlas-SNP	.											.	RPSA	15	.	0			c.T516C						.						151	151	151					3																	39453157		2203	4300	6503	SO:0001819	synonymous_variant	3921	exon4			AGTGGGTTTGATG	S37431	CCDS2686.1	3p21.3	2014-09-17	2002-08-29	2005-02-11	ENSG00000168028	ENSG00000168028			6502	protein-coding gene	gene with protein product		150370	"laminin receptor 1 (67kD, ribosomal protein SA)"	LAMR1		1534510, 8760291	Standard	NM_001012321		Approved	LRP, 37LRP, p40, SA	uc003cjp.3	P08865	OTTHUMG00000131296	ENST00000301821.6:c.516T>C	chr3.hg19:g.39453157T>C		112.0	0.0		83.0	4.0	NM_001012321		Silent	SNP	ENST00000301821.6	hg19	CCDS2686.1																																																																																			.	.		0.512	RPSA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254064.3	NM_002295		C	39453157	T	C	39453157	2	2	91	1	0	0	0	0	0	0	0	1	13678	1712	60	2		2	RPSA	3	39453157	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	913994	39453157	158569273	127	12201										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266104	41266104	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acagtcttacctggactctgGaatccattctggtgccacta	8	12	3	0	rs28931589|rs121913416		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:41266104G>T	ENST00000349496.5	+	3	381	c.101G>T	c.(100-102)gGa>gTa	p.G34V	CTNNB1_ENST00000396185.3_Missense_Mutation_p.G34V|CTNNB1_ENST00000405570.1_Missense_Mutation_p.G34V|CTNNB1_ENST00000453024.1_Missense_Mutation_p.G27V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.G34V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	34			G -> E (in PTR). {ECO:0000269|PubMed:10192393}.|G -> R (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|G -> V (in hepatoblastoma; dbSNP:rs28931589). {ECO:0000269|PubMed:9927029}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.G34E(73)|p.G34V(72)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTGGACTCTGGAATCCATTCT	0.488	G34E(AGS_STOMACH)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.G34V	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,161	CTNNB1	4904	.	276	Substitution - Missense(145)|Deletion - In frame(105)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(146)|endometrium(30)|large_intestine(27)|stomach(21)|central_nervous_system(20)|skin(8)|pancreas(8)|ovary(6)|small_intestine(2)|lung(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|pituitary(1)|prostate(1)|bone(1)	c.G101T						.						93	78	83					3																	41266104		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACTCTGGAATCCA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.101G>T	chr3.hg19:g.41266104G>T	ENSP00000344456:p.Gly34Val	260.0	1.0		209.0	13.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.450603	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-31.2232	19.9596	0.97236	0.0:0.0:1.0:0.0	rs28931589	34	P35222	CTNB1_HUMAN	V	27;34;34;34;34;27;34;34;34	ENSP00000400508:G27V;ENSP00000385604:G34V;ENSP00000412219:G34V;ENSP00000379486:G34V;ENSP00000344456:G34V;ENSP00000411226:G27V;ENSP00000379488:G34V;ENSP00000409302:G34V;ENSP00000401599:G34V	ENSP00000344456:G34V	G	+	2	0	CTNNB1	41241108	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GGA	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266104	G	T	41266104	3	4	91	1	0	0	0	0	1	0	0	0	4018	1174	41	3	107	3	CTNNB1	3	41266104	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	1812947	41266104	156756326	128	12202										
LRRC2	79442	hgsc.bcm.edu	37	chr3	46569020	46569020	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aggttcagcatggaatagggAaggtaggtcaacttgttttt	13	4	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:46569020A>G	ENST00000395905.3	-	7	1217	c.825T>C	c.(823-825)ctT>ctC	p.L275L	LRRC2_ENST00000296144.3_Silent_p.L275L	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	275										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		TGGAATAGGGAAGGTAGGTCA	0.458																																					p.L275L		Atlas-SNP	.											.	LRRC2	37	.	0			c.T825C						.						107	100	102					3																	46569020		2203	4300	6503	SO:0001819	synonymous_variant	79442	exon7			ATAGGGAAGGTAG	AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"leucine-rich repeat-containing 2"			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.825T>C	chr3.hg19:g.46569020A>G		99.0	0.0		100.0	4.0	NM_024512	B2RDQ7|Q96LT5	Silent	SNP	ENST00000395905.3	hg19	CCDS2741.1																																																																																			.	.		0.458	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2			G	46569020	A	G	46569020	2	3	91	1	0	0	0	0	0	0	0	1	8985	233	9	2		2	LRRC2	3	46569020	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	5302916	46569020	151453410	129	12203										
ALS2CL	259173	hgsc.bcm.edu	37	chr3	46722798	46722798	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctctcccagtggcccgtgtaCctgaagggctggggggcctg	16	13	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:46722798C>T	ENST00000318962.4	-	13	1457	c.1374G>A	c.(1372-1374)agG>agA	p.R458R	ALS2CL_ENST00000415953.1_Silent_p.R458R	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	458					endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		GGCCCGTGTACCTGAAGGGCT	0.662																																					p.R458R		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G1374A						.						78	85	82					3																	46722798		2203	4300	6503	SO:0001819	synonymous_variant	259173	exon13			CGTGTACCTGAAG	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.1374G>A	chr3.hg19:g.46722798C>T		211.0	0.0		152.0	53.0	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Silent	SNP	ENST00000318962.4	hg19	CCDS2743.1																																																																																			.	.		0.662	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129		T	46722798	C	T	46722798	2	4	91	1	0	0	0	0	0	0	0	1	551	506	18	3		3	ALS2CL	3	46722798	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	153778	46722798	151299632	130	12204										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47043918	47043918	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgctaagagccacgaccttAtgtcaggtttctggaatgcc	10	10	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:47043918A>T	ENST00000450053.3	+	32	5388	c.5209A>T	c.(5209-5211)Atg>Ttg	p.M1737L	NBEAL2_ENST00000292309.5_Missense_Mutation_p.M1553L|NBEAL2_ENST00000383740.2_Missense_Mutation_p.M16L	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1737					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CCACGACCTTATGTCAGGTTT	0.587																																					p.M1737L		Atlas-SNP	.											.	NBEAL2	267	.	0			c.A5209T						.						75	77	76					3																	47043918		2099	4206	6305	SO:0001583	missense	23218	exon32			GACCTTATGTCAG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.5209A>T	chr3.hg19:g.47043918A>T	ENSP00000415034:p.Met1737Leu	92.0	0.0		91.0	26.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	25.8|25.8|25.8	4.679318|4.679318|4.679318	0.88542|0.88542|0.88542	.|.|.	.|.|.	ENSG00000160796|ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000292309;ENST00000383740;ENST00000450053|ENST00000443829	T|T;T;T|.	0.58060|0.56776|.	0.36|0.5;1.14;0.44|.	4.84|4.84|4.84	4.84|4.84|4.84	0.62591|0.62591|0.62591	.|.|.	.|0.046774|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|T	0.63498|0.63498|0.63498	0.2516|0.2516|0.2516	L|L|L	0.54323|0.54323|0.54323	1.7|1.7|1.7	0.53688|0.53688|0.53688	D|D|D	0.999971|0.999971|0.999971	.|B;P|.	.|0.34462|.	.|0.264;0.454|.	.|B;B|.	.|0.37601|.	.|0.082;0.254|.	T|T|T	0.62091|0.62091|0.62091	-0.6927|-0.6927|-0.6927	7|10|5	0.54805|0.36615|.	T|T|.	0.06|0.2|.	.|.|.	13.4524|13.4524|13.4524	0.61178|0.61178|0.61178	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|1553;1737|.	.|Q6ZNJ1-2;Q6ZNJ1|.	.|.;NBEL2_HUMAN|.	F|L|F	1024|1553;16;1737|105	ENSP00000410405:L1024F|ENSP00000292309:M1553L;ENSP00000373246:M16L;ENSP00000415034:M1737L|.	ENSP00000410405:L1024F|ENSP00000292309:M1553L|.	L|M|Y	+|+|+	3|1|2	2|0|0	NBEAL2|NBEAL2|NBEAL2	47018922|47018922|47018922	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.974000|0.974000|0.974000	0.67602|0.67602|0.67602	9.106000|9.106000|9.106000	0.94253|0.94253|0.94253	2.045000|2.045000|2.045000	0.60652|0.60652|0.60652	0.529000|0.529000|0.529000	0.55759|0.55759|0.55759	TTA|ATG|TAT	.	.		0.587	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47043918	A	T	47043918	3	4	91	1	0	0	0	0	1	0	0	0	10198	449	16	4	5335	4	NBEAL2	3	47043918	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	321120	47043918	150978512	131	12205										
PTPN23	25930	hgsc.bcm.edu	37	chr3	47454662	47454662	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctggatccactctggacacTcaacaagacctgaacaggtt	8	12	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:47454662T>C	ENST00000265562.4	+	25	4975	c.4898T>C	c.(4897-4899)cTc>cCc	p.L1633P	PTPN23_ENST00000431726.1_Missense_Mutation_p.L1507P	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1633					cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTCTGGACACTCAACAAGACC	0.572																																					p.L1633P		Atlas-SNP	.											.	PTPN23	85	.	0			c.T4898C						.						71	72	71					3																	47454662		2202	4291	6493	SO:0001583	missense	25930	exon25			GGACACTCAACAA	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.4898T>C	chr3.hg19:g.47454662T>C	ENSP00000265562:p.Leu1633Pro	94.0	0.0		87.0	4.0	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	hg19	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.970869	0.53614	.	.	ENSG00000076201	ENST00000265562	T	0.13901	2.55	4.35	4.35	0.52113	.	0.000000	0.64402	D	0.000017	T	0.25791	0.0628	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.01988	-1.1234	10	0.87932	D	0	-26.5951	12.6561	0.56788	0.0:0.0:0.0:1.0	.	1633	Q9H3S7	PTN23_HUMAN	P	1633	ENSP00000265562:L1633P	ENSP00000265562:L1633P	L	+	2	0	PTPN23	47429666	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.147000	0.77382	1.805000	0.52779	0.460000	0.39030	CTC	.	.		0.572	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		C	47454662	T	C	47454662	3	2	91	1	0	0	0	0	1	0	0	0	12803	1551	54	2	4996	2	PTPN23	3	47454662	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	410744	47454662	150567768	132	12206										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49162306	49162306	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacagttggcaccggccaccTggccttgatgggtccccaaa	11	15	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:49162306T>C	ENST00000418109.1	-	22	3101	c.2937A>G	c.(2935-2937)ccA>ccG	p.P979P	LAMB2_ENST00000305544.4_Silent_p.P979P|LAMB2_ENST00000464891.1_5'UTR	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	979	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ACCGGCCACCTGGCCTTGATG	0.602																																					p.P979P		Atlas-SNP	.											.	LAMB2	156	.	0			c.A2937G						.						87	77	81					3																	49162306		2203	4300	6503	SO:0001819	synonymous_variant	3913	exon21			GCCACCTGGCCTT		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.2937A>G	chr3.hg19:g.49162306T>C		54.0	0.0		43.0	4.0	NM_002292	Q16321	Silent	SNP	ENST00000418109.1	hg19	CCDS2789.1																																																																																			.	.		0.602	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		C	49162306	T	C	49162306	2	2	91	1	0	0	0	0	0	0	0	1	8620	1567	55	2		2	LAMB2	3	49162306	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1707644	49162306	148860124	133	12207										
GNAT1	2779	hgsc.bcm.edu	37	chr3	50231568	50231568	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctcggagcgcaagaagtggAtccactgcttcgagggcgtg	16	10	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:50231568A>G	ENST00000433068.1	+	6	678	c.622A>G	c.(622-624)Atc>Gtc	p.I208V	GNAT1_ENST00000232461.3_Missense_Mutation_p.I208V|GNAT1_ENST00000481246.1_3'UTR	NM_000172.3	NP_000163.2	P11488	GNAT1_HUMAN	guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1	208					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell proliferation (GO:0008283)|cellular response to electrical stimulus (GO:0071257)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|phototransduction, visible light (GO:0007603)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to light intensity (GO:0009642)|response to light stimulus (GO:0009416)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	acyl binding (GO:0000035)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		CAAGAAGTGGATCCACTGCTT	0.667																																					p.I208V		Atlas-SNP	.											.	GNAT1	39	.	0			c.A622G						.						65	59	61					3																	50231568		2203	4300	6503	SO:0001583	missense	2779	exon6			AAGTGGATCCACT		CCDS2812.1	3p21	2014-01-28			ENSG00000114349	ENSG00000114349			4393	protein-coding gene	gene with protein product		139330					Standard	NM_000172		Approved	CSNBAD3	uc003cyl.2	P11488	OTTHUMG00000156808	ENST00000433068.1:c.622A>G	chr3.hg19:g.50231568A>G	ENSP00000387555:p.Ile208Val	91.0	0.0		88.0	4.0	NM_144499	Q4VBN2	Missense_Mutation	SNP	ENST00000433068.1	hg19	CCDS2812.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.193651	0.78902	.	.	ENSG00000114349	ENST00000232461;ENST00000433068	D;D	0.88509	-2.39;-2.39	4.49	4.49	0.54785	.	0.048531	0.85682	D	0.000000	D	0.90696	0.7081	M	0.85099	2.735	0.58432	D	0.999997	B	0.31459	0.324	B	0.37601	0.254	D	0.91411	0.5151	10	0.87932	D	0	.	12.9261	0.58260	1.0:0.0:0.0:0.0	.	208	P11488	GNAT1_HUMAN	V	208	ENSP00000232461:I208V;ENSP00000387555:I208V	ENSP00000232461:I208V	I	+	1	0	GNAT1	50206572	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.894000	0.92506	1.908000	0.55244	0.459000	0.35465	ATC	.	.		0.667	GNAT1-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345957.1	NM_000172		G	50231568	A	G	50231568	3	3	91	1	0	0	0	0	1	0	0	0	6519	333	12	2	644	2	GNAT1	3	50231568	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1069262	50231568	147790862	134	12208										
SLC38A3	10991	hgsc.bcm.edu	37	chr3	50251833	50251833	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccaccctgacctgtgcctacAggtcgaggaccctgcacgga	11	16	0	1	rs397812056|rs5848902|rs201228948		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:50251833A>G	ENST00000420502.1	+	0	255									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		CTGTGCCTACAGGTCGAGGAC	0.607																																					.		Atlas-SNP	.											.	SLC38A3	22	.	0			c.102-1A>G						.						23	27	26					3																	50251833		2041	4186	6227			10991	exon3			GCCTACAGGTCGA	U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"Solute carriers"	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		chr3.hg19:g.50251833A>G		68.0	0.0		61.0	5.0	NM_006841		Splice_Site	SNP	ENST00000420502.1	hg19																																																																																				.	.		0.607	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841		G	50251833	A	G	50251833	1	3	91	0	1	0	0	0	0	0	0	0	14620	202	7	2		2	SLC38A3	3	50251833	RNA	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	20265	50251833	147770597	135	12209										
ZMYND10	51364	hgsc.bcm.edu	37	chr3	50380447	50380447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggctcaaggtgctgagagagAggctaggggcagggacgttg	20	6	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:50380447A>G	ENST00000231749.3	-	7	1874	c.602T>C	c.(601-603)cTc>cCc	p.L201P	ZMYND10_ENST00000360165.3_Intron|RASSF1_ENST00000488024.1_5'Flank|ZMYND10-AS1_ENST00000440013.1_RNA|RASSF1_ENST00000357043.2_5'Flank|ZMYND10_ENST00000490675.1_5'Flank|RASSF1_ENST00000359365.4_5'Flank	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	201					inner dynein arm assembly (GO:0036159)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)	centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|urinary_tract(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCTGAGAGAGAGGCTAGGGGC	0.627										TSP Lung(30;0.18)																											p.L201P		Atlas-SNP	.											.	ZMYND10	37	.	0			c.T602C						.						144	131	135					3																	50380447		2203	4300	6503	SO:0001583	missense	51364	exon7			AGAGAGAGGCTAG	U70824	CCDS2825.1	3p21.3	2014-02-03			ENSG00000004838	ENSG00000004838		"Zinc fingers, MYND-type"	19412	protein-coding gene	gene with protein product		607070				12629521, 23891469	Standard	NM_015896		Approved	BLU, CILD22	uc003dag.1	O75800	OTTHUMG00000156874	ENST00000231749.3:c.602T>C	chr3.hg19:g.50380447A>G	ENSP00000231749:p.Leu201Pro	172.0	0.0		143.0	6.0	NM_015896	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Missense_Mutation	SNP	ENST00000231749.3	hg19	CCDS2825.1	.	.	.	.	.	.	.	.	.	.	A	18.39	3.612870	0.66672	.	.	ENSG00000004838	ENST00000231749;ENST00000442887	T;T	0.30448	1.53;1.53	5.55	5.55	0.83447	.	0.218577	0.38217	N	0.001775	T	0.54727	0.1876	M	0.88241	2.94	0.80722	D	1	P	0.49862	0.929	P	0.53102	0.718	T	0.64931	-0.6291	10	0.87932	D	0	-11.4017	14.8803	0.70528	1.0:0.0:0.0:0.0	.	201	O75800	ZMY10_HUMAN	P	201;158	ENSP00000231749:L201P;ENSP00000393687:L158P	ENSP00000231749:L201P	L	-	2	0	ZMYND10	50355451	1.000000	0.71417	1.000000	0.80357	0.540000	0.34992	6.998000	0.76277	2.122000	0.65172	0.459000	0.35465	CTC	.	.		0.627	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896		G	50380447	A	G	50380447	3	3	91	1	0	0	0	0	1	0	0	0	17720	304	11	2	744	2	ZMYND10	3	50380447	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	128614	50380447	147641983	136	12210										
TLR9	54106	hgsc.bcm.edu	37	chr3	52257674	52257674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagcagatactccaggctggAaggcaggttgcggggcacca	15	11	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:52257674A>G	ENST00000360658.2	-	2	1291	c.658T>C	c.(658-660)Tcc>Ccc	p.S220P	TLR9_ENST00000494383.1_Missense_Mutation_p.F373S|TLR9_ENST00000597542.1_Missense_Mutation_p.S244P	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	220					defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	TCCAGGCTGGAAGGCAGGTTG	0.632																																					p.S220P		Atlas-SNP	.											.	TLR9	72	.	0			c.T658C						.						39	32	34					3																	52257674		2203	4300	6503	SO:0001583	missense	54106	exon2			GGCTGGAAGGCAG	AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"CD molecules"	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.658T>C	chr3.hg19:g.52257674A>G	ENSP00000353874:p.Ser220Pro	113.0	0.0		87.0	4.0	NM_017442	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	hg19	CCDS2848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.388|3.388	-0.124873|-0.124873	0.06795|0.06795	.|.	.|.	ENSG00000173366|ENSG00000239732	ENST00000494383|ENST00000360658	.|T	.|0.57436	.|0.4	5.57|5.57	3.64|3.64	0.41730|0.41730	.|.	.|0.468826	.|0.15943	.|N	.|0.237118	T|T	0.32793|0.32793	0.0841|0.0841	N|N	0.21545|0.21545	0.675|0.675	0.26498|0.26498	N|N	0.974812|0.974812	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.15263|0.15263	-1.0443|-1.0443	5|10	.|0.16896	.|T	.|0.51	.|.	6.5276|6.5276	0.22309|0.22309	0.1879:0.1646:0.6475:0.0|0.1879:0.1646:0.6475:0.0	.|.	.|317;220	.|B4E0A1;Q9NR96	.|.;TLR9_HUMAN	S|P	373|220	.|ENSP00000353874:S220P	.|ENSP00000353874:S220P	F|S	-|-	2|1	0|0	RP11-330H6.5|TLR9	52232714|52232714	0.000000|0.000000	0.05858|0.05858	1.000000|1.000000	0.80357|0.80357	0.547000|0.547000	0.35210|0.35210	-0.426000|-0.426000	0.07008|0.07008	1.329000|1.329000	0.45376|0.45376	-0.242000|-0.242000	0.12053|0.12053	TTC|TCC	.	.		0.632	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1			G	52257674	A	G	52257674	3	3	91	1	0	0	0	0	1	0	0	0	15973	246	9	2	2444	2	TLR9	3	52257674	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1877227	52257674	145764756	137	12211										
RFT1	91869	hgsc.bcm.edu	37	chr3	53126534	53126534	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatccgaatgcccatgttaaAgcagttggccaagatgaagc	11	9	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:53126534A>G	ENST00000296292.3	-	12	1370	c.1309T>C	c.(1309-1311)Ttt>Ctt	p.F437L	RFT1_ENST00000394738.3_Missense_Mutation_p.F398L|RP11-894J14.5_ENST00000607203.1_Intron	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	437					carbohydrate transport (GO:0008643)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		CCCATGTTAAAGCAGTTGGCC	0.562																																					p.F437L		Atlas-SNP	.											.	RFT1	34	.	0			c.T1309C						.						83	71	75					3																	53126534		2203	4300	6503	SO:0001583	missense	91869	exon12			TGTTAAAGCAGTT	AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933			30220	protein-coding gene	gene with protein product	"congenital disorder of glycosylation 1N"	611908	"RFT1, requiring fifty three 1 homolog (S. cerevisiae)"			12477932	Standard	NM_052859		Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000296292.3:c.1309T>C	chr3.hg19:g.53126534A>G	ENSP00000296292:p.Phe437Leu	78.0	0.0		83.0	4.0	NM_052859	Q96J03	Missense_Mutation	SNP	ENST00000296292.3	hg19	CCDS2869.1	.	.	.	.	.	.	.	.	.	.	A	7.966	0.748034	0.15710	.	.	ENSG00000163933	ENST00000296292;ENST00000394738	D;D	0.82893	-1.66;-1.66	5.33	4.16	0.48862	.	0.320109	0.38381	N	0.001717	T	0.61527	0.2354	N	0.03930	-0.32	0.44061	D	0.996801	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.51896	-0.8647	10	0.15499	T	0.54	.	10.3826	0.44121	0.9203:0.0:0.0797:0.0	.	398;437	B5MDE0;Q96AA3	.;RFT1_HUMAN	L	437;398	ENSP00000296292:F437L;ENSP00000378223:F398L	ENSP00000296292:F437L	F	-	1	0	RFT1	53101574	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.064000	0.49986	0.851000	0.35264	0.379000	0.24179	TTT	.	.		0.562	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859		G	53126534	A	G	53126534	3	3	91	1	0	0	0	0	1	0	0	0	13272	72	3	2	324	2	RFT1	3	53126534	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	868860	53126534	144895896	138	12212										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64524966	64524966	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtccttgcaaactgtaagtcAgtggctgtggggtggagaag	16	6	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:64524966A>G	ENST00000498707.1	-	37	5868	c.5526T>C	c.(5524-5526)acT>acC	p.T1842T	ADAMTS9_ENST00000295903.4_Silent_p.T1814T	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1842	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		ACTGTAAGTCAGTGGCTGTGG	0.537																																					p.T1842T		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.T5526C						.						96	85	88					3																	64524966		2203	4300	6503	SO:0001819	synonymous_variant	56999	exon37			TAAGTCAGTGGCT	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.5526T>C	chr3.hg19:g.64524966A>G		105.0	0.0		88.0	5.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Silent	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	A	8.017	0.758879	0.15846	.	.	ENSG00000163638	ENST00000481060	.	.	.	5.62	-11.2	0.00127	.	.	.	.	.	T	0.35307	0.0927	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47799	-0.9089	4	.	.	.	.	4.6343	0.12516	0.2499:0.4312:0.2303:0.0886	.	.	.	.	P	898	.	.	L	-	2	0	ADAMTS9	64500006	0.052000	0.20516	0.896000	0.35187	0.734000	0.41952	-0.556000	0.05992	-1.368000	0.02149	-0.468000	0.05107	CTG	.	.		0.537	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			G	64524966	A	G	64524966	2	3	91	1	0	0	0	0	0	0	0	1	273	175	7	2		2	ADAMTS9	3	64524966	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	11398432	64524966	133497464	139	12213										
MAGI1	9223	hgsc.bcm.edu	37	chr3	65342529	65342529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcgctcggcctgcgcgtcccTccgtccctccggcgcccggt	13	21	0	0	rs544348166		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:65342529T>C	ENST00000402939.2	-	23	3912	c.3913A>G	c.(3913-3915)Agg>Ggg	p.R1305G	RP11-88H12.2_ENST00000602316.1_RNA|MAGI1_ENST00000330909.8_3'UTR	NM_001033057.1	NP_001028229.1	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	1334					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		TGCGCGTCCCTCCGTCCCTCC	0.682													T|||	1	0.000199681	0	0	5008	,	,		11789	0		0	False		,,,				2504	0.001				p.R1305G		Atlas-SNP	.											.	MAGI1	481	.	0			c.A3913G						.						55	56	56					3																	65342529		2203	4300	6503	SO:0001583	missense	9223	exon23			CGTCCCTCCGTCC	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000402939.2:c.3913A>G	chr3.hg19:g.65342529T>C	ENSP00000385450:p.Arg1305Gly	146.0	0.0		161.0	11.0	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000402939.2	hg19	CCDS33780.1	.	.	.	.	.	.	.	.	.	.	T	1.874	-0.459500	0.04508	.	.	ENSG00000151276	ENST00000402939	T	0.13089	2.62	5.04	5.04	0.67666	.	0.128295	0.50627	D	0.000102	T	0.10294	0.0252	L	0.32530	0.975	0.45284	D	0.998283	B	0.24721	0.11	B	0.19391	0.025	T	0.18085	-1.0348	10	0.20046	T	0.44	-15.7152	10.6071	0.45400	0.0:0.0:0.3038:0.6962	.	1305	Q96QZ7-2	.	G	1305	ENSP00000385450:R1305G	ENSP00000385450:R1305G	R	-	1	2	MAGI1	65317569	0.997000	0.39634	0.616000	0.29078	0.026000	0.11368	2.755000	0.47540	1.888000	0.54679	0.533000	0.62120	AGG	.	.		0.682	MAGI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349126.1	NM_004742		C	65342529	T	C	65342529	3	2	91	1	0	0	0	0	1	0	0	0	9199	1550	54	2	479	2	MAGI1	3	65342529	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	817563	65342529	132679901	140	12214										
IQCB1	9657	hgsc.bcm.edu	37	chr3	121527778	121527778	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttaccattctgaataagttCaacatggcctcccaaaagcc	5	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:121527778C>A	ENST00000310864.6	-	6	686	c.472G>T	c.(472-474)Gaa>Taa	p.E158*	IQCB1_ENST00000349820.6_Nonsense_Mutation_p.E158*	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	158					cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)			NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		TGAATAAGTTCAACATGGCCT	0.338																																					p.E158X		Atlas-SNP	.											.	IQCB1	50	.	0			c.G472T						.						58	65	62					3																	121527778		2203	4300	6503	SO:0001587	stop_gained	9657	exon6			TAAGTTCAACATG	D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"nephrocystin-5"	609237	"IQ calmodulin-binding motif containing 1"			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.472G>T	chr3.hg19:g.121527778C>A	ENSP00000311505:p.Glu158*	240.0	0.0		271.0	103.0	NM_001023570	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Nonsense_Mutation	SNP	ENST00000310864.6	hg19	CCDS33837.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.344418	0.82022	.	.	ENSG00000173226	ENST00000310864;ENST00000349820	.	.	.	5.54	4.67	0.58626	.	0.380726	0.32935	N	0.005467	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-6.5529	12.1582	0.54089	0.0:0.1807:0.8193:0.0	.	.	.	.	X	158	.	ENSP00000311505:E158X	E	-	1	0	IQCB1	123010468	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	3.495000	0.53280	1.579000	0.49836	-0.171000	0.13296	GAA	.	.		0.338	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642		A	121527778	C	A	121527778	4	1	91	1	0	0	0	0	0	1	0	0	7812	835	29	3	1364	3	IQCB1	3	121527778	Nonsense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	56185249	121527778	76494652	141	12215										
HEG1	57493	hgsc.bcm.edu	37	chr3	124724182	124724182	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttgtattaagaaaagttctcTttaatttaaactctgtcacg	5	6	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:124724182T>C	ENST00000311127.4	-	9	3291	c.3224A>G	c.(3223-3225)aAg>aGg	p.K1075R		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	1075					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						AAAAGTTCTCTTTAATTTAAA	0.348																																					p.K1075R		Atlas-SNP	.											.	HEG1	109	.	0			c.A3224G						.						67	66	66					3																	124724182		1829	4090	5919	SO:0001583	missense	57493	exon9			GTTCTCTTTAATT	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.3224A>G	chr3.hg19:g.124724182T>C	ENSP00000311502:p.Lys1075Arg	88.0	0.0		58.0	4.0	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	hg19	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.004702	0.35320	.	.	ENSG00000173706	ENST00000311127	D	0.88509	-2.39	5.08	3.92	0.45320	.	0.184817	0.25419	U	0.030811	T	0.77075	0.4077	N	0.17082	0.46	0.25578	N	0.986825	B	0.27882	0.192	B	0.24701	0.055	T	0.66396	-0.5934	10	0.45353	T	0.12	.	5.8174	0.18500	0.0:0.096:0.1719:0.7321	.	1075	Q9ULI3	HEG1_HUMAN	R	1075	ENSP00000311502:K1075R	ENSP00000311502:K1075R	K	-	2	0	HEG1	126206872	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	1.973000	0.40550	2.144000	0.66660	0.460000	0.39030	AAG	.	.		0.348	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		C	124724182	T	C	124724182	3	2	91	1	0	0	0	0	1	0	0	0	7053	1609	56	2	957	2	HEG1	3	124724182	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3196404	124724182	73298248	142	12216										
CCDC37	348807	hgsc.bcm.edu	37	chr3	126152005	126152005	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcagctgagctggagctcaaAgcccgagtcttccacttcgg	12	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:126152005A>G	ENST00000352312.1	+	14	1479	c.1380A>G	c.(1378-1380)aaA>aaG	p.K460K	CCDC37_ENST00000393425.1_Silent_p.K461K|CCDC37_ENST00000505024.1_Silent_p.K461K	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	460										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		TGGAGCTCAAAGCCCGAGTCT	0.602																																					p.K460K		Atlas-SNP	.											.	CCDC37	69	.	0			c.A1380G						.						135	122	126					3																	126152005		2203	4300	6503	SO:0001819	synonymous_variant	348807	exon14			GCTCAAAGCCCGA	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1380A>G	chr3.hg19:g.126152005A>G		113.0	0.0		100.0	4.0	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	hg19	CCDS3037.1																																																																																			.	.		0.602	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		G	126152005	A	G	126152005	2	3	91	1	0	0	0	0	0	0	0	1	2811	69	3	2		2	CCDC37	3	126152005	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1427823	126152005	71870425	143	12217										
COPG	22820	hgsc.bcm.edu	37	chr3	128984637	128984637	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catgaggaggtccgggcaggTaggtctgagccagggctgaa	18	8	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:128984637T>C	ENST00000314797.6	+	14	1572		c.e14+2			NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1						COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										TCCGGGCAGGTAGGTCTGAGC	0.542																																					.		Atlas-SNP	.											.	.	.	.	0			c.1468+2T>C						.						44	37	40					3																	128984637		2203	4300	6503	SO:0001630	splice_region_variant	22820	exon14			GGCAGGTAGGTCT	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"coat protein gamma-cop"	615525	"coatomer protein complex, subunit gamma"	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.1468+2T>C	chr3.hg19:g.128984637T>C		123.0	0.0		96.0	4.0	NM_016128	A8K6M8|B3KMF6|Q54AC4	Splice_Site	SNP	ENST00000314797.6	hg19	CCDS33851.1	.	.	.	.	.	.	.	.	.	.	T	12.91	2.079215	0.36662	.	.	ENSG00000181789	ENST00000314797	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4129	0.67128	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	COPG	130467327	1.000000	0.71417	0.933000	0.37362	0.172000	0.22775	7.827000	0.86722	2.288000	0.76882	0.533000	0.62120	.	.	.		0.542	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128	Intron	C	128984637	T	C	128984637	5	2	91	1	0	0	0	0	0	0	1	0	3733	1652	57	2	1524	2	COPG	3	128984637	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2832632	128984637	69037793	144	12218										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130174346	130174346	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttgggaggtaatggcttcaTtggccaagaattaaattctg	11	5	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:130174346T>C	ENST00000432398.2	+	37	7120	c.6626T>C	c.(6625-6627)aTt>aCt	p.I2209T	COL6A5_ENST00000265379.6_Missense_Mutation_p.I2209T	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2209	Nonhelical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						AATGGCTTCATTGGCCAAGAA	0.378																																					p.I2209T		Atlas-SNP	.											.	COL6A5	205	.	0			c.T6626C						.						43	43	43					3																	130174346		1807	4068	5875	SO:0001583	missense	256076	exon37			GCTTCATTGGCCA	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.6626T>C	chr3.hg19:g.130174346T>C	ENSP00000390895:p.Ile2209Thr	301.0	0.0		277.0	38.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.	.	.	.	.	.	.	.	.	.	T	3.259	-0.151527	0.06585	.	.	ENSG00000172752	ENST00000432398;ENST00000265379;ENST00000373157;ENST00000512482	D;D;T;T	0.90324	-2.56;-2.65;-1.06;-0.91	4.38	0.641	0.17759	.	1.544370	0.04444	N	0.371447	D	0.84000	0.5376	L	0.44542	1.39	0.09310	N	1	B;B	0.15473	0.008;0.013	B;B	0.19391	0.011;0.025	T	0.64968	-0.6282	10	0.07482	T	0.82	.	3.6008	0.08024	0.0:0.2095:0.1963:0.5943	.	2209;2209	A8TX70;A8TX70-2	CO6A5_HUMAN;.	T	2209;2209;152;44	ENSP00000390895:I2209T;ENSP00000265379:I2209T;ENSP00000362250:I152T;ENSP00000424968:I44T	ENSP00000265379:I2209T	I	+	2	0	COL6A5	131657036	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.018000	0.12568	0.022000	0.15160	-0.299000	0.09455	ATT	.	.		0.378	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		C	130174346	T	C	130174346	3	2	91	1	0	0	0	0	1	0	0	0	3704	1493	52	2	6768	2	COL6A5	3	130174346	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1189709	130174346	67848084	145	12219										
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132172158	132172158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcagcatttatttgcgtcagAgcaaagagaagagattatta	10	5	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:132172158A>G	ENST00000260818.6	+	7	802	c.554A>G	c.(553-555)gAg>gGg	p.E185G	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	185					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TTTGCGTCAGAGCAAAGAGAA	0.343																																					p.E185G		Atlas-SNP	.											.	DNAJC13	253	.	0			c.A554G						.						39	40	40					3																	132172158		2201	4300	6501	SO:0001583	missense	23317	exon7			CGTCAGAGCAAAG	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.554A>G	chr3.hg19:g.132172158A>G	ENSP00000260818:p.Glu185Gly	119.0	0.0		118.0	5.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	hg19	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.044640	0.55110	.	.	ENSG00000138246	ENST00000260818	T	0.42513	0.97	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.59865	0.2225	L	0.58810	1.83	0.80722	D	1	P;D	0.57899	0.67;0.981	B;D	0.67900	0.328;0.954	T	0.56565	-0.7958	10	0.35671	T	0.21	.	16.2214	0.82262	1.0:0.0:0.0:0.0	.	185;185	A7E2Y5;O75165	.;DJC13_HUMAN	G	185	ENSP00000260818:E185G	ENSP00000260818:E185G	E	+	2	0	DNAJC13	133654848	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.730000	0.91510	2.219000	0.72066	0.528000	0.53228	GAG	.	.		0.343	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		G	132172158	A	G	132172158	3	3	91	1	0	0	0	0	1	0	0	0	4634	304	11	2	576	2	DNAJC13	3	132172158	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1997812	132172158	65850272	146	12220										
CEP63	80254	hgsc.bcm.edu	37	chr3	134270790	134270790	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gattttggatcagctggagtCactcaaattagaaaatcgtc	9	7	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:134270790C>T	ENST00000337090.3	+	12	1576	c.1403C>T	c.(1402-1404)tCa>tTa	p.S468L	CEP63_ENST00000354446.3_Missense_Mutation_p.S422L|CEP63_ENST00000332047.5_Missense_Mutation_p.S422L|CEP63_ENST00000513612.2_Missense_Mutation_p.S468L|CEP63_ENST00000606977.1_Missense_Mutation_p.S468L|CEP63_ENST00000383229.3_Missense_Mutation_p.S468L			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	468					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CAGCTGGAGTCACTCAAATTA	0.308																																					p.S468L		Atlas-SNP	.											.	CEP63	56	.	0			c.C1403T						.						82	93	89					3																	134270790		2203	4296	6499	SO:0001583	missense	80254	exon13			TGGAGTCACTCAA	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1403C>T	chr3.hg19:g.134270790C>T	ENSP00000336524:p.Ser468Leu	83.0	0.0		93.0	4.0	NM_025180	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	hg19	CCDS3086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.77|15.77	2.932417|2.932417	0.52866|0.52866	.|.	.|.	ENSG00000182923|ENSG00000182923	ENST00000504929|ENST00000332047;ENST00000354446;ENST00000337090;ENST00000383229;ENST00000513612;ENST00000514678	.|T;T;T;T;T;T	.|0.32515	.|1.52;1.91;2.27;1.54;2.27;1.45	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	.|0.148621	.|0.42821	.|D	.|0.000660	T|T	0.43523|0.43523	0.1251|0.1251	L|L	0.54323|0.54323	1.7|1.7	0.34030|0.34030	D|D	0.653712|0.653712	.|D;B;P;B	.|0.57899	.|0.981;0.034;0.825;0.16	.|P;B;B;B	.|0.54026	.|0.74;0.023;0.175;0.088	T|T	0.53436|0.53436	-0.8439|-0.8439	5|10	.|0.41790	.|T	.|0.15	-3.0335|-3.0335	16.877|16.877	0.86054|0.86054	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|468;468;422;422	.|Q96MT8;Q96MT8-2;Q96MT8-4;Q96MT8-3	.|CEP63_HUMAN;.;.;.	Y|L	157|422;422;468;468;468;141	.|ENSP00000328382:S422L;ENSP00000346432:S422L;ENSP00000336524:S468L;ENSP00000372716:S468L;ENSP00000426129:S468L;ENSP00000427526:S141L	.|ENSP00000328382:S422L	H|S	+|+	1|2	0|0	CEP63|CEP63	135753480|135753480	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.459000|0.459000	0.32528|0.32528	5.075000|5.075000	0.64407|0.64407	2.724000|2.724000	0.93272|0.93272	0.585000|0.585000	0.79938|0.79938	CAC|TCA	.	.		0.308	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180		T	134270790	C	T	134270790	3	4	91	1	0	0	0	0	1	0	0	0	3259	838	29	3	1445	3	CEP63	3	134270790	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2098632	134270790	63751640	147	12221										
ATR	545	hgsc.bcm.edu	37	chr3	142226796	142226796	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taaaaatccaagatgttcctGaatattttgcttcttttctg	5	7	2	2	rs139135398		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:142226796G>T	ENST00000350721.4	-	28	5129	c.5008C>A	c.(5008-5010)Cag>Aag	p.Q1670K	ATR_ENST00000383101.3_Missense_Mutation_p.Q1606K	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1670	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						AGATGTTCCTGAATATTTTGC	0.333								Other conserved DNA damage response genes																													p.Q1670K		Atlas-SNP	.											.	ATR	285	.	0			c.C5008A						.						58	59	59					3																	142226796		2203	4300	6503	SO:0001583	missense	545	exon28			GTTCCTGAATATT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5008C>A	chr3.hg19:g.142226796G>T	ENSP00000343741:p.Gln1670Lys	111.0	0.0		92.0	4.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916713	0.92249	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.20881	2.04;2.04	5.42	5.42	0.78866	PIK-related kinase (1);Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	M	0.72894	2.215	0.80722	D	1	D	0.59357	0.985	P	0.57960	0.83	T	0.15150	-1.0447	10	0.12103	T	0.63	-7.2528	19.2145	0.93770	0.0:0.0:1.0:0.0	.	1670	Q13535	ATR_HUMAN	K	1670;1606	ENSP00000343741:Q1670K;ENSP00000372581:Q1606K	ENSP00000343741:Q1670K	Q	-	1	0	ATR	143709486	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.605000	0.98321	2.536000	0.85505	0.591000	0.81541	CAG	.	G|1.000;C|0.000		0.333	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142226796	G	T	142226796	3	4	91	1	0	0	0	0	1	0	0	0	1204	1299	45	3	3006	3	ATR	3	142226796	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	7956006	142226796	55795634	148	12222										
ATR	545	hgsc.bcm.edu	37	chr3	142226823	142226823	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttgcttcttttctgtaataaAtgattcaaagtgcattacag	6	6	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:142226823A>G	ENST00000350721.4	-	28	5102	c.4981T>C	c.(4981-4983)Ttt>Ctt	p.F1661L	ATR_ENST00000383101.3_Missense_Mutation_p.F1597L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1661	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TCTGTAATAAATGATTCAAAG	0.373								Other conserved DNA damage response genes																													p.F1661L		Atlas-SNP	.											.	ATR	285	.	0			c.T4981C						.						70	71	70					3																	142226823		2203	4300	6503	SO:0001583	missense	545	exon28			TAATAAATGATTC	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.4981T>C	chr3.hg19:g.142226823A>G	ENSP00000343741:p.Phe1661Leu	139.0	0.0		114.0	5.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	A	18.47	3.630358	0.67015	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.22539	1.95;1.95	5.42	5.42	0.78866	PIK-related kinase (1);Tetratricopeptide-like helical (1);	0.117930	0.64402	D	0.000013	T	0.19765	0.0475	L	0.56769	1.78	0.58432	D	0.999999	P	0.46064	0.872	B	0.35114	0.196	T	0.06679	-1.0813	10	0.20046	T	0.44	-21.118	15.4559	0.75314	1.0:0.0:0.0:0.0	.	1661	Q13535	ATR_HUMAN	L	1661;1597	ENSP00000343741:F1661L;ENSP00000372581:F1597L	ENSP00000343741:F1661L	F	-	1	0	ATR	143709513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.140000	0.71738	2.051000	0.60960	0.482000	0.46254	TTT	.	.		0.373	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		G	142226823	A	G	142226823	3	3	91	1	0	0	0	0	1	0	0	0	1204	101	4	2	3033	2	ATR	3	142226823	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	27	142226823	55795607	149	12223										
ATR	545	hgsc.bcm.edu	37	chr3	142272231	142272231	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcaaatggtaccaaatctccTtttgcggccctaaaattaaa	6	10	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:142272231T>C	ENST00000350721.4	-	13	2764	c.2643A>G	c.(2641-2643)aaA>aaG	p.K881K	ATR_ENST00000383101.3_Silent_p.K817K	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	881					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CCAAATCTCCTTTTGCGGCCC	0.393								Other conserved DNA damage response genes																													p.K881K		Atlas-SNP	.											.	ATR	285	.	0			c.A2643G						.						52	51	51					3																	142272231		2203	4300	6503	SO:0001819	synonymous_variant	545	exon13			ATCTCCTTTTGCG	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.2643A>G	chr3.hg19:g.142272231T>C		112.0	0.0		97.0	4.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.393	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		C	142272231	T	C	142272231	2	2	91	1	0	0	0	0	0	0	0	1	1204	1606	56	2		2	ATR	3	142272231	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	45408	142272231	55750199	150	12224										
AADAC	13	hgsc.bcm.edu	37	chr3	151545789	151545789	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtcatcacctgtcaatatgaTctcttaagagatgatggact	8	8	4	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:151545789T>C	ENST00000232892.7	+	5	1155	c.1029T>C	c.(1027-1029)gaT>gaC	p.D343D	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	343					positive regulation of triglyceride catabolic process (GO:0010898)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|deacetylase activity (GO:0019213)|lipase activity (GO:0016298)|serine hydrolase activity (GO:0017171)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(5)|skin(2)	19		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			GTCAATATGATCTCTTAAGAG	0.463																																					p.D343D	Ovarian(30;839 841 2699 32801 46334)	Atlas-SNP	.											.	AADAC	49	.	0			c.T1029C						.						97	88	91					3																	151545789		2203	4300	6503	SO:0001819	synonymous_variant	13	exon5			ATATGATCTCTTA	L32179	CCDS33877.1	3q25.1	2014-03-18	2012-07-13		ENSG00000114771	ENSG00000114771	3.1.1.3		17	protein-coding gene	gene with protein product		600338	"arylacetamide deacetylase (esterase)"			8063807	Standard	XM_005247103		Approved	DAC, CES5A1	uc003eze.3	P22760	OTTHUMG00000159876	ENST00000232892.7:c.1029T>C	chr3.hg19:g.151545789T>C		164.0	0.0		98.0	4.0	NM_001086	A8K3L3|D3DNJ6|Q8N1A9	Silent	SNP	ENST00000232892.7	hg19	CCDS33877.1																																																																																			.	.		0.463	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086		C	151545789	T	C	151545789	2	2	91	1	0	0	0	0	0	0	0	1	10	1432	50	2		2	AADAC	3	151545789	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9273558	151545789	46476641	151	12225										
DHX36	170506	hgsc.bcm.edu	37	chr3	153998561	153998561	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcctgctgtacctgaatttaTattagattctggatctttag	7	7	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:153998561T>C	ENST00000496811.1	-	21	2547	c.2467A>G	c.(2467-2469)Ata>Gta	p.I823V	DHX36_ENST00000308361.6_Missense_Mutation_p.I794V|DHX36_ENST00000329463.5_Missense_Mutation_p.I809V|DHX36_ENST00000544526.1_Missense_Mutation_p.I809V	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	823					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CCTGAATTTATATTAGATTCT	0.383																																					p.I823V		Atlas-SNP	.											.	DHX36	98	.	0			c.A2467G						.						100	106	104					3																	153998561		2203	4300	6503	SO:0001583	missense	170506	exon21			AATTTATATTAGA	AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.2467A>G	chr3.hg19:g.153998561T>C	ENSP00000417078:p.Ile823Val	109.0	0.0		88.0	4.0	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Missense_Mutation	SNP	ENST00000496811.1	hg19	CCDS3171.1	.	.	.	.	.	.	.	.	.	.	T	7.755	0.704075	0.15172	.	.	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	T;T;T;T;T	0.03152	4.2;4.11;4.03;4.03;4.19	5.65	4.49	0.54785	Domain of unknown function DUF1605 (1);	0.175651	0.64402	N	0.000011	T	0.02494	0.0076	N	0.11756	0.17	0.38706	D	0.953092	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.50600	-0.8809	10	0.16420	T	0.52	.	11.5378	0.50648	0.0:0.0699:0.0:0.9301	.	809;794;823	Q9H2U1-2;Q9H2U1-3;Q9H2U1	.;.;DHX36_HUMAN	V	823;794;809;809;737	ENSP00000417078:I823V;ENSP00000309296:I794V;ENSP00000444247:I809V;ENSP00000330113:I809V;ENSP00000419862:I737V	ENSP00000309296:I794V	I	-	1	0	DHX36	155481255	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	2.773000	0.47686	0.974000	0.38366	0.528000	0.53228	ATA	.	.		0.383	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		C	153998561	T	C	153998561	3	2	91	1	0	0	0	0	1	0	0	0	4511	1406	49	2	579	2	DHX36	3	153998561	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2452772	153998561	44023869	152	12226										
GMPS	8833	hgsc.bcm.edu	37	chr3	155629067	155629067	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aagcttggaattcaggtcaaAggtattgaagaacctcagaa	10	6	3	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:155629067A>G	ENST00000496455.2	+	7	1220	c.885A>G	c.(883-885)aaA>aaG	p.K295K	GMPS_ENST00000295920.7_Splice_Site_p.K196K	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase	295	GMPS ATP-PPase. {ECO:0000255|PROSITE- ProRule:PRU00886}.				glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|GMP synthase (glutamine-hydrolyzing) activity (GO:0003922)|GMP synthase activity (GO:0003921)|pyrophosphatase activity (GO:0016462)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamine(DB00130)	TTCAGGTCAAAGGTATTGAAG	0.358			T	MLL	AML																																p.K295K	Ovarian(153;896 1876 4149 15499 28134)	Atlas-SNP	.		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	.	GMPS	70	.	0			c.A885G						.						62	57	58					3																	155629067		1839	4096	5935	SO:0001630	splice_region_variant	8833	exon7			GGTCAAAGGTATT	U10860	CCDS46941.1	3q25.31	2013-06-18	2013-06-18		ENSG00000163655	ENSG00000163655	6.3.5.2		4378	protein-coding gene	gene with protein product	"GMP synthase"	600358	"guanine monphosphate synthetase"			8089153, 9195163	Standard	NM_003875		Approved		uc003faq.3	P49915	OTTHUMG00000158551	ENST00000496455.2:c.886+1A>G	chr3.hg19:g.155629067A>G		117.0	0.0		89.0	4.0	NM_003875	A8K639|B4DXV7|F8W720	Silent	SNP	ENST00000496455.2	hg19	CCDS46941.1																																																																																			.	.		0.358	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351260.2		Silent	G	155629067	A	G	155629067	5	3	91	1	0	0	0	0	0	0	1	0	6506	86	3	2	911	2	GMPS	3	155629067	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1630506	155629067	42393363	153	12227										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164906629	164906629	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aacaaagactgctgagaaaaAcagaaccagcaggctgagaa	10	8	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:164906629A>G	ENST00000475390.1	-	2	2433	c.1990T>C	c.(1990-1992)Ttt>Ctt	p.F664L	SLITRK3_ENST00000241274.3_Missense_Mutation_p.F664L			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	664					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						GCTGAGAAAAACAGAACCAGC	0.532										HNSCC(40;0.11)																											p.F664L		Atlas-SNP	.											.	SLITRK3	263	.	0			c.T1990C						.						47	48	47					3																	164906629		2203	4300	6503	SO:0001583	missense	22865	exon2			AGAAAAACAGAAC	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1990T>C	chr3.hg19:g.164906629A>G	ENSP00000420091:p.Phe664Leu	109.0	0.0		98.0	4.0	NM_014926	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	hg19	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.609455	0.46527	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.57436	0.4;0.4	4.85	4.85	0.62838	.	0.000000	0.35040	N	0.003490	T	0.45418	0.1341	L	0.55017	1.72	0.47994	D	0.999561	P	0.38827	0.649	B	0.33042	0.157	T	0.45745	-0.9240	10	0.33940	T	0.23	-15.6811	13.8456	0.63466	1.0:0.0:0.0:0.0	.	664	O94933	SLIK3_HUMAN	L	664	ENSP00000420091:F664L;ENSP00000241274:F664L	ENSP00000241274:F664L	F	-	1	0	SLITRK3	166389323	0.999000	0.42202	0.971000	0.41717	0.691000	0.40173	4.273000	0.58914	2.144000	0.66660	0.533000	0.62120	TTT	.	.		0.532	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		G	164906629	A	G	164906629	3	3	91	1	0	0	0	0	1	0	0	0	14759	43	2	2	947	2	SLITRK3	3	164906629	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	9277562	164906629	33115801	154	12228										
TBCCD1	55171	hgsc.bcm.edu	37	chr3	186272765	186272765	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cccccgccagagtgtctgagCtcttagccagtgtctgcttg	11	14	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:186272765C>T	ENST00000424280.1	-	5	1447	c.968G>A	c.(967-969)aGc>aAc	p.S323N	TBCCD1_ENST00000479590.1_5'Flank|TBCCD1_ENST00000338733.5_Missense_Mutation_p.S323N|TBCCD1_ENST00000446782.1_Missense_Mutation_p.S227N	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	323	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		AGTGTCTGAGCTCTTAGCCAG	0.468																																					p.S323N		Atlas-SNP	.											.	TBCCD1	42	.	0			c.G968A						.						121	110	113					3																	186272765		2203	4300	6503	SO:0001583	missense	55171	exon5			TCTGAGCTCTTAG	BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.968G>A	chr3.hg19:g.186272765C>T	ENSP00000411253:p.Ser323Asn	171.0	0.0		156.0	12.0	NM_001134415	B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	hg19	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.514052	0.64522	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000446782	D;D;D	0.84516	-1.84;-1.84;-1.86	5.88	5.88	0.94601	C-CAP/cofactor C-like domain (1);	0.146462	0.64402	D	0.000007	D	0.89343	0.6688	M	0.67953	2.075	0.39658	D	0.970572	D;P	0.53462	0.96;0.872	P;B	0.54706	0.759;0.342	D	0.88212	0.2891	10	0.35671	T	0.21	-15.5751	17.791	0.88552	0.0:1.0:0.0:0.0	.	227;323	G5E9J4;Q9NVR7	.;TBCC1_HUMAN	N	323;323;227	ENSP00000411253:S323N;ENSP00000341652:S323N;ENSP00000397091:S227N	ENSP00000341652:S323N	S	-	2	0	TBCCD1	187755459	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	4.737000	0.62066	2.805000	0.96524	0.552000	0.68991	AGC	.	.		0.468	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138		T	186272765	C	T	186272765	3	4	91	1	0	0	0	0	1	0	0	0	15647	797	28	3	717	3	TBCCD1	3	186272765	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	21366136	186272765	11749665	155	12229										
IL1RAP	3556	hgsc.bcm.edu	37	chr3	190366343	190366343	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaagagggctaagacggtgcTcacggtcattaaatggaaag	14	6	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:190366343T>C	ENST00000412504.2	+	11	1814	c.1562T>C	c.(1561-1563)cTc>cCc	p.L521P	IL1RAP_ENST00000447382.1_Missense_Mutation_p.L521P|IL1RAP_ENST00000072516.3_Missense_Mutation_p.L521P|IL1RAP_ENST00000439062.1_Missense_Mutation_p.L521P|IL1RAP_ENST00000317757.3_Intron|IL1RAP_ENST00000443369.2_Intron			Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein	521	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-2 biosynthetic process (GO:0042094)|protein complex assembly (GO:0006461)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		AAGACGGTGCTCACGGTCATT	0.498																																					p.L521P		Atlas-SNP	.											.	IL1RAP	96	.	0			c.T1562C						.						101	102	101					3																	190366343		2203	4300	6503	SO:0001583	missense	3556	exon11			CGGTGCTCACGGT	AB006537	CCDS3298.1, CCDS46982.1, CCDS54696.1	3q28	2013-01-11			ENSG00000196083	ENSG00000196083		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5995	protein-coding gene	gene with protein product		602626				9479509, 9065432	Standard	NM_002182		Approved	IL-1RAcP, IL1R3, C3orf13	uc003fsq.3	Q9NPH3	OTTHUMG00000156211	ENST00000412504.2:c.1562T>C	chr3.hg19:g.190366343T>C	ENSP00000412053:p.Leu521Pro	140.0	0.0		81.0	4.0	NM_001167929	B1NLD0|D3DNW0|O14915|Q86WJ7	Missense_Mutation	SNP	ENST00000412504.2	hg19	CCDS3298.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.369863	0.82573	.	.	ENSG00000196083	ENST00000072516;ENST00000412504;ENST00000439062;ENST00000447382	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	6.03	6.03	0.97812	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.433509	0.22103	N	0.064584	T	0.37679	0.1012	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.17258	-1.0375	10	0.62326	D	0.03	.	15.7535	0.78005	0.0:0.0:0.0:1.0	.	521	Q9NPH3	IL1AP_HUMAN	P	521	ENSP00000072516:L521P;ENSP00000412053:L521P;ENSP00000401132:L521P;ENSP00000390541:L521P	ENSP00000072516:L521P	L	+	2	0	IL1RAP	191849037	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.591000	0.82666	2.313000	0.78055	0.455000	0.32223	CTC	.	.		0.498	IL1RAP-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343497.1			C	190366343	T	C	190366343	3	2	91	1	0	0	0	0	1	0	0	0	7669	1551	54	2	1620	2	IL1RAP	3	190366343	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4093578	190366343	7656087	156	12230										
HTT	3064	hgsc.bcm.edu	37	chr4	3227454	3227454	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcgggagctggggagcatgaGctacaaactcggccaggtca	16	10	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:3227454G>T	ENST00000355072.5	+	57	7977	c.7832G>T	c.(7831-7833)aGc>aTc	p.S2611I		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2611					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GGGAGCATGAGCTACAAACTC	0.602																																					p.S2611I		Atlas-SNP	.											.	HTT	221	.	0			c.G7832T						.						28	32	31					4																	3227454		1997	4188	6185	SO:0001583	missense	3064	exon57			GCATGAGCTACAA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.7832G>T	chr4.hg19:g.3227454G>T	ENSP00000347184:p.Ser2611Ile	136.0	0.0		123.0	5.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.587627	0.46110	.	.	ENSG00000197386	ENST00000355072	T	0.05258	3.47	3.97	3.97	0.46021	.	0.254344	0.43260	D	0.000581	T	0.04998	0.0134	N	0.22421	0.69	0.27258	N	0.95869	P	0.39903	0.694	B	0.37943	0.261	T	0.34179	-0.9839	10	0.37606	T	0.19	.	11.3151	0.49388	0.0935:0.0:0.9065:0.0	.	2611	P42858	HD_HUMAN	I	2611	ENSP00000347184:S2611I	ENSP00000347184:S2611I	S	+	2	0	HTT	3197252	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	4.833000	0.62766	2.247000	0.74100	0.644000	0.83932	AGC	.	.		0.602	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3227454	G	T	3227454	3	4	91	1	0	0	0	0	1	0	0	0	7466	971	34	3	8058	3	HTT	4	3227454	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10		3227454	187926822	157	12231										
EVC2	132884	hgsc.bcm.edu	37	chr4	5624634	5624634	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtgctcctccatcaggctccTcttctggtgcaggtactggc	11	14	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:5624634T>C	ENST00000344408.5	-	14	2184	c.2131A>G	c.(2131-2133)Agg>Ggg	p.R711G	EVC2_ENST00000344938.1_Missense_Mutation_p.R711G|EVC2_ENST00000310917.2_Missense_Mutation_p.R631G	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	711					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						ATCAGGCTCCTCTTCTGGTGC	0.637																																					p.R711G		Atlas-SNP	.											.	EVC2	202	.	0			c.A2131G						.						63	62	62					4																	5624634		2203	4300	6503	SO:0001583	missense	132884	exon14			GGCTCCTCTTCTG	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2131A>G	chr4.hg19:g.5624634T>C	ENSP00000342144:p.Arg711Gly	160.0	0.0		135.0	7.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	T	6.206	0.406161	0.11754	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.75050	-0.9;-0.89;-0.9	5.12	-0.339	0.12647	.	1.004860	0.08010	N	0.990129	T	0.60945	0.2308	N	0.22421	0.69	0.25800	N	0.984521	B	0.10296	0.003	B	0.08055	0.003	T	0.44802	-0.9304	10	0.39692	T	0.17	-27.8752	11.5804	0.50887	0.0:0.0941:0.205:0.7009	.	711	Q86UK5	LBN_HUMAN	G	711;631;711	ENSP00000339954:R711G;ENSP00000311683:R631G;ENSP00000342144:R711G	ENSP00000311683:R631G	R	-	1	2	EVC2	5675535	0.315000	0.24571	0.556000	0.28293	0.001000	0.01503	0.085000	0.14912	-0.478000	0.06823	-0.648000	0.03929	AGG	.	.		0.637	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		C	5624634	T	C	5624634	3	2	91	1	0	0	0	0	1	0	0	0	5288	1550	54	2	1831	2	EVC2	4	5624634	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2397180	5624634	185529642	158	12232										
C1QTNF7	114905	hgsc.bcm.edu	37	chr4	15444246	15444246	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acaggaaaccatgatgtggcTtcggggtccacagtcatcta	11	10	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:15444246T>C	ENST00000444304.2	+	3	1019	c.693T>C	c.(691-693)gcT>gcC	p.A231A	C1QTNF7_ENST00000429690.1_Silent_p.A231A|C1QTNF7_ENST00000295297.4_Silent_p.A238A			Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7	231	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	16						ATGATGTGGCTTCGGGGTCCA	0.498																																					p.A238A		Atlas-SNP	.											.	C1QTNF7	36	.	0			c.T714C						.						88	91	90					4																	15444246		2203	4300	6503	SO:0001819	synonymous_variant	114905	exon3			TGTGGCTTCGGGG	AF329839	CCDS3414.1, CCDS47025.1	4p15.3	2008-08-29			ENSG00000163145	ENSG00000163145			14342	protein-coding gene	gene with protein product							Standard	NM_001135170		Approved	CTRP7	uc003gnp.3	Q9BXJ2	OTTHUMG00000097095	ENST00000444304.2:c.693T>C	chr4.hg19:g.15444246T>C		95.0	0.0		90.0	4.0	NM_001135170	B2RBT3|J3KPW3	Silent	SNP	ENST00000444304.2	hg19	CCDS3414.1																																																																																			.	.		0.498	C1QTNF7-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250891.2			C	15444246	T	C	15444246	2	2	91	1	0	0	0	0	0	0	0	1	1970	1596	56	2		2	C1QTNF7	4	15444246	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9819612	15444246	175710030	159	12233										
SEPSECS	51091	hgsc.bcm.edu	37	chr4	25156728	25156728	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctgctttcaggtctgtacgcAgctcgtcaccttccaaaaca	7	14	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:25156728A>G	ENST00000382103.2	-	5	665	c.593T>C	c.(592-594)cTg>cCg	p.L198P	SEPSECS_ENST00000302922.3_Missense_Mutation_p.L119P	NM_016955.3	NP_058651.3	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	198					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	pyridoxal phosphate binding (GO:0030170)|transferase activity, transferring selenium-containing groups (GO:0016785)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(2)|stomach(1)	8		Breast(46;0.173)				GTCTGTACGCAGCTCGTCACC	0.428																																					p.L198P		Atlas-SNP	.											.	SEPSECS	55	.	0			c.T593C						.						136	117	123					4																	25156728		2203	4300	6503	SO:0001583	missense	51091	exon5			GTACGCAGCTCGT	AJ238617	CCDS3432.1, CCDS3432.2	4p15.2	2008-10-27			ENSG00000109618	ENSG00000109618			30605	protein-coding gene	gene with protein product	"soluble liver antigen/liver pancreas antigen"	613009				16230358, 10931155, 17142313, 17194211	Standard	NM_016955		Approved	SLA/LP, SLA	uc003grg.3	Q9HD40	OTTHUMG00000128563	ENST00000382103.2:c.593T>C	chr4.hg19:g.25156728A>G	ENSP00000371535:p.Leu198Pro	109.0	0.0		101.0	11.0	NM_016955	A8K8W1|Q0D2P3|Q17RT1|Q9NXZ5|Q9UGM9|Q9Y353	Missense_Mutation	SNP	ENST00000382103.2	hg19	CCDS3432.2	.	.	.	.	.	.	.	.	.	.	A	22.8	4.333384	0.81801	.	.	ENSG00000109618	ENST00000302922;ENST00000382103	D;D	0.84370	-1.84;-1.84	5.37	5.37	0.77165	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.93387	0.7891	M	0.88842	2.985	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.94587	0.7784	10	0.87932	D	0	-5.2746	15.7032	0.77558	1.0:0.0:0.0:0.0	.	197;138;198	Q9HD40-3;A1A4F3;Q9HD40	.;.;SPCS_HUMAN	P	119;198	ENSP00000305956:L119P;ENSP00000371535:L198P	ENSP00000305956:L119P	L	-	2	0	SEPSECS	24765826	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	8.855000	0.92236	2.178000	0.69098	0.473000	0.43528	CTG	.	.		0.428	SEPSECS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250414.2	NM_016955		G	25156728	A	G	25156728	3	3	91	1	0	0	0	0	1	0	0	0	14073	188	7	2	940	2	SEPSECS	4	25156728	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	9712482	25156728	165997548	160	12234										
TBC1D19	55296	hgsc.bcm.edu	37	chr4	26755500	26755500	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctgatggaggtgacatcactGgctgcagctgaagtaaggat	14	7	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:26755500G>T	ENST00000264866.4	+	20	1772	c.1494G>T	c.(1492-1494)ctG>ctT	p.L498L	TBC1D19_ENST00000511789.1_Silent_p.L433L	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	498							Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				TGACATCACTGGCTGCAGCTG	0.483																																					p.L498L		Atlas-SNP	.											.	TBC1D19	53	.	0			c.G1494T						.						137	119	125					4																	26755500		2203	4300	6503	SO:0001819	synonymous_variant	55296	exon20			ATCACTGGCTGCA	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.1494G>T	chr4.hg19:g.26755500G>T		113.0	0.0		97.0	4.0	NM_018317	B9A6M0|Q9NUX1	Silent	SNP	ENST00000264866.4	hg19	CCDS3439.1																																																																																			.	.		0.483	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317		T	26755500	G	T	26755500	2	4	91	1	0	0	0	0	0	0	0	1	15622	1335	47	3		3	TBC1D19	4	26755500	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	1598772	26755500	164398776	161	12235										
UGDH	7358	hgsc.bcm.edu	37	chr4	39510222	39510222	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctacttctggcaaattcagAgcctcacagagataaaccaa	7	11	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:39510222A>G	ENST00000316423.6	-	7	1212	c.870T>C	c.(868-870)gcT>gcC	p.A290A	UGDH_ENST00000506179.1_Silent_p.A290A|UGDH_ENST00000507089.1_Silent_p.A193A|UGDH_ENST00000515398.1_5'Flank|UGDH_ENST00000501493.2_Silent_p.A223A	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	290					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)			breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						GCAAATTCAGAGCCTCACAGA	0.393																																					p.A290A		Atlas-SNP	.											.	UGDH	52	.	0			c.T870C						.						75	80	78					4																	39510222		2203	4300	6503	SO:0001819	synonymous_variant	7358	exon7			ATTCAGAGCCTCA	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"UDP-glucose dehydrogenase"			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.870T>C	chr4.hg19:g.39510222A>G		84.0	0.0		50.0	4.0	NM_003359	B3KUU2|B4DN25|O60589	Silent	SNP	ENST00000316423.6	hg19	CCDS3455.1																																																																																			.	.		0.393	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359		G	39510222	A	G	39510222	2	3	91	1	0	0	0	0	0	0	0	1	16955	291	11	2		2	UGDH	4	39510222	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	12754722	39510222	151644054	162	12236										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46067446	46067446	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgattaggagttgttatccaGtgagcatcagattttcttga	10	6	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:46067446G>A	ENST00000295452.4	-	4	644	c.477C>T	c.(475-477)caC>caT	p.H159H		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	159					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTGTTATCCAGTGAGCATCAG	0.353																																					p.H159H		Atlas-SNP	.											.	GABRG1	172	.	0			c.C477T						.						97	95	96					4																	46067446		2203	4300	6503	SO:0001819	synonymous_variant	2565	exon4			TATCCAGTGAGCA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.477C>T	chr4.hg19:g.46067446G>A		117.0	0.0		77.0	4.0	NM_173536	Q5H9T8	Silent	SNP	ENST00000295452.4	hg19	CCDS3470.1																																																																																			.	.		0.353	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		A	46067446	G	A	46067446	2	1	91	1	0	0	0	0	0	0	0	1	6179	1020	36	3		3	GABRG1	4	46067446	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	6557224	46067446	145086830	163	12237										
NPFFR2	10886	hgsc.bcm.edu	37	chr4	73013093	73013093	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcagaagatcattaagatgcTcctgattgtggccctgcttt	10	9	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:73013093T>C	ENST00000308744.6	+	4	1231	c.1133T>C	c.(1132-1134)cTc>cCc	p.L378P	NPFFR2_ENST00000344413.5_3'UTR|NPFFR2_ENST00000506359.1_3'UTR|NPFFR2_ENST00000358749.3_Missense_Mutation_p.L276P|NPFFR2_ENST00000395999.1_Missense_Mutation_p.L279P	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	378					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)	p.L378H(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			ATTAAGATGCTCCTGATTGTG	0.502																																					p.L378P		Atlas-SNP	.											NPFFR2,NS,carcinoma,0,1	NPFFR2	98	.	1	Substitution - Missense(1)	lung(1)	c.T1133C						.						89	85	86					4																	73013093		2203	4300	6503	SO:0001583	missense	10886	exon4			AGATGCTCCTGAT	AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"GPCR / Class A :  Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors"	4525	protein-coding gene	gene with protein product	"neuropeptide FF 2"	607449	"G protein-coupled receptor 74"	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.1133T>C	chr4.hg19:g.73013093T>C	ENSP00000307822:p.Leu378Pro	117.0	0.0		75.0	3.0	NM_004885	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	hg19	CCDS3551.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.873655	0.51695	.	.	ENSG00000056291	ENST00000308744;ENST00000395999;ENST00000358749	T;T;T	0.51574	0.7;0.7;0.7	5.82	5.82	0.92795	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000116	T	0.81819	0.4903	H	0.98951	4.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89340	0.3653	10	0.87932	D	0	.	15.8418	0.78852	0.0:0.0:0.0:1.0	.	279;378	Q9Y5X5-3;Q9Y5X5	.;NPFF2_HUMAN	P	378;279;276	ENSP00000307822:L378P;ENSP00000379321:L279P;ENSP00000351599:L276P	ENSP00000307822:L378P	L	+	2	0	NPFFR2	73231957	1.000000	0.71417	0.970000	0.41538	0.076000	0.17211	7.911000	0.87458	2.214000	0.71695	0.482000	0.46254	CTC	.	.		0.502	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		C	73013093	T	C	73013093	3	2	91	1	0	0	0	0	1	0	0	0	10587	1551	54	2	1153	2	NPFFR2	4	73013093	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	26945647	73013093	118141183	164	12238										
ALB	213	hgsc.bcm.edu	37	chr4	74274385	74274385	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggtgaaatggctgactgctgTgcaaaacaagaacctgagag	13	7	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:74274385T>C	ENST00000295897.4	+	4	434	c.345T>C	c.(343-345)tgT>tgC	p.C115C	ALB_ENST00000415165.2_Intron|ALB_ENST00000503124.1_Intron|ALB_ENST00000401494.3_Intron|ALB_ENST00000509063.1_Silent_p.C115C|ALB_ENST00000505649.1_3'UTR	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTGACTGCTGTGCAAAACAAG	0.438																																					p.C115C		Atlas-SNP	.											.	ALB	132	.	0			c.T345C						.						94	88	90					4																	74274385		2203	4300	6503	SO:0001819	synonymous_variant	213	exon4			CTGCTGTGCAAAA	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.345T>C	chr4.hg19:g.74274385T>C		212.0	0.0		118.0	5.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.438	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477		C	74274385	T	C	74274385	2	2	91	1	0	0	0	0	0	0	0	1	486	1702	59	2		2	ALB	4	74274385	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1261292	74274385	116879891	165	12239										
RASSF6	166824	hgsc.bcm.edu	37	chr4	74459214	74459214	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttcatactagtaaaagaagAgaatggcttctcatcttgta	7	7	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:74459214A>G	ENST00000342081.3	-	4	467	c.337T>C	c.(337-339)Tct>Cct	p.S113P	RASSF6_ENST00000307439.5_Missense_Mutation_p.S81P|RASSF6_ENST00000335049.5_Missense_Mutation_p.S69P|RASSF6_ENST00000395777.2_Missense_Mutation_p.S81P	NM_201431.2	NP_958834.1	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family member 6	113					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)					breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|pancreas(2)|skin(2)	17	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			GTAAAAGAAGAGAATGGCTTC	0.363																																					p.S113P		Atlas-SNP	.											.	RASSF6	68	.	0			c.T337C						.						116	117	117					4																	74459214		2203	4300	6503	SO:0001583	missense	166824	exon4			AAGAAGAGAATGG	AY217664	CCDS3558.1, CCDS3559.1, CCDS58904.1, CCDS58905.1	4q21.1	2008-02-22	2008-02-22		ENSG00000169435	ENSG00000169435			20796	protein-coding gene	gene with protein product		612620					Standard	NM_177532		Approved		uc003hhd.2	Q6ZTQ3	OTTHUMG00000130007	ENST00000342081.3:c.337T>C	chr4.hg19:g.74459214A>G	ENSP00000340578:p.Ser113Pro	191.0	0.0		149.0	6.0	NM_201431	Q68DT2|Q6PDA6|Q86WG9|Q86WH0	Missense_Mutation	SNP	ENST00000342081.3	hg19	CCDS3558.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.707539	0.00712	.	.	ENSG00000169435	ENST00000307439;ENST00000342081;ENST00000395777;ENST00000335049	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	5.42	1.28	0.21552	.	0.468479	0.26217	N	0.025656	T	0.09158	0.0226	N	0.00879	-1.12	0.35790	D	0.822346	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.0;0.001	T	0.33701	-0.9858	10	0.06365	T	0.9	-0.3215	8.4588	0.32915	0.3129:0.0:0.6871:0.0	.	69;81;113	Q6ZTQ3-3;Q6ZTQ3-4;Q6ZTQ3	.;.;RASF6_HUMAN	P	81;113;81;69	ENSP00000303877:S81P;ENSP00000340578:S113P;ENSP00000379123:S81P;ENSP00000335582:S69P	ENSP00000303877:S81P	S	-	1	0	RASSF6	74678078	1.000000	0.71417	0.985000	0.45067	0.095000	0.18619	1.046000	0.30354	0.176000	0.19873	-0.407000	0.06327	TCT	.	.		0.363	RASSF6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252279.1	NM_177532		G	74459214	A	G	74459214	3	3	91	1	0	0	0	0	1	0	0	0	13105	304	11	2	804	2	RASSF6	4	74459214	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	184829	74459214	116695062	166	12240										
C4orf22	255119	hgsc.bcm.edu	37	chr4	81283933	81283933	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaccctggcccgccagttggTggagctaggctaccgaggga	15	12	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:81283933T>C	ENST00000358105.3	+	2	186	c.137T>C	c.(136-138)gTg>gCg	p.V46A	C4orf22_ENST00000508675.1_Missense_Mutation_p.V46A|C4orf22_ENST00000512931.1_3'UTR	NM_152770.2	NP_689983.2	Q6V702	CD022_HUMAN	chromosome 4 open reading frame 22	46										NS(1)|large_intestine(3)|lung(5)|prostate(1)|skin(5)	15						CGCCAGTTGGTGGAGCTAGGC	0.448																																					p.V46A		Atlas-SNP	.											.	C4orf22	35	.	0			c.T137C						.						115	125	122					4																	81283933		2203	4300	6503	SO:0001583	missense	255119	exon2			AGTTGGTGGAGCT	BC034296	CCDS3587.1, CCDS56336.1	4q21.21	2008-02-05			ENSG00000197826	ENSG00000197826			28554	protein-coding gene	gene with protein product						12477932	Standard	NM_152770		Approved		uc010ijp.3	Q6V702	OTTHUMG00000130289	ENST00000358105.3:c.137T>C	chr4.hg19:g.81283933T>C	ENSP00000350818:p.Val46Ala	116.0	0.0		86.0	4.0	NM_152770	E7EQ13|Q6ZQY4|Q8N4G9	Missense_Mutation	SNP	ENST00000358105.3	hg19	CCDS3587.1	.	.	.	.	.	.	.	.	.	.	T	18.36	3.606437	0.66445	.	.	ENSG00000197826	ENST00000358105;ENST00000508675	T;T	0.34275	1.37;1.37	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000020	T	0.62816	0.2459	M	0.84683	2.71	0.44862	D	0.997874	D;P	0.89917	1.0;0.845	D;P	0.79784	0.993;0.646	T	0.65681	-0.6109	10	0.38643	T	0.18	.	14.3501	0.66694	0.0:0.0:0.0:1.0	.	46;46	E7EQ13;Q6V702	.;CD022_HUMAN	A	46	ENSP00000350818:V46A;ENSP00000425786:V46A	ENSP00000350818:V46A	V	+	2	0	C4orf22	81502957	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.413000	0.66399	2.091000	0.63221	0.477000	0.44152	GTG	.	.		0.448	C4orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252629.2	NM_152770		C	81283933	T	C	81283933	3	2	91	1	0	0	0	0	1	0	0	0	2257	1696	59	2	143	2	C4orf22	4	81283933	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	6824719	81283933	109870343	167	12241										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85731416	85731416	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctttccatagcaacgagcaAggatgtaatgtacacaaatc	7	9	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:85731416A>G	ENST00000295888.4	-	14	2376	c.1969T>C	c.(1969-1971)Ttg>Ctg	p.L657L	WDFY3_ENST00000322366.6_Silent_p.L657L|WDFY3-AS1_ENST00000510449.1_RNA	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	657					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GCAACGAGCAAGGATGTAATG	0.443																																					p.L657L		Atlas-SNP	.											.	WDFY3	314	.	0			c.T1969C						.						68	63	65					4																	85731416		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon14			CGAGCAAGGATGT	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.1969T>C	chr4.hg19:g.85731416A>G		87.0	0.0		47.0	4.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.		0.443	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		G	85731416	A	G	85731416	2	3	91	1	0	0	0	0	0	0	0	1	17285	69	3	2		2	WDFY3	4	85731416	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4447483	85731416	105422860	168	12242										
MEPE	56955	hgsc.bcm.edu	37	chr4	88766433	88766433	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgctatcagcaaactacatgAccaagaagaatatggcgcag	9	9	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:88766433A>G	ENST00000424957.3	+	4	486	c.413A>G	c.(412-414)gAc>gGc	p.D138G	MEPE_ENST00000497649.2_Missense_Mutation_p.D114G|MEPE_ENST00000540395.1_Missense_Mutation_p.D25G|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000560249.1_Missense_Mutation_p.D25G|MEPE_ENST00000361056.3_Missense_Mutation_p.D138G|MEPE_ENST00000395102.4_Missense_Mutation_p.D169G	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	138					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		AAACTACATGACCAAGAAGAA	0.418																																					p.D138G		Atlas-SNP	.											.	MEPE	86	.	0			c.A413G						.						70	68	69					4																	88766433		2203	4300	6503	SO:0001583	missense	56955	exon4			TACATGACCAAGA	AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.413A>G	chr4.hg19:g.88766433A>G	ENSP00000416984:p.Asp138Gly	182.0	0.0		86.0	4.0	NM_020203	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	hg19	CCDS3625.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.021259	0.35701	.	.	ENSG00000152595	ENST00000535138;ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.57436	4.32;0.42;0.4;0.46;4.32	4.84	-2.83	0.05769	.	0.620480	0.15238	N	0.273009	T	0.40272	0.1110	M	0.62088	1.915	0.09310	N	0.999994	P	0.34800	0.469	B	0.34590	0.186	T	0.26258	-1.0108	10	0.39692	T	0.17	-3.4702	3.3001	0.06980	0.4063:0.0:0.1726:0.4211	.	138	Q9NQ76	MEPE_HUMAN	G	138;138;169;114;25;138	ENSP00000416984:D138G;ENSP00000378534:D169G;ENSP00000422747:D114G;ENSP00000443491:D25G;ENSP00000354341:D138G	ENSP00000354341:D138G	D	+	2	0	MEPE	88985457	0.499000	0.26083	0.044000	0.18714	0.107000	0.19398	0.257000	0.18369	-0.628000	0.05582	0.533000	0.62120	GAC	.	.		0.418	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1			G	88766433	A	G	88766433	3	3	91	1	0	0	0	0	1	0	0	0	9487	275	10	2	423	2	MEPE	4	88766433	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3035017	88766433	102387843	169	12243										
CCDC109B	55013	hgsc.bcm.edu	37	chr4	110580168	110580168	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taatttttccttcttgtaggTtttgcgtgtgaagctgtgtg	11	5	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:110580168T>C	ENST00000394650.4	+	2	234	c.101T>C	c.(100-102)gTt>gCt	p.V34A	CCDC109B_ENST00000515114.1_3'UTR	NM_017918.4	NP_060388.2	Q9NWR8	MCUB_HUMAN	coiled-coil domain containing 109B	34					mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)	calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of membrane (GO:0031224)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium channel inhibitor activity (GO:0019855)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(1)	9				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)		TTCTTGTAGGTTTTGCGTGTG	0.318																																					p.V34A		Atlas-SNP	.											.	CCDC109B	47	.	0			c.T101C						.						214	178	189					4																	110580168		692	1591	2283	SO:0001630	splice_region_variant	55013	exon2			TGTAGGTTTTGCG	BC002633	CCDS3683.2	4q25	2011-05-24			ENSG00000005059	ENSG00000005059			26076	protein-coding gene	gene with protein product						12477932	Standard	NM_017918		Approved	FLJ20647	uc011cfs.2	Q9NWR8	OTTHUMG00000161103	ENST00000394650.4:c.100-1T>C	chr4.hg19:g.110580168T>C		182.0	0.0		103.0	6.0	NM_017918	A8K4Y3|Q6IAC1	Missense_Mutation	SNP	ENST00000394650.4	hg19	CCDS3683.2	.	.	.	.	.	.	.	.	.	.	T	9.020	0.984555	0.18889	.	.	ENSG00000005059	ENST00000394650;ENST00000452915	T;T	0.55052	0.54;0.54	4.86	3.66	0.41972	.	0.812536	0.09859	U	0.746452	T	0.41305	0.1153	L	0.27053	0.805	0.23933	N	0.996424	B;P	0.44139	0.243;0.827	B;B	0.40901	0.079;0.343	T	0.12243	-1.0555	10	0.39692	T	0.17	-0.167	10.2263	0.43227	0.0:0.0:0.1671:0.8329	.	34;13	Q9NWR8;C9JTJ6	C109B_HUMAN;.	A	34;13	ENSP00000378145:V34A;ENSP00000414591:V13A	ENSP00000378145:V34A	V	+	2	0	CCDC109B	110799617	0.999000	0.42202	0.634000	0.29324	0.066000	0.16364	2.038000	0.41184	0.704000	0.31869	0.529000	0.55759	GTT	.	.		0.318	CCDC109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254865.1	NM_017918	Missense_Mutation	C	110580168	T	C	110580168	5	2	91	1	0	0	0	0	0	0	1	0	2747	1739	60	2	107	2	CCDC109B	4	110580168	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	21813735	110580168	80574108	170	12244										
CASP6	839	hgsc.bcm.edu	37	chr4	110612018	110612018	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccacacaccttctgcaacagAgtaacacatgaggaagtcag	8	12	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:110612018A>G	ENST00000265164.2	-	6	708	c.631T>C	c.(631-633)Tct>Cct	p.S211P	CASP6_ENST00000510324.1_5'UTR|CASP6_ENST00000352981.3_Missense_Mutation_p.S122P|AC004067.5_ENST00000608733.1_RNA	NM_001226.3	NP_001217.2	P55212	CASP6_HUMAN	caspase 6, apoptosis-related cysteine peptidase	211					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|epithelial cell differentiation (GO:0030855)|proteolysis (GO:0006508)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)		TCTGCAACAGAGTAACACATG	0.443																																					p.S211P		Atlas-SNP	.											.	CASP6	25	.	0			c.T631C						.						189	163	172					4																	110612018		2203	4300	6503	SO:0001583	missense	839	exon6			CAACAGAGTAACA	U20536	CCDS3684.1, CCDS3685.1	4q25	2008-02-05	2005-08-17		ENSG00000138794	ENSG00000138794		"Caspases"	1507	protein-coding gene	gene with protein product		601532	"caspase 6, apoptosis-related cysteine protease"			8780721, 7796396	Standard	XM_005263271		Approved	MCH2	uc003hzn.1	P55212	OTTHUMG00000131914	ENST00000265164.2:c.631T>C	chr4.hg19:g.110612018A>G	ENSP00000265164:p.Ser211Pro	105.0	0.0		104.0	5.0	NM_001226	Q9BQE7	Missense_Mutation	SNP	ENST00000265164.2	hg19	CCDS3684.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.756726	0.89843	.	.	ENSG00000138794	ENST00000352981;ENST00000265164	T;T	0.57436	0.4;3.39	5.48	5.48	0.80851	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.052885	0.85682	D	0.000000	T	0.77592	0.4153	M	0.90309	3.105	0.80722	D	1	P;D	0.76494	0.684;0.999	P;D	0.77004	0.477;0.989	T	0.83009	-0.0173	10	0.87932	D	0	.	15.6181	0.76784	1.0:0.0:0.0:0.0	.	122;211	P55212-2;P55212	.;CASP6_HUMAN	P	122;211	ENSP00000285333:S122P;ENSP00000265164:S211P	ENSP00000265164:S211P	S	-	1	0	CASP6	110831467	1.000000	0.71417	0.994000	0.49952	0.892000	0.51952	8.933000	0.92911	2.101000	0.63845	0.529000	0.55759	TCT	.	.		0.443	CASP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254866.1	NM_001226		G	110612018	A	G	110612018	3	3	91	1	0	0	0	0	1	0	0	0	2677	304	11	2	258	2	CASP6	4	110612018	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	31850	110612018	80542258	171	12245										
CCNA2	890	hgsc.bcm.edu	37	chr4	122738818	122738818	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatttagtgtctctggtgggTtgaggagagaaacaccatga	14	5	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:122738818T>C	ENST00000274026.5	-	8	1577	c.1274A>G	c.(1273-1275)aAc>aGc	p.N425S		NM_001237.3	NP_001228	P20248	CCNA2_HUMAN	cyclin A2	425					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|organ regeneration (GO:0031100)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|response to estradiol (GO:0032355)|response to glucagon (GO:0033762)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	12						CTCTGGTGGGTTGAGGAGAGA	0.348																																					p.N425S		Atlas-SNP	.											.	CCNA2	30	.	0			c.A1274G						.						141	136	138					4																	122738818		2203	4300	6503	SO:0001583	missense	890	exon8			GGTGGGTTGAGGA		CCDS3723.1	4q27	2012-07-12			ENSG00000145386	ENSG00000145386			1578	protein-coding gene	gene with protein product		123835		CCNA, CCN1		1675006	Standard	NM_001237		Approved		uc003iec.4	P20248	OTTHUMG00000133072	ENST00000274026.5:c.1274A>G	chr4.hg19:g.122738818T>C	ENSP00000274026:p.Asn425Ser	104.0	0.0		86.0	4.0	NM_001237	A8K7B6|Q2M3U6|Q4W5P4|Q6LER8	Missense_Mutation	SNP	ENST00000274026.5	hg19	CCDS3723.1	.	.	.	.	.	.	.	.	.	.	T	9.432	1.085771	0.20390	.	.	ENSG00000145386	ENST00000274026	T	0.19532	2.14	6.16	3.73	0.42828	Cyclin, C-terminal (1);Cyclin-like (2);	0.393919	0.29508	N	0.011958	T	0.04861	0.0131	N	0.00453	-1.485	0.26776	N	0.969697	B	0.02656	0.0	B	0.01281	0.0	T	0.37407	-0.9707	10	0.12103	T	0.63	.	8.1586	0.31185	0.1208:0.0645:0.0:0.8147	.	425	P20248	CCNA2_HUMAN	S	425	ENSP00000274026:N425S	ENSP00000274026:N425S	N	-	2	0	CCNA2	122958268	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.712000	0.47186	0.547000	0.28938	0.528000	0.53228	AAC	.	.		0.348	CCNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256712.2	NM_001237		C	122738818	T	C	122738818	3	2	91	1	0	0	0	0	1	0	0	0	2912	1725	60	2	28	2	CCNA2	4	122738818	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	12126800	122738818	68415458	172	12246										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123210267	123210267	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttcctttgaacataatcttaCaactgatcttctaaaccact	2	11	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:123210267C>T	ENST00000264501.4	+	54	9681	c.9308C>T	c.(9307-9309)aCa>aTa	p.T3103I	KIAA1109_ENST00000455637.1_Missense_Mutation_p.T3103I|KIAA1109_ENST00000388738.3_Missense_Mutation_p.T3103I			Q2LD37	K1109_HUMAN	KIAA1109	3103					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CATAATCTTACAACTGATCTT	0.313																																					p.T3103I		Atlas-SNP	.											.	KIAA1109	424	.	0			c.C9308T						.						141	129	132					4																	123210267		1832	4084	5916	SO:0001583	missense	84162	exon52			ATCTTACAACTGA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.9308C>T	chr4.hg19:g.123210267C>T	ENSP00000264501:p.Thr3103Ile	165.0	0.0		113.0	5.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417393	0.83449	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637	T;T;T	0.36520	1.25;1.25;1.25	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.60612	0.2282	M	0.70595	2.14	0.49798	D	0.999826	D;D	0.76494	0.997;0.999	P;D	0.63488	0.899;0.915	T	0.62243	-0.6895	10	0.87932	D	0	.	20.0119	0.97458	0.0:1.0:0.0:0.0	.	3103;3103	Q2LD37-6;Q2LD37	.;K1109_HUMAN	I	3103	ENSP00000264501:T3103I;ENSP00000373390:T3103I;ENSP00000389925:T3103I	ENSP00000264501:T3103I	T	+	2	0	KIAA1109	123429717	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.888000	0.69758	2.712000	0.92718	0.650000	0.86243	ACA	.	.		0.313	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123210267	C	T	123210267	3	4	91	1	0	0	0	0	1	0	0	0	8217	478	17	3	9514	3	KIAA1109	4	123210267	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	471449	123210267	67944009	173	12247										
FAT4	79633	hgsc.bcm.edu	37	chr4	126371393	126371393	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccactttcttcccaagcaacTgttcacataactgtcactga	4	14	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:126371393T>C	ENST00000394329.3	+	9	9235	c.9222T>C	c.(9220-9222)acT>acC	p.T3074T	FAT4_ENST00000335110.5_Silent_p.T1372T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3074	Cadherin 29. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCCAAGCAACTGTTCACATAA	0.438																																					p.T3074T		Atlas-SNP	.											.	FAT4	1752	.	0			c.T9222C						.						98	93	94					4																	126371393		2203	4300	6503	SO:0001819	synonymous_variant	79633	exon9			AGCAACTGTTCAC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9222T>C	chr4.hg19:g.126371393T>C		135.0	0.0		97.0	4.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.		0.438	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126371393	T	C	126371393	2	2	91	1	0	0	0	0	0	0	0	1	5700	1567	55	2		2	FAT4	4	126371393	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3161126	126371393	64782883	174	12248										
PHF17	79960	hgsc.bcm.edu	37	chr4	129782996	129782996	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aagcacagctcacataggaaAcccgaggagagtcttggcaa	11	10	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:129782996A>G	ENST00000226319.6	+	9	1399	c.1119A>G	c.(1117-1119)aaA>aaG	p.K373K	PHF17_ENST00000511647.1_Silent_p.K373K|PHF17_ENST00000452328.2_Silent_p.K361K|PHF17_ENST00000413543.2_Silent_p.K373K|PHF17_ENST00000512960.1_Silent_p.K373K	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CACATAGGAAACCCGAGGAGA	0.562																																					p.K373K		Atlas-SNP	.											.	PHF17	63	.	0			c.A1119G						.						103	116	112					4																	129782996		2203	4300	6503	SO:0001819	synonymous_variant	79960	exon9			TAGGAAACCCGAG																												ENST00000226319.6:c.1119A>G	chr4.hg19:g.129782996A>G		167.0	0.0		92.0	4.0	NM_199320		Silent	SNP	ENST00000226319.6	hg19	CCDS34062.1																																																																																			.	.		0.562	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1			G	129782996	A	G	129782996	2	3	91	1	0	0	0	0	0	0	0	1	11837	40	2	2		2	PHF17	4	129782996	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3411603	129782996	61371280	175	12249										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148802995	148802995	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgattatttgcagggggacGgagaggtgttctttttgaaa	14	3	1	3	rs138388284		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:148802995G>T	ENST00000336498.3	+	10	1185	c.946G>T	c.(946-948)Gga>Tga	p.G316*	ARHGAP10_ENST00000414545.2_5'Flank	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		GCAGGGGGACGGAGAGGTGTT	0.413																																					p.G316X		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.G946T						.						154	150	152					4																	148802995		2203	4300	6503	SO:0001587	stop_gained	79658	exon10			GGGGACGGAGAGG	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.946G>T	chr4.hg19:g.148802995G>T	ENSP00000336923:p.Gly316*	187.0	0.0		110.0	38.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Nonsense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	G	38	6.804907	0.97853	.	.	ENSG00000071205	ENST00000336498	.	.	.	4.94	4.94	0.65067	.	0.110592	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	.	14.3287	0.66537	0.0:0.1492:0.8507:0.0	.	.	.	.	X	316	.	ENSP00000336923:G316X	G	+	1	0	ARHGAP10	149022445	0.085000	0.21516	0.783000	0.31826	0.053000	0.15095	1.461000	0.35255	2.284000	0.76573	0.591000	0.81541	GGA	.	G|1.000;A|0.000		0.413	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		T	148802995	G	T	148802995	4	4	91	1	0	0	0	0	0	1	0	0	862	1117	39	1	984	1	ARHGAP10	4	148802995	Nonsense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	19019999	148802995	42351281	176	12250										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148984403	148984403	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctttcacccgggtcgtcccCtttccccttttctcctcctg	5	19	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:148984403C>A	ENST00000336498.3	+	21	2371	c.2132C>A	c.(2131-2133)cCt>cAt	p.P711H	ARHGAP10_ENST00000414545.2_Intron	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		GGGTCGTCCCCTTTCCCCTTT	0.562																																					p.P711H		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.C2132A						.						152	107	122					4																	148984403		2203	4300	6503	SO:0001583	missense	79658	exon21			CGTCCCCTTTCCC	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.2132C>A	chr4.hg19:g.148984403C>A	ENSP00000336923:p.Pro711His	148.0	0.0		131.0	30.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.458566	0.43634	.	.	ENSG00000071205	ENST00000336498	T	0.10288	2.89	5.56	5.56	0.83823	Src homology-3 domain (1);	1.151220	0.06032	N	0.653185	T	0.10252	0.0251	N	0.14661	0.345	0.80722	D	1	D;B;B	0.55172	0.97;0.016;0.0	B;B;B	0.40901	0.343;0.005;0.001	T	0.43294	-0.9400	10	0.45353	T	0.12	.	16.4441	0.83910	0.0:1.0:0.0:0.0	.	144;292;711	Q9H7G7;Q86T21;A1A4S6	.;.;RHG10_HUMAN	H	711	ENSP00000336923:P711H	ENSP00000336923:P711H	P	+	2	0	ARHGAP10	149203853	0.006000	0.16342	0.006000	0.13384	0.020000	0.10135	1.978000	0.40598	2.615000	0.88500	0.555000	0.69702	CCT	.	.		0.562	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		A	148984403	C	A	148984403	3	1	91	1	0	0	0	0	1	0	0	0	862	681	24	3	2214	3	ARHGAP10	4	148984403	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	181408	148984403	42169873	177	12251										
FHDC1	85462	hgsc.bcm.edu	37	chr4	153884235	153884235	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctttgctcaaattggcagacAcaaaagcaaacaaacctggg	8	10	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:153884235A>G	ENST00000511601.1	+	8	1170	c.982A>G	c.(982-984)Aca>Gca	p.T328A	FHDC1_ENST00000260008.3_Missense_Mutation_p.T328A			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	328	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.								ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					ATTGGCAGACACAAAAGCAAA	0.398																																					p.T328A		Atlas-SNP	.											.	FHDC1	102	.	0			c.A982G						.						114	122	119					4																	153884235		2203	4300	6503	SO:0001583	missense	85462	exon7			GCAGACACAAAAG	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.982A>G	chr4.hg19:g.153884235A>G	ENSP00000427567:p.Thr328Ala	93.0	0.0		68.0	4.0	NM_033393		Missense_Mutation	SNP	ENST00000511601.1	hg19	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.714560	0.89112	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	T;T	0.21361	2.01;2.01	5.43	5.43	0.79202	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.55721	0.1938	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.66548	-0.5896	10	0.66056	D	0.02	.	15.5039	0.75722	1.0:0.0:0.0:0.0	.	328	Q9C0D6	FHDC1_HUMAN	A	328	ENSP00000427567:T328A;ENSP00000260008:T328A	ENSP00000260008:T328A	T	+	1	0	FHDC1	154103685	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.062000	0.61559	0.459000	0.35465	ACA	.	.		0.398	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		G	153884235	A	G	153884235	3	3	91	1	0	0	0	0	1	0	0	0	5884	159	6	2	1008	2	FHDC1	4	153884235	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4899832	153884235	37270041	178	12252										
TRIM2	23321	hgsc.bcm.edu	37	chr4	154216477	154216477	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcccgcaggtcctccagtcgCagctggatactctgctccag	10	16	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:154216477C>T	ENST00000437508.2	+	6	919	c.718C>T	c.(718-720)Cag>Tag	p.Q240*	TRIM2_ENST00000494872.1_3'UTR|TRIM2_ENST00000338700.5_Nonsense_Mutation_p.Q267*	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	240					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		CCTCCAGTCGCAGCTGGATAC	0.652																																					p.Q267X		Atlas-SNP	.											TRIM2_ENST00000338700,colon,carcinoma,0,2	TRIM2	105	.	0			c.C799T						.						22	21	22					4																	154216477		2203	4300	6503	SO:0001587	stop_gained	23321	exon6			CAGTCGCAGCTGG	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15974	protein-coding gene	gene with protein product		614141	"tripartite motif-containing 2"			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.718C>T	chr4.hg19:g.154216477C>T	ENSP00000415812:p.Gln240*	63.0	0.0		49.0	3.0	NM_015271	D3DP09|O60272|Q9BSI9|Q9UFZ1	Nonsense_Mutation	SNP	ENST00000437508.2	hg19	CCDS47147.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993509	0.93167	.	.	ENSG00000109654	ENST00000437508;ENST00000338700	.	.	.	5.31	5.31	0.75309	.	0.102561	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	1.0038	19.3326	0.94297	0.0:1.0:0.0:0.0	.	.	.	.	X	240;267	.	ENSP00000339659:Q267X	Q	+	1	0	TRIM2	154435927	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.411000	0.80078	2.639000	0.89480	0.561000	0.74099	CAG	.	.		0.652	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1			T	154216477	C	T	154216477	4	4	91	1	0	0	0	0	0	1	0	0	16509	711	25	3	821	3	TRIM2	4	154216477	Nonsense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	332242	154216477	36937799	179	12253										
IRF2	3660	hgsc.bcm.edu	37	chr4	185340657	185340657	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagtttctaaagagtggtgcAtctttttccacatcccaccc	6	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:185340657A>G	ENST00000393593.3	-	3	360	c.153T>C	c.(151-153)gaT>gaC	p.D51D	IRF2_ENST00000512020.1_5'UTR	NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	51					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		AGAGTGGTGCATCTTTTTCCA	0.393																																					p.D51D		Atlas-SNP	.											.	IRF2	53	.	0			c.T153C						.						140	141	141					4																	185340657		2203	4300	6503	SO:0001819	synonymous_variant	3660	exon3			TGGTGCATCTTTT		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.153T>C	chr4.hg19:g.185340657A>G		96.0	0.0		74.0	4.0	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Silent	SNP	ENST00000393593.3	hg19	CCDS3835.1																																																																																			.	.		0.393	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1			G	185340657	A	G	185340657	2	3	91	1	0	0	0	0	0	0	0	1	7837	214	8	2		2	IRF2	4	185340657	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	31124180	185340657	5813619	180	12254										
TRIML1	339976	hgsc.bcm.edu	37	chr4	189068092	189068092	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccgacaacccggaaagatttGaccagtctgcgactgtgctg	11	12	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:189068092G>A	ENST00000332517.3	+	6	1113	c.973G>A	c.(973-975)Gac>Aac	p.D325N	TRIML1_ENST00000507581.1_3'UTR	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	325	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D325H(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		GGAAAGATTTGACCAGTCTGC	0.547																																					p.D325N	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											TRIML1,NS,carcinoma,0,1	TRIML1	126	.	1	Substitution - Missense(1)	endometrium(1)	c.G973A						.						105	99	101					4																	189068092		2203	4300	6503	SO:0001583	missense	339976	exon6			AGATTTGACCAGT	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"RING-type (C3HC4) zinc fingers"	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.973G>A	chr4.hg19:g.189068092G>A	ENSP00000327738:p.Asp325Asn	127.0	0.0		109.0	5.0	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	hg19	CCDS3851.1	.	.	.	.	.	.	.	.	.	.	g	19.93	3.917648	0.73098	.	.	ENSG00000184108	ENST00000332517	T	0.15952	2.38	4.92	4.07	0.47477	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.000000	0.56097	D	0.000026	T	0.23410	0.0566	L	0.50919	1.6	0.37246	D	0.906365	D	0.57899	0.981	P	0.56514	0.8	T	0.01869	-1.1257	10	0.26408	T	0.33	-38.8901	6.7704	0.23591	0.1815:0.0:0.8185:0.0	.	325	Q8N9V2	TRIML_HUMAN	N	325	ENSP00000327738:D325N	ENSP00000327738:D325N	D	+	1	0	TRIML1	189305086	0.032000	0.19561	1.000000	0.80357	0.838000	0.47535	1.110000	0.31147	2.749000	0.94314	0.550000	0.68814	GAC	.	.		0.547	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556		A	189068092	G	A	189068092	3	1	91	1	0	0	0	0	1	0	0	0	16565	1290	45	3	995	3	TRIML1	4	189068092	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3727435	189068092	2086184	181	12255										
EXOC3	11336	hgsc.bcm.edu	37	chr5	466898	466898	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggacgccagccgtgacatgaAgcagaccatcatggagaccc	12	13	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:466898A>G	ENST00000512944.1	+	13	2312	c.2123A>G	c.(2122-2124)aAg>aGg	p.K708R	EXOC3_ENST00000315013.5_Missense_Mutation_p.K708R|CTD-2228K2.5_ENST00000510714.1_Intron	NM_007277.4	NP_009208.2	O60645	EXOC3_HUMAN	exocyst complex component 3	719					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|secretory granule membrane (GO:0030667)				breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(13)|ovary(1)|urinary_tract(1)	23		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CGTGACATGAAGCAGACCATC	0.647																																					p.K708R		Atlas-SNP	.											.	EXOC3	54	.	0			c.A2123G						.						47	57	54					5																	466898		2167	4257	6424	SO:0001583	missense	11336	exon13			ACATGAAGCAGAC	BC034427	CCDS54830.1	5p15.33	2013-01-22	2005-11-01	2005-11-01	ENSG00000180104	ENSG00000180104			30378	protein-coding gene	gene with protein product		608186	"SEC6-like 1 (S. cerevisiae)"	SEC6L1		8619474	Standard	XM_005248238		Approved	Sec6p	uc003jba.3	O60645	OTTHUMG00000162205	ENST00000512944.1:c.2123A>G	chr5.hg19:g.466898A>G	ENSP00000425587:p.Lys708Arg	147.0	0.0		109.0	6.0	NM_007277	Q6P2E8|Q8TEN6|Q8WUW0|Q96DI4	Missense_Mutation	SNP	ENST00000512944.1	hg19	CCDS54830.1	.	.	.	.	.	.	.	.	.	.	A	8.734	0.917369	0.17982	.	.	ENSG00000180104	ENST00000512944;ENST00000315013;ENST00000340158	T;T	0.05996	3.36;3.36	5.49	5.49	0.81192	.	0.047847	0.85682	D	0.000000	T	0.02970	0.0088	N	0.02802	-0.49	0.45554	D	0.998505	B	0.14012	0.009	B	0.16289	0.015	T	0.47699	-0.9097	10	0.09843	T	0.71	-43.9352	13.5419	0.61679	1.0:0.0:0.0:0.0	.	719	O60645	EXOC3_HUMAN	R	708;708;603	ENSP00000425587:K708R;ENSP00000323377:K708R	ENSP00000323377:K708R	K	+	2	0	EXOC3	519898	1.000000	0.71417	1.000000	0.80357	0.495000	0.33615	5.054000	0.64275	2.091000	0.63221	0.254000	0.18369	AAG	.	.		0.647	EXOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367882.1	NM_007277		G	466898	A	G	466898	3	3	91	1	0	0	0	0	1	0	0	0	5305	72	3	2	2169	2	EXOC3	5	466898	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10		466898	180448362	182	12256										
BRD9	65980	hgsc.bcm.edu	37	chr5	864653	864653	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggtcgtgggtgacgtctggcTgctccccgacactcaggcga	15	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:864653T>C	ENST00000467963.1	-	16	1890	c.1724A>G	c.(1723-1725)cAg>cGg	p.Q575R	BRD9_ENST00000483173.1_Missense_Mutation_p.Q522R|BRD9_ENST00000323510.4_Missense_Mutation_p.Q479R|BRD9_ENST00000388890.4_Missense_Mutation_p.Q459R	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	575					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			GACGTCTGGCTGCTCCCCGAC	0.557																																					p.Q575R		Atlas-SNP	.											.	BRD9	113	.	0			c.A1724G						.						73	74	74					5																	864653		2203	4300	6503	SO:0001583	missense	65980	exon16			TCTGGCTGCTCCC	AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310			25818	protein-coding gene	gene with protein product						12477932	Standard	NM_023924		Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.1724A>G	chr5.hg19:g.864653T>C	ENSP00000419765:p.Gln575Arg	70.0	0.0		63.0	4.0	NM_023924	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	Missense_Mutation	SNP	ENST00000467963.1	hg19	CCDS34127.2	.	.	.	.	.	.	.	.	.	.	t	18.51	3.639436	0.67244	.	.	ENSG00000028310	ENST00000323510;ENST00000388890;ENST00000483173;ENST00000467963	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.58680	0.2139	M	0.63428	1.95	0.80722	D	1	D;D;P;P	0.52996	0.957;0.957;0.921;0.921	P;P;P;P	0.52710	0.608;0.608;0.707;0.707	T	0.63717	-0.6574	10	0.87932	D	0	.	15.2034	0.73159	0.0:0.0:0.0:1.0	.	522;575;479;459	B4DMQ2;Q9H8M2;Q9H8M2-1;Q9H8M2-3	.;BRD9_HUMAN;.;.	R	479;459;522;575	ENSP00000323557:Q479R;ENSP00000373542:Q459R;ENSP00000419845:Q522R;ENSP00000419765:Q575R	ENSP00000323557:Q479R	Q	-	2	0	BRD9	917653	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	5.037000	0.64170	2.078000	0.62432	0.459000	0.35465	CAG	.	.		0.557	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354113.1	NM_023924		C	864653	T	C	864653	3	2	91	1	0	0	0	0	1	0	0	0	1509	1580	55	2	73	2	BRD9	5	864653	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	397755	864653	180050607	183	12257										
LPCAT1	79888	hgsc.bcm.edu	37	chr5	1463792	1463792	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagcttcttgcgaacaggctTccgcccagcgtctgagtttt	10	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:1463792T>C	ENST00000283415.3	-	14	1711	c.1579A>G	c.(1579-1581)Aag>Gag	p.K527E	LPCAT1_ENST00000503252.1_5'UTR	NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	527					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		CGAACAGGCTTCCGCCCAGCG	0.597																																					p.K527E		Atlas-SNP	.											.	LPCAT1	70	.	0			c.A1579G						.						56	59	58					5																	1463792		2203	4300	6503	SO:0001583	missense	79888	exon14			CAGGCTTCCGCCC	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"EF-hand domain containing"	25718	protein-coding gene	gene with protein product		610472	"acyltransferase like 2"	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.1579A>G	chr5.hg19:g.1463792T>C	ENSP00000283415:p.Lys527Glu	115.0	0.0		90.0	4.0	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Missense_Mutation	SNP	ENST00000283415.3	hg19	CCDS3864.1	.	.	.	.	.	.	.	.	.	.	T	10.65	1.410349	0.25465	.	.	ENSG00000153395	ENST00000283415	T	0.70045	-0.45	4.29	0.528	0.17089	.	0.693642	0.14799	N	0.297753	T	0.37945	0.1022	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.15150	-1.0447	10	0.21540	T	0.41	-7.8716	4.4181	0.11466	0.0:0.2028:0.1961:0.6011	.	527	Q8NF37	PCAT1_HUMAN	E	527	ENSP00000283415:K527E	ENSP00000283415:K527E	K	-	1	0	LPCAT1	1516792	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.428000	0.21395	-0.155000	0.11098	0.459000	0.35465	AAG	.	.		0.597	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830		C	1463792	T	C	1463792	3	2	91	1	0	0	0	0	1	0	0	0	8919	1792	62	2	29	2	LPCAT1	5	1463792	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	599139	1463792	179451468	184	12258										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5461628	5461628	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtgggatagaatatacaaaAgtagtaaaaggcttgaccaa	10	4	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:5461628A>G	ENST00000296564.7	+	13	2403	c.2181A>G	c.(2179-2181)aaA>aaG	p.K727K		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		727					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AATATACAAAAGTAGTAAAAG	0.388																																					p.K727K		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A2181G						.						54	51	52					5																	5461628		1851	4093	5944	SO:0001819	synonymous_variant	23379	exon13			TACAAAAGTAGTA																												ENST00000296564.7:c.2181A>G	chr5.hg19:g.5461628A>G		116.0	0.0		102.0	5.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	hg19	CCDS47187.1																																																																																			.	.		0.388	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			G	5461628	A	G	5461628	2	3	91	1	0	0	0	0	0	0	0	1	8211	69	3	2		2	KIAA0947	5	5461628	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3997836	5461628	175453632	185	12259										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5461675	5461675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttcacttcctcggtcagtatTtatgaaagctacaaaagatg	7	8	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:5461675T>C	ENST00000296564.7	+	13	2450	c.2228T>C	c.(2227-2229)tTt>tCt	p.F743S		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		743					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						CGGTCAGTATTTATGAAAGCT	0.363																																					p.F743S		Atlas-SNP	.											.	KIAA0947	301	.	0			c.T2228C						.						59	51	54					5																	5461675		1874	4096	5970	SO:0001583	missense	23379	exon13			CAGTATTTATGAA																												ENST00000296564.7:c.2228T>C	chr5.hg19:g.5461675T>C	ENSP00000296564:p.Phe743Ser	99.0	0.0		81.0	4.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.147369	0.77888	.	.	ENSG00000164151	ENST00000296564	T	0.12361	2.69	5.26	2.63	0.31362	.	0.545813	0.19575	N	0.111005	T	0.20981	0.0505	L	0.32530	0.975	0.09310	N	1	D	0.71674	0.998	D	0.69654	0.965	T	0.04693	-1.0933	10	0.34782	T	0.22	-21.5527	8.8379	0.35123	0.0:0.0:0.3738:0.6262	.	743	Q9Y2F5	K0947_HUMAN	S	743	ENSP00000296564:F743S	ENSP00000296564:F743S	F	+	2	0	KIAA0947	5514675	0.535000	0.26370	0.007000	0.13788	0.857000	0.48899	1.607000	0.36836	0.807000	0.34208	0.254000	0.18369	TTT	.	.		0.363	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			C	5461675	T	C	5461675	3	2	91	1	0	0	0	0	1	0	0	0	8211	1841	64	2	2278	2	KIAA0947	5	5461675	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	47	5461675	175453585	186	12260										
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9122917	9122917	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcgtccacggagaccacacAccaaagtgcccatccacggt	10	16	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:9122917A>G	ENST00000382496.5	-	14	2297	c.1632T>C	c.(1630-1632)ggT>ggC	p.G544G		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	544	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GAGACCACACACCAAAGTGCC	0.557																																					p.G544G		Atlas-SNP	.											.	SEMA5A	236	.	0			c.T1632C						.						63	63	63					5																	9122917		2203	4300	6503	SO:0001819	synonymous_variant	9037	exon14			CCACACACCAAAG	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1632T>C	chr5.hg19:g.9122917A>G		158.0	0.0		135.0	6.0	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	hg19	CCDS3875.1																																																																																			.	.		0.557	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			G	9122917	A	G	9122917	2	3	91	1	0	0	0	0	0	0	0	1	14052	146	6	2		2	SEMA5A	5	9122917	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3661242	9122917	171792343	187	12261										
FBXL7	23194	hgsc.bcm.edu	37	chr5	15936656	15936656	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccatccgctacctggacatGacggactgcttcgtgctgga	11	13	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:15936656G>A	ENST00000504595.1	+	4	1318	c.837G>A	c.(835-837)atG>atA	p.M279I	FBXL7_ENST00000329673.7_Missense_Mutation_p.M267I|MIR887_ENST00000401258.1_RNA|FBXL7_ENST00000510662.1_Missense_Mutation_p.M232I	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	279					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						ACCTGGACATGACGGACTGCT	0.612																																					p.M279I		Atlas-SNP	.											.	FBXL7	138	.	0			c.G837A						.						72	73	72					5																	15936656		2183	4285	6468	SO:0001583	missense	23194	exon4			GGACATGACGGAC	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.837G>A	chr5.hg19:g.15936656G>A	ENSP00000423630:p.Met279Ile	62.0	0.0		63.0	4.0	NM_012304	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	hg19	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.369911	0.61624	.	.	ENSG00000183580	ENST00000504595;ENST00000510662;ENST00000329673	T;T;T	0.49139	0.79;0.79;0.79	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.35307	0.0927	N	0.24115	0.695	0.80722	D	1	P	0.35844	0.524	B	0.29862	0.108	T	0.20773	-1.0265	10	0.41790	T	0.15	.	18.6513	0.91431	0.0:0.0:1.0:0.0	.	279	Q9UJT9	FBXL7_HUMAN	I	279;232;267	ENSP00000423630:M279I;ENSP00000425184:M232I;ENSP00000329632:M267I	ENSP00000329632:M267I	M	+	3	0	FBXL7	15989656	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.414000	0.81942	0.655000	0.94253	ATG	.	.		0.612	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		A	15936656	G	A	15936656	3	1	91	1	0	0	0	0	1	0	0	0	5732	1290	45	3	851	3	FBXL7	5	15936656	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	6813739	15936656	164978604	188	12262										
CDH18	1016	hgsc.bcm.edu	37	chr5	19544066	19544066	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctaatggtcccagtattggcAtcaatgttgaaaaatctgtc	8	8	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:19544066A>G	ENST00000507958.1	-	11	2292	c.1302T>C	c.(1300-1302)gaT>gaC	p.D434D	CDH18_ENST00000502796.1_Silent_p.D434D|CDH18_ENST00000274170.4_Silent_p.D434D|CDH18_ENST00000506372.1_Silent_p.D434D|CDH18_ENST00000511273.1_Silent_p.D434D|CDH18_ENST00000382275.1_Silent_p.D434D			Q13634	CAD18_HUMAN	cadherin 18, type 2	434	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CAGTATTGGCATCAATGTTGA	0.343																																					p.D434D		Atlas-SNP	.											.	CDH18	561	.	0			c.T1302C						.						124	117	119					5																	19544066		2203	4300	6503	SO:0001819	synonymous_variant	1016	exon9			ATTGGCATCAATG	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1302T>C	chr5.hg19:g.19544066A>G		169.0	0.0		114.0	6.0	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	hg19	CCDS3889.1																																																																																			.	.		0.343	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		G	19544066	A	G	19544066	2	3	91	1	0	0	0	0	0	0	0	1	3105	214	8	2		2	CDH18	5	19544066	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3607410	19544066	161371194	189	12263										
FYB	2533	hgsc.bcm.edu	37	chr5	39130699	39130699	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcgtgtggcttacctccactTccactctgactgtggctaga	10	13	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:39130699T>C	ENST00000351578.6	-	10	2023	c.1833A>G	c.(1831-1833)ggA>ggG	p.G611G	FYB_ENST00000540520.1_Silent_p.G621G|FYB_ENST00000512982.1_Silent_p.G611G|FYB_ENST00000515010.1_Silent_p.G611G|FYB_ENST00000505428.1_Silent_p.G611G	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	611					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			TACCTCCACTTCCACTCTGAC	0.333																																					p.G621G		Atlas-SNP	.											.	FYB	354	.	0			c.A1863G						.						77	71	73					5																	39130699		1891	4117	6008	SO:0001819	synonymous_variant	2533	exon10			TCCACTTCCACTC	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1833A>G	chr5.hg19:g.39130699T>C		72.0	0.0		73.0	5.0	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	hg19	CCDS47200.1																																																																																			.	.		0.333	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		C	39130699	T	C	39130699	2	2	91	1	0	0	0	0	0	0	0	1	6132	1770	62	2		2	FYB	5	39130699	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	19586633	39130699	141784561	190	12264										
FGF10	2255	hgsc.bcm.edu	37	chr5	44388683	44388683	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccaagggcttggcaggtgacAgggacggaagacaccaagaa	15	9	0	3	rs140279180	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:44388683A>G	ENST00000264664.4	-	1	216	c.102T>C	c.(100-102)ccT>ccC	p.P34P	RP11-473L15.2_ENST00000502457.1_RNA	NM_004465.1	NP_004456.1	O15520	FGF10_HUMAN	fibroblast growth factor 10	34					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchiole morphogenesis (GO:0060436)|bud elongation involved in lung branching (GO:0060449)|bud outgrowth involved in lung branching (GO:0060447)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell migration (GO:0010631)|epithelial cell proliferation (GO:0050673)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|ERK1 and ERK2 cascade (GO:0070371)|establishment of mitotic spindle orientation (GO:0000132)|Fc-epsilon receptor signaling pathway (GO:0038095)|female genitalia morphogenesis (GO:0048807)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|hair follicle morphogenesis (GO:0031069)|Harderian gland development (GO:0070384)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte proliferation (GO:0043616)|lacrimal gland development (GO:0032808)|limb bud formation (GO:0060174)|lung epithelium development (GO:0060428)|lung proximal/distal axis specification (GO:0061115)|lung saccule development (GO:0060430)|male genitalia morphogenesis (GO:0048808)|mammary gland bud formation (GO:0060615)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal-epithelial cell signaling involved in lung development (GO:0060496)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|metanephros morphogenesis (GO:0003338)|muscle cell fate commitment (GO:0042693)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|pancreas development (GO:0031016)|phosphatidylinositol-mediated signaling (GO:0048015)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of ATPase activity (GO:0032781)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urothelial cell proliferation (GO:0050677)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of white fat cell proliferation (GO:0070352)|prostatic bud formation (GO:0060513)|protein localization to cell surface (GO:0034394)|radial glial cell differentiation (GO:0060019)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of saliva secretion (GO:0046877)|regulation of smoothened signaling pathway (GO:0008589)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|salivary gland development (GO:0007431)|secretion by lung epithelial cell involved in lung growth (GO:0061033)|semicircular canal fusion (GO:0060879)|smooth muscle cell differentiation (GO:0051145)|somatic stem cell maintenance (GO:0035019)|spleen development (GO:0048536)|submandibular salivary gland formation (GO:0060661)|tear secretion (GO:0070075)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tissue regeneration (GO:0042246)|Type II pneumocyte differentiation (GO:0060510)|urothelial cell proliferation (GO:0050674)|white fat cell differentiation (GO:0050872)|wound healing (GO:0042060)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chemoattractant activity (GO:0042056)|fibroblast growth factor receptor binding (GO:0005104)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|type 2 fibroblast growth factor receptor binding (GO:0005111)			haematopoietic_and_lymphoid_tissue(1)|lung(11)|skin(1)	13	Lung NSC(6;1.12e-06)					GGCAGGTGACAGGGACGGAAG	0.572																																					p.P34P		Atlas-SNP	.											.	FGF10	40	.	0			c.T102C						.						55	51	52					5																	44388683		2203	4300	6503	SO:0001819	synonymous_variant	2255	exon1			GGTGACAGGGACG		CCDS3950.1	5p13-p12	2008-02-05			ENSG00000070193	ENSG00000070193			3666	protein-coding gene	gene with protein product		602115				9287324	Standard	NM_004465		Approved		uc003jog.1	O15520	OTTHUMG00000131153	ENST00000264664.4:c.102T>C	chr5.hg19:g.44388683A>G		128.0	0.0		141.0	6.0	NM_004465	C7FDY0|Q6FHR3|Q6FHT6|Q96P59	Silent	SNP	ENST00000264664.4	hg19	CCDS3950.1																																																																																			.	A|1.000;C|0.000		0.572	FGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253845.2	NM_004465		G	44388683	A	G	44388683	2	3	91	1	0	0	0	0	0	0	0	1	5847	175	7	2		2	FGF10	5	44388683	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	5257984	44388683	136526577	191	12265										
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64510631	64510631	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcatcttacctccagcacaAgtagctgagcattctgacca	8	13	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:64510631A>G								ADAMTS6 (16039 upstream) : ADAMTS6 (82403 downstream)																							CTCCAGCACAAGTAGCTGAGC	0.443																																					p.T855T		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.T2565C						.						130	114	119					5																	64510631		2203	4300	6503	SO:0001628	intergenic_variant	11174	exon20			AGCACAAGTAGCT																													chr5.hg19:g.64510631A>G		119.0	0.0		110.0	5.0	NM_197941		Silent	SNP		hg19																																																																																				.	.	0	0.443									G	64510631	A	G	64510631	1	3	91	0	1	0	0	0	0	0	0	0	270	59	3	2		2	ADAMTS6	5	64510631	IGR	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	20121948	64510631	116404629	192	12266										
PPWD1	23398	hgsc.bcm.edu	37	chr5	64868003	64868003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aggcttatccaaccagcgtaTgtttttcaccagatgggaag	10	9	1	1	rs373825399		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:64868003T>C	ENST00000261308.5	+	5	931	c.859T>C	c.(859-861)Tgt>Cgt	p.C287R	PPWD1_ENST00000538977.1_Missense_Mutation_p.C131R|PPWD1_ENST00000535264.1_Missense_Mutation_p.C257R	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	287					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		AACCAGCGTATGTTTTTCACC	0.338																																					p.C287R		Atlas-SNP	.											.	PPWD1	47	.	0			c.T859C						.	T	ARG/CYS	1,4405	2.1+/-5.4	0,1,2202	65	71	68		859	5.6	1	5		68	0,8600		0,0,4300	no	missense	PPWD1	NM_015342.2	180	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	287/647	64868003	1,13005	2203	4300	6503	SO:0001583	missense	23398	exon5			AGCGTATGTTTTT	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"WD repeat domain containing"	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.859T>C	chr5.hg19:g.64868003T>C	ENSP00000261308:p.Cys287Arg	84.0	0.0		75.0	4.0	NM_015342	B4DWR9|Q15002|Q7KZ89	Missense_Mutation	SNP	ENST00000261308.5	hg19	CCDS3985.1	.	.	.	.	.	.	.	.	.	.	T	9.671	1.146709	0.21288	2.27E-4	0.0	ENSG00000113593	ENST00000261308;ENST00000535264;ENST00000538977;ENST00000505380	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.215721	0.48286	D	0.000195	T	0.35307	0.0927	N	0.05124	-0.11	0.58432	D	0.999994	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.19192	-1.0313	10	0.32370	T	0.25	.	11.5435	0.50679	0.1416:0.0:0.0:0.8584	.	257;287	F5H7P7;Q96BP3	.;PPWD1_HUMAN	R	287;257;131;206	ENSP00000261308:C287R;ENSP00000442371:C257R;ENSP00000444496:C131R;ENSP00000423234:C206R	ENSP00000261308:C287R	C	+	1	0	PPWD1	64903759	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.444000	0.44890	2.125000	0.65367	0.459000	0.35465	TGT	.	.		0.338	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342		C	64868003	T	C	64868003	3	2	91	1	0	0	0	0	1	0	0	0	12426	1464	51	2	877	2	PPWD1	5	64868003	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	357372	64868003	116047257	193	12267										
TRIM23	373	hgsc.bcm.edu	37	chr5	64890421	64890421	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acaactttgcaagttcgctgTgtgcttcactaattctgtct	7	10	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:64890421T>C	ENST00000231524.9	-	10	1843	c.1472A>G	c.(1471-1473)cAc>cGc	p.H491R	TRIM23_ENST00000381018.3_Missense_Mutation_p.H491R|TRIM23_ENST00000274327.7_Missense_Mutation_p.H491R	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	491	ARF-like.				GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		AAGTTCGCTGTGTGCTTCACT	0.338																																					p.H491R		Atlas-SNP	.											.	TRIM23	73	.	0			c.A1472G						.						109	102	105					5																	64890421		2202	4300	6502	SO:0001583	missense	373	exon10			TCGCTGTGTGCTT	L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	660	protein-coding gene	gene with protein product		601747	"ADP-ribosylation factor domain protein 1, 64kDa", "tripartite motif-containing 23"	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.1472A>G	chr5.hg19:g.64890421T>C	ENSP00000231524:p.His491Arg	85.0	0.0		74.0	4.0	NM_033228	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	hg19	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	T	9.197	1.027585	0.19512	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	T;T;T	0.61392	0.11;0.11;0.11	5.64	5.64	0.86602	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.30759	0.0775	N	0.01473	-0.845	0.58432	D	0.999998	B;B;B	0.16603	0.0;0.002;0.018	B;B;B	0.20955	0.01;0.002;0.032	T	0.26503	-1.0101	10	0.13470	T	0.59	.	15.8515	0.78934	0.0:0.0:0.0:1.0	.	491;491;491	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	R	491	ENSP00000231524:H491R;ENSP00000370406:H491R;ENSP00000274327:H491R	ENSP00000231524:H491R	H	-	2	0	TRIM23	64926177	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.263000	0.72521	2.137000	0.66172	0.482000	0.46254	CAC	.	.		0.338	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		C	64890421	T	C	64890421	3	2	91	1	0	0	0	0	1	0	0	0	16512	1696	59	2	327	2	TRIM23	5	64890421	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	22418	64890421	116024839	194	12268										
SV2C	22987	hgsc.bcm.edu	37	chr5	75505685	75505685	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtggcatctacgcctctgccAtggcctgggccatcatcccg	11	16	3	0	rs370314313		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:75505685A>C	ENST00000502798.2	+	4	1328	c.886A>C	c.(886-888)Atg>Ctg	p.M296L	SV2C_ENST00000322285.7_Missense_Mutation_p.M296L	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	296					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CGCCTCTGCCATGGCCTGGGC	0.577																																					p.M296L		Atlas-SNP	.											.	SV2C	97	.	0			c.A886C						.	A	LEU/MET	0,4400		0,0,2200	55	58	57		886	5.1	1	5		57	1,8599	1.2+/-3.3	0,1,4299	no	missense	SV2C	NM_014979.1	15	0,1,6499	CC,CA,AA		0.0116,0.0,0.0077	possibly-damaging	296/728	75505685	1,12999	2200	4300	6500	SO:0001583	missense	22987	exon4			TCTGCCATGGCCT	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.886A>C	chr5.hg19:g.75505685A>C	ENSP00000423541:p.Met296Leu	106.0	0.0		79.0	4.0	NM_014979	Q496K1|Q9UPU8	Missense_Mutation	SNP	ENST00000502798.2	hg19	CCDS43331.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.314382	0.60414	0.0	1.16E-4	ENSG00000122012	ENST00000502798;ENST00000322285	T;T	0.50001	0.76;0.76	5.13	5.13	0.70059	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.31104	0.0786	N	0.16130	0.375	0.80722	D	1	B	0.13594	0.008	B	0.23150	0.044	T	0.11251	-1.0595	10	0.13108	T	0.6	-31.3584	14.6544	0.68823	1.0:0.0:0.0:0.0	.	296	Q496J9	SV2C_HUMAN	L	296	ENSP00000423541:M296L;ENSP00000316983:M296L	ENSP00000316983:M296L	M	+	1	0	SV2C	75541441	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.176000	0.94839	1.935000	0.56089	0.477000	0.44152	ATG	.	.		0.577	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4			C	75505685	A	C	75505685	3	2	91	1	0	0	0	0	1	0	0	0	15434	217	8	5	896	5	SV2C	5	75505685	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	10615264	75505685	105409575	195	12269										
AP3B1	8546	hgsc.bcm.edu	37	chr5	77563357	77563357	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tacctaccccaacaatccgcTtcatagcatccagtttagca	4	15	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:77563357T>C	ENST00000255194.6	-	2	366	c.191A>G	c.(190-192)aAg>aGg	p.K64R	AP3B1_ENST00000519295.1_Missense_Mutation_p.K15R	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	64					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		AACAATCCGCTTCATAGCATC	0.289									Hermansky-Pudlak syndrome																												p.K64R		Atlas-SNP	.											.	AP3B1	94	.	0			c.A191G						.						94	95	94					5																	77563357		2203	4298	6501	SO:0001583	missense	8546	exon2	Familial Cancer Database	HPS, HPS1-8	ATCCGCTTCATAG	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.191A>G	chr5.hg19:g.77563357T>C	ENSP00000255194:p.Lys64Arg	94.0	0.0		88.0	4.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.150497	0.78001	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760	T;T	0.30981	1.51;1.51	5.29	5.29	0.74685	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.164274	0.51477	D	0.000088	T	0.51534	0.1680	L	0.58428	1.81	0.58432	D	0.999999	D	0.71674	0.998	D	0.77557	0.99	T	0.54397	-0.8300	10	0.87932	D	0	-19.2682	14.2078	0.65746	0.0:0.0:0.0:1.0	.	64	O00203	AP3B1_HUMAN	R	64;15;64	ENSP00000255194:K64R;ENSP00000430597:K15R	ENSP00000255194:K64R	K	-	2	0	AP3B1	77599113	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	4.593000	0.61034	1.990000	0.58119	0.482000	0.46254	AAG	.	.		0.289	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			C	77563357	T	C	77563357	3	2	91	1	0	0	0	0	1	0	0	0	744	1609	56	2	3197	2	AP3B1	5	77563357	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2057672	77563357	103351903	196	12270										
RASGRF2	5924	hgsc.bcm.edu	37	chr5	80511700	80511700	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttcttttctttttagacaaaAgctctaatggacaaacttca	4	8	4	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:80511700A>G	ENST00000265080.4	+	24	3427	c.3360A>G	c.(3358-3360)aaA>aaG	p.K1120K	CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000503483.2_RNA	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	1120	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.|Responsible of the affinity for farnesylated versus geranylgeranylated Ras. {ECO:0000250}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		TTTAGACAAAAGCTCTAATGG	0.289																																					p.K1120K		Atlas-SNP	.											.	RASGRF2	165	.	0			c.A3360G						.						15	16	16					5																	80511700		2118	4226	6344	SO:0001819	synonymous_variant	5924	exon24			GACAAAAGCTCTA	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.3360A>G	chr5.hg19:g.80511700A>G		105.0	0.0		86.0	4.0	NM_006909	B9EG89|Q9UK56	Silent	SNP	ENST00000265080.4	hg19	CCDS4052.1																																																																																			.	.		0.289	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		G	80511700	A	G	80511700	2	3	91	1	0	0	0	0	0	0	0	1	13088	69	3	2		2	RASGRF2	5	80511700	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2948343	80511700	100403560	197	12271										
XRCC4	7518	hgsc.bcm.edu	37	chr5	82499472	82499472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aacaaaaatcagaagtttgcAtaataaattattaaatgcag	5	4	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:82499472A>G	ENST00000511817.1	+	5	664	c.584A>G	c.(583-585)cAt>cGt	p.H195R	XRCC4_ENST00000282268.3_Missense_Mutation_p.H195R|XRCC4_ENST00000338635.6_Missense_Mutation_p.H195R|XRCC4_ENST00000509268.1_3'UTR|XRCC4_ENST00000396027.4_Missense_Mutation_p.H195R			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	195	Interacts with LIG4.				cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		AGAAGTTTGCATAATAAATTA	0.328								Non-homologous end-joining																													p.H195R		Atlas-SNP	.											.	XRCC4	37	.	0			c.A584G						.						69	75	73					5																	82499472		2203	4299	6502	SO:0001583	missense	7518	exon5			GTTTGCATAATAA	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"X-ray repair, complementing defective, repair in Chinese hamster", "DNA repair protein XRCC4"	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.584A>G	chr5.hg19:g.82499472A>G	ENSP00000421491:p.His195Arg	92.0	0.0		94.0	4.0	NM_003401	A8K3X4|Q9BS72|Q9UP94	Missense_Mutation	SNP	ENST00000511817.1	hg19	CCDS4059.1	.	.	.	.	.	.	.	.	.	.	A	3.577	-0.086504	0.07097	.	.	ENSG00000152422	ENST00000282268;ENST00000338635;ENST00000396027;ENST00000511817	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	0.225	0.225	0.15325	.	0.212263	0.50627	N	0.000115	T	0.20170	0.0485	L	0.56769	1.78	0.25570	N	0.986905	B;B;B	0.15719	0.011;0.014;0.012	B;B;B	0.12837	0.005;0.008;0.007	T	0.15150	-1.0447	10	0.46703	T	0.11	-18.6796	4.823	0.13400	0.9998:0.0:2.0E-4:0.0	.	195;195;195	Q13426-2;Q13426;Q13426-3	.;XRCC4_HUMAN;.	R	195	ENSP00000282268:H195R;ENSP00000342011:H195R;ENSP00000379344:H195R;ENSP00000421491:H195R	ENSP00000282268:H195R	H	+	2	0	XRCC4	82535228	0.940000	0.31905	0.993000	0.49108	0.668000	0.39293	1.013000	0.29937	0.257000	0.21650	0.254000	0.18369	CAT	.	.		0.328	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550		G	82499472	A	G	82499472	3	3	91	1	0	0	0	0	1	0	0	0	17470	217	8	2	598	2	XRCC4	5	82499472	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1987772	82499472	98415788	198	12272										
ERAP1	51752	hgsc.bcm.edu	37	chr5	96119656	96119656	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagtttccacttcattcataTctcttttctccattaactta	2	11	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:96119656T>C	ENST00000443439.2	-	14	2138	c.2072A>G	c.(2071-2073)gAt>gGt	p.D691G	ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000512856.1_RNA|ERAP1_ENST00000296754.3_Missense_Mutation_p.D691G|CTD-2260A17.1_ENST00000602972.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	691					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TTCATTCATATCTCTTTTCTC	0.308																																					p.D691G		Atlas-SNP	.											.	ERAP1	59	.	0			c.A2072G						.						88	83	85					5																	96119656		2203	4300	6503	SO:0001583	missense	51752	exon14			TTCATATCTCTTT	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.2072A>G	chr5.hg19:g.96119656T>C	ENSP00000406304:p.Asp691Gly	110.0	0.0		89.0	4.0	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	hg19	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	T	10.29	1.309375	0.23821	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.06449	3.3;3.3	5.84	5.84	0.93424	.	0.262386	0.42420	D	0.000702	T	0.07954	0.0199	L	0.46614	1.455	0.58432	D	0.999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.12837	0.008;0.003;0.003	T	0.26985	-1.0087	10	0.17369	T	0.5	.	15.1933	0.73063	0.0:0.0:0.0:1.0	.	691;691;691	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	G	691	ENSP00000296754:D691G;ENSP00000406304:D691G	ENSP00000296754:D691G	D	-	2	0	ERAP1	96145412	1.000000	0.71417	0.994000	0.49952	0.988000	0.76386	4.552000	0.60747	2.232000	0.73038	0.533000	0.62120	GAT	.	.		0.308	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		C	96119656	T	C	96119656	3	2	91	1	0	0	0	0	1	0	0	0	5205	1435	50	2	810	2	ERAP1	5	96119656	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	13620184	96119656	84795604	199	12273										
ST8SIA4	7903	hgsc.bcm.edu	37	chr5	100222086	100222086	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgtcaatctcctttccacatTcactgtctaacagaatgcca	4	13	4	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:100222086T>C	ENST00000231461.5	-	3	774	c.464A>G	c.(463-465)gAa>gGa	p.E155G	ST8SIA4_ENST00000451528.2_Missense_Mutation_p.E155G|ST8SIA4_ENST00000507360.2_5'UTR	NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	155					axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		CTTTCCACATTCACTGTCTAA	0.388																																					p.E155G		Atlas-SNP	.											ST8SIA4,colon,carcinoma,0,2	ST8SIA4	77	.	0			c.A464G						.						83	83	83					5																	100222086		2203	4300	6503	SO:0001583	missense	7903	exon3			CCACATTCACTGT	L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532		"Sialyltransferases"	10871	protein-coding gene	gene with protein product	"ST8Sia IV"	602547	"sialyltransferase 8 (alpha-2, 8-polysialytransferase) D"	SIAT8D		7624364	Standard	NM_005668		Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.464A>G	chr5.hg19:g.100222086T>C	ENSP00000231461:p.Glu155Gly	201.0	0.0		169.0	7.0	NM_175052	A8KA07|G3V104|Q8N1F4|Q92693	Missense_Mutation	SNP	ENST00000231461.5	hg19	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	T	5.756	0.323932	0.10900	.	.	ENSG00000113532	ENST00000231461;ENST00000451528	T;T	0.28454	1.61;1.61	5.92	-1.81	0.07882	.	0.400705	0.26761	N	0.022637	T	0.05318	0.0141	N	0.00149	-1.99	0.25427	N	0.988219	B	0.02656	0.0	B	0.01281	0.0	T	0.43410	-0.9393	10	0.02654	T	1	-3.5454	13.1326	0.59391	0.0:0.6687:0.0:0.3313	.	155	Q92187	SIA8D_HUMAN	G	155	ENSP00000231461:E155G;ENSP00000428914:E155G	ENSP00000231461:E155G	E	-	2	0	ST8SIA4	100249985	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	0.871000	0.28023	-0.155000	0.11098	0.455000	0.32223	GAA	.	.		0.388	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668		C	100222086	T	C	100222086	3	2	91	1	0	0	0	0	1	0	0	0	15249	1783	62	2	631	2	ST8SIA4	5	100222086	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4102430	100222086	80693174	200	12274										
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109190938	109190938	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccaatggcaaataagttctCctcacctacccttgagctgc	6	14	2	1	rs3217225|rs200723635	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:109190938C>T	ENST00000261483.4	+	20	4126	c.3074C>T	c.(3073-3075)tCc>tTc	p.S1025F	MAN2A1_ENST00000505313.1_3'UTR	NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	1025					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		AATAAGTTCTCCTCACCTACC	0.403																																					p.S1025F		Atlas-SNP	.											MAN2A1,colon,carcinoma,0,1	MAN2A1	136	.	0			c.C3074T						.						163	117	132					5																	109190938		2202	4295	6497	SO:0001583	missense	4124	exon20			AGTTCTCCTCACC		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.3074C>T	chr5.hg19:g.109190938C>T	ENSP00000261483:p.Ser1025Phe	3.0	0.0		26.0	15.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	C	9.575	1.122145	0.20877	.	.	ENSG00000112893	ENST00000261483	T	0.80738	-1.41	5.07	1.88	0.25563	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	1.184260	0.05825	N	0.616516	T	0.71609	0.3360	L	0.34521	1.04	0.09310	N	1	B	0.10296	0.003	B	0.19666	0.026	T	0.58521	-0.7622	10	0.56958	D	0.05	1.7459	5.1539	0.15025	0.5166:0.3102:0.0:0.1732	.	1025	Q16706	MA2A1_HUMAN	F	1025	ENSP00000261483:S1025F	ENSP00000261483:S1025F	S	+	2	0	MAN2A1	109218837	0.407000	0.25352	0.001000	0.08648	0.007000	0.05969	3.958000	0.56737	0.412000	0.25729	-0.373000	0.07131	TCC	.	.		0.403	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			T	109190938	C	T	109190938	3	4	91	1	0	0	0	0	1	0	0	0	9223	855	30	3	3152	3	MAN2A1	5	109190938	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	8968852	109190938	71724322	201	12275										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112927702	112927702	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttacctacagggattttctAggatgtcttctgagattgga	10	6	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:112927702A>G	ENST00000161863.4	+	28	4252	c.4039A>G	c.(4039-4041)Agg>Ggg	p.R1347G		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1347	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GGGATTTTCTAGGATGTCTTC	0.418																																					p.R1347G		Atlas-SNP	.											.	YTHDC2	118	.	0			c.A4039G						.						47	45	46					5																	112927702		2201	4299	6500	SO:0001583	missense	64848	exon28			TTTTCTAGGATGT	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.4039A>G	chr5.hg19:g.112927702A>G	ENSP00000161863:p.Arg1347Gly	84.0	0.0		87.0	4.0	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	A	19.03	3.748349	0.69533	.	.	ENSG00000047188	ENST00000161863;ENST00000511372	T	0.36157	1.27	5.83	3.3	0.37823	YTH domain (2);	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	M	0.79614	2.46	0.80722	D	1	D	0.57257	0.979	D	0.65233	0.933	T	0.61038	-0.7143	10	0.87932	D	0	.	12.9384	0.58329	0.613:0.387:0.0:0.0	.	1347	Q9H6S0	YTDC2_HUMAN	G	1347;1257	ENSP00000161863:R1347G	ENSP00000161863:R1347G	R	+	1	2	YTHDC2	112955601	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.692000	0.47018	0.399000	0.25367	0.528000	0.53228	AGG	.	.		0.418	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		G	112927702	A	G	112927702	3	3	91	1	0	0	0	0	1	0	0	0	17512	411	15	2	4149	2	YTHDC2	5	112927702	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3736764	112927702	67987558	202	12276										
TIFAB	140947	hgsc.bcm.edu	37	chr5	134785146	134785146	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccaggcaacctggatctgctAccctgaaccagggggaggct	13	13	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:134785146A>G	ENST00000503143.2	-	0	0				TIFAB_ENST00000537858.1_Nonstop_Mutation_p.*162Q|CTB-138E5.1_ENST00000510230.1_RNA	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN								nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGGATCTGCTACCCTGAACCA	0.582																																					p.X162Q		Atlas-SNP	.											.	TIFAB	23	.	0			c.T484C						.						52	55	54					5																	134785146		1890	4117	6007	SO:0001631	upstream_gene_variant	497189	exon2			TCTGCTACCCTGA																													chr5.hg19:g.134785146A>G	Exception_encountered	90.0	0.0		81.0	4.0	NM_001099221		Missense_Mutation	SNP	ENST00000503143.2	hg19	CCDS4186.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.948404	0.00051	.	.	ENSG00000255833	ENST00000537858	.	.	.	5.28	-5.38	0.02673	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.3388	0.07111	0.085:0.2566:0.3544:0.3041	.	.	.	.	Q	162	.	.	X	-	1	0	TIFAB	134813045	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.454000	0.06770	-1.473000	0.01881	-1.525000	0.00928	TAG	.	.		0.582	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1			G	134785146	A	G	134785146	1	3	91	0	1	0	0	0	0	0	0	0	15910	404	14	2		2	TIFAB	5	134785146	5'Flank	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	21857444	134785146	46130114	203	12277										
PKD2L2	27039	hgsc.bcm.edu	37	chr5	137271514	137271514	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaacgcagagcagatgaaaaAatggaaagagaggcttgaga	13	4	0	5			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:137271514A>G	ENST00000508883.1	+	13	1726	c.1700A>G	c.(1699-1701)aAa>aGa	p.K567R	PKD2L2_ENST00000290431.5_Missense_Mutation_p.K567R|PKD2L2_ENST00000502810.1_Missense_Mutation_p.K545R|PKD2L2_ENST00000508638.1_Missense_Mutation_p.K466R|PKD2L2_ENST00000350250.4_Missense_Mutation_p.K533R			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	567					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CAGATGAAAAAATGGAAAGAG	0.388																																					p.K567R		Atlas-SNP	.											.	PKD2L2	68	.	0			c.A1700G						.						77	75	76					5																	137271514		1839	4104	5943	SO:0001583	missense	27039	exon13			TGAAAAAATGGAA	AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"Voltage-gated ion channels / Transient receptor potential cation channels"	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.1700A>G	chr5.hg19:g.137271514A>G	ENSP00000424725:p.Lys567Arg	71.0	0.0		92.0	4.0	NM_014386	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.86	1.469548	0.26423	.	.	ENSG00000078795	ENST00000350250;ENST00000508638;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T;T	0.72835	-0.31;0.21;-0.69;-0.23;-0.24	5.63	3.24	0.37175	.	0.157314	0.44688	N	0.000431	T	0.48333	0.1494	N	0.17474	0.49	0.23282	N	0.997982	B;B;B	0.17038	0.001;0.02;0.011	B;B;B	0.13407	0.002;0.008;0.009	T	0.25745	-1.0123	10	0.25106	T	0.35	-7.9694	5.5578	0.17125	0.7359:0.1739:0.0902:0.0	.	567;466;567	Q9NZM6;E9PC91;Q9NZM6-5	PK2L2_HUMAN;.;.	R	533;466;545;567;567	ENSP00000344177:K533R;ENSP00000423382:K466R;ENSP00000425513:K545R;ENSP00000424725:K567R;ENSP00000290431:K567R	ENSP00000290431:K567R	K	+	2	0	PKD2L2	137299413	0.977000	0.34250	0.980000	0.43619	0.991000	0.79684	1.162000	0.31786	0.505000	0.28104	-0.313000	0.08912	AAA	.	.		0.388	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		G	137271514	A	G	137271514	3	3	91	1	0	0	0	0	1	0	0	0	11977	14	1	2	1750	2	PKD2L2	5	137271514	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2486368	137271514	43643746	204	12278										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140180864	140180864	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcgcagcctcggaggtggggAgcggccagctccactactcc	14	15	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:140180864A>C	ENST00000522353.2	+	1	82	c.82A>C	c.(82-84)Agc>Cgc	p.S28R	PCDHA3_ENST00000532566.2_Missense_Mutation_p.S28R|PCDHA2_ENST00000520672.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	28					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGGTGGGGAGCGGCCAGCT	0.617																																					p.S28R		Atlas-SNP	.											.	PCDHA3	396	.	0			c.A82C						.						57	63	61					5																	140180864		2203	4300	6503	SO:0001583	missense	56145	exon1			GTGGGGAGCGGCC	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.82A>C	chr5.hg19:g.140180864A>C	ENSP00000429808:p.Ser28Arg	83.0	0.0		95.0	4.0	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	hg19	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	a	4.841	0.156425	0.09236	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.54071	0.67;0.59	4.65	3.49	0.39957	Cadherin (1);	0.000000	0.46758	U	0.000274	T	0.56601	0.1996	M	0.91768	3.24	0.20196	N	0.999921	B;B	0.26547	0.152;0.014	B;B	0.28709	0.093;0.031	T	0.57642	-0.7776	10	0.51188	T	0.08	.	4.7933	0.13259	0.6568:0.1611:0.1821:0.0	.	28;28	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	R	28	ENSP00000429808:S28R;ENSP00000434086:S28R	ENSP00000429808:S28R	S	+	1	0	PCDHA3	140161048	0.034000	0.19679	0.986000	0.45419	0.031000	0.12232	1.944000	0.40263	0.758000	0.33059	-0.333000	0.08304	AGC	.	.		0.617	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		C	140180864	A	C	140180864	3	2	91	1	0	0	0	0	1	0	0	0	11534	304	11	5	84	5	PCDHA3	5	140180864	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2909350	140180864	40734396	205	12279										
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140250200	140250200	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttgggcgaccgcgcgctgtcGagctacgtgtcggtgcacgc	16	13	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:140250200G>A	ENST00000398640.2	+	1	1512	c.1512G>A	c.(1510-1512)tcG>tcA	p.S504S	PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	504	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCGCTGTCGAGCTACGTGT	0.692																																					p.S504S		Atlas-SNP	.											.	PCDHA11	209	.	0			c.G1512A						.						61	67	65					5																	140250200		2203	4298	6501	SO:0001819	synonymous_variant	56138	exon1			GCTGTCGAGCTAC	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1512G>A	chr5.hg19:g.140250200G>A		114.0	0.0		142.0	11.0	NM_018902	B2RN58|O75279	Silent	SNP	ENST00000398640.2	hg19	CCDS47284.1																																																																																			.	.		0.692	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		A	140250200	G	A	140250200	2	1	91	1	0	0	0	0	0	0	0	1	11530	1045	37	1		1	PCDHA11	5	140250200	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	69336	140250200	40665060	206	12280										
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140480645	140480645	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cggtattctttgaaaatgaaAtgcatctgaaaatcctagaa	7	6	2	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:140480645A>G	ENST00000231130.2	+	1	412	c.412A>G	c.(412-414)Atg>Gtg	p.M138V	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	138	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGAAAATGAAATGCATCTGAA	0.398																																					p.M138V		Atlas-SNP	.											PCDHB3,colon,carcinoma,-1,1	PCDHB3	208	.	0			c.A412G						.						83	87	86					5																	140480645		2203	4300	6503	SO:0001583	missense	56132	exon1			AATGAAATGCATC	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.412A>G	chr5.hg19:g.140480645A>G	ENSP00000231130:p.Met138Val	65.0	0.0		87.0	4.0	NM_018937	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	hg19	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	A	7.759	0.705025	0.15172	.	.	ENSG00000113205	ENST00000231130	T	0.19105	2.17	5.08	5.08	0.68730	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.18467	0.0443	L	0.35723	1.085	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.09751	-1.0660	9	0.45353	T	0.12	.	10.7425	0.46162	0.8576:0.0:0.0:0.1424	.	138	Q9Y5E6	PCDB3_HUMAN	V	138	ENSP00000231130:M138V	ENSP00000231130:M138V	M	+	1	0	PCDHB3	140460829	0.000000	0.05858	0.998000	0.56505	0.997000	0.91878	-0.490000	0.06482	2.036000	0.60181	0.533000	0.62120	ATG	.	.		0.398	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		G	140480645	A	G	140480645	3	3	91	1	0	0	0	0	1	0	0	0	11552	101	4	2	414	2	PCDHB3	5	140480645	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	230445	140480645	40434615	207	12281										
KIF4B	285643	hgsc.bcm.edu	37	chr5	154394167	154394167	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatcagaaagacagaagaaaAccaaggctgaaggggatcgt	13	6	1	5			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:154394167A>C	ENST00000435029.4	+	1	908	c.748A>C	c.(748-750)Acc>Ccc	p.T250P		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	250	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			ACAGAAGAAAACCAAGGCTGA	0.428																																					p.T250P		Atlas-SNP	.											.	KIF4B	307	.	0			c.A748C						.						111	113	112					5																	154394167		2203	4300	6503	SO:0001583	missense	285643	exon1			AAGAAAACCAAGG	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"Kinesins"	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.748A>C	chr5.hg19:g.154394167A>C	ENSP00000387875:p.Thr250Pro	227.0	0.0		269.0	19.0	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	hg19	CCDS47324.1	.	.	.	.	.	.	.	.	.	.	a	16.48	3.134160	0.56828	.	.	ENSG00000226650	ENST00000435029	T	0.77489	-1.1	1.73	1.73	0.24493	Kinesin, motor domain (5);	.	.	.	.	D	0.89694	0.6789	H	0.95850	3.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88917	0.3363	9	0.87932	D	0	.	7.4446	0.27203	1.0:0.0:0.0:0.0	.	250	Q2VIQ3	KIF4B_HUMAN	P	250	ENSP00000387875:T250P	ENSP00000387875:T250P	T	+	1	0	KIF4B	154374360	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.389000	0.59639	1.070000	0.40811	0.533000	0.62120	ACC	.	.		0.428	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			C	154394167	A	C	154394167	3	2	91	1	0	0	0	0	1	0	0	0	8313	43	2	5	750	5	KIF4B	5	154394167	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	13913522	154394167	26521093	208	12282										
HAVCR1	26762	hgsc.bcm.edu	37	chr5	156479571	156479571	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gttgtcgttggaacagtcgtCattggaacagtcgttgtcgt	13	7	1	0	rs6149307|rs386693994|rs183130208|rs141023871	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:156479571C>T	ENST00000339252.3	-	3	1006	c.474G>A	c.(472-474)atG>atA	p.M158I	HAVCR1_ENST00000523175.1_Missense_Mutation_p.M158I|HAVCR1_ENST00000425854.1_Missense_Mutation_p.M158I|HAVCR1_ENST00000522693.1_Missense_Mutation_p.M158I|HAVCR1_ENST00000544197.1_Missense_Mutation_p.M158I	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)			endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GAACAGTCGTCATTGGAACAG	0.488																																					p.M158I		Atlas-SNP	.											.	HAVCR1	84	.	0			c.G474A						.						413	302	340					5																	156479571		2079	3991	6070	SO:0001583	missense	26762	exon4			AGTCGTCATTGGA	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"Immunoglobulin superfamily / V-set domain containing"	17866	protein-coding gene	gene with protein product	"T-cell immunoglobulin mucin family member 1"	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.474G>A	chr5.hg19:g.156479571C>T	ENSP00000344844:p.Met158Ile	8.0	0.0		339.0	38.0	NM_001099414	O43656	Missense_Mutation	SNP	ENST00000339252.3	hg19	CCDS43392.1	.	.	.	.	.	.	.	.	.	.	C	2.575	-0.298775	0.05532	.	.	ENSG00000113249	ENST00000522693;ENST00000523175;ENST00000339252;ENST00000425854;ENST00000544197;ENST00000518745	T;T;T;T;T;T	0.13901	2.55;2.6;2.6;2.55;2.6;2.57	1.56	-3.12	0.05282	.	.	.	.	.	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.31392	-0.9945	7	0.62326	D	0.03	.	0.1239	0.00067	0.2901:0.1916:0.1631:0.3551	.	.	.	.	I	158	ENSP00000428524:M158I;ENSP00000427898:M158I;ENSP00000344844:M158I;ENSP00000403333:M158I;ENSP00000440258:M158I;ENSP00000428422:M158I	ENSP00000344844:M158I	M	-	3	0	HAVCR1	156412149	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.878000	0.28126	-1.479000	0.01867	-0.507000	0.04495	ATG	.	.		0.488	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1			T	156479571	C	T	156479571	3	4	91	1	0	0	0	0	1	0	0	0	6982	826	29	3	644	3	HAVCR1	5	156479571	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2085404	156479571	24435689	209	12283										
ADRA1B	147	hgsc.bcm.edu	37	chr5	159399016	159399016	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagttcaagcgcgctttcgtGcgcatcctcgggtgccagtg	14	12	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:159399016G>A	ENST00000306675.3	+	2	1203	c.1080G>A	c.(1078-1080)gtG>gtA	p.V360V		NM_000679.3	NP_000670.1	P35368	ADA1B_HUMAN	adrenoceptor alpha 1B	360					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|adult heart development (GO:0007512)|behavioral response to cocaine (GO:0048148)|blood vessel remodeling (GO:0001974)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|multicellular organismal development (GO:0007275)|negative regulation of glycogen catabolic process (GO:0045818)|organ growth (GO:0035265)|positive regulation of glycogen catabolic process (GO:0045819)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of the force of heart contraction by epinephrine-norepinephrine (GO:0001997)|regulation of cardiac muscle contraction (GO:0055117)|regulation of vasoconstriction (GO:0019229)|response to amphetamine (GO:0001975)|response to morphine (GO:0043278)|vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure (GO:0001987)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)|protein heterodimerization activity (GO:0046982)			endometrium(3)|large_intestine(6)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acepromazine(DB01614)|Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Dapiprazole(DB00298)|Desipramine(DB01151)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Ziprasidone(DB00246)	GCGCTTTCGTGCGCATCCTCG	0.697																																					p.V360V		Atlas-SNP	.											.	ADRA1B	39	.	0			c.G1080A						.						19	20	20					5																	159399016		2199	4291	6490	SO:0001819	synonymous_variant	147	exon2			TTTCGTGCGCATC	L31773	CCDS4347.1	5q33.3	2012-08-08	2012-05-09		ENSG00000170214	ENSG00000170214		"GPCR / Class A : Adrenoceptors : alpha"	278	protein-coding gene	gene with protein product		104220	"adrenergic, alpha-1B-, receptor"				Standard	XM_005265818		Approved		uc003lxt.1	P35368	OTTHUMG00000130327	ENST00000306675.3:c.1080G>A	chr5.hg19:g.159399016G>A		83.0	0.0		89.0	4.0	NM_000679	B0LPE1	Silent	SNP	ENST00000306675.3	hg19	CCDS4347.1																																																																																			.	.		0.697	ADRA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252676.1			A	159399016	G	A	159399016	2	1	91	1	0	0	0	0	0	0	0	1	335	1306	46	3		3	ADRA1B	5	159399016	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	2919445	159399016	21516244	210	12284										
HK3	3101	hgsc.bcm.edu	37	chr5	176314004	176314004	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctcttggccctccctcaccTggtctaggccaagctgccta	8	17	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:176314004T>C	ENST00000292432.5	-	13	1947	c.1856A>G	c.(1855-1857)cAg>cGg	p.Q619R		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	619	Catalytic.|Glucose-binding. {ECO:0000255}.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCCCTCACCTGGTCTAGGCC	0.622																																					p.Q619R		Atlas-SNP	.											.	HK3	210	.	0			c.A1856G						.						55	48	50					5																	176314004		2203	4300	6503	SO:0001630	splice_region_variant	3101	exon13			CTCACCTGGTCTA		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1857+1A>G	chr5.hg19:g.176314004T>C		52.0	0.0		72.0	4.0	NM_002115	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	hg19	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.328492	0.41197	.	.	ENSG00000160883	ENST00000292432	D	0.98914	-5.23	5.0	5.0	0.66597	Hexokinase, conserved site (1);Hexokinase, N-terminal (1);	0.000000	0.51477	D	0.000096	D	0.95853	0.8650	N	0.11255	0.115	0.38068	D	0.936293	B	0.25719	0.132	B	0.34931	0.192	D	0.95163	0.8283	10	0.51188	T	0.08	-15.0804	14.6863	0.69052	0.0:0.0:0.0:1.0	.	619	P52790	HXK3_HUMAN	R	619	ENSP00000292432:Q619R	ENSP00000292432:Q619R	Q	-	2	0	HK3	176246610	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	2.609000	0.46317	1.880000	0.54463	0.454000	0.30748	CAG	.	.		0.622	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		Missense_Mutation	C	176314004	T	C	176314004	5	2	91	1	0	0	0	0	0	0	1	0	7201	1594	55	2	943	2	HK3	5	176314004	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	16914988	176314004	4601256	211	12285										
FGFR4	2264	hgsc.bcm.edu	37	chr5	176520392	176520392	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctccagcaggcagaaccaagTctcccactttgcagttctcc	7	16	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:176520392T>C	ENST00000292408.4	+	10	1496				FGFR4_ENST00000292410.3_Missense_Mutation_p.S373P|FGFR4_ENST00000393648.2_Intron|FGFR4_ENST00000393637.1_Missense_Mutation_p.S373P|FGFR4_ENST00000502906.1_Intron	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4						alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	CAGAACCAAGTCTCCCACTTT	0.627										TSP Lung(9;0.080)																											p.S373P		Atlas-SNP	.											.	FGFR4	174	.	0			c.T1117C						.						78	80	80					5																	176520392		2203	4300	6503	SO:0001627	intron_variant	2264	exon8			ACCAAGTCTCCCA	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1252-15T>C	chr5.hg19:g.176520392T>C		113.0	0.0		166.0	7.0	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	T	8.471	0.857541	0.17106	.	.	ENSG00000160867	ENST00000292410;ENST00000393637	T;T	0.78816	-1.21;-1.21	4.76	-2.17	0.07059	.	.	.	.	.	T	0.52025	0.1709	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29458	-1.0011	9	0.27082	T	0.32	.	5.301	0.15778	0.0:0.382:0.1581:0.4599	.	373	P22455-2	.	P	373	ENSP00000292410:S373P;ENSP00000377254:S373P	ENSP00000292410:S373P	S	+	1	0	FGFR4	176452998	0.008000	0.16893	0.001000	0.08648	0.671000	0.39405	0.419000	0.21247	-0.545000	0.06224	-0.451000	0.05528	TCT	.	.		0.627	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			C	176520392	T	C	176520392	1	2	91	0	1	0	0	0	0	0	0	0	5876	1667	58	2		2	FGFR4	5	176520392	Intron	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	206388	176520392	4394868	212	12286										
CDYL	9425	hgsc.bcm.edu	37	chr6	4892284	4892284	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgccagccagaagttcaggaAgaacacagctccatctctct	8	13	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:4892284A>G	ENST00000328908.5	+	4	655	c.524A>G	c.(523-525)aAg>aGg	p.K175R	CDYL_ENST00000472453.1_Intron|CDYL_ENST00000397588.3_Missense_Mutation_p.K121R|CDYL_ENST00000449732.2_5'UTR|CDYL_ENST00000343762.5_5'UTR			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	175	Interaction with EZH2.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		AAGTTCAGGAAGAACACAGCT	0.507																																					p.K121R		Atlas-SNP	.											.	CDYL	74	.	0			c.A362G						.						89	93	91					6																	4892284		2203	4300	6503	SO:0001583	missense	9425	exon2			TCAGGAAGAACAC	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"CDY-like, autosomal", "testis-specific chromodomain Y-like protein"	603778	"chromodomain protein, Y chromosome-like"			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.524A>G	chr6.hg19:g.4892284A>G	ENSP00000330512:p.Lys175Arg	87.0	0.0		92.0	4.0	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	hg19		.	.	.	.	.	.	.	.	.	.	A	10.15	1.269882	0.23221	.	.	ENSG00000153046	ENST00000328908;ENST00000397588	T;T	0.55588	0.89;0.51	5.79	2.02	0.26589	.	2.341570	0.01986	N	0.045182	T	0.18173	0.0436	N	0.21448	0.665	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.001	T	0.24799	-1.0150	10	0.28530	T	0.3	.	4.2753	0.10806	0.6459:0.0:0.2176:0.1365	.	121;175	Q9Y232-2;Q9Y232	.;CDYL1_HUMAN	R	175;121	ENSP00000330512:K175R;ENSP00000380718:K121R	ENSP00000330512:K175R	K	+	2	0	CDYL	4837283	1.000000	0.71417	0.975000	0.42487	0.993000	0.82548	2.489000	0.45285	0.107000	0.17824	0.528000	0.53228	AAG	.	.		0.507	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		G	4892284	A	G	4892284	3	3	91	1	0	0	0	0	1	0	0	0	3187	72	3	2	368	2	CDYL	6	4892284	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10		4892284	166222783	213	12287										
RIOK1	83732	hgsc.bcm.edu	37	chr6	7393524	7393524	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggttatgtctggaatggaggAagcaacccacaggtatttta	12	6	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:7393524A>G	ENST00000379834.2	+	2	771	c.264A>G	c.(262-264)ggA>ggG	p.G88G		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	88							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					GGAATGGAGGAAGCAACCCAC	0.408																																					p.G88G		Atlas-SNP	.											.	RIOK1	36	.	0			c.A264G						.						132	124	126					6																	7393524		2203	4300	6503	SO:0001819	synonymous_variant	83732	exon2			TGGAGGAAGCAAC	BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"RIO kinase 1 (yeast)"				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.264A>G	chr6.hg19:g.7393524A>G		133.0	0.0		141.0	8.0	NM_031480	B2RB28|Q8NDC8|Q96NV9	Silent	SNP	ENST00000379834.2	hg19	CCDS4500.1																																																																																			.	.		0.408	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480		G	7393524	A	G	7393524	2	3	91	1	0	0	0	0	0	0	0	1	13392	233	9	2		2	RIOK1	6	7393524	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2501240	7393524	163721543	214	12288										
DSP	1832	hgsc.bcm.edu	37	chr6	7581098	7581098	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aggaccaggatatcacgcggTtccagaactctctgaaagag	11	10	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:7581098T>C	ENST00000379802.3	+	23	5016	c.4675T>C	c.(4675-4677)Ttc>Ctc	p.F1559L	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1559	Central fibrous rod domain.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		TATCACGCGGTTCCAGAACTC	0.522																																					p.F1559L		Atlas-SNP	.											.	DSP	306	.	0			c.T4675C						.						76	81	79					6																	7581098		2203	4300	6503	SO:0001583	missense	1832	exon23			ACGCGGTTCCAGA	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.4675T>C	chr6.hg19:g.7581098T>C	ENSP00000369129:p.Phe1559Leu	82.0	0.0		99.0	4.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	T	0.104	-1.147277	0.01714	.	.	ENSG00000096696	ENST00000379802	T	0.65178	-0.14	5.58	3.05	0.35203	.	0.189188	0.37955	N	0.001865	T	0.07234	0.0183	N	0.00801	-1.175	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42361	-0.9456	10	0.02654	T	1	.	3.6866	0.08331	0.2897:0.1438:0.0:0.5665	.	1559	P15924	DESP_HUMAN	L	1559	ENSP00000369129:F1559L	ENSP00000369129:F1559L	F	+	1	0	DSP	7526097	0.647000	0.27304	0.570000	0.28473	0.572000	0.35998	1.153000	0.31676	0.337000	0.23665	0.533000	0.62120	TTC	.	.		0.522	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		C	7581098	T	C	7581098	3	2	91	1	0	0	0	0	1	0	0	0	4783	1725	60	2	4765	2	DSP	6	7581098	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	187574	7581098	163533969	215	12289										
DSP	1832	hgsc.bcm.edu	37	chr6	7585893	7585893	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggtagaagatatcactgggCtgcgccttctggaagccgcc	13	11	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:7585893C>T	ENST00000379802.3	+	24	8739	c.8398C>T	c.(8398-8400)Ctg>Ttg	p.L2800L	DSP_ENST00000418664.2_Silent_p.L2201L	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2800	4.5 X 38 AA tandem repeats (Domain C).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		TATCACTGGGCTGCGCCTTCT	0.552																																					p.L2800L		Atlas-SNP	.											.	DSP	306	.	0			c.C8398T						.						130	147	141					6																	7585893		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon24			ACTGGGCTGCGCC	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.8398C>T	chr6.hg19:g.7585893C>T		66.0	0.0		95.0	4.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.552	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7585893	C	T	7585893	2	4	91	1	0	0	0	0	0	0	0	1	4783	796	28	3		3	DSP	6	7585893	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	4795	7585893	163529174	216	12290										
ERVFRDE1	405754	hgsc.bcm.edu	37	chr6	11104838	11104838	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttattttcccaaaaaagagAatttcgagtttggtccaata	6	6	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:11104838A>G	ENST00000472091.1	-	2	1081	c.706T>C	c.(706-708)Tct>Cct	p.S236P	ERVFRD-1_ENST00000542862.1_Missense_Mutation_p.S236P|SMIM13_ENST00000416247.2_Intron	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	236					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						caaaaaagagaatttcgagtt	0.468																																					p.S236P		Atlas-SNP	.											.	ERVFRD-1	41	.	0			c.T706C						.						29	32	31					6																	11104838		2203	4300	6503	SO:0001583	missense	405754	exon2			AAAGAGAATTTCG	AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.706T>C	chr6.hg19:g.11104838A>G	ENSP00000420174:p.Ser236Pro	57.0	0.0		91.0	4.0	NM_207582		Missense_Mutation	SNP	ENST00000472091.1	hg19	CCDS4519.1	.	.	.	.	.	.	.	.	.	.	A	13.63	2.295281	0.40594	.	.	ENSG00000244476	ENST00000472091;ENST00000542862	T;T	0.14516	2.5;2.5	0.225	0.225	0.15325	.	.	.	.	.	T	0.02649	0.0080	N	0.22421	0.69	0.20926	N	0.99982	B	0.10296	0.003	B	0.18263	0.021	T	0.45011	-0.9290	8	0.45353	T	0.12	.	.	.	.	.	236	P60508	EFRD1_HUMAN	P	236	ENSP00000420174:S236P;ENSP00000444461:S236P	ENSP00000420174:S236P	S	-	1	0	ERVFRD-1	11212824	0.973000	0.33851	0.891000	0.34965	0.891000	0.51852	0.349000	0.20055	0.257000	0.21650	0.254000	0.18369	TCT	.	.		0.468	ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353776.1	NM_207582		G	11104838	A	G	11104838	3	3	91	1	0	0	0	0	1	0	0	0	5248	246	9	2	914	2	ERVFRDE1	6	11104838	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3518945	11104838	160010229	217	12291										
EDN1	1906	hgsc.bcm.edu	37	chr6	12296284	12296284	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agagcgttatgtgacccacaAccgagcacattggtgacaga	11	10	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:12296284A>G	ENST00000379375.5	+	5	890	c.623A>G	c.(622-624)aAc>aGc	p.N208S		NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	208					artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				GTGACCCACAACCGAGCACAT	0.547																																					p.N208S		Atlas-SNP	.											.	EDN1	23	.	0			c.A623G						.						131	122	125					6																	12296284		2203	4300	6503	SO:0001583	missense	1906	exon5			CCCACAACCGAGC	S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401		"Endogenous ligands"	3176	protein-coding gene	gene with protein product		131240					Standard	NM_001168319		Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.623A>G	chr6.hg19:g.12296284A>G	ENSP00000368683:p.Asn208Ser	86.0	0.0		109.0	5.0	NM_001955	Q96DA1	Missense_Mutation	SNP	ENST00000379375.5	hg19	CCDS4522.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.035233	0.35893	.	.	ENSG00000078401	ENST00000379375	D	0.85088	-1.94	5.93	5.93	0.95920	.	0.258675	0.45126	D	0.000381	D	0.86024	0.5834	L	0.35854	1.095	0.41107	D	0.985715	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	D	0.87471	0.2414	10	0.51188	T	0.08	-3.2364	14.9508	0.71071	1.0:0.0:0.0:0.0	.	208;208	Q6FH53;P05305	.;EDN1_HUMAN	S	208	ENSP00000368683:N208S	ENSP00000368683:N208S	N	+	2	0	EDN1	12404270	1.000000	0.71417	1.000000	0.80357	0.340000	0.28889	5.705000	0.68355	2.271000	0.75665	0.533000	0.62120	AAC	.	.		0.547	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039872.1	NM_001955		G	12296284	A	G	12296284	3	3	91	1	0	0	0	0	1	0	0	0	4918	43	2	2	641	2	EDN1	6	12296284	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1191446	12296284	158818783	218	12292										
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156943	26156943	+	Nonsense_Mutation	SNP	A	A	T													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgggttccttcaaactcaacAagaaggcggcctctggggaa							TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:26156943A>T	ENST00000304218.3	+	1	385	c.325A>T	c.(325-327)Aag>Tag	p.K109*	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	109	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						CAAACTCAACAAGAAGGCGGC	0.617																																					p.K109X		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.A325T						.						33	40	38					6																	26156943		2203	4300	6503	SO:0001587	stop_gained	3008	exon1			CTCAACAAGAAGG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"Histones / Replication-dependent"	4718	protein-coding gene	gene with protein product		142220	"H1 histone family, member 4", "histone 1, H1e"	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.325A>T	chr6.hg19:g.26156943A>T	ENSP00000307705:p.Lys109*	119.0	0.0		141.0	52.0	NM_005321	Q4VB25	Nonsense_Mutation	SNP	ENST00000304218.3	hg19	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	35	5.588280	0.96590	.	.	ENSG00000168298	ENST00000304218	.	.	.	5.35	5.35	0.76521	.	0.105304	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2553	14.7974	0.69886	1.0:0.0:0.0:0.0	.	.	.	.	X	109	.	ENSP00000307705:K109X	K	+	1	0	HIST1H1E	26264922	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.448000	0.80631	2.146000	0.66826	0.459000	0.35465	AAG	.	.		0.617	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		T	26156943	A	T	26156943	4	4	91	1	0	0	0	0	0	1	0	0	7135	131	5	4	327	4	HIST1H1E	6	26156943	Nonsense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	13860659	26156943	144958124	219	12293	51	2								
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156946	26156946	+	Nonsense_Mutation	SNP	A	A	T													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gttccttcaaactcaacaagAaggcggcctctggggaagcc							TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:26156946A>T	ENST00000304218.3	+	1	388	c.328A>T	c.(328-330)Aag>Tag	p.K110*	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	110					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						ACTCAACAAGAAGGCGGCCTC	0.627																																					p.K110X		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.A328T						.						33	39	37					6																	26156946		2203	4300	6503	SO:0001587	stop_gained	3008	exon1			AACAAGAAGGCGG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"Histones / Replication-dependent"	4718	protein-coding gene	gene with protein product		142220	"H1 histone family, member 4", "histone 1, H1e"	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.328A>T	chr6.hg19:g.26156946A>T	ENSP00000307705:p.Lys110*	110.0	0.0		146.0	55.0	NM_005321	Q4VB25	Nonsense_Mutation	SNP	ENST00000304218.3	hg19	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	35	5.574334	0.96553	.	.	ENSG00000168298	ENST00000304218	.	.	.	5.35	5.35	0.76521	.	0.152047	0.41194	D	0.000922	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.1063	14.7974	0.69886	1.0:0.0:0.0:0.0	.	.	.	.	X	110	.	ENSP00000307705:K110X	K	+	1	0	HIST1H1E	26264925	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	6.134000	0.71689	2.146000	0.66826	0.459000	0.35465	AAG	.	.		0.627	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		T	26156946	A	T	26156946	4	4	91	1	0	0	0	0	0	1	0	0	7135	247	9	4	330	4	HIST1H1E	6	26156946	Nonsense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3	26156946	144958121	220	12294	51	2								
TRIM39	56658	hgsc.bcm.edu	37	chr6	30297109	30297109	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taaattatggcagagacaagTctgttagaggctggggcctc	13	7	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:30297109T>C	ENST00000396547.1	+	2	175	c.15T>C	c.(13-15)agT>agC	p.S5S	HCG18_ENST00000454269.1_RNA|HCG18_ENST00000454129.1_RNA|TRIM39_ENST00000376656.4_Silent_p.S5S|HCG18_ENST00000444126.1_RNA|TRIM39-RPP21_ENST00000513556.1_5'Flank|TRIM39_ENST00000540416.1_Silent_p.S5S|TRIM39_ENST00000376659.5_Silent_p.S5S|HCG18_ENST00000412685.2_RNA|TRIM39_ENST00000396548.1_Silent_p.S5S|HCG18_ENST00000413358.2_RNA|HCG18_ENST00000602290.1_RNA|HCG18_ENST00000449544.1_RNA|HCG18_ENST00000426882.1_RNA|HCG18_ENST00000438412.1_RNA|HCG18_ENST00000602550.1_RNA|TRIM39_ENST00000396551.3_Silent_p.S5S			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	5					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						CAGAGACAAGTCTGTTAGAGG	0.453																																					p.S5S		Atlas-SNP	.											.	TRIM39	56	.	0			c.T15C						.						134	175	160					6																	30297109		1508	2707	4215	SO:0001819	synonymous_variant	56658	exon3			GACAAGTCTGTTA	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10065	protein-coding gene	gene with protein product		605700	"ring finger protein 23", "tripartite motif-containing 39"	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.15T>C	chr6.hg19:g.30297109T>C		63.0	0.0		75.0	4.0	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Silent	SNP	ENST00000396547.1	hg19	CCDS34377.1																																																																																			.	.		0.453	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016		C	30297109	T	C	30297109	2	2	91	1	0	0	0	0	0	0	0	1	16528	1664	58	2		2	TRIM39	6	30297109	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4140163	30297109	140817958	221	12295										
ABCF1	23	hgsc.bcm.edu	37	chr6	30550931	30550931	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccaggcggagatgtcctcccGccaagccatgttagaaaatg	11	12	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:30550931G>A	ENST00000326195.8	+	10	993	c.881G>A	c.(880-882)cGc>cAc	p.R294H	MIR877_ENST00000401282.1_RNA|ABCF1_ENST00000376545.3_Missense_Mutation_p.R256H|ABCF1_ENST00000396515.4_Intron	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	294					inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						ATGTCCTCCCGCCAAGCCATG	0.512																																					p.R294H		Atlas-SNP	.											.	ABCF1	61	.	0			c.G881A						.						94	100	98					6																	30550931		1510	2708	4218	SO:0001583	missense	23	exon10			CCTCCCGCCAAGC	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"ATP binding cassette transporters / subfamily F"	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.881G>A	chr6.hg19:g.30550931G>A	ENSP00000313603:p.Arg294His	77.0	0.0		89.0	4.0	NM_001025091	A2BF75|O14897|Q69YP6	Missense_Mutation	SNP	ENST00000326195.8	hg19	CCDS34380.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.429787	0.83776	.	.	ENSG00000204574	ENST00000326195;ENST00000376545;ENST00000455943;ENST00000441867	T;T;T	0.53857	0.6;0.94;0.79	5.41	4.55	0.56014	.	0.057428	0.64402	D	0.000001	T	0.55986	0.1955	L	0.59436	1.845	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.64877	0.93;0.93;0.93	T	0.59553	-0.7433	10	0.48119	T	0.1	-9.7828	12.9326	0.58294	0.0798:0.0:0.9202:0.0	.	256;294;294	Q2L6I2;Q8NE71;A2BF75	.;ABCF1_HUMAN;.	H	294;256;295;295	ENSP00000313603:R294H;ENSP00000365728:R256H;ENSP00000405512:R295H	ENSP00000313603:R294H	R	+	2	0	ABCF1	30658910	1.000000	0.71417	0.994000	0.49952	0.960000	0.62799	8.704000	0.91351	1.301000	0.44836	0.313000	0.20887	CGC	.	.		0.512	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			A	30550931	G	A	30550931	3	1	91	1	0	0	0	0	1	0	0	0	65	1087	38	1	919	1	ABCF1	6	30550931	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	253822	30550931	140564136	222	12296										
FLOT1	8870	hgsc.bcm.edu	37	chr6	30709964	30709964	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttgggccacaagtgaaaaaCatggttcaggctggagctgg	14	7	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:30709964C>T	ENST00000259874.5	-	0	1244				FLOT1_ENST00000456573.2_Start_Codon_SNP_p.M1I|XXbac-BPG252P9.10_ENST00000607333.1_RNA|FLOT1_ENST00000376389.3_Start_Codon_SNP_p.M1I|FLOT1_ENST00000470643.1_5'UTR	NM_003897.3	NP_003888.2	P46695	IEX1_HUMAN	immediate early response 3						anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glycolytic process (GO:0045820)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|negative regulation of systemic arterial blood pressure (GO:0003085)|positive regulation of protein catabolic process (GO:0045732)|regulation of DNA repair (GO:0006282)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of response to DNA damage stimulus (GO:2001020)|response to protozoan (GO:0001562)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)	1						AAGTGAAAAACATGGTTCAGG	0.597																																					p.M1I		Atlas-SNP	.											.	FLOT1	28	.	0			c.G3A						.						157	148	151					6																	30709964		1511	2709	4220	SO:0001628	intergenic_variant	10211	exon2			GAAAAACATGGTT	AF083421	CCDS4689.1	6p21.3	2010-02-17			ENSG00000137331	ENSG00000137331			5392	protein-coding gene	gene with protein product		602996				8603392, 9703517	Standard	NM_003897		Approved	IEX-1, DIF-2, PRG1, IEX-1L	uc003nrn.3	P46695	OTTHUMG00000031265		chr6.hg19:g.30709964C>T		72.0	0.0		93.0	4.0	NM_005803	Q5SU30|Q92691|Q93044	Missense_Mutation	SNP	ENST00000259874.5	hg19	CCDS4689.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.52|17.52	3.410420|3.410420	0.62399|0.62399	.|.	.|.	ENSG00000137312|ENSG00000137312	ENST00000418160|ENST00000376389;ENST00000456573;ENST00000438162;ENST00000445853;ENST00000416018;ENST00000454845	.|D;T;D;D;D;D	.|0.97352	.|-3.41;1.52;-3.8;-3.8;-4.35;-4.27	4.41|4.41	4.41|4.41	0.53225|0.53225	.|.	.|0.045756	.|0.85682	.|D	.|0.000000	D|D	0.92951|0.92951	0.7757|0.7757	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|B;B	.|0.24533	.|0.105;0.101	.|B;B	.|0.20955	.|0.032;0.02	D|D	0.92161|0.92161	0.5736|0.5736	5|9	0.87932|0.56958	D|D	0|0.05	0.6111|0.6111	14.8798|14.8798	0.70522|0.70522	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1;1	.|B4DVY7;O75955	.|.;FLOT1_HUMAN	Y|I	50|1	.|ENSP00000365569:M1I;ENSP00000394375:M1I;ENSP00000400615:M1I;ENSP00000398834:M1I;ENSP00000412058:M1I;ENSP00000391341:M1I	ENSP00000404300:C50Y|ENSP00000365569:M1I	C|M	-|-	2|3	0|0	FLOT1|FLOT1	30817943|30817943	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.651000|0.651000	0.38670|0.38670	6.264000|6.264000	0.72527|0.72527	2.435000|2.435000	0.82474|0.82474	0.462000|0.462000	0.41574|0.41574	TGT|ATG	.	.		0.597	IER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076578.2			T	30709964	C	T	30709964	1	4	91	0	1	0	0	0	0	0	0	0	5944	478	17	3		3	FLOT1	6	30709964	IGR	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	159033	30709964	140405103	223	12297										
BAT2	7916	hgsc.bcm.edu	37	chr6	31599743	31599743	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttcagagtatgaggaaatccCcaagcggcgccggcagcggg	15	11	1	2	rs545938957		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:31599743C>T	ENST00000376033.2	+	16	3527	c.3293C>T	c.(3292-3294)cCc>cTc	p.P1098L	PRRC2A_ENST00000376007.4_Missense_Mutation_p.P1098L	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1098	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GAGGAAATCCCCAAGCGGCGC	0.647																																					p.P1098L		Atlas-SNP	.											.	PRRC2A	152	.	0			c.C3293T						.						35	46	42					6																	31599743		1507	2708	4215	SO:0001583	missense	7916	exon16			AAATCCCCAAGCG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3293C>T	chr6.hg19:g.31599743C>T	ENSP00000365201:p.Pro1098Leu	50.0	0.0		74.0	4.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	hg19	CCDS4708.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.28|13.28	2.188734|2.188734	0.38609|0.38609	.|.	.|.	ENSG00000204469|ENSG00000204469	ENST00000376007;ENST00000376033;ENST00000376010|ENST00000424184;ENST00000435052	T;T|.	0.33438|.	1.41;1.41|.	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	0.000000|0.000000	0.52532|0.52532	D|D	0.000075|0.000075	T|T	0.67031|0.67031	0.2850|0.2850	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	T|T	0.70894|0.70894	-0.4748|-0.4748	10|7	0.87932|0.87932	D|D	0|0	-8.8398|-8.8398	16.9681|16.9681	0.86291|0.86291	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1098|.	P48634|.	PRC2A_HUMAN|.	L|S	1098;1098;323|1097;1086	ENSP00000365175:P1098L;ENSP00000365201:P1098L|.	ENSP00000365175:P1098L|ENSP00000407986:P1097S	P|P	+|+	2|1	0|0	PRRC2A|PRRC2A	31707722|31707722	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	7.314000|7.314000	0.78988|0.78988	2.562000|2.562000	0.86427|0.86427	0.655000|0.655000	0.94253|0.94253	CCC|CCA	.	.		0.647	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		T	31599743	C	T	31599743	3	4	91	1	0	0	0	0	1	0	0	0	1319	623	22	3	3351	3	BAT2	6	31599743	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	889779	31599743	139515324	224	12298										
APOM	55937	hgsc.bcm.edu	37	chr6	31623826	31623826	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccagtgccctgagcacagtcAactgacaactctgggcgtgg	12	13	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:31623826A>C	ENST00000375916.3	+	1	579	c.83A>C	c.(82-84)cAa>cCa	p.Q28P	C6orf47-AS1_ENST00000422049.1_RNA|APOM_ENST00000375918.2_Intron|APOM_ENST00000375920.4_Intron	NM_019101.2	NP_061974.2	O95445	APOM_HUMAN	apolipoprotein M	28				MFHQIWAALLYFYGIILNSIYQCPEHSQLTTLGVDGKE -> RFPDSIWGSRSDTSGSPQVPKLYFCGARRESPQPQT (in Ref. 3; AAF29014). {ECO:0000305}.	cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein metabolic process (GO:0042157)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|response to glucose (GO:0009749)|reverse cholesterol transport (GO:0043691)	discoidal high-density lipoprotein particle (GO:0034365)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|lipid transporter activity (GO:0005319)|phospholipid binding (GO:0005543)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(1)	7						GAGCACAGTCAACTGACAACT	0.532																																					p.Q28P	Colon(39;129 858 13764 41453 42617)	Atlas-SNP	.											.	APOM	12	.	0			c.A83C						.						63	41	49					6																	31623826		1510	2709	4219	SO:0001583	missense	55937	exon1			ACAGTCAACTGAC	AJ245434	CCDS4710.1, CCDS59004.1	6p21	2014-01-22			ENSG00000204444	ENSG00000204444		"Apolipoproteins", "Lipocalins"	13916	protein-coding gene	gene with protein product		606907				10531326, 11418126	Standard	NM_019101		Approved	ApoM, G3a, NG20	uc003nvl.3	O95445	OTTHUMG00000031250	ENST00000375916.3:c.83A>C	chr6.hg19:g.31623826A>C	ENSP00000365081:p.Gln28Pro	158.0	0.0		208.0	41.0	NM_019101	B0UX98|Q5SRP4|Q9P046|Q9UMP6	Missense_Mutation	SNP	ENST00000375916.3	hg19	CCDS4710.1	.	.	.	.	.	.	.	.	.	.	A	11.16	1.557628	0.27827	.	.	ENSG00000204444	ENST00000375916	.	.	.	5.34	-2.35	0.06684	.	0.279884	0.30085	N	0.010446	T	0.09069	0.0224	N	0.20401	0.57	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32025	-0.9922	9	0.41790	T	0.15	-12.5912	8.4387	0.32801	0.3283:0.5869:0.0848:0.0	.	28	O95445	APOM_HUMAN	P	28	.	ENSP00000365081:Q28P	Q	+	2	0	APOM	31731805	0.021000	0.18746	0.461000	0.27105	0.905000	0.53344	0.040000	0.13905	-0.253000	0.09514	0.402000	0.26972	CAA	.	.		0.532	APOM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076527.3	NM_019101		C	31623826	A	C	31623826	3	2	91	1	0	0	0	0	1	0	0	0	812	130	5	5	85	5	APOM	6	31623826	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	24083	31623826	139491241	225	12299										
DAAM2	23500	hgsc.bcm.edu	37	chr6	39869662	39869662	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgcaggcagctcgctggaggAgggaggagagttcgatgacc	18	8	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:39869662A>G	ENST00000398904.2	+	25	3238	c.3056A>G	c.(3055-3057)gAg>gGg	p.E1019G	DAAM2_ENST00000538976.1_Missense_Mutation_p.E1018G|RP11-61I13.3_ENST00000437947.1_RNA|DAAM2_ENST00000274867.4_Missense_Mutation_p.E1019G			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	1019	DAD. {ECO:0000255|PROSITE- ProRule:PRU00577}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					TCGCTGGAGGAGGGAGGAGAG	0.647																																					p.E1019G		Atlas-SNP	.											.	DAAM2	101	.	0			c.A3056G						.						32	41	38					6																	39869662		2109	4231	6340	SO:0001583	missense	23500	exon25			TGGAGGAGGGAGG	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.3056A>G	chr6.hg19:g.39869662A>G	ENSP00000381876:p.Glu1019Gly	26.0	0.0		66.0	11.0	NM_001201427	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.290024	0.59976	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.80824	-1.42;-1.42;-1.41	5.64	5.64	0.86602	Actin-binding FH2/DRF autoregulatory (1);Diaphanous autoregulatory (1);	0.068023	0.64402	D	0.000010	T	0.69242	0.3089	L	0.50333	1.59	0.80722	D	1	B;B	0.23891	0.042;0.093	B;B	0.26517	0.07;0.05	T	0.71062	-0.4701	10	0.56958	D	0.05	.	15.5198	0.75857	1.0:0.0:0.0:0.0	.	1018;1019	G5EA45;Q86T65	.;DAAM2_HUMAN	G	1019;1019;1018	ENSP00000274867:E1019G;ENSP00000381876:E1019G;ENSP00000437808:E1018G	ENSP00000274867:E1019G	E	+	2	0	DAAM2	39977640	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	5.425000	0.66470	2.145000	0.66743	0.533000	0.62120	GAG	.	.		0.647	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			G	39869662	A	G	39869662	3	3	91	1	0	0	0	0	1	0	0	0	4218	304	11	2	3147	2	DAAM2	6	39869662	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	8245836	39869662	131245405	226	12300										
PEX6	5190	hgsc.bcm.edu	37	chr6	42933450	42933450	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcctccagaatctccacttcGcccccggcttggggccaaag	9	17	1	1	rs267608241		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:42933450G>A	ENST00000304611.8	-	13	2509	c.2440C>T	c.(2440-2442)Cga>Tga	p.R814*	PEX6_ENST00000244546.4_Silent_p.G731G	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	814					ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			TCTCCACTTCGCCCCCGGCTT	0.562																																					p.R814X		Atlas-SNP	.											.	PEX6	44	.	0			c.C2440T						.						160	177	171					6																	42933450		2203	4300	6503	SO:0001587	stop_gained	5190	exon13			CACTTCGCCCCCG	U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"ATPases / AAA-type"	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.2440C>T	chr6.hg19:g.42933450G>A	ENSP00000303511:p.Arg814*	148.0	0.0		184.0	17.0	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Nonsense_Mutation	SNP	ENST00000304611.8	hg19	CCDS4877.1	.	.	.	.	.	.	.	.	.	.	G	40	8.021076	0.98613	.	.	ENSG00000124587	ENST00000304611	.	.	.	5.76	5.76	0.90799	.	0.109084	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.5604	14.4359	0.67279	0.0:0.0:0.8525:0.1474	.	.	.	.	X	814	.	ENSP00000303511:R814X	R	-	1	2	PEX6	43041428	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.022000	0.57203	2.724000	0.93272	0.563000	0.77884	CGA	.	.		0.562	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287		A	42933450	G	A	42933450	4	1	91	1	0	0	0	0	0	1	0	0	11759	1095	38	1	522	1	PEX6	6	42933450	Nonsense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3063788	42933450	128181617	227	12301										
SPATS1	221409	hgsc.bcm.edu	37	chr6	44336153	44336153	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggaatcccaaagttaactccAggcgacaatccatatatgta	7	10	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:44336153A>G	ENST00000288390.2	+	5	959	c.612A>G	c.(610-612)ccA>ccG	p.P204P	RP11-444E17.6_ENST00000505802.1_3'UTR|SPATS1_ENST00000323108.8_Silent_p.P204P			Q496A3	SPAS1_HUMAN	spermatogenesis associated, serine-rich 1	204										NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(5)|skin(1)|urinary_tract(1)	14	all_lung(25;0.00469)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AGTTAACTCCAGGCGACAATC	0.398																																					p.P204P		Atlas-SNP	.											.	SPATS1	61	.	0			c.A612G						.						122	119	120					6																	44336153		2203	4300	6503	SO:0001819	synonymous_variant	221409	exon6			AACTCCAGGCGAC	AK058171	CCDS4911.1	6p21.1	2003-08-08			ENSG00000249481	ENSG00000249481			22957	protein-coding gene	gene with protein product							Standard	NM_145026		Approved	SPATA8, FLJ25442, SRSP1	uc021yzz.1	Q496A3	OTTHUMG00000014764	ENST00000288390.2:c.612A>G	chr6.hg19:g.44336153A>G		62.0	0.0		88.0	4.0	NM_145026	Q496A2|Q496A5|Q96LJ0	Silent	SNP	ENST00000288390.2	hg19	CCDS4911.1																																																																																			.	.		0.398	SPATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040738.2	NM_145026		G	44336153	A	G	44336153	2	3	91	1	0	0	0	0	0	0	0	1	15033	175	7	2		2	SPATS1	6	44336153	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1402703	44336153	126778914	228	12302										
CDC5L	988	hgsc.bcm.edu	37	chr6	44414375	44414375	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agacgttcagcgacaacaagAaagagaaaaggaacttcaac	9	8	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:44414375A>G	ENST00000371477.3	+	16	2635	c.2336A>G	c.(2335-2337)gAa>gGa	p.E779G		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	779	Interaction with PLRG1.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)	p.E779G(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CGACAACAAGAAAGAGAAAAG	0.294																																					p.E779G		Atlas-SNP	.											CDC5L,colon,carcinoma,0,1	CDC5L	86	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2336G						.						106	113	111					6																	44414375		2203	4300	6503	SO:0001583	missense	988	exon16			AACAAGAAAGAGA	D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"CDC5 (cell division cycle 5, S. pombe, homolog)-like", "CDC5 cell division cycle 5-like (S. pombe)"			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.2336A>G	chr6.hg19:g.44414375A>G	ENSP00000360532:p.Glu779Gly	58.0	0.0		70.0	3.0	NM_001253	Q76N46|Q99974	Missense_Mutation	SNP	ENST00000371477.3	hg19	CCDS4912.1	.	.	.	.	.	.	.	.	.	.	A	19.64	3.866052	0.71949	.	.	ENSG00000096401	ENST00000371477	T	0.48522	0.81	6.01	6.01	0.97437	.	0.225469	0.52532	D	0.000067	T	0.37128	0.0992	M	0.72479	2.2	0.80722	D	1	P	0.41313	0.745	B	0.36134	0.218	T	0.44997	-0.9291	10	0.52906	T	0.07	-10.0754	16.5285	0.84344	1.0:0.0:0.0:0.0	.	779	Q99459	CDC5L_HUMAN	G	779	ENSP00000360532:E779G	ENSP00000360532:E779G	E	+	2	0	CDC5L	44522353	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	8.065000	0.89485	2.307000	0.77673	0.528000	0.53228	GAA	.	.		0.294	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			G	44414375	A	G	44414375	3	3	91	1	0	0	0	0	1	0	0	0	3084	246	9	2	2398	2	CDC5L	6	44414375	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	78222	44414375	126700692	229	12303										
GPR111	222611	hgsc.bcm.edu	37	chr6	47649442	47649442	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaatctcactgatttttgaaAagatcagcaagtcagaggag	10	6	3	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:47649442A>G	ENST00000296862.1	+	6	1147	c.1147A>G	c.(1147-1149)Aag>Gag	p.K383E	GPR111_ENST00000507065.1_Missense_Mutation_p.K315E|GPR111_ENST00000398742.2_Missense_Mutation_p.K315E			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	383					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						GATTTTTGAAAAGATCAGCAA	0.438																																					p.K315E		Atlas-SNP	.											.	GPR111	123	.	0			c.A943G						.						93	92	92					6																	47649442		1907	4137	6044	SO:0001583	missense	222611	exon7			TTTGAAAAGATCA	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"-", "GPCR / Class B : Orphans"	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.1147A>G	chr6.hg19:g.47649442A>G	ENSP00000296862:p.Lys383Glu	78.0	0.0		98.0	4.0	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	hg19		.	.	.	.	.	.	.	.	.	.	A	23.2	4.391015	0.82902	.	.	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.38240	1.92;1.9;1.15	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000003	T	0.54902	0.1887	M	0.83774	2.66	0.35076	D	0.762988	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.64740	-0.6336	10	0.54805	T	0.06	.	14.8206	0.70070	1.0:0.0:0.0:0.0	.	315;383	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	E	315;383;315	ENSP00000422934:K315E;ENSP00000296862:K383E;ENSP00000381727:K315E	ENSP00000296862:K383E	K	+	1	0	GPR111	47757401	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.977000	0.88081	2.099000	0.63709	0.477000	0.44152	AAG	.	.		0.438	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839		G	47649442	A	G	47649442	3	3	91	1	0	0	0	0	1	0	0	0	6636	15	1	2	961	2	GPR111	6	47649442	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3235067	47649442	123465625	230	12304										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72678720	72678720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acatggcgaagcctgctgccTgcaaaacaccaagaaatgct	9	12	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:72678720T>C	ENST00000521978.1	+	2	199	c.199T>C	c.(199-201)Tgc>Cgc	p.C67R	RIMS1_ENST00000520567.1_Missense_Mutation_p.C67R|RIMS1_ENST00000522291.1_Missense_Mutation_p.C67R|RIMS1_ENST00000264839.7_Missense_Mutation_p.C67R|RIMS1_ENST00000491071.2_Missense_Mutation_p.C67R|RIMS1_ENST00000517960.1_Missense_Mutation_p.C67R|RIMS1_ENST00000348717.5_Missense_Mutation_p.C67R|RIMS1_ENST00000518273.1_Missense_Mutation_p.C67R	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	67	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GCCTGCTGCCTGCAAAACACC	0.448																																					p.C67R		Atlas-SNP	.											.	RIMS1	278	.	0			c.T199C						.						132	137	136					6																	72678720		1936	4138	6074	SO:0001583	missense	22999	exon2			GCTGCCTGCAAAA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.199T>C	chr6.hg19:g.72678720T>C	ENSP00000428417:p.Cys67Arg	96.0	0.0		102.0	10.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.235682	0.58886	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91	5.31	4.14	0.48551	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE/PHD-type (1);	.	.	.	.	T	0.39436	0.1078	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41466	-0.9507	9	0.39692	T	0.17	.	8.1641	0.31215	0.0:0.094:0.0:0.906	.	67	Q86UR5	RIMS1_HUMAN	R	67	ENSP00000430101:C67R;ENSP00000275037:C67R;ENSP00000264839:C67R;ENSP00000429959:C67R;ENSP00000430408:C67R;ENSP00000430502:C67R;ENSP00000430932:C67R;ENSP00000428417:C67R	ENSP00000264839:C67R	C	+	1	0	RIMS1	72735441	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.427000	0.34881	1.990000	0.58119	0.533000	0.62120	TGC	.	.		0.448	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			C	72678720	T	C	72678720	3	2	91	1	0	0	0	0	1	0	0	0	13382	1580	55	2	205	2	RIMS1	6	72678720	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	25029278	72678720	98436347	231	12305										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84311120	84311120	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcaaatggatctgaaatctgTgcttcagagggaacagagga	13	6	3	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:84311120T>A	ENST00000439399.2	-	16	1510	c.1194A>T	c.(1192-1194)gcA>gcT	p.A398A	SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000428679.2_Silent_p.A398A|SNAP91_ENST00000521743.1_Silent_p.A398A|SNAP91_ENST00000437520.1_Intron|SNAP91_ENST00000195649.6_Silent_p.A398A|SNAP91_ENST00000369694.2_Silent_p.A398A|SNAP91_ENST00000521485.1_Silent_p.A398A|SNAP91_ENST00000520302.1_Silent_p.A396A	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	398	Ala-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		CTGAAATCTGTGCTTCAGAGG	0.448																																					p.A398A		Atlas-SNP	.											.	SNAP91	199	.	0			c.A1194T						.						91	91	91					6																	84311120		1941	4131	6072	SO:0001819	synonymous_variant	9892	exon15			AATCTGTGCTTCA	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1194A>T	chr6.hg19:g.84311120T>A		260.0	0.0		177.0	109.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Silent	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.526100	0.27299	.	.	ENSG00000065609	ENST00000369691	.	.	.	5.58	1.72	0.24424	.	.	.	.	.	T	0.28433	0.0703	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.15065	-1.0450	4	.	.	.	-11.017	2.8386	0.05522	0.2468:0.0671:0.1286:0.5575	.	.	.	.	S	58	.	.	T	-	1	0	SNAP91	84367839	0.998000	0.40836	0.999000	0.59377	0.989000	0.77384	0.368000	0.20399	0.054000	0.16065	0.460000	0.39030	ACA	.	.		0.448	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			A	84311120	T	A	84311120	2	1	91	1	0	0	0	0	0	0	0	1	14848	1683	59	4		4	SNAP91	6	84311120	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	11632400	84311120	86803947	232	12306										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87964908	87964908	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaaagcagaagaagagagagAtaaaacagttaagagagagg	13	2	0	6			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:87964908A>G	ENST00000369577.3	+	8	1604	c.1561A>G	c.(1561-1563)Ata>Gta	p.I521V	ZNF292_ENST00000339907.4_Missense_Mutation_p.I516V	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	521						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		GAAGAGAGAGATAAAACAGTT	0.403																																					p.I521V		Atlas-SNP	.											.	ZNF292	479	.	0			c.A1561G						.						114	105	108					6																	87964908		1876	4099	5975	SO:0001583	missense	23036	exon8			AGAGAGATAAAAC	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.1561A>G	chr6.hg19:g.87964908A>G	ENSP00000358590:p.Ile521Val	130.0	0.0		101.0	5.0	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	hg19	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.103979	0.37145	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.35421	1.31;1.31	5.87	5.87	0.94306	.	0.176797	0.64402	D	0.000013	T	0.36082	0.0954	L	0.50333	1.59	0.29927	N	0.822255	D	0.58268	0.982	P	0.55615	0.78	T	0.21415	-1.0246	10	0.44086	T	0.13	.	16.2631	0.82557	1.0:0.0:0.0:0.0	.	521	O60281	ZN292_HUMAN	V	521;516	ENSP00000358590:I521V;ENSP00000342847:I516V	ENSP00000342847:I516V	I	+	1	0	ZNF292	88021627	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.258000	0.65479	2.239000	0.73571	0.528000	0.53228	ATA	.	.		0.403	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		G	87964908	A	G	87964908	3	3	91	1	0	0	0	0	1	0	0	0	17841	333	12	2	1591	2	ZNF292	6	87964908	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3653788	87964908	83150159	233	12307										
GABRR1	2569	hgsc.bcm.edu	37	chr6	89890099	89890099	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcaccgagaggaacacgaacAcaaagctgacccagaggtag	12	11	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:89890099A>G	ENST00000454853.2	-	9	1168	c.1058T>C	c.(1057-1059)gTg>gCg	p.V353A	GABRR1_ENST00000435811.1_Missense_Mutation_p.V336A|GABRR1_ENST00000369451.3_Missense_Mutation_p.V266A	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	353					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	GAACACGAACACAAAGCTGAC	0.577																																					p.V353A		Atlas-SNP	.											.	GABRR1	63	.	0			c.T1058C						.						160	123	135					6																	89890099		2203	4300	6503	SO:0001583	missense	2569	exon9			ACGAACACAAAGC		CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4090	protein-coding gene	gene with protein product	"GABA(A) receptor, rho 1"	137161	"gamma-aminobutyric acid (GABA) receptor, rho 1"			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.1058T>C	chr6.hg19:g.89890099A>G	ENSP00000412673:p.Val353Ala	122.0	0.0		74.0	4.0	NM_002042	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Missense_Mutation	SNP	ENST00000454853.2	hg19	CCDS5019.2	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716499	0.89205	.	.	ENSG00000146276	ENST00000454853;ENST00000435811;ENST00000369451;ENST00000436331	D;D;D	0.86694	-2.16;-2.16;-2.16	5.07	5.07	0.68467	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.86690	0.5993	L	0.41236	1.265	0.52099	D	0.999948	P;D	0.59767	0.936;0.986	P;D	0.65140	0.737;0.932	D	0.86484	0.1793	9	.	.	.	-24.6553	14.8538	0.70319	1.0:0.0:0.0:0.0	.	336;353	P24046-2;P24046	.;GBRR1_HUMAN	A	353;336;266;266	ENSP00000412673:V353A;ENSP00000394687:V336A;ENSP00000358463:V266A	.	V	-	2	0	GABRR1	89946818	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.306000	0.78905	1.891000	0.54761	0.455000	0.32223	GTG	.	.		0.577	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2			G	89890099	A	G	89890099	3	3	91	1	0	0	0	0	1	0	0	0	6184	159	6	2	389	2	GABRR1	6	89890099	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1925191	89890099	81224968	234	12308										
C6orf186	728464	hgsc.bcm.edu	37	chr6	110644068	110644068	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctggagatctatatgccacCggggaccctgcaagagacag	13	11	1	2	rs545654177		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:110644068C>A	ENST00000338882.4	-	2	325	c.326G>T	c.(325-327)cGg>cTg	p.R109L	METTL24_ENST00000490043.1_5'UTR	NM_001123364.1	NP_001116836.1	Q5JXM2	MET24_HUMAN	methyltransferase like 24	109						extracellular region (GO:0005576)	methyltransferase activity (GO:0008168)	p.R109Q(1)									TATATGCCACCGGGGACCCTG	0.522																																					p.R109L		Atlas-SNP	.											C6orf186,colon,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G326T						.						55	53	54					6																	110644068		1568	3582	5150	SO:0001583	missense	728464	exon2			TGCCACCGGGGAC		CCDS43489.1	6q21	2012-03-08	2012-02-21	2012-02-21	ENSG00000053328	ENSG00000053328			21566	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 186"	C6orf186			Standard	NM_001123364		Approved	dJ71D21.2	uc010kdu.1	Q5JXM2	OTTHUMG00000015359	ENST00000338882.4:c.326G>T	chr6.hg19:g.110644068C>A	ENSP00000344071:p.Arg109Leu	46.0	0.0		46.0	2.0	NM_001123364	Q6ZSU5	Missense_Mutation	SNP	ENST00000338882.4	hg19	CCDS43489.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.482511	0.63962	.	.	ENSG00000053328	ENST00000338882	T	0.52754	0.65	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.59891	0.2227	M	0.65498	2.005	0.58432	D	0.999995	D	0.76494	0.999	D	0.79784	0.993	T	0.62656	-0.6808	10	0.62326	D	0.03	-22.4033	14.7961	0.69878	0.0:1.0:0.0:0.0	.	109	Q5JXM2	CF186_HUMAN	L	109	ENSP00000344071:R109L	ENSP00000344071:R109L	R	-	2	0	C6orf186	110750761	1.000000	0.71417	1.000000	0.80357	0.142000	0.21351	4.903000	0.63272	2.563000	0.86464	0.650000	0.86243	CGG	.	.		0.522	METTL24-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041794.1	NM_001123364		A	110644068	C	A	110644068	3	1	91	1	0	0	0	0	1	0	0	0	2349	652	23	1	790	1	C6orf186	6	110644068	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	20753969	110644068	60470999	235	12309										
LAMA4	3910	hgsc.bcm.edu	37	chr6	112435867	112435867	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggcagtcagttttctcaccTgtaattctgtgccatctgcc	9	12	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:112435867T>C	ENST00000230538.7	-	37	5602	c.5205A>G	c.(5203-5205)acA>acG	p.T1735T	LAMA4_ENST00000522006.1_Splice_Site_p.T1728T|LAMA4_ENST00000389463.4_Splice_Site_p.T1728T|LAMA4_ENST00000424408.2_Splice_Site_p.T1728T	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1735	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TTTTCTCACCTGTAATTCTGT	0.443																																					p.T1735T		Atlas-SNP	.											.	LAMA4	227	.	0			c.A5205G						.						114	103	107					6																	112435867		2203	4300	6503	SO:0001630	splice_region_variant	3910	exon37			CTCACCTGTAATT		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.5206+1A>G	chr6.hg19:g.112435867T>C		167.0	0.0		99.0	4.0	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	hg19	CCDS43491.1																																																																																			.	.		0.443	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	Silent	C	112435867	T	C	112435867	5	2	91	1	0	0	0	0	0	0	1	0	8617	1594	55	2	278	2	LAMA4	6	112435867	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1791799	112435867	58679200	236	12310										
STX7	8417	hgsc.bcm.edu	37	chr6	132796761	132796761	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctcaattcaggtgaatcttgAggtgttccaagttgattcag	10	7	4	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:132796761A>G	ENST00000367941.2	-	3	239	c.126T>C	c.(124-126)ccT>ccC	p.P42P	STX7_ENST00000448348.3_5'UTR|STX7_ENST00000367937.4_Silent_p.P42P	NM_003569.2	NP_003560.2	O15400	STX7_HUMAN	syntaxin 7	42					intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)|synaptic vesicle exocytosis (GO:0016079)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(1)|lung(5)	19	Breast(56;0.0615)			OV - Ovarian serous cystadenocarcinoma(155;0.00532)|GBM - Glioblastoma multiforme(226;0.0114)		GTGAATCTTGAGGTGTTCCAA	0.294																																					p.P42P		Atlas-SNP	.											.	STX7	25	.	0			c.T126C						.						74	70	72					6																	132796761		2201	4297	6498	SO:0001819	synonymous_variant	8417	exon3			ATCTTGAGGTGTT	U77942	CCDS5153.1	6q23.1	2008-02-05			ENSG00000079950	ENSG00000079950			11442	protein-coding gene	gene with protein product		603217				9358037	Standard	NM_003569		Approved		uc003qdg.2	O15400	OTTHUMG00000015577	ENST00000367941.2:c.126T>C	chr6.hg19:g.132796761A>G		63.0	0.0		62.0	4.0	NM_003569	E1P579|Q5SZW2|Q96ES9	Silent	SNP	ENST00000367941.2	hg19	CCDS5153.1																																																																																			.	.		0.294	STX7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042252.2			G	132796761	A	G	132796761	2	3	91	1	0	0	0	0	0	0	0	1	15365	291	11	2		2	STX7	6	132796761	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	20360894	132796761	38318306	237	12311										
ALDH8A1	64577	hgsc.bcm.edu	37	chr6	135239987	135239987	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcaccttcagcaagagctcTcttgacgtaacttctgacct	8	13	3	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:135239987T>C	ENST00000265605.2	-	7	1098	c.1030A>G	c.(1030-1032)Aga>Gga	p.R344G	ALDH8A1_ENST00000367847.2_Missense_Mutation_p.R294G|ALDH8A1_ENST00000367845.2_Missense_Mutation_p.R290G	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	344					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		GCAAGAGCTCTCTTGACGTAA	0.463																																					p.R344G		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.A1030G						.						102	108	106					6																	135239987		2203	4300	6503	SO:0001583	missense	64577	exon7			GAGCTCTCTTGAC	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"Aldehyde dehydrogenases"	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.1030A>G	chr6.hg19:g.135239987T>C	ENSP00000265605:p.Arg344Gly	124.0	0.0		106.0	6.0	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	hg19	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	T	5.017	0.188873	0.09547	.	.	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847;ENST00000460753	T;T;T;T	0.76839	-1.05;1.54;-1.05;-1.05	5.57	5.57	0.84162	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.445184	0.27155	N	0.020664	T	0.50786	0.1636	N	0.25380	0.74	0.22457	N	0.999083	B;B;B	0.13145	0.002;0.006;0.007	B;B;B	0.09377	0.002;0.003;0.004	T	0.35226	-0.9797	10	0.28530	T	0.3	.	15.73	0.77794	0.0:0.0:0.0:1.0	.	294;290;344	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	G	344;290;294;29	ENSP00000265605:R344G;ENSP00000356819:R290G;ENSP00000356821:R294G;ENSP00000437161:R29G	ENSP00000265605:R344G	R	-	1	2	ALDH8A1	135281680	0.753000	0.28349	0.497000	0.27552	0.150000	0.21749	3.104000	0.50306	2.116000	0.64780	0.533000	0.62120	AGA	.	.		0.463	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			C	135239987	T	C	135239987	3	2	91	1	0	0	0	0	1	0	0	0	505	1559	54	2	437	2	ALDH8A1	6	135239987	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2443226	135239987	35875080	238	12312										
ALDH8A1	64577	hgsc.bcm.edu	37	chr6	135253949	135253949	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggacctgacggttgccggaaTgcactcatccaggttggcgt	14	11	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:135253949T>C	ENST00000265605.2	-	5	882	c.814A>G	c.(814-816)Att>Gtt	p.I272V	ALDH8A1_ENST00000367847.2_Missense_Mutation_p.I222V|ALDH8A1_ENST00000367845.2_Missense_Mutation_p.I272V	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	272					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		GTTGCCGGAATGCACTCATCC	0.582																																					p.I272V		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.A814G						.						94	94	94					6																	135253949		2203	4300	6503	SO:0001583	missense	64577	exon5			CCGGAATGCACTC	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"Aldehyde dehydrogenases"	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.814A>G	chr6.hg19:g.135253949T>C	ENSP00000265605:p.Ile272Val	112.0	0.0		77.0	4.0	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	hg19	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.707381	0.00719	.	.	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	T;T;T	0.73681	-0.77;-0.77;-0.77	5.3	-1.66	0.08265	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.144549	0.64402	N	0.000009	T	0.18130	0.0435	N	0.01624	-0.795	0.41054	D	0.98532	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.11329	0.003;0.003;0.006	T	0.41610	-0.9499	10	0.02654	T	1	.	12.3445	0.55114	0.0:0.2474:0.0:0.7526	.	222;272;272	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	V	272;272;222	ENSP00000265605:I272V;ENSP00000356819:I272V;ENSP00000356821:I222V	ENSP00000265605:I272V	I	-	1	0	ALDH8A1	135295642	0.002000	0.14202	0.013000	0.15412	0.001000	0.01503	-0.076000	0.11412	-0.583000	0.05921	-0.410000	0.06199	ATT	.	.		0.582	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			C	135253949	T	C	135253949	3	2	91	1	0	0	0	0	1	0	0	0	505	1464	51	2	661	2	ALDH8A1	6	135253949	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	13962	135253949	35861118	239	12313										
FAM54A	113115	hgsc.bcm.edu	37	chr6	136564084	136564084	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catagatccacaattatcagAgtctacagagttcaagagcg	8	9	3	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:136564084A>G	ENST00000420702.1	-	4	585	c.196T>C	c.(196-198)Tct>Cct	p.S66P	MTFR2_ENST00000451457.2_Missense_Mutation_p.S66P	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	66					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											CAATTATCAGAGTCTACAGAG	0.378																																					p.S66P		Atlas-SNP	.											.	.	.	.	0			c.T196C						.						87	87	87					6																	136564084		2203	4300	6503	SO:0001583	missense	113115	exon4			TATCAGAGTCTAC	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"DUF729 domain containing 1", "family with sequence similarity 54, member A"	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.196T>C	chr6.hg19:g.136564084A>G	ENSP00000395232:p.Ser66Pro	71.0	0.0		56.0	4.0	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Missense_Mutation	SNP	ENST00000420702.1	hg19	CCDS5176.1	.	.	.	.	.	.	.	.	.	.	A	9.562	1.118771	0.20877	.	.	ENSG00000146410	ENST00000451457;ENST00000420702;ENST00000418509	T;T;T	0.46819	0.86;0.86;0.86	5.62	-2.01	0.07410	.	0.962031	0.08693	N	0.907605	T	0.09992	0.0245	N	0.17564	0.495	0.09310	N	1	B	0.16166	0.016	B	0.17979	0.02	T	0.31586	-0.9938	10	0.27785	T	0.31	-1.7625	4.9444	0.13982	0.4544:0.2768:0.2688:0.0	.	66	Q6P444	FA54A_HUMAN	P	66;66;23	ENSP00000407010:S66P;ENSP00000395232:S66P;ENSP00000410861:S23P	ENSP00000410861:S23P	S	-	1	0	FAM54A	136605777	0.000000	0.05858	0.027000	0.17364	0.661000	0.39034	-0.044000	0.12023	-0.208000	0.10171	0.533000	0.62120	TCT	.	.		0.378	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419		G	136564084	A	G	136564084	3	3	91	1	0	0	0	0	1	0	0	0	5590	304	11	2	981	2	FAM54A	6	136564084	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1310135	136564084	34550983	240	12314										
MAP3K5	4217	hgsc.bcm.edu	37	chr6	136935339	136935339	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gattttaatgaaaccattctCactgaaagagcccagatact	6	9	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:136935339C>A	ENST00000359015.4	-	16	2596	c.2236G>T	c.(2236-2238)Gag>Tag	p.E746*	MAP3K5_ENST00000355845.4_5'UTR	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	746	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		AAACCATTCTCACTGAAAGAG	0.393																																					p.E746X		Atlas-SNP	.											.	MAP3K5	136	.	0			c.G2236T						.						151	144	146					6																	136935339		2203	4300	6503	SO:0001587	stop_gained	4217	exon16			CATTCTCACTGAA	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6857	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 1"	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.2236G>T	chr6.hg19:g.136935339C>A	ENSP00000351908:p.Glu746*	113.0	0.0		87.0	4.0	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Nonsense_Mutation	SNP	ENST00000359015.4	hg19	CCDS5179.1	.	.	.	.	.	.	.	.	.	.	C	43	10.477992	0.99412	.	.	ENSG00000197442	ENST00000359015;ENST00000367768	.	.	.	5.2	5.2	0.72013	.	0.095780	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	12.4507	0.55675	0.0:0.9222:0.0:0.0778	.	.	.	.	X	746;826	.	ENSP00000351908:E746X	E	-	1	0	MAP3K5	136977032	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.634000	0.61325	2.565000	0.86533	0.650000	0.86243	GAG	.	.		0.393	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1			A	136935339	C	A	136935339	4	1	91	1	0	0	0	0	0	1	0	0	9262	835	29	3	1948	3	MAP3K5	6	136935339	Nonsense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	371255	136935339	34179728	241	12315										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138629880	138629880	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aatcttcctcccttaggaaaAggccaagctccagtgtttga	8	11	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:138629880A>G	ENST00000251691.4	+	24	4144	c.3978A>G	c.(3976-3978)aaA>aaG	p.K1326K		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CCTTAGGAAAAGGCCAAGCTC	0.443																																					p.K1326K		Atlas-SNP	.											.	KIAA1244	236	.	0			c.A3978G						.						142	139	140					6																	138629880		2203	4300	6503	SO:0001819	synonymous_variant	57221	exon24			AGGAAAAGGCCAA	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.3978A>G	chr6.hg19:g.138629880A>G		163.0	0.0		89.0	4.0	NM_020340		Silent	SNP	ENST00000251691.4	hg19	CCDS5189.2																																																																																			.	.		0.443	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		G	138629880	A	G	138629880	2	3	91	1	0	0	0	0	0	0	0	1	8226	69	3	2		2	KIAA1244	6	138629880	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1694541	138629880	32485187	242	12316										
IPCEF1	26034	hgsc.bcm.edu	37	chr6	154480993	154480993	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttttcaacagagggagaagaAggtgatttcttgagttcctg	12	5	2	5			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:154480993A>G	ENST00000265198.4	-	12	1439	c.1284T>C	c.(1282-1284)ccT>ccC	p.P428P	OPRM1_ENST00000337049.4_Intron|IPCEF1_ENST00000519344.1_Silent_p.P400P|IPCEF1_ENST00000422970.2_Silent_p.P429P|IPCEF1_ENST00000367220.4_Silent_p.P429P	NM_001130700.1|NM_015553.2	NP_001124172.1|NP_056368.1	Q8WWN9	ICEF1_HUMAN	interaction protein for cytohesin exchange factors 1	428					oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|positive regulation of GTP catabolic process (GO:0033126)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	oxygen transporter activity (GO:0005344)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	12						AGGGAGAAGAAGGTGATTTCT	0.458																																					p.P429P		Atlas-SNP	.											.	IPCEF1	45	.	0			c.T1287C						.						61	65	63					6																	154480993		2203	4300	6503	SO:0001819	synonymous_variant	26034	exon13			AGAAGAAGGTGAT	AB007863	CCDS5245.1, CCDS47509.1	6q25.2	2013-01-10			ENSG00000074706	ENSG00000074706		"Pleckstrin homology (PH) domain containing"	21204	protein-coding gene	gene with protein product	"phosphoinositide binding protein PIP3-E"					11804589, 19756519	Standard	NM_001130699		Approved	PIP3-E, KIAA0403	uc021zhc.1	Q8WWN9	OTTHUMG00000015872	ENST00000265198.4:c.1284T>C	chr6.hg19:g.154480993A>G		79.0	0.0		57.0	5.0	NM_001130699	A8K1K2|B7ZL78|B7ZL80|O43153|Q5HYL8	Silent	SNP	ENST00000265198.4	hg19	CCDS5245.1																																																																																			.	.		0.458	IPCEF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042789.2	NM_001130699		G	154480993	A	G	154480993	2	3	91	1	0	0	0	0	0	0	0	1	7800	59	3	2		2	IPCEF1	6	154480993	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	15851113	154480993	16634074	243	12317										
NOX3	50508	hgsc.bcm.edu	37	chr6	155750089	155750089	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cactccagcgaagatatggcTgggcactgcaccaagatgta	11	11	0	2	rs545302024	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:155750089T>C	ENST00000159060.2	-	9	1086	c.984A>G	c.(982-984)ccA>ccG	p.P328P		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	328	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.			P -> S (in Ref. 3; AAG15435). {ECO:0000305}.	detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		AAGATATGGCTGGGCACTGCA	0.567																																					p.P328P		Atlas-SNP	.											NOX3,NS,carcinoma,0,1	NOX3	93	.	0			c.A984G						.						80	81	81					6																	155750089		2203	4300	6503	SO:0001819	synonymous_variant	50508	exon9			TATGGCTGGGCAC	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.984A>G	chr6.hg19:g.155750089T>C		114.0	0.0		79.0	4.0	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	hg19	CCDS5250.1																																																																																			.	.		0.567	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			C	155750089	T	C	155750089	2	2	91	1	0	0	0	0	0	0	0	1	10566	1567	55	2		2	NOX3	6	155750089	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1269096	155750089	15364978	244	12318										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160469467	160469467	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gccatggacaactcaggggaAcatgtcacgtggaggaaata	13	8	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:160469467A>G	ENST00000356956.1	+	18	2554	c.2406A>G	c.(2404-2406)gaA>gaG	p.E802E		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	802					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	ACTCAGGGGAACATGTCACGT	0.453																																					p.E802E		Atlas-SNP	.											.	IGF2R	251	.	0			c.A2406G						.						135	114	121					6																	160469467		2203	4300	6503	SO:0001819	synonymous_variant	3482	exon18			AGGGGAACATGTC	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.2406A>G	chr6.hg19:g.160469467A>G		124.0	0.0		62.0	4.0	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	hg19	CCDS5273.1																																																																																			.	.		0.453	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		G	160469467	A	G	160469467	2	3	91	1	0	0	0	0	0	0	0	1	7585	40	2	2		2	IGF2R	6	160469467	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4719378	160469467	10645600	245	12319										
THBS2	7058	hgsc.bcm.edu	37	chr6	169626380	169626380	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acgtagggacaattgtctcgTtcattgaagacatctgtaag	10	7	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:169626380T>C	ENST00000366787.3	-	17	2682	c.2433A>G	c.(2431-2433)gaA>gaG	p.E811E	XXyac-YX65C7_A.2_ENST00000444188.1_RNA|THBS2_ENST00000488355.1_5'Flank	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	811					cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		AATTGTCTCGTTCATTGAAGA	0.468																																					p.E811E	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											THBS2,NS,carcinoma,0,1	THBS2	230	.	0			c.A2433G						.						93	88	89					6																	169626380		2203	4300	6503	SO:0001819	synonymous_variant	7058	exon17			GTCTCGTTCATTG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.2433A>G	chr6.hg19:g.169626380T>C		84.0	0.0		50.0	3.0	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	hg19	CCDS34574.1																																																																																			.	.		0.468	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		C	169626380	T	C	169626380	2	2	91	1	0	0	0	0	0	0	0	1	15869	1722	60	2		2	THBS2	6	169626380	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9156913	169626380	1488687	246	12320										
WDR27	253769	hgsc.bcm.edu	37	chr6	170002368	170002368	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccacaaggactgaaagcgaTtccacatggatagccgcggg	12	11	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:170002368T>C	ENST00000448612.1	-	23	2480	c.2371A>G	c.(2371-2373)Atc>Gtc	p.I791V	WDR27_ENST00000333572.6_Missense_Mutation_p.I791V|WDR27_ENST00000546525.1_5'UTR|WDR27_ENST00000423258.1_Missense_Mutation_p.I664V	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	761						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		CTGAAAGCGATTCCACATGGA	0.473																																					p.I791V		Atlas-SNP	.											.	WDR27	129	.	0			c.A2371G						.						36	39	38					6																	170002368		1924	4135	6059	SO:0001583	missense	253769	exon23			AAGCGATTCCACA	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"WD repeat domain containing"	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.2371A>G	chr6.hg19:g.170002368T>C	ENSP00000416289:p.Ile791Val	57.0	0.0		72.0	5.0	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	hg19	CCDS47520.2	.	.	.	.	.	.	.	.	.	.	T	0.063	-1.220356	0.01542	.	.	ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000423258	T;T;T	0.38077	5.1;1.16;5.1	4.56	-5.92	0.02261	.	.	.	.	.	T	0.04092	0.0114	N	0.16016	0.355	0.09310	N	1	B;B;B	0.20887	0.004;0.007;0.049	B;B;B	0.20184	0.002;0.003;0.028	T	0.38222	-0.9671	9	0.02654	T	1	-0.852	8.4385	0.32801	0.0:0.5975:0.1369:0.2656	.	791;664;791	F2Z2U5;A2RRH5-2;C9JGV0	.;.;.	V	791;791;664	ENSP00000416289:I791V;ENSP00000330265:I791V;ENSP00000397869:I664V	ENSP00000330265:I791V	I	-	1	0	WDR27	169744293	0.044000	0.20184	0.000000	0.03702	0.003000	0.03518	-0.027000	0.12371	-1.084000	0.03092	-0.417000	0.06048	ATC	.	.		0.473	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552		C	170002368	T	C	170002368	3	2	91	1	0	0	0	0	1	0	0	0	17299	1493	52	2	214	2	WDR27	6	170002368	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	375988	170002368	1112699	247	12321										
NUDT1	4521	hgsc.bcm.edu	37	chr7	2284331	2284331	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctttgggggcaaagtgcaagAaggagagaccatcgaggatg	16	6	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:2284331A>G	ENST00000397046.1	+	3	219	c.122A>G	c.(121-123)gAa>gGa	p.E41G	NUDT1_ENST00000397049.1_Missense_Mutation_p.E64G|FTSJ2_ENST00000242257.8_5'Flank|NUDT1_ENST00000397048.1_Missense_Mutation_p.E64G|FTSJ2_ENST00000440306.2_5'Flank|NUDT1_ENST00000339737.2_Missense_Mutation_p.E41G|NUDT1_ENST00000343985.4_Missense_Mutation_p.E64G|NUDT1_ENST00000356714.1_Missense_Mutation_p.E41G|FTSJ2_ENST00000486040.1_5'Flank	NM_198950.1	NP_945188.1	P36639	8ODP_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 1	82					ATP catabolic process (GO:0006200)|dATP catabolic process (GO:0046061)|dGTP catabolic process (GO:0006203)|DNA protection (GO:0042262)|DNA repair (GO:0006281)|GTP catabolic process (GO:0006184)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleotide catabolic process (GO:0006195)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity (GO:0035539)|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity (GO:0008413)|ATP diphosphatase activity (GO:0047693)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|snoRNA binding (GO:0030515)			large_intestine(3)|lung(8)|urinary_tract(1)	12		Ovarian(82;0.0253)|Melanoma(862;0.155)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.8e-14)|BRCA - Breast invasive adenocarcinoma(126;0.15)		AAAGTGCAAGAAGGAGAGACC	0.622								Modulation of nucleotide pools																													p.E64G		Atlas-SNP	.											.	NUDT1	22	.	0			c.A191G						.						43	43	43					7																	2284331		2203	4300	6503	SO:0001583	missense	4521	exon3			TGCAAGAAGGAGA	D16581	CCDS5329.1, CCDS5330.1	7p22	2008-07-18			ENSG00000106268	ENSG00000106268		"Nudix motif containing"	8048	protein-coding gene	gene with protein product	"mutT human homolog 1", "nudix motif 1", "8-oxo-7,8-dihydrodeoxyguanosine triphosphatase", "8-oxo-dGTPase", "7,8-dihydro-8-oxoguanine triphosphatase", "8-oxo-7,8-dihydroguanosine triphosphatase", "nucleoside diphosphate-linked moiety X-type motif 1"	600312		MTH1		7713494, 8226881	Standard	NM_002452		Approved		uc003slp.1	P36639	OTTHUMG00000023072	ENST00000397046.1:c.122A>G	chr7.hg19:g.2284331A>G	ENSP00000380239:p.Glu41Gly	65.0	0.0		67.0	4.0	NM_198949	A4D205|Q6LES7|Q6P0Y6|Q7Z7N6|Q8IV95|Q9UBM0|Q9UBM9	Missense_Mutation	SNP	ENST00000397046.1	hg19	CCDS5330.1	.	.	.	.	.	.	.	.	.	.	A	10.82	1.457932	0.26161	.	.	ENSG00000106268	ENST00000356714;ENST00000397049;ENST00000397046;ENST00000397048;ENST00000343985;ENST00000339737	T;T;T;T;T;T	0.09163	3.01;3.01;3.01;3.01;3.01;3.01	3.8	1.22	0.21188	NUDIX hydrolase (1);NUDIX hydrolase domain (3);NUDIX hydrolase, conserved site (1);NUDIX hydrolase domain-like (1);	0.792616	0.11873	N	0.521203	T	0.07999	0.0200	N	0.25094	0.71	0.28263	N	0.924759	B	0.30361	0.277	B	0.35182	0.197	T	0.38200	-0.9672	10	0.34782	T	0.22	-4.6872	6.7625	0.23548	0.535:0.3732:0.0918:0.0	.	82	P36639	8ODP_HUMAN	G	41;64;41;64;64;41	ENSP00000349148:E41G;ENSP00000380242:E64G;ENSP00000380239:E41G;ENSP00000380241:E64G;ENSP00000339503:E64G;ENSP00000343439:E41G	ENSP00000343439:E41G	E	+	2	0	NUDT1	2250857	0.845000	0.29573	0.938000	0.37757	0.616000	0.37450	2.490000	0.45294	0.019000	0.15079	0.379000	0.24179	GAA	.	.		0.622	NUDT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206922.1	NM_002452		G	2284331	A	G	2284331	3	3	91	1	0	0	0	0	1	0	0	0	10734	246	9	2	197	2	NUDT1	7	2284331	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10		2284331	156854332	248	12322										
CARD11	84433	hgsc.bcm.edu	37	chr7	2956991	2956991	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgacccgggggtcgcttgttGaaagcgcttcttctggctgc	14	11	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:2956991G>T	ENST00000396946.4	-	20	3039	c.2636C>A	c.(2635-2637)tCa>tAa	p.S879*		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	879					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GTCGCTTGTTGAAAGCGCTTC	0.552			Mis		DLBCL																																p.S879X		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.C2636A						.						39	52	47					7																	2956991		2203	4299	6502	SO:0001587	stop_gained	84433	exon20			CTTGTTGAAAGCG	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.2636C>A	chr7.hg19:g.2956991G>T	ENSP00000380150:p.Ser879*	60.0	0.0		57.0	4.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Nonsense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	39	7.837902	0.98516	.	.	ENSG00000198286	ENST00000396946	.	.	.	4.99	4.99	0.66335	.	0.371673	0.24640	N	0.036804	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.4471	11.9441	0.52918	0.0834:0.0:0.9166:0.0	.	.	.	.	X	879	.	ENSP00000380150:S879X	S	-	2	0	CARD11	2923517	0.944000	0.32072	0.008000	0.14137	0.456000	0.32438	5.617000	0.67716	2.308000	0.77769	0.561000	0.74099	TCA	.	.		0.552	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		T	2956991	G	T	2956991	4	4	91	1	0	0	0	0	0	1	0	0	2647	1294	45	3	852	3	CARD11	7	2956991	Nonsense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	672660	2956991	156181672	249	12323										
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4825066	4825066	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagccctgaggaagggggacTccgacctgcagaaagctgta	15	10	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:4825066T>C	ENST00000348624.4	+	8	1046	c.952T>C	c.(952-954)Tcc>Ccc	p.S318P	AP5Z1_ENST00000401897.1_Missense_Mutation_p.S318P	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	318					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											GAAGGGGGACTCCGACCTGCA	0.622																																					p.S318P		Atlas-SNP	.											.	.	.	.	0			c.T952C						.						35	42	40					7																	4825066		2081	4194	6275	SO:0001583	missense	9907	exon8			GGGGACTCCGACC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"KIAA0415"	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.952T>C	chr7.hg19:g.4825066T>C	ENSP00000297562:p.Ser318Pro	61.0	0.0		55.0	4.0	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	hg19	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.103961	0.56291	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.46063	0.88;0.88	5.48	-4.59	0.03400	.	0.346233	0.28453	N	0.015297	T	0.42988	0.1227	L	0.53249	1.67	0.09310	N	1	P	0.47106	0.89	P	0.46796	0.527	T	0.54990	-0.8210	10	0.48119	T	0.1	.	19.5099	0.95137	0.0:0.0:0.7208:0.2792	.	318	O43299	K0415_HUMAN	P	318	ENSP00000297562:S318P;ENSP00000384980:S318P	ENSP00000297562:S318P	S	+	1	0	KIAA0415	4791592	0.061000	0.20836	0.059000	0.19551	0.764000	0.43329	-0.153000	0.10144	-0.619000	0.05648	0.459000	0.35465	TCC	.	.		0.622	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			C	4825066	T	C	4825066	3	2	91	1	0	0	0	0	1	0	0	0	8184	1551	54	2	982	2	KIAA0415	7	4825066	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1868075	4825066	154313597	250	12324										
SNX13	23161	hgsc.bcm.edu	37	chr7	17915106	17915106	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttaaattaaaagaaaaccttCttcatctttgggggaagtgc	8	6	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:17915106C>T	ENST00000409389.1	-	7	833	c.661G>A	c.(661-663)Gaa>Aaa	p.E221K	SNX13_ENST00000428135.3_Missense_Mutation_p.E221K			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	221	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.E221*(1)		breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					AGAAAACCTTCTTCATCTTTG	0.363																																					p.E221K		Atlas-SNP	.											SNX13,colon,carcinoma,0,1	SNX13	113	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G661A						.						70	67	68					7																	17915106		1816	4085	5901	SO:0001583	missense	23161	exon7			AACCTTCTTCATC	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"Sorting nexins"	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.661G>A	chr7.hg19:g.17915106C>T	ENSP00000386705:p.Glu221Lys	74.0	1.0		54.0	3.0	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.57	1.678735	0.29783	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	T;T	0.17054	2.3;2.56	5.77	5.77	0.91146	Phox-associated domain (2);PX-associated, sorting nexin 13 (1);	0.044457	0.85682	D	0.000000	T	0.11836	0.0288	N	0.11789	0.175	0.80722	D	1	B;B;B;B	0.23377	0.053;0.084;0.049;0.068	B;B;B;B	0.22880	0.032;0.042;0.017;0.025	T	0.20974	-1.0259	10	0.13470	T	0.59	.	19.9808	0.97324	0.0:1.0:0.0:0.0	.	18;221;221;221	B3KN60;Q9Y5W8;B8ZZT9;Q9Y5W8-2	.;SNX13_HUMAN;.;.	K	221;221;269	ENSP00000386705:E221K;ENSP00000398789:E221K	ENSP00000242044:E269K	E	-	1	0	SNX13	17881631	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.085000	0.76875	2.714000	0.92807	0.655000	0.94253	GAA	.	.		0.363	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132		T	17915106	C	T	17915106	3	4	91	1	0	0	0	0	1	0	0	0	14899	922	32	3	2292	3	SNX13	7	17915106	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	13090040	17915106	141223557	251	12325										
DFNA5	1687	hgsc.bcm.edu	37	chr7	24756897	24756897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctggccgtccagtttcacgtAtaactcaatgacaccgtagg	9	12	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:24756897A>G	ENST00000342947.3	-	5	1098	c.673T>C	c.(673-675)Tac>Cac	p.Y225H	DFNA5_ENST00000419307.1_Missense_Mutation_p.Y61H|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000409970.1_Missense_Mutation_p.Y61H|DFNA5_ENST00000545231.1_Missense_Mutation_p.Y61H|DFNA5_ENST00000409775.3_Missense_Mutation_p.Y225H	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	225					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						AGTTTCACGTATAACTCAATG	0.572																																					p.Y225H	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.T673C						.						155	113	127					7																	24756897		2203	4300	6503	SO:0001583	missense	1687	exon5			TCACGTATAACTC	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.673T>C	chr7.hg19:g.24756897A>G	ENSP00000339587:p.Tyr225His	61.0	0.0		43.0	4.0	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	hg19	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.505486	0.44558	.	.	ENSG00000105928	ENST00000342947;ENST00000419307;ENST00000545231;ENST00000409970;ENST00000409775	T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93	5.7	4.52	0.55395	.	0.492653	0.22491	N	0.059365	T	0.46852	0.1414	M	0.72894	2.215	0.23401	N	0.997759	D;D	0.76494	0.999;0.999	D;D	0.72338	0.977;0.977	T	0.36890	-0.9729	10	0.30854	T	0.27	-14.1664	11.9919	0.53180	0.8547:0.1453:0.0:0.0	.	225;225	A4FTY0;O60443	.;DFNA5_HUMAN	H	225;61;61;61;225	ENSP00000339587:Y225H;ENSP00000401332:Y61H;ENSP00000442661:Y61H;ENSP00000387119:Y61H;ENSP00000386670:Y225H	ENSP00000339587:Y225H	Y	-	1	0	DFNA5	24723422	0.338000	0.24775	0.119000	0.21687	0.295000	0.27426	1.755000	0.38379	0.954000	0.37851	0.533000	0.62120	TAC	.	.		0.572	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		G	24756897	A	G	24756897	3	3	91	1	0	0	0	0	1	0	0	0	4456	449	16	2	841	2	DFNA5	7	24756897	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	6841791	24756897	134381766	252	12326										
CRHR2	1395	hgsc.bcm.edu	37	chr7	30704769	30704769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gataaaggtggtgatgaggtTccagtgaatcacattccgca	12	7	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:30704769T>C	ENST00000471646.1	-	5	877	c.460A>G	c.(460-462)Aac>Gac	p.N154D	CRHR2_ENST00000348438.4_Missense_Mutation_p.N181D|CRHR2_ENST00000506074.2_Missense_Mutation_p.N154D|CRHR2_ENST00000341843.4_Missense_Mutation_p.N140D	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	154					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GTGATGAGGTTCCAGTGAATC	0.562																																					p.N181D		Atlas-SNP	.											.	CRHR2	104	.	0			c.A541G						.						121	96	104					7																	30704769		2203	4300	6503	SO:0001583	missense	1395	exon6			TGAGGTTCCAGTG		CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"GPCR / Class B : Corticotropin-releasing factor receptors"	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.460A>G	chr7.hg19:g.30704769T>C	ENSP00000418722:p.Asn154Asp	117.0	0.0		97.0	4.0	NM_001202475	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Missense_Mutation	SNP	ENST00000471646.1	hg19	CCDS5429.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.675266	0.88445	.	.	ENSG00000106113	ENST00000471646;ENST00000348438;ENST00000341843;ENST00000506074	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	4.28	4.28	0.50868	GPCR, family 2-like (1);	0.046573	0.85682	D	0.000000	T	0.66046	0.2750	M	0.92691	3.335	0.80722	D	1	D;D;D;D;D	0.76494	0.99;0.997;0.999;0.999;0.995	D;D;D;D;D	0.72075	0.941;0.976;0.976;0.976;0.976	T	0.74677	-0.3585	10	0.87932	D	0	.	12.0279	0.53382	0.0:0.0:0.0:1.0	.	153;154;181;140;154	B3SXT0;B3SXS6;Q13324-2;Q13324-3;Q13324	.;.;.;.;CRFR2_HUMAN	D	154;181;140;154	ENSP00000418722:N154D;ENSP00000340943:N181D;ENSP00000344304:N140D;ENSP00000426498:N154D	ENSP00000344304:N140D	N	-	1	0	CRHR2	30671294	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.776000	0.85560	2.146000	0.66826	0.533000	0.62120	AAC	.	.		0.562	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3			C	30704769	T	C	30704769	3	2	91	1	0	0	0	0	1	0	0	0	3874	1783	62	2	807	2	CRHR2	7	30704769	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	5947872	30704769	128433894	253	12327										
AVL9	23080	hgsc.bcm.edu	37	chr7	32612832	32612832	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tagaagaagctctgatccagAtccatgatccagaactcagg	9	10	2	6			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:32612832A>G	ENST00000318709.4	+	12	1593	c.1372A>G	c.(1372-1374)Atc>Gtc	p.I458V	AVL9_ENST00000404479.1_Intron|AVL9_ENST00000409301.1_Missense_Mutation_p.I458V	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	458					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCTGATCCAGATCCATGATCC	0.507																																					p.I458V		Atlas-SNP	.											.	AVL9	66	.	0			c.A1372G						.						83	65	71					7																	32612832		2203	4300	6503	SO:0001583	missense	23080	exon12			ATCCAGATCCATG	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"KIAA0241"	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1372A>G	chr7.hg19:g.32612832A>G	ENSP00000315568:p.Ile458Val	98.0	0.0		102.0	5.0	NM_015060	Q92573	Missense_Mutation	SNP	ENST00000318709.4	hg19	CCDS34613.1	.	.	.	.	.	.	.	.	.	.	A	9.602	1.128856	0.21041	.	.	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000446718	T;T;T	0.42131	0.98;0.98;0.98	5.52	4.37	0.52481	.	0.108992	0.64402	N	0.000008	T	0.29458	0.0734	L	0.38531	1.155	0.80722	D	1	B;B	0.12630	0.003;0.006	B;B	0.20184	0.009;0.028	T	0.07009	-1.0795	10	0.16420	T	0.52	-10.2239	7.8191	0.29278	0.7763:0.0:0.2237:0.0	.	458;458	Q8NBF6-2;Q8NBF6	.;AVL9_HUMAN	V	458;458;458;389	ENSP00000315568:I458V;ENSP00000387011:I458V;ENSP00000395134:I389V	ENSP00000315568:I458V	I	+	1	0	AVL9	32579357	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.308000	0.59129	0.924000	0.37069	0.533000	0.62120	ATC	.	.		0.507	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		G	32612832	A	G	32612832	3	3	91	1	0	0	0	0	1	0	0	0	1228	333	12	2	1418	2	AVL9	7	32612832	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1908063	32612832	126525831	254	12328										
VPS41	27072	hgsc.bcm.edu	37	chr7	38765881	38765881	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caaaattgcacttcctggtcCacggttcttagcactgcaga	8	12	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:38765881C>T	ENST00000310301.4	-	29	2584	c.2530G>A	c.(2530-2532)Gga>Aga	p.G844R	VPS41_ENST00000395969.2_Missense_Mutation_p.G819R	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	844					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						CTTCCTGGTCCACGGTTCTTA	0.363																																					p.G844R		Atlas-SNP	.											.	VPS41	102	.	0			c.G2530A						.						137	123	128					7																	38765881		2203	4300	6503	SO:0001583	missense	27072	exon29			CTGGTCCACGGTT	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"vacuolar protein sorting 41 (yeast homolog)", "vacuolar protein sorting 41 (yeast)"			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.2530G>A	chr7.hg19:g.38765881C>T	ENSP00000309457:p.Gly844Arg	110.0	0.0		93.0	4.0	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	hg19	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.304227	0.60305	.	.	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.17370	2.28;2.28	5.51	5.51	0.81932	.	0.049153	0.85682	D	0.000000	T	0.13628	0.0330	N	0.25144	0.715	0.80722	D	1	B;B;B	0.23058	0.046;0.079;0.079	B;B;B	0.18263	0.017;0.021;0.021	T	0.11690	-1.0577	10	0.18276	T	0.48	-24.2966	19.0496	0.93038	0.0:1.0:0.0:0.0	.	844;819;844	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	R	844;819	ENSP00000309457:G844R;ENSP00000379297:G819R	ENSP00000309457:G844R	G	-	1	0	VPS41	38732406	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	6.463000	0.73530	2.590000	0.87494	0.650000	0.86243	GGA	.	.		0.363	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3			T	38765881	C	T	38765881	3	4	91	1	0	0	0	0	1	0	0	0	17225	603	21	3	38	3	VPS41	7	38765881	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	6153049	38765881	120372782	255	12329										
C7orf25	79020	hgsc.bcm.edu	37	chr7	42950513	42950513	+	5'UTR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagacatgctgtcagcattaTtcctttcctagggaaagaaa	8	9	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:42950513T>C	ENST00000350427.4	-	0	262				C7orf25_ENST00000447342.1_5'UTR|PSMA2_ENST00000442788.1_3'UTR|C7orf25_ENST00000438029.1_5'UTR|C7orf25_ENST00000431882.2_Missense_Mutation_p.N54S			Q9BPX7	CG025_HUMAN	chromosome 7 open reading frame 25											endometrium(6)|kidney(1)|large_intestine(7)|lung(2)|skin(1)	17						GTCAGCATTATTCCTTTCCTA	0.388																																					p.N54S		Atlas-SNP	.											.	C7orf25	36	.	0			c.A161G						.						91	89	90					7																	42950513		2202	4300	6502	SO:0001623	5_prime_UTR_variant	79020	exon2			GCATTATTCCTTT	BC001845	CCDS5466.1, CCDS47576.1	7p14.1	2011-11-24			ENSG00000136197	ENSG00000136197			21703	protein-coding gene	gene with protein product							Standard	NM_024054		Approved	MGC2821	uc003thx.4	Q9BPX7	OTTHUMG00000128869	ENST00000350427.4:c.-14A>G	chr7.hg19:g.42950513T>C		103.0	0.0		70.0	4.0	NM_001099858	A4D1V2|J3KR36|Q9H779	Missense_Mutation	SNP	ENST00000350427.4	hg19	CCDS5466.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.457279	0.43634	.	.	ENSG00000136197	ENST00000431882;ENST00000421724	T	0.39592	1.07	5.42	5.42	0.78866	.	.	.	.	.	T	0.24774	0.0601	N	0.08118	0	0.80722	D	1	B	0.18741	0.03	B	0.15870	0.014	T	0.07829	-1.0752	9	0.20519	T	0.43	.	15.4811	0.75528	0.0:0.0:0.0:1.0	.	54	B4DQM3	.	S	54;10	ENSP00000416290:N54S	ENSP00000395817:N10S	N	-	2	0	C7orf25	42917038	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	3.455000	0.52993	2.064000	0.61679	0.459000	0.35465	AAT	.	.		0.388	C7orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250814.2	NM_024054		C	42950513	T	C	42950513	1	2	91	0	1	0	0	0	0	0	0	0	2382	1493	52	2		2	C7orf25	7	42950513	5'UTR	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4184632	42950513	116188150	256	12330										
H2AFV	94239	hgsc.bcm.edu	37	chr7	44875219	44875219	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgcggagtgatacgctttacTttgagatccttagaagcatt	10	8	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:44875219T>C	ENST00000308153.4	-	4	325	c.234A>G	c.(232-234)aaA>aaG	p.K78K	H2AFV_ENST00000350771.3_Silent_p.K52K|H2AFV_ENST00000437072.1_Silent_p.K40K|H2AFV_ENST00000349299.3_Silent_p.K40K|H2AFV_ENST00000381124.5_Intron|H2AFV_ENST00000521529.1_Intron|H2AFV_ENST00000222690.6_Silent_p.K78K|H2AFV_ENST00000446531.1_Silent_p.K78K	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	78						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						TACGCTTTACTTTGAGATCCT	0.458																																					p.K78K		Atlas-SNP	.											.	H2AFV	14	.	0			c.A234G						.						113	94	100					7																	44875219		2203	4300	6503	SO:0001819	synonymous_variant	94239	exon4			CTTTACTTTGAGA	AF081192	CCDS5495.1, CCDS5496.1, CCDS5497.1, CCDS5498.1, CCDS47581.1	7p13	2011-01-27		2004-03-26	ENSG00000105968	ENSG00000105968		"Histones / Replication-independent"	20664	protein-coding gene	gene with protein product				H2AV			Standard	NM_012412		Approved	MGC10170, MGC10831, MGC1947	uc003tma.2	Q71UI9	OTTHUMG00000129217	ENST00000308153.4:c.234A>G	chr7.hg19:g.44875219T>C		132.0	0.0		82.0	6.0	NM_012412	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	Silent	SNP	ENST00000308153.4	hg19	CCDS5496.1																																																																																			.	.		0.458	H2AFV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251305.1	NM_012412		C	44875219	T	C	44875219	2	2	91	1	0	0	0	0	0	0	0	1	6936	1606	56	2		2	H2AFV	7	44875219	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1924706	44875219	114263444	257	12331										
CCM2	83605	hgsc.bcm.edu	37	chr7	45077891	45077891	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttaaacgagtattcctaaaaGgtgaaaagagtagagataag	10	3	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:45077891G>T	ENST00000258781.6	+	2	219	c.70G>T	c.(70-72)Ggt>Tgt	p.G24C	CCM2_ENST00000475551.1_Missense_Mutation_p.G18C|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000381112.3_Missense_Mutation_p.G45C|CCM2_ENST00000544363.1_Missense_Mutation_p.G24C|CCM2_ENST00000474617.1_Missense_Mutation_p.G18C|CCM2_ENST00000541586.1_Intron	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	24					blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						ATTCCTAAAAGGTGAAAAGAG	0.468																																					p.G45C		Atlas-SNP	.											.	CCM2	42	.	0			c.G133T						.						89	88	88					7																	45077891		2203	4300	6503	SO:0001583	missense	83605	exon2			CTAAAAGGTGAAA	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"malcavernin"	607929	"chromosome 7 open reading frame 22"	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.70G>T	chr7.hg19:g.45077891G>T	ENSP00000258781:p.Gly24Cys	93.0	0.0		71.0	4.0	NM_001029835	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Missense_Mutation	SNP	ENST00000258781.6	hg19	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625189	0.66901	.	.	ENSG00000136280	ENST00000258781;ENST00000544363;ENST00000543541;ENST00000475551;ENST00000381112;ENST00000474617	T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.72391	0.3454	M	0.67953	2.075	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.991;1.0;1.0;1.0	T	0.74090	-0.3777	10	0.87932	D	0	-18.6522	18.3739	0.90428	0.0:0.0:1.0:0.0	.	45;45;24;24	B7Z5A6;E9PDJ3;F5H0E1;Q9BSQ5	.;.;.;CCM2_HUMAN	C	24;24;24;18;45;18	ENSP00000258781:G24C;ENSP00000438035:G24C;ENSP00000417180:G18C;ENSP00000370503:G45C;ENSP00000419474:G18C	ENSP00000258781:G24C	G	+	1	0	CCM2	45044416	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.277000	0.95755	2.696000	0.92011	0.655000	0.94253	GGT	.	.		0.468	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443		T	45077891	G	T	45077891	3	4	91	1	0	0	0	0	1	0	0	0	2910	1000	35	3	173	3	CCM2	7	45077891	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	202672	45077891	114060772	258	12332										
COBL	23242	hgsc.bcm.edu	37	chr7	51085259	51085259	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctgttcattcacacgagcaAgggcacctgcagggaagaga	12	10	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:51085259A>G	ENST00000265136.7	-	13	3940	c.3775T>C	c.(3775-3777)Ttg>Ctg	p.L1259L	COBL_ENST00000395542.2_Silent_p.L1341L|RP4-724E13.2_ENST00000420449.1_RNA|RP4-724E13.2_ENST00000582616.1_RNA	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1259					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					CACACGAGCAAGGGCACCTGC	0.498																																					p.L1259L	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.T3775C						.						105	99	101					7																	51085259		2203	4300	6503	SO:0001819	synonymous_variant	23242	exon13			CGAGCAAGGGCAC	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3775T>C	chr7.hg19:g.51085259A>G		125.0	0.0		98.0	4.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	hg19	CCDS34637.1																																																																																			.	.		0.498	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		G	51085259	A	G	51085259	2	3	91	1	0	0	0	0	0	0	0	1	3655	69	3	2		2	COBL	7	51085259	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	6007368	51085259	108053404	259	12333										
COBL	23242	hgsc.bcm.edu	37	chr7	51096495	51096495	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacctccagaactctctgacTttcccaatgggctgagattc	7	14	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:51096495T>C	ENST00000265136.7	-	10	2463	c.2298A>G	c.(2296-2298)aaA>aaG	p.K766K	COBL_ENST00000395542.2_Silent_p.K848K	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	766					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					ACTCTCTGACTTTCCCAATGG	0.587																																					p.K766K	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.A2298G						.						50	50	50					7																	51096495		2203	4300	6503	SO:0001819	synonymous_variant	23242	exon10			TCTGACTTTCCCA	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.2298A>G	chr7.hg19:g.51096495T>C		150.0	0.0		86.0	5.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	hg19	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	T	0.505	-0.868926	0.02570	.	.	ENSG00000106078	ENST00000457306	.	.	.	5.83	-0.929	0.10444	.	.	.	.	.	.	.	.	.	.	.	0.19945	N	0.99994	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.2731	0.15636	0.0:0.2763:0.262:0.4617	.	.	.	.	.	-1	.	.	.	-	.	.	COBL	51063989	0.430000	0.25538	0.000000	0.03702	0.011000	0.07611	-0.022000	0.12480	-0.387000	0.07809	0.533000	0.62120	.	.	.		0.587	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		C	51096495	T	C	51096495	2	2	91	1	0	0	0	0	0	0	0	1	3655	1606	56	2		2	COBL	7	51096495	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	11236	51096495	108042168	260	12334										
ZNF716	441234	hgsc.bcm.edu	37	chr7	57522850	57522851	+	Missense_Mutation	DNP	AA	AA	TT													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agccccagaatataaagagaAatgagatggtagccaaacac							TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:57522850_57522851AA>TT	ENST00000420713.1	+	3	350_351	c.238_239AA>TT	c.(238-240)AAt>TTt	p.N80F		NM_001159279.1	NP_001152751.1	A6NP11	ZN716_HUMAN	zinc finger protein 716	80	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|lung(20)|ovary(2)	24						TATAAAGAGAAATGAGATGGTA	0.406																																					p.N80Y|p.N80I		Atlas-SNP	.											.	ZNF716	207	.	0			c.A238T|c.A239T						.																																			SO:0001583	missense	441234	exon3			AAGAGAAATGAGA|AGAGAAATGAGAT	AK131575	CCDS55112.1	7p11.1	2013-01-08			ENSG00000182111	ENSG00000182111		"Zinc fingers, C2H2-type", "-"	32458	protein-coding gene	gene with protein product							Standard	NM_001159279		Approved	FLJ46189	uc011kdi.1	A6NP11	OTTHUMG00000156689	Exception_encountered	chr7.hg19:g.57522850_57522851delinsTT	ENSP00000394248:p.Asn80Phe	41.0	0.0		34.0	9.0	NM_001159279		Missense_Mutation	SNP	ENST00000420713.1	hg19	CCDS55112.1																																																																																			.	.		0.406	ZNF716-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345309.1	NM_001159279		TT	57522851	AA	TT	57522850	3	4	91	1	0	0	0	0	1	0	0	0	18134	14	1	4	248	4	ZNF716	7	57522850	Missense_Mutation	DNP	AA	TCGA-DD-A119-01A-11D-A12Z-10	6426355	57522850	101615813	261	12335										
ZNF273	10793	hgsc.bcm.edu	37	chr7	64389279	64389279	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aatgtggcaaagcttttaacCggtcctcaaaccttactcga	7	11	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:64389279C>T	ENST00000476120.1	+	4	1644	c.1573C>T	c.(1573-1575)Cgg>Tgg	p.R525W	ZNF273_ENST00000527278.1_3'UTR|ZNF273_ENST00000319636.5_Missense_Mutation_p.R460W	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	525					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AGCTTTTAACCGGTCCTCAAA	0.388																																					p.R525W	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-SNP	.											.	ZNF273	45	.	0			c.C1573T						.						60	66	64					7																	64389279		2203	4300	6503	SO:0001583	missense	10793	exon4			TTTAACCGGTCCT	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"Zinc fingers, C2H2-type", "-"	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.1573C>T	chr7.hg19:g.64389279C>T	ENSP00000418719:p.Arg525Trp	113.0	0.0		127.0	6.0	NM_021148	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	hg19	CCDS5528.2	.	.	.	.	.	.	.	.	.	.	.	8.866	0.948193	0.18356	.	.	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.36520	1.25;1.25	1.16	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25082	0.0609	L	0.48642	1.525	0.09310	N	1	B	0.27316	0.175	B	0.20384	0.029	T	0.19745	-1.0296	9	0.26408	T	0.33	.	4.1332	0.10159	0.401:0.599:0.0:0.0	.	525	Q14593	ZN273_HUMAN	W	525;460	ENSP00000418719:R525W;ENSP00000324518:R460W	ENSP00000324518:R460W	R	+	1	2	ZNF273	64026714	0.000000	0.05858	0.771000	0.31576	0.771000	0.43674	-0.164000	0.09983	0.202000	0.20498	0.205000	0.17691	CGG	.	.		0.388	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1			T	64389279	C	T	64389279	3	4	91	1	0	0	0	0	1	0	0	0	17823	643	23	1	1587	1	ZNF273	7	64389279	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	6866429	64389279	94749384	262	12336										
ZNF92	168374	hgsc.bcm.edu	37	chr7	64864692	64864692	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttctcaacccttattacacaTcagataatttatactggaga	4	9	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:64864692T>C	ENST00000328747.7	+	4	1864	c.1665T>C	c.(1663-1665)caT>caC	p.H555H	ZNF92_ENST00000357512.2_Silent_p.H523H|ZNF92_ENST00000431504.1_Silent_p.H479H|ZNF92_ENST00000450302.2_Silent_p.H486H	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	555					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				TTATTACACATCAGATAATTT	0.348																																					p.H555H		Atlas-SNP	.											.	ZNF92	68	.	0			c.T1665C						.						42	49	47					7																	64864692		2203	4298	6501	SO:0001819	synonymous_variant	168374	exon4			TACACATCAGATA	M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"Zinc fingers, C2H2-type", "-"	13168	protein-coding gene	gene with protein product		603974	"zinc finger protein 92 (HTF12)"			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.1665T>C	chr7.hg19:g.64864692T>C		106.0	0.0		82.0	4.0	NM_152626	A6NNF9|Q8N492|Q8NB35	Silent	SNP	ENST00000328747.7	hg19	CCDS34646.1																																																																																			.	.		0.348	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626		C	64864692	T	C	64864692	2	2	91	1	0	0	0	0	0	0	0	1	18216	1432	50	2		2	ZNF92	7	64864692	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	475413	64864692	94273971	263	12337										
HIP1	3092	hgsc.bcm.edu	37	chr7	75184733	75184733	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtgtacctgcagacccagcGcagctgatgagaggaggttc	14	10	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:75184733G>A	ENST00000336926.6	-	19	1976	c.1950C>T	c.(1948-1950)tgC>tgT	p.C650C	HIP1_ENST00000434438.2_Silent_p.C650C	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	650					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CAGACCCAGCGCAGCTGATGA	0.542			T	PDGFRB	CMML																																p.C650C		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	HIP1,NS,carcinoma,0,1	HIP1	91	.	0			c.C1950T						.						87	70	76					7																	75184733		2203	4300	6503	SO:0001819	synonymous_variant	3092	exon19			CCCAGCGCAGCTG	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.1950C>T	chr7.hg19:g.75184733G>A		146.0	0.0		100.0	4.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	hg19	CCDS34669.1																																																																																			.	.		0.542	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		A	75184733	G	A	75184733	2	1	91	1	0	0	0	0	0	0	0	1	7123	1079	38	1		1	HIP1	7	75184733	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	10320041	75184733	83953930	264	12338										
CCDC146	57639	hgsc.bcm.edu	37	chr7	76883831	76883831	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttttttttgcagcttaaaggAagaaaaaatcatcatagtaa	6	4	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:76883831A>G	ENST00000285871.4	+	5	585	c.458A>G	c.(457-459)gAa>gGa	p.E153G	AC073635.5_ENST00000476561.2_RNA|CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	153										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				AGCTTAAAGGAAGAAAAAATC	0.294																																					p.E153G		Atlas-SNP	.											.	CCDC146	87	.	0			c.A458G						.						46	49	48					7																	76883831		2200	4295	6495	SO:0001583	missense	57639	exon5			TAAAGGAAGAAAA	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.458A>G	chr7.hg19:g.76883831A>G	ENSP00000285871:p.Glu153Gly	52.0	0.0		40.0	4.0	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	hg19	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	A	17.55	3.417321	0.62622	.	.	ENSG00000135205	ENST00000415750;ENST00000285871	D	0.83914	-1.78	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.90359	0.6983	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90074	0.4165	10	0.41790	T	0.15	-21.6388	13.899	0.63790	1.0:0.0:0.0:0.0	.	153	Q8IYE0	CC146_HUMAN	G	153	ENSP00000285871:E153G	ENSP00000285871:E153G	E	+	2	0	AC007000.1	76721767	1.000000	0.71417	0.997000	0.53966	0.522000	0.34438	5.832000	0.69337	2.227000	0.72691	0.455000	0.32223	GAA	.	.		0.294	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		G	76883831	A	G	76883831	3	3	91	1	0	0	0	0	1	0	0	0	2782	246	9	2	472	2	CCDC146	7	76883831	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1699098	76883831	82254832	265	12339										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91706167	91706167	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttgataattttgttattaaAgattacaaacttagaagagc	6	3	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:91706167A>G	ENST00000359028.2	+	30	6873		c.e30-1		AKAP9_ENST00000356239.3_Splice_Site|AKAP9_ENST00000358100.2_Splice_Site			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9						G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTGTTATTAAAGATTACAAAC	0.254			T	BRAF	papillary thyroid																																.		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.6613-2A>G						.						20	20	20					7																	91706167		2150	4238	6388	SO:0001630	splice_region_variant	10142	exon29			TATTAAAGATTAC	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.6649-1A>G	chr7.hg19:g.91706167A>G		171.0	0.0		121.0	5.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Splice_Site	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	A	20.5	4.005307	0.74932	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0786	0.80985	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AKAP9	91544103	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	7.422000	0.80217	2.254000	0.74563	0.460000	0.39030	.	.	.		0.254	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	Intron	G	91706167	A	G	91706167	5	3	91	1	0	0	0	0	0	0	1	0	459	86	3	2	6725	2	AKAP9	7	91706167	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	14822336	91706167	67432496	266	12340										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94057035	94057035	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acttctacagggctgaccagCctcgctcagcaccttctctc	7	17	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:94057035C>A	ENST00000297268.6	+	49	3835	c.3364C>A	c.(3364-3366)Cct>Act	p.P1122T		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1122				Missing (in Ref. 17; CAA23761). {ECO:0000305}.	blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GGCTGACCAGCCTCGCTCAGC	0.557										HNSCC(75;0.22)																											p.P1122T		Atlas-SNP	.											.	COL1A2	240	.	0			c.C3364A						.						100	99	99					7																	94057035		2203	4300	6503	SO:0001583	missense	1278	exon49			GACCAGCCTCGCT	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3364C>A	chr7.hg19:g.94057035C>A	ENSP00000297268:p.Pro1122Thr	86.0	0.0		95.0	4.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.848173	0.51164	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.89485	-2.52	5.71	5.71	0.89125	.	0.055529	0.64402	D	0.000001	D	0.92338	0.7569	L	0.55103	1.725	0.38795	D	0.955079	D	0.89917	1.0	D	0.80764	0.994	D	0.89134	0.3512	10	0.15499	T	0.54	.	17.7362	0.88394	0.0:1.0:0.0:0.0	.	1122	P08123	CO1A2_HUMAN	T	1122;1123	ENSP00000297268:P1122T	ENSP00000297268:P1122T	P	+	1	0	COL1A2	93894971	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.698000	0.54771	2.873000	0.98535	0.561000	0.74099	CCT	.	.		0.557	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		A	94057035	C	A	94057035	3	1	91	1	0	0	0	0	1	0	0	0	3680	739	26	3	3558	3	COL1A2	7	94057035	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2350868	94057035	65081628	267	12341										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98609873	98609873	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgacccgcctgcacaacctCgcccagttcgaaggcgggga	12	15	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:98609873C>T	ENST00000359863.4	+	72	11684	c.11475C>T	c.(11473-11475)ctC>ctT	p.L3825L	AC004893.11_ENST00000360902.1_RNA|TRRAP_ENST00000355540.3_Silent_p.L3796L|TRRAP_ENST00000446306.3_Silent_p.L3814L	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	3825	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TGCACAACCTCGCCCAGTTCG	0.652																																					p.L3825L		Atlas-SNP	.											.	TRRAP	863	.	0			c.C11475T						.						53	48	50					7																	98609873		2203	4300	6503	SO:0001819	synonymous_variant	8295	exon72			CAACCTCGCCCAG	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.11475C>T	chr7.hg19:g.98609873C>T		81.0	0.0		63.0	12.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	hg19	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	9.306	1.054218	0.19907	.	.	ENSG00000196367	ENST00000456197	.	.	.	5.16	-4.29	0.03721	.	.	.	.	.	T	0.53769	0.1817	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53809	-0.8386	4	.	.	.	.	10.3402	0.43873	0.0:0.2236:0.3968:0.3796	.	.	.	.	L	3554	.	.	S	+	2	0	TRRAP	98447809	0.022000	0.18835	0.967000	0.41034	0.993000	0.82548	-0.981000	0.03766	-0.770000	0.04614	-0.345000	0.07892	TCG	.	.		0.652	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		T	98609873	C	T	98609873	2	4	91	1	0	0	0	0	0	0	0	1	16616	871	31	1		1	TRRAP	7	98609873	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	4552838	98609873	60528790	268	12342										
STAG3	10734	hgsc.bcm.edu	37	chr7	99800175	99800175	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgctttatggggtgctggagAtggatgcagcctcagatgtt	15	6	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:99800175A>G	ENST00000426455.1	+	25	3069	c.2662A>G	c.(2662-2664)Atg>Gtg	p.M888V	STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000543273.1_RNA|STAG3_ENST00000394018.2_Missense_Mutation_p.M830V|STAG3_ENST00000317296.5_Missense_Mutation_p.M888V|GATS_ENST00000436886.2_3'UTR	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	888					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGTGCTGGAGATGGATGCAGC	0.517																																					p.M888V		Atlas-SNP	.											.	STAG3	121	.	0			c.A2662G						.						163	170	168					7																	99800175		2203	4300	6503	SO:0001583	missense	10734	exon25			CTGGAGATGGATG	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2662A>G	chr7.hg19:g.99800175A>G	ENSP00000400359:p.Met888Val	88.0	0.0		57.0	4.0	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	hg19	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	13.88	2.369405	0.42003	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000317296	T;T;T	0.20738	2.05;2.05;2.05	5.18	2.92	0.33932	.	0.343528	0.25143	N	0.032816	T	0.18383	0.0441	L	0.53561	1.675	0.80722	D	1	B;B;B	0.14438	0.001;0.01;0.004	B;B;B	0.12156	0.007;0.004;0.005	T	0.04509	-1.0946	10	0.45353	T	0.12	-8.28	6.2811	0.21007	0.6573:0.2074:0.0:0.1354	.	830;888;888	B4DZ10;D6W5U7;Q9UJ98	.;.;STAG3_HUMAN	V	888;830;888	ENSP00000400359:M888V;ENSP00000377586:M830V;ENSP00000319318:M888V	ENSP00000319318:M888V	M	+	1	0	STAG3	99638111	0.487000	0.25988	0.982000	0.44146	0.953000	0.61014	0.453000	0.21811	0.495000	0.27882	0.460000	0.39030	ATG	.	.		0.517	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		G	99800175	A	G	99800175	3	3	91	1	0	0	0	0	1	0	0	0	15259	333	12	2	2756	2	STAG3	7	99800175	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1190302	99800175	59338488	269	12343										
CUX1	1523	hgsc.bcm.edu	37	chr7	101839938	101839938	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agccaggaggaaagggaaagAccagcctgaaagtcggcgcc	15	10	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:101839938A>G	ENST00000292535.7	+	15	1285	c.1247A>G	c.(1246-1248)gAc>gGc	p.D416G	CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Intron|CUX1_ENST00000425244.2_Intron|SNORA48_ENST00000517015.1_RNA|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000549414.2_Missense_Mutation_p.D416G|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.D427G|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000556210.1_Intron|CUX1_ENST00000550008.2_Missense_Mutation_p.D416G|CUX1_ENST00000437600.4_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	416					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						AAAGGGAAAGACCAGCCTGAA	0.542																																					p.D427G		Atlas-SNP	.											.	CUX1	253	.	0			c.A1280G						.						38	48	44					7																	101839938		2198	4297	6495	SO:0001583	missense	1523	exon15			GGAAAGACCAGCC	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1247A>G	chr7.hg19:g.101839938A>G	ENSP00000292535:p.Asp416Gly	132.0	0.0		96.0	4.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.913591	0.72983	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008	T;T;T;T	0.61274	0.12;0.14;0.13;0.17	5.78	5.78	0.91487	.	0.057469	0.64402	D	0.000002	T	0.61726	0.2370	N	0.16743	0.435	0.80722	D	1	D;D	0.69078	0.996;0.997	P;D	0.66196	0.877;0.942	T	0.67810	-0.5574	10	0.72032	D	0.01	-29.1043	16.1054	0.81216	1.0:0.0:0.0:0.0	.	416;427	P39880;P39880-3	CUX1_HUMAN;.	G	427;416;416;416	ENSP00000353401:D427G;ENSP00000292535:D416G;ENSP00000446630:D416G;ENSP00000447373:D416G	ENSP00000292535:D416G	D	+	2	0	CUX1	101626658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.521000	0.90569	2.198000	0.70561	0.459000	0.35465	GAC	.	.		0.542	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		G	101839938	A	G	101839938	3	3	91	1	0	0	0	0	1	0	0	0	4066	275	10	2	1372	2	CUX1	7	101839938	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2039763	101839938	57298725	270	12344										
CFTR	1080	hgsc.bcm.edu	37	chr7	117232660	117232660	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atatattcaagaaggttatcTcaagaaactggcttggaaat	8	5	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:117232660T>C	ENST00000003084.6	+	14	2571	c.2439T>C	c.(2437-2439)tcT>tcC	p.S813S	CFTR_ENST00000454343.1_Silent_p.S752S	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	813					cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	GAAGGTTATCTCAAGAAACTG	0.418									Cystic Fibrosis																												p.S813S		Atlas-SNP	.											.	CFTR	171	.	0			c.T2439C						.						56	57	57					7																	117232660		2203	4300	6503	SO:0001819	synonymous_variant	1080	exon14	Familial Cancer Database	CF	GTTATCTCAAGAA	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.2439T>C	chr7.hg19:g.117232660T>C		83.0	0.0		61.0	4.0	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	hg19	CCDS5773.1																																																																																			.	.		0.418	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		C	117232660	T	C	117232660	2	2	91	1	0	0	0	0	0	0	0	1	3296	1538	54	2		2	CFTR	7	117232660	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	15392722	117232660	41906003	271	12345										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121652375	121652375	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acaagaaacctctgtttccaTttctagcaccaagggcatgt	7	11	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:121652375T>C	ENST00000393386.2	+	12	3686	c.3275T>C	c.(3274-3276)aTt>aCt	p.I1092T	PTPRZ1_ENST00000483028.1_Intron|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1092					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TCTGTTTCCATTTCTAGCACC	0.388																																					p.I1092T		Atlas-SNP	.											PTPRZ1_ENST00000393386,NS,carcinoma,0,2	PTPRZ1	605	.	0			c.T3275C						.						114	113	113					7																	121652375		2203	4300	6503	SO:0001583	missense	5803	exon12			TTTCCATTTCTAG	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.3275T>C	chr7.hg19:g.121652375T>C	ENSP00000377047:p.Ile1092Thr	139.0	0.0		92.0	4.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	T	7.681	0.689039	0.14973	.	.	ENSG00000106278	ENST00000393386	T	0.44881	0.91	5.32	-2.34	0.06704	.	1.440510	0.03998	N	0.296006	T	0.20981	0.0505	N	0.08118	0	0.20074	N	0.999934	B	0.02656	0.0	B	0.04013	0.001	T	0.15407	-1.0438	10	0.41790	T	0.15	.	3.5483	0.07836	0.1308:0.0764:0.4062:0.3866	.	1092	P23471	PTPRZ_HUMAN	T	1092	ENSP00000377047:I1092T	ENSP00000377047:I1092T	I	+	2	0	PTPRZ1	121439611	0.277000	0.24220	0.022000	0.16811	0.981000	0.71138	0.486000	0.22340	-0.270000	0.09285	0.454000	0.30748	ATT	.	.		0.388	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121652375	T	C	121652375	3	2	91	1	0	0	0	0	1	0	0	0	12829	1493	52	2	3321	2	PTPRZ1	7	121652375	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4419715	121652375	37486288	272	12346										
RNF148	378925	hgsc.bcm.edu	37	chr7	122342235	122342235	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaggtaaatagatacatgatGtaatggctcacccactgcat	8	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:122342235G>A	ENST00000434824.1	-	1	786	c.570C>T	c.(568-570)taC>taT	p.Y190Y	CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000313070.7_Intron|RNF148_ENST00000447240.1_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	190						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						GATACATGATGTAATGGCTCA	0.443																																					p.Y190Y		Atlas-SNP	.											.	RNF148	71	.	0			c.C570T						.						193	191	192					7																	122342235		2056	4213	6269	SO:0001819	synonymous_variant	378925	exon1			CATGATGTAATGG	BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"RING-type (C3HC4) zinc fingers"	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.570C>T	chr7.hg19:g.122342235G>A		97.0	0.0		84.0	4.0	NM_198085	A4D0X4|Q8N308	Silent	SNP	ENST00000434824.1	hg19	CCDS47692.1																																																																																			.	.		0.443	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085		A	122342235	G	A	122342235	2	1	91	1	0	0	0	0	0	0	0	1	13464	1372	48	3		3	RNF148	7	122342235	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	689860	122342235	36796428	273	12347										
CREB3L2	64764	hgsc.bcm.edu	37	chr7	137567210	137567210	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctccaggctggtctcattcgAgataatgaaatggggaagat	12	7	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:137567210A>G	ENST00000330387.6	-	11	1786	c.1435T>C	c.(1435-1437)Tcg>Ccg	p.S479P		NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	479					cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)		FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						GTCTCATTCGAGATAATGAAA	0.577			T	FUS	fibromyxoid sarcoma																																p.S479P		Atlas-SNP	.		Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	.	CREB3L2	62	.	0			c.T1435C						.						81	75	77					7																	137567210		2203	4300	6503	SO:0001583	missense	64764	exon11			CATTCGAGATAAT	AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158		"basic leucine zipper proteins"	23720	protein-coding gene	gene with protein product		608834					Standard	NM_194071		Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.1435T>C	chr7.hg19:g.137567210A>G	ENSP00000329140:p.Ser479Pro	115.0	0.0		122.0	5.0	NM_194071	Q6P454|Q6ZMR6	Missense_Mutation	SNP	ENST00000330387.6	hg19	CCDS34760.1	.	.	.	.	.	.	.	.	.	.	A	16.82	3.229194	0.58777	.	.	ENSG00000182158	ENST00000330387	T	0.59772	0.24	5.59	1.58	0.23477	.	0.683518	0.14898	N	0.291978	T	0.41971	0.1182	L	0.36672	1.1	0.80722	D	1	P	0.38978	0.652	B	0.35813	0.211	T	0.14309	-1.0477	10	0.37606	T	0.19	-16.7484	7.5023	0.27524	0.4328:0.4449:0.0:0.1223	.	479	Q70SY1	CR3L2_HUMAN	P	479	ENSP00000329140:S479P	ENSP00000329140:S479P	S	-	1	0	CREB3L2	137217750	1.000000	0.71417	0.298000	0.25002	0.996000	0.88848	1.881000	0.39638	0.373000	0.24621	0.454000	0.30748	TCG	.	.		0.577	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341462.1	NM_194071		G	137567210	A	G	137567210	3	3	91	1	0	0	0	0	1	0	0	0	3859	304	11	2	135	2	CREB3L2	7	137567210	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	15224975	137567210	21571453	274	12348										
OR9A4	130075	hgsc.bcm.edu	37	chr7	141619595	141619595	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccttcgggatggggtgaaacGctgctgtcaactattcagga	13	9	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:141619595G>T	ENST00000548136.1	+	1	979	c.920G>T	c.(919-921)cGc>cTc	p.R307L	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	307						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22	Melanoma(164;0.0171)					GGGGTGAAACGCTGCTGTCAA	0.428																																					p.R307L		Atlas-SNP	.											.	OR9A4	58	.	0			c.G920T						.						93	94	94					7																	141619595		2045	4228	6273	SO:0001583	missense	130075	exon1			TGAAACGCTGCTG		CCDS43661.1	7q34	2012-10-03			ENSG00000258083	ENSG00000258083		"GPCR / Class A : Olfactory receptors"	15095	protein-coding gene	gene with protein product							Standard	NM_001001656		Approved		uc003vwu.1	Q8NGU2	OTTHUMG00000158370	ENST00000548136.1:c.920G>T	chr7.hg19:g.141619595G>T	ENSP00000448789:p.Arg307Leu	69.0	0.0		61.0	24.0	NM_001001656	B9EGV6|Q6IFI4	Missense_Mutation	SNP	ENST00000548136.1	hg19	CCDS43661.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.612135	0.28712	.	.	ENSG00000258083	ENST00000548136	T	0.38560	1.13	3.71	-2.07	0.07276	.	.	.	.	.	T	0.34221	0.0890	L	0.42008	1.315	0.09310	N	1	B	0.19200	0.034	B	0.22601	0.04	T	0.40572	-0.9556	9	0.87932	D	0	-0.0715	10.694	0.45888	0.2205:0.0:0.7795:0.0	.	307	Q8NGU2	OR9A4_HUMAN	L	307	ENSP00000448789:R307L	ENSP00000386148:R307L	R	+	2	0	OR9A4	141266064	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.804000	0.04535	-0.394000	0.07727	-0.423000	0.05987	CGC	.	.		0.428	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656		T	141619595	G	T	141619595	3	4	91	1	0	0	0	0	1	0	0	0	11258	1087	38	1	922	1	OR9A4	7	141619595	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	4052385	141619595	17519068	275	12349										
FAM131B	9715	hgsc.bcm.edu	37	chr7	143054115	143054115	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgggtgcttgagccagggcaTctggaaaaagaatcatggag	15	6	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:143054115T>C	ENST00000409408.1	-	6	2235	c.527A>G	c.(526-528)gAt>gGt	p.D176G	FAM131B_ENST00000409222.3_Splice_Site_p.D176G|FAM131B_ENST00000409578.1_Splice_Site_p.D192G|FAM131B_ENST00000409346.1_Splice_Site_p.D176G|FAM131B_ENST00000443739.2_Splice_Site_p.D204G			Q86XD5	F131B_HUMAN	family with sequence similarity 131, member B	176										breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24	Melanoma(164;0.205)					AGCCAGGGCATCTGGAAAAAG	0.542																																					p.D204G		Atlas-SNP	.											.	FAM131B	104	.	0			c.A611G						.						35	31	33					7																	143054115		2203	4300	6503	SO:0001630	splice_region_variant	9715	exon7			AGGGCATCTGGAA	BC045611	CCDS5882.1, CCDS47734.1	7q34	2007-03-20			ENSG00000159784	ENSG00000159784			22202	protein-coding gene	gene with protein product							Standard	NM_014690		Approved	KIAA0773	uc010lpa.3	Q86XD5	OTTHUMG00000152697	ENST00000409408.1:c.527-1A>G	chr7.hg19:g.143054115T>C		74.0	0.0		74.0	4.0	NM_001031690	A4D2H6|A6NDW3|A8K605|B8ZZN2|D3DXE3|J3KQX2|Q7L0D6|Q86T97	Missense_Mutation	SNP	ENST00000409408.1	hg19	CCDS5882.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.197677	0.58126	.	.	ENSG00000159784	ENST00000443739;ENST00000409578;ENST00000409346;ENST00000452076;ENST00000409408;ENST00000409222	T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87	5.46	5.46	0.80206	.	0.199172	0.53938	D	0.000058	T	0.33059	0.0850	L	0.59436	1.845	0.52099	D	0.999945	B;P	0.45531	0.16;0.86	B;P	0.44561	0.117;0.453	T	0.12400	-1.0549	10	0.66056	D	0.02	.	15.5417	0.76057	0.0:0.0:0.0:1.0	.	192;176	Q86XD5-2;Q86XD5	.;F131B_HUMAN	G	204;192;176;180;176;176	ENSP00000410603:D204G;ENSP00000386568:D192G;ENSP00000386984:D176G;ENSP00000387017:D176G;ENSP00000387147:D176G	ENSP00000387147:D176G	D	-	2	0	FAM131B	142764237	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	2.713000	0.47194	2.072000	0.62099	0.533000	0.62120	GAT	.	.		0.542	FAM131B-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328057.1	NM_014690	Missense_Mutation	C	143054115	T	C	143054115	5	2	91	1	0	0	0	0	0	0	1	0	5445	1449	50	2	475	2	FAM131B	7	143054115	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1434520	143054115	16084548	276	12350										
ZNF777	27153	hgsc.bcm.edu	37	chr7	149133833	149133833	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agccgtgctcttccacctgtCccatcaggggctcaggtgtc	11	15	3	0	rs375051872		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:149133833C>T	ENST00000247930.4	-	5	1495	c.1172G>A	c.(1171-1173)gGa>gAa	p.G391E		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	391	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			TTCCACCTGTCCCATCAGGGG	0.597																																					p.G391E		Atlas-SNP	.											.	ZNF777	63	.	0			c.G1172A						.	C	GLU/GLY	1,3871		0,1,1935	68	70	70		1172	5.7	1	7		70	1,8249		0,1,4124	no	missense	ZNF777	NM_015694.2	98	0,2,6059	TT,TC,CC		0.0121,0.0258,0.0165	possibly-damaging	391/832	149133833	2,12120	1936	4125	6061	SO:0001583	missense	27153	exon5			ACCTGTCCCATCA	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"Zinc fingers, C2H2-type", "-"	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.1172G>A	chr7.hg19:g.149133833C>T	ENSP00000247930:p.Gly391Glu	94.0	0.0		90.0	5.0	NM_015694	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	hg19	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	C	19.07	3.756411	0.69648	2.58E-4	1.21E-4	ENSG00000196453	ENST00000247930;ENST00000314683	T	0.05996	3.36	5.66	5.66	0.87406	.	0.000000	0.53938	D	0.000055	T	0.13286	0.0322	L	0.29908	0.895	0.35148	D	0.769547	D	0.76494	0.999	D	0.76575	0.988	T	0.25745	-1.0123	10	0.23302	T	0.38	-16.2994	12.218	0.54416	0.1701:0.8299:0.0:0.0	.	391	Q9ULD5-2	.	E	391;134	ENSP00000247930:G391E	ENSP00000247930:G391E	G	-	2	0	ZNF777	148764766	0.329000	0.24696	0.977000	0.42913	0.959000	0.62525	1.119000	0.31258	2.662000	0.90505	0.555000	0.69702	GGA	.	.		0.597	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694		T	149133833	C	T	149133833	3	4	91	1	0	0	0	0	1	0	0	0	18165	855	30	3	1331	3	ZNF777	7	149133833	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	6079718	149133833	10004830	277	12351										
ABCF2	10061	hgsc.bcm.edu	37	chr7	150912710	150912710	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctgttgtttcccagtgagacCgtatcgcccaatgatcttcc	8	13	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:150912710C>A	ENST00000287844.2	-	13	1619	c.1510G>T	c.(1510-1512)Ggt>Tgt	p.G504C	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Missense_Mutation_p.G504C	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	504	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCAGTGAGACCGTATCGCCCA	0.517																																					p.G504C		Atlas-SNP	.											.	ABCF2	54	.	0			c.G1510T						.						320	281	294					7																	150912710		2203	4300	6503	SO:0001583	missense	10061	exon13			TGAGACCGTATCG	AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"ATP binding cassette transporters / subfamily F"	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.1510G>T	chr7.hg19:g.150912710C>A	ENSP00000287844:p.Gly504Cys	122.0	0.0		99.0	4.0	NM_005692	O60864|Q75MJ0|Q75MJ1|Q96TE8	Missense_Mutation	SNP	ENST00000287844.2	hg19	CCDS5923.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.314606	0.81358	.	.	ENSG00000033050	ENST00000222388;ENST00000287844	D;D	0.94931	-3.56;-3.56	5.76	5.76	0.90799	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.98526	0.9508	H	0.97918	4.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99466	1.0944	10	0.87932	D	0	-10.3108	18.9739	0.92728	0.0:1.0:0.0:0.0	.	504;504	Q9UG63;Q75MJ1	ABCF2_HUMAN;.	C	504	ENSP00000222388:G504C;ENSP00000287844:G504C	ENSP00000222388:G504C	G	-	1	0	ABCF2	150543643	1.000000	0.71417	0.945000	0.38365	0.487000	0.33371	7.237000	0.78164	2.706000	0.92434	0.655000	0.94253	GGT	.	.		0.517	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692		A	150912710	C	A	150912710	3	1	91	1	0	0	0	0	1	0	0	0	66	652	23	1	414	1	ABCF2	7	150912710	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1778877	150912710	8225953	278	12352										
XKR6	286046	hgsc.bcm.edu	37	chr8	10756400	10756400	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggctagcacccaagccagggAcatcagggaagtcacagagg	14	11	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:10756400A>G	ENST00000416569.2	-	3	1014	c.988T>C	c.(988-990)Tcc>Ccc	p.S330P	XKR6_ENST00000304437.2_Missense_Mutation_p.S51P	NM_173683.3	NP_775954.2	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related family, member 6	330						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(8)|ovary(2)|prostate(1)|skin(3)	31				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		CAAGCCAGGGACATCAGGGAA	0.572																																					p.S330P		Atlas-SNP	.											.	XKR6	85	.	0			c.T988C						.						93	83	87					8																	10756400		2203	4300	6503	SO:0001583	missense	286046	exon3			CCAGGGACATCAG	BC024146	CCDS5978.2	8p23.1	2009-05-27	2006-01-12	2005-07-28	ENSG00000171044	ENSG00000171044			27806	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 7", "chromosome 8 open reading frame 21", "X Kell blood group precursor-related family, member 6", "chromosome 8 open reading frame 5"	C8orf7, C8orf21, C8orf5			Standard	NM_173683		Approved		uc003wtk.1	Q5GH73	OTTHUMG00000129351	ENST00000416569.2:c.988T>C	chr8.hg19:g.10756400A>G	ENSP00000416707:p.Ser330Pro	111.0	0.0		43.0	6.0	NM_173683	Q8TBA0	Missense_Mutation	SNP	ENST00000416569.2	hg19	CCDS5978.2	.	.	.	.	.	.	.	.	.	.	A	17.65	3.441667	0.63067	.	.	ENSG00000171044	ENST00000304437;ENST00000416569	T;T	0.75367	-0.93;-0.93	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.88603	0.6481	M	0.91354	3.2	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.91037	0.4868	10	0.72032	D	0.01	-24.4852	14.297	0.66321	1.0:0.0:0.0:0.0	.	330	Q5GH73	XKR6_HUMAN	P	51;330	ENSP00000307120:S51P;ENSP00000416707:S330P	ENSP00000307120:S51P	S	-	1	0	XKR6	10793810	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	1.964000	0.57103	0.459000	0.35465	TCC	.	.		0.572	XKR6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383958.1	NM_173683		G	10756400	A	G	10756400	3	3	91	1	0	0	0	0	1	0	0	0	17450	275	10	2	941	2	XKR6	8	10756400	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10		10756400	135607622	279	12353										
XPO7	23039	hgsc.bcm.edu	37	chr8	21848326	21848326	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttctttttttcaatagagcgAgcacttttcatttttgggta	7	6	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:21848326A>G	ENST00000252512.9	+	18	2037	c.1937A>G	c.(1936-1938)gAg>gGg	p.E646G	XPO7_ENST00000434536.1_Missense_Mutation_p.E655G|XPO7_ENST00000433566.4_Missense_Mutation_p.E647G	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	646					mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		CAATAGAGCGAGCACTTTTCA	0.423																																					p.E646G		Atlas-SNP	.											.	XPO7	79	.	0			c.A1937G						.						157	151	153					8																	21848326		1862	4095	5957	SO:0001583	missense	23039	exon18			AGAGCGAGCACTT	AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"Exportins"	14108	protein-coding gene	gene with protein product		606140	"RAN binding protein 16"	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.1937A>G	chr8.hg19:g.21848326A>G	ENSP00000252512:p.Glu646Gly	88.0	0.0		21.0	4.0	NM_015024	O94846|Q6PJK9|Q8NEK7	Missense_Mutation	SNP	ENST00000252512.9	hg19	CCDS47818.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.843186	0.91197	.	.	ENSG00000130227	ENST00000434536;ENST00000252512;ENST00000433566	T;T;T	0.68624	-0.34;-0.34;-0.34	5.94	5.94	0.96194	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73984	0.3657	M	0.83774	2.66	0.80722	D	1	P;P;P	0.48640	0.749;0.913;0.913	B;P;P	0.45343	0.206;0.477;0.477	T	0.78006	-0.2373	10	0.51188	T	0.08	-19.812	16.0637	0.80856	1.0:0.0:0.0:0.0	.	647;655;646	E7ESC6;E9PEN8;Q9UIA9	.;.;XPO7_HUMAN	G	655;646;647	ENSP00000404853:E655G;ENSP00000252512:E646G;ENSP00000410249:E647G	ENSP00000252512:E646G	E	+	2	0	XPO7	21904272	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.313000	0.96297	2.274000	0.75844	0.528000	0.53228	GAG	.	.		0.423	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024		G	21848326	A	G	21848326	3	3	91	1	0	0	0	0	1	0	0	0	17464	304	11	2	2059	2	XPO7	8	21848326	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	11091926	21848326	124515696	280	12354										
HR	55806	hgsc.bcm.edu	37	chr8	21984816	21984816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gccgtgtgagccatgtcttcTtcagcttggtgtggtggctg	15	9	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:21984816T>C	ENST00000381418.4	-	3	2619	c.1139A>G	c.(1138-1140)aAg>aGg	p.K380R	HR_ENST00000312841.8_Missense_Mutation_p.K380R	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	380					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CCATGTCTTCTTCAGCTTGGT	0.662																																					p.K380R		Atlas-SNP	.											.	HR	71	.	0			c.A1139G						.						121	136	131					8																	21984816		2203	4300	6503	SO:0001583	missense	55806	exon3			GTCTTCTTCAGCT	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"hairless (mouse) homolog", "hairless homolog (mouse)"	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1139A>G	chr8.hg19:g.21984816T>C	ENSP00000370826:p.Lys380Arg	156.0	0.0		75.0	4.0	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	hg19	CCDS6022.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.836857	0.91117	.	.	ENSG00000168453	ENST00000381418;ENST00000312841	D;D	0.81739	-1.53;-1.52	6.04	6.04	0.98038	.	0.000000	0.64402	D	0.000011	D	0.84479	0.5481	L	0.36672	1.1	0.34520	D	0.708092	D;D	0.71674	0.998;0.997	D;D	0.80764	0.994;0.985	D	0.88893	0.3347	10	0.59425	D	0.04	-28.9319	12.9803	0.58559	0.0:0.0:0.0:1.0	.	380;380	O43593-2;O43593	.;HAIR_HUMAN	R	380	ENSP00000370826:K380R;ENSP00000326765:K380R	ENSP00000326765:K380R	K	-	2	0	HR	22040761	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	4.925000	0.63425	2.317000	0.78254	0.460000	0.39030	AAG	.	.		0.662	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			C	21984816	T	C	21984816	3	2	91	1	0	0	0	0	1	0	0	0	7356	1609	56	2	2498	2	HR	8	21984816	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	136490	21984816	124379206	281	12355										
DOCK5	80005	hgsc.bcm.edu	37	chr8	25191685	25191685	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acttgaaacctacatttacaAgcacttcagcgccactttgg	6	12	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:25191685A>G	ENST00000276440.7	+	21	2209	c.2165A>G	c.(2164-2166)aAg>aGg	p.K722R		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	722					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TACATTTACAAGCACTTCAGC	0.363																																					p.K722R	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.A2165G						.						147	143	145					8																	25191685		2203	4300	6503	SO:0001583	missense	80005	exon21			TTTACAAGCACTT		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.2165A>G	chr8.hg19:g.25191685A>G	ENSP00000276440:p.Lys722Arg	373.0	0.0		100.0	4.0	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	hg19	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.897626	0.91962	.	.	ENSG00000147459	ENST00000276440	T	0.20463	2.07	6.04	6.04	0.98038	Armadillo-type fold (1);	0.100947	0.64402	D	0.000003	T	0.32436	0.0829	M	0.72118	2.19	0.80722	D	1	P;P;P	0.47253	0.645;0.892;0.803	B;P;B	0.44732	0.313;0.459;0.313	T	0.08452	-1.0721	10	0.59425	D	0.04	.	16.5763	0.84648	1.0:0.0:0.0:0.0	.	712;497;722	D3DSS6;Q68DL4;Q9H7D0	.;.;DOCK5_HUMAN	R	722	ENSP00000276440:K722R	ENSP00000276440:K722R	K	+	2	0	DOCK5	25247602	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.339000	0.96797	2.317000	0.78254	0.459000	0.35465	AAG	.	.		0.363	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		G	25191685	A	G	25191685	3	3	91	1	0	0	0	0	1	0	0	0	4692	72	3	2	2247	2	DOCK5	8	25191685	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3206869	25191685	121172337	282	12356										
PPP2R2A	5520	hgsc.bcm.edu	37	chr8	26227714	26227714	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acagaaacacaaagcgagacAtaaccctagaagcatcgcgg	9	11	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:26227714A>G	ENST00000380737.3	+	10	1458	c.1129A>G	c.(1129-1131)Ata>Gta	p.I377V	PPP2R2A_ENST00000315985.7_Missense_Mutation_p.I387V	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	377					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		AAAGCGAGACATAACCCTAGA	0.413																																					p.I387V		Atlas-SNP	.											.	PPP2R2A	44	.	0			c.A1159G						.						80	75	77					8																	26227714		2203	4300	6503	SO:0001583	missense	5520	exon10			CGAGACATAACCC	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9304	protein-coding gene	gene with protein product	"PP2A subunit B isoform alpha"	604941	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.1129A>G	chr8.hg19:g.26227714A>G	ENSP00000370113:p.Ile377Val	200.0	0.0		108.0	5.0	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Missense_Mutation	SNP	ENST00000380737.3	hg19	CCDS34867.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.634009	0.00806	.	.	ENSG00000221914	ENST00000380737;ENST00000524169;ENST00000315985	T;T;T	0.39592	1.65;1.07;1.65	5.25	5.25	0.73442	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.147313	0.44097	U	0.000491	T	0.18467	0.0443	N	0.02685	-0.53	0.38222	D	0.940789	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.16305	-1.0407	10	0.02654	T	1	-20.2723	15.6084	0.76692	1.0:0.0:0.0:0.0	.	387;377;378	B4E1T7;P63151;Q6ZP32	.;2ABA_HUMAN;.	V	377;156;387	ENSP00000370113:I377V;ENSP00000430320:I156V;ENSP00000325074:I387V	ENSP00000325074:I387V	I	+	1	0	PPP2R2A	26283631	0.932000	0.31603	1.000000	0.80357	0.997000	0.91878	1.432000	0.34936	2.326000	0.78906	0.533000	0.62120	ATA	.	.		0.413	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717		G	26227714	A	G	26227714	3	3	91	1	0	0	0	0	1	0	0	0	12396	217	8	2	1208	2	PPP2R2A	8	26227714	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1036029	26227714	120136308	283	12357										
ELP3	55140	hgsc.bcm.edu	37	chr8	28016144	28016144	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	attcatcacaaagtacggccAtaccaggttagtctcttcat	6	11	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:28016144A>G	ENST00000256398.8	+	12	1628	c.1251A>G	c.(1249-1251)ccA>ccG	p.P417P	ELP3_ENST00000524103.1_Silent_p.P345P|ELP3_ENST00000537665.1_Silent_p.P298P|ELP3_ENST00000380353.4_Silent_p.P325P|ELP3_ENST00000521015.1_Silent_p.P403P|ELP3_ENST00000542181.1_Silent_p.P288P	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3	417	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		AAGTACGGCCATACCAGGTTA	0.493																																					p.P417P		Atlas-SNP	.											.	ELP3	36	.	0			c.A1251G						.						115	99	105					8																	28016144		2203	4300	6503	SO:0001819	synonymous_variant	55140	exon12			ACGGCCATACCAG		CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"Chromatin-modifying enzymes / K-acetyltransferases", "Elongator acetyltransferase complex subunits"	20696	protein-coding gene	gene with protein product		612722	"elongation protein 3 homolog (S. cerevisiae)"			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.1251A>G	chr8.hg19:g.28016144A>G		147.0	0.0		44.0	4.0	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Silent	SNP	ENST00000256398.8	hg19	CCDS6065.1																																																																																			.	.		0.493	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091		G	28016144	A	G	28016144	2	3	91	1	0	0	0	0	0	0	0	1	5083	204	8	2		2	ELP3	8	28016144	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1788430	28016144	118347878	284	12358										
HMBOX1	79618	hgsc.bcm.edu	37	chr8	28904937	28904937	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tatataattggtttgctaacAgaaggaaggagatcaagagg	12	3	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:28904937A>G	ENST00000397358.3	+	9	1701	c.997A>G	c.(997-999)Aga>Gga	p.R333G	HMBOX1_ENST00000558662.1_Missense_Mutation_p.R333G|HMBOX1_ENST00000287701.10_Missense_Mutation_p.R333G|RNA5SP260_ENST00000363849.1_RNA|HMBOX1_ENST00000524238.1_Missense_Mutation_p.R333G|HMBOX1_ENST00000519047.1_Missense_Mutation_p.R333G|HMBOX1_ENST00000355231.5_Missense_Mutation_p.R333G|HMBOX1_ENST00000523613.1_Missense_Mutation_p.R333G|HMBOX1_ENST00000517386.1_3'UTR|HMBOX1_ENST00000444075.1_Missense_Mutation_p.R333G	NM_024567.3	NP_078843.2	Q6NT76	HMBX1_HUMAN	homeobox containing 1	333					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	11		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)		GTTTGCTAACAGAAGGAAGGA	0.368																																					p.R333G		Atlas-SNP	.											HMBOX1,NS,carcinoma,0,1	HMBOX1	34	.	0			c.A997G						.						109	109	109					8																	28904937		2203	4300	6503	SO:0001583	missense	79618	exon9			GCTAACAGAAGGA	AY522342	CCDS6071.1	8p12	2013-05-23			ENSG00000147421	ENSG00000147421		"Homeoboxes / HNF class"	26137	protein-coding gene	gene with protein product	"homeobox telomere-binding protein 1"					16825764	Standard	NM_024567		Approved	HNF1LA, PBHNF, FLJ21616, HOT1	uc003xhd.4	Q6NT76	OTTHUMG00000172138	ENST00000397358.3:c.997A>G	chr8.hg19:g.28904937A>G	ENSP00000380516:p.Arg333Gly	142.0	0.0		69.0	3.0	NM_024567	A4K385|A8K3R8|B4DHY5|D3DSU0|Q3Y6P1|Q96GS5|Q9H701	Missense_Mutation	SNP	ENST00000397358.3	hg19	CCDS6071.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.043030	0.75732	.	.	ENSG00000147421	ENST00000287701;ENST00000444075;ENST00000519047;ENST00000397358;ENST00000524238;ENST00000517340;ENST00000355231	D;D;D;D;D	0.97529	-4.42;-4.42;-4.42;-4.42;-4.42	5.06	3.88	0.44766	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98820	0.9602	H	0.96720	3.87	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.991;1.0	D;D;D;D;D;D	0.91635	0.998;0.999;0.997;0.998;0.987;0.998	D	0.98440	1.0586	10	0.42905	T	0.14	.	11.6787	0.51444	0.846:0.154:0.0:0.0	.	333;333;333;333;333;333	Q6NT76-5;D3DSU2;Q6NT76-2;Q6NT76-3;Q6NT76;E5RGZ2	.;.;.;.;HMBX1_HUMAN;.	G	333	ENSP00000287701:R333G;ENSP00000401769:R333G;ENSP00000430059:R333G;ENSP00000380516:R333G;ENSP00000430110:R333G	ENSP00000287701:R333G	R	+	1	2	HMBOX1	28960856	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.183000	0.50918	0.755000	0.32990	0.477000	0.44152	AGA	.	.		0.368	HMBOX1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255267.4	NM_024567		G	28904937	A	G	28904937	3	3	91	1	0	0	0	0	1	0	0	0	7227	180	7	2	1023	2	HMBOX1	8	28904937	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	888793	28904937	117459085	285	12359										
MYST3	7994	hgsc.bcm.edu	37	chr8	41791422	41791422	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtcctggtaggcgccctcaTgctcactgctttcttcttga	9	13	4	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:41791422T>C	ENST00000396930.3	-	18	4859	c.4316A>G	c.(4315-4317)cAt>cGt	p.H1439R	KAT6A_ENST00000265713.2_Missense_Mutation_p.H1439R|KAT6A_ENST00000406337.1_Missense_Mutation_p.H1439R	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1439					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GGCGCCCTCATGCTCACTGCT	0.502																																					p.H1439R		Atlas-SNP	.											.	.	.	.	0			c.A4316G						.						118	110	113					8																	41791422		2203	4300	6503	SO:0001583	missense	7994	exon18			CCCTCATGCTCAC	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.4316A>G	chr8.hg19:g.41791422T>C	ENSP00000380136:p.His1439Arg	109.0	0.0		61.0	5.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.767305	0.31320	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.59083	0.29;0.29;0.29	5.96	5.96	0.96718	.	0.131092	0.53938	D	0.000054	T	0.35480	0.0933	N	0.08118	0	0.53688	D	0.999974	B	0.22414	0.069	B	0.21546	0.035	T	0.33701	-0.9858	10	0.02654	T	1	-13.3592	16.4311	0.83844	0.0:0.0:0.0:1.0	.	1439	Q92794	KAT6A_HUMAN	R	1439	ENSP00000265713:H1439R;ENSP00000385888:H1439R;ENSP00000380136:H1439R	ENSP00000265713:H1439R	H	-	2	0	KAT6A	41910579	1.000000	0.71417	0.867000	0.34043	0.502000	0.33828	5.650000	0.67944	2.277000	0.76020	0.528000	0.53228	CAT	.	.		0.502	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		C	41791422	T	C	41791422	3	2	91	1	0	0	0	0	1	0	0	0	10113	1464	51	2	1702	2	MYST3	8	41791422	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	12886485	41791422	104572600	286	12360										
MYST3	7994	hgsc.bcm.edu	37	chr8	41794799	41794799	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcatcatctgactcttcatcTtcttcttcatctttagactt	3	12	9	2	rs201760077|rs3837198	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:41794799T>A	ENST00000396930.3	-	17	3870	c.3327A>T	c.(3325-3327)gaA>gaT	p.E1109D	KAT6A_ENST00000265713.2_Missense_Mutation_p.E1109D|KAT6A_ENST00000406337.1_Missense_Mutation_p.E1109D	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1109					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										ACTCTTCATCTTCTTCTTCAT	0.403																																					p.E1109D		Atlas-SNP	.											.	.	.	.	0			c.A3327T						.						114	110	112					8																	41794799		2203	4300	6503	SO:0001583	missense	7994	exon17			TTCATCTTCTTCT	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.3327A>T	chr8.hg19:g.41794799T>A	ENSP00000380136:p.Glu1109Asp	100.0	0.0		31.0	4.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490030	0.26686	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000418721	T;T;T	0.60299	0.2;0.2;0.2	5.41	-10.8	0.00216	.	0.572288	0.16272	N	0.221734	T	0.25975	0.0633	L	0.29908	0.895	0.24514	N	0.994196	B	0.02656	0.0	B	0.01281	0.0	T	0.29366	-1.0014	10	0.13853	T	0.58	-1.715	0.3601	0.00363	0.3421:0.1983:0.2542:0.2054	.	1109	Q92794	KAT6A_HUMAN	D	1109;1109;1109;689	ENSP00000265713:E1109D;ENSP00000385888:E1109D;ENSP00000380136:E1109D	ENSP00000265713:E1109D	E	-	3	2	KAT6A	41913956	0.002000	0.14202	0.062000	0.19696	0.839000	0.47603	-1.778000	0.01778	-3.256000	0.00203	-1.412000	0.01120	GAA	.	.		0.403	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		A	41794799	T	A	41794799	3	1	91	1	0	0	0	0	1	0	0	0	10113	1606	56	4	2695	4	MYST3	8	41794799	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3377	41794799	104569223	287	12361										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73480279	73480279	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttccattttaaatttctacCggaccgggaaactccatatg	6	11	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:73480279C>T	ENST00000523207.1	+	2	898	c.310C>T	c.(310-312)Cgg>Tgg	p.R104W		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	104					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.R104W(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	AAATTTCTACCGGACCGGGAA	0.463																																					p.R104W		Atlas-SNP	.											KCNB2,NS,carcinoma,0,1	KCNB2	228	.	1	Substitution - Missense(1)	lung(1)	c.C310T						.						76	80	78					8																	73480279		2203	4300	6503	SO:0001583	missense	9312	exon2			TTCTACCGGACCG	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.310C>T	chr8.hg19:g.73480279C>T	ENSP00000430846:p.Arg104Trp	178.0	1.0		302.0	21.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.728234	0.69074	.	.	ENSG00000182674	ENST00000523207	T	0.80824	-1.42	6.17	4.22	0.49857	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.32918	U	0.005494	D	0.91768	0.7396	H	0.96398	3.815	0.50467	D	0.999875	D	0.89917	1.0	D	0.97110	1.0	D	0.92664	0.6144	10	0.87932	D	0	.	9.3834	0.38327	0.2288:0.6924:0.0:0.0788	.	104	Q92953	KCNB2_HUMAN	W	104	ENSP00000430846:R104W	ENSP00000430846:R104W	R	+	1	2	KCNB2	73642833	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	2.559000	0.45888	1.630000	0.50440	0.655000	0.94253	CGG	.	.		0.463	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		T	73480279	C	T	73480279	3	4	91	1	0	0	0	0	1	0	0	0	8022	643	23	1	312	1	KCNB2	8	73480279	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	31685480	73480279	72883743	288	12362										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77616406	77616406	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgtggaacgacacaacttgAtaatgaggtgccagagaaag	12	6	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:77616406A>G	ENST00000521891.2	+	2	531	c.83A>G	c.(82-84)gAt>gGt	p.D28G	ZFHX4_ENST00000050961.6_Missense_Mutation_p.D28G|ZFHX4_ENST00000455469.2_Missense_Mutation_p.D28G|ZFHX4_ENST00000518282.1_Missense_Mutation_p.D28G|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	28					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ACACAACTTGATAATGAGGTG	0.498										HNSCC(33;0.089)																											p.D28G		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A83G						.						60	61	61					8																	77616406		1995	4194	6189	SO:0001583	missense	79776	exon2			AACTTGATAATGA		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.83A>G	chr8.hg19:g.77616406A>G	ENSP00000430497:p.Asp28Gly	182.0	0.0		281.0	27.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	16.51	3.142703	0.57044	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000520307;ENST00000523885;ENST00000517585;ENST00000523809;ENST00000518282	T;T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.53	5.53	0.82687	.	0.000000	0.45867	U	0.000325	T	0.29355	0.0731	N	0.19112	0.55	0.58432	D	0.999998	D;D;D;P	0.61697	0.982;0.972;0.99;0.89	B;P;P;B	0.48840	0.388;0.453;0.592;0.419	T	0.05419	-1.0886	10	0.54805	T	0.06	.	15.827	0.78718	1.0:0.0:0.0:0.0	.	28;28;28;28	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	G	28	ENSP00000430497:D28G;ENSP00000399605:D28G;ENSP00000050961:D28G;ENSP00000428525:D28G;ENSP00000429495:D28G;ENSP00000427775:D28G;ENSP00000427739:D28G;ENSP00000430848:D28G	ENSP00000050961:D28G	D	+	2	0	ZFHX4	77778961	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.585000	0.67497	2.324000	0.78689	0.533000	0.62120	GAT	.	.		0.498	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		G	77616406	A	G	77616406	3	3	91	1	0	0	0	0	1	0	0	0	17650	333	12	2	85	2	ZFHX4	8	77616406	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4136127	77616406	68747616	289	12363										
STMN2	11075	hgsc.bcm.edu	37	chr8	80553709	80553709	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctcagaagccccacgaacttTagcttctccaaagaagaaag	7	12	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:80553709T>C	ENST00000220876.7	+	3	594	c.212T>C	c.(211-213)tTa>tCa	p.L71S	STMN2_ENST00000518491.1_Missense_Mutation_p.L60S|STMN2_ENST00000518111.1_Missense_Mutation_p.L71S	NM_001199214.1|NM_007029.3	NP_001186143.1|NP_008960.2	Q93045	STMN2_HUMAN	stathmin 2	71	Regulatory/phosphorylation domain. {ECO:0000255}.|SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				cellular response to nerve growth factor stimulus (GO:1990090)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|positive regulation of microtubule depolymerization (GO:0031117)|positive regulation of neuron projection development (GO:0010976)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)			CCACGAACTTTAGCTTCTCCA	0.463																																					p.L71S		Atlas-SNP	.											.	STMN2	23	.	0			c.T212C						.						70	67	68					8																	80553709		1889	4123	6012	SO:0001583	missense	11075	exon3			GAACTTTAGCTTC		CCDS43748.1, CCDS56542.1	8q21.13	2014-04-01	2014-04-01	2001-07-13	ENSG00000104435	ENSG00000104435			10577	protein-coding gene	gene with protein product		600621	"stathmin-like 2"	SCGN10		8622778, 12140291	Standard	NM_007029		Approved	SCG10	uc022awk.1	Q93045	OTTHUMG00000164610	ENST00000220876.7:c.212T>C	chr8.hg19:g.80553709T>C	ENSP00000220876:p.Leu71Ser	122.0	0.0		246.0	35.0	NM_007029	A8K9M2|G3V110|O14952|Q6PK68	Missense_Mutation	SNP	ENST00000220876.7	hg19	CCDS43748.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.455924	0.26161	.	.	ENSG00000104435	ENST00000220876;ENST00000518111;ENST00000518491	.	.	.	5.49	5.49	0.81192	.	0.540325	0.19802	N	0.105739	T	0.54208	0.1844	L	0.27053	0.805	0.35621	D	0.809458	D;D	0.59767	0.986;0.96	P;P	0.60473	0.875;0.761	T	0.62756	-0.6787	9	0.42905	T	0.14	-3.7681	10.0198	0.42035	0.0:0.0755:0.0:0.9245	.	71;71	B7Z4K3;Q93045	.;STMN2_HUMAN	S	71;71;60	.	ENSP00000220876:L71S	L	+	2	0	STMN2	80716264	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.698000	0.84413	2.073000	0.62155	0.383000	0.25322	TTA	.	.		0.463	STMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379261.2	NM_007029		C	80553709	T	C	80553709	3	2	91	1	0	0	0	0	1	0	0	0	15324	1764	61	2	222	2	STMN2	8	80553709	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2937303	80553709	65810313	290	12364										
CNBD1	168975	hgsc.bcm.edu	37	chr8	88218281	88218281	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aagttcctgaaaacaattccAgatttaacctttcagctaaa	4	9	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:88218281A>C	ENST00000518476.1	+	5	543	c.492A>C	c.(490-492)ccA>ccC	p.P164P	CNBD1_ENST00000522427.1_3'UTR	NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	164										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						AAACAATTCCAGATTTAACCT	0.373																																					p.P164P		Atlas-SNP	.											.	CNBD1	206	.	0			c.A492C						.						56	55	55					8																	88218281		1845	4076	5921	SO:0001819	synonymous_variant	168975	exon5			AATTCCAGATTTA	AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.492A>C	chr8.hg19:g.88218281A>C		63.0	0.0		113.0	5.0	NM_173538		Silent	SNP	ENST00000518476.1	hg19	CCDS55259.1																																																																																			.	.		0.373	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		C	88218281	A	C	88218281	2	2	91	1	0	0	0	0	0	0	0	1	3593	175	7	5		5	CNBD1	8	88218281	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	7664572	88218281	58145741	291	12365										
RECQL4	113655	hgsc.bcm.edu	37	chr8	145737638	145737638	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccttctcctcagcggtcaagTcccccgggctgcgaaggtgg	13	15	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:145737638T>C	ENST00000301327.4	+	0	1548				CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000532237.1_5'UTR|RECQL4_ENST00000428558.2_Missense_Mutation_p.D1042G	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			AGCGGTCAAGTCCCCCGGGCT	0.647																																					p.D1042G		Atlas-SNP	.											.	RECQL4	75	.	0			c.A3125G						.						35	40	38					8																	145737638		2065	4206	6271	SO:0001628	intergenic_variant	9401	exon19			GTCAAGTCCCCCG		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		chr8.hg19:g.145737638T>C		57.0	0.0		115.0	6.0	NM_004260		Missense_Mutation	SNP	ENST00000301327.4	hg19	CCDS6431.1																																																																																			.	.		0.647	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		C	145737638	T	C	145737638	1	2	91	0	1	0	0	0	0	0	0	0	13217	1667	58	2		2	RECQL4	8	145737638	IGR	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	57519357	145737638	626384	292	12366										
LRRC24	441381	hgsc.bcm.edu	37	chr8	145748134	145748134	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcgccggcgacagatcatggCgaccaggagcagcgccgtga	16	13	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:145748134C>T	ENST00000529415.2	-	5	1384	c.1267G>A	c.(1267-1269)Gcc>Acc	p.A423T	LRRC14_ENST00000292524.1_3'UTR|LRRC14_ENST00000528528.1_3'UTR|LRRC24_ENST00000533758.1_Missense_Mutation_p.A420T			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	423						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CAGATCATGGCGACCAGGAGC	0.711																																					p.A423T		Atlas-SNP	.											.	LRRC24	11	.	0			c.G1267A						.						6	6	6					8																	145748134		2132	4224	6356	SO:0001583	missense	441381	exon5			TCATGGCGACCAG	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"Immunoglobulin superfamily / I-set domain containing"	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.1267G>A	chr8.hg19:g.145748134C>T	ENSP00000434849:p.Ala423Thr	16.0	0.0		34.0	7.0	NM_001024678		Missense_Mutation	SNP	ENST00000529415.2	hg19	CCDS34969.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.732977	0.30684	.	.	ENSG00000254402	ENST00000529415;ENST00000533758	T;T	0.55930	0.63;0.49	4.73	1.28	0.21552	.	0.865932	0.10420	N	0.676868	T	0.36744	0.0978	N	0.24115	0.695	0.18873	N	0.999986	B;B	0.19706	0.038;0.022	B;B	0.18871	0.023;0.01	T	0.25012	-1.0144	10	0.35671	T	0.21	.	9.3443	0.38098	0.0:0.7528:0.0:0.2472	.	420;423	G3V1D8;Q50LG9	.;LRC24_HUMAN	T	423;420	ENSP00000434849:A423T;ENSP00000435653:A420T	ENSP00000434849:A423T	A	-	1	0	LRRC24	145718942	0.001000	0.12720	0.928000	0.36995	0.845000	0.48019	0.014000	0.13333	0.427000	0.26145	0.561000	0.74099	GCC	.	.		0.711	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678		T	145748134	C	T	145748134	3	4	91	1	0	0	0	0	1	0	0	0	8988	768	27	1	278	1	LRRC24	8	145748134	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	10496	145748134	615888	293	12367										
UHRF2	115426	hgsc.bcm.edu	37	chr9	6481676	6481676	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgtaaaactgattccagtgaAgttgtaaaggctggtgaaag	12	4	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:6481676A>G	ENST00000276893.5	+	7	1362	c.1194A>G	c.(1192-1194)gaA>gaG	p.E398E		NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	398					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		ATTCCAGTGAAGTTGTAAAGG	0.368																																					p.E398E		Atlas-SNP	.											.	UHRF2	50	.	0			c.A1194G						.						89	98	95					9																	6481676		2203	4299	6502	SO:0001819	synonymous_variant	115426	exon7			CAGTGAAGTTGTA	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	12557	protein-coding gene	gene with protein product	"Np95-like ring finger protein"	615211	"ubiquitin-like with PHD and ring finger domains 2"			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.1194A>G	chr9.hg19:g.6481676A>G		120.0	0.0		95.0	4.0	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Silent	SNP	ENST00000276893.5	hg19	CCDS6469.1																																																																																			.	.		0.368	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		G	6481676	A	G	6481676	2	3	91	1	0	0	0	0	0	0	0	1	16985	69	3	2		2	UHRF2	9	6481676	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10		6481676	134731755	294	12368										
UHRF2	115426	hgsc.bcm.edu	37	chr9	6493855	6493855	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatgagttcacatacactggAagcggtggtaaaaatcttgc	11	7	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:6493855A>G	ENST00000276893.5	+	10	1695	c.1527A>G	c.(1525-1527)ggA>ggG	p.G509G	UHRF2_ENST00000485617.2_3'UTR	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	509	Methyl-CpG binding and interaction with HDAC1.|YDG. {ECO:0000255|PROSITE- ProRule:PRU00358}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		CATACACTGGAAGCGGTGGTA	0.363																																					p.G509G		Atlas-SNP	.											.	UHRF2	50	.	0			c.A1527G						.						88	80	83					9																	6493855		2203	4300	6503	SO:0001819	synonymous_variant	115426	exon10			CACTGGAAGCGGT	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	12557	protein-coding gene	gene with protein product	"Np95-like ring finger protein"	615211	"ubiquitin-like with PHD and ring finger domains 2"			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.1527A>G	chr9.hg19:g.6493855A>G		120.0	0.0		74.0	4.0	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Silent	SNP	ENST00000276893.5	hg19	CCDS6469.1																																																																																			.	.		0.363	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		G	6493855	A	G	6493855	2	3	91	1	0	0	0	0	0	0	0	1	16985	233	9	2		2	UHRF2	9	6493855	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	12179	6493855	134719576	295	12369										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13188853	13188853	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcagtgcttctacagcttccTcaagactgctgttttccaag	7	12	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:13188853T>C	ENST00000319217.7	-	17	2541	c.2294A>G	c.(2293-2295)gAg>gGg	p.E765G	MPDZ_ENST00000546205.1_Missense_Mutation_p.E765G|MPDZ_ENST00000381015.4_Missense_Mutation_p.E765G|MPDZ_ENST00000536827.1_Missense_Mutation_p.E765G|MPDZ_ENST00000381022.2_Missense_Mutation_p.E765G|MPDZ_ENST00000541718.1_Missense_Mutation_p.E765G|MPDZ_ENST00000447879.1_Missense_Mutation_p.E765G	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	765	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TACAGCTTCCTCAAGACTGCT	0.468																																					p.E765G		Atlas-SNP	.											.	MPDZ	324	.	0			c.A2294G						.						240	238	238					9																	13188853		1990	4161	6151	SO:0001583	missense	8777	exon17			GCTTCCTCAAGAC	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2294A>G	chr9.hg19:g.13188853T>C	ENSP00000320006:p.Glu765Gly	141.0	0.0		97.0	4.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	T	29.4	5.005993	0.93287	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42;1.42;1.42	5.9	5.9	0.94986	.	0.000000	0.48286	D	0.000196	T	0.54029	0.1833	M	0.62209	1.925	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.53034	-0.8495	10	0.51188	T	0.08	.	16.3283	0.82996	0.0:0.0:0.0:1.0	.	765;765;765	B7ZMI4;O75970-3;O75970-2	.;.;.	G	765;765;765;765;765;765;715;765	ENSP00000320006:E765G;ENSP00000439807:E765G;ENSP00000370410:E765G;ENSP00000444151:E765G;ENSP00000415208:E765G;ENSP00000370403:E765G;ENSP00000446358:E765G	ENSP00000320006:E765G	E	-	2	0	MPDZ	13178853	1.000000	0.71417	0.988000	0.46212	0.991000	0.79684	4.784000	0.62411	2.257000	0.74773	0.533000	0.62120	GAG	.	.		0.468	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		C	13188853	T	C	13188853	3	2	91	1	0	0	0	0	1	0	0	0	9731	1551	54	2	3951	2	MPDZ	9	13188853	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	6694998	13188853	128024578	296	12370										
DENND4C	55667	hgsc.bcm.edu	37	chr9	19350716	19350716	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaaggaagaaactaatagagActacagcttcccagctggcc	9	10	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:19350716A>G	ENST00000380432.2	+	19	3512	c.3479A>G	c.(3478-3480)gAc>gGc	p.D1160G	DENND4C_ENST00000602925.1_Missense_Mutation_p.D1396G|DENND4C_ENST00000434457.2_Missense_Mutation_p.D1445G			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1160					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						ACTAATAGAGACTACAGCTTC	0.393																																					p.D1396G		Atlas-SNP	.											.	DENND4C	120	.	0			c.A4187G						.						63	62	62					9																	19350716		2203	4300	6503	SO:0001583	missense	55667	exon23			ATAGAGACTACAG	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.3479A>G	chr9.hg19:g.19350716A>G	ENSP00000369797:p.Asp1160Gly	94.0	0.0		70.0	5.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	A	10.87	1.473271	0.26423	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024;ENST00000380424	T;T	0.58506	0.33;0.33	5.61	5.61	0.85477	.	0.282354	0.28338	N	0.015720	T	0.42404	0.1201	L	0.27053	0.805	0.33684	D	0.612536	B;B;B;B	0.15930	0.015;0.004;0.007;0.001	B;B;B;B	0.18871	0.023;0.006;0.016;0.002	T	0.50972	-0.8764	10	0.22706	T	0.39	-18.6985	10.1977	0.43065	0.9259:0.0:0.0741:0.0	.	490;1160;342;1160	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	G	1160;633;342;490;633;342;157;31	ENSP00000305795:D633G;ENSP00000443804:D490G	ENSP00000305795:D633G	D	+	2	0	DENND4C	19340716	1.000000	0.71417	1.000000	0.80357	0.711000	0.40976	3.871000	0.56077	2.125000	0.65367	0.533000	0.62120	GAC	.	.		0.393	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		G	19350716	A	G	19350716	3	3	91	1	0	0	0	0	1	0	0	0	4437	275	10	2	3553	2	DENND4C	9	19350716	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	6161863	19350716	121862715	297	12371										
TEK	7010	hgsc.bcm.edu	37	chr9	27213566	27213566	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagattttggattgtcccgaGgtcaagaggtgtatgtgaaa	13	5	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:27213566G>A	ENST00000380036.4	+	18	3404	c.2962G>A	c.(2962-2964)Ggt>Agt	p.G988S	TEK_ENST00000406359.4_Missense_Mutation_p.G945S|TEK_ENST00000519097.1_Missense_Mutation_p.G840S	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	988	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	ATTGTCCCGAGGTCAAGAGGT	0.428																																					p.G988S		Atlas-SNP	.											.	TEK	250	.	0			c.G2962A						.						124	122	123					9																	27213566		2203	4300	6503	SO:0001583	missense	7010	exon18			TCCCGAGGTCAAG	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2962G>A	chr9.hg19:g.27213566G>A	ENSP00000369375:p.Gly988Ser	92.0	0.0		72.0	4.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	G	35	5.585865	0.96578	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359	D;D;D	0.81739	-1.53;-1.53;-1.53	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	D	0.000072	T	0.80199	0.4579	N	0.04636	-0.2	0.80722	D	1	D;D;D	0.89917	1.0;0.991;1.0	D;D;D	0.97110	1.0;0.97;1.0	D	0.83567	0.0110	10	0.41790	T	0.15	.	19.7221	0.96147	0.0:0.0:1.0:0.0	.	840;1021;988	E7EWI2;Q59HG2;Q02763	.;.;TIE2_HUMAN	S	840;988;945	ENSP00000430686:G840S;ENSP00000369375:G988S;ENSP00000383977:G945S	ENSP00000369375:G988S	G	+	1	0	TEK	27203566	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.679000	0.91253	0.655000	0.94253	GGT	.	.		0.428	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			A	27213566	G	A	27213566	3	1	91	1	0	0	0	0	1	0	0	0	15766	1000	35	3	3032	3	TEK	9	27213566	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	7862850	27213566	113999865	298	12372										
C9orf72	203228	hgsc.bcm.edu	37	chr9	27556627	27556627	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgtcttcttctgaagtggcTctccagaaggctgtcagctc	10	11	5	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:27556627T>C	ENST00000380003.3	-	8	1086	c.1023A>G	c.(1021-1023)agA>agG	p.R341R	C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	341					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		CTGAAGTGGCTCTCCAGAAGG	0.448																																					p.R341R		Atlas-SNP	.											.	C9orf72	48	.	0			c.A1023G						.						154	141	145					9																	27556627		2203	4300	6503	SO:0001819	synonymous_variant	203228	exon8			AGTGGCTCTCCAG	AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.1023A>G	chr9.hg19:g.27556627T>C		208.0	0.0		119.0	5.0	NM_018325	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Silent	SNP	ENST00000380003.3	hg19	CCDS6522.1																																																																																			.	.		0.448	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325		C	27556627	T	C	27556627	2	2	91	1	0	0	0	0	0	0	0	1	2497	1548	54	2		2	C9orf72	9	27556627	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	343061	27556627	113656804	299	12373										
GALT	2592	hgsc.bcm.edu	37	chr9	34649497	34649497	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctcctgcgctctgccactgTccggaaattcatggttggct	11	13	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:34649497T>C	ENST00000378842.3	+	10	1037	c.995T>C	c.(994-996)gTc>gCc	p.V332A	GALT_ENST00000556278.1_Intron|IL11RA_ENST00000555003.1_5'Flank|GALT_ENST00000450095.2_Missense_Mutation_p.V223A|GALT_ENST00000488412.2_3'UTR|IL11RA_ENST00000441545.2_5'Flank	NM_000155.3	NP_000146.2	P07902	GALT_HUMAN	galactose-1-phosphate uridylyltransferase	332					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)|UDP-glucose catabolic process (GO:0006258)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	UDP-glucose:hexose-1-phosphate uridylyltransferase activity (GO:0008108)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(2)|lung(5)|upper_aerodigestive_tract(1)	16	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		TCTGCCACTGTCCGGAAATTC	0.582									Galactosemia																												p.V332A		Atlas-SNP	.											.	GALT	29	.	0			c.T995C						.						119	112	114					9																	34649497		2203	4300	6503	SO:0001583	missense	2592	exon10	Familial Cancer Database	Galactose-1-Phosphate Uridyltransferase Deficiency	CCACTGTCCGGAA	M60091	CCDS6565.1, CCDS59122.1	9p13	2013-01-08			ENSG00000213930	ENSG00000213930	2.7.7.12		4135	protein-coding gene	gene with protein product		606999					Standard	NM_000155		Approved		uc003zve.4	P07902	OTTHUMG00000019836	ENST00000378842.3:c.995T>C	chr9.hg19:g.34649497T>C	ENSP00000368119:p.Val332Ala	117.0	0.0		92.0	4.0	NM_000155	B4E097|E7ET32|Q14355|Q14356|Q14357|Q14358|Q14359|Q14360|Q14361|Q14363|Q14364|Q14365|Q14369|Q14370|Q14371|Q14372|Q14373|Q14374|Q14375|Q14377|Q14378|Q14380|Q14381|Q14382|Q14383|Q14384|Q14385|Q14386|Q14387|Q14389|Q16766|Q53XK1|Q5VZ81|Q96BY1	Missense_Mutation	SNP	ENST00000378842.3	hg19	CCDS6565.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.855412	0.91355	.	.	ENSG00000213930	ENST00000450095;ENST00000378842	D;D	0.99503	-6.03;-6.03	5.2	5.2	0.72013	Histidine triad motif (1);Galactose-1-phosphate uridyl transferase, C-terminal (1);Histidine triad-like motif (1);	0.235140	0.34435	U	0.003979	D	0.99687	0.9882	H	0.96889	3.9	0.53688	D	0.999975	D;D	0.89917	1.0;1.0	D;D	0.83275	0.983;0.996	D	0.97401	0.9996	10	0.87932	D	0	-8.4733	13.888	0.63721	0.0:0.0:0.0:1.0	.	223;332	E7ET32;P07902	.;GALT_HUMAN	A	223;332	ENSP00000401956:V223A;ENSP00000368119:V332A	ENSP00000368119:V332A	V	+	2	0	GALT	34639497	0.995000	0.38212	0.993000	0.49108	0.971000	0.66376	7.562000	0.82300	1.967000	0.57214	0.454000	0.30748	GTC	.	.		0.582	GALT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052231.1	NM_000155		C	34649497	T	C	34649497	3	2	91	1	0	0	0	0	1	0	0	0	6238	1667	58	2	1033	2	GALT	9	34649497	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	7092870	34649497	106563934	300	12374										
IL11RA	3590	hgsc.bcm.edu	37	chr9	34656848	34656848	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acagcactgatgagggcaccTacatctgccagaccctggat	10	13	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:34656848T>C	ENST00000555003.1	+	4	1630	c.274T>C	c.(274-276)Tac>Cac	p.Y92H	IL11RA_ENST00000478802.2_3'UTR|GALT_ENST00000556278.1_Missense_Mutation_p.Y236H|IL11RA_ENST00000318041.9_Missense_Mutation_p.Y92H|IL11RA_ENST00000378817.4_Missense_Mutation_p.Y92H|IL11RA_ENST00000602473.1_Missense_Mutation_p.Y92H|IL11RA_ENST00000441545.2_Missense_Mutation_p.Y92H			Q14626	I11RA_HUMAN	interleukin 11 receptor, alpha	92	Ig-like C2-type.				developmental process (GO:0032502)|embryo implantation (GO:0007566)|head development (GO:0060322)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.174)	Oprelvekin(DB00038)	TGAGGGCACCTACATCTGCCA	0.612																																					p.Y92H		Atlas-SNP	.											.	IL11RA	34	.	0			c.T274C						.						68	60	63					9																	34656848		2203	4300	6503	SO:0001583	missense	3590	exon4			GGCACCTACATCT	Z38102	CCDS6567.1	9p13	2014-05-22			ENSG00000137070	ENSG00000137070		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5967	protein-coding gene	gene with protein product		600939				7670098	Standard	NM_001142784		Approved		uc011loq.3	Q14626	OTTHUMG00000019837	ENST00000555003.1:c.274T>C	chr9.hg19:g.34656848T>C	ENSP00000450565:p.Tyr92His	131.0	0.0		75.0	4.0	NM_001142784	Q16542|Q5VZ80|Q7KYJ7	Missense_Mutation	SNP	ENST00000555003.1	hg19	CCDS6567.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936705	0.73557	.	.	ENSG00000258728;ENSG00000137070;ENSG00000137070;ENSG00000137070;ENSG00000137070;ENSG00000137070;ENSG00000137070;ENSG00000137070	ENST00000556278;ENST00000555003;ENST00000441545;ENST00000556792;ENST00000378817;ENST00000318041;ENST00000556531;ENST00000555981	T;T;T;T;T;T;D;T	0.94758	-0.08;-0.08;-0.08;-0.08;-0.08;-0.08;-3.51;-0.08	5.34	5.34	0.76211	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	D	0.95962	0.8685	L	0.58101	1.795	0.51482	D	0.999927	D	0.89917	1.0	D	0.79108	0.992	D	0.95621	0.8681	10	0.52906	T	0.07	-14.6428	11.6292	0.51164	0.0:0.0:0.0:1.0	.	92	Q14626	I11RA_HUMAN	H	236;92;92;92;92;92;92;92	ENSP00000451792:Y236H;ENSP00000450565:Y92H;ENSP00000394391:Y92H;ENSP00000450543:Y92H;ENSP00000368094:Y92H;ENSP00000326500:Y92H;ENSP00000451447:Y92H;ENSP00000450640:Y92H	ENSP00000326500:Y92H	Y	+	1	0	RP11-195F19.29;IL11RA	34646848	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.056000	0.57448	2.242000	0.73789	0.533000	0.62120	TAC	.	.		0.612	IL11RA-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410625.1	NM_001142784		C	34656848	T	C	34656848	3	2	91	1	0	0	0	0	1	0	0	0	7632	1522	53	2	284	2	IL11RA	9	34656848	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	7351	34656848	106556583	301	12375										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35389938	35389938	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atcgtgtcaatcatagaggaAgataagaattcctacacacc	7	9	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:35389938A>G	ENST00000378495.3	+	24	3165	c.2943A>G	c.(2941-2943)gaA>gaG	p.E981E	UNC13B_ENST00000396787.1_Silent_p.E993E|UNC13B_ENST00000378496.4_Silent_p.E981E	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	981					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TCATAGAGGAAGATAAGAATT	0.493																																					p.E981E		Atlas-SNP	.											.	UNC13B	153	.	0			c.A2943G						.						230	217	221					9																	35389938		2203	4300	6503	SO:0001819	synonymous_variant	10497	exon24			AGAGGAAGATAAG	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.2943A>G	chr9.hg19:g.35389938A>G		167.0	0.0		109.0	5.0	NM_006377	Q5VYM8	Silent	SNP	ENST00000378495.3	hg19	CCDS6579.1																																																																																			.	.		0.493	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		G	35389938	A	G	35389938	2	3	91	1	0	0	0	0	0	0	0	1	17000	69	3	2		2	UNC13B	9	35389938	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	733090	35389938	105823493	302	12376										
GNE	10020	hgsc.bcm.edu	37	chr9	36222836	36222836	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttggccaaatttcctttccGccagggcagcacagttgcca	9	14	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:36222836G>A	ENST00000539815.1	-	8	1611	c.1571C>T	c.(1570-1572)gCg>gTg	p.A524V	GNE_ENST00000377902.5_Missense_Mutation_p.A524V|GNE_ENST00000539208.1_Missense_Mutation_p.A414V|GNE_ENST00000396594.3_Missense_Mutation_p.A555V|GNE_ENST00000543356.2_Missense_Mutation_p.A519V|GNE_ENST00000447283.2_Intron			Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	524	N-acetylmannosamine kinase.		A -> V (in IBM2). {ECO:0000269|PubMed:12409274}.		carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)			endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			TTTCCTTTCCGCCAGGGCAGC	0.512																																					p.A555V	GBM(184;106 2118 20004 35750 50727)	Atlas-SNP	.											.	GNE	141	.	0			c.C1664T	GRCh37	CM024159	GNE	M		.						153	150	151					9																	36222836		2203	4300	6503	SO:0001583	missense	10020	exon9			CTTTCCGCCAGGG	AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921			23657	protein-coding gene	gene with protein product		603824	"UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase"	IBM2		9305887, 9305888	Standard	NM_005476		Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539815.1:c.1571C>T	chr9.hg19:g.36222836G>A	ENSP00000439155:p.Ala524Val	159.0	0.0		96.0	4.0	NM_001128227	A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	Missense_Mutation	SNP	ENST00000539815.1	hg19	CCDS6602.1	.	.	.	.	.	.	.	.	.	.	G	34	5.334432	0.95758	.	.	ENSG00000159921	ENST00000377902;ENST00000396594;ENST00000339267;ENST00000539815;ENST00000543356;ENST00000539208	D;D;D;D	0.99232	-5.6;-5.6;-5.6;-5.6	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.99573	0.9846	H	0.94582	3.555	0.80722	D	1	D;D;D;D	0.89917	0.998;0.999;1.0;0.999	P;P;P;D	0.65773	0.856;0.898;0.898;0.938	D	0.98294	1.0515	10	0.87932	D	0	-21.442	17.9148	0.88945	0.0:0.0:1.0:0.0	.	414;483;555;524	F5H499;Q9Y223-3;Q9Y223-2;Q9Y223	.;.;.;GLCNE_HUMAN	V	524;555;519;524;496;414	ENSP00000367134:A524V;ENSP00000379839:A555V;ENSP00000439155:A524V;ENSP00000445117:A414V	ENSP00000340770:A519V	A	-	2	0	GNE	36212836	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.162000	0.94745	2.823000	0.97156	0.591000	0.81541	GCG	.	.		0.512	GNE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052412.4	NM_005476		A	36222836	G	A	36222836	3	1	91	1	0	0	0	0	1	0	0	0	6530	1087	38	1	613	1	GNE	9	36222836	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	832898	36222836	104990595	303	12377										
FBXO10	26267	hgsc.bcm.edu	37	chr9	37525156	37525156	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gccggcagcacggcccttgaAgatgtggttcccgctaaagt	13	12	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:37525156A>G	ENST00000432825.2	-	6	1768	c.1720T>C	c.(1720-1722)Ttc>Ctc	p.F574L	FBXO10_ENST00000541829.1_Missense_Mutation_p.F99L|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000543968.1_5'UTR	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	574					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		CGGCCCTTGAAGATGTGGTTC	0.547																																					p.F574L		Atlas-SNP	.											.	FBXO10	75	.	0			c.T1720C						.						34	34	34					9																	37525156		1953	4142	6095	SO:0001583	missense	26267	exon6			CCTTGAAGATGTG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"F-boxes /  "other""	13589	protein-coding gene	gene with protein product		609092	"F-box only protein 10"			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.1720T>C	chr9.hg19:g.37525156A>G	ENSP00000403802:p.Phe574Leu	88.0	0.0		78.0	4.0	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	hg19	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.987150	0.93106	.	.	ENSG00000147912	ENST00000432825;ENST00000541829	T;T	0.79454	-1.22;-1.27	4.96	4.96	0.65561	Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);	0.052247	0.85682	D	0.000000	D	0.83069	0.5174	M	0.68593	2.085	0.58432	D	0.999999	D;P;D	0.57257	0.979;0.507;0.972	P;B;P	0.57846	0.828;0.208;0.801	T	0.81531	-0.0890	10	0.27785	T	0.31	-21.0908	13.6457	0.62279	1.0:0.0:0.0:0.0	.	453;99;574	Q59F51;Q08AL4;Q9UK96	.;.;FBX10_HUMAN	L	574;99	ENSP00000403802:F574L;ENSP00000441307:F99L	ENSP00000403802:F574L	F	-	1	0	FBXO10	37515156	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.873000	0.92357	1.858000	0.53909	0.533000	0.62120	TTC	.	.		0.547	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3			G	37525156	A	G	37525156	3	3	91	1	0	0	0	0	1	0	0	0	5734	72	3	2	1174	2	FBXO10	9	37525156	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1302320	37525156	103688275	304	12378										
TJP2	9414	hgsc.bcm.edu	37	chr9	71845029	71845029	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaatggtaaggttcaagaagGgagacagcgtgggcctccgg	16	7	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:71845029G>A	ENST00000377245.4	+	11	1760	c.1552G>A	c.(1552-1554)Gga>Aga	p.G518R	TJP2_ENST00000453658.2_Missense_Mutation_p.G495R|TJP2_ENST00000535702.1_Missense_Mutation_p.G522R|TJP2_ENST00000539225.1_Missense_Mutation_p.G549R|TJP2_ENST00000265384.7_Missense_Mutation_p.G518R|TJP2_ENST00000348208.4_Missense_Mutation_p.G518R	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	518	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GTTCAAGAAGGGAGACAGCGT	0.483																																					p.G549R		Atlas-SNP	.											.	TJP2	120	.	0			c.G1645A						.						78	79	79					9																	71845029		2203	4300	6503	SO:0001583	missense	9414	exon11			AAGAAGGGAGACA	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"Friedreich ataxia region gene X104 (tight junction protein ZO-2)", "zona occludens 2"	607709	"deafness, autosomal dominant 51"	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1552G>A	chr9.hg19:g.71845029G>A	ENSP00000366453:p.Gly518Arg	123.0	0.0		80.0	4.0	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	hg19	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.749259	0.89753	.	.	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43;0.43	5.86	5.86	0.93980	PDZ/DHR/GLGF (3);	0.000000	0.85682	D	0.000000	T	0.74245	0.3691	M	0.83774	2.66	0.80722	D	1	D;D;D;D;D	0.89917	0.977;0.989;1.0;0.999;0.997	P;D;D;D;D	0.79784	0.847;0.962;0.966;0.993;0.973	T	0.76849	-0.2807	10	0.87932	D	0	.	14.699	0.69142	0.069:0.0:0.9309:0.0	.	549;522;518;518;518	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	R	495;518;518;518;522;549	ENSP00000392178:G495R;ENSP00000366453:G518R;ENSP00000345893:G518R;ENSP00000265384:G518R;ENSP00000442090:G522R;ENSP00000438262:G549R	ENSP00000265384:G518R	G	+	1	0	TJP2	71034849	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.975000	0.88055	2.937000	0.99478	0.650000	0.86243	GGA	.	.		0.483	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		A	71845029	G	A	71845029	3	1	91	1	0	0	0	0	1	0	0	0	15945	1233	43	3	1751	3	TJP2	9	71845029	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	34319873	71845029	69368402	305	12379										
PTAR1	375743	hgsc.bcm.edu	37	chr9	72356709	72356709	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	actaatgaaaatgacataccTcacgttccatgcagtggtaa	7	9	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:72356709T>C	ENST00000340434.4	-	3	325	c.322A>G	c.(322-324)Agg>Ggg	p.R108G	PTAR1_ENST00000377200.5_Intron	NM_001099666.1	NP_001093136.1	Q7Z6K3	PTAR1_HUMAN	protein prenyltransferase alpha subunit repeat containing 1	108					protein prenylation (GO:0018342)		protein prenyltransferase activity (GO:0008318)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)	5						ATGACATACCTCACGTTCCAT	0.333																																					p.R108G		Atlas-SNP	.											.	PTAR1	46	.	0			c.A322G						.						82	76	77					9																	72356709		1875	4118	5993	SO:0001630	splice_region_variant	375743	exon3			CATACCTCACGTT	BC053622	CCDS47978.1	9q21.13	2008-10-01			ENSG00000188647	ENSG00000188647		"Prenyltransferase alpha subunit repeat containing"	30449	protein-coding gene	gene with protein product						12477932	Standard	NM_001099666		Approved		uc004ahj.4	Q7Z6K3	OTTHUMG00000019982	ENST00000340434.4:c.323+1A>G	chr9.hg19:g.72356709T>C		133.0	0.0		99.0	4.0	NM_001099666	Q5T7V5|Q5T7V6	Missense_Mutation	SNP	ENST00000340434.4	hg19	CCDS47978.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.270626	0.80469	.	.	ENSG00000188647	ENST00000340434	T	0.70749	-0.51	5.74	5.74	0.90152	Protein prenyltransferase (1);	.	.	.	.	T	0.77103	0.4081	M	0.70595	2.14	0.80722	D	1	D	0.58620	0.983	P	0.49683	0.619	T	0.80845	-0.1200	9	0.87932	D	0	.	16.0405	0.80679	0.0:0.0:0.0:1.0	.	108	Q7Z6K3	PTAR1_HUMAN	G	108	ENSP00000344299:R108G	ENSP00000344299:R108G	R	-	1	2	PTAR1	71546529	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.519000	0.60517	2.187000	0.69744	0.519000	0.50382	AGG	.	.		0.333	PTAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052582.4	NM_001099666	Missense_Mutation	C	72356709	T	C	72356709	5	2	91	1	0	0	0	0	0	0	1	0	12736	1565	54	2	910	2	PTAR1	9	72356709	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	511680	72356709	68856722	306	12380										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79461504	79461504	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atctcctttagcacgagagaAgaggaagactctcggaactc	10	10	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:79461504A>G	ENST00000376718.3	-	4	558	c.435T>C	c.(433-435)tcT>tcC	p.S145S	PRUNE2_ENST00000376713.3_Silent_p.S145S|PRUNE2_ENST00000428286.1_5'UTR	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	145					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GCACGAGAGAAGAGGAAGACT	0.468																																					p.S145S		Atlas-SNP	.											.	PRUNE2	331	.	0			c.T435C						.						106	103	104					9																	79461504		2203	4300	6503	SO:0001819	synonymous_variant	158471	exon4			GAGAGAAGAGGAA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.435T>C	chr9.hg19:g.79461504A>G		114.0	0.0		80.0	5.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	hg19	CCDS47982.1																																																																																			.	.		0.468	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		G	79461504	A	G	79461504	2	3	91	1	0	0	0	0	0	0	0	1	12653	59	3	2		2	PRUNE2	9	79461504	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	7104795	79461504	61751927	307	12381										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79960046	79960046	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacaaagaatgaacttgttcAatacaatcaaaggtaagatt	6	6	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:79960046A>G	ENST00000360280.3	+	52	7537	c.7277A>G	c.(7276-7278)cAa>cGa	p.Q2426R	VPS13A_ENST00000376636.3_Missense_Mutation_p.Q2387R|VPS13A_ENST00000376634.4_Missense_Mutation_p.Q2426R|VPS13A_ENST00000357409.5_Missense_Mutation_p.Q2426R	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2426					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GAACTTGTTCAATACAATCAA	0.313																																					p.Q2426R		Atlas-SNP	.											.	VPS13A	735	.	0			c.A7277G						.						126	127	127					9																	79960046		2203	4298	6501	SO:0001583	missense	23230	exon52			TTGTTCAATACAA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.7277A>G	chr9.hg19:g.79960046A>G	ENSP00000353422:p.Gln2426Arg	104.0	0.0		88.0	4.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	2.662	-0.279511	0.05642	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.26	5.26	0.73747	Vacuolar protein sorting-associated protein (1);	0.670270	0.14937	N	0.289778	T	0.17746	0.0426	N	0.12182	0.205	0.80722	D	1	B;B;B;B	0.10296	0.001;0.003;0.002;0.002	B;B;B;B	0.11329	0.003;0.006;0.006;0.004	T	0.09357	-1.0678	10	0.19590	T	0.45	.	10.9338	0.47233	0.843:0.157:0.0:0.0	.	2387;2426;2426;2426	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	R	2426;2387;2426;2426	ENSP00000365821:Q2426R;ENSP00000365823:Q2387R;ENSP00000353422:Q2426R;ENSP00000349985:Q2426R	ENSP00000349985:Q2426R	Q	+	2	0	VPS13A	79149866	1.000000	0.71417	0.761000	0.31378	0.032000	0.12392	5.624000	0.67764	1.980000	0.57719	0.477000	0.44152	CAA	.	.		0.313	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		G	79960046	A	G	79960046	3	3	91	1	0	0	0	0	1	0	0	0	17204	130	5	2	7483	2	VPS13A	9	79960046	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	498542	79960046	61253385	308	12382										
GKAP1	80318	hgsc.bcm.edu	37	chr9	86395306	86395306	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ataagacttacctcagtcttTttactaatgtgatctgtaaa	5	7	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:86395306T>A	ENST00000376371.2	-	7	976	c.576A>T	c.(574-576)aaA>aaT	p.K192N	GKAP1_ENST00000376365.3_Missense_Mutation_p.K192N	NM_025211.3	NP_079487.2	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1	192					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)	14						CCTCAGTCTTTTTACTAATGT	0.249																																					p.K192N		Atlas-SNP	.											.	GKAP1	27	.	0			c.A576T						.						48	53	51					9																	86395306		2199	4285	6484	SO:0001583	missense	80318	exon7			AGTCTTTTTACTA	BC014476	CCDS35049.1, CCDS47988.1	9q22.1	2008-02-05			ENSG00000165113	ENSG00000165113			17496	protein-coding gene	gene with protein product	"cGMP-dependent protein kinase anchoring protein 42kDa"	611356					Standard	NM_025211		Approved	GKAP42, FKSG21	uc004amy.3	Q5VSY0	OTTHUMG00000020106	ENST00000376371.2:c.576A>T	chr9.hg19:g.86395306T>A	ENSP00000365550:p.Lys192Asn	280.0	0.0		243.0	17.0	NM_025211	Q96LI0|Q9BYI1|Q9BYI2|Q9H225	Missense_Mutation	SNP	ENST00000376371.2	hg19	CCDS35049.1	.	.	.	.	.	.	.	.	.	.	T	16.48	3.136019	0.56936	.	.	ENSG00000165113	ENST00000376371;ENST00000376365	.	.	.	5.19	4.05	0.47172	.	0.090473	0.85682	D	0.000000	T	0.66137	0.2759	L	0.49350	1.555	0.48087	D	0.999588	D;P	0.89917	1.0;0.661	D;B	0.85130	0.997;0.287	T	0.61422	-0.7066	9	0.26408	T	0.33	-16.4182	9.3504	0.38133	0.0:0.083:0.0:0.917	.	192;192	Q5VSY0-2;Q5VSY0	.;GKAP1_HUMAN	N	192	.	ENSP00000365544:K192N	K	-	3	2	GKAP1	85585126	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.837000	0.39201	0.923000	0.37045	0.460000	0.39030	AAA	.	.		0.249	GKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052839.2	NM_025211		A	86395306	T	A	86395306	3	1	91	1	0	0	0	0	1	0	0	0	6431	1838	64	4	552	4	GKAP1	9	86395306	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	6435260	86395306	54818125	309	12383										
FAM22F	54754	hgsc.bcm.edu	37	chr9	97080944	97080944	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttcttggacttgctggcagGagaaggtgatgggctgaggc	17	7	1	3	rs150455117	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:97080944G>C	ENST00000253262.4	-	7	2094	c.2074C>G	c.(2074-2076)Cct>Gct	p.P692A	NUTM2F_ENST00000335456.7_Intron|NUTM2F_ENST00000341207.4_Missense_Mutation_p.P677A	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	692																	TTGCTGGCAGGAGAAGGTGAT	0.607																																					p.P692A		Atlas-SNP	.											.	FAM22F	72	.	0			c.C2074G						.						21	19	20					9																	97080944		1843	4069	5912	SO:0001583	missense	54754	exon7			TGGCAGGAGAAGG		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"family with sequence similarity 22, member F"	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.2074C>G	chr9.hg19:g.97080944G>C	ENSP00000253262:p.Pro692Ala	390.0	0.0		312.0	21.0	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Missense_Mutation	SNP	ENST00000253262.4	hg19	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.581686	0.00879	.	.	ENSG00000130950	ENST00000253262;ENST00000341207;ENST00000375347	T;T	0.14640	2.49;2.52	1.52	-3.04	0.05412	Nuclear Testis protein, C-terminal (1);	2.077270	0.02242	N	0.065820	T	0.12561	0.0305	L	0.56769	1.78	0.09310	N	1	B	0.13594	0.008	B	0.16289	0.015	T	0.30621	-0.9972	10	0.09084	T	0.74	.	5.0244	0.14378	0.1751:0.5512:0.2738:0.0	.	692	A1L443	FA22F_HUMAN	A	692;677;526	ENSP00000253262:P692A;ENSP00000343865:P677A	ENSP00000253262:P692A	P	-	1	0	FAM22F	96120765	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.495000	0.06443	-1.287000	0.02381	-0.518000	0.04402	CCT	.	.		0.607	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561		C	97080944	G	C	97080944	3	2	91	1	0	0	0	0	1	0	0	0	5550	1174	41	4	200	4	FAM22F	9	97080944	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	10685638	97080944	44132487	310	12384										
ZNF782	158431	hgsc.bcm.edu	37	chr9	99580298	99580298	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catttatagggtttctccccTgtgtgagttctctgatgtac	9	9	2	2	rs561032098	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:99580298T>C	ENST00000481138.1	-	6	2668	c.2007A>G	c.(2005-2007)acA>acG	p.T669T	ZNF782_ENST00000535338.1_Silent_p.T537T|ZNF782_ENST00000466833.1_5'Flank	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	669					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				GTTTCTCCCCTGTGTGAGTTC	0.423																																					p.T669T		Atlas-SNP	.											.	ZNF782	64	.	0			c.A2007G						.						103	104	104					9																	99580298		2203	4300	6503	SO:0001819	synonymous_variant	158431	exon6			CTCCCCTGTGTGA	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"Zinc fingers, C2H2-type", "-"	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.2007A>G	chr9.hg19:g.99580298T>C		246.0	0.0		175.0	8.0	NM_001001662	B2RNR0	Silent	SNP	ENST00000481138.1	hg19	CCDS35075.1	.	.	.	.	.	.	.	.	.	.	t	7.390	0.630621	0.14322	.	.	ENSG00000196597	ENST00000289032	.	.	.	2.64	0.104	0.14531	.	.	.	.	.	T	0.51822	0.1697	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39165	-0.9627	4	.	.	.	.	6.321	0.21217	0.43:0.0:0.0:0.57	.	.	.	.	G	658	.	.	R	-	1	2	ZNF782	98620119	0.062000	0.20869	0.999000	0.59377	0.992000	0.81027	-0.986000	0.03747	0.000000	0.14550	0.533000	0.62120	AGG	.	.		0.423	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		C	99580298	T	C	99580298	2	2	91	1	0	0	0	0	0	0	0	1	18170	1567	55	2		2	ZNF782	9	99580298	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2499354	99580298	41633133	311	12385										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100074426	100074426	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagccaagagggaaaaagccCgagagagtgagaacaccatc	13	9	0	3	rs377165805		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:100074426C>A	ENST00000357054.1	+	18	1776	c.841C>A	c.(841-843)Cga>Aga	p.R281R	CCDC180_ENST00000529487.1_Silent_p.R142R|CCDC180_ENST00000375202.2_Silent_p.R142R|CCDC180_ENST00000460482.2_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000411667.2_Silent_p.R142R|CCDC180_ENST00000395220.1_Silent_p.R281R			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	281						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											GGAAAAAGCCCGAGAGAGTGA	0.557																																					p.R142R		Atlas-SNP	.											.	.	.	.	0			c.C424A						.						120	122	121					9																	100074426		2203	4300	6503	SO:0001819	synonymous_variant	0	exon4			AAAGCCCGAGAGA	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.841C>A	chr9.hg19:g.100074426C>A		95.0	0.0		73.0	4.0	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	hg19																																																																																				.	.		0.557	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		A	100074426	C	A	100074426	2	1	91	1	0	0	0	0	0	0	0	1	8249	644	23	1		1	KIAA1529	9	100074426	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	494128	100074426	41139005	312	12386										
IKBKAP	8518	hgsc.bcm.edu	37	chr9	111656321	111656321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccattttcttaagtgtattaAgaaatggaagatattctttg	7	4	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:111656321A>G	ENST00000374647.5	-	26	3069	c.2762T>C	c.(2761-2763)cTt>cCt	p.L921P	IKBKAP_ENST00000537196.1_Missense_Mutation_p.L572P	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	921					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						AAGTGTATTAAGAAATGGAAG	0.294																																					p.L921P		Atlas-SNP	.											.	IKBKAP	122	.	0			c.T2762C						.						83	80	81					9																	111656321		2203	4300	6503	SO:0001583	missense	8518	exon26			GTATTAAGAAATG	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"Elongator acetyltransferase complex subunits"	5959	protein-coding gene	gene with protein product	"elongator acetyltransferase complex subunit 1"	603722	"dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.2762T>C	chr9.hg19:g.111656321A>G	ENSP00000363779:p.Leu921Pro	118.0	0.0		69.0	4.0	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	hg19	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.390549	0.82902	.	.	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.59502	0.26;0.26	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.82323	0.5012	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87135	0.2199	10	0.87932	D	0	-18.042	14.3095	0.66407	1.0:0.0:0.0:0.0	.	921	O95163	ELP1_HUMAN	P	921;572	ENSP00000363779:L921P;ENSP00000439367:L572P	ENSP00000363779:L921P	L	-	2	0	IKBKAP	110696142	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.073000	0.93992	2.270000	0.75569	0.477000	0.44152	CTT	.	.		0.294	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1			G	111656321	A	G	111656321	3	3	91	1	0	0	0	0	1	0	0	0	7619	72	3	2	1284	2	IKBKAP	9	111656321	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	11581895	111656321	29557110	313	12387										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113169046	113169046	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaggtccacagttgactggtTtacagagaggaatctctgca	12	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:113169046T>C	ENST00000401783.2	-	38	9170	c.8834A>G	c.(8833-8835)aAa>aGa	p.K2945R	SVEP1_ENST00000297826.5_Missense_Mutation_p.K871R|SVEP1_ENST00000374469.1_Missense_Mutation_p.K2922R	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2945	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GTTGACTGGTTTACAGAGAGG	0.478																																					p.K2945R		Atlas-SNP	.											.	SVEP1	326	.	0			c.A8834G						.						187	183	184					9																	113169046		1959	4153	6112	SO:0001583	missense	79987	exon38			ACTGGTTTACAGA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8834A>G	chr9.hg19:g.113169046T>C	ENSP00000384917:p.Lys2945Arg	118.0	0.0		97.0	4.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	12.45	1.940874	0.34283	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.24151	1.87;1.87;1.87	5.57	4.4	0.53042	Complement control module (2);Sushi/SCR/CCP (1);	0.155382	0.56097	D	0.000027	T	0.19046	0.0457	L	0.42487	1.325	0.80722	D	1	P	0.38922	0.651	B	0.33521	0.165	T	0.03017	-1.1082	10	0.17369	T	0.5	.	11.7457	0.51819	0.1323:0.0:0.0:0.8677	.	2945	Q4LDE5	SVEP1_HUMAN	R	2945;2922;871	ENSP00000384917:K2945R;ENSP00000363593:K2922R;ENSP00000297826:K871R	ENSP00000297826:K871R	K	-	2	0	SVEP1	112208867	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	3.891000	0.56227	0.907000	0.36646	0.482000	0.46254	AAA	.	.		0.478	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113169046	T	C	113169046	3	2	91	1	0	0	0	0	1	0	0	0	15435	1841	64	2	1925	2	SVEP1	9	113169046	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1512725	113169046	28044385	314	12388										
SLC31A1	1317	hgsc.bcm.edu	37	chr9	116018546	116018546	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atggtggaggagacagcagcAtgatgatgatggtgagtgcc	17	5	0	5			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:116018546A>G	ENST00000374212.4	+	2	270	c.118A>G	c.(118-120)Atg>Gtg	p.M40V	CDC26_ENST00000490408.1_Intron|SLC31A1_ENST00000374210.6_Missense_Mutation_p.M40V	NM_001859.3	NP_001850.1	O15431	COPT1_HUMAN	solute carrier family 31 (copper transporter), member 1	40					cellular copper ion homeostasis (GO:0006878)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	copper ion transmembrane transporter activity (GO:0005375)|copper uptake transmembrane transporter activity (GO:0015088)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7					Bortezomib(DB00188)|Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	AGACAGCAGCATGATGATGAT	0.483																																					p.M40V	Ovarian(135;1049 1799 4519 17564 28677)	Atlas-SNP	.											.	SLC31A1	12	.	0			c.A118G						.						115	84	95					9																	116018546		2203	4300	6503	SO:0001583	missense	1317	exon2			AGCAGCATGATGA	U83460	CCDS6789.1	9q32	2013-07-17	2013-07-17		ENSG00000136868	ENSG00000136868		"Solute carriers"	11016	protein-coding gene	gene with protein product	copper transport 1 homolog (S. cerevisiae)	603085		COPT1		9207117	Standard	NM_001859		Approved	hCTR1, CTR1	uc004bgu.3	O15431	OTTHUMG00000020519	ENST00000374212.4:c.118A>G	chr9.hg19:g.116018546A>G	ENSP00000363329:p.Met40Val	203.0	0.0		166.0	7.0	NM_001859	A8K8Z6|Q53GR5|Q5T1M4	Missense_Mutation	SNP	ENST00000374212.4	hg19	CCDS6789.1	.	.	.	.	.	.	.	.	.	.	A	8.096	0.775624	0.16051	.	.	ENSG00000136868	ENST00000374212;ENST00000374210	T;T	0.66280	-0.16;-0.2	5.54	4.35	0.52113	.	0.234155	0.44285	D	0.000466	T	0.37758	0.1015	N	0.08118	0	0.80722	D	1	B;B	0.25667	0.131;0.009	B;B	0.22386	0.039;0.01	T	0.25916	-1.0118	10	0.30078	T	0.28	-12.7871	8.8623	0.35265	0.8342:0.0:0.0:0.1658	.	40;40	Q5T1M3;O15431	.;COPT1_HUMAN	V	40	ENSP00000363329:M40V;ENSP00000363327:M40V	ENSP00000363327:M40V	M	+	1	0	SLC31A1	115058367	0.999000	0.42202	0.999000	0.59377	0.947000	0.59692	1.699000	0.37804	2.095000	0.63458	0.460000	0.39030	ATG	.	.		0.483	SLC31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053715.1	NM_001859		G	116018546	A	G	116018546	3	3	91	1	0	0	0	0	1	0	0	0	14578	217	8	2	120	2	SLC31A1	9	116018546	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2849500	116018546	25194885	315	12389										
WDR31	114987	hgsc.bcm.edu	37	chr9	116079110	116079110	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	attcctctgttaaaacttgcAcacaataaggagatggcgtc	8	9	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:116079110A>G	ENST00000374193.4	-	11	1269	c.1023T>C	c.(1021-1023)tgT>tgC	p.C341C	WDR31_ENST00000461942.1_5'UTR|WDR31_ENST00000374195.3_Silent_p.C216C|WDR31_ENST00000341761.4_Silent_p.C340C	NM_001012361.2|NM_145241.3	NP_001012361.1|NP_660284.1	Q8NA23	WDR31_HUMAN	WD repeat domain 31	341										NS(1)|large_intestine(1)|lung(2)|prostate(2)	6						TAAAACTTGCACACAATAAGG	0.527																																					p.C341C		Atlas-SNP	.											.	WDR31	23	.	0			c.T1023C						.						141	128	132					9																	116079110		2203	4300	6503	SO:0001819	synonymous_variant	114987	exon11			ACTTGCACACAAT	BC012352	CCDS6792.1, CCDS35110.1	9q33.1	2013-01-09			ENSG00000148225	ENSG00000148225		"WD repeat domain containing"	21421	protein-coding gene	gene with protein product	"similar to spermatid WD-repeat protein"						Standard	NM_145241		Approved	FLJ35921	uc004bhb.3	Q8NA23	OTTHUMG00000020525	ENST00000374193.4:c.1023T>C	chr9.hg19:g.116079110A>G		90.0	0.0		56.0	4.0	NM_001012361	Q5W0T9|Q96EG8	Silent	SNP	ENST00000374193.4	hg19	CCDS35110.1																																																																																			.	.		0.527	WDR31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053734.2	NM_145241		G	116079110	A	G	116079110	2	3	91	1	0	0	0	0	0	0	0	1	17301	157	6	2		2	WDR31	9	116079110	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	60564	116079110	25134321	316	12390										
TNC	3371	hgsc.bcm.edu	37	chr9	117852928	117852928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctccagctcctccagtctgcTcagcagctccttaacatcag	6	17	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:117852928T>C	ENST00000350763.4	-	2	781	c.370A>G	c.(370-372)Agc>Ggc	p.S124G	TNC_ENST00000535648.1_Missense_Mutation_p.S124G|TNC_ENST00000423613.2_Missense_Mutation_p.S124G|TNC_ENST00000537320.1_Missense_Mutation_p.S124G|TNC_ENST00000340094.3_Missense_Mutation_p.S124G|TNC_ENST00000341037.4_Missense_Mutation_p.S124G|TNC_ENST00000346706.3_Missense_Mutation_p.S124G|TNC_ENST00000345230.3_Missense_Mutation_p.S124G|TNC_ENST00000542877.1_Missense_Mutation_p.S124G	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	124					bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TCCAGTCTGCTCAGCAGCTCC	0.592																																					p.S124G		Atlas-SNP	.											TNC,NS,carcinoma,0,1	TNC	282	.	0			c.A370G						.						139	150	146					9																	117852928		2203	4300	6503	SO:0001583	missense	3371	exon2			GTCTGCTCAGCAG		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.370A>G	chr9.hg19:g.117852928T>C	ENSP00000265131:p.Ser124Gly	95.0	1.0		94.0	4.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.931316	0.92389	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34	5.94	5.94	0.96194	.	0.244211	0.53938	D	0.000056	T	0.45256	0.1333	M	0.65975	2.015	0.48975	D	0.999735	P;P	0.51791	0.948;0.85	B;P	0.46208	0.441;0.507	T	0.48822	-0.9001	10	0.62326	D	0.03	.	15.5674	0.76303	0.0:0.0:0.0:1.0	.	124;124	E9PC84;P24821	.;TENA_HUMAN	G	124	ENSP00000344400:S124G;ENSP00000438152:S124G;ENSP00000344555:S124G;ENSP00000345861:S124G;ENSP00000265131:S124G;ENSP00000339553:S124G;ENSP00000411406:S124G;ENSP00000443478:S124G;ENSP00000442242:S124G	ENSP00000344400:S124G	S	-	1	0	TNC	116892749	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	6.152000	0.71812	2.261000	0.74972	0.533000	0.62120	AGC	.	.		0.592	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		C	117852928	T	C	117852928	3	2	91	1	0	0	0	0	1	0	0	0	16285	1551	54	2	6343	2	TNC	9	117852928	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1773818	117852928	23360503	317	12391										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123156882	123156882	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttgttcaaacaattttttaTgtagtttggtgacctctgcc	7	8	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:123156882T>A	ENST00000349780.4	-	36	5665	c.5486A>T	c.(5485-5487)cAt>cTt	p.H1829L	CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.H1750L|CDK5RAP2_ENST00000480467.1_5'UTR|CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.H1788L|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.H1797L	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1829	Interaction with PCNT and AKAP9.				brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						CAATTTTTTATGTAGTTTGGT	0.348																																					p.H1829L		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.A5486T						.						146	133	138					9																	123156882		2203	4300	6503	SO:0001583	missense	55755	exon36			TTTTTATGTAGTT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.5486A>T	chr9.hg19:g.123156882T>A	ENSP00000343818:p.His1829Leu	319.0	0.0		252.0	35.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	hg19	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	T	12.67	2.008474	0.35415	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000416449;ENST00000425647;ENST00000345313	T;T;T;T;T;T	0.23348	3.89;3.81;3.9;3.81;2.22;1.91	5.39	3.04	0.35103	.	0.578085	0.16911	N	0.194491	T	0.36082	0.0954	M	0.67953	2.075	0.30138	N	0.804181	P;B;P;P;P	0.47762	0.589;0.279;0.9;0.483;0.763	B;B;P;B;B	0.53185	0.114;0.124;0.72;0.058;0.229	T	0.33523	-0.9865	10	0.72032	D	0.01	.	5.7886	0.18347	0.0:0.2872:0.0:0.7128	.	839;1797;1750;1829;1223	Q5JTU8;Q96SN8-2;Q96SN8-4;Q96SN8;B1AMJ5	.;.;.;CK5P2_HUMAN;.	L	1797;1788;1829;1750;1223;839;1601	ENSP00000354065:H1797L;ENSP00000352258:H1788L;ENSP00000343818:H1829L;ENSP00000353317:H1750L;ENSP00000400395:H1223L;ENSP00000409941:H839L	ENSP00000341695:H1601L	H	-	2	0	CDK5RAP2	122196703	0.734000	0.28142	0.490000	0.27465	0.491000	0.33493	0.229000	0.17833	0.869000	0.35703	0.533000	0.62120	CAT	.	.		0.348	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		A	123156882	T	A	123156882	3	1	91	1	0	0	0	0	1	0	0	0	3148	1464	51	4	207	4	CDK5RAP2	9	123156882	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	5303954	123156882	18056549	318	12392										
RC3H2	54542	hgsc.bcm.edu	37	chr9	125642094	125642094	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aagtccacaaggccatgaacTactgttttaacagctaccat	6	11	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:125642094T>C	ENST00000373670.1	-	7	1752	c.1152A>G	c.(1150-1152)gtA>gtG	p.V384V	RC3H2_ENST00000335387.5_Silent_p.V384V|RC3H2_ENST00000423239.2_Silent_p.V384V|SNORD90_ENST00000391145.1_RNA|RC3H2_ENST00000357244.2_Silent_p.V384V|RC3H2_ENST00000373665.2_Silent_p.V384V			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	384					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						GGCCATGAACTACTGTTTTAA	0.438																																					p.V384V		Atlas-SNP	.											.	RC3H2	150	.	0			c.A1152G						.						69	69	69					9																	125642094		1872	4098	5970	SO:0001819	synonymous_variant	54542	exon8			ATGAACTACTGTT	AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"RING-type (C3HC4) zinc fingers", "Zinc fingers, CCCH-type domain containing"	21461	protein-coding gene	gene with protein product		615231	"membrane associated DNA binding protein", "ring finger and CCCH-type zinc finger domains 2"	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.1152A>G	chr9.hg19:g.125642094T>C		78.0	0.0		68.0	5.0	NM_018835	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Silent	SNP	ENST00000373670.1	hg19	CCDS43874.1																																																																																			.	.		0.438	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835		C	125642094	T	C	125642094	2	2	91	1	0	0	0	0	0	0	0	1	13182	1509	53	2		2	RC3H2	9	125642094	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2485212	125642094	15571337	319	12393										
ODF2	4957	hgsc.bcm.edu	37	chr9	131231625	131231625	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaatgcggttggttgtctgaAgtctgaggtgagggaggtag	19	3	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:131231625A>G	ENST00000434106.3	+	5	776	c.413A>G	c.(412-414)aAg>aGg	p.K138R	ODF2_ENST00000604420.1_Missense_Mutation_p.K138R|ODF2_ENST00000372807.5_Missense_Mutation_p.K133R|RP11-339B21.9_ENST00000420801.1_RNA|ODF2_ENST00000372791.3_Missense_Mutation_p.K119R|ODF2_ENST00000448249.3_Intron|ODF2_ENST00000372814.3_Missense_Mutation_p.K182R|ODF2_ENST00000393527.3_Missense_Mutation_p.K114R|ODF2_ENST00000546203.1_Missense_Mutation_p.K119R|ODF2_ENST00000444119.2_Missense_Mutation_p.K114R|ODF2_ENST00000535026.1_Intron|ODF2_ENST00000393533.2_Missense_Mutation_p.K138R|ODF2_ENST00000351030.3_Missense_Mutation_p.K133R	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	138					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						GGTTGTCTGAAGTCTGAGGTG	0.498																																					p.K202R		Atlas-SNP	.											.	ODF2	227	.	0			c.A605G						.						152	142	145					9																	131231625		2203	4300	6503	SO:0001583	missense	4957	exon5			GTCTGAAGTCTGA	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"cancer/testis antigen 134"	602015	"outer dense fibre of sperm tails 2"			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.413A>G	chr9.hg19:g.131231625A>G	ENSP00000403453:p.Lys138Arg	89.0	0.0		63.0	4.0	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	hg19	CCDS56588.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.370217	0.82573	.	.	ENSG00000136811	ENST00000393533;ENST00000372814;ENST00000351030;ENST00000372796;ENST00000303890;ENST00000444119;ENST00000434106;ENST00000546203;ENST00000446274;ENST00000372791	T;T;T;T;T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	5.97	5.97	0.96955	.	0.042327	0.85682	D	0.000000	T	0.81607	0.4858	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.996;0.999;0.998;0.998;0.998;0.996;0.999;0.984	T	0.81957	-0.0695	10	0.51188	T	0.08	-29.8851	15.2656	0.73657	1.0:0.0:0.0:0.0	.	119;133;72;138;133;119;138;114	Q5BJF6-8;Q5BJF6-4;Q5BJF6-2;B4DX73;B1AND4;Q5BJF6-5;Q5BJF6;Q5BJF6-3	.;.;.;.;.;.;ODFP2_HUMAN;.	R	138;182;133;138;114;114;138;119;119;119	ENSP00000377166:K138R;ENSP00000361901:K182R;ENSP00000342581:K133R;ENSP00000361882:K138R;ENSP00000307781:K114R;ENSP00000394506:K114R;ENSP00000403453:K138R;ENSP00000437579:K119R;ENSP00000415290:K119R;ENSP00000361877:K119R	ENSP00000307781:K114R	K	+	2	0	ODF2	130271446	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	6.649000	0.74364	2.285000	0.76669	0.477000	0.44152	AAG	.	.		0.498	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			G	131231625	A	G	131231625	3	3	91	1	0	0	0	0	1	0	0	0	10836	72	3	2	482	2	ODF2	9	131231625	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	5589531	131231625	9981806	320	12394										
LRRC8A	56262	hgsc.bcm.edu	37	chr9	131670854	131670855	+	Frame_Shift_Del	DEL	CT	CT	-													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcattgcccagctcacgggcCtcaaggagctgtggctctac							TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:131670854_131670855delCT	ENST00000259324.5	+	3	1934_1935	c.1411_1412delCT	c.(1411-1413)ctcfs	p.L471fs	LRRC8A_ENST00000372599.3_Frame_Shift_Del_p.L471fs|LRRC8A_ENST00000372600.4_Frame_Shift_Del_p.L471fs	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	471					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						GCTCACGGGCCTCAAGGAGCTG	0.629																																					p.470_471del		Atlas-INDEL	.											.	LRRC8A	69	.	0			c.1410_1411del						.																																			SO:0001589	frameshift_variant	56262	exon3			.	AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"leucine rich repeat containing 8"	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.1411_1412delCT	chr9.hg19:g.131670854_131670855delCT	ENSP00000259324:p.Leu471fs	68.0	0.0		40.0	11.0	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Frame_Shift_Del	DEL	ENST00000259324.5	hg19	CCDS35155.1																																																																																			.	.		0.629	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		-	131670855	CT	-	131670854	7	5	91	1	0	1	0	1	0	0	0	0	9030	681	24	0	1413	0	LRRC8A	9	131670854	Frame_Shift_Del	DEL	CT	TCGA-DD-A119-01A-11D-A12Z-10	439229	131670854	9542577	321	12395										
PHYHD1	254295	hgsc.bcm.edu	37	chr9	131689459	131689459	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	attctccacccaggaagaggAgcagcttcgagcccaggtag	12	12	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:131689459A>G	ENST00000372592.3	+	4	1109	c.176A>G	c.(175-177)gAg>gGg	p.E59G	PHYHD1_ENST00000353176.5_Missense_Mutation_p.E59G|PHYHD1_ENST00000308941.5_Missense_Mutation_p.E59G|PHYHD1_ENST00000421063.2_Missense_Mutation_p.E59G	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	59							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						CAGGAAGAGGAGCAGCTTCGA	0.582											OREG0019526	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E59G		Atlas-SNP	.											.	PHYHD1	29	.	0			c.A176G						.						137	118	124					9																	131689459		2203	4300	6503	SO:0001583	missense	254295	exon2			AAGAGGAGCAGCT	BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.176A>G	chr9.hg19:g.131689459A>G	ENSP00000361673:p.Glu59Gly	102.0	0.0	1589	70.0	4.0	NM_001100877	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Missense_Mutation	SNP	ENST00000372592.3	hg19	CCDS43885.1	.	.	.	.	.	.	.	.	.	.	A	15.58	2.876179	0.51801	.	.	ENSG00000175287	ENST00000372592;ENST00000428610;ENST00000308941;ENST00000419552;ENST00000353176;ENST00000426694;ENST00000421063	D;D;D	0.89810	-2.54;-2.57;-2.57	5.32	5.32	0.75619	.	0.100735	0.64402	D	0.000003	D	0.90868	0.7131	M	0.73598	2.24	0.58432	D	0.999999	P;P;D	0.54397	0.734;0.605;0.966	B;B;P	0.49887	0.373;0.412;0.625	D	0.91285	0.5054	10	0.51188	T	0.08	-23.6398	14.0941	0.65008	1.0:0.0:0.0:0.0	.	59;59;59	Q5SRE7-2;Q5SRE7;Q5SRE7-3	.;PHYD1_HUMAN;.	G	59	ENSP00000361673:E59G;ENSP00000340945:E59G;ENSP00000409928:E59G	ENSP00000309515:E59G	E	+	2	0	PHYHD1	130729280	1.000000	0.71417	0.998000	0.56505	0.324000	0.28378	3.925000	0.56484	2.002000	0.58637	0.533000	0.62120	GAG	.	.		0.582	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933		G	131689459	A	G	131689459	3	3	91	1	0	0	0	0	1	0	0	0	11874	304	11	2	182	2	PHYHD1	9	131689459	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	18605	131689459	9523972	322	12396										
PTGES	9536	hgsc.bcm.edu	37	chr9	132502117	132502117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaaaaggaaggggtagatggTctccatgtcgttccggtggg	17	6	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:132502117T>C	ENST00000340607.4	-	3	266	c.232A>G	c.(232-234)Acc>Gcc	p.T78A	PTGES_ENST00000481476.1_5'UTR	NM_004878.4	NP_004869.1	O14684	PTGES_HUMAN	prostaglandin E synthase	78					acute inflammatory response (GO:0002526)|arachidonic acid metabolic process (GO:0019369)|chronic inflammatory response (GO:0002544)|cyclooxygenase pathway (GO:0019371)|negative regulation of cell proliferation (GO:0008285)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|response to calcium ion (GO:0051592)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)	glutathione binding (GO:0043295)|prostaglandin-E synthase activity (GO:0050220)			lung(1)|skin(1)	2		Ovarian(14;0.00556)				GGGTAGATGGTCTCCATGTCG	0.572																																					p.T78A		Atlas-SNP	.											.	PTGES	7	.	0			c.A232G						.						69	44	52					9																	132502117		2192	4292	6484	SO:0001583	missense	9536	exon3			AGATGGTCTCCAT	AF010316	CCDS6927.1	9q34.3	2008-07-21			ENSG00000148344	ENSG00000148344			9599	protein-coding gene	gene with protein product	"microsomal glutathione S-transferase 1-like 1", "tumor protein p53 inducible protein 12", "p53-induced gene 12", "microsomal prostaglandin E synthase-1", "glutathione S-transferase 1-like 1", "MGST1-like 1"	605172		MGST1L1		9305847, 10091672	Standard	NM_004878		Approved	MGST-IV, PIG12, MGST1-L1, TP53I12	uc004byi.3	O14684	OTTHUMG00000020791	ENST00000340607.4:c.232A>G	chr9.hg19:g.132502117T>C	ENSP00000342385:p.Thr78Ala	118.0	0.0		90.0	4.0	NM_004878	O14900|Q5SZC0	Missense_Mutation	SNP	ENST00000340607.4	hg19	CCDS6927.1	.	.	.	.	.	.	.	.	.	.	T	18.56	3.650502	0.67472	.	.	ENSG00000148344	ENST00000340607	T	0.57273	0.41	4.6	4.6	0.57074	Membrane associated eicosanoid/glutathione metabolism-like domain (1);	0.138330	0.64402	D	0.000005	T	0.48095	0.1481	L	0.33485	1.01	0.47949	D	0.999557	B	0.23650	0.089	B	0.35114	0.196	T	0.52909	-0.8512	10	0.87932	D	0	-50.199	13.6096	0.62068	0.0:0.0:0.0:1.0	.	78	O14684	PTGES_HUMAN	A	78	ENSP00000342385:T78A	ENSP00000342385:T78A	T	-	1	0	PTGES	131541938	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.762000	0.85270	2.048000	0.60808	0.459000	0.35465	ACC	.	.		0.572	PTGES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054599.2	NM_004878		C	132502117	T	C	132502117	3	2	91	1	0	0	0	0	1	0	0	0	12759	1667	58	2	230	2	PTGES	9	132502117	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	812658	132502117	8711314	323	12397										
TOR1B	27348	hgsc.bcm.edu	37	chr9	132571282	132571282	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaaggacctggaacctgtacTgtctgtcggagtcttcaata	11	9	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:132571282T>C	ENST00000259339.2	+	4	800	c.740T>C	c.(739-741)cTg>cCg	p.L247P		NM_014506.1	NP_055321.1	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B)	247					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum organization (GO:0007029)|nuclear membrane organization (GO:0071763)|protein homooligomerization (GO:0051260)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)	12		Ovarian(14;0.0586)				GAACCTGTACTGTCTGTCGGA	0.502																																					p.L247P		Atlas-SNP	.											.	TOR1B	20	.	0			c.T740C						.						84	88	86					9																	132571282		2203	4300	6503	SO:0001583	missense	27348	exon4			CTGTACTGTCTGT	AF007872	CCDS6929.1	9q34	2008-07-21			ENSG00000136816	ENSG00000136816			11995	protein-coding gene	gene with protein product		608050				9288096, 10644435	Standard	NM_014506		Approved	DQ1, MGC4386	uc004byk.1	O14657	OTTHUMG00000020795	ENST00000259339.2:c.740T>C	chr9.hg19:g.132571282T>C	ENSP00000259339:p.Leu247Pro	95.0	0.0		78.0	4.0	NM_014506		Missense_Mutation	SNP	ENST00000259339.2	hg19	CCDS6929.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.336735	0.81801	.	.	ENSG00000136816	ENST00000259339;ENST00000437263	T	0.58210	0.35	4.72	4.72	0.59763	.	0.140502	0.48286	D	0.000199	T	0.76528	0.4000	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.82438	-0.0457	10	0.72032	D	0.01	-30.1219	13.5395	0.61666	0.0:0.0:0.0:1.0	.	247	O14657	TOR1B_HUMAN	P	247;216	ENSP00000259339:L247P	ENSP00000259339:L247P	L	+	2	0	TOR1B	131611103	0.954000	0.32549	0.974000	0.42286	0.971000	0.66376	7.327000	0.79147	1.979000	0.57680	0.528000	0.53228	CTG	.	.		0.502	TOR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054615.1	NM_014506		C	132571282	T	C	132571282	3	2	91	1	0	0	0	0	1	0	0	0	16389	1580	55	2	754	2	TOR1B	9	132571282	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	69165	132571282	8642149	324	12398										
TSC1	7248	hgsc.bcm.edu	37	chr9	135771990	135771990	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctctggggtagaaagctcgcTgctgctgctgctgctgcctc	13	13	1	1	rs397514812		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:135771990T>C	ENST00000298552.3	-	23	3348	c.3127A>G	c.(3127-3129)Agc>Ggc	p.S1043G	TSC1_ENST00000545250.1_Missense_Mutation_p.S992G|TSC1_ENST00000440111.2_Missense_Mutation_p.S1043G	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	1043	Poly-Ser.		Missing (in TSC1; unknown pathological significance; no effect on expression; no effect on subcellular localization; no effect on inhibition of TORC1 signaling). {ECO:0000269|PubMed:22161988}.		activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		GAAAGCTCgctgctgctgctg	0.642			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.S1043G		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	TSC1,colon,carcinoma,0,2	TSC1	167	.	1	Unknown(1)	bone(1)	c.A3127G						.						23	26	25					9																	135771990		2203	4299	6502	SO:0001583	missense	7248	exon23	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GCTCGCTGCTGCT	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.3127A>G	chr9.hg19:g.135771990T>C	ENSP00000298552:p.Ser1043Gly	55.0	1.0		34.0	3.0	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	hg19	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	T	9.298	1.052277	0.19827	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	D;D;T	0.82255	-1.59;-1.59;-1.4	3.95	3.95	0.45737	.	0.297282	0.36665	N	0.002471	D	0.86818	0.6024	M	0.64997	1.995	0.80722	D	1	D;P	0.58268	0.982;0.905	D;B	0.67548	0.952;0.423	D	0.83606	0.0131	10	0.18710	T	0.47	-4.8503	10.7727	0.46332	0.0:0.0:0.0:1.0	.	992;1043	B7Z897;Q92574	.;TSC1_HUMAN	G	1043;1043;992	ENSP00000298552:S1043G;ENSP00000394524:S1043G;ENSP00000444017:S992G	ENSP00000298552:S1043G	S	-	1	0	TSC1	134761811	1.000000	0.71417	0.961000	0.40146	0.822000	0.46500	2.796000	0.47869	1.405000	0.46838	0.338000	0.21704	AGC	.	.		0.642	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			C	135771990	T	C	135771990	3	2	91	1	0	0	0	0	1	0	0	0	16620	1580	55	2	371	2	TSC1	9	135771990	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3200708	135771990	5441441	325	12399										
GLT6D1	360203	hgsc.bcm.edu	37	chr9	138516329	138516329	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acccaggctcttcacatgcaCcagggggccatcgagccacc	10	17	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:138516329C>T	ENST00000371763.1	-	5	698	c.445G>A	c.(445-447)Gtg>Atg	p.V149M		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	149					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		TTCACATGCACCAGGGGGCCA	0.557																																					p.V149M		Atlas-SNP	.											.	GLT6D1	56	.	0			c.G445A						.						41	43	42					9																	138516329		1993	4157	6150	SO:0001583	missense	360203	exon5			CATGCACCAGGGG	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"Glycosyltransferase family 6 domain containing"	23671	protein-coding gene	gene with protein product		613699	"galactosyltransferase family 6 domain containing 1"	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.445G>A	chr9.hg19:g.138516329C>T	ENSP00000360829:p.Val149Met	80.0	0.0		47.0	4.0	NM_182974		Missense_Mutation	SNP	ENST00000371763.1	hg19	CCDS43900.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.971199	0.00457	.	.	ENSG00000204007	ENST00000371763	T	0.01178	5.22	3.43	-6.86	0.01676	.	1.441670	0.03843	N	0.271043	T	0.00384	0.0012	N	0.00729	-1.24	0.09310	N	1	B	0.22909	0.077	B	0.19148	0.024	T	0.42292	-0.9460	10	0.07175	T	0.84	-1.1801	3.553	0.07854	0.0988:0.392:0.2995:0.2097	.	149	Q7Z4J2	GL6D1_HUMAN	M	149	ENSP00000360829:V149M	ENSP00000360829:V149M	V	-	1	0	GLT6D1	137656150	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.876000	0.01633	-3.190000	0.00220	-1.181000	0.01715	GTG	.	.		0.557	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974		T	138516329	C	T	138516329	3	4	91	1	0	0	0	0	1	0	0	0	6476	507	18	3	389	3	GLT6D1	9	138516329	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2744339	138516329	2697102	326	12400										
LCN8	389812	hgsc.bcm.edu	37	chr9	139651509	139651509	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctgttatatgcaaccttcaCggtcaggttactcccgctca	7	14	3	0	rs140571672		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:139651509C>T	ENST00000316144.5	-	0	762				LCN8_ENST00000482893.1_5'UTR|LCN15_ENST00000482511.1_5'Flank|LCN8_ENST00000371688.3_Missense_Mutation_p.V46M	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15						lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						GCAACCTTCACGGTCAGGTTA	0.637																																					p.V46M		Atlas-SNP	.											.	LCN8	14	.	0			c.G136A						.	C	MET/VAL	0,4406		0,0,2203	49	43	45		136	2.6	0	9	dbSNP_134	45	2,8598	2.2+/-6.3	0,2,4298	no	missense	LCN8	NM_178469.3	21	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	46/153	139651509	2,13004	2203	4300	6503	SO:0001628	intergenic_variant	138307	exon2			CCTTCACGGTCAG		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"Lipocalins"	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943		chr9.hg19:g.139651509C>T		90.0	0.0		76.0	4.0	NM_178469		Missense_Mutation	SNP	ENST00000316144.5	hg19	CCDS7006.1	.	.	.	.	.	.	.	.	.	.	C	9.175	1.022095	0.19433	0.0	2.33E-4	ENSG00000204001	ENST00000371688	T	0.10763	2.84	3.47	2.57	0.30868	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.	.	.	.	T	0.08891	0.0220	L	0.35723	1.085	0.09310	N	1	D;P	0.58268	0.982;0.847	B;B	0.42593	0.392;0.188	T	0.24440	-1.0160	8	.	.	.	.	7.0423	0.25027	0.0:0.874:0.0:0.126	.	69;46	Q6JVE9;Q6JVE9-2	LCN8_HUMAN;.	M	46	ENSP00000360753:V46M	.	V	-	1	0	LCN8	138771330	0.598000	0.26882	0.032000	0.17829	0.070000	0.16714	1.531000	0.36018	1.053000	0.40415	-0.254000	0.11334	GTG	.	C|1.000;T|0.000		0.637	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347		T	139651509	C	T	139651509	1	4	91	0	1	0	0	0	0	0	0	0	8695	536	19	1		1	LCN8	9	139651509	IGR	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1135180	139651509	1561922	327	12401										
FBXW5	54461	hgsc.bcm.edu	37	chr9	139837940	139837940	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catacagccgctggaactccTcgtaccaggacatggccgct	10	15	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:139837940T>C	ENST00000325285.3	-	3	291	c.212A>G	c.(211-213)gAg>gGg	p.E71G	C8G_ENST00000224181.3_5'Flank|FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	71					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		CTGGAACTCCTCGTACCAGGA	0.662																																					p.E71G		Atlas-SNP	.											.	FBXW5	36	.	0			c.A212G						.						50	38	42					9																	139837940		2199	4299	6498	SO:0001583	missense	54461	exon3			AACTCCTCGTACC	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"F-boxes / WD-40 domains", "WD repeat domain containing"	13613	protein-coding gene	gene with protein product		609072	"F-box and WD-40 domain protein 5"				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.212A>G	chr9.hg19:g.139837940T>C	ENSP00000313034:p.Glu71Gly	71.0	0.0		62.0	4.0	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	hg19	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	t	10.83	1.461751	0.26248	.	.	ENSG00000159069	ENST00000325285;ENST00000428398;ENST00000443788	T;T;T	0.23348	1.91;1.91;1.91	4.58	4.58	0.56647	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);F-box domain, Skp2-like (1);	0.238551	0.42964	D	0.000624	T	0.15522	0.0374	N	0.24115	0.695	0.33244	D	0.55762	B	0.06786	0.001	B	0.06405	0.002	T	0.17137	-1.0379	10	0.20046	T	0.44	-7.7081	9.3994	0.38424	0.0:0.085:0.0:0.915	.	71	Q969U6	FBXW5_HUMAN	G	71	ENSP00000313034:E71G;ENSP00000404829:E71G;ENSP00000394011:E71G	ENSP00000313034:E71G	E	-	2	0	FBXW5	138957761	1.000000	0.71417	0.937000	0.37676	0.417000	0.31264	4.169000	0.58223	1.672000	0.50884	0.454000	0.30748	GAG	.	.		0.662	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		C	139837940	T	C	139837940	3	2	91	1	0	0	0	0	1	0	0	0	5776	1551	54	2	1516	2	FBXW5	9	139837940	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	186431	139837940	1375491	328	12402										
PITRM1	10531	hgsc.bcm.edu	37	chr10	3208567	3208567	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccatgggagtagtacggaacTgcacgctagggaaggagaat	15	7	0	1	rs4266975|rs148472807|rs28416720	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:3208567T>G	ENST00000224949.4	-	4	306	c.272A>C	c.(271-273)cAg>cCg	p.Q91P	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000451104.2_Missense_Mutation_p.Q59P|PITRM1_ENST00000380989.2_Missense_Mutation_p.Q91P|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	91					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						AGTACGGAACTGCACGCTAGG	0.493																																					p.Q91P		Atlas-SNP	.											PITRM1,colon,carcinoma,0,3	PITRM1	109	.	0			c.A272C						.						102	102	102					10																	3208567		2072	4187	6259	SO:0001583	missense	10531	exon4			CGGAACTGCACGC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.272A>C	chr10.hg19:g.3208567T>G	ENSP00000224949:p.Gln91Pro	38.0	0.0		25.0	6.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	hg19	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	t	9.750	1.167171	0.21621	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.25912	1.77;1.77;1.77	5.36	5.36	0.76844	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.051197	0.85682	D	0.000000	T	0.38585	0.1046	M	0.76002	2.32	0.80722	D	1	P;B;P;P;P;P	0.40332	0.609;0.261;0.713;0.457;0.457;0.612	B;B;P;B;B;B	0.45343	0.425;0.222;0.477;0.284;0.284;0.284	T	0.18903	-1.0322	10	0.37606	T	0.19	.	15.3402	0.74290	0.0:0.0:0.0:1.0	rs28416720	84;59;91;91;91;84	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3;B4DH07	.;.;.;.;PREP_HUMAN;.	P	91;84;91;59	ENSP00000224949:Q91P;ENSP00000370377:Q91P;ENSP00000401201:Q59P	ENSP00000224949:Q91P	Q	-	2	0	PITRM1	3198567	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	4.424000	0.59868	2.024000	0.59613	0.379000	0.24179	CAG	.	.		0.493	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			G	3208567	T	G	3208567	3	3	91	1	0	0	0	0	1	0	0	0	11962	1580	55	5	2937	5	PITRM1	10	3208567	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10		3208567	132326180	329	12403										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7247842	7247842	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	accagcccactgggaagatgTccatggattccacatcaaca	8	13	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:7247842T>C	ENST00000361972.4	-	12	1469	c.1379A>G	c.(1378-1380)gAc>gGc	p.D460G	SFMBT2_ENST00000397167.1_Missense_Mutation_p.D460G	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	460					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						TGGGAAGATGTCCATGGATTC	0.483																																					p.D460G		Atlas-SNP	.											.	SFMBT2	209	.	0			c.A1379G						.						120	106	111					10																	7247842		2203	4300	6503	SO:0001583	missense	57713	exon12			AAGATGTCCATGG	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.1379A>G	chr10.hg19:g.7247842T>C	ENSP00000355109:p.Asp460Gly	144.0	0.0		95.0	5.0	NM_001029880	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	hg19	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.814606	0.90790	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.50277	0.75;0.75	5.57	5.57	0.84162	.	0.042810	0.85682	D	0.000000	T	0.69205	0.3085	M	0.74467	2.265	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.73401	-0.3994	10	0.87932	D	0	.	15.742	0.77905	0.0:0.0:0.0:1.0	.	460	Q5VUG0	SMBT2_HUMAN	G	460	ENSP00000355109:D460G;ENSP00000380353:D460G	ENSP00000355109:D460G	D	-	2	0	SFMBT2	7287848	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.911000	0.87458	2.126000	0.65437	0.533000	0.62120	GAC	.	.		0.483	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		C	7247842	T	C	7247842	3	2	91	1	0	0	0	0	1	0	0	0	14173	1667	58	2	1345	2	SFMBT2	10	7247842	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4039275	7247842	128286905	330	12404										
ZEB1	6935	hgsc.bcm.edu	37	chr10	31815839	31815839	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagggcctgaaatcctctcgAatgagcacgtgggtgccagg	14	11	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:31815839A>G	ENST00000320985.10	+	9	3132	c.3022A>G	c.(3022-3024)Aat>Gat	p.N1008D	ZEB1_ENST00000446923.2_Missense_Mutation_p.N992D|ZEB1_ENST00000542815.3_Missense_Mutation_p.N941D|ZEB1_ENST00000560721.2_Missense_Mutation_p.N988D|ZEB1_ENST00000361642.5_Missense_Mutation_p.N1009D			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	1008	Glu-rich (acidic).				cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				AATCCTCTCGAATGAGCACGT	0.517																																					p.N1009D	Ovarian(40;423 959 14296 36701 49589)	Atlas-SNP	.											.	ZEB1	173	.	0			c.A3025G						.						80	70	73					10																	31815839		2203	4300	6503	SO:0001583	missense	6935	exon9			CTCTCGAATGAGC	AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.3022A>G	chr10.hg19:g.31815839A>G	ENSP00000319248:p.Asn1008Asp	77.0	0.0		66.0	4.0	NM_001174096	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	hg19	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	A	5.511	0.279239	0.10458	.	.	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000543514;ENST00000446923	T;T;T;T;T	0.13089	2.94;2.62;2.68;2.62;2.68	4.8	-2.06	0.07298	.	3.939600	0.00567	N	0.000282	T	0.10337	0.0253	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.20887	0.009;0.049;0.025;0.049;0.029	B;B;B;B;B	0.23018	0.043;0.016;0.028;0.01;0.006	T	0.31024	-0.9958	10	0.26408	T	0.33	2.9472	8.1131	0.30926	0.4587:0.1381:0.4032:0.0	.	941;992;988;1009;1008	F5H4I8;E9PCM7;Q5VZ84;Q2KJ05;P37275	.;.;.;.;ZEB1_HUMAN	D	790;1008;1009;1003;941;1008;988;899;992	ENSP00000444282:N790D;ENSP00000354487:N1009D;ENSP00000444891:N941D;ENSP00000319248:N1008D;ENSP00000391612:N992D	ENSP00000319248:N1008D	N	+	1	0	ZEB1	31855845	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.475000	0.06599	-0.305000	0.08831	0.477000	0.44152	AAT	.	.		0.517	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		G	31815839	A	G	31815839	3	3	91	1	0	0	0	0	1	0	0	0	17638	246	9	2	3070	2	ZEB1	10	31815839	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	24567997	31815839	103718908	331	12405										
NRP1	8829	hgsc.bcm.edu	37	chr10	33552610	33552610	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccagatttctagccggtcgtAgcgacagaacatcccccctg	9	15	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:33552610A>G	ENST00000265371.4	-	5	1147	c.622T>C	c.(622-624)Tac>Cac	p.Y208H	NRP1_ENST00000374823.5_Missense_Mutation_p.Y208H|NRP1_ENST00000374822.4_Missense_Mutation_p.Y208H|NRP1_ENST00000374821.5_Missense_Mutation_p.Y208H|NRP1_ENST00000432372.2_Missense_Mutation_p.Y208H|NRP1_ENST00000374875.1_Missense_Mutation_p.Y27H|NRP1_ENST00000374867.2_Missense_Mutation_p.Y208H|NRP1_ENST00000395995.1_Missense_Mutation_p.Y208H|NRP1_ENST00000374816.3_Missense_Mutation_p.Y208H			O14786	NRP1_HUMAN	neuropilin 1	208	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	AGCCGGTCGTAGCGACAGAAC	0.468																																					p.Y208H	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.T622C						.						59	59	59					10																	33552610		2203	4300	6503	SO:0001583	missense	8829	exon4			GGTCGTAGCGACA	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"CD molecules"	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.622T>C	chr10.hg19:g.33552610A>G	ENSP00000265371:p.Tyr208His	89.0	0.0		84.0	4.0	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Missense_Mutation	SNP	ENST00000265371.4	hg19	CCDS7177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.5|21.5	4.163909|4.163909	0.78226|0.78226	.|.	.|.	ENSG00000099250|ENSG00000099250	ENST00000455749|ENST00000265371;ENST00000374875;ENST00000374867;ENST00000395995;ENST00000374822;ENST00000374821;ENST00000374823;ENST00000374816;ENST00000374818	.|T;T;T;T;T;T;T;T	.|0.20881	.|2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04	5.76|5.76	5.76|5.76	0.90799|0.90799	.|CUB (5);	.|0.052690	.|0.85682	.|D	.|0.000000	T|T	0.51346|0.51346	0.1669|0.1669	M|M	0.83774|0.83774	2.66|2.66	0.80722|0.80722	D|D	1|1	.|D;D;D;B;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.396;1.0;1.0;1.0;1.0;1.0	.|D;D;D;P;D;D;D;D;D	.|0.91635	.|0.996;0.994;0.994;0.479;0.978;0.999;0.996;0.996;0.976	T|T	0.57694|0.57694	-0.7767|-0.7767	5|10	.|0.87932	.|D	.|0	-20.3856|-20.3856	16.0734|16.0734	0.80951|0.80951	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|208;208;208;208;208;208;208;27;208	.|A8K9V7;E7EX60;Q5T7F0;Q5T7F1;O14786-2;Q68DN3;O14786;Q5JWQ6;E9PEP6	.|.;.;.;.;.;.;NRP1_HUMAN;.;.	P|H	8|208;27;208;208;208;208;208;208;27	.|ENSP00000265371:Y208H;ENSP00000364009:Y27H;ENSP00000364001:Y208H;ENSP00000379317:Y208H;ENSP00000363955:Y208H;ENSP00000363954:Y208H;ENSP00000363956:Y208H;ENSP00000363949:Y208H	.|ENSP00000265371:Y208H	L|Y	-|-	2|1	0|0	NRP1|NRP1	33592616|33592616	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.921000|0.921000	0.55340|0.55340	9.339000|9.339000	0.96797|0.96797	2.195000|2.195000	0.70347|0.70347	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.		0.468	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2			G	33552610	A	G	33552610	3	3	91	1	0	0	0	0	1	0	0	0	10669	420	15	2	2216	2	NRP1	10	33552610	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1736771	33552610	101982137	332	12406										
ZNF33B	7582	hgsc.bcm.edu	37	chr10	43089012	43089012	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaaggtttctcacctgtgtgAgttctctggtgtactgtaag	11	7	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:43089012A>G	ENST00000359467.3	-	5	1500	c.1386T>C	c.(1384-1386)acT>acC	p.T462T	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	462					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						CACCTGTGTGAGTTCTCTGGT	0.398																																					p.T462T	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.T1386C						.						96	93	94					10																	43089012		2203	4300	6503	SO:0001819	synonymous_variant	7582	exon5			TGTGTGAGTTCTC	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"Zinc fingers, C2H2-type", "-"	13097	protein-coding gene	gene with protein product		194522	"zinc finger protein 33b (KOX 31)", "zinc finger protein 11B"	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1386T>C	chr10.hg19:g.43089012A>G		164.0	0.0		98.0	4.0	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Silent	SNP	ENST00000359467.3	hg19	CCDS7198.1																																																																																			.	.		0.398	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		G	43089012	A	G	43089012	2	3	91	1	0	0	0	0	0	0	0	1	17870	291	11	2		2	ZNF33B	10	43089012	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	9536402	43089012	92445735	333	12407										
ALOX5	240	hgsc.bcm.edu	37	chr10	45939627	45939627	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagccccgccaccgactgccAagggcgtggtgaccattgag	14	14	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:45939627A>G	ENST00000374391.2	+	13	1791	c.1738A>G	c.(1738-1740)Aag>Gag	p.K580E	ALOX5_ENST00000542434.1_Intron|RP11-67C2.2_ENST00000435635.1_RNA	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	580	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	ACCGACTGCCAAGGGCGTGGT	0.687																																					p.K580E		Atlas-SNP	.											.	ALOX5	88	.	0			c.A1738G						.						16	15	16					10																	45939627		2154	4245	6399	SO:0001583	missense	240	exon13			ACTGCCAAGGGCG	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"Arachidonate lipoxygenases"	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.1738A>G	chr10.hg19:g.45939627A>G	ENSP00000363512:p.Lys580Glu	109.0	0.0		74.0	4.0	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Missense_Mutation	SNP	ENST00000374391.2	hg19	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	A	33	5.211057	0.95069	.	.	ENSG00000012779	ENST00000374391	D	0.90900	-2.75	4.86	4.86	0.63082	Lipoxygenase, C-terminal (3);	0.045241	0.85682	D	0.000000	D	0.94006	0.8080	M	0.66439	2.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94137	0.7393	10	0.59425	D	0.04	-36.3065	12.4482	0.55664	1.0:0.0:0.0:0.0	.	548;580	E5FPY8;P09917	.;LOX5_HUMAN	E	580	ENSP00000363512:K580E	ENSP00000363512:K580E	K	+	1	0	ALOX5	45259633	1.000000	0.71417	0.985000	0.45067	0.969000	0.65631	9.091000	0.94151	2.048000	0.60808	0.528000	0.53228	AAG	.	.		0.687	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1			G	45939627	A	G	45939627	3	3	91	1	0	0	0	0	1	0	0	0	540	131	5	2	1788	2	ALOX5	10	45939627	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2850615	45939627	89595120	334	12408										
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49457197	49457197	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagaaagcagggctgaccagGggcaaaccacatagtccgag	13	11	0	2	rs142764597		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:49457197G>A	ENST00000374201.3	-	3	478	c.176C>T	c.(175-177)cCc>cTc	p.P59L	FRMPD2_ENST00000305531.3_Missense_Mutation_p.P57L|FRMPD2_ENST00000407470.4_Missense_Mutation_p.P50L	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	59	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		GGCTGACCAGGGGCAAACCAC	0.557																																					p.P59L		Atlas-SNP	.											.	FRMPD2	157	.	0			c.C176T						.						49	51	50					10																	49457197		2203	4300	6503	SO:0001583	missense	143162	exon3			GACCAGGGGCAAA	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.176C>T	chr10.hg19:g.49457197G>A	ENSP00000363317:p.Pro59Leu	89.0	0.0		83.0	4.0	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	hg19	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.690406	0.68271	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.36699	1.24;1.24;1.24	5.47	4.57	0.56435	KIND (2);	.	.	.	.	T	0.59542	0.2201	M	0.80982	2.52	0.47621	D	0.999479	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.63804	-0.6554	9	0.87932	D	0	.	10.1642	0.42871	0.0917:0.0:0.9083:0.0	.	57;59;50	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	L	59;57;50	ENSP00000363317:P59L;ENSP00000307079:P57L;ENSP00000384339:P50L	ENSP00000307079:P57L	P	-	2	0	FRMPD2	49127203	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	5.303000	0.65738	1.333000	0.45449	0.655000	0.94253	CCC	.	G|1.000;T|0.000		0.557	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		A	49457197	G	A	49457197	3	1	91	1	0	0	0	0	1	0	0	0	6066	1232	43	3	3861	3	FRMPD2	10	49457197	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3517570	49457197	86077550	335	12409										
C10orf72	196740	hgsc.bcm.edu	37	chr10	50256529	50256529	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggccagctccttacctttggCagggactgcgggaggaatgt	15	10	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:50256529C>T	ENST00000332853.4	-	6	792	c.769G>A	c.(769-771)Gcc>Acc	p.A257T		NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	257						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						TTACCTTTGGCAGGGACTGCG	0.547																																					p.A257T		Atlas-SNP	.											.	VSTM4	83	.	0			c.G769A						.						101	88	92					10																	50256529		2203	4300	6503	SO:0001583	missense	196740	exon6			CTTTGGCAGGGAC	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"Immunoglobulin superfamily / V-set domain containing"	26470	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 72"	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.769G>A	chr10.hg19:g.50256529C>T	ENSP00000331062:p.Ala257Thr	87.0	0.0		51.0	4.0	NM_001031746	B4DNI6|Q96MX7	Missense_Mutation	SNP	ENST00000332853.4	hg19	CCDS31198.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.499386	0.85069	.	.	ENSG00000165633	ENST00000332853	T	0.08634	3.07	6.17	6.17	0.99709	.	0.171431	0.50627	D	0.000108	T	0.17066	0.0410	N	0.19112	0.55	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.01702	-1.1292	10	0.45353	T	0.12	-36.3062	16.3795	0.83443	0.0:1.0:0.0:0.0	.	257	Q8IW00	VSTM4_HUMAN	T	257	ENSP00000331062:A257T	ENSP00000331062:A257T	A	-	1	0	VSTM4	49926535	0.996000	0.38824	0.993000	0.49108	0.916000	0.54674	4.440000	0.59975	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.547	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984		T	50256529	C	T	50256529	3	4	91	1	0	0	0	0	1	0	0	0	1617	710	25	3	205	3	C10orf72	10	50256529	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	799332	50256529	85278218	336	12410										
ERCC6	2074	hgsc.bcm.edu	37	chr10	50701191	50701191	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggtataggaaccggtttcaTgtagaattgccactctgaac	11	8	2	2	rs376250875		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:50701191T>C	ENST00000355832.5	-	8	1871	c.1793A>G	c.(1792-1794)cAt>cGt	p.H598R	ERCC6_ENST00000542458.1_Intron	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	598	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						ACCGGTTTCATGTAGAATTGC	0.413								Direct reversal of damage;Nucleotide excision repair (NER)																													p.T598R		Atlas-SNP	.											.	ERCC6	162	.	0			c.C1793G						.	T	ARG/HIS	1,4405	2.1+/-5.4	0,1,2202	107	90	96		1793	5.3	0.2	10		96	0,8600		0,0,4300	no	missense	ERCC6	NM_000124.2	29	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	probably-damaging	598/1494	50701191	1,13005	2203	4300	6503	SO:0001583	missense	2074	exon8			GTTTCATGTAGAA	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.1793A>G	chr10.hg19:g.50701191T>C	ENSP00000348089:p.His598Arg	138.0	0.0		98.0	4.0	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	hg19	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.329218	0.81690	2.27E-4	0.0	ENSG00000225830	ENST00000355832	D	0.94092	-3.35	5.31	5.31	0.75309	DEAD-like helicase (2);SNF2-related (1);	.	.	.	.	D	0.97099	0.9052	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97942	1.0326	9	0.87932	D	0	-21.1423	15.5582	0.76216	0.0:0.0:0.0:1.0	.	598	Q03468	ERCC6_HUMAN	R	598	ENSP00000348089:H598R	ENSP00000348089:H598R	H	-	2	0	ERCC6	50371197	1.000000	0.71417	0.225000	0.23894	0.962000	0.63368	7.997000	0.88414	2.135000	0.66039	0.455000	0.32223	CAT	.	.		0.413	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		C	50701191	T	C	50701191	3	2	91	1	0	0	0	0	1	0	0	0	5219	1464	51	2	2744	2	ERCC6	10	50701191	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	444662	50701191	84833556	337	12411										
ERCC6	2074	hgsc.bcm.edu	37	chr10	50701217	50701217	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	attgccactctgaacggaggCcaccacgtgtgaaattcctt	9	12	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:50701217C>T	ENST00000355832.5	-	8	1845	c.1767G>A	c.(1765-1767)tgG>tgA	p.W589*	ERCC6_ENST00000542458.1_Intron	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	589	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TGAACGGAGGCCACCACGTGT	0.448								Direct reversal of damage;Nucleotide excision repair (NER)																													p.F589L		Atlas-SNP	.											.	ERCC6	162	.	0			c.C1767A						.						122	103	110					10																	50701217		2203	4300	6503	SO:0001587	stop_gained	2074	exon8			CGGAGGCCACCAC	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.1767G>A	chr10.hg19:g.50701217C>T	ENSP00000348089:p.Trp589*	150.0	0.0		109.0	5.0	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	hg19	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	C	39	7.768210	0.98480	.	.	ENSG00000225830	ENST00000355832	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.2819	19.3425	0.94349	0.0:1.0:0.0:0.0	.	.	.	.	X	589	.	ENSP00000348089:W589X	W	-	3	0	ERCC6	50371223	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.776000	0.85560	2.643000	0.89663	0.557000	0.71058	TGG	.	.		0.448	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		T	50701217	C	T	50701217	4	4	91	1	0	0	0	0	0	1	0	0	5219	740	26	3	2770	3	ERCC6	10	50701217	Nonsense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	26	50701217	84833530	338	12412										
CHAT	1103	hgsc.bcm.edu	37	chr10	50830196	50830196	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctacaaggccctgctggacaGgtaggactgggagggtggtg	18	8	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:50830196G>T	ENST00000337653.2	+	5	905	c.752G>T	c.(751-753)aGc>aTc	p.S251I	CHAT_ENST00000460699.1_3'UTR|CHAT_ENST00000395562.2_Splice_Site_p.S169I|CHAT_ENST00000455728.2_Splice_Site_p.S133I|CHAT_ENST00000351556.3_Splice_Site_p.S133I|CHAT_ENST00000339797.1_Splice_Site_p.S133I|CHAT_ENST00000395559.2_Splice_Site_p.S133I	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	251					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	CTGCTGGACAGGTAGGACTGG	0.587																																					p.S251I		Atlas-SNP	.											.	CHAT	162	.	0			c.G752T						.						226	181	196					10																	50830196		2203	4300	6503	SO:0001630	splice_region_variant	1103	exon5			TGGACAGGTAGGA	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.752+1G>T	chr10.hg19:g.50830196G>T		147.0	0.0		100.0	4.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	hg19	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827050	0.50739	.	.	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	T;T;T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48;-1.48;-1.48	4.85	3.88	0.44766	.	0.280060	0.39544	N	0.001326	T	0.78786	0.4338	M	0.81341	2.54	0.49687	D	0.999818	B;P	0.41624	0.232;0.757	B;B	0.33799	0.051;0.17	D	0.83530	0.0090	10	0.56958	D	0.05	-24.6129	14.401	0.67047	0.0:0.3158:0.6842:0.0	.	133;251	F8W8I2;P28329	.;CLAT_HUMAN	I	133;133;133;251;169;133	ENSP00000343486:S133I;ENSP00000345878:S133I;ENSP00000378926:S133I;ENSP00000337103:S251I;ENSP00000378929:S169I;ENSP00000390521:S133I	ENSP00000337103:S251I	S	+	2	0	CHAT	50500202	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	1.702000	0.37836	2.233000	0.73108	0.561000	0.74099	AGC	.	.		0.587	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	Missense_Mutation	T	50830196	G	T	50830196	5	4	91	1	0	0	0	0	0	0	1	0	3315	1014	35	3	814	3	CHAT	10	50830196	Splice_Site	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	128979	50830196	84704551	339	12413										
CISD1	55847	hgsc.bcm.edu	37	chr10	60047332	60047332	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcttcctagttcccattctgTgatggggctcacacaaaaca	7	12	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:60047332T>C	ENST00000333926.5	+	3	465	c.249T>C	c.(247-249)tgT>tgC	p.C83C	CISD1_ENST00000488388.2_3'UTR	NM_018464.4	NP_060934.1	Q9NZ45	CISD1_HUMAN	CDGSH iron sulfur domain 1	83					regulation of cellular respiration (GO:0043457)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)			breast(1)	1						TCCCATTCTGTGATGGGGCTC	0.388																																					p.C83C		Atlas-SNP	.											.	CISD1	7	.	0			c.T249C						.						85	76	79					10																	60047332		2203	4300	6503	SO:0001819	synonymous_variant	55847	exon3			ATTCTGTGATGGG	AY960578	CCDS7251.1	10q21.3	2011-01-05	2007-08-10	2007-08-10	ENSG00000122873	ENSG00000122873		"CDGSH iron sulfur domain containing"	30880	protein-coding gene	gene with protein product		611932	"chromosome 10 open reading frame 70", "zinc finger, CDGSH-type domain 1"	C10orf70, ZCD1		17376863, 17584744	Standard	NM_018464		Approved	MDS029, mitoNEET	uc001jkc.5	Q9NZ45	OTTHUMG00000018266	ENST00000333926.5:c.249T>C	chr10.hg19:g.60047332T>C		134.0	0.0		99.0	4.0	NM_018464	Q1X902	Silent	SNP	ENST00000333926.5	hg19	CCDS7251.1																																																																																			.	.		0.388	CISD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048137.1	NM_018464		C	60047332	T	C	60047332	2	2	91	1	0	0	0	0	0	0	0	1	3437	1702	59	2		2	CISD1	10	60047332	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9217136	60047332	75487415	340	12414										
SUPV3L1	6832	hgsc.bcm.edu	37	chr10	70968547	70968547	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtcaggaaccttaaagagccAagctagaaggacacgcggca	12	10	1	2	rs370657076		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:70968547A>G	ENST00000359655.4	+	15	2177	c.2117A>G	c.(2116-2118)cAa>cGa	p.Q706R		NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	706	Interaction with LAMTOR5, important for protein stability.				ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTAAAGAGCCAAGCTAGAAGG	0.502																																					p.Q706R		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.A2117G						.	A	ARG/GLN	0,4406		0,0,2203	81	79	80		2117	-1.3	0.3	10		80	1,8599	1.2+/-3.3	0,1,4299	no	missense	SUPV3L1	NM_003171.3	43	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	706/787	70968547	1,13005	2203	4300	6503	SO:0001583	missense	6832	exon15			AGAGCCAAGCTAG	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"suppressor of var1 (S.cerevisiae) 3-like 1"			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.2117A>G	chr10.hg19:g.70968547A>G	ENSP00000352678:p.Gln706Arg	155.0	0.0		86.0	4.0	NM_003171	A8K301|O43630	Missense_Mutation	SNP	ENST00000359655.4	hg19	CCDS7287.1	.	.	.	.	.	.	.	.	.	.	A	2.513	-0.312547	0.05422	0.0	1.16E-4	ENSG00000156502	ENST00000359655	T	0.30182	1.54	5.9	-1.34	0.09143	.	0.788806	0.12345	N	0.477145	T	0.15305	0.0369	N	0.22421	0.69	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.31503	-0.9941	10	0.15952	T	0.53	-0.4303	5.8797	0.18848	0.3644:0.4659:0.0621:0.1076	.	706	Q8IYB8	SUV3_HUMAN	R	706	ENSP00000352678:Q706R	ENSP00000352678:Q706R	Q	+	2	0	SUPV3L1	70638553	0.000000	0.05858	0.272000	0.24630	0.100000	0.18952	-0.321000	0.08018	-0.125000	0.11703	-0.323000	0.08544	CAA	.	.		0.502	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171		G	70968547	A	G	70968547	3	3	91	1	0	0	0	0	1	0	0	0	15417	130	5	2	2175	2	SUPV3L1	10	70968547	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	10921215	70968547	64566200	341	12415										
PRF1	5551	hgsc.bcm.edu	37	chr10	72357981	72357981	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggaaccagacttgggagccTgatcacaggtgccaaggagg	16	9	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:72357981T>C	ENST00000441259.1	-	3	1656	c.1496A>G	c.(1495-1497)cAg>cGg	p.Q499R	PRF1_ENST00000373209.2_Missense_Mutation_p.Q499R	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	499					apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CTTGGGAGCCTGATCACAGGT	0.592			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.Q499R		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.A1496G						.						135	134	134					10																	72357981		2203	4300	6503	SO:0001583	missense	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GGAGCCTGATCAC	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"Perforin", "perforin 1 (preforming protein)"	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.1496A>G	chr10.hg19:g.72357981T>C	ENSP00000398568:p.Gln499Arg	103.0	0.0		88.0	4.0	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	hg19	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	T	1.891	-0.455536	0.04540	.	.	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.90620	-2.7;-2.7	5.97	-6.99	0.01605	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	2.233410	0.01456	N	0.015679	T	0.80265	0.4591	N	0.10972	0.075	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.72623	-0.4237	10	0.02654	T	1	-2.2068	18.8422	0.92189	0.0:0.7791:0.0:0.2209	.	499	P14222	PERF_HUMAN	R	499	ENSP00000362305:Q499R;ENSP00000398568:Q499R	ENSP00000316746:Q499R	Q	-	2	0	PRF1	72027987	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.642000	0.00204	-1.150000	0.02840	-0.256000	0.11100	CAG	.	.		0.592	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		C	72357981	T	C	72357981	3	2	91	1	0	0	0	0	1	0	0	0	12490	1580	55	2	175	2	PRF1	10	72357981	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1389434	72357981	63176766	342	12416										
CBARA1	10367	hgsc.bcm.edu	37	chr10	74267928	74267928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttactggaaagaacagttgTgaggaaaatgtagtctgaaa	11	4	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:74267928T>C	ENST00000361114.5	-	6	733	c.637A>G	c.(637-639)Aca>Gca	p.T213A	MICU1_ENST00000398763.4_5'UTR|MICU1_ENST00000401998.3_Missense_Mutation_p.T213A|MICU1_ENST00000398761.4_Missense_Mutation_p.T215A|MICU1_ENST00000418483.2_Intron	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	213					calcium ion import (GO:0070509)|calcium ion transmembrane import into mitochondrion (GO:0036444)|defense response (GO:0006952)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein homooligomerization (GO:0051260)	calcium channel complex (GO:0034704)|integral component of mitochondrial membrane (GO:0032592)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										AGAACAGTTGTGAGGAAAATG	0.333																																					p.T213A		Atlas-SNP	.											.	.	.	.	0			c.A637G						.						60	56	57					10																	74267928		1815	4086	5901	SO:0001583	missense	10367	exon6			CAGTTGTGAGGAA	Y17711	CCDS55714.1, CCDS55715.1	10q22.1	2013-01-10	2011-06-23	2011-06-23	ENSG00000107745	ENSG00000107745		"EF-hand domain containing"	1530	protein-coding gene	gene with protein product		605084	"calcium binding atopy-related autoantigen 1"	CBARA1		9806765, 20693986	Standard	NM_006077		Approved	CALC, EFHA3, FLJ12684	uc001jtb.2	Q9BPX6	OTTHUMG00000018437	ENST00000361114.5:c.637A>G	chr10.hg19:g.74267928T>C	ENSP00000354415:p.Thr213Ala	100.0	0.0		97.0	4.0	NM_001195518	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Missense_Mutation	SNP	ENST00000361114.5	hg19	CCDS55715.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.195170	0.78902	.	.	ENSG00000107745	ENST00000361114;ENST00000398761;ENST00000401998	T;T;T	0.79845	-1.31;-1.31;-1.31	5.23	5.23	0.72850	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.70193	0.3196	N	0.12182	0.205	0.80722	D	1	P	0.45715	0.865	P	0.45913	0.497	T	0.69829	-0.5039	10	0.23302	T	0.38	.	15.0724	0.72049	0.0:0.0:0.0:1.0	.	213	Q9BPX6	MICU1_HUMAN	A	213;215;213	ENSP00000354415:T213A;ENSP00000381745:T215A;ENSP00000384068:T213A	ENSP00000354415:T213A	T	-	1	0	MICU1	73937934	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.704000	0.84595	2.090000	0.63153	0.383000	0.25322	ACA	.	.		0.333	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077		C	74267928	T	C	74267928	3	2	91	1	0	0	0	0	1	0	0	0	2698	1696	59	2	821	2	CBARA1	10	74267928	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1909947	74267928	61266819	343	12417										
FUT11	170384	hgsc.bcm.edu	37	chr10	75532420	75532420	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgtggcgtcccggaaccgccGagcgctgagggactcgcgga	17	14	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:75532420G>A	ENST00000372841.3	+	1	372	c.329G>A	c.(328-330)cGa>cAa	p.R110Q	RMRPP1_ENST00000517236.1_RNA|AC022400.2_ENST00000595757.1_5'Flank|FUT11_ENST00000394790.1_Missense_Mutation_p.R110Q|FUT11_ENST00000465695.1_3'UTR	NM_173540.2	NP_775811.2	Q495W5	FUT11_HUMAN	fucosyltransferase 11 (alpha (1,3) fucosyltransferase)	110					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7	Prostate(51;0.0112)					CGGAACCGCCGAGCGCTGAGG	0.736																																					p.R110Q		Atlas-SNP	.											.	FUT11	30	.	0			c.G329A						.						5	5	5					10																	75532420		1954	3835	5789	SO:0001583	missense	170384	exon1			ACCGCCGAGCGCT	BC036037	CCDS7333.1, CCDS60558.1	10q22.3	2014-01-02			ENSG00000196968	ENSG00000196968		"Fucosyltransferases"	19233	protein-coding gene	gene with protein product						11698403, 24318988	Standard	NM_173540		Approved	MGC33202	uc001jva.3	Q495W5	OTTHUMG00000018483	ENST00000372841.3:c.329G>A	chr10.hg19:g.75532420G>A	ENSP00000361932:p.Arg110Gln	15.0	0.0		20.0	4.0	NM_173540	Q495W7|Q8IYE4	Missense_Mutation	SNP	ENST00000372841.3	hg19	CCDS7333.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.176976	0.38413	.	.	ENSG00000196968	ENST00000372841;ENST00000394790	T;T	0.25579	1.79;1.79	5.26	5.26	0.73747	.	0.459795	0.25285	N	0.031767	T	0.21674	0.0522	L	0.31371	0.925	0.09310	N	1	B;B;P	0.47545	0.045;0.062;0.897	B;B;P	0.45856	0.046;0.027;0.495	T	0.11299	-1.0593	10	0.19147	T	0.46	-33.8039	11.9208	0.52791	0.0811:0.0:0.9189:0.0	.	110;110;110	Q495W5;Q495W5-2;B2RC53	FUT11_HUMAN;.;.	Q	110	ENSP00000361932:R110Q;ENSP00000378270:R110Q	ENSP00000361932:R110Q	R	+	2	0	FUT11	75202426	0.990000	0.36364	0.007000	0.13788	0.039000	0.13416	5.570000	0.67398	2.466000	0.83321	0.462000	0.41574	CGA	.	.		0.736	FUT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048689.1	NM_173540		A	75532420	G	A	75532420	3	1	91	1	0	0	0	0	1	0	0	0	6111	1058	37	1	331	1	FUT11	10	75532420	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	1264492	75532420	60002327	344	12418										
MYST4	23522	hgsc.bcm.edu	37	chr10	76788662	76788662	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaagaggaggaggaggaggaAgaggaagaagaggaagaaga	21	0	0	6	rs546432678|rs544824146	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:76788662A>G	ENST00000287239.4	+	18	4569	c.4080A>G	c.(4078-4080)gaA>gaG	p.E1360E	KAT6B_ENST00000372711.1_Silent_p.E1177E|KAT6B_ENST00000372725.1_Silent_p.E1068E|KAT6B_ENST00000372724.1_Silent_p.E1068E|KAT6B_ENST00000372714.1_Silent_p.E1068E	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1360	Poly-Glu.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										aggaggaggaagaggaagaag	0.453													A|||	11	0.00219649	0	0	5008	,	,		20164	0		0	False		,,,				2504	0.0112				p.E1360E		Atlas-SNP	.											.	.	.	.	0			c.A4080G						.						43	42	42					10																	76788662		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon18			GGAGGAAGAGGAA	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.4080A>G	chr10.hg19:g.76788662A>G		37.0	0.0		39.0	5.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.453	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		G	76788662	A	G	76788662	2	3	91	1	0	0	0	0	0	0	0	1	10114	69	3	2		2	MYST4	10	76788662	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1256242	76788662	58746085	345	12419										
RPS24	6229	hgsc.bcm.edu	37	chr10	79795311	79795311	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggaaggcgacagtgcctaagAcagaaattcgggaaaaacta	12	7	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:79795311A>G	ENST00000372360.3	+	3	149	c.112A>G	c.(112-114)Aca>Gca	p.T38A	RPS24_ENST00000476545.1_3'UTR|RPS24_ENST00000360830.4_Missense_Mutation_p.T38A|RPS24_ENST00000435275.1_Missense_Mutation_p.T38A|RPS24_ENST00000440692.1_Missense_Mutation_p.T38A	NM_001026.4	NP_001017.1	P62847	RS24_HUMAN	ribosomal protein S24	38					cellular protein metabolic process (GO:0044267)|erythrocyte homeostasis (GO:0034101)|gene expression (GO:0010467)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|translation initiation factor binding (GO:0031369)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(2)|skin(1)	5	all_cancers(46;0.0343)|all_epithelial(25;0.000959)|Breast(12;0.00113)|Prostate(51;0.0095)		Epithelial(14;0.00128)|OV - Ovarian serous cystadenocarcinoma(4;0.00248)|all cancers(16;0.00428)			AGTGCCTAAGACAGAAATTCG	0.408																																					p.T38A		Atlas-SNP	.											.	RPS24	23	.	0			c.A112G						.						64	62	63					10																	79795311		2203	4300	6503	SO:0001583	missense	6229	exon3			CCTAAGACAGAAA	AB007159	CCDS7355.1, CCDS7356.1, CCDS44443.1	10q22	2011-04-06			ENSG00000138326	ENSG00000138326		"S ribosomal proteins"	10411	protein-coding gene	gene with protein product		602412				9027498, 9582194	Standard	NM_001142283		Approved	S24	uc001jzs.3	P62847	OTTHUMG00000018549	ENST00000372360.3:c.112A>G	chr10.hg19:g.79795311A>G	ENSP00000361435:p.Thr38Ala	71.0	0.0		70.0	4.0	NM_001142283	E7EPK6|P16632|Q5T0P7|Q5T0P8|Q7Z3D1	Missense_Mutation	SNP	ENST00000372360.3	hg19	CCDS7355.1	.	.	.	.	.	.	.	.	.	.	A	19.16	3.772812	0.69992	.	.	ENSG00000138326	ENST00000440692;ENST00000435275;ENST00000372360;ENST00000401656;ENST00000360830	.	.	.	5.07	5.07	0.68467	Ribosomal protein L23/L15e (1);Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.68622	0.3021	L	0.55481	1.735	0.80722	D	1	P;P;B;B	0.42248	0.473;0.774;0.329;0.329	B;P;B;B	0.51742	0.329;0.678;0.327;0.327	T	0.67554	-0.5641	8	.	.	.	.	14.8512	0.70297	1.0:0.0:0.0:0.0	.	38;38;38;38	P62847-3;E7EPK6;P62847;E7ETK0	.;.;RS24_HUMAN;.	A	38	.	.	T	+	1	0	RPS24	79465317	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	9.283000	0.95860	1.895000	0.54865	0.496000	0.49642	ACA	.	.		0.408	RPS24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048910.1	NM_001026		G	79795311	A	G	79795311	3	3	91	1	0	0	0	0	1	0	0	0	13650	275	10	2	122	2	RPS24	10	79795311	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3006649	79795311	55739436	346	12420										
MAT1A	4143	hgsc.bcm.edu	37	chr10	82049166	82049166	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtggtcacacaagccatccAccggtccattcatcttctca	6	15	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:82049166A>G	ENST00000372213.3	-	1	274	c.14T>C	c.(13-15)gTg>gCg	p.V5A		NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	5					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	CAAGCCATCCACCGGTCCATT	0.473																																					p.V5A		Atlas-SNP	.											.	MAT1A	52	.	0			c.T14C						.						172	154	160					10																	82049166		2203	4300	6503	SO:0001583	missense	4143	exon1			CCATCCACCGGTC		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"S-adenosylmethionine synthetase"	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.14T>C	chr10.hg19:g.82049166A>G	ENSP00000361287:p.Val5Ala	179.0	0.0		85.0	6.0	NM_000429	D3DWD5|Q5QP09	Missense_Mutation	SNP	ENST00000372213.3	hg19	CCDS7365.1	.	.	.	.	.	.	.	.	.	.	A	12.34	1.907577	0.33721	.	.	ENSG00000151224	ENST00000372213;ENST00000372206	D	0.96011	-3.88	5.34	5.34	0.76211	.	0.541473	0.19334	N	0.116836	D	0.86301	0.5900	N	0.02916	-0.46	0.35460	D	0.796464	B	0.02656	0.0	B	0.04013	0.001	D	0.83742	0.0204	10	0.10111	T	0.7	-25.9898	13.554	0.61749	1.0:0.0:0.0:0.0	.	5	Q00266	METK1_HUMAN	A	5	ENSP00000361287:V5A	ENSP00000361280:V5A	V	-	2	0	MAT1A	82039146	1.000000	0.71417	0.990000	0.47175	0.799000	0.45148	3.481000	0.53179	2.156000	0.67533	0.533000	0.62120	GTG	.	.		0.473	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429		G	82049166	A	G	82049166	3	3	91	1	0	0	0	0	1	0	0	0	9338	159	6	2	1209	2	MAT1A	10	82049166	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2253855	82049166	53485581	347	12421										
LRIT1	26103	hgsc.bcm.edu	37	chr10	86001096	86001096	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggccttgctgccatcacccaTgatatggaggctgcagctgc	12	13	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:86001096T>C	ENST00000372105.3	-	1	121	c.100A>G	c.(100-102)Atg>Gtg	p.M34V		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	34	LRRNT.					integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						CCATCACCCATGATATGGAGG	0.642																																					p.M34V		Atlas-SNP	.											.	LRIT1	73	.	0			c.A100G						.						34	34	34					10																	86001096		2203	4298	6501	SO:0001583	missense	26103	exon1			CACCCATGATATG	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	23404	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 9"		"leucine rich repeat containing 21"	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.100A>G	chr10.hg19:g.86001096T>C	ENSP00000361177:p.Met34Val	89.0	0.0		84.0	4.0	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	hg19	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	T	9.527	1.109711	0.20714	.	.	ENSG00000148602	ENST00000372105	T	0.32753	1.44	4.31	2.4	0.29515	Leucine-rich repeat-containing N-terminal (1);	0.172115	0.39834	N	0.001256	T	0.14399	0.0348	N	0.14661	0.345	0.22253	N	0.999258	B	0.02656	0.0	B	0.01281	0.0	T	0.31943	-0.9925	10	0.02654	T	1	.	11.5821	0.50898	0.0:0.0:0.5319:0.4681	.	34	Q9P2V4	LRIT1_HUMAN	V	34	ENSP00000361177:M34V	ENSP00000361177:M34V	M	-	1	0	LRIT1	85991076	1.000000	0.71417	0.998000	0.56505	0.791000	0.44710	0.975000	0.29449	0.423000	0.26033	-0.677000	0.03784	ATG	.	.		0.642	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		C	86001096	T	C	86001096	3	2	91	1	0	0	0	0	1	0	0	0	8956	1464	51	2	1787	2	LRIT1	10	86001096	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3951930	86001096	49533651	348	12422										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88259819	88259819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttttctgagacgaccagctTctcccaaatctgcaggagtg	9	11	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:88259819T>C	ENST00000298767.5	-	3	1653	c.1181A>G	c.(1180-1182)gAa>gGa	p.E394G		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	394	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						ACGACCAGCTTCTCCCAAATC	0.393																																					p.E394G		Atlas-SNP	.											.	WAPAL	81	.	0			c.A1181G						.						59	61	60					10																	88259819		2203	4300	6503	SO:0001583	missense	23063	exon3			CCAGCTTCTCCCA	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.1181A>G	chr10.hg19:g.88259819T>C	ENSP00000298767:p.Glu394Gly	163.0	0.0		113.0	5.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.057235	0.55325	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.37584	1.19	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.54838	0.1883	L	0.53249	1.67	0.80722	D	1	D;D;D	0.76494	0.987;0.987;0.999	P;P;D	0.67382	0.755;0.755;0.951	T	0.57860	-0.7738	10	0.87932	D	0	.	15.6594	0.77174	0.0:0.0:0.0:1.0	.	394;394;437	B2RTX8;Q7Z5K2;Q7Z5K2-2	.;WAPL_HUMAN;.	G	479;394;479	ENSP00000298767:E394G	ENSP00000298767:E394G	E	-	2	0	WAPAL	88249799	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.102000	0.63906	0.528000	0.53228	GAA	.	.		0.393	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		C	88259819	T	C	88259819	3	2	91	1	0	0	0	0	1	0	0	0	17263	1783	62	2	2459	2	WAPAL	10	88259819	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2258723	88259819	47274928	349	12423										
IFIT2	3433	hgsc.bcm.edu	37	chr10	91066406	91066406	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaaggtgaagaggaaggtgaAggagagaagttagttgaaga	18	0	0	6			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:91066406A>G	ENST00000371826.3	+	2	862	c.693A>G	c.(691-693)gaA>gaG	p.E231E	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	231					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				AGGAAGGTGAAGGAGAGAAGT	0.473																																					p.E231E		Atlas-SNP	.											.	IFIT2	39	.	0			c.A693G						.						74	73	73					10																	91066406		1980	4178	6158	SO:0001819	synonymous_variant	3433	exon2			AGGTGAAGGAGAG	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"Tetratricopeptide (TTC) repeat domain containing"	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.693A>G	chr10.hg19:g.91066406A>G		92.0	0.0		72.0	4.0	NM_001547	Q5T767	Silent	SNP	ENST00000371826.3	hg19	CCDS41548.1																																																																																			.	.		0.473	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547		G	91066406	A	G	91066406	2	3	91	1	0	0	0	0	0	0	0	1	7532	69	3	2		2	IFIT2	10	91066406	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2806587	91066406	44468341	350	12424										
IFIT1B	439996	hgsc.bcm.edu	37	chr10	91144106	91144106	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttgagatggcctatgttgacCtggctgaaacgtatgcagaa	12	7	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:91144106C>T	ENST00000371809.3	+	2	1116	c.1036C>T	c.(1036-1038)Ctg>Ttg	p.L346L	LIPA_ENST00000371837.1_Intron	NM_001010987.2	NP_001010987.1	Q5T764	IFT1B_HUMAN	interferon-induced protein with tetratricopeptide repeats 1B	346										endometrium(2)|large_intestine(3)|lung(8)	13						CTATGTTGACCTGGCTGAAAC	0.403																																					p.L346L		Atlas-SNP	.											.	IFIT1B	39	.	0			c.C1036T						.						69	66	67					10																	91144106		2203	4300	6503	SO:0001819	synonymous_variant	439996	exon2			GTTGACCTGGCTG		CCDS31242.1	10q23.31	2014-05-22	2010-03-22	2010-03-22	ENSG00000204010	ENSG00000204010		"Tetratricopeptide (TTC) repeat domain containing"	23442	protein-coding gene	gene with protein product			"interferon-induced protein with tetratricopeptide repeats 1-like"	IFIT1L			Standard	NM_001010987		Approved	bA149I23.6	uc001kgh.3	Q5T764	OTTHUMG00000018709	ENST00000371809.3:c.1036C>T	chr10.hg19:g.91144106C>T		60.0	0.0		61.0	4.0	NM_001010987	A7E245	Silent	SNP	ENST00000371809.3	hg19	CCDS31242.1																																																																																			.	.		0.403	IFIT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049296.3	NM_001010987		T	91144106	C	T	91144106	2	4	91	1	0	0	0	0	0	0	0	1	7531	680	24	3		3	IFIT1B	10	91144106	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	77700	91144106	44390641	351	12425										
TCTN3	26123	hgsc.bcm.edu	37	chr10	97453399	97453399	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cccccacaacgttttccctcAcctgggaagaggtccacagt	8	16	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:97453399A>G	ENST00000371217.5	-	1	280		c.e1+1		TCTN3_ENST00000430368.2_Splice_Site|TCTN3_ENST00000371209.5_Splice_Site|TCTN3_ENST00000265993.9_Splice_Site			Q6NUS6	TECT3_HUMAN	tectonic family member 3						apoptotic process (GO:0006915)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(3)|endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		GTTTTCCCTCACCTGGGAAGA	0.567											OREG0020392	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	TCTN3	66	.	0			c.256+2T>C						.						34	37	36					10																	97453399		692	1591	2283	SO:0001630	splice_region_variant	26123	exon2			TCCCTCACCTGGG	AK098295	CCDS31258.2, CCDS44461.1	10q24.1	2014-01-28	2007-08-20	2007-08-20	ENSG00000119977	ENSG00000119977		"Tectonic proteins"	24519	protein-coding gene	gene with protein product		613847	"chromosome 10 open reading frame 61"	C10orf61		12975309	Standard	NM_015631		Approved	DKFZP564D116, TECT3, JBTS18	uc001klb.4	Q6NUS6	OTTHUMG00000018814	ENST00000371217.5:c.256+1T>C	chr10.hg19:g.97453399A>G		72.0	0.0	1328	53.0	4.0	NM_015631	A6NIC8|B0QZ90|B4DR81|Q6P7P3|Q6UW27|Q6ZQQ0|Q8N7K1|Q8NBQ0|Q96GF7|Q9Y3U1	Splice_Site	SNP	ENST00000371217.5	hg19	CCDS31258.2	.	.	.	.	.	.	.	.	.	.	A	9.381	1.073010	0.20147	.	.	ENSG00000119977	ENST00000265993;ENST00000430368;ENST00000371217;ENST00000371209;ENST00000424175	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5619	0.45150	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TCTN3	97443389	1.000000	0.71417	1.000000	0.80357	0.037000	0.13140	3.854000	0.55949	2.274000	0.75844	0.533000	0.62120	.	.	.		0.567	TCTN3-009	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000471858.1	NM_015631	Intron	G	97453399	A	G	97453399	5	3	91	1	0	0	0	0	0	0	1	0	15739	173	6	2	1621	2	TCTN3	10	97453399	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	6309293	97453399	38081348	352	12426										
C10orf12	26148	hgsc.bcm.edu	37	chr10	98743214	98743214	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaggtagacaacgaaaacacCcagcagaaagatgatgagag	12	7	0	5			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:98743214C>A	ENST00000286067.2	+	1	2174	c.2067C>A	c.(2065-2067)acC>acA	p.T689T		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	689										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		ACGAAAACACCCAGCAGAAAG	0.522																																					p.T689T		Atlas-SNP	.											.	C10orf12	94	.	0			c.C2067A						.						77	68	71					10																	98743214		2203	4300	6503	SO:0001819	synonymous_variant	26148	exon1			AAACACCCAGCAG	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.2067C>A	chr10.hg19:g.98743214C>A		84.0	0.0		57.0	4.0	NM_015652	Q9H945|Q9Y457	Silent	SNP	ENST00000286067.2	hg19	CCDS7452.1																																																																																			.	.		0.522	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		A	98743214	C	A	98743214	2	1	91	1	0	0	0	0	0	0	0	1	1591	610	22	3		3	C10orf12	10	98743214	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1289815	98743214	36791533	353	12427										
ANKRD2	26287	hgsc.bcm.edu	37	chr10	99342105	99342105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgctgcacgtggcagtccggAcagggcaggtggagattgtg	18	9	0	1	rs534926101		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:99342105A>G	ENST00000307518.5	+	7	1036	c.769A>G	c.(769-771)Aca>Gca	p.T257A	HOGA1_ENST00000370646.4_5'Flank|HOGA1_ENST00000370647.4_5'Flank|ANKRD2_ENST00000455090.1_Intron|PI4K2A_ENST00000370649.3_5'Flank|ANKRD2_ENST00000370655.1_Missense_Mutation_p.T230A|PI4K2A_ENST00000555577.1_5'Flank|ANKRD2_ENST00000298808.5_Intron			Q9GZV1	ANKR2_HUMAN	ankyrin repeat domain 2 (stretch responsive muscle)	257					muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|euchromatin (GO:0000791)|I band (GO:0031674)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	protein kinase B binding (GO:0043422)|structural constituent of muscle (GO:0008307)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7		all_hematologic(284;1.95e-06)|Colorectal(252;0.0163)		Epithelial(162;1.18e-94)|all cancers(201;9.31e-86)|BRCA - Breast invasive adenocarcinoma(275;0.0233)|STAD - Stomach adenocarcinoma(243;0.181)|KIRC - Kidney renal clear cell carcinoma(50;0.206)|Kidney(138;0.241)		GGCAGTCCGGACAGGGCAGGT	0.622																																					p.T257A		Atlas-SNP	.											.	ANKRD2	27	.	0			c.A769G						.						55	42	47					10																	99342105		2189	4287	6476	SO:0001583	missense	26287	exon7			GTCCGGACAGGGC	AJ304805	CCDS7466.1, CCDS44468.1	10q23	2013-01-10			ENSG00000165887	ENSG00000165887		"Ankyrin repeat domain containing"	495	protein-coding gene	gene with protein product		610734				10873377, 15136035, 15677738	Standard	NM_001129981		Approved	ARPP	uc001knw.3	Q9GZV1	OTTHUMG00000018860	ENST00000307518.5:c.769A>G	chr10.hg19:g.99342105A>G	ENSP00000306163:p.Thr257Ala	113.0	0.0		65.0	5.0	NM_020349	Q3B778|Q5T456|Q70EZ9|Q8WUD7|Q96MG0|Q9NQC9	Missense_Mutation	SNP	ENST00000307518.5	hg19	CCDS7466.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.304274	0.60305	.	.	ENSG00000165887	ENST00000307518;ENST00000370655	T;T	0.61980	0.06;0.06	5.6	5.6	0.85130	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000001	T	0.62768	0.2455	N	0.16016	0.355	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.59600	-0.7424	10	0.15066	T	0.55	-15.7438	14.7787	0.69749	1.0:0.0:0.0:0.0	.	257	Q9GZV1	ANKR2_HUMAN	A	257;230	ENSP00000306163:T257A;ENSP00000359689:T230A	ENSP00000306163:T257A	T	+	1	0	ANKRD2	99332095	1.000000	0.71417	0.983000	0.44433	0.039000	0.13416	8.102000	0.89548	2.131000	0.65755	0.533000	0.62120	ACA	.	.		0.622	ANKRD2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	99342105	A	G	99342105	3	3	91	1	0	0	0	0	1	0	0	0	647	275	10	2	795	2	ANKRD2	10	99342105	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	598891	99342105	36192642	354	12428										
C10orf28	27291	hgsc.bcm.edu	37	chr10	100003864	100003864	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acagagagaaagcggttggaAgccaagcaacgggaagacat	14	7	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:100003864A>G	ENST00000298999.3	+	10	2589	c.2286A>G	c.(2284-2286)gaA>gaG	p.E762E	R3HCC1L_ENST00000370584.3_Silent_p.E762E|R3HCC1L_ENST00000370586.2_Silent_p.E168E|R3HCC1L_ENST00000314594.5_Silent_p.E178E	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	776							nucleotide binding (GO:0000166)										AGCGGTTGGAAGCCAAGCAAC	0.393																																					p.E776E		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.A2328G						.						123	113	116					10																	100003864		2203	4300	6503	SO:0001819	synonymous_variant	27291	exon11			GTTGGAAGCCAAG	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 28"	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.2286A>G	chr10.hg19:g.100003864A>G		112.0	0.0		87.0	4.0	NM_001256619	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Silent	SNP	ENST00000298999.3	hg19	CCDS31267.1																																																																																			.	.		0.393	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472		G	100003864	A	G	100003864	2	3	91	1	0	0	0	0	0	0	0	1	1603	69	3	2		2	C10orf28	10	100003864	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	661759	100003864	35530883	355	12429										
CNNM1	26507	hgsc.bcm.edu	37	chr10	101136951	101136951	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctgactactcagtccacatCctcagcgatgtgcagtttgt	8	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:101136951C>A	ENST00000356713.4	+	7	2605	c.2316C>A	c.(2314-2316)atC>atA	p.I772I	CNNM1_ENST00000370534.4_Silent_p.I428I|CNNM1_ENST00000370528.3_Silent_p.I701I|CNNM1_ENST00000488090.1_3'UTR|CNNM1_ENST00000446890.1_Silent_p.I701I	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	772					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		CAGTCCACATCCTCAGCGATG	0.562																																					p.I772I		Atlas-SNP	.											.	CNNM1	101	.	0			c.C2316A						.						135	100	112					10																	101136951		2203	4300	6503	SO:0001819	synonymous_variant	26507	exon7			CCACATCCTCAGC	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"cyclin M1"	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.2316C>A	chr10.hg19:g.101136951C>A		154.0	0.0		100.0	4.0	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	hg19	CCDS7478.2																																																																																			.	.		0.562	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348		A	101136951	C	A	101136951	2	1	91	1	0	0	0	0	0	0	0	1	3614	845	30	3		3	CNNM1	10	101136951	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1133087	101136951	34397796	356	12430										
HPS6	79803	hgsc.bcm.edu	37	chr10	103827332	103827332	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgtgcccaccagaactggctCcagctgagctcctgcttcta	9	15	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:103827332C>T	ENST00000299238.5	+	1	2186	c.2101C>T	c.(2101-2103)Cca>Tca	p.P701S		NM_024747.5	NP_079023.2	Q86YV9	HPS6_HUMAN	Hermansky-Pudlak syndrome 6	701					blood coagulation (GO:0007596)|melanocyte differentiation (GO:0030318)|organelle organization (GO:0006996)|protein localization to membrane (GO:0072657)	BLOC-2 complex (GO:0031084)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|Rab GTPase binding (GO:0017137)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)	11		Colorectal(252;0.122)		Epithelial(162;5.93e-08)|all cancers(201;1.03e-06)		AGAACTGGCTCCAGCTGAGCT	0.617									Hermansky-Pudlak syndrome																												p.P701S		Atlas-SNP	.											.	HPS6	38	.	0			c.C2101T						.						53	57	55					10																	103827332		2203	4300	6503	SO:0001583	missense	79803	exon1	Familial Cancer Database	HPS, HPS1-8	CTGGCTCCAGCTG	BC009258	CCDS7527.1	10q24.32	2014-06-18			ENSG00000166189	ENSG00000166189			18817	protein-coding gene	gene with protein product		607522				12548288	Standard	NM_024747		Approved	FLJ22501	uc001kuj.3	Q86YV9	OTTHUMG00000018945	ENST00000299238.5:c.2101C>T	chr10.hg19:g.103827332C>T	ENSP00000299238:p.Pro701Ser	55.0	0.0		56.0	4.0	NM_024747	Q5VV69|Q9H685	Missense_Mutation	SNP	ENST00000299238.5	hg19	CCDS7527.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843076	0.51057	.	.	ENSG00000166189	ENST00000299238	T	0.80123	-1.34	4.85	4.85	0.62838	.	0.304358	0.31624	N	0.007329	T	0.78629	0.4313	L	0.54323	1.7	0.32302	N	0.564953	P	0.47910	0.902	P	0.46543	0.52	T	0.83190	-0.0084	10	0.49607	T	0.09	-8.5036	10.2382	0.43297	0.1491:0.7061:0.1447:0.0	.	701	Q86YV9	HPS6_HUMAN	S	701	ENSP00000299238:P701S	ENSP00000299238:P701S	P	+	1	0	HPS6	103817322	0.994000	0.37717	1.000000	0.80357	0.982000	0.71751	1.838000	0.39211	2.520000	0.84964	0.561000	0.74099	CCA	.	.		0.617	HPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050018.2	NM_024747		T	103827332	C	T	103827332	3	4	91	1	0	0	0	0	1	0	0	0	7352	855	30	3	2103	3	HPS6	10	103827332	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2690381	103827332	31707415	357	12431										
NFKB2	4791	hgsc.bcm.edu	37	chr10	104160556	104160556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacagagatggaggagctggGgttggtcacccatctggtca	15	9	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:104160556G>A	ENST00000369966.3	+	17	2193	c.1943G>A	c.(1942-1944)gGg>gAg	p.G648E	NFKB2_ENST00000428099.1_Missense_Mutation_p.G648E|NFKB2_ENST00000189444.6_Missense_Mutation_p.G648E	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	648			Missing (in truncated form EB308).		extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	GAGGAGCTGGGGTTGGTCACC	0.632			T	IGH@	B-NHL																																p.G648E		Atlas-SNP	.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	.	NFKB2	48	.	0			c.G1943A						.						25	29	28					10																	104160556		2016	4177	6193	SO:0001583	missense	4791	exon17			AGCTGGGGTTGGT	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"Ankyrin repeat domain containing"	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.1943G>A	chr10.hg19:g.104160556G>A	ENSP00000358983:p.Gly648Glu	115.0	0.0		100.0	4.0	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	hg19	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.486303	0.44147	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.58940	0.3;0.3;0.3	4.43	4.43	0.53597	Ankyrin repeat-containing domain (4);	0.177576	0.49916	D	0.000133	T	0.22513	0.0543	N	0.01668	-0.77	0.32311	N	0.563732	P;P	0.43231	0.801;0.801	B;B	0.41374	0.355;0.355	T	0.45702	-0.9243	10	0.05351	T	0.99	.	5.9021	0.18972	0.2381:0.0:0.7619:0.0	.	648;648	Q00653;A8K9D9	NFKB2_HUMAN;.	E	648	ENSP00000410256:G648E;ENSP00000358983:G648E;ENSP00000189444:G648E	ENSP00000189444:G648E	G	+	2	0	NFKB2	104150546	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.852000	0.55934	2.478000	0.83669	0.561000	0.74099	GGG	.	.		0.632	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			A	104160556	G	A	104160556	3	1	91	1	0	0	0	0	1	0	0	0	10385	1232	43	3	2005	3	NFKB2	10	104160556	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	333224	104160556	31374191	358	12432										
PSD	5662	hgsc.bcm.edu	37	chr10	104164802	104164802	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctgaaagggccttcccaggcTtgtactcctcctgcaggggt	12	13	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:104164802T>C	ENST00000020673.5	-	14	2934	c.2408A>G	c.(2407-2409)aAg>aGg	p.K803R	PSD_ENST00000406432.1_Missense_Mutation_p.K803R	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	803	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CTTCCCAGGCTTGTACTCCTC	0.617																																					p.K803R		Atlas-SNP	.											PSD_ENST00000020673,NS,carcinoma,0,2	PSD	164	.	0			c.A2408G						.						77	70	73					10																	104164802		2203	4300	6503	SO:0001583	missense	5662	exon15			CCAGGCTTGTACT	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.2408A>G	chr10.hg19:g.104164802T>C	ENSP00000020673:p.Lys803Arg	162.0	1.0		125.0	6.0	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	hg19	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	T	11.20	1.568739	0.28003	.	.	ENSG00000059915	ENST00000020673;ENST00000541902;ENST00000406432	T;T	0.38722	1.12;1.12	4.81	4.81	0.61882	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.336296	0.30859	N	0.008724	T	0.28764	0.0713	N	0.25094	0.71	0.27671	N	0.946755	B;B;B	0.12630	0.0;0.006;0.001	B;B;B	0.17098	0.004;0.017;0.007	T	0.10109	-1.0644	10	0.13108	T	0.6	.	14.5823	0.68300	0.0:0.0:0.0:1.0	.	803;706;424	A5PKW4;Q86YI3;A5PKW4-2	PSD1_HUMAN;.;.	R	803;706;803	ENSP00000020673:K803R;ENSP00000384830:K803R	ENSP00000020673:K803R	K	-	2	0	PSD	104154792	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.382000	0.59594	2.033000	0.60031	0.449000	0.29647	AAG	.	.		0.617	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			C	104164802	T	C	104164802	3	2	91	1	0	0	0	0	1	0	0	0	12658	1609	56	2	682	2	PSD	10	104164802	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4246	104164802	31369945	359	12433										
TRIM8	81603	hgsc.bcm.edu	37	chr10	104414949	104414949	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctagacaaggcccaggccaAgttctgcagcgagaacgcag	12	13	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:104414949A>G	ENST00000302424.7	+	3	901	c.779A>G	c.(778-780)aAg>aGg	p.K260R	TRIM8_ENST00000487927.1_3'UTR	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	260					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GCCCAGGCCAAGTTCTGCAGC	0.622																																					p.K260R		Atlas-SNP	.											.	TRIM8	35	.	0			c.A779G						.						58	54	55					10																	104414949		2203	4300	6503	SO:0001583	missense	81603	exon3			AGGCCAAGTTCTG	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15579	protein-coding gene	gene with protein product	"glioblastoma expressed ring finger protein"	606125	"ring finger protein 27", "tripartite motif-containing 8"	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.779A>G	chr10.hg19:g.104414949A>G	ENSP00000302120:p.Lys260Arg	124.0	0.0		96.0	4.0	NM_030912	A6NI31|Q9C028	Missense_Mutation	SNP	ENST00000302424.7	hg19	CCDS31274.1	.	.	.	.	.	.	.	.	.	.	A	12.47	1.946762	0.34377	.	.	ENSG00000171206	ENST00000302424;ENST00000369896	T	0.58060	0.36	5.55	5.55	0.83447	.	0.062472	0.64402	D	0.000004	T	0.36331	0.0963	N	0.14661	0.345	0.51482	D	0.99992	B	0.10296	0.003	B	0.04013	0.001	T	0.15435	-1.0437	10	0.20519	T	0.43	.	15.6992	0.77528	1.0:0.0:0.0:0.0	.	260	Q9BZR9	TRIM8_HUMAN	R	260;259	ENSP00000302120:K260R	ENSP00000302120:K260R	K	+	2	0	TRIM8	104404939	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.869000	0.75521	2.122000	0.65172	0.459000	0.35465	AAG	.	.		0.622	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912		G	104414949	A	G	104414949	3	3	91	1	0	0	0	0	1	0	0	0	16563	72	3	2	789	2	TRIM8	10	104414949	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	250147	104414949	31119798	360	12434										
SLK	9748	hgsc.bcm.edu	37	chr10	105750545	105750545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catattagcatcttgtgatcAcccaaatatagtcaagcttc	5	10	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:105750545A>G	ENST00000369755.3	+	2	808	c.263A>G	c.(262-264)cAc>cGc	p.H88R	SLK_ENST00000335753.4_Missense_Mutation_p.H88R	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	88	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TCTTGTGATCACCCAAATATA	0.353																																					p.H88R	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.A263G						.						128	119	122					10																	105750545		2203	4300	6503	SO:0001583	missense	9748	exon2			GTGATCACCCAAA		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.263A>G	chr10.hg19:g.105750545A>G	ENSP00000358770:p.His88Arg	114.0	0.0		127.0	37.0	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	hg19	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.816069	0.90790	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.78481	-1.18;-1.18	6.17	6.17	0.99709	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93579	0.7950	H	0.99261	4.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96145	0.9103	10	0.87932	D	0	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	88;88	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	R	88	ENSP00000336824:H88R;ENSP00000358770:H88R	ENSP00000336824:H88R	H	+	2	0	SLK	105740535	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.213000	0.95133	2.371000	0.80710	0.533000	0.62120	CAC	.	.		0.353	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		G	105750545	A	G	105750545	3	3	91	1	0	0	0	0	1	0	0	0	14763	159	6	2	269	2	SLK	10	105750545	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1335596	105750545	29784202	361	12435										
SMNDC1	10285	hgsc.bcm.edu	37	chr10	112054041	112054041	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtgaagcaaaaatactcctcTttacctaagggaaagaaaac	7	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:112054041T>C	ENST00000369603.5	-	6	787	c.584A>G	c.(583-585)aAg>aGg	p.K195R	SMNDC1_ENST00000369592.1_Missense_Mutation_p.K195R	NM_005871.3	NP_005862.1	O75940	SPF30_HUMAN	survival motor neuron domain containing 1	195					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	4		Breast(234;0.174)		Epithelial(162;6.86e-05)|all cancers(201;0.00149)|BRCA - Breast invasive adenocarcinoma(275;0.119)		AATACTCCTCTTTACCTAAGG	0.323																																					p.K195R		Atlas-SNP	.											.	SMNDC1	9	.	0			c.A584G						.						110	105	107					10																	112054041		2203	4300	6503	SO:0001583	missense	10285	exon6			CTCCTCTTTACCT	AF083385	CCDS7565.1	10q23	2013-01-23			ENSG00000119953	ENSG00000119953		"Tudor domain containing"	16900	protein-coding gene	gene with protein product	"splicing factor 30, survival of motor neuron-related", "tudor domain containing 16C"	603519				9731529, 9817934	Standard	NM_005871		Approved	SPF30, SMNR, TDRD16C	uc001kzc.4	O75940	OTTHUMG00000019036	ENST00000369603.5:c.584A>G	chr10.hg19:g.112054041T>C	ENSP00000358616:p.Lys195Arg	115.0	0.0		95.0	4.0	NM_005871	B2RA27|D3DRB1|Q5T3K6	Missense_Mutation	SNP	ENST00000369603.5	hg19	CCDS7565.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.306303	0.81247	.	.	ENSG00000119953	ENST00000369603;ENST00000369592	D;D	0.89485	-2.52;-2.52	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.92011	0.7469	L	0.46885	1.475	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	D	0.91304	0.5069	10	0.38643	T	0.18	-17.0481	16.1699	0.81801	0.0:0.0:0.0:1.0	.	195	O75940	SPF30_HUMAN	R	195	ENSP00000358616:K195R;ENSP00000358605:K195R	ENSP00000358605:K195R	K	-	2	0	SMNDC1	112044031	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.008000	0.88588	2.229000	0.72834	0.533000	0.62120	AAG	.	.		0.323	SMNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050325.2	NM_005871		C	112054041	T	C	112054041	3	2	91	1	0	0	0	0	1	0	0	0	14814	1609	56	2	136	2	SMNDC1	10	112054041	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	6303496	112054041	23480706	362	12436										
TACC2	10579	hgsc.bcm.edu	37	chr10	123842981	123842981	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aattcaggggctgccccagaAgcagaagtgaatgccgcttc	12	11	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:123842981A>G	ENST00000369005.1	+	4	1306	c.966A>G	c.(964-966)gaA>gaG	p.E322E	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515273.1_Silent_p.E322E|TACC2_ENST00000453444.2_Silent_p.E322E|TACC2_ENST00000334433.3_Silent_p.E322E|TACC2_ENST00000515603.1_Silent_p.E322E|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	322					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CTGCCCCAGAAGCAGAAGTGA	0.607																																					p.E322E		Atlas-SNP	.											.	TACC2	271	.	0			c.A966G						.						33	41	38					10																	123842981		2203	4299	6502	SO:0001819	synonymous_variant	10579	exon4			CCCAGAAGCAGAA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.966A>G	chr10.hg19:g.123842981A>G		64.0	0.0		61.0	5.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.607	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			G	123842981	A	G	123842981	2	3	91	1	0	0	0	0	0	0	0	1	15517	69	3	2		2	TACC2	10	123842981	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	11788940	123842981	11691766	363	12437										
LRRC56	115399	hgsc.bcm.edu	37	chr11	552650	552650	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cggagggtccctgaagagcaAgtgcaccaggcagagcccaa	14	12	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:552650A>G	ENST00000270115.7	+	13	1763	c.1263A>G	c.(1261-1263)caA>caG	p.Q421Q		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	421										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGAAGAGCAAGTGCACCAGG	0.687																																					p.Q421Q		Atlas-SNP	.											.	LRRC56	23	.	0			c.A1263G						.						24	27	26					11																	552650		2188	4295	6483	SO:0001819	synonymous_variant	115399	exon13			AGAGCAAGTGCAC		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.1263A>G	chr11.hg19:g.552650A>G		116.0	0.0		124.0	5.0	NM_198075	Q8N3Q4	Silent	SNP	ENST00000270115.7	hg19	CCDS7700.1																																																																																			.	.		0.687	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075		G	552650	A	G	552650	2	3	91	1	0	0	0	0	0	0	0	1	9021	69	3	2		2	LRRC56	11	552650	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10		552650	134453866	364	12438										
PNPLA2	57104	hgsc.bcm.edu	37	chr11	821745	821745	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagtttcctgctgaaggtccTgcctgctgatagccatgagc	11	12	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:821745T>C	ENST00000336615.4	+	3	507	c.305T>C	c.(304-306)cTg>cCg	p.L102P	AP006621.8_ENST00000528982.1_RNA|AP006621.8_ENST00000532946.1_RNA	NM_020376.3	NP_065109.1	Q96AD5	PLPL2_HUMAN	patatin-like phospholipase domain containing 2	102	Patatin.				acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of sequestering of triglyceride (GO:0010891)|phospholipid metabolic process (GO:0006644)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|lung(4)|prostate(1)|urinary_tract(1)	9		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.63e-25)|Epithelial(43;1.28e-24)|OV - Ovarian serous cystadenocarcinoma(40;7.09e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGAAGGTCCTGCCTGCTGAT	0.567																																					p.L102P		Atlas-SNP	.											.	PNPLA2	26	.	0			c.T305C						.						72	65	67					11																	821745		2203	4299	6502	SO:0001583	missense	57104	exon3			AGGTCCTGCCTGC	AJ278475	CCDS7718.1	11p15.5	2014-03-14			ENSG00000177666	ENSG00000177666	3.1.1.3	"Patatin-like phospholipase domain containing"	30802	protein-coding gene	gene with protein product		609059				8619474, 16799181, 19029121	Standard	NM_020376		Approved	desnutrin, TTS-2.2, ATGL, FP17548, iPLA2zeta	uc001lrt.3	Q96AD5	OTTHUMG00000133309	ENST00000336615.4:c.305T>C	chr11.hg19:g.821745T>C	ENSP00000337701:p.Leu102Pro	102.0	0.0		99.0	4.0	NM_020376	O60643|Q5EFF5|Q6XYE5|Q96ET6|Q9NQ61|Q9NQ62	Missense_Mutation	SNP	ENST00000336615.4	hg19	CCDS7718.1	.	.	.	.	.	.	.	.	.	.	T	16.38	3.105865	0.56291	.	.	ENSG00000177666	ENST00000336615	D	0.85013	-1.93	4.24	4.24	0.50183	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.077664	0.53938	D	0.000054	D	0.94182	0.8133	H	0.95679	3.705	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.95603	0.8665	10	0.87932	D	0	-15.3366	13.4886	0.61382	0.0:0.0:0.0:1.0	.	102	Q96AD5	PLPL2_HUMAN	P	102	ENSP00000337701:L102P	ENSP00000337701:L102P	L	+	2	0	PNPLA2	811745	1.000000	0.71417	0.700000	0.30305	0.055000	0.15305	7.753000	0.85153	1.781000	0.52344	0.459000	0.35465	CTG	.	.		0.567	PNPLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257106.1	NM_020376		C	821745	T	C	821745	3	2	91	1	0	0	0	0	1	0	0	0	12174	1580	55	2	311	2	PNPLA2	11	821745	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	269095	821745	134184771	365	12439										
MUC6	4588	hgsc.bcm.edu	37	chr11	1025876	1025876	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatgacgttctctgtcaggaTcttgaaggtgggctgtgagt	15	6	3	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:1025876T>C	ENST00000421673.2	-	22	2778	c.2728A>G	c.(2728-2730)Atc>Gtc	p.I910V		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	910	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCTGTCAGGATCTTGAAGGTG	0.647																																					p.I910V		Atlas-SNP	.											.	MUC6	408	.	0			c.A2728G						.						50	56	54					11																	1025876		2091	4210	6301	SO:0001583	missense	4588	exon22			TCAGGATCTTGAA	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.2728A>G	chr11.hg19:g.1025876T>C	ENSP00000406861:p.Ile910Val	113.0	0.0		81.0	4.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	T	0.026	-1.368889	0.01225	.	.	ENSG00000184956	ENST00000421673	T	0.57107	0.42	4.15	-2.45	0.06481	von Willebrand factor, type D domain (3);	.	.	.	.	T	0.26011	0.0634	N	0.11673	0.155	0.09310	N	1	B	0.25272	0.122	B	0.25884	0.064	T	0.29882	-0.9997	9	0.06625	T	0.88	.	9.5356	0.39220	0.0:0.4365:0.0:0.5635	.	910	Q6W4X9	MUC6_HUMAN	V	910	ENSP00000406861:I910V	ENSP00000406861:I910V	I	-	1	0	MUC6	1015876	0.006000	0.16342	0.025000	0.17156	0.373000	0.29922	0.056000	0.14256	-0.434000	0.07275	0.260000	0.18958	ATC	.	.		0.647	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		C	1025876	T	C	1025876	3	2	91	1	0	0	0	0	1	0	0	0	9989	1435	50	2	4639	2	MUC6	11	1025876	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	204131	1025876	133980640	366	12440										
C11orf40	143501	hgsc.bcm.edu	37	chr11	4592711	4592712	+	Missense_Mutation	DNP	TT	TT	AG													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtagaacacgatccatacagTttttccctgcaaagacctgg					rs78543312|rs78387367		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:4592711_4592712TT>AG	ENST00000307616.1	-	4	594_595	c.595_596AA>CT	c.(595-597)AAc>CTc	p.N199L		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	199										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		atccatacagtttttccCTGCA	0.441																																					p.N199I|p.N199H		Atlas-SNP	.											.	C11orf40	37	.	0			c.A596T|c.A595C						.																																			SO:0001583	missense	143501	exon4			ATACAGTTTTTCC|TACAGTTTTTCCC		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.595_596delinsAG	chr11.hg19:g.4592711_4592712delinsAG	ENSP00000302918:p.Asn199Leu	236.0|234.0	0.0		203.0|198.0	17.0|12.0	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	hg19	CCDS31354.1																																																																																			.	.		0.441	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663		AG	4592712	TT	AG	4592711	3	1	91	1	0	0	0	0	1	0	0	0	1641	1725	60	4	60	4	C11orf40	11	4592711	Missense_Mutation	DNP	TT	TCGA-DD-A119-01A-11D-A12Z-10	3566835	4592711	130413805	367	12441										
OR51B4	79339	hgsc.bcm.edu	37	chr11	5322255	5322255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aataagggctcaagccctacTctgcccagaaaataggcgaa	9	11	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:5322255T>C	ENST00000380224.1	-	1	971	c.922A>G	c.(922-924)Agt>Ggt	p.S308G	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	308					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAAGCCCTACTCTGCCCAGAA	0.403																																					p.S308G		Atlas-SNP	.											.	OR51B4	64	.	0			c.A922G						.						49	49	49					11																	5322255		2201	4297	6498	SO:0001583	missense	79339	exon1			CCCTACTCTGCCC	BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"GPCR / Class A : Olfactory receptors"	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.922A>G	chr11.hg19:g.5322255T>C	ENSP00000369573:p.Ser308Gly	84.0	0.0		72.0	4.0	NM_033179	A7MAV5|Q6NTD7	Missense_Mutation	SNP	ENST00000380224.1	hg19	CCDS7757.1	.	.	.	.	.	.	.	.	.	.	T	4.688	0.127852	0.08981	.	.	ENSG00000183251	ENST00000380224	T	0.00005	9.78	4.01	1.67	0.24075	.	1.351800	0.05103	N	0.487474	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	B	0.19331	0.035	B	0.14578	0.011	T	0.01228	-1.1412	10	0.32370	T	0.25	.	5.6113	0.17406	0.0:0.2286:0.0:0.7714	.	308	Q9Y5P0	O51B4_HUMAN	G	308	ENSP00000369573:S308G	ENSP00000369573:S308G	S	-	1	0	OR51B4	5278831	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.894000	0.28350	0.238000	0.21222	-0.256000	0.11100	AGT	.	.		0.403	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179		C	5322255	T	C	5322255	3	2	91	1	0	0	0	0	1	0	0	0	11099	1551	54	2	13	2	OR51B4	11	5322255	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	729544	5322255	129684261	368	12442										
TRIM3	10612	hgsc.bcm.edu	37	chr11	6471835	6471835	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atttcattcttgttgttcacAgccacaaaatggggccctga	8	10	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:6471835A>G	ENST00000525074.1	-	10	2281	c.1887T>C	c.(1885-1887)gcT>gcC	p.A629A	TRIM3_ENST00000536344.1_Silent_p.A510A|TRIM3_ENST00000359518.3_Silent_p.A629A|TRIM3_ENST00000537602.1_Silent_p.A551A|TRIM3_ENST00000345851.3_Silent_p.A629A	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	629					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTTGTTCACAGCCACAAAAT	0.478																																					p.A629A	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.T1887C						.						94	81	86					11																	6471835		2201	4296	6497	SO:0001819	synonymous_variant	10612	exon10			GTTCACAGCCACA	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10064	protein-coding gene	gene with protein product	"ring finger protein 22", "brain expressed ring finger", "tripartite motif protein TRIM3"	605493	"tripartite motif-containing 3"	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.1887T>C	chr11.hg19:g.6471835A>G		84.0	0.0		101.0	5.0	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	hg19	CCDS7764.1																																																																																			.	.		0.478	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458		G	6471835	A	G	6471835	2	3	91	1	0	0	0	0	0	0	0	1	16519	175	7	2		2	TRIM3	11	6471835	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1149580	6471835	128534681	369	12443										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6567219	6567219	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tagaggaggtggcctgtgggAccgtactgggtcctaatggt	17	7	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:6567219A>G	ENST00000527990.2	+	19	5050	c.5050A>G	c.(5050-5052)Acc>Gcc	p.T1684A	DNHD1_ENST00000254579.6_Missense_Mutation_p.T1684A			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1684					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GGCCTGTGGGACCGTACTGGG	0.587																																					p.T1684A		Atlas-SNP	.											.	DNHD1	198	.	0			c.A5050G						.						90	79	82					11																	6567219		692	1591	2283	SO:0001583	missense	144132	exon21			TGTGGGACCGTAC	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.5050A>G	chr11.hg19:g.6567219A>G	ENSP00000436180:p.Thr1684Ala	145.0	0.0		118.0	5.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.694861	0.00731	.	.	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.05319	3.46;3.46	5.56	-0.506	0.11989	.	0.419590	0.26590	N	0.023525	T	0.01523	0.0049	N	0.00771	-1.2	0.20975	N	0.999812	B	0.14805	0.011	B	0.15052	0.012	T	0.48127	-0.9062	10	0.02654	T	1	.	9.9803	0.41809	0.4312:0.0:0.5688:0.0	.	1684	Q96M86	DNHD1_HUMAN	A	1684	ENSP00000254579:T1684A;ENSP00000436180:T1684A	ENSP00000254579:T1684A	T	+	1	0	DNHD1	6523795	0.724000	0.28038	0.921000	0.36526	0.296000	0.27459	0.190000	0.17057	0.089000	0.17243	0.533000	0.62120	ACC	.	.		0.587	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		G	6567219	A	G	6567219	3	3	91	1	0	0	0	0	1	0	0	0	4670	275	10	2	5133	2	DNHD1	11	6567219	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	95384	6567219	128439297	370	12444										
ZNF215	7762	hgsc.bcm.edu	37	chr11	6977409	6977409	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttattcgacatcagatcattCacacaggagagaaaccctat	6	10	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:6977409C>T	ENST00000278319.5	+	7	1789	c.1201C>T	c.(1201-1203)Cac>Tac	p.H401Y	ZNF215_ENST00000529903.1_Intron|ZNF215_ENST00000414517.2_Missense_Mutation_p.H401Y	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	401					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		TCAGATCATTCACACAGGAGA	0.403																																					p.H401Y		Atlas-SNP	.											.	ZNF215	72	.	0			c.C1201T						.						74	72	73					11																	6977409		2201	4296	6497	SO:0001583	missense	7762	exon7			ATCATTCACACAG	AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"Zinc fingers, C2H2-type", "-", "-", "-"	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.1201C>T	chr11.hg19:g.6977409C>T	ENSP00000278319:p.His401Tyr	68.0	0.0		76.0	4.0	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	hg19	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.777075	0.90195	.	.	ENSG00000149054	ENST00000278319;ENST00000414517	T;T	0.67523	-0.27;-0.27	4.85	4.85	0.62838	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47852	D	0.000220	D	0.86037	0.5837	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89404	0.3698	10	0.87932	D	0	-8.6708	15.8711	0.79119	0.0:1.0:0.0:0.0	.	401	Q9UL58	ZN215_HUMAN	Y	401	ENSP00000278319:H401Y;ENSP00000393202:H401Y	ENSP00000278319:H401Y	H	+	1	0	ZNF215	6933985	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.504000	0.66968	2.689000	0.91719	0.655000	0.94253	CAC	.	.		0.403	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1			T	6977409	C	T	6977409	3	4	91	1	0	0	0	0	1	0	0	0	17786	826	29	3	1219	3	ZNF215	11	6977409	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	410190	6977409	128029107	371	12445										
RPL27A	6157	hgsc.bcm.edu	37	chr11	8704765	8704765	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acagccatccagactgaggaAgacccggaaacttaggggcc	12	12	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:8704765A>G	ENST00000314138.6	+	2	423	c.20A>G	c.(19-21)aAg>aGg	p.K7R	RPL27A_ENST00000526562.1_5'UTR|RPL27A_ENST00000531978.1_Missense_Mutation_p.K7R|RP11-152H18.4_ENST00000534169.1_RNA|SNORA45_ENST00000391305.1_RNA|RPL27A_ENST00000530913.1_5'Flank|SNORA3_ENST00000364113.1_RNA|RPL27A_ENST00000532359.1_Missense_Mutation_p.K7R|RPL27A_ENST00000530022.1_5'UTR|RPL27A_ENST00000524496.1_5'UTR	NM_000990.4	NP_000981.1	P46776	RL27A_HUMAN	ribosomal protein L27a	7					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|lung(1)	2				Epithelial(150;3.24e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGACTGAGGAAGACCCGGAAA	0.622																																					p.K7R		Atlas-SNP	.											.	RPL27A	5	.	0			c.A20G						.						69	71	70					11																	8704765		2201	4296	6497	SO:0001583	missense	6157	exon2			TGAGGAAGACCCG	U14968	CCDS7790.1	11p15	2011-04-06				ENSG00000166441		"L ribosomal proteins"	10329	protein-coding gene	gene with protein product		603637				7772601, 9582194	Standard	NM_000990		Approved	L27A	uc001mgs.4	P46776		ENST00000314138.6:c.20A>G	chr11.hg19:g.8704765A>G	ENSP00000346015:p.Lys7Arg	101.0	0.0		78.0	4.0	NM_000990	B2R4B3	Missense_Mutation	SNP	ENST00000314138.6	hg19	CCDS7790.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.3|23.3	4.403285|4.403285	0.83230|0.83230	.|.	.|.	ENSG00000166441|ENSG00000166441	ENST00000314138;ENST00000531978;ENST00000532359|ENST00000525981	.|.	.|.	.|.	4.96|4.96	4.96|4.96	0.65561|0.65561	Ribosomal protein L18e/L15P (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.78285|0.78285	0.4259|0.4259	M|M	0.84683|0.84683	2.71|2.71	0.80722|0.80722	D|D	1|1	P|.	0.42620|.	0.785|.	P|.	0.50049|.	0.629|.	T|T	0.81093|0.81093	-0.1089|-0.1089	9|5	0.72032|.	D|.	0.01|.	-18.0389|-18.0389	14.773|14.773	0.69693|0.69693	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	7|.	P46776|.	RL27A_HUMAN|.	R|G	7|2	.|.	ENSP00000346015:K7R|.	K|R	+|+	2|1	0|2	RPL27A|RPL27A	8661341|8661341	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.146000|8.146000	0.89626|0.89626	2.207000|2.207000	0.71202|0.71202	0.533000|0.533000	0.62120|0.62120	AAG|AGA	.	.		0.622	RPL27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386506.1	NM_000990		G	8704765	A	G	8704765	3	3	91	1	0	0	0	0	1	0	0	0	13591	72	3	2	26	2	RPL27A	11	8704765	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1727356	8704765	126301751	372	12446										
NUCB2	4925	hgsc.bcm.edu	37	chr11	17352477	17352477	+	Nonsense_Mutation	SNP	T	T	A													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcagatggaacaaaaaaaatTacaacaaggaattcctccat					rs535406012|rs3842269	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:17352477T>A	ENST00000529010.1	+	13	1421	c.1202T>A	c.(1201-1203)tTa>tAa	p.L401*	NUCB2_ENST00000458064.2_Nonsense_Mutation_p.L371*|NUCB2_ENST00000323688.6_Nonsense_Mutation_p.L401*	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	401	Binds to necdin. {ECO:0000250}.					cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						CAAAAAAAATTACAACAAGGA	0.323																																					p.L401X		Atlas-SNP	.											.	NUCB2	31	.	0			c.T1202A						.						47	42	44					11																	17352477		1800	4062	5862	SO:0001587	stop_gained	4925	exon13			AAAAATTACAACA	AF052642	CCDS41623.1	11p15.1	2013-01-10						"EF-hand domain containing"	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		ENST00000529010.1:c.1202T>A	chr11.hg19:g.17352477T>A	ENSP00000436455:p.Leu401*	300.0	0.0		304.0	17.0	NM_005013	A8K642|D3DQX5|Q8NFT5	Nonsense_Mutation	SNP	ENST00000529010.1	hg19	CCDS41623.1	.	.	.	.	.	.	.	.	.	.	T	37	6.521637	0.97633	.	.	ENSG00000070081	ENST00000323688;ENST00000529010;ENST00000458064	.	.	.	5.46	5.46	0.80206	.	0.481828	0.22040	N	0.065466	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-0.1802	9.9647	0.41717	0.0:0.076:0.0:0.924	.	.	.	.	X	401;401;371	.	ENSP00000320168:L401X	L	+	2	0	NUCB2	17309053	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.443000	0.44881	2.063000	0.61619	0.460000	0.39030	TTA	.	.		0.323	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013		A	17352477	T	A	17352477	4	1	91	1	0	0	0	0	0	1	0	0	10728	1764	61	4	1244	4	NUCB2	11	17352477	Nonsense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	8647712	17352477	117654039	373	12447	52	2								
NUCB2	4925	hgsc.bcm.edu	37	chr11	17352479	17352480	+	Missense_Mutation	DNP	CA	CA	TT													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agatggaacaaaaaaaattaCaacaaggaattcctccatca					rs189362726|rs535406012|rs3842269	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:17352479_17352480CA>TT	ENST00000529010.1	+	13	1423_1424	c.1204_1205CA>TT	c.(1204-1206)CAa>TTa	p.Q402L	NUCB2_ENST00000458064.2_Missense_Mutation_p.Q372L|NUCB2_ENST00000323688.6_Missense_Mutation_p.Q402L	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	402	Binds to necdin. {ECO:0000250}.		Missing. {ECO:0000269|PubMed:12087473, ECO:0000269|PubMed:14702039}.			cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AAAAAAATTACAACAAGGAATT	0.322																																					p.Q402X|p.Q402L		Atlas-SNP	.											.	NUCB2	31	.	0			c.C1204T|c.A1205T						.																																			SO:0001583	missense	4925	exon13			AAATTACAACAAG|AATTACAACAAGG	AF052642	CCDS41623.1	11p15.1	2013-01-10						"EF-hand domain containing"	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		Exception_encountered	chr11.hg19:g.17352479_17352480delinsTT	ENSP00000436455:p.Gln402Leu	9.0|6.0	0.0		43.0	18.0|20.0	NM_005013	A8K642|D3DQX5|Q8NFT5	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000529010.1	hg19	CCDS41623.1																																																																																			.	.		0.322	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013		TT	17352480	CA	TT	17352479	3	4	91	1	0	0	0	0	1	0	0	0	10728	479	17	3	1246	3	NUCB2	11	17352479	Missense_Mutation	DNP	CA	TCGA-DD-A119-01A-11D-A12Z-10	2	17352479	117654037	374	12448	52	2								
FIBIN	387758	hgsc.bcm.edu	37	chr11	27016470	27016470	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcggggatgcctactccaacTcggacaaatccctcactgag	9	14	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:27016470T>C	ENST00000318627.2	+	1	843	c.397T>C	c.(397-399)Tcg>Ccg	p.S133P		NM_203371.1	NP_976249.1	Q8TAL6	FIBIN_HUMAN	fin bud initiation factor homolog (zebrafish)	133						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)				breast(1)|endometrium(2)|lung(7)|upper_aerodigestive_tract(1)	11						CTACTCCAACTCGGACAAATC	0.582																																					p.S133P		Atlas-SNP	.											.	FIBIN	19	.	0			c.T397C						.						72	64	67					11																	27016470		2203	4299	6502	SO:0001583	missense	387758	exon1			TCCAACTCGGACA	BC026873	CCDS7861.1	11p14.2	2008-12-03				ENSG00000176971			33747	protein-coding gene	gene with protein product						17196583	Standard	NM_203371		Approved	MGC24932	uc001mrd.3	Q8TAL6		ENST00000318627.2:c.397T>C	chr11.hg19:g.27016470T>C	ENSP00000321962:p.Ser133Pro	43.0	0.0		51.0	5.0	NM_203371		Missense_Mutation	SNP	ENST00000318627.2	hg19	CCDS7861.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.228808	0.79576	.	.	ENSG00000176971	ENST00000318627	.	.	.	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.65491	0.2696	L	0.29908	0.895	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.65635	-0.6120	9	0.42905	T	0.14	-8.3857	15.0311	0.71708	0.0:0.0:0.0:1.0	.	133	Q8TAL6	FIBIN_HUMAN	P	133	.	ENSP00000321962:S133P	S	+	1	0	FIBIN	26973046	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.612000	0.82975	2.240000	0.73641	0.477000	0.44152	TCG	.	.		0.582	FIBIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387945.1	NM_203371		C	27016470	T	C	27016470	3	2	91	1	0	0	0	0	1	0	0	0	5893	1551	54	2	399	2	FIBIN	11	27016470	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9663991	27016470	107990046	375	12449										
QSER1	79832	hgsc.bcm.edu	37	chr11	32955843	32955843	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgcaggctgttgaagatggTgattctaaatctcattttca	9	6	3	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:32955843T>C	ENST00000399302.2	+	4	2987	c.2652T>C	c.(2650-2652)ggT>ggC	p.G884G	QSER1_ENST00000527788.1_Silent_p.G645G	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	884										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					TTGAAGATGGTGATTCTAAAT	0.388																																					p.G884G		Atlas-SNP	.											.	QSER1	153	.	0			c.T2652C						.						81	76	78					11																	32955843		1887	4118	6005	SO:0001819	synonymous_variant	79832	exon4			AGATGGTGATTCT	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.2652T>C	chr11.hg19:g.32955843T>C		189.0	0.0		112.0	5.0	NM_001076786	Q6ZU30|Q6ZUR5	Silent	SNP	ENST00000399302.2	hg19	CCDS41631.1																																																																																			.	.		0.388	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		C	32955843	T	C	32955843	2	2	91	1	0	0	0	0	0	0	0	1	12897	1683	59	2		2	QSER1	11	32955843	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	5939373	32955843	102050673	376	12450										
CD44	960	hgsc.bcm.edu	37	chr11	35222635	35222635	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catcgttatcacagtttcaaCcacaccacgggcttttgacc	6	14	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:35222635C>T	ENST00000428726.2	+	8	1052	c.929C>T	c.(928-930)aCc>aTc	p.T310I	CD44_ENST00000449691.2_Missense_Mutation_p.T310I|CD44_ENST00000526669.2_Intron|CD44_ENST00000433354.2_Missense_Mutation_p.T310I|CD44_ENST00000352818.4_Intron|CD44_ENST00000415148.2_Missense_Mutation_p.T267I|CD44_ENST00000278386.6_Intron|CD44_ENST00000434472.2_Intron|CD44_ENST00000437706.2_Missense_Mutation_p.T310I|CD44_ENST00000433892.2_Intron|CD44_ENST00000263398.6_Intron|CD44_ENST00000360158.4_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	310	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	ACAGTTTCAACCACACCACGG	0.463																																					p.T310I		Atlas-SNP	.											.	CD44	48	.	0			c.C929T						.						158	163	162					11																	35222635		2202	4298	6500	SO:0001583	missense	960	exon8			TTTCAACCACACC	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"CD molecules", "Blood group antigens", "Proteoglycans / Cell surface : Other"	1681	protein-coding gene	gene with protein product	"hematopoietic cell E- and L-selectin ligand", "chondroitin sulfate proteoglycan 8"	107269	"CD44 antigen (homing function and Indian blood group system)"	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.929C>T	chr11.hg19:g.35222635C>T	ENSP00000398632:p.Thr310Ile	62.0	0.0		67.0	4.0	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Missense_Mutation	SNP	ENST00000428726.2	hg19	CCDS7897.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.606861	0.46527	.	.	ENSG00000026508	ENST00000415148;ENST00000433354;ENST00000449691;ENST00000437706;ENST00000428726	T;T;T;T;T	0.21031	2.75;2.03;2.03;2.03;2.03	5.64	3.73	0.42828	.	0.340058	0.25464	N	0.030500	T	0.19805	0.0476	L	0.53249	1.67	0.47698	D	0.999494	B;B	0.17465	0.004;0.022	B;B	0.17433	0.007;0.018	T	0.03202	-1.1061	10	0.41790	T	0.15	-3.7328	8.3869	0.32505	0.0:0.7611:0.1543:0.0846	.	267;310	P16070-4;P16070	.;CD44_HUMAN	I	267;310;310;310;310	ENSP00000389830:T267I;ENSP00000414567:T310I;ENSP00000391008:T310I;ENSP00000403990:T310I;ENSP00000398632:T310I	ENSP00000389830:T267I	T	+	2	0	CD44	35179211	0.991000	0.36638	0.847000	0.33407	0.816000	0.46133	1.332000	0.33805	0.690000	0.31570	0.655000	0.94253	ACC	.	.		0.463	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610		T	35222635	C	T	35222635	3	4	91	1	0	0	0	0	1	0	0	0	3019	507	18	3	959	3	CD44	11	35222635	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2266792	35222635	99783881	377	12451										
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46456589	46456589	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	accagcacattcacggaagcTgcatcagacaaagaaagaaa	8	10	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:46456589T>C	ENST00000458649.2	-	13	3051		c.e13-2		AMBRA1_ENST00000314845.3_Splice_Site|AMBRA1_ENST00000534300.1_Splice_Site|AMBRA1_ENST00000528950.1_Splice_Site|AMBRA1_ENST00000298834.3_Splice_Site|AMBRA1_ENST00000426438.1_Splice_Site|AMBRA1_ENST00000533727.1_Splice_Site			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1						autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		TCACGGAAGCTGCATCAGACA	0.468																																					.		Atlas-SNP	.											.	AMBRA1	201	.	0			c.2363-2A>G						.						26	24	25					11																	46456589		2201	4299	6500	SO:0001630	splice_region_variant	55626	exon15			GGAAGCTGCATCA	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	25990	protein-coding gene	gene with protein product	"WD repeat domain 94", "DDB1 and CUL4 associated factor 3"	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.2633-2A>G	chr11.hg19:g.46456589T>C		78.0	0.0		96.0	4.0	NM_017749	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Splice_Site	SNP	ENST00000458649.2	hg19		.	.	.	.	.	.	.	.	.	.	T	26.7	4.763378	0.89932	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000458649;ENST00000528950	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4237	0.83790	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	AMBRA1	46413165	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.853000	0.86934	2.279000	0.76181	0.533000	0.62120	.	.	.		0.468	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	Intron	C	46456589	T	C	46456589	5	2	91	1	0	0	0	0	0	0	1	0	565	1594	55	2	1289	2	AMBRA1	11	46456589	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	11233954	46456589	88549927	378	12452										
OR4B1	119765	hgsc.bcm.edu	37	chr11	48239231	48239231	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atttacacactcaggaatgcAgaggtgaaaatcgccataag	9	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:48239231A>G	ENST00000309562.2	+	1	888	c.870A>G	c.(868-870)gcA>gcG	p.A290A		NM_001005470.1	NP_001005470.1	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B, member 1	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						TCAGGAATGCAGAGGTGAAAA	0.433																																					p.A290A		Atlas-SNP	.											.	OR4B1	52	.	0			c.A870G						.						73	68	70					11																	48239231		2201	4298	6499	SO:0001819	synonymous_variant	119765	exon1			GAATGCAGAGGTG	AB065848	CCDS31485.1	11p11.2	2012-08-09			ENSG00000175619	ENSG00000175619		"GPCR / Class A : Olfactory receptors"	8290	protein-coding gene	gene with protein product							Standard	NM_001005470		Approved	OST208	uc010rhs.2	Q8NGF8	OTTHUMG00000166576	ENST00000309562.2:c.870A>G	chr11.hg19:g.48239231A>G		61.0	0.0		74.0	4.0	NM_001005470	Q6IF75|Q96R64	Silent	SNP	ENST00000309562.2	hg19	CCDS31485.1																																																																																			.	.		0.433	OR4B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390554.1	NM_001005470		G	48239231	A	G	48239231	2	3	91	1	0	0	0	0	0	0	0	1	11053	175	7	2		2	OR4B1	11	48239231	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1782642	48239231	86767285	379	12453										
OR5M1	390168	hgsc.bcm.edu	37	chr11	56380553	56380553	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taagggatagtgaccagacaGacacagatgttcttggacat	11	7	1	4	rs200393978		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:56380553G>C	ENST00000526538.1	-	1	425	c.426C>G	c.(424-426)gtC>gtG	p.V142V		NM_001004740.1	NP_001004740.1	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M, member 1	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|upper_aerodigestive_tract(1)	12						TGACCAGACAGACACAGATGT	0.443																																					p.V142V		Atlas-SNP	.											.	OR5M1	92	.	0			c.C426G						.						133	115	120					11																	56380553		1971	4166	6137	SO:0001819	synonymous_variant	390168	exon1			CAGACAGACACAG	AB065742	CCDS53631.1	11q11	2012-08-09				ENSG00000255012		"GPCR / Class A : Olfactory receptors"	8352	protein-coding gene	gene with protein product							Standard	NM_001004740		Approved	OST050	uc001nja.1	Q8NGP8		ENST00000526538.1:c.426C>G	chr11.hg19:g.56380553G>C		197.0	0.0		168.0	9.0	NM_001004740	Q6IF60|Q96RB6	Silent	SNP	ENST00000526538.1	hg19	CCDS53631.1																																																																																			.	.		0.443	OR5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391610.1	NM_001004740		C	56380553	G	C	56380553	2	2	91	1	0	0	0	0	0	0	0	1	11181	929	33	4		4	OR5M1	11	56380553	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	8141322	56380553	78625963	380	12454										
SERPING1	710	hgsc.bcm.edu	37	chr11	57374013	57374013	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttcattgaccaaactttgaAagccaaggtaagttcttaac	6	8	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:57374013A>G	ENST00000278407.4	+	6	1249	c.1022A>G	c.(1021-1023)aAa>aGa	p.K341R	SERPING1_ENST00000340687.6_Missense_Mutation_p.K341R|SERPING1_ENST00000378323.4_Missense_Mutation_p.K346R|SERPING1_ENST00000403558.1_Missense_Mutation_p.K384R|SERPING1_ENST00000378324.2_Missense_Mutation_p.K289R	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	341					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						CAAACTTTGAAAGCCAAGGTA	0.408																																					p.K341R		Atlas-SNP	.											.	SERPING1	57	.	0			c.A1022G						.						173	164	167					11																	57374013		2201	4296	6497	SO:0001583	missense	710	exon5			CTTTGAAAGCCAA	X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"Serine (or cysteine) peptidase inhibitors"	1228	protein-coding gene	gene with protein product	"plasma protease C1 inhibitor", "angioedema, hereditary"	606860	"serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.1022A>G	chr11.hg19:g.57374013A>G	ENSP00000278407:p.Lys341Arg	82.0	0.0		65.0	4.0	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	hg19	CCDS7962.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.639032	0.47153	.	.	ENSG00000149131	ENST00000278407;ENST00000340687;ENST00000378323;ENST00000378324;ENST00000403558	D;D;D;D;D	0.88509	-2.39;-2.39;-2.39;-2.39;-2.39	5.49	4.37	0.52481	Serpin domain (3);	0.056073	0.64402	D	0.000001	D	0.85754	0.5770	M	0.64404	1.975	0.39768	D	0.972124	B;B;B;B	0.27140	0.153;0.169;0.153;0.153	B;B;B;B	0.26770	0.073;0.067;0.073;0.073	T	0.82184	-0.0583	10	0.45353	T	0.12	.	8.9441	0.35747	0.9144:0.0:0.0856:0.0	.	346;384;341;341	B4E1F0;E9PGN7;E9KL26;P05155	.;.;.;IC1_HUMAN	R	341;341;346;289;384	ENSP00000278407:K341R;ENSP00000341861:K341R;ENSP00000367574:K346R;ENSP00000367575:K289R;ENSP00000384420:K384R	ENSP00000278407:K341R	K	+	2	0	SERPING1	57130589	1.000000	0.71417	0.888000	0.34837	0.983000	0.72400	3.594000	0.54008	0.935000	0.37341	0.533000	0.62120	AAA	.	.		0.408	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062		G	57374013	A	G	57374013	3	3	91	1	0	0	0	0	1	0	0	0	14131	14	1	2	1040	2	SERPING1	11	57374013	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	993460	57374013	77632503	381	12455										
OR5B21	219968	hgsc.bcm.edu	37	chr11	58275280	58275280	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggcaaaccccacaaagaagAagaactgagctgcacatcca	8	12	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:58275280A>G	ENST00000360374.2	-	1	298	c.299T>C	c.(298-300)tTc>tCc	p.F100S		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CACAAAGAAGAAGAACTGAGC	0.547																																					p.F100S		Atlas-SNP	.											.	OR5B21	59	.	0			c.T299C						.						127	98	108					11																	58275280		2201	4295	6496	SO:0001583	missense	219968	exon1			AAGAAGAAGAACT		CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"GPCR / Class A : Olfactory receptors"	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.299T>C	chr11.hg19:g.58275280A>G	ENSP00000353537:p.Phe100Ser	123.0	0.0		94.0	4.0	NM_001005218		Missense_Mutation	SNP	ENST00000360374.2	hg19	CCDS31552.1	.	.	.	.	.	.	.	.	.	.	A	16.67	3.188781	0.57909	.	.	ENSG00000198283	ENST00000360374	T	0.00397	7.57	5.2	4.07	0.47477	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38837	U	0.001544	T	0.00384	0.0012	M	0.74389	2.26	0.29433	N	0.859748	P	0.43973	0.823	B	0.42827	0.399	T	0.31420	-0.9944	10	0.72032	D	0.01	-9.5501	5.4771	0.16702	0.765:0.0:0.0822:0.1528	.	100	A6NL26	OR5BL_HUMAN	S	100	ENSP00000353537:F100S	ENSP00000353537:F100S	F	-	2	0	OR5B21	58031856	0.006000	0.16342	0.980000	0.43619	0.998000	0.95712	0.425000	0.21346	0.994000	0.38892	0.533000	0.62120	TTC	.	.		0.547	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218		G	58275280	A	G	58275280	3	3	91	1	0	0	0	0	1	0	0	0	11160	246	9	2	632	2	OR5B21	11	58275280	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	901267	58275280	76731236	382	12456										
MS4A6A	64231	hgsc.bcm.edu	37	chr11	59947428	59947428	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ataccatcatgccacacaagAtctggatagtctgtgggaag	10	9	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:59947428A>G	ENST00000530839.1	-	4	650	c.158T>C	c.(157-159)aTc>aCc	p.I53T	MS4A6A_ENST00000529906.1_5'UTR|MS4A6A_ENST00000528851.1_Missense_Mutation_p.I53T|MS4A6A_ENST00000532169.1_Missense_Mutation_p.I53T|MS4A6A_ENST00000426738.2_Intron|MS4A6A_ENST00000533023.1_Intron|MS4A6A_ENST00000420732.2_Missense_Mutation_p.I53T|MS4A6A_ENST00000412309.2_Missense_Mutation_p.I81T|MS4A6A_ENST00000323961.3_Missense_Mutation_p.I53T|MS4A6A_ENST00000529054.1_Missense_Mutation_p.I81T	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	53						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GCCACACAAGATCTGGATAGT	0.443																																					p.I81T		Atlas-SNP	.											.	MS4A6A	85	.	0			c.T242C						.						92	85	88					11																	59947428		2201	4295	6496	SO:0001583	missense	64231	exon4			CACAAGATCTGGA	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.158T>C	chr11.hg19:g.59947428A>G	ENSP00000436979:p.Ile53Thr	153.0	0.0		145.0	6.0	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Missense_Mutation	SNP	ENST00000530839.1	hg19	CCDS7981.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.181779	0.38511	.	.	ENSG00000110077	ENST00000323961;ENST00000528851;ENST00000420732;ENST00000530839;ENST00000529054;ENST00000412309;ENST00000532169;ENST00000534596	T;T;T;T;T;T;T;T	0.27557	3.35;3.35;3.35;3.35;3.35;3.35;3.35;1.66	4.32	3.2	0.36748	.	0.207171	0.36972	N	0.002306	T	0.51991	0.1707	M	0.86097	2.795	0.80722	D	1	D;D;D;P	0.56287	0.969;0.975;0.975;0.94	P;D;D;P	0.68621	0.871;0.959;0.921;0.798	T	0.54754	-0.8246	9	.	.	.	.	5.951	0.19246	0.8842:0.0:0.1158:0.0	.	81;81;53;53	F8W9K1;E9PSA9;Q9H2W1;Q9H2W1-3	.;.;M4A6A_HUMAN;.	T	53;53;53;53;81;81;53;81	ENSP00000315878:I53T;ENSP00000431901:I53T;ENSP00000392921:I53T;ENSP00000436979:I53T;ENSP00000435844:I81T;ENSP00000403212:I81T;ENSP00000431266:I53T;ENSP00000433436:I81T	.	I	-	2	0	MS4A6A	59704004	0.978000	0.34361	0.979000	0.43373	0.380000	0.30137	2.367000	0.44213	1.929000	0.55896	0.533000	0.62120	ATC	.	.		0.443	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1			G	59947428	A	G	59947428	3	3	91	1	0	0	0	0	1	0	0	0	9873	333	12	2	635	2	MS4A6A	11	59947428	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1672148	59947428	75059088	383	12457										
MS4A14	84689	hgsc.bcm.edu	37	chr11	60165354	60165354	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atcctgcttgctctaatcatTgtgggctttggaactatatt	8	8	2	0	rs3217518	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:60165354T>A	ENST00000300187.6	+	2	445	c.168T>A	c.(166-168)atT>atA	p.I56I	MS4A14_ENST00000395005.2_Silent_p.I56I|MS4A14_ENST00000531787.1_Intron|MS4A14_ENST00000395001.1_De_novo_Start_InFrame|MS4A14_ENST00000531783.1_Silent_p.I56I	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	56						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						CTCTAATCATTGTGGGCTTTG	0.478																																					p.I56I		Atlas-SNP	.											.	MS4A14	120	.	0			c.T168A						.						112	78	91					11																	60165354		1817	2868	4685	SO:0001819	synonymous_variant	84689	exon2			AATCATTGTGGGC	AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"membrane-spanning 4-domains, subfamily A, member 16"	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.168T>A	chr11.hg19:g.60165354T>A		1.0	0.0		22.0	14.0	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Silent	SNP	ENST00000300187.6	hg19	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	T	8.441	0.850792	0.17034	.	.	ENSG00000166928	ENST00000534688	.	.	.	4.94	-1.76	0.08006	.	.	.	.	.	.	.	.	.	.	.	0.30288	N	0.790644	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.4396	4.4751	0.11731	0.0:0.3068:0.3384:0.3548	.	.	.	.	X	15	.	.	L	+	2	0	MS4A14	59921930	0.001000	0.12720	0.066000	0.19879	0.254000	0.26022	-0.793000	0.04589	-0.152000	0.11156	0.482000	0.46254	TTG	.	.		0.478	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			A	60165354	T	A	60165354	2	1	91	1	0	0	0	0	0	0	0	1	9867	1800	63	4		4	MS4A14	11	60165354	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	217926	60165354	74841162	384	12458										
VPS37C	55048	hgsc.bcm.edu	37	chr11	60900811	60900811	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtgctgaagaaaatttctcTggaagggagggcagaacgac	14	6	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:60900811T>C	ENST00000301765.5	-	4	498		c.e4-2			NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)						endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						AAAATTTCTCTGGAAGGGAGG	0.527																																					.		Atlas-SNP	.											.	VPS37C	30	.	0			c.266-2A>G						.						65	50	55					11																	60900811		2203	4299	6502	SO:0001630	splice_region_variant	55048	exon5			TTTCTCTGGAAGG	AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"vacuolar protein sorting 37C (yeast)"			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.266-2A>G	chr11.hg19:g.60900811T>C		69.0	0.0		61.0	4.0	NM_017966	Q8N3K4	Splice_Site	SNP	ENST00000301765.5	hg19	CCDS31573.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.956540	0.73902	.	.	ENSG00000167987	ENST00000301765;ENST00000540084;ENST00000538036	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3137	0.60394	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	VPS37C	60657387	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.060000	0.64312	1.880000	0.54463	0.459000	0.35465	.	.	.		0.527	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966	Intron	C	60900811	T	C	60900811	5	2	91	1	0	0	0	0	0	0	1	0	17222	1594	55	2	811	2	VPS37C	11	60900811	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	735457	60900811	74105705	385	12459										
DDB1	1642	hgsc.bcm.edu	37	chr11	61097525	61097525	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtacttcgctgtcaagataaAcagcaggtccttgctctccc	8	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:61097525A>G	ENST00000301764.7	-	3	629	c.232T>C	c.(232-234)Ttt>Ctt	p.F78L	DDB1_ENST00000545930.1_5'Flank|DDB1_ENST00000450997.2_Intron	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	78	Interaction with CDT1.|WD repeat beta-propeller A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						GTCAAGATAAACAGCAGGTCC	0.453								Nucleotide excision repair (NER)																													p.F78L		Atlas-SNP	.											.	DDB1	100	.	0			c.T232C						.						108	95	99					11																	61097525		2203	4299	6502	SO:0001583	missense	1642	exon3			AGATAAACAGCAG	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.232T>C	chr11.hg19:g.61097525A>G	ENSP00000301764:p.Phe78Leu	141.0	0.0		142.0	6.0	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Missense_Mutation	SNP	ENST00000301764.7	hg19	CCDS31576.1	.	.	.	.	.	.	.	.	.	.	A	33	5.197625	0.94997	.	.	ENSG00000167986	ENST00000301764;ENST00000539426;ENST00000535283;ENST00000542337;ENST00000543627	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.60869	0.2302	M	0.72894	2.215	0.80722	D	1	D;D	0.71674	0.968;0.998	P;D	0.68192	0.691;0.956	T	0.59963	-0.7355	10	0.30854	T	0.27	-16.3001	14.6448	0.68754	1.0:0.0:0.0:0.0	.	78;78	B7Z2A1;Q16531	.;DDB1_HUMAN	L	78;22;22;78;78	ENSP00000301764:F78L;ENSP00000445554:F22L;ENSP00000441825:F22L;ENSP00000444105:F78L	ENSP00000301764:F78L	F	-	1	0	DDB1	60854101	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.095000	0.94175	1.914000	0.55421	0.460000	0.39030	TTT	.	.		0.453	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		G	61097525	A	G	61097525	3	3	91	1	0	0	0	0	1	0	0	0	4325	43	2	2	3290	2	DDB1	11	61097525	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	196714	61097525	73908991	386	12460										
SCGB1A1	7356	hgsc.bcm.edu	37	chr11	62189867	62189867	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccaaaagcccagagaaagcaTcattaagctcatggtaacca	7	11	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:62189867T>C	ENST00000278282.2	+	2	291	c.230T>C	c.(229-231)aTc>aCc	p.I77T	SCGB1A1_ENST00000534397.1_Missense_Mutation_p.I42T|CTD-2531D15.4_ENST00000528983.1_RNA	NM_003357.4	NP_003348.1	P11684	UTER_HUMAN	secretoglobin, family 1A, member 1 (uteroglobin)	77					embryo implantation (GO:0007566)|female pregnancy (GO:0007565)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of inflammatory response (GO:0050727)|regulation of mRNA stability (GO:0043488)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fibroblast growth factor (GO:0071774)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to silicon dioxide (GO:0034021)|response to xenobiotic stimulus (GO:0009410)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nuclear envelope (GO:0005635)|rough endoplasmic reticulum (GO:0005791)|secretory granule (GO:0030141)	phospholipase A2 inhibitor activity (GO:0019834)			lung(1)	1						AGAGAAAGCATCATTAAGCTC	0.537																																					p.I77T		Atlas-SNP	.											.	SCGB1A1	5	.	0			c.T230C						.						118	105	110					11																	62189867		2202	4299	6501	SO:0001583	missense	7356	exon2			AAAGCATCATTAA		CCDS8020.1	11q12.3	2011-12-14	2002-03-22	2002-03-22	ENSG00000149021	ENSG00000149021		"Secretoglobins"	12523	protein-coding gene	gene with protein product	"Uteroglobin (Clara-cell specific 10-kD protein)"	192020	"uteroglobin"	UGB		1284526, 22155607	Standard	NM_003357		Approved	CC10, CCSP, CC16	uc001ntj.3	P11684	OTTHUMG00000167526	ENST00000278282.2:c.230T>C	chr11.hg19:g.62189867T>C	ENSP00000278282:p.Ile77Thr	97.0	0.0		71.0	4.0	NM_003357	B2R5F2|Q6FHH3|Q9UCM2|Q9UCM4	Missense_Mutation	SNP	ENST00000278282.2	hg19	CCDS8020.1	.	.	.	.	.	.	.	.	.	.	T	13.41	2.229648	0.39399	.	.	ENSG00000149021	ENST00000534397;ENST00000278282	T;T	0.18810	2.19;2.19	4.74	3.61	0.41365	.	1.410380	0.04639	N	0.404942	T	0.34919	0.0914	.	.	.	0.09310	N	1	P	0.48089	0.905	P	0.52823	0.71	T	0.11251	-1.0595	9	0.87932	D	0	-1.5553	7.1299	0.25496	0.0:0.1038:0.0:0.8962	.	77	P11684	UTER_HUMAN	T	42;77	ENSP00000432866:I42T;ENSP00000278282:I77T	ENSP00000278282:I77T	I	+	2	0	SCGB1A1	61946443	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	1.224000	0.32539	0.786000	0.33708	0.533000	0.62120	ATC	.	.		0.537	SCGB1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394925.1	NM_003357		C	62189867	T	C	62189867	3	2	91	1	0	0	0	0	1	0	0	0	13909	1435	50	2	236	2	SCGB1A1	11	62189867	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1092342	62189867	72816649	387	12461										
INTS5	80789	hgsc.bcm.edu	37	chr11	62416122	62416122	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctctccaacatggtttttgAgcgcatctaaaaagggcacc	9	11	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:62416122A>G	ENST00000330574.2	-	2	1482	c.1430T>C	c.(1429-1431)cTc>cCc	p.L477P	GANAB_ENST00000356638.3_5'Flank|GANAB_ENST00000534779.1_5'Flank|GANAB_ENST00000540933.1_5'Flank|GANAB_ENST00000346178.4_5'Flank	NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	477					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(6)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	36						ATGGTTTTTGAGCGCATCTAA	0.587																																					p.L477P		Atlas-SNP	.											.	INTS5	81	.	0			c.T1430C						.						77	79	78					11																	62416122		2202	4299	6501	SO:0001583	missense	80789	exon2			TTTTTGAGCGCAT	AK123587	CCDS8027.1	11q12.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000185085	ENSG00000185085			29352	protein-coding gene	gene with protein product		611349	"KIAA1698"	KIAA1698		16239144	Standard	NM_030628		Approved	INT5	uc001nud.3	Q6P9B9	OTTHUMG00000167605	ENST00000330574.2:c.1430T>C	chr11.hg19:g.62416122A>G	ENSP00000327889:p.Leu477Pro	66.0	0.0		69.0	4.0	NM_030628	Q8N6W5|Q9C0G5	Missense_Mutation	SNP	ENST00000330574.2	hg19	CCDS8027.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.155447	0.38021	.	.	ENSG00000185085	ENST00000330574	.	.	.	4.87	4.87	0.63330	.	0.084051	0.49916	D	0.000121	T	0.61502	0.2352	N	0.24115	0.695	0.52501	D	0.999959	D	0.76494	0.999	D	0.69479	0.964	T	0.66316	-0.5954	9	0.87932	D	0	.	12.476	0.55814	1.0:0.0:0.0:0.0	.	477	Q6P9B9	INT5_HUMAN	P	477	.	ENSP00000327889:L477P	L	-	2	0	INTS5	62172698	1.000000	0.71417	0.108000	0.21378	0.554000	0.35429	8.598000	0.90852	2.052000	0.61016	0.533000	0.62120	CTC	.	.		0.587	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628		G	62416122	A	G	62416122	3	3	91	1	0	0	0	0	1	0	0	0	7790	304	11	2	1633	2	INTS5	11	62416122	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	226255	62416122	72590394	388	12462										
ATL3	25923	hgsc.bcm.edu	37	chr11	63396832	63396832	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggatggtcttccaacaactgCatccctcacagtggcctgag	10	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:63396832C>A	ENST00000398868.3	-	13	1861	c.1585G>T	c.(1585-1587)Gca>Tca	p.A529S	ATL3_ENST00000538786.1_Missense_Mutation_p.A511S|ATL3_ENST00000332645.4_Missense_Mutation_p.A556S	NM_015459.3	NP_056274.3	Q6DD88	ATLA3_HUMAN	atlastin GTPase 3	529					endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	11						CCAACAACTGCATCCCTCACA	0.388																																					p.A529S		Atlas-SNP	.											.	ATL3	31	.	0			c.G1585T						.						124	117	119					11																	63396832		1905	4120	6025	SO:0001583	missense	25923	exon13			CAACTGCATCCCT		CCDS41663.1, CCDS73309.1	11q13.1	2008-09-17			ENSG00000184743	ENSG00000184743			24526	protein-coding gene	gene with protein product		609369				18270207	Standard	XM_005273891		Approved	DKFZP564J0863	uc001nxk.1	Q6DD88	OTTHUMG00000167854	ENST00000398868.3:c.1585G>T	chr11.hg19:g.63396832C>A	ENSP00000381844:p.Ala529Ser	277.0	0.0		249.0	102.0	NM_015459	Q8N7W5|Q9H8Q5|Q9UFL1	Missense_Mutation	SNP	ENST00000398868.3	hg19	CCDS41663.1	.	.	.	.	.	.	.	.	.	.	C	8.508	0.865783	0.17250	.	.	ENSG00000184743	ENST00000398868;ENST00000332645;ENST00000538786	T;T;T	0.80480	-1.25;-1.38;-1.24	5.63	1.39	0.22231	.	0.572977	0.18801	N	0.130797	T	0.52948	0.1766	N	0.04959	-0.14	0.09310	N	1	B	0.28820	0.224	B	0.24701	0.055	T	0.38564	-0.9655	10	0.29301	T	0.29	-7.3235	1.6857	0.02841	0.1828:0.4839:0.155:0.1782	.	529	Q6DD88	ATLA3_HUMAN	S	529;556;511	ENSP00000381844:A529S;ENSP00000329034:A556S;ENSP00000437593:A511S	ENSP00000329034:A556S	A	-	1	0	ATL3	63153408	0.002000	0.14202	0.425000	0.26659	0.009000	0.06853	0.010000	0.13242	0.298000	0.22638	-0.274000	0.10170	GCA	.	.		0.388	ATL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396637.1	NM_015459		A	63396832	C	A	63396832	3	1	91	1	0	0	0	0	1	0	0	0	1108	710	25	3	44	3	ATL3	11	63396832	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	980710	63396832	71609684	389	12463										
KCNK4	50801	hgsc.bcm.edu	37	chr11	64060629	64060629	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggaggtccgagagaagttcCtgagggcccatccgtgtgtg	17	9	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:64060629C>A	ENST00000539216.1	+	1	499	c.139C>A	c.(139-141)Ctg>Atg	p.L47M	RP11-783K16.10_ENST00000539086.1_RNA|Y_RNA_ENST00000384297.1_RNA|KCNK4_ENST00000422670.2_Missense_Mutation_p.L47M|KCNK4_ENST00000538767.1_Intron|KCNK4_ENST00000394525.2_Missense_Mutation_p.L47M|KCNK4_ENST00000539651.1_Intron			Q9NYG8	KCNK4_HUMAN	potassium channel, subfamily K, member 4	47					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(2)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	10						AGAGAAGTTCCTGAGGGCCCA	0.667																																					p.L47M		Atlas-SNP	.											.	KCNK4	22	.	0			c.C139A						.						39	37	37					11																	64060629		1872	3553	5425	SO:0001583	missense	50801	exon2			AAGTTCCTGAGGG	AF247042	CCDS8067.1	11q13	2012-03-07			ENSG00000182450	ENSG00000182450		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6279	protein-coding gene	gene with protein product		605720				10767409, 16382106	Standard	NM_033310		Approved	K2p4.1, TRAAK	uc001nzk.1	Q9NYG8	OTTHUMG00000168006	ENST00000539216.1:c.139C>A	chr11.hg19:g.64060629C>A	ENSP00000444948:p.Leu47Met	74.0	0.0		68.0	4.0	NM_033310	B5TJL1|Q96T94	Missense_Mutation	SNP	ENST00000539216.1	hg19	CCDS8067.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.922849	0.73213	.	.	ENSG00000182450	ENST00000422670;ENST00000539852;ENST00000394525;ENST00000544845;ENST00000539216	T;T;T	0.20069	2.1;2.1;2.1	4.28	3.35	0.38373	.	0.186190	0.36200	N	0.002725	T	0.38639	0.1048	M	0.71036	2.16	0.47584	D	0.999462	D	0.54964	0.969	P	0.60012	0.867	T	0.15178	-1.0446	10	0.46703	T	0.11	.	11.1218	0.48296	0.1862:0.8138:0.0:0.0	.	47	Q9NYG8	KCNK4_HUMAN	M	47;72;47;109;47	ENSP00000402797:L47M;ENSP00000378033:L47M;ENSP00000444948:L47M	ENSP00000378033:L47M	L	+	1	2	KCNK4	63817205	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.478000	0.60230	0.989000	0.38761	0.455000	0.32223	CTG	.	.		0.667	KCNK4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396430.1	NM_033311		A	64060629	C	A	64060629	3	1	91	1	0	0	0	0	1	0	0	0	8077	680	24	3	141	3	KCNK4	11	64060629	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	663797	64060629	70945887	390	12464										
MEN1	4221	hgsc.bcm.edu	37	chr11	64577196	64577196	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccttgaagtaggagcggctgAggctgttccatatgacatcg	13	9	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:64577196A>G	ENST00000337652.1	-	2	889	c.386T>C	c.(385-387)cTc>cCc	p.L129P	MEN1_ENST00000377321.1_Missense_Mutation_p.L129P|MEN1_ENST00000315422.4_Missense_Mutation_p.L129P|MEN1_ENST00000394374.2_Missense_Mutation_p.L129P|MEN1_ENST00000377326.3_Missense_Mutation_p.L129P|MEN1_ENST00000377316.2_Missense_Mutation_p.L129P|MEN1_ENST00000394376.1_Missense_Mutation_p.L129P|MEN1_ENST00000312049.6_Missense_Mutation_p.L129P|MEN1_ENST00000443283.1_Missense_Mutation_p.L129P|MEN1_ENST00000377313.1_Missense_Mutation_p.L129P	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	129					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.I125fs*53(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						GGAGCGGCTGAGGCTGTTCCA	0.572			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												p.L129P	Esophageal Squamous(1;83 158 15500 18603 18803 29295)	Atlas-SNP	.	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	.	MEN1	442	.	1	Deletion - Frameshift(1)	parathyroid(1)	c.T386C						.						114	115	115					11																	64577196		2201	4297	6498	SO:0001583	missense	4221	exon2	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	CGGCTGAGGCTGT	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.386T>C	chr11.hg19:g.64577196A>G	ENSP00000337088:p.Leu129Pro	106.0	0.0		118.0	8.0	NM_130800	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	hg19	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.271310	0.80469	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873;ENST00000450708;ENST00000413626;ENST00000429702;ENST00000424912	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.99719	-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52	4.93	4.93	0.64822	.	0.000000	0.64402	D	0.000002	D	0.99542	0.9836	M	0.67397	2.05	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.997;0.999	D	0.98014	1.0367	10	0.87932	D	0	-28.6783	12.8611	0.57913	1.0:0.0:0.0:0.0	.	129;129;129	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	P	129	ENSP00000366533:L129P;ENSP00000366538:L129P;ENSP00000366543:L129P;ENSP00000308975:L129P;ENSP00000323747:L129P;ENSP00000337088:L129P;ENSP00000377901:L129P;ENSP00000377899:L129P;ENSP00000396940:L129P;ENSP00000366530:L129P;ENSP00000413944:L129P;ENSP00000394933:L129P;ENSP00000411218:L129P;ENSP00000402752:L129P;ENSP00000388016:L129P	ENSP00000308975:L129P	L	-	2	0	MEN1	64333772	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	8.364000	0.90105	1.988000	0.58038	0.402000	0.26972	CTC	.	.		0.572	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			G	64577196	A	G	64577196	3	3	91	1	0	0	0	0	1	0	0	0	9481	304	11	2	1497	2	MEN1	11	64577196	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	516567	64577196	70429320	391	12465										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65351097	65351097	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggctggggtcttgggaaatgAgaaggggaaagaagctgagg	20	3	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:65351097A>G	ENST00000309295.4	+	9	3219	c.2954A>G	c.(2953-2955)gAg>gGg	p.E985G		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	985						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						TTGGGAAATGAGAAGGGGAAA	0.602																																					p.E985G		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.A2954G						.						14	15	14					11																	65351097		1846	4093	5939	SO:0001583	missense	254102	exon9			GAAATGAGAAGGG	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.2954A>G	chr11.hg19:g.65351097A>G	ENSP00000312671:p.Glu985Gly	80.0	0.0		83.0	4.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.883|6.883	0.532444|0.532444	0.13127|0.13127	.|.	.|.	ENSG00000173442|ENSG00000173442	ENST00000309295|ENST00000533465	T|.	0.66638|.	-0.22|.	4.87|4.87	2.49|2.49	0.30216|0.30216	.|.	0.894455|.	0.09376|.	N|.	0.810556|.	T|.	0.28599|.	0.0708|.	L|L	0.27053|0.27053	0.805|0.805	0.30589|0.30589	N|N	0.761684|0.761684	B|.	0.06786|.	0.001|.	B|.	0.04013|.	0.001|.	T|.	0.26503|.	-1.0101|.	10|.	0.32370|.	T|.	0.25|.	.|.	4.5776|4.5776	0.12241|0.12241	0.7238:0.0:0.0973:0.179|0.7238:0.0:0.0973:0.179	.|.	985|.	Q8N3D4|.	EH1L1_HUMAN|.	G|W	985|34	ENSP00000312671:E985G|.	ENSP00000312671:E985G|.	E|X	+|+	2|3	0|0	EHBP1L1|EHBP1L1	65107673|65107673	0.318000|0.318000	0.24598|0.24598	0.089000|0.089000	0.20774|0.20774	0.255000|0.255000	0.26057|0.26057	0.987000|0.987000	0.29603|0.29603	0.666000|0.666000	0.31087|0.31087	0.358000|0.358000	0.22013|0.22013	GAG|TGA	.	.		0.602	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		G	65351097	A	G	65351097	3	3	91	1	0	0	0	0	1	0	0	0	4978	304	11	2	2988	2	EHBP1L1	11	65351097	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	773901	65351097	69655419	392	12466										
OVOL1	5017	hgsc.bcm.edu	37	chr11	65562182	65562182	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	accttcgacctcaagagacaCgtccgaactcacactggtaa	7	14	2	1	rs377708693		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:65562182C>T	ENST00000335987.3	+	3	844	c.492C>T	c.(490-492)caC>caT	p.H164H	RP11-770G2.5_ENST00000531155.1_RNA|OVOL1_ENST00000532448.1_Silent_p.H102H	NM_004561.3	NP_004552.2	O14753	OVOL1_HUMAN	ovo-like zinc finger 1	164					cytoskeleton organization (GO:0007010)|epidermal cell differentiation (GO:0009913)|germline cell cycle switching, mitotic to meiotic cell cycle (GO:0051729)|kidney development (GO:0001822)|mesoderm development (GO:0007498)|negative regulation of meiotic cell cycle phase transition (GO:1901994)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.H164H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6				READ - Rectum adenocarcinoma(159;0.17)		TCAAGAGACACGTCCGAACTC	0.617													C|||	1	0.000199681	0	0	5008	,	,		21988	0		0	False		,,,				2504	0.001				p.H164H		Atlas-SNP	.											OVOL1,NS,carcinoma,0,1	OVOL1	15	.	1	Substitution - coding silent(1)	endometrium(1)	c.C492T						.	C		0,4402		0,0,2201	123	96	105		492	-5.8	0.8	11		105	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	OVOL1	NM_004561.3		0,1,6497	TT,TC,CC		0.0116,0.0,0.0077		164/268	65562182	1,12995	2201	4297	6498	SO:0001819	synonymous_variant	5017	exon3			GAGACACGTCCGA	BC059408	CCDS8112.1	11q13	2013-10-17	2013-10-17		ENSG00000172818	ENSG00000172818		"Zinc fingers, C2H2-type"	8525	protein-coding gene	gene with protein product		602313	"ovo (Drosophila) homolog-like 1", "ovo-like 1(Drosophila)"			9383297	Standard	NM_004561		Approved	HOVO1	uc001ofp.3	O14753	OTTHUMG00000166600	ENST00000335987.3:c.492C>T	chr11.hg19:g.65562182C>T		70.0	0.0		58.0	3.0	NM_004561	Q6PCB1	Silent	SNP	ENST00000335987.3	hg19	CCDS8112.1																																																																																			.	.		0.617	OVOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390690.1	NM_004561		T	65562182	C	T	65562182	2	4	91	1	0	0	0	0	0	0	0	1	11335	535	19	1		1	OVOL1	11	65562182	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	211085	65562182	69444334	393	12467										
DPP3	10072	hgsc.bcm.edu	37	chr11	66249887	66249887	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctcttccgcgcccaggacccCgaccagctgcgccaacatgc	9	20	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:66249887C>T	ENST00000360510.2	+	2	281	c.216C>T	c.(214-216)ccC>ccT	p.P72P	DPP3_ENST00000531863.1_Silent_p.P92P|CTD-3074O7.5_ENST00000527274.2_RNA|CTD-3074O7.5_ENST00000533502.1_RNA|CTD-3074O7.5_ENST00000527092.1_RNA|DPP3_ENST00000532677.1_Silent_p.P91P|DPP3_ENST00000541961.1_Silent_p.P72P|DPP3_ENST00000530165.1_Silent_p.P72P|CTD-3074O7.5_ENST00000525142.1_RNA|DPP3_ENST00000453114.1_Silent_p.P72P			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	72					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						CCCAGGACCCCGACCAGCTGC	0.632																																					p.P72P		Atlas-SNP	.											.	DPP3	61	.	0			c.C216T						.						41	43	42					11																	66249887		2200	4295	6495	SO:0001819	synonymous_variant	10072	exon2			GGACCCCGACCAG	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"dipeptidylpeptidase III", "dipeptidylpeptidase 3"			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.216C>T	chr11.hg19:g.66249887C>T		30.0	0.0		34.0	4.0	NM_001256670	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Silent	SNP	ENST00000360510.2	hg19	CCDS8141.1																																																																																			.	.		0.632	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2			T	66249887	C	T	66249887	2	4	91	1	0	0	0	0	0	0	0	1	4730	639	23	1		1	DPP3	11	66249887	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	687705	66249887	68756629	394	12468										
PC	5091	hgsc.bcm.edu	37	chr11	66636393	66636393	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaagtagtgcttgccgtgccTgtccaccaggaactccacgg	12	13	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:66636393T>C	ENST00000393958.2	-	9	1039	c.946A>G	c.(946-948)Agg>Ggg	p.R316G	PC_ENST00000355677.3_Missense_Mutation_p.R316G|PC_ENST00000393955.2_Missense_Mutation_p.R316G|PC_ENST00000393960.1_Missense_Mutation_p.R316G|PC_ENST00000524491.1_Missense_Mutation_p.R276G	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	316	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	TTGCCGTGCCTGTCCACCAGG	0.662																																					p.R316G		Atlas-SNP	.											.	PC	116	.	0			c.A946G						.						94	82	86					11																	66636393		2200	4295	6495	SO:0001583	missense	5091	exon9			CGTGCCTGTCCAC	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.946A>G	chr11.hg19:g.66636393T>C	ENSP00000377530:p.Arg316Gly	181.0	0.0		148.0	7.0	NM_000920	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	hg19	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.357478	0.41801	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677	D;D;D;D;D	0.97688	-4.49;-4.49;-4.49;-4.49;-4.49	4.36	3.2	0.36748	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.487758	0.17767	N	0.162713	D	0.90810	0.7114	N	0.05050	-0.12	0.28376	N	0.919783	B	0.02656	0.0	B	0.06405	0.002	T	0.81099	-0.1086	10	0.10377	T	0.69	-9.4352	9.118	0.36769	0.0:0.0:0.1854:0.8146	.	316	P11498	PYC_HUMAN	G	316;316;316;276;316	ENSP00000377527:R316G;ENSP00000377530:R316G;ENSP00000377532:R316G;ENSP00000434192:R276G;ENSP00000347900:R316G	ENSP00000347900:R316G	R	-	1	2	PC	66392969	0.996000	0.38824	0.633000	0.29310	0.861000	0.49209	1.935000	0.40173	0.511000	0.28236	0.459000	0.35465	AGG	.	.		0.662	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		C	66636393	T	C	66636393	3	2	91	1	0	0	0	0	1	0	0	0	11506	1579	55	2	2646	2	PC	11	66636393	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	386506	66636393	68370123	395	12469										
KDM2A	22992	hgsc.bcm.edu	37	chr11	67020287	67020287	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgacctcagttggaccaacaTctctaaaaagcaactgacat	6	11	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:67020287T>C	ENST00000529006.2	+	18	3337	c.2891T>C	c.(2890-2892)aTc>aCc	p.I964T	KDM2A_ENST00000308783.5_Missense_Mutation_p.I422T|KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000530342.1_Missense_Mutation_p.I525T|KDM2A_ENST00000398645.2_3'UTR	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	964					histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						TGGACCAACATCTCTAAAAAG	0.532											OREG0021121	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I964T		Atlas-SNP	.											.	KDM2A	80	.	0			c.T2891C						.						70	69	70					11																	67020287		1975	4160	6135	SO:0001583	missense	22992	exon18			CCAACATCTCTAA	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13606	protein-coding gene	gene with protein product	"F-box protein FBL11", "jumonji C domain-containing histone demethylase 1A"	605657	"F-box and leucine-rich repeat protein 11"	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.2891T>C	chr11.hg19:g.67020287T>C	ENSP00000432786:p.Ile964Thr	86.0	0.0	1096	73.0	4.0	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Missense_Mutation	SNP	ENST00000529006.2	hg19	CCDS44657.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.720220	0.89205	.	.	ENSG00000173120	ENST00000529006;ENST00000530342;ENST00000308783	T;T;T	0.37058	1.22;1.22;1.22	5.44	5.44	0.79542	.	0.108661	0.64402	D	0.000004	T	0.42585	0.1209	M	0.77486	2.375	0.80722	D	1	P;P;B	0.40144	0.458;0.704;0.319	B;B;B	0.36922	0.218;0.236;0.1	T	0.50759	-0.8790	10	0.62326	D	0.03	-10.9482	15.6519	0.77104	0.0:0.0:0.0:1.0	.	525;422;964	E9PIL6;D4QA03;Q9Y2K7	.;.;KDM2A_HUMAN	T	964;525;422	ENSP00000432786:I964T;ENSP00000435776:I525T;ENSP00000309302:I422T	ENSP00000309302:I422T	I	+	2	0	KDM2A	66776863	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.841000	0.86834	2.285000	0.76669	0.528000	0.53228	ATC	.	.		0.532	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308		C	67020287	T	C	67020287	3	2	91	1	0	0	0	0	1	0	0	0	8133	1435	50	2	2957	2	KDM2A	11	67020287	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	383894	67020287	67986229	396	12470										
P2RY2	5029	hgsc.bcm.edu	37	chr11	72945625	72945625	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcgtcttacgacctctgcgcTccctgcgctggggccgggcc	14	17	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:72945625T>C	ENST00000311131.2	+	3	888	c.421T>C	c.(421-423)Tcc>Ccc	p.S141P	P2RY2_ENST00000393596.2_Missense_Mutation_p.S141P|P2RY2_ENST00000393597.2_Missense_Mutation_p.S141P	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	141					cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	ACCTCTGCGCTCCCTGCGCTG	0.667																																					p.S141P		Atlas-SNP	.											.	P2RY2	54	.	0			c.T421C						.						62	59	60					11																	72945625		2200	4293	6493	SO:0001583	missense	5029	exon3			CTGCGCTCCCTGC	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.421T>C	chr11.hg19:g.72945625T>C	ENSP00000310305:p.Ser141Pro	41.0	0.0		74.0	4.0	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	hg19	CCDS8219.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.197562	0.58126	.	.	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.38722	1.12;1.12;1.12	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67683	0.2919	M	0.85041	2.73	0.50813	D	0.999899	D	0.71674	0.998	D	0.75484	0.986	T	0.73069	-0.4099	10	0.59425	D	0.04	.	14.5447	0.68020	0.0:0.0:0.0:1.0	.	141	P41231	P2RY2_HUMAN	P	141	ENSP00000377222:S141P;ENSP00000310305:S141P;ENSP00000377221:S141P	ENSP00000310305:S141P	S	+	1	0	P2RY2	72623273	0.845000	0.29573	0.882000	0.34594	0.912000	0.54170	2.238000	0.43070	2.039000	0.60335	0.533000	0.62120	TCC	.	.		0.667	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072		C	72945625	T	C	72945625	3	2	91	1	0	0	0	0	1	0	0	0	11361	1551	54	2	423	2	P2RY2	11	72945625	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	5925338	72945625	62060891	397	12471										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73824846	73824846	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccatctgtaattttactggAggcgagtcgaacaacctcag	9	10	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:73824846A>G	ENST00000334126.7	-	11	2048	c.1822T>C	c.(1822-1824)Tcc>Ccc	p.S608P	C2CD3_ENST00000313663.7_Missense_Mutation_p.S608P			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	608					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					ATTTTACTGGAGGCGAGTCGA	0.393																																					p.S608P		Atlas-SNP	.											.	C2CD3	288	.	0			c.T1822C						.						129	126	127					11																	73824846		2200	4293	6493	SO:0001583	missense	26005	exon11			TACTGGAGGCGAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1822T>C	chr11.hg19:g.73824846A>G	ENSP00000334379:p.Ser608Pro	90.0	0.0		76.0	5.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	A	23.6	4.431412	0.83776	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.19105	2.17;2.23	5.27	5.27	0.74061	C2 calcium-dependent membrane targeting (1);	0.062950	0.64402	D	0.000003	T	0.45558	0.1348	M	0.71581	2.175	0.39755	D	0.971948	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.50583	-0.8811	10	0.87932	D	0	-10.2501	13.4225	0.61007	1.0:0.0:0.0:0.0	.	608;608	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	P	608	ENSP00000334379:S608P;ENSP00000323339:S608P	ENSP00000323339:S608P	S	-	1	0	C2CD3	73502494	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.086000	0.76885	1.996000	0.58369	0.374000	0.22700	TCC	.	.		0.393	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		G	73824846	A	G	73824846	3	3	91	1	0	0	0	0	1	0	0	0	2156	304	11	2	4153	2	C2CD3	11	73824846	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	879221	73824846	61181670	398	12472										
DLG2	1740	hgsc.bcm.edu	37	chr11	83173062	83173062	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tacctgtaaaatattctccaAattcttgttctagcttaatt	3	8	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:83173062A>G	ENST00000532653.1	-	22	2737	c.2435T>C	c.(2434-2436)tTt>tCt	p.F812S	DLG2_ENST00000404783.3_Missense_Mutation_p.F308S|DLG2_ENST00000531015.1_Missense_Mutation_p.F797S|DLG2_ENST00000376104.2_Missense_Mutation_p.F935S|DLG2_ENST00000398309.2_Missense_Mutation_p.F830S|DLG2_ENST00000426717.2_Missense_Mutation_p.F294S|DLG2_ENST00000524982.1_Missense_Mutation_p.F826S|DLG2_ENST00000330014.6_Missense_Mutation_p.F751S|DLG2_ENST00000376106.3_Missense_Mutation_p.F294S|DLG2_ENST00000280241.8_Missense_Mutation_p.F869S|DLG2_ENST00000543673.1_Missense_Mutation_p.F935S|DLG2_ENST00000418306.2_Missense_Mutation_p.F709S|DLG2_ENST00000537455.1_Missense_Mutation_p.F580S			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	536					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				ATATTCTCCAAATTCTTGTTC	0.413																																					p.F935S		Atlas-SNP	.											.	DLG2	448	.	0			c.T2804C						.						153	146	148					11																	83173062		1867	4121	5988	SO:0001583	missense	1740	exon27			TCTCCAAATTCTT	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.2435T>C	chr11.hg19:g.83173062A>G	ENSP00000435849:p.Phe812Ser	552.0	0.0		496.0	53.0	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	hg19		.	.	.	.	.	.	.	.	.	.	A	22.3	4.272603	0.80580	.	.	ENSG00000150672	ENST00000398309;ENST00000426717;ENST00000376104;ENST00000418306;ENST00000543673;ENST00000280241;ENST00000404783;ENST00000330014;ENST00000537455;ENST00000376106;ENST00000524982;ENST00000532653;ENST00000546021;ENST00000531015	T;T;T;T;T;T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	5.01	5.01	0.66863	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.000000	0.64402	D	0.000001	T	0.67078	0.2855	M	0.72576	2.205	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.996;0.999;0.995;1.0;1.0;0.992	D;D;D;D;D;D;D;D	0.97110	1.0;0.997;0.978;0.995;0.967;0.999;0.999;0.977	T	0.68557	-0.5377	9	.	.	.	.	14.8932	0.70625	1.0:0.0:0.0:0.0	.	797;812;826;751;308;935;830;709	E9PIW2;B7Z2T4;E9PN83;B7Z264;B5MCC5;Q15700-2;Q15700;Q15700-3	.;.;.;.;.;.;DLG2_HUMAN;.	S	830;294;935;709;935;869;308;751;580;294;826;812;935;797	ENSP00000381355:F830S;ENSP00000393049:F294S;ENSP00000365272:F935S;ENSP00000402275:F709S;ENSP00000441994:F935S;ENSP00000280241:F869S;ENSP00000385113:F308S;ENSP00000381353:F751S;ENSP00000443248:F580S;ENSP00000365274:F294S;ENSP00000432894:F826S;ENSP00000435849:F812S;ENSP00000433848:F797S	.	F	-	2	0	DLG2	82850710	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.761000	0.91691	2.106000	0.64143	0.533000	0.62120	TTT	.	.		0.413	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		G	83173062	A	G	83173062	3	3	91	1	0	0	0	0	1	0	0	0	4557	14	1	2	131	2	DLG2	11	83173062	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	9348216	83173062	51833454	399	12473										
MED17	9440	hgsc.bcm.edu	37	chr11	93528080	93528080	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttcttgtctttcaggttcccCacattggcagacaaaattag	7	10	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:93528080C>T	ENST00000251871.3	+	6	1153	c.866C>T	c.(865-867)cCa>cTa	p.P289L	MED17_ENST00000533367.1_Intron|snoU13_ENST00000459243.1_RNA	NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	289					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			large_intestine(2)|lung(11)|ovary(1)	14		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TCAGGTTCCCCACATTGGCAG	0.338																																					p.P289L		Atlas-SNP	.											.	MED17	37	.	0			c.C866T						.						74	77	76					11																	93528080		2201	4297	6498	SO:0001583	missense	9440	exon6			GTTCCCCACATTG	AF104254	CCDS8295.1	11q21	2007-07-30	2007-07-30	2007-07-30	ENSG00000042429	ENSG00000042429			2375	protein-coding gene	gene with protein product		603810	"cofactor required for Sp1 transcriptional activation, subunit 6 (77kD)", "cofactor required for Sp1 transcriptional activation, subunit 6, 77kDa"	CRSP6		9989412, 10198638	Standard	NM_004268		Approved	CRSP77, TRAP80, DRIP80	uc001pem.4	Q9NVC6	OTTHUMG00000167497	ENST00000251871.3:c.866C>T	chr11.hg19:g.93528080C>T	ENSP00000251871:p.Pro289Leu	99.0	0.0		84.0	4.0	NM_004268	B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Missense_Mutation	SNP	ENST00000251871.3	hg19	CCDS8295.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.360129	0.41801	.	.	ENSG00000042429	ENST00000251871;ENST00000427225	T	0.52754	0.65	5.57	5.57	0.84162	.	0.048996	0.85682	D	0.000000	T	0.38214	0.1032	L	0.38175	1.15	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.12016	-1.0564	10	0.27082	T	0.32	-16.3463	13.7988	0.63188	0.0:0.9268:0.0:0.0732	.	289	Q9NVC6	MED17_HUMAN	L	289;259	ENSP00000251871:P289L	ENSP00000251871:P289L	P	+	2	0	MED17	93167728	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.665000	0.54532	2.639000	0.89480	0.655000	0.94253	CCA	.	.		0.338	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268		T	93528080	C	T	93528080	3	4	91	1	0	0	0	0	1	0	0	0	9444	594	21	3	888	3	MED17	11	93528080	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	10355018	93528080	41478436	400	12474										
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93844145	93844145	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cattgaactgtttgcagatcAcccagggacatggctgctac	10	11	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:93844145A>G	ENST00000315765.9	+	18	3130	c.3122A>G	c.(3121-3123)cAc>cGc	p.H1041R		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	1041	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TTTGCAGATCACCCAGGGACA	0.438																																					p.H1041R		Atlas-SNP	.											.	HEPHL1	144	.	0			c.A3122G						.						82	83	83					11																	93844145		2108	4251	6359	SO:0001583	missense	341208	exon18			CAGATCACCCAGG	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.3122A>G	chr11.hg19:g.93844145A>G	ENSP00000313699:p.His1041Arg	134.0	0.0		125.0	5.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	A	15.60	2.880444	0.51801	.	.	ENSG00000181333	ENST00000315765	D	0.99619	-6.28	5.97	5.97	0.96955	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.045878	0.85682	D	0.000000	D	0.98068	0.9363	N	0.21194	0.64	0.35325	D	0.785137	B	0.30542	0.284	B	0.27887	0.084	D	0.99975	1.2176	10	0.59425	D	0.04	0.0867	16.4566	0.84019	1.0:0.0:0.0:0.0	.	1041	Q6MZM0	HPHL1_HUMAN	R	1041	ENSP00000313699:H1041R	ENSP00000313699:H1041R	H	+	2	0	HEPHL1	93483793	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.865000	0.75500	2.291000	0.77112	0.533000	0.62120	CAC	.	.		0.438	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		G	93844145	A	G	93844145	3	3	91	1	0	0	0	0	1	0	0	0	7064	159	6	2	3192	2	HEPHL1	11	93844145	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	316065	93844145	41162371	401	12475										
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93845031	93845031	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagattaccagcaagtccagTcctgtgctctccccacggat	8	15	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:93845031T>C	ENST00000315765.9	+	20	3459	c.3451T>C	c.(3451-3453)Tcc>Ccc	p.S1151P		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	1151					copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				GCAAGTCCAGTCCTGTGCTCT	0.527																																					p.S1151P		Atlas-SNP	.											.	HEPHL1	144	.	0			c.T3451C						.						184	179	181					11																	93845031		2026	4192	6218	SO:0001583	missense	341208	exon20			GTCCAGTCCTGTG	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.3451T>C	chr11.hg19:g.93845031T>C	ENSP00000313699:p.Ser1151Pro	138.0	0.0		94.0	4.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.480697	0.44044	.	.	ENSG00000181333	ENST00000315765	D	0.99304	-5.72	5.45	1.38	0.22167	.	.	.	.	.	D	0.96405	0.8827	N	0.19112	0.55	0.28284	N	0.92386	P	0.37466	0.596	B	0.34991	0.193	D	0.93821	0.7119	9	0.54805	T	0.06	-4.5314	9.2422	0.37504	0.4762:0.0:0.0:0.5238	.	1151	Q6MZM0	HPHL1_HUMAN	P	1151	ENSP00000313699:S1151P	ENSP00000313699:S1151P	S	+	1	0	HEPHL1	93484679	0.993000	0.37304	1.000000	0.80357	0.873000	0.50193	0.141000	0.16076	0.311000	0.23014	0.459000	0.35465	TCC	.	.		0.527	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		C	93845031	T	C	93845031	3	2	91	1	0	0	0	0	1	0	0	0	7064	1667	58	2	3529	2	HEPHL1	11	93845031	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	886	93845031	41161485	402	12476										
EXPH5	23086	hgsc.bcm.edu	37	chr11	108398908	108398908	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggaggtcctgcatggccatcAcatctgtggaaataatttga	11	8	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:108398908A>G	ENST00000265843.4	-	4	557	c.447T>C	c.(445-447)tgT>tgC	p.C149C	EXPH5_ENST00000443411.1_Intron|EXPH5_ENST00000525344.1_Silent_p.C142C|EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Silent_p.C73C	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	149					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CATGGCCATCACATCTGTGGA	0.398																																					p.C149C		Atlas-SNP	.											.	EXPH5	193	.	0			c.T447C						.						88	86	86					11																	108398908		2201	4298	6499	SO:0001819	synonymous_variant	23086	exon4			GCCATCACATCTG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.447T>C	chr11.hg19:g.108398908A>G		84.0	0.0		66.0	4.0	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	hg19	CCDS8341.1																																																																																			.	.		0.398	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		G	108398908	A	G	108398908	2	3	91	1	0	0	0	0	0	0	0	1	5324	157	6	2		2	EXPH5	11	108398908	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	14553877	108398908	26607608	403	12477										
EXPH5	23086	hgsc.bcm.edu	37	chr11	108464205	108464205	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttccagcacctgaaggatcTtcctggcctcttcgtcattt	7	13	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:108464205T>C	ENST00000265843.4	-	1	169	c.59A>G	c.(58-60)aAg>aGg	p.K20R	EXPH5_ENST00000525344.1_Missense_Mutation_p.K13R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	20	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTGAAGGATCTTCCTGGCCTC	0.478																																					p.K20R		Atlas-SNP	.											.	EXPH5	193	.	0			c.A59G						.						120	116	117					11																	108464205		2201	4298	6499	SO:0001583	missense	23086	exon1			AGGATCTTCCTGG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.59A>G	chr11.hg19:g.108464205T>C	ENSP00000265843:p.Lys20Arg	202.0	0.0		199.0	8.0	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	hg19	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.062149	0.76187	.	.	ENSG00000110723	ENST00000265843;ENST00000525344	T;T	0.02631	4.22;4.24	5.22	2.73	0.32206	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);	0.440551	0.19410	N	0.114963	T	0.05823	0.0152	L	0.47716	1.5	0.80722	D	1	P	0.50156	0.932	P	0.51135	0.66	T	0.38286	-0.9668	10	0.48119	T	0.1	-6.9512	9.9736	0.41770	0.0:0.0:0.3285:0.6715	.	20	Q8NEV8	EXPH5_HUMAN	R	20;13	ENSP00000265843:K20R;ENSP00000432546:K13R	ENSP00000265843:K20R	K	-	2	0	EXPH5	107969415	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.278000	0.33179	0.257000	0.21650	0.379000	0.24179	AAG	.	.		0.478	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		C	108464205	T	C	108464205	3	2	91	1	0	0	0	0	1	0	0	0	5324	1609	56	2	5934	2	EXPH5	11	108464205	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	65297	108464205	26542311	404	12478										
NCAM1	4684	hgsc.bcm.edu	37	chr11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccctcccagccagcagattaCaatgctgccaaactaaggat					rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				RP11-629G13.1_ENST00000500537.2_RNA|NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000532002.1_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		1.0	1.0		32.0	32.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		-	112832363	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	112832332	6	5	91	0	1	1	0	1	0	0	0	0	10211	493	17	0		0	NCAM1	11	112832332	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	TCGA-DD-A119-01A-11D-A12Z-10	4368127	112832332	22174184	405	12479										
PAFAH1B2	5049	hgsc.bcm.edu	37	chr11	117031926	117031926	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	attgggggagatacaacaagAcatgttttgtggagactaaa	12	4	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:117031926A>G	ENST00000527958.1	+	4	396	c.237A>G	c.(235-237)agA>agG	p.R79R	PAFAH1B2_ENST00000419197.2_Silent_p.R79R|PAFAH1B2_ENST00000530272.1_Silent_p.R79R|PAFAH1B2_ENST00000526888.1_Intron|PAFAH1B2_ENST00000529887.2_Silent_p.R79R	NM_002572.3	NP_002563.1	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa)	79					brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|positive regulation of macroautophagy (GO:0016239)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)		ATACAACAAGACATGTTTTGT	0.348			T	IGH@	MLCLS																																p.R79R		Atlas-SNP	.		Dom	yes		11	11q23	5049	"platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa"		L	.	PAFAH1B2	19	.	0			c.A237G						.						112	117	115					11																	117031926		2201	4296	6497	SO:0001819	synonymous_variant	5049	exon4			AACAAGACATGTT	D63390	CCDS8380.1, CCDS53713.1, CCDS53714.1, CCDS53715.1	11q23	2011-10-24	2010-02-10			ENSG00000168092			8575	protein-coding gene	gene with protein product	"PAF-AH1b alpha 2 subunit"	602508	"platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa", "platelet-activating factor acetylhydrolase, isoform Ib, subunit 2 (30kDa)"			9144386, 9693049	Standard	NM_002572		Approved		uc001pqe.2	P68402		ENST00000527958.1:c.237A>G	chr11.hg19:g.117031926A>G		116.0	0.0		107.0	5.0	NM_001184747	A8DPS5|A8DPS6|A8DPS7|E9PEJ5|E9PLP3|O00687|Q29459|Q6IBR6	Silent	SNP	ENST00000527958.1	hg19	CCDS8380.1																																																																																			.	.		0.348	PAFAH1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392826.1	NM_002572		G	117031926	A	G	117031926	2	3	91	1	0	0	0	0	0	0	0	1	11394	272	10	2		2	PAFAH1B2	11	117031926	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4199594	117031926	17974590	406	12480										
CEP164	22897	hgsc.bcm.edu	37	chr11	117222658	117222658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taagaagaagaaaaaaaaaaAggaaaagaaagacaagaagg	10	1	0	6			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:117222658A>G	ENST00000278935.3	+	5	494	c.347A>G	c.(346-348)aAg>aGg	p.K116R		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	116	Interaction with ATRIP.|Lys-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		aaaaaaaaaaaggaaaagaaa	0.502																																					p.K116R		Atlas-SNP	.											CEP164,caecum,carcinoma,0,1	CEP164	121	.	0			c.A347G						.						33	34	34					11																	117222658		2201	4296	6497	SO:0001583	missense	22897	exon4			AAAAAAAGGAAAA	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.347A>G	chr11.hg19:g.117222658A>G	ENSP00000278935:p.Lys116Arg	76.0	1.0		73.0	3.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	hg19	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744661	0.49151	.	.	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000533570;ENST00000529538	T;T;T;T	0.76060	-0.34;-0.03;-0.29;-0.99	5.95	4.82	0.62117	.	0.243999	0.29172	N	0.012934	T	0.80221	0.4583	M	0.62723	1.935	0.34770	D	0.733632	D;P;B;D	0.56521	0.959;0.482;0.023;0.976	P;B;B;P	0.56960	0.65;0.11;0.01;0.81	D	0.85776	0.1358	10	0.62326	D	0.03	-27.2573	11.2799	0.49188	0.9276:0.0:0.0724:0.0	.	116;70;116;116	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	R	70;116;70;70;116;116	ENSP00000436034:K70R;ENSP00000278935:K116R;ENSP00000435759:K70R;ENSP00000431302:K116R	ENSP00000278935:K116R	K	+	2	0	CEP164	116727868	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.713000	0.91408	1.068000	0.40764	0.533000	0.62120	AAG	.	.		0.502	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		G	117222658	A	G	117222658	3	3	91	1	0	0	0	0	1	0	0	0	3251	72	3	2	357	2	CEP164	11	117222658	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	190732	117222658	17783858	407	12481										
HINFP	25988	hgsc.bcm.edu	37	chr11	119004976	119004976	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggagccaggacgtaaggaagAggaagaggagggcaagggta	20	4	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:119004976A>G	ENST00000350777.2	+	10	1385	c.1322A>G	c.(1321-1323)gAg>gGg	p.E441G	HINFP_ENST00000527410.1_3'UTR	NM_001243259.1|NM_015517.4|NM_198971.2	NP_001230188.1|NP_056332.2|NP_945322.1	Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	441	Interaction with NPAT.|Poly-Glu.				DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CGTAAGGAAGAGGAAGAGGAG	0.582											OREG0021397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E441G		Atlas-SNP	.											.	HINFP	50	.	0			c.A1322G						.						100	98	99					11																	119004976		2200	4295	6495	SO:0001583	missense	25988	exon11			AGGAAGAGGAAGA	AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273		"Zinc fingers, C2H2-type"	17850	protein-coding gene	gene with protein product	"histone nuclear factor P"	607099	"MBD2-interacting zinc finger 1", "MBD2-interacting zinc finger"	MIZF		11553631	Standard	NM_015517		Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000350777.2:c.1322A>G	chr11.hg19:g.119004976A>G	ENSP00000318085:p.Glu441Gly	118.0	0.0	1492	90.0	4.0	NM_015517	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	Missense_Mutation	SNP	ENST00000350777.2	hg19	CCDS8414.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.704586	0.48412	.	.	ENSG00000172273	ENST00000350777	T	0.10192	2.9	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000001	T	0.10723	0.0262	L	0.43152	1.355	0.80722	D	1	P	0.40970	0.734	B	0.37731	0.257	T	0.15093	-1.0449	10	0.29301	T	0.29	1.7937	13.32	0.60428	1.0:0.0:0.0:0.0	.	441	Q9BQA5	HINFP_HUMAN	G	441	ENSP00000318085:E441G	ENSP00000318085:E441G	E	+	2	0	HINFP	118510186	0.877000	0.30153	0.405000	0.26409	0.790000	0.44656	2.810000	0.47979	2.163000	0.67991	0.533000	0.62120	GAG	.	.		0.582	HINFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388201.2	NM_015517		G	119004976	A	G	119004976	3	3	91	1	0	0	0	0	1	0	0	0	7119	304	11	2	1356	2	HINFP	11	119004976	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1782318	119004976	16001540	408	12482										
TRIM29	23650	hgsc.bcm.edu	37	chr11	120007994	120007994	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tatgattcttgtgctcctggAacatgcaaaggtagcagatg	11	7	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:120007994A>G	ENST00000341846.5	-	1	1167	c.746T>C	c.(745-747)tTc>tCc	p.F249S		NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	249					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		GTGCTCCTGGAACATGCAAAG	0.607																																					p.F249S		Atlas-SNP	.											.	TRIM29	78	.	0			c.T746C						.						96	89	91					11																	120007994		2203	4300	6503	SO:0001583	missense	23650	exon1			TCCTGGAACATGC	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"Tripartite motif containing / Tripartite motif containing"	17274	protein-coding gene	gene with protein product	"tripartite motif protein TRIM29", "ataxia-telangiectasia group D-associated protein"	610658	"tripartite motif-containing 29"			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.746T>C	chr11.hg19:g.120007994A>G	ENSP00000343129:p.Phe249Ser	96.0	0.0		94.0	5.0	NM_012101	Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	hg19	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.013488	0.75161	.	.	ENSG00000137699	ENST00000341846	T	0.39997	1.05	5.91	4.77	0.60923	Zinc finger, B-box (3);	0.000000	0.85682	D	0.000000	T	0.39064	0.1064	N	0.03224	-0.385	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.41106	-0.9527	9	.	.	.	.	13.3279	0.60469	0.868:0.1319:0.0:0.0	.	249	Q14134	TRI29_HUMAN	S	249	ENSP00000343129:F249S	.	F	-	2	0	TRIM29	119513204	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.193000	0.72075	1.041000	0.40125	0.533000	0.62120	TTC	.	.		0.607	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101		G	120007994	A	G	120007994	3	3	91	1	0	0	0	0	1	0	0	0	16518	246	9	2	1056	2	TRIM29	11	120007994	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1003018	120007994	14998522	409	12483										
OAF	220323	hgsc.bcm.edu	37	chr11	120096467	120096467	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacccagctgcagcacaatgAgatcatccccagtgaggcca	9	15	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:120096467A>G	ENST00000328965.4	+	2	842	c.329A>G	c.(328-330)gAg>gGg	p.E110G	OAF_ENST00000531220.1_5'UTR	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	110						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(5)	6		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		CAGCACAATGAGATCATCCCC	0.647																																					p.E110G		Atlas-SNP	.											.	OAF	12	.	0			c.A329G						.						127	122	124					11																	120096467		2203	4300	6503	SO:0001583	missense	220323	exon2			ACAATGAGATCAT	BC047726	CCDS8430.1	11q23.3	2010-11-23			ENSG00000184232	ENSG00000184232			28752	protein-coding gene	gene with protein product						12477932	Standard	NM_178507		Approved	MGC52117	uc001pxb.3	Q86UD1	OTTHUMG00000166139	ENST00000328965.4:c.329A>G	chr11.hg19:g.120096467A>G	ENSP00000332613:p.Glu110Gly	62.0	0.0		70.0	4.0	NM_178507		Missense_Mutation	SNP	ENST00000328965.4	hg19	CCDS8430.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.904200	0.92035	.	.	ENSG00000184232	ENST00000328965	T	0.37584	1.19	4.96	4.96	0.65561	.	0.116380	0.56097	D	0.000025	T	0.53626	0.1808	M	0.72118	2.19	0.80722	D	1	D	0.63046	0.992	P	0.57101	0.813	T	0.59778	-0.7390	10	0.72032	D	0.01	-21.2797	14.6307	0.68653	1.0:0.0:0.0:0.0	.	110	Q86UD1	OAF_HUMAN	G	110	ENSP00000332613:E110G	ENSP00000332613:E110G	E	+	2	0	OAF	119601677	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.629000	0.90983	1.852000	0.53769	0.459000	0.35465	GAG	.	.		0.647	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507		G	120096467	A	G	120096467	3	3	91	1	0	0	0	0	1	0	0	0	10807	304	11	2	335	2	OAF	11	120096467	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	88473	120096467	14910049	410	12484										
OR8B4	283162	hgsc.bcm.edu	37	chr11	124294157	124294157	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgctggatagcatggtgattActccaacaacaatgaaaaat	8	7	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:124294157A>T	ENST00000356130.3	-	1	632	c.611T>A	c.(610-612)gTa>gAa	p.V204E		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CATGGTGATTACTCCAACAAC	0.468																																					p.V204E		Atlas-SNP	.											.	OR8B4	60	.	0			c.T611A						.						84	67	73					11																	124294157		2201	4299	6500	SO:0001583	missense	283162	exon1			GTGATTACTCCAA	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"GPCR / Class A : Olfactory receptors"	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.611T>A	chr11.hg19:g.124294157A>T	ENSP00000348449:p.Val204Glu	126.0	0.0		112.0	6.0	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	hg19	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	a	5.455	0.269109	0.10349	.	.	ENSG00000198657	ENST00000356130	T	0.40225	1.04	4.02	0.421	0.16451	GPCR, rhodopsin-like superfamily (1);	1.353600	0.05172	N	0.499731	T	0.44973	0.1319	M	0.78801	2.425	0.09310	N	1	B	0.29671	0.254	B	0.31337	0.128	T	0.44360	-0.9333	10	0.87932	D	0	.	4.6979	0.12813	0.6613:0.1626:0.1761:0.0	.	204	Q96RC9	OR8B4_HUMAN	E	204	ENSP00000348449:V204E	ENSP00000348449:V204E	V	-	2	0	OR8B4	123799367	0.000000	0.05858	0.002000	0.10522	0.023000	0.10783	0.406000	0.21032	0.065000	0.16485	0.529000	0.55759	GTA	.	.		0.468	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196		T	124294157	A	T	124294157	3	4	91	1	0	0	0	0	1	0	0	0	11238	391	14	4	320	4	OR8B4	11	124294157	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4197690	124294157	10712359	411	12485										
ROBO4	54538	hgsc.bcm.edu	37	chr11	124764172	124764172	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agccacttgcacgcagtaggAgcctggcatatgggtggcga	15	10	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:124764172A>G	ENST00000306534.3	-	8	1728	c.1243T>C	c.(1243-1245)Tcc>Ccc	p.S415P	ROBO4_ENST00000526899.1_5'Flank|ROBO4_ENST00000533054.1_Missense_Mutation_p.S270P	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	415	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.S415A(1)		NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		ACGCAGTAGGAGCCTGGCATA	0.607																																					p.S415P		Atlas-SNP	.											ROBO4,colon,carcinoma,0,1	ROBO4	130	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1243C						.						105	83	91					11																	124764172		2201	4299	6500	SO:0001583	missense	54538	exon8			AGTAGGAGCCTGG	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.1243T>C	chr11.hg19:g.124764172A>G	ENSP00000304945:p.Ser415Pro	132.0	0.0		109.0	5.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	hg19	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.451082	0.63290	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.58652	0.32;0.32	4.93	4.93	0.64822	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.227101	0.22905	N	0.054205	T	0.69486	0.3116	M	0.65975	2.015	0.33960	D	0.645526	D;D	0.71674	0.993;0.998	P;D	0.64321	0.801;0.924	T	0.77275	-0.2648	10	0.39692	T	0.17	.	10.9978	0.47587	1.0:0.0:0.0:0.0	.	305;415	Q8WZ75-3;Q8WZ75	.;ROBO4_HUMAN	P	415;305;270	ENSP00000304945:S415P;ENSP00000437129:S270P	ENSP00000304945:S415P	S	-	1	0	ROBO4	124269382	0.999000	0.42202	0.999000	0.59377	0.848000	0.48234	1.518000	0.35877	1.851000	0.53745	0.533000	0.62120	TCC	.	.		0.607	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		G	124764172	A	G	124764172	3	3	91	1	0	0	0	0	1	0	0	0	13531	304	11	2	1824	2	ROBO4	11	124764172	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	470015	124764172	10242344	412	12486										
NFRKB	4798	hgsc.bcm.edu	37	chr11	129752348	129752348	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctctgttgctcacttactcTtccttgatagcaggaattgc	7	11	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:129752348T>C	ENST00000446488.3	-	9	1183	c.1080A>G	c.(1078-1080)gaA>gaG	p.E360E	NFRKB_ENST00000524746.1_Silent_p.E360E|NFRKB_ENST00000304521.5_Silent_p.E360E|NFRKB_ENST00000524794.1_Silent_p.E385E	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	360					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		TCACTTACTCTTCCTTGATAG	0.547																																					p.E385E		Atlas-SNP	.											.	NFRKB	101	.	0			c.A1155G						.						122	125	124					11																	129752348		2201	4297	6498	SO:0001819	synonymous_variant	4798	exon8			TTACTCTTCCTTG		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"INO80 complex subunits"	7802	protein-coding gene	gene with protein product	"nuclear factor related to kappa B binding protein", "DNA-binding protein R kappa B", "INO80 complex subunit G"	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.1080A>G	chr11.hg19:g.129752348T>C		96.0	0.0		120.0	6.0	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	hg19	CCDS44770.1																																																																																			.	.		0.547	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		C	129752348	T	C	129752348	2	2	91	1	0	0	0	0	0	0	0	1	10393	1606	56	2		2	NFRKB	11	129752348	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4988176	129752348	5254168	413	12487										
SLC6A13	6540	hgsc.bcm.edu	37	chr12	352865	352865	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctcaaagatggggcagatcTtcctccaggctgtgacgcct	11	13	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:352865T>C	ENST00000343164.4	-	3	369	c.317A>G	c.(316-318)aAg>aGg	p.K106R	SLC6A13_ENST00000445055.2_Intron	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	106					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GGGGCAGATCTTCCTCCAGGC	0.502																																					p.K106R		Atlas-SNP	.											.	SLC6A13	62	.	0			c.A317G						.						118	97	104					12																	352865		2203	4300	6503	SO:0001583	missense	6540	exon3			CAGATCTTCCTCC	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.317A>G	chr12.hg19:g.352865T>C	ENSP00000339260:p.Lys106Arg	134.0	0.0		114.0	5.0	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	hg19	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	T	14.86	2.662792	0.47572	.	.	ENSG00000010379	ENST00000313154;ENST00000343164	T	0.74632	-0.86	6.17	3.78	0.43462	.	0.239426	0.49305	N	0.000154	T	0.61160	0.2325	N	0.20986	0.625	0.80722	D	1	B;B	0.19583	0.037;0.015	B;B	0.32289	0.143;0.143	T	0.50617	-0.8807	10	0.30078	T	0.28	.	8.5203	0.33270	0.0:0.2629:0.0:0.7371	.	85;106	B4DJS3;Q9NSD5	.;S6A13_HUMAN	R	85;106	ENSP00000339260:K106R	ENSP00000318097:K85R	K	-	2	0	SLC6A13	223126	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.245000	0.32790	0.539000	0.28788	0.533000	0.62120	AAG	.	.		0.502	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		C	352865	T	C	352865	3	2	91	1	0	0	0	0	1	0	0	0	14691	1609	56	2	1543	2	SLC6A13	12	352865	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10		352865	133499030	414	12488										
EFCAB4B	84766	hgsc.bcm.edu	37	chr12	3788250	3788250	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctgacttgggttattctggcTgaagaagaagtgacctgggg	15	6	1	5			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:3788250T>C	ENST00000252322.1	-	6	823	c.355A>G	c.(355-357)Agc>Ggc	p.S119G	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.S119G|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.S119G	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		119	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TTATTCTGGCTGAAGAAGAAG	0.532																																					p.S119G		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.A355G						.						115	99	104					12																	3788250		2203	4300	6503	SO:0001583	missense	84766	exon6			TCTGGCTGAAGAA																												ENST00000252322.1:c.355A>G	chr12.hg19:g.3788250T>C	ENSP00000252322:p.Ser119Gly	130.0	0.0		69.0	4.0	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	hg19	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490302	0.26686	.	.	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.24350	1.86;1.86;1.86	4.76	3.6	0.41247	EF-hand-like domain (1);	0.102697	0.64402	D	0.000001	T	0.13884	0.0336	N	0.24115	0.695	0.26995	N	0.96505	B;B;B	0.13145	0.003;0.0;0.007	B;B;B	0.10450	0.003;0.001;0.005	T	0.30179	-0.9987	10	0.12430	T	0.62	-14.8863	7.2263	0.26018	0.0:0.1036:0.0:0.8964	.	119;119;119	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	G	119	ENSP00000409382:S119G;ENSP00000412496:S119G;ENSP00000252322:S119G	ENSP00000252322:S119G	S	-	1	0	EFCAB4B	3658511	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.128000	0.31369	0.660000	0.30964	0.459000	0.35465	AGC	.	.		0.532	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1			C	3788250	T	C	3788250	3	2	91	1	0	0	0	0	1	0	0	0	4939	1580	55	2	2092	2	EFCAB4B	12	3788250	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3435385	3788250	130063645	415	12489										
PARP11	57097	hgsc.bcm.edu	37	chr12	3931065	3931065	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aagaactcccacaaatctagGttttgaattctctgaattct	5	9	3	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:3931065G>A	ENST00000228820.4	-	6	666	c.522C>T	c.(520-522)aaC>aaT	p.N174N	PARP11_ENST00000397096.2_Silent_p.N167N|PARP11_ENST00000447133.3_Silent_p.N93N|PARP11_ENST00000476985.1_5'UTR|PARP11_ENST00000427057.2_Silent_p.N93N	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	167	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.						NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	17			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			ACAAATCTAGGTTTTGAATTC	0.338																																					p.N174N		Atlas-SNP	.											.	PARP11	39	.	0			c.C522T						.						73	79	77					12																	3931065		2202	4300	6502	SO:0001819	synonymous_variant	57097	exon6			ATCTAGGTTTTGA	AF263540	CCDS8523.2, CCDS66281.1	12p13.3	2014-01-28	2004-08-25	2004-08-26	ENSG00000111224	ENSG00000111224		"Poly (ADP-ribose) polymerases"	1186	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 6"	C12orf6		15273990	Standard	NM_001286522		Approved		uc001qml.2	Q9NR21	OTTHUMG00000156442	ENST00000228820.4:c.522C>T	chr12.hg19:g.3931065G>A		119.0	0.0		90.0	4.0	NM_020367	B4DRQ0|Q68DS1|Q8N5Y9	Silent	SNP	ENST00000228820.4	hg19	CCDS8523.2																																																																																			.	.		0.338	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1			A	3931065	G	A	3931065	2	1	91	1	0	0	0	0	0	0	0	1	11465	1252	44	3		3	PARP11	12	3931065	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	142815	3931065	129920830	416	12490										
FGF6	2251	hgsc.bcm.edu	37	chr12	4553334	4553334	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcctttactgttcatggcaaCgaagagggcacttctcactc	8	12	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:4553334C>T	ENST00000228837.2	-	2	458	c.415G>A	c.(415-417)Gtt>Att	p.V139I		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	139					angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)	p.V139I(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			TTCATGGCAACGAAGAGGGCA	0.512																																					p.V139I		Atlas-SNP	.											FGF6,NS,carcinoma,0,1	FGF6	40	.	1	Substitution - Missense(1)	prostate(1)	c.G415A						.						106	81	89					12																	4553334		2203	4300	6503	SO:0001583	missense	2251	exon2			TGGCAACGAAGAG	X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"Endogenous ligands"	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.415G>A	chr12.hg19:g.4553334C>T	ENSP00000228837:p.Val139Ile	103.0	0.0		95.0	24.0	NM_020996	Q0VAE1	Missense_Mutation	SNP	ENST00000228837.2	hg19	CCDS8527.1	.	.	.	.	.	.	.	.	.	.	c	8.440	0.850726	0.17034	.	.	ENSG00000111241	ENST00000543077;ENST00000228837	D;T	0.85861	-2.04;1.5	5.63	-3.46	0.04767	.	0.271169	0.41605	N	0.000859	T	0.77198	0.4095	L	0.43923	1.385	0.40032	D	0.975543	B	0.13594	0.008	B	0.17433	0.018	T	0.55786	-0.8086	10	0.42905	T	0.14	.	13.631	0.62196	0.0:0.4678:0.0:0.5322	.	139	P10767	FGF6_HUMAN	I	18;139	ENSP00000445479:V18I;ENSP00000228837:V139I	ENSP00000228837:V139I	V	-	1	0	FGF6	4423595	0.002000	0.14202	0.017000	0.16124	0.633000	0.38033	-1.160000	0.03147	-1.177000	0.02744	-2.144000	0.00337	GTT	.	.		0.512	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996		T	4553334	C	T	4553334	3	4	91	1	0	0	0	0	1	0	0	0	5864	536	19	1	219	1	FGF6	12	4553334	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	622269	4553334	129298561	417	12491										
APOBEC1	339	hgsc.bcm.edu	37	chr12	7805229	7805229	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggacaagaaccaggtgatggAgcagctcatggatgggtgaa	16	6	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:7805229A>G	ENST00000229304.4	-	3	267	c.247T>C	c.(247-249)Tcc>Ccc	p.S83P		NM_001644.3	NP_001635.2	P41238	ABEC1_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	83				S -> T (in Ref. 5; AAD10701). {ECO:0000305}.	cellular response to insulin stimulus (GO:0032869)|cytidine deamination (GO:0009972)|cytidine to uridine editing (GO:0016554)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|gene expression (GO:0010467)|lipid metabolic process (GO:0006629)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein transport (GO:0042953)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to osmotic stress (GO:0006970)|response to zinc ion (GO:0010043)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	AU-rich element binding (GO:0017091)|cytidine deaminase activity (GO:0004126)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|stomach(1)	17						CAGGTGATGGAGCAGCTCATG	0.468																																					p.S83P	Pancreas(135;929 1826 4531 10527 41012)	Atlas-SNP	.											.	APOBEC1	43	.	0			c.T247C						.						48	47	47					12																	7805229		2203	4300	6503	SO:0001583	missense	339	exon3			TGATGGAGCAGCT	U72891	CCDS8579.1	12p13.1	2007-02-01			ENSG00000111701	ENSG00000111701		"Apolipoprotein B mRNA editing enzymes"	604	protein-coding gene	gene with protein product		600130					Standard	XM_005253355		Approved	BEDP, CDAR1, APOBEC-1, HEPR	uc001qtb.3	P41238	OTTHUMG00000141288	ENST00000229304.4:c.247T>C	chr12.hg19:g.7805229A>G	ENSP00000229304:p.Ser83Pro	94.0	0.0		64.0	4.0	NM_001644	Q9UE64|Q9UM71	Missense_Mutation	SNP	ENST00000229304.4	hg19	CCDS8579.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.237759	0.58886	.	.	ENSG00000111701	ENST00000229304	T	0.66460	-0.21	4.48	3.23	0.37069	APOBEC-like, N-terminal (1);APOBEC/CMP deaminase, zinc-binding (1);	0.236214	0.30528	N	0.009438	T	0.76478	0.3993	M	0.79805	2.47	0.27360	N	0.955992	D	0.65815	0.995	D	0.63283	0.913	T	0.66952	-0.5793	10	0.51188	T	0.08	-13.8594	6.849	0.24005	0.7934:0.0:0.0:0.2066	.	83	P41238	ABEC1_HUMAN	P	83	ENSP00000229304:S83P	ENSP00000229304:S83P	S	-	1	0	APOBEC1	7696496	1.000000	0.71417	0.999000	0.59377	0.886000	0.51366	0.820000	0.27323	1.805000	0.52779	0.379000	0.24179	TCC	.	.		0.468	APOBEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280523.1	NM_001644		G	7805229	A	G	7805229	3	3	91	1	0	0	0	0	1	0	0	0	787	304	11	2	475	2	APOBEC1	12	7805229	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3251895	7805229	126046666	418	12492										
FOXJ2	55810	hgsc.bcm.edu	37	chr12	8202064	8202064	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacttccttactcagactggTcacgtgccccctcaaggggg	10	15	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:8202064T>C	ENST00000162391.3	+	9	2579	c.1434T>C	c.(1432-1434)ggT>ggC	p.G478G	FOXJ2_ENST00000428177.2_Silent_p.G478G	NM_018416.2	NP_060886.1	Q9P0K8	FOXJ2_HUMAN	forkhead box J2	478					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	16				Kidney(36;0.0944)		CTCAGACTGGTCACGTGCCCC	0.592																																					p.G478G		Atlas-SNP	.											.	FOXJ2	43	.	0			c.T1434C						.						141	105	117					12																	8202064		2203	4300	6503	SO:0001819	synonymous_variant	55810	exon9			GACTGGTCACGTG	AF155132	CCDS8587.1	12p13.31	2006-12-15				ENSG00000065970		"Forkhead boxes"	24818	protein-coding gene	gene with protein product						10777590, 10966786	Standard	NM_018416		Approved	FHX	uc001qtu.3	Q9P0K8		ENST00000162391.3:c.1434T>C	chr12.hg19:g.8202064T>C		81.0	0.0		70.0	4.0	NM_018416	A0AVK4|B2RMP3|Q96PS9|Q9NSN5	Silent	SNP	ENST00000162391.3	hg19	CCDS8587.1																																																																																			.	.		0.592	FOXJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400088.1	NM_018416		C	8202064	T	C	8202064	2	2	91	1	0	0	0	0	0	0	0	1	6020	1654	58	2		2	FOXJ2	12	8202064	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	396835	8202064	125649831	419	12493										
C3AR1	719	hgsc.bcm.edu	37	chr12	8212440	8212440	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagcgatccaggctaatggcAgtaagcaggaagacactggc	13	10	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:8212440A>G	ENST00000307637.4	-	2	545	c.342T>C	c.(340-342)acT>acC	p.T114T		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	114					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		GGCTAATGGCAGTAAGCAGGA	0.517																																					p.T114T		Atlas-SNP	.											.	C3AR1	61	.	0			c.T342C						.						182	148	160					12																	8212440		2203	4300	6503	SO:0001819	synonymous_variant	719	exon2			AATGGCAGTAAGC	U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"Complement system", "GPCR / Class A : Complement component receptors"	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.342T>C	chr12.hg19:g.8212440A>G		162.0	0.0		81.0	4.0	NM_004054	O43771|Q92868	Silent	SNP	ENST00000307637.4	hg19	CCDS8588.1																																																																																			.	.		0.517	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1			G	8212440	A	G	8212440	2	3	91	1	0	0	0	0	0	0	0	1	2207	175	7	2		2	C3AR1	12	8212440	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	10376	8212440	125639455	420	12494										
PZP	5858	hgsc.bcm.edu	37	chr12	9318676	9318676	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caccaactcccagatccaagTctcaggaaaatagcttcgca	6	14	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:9318676T>C	ENST00000261336.2	-	18	2258	c.2230A>G	c.(2230-2232)Act>Gct	p.T744A	PZP_ENST00000381997.2_Missense_Mutation_p.T613A|PZP_ENST00000539983.1_5'UTR	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	744					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CAGATCCAAGTCTCAGGAAAA	0.428																																					p.T744A	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A2230G						.						152	142	146					12																	9318676		2203	4300	6503	SO:0001583	missense	5858	exon18			TCCAAGTCTCAGG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2230A>G	chr12.hg19:g.9318676T>C	ENSP00000261336:p.Thr744Ala	135.0	0.0		89.0	5.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	19.39	3.818181	0.71028	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.29655	1.56;1.56	3.85	3.85	0.44370	Alpha-2-macroglobulin (1);	0.094329	0.44285	U	0.000465	T	0.56217	0.1970	M	0.87381	2.88	0.26229	N	0.979042	D;D;D	0.67145	0.976;0.996;0.995	D;D;D	0.68621	0.912;0.959;0.946	T	0.52653	-0.8547	10	0.62326	D	0.03	.	10.6921	0.45877	0.0:0.0:0.0:1.0	.	744;613;744	B2R950;P20742-2;P20742	.;.;PZP_HUMAN	A	744;613	ENSP00000261336:T744A;ENSP00000371427:T613A	ENSP00000261336:T744A	T	-	1	0	PZP	9209943	1.000000	0.71417	1.000000	0.80357	0.664000	0.39144	4.955000	0.63638	1.707000	0.51288	0.383000	0.25322	ACT	.	.		0.428	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		C	9318676	T	C	9318676	3	2	91	1	0	0	0	0	1	0	0	0	12884	1667	58	2	2294	2	PZP	12	9318676	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1106236	9318676	124533219	421	12495										
KLRF1	51348	hgsc.bcm.edu	37	chr12	9994450	9994450	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caaataccaagggaagtgttGttattggttctctaatgaga	10	5	1	1	rs3052097|rs111928232		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:9994450G>A	ENST00000279544.3	+	4	441	c.377G>A	c.(376-378)tGt>tAt	p.C126Y	KLRF1_ENST00000354855.3_Intron|KLRF1_ENST00000324214.4_Missense_Mutation_p.C76Y|KLRF1_ENST00000537723.1_Intron	NM_016523.1	NP_057607	Q9NZS2	KLRF1_HUMAN	killer cell lectin-like receptor subfamily F, member 1	126	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|MHC class I receptor activity (GO:0032393)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)	13						GGGAAGTGTTGTTATTGGTTC	0.323																																					p.C126Y		Atlas-SNP	.											.	KLRF1	27	.	0			c.G377A						.						142	134	136					12																	9994450		1842	4083	5925	SO:0001583	missense	51348	exon4			AGTGTTGTTATTG	AF175206	CCDS41750.1	12p13.31	2011-08-30			ENSG00000150045	ENSG00000150045		"Killer cell lectin-like receptors", "C-type lectin domain containing"	13342	protein-coding gene	gene with protein product		605029				10671213	Standard	NM_001291823		Approved	CLEC5C, NKp80	uc021qux.1	Q9NZS2		ENST00000279544.3:c.377G>A	chr12.hg19:g.9994450G>A	ENSP00000279544:p.Cys126Tyr	230.0	0.0		221.0	13.0	NM_016523	Q4KMT5|Q96PR2|Q96PR3|Q9NZS1	Missense_Mutation	SNP	ENST00000279544.3	hg19	CCDS41750.1	.	.	.	.	.	.	.	.	.	.	-	4.237	0.042890	0.08196	.	.	ENSG00000150045	ENST00000324214;ENST00000279544	T;T	0.38401	1.14;1.14	.	.	.	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	.	.	.	.	T	0.62708	0.2450	M	0.91090	3.175	0.80722	D	1	D;D	0.89917	1.0;0.988	D;D	0.87578	0.998;0.983	T	0.65162	-0.6235	6	.	.	.	.	.	.	.	.	126;76	Q9NZS2;Q9NZS2-2	KLRF1_HUMAN;.	Y	76;126	ENSP00000322487:C76Y;ENSP00000279544:C126Y	.	C	+	2	0	KLRF1	9885717	1.000000	0.71417	0.998000	0.56505	0.846000	0.48090	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	TGT	.	G|0.500;A|0.500		0.323	KLRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399535.1	NM_016523		A	9994450	G	A	9994450	3	1	91	1	0	0	0	0	1	0	0	0	8429	1377	48	3	391	3	KLRF1	12	9994450	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	675774	9994450	123857445	422	12496										
LRP6	4040	hgsc.bcm.edu	37	chr12	12279675	12279675	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtggcacataaccaagaggcAcagaagctggtccatgaact	11	10	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:12279675A>G	ENST00000261349.4	-	20	4338	c.4262T>C	c.(4261-4263)gTg>gCg	p.V1421A	LRP6_ENST00000540415.1_Intron|LRP6_ENST00000543091.1_Missense_Mutation_p.V1376A|BCL2L14_ENST00000396369.1_Intron	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1421					anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				ACCAAGAGGCACAGAAGCTGG	0.458																																					p.V1421A		Atlas-SNP	.											.	LRP6	170	.	0			c.T4262C						.						197	160	173					12																	12279675		2203	4300	6503	SO:0001583	missense	4040	exon20			AGAGGCACAGAAG	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.4262T>C	chr12.hg19:g.12279675A>G	ENSP00000261349:p.Val1421Ala	132.0	0.0		106.0	5.0	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813240	0.50527	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	T;T	0.36520	1.25;1.25	5.7	5.7	0.88788	.	0.000000	0.53938	D	0.000042	T	0.50463	0.1617	L	0.50333	1.59	0.80722	D	1	D;D	0.65815	0.99;0.995	D;D	0.73380	0.98;0.917	T	0.40887	-0.9539	10	0.08179	T	0.78	.	15.96	0.79923	1.0:0.0:0.0:0.0	.	1376;1421	F5H7J9;O75581	.;LRP6_HUMAN	A	1421;1376	ENSP00000261349:V1421A;ENSP00000442472:V1376A	ENSP00000261349:V1421A	V	-	2	0	LRP6	12170942	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.923000	0.92808	2.165000	0.68154	0.460000	0.39030	GTG	.	.		0.458	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			G	12279675	A	G	12279675	3	3	91	1	0	0	0	0	1	0	0	0	8971	159	6	2	595	2	LRP6	12	12279675	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2285225	12279675	121572220	423	12497										
PTPRO	5800	hgsc.bcm.edu	37	chr12	15704607	15704607	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agcatctgcagatggctaggTaagttaagttttactaatat	9	5	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:15704607T>C	ENST00000281171.4	+	15	2888		c.e15+2		PTPRO_ENST00000445537.2_Splice_Site|PTPRO_ENST00000544244.1_Splice_Site|PTPRO_ENST00000348962.2_Splice_Site|PTPRO_ENST00000442921.2_Splice_Site|PTPRO_ENST00000542557.1_Splice_Site	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O						axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				GATGGCTAGGTAAGTTAAGTT	0.353																																					.		Atlas-SNP	.											.	PTPRO	148	.	0			c.2558+2T>C						.						133	119	124					12																	15704607		2203	4300	6503	SO:0001630	splice_region_variant	5800	exon15			GCTAGGTAAGTTA	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9678	protein-coding gene	gene with protein product	"osteoclastic transmembrane protein-tyrosine phosphatase"	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.2558+2T>C	chr12.hg19:g.15704607T>C		128.0	0.0		84.0	4.0	NM_030667	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Splice_Site	SNP	ENST00000281171.4	hg19	CCDS8675.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.946854	0.53186	.	.	ENSG00000151490	ENST00000281171;ENST00000348962;ENST00000442921;ENST00000542557;ENST00000445537;ENST00000544244	.	.	.	5.03	3.85	0.44370	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9622	0.53015	0.0:0.0:0.1452:0.8548	.	.	.	.	.	-1	.	.	.	+	.	.	PTPRO	15595874	1.000000	0.71417	0.919000	0.36401	0.776000	0.43924	6.961000	0.76042	0.892000	0.36259	0.421000	0.28195	.	.	.		0.353	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1		Intron	C	15704607	T	C	15704607	5	2	91	1	0	0	0	0	0	0	1	0	12824	1652	57	2	2618	2	PTPRO	12	15704607	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3424932	15704607	118147288	424	12498										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19410367	19410367	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catgctctttttctatttagActtcacgagcttcaaaaaaa	4	9	4	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:19410367A>G	ENST00000299275.6	+	6	439	c.433A>G	c.(433-435)Act>Gct	p.T145A	PLEKHA5_ENST00000424268.1_Splice_Site_p.T37A|PLEKHA5_ENST00000355397.3_Splice_Site_p.T145A|PLEKHA5_ENST00000309364.4_Splice_Site_p.T145A|PLEKHA5_ENST00000429027.2_Splice_Site_p.T145A|PLEKHA5_ENST00000539256.1_5'UTR|PLEKHA5_ENST00000317589.4_Splice_Site_p.T145A|PLEKHA5_ENST00000359180.3_Splice_Site_p.T145A|PLEKHA5_ENST00000543806.1_Splice_Site_p.T37A|PLEKHA5_ENST00000538714.1_Splice_Site_p.T145A	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	145					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					TTCTATTTAGACTTCACGAGC	0.333																																					p.T145A	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A433G						.						69	77	74					12																	19410367		2203	4298	6501	SO:0001630	splice_region_variant	54477	exon6			ATTTAGACTTCAC	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.433-1A>G	chr12.hg19:g.19410367A>G		84.0	0.0		79.0	4.0	NM_001143821	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	3.063	-0.192906	0.06259	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000309364;ENST00000412219;ENST00000429027;ENST00000299275;ENST00000538714;ENST00000538305;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T;T	0.12039	2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72	4.93	2.43	0.29744	.	0.322311	0.33670	N	0.004672	T	0.03651	0.0104	N	0.00926	-1.1	0.80722	D	1	B;B;B;B;B;P	0.35575	0.114;0.162;0.101;0.036;0.044;0.51	B;B;B;B;B;B	0.36567	0.078;0.075;0.034;0.006;0.012;0.228	T	0.45891	-0.9230	9	.	.	.	-11.6171	6.2473	0.20825	0.7043:0.0:0.0793:0.2164	.	145;37;37;145;145;145	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;Q9HAU0;Q9HAU0-2	.;.;.;.;PKHA5_HUMAN;.	A	145;145;145;145;145;145;145;145;145;37;37;37;37	ENSP00000325155:T145A;ENSP00000347560:T145A;ENSP00000352104:T145A;ENSP00000311239:T145A;ENSP00000404296:T145A;ENSP00000299275:T145A;ENSP00000439673:T145A;ENSP00000446308:T37A;ENSP00000400411:T37A;ENSP00000439837:T37A;ENSP00000440371:T37A	.	T	+	1	0	PLEKHA5	19301634	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	3.219000	0.51200	0.910000	0.36722	-0.256000	0.11100	ACT	.	.		0.333	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	Missense_Mutation	G	19410367	A	G	19410367	5	3	91	1	0	0	0	0	0	0	1	0	12068	289	10	2	455	2	PLEKHA5	12	19410367	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3705760	19410367	114441528	425	12499										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19499936	19499936	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tacaatctttaggaagaggaAgtagtcccacctcgtcctcc	8	12	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:19499936A>G	ENST00000299275.6	+	18	2406				PLEKHA5_ENST00000424268.1_Silent_p.E729E|PLEKHA5_ENST00000355397.3_Intron|PLEKHA5_ENST00000429027.2_Silent_p.E906E|PLEKHA5_ENST00000539256.1_Intron|PLEKHA5_ENST00000317589.4_Silent_p.E803E|PLEKHA5_ENST00000359180.3_Intron|PLEKHA5_ENST00000543806.1_Silent_p.E722E|PLEKHA5_ENST00000538714.1_Intron	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5						reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					AGGAAGAGGAAGTAGTCCCAC	0.418																																					p.E906E	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A2718G						.						60	54	56					12																	19499936		692	1591	2283	SO:0001627	intron_variant	54477	exon24			AGAGGAAGTAGTC	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2400+1114A>G	chr12.hg19:g.19499936A>G		128.0	0.0		78.0	4.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Silent	SNP	ENST00000299275.6	hg19	CCDS8682.1																																																																																			.	.		0.418	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		G	19499936	A	G	19499936	1	3	91	0	1	0	0	0	0	0	0	0	12068	69	3	2		2	PLEKHA5	12	19499936	Intron	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	89569	19499936	114351959	426	12500										
MED21	9412	hgsc.bcm.edu	37	chr12	27181241	27181241	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctagcttgtataagctagaAgaagaaaaccatgaagctgc	10	7	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:27181241A>G	ENST00000282892.3	+	4	312	c.282A>G	c.(280-282)gaA>gaG	p.E94E	MED21_ENST00000536503.1_3'UTR|MED21_ENST00000546323.1_Silent_p.E94E	NM_001271811.1|NM_004264.3	NP_001258740.1|NP_004255.2	Q13503	MED21_HUMAN	mediator complex subunit 21	94					blastocyst development (GO:0001824)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	mediator complex (GO:0016592)	DNA-directed RNA polymerase activity (GO:0003899)|transcription coactivator activity (GO:0003713)					Colorectal(261;0.0847)					ATAAGCTAGAAGAAGAAAACC	0.368																																					p.E94E		Atlas-SNP	.											.	MED21	7	.	0			c.A282G						.						134	135	135					12																	27181241		2203	4300	6503	SO:0001819	synonymous_variant	9412	exon4			GCTAGAAGAAGAA	U46837	CCDS8711.1	12p12	2007-07-30	2007-07-30	2007-07-30		ENSG00000152944			11473	protein-coding gene	gene with protein product		603800	"SRB7 (suppressor of RNA polymerase B, yeast) homolog", "SRB7 suppressor of RNA polymerase B homolog (yeast)"	SURB7		8598913	Standard	NM_004264		Approved	SRB7	uc001rhp.2	Q13503		ENST00000282892.3:c.282A>G	chr12.hg19:g.27181241A>G		90.0	0.0		74.0	4.0	NM_004264	B2R4I3|Q6IB05|Q92811	Silent	SNP	ENST00000282892.3	hg19	CCDS8711.1																																																																																			.	.		0.368	MED21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403262.1	NM_004264		G	27181241	A	G	27181241	2	3	91	1	0	0	0	0	0	0	0	1	9448	69	3	2		2	MED21	12	27181241	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	7681305	27181241	106670654	427	12501										
DENND5B	160518	hgsc.bcm.edu	37	chr12	31605207	31605207	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtacagacattgccgttcttTttgtcattgaccaagtcttt	7	9	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:31605207T>C	ENST00000389082.5	-	5	1560	c.1296A>G	c.(1294-1296)aaA>aaG	p.K432K	DENND5B_ENST00000536562.1_Silent_p.K467K|DENND5B_ENST00000306833.6_Silent_p.K467K|snoU13_ENST00000458765.1_RNA|DENND5B_ENST00000354285.4_Silent_p.K454K	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	432					positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TGCCGTTCTTTTTGTCATTGA	0.458																																					p.K432K		Atlas-SNP	.											DENND5B,caecum,carcinoma,0,1	DENND5B	114	.	0			c.A1296G						.						142	138	139					12																	31605207		1925	4134	6059	SO:0001819	synonymous_variant	160518	exon5			GTTCTTTTTGTCA	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.1296A>G	chr12.hg19:g.31605207T>C		144.0	0.0		88.0	4.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Silent	SNP	ENST00000389082.5	hg19	CCDS44857.1																																																																																			.	.		0.458	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		C	31605207	T	C	31605207	2	2	91	1	0	0	0	0	0	0	0	1	4439	1838	64	2		2	DENND5B	12	31605207	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4423966	31605207	102246688	428	12502										
FGD4	121512	hgsc.bcm.edu	37	chr12	32735126	32735126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtgaggaggagaaagctgccActcttagctcagatacttct	11	9	3	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:32735126A>G	ENST00000427716.2	+	4	749	c.325A>G	c.(325-327)Act>Gct	p.T109A	FGD4_ENST00000531134.1_Missense_Mutation_p.T194A|FGD4_ENST00000472289.1_Missense_Mutation_p.T109A|FGD4_ENST00000534526.2_Missense_Mutation_p.T246A|FGD4_ENST00000546442.1_Missense_Mutation_p.T16A|FGD4_ENST00000266482.3_5'UTR|FGD4_ENST00000525053.1_Missense_Mutation_p.T221A	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	109	Actin filament-binding. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					GAAAGCTGCCACTCTTAGCTC	0.473																																					p.T109A		Atlas-SNP	.											.	FGD4	86	.	0			c.A325G						.						161	127	139					12																	32735126		2203	4300	6503	SO:0001583	missense	121512	exon4			GCTGCCACTCTTA	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.325A>G	chr12.hg19:g.32735126A>G	ENSP00000394487:p.Thr109Ala	162.0	0.0		100.0	5.0	NM_139241	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	hg19	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	A	3.830	-0.036041	0.07497	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000472289;ENST00000427716;ENST00000546442;ENST00000525053;ENST00000395742	T;T;T;T;T	0.68765	-0.35;-0.35;-0.34;-0.32;-0.35	4.91	-2.4	0.06583	.	1.440510	0.04464	N	0.374939	T	0.40094	0.1103	N	0.08118	0	0.09310	N	1	B;B;B;B	0.11235	0.0;0.0;0.0;0.004	B;B;B;B	0.09377	0.0;0.0;0.0;0.004	T	0.24119	-1.0169	10	0.08837	T	0.75	0.263	6.275	0.20975	0.3963:0.2885:0.3152:0.0	.	221;194;109;109	E9PJX4;B7Z493;Q96M96;E9PQT1	.;.;FGD4_HUMAN;.	A	246;194;109;109;16;221;90	ENSP00000449273:T246A;ENSP00000431323:T194A;ENSP00000394487:T109A;ENSP00000446695:T16A;ENSP00000433666:T221A	ENSP00000379089:T109A	T	+	1	0	FGD4	32626393	0.000000	0.05858	0.000000	0.03702	0.354000	0.29330	-1.203000	0.03019	-0.385000	0.07833	0.383000	0.25322	ACT	.	.		0.473	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		G	32735126	A	G	32735126	3	3	91	1	0	0	0	0	1	0	0	0	5843	159	6	2	331	2	FGD4	12	32735126	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1129919	32735126	101116769	429	12503										
DNM1L	10059	hgsc.bcm.edu	37	chr12	32854462	32854462	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caactggtccatgtttcacaAgaagataaacggaaaacaac	7	9	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:32854462A>G	ENST00000549701.1	+	2	290	c.216A>G	c.(214-216)caA>caG	p.Q72Q	DNM1L_ENST00000547312.1_Silent_p.Q72Q|DNM1L_ENST00000553257.1_Silent_p.Q72Q|DNM1L_ENST00000452533.2_Silent_p.Q72Q|DNM1L_ENST00000548671.1_3'UTR|DNM1L_ENST00000414834.2_Missense_Mutation_p.K4R|DNM1L_ENST00000358214.5_Silent_p.Q72Q|DNM1L_ENST00000266481.6_Silent_p.Q72Q|DNM1L_ENST00000381000.4_Silent_p.Q72Q			O00429	DNM1L_HUMAN	dynamin 1-like	72	Dynamin-type G.|GTPase domain.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					ATGTTTCACAAGAAGATAAAC	0.403																																					p.Q72Q		Atlas-SNP	.											.	DNM1L	52	.	0			c.A216G						.						85	88	87					12																	32854462		2203	4300	6503	SO:0001819	synonymous_variant	10059	exon2			TTCACAAGAAGAT	AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.216A>G	chr12.hg19:g.32854462A>G		93.0	0.0		88.0	4.0	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Silent	SNP	ENST00000549701.1	hg19	CCDS8729.1	.	.	.	.	.	.	.	.	.	.	a	13.25	2.179630	0.38511	.	.	ENSG00000087470	ENST00000414834	T	0.79653	-1.29	5.58	-1.55	0.08558	.	.	.	.	.	T	0.66973	0.2844	.	.	.	0.22317	N	0.999208	B	0.02656	0.0	B	0.01281	0.0	T	0.56456	-0.7976	8	0.87932	D	0	.	3.4462	0.07481	0.4556:0.3351:0.0693:0.1401	.	4	B4DGC9	.	R	4	ENSP00000404160:K4R	ENSP00000404160:K4R	K	+	2	0	DNM1L	32745729	0.442000	0.25633	0.996000	0.52242	0.991000	0.79684	-0.048000	0.11944	-0.174000	0.10743	0.520000	0.50463	AAG	.	.		0.403	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062		G	32854462	A	G	32854462	2	3	91	1	0	0	0	0	0	0	0	1	4673	69	3	2		2	DNM1L	12	32854462	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	119336	32854462	100997433	430	12504										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41337846	41337846	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aatgccgatatcacagttggAgaaaacgccaccatgcagtg	10	10	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:41337846A>G	ENST00000551295.2	+	14	1674	c.1557A>G	c.(1555-1557)ggA>ggG	p.G519G	CNTN1_ENST00000547702.1_Silent_p.G519G|CNTN1_ENST00000347616.1_Silent_p.G519G|CNTN1_ENST00000547849.1_Silent_p.G519G|CNTN1_ENST00000360099.3_Silent_p.G519G|CNTN1_ENST00000348761.2_Silent_p.G508G	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	519	Ig-like C2-type 6.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TCACAGTTGGAGAAAACGCCA	0.383																																					p.G519G		Atlas-SNP	.											.	CNTN1	207	.	0			c.A1557G						.						151	121	131					12																	41337846		2203	4299	6502	SO:0001819	synonymous_variant	1272	exon14			AGTTGGAGAAAAC	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1557A>G	chr12.hg19:g.41337846A>G		132.0	0.0		74.0	4.0	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Silent	SNP	ENST00000551295.2	hg19	CCDS8737.1																																																																																			.	.		0.383	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		G	41337846	A	G	41337846	2	3	91	1	0	0	0	0	0	0	0	1	3642	291	11	2		2	CNTN1	12	41337846	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	8483384	41337846	92514049	431	12505										
H1FNT	341567	hgsc.bcm.edu	37	chr12	48723755	48723755	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtgaaggaagacaccacgccGaggtcagggaaggacaagag	16	8	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:48723755G>C	ENST00000335017.1	+	1	993	c.681G>C	c.(679-681)ccG>ccC	p.P227P		NM_181788.1	NP_861453.1	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	227					chromosome condensation (GO:0030261)|multicellular organismal development (GO:0007275)|sperm chromatin condensation (GO:0035092)|spermatid nucleus elongation (GO:0007290)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	13						ACACCACGCCGAGGTCAGGGA	0.657																																					p.P227P		Atlas-SNP	.											H1FNT,NS,carcinoma,0,1	H1FNT	30	.	0			c.G681C						.						55	64	61					12																	48723755		2189	4294	6483	SO:0001819	synonymous_variant	341567	exon1			CACGCCGAGGTCA	AY302593	CCDS8762.1	12q13.11	2011-01-27				ENSG00000187166		"Histones / Replication-independent"	24893	protein-coding gene	gene with protein product						15710904	Standard	NM_181788		Approved	HANP1, H1T2	uc001rrm.3	Q75WM6		ENST00000335017.1:c.681G>C	chr12.hg19:g.48723755G>C		51.0	1.0		37.0	8.0	NM_181788	Q147U8|Q5GKZ5|Q7Z694	Silent	SNP	ENST00000335017.1	hg19	CCDS8762.1																																																																																			.	.		0.657	H1FNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406516.1	NM_181788		C	48723755	G	C	48723755	2	2	91	1	0	0	0	0	0	0	0	1	6930	1045	37	4		4	H1FNT	12	48723755	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	7385909	48723755	85128140	432	12506										
ADCY6	112	hgsc.bcm.edu	37	chr12	49168824	49168824	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aggctccgaagcggggatccAccttccgggagtactgaggg	16	11	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:49168824A>G	ENST00000307885.4	-	11	2688	c.1994T>C	c.(1993-1995)gTg>gCg	p.V665A	ADCY6_ENST00000357869.3_Missense_Mutation_p.V665A|ADCY6_ENST00000552090.1_5'UTR|ADCY6_ENST00000550422.1_Missense_Mutation_p.V665A	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	665					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						GCGGGGATCCACCTTCCGGGA	0.597																																					p.V665A		Atlas-SNP	.											.	ADCY6	81	.	0			c.T1994C						.						65	56	59					12																	49168824		2181	4268	6449	SO:0001583	missense	112	exon12			GGATCCACCTTCC		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"Adenylate cyclases"	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.1994T>C	chr12.hg19:g.49168824A>G	ENSP00000311405:p.Val665Ala	100.0	0.0		85.0	5.0	NM_020983	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	hg19	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.489498	0.44249	.	.	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.34859	1.34;1.34;1.34	4.63	4.63	0.57726	.	0.074628	0.52532	D	0.000072	T	0.41465	0.1160	L	0.58101	1.795	0.58432	D	0.999994	P;P	0.40681	0.486;0.727	B;P	0.45660	0.356;0.489	T	0.20638	-1.0269	10	0.28530	T	0.3	.	13.7149	0.62691	1.0:0.0:0.0:0.0	.	665;665	O43306-2;O43306	.;ADCY6_HUMAN	A	665	ENSP00000350536:V665A;ENSP00000446730:V665A;ENSP00000311405:V665A	ENSP00000311405:V665A	V	-	2	0	ADCY6	47455091	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.683000	0.91236	2.026000	0.59711	0.533000	0.62120	GTG	.	.		0.597	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		G	49168824	A	G	49168824	3	3	91	1	0	0	0	0	1	0	0	0	298	159	6	2	1556	2	ADCY6	12	49168824	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	445069	49168824	84683071	433	12507										
DDN	23109	hgsc.bcm.edu	37	chr12	49391772	49391772	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccgctccacagcctggggatCcccccaagagaccttgcccc	9	20	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:49391772C>A	ENST00000421952.2	-	2	908	c.887G>T	c.(886-888)gGa>gTa	p.G296V	RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	296						cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						GCCTGGGGATCCCCCCAAGAG	0.657																																					p.G296V		Atlas-SNP	.											DDN_ENST00000421952,NS,carcinoma,0,2	DDN	54	.	0			c.G887T						.						52	61	57					12																	49391772		2203	4299	6502	SO:0001583	missense	23109	exon2			GGGGATCCCCCCA	AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.887G>T	chr12.hg19:g.49391772C>A	ENSP00000390590:p.Gly296Val	100.0	0.0		54.0	3.0	NM_015086		Missense_Mutation	SNP	ENST00000421952.2	hg19	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	C	18.34	3.602955	0.66445	.	.	ENSG00000181418	ENST00000421952	T	0.64085	-0.08	4.09	4.09	0.47781	.	0.000000	0.44902	D	0.000409	T	0.67154	0.2863	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.69316	-0.5177	10	0.54805	T	0.06	-7.7903	14.2411	0.65956	0.0:1.0:0.0:0.0	.	296	O94850	DEND_HUMAN	V	296	ENSP00000390590:G296V	ENSP00000390590:G296V	G	-	2	0	DDN	47678039	0.099000	0.21834	0.995000	0.50966	0.996000	0.88848	2.370000	0.44240	2.583000	0.87209	0.561000	0.74099	GGA	.	.		0.657	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			A	49391772	C	A	49391772	3	1	91	1	0	0	0	0	1	0	0	0	4335	855	30	3	1252	3	DDN	12	49391772	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	222948	49391772	84460123	434	12508										
PRPF40B	25766	hgsc.bcm.edu	37	chr12	50036726	50036726	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctagcagactgaatgccagcAcctccacaccaaaggccgaa	8	15	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:50036726A>G	ENST00000380281.1	+	21	2133	c.2069A>G	c.(2068-2070)cAc>cGc	p.H690R	PRPF40B_ENST00000261897.1_Missense_Mutation_p.H677R|FMNL3_ENST00000335154.5_3'UTR|PRPF40B_ENST00000548825.2_Missense_Mutation_p.H711R			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	690					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						GAATGCCAGCACCTCCACACC	0.542																																					p.H711R		Atlas-SNP	.											.	PRPF40B	83	.	0			c.A2132G						.						125	103	110					12																	50036726		2203	4300	6503	SO:0001583	missense	25766	exon22			GCCAGCACCTCCA	AF049525	CCDS31796.1, CCDS31796.2	12q13.12	2014-09-17	2006-04-04			ENSG00000110844			25031	protein-coding gene	gene with protein product	"Huntingtin interacting protein C"		"PRP40 pre-mRNA processing factor 40 homolog B (yeast)"			9700202	Standard	NM_001031698		Approved	HYPC	uc001rus.2	Q6NWY9		ENST00000380281.1:c.2069A>G	chr12.hg19:g.50036726A>G	ENSP00000369634:p.His690Arg	138.0	0.0		120.0	5.0	NM_001031698	O75401|Q6PI09|Q6ZWB3|Q8NCZ1|Q9H5G4|Q9NT95	Missense_Mutation	SNP	ENST00000380281.1	hg19		.	.	.	.	.	.	.	.	.	.	A	22.7	4.323693	0.81580	.	.	ENSG00000110844	ENST00000261897;ENST00000380281	T;T	0.22945	1.95;1.93	4.63	4.63	0.57726	.	0.000000	0.64402	D	0.000007	T	0.51805	0.1696	M	0.85859	2.78	0.80722	D	1	D;D;D	0.61080	0.981;0.989;0.989	D;D;D	0.75020	0.966;0.985;0.985	T	0.53287	-0.8460	10	0.25751	T	0.34	-16.018	13.4498	0.61163	1.0:0.0:0.0:0.0	.	690;677;689	Q6NWY9;Q6NWY9-2;Q6NWY9-3	PR40B_HUMAN;.;.	R	677;690	ENSP00000261897:H677R;ENSP00000369634:H690R	ENSP00000261897:H677R	H	+	2	0	PRPF40B	48322993	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.871000	0.92346	2.092000	0.63282	0.459000	0.35465	CAC	.	.		0.542	PRPF40B-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000404838.1	NM_012272		G	50036726	A	G	50036726	3	3	91	1	0	0	0	0	1	0	0	0	12584	159	6	2	2151	2	PRPF40B	12	50036726	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	644954	50036726	83815169	435	12509										
KRT84	3890	hgsc.bcm.edu	37	chr12	52779324	52779324	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgctgaacaagagctgaagtTgcccacccggtgaccagagc	12	12	0	5			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:52779324T>C	ENST00000257951.3	-	1	112	c.46A>G	c.(46-48)Aac>Gac	p.N16D	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	16	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GAGCTGAAGTTGCCCACCCGG	0.572																																					p.N16D		Atlas-SNP	.											.	KRT84	61	.	0			c.A46G						.						85	93	90					12																	52779324		2203	4300	6503	SO:0001583	missense	3890	exon1			TGAAGTTGCCCAC	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"-", "Intermediate filaments type II, keratins (basic)"	6461	protein-coding gene	gene with protein product	"hard keratin type II 4"	602766	"keratin, hair, basic, 4"	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.46A>G	chr12.hg19:g.52779324T>C	ENSP00000257951:p.Asn16Asp	83.0	0.0		61.0	4.0	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	hg19	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	T	10.47	1.358873	0.24598	.	.	ENSG00000161849	ENST00000257951	T	0.81078	-1.45	5.06	3.9	0.45041	.	0.448207	0.19373	N	0.115847	T	0.66197	0.2765	N	0.17631	0.505	0.09310	N	1	B	0.31125	0.309	B	0.25140	0.058	T	0.58853	-0.7563	10	0.51188	T	0.08	.	11.16	0.48509	0.0:0.0727:0.0:0.9273	.	16	Q9NSB2	KRT84_HUMAN	D	16	ENSP00000257951:N16D	ENSP00000257951:N16D	N	-	1	0	KRT84	51065591	0.051000	0.20477	0.884000	0.34674	0.415000	0.31203	1.240000	0.32731	1.053000	0.40415	0.443000	0.29094	AAC	.	.		0.572	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		C	52779324	T	C	52779324	3	2	91	1	0	0	0	0	1	0	0	0	8507	1812	63	2	1792	2	KRT84	12	52779324	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2742598	52779324	81072571	436	12510										
NXPH4	11247	hgsc.bcm.edu	37	chr12	57619481	57619481	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgactacaaactggtgcagaAggtgtgcccagactataact	10	9	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:57619481A>G	ENST00000349394.5	+	2	1053	c.878A>G	c.(877-879)aAg>aGg	p.K293R	Y_RNA_ENST00000365197.1_RNA	NM_007224.3	NP_009155.1	O95158	NXPH4_HUMAN	neurexophilin 4	293	V (Cys-rich).				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)	10						CTGGTGCAGAAGGTGTGCCCA	0.572																																					p.K293R		Atlas-SNP	.											.	NXPH4	40	.	0			c.A878G						.						62	69	67					12																	57619481		2203	4300	6503	SO:0001583	missense	11247	exon2			TGCAGAAGGTGTG	AF043469	CCDS8933.1	12q13.3	2014-09-04			ENSG00000182379	ENSG00000182379			8078	protein-coding gene	gene with protein product		604637				9570794	Standard	NM_007224		Approved	NPH4	uc009zpj.4	O95158	OTTHUMG00000171241	ENST00000349394.5:c.878A>G	chr12.hg19:g.57619481A>G	ENSP00000333593:p.Lys293Arg	52.0	0.0		53.0	5.0	NM_007224	A8K4I4|Q7Z6L3|Q8N462	Missense_Mutation	SNP	ENST00000349394.5	hg19	CCDS8933.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.444454	0.83993	.	.	ENSG00000182379	ENST00000349394	.	.	.	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.69904	0.3163	L	0.52905	1.665	0.52099	D	0.999941	D	0.89917	1.0	D	0.87578	0.998	T	0.73164	-0.4069	9	0.87932	D	0	-21.6572	12.3172	0.54964	1.0:0.0:0.0:0.0	.	293	O95158	NXPH4_HUMAN	R	293	.	ENSP00000333593:K293R	K	+	2	0	NXPH4	55905748	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.859000	0.92264	1.744000	0.51775	0.460000	0.39030	AAG	.	.		0.572	NXPH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412474.1	NM_007224		G	57619481	A	G	57619481	3	3	91	1	0	0	0	0	1	0	0	0	10802	72	3	2	884	2	NXPH4	12	57619481	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4840157	57619481	76232414	437	12511										
MON2	23041	hgsc.bcm.edu	37	chr12	62887709	62887709	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgaagcactgaaagagaacAgctcagaggttgtacagcct	11	8	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:62887709A>G	ENST00000393632.2	+	3	581	c.190A>G	c.(190-192)Agc>Ggc	p.S64G	MON2_ENST00000393630.3_Missense_Mutation_p.S64G|MON2_ENST00000549378.1_Intron|MON2_ENST00000280379.6_Missense_Mutation_p.S64G|MON2_ENST00000552738.1_Missense_Mutation_p.S64G|MON2_ENST00000552115.1_Missense_Mutation_p.S64G|MON2_ENST00000546600.1_Missense_Mutation_p.S64G|MON2_ENST00000393629.2_Missense_Mutation_p.S64G	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	64					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		GAAAGAGAACAGCTCAGAGGT	0.333																																					p.S64G		Atlas-SNP	.											.	MON2	160	.	0			c.A190G						.						79	67	71					12																	62887709		2202	4300	6502	SO:0001583	missense	23041	exon3			GAGAACAGCTCAG		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.190A>G	chr12.hg19:g.62887709A>G	ENSP00000377252:p.Ser64Gly	142.0	0.0		86.0	4.0	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	A	19.16	3.773486	0.69992	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629;ENST00000552115	T;T;T;T;T;T;T	0.66460	-0.2;-0.21;-0.21;-0.2;-0.2;-0.21;1.4	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.75012	0.3792	L	0.58810	1.83	0.80722	D	1	D;P;P;D	0.54047	0.964;0.776;0.544;0.963	P;P;B;P	0.56434	0.632;0.583;0.257;0.798	T	0.74728	-0.3567	9	.	.	.	-9.3819	15.8953	0.79329	1.0:0.0:0.0:0.0	.	64;64;64;64	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-4	.;.;.;.	G	64	ENSP00000377252:S64G;ENSP00000377250:S64G;ENSP00000280379:S64G;ENSP00000447407:S64G;ENSP00000449215:S64G;ENSP00000377249:S64G;ENSP00000446635:S64G	.	S	+	1	0	MON2	61173976	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.163000	0.67991	0.482000	0.46254	AGC	.	.		0.333	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		G	62887709	A	G	62887709	3	3	91	1	0	0	0	0	1	0	0	0	9709	188	7	2	200	2	MON2	12	62887709	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	5268228	62887709	70964186	438	12512										
TBK1	29110	hgsc.bcm.edu	37	chr12	64878199	64878199	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggaaggctggcacaacattTccctaaaactactgaggaaa	9	9	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:64878199T>C	ENST00000331710.5	+	9	1448	c.1109T>C	c.(1108-1110)tTc>tCc	p.F370S		NM_013254.3	NP_037386.1	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	370	Ubiquitin-like.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of gene expression (GO:0010629)|negative regulation of type I interferon production (GO:0032480)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon production (GO:0032606)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)	ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)	20				GBM - Glioblastoma multiforme(28;0.0386)		GCACAACATTTCCCTAAAACT	0.363																																					p.F370S		Atlas-SNP	.											.	TBK1	149	.	0			c.T1109C						.						59	61	61					12																	64878199		2203	4300	6503	SO:0001583	missense	29110	exon9			AACATTTCCCTAA	AF191838	CCDS8968.1	12q14.2	2006-06-10			ENSG00000183735	ENSG00000183735			11584	protein-coding gene	gene with protein product		604834				10581243, 10783893	Standard	NM_013254		Approved	NAK	uc001ssc.2	Q9UHD2	OTTHUMG00000168796	ENST00000331710.5:c.1109T>C	chr12.hg19:g.64878199T>C	ENSP00000329967:p.Phe370Ser	141.0	0.0		98.0	4.0	NM_013254	A8K4S4|Q8IYV3|Q9NUJ5	Missense_Mutation	SNP	ENST00000331710.5	hg19	CCDS8968.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.814078	0.70912	.	.	ENSG00000183735	ENST00000331710	T	0.68331	-0.32	5.07	5.07	0.68467	.	0.094445	0.64402	D	0.000001	T	0.72779	0.3503	L	0.34521	1.04	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.71556	-0.4557	9	.	.	.	-2.3032	15.533	0.75980	0.0:0.0:0.0:1.0	.	370	Q9UHD2	TBK1_HUMAN	S	370	ENSP00000329967:F370S	.	F	+	2	0	TBK1	63164466	1.000000	0.71417	0.996000	0.52242	0.328000	0.28507	6.623000	0.74238	2.212000	0.71576	0.460000	0.39030	TTC	.	.		0.363	TBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401130.1	NM_013254		C	64878199	T	C	64878199	3	2	91	1	0	0	0	0	1	0	0	0	15652	1783	62	2	1139	2	TBK1	12	64878199	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1990490	64878199	68973696	439	12513										
CPM	1368	hgsc.bcm.edu	37	chr12	69326513	69326513	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acagaactgtagttttgggcAacagtcttcaaaaacgcttc	8	9	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:69326513A>G	ENST00000551568.1	-	2	165	c.105T>C	c.(103-105)gtT>gtC	p.V35V	CPM_ENST00000546373.1_Silent_p.V35V|CPM_ENST00000338356.3_Silent_p.V35V	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	35					anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			AGTTTTGGGCAACAGTCTTCA	0.517																																					p.V35V		Atlas-SNP	.											.	CPM	30	.	0			c.T105C						.						137	130	133					12																	69326513		2203	4300	6503	SO:0001819	synonymous_variant	1368	exon2			TTGGGCAACAGTC	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"renal carboxypeptidase", "urinary carboxypeptidase B"	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.105T>C	chr12.hg19:g.69326513A>G		156.0	0.0		108.0	5.0	NM_001005502	B2R800|Q9H2K9	Silent	SNP	ENST00000551568.1	hg19	CCDS8987.1																																																																																			.	.		0.517	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320		G	69326513	A	G	69326513	2	3	91	1	0	0	0	0	0	0	0	1	3810	117	5	2		2	CPM	12	69326513	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4448314	69326513	64525382	440	12514										
FRS2	10818	hgsc.bcm.edu	37	chr12	69968235	69968235	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcaacaactcagctcagagaAgaactgcattattaaactat	5	9	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:69968235A>G	ENST00000550389.1	+	7	1273	c.1027A>G	c.(1027-1029)Aga>Gga	p.R343G	FRS2_ENST00000397997.2_Missense_Mutation_p.R343G|FRS2_ENST00000299293.2_Missense_Mutation_p.R343G|FRS2_ENST00000549921.1_Missense_Mutation_p.R343G	NM_001278353.1|NM_001278357.1	NP_001265282.1|NP_001265286.1	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	343					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification, embryo (GO:0008595)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation with mouth forming second (GO:0001702)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lens fiber cell development (GO:0070307)|neuroblast proliferation (GO:0007405)|neurotrophin TRK receptor signaling pathway (GO:0048011)|optic placode formation involved in camera-type eye formation (GO:0046619)|organ induction (GO:0001759)|phosphatidylinositol-mediated signaling (GO:0048015)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of apoptotic process (GO:0042981)|regulation of epithelial cell proliferation (GO:0050678)|regulation of ERK1 and ERK2 cascade (GO:0070372)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatase activator activity (GO:0019211)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			AGCTCAGAGAAGAACTGCATT	0.453																																					p.R343G		Atlas-SNP	.											.	FRS2	88	.	0			c.A1027G						.						66	65	65					12																	69968235		1894	4124	6018	SO:0001583	missense	10818	exon10			CAGAGAAGAACTG	AF036717	CCDS41809.1	12q15	2008-02-05				ENSG00000166225			16971	protein-coding gene	gene with protein product		607743				8761293, 9660748	Standard	NM_001278351		Approved	SNT-1, FRS2alpha, SNT1, FRS2A	uc001suz.3	Q8WU20		ENST00000550389.1:c.1027A>G	chr12.hg19:g.69968235A>G	ENSP00000447241:p.Arg343Gly	89.0	0.0		64.0	4.0	NM_001042555	B0LPF2|B2R684|O43558|Q7LDQ6	Missense_Mutation	SNP	ENST00000550389.1	hg19	CCDS41809.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.995471	0.54147	.	.	ENSG00000166225	ENST00000299293;ENST00000549921;ENST00000550389;ENST00000397997	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	6.04	6.04	0.98038	.	0.043348	0.85682	D	0.000000	T	0.51753	0.1693	L	0.42245	1.32	0.44771	D	0.997779	D	0.57899	0.981	D	0.67231	0.95	T	0.42085	-0.9472	9	.	.	.	-11.0668	16.6244	0.84952	1.0:0.0:0.0:0.0	.	343	Q8WU20	FRS2_HUMAN	G	343	ENSP00000299293:R343G;ENSP00000450048:R343G;ENSP00000447241:R343G;ENSP00000381083:R343G	.	R	+	1	2	FRS2	68254502	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.134000	0.57990	2.323000	0.78572	0.529000	0.55759	AGA	.	.		0.453	FRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403760.1	NM_006654		G	69968235	A	G	69968235	3	3	91	1	0	0	0	0	1	0	0	0	6069	64	3	2	1045	2	FRS2	12	69968235	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	641722	69968235	63883660	441	12515										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70989899	70989899	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctgtgatggcaatattgtaTttactaccagcagtgagatt	10	6	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:70989899T>C	ENST00000261266.5	-	3	563	c.534A>G	c.(532-534)aaA>aaG	p.K178K	PTPRB_ENST00000538708.1_Silent_p.K178K|PTPRB_ENST00000451516.2_Silent_p.K178K|PTPRB_ENST00000551525.1_Silent_p.K395K|PTPRB_ENST00000550857.1_Silent_p.K178K|PTPRB_ENST00000550358.1_Silent_p.K396K|PTPRB_ENST00000334414.6_Silent_p.K396K|PTPRB_ENST00000538174.2_5'UTR	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	178	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CAATATTGTATTTACTACCAG	0.333																																					p.K396K		Atlas-SNP	.											.	PTPRB	676	.	0			c.A1188G						.						69	67	68					12																	70989899		1843	4086	5929	SO:0001819	synonymous_variant	5787	exon5			ATTGTATTTACTA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.534A>G	chr12.hg19:g.70989899T>C		149.0	0.0		98.0	5.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.333	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			C	70989899	T	C	70989899	2	2	91	1	0	0	0	0	0	0	0	1	12811	1490	52	2		2	PTPRB	12	70989899	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1021664	70989899	62861996	442	12516										
GLIPR1L2	144321	hgsc.bcm.edu	37	chr12	75816822	75816822	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cataatggattggacaagaaAaataagcgattgaacactag	9	5	0	2	rs75261424		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:75816822A>G	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000320460.4_Silent_p.K241K|GLIPR1L2_ENST00000441218.1_Intron|GLIPR1L2_ENST00000435775.1_Intron|GLIPR1L2_ENST00000378692.3_Intron	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2							integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						TGGACAAGAAAAATAAGCGAT	0.313																																					p.K241K		Atlas-SNP	.											.	GLIPR1L2	54	.	0			c.A723G						.						109	111	110					12																	75816822		2203	4300	6503	SO:0001627	intron_variant	144321	exon4			CAAGAAAAATAAG	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.670+53A>G	chr12.hg19:g.75816822A>G		124.0	0.0		113.0	7.0	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Silent	SNP	ENST00000550916.1	hg19	CCDS58258.1																																																																																			.	.		0.313	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436		G	75816822	A	G	75816822	1	3	91	0	1	0	0	0	0	0	0	0	6451	11	1	2		2	GLIPR1L2	12	75816822	Intron	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4826923	75816822	58035073	443	12517										
ATP2B1	490	hgsc.bcm.edu	37	chr12	90014010	90014010	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaggtaatccaccctctttcTctggtggctataagagaaaa	9	9	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:90014010T>C	ENST00000428670.3	-	11	2051	c.1595A>G	c.(1594-1596)gAg>gGg	p.E532G	ATP2B1_ENST00000359142.3_Missense_Mutation_p.E532G|ATP2B1_ENST00000348959.3_Missense_Mutation_p.E532G|ATP2B1_ENST00000261173.2_Missense_Mutation_p.E532G|ATP2B1_ENST00000393164.2_Missense_Mutation_p.E275G			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	532					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						ACCCTCTTTCTCTGGTGGCTA	0.338																																					p.E532G		Atlas-SNP	.											.	ATP2B1	191	.	0			c.A1595G						.						63	63	63					12																	90014010		2203	4300	6503	SO:0001583	missense	490	exon10			TCTTTCTCTGGTG	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.1595A>G	chr12.hg19:g.90014010T>C	ENSP00000392043:p.Glu532Gly	139.0	0.0		96.0	4.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	hg19	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.301762	0.81136	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.68961	0.3058	N	0.16307	0.4	0.80722	D	1	D;B;B	0.89917	1.0;0.189;0.092	D;B;B	0.80764	0.994;0.125;0.056	T	0.68857	-0.5298	9	.	.	.	-24.6541	15.5449	0.76090	0.0:0.0:0.0:1.0	.	532;532;532	P20020-3;P20020-2;P20020-6	.;.;.	G	532;532;532;532;275	ENSP00000261173:E532G;ENSP00000343599:E532G;ENSP00000352054:E532G;ENSP00000392043:E532G;ENSP00000376869:E275G	.	E	-	2	0	ATP2B1	88538141	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	8.008000	0.88588	2.070000	0.61991	0.383000	0.25322	GAG	.	.		0.338	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		C	90014010	T	C	90014010	3	2	91	1	0	0	0	0	1	0	0	0	1139	1551	54	2	2269	2	ATP2B1	12	90014010	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	14197188	90014010	43837885	444	12518										
C12orf12	196477	hgsc.bcm.edu	37	chr12	91348403	91348403	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggagcacccgggcgccttcgAtggcaggacgaccaggagct	16	13	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:91348403A>G	ENST00000358859.2	-	1	550	c.117T>C	c.(115-117)caT>caC	p.H39H	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	39																	GGCGCCTTCGATGGCAGGACG	0.662																																					p.H39H		Atlas-SNP	.											.	.	.	.	0			c.T117C						.						21	20	20					12																	91348403		2203	4300	6503	SO:0001819	synonymous_variant	196477	exon1			CCTTCGATGGCAG	BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 12"	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.117T>C	chr12.hg19:g.91348403A>G		34.0	0.0		47.0	5.0	NM_152638	Q8TC47	Silent	SNP	ENST00000358859.2	hg19	CCDS9036.1																																																																																			.	.		0.662	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		G	91348403	A	G	91348403	2	3	91	1	0	0	0	0	0	0	0	1	1678	330	12	2		2	C12orf12	12	91348403	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1334393	91348403	42503492	445	12519										
POLR3B	55703	hgsc.bcm.edu	37	chr12	106824062	106824062	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccctacagggaaattggtcTttaaagagatttaaaatgga	9	5	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:106824062T>C	ENST00000228347.4	+	14	1497	c.1275T>C	c.(1273-1275)tcT>tcC	p.S425S	POLR3B_ENST00000539066.1_Silent_p.S367S	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	425					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GAAATTGGTCTTTAAAGAGAT	0.443																																					p.S425S		Atlas-SNP	.											.	POLR3B	123	.	0			c.T1275C						.						101	111	108					12																	106824062		2203	4300	6503	SO:0001819	synonymous_variant	55703	exon14			TTGGTCTTTAAAG	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1275T>C	chr12.hg19:g.106824062T>C		76.0	0.0		92.0	4.0	NM_018082	A8K6H0|B3KV73|F5H1E6|Q9NW59	Silent	SNP	ENST00000228347.4	hg19	CCDS9105.1																																																																																			.	.		0.443	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		C	106824062	T	C	106824062	2	2	91	1	0	0	0	0	0	0	0	1	12238	1596	56	2		2	POLR3B	12	106824062	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	15475659	106824062	27027833	446	12520										
MYO1H	283446	hgsc.bcm.edu	37	chr12	109853345	109853345	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcgtagccgtaagctggctgGtccaaagggccgaaagagga	15	9	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:109853345G>A	ENST00000431443.2	+	14	1499	c.1499G>A	c.(1498-1500)gGt>gAt	p.G500D	MYO1H_ENST00000310903.5_Missense_Mutation_p.G490D	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	500	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						AAGCTGGCTGGTCCAAAGGGC	0.517																																					p.G490D		Atlas-SNP	.											.	MYO1H	98	.	0			c.G1469A						.						47	48	48					12																	109853345		1938	4158	6096	SO:0001583	missense	283446	exon14			TGGCTGGTCCAAA		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.1499G>A	chr12.hg19:g.109853345G>A	ENSP00000444076:p.Gly500Asp	71.0	0.0		80.0	4.0	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	hg19		.	.	.	.	.	.	.	.	.	.	G	4.082	0.013064	0.07912	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	T;T	0.71698	-0.59;-0.59	5.5	3.66	0.41972	.	.	.	.	.	T	0.27419	0.0673	N	0.00298	-1.69	0.36097	D	0.843858	B	0.15141	0.012	B	0.19946	0.027	T	0.43114	-0.9411	9	0.02654	T	1	.	5.9099	0.19023	0.3367:0.0:0.6633:0.0	.	490	F5H3C6	.	D	490;500	ENSP00000439182:G490D;ENSP00000444076:G500D	ENSP00000439182:G490D	G	+	2	0	MYO1H	108337728	1.000000	0.71417	0.097000	0.21041	0.916000	0.54674	5.495000	0.66912	1.310000	0.45006	0.655000	0.94253	GGT	.	.		0.517	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		A	109853345	G	A	109853345	3	1	91	1	0	0	0	0	1	0	0	0	10084	1261	44	3	1523	3	MYO1H	12	109853345	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3029283	109853345	23998550	447	12521										
ERP29	10961	hgsc.bcm.edu	37	chr12	112451275	112451275	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caggaacccggcgatatggcTgccgctgtgccccgcgccgc	14	17	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:112451275T>C	ENST00000261735.3	+	1	156	c.6T>C	c.(4-6)gcT>gcC	p.A2A	TMEM116_ENST00000552839.2_5'Flank|TMEM116_ENST00000552374.2_5'Flank|TMEM116_ENST00000355445.3_5'Flank|ERP29_ENST00000455836.1_Silent_p.A2A|TMEM116_ENST00000437003.2_5'Flank|TMEM116_ENST00000549537.2_5'Flank|TMEM116_ENST00000550831.3_5'Flank|TMEM116_ENST00000354825.3_5'Flank	NM_006817.3	NP_006808.1	P30040	ERP29_HUMAN	endoplasmic reticulum protein 29	2					intracellular protein transport (GO:0006886)|protein folding (GO:0006457)|protein secretion (GO:0009306)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	5						GCGATATGGCTGCCGCTGTGC	0.682																																					p.A2A		Atlas-SNP	.											.	ERP29	17	.	0			c.T6C						.						53	59	57					12																	112451275		2203	4298	6501	SO:0001819	synonymous_variant	10961	exon1			TATGGCTGCCGCT	X94910	CCDS9158.1, CCDS44977.1	12q24.13	2011-10-19	2005-10-05	2005-10-05		ENSG00000089248		"Protein disulfide isomerases"	13799	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 9"	602287	"chromosome 12 open reading frame 8"	C12orf8		9738895, 9037184	Standard	NM_006817		Approved	ERp28, ERp31, ERp29, PDI-DB, PDIA9	uc001ttk.1	P30040	OTTHUMG00000169637	ENST00000261735.3:c.6T>C	chr12.hg19:g.112451275T>C		58.0	0.0		86.0	4.0	NM_001034025	C9J183|Q3MJC3|Q6FHT4	Silent	SNP	ENST00000261735.3	hg19	CCDS9158.1																																																																																			.	.		0.682	ERP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405200.1			C	112451275	T	C	112451275	2	2	91	1	0	0	0	0	0	0	0	1	5244	1567	55	2		2	ERP29	12	112451275	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2597930	112451275	21400620	448	12522										
OAS1	4938	hgsc.bcm.edu	37	chr12	113357213	113357213	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggctgaaagcaacagtgcagAcgatgagaccgacgatccca	12	11	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:113357213A>G	ENST00000202917.5	+	6	1321	c.1058A>G	c.(1057-1059)gAc>gGc	p.D353G	OAS1_ENST00000445409.2_Intron|OAS1_ENST00000551241.1_Intron|RP1-71H24.1_ENST00000552784.1_RNA	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	353					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						AACAGTGCAGACGATGAGACC	0.488																																					p.D353G		Atlas-SNP	.											.	OAS1	128	.	0			c.A1058G						.						87	86	87					12																	113357213		2203	4300	6503	SO:0001583	missense	4938	exon6			GTGCAGACGATGA	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"2',5'-oligoadenylate synthetase 1 (40-46 kD)"	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.1058A>G	chr12.hg19:g.113357213A>G	ENSP00000202917:p.Asp353Gly	78.0	0.0		85.0	4.0	NM_016816	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	hg19	CCDS41838.1	.	.	.	.	.	.	.	.	.	.	A	7.064	0.566970	0.13560	.	.	ENSG00000089127	ENST00000202917	T	0.05258	3.47	2.38	-0.113	0.13568	.	.	.	.	.	T	0.02649	0.0080	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48647	-0.9017	9	0.15066	T	0.55	.	4.3968	0.11367	0.6134:0.0:0.3866:0.0	.	353	P00973	OAS1_HUMAN	G	353	ENSP00000202917:D353G	ENSP00000202917:D353G	D	+	2	0	OAS1	111841596	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.513000	0.06305	-0.026000	0.13895	0.455000	0.32223	GAC	.	.		0.488	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2			G	113357213	A	G	113357213	3	3	91	1	0	0	0	0	1	0	0	0	10808	275	10	2	1137	2	OAS1	12	113357213	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	905938	113357213	20494682	449	12523										
IQCD	115811	hgsc.bcm.edu	37	chr12	113633675	113633675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctcctccctgtgaacagcgTccagatcctccaactcctcc	5	19	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:113633675T>C	ENST00000416617.2	-	5	1245	c.1055A>G	c.(1054-1056)gAc>gGc	p.D352G	IQCD_ENST00000299732.2_Missense_Mutation_p.D250G			Q96DY2	IQCD_HUMAN	IQ motif containing D	352										endometrium(2)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						GTGAACAGCGTCCAGATCCTC	0.632																																					p.D250G		Atlas-SNP	.											.	IQCD	32	.	0			c.A749G						.						51	47	48					12																	113633675		2203	4300	6503	SO:0001583	missense	115811	exon3			ACAGCGTCCAGAT	BC013151	CCDS9167.1	12q24.21	2014-07-18				ENSG00000166578			25168	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 10"					23427265, 24804578	Standard	NM_138451		Approved	DRC10, CFAP84	uc001tuu.3	Q96DY2		ENST00000416617.2:c.1055A>G	chr12.hg19:g.113633675T>C	ENSP00000400669:p.Asp352Gly	98.0	0.0		81.0	4.0	NM_138451	Q6ZSU0	Missense_Mutation	SNP	ENST00000416617.2	hg19		.	.	.	.	.	.	.	.	.	.	T	8.935	0.964391	0.18583	.	.	ENSG00000166578	ENST00000299732;ENST00000416617	T;T	0.46451	2.98;0.87	4.29	4.29	0.51040	.	.	.	.	.	T	0.36853	0.0982	.	.	.	0.80722	D	1	B	0.27679	0.185	B	0.28553	0.091	T	0.31336	-0.9947	8	0.56958	D	0.05	-9.3408	12.5394	0.56161	0.0:0.0:0.0:1.0	.	250	Q96DY2-2	.	G	250;352	ENSP00000299732:D250G;ENSP00000400669:D352G	ENSP00000299732:D250G	D	-	2	0	IQCD	112118058	0.133000	0.22466	0.808000	0.32385	0.003000	0.03518	2.823000	0.48081	1.804000	0.52760	0.459000	0.35465	GAC	.	.		0.632	IQCD-004	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000405327.1	NM_138451		C	113633675	T	C	113633675	3	2	91	1	0	0	0	0	1	0	0	0	7814	1667	58	2	298	2	IQCD	12	113633675	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	276462	113633675	20218220	450	12524										
VSIG10	54621	hgsc.bcm.edu	37	chr12	118533406	118533406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctggcaggtgtagattcccTcatctcccaggctcagcgat	10	14	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:118533406T>C	ENST00000359236.5	-	2	569	c.293A>G	c.(292-294)gAg>gGg	p.E98G	VSIG10_ENST00000536905.1_5'UTR	NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	98	Ig-like C2-type 1.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						GTAGATTCCCTCATCTCCCAG	0.592																																					p.E98G		Atlas-SNP	.											.	VSIG10	41	.	0			c.A293G						.						88	96	93					12																	118533406		2116	4243	6359	SO:0001583	missense	54621	exon2			ATTCCCTCATCTC		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.293A>G	chr12.hg19:g.118533406T>C	ENSP00000352172:p.Glu98Gly	83.0	0.0		92.0	5.0	NM_019086	Q9NWQ7	Missense_Mutation	SNP	ENST00000359236.5	hg19	CCDS44992.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.712689	0.48517	.	.	ENSG00000176834	ENST00000359236;ENST00000538357	T;T	0.67698	-0.28;-0.28	4.99	2.46	0.29980	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.155706	0.30210	N	0.010146	T	0.75889	0.3911	M	0.73430	2.235	0.34189	D	0.67189	D	0.65815	0.995	D	0.63703	0.917	T	0.79725	-0.1683	10	0.32370	T	0.25	-18.387	10.1025	0.42513	0.0:0.0:0.3214:0.6786	.	98	Q8N0Z9	VSI10_HUMAN	G	98	ENSP00000352172:E98G;ENSP00000442861:E98G	ENSP00000352172:E98G	E	-	2	0	VSIG10	117017789	0.722000	0.28017	0.992000	0.48379	0.177000	0.22998	1.256000	0.32921	0.905000	0.36596	0.533000	0.62120	GAG	.	.		0.592	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086		C	118533406	T	C	118533406	3	2	91	1	0	0	0	0	1	0	0	0	17238	1551	54	2	1361	2	VSIG10	12	118533406	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4899731	118533406	15318489	451	12525										
GPR133	283383	hgsc.bcm.edu	37	chr12	131616271	131616271	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccatggtttcttgtgcaggTcaacattggcatcctcatcg	9	11	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:131616271T>C	ENST00000261654.5	+	21	2736	c.2177T>C	c.(2176-2178)gTc>gCc	p.V726A	GPR133_ENST00000535015.1_Splice_Site_p.V758A|GPR133_ENST00000376682.4_Splice_Site_p.V412A|GPR133_ENST00000543617.1_Splice_Site_p.V245A|GPR133_ENST00000540207.1_3'UTR	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	726					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		CTTGTGCAGGTCAACATTGGC	0.587																																					p.V726A		Atlas-SNP	.											.	GPR133	136	.	0			c.T2177C						.						153	116	129					12																	131616271		2203	4300	6503	SO:0001630	splice_region_variant	283383	exon21			TGCAGGTCAACAT	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"-", "GPCR / Class B : Orphans"	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.2176-1T>C	chr12.hg19:g.131616271T>C		140.0	0.0		167.0	7.0	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	hg19	CCDS9272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.02|17.02	3.282762|3.282762	0.59867|0.59867	.|.	.|.	ENSG00000111452|ENSG00000111452	ENST00000335486|ENST00000261654;ENST00000535015;ENST00000376682;ENST00000543617	.|T;T;T;T	.|0.55052	.|0.54;0.54;1.24;1.24	4.39|4.39	4.39|4.39	0.52855|0.52855	.|GPCR, family 2-like (1);	.|0.000000	.|0.64402	.|U	.|0.000001	T|T	0.64294|0.64294	0.2585|0.2585	L|L	0.55990|0.55990	1.75|1.75	0.80722|0.80722	D|D	1|1	.|P;D;P	.|0.61080	.|0.608;0.989;0.743	.|P;D;P	.|0.68039	.|0.852;0.955;0.613	T|T	0.64483|0.64483	-0.6397|-0.6397	5|10	.|0.45353	.|T	.|0.12	.|.	11.8298|11.8298	0.52288|0.52288	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|758;79;726	.|B7ZLF7;Q9NSM3;Q6QNK2	.|.;.;GP133_HUMAN	P|A	80|726;758;412;245	.|ENSP00000261654:V726A;ENSP00000444425:V758A;ENSP00000365872:V412A;ENSP00000438021:V245A	.|ENSP00000261654:V726A	S|V	+|+	1|2	0|0	GPR133|GPR133	130182224|130182224	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.837000|0.837000	0.47467|0.47467	4.951000|4.951000	0.63610|0.63610	1.721000|1.721000	0.51461|0.51461	0.402000|0.402000	0.26972|0.26972	TCA|GTC	.	.		0.587	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	Missense_Mutation	C	131616271	T	C	131616271	5	2	91	1	0	0	0	0	0	0	1	0	6651	1681	58	2	2259	2	GPR133	12	131616271	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	13082865	131616271	2235624	452	12526										
EP400	57634	hgsc.bcm.edu	37	chr12	132549247	132549247	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aatgcagaagcagaaactgcAgatgcccccgcagcccccac	9	16	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:132549247A>G	ENST00000333577.4	+	49	8586	c.8477A>G	c.(8476-8478)cAg>cGg	p.Q2826R	EP400_ENST00000332482.4_Missense_Mutation_p.Q2753R|EP400_ENST00000330386.6_Missense_Mutation_p.Q2709R|EP400_ENST00000389562.2_Missense_Mutation_p.Q2789R|EP400_ENST00000389561.2_Missense_Mutation_p.Q2790R			Q96L91	EP400_HUMAN	E1A binding protein p400	2826					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CAGAAACTGCAGATGCCCCCG	0.542																																					p.Q2790R		Atlas-SNP	.											.	EP400	370	.	0			c.A8369G						.						36	48	44					12																	132549247		2202	4300	6502	SO:0001583	missense	57634	exon48			AACTGCAGATGCC	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8477A>G	chr12.hg19:g.132549247A>G	ENSP00000333602:p.Gln2826Arg	64.0	0.0		64.0	4.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	hg19		.	.	.	.	.	.	.	.	.	.	A	15.49	2.848961	0.51164	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.90844	-2.74;-2.74;-2.71;-2.72;-2.71	4.83	4.83	0.62350	.	0.066245	0.64402	D	0.000009	D	0.91222	0.7234	L	0.29908	0.895	0.39818	D	0.972799	D;D;D;D	0.67145	0.985;0.996;0.996;0.996	P;D;D;D	0.75484	0.696;0.986;0.986;0.986	D	0.89729	0.3925	10	0.23302	T	0.38	.	14.0591	0.64788	1.0:0.0:0.0:0.0	.	2826;2790;2709;2789	Q96L91;Q96L91-2;Q96L91-4;Q96L91-5	EP400_HUMAN;.;.;.	R	2826;2790;2789;2753;2709;2790	ENSP00000333602:Q2826R;ENSP00000374212:Q2790R;ENSP00000374213:Q2789R;ENSP00000331737:Q2753R;ENSP00000330620:Q2709R	ENSP00000330620:Q2709R	Q	+	2	0	EP400	131115200	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	8.063000	0.89482	1.813000	0.52934	0.402000	0.26972	CAG	.	.		0.542	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		G	132549247	A	G	132549247	3	3	91	1	0	0	0	0	1	0	0	0	5151	188	7	2	8552	2	EP400	12	132549247	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	932976	132549247	1302648	453	12527										
GALNT9	50614	hgsc.bcm.edu	37	chr12	132688051	132688051	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cggcctgtgggggactcaccGacatggggatgttccaggcc	16	12	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:132688051G>A	ENST00000328957.8	-	7	1261	c.1262C>T	c.(1261-1263)tCg>tTg	p.S421L	GALNT9_ENST00000541995.1_Splice_Site_p.S55L|GALNT9_ENST00000535228.1_Splice_Site_p.S172L|GALNT9_ENST00000397325.2_Splice_Site_p.S55L	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	421					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.S421L(1)|p.S55L(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		GGGACTCACCGACATGGGGAT	0.682																																					p.S421L	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											GALNT9_ENST00000328957,NS,carcinoma,0,2	GALNT9	74	.	2	Substitution - Missense(2)	lung(2)	c.C1262T						.						43	46	45					12																	132688051		2073	4199	6272	SO:0001630	splice_region_variant	50614	exon7			CTCACCGACATGG	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4131	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 9"	606251	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.1263+1C>T	chr12.hg19:g.132688051G>A		65.0	0.0		74.0	4.0	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Missense_Mutation	SNP	ENST00000328957.8	hg19		.	.	.	.	.	.	.	.	.	.	g	12.27	1.887299	0.33348	.	.	ENSG00000182870	ENST00000397325;ENST00000328957;ENST00000535228;ENST00000541995;ENST00000538356	T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55	3.87	2.97	0.34412	.	0.220504	0.45126	D	0.000382	T	0.47728	0.1461	N	0.12182	0.205	0.21719	N	0.999571	B;B;B	0.20887	0.049;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.30268	-0.9984	10	0.30854	T	0.27	.	8.4984	0.33144	0.0883:0.1557:0.756:0.0	.	172;421;278	B3KNR7;Q9HCQ5;B3KP58	.;GALT9_HUMAN;.	L	55;421;172;55;55	ENSP00000380488:S55L;ENSP00000329846:S421L;ENSP00000439745:S172L;ENSP00000440544:S55L;ENSP00000444709:S55L	ENSP00000329846:S421L	S	-	2	0	GALNT9	131254004	0.998000	0.40836	0.565000	0.28409	0.375000	0.29983	2.717000	0.47227	0.714000	0.32081	0.448000	0.29417	TCG	.	.		0.682	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	Missense_Mutation	A	132688051	G	A	132688051	5	1	91	1	0	0	0	0	0	0	1	0	6228	1072	37	1	569	1	GALNT9	12	132688051	Splice_Site	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	138804	132688051	1163844	454	12528										
POLE	5426	hgsc.bcm.edu	37	chr12	133218836	133218836	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccatgacaagacagttgtcAtcagcctcctttccacccag	6	15	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:133218836A>G	ENST00000320574.5	-	38	5143	c.5100T>C	c.(5098-5100)gaT>gaC	p.D1700D	POLE_ENST00000434528.3_5'Flank|POLE_ENST00000535270.1_Silent_p.D1673D	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1700					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GACAGTTGTCATCAGCCTCCT	0.592								DNA polymerases (catalytic subunits)																													p.D1700D		Atlas-SNP	.											.	POLE	416	.	0			c.T5100C						.						135	123	127					12																	133218836		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon38			GTTGTCATCAGCC		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.5100T>C	chr12.hg19:g.133218836A>G		114.0	0.0		99.0	4.0	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	hg19	CCDS9278.1																																																																																			.	.		0.592	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		G	133218836	A	G	133218836	2	3	91	1	0	0	0	0	0	0	0	1	12205	214	8	2		2	POLE	12	133218836	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	530785	133218836	633059	455	12529										
SKA3	221150	hgsc.bcm.edu	37	chr13	21742126	21742126	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccttttaacagagctgcttaCcttttattattcctcgcatt	4	11	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:21742126C>A	ENST00000314759.5	-	4	868		c.e4+1		SKA3_ENST00000400018.3_Splice_Site	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3						chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GAGCTGCTTACCTTTTATTAT	0.284																																					.		Atlas-SNP	.											.	SKA3	76	.	0			c.743+1G>T						.						63	58	60					13																	21742126		2203	4297	6500	SO:0001630	splice_region_variant	221150	exon5			TGCTTACCTTTTA	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 3"	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.743+1G>T	chr13.hg19:g.21742126C>A		142.0	0.0		120.0	15.0	NM_001166017	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Splice_Site	SNP	ENST00000314759.5	hg19	CCDS31946.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.052163	0.36181	.	.	ENSG00000165480	ENST00000314759;ENST00000400018	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6803	0.77364	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SKA3	20640126	1.000000	0.71417	1.000000	0.80357	0.302000	0.27658	4.395000	0.59678	2.777000	0.95525	0.655000	0.94253	.	.	.		0.284	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	Intron	A	21742126	C	A	21742126	5	1	91	1	0	0	0	0	0	0	1	0	14369	521	18	3	565	3	SKA3	13	21742126	Splice_Site	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10		21742126	93427752	456	12530										
SACS	26278	hgsc.bcm.edu	37	chr13	23906630	23906630	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccatcttctaccatcacaaaAgcaacccctcgcaactgaaa	3	16	3	1	rs148605896		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:23906630A>G	ENST00000382292.3	-	9	11658	c.11385T>C	c.(11383-11385)gcT>gcC	p.A3795A	SACS_ENST00000402364.1_Silent_p.A3045A|SACS_ENST00000382298.3_Silent_p.A3795A			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3795					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CCATCACAAAAGCAACCCCTC	0.368																																					p.A3795A		Atlas-SNP	.											.	SACS	871	.	0			c.T11385C						.						88	85	86					13																	23906630		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			CACAAAAGCAACC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.11385T>C	chr13.hg19:g.23906630A>G		120.0	0.0		110.0	5.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	A|0.999;C|0.001		0.368	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23906630	A	G	23906630	2	3	91	1	0	0	0	0	0	0	0	1	13819	59	3	2		2	SACS	13	23906630	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2164504	23906630	91263248	457	12531										
SACS	26278	hgsc.bcm.edu	37	chr13	23911630	23911630	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agaaccataagggaatctccCatctttaatatcaaataact	4	9	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:23911630C>T	ENST00000382292.3	-	9	6658	c.6385G>A	c.(6385-6387)Ggg>Agg	p.G2129R	SACS_ENST00000402364.1_Missense_Mutation_p.G1379R|SACS_ENST00000382298.3_Missense_Mutation_p.G2129R			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2129					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GGGAATCTCCCATCTTTAATA	0.378																																					p.G2129R		Atlas-SNP	.											.	SACS	871	.	0			c.G6385A						.						52	56	55					13																	23911630		2203	4297	6500	SO:0001583	missense	26278	exon10			ATCTCCCATCTTT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.6385G>A	chr13.hg19:g.23911630C>T	ENSP00000371729:p.Gly2129Arg	131.0	0.0		94.0	4.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	15.11	2.737234	0.49045	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88431	-2.24;-2.38;-2.24	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.93562	0.7945	L	0.54323	1.7	0.58432	D	0.999995	D	0.89917	1.0	D	0.87578	0.998	D	0.93466	0.6815	10	0.72032	D	0.01	.	20.1306	0.97998	0.0:1.0:0.0:0.0	.	2129	Q9NZJ4	SACS_HUMAN	R	2129;1379;2129	ENSP00000371729:G2129R;ENSP00000385844:G1379R;ENSP00000371735:G2129R	ENSP00000371729:G2129R	G	-	1	0	SACS	22809630	1.000000	0.71417	0.994000	0.49952	0.059000	0.15707	7.487000	0.81328	2.751000	0.94390	0.655000	0.94253	GGG	.	.		0.378	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23911630	C	T	23911630	3	4	91	1	0	0	0	0	1	0	0	0	13819	594	21	3	7358	3	SACS	13	23911630	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	5000	23911630	91258248	458	12532										
FAM123A	219287	hgsc.bcm.edu	37	chr13	25744544	25744544	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctttttagacagagccggcTtgcctggcccggggacatgc	13	12	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:25744544T>C	ENST00000515384.1	-	1	1881	c.1214A>G	c.(1213-1215)aAg>aGg	p.K405R	AMER2_ENST00000381853.3_Missense_Mutation_p.K286R|AMER2-AS1_ENST00000413501.1_lincRNA|AMER2_ENST00000357816.2_Missense_Mutation_p.K286R			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	405					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)										CAGAGCCGGCTTGCCTGGCCC	0.577																																					p.K405R		Atlas-SNP	.											.	.	.	.	0			c.A1214G						.						30	33	32					13																	25744544		2203	4300	6503	SO:0001583	missense	219287	exon1			GCCGGCTTGCCTG	AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"-"	26360	protein-coding gene	gene with protein product		614659	"family with sequence similarity 123A"	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1214A>G	chr13.hg19:g.25744544T>C	ENSP00000426528:p.Lys405Arg	60.0	0.0		45.0	4.0	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	hg19	CCDS53859.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.867607	0.51588	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.17528	2.27;2.27;2.27	4.42	4.42	0.53409	.	0.252962	0.36167	N	0.002741	T	0.16257	0.0391	L	0.46157	1.445	0.37051	D	0.89758	P;P	0.37914	0.611;0.557	B;B	0.35114	0.196;0.124	T	0.13124	-1.0521	10	0.44086	T	0.13	-18.2309	13.0064	0.58707	0.0:0.0:0.0:1.0	.	405;286	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	R	286;286;405	ENSP00000350469:K286R;ENSP00000371277:K286R;ENSP00000426528:K405R	ENSP00000350469:K286R	K	-	2	0	FAM123A	24642544	1.000000	0.71417	0.989000	0.46669	0.908000	0.53690	3.647000	0.54403	1.851000	0.53745	0.459000	0.35465	AAG	.	.		0.577	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704		C	25744544	T	C	25744544	3	2	91	1	0	0	0	0	1	0	0	0	5427	1609	56	2	805	2	FAM123A	13	25744544	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1832914	25744544	89425334	459	12533										
PRHOXNB	646625	hgsc.bcm.edu	37	chr13	28562605	28562605	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atacggaagccttacctgacTgtgcaagggcatcaataaag	10	9	1	1	rs3897926	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:28562605T>C	ENST00000332715.5	-	1	186	c.170A>G	c.(169-171)cAg>cGg	p.Q57R	RN7SL272P_ENST00000487762.2_RNA	NM_001105577.1	NP_001099047.1	A6NGE7	URAD_HUMAN	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase	57			Q -> P (in dbSNP:rs3897926).		allantoin biosynthetic process (GO:0019428)|purine nucleobase metabolic process (GO:0006144)|urate catabolic process (GO:0019628)	peroxisome (GO:0005777)	carboxy-lyase activity (GO:0016831)	p.Q57P(1)									CTTACCTGACTGTGCAAGGGC	0.433																																					p.Q57R		Atlas-SNP	.											PRHOXNB,NS,carcinoma,0,1	PRHOXNB	6	.	1	Substitution - Missense(1)	stomach(1)	c.A170G						.						71	66	68					13																	28562605		1876	4114	5990	SO:0001583	missense	646625	exon1			CCTGACTGTGCAA		CCDS45020.1	13q12.2	2014-04-09	2013-06-18	2013-06-18	ENSG00000183463	ENSG00000183463	4.1.1.n1		17785	protein-coding gene	gene with protein product	"OHCU decarboxylase"	615804	"parahox cluster neighbor"	PRHOXNB		16462750	Standard	NM_001105577		Approved		uc010aan.1	A6NGE7	OTTHUMG00000186217	ENST00000332715.5:c.170A>G	chr13.hg19:g.28562605T>C	ENSP00000333490:p.Gln57Arg	82.0	0.0		68.0	3.0	NM_001105577		Missense_Mutation	SNP	ENST00000332715.5	hg19	CCDS45020.1	.	.	.	.	.	.	.	.	.	.	T	4.980	0.182035	0.09495	.	.	ENSG00000183463	ENST00000332715	T	0.39997	1.05	5.2	-2.01	0.07410	2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 1 (1);Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase (2);	0.537574	0.18843	N	0.129613	T	0.13286	0.0322	N	0.03903	-0.33	0.80722	P	0.0	B	0.10296	0.003	B	0.11329	0.006	T	0.18587	-1.0332	9	0.14656	T	0.56	-0.8652	3.3162	0.07034	0.405:0.168:0.0:0.427	.	57	A6NGE7	URAD_HUMAN	R	57	ENSP00000333490:Q57R	ENSP00000333490:Q57R	Q	-	2	0	PRHOXNB	27460605	0.000000	0.05858	0.016000	0.15963	0.713000	0.41058	-0.723000	0.04952	-0.313000	0.08728	0.482000	0.46254	CAG	.	T|0.723;G|0.277		0.433	URAD-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472432.1			C	28562605	T	C	28562605	3	2	91	1	0	0	0	0	1	0	0	0	12496	1580	55	2	359	2	PRHOXNB	13	28562605	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2818061	28562605	86607273	460	12534										
FLT1	2321	hgsc.bcm.edu	37	chr13	28913323	28913323	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acccagtttaagtctctcccGggcaaactcccacttgctgg	8	15	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:28913323G>A	ENST00000282397.4	-	17	2721	c.2470C>T	c.(2470-2472)Cgg>Tgg	p.R824W	FLT1_ENST00000540678.1_Missense_Mutation_p.R42W	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	824					blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGTCTCTCCCGGGCAAACTCC	0.418																																					p.R824W		Atlas-SNP	.											.	FLT1	393	.	0			c.C2470T						.						78	77	77					13																	28913323		2203	4300	6503	SO:0001583	missense	2321	exon17			TCTCCCGGGCAAA	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2470C>T	chr13.hg19:g.28913323G>A	ENSP00000282397:p.Arg824Trp	124.0	0.0		88.0	4.0	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	hg19	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.911144	0.72983	.	.	ENSG00000102755	ENST00000282397;ENST00000540678	D;D	0.89552	-2.53;-2.53	5.52	4.63	0.57726	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.94159	0.8126	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94445	0.7662	10	0.87932	D	0	.	14.6701	0.68937	0.0:0.0:0.7069:0.2931	.	824	P17948	VGFR1_HUMAN	W	824;42	ENSP00000282397:R824W;ENSP00000443311:R42W	ENSP00000282397:R824W	R	-	1	2	FLT1	27811323	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.074000	0.41529	2.761000	0.94854	0.655000	0.94253	CGG	.	.		0.418	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			A	28913323	G	A	28913323	3	1	91	1	0	0	0	0	1	0	0	0	5949	1115	39	1	1602	1	FLT1	13	28913323	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	350718	28913323	86256555	461	12535										
BRCA2	675	hgsc.bcm.edu	37	chr13	32914823	32914823	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaatacttcctcgtgttgatAagagaaacccagagcactgt	8	9	0	3	rs397507369|rs80359574|rs587781470		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:32914823A>G	ENST00000380152.3	+	11	6564	c.6331A>G	c.(6331-6333)Aag>Gag	p.K2111E	BRCA2_ENST00000544455.1_Missense_Mutation_p.K2111E			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2111					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TCGTGTTGATAAGAGAAACCC	0.343			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.K2111E	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2	812	.	0			c.A6331G						.						40	42	41					13																	32914823		2203	4297	6500	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	GTTGATAAGAGAA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.6331A>G	chr13.hg19:g.32914823A>G	ENSP00000369497:p.Lys2111Glu	102.0	0.0		96.0	4.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	6.836	0.523531	0.13066	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00705	5.81;5.81	5.49	-0.7	0.11273	.	0.904941	0.09578	N	0.783329	T	0.00754	0.0025	L	0.38838	1.175	0.09310	N	1	B	0.22276	0.067	B	0.18263	0.021	T	0.44128	-0.9348	10	0.10636	T	0.68	.	10.0594	0.42266	0.571:0.0:0.429:0.0	.	2111	P51587	BRCA2_HUMAN	E	2111	ENSP00000369497:K2111E;ENSP00000439902:K2111E	ENSP00000369497:K2111E	K	+	1	0	BRCA2	31812823	0.000000	0.05858	0.000000	0.03702	0.356000	0.29392	0.419000	0.21247	0.085000	0.17107	0.482000	0.46254	AAG	.	.		0.343	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32914823	A	G	32914823	3	3	91	1	0	0	0	0	1	0	0	0	1501	363	13	2	6369	2	BRCA2	13	32914823	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4001500	32914823	82255055	462	12536										
N4BP2L2	10443	hgsc.bcm.edu	37	chr13	33012840	33012840	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atctttagtgtcttccagtcAaggggaaccacatagtcatc	8	10	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:33012840A>G	ENST00000504114.1	-	7	2230	c.2139T>C	c.(2137-2139)ctT>ctC	p.L713L	N4BP2L2_ENST00000380121.3_5'UTR|N4BP2L2_ENST00000357505.6_Silent_p.L713L|N4BP2L2_ENST00000399396.3_Silent_p.L728L|N4BP2L2_ENST00000446957.2_Silent_p.L631L			Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	0					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TCTTCCAGTCAAGGGGAACCA	0.393																																					p.L728L		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.T2184C						.						101	101	101					13																	33012840		1952	4164	6116	SO:0001819	synonymous_variant	10443	exon8			CCAGTCAAGGGGA	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"phosphonoformate immuno-associated protein 5"	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000504114.1:c.2139T>C	chr13.hg19:g.33012840A>G		96.0	0.0		111.0	5.0	NM_033111	A3KME8	Silent	SNP	ENST00000504114.1	hg19																																																																																				.	.		0.393	N4BP2L2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000361380.1	NM_014887		G	33012840	A	G	33012840	2	3	91	1	0	0	0	0	0	0	0	1	10121	117	5	2		2	N4BP2L2	13	33012840	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	98017	33012840	82157038	463	12537										
NBEA	26960	hgsc.bcm.edu	37	chr13	36229065	36229065	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atacaaatcaatgcacattgTtttgtggtaacagcagataa	7	6	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:36229065T>C	ENST00000400445.3	+	53	8580	c.8046T>C	c.(8044-8046)tgT>tgC	p.C2682C	NBEA_ENST00000379922.3_Silent_p.C260C|NBEA_ENST00000537702.1_Silent_p.C475C|NBEA_ENST00000540320.1_Silent_p.C2682C|NBEA_ENST00000310336.4_Silent_p.C2682C|NBEA_ENST00000379939.2_Silent_p.C2679C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2682					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ATGCACATTGTTTTGTGGTAA	0.358																																					p.C2682C		Atlas-SNP	.											.	NBEA	340	.	0			c.T8046C						.						110	103	105					13																	36229065		1863	4096	5959	SO:0001819	synonymous_variant	26960	exon53			ACATTGTTTTGTG	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.8046T>C	chr13.hg19:g.36229065T>C		127.0	0.0		92.0	4.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.358	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		C	36229065	T	C	36229065	2	2	91	1	0	0	0	0	0	0	0	1	10196	1731	60	2		2	NBEA	13	36229065	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3216225	36229065	78940813	464	12538										
FAM48A	55578	hgsc.bcm.edu	37	chr13	37586423	37586423	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgttcttgactggttgaaccTtgctcagaaccctgaataaa	8	9	2	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:37586423T>C	ENST00000350612.6	-	24	2224	c.2004A>G	c.(2002-2004)caA>caG	p.Q668Q	SUPT20H_ENST00000360252.4_Silent_p.Q669Q|SUPT20H_ENST00000356185.3_Silent_p.Q669Q|SUPT20H_ENST00000475892.1_Silent_p.Q747Q|SUPT20H_ENST00000464744.1_Silent_p.Q669Q	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	668	Gln-rich.				autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										TGGTTGAACCTTGCTCAGAAC	0.368																																					p.Q669Q		Atlas-SNP	.											.	.	.	.	0			c.A2007G						.						138	139	139					13																	37586423		2203	4300	6503	SO:0001819	synonymous_variant	55578	exon24			TGAACCTTGCTCA	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.2004A>G	chr13.hg19:g.37586423T>C		53.0	0.0		50.0	5.0	NM_017569	E7ER46|Q71RF3|Q9Y6A6	Silent	SNP	ENST00000350612.6	hg19	CCDS31959.1	.	.	.	.	.	.	.	.	.	.	T	8.149	0.786994	0.16189	.	.	ENSG00000102710	ENST00000469488	.	.	.	5.64	3.17	0.36434	.	.	.	.	.	T	0.55130	0.1901	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45977	-0.9224	4	.	.	.	-1.3626	6.6608	0.23012	0.1353:0.0781:0.0:0.7866	.	.	.	.	R	211	.	.	K	-	2	0	FAM48A	36484423	1.000000	0.71417	0.995000	0.50966	0.957000	0.61999	3.227000	0.51262	0.400000	0.25396	0.379000	0.24179	AAG	.	.		0.368	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		C	37586423	T	C	37586423	2	2	91	1	0	0	0	0	0	0	0	1	5580	1606	56	2		2	FAM48A	13	37586423	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1357358	37586423	77583455	465	12539										
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42306265	42306265	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgtctttaaccgaaggctgaAgcgtaagagtttgtactgtg	12	7	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:42306265A>G	ENST00000379310.3	-	22	2521	c.2453T>C	c.(2452-2454)cTt>cCt	p.L818P	VWA8_ENST00000281496.6_Missense_Mutation_p.L818P	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	818						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										CGAAGGCTGAAGCGTAAGAGT	0.328																																					p.L818P		Atlas-SNP	.											.	.	.	.	0			c.T2453C						.						90	89	89					13																	42306265		2203	4300	6503	SO:0001583	missense	23078	exon22			GGCTGAAGCGTAA	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.2453T>C	chr13.hg19:g.42306265A>G	ENSP00000368612:p.Leu818Pro	51.0	0.0		32.0	4.0	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	hg19	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.534102	0.85812	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	T;T	0.54866	0.55;0.55	5.94	5.94	0.96194	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.067028	0.64402	D	0.000013	T	0.72326	0.3446	M	0.74546	2.27	0.80722	D	1	D	0.61697	0.99	D	0.69142	0.962	T	0.75216	-0.3396	10	0.66056	D	0.02	.	16.4075	0.83691	1.0:0.0:0.0:0.0	.	818	A3KMH1	K0564_HUMAN	P	722;818;818	ENSP00000368612:L818P;ENSP00000281496:L818P	ENSP00000251030:L722P	L	-	2	0	KIAA0564	41204265	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.272000	0.72575	2.275000	0.75901	0.528000	0.53228	CTT	.	.		0.328	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		G	42306265	A	G	42306265	3	3	91	1	0	0	0	0	1	0	0	0	8194	72	3	2	3364	2	KIAA0564	13	42306265	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4719842	42306265	72863613	466	12540										
KPNA3	3839	hgsc.bcm.edu	37	chr13	50285129	50285129	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttacctccatctgtcaagtaTgacagagcccaaacagtgtc	7	12	2	2	rs370734199		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:50285129T>C	ENST00000261667.3	-	11	1215	c.801A>G	c.(799-801)tcA>tcG	p.S267S		NM_002267.3	NP_002258.2	O00505	IMA4_HUMAN	karyopherin alpha 3 (importin alpha 4)	267					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)|protein complex assembly (GO:0006461)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(4)	21		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)		CTGTCAAGTATGACAGAGCCC	0.398																																					p.S267S		Atlas-SNP	.											.	KPNA3	53	.	0			c.A801G						.						75	66	69					13																	50285129		2203	4300	6503	SO:0001819	synonymous_variant	3839	exon11			CAAGTATGACAGA	D89618	CCDS9421.1	13q14.3	2013-02-14			ENSG00000102753	ENSG00000102753		"Importins", "Armadillo repeat containing"	6396	protein-coding gene	gene with protein product		601892				9154134, 9435235	Standard	NM_002267		Approved	SRP1gamma, SRP4, hSRP1, IPOA4	uc001vdj.2	O00505	OTTHUMG00000016922	ENST00000261667.3:c.801A>G	chr13.hg19:g.50285129T>C		100.0	0.0		68.0	4.0	NM_002267	O00191|O43195|Q5JVM9|Q96AA7	Silent	SNP	ENST00000261667.3	hg19	CCDS9421.1																																																																																			.	.		0.398	KPNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044939.2	NM_002267		C	50285129	T	C	50285129	2	2	91	1	0	0	0	0	0	0	0	1	8440	1451	51	2		2	KPNA3	13	50285129	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	7978864	50285129	64884749	467	12541										
PIBF1	10464	hgsc.bcm.edu	37	chr13	73401963	73401963	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttagtgttcgctgtgctcaTgaagaggatcgccttgaaag	12	8	1	3	rs552358739	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:73401963T>C	ENST00000326291.6	+	8	1346	c.1008T>C	c.(1006-1008)caT>caC	p.H336H		NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	336						centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		GCTGTGCTCATGAAGAGGATC	0.398													T|||	2	0.000399361	0	0	5008	,	,		15434	0.002		0	False		,,,				2504	0				p.H336H		Atlas-SNP	.											.	PIBF1	65	.	0			c.T1008C						.						104	93	97					13																	73401963		2203	4300	6503	SO:0001819	synonymous_variant	10464	exon8			TGCTCATGAAGAG	AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"progesterone-induced blocking factor 1"	607532	"chromosome 13 open reading frame 24"	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.1008T>C	chr13.hg19:g.73401963T>C		73.0	0.0		50.0	4.0	NM_006346	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Silent	SNP	ENST00000326291.6	hg19	CCDS31991.1																																																																																			.	.		0.398	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346		C	73401963	T	C	73401963	2	2	91	1	0	0	0	0	0	0	0	1	11888	1461	51	2		2	PIBF1	13	73401963	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	23116834	73401963	41767915	468	12542										
NALCN	259232	hgsc.bcm.edu	37	chr13	102047689	102047689	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agaaatgacgctgatgatggCacagatgcgcagcaaagagt	13	7	0	6			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:102047689C>A	ENST00000251127.6	-	3	217	c.136G>T	c.(136-138)Gcc>Tcc	p.A46S	NALCN_ENST00000376196.3_Missense_Mutation_p.A46S|NALCN_ENST00000470333.1_5'UTR|NALCN_ENST00000376200.5_Missense_Mutation_p.A46S	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	46					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTGATGATGGCACAGATGCGC	0.423																																					p.A46S		Atlas-SNP	.											.	NALCN	431	.	0			c.G136T						.						129	105	113					13																	102047689		2203	4300	6503	SO:0001583	missense	259232	exon3			TGATGGCACAGAT	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.136G>T	chr13.hg19:g.102047689C>A	ENSP00000251127:p.Ala46Ser	89.0	0.0		64.0	4.0	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.843579	0.91197	.	.	ENSG00000102452	ENST00000251127;ENST00000376196;ENST00000376200;ENST00000449582	D;D;D	0.97404	-4.37;-4.37;-4.37	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.96358	0.8812	L	0.56769	1.78	0.80722	D	1	P;P	0.41929	0.765;0.765	B;B	0.43052	0.353;0.406	D	0.95560	0.8628	10	0.35671	T	0.21	.	19.7619	0.96323	0.0:1.0:0.0:0.0	.	46;46	F2Z323;Q8IZF0	.;NALCN_HUMAN	S	46	ENSP00000251127:A46S;ENSP00000365367:A46S;ENSP00000365373:A46S	ENSP00000251127:A46S	A	-	1	0	NALCN	100845690	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.487000	0.81328	2.681000	0.91329	0.561000	0.74099	GCC	.	.		0.423	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		A	102047689	C	A	102047689	3	1	91	1	0	0	0	0	1	0	0	0	10157	710	25	3	5248	3	NALCN	13	102047689	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	28645726	102047689	13122189	469	12543										
C13orf16	121793	hgsc.bcm.edu	37	chr13	111995257	111995257	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtgctgggccctcgatgaagAgtgacgaggataaggatgat	16	6	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:111995257A>G	ENST00000283547.1	+	5	523	c.394A>G	c.(394-396)Agt>Ggt	p.S132G		NM_152324.1	NP_689537.1	Q8N6K0	TEX29_HUMAN	testis expressed 29	132						integral component of membrane (GO:0016021)											CTCGATGAAGAGTGACGAGGA	0.577																																					p.S132G		Atlas-SNP	.											.	.	.	.	0			c.A394G						.						84	80	81					13																	111995257		2203	4300	6503	SO:0001583	missense	121793	exon5			ATGAAGAGTGACG	BC029889	CCDS9522.1	13q34	2012-03-23	2012-02-07	2012-02-07	ENSG00000153495	ENSG00000153495			20370	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 16"	C13orf16			Standard	NM_152324		Approved	bA474D23.1, MGC35169	uc001vsa.3	Q8N6K0	OTTHUMG00000017358	ENST00000283547.1:c.394A>G	chr13.hg19:g.111995257A>G	ENSP00000283547:p.Ser132Gly	68.0	0.0		52.0	4.0	NM_152324		Missense_Mutation	SNP	ENST00000283547.1	hg19	CCDS9522.1	.	.	.	.	.	.	.	.	.	.	A	6.325	0.428126	0.11987	.	.	ENSG00000153495	ENST00000283547	.	.	.	1.65	-3.3	0.05003	.	8.714320	0.00465	N	0.000116	T	0.19604	0.0471	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.04767	-1.0928	9	0.30078	T	0.28	0.0149	0.0801	0.00031	0.3194:0.241:0.201:0.2386	.	132	Q8N6K0	CM016_HUMAN	G	132	.	ENSP00000283547:S132G	S	+	1	0	C13orf16	110793258	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.432000	0.06956	-0.952000	0.03649	0.379000	0.24179	AGT	.	.		0.577	TEX29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045812.2	NM_152324		G	111995257	A	G	111995257	3	3	91	1	0	0	0	0	1	0	0	0	1721	304	11	2	408	2	C13orf16	13	111995257	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	9947568	111995257	3174621	470	12544										
LAMP1	3916	hgsc.bcm.edu	37	chr13	113973926	113973926	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggacctgcctgctggccagCatggggctgcagctgaacct	15	13	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:113973926C>T	ENST00000332556.4	+	5	899	c.705C>T	c.(703-705)agC>agT	p.S235S	LAMP1_ENST00000397181.3_Silent_p.S182S	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	235	Second lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			TGCTGGCCAGCATGGGGCTGC	0.677																																					p.S235S		Atlas-SNP	.											.	LAMP1	41	.	0			c.C705T						.						48	57	54					13																	113973926		2051	4174	6225	SO:0001819	synonymous_variant	3916	exon5			GGCCAGCATGGGG	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.705C>T	chr13.hg19:g.113973926C>T		43.0	0.0		35.0	4.0	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Silent	SNP	ENST00000332556.4	hg19	CCDS41909.1																																																																																			.	.		0.677	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			T	113973926	C	T	113973926	2	4	91	1	0	0	0	0	0	0	0	1	8626	709	25	3		3	LAMP1	13	113973926	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1978669	113973926	1195952	471	12545										
OR4K14	122740	hgsc.bcm.edu	37	chr14	20482991	20482991	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atatggccacatatctgtcaTaggccatggaaaccaggagc	10	10	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:20482991T>C	ENST00000305045.2	-	1	361	c.362A>G	c.(361-363)tAt>tGt	p.Y121C		NM_001004712.1	NP_001004712.1	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K, member 14	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(20)|skin(6)	37	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)		ATATCTGTCATAGGCCATGGA	0.468																																					p.Y121C		Atlas-SNP	.											.	OR4K14	86	.	0			c.A362G						.						96	93	94					14																	20482991		2203	4300	6503	SO:0001583	missense	122740	exon1			CTGTCATAGGCCA		CCDS32027.1	14q11.2	2013-09-23			ENSG00000169484	ENSG00000169484		"GPCR / Class A : Olfactory receptors"	15352	protein-coding gene	gene with protein product							Standard	NM_001004712		Approved		uc010tky.2	Q8NGD5	OTTHUMG00000170780	ENST00000305045.2:c.362A>G	chr14.hg19:g.20482991T>C	ENSP00000305011:p.Tyr121Cys	124.0	0.0		86.0	4.0	NM_001004712	Q6IEU1|Q96R71	Missense_Mutation	SNP	ENST00000305045.2	hg19	CCDS32027.1	.	.	.	.	.	.	.	.	.	.	.	16.16	3.044397	0.55110	.	.	ENSG00000169484	ENST00000305045	T	0.00490	7.03	4.04	4.04	0.47022	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40640	N	0.001053	T	0.01489	0.0048	M	0.89658	3.05	0.31676	N	0.643736	D	0.67145	0.996	P	0.60886	0.88	T	0.02654	-1.1128	10	0.72032	D	0.01	.	12.097	0.53761	0.0:0.0:0.0:1.0	.	121	Q8NGD5	OR4KE_HUMAN	C	121	ENSP00000305011:Y121C	ENSP00000305011:Y121C	Y	-	2	0	OR4K14	19552831	0.990000	0.36364	1.000000	0.80357	0.966000	0.64601	0.207000	0.17395	1.695000	0.51148	0.413000	0.27773	TAT	.	.		0.468	OR4K14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410343.1			C	20482991	T	C	20482991	3	2	91	1	0	0	0	0	1	0	0	0	11078	1406	49	2	573	2	OR4K14	14	20482991	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10		20482991	86866549	472	12546										
OR6S1	341799	hgsc.bcm.edu	37	chr14	21109228	21109228	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcaaggaagatacaatgacgAgggaggccaggacaaagtca	14	7	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:21109228A>G	ENST00000320704.3	-	1	622	c.623T>C	c.(622-624)cTc>cCc	p.L208P		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		TACAATGACGAGGGAGGCCAG	0.577																																					p.L208P		Atlas-SNP	.											.	OR6S1	49	.	0			c.T623C						.						90	90	90					14																	21109228		2203	4300	6503	SO:0001583	missense	341799	exon1			ATGACGAGGGAGG	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"GPCR / Class A : Olfactory receptors"	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.623T>C	chr14.hg19:g.21109228A>G	ENSP00000313110:p.Leu208Pro	67.0	0.0		46.0	4.0	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	hg19	CCDS32038.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.826478	0.50739	.	.	ENSG00000181803	ENST00000320704	T	0.44881	0.91	5.62	5.62	0.85841	GPCR, rhodopsin-like superfamily (1);	0.349077	0.20846	N	0.084603	T	0.53883	0.1824	L	0.39245	1.2	0.21220	N	0.999757	D	0.63880	0.993	D	0.65323	0.934	T	0.50849	-0.8779	10	0.87932	D	0	-9.0646	13.7709	0.63023	1.0:0.0:0.0:0.0	.	208	Q8NH40	OR6S1_HUMAN	P	208	ENSP00000313110:L208P	ENSP00000313110:L208P	L	-	2	0	OR6S1	20179068	0.000000	0.05858	0.798000	0.32154	0.926000	0.56050	1.250000	0.32850	2.124000	0.65301	0.533000	0.62120	CTC	.	.		0.577	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1			G	21109228	A	G	21109228	3	3	91	1	0	0	0	0	1	0	0	0	11218	304	11	2	376	2	OR6S1	14	21109228	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	626237	21109228	86240312	473	12547										
MMP14	4323	hgsc.bcm.edu	37	chr14	23310816	23310816	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagaagttttacggcttgcaAgtaacaggcaaagctgatgc	11	8	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:23310816A>G	ENST00000311852.6	+	2	486	c.225A>G	c.(223-225)caA>caG	p.Q75Q	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	75					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	ACGGCTTGCAAGTAACAGGCA	0.567																																					p.Q75Q		Atlas-SNP	.											.	MMP14	40	.	0			c.A225G						.						96	73	81					14																	23310816		2203	4300	6503	SO:0001819	synonymous_variant	4323	exon2			CTTGCAAGTAACA		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"membrane type 1 metalloprotease"	600754	"matrix metalloproteinase 14 (membrane-inserted)"			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.225A>G	chr14.hg19:g.23310816A>G		48.0	0.0		44.0	4.0	NM_004995	A8K5L0|Q6GSF3|Q92678	Silent	SNP	ENST00000311852.6	hg19	CCDS9577.1																																																																																			.	.		0.567	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995		G	23310816	A	G	23310816	2	3	91	1	0	0	0	0	0	0	0	1	9662	69	3	2		2	MMP14	14	23310816	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2201588	23310816	84038724	474	12548										
DHRS2	10202	hgsc.bcm.edu	37	chr14	24112421	24112421	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gccagttgctgccctacatgGagaacaggtatggcagggcg	15	10	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:24112421G>A	ENST00000250383.6	+	5	957	c.481G>A	c.(481-483)Gag>Aag	p.E161K	DHRS2_ENST00000344777.7_Missense_Mutation_p.E161K	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	161					C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		GCCCTACATGGAGAACAGGTA	0.582																																					p.E161K		Atlas-SNP	.											DHRS2_ENST00000344777,NS,carcinoma,0,2	DHRS2	78	.	0			c.G481A						.						139	137	138					14																	24112421		2203	4300	6503	SO:0001583	missense	10202	exon5			TACATGGAGAACA		CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18349	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 25C, member 1"	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.481G>A	chr14.hg19:g.24112421G>A	ENSP00000250383:p.Glu161Lys	85.0	0.0		58.0	3.0	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	ENST00000250383.6	hg19	CCDS9604.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.56|12.56	1.974175|1.974175	0.34848|0.34848	.|.	.|.	ENSG00000100867|ENSG00000100867	ENST00000432832;ENST00000250383;ENST00000344777;ENST00000553600|ENST00000557535	T;T;T;T|.	0.19532|.	2.14;2.14;2.14;2.14|.	4.6|4.6	4.6|4.6	0.57074|0.57074	.|.	0.234355|.	0.42294|.	D|.	0.000722|.	T|T	0.32255|0.32255	0.0823|0.0823	N|N	0.04162|0.04162	-0.26|-0.26	0.47441|0.47441	D|D	0.999422|0.999422	B;B;B|.	0.33212|.	0.055;0.402;0.007|.	B;B;B|.	0.27380|.	0.035;0.079;0.013|.	T|T	0.15263|0.15263	-1.0443|-1.0443	10|5	0.05833|.	T|.	0.94|.	.|.	11.0392|11.0392	0.47820|0.47820	0.0:0.1884:0.8116:0.0|0.0:0.1884:0.8116:0.0	.|.	161;161;139|.	C9JZP6;D3DS54;Q13268-2|.	.;.;.|.	K|E	161;161;161;61|76	ENSP00000401213:E161K;ENSP00000250383:E161K;ENSP00000344674:E161K;ENSP00000451485:E61K|.	ENSP00000250383:E161K|.	E|G	+|+	1|2	0|0	DHRS2|DHRS2	23182261|23182261	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.574000|0.574000	0.36063|0.36063	4.151000|4.151000	0.58105|0.58105	2.533000|2.533000	0.85409|0.85409	0.563000|0.563000	0.77884|0.77884	GAG|GGA	.	.		0.582	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908		A	24112421	G	A	24112421	3	1	91	1	0	0	0	0	1	0	0	0	4492	1175	41	3	495	3	DHRS2	14	24112421	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	801605	24112421	83237119	475	12549										
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24533482	24533482	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacctgggactcgtcaggagAatgggatggccacccgcctg	14	13	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:24533482A>G	ENST00000342740.5	+	32	3161	c.3007A>G	c.(3007-3009)Aat>Gat	p.N1003D	LRRC16B_ENST00000334420.7_Missense_Mutation_p.N99D	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1003						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TCGTCAGGAGAATGGGATGGC	0.567																																					p.N1003D		Atlas-SNP	.											.	LRRC16B	120	.	0			c.A3007G						.						62	51	54					14																	24533482		2203	4300	6503	SO:0001583	missense	90668	exon32			CAGGAGAATGGGA	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.3007A>G	chr14.hg19:g.24533482A>G	ENSP00000340467:p.Asn1003Asp	51.0	0.0		56.0	4.0	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	hg19	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.328354	0.60743	.	.	ENSG00000186648	ENST00000342740;ENST00000334420	T;T	0.56941	0.43;0.43	5.28	5.28	0.74379	.	0.000000	0.45606	D	0.000343	T	0.61489	0.2351	L	0.46157	1.445	0.38364	D	0.944697	D;P	0.64830	0.994;0.882	D;B	0.68039	0.955;0.332	T	0.61158	-0.7119	10	0.24483	T	0.36	-18.0226	11.6259	0.51145	1.0:0.0:0.0:0.0	.	99;1003	Q8ND23-2;Q8ND23	.;LR16B_HUMAN	D	1003;99	ENSP00000340467:N1003D;ENSP00000334701:N99D	ENSP00000334701:N99D	N	+	1	0	LRRC16B	23603322	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.348000	0.52209	1.998000	0.58463	0.533000	0.62120	AAT	.	.		0.567	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		G	24533482	A	G	24533482	3	3	91	1	0	0	0	0	1	0	0	0	8981	246	9	2	3133	2	LRRC16B	14	24533482	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	421061	24533482	82816058	476	12550										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33293955	33293955	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttctaaaccttcatgaaaaAcgacatagaaatatgcatag	5	8	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:33293955A>G	ENST00000280979.4	+	13	7106	c.6936A>G	c.(6934-6936)aaA>aaG	p.K2312K	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2312					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TTCATGAAAAACGACATAGAA	0.418																																					p.K2312K	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.A6936G						.						65	69	68					14																	33293955		2146	4282	6428	SO:0001819	synonymous_variant	9472	exon13			TGAAAAACGACAT	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6936A>G	chr14.hg19:g.33293955A>G		137.0	0.0		111.0	5.0	NM_004274	A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	hg19	CCDS9644.1																																																																																			.	.		0.418	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		G	33293955	A	G	33293955	2	3	91	1	0	0	0	0	0	0	0	1	455	40	2	2		2	AKAP6	14	33293955	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	8760473	33293955	74055585	477	12551										
KIAA0391	9692	hgsc.bcm.edu	37	chr14	35596745	35596745	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagctgagtccagaagaataTgaatgtcttaagggaaaaat	10	5	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:35596745T>C	ENST00000557565.1	+	4	1476	c.1095T>C	c.(1093-1095)taT>taC	p.Y365Y	KIAA0391_ENST00000603588.1_3'UTR|KIAA0391_ENST00000321130.10_Silent_p.Y349Y|KIAA0391_ENST00000604948.1_Silent_p.Y270Y|KIAA0391_ENST00000534898.4_Silent_p.Y365Y|KIAA0391_ENST00000605870.1_5'UTR|KIAA0391_ENST00000603544.1_Silent_p.Y349Y|KIAA0391_ENST00000250377.7_Silent_p.Y270Y	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	365					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		CAGAAGAATATGAATGTCTTA	0.358																																					p.Y365Y		Atlas-SNP	.											.	KIAA0391	35	.	0			c.T1095C						.						82	82	82					14																	35596745		2203	4300	6503	SO:0001819	synonymous_variant	9692	exon4			AGAATATGAATGT	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 3", "proteinaceous RNase P"	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.1095T>C	chr14.hg19:g.35596745T>C		110.0	0.0		92.0	4.0	NM_014672	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Silent	SNP	ENST00000557565.1	hg19	CCDS32063.1																																																																																			.	.		0.358	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		C	35596745	T	C	35596745	2	2	91	1	0	0	0	0	0	0	0	1	8181	1471	51	2		2	KIAA0391	14	35596745	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2302790	35596745	71752795	478	12552										
CLEC14A	161198	hgsc.bcm.edu	37	chr14	38724408	38724408	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccccagctcgaagcccgtagCacattcgcaggcaaagcctc	9	17	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:38724408C>A	ENST00000342213.2	-	1	1166	c.820G>T	c.(820-822)Gct>Tct	p.A274S		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	274	EGF-like.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		AAGCCCGTAGCACATTCGCAG	0.662																																					p.A274S		Atlas-SNP	.											CLEC14A,NS,carcinoma,0,1	CLEC14A	83	.	0			c.G820T						.						63	69	67					14																	38724408		2203	4300	6503	SO:0001583	missense	161198	exon1			CCGTAGCACATTC		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"C-type lectin domain containing"	19832	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 27"	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.820G>T	chr14.hg19:g.38724408C>A	ENSP00000353013:p.Ala274Ser	74.0	0.0		59.0	3.0	NM_175060	Q695G9|Q6PWT6|Q8N5V5	Missense_Mutation	SNP	ENST00000342213.2	hg19	CCDS9667.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.867327	0.32977	.	.	ENSG00000176435	ENST00000342213;ENST00000546356	D	0.95622	-3.76	3.91	3.91	0.45181	Epidermal growth factor-like (1);	0.127905	0.30101	N	0.010420	D	0.94142	0.8121	N	0.20986	0.625	0.32366	N	0.556535	D	0.64830	0.994	D	0.62955	0.909	D	0.92674	0.6152	10	0.32370	T	0.25	-9.0137	11.7127	0.51635	0.0:1.0:0.0:0.0	.	274	Q86T13	CLC14_HUMAN	S	274;39	ENSP00000353013:A274S	ENSP00000353013:A274S	A	-	1	0	CLEC14A	37794159	0.993000	0.37304	0.953000	0.39169	0.611000	0.37282	1.858000	0.39408	2.498000	0.84270	0.591000	0.81541	GCT	.	.		0.662	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		A	38724408	C	A	38724408	3	1	91	1	0	0	0	0	1	0	0	0	3501	710	25	3	656	3	CLEC14A	14	38724408	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	3127663	38724408	68625132	479	12553										
C14orf138	79609	hgsc.bcm.edu	37	chr14	50583176	50583176	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccacgccaccggagctatacTgctgtagtcgtagcactgta	10	13	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:50583176T>C	ENST00000395860.2	-	1	99	c.95A>G	c.(94-96)cAg>cGg	p.Q32R	VCPKMT_ENST00000395859.2_Missense_Mutation_p.Q32R	NM_024558.2	NP_078834.2	Q9H867	MT21D_HUMAN	valosin containing protein lysine (K) methyltransferase	32					peptidyl-lysine trimethylation (GO:0018023)	cytoplasm (GO:0005737)	protein-lysine N-methyltransferase activity (GO:0016279)										GGAGCTATACTGCTGTAGTCG	0.597																																					p.Q32R		Atlas-SNP	.											.	METTL21D	11	.	0			c.A95G						.						59	63	62					14																	50583176		2203	4300	6503	SO:0001583	missense	79609	exon1			CTATACTGCTGTA	AK023982	CCDS9696.2, CCDS41951.1	14q21.3	2013-09-30	2013-09-30	2013-09-30	ENSG00000100483	ENSG00000100483			20352	protein-coding gene	gene with protein product		615260	"chromosome 14 open reading frame 138", "methyltransferase like 21D"	C14orf138, METTL21D		22948820	Standard	NR_049738		Approved	VCP-KMT	uc001wxo.1	Q9H867	OTTHUMG00000029531	ENST00000395860.2:c.95A>G	chr14.hg19:g.50583176T>C	ENSP00000379201:p.Gln32Arg	98.0	0.0		84.0	4.0	NM_024558	B7ZLA3|B7ZLA4|Q2M2X3|Q86T12	Missense_Mutation	SNP	ENST00000395860.2	hg19	CCDS9696.2	.	.	.	.	.	.	.	.	.	.	T	29.1	4.975096	0.92919	.	.	ENSG00000100483	ENST00000395859;ENST00000395860	T;T	0.07688	3.17;3.17	6.06	4.93	0.64822	.	0.050670	0.85682	D	0.000000	T	0.32496	0.0831	M	0.88310	2.945	0.54753	D	0.999982	D;D	0.76494	0.999;0.997	D;D	0.69307	0.963;0.927	T	0.18429	-1.0337	10	0.72032	D	0.01	-4.084	12.113	0.53850	0.0:0.0665:0.0:0.9335	.	32;32	B7ZLA4;Q9H867	.;MT21D_HUMAN	R	32	ENSP00000379200:Q32R;ENSP00000379201:Q32R	ENSP00000379200:Q32R	Q	-	2	0	METTL21D	49652926	1.000000	0.71417	0.997000	0.53966	0.970000	0.65996	7.115000	0.77110	1.122000	0.41944	0.528000	0.53228	CAG	.	.		0.597	VCPKMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276877.1	NM_024558		C	50583176	T	C	50583176	3	2	91	1	0	0	0	0	1	0	0	0	1748	1580	55	2	618	2	C14orf138	14	50583176	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	11858768	50583176	56766364	480	12554										
DHRS7	51635	hgsc.bcm.edu	37	chr14	60619873	60619873	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agagaacgctgggacattccAccattgttgaccagaatgtc	10	10	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:60619873A>G	ENST00000216500.5	-	5	872	c.417T>C	c.(415-417)ggT>ggC	p.G139G	DHRS7_ENST00000536410.2_Silent_p.G89G|PCNXL4_ENST00000553898.1_Intron|DHRS7_ENST00000557185.1_Silent_p.G139G|DHRS7_ENST00000553986.1_5'UTR|PCNXL4_ENST00000406949.1_Intron			Q9Y394	DHRS7_HUMAN	dehydrogenase/reductase (SDR family) member 7	139						membrane (GO:0016020)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	5				OV - Ovarian serous cystadenocarcinoma(108;0.121)		GGGACATTCCACCATTGTTGA	0.428																																					p.G139G		Atlas-SNP	.											.	DHRS7	31	.	0			c.T417C						.						96	87	90					14																	60619873		2203	4300	6503	SO:0001819	synonymous_variant	51635	exon4			CATTCCACCATTG	AF151844	CCDS9743.1	14q23.1	2011-09-20			ENSG00000100612	ENSG00000100612		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	21524	protein-coding gene	gene with protein product	"retinal short-chain dehydrogenase/reductase 4", "short chain dehydrogenase/reductase family 34C, member 1"	612833				10800688, 10810093, 19027726	Standard	NM_016029		Approved	retDSR4, SDR34C1	uc001xes.3	Q9Y394	OTTHUMG00000140331	ENST00000216500.5:c.417T>C	chr14.hg19:g.60619873A>G		123.0	0.0		102.0	5.0	NM_016029	B2R896|Q9UKU2	Silent	SNP	ENST00000216500.5	hg19	CCDS9743.1	.	.	.	.	.	.	.	.	.	.	A	4.680	0.126440	0.08931	.	.	ENSG00000100612	ENST00000557751;ENST00000554101	.	.	.	5.95	0.798	0.18660	.	.	.	.	.	T	0.45216	0.1331	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21999	-1.0229	4	.	.	.	.	3.5656	0.07899	0.4401:0.0:0.1984:0.3614	.	.	.	.	A	7;134	.	.	V	-	2	0	DHRS7	59689626	0.932000	0.31603	0.984000	0.44739	0.402000	0.30811	0.172000	0.16704	-0.090000	0.12462	-0.371000	0.07208	GTG	.	.		0.428	DHRS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276947.2	NM_016029		G	60619873	A	G	60619873	2	3	91	1	0	0	0	0	0	0	0	1	4497	146	6	2		2	DHRS7	14	60619873	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	10036697	60619873	46729667	481	12555										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64630170	64630170	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaagcctttctccaaaattcCagtgtcctggatcgactccc	7	14	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:64630170C>A	ENST00000344113.4	+	89	16562	c.16350C>A	c.(16348-16350)tcC>tcA	p.S5450S	SYNE2_ENST00000357395.3_Silent_p.S1835S|SYNE2_ENST00000555002.1_Silent_p.S2084S|SYNE2_ENST00000358025.3_Silent_p.S5450S|SYNE2_ENST00000394768.2_Silent_p.S1835S|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Silent_p.S5367S	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5450					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TCCAAAATTCCAGTGTCCTGG	0.522																																					p.S5450S		Atlas-SNP	.											.	SYNE2	577	.	0			c.C16350A						.						76	79	78					14																	64630170		2203	4300	6503	SO:0001819	synonymous_variant	23224	exon89			AAATTCCAGTGTC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.16350C>A	chr14.hg19:g.64630170C>A		106.0	0.0		97.0	4.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.522	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64630170	C	A	64630170	2	1	91	1	0	0	0	0	0	0	0	1	15461	581	21	3		3	SYNE2	14	64630170	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	4010297	64630170	42719370	482	12556										
YLPM1	56252	hgsc.bcm.edu	37	chr14	75301993	75301993	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgggcagacctggaagagaAgaaggatgcagataggaaaa	15	4	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:75301993A>G	ENST00000552421.1	+	19	4326	c.4202A>G	c.(4201-4203)aAg>aGg	p.K1401R	YLPM1_ENST00000325680.7_Missense_Mutation_p.K2107R			P49750	YLPM1_HUMAN	YLP motif containing 1	1912					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CTGGAAGAGAAGAAGGATGCA	0.468																																					p.K2107R		Atlas-SNP	.											.	YLPM1	298	.	0			c.A6320G						.						102	101	101					14																	75301993		1883	4121	6004	SO:0001583	missense	56252	exon20			AAGAGAAGAAGGA	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.4202A>G	chr14.hg19:g.75301993A>G	ENSP00000447921:p.Lys1401Arg	106.0	0.0		100.0	4.0	NM_019589	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.66	2.602157	0.46423	.	.	ENSG00000119596	ENST00000552421;ENST00000325680	.	.	.	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000001	T	0.49338	0.1551	N	0.04203	-0.255	0.80722	D	1	D	0.63880	0.993	D	0.63488	0.915	T	0.57585	-0.7786	9	0.33940	T	0.23	-13.4137	15.8972	0.79344	1.0:0.0:0.0:0.0	.	2107	P49750-4	.	R	1401;2107	.	ENSP00000324463:K2107R	K	+	2	0	YLPM1	74371746	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.157000	0.67596	0.460000	0.39030	AAG	.	.		0.468	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		G	75301993	A	G	75301993	3	3	91	1	0	0	0	0	1	0	0	0	17501	72	3	2	6398	2	YLPM1	14	75301993	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	10671823	75301993	32047547	483	12557										
POMT2	29954	hgsc.bcm.edu	37	chr14	77765880	77765880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tatgaggcacaggacacgagCagtcaggtgttttcccacag	12	10	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:77765880C>T	ENST00000261534.4	-	7	1043	c.841G>A	c.(841-843)Gct>Act	p.A281T		NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	281						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		AGGACACGAGCAGTCAGGTGT	0.507																																					p.A281T		Atlas-SNP	.											.	POMT2	47	.	0			c.G841A						.						137	111	119					14																	77765880		2203	4300	6503	SO:0001583	missense	29954	exon7			CACGAGCAGTCAG	AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.841G>A	chr14.hg19:g.77765880C>T	ENSP00000261534:p.Ala281Thr	95.0	0.0		124.0	5.0	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	hg19	CCDS9857.1	.	.	.	.	.	.	.	.	.	.	C	36	5.598825	0.96614	.	.	ENSG00000009830	ENST00000261534	D	0.86769	-2.17	5.41	5.41	0.78517	Glycosyl transferase, family 39 (1);	0.000000	0.85682	D	0.000000	D	0.93933	0.8058	M	0.83692	2.655	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	D	0.93826	0.7123	10	0.51188	T	0.08	-9.8709	19.187	0.93648	0.0:1.0:0.0:0.0	.	281	Q9UKY4	POMT2_HUMAN	T	281	ENSP00000261534:A281T	ENSP00000261534:A281T	A	-	1	0	POMT2	76835633	1.000000	0.71417	0.996000	0.52242	0.890000	0.51754	7.036000	0.76524	2.515000	0.84797	0.655000	0.94253	GCT	.	.		0.507	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382		T	77765880	C	T	77765880	3	4	91	1	0	0	0	0	1	0	0	0	12255	710	25	3	1471	3	POMT2	14	77765880	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2463887	77765880	29583660	484	12558										
FOXN3	1112	hgsc.bcm.edu	37	chr14	89878687	89878687	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttctaatcggatgtcaggcAgagaaaagtcgaggtcatcg	12	8	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:89878687A>G	ENST00000345097.4	-	2	250	c.134T>C	c.(133-135)cTg>cCg	p.L45P	FOXN3_ENST00000555353.1_Missense_Mutation_p.L45P|RP11-33N16.3_ENST00000555070.1_RNA|RP11-33N16.2_ENST00000556383.1_RNA|FOXN3_ENST00000261302.5_Missense_Mutation_p.L45P|FOXN3_ENST00000557258.1_Missense_Mutation_p.L45P	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	45					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GATGTCAGGCAGAGAAAAGTC	0.532																																					p.L45P		Atlas-SNP	.											.	FOXN3	78	.	0			c.T134C						.						90	84	86					14																	89878687		2203	4300	6503	SO:0001583	missense	1112	exon2			TCAGGCAGAGAAA		CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254		"Forkhead boxes"	1928	protein-coding gene	gene with protein product		602628	"chromosome 14 open reading frame 116", "checkpoint suppressor 1"	C14orf116, CHES1		9154802	Standard	NM_005197		Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.134T>C	chr14.hg19:g.89878687A>G	ENSP00000343288:p.Leu45Pro	92.0	0.0		83.0	4.0	NM_005197	Q96II7|Q9UIE7	Missense_Mutation	SNP	ENST00000345097.4	hg19	CCDS41977.1	.	.	.	.	.	.	.	.	.	.	A	10.09	1.253771	0.22965	.	.	ENSG00000053254	ENST00000345097;ENST00000261302;ENST00000557258;ENST00000555353;ENST00000555855;ENST00000555034;ENST00000553904	T;T;T;T;D	0.95724	-0.03;-0.03;-0.03;-0.03;-3.79	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000007	D	0.91703	0.7377	L	0.43152	1.355	0.80722	D	1	B;B	0.14805	0.009;0.011	B;B	0.16289	0.004;0.015	D	0.87527	0.2450	10	0.30078	T	0.28	.	9.7105	0.40243	0.9226:0.0:0.0774:0.0	.	45;45	O00409;O00409-2	FOXN3_HUMAN;.	P	45	ENSP00000343288:L45P;ENSP00000261302:L45P;ENSP00000452005:L45P;ENSP00000452227:L45P;ENSP00000451135:L45P	ENSP00000261302:L45P	L	-	2	0	FOXN3	88948440	1.000000	0.71417	0.936000	0.37596	0.329000	0.28539	4.205000	0.58466	2.012000	0.59069	0.528000	0.53228	CTG	.	.		0.532	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410902.2	NM_005197		G	89878687	A	G	89878687	3	3	91	1	0	0	0	0	1	0	0	0	6029	188	7	2	1362	2	FOXN3	14	89878687	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	12112807	89878687	17470853	485	12559										
RPS6KA5	9252	hgsc.bcm.edu	37	chr14	91369167	91369167	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	attacctgaaacagcttctcAgaactctggggcagggctgc	11	11	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:91369167A>G	ENST00000261991.3	-	9	1277	c.1104T>C	c.(1102-1104)tcT>tcC	p.S368S	RPS6KA5_ENST00000536315.2_Silent_p.S289S|RPS6KA5_ENST00000418736.2_Silent_p.S368S	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	368	AGC-kinase C-terminal.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		ACAGCTTCTCAGAACTCTGGG	0.413																																					p.S368S		Atlas-SNP	.											.	RPS6KA5	135	.	0			c.T1104C						.						82	75	77					14																	91369167		2203	4300	6503	SO:0001819	synonymous_variant	9252	exon9			CTTCTCAGAACTC	AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"ribosomal protein S6 kinase, 90kD, polypeptide 5"			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.1104T>C	chr14.hg19:g.91369167A>G		168.0	0.0		125.0	5.0	NM_182398	O95316|Q96AF7	Silent	SNP	ENST00000261991.3	hg19	CCDS9893.1																																																																																			.	.		0.413	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		G	91369167	A	G	91369167	2	3	91	1	0	0	0	0	0	0	0	1	13669	175	7	2		2	RPS6KA5	14	91369167	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1490480	91369167	15980373	486	12560										
GPR68	8111	hgsc.bcm.edu	37	chr14	91700443	91700443	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcacccagcgggtaggcctCcctggcccggccggtcctgg	16	17	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:91700443C>T	ENST00000531499.2	-	2	1291	c.952G>A	c.(952-954)Gag>Aag	p.E318K	GPR68_ENST00000238699.3_Missense_Mutation_p.E328K|GPR68_ENST00000529300.1_5'Flank|GPR68_ENST00000535815.1_Missense_Mutation_p.E318K			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	318					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		GGGTAGGCCTCCCTGGCCCGG	0.731																																					p.E318K		Atlas-SNP	.											.	GPR68	32	.	0			c.G952A						.						7	10	9					14																	91700443		1923	3691	5614	SO:0001583	missense	8111	exon2			AGGCCTCCCTGGC	U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"GPCR / Class A : Orphans"	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.952G>A	chr14.hg19:g.91700443C>T	ENSP00000434045:p.Glu318Lys	18.0	0.0		23.0	6.0	NM_001177676	Q13334|Q4VBB4|Q6IX34	Missense_Mutation	SNP	ENST00000531499.2	hg19	CCDS9894.2	.	.	.	.	.	.	.	.	.	.	C	12.55	1.972256	0.34754	.	.	ENSG00000119714	ENST00000531499;ENST00000238699;ENST00000535815;ENST00000529102	T;T;T;T	0.62498	0.03;0.02;0.03;0.04	5.26	3.39	0.38822	.	0.192813	0.31092	N	0.008273	T	0.44932	0.1317	L	0.27053	0.805	0.27758	N	0.943931	B;B	0.19200	0.034;0.034	B;B	0.20577	0.03;0.03	T	0.28299	-1.0048	10	0.22706	T	0.39	.	8.9293	0.35661	0.0:0.7721:0.149:0.0789	.	318;318	Q6NWR5;Q15743	.;OGR1_HUMAN	K	318;328;318;318	ENSP00000434045:E318K;ENSP00000238699:E328K;ENSP00000440797:E318K;ENSP00000432740:E318K	ENSP00000238699:E328K	E	-	1	0	GPR68	90770196	0.992000	0.36948	0.887000	0.34795	0.603000	0.37013	1.735000	0.38176	0.572000	0.29383	0.555000	0.69702	GAG	.	.		0.731	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2			T	91700443	C	T	91700443	3	4	91	1	0	0	0	0	1	0	0	0	6715	864	30	3	149	3	GPR68	14	91700443	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	331276	91700443	15649097	487	12561										
SERPINA11	256394	hgsc.bcm.edu	37	chr14	94914957	94914957	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aagcaaaattggtaatggtgGgtgtgattctgtggtaggcg	16	3	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:94914957G>A	ENST00000334708.3	-	2	219	c.155C>T	c.(154-156)cCc>cTc	p.P52L	RP11-349I1.2_ENST00000536735.1_RNA	NM_001080451.1	NP_001073920.1	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	52					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(14)|skin(1)|upper_aerodigestive_tract(1)	24				COAD - Colon adenocarcinoma(157;0.211)		GGTAATGGTGGGTGTGATTCT	0.567																																					p.P52L		Atlas-SNP	.											.	SERPINA11	53	.	0			c.C155T						.						122	134	130					14																	94914957		2203	4300	6503	SO:0001583	missense	256394	exon2			ATGGTGGGTGTGA	BX248259	CCDS32149.1	14q32.13	2014-02-18	2005-08-18		ENSG00000186910	ENSG00000186910		"Serine (or cysteine) peptidase inhibitors"	19193	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11"			15014966, 24172014	Standard	NM_001080451		Approved		uc001ydd.1	Q86U17	OTTHUMG00000171348	ENST00000334708.3:c.155C>T	chr14.hg19:g.94914957G>A	ENSP00000335024:p.Pro52Leu	96.0	0.0		92.0	4.0	NM_001080451	B2RV07	Missense_Mutation	SNP	ENST00000334708.3	hg19	CCDS32149.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.622231	0.66787	.	.	ENSG00000186910	ENST00000334708	D	0.87256	-2.23	4.85	4.85	0.62838	Serpin domain (1);	0.000000	0.64402	D	0.000009	D	0.91643	0.7359	M	0.72894	2.215	0.48830	D	0.999715	D	0.63046	0.992	D	0.63597	0.916	D	0.91936	0.5559	10	0.59425	D	0.04	.	13.5049	0.61479	0.0773:0.0:0.9227:0.0	.	52	Q86U17	SPA11_HUMAN	L	52	ENSP00000335024:P52L	ENSP00000335024:P52L	P	-	2	0	SERPINA11	93984710	1.000000	0.71417	0.999000	0.59377	0.528000	0.34623	5.441000	0.66569	2.516000	0.84829	0.655000	0.94253	CCC	.	.		0.567	SERPINA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413091.1	NM_001080451		A	94914957	G	A	94914957	3	1	91	1	0	0	0	0	1	0	0	0	14103	1232	43	3	1129	3	SERPINA11	14	94914957	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3214514	94914957	12434583	488	12562										
TCL1B	9623	hgsc.bcm.edu	37	chr14	96157133	96157133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgcatacccgggagctactcTcctccggccagatgcccttc	9	17	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:96157133T>C	ENST00000340722.7	+	2	274	c.223T>C	c.(223-225)Tcc>Ccc	p.S75P	RP11-1070N10.6_ENST00000461160.1_RNA	NM_004918.3	NP_004909.1	O95988	TCL1B_HUMAN	T-cell leukemia/lymphoma 1B	75										cervix(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		GGAGCTACTCTCCTCCGGCCA	0.582																																					p.S75P		Atlas-SNP	.											.	TCL1B	30	.	0			c.T223C						.						106	105	105					14																	96157133		2203	4300	6503	SO:0001583	missense	9623	exon2			CTACTCTCCTCCG	AB018563	CCDS32151.1	14q32.1	2008-09-05			ENSG00000213231	ENSG00000213231			11649	protein-coding gene	gene with protein product		603769				10077617	Standard	NM_004918		Approved	TML1	uc001yez.3	O95988	OTTHUMG00000028912	ENST00000340722.7:c.223T>C	chr14.hg19:g.96157133T>C	ENSP00000343223:p.Ser75Pro	76.0	0.0		95.0	6.0	NM_004918	A6NEK7|Q6IAR7|Q9UBQ4	Missense_Mutation	SNP	ENST00000340722.7	hg19	CCDS32151.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.345544	0.24426	.	.	ENSG00000213231	ENST00000340722;ENST00000538038	T	0.28895	1.59	3.0	-2.93	0.05598	.	.	.	.	.	T	0.17152	0.0412	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.25187	-1.0139	9	0.30854	T	0.27	-0.8758	7.98	0.30177	0.0:0.6107:0.0:0.3893	.	75	O95988	TCL1B_HUMAN	P	75	ENSP00000343223:S75P	ENSP00000343223:S75P	S	+	1	0	TCL1B	95226886	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.504000	0.00964	-0.558000	0.06118	0.379000	0.24179	TCC	.	.		0.582	TCL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315123.2			C	96157133	T	C	96157133	3	2	91	1	0	0	0	0	1	0	0	0	15720	1551	54	2	229	2	TCL1B	14	96157133	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1242176	96157133	11192407	489	12563										
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102551266	102551266	+	Missense_Mutation	SNP	T	T	C													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctctttctcttctttttcttTttcttcttctttgtcttcct							TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:102551266T>C	ENST00000216281.8	-	5	938	c.733A>G	c.(733-735)Aaa>Gaa	p.K245E	HSP90AA1_ENST00000441629.2_Missense_Mutation_p.K66E|HSP90AA1_ENST00000334701.7_Missense_Mutation_p.K367E	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	245					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)	p.E366fs*72(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	tctttttctttttcttcttct	0.378																																					p.K367E		Atlas-SNP	.											.,1	HSP90AA1	65	.	1	Deletion - Frameshift(1)	ovary(1)	c.A1099G						.						54	51	52					14																	102551266		2203	4300	6503	SO:0001583	missense	3320	exon6			TTTCTTTTTCTTC	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.733A>G	chr14.hg19:g.102551266T>C	ENSP00000216281:p.Lys245Glu	249.0	0.0		189.0	9.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Missense_Mutation	SNP	ENST00000216281.8	hg19	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	t	2.275	-0.366010	0.05069	.	.	ENSG00000080824	ENST00000216281;ENST00000334701;ENST00000441629	T;T;T	0.57107	0.42;0.42;0.42	4.37	3.22	0.36961	.	0.557487	0.16271	N	0.221780	T	0.23649	0.0572	N	0.04162	-0.26	0.19775	N	0.999954	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.18871	-1.0323	10	0.02654	T	1	-22.5825	9.1829	0.37152	0.0:0.089:0.0:0.911	.	66;367;245	Q86U12;P07900-2;P07900	.;.;HS90A_HUMAN	E	245;367;66	ENSP00000216281:K245E;ENSP00000335153:K367E;ENSP00000396189:K66E	ENSP00000216281:K245E	K	-	1	0	HSP90AA1	101621019	0.810000	0.29049	0.390000	0.26220	0.768000	0.43524	1.460000	0.35244	1.748000	0.51833	0.482000	0.46254	AAA	.	.		0.378	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		C	102551266	T	C	102551266	3	2	91	1	0	0	0	0	1	0	0	0	7410	1850	64	2	1493	2	HSP90AA1	14	102551266	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	6394133	102551266	4798274	490	12564	53	2								
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102551269	102551269	+	Missense_Mutation	SNP	C	C	T													0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttctcttctttttctttttCttcttctttgtcttcctttt					rs3208444		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:102551269C>T	ENST00000216281.8	-	5	935	c.730G>A	c.(730-732)Gaa>Aaa	p.E244K	HSP90AA1_ENST00000441629.2_Missense_Mutation_p.E65K|HSP90AA1_ENST00000334701.7_Missense_Mutation_p.E366K	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	244					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)	p.E366fs*72(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	ttttctttttcttcttctttg	0.383																																					p.E366K		Atlas-SNP	.											.	HSP90AA1	65	.	1	Deletion - Frameshift(1)	ovary(1)	c.G1096A						.						53	50	51					14																	102551269		2203	4300	6503	SO:0001583	missense	3320	exon6			CTTTTTCTTCTTC	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.730G>A	chr14.hg19:g.102551269C>T	ENSP00000216281:p.Glu244Lys	246.0	0.0		186.0	11.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Missense_Mutation	SNP	ENST00000216281.8	hg19	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	c	11.92	1.781836	0.31502	.	.	ENSG00000080824	ENST00000216281;ENST00000334701;ENST00000441629	T;T;T	0.59083	0.29;0.29;0.29	4.37	3.4	0.38934	.	0.579755	0.15072	U	0.282125	T	0.40498	0.1119	N	0.20766	0.605	0.53005	D	0.999964	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.09377	0.003;0.004;0.003	T	0.18713	-1.0328	10	0.15952	T	0.53	-12.6218	13.6002	0.62015	0.0:0.8432:0.1568:0.0	rs3208444	65;366;244	Q86U12;P07900-2;P07900	.;.;HS90A_HUMAN	K	244;366;65	ENSP00000216281:E244K;ENSP00000335153:E366K;ENSP00000396189:E65K	ENSP00000216281:E244K	E	-	1	0	HSP90AA1	101621022	0.009000	0.17119	0.449000	0.26957	0.672000	0.39443	1.078000	0.30754	2.152000	0.67230	0.591000	0.81541	GAA	.	.		0.383	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		T	102551269	C	T	102551269	3	4	91	1	0	0	0	0	1	0	0	0	7410	922	32	3	1496	3	HSP90AA1	14	102551269	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	3	102551269	4798271	491	12565	53	2								
GPR132	29933	hgsc.bcm.edu	37	chr14	105517339	105517339	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacacagtgggctcagcaggActcctcaatcagcctctttg	9	14	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:105517339A>G	ENST00000329797.3	-	4	2046	c.1135T>C	c.(1135-1137)Tcc>Ccc	p.S379P	GPR132_ENST00000392585.2_Missense_Mutation_p.S370P|GPR132_ENST00000546679.1_5'Flank|GPR132_ENST00000539291.2_Missense_Mutation_p.S379P	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	379					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		GCTCAGCAGGACTCCTCAATC	0.647																																					p.S379P		Atlas-SNP	.											.	GPR132	40	.	0			c.T1135C						.						58	52	54					14																	105517339		2203	4300	6503	SO:0001583	missense	29933	exon4			AGCAGGACTCCTC	AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"GPCR / Class A : Orphans"	17482	protein-coding gene	gene with protein product	"G2 accumulation"	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.1135T>C	chr14.hg19:g.105517339A>G	ENSP00000328818:p.Ser379Pro	124.0	0.0		99.0	5.0	NM_013345	A8K7X7|B4E144|Q9BSU2	Missense_Mutation	SNP	ENST00000329797.3	hg19	CCDS9997.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.780763	0.31502	.	.	ENSG00000183484	ENST00000329797;ENST00000392585;ENST00000539291	T;T;T	0.38887	1.11;1.14;1.11	2.56	-2.83	0.05769	.	1.607050	0.04698	N	0.415371	T	0.24044	0.0582	N	0.19112	0.55	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.08055	0.003;0.003	T	0.11792	-1.0573	10	0.33141	T	0.24	.	3.4172	0.07380	0.3461:0.0:0.4416:0.2122	.	370;379	B4E144;Q9UNW8	.;GP132_HUMAN	P	379;370;379	ENSP00000328818:S379P;ENSP00000376364:S370P;ENSP00000438094:S379P	ENSP00000328818:S379P	S	-	1	0	GPR132	104588384	0.000000	0.05858	0.003000	0.11579	0.558000	0.35554	-1.056000	0.03489	-0.692000	0.05128	0.379000	0.24179	TCC	.	.		0.647	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345		G	105517339	A	G	105517339	3	3	91	1	0	0	0	0	1	0	0	0	6650	275	10	2	11	2	GPR132	14	105517339	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2966070	105517339	1832201	492	12566										
MKRN3	7681	hgsc.bcm.edu	37	chr15	23811668	23811668	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggttgcggttttgctattatGcttccaggggagtttgcttt	13	6	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:23811668G>A	ENST00000314520.3	+	1	1215	c.739G>A	c.(739-741)Gct>Act	p.A247T	MKRN3_ENST00000568252.1_Intron|MKRN3_ENST00000568945.1_3'UTR|RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000564592.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	247					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		TTGCTATTATGCTTCCAGGGG	0.577																																					p.A247T		Atlas-SNP	.											MKRN3,right_upper_lobe,carcinoma,0,1	MKRN3	155	.	0			c.G739A						.						99	105	103					15																	23811668		2203	4300	6503	SO:0001583	missense	7681	exon1			TATTATGCTTCCA	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"RING-type (C3HC4) zinc fingers"	7114	protein-coding gene	gene with protein product	"zinc finger protein 127"	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.739G>A	chr15.hg19:g.23811668G>A	ENSP00000313881:p.Ala247Thr	69.0	0.0		66.0	3.0	NM_005664		Missense_Mutation	SNP	ENST00000314520.3	hg19	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.653168	0.47362	.	.	ENSG00000179455	ENST00000314520	T	0.41758	0.99	4.07	3.14	0.36123	Zinc finger, CCCH-type (2);	0.241045	0.40222	N	0.001143	T	0.66973	0.2844	M	0.91717	3.235	0.58432	D	0.999992	D	0.89917	1.0	D	0.72075	0.976	T	0.70447	-0.4869	10	0.33141	T	0.24	.	11.4389	0.50086	0.0:0.0:0.8184:0.1815	.	247	Q13064	MKRN3_HUMAN	T	247	ENSP00000313881:A247T	ENSP00000313881:A247T	A	+	1	0	MKRN3	21362761	1.000000	0.71417	0.024000	0.17045	0.005000	0.04900	7.156000	0.77453	1.288000	0.44600	-0.182000	0.12963	GCT	.	.		0.577	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664		A	23811668	G	A	23811668	3	1	91	1	0	0	0	0	1	0	0	0	9617	1319	46	3	741	3	MKRN3	15	23811668	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10		23811668	78719724	493	12567										
HERC2	8924	hgsc.bcm.edu	37	chr15	28493786	28493786	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgcagtaacaaatccaatgaAgcagatctttcacgactgtg	8	10	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:28493786A>G	ENST00000261609.7	-	21	3255	c.3147T>C	c.(3145-3147)gcT>gcC	p.A1049A		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		AATCCAATGAAGCAGATCTTT	0.388																																					p.A1049A		Atlas-SNP	.											.	HERC2	501	.	0			c.T3147C						.						104	94	98					15																	28493786		2203	4300	6503	SO:0001819	synonymous_variant	8924	exon21			CAATGAAGCAGAT	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.3147T>C	chr15.hg19:g.28493786A>G		125.0	0.0		82.0	4.0	NM_004667		Silent	SNP	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.388	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		G	28493786	A	G	28493786	2	3	91	1	0	0	0	0	0	0	0	1	7067	59	3	2		2	HERC2	15	28493786	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4682118	28493786	74037606	494	12568										
FMN1	342184	hgsc.bcm.edu	37	chr15	33359640	33359640	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctggccaccatcatcagagTcagaatcactggtggtgtgc	11	12	4	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:33359640T>C	ENST00000559047.1	-	3	2043				FMN1_ENST00000334528.9_Missense_Mutation_p.D149G|FMN1_ENST00000558197.1_Missense_Mutation_p.D149G|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000561249.1_Intron			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		ATCATCAGAGTCAGAATCACT	0.517																																					p.D149G		Atlas-SNP	.											.	FMN1	174	.	0			c.A446G						.						74	75	75					15																	33359640		2019	4180	6199	SO:0001627	intron_variant	342184	exon1			TCAGAGTCAGAAT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-2365A>G	chr15.hg19:g.33359640T>C		124.0	0.0		94.0	5.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.79	2.343388	0.41498	.	.	ENSG00000248905	ENST00000334528	T	0.41400	1.0	5.66	4.48	0.54585	.	.	.	.	.	T	0.60117	0.2244	.	.	.	.	.	.	D;D	0.76494	0.999;0.961	D;P	0.65443	0.935;0.616	T	0.71076	-0.4697	7	0.56958	D	0.05	.	12.455	0.55700	0.0:0.0:0.1398:0.8602	.	149;149	Q68DA7-3;Q68DA7-5	.;.	G	149	ENSP00000333950:D149G	ENSP00000333950:D149G	D	-	2	0	FMN1	31146932	0.921000	0.31238	0.797000	0.32132	0.676000	0.39594	2.169000	0.42434	2.157000	0.67596	0.533000	0.62120	GAC	.	.		0.517	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		C	33359640	T	C	33359640	1	2	91	0	1	0	0	0	0	0	0	0	5957	1667	58	2		2	FMN1	15	33359640	Intron	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4865854	33359640	69171752	495	12569										
PGBD4	161779	hgsc.bcm.edu	37	chr15	34395101	34395101	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtttcaaaaattactagagaAacaaatgcccaagctgcctt	6	9	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:34395101A>G	ENST00000397766.2	+	1	828	c.369A>G	c.(367-369)gaA>gaG	p.E123E	EMC7_ENST00000256545.4_5'Flank|EMC7_ENST00000532113.1_5'Flank	NM_152595.4	NP_689808.2	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	123										breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)|prostate(1)	16		all_lung(180;1.76e-08)		all cancers(64;1.22e-17)|GBM - Glioblastoma multiforme(113;1.78e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0242)		TTACTAGAGAAACAAATGCCC	0.428																																					p.E123E		Atlas-SNP	.											.	PGBD4	58	.	0			c.A369G						.						53	55	54					15																	34395101		2201	4298	6499	SO:0001819	synonymous_variant	161779	exon1			TAGAGAAACAAAT	AK057200	CCDS10033.1	15q13.1	2002-10-25			ENSG00000182405	ENSG00000182405			19401	protein-coding gene	gene with protein product							Standard	NM_152595		Approved	FLJ32638, FLJ37497	uc001zho.3	Q96DM1	OTTHUMG00000129370	ENST00000397766.2:c.369A>G	chr15.hg19:g.34395101A>G		118.0	0.0		78.0	4.0	NM_152595	A1L487|A8K0C6|Q8N9E8	Silent	SNP	ENST00000397766.2	hg19	CCDS10033.1																																																																																			.	.		0.428	PGBD4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251522.1			G	34395101	A	G	34395101	2	3	91	1	0	0	0	0	0	0	0	1	11792	11	1	2		2	PGBD4	15	34395101	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1035461	34395101	68136291	496	12570										
C15orf55	256646	hgsc.bcm.edu	37	chr15	34640689	34640689	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgtgcccctggaaaaagcttGgccagggccacatgggacaa	13	11	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:34640689G>A	ENST00000333756.4	+	2	691	c.536G>A	c.(535-537)tGg>tAg	p.W179*	NUTM1_ENST00000537011.1_Nonsense_Mutation_p.W207*|NUTM1_ENST00000438749.3_Nonsense_Mutation_p.W197*	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	179	Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)											GAAAAAGCTTGGCCAGGGCCA	0.587																																					p.W179X		Atlas-SNP	.											.	C15orf55	110	.	0			c.G536A						.						32	32	32					15																	34640689		2201	4298	6499	SO:0001587	stop_gained	256646	exon2			AAGCTTGGCCAGG	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"nuclear protein in testis"	608963	"chromosome 15 open reading frame 55"	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.536G>A	chr15.hg19:g.34640689G>A	ENSP00000329448:p.Trp179*	63.0	0.0		56.0	4.0	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Nonsense_Mutation	SNP	ENST00000333756.4	hg19	CCDS32190.1	.	.	.	.	.	.	.	.	.	.	G	36	5.907219	0.97093	.	.	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000354999;ENST00000333756	.	.	.	5.69	3.83	0.44106	.	0.000000	0.53938	D	0.000044	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	9.4628	0.38796	0.0767:0.1425:0.7808:0.0	.	.	.	.	X	207;197;179;179	.	ENSP00000329448:W179X	W	+	2	0	C15orf55	32427981	1.000000	0.71417	0.995000	0.50966	0.099000	0.18886	2.375000	0.44283	0.775000	0.33450	-0.126000	0.14955	TGG	.	.		0.587	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		A	34640689	G	A	34640689	4	1	91	1	0	0	0	0	0	1	0	0	1805	1357	47	3	542	3	C15orf55	15	34640689	Nonsense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	245588	34640689	67890703	497	12571										
C15orf41	84529	hgsc.bcm.edu	37	chr15	37001438	37001438	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctgtagatgaagatcagcttCgtgcaaagggttatgacaaa	11	6	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:37001438C>A	ENST00000566621.1	+	9	809	c.559C>A	c.(559-561)Cgt>Agt	p.R187S	C15orf41_ENST00000565792.1_3'UTR|C15orf41_ENST00000562489.1_Missense_Mutation_p.R11S|C15orf41_ENST00000567389.1_Missense_Mutation_p.R89S|C15orf41_ENST00000437989.2_Missense_Mutation_p.R187S|C15orf41_ENST00000562877.1_Missense_Mutation_p.R89S|C15orf41_ENST00000338183.4_Missense_Mutation_p.R89S|C15orf41_ENST00000569302.1_Missense_Mutation_p.R187S	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	187										kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		AGATCAGCTTCGTGCAAAGGG	0.299																																					p.R187S		Atlas-SNP	.											.	C15orf41	24	.	0			c.C559A						.						100	97	98					15																	37001438		1821	4075	5896	SO:0001583	missense	84529	exon9			CAGCTTCGTGCAA	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.559C>A	chr15.hg19:g.37001438C>A	ENSP00000455397:p.Arg187Ser	153.0	0.0		93.0	4.0	NM_001130010	B2RD87	Missense_Mutation	SNP	ENST00000566621.1	hg19	CCDS45215.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.484981	0.63962	.	.	ENSG00000186073	ENST00000437989;ENST00000338183	T	0.68025	-0.3	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.84727	0.5536	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86020	0.1506	10	0.72032	D	0.01	-11.6817	20.0359	0.97557	0.0:1.0:0.0:0.0	.	187	Q9Y2V0	CO041_HUMAN	S	187;89	ENSP00000401362:R187S	ENSP00000342433:R89S	R	+	1	0	C15orf41	34788730	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.933000	0.70130	2.805000	0.96524	0.655000	0.94253	CGT	.	.		0.299	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499		A	37001438	C	A	37001438	3	1	91	1	0	0	0	0	1	0	0	0	1797	884	31	1	593	1	C15orf41	15	37001438	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2360749	37001438	65529954	498	12572										
EXD1	161829	hgsc.bcm.edu	37	chr15	41482300	41482300	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtaaagagggtgaaacaggTcggatgaaccatacttctgg	13	6	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:41482300T>C	ENST00000314992.5	-	9	907	c.717A>G	c.(715-717)cgA>cgG	p.R239R	EXD1_ENST00000458580.2_Silent_p.R297R|RN7SL497P_ENST00000476341.2_RNA	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	239							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						GTGAAACAGGTCGGATGAACC	0.428																																					p.R239R		Atlas-SNP	.											.	EXD1	52	.	0			c.A717G						.						118	119	119					15																	41482300		2203	4300	6503	SO:0001819	synonymous_variant	161829	exon9			AACAGGTCGGATG	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"exonuclease 3'-5' domain-like 1"	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.717A>G	chr15.hg19:g.41482300T>C		98.0	0.0		90.0	4.0	NM_152596	A8K909|B7Z839|Q6ZW94	Silent	SNP	ENST00000314992.5	hg19	CCDS10072.1																																																																																			.	.		0.428	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596		C	41482300	T	C	41482300	2	2	91	1	0	0	0	0	0	0	0	1	5299	1654	58	2		2	EXD1	15	41482300	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4480862	41482300	61049092	499	12573										
RPAP1	26015	hgsc.bcm.edu	37	chr15	41819624	41819624	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agaagctgtccctttaccttGatgacatcatgtcgggccag	10	11	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:41819624G>T	ENST00000304330.4	-	12	1724	c.1608C>A	c.(1606-1608)atC>atA	p.I536I	RPAP1_ENST00000561603.1_Silent_p.I536I|RPAP1_ENST00000568413.1_5'Flank	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	536						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CCTTTACCTTGATGACATCAT	0.542																																					p.I536I		Atlas-SNP	.											.	RPAP1	111	.	0			c.C1608A						.						89	90	90					15																	41819624		2203	4300	6503	SO:0001819	synonymous_variant	26015	exon12			TACCTTGATGACA	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.1608C>A	chr15.hg19:g.41819624G>T		117.0	0.0		96.0	4.0	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	ENST00000304330.4	hg19	CCDS10079.1																																																																																			.	.		0.542	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		T	41819624	G	T	41819624	2	4	91	1	0	0	0	0	0	0	0	1	13556	1280	45	3		3	RPAP1	15	41819624	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	337324	41819624	60711768	500	12574										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42167762	42167762	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acttgcttctcaggccttgaAgcctggtctgtatgtcctcc	9	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:42167762A>G	ENST00000320955.6	-	22	4408	c.4181T>C	c.(4180-4182)cTt>cCt	p.L1394P		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1394					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CAGGCCTTGAAGCCTGGTCTG	0.587																																					p.L1359P		Atlas-SNP	.											.	SPTBN5	171	.	0			c.T4076C						.						49	53	52					15																	42167762		2097	4212	6309	SO:0001583	missense	51332	exon22			CCTTGAAGCCTGG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.4181T>C	chr15.hg19:g.42167762A>G	ENSP00000317790:p.Leu1394Pro	117.0	0.0		97.0	4.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	12.15	1.850211	0.32699	.	.	ENSG00000137877	ENST00000320955	T	0.56611	0.45	5.48	5.48	0.80851	.	0.374643	0.23228	N	0.050497	T	0.73337	0.3574	M	0.81942	2.565	0.18873	N	0.999982	D	0.89917	1.0	D	0.75020	0.985	T	0.68704	-0.5338	10	0.87932	D	0	.	14.5835	0.68308	1.0:0.0:0.0:0.0	.	1394	Q9NRC6	SPTN5_HUMAN	P	1394	ENSP00000317790:L1394P	ENSP00000317790:L1394P	L	-	2	0	SPTBN5	39955054	0.166000	0.22962	0.053000	0.19242	0.005000	0.04900	2.641000	0.46587	2.073000	0.62155	0.529000	0.55759	CTT	.	.		0.587	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		G	42167762	A	G	42167762	3	3	91	1	0	0	0	0	1	0	0	0	15137	72	3	2	7031	2	SPTBN5	15	42167762	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	348138	42167762	60363630	501	12575										
TMEM87A	25963	hgsc.bcm.edu	37	chr15	42531866	42531866	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taaataatataaagtcacttAcaatcatcaagggatagtct	5	6	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:42531866A>G	ENST00000389834.4	-	8	949		c.e8+1		TMEM87A_ENST00000448392.1_Splice_Site	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A							integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		AAAGTCACTTACAATCATCAA	0.368																																					.		Atlas-SNP	.											.	TMEM87A	56	.	0			c.684+2T>C						.						122	122	122					15																	42531866		2203	4298	6501	SO:0001630	splice_region_variant	25963	exon9			TCACTTACAATCA	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.684+1T>C	chr15.hg19:g.42531866A>G		99.0	0.0		82.0	4.0	NM_015497	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Splice_Site	SNP	ENST00000389834.4	hg19	CCDS32205.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.531829	0.85706	.	.	ENSG00000103978	ENST00000389834;ENST00000448392;ENST00000535305	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1026	0.72292	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM87A	40319158	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.557000	0.90700	2.140000	0.66376	0.482000	0.46254	.	.	.		0.368	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497	Intron	G	42531866	A	G	42531866	5	3	91	1	0	0	0	0	0	0	1	0	16225	405	14	2	1033	2	TMEM87A	15	42531866	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	364104	42531866	59999526	502	12576										
C15orf63	25764	hgsc.bcm.edu	37	chr15	44093963	44093963	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aacgcagtttgcgggaacacAtgggcaacgtggtagaggcg	16	8	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:44093963A>G	ENST00000406925.1	+	5	4460	c.349A>G	c.(349-351)Atg>Gtg	p.M117V	SERINC4_ENST00000249714.3_5'Flank|SERINC4_ENST00000319327.6_5'Flank|SERF2_ENST00000594896.1_Missense_Mutation_p.M163V|HYPK_ENST00000442995.2_Missense_Mutation_p.M117V|SERF2_ENST00000600633.1_Missense_Mutation_p.M117V|RP11-296A16.1_ENST00000417761.2_5'Flank|HYPK_ENST00000458412.1_3'UTR|SERINC4_ENST00000299969.6_5'Flank			Q9NX55	HYPK_HUMAN	huntingtin interacting protein K	117						cytoplasm (GO:0005737)|nucleus (GO:0005634)							all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		GBM - Glioblastoma multiforme(94;8.1e-07)		GCGGGAACACATGGGCAACGT	0.418																																					p.M117V		Atlas-SNP	.											.	.	.	.	0			c.A349G						.						97	90	92					15																	44093963		2198	4298	6496	SO:0001583	missense	25764	exon4			GAACACATGGGCA	AF049613	CCDS10104.1	15q14	2012-10-08	2012-10-08	2012-10-08	ENSG00000242028	ENSG00000242028			18418	protein-coding gene	gene with protein product	"Huntingtin yeast partner K"	612784	"chromosome 15 open reading frame 63"	C15orf63		9700202, 20154145	Standard	NM_016400		Approved	HSPC136, FLJ20431	uc001ztf.3	Q9NX55	OTTHUMG00000060146	ENST00000406925.1:c.349A>G	chr15.hg19:g.44093963A>G	ENSP00000384474:p.Met117Val	81.0	0.0		97.0	4.0	NM_016400	C9JKJ0|O75408|Q8WUW8|Q9P024	Missense_Mutation	SNP	ENST00000406925.1	hg19	CCDS10104.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494575	0.64186	.	.	ENSG00000242028	ENST00000406925;ENST00000442995	T;T	0.43688	0.94;0.94	5.34	5.34	0.76211	.	0.071805	0.85682	D	0.000000	T	0.34279	0.0892	L	0.36672	1.1	0.80722	D	1	B	0.27117	0.168	B	0.22386	0.039	T	0.09100	-1.0690	10	0.31617	T	0.26	-26.6856	15.4877	0.75578	1.0:0.0:0.0:0.0	.	117	Q9NX55	HYPK_HUMAN	V	117	ENSP00000384474:M117V;ENSP00000401155:M117V	ENSP00000384474:M117V	M	+	1	0	C15orf63	41881255	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.919000	0.70005	2.248000	0.74166	0.533000	0.62120	ATG	.	.		0.418	HYPK-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133876.3	NM_016400		G	44093963	A	G	44093963	3	3	91	1	0	0	0	0	1	0	0	0	1811	217	8	2	363	2	C15orf63	15	44093963	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1562097	44093963	58437429	503	12577										
SHF	90525	hgsc.bcm.edu	37	chr15	45467612	45467612	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctgagttgctgtctccttggAgccccggatctctgccggag	13	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:45467612A>G	ENST00000560734.1	-	3	652	c.652T>C	c.(652-654)Tcc>Ccc	p.S218P	SHF_ENST00000560540.1_Missense_Mutation_p.S218P|SHF_ENST00000561091.1_5'UTR|SHF_ENST00000318390.6_Missense_Mutation_p.S210P|SHF_ENST00000290894.8_Missense_Mutation_p.S153P|SHF_ENST00000458022.2_Missense_Mutation_p.S16P|RP11-519G16.2_ENST00000560034.1_RNA|SHF_ENST00000560471.1_Missense_Mutation_p.S218P					Src homology 2 domain containing F											endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		GTCTCCTTGGAGCCCCGGATC	0.637																																					p.S153P		Atlas-SNP	.											.	SHF	27	.	0			c.T457C						.						35	28	31					15																	45467612		2195	4296	6491	SO:0001583	missense	90525	exon4			CCTTGGAGCCCCG	BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"SH2 domain containing"	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000560734.1:c.652T>C	chr15.hg19:g.45467612A>G	ENSP00000453168:p.Ser218Pro	75.0	0.0		75.0	4.0	NM_138356		Missense_Mutation	SNP	ENST00000560734.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.94	1.492540	0.26774	.	.	ENSG00000138606	ENST00000290894;ENST00000361989;ENST00000318390;ENST00000458022;ENST00000413198	T;T;T	0.30448	1.53;1.53;1.53	5.25	5.25	0.73442	.	0.201227	0.44483	D	0.000455	T	0.47303	0.1438	L	0.58510	1.815	0.34878	D	0.744315	D;D;B;B;B	0.71674	0.983;0.998;0.023;0.039;0.023	P;P;B;B;B	0.62649	0.791;0.905;0.007;0.028;0.017	T	0.58885	-0.7557	10	0.36615	T	0.2	-10.114	13.1129	0.59283	1.0:0.0:0.0:0.0	.	16;153;143;210;153	Q8N9I8;E7EV73;E7EWB7;F8W6K9;Q7M4L6	.;.;.;.;SHF_HUMAN	P	153;153;210;16;143	ENSP00000290894:S153P;ENSP00000315978:S210P;ENSP00000411530:S16P	ENSP00000290894:S153P	S	-	1	0	SHF	43254904	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.330000	0.52068	1.981000	0.57761	0.402000	0.26972	TCC	.	.		0.637	SHF-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000416338.1	NM_138356		G	45467612	A	G	45467612	3	3	91	1	0	0	0	0	1	0	0	0	14292	304	11	2	834	2	SHF	15	45467612	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1373649	45467612	57063780	504	12578										
SQRDL	58472	hgsc.bcm.edu	37	chr15	45965905	45965905	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agctctgcaggacttcaaagAgggcaatgccatcttcacct	9	12	4	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:45965905A>G	ENST00000260324.7	+	5	946	c.560A>G	c.(559-561)gAg>gGg	p.E187G	SQRDL_ENST00000568606.1_Missense_Mutation_p.E187G|RP11-96O20.4_ENST00000564080.1_Missense_Mutation_p.E187G	NM_021199.3	NP_067022.1	Q9Y6N5	SQRD_HUMAN	sulfide quinone reductase-like (yeast)	187					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial inner membrane (GO:0005743)	sulfide:quinone oxidoreductase activity (GO:0070224)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	11		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		GACTTCAAAGAGGGCAATGCC	0.453																																					p.E187G		Atlas-SNP	.											.	SQRDL	27	.	0			c.A560G						.						140	128	132					15																	45965905		2198	4297	6495	SO:0001583	missense	58472	exon5			TCAAAGAGGGCAA	AF042284	CCDS10127.1	15q21.1	2010-08-05			ENSG00000137767	ENSG00000137767			20390	protein-coding gene	gene with protein product						10810093, 10224084	Standard	NM_021199		Approved	CGI-44	uc001zvu.4	Q9Y6N5	OTTHUMG00000131476	ENST00000260324.7:c.560A>G	chr15.hg19:g.45965905A>G	ENSP00000260324:p.Glu187Gly	130.0	0.0		109.0	5.0	NM_021199	Q9UQM8	Missense_Mutation	SNP	ENST00000260324.7	hg19	CCDS10127.1	.	.	.	.	.	.	.	.	.	.	A	6.130	0.392133	0.11581	.	.	ENSG00000137767	ENST00000260324	T	0.45276	0.9	5.62	5.62	0.85841	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.094126	0.64402	D	0.000001	T	0.16385	0.0394	N	0.01576	-0.805	0.51012	D	0.999908	B	0.02656	0.0	B	0.11329	0.006	T	0.20672	-1.0268	10	0.02654	T	1	-10.0801	14.6676	0.68921	1.0:0.0:0.0:0.0	.	187	Q9Y6N5	SQRD_HUMAN	G	187	ENSP00000260324:E187G	ENSP00000260324:E187G	E	+	2	0	SQRDL	43753197	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	7.338000	0.79269	2.146000	0.66826	0.460000	0.39030	GAG	.	.		0.453	SQRDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254319.2			G	45965905	A	G	45965905	3	3	91	1	0	0	0	0	1	0	0	0	15144	304	11	2	574	2	SQRDL	15	45965905	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	498293	45965905	56565487	505	12579										
DTWD1	56986	hgsc.bcm.edu	37	chr15	49935632	49935632	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttgaagccatttactactttCtggtagactaccatactgat	6	9	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:49935632C>T	ENST00000251250.6	+	6	979	c.772C>T	c.(772-774)Ctg>Ttg	p.L258L	DTWD1_ENST00000403028.3_Silent_p.L258L|DTWD1_ENST00000415425.1_Silent_p.L171L|DTWD1_ENST00000558653.1_Silent_p.L258L	NM_020234.5	NP_064619.2	Q8N5C7	DTWD1_HUMAN	DTW domain containing 1	258										endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;0.0384)		all cancers(107;3.27e-08)|GBM - Glioblastoma multiforme(94;7.6e-05)		TTACTACTTTCTGGTAGACTA	0.323																																					p.L258L		Atlas-SNP	.											.	DTWD1	22	.	0			c.C772T						.						57	63	61					15																	49935632		2194	4293	6487	SO:0001819	synonymous_variant	56986	exon5			TACTTTCTGGTAG	BC032535	CCDS10132.1	15q21.2	2005-08-09			ENSG00000104047	ENSG00000104047			30926	protein-coding gene	gene with protein product							Standard	NM_020234		Approved	MDS009, MGC111207	uc001zxs.3	Q8N5C7	OTTHUMG00000131567	ENST00000251250.6:c.772C>T	chr15.hg19:g.49935632C>T		255.0	0.0		220.0	13.0	NM_001144955	Q567Q3|Q8WVG9|Q9NRU6	Silent	SNP	ENST00000251250.6	hg19	CCDS10132.1																																																																																			.	.		0.323	DTWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254431.2	NM_020234		T	49935632	C	T	49935632	2	4	91	1	0	0	0	0	0	0	0	1	4793	912	32	3		3	DTWD1	15	49935632	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	3969727	49935632	52595760	506	12580										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54529885	54529885	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acatccctaaataatgaggaActggtaagtactagatattg	8	6	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:54529885A>G	ENST00000260323.11	+	6	3225	c.3225A>G	c.(3223-3225)gaA>gaG	p.E1075E	UNC13C_ENST00000537900.1_Silent_p.E1073E|UNC13C_ENST00000545554.1_Silent_p.E1075E	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1075					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ATAATGAGGAACTGGTAAGTA	0.388																																					p.E1075E		Atlas-SNP	.											.	UNC13C	674	.	0			c.A3225G						.						77	73	74					15																	54529885		1885	4093	5978	SO:0001819	synonymous_variant	440279	exon5			TGAGGAACTGGTA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.3225A>G	chr15.hg19:g.54529885A>G		112.0	0.0		82.0	4.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.388	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		G	54529885	A	G	54529885	2	3	91	1	0	0	0	0	0	0	0	1	17001	40	2	2		2	UNC13C	15	54529885	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4594253	54529885	48001507	507	12581										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54707196	54707196	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttaggtttcctcaagagctgAacatgggaaaaataagtgcc	10	7	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:54707196A>T	ENST00000260323.11	+	18	4864	c.4864A>T	c.(4864-4866)Aac>Tac	p.N1622Y	UNC13C_ENST00000537900.1_Missense_Mutation_p.N1620Y|UNC13C_ENST00000545554.1_Missense_Mutation_p.N1622Y	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1622					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCAAGAGCTGAACATGGGAAA	0.303																																					p.N1622Y		Atlas-SNP	.											.	UNC13C	674	.	0			c.A4864T						.						101	100	100					15																	54707196		1815	4066	5881	SO:0001583	missense	440279	exon17			GAGCTGAACATGG	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.4864A>T	chr15.hg19:g.54707196A>T	ENSP00000260323:p.Asn1622Tyr	125.0	0.0		111.0	5.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.330404	0.81690	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.82081	-1.57;-1.57;-1.57	5.61	5.61	0.85477	Calcium-dependent secretion activator (1);	0.092243	0.64402	D	0.000001	D	0.91509	0.7319	M	0.85945	2.785	0.54753	D	0.999988	D;D	0.89917	1.0;1.0	D;D	0.91635	0.99;0.999	D	0.92734	0.6202	10	0.87932	D	0	.	13.7525	0.62917	1.0:0.0:0.0:0.0	.	1622;1622	F5H090;Q8NB66	.;UN13C_HUMAN	Y	1622;1622;1620	ENSP00000260323:N1622Y;ENSP00000438156:N1622Y;ENSP00000442569:N1620Y	ENSP00000260323:N1622Y	N	+	1	0	UNC13C	52494488	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.489000	0.90461	2.138000	0.66242	0.533000	0.62120	AAC	.	.		0.303	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54707196	A	T	54707196	3	4	91	1	0	0	0	0	1	0	0	0	17001	246	9	4	4930	4	UNC13C	15	54707196	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	177311	54707196	47824196	508	12582										
TPM1	7168	hgsc.bcm.edu	37	chr15	63349281	63349281	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcaacagctttgcagaagcTggaggaagctgagaaggcag	16	7	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:63349281T>C	ENST00000403994.3	+	3	418	c.338T>C	c.(337-339)cTg>cCg	p.L113P	TPM1_ENST00000317516.7_Missense_Mutation_p.L77P|TPM1_ENST00000334895.5_Missense_Mutation_p.L77P|TPM1_ENST00000560959.1_Missense_Mutation_p.L77P|TPM1_ENST00000288398.6_Missense_Mutation_p.L113P|TPM1_ENST00000559397.1_Missense_Mutation_p.L113P|TPM1_ENST00000404484.4_Missense_Mutation_p.L77P|TPM1_ENST00000559281.1_Missense_Mutation_p.L77P|TPM1_ENST00000357980.4_Missense_Mutation_p.L155P|TPM1_ENST00000358278.3_Missense_Mutation_p.L113P|TPM1_ENST00000267996.7_Missense_Mutation_p.L113P|TPM1_ENST00000559556.1_Missense_Mutation_p.L113P|TPM1_ENST00000560445.1_Intron	NM_001018005.1	NP_001018005.1	P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	113					cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						TTGCAGAAGCTGGAGGAAGCT	0.547																																					p.L113P		Atlas-SNP	.											.	TPM1	59	.	0			c.T338C						.						103	97	99					15																	63349281		2203	4300	6503	SO:0001583	missense	7168	exon3			AGAAGCTGGAGGA	AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416		"Tropomyosins"	12010	protein-coding gene	gene with protein product		191010	"chromosome 15 open reading frame 13", "cardiomyopathy, hypertrophic 3"	C15orf13, CMH3		10343096, 8205619	Standard	XM_005254637		Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000403994.3:c.338T>C	chr15.hg19:g.63349281T>C	ENSP00000385107:p.Leu113Pro	86.0	0.0		84.0	4.0	NM_001018007	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Missense_Mutation	SNP	ENST00000403994.3	hg19	CCDS45273.1	.	.	.	.	.	.	.	.	.	.	T	18.60	3.658219	0.67586	.	.	ENSG00000140416	ENST00000288398;ENST00000267996;ENST00000358278;ENST00000403994;ENST00000357980;ENST00000404484;ENST00000334895;ENST00000317516	D;D;D;D;D;D	0.99194	-5.54;-5.54;-5.54;-5.54;-5.54;-5.54	5.72	5.72	0.89469	.	0.000000	0.41001	D	0.000979	D	0.99641	0.9868	H	0.99299	4.505	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;0.998;1.0;1.0;0.998;0.998;1.0;1.0;0.998	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;0.995;1.0;1.0;1.0;0.994;1.0;0.998;0.991;0.997;0.996;1.0;0.994	D	0.97366	0.9973	10	0.87932	D	0	-11.1461	15.1809	0.72956	0.0:0.0:0.0:1.0	.	77;77;113;79;77;77;113;155;113;113;113;113;113;113	B7Z722;B7Z596;P09493-6;F5H7S3;D9YZV7;Q1ZYL5;D9YZV4;Q6ZN40;D9YZV8;D9YZV5;Q9Y427;D9YZV3;D9YZV2;P09493	.;.;.;.;.;.;.;.;.;.;.;.;.;TPM1_HUMAN	P	113;113;113;113;155;135;77;79	ENSP00000288398:L113P;ENSP00000267996:L113P;ENSP00000351022:L113P;ENSP00000385107:L113P;ENSP00000350667:L155P;ENSP00000334624:L77P	ENSP00000267996:L113P	L	+	2	0	TPM1	61136334	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.040000	0.89188	2.187000	0.69744	0.482000	0.46254	CTG	.	.		0.547	TPM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417083.2	NM_001018004		C	63349281	T	C	63349281	3	2	91	1	0	0	0	0	1	0	0	0	16420	1580	55	2	614	2	TPM1	15	63349281	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	8642085	63349281	39182111	509	12583										
ANKDD1A	348094	hgsc.bcm.edu	37	chr15	65219192	65219192	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggctgtgaccacaatgtcaaAgacaaggtaccgtgtccgtg	12	10	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:65219192A>G	ENST00000380230.3	+	6	593	c.564A>G	c.(562-564)aaA>aaG	p.K188K	ANKDD1A_ENST00000357698.3_Silent_p.K188K|ANKDD1A_ENST00000496660.1_Silent_p.K97K|ANKDD1A_ENST00000491145.1_3'UTR|ANKDD1A_ENST00000319580.8_3'UTR|AC069368.3_ENST00000437723.1_Intron|ANKDD1A_ENST00000395720.1_Silent_p.K188K|ANKDD1A_ENST00000395723.1_Silent_p.K97K	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	188					signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						ACAATGTCAAAGACAAGGTAC	0.617																																					p.K188K		Atlas-SNP	.											.	ANKDD1A	47	.	0			c.A564G						.						111	93	99					15																	65219192		2202	4299	6501	SO:0001819	synonymous_variant	348094	exon6			TGTCAAAGACAAG		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.564A>G	chr15.hg19:g.65219192A>G		112.0	0.0		63.0	4.0	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Silent	SNP	ENST00000380230.3	hg19	CCDS10197.2																																																																																			.	.		0.617	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703		G	65219192	A	G	65219192	2	3	91	1	0	0	0	0	0	0	0	1	624	69	3	2		2	ANKDD1A	15	65219192	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1869911	65219192	37312200	510	12584										
CILP	8483	hgsc.bcm.edu	37	chr15	65499173	65499173	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agcagttctggccaggccgcTgctccctgttgaggcaccag	13	14	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:65499173T>C	ENST00000261883.4	-	4	537	c.371A>G	c.(370-372)cAg>cGg	p.Q124R		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	124					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						GCCAGGCCGCTGCTCCCTGTT	0.642																																					p.Q124R		Atlas-SNP	.											.	CILP	124	.	0			c.A371G						.						56	59	58					15																	65499173		2201	4299	6500	SO:0001583	missense	8483	exon4			GGCCGCTGCTCCC	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.371A>G	chr15.hg19:g.65499173T>C	ENSP00000261883:p.Gln124Arg	60.0	0.0		45.0	4.0	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	hg19	CCDS10203.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.190444	0.78789	.	.	ENSG00000138615	ENST00000261883	T	0.22743	1.94	5.3	5.3	0.74995	.	0.246394	0.43747	D	0.000532	T	0.44932	0.1317	M	0.94101	3.495	0.58432	D	0.999996	D	0.53312	0.959	P	0.50109	0.631	T	0.57619	-0.7780	10	0.45353	T	0.12	-4.0081	13.2541	0.60068	0.0:0.0:0.0:1.0	.	124	O75339	CILP1_HUMAN	R	124	ENSP00000261883:Q124R	ENSP00000261883:Q124R	Q	-	2	0	CILP	63286226	1.000000	0.71417	0.997000	0.53966	0.550000	0.35303	7.756000	0.85195	2.231000	0.72958	0.459000	0.35465	CAG	.	.		0.642	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		C	65499173	T	C	65499173	3	2	91	1	0	0	0	0	1	0	0	0	3431	1580	55	2	3207	2	CILP	15	65499173	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	279981	65499173	37032219	511	12585										
ITGA11	22801	hgsc.bcm.edu	37	chr15	68599732	68599732	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agatgaaggggctgtggaacTgcctctgcaaggctgcgttg	16	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:68599732T>C	ENST00000315757.7	-	28	3421	c.3335A>G	c.(3334-3336)cAg>cGg	p.Q1112R	ITGA11_ENST00000423218.2_Missense_Mutation_p.Q1113R	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	1112					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						GCTGTGGAACTGCCTCTGCAA	0.572											OREG0023219	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q1112R		Atlas-SNP	.											.	ITGA11	110	.	0			c.A3335G						.						37	48	44					15																	68599732		1967	4109	6076	SO:0001583	missense	22801	exon28			TGGAACTGCCTCT	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.3335A>G	chr15.hg19:g.68599732T>C	ENSP00000327290:p.Gln1112Arg	88.0	0.0	1108	86.0	6.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	hg19	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	T	12.86	2.063102	0.36373	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.41400	1.0;1.0	4.73	4.73	0.59995	.	0.429079	0.27558	N	0.018823	T	0.30727	0.0774	N	0.25647	0.755	0.28611	N	0.908682	B;B	0.09022	0.0;0.002	B;B	0.06405	0.001;0.002	T	0.15009	-1.0452	10	0.34782	T	0.22	.	13.3728	0.60723	0.0:0.0:0.0:1.0	.	1112;1112	A8K8T0;Q9UKX5	.;ITA11_HUMAN	R	1112;1113;747	ENSP00000327290:Q1112R;ENSP00000403392:Q1113R	ENSP00000327290:Q1112R	Q	-	2	0	ITGA11	66386786	0.997000	0.39634	1.000000	0.80357	0.990000	0.78478	1.690000	0.37711	1.903000	0.55091	0.454000	0.30748	CAG	.	.		0.572	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		C	68599732	T	C	68599732	3	2	91	1	0	0	0	0	1	0	0	0	7883	1580	55	2	243	2	ITGA11	15	68599732	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3100559	68599732	33931660	512	12586										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72119321	72119321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctgctttttaagttgctttCgcaacttgctggaaggttca	10	8	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:72119321C>T	ENST00000356056.5	-	42	7719	c.7247G>A	c.(7246-7248)cGa>cAa	p.R2416Q	MYO9A_ENST00000424560.1_Missense_Mutation_p.R2487Q|MYO9A_ENST00000444904.1_Missense_Mutation_p.R2397Q|MYO9A_ENST00000564571.1_3'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	2416	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AAGTTGCTTTCGCAACTTGCT	0.438																																					p.R2416Q		Atlas-SNP	.											.	MYO9A	203	.	0			c.G7247A						.						60	62	61					15																	72119321		2199	4297	6496	SO:0001583	missense	4649	exon42			TGCTTTCGCAACT	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.7247G>A	chr15.hg19:g.72119321C>T	ENSP00000348349:p.Arg2416Gln	59.0	0.0		59.0	7.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.254107	0.39896	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.90563	-2.64;-2.69;-2.63	5.55	2.66	0.31614	.	.	.	.	.	D	0.85986	0.5825	L	0.51422	1.61	0.22424	N	0.999114	B;B	0.25312	0.123;0.052	B;B	0.14023	0.01;0.008	T	0.74321	-0.3703	9	0.44086	T	0.13	.	8.7956	0.34876	0.0:0.712:0.0:0.288	.	2416;2180	B2RTY4;B2RTY4-5	MYO9A_HUMAN;.	Q	2416;2487;2397	ENSP00000348349:R2416Q;ENSP00000399162:R2487Q;ENSP00000398250:R2397Q	ENSP00000348349:R2416Q	R	-	2	0	MYO9A	69906375	0.032000	0.19561	0.123000	0.21794	0.825000	0.46686	0.720000	0.25896	0.303000	0.22785	-0.137000	0.14449	CGA	.	.		0.438	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		T	72119321	C	T	72119321	3	4	91	1	0	0	0	0	1	0	0	0	10093	884	31	1	403	1	MYO9A	15	72119321	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	3519589	72119321	30412071	513	12587										
ZNF592	9640	hgsc.bcm.edu	37	chr15	85327556	85327556	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtgaaaaaggctgccccactGattgtagaggtcttcaacaa	10	9	2	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:85327556G>T	ENST00000560079.2	+	4	1938	c.1650G>T	c.(1648-1650)ctG>ctT	p.L550L	ZNF592_ENST00000299927.3_Silent_p.L550L	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	550					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CTGCCCCACTGATTGTAGAGG	0.582																																					p.L550L		Atlas-SNP	.											ZNF592,NS,carcinoma,0,1	ZNF592	95	.	0			c.G1650T						.						88	89	89					15																	85327556		2203	4299	6502	SO:0001819	synonymous_variant	9640	exon4			CCCACTGATTGTA	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"Zinc fingers, C2H2-type"	28986	protein-coding gene	gene with protein product		613624	"spinocerebellar ataxia, autosomal recessive 5"	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.1650G>T	chr15.hg19:g.85327556G>T		103.0	0.0		63.0	3.0	NM_014630	Q2M1T2|Q504Y9	Silent	SNP	ENST00000560079.2	hg19	CCDS32317.1																																																																																			.	.		0.582	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		T	85327556	G	T	85327556	2	4	91	1	0	0	0	0	0	0	0	1	18037	1277	45	3		3	ZNF592	15	85327556	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	13208235	85327556	17203836	514	12588										
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85476374	85476374	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acctgcactctcactcttgcAgatcgatgccacctcgttga	7	15	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:85476374A>G	ENST00000286749.3	+	12	1173		c.e12-1		SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000394573.1_Splice_Site|SLC28A1_ENST00000537624.1_Splice_Site|SLC28A1_ENST00000537216.1_Splice_Site			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1						nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TCACTCTTGCAGATCGATGCC	0.582																																					.		Atlas-SNP	.											.	SLC28A1	118	.	0			c.1084-2A>G						.						194	168	177					15																	85476374		2203	4299	6502	SO:0001630	splice_region_variant	9154	exon13			TCTTGCAGATCGA	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"Solute carriers"	11001	protein-coding gene	gene with protein product		606207	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.1084-1A>G	chr15.hg19:g.85476374A>G		173.0	0.0		121.0	5.0	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Splice_Site	SNP	ENST00000286749.3	hg19	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	A	18.70	3.679187	0.68042	.	.	ENSG00000156222	ENST00000537216;ENST00000537624;ENST00000286749;ENST00000394573	.	.	.	4.4	4.4	0.53042	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6471	0.51267	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC28A1	83277378	1.000000	0.71417	0.973000	0.42090	0.803000	0.45373	8.204000	0.89741	1.840000	0.53500	0.460000	0.39030	.	.	.		0.582	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		Intron	G	85476374	A	G	85476374	5	3	91	1	0	0	0	0	0	0	1	0	14546	202	7	2	1195	2	SLC28A1	15	85476374	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	148818	85476374	17055018	515	12589										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88423565	88423565	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agatctcccagaggatcaccCcgaagctccatacatcactc	6	16	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:88423565C>T	ENST00000360948.2	-	18	2431	c.2270G>A	c.(2269-2271)gGg>gAg	p.G757E	NTRK3_ENST00000557856.1_Missense_Mutation_p.G735E|NTRK3_ENST00000355254.2_Missense_Mutation_p.G743E|NTRK3_ENST00000357724.2_Missense_Mutation_p.G749E|NTRK3_ENST00000394480.2_Missense_Mutation_p.G743E	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	757	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			GAGGATCACCCCGAAGCTCCA	0.512			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.G757E		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.G2270A						.						131	115	120					15																	88423565		2201	4299	6500	SO:0001583	missense	4916	exon19			ATCACCCCGAAGC	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.2270G>A	chr15.hg19:g.88423565C>T	ENSP00000354207:p.Gly757Glu	167.0	0.0		131.0	6.0	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.966557	0.92855	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254	D;D;D;D	0.99158	-5.5;-5.5;-5.5;-5.5	5.34	5.34	0.76211	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99677	0.9879	H	0.99545	4.62	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97157	0.9835	10	0.87932	D	0	.	17.5974	0.88016	0.0:1.0:0.0:0.0	.	735;743;757	B7Z4C5;Q16288-3;Q16288	.;.;NTRK3_HUMAN	E	743;757;749;743	ENSP00000377990:G743E;ENSP00000354207:G757E;ENSP00000350356:G749E;ENSP00000347397:G743E	ENSP00000347397:G743E	G	-	2	0	NTRK3	86224569	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.514000	0.81750	2.482000	0.83794	0.655000	0.94253	GGG	.	.		0.512	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				T	88423565	C	T	88423565	3	4	91	1	0	0	0	0	1	0	0	0	10717	623	22	3	257	3	NTRK3	15	88423565	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2947191	88423565	14107827	516	12590										
BLM	641	hgsc.bcm.edu	37	chr15	91328233	91328233	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagagagatgggctcgctgcTcttgcttaccatgctggcct	12	12	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:91328233T>C	ENST00000355112.3	+	14	2863	c.2745T>C	c.(2743-2745)gcT>gcC	p.A915A	BLM_ENST00000560509.1_Silent_p.A915A|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	915	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			GGCTCGCTGCTCTTGCTTACC	0.468			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.A915A		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	.	BLM	122	.	0			c.T2745C						.						102	91	95					15																	91328233		2198	4298	6496	SO:0001819	synonymous_variant	641	exon14	Familial Cancer Database		CGCTGCTCTTGCT	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"Bloom syndrome"			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.2745T>C	chr15.hg19:g.91328233T>C		99.0	0.0		84.0	4.0	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	hg19	CCDS10363.1																																																																																			.	.		0.468	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			C	91328233	T	C	91328233	2	2	91	1	0	0	0	0	0	0	0	1	1445	1538	54	2		2	BLM	15	91328233	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2904668	91328233	11203159	517	12591										
FES	2242	hgsc.bcm.edu	37	chr15	91434318	91434318	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggtggctgagctgctggtgcActctggggacttcctggtgc	17	10	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:91434318A>G	ENST00000328850.3	+	11	1569	c.1427A>G	c.(1426-1428)cAc>cGc	p.H476R	FES_ENST00000444422.2_Intron|FES_ENST00000414248.2_Intron|FES_ENST00000394300.3_Missense_Mutation_p.H418R|FES_ENST00000450438.2_Intron|FES_ENST00000394302.1_Intron	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	476	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)			lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			CTGCTGGTGCACTCTGGGGAC	0.647																																					p.H476R		Atlas-SNP	.											.	FES	102	.	0			c.A1427G						.						96	73	81					15																	91434318		2195	4293	6488	SO:0001583	missense	2242	exon11			TGGTGCACTCTGG	X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"SH2 domain containing"	3657	protein-coding gene	gene with protein product	"Oncogene FES, feline sarcoma virus", "c-fes/fps protein"	190030	"feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog", "feline sarcoma oncogene"			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.1427A>G	chr15.hg19:g.91434318A>G	ENSP00000331504:p.His476Arg	91.0	0.0		104.0	5.0	NM_002005	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Missense_Mutation	SNP	ENST00000328850.3	hg19	CCDS10365.1	.	.	.	.	.	.	.	.	.	.	A	4.210	0.037720	0.08148	.	.	ENSG00000182511	ENST00000328850;ENST00000394300	T;T	0.61510	0.1;0.1	4.63	3.51	0.40186	SH2 motif (4);	0.269317	0.38959	N	0.001518	T	0.30885	0.0779	N	0.03881	-0.34	0.21861	N	0.999507	B;B;B	0.15473	0.007;0.01;0.013	B;B;B	0.15870	0.014;0.006;0.01	T	0.18335	-1.0340	10	0.44086	T	0.13	-20.1774	8.0094	0.30344	0.8162:0.0:0.1838:0.0	.	458;418;476	B4DUD9;P07332-3;P07332	.;.;FES_HUMAN	R	476;418	ENSP00000331504:H476R;ENSP00000377837:H418R	ENSP00000331504:H476R	H	+	2	0	FES	89235322	0.036000	0.19791	0.013000	0.15412	0.184000	0.23303	3.041000	0.49807	0.817000	0.34445	0.392000	0.25879	CAC	.	.		0.647	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005		G	91434318	A	G	91434318	3	3	91	1	0	0	0	0	1	0	0	0	5828	159	6	2	1465	2	FES	15	91434318	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	106085	91434318	11097074	518	12592										
UNC45A	55898	hgsc.bcm.edu	37	chr15	91491925	91491925	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttgcggtggcctcagcgctGgtgaactgcaccaacagcta	12	12	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:91491925G>A	ENST00000418476.2	+	13	1819	c.1779G>A	c.(1777-1779)ctG>ctA	p.L593L	UNC45A_ENST00000394275.2_Silent_p.L578L	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	593					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CCTCAGCGCTGGTGAACTGCA	0.587																																					p.L593L		Atlas-SNP	.											.	UNC45A	57	.	0			c.G1779A						.						74	60	65					15																	91491925		2198	4298	6496	SO:0001819	synonymous_variant	55898	exon13			AGCGCTGGTGAAC		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"smooth muscle cell associated protein-1"	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.1779G>A	chr15.hg19:g.91491925G>A		88.0	0.0		93.0	4.0	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Silent	SNP	ENST00000418476.2	hg19	CCDS10367.1																																																																																			.	.		0.587	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671		A	91491925	G	A	91491925	2	1	91	1	0	0	0	0	0	0	0	1	17003	1335	47	3		3	UNC45A	15	91491925	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	57607	91491925	11039467	519	12593										
ARRDC4	91947	hgsc.bcm.edu	37	chr15	98512600	98512600	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgcattatcagagtggactaTtccttagctgtaagcaaagc	9	8	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:98512600T>C	ENST00000268042.6	+	5	1037	c.873T>C	c.(871-873)taT>taC	p.Y291Y	ARRDC4_ENST00000538249.1_Silent_p.Y204Y	NM_183376.2	NP_899232.2	Q8NCT1	ARRD4_HUMAN	arrestin domain containing 4	291					positive regulation of ubiquitin-protein transferase activity (GO:0051443)	endosome (GO:0005768)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|skin(3)	16	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)			GAGTGGACTATTCCTTAGCTG	0.393																																					p.Y291Y		Atlas-SNP	.											.	ARRDC4	30	.	0			c.T873C						.						91	82	85					15																	98512600		2197	4298	6495	SO:0001819	synonymous_variant	91947	exon5			GGACTATTCCTTA	BC028704	CCDS10377.1	15q26.2	2005-08-16			ENSG00000140450	ENSG00000140450			28087	protein-coding gene	gene with protein product						12477932	Standard	NM_183376		Approved	FLJ36045	uc010bom.3	Q8NCT1	OTTHUMG00000149849	ENST00000268042.6:c.873T>C	chr15.hg19:g.98512600T>C		121.0	0.0		89.0	4.0	NM_183376	Q6NSI9	Silent	SNP	ENST00000268042.6	hg19	CCDS10377.1																																																																																			.	.		0.393	ARRDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313535.1	NM_183376		C	98512600	T	C	98512600	2	2	91	1	0	0	0	0	0	0	0	1	985	1500	52	2		2	ARRDC4	15	98512600	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	7020675	98512600	4018792	520	12594										
CCNF	899	hgsc.bcm.edu	37	chr16	2503452	2503452	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgtgctgcattaggagtgacAcaagacagccccgacccccc	10	15	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:2503452A>G	ENST00000397066.4	+	15	1717	c.1629A>G	c.(1627-1629)acA>acG	p.T543T	RP11-715J22.3_ENST00000561653.1_RNA|RP11-715J22.4_ENST00000566085.1_lincRNA	NM_001761.2	NP_001752.2	P41002	CCNF_HUMAN	cyclin F	543					mitotic nuclear division (GO:0007067)|negative regulation of centrosome duplication (GO:0010826)|placenta development (GO:0001890)|protein ubiquitination (GO:0016567)|re-entry into mitotic cell cycle (GO:0000320)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	centriole (GO:0005814)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(2)|lung(5)|prostate(4)|skin(1)	20		Ovarian(90;0.17)				TAGGAGTGACACAAGACAGCC	0.627																																					p.T543T		Atlas-SNP	.											.	CCNF	110	.	0			c.A1629G						.						90	83	85					16																	2503452		2198	4300	6498	SO:0001819	synonymous_variant	899	exon15			AGTGACACAAGAC	Z36714	CCDS10467.1	16p13.3	2008-02-05			ENSG00000162063	ENSG00000162063		"F-boxes /  "other""	1591	protein-coding gene	gene with protein product		600227				7896286	Standard	NM_001761		Approved	FBX1, FBXO1	uc002cqd.1	P41002	OTTHUMG00000128858	ENST00000397066.4:c.1629A>G	chr16.hg19:g.2503452A>G		70.0	0.0		65.0	4.0	NM_001761	B2R8H3|Q96EG9	Silent	SNP	ENST00000397066.4	hg19	CCDS10467.1																																																																																			.	.		0.627	CCNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250801.1	NM_001761		G	2503452	A	G	2503452	2	3	91	1	0	0	0	0	0	0	0	1	2924	146	6	2		2	CCNF	16	2503452	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10		2503452	87851301	521	12595										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3799678	3799678	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttttcaaactgatcctttgaAattgtccttgttttaaaata	4	6	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:3799678A>G	ENST00000262367.5	-	21	4595	c.3786T>C	c.(3784-3786)atT>atC	p.I1262I	CREBBP_ENST00000382070.3_Silent_p.I1224I	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1262	Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GATCCTTTGAAATTGTCCTTG	0.284			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.I1262I		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.T3786C						.						83	78	80					16																	3799678		2194	4298	6492	SO:0001819	synonymous_variant	1387	exon21			CTTTGAAATTGTC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.3786T>C	chr16.hg19:g.3799678A>G		114.0	0.0		123.0	5.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.		0.284	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		G	3799678	A	G	3799678	2	3	91	1	0	0	0	0	0	0	0	1	3863	10	1	2		2	CREBBP	16	3799678	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1296226	3799678	86555075	522	12596										
ADCY9	115	hgsc.bcm.edu	37	chr16	4164949	4164949	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taatgccgggcgtacagcttGgtgaaggtaaacagaaagaa	13	6	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:4164949G>T	ENST00000294016.3	-	2	1033	c.495C>A	c.(493-495)acC>acA	p.T165T		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	165					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CGTACAGCTTGGTGAAGGTAA	0.592																																					p.T165T		Atlas-SNP	.											.	ADCY9	151	.	0			c.C495A						.						86	84	85					16																	4164949		2197	4300	6497	SO:0001819	synonymous_variant	115	exon2			CAGCTTGGTGAAG	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.495C>A	chr16.hg19:g.4164949G>T		70.0	0.0		50.0	4.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	hg19	CCDS32382.1																																																																																			.	.		0.592	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			T	4164949	G	T	4164949	2	4	91	1	0	0	0	0	0	0	0	1	301	1335	47	3		3	ADCY9	16	4164949	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	365271	4164949	86189804	523	12597										
VASN	114990	hgsc.bcm.edu	37	chr16	4432547	4432547	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcggggaggcccatacacccCcagccgtccactccaaccac	9	20	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:4432547C>T	ENST00000304735.3	+	2	1824	c.1669C>T	c.(1669-1671)Cca>Tca	p.P557S	CORO7_ENST00000539968.1_Intron|CORO7_ENST00000251166.4_Intron|CORO7_ENST00000537233.2_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000423908.2_Intron|CORO7_ENST00000574025.1_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	557	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						CCATACACCCCCAGCCGTCCA	0.736																																					p.P557S		Atlas-SNP	.											.	VASN	21	.	0			c.C1669T						.						11	17	15					16																	4432547		2153	4249	6402	SO:0001583	missense	114990	exon2			ACACCCCCAGCCG	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"slit-like 2 (Drosophila)"	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.1669C>T	chr16.hg19:g.4432547C>T	ENSP00000306864:p.Pro557Ser	34.0	0.0		46.0	4.0	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Missense_Mutation	SNP	ENST00000304735.3	hg19	CCDS10514.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.632559	0.29068	.	.	ENSG00000168140	ENST00000304735	T	0.55930	0.49	5.22	3.22	0.36961	.	0.609808	0.16478	N	0.212668	T	0.36524	0.0970	N	0.24115	0.695	0.09310	N	1	B	0.26081	0.141	B	0.31016	0.123	T	0.19160	-1.0314	10	0.06625	T	0.88	-6.3503	12.9558	0.58427	0.0:0.6888:0.3112:0.0	.	557	Q6EMK4	VASN_HUMAN	S	557	ENSP00000306864:P557S	ENSP00000306864:P557S	P	+	1	0	VASN	4372548	0.000000	0.05858	0.010000	0.14722	0.892000	0.51952	1.115000	0.31209	0.569000	0.29329	0.655000	0.94253	CCA	.	.		0.736	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440		T	4432547	C	T	4432547	3	4	91	1	0	0	0	0	1	0	0	0	17142	623	22	3	1671	3	VASN	16	4432547	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	267598	4432547	85922206	524	12598										
PPL	5493	hgsc.bcm.edu	37	chr16	4942072	4942072	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccagcagctgcaggaggtgcTcgtatttccggttggtgtcc	14	11	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:4942072T>C	ENST00000345988.2	-	15	1882	c.1793A>G	c.(1792-1794)gAg>gGg	p.E598G	PPL_ENST00000590782.2_Missense_Mutation_p.E596G	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	598					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CAGGAGGTGCTCGTATTTCCG	0.677																																					p.E598G		Atlas-SNP	.											.	PPL	168	.	0			c.A1793G						.						63	62	62					16																	4942072		2197	4300	6497	SO:0001583	missense	5493	exon15			AGGTGCTCGTATT	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.1793A>G	chr16.hg19:g.4942072T>C	ENSP00000340510:p.Glu598Gly	105.0	0.0		88.0	4.0	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	hg19	CCDS10526.1	.	.	.	.	.	.	.	.	.	.	T	11.95	1.791649	0.31685	.	.	ENSG00000118898	ENST00000345988	T	0.37584	1.19	5.35	5.35	0.76521	.	0.573319	0.17738	N	0.163672	T	0.30947	0.0781	L	0.44542	1.39	0.34790	D	0.735676	B	0.32245	0.361	B	0.21708	0.036	T	0.42515	-0.9447	10	0.40728	T	0.16	.	15.3443	0.74324	0.0:0.0:0.0:1.0	.	598	O60437	PEPL_HUMAN	G	598	ENSP00000340510:E598G	ENSP00000340510:E598G	E	-	2	0	PPL	4882073	1.000000	0.71417	1.000000	0.80357	0.222000	0.24845	5.499000	0.66937	2.038000	0.60285	0.448000	0.29417	GAG	.	.		0.677	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705		C	4942072	T	C	4942072	3	2	91	1	0	0	0	0	1	0	0	0	12346	1551	54	2	3509	2	PPL	16	4942072	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	509525	4942072	85412681	525	12599										
TXNDC11	51061	hgsc.bcm.edu	37	chr16	11785663	11785663	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atttcaaaaaagctgcactgTggcacgctgaccgagctcgg	11	11	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:11785663T>C	ENST00000356957.3	-	9	1571	c.1464A>G	c.(1462-1464)ccA>ccG	p.P488P	TXNDC11_ENST00000570917.1_5'Flank|TXNDC11_ENST00000283033.5_Silent_p.P461P			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	488					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						AGCTGCACTGTGGCACGCTGA	0.532																																					p.P461P		Atlas-SNP	.											.	TXNDC11	75	.	0			c.A1383G						.						52	53	53					16																	11785663		2197	4300	6497	SO:0001819	synonymous_variant	51061	exon8			GCACTGTGGCACG	BC013727	CCDS32387.1	16p13.13	2008-09-29				ENSG00000153066			28030	protein-coding gene	gene with protein product	"EF-hand binding protein 1"					8619474, 9110174	Standard	XM_005255346		Approved	EFP1	uc002dbg.1	Q6PKC3		ENST00000356957.3:c.1464A>G	chr16.hg19:g.11785663T>C		77.0	0.0		93.0	4.0	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Silent	SNP	ENST00000356957.3	hg19																																																																																				.	.		0.532	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914		C	11785663	T	C	11785663	2	2	91	1	0	0	0	0	0	0	0	1	16807	1683	59	2		2	TXNDC11	16	11785663	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	6843591	11785663	78569090	526	12600										
SMG1	23049	hgsc.bcm.edu	37	chr16	18849391	18849391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggtgatctctcgctccatcTctctcttgctctgcttgctc	8	15	4	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:18849391T>C	ENST00000446231.2	-	45	7770	c.7358A>G	c.(7357-7359)gAg>gGg	p.E2453G	SMG1_ENST00000389467.3_Missense_Mutation_p.E2453G			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2453	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TCGCTCCATCTCTCTCTTGCT	0.527																																					p.E2453G		Atlas-SNP	.											.	SMG1	401	.	0			c.A7358G						.						38	41	40					16																	18849391		2069	4205	6274	SO:0001583	missense	23049	exon45			TCCATCTCTCTCT	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.7358A>G	chr16.hg19:g.18849391T>C	ENSP00000402515:p.Glu2453Gly	144.0	0.0		123.0	5.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.295773	0.81025	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01185	5.21;5.21	5.72	5.72	0.89469	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (2);	0.000000	0.64402	D	0.000001	T	0.02418	0.0074	L	0.31420	0.93	0.51012	D	0.999901	D	0.55172	0.97	P	0.51895	0.683	T	0.66716	-0.5853	10	0.56958	D	0.05	.	16.2988	0.82793	0.0:0.0:0.0:1.0	.	2453	Q96Q15	SMG1_HUMAN	G	2453	ENSP00000402515:E2453G;ENSP00000374118:E2453G	ENSP00000374118:E2453G	E	-	2	0	SMG1	18756892	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.243000	0.72384	2.311000	0.77944	0.533000	0.62120	GAG	.	.		0.527	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		C	18849391	T	C	18849391	3	2	91	1	0	0	0	0	1	0	0	0	14810	1551	54	2	3703	2	SMG1	16	18849391	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	7063728	18849391	71505362	527	12601										
HS3ST2	9956	hgsc.bcm.edu	37	chr16	22926348	22926348	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cactcaagaggctcctcgacGcatcttcaacatgtcccgag	8	15	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:22926348G>T	ENST00000261374.3	+	2	1003	c.569G>T	c.(568-570)cGc>cTc	p.R190L		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	190					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)			breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		GCTCCTCGACGCATCTTCAAC	0.577																																					p.R190L		Atlas-SNP	.											HS3ST2,colon,carcinoma,0,1	HS3ST2	59	.	0			c.G569T						.						110	100	103					16																	22926348		2197	4300	6497	SO:0001583	missense	9956	exon2			CTCGACGCATCTT	AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"Sulfotransferases, membrane-bound"	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.569G>T	chr16.hg19:g.22926348G>T	ENSP00000261374:p.Arg190Leu	80.0	0.0		64.0	3.0	NM_006043	Q52LZ1	Missense_Mutation	SNP	ENST00000261374.3	hg19	CCDS10606.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.015657	0.54468	.	.	ENSG00000122254	ENST00000261374;ENST00000540146	T	0.48522	0.81	5.25	4.3	0.51218	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.72203	0.3431	M	0.89478	3.035	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78109	-0.2332	10	0.87932	D	0	.	13.1286	0.59369	0.0769:0.0:0.9231:0.0	.	190	Q9Y278	HS3S2_HUMAN	L	190;198	ENSP00000261374:R190L	ENSP00000261374:R190L	R	+	2	0	HS3ST2	22833849	1.000000	0.71417	0.066000	0.19879	0.279000	0.26890	7.863000	0.87023	1.225000	0.43566	0.561000	0.74099	CGC	.	.		0.577	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043		T	22926348	G	T	22926348	3	4	91	1	0	0	0	0	1	0	0	0	7373	1087	38	1	575	1	HS3ST2	16	22926348	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	4076957	22926348	67428405	528	12602										
ZNF689	115509	hgsc.bcm.edu	37	chr16	30615611	30615611	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcgttgcccctctgactggAgcccccgatagcagatctag	12	14	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:30615611A>G	ENST00000287461.3	-	3	1814	c.1477T>C	c.(1477-1479)Tcc>Ccc	p.S493P	ZNF689_ENST00000566673.1_5'Flank|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	493					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			CTCTGACTGGAGCCCCCGATA	0.582																																					p.S493P		Atlas-SNP	.											.	ZNF689	48	.	0			c.T1477C						.						31	31	31					16																	30615611		2197	4300	6497	SO:0001583	missense	115509	exon3			GACTGGAGCCCCC	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"Zinc fingers, C2H2-type", "-"	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.1477T>C	chr16.hg19:g.30615611A>G	ENSP00000287461:p.Ser493Pro	85.0	0.0		84.0	4.0	NM_138447	Q658J5	Missense_Mutation	SNP	ENST00000287461.3	hg19	CCDS10686.1	.	.	.	.	.	.	.	.	.	.	a	0.921	-0.715753	0.03206	.	.	ENSG00000156853	ENST00000287461;ENST00000443190	T	0.06933	3.24	4.38	-4.12	0.03916	.	0.589368	0.15468	N	0.260742	T	0.02610	0.0079	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36432	-0.9748	10	0.27082	T	0.32	-3.2162	1.1893	0.01862	0.3564:0.2821:0.2294:0.1321	.	493	Q96CS4	ZN689_HUMAN	P	493;491	ENSP00000287461:S493P	ENSP00000287461:S493P	S	-	1	0	ZNF689	30523112	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	0.088000	0.14979	-0.729000	0.04875	-0.384000	0.06662	TCC	.	.		0.582	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		G	30615611	A	G	30615611	3	3	91	1	0	0	0	0	1	0	0	0	18109	304	11	2	29	2	ZNF689	16	30615611	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	7689263	30615611	59739142	529	12603										
RNF40	9810	hgsc.bcm.edu	37	chr16	30783507	30783507	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccaggaggagatcaaggagtAcaaggtggggctgtgggcca	18	7	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:30783507A>G	ENST00000324685.6	+	19	3260	c.2825A>G	c.(2824-2826)tAc>tGc	p.Y942C	RNF40_ENST00000357890.5_Missense_Mutation_p.Y842C|RNF40_ENST00000402121.3_Missense_Mutation_p.Y634C|RNF40_ENST00000563683.1_Missense_Mutation_p.Y902C|RNF40_ENST00000567365.1_3'UTR	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	942					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			ATCAAGGAGTACAAGGTGGGG	0.557																																					p.Y942C		Atlas-SNP	.											.	RNF40	83	.	0			c.A2825G						.						65	40	48					16																	30783507		2104	4119	6223	SO:0001583	missense	9810	exon19			AGGAGTACAAGGT	AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"RING-type (C3HC4) zinc fingers"	16867	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"	607700	"ring finger protein 40"			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.2825A>G	chr16.hg19:g.30783507A>G	ENSP00000325677:p.Tyr942Cys	101.0	0.0		88.0	4.0	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	hg19	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.983542	0.74474	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000402121;ENST00000538323	T;T;T	0.36520	1.25;1.27;1.27	5.58	5.58	0.84498	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.60818	0.2298	M	0.73598	2.24	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.984;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.996;0.924;0.983;0.987;0.987	T	0.65327	-0.6195	10	0.87932	D	0	-15.1456	14.741	0.69455	1.0:0.0:0.0:0.0	.	274;634;842;941;942	F6SYU7;F8W8Z4;O75150-4;A8K6K1;O75150	.;.;.;.;BRE1B_HUMAN	C	942;842;634;274	ENSP00000325677:Y942C;ENSP00000350563:Y842C;ENSP00000384942:Y634C	ENSP00000325677:Y942C	Y	+	2	0	RNF40	30691008	1.000000	0.71417	1.000000	0.80357	0.775000	0.43874	8.952000	0.93031	2.135000	0.66039	0.533000	0.62120	TAC	.	.		0.557	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771		G	30783507	A	G	30783507	3	3	91	1	0	0	0	0	1	0	0	0	13508	391	14	2	2895	2	RNF40	16	30783507	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	167896	30783507	59571246	530	12604										
ITGAX	3687	hgsc.bcm.edu	37	chr16	31384577	31384577	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acctgatacccagcttgaagTccctgctggtggggagtaac	12	11	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:31384577T>C	ENST00000268296.4	+	20	2495	c.2374T>C	c.(2374-2376)Tcc>Ccc	p.S792P	ITGAX_ENST00000562522.1_Missense_Mutation_p.S792P	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	792					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CAGCTTGAAGTCCCTGCTGGT	0.537																																					p.S792P		Atlas-SNP	.											.	ITGAX	198	.	0			c.T2374C						.						107	88	94					16																	31384577		2197	4300	6497	SO:0001583	missense	3687	exon20			TTGAAGTCCCTGC	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.2374T>C	chr16.hg19:g.31384577T>C	ENSP00000268296:p.Ser792Pro	128.0	0.0		99.0	4.0	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	hg19	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	A	18.89	3.719230	0.68844	.	.	ENSG00000140678	ENST00000268296	T	0.47177	0.85	4.89	4.89	0.63831	Integrin alpha-2 (1);	.	.	.	.	T	0.27241	0.0668	N	0.08118	0	0.19300	N	0.999972	B	0.24533	0.105	B	0.15484	0.013	T	0.15206	-1.0445	9	0.42905	T	0.14	.	9.2372	0.37473	0.8385:0.0:0.0:0.1615	.	792	P20702	ITAX_HUMAN	P	792	ENSP00000268296:S792P	ENSP00000268296:S792P	S	+	1	0	ITGAX	31292078	0.986000	0.35501	0.463000	0.27130	0.471000	0.32888	2.459000	0.45023	1.003000	0.39130	-0.336000	0.08194	TCC	.	.		0.537	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		C	31384577	T	C	31384577	3	2	91	1	0	0	0	0	1	0	0	0	7898	1667	58	2	2452	2	ITGAX	16	31384577	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	601070	31384577	58970176	531	12605										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31927484	31927484	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tacaaatgtgaagaatgtggCaaagccttcaactataggtc	9	7	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:31927484C>T	ENST00000300870.10	+	4	2123	c.1914C>T	c.(1912-1914)ggC>ggT	p.G638G		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	638					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						AAGAATGTGGCAAAGCCTTCA	0.413																																					p.G638G		Atlas-SNP	.											.	ZNF267	94	.	0			c.C1914T						.						73	75	74					16																	31927484		2197	4300	6497	SO:0001819	synonymous_variant	10308	exon4			ATGTGGCAAAGCC	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.1914C>T	chr16.hg19:g.31927484C>T		92.0	0.0		69.0	4.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Silent	SNP	ENST00000300870.10	hg19	CCDS32440.1																																																																																			.	.		0.413	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		T	31927484	C	T	31927484	2	4	91	1	0	0	0	0	0	0	0	1	17821	697	25	3		3	ZNF267	16	31927484	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	542907	31927484	58427269	532	12606										
CYLD	1540	hgsc.bcm.edu	37	chr16	50818357	50818357	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acagaaattgttaatcctctGagaatgtaagtagaaaacaa	7	5	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:50818357G>A	ENST00000427738.3	+	11	2149	c.1944G>A	c.(1942-1944)ctG>ctA	p.L648L	CYLD_ENST00000566206.1_Silent_p.L645L|CYLD_ENST00000569418.1_Silent_p.L645L|CYLD_ENST00000564326.1_Silent_p.L645L|CYLD_ENST00000311559.9_Silent_p.L648L|CYLD_ENST00000540145.1_Silent_p.L648L|RP11-327F22.4_ENST00000564510.1_RNA|RP11-327F22.4_ENST00000575917.1_RNA|CYLD_ENST00000398568.2_Silent_p.L645L|CYLD_ENST00000568704.2_Silent_p.L463L			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	648	USP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				TTAATCCTCTGAGAATGTAAG	0.333			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.L648L		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	CYLD,right_upper_lobe,carcinoma,0,1	CYLD	150	.	0			c.G1944A						.						95	88	90					16																	50818357		1834	4086	5920	SO:0001819	synonymous_variant	1540	exon13	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	TCCTCTGAGAATG	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1944G>A	chr16.hg19:g.50818357G>A		62.0	0.0		47.0	2.0	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Silent	SNP	ENST00000427738.3	hg19	CCDS45482.1																																																																																			.	.		0.333	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			A	50818357	G	A	50818357	2	1	91	1	0	0	0	0	0	0	0	1	4145	1277	45	3		3	CYLD	16	50818357	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	18890873	50818357	39536396	533	12607										
SLC12A3	6559	hgsc.bcm.edu	37	chr16	56924197	56924197	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctttccagtgatgcctttgAtttcaactatggcgtgtgtg	10	8	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:56924197A>G	ENST00000563236.1	+	19	2322	c.2297A>G	c.(2296-2298)gAt>gGt	p.D766G	SLC12A3_ENST00000438926.2_Missense_Mutation_p.D766G|SLC12A3_ENST00000262502.5_Missense_Mutation_p.D765G|SLC12A3_ENST00000566786.1_Missense_Mutation_p.D765G			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	766				D -> E (in Ref. 1; AAC50355). {ECO:0000305}.	chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	GATGCCTTTGATTTCAACTAT	0.562																																					p.D766G		Atlas-SNP	.											.	SLC12A3	99	.	0			c.A2297G						.						206	145	165					16																	56924197		2198	4300	6498	SO:0001583	missense	6559	exon19			CCTTTGATTTCAA		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"Solute carriers"	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.2297A>G	chr16.hg19:g.56924197A>G	ENSP00000456149:p.Asp766Gly	91.0	0.0		89.0	4.0	NM_001126108	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	hg19	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.674030	0.88445	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	5.63	5.63	0.86233	.	0.150659	0.64402	D	0.000017	D	0.85296	0.5664	M	0.93106	3.38	0.80722	D	1	B;D;D	0.76494	0.338;0.999;0.999	B;D;D	0.71414	0.211;0.94;0.973	D	0.88846	0.3316	9	0.72032	D	0.01	.	15.0231	0.71647	1.0:0.0:0.0:0.0	.	765;766;766	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	G	765;766	.	ENSP00000262502:D766G	D	+	2	0	SLC12A3	55481698	1.000000	0.71417	0.998000	0.56505	0.794000	0.44872	9.281000	0.95811	2.137000	0.66172	0.533000	0.62120	GAT	.	.		0.562	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			G	56924197	A	G	56924197	3	3	91	1	0	0	0	0	1	0	0	0	14399	333	12	2	2371	2	SLC12A3	16	56924197	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	6105840	56924197	33430556	534	12608										
NLRC5	84166	hgsc.bcm.edu	37	chr16	57067552	57067552	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaaagtgacggccagaggaaAggggctcagagcagaagctt	16	7	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:57067552A>G	ENST00000262510.6	+	12	2739	c.2514A>G	c.(2512-2514)aaA>aaG	p.K838K	NLRC5_ENST00000436936.1_Silent_p.K838K|NLRC5_ENST00000308149.7_Silent_p.K838K|NLRC5_ENST00000539144.1_Silent_p.K838K	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	838					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GCCAGAGGAAAGGGGCTCAGA	0.557																																					p.K838K		Atlas-SNP	.											.	NLRC5	186	.	0			c.A2514G						.						101	93	96					16																	57067552		2198	4300	6498	SO:0001819	synonymous_variant	84166	exon11			GAGGAAAGGGGCT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2514A>G	chr16.hg19:g.57067552A>G		67.0	0.0		70.0	4.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	hg19	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	A	0.049	-1.255598	0.01457	.	.	ENSG00000140853	ENST00000538805	.	.	.	3.98	1.45	0.22620	.	.	.	.	.	T	0.25568	0.0622	.	.	.	0.20196	N	0.99993	.	.	.	.	.	.	T	0.23404	-1.0189	4	.	.	.	.	5.2672	0.15605	0.6982:0.0:0.3018:0.0	.	.	.	.	G	591	.	.	R	+	1	2	NLRC5	55625053	0.931000	0.31567	0.018000	0.16275	0.053000	0.15095	0.013000	0.13310	0.264000	0.21851	-0.274000	0.10170	AGG	.	.		0.557	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		G	57067552	A	G	57067552	2	3	91	1	0	0	0	0	0	0	0	1	10479	69	3	2		2	NLRC5	16	57067552	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	143355	57067552	33287201	535	12609										
CNGB1	1258	hgsc.bcm.edu	37	chr16	57998104	57998104	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtaagggcagcctccttggTctctggaaaagaatctctca	10	10	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:57998104T>C	ENST00000251102.8	-	4	280	c.220A>G	c.(220-222)Acc>Gcc	p.T74A	CNGB1_ENST00000564448.1_Missense_Mutation_p.T74A|CNGB1_ENST00000311183.4_Missense_Mutation_p.T74A	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	74					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						GCCTCCTTGGTCTCTGGAAAA	0.557																																					p.T74A	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.A220G						.						68	73	72					16																	57998104		1899	4114	6013	SO:0001583	missense	1258	exon4			CCTTGGTCTCTGG	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2151	protein-coding gene	gene with protein product	"glutamic acid-rich protein"	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.220A>G	chr16.hg19:g.57998104T>C	ENSP00000251102:p.Thr74Ala	83.0	0.0		89.0	4.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	hg19	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	T	11.64	1.699215	0.30142	.	.	ENSG00000070729	ENST00000251102;ENST00000311183	D;T	0.96587	-4.06;0.92	3.9	3.9	0.45041	.	0.197173	0.25233	N	0.032152	D	0.94321	0.8175	L	0.27053	0.805	0.20821	N	0.999842	D;P	0.56035	0.974;0.884	P;B	0.54499	0.754;0.268	D	0.88495	0.3078	10	0.56958	D	0.05	.	9.4298	0.38604	0.0:0.0:0.0:1.0	.	74;74	Q14028-3;Q14028	.;CNGB1_HUMAN	A	74	ENSP00000251102:T74A;ENSP00000311670:T74A	ENSP00000251102:T74A	T	-	1	0	CNGB1	56555605	0.857000	0.29778	0.998000	0.56505	0.410000	0.31052	1.028000	0.30128	1.998000	0.58463	0.533000	0.62120	ACC	.	.		0.557	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		C	57998104	T	C	57998104	3	2	91	1	0	0	0	0	1	0	0	0	3602	1667	58	2	3685	2	CNGB1	16	57998104	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	930552	57998104	32356649	536	12610										
LRRC29	26231	hgsc.bcm.edu	37	chr16	67241508	67241508	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggctggttactgacctggccTcagagtgttagggtcaggtc	15	9	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:67241508T>C	ENST00000409037.1	-	4	1568	c.672A>G	c.(670-672)tgA>tgG	p.*224W	LRRC29_ENST00000393992.1_Nonstop_Mutation_p.*224W|LRRC29_ENST00000341546.3_Nonstop_Mutation_p.*224W|LRRC29_ENST00000462169.1_5'Flank|LRRC29_ENST00000409509.1_Nonstop_Mutation_p.*224W			Q8WV35	LRC29_HUMAN	leucine rich repeat containing 29	0										autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		TGACCTGGCCTCAGAGTGTTA	0.627																																					p.X224W		Atlas-SNP	.											.	LRRC29	13	.	0			c.A672G						.						44	39	40					16																	67241508		2198	4299	6497	SO:0001578	stop_lost	26231	exon6			CTGGCCTCAGAGT	AF176701	CCDS32465.1	16q22.1	2008-02-05	2004-08-23	2004-08-26	ENSG00000125122	ENSG00000125122			13605	protein-coding gene	gene with protein product			"F-box and leucine-rich repeat protein 9"	FBXL9		10531037	Standard	NM_012163		Approved	FBL9	uc002esf.3	Q8WV35	OTTHUMG00000154403	ENST00000409037.1:c.672A>G	chr16.hg19:g.67241508T>C	ENSP00000387318:p.*224Cysext*5	61.0	0.0		53.0	4.0	NM_001004055	B2RE92|Q9UKA0	Missense_Mutation	SNP	ENST00000409037.1	hg19	CCDS32465.1	.	.	.	.	.	.	.	.	.	.	T	16.43	3.120864	0.56613	.	.	ENSG00000125122	ENST00000409509;ENST00000393992;ENST00000409037;ENST00000341546	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6818	0.45819	0.0:0.0:0.0:1.0	.	.	.	.	W	224	.	.	X	-	3	0	LRRC29	65799009	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	2.561000	0.45905	2.096000	0.63516	0.533000	0.62120	TGA	.	.		0.627	LRRC29-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335073.1	NM_012163		C	67241508	T	C	67241508	4	2	91	1	0	0	0	0	0	0	0	0	8992	1564	54	2	3	2	LRRC29	16	67241508	Nonstop_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9243404	67241508	23113245	537	12611										
CTCF	10664	hgsc.bcm.edu	37	chr16	67644896	67644896	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggtgaggtggtccaggatgTcaacagcagtgtacagatgg	17	6	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:67644896T>C	ENST00000264010.4	+	3	605	c.161T>C	c.(160-162)gTc>gCc	p.V54A	CTCF_ENST00000401394.1_Intron	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	54					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		GTCCAGGATGTCAACAGCAGT	0.557																																					p.V54A	Colon(175;1200 1966 6945 23069 27405)	Atlas-SNP	.											.	CTCF	193	.	0			c.T161C						.						89	87	88					16																	67644896		2198	4300	6498	SO:0001583	missense	10664	exon3			AGGATGTCAACAG	U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"Zinc fingers, C2H2-type"	13723	protein-coding gene	gene with protein product	"11 zinc finger transcriptional repressor"	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.161T>C	chr16.hg19:g.67644896T>C	ENSP00000264010:p.Val54Ala	80.0	0.0		56.0	4.0	NM_006565	B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	ENST00000264010.4	hg19	CCDS10841.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.898288	0.52227	.	.	ENSG00000102974	ENST00000264010	T	0.08984	3.03	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000009	T	0.15003	0.0362	N	0.24115	0.695	0.80722	D	1	P	0.49447	0.924	P	0.59424	0.857	T	0.03413	-1.1039	10	0.49607	T	0.09	-1.9744	15.2015	0.73142	0.0:0.0:0.0:1.0	.	54	P49711	CTCF_HUMAN	A	54	ENSP00000264010:V54A	ENSP00000264010:V54A	V	+	2	0	CTCF	66202397	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.381000	0.44336	2.178000	0.69098	0.533000	0.62120	GTC	.	.		0.557	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2	NM_006565		C	67644896	T	C	67644896	3	2	91	1	0	0	0	0	1	0	0	0	4002	1667	58	2	163	2	CTCF	16	67644896	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	403388	67644896	22709857	538	12612										
EDC4	23644	hgsc.bcm.edu	37	chr16	67918040	67918040	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgcatggcctcgtgacccccAgcctcccttagctgctaagc	9	17	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:67918040A>G	ENST00000358933.5	+	29	4434	c.4195A>G	c.(4195-4197)Agc>Ggc	p.S1399G	CTC-479C5.10_ENST00000572067.1_lincRNA|NRN1L_ENST00000576147.1_5'Flank|NRN1L_ENST00000339176.3_5'Flank	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	1399					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)		p.S1399C(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		CGTGACCCCCAGCCTCCCTTA	0.622											OREG0023890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1399G		Atlas-SNP	.											EDC4,NS,carcinoma,0,1	EDC4	101	.	1	Substitution - Missense(1)	lung(1)	c.A4195G						.						49	37	41					16																	67918040		2198	4300	6498	SO:0001583	missense	23644	exon29			ACCCCCAGCCTCC	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.4195A>G	chr16.hg19:g.67918040A>G	ENSP00000351811:p.Ser1399Gly	36.0	0.0	1103	39.0	2.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	hg19	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	A	14.31	2.497317	0.44455	.	.	ENSG00000038358	ENST00000358933	.	.	.	4.94	2.7	0.31948	.	0.303191	0.32901	N	0.005501	T	0.11196	0.0273	N	0.00926	-1.1	0.24490	N	0.994307	B	0.06786	0.001	B	0.01281	0.0	T	0.17806	-1.0357	9	0.35671	T	0.21	-3.2229	6.4914	0.22117	0.7283:0.1506:0.121:0.0	.	1399	Q6P2E9	EDC4_HUMAN	G	1399	.	ENSP00000351811:S1399G	S	+	1	0	EDC4	66475541	0.998000	0.40836	0.994000	0.49952	0.980000	0.70556	3.776000	0.55356	0.992000	0.38840	0.528000	0.53228	AGC	.	.		0.622	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		G	67918040	A	G	67918040	3	3	91	1	0	0	0	0	1	0	0	0	4910	188	7	2	4309	2	EDC4	16	67918040	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	273144	67918040	22436713	539	12613										
NFATC3	4775	hgsc.bcm.edu	37	chr16	68208375	68208375	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggttgtgactggatctaatTttcttccagaatccaaaatc	7	8	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:68208375T>C	ENST00000346183.3	+	6	1897	c.1873T>C	c.(1873-1875)Ttt>Ctt	p.F625L	NFATC3_ENST00000349223.5_Missense_Mutation_p.F625L|NFATC3_ENST00000329524.4_Missense_Mutation_p.F625L|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Missense_Mutation_p.F625L	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	625					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		TGGATCTAATTTTCTTCCAGA	0.358																																					p.F625L		Atlas-SNP	.											.	NFATC3	190	.	0			c.T1873C						.						153	160	157					16																	68208375		2198	4300	6498	SO:0001583	missense	4775	exon6			TCTAATTTTCTTC	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"Nuclear factor of activated T-cells"	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.1873T>C	chr16.hg19:g.68208375T>C	ENSP00000300659:p.Phe625Leu	104.0	0.0		74.0	4.0	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	hg19	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.462054	0.43736	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524;ENST00000535127	T;T;T	0.15372	2.43;2.43;2.44	5.62	4.53	0.55603	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.048303	0.85682	D	0.000000	T	0.41465	0.1160	M	0.80183	2.485	0.80722	D	1	D;D;D;D	0.71674	0.998;0.961;0.998;0.998	D;B;D;D	0.70716	0.97;0.253;0.97;0.97	T	0.31806	-0.9930	10	0.56958	D	0.05	-16.6876	11.4406	0.50094	0.0:0.0703:0.0:0.9297	.	625;625;625;625	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	L	625;625;625;146	ENSP00000264008:F625L;ENSP00000300659:F625L;ENSP00000331324:F625L	ENSP00000331324:F625L	F	+	1	0	NFATC3	66765876	1.000000	0.71417	1.000000	0.80357	0.006000	0.05464	5.030000	0.64128	0.980000	0.38523	-0.353000	0.07706	TTT	.	.		0.358	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		C	68208375	T	C	68208375	3	2	91	1	0	0	0	0	1	0	0	0	10373	1841	64	2	1895	2	NFATC3	16	68208375	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	290335	68208375	22146378	540	12614										
CHTF8	54921	hgsc.bcm.edu	37	chr16	69154536	69154536	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acaggatatgatgccccacgAtcagcacagggattcccttt	9	12	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:69154536A>G	ENST00000448552.2	-	4	279	c.158T>C	c.(157-159)aTc>aCc	p.I53T	CHTF8_ENST00000574807.1_5'Flank|CHTF8_ENST00000520529.1_3'UTR|CHTF8_ENST00000522091.1_3'UTR|CHTF8_ENST00000518041.1_Intron|CHTF8_ENST00000306585.6_5'UTR|CHTF8_ENST00000519520.1_3'UTR|CHTF8_ENST00000398235.2_Missense_Mutation_p.I53T|CHTF8_ENST00000523421.1_Intron	NM_001039690.3|NM_001040146.3	NP_001034779.1|NP_001035236.1	P0CG13	CTF8_HUMAN	CTF8, chromosome transmission fidelity factor 8 homolog (S. cerevisiae)	53					cell cycle (GO:0007049)|DNA replication (GO:0006260)	nucleus (GO:0005634)	DNA binding (GO:0003677)										ATGCCCCACGATCAGCACAGG	0.522																																					p.I53T		Atlas-SNP	.											.	CHTF8	5	.	0			c.T158C						.						96	95	95					16																	69154536		1963	4150	6113	SO:0001583	missense	54921	exon4			CCCACGATCAGCA		CCDS42185.1	16q22.1	2009-01-14				ENSG00000168802			24353	protein-coding gene	gene with protein product		613202				12766176	Standard	NM_001039690		Approved	FLJ20400, CTF8, DERPC	uc002ewo.2	P0CG12		ENST00000448552.2:c.158T>C	chr16.hg19:g.69154536A>G	ENSP00000408367:p.Ile53Thr	90.0	0.0		79.0	4.0	NM_001039690	A8MYX8|Q71E72|Q8NDH8|Q8WV66|Q9NX73	Missense_Mutation	SNP	ENST00000448552.2	hg19	CCDS42185.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.410696	0.42817	.	.	ENSG00000168802	ENST00000448552;ENST00000398235	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	T	0.48589	0.1508	L	0.37850	1.14	0.80722	D	1	P	0.34684	0.463	B	0.34180	0.177	T	0.45440	-0.9261	8	0.30078	T	0.28	.	15.2868	0.73833	1.0:0.0:0.0:0.0	.	53	P0CG13	CTF8_HUMAN	T	53	.	ENSP00000381290:I53T	I	-	2	0	CHTF8	67712037	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.499000	0.90494	2.144000	0.66660	0.533000	0.62120	ATC	.	.		0.522	CHTF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376352.2	NM_017804		G	69154536	A	G	69154536	3	3	91	1	0	0	0	0	1	0	0	0	3417	333	12	2	211	2	CHTF8	16	69154536	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	946161	69154536	21200217	541	12615										
NIP7	51388	hgsc.bcm.edu	37	chr16	69375544	69375544	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aatatgtgcggcatgaagagAcgttgacttaaaacgaagcc	11	7	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:69375544A>G	ENST00000254940.5	+	5	932	c.532A>G	c.(532-534)Acg>Gcg	p.T178A	RP11-343C2.7_ENST00000564737.1_Intron|COG8_ENST00000562081.1_5'Flank|COG8_ENST00000306875.4_5'Flank|RP11-343C2.9_ENST00000563634.1_Intron|NIP7_ENST00000254941.6_Missense_Mutation_p.T131A	NM_016101.4	NP_057185.1	Q9Y221	NIP7_HUMAN	NIP7, nucleolar pre-rRNA processing protein	178	C-terminal domain.				ribosome assembly (GO:0042255)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Ovarian(137;0.101)				GCATGAAGAGACGTTGACTTA	0.468																																					p.T178A		Atlas-SNP	.											.	NIP7	20	.	0			c.A532G						.						146	143	144					16																	69375544		2198	4300	6498	SO:0001583	missense	51388	exon5			GAAGAGACGTTGA	AB112439	CCDS10877.1, CCDS56003.1	16q22.1	2013-03-04	2013-03-04		ENSG00000132603	ENSG00000132603			24328	protein-coding gene	gene with protein product			"nuclear import 7 homolog (S. cerevisiae)"			14660641, 22195017	Standard	NM_016101		Approved	CGI-37, FLJ10296, HSPC031, KD93	uc002exa.3	Q9Y221	OTTHUMG00000137568	ENST00000254940.5:c.532A>G	chr16.hg19:g.69375544A>G	ENSP00000254940:p.Thr178Ala	137.0	0.0		84.0	5.0	NM_016101	B2RD04|Q9NZZ0	Missense_Mutation	SNP	ENST00000254940.5	hg19	CCDS10877.1	.	.	.	.	.	.	.	.	.	.	A	13.94	2.386563	0.42308	.	.	ENSG00000132603	ENST00000254940;ENST00000254941	.	.	.	5.44	5.44	0.79542	.	0.047928	0.85682	D	0.000000	T	0.60287	0.2257	L	0.59436	1.845	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.14578	0.011;0.003	T	0.57195	-0.7853	9	0.41790	T	0.15	0.2163	15.7961	0.78412	1.0:0.0:0.0:0.0	.	131;178	Q9Y221-2;Q9Y221	.;NIP7_HUMAN	A	178;131	.	ENSP00000254940:T178A	T	+	1	0	NIP7	67933045	1.000000	0.71417	0.993000	0.49108	0.568000	0.35870	6.962000	0.76048	2.188000	0.69820	0.459000	0.35465	ACG	.	.		0.468	NIP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268947.2	NM_016101		G	69375544	A	G	69375544	3	3	91	1	0	0	0	0	1	0	0	0	10430	275	10	2	550	2	NIP7	16	69375544	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	221008	69375544	20979209	542	12616										
GLG1	2734	hgsc.bcm.edu	37	chr16	74528672	74528672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acttaccttttcactcatggAttcttcaaatttatggttaa	4	8	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:74528672A>G	ENST00000422840.2	-	6	1035	c.1036T>C	c.(1036-1038)Tcc>Ccc	p.S346P	GLG1_ENST00000447066.2_Missense_Mutation_p.S335P|GLG1_ENST00000205061.5_Missense_Mutation_p.S346P	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	346					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						TCACTCATGGATTCTTCAAAT	0.343																																					p.S346P		Atlas-SNP	.											.	GLG1	106	.	0			c.T1036C						.						88	87	88					16																	74528672		2198	4300	6498	SO:0001583	missense	2734	exon6			TCATGGATTCTTC		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.1036T>C	chr16.hg19:g.74528672A>G	ENSP00000405984:p.Ser346Pro	94.0	0.0		88.0	4.0	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	hg19	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.502617	0.44455	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.94	5.94	0.96194	.	0.063063	0.64402	D	0.000004	T	0.44265	0.1285	L	0.32530	0.975	0.58432	D	0.999999	B;B;P	0.42584	0.003;0.005;0.784	B;B;B	0.38880	0.009;0.005;0.284	T	0.38650	-0.9651	9	0.38643	T	0.18	-7.8662	16.4075	0.83691	1.0:0.0:0.0:0.0	.	346;346;335	Q92896;Q92896-2;B7Z8Y4	GSLG1_HUMAN;.;.	P	346;335;346	.	ENSP00000205061:S346P	S	-	1	0	GLG1	73086173	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.122000	0.57910	2.275000	0.75901	0.528000	0.53228	TCC	.	.		0.343	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		G	74528672	A	G	74528672	3	3	91	1	0	0	0	0	1	0	0	0	6444	333	12	2	2667	2	GLG1	16	74528672	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	5153128	74528672	15826081	543	12617										
ZFP1	162239	hgsc.bcm.edu	37	chr16	75203861	75203861	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cccaaaagtttgaactcaccAcacaccagagaattcataca	4	13	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:75203861A>G	ENST00000393430.2	+	4	977	c.853A>G	c.(853-855)Aca>Gca	p.T285A	ZFP1_ENST00000570010.1_Missense_Mutation_p.T285A|ZFP1_ENST00000464850.1_3'UTR|ZFP1_ENST00000568079.1_3'UTR|ZFP1_ENST00000332307.4_Missense_Mutation_p.T252A			Q6P2D0	ZFP1_HUMAN	ZFP1 zinc finger protein	285					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(4)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	12						TGAACTCACCACACACCAGAG	0.418																																					p.T285A	NSCLC(187;1429 2122 10143 20357 42217)	Atlas-SNP	.											.	ZFP1	28	.	0			c.A853G						.						72	72	72					16																	75203861		2198	4300	6498	SO:0001583	missense	162239	exon4			CTCACCACACACC	AK094761	CCDS10914.2	16q22.3	2013-01-08	2012-11-27		ENSG00000184517	ENSG00000184517		"Zinc fingers, C2H2-type", "-"	23328	protein-coding gene	gene with protein product			"zinc finger protein 1 homolog (mouse)", "zinc finger protein 1"			2574853	Standard	NM_153688		Approved	FLJ34243, ZNF475	uc002fdo.3	Q6P2D0	OTTHUMG00000137602	ENST00000393430.2:c.853A>G	chr16.hg19:g.75203861A>G	ENSP00000377080:p.Thr285Ala	118.0	0.0		81.0	4.0	NM_153688	A8K5Q7|B4DKG9|Q8N188|Q8N9F9	Missense_Mutation	SNP	ENST00000393430.2	hg19	CCDS10914.2	.	.	.	.	.	.	.	.	.	.	A	3.669	-0.067883	0.07228	.	.	ENSG00000184517	ENST00000332307;ENST00000393430	T	0.07216	3.21	4.64	4.64	0.57946	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000134	T	0.03477	0.0100	N	0.05351	-0.065	0.21105	N	0.999788	P	0.41450	0.75	B	0.33960	0.173	T	0.41680	-0.9495	10	0.08381	T	0.77	-23.7449	12.6831	0.56932	1.0:0.0:0.0:0.0	.	285	Q6P2D0	ZFP1_HUMAN	A	285	ENSP00000377080:T285A	ENSP00000333192:T285A	T	+	1	0	ZFP1	73761362	0.000000	0.05858	0.992000	0.48379	0.992000	0.81027	-0.121000	0.10643	2.308000	0.77769	0.533000	0.62120	ACA	.	.		0.418	ZFP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269013.2	NM_153688		G	75203861	A	G	75203861	3	3	91	1	0	0	0	0	1	0	0	0	17651	159	6	2	863	2	ZFP1	16	75203861	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	675189	75203861	15150892	544	12618										
WWOX	51741	hgsc.bcm.edu	37	chr16	78466543	78466543	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctctccccacgcggggtcaCgtcgaacgcagtgcatcctg	11	17	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:78466543C>T	ENST00000566780.1	+	8	1316	c.950C>T	c.(949-951)aCg>aTg	p.T317M	WWOX_ENST00000539474.2_Intron|WWOX_ENST00000408984.3_Missense_Mutation_p.T317M|WWOX_ENST00000402655.2_Intron|WWOX_ENST00000406884.2_Intron	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	317	Interaction with MAPT. {ECO:0000250}.				cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)			large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		CGCGGGGTCACGTCGAACGCA	0.537																																					p.T317M		Atlas-SNP	.											.	WWOX	98	.	0			c.C950T						.						141	144	143					16																	78466543		2082	4213	6295	SO:0001583	missense	51741	exon8			GGGTCACGTCGAA	AF187015	CCDS42196.1, CCDS42197.1	16q23.3-q24.1	2012-08-15	2002-01-14		ENSG00000186153	ENSG00000186153	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	12799	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 41C, member 1"	605131	"WW domain-containing oxidoreductase"			10786676, 10861292, 19027726	Standard	XR_243411		Approved	FOR, WOX1, SDR41C1	uc002ffk.3	Q9NZC7	OTTHUMG00000176851	ENST00000566780.1:c.950C>T	chr16.hg19:g.78466543C>T	ENSP00000457230:p.Thr317Met	179.0	0.0		129.0	6.0	NM_016373	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	hg19	CCDS42196.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152312	0.57259	.	.	ENSG00000186153	ENST00000408984	T	0.24350	1.86	5.93	5.93	0.95920	NAD(P)-binding domain (1);	0.237347	0.41938	D	0.000798	T	0.55000	0.1893	M	0.89287	3.02	0.47737	D	0.999506	D	0.76494	0.999	P	0.56216	0.794	T	0.62676	-0.6804	10	0.87932	D	0	.	20.3261	0.98701	0.0:1.0:0.0:0.0	.	317	Q9NZC7	WWOX_HUMAN	M	317	ENSP00000386161:T317M	ENSP00000386161:T317M	T	+	2	0	WWOX	77024044	0.998000	0.40836	0.965000	0.40720	0.130000	0.20726	3.738000	0.55067	2.814000	0.96858	0.655000	0.94253	ACG	.	.		0.537	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1			T	78466543	C	T	78466543	3	4	91	1	0	0	0	0	1	0	0	0	17429	536	19	1	1042	1	WWOX	16	78466543	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	3262682	78466543	11888210	545	12619										
LRRC50	123872	hgsc.bcm.edu	37	chr16	84199541	84199541	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggagaggaaaagacagagagAgagtcaagagagaggtatgc	17	3	1	6			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:84199541A>G	ENST00000378553.5	+	7	1140	c.1016A>G	c.(1015-1017)gAg>gGg	p.E339G	DNAAF1_ENST00000563818.1_3'UTR|DNAAF1_ENST00000334315.5_Missense_Mutation_p.E339G	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	339					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						AGACAGAGAGAGAGTCAAGAG	0.522																																					p.E339G		Atlas-SNP	.											.	DNAAF1	81	.	0			c.A1016G						.						148	138	141					16																	84199541		2200	4300	6500	SO:0001583	missense	123872	exon7			AGAGAGAGAGTCA	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"outer row dynein assembly 7 homolog (Chlamydomonas)"	613190	"leucine rich repeat containing 50"	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1016A>G	chr16.hg19:g.84199541A>G	ENSP00000367815:p.Glu339Gly	116.0	0.0		94.0	4.0	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	hg19	CCDS10943.2	.	.	.	.	.	.	.	.	.	.	A	12.59	1.984904	0.35036	.	.	ENSG00000154099	ENST00000334315;ENST00000378553	T;T	0.38240	1.15;1.61	5.66	-3.15	0.05233	.	0.389186	0.24557	N	0.037519	T	0.23846	0.0577	L	0.46157	1.445	0.09310	N	1	B;B	0.24768	0.111;0.028	B;B	0.22753	0.041;0.027	T	0.15780	-1.0425	10	0.27785	T	0.31	-3.3565	7.9681	0.30111	0.3761:0.4341:0.1898:0.0	.	87;339	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	G	339	ENSP00000334593:E339G;ENSP00000367815:E339G	ENSP00000334593:E339G	E	+	2	0	DNAAF1	82757042	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.380000	0.20602	-0.642000	0.05480	-0.297000	0.09499	GAG	.	.		0.522	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452		G	84199541	A	G	84199541	3	3	91	1	0	0	0	0	1	0	0	0	9018	304	11	2	1042	2	LRRC50	16	84199541	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	5732998	84199541	6155212	546	12620										
MVD	4597	hgsc.bcm.edu	37	chr16	88721665	88721665	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggtggatgatgcgccaggagAtggcattgaggtaagagatg	18	4	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:88721665A>G	ENST00000301012.3	-	7	868	c.839T>C	c.(838-840)aTc>aCc	p.I280T	MVD_ENST00000568709.1_5'Flank	NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	280					cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GCGCCAGGAGATGGCATTGAG	0.647																																					p.I280T		Atlas-SNP	.											.	MVD	27	.	0			c.T839C						.						251	192	212					16																	88721665		2189	4293	6482	SO:0001583	missense	4597	exon7			CAGGAGATGGCAT	U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4.1.1.33		7529	protein-coding gene	gene with protein product	"mevalonate pyrophosphate decarboxylase"	603236				8626466	Standard	NM_002461		Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.839T>C	chr16.hg19:g.88721665A>G	ENSP00000301012:p.Ile280Thr	98.0	0.0		119.0	5.0	NM_002461	Q53Y65	Missense_Mutation	SNP	ENST00000301012.3	hg19	CCDS10968.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.003|0.003	-2.450778|-2.450778	0.00175|0.00175	.|.	.|.	ENSG00000167508|ENSG00000167508	ENST00000301012|ENST00000378400	T|.	0.28454|.	1.61|.	4.26|4.26	1.12|1.12	0.20585|0.20585	.|.	0.417901|.	0.26723|.	N|.	0.022833|.	T|T	0.08403|0.08403	0.0209|0.0209	N|N	0.00413|0.00413	-1.525|-1.525	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.26608|0.26608	-1.0098|-1.0098	10|6	0.08179|0.87932	T|D	0.78|0	-20.7405|-20.7405	7.6388|7.6388	0.28282|0.28282	0.5585:0.0:0.4415:0.0|0.5585:0.0:0.4415:0.0	.|.	280|.	P53602|.	MVD1_HUMAN|.	T|P	280|108	ENSP00000301012:I280T|.	ENSP00000301012:I280T|ENSP00000367653:S108P	I|S	-|-	2|1	0|0	MVD|MVD	87249166|87249166	0.034000|0.034000	0.19679|0.19679	0.064000|0.064000	0.19789|0.19789	0.028000|0.028000	0.11728|0.11728	2.503000|2.503000	0.45407|0.45407	0.041000|0.041000	0.15688|0.15688	-0.415000|-0.415000	0.06103|0.06103	ATC|TCT	.	.		0.647	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269547.2	NM_002461		G	88721665	A	G	88721665	3	3	91	1	0	0	0	0	1	0	0	0	10003	333	12	2	379	2	MVD	16	88721665	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4522124	88721665	1633088	547	12621										
FAM57A	79850	hgsc.bcm.edu	37	chr17	644578	644578	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccttctgtacaaggtgaatgGaatcctcacgctggccacct	9	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:644578G>A	ENST00000308278.8	+	5	778	c.542G>A	c.(541-543)gGa>gAa	p.G181E	FAM57A_ENST00000301324.8_Missense_Mutation_p.G149E|FAM57A_ENST00000572018.1_3'UTR	NM_024792.1	NP_079068.1	Q8TBR7	FA57A_HUMAN	family with sequence similarity 57, member A	181	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G181E(1)		cervix(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(2)|urinary_tract(2)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0217)		AAGGTGAATGGAATCCTCACG	0.542																																					p.G181E		Atlas-SNP	.											FAM57A,NS,carcinoma,0,1	FAM57A	17	.	1	Substitution - Missense(1)	prostate(1)	c.G542A						.						150	131	137					17																	644578		2203	4300	6503	SO:0001583	missense	79850	exon5			TGAATGGAATCCT	AK025935	CCDS10996.1	17p13.3	2014-08-14				ENSG00000167695			29646	protein-coding gene	gene with protein product		611627				12270127	Standard	NM_024792		Approved	FLJ22282, CT120	uc002frp.3	Q8TBR7		ENST00000308278.8:c.542G>A	chr17.hg19:g.644578G>A	ENSP00000312017:p.Gly181Glu	213.0	2.0		115.0	5.0	NM_024792	A8K7Q0|Q7Z464|Q96D97|Q9H6H3	Missense_Mutation	SNP	ENST00000308278.8	hg19	CCDS10996.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.472963	0.84640	.	.	ENSG00000167695	ENST00000308278;ENST00000301324;ENST00000451373	D;D	0.87256	-2.23;-2.23	6.17	5.15	0.70609	TRAM/LAG1/CLN8 homology domain (3);	0.047993	0.85682	D	0.000000	D	0.94331	0.8178	M	0.88979	2.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.94720	0.7900	10	0.87932	D	0	-12.009	16.1997	0.82060	0.0:0.1327:0.8673:0.0	.	149;181	Q8TBR7-1;Q8TBR7	.;FA57A_HUMAN	E	181;149;254	ENSP00000312017:G181E;ENSP00000301324:G149E	ENSP00000301324:G149E	G	+	2	0	FAM57A	591328	1.000000	0.71417	0.999000	0.59377	0.662000	0.39071	7.845000	0.86875	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.542	FAM57A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437155.2	NM_024792		A	644578	G	A	644578	3	1	91	1	0	0	0	0	1	0	0	0	5596	1174	41	3	560	3	FAM57A	17	644578	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10		644578	80550632	548	12622										
SMG6	23293	hgsc.bcm.edu	37	chr17	2202373	2202373	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctcatggtgctggtaggtagAgggctacacacatactgtcc	12	10	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:2202373A>G	ENST00000263073.6	-	2	1724	c.1674T>C	c.(1672-1674)ccT>ccC	p.P558P	SMG6_ENST00000544865.1_Silent_p.P527P	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	558					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TGGTAGGTAGAGGGCTACACA	0.582																																					p.P558P	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.T1674C						.						199	186	191					17																	2202373		2203	4300	6503	SO:0001819	synonymous_variant	23293	exon2			AGGTAGAGGGCTA	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"EST1 telomerase component homolog A (S. cerevisiae)"	610963	"chromosome 17 open reading frame 31", "smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.1674T>C	chr17.hg19:g.2202373A>G		170.0	0.0		84.0	5.0	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	hg19	CCDS11016.1																																																																																			.	.		0.582	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			G	2202373	A	G	2202373	2	3	91	1	0	0	0	0	0	0	0	1	14812	291	11	2		2	SMG6	17	2202373	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1557795	2202373	78992837	549	12623										
OR1E2	8388	hgsc.bcm.edu	37	chr17	3336727	3336727	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcggtgtagtgcaggaggaAgcagatggcggtgtagtgca	20	5	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:3336727A>G	ENST00000248384.1	-	1	408	c.409T>C	c.(409-411)Ttc>Ctc	p.F137L		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	137					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						TGCAGGAGGAAGCAGATGGCG	0.552																																					p.F137L		Atlas-SNP	.											.	OR1E2	25	.	0			c.T409C						.						92	76	82					17																	3336727		2203	4300	6503	SO:0001583	missense	8388	exon1			GGAGGAAGCAGAT	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"GPCR / Class A : Olfactory receptors"	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.409T>C	chr17.hg19:g.3336727A>G	ENSP00000248384:p.Phe137Leu	260.0	0.0		116.0	6.0	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	hg19	CCDS11026.1	.	.	.	.	.	.	.	.	.	.	A	7.739	0.700830	0.15172	.	.	ENSG00000127780	ENST00000248384	T	0.01821	4.62	.	.	.	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.49466	-0.8937	5	0.87932	D	0	.	.	.	.	.	137	P47887	OR1E2_HUMAN	L	137	ENSP00000248384:F137L	ENSP00000248384:F137L	F	-	1	0	OR1E2	3283477	.	.	0.958000	0.39756	0.305000	0.27757	.	.	0.000000	0.14550	0.000000	0.15137	TTC	.	.		0.552	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1			G	3336727	A	G	3336727	3	3	91	1	0	0	0	0	1	0	0	0	10964	72	3	2	565	2	OR1E2	17	3336727	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1134354	3336727	77858483	550	12624										
SPATA22	84690	hgsc.bcm.edu	37	chr17	3365782	3365782	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttaagtagactcacctccaAccaccctggcttcttccagt	5	15	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:3365782A>G	ENST00000573128.1	-	5	807	c.324T>C	c.(322-324)ggT>ggC	p.G108G	SPATA22_ENST00000355380.4_Silent_p.G65G|SPATA22_ENST00000572969.1_Silent_p.G108G|SPATA22_ENST00000397168.3_Silent_p.G108G|SPATA22_ENST00000268981.5_Silent_p.G108G|SPATA22_ENST00000541913.1_Silent_p.G92G|SPATA22_ENST00000575375.1_Silent_p.G108G			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	108					fertilization (GO:0009566)|gamete generation (GO:0007276)|meiotic DNA repair synthesis (GO:0000711)|regulation of meiotic cell cycle (GO:0051445)|reproductive system development (GO:0061458)|synapsis (GO:0007129)	chromosome (GO:0005694)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)	19						CTCACCTCCAACCACCCTGGC	0.403																																					p.G108G		Atlas-SNP	.											.	SPATA22	49	.	0			c.T324C						.						104	105	105					17																	3365782		2203	4300	6503	SO:0001819	synonymous_variant	84690	exon5			CCTCCAACCACCC	AY035868	CCDS11027.1, CCDS54066.1, CCDS54067.1	17p13.3	2005-12-19							30705	protein-coding gene	gene with protein product						12477932	Standard	NM_001170696		Approved	NYD-SP20	uc002fvn.3	Q8NHS9		ENST00000573128.1:c.324T>C	chr17.hg19:g.3365782A>G		122.0	0.0		64.0	4.0	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Silent	SNP	ENST00000573128.1	hg19	CCDS11027.1																																																																																			.	.		0.403	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598		G	3365782	A	G	3365782	2	3	91	1	0	0	0	0	0	0	0	1	15023	30	2	2		2	SPATA22	17	3365782	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	29055	3365782	77829428	551	12625										
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3917468	3917468	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catgtcggaggtgaagcggtAatacagagtgtctcctaggc	14	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:3917468A>G	ENST00000381638.2	-	51	8453	c.8329T>C	c.(8329-8331)Tac>Cac	p.Y2777H		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2777							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						GTGAAGCGGTAATACAGAGTG	0.562																																					p.Y2777H		Atlas-SNP	.											.	ZZEF1	195	.	0			c.T8329C						.						93	76	82					17																	3917468		2203	4300	6503	SO:0001583	missense	23140	exon51			AGCGGTAATACAG	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.8329T>C	chr17.hg19:g.3917468A>G	ENSP00000371051:p.Tyr2777His	156.0	0.0		85.0	5.0	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	hg19	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.894978	0.91962	.	.	ENSG00000074755	ENST00000381638	T	0.26223	1.75	5.69	5.69	0.88448	.	0.063428	0.64402	D	0.000003	T	0.41858	0.1177	L	0.32530	0.975	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.33675	-0.9859	10	0.87932	D	0	-15.9479	15.945	0.79787	1.0:0.0:0.0:0.0	.	2777	O43149	ZZEF1_HUMAN	H	2777	ENSP00000371051:Y2777H	ENSP00000371051:Y2777H	Y	-	1	0	ZZEF1	3864217	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.957000	0.93082	2.159000	0.67721	0.533000	0.62120	TAC	.	.		0.562	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		G	3917468	A	G	3917468	3	3	91	1	0	0	0	0	1	0	0	0	18270	362	13	2	576	2	ZZEF1	17	3917468	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	551686	3917468	77277742	552	12626										
CAMTA2	23125	hgsc.bcm.edu	37	chr17	4883056	4883056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctggggggtcggagcagggaTgcttggagcttcgtcactga	18	8	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:4883056T>C	ENST00000348066.3	-	9	1684	c.1561A>G	c.(1561-1563)Atc>Gtc	p.I521V	CAMTA2_ENST00000361571.5_Missense_Mutation_p.I520V|CAMTA2_ENST00000572543.1_Missense_Mutation_p.I526V|CAMTA2_ENST00000414043.3_Missense_Mutation_p.I544V|CAMTA2_ENST00000358183.4_Missense_Mutation_p.I521V|CAMTA2_ENST00000381311.5_Missense_Mutation_p.I523V|CAMTA2_ENST00000571831.1_5'Flank	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	521					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GGAGCAGGGATGCTTGGAGCT	0.557																																					p.I544V		Atlas-SNP	.											.	CAMTA2	93	.	0			c.A1630G						.						132	131	131					17																	4883056		2203	4300	6503	SO:0001583	missense	23125	exon9			CAGGGATGCTTGG	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.1561A>G	chr17.hg19:g.4883056T>C	ENSP00000321813:p.Ile521Val	91.0	0.0		42.0	4.0	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	hg19	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	T	3.368	-0.129134	0.06753	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.31247	2.71;1.73;1.5;1.73;1.51	4.79	-3.37	0.04898	.	0.844005	0.10161	N	0.708334	T	0.09862	0.0242	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001	T	0.34179	-0.9839	10	0.15499	T	0.54	-1.43	4.7504	0.13057	0.1368:0.5329:0.1394:0.1909	.	497;544;523;521;520	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	V	544;523;520;521;521	ENSP00000412886:I544V;ENSP00000370712:I523V;ENSP00000354828:I520V;ENSP00000350910:I521V;ENSP00000321813:I521V	ENSP00000321813:I521V	I	-	1	0	CAMTA2	4823780	0.000000	0.05858	0.162000	0.22713	0.726000	0.41606	-0.646000	0.05403	-0.476000	0.06842	0.533000	0.62120	ATC	.	.		0.557	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099		C	4883056	T	C	4883056	3	2	91	1	0	0	0	0	1	0	0	0	2616	1464	51	2	2157	2	CAMTA2	17	4883056	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	965588	4883056	76312154	553	12627										
FAM64A	54478	hgsc.bcm.edu	37	chr17	6352638	6352638	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttctttcatgcagcgagtcTgacagtgacctagagcctgt	10	10	3	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:6352638T>C	ENST00000250056.8	+	4	680	c.597T>C	c.(595-597)tcT>tcC	p.S199S	FAM64A_ENST00000572595.2_Silent_p.S230S|FAM64A_ENST00000576056.1_Silent_p.S199S|FAM64A_ENST00000572447.1_Silent_p.S199S|FAM64A_ENST00000570337.2_Silent_p.S199S|FAM64A_ENST00000571373.1_Silent_p.S199S	NM_001195228.1	NP_001182157.1	Q9BSJ6	FA64A_HUMAN	family with sequence similarity 64, member A	199			S -> C (in dbSNP:rs16955870).		mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				COAD - Colon adenocarcinoma(228;0.141)		GCAGCGAGTCTGACAGTGACC	0.567																																					p.S199S		Atlas-SNP	.											.	FAM64A	20	.	0			c.T597C						.						100	98	99					17																	6352638		2203	4300	6503	SO:0001819	synonymous_variant	54478	exon4			CGAGTCTGACAGT		CCDS32541.1, CCDS56016.1	17p13.2	2013-10-11			ENSG00000129195	ENSG00000129195			25483	protein-coding gene	gene with protein product	"CALM interacting protein expressed in thymus and spleen"					19383357, 16491119	Standard	NM_019013		Approved	FLJ10156, FLJ10491, CATS	uc002gcw.2	Q9BSJ6	OTTHUMG00000177832	ENST00000250056.8:c.597T>C	chr17.hg19:g.6352638T>C		134.0	0.0		85.0	4.0	NM_019013	Q96CT4|Q9NVV1|Q9NWB5	Silent	SNP	ENST00000250056.8	hg19	CCDS56016.1																																																																																			.	.		0.567	FAM64A-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439156.1	NM_019013		C	6352638	T	C	6352638	2	2	91	1	0	0	0	0	0	0	0	1	5606	1567	55	2		2	FAM64A	17	6352638	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1469582	6352638	74842572	554	12628										
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6367544	6367544	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccaggcgccggggccgcggcAcattgtatgtgatgcgacca	15	13	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:6367544A>G	ENST00000262483.8	-	16	2189	c.2102T>C	c.(2101-2103)gTg>gCg	p.V701A	PITPNM3_ENST00000576664.1_5'UTR|PITPNM3_ENST00000421306.3_Missense_Mutation_p.V665A	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	701					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		GGGCCGCGGCACATTGTATGT	0.577																																					p.V701A		Atlas-SNP	.											.	PITPNM3	91	.	0			c.T2102C						.						81	80	80					17																	6367544		2203	4300	6503	SO:0001583	missense	83394	exon16			CGCGGCACATTGT	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.2102T>C	chr17.hg19:g.6367544A>G	ENSP00000262483:p.Val701Ala	100.0	0.0		63.0	4.0	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	hg19	CCDS11076.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.021258	0.54576	.	.	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.50548	0.74;0.75	4.65	4.65	0.58169	.	0.192544	0.44285	D	0.000463	T	0.45216	0.1331	L	0.55990	1.75	0.40089	D	0.976238	P;B	0.44521	0.837;0.293	B;B	0.41412	0.356;0.108	T	0.54063	-0.8349	10	0.87932	D	0	.	12.3053	0.54898	1.0:0.0:0.0:0.0	.	665;701	F8WEW5;Q9BZ71	.;PITM3_HUMAN	A	701;665	ENSP00000262483:V701A;ENSP00000407882:V665A	ENSP00000262483:V701A	V	-	2	0	PITPNM3	6308268	1.000000	0.71417	0.931000	0.37212	0.506000	0.33950	9.235000	0.95353	1.855000	0.53841	0.418000	0.28097	GTG	.	.		0.577	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		G	6367544	A	G	6367544	3	3	91	1	0	0	0	0	1	0	0	0	11961	159	6	2	842	2	PITPNM3	17	6367544	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	14906	6367544	74827666	555	12629										
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6386875	6386875	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcctcagagcagatggcaggAcaggggacgaacttgatgag	16	8	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:6386875A>G	ENST00000262483.8	-	6	636	c.549T>C	c.(547-549)tgT>tgC	p.C183C	PITPNM3_ENST00000421306.3_Silent_p.C147C	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	183					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		AGATGGCAGGACAGGGGACGA	0.572																																					p.C183C		Atlas-SNP	.											.	PITPNM3	91	.	0			c.T549C						.						142	97	112					17																	6386875		2203	4300	6503	SO:0001819	synonymous_variant	83394	exon6			GGCAGGACAGGGG	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.549T>C	chr17.hg19:g.6386875A>G		200.0	0.0		83.0	4.0	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	hg19	CCDS11076.1																																																																																			.	.		0.572	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		G	6386875	A	G	6386875	2	3	91	1	0	0	0	0	0	0	0	1	11961	273	10	2		2	PITPNM3	17	6386875	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	19331	6386875	74808335	556	12630										
TMEM95	339168	hgsc.bcm.edu	37	chr17	7259191	7259191	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtctcctcactcccttcataTtggagttggcttcgaaagac	8	12	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:7259191T>C	ENST00000576060.1	+	3	288	c.261T>C	c.(259-261)taT>taC	p.Y87Y	TMEM95_ENST00000330767.4_Silent_p.Y87Y|TMEM95_ENST00000389982.4_Silent_p.Y87Y|RP11-542C16.1_ENST00000572417.1_RNA			Q3KNT9	TMM95_HUMAN	transmembrane protein 95	87						integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)	3		Prostate(122;0.173)				TCCCTTCATATTGGAGTTGGC	0.577											OREG0024137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y87Y		Atlas-SNP	.											.	TMEM95	11	.	0			c.T261C						.						98	83	88					17																	7259191		2203	4300	6503	SO:0001819	synonymous_variant	339168	exon3			TTCATATTGGAGT		CCDS32546.1	17p13.1	2005-12-15			ENSG00000182896	ENSG00000182896			27898	protein-coding gene	gene with protein product						12975309	Standard	NM_198154		Approved	MGC129793, UNQ9390	uc002ggf.1	Q3KNT9	OTTHUMG00000132899	ENST00000576060.1:c.261T>C	chr17.hg19:g.7259191T>C		130.0	0.0	640	72.0	4.0	NM_198154	B7WPI7|Q6UXT3|Q8IW68	Silent	SNP	ENST00000576060.1	hg19																																																																																				.	.		0.577	TMEM95-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440555.2	NM_198154		C	7259191	T	C	7259191	2	2	91	1	0	0	0	0	0	0	0	1	16238	1500	52	2		2	TMEM95	17	7259191	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	872316	7259191	73936019	557	12631										
TMEM102	284114	hgsc.bcm.edu	37	chr17	7340050	7340050	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgaaagcccagtcccaaagcCgtcggaggctcgggaagcgt	14	13	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:7340050C>T	ENST00000323206.1	+	3	1025	c.752C>T	c.(751-753)cCg>cTg	p.P251L	RP11-104H15.8_ENST00000576615.1_RNA|FGF11_ENST00000293829.4_5'Flank|RP11-104H15.7_ENST00000575310.1_RNA|RP11-104H15.10_ENST00000575331.1_RNA|RP11-104H15.9_ENST00000570444.1_RNA|FGF11_ENST00000575235.1_5'Flank|TMEM102_ENST00000396568.1_Missense_Mutation_p.P251L	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	251					apoptotic process (GO:0006915)|positive regulation of cell adhesion (GO:0045785)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				kidney(1)|lung(3)|skin(1)	5		Prostate(122;0.173)				GTCCCAAAGCCGTCGGAGGCT	0.607																																					p.P251L		Atlas-SNP	.											.	TMEM102	11	.	0			c.C752T						.						77	80	79					17																	7340050		2203	4300	6503	SO:0001583	missense	284114	exon3			CAAAGCCGTCGGA	AK094197	CCDS11104.1	17p13.1	2008-04-21			ENSG00000181284	ENSG00000181284			26722	protein-coding gene	gene with protein product		613936				12477932	Standard	NM_178518		Approved	FLJ36878	uc002ggx.1	Q8N9M5	OTTHUMG00000132901	ENST00000323206.1:c.752C>T	chr17.hg19:g.7340050C>T	ENSP00000315387:p.Pro251Leu	105.0	0.0		72.0	4.0	NM_178518	D3DTP8	Missense_Mutation	SNP	ENST00000323206.1	hg19	CCDS11104.1	.	.	.	.	.	.	.	.	.	.	C	6.007	0.369720	0.11352	.	.	ENSG00000181284	ENST00000323206;ENST00000396568	T;T	0.41400	1.0;1.0	4.7	1.57	0.23409	.	0.814572	0.10946	N	0.616737	T	0.28034	0.0691	L	0.29908	0.895	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.26360	-1.0105	10	0.72032	D	0.01	-13.1651	4.4547	0.11637	0.1759:0.6361:0.0:0.188	.	251	Q8N9M5	TM102_HUMAN	L	251	ENSP00000315387:P251L;ENSP00000379815:P251L	ENSP00000315387:P251L	P	+	2	0	TMEM102	7280774	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	0.013000	0.13310	0.290000	0.22444	0.561000	0.74099	CCG	.	.		0.607	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518		T	7340050	C	T	7340050	3	4	91	1	0	0	0	0	1	0	0	0	16032	652	23	1	758	1	TMEM102	17	7340050	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	80859	7340050	73855160	558	12632										
ALOXE3	59344	hgsc.bcm.edu	37	chr17	8011902	8011902	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtagcccacgatttctgagAcaaagctgcaggaaagagat	11	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:8011902A>G	ENST00000448843.2	-	13	1908	c.1568T>C	c.(1567-1569)gTc>gCc	p.V523A	ALOXE3_ENST00000318227.3_Missense_Mutation_p.V655A|ALOXE3_ENST00000380149.1_Missense_Mutation_p.V679A	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3	523	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|fat cell differentiation (GO:0045444)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|sensory perception of pain (GO:0019233)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)	hepoxilin A3 synthase activity (GO:0051120)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	31						GATTTCTGAGACAAAGCTGCA	0.572																																					p.V655A		Atlas-SNP	.											.	ALOXE3	145	.	0			c.T1964C						.						75	73	74					17																	8011902		2203	4300	6503	SO:0001583	missense	59344	exon13			TCTGAGACAAAGC	AJ269499	CCDS11130.1, CCDS54084.1	17p13.1	2009-07-10			ENSG00000179148	ENSG00000179148	1.13.11.-	"Arachidonate lipoxygenases"	13743	protein-coding gene	gene with protein product		607206					Standard	NM_021628		Approved	eLOX3, E-LOX	uc010vuo.2	Q9BYJ1	OTTHUMG00000108179	ENST00000448843.2:c.1568T>C	chr17.hg19:g.8011902A>G	ENSP00000400581:p.Val523Ala	82.0	0.0		58.0	4.0	NM_001165960	B2R981|B7Z3W0|Q3ZB74|Q9H4F2|Q9HC22	Missense_Mutation	SNP	ENST00000448843.2	hg19	CCDS11130.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.400843	0.83120	.	.	ENSG00000179148	ENST00000380149;ENST00000318227;ENST00000448843	D;D;D	0.82803	-1.65;-1.65;-1.65	4.85	4.85	0.62838	Lipoxygenase, C-terminal (3);	0.058203	0.64402	D	0.000002	D	0.88980	0.6585	M	0.68952	2.095	0.58432	D	0.999999	D;D;D	0.63880	0.99;0.993;0.993	D;D;D	0.67382	0.91;0.951;0.951	D	0.89834	0.3998	10	0.62326	D	0.03	-35.6089	13.5611	0.61790	1.0:0.0:0.0:0.0	.	655;523;523	B7Z3W0;Q9BYJ1;B3KVD2	.;LOXE3_HUMAN;.	A	679;655;523	ENSP00000369494:V679A;ENSP00000314879:V655A;ENSP00000400581:V523A	ENSP00000314879:V655A	V	-	2	0	ALOXE3	7952627	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.725000	0.61979	2.051000	0.60960	0.460000	0.39030	GTC	.	.		0.572	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1			G	8011902	A	G	8011902	3	3	91	1	0	0	0	0	1	0	0	0	542	275	10	2	583	2	ALOXE3	17	8011902	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	671852	8011902	73183308	559	12633										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18063265	18063265	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcagctgtgcggggaccatgAggtcatgcgggatgaatgtt	16	7	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:18063265A>G	ENST00000205890.5	+	56	9658	c.9320A>G	c.(9319-9321)gAg>gGg	p.E3107G	MYO15A_ENST00000451725.2_5'UTR|MYO15A_ENST00000418233.3_Missense_Mutation_p.E371G	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3107	MyTH4 2. {ECO:0000255|PROSITE- ProRule:PRU00359}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					GGGGACCATGAGGTCATGCGG	0.532																																					p.E3107G		Atlas-SNP	.											.	MYO15A	268	.	0			c.A9320G						.						104	106	105					17																	18063265		2105	4225	6330	SO:0001583	missense	51168	exon55			ACCATGAGGTCAT	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.9320A>G	chr17.hg19:g.18063265A>G	ENSP00000205890:p.Glu3107Gly	95.0	0.0		66.0	4.0	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	A	13.24	2.179418	0.38511	.	.	ENSG00000091536	ENST00000205890;ENST00000418233;ENST00000556535	D;D	0.92446	-3.04;-3.04	5.6	5.6	0.85130	MyTH4 domain (3);	.	.	.	.	D	0.89739	0.6802	L	0.38733	1.17	0.80722	D	1	B;B;B;B	0.28783	0.018;0.222;0.217;0.037	B;B;B;B	0.37943	0.039;0.261;0.121;0.055	D	0.86719	0.1941	9	0.25751	T	0.34	.	15.7766	0.78224	1.0:0.0:0.0:0.0	.	96;371;3107;114	B4DLV9;B4DFC7;Q9UKN7;Q8TCK0	.;.;MYO15_HUMAN;.	G	3107;96;61	ENSP00000205890:E3107G;ENSP00000451782:E61G	ENSP00000205890:E3107G	E	+	2	0	MYO15A	18003990	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.985000	0.70556	2.143000	0.66587	0.459000	0.35465	GAG	.	.		0.532	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		G	18063265	A	G	18063265	3	3	91	1	0	0	0	0	1	0	0	0	10072	304	11	2	9534	2	MYO15A	17	18063265	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	10051363	18063265	63131945	560	12634										
CYTSB	92521	hgsc.bcm.edu	37	chr17	20108053	20108053	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctatgataagagctcttgagGagaagaacaagaactttcag	10	6	2	6			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:20108053G>A	ENST00000261503.5	+	4	742	c.691G>A	c.(691-693)Gag>Aag	p.E231K	SPECC1_ENST00000584527.1_5'Flank|SPECC1_ENST00000395530.2_Missense_Mutation_p.E150K|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395527.4_Missense_Mutation_p.E231K|SPECC1_ENST00000395525.3_Missense_Mutation_p.E150K|SPECC1_ENST00000395522.2_Missense_Mutation_p.E150K|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395529.3_Missense_Mutation_p.E231K|SPECC1_ENST00000472876.1_Intron	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	231					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		AGCTCTTGAGGAGAAGAACAA	0.478																																					p.E231K		Atlas-SNP	.											.	SPECC1	100	.	0			c.G691A						.						131	145	140					17																	20108053		2203	4300	6503	SO:0001583	missense	92521	exon4			CTTGAGGAGAAGA	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"sperm antigen HCMOGT 1", "cytokinesis and spindle organization B", "cytospin B"	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.691G>A	chr17.hg19:g.20108053G>A	ENSP00000261503:p.Glu231Lys	87.0	0.0		87.0	7.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	hg19	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	G	32	5.184086	0.94885	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.75050	-0.9;2.1;2.15;2.14	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.85509	0.5713	M	0.71036	2.16	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;0.999;1.0	D;D;D;D;D	0.85130	0.994;0.997;0.997;0.997;0.979	D	0.86658	0.1902	10	0.72032	D	0.01	-31.671	16.7847	0.85571	0.0:0.0:1.0:0.0	.	231;150;150;231;231	A8MV89;Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;.;CYTSB_HUMAN	K	231;231;231;150;150;150	ENSP00000261503:E231K;ENSP00000378900:E231K;ENSP00000378893:E150K;ENSP00000378896:E150K	ENSP00000261503:E231K	E	+	1	0	SPECC1	20048645	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.167000	0.94773	2.642000	0.89623	0.655000	0.94253	GAG	.	.		0.478	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904		A	20108053	G	A	20108053	3	1	91	1	0	0	0	0	1	0	0	0	4212	1175	41	3	745	3	CYTSB	17	20108053	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	2044788	20108053	61087157	561	12635										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27025001	27025001	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttcatctgtgcctgcaaggaActgcccggcaagttcctact	9	13	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:27025001A>G	ENST00000314616.6	+	32	4684	c.4401A>G	c.(4399-4401)gaA>gaG	p.E1467E	SUPT6H_ENST00000347486.4_Silent_p.E1467E	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1467					chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CCTGCAAGGAACTGCCCGGCA	0.537																																					p.E1467E		Atlas-SNP	.											.	SUPT6H	165	.	0			c.A4401G						.						75	73	73					17																	27025001		2203	4300	6503	SO:0001819	synonymous_variant	6830	exon32			CAAGGAACTGCCC	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.4401A>G	chr17.hg19:g.27025001A>G		47.0	0.0		58.0	4.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.537	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		G	27025001	A	G	27025001	2	3	91	1	0	0	0	0	0	0	0	1	15415	40	2	2		2	SUPT6H	17	27025001	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	6916948	27025001	54170209	562	12636										
RAB34	83871	hgsc.bcm.edu	37	chr17	27042082	27042082	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agactgcccagtactcagccTtcatctcctgggccacctgg	9	16	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:27042082T>C	ENST00000395245.3	-	8	1198	c.572A>G	c.(571-573)aAg>aGg	p.K191R	RAB34_ENST00000395242.2_Missense_Mutation_p.K192R|RAB34_ENST00000301043.6_Missense_Mutation_p.K191R|RAB34_ENST00000450529.1_Missense_Mutation_p.K183R|RAB34_ENST00000436730.3_Missense_Mutation_p.K191R|RAB34_ENST00000453384.3_Splice_Site_p.K249R|RAB34_ENST00000447716.1_Missense_Mutation_p.K248R|RAB34_ENST00000415040.2_Missense_Mutation_p.K169R|RAB34_ENST00000395243.3_Missense_Mutation_p.K183R	NM_001256281.1|NM_031934.5	NP_001243210.1|NP_114140.4	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family	191					antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					GTACTCAGCCTTCATCTCCTG	0.587																																					p.K249R	Pancreas(175;216 2049 29940 32498 41589)	Atlas-SNP	.											.	RAB34	44	.	0			c.A746G						.						86	74	78					17																	27042082		2203	4300	6503	SO:0001583	missense	83871	exon9			TCAGCCTTCATCT	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"RAB, member RAS oncogene"	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680	ENST00000395245.3:c.572A>G	chr17.hg19:g.27042082T>C	ENSP00000378666:p.Lys191Arg	86.0	0.0		70.0	4.0	NM_001142625	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Missense_Mutation	SNP	ENST00000395245.3	hg19	CCDS11240.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.65|12.65	2.001371|2.001371	0.35320|0.35320	.|.	.|.	ENSG00000109113|ENSG00000109113	ENST00000453384;ENST00000447716;ENST00000301043;ENST00000395243;ENST00000415040;ENST00000450529;ENST00000395242;ENST00000395245;ENST00000436730;ENST00000430132;ENST00000412625;ENST00000353676|ENST00000419712	T;T;T;T;T;T;T;T;T|.	0.80304|.	-1.1;-1.36;-1.36;-1.36;-1.36;-1.36;-1.36;-1.36;-1.36|.	5.01|5.01	5.01|5.01	0.66863|0.66863	Small GTP-binding protein domain (1);|.	0.268600|.	0.38778|.	N|.	0.001569|.	T|T	0.47377|0.47377	0.1442|0.1442	N|N	0.25789|0.25789	0.76|0.76	.|.	.|.	.|.	B;B;B;B;B;B;B|.	0.18610|.	0.029;0.001;0.002;0.002;0.004;0.005;0.001|.	B;B;B;B;B;B;B|.	0.15484|.	0.012;0.005;0.005;0.007;0.012;0.013;0.005|.	T|T	0.56649|0.56649	-0.7944|-0.7944	9|4	0.18710|.	T|.	0.47|.	-22.8504|-22.8504	13.7031|13.7031	0.62622|0.62622	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	249;169;183;214;206;192;191|.	E7ES60;E9PEJ9;Q9BZG1-2;C9JI96;B4DNC0;A8MYQ9;Q9BZG1|.	.;.;.;.;.;.;RAB34_HUMAN|.	R|G	249;248;191;183;169;206;192;191;214;192;191;191|212	ENSP00000413156:K249R;ENSP00000410403:K248R;ENSP00000301043:K191R;ENSP00000378664:K183R;ENSP00000410279:K169R;ENSP00000378663:K192R;ENSP00000378666:K191R;ENSP00000398706:K191R;ENSP00000226259:K191R|.	ENSP00000301043:K191R|.	K|R	-|-	2|1	0|2	RAB34|RAB34	24066209|24066209	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	3.085000|3.085000	0.50151|0.50151	2.107000|2.107000	0.64212|0.64212	0.379000|0.379000	0.24179|0.24179	AAG|AGA	.	.		0.587	RAB34-018	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345906.1	NM_031934		C	27042082	T	C	27042082	3	2	91	1	0	0	0	0	1	0	0	0	12939	1623	56	2	283	2	RAB34	17	27042082	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	17081	27042082	54153128	563	12637										
PIPOX	51268	hgsc.bcm.edu	37	chr17	27371932	27371932	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acaaagccggataatccgaaAggcgtacctggaagactttt	10	9	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:27371932A>G	ENST00000323372.4	+	2	496	c.170A>G	c.(169-171)aAg>aGg	p.K57R	PIPOX_ENST00000583215.1_3'UTR	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	57					L-lysine catabolic process to acetyl-CoA via L-pipecolate (GO:0033514)|oxidation-reduction process (GO:0055114)|tetrahydrofolate metabolic process (GO:0046653)	peroxisome (GO:0005777)	L-pipecolate oxidase activity (GO:0050031)|receptor binding (GO:0005102)|sarcosine oxidase activity (GO:0008115)			endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10	Lung NSC(42;0.015)		Epithelial(11;9.87e-06)|BRCA - Breast invasive adenocarcinoma(11;3.92e-05)|all cancers(11;5.59e-05)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)		Glycine(DB00145)	ATAATCCGAAAGGCGTACCTG	0.522																																					p.K57R		Atlas-SNP	.											.	PIPOX	42	.	0			c.A170G						.						127	112	117					17																	27371932		2203	4300	6503	SO:0001583	missense	51268	exon2			TCCGAAAGGCGTA	AF134593	CCDS11248.1	17p13.2	2008-07-18			ENSG00000179761	ENSG00000179761			17804	protein-coding gene	gene with protein product	"L-pipecolic acid oxidase"					10772957, 10642506	Standard	NM_016518		Approved	LPIPOX	uc002hdr.1	Q9P0Z9	OTTHUMG00000132679	ENST00000323372.4:c.170A>G	chr17.hg19:g.27371932A>G	ENSP00000317721:p.Lys57Arg	147.0	0.0		114.0	5.0	NM_016518	B3KNH0|Q96H28|Q9C070	Missense_Mutation	SNP	ENST00000323372.4	hg19	CCDS11248.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.611071	0.28712	.	.	ENSG00000179761	ENST00000323372	T	0.80994	-1.44	5.8	1.45	0.22620	FAD dependent oxidoreductase (1);	0.236909	0.49305	N	0.000156	T	0.56247	0.1972	N	0.05351	-0.065	0.38045	D	0.935605	B	0.10296	0.003	B	0.16289	0.015	T	0.41052	-0.9530	10	0.14656	T	0.56	-6.9605	7.1044	0.25356	0.5947:0.0:0.4053:0.0	.	57	Q9P0Z9	SOX_HUMAN	R	57	ENSP00000317721:K57R	ENSP00000317721:K57R	K	+	2	0	PIPOX	24396058	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	2.181000	0.42547	0.637000	0.30526	0.528000	0.53228	AAG	.	.		0.522	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518		G	27371932	A	G	27371932	3	3	91	1	0	0	0	0	1	0	0	0	11952	72	3	2	176	2	PIPOX	17	27371932	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	329850	27371932	53823278	564	12638										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27414105	27414105	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatcccgctcctcagtcagcTtctccatgttttccttgaga	7	14	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:27414105T>A	ENST00000527372.1	-	38	5741	c.5561A>T	c.(5560-5562)aAg>aTg	p.K1854M	MYO18A_ENST00000533112.1_Missense_Mutation_p.K1817M|MYO18A_ENST00000354329.4_Missense_Mutation_p.K1854M|MYO18A_ENST00000531253.1_Missense_Mutation_p.K1854M|MYO18A_ENST00000529578.1_5'UTR|TIAF1_ENST00000408971.2_De_novo_Start_InFrame	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1854					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CTCAGTCAGCTTCTCCATGTT	0.592																																					p.K1854M	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.A5561T						.						97	101	100					17																	27414105		2042	4191	6233	SO:0001583	missense	399687	exon38			GTCAGCTTCTCCA	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.5561A>T	chr17.hg19:g.27414105T>A	ENSP00000437073:p.Lys1854Met	174.0	0.0		144.0	52.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.4|28.4	4.917267|4.917267	0.92249|0.92249	.|.	.|.	ENSG00000196535|ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000529799;ENST00000540575;ENST00000458428;ENST00000546105|ENST00000527859	D;D;D;D|.	0.90197|.	-2.4;-2.63;-2.38;-2.4|.	5.18|5.18	5.18|5.18	0.71444|0.71444	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75903|0.75903	0.3913|0.3913	M|M	0.78456|0.78456	2.415|2.415	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.998;0.999;0.999;0.998|.	T|T	0.77083|0.77083	-0.2719|-0.2719	10|5	0.87932|.	D|.	0|.	.|.	15.5158|15.5158	0.75822|0.75822	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1457;1817;1854;1854|.	F8W6Y3;Q92614-3;Q92614-4;Q92614|.	.;.;.;MY18A_HUMAN|.	M|C	1854;1817;1817;1854;1854;750;750;1457;135|117	ENSP00000346291:K1854M;ENSP00000435932:K1817M;ENSP00000434228:K1854M;ENSP00000437073:K1854M|.	ENSP00000346291:K1854M|.	K|S	-|-	2|1	0|0	MYO18A|MYO18A	24438231|24438231	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	7.217000|7.217000	0.77982|0.77982	2.317000|2.317000	0.78254|0.78254	0.459000|0.459000	0.35465|0.35465	AAG|AGC	.	.		0.592	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		A	27414105	T	A	27414105	3	1	91	1	0	0	0	0	1	0	0	0	10074	1609	56	4	623	4	MYO18A	17	27414105	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	42173	27414105	53781105	565	12639										
AP2B1	163	hgsc.bcm.edu	37	chr17	33925250	33925250	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttgctctcatctcttgcaggAgaaatatttgaactaaaagc	7	8	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:33925250A>G	ENST00000262325.7	+	3	592	c.39A>G	c.(37-39)ggA>ggG	p.G13G	AP2B1_ENST00000312678.8_Splice_Site_p.G13G|AP2B1_ENST00000592545.1_Splice_Site_p.G13G|AP2B1_ENST00000537622.2_Splice_Site_p.G13G|AP2B1_ENST00000538556.1_5'UTR|AP2B1_ENST00000589344.1_Splice_Site_p.G13G	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	13					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		CTCTTGCAGGAGAAATATTTG	0.418																																					p.G13G		Atlas-SNP	.											.	AP2B1	70	.	0			c.A39G						.						77	74	75					17																	33925250		2203	4300	6503	SO:0001630	splice_region_variant	163	exon3			TGCAGGAGAAATA	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.38-1A>G	chr17.hg19:g.33925250A>G		110.0	0.0		85.0	4.0	NM_001282	A6NJP3|P21851|Q7Z451|Q96J19	Silent	SNP	ENST00000262325.7	hg19	CCDS32622.1																																																																																			.	.		0.418	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1		Silent	G	33925250	A	G	33925250	5	3	91	1	0	0	0	0	0	0	1	0	741	318	11	2	45	2	AP2B1	17	33925250	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	6511145	33925250	47269960	566	12640										
CCL5	6352	hgsc.bcm.edu	37	chr17	34205643	34205643	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agggtgtggtgtccgaggaaTctggaagaggaaaggaagga	19	3	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:34205643T>C	ENST00000293272.3	-	2	279	c.77A>G	c.(76-78)tAt>tGt	p.Y26C	AC015849.2_ENST00000413928.1_RNA|CCL5_ENST00000366113.3_Splice_Site_p.Y26C	NM_002985.2	NP_002976.2	P13501	CCL5_HUMAN	chemokine (C-C motif) ligand 5	26		Cleavage; by DPP4.			activation of phospholipase D activity (GO:0031584)|calcium ion transport (GO:0006816)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|cellular protein complex assembly (GO:0043623)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|eosinophil chemotaxis (GO:0048245)|exocytosis (GO:0006887)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage chemotaxis (GO:0048246)|MAPK cascade (GO:0000165)|monocyte chemotaxis (GO:0002548)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of T cell apoptotic process (GO:0070233)|negative regulation of viral genome replication (GO:0045071)|neutrophil activation (GO:0042119)|positive chemotaxis (GO:0050918)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of cellular biosynthetic process (GO:0031328)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of innate immune response (GO:0045089)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell apoptotic process (GO:0070234)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of translational initiation (GO:0045948)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|positive regulation of viral genome replication (GO:0045070)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein tetramerization (GO:0051262)|regulation of chronic inflammatory response (GO:0002676)|regulation of insulin secretion (GO:0050796)|regulation of neuron death (GO:1901214)|regulation of T cell activation (GO:0050863)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|CCR4 chemokine receptor binding (GO:0031729)|CCR5 chemokine receptor binding (GO:0031730)|chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)|chemokine receptor antagonist activity (GO:0046817)|chemokine receptor binding (GO:0042379)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase activator activity (GO:0016004)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|receptor signaling protein tyrosine kinase activator activity (GO:0030298)			breast(1)|kidney(1)|lung(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0183)		GTCCGAGGAATCTGGAAGAGG	0.483																																					p.Y26C		Atlas-SNP	.											.	CCL5	6	.	0			c.A77G						.						95	93	94					17																	34205643		2203	4300	6503	SO:0001630	splice_region_variant	6352	exon2			GAGGAATCTGGAA	AF043341	CCDS11300.1	17q11.2-q12	2014-04-17	2002-08-22	2002-08-23	ENSG00000161570	ENSG00000271503		"Chemokine ligands", "Endogenous ligands"	10632	protein-coding gene	gene with protein product	"T-cell specific protein p288", "T-cell specific RANTES protein", "SIS-delta", "regulated upon activation, normally T-expressed, and presumably secreted", "beta-chemokine RANTES", "small inducible cytokine subfamily A (Cys-Cys), member 5"	187011	"small inducible cytokine A5 (RANTES)"	D17S136E, SCYA5		1691736	Standard	NM_002985		Approved	RANTES, SISd, TCP228, MGC17164	uc002hkf.3	P13501	OTTHUMG00000188396	ENST00000293272.3:c.77-1A>G	chr17.hg19:g.34205643T>C		112.0	0.0		75.0	4.0	NM_002985	O43646|Q0QVW8|Q4ZGJ1|Q9NYA2|Q9UBG2|Q9UC99	Missense_Mutation	SNP	ENST00000293272.3	hg19	CCDS11300.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.963544	0.53507	.	.	ENSG00000161570	ENST00000293272;ENST00000366113	T;T	0.02369	4.32;4.32	5.39	5.39	0.77823	Chemokine interleukin-8-like domain (1);	0.488660	0.21839	N	0.068354	T	0.05135	0.0137	.	.	.	0.49483	D	0.999794	P	0.51537	0.946	P	0.46543	0.52	T	0.46898	-0.9158	9	0.42905	T	0.14	.	11.7182	0.51666	0.0:0.0:0.0:1.0	.	26	P13501	CCL5_HUMAN	C	26	ENSP00000293272:Y26C;ENSP00000375216:Y26C	ENSP00000293272:Y26C	Y	-	2	0	CCL5	31229756	1.000000	0.71417	1.000000	0.80357	0.598000	0.36846	1.134000	0.31442	2.266000	0.75297	0.533000	0.62120	TAT	.	.		0.483	CCL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256486.3	NM_002985	Missense_Mutation	C	34205643	T	C	34205643	5	2	91	1	0	0	0	0	0	0	1	0	2907	1449	50	2	206	2	CCL5	17	34205643	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	280393	34205643	46989567	567	12641										
GRB7	2886	hgsc.bcm.edu	37	chr17	37901211	37901211	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgagcagagccgcacctgcTggctggctgccttccgcctc	12	16	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:37901211T>C	ENST00000309156.4	+	9	1242	c.985T>C	c.(985-987)Tgg>Cgg	p.W329R	GRB7_ENST00000309185.3_Missense_Mutation_p.W329R|GRB7_ENST00000394211.3_Missense_Mutation_p.W329R|GRB7_ENST00000394209.2_Missense_Mutation_p.W329R|GRB7_ENST00000445327.2_Missense_Mutation_p.W352R|GRB7_ENST00000394204.1_Missense_Mutation_p.W329R	NM_005310.3	NP_005301.2	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7	329	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|leukocyte migration (GO:0050900)|negative regulation of translation (GO:0017148)|positive regulation of cell migration (GO:0030335)|positive regulation of signal transduction (GO:0009967)|stress granule assembly (GO:0034063)	cell projection (GO:0042995)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCGCACCTGCTGGCTGGCTGC	0.612																																					p.W352R		Atlas-SNP	.											.	GRB7	48	.	0			c.T1054C						.						37	40	39					17																	37901211		2202	4300	6502	SO:0001583	missense	2886	exon9			ACCTGCTGGCTGG	D43772	CCDS11345.1, CCDS56028.1	17q12	2013-02-14			ENSG00000141738	ENSG00000141738		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4567	protein-coding gene	gene with protein product		601522					Standard	NM_005310		Approved		uc021twu.1	Q14451	OTTHUMG00000133253	ENST00000309156.4:c.985T>C	chr17.hg19:g.37901211T>C	ENSP00000310771:p.Trp329Arg	84.0	0.0		83.0	4.0	NM_001242442	B2RAV1|B3KNL0|B3KWP9|B7WP75|J3KQM4|Q53YD3|Q92568|Q96DF9|Q9Y220	Missense_Mutation	SNP	ENST00000309156.4	hg19	CCDS11345.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.320788	0.81469	.	.	ENSG00000141738	ENST00000309185;ENST00000309156;ENST00000394211;ENST00000394209;ENST00000445327;ENST00000394204	D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	5.17	5.17	0.71159	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.108901	0.64402	D	0.000002	D	0.94105	0.8110	M	0.78916	2.43	0.80722	D	1	D;D	0.89917	0.973;1.0	P;D	0.87578	0.661;0.998	D	0.94802	0.7971	10	0.87932	D	0	-16.4513	14.836	0.70183	0.0:0.0:0.0:1.0	.	329;329	Q14451-2;Q14451	.;GRB7_HUMAN	R	329;329;329;329;352;329	ENSP00000311752:W329R;ENSP00000310771:W329R;ENSP00000377761:W329R;ENSP00000377759:W329R;ENSP00000403459:W352R;ENSP00000377754:W329R	ENSP00000310771:W329R	W	+	1	0	GRB7	35154737	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.760000	0.85248	2.165000	0.68154	0.459000	0.35465	TGG	.	.		0.612	GRB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257024.2	NM_005310		C	37901211	T	C	37901211	3	2	91	1	0	0	0	0	1	0	0	0	6768	1580	55	2	1015	2	GRB7	17	37901211	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3695568	37901211	43293999	568	12642										
MED24	9862	hgsc.bcm.edu	37	chr17	38179530	38179530	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttgatgggccgcttgggggGcagcaggttccagtagggca	18	8	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:38179530G>A	ENST00000394128.2	-	20	2185	c.2104C>T	c.(2104-2106)Ccc>Tcc	p.P702S	MED24_ENST00000394126.1_Missense_Mutation_p.P727S|MED24_ENST00000394127.2_Missense_Mutation_p.P689S|MED24_ENST00000356271.3_Missense_Mutation_p.P689S|MED24_ENST00000501516.3_Missense_Mutation_p.P721S	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	702					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CGCTTGGGGGGCAGCAGGTTC	0.602																																					p.P702S		Atlas-SNP	.											.	MED24	89	.	0			c.C2104T						.						57	51	53					17																	38179530		2203	4300	6503	SO:0001583	missense	9862	exon20			TGGGGGGCAGCAG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2104C>T	chr17.hg19:g.38179530G>A	ENSP00000377686:p.Pro702Ser	128.0	0.0		94.0	20.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	hg19	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.908418	0.52333	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000535508;ENST00000501516;ENST00000431269	T;T;T	0.44482	0.92;0.92;0.92	4.43	4.43	0.53597	Mediator complex, subunit Med24, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.59459	0.2195	L	0.51422	1.61	0.80722	D	1	D;D;P;D;D;D	0.89917	1.0;1.0;0.81;1.0;1.0;1.0	D;D;P;D;D;D	0.91635	0.998;0.998;0.498;0.998;0.999;0.998	T	0.61302	-0.7090	10	0.51188	T	0.08	-25.0801	17.2528	0.87047	0.0:0.0:1.0:0.0	.	652;612;612;689;702;644	F5H5K2;F8W9R9;B4E1A5;O75448-2;O75448;F5H0K1	.;.;.;.;MED24_HUMAN;.	S	702;702;702;652;689;644;263;173;612	ENSP00000377686:P702S;ENSP00000443344:P652S;ENSP00000377685:P689S	ENSP00000348610:P702S	P	-	1	0	MED24	35433056	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.653000	0.83643	2.280000	0.76307	0.561000	0.74099	CCC	.	.		0.602	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		A	38179530	G	A	38179530	3	1	91	1	0	0	0	0	1	0	0	0	9451	1203	42	3	893	3	MED24	17	38179530	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	278319	38179530	43015680	569	12643										
KRT19	3880	hgsc.bcm.edu	37	chr17	39680207	39680207	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgcgccagctgggctccaaAgcgcgcctccgtttctgcca	11	16	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:39680207A>G	ENST00000361566.3	-	6	1051	c.991T>C	c.(991-993)Ttt>Ctt	p.F331L	KRT15_ENST00000393974.3_5'Flank|KRT15_ENST00000393976.2_5'Flank|KRT15_ENST00000254043.3_5'Flank	NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	331	Coil 2.|Necessary for interaction with PNN.|Rod.				cell differentiation involved in embryonic placenta development (GO:0060706)|response to estrogen (GO:0043627)|sarcomere organization (GO:0045214)|viral process (GO:0016032)	cell periphery (GO:0071944)|costamere (GO:0043034)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12		Breast(137;0.00038)				TGGGCTCCAAAGCGCGCCTCC	0.597																																					p.F331L		Atlas-SNP	.											.	KRT19	41	.	0			c.T991C						.						40	41	41					17																	39680207		2203	4299	6502	SO:0001583	missense	3880	exon6			CTCCAAAGCGCGC		CCDS11399.1	17q21.2	2013-06-20			ENSG00000171345	ENSG00000171345		"-", "Intermediate filaments type I, keratins (acidic)"	6436	protein-coding gene	gene with protein product	"keratin, type I cytoskeletal 19", "keratin, type I, 40-kd", "cytokeratin 19", "40-kDa keratin intermediate filament"	148020				16831889	Standard	NM_002276		Approved	K19, CK19, K1CS, MGC15366		P08727	OTTHUMG00000133422	ENST00000361566.3:c.991T>C	chr17.hg19:g.39680207A>G	ENSP00000355124:p.Phe331Leu	96.0	0.0		121.0	5.0	NM_002276	B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Missense_Mutation	SNP	ENST00000361566.3	hg19	CCDS11399.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.239879	0.58995	.	.	ENSG00000171345	ENST00000361566	D	0.87571	-2.27	5.17	5.17	0.71159	Filament (1);	0.300651	0.23975	N	0.042732	D	0.87795	0.6267	L	0.56280	1.765	0.37628	D	0.921553	B;B	0.29341	0.027;0.242	B;B	0.39935	0.082;0.314	D	0.89297	0.3623	10	0.87932	D	0	.	15.0761	0.72077	1.0:0.0:0.0:0.0	.	494;331	B4DE59;P08727	.;K1C19_HUMAN	L	331	ENSP00000355124:F331L	ENSP00000355124:F331L	F	-	1	0	KRT19	36933733	0.947000	0.32204	0.104000	0.21259	0.222000	0.24845	7.406000	0.80017	1.963000	0.57068	0.454000	0.30748	TTT	.	.		0.597	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257285.1	NM_002276		G	39680207	A	G	39680207	3	3	91	1	0	0	0	0	1	0	0	0	8465	72	3	2	215	2	KRT19	17	39680207	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1500677	39680207	41515003	570	12644										
CCR10	2826	hgsc.bcm.edu	37	chr17	40831707	40831707	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcagcctccgcaggtcctggCggaagcgcaggcccaggaag	16	14	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:40831707C>T	ENST00000332438.4	-	2	972	c.953G>A	c.(952-954)cGc>cAc	p.R318H	CNTNAP1_ENST00000264638.4_5'Flank|PLEKHH3_ENST00000591022.1_5'Flank|PLEKHH3_ENST00000293349.6_5'Flank|CTD-3193K9.4_ENST00000593139.1_RNA|PLEKHH3_ENST00000412503.1_5'Flank|CCR10_ENST00000591765.1_Missense_Mutation_p.R96H	NM_016602.2	NP_057686.2	P46092	CCR10_HUMAN	chemokine (C-C motif) receptor 10	318					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)			lung(1)|ovary(1)|skin(1)	3		Breast(137;0.000153)		BRCA - Breast invasive adenocarcinoma(366;0.14)		CAGGTCCTGGCGGAAGCGCAG	0.701																																					p.R318H		Atlas-SNP	.											.	CCR10	7	.	0			c.G953A						.						13	13	13					17																	40831707		2174	4252	6426	SO:0001583	missense	2826	exon2			TCCTGGCGGAAGC	AF215981	CCDS11435.1	17q21.1-q21.3	2012-08-08	2004-11-12	2004-11-12	ENSG00000184451	ENSG00000184451		"GPCR / Class A : Chemokine receptors : C-C motif"	4474	protein-coding gene	gene with protein product		600240	"G protein-coupled receptor 2"	GPR2		7851889	Standard	NM_016602		Approved		uc002iax.4	P46092	OTTHUMG00000132301	ENST00000332438.4:c.953G>A	chr17.hg19:g.40831707C>T	ENSP00000332504:p.Arg318His	59.0	0.0		63.0	20.0	NM_016602	Q4V749|Q6T7X2|Q9NZG2	Missense_Mutation	SNP	ENST00000332438.4	hg19	CCDS11435.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.790650	0.90367	.	.	ENSG00000184451	ENST00000332438	T	0.58358	0.34	4.22	4.22	0.49857	.	0.000000	0.40064	N	0.001189	T	0.53578	0.1805	N	0.08118	0	0.50039	D	0.999841	D	0.89917	1.0	D	0.85130	0.997	T	0.65500	-0.6153	10	0.87932	D	0	.	15.5224	0.75875	0.0:1.0:0.0:0.0	.	318	P46092	CCR10_HUMAN	H	318	ENSP00000332504:R318H	ENSP00000332504:R318H	R	-	2	0	CCR10	38085233	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	5.516000	0.67055	2.185000	0.69588	0.313000	0.20887	CGC	.	.		0.701	CCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255406.1	NM_016602		T	40831707	C	T	40831707	3	4	91	1	0	0	0	0	1	0	0	0	2942	768	27	1	139	1	CCR10	17	40831707	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1151500	40831707	40363503	571	12645										
PLEKHM1	9842	hgsc.bcm.edu	37	chr17	43516846	43516846	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctgggtgtcccgcatacctgActgtggtgtcaaactcaaag	11	11	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:43516846A>G	ENST00000430334.3	-	11	3189	c.3056T>C	c.(3055-3057)gTc>gCc	p.V1019A	PLEKHM1_ENST00000421073.2_Missense_Mutation_p.V930A|PLEKHM1_ENST00000580404.1_5'UTR	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	1019					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CGCATACCTGACTGTGGTGTC	0.632																																					p.V1019A		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.T3056C						.						90	75	80					17																	43516846		2203	4300	6503	SO:0001583	missense	9842	exon11			TACCTGACTGTGG	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"Pleckstrin homology (PH) domain containing"	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.3056T>C	chr17.hg19:g.43516846A>G	ENSP00000389913:p.Val1019Ala	145.0	0.0		101.0	5.0	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Missense_Mutation	SNP	ENST00000430334.3	hg19	CCDS32671.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.575360	0.28092	.	.	ENSG00000225190	ENST00000430334;ENST00000421073	T;T	0.63255	-0.03;-0.03	5.08	1.6	0.23607	Protein kinase C-like, phorbol ester/diacylglycerol binding (2);	0.786081	0.11452	N	0.562701	T	0.36166	0.0957	N	0.10945	0.07	0.25339	N	0.988968	B;B	0.19445	0.029;0.036	B;B	0.20577	0.029;0.03	T	0.24261	-1.0165	10	0.11485	T	0.65	.	6.2057	0.20602	0.5906:0.0:0.4094:0.0	.	930;1019	F8W648;Q9Y4G2	.;PKHM1_HUMAN	A	1019;930	ENSP00000389913:V1019A;ENSP00000414352:V930A	ENSP00000414352:V930A	V	-	2	0	PLEKHM1	40872629	0.994000	0.37717	0.995000	0.50966	0.791000	0.44710	2.031000	0.41117	0.434000	0.26340	-0.475000	0.04921	GTC	.	.		0.632	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798		G	43516846	A	G	43516846	3	3	91	1	0	0	0	0	1	0	0	0	12089	275	10	2	122	2	PLEKHM1	17	43516846	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2685139	43516846	37678364	572	12646										
NPEPPS	9520	hgsc.bcm.edu	37	chr17	45679095	45679095	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtggttttgaaaaatgtcaaAccagaccaatgggtgaaggt	12	5	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:45679095A>G	ENST00000322157.4	+	15	1959	c.1722A>G	c.(1720-1722)aaA>aaG	p.K574K	RP11-580I16.2_ENST00000582066.1_RNA|RP11-580I16.2_ENST00000582389.1_RNA|NPEPPS_ENST00000544660.1_Silent_p.K494K|NPEPPS_ENST00000530173.1_Silent_p.K570K	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	574					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						AAAATGTCAAACCAGACCAAT	0.388																																					p.K574K		Atlas-SNP	.											.	NPEPPS	59	.	0			c.A1722G						.						100	96	97					17																	45679095		1846	4085	5931	SO:0001819	synonymous_variant	9520	exon15			TGTCAAACCAGAC	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"puromycin-sensitive aminopeptidase", "metalloproteinase MP100"	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1722A>G	chr17.hg19:g.45679095A>G		147.0	0.0		118.0	5.0	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Silent	SNP	ENST00000322157.4	hg19	CCDS45721.1																																																																																			.	.		0.388	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310		G	45679095	A	G	45679095	2	3	91	1	0	0	0	0	0	0	0	1	10584	40	2	2		2	NPEPPS	17	45679095	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2162249	45679095	35516115	573	12647										
TBX21	30009	hgsc.bcm.edu	37	chr17	45822240	45822240	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cccagccgcttctaccccgaCcttcctggccaggcgaagga	10	18	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:45822240C>T	ENST00000177694.1	+	6	1327	c.1116C>T	c.(1114-1116)gaC>gaT	p.D372D		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	372					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						TCTACCCCGACCTTCCTGGCC	0.612																																					p.D372D		Atlas-SNP	.											.	TBX21	50	.	0			c.C1116T						.						85	83	84					17																	45822240		2203	4300	6503	SO:0001819	synonymous_variant	30009	exon6			CCCCGACCTTCCT	AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"T-boxes"	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.1116C>T	chr17.hg19:g.45822240C>T		75.0	0.0		66.0	4.0	NM_013351		Silent	SNP	ENST00000177694.1	hg19	CCDS11514.1																																																																																			.	.		0.612	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351		T	45822240	C	T	45822240	2	4	91	1	0	0	0	0	0	0	0	1	15672	506	18	3		3	TBX21	17	45822240	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	143145	45822240	35372970	574	12648										
NFE2L1	4779	hgsc.bcm.edu	37	chr17	46128683	46128683	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttggatggctatggtatccAccccaagagcatagacctgg	11	11	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:46128683A>G	ENST00000362042.3	+	2	819	c.203A>G	c.(202-204)cAc>cGc	p.H68R	NFE2L1_ENST00000585291.1_Missense_Mutation_p.H68R|NFE2L1_ENST00000357480.5_Missense_Mutation_p.H68R|NFE2L1_ENST00000361665.3_Missense_Mutation_p.H68R	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	68					anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TATGGTATCCACCCCAAGAGC	0.567																																					p.H68R		Atlas-SNP	.											.	NFE2L1	60	.	0			c.A203G						.						107	103	104					17																	46128683		2203	4300	6503	SO:0001583	missense	4779	exon2			GTATCCACCCCAA	AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"basic leucine zipper proteins"	7781	protein-coding gene	gene with protein product		163260	"nuclear factor (erythroid-derived 2)-like 1"	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.203A>G	chr17.hg19:g.46128683A>G	ENSP00000354855:p.His68Arg	99.0	0.0		81.0	4.0	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Missense_Mutation	SNP	ENST00000362042.3	hg19	CCDS11524.1	.	.	.	.	.	.	.	.	.	.	A	11.74	1.727972	0.30593	.	.	ENSG00000082641	ENST00000362042;ENST00000361665;ENST00000357480	T;T	0.26373	2.16;1.74	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.52058	0.1711	M	0.79258	2.445	0.80722	D	1	D;D;D	0.89917	0.984;0.999;1.0	D;D;D	0.85130	0.964;0.994;0.997	T	0.57825	-0.7744	10	0.87932	D	0	-21.2442	13.8987	0.63790	1.0:0.0:0.0:0.0	.	68;68;68	A3KMG6;Q14494-2;Q14494	.;.;NF2L1_HUMAN	R	87;68;68	ENSP00000355190:H68R;ENSP00000350072:H68R	ENSP00000350072:H68R	H	+	2	0	NFE2L1	43483682	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.236000	0.95360	1.938000	0.56188	0.460000	0.39030	CAC	.	.		0.567	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204		G	46128683	A	G	46128683	3	3	91	1	0	0	0	0	1	0	0	0	10376	159	6	2	205	2	NFE2L1	17	46128683	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	306443	46128683	35066527	575	12649										
NFE2L1	4779	hgsc.bcm.edu	37	chr17	46136184	46136184	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaaggcagttcttcctcttcTtcctcctcctcttcctcttc	4	17	5	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:46136184T>C	ENST00000362042.3	+	6	2116	c.1500T>C	c.(1498-1500)tcT>tcC	p.S500S	RP5-890E16.4_ENST00000583349.1_RNA|NFE2L1_ENST00000585291.1_Silent_p.S470S|NFE2L1_ENST00000357480.5_Silent_p.S470S|NFE2L1_ENST00000583378.1_Silent_p.S301S|NFE2L1_ENST00000536222.1_Silent_p.S344S|NFE2L1_ENST00000361665.3_Silent_p.S489S|NFE2L1_ENST00000582155.1_Silent_p.S312S	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	500	Poly-Ser.				anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						cttcctcttcttcctcctcct	0.537																																					p.S500S		Atlas-SNP	.											.	NFE2L1	60	.	0			c.T1500C						.						81	80	80					17																	46136184		2203	4300	6503	SO:0001819	synonymous_variant	4779	exon6			CTCTTCTTCCTCC	AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"basic leucine zipper proteins"	7781	protein-coding gene	gene with protein product		163260	"nuclear factor (erythroid-derived 2)-like 1"	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.1500T>C	chr17.hg19:g.46136184T>C		71.0	0.0		87.0	4.0	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Silent	SNP	ENST00000362042.3	hg19	CCDS11524.1																																																																																			.	.		0.537	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204		C	46136184	T	C	46136184	2	2	91	1	0	0	0	0	0	0	0	1	10376	1596	56	2		2	NFE2L1	17	46136184	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	7501	46136184	35059026	576	12650										
SPOP	8405	hgsc.bcm.edu	37	chr17	47677854	47677854	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gacaccaccattgacttccaCccagaggtctccaagacatc	6	16	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:47677854C>T	ENST00000393328.2	-	11	1376	c.1011G>A	c.(1009-1011)ggG>ggA	p.G337G	SPOP_ENST00000503676.1_Silent_p.G337G|SPOP_ENST00000393331.3_Silent_p.G337G|SPOP_ENST00000347630.2_Silent_p.G337G|SPOP_ENST00000504102.1_Silent_p.G337G	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	337	Important for homodimerization.				glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						TTGACTTCCACCCAGAGGTCT	0.537										Prostate(2;0.17)																											p.G337G		Atlas-SNP	.											.	SPOP	91	.	0			c.G1011A						.						106	100	102					17																	47677854		2203	4300	6503	SO:0001819	synonymous_variant	8405	exon10			CTTCCACCCAGAG	AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"BTB/POZ domain containing"	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.1011G>A	chr17.hg19:g.47677854C>T		89.0	0.0		82.0	4.0	NM_001007228	B2R6S3|D3DTW7|Q53HJ1	Silent	SNP	ENST00000393328.2	hg19	CCDS11551.1																																																																																			.	.		0.537	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563		T	47677854	C	T	47677854	2	4	91	1	0	0	0	0	0	0	0	1	15099	494	18	3		3	SPOP	17	47677854	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1541670	47677854	33517356	577	12651										
SPAG9	9043	hgsc.bcm.edu	37	chr17	49072445	49072445	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcctgatctaacttatctaaActactctgagaggcacttcg	6	11	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:49072445A>G	ENST00000262013.7	-	18	2407	c.2199T>C	c.(2197-2199)agT>agC	p.S733S	SPAG9_ENST00000357122.4_Silent_p.S719S|SPAG9_ENST00000510283.1_Silent_p.S576S|SPAG9_ENST00000505279.1_Silent_p.S723S	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	733					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			ACTTATCTAAACTACTCTGAG	0.398																																					p.S733S		Atlas-SNP	.											.	SPAG9	151	.	0			c.T2199C						.						167	145	152					17																	49072445		2203	4300	6503	SO:0001819	synonymous_variant	9043	exon18			ATCTAAACTACTC	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2199T>C	chr17.hg19:g.49072445A>G		97.0	0.0		79.0	4.0	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Silent	SNP	ENST00000262013.7	hg19	CCDS45740.1																																																																																			.	.		0.398	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		G	49072445	A	G	49072445	2	3	91	1	0	0	0	0	0	0	0	1	15000	40	2	2		2	SPAG9	17	49072445	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1394591	49072445	32122765	578	12652										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901222	51901222	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttcgatgacaaagcctccaaCgagttggtgtaccagttcac	9	11	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:51901222C>T	ENST00000268919.4	+	1	984	c.828C>T	c.(826-828)aaC>aaT	p.N276N		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	276	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AAGCCTCCAACGAGTTGGTGT	0.562																																					p.N276N		Atlas-SNP	.											.	KIF2B	254	.	0			c.C828T						.						114	95	101					17																	51901222		2203	4300	6503	SO:0001819	synonymous_variant	84643	exon1			CTCCAACGAGTTG	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.828C>T	chr17.hg19:g.51901222C>T		102.0	0.0		112.0	36.0	NM_032559	Q96MA2|Q9BXG6	Silent	SNP	ENST00000268919.4	hg19	CCDS32685.1																																																																																			.	.		0.562	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51901222	C	T	51901222	2	4	91	1	0	0	0	0	0	0	0	1	8307	535	19	1		1	KIF2B	17	51901222	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2828777	51901222	29293988	579	12653										
TRIM25	7706	hgsc.bcm.edu	37	chr17	54969476	54969476	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagagcagtatgtgaacctcTggggatgcggccggtagttc	16	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:54969476T>C	ENST00000316881.4	-	9	1527	c.1478A>G	c.(1477-1479)cAg>cGg	p.Q493R	MIR3614_ENST00000581261.1_RNA|RP11-670E13.5_ENST00000574826.1_RNA|TRIM25_ENST00000537230.1_Missense_Mutation_p.Q493R|TRIM25_ENST00000573108.1_5'Flank	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	493	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)|response to estrogen (GO:0043627)|response to vitamin D (GO:0033280)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Breast(9;6.15e-08)					TGTGAACCTCTGGGGATGCGG	0.547																																					p.Q493R		Atlas-SNP	.											.	TRIM25	52	.	0			c.A1478G						.						82	78	80					17																	54969476		2203	4300	6503	SO:0001583	missense	7706	exon9			AACCTCTGGGGAT	D21205	CCDS11591.1	17q23.1	2013-01-09	2011-01-25	2004-03-30				"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	12932	protein-coding gene	gene with protein product		600453	"zinc finger protein 147 (estrogen-responsive finger protein)", "tripartite motif-containing 25"	ZNF147		7789997	Standard	NM_005082		Approved	EFP, RNF147	uc002iut.3	Q14258		ENST00000316881.4:c.1478A>G	chr17.hg19:g.54969476T>C	ENSP00000323889:p.Gln493Arg	79.0	0.0		72.0	4.0	NM_005082		Missense_Mutation	SNP	ENST00000316881.4	hg19	CCDS11591.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.253404	0.59212	.	.	ENSG00000121060	ENST00000316881;ENST00000537230	T;T	0.10668	2.85;2.85	4.84	3.76	0.43208	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	0.238747	0.29684	N	0.011479	T	0.12987	0.0315	L	0.50919	1.6	0.35027	D	0.758394	P	0.35468	0.503	B	0.40228	0.323	T	0.14924	-1.0455	10	0.46703	T	0.11	.	9.8174	0.40860	0.0:0.0818:0.0:0.9182	.	493	Q14258	TRI25_HUMAN	R	493	ENSP00000323889:Q493R;ENSP00000445961:Q493R	ENSP00000323889:Q493R	Q	-	2	0	TRIM25	52324475	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	1.549000	0.36212	1.807000	0.52817	0.418000	0.28097	CAG	.	.		0.547	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082		C	54969476	T	C	54969476	3	2	91	1	0	0	0	0	1	0	0	0	16514	1580	55	2	418	2	TRIM25	17	54969476	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3068254	54969476	26225734	580	12654										
MKS1	54903	hgsc.bcm.edu	37	chr17	56290446	56290446	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctgcttctccccctccgtcTcaatcctgtaaggtcaaaac	5	17	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:56290446T>C	ENST00000393119.2	-	8	829	c.755A>G	c.(754-756)gAg>gGg	p.E252G	MKS1_ENST00000337050.7_Missense_Mutation_p.E252G|MKS1_ENST00000546108.1_Missense_Mutation_p.E49G|MKS1_ENST00000537529.2_Missense_Mutation_p.E242G|MKS1_ENST00000313863.6_Missense_Mutation_p.E252G	NM_017777.3	NP_060247.2	Q9NXB0	MKS1_HUMAN	Meckel syndrome, type 1	252					branching morphogenesis of an epithelial tube (GO:0048754)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						CCCCTCCGTCTCAATCCTGTA	0.557																																					p.E252G		Atlas-SNP	.											.	MKS1	100	.	0			c.A755G						.						64	65	64					17																	56290446		1924	4133	6057	SO:0001583	missense	54903	exon8			TCCGTCTCAATCC	DQ185029	CCDS11603.2, CCDS54148.1	17q21-q24	2014-09-17			ENSG00000011143	ENSG00000011143			7121	protein-coding gene	gene with protein product	"POC12 centriolar protein homolog (Chlamydomonas)"	609883		MKS		7550354, 16415886, 18327255	Standard	NM_017777		Approved	FLJ20345, POC12, BBS13	uc002ivr.2	Q9NXB0	OTTHUMG00000133714	ENST00000393119.2:c.755A>G	chr17.hg19:g.56290446T>C	ENSP00000376827:p.Glu252Gly	74.0	0.0		53.0	4.0	NM_017777	B7WNX4|F5H885|Q284T0|Q96G13	Missense_Mutation	SNP	ENST00000393119.2	hg19	CCDS11603.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.12|16.12	3.033549|3.033549	0.54896|0.54896	.|.	.|.	ENSG00000011143|ENSG00000011143	ENST00000537529;ENST00000393120;ENST00000393119;ENST00000337050;ENST00000546108|ENST00000313863	T;T;T;T|.	0.76709|.	-0.61;-0.59;-0.35;-1.04|.	5.8|5.8	4.68|4.68	0.58851|0.58851	.|.	1.812070|.	0.02289|.	N|.	0.070158|.	T|T	0.70456|0.70456	0.3226|0.3226	M|M	0.69823|0.69823	2.125|2.125	0.54753|0.54753	D|D	0.999988|0.999988	D;P|.	0.60160|.	0.987;0.856|.	P;B|.	0.54856|.	0.762;0.345|.	T|T	0.70813|0.70813	-0.4770|-0.4770	9|5	.|.	.|.	.|.	-34.3665|-34.3665	11.3497|11.3497	0.49581|0.49581	0.1354:0.0:0.0:0.8646|0.1354:0.0:0.0:0.8646	.|.	252;252|.	A8MPP8;Q9NXB0|.	.;MKS1_HUMAN|.	G|G	242;252;252;252;49|253	ENSP00000442096:E242G;ENSP00000376827:E252G;ENSP00000338407:E252G;ENSP00000443012:E49G|.	.|.	E|R	-|-	2|1	0|2	MKS1|MKS1	53645445|53645445	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.270000|0.270000	0.26580|0.26580	3.900000|3.900000	0.56295|0.56295	2.203000|2.203000	0.70933|0.70933	0.523000|0.523000	0.50628|0.50628	GAG|AGA	.	.		0.557	MKS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258015.2	NM_017777		C	56290446	T	C	56290446	3	2	91	1	0	0	0	0	1	0	0	0	9618	1551	54	2	968	2	MKS1	17	56290446	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1320970	56290446	24904764	581	12655										
LPO	4025	hgsc.bcm.edu	37	chr17	56345321	56345321	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttgctcagccatcgacaagcTggacctgtcaccctgggcct	10	15	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:56345321T>C	ENST00000262290.4	+	13	2421	c.2105T>C	c.(2104-2106)cTg>cCg	p.L702P	LPO_ENST00000543544.1_Missense_Mutation_p.L643P|LPO_ENST00000582328.1_Missense_Mutation_p.L619P|LPO_ENST00000421678.2_Missense_Mutation_p.L619P	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	702					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						ATCGACAAGCTGGACCTGTCA	0.562																																					p.L702P		Atlas-SNP	.											.	LPO	73	.	0			c.T2105C						.						81	69	73					17																	56345321		2203	4300	6503	SO:0001583	missense	4025	exon13			ACAAGCTGGACCT	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.2105T>C	chr17.hg19:g.56345321T>C	ENSP00000262290:p.Leu702Pro	105.0	0.0		77.0	4.0	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Missense_Mutation	SNP	ENST00000262290.4	hg19	CCDS32689.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.013160	0.75161	.	.	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576	T;T;T	0.74737	-0.87;-0.87;-0.87	5.34	5.34	0.76211	.	0.070276	0.64402	D	0.000016	D	0.88709	0.6510	M	0.92604	3.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.90182	0.4243	10	0.45353	T	0.12	.	14.145	0.65344	0.0:0.0:0.0:1.0	.	619;702	E7EMJ3;P22079	.;PERL_HUMAN	P	702;619;643;447	ENSP00000262290:L702P;ENSP00000400245:L619P;ENSP00000445344:L643P	ENSP00000262290:L702P	L	+	2	0	LPO	53700320	0.945000	0.32115	1.000000	0.80357	0.819000	0.46315	6.718000	0.74713	2.029000	0.59856	0.533000	0.62120	CTG	.	.		0.562	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1			C	56345321	T	C	56345321	3	2	91	1	0	0	0	0	1	0	0	0	8931	1580	55	2	2151	2	LPO	17	56345321	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	54875	56345321	24849889	582	12656										
MTMR4	9110	hgsc.bcm.edu	37	chr17	56586080	56586080	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgtgctggtcctcctcggtcAgccccaggcaccaggcatgg	13	15	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:56586080A>G	ENST00000323456.5	-	6	540	c.416T>C	c.(415-417)cTg>cCg	p.L139P	MTMR4_ENST00000579925.1_Missense_Mutation_p.L139P	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	139					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTCCTCGGTCAGCCCCAGGCA	0.577																																					p.L139P		Atlas-SNP	.											.	MTMR4	91	.	0			c.T416C						.						75	59	64					17																	56586080		2203	4300	6503	SO:0001583	missense	9110	exon6			TCGGTCAGCCCCA	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.416T>C	chr17.hg19:g.56586080A>G	ENSP00000325285:p.Leu139Pro	118.0	0.0		86.0	26.0	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Missense_Mutation	SNP	ENST00000323456.5	hg19	CCDS11608.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.778475	0.31502	.	.	ENSG00000108389	ENST00000323456	D	0.93712	-3.27	5.91	5.91	0.95273	.	0.316163	0.29995	N	0.010672	D	0.92446	0.7602	L	0.40543	1.245	0.80722	D	1	D	0.54397	0.966	P	0.49421	0.61	D	0.93097	0.6505	10	0.66056	D	0.02	.	15.5248	0.75894	1.0:0.0:0.0:0.0	.	139	Q9NYA4	MTMR4_HUMAN	P	139	ENSP00000325285:L139P	ENSP00000325285:L139P	L	-	2	0	MTMR4	53941079	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	2.881000	0.48538	2.269000	0.75478	0.533000	0.62120	CTG	.	.		0.577	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687		G	56586080	A	G	56586080	3	3	91	1	0	0	0	0	1	0	0	0	9955	188	7	2	3227	2	MTMR4	17	56586080	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	240759	56586080	24609130	583	12657										
C17orf64	124773	hgsc.bcm.edu	37	chr17	58508620	58508620	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cccagaaactccagagactgAaccgtaagaagaccaactgg	9	12	0	5			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:58508620A>G	ENST00000269127.4	+	6	788	c.704A>G	c.(703-705)gAa>gGa	p.E235G	RPL12P38_ENST00000588627.1_RNA	NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	235										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			CCAGAGACTGAACCGTAAGAA	0.453																																					p.E235G		Atlas-SNP	.											.	C17orf64	19	.	0			c.A704G						.						42	54	50					17																	58508620		2203	4300	6503	SO:0001583	missense	124773	exon6			AGACTGAACCGTA	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.704A>G	chr17.hg19:g.58508620A>G	ENSP00000269127:p.Glu235Gly	109.0	0.0		84.0	5.0	NM_181707	Q8IY87	Missense_Mutation	SNP	ENST00000269127.4	hg19	CCDS32698.2	.	.	.	.	.	.	.	.	.	.	A	4.088	0.014223	0.07959	.	.	ENSG00000141371	ENST00000269127	.	.	.	4.42	-4.73	0.03259	.	1.446720	0.04997	U	0.468448	T	0.14570	0.0352	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16837	-1.0389	9	0.15066	T	0.55	1.8762	3.916	0.09224	0.4688:0.0:0.2506:0.2806	.	235	Q86WR6	CQ064_HUMAN	G	235	.	ENSP00000269127:E235G	E	+	2	0	C17orf64	55863402	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.020000	0.12525	-0.698000	0.05085	-0.242000	0.12053	GAA	.	.		0.453	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707		G	58508620	A	G	58508620	3	3	91	1	0	0	0	0	1	0	0	0	1874	246	9	2	726	2	C17orf64	17	58508620	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1922540	58508620	22686590	584	12658										
INTS2	57508	hgsc.bcm.edu	37	chr17	59981858	59981858	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggccagtagcatacaaaaggAaagtgaaacaaagcgaaccc	10	9	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:59981858A>G	ENST00000444766.3	-	9	1369	c.1294T>C	c.(1294-1296)Tcc>Ccc	p.S432P	INTS2_ENST00000251334.6_Missense_Mutation_p.S424P	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	432					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						ATACAAAAGGAAAGTGAAACA	0.403																																					p.S432P		Atlas-SNP	.											.	INTS2	89	.	0			c.T1294C						.						81	82	82					17																	59981858		1932	4111	6043	SO:0001583	missense	57508	exon9			AAAAGGAAAGTGA	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.1294T>C	chr17.hg19:g.59981858A>G	ENSP00000414237:p.Ser432Pro	129.0	0.0		94.0	4.0	NM_020748	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	hg19	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.994479	0.93167	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.46451	0.87	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.54967	0.1891	L	0.47716	1.5	0.80722	D	1	D	0.69078	0.997	D	0.63793	0.918	T	0.52555	-0.8560	9	.	.	.	-5.8668	15.3009	0.73949	1.0:0.0:0.0:0.0	.	432	Q9H0H0	INT2_HUMAN	P	432;431	ENSP00000414237:S432P	.	S	-	1	0	INTS2	57336640	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	8.618000	0.90932	2.020000	0.59435	0.383000	0.25322	TCC	.	.		0.403	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		G	59981858	A	G	59981858	3	3	91	1	0	0	0	0	1	0	0	0	7787	246	9	2	2388	2	INTS2	17	59981858	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1473238	59981858	21213352	585	12659										
ACE	1636	hgsc.bcm.edu	37	chr17	61560881	61560881	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaaacccactttgatgctggAgctaagtttcatgttccaaa	8	9	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:61560881A>G	ENST00000290866.4	+	10	1572	c.1548A>G	c.(1546-1548)ggA>ggG	p.G516G	ACE_ENST00000490216.2_5'Flank|ACE_ENST00000538928.1_Missense_Mutation_p.E468G|ACE_ENST00000428043.1_Silent_p.G516G|ACE_ENST00000584529.1_3'UTR|ACE_ENST00000413513.3_5'Flank|ACE_ENST00000290863.6_5'Flank|ACE_ENST00000421982.2_5'Flank|ACE_ENST00000577647.1_5'Flank	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	516	Peptidase M2 1.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	TTGATGCTGGAGCTAAGTTTC	0.498																																					p.G516G		Atlas-SNP	.											.	ACE	187	.	0			c.A1548G						.						145	134	138					17																	61560881		2203	4300	6503	SO:0001819	synonymous_variant	1636	exon10			TGCTGGAGCTAAG	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.1548A>G	chr17.hg19:g.61560881A>G		156.0	0.0		106.0	5.0	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Silent	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	A	14.00	2.405739	0.42715	.	.	ENSG00000159640	ENST00000538928	T	0.34275	1.37	4.9	0.00178	0.14048	.	.	.	.	.	T	0.19725	0.0474	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.08680	-1.0710	7	.	.	.	-13.7745	5.723	0.17998	0.4736:0.0:0.3945:0.1319	.	468	F5H1K1	.	G	468	ENSP00000439591:E468G	.	E	+	2	0	ACE	58914613	0.346000	0.24844	0.997000	0.53966	0.986000	0.74619	-0.463000	0.06696	0.046000	0.15833	0.374000	0.22700	GAG	.	.		0.498	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			G	61560881	A	G	61560881	2	3	91	1	0	0	0	0	0	0	0	1	136	291	11	2		2	ACE	17	61560881	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1579023	61560881	19634329	586	12660										
FTSJ3	5705	hgsc.bcm.edu	37	chr17	61902423	61902423	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cacacctttggcttcttcttAgtaaccaattcagtaacggt	6	11	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:61902423A>G	ENST00000310144.6	+	0	0				PSMC5_ENST00000580864.1_5'Flank|PSMC5_ENST00000581882.1_5'Flank|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000375812.4_5'Flank|FTSJ3_ENST00000427159.2_Silent_p.T232T	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						GCTTCTTCTTAGTAACCAATT	0.488																																					p.T232T		Atlas-SNP	.											.	FTSJ3	63	.	0			c.T696C						.						95	102	100					17																	61902423		2203	4300	6503	SO:0001631	upstream_gene_variant	117246	exon8			CTTCTTAGTAACC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195			chr17.hg19:g.61902423A>G	Exception_encountered	98.0	0.0		86.0	5.0	NM_017647	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Silent	SNP	ENST00000310144.6	hg19	CCDS11645.1																																																																																			.	.		0.488	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		G	61902423	A	G	61902423	1	3	91	0	1	0	0	0	0	0	0	0	6097	407	15	2		2	FTSJ3	17	61902423	5'Flank	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	341542	61902423	19292787	587	12661										
SMARCD2	6603	hgsc.bcm.edu	37	chr17	61914400	61914400	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagactctggaacaagctccCggatctgaaggaaggtagca	13	9	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:61914400C>T	ENST00000448276.2	-	4	714	c.449G>A	c.(448-450)cGg>cAg	p.R150Q	SMARCD2_ENST00000323347.10_Missense_Mutation_p.R102Q|SMARCD2_ENST00000225742.9_Missense_Mutation_p.R75Q|RN7SL805P_ENST00000581353.1_RNA	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	150					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						AACAAGCTCCCGGATCTGAAG	0.557																																					p.R150Q		Atlas-SNP	.											.	SMARCD2	29	.	0			c.G449A						.						55	56	56					17																	61914400		2001	4194	6195	SO:0001583	missense	6603	exon4			AGCTCCCGGATCT	U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60B", "Swp73-like protein", "chromatin remodeling complex BAF60B subunit", "SWI/SNF complex 60 kDa subunit B"	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.449G>A	chr17.hg19:g.61914400C>T	ENSP00000392617:p.Arg150Gln	77.0	0.0		71.0	4.0	NM_001098426	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Missense_Mutation	SNP	ENST00000448276.2	hg19	CCDS45756.1	.	.	.	.	.	.	.	.	.	.	.	22.4	4.290308	0.80914	.	.	ENSG00000108604	ENST00000448276;ENST00000225742;ENST00000450364;ENST00000323347	T;T;T	0.57595	0.39;0.81;0.39	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.73536	0.3599	M	0.76938	2.355	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	P;D;D	0.79108	0.863;0.992;0.992	T	0.75622	-0.3254	10	0.72032	D	0.01	-1.2528	16.9239	0.86170	0.0:1.0:0.0:0.0	.	102;113;150	Q92925-3;B9EGA3;Q92925	.;.;SMRD2_HUMAN	Q	150;92;113;102	ENSP00000392617:R150Q;ENSP00000225742:R92Q;ENSP00000318451:R102Q	ENSP00000225742:R92Q	R	-	2	0	SMARCD2	59268132	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	7.651000	0.83577	2.865000	0.98341	0.655000	0.94253	CGG	.	.		0.557	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426		T	61914400	C	T	61914400	3	4	91	1	0	0	0	0	1	0	0	0	14793	652	23	1	1186	1	SMARCD2	17	61914400	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	11977	61914400	19280810	588	12662										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62022142	62022142	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtagaggtacatgtagaggTtcacctcgtactgcggctgc	13	9	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:62022142T>C	ENST00000435607.1	-	21	3879	c.3803A>G	c.(3802-3804)aAc>aGc	p.N1268S	SCN4A_ENST00000578147.1_Missense_Mutation_p.N1268S	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1268					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.N1268S(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CATGTAGAGGTTCACCTCGTA	0.562																																					p.N1268S		Atlas-SNP	.											SCN4A,colon,carcinoma,0,1	SCN4A	205	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3803G						.						128	130	129					17																	62022142		2178	4292	6470	SO:0001583	missense	6329	exon21			TAGAGGTTCACCT	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.3803A>G	chr17.hg19:g.62022142T>C	ENSP00000396320:p.Asn1268Ser	108.0	1.0		90.0	5.0	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.862049	0.71949	.	.	ENSG00000007314	ENST00000435607	D	0.98296	-4.85	3.49	3.49	0.39957	Ion transport (1);	0.114478	0.64402	D	0.000014	D	0.97207	0.9087	L	0.31207	0.915	0.51012	D	0.999909	D	0.63880	0.993	P	0.61874	0.895	D	0.96063	0.9040	10	0.36615	T	0.2	.	11.6187	0.51104	0.0:0.0:0.0:1.0	.	1268	P35499	SCN4A_HUMAN	S	1268	ENSP00000396320:N1268S	ENSP00000396320:N1268S	N	-	2	0	SCN4A	59375874	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	7.825000	0.86693	1.596000	0.50062	0.379000	0.24179	AAC	.	.		0.562	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		C	62022142	T	C	62022142	3	2	91	1	0	0	0	0	1	0	0	0	13935	1725	60	2	1723	2	SCN4A	17	62022142	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	107742	62022142	19173068	589	12663										
ABCA8	10351	hgsc.bcm.edu	37	chr17	66873815	66873815	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctccaccgctccctttcagTagcacctgcagatgaaagtt	7	15	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:66873815T>C	ENST00000269080.2	-	31	4061	c.3924A>G	c.(3922-3924)ctA>ctG	p.L1308L	ABCA8_ENST00000430352.2_Silent_p.L1348L|ABCA8_ENST00000586539.1_Silent_p.L1348L	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1308	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					TCCCTTTCAGTAGCACCTGCA	0.537																																					p.L1308L		Atlas-SNP	.											.	ABCA8	213	.	0			c.A3924G						.						81	74	76					17																	66873815		2203	4300	6503	SO:0001819	synonymous_variant	10351	exon31			TTTCAGTAGCACC	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3924A>G	chr17.hg19:g.66873815T>C		95.0	0.0		62.0	4.0	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	hg19	CCDS11680.1																																																																																			.	.		0.537	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		C	66873815	T	C	66873815	2	2	91	1	0	0	0	0	0	0	0	1	38	1625	57	2		2	ABCA8	17	66873815	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4851673	66873815	14321395	590	12664										
ABCA8	10351	hgsc.bcm.edu	37	chr17	66890418	66890418	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aactgggaagcaattcaatcTtttggcattgcatgctaacg	9	8	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:66890418T>C	ENST00000269080.2	-	21	2949	c.2812A>G	c.(2812-2814)Aga>Gga	p.R938G	ABCA8_ENST00000430352.2_Missense_Mutation_p.R978G|ABCA8_ENST00000586539.1_Missense_Mutation_p.R978G	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	938					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					CAATTCAATCTTTTGGCATTG	0.313																																					p.R938G		Atlas-SNP	.											.	ABCA8	213	.	0			c.A2812G						.						68	62	64					17																	66890418		2203	4300	6503	SO:0001583	missense	10351	exon21			TCAATCTTTTGGC	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.2812A>G	chr17.hg19:g.66890418T>C	ENSP00000269080:p.Arg938Gly	71.0	0.0		80.0	4.0	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	hg19	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812218	0.50527	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225	D;D	0.85702	-2.02;-2.02	5.08	5.08	0.68730	.	0.000000	0.64402	D	0.000013	D	0.86994	0.6067	M	0.83384	2.64	0.35528	D	0.802039	B;B;B;B;B	0.30664	0.154;0.289;0.021;0.039;0.097	B;B;B;B;B	0.40477	0.132;0.33;0.029;0.099;0.16	D	0.86141	0.1581	10	0.17832	T	0.49	.	11.4185	0.49967	0.0:0.0:0.0:1.0	.	917;978;978;978;938	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	G	938;978;917	ENSP00000269080:R938G;ENSP00000402814:R978G	ENSP00000269080:R938G	R	-	1	2	ABCA8	64402013	0.006000	0.16342	1.000000	0.80357	0.962000	0.63368	1.194000	0.32174	2.260000	0.74910	0.533000	0.62120	AGA	.	.		0.313	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		C	66890418	T	C	66890418	3	2	91	1	0	0	0	0	1	0	0	0	38	1617	56	2	2005	2	ABCA8	17	66890418	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	16603	66890418	14304792	591	12665										
ARMC7	79637	hgsc.bcm.edu	37	chr17	73124841	73124841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcacgcaggaggtgtcccacTcatcatcaactgcctatcca	8	15	3	0	rs374083928	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:73124841T>C	ENST00000245543.1	+	3	607	c.305T>C	c.(304-306)cTc>cCc	p.L102P	ARMC7_ENST00000579096.1_3'UTR|NT5C_ENST00000579082.1_5'Flank|ARMC7_ENST00000581078.1_Missense_Mutation_p.S81P	NM_024585.2	NP_078861.1	Q9H6L4	ARMC7_HUMAN	armadillo repeat containing 7	102						cytoplasm (GO:0005737)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|pancreas(3)	9	all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)			GGTGTCCCACTCATCATCAAC	0.612																																					p.L102P		Atlas-SNP	.											.,1	ARMC7	14	.	0			c.T305C						.						69	53	58					17																	73124841		2203	4300	6503	SO:0001583	missense	79637	exon3			TCCCACTCATCAT	AK025813	CCDS11714.1	17q25	2013-02-14				ENSG00000125449		"Armadillo repeat containing"	26168	protein-coding gene	gene with protein product						12477932	Standard	NM_024585		Approved	FLJ22160	uc002jmw.1	Q9H6L4		ENST00000245543.1:c.305T>C	chr17.hg19:g.73124841T>C	ENSP00000245543:p.Leu102Pro	122.0	1.0		119.0	6.0	NM_024585	B4DVA4	Missense_Mutation	SNP	ENST00000245543.1	hg19	CCDS11714.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.675109	0.29783	.	.	ENSG00000125449	ENST00000245543	T	0.65732	-0.17	4.97	2.63	0.31362	Armadillo-like helical (1);Armadillo-type fold (1);	0.263954	0.32258	N	0.006355	T	0.49355	0.1552	L	0.53249	1.67	0.58432	D	0.999993	B	0.15719	0.014	B	0.22152	0.038	T	0.48603	-0.9021	10	0.30078	T	0.28	.	3.1657	0.06535	0.2061:0.1592:0.0:0.6346	.	102	Q9H6L4	ARMC7_HUMAN	P	102	ENSP00000245543:L102P	ENSP00000245543:L102P	L	+	2	0	ARMC7	70636436	1.000000	0.71417	0.996000	0.52242	0.840000	0.47671	3.182000	0.50910	2.007000	0.58848	0.533000	0.62120	CTC	.	.		0.612	ARMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445846.1	NM_024585		C	73124841	T	C	73124841	3	2	91	1	0	0	0	0	1	0	0	0	956	1551	54	2	315	2	ARMC7	17	73124841	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	6234423	73124841	8070369	592	12666										
ENGASE	64772	hgsc.bcm.edu	37	chr17	77075681	77075681	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caccattcccccagtgggctGgaccaacactgcccacaggc	9	18	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:77075681G>C	ENST00000579016.1	+	4	527	c.527G>C	c.(526-528)tGg>tCg	p.W176S	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	176						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CCAGTGGGCTGGACCAACACT	0.607																																					p.W176S		Atlas-SNP	.											.	ENGASE	55	.	0			c.G527C						.						90	112	105					17																	77075681		2118	4220	6338	SO:0001583	missense	64772	exon4			TGGGCTGGACCAA	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.527G>C	chr17.hg19:g.77075681G>C	ENSP00000462333:p.Trp176Ser	123.0	0.0		124.0	52.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	hg19	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	G	17.52	3.409801	0.62399	.	.	ENSG00000167280	ENST00000311595;ENST00000545583	.	.	.	5.22	5.22	0.72569	Glycoside hydrolase, family 85 (1);	0.057777	0.85682	D	0.000000	D	0.86368	0.5916	M	0.94142	3.5	0.80722	D	1	D;D	0.61080	0.972;0.989	D;D	0.66847	0.929;0.947	D	0.89986	0.4104	9	0.72032	D	0.01	-0.1925	17.3151	0.87221	0.0:0.0:1.0:0.0	.	176;176	Q8NFI3;Q8NFI3-3	ENASE_HUMAN;.	S	176	.	ENSP00000308158:W176S	W	+	2	0	ENGASE	74587276	1.000000	0.71417	1.000000	0.80357	0.431000	0.31685	9.007000	0.93597	2.587000	0.87381	0.655000	0.94253	TGG	.	.		0.607	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		C	77075681	G	C	77075681	3	2	91	1	0	0	0	0	1	0	0	0	5120	1357	47	4	541	4	ENGASE	17	77075681	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	3950840	77075681	4119529	593	12667										
SLC38A10	124565	hgsc.bcm.edu	37	chr17	79234066	79234066	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgcgctgcctccaccttcatCaaaccctcggcctctccaag	6	20	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:79234066C>T	ENST00000374759.3	-	11	1643	c.1260G>A	c.(1258-1260)ttG>ttA	p.L420L	SLC38A10_ENST00000288439.5_Silent_p.L420L|SLC38A10_ENST00000546352.1_5'Flank	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	420					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCACCTTCATCAAACCCTCGG	0.647																																					p.L420L		Atlas-SNP	.											.	SLC38A10	133	.	0			c.G1260A						.						24	25	25					17																	79234066		2199	4291	6490	SO:0001819	synonymous_variant	124565	exon11			CTTCATCAAACCC	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.1260G>A	chr17.hg19:g.79234066C>T		63.0	0.0		50.0	17.0	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	hg19	CCDS42397.1																																																																																			.	.		0.647	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		T	79234066	C	T	79234066	2	4	91	1	0	0	0	0	0	0	0	1	14617	825	29	3		3	SLC38A10	17	79234066	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2158385	79234066	1961144	594	12668										
TBCD	6904	hgsc.bcm.edu	37	chr17	80828170	80828170	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgcagcgtgggcaccaacgtCagggacgccgcctgctacgt	14	14	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:80828170C>A	ENST00000355528.4	+	14	1519	c.1389C>A	c.(1387-1389)gtC>gtA	p.V463V	TBCD_ENST00000397466.2_Silent_p.V77V|TBCD_ENST00000539345.2_Silent_p.V463V	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	463					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			GCACCAACGTCAGGGACGCCG	0.617																																					p.V463V		Atlas-SNP	.											.	TBCD	94	.	0			c.C1389A						.						48	56	53					17																	80828170		2148	4244	6392	SO:0001819	synonymous_variant	6904	exon14			CAACGTCAGGGAC	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"tubulin-specific chaperone d"				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.1389C>A	chr17.hg19:g.80828170C>A		90.0	0.0		97.0	6.0	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Silent	SNP	ENST00000355528.4	hg19	CCDS45818.1																																																																																			.	.		0.617	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		A	80828170	C	A	80828170	2	1	91	1	0	0	0	0	0	0	0	1	15648	813	29	3		3	TBCD	17	80828170	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1594104	80828170	367040	595	12669										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8718463	8718463	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctgagatggaagagatgagAgacagttatttagaggaaga	15	2	0	6			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:8718463A>G	ENST00000306329.11	+	2	1095	c.1095A>G	c.(1093-1095)agA>agG	p.R365R	SOGA2_ENST00000400050.3_Silent_p.R5R|SOGA2_ENST00000359865.3_Silent_p.R5R|SOGA2_ENST00000306285.7_5'UTR|Y_RNA_ENST00000516510.1_RNA|SOGA2_ENST00000517570.1_Silent_p.R5R																							AAGAGATGAGAGACAGTTATT	0.448																																					p.R5R		Atlas-SNP	.											.	.	.	.	0			c.A15G						.						97	92	94					18																	8718463		2203	4300	6503	SO:0001819	synonymous_variant	23255	exon3			GATGAGAGACAGT																												ENST00000306329.11:c.1095A>G	chr18.hg19:g.8718463A>G		125.0	0.0		93.0	4.0	NM_015210		Silent	SNP	ENST00000306329.11	hg19																																																																																				.	.		0.448	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			G	8718463	A	G	8718463	2	3	91	1	0	0	0	0	0	0	0	1	8203	301	11	2		2	KIAA0802	18	8718463	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10		8718463	69358785	596	12670										
PPP4R1	9989	hgsc.bcm.edu	37	chr18	9593834	9593834	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctctttcatcatcgcagactTccctcaaggtatcgagcaaa	6	13	4	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:9593834T>C	ENST00000400556.3	-	4	300	c.227A>G	c.(226-228)gAa>gGa	p.E76G	PPP4R1_ENST00000580583.1_5'UTR|PPP4R1_ENST00000400555.3_Missense_Mutation_p.E59G	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	76					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						ATCGCAGACTTCCCTCAAGGT	0.368																																					p.E76G	Melanoma(188;1232 2082 5061 11948 35994)	Atlas-SNP	.											.	PPP4R1	63	.	0			c.A227G						.						102	95	97					18																	9593834		1911	4137	6048	SO:0001583	missense	9989	exon4			CAGACTTCCCTCA	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.227A>G	chr18.hg19:g.9593834T>C	ENSP00000383402:p.Glu76Gly	89.0	0.0		91.0	4.0	NM_001042388	Q99774|Q9UNQ7	Missense_Mutation	SNP	ENST00000400556.3	hg19	CCDS42412.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.207615	0.39003	.	.	ENSG00000154845	ENST00000400556;ENST00000400555	T;T	0.18502	2.21;2.21	5.3	5.3	0.74995	Armadillo-like helical (1);Armadillo-type fold (1);	0.252844	0.36002	N	0.002853	T	0.17789	0.0427	L	0.48642	1.525	0.48236	D	0.99961	B;B;B	0.21606	0.058;0.026;0.044	B;B;B	0.23852	0.033;0.022;0.049	T	0.03807	-1.1002	9	.	.	.	-19.2209	15.0953	0.72229	0.0:0.0:0.0:1.0	.	59;76;59	A8K923;Q8TF05;Q8TF05-2	.;PP4R1_HUMAN;.	G	76;59	ENSP00000383402:E76G;ENSP00000383401:E59G	.	E	-	2	0	PPP4R1	9583834	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.162000	0.58177	2.240000	0.73641	0.477000	0.44152	GAA	.	.		0.368	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134		C	9593834	T	C	9593834	3	2	91	1	0	0	0	0	1	0	0	0	12415	1783	62	2	2693	2	PPP4R1	18	9593834	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	875371	9593834	68483414	597	12671										
GNAL	2774	hgsc.bcm.edu	37	chr18	11862404	11862404	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttctttgcagcttcctggaaAgaatcgacagcgtcagcttg	10	10	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:11862404A>G	ENST00000423027.3	+	6	823	c.502A>G	c.(502-504)Aga>Gga	p.R168G	GNAL_ENST00000269162.5_Missense_Mutation_p.R168G|GNAL_ENST00000602628.1_5'UTR|GNAL_ENST00000535121.1_Missense_Mutation_p.R168G|GNAL_ENST00000334049.6_Missense_Mutation_p.R245G			P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type	168					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|response to amphetamine (GO:0001975)|response to caffeine (GO:0031000)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)	12						CTTCCTGGAAAGAATCGACAG	0.507																																					p.R245G		Atlas-SNP	.											.	GNAL	59	.	0			c.A733G						.						94	79	84					18																	11862404		2203	4300	6503	SO:0001583	missense	2774	exon6			CTGGAAAGAATCG	AF493893	CCDS11851.1, CCDS11852.1, CCDS58614.1	18p11.22-p11.21	2003-12-17			ENSG00000141404	ENSG00000141404			4388	protein-coding gene	gene with protein product		139312				1302014	Standard	NM_182978		Approved		uc002kqc.3	P38405	OTTHUMG00000131660	ENST00000423027.3:c.502A>G	chr18.hg19:g.11862404A>G	ENSP00000408489:p.Arg168Gly	88.0	0.0		76.0	6.0	NM_182978	B7ZA26|Q86XU3	Missense_Mutation	SNP	ENST00000423027.3	hg19	CCDS11852.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.030689	0.54790	.	.	ENSG00000141404	ENST00000540217;ENST00000334049;ENST00000535121;ENST00000269162;ENST00000423027	D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51	5.1	2.68	0.31781	G protein alpha subunit, helical insertion (2);	0.084546	0.85682	D	0.000000	D	0.89777	0.6813	L	0.59967	1.855	0.80722	D	1	P;P	0.47604	0.776;0.898	P;P	0.55508	0.601;0.777	D	0.87055	0.2149	10	0.59425	D	0.04	.	7.4967	0.27494	0.768:0.1559:0.0761:0.0	.	168;245	P38405;Q86XU3	GNAL_HUMAN;.	G	107;245;168;168;168	ENSP00000334051:R245G;ENSP00000439023:R168G;ENSP00000269162:R168G;ENSP00000408489:R168G	ENSP00000269162:R168G	R	+	1	2	GNAL	11852404	1.000000	0.71417	0.629000	0.29254	0.987000	0.75469	6.928000	0.75846	0.275000	0.22094	0.459000	0.35465	AGA	.	.		0.507	GNAL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254561.2	NM_182978, NM_002071		G	11862404	A	G	11862404	3	3	91	1	0	0	0	0	1	0	0	0	6515	64	3	2	904	2	GNAL	18	11862404	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2268570	11862404	66214844	598	12672										
TAF4B	6875	hgsc.bcm.edu	37	chr18	23915177	23915177	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatccagaacagctgagattAaagcagaaagccaaagaggt	11	7	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:23915177A>G	ENST00000269142.5	+	13	3296	c.2298A>G	c.(2296-2298)ttA>ttG	p.L766L	TAF4B_ENST00000578121.1_Silent_p.L771L	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	766					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			AGCTGAGATTAAAGCAGAAAG	0.388																																					p.L766L		Atlas-SNP	.											.	TAF4B	71	.	0			c.A2298G						.						110	103	105					18																	23915177		1865	4101	5966	SO:0001819	synonymous_variant	6875	exon13			GAGATTAAAGCAG	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.2298A>G	chr18.hg19:g.23915177A>G		119.0	0.0		96.0	4.0	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	hg19	CCDS42421.1																																																																																			.	.		0.388	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		G	23915177	A	G	23915177	2	3	91	1	0	0	0	0	0	0	0	1	15542	359	13	2		2	TAF4B	18	23915177	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	12052773	23915177	54162071	599	12673										
MEP1B	4225	hgsc.bcm.edu	37	chr18	29790544	29790544	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggaaagtagaacgctgtacCctaaaagaggatttcagtgc	11	7	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:29790544C>A	ENST00000269202.6	+	10	1047	c.1000C>A	c.(1000-1002)Cct>Act	p.P334T	MEP1B_ENST00000581447.1_Missense_Mutation_p.P334T	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	334	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						AACGCTGTACCCTAAAAGAGG	0.413																																					p.P334T		Atlas-SNP	.											.	MEP1B	54	.	0			c.C1000A						.						90	85	87					18																	29790544		1887	4104	5991	SO:0001583	missense	4225	exon10			CTGTACCCTAAAA	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.1000C>A	chr18.hg19:g.29790544C>A	ENSP00000269202:p.Pro334Thr	82.0	0.0		58.0	25.0	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	hg19	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.502801	0.85176	.	.	ENSG00000141434	ENST00000269202	T	0.02103	4.45	5.33	5.33	0.75918	Concanavalin A-like lectin/glucanase (1);MAM domain (4);	0.000000	0.85682	D	0.000000	T	0.13200	0.0320	M	0.87038	2.855	0.80722	D	1	D	0.54207	0.965	P	0.56163	0.793	T	0.00380	-1.1776	10	0.87932	D	0	-19.3465	19.0127	0.92881	0.0:1.0:0.0:0.0	.	334	Q16820	MEP1B_HUMAN	T	334	ENSP00000269202:P334T	ENSP00000269202:P334T	P	+	1	0	MEP1B	28044542	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.439000	0.80444	2.507000	0.84556	0.585000	0.79938	CCT	.	.		0.413	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		A	29790544	C	A	29790544	3	1	91	1	0	0	0	0	1	0	0	0	9485	623	22	3	1038	3	MEP1B	18	29790544	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	5875367	29790544	48286704	600	12674										
C18orf54	162681	hgsc.bcm.edu	37	chr18	51889221	51889221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aattaccaaagtccatgaaaAaggatgacagtccttgctca	7	9	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:51889221A>G	ENST00000300091.5	+	4	1002	c.670A>G	c.(670-672)Aag>Gag	p.K224E	C18orf54_ENST00000578138.1_Missense_Mutation_p.K3E|C18orf54_ENST00000382911.4_Missense_Mutation_p.K385E	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	224						extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)		GTCCATGAAAAAGGATGACAG	0.348																																					p.K224E		Atlas-SNP	.											.	C18orf54	40	.	0			c.A670G						.						87	86	86					18																	51889221		2203	4300	6503	SO:0001583	missense	162681	exon4			ATGAAAAAGGATG	AK126503	CCDS11956.1, CCDS74223.1	18q21	2012-10-24			ENSG00000166845	ENSG00000166845			13796	protein-coding gene	gene with protein product	"lung adenoma susceptibility protein 2"	613258					Standard	XM_005258201		Approved	MGC33382, LAS2	uc031rij.1	Q8IYD9	OTTHUMG00000132703	ENST00000300091.5:c.670A>G	chr18.hg19:g.51889221A>G	ENSP00000300091:p.Lys224Glu	101.0	0.0		81.0	4.0	NM_173529	I7HFJ6|Q6MZU3|Q6ZTL6	Missense_Mutation	SNP	ENST00000300091.5	hg19	CCDS11956.1	.	.	.	.	.	.	.	.	.	.	A	9.452	1.090743	0.20471	.	.	ENSG00000166845	ENST00000300091;ENST00000382911	T;T	0.17854	2.25;2.25	5.12	3.95	0.45737	.	0.480335	0.23358	N	0.049045	T	0.13628	0.0330	L	0.55481	1.735	0.27894	N	0.939224	B;B	0.32829	0.053;0.386	B;B	0.25291	0.015;0.059	T	0.15350	-1.0440	10	0.34782	T	0.22	-0.0055	6.552	0.22440	0.6711:0.181:0.0:0.1479	.	385;224	Q8IYD9-2;Q8IYD9	.;CR054_HUMAN	E	224;385	ENSP00000300091:K224E;ENSP00000372368:K385E	ENSP00000300091:K224E	K	+	1	0	C18orf54	50143219	0.972000	0.33761	0.925000	0.36789	0.882000	0.50991	1.215000	0.32431	0.778000	0.33520	0.402000	0.26972	AAG	.	.		0.348	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256001.1	NM_173529		G	51889221	A	G	51889221	3	3	91	1	0	0	0	0	1	0	0	0	1906	15	1	2	680	2	C18orf54	18	51889221	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	22098677	51889221	26188027	601	12675										
RNF152	220441	hgsc.bcm.edu	37	chr18	59483299	59483299	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gctgttcagcagggatggtcAccacggtgacggacttctgc	14	11	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:59483299A>G	ENST00000312828.3	-	2	1497	c.398T>C	c.(397-399)gTg>gCg	p.V133A		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	133					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				AGGGATGGTCACCACGGTGAC	0.677																																					p.V133A		Atlas-SNP	.											.	RNF152	37	.	0			c.T398C						.						56	58	58					18																	59483299		2203	4300	6503	SO:0001583	missense	220441	exon2			ATGGTCACCACGG	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"RING-type (C3HC4) zinc fingers"	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.398T>C	chr18.hg19:g.59483299A>G	ENSP00000316628:p.Val133Ala	107.0	0.0		68.0	4.0	NM_173557	B3KV99|Q52LA4	Missense_Mutation	SNP	ENST00000312828.3	hg19	CCDS11978.1	.	.	.	.	.	.	.	.	.	.	A	17.22	3.333643	0.60853	.	.	ENSG00000176641	ENST00000312828	D	0.84516	-1.86	4.82	4.82	0.62117	.	0.148937	0.42821	D	0.000646	T	0.76990	0.4065	N	0.24115	0.695	0.43050	D	0.99465	B	0.21147	0.052	B	0.19391	0.025	T	0.74147	-0.3759	10	0.45353	T	0.12	-10.2772	14.5495	0.68057	1.0:0.0:0.0:0.0	.	133	Q8N8N0	RN152_HUMAN	A	133	ENSP00000316628:V133A	ENSP00000316628:V133A	V	-	2	0	RNF152	57634279	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.965000	0.87945	2.046000	0.60703	0.533000	0.62120	GTG	.	.		0.677	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557		G	59483299	A	G	59483299	3	3	91	1	0	0	0	0	1	0	0	0	13468	159	6	2	217	2	RNF152	18	59483299	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	7594078	59483299	18593949	602	12676										
PHLPP1	23239	hgsc.bcm.edu	37	chr18	60642674	60642674	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcttggtggtgccgctgtccTttgtcatatcaagcatgacc	11	11	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:60642674T>C	ENST00000262719.5	+	16	4034	c.3800T>C	c.(3799-3801)cTt>cCt	p.L1267P	PHLPP1_ENST00000400316.4_Missense_Mutation_p.L755P			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	1267	PP2C-like.				apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						GCCGCTGTCCTTTGTCATATC	0.522																																					p.L1267P		Atlas-SNP	.											.	PHLPP1	164	.	0			c.T3800C						.						157	151	153					18																	60642674		2034	4182	6216	SO:0001583	missense	23239	exon16			CTGTCCTTTGTCA	AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.3800T>C	chr18.hg19:g.60642674T>C	ENSP00000262719:p.Leu1267Pro	145.0	0.0		141.0	6.0	NM_194449	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Missense_Mutation	SNP	ENST00000262719.5	hg19	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	T	27.1	4.796057	0.90453	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	T;T	0.19532	2.14;2.14	5.28	5.28	0.74379	Protein phosphatase 2C-like (4);	.	.	.	.	T	0.43634	0.1256	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.18871	-1.0323	9	0.38643	T	0.18	-12.2446	15.374	0.74590	0.0:0.0:0.0:1.0	.	1267	O60346	PHLP1_HUMAN	P	755;1267	ENSP00000383170:L755P;ENSP00000262719:L1267P	ENSP00000262719:L1267P	L	+	2	0	PHLPP1	58793654	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	7.841000	0.86834	2.220000	0.72140	0.454000	0.30748	CTT	.	.		0.522	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		C	60642674	T	C	60642674	3	2	91	1	0	0	0	0	1	0	0	0	11863	1609	56	2	3862	2	PHLPP1	18	60642674	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1159375	60642674	17434574	603	12677										
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72998514	72998514	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagtcagccaaggatcagaaAgcagcgaacccgtacgtcac	11	12	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:72998514A>G	ENST00000580243.1	+	2	1500	c.1152A>G	c.(1150-1152)aaA>aaG	p.K384K	TSHZ1_ENST00000322038.5_Silent_p.K339K			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	384					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		AGGATCAGAAAGCAGCGAACC	0.622																																					p.K339K		Atlas-SNP	.											.	TSHZ1	104	.	0			c.A1017G						.						104	109	107					18																	72998514		2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			TCAGAAAGCAGCG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	10669	protein-coding gene	gene with protein product		614427	"serologically defined colon cancer antigen 33", "teashirt zinc finger 1", "teashirt family zinc finger 1"	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1152A>G	chr18.hg19:g.72998514A>G		97.0	0.0		66.0	5.0	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	hg19																																																																																				.	.		0.622	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		G	72998514	A	G	72998514	2	3	91	1	0	0	0	0	0	0	0	1	16638	69	3	2		2	TSHZ1	18	72998514	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	12355840	72998514	5078734	604	12678										
C19orf21	126353	hgsc.bcm.edu	37	chr19	758323	758323	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcggaggccaaggctgcgacTtcaccaaaggccacgatgtc	13	13	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:758323T>C	ENST00000215582.6	+	2	1480	c.1377T>C	c.(1375-1377)acT>acC	p.T459T		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	459					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											AGGCTGCGACTTCACCAAAGG	0.622																																					p.T459T		Atlas-SNP	.											.	C19orf21	56	.	0			c.T1377C						.						50	41	44					19																	758323		2203	4300	6503	SO:0001819	synonymous_variant	126353	exon2			TGCGACTTCACCA	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.1377T>C	chr19.hg19:g.758323T>C		75.0	0.0		81.0	4.0	NM_173481		Silent	SNP	ENST00000215582.6	hg19	CCDS12042.1																																																																																			.	.		0.622	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		C	758323	T	C	758323	2	2	91	1	0	0	0	0	0	0	0	1	1915	1596	56	2		2	C19orf21	19	758323	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10		758323	58370660	605	12679										
ABCA7	10347	hgsc.bcm.edu	37	chr19	1043779	1043779	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggatgtccgggaggtgtgggAgatgctgggaccccggatct	19	8	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:1043779A>G	ENST00000263094.6	+	10	1217	c.986A>G	c.(985-987)gAg>gGg	p.E329G	ABCA7_ENST00000435683.2_Missense_Mutation_p.E191G|ABCA7_ENST00000433129.1_Missense_Mutation_p.E329G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	329					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGTGTGGGAGATGCTGGGA	0.632																																					p.E329G		Atlas-SNP	.											.	ABCA7	174	.	0			c.A986G						.						169	165	167					19																	1043779		2203	4300	6503	SO:0001583	missense	10347	exon10			TGTGGGAGATGCT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.986A>G	chr19.hg19:g.1043779A>G	ENSP00000263094:p.Glu329Gly	76.0	0.0		62.0	8.0	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	A	10.80	1.451769	0.26074	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.85702	-2.02;-2.02	4.33	-8.66	0.00866	.	.	.	.	.	T	0.63710	0.2534	N	0.05510	-0.035	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.15052	0.012;0.005	T	0.51903	-0.8646	9	0.37606	T	0.19	.	6.4939	0.22132	0.4551:0.321:0.2239:0.0	.	191;329	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	G	329	ENSP00000263094:E329G;ENSP00000414062:E329G	ENSP00000263094:E329G	E	+	2	0	ABCA7	994779	0.000000	0.05858	0.001000	0.08648	0.070000	0.16714	-0.637000	0.05459	-1.689000	0.01434	-0.640000	0.03970	GAG	.	.		0.632	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		G	1043779	A	G	1043779	3	3	91	1	0	0	0	0	1	0	0	0	37	304	11	2	1020	2	ABCA7	19	1043779	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	285456	1043779	58085204	606	12680										
KDM4B	23030	hgsc.bcm.edu	37	chr19	5041177	5041177	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cccgcggcaccaggactttgAtgaccttgaacgcaaatact	9	13	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:5041177A>G	ENST00000159111.4	+	5	565	c.347A>G	c.(346-348)gAt>gGt	p.D116G	KDM4B_ENST00000381759.4_Missense_Mutation_p.D116G|KDM4B_ENST00000536461.1_Missense_Mutation_p.D116G	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	116					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						CAGGACTTTGATGACCTTGAA	0.557																																					p.D116G		Atlas-SNP	.											.	KDM4B	120	.	0			c.A347G						.						133	119	123					19																	5041177		2203	4300	6503	SO:0001583	missense	23030	exon5			ACTTTGATGACCT	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.347A>G	chr19.hg19:g.5041177A>G	ENSP00000159111:p.Asp116Gly	126.0	0.0		92.0	4.0	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	hg19	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.284955	0.59867	.	.	ENSG00000127663	ENST00000159111;ENST00000381759;ENST00000536461	T;T;T	0.50813	0.73;0.73;0.73	4.62	4.62	0.57501	.	0.117692	0.56097	D	0.000027	T	0.46580	0.1400	L	0.53729	1.69	0.80722	D	1	B;B;B	0.28378	0.021;0.209;0.012	B;B;B	0.31946	0.01;0.138;0.004	T	0.50338	-0.8840	10	0.56958	D	0.05	-36.0385	14.1735	0.65525	1.0:0.0:0.0:0.0	.	116;116;116	F5GX28;O94953-2;O94953	.;.;KDM4B_HUMAN	G	116	ENSP00000159111:D116G;ENSP00000371178:D116G;ENSP00000440495:D116G	ENSP00000159111:D116G	D	+	2	0	KDM4B	4992177	1.000000	0.71417	0.963000	0.40424	0.664000	0.39144	8.972000	0.93424	1.943000	0.56356	0.459000	0.35465	GAT	.	.		0.557	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		G	5041177	A	G	5041177	3	3	91	1	0	0	0	0	1	0	0	0	8138	333	12	2	357	2	KDM4B	19	5041177	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3997398	5041177	54087806	607	12681										
SAFB	6294	hgsc.bcm.edu	37	chr19	5654111	5654111	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatgataaatgtgacagaaaAgatgatgctaagaagggtga	13	2	0	7			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:5654111A>G	ENST00000292123.5	+	12	1673	c.1566A>G	c.(1564-1566)aaA>aaG	p.K522K	SAFB_ENST00000588852.1_Silent_p.K522K|SAFB_ENST00000538656.1_Silent_p.K365K|SAFB_ENST00000592224.1_Silent_p.K522K|SAFB_ENST00000454510.1_Silent_p.K453K|SAFB_ENST00000433404.1_Silent_p.K352K	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	522					chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GTGACAGAAAAGATGATGCTA	0.468																																					p.K522K	Colon(88;338 1345 6184 8214 20897)	Atlas-SNP	.											.	SAFB	74	.	0			c.A1566G						.						107	101	103					19																	5654111		2203	4300	6503	SO:0001819	synonymous_variant	6294	exon12			CAGAAAAGATGAT	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"RNA binding motif (RRM) containing"	10520	protein-coding gene	gene with protein product	"Hsp27 ERE-TATA binding protein"	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.1566A>G	chr19.hg19:g.5654111A>G		91.0	0.0		66.0	4.0	NM_002967	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Silent	SNP	ENST00000292123.5	hg19	CCDS12142.1																																																																																			.	.		0.468	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2			G	5654111	A	G	5654111	2	3	91	1	0	0	0	0	0	0	0	1	13821	69	3	2		2	SAFB	19	5654111	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	612934	5654111	53474872	608	12682										
VAV1	7409	hgsc.bcm.edu	37	chr19	6853046	6853046	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctggacaccaccttgcagtTccccttcaaggagcctgaaa	8	14	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:6853046T>C	ENST00000602142.1	+	25	2370	c.2288T>C	c.(2287-2289)tTc>tCc	p.F763S	VAV1_ENST00000596764.1_Missense_Mutation_p.F731S|VAV1_ENST00000539284.1_Missense_Mutation_p.F666S|VAV1_ENST00000304076.2_Missense_Mutation_p.F741S|VAV1_ENST00000599806.1_Missense_Mutation_p.F708S	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	763	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						ACCTTGCAGTTCCCCTTCAAG	0.542																																					p.F763S		Atlas-SNP	.											.	VAV1	140	.	0			c.T2288C						.						88	81	84					19																	6853046		2203	4300	6503	SO:0001583	missense	7409	exon25			TGCAGTTCCCCTT		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12657	protein-coding gene	gene with protein product		164875	"vav 1 oncogene"	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.2288T>C	chr19.hg19:g.6853046T>C	ENSP00000472929:p.Phe763Ser	107.0	0.0		95.0	5.0	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	hg19	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.501424	0.26861	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T	0.75477	-0.94	4.36	3.32	0.38043	SH2 motif (2);	0.321581	0.29185	N	0.012883	T	0.62901	0.2466	L	0.31371	0.925	0.33694	D	0.613715	B;B;B;B	0.31009	0.014;0.238;0.021;0.303	B;B;B;B	0.36808	0.044;0.058;0.032;0.233	T	0.67891	-0.5553	10	0.59425	D	0.04	.	6.9586	0.24585	0.3717:0.0:0.0:0.6283	.	666;763;708;763	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	S	763;666	ENSP00000443242:F666S	ENSP00000302269:F763S	F	+	2	0	VAV1	6804046	0.759000	0.28416	0.997000	0.53966	0.813000	0.45954	0.651000	0.24873	0.687000	0.31509	0.460000	0.39030	TTC	.	.		0.542	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1			C	6853046	T	C	6853046	3	2	91	1	0	0	0	0	1	0	0	0	17146	1783	62	2	2386	2	VAV1	19	6853046	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1198935	6853046	52275937	609	12683										
INSR	3643	hgsc.bcm.edu	37	chr19	7267868	7267868	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agcaattctccagctcatgcAacctagtgaggttgttccgg	10	11	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:7267868A>G	ENST00000302850.5	-	2	282	c.140T>C	c.(139-141)tTg>tCg	p.L47S	INSR_ENST00000341500.5_Missense_Mutation_p.L47S	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	47	Leu-rich.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""Insulin(DB00071)|""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	CAGCTCATGCAACCTAGTGAG	0.488																																					p.L47S		Atlas-SNP	.											.	INSR	265	.	0			c.T140C						.						59	54	55					19																	7267868		2203	4300	6503	SO:0001583	missense	3643	exon2			TCATGCAACCTAG	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"CD molecules", "Fibronectin type III domain containing"	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.140T>C	chr19.hg19:g.7267868A>G	ENSP00000303830:p.Leu47Ser	69.0	0.0		68.0	4.0	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	hg19	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.777137	0.49786	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	D;D	0.83914	-1.78;-1.78	5.06	5.06	0.68205	.	0.000000	0.35096	U	0.003442	D	0.88746	0.6520	L	0.58810	1.83	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.996	D	0.89728	0.3924	10	0.87932	D	0	.	12.802	0.57591	1.0:0.0:0.0:0.0	.	38;47;47	Q86WY9;P06213-2;P06213	.;.;INSR_HUMAN	S	47	ENSP00000303830:L47S;ENSP00000342838:L47S	ENSP00000303830:L47S	L	-	2	0	INSR	7218868	1.000000	0.71417	0.396000	0.26296	0.217000	0.24651	8.844000	0.92147	1.907000	0.55213	0.377000	0.23210	TTG	.	.		0.488	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			G	7267868	A	G	7267868	3	3	91	1	0	0	0	0	1	0	0	0	7782	131	5	2	4092	2	INSR	19	7267868	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	414822	7267868	51861115	610	12684										
PCP2	126006	hgsc.bcm.edu	37	chr19	7696666	7696666	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgagcaggggttggggactgAgggtcccagctcgtttctgt	17	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:7696666A>G	ENST00000311069.5	-	4	610	c.320T>C	c.(319-321)cTc>cCc	p.L107P	XAB2_ENST00000358368.4_5'Flank|CTD-3214H19.4_ENST00000595866.1_Intron|PET100_ENST00000594797.1_3'UTR|PCP2_ENST00000598935.1_Missense_Mutation_p.L91P|CTD-3214H19.6_ENST00000601797.1_RNA|XAB2_ENST00000534844.1_5'Flank	NM_174895.1	NP_777555.1	Q8IVA1	PCP2_HUMAN	Purkinje cell protein 2	107					rhodopsin mediated signaling pathway (GO:0016056)	neuronal cell body (GO:0043025)	GTPase regulator activity (GO:0030695)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|urinary_tract(1)	2						TTGGGGACTGAGGGTCCCAGC	0.677																																					p.L107P		Atlas-SNP	.											.	PCP2	6	.	0			c.T320C						.						61	58	59					19																	7696666		2202	4290	6492	SO:0001583	missense	126006	exon4			GGACTGAGGGTCC	BC025387	CCDS32893.1, CCDS62521.1	19p13.3	2008-02-05				ENSG00000174788			30209	protein-coding gene	gene with protein product						12477932	Standard	NM_174895		Approved	MGC41903, GPSM4	uc031rjd.1	Q8IVA1		ENST00000311069.5:c.320T>C	chr19.hg19:g.7696666A>G	ENSP00000310585:p.Leu107Pro	78.0	0.0		99.0	7.0	NM_174895	M0R2R7|Q3KRG7	Missense_Mutation	SNP	ENST00000311069.5	hg19	CCDS32893.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.326551	0.60743	.	.	ENSG00000174788	ENST00000311069	.	.	.	4.63	2.41	0.29592	.	0.794590	0.10342	N	0.686157	T	0.37156	0.0993	N	0.19112	0.55	0.58432	D	0.999996	D	0.61697	0.99	P	0.51615	0.675	T	0.26258	-1.0108	9	0.29301	T	0.29	-28.547	4.2383	0.10637	0.5832:0.2276:0.0:0.1892	.	107	Q8IVA1	PCP2_HUMAN	P	107	.	ENSP00000310585:L107P	L	-	2	0	PCP2	7602666	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	0.601000	0.24119	1.730000	0.51580	0.459000	0.35465	CTC	.	.		0.677	PCP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461026.2	XM_058956		G	7696666	A	G	7696666	3	3	91	1	0	0	0	0	1	0	0	0	11606	304	11	2	94	2	PCP2	19	7696666	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	428798	7696666	51432317	611	12685										
HNRNPM	4670	hgsc.bcm.edu	37	chr19	8550522	8550522	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcgtccctgggatcgagaggAtgggtcctggcattgaccgc	16	11	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:8550522A>G	ENST00000325495.4	+	14	1251	c.1210A>G	c.(1210-1212)Atg>Gtg	p.M404V	HNRNPM_ENST00000348943.3_Missense_Mutation_p.M365V	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	404	27 X 6 AA repeats of [GEVSTPAN]-[ILMV]- [DE]-[RH]-[MLVI]-[GAV].				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						GATCGAGAGGATGGGTCCTGG	0.642																																					p.M404V		Atlas-SNP	.											.	HNRNPM	61	.	0			c.A1210G						.						122	128	126					19																	8550522		2203	4300	6503	SO:0001583	missense	4670	exon14			GAGAGGATGGGTC	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.1210A>G	chr19.hg19:g.8550522A>G	ENSP00000325376:p.Met404Val	62.0	0.0		74.0	4.0	NM_005968	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Missense_Mutation	SNP	ENST00000325495.4	hg19	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	A	15.55	2.865759	0.51588	.	.	ENSG00000099783	ENST00000325495;ENST00000348943;ENST00000544159	T;T	0.14022	2.54;2.84	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.24774	0.0601	L	0.48986	1.54	0.48087	D	0.99958	P;B;D;P	0.58970	0.817;0.323;0.984;0.665	B;B;P;B	0.55871	0.164;0.267;0.786;0.157	T	0.00645	-1.1629	10	0.36615	T	0.2	.	13.2541	0.60068	1.0:0.0:0.0:0.0	.	244;404;365;289	Q7KYM9;P52272;P52272-2;Q59ES8	.;HNRPM_HUMAN;.;.	V	404;365;289	ENSP00000325376:M404V;ENSP00000325732:M365V	ENSP00000325376:M404V	M	+	1	0	HNRNPM	8456522	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.231000	0.72307	2.155000	0.67459	0.402000	0.26972	ATG	.	.		0.642	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1			G	8550522	A	G	8550522	3	3	91	1	0	0	0	0	1	0	0	0	7280	333	12	2	1264	2	HNRNPM	19	8550522	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	853856	8550522	50578461	612	12686										
ZNF699	374879	hgsc.bcm.edu	37	chr19	9406618	9406618	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taggtgttcggtgagggatgAggaacgactaaaggtcttcc	15	6	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:9406618A>G	ENST00000591998.1	-	6	1690	c.1462T>C	c.(1462-1464)Tca>Cca	p.S488P	ZNF699_ENST00000308650.3_Missense_Mutation_p.S488P|CTC-325H20.4_ENST00000591336.1_RNA			Q32M78	ZN699_HUMAN	zinc finger protein 699	488					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GTGAGGGATGAGGAACGACTA	0.458																																					p.S488P		Atlas-SNP	.											.	ZNF699	67	.	0			c.T1462C						.						80	85	83					19																	9406618		2200	4297	6497	SO:0001583	missense	374879	exon5			GGGATGAGGAACG	BC109268	CCDS42495.1	19p13.2	2013-01-08				ENSG00000196110		"Zinc fingers, C2H2-type", "-"	24750	protein-coding gene	gene with protein product	hangover homolog (Drosophila)	609571				16940975	Standard	NM_198535		Approved	FLJ38144, hang	uc002mlc.1	Q32M78		ENST00000591998.1:c.1462T>C	chr19.hg19:g.9406618A>G	ENSP00000467723:p.Ser488Pro	136.0	0.0		94.0	4.0	NM_198535	Q8N9A1	Missense_Mutation	SNP	ENST00000591998.1	hg19	CCDS42495.1	.	.	.	.	.	.	.	.	.	.	A	14.57	2.574165	0.45902	.	.	ENSG00000196110	ENST00000308650	T	0.07908	3.15	3.3	3.3	0.37823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.31221	N	0.008024	T	0.23094	0.0558	M	0.71871	2.18	0.09310	N	1	D	0.76494	0.999	D	0.66716	0.946	T	0.01169	-1.1430	10	0.66056	D	0.02	.	10.254	0.43385	1.0:0.0:0.0:0.0	.	488	Q32M78	ZN699_HUMAN	P	488	ENSP00000311596:S488P	ENSP00000311596:S488P	S	-	1	0	ZNF699	9267618	0.008000	0.16893	0.043000	0.18650	0.957000	0.61999	2.114000	0.41911	1.751000	0.51876	0.454000	0.30748	TCA	.	.		0.458	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535		G	9406618	A	G	9406618	3	3	91	1	0	0	0	0	1	0	0	0	18116	304	11	2	470	2	ZNF699	19	9406618	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	856096	9406618	49722365	613	12687										
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11560105	11560105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcctcctgtgcgggaaagagAccatggtgaccagcaccaca	12	13	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:11560105A>G	ENST00000589838.1	+	16	1465	c.1465A>G	c.(1465-1467)Acc>Gcc	p.T489A	PRKCSH_ENST00000592741.1_Missense_Mutation_p.T496A|PRKCSH_ENST00000591462.1_Missense_Mutation_p.T486A|PRKCSH_ENST00000587327.1_Missense_Mutation_p.T486A|PRKCSH_ENST00000412601.1_Missense_Mutation_p.T486A|PRKCSH_ENST00000252455.2_Missense_Mutation_p.T489A			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	489					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						CGGGAAAGAGACCATGGTGAC	0.697																																					p.T489A		Atlas-SNP	.											.	PRKCSH	55	.	0			c.A1465G						.						60	55	56					19																	11560105		2203	4300	6503	SO:0001583	missense	5589	exon17			AAAGAGACCATGG		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"EF-hand domain containing"	9411	protein-coding gene	gene with protein product		177060	"polycystic liver disease"	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.1465A>G	chr19.hg19:g.11560105A>G	ENSP00000465461:p.Thr489Ala	72.0	0.0		89.0	5.0	NM_002743	A8K318|Q96BU9|Q96D06|Q9P0W9	Missense_Mutation	SNP	ENST00000589838.1	hg19	CCDS32911.1	.	.	.	.	.	.	.	.	.	.	A	12.84	2.060014	0.36373	.	.	ENSG00000130175	ENST00000252455;ENST00000412601	D;D	0.81996	-1.56;-1.56	3.72	3.72	0.42706	Mannose-6-phosphate receptor, binding (1);	0.060522	0.64402	D	0.000004	D	0.88066	0.6337	M	0.79123	2.44	0.47819	D	0.999526	D;D;P;D	0.64830	0.984;0.994;0.629;0.994	P;D;B;D	0.64237	0.78;0.923;0.439;0.923	D	0.87571	0.2478	10	0.56958	D	0.05	-10.354	7.3549	0.26713	0.8044:0.0:0.0:0.1956	.	496;496;486;489	E7EQZ9;B4DJQ5;A8K318;P14314	.;.;.;GLU2B_HUMAN	A	489;486	ENSP00000252455:T489A;ENSP00000395616:T486A	ENSP00000252455:T489A	T	+	1	0	PRKCSH	11421105	1.000000	0.71417	0.848000	0.33437	0.330000	0.28571	4.618000	0.61211	1.543000	0.49345	0.460000	0.39030	ACC	.	.		0.697	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			G	11560105	A	G	11560105	3	3	91	1	0	0	0	0	1	0	0	0	12528	275	10	2	1548	2	PRKCSH	19	11560105	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2153487	11560105	47568878	614	12688										
ZNF844	284391	hgsc.bcm.edu	37	chr19	12186579	12186579	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctcagcatatatcttatacAtgaacgagttcacactggag	7	9	3	1	rs537864739		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:12186579A>G	ENST00000439326.3	+	4	819	c.644A>G	c.(643-645)cAt>cGt	p.H215R	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	215					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						TATCTTATACATGAACGAGTT	0.358													.|||	1	0.000199681	8e-04	0	5008	,	,		22325	0		0	False		,,,				2504	0				p.H215R		Atlas-SNP	.											.	ZNF844	69	.	0			c.A644G						.						39	34	35					19																	12186579		692	1591	2283	SO:0001583	missense	284391	exon4			TTATACATGAACG	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"Zinc fingers, C2H2-type", "-"	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.644A>G	chr19.hg19:g.12186579A>G	ENSP00000392024:p.His215Arg	138.0	0.0		92.0	4.0	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	hg19	CCDS45985.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.145874	0.57044	.	.	ENSG00000223547	ENST00000439326;ENST00000541708;ENST00000535505;ENST00000550826	D;D	0.86865	-2.18;-2.18	2.29	2.29	0.28610	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94755	0.8307	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.94229	0.7474	9	0.87932	D	0	.	9.2449	0.37520	1.0:0.0:0.0:0.0	.	215	Q08AG5	ZN844_HUMAN	R	215;215;190;58	ENSP00000392024:H215R;ENSP00000448588:H58R	ENSP00000392024:H215R	H	+	2	0	ZNF844	12047579	0.992000	0.36948	0.003000	0.11579	0.200000	0.23975	5.061000	0.64319	1.043000	0.40175	0.172000	0.16884	CAT	.	.		0.358	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			G	12186579	A	G	12186579	3	3	91	1	0	0	0	0	1	0	0	0	18205	217	8	2	658	2	ZNF844	19	12186579	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	626474	12186579	46942404	615	12689										
CD97	976	hgsc.bcm.edu	37	chr19	14516617	14516617	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgctgtcactcttctgcctgCtgctgtgcatcctcactttc	7	16	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:14516617C>T	ENST00000242786.5	+	14	1767	c.1687C>T	c.(1687-1689)Ctg>Ttg	p.L563L	CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000357355.3_Silent_p.L514L|CD97_ENST00000358600.3_Silent_p.L470L	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	563					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTTCTGCCTGCTGCTGTGCAT	0.622																																					p.L563L		Atlas-SNP	.											.	CD97	86	.	0			c.C1687T						.						180	139	153					19																	14516617		2203	4300	6503	SO:0001819	synonymous_variant	976	exon14			TGCCTGCTGCTGT		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.1687C>T	chr19.hg19:g.14516617C>T		107.0	0.0		85.0	4.0	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Silent	SNP	ENST00000242786.5	hg19	CCDS32929.1																																																																																			.	.		0.622	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		T	14516617	C	T	14516617	2	4	91	1	0	0	0	0	0	0	0	1	3051	796	28	3		3	CD97	19	14516617	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2330038	14516617	44612366	616	12690										
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15067448	15067448	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggtgtacatgcccagctgacCccccaggacggccatgtctt	11	15	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:15067448C>T	ENST00000221742.3	-	6	1016	c.1009G>A	c.(1009-1011)Ggt>Agt	p.G337S	SLC1A6_ENST00000600144.1_Intron|SLC1A6_ENST00000430939.2_Missense_Mutation_p.G273S	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	337					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						CCCAGCTGACCCCCCAGGACG	0.582																																					p.G337S		Atlas-SNP	.											.	SLC1A6	111	.	0			c.G1009A						.						143	124	130					19																	15067448		2203	4300	6503	SO:0001583	missense	6511	exon6			GCTGACCCCCCAG		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1009G>A	chr19.hg19:g.15067448C>T	ENSP00000221742:p.Gly337Ser	109.0	0.0		84.0	8.0	NM_005071	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	hg19	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	c	14.32	2.499178	0.44455	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.58940	0.36;0.3	3.97	3.97	0.46021	.	0.152513	0.64402	D	0.000018	T	0.52757	0.1754	L	0.27053	0.805	0.80722	D	1	B;B	0.24823	0.112;0.001	B;B	0.42062	0.374;0.009	T	0.49331	-0.8951	10	0.23891	T	0.37	-6.5217	13.9019	0.63809	0.0:1.0:0.0:0.0	.	273;337	E7EV13;P48664	.;EAA4_HUMAN	S	273;337	ENSP00000409386:G273S;ENSP00000221742:G337S	ENSP00000221742:G337S	G	-	1	0	SLC1A6	14928448	0.974000	0.33945	1.000000	0.80357	0.933000	0.57130	2.444000	0.44890	2.229000	0.72834	0.596000	0.82720	GGT	.	.		0.582	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		T	15067448	C	T	15067448	3	4	91	1	0	0	0	0	1	0	0	0	14451	623	22	3	701	3	SLC1A6	19	15067448	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	550831	15067448	44061535	617	12691										
AKAP8	10270	hgsc.bcm.edu	37	chr19	15472941	15472941	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctggaggaactccacggtctTgtcgggcagcttggtgctta	14	10	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:15472941T>C	ENST00000269701.2	-	10	1342	c.1282A>G	c.(1282-1284)Aag>Gag	p.K428E		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	428					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						TCCACGGTCTTGTCGGGCAGC	0.542																																					p.K428E	GBM(190;1671 2163 3274 27186 30476)	Atlas-SNP	.											.	AKAP8	68	.	0			c.A1282G						.						87	82	84					19																	15472941		2203	4300	6503	SO:0001583	missense	10270	exon10			CGGTCTTGTCGGG	Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"A-kinase anchor proteins"	378	protein-coding gene	gene with protein product	"A-kinase anchor protein, 95kDa"	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.1282A>G	chr19.hg19:g.15472941T>C	ENSP00000269701:p.Lys428Glu	77.0	0.0		74.0	4.0	NM_005858		Missense_Mutation	SNP	ENST00000269701.2	hg19	CCDS12329.1	.	.	.	.	.	.	.	.	.	.	T	17.49	3.402471	0.62288	.	.	ENSG00000105127	ENST00000269701;ENST00000537303	T	0.43688	0.94	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000009	T	0.41650	0.1168	L	0.29908	0.895	0.28242	N	0.925637	D;D	0.56746	0.977;0.977	P;P	0.52424	0.698;0.698	T	0.38520	-0.9657	10	0.56958	D	0.05	-34.2549	10.7411	0.46154	0.0:0.0:0.1594:0.8406	.	428;428	Q8NE02;O43823	.;AKAP8_HUMAN	E	428;177	ENSP00000269701:K428E	ENSP00000269701:K428E	K	-	1	0	AKAP8	15333941	1.000000	0.71417	1.000000	0.80357	0.438000	0.31896	2.842000	0.48230	2.096000	0.63516	0.379000	0.24179	AAG	.	.		0.542	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858		C	15472941	T	C	15472941	3	2	91	1	0	0	0	0	1	0	0	0	457	1821	63	2	816	2	AKAP8	19	15472941	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	405493	15472941	43656042	618	12692										
RASAL3	64926	hgsc.bcm.edu	37	chr19	15565287	15565287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catccacatccaccatggctAcctggtccaggaagcattgc	8	15	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:15565287A>G	ENST00000343625.7	-	13	2130	c.2045T>C	c.(2044-2046)gTa>gCa	p.V682A	RASAL3_ENST00000608577.1_5'Flank	NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	682					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						CACCATGGCTACCTGGTCCAG	0.557											OREG0025322	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V682A		Atlas-SNP	.											.	RASAL3	49	.	0			c.T2045C						.						87	97	94					19																	15565287		2106	4216	6322	SO:0001583	missense	64926	exon13			ATGGCTACCTGGT		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.2045T>C	chr19.hg19:g.15565287A>G	ENSP00000341905:p.Val682Ala	130.0	0.0	703	128.0	6.0	NM_022904	Q8N2T9|Q9H735	Missense_Mutation	SNP	ENST00000343625.7	hg19	CCDS46006.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.991511	0.74703	.	.	ENSG00000105122	ENST00000343625	D	0.84589	-1.87	5.29	5.29	0.74685	Rho GTPase activation protein (1);Ras GTPase-activating protein (2);	0.000000	0.34507	U	0.003905	D	0.90665	0.7072	M	0.69823	2.125	0.43874	D	0.996482	D;D	0.76494	0.999;0.999	D;P	0.66084	0.941;0.874	D	0.91680	0.5357	10	0.87932	D	0	.	13.1841	0.59672	1.0:0.0:0.0:0.0	.	682;682	Q86YV0-2;Q86YV0	.;RASL3_HUMAN	A	682	ENSP00000341905:V682A	ENSP00000341905:V682A	V	-	2	0	RASAL3	15426287	0.651000	0.27340	1.000000	0.80357	0.980000	0.70556	3.598000	0.54038	2.008000	0.58898	0.459000	0.35465	GTA	.	.		0.557	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904		G	15565287	A	G	15565287	3	3	91	1	0	0	0	0	1	0	0	0	13080	391	14	2	1014	2	RASAL3	19	15565287	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	92346	15565287	43563696	619	12693										
RASAL3	64926	hgsc.bcm.edu	37	chr19	15569377	15569377	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cccccaggaggctggggtgcAgtggccagatccgcacatcc	14	15	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:15569377A>G	ENST00000343625.7	-	7	837	c.752T>C	c.(751-753)cTg>cCg	p.L251P	RASAL3_ENST00000608577.1_5'Flank	NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	251	PH.		L -> V (in dbSNP:rs58123634).		negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						GCTGGGGTGCAGTGGCCAGAT	0.642																																					p.L251P		Atlas-SNP	.											.	RASAL3	49	.	0			c.T752C						.						40	45	43					19																	15569377		2095	4223	6318	SO:0001583	missense	64926	exon7			GGGTGCAGTGGCC		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.752T>C	chr19.hg19:g.15569377A>G	ENSP00000341905:p.Leu251Pro	113.0	0.0		95.0	6.0	NM_022904	Q8N2T9|Q9H735	Missense_Mutation	SNP	ENST00000343625.7	hg19	CCDS46006.1	.	.	.	.	.	.	.	.	.	.	A	19.11	3.764256	0.69878	.	.	ENSG00000105122	ENST00000343625	D	0.92752	-3.1	4.47	4.47	0.54385	Pleckstrin homology domain (1);	0.000000	0.26948	U	0.021700	D	0.94042	0.8091	L	0.57536	1.79	0.80722	D	1	D	0.76494	0.999	D	0.69307	0.963	D	0.93341	0.6710	10	0.44086	T	0.13	.	11.6946	0.51536	1.0:0.0:0.0:0.0	.	251	Q86YV0	RASL3_HUMAN	P	251	ENSP00000341905:L251P	ENSP00000341905:L251P	L	-	2	0	RASAL3	15430377	0.709000	0.27886	0.994000	0.49952	0.560000	0.35617	4.484000	0.60271	1.662000	0.50781	0.402000	0.26972	CTG	.	.		0.642	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904		G	15569377	A	G	15569377	3	3	91	1	0	0	0	0	1	0	0	0	13080	188	7	2	2331	2	RASAL3	19	15569377	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	4090	15569377	43559606	620	12694										
SIN3B	23309	hgsc.bcm.edu	37	chr19	16952755	16952755	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccagaaatctacaggtcattCctggagatcctgcacacgta	8	12	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:16952755C>A	ENST00000248054.5	+	4	579	c.558C>A	c.(556-558)ttC>ttA	p.F186L	SIN3B_ENST00000379803.1_Missense_Mutation_p.F186L|SIN3B_ENST00000596802.1_Missense_Mutation_p.F186L|CTD-2538G9.5_ENST00000600987.1_RNA					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						ACAGGTCATTCCTGGAGATCC	0.463																																					p.F186L		Atlas-SNP	.											.	SIN3B	90	.	0			c.C558A						.						72	68	69					19																	16952755		2203	4300	6503	SO:0001583	missense	23309	exon4			GTCATTCCTGGAG	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.558C>A	chr19.hg19:g.16952755C>A	ENSP00000248054:p.Phe186Leu	168.0	0.0		143.0	6.0	NM_015260		Missense_Mutation	SNP	ENST00000248054.5	hg19		.	.	.	.	.	.	.	.	.	.	C	19.73	3.882872	0.72410	.	.	ENSG00000127511	ENST00000379803;ENST00000248054	T;T	0.81247	-1.47;-1.29	5.22	4.19	0.49359	.	0.000000	0.85682	D	0.000000	D	0.91168	0.7218	H	0.95712	3.71	0.54753	D	0.999987	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.98;0.999	D	0.91355	0.5107	10	0.51188	T	0.08	-2.1933	8.8518	0.35203	0.0:0.8382:0.0:0.1618	.	186;186;186	O75182-2;O75182;O75182-3	.;SIN3B_HUMAN;.	L	186	ENSP00000369131:F186L;ENSP00000248054:F186L	ENSP00000248054:F186L	F	+	3	2	SIN3B	16813755	0.994000	0.37717	0.999000	0.59377	0.880000	0.50808	0.677000	0.25262	2.427000	0.82271	0.557000	0.71058	TTC	.	.		0.463	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		A	16952755	C	A	16952755	3	1	91	1	0	0	0	0	1	0	0	0	14341	854	30	3	572	3	SIN3B	19	16952755	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1383378	16952755	42176228	621	12695										
OCEL1	79629	hgsc.bcm.edu	37	chr19	17339715	17339715	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgatgaccaaggagacagcgAgggctccgtgtacttctaag	13	10	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:17339715A>G	ENST00000215061.4	+	6	820	c.776A>G	c.(775-777)gAg>gGg	p.E259G	OCEL1_ENST00000597836.1_Missense_Mutation_p.E203G|OCEL1_ENST00000601529.1_3'UTR	NM_024578.1	NP_078854.1	Q9H607	OCEL1_HUMAN	occludin/ELL domain containing 1	259										central_nervous_system(2)|endometrium(2)|kidney(1)|lung(2)	7						GGAGACAGCGAGGGCTCCGTG	0.542																																					p.E259G		Atlas-SNP	.											.	OCEL1	20	.	0			c.A776G						.						103	92	96					19																	17339715		2203	4300	6503	SO:0001583	missense	79629	exon6			ACAGCGAGGGCTC	BC029361	CCDS12351.1	19p13.11	2008-02-05				ENSG00000099330			26221	protein-coding gene	gene with protein product						12477932	Standard	NM_024578		Approved	FLJ22709	uc002nfp.3	Q9H607		ENST00000215061.4:c.776A>G	chr19.hg19:g.17339715A>G	ENSP00000215061:p.Glu259Gly	22.0	0.0		19.0	4.0	NM_024578		Missense_Mutation	SNP	ENST00000215061.4	hg19	CCDS12351.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.369493	0.42003	.	.	ENSG00000099330	ENST00000215061	T	0.38077	1.16	4.45	4.45	0.53987	.	0.352018	0.25394	N	0.030993	T	0.47040	0.1424	L	0.47716	1.5	0.20764	N	0.99985	D	0.76494	0.999	D	0.66716	0.946	T	0.31833	-0.9929	10	0.72032	D	0.01	-17.9301	7.3058	0.26447	0.8041:0.0:0.0:0.1959	.	259	Q9H607	OCEL1_HUMAN	G	259	ENSP00000215061:E259G	ENSP00000215061:E259G	E	+	2	0	OCEL1	17200715	0.985000	0.35326	0.981000	0.43875	0.213000	0.24496	2.629000	0.46485	1.866000	0.54105	0.402000	0.26972	GAG	.	.		0.542	OCEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463307.1	NM_024578		G	17339715	A	G	17339715	3	3	91	1	0	0	0	0	1	0	0	0	10825	304	11	2	798	2	OCEL1	19	17339715	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	386960	17339715	41789268	622	12696										
TM6SF2	53345	hgsc.bcm.edu	37	chr19	19381177	19381177	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cttggtgtagaactccatgaAgcccaccacatagctgtctt	8	12	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:19381177A>G	ENST00000389363.4	-	3	346	c.274T>C	c.(274-276)Ttc>Ctc	p.F92L	AC138430.4_ENST00000586064.2_RNA|TM6SF2_ENST00000586107.1_Intron	NM_001001524.2	NP_001001524.2	Q9BZW4	TM6S2_HUMAN	transmembrane 6 superfamily member 2	92						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14			Epithelial(12;0.0151)			AACTCCATGAAGCCCACCACA	0.617																																					p.F92L		Atlas-SNP	.											.	TM6SF2	39	.	0			c.T274C						.						42	45	44					19																	19381177		2005	4170	6175	SO:0001583	missense	53345	exon3			CCATGAAGCCCAC	AF255923	CCDS42528.1	19p13.3-p12	2008-02-05							11861	protein-coding gene	gene with protein product		606563				11124529	Standard	NM_001001524		Approved	Lpr4	uc002nmd.1	Q9BZW4		ENST00000389363.4:c.274T>C	chr19.hg19:g.19381177A>G	ENSP00000374014:p.Phe92Leu	102.0	0.0		90.0	4.0	NM_001001524	Q0IJ64	Missense_Mutation	SNP	ENST00000389363.4	hg19	CCDS42528.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.502192	0.44455	.	.	ENSG00000213996	ENST00000389363;ENST00000431465;ENST00000269990	T	0.52754	0.65	5.31	3.16	0.36331	.	0.000000	0.39475	U	0.001360	T	0.39145	0.1067	L	0.49640	1.575	0.44587	D	0.997553	B	0.17465	0.022	B	0.12156	0.007	T	0.22452	-1.0216	10	0.42905	T	0.14	-13.1688	8.7867	0.34825	0.8339:0.0:0.1661:0.0	.	92	Q9BZW4	TM6S2_HUMAN	L	92	ENSP00000374014:F92L	ENSP00000269990:F92L	F	-	1	0	TM6SF2	19242177	1.000000	0.71417	0.999000	0.59377	0.228000	0.25075	4.465000	0.60141	0.818000	0.34468	0.413000	0.27773	TTC	.	.		0.617	TM6SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460122.2	NM_203510		G	19381177	A	G	19381177	3	3	91	1	0	0	0	0	1	0	0	0	15988	72	3	2	891	2	TM6SF2	19	19381177	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2041462	19381177	39747806	623	12697										
CILP2	148113	hgsc.bcm.edu	37	chr19	19650506	19650506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agacgccacccccaccgaggAgccaatggcgactgcactgg	12	16	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:19650506A>G	ENST00000291495.5	+	2	168	c.83A>G	c.(82-84)gAg>gGg	p.E28G	CILP2_ENST00000586018.1_Missense_Mutation_p.E28G	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	28						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCCACCGAGGAGCCAATGGCG	0.647																																					p.E28G		Atlas-SNP	.											.	CILP2	84	.	0			c.A83G						.						88	90	89					19																	19650506		2203	4300	6503	SO:0001583	missense	148113	exon2			CCGAGGAGCCAAT	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.83A>G	chr19.hg19:g.19650506A>G	ENSP00000291495:p.Glu28Gly	105.0	0.0		99.0	4.0	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	hg19	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	a	14.46	2.542691	0.45280	.	.	ENSG00000160161	ENST00000291495	T	0.54675	0.56	3.42	0.164	0.14990	.	0.147700	0.30028	N	0.010585	T	0.31888	0.0811	L	0.29908	0.895	0.29199	N	0.875351	P;B	0.47409	0.895;0.436	B;B	0.38056	0.264;0.049	T	0.32268	-0.9913	10	0.72032	D	0.01	-14.8919	5.7698	0.18247	0.6397:0.0:0.3603:0.0	.	28;28	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	G	28	ENSP00000291495:E28G	ENSP00000291495:E28G	E	+	2	0	CILP2	19511506	1.000000	0.71417	0.926000	0.36857	0.254000	0.26022	1.051000	0.30417	-0.034000	0.13713	0.364000	0.22116	GAG	.	.		0.647	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		G	19650506	A	G	19650506	3	3	91	1	0	0	0	0	1	0	0	0	3432	304	11	2	89	2	CILP2	19	19650506	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	269329	19650506	39478477	624	12698										
ZNF506	440515	hgsc.bcm.edu	37	chr19	19917871	19917871	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggccacatctctaaattgcaAtggtccctgaaaaaaacaca	6	11	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:19917871A>G	ENST00000540806.2	-	2	98	c.10T>C	c.(10-12)Ttg>Ctg	p.L4L	ZNF506_ENST00000545006.1_Silent_p.L4L|CTC-559E9.6_ENST00000589657.1_RNA|ZNF506_ENST00000450683.2_Silent_p.L4L|ZNF506_ENST00000587461.1_Silent_p.L4L|ZNF506_ENST00000587452.1_Silent_p.L4L|CTC-559E9.6_ENST00000591884.1_RNA|CTC-559E9.4_ENST00000590274.1_lincRNA|ZNF506_ENST00000443905.2_Silent_p.L4L			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	4	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						CTAAATTGCAATGGTCCCTGA	0.418																																					p.L4L		Atlas-SNP	.											.	ZNF506	36	.	0			c.T10C						.						80	88	85					19																	19917871		2199	4299	6498	SO:0001819	synonymous_variant	440515	exon2			ATTGCAATGGTCC	AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"Zinc fingers, C2H2-type", "-"	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.10T>C	chr19.hg19:g.19917871A>G		112.0	0.0		87.0	4.0	NM_001099269	B3KTH6	Silent	SNP	ENST00000540806.2	hg19	CCDS42531.1																																																																																			.	.		0.418	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218		G	19917871	A	G	19917871	2	3	91	1	0	0	0	0	0	0	0	1	17967	98	4	2		2	ZNF506	19	19917871	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	267365	19917871	39211112	625	12699										
ZNF714	148206	hgsc.bcm.edu	37	chr19	21299777	21299777	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aggtgtacaaaaaaggttatGaactaaaccagtgtttgaca	9	5	0	2	rs111443257		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:21299777G>A	ENST00000596143.1	+	5	632	c.307G>A	c.(307-309)Gaa>Aaa	p.E103K	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AAAAGGTTATGAACTAAACCA	0.328																																					p.E103K		Atlas-SNP	.											.	ZNF714	121	.	0			c.G307A						.						39	38	38					19																	21299777		2190	4291	6481	SO:0001583	missense	148206	exon5			GGTTATGAACTAA	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.307G>A	chr19.hg19:g.21299777G>A	ENSP00000472368:p.Glu103Lys	291.0	0.0		256.0	14.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	0.388	-0.924824	0.02377	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.394	0.394	0.16299	.	.	.	.	.	T	0.22322	0.0538	L	0.27975	0.815	0.09310	N	1	B;P	0.37781	0.004;0.608	B;B	0.35413	0.004;0.202	T	0.14062	-1.0486	7	0.56958	D	0.05	.	.	.	.	.	104;103	Q96N38-2;A6NEM4	.;.	K	103	.	ENSP00000291770:E103K	E	+	1	0	ZNF714	21091617	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	-0.857000	0.04286	0.452000	0.26830	0.456000	0.33151	GAA	.	.		0.328	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		A	21299777	G	A	21299777	3	1	91	1	0	0	0	0	1	0	0	0	18133	1291	45	3	317	3	ZNF714	19	21299777	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	1381906	21299777	37829206	626	12700										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22154522	22154522	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtttctctccagtatgaattCtcttatgttccataaggttt	6	8	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:22154522C>T	ENST00000397126.4	-	4	3462	c.3314G>A	c.(3313-3315)aGa>aAa	p.R1105K	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	1105					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R977I(2)|p.R1105I(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGTATGAATTCTCTTATGTTC	0.393																																					p.R1105K		Atlas-SNP	.											ZNF208_ENST00000428290,colon,carcinoma,0,3	ZNF208	817	.	3	Substitution - Missense(3)	large_intestine(3)	c.G3314A						.						65	68	67					19																	22154522		2086	4239	6325	SO:0001583	missense	7757	exon4			TGAATTCTCTTAT	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.3314G>A	chr19.hg19:g.22154522C>T	ENSP00000380315:p.Arg1105Lys	63.0	0.0		92.0	7.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	7.902	0.734632	0.15574	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.02197	4.4	2.59	1.06	0.20224	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02649	0.0080	.	.	.	0.09310	N	1	B	0.29627	0.252	B	0.34590	0.186	T	0.45411	-0.9263	8	0.45353	T	0.12	.	9.2481	0.37539	0.0:0.8399:0.0:0.16	.	977	O43345	ZN208_HUMAN	K	1105;977	ENSP00000380315:R1105K	ENSP00000380315:R1105K	R	-	2	0	ZNF208	21946362	0.000000	0.05858	0.003000	0.11579	0.124000	0.20399	-0.834000	0.04391	1.029000	0.39812	0.297000	0.19635	AGA	.	.		0.393	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22154522	C	T	22154522	3	4	91	1	0	0	0	0	1	0	0	0	17781	913	32	3	532	3	ZNF208	19	22154522	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	854745	22154522	36974461	627	12701										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363103	22363103	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catttgtaaggtttctctgcAgcatgaattctcttgtgttt	8	7	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:22363103A>G	ENST00000397121.2	-	3	1733	c.1416T>C	c.(1414-1416)gcT>gcC	p.A472A		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	472					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				GTTTCTCTGCAGCATGAATTC	0.393																																					p.A472A		Atlas-SNP	.											.	ZNF676	146	.	0			c.T1416C						.						116	120	119					19																	22363103		2146	4271	6417	SO:0001819	synonymous_variant	163223	exon3			CTCTGCAGCATGA	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.1416T>C	chr19.hg19:g.22363103A>G		93.0	0.0		73.0	4.0	NM_001001411	A8MVX5	Silent	SNP	ENST00000397121.2	hg19	CCDS42539.1																																																																																			.	.		0.393	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		G	22363103	A	G	22363103	2	3	91	1	0	0	0	0	0	0	0	1	18098	175	7	2		2	ZNF676	19	22363103	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	208581	22363103	36765880	628	12702										
CEBPA	1050	hgsc.bcm.edu	37	chr19	33793069	33793069	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gccttctcctgctgccggctGtgctggaacaggtcggccag	14	14	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:33793069G>A	ENST00000498907.2	-	1	401	c.252C>T	c.(250-252)caC>caT	p.H84H	CTD-2540B15.9_ENST00000593041.1_lincRNA|CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.7_ENST00000587312.1_RNA|CTD-2540B15.11_ENST00000589932.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	84					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Y7_G130del(1)|p.L78_A174del(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					GCTGCCGGCTGTGCTGGAACA	0.741			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.H84H		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	.	CEBPA	986	.	2	Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(2)	c.C252T						.						3	4	4					19																	33793069		1098	2308	3406	SO:0001819	synonymous_variant	1050	exon1	Familial Cancer Database	Familial AML	CCGGCTGTGCTGG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.252C>T	chr19.hg19:g.33793069G>A		66.0	0.0		74.0	4.0	NM_004364	A7LNP2|P78319|Q05CA4	Silent	SNP	ENST00000498907.2	hg19	CCDS54243.1																																																																																			.	.		0.741	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		A	33793069	G	A	33793069	2	1	91	1	0	0	0	0	0	0	0	1	3201	1368	48	3		3	CEBPA	19	33793069	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	11429966	33793069	25335914	629	12703										
HAMP	57817	hgsc.bcm.edu	37	chr19	35775715	35775715	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggacaacttgcagagctgcaAccccaggacagagctggagc	13	12	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:35775715A>G	ENST00000598398.1	+	3	410	c.114A>G	c.(112-114)caA>caG	p.Q38Q	HAMP_ENST00000222304.3_Silent_p.Q38Q	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide	38					cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|immune response (GO:0006955)|killing of cells of other organism (GO:0031640)	apical cortex (GO:0045179)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CAGAGCTGCAACCCCAGGACA	0.637																																					p.Q38Q		Atlas-SNP	.											.	HAMP	14	.	0			c.A114G						.						86	84	85					19																	35775715		2203	4300	6503	SO:0001819	synonymous_variant	57817	exon2			GCTGCAACCCCAG	AF309489	CCDS12454.1	19q13.1	2014-09-17				ENSG00000105697			15598	protein-coding gene	gene with protein product		606464				11034317, 11113132	Standard	NM_021175		Approved	LEAP-1, HEPC, HFE2B, LEAP1	uc002nyw.3	P81172		ENST00000598398.1:c.114A>G	chr19.hg19:g.35775715A>G		98.0	0.0		81.0	4.0	NM_021175	Q1HE14|Q9BY68	Silent	SNP	ENST00000598398.1	hg19	CCDS12454.1																																																																																			.	.		0.637	HAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466067.1	NM_021175		G	35775715	A	G	35775715	2	3	91	1	0	0	0	0	0	0	0	1	6957	40	2	2		2	HAMP	19	35775715	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1982646	35775715	23353268	630	12704										
MLL4	9757	hgsc.bcm.edu	37	chr19	36221615	36221615	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcccacatgccaggtgctccCgtctgtactggagcacagtg	11	14	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:36221615C>A	ENST00000222270.7	+	26	5284	c.5284C>A	c.(5284-5286)Cgt>Agt	p.R1762S	KMT2B_ENST00000420124.1_Missense_Mutation_p.R1762S|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1762	FYR N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00875}.				chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R1764C(1)									CAGGTGCTCCCGTCTGTACTG	0.612																																					p.R1762S		Atlas-SNP	.											MLL4,NS,carcinoma,0,2	MLL4	229	.	1	Substitution - Missense(1)	endometrium(1)	c.C5284A						.						65	68	67					19																	36221615		2004	4182	6186	SO:0001583	missense	8085	exon26			TGCTCCCGTCTGT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5284C>A	chr19.hg19:g.36221615C>A	ENSP00000222270:p.Arg1762Ser	83.0	0.0		58.0	4.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.946063	0.53079	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.89939	-2.59;-2.59	5.97	3.71	0.42584	FY-rich, N-terminal (1);FY-rich, N-terminal subgroup (1);	0.000000	0.45606	D	0.000345	D	0.95014	0.8386	M	0.90309	3.105	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	D	0.95879	0.8897	10	0.87932	D	0	.	13.8947	0.63764	0.2769:0.723:0.0:0.0	.	1762	Q9UMN6	MLL4_HUMAN	S	1762	ENSP00000222270:R1762S;ENSP00000398837:R1762S	ENSP00000222270:R1762S	R	+	1	0	AD000671.1	40913455	0.338000	0.24775	0.998000	0.56505	0.989000	0.77384	0.780000	0.26760	1.500000	0.48636	0.655000	0.94253	CGT	.	.		0.612	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		A	36221615	C	A	36221615	3	1	91	1	0	0	0	0	1	0	0	0	9632	652	23	1	5386	1	MLL4	19	36221615	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	445900	36221615	22907368	631	12705										
MLL4	9757	hgsc.bcm.edu	37	chr19	36223465	36223465	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggactgagcccttccaggaAgagattgtagccgctggggc	16	10	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:36223465A>G	ENST00000222270.7	+	28	6015	c.6015A>G	c.(6013-6015)gaA>gaG	p.E2005E	KMT2B_ENST00000420124.1_Silent_p.E2005E|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2005					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CCTTCCAGGAAGAGATTGTAG	0.667																																					p.E2005E		Atlas-SNP	.											.	MLL4	229	.	0			c.A6015G						.						26	32	30					19																	36223465		1971	4144	6115	SO:0001819	synonymous_variant	8085	exon28			CCAGGAAGAGATT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.6015A>G	chr19.hg19:g.36223465A>G		91.0	0.0		77.0	7.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.667	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		G	36223465	A	G	36223465	2	3	91	1	0	0	0	0	0	0	0	1	9632	69	3	2		2	MLL4	19	36223465	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1850	36223465	22905518	632	12706										
SIRT2	22933	hgsc.bcm.edu	37	chr19	39389044	39389044	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctcctgcaccttccctgccTgggtctccagagggtgagag	12	15	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:39389044T>C	ENST00000249396.7	-	2	339	c.38A>G	c.(37-39)cAg>cGg	p.Q13R	NFKBIB_ENST00000572515.1_5'Flank|SIRT2_ENST00000392081.2_Intron|SIRT2_ENST00000358931.5_Missense_Mutation_p.Q13R|SIRT2_ENST00000481381.1_5'UTR|NFKBIB_ENST00000392079.3_5'Flank|NFKBIB_ENST00000313582.5_5'Flank	NM_012237.3	NP_036369.2	Q8IXJ6	SIR2_HUMAN	sirtuin 2	13					autophagy (GO:0006914)|cellular lipid catabolic process (GO:0044242)|cellular response to caloric restriction (GO:0061433)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to hypoxia (GO:0071456)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to oxidative stress (GO:0034599)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|chromatin silencing at telomere (GO:0006348)|gene silencing (GO:0016458)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|innate immune response (GO:0045087)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|myelination in peripheral nervous system (GO:0022011)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)|negative regulation of defense response to bacterium (GO:1900425)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of oligodendrocyte progenitor proliferation (GO:0070446)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cell division (GO:0051781)|positive regulation of DNA binding (GO:0043388)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of meiosis (GO:0045836)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)|protein kinase B signaling (GO:0043491)|regulation of cell cycle (GO:0051726)|regulation of exit from mitosis (GO:0007096)|regulation of myelination (GO:0031641)|regulation of phosphorylation (GO:0042325)|response to redox state (GO:0051775)|ripoptosome assembly involved in necroptotic process (GO:1901026)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)	centriole (GO:0005814)|centrosome (GO:0005813)|chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|glial cell projection (GO:0097386)|juxtaparanode region of axon (GO:0044224)|lateral loop (GO:0043219)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|myelin sheath (GO:0043209)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|spindle (GO:0005819)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|NAD-dependent protein deacetylase activity (GO:0034979)|protein deacetylase activity (GO:0033558)|transcription factor binding (GO:0008134)|tubulin deacetylase activity (GO:0042903)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(5)|skin(1)	9	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00125)|LUSC - Lung squamous cell carcinoma(53;0.00191)			CTTCCCTGCCTGGGTCTCCAG	0.602																																					p.Q13R		Atlas-SNP	.											.	SIRT2	29	.	0			c.A38G						.						73	52	59					19																	39389044		2203	4300	6503	SO:0001583	missense	22933	exon2			CCTGCCTGGGTCT	AF083107	CCDS12523.1, CCDS46069.1, CCDS74361.1	19q13	2010-06-25	2010-06-25		ENSG00000068903	ENSG00000068903			10886	protein-coding gene	gene with protein product		604480	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 2", "sirtuin (silent mating type information regulation 2 homolog) 2 (S. cerevisiae)"	SIR2L		10393250, 10381378	Standard	NM_012237		Approved		uc002ojt.2	Q8IXJ6	OTTHUMG00000150480	ENST00000249396.7:c.38A>G	chr19.hg19:g.39389044T>C	ENSP00000249396:p.Gln13Arg	73.0	0.0		89.0	4.0	NM_012237	A8K3V1|B2RB45|O95889|Q924Y7|Q9P0G8|Q9UNT0|Q9Y6E9|U5TP13	Missense_Mutation	SNP	ENST00000249396.7	hg19	CCDS12523.1	.	.	.	.	.	.	.	.	.	.	T	11.61	1.690352	0.29962	.	.	ENSG00000068903	ENST00000249396;ENST00000358931	T;T	0.42900	1.52;0.96	3.22	3.22	0.36961	.	.	.	.	.	T	0.33673	0.0871	N	0.08118	0	0.28455	N	0.916147	P	0.45126	0.851	P	0.55391	0.775	T	0.10683	-1.0619	9	0.23302	T	0.38	-4.1004	8.2043	0.31443	0.0:0.0:0.0:1.0	.	13	Q8IXJ6	SIRT2_HUMAN	R	13	ENSP00000249396:Q13R;ENSP00000351809:Q13R	ENSP00000249396:Q13R	Q	-	2	0	SIRT2	44080884	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.057000	0.49931	1.703000	0.51240	0.379000	0.24179	CAG	.	.		0.602	SIRT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318278.1			C	39389044	T	C	39389044	3	2	91	1	0	0	0	0	1	0	0	0	14353	1580	55	2	1191	2	SIRT2	19	39389044	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3165579	39389044	19739939	633	12707										
PAF1	55588	hgsc.bcm.edu	37	chr19	39880716	39880716	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccttagtctcacctgttctGgtcgaaggggtaggtgatga	13	8	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:39880716G>T	ENST00000599213.2	+	0	0				PAF1_ENST00000595564.1_Missense_Mutation_p.Q45K|MED29_ENST00000315588.5_5'Flank|PAF1_ENST00000221266.7_Missense_Mutation_p.Q45K|MED29_ENST00000594368.1_5'Flank|PAF1_ENST00000221265.3_Missense_Mutation_p.Q55K			Q9NX70	MED29_HUMAN	mediator complex subunit 29						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mediator complex (GO:0016592)|nucleus (GO:0005634)				lung(2)|ovary(1)|pancreas(1)	4	all_cancers(60;7.82e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;1.04e-26)|all cancers(26;7.68e-24)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			CACCTGTTCTGGTCGAAGGGG	0.527																																					p.Q55K		Atlas-SNP	.											.	PAF1	43	.	0			c.C163A						.						155	151	153					19																	39880716		2203	4300	6503	SO:0001631	upstream_gene_variant	54623	exon3			TGTTCTGGTCGAA	AL137304, AY729650	CCDS33021.1	19q13.2	2007-07-30	2007-07-30	2007-07-30		ENSG00000063322			23074	protein-coding gene	gene with protein product		612914	"intersex-like (Drosophila)"	IXL		15555573	Standard	NM_017592		Approved	DKFZp434H247	uc010xux.3	Q9NX70			chr19.hg19:g.39880716G>T	Exception_encountered	90.0	0.0		79.0	4.0	NM_019088	B4DNQ6|M0R2E4|Q5XX09|Q9NTF4	Missense_Mutation	SNP	ENST00000599213.2	hg19		.	.	.	.	.	.	.	.	.	.	g	13.38	2.219967	0.39201	.	.	ENSG00000006712	ENST00000221265;ENST00000221266	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.29288	0.0729	N	0.10874	0.06	0.80722	D	1	B;B	0.28605	0.217;0.159	B;B	0.19946	0.016;0.027	T	0.18713	-1.0328	9	0.06099	T	0.92	-28.8987	15.0781	0.72093	0.0:0.0:1.0:0.0	.	45;55	F8W9Q2;Q8N7H5	.;PAF1_HUMAN	K	55;45	.	ENSP00000221265:Q55K	Q	-	1	0	PAF1	44572556	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.671000	0.74472	2.937000	0.99478	0.651000	0.88453	CAG	.	.		0.527	MED29-011	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470870.1	XM_290829		T	39880716	G	T	39880716	1	4	91	0	1	0	0	0	0	0	0	0	11392	1357	47	3		3	PAF1	19	39880716	5'Flank	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	491672	39880716	19248267	634	12708										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42874933	42874933	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aataacagctatggggagaaAtgcgagagctgcctgcaggg	15	7	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:42874933A>G	ENST00000251268.6	+	40	7086	c.7086A>G	c.(7084-7086)aaA>aaG	p.K2362K	MEGF8_ENST00000334370.4_Silent_p.K2295K|MEGF8_ENST00000378073.4_Start_Codon_SNP_p.M1V	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2362					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				ATGGGGAGAAATGCGAGAGCT	0.632																																					p.K2362K		Atlas-SNP	.											.	MEGF8	358	.	0			c.A7086G						.						63	54	57					19																	42874933		2201	4295	6496	SO:0001819	synonymous_variant	1954	exon40			GGAGAAATGCGAG	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.7086A>G	chr19.hg19:g.42874933A>G		66.0	0.0		80.0	4.0	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	A	15.17	2.752735	0.49362	.	.	ENSG00000105429	ENST00000378073	.	.	.	4.96	-5.22	0.02806	.	.	.	.	.	T	0.59362	0.2188	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40942	-0.9536	7	0.87932	D	0	-3.8313	19.3059	0.94163	0.197:0.0:0.803:0.0	.	1	F5GZG7	.	V	1	.	ENSP00000367313:M1V	M	+	1	0	MEGF8	47566773	0.947000	0.32204	0.830000	0.32933	0.904000	0.53231	0.042000	0.13949	-1.128000	0.02922	-0.441000	0.05720	ATG	.	.		0.632	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		G	42874933	A	G	42874933	2	3	91	1	0	0	0	0	0	0	0	1	9472	98	4	2		2	MEGF8	19	42874933	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2994217	42874933	16254050	635	12709										
TEX101	83639	hgsc.bcm.edu	37	chr19	43920080	43920080	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccagaagaagccatgggaacCcctcgtatccagcatttgct	9	13	0	2	rs149972012		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:43920080C>T	ENST00000598265.1	+	2	175	c.9C>T	c.(7-9)acC>acT	p.T3T	TEX101_ENST00000601707.1_3'UTR|TEX101_ENST00000253435.7_Silent_p.T21T|TEX101_ENST00000602198.1_Silent_p.T21T	NM_001130011.1	NP_001123483.1	Q9BY14	TX101_HUMAN	testis expressed 101	3						acrosomal membrane (GO:0002080)|anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				large_intestine(1)|lung(12)|ovary(1)|skin(1)	15		Prostate(69;0.0199)				CCATGGGAACCCCTCGTATCC	0.542																																					p.T21T		Atlas-SNP	.											.	TEX101	28	.	0			c.C63T						.	C	,	5,4401	9.9+/-24.2	0,5,2198	194	185	188		9,63	-2.2	0	19	dbSNP_134	188	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TEX101	NM_001130011.1,NM_031451.4	,	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	,	3/250,21/268	43920080	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	83639	exon5			GGGAACCCCTCGT	AF241268	CCDS12619.1, CCDS59393.1	19q13.31	2013-06-06	2007-03-13			ENSG00000131126			30722	protein-coding gene	gene with protein product	"cancer/testis antigen 131", "spermatogenesis associated 44"	612665	"testis expressed sequence 101"			16388701, 16516155	Standard	NM_031451		Approved	MGC4766, SGRG, CT131, SPATA44	uc010xwo.2	Q9BY14		ENST00000598265.1:c.9C>T	chr19.hg19:g.43920080C>T		192.0	0.0		158.0	70.0	NM_031451	Q7L5R2|Q9BPY7	Silent	SNP	ENST00000598265.1	hg19	CCDS59393.1																																																																																			.	C|1.000;T|0.000		0.542	TEX101-004	KNOWN	non_canonical_other|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000463176.1	NM_031451		T	43920080	C	T	43920080	2	4	91	1	0	0	0	0	0	0	0	1	15788	610	22	3		3	TEX101	19	43920080	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1045147	43920080	15208903	636	12710										
ZNF223	7766	hgsc.bcm.edu	37	chr19	44571110	44571110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agccatacaaatgtgacaagTgtgggaagagctacattact	10	7	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:44571110T>C	ENST00000434772.3	+	5	1384	c.1129T>C	c.(1129-1131)Tgt>Cgt	p.C377R	ZNF223_ENST00000591793.1_Missense_Mutation_p.C487R	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				ATGTGACAAGTGTGGGAAGAG	0.443																																					p.C377R		Atlas-SNP	.											.	ZNF223	61	.	0			c.T1129C						.						92	87	88					19																	44571110		2203	4300	6503	SO:0001583	missense	7766	exon5			GACAAGTGTGGGA	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"Zinc fingers, C2H2-type", "-"	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.1129T>C	chr19.hg19:g.44571110T>C	ENSP00000401947:p.Cys377Arg	142.0	0.0		86.0	4.0	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Missense_Mutation	SNP	ENST00000434772.3	hg19	CCDS12635.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.370067	0.82573	.	.	ENSG00000178386	ENST00000434772	D	0.85955	-2.05	2.46	2.46	0.29980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94155	0.8125	H	0.97540	4.025	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93926	0.7210	9	0.87932	D	0	.	9.5423	0.39260	0.0:0.0:0.0:1.0	.	377	Q9UK11	ZN223_HUMAN	R	377	ENSP00000401947:C377R	ENSP00000401947:C377R	C	+	1	0	ZNF223	49262950	1.000000	0.71417	0.269000	0.24586	0.939000	0.58152	5.547000	0.67249	1.118000	0.41863	0.260000	0.18958	TGT	.	.		0.443	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2			C	44571110	T	C	44571110	3	2	91	1	0	0	0	0	1	0	0	0	17792	1696	59	2	1143	2	ZNF223	19	44571110	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	651030	44571110	14557873	637	12711										
ZNF180	7733	hgsc.bcm.edu	37	chr19	44983588	44983588	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caagtaccctgttcctcccgTgtgaagtccacagtcacaat	7	14	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:44983588T>C	ENST00000221327.4	-	4	527	c.246A>G	c.(244-246)acA>acG	p.T82T	ZNF180_ENST00000592529.1_Silent_p.T55T|ZNF180_ENST00000587047.1_Intron|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000586637.1_Missense_Mutation_p.T92A|ZNF180_ENST00000391956.4_Silent_p.T57T	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	82	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				GTTCCTCCCGTGTGAAGTCCA	0.493																																					p.T82T	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.A246G						.						118	110	113					19																	44983588		2203	4300	6503	SO:0001819	synonymous_variant	7733	exon4			CTCCCGTGTGAAG	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.246A>G	chr19.hg19:g.44983588T>C		133.0	0.0		92.0	4.0	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	hg19	CCDS12639.1																																																																																			.	.		0.493	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		C	44983588	T	C	44983588	2	2	91	1	0	0	0	0	0	0	0	1	17763	1683	59	2		2	ZNF180	19	44983588	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	412478	44983588	14145395	638	12712										
CEACAM20	125931	hgsc.bcm.edu	37	chr19	45015089	45015089	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagtgtggcataaacataccTcatagattgactccatgttt	7	9	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:45015089T>C	ENST00000454753.1	-	0	2015							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				TAAACATACCTCATAGATTGA	0.458																																					p.E579G		Atlas-SNP	.											.	CEACAM20	31	.	0			c.A1736G						.						85	86	86					19																	45015089		1874	4110	5984			125931	exon12			CATACCTCATAGA	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Immunoglobulin superfamily / I-set domain containing"	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		chr19.hg19:g.45015089T>C		137.0	0.0		124.0	5.0	NM_001102597		Missense_Mutation	SNP	ENST00000454753.1	hg19																																																																																				.	.		0.458	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444		C	45015089	T	C	45015089	1	2	91	0	1	0	0	0	0	0	0	0	3193	1565	54	2		2	CEACAM20	19	45015089	RNA	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	31501	45015089	14113894	639	12713										
CLPTM1	1209	hgsc.bcm.edu	37	chr19	45493763	45493763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tctacatcctggacaacgagAccaacttcgtggtccaggtc	9	13	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:45493763A>G	ENST00000337392.5	+	10	1393	c.1243A>G	c.(1243-1245)Acc>Gcc	p.T415A	CLPTM1_ENST00000541297.2_Missense_Mutation_p.T401A|CLPTM1_ENST00000546079.1_Missense_Mutation_p.T313A	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	415					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		GGACAACGAGACCAACTTCGT	0.602																																					p.T415A		Atlas-SNP	.											.	CLPTM1	109	.	0			c.A1243G						.						127	117	120					19																	45493763		2203	4300	6503	SO:0001583	missense	1209	exon10			AACGAGACCAACT	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.1243A>G	chr19.hg19:g.45493763A>G	ENSP00000336994:p.Thr415Ala	131.0	0.0		123.0	5.0	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	hg19	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.101075	0.76983	.	.	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	5.22	5.22	0.72569	.	0.052052	0.85682	D	0.000000	T	0.67534	0.2903	M	0.81802	2.56	0.80722	D	1	P;P	0.37352	0.591;0.497	B;B	0.41135	0.158;0.348	T	0.70788	-0.4777	9	0.48119	T	0.1	-40.3779	13.0899	0.59162	1.0:0.0:0.0:0.0	.	401;415	F5H8J3;O96005	.;CLPT1_HUMAN	A	313;401;415;415	.	ENSP00000336994:T415A	T	+	1	0	CLPTM1	50185603	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.654000	0.91092	1.986000	0.57962	0.397000	0.26171	ACC	.	.		0.602	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294		G	45493763	A	G	45493763	3	3	91	1	0	0	0	0	1	0	0	0	3556	275	10	2	1281	2	CLPTM1	19	45493763	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	478674	45493763	13635220	640	12714										
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305720	48305720	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcctgggatcgggcctgggTttgggcctgggatcgggcct	20	10	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:48305720T>A	ENST00000322175.3	-	2	703	c.548A>T	c.(547-549)aAc>aTc	p.N183I	TPRX1_ENST00000543508.1_Missense_Mutation_p.N173I|TPRX1_ENST00000535759.1_Missense_Mutation_p.N280I	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	183	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.N183I(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		cgggcctgggtttgggcctgg	0.657																																					p.N183I	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,NS,carcinoma,0,1	TPRX1	46	.	1	Substitution - Missense(1)	endometrium(1)	c.A548T						.						14	12	13					19																	48305720		1705	3156	4861	SO:0001583	missense	284355	exon2			CCTGGGTTTGGGC		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"Homeoboxes / PRD class"	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.548A>T	chr19.hg19:g.48305720T>A	ENSP00000323455:p.Asn183Ile	89.0	2.0		67.0	7.0	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	hg19	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	a	1.744	-0.491054	0.04322	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.42900	0.96;0.96;0.96	0.303	-0.607	0.11615	.	.	.	.	.	T	0.19248	0.0462	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16217	-1.0410	8	0.30854	T	0.27	.	.	.	.	.	183	Q8N7U7	TPRX1_HUMAN	I	183;280;173	ENSP00000323455:N183I;ENSP00000438832:N280I;ENSP00000438712:N173I	ENSP00000323455:N183I	N	-	2	0	TPRX1	52997532	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.060000	0.01392	-2.335000	0.00629	-2.486000	0.00196	AAC	.	.		0.657	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		A	48305720	T	A	48305720	3	1	91	1	0	0	0	0	1	0	0	0	16437	1725	60	4	691	4	TPRX1	19	48305720	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2811957	48305720	10823263	641	12715										
LMTK3	114783	hgsc.bcm.edu	37	chr19	49001397	49001397	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctctggggacctcagctcccCattctccagcgctttctcct	7	18	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:49001397C>T	ENST00000600059.1	-	11	3156	c.2929G>A	c.(2929-2931)Ggg>Agg	p.G977R	LMTK3_ENST00000270238.3_Missense_Mutation_p.G1006R			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	977	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		CTCAGCTCCCCATTCTCCAGC	0.637																																					p.G1006R		Atlas-SNP	.											.	LMTK3	125	.	0			c.G3016A						.						105	111	109					19																	49001397		1907	4119	6026	SO:0001583	missense	114783	exon12			GCTCCCCATTCTC	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 101"						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.2929G>A	chr19.hg19:g.49001397C>T	ENSP00000472020:p.Gly977Arg	160.0	0.0		122.0	5.0	NM_001080434	Q4G0U1	Missense_Mutation	SNP	ENST00000600059.1	hg19		.	.	.	.	.	.	.	.	.	.	C	5.475	0.272724	0.10349	.	.	ENSG00000142235	ENST00000270238	D	0.88896	-2.44	4.23	3.17	0.36434	.	0.089661	0.39985	N	0.001217	T	0.79064	0.4383	N	0.24115	0.695	0.26218	N	0.979191	B	0.30584	0.286	B	0.21546	0.035	T	0.71794	-0.4485	10	0.66056	D	0.02	.	9.6468	0.39872	0.2092:0.7907:0.0:0.0	.	977	Q96Q04	LMTK3_HUMAN	R	1006	ENSP00000270238:G1006R	ENSP00000270238:G1006R	G	-	1	0	LMTK3	53693209	0.994000	0.37717	0.996000	0.52242	0.034000	0.12701	2.662000	0.46766	0.904000	0.36572	-0.556000	0.04195	GGG	.	.		0.637	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895		T	49001397	C	T	49001397	3	4	91	1	0	0	0	0	1	0	0	0	8869	594	21	3	1473	3	LMTK3	19	49001397	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	695677	49001397	10127586	642	12716										
VSTM1	284415	hgsc.bcm.edu	37	chr19	54545427	54545427	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tatgccaagcatctacctctTggtggattcctcagatgatg	9	10	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:54545427T>C	ENST00000338372.2	-	6	686	c.511A>G	c.(511-513)Aag>Gag	p.K171E	VSTM1_ENST00000376626.1_Missense_Mutation_p.K140E|VSTM1_ENST00000366170.2_Missense_Mutation_p.K83E|VSTM1_ENST00000425006.2_3'UTR	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	171					immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		ATCTACCTCTTGGTGGATTCC	0.507																																					p.K171E		Atlas-SNP	.											.	VSTM1	30	.	0			c.A511G						.						148	152	151					19																	54545427		2203	4300	6503	SO:0001583	missense	284415	exon6			ACCTCTTGGTGGA	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.511A>G	chr19.hg19:g.54545427T>C	ENSP00000343366:p.Lys171Glu	123.0	0.0		92.0	4.0	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Missense_Mutation	SNP	ENST00000338372.2	hg19	CCDS12872.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.057261	0.36277	.	.	ENSG00000189068	ENST00000419106;ENST00000338372;ENST00000376626;ENST00000366170	T;T;T;T	0.44482	2.58;6.81;6.49;0.92	3.24	0.898	0.19264	.	0.497894	0.14973	N	0.287670	T	0.22205	0.0535	L	0.29908	0.895	0.09310	N	0.999995	B;B	0.30584	0.286;0.286	B;B	0.20384	0.029;0.029	T	0.10382	-1.0632	10	0.31617	T	0.26	-4.4272	3.0861	0.06278	0.0:0.1536:0.2457:0.6007	.	140;171	D2DJS4;Q6UX27	.;VSTM1_HUMAN	E	61;171;140;83	ENSP00000409412:K61E;ENSP00000343366:K171E;ENSP00000365813:K140E;ENSP00000444153:K83E	ENSP00000343366:K171E	K	-	1	0	VSTM1	59237239	0.004000	0.15560	0.127000	0.21898	0.003000	0.03518	-0.405000	0.07196	0.130000	0.18549	-0.394000	0.06481	AAG	.	.		0.507	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481		C	54545427	T	C	54545427	3	2	91	1	0	0	0	0	1	0	0	0	17243	1821	63	2	215	2	VSTM1	19	54545427	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	5544030	54545427	4583556	643	12717										
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55597306	55597306	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acttccaggcccgcaacagcAgtgagctgtcggtcaagcag	12	13	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:55597306A>G	ENST00000201647.6	+	15	1539	c.1483A>G	c.(1483-1485)Agt>Ggt	p.S495G	EPS8L1_ENST00000245618.5_Missense_Mutation_p.S368G|EPS8L1_ENST00000588359.1_Missense_Mutation_p.S181G|EPS8L1_ENST00000586329.1_Missense_Mutation_p.S509G|EPS8L1_ENST00000540810.1_Missense_Mutation_p.S431G	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	495	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CCGCAACAGCAGTGAGCTGTC	0.577																																					p.S495G	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.A1483G						.						69	66	67					19																	55597306		2203	4300	6503	SO:0001583	missense	54869	exon15			AACAGCAGTGAGC	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.1483A>G	chr19.hg19:g.55597306A>G	ENSP00000201647:p.Ser495Gly	68.0	0.0		100.0	4.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	hg19	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	A	19.09	3.759217	0.69763	.	.	ENSG00000131037	ENST00000310075;ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.27720	1.65;1.65;1.65	4.43	4.43	0.53597	Src homology-3 domain (4);	0.153050	0.53938	D	0.000041	T	0.31167	0.0788	N	0.05414	-0.055	0.47123	D	0.999324	P;D;B;D	0.69078	0.928;0.995;0.34;0.997	P;D;B;P	0.64410	0.632;0.925;0.153;0.908	T	0.25847	-1.0120	10	0.49607	T	0.09	-19.6723	11.9022	0.52690	1.0:0.0:0.0:0.0	.	509;274;368;495	Q8TE68-3;Q8TE68-4;Q8TE68-2;Q8TE68	.;.;.;ES8L1_HUMAN	G	509;495;431;368;181	ENSP00000201647:S495G;ENSP00000437541:S431G;ENSP00000245618:S368G	ENSP00000201647:S495G	S	+	1	0	EPS8L1	60289118	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	7.850000	0.86915	1.775000	0.52247	0.397000	0.26171	AGT	.	.		0.577	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		G	55597306	A	G	55597306	3	3	91	1	0	0	0	0	1	0	0	0	5197	188	7	2	1589	2	EPS8L1	19	55597306	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1051879	55597306	3531677	644	12718										
PTPRH	5794	hgsc.bcm.edu	37	chr19	55697237	55697237	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggacacacgcacctggaggAgcagcagttcccgcaccgtc	12	15	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:55697237A>G	ENST00000376350.3	-	17	2916	c.2894T>C	c.(2893-2895)cTc>cCc	p.L965P	PTPRH_ENST00000263434.5_Missense_Mutation_p.L787P	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	965	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CACCTGGAGGAGCAGCAGTTC	0.627																																					p.L965P		Atlas-SNP	.											.	PTPRH	139	.	0			c.T2894C						.						88	74	79					19																	55697237		2203	4300	6503	SO:0001583	missense	5794	exon17			TGGAGGAGCAGCA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.2894T>C	chr19.hg19:g.55697237A>G	ENSP00000365528:p.Leu965Pro	100.0	0.0		88.0	5.0	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	hg19	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.247235	0.59103	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	D;D	0.85955	-2.05;-2.05	4.68	4.68	0.58851	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.499063	0.15092	N	0.281037	D	0.94456	0.8216	H	0.96080	3.765	0.24885	N	0.992207	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.987	D	0.88001	0.2756	10	0.87932	D	0	.	12.0896	0.53717	1.0:0.0:0.0:0.0	.	787;965	C9JCH2;Q9HD43	.;PTPRH_HUMAN	P	965;787	ENSP00000365528:L965P;ENSP00000263434:L787P	ENSP00000263434:L787P	L	-	2	0	PTPRH	60389049	0.997000	0.39634	0.005000	0.12908	0.122000	0.20287	5.461000	0.66699	2.121000	0.65114	0.529000	0.55759	CTC	.	.		0.627	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			G	55697237	A	G	55697237	3	3	91	1	0	0	0	0	1	0	0	0	12818	304	11	2	469	2	PTPRH	19	55697237	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	99931	55697237	3431746	645	12719										
ZNF470	388566	hgsc.bcm.edu	37	chr19	57088312	57088312	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tactcttattgaaaaaagagAtcactctaacaaatctggga	6	7	4	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:57088312A>G	ENST00000330619.8	+	6	1201	c.515A>G	c.(514-516)gAt>gGt	p.D172G	ZNF470_ENST00000391709.3_Missense_Mutation_p.D172G|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	172					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		GAAAAAAGAGATCACTCTAAC	0.323																																					p.D172G		Atlas-SNP	.											.	ZNF470	103	.	0			c.A515G						.						50	52	51					19																	57088312		2203	4300	6503	SO:0001583	missense	388566	exon6			AAAGAGATCACTC	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.515A>G	chr19.hg19:g.57088312A>G	ENSP00000333223:p.Asp172Gly	156.0	0.0		132.0	6.0	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	hg19	CCDS33122.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.171175	0.00315	.	.	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.06294	3.32;3.32	3.2	2.18	0.27775	.	.	.	.	.	T	0.03178	0.0093	N	0.08118	0	0.09310	N	1	B	0.24186	0.099	B	0.14578	0.011	T	0.44892	-0.9298	9	0.32370	T	0.25	.	6.7702	0.23589	0.8826:0.0:0.1174:0.0	.	172	Q6ECI4	ZN470_HUMAN	G	172	ENSP00000375590:D172G;ENSP00000333223:D172G	ENSP00000333223:D172G	D	+	2	0	ZNF470	61780124	0.001000	0.12720	0.001000	0.08648	0.032000	0.12392	1.101000	0.31037	0.620000	0.30215	-0.351000	0.07748	GAT	.	.		0.323	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		G	57088312	A	G	57088312	3	3	91	1	0	0	0	0	1	0	0	0	17944	333	12	2	529	2	ZNF470	19	57088312	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1391075	57088312	2040671	646	12720										
ZIM2	23619	hgsc.bcm.edu	37	chr19	57286250	57286250	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtcacaacactggcaggctcTctctccaacgtagtcatgtt	8	13	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:57286250T>C	ENST00000391708.3	-	12	1932	c.1390A>G	c.(1390-1392)Aga>Gga	p.R464G	AC006115.3_ENST00000595954.1_RNA|AC006115.3_ENST00000597946.1_RNA|AC006115.3_ENST00000594400.1_RNA|ZIM2_ENST00000593711.1_Missense_Mutation_p.R464G|ZIM2_ENST00000221722.5_Missense_Mutation_p.R464G|ZIM2_ENST00000599935.1_Missense_Mutation_p.R464G|ZIM2_ENST00000601070.1_Missense_Mutation_p.R464G	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	464					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		TGGCAGGCTCTCTCTCCAACG	0.478																																					p.R464G		Atlas-SNP	.											.	ZIM2	511	.	0			c.A1390G						.						88	70	76					19																	57286250		2203	4300	6503	SO:0001583	missense	23619	exon11			AGGCTCTCTCTCC	AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"Zinc fingers, C2H2-type"	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.1390A>G	chr19.hg19:g.57286250T>C	ENSP00000375589:p.Arg464Gly	86.0	0.0		79.0	4.0	NM_015363	Q2M3K1	Missense_Mutation	SNP	ENST00000391708.3	hg19	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.288519	0.23478	.	.	ENSG00000198300	ENST00000391708;ENST00000221722	T;T	0.05081	3.5;3.5	4.96	2.8	0.32819	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08846	0.0219	L	0.52823	1.66	.	.	.	P	0.50272	0.933	B	0.42692	0.395	T	0.13308	-1.0514	8	0.87932	D	0	.	10.506	0.44834	0.0:0.0:0.5025:0.4975	.	464	Q9NZV7	ZIM2_HUMAN	G	464	ENSP00000375589:R464G;ENSP00000221722:R464G	ENSP00000221722:R464G	R	-	1	2	ZIM2	61978062	0.689000	0.27690	0.012000	0.15200	0.373000	0.29922	2.802000	0.47916	0.341000	0.23771	-0.316000	0.08728	AGA	.	.		0.478	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2			C	57286250	T	C	57286250	3	2	91	1	0	0	0	0	1	0	0	0	17699	1559	54	2	197	2	ZIM2	19	57286250	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	197938	57286250	1842733	647	12721										
ZNF543	125919	hgsc.bcm.edu	37	chr19	57839824	57839824	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtttcattcgacactacatcAtccacacgggagagaagccc	8	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:57839824A>G	ENST00000321545.4	+	4	1339	c.994A>G	c.(994-996)Atc>Gtc	p.I332V		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	332					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		ACACTACATCATCCACACGGG	0.512																																					p.I332V		Atlas-SNP	.											.	ZNF543	61	.	0			c.A994G						.						74	75	75					19																	57839824		2203	4300	6503	SO:0001583	missense	125919	exon4			TACATCATCCACA	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"Zinc fingers, C2H2-type", "-"	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.994A>G	chr19.hg19:g.57839824A>G	ENSP00000322545:p.Ile332Val	98.0	0.0		67.0	4.0	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	hg19	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	A	9.782	1.175449	0.21704	.	.	ENSG00000178229	ENST00000321545	T	0.16324	2.35	3.0	1.9	0.25705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10208	0.0250	N	0.17379	0.485	0.19945	N	0.999942	B	0.21225	0.053	B	0.28849	0.095	T	0.34976	-0.9807	9	0.49607	T	0.09	.	3.0895	0.06289	0.6653:0.0:0.1218:0.2128	.	332	Q08ER8	ZN543_HUMAN	V	332	ENSP00000322545:I332V	ENSP00000322545:I332V	I	+	1	0	ZNF543	62531636	0.000000	0.05858	0.970000	0.41538	0.890000	0.51754	1.146000	0.31589	0.310000	0.22990	0.459000	0.35465	ATC	.	.		0.512	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		G	57839824	A	G	57839824	3	3	91	1	0	0	0	0	1	0	0	0	17991	217	8	2	1008	2	ZNF543	19	57839824	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	553574	57839824	1289159	648	12722										
A1BG	1	hgsc.bcm.edu	37	chr19	58863849	58863849	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cccgcagcacacctcggcacActgctgttgttttcaggccg	10	16	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:58863849A>G	ENST00000263100.3	-	4	474	c.413T>C	c.(412-414)gTg>gCg	p.V138A	A1BG-AS1_ENST00000595302.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000599728.1_RNA	NM_130786.3	NP_570602.2	P04217	A1BG_HUMAN	alpha-1-B glycoprotein	138	Ig-like V-type 2.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)	15		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)		ACCTCGGCACACTGCTGTTGT	0.632																																					p.V138A		Atlas-SNP	.											.	A1BG	40	.	0			c.T413C						.						102	107	105					19																	58863849		2203	4300	6503	SO:0001583	missense	1	exon4			CGGCACACTGCTG		CCDS12976.1	19q13.43	2013-10-15			ENSG00000121410	ENSG00000121410		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5	protein-coding gene	gene with protein product		138670				2591067	Standard	NM_130786		Approved		uc002qsd.4	P04217	OTTHUMG00000183507	ENST00000263100.3:c.413T>C	chr19.hg19:g.58863849A>G	ENSP00000263100:p.Val138Ala	67.0	0.0		78.0	4.0	NM_130786	A8K052|Q68CK0|Q8IYJ6|Q96P39	Missense_Mutation	SNP	ENST00000263100.3	hg19	CCDS12976.1	.	.	.	.	.	.	.	.	.	.	A	7.800	0.713499	0.15306	.	.	ENSG00000121410	ENST00000263100;ENST00000453054	T	0.09538	2.97	3.39	-0.268	0.12934	Immunoglobulin-like fold (1);	1.307360	0.05638	N	0.582894	T	0.12561	0.0305	L	0.54323	1.7	0.09310	N	1	B	0.22146	0.065	B	0.29598	0.104	T	0.46303	-0.9201	10	0.15499	T	0.54	.	9.0994	0.36658	0.3965:0.6035:0.0:0.0	.	138	P04217	A1BG_HUMAN	A	138;16	ENSP00000263100:V138A	ENSP00000263100:V138A	V	-	2	0	A1BG	63555661	0.000000	0.05858	0.131000	0.22000	0.017000	0.09413	-0.751000	0.04803	-0.125000	0.11703	0.460000	0.39030	GTG	.	.		0.632	A1BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466930.1	NM_130786		G	58863849	A	G	58863849	3	3	91	1	0	0	0	0	1	0	0	0	1	159	6	2	1094	2	A1BG	19	58863849	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1024025	58863849	265134	649	12723										
CHGB	1114	hgsc.bcm.edu	37	chr20	5903053	5903053	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgaagtaagattgttaagagAcccagctgatgcctcggaag	12	7	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:5903053A>G	ENST00000378961.4	+	4	467	c.263A>G	c.(262-264)gAc>gGc	p.D88G		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	88						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						TTGTTAAGAGACCCAGCTGAT	0.473																																					p.D88G		Atlas-SNP	.											.	CHGB	112	.	0			c.A263G						.						58	59	59					20																	5903053		2203	4300	6503	SO:0001583	missense	1114	exon4			TAAGAGACCCAGC		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.263A>G	chr20.hg19:g.5903053A>G	ENSP00000368244:p.Asp88Gly	121.0	0.0		116.0	5.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	hg19	CCDS13092.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.376473	0.61735	.	.	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.02916	4.11;4.11	5.77	5.77	0.91146	.	0.290166	0.31082	N	0.008285	T	0.09468	0.0233	M	0.69823	2.125	0.31460	N	0.669675	D	0.56746	0.977	P	0.54889	0.763	T	0.02437	-1.1159	10	0.87932	D	0	-29.2125	10.1671	0.42886	0.9251:0.0:0.0749:0.0	.	88	P05060	SCG1_HUMAN	G	88;68	ENSP00000368244:D88G;ENSP00000416643:D68G	ENSP00000368244:D88G	D	+	2	0	CHGB	5851053	1.000000	0.71417	0.998000	0.56505	0.444000	0.32077	6.353000	0.73032	2.197000	0.70478	0.533000	0.62120	GAC	.	.		0.473	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		G	5903053	A	G	5903053	3	3	91	1	0	0	0	0	1	0	0	0	3341	275	10	2	277	2	CHGB	20	5903053	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10		5903053	57122467	650	12724										
SPTLC3	55304	hgsc.bcm.edu	37	chr20	13071736	13071736	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taattttatgtgcaggcaccTtggataagcacaaggagttg	11	6	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:13071736T>A	ENST00000399002.2	+	5	887	c.613T>A	c.(613-615)Ttg>Atg	p.L205M	SPTLC3_ENST00000378194.4_Missense_Mutation_p.L205M	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	205					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						TGCAGGCACCTTGGATAAGCA	0.428																																					p.L205M		Atlas-SNP	.											.	SPTLC3	78	.	0			c.T613A						.						170	169	169					20																	13071736		1900	4126	6026	SO:0001583	missense	55304	exon5			GGCACCTTGGATA	AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"chromosome 20 open reading frame 38", "serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.613T>A	chr20.hg19:g.13071736T>A	ENSP00000381968:p.Leu205Met	201.0	0.0		158.0	53.0	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Missense_Mutation	SNP	ENST00000399002.2	hg19	CCDS13115.2	.	.	.	.	.	.	.	.	.	.	T	9.789	1.177390	0.21787	.	.	ENSG00000172296	ENST00000399002;ENST00000378194	D;D	0.90676	-2.71;-2.71	5.44	-1.46	0.08800	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.363501	0.25823	N	0.028065	T	0.80248	0.4588	L	0.33485	1.01	0.37988	D	0.933822	B	0.17667	0.023	B	0.28553	0.091	T	0.62300	-0.6883	10	0.27082	T	0.32	-6.3789	1.2822	0.02043	0.2561:0.3455:0.1195:0.2789	.	205	Q9NUV7	SPTC3_HUMAN	M	205	ENSP00000381968:L205M;ENSP00000367436:L205M	ENSP00000367436:L205M	L	+	1	2	SPTLC3	13019736	0.969000	0.33509	0.991000	0.47740	0.418000	0.31294	0.472000	0.22116	0.073000	0.16731	0.524000	0.50904	TTG	.	.		0.428	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327		A	13071736	T	A	13071736	3	1	91	1	0	0	0	0	1	0	0	0	15140	1606	56	4	631	4	SPTLC3	20	13071736	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	7168683	13071736	49953784	651	12725										
MACROD2	140733	hgsc.bcm.edu	37	chr20	15967784	15967784	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccattaacagaggaccaagaAgaaaaagaaggtgaaaaagg	11	5	0	5			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:15967784A>G	ENST00000310348.4	+	15	1134	c.1134A>G	c.(1132-1134)gaA>gaG	p.E378E	MACROD2_ENST00000402914.1_Silent_p.E143E|MACROD2_ENST00000217246.4_Silent_p.E378E|MACROD2_ENST00000378058.3_Silent_p.E143E|MACROD2_ENST00000407045.3_Silent_p.E29E			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	378	Glu-rich.				brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				AGGACCAAGAAGAAAAAGAAG	0.383																																					p.E378E		Atlas-SNP	.											.	MACROD2	34	.	0			c.A1134G						.						113	111	112					20																	15967784		2203	4300	6503	SO:0001819	synonymous_variant	140733	exon15			CCAAGAAGAAAAA	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"chromosome 20 open reading frame 133"	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.1134A>G	chr20.hg19:g.15967784A>G		91.0	0.0		78.0	4.0	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Silent	SNP	ENST00000310348.4	hg19	CCDS13120.2																																																																																			.	.		0.383	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676		G	15967784	A	G	15967784	2	3	91	1	0	0	0	0	0	0	0	1	9155	69	3	2		2	MACROD2	20	15967784	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2896048	15967784	47057736	652	12726										
GZF1	64412	hgsc.bcm.edu	37	chr20	23345920	23345920	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaagcagggccggaggaggaAgaggaggaggaggaggagga	23	3	0	1	rs547594353|rs146870841	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:23345920A>G	ENST00000338121.5	+	2	977	c.900A>G	c.(898-900)gaA>gaG	p.E300E	GZF1_ENST00000544236.1_Intron|GZF1_ENST00000542987.1_Intron|GZF1_ENST00000461789.1_3'UTR|GZF1_ENST00000377051.2_Silent_p.E300E			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	300					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					Cggaggaggaagaggaggagg	0.527																																					p.E300E		Atlas-SNP	.											.,1	GZF1	61	.	0			c.A900G						.	A		0,4406		0,0,2203	48	53	52		900	-8	0	20	dbSNP_134	52	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous	GZF1	NM_022482.3		0,3,6500	GG,GA,AA		0.0349,0.0,0.0231		300/712	23345920	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	64412	exon1			GGAGGAAGAGGAG	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	15808	protein-coding gene	gene with protein product		613842	"zinc finger protein 336"	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.900A>G	chr20.hg19:g.23345920A>G		69.0	0.0		74.0	3.0	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Silent	SNP	ENST00000338121.5	hg19	CCDS13151.1																																																																																			.	A|1.000;G|0.000		0.527	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482		G	23345920	A	G	23345920	2	3	91	1	0	0	0	0	0	0	0	1	6923	69	3	2		2	GZF1	20	23345920	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	7378136	23345920	39679600	653	12727										
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36851965	36851965	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccccccaggggggtcggccTtctcgaattcctcgatggaa	12	14	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:36851965T>C	ENST00000279024.4	-	9	2514	c.2243A>G	c.(2242-2244)aAg>aGg	p.K748R		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	748										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GGGGTCGGCCTTCTCGAATTC	0.612																																					p.K748R		Atlas-SNP	.											.	KIAA1755	145	.	0			c.A2243G						.						50	48	49					20																	36851965		2203	4300	6503	SO:0001583	missense	85449	exon9			TCGGCCTTCTCGA	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2243A>G	chr20.hg19:g.36851965T>C	ENSP00000279024:p.Lys748Arg	94.0	0.0		82.0	4.0	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	T	4.279	0.050887	0.08243	.	.	ENSG00000149633	ENST00000279024;ENST00000373398;ENST00000435901	T;T	0.22945	3.34;1.93	4.46	3.36	0.38483	.	0.130493	0.34906	N	0.003596	T	0.15869	0.0382	L	0.29908	0.895	0.32929	D	0.516869	B	0.14012	0.009	B	0.09377	0.004	T	0.17992	-1.0351	10	0.20519	T	0.43	.	8.0775	0.30724	0.0:0.0979:0.0:0.9021	.	748	Q5JYT7	K1755_HUMAN	R	748;256;47	ENSP00000279024:K748R;ENSP00000393503:K47R	ENSP00000279024:K748R	K	-	2	0	KIAA1755	36285379	0.998000	0.40836	0.982000	0.44146	0.031000	0.12232	1.558000	0.36309	0.754000	0.32968	0.418000	0.28097	AAG	.	.		0.612	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		C	36851965	T	C	36851965	3	2	91	1	0	0	0	0	1	0	0	0	8266	1609	56	2	1383	2	KIAA1755	20	36851965	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	13506045	36851965	26173555	654	12728										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44685068	44685068	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctccccgtccccaggggaggAgcctgagggggaaggggaga	19	11	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:44685068A>G	ENST00000454036.2	+	23	3093	c.3044A>G	c.(3043-3045)gAg>gGg	p.E1015G	SLC12A5_ENST00000243964.3_Missense_Mutation_p.E992G	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	1015					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCAGGGGAGGAGCCTGAGGGG	0.607																																					p.E1015G		Atlas-SNP	.											.	SLC12A5	181	.	0			c.A3044G						.						39	37	38					20																	44685068		2203	4300	6503	SO:0001583	missense	57468	exon23			GGGAGGAGCCTGA	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.3044A>G	chr20.hg19:g.44685068A>G	ENSP00000387694:p.Glu1015Gly	80.0	0.0		87.0	4.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	hg19	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	A	7.247	0.602362	0.13939	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	T;T	0.42131	0.98;0.98	5.14	5.14	0.70334	.	0.375027	0.27105	N	0.020908	T	0.24586	0.0596	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.10450	0.001;0.005	T	0.06935	-1.0799	10	0.24483	T	0.36	.	14.2969	0.66318	1.0:0.0:0.0:0.0	.	1015;992	Q9H2X9;Q9H2X9-2	S12A5_HUMAN;.	G	1015;992	ENSP00000387694:E1015G;ENSP00000243964:E992G	ENSP00000243964:E992G	E	+	2	0	SLC12A5	44118475	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	4.682000	0.61671	2.155000	0.67459	0.459000	0.35465	GAG	.	.		0.607	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			G	44685068	A	G	44685068	3	3	91	1	0	0	0	0	1	0	0	0	14401	304	11	2	3190	2	SLC12A5	20	44685068	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	7833103	44685068	18340452	655	12729										
STAU1	6780	hgsc.bcm.edu	37	chr20	47734536	47734536	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtgtgatgtccttgactaacTcctacagcctgggcgacctc	10	13	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:47734536T>C	ENST00000371856.2	-	11	1697	c.1287A>G	c.(1285-1287)ggA>ggG	p.G429G	STAU1_ENST00000371802.1_Silent_p.G354G|STAU1_ENST00000371828.3_Silent_p.G354G|STAU1_ENST00000347458.5_Silent_p.G348G|STAU1_ENST00000340954.7_Silent_p.G348G|STAU1_ENST00000360426.4_Silent_p.G348G|STAU1_ENST00000371792.1_Silent_p.G346G	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	429					intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			CTTGACTAACTCCTACAGCCT	0.522																																					p.G429G		Atlas-SNP	.											.	STAU1	54	.	0			c.A1287G						.						126	123	124					20																	47734536		2203	4300	6503	SO:0001819	synonymous_variant	6780	exon11			ACTAACTCCTACA		CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 150"	601716	"staufen (Drosophila, RNA-binding protein)", "staufen, RNA binding protein (Drosophila)", "staufen, RNA binding protein, homolog 1 (Drosophila)"	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.1287A>G	chr20.hg19:g.47734536T>C		113.0	0.0		86.0	5.0	NM_017453	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Silent	SNP	ENST00000371856.2	hg19	CCDS13414.1																																																																																			.	.		0.522	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453		C	47734536	T	C	47734536	2	2	91	1	0	0	0	0	0	0	0	1	15287	1538	54	2		2	STAU1	20	47734536	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3049468	47734536	15290984	656	12730										
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51872705	51872705	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagtcactggctggccaacgTcaagtaccagcttaggaaaa	10	11	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:51872705T>C	ENST00000371497.5	+	2	3595	c.2708T>C	c.(2707-2709)gTc>gCc	p.V903A	TSHZ2_ENST00000603338.2_Missense_Mutation_p.V900A|TSHZ2_ENST00000329613.6_Missense_Mutation_p.V900A|RP4-678D15.1_ENST00000606932.1_RNA	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	903					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			CTGGCCAACGTCAAGTACCAG	0.488																																					p.V903A		Atlas-SNP	.											.	TSHZ2	209	.	0			c.T2708C						.						70	69	70					20																	51872705		2203	4300	6503	SO:0001583	missense	128553	exon2			CCAACGTCAAGTA	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2708T>C	chr20.hg19:g.51872705T>C	ENSP00000360552:p.Val903Ala	136.0	0.0		108.0	5.0	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.127114	0.77549	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.26810	1.72;1.71	5.8	5.8	0.92144	Homeobox (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.46425	0.1392	L	0.49126	1.545	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	T	0.42155	-0.9468	10	0.87932	D	0	-18.2384	16.1354	0.81481	0.0:0.0:0.0:1.0	.	903	Q9NRE2	TSH2_HUMAN	A	903;900;429	ENSP00000360552:V903A;ENSP00000333114:V900A	ENSP00000333114:V900A	V	+	2	0	TSHZ2	51306112	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.693000	0.84214	2.206000	0.71126	0.523000	0.50628	GTC	.	.		0.488	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		C	51872705	T	C	51872705	3	2	91	1	0	0	0	0	1	0	0	0	16639	1667	58	2	2714	2	TSHZ2	20	51872705	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	4138169	51872705	11152815	657	12731										
CASS4	57091	hgsc.bcm.edu	37	chr20	55025710	55025710	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagccccaagaaggcaggacTccatcccccagacagccaag	9	17	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:55025710T>C	ENST00000360314.3	+	5	842	c.617T>C	c.(616-618)cTc>cCc	p.L206P	CASS4_ENST00000371336.3_Missense_Mutation_p.L206P|CASS4_ENST00000434344.1_Missense_Mutation_p.L206P	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	206					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						AAGGCAGGACTCCATCCCCCA	0.483																																					p.L206P		Atlas-SNP	.											.	CASS4	121	.	0			c.T617C						.						96	71	80					20																	55025710		2203	4300	6503	SO:0001583	missense	57091	exon4			CAGGACTCCATCC	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"Cas scaffolding proteins"	15878	protein-coding gene	gene with protein product	"HEF-like protein", "HEF1-Efs-p130Cas-like"		"chromosome 20 open reading frame 32"	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.617T>C	chr20.hg19:g.55025710T>C	ENSP00000353462:p.Leu206Pro	120.0	0.0		91.0	5.0	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	hg19	CCDS33492.1	.	.	.	.	.	.	.	.	.	.	T	9.102	1.004418	0.19199	.	.	ENSG00000087589	ENST00000360314;ENST00000371336;ENST00000434344	T;T;T	0.20881	2.54;2.54;2.04	4.99	1.41	0.22369	.	1.471490	0.04517	N	0.383859	T	0.38374	0.1038	M	0.63428	1.95	0.18873	N	0.999989	D;D;D;B	0.71674	0.991;0.994;0.998;0.016	P;P;D;B	0.63381	0.556;0.906;0.914;0.008	T	0.09228	-1.0684	10	0.34782	T	0.22	-1.8146	5.496	0.16804	0.0:0.0939:0.3955:0.5106	.	152;206;206;206	B4DII4;Q9NQ75-3;Q9NQ75-2;Q9NQ75	.;.;.;CASS4_HUMAN	P	206	ENSP00000353462:L206P;ENSP00000360387:L206P;ENSP00000410027:L206P	ENSP00000353462:L206P	L	+	2	0	CASS4	54459117	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	0.145000	0.16157	0.062000	0.16340	0.533000	0.62120	CTC	.	.		0.483	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		C	55025710	T	C	55025710	3	2	91	1	0	0	0	0	1	0	0	0	2685	1551	54	2	631	2	CASS4	20	55025710	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3153005	55025710	7999810	658	12732										
EDN3	1908	hgsc.bcm.edu	37	chr20	57896094	57896094	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agacggtgccctatggactgTccaactacagaggaagcttc	11	11	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:57896094T>C	ENST00000337938.2	+	3	774	c.388T>C	c.(388-390)Tcc>Ccc	p.S130P	EDN3_ENST00000371025.3_Missense_Mutation_p.S130P|EDN3_ENST00000395654.3_Missense_Mutation_p.S130P|EDN3_ENST00000311585.7_Missense_Mutation_p.S130P|EDN3_ENST00000371028.2_Missense_Mutation_p.S130P	NM_207034.1	NP_996917.1	P14138	EDN3_HUMAN	endothelin 3	130					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inositol phosphate-mediated signaling (GO:0048016)|melanocyte differentiation (GO:0030318)|multicellular organismal development (GO:0007275)|neural crest cell migration (GO:0001755)|neuron differentiation (GO:0030182)|neutrophil chemotaxis (GO:0030593)|peptide hormone secretion (GO:0030072)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|regulation of developmental pigmentation (GO:0048070)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|signal transduction (GO:0007165)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	19	all_lung(29;0.0115)					CTATGGACTGTCCAACTACAG	0.612																																					p.S130P		Atlas-SNP	.											.	EDN3	83	.	0			c.T388C						.						89	77	81					20																	57896094		2203	4300	6503	SO:0001583	missense	1908	exon3			GGACTGTCCAACT	X52001	CCDS13477.1, CCDS13478.1, CCDS13479.1	20q13.2-q13.3	2013-02-26			ENSG00000124205	ENSG00000124205		"Endogenous ligands"	3178	protein-coding gene	gene with protein product		131242					Standard	NM_000114		Approved	ET3	uc002yaq.3	P14138	OTTHUMG00000032867	ENST00000337938.2:c.388T>C	chr20.hg19:g.57896094T>C	ENSP00000337128:p.Ser130Pro	118.0	0.0		95.0	4.0	NM_207034	E1P5I5|Q03229|Q7Z6D2|Q9UGT7	Missense_Mutation	SNP	ENST00000337938.2	hg19	CCDS13477.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.029868	0.75504	.	.	ENSG00000124205	ENST00000337938;ENST00000311585;ENST00000371028;ENST00000371025;ENST00000395654	D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	D	0.91181	0.7222	M	0.62723	1.935	0.38107	D	0.93745	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.72338	0.977;0.965;0.949;0.961	D	0.92226	0.5788	10	0.54805	T	0.06	-41.3052	11.1433	0.48415	0.0:0.0:0.0:1.0	.	130;130;130;130	P14138-2;Q7Z6D2;P14138;Q4FAT2	.;.;EDN3_HUMAN;.	P	130	ENSP00000337128:S130P;ENSP00000311854:S130P;ENSP00000360067:S130P;ENSP00000360064:S130P;ENSP00000379015:S130P	ENSP00000311854:S130P	S	+	1	0	EDN3	57329489	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	2.877000	0.48506	1.951000	0.56629	0.459000	0.35465	TCC	.	.		0.612	EDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079919.2	NM_000114		C	57896094	T	C	57896094	3	2	91	1	0	0	0	0	1	0	0	0	4920	1667	58	2	398	2	EDN3	20	57896094	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	2870384	57896094	5129426	659	12733										
COL9A3	1299	hgsc.bcm.edu	37	chr20	61460123	61460123	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cccttgtccccagggcatgcCgggcaaggacggccagaatg	14	14	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:61460123C>T	ENST00000343916.3	+	18	911	c.908C>T	c.(907-909)cCg>cTg	p.P303L		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	303	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					CAGGGCATGCCGGGCAAGGAC	0.682																																					p.P303L		Atlas-SNP	.											COL9A3,right_lower_lobe,carcinoma,0,1	COL9A3	70	.	0			c.C908T						.						49	46	47					20																	61460123		2201	4299	6500	SO:0001583	missense	1299	exon18			GCATGCCGGGCAA	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2219	protein-coding gene	gene with protein product	"collagen type IX proteoglycan"	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.908C>T	chr20.hg19:g.61460123C>T	ENSP00000341640:p.Pro303Leu	59.0	0.0		56.0	4.0	NM_001853	Q13681|Q9H4G9|Q9UPE2	Missense_Mutation	SNP	ENST00000343916.3	hg19	CCDS13505.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.121043	0.77436	.	.	ENSG00000092758	ENST00000343916	D	0.97066	-4.23	3.93	3.93	0.45458	.	0.119276	0.64402	D	0.000019	D	0.97870	0.9300	M	0.82433	2.59	0.80722	D	1	D	0.76494	0.999	P	0.57283	0.817	D	0.98387	1.0561	10	0.66056	D	0.02	.	15.0251	0.71663	0.0:1.0:0.0:0.0	.	303	Q14050	CO9A3_HUMAN	L	303	ENSP00000341640:P303L	ENSP00000341640:P303L	P	+	2	0	COL9A3	60930568	0.989000	0.36119	0.995000	0.50966	0.740000	0.42216	2.883000	0.48554	2.200000	0.70718	0.448000	0.29417	CCG	.	.		0.682	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853		T	61460123	C	T	61460123	3	4	91	1	0	0	0	0	1	0	0	0	3711	652	23	1	978	1	COL9A3	20	61460123	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	3564029	61460123	1565397	660	12734										
YTHDF1	54915	hgsc.bcm.edu	37	chr20	61835049	61835049	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtggtgaggtatggaatcggAgggtcccctgcagtagacca	16	8	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:61835049A>G	ENST00000370339.3	-	4	584	c.243T>C	c.(241-243)ccT>ccC	p.P81P	YTHDF1_ENST00000370333.4_Silent_p.P31P|YTHDF1_ENST00000370334.4_Intron	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	81							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						ATGGAATCGGAGGGTCCCCTG	0.557																																					p.P81P		Atlas-SNP	.											.	YTHDF1	66	.	0			c.T243C						.						104	109	107					20																	61835049		2203	4300	6503	SO:0001819	synonymous_variant	54915	exon4			AATCGGAGGGTCC	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"YTH domain family 1"	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.243T>C	chr20.hg19:g.61835049A>G		124.0	0.0		102.0	5.0	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Silent	SNP	ENST00000370339.3	hg19	CCDS13511.1																																																																																			.	.		0.557	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798		G	61835049	A	G	61835049	2	3	91	1	0	0	0	0	0	0	0	1	17513	291	11	2		2	YTHDF1	20	61835049	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	374926	61835049	1190471	661	12735										
OPRL1	4987	hgsc.bcm.edu	37	chr20	62729930	62729930	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cagccgagcagcgagactgcCgtggccattctgcgcttctg	13	14	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:62729930C>T	ENST00000349451.3	+	6	1303	c.891C>T	c.(889-891)gcC>gcT	p.A297A	OPRL1_ENST00000355631.4_Silent_p.A297A|OPRL1_ENST00000336866.2_Silent_p.A297A	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	297					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavior (GO:0007610)|opioid receptor signaling pathway (GO:0038003)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|nociceptin receptor activity (GO:0001626)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					GCGAGACTGCCGTGGCCATTC	0.632																																					p.A297A		Atlas-SNP	.											.	OPRL1	47	.	0			c.C891T						.						81	68	73					20																	62729930		2201	4295	6496	SO:0001819	synonymous_variant	4987	exon4			GACTGCCGTGGCC		CCDS13556.1	20q13.33	2012-08-08			ENSG00000125510	ENSG00000125510		"GPCR / Class A : Opioid receptors"	8155	protein-coding gene	gene with protein product	"LC132 receptor-like", "orphanin FQ receptor", "kappa3-related opioid receptor"	602548				8137918	Standard	NM_000913		Approved	NOCIR, ORL1, OOR, KOR-3	uc021wgs.1	P41146	OTTHUMG00000033027	ENST00000349451.3:c.891C>T	chr20.hg19:g.62729930C>T		104.0	0.0		96.0	38.0	NM_000913	Q8TD34|Q8WYH9|Q9H4K4	Silent	SNP	ENST00000349451.3	hg19	CCDS13556.1																																																																																			.	.		0.632	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647		T	62729930	C	T	62729930	2	4	91	1	0	0	0	0	0	0	0	1	10895	639	23	1		1	OPRL1	20	62729930	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	894881	62729930	295590	662	12736										
CXADR	1525	hgsc.bcm.edu	37	chr21	18933790	18933790	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaaaggaagttcatcacgatAtcaggtaattaagtgagaca	9	5	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:18933790A>G	ENST00000284878.7	+	6	1577	c.829A>G	c.(829-831)Atc>Gtc	p.I277V	CXADR_ENST00000400166.1_Intron|CXADR_ENST00000356275.6_Intron|CXADR_ENST00000306618.10_Missense_Mutation_p.I236V|CXADR_ENST00000400165.1_Intron|CXADR_ENST00000400169.1_Missense_Mutation_p.I277V	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	277					actin cytoskeleton reorganization (GO:0031532)|AV node cell to bundle of His cell communication (GO:0086067)|blood coagulation (GO:0007596)|cardiac muscle fiber development (GO:0048739)|cell-cell junction organization (GO:0045216)|defense response to virus (GO:0051607)|epithelial structure maintenance (GO:0010669)|gamma-delta T cell activation (GO:0046629)|germ cell migration (GO:0008354)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|homotypic cell-cell adhesion (GO:0034109)|leukocyte migration (GO:0050900)|mitochondrion organization (GO:0007005)|neutrophil chemotaxis (GO:0030593)|regulation of immune response (GO:0050776)|transepithelial transport (GO:0070633)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|adherens junction (GO:0005912)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|filopodium (GO:0030175)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|cell adhesion molecule binding (GO:0050839)|connexin binding (GO:0071253)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|virus receptor activity (GO:0001618)			endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		TCATCACGATATCAGGTAATT	0.363																																					p.I277V		Atlas-SNP	.											.	CXADR	44	.	0			c.A829G						.						71	70	71					21																	18933790		2203	4300	6503	SO:0001583	missense	1525	exon6			CACGATATCAGGT	Y07593	CCDS33519.1, CCDS56204.1, CCDS56205.1, CCDS56206.1, CCDS56207.1	21q21.1	2013-01-29			ENSG00000154639	ENSG00000154639		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2559	protein-coding gene	gene with protein product		602621				9036860, 9096397	Standard	NM_001338		Approved	CAR	uc002yki.3	P78310	OTTHUMG00000074508	ENST00000284878.7:c.829A>G	chr21.hg19:g.18933790A>G	ENSP00000284878:p.Ile277Val	240.0	0.0		179.0	11.0	NM_001207066	B2R8V8|B7WPI3|D3YHP0|O00694|Q8WWT6|Q8WWT7|Q8WWT8|Q9UKV4	Missense_Mutation	SNP	ENST00000284878.7	hg19	CCDS33519.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.983826	0.74474	.	.	ENSG00000154639	ENST00000284878;ENST00000400169;ENST00000306618	T;T;D	0.91237	-1.23;-1.26;-2.81	4.49	4.49	0.54785	.	0.045406	0.85682	D	0.000000	D	0.93966	0.8068	M	0.82517	2.595	0.53688	D	0.999978	D;D	0.65815	0.992;0.995	P;P	0.59761	0.729;0.863	D	0.93084	0.6494	10	0.30854	T	0.27	.	13.2808	0.60212	1.0:0.0:0.0:0.0	.	277;277	B7WPI3;P78310	.;CXAR_HUMAN	V	277;277;236	ENSP00000284878:I277V;ENSP00000383033:I277V;ENSP00000303395:I236V	ENSP00000284878:I277V	I	+	1	0	CXADR	17855661	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.030000	0.88816	1.799000	0.52666	0.482000	0.46254	ATC	.	.		0.363	CXADR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000158209.1			G	18933790	A	G	18933790	3	3	91	1	0	0	0	0	1	0	0	0	4078	449	16	2	851	2	CXADR	21	18933790	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10		18933790	29196105	663	12737										
KRTAP26-1	388818	hgsc.bcm.edu	37	chr21	31692292	31692292	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cgatggaggtgagaggaataTggcgggaggttctgagagat	19	3	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:31692292T>G	ENST00000360542.3	-	1	315	c.62A>C	c.(61-63)cAt>cCt	p.H21P		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	21						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GAGAGGAATATGGCGGGAGGT	0.532																																					p.H21P		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.A62C						.						53	56	55					21																	31692292		2203	4300	6503	SO:0001583	missense	388818	exon1			GGAATATGGCGGG	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"Keratin associated proteins"	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.62A>C	chr21.hg19:g.31692292T>G	ENSP00000353742:p.His21Pro	136.0	0.0		109.0	16.0	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	hg19	CCDS13588.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.877962	0.33162	.	.	ENSG00000197683	ENST00000360542	T	0.03272	3.99	4.95	2.34	0.29019	.	0.521049	0.18487	N	0.139742	T	0.04363	0.0120	L	0.47716	1.5	0.23260	N	0.998028	B	0.24721	0.11	B	0.27262	0.078	T	0.33854	-0.9852	10	0.36615	T	0.2	-11.6437	8.6875	0.34247	0.0:0.0:0.3806:0.6193	.	21	Q6PEX3	KR261_HUMAN	P	21	ENSP00000353742:H21P	ENSP00000353742:H21P	H	-	2	0	KRTAP26-1	30614163	0.892000	0.30473	0.262000	0.24481	0.260000	0.26232	1.198000	0.32223	0.949000	0.37715	-0.316000	0.08728	CAT	.	.		0.532	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405		G	31692292	T	G	31692292	3	3	91	1	0	0	0	0	1	0	0	0	8552	1464	51	5	574	5	KRTAP26-1	21	31692292	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	12758502	31692292	16437603	664	12738										
KRTAP27-1	643812	hgsc.bcm.edu	37	chr21	31709981	31709981	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtgaatggcagtggctatgAggcatattgctaaaaatcct	11	6	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:31709981A>G	ENST00000382835.2	-	1	31	c.6T>C	c.(4-6)ccT>ccC	p.P2P		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	2						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						AGTGGCTATGAGGCATATTGC	0.418																																					p.P2P		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.T6C						.						66	66	66					21																	31709981		2203	4299	6502	SO:0001819	synonymous_variant	643812	exon1			GCTATGAGGCATA	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"Keratin associated proteins"	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.6T>C	chr21.hg19:g.31709981A>G		214.0	0.0		132.0	7.0	NM_001077711		Silent	SNP	ENST00000382835.2	hg19	CCDS33532.1																																																																																			.	.		0.418	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711		G	31709981	A	G	31709981	2	3	91	1	0	0	0	0	0	0	0	1	8553	291	11	2		2	KRTAP27-1	21	31709981	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	17689	31709981	16419914	665	12739										
DONSON	29980	hgsc.bcm.edu	37	chr21	34957031	34957031	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggtggagccaatagataaggCtctgctggaaggtacaacgg	15	7	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:34957031C>A	ENST00000303071.5	-	4	716	c.650G>T	c.(649-651)aGc>aTc	p.S217I	DONSON_ENST00000453626.1_Missense_Mutation_p.S217I|DONSON_ENST00000303113.6_Splice_Site_p.S203I|DONSON_ENST00000432378.1_Missense_Mutation_p.S217I|AP000304.12_ENST00000429238.1_Missense_Mutation_p.E178D	NM_017613.3	NP_060083.1	Q9NYP3	DONS_HUMAN	downstream neighbor of SON	217					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|ovary(1)	11						ATAGATAAGGCTCTGCTGGAA	0.453																																					p.S217I		Atlas-SNP	.											.	DONSON	34	.	0			c.G650T						.						78	67	71					21																	34957031		2203	4300	6503	SO:0001583	missense	29980	exon4			ATAAGGCTCTGCT	AF000002	CCDS13632.1	21q22.1	2008-07-31			ENSG00000159147	ENSG00000159147			2993	protein-coding gene	gene with protein product		611428		C21orf60		10773462, 10950926	Standard	NM_017613		Approved	B17, C2TA, DKFZP434M035	uc002ysk.4	Q9NYP3	OTTHUMG00000065904	ENST00000303071.5:c.650G>T	chr21.hg19:g.34957031C>A	ENSP00000307143:p.Ser217Ile	134.0	0.0		100.0	4.0	NM_017613	Q8NC53|Q9NSR9|Q9NVZ5|Q9NYP1|Q9NYP2	Missense_Mutation	SNP	ENST00000303071.5	hg19	CCDS13632.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	25.7|25.7|25.7	4.665866|4.665866|4.665866	0.88251|0.88251|0.88251	.|.|.	.|.|.	ENSG00000159147|ENSG00000159147;ENSG00000249209|ENSG00000159147	ENST00000437395|ENST00000440810;ENST00000429238|ENST00000303113;ENST00000453626;ENST00000303071;ENST00000432378	.|.|.	.|.|.	.|.|.	5.99|5.99|5.99	4.14|4.14|4.14	0.48551|0.48551|0.48551	.|.|.	.|.|0.117155	.|.|0.85682	.|.|D	.|.|0.000000	T|T|T	0.61553|0.61553|0.61553	0.2356|0.2356|0.2356	M|M|M	0.64404|0.64404|0.64404	1.975|1.975|1.975	0.49687|0.49687|0.49687	D|D|D	0.999811|0.999811|0.999811	.|.|B;B;B	.|.|0.31209	.|.|0.313;0.168;0.313	.|.|B;B;B	.|.|0.36030	.|.|0.216;0.153;0.216	T|T|T	0.65569|0.65569|0.65569	-0.6136|-0.6136|-0.6136	5|5|9	.|.|0.72032	.|.|D	.|.|0.01	-36.6994|-36.6994|-36.6994	11.6527|11.6527|11.6527	0.51299|0.51299|0.51299	0.0:0.804:0.1274:0.0685|0.0:0.804:0.1274:0.0685|0.0:0.804:0.1274:0.0685	.|.|.	.|.|203;217;217	.|.|F8W8A5;C9J4K5;Q9NYP3	.|.|.;.;DONS_HUMAN	S|D|I	188|75;178|203;217;217;217	.|.|.	.|.|ENSP00000307143:S217I	A|E|S	-|-|-	1|3|2	0|2|0	DONSON|DONSON;AP000304.12|DONSON	33878901|33878901|33878901	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.999000|0.999000|0.999000	0.59377|0.59377|0.59377	0.974000|0.974000|0.974000	0.67602|0.67602|0.67602	2.976000|2.976000|2.976000	0.49289|0.49289|0.49289	1.499000|1.499000|1.499000	0.48617|0.48617|0.48617	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GCC|GAG|AGC	.	.		0.453	DONSON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141184.1	NM_017613		A	34957031	C	A	34957031	3	1	91	1	0	0	0	0	1	0	0	0	4708	797	28	3	1078	3	DONSON	21	34957031	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	3247050	34957031	13172864	666	12740										
HLCS	3141	hgsc.bcm.edu	37	chr21	38309237	38309237	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagggcttcctgggagtcggAgcccacatagaggaggatgt	17	8	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:38309237A>G	ENST00000399120.1	-	5	1738	c.508T>C	c.(508-510)Tcc>Ccc	p.S170P	HLCS_ENST00000336648.4_Missense_Mutation_p.S170P	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	170					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	TGGGAGTCGGAGCCCACATAG	0.577																																					p.S170P		Atlas-SNP	.											.	HLCS	64	.	0			c.T508C						.						68	60	63					21																	38309237		2203	4300	6503	SO:0001583	missense	3141	exon5			AGTCGGAGCCCAC		CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)", "holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.508T>C	chr21.hg19:g.38309237A>G	ENSP00000382071:p.Ser170Pro	157.0	0.0		95.0	4.0	NM_000411	B2RAH1|D3DSG6|Q99451	Missense_Mutation	SNP	ENST00000399120.1	hg19	CCDS13647.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.429202	0.43122	.	.	ENSG00000159267	ENST00000399120;ENST00000336648	D;D	0.98345	-4.88;-4.88	5.91	-3.88	0.04205	.	0.648921	0.17681	N	0.165616	D	0.95046	0.8396	L	0.55481	1.735	0.20307	N	0.999915	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.003	D	0.87120	0.2190	10	0.26408	T	0.33	.	9.615	0.39685	0.3517:0.1252:0.5231:0.0	.	170;170	B2RAH1;P50747	.;BPL1_HUMAN	P	170	ENSP00000382071:S170P;ENSP00000338387:S170P	ENSP00000338387:S170P	S	-	1	0	HLCS	37231107	0.985000	0.35326	0.135000	0.22099	0.902000	0.53008	0.511000	0.22739	-0.582000	0.05929	-0.250000	0.11733	TCC	.	.		0.577	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2			G	38309237	A	G	38309237	3	3	91	1	0	0	0	0	1	0	0	0	7222	304	11	2	1704	2	HLCS	21	38309237	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3352206	38309237	9820658	667	12741										
TTC3	7267	hgsc.bcm.edu	37	chr21	38573864	38573864	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atcaggagctgccttcctgcTcttctaggtagtcacacttc	8	13	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:38573864T>C	ENST00000399017.2	+	46	8814	c.6067T>C	c.(6067-6069)Tct>Cct	p.S2023P	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Missense_Mutation_p.S2023P|TTC3_ENST00000354749.2_Missense_Mutation_p.S2023P	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	2023					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GCCTTCCTGCTCTTCTAGGTA	0.498																																					p.S2023P	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.T6067C						.						58	56	57					21																	38573864		2203	4300	6503	SO:0001583	missense	7267	exon46			TCCTGCTCTTCTA	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.6067T>C	chr21.hg19:g.38573864T>C	ENSP00000381981:p.Ser2023Pro	86.0	0.0		74.0	4.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.46|12.46	1.944531|1.944531	0.34283|0.34283	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000428693|ENST00000355666;ENST00000399017;ENST00000354749	.|T;T;T	.|0.08984	.|3.03;3.03;3.03	3.95|3.95	1.52|1.52	0.23074|0.23074	.|.	.|.	.|.	.|.	.|.	T|T	0.07369|0.07369	0.0186|0.0186	L|L	0.46157|0.46157	1.445|1.445	0.09310|0.09310	N|N	1|1	.|B	.|0.29909	.|0.261	.|B	.|0.23018	.|0.043	T|T	0.31194|0.31194	-0.9952|-0.9952	5|9	.|0.87932	.|D	.|0	-0.0249|-0.0249	5.1189|5.1189	0.14851|0.14851	0.0:0.2776:0.0:0.7224|0.0:0.2776:0.0:0.7224	.|.	.|2023	.|P53804	.|TTC3_HUMAN	P|P	314|2023	.|ENSP00000347889:S2023P;ENSP00000381981:S2023P;ENSP00000346791:S2023P	.|ENSP00000346791:S2023P	L|S	+|+	2|1	0|0	TTC3|TTC3	37495734|37495734	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.199000|0.199000	0.17237|0.17237	0.205000|0.205000	0.20568|0.20568	-0.256000|-0.256000	0.11100|0.11100	CTC|TCT	.	.		0.498	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			C	38573864	T	C	38573864	3	2	91	1	0	0	0	0	1	0	0	0	16712	1551	54	2	6245	2	TTC3	21	38573864	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	264627	38573864	9556031	668	12742										
ETS2	2114	hgsc.bcm.edu	37	chr21	40191431	40191431	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggttgtctttgccagggacTcccaaagaccacgactcccc	9	15	1	1	rs457705	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:40191431T>C	ENST00000360214.3	+	9	1276	c.816T>C	c.(814-816)acT>acC	p.T272T	ETS2_ENST00000360938.3_Silent_p.T272T	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	272					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				TGCCAGGGACTCCCAAAGACC	0.547																																					p.T412T		Atlas-SNP	.											ETS2_ENST00000360214,NS,carcinoma,0,2	ETS2	87	.	0			c.T1236C						.						71	64	66					21																	40191431		2203	4300	6503	SO:0001819	synonymous_variant	2114	exon9			AGGGACTCCCAAA		CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.816T>C	chr21.hg19:g.40191431T>C		72.0	1.0		39.0	3.0	NM_001256295	A6NM68|D3DSH6|Q53Y89	Silent	SNP	ENST00000360214.3	hg19	CCDS13659.1																																																																																			.	T|0.298;G|0.702		0.547	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1			C	40191431	T	C	40191431	2	2	91	1	0	0	0	0	0	0	0	1	5278	1538	54	2		2	ETS2	21	40191431	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1617567	40191431	7938464	669	12743										
TMPRSS3	64699	hgsc.bcm.edu	37	chr21	43808513	43808513	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaaatgctctttaacttaccTtgggaaacccagttgggcac	9	10	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:43808513T>C	ENST00000291532.3	-	5	1400	c.445A>G	c.(445-447)Agc>Ggc	p.S149G	TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000433957.2_Splice_Site_p.S149G|TMPRSS3_ENST00000398405.1_Splice_Site_p.S147G|TMPRSS3_ENST00000380399.1_Splice_Site_p.S233G|TMPRSS3_ENST00000398397.3_Splice_Site_p.S149G	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	149	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						TTAACTTACCTTGGGAAACCC	0.473																																					p.S149G		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.A445G						.						116	108	111					21																	43808513		2203	4300	6503	SO:0001630	splice_region_variant	64699	exon5			CTTACCTTGGGAA	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"Serine peptidases / Transmembrane"	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.446+1A>G	chr21.hg19:g.43808513T>C		153.0	0.0		94.0	4.0	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	hg19	CCDS13686.1	.	.	.	.	.	.	.	.	.	.	T	17.15	3.316263	0.60524	.	.	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64	4.94	4.94	0.65067	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.050337	0.85682	D	0.000000	T	0.45558	0.1348	L	0.45581	1.43	0.80722	D	1	P;P;B	0.46142	0.724;0.873;0.153	B;B;B	0.44044	0.19;0.439;0.068	T	0.38735	-0.9647	9	.	.	.	.	14.601	0.68441	0.0:0.0:0.0:1.0	.	149;149;149	P57727-3;P57727-5;P57727	.;.;TMPS3_HUMAN	G	149;149;147;233;149	ENSP00000291532:S149G;ENSP00000411013:S149G;ENSP00000381442:S147G;ENSP00000369762:S233G;ENSP00000381434:S149G	.	S	-	1	0	TMPRSS3	42681582	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	6.190000	0.72057	1.849000	0.53698	0.402000	0.26972	AGC	.	.		0.473	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		Missense_Mutation	C	43808513	T	C	43808513	5	2	91	1	0	0	0	0	0	0	1	0	16263	1623	56	2	1038	2	TMPRSS3	21	43808513	Splice_Site	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	3617082	43808513	4321382	670	12744										
PDE9A	5152	hgsc.bcm.edu	37	chr21	44174131	44174131	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tccagagaccatcgaggcccTgcggaagccgacctttgacg	12	14	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:44174131T>C	ENST00000291539.6	+	10	827	c.767T>C	c.(766-768)cTg>cCg	p.L256P	PDE9A_ENST00000398225.3_Missense_Mutation_p.L215P|PDE9A_ENST00000328862.6_Missense_Mutation_p.L230P|PDE9A_ENST00000398224.3_Missense_Mutation_p.L129P|PDE9A_ENST00000398232.3_Missense_Mutation_p.L189P|PDE9A_ENST00000539837.1_Missense_Mutation_p.L128P|PDE9A_ENST00000335440.6_Missense_Mutation_p.L154P|PDE9A_ENST00000398227.3_Missense_Mutation_p.L96P|PDE9A_ENST00000335512.4_Missense_Mutation_p.L196P|PDE9A_ENST00000380328.2_Missense_Mutation_p.L203P|PDE9A_ENST00000349112.3_Missense_Mutation_p.L128P|PDE9A_ENST00000398229.3_Missense_Mutation_p.L122P|PDE9A_ENST00000398234.3_Missense_Mutation_p.L155P|PDE9A_ENST00000398236.3_Missense_Mutation_p.L170P|PDE9A_ENST00000470987.1_3'UTR	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	256					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	ATCGAGGCCCTGCGGAAGCCG	0.597																																					p.L256P		Atlas-SNP	.											.	PDE9A	69	.	0			c.T767C						.						70	57	62					21																	44174131		2203	4300	6503	SO:0001583	missense	5152	exon10			AGGCCCTGCGGAA	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"Phosphodiesterases"	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.767T>C	chr21.hg19:g.44174131T>C	ENSP00000291539:p.Leu256Pro	49.0	0.0		52.0	4.0	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	hg19	CCDS13690.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.170944	0.78452	.	.	ENSG00000160191	ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000328862;ENST00000335440;ENST00000398225;ENST00000398229;ENST00000398227;ENST00000349112;ENST00000398224	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.79554	-0.92;-1.13;-0.79;-1.28;-0.97;-0.89;-0.83;-0.93;-1.16;-0.79;-1.14;-1.14;-1.08;-0.85	4.54	4.54	0.55810	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.184656	0.38778	N	0.001564	D	0.89750	0.6805	M	0.85373	2.75	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.85130	0.996;0.996;0.996;0.996;0.996;0.997;0.995;0.994;0.996;0.996;0.996;0.997;0.997;0.996;0.996;0.986	D	0.91202	0.4992	10	0.87932	D	0	.	12.5263	0.56087	0.0:0.0:0.0:1.0	.	128;189;170;155;230;215;148;196;39;96;122;128;154;203;129;256	F5GWD0;O76083-13;O76083-8;O76083-6;O76083-15;O76083-14;O76083-16;O76083-2;O76083-10;O76083-9;O76083-11;O76083-4;O76083-12;O76083-5;O76083-3;O76083	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;PDE9A_HUMAN	P	196;128;256;203;189;155;170;230;154;215;122;96;128;129	ENSP00000335242:L196P;ENSP00000441899:L128P;ENSP00000291539:L256P;ENSP00000369685:L203P;ENSP00000381287:L189P;ENSP00000381289:L155P;ENSP00000381291:L170P;ENSP00000328699:L230P;ENSP00000335365:L154P;ENSP00000381281:L215P;ENSP00000381285:L122P;ENSP00000381283:L96P;ENSP00000344730:L128P;ENSP00000381280:L129P	ENSP00000291539:L256P	L	+	2	0	PDE9A	43047200	1.000000	0.71417	0.467000	0.27180	0.944000	0.59088	7.205000	0.77881	1.705000	0.51264	0.454000	0.30748	CTG	.	.		0.597	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			C	44174131	T	C	44174131	3	2	91	1	0	0	0	0	1	0	0	0	11664	1580	55	2	885	2	PDE9A	21	44174131	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	365618	44174131	3955764	671	12745										
PKNOX1	5316	hgsc.bcm.edu	37	chr21	44430256	44430256	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acttctgccagttttgatgtAgacatcgaaaattttgtaag	8	6	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:44430256A>G	ENST00000291547.5	+	4	484	c.273A>G	c.(271-273)gtA>gtG	p.V91V	PKNOX1_ENST00000432907.2_Intron	NM_004571.3	NP_004562.2	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	91					angiogenesis (GO:0001525)|camera-type eye development (GO:0043010)|erythrocyte differentiation (GO:0030218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|prostate(1)	22						GTTTTGATGTAGACATCGAAA	0.338																																					p.V91V		Atlas-SNP	.											.	PKNOX1	40	.	0			c.A273G						.						68	67	67					21																	44430256		2203	4300	6503	SO:0001819	synonymous_variant	5316	exon4			TGATGTAGACATC		CCDS13692.1, CCDS68211.1	21q22.3	2011-06-20			ENSG00000160199	ENSG00000160199		"Homeoboxes / TALE class"	9022	protein-coding gene	gene with protein product		602100				9479508	Standard	NM_001286258		Approved	PREP1	uc002zcq.1	P55347	OTTHUMG00000086833	ENST00000291547.5:c.273A>G	chr21.hg19:g.44430256A>G		66.0	0.0		53.0	4.0	NM_004571	O00528|Q8IWT7	Silent	SNP	ENST00000291547.5	hg19	CCDS13692.1																																																																																			.	.		0.338	PKNOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195520.3			G	44430256	A	G	44430256	2	3	91	1	0	0	0	0	0	0	0	1	11991	407	15	2		2	PKNOX1	21	44430256	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	256125	44430256	3699639	672	12746										
SIK1	150094	hgsc.bcm.edu	37	chr21	44838374	44838374	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggtcagacaactgtcagagcTggttccctctgcaggacttg	12	11	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:44838374T>C	ENST00000270162.6	-	12	1642	c.1510A>G	c.(1510-1512)Agc>Ggc	p.S504G		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	504					cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	CTGTCAGAGCTGGTTCCCTCT	0.642																																					p.S504G		Atlas-SNP	.											.	SIK1	65	.	0			c.A1510G						.						37	39	38					21																	44838374		2202	4300	6502	SO:0001583	missense	150094	exon12			CAGAGCTGGTTCC	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"myocardial SNF1-like kinase"	605705	"SNF1-like kinase"	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.1510A>G	chr21.hg19:g.44838374T>C	ENSP00000270162:p.Ser504Gly	85.0	0.0		69.0	5.0	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	hg19	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.803053	0.31869	.	.	ENSG00000142178	ENST00000270162	T	0.73681	-0.77	4.79	4.79	0.61399	.	0.110591	0.64402	D	0.000005	T	0.71634	0.3363	M	0.72118	2.19	0.43313	D	0.995329	B	0.21071	0.051	B	0.14023	0.01	T	0.67929	-0.5543	10	0.22706	T	0.39	.	14.3387	0.66608	0.0:0.0:0.0:1.0	.	504	P57059	SIK1_HUMAN	G	504	ENSP00000270162:S504G	ENSP00000270162:S504G	S	-	1	0	SIK1	43662802	1.000000	0.71417	1.000000	0.80357	0.254000	0.26022	5.626000	0.67777	1.790000	0.52503	0.533000	0.62120	AGC	.	.		0.642	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		C	44838374	T	C	44838374	3	2	91	1	0	0	0	0	1	0	0	0	14332	1580	55	2	853	2	SIK1	21	44838374	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	408118	44838374	3291521	673	12747										
C21orf2	755	hgsc.bcm.edu	37	chr21	45755646	45755646	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcaggagcgaggtacctgagCgtgatcacctccaggctggg	16	11	1	2	rs146104157	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:45755646C>A	ENST00000339818.4	-	3	345	c.138G>T	c.(136-138)acG>acT	p.T46T	C21orf2_ENST00000397956.3_Silent_p.T46T|C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000325223.7_Silent_p.T46T|AP001062.7_ENST00000448927.1_RNA	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	46					cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		GGTACCTGAGCGTGATCACCT	0.607																																					p.T46T		Atlas-SNP	.											.	C21orf2	10	.	0			c.G138T						.						65	42	50					21																	45755646		2202	4294	6496	SO:0001819	synonymous_variant	755	exon3			CCTGAGCGTGATC	Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"nuclear encoded mitochondrial protein", "leucine rich repeat containing 76"	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.138G>T	chr21.hg19:g.45755646C>A		139.0	0.0		100.0	4.0	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Silent	SNP	ENST00000339818.4	hg19	CCDS13709.1																																																																																			.	C|0.997;T|0.003		0.607	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928		A	45755646	C	A	45755646	2	1	91	1	0	0	0	0	0	0	0	1	2125	755	27	1		1	C21orf2	21	45755646	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	917272	45755646	2374249	674	12748										
TRPM2	7226	hgsc.bcm.edu	37	chr21	45833912	45833912	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctactctgcctctacctgcTcttcaccaacatcctgctgc	4	19	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:45833912T>C	ENST00000397928.1	+	20	3546	c.3101T>C	c.(3100-3102)cTc>cCc	p.L1034P	AP001065.2_ENST00000456880.1_RNA|TRPM2_ENST00000300482.5_Missense_Mutation_p.L1034P|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.L1034P|TRPM2_ENST00000300481.9_Missense_Mutation_p.L1014P|AP001065.2_ENST00000423310.1_RNA	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1034					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						CTCTACCTGCTCTTCACCAAC	0.652																																					p.L1034P		Atlas-SNP	.											.	TRPM2	196	.	0			c.T3101C						.						230	229	230					21																	45833912		2203	4300	6503	SO:0001583	missense	7226	exon20			ACCTGCTCTTCAC	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.3101T>C	chr21.hg19:g.45833912T>C	ENSP00000381023:p.Leu1034Pro	75.0	0.0		52.0	4.0	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	hg19	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.503139	0.85176	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	D;D;D;D	0.98732	-5.1;-5.1;-5.1;-5.1	4.65	4.65	0.58169	Ion transport (1);	0.000000	0.64402	D	0.000002	D	0.99275	0.9747	M	0.93016	3.37	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98974	1.0802	10	0.87932	D	0	-36.9905	14.3827	0.66921	0.0:0.0:0.0:1.0	.	1034;820;1034	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	P	1034;1034;1014;1034	ENSP00000300482:L1034P;ENSP00000381023:L1034P;ENSP00000300481:L1014P;ENSP00000381026:L1034P	ENSP00000300481:L1014P	L	+	2	0	TRPM2	44658340	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.652000	0.83633	1.868000	0.54150	0.482000	0.46254	CTC	.	.		0.652	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		C	45833912	T	C	45833912	3	2	91	1	0	0	0	0	1	0	0	0	16601	1551	54	2	3179	2	TRPM2	21	45833912	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	78266	45833912	2295983	675	12749										
PCNT	5116	hgsc.bcm.edu	37	chr21	47786943	47786943	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttgactcaagagttggagaaActgaagcggaaacacgaagg	13	6	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:47786943A>G	ENST00000359568.5	+	15	3161	c.3054A>G	c.(3052-3054)aaA>aaG	p.K1018K	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1018					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AGTTGGAGAAACTGAAGCGGA	0.547																																					p.K1018K		Atlas-SNP	.											.	PCNT	283	.	0			c.A3054G						.						91	100	97					21																	47786943		2203	4300	6503	SO:0001819	synonymous_variant	5116	exon15			GGAGAAACTGAAG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.3054A>G	chr21.hg19:g.47786943A>G		94.0	0.0		77.0	4.0	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	hg19	CCDS33592.1																																																																																			.	.		0.547	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		G	47786943	A	G	47786943	2	3	91	1	0	0	0	0	0	0	0	1	11599	40	2	2		2	PCNT	21	47786943	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1953031	47786943	342952	676	12750										
CDC45	8318	hgsc.bcm.edu	37	chr22	19502321	19502321	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tggaactcgccaagaagcagCtgcgagccacccagcagacc	11	15	0	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:19502321C>T	ENST00000407835.1	+	15	1523	c.1267C>T	c.(1267-1269)Ctg>Ttg	p.L423L	CDC45_ENST00000404724.3_Silent_p.L377L|CDC45_ENST00000437685.2_Silent_p.L455L|CDC45_ENST00000263201.1_Silent_p.L423L			O75419	CDC45_HUMAN	cell division cycle 45	423					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						CAAGAAGCAGCTGCGAGCCAC	0.572																																					p.L455L		Atlas-SNP	.											.	CDC45	48	.	0			c.C1363T						.						109	93	99					22																	19502321		2203	4300	6503	SO:0001819	synonymous_variant	8318	exon15			AAGCAGCTGCGAG	AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"human CDC45"	603465	"CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like", "CDC45 cell division cycle 45-like (S. cerevisiae)", "cell division cycle 45 homolog (S. cerevisiae)"	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.1267C>T	chr22.hg19:g.19502321C>T		74.0	0.0		59.0	4.0	NM_001178010	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Silent	SNP	ENST00000407835.1	hg19	CCDS13762.1																																																																																			.	.		0.572	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504		T	19502321	C	T	19502321	2	4	91	1	0	0	0	0	0	0	0	1	3083	796	28	3		3	CDC45	22	19502321	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10		19502321	31802245	677	12751										
ZNF74	7625	hgsc.bcm.edu	37	chr22	20755034	20755034	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatgttggagaactaccagaAccttcttgccctaggtaaaa	9	9	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:20755034A>G	ENST00000400451.2	+	3	747	c.233A>G	c.(232-234)aAc>aGc	p.N78S	ZNF74_ENST00000405993.1_Missense_Mutation_p.N78S|ZNF74_ENST00000357502.5_Silent_p.E83E|ZNF74_ENST00000403682.3_Silent_p.E49E|ZNF74_ENST00000356671.5_Missense_Mutation_p.N78S	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	78	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			AACTACCAGAACCTTCTTGCC	0.552																																					p.N78S		Atlas-SNP	.											.	ZNF74	54	.	0			c.A233G						.						100	116	111					22																	20755034		2197	4295	6492	SO:0001583	missense	7625	exon3			ACCAGAACCTTCT	X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"Zinc fingers, C2H2-type", "-"	13144	protein-coding gene	gene with protein product		194548	"zinc finger protein 74 (Cos52)"			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.233A>G	chr22.hg19:g.20755034A>G	ENSP00000383301:p.Asn78Ser	157.0	0.0		123.0	5.0	NM_003426	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Missense_Mutation	SNP	ENST00000400451.2	hg19	CCDS42982.1	.	.	.	.	.	.	.	.	.	.	A	15.83	2.949996	0.53186	.	.	ENSG00000185252	ENST00000400451;ENST00000356671;ENST00000405993	T;T;T	0.02525	4.26;4.26;4.26	3.37	3.37	0.38596	Krueppel-associated box (4);	0.000000	0.38436	N	0.001686	T	0.08492	0.0211	M	0.81802	2.56	0.22280	N	0.999237	D	0.59767	0.986	P	0.56612	0.802	T	0.14615	-1.0466	10	0.28530	T	0.3	.	5.3694	0.16131	0.8724:0.0:0.1276:0.0	.	78	Q16587	ZNF74_HUMAN	S	78	ENSP00000383301:N78S;ENSP00000349098:N78S;ENSP00000385855:N78S	ENSP00000349098:N78S	N	+	2	0	ZNF74	19085034	0.997000	0.39634	1.000000	0.80357	0.992000	0.81027	3.557000	0.53741	1.768000	0.52137	0.533000	0.62120	AAC	.	.		0.552	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426		G	20755034	A	G	20755034	3	3	91	1	0	0	0	0	1	0	0	0	18142	43	2	2	243	2	ZNF74	22	20755034	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1252713	20755034	30549532	678	12752										
CCDC116	164592	hgsc.bcm.edu	37	chr22	21990761	21990761	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gttcacgaagaagaagccgcTgccctccatctcgtcgaagt	10	13	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:21990761T>C	ENST00000292779.3	+	5	1405	c.1244T>C	c.(1243-1245)cTg>cCg	p.L415P		NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	415										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					AAGAAGCCGCTGCCCTCCATC	0.607																																					p.L415P		Atlas-SNP	.											.	CCDC116	56	.	0			c.T1244C						.						51	48	49					22																	21990761		2203	4300	6503	SO:0001583	missense	164592	exon5			AGCCGCTGCCCTC	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.1244T>C	chr22.hg19:g.21990761T>C	ENSP00000292779:p.Leu415Pro	94.0	0.0		68.0	4.0	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	hg19	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.628058	0.46944	.	.	ENSG00000161180	ENST00000292779	T	0.19394	2.15	4.47	-0.138	0.13464	.	1.652160	0.03980	N	0.293173	T	0.17323	0.0416	L	0.38175	1.15	0.09310	N	0.999995	P	0.39157	0.662	B	0.38655	0.278	T	0.22138	-1.0225	10	0.87932	D	0	.	3.027	0.06094	0.1883:0.3181:0.0:0.4936	.	415	Q8IYX3-2	.	P	415	ENSP00000292779:L415P	ENSP00000292779:L415P	L	+	2	0	CCDC116	20320761	0.000000	0.05858	0.091000	0.20842	0.086000	0.17979	0.154000	0.16343	0.020000	0.15106	-0.361000	0.07541	CTG	.	.		0.607	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612		C	21990761	T	C	21990761	3	2	91	1	0	0	0	0	1	0	0	0	2755	1580	55	2	1258	2	CCDC116	22	21990761	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1235727	21990761	29313805	679	12753										
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26771552	26771552	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgtgttcagtagcagaagcgGcagcagagacgtcgctggaa	15	8	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:26771552G>T	ENST00000248933.6	+	15	2934	c.2839G>T	c.(2839-2841)Gca>Tca	p.A947S	SEZ6L_ENST00000404234.3_Missense_Mutation_p.A946S|SEZ6L_ENST00000494013.1_3'UTR|SEZ6L_ENST00000343706.4_Missense_Mutation_p.A871S|SEZ6L_ENST00000411842.2_Intron|SEZ6L_ENST00000360929.3_Missense_Mutation_p.A872S|SEZ6L_ENST00000403121.1_Missense_Mutation_p.A643S|SEZ6L_ENST00000402979.1_Missense_Mutation_p.A719S|SEZ6L_ENST00000529632.2_Missense_Mutation_p.A936S			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	947					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						AGCAGAAGCGGCAGCAGAGAC	0.567																																					p.A947S		Atlas-SNP	.											.	SEZ6L	174	.	0			c.G2839T						.						87	72	77					22																	26771552		2203	4300	6503	SO:0001583	missense	23544	exon15			GAAGCGGCAGCAG	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.2839G>T	chr22.hg19:g.26771552G>T	ENSP00000248933:p.Ala947Ser	114.0	0.0		64.0	26.0	NM_021115	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	hg19	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.248544	0.39797	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.29655	1.9;2.0;2.12;1.87;1.69;1.56;1.88	5.33	5.33	0.75918	.	0.000000	0.56097	D	0.000031	T	0.43809	0.1264	L	0.34521	1.04	0.80722	D	1	D;D;B;D;P;D;D	0.89917	1.0;0.989;0.0;0.995;0.628;0.989;0.989	D;P;B;P;B;P;P	0.80764	0.994;0.804;0.0;0.814;0.415;0.804;0.804	T	0.11108	-1.0601	10	0.16420	T	0.52	.	18.0393	0.89314	0.0:0.0:1.0:0.0	.	934;936;643;871;872;946;947	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	S	946;936;872;947;871;643;719	ENSP00000384772:A946S;ENSP00000437037:A936S;ENSP00000354185:A872S;ENSP00000248933:A947S;ENSP00000342661:A871S;ENSP00000384838:A643S;ENSP00000384733:A719S	ENSP00000248933:A947S	A	+	1	0	SEZ6L	25101552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.214000	0.65236	2.502000	0.84385	0.555000	0.69702	GCA	.	.		0.567	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			T	26771552	G	T	26771552	3	4	91	1	0	0	0	0	1	0	0	0	14158	1203	42	3	2897	3	SEZ6L	22	26771552	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	4780791	26771552	24533014	680	12754										
THOC5	8563	hgsc.bcm.edu	37	chr22	29917065	29917065	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caggatacaagcaactcaggActgagtcaggagacagcaag	12	9	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:29917065A>G	ENST00000490103.1	-	13	1321	c.1199T>C	c.(1198-1200)gTc>gCc	p.V400A	THOC5_ENST00000397872.1_Missense_Mutation_p.V400A|THOC5_ENST00000397873.2_Missense_Mutation_p.V400A|CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Missense_Mutation_p.V400A	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	400					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCAACTCAGGACTGAGTCAGG	0.453																																					p.V400A		Atlas-SNP	.											.	THOC5	58	.	0			c.T1199C						.						133	136	135					22																	29917065		2203	4300	6503	SO:0001583	missense	8563	exon14			CTCAGGACTGAGT	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"THO complex subunits"	19074	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 79"	612733	"chromosome 22 open reading frame 19"	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1199T>C	chr22.hg19:g.29917065A>G	ENSP00000420306:p.Val400Ala	92.0	0.0		93.0	4.0	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	hg19	CCDS13859.1	.	.	.	.	.	.	.	.	.	.	A	19.77	3.889409	0.72524	.	.	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	5.82	5.82	0.92795	.	0.175441	0.49916	D	0.000130	T	0.24275	0.0588	L	0.34521	1.04	0.46478	D	0.999061	B	0.23185	0.081	B	0.25506	0.061	T	0.02852	-1.1102	10	0.66056	D	0.02	-20.9404	15.8454	0.78883	1.0:0.0:0.0:0.0	.	400	Q13769	THOC5_HUMAN	A	400	ENSP00000420306:V400A;ENSP00000380970:V400A;ENSP00000380969:V400A;ENSP00000380971:V400A	ENSP00000380969:V400A	V	-	2	0	THOC5	28247065	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.530000	0.90606	2.222000	0.72286	0.533000	0.62120	GTC	.	.		0.453	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678		G	29917065	A	G	29917065	3	3	91	1	0	0	0	0	1	0	0	0	15883	275	10	2	884	2	THOC5	22	29917065	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3145513	29917065	21387501	681	12755										
UQCR10	29796	hgsc.bcm.edu	37	chr22	30165668	30165668	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcttgtctttaaaatgcagaAgctgtggaaacacatcaagc	8	8	3	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:30165668A>G	ENST00000330029.6	+	2	182	c.152A>G	c.(151-153)aAg>aGg	p.K51R	ZMAT5_ENST00000397781.3_5'Flank|UQCR10_ENST00000401406.3_3'UTR|ZMAT5_ENST00000344318.3_5'Flank	NM_001003684.1|NM_013387.3	NP_001003684.1|NP_037519.2	Q9UDW1	QCR9_HUMAN	ubiquinol-cytochrome c reductase, complex III subunit X	51					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	5						AAAATGCAGAAGCTGTGGAAA	0.493																																					p.K51R		Atlas-SNP	.											.	UQCR10	10	.	0			c.A152G						.						65	70	68					22																	30165668		1897	4118	6015	SO:0001630	splice_region_variant	29796	exon2			TGCAGAAGCTGTG	AB028598	CCDS46680.1, CCDS46681.1	22q12.2	2011-07-04			ENSG00000184076	ENSG00000184076		"Mitochondrial respiratory chain complex / Complex III"	30863	protein-coding gene	gene with protein product	"ubiquinol-cytochrome c reductase, complex III subunit X, 7.2kDa", "complex III subunit 9"	610843				11042152	Standard	NM_013387		Approved	HSPC051, UCRC, QCR9, UCCR7.2	uc003agq.1	Q9UDW1	OTTHUMG00000151283	ENST00000330029.6:c.151-1A>G	chr22.hg19:g.30165668A>G		154.0	0.0		134.0	6.0	NM_013387	B5MCM5|Q9T2V6	Missense_Mutation	SNP	ENST00000330029.6	hg19	CCDS46680.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.91|13.91	2.378985|2.378985	0.42207|0.42207	.|.	.|.	ENSG00000184076|ENSG00000184076	ENST00000330029;ENST00000406782|ENST00000332801	T|.	0.57107|.	0.42|.	4.72|4.72	4.72|4.72	0.59763|0.59763	.|.	.|0.289711	.|0.25006	.|N	.|0.033872	T|T	0.67021|0.67021	0.2849|0.2849	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	P|.	0.39157|.	0.662|.	P|.	0.48654|.	0.585|.	T|T	0.70565|0.70565	-0.4837|-0.4837	8|6	0.33141|0.87932	T|D	0.24|0	-0.9291|-0.9291	10.795|10.795	0.46455|0.46455	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	51|.	Q9UDW1|.	QCR9_HUMAN|.	R|G	51;70|51	ENSP00000332887:K51R|.	ENSP00000332887:K51R|ENSP00000333278:S51G	K|S	+|+	2|1	0|0	UQCR10|UQCR10	28495668|28495668	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	6.697000|6.697000	0.74603|0.74603	2.110000|2.110000	0.64415|0.64415	0.529000|0.529000	0.55759|0.55759	AAG|AGC	.	.		0.493	UQCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322081.1	NM_013387	Missense_Mutation	G	30165668	A	G	30165668	5	3	91	1	0	0	0	0	0	0	1	0	17031	86	3	2	197	2	UQCR10	22	30165668	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	248603	30165668	21138898	682	12756										
PES1	23481	hgsc.bcm.edu	37	chr22	30975865	30975865	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccagagaagtactctgccacGgggagaaggagcctggcgtt	15	10	1	2	rs200700442|rs140808409	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:30975865G>T	ENST00000405677.1	-	14	1753	c.810C>A	c.(808-810)ccC>ccA	p.P270P	PES1_ENST00000402281.1_Silent_p.P270P|PES1_ENST00000335214.6_Silent_p.P404P|PES1_ENST00000354694.7_Silent_p.P409P|PES1_ENST00000402284.3_Silent_p.P392P	NM_001282328.1	NP_001269257.1			pescadillo ribosomal biogenesis factor 1											breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	29						ACTCTGCCACGGGGAGAAGGA	0.582																																					p.P409P		Atlas-SNP	.											.	PES1	55	.	0			c.C1227A						.						88	93	92					22																	30975865		2203	4300	6503	SO:0001819	synonymous_variant	23481	exon12			TGCCACGGGGAGA	U78310	CCDS13880.1, CCDS58802.1, CCDS74842.1	22q12.1	2012-02-23	2012-02-23		ENSG00000100029	ENSG00000100029			8848	protein-coding gene	gene with protein product		605819	"pescadillo (zebrafish) homolog 1, containing BRCT domain", "pescadillo homolog 1, containing BRCT domain (zebrafish)"			8985183, 10591208, 17353269	Standard	NM_014303		Approved	PES	uc003aij.2	O00541	OTTHUMG00000151077	ENST00000405677.1:c.810C>A	chr22.hg19:g.30975865G>T		79.0	0.0		81.0	6.0	NM_014303		Silent	SNP	ENST00000405677.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.288	1.049937	0.19827	.	.	ENSG00000100029	ENST00000441668	.	.	.	4.89	-9.78	0.00496	.	.	.	.	.	T	0.46580	0.1400	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55872	-0.8072	4	.	.	.	-10.6129	8.5608	0.33509	0.6373:0.2022:0.0906:0.0699	.	.	.	.	S	16	.	.	R	-	1	0	PES1	29305865	0.000000	0.05858	0.638000	0.29380	0.978000	0.69477	-3.878000	0.00344	-2.072000	0.00879	-0.878000	0.02970	CGT	.	G|0.980;A|0.020		0.582	PES1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000321189.2	NM_014303		T	30975865	G	T	30975865	2	4	91	1	0	0	0	0	0	0	0	1	11742	1103	39	1		1	PES1	22	30975865	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	810197	30975865	20328701	683	12757										
SMTN	6525	hgsc.bcm.edu	37	chr22	31487265	31487265	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggaggagggccccagggggcGgggcttggctgctaggcccc	21	12	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:31487265G>T	ENST00000347557.2	+	10	1474	c.1256G>T	c.(1255-1257)cGg>cTg	p.R419L	SMTN_ENST00000358743.1_Missense_Mutation_p.R419L|SMTN_ENST00000333137.7_Missense_Mutation_p.R419L|SMTN_ENST00000404574.1_5'Flank	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	419					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)	p.R419Q(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						CCCAGGGGGCGGGGCTTGGCT	0.697																																					p.R475L		Atlas-SNP	.											SMTN_ENST00000404496,NS,carcinoma,+1,1	SMTN	219	.	1	Substitution - Missense(1)	pancreas(1)	c.G1424T						.						6	7	7					22																	31487265		2091	4144	6235	SO:0001583	missense	6525	exon9			GGGGGCGGGGCTT	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.1256G>T	chr22.hg19:g.31487265G>T	ENSP00000328635:p.Arg419Leu	37.0	0.0		37.0	2.0	NM_001207018	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	hg19	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.223322	0.79464	.	.	ENSG00000183963	ENST00000358743;ENST00000347557;ENST00000333137;ENST00000329852;ENST00000404496	T;T;T	0.69435	0.02;-0.4;-0.39	5.22	4.21	0.49690	.	.	.	.	.	T	0.76442	0.3988	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D;D	0.76494	0.998;0.998;0.997;0.998;0.997;0.999	D;D;D;D;D;D	0.78314	0.991;0.936;0.987;0.936;0.987;0.968	T	0.78247	-0.2278	9	0.72032	D	0.01	-23.7183	11.995	0.53196	0.0818:0.0:0.9182:0.0	.	475;473;411;419;419;419	E7ETT8;B4E229;B5MC56;E7EWD0;P53814;P53814-5	.;.;.;.;SMTN_HUMAN;.	L	419;419;419;417;411	ENSP00000351593:R419L;ENSP00000328635:R419L;ENSP00000329532:R419L	ENSP00000329393:R417L	R	+	2	0	SMTN	29817265	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	4.107000	0.57811	1.354000	0.45846	0.491000	0.48974	CGG	.	.		0.697	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		T	31487265	G	T	31487265	3	4	91	1	0	0	0	0	1	0	0	0	14829	1116	39	1	1290	1	SMTN	22	31487265	Missense_Mutation	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	511400	31487265	19817301	684	12758										
C22orf30	253143	hgsc.bcm.edu	37	chr22	32109192	32109192	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctttaaaaaggcagaacttcTgattttacctatttttctcc	4	9	2	2	rs532999755		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:32109192T>C	ENST00000327423.6	-	4	4822	c.4633A>G	c.(4633-4635)Aga>Gga	p.R1545G	PRR14L_ENST00000397493.2_Missense_Mutation_p.R1545G|PRR14L_ENST00000434485.1_Missense_Mutation_p.R1545G	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1545										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GCAGAACTTCTGATTTTACCT	0.418																																					p.R1545G		Atlas-SNP	.											.	PRR14L	198	.	0			c.A4633G						.						69	61	64					22																	32109192		692	1591	2283	SO:0001583	missense	253143	exon4			AACTTCTGATTTT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 30"	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.4633A>G	chr22.hg19:g.32109192T>C	ENSP00000331845:p.Arg1545Gly	92.0	0.0		85.0	4.0	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	hg19	CCDS13900.2	.	.	.	.	.	.	.	.	.	.	T	11.60	1.685573	0.29962	.	.	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.09445	2.98;3.0;2.98	5.38	0.273	0.15650	.	0.534999	0.17011	N	0.190526	T	0.07818	0.0196	L	0.44542	1.39	0.09310	N	1	B;B;B	0.22003	0.063;0.01;0.063	B;B;B	0.19946	0.027;0.006;0.027	T	0.32719	-0.9896	9	.	.	.	-0.6826	5.0789	0.14646	0.0:0.1719:0.2524:0.5757	.	1545;1545;1545	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	G	1545	ENSP00000380630:R1545G;ENSP00000331845:R1545G;ENSP00000388314:R1545G	.	R	-	1	2	PRR14L	30439192	0.000000	0.05858	0.008000	0.14137	0.975000	0.68041	0.213000	0.17521	0.345000	0.23873	0.533000	0.62120	AGA	.	.		0.418	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566		C	32109192	T	C	32109192	3	2	91	1	0	0	0	0	1	0	0	0	2144	1588	55	2	1846	2	C22orf30	22	32109192	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	621927	32109192	19195374	685	12759										
C22orf28	51493	hgsc.bcm.edu	37	chr22	32795593	32795593	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cctccaaagtgagttacctgAggaaggcctcttttcttcgc	9	12	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:32795593A>G	ENST00000216038.5	-	6	749	c.651T>C	c.(649-651)ccT>ccC	p.P217P	RTCB_ENST00000476619.1_5'UTR|RTCB_ENST00000451746.2_Intron	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		GAGTTACCTGAGGAAGGCCTC	0.418																																					p.P217P		Atlas-SNP	.											.	C22orf28	43	.	0			c.T651C						.						136	131	133					22																	32795593		2203	4300	6503	SO:0001819	synonymous_variant	51493	exon6			TACCTGAGGAAGG	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"focal adhesion-associated protein"	613901	"chromosome 22 open reading frame 28"	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.651T>C	chr22.hg19:g.32795593A>G		129.0	0.0		124.0	5.0	NM_014306		Silent	SNP	ENST00000216038.5	hg19	CCDS13905.1																																																																																			.	.		0.418	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306		G	32795593	A	G	32795593	2	3	91	1	0	0	0	0	0	0	0	1	2142	291	11	2		2	C22orf28	22	32795593	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	686401	32795593	18508973	686	12760										
HMGXB4	10042	hgsc.bcm.edu	37	chr22	35661108	35661108	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcctaggacatgagttacagAgctttctgaaaacagcccgg	10	10	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:35661108A>G	ENST00000216106.5	+	5	855	c.727A>G	c.(727-729)Agc>Ggc	p.S243G	HMGXB4_ENST00000444518.2_Missense_Mutation_p.S134G	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	243					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGAGTTACAGAGCTTTCTGAA	0.498																																					p.S243G		Atlas-SNP	.											.	HMGXB4	52	.	0			c.A727G						.						80	86	84					22																	35661108		2203	4300	6503	SO:0001583	missense	10042	exon5			TTACAGAGCTTTC	AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"High mobility group / Non-canonical"	5003	protein-coding gene	gene with protein product		604702	"high-mobility group protein 2-like 1"	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.727A>G	chr22.hg19:g.35661108A>G	ENSP00000216106:p.Ser243Gly	142.0	0.0		132.0	16.0	NM_001003681	O75672|O75673|Q9UMT5	Missense_Mutation	SNP	ENST00000216106.5	hg19	CCDS33641.1	.	.	.	.	.	.	.	.	.	.	A	10.08	1.252352	0.22880	.	.	ENSG00000100281	ENST00000420166;ENST00000444518;ENST00000455359;ENST00000216106	T;T;T;T	0.49720	0.77;2.12;0.78;2.12	5.81	3.7	0.42460	.	0.062472	0.64402	N	0.000002	T	0.33352	0.0860	L	0.27053	0.805	0.28140	N	0.929847	B	0.02656	0.0	B	0.04013	0.001	T	0.27839	-1.0062	10	0.87932	D	0	-5.6282	8.9631	0.35860	0.7914:0.0:0.2086:0.0	.	243	Q9UGU5	HMGX4_HUMAN	G	134;134;134;243	ENSP00000401658:S134G;ENSP00000398302:S134G;ENSP00000415500:S134G;ENSP00000216106:S243G	ENSP00000216106:S243G	S	+	1	0	HMGXB4	33991108	1.000000	0.71417	0.998000	0.56505	0.019000	0.09904	3.133000	0.50531	0.483000	0.27608	-0.256000	0.11100	AGC	.	.		0.498	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487		G	35661108	A	G	35661108	3	3	91	1	0	0	0	0	1	0	0	0	7248	304	11	2	741	2	HMGXB4	22	35661108	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2865515	35661108	15643458	687	12761										
APOL3	80833	hgsc.bcm.edu	37	chr22	36537572	36537572	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctggcttgcctgatggcacgGatttcactcccaatggtttg	11	11	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:36537572G>T	ENST00000349314.2	-	3	922	c.885C>A	c.(883-885)atC>atA	p.I295I	APOL3_ENST00000361710.2_Silent_p.I95I|APOL3_ENST00000487423.1_5'Flank|APOL3_ENST00000397293.2_Silent_p.I224I|APOL3_ENST00000397287.2_Silent_p.I95I|APOL3_ENST00000424878.2_Silent_p.I95I	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	295					inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|signal transducer activity (GO:0004871)			endometrium(2)|large_intestine(1)|lung(1)|stomach(1)	5						TGATGGCACGGATTTCACTCC	0.493																																					p.I295I		Atlas-SNP	.											.	APOL3	60	.	0			c.C885A						.						74	74	74					22																	36537572		2203	4300	6503	SO:0001819	synonymous_variant	80833	exon3			GGCACGGATTTCA	AF305227	CCDS13922.1, CCDS13924.1	22q13.1	2013-01-24			ENSG00000128284	ENSG00000128284		"Apolipoproteins"	14868	protein-coding gene	gene with protein product		607253				11374903	Standard	NM_145640		Approved	CG12-1, APOLIII	uc003aot.3	O95236	OTTHUMG00000150632	ENST00000349314.2:c.885C>A	chr22.hg19:g.36537572G>T		91.0	0.0		83.0	4.0	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Silent	SNP	ENST00000349314.2	hg19	CCDS13922.1																																																																																			.	.		0.493	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641		T	36537572	G	T	36537572	2	4	91	1	0	0	0	0	0	0	0	1	807	1164	41	3		3	APOL3	22	36537572	Silent	SNP	G	TCGA-DD-A119-01A-11D-A12Z-10	876464	36537572	14766994	688	12762										
CSF2RB	1439	hgsc.bcm.edu	37	chr22	37334252	37334252	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaacccaggggaacgcccggCagatgtgtccccaacatccc	11	16	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:37334252C>T	ENST00000403662.3	+	14	2624	c.2402C>T	c.(2401-2403)gCa>gTa	p.A801V	CSF2RB_ENST00000536485.1_Missense_Mutation_p.A748V|CSF2RB_ENST00000406230.1_Missense_Mutation_p.A807V|CSF2RB_ENST00000262825.5_Missense_Mutation_p.A807V			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	801					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GAACGCCCGGCAGATGTGTCC	0.662																																					p.A801V		Atlas-SNP	.											.	CSF2RB	104	.	0			c.C2402T						.						65	69	67					22																	37334252		2203	4300	6503	SO:0001583	missense	1439	exon14			GCCCGGCAGATGT	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"CD molecules", "Fibronectin type III domain containing"	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.2402C>T	chr22.hg19:g.37334252C>T	ENSP00000384053:p.Ala801Val	54.0	0.0		51.0	4.0	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	hg19	CCDS13936.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.047510	0.36085	.	.	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.91945	-2.43;-2.94;-2.94;-2.94	5.4	-7.21	0.01490	.	0.777720	0.10890	N	0.622791	D	0.82435	0.5036	L	0.57536	1.79	0.09310	N	1	B;B	0.28783	0.222;0.067	B;B	0.17433	0.018;0.005	T	0.69068	-0.5243	10	0.23891	T	0.37	-2.2166	0.2917	0.00259	0.3202:0.1836:0.1457:0.3505	.	807;801	P32927-2;P32927	.;IL3RB_HUMAN	V	801;801;807;807;748	ENSP00000384053:A801V;ENSP00000262825:A807V;ENSP00000385271:A807V;ENSP00000440003:A748V	ENSP00000262825:A807V	A	+	2	0	CSF2RB	35664198	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.728000	0.04925	-0.846000	0.04174	-0.300000	0.09419	GCA	.	.		0.662	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395		T	37334252	C	T	37334252	3	4	91	1	0	0	0	0	1	0	0	0	3937	710	25	3	2452	3	CSF2RB	22	37334252	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	796680	37334252	13970314	689	12763										
CARD10	29775	hgsc.bcm.edu	37	chr22	37888763	37888763	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	acgggccgcagggcagacacCagtagcggccgcaccaaact	13	15	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:37888763C>A	ENST00000403299.1	-	18	2739	c.2523G>T	c.(2521-2523)ctG>ctT	p.L841L	CARD10_ENST00000406271.3_Silent_p.L555L|CARD10_ENST00000251973.5_Silent_p.L841L			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	841					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					GGGCAGACACCAGTAGCGGCC	0.657																																					p.L841L		Atlas-SNP	.											.	CARD10	55	.	0			c.G2523T						.						31	31	31					22																	37888763		2203	4299	6502	SO:0001819	synonymous_variant	29775	exon17			AGACACCAGTAGC	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.2523G>T	chr22.hg19:g.37888763C>A		108.0	0.0		92.0	5.0	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	hg19	CCDS13948.1																																																																																			.	.		0.657	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		A	37888763	C	A	37888763	2	1	91	1	0	0	0	0	0	0	0	1	2646	581	21	3		3	CARD10	22	37888763	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	554511	37888763	13415803	690	12764										
FAM83F	113828	hgsc.bcm.edu	37	chr22	40415308	40415308	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtatttcctggagatgtgtcAggacctgcagctcactgact	11	10	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:40415308A>G	ENST00000333407.6	+	2	720	c.626A>G	c.(625-627)cAg>cGg	p.Q209R	FAM83F_ENST00000473717.1_Missense_Mutation_p.Q41R	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	209										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						GAGATGTGTCAGGACCTGCAG	0.542																																					p.Q209R		Atlas-SNP	.											.	FAM83F	29	.	0			c.A626G						.						153	117	129					22																	40415308		2203	4300	6503	SO:0001583	missense	113828	exon2			TGTGTCAGGACCT		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.626A>G	chr22.hg19:g.40415308A>G	ENSP00000330432:p.Gln209Arg	114.0	0.0		116.0	5.0	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	hg19	CCDS14000.2	.	.	.	.	.	.	.	.	.	.	A	8.026	0.760733	0.15914	.	.	ENSG00000133477	ENST00000333407	T	0.11712	2.75	4.94	0.291	0.15732	.	0.554792	0.18621	N	0.135853	T	0.06142	0.0159	N	0.16478	0.41	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.36407	-0.9749	10	0.31617	T	0.26	-7.835	9.5473	0.39288	0.6013:0.0:0.3987:0.0	.	209	Q8NEG4	FA83F_HUMAN	R	209	ENSP00000330432:Q209R	ENSP00000330432:Q209R	Q	+	2	0	FAM83F	38745254	0.439000	0.25610	0.977000	0.42913	0.703000	0.40648	0.212000	0.17497	0.068000	0.16574	-0.379000	0.06801	CAG	.	.		0.542	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435		G	40415308	A	G	40415308	3	3	91	1	0	0	0	0	1	0	0	0	5646	188	7	2	632	2	FAM83F	22	40415308	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	2526545	40415308	10889258	691	12765										
EP300	2033	hgsc.bcm.edu	37	chr22	41513713	41513713	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccgagggcgacagaatatgcAgtacccaaacccaggcatgg	12	12	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:41513713A>G	ENST00000263253.7	+	2	1836	c.617A>G	c.(616-618)cAg>cGg	p.Q206R		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	206					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CAGAATATGCAGTACCCAAAC	0.532			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.Q206R		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.A617G						.						84	67	73					22																	41513713		2203	4300	6503	SO:0001583	missense	2033	exon2	Familial Cancer Database	Broad Thumb-Hallux syndrome	ATATGCAGTACCC	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.617A>G	chr22.hg19:g.41513713A>G	ENSP00000263253:p.Gln206Arg	115.0	0.0		73.0	5.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	16.45	3.125639	0.56721	.	.	ENSG00000100393	ENST00000263253	D	0.84146	-1.81	6.11	5.05	0.67936	.	0.153176	0.29587	N	0.011734	D	0.85287	0.5662	L	0.43152	1.355	0.31138	N	0.706986	D	0.53745	0.962	P	0.55055	0.767	T	0.82778	-0.0289	10	0.25106	T	0.35	-6.0963	12.3775	0.55289	0.778:0.222:0.0:0.0	.	206	Q09472	EP300_HUMAN	R	206	ENSP00000263253:Q206R	ENSP00000263253:Q206R	Q	+	2	0	EP300	39843659	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.694000	0.47035	2.343000	0.79666	0.496000	0.49642	CAG	.	.		0.532	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41513713	A	G	41513713	3	3	91	1	0	0	0	0	1	0	0	0	5150	188	7	2	623	2	EP300	22	41513713	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1098405	41513713	9790853	692	12766										
ACO2	50	hgsc.bcm.edu	37	chr22	41913597	41913597	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttccgtgttcccttacaaccAcaggatgaagaagtacctga	8	11	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:41913597A>G	ENST00000216254.4	+	7	924	c.902A>G	c.(901-903)cAc>cGc	p.H301R	ACO2_ENST00000466237.1_3'UTR|ACO2_ENST00000396512.3_Missense_Mutation_p.H326R	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	301					cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						CCTTACAACCACAGGATGAAG	0.607											OREG0026588	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H301R		Atlas-SNP	.											.	ACO2	58	.	0			c.A902G						.						84	63	70					22																	41913597		2203	4300	6503	SO:0001583	missense	50	exon7			ACAACCACAGGAT	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"aconitate hydratase, mitochondrial"	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.902A>G	chr22.hg19:g.41913597A>G	ENSP00000216254:p.His301Arg	77.0	0.0	904	78.0	4.0	NM_001098	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Missense_Mutation	SNP	ENST00000216254.4	hg19	CCDS14017.1	.	.	.	.	.	.	.	.	.	.	A	14.04	2.416156	0.42918	.	.	ENSG00000100412	ENST00000541439;ENST00000544234;ENST00000216254;ENST00000396512	T;T	0.75704	-0.96;-0.96	5.86	5.86	0.93980	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 2 (1);	0.133241	0.64402	D	0.000002	T	0.66733	0.2819	L	0.39514	1.22	0.44129	D	0.996916	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.63056	-0.6722	10	0.49607	T	0.09	.	13.0777	0.59097	0.7998:0.2002:0.0:0.0	.	326;301	A2A274;Q99798	.;ACON_HUMAN	R	22;282;301;326	ENSP00000216254:H301R;ENSP00000379769:H326R	ENSP00000216254:H301R	H	+	2	0	ACO2	40243543	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	3.832000	0.55783	2.241000	0.73720	0.482000	0.46254	CAC	.	.		0.607	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098		G	41913597	A	G	41913597	3	3	91	1	0	0	0	0	1	0	0	0	147	159	6	2	928	2	ACO2	22	41913597	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	399884	41913597	9390969	693	12767										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51160246	51160246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cactcgctggcccgggccccTcgcccaccacggtgcccagc	11	22	0	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:51160246T>C	ENST00000414786.2	+	21	4170	c.3943T>C	c.(3943-3945)Tcg>Ccg	p.S1315P	SHANK3_ENST00000445220.2_Missense_Mutation_p.S1331P|SHANK3_ENST00000262795.3_Missense_Mutation_p.S1345P			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1329	Pro-rich.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CCCGGGCCCCTCGCCCACCAC	0.706																																					p.S1315P		Atlas-SNP	.											.	SHANK3	96	.	0			c.T3943C						.						6	8	7					22																	51160246		1881	4040	5921	SO:0001583	missense	85358	exon21			GGCCCCTCGCCCA	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.3943T>C	chr22.hg19:g.51160246T>C	ENSP00000464552:p.Ser1315Pro	53.0	0.0		23.0	4.0	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	T	8.260	0.810974	0.16537	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.20738	2.05;2.05	4.93	1.46	0.22682	.	1.561710	0.03411	N	0.204853	T	0.17066	0.0410	N	0.25890	0.77	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.26985	-1.0087	10	0.34782	T	0.22	.	8.2873	0.31937	0.0:0.2586:0.0:0.7414	.	1329;1330;1345	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	P	1345;1331	ENSP00000442518:S1345P;ENSP00000446078:S1331P	ENSP00000442518:S1345P	S	+	1	0	SHANK3	49507112	0.002000	0.14202	0.394000	0.26270	0.484000	0.33280	0.402000	0.20965	0.212000	0.20703	0.379000	0.24179	TCG	.	.		0.706	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		C	51160246	T	C	51160246	3	2	91	1	0	0	0	0	1	0	0	0	14281	1551	54	2	4119	2	SHANK3	22	51160246	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9246649	51160246	144320	694	12768										
SFRS17A	8227	hgsc.bcm.edu	37	chrX	1712975	1712975	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gggccgcaacttccacacctTcagtttcggggggcacttga	12	13	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:1712975T>C	ENST00000313871.3	+	2	816	c.620T>C	c.(619-621)tTc>tCc	p.F207S	AKAP17A_ENST00000381261.3_Missense_Mutation_p.F207S	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	207	RRM.				B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						TTCCACACCTTCAGTTTCGGG	0.587																																					p.F207S		Atlas-SNP	.											.	AKAP17A	46	.	0			c.T620C						.						132	122	125					X																	1712975		2203	4296	6499	SO:0001583	missense	8227	exon2			ACACCTTCAGTTT	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"Pseudoautosomal regions / PAR1", "A-kinase anchor proteins"	18783	protein-coding gene	gene with protein product		312095, 465000	"chromosome X and Y open reading frame 3", "splicing factor, arginine/serine-rich 17A"	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.620T>C	chrX.hg19:g.1712975T>C	ENSP00000324827:p.Phe207Ser	87.0	0.0		93.0	4.0	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Missense_Mutation	SNP	ENST00000313871.3	hg19	CCDS14116.1	.	.	.	.	.	.	.	.	.	.	t	10.68	1.419356	0.25552	.	.	ENSG00000197976	ENST00000313871;ENST00000381261	T;T	0.29917	1.55;1.55	1.83	1.83	0.25207	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	U	0.000000	T	0.49541	0.1563	.	.	.	0.31688	N	0.642274	D;D	0.71674	0.998;0.997	D;D	0.83275	0.943;0.996	T	0.56715	-0.7933	9	0.59425	D	0.04	.	9.5435	0.39266	0.0:0.0:0.0:1.0	.	207;207	Q02040-3;Q02040	.;AK17A_HUMAN	S	207	ENSP00000324827:F207S;ENSP00000370660:F207S	ENSP00000324827:F207S	F	+	2	0	AKAP17A	1672975	1.000000	0.71417	0.018000	0.16275	0.362000	0.29581	5.773000	0.68898	0.582000	0.29556	0.084000	0.15446	TTC	.	.		0.587	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		C	1712975	T	C	1712975	3	2	91	1	0	0	0	0	1	0	0	0	14188	1783	62	2	622	2	SFRS17A	23	1712975	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10		1712975	153557585	695	12769										
ARSH	347527	hgsc.bcm.edu	37	chrX	2928166	2928166	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	cccaagtcgggctgccttccTgaccggccggtaccccatca	10	18	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:2928166T>C	ENST00000381130.2	+	2	188	c.188T>C	c.(187-189)cTg>cCg	p.L63P		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	63					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				GCTGCCTTCCTGACCGGCCGG	0.502																																					p.L63P		Atlas-SNP	.											.	ARSH	72	.	0			c.T188C						.						59	45	49					X																	2928166		2203	4300	6503	SO:0001583	missense	347527	exon2			CCTTCCTGACCGG	AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"Arylsulfatase family"	32488	protein-coding gene	gene with protein product		300586	"arylsulfatase H"			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.188T>C	chrX.hg19:g.2928166T>C	ENSP00000370522:p.Leu63Pro	124.0	0.0		106.0	5.0	NM_001011719		Missense_Mutation	SNP	ENST00000381130.2	hg19	CCDS35198.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.617479	0.46736	.	.	ENSG00000205667	ENST00000381130	D	0.99338	-5.76	3.58	3.58	0.41010	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase, conserved site (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.061108	0.64402	D	0.000004	D	0.99674	0.9878	H	0.99444	4.57	0.52501	D	0.99995	D	0.89917	1.0	D	0.87578	0.998	D	0.97411	1.0002	10	0.87932	D	0	.	11.7444	0.51811	0.0:0.0:0.0:1.0	.	63	Q5FYA8	ARSH_HUMAN	P	63	ENSP00000370522:L63P	ENSP00000370522:L63P	L	+	2	0	ARSH	2938166	1.000000	0.71417	0.576000	0.28549	0.213000	0.24496	3.578000	0.53892	1.273000	0.44346	0.486000	0.48141	CTG	.	.		0.502	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719		C	2928166	T	C	2928166	3	2	91	1	0	0	0	0	1	0	0	0	993	1580	55	2	194	2	ARSH	23	2928166	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1215191	2928166	152342394	696	12770										
GPR143	4935	hgsc.bcm.edu	37	chrX	9711666	9711666	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gatcacggctcccatcctccTctcgttctccgtgtaaatgc	7	16	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:9711666T>C	ENST00000467482.1	-	6	852	c.706A>G	c.(706-708)Agg>Ggg	p.R236G	GPR143_ENST00000380929.2_Missense_Mutation_p.R256G			P51810	GP143_HUMAN	G protein-coupled receptor 143	236	Necessary for its G protein-activation ability and normal distribution of melanosomes.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|eye pigment biosynthetic process (GO:0006726)|G-protein coupled receptor signaling pathway (GO:0007186)|melanosome localization (GO:0032400)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|neuropeptide signaling pathway (GO:0007218)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of calcium-mediated signaling (GO:0050848)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|G-protein coupled receptor activity (GO:0004930)|L-DOPA binding (GO:0072544)|L-DOPA receptor activity (GO:0035643)|tyrosine binding (GO:0072545)			endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Hepatocellular(5;0.000888)				CCCATCCTCCTCTCGTTCTCC	0.378																																					p.R236G		Atlas-SNP	.											.	GPR143	37	.	0			c.A706G						.						164	141	149					X																	9711666		2203	4300	6503	SO:0001583	missense	4935	exon6			TCCTCCTCTCGTT	Z48804	CCDS14134.1, CCDS14134.2	Xp22.3	2013-09-27	2003-12-01		ENSG00000101850	ENSG00000101850		"GPCR / Unclassified : 7TM orphan receptors"	20145	protein-coding gene	gene with protein product	"ocular albinism 1"	300808	"ocular albinism 1 (Nettleship-Falls)"	OA1		7647783, 10471510	Standard	NM_000273		Approved		uc004cst.2	P51810	OTTHUMG00000021118	ENST00000467482.1:c.706A>G	chrX.hg19:g.9711666T>C	ENSP00000417161:p.Arg236Gly	67.0	0.0		70.0	4.0	NM_000273	Q6NTI7	Missense_Mutation	SNP	ENST00000467482.1	hg19	CCDS14134.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.13|18.13	3.556439|3.556439	0.65425|0.65425	.|.	.|.	ENSG00000101850|ENSG00000101850	ENST00000447366|ENST00000467482;ENST00000380929;ENST00000431126	D|D;D;D	0.99399|0.99413	-5.83|-5.86;-5.86;-5.86	5.15|5.15	3.95|3.95	0.45737|0.45737	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99384|0.99384	0.9783|0.9783	M|M	0.80616|0.80616	2.505|2.505	0.53688|0.53688	D|D	0.999976|0.999976	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.99204|0.99204	1.0874|1.0874	6|10	.|0.62326	.|D	.|0.03	-9.3567|-9.3567	10.3836|10.3836	0.44125|0.44125	0.0:0.0:0.1626:0.8374|0.0:0.0:0.1626:0.8374	.|.	.|236	.|P51810	.|GP143_HUMAN	G|G	171|236;256;152	ENSP00000390546:E171G|ENSP00000417161:R236G;ENSP00000370316:R256G;ENSP00000406138:R152G	.|ENSP00000370316:R256G	E|R	-|-	2|1	0|2	GPR143|GPR143	9671666|9671666	1.000000|1.000000	0.71417|0.71417	0.957000|0.957000	0.39632|0.39632	0.777000|0.777000	0.43975|0.43975	2.492000|2.492000	0.45311|0.45311	0.594000|0.594000	0.29761|0.29761	0.417000|0.417000	0.27973|0.27973	GAG|AGG	.	.		0.378	GPR143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055714.2	NM_000273		C	9711666	T	C	9711666	3	2	91	1	0	0	0	0	1	0	0	0	6659	1550	54	2	524	2	GPR143	23	9711666	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	6783500	9711666	145558894	697	12771										
TLR8	51311	hgsc.bcm.edu	37	chrX	12938298	12938298	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tttaagaggttatgtgttccAggaactcagagaagatgatt	11	4	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:12938298A>G	ENST00000218032.6	+	2	1226	c.1139A>G	c.(1138-1140)cAg>cGg	p.Q380R	TLR8_ENST00000311912.5_Missense_Mutation_p.Q398R	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	380					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TATGTGTTCCAGGAACTCAGA	0.358																																					p.Q380R		Atlas-SNP	.											.	TLR8	134	.	0			c.A1139G						.						82	85	84					X																	12938298		2201	4300	6501	SO:0001583	missense	51311	exon2			TGTTCCAGGAACT	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1139A>G	chrX.hg19:g.12938298A>G	ENSP00000218032:p.Gln380Arg	63.0	0.0		59.0	4.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	A	7.190	0.591284	0.13812	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.30448	1.53;1.7	5.67	4.51	0.55191	.	0.198166	0.24856	N	0.035058	T	0.19644	0.0472	N	0.25060	0.705	0.24994	N	0.991519	B;B	0.22746	0.074;0.074	B;B	0.17979	0.02;0.02	T	0.16719	-1.0393	10	0.22706	T	0.39	.	10.7201	0.46036	0.9244:0.0:0.0756:0.0	.	380;398	Q9NR97;D1CS70	TLR8_HUMAN;.	R	380;398	ENSP00000218032:Q380R;ENSP00000312082:Q398R	ENSP00000218032:Q380R	Q	+	2	0	TLR8	12848219	0.976000	0.34144	0.914000	0.36105	0.437000	0.31866	2.446000	0.44908	0.877000	0.35895	0.486000	0.48141	CAG	.	.		0.358	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		G	12938298	A	G	12938298	3	3	91	1	0	0	0	0	1	0	0	0	15972	188	7	2	1145	2	TLR8	23	12938298	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3226632	12938298	142332262	698	12772										
PIR	8544	hgsc.bcm.edu	37	chrX	15477841	15477841	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	agtcttcatgggccatgctgCccccttccaggaggtaggat	12	12	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:15477841C>T	ENST00000380421.3	-	4	672	c.212G>A	c.(211-213)gGc>gAc	p.G71D	PIR_ENST00000476381.1_5'UTR|PIR_ENST00000380420.5_Missense_Mutation_p.G71D	NM_001018109.2|NM_003662.3	NP_001018119.1|NP_003653.1	O00625	PIR_HUMAN	pirin (iron-binding nuclear protein)	71					monocyte differentiation (GO:0030224)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|quercetin 2,3-dioxygenase activity (GO:0008127)|transcription cofactor activity (GO:0003712)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9	Hepatocellular(33;0.183)					GGCCATGCTGCCCCCTTCCAG	0.413																																					p.G71D	Ovarian(180;1587 2015 10555 34192 51653)	Atlas-SNP	.											.	PIR	22	.	0			c.G212A						.						205	200	202					X																	15477841		2203	4300	6503	SO:0001583	missense	8544	exon4			ATGCTGCCCCCTT	Y07868	CCDS14167.1	Xp22.31	2008-02-05			ENSG00000087842	ENSG00000087842			30048	protein-coding gene	gene with protein product		300931				9079676	Standard	NM_003662		Approved		uc004cwv.3	O00625	OTTHUMG00000021176	ENST00000380421.3:c.212G>A	chrX.hg19:g.15477841C>T	ENSP00000369786:p.Gly71Asp	112.0	0.0		84.0	4.0	NM_001018109	Q5U0G0|Q6FHD2	Missense_Mutation	SNP	ENST00000380421.3	hg19	CCDS14167.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.425097	0.83667	.	.	ENSG00000087842	ENST00000380420;ENST00000380421	T;T	0.43294	0.95;0.95	5.98	5.98	0.97165	Cupin, RmlC-type (1);RmlC-like jelly roll fold (1);Pirin, N-terminal (1);	0.063149	0.64402	D	0.000007	T	0.81777	0.4894	H	0.99874	4.875	0.46521	D	0.999083	D	0.89917	1.0	D	0.97110	1.0	D	0.90115	0.4195	10	0.72032	D	0.01	-23.1464	16.5188	0.84308	0.0:1.0:0.0:0.0	.	71	O00625	PIR_HUMAN	D	71	ENSP00000369785:G71D;ENSP00000369786:G71D	ENSP00000369785:G71D	G	-	2	0	PIR	15387762	0.987000	0.35691	0.946000	0.38457	0.992000	0.81027	4.445000	0.60007	2.508000	0.84585	0.600000	0.82982	GGC	.	.		0.413	PIR-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055863.1	NM_003662		T	15477841	C	T	15477841	3	4	91	1	0	0	0	0	1	0	0	0	11953	739	26	3	688	3	PIR	23	15477841	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	2539543	15477841	139792719	699	12773										
PDK3	5165	hgsc.bcm.edu	37	chrX	24521601	24521601	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggttttataccaaccgcatcTctttccgcatgcttattaat	5	11	1	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:24521601T>C	ENST00000379162.4	+	4	713	c.478T>C	c.(478-480)Tct>Cct	p.S160P	PDK3_ENST00000441463.2_Missense_Mutation_p.S160P	NM_005391.4	NP_005382.1	Q15120	PDK3_HUMAN	pyruvate dehydrogenase kinase, isozyme 3	160	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cell death (GO:0008219)|cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to glucose stimulus (GO:0071333)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|peptidyl-serine phosphorylation (GO:0018105)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|regulation of reactive oxygen species metabolic process (GO:2000377)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			NS(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CAACCGCATCTCTTTCCGCAT	0.388																																					p.S160P		Atlas-SNP	.											.	PDK3	86	.	0			c.T478C						.						114	103	107					X																	24521601		2203	4300	6503	SO:0001583	missense	5165	exon4			CGCATCTCTTTCC	L42452	CCDS14212.1, CCDS48088.1	Xp22.12	2008-02-05	2005-11-16		ENSG00000067992	ENSG00000067992			8811	protein-coding gene	gene with protein product		300906	"pyruvate dehydrogenase kinase, isoenzyme 3"			7499431	Standard	NM_001142386		Approved		uc004dbh.3	Q15120	OTTHUMG00000021269	ENST00000379162.4:c.478T>C	chrX.hg19:g.24521601T>C	ENSP00000368460:p.Ser160Pro	115.0	0.0		98.0	4.0	NM_005391	B4DXG6	Missense_Mutation	SNP	ENST00000379162.4	hg19	CCDS14212.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846122	0.71603	.	.	ENSG00000067992	ENST00000379162;ENST00000441463	T;T	0.35605	1.36;1.3	5.94	5.94	0.96194	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal (3);	0.098003	0.64402	D	0.000001	T	0.51753	0.1693	M	0.83603	2.65	0.80722	D	1	B;B	0.26147	0.143;0.143	B;B	0.38056	0.264;0.177	T	0.54186	-0.8331	10	0.59425	D	0.04	.	15.3771	0.74615	0.0:0.0:0.0:1.0	.	160;160	B4DXG6;Q15120	.;PDK3_HUMAN	P	160	ENSP00000368460:S160P;ENSP00000387536:S160P	ENSP00000368460:S160P	S	+	1	0	PDK3	24431522	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.013000	0.88655	2.015000	0.59207	0.483000	0.47432	TCT	.	.		0.388	PDK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056097.1	NM_005391		C	24521601	T	C	24521601	3	2	91	1	0	0	0	0	1	0	0	0	11686	1551	54	2	492	2	PDK3	23	24521601	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9043760	24521601	130748959	700	12774										
DMD	1756	hgsc.bcm.edu	37	chrX	32366626	32366626	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctgagttaaactgctccaatTccttcaaaggaatggaggcc	9	10	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:32366626T>C	ENST00000357033.4	-	38	5551	c.5345A>G	c.(5344-5346)gAa>gGa	p.E1782G	DMD_ENST00000378677.2_Missense_Mutation_p.E1778G	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1782	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				CTGCTCCAATTCCTTCAAAGG	0.323																																					p.E1782G		Atlas-SNP	.											.	DMD	2127	.	0			c.A5345G						.						73	65	68					X																	32366626		2202	4298	6500	SO:0001583	missense	1756	exon38			TCCAATTCCTTCA	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.5345A>G	chrX.hg19:g.32366626T>C	ENSP00000354923:p.Glu1782Gly	106.0	0.0		74.0	5.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.088119	0.55968	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000493412	T;T;T	0.62105	0.05;0.06;0.93	5.49	5.49	0.81192	.	0.000000	0.38111	U	0.001819	T	0.61476	0.2350	N	0.08118	0	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.979;0.998;0.998;0.998	D;P;D;D;D	0.78314	0.991;0.702;0.979;0.991;0.991	T	0.65837	-0.6071	10	0.34782	T	0.22	.	14.6635	0.68891	0.0:0.0:0.0:1.0	.	1774;1782;1778;441;438	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	G	1774;441;438;1778;1782;1782;1659;1	ENSP00000367948:E1778G;ENSP00000354923:E1782G;ENSP00000417725:E1G	ENSP00000354923:E1782G	E	-	2	0	DMD	32276547	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.332000	0.72934	1.844000	0.53588	0.376000	0.23039	GAA	.	.		0.323	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		C	32366626	T	C	32366626	3	2	91	1	0	0	0	0	1	0	0	0	4582	1783	62	2	6028	2	DMD	23	32366626	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	7845025	32366626	122903934	701	12775										
SYN1	6853	hgsc.bcm.edu	37	chrX	47464463	47464463	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atgcagtcgaaccatctgggCaaactatgagaaccaggaga	11	9	1	2	rs143341539		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:47464463C>T	ENST00000295987.7	-	5	812	c.688G>A	c.(688-690)Gcc>Acc	p.A230T	SYN1_ENST00000340666.4_Missense_Mutation_p.A230T	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	230	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						ACCATCTGGGCAAACTATGAG	0.468																																					p.A230T		Atlas-SNP	.											.	SYN1	84	.	0			c.G688A						.	C	THR/ALA,THR/ALA	0,3835		0,0,1632,571	89	76	80		688,688	4.9	1	X	dbSNP_134	80	1,6727		0,1,2427,1872	no	missense,missense	SYN1	NM_006950.3,NM_133499.2	58,58	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	probably-damaging,probably-damaging	230/706,230/670	47464463	1,10562	2203	4300	6503	SO:0001583	missense	6853	exon5			TCTGGGCAAACTA		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.688G>A	chrX.hg19:g.47464463C>T	ENSP00000295987:p.Ala230Thr	114.0	0.0		95.0	4.0	NM_006950	B1AJQ1|O75825|Q5H9A9	Missense_Mutation	SNP	ENST00000295987.7	hg19	CCDS14280.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.862415	0.71949	0.0	1.49E-4	ENSG00000008056	ENST00000295987;ENST00000340666	T;T	0.34072	1.81;1.38	4.88	4.88	0.63580	ATP-grasp fold, subdomain 2 (1);Synapsin, ATP-binding domain (1);	0.000000	0.64402	D	0.000002	T	0.57917	0.2086	M	0.84219	2.685	0.44110	D	0.99688	D;D	0.67145	0.993;0.996	D;P	0.63703	0.917;0.817	T	0.63673	-0.6584	10	0.72032	D	0.01	-2.8311	10.0826	0.42399	0.2005:0.7995:0.0:0.0	.	230;230	P17600;P17600-2	SYN1_HUMAN;.	T	230	ENSP00000295987:A230T;ENSP00000343206:A230T	ENSP00000295987:A230T	A	-	1	0	SYN1	47349407	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	1.617000	0.36943	2.152000	0.67230	0.544000	0.68410	GCC	.	C|1.000;T|0.000		0.468	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950		T	47464463	C	T	47464463	3	4	91	1	0	0	0	0	1	0	0	0	15455	710	25	3	1465	3	SYN1	23	47464463	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	15097837	47464463	107806097	702	12776										
ZNF182	7569	hgsc.bcm.edu	37	chrX	47842408	47842408	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	attcttctacctccaacttgAggatgaggtttggtttggta	10	7	2	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:47842408A>G	ENST00000396965.1	-	6	580	c.230T>C	c.(229-231)cTc>cCc	p.L77P	ZNF182_ENST00000376943.3_Missense_Mutation_p.L58P|ZNF182_ENST00000305127.6_Missense_Mutation_p.L77P	NM_001178099.1	NP_001171570.1	P17025	ZN182_HUMAN	zinc finger protein 182	77	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)	22						CTCCAACTTGAGGATGAGGTT	0.458																																					p.L77P		Atlas-SNP	.											.	ZNF182	117	.	0			c.T230C						.						128	100	110					X																	47842408		2203	4300	6503	SO:0001583	missense	7569	exon6			AACTTGAGGATGA	AK122874, R98366	CCDS35235.1, CCDS35236.1	Xp11.23	2013-01-08	2006-05-10	2006-05-10	ENSG00000147118	ENSG00000147118		"Zinc fingers, C2H2-type", "-"	13001	protein-coding gene	gene with protein product		314993	"zinc finger protein 182 (HHZ150)", "zinc finger protein 21 (KOX 14)"	ZNF21		8088786, 2014798, 8914609	Standard	NM_001178099		Approved	KOX14, HHZ150, Zfp182	uc004dit.3	P17025	OTTHUMG00000021460	ENST00000396965.1:c.230T>C	chrX.hg19:g.47842408A>G	ENSP00000380165:p.Leu77Pro	81.0	0.0		75.0	4.0	NM_006962	A2IDD7|Q3KP67|Q96QH7	Missense_Mutation	SNP	ENST00000396965.1	hg19	CCDS35236.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.221206	0.39201	.	.	ENSG00000147118	ENST00000376943;ENST00000396965;ENST00000305127	T;T;T	0.00892	5.57;5.57;5.57	4.42	4.42	0.53409	Krueppel-associated box (3);	.	.	.	.	T	0.01765	0.0056	L	0.29908	0.895	0.49389	D	0.999781	P;P;D	0.57571	0.874;0.823;0.98	B;B;P	0.58013	0.24;0.392;0.831	T	0.74420	-0.3671	9	0.33141	T	0.24	.	9.0057	0.36111	1.0:0.0:0.0:0.0	.	58;58;77	B4DRM0;Q96QH7;P17025	.;.;ZN182_HUMAN	P	58;77;77	ENSP00000366142:L58P;ENSP00000380165:L77P;ENSP00000306351:L77P	ENSP00000306351:L77P	L	-	2	0	ZNF182	47727352	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.542000	0.36137	1.948000	0.56530	0.486000	0.48141	CTC	.	.		0.458	ZNF182-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277055.1	NM_006962		G	47842408	A	G	47842408	3	3	91	1	0	0	0	0	1	0	0	0	17765	304	11	2	1697	2	ZNF182	23	47842408	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	377945	47842408	107428152	703	12777										
WDR13	64743	hgsc.bcm.edu	37	chrX	48458002	48458002	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggcagcgtggtgcccacgtcAgcagcagaggcaagtcgggc	17	12	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:48458002A>G	ENST00000218056.5	+	4	925	c.420A>G	c.(418-420)tcA>tcG	p.S140S	WDR13_ENST00000492715.1_3'UTR|WDR13_ENST00000376729.5_Silent_p.S140S	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	140						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						TGCCCACGTCAGCAGCAGAGG	0.612																																					p.S140S		Atlas-SNP	.											.	WDR13	96	.	0			c.A420G						.						82	71	74					X																	48458002		2203	4300	6503	SO:0001819	synonymous_variant	64743	exon4			CACGTCAGCAGCA	AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"WD repeat domain containing"	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.420A>G	chrX.hg19:g.48458002A>G		92.0	0.0		84.0	4.0	NM_017883	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Silent	SNP	ENST00000218056.5	hg19	CCDS14302.1																																																																																			.	.		0.612	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2			G	48458002	A	G	48458002	2	3	91	1	0	0	0	0	0	0	0	1	17290	175	7	2		2	WDR13	23	48458002	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	615594	48458002	106812558	704	12778										
CCNB3	85417	hgsc.bcm.edu	37	chrX	50053332	50053332	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gagaaaagcaccatggaagaAgagtcccttatcaataagct	9	8	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:50053332A>G	ENST00000376042.1	+	6	2461	c.2163A>G	c.(2161-2163)gaA>gaG	p.E721E	CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Silent_p.E721E			Q8WWL7	CCNB3_HUMAN	cyclin B3	721					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					CCATGGAAGAAGAGTCCCTTA	0.453																																					p.E721E		Atlas-SNP	.											.	CCNB3	367	.	0			c.A2163G						.						38	36	37					X																	50053332		2203	4300	6503	SO:0001819	synonymous_variant	85417	exon5			GGAAGAAGAGTCC	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.2163A>G	chrX.hg19:g.50053332A>G		194.0	0.0		177.0	8.0	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Silent	SNP	ENST00000376042.1	hg19	CCDS14331.1																																																																																			.	.		0.453	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			G	50053332	A	G	50053332	2	3	91	1	0	0	0	0	0	0	0	1	2916	69	3	2		2	CCNB3	23	50053332	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1595330	50053332	105217228	705	12779										
KDM5C	8242	hgsc.bcm.edu	37	chrX	53223019	53223019	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gtcacactgtctccattctcCagtaagccctggacctgcgg	9	15	3	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:53223019C>T	ENST00000375401.3	-	24	4585	c.4053G>A	c.(4051-4053)ctG>ctA	p.L1351L	KDM5C_ENST00000375379.3_Silent_p.L1351L|KDM5C_ENST00000452825.3_Silent_p.L1284L|KDM5C_ENST00000375383.3_Silent_p.L1310L|KDM5C_ENST00000404049.3_Silent_p.L1350L	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1351					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						CTCCATTCTCCAGTAAGCCCT	0.567			"N, F, S"		clear cell renal carcinoma																																p.L1351L		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G4053A						.						109	80	90					X																	53223019		2203	4300	6503	SO:0001819	synonymous_variant	8242	exon24			ATTCTCCAGTAAG	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11114	protein-coding gene	gene with protein product		314690	"Jumonji, AT rich interactive domain 1C (RBP2-like)", "Smcy homolog, X-linked (mouse)", "jumonji, AT rich interactive domain 1C", "mental retardation, X-linked 13"	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.4053G>A	chrX.hg19:g.53223019C>T		93.0	0.0		79.0	4.0	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Silent	SNP	ENST00000375401.3	hg19	CCDS14351.1																																																																																			.	.		0.567	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		T	53223019	C	T	53223019	2	4	91	1	0	0	0	0	0	0	0	1	8144	581	21	3		3	KDM5C	23	53223019	Silent	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	3169687	53223019	102047541	706	12780										
PHF8	23133	hgsc.bcm.edu	37	chrX	54011486	54011486	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ggggtgcgctgggaagcaggActgttagacactgtgcccag	17	9	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:54011486A>G	ENST00000357988.5	-	18	2770	c.2412T>C	c.(2410-2412)agT>agC	p.S804S	PHF8_ENST00000338946.6_Silent_p.S667S|PHF8_ENST00000322659.8_Silent_p.S751S|PHF8_ENST00000338154.6_Silent_p.S768S	NM_001184896.1	NP_001171825.1	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	804	Ser-rich.				brain development (GO:0007420)|G1/S transition of mitotic cell cycle (GO:0000082)|histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of chromatin silencing at rDNA (GO:0061188)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	40						GGGAAGCAGGACTGTTAGACA	0.637																																					p.S804S		Atlas-SNP	.											.	PHF8	198	.	0			c.T2412C						.						68	55	60					X																	54011486		2203	4300	6503	SO:0001819	synonymous_variant	23133	exon18			AGCAGGACTGTTA	AB029034	CCDS14355.1, CCDS55418.1, CCDS55419.1, CCDS55420.1	Xp11.22	2013-01-28			ENSG00000172943	ENSG00000172943		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	20672	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1F"	300560				10470851, 20023638, 20644565	Standard	NM_015107		Approved	ZNF422, KIAA1111, JHDM1F	uc004dsu.3	Q9UPP1	OTTHUMG00000021622	ENST00000357988.5:c.2412T>C	chrX.hg19:g.54011486A>G		52.0	0.0		46.0	4.0	NM_001184896	B3KMV4|B7Z911|Q5H9U5|Q5JPR9|Q5JPS0|Q5JPS2|Q5JPS3|Q5VUJ4|Q7Z6D4|Q9HAH2	Silent	SNP	ENST00000357988.5	hg19	CCDS55420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.979|9.979	1.227489|1.227489	0.22542|0.22542	.|.	.|.	ENSG00000172943|ENSG00000172943	ENST00000443302|ENST00000396282;ENST00000375189	T|.	0.48836|.	0.8|.	5.74|5.74	1.88|1.88	0.25563|0.25563	.|.	0.341060|.	0.37577|.	N|.	0.002036|.	T|T	0.38295|0.38295	0.1035|0.1035	.|.	.|.	.|.	0.30323|0.30323	N|N	0.78743|0.78743	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.46610|0.46610	-0.9179|-0.9179	7|5	0.24483|0.87932	T|D	0.36|0	-13.8079|-13.8079	3.2386|3.2386	0.06773|0.06773	0.4701:0.2157:0.3142:0.0|0.4701:0.2157:0.3142:0.0	.|.	.|.	.|.	.|.	P|A	532|672;244	ENSP00000397129:S532P|.	ENSP00000397129:S532P|ENSP00000364335:V244A	S|V	-|-	1|2	0|0	PHF8|PHF8	54028211|54028211	0.108000|0.108000	0.22018|0.22018	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	0.561000|0.561000	0.23515|0.23515	0.804000|0.804000	0.34136|0.34136	0.486000|0.486000	0.48141|0.48141	TCC|GTC	.	.		0.637	PHF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056784.2	NM_015107		G	54011486	A	G	54011486	2	3	91	1	0	0	0	0	0	0	0	1	11849	272	10	2		2	PHF8	23	54011486	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	788467	54011486	101259074	707	12781										
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54786268	54786268	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gcctggattgagcctccagcTttccaaacattaactgtgtc	8	12	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:54786268T>C	ENST00000218436.6	-	7	1025	c.996A>G	c.(994-996)aaA>aaG	p.K332K		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	332	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										AGCCTCCAGCTTTCCAAACAT	0.478																																					p.K332K		Atlas-SNP	.											.	.	.	.	0			c.A996G						.						162	121	135					X																	54786268		2203	4300	6503	SO:0001819	synonymous_variant	347365	exon7			TCCAGCTTTCCAA	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.996A>G	chrX.hg19:g.54786268T>C		119.0	0.0		93.0	4.0	NM_198510	A6NN03	Silent	SNP	ENST00000218436.6	hg19	CCDS14361.1																																																																																			.	.		0.478	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		C	54786268	T	C	54786268	2	2	91	1	0	0	0	0	0	0	0	1	7917	1606	56	2		2	ITIH5L	23	54786268	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	774782	54786268	100484292	708	12782										
ZC3H12B	340554	hgsc.bcm.edu	37	chrX	64709115	64709115	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	taatgatgtattggcagagcTtgtcagacttgggaacaaag	12	5	1	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:64709115T>C	ENST00000338957.4	+	1	501	c.434T>C	c.(433-435)cTt>cCt	p.L145P	ZC3H12B_ENST00000423889.3_Missense_Mutation_p.L134P	NM_001010888.3	NP_001010888.3	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	145							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TTGGCAGAGCTTGTCAGACTT	0.478																																					p.L145P		Atlas-SNP	.											.	ZC3H12B	144	.	0			c.T434C						.						86	83	84					X																	64709115		1938	4128	6066	SO:0001583	missense	340554	exon1			CAGAGCTTGTCAG	BX647241	CCDS48131.1, CCDS48131.2	Xq12	2012-07-05	2005-06-14	2005-06-14	ENSG00000102053	ENSG00000102053		"Zinc fingers, CCCH-type domain containing"	17407	protein-coding gene	gene with protein product	"MCP induced protein 2"	300889	"chromosome X open reading frame 32"	CXorf32		18178554	Standard	NM_001010888		Approved	MCPIP2	uc010nko.3	Q5HYM0	OTTHUMG00000021719	ENST00000338957.4:c.434T>C	chrX.hg19:g.64709115T>C	ENSP00000340839:p.Leu145Pro	78.0	0.0		74.0	4.0	NM_001010888	B2RTQ3|E9PAJ6|Q5H9C0	Missense_Mutation	SNP	ENST00000338957.4	hg19	CCDS48131.2	.	.	.	.	.	.	.	.	.	.	T	19.20	3.781242	0.70222	.	.	ENSG00000102053	ENST00000338957;ENST00000423889	T;T	0.61627	0.09;0.11	5.36	5.36	0.76844	.	0.458821	0.17941	N	0.156844	T	0.75280	0.3828	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77587	-0.2532	10	0.87932	D	0	-28.8678	13.1206	0.59325	0.0:0.0:0.0:1.0	.	134	Q5HYM0	ZC12B_HUMAN	P	145;134	ENSP00000340839:L145P;ENSP00000408077:L134P	ENSP00000340839:L145P	L	+	2	0	ZC3H12B	64625840	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.423000	0.80229	1.983000	0.57843	0.412000	0.27726	CTT	.	.		0.478	ZC3H12B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378734.2	XM_293334		C	64709115	T	C	64709115	3	2	91	1	0	0	0	0	1	0	0	0	17577	1609	56	2	436	2	ZC3H12B	23	64709115	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	9922847	64709115	90561445	709	12783										
FOXO4	4303	hgsc.bcm.edu	37	chrX	70320733	70320733	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ccccaagaagaaaccatctgTgctgccagctccacccgaag	8	16	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:70320733T>C	ENST00000374259.3	+	2	985	c.653T>C	c.(652-654)gTg>gCg	p.V218A	FOXO4_ENST00000341558.3_Missense_Mutation_p.V163A	NM_001170931.1|NM_005938.3	NP_001164402.1|NP_005929.2	P98177	FOXO4_HUMAN	forkhead box O4	218					cell cycle arrest (GO:0007050)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mitotic G2 DNA damage checkpoint (GO:0007095)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of smooth muscle cell differentiation (GO:0051151)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)	18	Renal(35;0.156)					AAACCATCTGTGCTGCCAGCT	0.642											OREG0019856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V218A		Atlas-SNP	.											.	FOXO4	60	.	0			c.T653C						.						21	22	22					X																	70320733		1952	4136	6088	SO:0001583	missense	4303	exon2			CATCTGTGCTGCC		CCDS43969.1, CCDS55440.1	Xq13.1	2008-02-05	2007-05-02	2007-05-02	ENSG00000184481	ENSG00000184481		"Forkhead boxes"	7139	protein-coding gene	gene with protein product		300033	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 7", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7"	MLLT7		7529552	Standard	NM_005938		Approved	AFX1	uc004dys.2	P98177	OTTHUMG00000021789	ENST00000374259.3:c.653T>C	chrX.hg19:g.70320733T>C	ENSP00000363377:p.Val218Ala	33.0	0.0	1121	39.0	4.0	NM_005938	B7WPJ7|O43821|Q13720|Q3KPF1|Q8TDK9	Missense_Mutation	SNP	ENST00000374259.3	hg19	CCDS43969.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.210425	0.00292	.	.	ENSG00000184481	ENST00000374259;ENST00000341558	D;D	0.95412	-3.48;-3.7	5.11	1.14	0.20703	.	0.325828	0.26776	N	0.022542	D	0.83751	0.5322	N	0.04880	-0.145	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.002;0.001	T	0.71090	-0.4693	10	0.09338	T	0.73	-19.6219	4.8266	0.13419	0.0:0.1744:0.1557:0.6699	.	218;163;218	B4DTB6;P98177-2;P98177	.;.;FOXO4_HUMAN	A	218;163	ENSP00000363377:V218A;ENSP00000342209:V163A	ENSP00000342209:V163A	V	+	2	0	FOXO4	70237458	0.852000	0.29690	0.019000	0.16419	0.005000	0.04900	0.608000	0.24223	0.232000	0.21100	0.422000	0.28245	GTG	.	.		0.642	FOXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057115.1	NM_005938		C	70320733	T	C	70320733	3	2	91	1	0	0	0	0	1	0	0	0	6033	1696	59	2	659	2	FOXO4	23	70320733	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	5611618	70320733	84949827	710	12784										
TAF1	6872	hgsc.bcm.edu	37	chrX	70601683	70601683	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atatggacgctgggaggacaAtatcatttgggatgctcagg	14	6	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:70601683A>G	ENST00000373790.4	+	9	1499	c.1448A>G	c.(1447-1449)aAt>aGt	p.N483S	TAF1_ENST00000276072.3_Missense_Mutation_p.N504S|TAF1_ENST00000423759.1_Missense_Mutation_p.N504S|TAF1_ENST00000449580.1_Missense_Mutation_p.N483S	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	483					cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				TGGGAGGACAATATCATTTGG	0.458																																					p.N504S		Atlas-SNP	.											.	TAF1	439	.	0			c.A1511G						.						144	115	125					X																	70601683		2203	4300	6503	SO:0001583	missense	6872	exon9			AGGACAATATCAT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.1448A>G	chrX.hg19:g.70601683A>G	ENSP00000362895:p.Asn483Ser	110.0	0.0		70.0	4.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	16.72	3.200855	0.58234	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.10860	2.83;2.91;2.88;2.83	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.14700	0.0355	L	0.54323	1.7	0.58432	D	0.999999	B;B	0.28584	0.138;0.216	B;B	0.33846	0.119;0.171	T	0.03728	-1.1009	10	0.30854	T	0.27	.	14.5732	0.68226	1.0:0.0:0.0:0.0	.	483;504	P21675;P21675-2	TAF1_HUMAN;.	S	483;483;504;504	ENSP00000362895:N483S;ENSP00000389000:N483S;ENSP00000406549:N504S;ENSP00000276072:N504S	ENSP00000276072:N504S	N	+	2	0	TAF1	70518408	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.125000	0.77193	1.821000	0.53095	0.481000	0.45027	AAT	.	.		0.458	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		G	70601683	A	G	70601683	3	3	91	1	0	0	0	0	1	0	0	0	15528	101	4	2	1545	2	TAF1	23	70601683	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	280950	70601683	84668877	711	12785										
RGAG4	340526	hgsc.bcm.edu	37	chrX	71349868	71349868	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaagtgggactcgattctggTtcctccgtctgctaggctgt	13	10	2	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:71349868T>C	ENST00000545866.1	-	1	1890	c.1523A>G	c.(1522-1524)aAc>aGc	p.N508S	NHSL2_ENST00000540800.1_Intron|RGAG4_ENST00000609883.1_Missense_Mutation_p.N508S	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	508										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					TCGATTCTGGTTCCTCCGTCT	0.557																																					p.N508S		Atlas-SNP	.											.	RGAG4	63	.	0			c.A1523G						.						53	55	54					X																	71349868		2030	4148	6178	SO:0001583	missense	340526	exon1			TTCTGGTTCCTCC	AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.1523A>G	chrX.hg19:g.71349868T>C	ENSP00000441366:p.Asn508Ser	140.0	0.0		122.0	5.0	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	hg19	CCDS55446.1	.	.	.	.	.	.	.	.	.	.	T	11.26	1.587655	0.28268	.	.	ENSG00000242732	ENST00000545866;ENST00000479991	T;T	0.14893	2.47;2.47	3.89	0.0353	0.14187	.	.	.	.	.	T	0.07007	0.0178	N	0.08118	0	0.21220	N	0.999754	B	0.17038	0.02	B	0.09377	0.004	T	0.42015	-0.9476	8	.	.	.	.	5.8822	0.18862	0.0:0.3757:0.0:0.6243	.	508	Q5HYW3	RGAG4_HUMAN	S	508	ENSP00000441366:N508S;ENSP00000418667:N508S	.	N	-	2	0	RGAG4	71266593	0.998000	0.40836	0.997000	0.53966	0.720000	0.41350	0.012000	0.13287	-0.091000	0.12440	0.417000	0.27973	AAC	.	.		0.557	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455		C	71349868	T	C	71349868	3	2	91	1	0	0	0	0	1	0	0	0	13290	1725	60	2	190	2	RGAG4	23	71349868	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	748185	71349868	83920692	712	12786										
DACH2	117154	hgsc.bcm.edu	37	chrX	86069720	86069720	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaaagcgcctgaagaaggagAaaaaaaccaagagaaaattg	10	5	0	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:86069720A>G	ENST00000373125.4	+	10	1567	c.1567A>G	c.(1567-1569)Aaa>Gaa	p.K523E	DACH2_ENST00000510272.1_Missense_Mutation_p.K304E|DACH2_ENST00000373131.1_Missense_Mutation_p.K510E|DACH2_ENST00000508860.1_Missense_Mutation_p.K356E	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	523	DACHbox-C.				development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						GAAGAAGGAGAAAAAAACCAA	0.428																																					p.K523E		Atlas-SNP	.											.	DACH2	263	.	0			c.A1567G						.						58	55	56					X																	86069720		2203	4300	6503	SO:0001583	missense	117154	exon10			AAGGAGAAAAAAA	AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.1567A>G	chrX.hg19:g.86069720A>G	ENSP00000362217:p.Lys523Glu	41.0	0.0		46.0	4.0	NM_053281	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	hg19	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.970788	0.74246	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297;ENST00000484479	D;D	0.88741	-2.37;-2.42	4.76	4.76	0.60689	.	0.000000	0.64402	D	0.000001	D	0.93416	0.7900	M	0.72894	2.215	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.998;0.998	D;D;D;D	0.87578	0.998;0.998;0.991;0.989	D	0.93778	0.7081	10	0.62326	D	0.03	.	13.4743	0.61299	1.0:0.0:0.0:0.0	.	389;523;510;523	Q1RMF5;A8K3I1;Q96NX9-2;Q96NX9	.;.;.;DACH2_HUMAN	E	523;510;523;356;304;356;188	ENSP00000362223:K510E;ENSP00000362217:K523E	ENSP00000345134:K523E	K	+	1	0	DACH2	85956376	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	8.793000	0.91862	1.553000	0.49476	0.339000	0.21740	AAA	.	.		0.428	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		G	86069720	A	G	86069720	3	3	91	1	0	0	0	0	1	0	0	0	4223	247	9	2	1605	2	DACH2	23	86069720	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	14719852	86069720	69200840	713	12787										
NXF3	56000	hgsc.bcm.edu	37	chrX	102339711	102339711	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcttgctgctgatgggatgaAgaatgcatgccaggattgac	13	7	1	4			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:102339711A>G	ENST00000395065.3	-	2	230	c.129T>C	c.(127-129)tcT>tcC	p.S43S	NXF3_ENST00000425644.1_5'UTR|NXF3_ENST00000425463.2_Intron	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	43					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)			NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						GATGGGATGAAGAATGCATGC	0.458																																					p.S43S		Atlas-SNP	.											.	NXF3	81	.	0			c.T129C						.						254	204	221					X																	102339711		2203	4300	6503	SO:0001819	synonymous_variant	56000	exon2			GGATGAAGAATGC	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.129T>C	chrX.hg19:g.102339711A>G		130.0	0.0		113.0	5.0	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Silent	SNP	ENST00000395065.3	hg19	CCDS14503.1																																																																																			.	.		0.458	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		G	102339711	A	G	102339711	2	3	91	1	0	0	0	0	0	0	0	1	10794	59	3	2		2	NXF3	23	102339711	Silent	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	16269991	102339711	52930849	714	12788										
MCART6	401612	hgsc.bcm.edu	37	chrX	103349276	103349276	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	gaactaggcaggtgattgttCcattgacactaccagacacc	9	11	0	3			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:103349276C>T	ENST00000357421.4	-	2	845	c.665G>A	c.(664-666)gGa>gAa	p.G222E		NM_001012755.3	NP_001012773.2	Q5H9E4	S2553_HUMAN	solute carrier family 25, member 53	222					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											GGTGATTGTTCCATTGACACT	0.522																																					p.G222E		Atlas-SNP	.											.	.	.	.	0			c.G665A						.						71	69	69					X																	103349276		2203	4300	6503	SO:0001583	missense	401612	exon2			ATTGTTCCATTGA		CCDS35363.1	Xq22.2	2013-05-22	2012-03-29	2012-03-29	ENSG00000176274	ENSG00000269743		"Solute carriers"	31894	protein-coding gene	gene with protein product			"mitochondrial carrier triple repeat 6"	MCART6			Standard	NM_001012755		Approved		uc004elu.3	Q5H9E4	OTTHUMG00000022124	ENST00000357421.4:c.665G>A	chrX.hg19:g.103349276C>T	ENSP00000361681:p.Gly222Glu	107.0	0.0		82.0	5.0	NM_001012755	B2RTT9	Missense_Mutation	SNP	ENST00000357421.4	hg19	CCDS35363.1	.	.	.	.	.	.	.	.	.	.	c	13.17	2.158299	0.38119	.	.	ENSG00000176274	ENST00000357421	D	0.85171	-1.95	4.18	4.18	0.49190	Mitochondrial carrier domain (2);	0.145961	0.46442	D	0.000293	D	0.84101	0.5398	M	0.72894	2.215	0.42889	D	0.994194	B	0.15719	0.014	B	0.20184	0.028	D	0.83794	0.0232	10	0.72032	D	0.01	-19.2128	13.1831	0.59666	0.0:1.0:0.0:0.0	.	222	Q5H9E4	MCAR6_HUMAN	E	222	ENSP00000361681:G222E	ENSP00000361681:G222E	G	-	2	0	MCART6	103235932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.415000	0.52700	2.061000	0.61500	0.594000	0.82650	GGA	.	.		0.522	SLC25A53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057761.1	NM_001012755		T	103349276	C	T	103349276	3	4	91	1	0	0	0	0	1	0	0	0	9380	855	30	3	262	3	MCART6	23	103349276	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	1009565	103349276	51921284	715	12789										
GUCY2F	2986	hgsc.bcm.edu	37	chrX	108628445	108628445	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	attccatccgagaagctgtgTtcacagtgtctccaaacaag	8	11	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:108628445T>C	ENST00000218006.2	-	16	3314	c.3023A>G	c.(3022-3024)aAc>aGc	p.N1008S		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	1008	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						AGAAGCTGTGTTCACAGTGTC	0.488																																					p.N1008S		Atlas-SNP	.											.	GUCY2F	178	.	0			c.A3023G						.						139	99	113					X																	108628445		2203	4300	6503	SO:0001583	missense	2986	exon16			GCTGTGTTCACAG	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.3023A>G	chrX.hg19:g.108628445T>C	ENSP00000218006:p.Asn1008Ser	97.0	0.0		99.0	4.0	NM_001522	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	hg19	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.968721	0.53614	.	.	ENSG00000101890	ENST00000218006	D	0.88124	-2.34	3.97	3.97	0.46021	Adenylyl cyclase class-3/4/guanylyl cyclase, conserved site (1);Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.153676	0.56097	D	0.000031	D	0.92773	0.7702	M	0.91249	3.19	0.34090	D	0.660587	D	0.63046	0.992	P	0.58331	0.837	D	0.95788	0.8822	10	0.87932	D	0	.	10.2551	0.43392	0.0:0.0:0.0:1.0	.	1008	P51841	GUC2F_HUMAN	S	1008	ENSP00000218006:N1008S	ENSP00000218006:N1008S	N	-	2	0	GUCY2F	108515101	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	3.898000	0.56281	1.781000	0.52344	0.486000	0.48141	AAC	.	.		0.488	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		C	108628445	T	C	108628445	3	2	91	1	0	0	0	0	1	0	0	0	6907	1725	60	2	319	2	GUCY2F	23	108628445	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	5279169	108628445	46642115	716	12790										
AMOT	154796	hgsc.bcm.edu	37	chrX	112021881	112021881	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ttccagagtattggagtggaAcacaggcccatctaaatgga	11	8	1	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:112021881A>G	ENST00000524145.1	-	12	3243	c.3169T>C	c.(3169-3171)Ttc>Ctc	p.F1057L	AMOT_ENST00000371962.1_Missense_Mutation_p.F825L|AMOT_ENST00000371959.3_Missense_Mutation_p.F1057L|MIR4329_ENST00000582643.1_RNA|AMOT_ENST00000304758.1_Missense_Mutation_p.F648L			Q4VCS5	AMOT_HUMAN	angiomotin	1057					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						TTGGAGTGGAACACAGGCCCA	0.433																																					p.F1057L		Atlas-SNP	.											.	AMOT	204	.	0			c.T3169C						.						169	156	160					X																	112021881		2203	4300	6503	SO:0001583	missense	154796	exon11			AGTGGAACACAGG	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.3169T>C	chrX.hg19:g.112021881A>G	ENSP00000429013:p.Phe1057Leu	89.0	0.0		79.0	4.0	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	hg19	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	A	15.22	2.768448	0.49680	.	.	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145	T;T;T;T	0.18657	2.2;2.24;2.48;2.24	6.01	3.52	0.40303	.	0.235189	0.32343	N	0.006229	T	0.10680	0.0261	N	0.19112	0.55	0.33031	D	0.53019	B	0.02656	0.0	B	0.06405	0.002	T	0.16541	-1.0399	10	0.08599	T	0.76	-7.9949	8.5959	0.33714	0.7442:0.1289:0.0:0.1268	.	1057	Q4VCS5	AMOT_HUMAN	L	648;1057;825;1057	ENSP00000305557:F648L;ENSP00000361027:F1057L;ENSP00000361030:F825L;ENSP00000429013:F1057L	ENSP00000305557:F648L	F	-	1	0	AMOT	111908537	1.000000	0.71417	0.978000	0.43139	0.965000	0.64279	5.024000	0.64090	2.020000	0.59435	0.486000	0.48141	TTC	.	.		0.433	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		G	112021881	A	G	112021881	3	3	91	1	0	0	0	0	1	0	0	0	582	43	2	2	89	2	AMOT	23	112021881	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	3393436	112021881	43248679	717	12791										
KLHL13	90293	hgsc.bcm.edu	37	chrX	117079481	117079481	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tgcaaatgggatgagaggccCatttcgctgcctccaaggga	13	10	0	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:117079481C>T	ENST00000262820.3	-	2	1065	c.156G>A	c.(154-156)atG>atA	p.M52I	KLHL13_ENST00000371876.1_Start_Codon_SNP_p.M1I|KLHL13_ENST00000371878.1_Start_Codon_SNP_p.M1I|KLHL13_ENST00000469946.1_Start_Codon_SNP_p.M1I|KLHL13_ENST00000545703.1_Missense_Mutation_p.M10I|KLHL13_ENST00000539496.1_Missense_Mutation_p.M55I|KLHL13_ENST00000540167.1_Missense_Mutation_p.M36I|KLHL13_ENST00000541812.1_Missense_Mutation_p.M36I|KLHL13_ENST00000371882.1_Start_Codon_SNP_p.M1I	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	52					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						ATGAGAGGCCCATTTCGCTGC	0.433																																					p.M55I		Atlas-SNP	.											.	KLHL13	87	.	0			c.G165A						.						104	85	92					X																	117079481		2203	4300	6503	SO:0001583	missense	90293	exon3			GAGGCCCATTTCG	AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"Kelch-like", "BTB/POZ domain containing"	22931	protein-coding gene	gene with protein product		300655	"BTB and kelch domain containing 2, KIAA1309", "kelch-like 13 (Drosophila)"	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.156G>A	chrX.hg19:g.117079481C>T	ENSP00000262820:p.Met52Ile	126.0	0.0		97.0	4.0	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Missense_Mutation	SNP	ENST00000262820.3	hg19	CCDS14571.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372477	0.61624	.	.	ENSG00000003096	ENST00000371882;ENST00000371876;ENST00000371878;ENST00000447671;ENST00000541812;ENST00000540167;ENST00000539496;ENST00000262820;ENST00000545703;ENST00000469946;ENST00000453826	T;T;T;T;T;T;T;T;T;T	0.70282	-0.38;-0.38;-0.38;-0.38;-0.36;-0.36;-0.47;-0.47;-0.44;-0.38	5.09	5.09	0.68999	.	0.077063	0.85682	D	0.000000	T	0.52517	0.1739	N	0.08118	0	0.80722	D	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.48433	-0.9036	10	0.35671	T	0.21	.	16.4339	0.83864	0.0:1.0:0.0:0.0	.	36;55;46;52	Q9P2N7-3;Q9P2N7-5;Q9P2N7-4;Q9P2N7	.;.;.;KLH13_HUMAN	I	1;1;1;1;36;36;55;52;10;1;1	ENSP00000360949:M1I;ENSP00000360943:M1I;ENSP00000360945:M1I;ENSP00000412640:M1I;ENSP00000444450:M36I;ENSP00000441029:M36I;ENSP00000443191:M55I;ENSP00000262820:M52I;ENSP00000440707:M10I;ENSP00000419803:M1I	ENSP00000262820:M52I	M	-	3	0	KLHL13	116963509	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.209000	0.65208	2.490000	0.84030	0.594000	0.82650	ATG	.	.		0.433	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495		T	117079481	C	T	117079481	3	4	91	1	0	0	0	0	1	0	0	0	8378	594	21	3	1835	3	KLHL13	23	117079481	Missense_Mutation	SNP	C	TCGA-DD-A119-01A-11D-A12Z-10	5057600	117079481	38191079	718	12792										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118284386	118284386	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	ctccttcttgcctttgtaagTcaaccaaagacaactgcaac	5	13	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:118284386T>C	ENST00000402510.2	-	1	156	c.157A>G	c.(157-159)Act>Gct	p.T53A		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	53										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						CCTTTGTAAGTCAACCAAAGA	0.597																																					p.T53A		Atlas-SNP	.											.	KIAA1210	171	.	0			c.A157G						.						47	51	50					X																	118284386		2000	4151	6151	SO:0001583	missense	57481	exon1			TGTAAGTCAACCA	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.157A>G	chrX.hg19:g.118284386T>C	ENSP00000384670:p.Thr53Ala	88.0	0.0		87.0	5.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	T	9.486	1.099506	0.20552	.	.	ENSG00000250423	ENST00000402510	T	0.11169	2.8	3.74	1.19	0.21007	.	.	.	.	.	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	P	0.40731	0.728	B	0.30105	0.111	T	0.35674	-0.9779	9	0.87932	D	0	.	3.5273	0.07763	0.2208:0.0:0.2583:0.521	.	53	Q9ULL0	K1210_HUMAN	A	53	ENSP00000384670:T53A	ENSP00000384670:T53A	T	-	1	0	RP13-347D8.6	118168414	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.164000	0.09983	0.117000	0.18138	0.486000	0.48141	ACT	.	.		0.597	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		C	118284386	T	C	118284386	3	2	91	1	0	0	0	0	1	0	0	0	8223	1667	58	2	5028	2	KIAA1210	23	118284386	Missense_Mutation	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1204905	118284386	36986174	719	12793										
ZDHHC9	51114	hgsc.bcm.edu	37	chrX	128975901	128975901	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	catttccgtgtcaccttcttTctcaccaccatcacagacat	3	16	4	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:128975901T>C	ENST00000357166.6	-	3	412	c.21A>G	c.(19-21)agA>agG	p.R7R	ZDHHC9_ENST00000371064.3_Silent_p.R7R	NM_016032.3	NP_057116.2	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC-type containing 9	7					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|Ras palmitoyltransferase activity (GO:0043849)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	19						TCACCTTCTTTCTCACCACCA	0.498																																					p.R7R		Atlas-SNP	.											.	ZDHHC9	41	.	0			c.A21G						.						171	137	148					X																	128975901		2203	4300	6503	SO:0001819	synonymous_variant	51114	exon2			CTTCTTTCTCACC	AF151847	CCDS35395.1	Xq26.1	2008-02-05			ENSG00000188706	ENSG00000188706		"Zinc fingers, DHHC-type"	18475	protein-coding gene	gene with protein product		300646	"zinc finger, DHHC-type containing 10", "chromosome X open reading frame 11"	ZDHHC10, CXorf11		10810093	Standard	NM_001008222		Approved	ZNF379, CGI-89, ZNF380	uc004euw.3	Q9Y397	OTTHUMG00000022375	ENST00000357166.6:c.21A>G	chrX.hg19:g.128975901T>C		112.0	0.0		103.0	6.0	NM_001008222	B4F6G2|D3DTF9|Q59EK4|Q5JSW5|Q8WWS7|Q9BPY4|Q9NSP0|Q9NVL0|Q9NVR6	Silent	SNP	ENST00000357166.6	hg19	CCDS35395.1																																																																																			.	.		0.498	ZDHHC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058213.1	NM_016032		C	128975901	T	C	128975901	2	2	91	1	0	0	0	0	0	0	0	1	17637	1780	62	2		2	ZDHHC9	23	128975901	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	10691515	128975901	26294659	720	12794										
CXorf48	54967	hgsc.bcm.edu	37	chrX	134292208	134292208	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	tcagtggaatattcaacttcTaacaagtcacccttataagg	6	9	4	0			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:134292208T>C	ENST00000276241.6	-	4	679	c.453A>G	c.(451-453)ttA>ttG	p.L151L	CXorf48_ENST00000344129.2_Silent_p.L151L	NM_001031705.2	NP_001026875.1	Q8WUE5	CT55_HUMAN		151										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)	5	Acute lymphoblastic leukemia(192;0.000127)					ATTCAACTTCTAACAAGTCAC	0.383																																					p.L151L		Atlas-SNP	.											.	CXorf48	17	.	0			c.A453G						.						101	90	94					X																	134292208		2203	4300	6503	SO:0001819	synonymous_variant	54967	exon4			AACTTCTAACAAG																												ENST00000276241.6:c.453A>G	chrX.hg19:g.134292208T>C		97.0	0.0		98.0	4.0	NM_017863	Q9NWY8	Silent	SNP	ENST00000276241.6	hg19	CCDS35400.1																																																																																			.	.		0.383	CXorf48-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058404.1			C	134292208	T	C	134292208	2	2	91	1	0	0	0	0	0	0	0	1	4113	1519	53	2		2	CXorf48	23	134292208	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	5316307	134292208	20978352	721	12795										
GPR112	139378	hgsc.bcm.edu	37	chrX	135430116	135430116	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	caggatacttcatttgtagaTaccacaacttccagctcaac	5	12	2	1			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:135430116T>C	ENST00000394143.1	+	6	4542	c.4251T>C	c.(4249-4251)gaT>gaC	p.D1417D	GPR112_ENST00000370652.1_Silent_p.D1417D|GPR112_ENST00000394141.1_Silent_p.D1212D|GPR112_ENST00000412101.1_Silent_p.D1212D|GPR112_ENST00000287534.4_Silent_p.D1354D	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1417					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CATTTGTAGATACCACAACTT	0.428																																					p.D1417D		Atlas-SNP	.											.	GPR112	459	.	0			c.T4251C						.						147	139	142					X																	135430116		2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			TGTAGATACCACA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4251T>C	chrX.hg19:g.135430116T>C		106.0	0.0		86.0	4.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	hg19	CCDS35409.1																																																																																			.	.		0.428	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			C	135430116	T	C	135430116	2	2	91	1	0	0	0	0	0	0	0	1	6637	1403	49	2		2	GPR112	23	135430116	Silent	SNP	T	TCGA-DD-A119-01A-11D-A12Z-10	1137908	135430116	19840444	722	12796										
AFF2	2334	hgsc.bcm.edu	37	chrX	148069086	148069086	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	aaactgacaagagaaaacaaAggtatgctcatctgttctac	7	8	3	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:148069086A>G	ENST00000370460.2	+	20	4292	c.3813A>G	c.(3811-3813)aaA>aaG	p.K1271K	AFF2_ENST00000342251.3_Splice_Site_p.K1238K|AFF2_ENST00000370457.5_Splice_Site_p.K1236K|AFF2_ENST00000286437.5_Splice_Site_p.K912K	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1271					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GAGAAAACAAAGGTATGCTCA	0.453																																					p.K1271K		Atlas-SNP	.											.	AFF2	679	.	0			c.A3813G						.						158	122	134					X																	148069086		2203	4300	6503	SO:0001630	splice_region_variant	2334	exon20			AAACAAAGGTATG	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.3814+1A>G	chrX.hg19:g.148069086A>G		124.0	0.0		97.0	4.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	hg19	CCDS14684.1																																																																																			.	.		0.453	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	Silent	G	148069086	A	G	148069086	5	3	91	1	0	0	0	0	0	0	1	0	357	86	3	2	3946	2	AFF2	23	148069086	Splice_Site	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	12638970	148069086	7201474	723	12797										
MTMR1	8776	hgsc.bcm.edu	37	chrX	149905886	149905886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0235783633841886	17	1	0.95849657660922	1.73375116063138	0.904565822938113	0.000306669346181528	0.0142984582657137	0	atttgaaactctcgtagaaaAggagtggataagctttggac	11	5	1	2			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:149905886A>G	ENST00000370390.3	+	11	1572	c.1415A>G	c.(1414-1416)aAg>aGg	p.K472R	MTMR1_ENST00000451863.2_Missense_Mutation_p.K472R|MTMR1_ENST00000541925.1_Missense_Mutation_p.K378R|MTMR1_ENST00000445323.2_Missense_Mutation_p.K480R|MTMR1_ENST00000538506.1_Missense_Mutation_p.K297R|MTMR1_ENST00000544228.1_Missense_Mutation_p.K472R	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	472	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					CTCGTAGAAAAGGAGTGGATA	0.453																																					p.K472R		Atlas-SNP	.											.	MTMR1	82	.	0			c.A1415G						.						145	123	130					X																	149905886		2203	4300	6503	SO:0001583	missense	8776	exon11			TAGAAAAGGAGTG	U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.1415A>G	chrX.hg19:g.149905886A>G	ENSP00000359417:p.Lys472Arg	103.0	0.0		88.0	4.0	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Missense_Mutation	SNP	ENST00000370390.3	hg19	CCDS14695.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.332574	0.81801	.	.	ENSG00000063601	ENST00000541925;ENST00000370390;ENST00000445323;ENST00000544228;ENST00000451863;ENST00000538506	D;D;D;D;D;D	0.94376	-3.41;-3.41;-3.41;-3.41;-3.41;-3.41	4.88	4.88	0.63580	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.95915	0.8670	M	0.76574	2.34	0.53005	D	0.999966	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.989	D	0.95296	0.8399	10	0.41790	T	0.15	.	12.327	0.55018	1.0:0.0:0.0:0.0	.	472;480	Q13613;F8WA39	MTMR1_HUMAN;.	R	378;472;480;472;472;297	ENSP00000441879:K378R;ENSP00000359417:K472R;ENSP00000414178:K480R;ENSP00000440534:K472R;ENSP00000387446:K472R;ENSP00000443444:K297R	ENSP00000359417:K472R	K	+	2	0	MTMR1	149656544	1.000000	0.71417	0.999000	0.59377	0.945000	0.59286	9.339000	0.96797	1.619000	0.50296	0.441000	0.28932	AAG	.	.		0.453	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789		G	149905886	A	G	149905886	3	3	91	1	0	0	0	0	1	0	0	0	9947	72	3	2	1457	2	MTMR1	23	149905886	Missense_Mutation	SNP	A	TCGA-DD-A119-01A-11D-A12Z-10	1836800	149905886	5364674	724	12798										
AJAP1	55966	hgsc.bcm.edu	37	chr1	4772503	4772503	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cccacgggggacgaggaggcCctggagtccaacacatttcc	13	14	0	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:4772503C>G	ENST00000378191.4	+	2	954	c.573C>G	c.(571-573)gcC>gcG	p.A191A	AJAP1_ENST00000378190.3_Silent_p.A191A	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	191	Thr-rich.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		ACGAGGAGGCCCTGGAGTCCA	0.647																																					p.A191A		Atlas-SNP	.											.	AJAP1	68	.	0			c.C573G						.						27	26	26					1																	4772503		2201	4299	6500	SO:0001819	synonymous_variant	55966	exon2			GGAGGCCCTGGAG	AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"transmembrane protein SHREW1"	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.573C>G	chr1.hg19:g.4772503C>G		10.0	0.0		29.0	11.0	NM_018836	Q9Y229	Silent	SNP	ENST00000378191.4	hg19	CCDS54.1																																																																																			.	.		0.647	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836		G	4772503	C	G	4772503	2	3	92	1	0	0	0	0	0	0	0	1	438	610	22	4		4	AJAP1	1	4772503	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10		4772503	244478118	1	12799										
MTOR	2475	hgsc.bcm.edu	37	chr1	11169374	11169374	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cttatctcgaaccctgttaaTaatctggatagctttcttat	5	9	3	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:11169374T>A	ENST00000361445.4	-	56	7577	c.7501A>T	c.(7501-7503)Att>Ttt	p.I2501F	MTOR_ENST00000376838.1_Missense_Mutation_p.I706F	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2501	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	ACCCTGTTAATAATCTGGATA	0.413																																					p.I2501F		Atlas-SNP	.											.	MTOR	327	.	0			c.A7501T						.						177	156	163					1																	11169374		2203	4300	6503	SO:0001583	missense	2475	exon56			TGTTAATAATCTG	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.7501A>T	chr1.hg19:g.11169374T>A	ENSP00000354558:p.Ile2501Phe	92.0	0.0		119.0	9.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.180381	0.78677	.	.	ENSG00000198793	ENST00000361445;ENST00000376838;ENST00000455339	T;T;T	0.28454	3.1;2.84;1.61	5.82	5.82	0.92795	Phosphatidylinositol 3-/4-kinase, catalytic (2);	0.000000	0.85682	D	0.000000	T	0.52741	0.1753	M	0.85197	2.74	0.80722	D	1	D	0.62365	0.991	P	0.54924	0.764	T	0.61178	-0.7115	10	0.72032	D	0.01	-1.8424	13.9151	0.63893	0.0:0.0:0.0:1.0	.	2501	P42345	MTOR_HUMAN	F	2501;706;157	ENSP00000354558:I2501F;ENSP00000366034:I706F;ENSP00000398745:I157F	ENSP00000354558:I2501F	I	-	1	0	MTOR	11091961	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	7.466000	0.80914	2.223000	0.72356	0.482000	0.46254	ATT	.	.		0.413	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		A	11169374	T	A	11169374	3	1	92	1	0	0	0	0	1	0	0	0	9963	1406	49	4	160	4	MTOR	1	11169374	Missense_Mutation	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	6396871	11169374	238081247	2	12800										
HNRNPCL1	343069	hgsc.bcm.edu	37	chr1	12907351	12907351	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttgatcaactccagctggtcAtccccctgatcttcattaac	5	14	4	2	rs2359485		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:12907351A>G	ENST00000317869.6	-	2	1017	c.792T>C	c.(790-792)gaT>gaC	p.D264D		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	264						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						CCAGCTGGTCATCCCCCTGAT	0.502																																					p.D264D		Atlas-SNP	.											.	HNRNPCL1	68	.	0			c.T792C						.						140	153	149					1																	12907351		2203	4300	6503	SO:0001819	synonymous_variant	343069	exon2			CTGGTCATCCCCC	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"RNA binding motif (RRM) containing"	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.792T>C	chr1.hg19:g.12907351A>G		103.0	0.0		192.0	29.0	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	hg19	CCDS30591.1																																																																																			.	A|0.500;G|0.500		0.502	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631		G	12907351	A	G	12907351	2	3	92	1	0	0	0	0	0	0	0	1	7272	214	8	2		2	HNRNPCL1	1	12907351	Silent	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	1737977	12907351	236343270	3	12801										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32151735	32151735	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gccccactggtcctggtggcCcctgcatgttaagacgctac	11	15	0	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:32151735C>T	ENST00000373672.3	-	28	2357	c.1841G>A	c.(1840-1842)gGg>gAg	p.G614E	COL16A1_ENST00000271069.6_Splice_Site_p.G613E|COL16A1_ENST00000373668.3_Splice_Site_p.G614E	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	614	Collagen-like 2.|Triple-helical region 7 (COL7) with 1 imperfection.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TCCTGGTGGCCCCTGCATGTT	0.587																																					p.G614E	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.G1841A						.						100	111	107					1																	32151735		2120	4224	6344	SO:0001630	splice_region_variant	1307	exon28			GGTGGCCCCTGCA	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.1840-1G>A	chr1.hg19:g.32151735C>T		85.0	0.0		126.0	70.0	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.273439	0.40194	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668	D;D;D	0.99619	-6.28;-3.27;-6.28	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.99757	0.9902	H	0.95950	3.745	0.48395	D	0.999644	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.97318	0.9942	10	0.87932	D	0	.	15.3516	0.74393	0.0:1.0:0.0:0.0	.	614;614;614	A6NCT7;Q07092;Q07092-2	.;COGA1_HUMAN;.	E	614;613;614	ENSP00000362776:G614E;ENSP00000271069:G613E;ENSP00000362772:G614E	ENSP00000271069:G613E	G	-	2	0	COL16A1	31924322	0.979000	0.34478	0.957000	0.39632	0.054000	0.15201	2.711000	0.47177	2.771000	0.95319	0.563000	0.77884	GGG	.	.		0.587	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	Missense_Mutation	T	32151735	C	T	32151735	5	4	92	1	0	0	0	0	0	0	1	0	3675	637	22	3	3149	3	COL16A1	1	32151735	Splice_Site	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	19244384	32151735	217098886	4	12802										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35852772	35852772	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctgcagctggtctccagcgtCtcgctgcccagtcccagcat	10	17	2	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:35852772C>T	ENST00000314607.6	+	12	2085	c.2005C>T	c.(2005-2007)Ctc>Ttc	p.L669F	ZMYM4_ENST00000373297.2_Missense_Mutation_p.L580F	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	669					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCTCCAGCGTCTCGCTGCCCA	0.522																																					p.L669F		Atlas-SNP	.											.	ZMYM4	143	.	0			c.C2005T						.						94	72	79					1																	35852772		2203	4300	6503	SO:0001583	missense	9202	exon12			CAGCGTCTCGCTG	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.2005C>T	chr1.hg19:g.35852772C>T	ENSP00000322915:p.Leu669Phe	68.0	0.0		87.0	8.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	hg19	CCDS389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.39|12.39	1.923056|1.923056	0.33908|0.33908	.|.	.|.	ENSG00000146463|ENSG00000146463	ENST00000314607;ENST00000373297|ENST00000457946	T;T|.	0.25579|.	1.82;1.79|.	5.66|5.66	4.74|4.74	0.60224|0.60224	.|.	0.173360|.	0.36703|.	N|.	0.002444|.	T|T	0.65954|0.65954	0.2741|0.2741	M|M	0.70595|0.70595	2.14|2.14	0.38565|0.38565	D|D	0.949817|0.949817	D|.	0.69078|.	0.997|.	D|.	0.72075|.	0.976|.	T|T	0.68477|0.68477	-0.5398|-0.5398	10|5	0.24483|.	T|.	0.36|.	-10.598|-10.598	10.2861|10.2861	0.43568|0.43568	0.0:0.7901:0.0:0.2099|0.0:0.7901:0.0:0.2099	.|.	669|.	Q5VZL5|.	ZMYM4_HUMAN|.	F|F	669;580|328	ENSP00000322915:L669F;ENSP00000362394:L580F|.	ENSP00000322915:L669F|.	L|S	+|+	1|2	0|0	ZMYM4|ZMYM4	35625359|35625359	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.588000|0.588000	0.36517|0.36517	1.958000|1.958000	0.40402|0.40402	1.363000|1.363000	0.46019|0.46019	0.655000|0.655000	0.94253|0.94253	CTC|TCT	.	.		0.522	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		T	35852772	C	T	35852772	3	4	92	1	0	0	0	0	1	0	0	0	17717	913	32	3	2051	3	ZMYM4	1	35852772	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	3701037	35852772	213397849	5	12803										
COL8A2	1296	hgsc.bcm.edu	37	chr1	36565805	36565805	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agcaccagcaccagtagcagCagcagcagcgaagacagggg	14	12	0	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:36565805C>T	ENST00000397799.1	-	3	263	c.39G>A	c.(37-39)ctG>ctA	p.L13L	COL8A2_ENST00000303143.4_Silent_p.L13L|COL8A2_ENST00000481785.1_5'UTR			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	13					angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ccagtagcagcagcagcagcG	0.652											OREG0013361	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L13L		Atlas-SNP	.											.	COL8A2	41	.	0			c.G39A						.						10	10	10					1																	36565805		2191	4281	6472	SO:0001819	synonymous_variant	1296	exon1			TAGCAGCAGCAGC	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"Collagens"	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.39G>A	chr1.hg19:g.36565805C>T		9.0	0.0	863	25.0	14.0	NM_005202	Q5JV31|Q8TEJ5	Silent	SNP	ENST00000397799.1	hg19	CCDS403.1																																																																																			.	.		0.652	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202		T	36565805	C	T	36565805	2	4	92	1	0	0	0	0	0	0	0	1	3708	697	25	3		3	COL8A2	1	36565805	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	713033	36565805	212684816	6	12804										
INSL5	10022	hgsc.bcm.edu	37	chr1	67266850	67266850	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agactccttgctccgcacttCtgagatggcaaataggacag	10	11	1	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:67266850C>A	ENST00000304526.2	-	1	89	c.55G>T	c.(55-57)Gaa>Taa	p.E19*		NM_005478.4	NP_005469.2	Q9Y5Q6	INSL5_HUMAN	insulin-like 5	19						extracellular region (GO:0005576)				breast(2)|endometrium(1)|lung(5)	8						CTCCGCACTTCTGAGATGGCA	0.443																																					p.E19X		Atlas-SNP	.											.	INSL5	26	.	0			c.G55T						.						81	80	81					1																	67266850		2203	4300	6503	SO:0001587	stop_gained	10022	exon1			GCACTTCTGAGAT	AF133816	CCDS634.1	1p31.3	2013-02-26			ENSG00000172410	ENSG00000172410		"Endogenous ligands"	6088	protein-coding gene	gene with protein product	"prepro-INSL5"	606413				10458910	Standard	NM_005478		Approved		uc001dcw.3	Q9Y5Q6	OTTHUMG00000009164	ENST00000304526.2:c.55G>T	chr1.hg19:g.67266850C>A	ENSP00000302724:p.Glu19*	64.0	0.0		58.0	25.0	NM_005478	Q3MIY4|Q5VYD8	Nonsense_Mutation	SNP	ENST00000304526.2	hg19	CCDS634.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.014391	0.75161	.	.	ENSG00000172410	ENST00000304526	.	.	.	4.48	4.48	0.54585	.	0.189536	0.32852	N	0.005563	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-2.8317	14.7095	0.69218	0.0:1.0:0.0:0.0	.	.	.	.	X	19	.	ENSP00000302724:E19X	E	-	1	0	INSL5	67039438	0.182000	0.23173	0.033000	0.17914	0.081000	0.17604	2.127000	0.42035	2.296000	0.77279	0.655000	0.94253	GAA	.	.		0.443	INSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025403.1	NM_005478		A	67266850	C	A	67266850	4	1	92	1	0	0	0	0	0	1	0	0	7778	922	32	3	360	3	INSL5	1	67266850	Nonsense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	30701045	67266850	181983771	7	12805										
DEPDC1	55635	hgsc.bcm.edu	37	chr1	68955231	68955232	+	Frame_Shift_Ins	INS	-	-	T													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tggaaaagttctctatgttgINSttttttctcaattctggata							TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:68955231_68955232insT	ENST00000456315.2	-	3	488_489	c.374_375insA	c.(373-375)aacfs	p.N125fs	DEPDC1_ENST00000370966.5_Frame_Shift_Ins_p.N125fs	NM_001114120.1	NP_001107592.1	Q5TB30	DEP1A_HUMAN	DEP domain containing 1	125					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)		TCTCTATGTTGTTTTTTCTCAA	0.317																																					p.N125fs		Atlas-Indel,Pindel	.											.	DEPDC1	102	.	0			c.375_376insA						.																																			SO:0001589	frameshift_variant	55635	exon3			.	AK000361	CCDS644.1, CCDS44159.1	1p31.2	2008-08-19			ENSG00000024526	ENSG00000024526			22949	protein-coding gene	gene with protein product		612002					Standard	NM_001114120		Approved	DEP.8, FLJ20354, SDP35, DEPDC1A	uc001dem.4	Q5TB30	OTTHUMG00000009212	ENST00000456315.2:c.375dupA	chr1.hg19:g.68955237_68955237dupT	ENSP00000412292:p.Asn125fs	157.0	0.0		333.0	29.0	NM_017779	A8QXE0|A8QXE1|Q05DU3|Q5TB28|Q9H9I3|Q9NX21|Q9NXZ0	Frame_Shift_Ins	INS	ENST00000456315.2	hg19	CCDS44159.1																																																																																			.	.		0.317	DEPDC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025514.2	NM_017779		T	68955232	-	T	68955231	7	5	92	1	0	1	1	0	0	0	0	0	4441	1368	48	0	2100	0	DEPDC1	1	68955231	Frame_Shift_Ins	INS	-	TCGA-DD-A11A-01A-11D-A12Z-10	1688381	68955231	180295390	8	12806										
ANKRD13C	81573	hgsc.bcm.edu	37	chr1	70740488	70740488	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tttgcacaccaattctctacCcagatgaggagctctaaaat	6	11	2	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:70740488C>G	ENST00000370944.4	-	11	1622	c.1309G>C	c.(1309-1311)Ggt>Cgt	p.G437R	ANKRD13C_ENST00000262346.6_Missense_Mutation_p.G402R|ANKRD13C_ENST00000464236.1_5'UTR	NM_030816.4	NP_110443.3	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C	437					protein retention in ER lumen (GO:0006621)|regulation of anoikis (GO:2000209)|regulation of receptor biosynthetic process (GO:0010869)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	19						AATTCTCTACCCAGATGAGGA	0.378																																					p.G437R		Atlas-SNP	.											.	ANKRD13C	36	.	0			c.G1309C						.						152	153	153					1																	70740488		2203	4300	6503	SO:0001583	missense	81573	exon11			CTCTACCCAGATG		CCDS648.2	1p32.3-p31.3	2013-01-10			ENSG00000118454	ENSG00000118454		"Ankyrin repeat domain containing"	25374	protein-coding gene	gene with protein product		615125				11230166	Standard	NM_030816		Approved	DKFZP566D1346, dJ677H15.3	uc001dex.4	Q8N6S4	OTTHUMG00000009343	ENST00000370944.4:c.1309G>C	chr1.hg19:g.70740488C>G	ENSP00000359982:p.Gly437Arg	79.0	0.0		141.0	26.0	NM_030816	B3KQ97|Q5VYH4|Q5VYH5|Q6PJE4|Q9H0N9	Missense_Mutation	SNP	ENST00000370944.4	hg19	CCDS648.2	.	.	.	.	.	.	.	.	.	.	C	24.2	4.502021	0.85176	.	.	ENSG00000118454	ENST00000370944;ENST00000262346	T;T	0.53206	0.63;0.63	5.19	4.26	0.50523	.	0.047258	0.85682	D	0.000000	T	0.66587	0.2804	M	0.86651	2.83	0.80722	D	1	P;D	0.89917	0.936;1.0	P;D	0.77004	0.839;0.989	T	0.72571	-0.4253	10	0.87932	D	0	-2.7546	14.3123	0.66424	0.0:0.9233:0.0:0.0767	.	402;437	Q8N6S4-2;Q8N6S4	.;AN13C_HUMAN	R	437;402	ENSP00000359982:G437R;ENSP00000262346:G402R	ENSP00000262346:G402R	G	-	1	0	ANKRD13C	70513076	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.613000	0.67688	2.593000	0.87608	0.563000	0.77884	GGT	.	.		0.378	ANKRD13C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025903.1	NM_030816		G	70740488	C	G	70740488	3	3	92	1	0	0	0	0	1	0	0	0	643	623	22	4	328	4	ANKRD13C	1	70740488	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	1785257	70740488	178510133	9	12807										
UBE2Q1	55585	hgsc.bcm.edu	37	chr1	154527970	154527970	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgagggaggttatagagtttAcacaggtcggagatgatcct	14	5	0	4			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:154527970A>C	ENST00000292211.4	-	3	550	c.471T>G	c.(469-471)tgT>tgG	p.C157W	UBE2Q1-AS1_ENST00000441613.1_RNA|UBE2Q1_ENST00000497453.1_5'UTR	NM_017582.6	NP_060052.3	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q family member 1	157					embryo implantation (GO:0007566)|fertilization (GO:0009566)|mating behavior (GO:0007617)|prolactin secretion (GO:0070459)|protein ubiquitination (GO:0016567)|reproductive system development (GO:0061458)|suckling behavior (GO:0001967)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TATAGAGTTTACACAGGTCGG	0.537																																					p.C157W		Atlas-SNP	.											.	UBE2Q1	35	.	0			c.T471G						.						151	144	147					1																	154527970		2203	4300	6503	SO:0001583	missense	55585	exon3			GAGTTTACACAGG	AJ243666	CCDS1069.1	1q22	2008-05-02	2008-05-02	2005-08-05	ENSG00000160714	ENSG00000160714		"Ubiquitin-conjugating enzymes E2"	15698	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2Q (putative)"	UBE2Q			Standard	NM_017582		Approved	PRO3094, NICE-5	uc001fff.1	Q7Z7E8	OTTHUMG00000037265	ENST00000292211.4:c.471T>G	chr1.hg19:g.154527970A>C	ENSP00000292211:p.Cys157Trp	66.0	0.0		126.0	50.0	NM_017582	B4DF92|Q3B841|Q5I0X2|Q6IS04|Q6P7P2|Q96MV4|Q9BVX5|Q9UGL6	Missense_Mutation	SNP	ENST00000292211.4	hg19	CCDS1069.1	.	.	.	.	.	.	.	.	.	.	A	17.57	3.423085	0.62733	.	.	ENSG00000160714	ENST00000292211	.	.	.	4.73	3.62	0.41486	.	0.000000	0.85682	D	0.000000	T	0.40595	0.1123	L	0.52573	1.65	0.80722	D	1	D	0.55172	0.97	P	0.52031	0.688	T	0.50750	-0.8791	9	0.87932	D	0	-8.4796	4.549	0.12103	0.7564:0.0:0.2436:0.0	.	157	Q7Z7E8	UB2Q1_HUMAN	W	157	.	ENSP00000292211:C157W	C	-	3	2	UBE2Q1	152794594	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.214000	0.51161	2.123000	0.65237	0.374000	0.22700	TGT	.	.		0.537	UBE2Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090704.1	NM_017582		C	154527970	A	C	154527970	3	2	92	1	0	0	0	0	1	0	0	0	16884	389	14	5	841	5	UBE2Q1	1	154527970	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	83787482	154527970	94722651	10	12808										
PBX1	5087	hgsc.bcm.edu	37	chr1	164781342	164781342	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cactgctaccaatgtgtcagCccatggaagccaagctaact	8	13	1	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:164781342C>A	ENST00000420696.2	+	6	1141	c.953C>A	c.(952-954)gCc>gAc	p.A318D	PBX1_ENST00000560641.1_Missense_Mutation_p.A213D|PBX1_ENST00000559240.1_Intron|PBX1_ENST00000367897.1_Missense_Mutation_p.A318D|PBX1_ENST00000401534.1_Missense_Mutation_p.A318D|PBX1_ENST00000540236.1_Missense_Mutation_p.A318D|PBX1_ENST00000540246.1_Missense_Mutation_p.A213D	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	318					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						AATGTGTCAGCCCATGGAAGC	0.443			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.A318D		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1	60	.	0			c.C953A						.						113	92	99					1																	164781342		2203	4300	6503	SO:0001583	missense	5087	exon6			TGTCAGCCCATGG	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"Homeoboxes / TALE class"	8632	protein-coding gene	gene with protein product		176310	"pre-B-cell leukemia transcription factor 1"				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.953C>A	chr1.hg19:g.164781342C>A	ENSP00000405890:p.Ala318Asp	87.0	0.0		180.0	26.0	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	hg19	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	C	17.86	3.491971	0.64074	.	.	ENSG00000185630	ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	D;D;D;D;D	0.89617	-2.43;-2.34;-2.44;-2.34;-2.54	5.8	5.8	0.92144	.	0.049382	0.85682	D	0.000000	T	0.81559	0.4848	L	0.59436	1.845	.	.	.	B;B;B;B;B	0.26672	0.073;0.073;0.156;0.073;0.025	B;B;B;B;B	0.32022	0.044;0.04;0.139;0.027;0.045	T	0.77159	-0.2690	9	0.23891	T	0.37	-11.2817	12.9399	0.58337	0.0:0.9256:0.0:0.0744	.	213;318;318;318;318	B7Z774;A8K5V0;F5H4U9;P40424;Q53YC7	.;.;.;PBX1_HUMAN;.	D	318;318;318;318;213	ENSP00000405890:A318D;ENSP00000356872:A318D;ENSP00000439943:A318D;ENSP00000384856:A318D;ENSP00000440869:A213D	ENSP00000356872:A318D	A	+	2	0	PBX1	163047966	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.601000	0.61090	2.732000	0.93576	0.650000	0.86243	GCC	.	.		0.443	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		A	164781342	C	A	164781342	3	1	92	1	0	0	0	0	1	0	0	0	11501	739	26	3	975	3	PBX1	1	164781342	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	10253372	164781342	84469279	11	12809										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179631316	179631316	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgggatgagaactggttaccTctacaggctaagatgggaaa	13	6	1	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:179631316T>A	ENST00000367614.1	+	14	2597	c.2238T>A	c.(2236-2238)ccT>ccA	p.P746P	TDRD5_ENST00000294848.8_Silent_p.P746P|TDRD5_ENST00000444136.1_Silent_p.P800P	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	746					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						ACTGGTTACCTCTACAGGCTA	0.443																																					p.P800P		Atlas-SNP	.											.	TDRD5	149	.	0			c.T2400A						.						155	133	140					1																	179631316		2203	4300	6503	SO:0001819	synonymous_variant	163589	exon15			GTTACCTCTACAG	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2238T>A	chr1.hg19:g.179631316T>A		36.0	0.0		76.0	43.0	NM_001199085	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.		0.443	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		A	179631316	T	A	179631316	2	1	92	1	0	0	0	0	0	0	0	1	15748	1538	54	4		4	TDRD5	1	179631316	Silent	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	14849974	179631316	69619305	12	12810										
GLT25D2	23127	hgsc.bcm.edu	37	chr1	183944304	183944304	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gtttcatcacatgggcaaacCgggaggttggccagtgcttt	13	9	2	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:183944304C>T	ENST00000361927.4	-	3	790	c.419G>A	c.(418-420)cGg>cAg	p.R140Q	COLGALT2_ENST00000546159.1_Missense_Mutation_p.R140Q	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	140					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										ATGGGCAAACCGGGAGGTTGG	0.433																																					p.R140Q		Atlas-SNP	.											GLT25D2,caecum,carcinoma,0,1	.	.	.	0			c.G419A						.						97	91	93					1																	183944304		2203	4300	6503	SO:0001583	missense	23127	exon3			GCAAACCGGGAGG	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.419G>A	chr1.hg19:g.183944304C>T	ENSP00000354960:p.Arg140Gln	23.0	0.0		60.0	12.0	NM_015101	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	hg19	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	C	36	5.848955	0.97023	.	.	ENSG00000198756	ENST00000546159;ENST00000361927	T;T	0.24151	1.87;1.87	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.61800	0.2376	M	0.91920	3.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.964;0.99	T	0.71474	-0.4582	10	0.87932	D	0	-33.9366	19.1269	0.93388	0.0:1.0:0.0:0.0	.	140;140	F5H3T5;Q8IYK4	.;GT252_HUMAN	Q	140	ENSP00000439112:R140Q;ENSP00000354960:R140Q	ENSP00000354960:R140Q	R	-	2	0	GLT25D2	182210927	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.531000	0.81973	2.583000	0.87209	0.650000	0.86243	CGG	.	.		0.433	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		T	183944304	C	T	183944304	3	4	92	1	0	0	0	0	1	0	0	0	6475	652	23	1	1501	1	GLT25D2	1	183944304	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	4312988	183944304	65306317	13	12811										
CR1	1378	hgsc.bcm.edu	37	chr1	207789962	207789962	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agctatccttaatgggagacAcacaggaactccctttggag	10	10	0	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:207789962A>T	ENST00000367049.4	+	41	6704	c.6704A>T	c.(6703-6705)cAc>cTc	p.H2235L	CR1_ENST00000400960.2_Missense_Mutation_p.H1785L|CR1_ENST00000367051.1_Missense_Mutation_p.H1785L|CR1_ENST00000367053.1_Missense_Mutation_p.H1785L|CR1_ENST00000367052.1_Missense_Mutation_p.H1785L	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1785					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						AATGGGAGACACACAGGAACT	0.413																																					p.H2235L		Atlas-SNP	.											.	CR1	354	.	0			c.A6704T						.						118	111	113					1																	207789962		1841	4084	5925	SO:0001583	missense	1378	exon41			GGAGACACACAGG	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6704A>T	chr1.hg19:g.207789962A>T	ENSP00000356016:p.His2235Leu	111.0	0.0		173.0	42.0	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	hg19	CCDS44308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.86|12.86	2.063506|2.063506	0.36373|0.36373	.|.	.|.	ENSG00000203710|ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049|ENST00000529814	T;T;T;T;T|.	0.60548|.	0.18;0.18;0.18;0.18;0.18|.	4.3|4.3	4.3|4.3	0.51218|0.51218	Complement control module (2);Sushi/SCR/CCP (3);|.	.|.	.|.	.|.	.|.	T|T	0.39989|0.39989	0.1099|0.1099	L|L	0.41710|0.41710	1.295|1.295	0.09310|0.09310	N|N	1|1	D;D|.	0.76494|.	0.989;0.999|.	P;D|.	0.85130|.	0.835;0.997|.	T|T	0.22382|0.22382	-1.0218|-1.0218	9|5	0.02654|.	T|.	1|.	.|.	10.1339|10.1339	0.42695|0.42695	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1785;2235|.	P17927;E9PDY4|.	CR1_HUMAN;.|.	L|S	1785;1785;1785;1785;2235|408	ENSP00000356019:H1785L;ENSP00000356018:H1785L;ENSP00000356020:H1785L;ENSP00000383744:H1785L;ENSP00000356016:H2235L|.	ENSP00000356016:H2235L|.	H|T	+|+	2|1	0|0	CR1|CR1	205856585|205856585	0.019000|0.019000	0.18553|0.18553	0.026000|0.026000	0.17262|0.17262	0.327000|0.327000	0.28475|0.28475	2.555000|2.555000	0.45854|0.45854	2.171000|2.171000	0.68590|0.68590	0.496000|0.496000	0.49642|0.49642	CAC|ACA	.	.		0.413	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		T	207789962	A	T	207789962	3	4	92	1	0	0	0	0	1	0	0	0	3842	159	6	4	6866	4	CR1	1	207789962	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	23845658	207789962	41460659	14	12812										
USH2A	7399	hgsc.bcm.edu	37	chr1	216369968	216369974	+	Frame_Shift_Del	DEL	TTTCCTC	TTTCCTC	-													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgatgtcataccccacaactTttcctcttgtaacattatct							TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	TTTCCTC	TTTCCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:216369968_216369974delTTTCCTC	ENST00000307340.3	-	19	4558_4564	c.4172_4178delGAGGAAA	c.(4171-4179)agaggaaaafs	p.RGK1391fs	USH2A_ENST00000366943.2_Frame_Shift_Del_p.RGK1391fs|RP5-1099E6.3_ENST00000420867.1_RNA|USH2A_ENST00000366942.3_Frame_Shift_Del_p.RGK1391fs	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1391	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CCCCACAACTTTTCCTCTTGTAACATT	0.406										HNSCC(13;0.011)																											p.1391_1393del		Pindel	.											USH2A,NS,carcinoma,0,1	USH2A	1168	.	0			c.4173_4179del	GRCh37	CM071123	USH2A	M		.																																			SO:0001589	frameshift_variant	7399	exon19			.	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.4172_4178delGAGGAAA	chr1.hg19:g.216369968_216369974delTTTCCTC	ENSP00000305941:p.Arg1391fs	0.0	0.0		10.0	10.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Frame_Shift_Del	DEL	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.406	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		-	216369974	TTTCCTC	-	216369968	7	5	92	1	0	1	0	1	0	0	0	0	17051	1841	64	0	11660	0	USH2A	1	216369968	Frame_Shift_Del	DEL	TTTCCTC	TCGA-DD-A11A-01A-11D-A12Z-10	8580006	216369968	32880653	15	12813										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228511096	228511096	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tatcctgtgagctttgactgCgtggtgacaggtcagcccat	12	10	1	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:228511096C>T	ENST00000422127.1	+	56	15485	c.15441C>T	c.(15439-15441)tgC>tgT	p.C5147C	OBSCN_ENST00000284548.11_Silent_p.C5147C|OBSCN_ENST00000366707.4_Silent_p.C2781C|OBSCN_ENST00000570156.2_Silent_p.C6104C|OBSCN_ENST00000366709.4_Silent_p.C2266C	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5147	Ig-like 49.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTTTGACTGCGTGGTGACAG	0.532																																					p.C6104C		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C18312T						.						80	82	82					1																	228511096		2139	4244	6383	SO:0001819	synonymous_variant	84033	exon67			TGACTGCGTGGTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15441C>T	chr1.hg19:g.228511096C>T		54.0	0.0		141.0	27.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.532	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228511096	C	T	228511096	2	4	92	1	0	0	0	0	0	0	0	1	10821	776	27	1		1	OBSCN	1	228511096	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	12141128	228511096	20739525	16	12814										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245862258	245862258	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agaggatcgccgaggtccgcGcgaagtacgagtggctgatg	17	9	0	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:245862258G>A	ENST00000407071.2	+	14	6537	c.6097G>A	c.(6097-6099)Gcg>Acg	p.A2033T	KIF26B_ENST00000366518.4_Missense_Mutation_p.A1652T	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	2033					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			CGAGGTCCGCGCGAAGTACGA	0.567																																					p.A2033T		Atlas-SNP	.											.	KIF26B	343	.	0			c.G6097A						.						73	80	78					1																	245862258		2105	4222	6327	SO:0001583	missense	55083	exon14			GTCCGCGCGAAGT	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.6097G>A	chr1.hg19:g.245862258G>A	ENSP00000385545:p.Ala2033Thr	46.0	0.0		97.0	72.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.458239	0.84317	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	D;D	0.82433	-1.61;-1.6	5.82	5.82	0.92795	.	.	.	.	.	D	0.90352	0.6981	M	0.65975	2.015	0.58432	D	0.999999	D	0.89917	1.0	D	0.66602	0.945	D	0.90525	0.4491	9	0.87932	D	0	.	20.099	0.97865	0.0:0.0:1.0:0.0	.	2033	Q2KJY2	KI26B_HUMAN	T	2033;1652;1649	ENSP00000385545:A2033T;ENSP00000355475:A1652T	ENSP00000355475:A1652T	A	+	1	0	KIF26B	243928881	1.000000	0.71417	0.991000	0.47740	0.678000	0.39670	9.838000	0.99474	2.752000	0.94435	0.655000	0.94253	GCG	.	.		0.567	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245862258	G	A	245862258	3	1	92	1	0	0	0	0	1	0	0	0	8304	1087	38	1	6151	1	KIF26B	1	245862258	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	17351162	245862258	3388363	17	12815										
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112614	248112614	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agggtcttggatcataggctCgatcaatgcttgtgctcaca	11	9	4	0	rs536751971		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:248112614C>A	ENST00000357191.3	+	1	455	c.455C>A	c.(454-456)tCg>tAg	p.S152*	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	152						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			ATCATAGGCTCGATCAATGCT	0.438																																					p.S152X		Atlas-SNP	.											OR2L8,NS,carcinoma,0,1	OR2L8	92	.	0			c.C455A						.						245	190	208					1																	248112614		2203	4300	6503	SO:0001587	stop_gained	391190	exon1			TAGGCTCGATCAA	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.455C>A	chr1.hg19:g.248112614C>A	ENSP00000349719:p.Ser152*	156.0	0.0		529.0	117.0	NM_001001963	Q6IF03	Nonsense_Mutation	SNP	ENST00000357191.3	hg19	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	14.04	2.415572	0.42817	.	.	ENSG00000196936	ENST00000357191	.	.	.	1.64	1.64	0.23874	.	1.218230	0.06416	U	0.721499	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.6931	0.08354	0.0:0.5144:0.0:0.4856	.	.	.	.	X	152	.	ENSP00000349719:S152X	S	+	2	0	OR2L8	246179237	0.000000	0.05858	0.008000	0.14137	0.281000	0.26958	-0.605000	0.05661	0.905000	0.36596	0.479000	0.44913	TCG	.	.		0.438	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			A	248112614	C	A	248112614	4	1	92	1	0	0	0	0	0	1	0	0	11018	893	31	1	457	1	OR2L8	1	248112614	Nonsense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	2250356	248112614	1138007	18	12816										
OR2T33	391195	hgsc.bcm.edu	37	chr1	248436686	248436686	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cacccaggagccaacacgacAtggtcatcctcaggcacagc	9	16	2	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr1:248436686A>G	ENST00000318021.2	-	1	452	c.431T>C	c.(430-432)aTg>aCg	p.M144T		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	144						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CCAACACGACATGGTCATCCT	0.572																																					p.M144T		Atlas-SNP	.											.	OR2T33	133	.	0			c.T431C						.						143	136	138					1																	248436686		2203	4300	6503	SO:0001583	missense	391195	exon1			CACGACATGGTCA		CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"GPCR / Class A : Olfactory receptors"	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.431T>C	chr1.hg19:g.248436686A>G	ENSP00000324687:p.Met144Thr	175.0	0.0		650.0	177.0	NM_001004695	B2RNN0	Missense_Mutation	SNP	ENST00000318021.2	hg19	CCDS31109.1	.	.	.	.	.	.	.	.	.	.	-	0.655	-0.807933	0.02819	.	.	ENSG00000177212	ENST00000318021	T	0.35973	1.28	2.7	-1.45	0.08828	GPCR, rhodopsin-like superfamily (1);	1.861850	0.03589	U	0.231619	T	0.14614	0.0353	N	0.02181	-0.65	0.09310	N	1	B	0.11235	0.004	B	0.19946	0.027	T	0.14839	-1.0458	10	0.29301	T	0.29	.	4.447	0.11602	0.4771:0.1676:0.3552:0.0	.	144	Q8NG76	O2T33_HUMAN	T	144	ENSP00000324687:M144T	ENSP00000324687:M144T	M	-	2	0	OR2T33	246503309	0.001000	0.12720	0.000000	0.03702	0.035000	0.12851	0.625000	0.24477	-0.348000	0.08286	0.404000	0.27445	ATG	.	.		0.572	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695		G	248436686	A	G	248436686	3	3	92	1	0	0	0	0	1	0	0	0	11033	217	8	2	534	2	OR2T33	1	248436686	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	324072	248436686	813935	19	12817										
GRHL1	29841	hgsc.bcm.edu	37	chr2	10132262	10132262	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gtgcactttgccaacttgcaGcggggcactcatgtaggtaa	12	10	1	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr2:10132262G>A	ENST00000324907.9	+	11	1585	c.1449G>A	c.(1447-1449)caG>caA	p.Q483Q	GRHL1_ENST00000405379.2_Silent_p.Q483Q|GRHL1_ENST00000324883.5_Silent_p.Q294Q	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	483					cellular lipid metabolic process (GO:0044255)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		CCAACTTGCAGCGGGGCACTC	0.483																																					p.Q483Q		Atlas-SNP	.											.	GRHL1	95	.	0			c.G1449A						.						109	94	99					2																	10132262		2203	4300	6503	SO:0001819	synonymous_variant	29841	exon11			CTTGCAGCGGGGC	AF198489	CCDS33144.1, CCDS33144.2	2p25.2	2008-02-05	2005-07-11	2005-07-11	ENSG00000134317	ENSG00000134317			17923	protein-coding gene	gene with protein product		609786	"transcription factor CP2-like 2"	TFCP2L2		10644752, 12393799	Standard	NM_198182		Approved	LBP-32, MGR	uc002raa.3	Q9NZI5	OTTHUMG00000151704	ENST00000324907.9:c.1449G>A	chr2.hg19:g.10132262G>A		66.0	0.0		162.0	65.0	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Silent	SNP	ENST00000324907.9	hg19	CCDS33144.2																																																																																			.	.		0.483	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		A	10132262	G	A	10132262	2	1	92	1	0	0	0	0	0	0	0	1	6772	962	34	3		3	GRHL1	2	10132262	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10		10132262	233067111	20	12818										
ASXL2	55252	hgsc.bcm.edu	37	chr2	26101043	26101044	+	Frame_Shift_Ins	INS	-	-	G													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctcccccttaccgtcttggcINSggcctccgcccaggtcctgc							TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr2:26101043_26101044insG	ENST00000435504.4	-	1	341_342	c.48_49insC	c.(46-51)gccgccfs	p.A17fs	ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000336112.4_5'UTR			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	17					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)	p.A17S(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACCGTCTTGGCGGCCTCCGCCC	0.663																																					p.A17fs		Atlas-INDEL	.											ASXL2_ENST00000435504,NS,carcinoma,0,1	ASXL2	217	.	1	Substitution - Missense(1)	prostate(1)	c.49_50insC						.																																			SO:0001589	frameshift_variant	55252	exon1			.			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.49dupC	chr2.hg19:g.26101045_26101045dupG	ENSP00000391447:p.Ala17fs	36.0	0.0		127.0	10.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Frame_Shift_Ins	INS	ENST00000435504.4	hg19																																																																																				.	.		0.663	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		G	26101044	-	G	26101043	7	5	92	1	0	1	1	0	0	0	0	0	1067	768	27	0	4306	0	ASXL2	2	26101043	Frame_Shift_Ins	INS	-	TCGA-DD-A11A-01A-11D-A12Z-10	15968781	26101043	217098330	21	12819										
NLRC4	58484	hgsc.bcm.edu	37	chr2	32466120	32466120	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	acctagttttatagcatcttCttcattcatctttatgttat	3	8	5	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr2:32466120C>G	ENST00000404025.2	-	6	2820	c.2332G>C	c.(2332-2334)Gaa>Caa	p.E778Q	NLRC4_ENST00000360906.5_Missense_Mutation_p.E778Q|NLRC4_ENST00000402280.1_Missense_Mutation_p.E778Q|NLRC4_ENST00000342905.6_Missense_Mutation_p.E113Q			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	778					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					ATAGCATCTTCTTCATTCATC	0.358																																					p.E778Q		Atlas-SNP	.											.	NLRC4	165	.	0			c.G2332C						.						231	220	224					2																	32466120		2203	4300	6503	SO:0001583	missense	58484	exon5			CATCTTCTTCATT	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.2332G>C	chr2.hg19:g.32466120C>G	ENSP00000385090:p.Glu778Gln	54.0	0.0		130.0	14.0	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	hg19	CCDS33174.1	.	.	.	.	.	.	.	.	.	.	C	6.492	0.459053	0.12342	.	.	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000342905;ENST00000404025	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	3.6	3.6	0.41247	.	0.000000	0.34628	N	0.003820	T	0.38268	0.1034	L	0.43152	1.355	0.26350	N	0.977228	P;B	0.40476	0.718;0.442	B;B	0.35688	0.208;0.103	T	0.50783	-0.8787	9	0.26408	T	0.33	-7.4064	8.9962	0.36055	0.0:0.892:0.0:0.108	.	113;778	Q9NPP4-2;Q9NPP4	.;NLRC4_HUMAN	Q	778;778;113;778	ENSP00000354159:E778Q;ENSP00000385428:E778Q;ENSP00000339666:E113Q;ENSP00000385090:E778Q	ENSP00000339666:E113Q	E	-	1	0	NLRC4	32319624	0.066000	0.20996	0.968000	0.41197	0.338000	0.28826	0.700000	0.25601	2.306000	0.77630	0.467000	0.42956	GAA	.	.		0.358	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		G	32466120	C	G	32466120	3	3	92	1	0	0	0	0	1	0	0	0	10478	922	32	4	762	4	NLRC4	2	32466120	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	6365077	32466120	210733253	22	12820										
GLI2	2736	hgsc.bcm.edu	37	chr2	121726310	121726310	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgtcccgtttctccagcccgCgggtgacgccccgcctgagc	12	18	1	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr2:121726310C>T	ENST00000452319.1	+	6	724	c.664C>T	c.(664-666)Cgg>Tgg	p.R222W	GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_5'UTR|GLI2_ENST00000361492.4_Missense_Mutation_p.R222W					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CTCCAGCCCGCGGGTGACGCC	0.642																																					p.R222W		Atlas-SNP	.											.	GLI2	187	.	0			c.C664T						.						61	61	61					2																	121726310		2203	4300	6503	SO:0001583	missense	2736	exon5			AGCCCGCGGGTGA		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.664C>T	chr2.hg19:g.121726310C>T	ENSP00000390436:p.Arg222Trp	30.0	0.0		102.0	11.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.82|16.82	3.228879|3.228879	0.58777|0.58777	.|.	.|.	ENSG00000074047|ENSG00000074047	ENST00000440937;ENST00000360874|ENST00000452319;ENST00000361492	.|T;T	.|0.71341	.|-0.56;-0.56	4.91|4.91	4.01|4.01	0.46588|0.46588	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.84529|0.84529	0.5492|0.5492	M|M	0.85777|0.85777	2.775|2.775	0.80722|0.80722	D|D	1|1	B|D;D	0.26975|0.89917	0.165|1.0;1.0	B|D;D	0.22152|0.91635	0.038|0.999;0.998	D|D	0.86936|0.86936	0.2076|0.2076	8|10	0.72032|0.87932	D|D	0.01|0	.|.	13.1307|13.1307	0.59380|0.59380	0.3111:0.6889:0.0:0.0|0.3111:0.6889:0.0:0.0	.|.	92|222;222	F5H4D9|P10070;Q0VGA0	.|GLI2_HUMAN;.	V|W	92;84|222	.|ENSP00000390436:R222W;ENSP00000354586:R222W	ENSP00000441454:A84V|ENSP00000354586:R222W	A|R	+|+	2|1	0|2	GLI2|GLI2	121442780|121442780	0.058000|0.058000	0.20735|0.20735	0.713000|0.713000	0.30519|0.30519	0.597000|0.597000	0.36814|0.36814	0.436000|0.436000	0.21526|0.21526	1.250000|1.250000	0.43966|0.43966	-0.274000|-0.274000	0.10170|0.10170	GCG|CGG	.	.		0.642	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121726310	C	T	121726310	3	4	92	1	0	0	0	0	1	0	0	0	6446	759	27	1	682	1	GLI2	2	121726310	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	89260190	121726310	121473063	23	12821										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141264466	141264466	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tatggcacatgaaagcatttTcatcacatgtattattggga	8	6	2	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr2:141264466T>G	ENST00000389484.3	-	53	9391	c.8420A>C	c.(8419-8421)gAa>gCa	p.E2807A		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2807	LDL-receptor class A 18. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GAAAGCATTTTCATCACATGT	0.388										TSP Lung(27;0.18)																											p.E2807A	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A8420C						.						122	113	116					2																	141264466		2203	4300	6503	SO:0001583	missense	53353	exon53			GCATTTTCATCAC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8420A>C	chr2.hg19:g.141264466T>G	ENSP00000374135:p.Glu2807Ala	99.0	0.0		185.0	79.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.123766	0.56613	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	T	0.40756	1.02	5.65	3.29	0.37713	.	0.067036	0.64402	D	0.000015	T	0.25232	0.0613	N	0.13235	0.315	0.43000	D	0.994512	B	0.31125	0.309	B	0.37550	0.253	T	0.03957	-1.0989	10	0.10111	T	0.7	.	9.6567	0.39930	0.0:0.1409:0.0:0.8591	.	2807	Q9NZR2	LRP1B_HUMAN	A	2807;2745	ENSP00000374135:E2807A	ENSP00000374135:E2807A	E	-	2	0	LRP1B	140980936	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	3.256000	0.51492	0.966000	0.38159	0.533000	0.62120	GAA	.	.		0.388	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141264466	T	G	141264466	3	3	92	1	0	0	0	0	1	0	0	0	8964	1783	62	5	5535	5	LRP1B	2	141264466	Missense_Mutation	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	19538156	141264466	101934907	24	12822										
NEB	4703	hgsc.bcm.edu	37	chr2	152552146	152552146	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ataaaagcaggagtatcaggGgggatatggcacttgaactt	13	5	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr2:152552146G>C	ENST00000172853.10	-	18	1767	c.1620C>G	c.(1618-1620)ccC>ccG	p.P540P	NEB_ENST00000409198.1_Silent_p.P540P|NEB_ENST00000427231.2_Silent_p.P540P|NEB_ENST00000603639.1_Silent_p.P540P|NEB_ENST00000604864.1_Silent_p.P540P|NEB_ENST00000397345.3_Silent_p.P540P			P20929	NEBU_HUMAN	nebulin	540					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GAGTATCAGGGGGGATATGGC	0.388																																					p.P540P		Atlas-SNP	.											.	NEB	1697	.	0			c.C1620G						.						132	129	130					2																	152552146		1906	4128	6034	SO:0001819	synonymous_variant	4703	exon18			ATCAGGGGGGATA	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.1620C>G	chr2.hg19:g.152552146G>C		111.0	0.0		167.0	16.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	.		0.388	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		C	152552146	G	C	152552146	2	2	92	1	0	0	0	0	0	0	0	1	10311	1219	43	4		4	NEB	2	152552146	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	11287680	152552146	90647227	25	12823										
TTN	7273	hgsc.bcm.edu	37	chr2	179588199	179588199	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gccagcgttgttagaaaccaCacaggtgtattccccactct	8	13	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr2:179588199C>T	ENST00000591111.1	-	72	20901	c.20677G>A	c.(20677-20679)Gtg>Atg	p.V6893M	TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V7210M|TTN_ENST00000342992.6_Missense_Mutation_p.V5966M|RP11-171I2.1_ENST00000590024.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12484	Ig-like 50.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTAGAAACCACACAGGTGTAT	0.418																																					p.V7210M		Atlas-SNP	.											.	TTN	18412	.	0			c.G21628A						.						81	80	80					2																	179588199		1916	4137	6053	SO:0001583	missense	7273	exon74			AAACCACACAGGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.20677G>A	chr2.hg19:g.179588199C>T	ENSP00000465570:p.Val6893Met	93.0	0.0		118.0	38.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	7.445	0.641575	0.14451	.	.	ENSG00000155657	ENST00000342992	T	0.68765	-0.35	6.06	4.21	0.49690	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67126	0.2860	L	0.59436	1.845	0.80722	D	1	B	0.33826	0.427	B	0.40782	0.34	T	0.70992	-0.4721	9	0.87932	D	0	.	12.0719	0.53622	0.0:0.7074:0.2235:0.0691	.	6893	Q8WZ42	TITIN_HUMAN	M	5966	ENSP00000343764:V5966M	ENSP00000343764:V5966M	V	-	1	0	TTN	179296444	0.881000	0.30235	1.000000	0.80357	0.802000	0.45316	0.181000	0.16880	1.574000	0.49760	0.650000	0.86243	GTG	.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179588199	C	T	179588199	3	4	92	1	0	0	0	0	1	0	0	0	16750	478	17	3	83057	3	TTN	2	179588199	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	27036053	179588199	63611174	26	12824										
TTN	7273	hgsc.bcm.edu	37	chr2	179638382	179638382	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gtcacatcagggactgacacCttacattcaagcacagcctt	7	13	3	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr2:179638382C>A	ENST00000591111.1	-	32	7625	c.7401G>T	c.(7399-7401)aaG>aaT	p.K2467N	TTN_ENST00000359218.5_Missense_Mutation_p.K2421N|TTN_ENST00000460472.2_Missense_Mutation_p.K2421N|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K2421N|TTN_ENST00000589042.1_Missense_Mutation_p.K2467N|TTN_ENST00000342992.6_Missense_Mutation_p.K2467N|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.K2467N|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12789	Ig-like 14.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGACTGACACCTTACATTCAA	0.418																																					p.K2467N		Atlas-SNP	.											.	TTN	18412	.	0			c.G7401T						.						103	96	98					2																	179638382		2203	4300	6503	SO:0001583	missense	7273	exon32			TGACACCTTACAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.7401G>T	chr2.hg19:g.179638382C>A	ENSP00000465570:p.Lys2467Asn	126.0	0.0		263.0	15.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.719	1.159063	0.21454	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	5.82	0.456	0.16655	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.78362	0.4271	M	0.70595	2.14	0.25367	N	0.988738	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.998;0.998;0.998;0.999	T	0.67608	-0.5627	9	0.87932	D	0	.	10.7519	0.46213	0.0:0.5099:0.0:0.4901	.	2421;2421;2421;2467;2467	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	N	2467;2421;2421;2421;2421;2467	ENSP00000343764:K2467N;ENSP00000434586:K2421N;ENSP00000340554:K2421N;ENSP00000352154:K2421N;ENSP00000354117:K2467N	ENSP00000340554:K2421N	K	-	3	2	TTN	179346627	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	1.156000	0.31712	0.126000	0.18424	-0.133000	0.14855	AAG	.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179638382	C	A	179638382	3	1	92	1	0	0	0	0	1	0	0	0	16750	680	24	3	103911	3	TTN	2	179638382	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	50183	179638382	63560991	27	12825										
TTN	7273	hgsc.bcm.edu	37	chr2	179659228	179659228	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctcactctggccatatcaacGgcagcaacaacagtcgcaac	7	15	3	0	rs549880126		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr2:179659228G>C	ENST00000591111.1	-	8	1520	c.1296C>G	c.(1294-1296)gcC>gcG	p.A432A	TTN_ENST00000359218.5_Silent_p.A432A|TTN_ENST00000460472.2_Silent_p.A432A|TTN_ENST00000342175.6_Silent_p.A432A|TTN_ENST00000589042.1_Silent_p.A432A|TTN_ENST00000342992.6_Silent_p.A432A|TTN_ENST00000360870.5_Silent_p.A432A			Q8WZ42	TITIN_HUMAN	titin	0	Ala-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCATATCAACGGCAGCAACAA	0.468																																					p.A432A		Atlas-SNP	.											.	TTN	18412	.	0			c.C1296G						.						147	134	138					2																	179659228		2203	4300	6503	SO:0001819	synonymous_variant	7273	exon8			ATCAACGGCAGCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.1296C>G	chr2.hg19:g.179659228G>C		71.0	0.0		100.0	38.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179659228	G	C	179659228	2	2	92	1	0	0	0	0	0	0	0	1	16750	1103	39	4		4	TTN	2	179659228	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	20846	179659228	63540145	28	12826										
TOP2B	7155	hgsc.bcm.edu	37	chr3	25665077	25665077	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttccctagcatcatagttggGtagtttacaagcccatccag	8	11	1	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:25665077G>A	ENST00000264331.4	-	21	2655	c.2656C>T	c.(2656-2658)Ccc>Tcc	p.P886S	TOP2B_ENST00000435706.2_Missense_Mutation_p.P881S	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	886					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	TCATAGTTGGGTAGTTTACAA	0.388																																					p.P881S		Atlas-SNP	.											TOP2B,caecum,carcinoma,0,1	TOP2B	98	.	0			c.C2641T						.						121	115	117					3																	25665077		1921	4137	6058	SO:0001583	missense	7155	exon21			AGTTGGGTAGTTT	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.2656C>T	chr3.hg19:g.25665077G>A	ENSP00000264331:p.Pro886Ser	135.0	0.0		277.0	65.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	hg19		.	.	.	.	.	.	.	.	.	.	G	31	5.071559	0.93950	.	.	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225	T;T	0.57907	0.37;0.37	5.64	5.64	0.86602	.	0.045861	0.85682	D	0.000000	T	0.75946	0.3919	M	0.89534	3.04	0.80722	D	1	D	0.60160	0.987	P	0.57846	0.828	T	0.80099	-0.1524	10	0.62326	D	0.03	-7.3621	20.0639	0.97700	0.0:0.0:1.0:0.0	.	881	Q02880-2	.	S	881;886;881	ENSP00000396704:P881S;ENSP00000264331:P886S	ENSP00000264331:P886S	P	-	1	0	TOP2B	25640081	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	9.766000	0.98957	2.817000	0.96982	0.557000	0.71058	CCC	.	.		0.388	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				A	25665077	G	A	25665077	3	1	92	1	0	0	0	0	1	0	0	0	16381	1261	44	3	2288	3	TOP2B	3	25665077	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10		25665077	172357353	29	12827										
OXSM	54995	hgsc.bcm.edu	37	chr3	25835782	25835782	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgctgggagctgcaggggcaGtcgaggcagcttttaccaca	15	10	0	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:25835782G>T	ENST00000280701.3	+	3	1276	c.1177G>T	c.(1177-1179)Gtc>Ttc	p.V393F	OXSM_ENST00000420173.2_Missense_Mutation_p.V310F	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	393					acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						TGCAGGGGCAGTCGAGGCAGC	0.433																																					p.V393F		Atlas-SNP	.											.	OXSM	54	.	0			c.G1177T						.						99	99	99					3																	25835782		2203	4300	6503	SO:0001583	missense	54995	exon3			GGGGCAGTCGAGG	BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	ENST00000280701.3:c.1177G>T	chr3.hg19:g.25835782G>T	ENSP00000280701:p.Val393Phe	89.0	0.0		122.0	18.0	NM_017897		Missense_Mutation	SNP	ENST00000280701.3	hg19	CCDS2643.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.677468	0.47886	.	.	ENSG00000151093	ENST00000280701;ENST00000420173	.	.	.	5.52	1.6	0.23607	Beta-ketoacyl synthase, C-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.545762	0.19448	N	0.114004	T	0.50343	0.1610	M	0.64260	1.97	0.09310	N	1	D;P	0.71674	0.998;0.65	D;P	0.67382	0.951;0.751	T	0.41052	-0.9530	9	0.72032	D	0.01	-4.6058	1.3158	0.02107	0.2565:0.2619:0.3475:0.1341	.	310;393	Q9NWU1-2;Q9NWU1	.;OXSM_HUMAN	F	393;310	.	ENSP00000280701:V393F	V	+	1	0	OXSM	25810786	0.018000	0.18449	0.000000	0.03702	0.573000	0.36030	1.037000	0.30241	0.299000	0.22661	0.655000	0.94253	GTC	.	.		0.433	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		T	25835782	G	T	25835782	3	4	92	1	0	0	0	0	1	0	0	0	11344	1029	36	3	1183	3	OXSM	3	25835782	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	170705	25835782	172186648	30	12828										
PRSS50	29122	hgsc.bcm.edu	37	chr3	46755769	46755769	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gaatggtccttcaacacataGtccgtgccaggcaggcagat	11	11	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:46755769G>A	ENST00000460241.1	-	9	2363	c.693C>T	c.(691-693)gaC>gaT	p.D231D	PRSS50_ENST00000315170.7_Silent_p.D231D			Q9UI38	TSP50_HUMAN	protease, serine, 50	231	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						TCAACACATAGTCCGTGCCAG	0.607																																					p.D231D	Pancreas(41;915 1239 11561 17469)	Atlas-SNP	.											.	PRSS50	35	.	0			c.C693T						.						124	93	103					3																	46755769		2203	4300	6503	SO:0001819	synonymous_variant	29122	exon4			CACATAGTCCGTG	AF100707	CCDS2745.1	3p21.31	2011-05-24			ENSG00000206549	ENSG00000206549		"Serine peptidases / Serine peptidases"	17910	protein-coding gene	gene with protein product	"cancer/testis antigen 20", "testes specific protease 50"	607950				10397268	Standard	NM_013270		Approved	TSP50, CT20	uc003cqe.1	Q9UI38	OTTHUMG00000164067	ENST00000460241.1:c.693C>T	chr3.hg19:g.46755769G>A		50.0	0.0		86.0	61.0	NM_013270		Silent	SNP	ENST00000460241.1	hg19	CCDS2745.1																																																																																			.	.		0.607	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1			A	46755769	G	A	46755769	2	1	92	1	0	0	0	0	0	0	0	1	12643	1020	36	3		3	PRSS50	3	46755769	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	20919987	46755769	151266661	31	12829										
KLHL18	23276	hgsc.bcm.edu	37	chr3	47371491	47371491	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ccagtttgctgagacaatgaTgtgtgctgtgctgtacgacg	13	8	0	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:47371491T>C	ENST00000232766.5	+	4	472	c.452T>C	c.(451-453)aTg>aCg	p.M151T	KLHL18_ENST00000455924.2_Missense_Mutation_p.M39T	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	151	BACK.									endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	21		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		GAGACAATGATGTGTGCTGTG	0.488																																					p.M151T		Atlas-SNP	.											.	KLHL18	46	.	0			c.T452C						.						120	118	119					3																	47371491		2203	4300	6503	SO:0001583	missense	23276	exon4			CAATGATGTGTGC	AB018338	CCDS33749.1	3p21	2013-01-30	2013-01-30		ENSG00000114648	ENSG00000114648		"Kelch-like", "BTB/POZ domain containing"	29120	protein-coding gene	gene with protein product			"kelch-like 18 (Drosophila)"			9872452	Standard	NM_025010		Approved	KIAA0795, FLJ13703	uc003crd.3	O94889	OTTHUMG00000156522	ENST00000232766.5:c.452T>C	chr3.hg19:g.47371491T>C	ENSP00000232766:p.Met151Thr	49.0	0.0		123.0	19.0	NM_025010	A8K612|Q7Z3E8|Q8N125	Missense_Mutation	SNP	ENST00000232766.5	hg19	CCDS33749.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.617891	0.66787	.	.	ENSG00000114648	ENST00000232766;ENST00000455924	T;T	0.67523	-0.27;-0.27	4.94	4.94	0.65067	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	T	0.64962	0.2646	N	0.25245	0.725	0.80722	D	1	D;P;P	0.58970	0.984;0.458;0.902	P;B;P	0.58620	0.842;0.183;0.52	T	0.61088	-0.7133	10	0.21014	T	0.42	.	13.5678	0.61828	0.0:0.0:0.0:1.0	.	2;151;86	Q647K1;O94889;O94889-2	.;KLH18_HUMAN;.	T	151;39	ENSP00000232766:M151T;ENSP00000405585:M39T	ENSP00000232766:M151T	M	+	2	0	KLHL18	47346495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.903000	0.69877	2.085000	0.62840	0.383000	0.25322	ATG	.	.		0.488	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344493.1	NM_025010		C	47371491	T	C	47371491	3	2	92	1	0	0	0	0	1	0	0	0	8382	1464	51	2	466	2	KLHL18	3	47371491	Missense_Mutation	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	615722	47371491	150650939	32	12830										
MST1R	4486	hgsc.bcm.edu	37	chr3	49936589	49936589	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	acatacaatgcagtgacctgTactggtcccaacagcccatt	7	13	0	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:49936589T>C	ENST00000296474.3	-	2	1365	c.1338A>G	c.(1336-1338)gtA>gtG	p.V446V	CTD-2330K9.2_ENST00000435478.1_RNA|MST1R_ENST00000344206.4_Silent_p.V446V	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	446	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		CAGTGACCTGTACTGGTCCCA	0.572																																					p.V446V		Atlas-SNP	.											.	MST1R	205	.	0			c.A1338G						.						208	182	191					3																	49936589		2203	4300	6503	SO:0001819	synonymous_variant	4486	exon2			GACCTGTACTGGT	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.1338A>G	chr3.hg19:g.49936589T>C		63.0	0.0		109.0	12.0	NM_001244937	B5A944|B5A945|B5A946|B5A947	Silent	SNP	ENST00000296474.3	hg19	CCDS2807.1																																																																																			.	.		0.572	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			C	49936589	T	C	49936589	2	2	92	1	0	0	0	0	0	0	0	1	9900	1625	57	2		2	MST1R	3	49936589	Silent	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	2565098	49936589	148085841	33	12831										
ATXN7	6314	hgsc.bcm.edu	37	chr3	63975996	63975996	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gaaggcgatgacaaagaagaGtctgttgaaaaactggactg	13	5	1	4			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:63975996G>T	ENST00000295900.6	+	10	2056	c.1506G>T	c.(1504-1506)gaG>gaT	p.E502D	ATXN7_ENST00000538065.1_Missense_Mutation_p.E502D|ATXN7_ENST00000398590.3_Missense_Mutation_p.E502D|ATXN7_ENST00000484332.1_Missense_Mutation_p.E357D|ATXN7_ENST00000487717.1_Missense_Mutation_p.E502D	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	502					cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		ACAAAGAAGAGTCTGTTGAAA	0.552																																					p.E502D		Atlas-SNP	.											.	ATXN7	126	.	0			c.G1506T						.						106	113	111					3																	63975996		2055	4199	6254	SO:0001583	missense	6314	exon10			AGAAGAGTCTGTT	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"Ataxins"	10560	protein-coding gene	gene with protein product		607640	"spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.1506G>T	chr3.hg19:g.63975996G>T	ENSP00000295900:p.Glu502Asp	57.0	0.0		110.0	19.0	NM_000333	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	ENST00000295900.6	hg19	CCDS43102.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759417	0.69763	.	.	ENSG00000163635	ENST00000398590;ENST00000295900;ENST00000487717;ENST00000538065;ENST00000484332	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	5.91	4.86	0.63082	.	0.165282	0.56097	D	0.000035	T	0.56247	0.1972	L	0.45422	1.42	0.58432	D	0.999997	P;P;D	0.69078	0.603;0.724;0.997	B;B;D	0.79108	0.089;0.183;0.992	T	0.52366	-0.8585	10	0.45353	T	0.12	-16.3957	15.9733	0.80036	0.0746:0.0:0.9254:0.0	.	357;502;502	E9PHP9;O15265-2;O15265	.;.;ATX7_HUMAN	D	502;502;502;502;357	ENSP00000381590:E502D;ENSP00000295900:E502D;ENSP00000420234:E502D;ENSP00000439585:E502D;ENSP00000428277:E357D	ENSP00000295900:E502D	E	+	3	2	ATXN7	63951036	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.495000	0.35627	2.808000	0.96608	0.655000	0.94253	GAG	.	.		0.552	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333		T	63975996	G	T	63975996	3	4	92	1	0	0	0	0	1	0	0	0	1215	1020	36	3	1604	3	ATXN7	3	63975996	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	14039407	63975996	134046434	34	12832										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64084858	64084858	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctcatcgcttgtgacgtatcGcaggcgcgctggctggggga	16	11	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:64084858G>T	ENST00000295902.6	-	8	2989	c.2404C>A	c.(2404-2406)Cga>Aga	p.R802R	PRICKLE2-AS1_ENST00000460946.1_RNA|PRICKLE2_ENST00000564377.1_Silent_p.R858R|RP11-129B22.1_ENST00000482609.1_RNA|PRICKLE2-AS1_ENST00000476308.1_RNA	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	802					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R802*(1)		breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		GTGACGTATCGCAGGCGCGCT	0.552																																					p.R802R		Atlas-SNP	.											PRICKLE2,NS,carcinoma,0,1	PRICKLE2	88	.	1	Substitution - Nonsense(1)	prostate(1)	c.C2404A						.						88	86	87					3																	64084858		2203	4300	6503	SO:0001819	synonymous_variant	166336	exon8			CGTATCGCAGGCG	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.2404C>A	chr3.hg19:g.64084858G>T		80.0	0.0		119.0	19.0	NM_198859	Q0VF44	Silent	SNP	ENST00000295902.6	hg19	CCDS2902.1																																																																																			.	.		0.552	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		T	64084858	G	T	64084858	2	4	92	1	0	0	0	0	0	0	0	1	12499	1095	38	1		1	PRICKLE2	3	64084858	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	108862	64084858	133937572	35	12833										
RETNLB	84666	hgsc.bcm.edu	37	chr3	108474715	108474716	+	Frame_Shift_Ins	INS	-	-	C													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gctgaacatcccacgaaccaINScagccatagccacaagcaca							TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:108474715_108474716insC	ENST00000295755.6	-	3	443_444	c.245_246insG	c.(244-246)tgtfs	p.C82fs	RETNLB_ENST00000482939.1_Intron	NM_032579.2	NP_115968.1	Q9BQ08	RETNB_HUMAN	resistin like beta	82					cell proliferation (GO:0008283)	extracellular region (GO:0005576)				endometrium(1)|kidney(3)|lung(10)|prostate(1)|skin(1)	16						CCCACGAACCACAGCCATAGCC	0.579																																					p.C82fs		Atlas-INDEL	.											.	RETNLB	38	.	0			c.246_247insG						.																																			SO:0001589	frameshift_variant	84666	exon3			.	AF290873	CCDS2953.1	3q13.1	2008-02-05			ENSG00000163515	ENSG00000163515			20388	protein-coding gene	gene with protein product		605645				10921885, 12574343	Standard	NM_032579		Approved	HXCP2, FIZZ2, RELMb	uc003dxh.2	Q9BQ08	OTTHUMG00000159393	ENST00000295755.6:c.246dupG	chr3.hg19:g.108474716_108474716dupC	ENSP00000295755:p.Cys82fs	62.0	0.0		311.0	27.0	NM_032579	Q14D27	Frame_Shift_Ins	INS	ENST00000295755.6	hg19	CCDS2953.1																																																																																			.	.		0.579	RETNLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355093.1			C	108474716	-	C	108474715	7	5	92	1	0	1	1	0	0	0	0	0	13252	157	6	0	93	0	RETNLB	3	108474715	Frame_Shift_Ins	INS	-	TCGA-DD-A11A-01A-11D-A12Z-10	44389857	108474715	89547715	36	12834										
C3orf15	89876	hgsc.bcm.edu	37	chr3	119421979	119421980	+	Frame_Shift_Ins	INS	-	-	C													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	aaccatcgaggagccccaggINScccagccgcaggtgtctcaa							TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:119421979_119421980insC	ENST00000273390.5	+	1	111_112	c.34_35insC	c.(34-36)gccfs	p.A12fs	MAATS1_ENST00000463700.1_Frame_Shift_Ins_p.A12fs	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	12						mitochondrion (GO:0005739)											GGAGCCCCAGGCCCAGCCGCAG	0.639																																					p.A12fs		Atlas-INDEL	.											.	.	.	.	0			c.34_35insC						.																																			SO:0001589	frameshift_variant	89876	exon1			.	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"AMY-1-associating protein expressed in testis 1", "MYCBP-binding protein", "spermatogenesis associated 26"	609910	"chromosome 3 open reading frame 15", "MYCBP/AMY-1-associated, testis expressed 1"	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.37dupC	chr3.hg19:g.119421982_119421982dupC	ENSP00000273390:p.Ala12fs	34.0	0.0		95.0	11.0	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Frame_Shift_Ins	INS	ENST00000273390.5	hg19	CCDS2994.1																																																																																			.	.		0.639	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364		C	119421980	-	C	119421979	7	5	92	1	0	1	1	0	0	0	0	0	2211	1203	42	0	36	0	C3orf15	3	119421979	Frame_Shift_Ins	INS	-	TCGA-DD-A11A-01A-11D-A12Z-10	10947264	119421979	78600451	37	12835										
GSK3B	2932	hgsc.bcm.edu	37	chr3	119635000	119635000	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	atggatataggctaaacttcGgaacagctgatacatataca	8	7	0	1	rs201787969		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:119635000G>A	ENST00000264235.8	-	5	1481	c.499C>T	c.(499-501)Cga>Tga	p.R167*	GSK3B_ENST00000316626.5_Nonsense_Mutation_p.R167*	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	167	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	GCTAAACTTCGGAACAGCTGA	0.348																																					p.R167X		Atlas-SNP	.											GSK3B_ENST00000316626,NS,carcinoma,0,2	GSK3B	119	.	0			c.C499T						.						81	84	83					3																	119635000		2203	4300	6503	SO:0001587	stop_gained	2932	exon5			AACTTCGGAACAG	BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701			4617	protein-coding gene	gene with protein product		605004				10486203	Standard	NM_002093		Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.499C>T	chr3.hg19:g.119635000G>A	ENSP00000264235:p.Arg167*	47.0	0.0		77.0	8.0	NM_002093	D3DN89|Q9BWH3|Q9UL47	Nonsense_Mutation	SNP	ENST00000264235.8	hg19	CCDS54628.1	.	.	.	.	.	.	.	.	.	.	G	37	6.481761	0.97603	.	.	ENSG00000082701	ENST00000264235;ENST00000316626	.	.	.	4.89	2.99	0.34606	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0915	13.4517	0.61174	0.0:0.0:0.6701:0.3299	.	.	.	.	X	167	.	ENSP00000264235:R167X	R	-	1	2	GSK3B	121117690	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.621000	0.54210	0.684000	0.31448	0.563000	0.77884	CGA	.	.		0.348	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258240.2			A	119635000	G	A	119635000	4	1	92	1	0	0	0	0	0	1	0	0	6833	1124	39	1	834	1	GSK3B	3	119635000	Nonsense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	213021	119635000	78387430	38	12836										
DNAJB8	165721	hgsc.bcm.edu	37	chr3	128181899	128181899	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	acagccagcacggtcatacaGggagcgtttcttggagtcag	13	10	3	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:128181899G>A	ENST00000469083.1	-	2	2747	c.190C>T	c.(190-192)Ctg>Ttg	p.L64L	DNAJB8-AS1_ENST00000471626.1_RNA|DNAJB8_ENST00000319153.3_Silent_p.L64L			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	64	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		CGGTCATACAGGGAGCGTTTC	0.602																																					p.L64L		Atlas-SNP	.											.	DNAJB8	34	.	0			c.C190T						.						126	127	126					3																	128181899		2203	4300	6503	SO:0001819	synonymous_variant	165721	exon3			CATACAGGGAGCG		CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"Heat shock proteins / DNAJ (HSP40)"	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.190C>T	chr3.hg19:g.128181899G>A		56.0	0.0		120.0	14.0	NM_153330	B3KWV7	Silent	SNP	ENST00000469083.1	hg19	CCDS3048.1																																																																																			.	.		0.602	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330		A	128181899	G	A	128181899	2	1	92	1	0	0	0	0	0	0	0	1	4628	991	35	3		3	DNAJB8	3	128181899	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	8546899	128181899	69840531	39	12837										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129303388	129303388	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	aggctgggcaggctgcccgaGatctgcaggatcatgccctg	15	12	2	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:129303388G>A	ENST00000324093.4	-	6	2047	c.1869C>T	c.(1867-1869)atC>atT	p.I623I	PLXND1_ENST00000393239.1_Silent_p.I623I	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	623					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GGCTGCCCGAGATCTGCAGGA	0.647																																					p.I623I	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C1869T						.						59	57	57					3																	129303388		2203	4300	6503	SO:0001819	synonymous_variant	23129	exon6			GCCCGAGATCTGC	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.1869C>T	chr3.hg19:g.129303388G>A		35.0	0.0		92.0	41.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	hg19	CCDS33854.1																																																																																			.	.		0.647	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		A	129303388	G	A	129303388	2	1	92	1	0	0	0	0	0	0	0	1	12136	932	33	3		3	PLXND1	3	129303388	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	1121489	129303388	68719042	40	12838										
SLCO2A1	6578	hgsc.bcm.edu	37	chr3	133673915	133673915	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agccagcagctgggcaaccaCcatcaggccccacatgctgc	10	17	1	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:133673915C>T	ENST00000310926.4	-	4	793	c.520G>A	c.(520-522)Gtg>Atg	p.V174M	SLCO2A1_ENST00000493729.1_Intron|SLCO2A1_ENST00000478651.1_5'Flank	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	174					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	TGGGCAACCACCATCAGGCCC	0.597																																					p.V174M		Atlas-SNP	.											.	SLCO2A1	72	.	0			c.G520A						.						71	71	71					3																	133673915		2203	4300	6503	SO:0001583	missense	6578	exon4			CAACCACCATCAG		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"Solute carriers"	10955	protein-coding gene	gene with protein product		601460	"solute carrier family 21 (prostaglandin transporter), member 2", "matrin F/G 1"	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.520G>A	chr3.hg19:g.133673915C>T	ENSP00000311291:p.Val174Met	59.0	0.0		131.0	56.0	NM_005630	Q86V98|Q8IUN2	Missense_Mutation	SNP	ENST00000310926.4	hg19	CCDS3084.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.542741	0.45280	.	.	ENSG00000174640	ENST00000310926	T	0.59906	0.23	5.89	4.1	0.47936	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.146813	0.64402	N	0.000009	T	0.67411	0.2890	L	0.45470	1.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.991;0.995	T	0.67086	-0.5759	10	0.56958	D	0.05	.	11.0765	0.48034	0.1296:0.8042:0.0:0.0662	.	174;174	F8W9W8;Q92959	.;SO2A1_HUMAN	M	174	ENSP00000311291:V174M	ENSP00000311291:V174M	V	-	1	0	SLCO2A1	135156605	1.000000	0.71417	0.995000	0.50966	0.053000	0.15095	7.518000	0.81795	0.826000	0.34661	-0.314000	0.08810	GTG	.	.		0.597	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630		T	133673915	C	T	133673915	3	4	92	1	0	0	0	0	1	0	0	0	14741	507	18	3	1455	3	SLCO2A1	3	133673915	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	4370527	133673915	64348515	41	12839										
PHC3	80012	hgsc.bcm.edu	37	chr3	169846627	169846627	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctgcaccaaaacctggccctGggacagaatttcaggctgca	10	13	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr3:169846627G>C	ENST00000494943.1	-	8	1665	c.1597C>G	c.(1597-1599)Cag>Gag	p.Q533E	PHC3_ENST00000467570.1_Missense_Mutation_p.Q492E|PHC3_ENST00000495893.2_Missense_Mutation_p.Q545E			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	533	Gln-rich.|Pro-rich.				multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			ACCTGGCCCTGGGACAGAATT	0.512																																					p.Q545E		Atlas-SNP	.											.	PHC3	113	.	0			c.C1633G						.						129	131	131					3																	169846627		1947	4141	6088	SO:0001583	missense	80012	exon8			GGCCCTGGGACAG		CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"Sterile alpha motif (SAM) domain containing"	15682	protein-coding gene	gene with protein product	"early development regulator 3", "polyhomeotic like 3"		"polyhomeotic like 3 (Drosophila)"			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.1597C>G	chr3.hg19:g.169846627G>C	ENSP00000420271:p.Gln533Glu	64.0	0.0		86.0	31.0	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Missense_Mutation	SNP	ENST00000494943.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.99	2.995155	0.54147	.	.	ENSG00000173889	ENST00000494943;ENST00000495893;ENST00000467570	T;T	0.31769	1.48;1.48	5.69	5.69	0.88448	.	0.189604	0.37136	N	0.002223	T	0.38268	0.1034	L	0.36672	1.1	0.80722	D	1	P;B;P;B	0.43578	0.811;0.187;0.713;0.091	P;B;P;B	0.54924	0.764;0.152;0.68;0.068	T	0.02639	-1.1130	10	0.02654	T	1	-1.2302	19.8034	0.96518	0.0:0.0:1.0:0.0	.	492;492;533;545	B4E2T1;E7EX82;Q8NDX5;Q8NDX5-7	.;.;PHC3_HUMAN;.	E	533;545;492	ENSP00000420271:Q533E;ENSP00000420294:Q545E	ENSP00000419089:Q492E	Q	-	1	0	PHC3	171329321	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.081000	0.64444	2.670000	0.90874	0.563000	0.77884	CAG	.	.		0.512	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947		C	169846627	G	C	169846627	3	2	92	1	0	0	0	0	1	0	0	0	11827	1357	47	4	1386	4	PHC3	3	169846627	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	36172712	169846627	28175803	42	12840										
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15601277	15601277	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agaaaaaagtcaaggagaagAtgtagaagatgaccacagag	12	4	1	7			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr4:15601277A>G	ENST00000503292.1	+	37	4802	c.4622A>G	c.(4621-4623)gAt>gGt	p.D1541G	CC2D2A_ENST00000389652.5_Missense_Mutation_p.D1433G|CC2D2A_ENST00000413206.1_Missense_Mutation_p.D1541G|CC2D2A_ENST00000424120.1_Missense_Mutation_p.D1541G	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	1541					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						CAAGGAGAAGATGTAGAAGAT	0.448																																					p.D1541G		Atlas-SNP	.											.	CC2D2A	158	.	0			c.A4622G						.						75	70	72					4																	15601277		1920	4141	6061	SO:0001583	missense	57545	exon37			GAGAAGATGTAGA	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.4622A>G	chr4.hg19:g.15601277A>G	ENSP00000421809:p.Asp1541Gly	109.0	0.0		273.0	20.0	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Missense_Mutation	SNP	ENST00000503292.1	hg19	CCDS47026.1	.	.	.	.	.	.	.	.	.	.	A	9.556	1.117098	0.20795	.	.	ENSG00000048342	ENST00000424120;ENST00000413206;ENST00000426932;ENST00000510333;ENST00000503292;ENST00000389652	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.75	3.26	0.37387	.	0.126124	0.51477	D	0.000086	T	0.61451	0.2348	L	0.56396	1.775	0.80722	D	1	B;B	0.13594	0.008;0.001	B;B	0.15870	0.014;0.006	T	0.50642	-0.8804	10	0.17832	T	0.49	.	8.5037	0.33175	0.8009:0.1314:0.0677:0.0	.	1541;1433	Q9P2K1;Q9P2K1-2	C2D2A_HUMAN;.	G	1541;1541;1433;1433;1541;1433	ENSP00000403465:D1541G;ENSP00000398391:D1541G;ENSP00000421809:D1541G;ENSP00000374303:D1433G	ENSP00000374303:D1433G	D	+	2	0	CC2D2A	15210375	0.999000	0.42202	0.276000	0.24689	0.376000	0.30014	4.146000	0.58072	0.427000	0.26145	0.528000	0.53228	GAT	.	.		0.448	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		G	15601277	A	G	15601277	3	3	92	1	0	0	0	0	1	0	0	0	2730	333	12	2	4963	2	CC2D2A	4	15601277	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10		15601277	175552999	43	12841										
PPARGC1A	10891	hgsc.bcm.edu	37	chr4	23815325	23815325	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	aggtttaccttgaagaggatCtactgcctggagaccttgat	11	8	1	4			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr4:23815325C>A	ENST00000264867.2	-	8	1900	c.1781G>T	c.(1780-1782)aGa>aTa	p.R594I	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	594	Arg/Ser-rich.|Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				TGAAGAGGATCTACTGCCTGG	0.403																																					p.R594I	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.G1781T						.						60	61	61					4																	23815325		2203	4300	6503	SO:0001583	missense	10891	exon8			GAGGATCTACTGC	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"RNA binding motif (RRM) containing"	9237	protein-coding gene	gene with protein product		604517	"peroxisome proliferative activated receptor, gamma, coactivator 1", "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.1781G>T	chr4.hg19:g.23815325C>A	ENSP00000264867:p.Arg594Ile	52.0	0.0		52.0	9.0	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	hg19	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	C	17.14	3.313073	0.60414	.	.	ENSG00000109819	ENST00000264867	T	0.40225	1.04	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.68311	0.2987	M	0.78049	2.395	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.65849	-0.6068	10	0.51188	T	0.08	-5.1764	20.8598	0.99761	0.0:1.0:0.0:0.0	.	594	Q9UBK2	PRGC1_HUMAN	I	594	ENSP00000264867:R594I	ENSP00000264867:R594I	R	-	2	0	PPARGC1A	23424423	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.684000	0.74538	2.937000	0.99478	0.650000	0.86243	AGA	.	.		0.403	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261		A	23815325	C	A	23815325	3	1	92	1	0	0	0	0	1	0	0	0	12309	913	32	3	639	3	PPARGC1A	4	23815325	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	8214048	23815325	167338951	44	12842										
BEND4	389206	hgsc.bcm.edu	37	chr4	42145706	42145706	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	actggctgacgaggggtttgGagttggaaagcttcccgaga	16	7	0	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr4:42145706G>T	ENST00000502486.1	-	3	1372	c.793C>A	c.(793-795)Cca>Aca	p.P265T	BEND4_ENST00000504360.1_Missense_Mutation_p.P261T	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	265										NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						GAGGGGTTTGGAGTTGGAAAG	0.488																																					p.P265T		Atlas-SNP	.											.	BEND4	67	.	0			c.C793A						.						87	88	88					4																	42145706		1909	4114	6023	SO:0001583	missense	389206	exon3			GGTTTGGAGTTGG	AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"BEN domain containing"	23815	protein-coding gene	gene with protein product			"coiled-coil domain containing 4"	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.793C>A	chr4.hg19:g.42145706G>T	ENSP00000421169:p.Pro265Thr	78.0	0.0		158.0	11.0	NM_001159547	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Missense_Mutation	SNP	ENST00000502486.1	hg19	CCDS47048.1	.	.	.	.	.	.	.	.	.	.	G	6.044	0.376490	0.11466	.	.	ENSG00000188848	ENST00000411720;ENST00000502486;ENST00000504360	.	.	.	5.52	2.77	0.32553	.	0.317042	0.35067	N	0.003470	T	0.35307	0.0927	N	0.08118	0	0.35096	D	0.764746	B;B;B	0.26547	0.152;0.094;0.152	B;B;B	0.27500	0.08;0.023;0.08	T	0.37244	-0.9714	9	0.54805	T	0.06	-15.8412	16.5549	0.84482	0.0:0.3682:0.6318:0.0	.	187;265;265	Q6ZU67-3;Q6ZU67;Q6ZU67-2	.;BEND4_HUMAN;.	T	136;265;261	.	ENSP00000412495:P136T	P	-	1	0	BEND4	41840463	1.000000	0.71417	0.062000	0.19696	0.001000	0.01503	3.989000	0.56958	0.259000	0.21709	-0.175000	0.13238	CCA	.	.		0.488	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406		T	42145706	G	T	42145706	3	4	92	1	0	0	0	0	1	0	0	0	1400	1174	41	3	827	3	BEND4	4	42145706	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	18330381	42145706	149008570	45	12843										
HERC3	8916	hgsc.bcm.edu	37	chr4	89591339	89591339	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgatacattttacattcctgAgatttccaatctcgtggaca	6	9	1	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr4:89591339A>T	ENST00000402738.1	+	16	2086	c.1847A>T	c.(1846-1848)gAg>gTg	p.E616V	HERC3_ENST00000543130.1_Missense_Mutation_p.E60V|HERC3_ENST00000264345.3_Missense_Mutation_p.E616V	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	616					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TACATTCCTGAGATTTCCAAT	0.363																																					p.E616V		Atlas-SNP	.											.	HERC3	82	.	0			c.A1847T						.						134	129	131					4																	89591339		2203	4300	6503	SO:0001583	missense	8916	exon16			TTCCTGAGATTTC	D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"hect domain and RLD 3"			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.1847A>T	chr4.hg19:g.89591339A>T	ENSP00000385684:p.Glu616Val	82.0	0.0		89.0	31.0	NM_014606	A8K1S5|Q8IXX3	Missense_Mutation	SNP	ENST00000402738.1	hg19	CCDS34028.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.602872	0.87157	.	.	ENSG00000138641	ENST00000402738;ENST00000264345;ENST00000543130;ENST00000512194	T;T;T;T	0.75260	0.82;0.82;1.13;-0.92	4.68	4.68	0.58851	.	0.051936	0.85682	D	0.000000	D	0.82435	0.5036	L	0.61036	1.89	0.80722	D	1	D	0.67145	0.996	P	0.62649	0.905	D	0.84386	0.0552	10	0.62326	D	0.03	.	14.5861	0.68326	1.0:0.0:0.0:0.0	.	616	Q15034	HERC3_HUMAN	V	616;616;60;17	ENSP00000385684:E616V;ENSP00000264345:E616V;ENSP00000441703:E60V;ENSP00000421021:E17V	ENSP00000264345:E616V	E	+	2	0	HERC3	89810362	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.709000	0.91379	2.092000	0.63282	0.482000	0.46254	GAG	.	.		0.363	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606		T	89591339	A	T	89591339	3	4	92	1	0	0	0	0	1	0	0	0	7068	304	11	4	1901	4	HERC3	4	89591339	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	47445633	89591339	101562937	46	12844										
FAT4	79633	hgsc.bcm.edu	37	chr4	126369855	126369855	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctgttagattcgtgaataagGccgatttccctaaagtgaga	10	7	0	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr4:126369855G>A	ENST00000394329.3	+	9	7697	c.7684G>A	c.(7684-7686)Gcc>Acc	p.A2562T	FAT4_ENST00000335110.5_Missense_Mutation_p.A860T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2562	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CGTGAATAAGGCCGATTTCCC	0.423																																					p.A2562T		Atlas-SNP	.											.	FAT4	1752	.	0			c.G7684A						.						79	78	78					4																	126369855		2203	4298	6501	SO:0001583	missense	79633	exon9			AATAAGGCCGATT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.7684G>A	chr4.hg19:g.126369855G>A	ENSP00000377862:p.Ala2562Thr	42.0	0.0		25.0	12.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	17.35	3.368545	0.61624	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.60797	0.16;0.16	5.92	5.92	0.95590	Cadherin (2);	0.000000	0.34088	U	0.004277	T	0.68531	0.3011	M	0.62266	1.93	0.58432	D	0.999997	P;P;P	0.50272	0.933;0.709;0.808	P;B;B	0.51582	0.674;0.133;0.26	T	0.68017	-0.5520	10	0.52906	T	0.07	.	20.3343	0.98733	0.0:0.0:1.0:0.0	.	860;2562;2562	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	T	2562;860	ENSP00000377862:A2562T;ENSP00000335169:A860T	ENSP00000335169:A860T	A	+	1	0	FAT4	126589305	1.000000	0.71417	0.997000	0.53966	0.841000	0.47740	9.666000	0.98612	2.822000	0.97130	0.650000	0.86243	GCC	.	.		0.423	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126369855	G	A	126369855	3	1	92	1	0	0	0	0	1	0	0	0	5700	1203	42	3	7718	3	FAT4	4	126369855	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	36778516	126369855	64784421	47	12845										
FAT4	79633	hgsc.bcm.edu	37	chr4	126371628	126371628	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	taacactagccaaagctcttGattatgagctatgccagaaa	7	9	1	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr4:126371628G>C	ENST00000394329.3	+	9	9470	c.9457G>C	c.(9457-9459)Gat>Cat	p.D3153H	FAT4_ENST00000335110.5_Missense_Mutation_p.D1451H	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3153	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CAAAGCTCTTGATTATGAGCT	0.388																																					p.D3153H		Atlas-SNP	.											.	FAT4	1752	.	0			c.G9457C						.						80	81	81					4																	126371628		2203	4300	6503	SO:0001583	missense	79633	exon9			GCTCTTGATTATG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9457G>C	chr4.hg19:g.126371628G>C	ENSP00000377862:p.Asp3153His	75.0	0.0		67.0	11.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	15.37	2.814864	0.50527	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.04234	3.67;3.67	5.63	5.63	0.86233	Cadherin (4);Cadherin-like (1);	0.000000	0.35378	U	0.003259	T	0.41696	0.1170	H	0.99058	4.415	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.66081	-0.6012	10	0.87932	D	0	.	19.7096	0.96089	0.0:0.0:1.0:0.0	.	1451;3153;3153	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	H	3153;1451	ENSP00000377862:D3153H;ENSP00000335169:D1451H	ENSP00000335169:D1451H	D	+	1	0	FAT4	126591078	1.000000	0.71417	0.997000	0.53966	0.197000	0.23852	9.666000	0.98612	2.652000	0.90054	0.655000	0.94253	GAT	.	.		0.388	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126371628	G	C	126371628	3	2	92	1	0	0	0	0	1	0	0	0	5700	1290	45	4	9491	4	FAT4	4	126371628	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	1773	126371628	64782648	48	12846										
MAP9	79884	hgsc.bcm.edu	37	chr4	156289738	156289738	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agtttagtggtagtgctaacCtcaggatcaaggttttcaga	11	6	3	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr4:156289738C>A	ENST00000311277.4	-	5	971	c.708G>T	c.(706-708)gaG>gaT	p.E236D	AC097467.2_ENST00000597831.1_RNA|AC097467.2_ENST00000598890.1_RNA|AC097467.2_ENST00000596165.1_RNA|MAP9_ENST00000379248.2_Missense_Mutation_p.E163D|AC097467.2_ENST00000600928.1_RNA|MAP9_ENST00000515654.1_Splice_Site_p.E236D	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	236					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		TAGTGCTAACCTCAGGATCAA	0.373																																					p.E236D		Atlas-SNP	.											.	MAP9	79	.	0			c.G708T						.						99	90	93					4																	156289738		2203	4300	6503	SO:0001630	splice_region_variant	79884	exon5			GCTAACCTCAGGA	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"aster-associated protein"	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.708+1G>T	chr4.hg19:g.156289738C>A		110.0	0.0		88.0	29.0	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	hg19	CCDS35493.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.444329	0.43429	.	.	ENSG00000164114	ENST00000311277;ENST00000515654;ENST00000433024;ENST00000393836;ENST00000379248	T;T;T;T	0.59224	1.21;1.86;0.5;0.28	5.09	4.23	0.50019	.	0.371784	0.23268	N	0.050055	T	0.66674	0.2813	M	0.66939	2.045	0.32156	N	0.58356	P;D;P;P	0.65815	0.877;0.995;0.787;0.787	P;P;B;B	0.57371	0.464;0.819;0.218;0.218	T	0.73751	-0.3884	10	0.66056	D	0.02	-1.4673	10.0248	0.42066	0.0:0.9011:0.0:0.0989	.	235;163;236;236	B4DVG9;A8MSM7;B9EJB6;Q49MG5	.;.;.;MAP9_HUMAN	D	236;236;235;236;163	ENSP00000310593:E236D;ENSP00000427402:E236D;ENSP00000394048:E235D;ENSP00000368550:E163D	ENSP00000310593:E236D	E	-	3	2	MAP9	156509188	1.000000	0.71417	0.986000	0.45419	0.134000	0.20937	2.641000	0.46587	2.520000	0.84964	0.467000	0.42956	GAG	.	.		0.373	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	Missense_Mutation	A	156289738	C	A	156289738	5	1	92	1	0	0	0	0	0	0	1	0	9279	695	24	3	1275	3	MAP9	4	156289738	Splice_Site	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	29918110	156289738	34864538	49	12847										
CBR4	84869	hgsc.bcm.edu	37	chr4	169923357	169923357	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttttaagccaacaatgcttcCtaggacaaaaaaaaaaaaaa	4	7	0	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr4:169923357C>G	ENST00000306193.3	-	4	569		c.e4-1		CBR4_ENST00000504480.1_Splice_Site|CBR4_ENST00000509108.1_Splice_Site	NM_032783.4	NP_116172.2	Q8N4T8	CBR4_HUMAN	carbonyl reductase 4						daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|fatty acid biosynthetic process (GO:0006633)|protein homotetramerization (GO:0051289)	mitochondrial matrix (GO:0005759)	NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|NADPH binding (GO:0070402)|NADPH dehydrogenase (quinone) activity (GO:0008753)|quinone binding (GO:0048038)			kidney(1)|large_intestine(2)|lung(2)	5		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)		ACAATGCTTCCTAGGACaaaa	0.328																																					.		Atlas-SNP	.											.	CBR4	15	.	0			c.401-1G>C						.						29	29	29					4																	169923357		2201	4299	6500	SO:0001630	splice_region_variant	84869	exon5			TGCTTCCTAGGAC	BC021973	CCDS3812.1	4q32.3	2013-10-11			ENSG00000145439	ENSG00000145439	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	25891	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 45C, member 1"					19027726	Standard	NM_032783		Approved	FLJ14431, SDR45C1	uc003iry.3	Q8N4T8	OTTHUMG00000161025	ENST00000306193.3:c.401-1G>C	chr4.hg19:g.169923357C>G		31.0	0.0		49.0	24.0	NM_032783	Q8WTW8|Q96K93	Splice_Site	SNP	ENST00000306193.3	hg19	CCDS3812.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.941649	0.53079	.	.	ENSG00000145439	ENST00000306193;ENST00000504480;ENST00000504561	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4136	0.94685	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CBR4	170159932	1.000000	0.71417	0.999000	0.59377	0.806000	0.45545	6.134000	0.71689	2.596000	0.87737	0.305000	0.20034	.	.	.		0.328	CBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363441.2	NM_032783	Intron	G	169923357	C	G	169923357	5	3	92	1	0	0	0	0	0	0	1	0	2712	695	24	4	321	4	CBR4	4	169923357	Splice_Site	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	13633619	169923357	21230919	50	12848										
EMB	133418	hgsc.bcm.edu	37	chr5	49724007	49724007	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	atatgttatgactctccaagGaaaagttatttgccattatt	6	6	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr5:49724007G>A	ENST00000303221.5	-	2	382	c.167C>T	c.(166-168)tCc>tTc	p.S56F	EMB_ENST00000506190.1_5'UTR|EMB_ENST00000514111.1_Missense_Mutation_p.S6F|EMB_ENST00000508934.1_Missense_Mutation_p.S56F	NM_198449.2	NP_940851.1	Q6PCB8	EMB_HUMAN	embigin	56					cell adhesion (GO:0007155)|plasma membrane lactate transport (GO:0035879)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	organic cyclic compound binding (GO:0097159)			breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	15	Lung SC(58;0.218)	Lung NSC(810;0.0795)				ACTCTCCAAGGAAAAGTTATT	0.318																																					p.S56F		Atlas-SNP	.											.	EMB	42	.	0			c.C167T						.						112	113	113					5																	49724007		2203	4300	6503	SO:0001583	missense	133418	exon2			TCCAAGGAAAAGT	BC059398	CCDS3953.1	5q11.1	2013-01-29	2010-06-24		ENSG00000170571	ENSG00000170571		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30465	protein-coding gene	gene with protein product		615669	"embigin homolog (mouse)"			9438341	Standard	NM_198449		Approved	MGC71745	uc003jom.3	Q6PCB8	OTTHUMG00000131161	ENST00000303221.5:c.167C>T	chr5.hg19:g.49724007G>A	ENSP00000302289:p.Ser56Phe	55.0	0.0		78.0	16.0	NM_198449	B7Z6S3|B7Z902	Missense_Mutation	SNP	ENST00000303221.5	hg19	CCDS3953.1	.	.	.	.	.	.	.	.	.	.	G	9.241	1.038241	0.19669	.	.	ENSG00000170571	ENST00000303221;ENST00000508934;ENST00000514111	T;T;T	0.60424	0.73;0.19;0.68	4.2	4.2	0.49525	.	0.896581	0.09633	N	0.775980	T	0.59487	0.2197	L	0.27053	0.805	0.29338	N	0.866241	D;D	0.58970	0.984;0.984	P;P	0.57371	0.819;0.819	T	0.51601	-0.8685	9	.	.	.	-0.531	12.3678	0.55238	0.0:0.0:1.0:0.0	.	56;56	D6RDX7;Q6PCB8	.;EMB_HUMAN	F	56;56;6	ENSP00000302289:S56F;ENSP00000425215:S56F;ENSP00000426404:S6F	.	S	-	2	0	EMB	49759764	1.000000	0.71417	0.978000	0.43139	0.031000	0.12232	3.755000	0.55197	2.642000	0.89623	0.655000	0.94253	TCC	.	.		0.318	EMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253853.1	NM_198449		A	49724007	G	A	49724007	3	1	92	1	0	0	0	0	1	0	0	0	5087	1174	41	3	848	3	EMB	5	49724007	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10		49724007	131191253	51	12849										
MOCS2	4338	hgsc.bcm.edu	37	chr5	52405551	52405551	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gccacccttacctggcacagCggcaccatcccgcctaggac	9	19	0	0	rs397518417		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr5:52405551C>T	ENST00000361377.4	-	1	50	c.9G>A	c.(7-9)ccG>ccA	p.P3P	MOCS2_ENST00000584946.1_Silent_p.P3P|MOCS2_ENST00000396954.3_5'UTR|CTD-2366F13.1_ENST00000512301.1_RNA|CTD-2366F13.1_ENST00000502171.2_RNA|CTD-2366F13.1_ENST00000499459.2_RNA|MOCS2_ENST00000450852.3_Silent_p.P3P|MOCS2_ENST00000510818.2_Silent_p.P3P|MOCS2_ENST00000508922.1_Silent_p.P3P|MOCS2_ENST00000582677.1_Silent_p.P3P|MOCS2_ENST00000527216.1_Intron					molybdenum cofactor synthesis 2											endometrium(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(810;3.08e-05)|Breast(144;0.0848)				CCTGGCACAGCGGCACCATCC	0.711																																					p.P3P		Atlas-SNP	.											.	MOCS2	28	.	0			c.G9A						.						13	23	20					5																	52405551		1968	3956	5924	SO:0001819	synonymous_variant	4338	exon1			GCACAGCGGCACC	AF117815	CCDS3958.1, CCDS47205.1	5q11	2008-02-05			ENSG00000164172	ENSG00000164172			7193	protein-coding gene	gene with protein product		603708				10053004, 9889283	Standard	NM_004531		Approved	MOCO1	uc003joz.3	O96007	OTTHUMG00000096981	ENST00000361377.4:c.9G>A	chr5.hg19:g.52405551C>T		31.0	0.0		49.0	19.0	NM_176806		Silent	SNP	ENST00000361377.4	hg19	CCDS47205.1																																																																																			.	.		0.711	MOCS2-004	KNOWN	alternative_3_UTR|NMD_exception|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000367796.3	NM_183418		T	52405551	C	T	52405551	2	4	92	1	0	0	0	0	0	0	0	1	9700	755	27	1		1	MOCS2	5	52405551	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	2681544	52405551	128509709	52	12850										
ANKRD32	84250	hgsc.bcm.edu	37	chr5	94025298	94025298	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	aaaaagatgaattttcacaaGactaatctaaaaggtattcc	5	6	2	3	rs367590507		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr5:94025298G>T	ENST00000265140.5	+	18	2825	c.2406G>T	c.(2404-2406)aaG>aaT	p.K802N		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	802						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		ATTTTCACAAGACTAATCTAA	0.323																																					p.K802N		Atlas-SNP	.											.	ANKRD32	117	.	0			c.G2406T						.						43	46	45					5																	94025298		2202	4298	6500	SO:0001583	missense	84250	exon18			TCACAAGACTAAT	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"Ankyrin repeat domain containing"	25408	protein-coding gene	gene with protein product			"BRCT domain containing 1"	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.2406G>T	chr5.hg19:g.94025298G>T	ENSP00000265140:p.Lys802Asn	66.0	0.0		82.0	25.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Missense_Mutation	SNP	ENST00000265140.5	hg19	CCDS4071.2	.	.	.	.	.	.	.	.	.	.	G	16.22	3.062451	0.55432	.	.	ENSG00000133302	ENST00000265140	T	0.63913	-0.07	5.67	2.91	0.33838	Ankyrin repeat-containing domain (3);	0.066807	0.56097	D	0.000027	T	0.59569	0.2203	N	0.16567	0.415	0.30410	N	0.779197	D	0.76494	0.999	D	0.69824	0.966	T	0.58825	-0.7568	10	0.66056	D	0.02	.	6.5315	0.22330	0.2064:0.1303:0.6632:0.0	.	802	Q9BQI6	ANR32_HUMAN	N	802	ENSP00000265140:K802N	ENSP00000265140:K802N	K	+	3	2	ANKRD32	94051054	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.039000	0.30266	0.414000	0.25790	0.655000	0.94253	AAG	.	.		0.323	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290		T	94025298	G	T	94025298	3	4	92	1	0	0	0	0	1	0	0	0	660	933	33	3	2472	3	ANKRD32	5	94025298	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	41619747	94025298	86889962	53	12851										
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125759319	125759319	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	atgactgaactacagcaagaTgtggaagacacaaagcctgc	10	9	0	4			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr5:125759319T>C	ENST00000285689.3	+	1	482	c.21T>C	c.(19-21)gaT>gaC	p.D7D	GRAMD3_ENST00000513040.1_Intron|GRAMD3_ENST00000514932.1_3'UTR|GRAMD3_ENST00000544396.1_5'UTR|GRAMD3_ENST00000543198.1_Silent_p.D7D|GRAMD3_ENST00000542322.1_Start_Codon_SNP_p.M1T|GRAMD3_ENST00000515200.1_Silent_p.D7D	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	7						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		TACAGCAAGATGTGGAAGACA	0.612																																					p.M1T		Atlas-SNP	.											.	GRAMD3	30	.	0			c.T2C						.						67	63	64					5																	125759319		2203	4300	6503	SO:0001819	synonymous_variant	65983	exon1			GCAAGATGTGGAA	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"HCV NS3 transactivated protein 2"					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.21T>C	chr5.hg19:g.125759319T>C		56.0	0.0		114.0	63.0	NM_001146321	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	hg19	CCDS4136.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.651935	0.29336	.	.	ENSG00000155324	ENST00000542322	T	0.33438	1.41	5.62	1.96	0.26148	.	.	.	.	.	T	0.22666	0.0547	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.06734	-1.0810	8	0.87932	D	0	.	6.4038	0.21652	0.0:0.0849:0.3312:0.5839	.	1	B7Z3R1	.	T	1	ENSP00000441876:M1T	ENSP00000441876:M1T	M	+	2	0	GRAMD3	125787218	1.000000	0.71417	1.000000	0.80357	0.396000	0.30629	0.233000	0.17911	0.406000	0.25560	0.533000	0.62120	ATG	.	.		0.612	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927		C	125759319	T	C	125759319	2	2	92	1	0	0	0	0	0	0	0	1	6760	1464	51	2		2	GRAMD3	5	125759319	Silent	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	31734021	125759319	55155941	54	12852										
DDX46	9879	hgsc.bcm.edu	37	chr5	134143603	134143603	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgaggattatgtacacagagCagggcggactggaagagcag	16	6	0	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr5:134143603C>T	ENST00000354283.4	+	16	2255	c.2120C>T	c.(2119-2121)gCa>gTa	p.A707V	DDX46_ENST00000452510.2_Missense_Mutation_p.A707V			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	707	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GTACACAGAGCAGGGCGGACT	0.383																																					p.A707V	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.C2120T						.						60	62	62					5																	134143603		2203	4300	6503	SO:0001583	missense	9879	exon16			ACAGAGCAGGGCG		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.2120C>T	chr5.hg19:g.134143603C>T	ENSP00000346236:p.Ala707Val	77.0	0.0		90.0	24.0	NM_014829	O94894|Q96EI0|Q9Y658	Missense_Mutation	SNP	ENST00000354283.4	hg19	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	C	9.778	1.174651	0.21704	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	T;T	0.75260	-0.92;-0.92	5.49	5.49	0.81192	Helicase, C-terminal (3);	0.045148	0.85682	D	0.000000	T	0.45296	0.1335	N	0.00572	-1.36	0.80722	D	1	B	0.15930	0.015	B	0.28139	0.086	T	0.56414	-0.7983	10	0.02654	T	1	-18.615	19.744	0.96245	0.0:1.0:0.0:0.0	.	707	Q7L014	DDX46_HUMAN	V	707	ENSP00000416534:A707V;ENSP00000346236:A707V	ENSP00000346236:A707V	A	+	2	0	DDX46	134171502	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.983000	0.70540	2.746000	0.94184	0.561000	0.74099	GCA	.	.		0.383	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		T	134143603	C	T	134143603	3	4	92	1	0	0	0	0	1	0	0	0	4366	710	25	3	2182	3	DDX46	5	134143603	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	8384284	134143603	46771657	55	12853										
ARSI	340075	hgsc.bcm.edu	37	chr5	149677216	149677216	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ggtctcctgtcagcagcttcCactcacccacgcggatggca	10	16	3	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr5:149677216C>T	ENST00000328668.7	-	2	1850	c.1271G>A	c.(1270-1272)tGg>tAg	p.W424*		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	424					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAGCAGCTTCCACTCACCCAC	0.622																																					p.W424X		Atlas-SNP	.											.	ARSI	65	.	0			c.G1271A						.						34	38	36					5																	149677216		2203	4300	6503	SO:0001587	stop_gained	340075	exon2			AGCTTCCACTCAC	AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"Arylsulfatase family"	32521	protein-coding gene	gene with protein product		610009	"arylsulfatase I"			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.1271G>A	chr5.hg19:g.149677216C>T	ENSP00000333395:p.Trp424*	35.0	0.0		66.0	24.0	NM_001012301	A1L3B0|B3KV22|B7XD03	Nonsense_Mutation	SNP	ENST00000328668.7	hg19	CCDS34275.1	.	.	.	.	.	.	.	.	.	.	C	35	5.459116	0.96240	.	.	ENSG00000183876	ENST00000328668;ENST00000515301	.	.	.	4.45	4.45	0.53987	.	0.121961	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.3903	0.55355	0.1682:0.8318:0.0:0.0	.	.	.	.	X	424;281	.	ENSP00000333395:W424X	W	-	2	0	ARSI	149657409	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.772000	0.68889	2.296000	0.77279	0.561000	0.74099	TGG	.	.		0.622	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301		T	149677216	C	T	149677216	4	4	92	1	0	0	0	0	0	1	0	0	994	595	21	3	442	3	ARSI	5	149677216	Nonsense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	15533613	149677216	31238044	56	12854										
HDGFL1	154150	hgsc.bcm.edu	37	chr6	22570186	22570186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	acgctggtggcggcggcgacGaattggggaagccggacgac	19	10	0	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:22570186G>A	ENST00000230012.3	+	1	509	c.382G>A	c.(382-384)Gaa>Aaa	p.E128K	HDGFL1_ENST00000510882.2_Missense_Mutation_p.E128K	NM_138574.2	NP_612641.2	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1	128										kidney(1)|large_intestine(3)|lung(7)	11	Ovarian(93;0.163)					CGGCGGCGACGAATTGGGGAA	0.701																																					p.E128K		Atlas-SNP	.											.	HDGFL1	33	.	0			c.G382A						.						6	6	6					6																	22570186		2018	4000	6018	SO:0001583	missense	154150	exon1			GGCGACGAATTGG	AK056824	CCDS34347.1	6p22.2	2008-02-05	2005-04-07	2005-04-07	ENSG00000112273	ENSG00000112273			21095	protein-coding gene	gene with protein product			"PWWP domain containing 1"	PWWP1			Standard	NM_138574		Approved	dJ309H15.1	uc003nds.3	Q5TGJ6	OTTHUMG00000016206	ENST00000230012.3:c.382G>A	chr6.hg19:g.22570186G>A	ENSP00000230012:p.Glu128Lys	28.0	0.0		94.0	38.0	NM_138574	Q96MJ6	Missense_Mutation	SNP	ENST00000230012.3	hg19	CCDS34347.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.723361	0.30503	.	.	ENSG00000112273	ENST00000230012;ENST00000510882	T;T	0.33865	1.39;1.39	2.8	-3.49	0.04724	.	0.579894	0.16944	N	0.193177	T	0.08626	0.0214	L	0.45137	1.4	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.25152	-1.0140	10	0.40728	T	0.16	-12.1753	4.1988	0.10455	0.4156:0.3428:0.2416:0.0	.	128	Q5TGJ6	HDGL1_HUMAN	K	128	ENSP00000230012:E128K;ENSP00000442129:E128K	ENSP00000230012:E128K	E	+	1	0	HDGFL1	22678165	0.004000	0.15560	0.000000	0.03702	0.070000	0.16714	0.700000	0.25601	-0.950000	0.03659	0.491000	0.48974	GAA	.	.		0.701	HDGFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043500.1	NM_138574		A	22570186	G	A	22570186	3	1	92	1	0	0	0	0	1	0	0	0	7028	1059	37	1	384	1	HDGFL1	6	22570186	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10		22570186	148544881	57	12855										
HIST1H2BD	3017	hgsc.bcm.edu	37	chr6	26158595	26158595	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	atggggatcatgaattccttCgtcaacgacatcttcgagcg	10	10	3	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:26158595C>T	ENST00000289316.2	+	1	222	c.198C>T	c.(196-198)ttC>ttT	p.F66F	HIST1H2BD_ENST00000377777.4_Silent_p.F66F	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	66					chromatin organization (GO:0006325)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	24						TGAATTCCTTCGTCAACGACA	0.577																																					p.F66F		Atlas-SNP	.											.	HIST1H2BD	45	.	0			c.C198T						.						180	169	173					6																	26158595		2203	4300	6503	SO:0001819	synonymous_variant	3017	exon1			TTCCTTCGTCAAC	M60751	CCDS4587.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158373	ENSG00000158373		"Histones / Replication-dependent"	4747	protein-coding gene	gene with protein product		602799	"H2B histone family, member B", "histone 1, H2bd"	H2BFB		1916825, 12408966	Standard	NM_021063		Approved	H2B/b	uc003ngr.3	P58876	OTTHUMG00000014426	ENST00000289316.2:c.198C>T	chr6.hg19:g.26158595C>T		106.0	0.0		202.0	26.0	NM_021063		Silent	SNP	ENST00000289316.2	hg19	CCDS4587.1																																																																																			.	.		0.577	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063		T	26158595	C	T	26158595	2	4	92	1	0	0	0	0	0	0	0	1	7152	883	31	1		1	HIST1H2BD	6	26158595	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	3588409	26158595	144956472	58	12856										
GABBR1	2550	hgsc.bcm.edu	37	chr6	29574930	29574930	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gtgaagaccgtgtggacccaCcaaatcttggtgaacatgga	12	9	1	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:29574930C>A	ENST00000377034.4	-	17	2393	c.2058G>T	c.(2056-2058)tgG>tgT	p.W686C	GABBR1_ENST00000376977.3_3'UTR|GABBR1_ENST00000355973.3_Missense_Mutation_p.W569C|GABBR1_ENST00000377012.4_Missense_Mutation_p.W569C|GABBR1_ENST00000377016.4_Missense_Mutation_p.W624C	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	686					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	TGTGGACCCACCAAATCTTGG	0.577																																					p.W686C		Atlas-SNP	.											.	GABBR1	95	.	0			c.G2058T						.						114	110	111					6																	29574930		2203	4300	6503	SO:0001583	missense	2550	exon17			GACCCACCAAATC	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.2058G>T	chr6.hg19:g.29574930C>A	ENSP00000366233:p.Trp686Cys	65.0	0.0		183.0	18.0	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	hg19	CCDS4663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.3|21.3	4.129378|4.129378	0.77549|0.77549	.|.	.|.	ENSG00000204681|ENSG00000204681	ENST00000485026|ENST00000355973;ENST00000377016;ENST00000377012;ENST00000377034	.|D;D;D;D	.|0.88201	.|-2.35;-2.35;-2.35;-2.35	4.57|4.57	4.57|4.57	0.56435|0.56435	.|GPCR, family 3, C-terminal (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94598|0.94598	0.8259|0.8259	M|M	0.90483|0.90483	3.12|3.12	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.999;0.999	D|D	0.95655|0.95655	0.8710|0.8710	5|10	.|0.87932	.|D	.|0	-5.0204|-5.0204	14.8623|14.8623	0.70389|0.70389	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|624;686;569	.|Q9UBS5-3;Q9UBS5;Q5SUJ9	.|.;GABR1_HUMAN;.	L|C	67|569;624;569;686	.|ENSP00000348248:W569C;ENSP00000366215:W624C;ENSP00000366211:W569C;ENSP00000366233:W686C	.|ENSP00000348248:W569C	V|W	-|-	1|3	0|0	GABBR1|GABBR1	29682909|29682909	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.908000|0.908000	0.53690|0.53690	7.357000|7.357000	0.79456|0.79456	2.075000|2.075000	0.62263|0.62263	0.563000|0.563000	0.77884|0.77884	GTG|TGG	.	.		0.577	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			A	29574930	C	A	29574930	3	1	92	1	0	0	0	0	1	0	0	0	6163	508	18	3	855	3	GABBR1	6	29574930	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	3416335	29574930	141540137	59	12857										
HLA-A	3105	hgsc.bcm.edu	37	chr6	29911899	29911900	+	Splice_Site	INS	-	-	C													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttctgactcttcccgtcagaINScccccccaagacacatatga					rs199474608|rs199474609|rs386698554|rs377011235|rs41544717		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:29911899_29911900insC	ENST00000396634.1	+	6	961_962	c.620_621insC	c.(619-624)gacccc>gaCcccc	p.DP207fs	HLA-A_ENST00000376806.5_Splice_Site_p.DP207fs|HLA-A_ENST00000376809.5_Splice_Site_p.DP207fs|HLA-A_ENST00000376802.2_Splice_Site_p.DP207fs			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	207	Alpha-3.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TTCCCGTCAGACCCCCCCAAGA	0.574									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.D207fs		Pindel	.											.	HLA-A	89	.	0			c.620_621insC						.																																			SO:0001630	splice_region_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	.	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.620-1->C	chr6.hg19:g.29911906_29911906dupC		0.0	0.0		17.0	17.0	NM_002116	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Frame_Shift_Ins	INS	ENST00000396634.1	hg19	CCDS34373.1																																																																																			.	.		0.574	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	Frame_Shift_Ins	C	29911900	-	C	29911899	8	5	92	1	0	1	1	0	0	0	1	0	7204	289	10	0	634	0	HLA-A	6	29911899	Splice_Site	INS	-	TCGA-DD-A11A-01A-11D-A12Z-10	336969	29911899	141203168	60	12858										
MUC21	394263	hgsc.bcm.edu	37	chr6	30954774	30954774	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ggcacagccaccaactctgaGtccagcacagtgtccagtgg	11	14	1	1	rs41288649		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:30954774G>C	ENST00000376296.3	+	2	1063	c.822G>C	c.(820-822)gaG>gaC	p.E274D	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	274	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAACTCTGAGTCCAGCACAG	0.612																																					p.E274D		Atlas-SNP	.											.	MUC21	98	.	0			c.G822C						.						185	181	182					6																	30954774		2203	4300	6503	SO:0001583	missense	394263	exon2			CTCTGAGTCCAGC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.822G>C	chr6.hg19:g.30954774G>C	ENSP00000365473:p.Glu274Asp	72.0	0.0		234.0	25.0	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	hg19	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	7.723	0.697571	0.15106	.	.	ENSG00000204544	ENST00000376296	T	0.01963	4.53	3.7	-3.24	0.05094	.	.	.	.	.	T	0.00552	0.0018	L	0.29908	0.895	0.09310	N	1	P	0.40834	0.73	B	0.37451	0.25	T	0.48080	-0.9066	8	.	.	.	0.085	4.9779	0.14149	0.291:0.3326:0.3764:0.0	.	274	Q5SSG8	MUC21_HUMAN	D	274	ENSP00000365473:E274D	.	E	+	3	2	MUC21	31062753	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	-2.404000	0.01045	-0.243000	0.09653	0.472000	0.43445	GAG	.	G|0.500;C|0.500		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		C	30954774	G	C	30954774	3	2	92	1	0	0	0	0	1	0	0	0	9986	1020	36	4	828	4	MUC21	6	30954774	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	1042875	30954774	140160293	61	12859										
HSPA1L	3305	hgsc.bcm.edu	37	chr6	31778842	31778842	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctgcacacaactcttcaaatCgagctctggtgatggatgta	9	10	3	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:31778842C>T	ENST00000375654.4	-	2	1097	c.908G>A	c.(907-909)cGa>cAa	p.R303Q	HSPA1L_ENST00000417199.3_Missense_Mutation_p.R303Q	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	303					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						CTCTTCAAATCGAGCTCTGGT	0.483																																					p.R303Q		Atlas-SNP	.											.	HSPA1L	185	.	0			c.G908A						.						70	74	73					6																	31778842		2203	4300	6503	SO:0001583	missense	3305	exon2			TCAAATCGAGCTC	D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"Heat shock proteins / HSP70"	5234	protein-coding gene	gene with protein product		140559	"heat shock 70kD protein-like 1"			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.908G>A	chr6.hg19:g.31778842C>T	ENSP00000364805:p.Arg303Gln	58.0	0.0		113.0	60.0	NM_005527	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Missense_Mutation	SNP	ENST00000375654.4	hg19	CCDS34413.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.263130	0.59431	.	.	ENSG00000204390	ENST00000375654;ENST00000417199;ENST00000375653;ENST00000424494	T;T	0.01005	5.45;5.45	5.4	5.4	0.78164	.	0.000000	0.31772	N	0.007091	T	0.00906	0.0030	M	0.64080	1.96	0.80722	D	1	B	0.21606	0.058	B	0.17722	0.019	T	0.55528	-0.8127	10	0.87932	D	0	-7.9667	16.7132	0.85391	0.0:1.0:0.0:0.0	.	303	P34931	HS71L_HUMAN	Q	303;303;248;193	ENSP00000364805:R303Q;ENSP00000387691:R303Q	ENSP00000364804:R248Q	R	-	2	0	HSPA1L	31886821	1.000000	0.71417	0.980000	0.43619	0.695000	0.40330	5.899000	0.69846	2.810000	0.96702	0.585000	0.79938	CGA	.	.		0.483	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			T	31778842	C	T	31778842	3	4	92	1	0	0	0	0	1	0	0	0	7419	884	31	1	1021	1	HSPA1L	6	31778842	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	824068	31778842	139336225	62	12860										
HLA-DPB1	3115	hgsc.bcm.edu	37	chr6	33053656	33053656	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ggcatcttcatgcacaggagGagcaagaaaggtgagaaagc	14	7	2	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:33053656G>T	ENST00000418931.2	+	4	863	c.747G>T	c.(745-747)agG>agT	p.R249S		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	249					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						TGCACAGGAGGAGCAAGAAAG	0.532																																					p.R249S		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.G747T						.						87	82	84					6																	33053656		2203	4300	6503	SO:0001583	missense	3115	exon4			CAGGAGGAGCAAG		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.747G>T	chr6.hg19:g.33053656G>T	ENSP00000408146:p.Arg249Ser	51.0	0.0		116.0	8.0	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	hg19	CCDS4765.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	16.43|16.43|16.43	3.121594|3.121594|3.121594	0.56613|0.56613|0.56613	.|.|.	.|.|.	ENSG00000223865|ENSG00000223865|ENSG00000223865	ENST00000422592|ENST00000416804|ENST00000418931;ENST00000411942;ENST00000428835	.|.|T;T	.|.|0.00808	.|.|5.78;5.67	4.03|4.03|4.03	1.24|1.24|1.24	0.21308|0.21308|0.21308	.|.|.	.|.|0.184300	.|.|0.42964	.|.|D	.|.|0.000624	.|T|T	.|0.01765|0.01765	.|0.0056|0.0056	M|M|M	0.87456|0.87456|0.87456	2.885|2.885|2.885	0.09310|0.09310|0.09310	N|N|N	0.999998|0.999998|0.999998	.|.|D;D;D	.|.|0.76494	.|.|0.997;0.999;0.999	.|.|D;D;D	.|.|0.64506	.|.|0.926;0.926;0.926	.|T|T	.|0.35773|0.35773	.|-0.9775|-0.9775	.|5|10	0.52906|.|0.87932	T|.|D	0.07|.|0	.|.|.	6.5722|6.5722|6.5722	0.22545|0.22545|0.22545	0.2937:0.0:0.7063:0.0|0.2937:0.0:0.7063:0.0|0.2937:0.0:0.7063:0.0	.|.|.	.|.|215;259;249	.|.|A2ALJ6;Q59GY1;P04440	.|.|.;.;DPB1_HUMAN	X|V|S	60|216|249;219;226	.|.|ENSP00000408146:R249S;ENSP00000412654:R226S	ENSP00000413559:E60X|.|ENSP00000389210:R219S	E|G|R	+|+|+	1|2|3	0|0|2	HLA-DPB1|HLA-DPB1|HLA-DPB1	33161634|33161634|33161634	0.003000|0.003000|0.003000	0.15002|0.15002|0.15002	0.003000|0.003000|0.003000	0.11579|0.11579|0.11579	0.341000|0.341000|0.341000	0.28922|0.28922|0.28922	0.325000|0.325000|0.325000	0.19628|0.19628|0.19628	0.130000|0.130000|0.130000	0.18549|0.18549|0.18549	0.643000|0.643000|0.643000	0.83706|0.83706|0.83706	GAG|GGA|AGG	.	.		0.532	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121		T	33053656	G	T	33053656	3	4	92	1	0	0	0	0	1	0	0	0	7212	1165	41	3	761	3	HLA-DPB1	6	33053656	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	1274814	33053656	138061411	63	12861										
PPIL1	51645	hgsc.bcm.edu	37	chr6	36823793	36823793	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tctggccccgcattggccatTgcgagaattccagcccctgg	11	15	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:36823793T>C	ENST00000373699.5	-	4	548	c.297A>G	c.(295-297)gcA>gcG	p.A99A	PPIL1_ENST00000483552.1_5'UTR	NM_016059.4	NP_057143.1	Q9Y3C6	PPIL1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 1	99	Cyclosporin A binding.|PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			lung(1)|ovary(1)	2						CATTGGCCATTGCGAGAATTC	0.537																																					p.A99A		Atlas-SNP	.											.	PPIL1	6	.	0			c.A297G						.						40	40	40					6																	36823793		2203	4300	6503	SO:0001819	synonymous_variant	51645	exon4			GGCCATTGCGAGA	AF090992	CCDS4826.1	6p21.1	2008-08-29			ENSG00000137168	ENSG00000137168			9260	protein-coding gene	gene with protein product		601301				10072585, 8978786	Standard	NM_016059		Approved	CYPL1	uc003omu.2	Q9Y3C6	OTTHUMG00000014612	ENST00000373699.5:c.297A>G	chr6.hg19:g.36823793T>C		28.0	0.0		63.0	35.0	NM_016059	O15001|Q5TDC9	Silent	SNP	ENST00000373699.5	hg19	CCDS4826.1																																																																																			.	.		0.537	PPIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040382.1			C	36823793	T	C	36823793	2	2	92	1	0	0	0	0	0	0	0	1	12338	1799	63	2		2	PPIL1	6	36823793	Silent	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	3770137	36823793	134291274	64	12862										
MOCS1	4337	hgsc.bcm.edu	37	chr6	39895091	39895091	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgaggttgcacttctctgtgAgggagatccgcaggtagctg	15	8	1	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:39895091A>G	ENST00000340692.5	-	2	230	c.227T>C	c.(226-228)cTc>cCc	p.L76P	MOCS1_ENST00000308559.7_Missense_Mutation_p.L76P|MOCS1_ENST00000373186.4_Missense_Mutation_p.L76P|MOCS1_ENST00000373195.3_Intron|MOCS1_ENST00000432280.2_Missense_Mutation_p.L47P|MOCS1_ENST00000373175.4_Missense_Mutation_p.L47P|MOCS1_ENST00000425303.2_Missense_Mutation_p.L76P|MOCS1_ENST00000373188.2_Missense_Mutation_p.L76P			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	76	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					CTTCTCTGTGAGGGAGATCCG	0.617																																					p.L76P	NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	Atlas-SNP	.											.	MOCS1	87	.	0			c.T227C						.						38	38	38					6																	39895091		2202	4297	6499	SO:0001583	missense	4337	exon1			TCTGTGAGGGAGA	AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.227T>C	chr6.hg19:g.39895091A>G	ENSP00000344794:p.Leu76Pro	33.0	0.0		101.0	17.0	NM_005943	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	hg19		.	.	.	.	.	.	.	.	.	.	A	25.5	4.649040	0.87958	.	.	ENSG00000124615	ENST00000373186;ENST00000308559;ENST00000373175;ENST00000373188;ENST00000340692;ENST00000425303;ENST00000432280	D;D;D;D;D;D;D	0.92397	-3.03;-3.03;-3.03;-3.03;-3.03;-3.03;-3.03	5.44	5.44	0.79542	Elongator protein 3/MiaB/NifB (1);Aldolase-type TIM barrel (1);Radical SAM (1);MoaA/nifB/pqqE, iron-sulphur binding, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97520	0.9188	H	0.97962	4.115	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.994;0.999;0.998;0.994	D	0.99078	1.0836	9	.	.	.	-27.7589	15.438	0.75162	1.0:0.0:0.0:0.0	.	76;76;76;76	Q9NZB8-5;Q9NZB8;Q9NZB8-8;Q9NZB8-6	.;MOCS1_HUMAN;.;.	P	76;76;47;76;76;76;47	ENSP00000362282:L76P;ENSP00000309843:L76P;ENSP00000362270:L47P;ENSP00000362284:L76P;ENSP00000344794:L76P;ENSP00000416478:L76P;ENSP00000410809:L47P	.	L	-	2	0	MOCS1	40003069	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.130000	0.89598	2.182000	0.69389	0.482000	0.46254	CTC	.	.		0.617	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943		G	39895091	A	G	39895091	3	3	92	1	0	0	0	0	1	0	0	0	9699	304	11	2	966	2	MOCS1	6	39895091	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	3071298	39895091	131219976	65	12863										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136582246	136582439	+	Stop_Codon_Del	DEL	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	-													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttgtaatcttacttcatattTattattcctaaaagagagag					rs376948280|rs537502804|rs562481221|rs527483217|rs62431283|rs112744301|rs62431282|rs370252607|rs570210520|rs111800140|rs193167212|rs375440569	byFrequency	TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:136582246_136582439delTGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	ENST00000531224.1	-	0	2973_3017				BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000530767.1_Stop_Codon_Del|BCLAF1_ENST00000031135.9_Stop_Codon_Del|BCLAF1_ENST00000527536.1_Stop_Codon_Del|BCLAF1_ENST00000353331.4_Stop_Codon_Del|BCLAF1_ENST00000527759.1_Stop_Codon_Del|BCLAF1_ENST00000392348.2_Stop_Codon_Del	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1						apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		ACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATTTTATACCTTTTCTTCCTTGCGTCTGTCCTTCTTTTCTTCATTATTTTCCATGG	0.315																																					p.920_921del	Colon(142;1534 1789 5427 7063 28491)	Pindel	.											.	BCLAF1	203	.	0			c.2758_3016del						.																																			SO:0001567	stop_retained_variant	9774	exon13			.	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	Exception_encountered	chr6.hg19:g.136582246_136582439delTGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	Exception_encountered	0.0	0.0		14.0	14.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Frame_Shift_Del	DEL	ENST00000531224.1	hg19	CCDS5177.1																																																																																			.	.		0.315	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		-	136582439	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	-	136582246	7	5	92	1	0	1	0	1	0	0	0	0	1383	1769	61	0	1	0	BCLAF1	6	136582246	Stop_Codon_Del	DEL	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TCGA-DD-A11A-01A-11D-A12Z-10	96687155	136582246	34532821	66	12864										
MAP3K5	4217	hgsc.bcm.edu	37	chr6	136913604	136913604	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agtgtccgaattcccttgacAtctctttctccgcaggactt	7	13	2	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr6:136913604A>G	ENST00000359015.4	-	22	3387	c.3027T>C	c.(3025-3027)gaT>gaC	p.D1009D	MAP3K5_ENST00000355845.4_Silent_p.D256D	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	1009					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		TTCCCTTGACATCTCTTTCTC	0.473																																					p.D1009D		Atlas-SNP	.											.	MAP3K5	136	.	0			c.T3027C						.						149	149	149					6																	136913604		2203	4300	6503	SO:0001819	synonymous_variant	4217	exon22			CTTGACATCTCTT	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6857	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 1"	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.3027T>C	chr6.hg19:g.136913604A>G		66.0	0.0		99.0	16.0	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	hg19	CCDS5179.1																																																																																			.	.		0.473	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1			G	136913604	A	G	136913604	2	3	92	1	0	0	0	0	0	0	0	1	9262	214	8	2		2	MAP3K5	6	136913604	Silent	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	331358	136913604	34201463	67	12865										
AQP1	358	hgsc.bcm.edu	37	chr7	30951862	30951862	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cgtcgccaccgccatcctctCaggcatcacctcctccctga	6	21	2	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:30951862C>T	ENST00000311813.4	+	1	393	c.338C>T	c.(337-339)tCa>tTa	p.S113L	AQP1_ENST00000434909.2_Missense_Mutation_p.S173L|AQP1_ENST00000509504.1_Missense_Mutation_p.S290L	NM_198098.2	NP_932766.1	P29972	AQP1_HUMAN	aquaporin 1 (Colton blood group)	113					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|camera-type eye morphogenesis (GO:0048593)|carbon dioxide transmembrane transport (GO:0035378)|carbon dioxide transport (GO:0015670)|cation transmembrane transport (GO:0098655)|cell volume homeostasis (GO:0006884)|cellular homeostasis (GO:0019725)|cellular hyperosmotic response (GO:0071474)|cellular response to cAMP (GO:0071320)|cellular response to copper ion (GO:0071280)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to inorganic substance (GO:0071241)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mercury ion (GO:0071288)|cellular response to nitric oxide (GO:0071732)|cellular response to retinoic acid (GO:0071300)|cellular response to salt stress (GO:0071472)|cellular response to stress (GO:0033554)|cellular response to UV (GO:0034644)|cerebrospinal fluid secretion (GO:0033326)|cGMP biosynthetic process (GO:0006182)|corticotropin secretion (GO:0051458)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|glomerular filtration (GO:0003094)|glycerol transport (GO:0015793)|hyperosmotic salinity response (GO:0042538)|lateral ventricle development (GO:0021670)|lipid digestion (GO:0044241)|maintenance of symbiont-containing vacuole by host (GO:0085018)|metanephric descending thin limb development (GO:0072220)|metanephric glomerulus vasculature development (GO:0072239)|metanephric proximal convoluted tubule segment 2 development (GO:0072232)|metanephric proximal straight tubule development (GO:0072230)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|nitric oxide transport (GO:0030185)|odontogenesis (GO:0042476)|pancreatic juice secretion (GO:0030157)|positive regulation of angiogenesis (GO:0045766)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of saliva secretion (GO:0046878)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|renal water absorption (GO:0070295)|renal water transport (GO:0003097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|secretory granule organization (GO:0033363)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)|transepithelial water transport (GO:0035377)|transmembrane transport (GO:0055085)|water transport (GO:0006833)|wound healing (GO:0042060)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|symbiont-containing vacuole (GO:0020003)	ammonium transmembrane transporter activity (GO:0008519)|carbon dioxide transmembrane transporter activity (GO:0035379)|glycerol transmembrane transporter activity (GO:0015168)|intracellular cGMP activated cation channel activity (GO:0005223)|nitric oxide transmembrane transporter activity (GO:0030184)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)|transmembrane transporter activity (GO:0022857)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			kidney(1)|large_intestine(2)|lung(9)	12		Melanoma(862;0.16)			Acetazolamide(DB00819)	GCCATCCTCTCAGGCATCACC	0.617																																					p.S113L		Atlas-SNP	.											.	AQP1	38	.	0			c.C338T						.						87	91	90					7																	30951862		2203	4300	6503	SO:0001583	missense	358	exon1			TCCTCTCAGGCAT	M77829	CCDS5431.1, CCDS55096.1, CCDS55097.1, CCDS55098.1	7p14	2014-07-19	2014-01-02		ENSG00000240583	ENSG00000240583		"Ion channels / Aquaporins", "Blood group antigens"	633	protein-coding gene	gene with protein product		107776	"Colton blood group", "aquaporin 1 (channel-forming integral protein, 28kDa)", "aquaporin 1 (channel-forming integral protein, 28kDa, CO blood group)", "aquaporin 1"	CO		1722319, 3166547	Standard	NM_198098		Approved	CHIP28		P29972	OTTHUMG00000023944	ENST00000311813.4:c.338C>T	chr7.hg19:g.30951862C>T	ENSP00000311165:p.Ser113Leu	15.0	0.0		82.0	10.0	NM_198098	B5BU39|E7EM69|E9PC21|F5GY19|Q8TBI5|Q8TDC1	Missense_Mutation	SNP	ENST00000311813.4	hg19	CCDS5431.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.844051	0.51164	.	.	ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000250424	ENST00000434909;ENST00000265298;ENST00000311813;ENST00000413400;ENST00000509504	D;D;D	0.92545	-3.06;-3.06;-3.06	4.46	4.46	0.54185	Aquaporin-like (2);	0.206480	0.43919	D	0.000510	D	0.90424	0.7002	N	0.11560	0.145	0.80722	D	1	D;D	0.69078	0.997;0.995	D;P	0.64410	0.925;0.827	D	0.91315	0.5077	10	0.46703	T	0.11	-1.4045	15.0132	0.71565	0.0:1.0:0.0:0.0	.	173;113	B4E220;P29972	.;AQP1_HUMAN	L	173;18;113;98;290	ENSP00000395059:S173L;ENSP00000311165:S113L;ENSP00000421315:S290L	ENSP00000265298:S18L	S	+	2	0	RP5-877J2.1;AQP1	30918387	0.725000	0.28048	0.971000	0.41717	0.526000	0.34562	1.301000	0.33447	2.490000	0.84030	0.561000	0.74099	TCA	.	.		0.617	AQP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215002.3	NM_000385		T	30951862	C	T	30951862	3	4	92	1	0	0	0	0	1	0	0	0	821	838	29	3	340	3	AQP1	7	30951862	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10		30951862	128186801	68	12866										
NPSR1	387129	hgsc.bcm.edu	37	chr7	34698055	34698055	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	acttcacagagggcagcttcGattccagtgggaccgggcag	14	11	1	1	rs267601495		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:34698055G>A	ENST00000360581.1	+	1	159	c.31G>A	c.(31-33)Gat>Aat	p.D11N	NPSR1-AS1_ENST00000419766.1_RNA|NPSR1_ENST00000381553.3_Missense_Mutation_p.D11N|NPSR1_ENST00000381539.3_Missense_Mutation_p.D11N|NPSR1_ENST00000381542.1_Missense_Mutation_p.D11N|AC005493.1_ENST00000399077.1_Intron|NPSR1_ENST00000531252.1_Missense_Mutation_p.D11N|NPSR1_ENST00000359791.1_Missense_Mutation_p.D11N|NPSR1_ENST00000465305.1_Missense_Mutation_p.D11N	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	11						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)	p.D11H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	GGGCAGCTTCGATTCCAGTGG	0.572																																					p.D11N		Atlas-SNP	.											NPSR1_ENST00000359791,colon,carcinoma,0,3	NPSR1	134	.	1	Substitution - Missense(1)	skin(1)	c.G31A						.						102	91	95					7																	34698055		2203	4300	6503	SO:0001583	missense	387129	exon1			AGCTTCGATTCCA	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"GPCR / Class A : Neuropeptide receptors : S"	23631	protein-coding gene	gene with protein product		608595	"G protein-coupled receptor 154"	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.31G>A	chr7.hg19:g.34698055G>A	ENSP00000353788:p.Asp11Asn	60.0	0.0		106.0	38.0	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	hg19	CCDS5444.1	.	.	.	.	.	.	.	.	.	.	G	5.696	0.312915	0.10789	.	.	ENSG00000187258	ENST00000381553;ENST00000465305;ENST00000360581;ENST00000381542;ENST00000359791;ENST00000531252;ENST00000381539	T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5	3.84	-6.33	0.01988	.	1.739720	0.03061	N	0.155829	T	0.11410	0.0278	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B	0.09022	0.0;0.002;0.0;0.001;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.001;0.0;0.001;0.0;0.0	T	0.12682	-1.0538	10	0.17369	T	0.5	0.3602	1.1791	0.01841	0.2309:0.2662:0.3298:0.1731	.	11;11;11;11;11;11	B7ZMA2;Q6W5P4-5;Q6W5P4-2;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;.;.;NPSR1_HUMAN	N	11	ENSP00000370965:D11N;ENSP00000434955:D11N;ENSP00000353788:D11N;ENSP00000370953:D11N;ENSP00000352839:D11N;ENSP00000433258:D11N;ENSP00000370950:D11N	ENSP00000352839:D11N	D	+	1	0	NPSR1	34664580	0.000000	0.05858	0.000000	0.03702	0.169000	0.22640	-1.229000	0.02945	-1.277000	0.02411	-0.367000	0.07326	GAT	.	.		0.572	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173		A	34698055	G	A	34698055	3	1	92	1	0	0	0	0	1	0	0	0	10609	1058	37	1	33	1	NPSR1	7	34698055	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	3746193	34698055	124440608	69	12867										
AEBP1	165	hgsc.bcm.edu	37	chr7	44149823	44149823	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cagaccggtgccactgaggaCgactactatgatggtgcgtg	14	10	0	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:44149823C>A	ENST00000223357.3	+	11	1583	c.1278C>A	c.(1276-1278)gaC>gaA	p.D426E	AEBP1_ENST00000450684.2_5'Flank|MIR4649_ENST00000582839.1_RNA	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	426	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.|Interaction with MAPK1 and MAPK3. {ECO:0000250}.|Required for DNA-binding and interaction with NFKBIA. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						CCACTGAGGACGACTACTATG	0.632																																					p.D426E		Atlas-SNP	.											.	AEBP1	102	.	0			c.C1278A						.						96	79	85					7																	44149823		2203	4300	6503	SO:0001583	missense	165	exon11			TGAGGACGACTAC	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"aortic carboxypeptidase-like protein", "adipocyte enhancer binding protein 1"	602981	"AE-binding protein 1"			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.1278C>A	chr7.hg19:g.44149823C>A	ENSP00000223357:p.Asp426Glu	57.0	0.0		138.0	14.0	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	hg19	CCDS5476.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.406636	0.42715	.	.	ENSG00000106624	ENST00000223357	D	0.99270	-5.66	5.24	-2.29	0.06805	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.97685	0.9241	L	0.37561	1.115	0.80722	D	1	P	0.43477	0.808	P	0.47705	0.555	D	0.94444	0.7661	10	0.54805	T	0.06	-44.4846	12.4051	0.55434	0.0:0.3852:0.0:0.6148	.	426	Q8IUX7	AEBP1_HUMAN	E	426	ENSP00000223357:D426E	ENSP00000223357:D426E	D	+	3	2	AEBP1	44116348	0.000000	0.05858	0.994000	0.49952	0.552000	0.35366	-2.477000	0.00985	-0.316000	0.08690	0.561000	0.74099	GAC	.	.		0.632	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		A	44149823	C	A	44149823	3	1	92	1	0	0	0	0	1	0	0	0	349	535	19	1	1320	1	AEBP1	7	44149823	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	9451768	44149823	114988840	70	12868										
FZD9	8326	hgsc.bcm.edu	37	chr7	72849249	72849250	+	In_Frame_Ins	INS	-	-	CAG													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cgggcgcgctctacgtgatcINScaggagggcctggagaacac							TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:72849249_72849250insCAG	ENST00000344575.3	+	1	1141_1142	c.912_913insCAG	c.(913-915)cag>CAGcag	p.305_305Q>QQ		NM_003508.2	NP_003499.1	O00144	FZD9_HUMAN	frizzled class receptor 9	305					B cell differentiation (GO:0030183)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|learning or memory (GO:0007611)|nervous system development (GO:0007399)|neuroblast proliferation (GO:0007405)|vasculature development (GO:0001944)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|skin(1)	14		Lung NSC(55;0.0659)|all_lung(88;0.152)				TCTACGTGATCCAGGAGGGCCT	0.649																																					p.I304delinsIQ	Pancreas(144;909 1878 36867 38226 39554)	Atlas-Indel,Pindel	.											.	FZD9	51	.	0			c.912_913insCAG						.																																			SO:0001652	inframe_insertion	8326	exon1			.	U82169	CCDS5548.1	7q11.23	2014-01-29	2014-01-29		ENSG00000188763	ENSG00000188763		"GPCR / Class F : Frizzled receptors", "CD molecules"	4047	protein-coding gene	gene with protein product		601766	"frizzled (Drosophila) homolog 9", "frizzled homolog 9 (Drosophila)", "frizzled 9, seven transmembrane spanning receptor", "frizzled family receptor 9"			9147651, 10198163	Standard	NM_003508		Approved	FZD3, CD349	uc003tyb.3	O00144	OTTHUMG00000023051	ENST00000344575.3:c.913_915dupCAG	chr7.hg19:g.72849250_72849252dupCAG	ENSP00000345785:p.Gln305dup	36.0	0.0		110.0	20.0	NM_003508		In_Frame_Ins	INS	ENST00000344575.3	hg19	CCDS5548.1																																																																																			.	.		0.649	FZD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252120.1			CAG	72849250	-	CAG	72849249	7	5	92	1	0	1	1	0	0	0	0	0	6145	845	30	0	914	0	FZD9	7	72849249	In_Frame_Ins	INS	-	TCGA-DD-A11A-01A-11D-A12Z-10	28699426	72849249	86289414	71	12869										
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72903721	72903721	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgctggcacgttactgatgaTctaggttaaaaagaaacaaa	9	6	1	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:72903721T>C	ENST00000339594.4	-	6	1032	c.694A>G	c.(694-696)Atc>Gtc	p.I232V	BAZ1B_ENST00000404251.1_Splice_Site_p.I232V	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	232	Mediates the tyrosine-protein kinase activity.				cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				TTACTGATGATCTAGGTTAAA	0.393																																					p.I232V	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.A694G						.						108	94	99					7																	72903721		2203	4300	6503	SO:0001630	splice_region_variant	9031	exon6			TGATGATCTAGGT	AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.694-1A>G	chr7.hg19:g.72903721T>C		92.0	0.0		229.0	120.0	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	hg19	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	T	4.518	0.096070	0.08681	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.57436	0.4;0.4	5.88	4.72	0.59763	.	0.113674	0.64402	N	0.000009	T	0.25865	0.0630	N	0.08118	0	0.38723	D	0.953488	B	0.02656	0.0	B	0.04013	0.001	T	0.14727	-1.0462	10	0.05721	T	0.95	-9.0796	8.3585	0.32344	0.0:0.1502:0.0:0.8498	.	232	Q9UIG0	BAZ1B_HUMAN	V	232	ENSP00000342434:I232V;ENSP00000385442:I232V	ENSP00000342434:I232V	I	-	1	0	BAZ1B	72541657	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.480000	0.53172	1.050000	0.40346	0.533000	0.62120	ATC	.	.		0.393	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	Missense_Mutation	C	72903721	T	C	72903721	5	2	92	1	0	0	0	0	0	0	1	0	1330	1449	50	2	3813	2	BAZ1B	7	72903721	Splice_Site	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	54472	72903721	86234942	72	12870										
PCLO	27445	hgsc.bcm.edu	37	chr7	82583266	82583266	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	atcaaacacggtttcggataAgctactttttgttcgttcgg	9	8	1	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:82583266A>G	ENST00000333891.9	-	5	7340	c.7003T>C	c.(7003-7005)Tta>Cta	p.L2335L	PCLO_ENST00000423517.2_Silent_p.L2335L	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GTTTCGGATAAGCTACTTTTT	0.423																																					p.L2335L		Atlas-SNP	.											.	PCLO	1506	.	0			c.T7003C						.						108	109	109					7																	82583266		1859	4102	5961	SO:0001819	synonymous_variant	27445	exon5			CGGATAAGCTACT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.7003T>C	chr7.hg19:g.82583266A>G		120.0	0.0		360.0	82.0	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.423	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82583266	A	G	82583266	2	3	92	1	0	0	0	0	0	0	0	1	11592	69	3	2		2	PCLO	7	82583266	Silent	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	9679545	82583266	76555397	73	12871										
RINT1	60561	hgsc.bcm.edu	37	chr7	105195558	105195558	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tagtagatgattttaggataCgattaacacaagtgatgaaa	9	3	0	4			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:105195558C>T	ENST00000257700.2	+	11	1786	c.1555C>T	c.(1555-1557)Cga>Tga	p.R519*		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	519	RINT1/TIP20. {ECO:0000255|PROSITE- ProRule:PRU00717}.				G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TTTTAGGATACGATTAACACA	0.393																																					p.R519X		Atlas-SNP	.											.	RINT1	65	.	0			c.C1555T						.						156	154	155					7																	105195558		2203	4300	6503	SO:0001587	stop_gained	60561	exon11			AGGATACGATTAA	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.1555C>T	chr7.hg19:g.105195558C>T	ENSP00000257700:p.Arg519*	68.0	0.0		123.0	8.0	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Nonsense_Mutation	SNP	ENST00000257700.2	hg19	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	C	40	8.473654	0.98827	.	.	ENSG00000135249	ENST00000257700	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.8305	20.2245	0.98337	0.0:1.0:0.0:0.0	.	.	.	.	X	519	.	ENSP00000257700:R519X	R	+	1	2	RINT1	104982794	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.129000	0.57957	2.770000	0.95276	0.650000	0.86243	CGA	.	.		0.393	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		T	105195558	C	T	105195558	4	4	92	1	0	0	0	0	0	1	0	0	13391	528	19	1	1597	1	RINT1	7	105195558	Nonsense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	22612292	105195558	53943105	74	12872										
SPAM1	6677	hgsc.bcm.edu	37	chr7	123594436	123594436	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tttgaacactcagcagtctcCtgtagctgctacactctatg	7	12	3	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:123594436C>T	ENST00000439500.1	+	4	1425	c.812C>T	c.(811-813)cCt>cTt	p.P271L	SPAM1_ENST00000223028.7_Missense_Mutation_p.P271L|SPAM1_ENST00000340011.5_Missense_Mutation_p.P271L|SPAM1_ENST00000460182.1_Missense_Mutation_p.P271L|SPAM1_ENST00000402183.2_Missense_Mutation_p.P271L	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	271					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CAGCAGTCTCCTGTAGCTGCT	0.418																																					p.P271L		Atlas-SNP	.											.	SPAM1	195	.	0			c.C812T						.						113	105	108					7																	123594436		2203	4300	6503	SO:0001583	missense	6677	exon3			AGTCTCCTGTAGC	L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.812C>T	chr7.hg19:g.123594436C>T	ENSP00000402123:p.Pro271Leu	71.0	0.0		107.0	12.0	NM_153189	Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	hg19	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.354418	0.41700	.	.	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000340011;ENST00000439500;ENST00000223028	T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87	6.13	4.34	0.51931	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.900897	0.09753	N	0.760366	T	0.18002	0.0432	N	0.20685	0.6	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.28106	-1.0054	9	.	.	.	-4.201	11.6139	0.51078	0.1232:0.8123:0.0:0.0645	.	271;271	Q8TC30;P38567	.;HYALP_HUMAN	L	271	ENSP00000386028:P271L;ENSP00000417934:P271L;ENSP00000345849:P271L;ENSP00000402123:P271L;ENSP00000223028:P271L	.	P	+	2	0	SPAM1	123381672	0.208000	0.23494	0.001000	0.08648	0.000000	0.00434	3.688000	0.54699	0.906000	0.36621	-0.201000	0.12746	CCT	.	.		0.418	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			T	123594436	C	T	123594436	3	4	92	1	0	0	0	0	1	0	0	0	15001	681	24	3	814	3	SPAM1	7	123594436	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	18398878	123594436	35544227	75	12873										
SLC13A4	26266	hgsc.bcm.edu	37	chr7	135390908	135390908	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cctcttcggtgttggagttgCccgccacgagctgctcgtcc	12	15	1	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:135390908C>T	ENST00000354042.4	-	4	1195	c.506G>A	c.(505-507)gGc>gAc	p.G169D	RP11-644N4.1_ENST00000609370.1_RNA	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	169					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						GTTGGAGTTGCCCGCCACGAG	0.617																																					p.G169D		Atlas-SNP	.											.	SLC13A4	56	.	0			c.G506A						.						103	89	94					7																	135390908		2203	4300	6503	SO:0001583	missense	26266	exon4			GAGTTGCCCGCCA	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.506G>A	chr7.hg19:g.135390908C>T	ENSP00000297282:p.Gly169Asp	41.0	0.0		108.0	13.0	NM_012450	A4D1Q4|Q8N631	Missense_Mutation	SNP	ENST00000354042.4	hg19	CCDS5840.1	.	.	.	.	.	.	.	.	.	.	C	9.560	1.118121	0.20877	.	.	ENSG00000164707	ENST00000354042	T	0.02787	4.16	5.0	-0.336	0.12658	.	0.781774	0.11805	N	0.527708	T	0.03178	0.0093	L	0.38838	1.175	0.09310	N	1	P	0.42161	0.772	B	0.43575	0.424	T	0.46275	-0.9203	10	0.17369	T	0.5	.	9.3835	0.38329	0.0:0.4104:0.4426:0.147	.	169	Q9UKG4	S13A4_HUMAN	D	169	ENSP00000297282:G169D	ENSP00000297282:G169D	G	-	2	0	SLC13A4	135041448	0.032000	0.19561	0.000000	0.03702	0.469000	0.32828	0.211000	0.17474	-0.383000	0.07858	-1.943000	0.00494	GGC	.	.		0.617	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		T	135390908	C	T	135390908	3	4	92	1	0	0	0	0	1	0	0	0	14409	739	26	3	1426	3	SLC13A4	7	135390908	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	11796472	135390908	23747755	76	12874										
OR9A2	135924	hgsc.bcm.edu	37	chr7	142724155	142724155	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tagcaaaaagaatgtggtgtAgtccttgggacccagggaag	14	6	0	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:142724155A>C	ENST00000350513.2	-	1	127	c.65T>G	c.(64-66)cTa>cGa	p.L22R		NM_001001658.1	NP_001001658.1	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A, member 2	22						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(3)|endometrium(4)|large_intestine(1)|lung(14)|skin(3)	25	Melanoma(164;0.059)					AATGTGGTGTAGTCCTTGGGA	0.423																																					p.L22R		Atlas-SNP	.											.	OR9A2	52	.	0			c.T65G						.						81	81	81					7																	142724155		2203	4300	6503	SO:0001583	missense	135924	exon1			TGGTGTAGTCCTT		CCDS34767.1	7q34	2014-07-10			ENSG00000179468	ENSG00000179468		"GPCR / Class A : Olfactory receptors"	15093	protein-coding gene	gene with protein product							Standard	NM_001001658		Approved		uc003wcc.1	Q8NGT5	OTTHUMG00000158386	ENST00000350513.2:c.65T>G	chr7.hg19:g.142724155A>C	ENSP00000316518:p.Leu22Arg	82.0	0.0		146.0	51.0	NM_001001658	B9EH51|Q6IF71|Q8NGD9	Missense_Mutation	SNP	ENST00000350513.2	hg19	CCDS34767.1	.	.	.	.	.	.	.	.	.	.	A	9.476	1.096856	0.20552	.	.	ENSG00000179468	ENST00000350513	T	0.05580	3.42	4.31	1.86	0.25419	.	0.319950	0.17220	U	0.182349	T	0.10165	0.0249	M	0.87038	2.855	0.09310	N	1	B	0.12630	0.006	B	0.16289	0.015	T	0.31806	-0.9930	10	0.87932	D	0	-0.95	2.8423	0.05533	0.6109:0.0:0.2026:0.1865	.	22	Q8NGT5	OR9A2_HUMAN	R	22	ENSP00000316518:L22R	ENSP00000316518:L22R	L	-	2	0	OR9A2	142434277	0.006000	0.16342	0.000000	0.03702	0.010000	0.07245	2.360000	0.44151	0.279000	0.22186	-0.509000	0.04479	CTA	.	.		0.423	OR9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350862.1			C	142724155	A	C	142724155	3	2	92	1	0	0	0	0	1	0	0	0	11257	420	15	5	871	5	OR9A2	7	142724155	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	7333247	142724155	16414508	77	12875										
GALNTL5	168391	hgsc.bcm.edu	37	chr7	151664464	151664464	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	aaagccaggagcctctgtcaGcttggtcccctggaaaaaaa	10	11	2	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:151664464G>A	ENST00000392800.2	+	2	387	c.133G>A	c.(133-135)Gct>Act	p.A45T	GALNTL5_ENST00000431418.2_Missense_Mutation_p.A45T	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	45					spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		GCCTCTGTCAGCTTGGTCCCC	0.428																																					p.A45T		Atlas-SNP	.											.	GALNTL5	87	.	0			c.G133A						.						62	63	63					7																	151664464		2203	4300	6503	SO:0001583	missense	168391	exon2			CTGTCAGCTTGGT	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"Glycosyltransferase family 2 domain containing"	21725	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 5"	615133	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.133G>A	chr7.hg19:g.151664464G>A	ENSP00000376548:p.Ala45Thr	97.0	0.0		170.0	116.0	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	hg19	CCDS5929.1	.	.	.	.	.	.	.	.	.	.	G	9.617	1.132789	0.21041	.	.	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.59224	0.28;0.28	4.33	-8.67	0.00863	.	1.962090	0.02605	N	0.101470	T	0.33323	0.0859	N	0.22421	0.69	0.09310	N	1	B	0.22604	0.072	B	0.18871	0.023	T	0.11567	-1.0582	10	0.21014	T	0.42	.	2.7292	0.05222	0.5072:0.2096:0.1778:0.1054	.	45	Q7Z4T8	GLTL5_HUMAN	T	45	ENSP00000392582:A45T;ENSP00000376548:A45T	ENSP00000376548:A45T	A	+	1	0	GALNTL5	151295397	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-1.359000	0.02602	-1.821000	0.01213	0.650000	0.86243	GCT	.	.		0.428	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292		A	151664464	G	A	151664464	3	1	92	1	0	0	0	0	1	0	0	0	6232	971	34	3	135	3	GALNTL5	7	151664464	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	8940309	151664464	7474199	78	12876										
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154760558	154760558	+	Silent	SNP	T	T	C													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gcttgctgctgctgctgctgTtgctgtgaaaatggatgcgg							TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:154760558T>C	ENST00000404141.1	-	7	1507	c.1353A>G	c.(1351-1353)caA>caG	p.Q451Q	PAXIP1_ENST00000397192.1_Silent_p.Q451Q|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	451	Gln-rich.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		gctgctgctgttgctgTGAAA	0.567																																					p.Q451Q		Atlas-SNP	.											.	PAXIP1	150	.	0			c.A1353G						.						24	26	25					7																	154760558		1840	3458	5298	SO:0001819	synonymous_variant	22976	exon7			CTGCTGTTGCTGT	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1353A>G	chr7.hg19:g.154760558T>C		46.0	0.0		130.0	16.0	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Silent	SNP	ENST00000404141.1	hg19	CCDS47753.1																																																																																			.	.		0.567	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		C	154760558	T	C	154760558	2	2	92	1	0	0	0	0	0	0	0	1	11496	1722	60	2		2	PAXIP1	7	154760558	Silent	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	3096094	154760558	4378105	79	12877	54	2								
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154760561	154760561	+	Silent	SNP	C	C	T													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgctgctgctgctgctgttgCtgtgaaaatggatgcggcgg							TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr7:154760561C>T	ENST00000404141.1	-	7	1504	c.1350G>A	c.(1348-1350)caG>caA	p.Q450Q	PAXIP1_ENST00000397192.1_Silent_p.Q450Q|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	450	Gln-rich.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		gctgctgttgctgTGAAAATG	0.562																																					p.Q450Q		Atlas-SNP	.											.	PAXIP1	150	.	0			c.G1350A						.						23	26	25					7																	154760561		1829	3462	5291	SO:0001819	synonymous_variant	22976	exon7			CTGTTGCTGTGAA	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1350G>A	chr7.hg19:g.154760561C>T		46.0	0.0		130.0	12.0	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Silent	SNP	ENST00000404141.1	hg19	CCDS47753.1																																																																																			.	.		0.562	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		T	154760561	C	T	154760561	2	4	92	1	0	0	0	0	0	0	0	1	11496	796	28	3		3	PAXIP1	7	154760561	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	3	154760561	4378102	80	12878	54	2								
SLC7A2	6542	hgsc.bcm.edu	37	chr8	17421125	17421125	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ccctcaggttccattcttacCatttttgccagcgttcagca	6	14	3	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr8:17421125C>A	ENST00000494857.1	+	12	1903	c.1685C>A	c.(1684-1686)cCa>cAa	p.P562Q	SLC7A2_ENST00000004531.10_Missense_Mutation_p.P602Q|SLC7A2_ENST00000398090.3_Missense_Mutation_p.P601Q|SLC7A2_ENST00000522656.1_Missense_Mutation_p.P562Q|SLC7A2_ENST00000470360.1_Missense_Mutation_p.P601Q	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	562					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	CCATTCTTACCATTTTTGCCA	0.413																																					p.P602Q		Atlas-SNP	.											.	SLC7A2	157	.	0			c.C1805A						.						251	238	243					8																	17421125		2203	4300	6503	SO:0001583	missense	6542	exon11			TCTTACCATTTTT	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"Solute carriers"	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.1685C>A	chr8.hg19:g.17421125C>A	ENSP00000419140:p.Pro562Gln	126.0	0.0		343.0	73.0	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	hg19	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.483271	0.84854	.	.	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	D;D;D;D;D	0.95588	-3.46;-3.46;-3.75;-3.6;-3.75	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.98814	0.9600	H	0.98027	4.13	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.99107	1.0845	10	0.87932	D	0	.	20.2344	0.98354	0.0:1.0:0.0:0.0	.	602;601;562	P52569-3;P52569-2;P52569	.;.;CTR2_HUMAN	Q	562;562;601;602;601	ENSP00000419140:P562Q;ENSP00000430464:P562Q;ENSP00000419873:P601Q;ENSP00000004531:P602Q;ENSP00000381164:P601Q	ENSP00000004531:P602Q	P	+	2	0	SLC7A2	17465399	1.000000	0.71417	0.357000	0.25798	0.838000	0.47535	7.818000	0.86416	2.854000	0.98071	0.655000	0.94253	CCA	.	.		0.413	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046		A	17421125	C	A	17421125	3	1	92	1	0	0	0	0	1	0	0	0	14712	594	21	3	1988	3	SLC7A2	8	17421125	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10		17421125	128942897	81	12879										
SLC18A1	6570	hgsc.bcm.edu	37	chr8	20004896	20004896	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttacaatggcaccaccggtgGatggacctgggagggataca	14	9	0	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr8:20004896G>T	ENST00000276373.5	-	15	1603	c.1337C>A	c.(1336-1338)tCc>tAc	p.S446Y	SLC18A1_ENST00000381608.4_Intron|SLC18A1_ENST00000265808.7_Missense_Mutation_p.S414Y|SLC18A1_ENST00000440926.1_Missense_Mutation_p.S446Y|SLC18A1_ENST00000519026.1_Missense_Mutation_p.S414Y|SLC18A1_ENST00000437980.1_Intron	NM_003053.3	NP_003044.1	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 1	446					monoamine transport (GO:0015844)|neurotransmitter transport (GO:0006836)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	drug transmembrane transporter activity (GO:0015238)|monoamine transmembrane transporter activity (GO:0008504)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29				Colorectal(74;0.0747)	Ephedra(DB01363)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Reserpine(DB00206)	ACCACCGGTGGATGGACCTGG	0.542																																					p.S446Y		Atlas-SNP	.											.	SLC18A1	68	.	0			c.C1337A						.						77	67	70					8																	20004896		2203	4300	6503	SO:0001583	missense	6570	exon15			CCGGTGGATGGAC		CCDS6013.1, CCDS47814.1, CCDS47815.1	8p21.3	2013-07-18	2013-07-18		ENSG00000036565	ENSG00000036565		"Solute carriers"	10934	protein-coding gene	gene with protein product		193002		VMAT1, VAT1			Standard	NM_003053		Approved	CGAT	uc003wzm.3	P54219	OTTHUMG00000097017	ENST00000276373.5:c.1337C>A	chr8.hg19:g.20004896G>T	ENSP00000276373:p.Ser446Tyr	54.0	0.0		79.0	13.0	NM_003053	E9PDJ5|Q9BRE4	Missense_Mutation	SNP	ENST00000276373.5	hg19	CCDS6013.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.229561	0.58777	.	.	ENSG00000036565	ENST00000265808;ENST00000276373;ENST00000440926;ENST00000519026	T;T;T;T	0.80738	0.37;-1.41;-1.41;0.37	4.88	4.88	0.63580	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.110707	0.64402	D	0.000005	D	0.89501	0.6733	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.90054	0.4151	10	0.54805	T	0.06	-19.284	16.7583	0.85506	0.0:0.0:1.0:0.0	.	414;446	E9PDJ5;P54219	.;VMAT1_HUMAN	Y	414;446;446;414	ENSP00000265808:S414Y;ENSP00000276373:S446Y;ENSP00000387549:S446Y;ENSP00000429664:S414Y	ENSP00000265808:S414Y	S	-	2	0	SLC18A1	20049176	1.000000	0.71417	0.989000	0.46669	0.254000	0.26022	9.417000	0.97391	2.543000	0.85770	0.462000	0.41574	TCC	.	.		0.542	SLC18A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214106.1			T	20004896	G	T	20004896	3	4	92	1	0	0	0	0	1	0	0	0	14440	1174	41	3	248	3	SLC18A1	8	20004896	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	2583771	20004896	126359126	82	12880										
NCOA2	10499	hgsc.bcm.edu	37	chr8	71039123	71039123	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gctcatagttgctggcatacCactaggagccaccatgcttg	10	12	1	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr8:71039123C>T	ENST00000452400.2	-	19	4022	c.3841G>A	c.(3841-3843)Ggt>Agt	p.G1281S	NCOA2_ENST00000267974.4_Missense_Mutation_p.G369S	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	1281					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			GCTGGCATACCACTAGGAGCC	0.493			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.G1281S		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.G3841A						.						155	147	149					8																	71039123		1982	4157	6139	SO:0001583	missense	10499	exon19			GCATACCACTAGG	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.3841G>A	chr8.hg19:g.71039123C>T	ENSP00000399968:p.Gly1281Ser	71.0	0.0		149.0	23.0	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	hg19	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.611027	0.66558	.	.	ENSG00000140396	ENST00000452400;ENST00000267974	T;T	0.26373	1.74;1.74	5.97	5.97	0.96955	Domain of unknown function DUF1518 (1);	0.000000	0.85682	D	0.000000	T	0.40145	0.1105	L	0.31065	0.9	0.58432	D	0.999993	D;D	0.76494	0.999;0.998	D;D	0.70935	0.971;0.966	T	0.02533	-1.1145	10	0.21014	T	0.42	.	20.4388	0.99107	0.0:1.0:0.0:0.0	.	369;1281	F8WAJ2;Q15596	.;NCOA2_HUMAN	S	1281;369	ENSP00000399968:G1281S;ENSP00000267974:G369S	ENSP00000267974:G369S	G	-	1	0	NCOA2	71201677	1.000000	0.71417	0.997000	0.53966	0.787000	0.44495	4.552000	0.60747	2.836000	0.97738	0.655000	0.94253	GGT	.	.		0.493	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			T	71039123	C	T	71039123	3	4	92	1	0	0	0	0	1	0	0	0	10238	594	21	3	573	3	NCOA2	8	71039123	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	51034227	71039123	75324899	83	12881										
EYA1	2138	hgsc.bcm.edu	37	chr8	72233982	72233982	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tactcaccatatgaggaaatGccgtacggctgtcctggctg	11	11	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr8:72233982G>T	ENST00000340726.3	-	6	1044	c.405C>A	c.(403-405)ggC>ggA	p.G135G	EYA1_ENST00000388740.3_Silent_p.G102G|EYA1_ENST00000388741.2_Silent_p.G101G|EYA1_ENST00000388742.4_Silent_p.G135G|EYA1_ENST00000388743.2_Silent_p.G134G|EYA1_ENST00000419131.1_Silent_p.G135G|EYA1_ENST00000303824.7_Silent_p.G134G	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	135					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			ATGAGGAAATGCCGTACGGCT	0.483																																					p.G135G		Atlas-SNP	.											.	EYA1	108	.	0			c.C405A	GRCh37	CD972191	EYA1	D		.						143	100	115					8																	72233982		2203	4300	6503	SO:0001819	synonymous_variant	2138	exon5			GGAAATGCCGTAC	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"Protein tyrosine phosphatases / Asp-based PTPs"	3519	protein-coding gene	gene with protein product		601653	"eyes absent (Drosophila) homolog 1", "eyes absent homolog 1 (Drosophila)"	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.405C>A	chr8.hg19:g.72233982G>T		112.0	0.0		313.0	41.0	NM_172059	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Silent	SNP	ENST00000340726.3	hg19	CCDS34906.1																																																																																			.	.		0.483	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		T	72233982	G	T	72233982	2	4	92	1	0	0	0	0	0	0	0	1	5330	1306	46	3		3	EYA1	8	72233982	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	1194859	72233982	74130040	84	12882										
PTDSS1	9791	hgsc.bcm.edu	37	chr8	97345763	97345763	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	aaggaatcggcattccaagtCaaaagtcaccaatggcgttg	10	9	2	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr8:97345763C>T	ENST00000517309.1	+	13	1717	c.1391C>T	c.(1390-1392)tCa>tTa	p.S464L	PTDSS1_ENST00000522072.1_Intron|PTDSS1_ENST00000455950.2_Missense_Mutation_p.S318L	NM_014754.1	NP_055569.1	P48651	PTSS1_HUMAN	phosphatidylserine synthase 1	464					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|stomach(1)	29	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)	CATTCCAAGTCAAAAGTCACC	0.468											OREG0018880	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S464L		Atlas-SNP	.											.	PTDSS1	70	.	0			c.C1391T						.						160	149	153					8																	97345763		2203	4300	6503	SO:0001583	missense	9791	exon13			CCAAGTCAAAAGT	D14694	CCDS6271.1	8q22	2008-05-02			ENSG00000156471	ENSG00000156471			9587	protein-coding gene	gene with protein product		612792					Standard	NM_014754		Approved	KIAA0024, PSSA, PSS1	uc003yht.1	P48651	OTTHUMG00000164687	ENST00000517309.1:c.1391C>T	chr8.hg19:g.97345763C>T	ENSP00000430548:p.Ser464Leu	64.0	0.0	1327	113.0	17.0	NM_014754	E5RFC5|Q9BUQ5	Missense_Mutation	SNP	ENST00000517309.1	hg19	CCDS6271.1	.	.	.	.	.	.	.	.	.	.	C	16.63	3.175674	0.57692	.	.	ENSG00000156471	ENST00000517309;ENST00000455950	T;T	0.46819	0.86;0.86	5.55	4.64	0.57946	.	0.140810	0.49305	D	0.000141	T	0.37293	0.0998	L	0.29908	0.895	0.42822	D	0.993992	B	0.17038	0.02	B	0.12156	0.007	T	0.27839	-1.0062	10	0.62326	D	0.03	-16.6697	13.7698	0.63018	0.0:0.8471:0.1529:0.0	.	464	P48651	PTSS1_HUMAN	L	464;318	ENSP00000430548:S464L;ENSP00000401248:S318L	ENSP00000401248:S318L	S	+	2	0	PTDSS1	97414939	0.998000	0.40836	0.972000	0.41901	0.996000	0.88848	2.930000	0.48924	2.602000	0.87976	0.655000	0.94253	TCA	.	.		0.468	PTDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379743.2			T	97345763	C	T	97345763	3	4	92	1	0	0	0	0	1	0	0	0	12748	838	29	3	1441	3	PTDSS1	8	97345763	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	25111781	97345763	49018259	85	12883										
ZC3H3	23144	hgsc.bcm.edu	37	chr8	144550407	144550407	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tggacacatggtgggagaagGggcaggtcccatccgttttc	15	9	0	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr8:144550407G>T	ENST00000262577.5	-	8	2178	c.2147C>A	c.(2146-2148)cCc>cAc	p.P716H		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	716					mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			GTGGGAGAAGGGGCAGGTCCC	0.667																																					p.P716H		Atlas-SNP	.											ZC3H3,NS,malignant_melanoma,0,1	ZC3H3	75	.	0			c.C2147A						.						69	64	66					8																	144550407		2203	4300	6503	SO:0001583	missense	23144	exon8			GAGAAGGGGCAGG	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"Zinc fingers, CCCH-type domain containing"	28972	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 3"	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.2147C>A	chr8.hg19:g.144550407G>T	ENSP00000262577:p.Pro716His	24.0	0.0		58.0	20.0	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	hg19	CCDS6402.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.447515	0.84101	.	.	ENSG00000014164	ENST00000262577	D	0.85088	-1.94	5.4	4.52	0.55395	Zinc finger, CCCH-type (2);	0.058787	0.64402	N	0.000002	D	0.92221	0.7533	M	0.80746	2.51	0.58432	D	0.99999	D	0.76494	0.999	D	0.77557	0.99	D	0.93150	0.6549	10	0.72032	D	0.01	-21.9847	15.4404	0.75178	0.0:0.0:0.8599:0.1401	.	716	Q8IXZ2	ZC3H3_HUMAN	H	716	ENSP00000262577:P716H	ENSP00000262577:P716H	P	-	2	0	ZC3H3	144621550	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.011000	0.93618	1.259000	0.44117	0.655000	0.94253	CCC	.	.		0.667	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117		T	144550407	G	T	144550407	3	4	92	1	0	0	0	0	1	0	0	0	17584	1232	43	3	719	3	ZC3H3	8	144550407	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	47204644	144550407	1813615	86	12884										
CPSF1	29894	hgsc.bcm.edu	37	chr8	145623090	145623090	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ggcacagcgtaatcaccttgGactgctgtggggagaggggt	17	8	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr8:145623090G>C	ENST00000349769.3	-	21	2172	c.2078C>G	c.(2077-2079)tCc>tGc	p.S693C	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	693					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			AATCACCTTGGACTGCTGTGG	0.697																																					p.S693C	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.C2078G						.						27	30	29					8																	145623090		2203	4298	6501	SO:0001583	missense	29894	exon21			ACCTTGGACTGCT	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.2078C>G	chr8.hg19:g.145623090G>C	ENSP00000339353:p.Ser693Cys	15.0	0.0		41.0	10.0	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	hg19	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.198604	0.58126	.	.	ENSG00000071894	ENST00000349769	T	0.34275	1.37	5.61	4.73	0.59995	.	0.123358	0.56097	D	0.000025	T	0.51483	0.1677	L	0.55481	1.735	0.53688	D	0.999976	D	0.76494	0.999	D	0.65987	0.94	T	0.51076	-0.8751	10	0.51188	T	0.08	-13.0961	12.0782	0.53655	0.0:0.0:0.8283:0.1717	.	693	Q10570	CPSF1_HUMAN	C	693	ENSP00000339353:S693C	ENSP00000339353:S693C	S	-	2	0	CPSF1	145593898	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	6.586000	0.74067	1.362000	0.46000	0.491000	0.48974	TCC	.	.		0.697	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		C	145623090	G	C	145623090	3	2	92	1	0	0	0	0	1	0	0	0	3826	1174	41	4	2325	4	CPSF1	8	145623090	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	1072683	145623090	740932	87	12885										
SH3GL2	6456	hgsc.bcm.edu	37	chr9	17795714	17795714	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttcttccccatcaattatgtGgaaattctggttgccctgcc	7	12	3	0	rs371297260		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr9:17795714G>A	ENST00000380607.4	+	9	1152	c.1032G>A	c.(1030-1032)gtG>gtA	p.V344V	SH3GL2_ENST00000537391.1_Silent_p.V297V	NM_003026.2	NP_003017.1	Q99962	SH3G2_HUMAN	SH3-domain GRB2-like 2	344	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of receptor internalization (GO:0002090)|signal transduction (GO:0007165)|synaptic vesicle endocytosis (GO:0048488)	clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)		TCAATTATGTGGAAATTCTGG	0.483																																					p.V344V		Atlas-SNP	.											.	SH3GL2	60	.	0			c.G1032A						.	G		1,4405	2.1+/-5.4	0,1,2202	98	84	89		1032	4.7	1	9		89	0,8600		0,0,4300	no	coding-synonymous	SH3GL2	NM_003026.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		344/353	17795714	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6456	exon9			TTATGTGGAAATT	X99657	CCDS6483.1	9p22	2008-02-05			ENSG00000107295	ENSG00000107295			10831	protein-coding gene	gene with protein product		604465				9169142	Standard	XM_005251549		Approved	SH3P4, SH3D2A, CNSA2, EEN-B1	uc003zna.3	Q99962	OTTHUMG00000019601	ENST00000380607.4:c.1032G>A	chr9.hg19:g.17795714G>A		109.0	0.0		277.0	59.0	NM_003026	B2R618|Q9NQK5	Silent	SNP	ENST00000380607.4	hg19	CCDS6483.1																																																																																			.	.		0.483	SH3GL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051796.1	NM_003026		A	17795714	G	A	17795714	2	1	92	1	0	0	0	0	0	0	0	1	14266	1335	47	3		3	SH3GL2	9	17795714	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10		17795714	123417717	88	12886										
KLHL9	55958	hgsc.bcm.edu	37	chr9	21334288	21334288	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tcgttcaaaagggagttttaGaaactccccagtactcaata	7	9	2	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr9:21334288G>A	ENST00000359039.4	-	1	1091	c.571C>T	c.(571-573)Cta>Tta	p.L191L	KLHL9_ENST00000537938.1_Silent_p.L123L			Q9P2J3	KLHL9_HUMAN	kelch-like family member 9	191	BACK.				cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|midbody (GO:0030496)				endometrium(9)|large_intestine(7)|lung(10)|ovary(4)|skin(2)	32				Lung(24;8.52e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.118)		GGGAGTTTTAGAAACTCCCCA	0.388																																					p.L191L		Atlas-SNP	.											.	KLHL9	61	.	0			c.C571T						.						49	53	52					9																	21334288		2203	4300	6503	SO:0001819	synonymous_variant	55958	exon1			GTTTTAGAAACTC	AB037775	CCDS6503.1	9p22	2013-01-30	2013-01-30		ENSG00000198642	ENSG00000198642		"Kelch-like", "BTB/POZ domain containing"	18732	protein-coding gene	gene with protein product		611201	"kelch-like 9 (Drosophila)"				Standard	NM_018847		Approved	KIAA1354, FLJ13568	uc003zoy.3	Q9P2J3	OTTHUMG00000019669	ENST00000359039.4:c.571C>T	chr9.hg19:g.21334288G>A		42.0	0.0		40.0	9.0	NM_018847	Q8TCQ2	Silent	SNP	ENST00000359039.4	hg19	CCDS6503.1																																																																																			.	.		0.388	KLHL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051898.2	NM_018847		A	21334288	G	A	21334288	2	1	92	1	0	0	0	0	0	0	0	1	8405	933	33	3		3	KLHL9	9	21334288	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	3538574	21334288	119879143	89	12887										
CBWD6	644019	hgsc.bcm.edu	37	chr9	69256787	69256893	+	Splice_Site	DEL	CACATTCCTCACTTCACTGAACAGCAGAGGCAACCGTTTCTAAGTTCCAGCCACTCTTCATAGAGCTCTCCACCTTGGCTGACAGCTAAGGATTTCTCCAGCGCACT	CACATTCCTCACTTCACTGAACAGCAGAGGCAACCGTTTCTAAGTTCCAGCCACTCTTCATAGAGCTCTCCACCTTGGCTGACAGCTAAGGATTTCTCCAGCGCACT	-													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	atgtacacagtaaacacattCctcacttcactgaacagcag					rs199904980|rs368164842|rs62557779|rs370995342|rs111966921|rs113407575	byFrequency	TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	CACATTCCTCACTTCACTGAACAGCAGAGGCAACCGTTTCTAAGTTCCAGCCACTCTTCATAGAGCTCTCCACCTTGGCTGACAGCTAAGGATTTCTCCAGCGCACT	CACATTCCTCACTTCACTGAACAGCAGAGGCAACCGTTTCTAAGTTCCAGCCACTCTTCATAGAGCTCTCCACCTTGGCTGACAGCTAAGGATTTCTCCAGCGCACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr9:69256787_69256893delCACATTCCTCACTTCACTGAACAGCAGAGGCAACCGTTTCTAAGTTCCAGCCACTCTTCATAGAGCTCTCCACCTTGGCTGACAGCTAAGGATTTCTCCAGCGCACT	ENST00000377457.5	-	3	347_444	c.242_339delAGTGCGCTGGAGAAATCCTTAGCTGTCAGCCAAGGTGGAGAGCTCTATGAAGAGTGGCTGGAACTTAGAAACGGTTGCCTCTGCTGTTCAGTGAAGTGAGGAATGTG	c.(241-339)gagtgcgctggagaaatccttagctgtcagccaaggtggagagctctatgaagagtggctggaacttagaaacggttgcctctgctgttcagtgaagtg>g	p.ECAGEILSCQPRWRAL*RVAGT*KRLPLLFSEV81fs	CBWD6_ENST00000377449.1_Splice_Site_p.ECAGEILSCQPRWRAL*RVAGT*KRLPLLFSEV45fs|CBWD6_ENST00000382399.4_Splice_Site_p.ECAGEILSCQPRWRAL*RVAGT*KRLPLLFSEV81fs|CBWD6_ENST00000377441.1_Stop_Codon_Del	NM_001085457.1	NP_001078926.1	Q4V339	CBWD6_HUMAN	COBW domain containing 6	81							ATP binding (GO:0005524)			lung(4)	4						TAAACACATTCCTCACTTCACTGAACAGCAGAGGCAACCGTTTCTAAGTTCCAGCCACTCTTCATAGAGCTCTCCACCTTGGCTGACAGCTAAGGATTTCTCCAGCGCACTTCCTAGAATAAATAAC	0.352																																					p.82_113del		Pindel	.											.	CBWD6	19	.	0			c.245_338del						.																																			SO:0001630	splice_region_variant	644019	exon3			.		CCDS43827.1	9q13	2006-06-30			ENSG00000204790	ENSG00000204790			31978	protein-coding gene	gene with protein product							Standard	NM_001085457		Approved	OTTHUMG00000066820	uc004afj.4	Q4V339	OTTHUMG00000066820	ENST00000377457.5:c.338+1AGTGCGCTGGAGAAATCCTTAGCTGTCAGCCAAGGTGGAGAGCTCTATGAAGAGTGGCTGGAACTTAGAAACGGTTGCCTCTGCTGTTCAGTGAAGTGAGGAATGTG>-	chr9.hg19:g.69256787_69256893delCACATTCCTCACTTCACTGAACAGCAGAGGCAACCGTTTCTAAGTTCCAGCCACTCTTCATAGAGCTCTCCACCTTGGCTGACAGCTAAGGATTTCTCCAGCGCACT		0.0	0.0		18.0	18.0	NM_001085457		Frame_Shift_Del	DEL	ENST00000377457.5	hg19	CCDS43827.1																																																																																			.	.		0.352	CBWD6-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143172.2	XM_928822	Frame_Shift_Del	-	69256893	CACATTCCTCACTTCACTGAACAGCAGAGGCAACCGTTTCTAAGTTCCAGCCACTCTTCATAGAGCTCTCCACCTTGGCTGACAGCTAAGGATTTCTCCAGCGCACT	-	69256787	8	5	92	1	0	1	0	1	0	0	1	0	2718	870	30	0		0	CBWD6	9	69256787	Splice_Site	DEL	CACATTCCTCACTTCACTGAACAGCAGAGGCAACCGTTTCTAAGTTCCAGCCACTCTTCATAGAGCTCTCCACCTTGGCTGACAGCTAAGGATTTCTCCAGCGCACT	TCGA-DD-A11A-01A-11D-A12Z-10	47922499	69256787	71956644	90	12888										
IKBKAP	8518	hgsc.bcm.edu	37	chr9	111658811	111658811	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agctaccatgaggaccaaatCaaagtcataggtgccaagag	10	9	2	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr9:111658811C>G	ENST00000374647.5	-	25	3008	c.2701G>C	c.(2701-2703)Gat>Cat	p.D901H	IKBKAP_ENST00000537196.1_Missense_Mutation_p.D552H	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	901					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						AGGACCAAATCAAAGTCATAG	0.388																																					p.D901H		Atlas-SNP	.											.	IKBKAP	122	.	0			c.G2701C						.						111	101	104					9																	111658811		2203	4300	6503	SO:0001583	missense	8518	exon25			CCAAATCAAAGTC	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"Elongator acetyltransferase complex subunits"	5959	protein-coding gene	gene with protein product	"elongator acetyltransferase complex subunit 1"	603722	"dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.2701G>C	chr9.hg19:g.111658811C>G	ENSP00000363779:p.Asp901His	82.0	0.0		93.0	31.0	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	hg19	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	C	18.87	3.714445	0.68730	.	.	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.27890	1.64;1.64	5.13	4.22	0.49857	.	0.051676	0.85682	D	0.000000	T	0.51873	0.1700	M	0.70787	2.145	0.32810	D	0.501346	D	0.76494	0.999	D	0.70016	0.967	T	0.66101	-0.6007	10	0.62326	D	0.03	-15.7408	12.1646	0.54123	0.0:0.9146:0.0:0.0854	.	901	O95163	ELP1_HUMAN	H	901;552	ENSP00000363779:D901H;ENSP00000439367:D552H	ENSP00000363779:D901H	D	-	1	0	IKBKAP	110698632	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.472000	0.60189	1.264000	0.44198	0.563000	0.77884	GAT	.	.		0.388	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1			G	111658811	C	G	111658811	3	3	92	1	0	0	0	0	1	0	0	0	7619	826	29	4	1349	4	IKBKAP	9	111658811	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	42402024	111658811	29554620	91	12889										
PRKCQ	5588	hgsc.bcm.edu	37	chr10	6553138	6553138	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	acatggtaggctttttctggAtatacatctgcccgttctct	8	10	3	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr10:6553138A>T	ENST00000263125.5	-	3	236	c.137T>A	c.(136-138)aTc>aAc	p.I46N	PRKCQ_ENST00000539722.1_5'UTR|PRKCQ_ENST00000397176.2_Missense_Mutation_p.I46N	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	46	C2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	CTTTTTCTGGATATACATCTG	0.453																																					p.I46N	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											.	PRKCQ	113	.	0			c.T137A						.						146	129	135					10																	6553138		2203	4300	6503	SO:0001583	missense	5588	exon3			TTCTGGATATACA	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.137T>A	chr10.hg19:g.6553138A>T	ENSP00000263125:p.Ile46Asn	98.0	0.0		98.0	46.0	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Missense_Mutation	SNP	ENST00000263125.5	hg19	CCDS7079.1	.	.	.	.	.	.	.	.	.	.	A	14.57	2.575291	0.45902	.	.	ENSG00000065675	ENST00000263125;ENST00000397176	T;T	0.69806	-0.43;-0.36	5.33	5.33	0.75918	C2 calcium/lipid-binding domain, CaLB (1);	0.302177	0.36665	N	0.002477	T	0.61135	0.2323	L	0.29908	0.895	0.80722	D	1	B;B	0.28128	0.089;0.201	B;B	0.35655	0.207;0.092	T	0.63571	-0.6607	10	0.72032	D	0.01	.	15.6241	0.76840	1.0:0.0:0.0:0.0	.	46;46	Q04759-2;Q04759	.;KPCT_HUMAN	N	46	ENSP00000263125:I46N;ENSP00000380361:I46N	ENSP00000263125:I46N	I	-	2	0	PRKCQ	6593144	1.000000	0.71417	0.965000	0.40720	0.802000	0.45316	5.182000	0.65059	2.145000	0.66743	0.533000	0.62120	ATC	.	.		0.453	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257		T	6553138	A	T	6553138	3	4	92	1	0	0	0	0	1	0	0	0	12527	333	12	4	2047	4	PRKCQ	10	6553138	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10		6553138	128981609	92	12890										
C10orf12	26148	hgsc.bcm.edu	37	chr10	98743690	98743690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	caagaaaaggtcacggaaatGtaggagttcattggagagtc	13	5	2	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr10:98743690G>A	ENST00000286067.2	+	1	2650	c.2543G>A	c.(2542-2544)tGt>tAt	p.C848Y		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	848										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		TCACGGAAATGTAGGAGTTCA	0.378																																					p.C848Y		Atlas-SNP	.											.	C10orf12	94	.	0			c.G2543A						.						81	76	78					10																	98743690		2203	4300	6503	SO:0001583	missense	26148	exon1			GGAAATGTAGGAG	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.2543G>A	chr10.hg19:g.98743690G>A	ENSP00000286067:p.Cys848Tyr	82.0	0.0		113.0	29.0	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	hg19	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	G	5.055	0.195766	0.09599	.	.	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.08370	3.1	5.95	5.05	0.67936	.	0.739585	0.12696	N	0.446733	T	0.09818	0.0241	L	0.53249	1.67	0.09310	N	0.999999	B	0.22080	0.064	B	0.16289	0.015	T	0.20472	-1.0274	10	0.59425	D	0.04	-0.4738	6.8695	0.24113	0.1422:0.0:0.7146:0.1432	.	848	Q8N655	CJ012_HUMAN	Y	848;682	ENSP00000286067:C848Y	ENSP00000286067:C848Y	C	+	2	0	C10orf12	98733680	0.999000	0.42202	0.715000	0.30552	0.001000	0.01503	3.339000	0.52135	1.527000	0.49086	0.655000	0.94253	TGT	.	.		0.378	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		A	98743690	G	A	98743690	3	1	92	1	0	0	0	0	1	0	0	0	1591	1377	48	3	2545	3	C10orf12	10	98743690	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	92190552	98743690	36791057	93	12891										
MUC6	4588	hgsc.bcm.edu	37	chr11	1017945	1017945	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gagtcaccaaagaggtggagAaaggtggaacgtgagtggga	18	4	1	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr11:1017945A>G	ENST00000421673.2	-	31	4906	c.4856T>C	c.(4855-4857)tTc>tCc	p.F1619S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1619	Approximate repeats.|Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGAGGTGGAGAAAGGTGGAAC	0.542																																					p.F1619S		Atlas-SNP	.											.	MUC6	408	.	0			c.T4856C						.																																			SO:0001583	missense	4588	exon31			GTGGAGAAAGGTG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4856T>C	chr11.hg19:g.1017945A>G	ENSP00000406861:p.Phe1619Ser	174.0	0.0		771.0	31.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	A	0.026	-1.375208	0.01214	.	.	ENSG00000184956	ENST00000421673	T	0.19669	2.13	2.39	-1.65	0.08291	.	.	.	.	.	T	0.14227	0.0344	L	0.41710	1.295	0.09310	N	1	B	0.29341	0.242	B	0.35931	0.214	T	0.39860	-0.9593	9	0.06625	T	0.88	.	6.4604	0.21954	0.6729:0.0:0.3271:0.0	.	1619	Q6W4X9	MUC6_HUMAN	S	1619	ENSP00000406861:F1619S	ENSP00000406861:F1619S	F	-	2	0	MUC6	1007945	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.579000	0.05834	-0.502000	0.06596	-0.917000	0.02746	TTC	.	.		0.542	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		G	1017945	A	G	1017945	3	3	92	1	0	0	0	0	1	0	0	0	9989	246	9	2	2475	2	MUC6	11	1017945	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10		1017945	133988571	94	12892										
TPH1	7166	hgsc.bcm.edu	37	chr11	18050909	18050909	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cctttggaatggggtctccaCtaatgagataaagggaagga	13	6	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr11:18050909C>G	ENST00000250018.2	-	5	1033		c.e5-1		TPH1_ENST00000341556.2_Splice_Site	NM_004179.2	NP_004170.1	P17752	TPH1_HUMAN	tryptophan hydroxylase 1						aromatic amino acid family metabolic process (GO:0009072)|bone remodeling (GO:0046849)|cellular nitrogen compound metabolic process (GO:0034641)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|mammary gland alveolus development (GO:0060749)|negative regulation of ossification (GO:0030279)|response to immobilization stress (GO:0035902)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(14)|prostate(1)|stomach(1)	25					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	GGGGTCTCCACTAATGAGATA	0.383																																					.		Atlas-SNP	.											.	TPH1	44	.	0			c.471-1G>C						.						149	155	153					11																	18050909		2200	4293	6493	SO:0001630	splice_region_variant	7166	exon6			TCTCCACTAATGA	X52836	CCDS7829.1	11p15.3-p14	2012-10-02	2008-07-31	2003-04-04	ENSG00000129167	ENSG00000129167	1.14.16.4		12008	protein-coding gene	gene with protein product	"tryptophan 5-monooxygenase"	191060	"tryptophan hydroxylase (tryptophan 5-monooxygenase)"	TPRH, TPH		1463016	Standard	NM_004179		Approved		uc001mnp.2	P17752	OTTHUMG00000166421	ENST00000250018.2:c.471-1G>C	chr11.hg19:g.18050909C>G		60.0	0.0		63.0	17.0	NM_004179	D3DQX6|O95188|O95189|Q16736|Q3KPG8	Splice_Site	SNP	ENST00000250018.2	hg19	CCDS7829.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.573105	0.65765	.	.	ENSG00000129167	ENST00000250018;ENST00000341556	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0942	0.97832	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TPH1	18007485	1.000000	0.71417	0.999000	0.59377	0.585000	0.36419	7.738000	0.84966	2.756000	0.94617	0.650000	0.86243	.	.	.		0.383	TPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389696.1	NM_004179	Intron	G	18050909	C	G	18050909	5	3	92	1	0	0	0	0	0	0	1	0	16416	579	20	4	888	4	TPH1	11	18050909	Splice_Site	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	17032964	18050909	116955607	95	12893										
HPS5	11234	hgsc.bcm.edu	37	chr11	18339305	18339305	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tcaagaaattcacctttagaCgactggagtccagccgcagg	10	11	2	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr11:18339305C>T	ENST00000349215.3	-	2	378	c.101G>A	c.(100-102)cGt>cAt	p.R34H	HPS5_ENST00000531848.1_Intron|HPS5_ENST00000396253.3_Intron|HPS5_ENST00000438420.2_Intron	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	34					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CACCTTTAGACGACTGGAGTC	0.463									Hermansky-Pudlak syndrome																												p.R34H		Atlas-SNP	.											.	HPS5	70	.	0			c.G101A						.						59	53	55					11																	18339305		2199	4293	6492	SO:0001583	missense	11234	exon2	Familial Cancer Database	HPS, HPS1-8	TTTAGACGACTGG	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.101G>A	chr11.hg19:g.18339305C>T	ENSP00000265967:p.Arg34His	59.0	0.0		96.0	22.0	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	hg19	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	C	34	5.345874	0.95807	.	.	ENSG00000110756	ENST00000349215	T	0.63255	-0.03	5.05	5.05	0.67936	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.71281	0.3321	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.917;1.0	T	0.75505	-0.3294	10	0.87932	D	0	.	18.4032	0.90525	0.0:1.0:0.0:0.0	.	50;34	Q8IZE8;Q9UPZ3	.;HPS5_HUMAN	H	34	ENSP00000265967:R34H	ENSP00000265967:R34H	R	-	2	0	HPS5	18295881	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.445000	0.80570	2.334000	0.79466	0.591000	0.81541	CGT	.	.		0.463	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507		T	18339305	C	T	18339305	3	4	92	1	0	0	0	0	1	0	0	0	7351	536	19	1	3376	1	HPS5	11	18339305	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	288396	18339305	116667211	96	12894										
PHF21A	51317	hgsc.bcm.edu	37	chr11	45975168	45975168	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tcatctgtttctgtgtgagaTttaactgtctaggagagaaa	10	5	4	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr11:45975168T>C	ENST00000418153.2	-	10	1201	c.1002A>G	c.(1000-1002)aaA>aaG	p.K334K	PHF21A_ENST00000323180.6_Silent_p.K335K|PHF21A_ENST00000257821.4_Silent_p.K335K|PHF21A_ENST00000527753.1_5'UTR			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	334					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						CTGTGTGAGATTTAACTGTCT	0.388																																					p.K335K		Atlas-SNP	.											.	PHF21A	107	.	0			c.A1005G						.						107	97	100					11																	45975168		2202	4299	6501	SO:0001819	synonymous_variant	51317	exon10			GTGAGATTTAACT	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.1002A>G	chr11.hg19:g.45975168T>C		126.0	0.0		396.0	190.0	NM_016621	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Silent	SNP	ENST00000418153.2	hg19	CCDS44578.1																																																																																			.	.		0.388	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		C	45975168	T	C	45975168	2	2	92	1	0	0	0	0	0	0	0	1	11842	1490	52	2		2	PHF21A	11	45975168	Silent	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	27635863	45975168	89031348	97	12895										
OR4A16	81327	hgsc.bcm.edu	37	chr11	55111334	55111334	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	taatctcctgtggagtcatcCtaaacttccttaaaacttac	4	11	2	0	rs548070218		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr11:55111334C>A	ENST00000314721.2	+	1	708	c.658C>A	c.(658-660)Cta>Ata	p.L220I		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						TGGAGTCATCCTAAACTTCCT	0.443																																					p.L220I		Atlas-SNP	.											.	OR4A16	120	.	0			c.C658A						.						171	158	162					11																	55111334		2201	4296	6497	SO:0001583	missense	81327	exon1			GTCATCCTAAACT	AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"GPCR / Class A : Olfactory receptors"	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.658C>A	chr11.hg19:g.55111334C>A	ENSP00000325128:p.Leu220Ile	138.0	0.0		342.0	76.0	NM_001005274	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	hg19	CCDS31499.1	.	.	.	.	.	.	.	.	.	.	c	10.11	1.259097	0.23051	.	.	ENSG00000181961	ENST00000314721	T	0.00152	8.66	2.54	1.58	0.23477	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00210	0.0006	L	0.48642	1.525	0.24991	N	0.991537	P	0.45011	0.848	P	0.50934	0.654	T	0.41928	-0.9481	9	0.87932	D	0	.	4.2522	0.10700	0.0:0.6327:0.0:0.3673	.	220	Q8NH70	O4A16_HUMAN	I	220	ENSP00000325128:L220I	ENSP00000325128:L220I	L	+	1	2	OR4A16	54867910	0.000000	0.05858	0.378000	0.26068	0.067000	0.16453	-2.213000	0.01224	0.370000	0.24538	0.423000	0.28283	CTA	.	.		0.443	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		A	55111334	C	A	55111334	3	1	92	1	0	0	0	0	1	0	0	0	11050	680	24	3	660	3	OR4A16	11	55111334	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	9136166	55111334	79895182	98	12896										
OR8H2	390151	hgsc.bcm.edu	37	chr11	55872714	55872714	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ccatgtattttttccttactCacctgtcatttattgacctc	3	12	2	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr11:55872714C>A	ENST00000313503.1	+	1	196	c.196C>A	c.(196-198)Cac>Aac	p.H66N		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H66Y(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					TTTCCTTACTCACCTGTCATT	0.428										HNSCC(53;0.14)																											p.H66N		Atlas-SNP	.											OR8H2,NS,carcinoma,0,1	OR8H2	117	.	1	Substitution - Missense(1)	lung(1)	c.C196A						.						232	218	223					11																	55872714		2201	4292	6493	SO:0001583	missense	390151	exon1			CTTACTCACCTGT	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"GPCR / Class A : Olfactory receptors"	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.196C>A	chr11.hg19:g.55872714C>A	ENSP00000323982:p.His66Asn	99.0	0.0		184.0	18.0	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	hg19	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	c	0.011	-1.709980	0.00712	.	.	ENSG00000181767	ENST00000313503	T	0.00892	5.57	3.58	2.54	0.30619	GPCR, rhodopsin-like superfamily (1);	0.228496	0.31519	N	0.007516	T	0.00412	0.0013	N	0.02142	-0.665	0.09310	N	1	B	0.34290	0.447	B	0.34242	0.178	T	0.48410	-0.9038	10	0.02654	T	1	.	6.119	0.20142	0.2702:0.6231:0.0:0.1067	.	66	Q8N162	OR8H2_HUMAN	N	66	ENSP00000323982:H66N	ENSP00000323982:H66N	H	+	1	0	OR8H2	55629290	0.000000	0.05858	0.894000	0.35097	0.612000	0.37316	-0.085000	0.11250	1.952000	0.56665	0.440000	0.28878	CAC	.	.		0.428	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200		A	55872714	C	A	55872714	3	1	92	1	0	0	0	0	1	0	0	0	11247	826	29	3	198	3	OR8H2	11	55872714	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	761380	55872714	79133802	99	12897										
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94353216	94353216	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ccggggaactgttagtcctaCctactataatgtcatctatg	8	10	2	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr11:94353216C>A	ENST00000299001.6	+	19	2559	c.2348C>A	c.(2347-2349)aCc>aAc	p.T783N	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA|PIWIL4_ENST00000537419.1_Missense_Mutation_p.T134N	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	783	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GTTAGTCCTACCTACTATAAT	0.458																																					p.T783N		Atlas-SNP	.											.	PIWIL4	70	.	0			c.C2348A						.						86	81	83					11																	94353216		2201	4298	6499	SO:0001583	missense	143689	exon19			GTCCTACCTACTA	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.2348C>A	chr11.hg19:g.94353216C>A	ENSP00000299001:p.Thr783Asn	88.0	0.0		89.0	13.0	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	hg19	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.519264	0.64634	.	.	ENSG00000134627	ENST00000299001;ENST00000537419	T;T	0.34275	1.37;1.37	5.39	5.39	0.77823	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.64402	D	0.000004	T	0.74779	0.3761	H	0.97315	3.98	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.84533	0.0634	10	0.87932	D	0	-18.4737	17.9256	0.88982	0.0:1.0:0.0:0.0	.	783	Q7Z3Z4	PIWL4_HUMAN	N	783;134	ENSP00000299001:T783N;ENSP00000439710:T134N	ENSP00000299001:T783N	T	+	2	0	PIWIL4	93992864	1.000000	0.71417	0.974000	0.42286	0.181000	0.23173	7.306000	0.78905	2.542000	0.85734	0.561000	0.74099	ACC	.	.		0.458	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		A	94353216	C	A	94353216	3	1	92	1	0	0	0	0	1	0	0	0	11969	507	18	3	2422	3	PIWIL4	11	94353216	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	38480502	94353216	40653300	100	12898										
NCAM1	4684	hgsc.bcm.edu	37	chr11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ccctcccagccagcagattaCaatgctgccaaactaaggat					rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000500537.2_RNA|RP11-629G13.1_ENST00000532002.1_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		0.0	0.0		22.0	22.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		-	112832363	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	112832332	6	5	92	0	1	1	0	1	0	0	0	0	10211	493	17	0		0	NCAM1	11	112832332	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	TCGA-DD-A11A-01A-11D-A12Z-10	18479116	112832332	22174184	101	12899										
APOC3	345	hgsc.bcm.edu	37	chr11	116701502	116701502	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tcctcaggagcttcagaggcCgaggatgcctcccttctcag	11	14	3	1	rs372158089		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr11:116701502C>T	ENST00000227667.3	+	3	131	c.69C>T	c.(67-69)gcC>gcT	p.A23A	APOC3_ENST00000375345.1_Silent_p.A41A|APOC3_ENST00000470144.1_3'UTR	NM_000040.1	NP_000031.1	P02656	APOC3_HUMAN	apolipoprotein C-III	23					cellular response to glucose stimulus (GO:0071333)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle remodeling (GO:0034375)|inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of cholesterol import (GO:0060621)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of high-density lipoprotein particle clearance (GO:0010987)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of triglyceride catabolic process (GO:0010897)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|negative regulation of very-low-density lipoprotein particle remodeling (GO:0010903)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	cholesterol binding (GO:0015485)|enzyme regulator activity (GO:0030234)|high-density lipoprotein particle receptor binding (GO:0070653)|lipase inhibitor activity (GO:0055102)|phospholipid binding (GO:0005543)			endometrium(1)|lung(6)	7	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		CTTCAGAGGCCGAGGATGCCT	0.627													C|||	1	0.000199681	0	0	5008	,	,		16260	0		0	False		,,,				2504	0.001				p.A23A	GBM(81;259 1650 7161 35190)	Atlas-SNP	.											.	APOC3	8	.	0			c.C69T						.	C		1,4401	2.1+/-5.4	0,1,2200	45	40	42		69	-9.9	0	11		42	0,8592		0,0,4296	no	coding-synonymous	APOC3	NM_000040.1		0,1,6496	TT,TC,CC		0.0,0.0227,0.0077		23/100	116701502	1,12993	2201	4296	6497	SO:0001819	synonymous_variant	345	exon3			AGAGGCCGAGGAT	X01388	CCDS8377.1	11q23.3	2013-01-24			ENSG00000110245	ENSG00000110245		"Apolipoproteins"	610	protein-coding gene	gene with protein product		107720					Standard	NM_000040		Approved		uc001ppt.1	P02656	OTTHUMG00000046115	ENST00000227667.3:c.69C>T	chr11.hg19:g.116701502C>T		47.0	0.0		38.0	6.0	NM_000040	Q08E83|Q6Q786	Silent	SNP	ENST00000227667.3	hg19	CCDS8377.1																																																																																			.	.		0.627	APOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106284.2	NM_000040		T	116701502	C	T	116701502	2	4	92	1	0	0	0	0	0	0	0	1	799	639	23	1		1	APOC3	11	116701502	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	3869170	116701502	18305014	102	12900										
ERC1	23085	hgsc.bcm.edu	37	chr12	1192560	1192560	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cgtattgagactcaaaagcaGaccctaaatgctcgggatga	10	9	1	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr12:1192560G>C	ENST00000397203.2	+	3	1306	c.900G>C	c.(898-900)caG>caC	p.Q300H	ERC1_ENST00000360905.4_Missense_Mutation_p.Q300H|ERC1_ENST00000543086.3_Missense_Mutation_p.Q300H|ERC1_ENST00000589028.1_Missense_Mutation_p.Q300H|ERC1_ENST00000355446.5_Missense_Mutation_p.Q300H|ERC1_ENST00000546231.2_Missense_Mutation_p.Q300H			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	300					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			CTCAAAAGCAGACCCTAAATG	0.473																																					p.Q300H		Atlas-SNP	.											.	ERC1	95	.	0			c.G900C						.						65	66	66					12																	1192560		2203	4300	6503	SO:0001583	missense	23085	exon3			AAAGCAGACCCTA	AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"RAB6 interacting protein 2"	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.900G>C	chr12.hg19:g.1192560G>C	ENSP00000380386:p.Gln300His	49.0	0.0		38.0	9.0	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	hg19	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	G	12.44	1.937699	0.34189	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000543086;ENST00000542302;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394;ENST00000538971	T;T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.56	-1.25	0.09405	.	0.000000	0.85682	D	0.000000	T	0.45716	0.1356	L	0.56769	1.78	0.47698	D	0.999498	B;B;B;B	0.22541	0.033;0.001;0.002;0.071	B;B;B;B	0.33690	0.036;0.004;0.003;0.168	T	0.50294	-0.8845	10	0.72032	D	0.01	-18.95	12.7244	0.57162	0.2798:0.0:0.7202:0.0	.	76;300;300;300	F5H327;Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;.;RB6I2_HUMAN	H	300;300;300;300;300;300;300;300;300;300;76	ENSP00000340054:Q300H;ENSP00000380386:Q300H;ENSP00000438546:Q300H;ENSP00000445336:Q300H;ENSP00000442739:Q300H;ENSP00000347621:Q300H;ENSP00000354158:Q300H;ENSP00000410064:Q300H	ENSP00000340054:Q300H	Q	+	3	2	ERC1	1062821	1.000000	0.71417	0.996000	0.52242	0.943000	0.58893	0.640000	0.24705	-0.144000	0.11314	0.655000	0.94253	CAG	.	.		0.473	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		C	1192560	G	C	1192560	3	2	92	1	0	0	0	0	1	0	0	0	5212	933	33	4	906	4	ERC1	12	1192560	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10		1192560	132659335	103	12901										
CELA1	1990	hgsc.bcm.edu	37	chr12	51740405	51740433	+	Start_Codon_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cgactggaccatatccacttAccataaaggaccagcatgtt					rs150350903|rs573952082|rs201074609|rs141305161|rs117443541|rs377599213|rs143199509|rs61761206|rs148235680|rs370927847|rs148270827|rs116944010|rs386762976|rs149358345|rs55827519	byFrequency	TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr12:51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC	ENST00000293636.1	-	0	30_57					NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1						exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)|p.L4P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ATATCCACTTACCATAAAGGACCAGCATGTTGCCGATGGAGTAGACCAC	0.524																																					p.3_6del		Pindel	.											.	CELA1	39	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.8_16del						.																																			SO:0001582	initiator_codon_variant	1990	exon1			.		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"elastase 1, pancreatic"	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523		chr12.hg19:g.51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC		0.0	0.0		20.0	20.0	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	In_Frame_Del	DEL	ENST00000293636.1	hg19	CCDS8812.1																																																																																			.	-|0.574;CACCAGGAAGCG|0.426		0.524	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971		-	51740433	CTGGACCATATCCACTTACCATAAAGGAC	-	51740405	7	5	92	1	0	1	0	1	0	0	0	0	3212	405	14	0	790	0	CELA1	12	51740405	Start_Codon_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	TCGA-DD-A11A-01A-11D-A12Z-10	50547845	51740405	82111490	104	12902										
ESPL1	9700	hgsc.bcm.edu	37	chr12	53670586	53670586	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ggcctgggcacgagccacccAcctggtagaactggctcagg	14	14	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr12:53670586A>T	ENST00000257934.4	+	8	1974	c.1883A>T	c.(1882-1884)cAc>cTc	p.H628L	ESPL1_ENST00000552462.1_Missense_Mutation_p.H628L	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	628					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						CGAGCCACCCACCTGGTAGAA	0.612																																					p.H628L	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.A1883T						.						59	65	63					12																	53670586		2203	4299	6502	SO:0001583	missense	9700	exon8			CCACCCACCTGGT	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"separin", "separase", "separin, cysteine protease"	604143	"extra spindle poles like 1 (S. cerevisiae)"			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.1883A>T	chr12.hg19:g.53670586A>T	ENSP00000257934:p.His628Leu	15.0	0.0		42.0	14.0	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	hg19	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.019977	0.35606	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.12465	2.68;2.68	5.38	5.38	0.77491	.	0.323012	0.34245	N	0.004124	T	0.14356	0.0347	M	0.63428	1.95	0.27089	N	0.962896	B	0.23442	0.085	B	0.16722	0.016	T	0.10314	-1.0635	10	0.33141	T	0.24	.	8.4595	0.32919	0.7308:0.0:0.0:0.2692	.	628	Q14674	ESPL1_HUMAN	L	628;303;628	ENSP00000257934:H628L;ENSP00000449831:H628L	ENSP00000257934:H628L	H	+	2	0	ESPL1	51956853	0.940000	0.31905	0.998000	0.56505	0.997000	0.91878	1.960000	0.40422	2.262000	0.75019	0.528000	0.53228	CAC	.	.		0.612	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		T	53670586	A	T	53670586	3	4	92	1	0	0	0	0	1	0	0	0	5255	159	6	4	1909	4	ESPL1	12	53670586	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	1930181	53670586	80181309	105	12903										
SRGAP1	57522	hgsc.bcm.edu	37	chr12	64505683	64505683	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gaaattatcaaaaccatcatCatccaccatgagactatttt	3	10	3	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr12:64505683C>T	ENST00000355086.3	+	17	2585	c.2061C>T	c.(2059-2061)atC>atT	p.I687I	RP11-196H14.4_ENST00000535806.1_RNA|SRGAP1_ENST00000357825.3_Silent_p.I664I|SRGAP1_ENST00000543397.1_Silent_p.I624I	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	687	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		AAACCATCATCATCCACCATG	0.423																																					p.I687I		Atlas-SNP	.											.	SRGAP1	146	.	0			c.C2061T						.						171	151	158					12																	64505683		2203	4300	6503	SO:0001819	synonymous_variant	57522	exon17			CATCATCATCCAC	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.2061C>T	chr12.hg19:g.64505683C>T		96.0	0.0		150.0	18.0	NM_020762	Q9H8A3|Q9P2P2	Silent	SNP	ENST00000355086.3	hg19	CCDS8967.1																																																																																			.	.		0.423	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			T	64505683	C	T	64505683	2	4	92	1	0	0	0	0	0	0	0	1	15160	816	29	3		3	SRGAP1	12	64505683	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	10835097	64505683	69346212	106	12904										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70954625	70954625	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gagaatcagctcataaaagtCaaagtccccagaggctggac	10	10	3	2	rs112738980		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr12:70954625C>G	ENST00000261266.5	-	15	3633	c.3604G>C	c.(3604-3606)Gac>Cac	p.D1202H	PTPRB_ENST00000550358.1_Missense_Mutation_p.D1332H|PTPRB_ENST00000550857.1_Missense_Mutation_p.D1112H|PTPRB_ENST00000538708.1_Missense_Mutation_p.D1112H|PTPRB_ENST00000451516.2_Missense_Mutation_p.D1112H|PTPRB_ENST00000334414.6_Missense_Mutation_p.D1420H|PTPRB_ENST00000551525.1_Missense_Mutation_p.D1419H	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1202	Fibronectin type-III 14. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TCATAAAAGTCAAAGTCCCCA	0.498																																					p.D1420H		Atlas-SNP	.											.	PTPRB	676	.	0			c.G4258C						.						91	85	87					12																	70954625		1896	4123	6019	SO:0001583	missense	5787	exon17			AAAAGTCAAAGTC	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.3604G>C	chr12.hg19:g.70954625C>G	ENSP00000261266:p.Asp1202His	90.0	0.0		138.0	15.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.232757	0.79688	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26;0.26;0.26;0.26	5.43	5.43	0.79202	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.095331	0.64402	D	0.000001	T	0.78220	0.4249	M	0.84082	2.675	0.53688	D	0.999978	P;P;D;P;D;D;D	0.71674	0.906;0.822;0.996;0.835;0.998;0.978;0.984	P;P;D;B;D;D;P	0.65987	0.794;0.794;0.93;0.356;0.94;0.918;0.834	T	0.81324	-0.0984	10	0.72032	D	0.01	.	19.2383	0.93871	0.0:1.0:0.0:0.0	.	1112;1112;1299;1419;1420;1202;1332	P23467-2;F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;PTPRB_HUMAN;.	H	1420;1112;1332;1112;1112;1202;1419;1299	ENSP00000334928:D1420H;ENSP00000393028:D1112H;ENSP00000448058:D1332H;ENSP00000438927:D1112H;ENSP00000447302:D1112H;ENSP00000261266:D1202H;ENSP00000448349:D1419H;ENSP00000446982:D1299H	ENSP00000261266:D1202H	D	-	1	0	PTPRB	69240892	0.968000	0.33430	0.994000	0.49952	0.948000	0.59901	2.243000	0.43115	2.528000	0.85240	0.558000	0.71614	GAC	.	.		0.498	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			G	70954625	C	G	70954625	3	3	92	1	0	0	0	0	1	0	0	0	12811	826	29	4	2461	4	PTPRB	12	70954625	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	6448942	70954625	62897270	107	12905										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70984008	70984008	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctccaggtttgcaactttgtCtggaactaaacggtgaaatg	10	8	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr12:70984008C>G	ENST00000261266.5	-	6	1161	c.1132G>C	c.(1132-1134)Gac>Cac	p.D378H	PTPRB_ENST00000550358.1_Missense_Mutation_p.D596H|PTPRB_ENST00000550857.1_Intron|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000538708.1_Missense_Mutation_p.D378H|PTPRB_ENST00000451516.2_Intron|PTPRB_ENST00000334414.6_Missense_Mutation_p.D596H|PTPRB_ENST00000551525.1_Missense_Mutation_p.D595H	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	378	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			GCAACTTTGTCTGGAACTAAA	0.453											OREG0021990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D596H		Atlas-SNP	.											.	PTPRB	676	.	0			c.G1786C						.						115	111	112					12																	70984008		1917	4129	6046	SO:0001583	missense	5787	exon8			CTTTGTCTGGAAC	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1132G>C	chr12.hg19:g.70984008C>G	ENSP00000261266:p.Asp378His	99.0	0.0	1126	227.0	25.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.920749	0.52653	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T	0.05081	3.5;3.5;3.5;3.5;3.5;3.5	5.85	3.91	0.45181	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.671921	0.15965	N	0.236042	T	0.11410	0.0278	N	0.22421	0.69	0.80722	D	1	P;P;P;B;P;P	0.46912	0.702;0.84;0.702;0.313;0.544;0.886	P;P;P;B;P;P	0.54590	0.525;0.756;0.642;0.402;0.653;0.693	T	0.25745	-1.0123	10	0.45353	T	0.12	.	16.154	0.81644	0.0:0.6324:0.3676:0.0	.	378;475;595;596;378;596	F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;PTPRB_HUMAN;.	H	596;596;596;378;378;595;475	ENSP00000334928:D596H;ENSP00000448058:D596H;ENSP00000438927:D378H;ENSP00000261266:D378H;ENSP00000448349:D595H;ENSP00000446982:D475H	ENSP00000261266:D378H	D	-	1	0	PTPRB	69270275	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	2.269000	0.43346	1.451000	0.47736	0.655000	0.94253	GAC	.	.		0.453	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			G	70984008	C	G	70984008	3	3	92	1	0	0	0	0	1	0	0	0	12811	913	32	4	4969	4	PTPRB	12	70984008	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	29383	70984008	62867887	108	12906										
GLIPR1	11010	hgsc.bcm.edu	37	chr12	75875766	75875766	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gggtctgtgcccattttttcTgtgtcttccgccatcacaaa	8	12	4	0	rs373244879		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr12:75875766T>A	ENST00000266659.3	+	2	528	c.327T>A	c.(325-327)tcT>tcA	p.S109S	RP11-585P4.5_ENST00000547326.1_RNA	NM_006851.2	NP_006842.2	P48060	GLIP1_HUMAN	GLI pathogenesis-related 1	109	SCP.				cellular lipid metabolic process (GO:0044255)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	14						CCATTTTTTCTGTGTCTTCCG	0.473																																					p.S109S		Atlas-SNP	.											.	GLIPR1	33	.	0			c.T327A						.						118	102	107					12																	75875766		2203	4300	6503	SO:0001819	synonymous_variant	11010	exon2			TTTTTCTGTGTCT	U16307	CCDS9011.1	12q14.1	2008-08-15	2008-08-15			ENSG00000139278			17001	protein-coding gene	gene with protein product		602692	"GLI pathogenesis-related 1 (glioma)"			7607567, 8973356	Standard	NM_006851		Approved	RTVP1, GliPR	uc001sxs.3	P48060	OTTHUMG00000169757	ENST00000266659.3:c.327T>A	chr12.hg19:g.75875766T>A		77.0	0.0		143.0	32.0	NM_006851	A7YET6|F8VUC2|Q15409|Q969K2	Silent	SNP	ENST00000266659.3	hg19	CCDS9011.1																																																																																			.	.		0.473	GLIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405722.1	NM_006851		A	75875766	T	A	75875766	2	1	92	1	0	0	0	0	0	0	0	1	6449	1567	55	4		4	GLIPR1	12	75875766	Silent	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	4891758	75875766	57976129	109	12907										
RNF17	56163	hgsc.bcm.edu	37	chr13	25435486	25435486	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttgctgtatcctgatataccCcagttttgtattccttgtca	6	10	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr13:25435486C>T	ENST00000255324.5	+	27	3907	c.3855C>T	c.(3853-3855)ccC>ccT	p.P1285P	RNF17_ENST00000381921.1_Silent_p.P1285P|RNF17_ENST00000339524.3_Silent_p.P337P	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1285	Tudor 3. {ECO:0000255|PROSITE- ProRule:PRU00211}.				multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		CTGATATACCCCAGTTTTGTA	0.313																																					p.P1285P		Atlas-SNP	.											.	RNF17	259	.	0			c.C3855T						.						221	223	222					13																	25435486		2203	4300	6503	SO:0001819	synonymous_variant	56163	exon27			TATACCCCAGTTT	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.3855C>T	chr13.hg19:g.25435486C>T		114.0	0.0		216.0	28.0	NM_031277	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	hg19	CCDS9308.2																																																																																			.	.		0.313	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		T	25435486	C	T	25435486	2	4	92	1	0	0	0	0	0	0	0	1	13476	610	22	3		3	RNF17	13	25435486	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10		25435486	89734392	110	12908										
FAM48A	55578	hgsc.bcm.edu	37	chr13	37619483	37619483	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctcttgcataacaagcttctCtaacaagttcacatttcttc	3	12	4	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr13:37619483C>T	ENST00000350612.6	-	6	413	c.193G>A	c.(193-195)Gag>Aag	p.E65K	SUPT20H_ENST00000360252.4_Missense_Mutation_p.E66K|SUPT20H_ENST00000464744.1_Missense_Mutation_p.E66K|SUPT20H_ENST00000475892.1_Missense_Mutation_p.E65K|SUPT20H_ENST00000470359.2_5'UTR|SUPT20H_ENST00000356185.3_Missense_Mutation_p.E66K|SUPT20H_ENST00000542180.1_Missense_Mutation_p.E53K	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	65					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										ACAAGCTTCTCTAACAAGTTC	0.353																																					p.E66K		Atlas-SNP	.											.	.	.	.	0			c.G196A						.						105	94	97					13																	37619483		2203	4300	6503	SO:0001583	missense	55578	exon6			GCTTCTCTAACAA	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.193G>A	chr13.hg19:g.37619483C>T	ENSP00000218894:p.Glu65Lys	67.0	0.0		60.0	19.0	NM_017569	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	hg19	CCDS31959.1	.	.	.	.	.	.	.	.	.	.	C	33	5.265120	0.95399	.	.	ENSG00000102710	ENST00000360252;ENST00000475892;ENST00000350612;ENST00000356185;ENST00000536874;ENST00000464744;ENST00000542180;ENST00000497318	T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.69151	0.3079	M	0.82056	2.57	0.80722	D	1	D;D;D;D;D;D	0.76494	0.995;0.997;0.997;0.995;0.993;0.999	D;D;D;D;D;D	0.74674	0.973;0.973;0.968;0.973;0.941;0.984	T	0.70956	-0.4731	10	0.87932	D	0	-16.4567	20.4777	0.99188	0.0:1.0:0.0:0.0	.	53;65;65;66;66;65	B4E2D5;B3KNI1;E7ER46;A8K8L1;Q8NEM7-2;Q8NEM7	.;.;.;.;.;FA48A_HUMAN	K	66;65;65;66;65;66;53;66	ENSP00000353388:E66K;ENSP00000417510:E65K;ENSP00000218894:E65K;ENSP00000348512:E66K;ENSP00000419754:E66K;ENSP00000439000:E53K;ENSP00000420170:E66K	ENSP00000218894:E65K	E	-	1	0	FAM48A	36517483	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.875000	0.69660	2.840000	0.97914	0.655000	0.94253	GAG	.	.		0.353	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		T	37619483	C	T	37619483	3	4	92	1	0	0	0	0	1	0	0	0	5580	922	32	3	2230	3	FAM48A	13	37619483	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	12183997	37619483	77550395	111	12909										
FREM2	341640	hgsc.bcm.edu	37	chr13	39265592	39265592	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tcacactgggcatgaattttAcccaggatgaagtagacaga	10	8	1	4			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr13:39265592A>G	ENST00000280481.7	+	1	4327	c.4111A>G	c.(4111-4113)Acc>Gcc	p.T1371A		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1371					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CATGAATTTTACCCAGGATGA	0.393																																					p.T1371A		Atlas-SNP	.											.	FREM2	385	.	0			c.A4111G						.						68	66	67					13																	39265592		2203	4300	6503	SO:0001583	missense	341640	exon1			AATTTTACCCAGG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.4111A>G	chr13.hg19:g.39265592A>G	ENSP00000280481:p.Thr1371Ala	76.0	0.0		91.0	10.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	A	18.93	3.728121	0.69074	.	.	ENSG00000150893	ENST00000280481	T	0.61510	0.1	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.82559	0.5063	H	0.94771	3.58	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.87648	0.2526	10	0.87932	D	0	.	16.1699	0.81801	1.0:0.0:0.0:0.0	.	1371	Q5SZK8	FREM2_HUMAN	A	1371	ENSP00000280481:T1371A	ENSP00000280481:T1371A	T	+	1	0	FREM2	38163592	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.335000	0.96500	2.217000	0.71921	0.533000	0.62120	ACC	.	.		0.393	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39265592	A	G	39265592	3	3	92	1	0	0	0	0	1	0	0	0	6053	391	14	2	4113	2	FREM2	13	39265592	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	1646109	39265592	75904286	112	12910										
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60498943	60498943	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	attttagaatctaaaaacttAagttctttaatttttttctt	2	4	3	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr13:60498943A>C	ENST00000400324.4	-	18	2356	c.2136T>G	c.(2134-2136)ctT>ctG	p.L712L	DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400330.1_Silent_p.L712L|DIAPH3_ENST00000267215.4_Silent_p.L712L|DIAPH3_ENST00000400320.1_Silent_p.L666L|DIAPH3_ENST00000400319.1_Silent_p.L642L|DIAPH3_ENST00000377908.2_Silent_p.L701L	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	712	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		CTAAAAACTTAAGTTCTTTAA	0.299																																					p.L712L		Atlas-SNP	.											.	DIAPH3	139	.	0			c.T2136G						.						44	45	45					13																	60498943		1778	4035	5813	SO:0001819	synonymous_variant	81624	exon18			AAACTTAAGTTCT	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.2136T>G	chr13.hg19:g.60498943A>C		148.0	0.0		239.0	50.0	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	hg19	CCDS41898.1																																																																																			.	.		0.299	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		C	60498943	A	C	60498943	2	2	92	1	0	0	0	0	0	0	0	1	4522	349	13	5		5	DIAPH3	13	60498943	Silent	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	21233351	60498943	54670935	113	12911										
ITGBL1	9358	hgsc.bcm.edu	37	chr13	102366888	102366888	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gactgcgacaaacatgatggTctcatttgtacaggtgcagt	11	8	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr13:102366888T>G	ENST00000376180.3	+	10	1599	c.1380T>G	c.(1378-1380)ggT>ggG	p.G460G	ITGBL1_ENST00000545560.2_Silent_p.G319G|RP11-397O8.7_ENST00000606869.1_lincRNA|ITGBL1_ENST00000376162.3_Silent_p.G367G	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	460	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)				breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AACATGATGGTCTCATTTGTA	0.433																																					p.G460G		Atlas-SNP	.											.	ITGBL1	83	.	0			c.T1380G						.						344	320	328					13																	102366888		2203	4300	6503	SO:0001819	synonymous_variant	9358	exon10			TGATGGTCTCATT	AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"ten integrin EGF-like repeat domains protein", "ITGBL1, integrin beta-like 1"	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.1380T>G	chr13.hg19:g.102366888T>G		105.0	0.0		208.0	50.0	NM_004791	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Silent	SNP	ENST00000376180.3	hg19	CCDS9499.1																																																																																			.	.		0.433	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791		G	102366888	T	G	102366888	2	3	92	1	0	0	0	0	0	0	0	1	7911	1654	58	5		5	ITGBL1	13	102366888	Silent	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	41867945	102366888	12802990	114	12912										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25959333	25959333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ggcagctgggtgtgaacctcCgcaggaagtcttctatcgtc	13	11	2	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr15:25959333C>T	ENST00000356865.6	-	10	1943	c.1832G>A	c.(1831-1833)cGg>cAg	p.R611Q		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	611					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TGTGAACCTCCGCAGGAAGTC	0.592																																					p.R611Q		Atlas-SNP	.											.	ATP10A	270	.	0			c.G1832A						.						46	51	49					15																	25959333		2203	4300	6503	SO:0001583	missense	57194	exon10			AACCTCCGCAGGA	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1832G>A	chr15.hg19:g.25959333C>T	ENSP00000349325:p.Arg611Gln	16.0	0.0		31.0	12.0	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	9.027	0.986406	0.18889	.	.	ENSG00000206190	ENST00000356865	T	0.10005	2.92	4.41	2.49	0.30216	HAD-like domain (1);	0.269079	0.37437	N	0.002095	T	0.05868	0.0153	N	0.21194	0.64	0.39530	D	0.968651	B	0.25521	0.128	B	0.20955	0.032	T	0.32903	-0.9889	10	0.09084	T	0.74	-30.2031	8.8515	0.35203	0.149:0.7722:0.0:0.0788	.	611	O60312	AT10A_HUMAN	Q	611	ENSP00000349325:R611Q	ENSP00000349325:R611Q	R	-	2	0	ATP10A	23510426	0.994000	0.37717	0.026000	0.17262	0.057000	0.15508	4.174000	0.58256	0.484000	0.27630	-0.140000	0.14226	CGG	.	.		0.592	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25959333	C	T	25959333	3	4	92	1	0	0	0	0	1	0	0	0	1116	652	23	1	2715	1	ATP10A	15	25959333	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10		25959333	76572059	115	12913										
HERC2	8924	hgsc.bcm.edu	37	chr15	28457606	28457606	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctgacctgcaaaggcctgttTagtcgatttctttattttgt	8	8	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr15:28457606T>A	ENST00000261609.7	-	43	7018	c.6910A>T	c.(6910-6912)Aaa>Taa	p.K2304*		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		AAGGCCTGTTTAGTCGATTTC	0.453																																					p.K2304X		Atlas-SNP	.											.	HERC2	501	.	0			c.A6910T						.						107	96	100					15																	28457606		2203	4297	6500	SO:0001587	stop_gained	8924	exon43			CCTGTTTAGTCGA	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.6910A>T	chr15.hg19:g.28457606T>A	ENSP00000261609:p.Lys2304*	185.0	0.0		921.0	162.0	NM_004667		Nonsense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	T	46	12.694378	0.99689	.	.	ENSG00000128731	ENST00000261609	.	.	.	4.53	4.53	0.55603	.	0.329464	0.31438	N	0.007648	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	14.0351	0.64640	0.0:0.0:0.0:1.0	.	.	.	.	X	2304	.	ENSP00000261609:K2304X	K	-	1	0	HERC2	26131201	0.996000	0.38824	0.957000	0.39632	0.060000	0.15804	4.343000	0.59348	1.899000	0.54978	0.254000	0.18369	AAA	.	.		0.453	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28457606	T	A	28457606	4	1	92	1	0	0	0	0	0	1	0	0	7067	1763	61	4	7798	4	HERC2	15	28457606	Nonsense_Mutation	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	2498273	28457606	74073786	116	12914										
TYRO3	7301	hgsc.bcm.edu	37	chr15	41854881	41854881	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	aggaactacgaagatcggggGacccgctccctctccatctg	11	14	2	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr15:41854881G>A	ENST00000263798.3	+	4	769	c.545G>A	c.(544-546)gGa>gAa	p.G182E	TYRO3_ENST00000559066.1_Missense_Mutation_p.G137E	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	182	Ig-like C2-type 2.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		AAGATCGGGGGACCCGCTCCC	0.577																																					p.G182E		Atlas-SNP	.											.	TYRO3	169	.	0			c.G545A						.						46	44	45					15																	41854881		2203	4300	6503	SO:0001583	missense	7301	exon4			TCGGGGGACCCGC	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.545G>A	chr15.hg19:g.41854881G>A	ENSP00000263798:p.Gly182Glu	42.0	0.0		47.0	31.0	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	hg19	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	g	9.032	0.987648	0.18966	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	T	0.74002	-0.8	4.8	-0.989	0.10242	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.625022	0.13249	N	0.402233	T	0.33527	0.0866	N	0.01352	-0.895	0.09310	N	0.999999	B	0.06786	0.001	B	0.04013	0.001	T	0.38156	-0.9674	10	0.02654	T	1	-0.0368	2.956	0.05876	0.5108:0.1131:0.2483:0.1278	.	182	Q06418	TYRO3_HUMAN	E	114;182	ENSP00000263798:G182E	ENSP00000263798:G182E	G	+	2	0	TYRO3	39642173	0.774000	0.28592	0.361000	0.25849	0.892000	0.51952	0.271000	0.18626	-0.094000	0.12374	0.472000	0.43445	GGA	.	.		0.577	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2			A	41854881	G	A	41854881	3	1	92	1	0	0	0	0	1	0	0	0	16829	1174	41	3	559	3	TYRO3	15	41854881	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	13397275	41854881	60676511	117	12915										
CTDSPL2	51496	hgsc.bcm.edu	37	chr15	44811383	44811383	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttaggcaccggcttttccgtGaacattgtgtttgtgtacaa	10	8	0	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr15:44811383G>A	ENST00000260327.4	+	11	1692	c.1129G>A	c.(1129-1131)Gaa>Aaa	p.E377K	CTDSPL2_ENST00000558966.1_Missense_Mutation_p.E377K|CTDSPL2_ENST00000396780.1_Missense_Mutation_p.E305K|CTDSPL2_ENST00000558373.1_Missense_Mutation_p.E305K|CTD-2329K10.1_ENST00000561324.1_RNA	NM_016396.2	NP_057480.2	Q05D32	CTSL2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	377	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.						phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	13		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)		GCTTTTCCGTGAACATTGTGT	0.284																																					p.E377K		Atlas-SNP	.											.	CTDSPL2	31	.	0			c.G1129A						.						26	28	27					15																	44811383		2188	4293	6481	SO:0001583	missense	51496	exon11			TTCCGTGAACATT	AF161478	CCDS10110.1	15q15.3-q21.1	2010-06-21			ENSG00000137770	ENSG00000137770		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	26936	protein-coding gene	gene with protein product							Standard	NM_016396		Approved	HSPC129, FLJ10523	uc001ztr.3	Q05D32	OTTHUMG00000131159	ENST00000260327.4:c.1129G>A	chr15.hg19:g.44811383G>A	ENSP00000260327:p.Glu377Lys	75.0	0.0		109.0	27.0	NM_016396	Q3ZTU1|Q6AI06|Q8IYI9|Q9NVT2|Q9NZX8|Q9P030	Missense_Mutation	SNP	ENST00000260327.4	hg19	CCDS10110.1	.	.	.	.	.	.	.	.	.	.	G	32	5.164126	0.94727	.	.	ENSG00000137770	ENST00000260327;ENST00000396780	T;T	0.19105	2.17;2.17	5.66	5.66	0.87406	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.55081	0.1898	M	0.87827	2.91	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.81914	0.946;0.995	T	0.61496	-0.7051	10	0.87932	D	0	-14.6475	19.7309	0.96181	0.0:0.0:1.0:0.0	.	305;377	Q05D32-2;Q05D32	.;CTSL2_HUMAN	K	377;305	ENSP00000260327:E377K;ENSP00000380000:E305K	ENSP00000260327:E377K	E	+	1	0	CTDSPL2	42598675	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.837000	0.99465	2.669000	0.90835	0.557000	0.71058	GAA	.	.		0.284	CTDSPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253851.1	NM_016396		A	44811383	G	A	44811383	3	1	92	1	0	0	0	0	1	0	0	0	4008	1291	45	3	1167	3	CTDSPL2	15	44811383	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	2956502	44811383	57720009	118	12916										
MYO1E	4643	hgsc.bcm.edu	37	chr15	59464100	59464100	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cacctccactactcacctgaGggacacagacaagatccgtt	7	15	1	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr15:59464100G>A	ENST00000288235.4	-	22	2875	c.2476C>T	c.(2476-2478)Ctc>Ttc	p.L826F	MIR2116_ENST00000517221.1_RNA	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	826	Myosin tail. {ECO:0000255}.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		ACTCACCTGAGGGACACAGAC	0.562																																					p.L826F		Atlas-SNP	.											.	MYO1E	99	.	0			c.C2476T						.						132	116	121					15																	59464100		2191	4291	6482	SO:0001583	missense	4643	exon22			ACCTGAGGGACAC	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.2476C>T	chr15.hg19:g.59464100G>A	ENSP00000288235:p.Leu826Phe	49.0	0.0		87.0	19.0	NM_004998	Q14778	Missense_Mutation	SNP	ENST00000288235.4	hg19	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.769950	0.49680	.	.	ENSG00000157483	ENST00000288235	T	0.50001	0.76	5.05	5.05	0.67936	Myosin tail 2 (1);	0.000000	0.85682	D	0.000000	T	0.71117	0.3302	M	0.90145	3.09	0.80722	D	1	D	0.67145	0.996	D	0.74348	0.983	T	0.76189	-0.3050	10	0.87932	D	0	.	10.2432	0.43326	0.1516:0.0:0.8484:0.0	.	826	Q12965	MYO1E_HUMAN	F	826	ENSP00000288235:L826F	ENSP00000288235:L826F	L	-	1	0	MYO1E	57251392	1.000000	0.71417	1.000000	0.80357	0.564000	0.35744	5.563000	0.67352	2.640000	0.89533	0.561000	0.74099	CTC	.	.		0.562	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		A	59464100	G	A	59464100	3	1	92	1	0	0	0	0	1	0	0	0	10081	1000	35	3	878	3	MYO1E	15	59464100	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	14652717	59464100	43067292	119	12917										
ATP2A1	487	hgsc.bcm.edu	37	chr16	28913552	28913552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gcctgaggccctgatcccggTgcagctgctatgggtgaact	14	12	0	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr16:28913552T>C	ENST00000357084.3	+	17	2636	c.2369T>C	c.(2368-2370)gTg>gCg	p.V790A	ATP2A1_ENST00000395503.4_Missense_Mutation_p.V790A|ATP2A1_ENST00000536376.1_Missense_Mutation_p.V665A	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	790	Interacts with phospholamban 2. {ECO:0000250}.				apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						CTGATCCCGGTGCAGCTGCTA	0.662																																					p.V790A		Atlas-SNP	.											.	ATP2A1	116	.	0			c.T2369C						.						73	78	76					16																	28913552		2197	4300	6497	SO:0001583	missense	487	exon17			TCCCGGTGCAGCT		CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"ATPases / P-type"	811	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 1", "calcium pump 1"	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.2369T>C	chr16.hg19:g.28913552T>C	ENSP00000349595:p.Val790Ala	58.0	0.0		135.0	44.0	NM_004320	A8K5J9|B3KY17|O14984	Missense_Mutation	SNP	ENST00000357084.3	hg19	CCDS10643.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.107243	0.77096	.	.	ENSG00000196296	ENST00000357084;ENST00000395503;ENST00000395498;ENST00000536376	D;D;D	0.97831	-4.56;-4.56;-4.56	4.95	3.85	0.44370	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.98248	0.9420	M	0.82433	2.59	0.58432	D	0.999995	D;P;P	0.56746	0.977;0.618;0.564	P;P;P	0.62649	0.905;0.697;0.625	D	0.98231	1.0483	10	0.87932	D	0	.	9.8633	0.41127	0.0:0.0829:0.0:0.9171	.	665;790;790	B3KY17;O14983;O14983-2	.;AT2A1_HUMAN;.	A	790;790;827;665	ENSP00000349595:V790A;ENSP00000378879:V790A;ENSP00000443101:V665A	ENSP00000349595:V790A	V	+	2	0	ATP2A1	28821053	1.000000	0.71417	0.998000	0.56505	0.805000	0.45488	7.844000	0.86867	0.899000	0.36444	0.459000	0.35465	GTG	.	.		0.662	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320		C	28913552	T	C	28913552	3	2	92	1	0	0	0	0	1	0	0	0	1136	1696	59	2	2435	2	ATP2A1	16	28913552	Missense_Mutation	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10		28913552	61441201	120	12918										
SPIRE2	84501	hgsc.bcm.edu	37	chr16	89924764	89924764	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agggtttggctctctgccctGcatcctcaacgcctgctccg	10	16	2	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr16:89924764G>T	ENST00000378247.3	+	8	1164	c.1121G>T	c.(1120-1122)tGc>tTc	p.C374F	SPIRE2_ENST00000393062.2_Missense_Mutation_p.C374F	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	374					actin cytoskeleton organization (GO:0030036)|cleavage furrow formation (GO:0036089)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|intracellular transport (GO:0046907)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		TCTCTGCCCTGCATCCTCAAC	0.672																																					p.C374F		Atlas-SNP	.											.	SPIRE2	63	.	0			c.G1121T						.						101	108	106					16																	89924764		2198	4299	6497	SO:0001583	missense	84501	exon8			TGCCCTGCATCCT	AL834408	CCDS32516.1	16q24	2013-08-27	2013-08-27			ENSG00000204991			30623	protein-coding gene	gene with protein product		609217	"spire homolog 2 (Drosophila)", "spire family actin nucleation factor 2"			11347906	Standard	NM_032451		Approved	spir-2, KIAA1832	uc002foz.1	Q8WWL2		ENST00000378247.3:c.1121G>T	chr16.hg19:g.89924764G>T	ENSP00000367494:p.Cys374Phe	41.0	0.0		60.0	24.0	NM_032451	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Missense_Mutation	SNP	ENST00000378247.3	hg19	CCDS32516.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.689927	0.68271	.	.	ENSG00000204991	ENST00000378247;ENST00000393062	T;T	0.46063	0.89;0.88	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.66636	0.2809	M	0.76838	2.35	0.80722	D	1	D;D;D;D	0.89917	0.993;1.0;0.998;1.0	P;D;D;D	0.91635	0.884;0.999;0.93;0.999	T	0.67677	-0.5609	10	0.48119	T	0.1	-37.2302	17.6972	0.88285	0.0:0.0:1.0:0.0	.	241;374;326;374	Q8WWL2-4;Q8WWL2-2;Q8WWL2-3;Q8WWL2	.;.;.;SPIR2_HUMAN	F	374	ENSP00000367494:C374F;ENSP00000376782:C374F	ENSP00000367494:C374F	C	+	2	0	SPIRE2	88452265	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.927000	0.92846	2.537000	0.85549	0.655000	0.94253	TGC	.	.		0.672	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462		T	89924764	G	T	89924764	3	4	92	1	0	0	0	0	1	0	0	0	15087	1319	46	3	1151	3	SPIRE2	16	89924764	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	61011212	89924764	429989	121	12919										
PRDM7	11105	hgsc.bcm.edu	37	chr16	90126813	90126813	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	atgcccagttcctggccataCtcatccccataccagaccag	6	17	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr16:90126813C>G	ENST00000449207.2	-	9	1188	c.1169G>C	c.(1168-1170)aGt>aCt	p.S390T	PRDM7_ENST00000325921.6_Intron|PRDM7_ENST00000407825.1_Intron	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	390					regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)			lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		CCTGGCCATACTCATCCCCAT	0.512																																					p.S390T		Atlas-SNP	.											.	PRDM7	53	.	0			c.G1169C						.						125	124	125					16																	90126813		1943	4133	6076	SO:0001583	missense	11105	exon9			GCCATACTCATCC	AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"Zinc fingers, C2H2-type", "-"	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.1169G>C	chr16.hg19:g.90126813C>G	ENSP00000396732:p.Ser390Thr	122.0	0.0		181.0	63.0	NM_001098173	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	hg19	CCDS45557.1	.	.	.	.	.	.	.	.	.	.	.	0.785	-0.760829	0.02996	.	.	ENSG00000126856	ENST00000449207	T	0.11495	2.77	2.23	-0.309	0.12769	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	0.51233	D	0.999911	B	0.17038	0.02	B	0.15870	0.014	T	0.42649	-0.9439	8	.	.	.	-8.8469	2.8348	0.05510	0.0:0.4952:0.3051:0.1997	.	390	Q9NQW5	PRDM7_HUMAN	T	390	ENSP00000396732:S390T	.	S	-	2	0	PRDM7	88654314	0.920000	0.31207	0.875000	0.34327	0.328000	0.28507	0.290000	0.18975	0.246000	0.21394	0.485000	0.47835	AGT	.	.		0.512	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1			G	90126813	C	G	90126813	3	3	92	1	0	0	0	0	1	0	0	0	12473	565	20	4	317	4	PRDM7	16	90126813	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	202049	90126813	227940	122	12920										
SGSM2	9905	hgsc.bcm.edu	37	chr17	2282393	2282393	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ggcagccaggcacatctcatCggagcactttgtcctgttca	10	13	2	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:2282393C>T	ENST00000426855.2	+	22	3003	c.2828C>T	c.(2827-2829)tCg>tTg	p.S943L	SGSM2_ENST00000574563.1_Missense_Mutation_p.S943L|SGSM2_ENST00000268989.3_Missense_Mutation_p.S988L|RP1-59D14.5_ENST00000574290.1_RNA|RP1-59D14.5_ENST00000573007.1_RNA	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	943					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		CACATCTCATCGGAGCACTTT	0.547																																					p.S988L		Atlas-SNP	.											.	SGSM2	60	.	0			c.C2963T						.						197	139	158					17																	2282393		2203	4300	6503	SO:0001583	missense	9905	exon23			TCTCATCGGAGCA	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"Small G protein signaling modulators"	29026	protein-coding gene	gene with protein product		611418	"RUN and TBC1 domain containing 1"	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.2828C>T	chr17.hg19:g.2282393C>T	ENSP00000415107:p.Ser943Leu	114.0	0.0		155.0	60.0	NM_014853	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Missense_Mutation	SNP	ENST00000426855.2	hg19	CCDS45570.1	.	.	.	.	.	.	.	.	.	.	C	34	5.352908	0.95830	.	.	ENSG00000141258	ENST00000268989;ENST00000426855	T;T	0.21361	2.01;2.01	5.43	5.43	0.79202	Rab-GAP/TBC domain (3);	0.000000	0.85682	D	0.000000	T	0.56337	0.1978	M	0.89840	3.065	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.993;0.993;0.995	T	0.65573	-0.6135	10	0.87932	D	0	-0.0013	18.2136	0.89878	0.0:1.0:0.0:0.0	.	943;943;943;988	O43147-5;B9A6J3;O43147;O43147-2	.;.;SGSM2_HUMAN;.	L	988;943	ENSP00000268989:S988L;ENSP00000415107:S943L	ENSP00000268989:S988L	S	+	2	0	SGSM2	2229143	1.000000	0.71417	0.453000	0.27007	0.952000	0.60782	7.798000	0.85924	2.572000	0.86782	0.561000	0.74099	TCG	.	.		0.547	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853		T	2282393	C	T	2282393	3	4	92	1	0	0	0	0	1	0	0	0	14238	893	31	1	3053	1	SGSM2	17	2282393	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10		2282393	78912817	123	12921										
SPAG7	9552	hgsc.bcm.edu	37	chr17	4864100	4864100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cccttttacgaaactccactTtctgttgtttctcttgctct	4	13	3	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:4864100T>C	ENST00000206020.3	-	2	201	c.134A>G	c.(133-135)aAa>aGa	p.K45R	SPAG7_ENST00000575142.1_Missense_Mutation_p.K34R|SPAG7_ENST00000573366.1_5'UTR	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	45						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						AAACTCCACTTTCTGTTGTTT	0.478																																					p.K45R		Atlas-SNP	.											.	SPAG7	22	.	0			c.A134G						.						173	164	167					17																	4864100		1880	4117	5997	SO:0001583	missense	9552	exon2			TCCACTTTCTGTT	AF047437	CCDS42240.1	17p13.2	2008-07-18				ENSG00000091640			11216	protein-coding gene	gene with protein product		610056				9653160	Standard	NM_004890		Approved	FSA-1, ACRP, MGC20134	uc002gae.3	O75391		ENST00000206020.3:c.134A>G	chr17.hg19:g.4864100T>C	ENSP00000206020:p.Lys45Arg	136.0	0.0		198.0	151.0	NM_004890	Q96EU5	Missense_Mutation	SNP	ENST00000206020.3	hg19	CCDS42240.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.151909	0.38021	.	.	ENSG00000091640	ENST00000206020	.	.	.	5.24	5.24	0.73138	Single-stranded nucleic acid binding R3H (1);	0.000000	0.85682	D	0.000000	T	0.53610	0.1807	M	0.65975	2.015	0.80722	D	1	B	0.34290	0.447	B	0.28638	0.092	T	0.58470	-0.7631	9	0.51188	T	0.08	-5.2553	13.1387	0.59423	0.0:0.0:0.0:1.0	.	45	O75391	SPAG7_HUMAN	R	45	.	ENSP00000206020:K45R	K	-	2	0	SPAG7	4804823	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.302000	0.65733	2.202000	0.70862	0.533000	0.62120	AAA	.	.		0.478	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890		C	4864100	T	C	4864100	3	2	92	1	0	0	0	0	1	0	0	0	14998	1841	64	2	573	2	SPAG7	17	4864100	Missense_Mutation	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	2581707	4864100	76331110	124	12922										
TP53	7157	hgsc.bcm.edu	37	chr17	7578454	7578455	+	In_Frame_Ins	INS	-	-	CGCGGA													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctgcttgtagatggccatggINScgcggacgcgggtgccgggc							TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:7578454_7578455insCGCGGA	ENST00000269305.4	-	5	664_665	c.475_476insTCCGCG	c.(475-477)gcc>gTCCGCGcc	p.158_159insVR	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_In_Frame_Ins_p.158_159insVR|TP53_ENST00000420246.2_In_Frame_Ins_p.158_159insVR|TP53_ENST00000413465.2_In_Frame_Ins_p.158_159insVR|TP53_ENST00000455263.2_In_Frame_Ins_p.158_159insVR|TP53_ENST00000445888.2_In_Frame_Ins_p.158_159insVR	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	158	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		A -> D (in sporadic cancers; somatic mutation).|A -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|A -> G (in sporadic cancers; somatic mutation).|A -> P (in sporadic cancers; somatic mutation).|A -> S (in sporadic cancers; somatic mutation).|A -> T (in sporadic cancers; somatic mutation).|A -> V (in sporadic cancers; somatic mutation).|R -> C (in sporadic cancers; somatic mutation).|R -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.A159V(33)|p.A159P(19)|p.0?(8)|p.A159T(7)|p.A159D(7)|p.R158fs(6)|p.R158fs*11(6)|p.A159fs*11(4)|p.A159S(4)|p.R65fs(2)|p.A27P(2)|p.R158_A159delRA(2)|p.R156_I162delRVRAMAI(2)|p.V157fs*9(2)|p.R26fs(2)|p.A66P(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156fs*18(1)|p.R26fs*11(1)|p.R156_A161del(1)|p.R158_A159insXX(1)|p.V157_M160delVRAM(1)|p.A66V(1)|p.S149fs*72(1)|p.A159fs*21(1)|p.T155_A161delTRVRAMA(1)|p.R65fs*11(1)|p.A27V(1)|p.R156fs*20(1)|p.V157_I162delVRAMAI(1)|p.A159_Q167delAMAIYKQSQ(1)|p.V157fs*21(1)|p.R158fs*8(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGCCATGGCGCGGACGCGG	0.629		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.A159delinsVRA	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,bladder,carcinoma,0,1	TP53	33396	.	127	Substitution - Missense(76)|Deletion - Frameshift(18)|Deletion - In frame(12)|Complex(10)|Whole gene deletion(8)|Complex - frameshift(2)|Insertion - In frame(1)	lung(27)|central_nervous_system(20)|large_intestine(15)|oesophagus(10)|stomach(9)|breast(9)|liver(8)|ovary(6)|upper_aerodigestive_tract(4)|haematopoietic_and_lymphoid_tissue(4)|urinary_tract(4)|bone(4)|pancreas(2)|thyroid(1)|soft_tissue(1)|endometrium(1)|skin(1)|prostate(1)	c.476_477insTCCGCG						.																																			SO:0001652	inframe_insertion	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.470_475dupTCCGCG	chr17.hg19:g.7578455_7578460dupCGCGGA	ENSP00000269305:p.Val157_Arg158dup	32.0	0.0		33.0	12.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	In_Frame_Ins	INS	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.629	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		CGCGGA	7578455	-	CGCGGA	7578454	7	5	92	1	0	1	1	0	0	0	0	0	16396	1203	42	0	822	0	TP53	17	7578454	In_Frame_Ins	INS	-	TCGA-DD-A11A-01A-11D-A12Z-10	2714354	7578454	73616756	125	12923										
FAM18B2	201158	hgsc.bcm.edu	37	chr17	15449210	15449210	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gattcagcctctgacacagtTttattctcttgagaggactc	8	10	3	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:15449210T>G	ENST00000225576.3	-	5	446	c.351A>C	c.(349-351)aaA>aaC	p.K117N	TVP23C_ENST00000584811.1_Missense_Mutation_p.K53N|TVP23C_ENST00000438826.3_Missense_Mutation_p.K117N|TVP23C_ENST00000518321.1_Missense_Mutation_p.K117N|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.K117N|TVP23C_ENST00000428082.2_Missense_Mutation_p.K117N|TVP23C_ENST00000519970.1_Missense_Mutation_p.K31N	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)	117						integral component of membrane (GO:0016021)											CTGACACAGTTTTATTCTCTT	0.323																																					p.K117N		Atlas-SNP	.											.	.	.	.	0			c.A351C						.						103	103	103					17																	15449210		2203	4297	6500	SO:0001583	missense	201158	exon5			CACAGTTTTATTC	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"family with sequence similarity 18, member B2"	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.351A>C	chr17.hg19:g.15449210T>G	ENSP00000225576:p.Lys117Asn	114.0	0.0		267.0	99.0	NM_145301	Q3LIC7	Missense_Mutation	SNP	ENST00000225576.3	hg19	CCDS11170.1	.	.	.	.	.	.	.	.	.	.	.	4.724	0.134640	0.09032	.	.	ENSG00000259024;ENSG00000259024;ENSG00000259024;ENSG00000175106;ENSG00000175106;ENSG00000175106;ENSG00000175106;ENSG00000175106	ENST00000522212;ENST00000557349;ENST00000481756;ENST00000519970;ENST00000225576;ENST00000428082;ENST00000438826;ENST00000419890	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.17	2.93	0.34026	.	0.215756	0.41097	D	0.000953	T	0.38081	0.1027	L	0.59436	1.845	0.23598	N	0.997326	B;B;B;B	0.34103	0.003;0.437;0.001;0.437	B;B;B;B	0.37091	0.012;0.241;0.007;0.241	T	0.23119	-1.0197	10	0.39692	T	0.17	.	8.451	0.32871	0.0:0.1653:0.0:0.8347	.	117;31;117;117	Q96ET8-2;B4E0Q0;Q96ET8-3;Q96ET8	.;.;.;F18B2_HUMAN	N	117;31;31;31;117;117;117;53	ENSP00000429865:K117N;ENSP00000428961:K31N;ENSP00000225576:K117N;ENSP00000406387:K117N;ENSP00000413355:K117N;ENSP00000409988:K53N	ENSP00000225576:K117N	K	-	3	2	RP11-726O12.1;FAM18B2	15389935	0.034000	0.19679	0.076000	0.20297	0.165000	0.22458	0.090000	0.15025	0.907000	0.36646	0.528000	0.53228	AAA	.	.		0.323	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301		G	15449210	T	G	15449210	3	3	92	1	0	0	0	0	1	0	0	0	5525	1838	64	5	641	5	FAM18B2	17	15449210	Missense_Mutation	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	7870756	15449210	65746000	126	12924										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18058480	18058480	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cggaaagcgtgaagcgggccGtggtcagcactgcacgagac	16	11	1	2	rs367717396		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:18058480G>A	ENST00000205890.5	+	46	8619	c.8281G>A	c.(8281-8283)Gtg>Atg	p.V2761M	MYO15A_ENST00000585180.1_Missense_Mutation_p.V25M|MYO15A_ENST00000418233.3_Missense_Mutation_p.V25M	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2761	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.V2761M(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					GAAGCGGGCCGTGGTCAGCAC	0.632													G|||	1	0.000199681	8e-04	0	5008	,	,		18625	0		0	False		,,,				2504	0				p.V2761M		Atlas-SNP	.											MYO15A,NS,carcinoma,0,1	MYO15A	268	.	1	Substitution - Missense(1)	lung(1)	c.G8281A						.	G	MET/VAL	0,4220		0,0,2110	45	55	52		8281	4.1	0.5	17		52	1,8447		0,1,4223	no	missense	MYO15A	NM_016239.3	21	0,1,6333	AA,AG,GG		0.0118,0.0,0.0079	possibly-damaging	2761/3531	18058480	1,12667	2110	4224	6334	SO:0001583	missense	51168	exon45			CGGGCCGTGGTCA	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8281G>A	chr17.hg19:g.18058480G>A	ENSP00000205890:p.Val2761Met	19.0	0.0		48.0	25.0	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	G	8.308	0.821400	0.16678	0.0	1.18E-4	ENSG00000091536	ENST00000205890	D	0.89939	-2.59	5.1	4.12	0.48240	.	.	.	.	.	D	0.90631	0.7062	M	0.78049	2.395	0.80722	D	1	P;D	0.64830	0.951;0.994	P;P	0.54965	0.726;0.765	D	0.90331	0.4352	9	0.72032	D	0.01	.	4.8201	0.13387	0.3075:0.0:0.6925:0.0	.	25;2761	B4DFC7;Q9UKN7	.;MYO15_HUMAN	M	2761	ENSP00000205890:V2761M	ENSP00000205890:V2761M	V	+	1	0	MYO15A	17999205	1.000000	0.71417	0.484000	0.27391	0.113000	0.19764	4.470000	0.60175	2.363000	0.80096	0.561000	0.74099	GTG	.	.		0.632	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		A	18058480	G	A	18058480	3	1	92	1	0	0	0	0	1	0	0	0	10072	1145	40	1	8455	1	MYO15A	17	18058480	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	2609270	18058480	63136730	127	12925										
TOP3A	7156	hgsc.bcm.edu	37	chr17	18188782	18188782	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttgtctggggtgaggcccacGtacatccgggctttgatggt	15	9	1	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:18188782G>A	ENST00000321105.5	-	14	1864	c.1650C>T	c.(1648-1650)taC>taT	p.Y550Y	TOP3A_ENST00000540524.1_Silent_p.Y80Y|TOP3A_ENST00000542570.1_Silent_p.Y455Y	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	550					DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						TGAGGCCCACGTACATCCGGG	0.582																																					p.Y550Y		Atlas-SNP	.											.	TOP3A	85	.	0			c.C1650T						.						120	83	96					17																	18188782		2203	4300	6503	SO:0001819	synonymous_variant	7156	exon14			GCCCACGTACATC	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 7"	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.1650C>T	chr17.hg19:g.18188782G>A		63.0	0.0		169.0	82.0	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Silent	SNP	ENST00000321105.5	hg19	CCDS11194.1																																																																																			.	.		0.582	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			A	18188782	G	A	18188782	2	1	92	1	0	0	0	0	0	0	0	1	16382	1140	40	1		1	TOP3A	17	18188782	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	130302	18188782	63006428	128	12926										
SMCR8	140775	hgsc.bcm.edu	37	chr17	18221376	18221376	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tatctttgtccccagctatgGctgctacgctaagcccgtga	9	13	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:18221376G>T	ENST00000406438.3	+	1	2753	c.2273G>T	c.(2272-2274)gGc>gTc	p.G758V		NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	758						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						CCCAGCTATGGCTGCTACGCT	0.522																																					p.G758V		Atlas-SNP	.											.	SMCR8	62	.	0			c.G2273T						.						132	113	119					17																	18221376		2203	4300	6503	SO:0001583	missense	140775	exon1			GCTATGGCTGCTA	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.2273G>T	chr17.hg19:g.18221376G>T	ENSP00000385025:p.Gly758Val	53.0	0.0		101.0	26.0	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	hg19	CCDS11195.2	.	.	.	.	.	.	.	.	.	.	G	21.1	4.096642	0.76870	.	.	ENSG00000176994	ENST00000406438	T	0.25579	1.79	5.55	5.55	0.83447	.	0.166916	0.52532	D	0.000072	T	0.39118	0.1066	L	0.56769	1.78	0.80722	D	1	D	0.56521	0.976	P	0.49421	0.61	T	0.17167	-1.0378	10	0.66056	D	0.02	-13.0526	19.861	0.96785	0.0:0.0:1.0:0.0	.	758	Q8TEV9	SMCR8_HUMAN	V	758	ENSP00000385025:G758V	ENSP00000385025:G758V	G	+	2	0	SMCR8	18162101	1.000000	0.71417	0.727000	0.30756	0.991000	0.79684	9.358000	0.97109	2.767000	0.95098	0.655000	0.94253	GGC	.	.		0.522	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		T	18221376	G	T	18221376	3	4	92	1	0	0	0	0	1	0	0	0	14807	1203	42	3	2275	3	SMCR8	17	18221376	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	32594	18221376	62973834	129	12927										
KRT35	3886	hgsc.bcm.edu	37	chr17	39635729	39635729	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgatgtctgactccaccagcTgccgcagggacacctccgtc	10	16	1	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:39635729T>A	ENST00000393989.1	-	3	623	c.581A>T	c.(580-582)cAg>cTg	p.Q194L	KRT35_ENST00000246639.2_Missense_Mutation_p.Q164L	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	194	Coil 1B.|Rod.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				CTCCACCAGCTGCCGCAGGGA	0.587																																					p.Q194L		Atlas-SNP	.											.	KRT35	58	.	0			c.A581T						.						86	82	83					17																	39635729		2203	4300	6503	SO:0001583	missense	3886	exon3			ACCAGCTGCCGCA	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"-", "Intermediate filaments type I, keratins (acidic)"	6453	protein-coding gene	gene with protein product	"hard keratin type I 5"	602764	"keratin, hair, acidic, 5"	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.581A>T	chr17.hg19:g.39635729T>A	ENSP00000377558:p.Gln194Leu	75.0	0.0		184.0	16.0	NM_002280	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	hg19	CCDS11394.2	.	.	.	.	.	.	.	.	.	.	T	17.48	3.399813	0.62177	.	.	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.89415	-2.51;-2.51	4.47	4.47	0.54385	Filament (1);	0.000000	0.48767	D	0.000178	D	0.89336	0.6686	M	0.74467	2.265	0.38662	D	0.9521	B	0.31625	0.332	B	0.41036	0.346	D	0.88947	0.3384	10	0.45353	T	0.12	.	8.8939	0.35451	0.1664:0.0:0.0:0.8336	.	194	Q92764	KRT35_HUMAN	L	164;194	ENSP00000246639:Q164L;ENSP00000377558:Q194L	ENSP00000246639:Q164L	Q	-	2	0	KRT35	36889255	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.579000	0.46059	1.988000	0.58038	0.533000	0.62120	CAG	.	.		0.587	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280		A	39635729	T	A	39635729	3	1	92	1	0	0	0	0	1	0	0	0	8481	1580	55	4	806	4	KRT35	17	39635729	Missense_Mutation	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	21414353	39635729	41559481	130	12928										
CDC27	996	hgsc.bcm.edu	37	chr17	45234594	45234729	+	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cactagaatataagacacttAcaattgtgtcctggggtgtt					rs149474782|rs113608268|rs370849730|rs78395997|rs76624491|rs370261409|rs75353677|rs368304141|rs376818791|rs372212798|rs375653477|rs374472811|rs76359747|rs147617501|rs374614181|rs78108688|rs142987740|rs143453365|rs75990396|rs144985864|rs367644695|rs202182614|rs139751753|rs11570485|rs372926889|rs140171160|rs368750026|rs201098929|rs199899451|rs75175938|rs200340309|rs537990668	byFrequency	TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	ENST00000066544.3	-	6	590_724	c.497_631delAGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG	c.(496-633)cagttcttacggaaacaccccaggacacaattgtaagtgtcttatattctagtgttcaaaatattatgaaaactacaaagaatgatctgaactaaataatatattgtgaatgacttggtagaaattttctgtttcaga>cga	p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000531206.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000446365.2_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF105fs|CDC27_ENST00000527547.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.T167T(7)|p.T171T(3)|p.V201I(2)|p.E199E(2)|p.T200T(2)|p.L173S(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACTGTCTCAGGCTGTCTGTGAGATAAACTATGATTAGGTACTTGTGTTGTGCAAGAGTTGGGCAGACAGTTGCTAAAGTTCTGTAAAGATGTGAATTTAAATGTTTGGTCAGGATC	0.342																																					p.201_211del		Pindel	.											.	CDC27	337	.	17	Substitution - coding silent(14)|Substitution - Missense(3)	large_intestine(6)|prostate(6)|kidney(4)|NS(1)	c.601_631del						.																																			SO:0001630	splice_region_variant	996	exon6			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.631-104AGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG>-	chr17.hg19:g.45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT		0.0	0.0		10.0	10.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.342	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Frame_Shift_Del	-	45234729	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	45234594	8	5	92	1	0	1	0	1	0	0	1	0	3068	405	14	0	1916	0	CDC27	17	45234594	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	TCGA-DD-A11A-01A-11D-A12Z-10	5598865	45234594	35960616	131	12929										
MRC2	9902	hgsc.bcm.edu	37	chr17	60757607	60757607	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tgcggtgctggacctggcctCcctgcagtgggtggccatgc	16	13	0	0	rs370911684		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:60757607C>T	ENST00000303375.5	+	15	2777	c.2375C>T	c.(2374-2376)tCc>tTc	p.S792F	MRC2_ENST00000446119.2_5'Flank	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	792	C-type lectin 4. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						GACCTGGCCTCCCTGCAGTGG	0.657																																					p.S792F		Atlas-SNP	.											.	MRC2	126	.	0			c.C2375T						.						60	57	58					17																	60757607		2203	4300	6503	SO:0001583	missense	9902	exon15			TGGCCTCCCTGCA	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.2375C>T	chr17.hg19:g.60757607C>T	ENSP00000307513:p.Ser792Phe	46.0	0.0		131.0	30.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.692791	0.68271	.	.	ENSG00000011028	ENST00000303375	T	0.20332	2.08	5.41	4.38	0.52667	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.178752	0.49916	D	0.000121	T	0.38134	0.1029	L	0.42632	1.34	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	T	0.13899	-1.0492	10	0.66056	D	0.02	-38.795	15.5958	0.76578	0.0:0.8622:0.1378:0.0	.	792	Q9UBG0	MRC2_HUMAN	F	792	ENSP00000307513:S792F	ENSP00000307513:S792F	S	+	2	0	MRC2	58111339	1.000000	0.71417	1.000000	0.80357	0.608000	0.37181	2.425000	0.44723	2.539000	0.85634	0.305000	0.20034	TCC	.	.		0.657	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			T	60757607	C	T	60757607	3	4	92	1	0	0	0	0	1	0	0	0	9767	855	30	3	2433	3	MRC2	17	60757607	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	15523013	60757607	20437603	132	12930										
ABCA8	10351	hgsc.bcm.edu	37	chr17	66873752	66873752	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	actgtcaggttgggccacagCgcgttctcctgagggcagta	14	11	2	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:66873752C>T	ENST00000269080.2	-	31	4124	c.3987G>A	c.(3985-3987)gcG>gcA	p.A1329A	ABCA8_ENST00000586539.1_Silent_p.A1369A|ABCA8_ENST00000430352.2_Silent_p.A1369A	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1329	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					TGGGCCACAGCGCGTTCTCCT	0.602																																					p.A1329A		Atlas-SNP	.											.	ABCA8	213	.	0			c.G3987A						.						141	120	127					17																	66873752		2203	4300	6503	SO:0001819	synonymous_variant	10351	exon31			CCACAGCGCGTTC	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3987G>A	chr17.hg19:g.66873752C>T		42.0	0.0		120.0	23.0	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	hg19	CCDS11680.1																																																																																			.	.		0.602	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		T	66873752	C	T	66873752	2	4	92	1	0	0	0	0	0	0	0	1	38	755	27	1		1	ABCA8	17	66873752	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	6116145	66873752	14321458	133	12931										
QRICH2	84074	hgsc.bcm.edu	37	chr17	74288539	74288571	+	In_Frame_Del	DEL	CTGCACCAGGTGGGACCAAACCACGCTGATGAT	CTGCACCAGGTGGGACCAAACCACGCTGATGAT	-													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttggaccaaaccacgctgatCtgcaccaggtgggaccaaac					rs557984318|rs77671598|rs35035566|rs370061384|rs79093440|rs34007000	byFrequency	TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	CTGCACCAGGTGGGACCAAACCACGCTGATGAT	CTGCACCAGGTGGGACCAAACCACGCTGATGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:74288539_74288571delCTGCACCAGGTGGGACCAAACCACGCTGATGAT	ENST00000262765.5	-	4	1918_1950	c.1739_1771delATCATCAGCGTGGTTTGGTCCCACCTGGTGCAG	c.(1738-1773)gatcatcagcgtggtttggtcccacctggtgcagat>gat	p.580_591DHQRGLVPPGAD>D		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	580	Gln-rich.							p.H581Q(5)|p.Q582R(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CCACGCTGATCTGCACCAGGTGGGACCAAACCACGCTGATGATCTGCACGAGG	0.536																																					p.580_591del		Pindel	.											.	QRICH2	143	.	6	Substitution - Missense(6)	kidney(4)|lung(2)	c.1740_1772del						.																																			SO:0001651	inframe_deletion	84074	exon4			.	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.1739_1771delATCATCAGCGTGGTTTGGTCCCACCTGGTGCAG	chr17.hg19:g.74288539_74288571delCTGCACCAGGTGGGACCAAACCACGCTGATGAT	ENSP00000262765:p.Asp580_Ala590del	0.0	0.0		12.0	12.0	NM_032134	A2RRE1|Q96LM3	In_Frame_Del	DEL	ENST00000262765.5	hg19	CCDS32741.1																																																																																			.	.		0.536	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		-	74288571	CTGCACCAGGTGGGACCAAACCACGCTGATGAT	-	74288539	7	5	92	1	0	1	0	1	0	0	0	0	12895	913	32	0	3284	0	QRICH2	17	74288539	In_Frame_Del	DEL	CTGCACCAGGTGGGACCAAACCACGCTGATGAT	TCGA-DD-A11A-01A-11D-A12Z-10	7414787	74288539	6906671	134	12932										
CCDC57	284001	hgsc.bcm.edu	37	chr17	80136965	80136965	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cttttggatctggtccctttCaatgtcatcacagcggcgct	9	12	4	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr17:80136965C>T	ENST00000389641.4	-	9	1348	c.1312G>A	c.(1312-1314)Gaa>Aaa	p.E438K	CCDC57_ENST00000392347.1_Missense_Mutation_p.E438K|CCDC57_ENST00000327026.3_Intron|CCDC57_ENST00000392343.3_Missense_Mutation_p.E438K			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	438										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			TGGTCCCTTTCAATGTCATCA	0.607																																					p.E438K		Atlas-SNP	.											.	CCDC57	102	.	0			c.G1312A						.						58	63	61					17																	80136965		2082	4207	6289	SO:0001583	missense	284001	exon9			CCCTTTCAATGTC	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.1312G>A	chr17.hg19:g.80136965C>T	ENSP00000374292:p.Glu438Lys	49.0	0.0		123.0	24.0	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Missense_Mutation	SNP	ENST00000389641.4	hg19		.	.	.	.	.	.	.	.	.	.	C	18.40	3.616639	0.66672	.	.	ENSG00000176155	ENST00000389641;ENST00000392347;ENST00000392343	T;T;T	0.31769	2.72;2.72;1.48	5.52	5.52	0.82312	.	0.149714	0.45606	D	0.000358	T	0.54631	0.1870	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.53315	-0.8456	10	0.48119	T	0.1	-30.6164	14.9303	0.70908	0.0:1.0:0.0:0.0	.	438;438	Q2TAC2-2;Q2TAC2	.;CCD57_HUMAN	K	438	ENSP00000374292:E438K;ENSP00000376158:E438K;ENSP00000376154:E438K	ENSP00000374292:E438K	E	-	1	0	CCDC57	77730254	0.993000	0.37304	0.472000	0.27241	0.306000	0.27790	3.418000	0.52721	2.581000	0.87130	0.557000	0.71058	GAA	.	.		0.607	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		T	80136965	C	T	80136965	3	4	92	1	0	0	0	0	1	0	0	0	2829	835	29	3	1471	3	CCDC57	17	80136965	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	5848426	80136965	1058245	135	12933										
ARHGAP28	79822	hgsc.bcm.edu	37	chr18	6887166	6887166	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ttcttgttaggagggcctcaCgtcaaagtacagtttcaagc	10	9	4	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr18:6887166C>T	ENST00000383472.4	+	12	1568	c.1464C>T	c.(1462-1464)caC>caT	p.H488H	ARHGAP28_ENST00000419673.2_Silent_p.H329H|ARHGAP28_ENST00000262227.3_Silent_p.H436H|ARHGAP28_ENST00000418986.1_Silent_p.H329H|ARHGAP28_ENST00000532996.1_Silent_p.H311H|ARHGAP28_ENST00000531294.1_Silent_p.H324H|ARHGAP28_ENST00000314319.3_Silent_p.H329H|ARHGAP28_ENST00000400091.2_Silent_p.H488H			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	488	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				GAGGGCCTCACGTCAAAGTAC	0.493																																					p.H329H		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.C987T						.						148	125	133					18																	6887166		2203	4300	6503	SO:0001819	synonymous_variant	79822	exon11			GCCTCACGTCAAA	BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"Rho GTPase activating proteins"	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.1464C>T	chr18.hg19:g.6887166C>T		91.0	0.0		106.0	27.0	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Silent	SNP	ENST00000383472.4	hg19																																																																																				.	.		0.493	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108		T	6887166	C	T	6887166	2	4	92	1	0	0	0	0	0	0	0	1	877	535	19	1		1	ARHGAP28	18	6887166	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10		6887166	71190082	136	12934										
AQP4	361	hgsc.bcm.edu	37	chr18	24442273	24442273	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tggcgatgctgatcttcctgGtgcacaccatggccacagtc	11	13	1	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr18:24442273G>T	ENST00000383168.4	-	2	448	c.320C>A	c.(319-321)aCc>aAc	p.T107N	AQP4-AS1_ENST00000578701.1_RNA|AQP4_ENST00000583022.1_5'Flank|AQP4-AS1_ENST00000568797.1_RNA|AQP4-AS1_ENST00000579964.1_RNA|AQP4-AS1_ENST00000582605.1_RNA|AQP4_ENST00000581374.1_Missense_Mutation_p.T85N|AQP4_ENST00000440832.3_Missense_Mutation_p.T85N	NM_001650.4|NM_004028.3	NP_001641.1|NP_004019.1	P55087	AQP4_HUMAN	aquaporin 4	107					carbon dioxide transport (GO:0015670)|cellular response to estradiol stimulus (GO:0071392)|cellular response to interferon-gamma (GO:0071346)|female pregnancy (GO:0007565)|hyperosmotic salinity response (GO:0042538)|multicellular organismal water homeostasis (GO:0050891)|protein homooligomerization (GO:0051260)|renal water absorption (GO:0070295)|response to glucocorticoid (GO:0051384)|response to radiation (GO:0009314)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)	porin activity (GO:0015288)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			kidney(2)|large_intestine(3)|lung(5)|skin(1)	11	all_cancers(21;0.0172)|Lung NSC(5;0.00299)|all_lung(6;0.00747)|Ovarian(20;0.124)					GATCTTCCTGGTGCACACCAT	0.557																																					p.T107N		Atlas-SNP	.											.	AQP4	27	.	0			c.C320A						.						106	89	95					18																	24442273		2203	4300	6503	SO:0001583	missense	361	exon2			TTCCTGGTGCACA	U63622	CCDS11889.1, CCDS58617.1	18q11.2-q12.1	2005-09-20			ENSG00000171885	ENSG00000171885		"Ion channels / Aquaporins"	637	protein-coding gene	gene with protein product		600308				7528931	Standard	NM_001650		Approved	MIWC	uc002kwa.3	P55087	OTTHUMG00000131955	ENST00000383168.4:c.320C>A	chr18.hg19:g.24442273G>T	ENSP00000372654:p.Thr107Asn	37.0	0.0		51.0	13.0	NM_001650	P78564	Missense_Mutation	SNP	ENST00000383168.4	hg19	CCDS11889.1	.	.	.	.	.	.	.	.	.	.	G	17.90	3.500913	0.64298	.	.	ENSG00000171885	ENST00000383168;ENST00000440832;ENST00000383170	D	0.93019	-3.15	5.57	5.57	0.84162	Aquaporin-like (2);	0.000000	0.85682	D	0.000000	D	0.91606	0.7348	L	0.53729	1.69	0.80722	D	1	P	0.40681	0.727	B	0.41174	0.349	D	0.92024	0.5628	10	0.72032	D	0.01	.	12.843	0.57813	0.0748:0.0:0.9252:0.0	.	107	P55087	AQP4_HUMAN	N	107;87;114	ENSP00000372654:T107N	ENSP00000372654:T107N	T	-	2	0	AQP4	22696271	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.462000	0.73526	2.614000	0.88457	0.462000	0.41574	ACC	.	.		0.557	AQP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254914.2	NM_001650, NM_004028		T	24442273	G	T	24442273	3	4	92	1	0	0	0	0	1	0	0	0	828	1261	44	3	667	3	AQP4	18	24442273	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	17555107	24442273	53634975	137	12935										
SLC25A23	79085	hgsc.bcm.edu	37	chr19	6458301	6458301	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	attcctccaggtcgagcccgCcatctgggtcagcatcaccc	9	17	3	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr19:6458301C>T	ENST00000301454.4	-	2	297	c.191G>A	c.(190-192)gGc>gAc	p.G64D	SLC25A23_ENST00000334510.5_Missense_Mutation_p.G64D	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	64					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						GTCGAGCCCGCCATCTGGGTC	0.577																																					p.G64D		Atlas-SNP	.											.	SLC25A23	43	.	0			c.G191A						.						36	30	32					19																	6458301		2203	4300	6503	SO:0001583	missense	79085	exon2			AGCCCGCCATCTG	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"Solute carriers", "EF-hand domain containing"	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.191G>A	chr19.hg19:g.6458301C>T	ENSP00000301454:p.Gly64Asp	13.0	0.0		13.0	12.0	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Missense_Mutation	SNP	ENST00000301454.4	hg19	CCDS32882.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.079290	0.76528	.	.	ENSG00000125648	ENST00000264088;ENST00000301454;ENST00000334510	T;T;D	0.83837	0.1;0.1;-1.77	4.72	2.39	0.29439	EF-hand-like domain (1);	0.235256	0.42420	N	0.000713	D	0.86810	0.6022	M	0.90814	3.15	0.52501	D	0.999955	B	0.28291	0.206	B	0.37387	0.248	D	0.84430	0.0576	10	0.56958	D	0.05	-2.5106	11.7402	0.51788	0.3212:0.6788:0.0:0.0	.	64	Q9BV35	SCMC3_HUMAN	D	64	ENSP00000264088:G64D;ENSP00000301454:G64D;ENSP00000334537:G64D	ENSP00000264088:G64D	G	-	2	0	SLC25A23	6409301	0.941000	0.31946	0.002000	0.10522	0.858000	0.48976	2.119000	0.41958	0.325000	0.23359	0.462000	0.41574	GGC	.	.		0.577	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103		T	6458301	C	T	6458301	3	4	92	1	0	0	0	0	1	0	0	0	14501	739	26	3	1251	3	SLC25A23	19	6458301	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10		6458301	52670682	138	12936										
MAP1S	55201	hgsc.bcm.edu	37	chr19	17831786	17831786	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	atcctggcgtctgcaaccttGatgaacagctcaaggtcttt	9	11	3	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr19:17831786G>C	ENST00000324096.4	+	2	311	c.160G>C	c.(160-162)Gat>Cat	p.D54H	MAP1S_ENST00000544059.2_Missense_Mutation_p.D28H|MAP1S_ENST00000597681.1_Intron	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	54	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CTGCAACCTTGATGAACAGCT	0.587																																					p.D54H		Atlas-SNP	.											.	MAP1S	74	.	0			c.G160C						.						148	130	136					19																	17831786		2203	4300	6503	SO:0001583	missense	55201	exon2			AACCTTGATGAAC	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.160G>C	chr19.hg19:g.17831786G>C	ENSP00000325313:p.Asp54His	65.0	0.0		104.0	23.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	hg19	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	g	16.81	3.224656	0.58668	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.21932	1.98;1.98	3.87	3.87	0.44632	.	0.000000	0.49305	D	0.000153	T	0.43700	0.1259	M	0.67397	2.05	0.80722	D	1	D;D;D	0.89917	0.996;0.998;1.0	D;D;D	0.91635	0.918;0.919;0.999	T	0.46020	-0.9221	10	0.87932	D	0	-16.1082	13.6604	0.62363	0.0:0.0:1.0:0.0	.	28;54;54	B4DH53;A8K940;Q66K74	.;.;MAP1S_HUMAN	H	54;28	ENSP00000325313:D54H;ENSP00000439243:D28H	ENSP00000325313:D54H	D	+	1	0	MAP1S	17692786	1.000000	0.71417	0.487000	0.27428	0.082000	0.17680	6.993000	0.76245	1.863000	0.54032	0.486000	0.48141	GAT	.	.		0.587	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		C	17831786	G	C	17831786	3	2	92	1	0	0	0	0	1	0	0	0	9243	1290	45	4	166	4	MAP1S	19	17831786	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	11373485	17831786	41297197	139	12937										
PDCD2L	84306	hgsc.bcm.edu	37	chr19	34916969	34916969	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ggcccccaaatcatcagactCccatggaagaattttgtatt	7	11	2	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr19:34916969C>G	ENST00000246535.3	+	7	1068	c.1021C>G	c.(1021-1023)Ccc>Gcc	p.P341A	PDCD2L_ENST00000587065.2_Missense_Mutation_p.P39A|UBA2_ENST00000246548.4_5'Flank|CTD-2588C8.8_ENST00000592220.1_RNA|UBA2_ENST00000439527.2_5'Flank	NM_032346.1	NP_115722.1	Q9BRP1	PDD2L_HUMAN	programmed cell death 2-like	341					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			TCATCAGACTCCCATGGAAGA	0.328																																					p.P341A		Atlas-SNP	.											.	PDCD2L	27	.	0			c.C1021G						.						80	83	82					19																	34916969		2203	4300	6503	SO:0001583	missense	84306	exon7			CAGACTCCCATGG	BC006146	CCDS12438.1	19q13.11	2008-02-05				ENSG00000126249			28194	protein-coding gene	gene with protein product		615661				16311922	Standard	NM_032346		Approved	MGC13096	uc002nvj.3	Q9BRP1		ENST00000246535.3:c.1021C>G	chr19.hg19:g.34916969C>G	ENSP00000246535:p.Pro341Ala	67.0	0.0		67.0	23.0	NM_032346		Missense_Mutation	SNP	ENST00000246535.3	hg19	CCDS12438.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.693910	0.30052	.	.	ENSG00000126249	ENST00000246535	.	.	.	5.56	4.53	0.55603	Programmed cell death protein 2, C-terminal (1);	0.103148	0.64402	D	0.000003	T	0.56558	0.1993	L	0.51422	1.61	0.48511	D	0.999668	P	0.48407	0.91	P	0.46237	0.508	T	0.56523	-0.7965	9	0.37606	T	0.19	-15.6775	13.6521	0.62316	0.0:0.9245:0.0:0.0755	.	341	Q9BRP1	PDD2L_HUMAN	A	341	.	ENSP00000246535:P341A	P	+	1	0	PDCD2L	39608809	0.992000	0.36948	0.837000	0.33122	0.117000	0.20001	4.175000	0.58263	1.372000	0.46190	-0.128000	0.14901	CCC	.	.		0.328	PDCD2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459251.3	NM_032346		G	34916969	C	G	34916969	3	3	92	1	0	0	0	0	1	0	0	0	11629	855	30	4	1047	4	PDCD2L	19	34916969	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	17085183	34916969	24212014	140	12938										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44739856	44739856	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ctcaggctgcacattttcacAtccatcagagagtccacact	6	14	3	1			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr19:44739856A>T	ENST00000313040.7	+	6	1478	c.1273A>T	c.(1273-1275)Atc>Ttc	p.I425F	ZNF227_ENST00000391961.2_Missense_Mutation_p.I374F|ZNF227_ENST00000589005.1_Missense_Mutation_p.I374F	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	425					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				ACATTTTCACATCCATCAGAG	0.488																																					p.I425F		Atlas-SNP	.											.	ZNF227	62	.	0			c.A1273T						.						84	87	86					19																	44739856		2203	4300	6503	SO:0001583	missense	7770	exon6			TTTCACATCCATC	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.1273A>T	chr19.hg19:g.44739856A>T	ENSP00000321049:p.Ile425Phe	40.0	0.0		46.0	11.0	NM_182490	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	hg19	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.030064	0.54790	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980;ENST00000377916	T;T	0.01005	5.45;5.45	4.12	4.12	0.48240	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02230	0.0069	L	0.33710	1.025	0.23994	N	0.996235	D;D;P;D	0.65815	0.995;0.993;0.955;0.995	D;P;P;D	0.63597	0.916;0.867;0.679;0.916	T	0.57808	-0.7747	9	0.19147	T	0.46	.	11.7334	0.51750	1.0:0.0:0.0:0.0	.	346;404;377;425	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	F	425;382;374;404;126	ENSP00000321049:I425F;ENSP00000375823:I374F	ENSP00000321049:I425F	I	+	1	0	ZNF227	49431696	0.000000	0.05858	0.997000	0.53966	0.951000	0.60555	-0.378000	0.07446	1.802000	0.52723	0.460000	0.39030	ATC	.	.		0.488	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		T	44739856	A	T	44739856	3	4	92	1	0	0	0	0	1	0	0	0	17796	217	8	4	1287	4	ZNF227	19	44739856	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	9822887	44739856	14389127	141	12939										
ZNF578	147660	hgsc.bcm.edu	37	chr19	53014087	53014087	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	aggcatgctggaaacaagccTattaaagatcagcttggatt	10	7	1	1	rs556778715		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr19:53014087T>A	ENST00000421239.2	+	6	697	c.453T>A	c.(451-453)ccT>ccA	p.P151P	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GAAACAAGCCTATTAAAGATC	0.403																																					p.P151P		Atlas-SNP	.											.	.	.	.	0			c.T453A						.						154	154	154					19																	53014087		2203	4300	6503	SO:0001819	synonymous_variant	147660	exon6			CAAGCCTATTAAA	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.453T>A	chr19.hg19:g.53014087T>A		121.0	0.0		168.0	50.0	NM_001099694	B4DR51|I3L1Y6	Silent	SNP	ENST00000421239.2	hg19	CCDS54310.1																																																																																			.	.		0.403	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		A	53014087	T	A	53014087	2	1	92	1	0	0	0	0	0	0	0	1	18025	1509	53	4		4	ZNF578	19	53014087	Silent	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10	8274231	53014087	6114896	142	12940										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53854648	53854648	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	cagataatccatttaggagcGaaacaatataaatgtgatgt	8	5	0	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr19:53854648G>A	ENST00000595091.1	+	5	939	c.720G>A	c.(718-720)gcG>gcA	p.A240A	ZNF845_ENST00000458035.1_Silent_p.A240A			Q96IR2	ZN845_HUMAN	zinc finger protein 845	240					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						ATTTAGGAGCGAAACAATATA	0.363																																					p.A240A		Atlas-SNP	.											.	ZNF845	101	.	0			c.G720A						.						99	83	88					19																	53854648		692	1591	2283	SO:0001819	synonymous_variant	91664	exon4			AGGAGCGAAACAA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.720G>A	chr19.hg19:g.53854648G>A		110.0	0.0		149.0	8.0	NM_138374		Silent	SNP	ENST00000595091.1	hg19	CCDS46170.1																																																																																			.	.		0.363	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		A	53854648	G	A	53854648	2	1	92	1	0	0	0	0	0	0	0	1	18206	1045	37	1		1	ZNF845	19	53854648	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10	840561	53854648	5274335	143	12941										
TSEN34	79042	hgsc.bcm.edu	37	chr19	54695669	54695669	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	ccgtcgtcaggagctcctggAgaagattacggagggccagg	16	10	1	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr19:54695669A>G	ENST00000396383.1	+	3	652	c.341A>G	c.(340-342)gAg>gGg	p.E114G	MBOAT7_ENST00000391754.1_5'Flank|MBOAT7_ENST00000474910.1_5'Flank|CTD-3093M3.1_ENST00000594382.1_lincRNA|TSEN34_ENST00000396388.2_Missense_Mutation_p.E114G|MBOAT7_ENST00000245615.1_5'Flank|TSEN34_ENST00000302937.4_Missense_Mutation_p.E114G|MBOAT7_ENST00000431666.2_5'Flank|TSEN34_ENST00000429671.2_Missense_Mutation_p.E114G|MBOAT7_ENST00000338624.6_5'Flank			Q9BSV6	SEN34_HUMAN	TSEN34 tRNA splicing endonuclease subunit	114					mRNA processing (GO:0006397)|tRNA-type intron splice site recognition and cleavage (GO:0000379)	tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	10	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GAGCTCCTGGAGAAGATTACG	0.627																																					p.E114G	Esophageal Squamous(37;841 964 4869 42824)	Atlas-SNP	.											.	TSEN34	17	.	0			c.A341G						.						44	47	46					19																	54695669		1894	4106	6000	SO:0001583	missense	79042	exon3			TCCTGGAGAAGAT	AF211970	CCDS42609.1, CCDS74446.1	19q13.4	2013-08-06	2013-08-06	2005-03-12	ENSG00000170892	ENSG00000170892		"tRNA splicing endonuclease subunits"	15506	protein-coding gene	gene with protein product		608754	"leukocyte receptor cluster (LRC) member 5", "tRNA splicing endonuclease 34 homolog (SEN34, S. cerevisiae)", "tRNA splicing endonuclease 34 homolog (S. cerevisiae)"	LENG5		10941842, 15109492	Standard	NM_024075		Approved	SEN34, SEN34L	uc002qdw.3	Q9BSV6	OTTHUMG00000066515	ENST00000396383.1:c.341A>G	chr19.hg19:g.54695669A>G	ENSP00000379667:p.Glu114Gly	30.0	0.0		46.0	10.0	NM_024075	A6NNB1|B0V3J1|Q9BVT1|Q9H6H5	Missense_Mutation	SNP	ENST00000396383.1	hg19	CCDS42609.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.087343	0.55968	.	.	ENSG00000170892	ENST00000455798;ENST00000456872;ENST00000302937;ENST00000429671;ENST00000396383;ENST00000396388	T;T;T;T;T;T	0.67523	-0.26;-0.27;-0.24;-0.25;-0.24;-0.24	4.36	4.36	0.52297	.	0.593383	0.18153	N	0.150014	T	0.57695	0.2071	L	0.47716	1.5	0.33031	D	0.530226	B;B	0.26672	0.156;0.094	B;B	0.21917	0.037;0.023	T	0.65080	-0.6255	10	0.36615	T	0.2	.	11.3906	0.49811	1.0:0.0:0.0:0.0	.	114;114	E7EQB3;Q9BSV6	.;SEN34_HUMAN	G	114;117;114;114;114;114	ENSP00000400743:E114G;ENSP00000408689:E117G;ENSP00000305524:E114G;ENSP00000397402:E114G;ENSP00000379667:E114G;ENSP00000379671:E114G	ENSP00000305524:E114G	E	+	2	0	TSEN34	59387481	0.778000	0.28640	0.928000	0.36995	0.991000	0.79684	1.916000	0.39986	1.761000	0.52028	0.459000	0.35465	GAG	.	.		0.627	TSEN34-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142200.1	NM_024075		G	54695669	A	G	54695669	3	3	92	1	0	0	0	0	1	0	0	0	16628	304	11	2	347	2	TSEN34	19	54695669	Missense_Mutation	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	841021	54695669	4433314	144	12942										
DSN1	79980	hgsc.bcm.edu	37	chr20	35383170	35383170	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	caagagacaagcttaccgagCtgtactgacaccttctggaa	9	11	1	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr20:35383170C>T	ENST00000426836.1	-	10	1329	c.957G>A	c.(955-957)caG>caA	p.Q319Q	DSN1_ENST00000373745.3_Silent_p.Q319Q|DSN1_ENST00000373734.4_Silent_p.Q212Q|DSN1_ENST00000473615.1_5'UTR|DSN1_ENST00000448110.2_Silent_p.Q303Q|DSN1_ENST00000373740.3_Silent_p.Q247Q|DSN1_ENST00000373750.4_Silent_p.Q319Q	NM_001145316.1	NP_001138788.1	Q9H410	DSN1_HUMAN	DSN1, MIS12 kinetochore complex component	319					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|MIS12/MIND type complex (GO:0000444)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	16		Myeloproliferative disorder(115;0.00874)				GCTTACCGAGCTGTACTGACA	0.478																																					p.Q319Q		Atlas-SNP	.											.	DSN1	32	.	0			c.G957A						.						97	76	83					20																	35383170		2203	4300	6503	SO:0001819	synonymous_variant	79980	exon10			ACCGAGCTGTACT	AK023408	CCDS13286.1, CCDS46596.1, CCDS46597.1	20q11.23	2013-07-03	2013-07-03	2006-11-07	ENSG00000149636	ENSG00000149636			16165	protein-coding gene	gene with protein product	"kinetochore null 3 homolog (C. elegans)"	609175	"chromosome 20 open reading frame 172", "DSN1, MIND kinetochore complex component, homolog (S. cerevisiae)"	C20orf172		16585270, 20819937	Standard	NM_001145315		Approved	dJ469A13.2, MIS13, KNL3, hKNL-3	uc002xfz.3	Q9H410	OTTHUMG00000032396	ENST00000426836.1:c.957G>A	chr20.hg19:g.35383170C>T		33.0	0.0		74.0	17.0	NM_001145315	B4DWT2|E1P5U9|Q5JW55|Q5JW56|Q9H8P4	Silent	SNP	ENST00000426836.1	hg19	CCDS13286.1																																																																																			.	.		0.478	DSN1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079043.2	NM_024918		T	35383170	C	T	35383170	2	4	92	1	0	0	0	0	0	0	0	1	4782	796	28	3		3	DSN1	20	35383170	Silent	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10		35383170	27642350	145	12943										
OPRL1	4987	hgsc.bcm.edu	37	chr20	62729669	62729676	+	Frame_Shift_Del	DEL	CTGGGGCC	CTGGGGCC	-													0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	atccctacccctcaggattaCtggggcccggtgtttgccat							TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	CTGGGGCC	CTGGGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr20:62729669_62729676delCTGGGGCC	ENST00000349451.3	+	6	1042_1049	c.630_637delCTGGGGCC	c.(628-639)tactggggcccgfs	p.WGP211fs	OPRL1_ENST00000355631.4_Frame_Shift_Del_p.WGP211fs|OPRL1_ENST00000336866.2_Frame_Shift_Del_p.WGP211fs	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	211					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavior (GO:0007610)|opioid receptor signaling pathway (GO:0038003)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|nociceptin receptor activity (GO:0001626)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					CTCAGGATTACTGGGGCCCGGTGTTTGC	0.62																																					p.210_212del		Atlas-Indel,Pindel	.											.	OPRL1	47	.	0			c.629_636del						.																																			SO:0001589	frameshift_variant	4987	exon4			.		CCDS13556.1	20q13.33	2012-08-08			ENSG00000125510	ENSG00000125510		"GPCR / Class A : Opioid receptors"	8155	protein-coding gene	gene with protein product	"LC132 receptor-like", "orphanin FQ receptor", "kappa3-related opioid receptor"	602548				8137918	Standard	NM_000913		Approved	NOCIR, ORL1, OOR, KOR-3	uc021wgs.1	P41146	OTTHUMG00000033027	ENST00000349451.3:c.630_637delCTGGGGCC	chr20.hg19:g.62729669_62729676delCTGGGGCC	ENSP00000336764:p.Trp211fs	116.0	0.0		257.0	19.0	NM_000913	Q8TD34|Q8WYH9|Q9H4K4	Frame_Shift_Del	DEL	ENST00000349451.3	hg19	CCDS13556.1																																																																																			.	.		0.62	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647		-	62729676	CTGGGGCC	-	62729669	7	5	92	1	0	1	0	1	0	0	0	0	10895	576	20	0	640	0	OPRL1	20	62729669	Frame_Shift_Del	DEL	CTGGGGCC	TCGA-DD-A11A-01A-11D-A12Z-10	27346499	62729669	295851	146	12944										
BACH1	571	hgsc.bcm.edu	37	chr21	30699058	30699058	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agtgcccaactgaaaaatcaGaagtgactcctttcccccac	6	14	1	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr21:30699058G>A	ENST00000399921.1	+	3	1156	c.913G>A	c.(913-915)Gaa>Aaa	p.E305K	BACH1_ENST00000286800.3_Missense_Mutation_p.E305K	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						TGAAAAATCAGAAGTGACTCC	0.388																																					p.E305K		Atlas-SNP	.											.	BACH1	66	.	0			c.G913A						.						110	114	113					21																	30699058		2203	4300	6503	SO:0001583	missense	571	exon3			AAATCAGAAGTGA	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"BTB/POZ domain containing", "basic leucine zipper proteins"	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.913G>A	chr21.hg19:g.30699058G>A	ENSP00000382805:p.Glu305Lys	36.0	0.0		23.0	9.0	NM_206866	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000399921.1	hg19	CCDS13585.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.633614	0.47049	.	.	ENSG00000156273	ENST00000286800;ENST00000399921	T;T	0.71817	-0.6;-0.6	5.65	3.8	0.43715	.	0.423319	0.26029	N	0.026773	T	0.53110	0.1776	N	0.19112	0.55	0.09310	N	1	B	0.31680	0.335	B	0.25140	0.058	T	0.26052	-1.0114	10	0.14656	T	0.56	-12.5395	16.7676	0.85528	0.0:0.2164:0.7836:0.0	.	305	O14867	BACH1_HUMAN	K	305	ENSP00000286800:E305K;ENSP00000382805:E305K	ENSP00000286800:E305K	E	+	1	0	BACH1	29620929	0.984000	0.35163	0.004000	0.12327	0.969000	0.65631	4.010000	0.57117	0.891000	0.36235	0.655000	0.94253	GAA	.	.		0.388	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		A	30699058	G	A	30699058	3	1	92	1	0	0	0	0	1	0	0	0	1283	943	33	3	919	3	BACH1	21	30699058	Missense_Mutation	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10		30699058	17430837	147	12945										
AIRE	326	hgsc.bcm.edu	37	chr21	45712255	45712255	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agccccgggcagaggagcccCggccccaggagccacccgtg	15	18	0	1	rs376901046		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr21:45712255C>T	ENST00000291582.5	+	9	1193	c.1066C>T	c.(1066-1068)Cgg>Tgg	p.R356W	AIRE_ENST00000355347.4_Missense_Mutation_p.R149W|AIRE_ENST00000329347.4_Missense_Mutation_p.R149W	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	356					humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		AGAGGAGCCCCGGCCCCAGGA	0.706									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				C|||	1	0.000199681	0	0	5008	,	,		14318	0		0	False		,,,				2504	0.001				p.R356W		Atlas-SNP	.											.	AIRE	61	.	0			c.C1066T						.	C	TRP/ARG,TRP/ARG	0,4268		0,0,2134	12	17	15		1066,475	0.7	0	21		15	3,8467		0,3,4232	no	missense,missense	AIRE	NM_000383.2,NM_000658.2	101,101	0,3,6366	TT,TC,CC		0.0354,0.0,0.0236	probably-damaging,probably-damaging	356/546,159/349	45712255	3,12735	2134	4235	6369	SO:0001583	missense	326	exon9	Familial Cancer Database	APECED	GAGCCCCGGCCCC	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"Zinc fingers, PHD-type"	360	protein-coding gene	gene with protein product	"autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"	607358	"autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.1066C>T	chr21.hg19:g.45712255C>T	ENSP00000291582:p.Arg356Trp	28.0	0.0		32.0	11.0	NM_000383	B2RP50|O43922|O43932|O75745	Missense_Mutation	SNP	ENST00000291582.5	hg19	CCDS13706.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.053313	0.36181	0.0	3.54E-4	ENSG00000160224	ENST00000291582;ENST00000337909;ENST00000397994;ENST00000355347;ENST00000329347	D;D;D	0.96885	-3.72;-4.16;-4.04	4.27	0.706	0.18133	.	2.392740	0.02114	N	0.055069	D	0.96981	0.9014	L	0.57536	1.79	0.09310	N	1	D;D	0.76494	0.999;0.993	P;P	0.62014	0.897;0.548	D	0.87388	0.2361	10	0.62326	D	0.03	-33.7671	6.2932	0.21071	0.413:0.4236:0.1634:0.0	.	159;356	B2RP50;O43918	.;AIRE_HUMAN	W	356;159;159;149;149	ENSP00000291582:R356W;ENSP00000347505:R149W;ENSP00000331055:R149W	ENSP00000291582:R356W	R	+	1	2	AIRE	44536683	0.000000	0.05858	0.039000	0.18376	0.126000	0.20510	-0.058000	0.11750	0.243000	0.21327	0.462000	0.41574	CGG	.	.		0.706	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2			T	45712255	C	T	45712255	3	4	92	1	0	0	0	0	1	0	0	0	437	643	23	1	1388	1	AIRE	21	45712255	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	15013197	45712255	2417640	148	12946										
PI4KA	5297	hgsc.bcm.edu	37	chr22	21161719	21161719	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gagagggtcactgaaggaagTgtagtagagatcagcactgg	16	5	2	3	rs542084506		TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr22:21161719T>C	ENST00000572273.1	-	10	1155	c.925A>G	c.(925-927)Act>Gct	p.T309A	PI4KA_ENST00000255882.6_Missense_Mutation_p.T367A			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	309					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			CTGAAGGAAGTGTAGTAGAGA	0.507													T|||	1	0.000199681	8e-04	0	5008	,	,		21855	0		0	False		,,,				2504	0				p.T367A	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.A1099G						.						175	121	140					22																	21161719		2203	4300	6503	SO:0001583	missense	5297	exon10			AGGAAGTGTAGTA	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.925A>G	chr22.hg19:g.21161719T>C	ENSP00000458238:p.Thr309Ala	45.0	0.0		54.0	28.0	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.34	2.805680	0.50315	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.24	0.382	0.16234	.	0.399434	0.28354	N	0.015648	T	0.27419	0.0673	N	0.08118	0	0.80722	D	1	B;B	0.13145	0.007;0.0	B;B	0.12156	0.007;0.0	T	0.03325	-1.1048	9	0.49607	T	0.09	-17.1863	7.0933	0.25295	0.3425:0.0693:0.0:0.5881	.	367;309	D3DX33;P42356	.;PI4KA_HUMAN	A	309	.	ENSP00000255882:T309A	T	-	1	0	PI4KA	19491719	1.000000	0.71417	0.603000	0.28903	0.986000	0.74619	2.730000	0.47335	0.086000	0.17137	-0.336000	0.08194	ACT	.	.		0.507	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		C	21161719	T	C	21161719	3	2	92	1	0	0	0	0	1	0	0	0	11882	1696	59	2	5393	2	PI4KA	22	21161719	Missense_Mutation	SNP	T	TCGA-DD-A11A-01A-11D-A12Z-10		21161719	30142847	149	12947										
TCF20	6942	hgsc.bcm.edu	37	chr22	42607990	42607990	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	gtgctgtgctgcagcaattaCtccctgagcagaaccgctgc	11	13	0	2			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chr22:42607990C>G	ENST00000359486.3	-	1	3458	c.3322G>C	c.(3322-3324)Gta>Cta	p.V1108L	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Missense_Mutation_p.V1108L	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1108					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						GCAGCAATTACTCCCTGAGCA	0.507																																					p.V1108L		Atlas-SNP	.											.	TCF20	164	.	0			c.G3322C						.						78	77	77					22																	42607990		2203	4300	6503	SO:0001583	missense	6942	exon1			CAATTACTCCCTG	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.3322G>C	chr22.hg19:g.42607990C>G	ENSP00000352463:p.Val1108Leu	38.0	0.0		52.0	7.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.307250	0.81247	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.63580	-0.05;-0.05	5.91	5.91	0.95273	.	0.100298	0.44483	D	0.000454	T	0.52435	0.1734	N	0.19112	0.55	0.80722	D	1	P;P	0.42518	0.782;0.675	B;B	0.43478	0.421;0.241	T	0.45175	-0.9279	10	0.17832	T	0.49	-12.8393	18.4788	0.90804	0.0:1.0:0.0:0.0	.	1108;1108	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	L	1108	ENSP00000352463:V1108L;ENSP00000335561:V1108L	ENSP00000335561:V1108L	V	-	1	0	TCF20	40937934	1.000000	0.71417	0.973000	0.42090	0.940000	0.58332	4.989000	0.63870	2.802000	0.96397	0.655000	0.94253	GTA	.	.		0.507	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		G	42607990	C	G	42607990	3	3	92	1	0	0	0	0	1	0	0	0	15705	565	20	4	2598	4	TCF20	22	42607990	Missense_Mutation	SNP	C	TCGA-DD-A11A-01A-11D-A12Z-10	21446271	42607990	8696576	150	12948										
CDKL5	6792	hgsc.bcm.edu	37	chrX	18622799	18622799	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	agtagccattcccattcactGtctgcacctcacgaatcttt	5	14	4	0			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chrX:18622799G>A	ENST00000379989.3	+	13	2040	c.1755G>A	c.(1753-1755)ctG>ctA	p.L585L	CDKL5_ENST00000379996.3_Silent_p.L585L|CDKL5_ENST00000463994.1_3'UTR	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	585					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					CCCATTCACTGTCTGCACCTC	0.507																																					p.L585L		Atlas-SNP	.											.	CDKL5	124	.	0			c.G1755A						.						146	141	143					X																	18622799		2203	4300	6503	SO:0001819	synonymous_variant	6792	exon12			TTCACTGTCTGCA	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"Cyclin-dependent kinases"	11411	protein-coding gene	gene with protein product		300203	"serine/threonine kinase 9"	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.1755G>A	chrX.hg19:g.18622799G>A		36.0	0.0		49.0	32.0	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Silent	SNP	ENST00000379989.3	hg19	CCDS14186.1																																																																																			.	.		0.507	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159		A	18622799	G	A	18622799	2	1	92	1	0	0	0	0	0	0	0	1	3159	1364	48	3		3	CDKL5	23	18622799	Silent	SNP	G	TCGA-DD-A11A-01A-11D-A12Z-10		18622799	136647761	151	12949										
FMR1NB	158521	hgsc.bcm.edu	37	chrX	147084806	147084806	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.112582781456954	17	1	1.66719298245614	2.70983379501385	1.31343984962406	0.530264956619443	1	0	tctctggaagaagattccgcAttggaagctttgctgaattt	10	7	1	3			TCGA-DD-A11A-01A-11D-A12Z-10	TCGA-DD-A11A-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3387dbca-ef9a-4ffe-94f2-e002df056e64	926ba7c3-0c83-4e06-8ba2-ed15ba1f87a5	g.chrX:147084806A>C	ENST00000370467.3	+	2	437	c.363A>C	c.(361-363)gcA>gcC	p.A121A		NM_152578.2	NP_689791.1	Q8N0W7	FMR1N_HUMAN	fragile X mental retardation 1 neighbor	121						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)				breast(2)|cervix(1)|endometrium(3)|large_intestine(7)|lung(10)|ovary(1)|skin(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					AAGATTCCGCATTGGAAGCTT	0.358																																					p.A121A		Atlas-SNP	.											.	FMR1NB	51	.	0			c.A363C						.						113	105	108					X																	147084806		2203	4300	6503	SO:0001819	synonymous_variant	158521	exon2			TTCCGCATTGGAA		CCDS14683.1	Xq28	2009-03-25			ENSG00000176988	ENSG00000176988			26372	protein-coding gene	gene with protein product	"cancer/testis antigen 37"					12601173	Standard	NM_152578		Approved	FLJ25736, NY-SAR-35, CT37	uc004fcm.3	Q8N0W7	OTTHUMG00000022608	ENST00000370467.3:c.363A>C	chrX.hg19:g.147084806A>C		113.0	0.0		204.0	13.0	NM_152578	D3DWT3	Silent	SNP	ENST00000370467.3	hg19	CCDS14683.1																																																																																			.	.		0.358	FMR1NB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058667.1	NM_152578		C	147084806	A	C	147084806	2	2	92	1	0	0	0	0	0	0	0	1	5969	204	8	5		5	FMR1NB	23	147084806	Silent	SNP	A	TCGA-DD-A11A-01A-11D-A12Z-10	128462007	147084806	8185754	152	12950										
KAZ	23254	hgsc.bcm.edu	37	chr1	14925544	14925544	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	cgcatcgatggggcggtccaGtcggccagccaggaggtgac	17	12	0	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr1:14925544G>C	ENST00000376030.2	+	1	345	c.51G>C	c.(49-51)caG>caC	p.Q17H	KAZN_ENST00000422387.2_Missense_Mutation_p.Q17H|KAZN_ENST00000503743.1_Missense_Mutation_p.Q17H	NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	17					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						GGGCGGTCCAGTCGGCCAGCC	0.667																																					p.Q17H		Atlas-SNP	.											.	KAZN	57	.	0			c.G51C						.						31	37	35					1																	14925544		1967	4136	6103	SO:0001583	missense	23254	exon1			GGTCCAGTCGGCC	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.51G>C	chr1.hg19:g.14925544G>C	ENSP00000365198:p.Gln17His	142.0	1.0		67.0	50.0	NM_015209	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	hg19	CCDS152.2	.	.	.	.	.	.	.	.	.	.	G	22.4	4.280690	0.80692	.	.	ENSG00000189337	ENST00000376030;ENST00000503743;ENST00000422387	T;T;T	0.51325	0.71;0.71;0.71	3.98	3.98	0.46160	.	0.124322	0.31268	U	0.007953	T	0.54078	0.1836	L	0.50333	1.59	0.80722	D	1	D;D	0.61080	0.987;0.989	P;P	0.53912	0.693;0.737	T	0.60311	-0.7288	10	0.87932	D	0	-15.2006	13.4971	0.61432	0.0:0.0:1.0:0.0	.	17;17	Q674X7-2;Q674X7	.;KAZRN_HUMAN	H	17	ENSP00000365198:Q17H;ENSP00000426015:Q17H;ENSP00000391728:Q17H	ENSP00000365198:Q17H	Q	+	3	2	KAZN	14798131	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.168000	0.71908	1.739000	0.51704	0.313000	0.20887	CAG	.	.		0.667	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		C	14925544	G	C	14925544	3	2	93	1	0	0	0	0	1	0	0	0	7997	1020	36	4	53	4	KAZ	1	14925544	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10		14925544	234325077	1	12951										
TTC24	164118	hgsc.bcm.edu	37	chr1	156552954	156552954	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	gcatgccctgcaggctgcccGggactctggtaagcgtgaga	15	12	1	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr1:156552954G>T	ENST00000368237.3	+	3	1031	c.1031G>T	c.(1030-1032)cGg>cTg	p.R344L	TTC24_ENST00000368236.3_Missense_Mutation_p.R344L|TTC24_ENST00000478081.1_Intron			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	344										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAGGCTGCCCGGGACTCTGGT	0.652																																					p.R344L		Atlas-SNP	.											.	TTC24	46	.	0			c.G1031T						.						38	41	40					1																	156552954		1981	4148	6129	SO:0001583	missense	164118	exon4			CTGCCCGGGACTC		CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"Tetratricopeptide (TTC) repeat domain containing"	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.1031G>T	chr1.hg19:g.156552954G>T	ENSP00000357220:p.Arg344Leu	288.0	0.0		253.0	70.0	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	hg19	CCDS53379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.58|12.58	1.981317|1.981317	0.34942|0.34942	.|.	.|.	ENSG00000187862|ENSG00000187862	ENST00000340086;ENST00000413282|ENST00000368236;ENST00000368237	.|D;D	.|0.95035	.|-3.59;-3.59	4.87|4.87	-0.252|-0.252	0.12999|0.12999	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.|0.531595	.|0.15832	.|N	.|0.242466	D|D	0.86900|0.86900	0.6044|0.6044	M|M	0.67700|0.67700	2.07|2.07	0.26495|0.26495	N|N	0.974872|0.974872	.|P	.|0.38992	.|0.653	.|B	.|0.36504	.|0.226	T|T	0.80527|0.80527	-0.1343|-0.1343	5|10	.|0.59425	.|D	.|0.04	-4.733|-4.733	8.948|8.948	0.35771|0.35771	0.5517:0.0:0.4483:0.0|0.5517:0.0:0.4483:0.0	.|.	.|344	.|A2A3L6	.|TTC24_HUMAN	W|L	117;109|344	.|ENSP00000357219:R344L;ENSP00000357220:R344L	.|ENSP00000357219:R344L	G|R	+|+	1|2	0|0	TTC24|TTC24	154819578|154819578	0.949000|0.949000	0.32298|0.32298	0.628000|0.628000	0.29241|0.29241	0.487000|0.487000	0.33371|0.33371	0.722000|0.722000	0.25925|0.25925	0.086000|0.086000	0.17137|0.17137	0.455000|0.455000	0.32223|0.32223	GGG|CGG	.	.		0.652	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		T	156552954	G	T	156552954	3	4	93	1	0	0	0	0	1	0	0	0	16707	1116	39	1	1041	1	TTC24	1	156552954	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10	141627410	156552954	92697667	2	12952										
VANGL2	57216	hgsc.bcm.edu	37	chr1	160388964	160388964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ggcactgctgtctttcctcaCgcctctggccttcctgctgc	9	17	3	0			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr1:160388964C>T	ENST00000368061.2	+	4	839	c.365C>T	c.(364-366)aCg>aTg	p.T122M		NM_020335.2	NP_065068.1	Q9ULK5	VANG2_HUMAN	VANGL planar cell polarity protein 2	122					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|cell migration involved in kidney development (GO:0035787)|cochlea morphogenesis (GO:0090103)|convergent extension involved in axis elongation (GO:0060028)|convergent extension involved in neural plate elongation (GO:0022007)|digestive tract morphogenesis (GO:0048546)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity involved in neural tube closure (GO:0090177)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|glomerulus development (GO:0032835)|hair follicle development (GO:0001942)|heart looping (GO:0001947)|inner ear receptor stereocilium organization (GO:0060122)|kidney morphogenesis (GO:0060993)|lateral sprouting involved in lung morphogenesis (GO:0060490)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in axis elongation (GO:0003402)|planar cell polarity pathway involved in heart morphogenesis (GO:0061346)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|positive regulation of JUN kinase activity (GO:0043507)|post-anal tail morphogenesis (GO:0036342)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Wnt signaling pathway (GO:0030111)|Rho protein signal transduction (GO:0007266)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell pole (GO:0060187)|cell-cell junction (GO:0005911)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)				biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	37	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TCTTTCCTCACGCCTCTGGCC	0.662																																					p.T122M		Atlas-SNP	.											.	VANGL2	83	.	0			c.C365T						.						59	58	58					1																	160388964		2203	4300	6503	SO:0001583	missense	57216	exon4			TCCTCACGCCTCT	AB033041	CCDS30915.1	1q22-q23	2013-03-05	2013-03-05		ENSG00000162738	ENSG00000162738			15511	protein-coding gene	gene with protein product	"vang, van gogh-like 2", "loop-tail-associated protein", "strabismus"	600533	"vang (van gogh, Drosophila)-like 2, vang, van gogh-like 2 (Drosophila)", "vang-like 2 (van gogh, Drosophila)"			11431695	Standard	NM_020335		Approved	KIAA1215, LTAP, LPP1, STBM, STB1, STBM1, MGC119403, MGC119404	uc001fwc.2	Q9ULK5	OTTHUMG00000033122	ENST00000368061.2:c.365C>T	chr1.hg19:g.160388964C>T	ENSP00000357040:p.Thr122Met	49.0	0.0		66.0	17.0	NM_020335	D3DVE9|Q5T212	Missense_Mutation	SNP	ENST00000368061.2	hg19	CCDS30915.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.057332	0.76074	.	.	ENSG00000162738	ENST00000368061	D	0.83075	-1.68	4.93	3.94	0.45596	.	0.000000	0.85682	D	0.000000	D	0.89608	0.6764	M	0.84219	2.685	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.90763	0.4666	10	0.87932	D	0	-20.8955	13.7554	0.62933	0.0:0.845:0.155:0.0	.	122	Q9ULK5	VANG2_HUMAN	M	122	ENSP00000357040:T122M	ENSP00000357040:T122M	T	+	2	0	VANGL2	158655588	1.000000	0.71417	0.990000	0.47175	0.878000	0.50629	5.635000	0.67841	2.433000	0.82419	0.563000	0.77884	ACG	.	.		0.662	VANGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080677.1	NM_020335		T	160388964	C	T	160388964	3	4	93	1	0	0	0	0	1	0	0	0	17135	536	19	1	375	1	VANGL2	1	160388964	Missense_Mutation	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10	3836010	160388964	88861657	3	12953										
C1orf226	400793	hgsc.bcm.edu	37	chr1	162353415	162353415	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tggcagcccccctcctcaggCacggacctccagcctcgaca	9	20	1	0			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr1:162353415C>T	ENST00000458626.2	+	2	933	c.761C>T	c.(760-762)gCa>gTa	p.A254V	C1orf226_ENST00000426197.2_Missense_Mutation_p.A297V	NM_001085375.1	NP_001078844.1	A1L170	CA226_HUMAN	chromosome 1 open reading frame 226	254										central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12						CCTCCTCAGGCACGGACCTCC	0.607																																					p.A297V		Atlas-SNP	.											.	C1orf226	49	.	0			c.C890T						.						21	24	23					1																	162353415		2015	4178	6193	SO:0001583	missense	400793	exon3			CTCAGGCACGGAC	AI480219, AK023199, AK125122, AL512785, BC127743	CCDS44268.1, CCDS53422.1	1q23.3	2013-10-11			ENSG00000239887	ENSG00000239887			34351	protein-coding gene	gene with protein product						14702039	Standard	NM_001085375		Approved	FLJ13137	uc010pkt.1	A1L170	OTTHUMG00000031376	ENST00000458626.2:c.761C>T	chr1.hg19:g.162353415C>T	ENSP00000437071:p.Ala254Val	44.0	0.0		42.0	14.0	NM_001135240	B4DF31	Missense_Mutation	SNP	ENST00000458626.2	hg19	CCDS53422.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.459629	0.43736	.	.	ENSG00000239887	ENST00000426197;ENST00000458626	.	.	.	5.62	4.71	0.59529	.	.	.	.	.	T	0.32585	0.0834	N	0.24115	0.695	.	.	.	P;D	0.53619	0.585;0.961	B;P	0.47645	0.399;0.553	T	0.09729	-1.0661	6	.	.	.	-9.5985	18.2171	0.89889	0.0:0.8776:0.1224:0.0	.	297;254	A1L170-2;A1L170	.;CA226_HUMAN	V	297;254	.	.	A	+	2	0	C1orf226	160620039	0.021000	0.18746	0.967000	0.41034	0.070000	0.16714	0.777000	0.26718	0.734000	0.32515	-0.795000	0.03280	GCA	.	.		0.607	C1orf226-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076793.2	NM_001085375		T	162353415	C	T	162353415	3	4	93	1	0	0	0	0	1	0	0	0	2034	710	25	3	900	3	C1orf226	1	162353415	Missense_Mutation	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10	1964451	162353415	86897206	4	12954										
APOBEC4	403314	hgsc.bcm.edu	37	chr1	183617170	183617170	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tcctgagcttttgtgtttggAttcctttttgtctggagaag	11	6	1	2			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr1:183617170A>T	ENST00000308641.4	-	2	1018	c.747T>A	c.(745-747)aaT>aaA	p.N249K	RGL1_ENST00000304685.4_Intron|APOBEC4_ENST00000481562.1_Intron|RGL1_ENST00000536277.1_Intron	NM_203454.2	NP_982279.1	Q8WW27	ABEC4_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	249					mRNA processing (GO:0006397)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(6)|skin(1)	21						TTGTGTTTGGATTCCTTTTTG	0.458																																					p.N249K		Atlas-SNP	.											.	APOBEC4	45	.	0			c.T747A						.						102	106	105					1																	183617170		2203	4300	6503	SO:0001583	missense	403314	exon2			GTTTGGATTCCTT	BC021711	CCDS1358.1	1q25.3	2008-02-05	2005-10-27	2005-10-27	ENSG00000173627	ENSG00000173627		"Apolipoprotein B mRNA editing enzymes"	32152	protein-coding gene	gene with protein product		609908	"chromosome 1 open reading frame 169"	C1orf169		16082223	Standard	NM_203454		Approved	MGC26594, FLJ25691, RP1-127C7.4	uc001gqn.3	Q8WW27	OTTHUMG00000035459	ENST00000308641.4:c.747T>A	chr1.hg19:g.183617170A>T	ENSP00000310622:p.Asn249Lys	841.0	0.0		687.0	181.0	NM_203454	Q8N7F6	Missense_Mutation	SNP	ENST00000308641.4	hg19	CCDS1358.1	.	.	.	.	.	.	.	.	.	.	A	6.837	0.523599	0.13066	.	.	ENSG00000173627	ENST00000308641	T	0.13778	2.56	5.15	3.8	0.43715	.	0.621363	0.14561	N	0.312068	T	0.13970	0.0338	L	0.59436	1.845	0.09310	N	0.999992	B	0.32245	0.361	B	0.33042	0.157	T	0.17992	-1.0351	10	0.56958	D	0.05	-18.7721	5.1447	0.14979	0.7218:0.0:0.2782:0.0	.	249	Q8WW27	ABEC4_HUMAN	K	249	ENSP00000310622:N249K	ENSP00000310622:N249K	N	-	3	2	APOBEC4	181883793	0.985000	0.35326	0.102000	0.21198	0.151000	0.21798	1.019000	0.30014	1.942000	0.56320	0.533000	0.62120	AAT	.	.		0.458	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454		T	183617170	A	T	183617170	3	4	93	1	0	0	0	0	1	0	0	0	796	330	12	4	360	4	APOBEC4	1	183617170	Missense_Mutation	SNP	A	TCGA-DD-A11B-01A-11D-A12Z-10	21263755	183617170	65633451	5	12955										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133538773	133538773	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	aagcattacttgatccacttTctgtctgtggagctgctttc	8	10	2	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr2:133538773T>G	ENST00000409261.1	-	15	5274	c.4901A>C	c.(4900-4902)gAa>gCa	p.E1634A	NCKAP5_ENST00000473859.1_5'UTR|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.E1634A	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1634										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TGATCCACTTTCTGTCTGTGG	0.453																																					p.E1634A		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A4901C						.						109	107	108					2																	133538773		1900	4122	6022	SO:0001583	missense	344148	exon15			CCACTTTCTGTCT	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.4901A>C	chr2.hg19:g.133538773T>G	ENSP00000387128:p.Glu1634Ala	568.0	0.0		275.0	124.0	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	hg19	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	T	14.93	2.682606	0.47991	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.11277	2.79;2.79	5.35	4.21	0.49690	.	0.000000	0.32836	U	0.005599	T	0.11110	0.0271	L	0.29908	0.895	0.80722	D	1	D	0.55385	0.971	P	0.47075	0.536	T	0.03524	-1.1028	10	0.72032	D	0.01	.	9.668	0.39996	0.0:0.0779:0.0:0.9221	.	1634	O14513	NCKP5_HUMAN	A	1634	ENSP00000387128:E1634A;ENSP00000380603:E1634A	ENSP00000380603:E1634A	E	-	2	0	NCKAP5	133255243	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	4.150000	0.58098	1.059000	0.40554	0.533000	0.62120	GAA	.	.		0.453	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		G	133538773	T	G	133538773	3	3	93	1	0	0	0	0	1	0	0	0	10232	1783	62	5	852	5	NCKAP5	2	133538773	Missense_Mutation	SNP	T	TCGA-DD-A11B-01A-11D-A12Z-10		133538773	109660600	6	12956										
SESTD1	91404	hgsc.bcm.edu	37	chr2	180036920	180036920	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tatcccagaattcatctggcTttaccacacaaacaagggac	6	12	2	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr2:180036920T>C	ENST00000428443.3	-	5	612	c.296A>G	c.(295-297)aAg>aGg	p.K99R	SESTD1_ENST00000486468.1_5'UTR	NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	99	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			TTCATCTGGCTTTACCACACA	0.308																																					p.K99R		Atlas-SNP	.											.	SESTD1	66	.	0			c.A296G						.						98	101	100					2																	180036920		2203	4300	6503	SO:0001583	missense	91404	exon5			TCTGGCTTTACCA	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.296A>G	chr2.hg19:g.180036920T>C	ENSP00000415332:p.Lys99Arg	350.0	0.0		195.0	77.0	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	hg19	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	T	12.96	2.094321	0.36952	.	.	ENSG00000187231	ENST00000428443;ENST00000440010;ENST00000435047	D;T;T	0.84442	-1.85;-0.01;-0.01	5.15	5.15	0.70609	Cellular retinaldehyde-binding/triple function, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80053	0.4553	N	0.01751	-0.74	0.80722	D	1	D	0.57257	0.979	D	0.71414	0.973	T	0.81656	-0.0834	9	.	.	.	-11.6898	14.9769	0.71281	0.0:0.0:0.0:1.0	.	99	Q86VW0	SESD1_HUMAN	R	99	ENSP00000415332:K99R;ENSP00000416164:K99R;ENSP00000410286:K99R	.	K	-	2	0	SESTD1	179745165	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.958000	0.87877	1.942000	0.56320	0.454000	0.30748	AAG	.	.		0.308	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		C	180036920	T	C	180036920	3	2	93	1	0	0	0	0	1	0	0	0	14142	1609	56	2	1850	2	SESTD1	2	180036920	Missense_Mutation	SNP	T	TCGA-DD-A11B-01A-11D-A12Z-10	46498147	180036920	63162453	7	12957										
TRAK2	66008	hgsc.bcm.edu	37	chr2	202245372	202245372	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tcctccttagtccacctaatAaactgctacctgaatttaaa	3	12	0	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr2:202245372A>T	ENST00000332624.3	-	16	3067	c.2639T>A	c.(2638-2640)tTa>tAa	p.L880*		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	880					protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						TCCACCTAATAAACTGCTACC	0.463																																					p.L880X		Atlas-SNP	.											.	TRAK2	62	.	0			c.T2639A						.						76	75	75					2																	202245372		2203	4300	6503	SO:0001587	stop_gained	66008	exon16			CCTAATAAACTGC	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"gamma-aminobutyric acid(A) receptor-interacting factor", "milton homolog 2 (Drosophila)", "O-linked N-acetylglucosamine transferase interacting protein 98"	607334	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.2639T>A	chr2.hg19:g.202245372A>T	ENSP00000328875:p.Leu880*	236.0	0.0		127.0	52.0	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Nonsense_Mutation	SNP	ENST00000332624.3	hg19	CCDS2347.1	.	.	.	.	.	.	.	.	.	.	A	41	8.904768	0.98998	.	.	ENSG00000115993	ENST00000332624	.	.	.	6.17	6.17	0.99709	.	0.087590	0.44483	D	0.000455	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	.	.	.	X	880	.	ENSP00000328875:L880X	L	-	2	0	TRAK2	201953617	1.000000	0.71417	0.035000	0.18076	0.459000	0.32528	8.627000	0.90974	2.371000	0.80710	0.533000	0.62120	TTA	.	.		0.463	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049		T	202245372	A	T	202245372	4	4	93	1	0	0	0	0	0	1	0	0	16465	372	13	4	109	4	TRAK2	2	202245372	Nonsense_Mutation	SNP	A	TCGA-DD-A11B-01A-11D-A12Z-10	22208452	202245372	40954001	8	12958										
OGG1	4968	hgsc.bcm.edu	37	chr3	9792677	9792677	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	agtggtgtactagcggatcaAgtatggacactgactcagac	12	8	2	2			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr3:9792677A>C	ENST00000344629.7	+	2	529	c.186A>C	c.(184-186)caA>caC	p.Q62H	OGG1_ENST00000302008.8_Missense_Mutation_p.Q62H|OGG1_ENST00000349503.5_Missense_Mutation_p.Q62H|OGG1_ENST00000302003.7_Missense_Mutation_p.Q62H|OGG1_ENST00000449570.2_Missense_Mutation_p.Q62H|OGG1_ENST00000383826.5_Missense_Mutation_p.Q62H|OGG1_ENST00000339511.5_Missense_Mutation_p.Q62H|OGG1_ENST00000302036.7_Missense_Mutation_p.Q62H|OGG1_ENST00000436092.1_3'UTR			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	62					acute inflammatory response (GO:0002526)|base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cellular response to cadmium ion (GO:0071276)|depurination (GO:0045007)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity (GO:0034039)|damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534)			kidney(2)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8	Medulloblastoma(99;0.227)					TAGCGGATCAAGTATGGACAC	0.577								Base excision repair (BER), DNA glycosylases																													p.Q62H		Atlas-SNP	.											.	OGG1	57	.	0			c.A186C						.						116	89	98					3																	9792677		2203	4300	6503	SO:0001583	missense	4968	exon2			GGATCAAGTATGG	U96710	CCDS2576.1, CCDS2577.1, CCDS2578.1, CCDS2579.1, CCDS2580.1, CCDS2581.1, CCDS43046.1, CCDS46742.1	3p26	2010-11-23			ENSG00000114026	ENSG00000114026	3.2.2.-, 4.2.99.18		8125	protein-coding gene	gene with protein product	"8-hydroxyguanine DNA glycosylase", "OGG1 type 1e", "OGG1 type 1d", "OGG1 type 1g", "OGG1 type 1h"	601982				9207108, 10449904	Standard	NM_002542		Approved	HMMH, HOGG1, OGH1, MUTM	uc003bsj.3	O15527	OTTHUMG00000097091	ENST00000344629.7:c.186A>C	chr3.hg19:g.9792677A>C	ENSP00000342851:p.Gln62His	139.0	0.0		71.0	24.0	NM_016819	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	hg19	CCDS2581.1	.	.	.	.	.	.	.	.	.	.	A	8.800	0.932625	0.18131	.	.	ENSG00000114026	ENST00000302003;ENST00000344629;ENST00000302036;ENST00000349503;ENST00000339511;ENST00000449570;ENST00000302008;ENST00000383826	T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	5.54	0.888	0.19206	8-oxoguanine DNA glycosylase, N-terminal (1);Transcription factor TFIID, C-terminal/DNA glycosylase, N-terminal (1);	0.248639	0.41605	D	0.000851	T	0.43233	0.1238	N	0.16037	0.36	0.33408	D	0.578254	B;D;D;P;B;P;B;P	0.62365	0.002;0.961;0.991;0.874;0.002;0.874;0.001;0.748	B;P;P;B;B;B;B;B	0.55667	0.03;0.781;0.469;0.335;0.005;0.335;0.0;0.165	T	0.54563	-0.8275	10	0.49607	T	0.09	-2.3299	8.0951	0.30824	0.1389:0.3387:0.5224:0.0	.	62;62;62;62;62;62;62;62	E5KPM8;E5KPM6;E5KPM5;E5KPM7;E5KPM9;E5KPN0;O15527;O15527-2	.;.;.;.;.;.;OGG1_HUMAN;.	H	62	ENSP00000305584:Q62H;ENSP00000342851:Q62H;ENSP00000306561:Q62H;ENSP00000303132:Q62H;ENSP00000345520:Q62H;ENSP00000403598:Q62H;ENSP00000305527:Q62H;ENSP00000373337:Q62H	ENSP00000305584:Q62H	Q	+	3	2	OGG1	9767677	0.957000	0.32711	0.266000	0.24541	0.156000	0.22039	0.040000	0.13905	0.129000	0.18514	0.533000	0.62120	CAA	.	.		0.577	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821		C	9792677	A	C	9792677	3	2	93	1	0	0	0	0	1	0	0	0	10854	69	3	5	192	5	OGG1	3	9792677	Missense_Mutation	SNP	A	TCGA-DD-A11B-01A-11D-A12Z-10		9792677	188229753	9	12959										
ENTPD3	956	hgsc.bcm.edu	37	chr3	40442397	40442397	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ttattcagtatggtattgtgCtggatgccgggtcttcaaga	12	6	3	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr3:40442397C>T	ENST00000301825.3	+	4	299	c.181C>T	c.(181-183)Ctg>Ttg	p.L61L	ENTPD3_ENST00000456402.1_Silent_p.L61L|ENTPD3-AS1_ENST00000425156.1_RNA|ENTPD3-AS1_ENST00000452768.1_RNA|ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3_ENST00000445129.1_Silent_p.L61L	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	61					nucleoside diphosphate catabolic process (GO:0009134)|nucleoside triphosphate catabolic process (GO:0009143)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		TGGTATTGTGCTGGATGCCGG	0.483																																					p.L61L		Atlas-SNP	.											.	ENTPD3	48	.	0			c.C181T						.						194	198	197					3																	40442397		2203	4300	6503	SO:0001819	synonymous_variant	956	exon4			ATTGTGCTGGATG	AF039917	CCDS2691.1, CCDS74919.1	3p21.3	2004-02-26			ENSG00000168032	ENSG00000168032			3365	protein-coding gene	gene with protein product		603161		CD39L3		9676430	Standard	XM_005265605		Approved	NTPDase-3, HB6	uc003ckd.4	O75355	OTTHUMG00000131390	ENST00000301825.3:c.181C>T	chr3.hg19:g.40442397C>T		439.0	0.0		157.0	68.0	NM_001248	B2R8D0|G5E9N0|O60495|Q8N6K2	Silent	SNP	ENST00000301825.3	hg19	CCDS2691.1																																																																																			.	.		0.483	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248		T	40442397	C	T	40442397	2	4	93	1	0	0	0	0	0	0	0	1	5142	796	28	3		3	ENTPD3	3	40442397	Silent	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10	30649720	40442397	157580033	10	12960										
TRPC1	7220	hgsc.bcm.edu	37	chr3	142525018	142525018	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tgtcaaaattccgaaatgaaAtaagggatttacttggcttt	8	5	1	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr3:142525018A>G	ENST00000476941.1	+	13	2809	c.2323A>G	c.(2323-2325)Ata>Gta	p.I775V	TRPC1_ENST00000273482.6_Missense_Mutation_p.I741V	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	775					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						CCGAAATGAAATAAGGGATTT	0.348																																					p.I775V		Atlas-SNP	.											.	TRPC1	82	.	0			c.A2323G						.						78	78	78					3																	142525018		2203	4300	6503	SO:0001583	missense	7220	exon13			AATGAAATAAGGG	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"Voltage-gated ion channels / Transient receptor potential cation channels"	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.2323A>G	chr3.hg19:g.142525018A>G	ENSP00000419313:p.Ile775Val	303.0	0.0		219.0	95.0	NM_001251845	Q14CE4	Missense_Mutation	SNP	ENST00000476941.1	hg19	CCDS58856.1	.	.	.	.	.	.	.	.	.	.	A	9.280	1.047830	0.19827	.	.	ENSG00000144935	ENST00000476941;ENST00000273482	T;T	0.80123	-1.34;-1.34	5.59	5.59	0.84812	.	0.037965	0.85682	D	0.000000	T	0.50599	0.1625	N	0.00313	-1.665	0.46203	D	0.998923	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.55049	-0.8201	10	0.19590	T	0.45	-27.4427	15.7661	0.78128	1.0:0.0:0.0:0.0	.	775;741	P48995;P48995-2	TRPC1_HUMAN;.	V	775;741	ENSP00000419313:I775V;ENSP00000273482:I741V	ENSP00000273482:I741V	I	+	1	0	TRPC1	144007708	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.942000	0.92970	2.134000	0.65973	0.460000	0.39030	ATA	.	.		0.348	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304		G	142525018	A	G	142525018	3	3	93	1	0	0	0	0	1	0	0	0	16593	101	4	2	2267	2	TRPC1	3	142525018	Missense_Mutation	SNP	A	TCGA-DD-A11B-01A-11D-A12Z-10	102082621	142525018	55497412	11	12961										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164907129	164907129	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	gcatgaggctgaaggctgcaGgctggatttcccggatgaca	15	9	0	3			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr3:164907129G>A	ENST00000475390.1	-	2	1933	c.1490C>T	c.(1489-1491)cCt>cTt	p.P497L	SLITRK3_ENST00000241274.3_Missense_Mutation_p.P497L			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	497					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						GAAGGCTGCAGGCTGGATTTC	0.498										HNSCC(40;0.11)																											p.P497L		Atlas-SNP	.											.	SLITRK3	263	.	0			c.C1490T						.						69	73	71					3																	164907129		2203	4300	6503	SO:0001583	missense	22865	exon2			GCTGCAGGCTGGA	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1490C>T	chr3.hg19:g.164907129G>A	ENSP00000420091:p.Pro497Leu	88.0	0.0		43.0	23.0	NM_014926	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	hg19	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	G	18.98	3.738472	0.69304	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.52526	0.66;0.66	5.13	5.13	0.70059	.	0.000000	0.37483	N	0.002077	T	0.67692	0.2920	M	0.61387	1.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68743	-0.5328	10	0.66056	D	0.02	-12.8839	18.7378	0.91763	0.0:0.0:1.0:0.0	.	497	O94933	SLIK3_HUMAN	L	497	ENSP00000420091:P497L;ENSP00000241274:P497L	ENSP00000241274:P497L	P	-	2	0	SLITRK3	166389823	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.601000	0.98297	2.830000	0.97506	0.655000	0.94253	CCT	.	.		0.498	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		A	164907129	G	A	164907129	3	1	93	1	0	0	0	0	1	0	0	0	14759	1000	35	3	1447	3	SLITRK3	3	164907129	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10	22382111	164907129	33115301	12	12962										
C6	729	hgsc.bcm.edu	37	chr5	41201723	41201723	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tctcccaggaggcagttgatGgggcatctttgccagttaca	12	10	2	1	rs398122811		TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr5:41201723G>A	ENST00000263413.3	-	3	501	c.237C>T	c.(235-237)ccC>ccT	p.P79P	C6_ENST00000337836.5_Silent_p.P79P	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	79	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				GGCAGTTGATGGGGCATCTTT	0.428																																					p.P79P		Atlas-SNP	.											C6,NS,carcinoma,0,1	C6	197	.	0			c.C237T	GRCh37	CD961874	C6	D		.						109	105	106					5																	41201723		2203	4300	6503	SO:0001819	synonymous_variant	729	exon3			GTTGATGGGGCAT	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"Complement system"	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.237C>T	chr5.hg19:g.41201723G>A		456.0	0.0		183.0	79.0	NM_001115131		Silent	SNP	ENST00000263413.3	hg19	CCDS3936.1																																																																																			.	.		0.428	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			A	41201723	G	A	41201723	2	1	93	1	0	0	0	0	0	0	0	1	2317	1335	47	3		3	C6	5	41201723	Silent	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10		41201723	139713537	13	12963										
PLAC8L1	153770	hgsc.bcm.edu	37	chr5	145483862	145483862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	acacctgaagaagttacttcCaaaccaattcatagtgagaa	6	9	1	3			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr5:145483862C>T	ENST00000311450.4	-	1	70	c.13G>A	c.(13-15)Gga>Aga	p.G5R	RP11-118M9.3_ENST00000514002.1_RNA	NM_001029869.1	NP_001025040.1	A1L4L8	PL8L1_HUMAN	PLAC8-like 1	5										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|stomach(2)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGTTACTTCCAAACCAATTC	0.383																																					p.G5R		Atlas-SNP	.											.	PLAC8L1	17	.	0			c.G13A						.						111	109	109					5																	145483862		2203	4300	6503	SO:0001583	missense	153770	exon1			TACTTCCAAACCA		CCDS34264.1	5q32	2008-02-05			ENSG00000173261	ENSG00000173261			31746	protein-coding gene	gene with protein product							Standard	XM_005268381		Approved		uc003lnv.3	A1L4L8	OTTHUMG00000163418	ENST00000311450.4:c.13G>A	chr5.hg19:g.145483862C>T	ENSP00000309087:p.Gly5Arg	300.0	0.0		135.0	52.0	NM_001029869		Missense_Mutation	SNP	ENST00000311450.4	hg19	CCDS34264.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.262040	0.39995	.	.	ENSG00000173261	ENST00000311450	T	0.47869	0.83	4.65	2.87	0.33458	.	0.426594	0.20221	N	0.096684	T	0.32041	0.0816	L	0.27053	0.805	0.30565	N	0.764089	B	0.22080	0.064	B	0.20767	0.031	T	0.30592	-0.9973	10	0.87932	D	0	-3.1067	6.963	0.24608	0.0:0.7926:0.0:0.2074	.	5	A1L4L8	PL8L1_HUMAN	R	5	ENSP00000309087:G5R	ENSP00000309087:G5R	G	-	1	0	PLAC8L1	145464055	0.996000	0.38824	0.996000	0.52242	0.132000	0.20833	0.281000	0.18810	0.697000	0.31718	0.563000	0.77884	GGA	.	.		0.383	PLAC8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373290.1	XM_087761		T	145483862	C	T	145483862	3	4	93	1	0	0	0	0	1	0	0	0	12025	603	21	3	536	3	PLAC8L1	5	145483862	Missense_Mutation	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10	104282139	145483862	35431398	14	12964										
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74227627	74227628	+	Missense_Mutation	DNP	GT	GT	AA													0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tgatgacacccaccgcaactGtctgtctcatatcacgaaca							TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr6:74227627_74227628GT>AA	ENST00000316292.9	-	7	2285_2286	c.1294_1295AC>TT	c.(1294-1296)ACa>TTa	p.T432L	EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000309268.6_Missense_Mutation_p.T432L|EEF1A1_ENST00000331523.2_Missense_Mutation_p.T432L	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	432					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						CACCGCAACTGTCTGTCTCATA	0.401											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T432I|p.T432S		Atlas-SNP	.											.	EEF1A1	56	.	0			c.C1295T|c.A1294T						.																																			SO:0001583	missense	1915	exon8			GCAACTGTCTGTC|CAACTGTCTGTCT	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1294_1295delinsAA	chr6.hg19:g.74227627_74227628delinsAA	ENSP00000339063:p.Thr432Leu	239.0|240.0	0.0	1151	114.0|112.0	40.0	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1																																																																																			.	.		0.401	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		AA	74227628	GT	AA	74227627	3	1	93	1	0	0	0	0	1	0	0	0	4925	1377	48	3	97	3	EEF1A1	6	74227627	Missense_Mutation	DNP	GT	TCGA-DD-A11B-01A-11D-A12Z-10		74227627	96887440	15	12965										
RNF216	54476	hgsc.bcm.edu	37	chr7	5681008	5681008	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	cagcagtcattttttcttcaCtgaaataagaaaacataatt	4	7	3	2			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr7:5681008C>A	ENST00000425013.2	-	15	2213		c.e15-1		RNF216_ENST00000389902.3_Splice_Site|RNF216_ENST00000469375.1_Splice_Site	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216						apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		TTTTTCTTCACTGAAATAAGA	0.403																																					.		Atlas-SNP	.											.	RNF216	71	.	0			c.1989-1G>T						.						45	46	45					7																	5681008		2203	4300	6503	SO:0001630	splice_region_variant	54476	exon16			TCTTCACTGAAAT	AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"RING-type (C3HC4) zinc fingers"	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.1989-1G>T	chr7.hg19:g.5681008C>A		127.0	0.0		90.0	42.0	NM_207116	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Splice_Site	SNP	ENST00000425013.2	hg19	CCDS34595.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.300859	0.81136	.	.	ENSG00000011275	ENST00000425013;ENST00000389902;ENST00000458425	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.871	0.88811	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RNF216	5647534	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	7.194000	0.77789	2.444000	0.82710	0.563000	0.77884	.	.	.		0.403	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111	Intron	A	5681008	C	A	5681008	5	1	93	1	0	0	0	0	0	0	1	0	13495	579	20	3	624	3	RNF216	7	5681008	Splice_Site	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10		5681008	153457655	16	12966										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107704297	107704298	+	Frame_Shift_Del	DEL	CT	CT	-													0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ttgtgcaaacatcgaaggcaCtcccctgttacccggctgca							TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr7:107704297_107704298delCT	ENST00000388781.3	-	22	3052_3053	c.2969_2970delAG	c.(2968-2970)gagfs	p.E990fs	LAMB4_ENST00000205386.4_Frame_Shift_Del_p.E990fs|LAMB4_ENST00000388780.3_Frame_Shift_Del_p.E990fs	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	990	Laminin EGF-like 10. {ECO:0000255|PROSITE-ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						ATCGAAGGCACTCCCCTGTTAC	0.51																																					p.990_991del		Atlas-Indel,Pindel	.											.	LAMB4	253	.	0			c.2970_2971del						.																																			SO:0001589	frameshift_variant	22798	exon22			.	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2969_2970delAG	chr7.hg19:g.107704297_107704298delCT	ENSP00000373433:p.Glu990fs	508.0	0.0		180.0	65.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Frame_Shift_Del	DEL	ENST00000388781.3	hg19	CCDS34732.1																																																																																			.	.		0.51	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		-	107704298	CT	-	107704297	7	5	93	1	0	1	0	1	0	0	0	0	8622	564	20	0	2367	0	LAMB4	7	107704297	Frame_Shift_Del	DEL	CT	TCGA-DD-A11B-01A-11D-A12Z-10	102023289	107704297	51434366	17	12967										
RAB2A	5862	hgsc.bcm.edu	37	chr8	61496802	61496802	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tttcgttccatcacaaggtcGtattacagaggtgcagcagg	11	9	1	1	rs535641144		TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr8:61496802G>T	ENST00000262646.7	+	4	573	c.222G>T	c.(220-222)tcG>tcT	p.S74S	RAB2A_ENST00000531289.1_Silent_p.S50S|RAB2A_ENST00000530071.1_3'UTR|RAB2A_ENST00000529579.1_Silent_p.S74S	NM_002865.2	NP_002856.1	P61019	RAB2A_HUMAN	RAB2A, member RAS oncogene family	74					ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|lung(4)	6			BRCA - Breast invasive adenocarcinoma(89;0.0805)			TCACAAGGTCGTATTACAGAG	0.363																																					p.S74S		Atlas-SNP	.											.	RAB2A	21	.	0			c.G222T						.						157	155	156					8																	61496802		2203	4300	6503	SO:0001819	synonymous_variant	5862	exon4			AAGGTCGTATTAC		CCDS6175.1, CCDS56537.1	8q12.1	2007-01-15	2007-01-15	2007-01-15	ENSG00000104388	ENSG00000104388		"RAB, member RAS oncogene"	9763	protein-coding gene	gene with protein product		179509	"RAB2, member RAS oncogene family"	RAB2			Standard	NM_002865		Approved		uc003xud.2	P61019	OTTHUMG00000134298	ENST00000262646.7:c.222G>T	chr8.hg19:g.61496802G>T		167.0	0.0		115.0	39.0	NM_002865	B2R5W8|B4DMQ5|P08886	Silent	SNP	ENST00000262646.7	hg19	CCDS6175.1																																																																																			.	.		0.363	RAB2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259145.2			T	61496802	G	T	61496802	2	4	93	1	0	0	0	0	0	0	0	1	12932	1132	40	1		1	RAB2A	8	61496802	Silent	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10		61496802	84867220	18	12968										
MFSD3	113655	hgsc.bcm.edu	37	chr8	145735131	145735131	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tggggccgggcaataccgtgCaggtggtcgcgtacaagctg	17	10	0	0			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr8:145735131C>T	ENST00000301327.4	+	1	675	c.415C>T	c.(415-417)Cag>Tag	p.Q139*	CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000532237.1_5'Flank	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3	139	Leu-rich.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CAATACCGTGCAGGTGGTCGC	0.692											OREG0019059	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q139X		Atlas-SNP	.											.	MFSD3	17	.	0			c.C415T						.						8	8	8					8																	145735131		2125	4213	6338	SO:0001587	stop_gained	113655	exon1			ACCGTGCAGGTGG		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177	ENST00000301327.4:c.415C>T	chr8.hg19:g.145735131C>T	ENSP00000301327:p.Gln139*	50.0	0.0	1696	60.0	27.0	NM_138431		Nonsense_Mutation	SNP	ENST00000301327.4	hg19	CCDS6431.1	.	.	.	.	.	.	.	.	.	.	C	35	5.506859	0.96386	.	.	ENSG00000167700	ENST00000301327	.	.	.	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-18.3085	16.1659	0.81754	0.0:1.0:0.0:0.0	.	.	.	.	X	139	.	ENSP00000301327:Q139X	Q	+	1	0	MFSD3	145705939	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	5.256000	0.65468	2.484000	0.83849	0.561000	0.74099	CAG	.	.		0.692	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		T	145735131	C	T	145735131	4	4	93	1	0	0	0	0	0	1	0	0	9541	711	25	3	417	3	MFSD3	8	145735131	Nonsense_Mutation	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10	84238329	145735131	628891	19	12969										
S1PR3	1903	hgsc.bcm.edu	37	chr9	91616620	91616620	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ggctcattgccttcacgctgGgcgccctgcccattctgggc	12	16	3	0			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr9:91616620G>T	ENST00000375846.3	+	1	5200	c.505G>T	c.(505-507)Ggc>Tgc	p.G169C	S1PR3_ENST00000358157.2_Missense_Mutation_p.G169C			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	169					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						CTTCACGCTGGGCGCCCTGCC	0.567											OREG0019291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G169C		Atlas-SNP	.											.	S1PR3	49	.	0			c.G505T						.						164	117	133					9																	91616620		2203	4300	6503	SO:0001583	missense	1903	exon2			ACGCTGGGCGCCC	AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3167	protein-coding gene	gene with protein product	"sphingosine-1-phosphate receptor 3"	601965	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.505G>T	chr9.hg19:g.91616620G>T	ENSP00000365006:p.Gly169Cys	131.0	0.0	1283	50.0	39.0	NM_005226	Q5SQD8|Q7Z5I2	Missense_Mutation	SNP	ENST00000375846.3	hg19	CCDS6680.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.997500	0.74818	.	.	ENSG00000213694	ENST00000358157;ENST00000375846	T;T	0.37584	1.19;1.19	5.41	5.41	0.78517	GPCR, rhodopsin-like superfamily (1);	0.121539	0.56097	D	0.000033	T	0.67297	0.2878	M	0.87617	2.895	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.72374	-0.4313	10	0.87932	D	0	.	19.3785	0.94521	0.0:0.0:1.0:0.0	.	169	Q99500	S1PR3_HUMAN	C	169	ENSP00000350878:G169C;ENSP00000365006:G169C	ENSP00000350878:G169C	G	+	1	0	S1PR3	90806440	1.000000	0.71417	0.999000	0.59377	0.526000	0.34562	9.478000	0.97927	2.815000	0.96918	0.561000	0.74099	GGC	.	.		0.567	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226		T	91616620	G	T	91616620	3	4	93	1	0	0	0	0	1	0	0	0	13810	1232	43	3	507	3	S1PR3	9	91616620	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10		91616620	49596811	20	12970										
ALAD	210	hgsc.bcm.edu	37	chr9	116152930	116152930	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ctggcggctctcctcagcccGgaatgctccgttttcactca	9	16	4	0			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr9:116152930G>A	ENST00000409155.3	-	6	620	c.424C>T	c.(424-426)Cgg>Tgg	p.R142W	ALAD_ENST00000277315.5_Missense_Mutation_p.R125W|ALAD_ENST00000482001.1_5'Flank	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	142					cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1)	9					Aminolevulinic acid(DB00855)	TCCTCAGCCCGGAATGCTCCG	0.627																																					p.R142W		Atlas-SNP	.											.	ALAD	36	.	0			c.C424T						.						35	37	36					9																	116152930		2203	4300	6503	SO:0001583	missense	210	exon6			CAGCCCGGAATGC	M13928	CCDS6794.2	9q32	2010-04-29	2010-04-29		ENSG00000148218	ENSG00000148218	4.2.1.24		395	protein-coding gene	gene with protein product	"porphobilinogen synthase"	125270	"aminolevulinate, delta-, dehydratase"			6839527, 6378062	Standard	NM_000031		Approved	ALADH, PBGS	uc011lxf.2	P13716	OTTHUMG00000020522	ENST00000409155.3:c.424C>T	chr9.hg19:g.116152930G>A	ENSP00000386284:p.Arg142Trp	54.0	0.0		15.0	9.0	NM_000031	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Missense_Mutation	SNP	ENST00000409155.3	hg19	CCDS6794.2	.	.	.	.	.	.	.	.	.	.	G	18.57	3.652626	0.67472	.	.	ENSG00000148218	ENST00000409155;ENST00000277315	D;D	0.87334	-2.24;-2.24	5.8	4.9	0.64082	Aldolase-type TIM barrel (1);	1.098010	0.06621	N	0.757457	D	0.90017	0.6883	L	0.46157	1.445	0.23459	N	0.997634	D;P;D	0.57899	0.96;0.875;0.981	P;P;P	0.53722	0.594;0.678;0.733	T	0.79769	-0.1664	10	0.62326	D	0.03	1.7263	14.9393	0.70980	0.0:0.0:0.8558:0.1442	.	142;125;171	P13716;B7Z3I9;P13716-2	HEM2_HUMAN;.;.	W	142;125	ENSP00000386284:R142W;ENSP00000277315:R125W	ENSP00000277315:R125W	R	-	1	2	ALAD	115192751	0.995000	0.38212	0.125000	0.21846	0.765000	0.43378	2.472000	0.45136	1.425000	0.47237	0.655000	0.94253	CGG	.	.		0.627	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945		A	116152930	G	A	116152930	3	1	93	1	0	0	0	0	1	0	0	0	483	1115	39	1	596	1	ALAD	9	116152930	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10	24536310	116152930	25060501	21	12971										
SLC2A6	11182	hgsc.bcm.edu	37	chr9	136339125	136339125	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	agacgaagagcagcaccttgCggcctgcgaggtccatggtg	15	11	0	2			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr9:136339125C>A	ENST00000371899.4	-	7	1090	c.1013G>T	c.(1012-1014)cGc>cTc	p.R338L	SLC2A6_ENST00000485978.1_5'UTR|SLC2A6_ENST00000371897.4_Missense_Mutation_p.R338L	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	338					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		CAGCACCTTGCGGCCTGCGAG	0.692																																					p.R338L		Atlas-SNP	.											.	SLC2A6	31	.	0			c.G1013T						.						35	30	32					9																	136339125		2201	4299	6500	SO:0001583	missense	11182	exon7			ACCTTGCGGCCTG	AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"Solute carriers"	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.1013G>T	chr9.hg19:g.136339125C>A	ENSP00000360966:p.Arg338Leu	71.0	0.0		24.0	15.0	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	hg19	CCDS6975.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.341124	0.81911	.	.	ENSG00000160326	ENST00000371897;ENST00000371899	D;D	0.83914	-1.78;-1.78	5.37	5.37	0.77165	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Sugar transporter, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.93552	0.7942	H	0.95679	3.705	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95054	0.8189	10	0.87932	D	0	.	14.6331	0.68671	0.1459:0.8541:0.0:0.0	.	338;338	Q9UGQ3-2;Q9UGQ3	.;GTR6_HUMAN	L	338	ENSP00000360964:R338L;ENSP00000360966:R338L	ENSP00000360964:R338L	R	-	2	0	SLC2A6	135328946	1.000000	0.71417	0.999000	0.59377	0.812000	0.45895	5.449000	0.66619	2.532000	0.85374	0.561000	0.74099	CGC	.	.		0.692	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585		A	136339125	C	A	136339125	3	1	93	1	0	0	0	0	1	0	0	0	14564	768	27	1	526	1	SLC2A6	9	136339125	Missense_Mutation	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10	20186195	136339125	4874306	22	12972										
MUC2	4583	hgsc.bcm.edu	37	chr11	1096485	1096485	+	Frame_Shift_Del	DEL	G	G	-													0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	cactgcgatcccaacgacaaGgtgtcctgtccccgcaccct							TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr11:1096485delG	ENST00000441003.2	+	34	6537	c.6510delG	c.(6508-6510)aagfs	p.K2170fs	MUC2_ENST00000361558.6_Frame_Shift_Del_p.K308fs	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4532					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCAACGACAAGGTGTCCTGTC	0.592																																					p.K2166fs		Atlas-Indel,Pindel	.											.	MUC2	614	.	0			c.6497delA						.						109	120	116					11																	1096485		2183	4268	6451	SO:0001589	frameshift_variant	4583	exon35			.	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.6510delG	chr11.hg19:g.1096485delG	ENSP00000415183:p.Lys2170fs	89.0	0.0		49.0	23.0	NM_002457	Q14878	Frame_Shift_Del	DEL	ENST00000441003.2	hg19																																																																																				.	.		0.592	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		-	1096485	G	-	1096485	7	5	93	1	0	1	0	1	0	0	0	0	9984	991	35	0	6636	0	MUC2	11	1096485	Frame_Shift_Del	DEL	G	TCGA-DD-A11B-01A-11D-A12Z-10		1096485	133910031	23	12973										
SOX6	55553	hgsc.bcm.edu	37	chr11	15994640	15994640	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	acacctgttcctgtggtgatTggaatctgaggctgttgcct	12	9	1	2			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr11:15994640T>A	ENST00000352083.6	-	16	2279	c.2202A>T	c.(2200-2202)ccA>ccT	p.P734P	SOX6_ENST00000316399.6_Silent_p.P714P|SOX6_ENST00000396356.3_Silent_p.P714P|SOX6_ENST00000527619.1_Silent_p.P710P|SOX6_ENST00000528252.1_Silent_p.P707P|SOX6_ENST00000528429.1_Silent_p.P734P			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	734					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						CTGTGGTGATTGGAATCTGAG	0.443																																					p.P747P		Atlas-SNP	.											.	SOX6	149	.	0			c.A2241T						.						77	78	78					11																	15994640		2200	4294	6494	SO:0001819	synonymous_variant	55553	exon16			GGTGATTGGAATC	AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"SRY (sex determining region Y)-boxes"	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.2202A>T	chr11.hg19:g.15994640T>A		196.0	0.0		125.0	60.0	NM_001145819	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Silent	SNP	ENST00000352083.6	hg19																																																																																				.	.		0.443	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326		A	15994640	T	A	15994640	2	1	93	1	0	0	0	0	0	0	0	1	14970	1799	63	4		4	SOX6	11	15994640	Silent	SNP	T	TCGA-DD-A11B-01A-11D-A12Z-10	14898155	15994640	119011876	24	12974										
SSRP1	6749	hgsc.bcm.edu	37	chr11	57100232	57100232	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	agatccgaatgtcataacgaCcacgaggagtcagacactgc	10	11	2	2			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr11:57100232C>T	ENST00000278412.2	-	6	901	c.635G>A	c.(634-636)gGt>gAt	p.G212D		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	212					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(4)	23						GTCATAACGACCACGAGGAGT	0.522																																					p.G212D	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.G635A						.						91	86	88					11																	57100232		2201	4296	6497	SO:0001583	missense	6749	exon6			TAACGACCACGAG	M86737	CCDS7952.1	11q12	2008-02-05			ENSG00000149136	ENSG00000149136			11327	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 80 kDa subunit"	604328				1372440	Standard	NM_003146		Approved	FACT80	uc001njt.3	Q08945	OTTHUMG00000167024	ENST00000278412.2:c.635G>A	chr11.hg19:g.57100232C>T	ENSP00000278412:p.Gly212Asp	129.0	0.0		83.0	41.0	NM_003146	Q5BJG8	Missense_Mutation	SNP	ENST00000278412.2	hg19	CCDS7952.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.031245	0.54790	.	.	ENSG00000149136	ENST00000278412;ENST00000526696;ENST00000529002	T;T;T	0.64260	-0.09;-0.09;-0.09	5.97	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.84406	0.5465	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89005	0.3424	10	0.87932	D	0	-20.1083	16.2813	0.82687	0.1337:0.8663:0.0:0.0	.	212	Q08945	SSRP1_HUMAN	D	212;115;115	ENSP00000278412:G212D;ENSP00000431154:G115D;ENSP00000434546:G115D	ENSP00000278412:G212D	G	-	2	0	SSRP1	56856808	1.000000	0.71417	0.990000	0.47175	0.098000	0.18820	6.738000	0.74822	1.521000	0.48983	0.561000	0.74099	GGT	.	.		0.522	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146		T	57100232	C	T	57100232	3	4	93	1	0	0	0	0	1	0	0	0	15209	507	18	3	1542	3	SSRP1	11	57100232	Missense_Mutation	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10	41105592	57100232	77906284	25	12975										
OVCH1	341350	hgsc.bcm.edu	37	chr12	29597095	29597095	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	taccccatagtagttctgtgAgaatttcttgggatctgcat	9	8	3	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr12:29597095A>G	ENST00000318184.5	-	24	2999	c.3000T>C	c.(2998-3000)tcT>tcC	p.S1000S	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	1000						extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TAGTTCTGTGAGAATTTCTTG	0.408																																					p.S1000S		Atlas-SNP	.											.	OVCH1	195	.	0			c.T3000C						.						200	199	199					12																	29597095		1828	4086	5914	SO:0001819	synonymous_variant	341350	exon24			TCTGTGAGAATTT	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.3000T>C	chr12.hg19:g.29597095A>G		123.0	0.0		73.0	25.0	NM_183378		Silent	SNP	ENST00000318184.5	hg19																																																																																				.	.		0.408	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		G	29597095	A	G	29597095	2	3	93	1	0	0	0	0	0	0	0	1	11332	291	11	2		2	OVCH1	12	29597095	Silent	SNP	A	TCGA-DD-A11B-01A-11D-A12Z-10		29597095	104254800	26	12976										
KIF21A	55605	hgsc.bcm.edu	37	chr12	39688230	39688230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ctatcttcattcatgtttaaTtactggcaatatcttccccc	3	12	4	0			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr12:39688230T>C	ENST00000361418.5	-	38	5036	c.5021A>G	c.(5020-5022)aAt>aGt	p.N1674S	KIF21A_ENST00000544797.2_Missense_Mutation_p.N1637S|KIF21A_ENST00000395670.3_Missense_Mutation_p.N1675S|KIF21A_ENST00000361961.3_Missense_Mutation_p.N1661S|KIF21A_ENST00000541463.2_Missense_Mutation_p.N1621S			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1674					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				TCATGTTTAATTACTGGCAAT	0.373																																					p.N1674S		Atlas-SNP	.											.	KIF21A	238	.	0			c.A5021G						.						127	115	119					12																	39688230		2203	4300	6503	SO:0001583	missense	55605	exon38			GTTTAATTACTGG	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.5021A>G	chr12.hg19:g.39688230T>C	ENSP00000354878:p.Asn1674Ser	319.0	1.0		104.0	36.0	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	hg19	CCDS53776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.69|11.69	1.713169|1.713169	0.30413|0.30413	.|.	.|.	ENSG00000139116|ENSG00000139116	ENST00000552961|ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463	.|T;T;T;T;T;T	.|0.70516	.|-0.47;-0.41;0.4;-0.49;-0.36;-0.48	5.13|5.13	1.5|1.5	0.22942|0.22942	.|.	.|0.122003	.|0.36134	.|N	.|0.002765	T|T	0.72479|0.72479	0.3465|0.3465	L|L	0.34521|0.34521	1.04|1.04	0.30499|0.30499	N|N	0.770573|0.770573	.|D;B;D;D;D;D	.|0.76494	.|0.974;0.005;0.997;0.974;0.99;0.999	.|D;B;D;D;D;D	.|0.77557	.|0.953;0.007;0.97;0.969;0.979;0.99	T|T	0.69847|0.69847	-0.5034|-0.5034	5|10	.|0.54805	.|T	.|0.06	.|.	9.0609|9.0609	0.36433|0.36433	0.0:0.211:0.0:0.789|0.0:0.211:0.0:0.789	.|.	.|1637;1621;1674;1661;1627;661	.|F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2;Q7Z4S6-3;F5H0V8	.|.;.;KI21A_HUMAN;.;.;.	V|S	975|1661;1675;1627;661;655;1637;1674;1621	.|ENSP00000354851:N1661S;ENSP00000379029:N1675S;ENSP00000448792:N655S;ENSP00000445606:N1637S;ENSP00000354878:N1674S;ENSP00000438075:N1621S	.|ENSP00000344501:N1627S	I|N	-|-	1|2	0|0	KIF21A|KIF21A	37974497|37974497	1.000000|1.000000	0.71417|0.71417	0.956000|0.956000	0.39512|0.39512	0.305000|0.305000	0.27757|0.27757	0.602000|0.602000	0.24134|0.24134	0.014000|0.014000	0.14944|0.14944	-0.280000|-0.280000	0.10049|0.10049	ATT|AAT	.	.		0.373	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		C	39688230	T	C	39688230	3	2	93	1	0	0	0	0	1	0	0	0	8297	1493	52	2	7	2	KIF21A	12	39688230	Missense_Mutation	SNP	T	TCGA-DD-A11B-01A-11D-A12Z-10	10091135	39688230	94163665	27	12977										
MORN3	283385	hgsc.bcm.edu	37	chr12	122097220	122097220	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ttccagtccccctcatagatGgctcctttcttcttccagac	5	16	3	2			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr12:122097220G>A	ENST00000355329.3	-	2	350	c.180C>T	c.(178-180)gcC>gcT	p.A60A		NM_173855.4	NP_776254.3	Q6PF18	MORN3_HUMAN	MORN repeat containing 3	60						nucleus (GO:0005634)				breast(2)|large_intestine(1)|lung(4)|skin(1)|stomach(1)	9	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000409)|Epithelial(86;0.00145)		CCTCATAGATGGCTCCTTTCT	0.592																																					p.A60A		Atlas-SNP	.											.	MORN3	20	.	0			c.C180T						.						137	108	118					12																	122097220		2203	4300	6503	SO:0001819	synonymous_variant	283385	exon2			ATAGATGGCTCCT	BC057760	CCDS31917.1	12q24.31	2006-01-17			ENSG00000139714	ENSG00000139714			29807	protein-coding gene	gene with protein product							Standard	NM_173855		Approved		uc001uax.3	Q6PF18	OTTHUMG00000169075	ENST00000355329.3:c.180C>T	chr12.hg19:g.122097220G>A		210.0	0.0		94.0	33.0	NM_173855	Q86YQ9	Silent	SNP	ENST00000355329.3	hg19	CCDS31917.1																																																																																			.	.		0.592	MORN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402154.1	NM_173855		A	122097220	G	A	122097220	2	1	93	1	0	0	0	0	0	0	0	1	9718	1335	47	3		3	MORN3	12	122097220	Silent	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10	82408990	122097220	11754675	28	12978										
TSC22D1	8848	hgsc.bcm.edu	37	chr13	45147977	45147977	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	aaggtggaacctgggtagagGgctgctgcactgcagtaggt	17	7	0	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr13:45147977G>A	ENST00000458659.2	-	1	2724	c.2234C>T	c.(2233-2235)cCc>cTc	p.P745L	TSC22D1_ENST00000501704.2_Intron|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	745	Gln-rich.				negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		CTGGGTAGAGGGCTGCTGCAC	0.522																																					p.P745L		Atlas-SNP	.											.	TSC22D1	88	.	0			c.C2234T						.						58	60	59					13																	45147977		2203	4300	6503	SO:0001583	missense	8848	exon1			GTAGAGGGCTGCT	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"transforming growth factor beta 1 induced transcript 4"	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.2234C>T	chr13.hg19:g.45147977G>A	ENSP00000397435:p.Pro745Leu	120.0	0.0		88.0	34.0	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	hg19	CCDS31966.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.811732	0.32053	.	.	ENSG00000102804	ENST00000458659	T	0.36520	1.25	4.77	3.92	0.45320	.	0.515734	0.17667	N	0.166110	T	0.26011	0.0634	L	0.27053	0.805	0.80722	D	1	B	0.27823	0.19	B	0.24006	0.05	T	0.05699	-1.0869	10	0.44086	T	0.13	.	12.1484	0.54036	0.0828:0.0:0.9172:0.0	.	745	Q15714	T22D1_HUMAN	L	745	ENSP00000397435:P745L	ENSP00000397435:P745L	P	-	2	0	TSC22D1	44045977	0.984000	0.35163	0.868000	0.34077	0.849000	0.48306	1.812000	0.38952	1.226000	0.43582	0.462000	0.41574	CCC	.	.		0.522	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		A	45147977	G	A	45147977	3	1	93	1	0	0	0	0	1	0	0	0	16622	1232	43	3	1128	3	TSC22D1	13	45147977	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10		45147977	70021901	29	12979										
C14orf145	145508	hgsc.bcm.edu	37	chr14	80971304	80971304	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	aggaagcgactgtgatcctgCcaagaggatgagtgatctaa	13	7	1	4			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr14:80971304C>A	ENST00000555265.1	-	24	3507	c.3132G>T	c.(3130-3132)tgG>tgT	p.W1044C	CEP128_ENST00000281129.3_Missense_Mutation_p.W1044C|CEP128_ENST00000553717.1_5'UTR			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	1044						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TGTGATCCTGCCAAGAGGATG	0.403																																					p.W1044C		Atlas-SNP	.											.	CEP128	146	.	0			c.G3132T						.						69	67	67					14																	80971304		2203	4300	6503	SO:0001583	missense	145508	exon23			ATCCTGCCAAGAG	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.3132G>T	chr14.hg19:g.80971304C>A	ENSP00000451162:p.Trp1044Cys	78.0	0.0		23.0	7.0	NM_152446	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	hg19	CCDS32130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.352|4.352	0.064812|0.064812	0.08388|0.08388	.|.	.|.	ENSG00000100629|ENSG00000100629	ENST00000556061|ENST00000281129;ENST00000555265	.|T;T	.|0.33216	.|1.42;1.42	5.32|5.32	4.42|4.42	0.53409|0.53409	.|.	.|0.500009	.|0.18843	.|N	.|0.129630	T|T	0.18383|0.18383	0.0441|0.0441	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	D|D	1|1	.|B	.|0.16802	.|0.019	.|B	.|0.16289	.|0.015	T|T	0.04216|0.04216	-1.0968|-1.0968	5|10	.|0.35671	.|T	.|0.21	.|.	12.1086|12.1086	0.53825|0.53825	0.0:0.8287:0.1713:0.0|0.0:0.8287:0.1713:0.0	.|.	.|1044	.|Q6ZU80	.|CE128_HUMAN	S|C	110|1044	.|ENSP00000281129:W1044C;ENSP00000451162:W1044C	.|ENSP00000281129:W1044C	A|W	-|-	1|3	0|0	CEP128|CEP128	80041057|80041057	1.000000|1.000000	0.71417|0.71417	0.964000|0.964000	0.40570|0.40570	0.066000|0.066000	0.16364|0.16364	1.978000|1.978000	0.40598|0.40598	1.440000|1.440000	0.47531|0.47531	0.650000|0.650000	0.86243|0.86243	GCA|TGG	.	.		0.403	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		A	80971304	C	A	80971304	3	1	93	1	0	0	0	0	1	0	0	0	1751	740	26	3	160	3	C14orf145	14	80971304	Missense_Mutation	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10		80971304	26378236	30	12980										
AXIN1	8312	hgsc.bcm.edu	37	chr16	348180	348180	+	Frame_Shift_Del	DEL	G	G	-													0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ggcgggaagtggtgccaagcGggggcgggaggcagcttgtg							TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr16:348180delG	ENST00000262320.3	-	6	1697	c.1326delC	c.(1324-1326)cccfs	p.P442fs	AXIN1_ENST00000481769.1_5'UTR|AXIN1_ENST00000354866.3_Frame_Shift_Del_p.P442fs	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	442	Interaction with CTNNB1. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GGTGCCAAGCGGGGGCGGGAG	0.667											OREG0003699	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.A443fs		Atlas-INDEL	.											.,1	AXIN1	290	.	0			c.1327delG						.																																			SO:0001589	frameshift_variant	8312	exon6			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1326delC	chr16.hg19:g.348180delG	ENSP00000262320:p.Pro442fs	54.0	0.0	587	11.0	10.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Del	DEL	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.667	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			-	348180	G	-	348180	7	5	93	1	0	1	0	1	0	0	0	0	1236	1103	39	0	1286	0	AXIN1	16	348180	Frame_Shift_Del	DEL	G	TCGA-DD-A11B-01A-11D-A12Z-10		348180	90006573	31	12981										
SALL1	6299	hgsc.bcm.edu	37	chr16	51171120	51171120	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ttttctccaggccggccaggGgagcattgggctctgagttc	14	11	2	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr16:51171120G>A	ENST00000251020.4	-	3	3911	c.3878C>T	c.(3877-3879)cCc>cTc	p.P1293L	SALL1_ENST00000566102.1_3'UTR|SALL1_ENST00000440970.1_Missense_Mutation_p.P1196L|SALL1_ENST00000541611.1_Missense_Mutation_p.P116L	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1293					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GCCGGCCAGGGGAGCATTGGG	0.577																																					p.P1293L	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C3878T						.						73	69	70					16																	51171120		2198	4300	6498	SO:0001583	missense	6299	exon3			GCCAGGGGAGCAT	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3878C>T	chr16.hg19:g.51171120G>A	ENSP00000251020:p.Pro1293Leu	180.0	0.0		44.0	29.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.617114	0.46736	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559;ENST00000541611	T;T;T	0.50813	0.73;0.73;0.73	5.8	5.8	0.92144	.	0.050430	0.85682	D	0.000000	T	0.51075	0.1653	L	0.43923	1.385	0.80722	D	1	B;P	0.40180	0.006;0.705	B;B	0.44044	0.006;0.439	T	0.49293	-0.8955	10	0.54805	T	0.06	.	20.0486	0.97617	0.0:0.0:1.0:0.0	.	1293;116	Q9NSC2;F5H733	SALL1_HUMAN;.	L	1293;1196;1257;116	ENSP00000251020:P1293L;ENSP00000407914:P1196L;ENSP00000442827:P116L	ENSP00000251020:P1293L	P	-	2	0	SALL1	49728621	1.000000	0.71417	0.918000	0.36340	0.896000	0.52359	8.040000	0.89188	2.752000	0.94435	0.643000	0.83706	CCC	.	.		0.577	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51171120	G	A	51171120	3	1	93	1	0	0	0	0	1	0	0	0	13825	1232	43	3	100	3	SALL1	16	51171120	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10	50822940	51171120	39183633	32	12982										
MIS12	79003	hgsc.bcm.edu	37	chr17	5392627	5392627	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tagaagagcaaaaaattgttCaggccaaactcaaacagacg	8	8	2	3			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr17:5392627C>T	ENST00000381165.3	+	3	998	c.445C>T	c.(445-447)Cag>Tag	p.Q149*	DERL2_ENST00000571968.1_5'Flank|MIS12_ENST00000573759.1_Nonsense_Mutation_p.Q149*	NM_001258217.1|NM_001258219.1|NM_001258220.1|NM_024039.2	NP_001245146.1|NP_001245148.1|NP_001245149.1|NP_076944.1			MIS12 kinetochore complex component											central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(2)	12						AAAAATTGTTCAGGCCAAACT	0.398																																					p.Q149X		Atlas-SNP	.											.	MIS12	19	.	0			c.C445T						.						164	160	161					17																	5392627		2203	4300	6503	SO:0001587	stop_gained	79003	exon2			ATTGTTCAGGCCA	AL136906	CCDS11074.1	17p13.3	2013-07-03	2013-07-03		ENSG00000167842	ENSG00000167842			24967	protein-coding gene	gene with protein product		609178	"MIS12, MIND kinetochore complex component, homolog (yeast)", "MIS12, MIND kinetochore complex component, homolog (S. pombe)"			11230166, 12515822	Standard	NM_001258217		Approved	MGC2488, hMIS12, KNTC2AP, MTW1	uc031qyj.1	Q9H081	OTTHUMG00000102042	ENST00000381165.3:c.445C>T	chr17.hg19:g.5392627C>T	ENSP00000370557:p.Gln149*	202.0	0.0		102.0	9.0	NM_001258220		Nonsense_Mutation	SNP	ENST00000381165.3	hg19	CCDS11074.1	.	.	.	.	.	.	.	.	.	.	C	36	5.656557	0.96724	.	.	ENSG00000167842	ENST00000381165	.	.	.	5.81	1.25	0.21368	.	0.275260	0.42172	D	0.000743	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-13.354	10.14	0.42730	0.3616:0.4154:0.223:0.0	.	.	.	.	X	149	.	ENSP00000370557:Q149X	Q	+	1	0	MIS12	5333351	0.930000	0.31532	0.990000	0.47175	0.998000	0.95712	1.487000	0.35540	0.022000	0.15160	0.591000	0.81541	CAG	.	.		0.398	MIS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219827.1	NM_024039		T	5392627	C	T	5392627	4	4	93	1	0	0	0	0	0	1	0	0	9603	827	29	3	447	3	MIS12	17	5392627	Nonsense_Mutation	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10		5392627	75802583	33	12983										
SREBF1	6720	hgsc.bcm.edu	37	chr17	17719328	17719328	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	aggcaggcctggcgggcactGctcaggaagaagcgctgtag	17	10	1	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr17:17719328G>A	ENST00000261646.5	-	12	2413	c.2229C>T	c.(2227-2229)agC>agT	p.S743S	SREBF1_ENST00000355815.4_Silent_p.S773S|SREBF1_ENST00000395757.1_Silent_p.S489S|MIR33B_ENST00000385104.1_RNA|SREBF1_ENST00000338854.5_Silent_p.S743S	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	743					aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						GGCGGGCACTGCTCAGGAAGA	0.677																																					p.S773S		Atlas-SNP	.											.	SREBF1	47	.	0			c.C2319T						.						40	43	42					17																	17719328		2203	4299	6502	SO:0001819	synonymous_variant	6720	exon13			GGCACTGCTCAGG	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"Basic helix-loop-helix proteins"	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.2229C>T	chr17.hg19:g.17719328G>A		130.0	0.0		57.0	21.0	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Silent	SNP	ENST00000261646.5	hg19	CCDS11189.1	.	.	.	.	.	.	.	.	.	.	G	9.624	1.134561	0.21123	.	.	ENSG00000072310	ENST00000395751	.	.	.	5.2	-3.49	0.04724	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-22.0331	12.1669	0.54135	0.4434:0.0:0.5566:0.0	.	.	.	.	X	751	.	.	Q	-	1	0	SREBF1	17660053	1.000000	0.71417	0.575000	0.28536	0.858000	0.48976	0.886000	0.28241	-0.495000	0.06659	-0.291000	0.09656	CAG	.	.		0.677	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		A	17719328	G	A	17719328	2	1	93	1	0	0	0	0	0	0	0	1	15156	1310	46	3		3	SREBF1	17	17719328	Silent	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10	12326701	17719328	63475882	34	12984										
VEZF1	7716	hgsc.bcm.edu	37	chr17	56052168	56052168	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ctgtgactgggtttgacataGtcccagacgacacagaggat	12	9	0	4			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr17:56052168G>C	ENST00000581208.1	-	6	1272	c.1232C>G	c.(1231-1233)aCt>aGt	p.T411S	VEZF1_ENST00000584396.1_Missense_Mutation_p.T402S	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	411	4 X 7 AA repeats of P-[LV]-T-[IL]-T-[ST]- P.				angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						GTTTGACATAGTCCCAGACGA	0.468																																					p.T411S		Atlas-SNP	.											.	VEZF1	50	.	0			c.C1232G						.						161	157	158					17																	56052168		2203	4300	6503	SO:0001583	missense	7716	exon6			GACATAGTCCCAG	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"Zinc fingers, C2H2-type"	12949	protein-coding gene	gene with protein product		606747	"zinc finger protein 161"	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.1232C>G	chr17.hg19:g.56052168G>C	ENSP00000462337:p.Thr411Ser	333.0	0.0		177.0	74.0	NM_007146		Missense_Mutation	SNP	ENST00000581208.1	hg19	CCDS32687.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.883171	0.51908	.	.	ENSG00000136451	ENST00000258963	.	.	.	6.06	6.06	0.98353	.	0.433958	0.28688	N	0.014477	T	0.39279	0.1072	N	0.14661	0.345	0.58432	D	0.999995	P	0.38827	0.649	B	0.33042	0.157	T	0.38265	-0.9669	9	0.54805	T	0.06	-9.2383	20.6208	0.99490	0.0:0.0:1.0:0.0	.	411	Q14119	VEZF1_HUMAN	S	411	.	ENSP00000258963:T411S	T	-	2	0	VEZF1	53407167	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	6.946000	0.75953	2.882000	0.98803	0.655000	0.94253	ACT	.	.		0.468	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1			C	56052168	G	C	56052168	3	2	93	1	0	0	0	0	1	0	0	0	17170	1029	36	4	337	4	VEZF1	17	56052168	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10	38332840	56052168	25143042	35	12985										
CLTC	1213	hgsc.bcm.edu	37	chr17	57738828	57738828	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ttcttcgtactccagacactAtccgtcggttccagagtgtc	8	13	1	2			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr17:57738828A>G	ENST00000269122.3	+	8	1466	c.1192A>G	c.(1192-1194)Atc>Gtc	p.I398V	CLTC_ENST00000579456.1_Intron|CLTC_ENST00000393043.1_Missense_Mutation_p.I398V	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	398	Globular terminal domain.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TCCAGACACTATCCGTCGGTT	0.448			T	"ALK, TFE3"	"ALCL, renal "																																p.I398V		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.A1192G						.						133	121	125					17																	57738828		2203	4300	6503	SO:0001583	missense	1213	exon8			GACACTATCCGTC	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.1192A>G	chr17.hg19:g.57738828A>G	ENSP00000269122:p.Ile398Val	150.0	0.0		83.0	32.0	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.907204	0.52333	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.51817	0.69;0.69	5.78	5.78	0.91487	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58366	0.2117	M	0.73598	2.24	0.80722	D	1	B;B	0.17038	0.0;0.02	B;B	0.37550	0.004;0.253	T	0.56798	-0.7919	10	0.40728	T	0.16	-20.971	16.1215	0.81361	1.0:0.0:0.0:0.0	.	398;398	Q00610;Q00610-2	CLH1_HUMAN;.	V	398	ENSP00000269122:I398V;ENSP00000376763:I398V	ENSP00000269122:I398V	I	+	1	0	CLTC	55093610	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	9.339000	0.96797	2.208000	0.71279	0.528000	0.53228	ATC	.	.		0.448	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		G	57738828	A	G	57738828	3	3	93	1	0	0	0	0	1	0	0	0	3568	449	16	2	1222	2	CLTC	17	57738828	Missense_Mutation	SNP	A	TCGA-DD-A11B-01A-11D-A12Z-10	1686660	57738828	23456382	36	12986										
CCDC40	55036	hgsc.bcm.edu	37	chr17	78011929	78011929	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	tctctaaaaccaggtcccatCcggaagatggatcggcttct	9	12	2	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr17:78011929C>T	ENST00000397545.4	+	2	64	c.37C>T	c.(37-39)Ccg>Tcg	p.P13S	CCDC40_ENST00000374876.4_Missense_Mutation_p.P13S|CCDC40_ENST00000374877.3_Missense_Mutation_p.P13S|CCDC40_ENST00000269318.5_Missense_Mutation_p.P13S|TBC1D16_ENST00000310924.2_5'Flank	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	13					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			CAGGTCCCATCCGGAAGATGG	0.418																																					p.P13S		Atlas-SNP	.											.	CCDC40	198	.	0			c.C37T						.						60	60	60					17																	78011929		1831	4080	5911	SO:0001583	missense	55036	exon2			TCCCATCCGGAAG	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.37C>T	chr17.hg19:g.78011929C>T	ENSP00000380679:p.Pro13Ser	110.0	0.0		73.0	35.0	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Missense_Mutation	SNP	ENST00000397545.4	hg19	CCDS42395.1	.	.	.	.	.	.	.	.	.	.	C	7.950	0.744705	0.15710	.	.	ENSG00000141519	ENST00000374877;ENST00000269318;ENST00000374876;ENST00000397545	T;T;T;T	0.48201	0.84;0.82;0.84;0.89	3.11	2.14	0.27477	.	.	.	.	.	T	0.33118	0.0852	N	0.14661	0.345	0.09310	N	0.999999	D;B	0.54964	0.969;0.421	P;B	0.50314	0.637;0.055	T	0.09465	-1.0673	9	0.16420	T	0.52	-2.15	6.248	0.20830	0.0:0.8614:0.0:0.1386	.	13;13	Q4G0X9-5;Q4G0X9	.;CCD40_HUMAN	S	13	ENSP00000364011:P13S;ENSP00000269318:P13S;ENSP00000364010:P13S;ENSP00000380679:P13S	ENSP00000269318:P13S	P	+	1	0	CCDC40	75626524	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.401000	0.20948	0.878000	0.35920	0.563000	0.77884	CCG	.	.		0.418	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		T	78011929	C	T	78011929	3	4	93	1	0	0	0	0	1	0	0	0	2814	855	30	3	43	3	CCDC40	17	78011929	Missense_Mutation	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10	20273101	78011929	3183281	37	12987										
STK11	6794	hgsc.bcm.edu	37	chr19	1221320	1221320	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ccgggcgactgtggccccccGctctctgacctgctgaaagg	13	16	1	2			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr19:1221320G>A	ENST00000326873.7	+	6	2016	c.843G>A	c.(841-843)ccG>ccA	p.P281P		NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	281	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> L (in ovarian carcinoma; somatic mutation). {ECO:0000269|PubMed:10429654}.		activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.L282fs*3(3)|p.?(2)|p.Y246fs*3(1)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGGCCCCCCGCTCTCTGACC	0.617		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																											p.P281P		Atlas-SNP	.	yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	.	STK11	410	.	26	Whole gene deletion(20)|Insertion - Frameshift(3)|Unknown(2)|Deletion - Frameshift(1)	cervix(14)|lung(8)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.G843A	GRCh37	CD982962	STK11	D		.						32	35	34					19																	1221320		1919	4103	6022	SO:0001819	synonymous_variant	6794	exon6	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	CCCCCCGCTCTCT	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"polarization-related protein LKB1"	602216	"serine/threonine kinase 11 (Peutz-Jeghers syndrome)"			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.843G>A	chr19.hg19:g.1221320G>A		41.0	0.0		43.0	16.0	NM_000455	B2RBX7|E7EW76	Silent	SNP	ENST00000326873.7	hg19	CCDS45896.1																																																																																			.	.		0.617	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		A	1221320	G	A	1221320	2	1	93	1	0	0	0	0	0	0	0	1	15302	1074	38	1		1	STK11	19	1221320	Silent	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10		1221320	57907663	38	12988										
C3	718	hgsc.bcm.edu	37	chr19	6682236	6682236	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	agtggcatcctggtctccccGgtacctggatagtgcagaaa	12	11	1	1	rs148227405		TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr19:6682236G>C	ENST00000245907.6	-	34	4269	c.4177C>G	c.(4177-4179)Cgg>Ggg	p.R1393G	C3_ENST00000599668.1_5'Flank	NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1393					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGGTCTCCCCGGTACCTGGAT	0.532																																					p.R1393G		Atlas-SNP	.											.	C3	192	.	0			c.C4177G						.						70	64	66					19																	6682236		2203	4300	6503	SO:0001583	missense	718	exon34			CTCCCCGGTACCT	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.4177C>G	chr19.hg19:g.6682236G>C	ENSP00000245907:p.Arg1393Gly	133.0	0.0		55.0	20.0	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.745870	0.30955	.	.	ENSG00000125730	ENST00000245907	T	0.30182	1.54	5.78	4.74	0.60224	Alpha-macroglobulin, receptor-binding (2);	0.654672	0.16237	N	0.223340	T	0.26159	0.0638	L	0.40543	1.245	0.23238	N	0.998061	B	0.30563	0.285	B	0.30716	0.119	T	0.13124	-1.0521	10	0.22109	T	0.4	.	12.8817	0.58020	0.0807:0.0:0.9193:0.0	.	1393	P01024	CO3_HUMAN	G	1393	ENSP00000245907:R1393G	ENSP00000245907:R1393G	R	-	1	2	C3	6633236	0.998000	0.40836	1.000000	0.80357	0.540000	0.34992	2.010000	0.40913	1.407000	0.46875	0.586000	0.80456	CGG	.	G|1.000;A|0.000		0.532	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		C	6682236	G	C	6682236	3	2	93	1	0	0	0	0	1	0	0	0	2206	1115	39	4	846	4	C3	19	6682236	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10	5460916	6682236	52446747	39	12989										
RGL3	57139	hgsc.bcm.edu	37	chr19	11517408	11517408	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ggatcctcaccaagtctatgAgggtcagctgctcggccacc	11	14	3	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr19:11517408A>T	ENST00000380456.3	-	6	833	c.770T>A	c.(769-771)cTc>cAc	p.L257H	RGL3_ENST00000393423.3_Missense_Mutation_p.L257H|Y_RNA_ENST00000365487.1_RNA	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	257	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						CAAGTCTATGAGGGTCAGCTG	0.632																																					p.L257H	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.T770A						.						43	36	38					19																	11517408		2203	4300	6503	SO:0001583	missense	57139	exon6			TCTATGAGGGTCA	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.770T>A	chr19.hg19:g.11517408A>T	ENSP00000369823:p.Leu257His	61.0	0.0		30.0	18.0	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	hg19	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	A	14.30	2.493475	0.44352	.	.	ENSG00000205517	ENST00000342684;ENST00000393423;ENST00000380456	T;T	0.38240	1.15;1.15	4.25	4.25	0.50352	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.200500	0.32769	N	0.005679	T	0.66587	0.2804	M	0.92691	3.335	0.31238	N	0.695552	P;D;P;D	0.89917	0.948;1.0;0.948;1.0	P;D;P;D	0.80764	0.805;0.994;0.805;0.987	T	0.75671	-0.3237	10	0.87932	D	0	.	12.4652	0.55753	1.0:0.0:0.0:0.0	.	257;257;257;54	Q3MIN7;B5ME84;B7ZL22;Q8TEP0	RGL3_HUMAN;.;.;.	H	54;257;257	ENSP00000377075:L257H;ENSP00000369823:L257H	ENSP00000344665:L54H	L	-	2	0	RGL3	11378408	0.001000	0.12720	0.355000	0.25773	0.407000	0.30961	1.302000	0.33459	1.775000	0.52247	0.482000	0.46254	CTC	.	.		0.632	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867		T	11517408	A	T	11517408	3	4	93	1	0	0	0	0	1	0	0	0	13293	304	11	4	1436	4	RGL3	19	11517408	Missense_Mutation	SNP	A	TCGA-DD-A11B-01A-11D-A12Z-10	4835172	11517408	47611575	40	12990										
MAST1	22983	hgsc.bcm.edu	37	chr19	12975699	12975699	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	cgcatgtactttgctgagacGgtgctagccctggagtattt	12	9	0	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr19:12975699G>T	ENST00000251472.4	+	13	1482	c.1443G>T	c.(1441-1443)acG>acT	p.T481T		NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1											NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						TTGCTGAGACGGTGCTAGCCC	0.582																																					p.T481T		Atlas-SNP	.											.	MAST1	214	.	0			c.G1443T						.						145	129	135					19																	12975699		2203	4300	6503	SO:0001819	synonymous_variant	22983	exon13			TGAGACGGTGCTA	AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.1443G>T	chr19.hg19:g.12975699G>T		182.0	0.0		54.0	26.0	NM_014975		Silent	SNP	ENST00000251472.4	hg19	CCDS32921.1																																																																																			.	.		0.582	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975		T	12975699	G	T	12975699	2	4	93	1	0	0	0	0	0	0	0	1	9333	1103	39	1		1	MAST1	19	12975699	Silent	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10	1458291	12975699	46153284	41	12991										
BRD4	23476	hgsc.bcm.edu	37	chr19	15350762	15350762	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ttgctggggtggagactggtGggtcaggctctggaactgtg	19	6	2	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr19:15350762G>A	ENST00000263377.2	-	15	3462	c.3241C>T	c.(3241-3243)Cac>Tac	p.H1081Y		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1081	C-terminal (CTD) region.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			GGAGACTGGTGGGTCAGGCTC	0.602			T	C15orf55	lethal midline carcinoma of young people																																p.H1081Y		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.C3241T						.						75	72	73					19																	15350762		2203	4300	6503	SO:0001583	missense	23476	exon15			ACTGGTGGGTCAG	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.3241C>T	chr19.hg19:g.15350762G>A	ENSP00000263377:p.His1081Tyr	129.0	0.0		96.0	43.0	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	hg19	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.131823	0.37630	.	.	ENSG00000141867	ENST00000263377	T	0.34859	1.34	4.62	3.58	0.41010	.	0.254840	0.27917	N	0.017340	T	0.31888	0.0811	L	0.46157	1.445	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14117	-1.0484	10	0.72032	D	0.01	-9.0751	11.4752	0.50293	0.0904:0.0:0.9096:0.0	.	1081	O60885	BRD4_HUMAN	Y	1081	ENSP00000263377:H1081Y	ENSP00000263377:H1081Y	H	-	1	0	BRD4	15211762	1.000000	0.71417	0.997000	0.53966	0.970000	0.65996	9.066000	0.93949	0.915000	0.36847	0.561000	0.74099	CAC	.	.		0.602	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		A	15350762	G	A	15350762	3	1	93	1	0	0	0	0	1	0	0	0	1506	1348	47	3	871	3	BRD4	19	15350762	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10	2375063	15350762	43778221	42	12992										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22364225	22364225	+	Frame_Shift_Del	DEL	A	A	-													0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	aaactctggttaagtttattAtaaccttctttgtgcacgtt							TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr19:22364225delA	ENST00000397121.2	-	3	611	c.294delT	c.(292-294)tatfs	p.Y98fs		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	98					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TAAGTTTATTATAACCTTCTT	0.308																																					p.N99fs		Atlas-Indel,Pindel	.											.	ZNF676	146	.	0			c.295delA						.						134	123	127					19																	22364225		1976	4181	6157	SO:0001589	frameshift_variant	163223	exon3			.	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.294delT	chr19.hg19:g.22364225delA	ENSP00000380310:p.Tyr98fs	565.0	0.0		167.0	78.0	NM_001001411	A8MVX5	Frame_Shift_Del	DEL	ENST00000397121.2	hg19	CCDS42539.1																																																																																			.	.		0.308	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		-	22364225	A	-	22364225	7	5	93	1	0	1	0	1	0	0	0	0	18098	456	16	0	1476	0	ZNF676	19	22364225	Frame_Shift_Del	DEL	A	TCGA-DD-A11B-01A-11D-A12Z-10	7013463	22364225	36764758	43	12993										
KIAA0355	9710	hgsc.bcm.edu	37	chr19	34791642	34791642	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	aagtatctggatgccctgaaCgtcttctgccgtgccagtac	10	12	3	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr19:34791642C>T	ENST00000299505.6	+	2	1137	c.264C>T	c.(262-264)aaC>aaT	p.N88N		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	88										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					ATGCCCTGAACGTCTTCTGCC	0.557																																					p.N88N		Atlas-SNP	.											.	KIAA0355	105	.	0			c.C264T						.						77	66	70					19																	34791642		2203	4300	6503	SO:0001819	synonymous_variant	9710	exon2			CCTGAACGTCTTC		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.264C>T	chr19.hg19:g.34791642C>T		148.0	0.0		72.0	5.0	NM_014686	Q2M3W4	Silent	SNP	ENST00000299505.6	hg19	CCDS12436.1																																																																																			.	.		0.557	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686		T	34791642	C	T	34791642	2	4	93	1	0	0	0	0	0	0	0	1	8179	535	19	1		1	KIAA0355	19	34791642	Silent	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10	12427417	34791642	24337341	44	12994										
ZNF302	55900	hgsc.bcm.edu	37	chr19	35174079	35174079	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ggtctttccgtaactaagccAtatgtgatcatgttattgga	9	7	2	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr19:35174079A>G	ENST00000446502.2	+	5	490	c.282A>G	c.(280-282)ccA>ccG	p.P94P	ZNF302_ENST00000457781.2_Silent_p.P50P|ZNF302_ENST00000423823.2_Silent_p.P50P|ZNF302_ENST00000505242.1_Silent_p.P50P|ZNF302_ENST00000505365.2_Silent_p.P50P|ZNF302_ENST00000509528.1_Intron|ZNF302_ENST00000507959.1_Silent_p.P51P			Q9NR11	ZN302_HUMAN	zinc finger protein 302	50					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TAACTAAGCCATATGTGATCA	0.413																																					p.P50P		Atlas-SNP	.											.	ZNF302	27	.	0			c.A150G						.						120	118	119					19																	35174079		2203	4300	6503	SO:0001819	synonymous_variant	55900	exon4			TAAGCCATATGTG	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"Zinc fingers, C2H2-type", "-"	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.282A>G	chr19.hg19:g.35174079A>G		175.0	0.0		108.0	44.0	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Silent	SNP	ENST00000446502.2	hg19																																																																																				.	.		0.413	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1			G	35174079	A	G	35174079	2	3	93	1	0	0	0	0	0	0	0	1	17847	204	8	2		2	ZNF302	19	35174079	Silent	SNP	A	TCGA-DD-A11B-01A-11D-A12Z-10	382437	35174079	23954904	45	12995										
MLL4	9757	hgsc.bcm.edu	37	chr19	36211168	36211168	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ggctcccctttgtgatcaagTttgtttcaagggccaaaaaa	9	9	2	1	rs540162147		TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr19:36211168T>C	ENST00000222270.7	+	3	919	c.919T>C	c.(919-921)Ttt>Ctt	p.F307L	KMT2B_ENST00000420124.1_Missense_Mutation_p.F307L|KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000341701.1_Missense_Mutation_p.F307L	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	307					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TGTGATCAAGTTTGTTTCAAG	0.577													T|||	1	0.000199681	0	0	5008	,	,		14313	0		0	False		,,,				2504	0.001				p.F307L		Atlas-SNP	.											.	MLL4	229	.	0			c.T919C						.						18	22	21					19																	36211168		1951	4133	6084	SO:0001583	missense	8085	exon3			ATCAAGTTTGTTT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.919T>C	chr19.hg19:g.36211168T>C	ENSP00000222270:p.Phe307Leu	72.0	0.0		66.0	27.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	T	11.06	1.527193	0.27299	.	.	ENSG00000105663	ENST00000222270;ENST00000420124;ENST00000341701	D;D;T	0.87887	-2.31;-2.31;0.14	4.17	3.14	0.36123	.	0.205285	0.24098	U	0.041575	T	0.74801	0.3764	N	0.14661	0.345	0.30078	N	0.809429	B	0.13594	0.008	B	0.11329	0.006	T	0.69176	-0.5214	10	0.87932	D	0	.	7.5273	0.27662	0.0:0.0:0.2195:0.7805	.	307	Q9UMN6	MLL4_HUMAN	L	307	ENSP00000222270:F307L;ENSP00000398837:F307L;ENSP00000345761:F307L	ENSP00000222270:F307L	F	+	1	0	AD000671.1	40903008	1.000000	0.71417	1.000000	0.80357	0.082000	0.17680	2.446000	0.44908	0.611000	0.30052	-0.648000	0.03929	TTT	.	.		0.577	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		C	36211168	T	C	36211168	3	2	93	1	0	0	0	0	1	0	0	0	9632	1725	60	2	929	2	MLL4	19	36211168	Missense_Mutation	SNP	T	TCGA-DD-A11B-01A-11D-A12Z-10	1037089	36211168	22917815	46	12996										
KLHDC7B	113730	hgsc.bcm.edu	37	chr22	50987578	50987578	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	cctgcatgtgttcaacccccGggagaacacctggcggcccc	11	17	1	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chr22:50987578G>A	ENST00000395676.2	+	1	1117	c.983G>A	c.(982-984)cGg>cAg	p.R328Q	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	328										central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	14		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TTCAACCCCCGGGAGAACACC	0.716																																					p.R328Q		Atlas-SNP	.											.	KLHDC7B	39	.	0			c.G983A						.						36	46	43					22																	50987578		2057	4105	6162	SO:0001583	missense	113730	exon1			ACCCCCGGGAGAA	BC009980	CCDS14097.2	22q13.33	2006-11-29		2005-12-13	ENSG00000130487	ENSG00000130487			25145	protein-coding gene	gene with protein product							Standard	NM_138433		Approved	MGC16635	uc003bmi.3	Q96G42	OTTHUMG00000150250	ENST00000395676.2:c.983G>A	chr22.hg19:g.50987578G>A	ENSP00000379034:p.Arg328Gln	8.0	0.0		24.0	7.0	NM_138433		Missense_Mutation	SNP	ENST00000395676.2	hg19	CCDS14097.2	.	.	.	.	.	.	.	.	.	.	G	13.33	2.203681	0.38905	.	.	ENSG00000130487	ENST00000395676	T	0.66280	-0.2	4.99	-4.36	0.03645	Kelch-type beta propeller (1);	2.202390	0.02891	N	0.134118	T	0.30103	0.0754	N	0.01576	-0.805	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.33523	-0.9865	10	0.09843	T	0.71	.	9.116	0.36758	0.3541:0.1209:0.5249:0.0	.	328	Q96G42	KLD7B_HUMAN	Q	328	ENSP00000379034:R328Q	ENSP00000379034:R328Q	R	+	2	0	KLHDC7B	49334444	0.000000	0.05858	0.006000	0.13384	0.646000	0.38490	-1.269000	0.02834	-0.685000	0.05177	-0.683000	0.03753	CGG	.	.		0.716	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433		A	50987578	G	A	50987578	3	1	93	1	0	0	0	0	1	0	0	0	8370	1116	39	1	985	1	KLHDC7B	22	50987578	Missense_Mutation	SNP	G	TCGA-DD-A11B-01A-11D-A12Z-10		50987578	316988	47	12997										
MTM1	4534	hgsc.bcm.edu	37	chrX	149814213	149814213	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0416666666666667	2	1	0.634029441971927	0	0.729133858267716	0.333333333333333	1	0	ttgtgcgttgcagtcagcctCttgtcggtatgagtgggaaa	14	7	2	1			TCGA-DD-A11B-01A-11D-A12Z-10	TCGA-DD-A11B-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0642c1b7-0644-41ae-b17a-db7e1cffcb72	353422f9-5ae7-40a6-99ef-18d0b2562c39	g.chrX:149814213C>T	ENST00000370396.2	+	9	790	c.736C>T	c.(736-738)Ctt>Ttt	p.L246F	MTM1_ENST00000413012.2_Missense_Mutation_p.L209F|MTM1_ENST00000306167.7_3'UTR|MTM1_ENST00000543350.1_Missense_Mutation_p.L131F|MTM1_ENST00000542741.1_Missense_Mutation_p.L151F	NM_000252.2	NP_000243.1	Q13496	MTM1_HUMAN	myotubularin 1	246	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				endosome to lysosome transport (GO:0008333)|intermediate filament organization (GO:0045109)|mitochondrion distribution (GO:0048311)|mitochondrion morphogenesis (GO:0070584)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|protein transport (GO:0015031)|regulation of vacuole organization (GO:0044088)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	intermediate filament binding (GO:0019215)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Acute lymphoblastic leukemia(192;6.56e-05)					CAGTCAGCCTCTTGTCGGTAT	0.378																																					p.L246F		Atlas-SNP	.											.	MTM1	89	.	0			c.C736T						.						180	153	162					X																	149814213		2203	4300	6503	SO:0001583	missense	4534	exon9			CAGCCTCTTGTCG	U46024	CCDS14694.1	Xq27.3-q28	2014-09-17			ENSG00000171100	ENSG00000171100		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7448	protein-coding gene	gene with protein product		300415	"myotubular myopathy 1"				Standard	NM_000252		Approved		uc004fef.4	Q13496	OTTHUMG00000024158	ENST00000370396.2:c.736C>T	chrX.hg19:g.149814213C>T	ENSP00000359423:p.Leu246Phe	220.0	0.0		119.0	104.0	NM_000252	A6NDB1|B7Z491|F2Z330|Q8NEL1	Missense_Mutation	SNP	ENST00000370396.2	hg19	CCDS14694.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.677584	0.88445	.	.	ENSG00000171100	ENST00000370396;ENST00000542741;ENST00000543350;ENST00000413012	D;D;D;D	0.94457	-3.43;-3.43;-3.43;-3.43	5.93	5.93	0.95920	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.000000	0.85682	D	0.000000	D	0.98137	0.9385	H	0.94183	3.505	0.48087	D	0.999587	D;D	0.59357	0.969;0.985	D;D	0.69142	0.924;0.962	D	0.98900	1.0776	10	0.87932	D	0	.	19.2929	0.94110	0.0:1.0:0.0:0.0	.	209;246	B7Z491;Q13496	.;MTM1_HUMAN	F	246;151;131;209	ENSP00000359423:L246F;ENSP00000444015:L151F;ENSP00000439784:L131F;ENSP00000389157:L209F	ENSP00000359423:L246F	L	+	1	0	MTM1	149564871	0.977000	0.34250	1.000000	0.80357	0.994000	0.84299	2.467000	0.45093	2.508000	0.84585	0.594000	0.82650	CTT	.	.		0.378	MTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060847.3	NM_000252		T	149814213	C	T	149814213	3	4	93	1	0	0	0	0	1	0	0	0	9946	913	32	3	766	3	MTM1	23	149814213	Missense_Mutation	SNP	C	TCGA-DD-A11B-01A-11D-A12Z-10		149814213	5456347	48	12998										
PRAMEF2	65122	hgsc.bcm.edu	37	chr1	12920107	12920107	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tgatcaccttcttcagtgggCacctggaacagctgatcagg	11	11	4	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:12920107C>T	ENST00000240189.2	+	3	934	c.847C>T	c.(847-849)Cac>Tac	p.H283Y		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	283					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTTCAGTGGGCACCTGGAACA	0.463																																					p.H283Y		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.C847T						.						80	81	81					1																	12920107		2202	4294	6496	SO:0001583	missense	65122	exon3			AGTGGGCACCTGG		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"-"	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.847C>T	chr1.hg19:g.12920107C>T	ENSP00000240189:p.His283Tyr	91.0	0.0		58.0	20.0	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	hg19	CCDS149.1	.	.	.	.	.	.	.	.	.	.	C	0.065	-1.214119	0.01555	.	.	ENSG00000120952	ENST00000240189	T	0.00949	5.51	0.833	0.833	0.18875	.	1.018660	0.07819	N	0.959497	T	0.01124	0.0037	L	0.43152	1.355	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	T	0.45659	-0.9246	10	0.39692	T	0.17	.	5.0256	0.14383	0.0:1.0:0.0:0.0	.	283	O60811	PRAM2_HUMAN	Y	283	ENSP00000240189:H283Y	ENSP00000240189:H283Y	H	+	1	0	PRAMEF2	12842694	0.000000	0.05858	0.004000	0.12327	0.007000	0.05969	-0.334000	0.07883	0.753000	0.32945	0.184000	0.17185	CAC	.	.		0.463	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014		T	12920107	C	T	12920107	3	4	94	1	0	0	0	0	1	0	0	0	12447	710	25	3	853	3	PRAMEF2	1	12920107	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10		12920107	236330514	1	12999										
SPEN	23013	hgsc.bcm.edu	37	chr1	16257658	16257658	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ccttccgttgggcctccaagTgtcacagtcgtaactctaga	9	13	2	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:16257658T>G	ENST00000375759.3	+	11	5127	c.4923T>G	c.(4921-4923)agT>agG	p.S1641R		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1641					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GGCCTCCAAGTGTCACAGTCG	0.478																																					p.S1641R		Atlas-SNP	.											.	SPEN	374	.	0			c.T4923G						.						154	165	161					1																	16257658		2203	4300	6503	SO:0001583	missense	23013	exon11			TCCAAGTGTCACA		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.4923T>G	chr1.hg19:g.16257658T>G	ENSP00000364912:p.Ser1641Arg	68.0	0.0		64.0	20.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	T	10.67	1.415399	0.25552	.	.	ENSG00000065526	ENST00000375759	T	0.09538	2.97	5.28	-4.5	0.03493	.	.	.	.	.	T	0.04679	0.0127	N	0.19112	0.55	0.09310	N	1	P	0.34780	0.468	B	0.32864	0.154	T	0.38693	-0.9649	9	0.30854	T	0.27	0.6893	2.3616	0.04308	0.1527:0.3313:0.0862:0.4298	.	1641	Q96T58	MINT_HUMAN	R	1641	ENSP00000364912:S1641R	ENSP00000364912:S1641R	S	+	3	2	SPEN	16130245	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.769000	0.04710	-0.291000	0.09012	0.383000	0.25322	AGT	.	.		0.478	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16257658	T	G	16257658	3	3	94	1	0	0	0	0	1	0	0	0	15053	1693	59	5	4965	5	SPEN	1	16257658	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	3337551	16257658	232992963	2	13000										
PHC2	1912	hgsc.bcm.edu	37	chr1	33799862	33799862	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	atgccggggctgctgaggtcGgtcagtgcatgaacaatgcc	15	10	1	2	rs370099521		TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:33799862G>A	ENST00000257118.5	-	9	1640	c.1587C>T	c.(1585-1587)acC>acT	p.T529T	RN7SKP16_ENST00000410180.1_RNA|MIR3605_ENST00000583214.1_RNA|PHC2_ENST00000485928.1_5'UTR|PHC2_ENST00000373422.3_Silent_p.T135T|PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000419414.2_Silent_p.T530T|PHC2_ENST00000431992.1_Silent_p.T500T|PHC2_ENST00000373418.3_5'UTR	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	529					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				TGCTGAGGTCGGTCAGTGCAT	0.592																																					p.T529T		Atlas-SNP	.											.	PHC2	78	.	0			c.C1587T						.						107	103	105					1																	33799862		2203	4300	6503	SO:0001819	synonymous_variant	1912	exon9			GAGGTCGGTCAGT	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"Sterile alpha motif (SAM) domain containing"	3183	protein-coding gene	gene with protein product		602979	"early development regulator 2 (homolog of polyhomeotic 2)", "polyhomeotic-like 2 (Drosophila)"	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.1587C>T	chr1.hg19:g.33799862G>A		98.0	0.0		108.0	48.0	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Silent	SNP	ENST00000257118.5	hg19	CCDS378.1																																																																																			.	.		0.592	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		A	33799862	G	A	33799862	2	1	94	1	0	0	0	0	0	0	0	1	11826	1103	39	1		1	PHC2	1	33799862	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	17542204	33799862	215450759	3	13001										
WDR65	149465	hgsc.bcm.edu	37	chr1	43649280	43649280	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	aggtgagcttcagtccacagGataacactcaggtgtgtgtc	12	9	2	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:43649280G>C	ENST00000372492.4	+	4	817	c.493G>C	c.(493-495)Gat>Cat	p.D165H	WDR65_ENST00000528956.1_Missense_Mutation_p.D165H	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		165										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CAGTCCACAGGATAACACTCA	0.388																																					p.D165H		Atlas-SNP	.											.	WDR65	76	.	0			c.G493C						.						74	76	75					1																	43649280		2203	4300	6503	SO:0001583	missense	149465	exon4			CCACAGGATAACA																												ENST00000372492.4:c.493G>C	chr1.hg19:g.43649280G>C	ENSP00000361570:p.Asp165His	140.0	0.0		80.0	40.0	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	hg19		.	.	.	.	.	.	.	.	.	.	G	21.3	4.121368	0.77436	.	.	ENSG00000243710	ENST00000372492;ENST00000528956;ENST00000529956	T;T;T	0.32515	4.96;1.45;4.96	5.66	5.66	0.87406	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.051667	0.85682	D	0.000000	T	0.64494	0.2603	M	0.88704	2.975	0.54753	D	0.999988	D;D	0.89917	1.0;1.0	D;D	0.81914	0.994;0.995	T	0.69206	-0.5206	10	0.56958	D	0.05	.	19.7559	0.96291	0.0:0.0:1.0:0.0	.	165;165	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	H	165	ENSP00000361570:D165H;ENSP00000435310:D165H;ENSP00000434133:D165H	ENSP00000361570:D165H	D	+	1	0	WDR65	43421867	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.232000	0.78116	2.656000	0.90262	0.655000	0.94253	GAT	.	.		0.388	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			C	43649280	G	C	43649280	3	2	94	1	0	0	0	0	1	0	0	0	17331	1174	41	4	503	4	WDR65	1	43649280	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	9849418	43649280	205601341	4	13002										
TAL1	6886	hgsc.bcm.edu	37	chr1	47685719	47685719	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cggaggatctcattcttgctGagcttcttgtccgggggatg	14	9	3	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:47685719G>A	ENST00000294339.3	-	4	1245	c.669C>T	c.(667-669)ctC>ctT	p.L223L	TAL1_ENST00000371884.2_Silent_p.L223L|TAL1_ENST00000371883.3_Silent_p.L225L|TAL1_ENST00000459729.1_5'UTR	NM_003189.2	NP_003180.1	P17542	TAL1_HUMAN	T-cell acute lymphocytic leukemia 1	223	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				angiogenesis (GO:0001525)|astrocyte fate commitment (GO:0060018)|basophil differentiation (GO:0030221)|cell fate commitment (GO:0045165)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|hemangioblast cell differentiation (GO:0060217)|hematopoietic stem cell differentiation (GO:0060218)|hemopoiesis (GO:0030097)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|platelet formation (GO:0030220)|positive regulation of cell division (GO:0051781)|positive regulation of chromatin assembly or disassembly (GO:0045799)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell proliferation (GO:0042127)|regulation of mast cell differentiation (GO:0060375)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord association neuron differentiation (GO:0021527)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|E-box binding (GO:0070888)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			haematopoietic_and_lymphoid_tissue(1)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	15						CATTCTTGCTGAGCTTCTTGT	0.592			T	"TRD@, SIL"	lymphoblastic leukemia/biphasic																																p.L223L		Atlas-SNP	.		Dom	yes		1	1p32	6886	T-cell acute lymphocytic leukemia 1 (SCL)		L	.	TAL1	31	.	0			c.C669T						.						64	62	63					1																	47685719		2203	4300	6503	SO:0001819	synonymous_variant	6886	exon4			CTTGCTGAGCTTC	M29038	CCDS547.1	1p32	2013-05-21	2001-12-04		ENSG00000162367	ENSG00000162367		"Basic helix-loop-helix proteins"	11556	protein-coding gene	gene with protein product		187040		TCL5		2740341	Standard	NM_001287347		Approved	SCL, bHLHa17	uc009vyq.2	P17542	OTTHUMG00000007847	ENST00000294339.3:c.669C>T	chr1.hg19:g.47685719G>A		224.0	0.0		178.0	71.0	NM_003189	D3DQ24	Silent	SNP	ENST00000294339.3	hg19	CCDS547.1																																																																																			.	.		0.592	TAL1-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021640.1	NM_003189		A	47685719	G	A	47685719	2	1	94	1	0	0	0	0	0	0	0	1	15556	1277	45	3		3	TAL1	1	47685719	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	4036439	47685719	201564902	5	13003										
GBP2	2634	hgsc.bcm.edu	37	chr1	89573964	89573964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cgaatccctccttgagaaggCgttcctgttcctaaaaggga	10	11	0	1	rs200077424		TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:89573964C>T	ENST00000370466.3	-	11	1938	c.1670G>A	c.(1669-1671)cGc>cAc	p.R557H	GBP2_ENST00000463660.1_5'Flank	NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN	guanylate binding protein 2, interferon-inducible	557					cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R557H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		CTTGAGAAGGCGTTCCTGTTC	0.408																																					p.R557H		Atlas-SNP	.											GBP2,NS,carcinoma,0,1	GBP2	58	.	1	Substitution - Missense(1)	endometrium(1)	c.G1670A						.						122	113	116					1																	89573964		2203	4300	6503	SO:0001583	missense	2634	exon11			AGAAGGCGTTCCT	BC073163	CCDS719.1	1p22.2	2008-02-05			ENSG00000162645	ENSG00000162645			4183	protein-coding gene	gene with protein product		600412				1715024	Standard	NM_004120		Approved		uc001dmz.1	P32456	OTTHUMG00000010662	ENST00000370466.3:c.1670G>A	chr1.hg19:g.89573964C>T	ENSP00000359497:p.Arg557His	74.0	0.0		52.0	20.0	NM_004120	Q6GPH0|Q6IAU2|Q86TB0	Missense_Mutation	SNP	ENST00000370466.3	hg19	CCDS719.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.680795	0.47886	.	.	ENSG00000162645	ENST00000370466	T	0.55760	0.5	4.29	-6.79	0.01715	Guanylate-binding protein, C-terminal (3);	2.631740	0.03031	U	0.152049	T	0.42988	0.1227	M	0.81802	2.56	0.09310	N	1	D	0.55605	0.972	P	0.51355	0.667	T	0.55211	-0.8176	10	0.59425	D	0.04	-10.6503	7.0098	0.24855	0.2258:0.1683:0.0:0.6059	.	557	P32456	GBP2_HUMAN	H	557	ENSP00000359497:R557H	ENSP00000359497:R557H	R	-	2	0	GBP2	89346552	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-6.050000	0.00083	-1.516000	0.01782	-0.152000	0.13540	CGC	.	C|0.999;T|0.001		0.408	GBP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029406.2	NM_004120		T	89573964	C	T	89573964	3	4	94	1	0	0	0	0	1	0	0	0	6282	768	27	1	109	1	GBP2	1	89573964	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	41888245	89573964	159676657	6	13004										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103461593	103461593	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ataggaccttgtggaccaggGggaccctgaaatagatgaat	13	7	0	3			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:103461593G>A	ENST00000370096.3	-	27	2559	c.2247C>T	c.(2245-2247)ccC>ccT	p.P749P	COL11A1_ENST00000512756.1_Silent_p.P633P|COL11A1_ENST00000353414.4_Silent_p.P710P|COL11A1_ENST00000358392.2_Silent_p.P761P	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	749	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GTGGACCAGGGGGACCCTGAA	0.363																																					p.P761P		Atlas-SNP	.											.	COL11A1	972	.	0			c.C2283T						.						40	44	43					1																	103461593		2201	4300	6501	SO:0001819	synonymous_variant	1301	exon27			ACCAGGGGGACCC	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2247C>T	chr1.hg19:g.103461593G>A		88.0	0.0		20.0	16.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.363	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103461593	G	A	103461593	2	1	94	1	0	0	0	0	0	0	0	1	3669	1219	43	3		3	COL11A1	1	103461593	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	13887629	103461593	145789028	7	13005										
ANKRD34A	284615	hgsc.bcm.edu	37	chr1	145474731	145474731	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tcccaggaccaagcgcaaatTggtgagacgccactccatgc	10	14	0	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:145474731T>A	ENST00000323397.4	+	4	2696	c.1403T>A	c.(1402-1404)tTg>tAg	p.L468*	RP11-315I20.1_ENST00000600340.1_RNA|LIX1L_ENST00000369308.3_5'Flank	NM_001039888.2	NP_001034977.1	Q69YU3	AN34A_HUMAN	ankyrin repeat domain 34A	468						cytoplasm (GO:0005737)				endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	20	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AAGCGCAAATTGGTGAGACGC	0.662																																					p.L468X		Atlas-SNP	.											.	ANKRD34A	52	.	0			c.T1403A						.						21	24	23					1																	145474731		2203	4300	6503	SO:0001587	stop_gained	284615	exon4			GCAAATTGGTGAG	AK128050	CCDS72874.1	1q21.1	2013-01-10	2007-11-20	2007-11-20	ENSG00000181039	ENSG00000272031		"Ankyrin repeat domain containing"	27639	protein-coding gene	gene with protein product			"ankyrin repeat domain 34"	ANKRD34			Standard	NM_001039888		Approved		uc001enq.1	Q69YU3	OTTHUMG00000013740	ENST00000323397.4:c.1403T>A	chr1.hg19:g.145474731T>A	ENSP00000314103:p.Leu468*	27.0	0.0		43.0	16.0	NM_001039888	B3KSU3	Nonsense_Mutation	SNP	ENST00000323397.4	hg19	CCDS30829.1	.	.	.	.	.	.	.	.	.	.	T	48	14.271858	0.99787	.	.	ENSG00000181039	ENST00000323397	.	.	.	5.22	5.22	0.72569	.	0.099140	0.31031	N	0.008393	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1908	13.1433	0.59446	0.0:0.0:0.0:1.0	.	.	.	.	X	468	.	ENSP00000314103:L468X	L	+	2	0	ANKRD34A	144186088	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.633000	0.61318	2.190000	0.69967	0.529000	0.55759	TTG	.	.		0.662	ANKRD34A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038512.1			A	145474731	T	A	145474731	4	1	94	1	0	0	0	0	0	1	0	0	662	1821	63	4	1405	4	ANKRD34A	1	145474731	Nonsense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	42013138	145474731	103775890	8	13006										
FLG	2312	hgsc.bcm.edu	37	chr1	152280175	152280175	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ggccacgtgtggactcttggTggctctgctgatggggccca	16	11	2	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:152280175T>C	ENST00000368799.1	-	3	7222	c.7187A>G	c.(7186-7188)cAc>cGc	p.H2396R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2396	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGACTCTTGGTGGCTCTGCTG	0.582									Ichthyosis																												p.H2396R		Atlas-SNP	.											.	FLG	900	.	0			c.A7187G						.						67	71	70					1																	152280175		2202	4279	6481	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCTTGGTGGCTCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7187A>G	chr1.hg19:g.152280175T>C	ENSP00000357789:p.His2396Arg	393.0	1.0		404.0	106.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	T	10.09	1.254229	0.22965	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01629	4.72	3.84	-1.46	0.08800	.	.	.	.	.	T	0.00815	0.0027	M	0.78223	2.4	0.09310	N	1	B	0.18741	0.03	B	0.15052	0.012	T	0.41124	-0.9526	9	0.30078	T	0.28	.	3.9105	0.09201	0.0:0.3241:0.1923:0.4836	.	2396	P20930	FILA_HUMAN	R	2396;306	ENSP00000357789:H2396R	ENSP00000271820:H306R	H	-	2	0	FLG	150546799	0.000000	0.05858	0.007000	0.13788	0.038000	0.13279	-0.412000	0.07132	-0.127000	0.11661	0.397000	0.26171	CAC	.	.		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152280175	T	C	152280175	3	2	94	1	0	0	0	0	1	0	0	0	5930	1696	59	2	5002	2	FLG	1	152280175	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	6805444	152280175	96970446	9	13007										
VANGL2	57216	hgsc.bcm.edu	37	chr1	160388869	160388869	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tcccatgatgacctcacacgCatcgccaaggacatggagga	10	13	1	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:160388869C>T	ENST00000368061.2	+	4	744	c.270C>T	c.(268-270)cgC>cgT	p.R90R		NM_020335.2	NP_065068.1	Q9ULK5	VANG2_HUMAN	VANGL planar cell polarity protein 2	90					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|cell migration involved in kidney development (GO:0035787)|cochlea morphogenesis (GO:0090103)|convergent extension involved in axis elongation (GO:0060028)|convergent extension involved in neural plate elongation (GO:0022007)|digestive tract morphogenesis (GO:0048546)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity involved in neural tube closure (GO:0090177)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|glomerulus development (GO:0032835)|hair follicle development (GO:0001942)|heart looping (GO:0001947)|inner ear receptor stereocilium organization (GO:0060122)|kidney morphogenesis (GO:0060993)|lateral sprouting involved in lung morphogenesis (GO:0060490)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in axis elongation (GO:0003402)|planar cell polarity pathway involved in heart morphogenesis (GO:0061346)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|positive regulation of JUN kinase activity (GO:0043507)|post-anal tail morphogenesis (GO:0036342)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Wnt signaling pathway (GO:0030111)|Rho protein signal transduction (GO:0007266)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell pole (GO:0060187)|cell-cell junction (GO:0005911)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)				biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	37	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ACCTCACACGCATCGCCAAGG	0.622																																					p.R90R		Atlas-SNP	.											.	VANGL2	83	.	0			c.C270T						.						117	113	114					1																	160388869		2203	4300	6503	SO:0001819	synonymous_variant	57216	exon4			CACACGCATCGCC	AB033041	CCDS30915.1	1q22-q23	2013-03-05	2013-03-05		ENSG00000162738	ENSG00000162738			15511	protein-coding gene	gene with protein product	"vang, van gogh-like 2", "loop-tail-associated protein", "strabismus"	600533	"vang (van gogh, Drosophila)-like 2, vang, van gogh-like 2 (Drosophila)", "vang-like 2 (van gogh, Drosophila)"			11431695	Standard	NM_020335		Approved	KIAA1215, LTAP, LPP1, STBM, STB1, STBM1, MGC119403, MGC119404	uc001fwc.2	Q9ULK5	OTTHUMG00000033122	ENST00000368061.2:c.270C>T	chr1.hg19:g.160388869C>T		67.0	0.0		115.0	21.0	NM_020335	D3DVE9|Q5T212	Silent	SNP	ENST00000368061.2	hg19	CCDS30915.1																																																																																			.	.		0.622	VANGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080677.1	NM_020335		T	160388869	C	T	160388869	2	4	94	1	0	0	0	0	0	0	0	1	17135	697	25	3		3	VANGL2	1	160388869	Silent	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	8108694	160388869	88861752	10	13008										
FAM20B	9917	hgsc.bcm.edu	37	chr1	179013021	179013021	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gtcgtgctgttagcaattctCcttgtcatttttatcttcac	6	10	4	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:179013021C>T	ENST00000263733.4	+	2	375	c.39C>T	c.(37-39)ctC>ctT	p.L13L		NM_014864.3	NP_055679.1	O75063	XYLK_HUMAN	family with sequence similarity 20, member B	13						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(3)	14						TAGCAATTCTCCTTGTCATTT	0.468																																					p.L13L		Atlas-SNP	.											.	FAM20B	38	.	0			c.C39T						.						99	85	90					1																	179013021		2203	4300	6503	SO:0001819	synonymous_variant	9917	exon2			AATTCTCCTTGTC	AB007944	CCDS1328.1	1q25.2	2013-04-29			ENSG00000116199	ENSG00000116199			23017	protein-coding gene	gene with protein product	"glycosaminoglycan xylosylkinase"	611063				9455484, 19473117	Standard	NM_014864		Approved	KIAA0475, GXK1	uc001gmc.3	O75063	OTTHUMG00000035073	ENST00000263733.4:c.39C>T	chr1.hg19:g.179013021C>T		127.0	0.0		209.0	75.0	NM_014864	Q5W0C3|Q5W0C4	Silent	SNP	ENST00000263733.4	hg19	CCDS1328.1																																																																																			.	.		0.468	FAM20B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084922.1	NM_014864		T	179013021	C	T	179013021	2	4	94	1	0	0	0	0	0	0	0	1	5543	842	30	3		3	FAM20B	1	179013021	Silent	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	18624152	179013021	70237600	11	13009										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200960199	200960199	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cgacacctcagccccagagtCcagcatgggtggctttagtc	11	14	1	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:200960199C>A	ENST00000422435.2	-	18	2849	c.2533G>T	c.(2533-2535)Gac>Tac	p.D845Y	KIF21B_ENST00000461742.2_Missense_Mutation_p.D845Y|KIF21B_ENST00000360529.5_Missense_Mutation_p.D845Y|KIF21B_ENST00000332129.2_Missense_Mutation_p.D845Y	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	845					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						GCCCCAGAGTCCAGCATGGGT	0.617																																					p.D845Y		Atlas-SNP	.											.	KIF21B	208	.	0			c.G2533T						.						69	72	71					1																	200960199		2203	4300	6503	SO:0001583	missense	23046	exon18			CAGAGTCCAGCAT	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.2533G>T	chr1.hg19:g.200960199C>A	ENSP00000411831:p.Asp845Tyr	121.0	0.0		171.0	47.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	hg19	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364284	0.82463	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.72167	-0.28;-0.59;-0.63;-0.32	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.81049	0.4742	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.76494	0.998;0.998;0.998;0.999	P;P;P;D	0.65874	0.87;0.87;0.87;0.939	T	0.81152	-0.1063	9	.	.	.	.	16.9766	0.86315	0.0:1.0:0.0:0.0	.	845;845;845;845	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	Y	845	ENSP00000328494:D845Y;ENSP00000353724:D845Y;ENSP00000433808:D845Y;ENSP00000411831:D845Y	.	D	-	1	0	KIF21B	199226822	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.381000	0.79718	2.305000	0.77605	0.591000	0.81541	GAC	.	.		0.617	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200960199	C	A	200960199	3	1	94	1	0	0	0	0	1	0	0	0	8298	855	30	3	2409	3	KIF21B	1	200960199	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	21947178	200960199	48290422	12	13010										
RBBP5	5929	hgsc.bcm.edu	37	chr1	205084043	205084043	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gtgtgccccacctgttaaagGtgcaagtcaaagccatgctg	11	11	1	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:205084043G>A	ENST00000264515.6	-	3	233	c.92C>T	c.(91-93)aCc>aTc	p.T31I	RBBP5_ENST00000367164.1_Missense_Mutation_p.T31I|RBBP5_ENST00000484379.1_5'UTR	NM_001193273.1|NM_005057.3	NP_001180202.1|NP_005048.2	Q15291	RBBP5_HUMAN	retinoblastoma binding protein 5	31					cellular response to DNA damage stimulus (GO:0006974)|histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	methylated histone binding (GO:0035064)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	27	Breast(84;0.0505)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			CCTGTTAAAGGTGCAAGTCAA	0.408																																					p.T31I		Atlas-SNP	.											.	RBBP5	45	.	0			c.C92T						.						53	48	49					1																	205084043		2203	4298	6501	SO:0001583	missense	5929	exon3			TTAAAGGTGCAAG	BC053856	CCDS30983.1, CCDS53463.1	1q32	2013-01-10	2001-11-28		ENSG00000117222	ENSG00000117222		"WD repeat domain containing"	9888	protein-coding gene	gene with protein product	"SWD1, Set1c WD40 repeat protein, homolog (S. cerevisiae)"	600697	"retinoblastoma-binding protein 5"			7558034	Standard	NM_005057		Approved	RBQ3, SWD1	uc001hbu.2	Q15291	OTTHUMG00000037104	ENST00000264515.6:c.92C>T	chr1.hg19:g.205084043G>A	ENSP00000264515:p.Thr31Ile	192.0	0.0		369.0	120.0	NM_005057	A8K272|Q7Z6D8|Q8NDZ7	Missense_Mutation	SNP	ENST00000264515.6	hg19	CCDS30983.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.226673	0.79576	.	.	ENSG00000117222	ENST00000264515;ENST00000367164	T;T	0.59502	0.26;0.26	5.82	5.82	0.92795	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.64560	0.2609	M	0.64170	1.965	0.80722	D	1	P;B;P	0.43169	0.687;0.397;0.8	P;B;B	0.45232	0.474;0.098;0.248	T	0.67078	-0.5761	10	0.66056	D	0.02	.	19.6939	0.96016	0.0:0.0:1.0:0.0	.	66;31;31	B4DMM7;Q15291-2;Q15291	.;.;RBBP5_HUMAN	I	31	ENSP00000264515:T31I;ENSP00000356132:T31I	ENSP00000264515:T31I	T	-	2	0	RBBP5	203350666	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.735000	0.98825	2.764000	0.94973	0.650000	0.86243	ACC	.	.		0.408	RBBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090077.1	NM_005057		A	205084043	G	A	205084043	3	1	94	1	0	0	0	0	1	0	0	0	13117	1261	44	3	1572	3	RBBP5	1	205084043	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	4123844	205084043	44166578	13	13011										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214557484	214557484	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gctggtggcaggtcgtggccGtgggtaggggggcggtggcc	24	8	0	0	rs200947677		TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:214557484G>A	ENST00000366956.5	-	13	1908	c.1714C>T	c.(1714-1716)Cgg>Tgg	p.R572W	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	572	Poly-Pro.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GGTCGTGGCCGTGGGTAGGGG	0.652																																					p.R572W	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											PTPN14,caecum,carcinoma,0,2	PTPN14	168	.	0			c.C1714T						.	G	TRP/ARG	0,4406		0,0,2203	42	46	45		1714	4.7	0.9	1		45	1,8599	1.2+/-3.3	0,1,4299	no	missense	PTPN14	NM_005401.4	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	572/1188	214557484	1,13005	2203	4300	6503	SO:0001583	missense	5784	exon13			GTGGCCGTGGGTA	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.1714C>T	chr1.hg19:g.214557484G>A	ENSP00000355923:p.Arg572Trp	55.0	0.0		54.0	18.0	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850976	0.71719	0.0	1.16E-4	ENSG00000152104	ENST00000366956	T	0.68765	-0.35	5.61	4.68	0.58851	.	0.194784	0.45606	D	0.000350	T	0.72162	0.3426	L	0.47716	1.5	0.80722	D	1	D	0.69078	0.997	P	0.56434	0.798	T	0.72200	-0.4362	10	0.38643	T	0.18	.	16.3998	0.83635	0.0:0.0:0.8676:0.1324	.	572	Q15678	PTN14_HUMAN	W	572	ENSP00000355923:R572W	ENSP00000355923:R572W	R	-	1	2	PTPN14	212624107	0.883000	0.30277	0.857000	0.33713	0.992000	0.81027	3.487000	0.53222	1.482000	0.48325	0.650000	0.86243	CGG	.	G|0.999;A|0.001		0.652	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		A	214557484	G	A	214557484	3	1	94	1	0	0	0	0	1	0	0	0	12796	1144	40	1	1877	1	PTPN14	1	214557484	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	9473441	214557484	34693137	14	13012										
ZNF695	57116	hgsc.bcm.edu	37	chr1	247162655	247162655	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ttcactcccacctacctgagTgtctggctgtcttctctgtg	8	14	4	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr1:247162655T>C	ENST00000339986.7	-	3	401	c.254A>G	c.(253-255)cAc>cGc	p.H85R	ZNF695_ENST00000487338.2_Missense_Mutation_p.H85R|ZNF695_ENST00000498046.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	85	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CCTACCTGAGTGTCTGGCTGT	0.483																																					p.H85R		Atlas-SNP	.											.	ZNF695	55	.	0			c.A254G						.						112	115	114					1																	247162655		2037	4235	6272	SO:0001583	missense	57116	exon3			CCTGAGTGTCTGG		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"Zinc fingers, C2H2-type", "-"	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.254A>G	chr1.hg19:g.247162655T>C	ENSP00000341236:p.His85Arg	310.0	0.0		196.0	85.0	NM_001204221	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	hg19	CCDS44344.1	.	.	.	.	.	.	.	.	.	.	T	0.898	-0.723208	0.03158	.	.	ENSG00000197472	ENST00000487338;ENST00000391780;ENST00000339986	T;T	0.05996	5.9;3.36	0.149	0.149	0.14863	Krueppel-associated box (1);	.	.	.	.	T	0.01905	0.0060	N	0.00972	-1.085	0.09310	N	1	P;P;P	0.42735	0.462;0.788;0.667	B;B;B	0.37989	0.227;0.124;0.262	T	0.41662	-0.9496	8	0.45353	T	0.12	.	.	.	.	.	85;73;85	Q8IW36;F2Z2N8;Q8IW36-1	ZN695_HUMAN;.;.	R	85	ENSP00000429736:H85R;ENSP00000341236:H85R	ENSP00000428213:H73R	H	-	2	0	ZNF695	245229278	0.287000	0.24315	0.114000	0.21550	0.115000	0.19883	0.939000	0.28978	0.166000	0.19597	0.164000	0.16699	CAC	.	.		0.483	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394		C	247162655	T	C	247162655	3	2	94	1	0	0	0	0	1	0	0	0	18113	1696	59	2	1301	2	ZNF695	1	247162655	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	32605171	247162655	2087966	15	13013										
OTX1	5013	hgsc.bcm.edu	37	chr2	63282697	63282698	+	Frame_Shift_Del	DEL	AG	AG	-													0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gcagagcgggagcggaaccaAgagccgcccagccaagaaga							TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr2:63282697_63282698delAG	ENST00000282549.2	+	5	587_588	c.311_312delAG	c.(310-312)aagfs	p.K104fs	OTX1_ENST00000366671.3_Frame_Shift_Del_p.K104fs	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	104					anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					AGCGGAACCAAGAGCCGCCCAG	0.649																																					p.104_104del		Atlas-Indel,Pindel	.											.	OTX1	49	.	0			c.310_311del						.																																			SO:0001589	frameshift_variant	5013	exon5			.		CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"Homeoboxes / PRD class"	8521	protein-coding gene	gene with protein product		600036	"orthodenticle (Drosophila) homolog 1", "orthodenticle homolog 1 (Drosophila)"			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.311_312delAG	chr2.hg19:g.63282699_63282700delAG	ENSP00000282549:p.Lys104fs	173.0	0.0		91.0	22.0	NM_014562	A6NHA2|B3KTJ4|Q53TG6	Frame_Shift_Del	DEL	ENST00000282549.2	hg19	CCDS1873.1																																																																																			.	.		0.649	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1			-	63282698	AG	-	63282697	7	5	94	1	0	1	0	1	0	0	0	0	11329	72	3	0	321	0	OTX1	2	63282697	Frame_Shift_Del	DEL	AG	TCGA-DD-A11C-01A-11D-A12Z-10		63282697	179916676	16	13014										
SUCLG1	8802	hgsc.bcm.edu	37	chr2	84660559	84660559	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tgccagatctggacacaatgCcttaacgaaagagaattcaa	8	9	2	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr2:84660559C>T	ENST00000393868.2	-	6	800	c.590G>A	c.(589-591)gGc>gAc	p.G197D	SUCLG1_ENST00000491123.1_5'Flank	NM_003849.3	NP_003840.2	P53597	SUCA_HUMAN	succinate-CoA ligase, alpha subunit	197					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			kidney(4)|large_intestine(4)|lung(2)	10					Succinic acid(DB00139)	GGACACAATGCCTTAACGAAA	0.393																																					p.G197D	Ovarian(48;203 1101 37206 40305 50790)	Atlas-SNP	.											.	SUCLG1	30	.	0			c.G590A						.						70	64	66					2																	84660559		2203	4300	6503	SO:0001630	splice_region_variant	8802	exon6			ACAATGCCTTAAC	Z68204	CCDS1967.2	2p11.3	2008-02-05	2008-01-08		ENSG00000163541	ENSG00000163541	6.2.1.4		11449	protein-coding gene	gene with protein product		611224	"succinate-CoA ligase, GDP-forming, alpha subunit"			9128182	Standard	NM_003849		Approved		uc002son.3	P53597	OTTHUMG00000130023	ENST00000393868.2:c.590-1G>A	chr2.hg19:g.84660559C>T		172.0	0.0		81.0	34.0	NM_003849	Q9BWB0|Q9UNP6	Missense_Mutation	SNP	ENST00000393868.2	hg19	CCDS1967.2	.	.	.	.	.	.	.	.	.	.	C	29.2	4.985575	0.93044	.	.	ENSG00000163541	ENST00000393868	D	0.86030	-2.06	5.83	5.83	0.93111	Succinyl-CoA synthetase-like (2);	0.046728	0.85682	D	0.000000	D	0.96084	0.8724	H	0.99877	4.88	0.80722	D	1	D;D	0.67145	0.991;0.996	P;P	0.62014	0.658;0.897	D	0.97912	1.0309	10	0.87932	D	0	.	17.6146	0.88064	0.0:1.0:0.0:0.0	.	197;197	B7Z438;P53597	.;SUCA_HUMAN	D	197	ENSP00000377446:G197D	ENSP00000377446:G197D	G	-	2	0	SUCLG1	84514070	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	7.818000	0.86416	2.758000	0.94735	0.655000	0.94253	GGC	.	.		0.393	SUCLG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252298.2	NM_003849	Missense_Mutation	T	84660559	C	T	84660559	5	4	94	1	0	0	0	0	0	0	1	0	15379	753	26	3	466	3	SUCLG1	2	84660559	Splice_Site	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	21377862	84660559	158538814	17	13015										
TANC1	85461	hgsc.bcm.edu	37	chr2	160053178	160053178	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cacagtgccctacggggccaCggtgacattctccagtacct	10	15	1	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr2:160053178C>T	ENST00000263635.6	+	18	3276	c.3039C>T	c.(3037-3039)caC>caT	p.H1013H	TANC1_ENST00000454300.1_Silent_p.H907H	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1013					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						TACGGGGCCACGGTGACATTC	0.627																																					p.H1013H		Atlas-SNP	.											.	TANC1	157	.	0			c.C3039T						.						59	64	62					2																	160053178		2103	4204	6307	SO:0001819	synonymous_variant	85461	exon18			GGGCCACGGTGAC	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.3039C>T	chr2.hg19:g.160053178C>T		106.0	0.0		100.0	35.0	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	hg19	CCDS42766.1																																																																																			.	.		0.627	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			T	160053178	C	T	160053178	2	4	94	1	0	0	0	0	0	0	0	1	15559	535	19	1		1	TANC1	2	160053178	Silent	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	75392619	160053178	83146195	18	13016										
PLEKHM3	389072	hgsc.bcm.edu	37	chr2	208865840	208865840	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gcgggccttgaagcaatggcTgctgctgttgctgctgctgc	15	11	0	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr2:208865840T>C	ENST00000427836.2	-	2	1013	c.524A>G	c.(523-525)cAg>cGg	p.Q175R	PLEKHM3_ENST00000457206.1_Missense_Mutation_p.Q175R|PLEKHM3_ENST00000389247.4_Missense_Mutation_p.Q175R	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	175	Poly-Gln.				intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AAGCAATGgctgctgctgttg	0.478																																					p.Q175R		Atlas-SNP	.											.	PLEKHM3	101	.	0			c.A524G						.						26	34	32					2																	208865840		2134	4268	6402	SO:0001583	missense	389072	exon2			AATGGCTGCTGCT	AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385		"Pleckstrin homology (PH) domain containing"	34006	protein-coding gene	gene with protein product	"differentiation associated protein"		"pleckstrin homology domain containing, family M, member 1-like"	PLEKHM1L		19028694	Standard	NM_001080475		Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.524A>G	chr2.hg19:g.208865840T>C	ENSP00000417003:p.Gln175Arg	168.0	0.0		156.0	84.0	NM_001080475	B9EKV2|Q8WW68	Missense_Mutation	SNP	ENST00000427836.2	hg19	CCDS42808.1	.	.	.	.	.	.	.	.	.	.	T	6.520	0.464167	0.12402	.	.	ENSG00000178385	ENST00000427836;ENST00000389247;ENST00000457206	D;D;D	0.82984	-1.65;-1.65;-1.67	4.42	3.29	0.37713	.	0.335412	0.27563	N	0.018819	T	0.60130	0.2245	N	0.08118	0	0.09310	N	0.999994	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.39860	-0.9593	10	0.15952	T	0.53	.	4.9311	0.13917	0.0:0.2102:0.0:0.7898	.	175;175	C9J119;Q6ZWE6	.;PKHM3_HUMAN	R	175	ENSP00000417003:Q175R;ENSP00000373899:Q175R;ENSP00000400150:Q175R	ENSP00000373899:Q175R	Q	-	2	0	PLEKHM3	208574085	0.017000	0.18338	0.986000	0.45419	0.250000	0.25880	0.190000	0.17057	1.960000	0.56953	0.449000	0.29647	CAG	.	.		0.478	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	NM_001080475		C	208865840	T	C	208865840	3	2	94	1	0	0	0	0	1	0	0	0	12091	1580	55	2	1789	2	PLEKHM3	2	208865840	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	48812662	208865840	34333533	19	13017										
USP40	55230	hgsc.bcm.edu	37	chr2	234394614	234394614	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	acctgtgtcctcagcagcacGtcctgggggctgtaccagaa	12	13	1	1	rs369926451		TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr2:234394614G>A	ENST00000427112.2	-	28	3239	c.3204C>T	c.(3202-3204)gaC>gaT	p.D1068D	USP40_ENST00000496298.1_5'UTR|USP40_ENST00000450966.1_Silent_p.D1080D|USP40_ENST00000251722.6_Silent_p.D1068D			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1068					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		TCAGCAGCACGTCCTGGGGGC	0.597																																					p.D1080D		Atlas-SNP	.											.	USP40	174	.	0			c.C3240T						.	G		1,3995		0,1,1997	10	11	11		3240	0.6	0.7	2		11	0,8296		0,0,4148	no	coding-synonymous	USP40	NM_018218.2		0,1,6145	AA,AG,GG		0.0,0.025,0.0081		1080/1248	234394614	1,12291	1998	4148	6146	SO:0001819	synonymous_variant	55230	exon28			CAGCACGTCCTGG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3204C>T	chr2.hg19:g.234394614G>A		22.0	0.0		9.0	9.0	NM_018218	Q6NX38|Q70EL0	Silent	SNP	ENST00000427112.2	hg19	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	G	8.169	0.791253	0.16258	2.5E-4	0.0	ENSG00000085982	ENST00000454354	.	.	.	5.75	0.614	0.17603	.	.	.	.	.	T	0.41442	0.1159	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22034	-1.0228	4	.	.	.	.	0.8175	0.01105	0.2516:0.3156:0.218:0.2148	.	.	.	.	M	36	.	.	T	-	2	0	USP40	234059353	0.002000	0.14202	0.666000	0.29783	0.995000	0.86356	-0.184000	0.09698	-0.176000	0.10707	0.650000	0.86243	ACG	.	.		0.597	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		A	234394614	G	A	234394614	2	1	94	1	0	0	0	0	0	0	0	1	17087	1136	40	1		1	USP40	2	234394614	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	25528774	234394614	8804759	20	13018										
SATB1	6304	hgsc.bcm.edu	37	chr3	18436227	18436227	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ttgaccaattgaggactgatAggtgttgatacgagcccagg	13	7	0	4			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr3:18436227A>T	ENST00000338745.6	-	7	2667	c.933T>A	c.(931-933)ccT>ccA	p.P311P	SATB1_ENST00000417717.2_Silent_p.P311P|SATB1_ENST00000475083.1_5'Flank|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Silent_p.P311P	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	311					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						GAGGACTGATAGGTGTTGATA	0.567																																					p.P311P		Atlas-SNP	.											.	SATB1	96	.	0			c.T933A						.						149	138	142					3																	18436227		2203	4300	6503	SO:0001819	synonymous_variant	6304	exon7			ACTGATAGGTGTT		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.933T>A	chr3.hg19:g.18436227A>T		156.0	0.0		103.0	60.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Silent	SNP	ENST00000338745.6	hg19	CCDS2631.1																																																																																			.	.		0.567	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		T	18436227	A	T	18436227	2	4	94	1	0	0	0	0	0	0	0	1	13868	407	15	4		4	SATB1	3	18436227	Silent	SNP	A	TCGA-DD-A11C-01A-11D-A12Z-10		18436227	179586203	21	13019										
CAMKV	79012	hgsc.bcm.edu	37	chr3	49897070	49897070	+	Frame_Shift_Del	DEL	G	G	-													0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tgacactgccatcagtggctGgggtggcacttccatctgtg							TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr3:49897070delG	ENST00000477224.1	-	11	1665	c.1187delC	c.(1186-1188)ccafs	p.P396fs	CAMKV_ENST00000488336.1_Frame_Shift_Del_p.P365fs|CAMKV_ENST00000498324.1_5'Flank|CAMKV_ENST00000296471.7_Frame_Shift_Del_p.P368fs|CAMKV_ENST00000467248.1_Frame_Shift_Del_p.P321fs|CAMKV_ENST00000463537.1_Frame_Shift_Del_p.Q328fs|CAMKV_ENST00000466940.1_Frame_Shift_Del_p.P322fs			Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	396	Ala-rich.					cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			central_nervous_system(1)|large_intestine(2)|lung(2)|ovary(2)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		ATCAGTGGCTGGGGTGGCACT	0.622																																					p.P396fs		Atlas-INDEL	.											.	CAMKV	84	.	0			c.1188delA						.						103	106	105					3																	49897070		2203	4299	6502	SO:0001589	frameshift_variant	79012	exon11			.	BC017363	CCDS33762.1	3p21.31	2005-03-04			ENSG00000164076	ENSG00000164076			28788	protein-coding gene	gene with protein product		614993				12477932	Standard	XM_005265478		Approved	MGC8407, VACAMKL	uc003cxt.1	Q8NCB2	OTTHUMG00000158288	ENST00000477224.1:c.1187delC	chr3.hg19:g.49897070delG	ENSP00000419195:p.Pro396fs	199.0	0.0		185.0	19.0	NM_024046	A6NFD4|Q6FIB8|Q8NBS8|Q8NC85|Q8NDU4|Q8WTT8|Q9BQC9|Q9H0Q5	Frame_Shift_Del	DEL	ENST00000477224.1	hg19	CCDS33762.1																																																																																			.	.		0.622	CAMKV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350584.4	NM_024046		-	49897070	G	-	49897070	7	5	94	1	0	1	0	1	0	0	0	0	2610	1348	47	0	322	0	CAMKV	3	49897070	Frame_Shift_Del	DEL	G	TCGA-DD-A11C-01A-11D-A12Z-10	31460843	49897070	148125360	22	13020										
RBM6	10180	hgsc.bcm.edu	37	chr3	50095360	50095360	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tatctgcctccttctcgaagGgaagggccaactttccgaag	10	12	2	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr3:50095360G>A	ENST00000266022.4	+	9	2152	c.1893G>A	c.(1891-1893)agG>agA	p.R631R	RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000539992.1_5'UTR|RBM6_ENST00000422955.1_Silent_p.R109R|RBM6_ENST00000443081.1_Silent_p.R499R|RBM6_ENST00000442092.1_Silent_p.R109R	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	631					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		CTTCTCGAAGGGAAGGGCCAA	0.507																																					p.R631R		Atlas-SNP	.											.	RBM6	85	.	0			c.G1893A						.						81	78	79					3																	50095360		2203	4300	6503	SO:0001819	synonymous_variant	10180	exon9			TCGAAGGGAAGGG	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"RNA binding motif (RRM) containing", "G patch domain containing"	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.1893G>A	chr3.hg19:g.50095360G>A		49.0	0.0		52.0	35.0	NM_005777	O60549|O75524|Q86SS3	Silent	SNP	ENST00000266022.4	hg19	CCDS2809.1																																																																																			.	.		0.507	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		A	50095360	G	A	50095360	2	1	94	1	0	0	0	0	0	0	0	1	13159	1223	43	3		3	RBM6	3	50095360	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	198290	50095360	147927070	23	13021										
CISH	1154	hgsc.bcm.edu	37	chr3	50645109	50645109	+	Frame_Shift_Del	DEL	C	C	-													0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tggcaggcagtccacgtcggCcaccagacggttgatgacaa							TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr3:50645109delC	ENST00000348721.3	-	3	886	c.706delG	c.(706-708)gccfs	p.A236fs	CISH_ENST00000443053.2_Frame_Shift_Del_p.A253fs	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein	236	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of signal transduction (GO:0009968)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				breast(2)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		TCCACGTCGGCCACCAGACGG	0.627																																					p.A253fs		Atlas-Indel,Pindel	.											.	CISH	27	.	0			c.758delC						.						72	73	73					3																	50645109		2203	4300	6503	SO:0001589	frameshift_variant	1154	exon4			.	Z77852	CCDS2831.1, CCDS46834.1	3p21.3	2013-02-14			ENSG00000114737	ENSG00000114737		"Suppressors of cytokine signaling", "SH2 domain containing"	1984	protein-coding gene	gene with protein product		602441				9465889, 7796808	Standard	NM_013324		Approved	CIS, G18, CIS-1, SOCS	uc003dax.3	Q9NSE2	OTTHUMG00000156853	ENST00000348721.3:c.706delG	chr3.hg19:g.50645109delC	ENSP00000294173:p.Ala236fs	138.0	0.0		76.0	46.0	NM_013324	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Frame_Shift_Del	DEL	ENST00000348721.3	hg19	CCDS2831.1																																																																																			.	.		0.627	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071		-	50645109	C	-	50645109	7	5	94	1	0	1	0	1	0	0	0	0	3439	739	26	0	74	0	CISH	3	50645109	Frame_Shift_Del	DEL	C	TCGA-DD-A11C-01A-11D-A12Z-10	549749	50645109	147377321	24	13022										
ARHGAP31	57514	hgsc.bcm.edu	37	chr3	119087231	119087231	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tgtttcaggcaagagtttggCtcagatcaatgtccagatct	10	8	4	3			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr3:119087231C>G	ENST00000264245.4	+	3	748	c.216C>G	c.(214-216)ggC>ggG	p.G72G		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	72	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						AAGAGTTTGGCTCAGATCAAT	0.522																																					p.G72G	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.C216G						.						129	122	124					3																	119087231		1967	4160	6127	SO:0001819	synonymous_variant	57514	exon3			GTTTGGCTCAGAT		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.216C>G	chr3.hg19:g.119087231C>G		86.0	0.0		86.0	57.0	NM_020754	Q9ULL6	Silent	SNP	ENST00000264245.4	hg19	CCDS43135.1																																																																																			.	.		0.522	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			G	119087231	C	G	119087231	2	3	94	1	0	0	0	0	0	0	0	1	880	784	28	4		4	ARHGAP31	3	119087231	Silent	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	68442122	119087231	78935199	25	13023										
PAK2	5062	hgsc.bcm.edu	37	chr3	196547330	196547330	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tactggatggcaccagaggtGgttacacggaaagcttatgg	14	7	0	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr3:196547330G>A	ENST00000327134.3	+	13	1564	c.1242G>A	c.(1240-1242)gtG>gtA	p.V414V		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	414	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)	p.V415F(1)|p.V414V(1)		breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		CACCAGAGGTGGTTACACGGA	0.488																																					p.V414V		Atlas-SNP	.											PAK2_ENST00000327134,NS,carcinoma,0,2	PAK2	113	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)	c.G1242A						.						155	130	138					3																	196547330		2203	4300	6503	SO:0001819	synonymous_variant	5062	exon13			AGAGGTGGTTACA	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"S6/H4 kinase"	605022	"p21 (CDKN1A)-activated kinase 2"			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.1242G>A	chr3.hg19:g.196547330G>A		135.0	0.0		146.0	40.0	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	hg19	CCDS3321.1	.	.	.	.	.	.	.	.	.	.	G	9.873	1.199547	0.22121	.	.	ENSG00000180370	ENST00000426668	.	.	.	4.69	3.8	0.43715	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7285	0.46083	0.0739:0.1311:0.795:0.0	.	.	.	.	X	157	.	.	W	+	2	0	PAK2	198031727	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.432000	0.34936	1.303000	0.44873	0.655000	0.94253	TGG	.	.		0.488	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577		A	196547330	G	A	196547330	2	1	94	1	0	0	0	0	0	0	0	1	11410	1335	47	3		3	PAK2	3	196547330	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	77460099	196547330	1475100	26	13024										
GUF1	60558	hgsc.bcm.edu	37	chr4	44697656	44697656	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	aaagctcattcaattggcaaAgccatatgtgaacggctgaa	9	8	2	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr4:44697656A>T	ENST00000281543.5	+	15	1934	c.1740A>T	c.(1738-1740)aaA>aaT	p.K580N	GUF1_ENST00000506793.1_3'UTR|RP11-700J17.1_ENST00000610260.1_RNA	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						CAATTGGCAAAGCCATATGTG	0.358																																					p.K580N		Atlas-SNP	.											.	GUF1	72	.	0			c.A1740T						.						65	67	66					4																	44697656		2203	4300	6503	SO:0001583	missense	60558	exon15			TGGCAAAGCCATA		CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.1740A>T	chr4.hg19:g.44697656A>T	ENSP00000281543:p.Lys580Asn	69.0	0.0		63.0	35.0	NM_021927		Missense_Mutation	SNP	ENST00000281543.5	hg19	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	A	16.10	3.028402	0.54790	.	.	ENSG00000151806	ENST00000281543	T	0.71103	-0.54	5.74	4.58	0.56647	GTP-binding protein LepA, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77498	0.4139	M	0.74389	2.26	0.58432	D	0.999999	D	0.56287	0.975	P	0.56514	0.8	T	0.79801	-0.1650	10	0.87932	D	0	-23.4571	7.8275	0.29324	0.8466:0.0:0.1534:0.0	.	580	Q8N442	GUF1_HUMAN	N	580	ENSP00000281543:K580N	ENSP00000281543:K580N	K	+	3	2	GUF1	44392413	0.998000	0.40836	0.992000	0.48379	0.057000	0.15508	3.069000	0.50026	2.183000	0.69458	0.533000	0.62120	AAA	.	.		0.358	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927		T	44697656	A	T	44697656	3	4	94	1	0	0	0	0	1	0	0	0	6908	69	3	4	1798	4	GUF1	4	44697656	Missense_Mutation	SNP	A	TCGA-DD-A11C-01A-11D-A12Z-10		44697656	146456620	27	13025										
CNGA1	1259	hgsc.bcm.edu	37	chr4	47939598	47939598	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gataatgatgacgatatacaTaacaaggttggaaatcctga	9	5	0	3			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr4:47939598T>C	ENST00000514170.1	-	11	1232	c.913A>G	c.(913-915)Atg>Gtg	p.M305V	CNGA1_ENST00000358519.4_Missense_Mutation_p.M305V|CNGA1_ENST00000544810.1_Missense_Mutation_p.M305V|CNGA1_ENST00000420489.2_Missense_Mutation_p.M305V|CNGA1_ENST00000402813.3_Missense_Mutation_p.M374V			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	305					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						ACGATATACATAACAAGGTTG	0.363																																					p.M374V		Atlas-SNP	.											.	CNGA1	74	.	0			c.A1120G						.						164	158	160					4																	47939598		1872	4104	5976	SO:0001583	missense	1259	exon10			TATACATAACAAG	M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.913A>G	chr4.hg19:g.47939598T>C	ENSP00000426862:p.Met305Val	140.0	0.0		92.0	43.0	NM_001142564	A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Missense_Mutation	SNP	ENST00000514170.1	hg19	CCDS43226.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.738312	0.49045	.	.	ENSG00000198515	ENST00000402813;ENST00000514170;ENST00000544810;ENST00000358519;ENST00000420489	D;D;D;D;D	0.97850	-4.57;-4.57;-4.57;-4.57;-4.57	5.09	5.09	0.68999	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.95037	0.8393	L	0.39566	1.225	0.49582	D	0.999806	B;B	0.18968	0.032;0.032	B;B	0.20577	0.03;0.03	D	0.93042	0.6458	10	0.18276	T	0.48	.	14.9022	0.70687	0.0:0.0:0.0:1.0	.	305;305	Q4W5E3;P29973	.;CNGA1_HUMAN	V	374;305;305;305;305	ENSP00000384264:M374V;ENSP00000426862:M305V;ENSP00000443401:M305V;ENSP00000351320:M305V;ENSP00000389881:M305V	ENSP00000351320:M305V	M	-	1	0	CNGA1	47634355	1.000000	0.71417	0.948000	0.38648	0.862000	0.49288	4.770000	0.62309	1.923000	0.55706	0.533000	0.62120	ATG	.	.		0.363	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2	NM_000087		C	47939598	T	C	47939598	3	2	94	1	0	0	0	0	1	0	0	0	3598	1406	49	2	1163	2	CNGA1	4	47939598	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	3241942	47939598	143214678	28	13026										
AFP	174	hgsc.bcm.edu	37	chr4	74319616	74319616	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	agtctgctttgctgaagaggTacatgcagctcatttcatac	9	9	3	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr4:74319616T>C	ENST00000395792.2	+	13	1885		c.e13+2		AFP_ENST00000506820.1_Splice_Site|AFP_ENST00000226359.2_Splice_Site	NM_001134.1	NP_001125.1	P02771	FETA_HUMAN	alpha-fetoprotein						ovulation from ovarian follicle (GO:0001542)|progesterone metabolic process (GO:0042448)|SMAD protein signal transduction (GO:0060395)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(3)|lung(13)|ovary(1)|skin(1)|urinary_tract(1)	22	Breast(15;0.00102)		Epithelial(6;2.42e-05)|all cancers(17;0.000268)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GCTGAAGAGGTACATGCAGCT	0.388									Alpha-Fetoprotein, Hereditary Persistence of																												.		Atlas-SNP	.											.	AFP	60	.	0			c.1785+2T>C						.						78	73	75					4																	74319616		2203	4300	6503	SO:0001630	splice_region_variant	174	exon13	Familial Cancer Database	HPAFP	AAGAGGTACATGC	V01514	CCDS3556.1	4q13.3	2012-05-16			ENSG00000081051	ENSG00000081051			317	protein-coding gene	gene with protein product		104150		HPAFP			Standard	NM_001134		Approved	FETA	uc003hgz.1	P02771	OTTHUMG00000130011	ENST00000395792.2:c.1785+2T>C	chr4.hg19:g.74319616T>C		184.0	0.0		122.0	9.0	NM_001134	B2RBU3	Splice_Site	SNP	ENST00000395792.2	hg19	CCDS3556.1	.	.	.	.	.	.	.	.	.	.	T	8.418	0.845661	0.16963	.	.	ENSG00000081051	ENST00000395792;ENST00000226359	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6488	0.45636	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	AFP	74538480	0.997000	0.39634	0.907000	0.35723	0.077000	0.17291	2.789000	0.47813	2.011000	0.59026	0.459000	0.35465	.	.	.		0.388	AFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252284.3		Intron	C	74319616	T	C	74319616	5	2	94	1	0	0	0	0	0	0	1	0	363	1652	57	2	1837	2	AFP	4	74319616	Splice_Site	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	26380018	74319616	116834660	29	13027										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183675952	183675952	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tcagtgccccatcctccctgGctgcttctccagatggtaca	8	16	2	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr4:183675952G>C	ENST00000511685.1	+	22	4555	c.4432G>C	c.(4432-4434)Gct>Cct	p.A1478P	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.A1478P			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1478					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										ATCCTCCCTGGCTGCTTCTCC	0.473																																					p.A1478P		Atlas-SNP	.											.	.	.	.	0			c.G4432C						.						82	83	83					4																	183675952		1987	4161	6148	SO:0001583	missense	55714	exon21			TCCCTGGCTGCTT	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.4432G>C	chr4.hg19:g.183675952G>C	ENSP00000424226:p.Ala1478Pro	91.0	0.0		43.0	21.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435939	0.83885	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.92647	-3.08;-3.08	5.16	5.16	0.70880	Six-bladed beta-propeller, TolB-like (1);	.	.	.	.	D	0.94735	0.8301	H	0.95151	3.63	0.80722	D	1	P	0.51791	0.948	B	0.41135	0.348	D	0.96381	0.9281	9	0.87932	D	0	.	18.8456	0.92205	0.0:0.0:1.0:0.0	.	1478	Q9P273	TEN3_HUMAN	P	1478	ENSP00000424226:A1478P;ENSP00000385276:A1478P	ENSP00000385276:A1478P	A	+	1	0	ODZ3	183912946	1.000000	0.71417	0.385000	0.26158	0.926000	0.56050	9.657000	0.98554	2.698000	0.92095	0.563000	0.77884	GCT	.	.		0.473	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			C	183675952	G	C	183675952	3	2	94	1	0	0	0	0	1	0	0	0	10845	1203	42	4	4514	4	ODZ3	4	183675952	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	109356336	183675952	7478324	30	13028										
CMBL	134147	hgsc.bcm.edu	37	chr5	10288612	10288612	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cagaggggtcccaaggctctTgccctacaaagaagtctgga	12	11	2	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr5:10288612T>A	ENST00000296658.3	-	3	665	c.245A>T	c.(244-246)cAa>cTa	p.Q82L	CMBL_ENST00000510532.1_5'UTR	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	82						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						CCAAGGCTCTTGCCCTACAAA	0.448																																					p.Q82L		Atlas-SNP	.											.	CMBL	24	.	0			c.A245T						.						95	90	91					5																	10288612		2203	4300	6503	SO:0001583	missense	134147	exon3			GGCTCTTGCCCTA		CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	"carboxymethylenebutenolidase-like (Pseudomonas)"			3804974, 20177059	Standard	NM_138809		Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.245A>T	chr5.hg19:g.10288612T>A	ENSP00000296658:p.Gln82Leu	57.0	0.0		60.0	16.0	NM_138809	D3DTC7|Q8TED6	Missense_Mutation	SNP	ENST00000296658.3	hg19	CCDS3878.1	.	.	.	.	.	.	.	.	.	.	T	15.75	2.924552	0.52653	.	.	ENSG00000164237	ENST00000296658	T	0.48201	0.82	5.48	4.31	0.51392	Dienelactone hydrolase (1);	0.246359	0.40469	N	0.001094	T	0.42449	0.1203	L	0.54323	1.7	0.43032	D	0.994604	B	0.30563	0.285	B	0.28916	0.096	T	0.37572	-0.9700	10	0.59425	D	0.04	-15.8316	10.4159	0.44322	0.0:0.0778:0.0:0.9222	.	82	Q96DG6	CMBL_HUMAN	L	82	ENSP00000296658:Q82L	ENSP00000296658:Q82L	Q	-	2	0	CMBL	10341612	0.999000	0.42202	0.171000	0.22900	0.899000	0.52679	4.149000	0.58091	0.898000	0.36418	0.459000	0.35465	CAA	.	.		0.448	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253689.1	NM_138809		A	10288612	T	A	10288612	3	1	94	1	0	0	0	0	1	0	0	0	3578	1812	63	4	508	4	CMBL	5	10288612	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10		10288612	170626648	31	13029										
PSD2	84249	hgsc.bcm.edu	37	chr5	139189232	139189232	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gacccagatgtggccttccaTggcctcagccttggcctctc	10	16	2	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr5:139189232T>C	ENST00000274710.3	+	2	412	c.207T>C	c.(205-207)caT>caC	p.H69H		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	69					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCCTTCCATGGCCTCAGCC	0.642																																					p.H69H		Atlas-SNP	.											.	PSD2	88	.	0			c.T207C						.						84	86	85					5																	139189232		2203	4300	6503	SO:0001819	synonymous_variant	84249	exon2			CTTCCATGGCCTC	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.207T>C	chr5.hg19:g.139189232T>C		231.0	0.0		168.0	88.0	NM_032289	D3DQD3|Q8N3J8	Silent	SNP	ENST00000274710.3	hg19	CCDS4216.1																																																																																			.	.		0.642	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		C	139189232	T	C	139189232	2	2	94	1	0	0	0	0	0	0	0	1	12659	1461	51	2		2	PSD2	5	139189232	Silent	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	128900620	139189232	41726028	32	13030										
MRPL22	29093	hgsc.bcm.edu	37	chr5	154346429	154346429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	agagtatattcagcagcttcGcagccggaccatcgttcaca	9	12	2	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr5:154346429G>A	ENST00000523037.1	+	7	634	c.593G>A	c.(592-594)cGc>cAc	p.R198H	MRPL22_ENST00000439747.3_Missense_Mutation_p.R224H|MRPL22_ENST00000265229.8_Missense_Mutation_p.R118H|MRPL22_ENST00000522038.1_Missense_Mutation_p.R204H|MRPL22_ENST00000518364.1_3'UTR	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	198					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CAGCAGCTTCGCAGCCGGACC	0.438																																					p.R198H		Atlas-SNP	.											MRPL22,colon,carcinoma,0,1	MRPL22	18	.	0			c.G593A						.						54	47	50					5																	154346429		2203	4300	6503	SO:0001583	missense	29093	exon7			AGCTTCGCAGCCG	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"Mitochondrial ribosomal proteins / large subunits"	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.593G>A	chr5.hg19:g.154346429G>A	ENSP00000431040:p.Arg198His	49.0	0.0		63.0	33.0	NM_014180	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Missense_Mutation	SNP	ENST00000523037.1	hg19	CCDS4331.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.506467	0.64410	.	.	ENSG00000082515	ENST00000523037;ENST00000265229;ENST00000439747;ENST00000522038	T;T;T;T	0.59772	0.28;0.4;0.24;0.27	5.8	5.8	0.92144	.	0.579484	0.18168	N	0.149546	T	0.74574	0.3734	M	0.79926	2.475	0.58432	D	0.999999	D	0.60575	0.988	P	0.55303	0.773	T	0.75958	-0.3134	10	0.54805	T	0.06	-1.2567	20.0415	0.97592	0.0:0.0:1.0:0.0	.	198	Q9NWU5	RM22_HUMAN	H	198;118;224;204	ENSP00000431040:R198H;ENSP00000265229:R118H;ENSP00000411177:R224H;ENSP00000429039:R204H	ENSP00000265229:R118H	R	+	2	0	MRPL22	154326622	0.996000	0.38824	0.800000	0.32199	0.138000	0.21146	4.728000	0.62000	2.745000	0.94114	0.563000	0.77884	CGC	.	.		0.438	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2			A	154346429	G	A	154346429	3	1	94	1	0	0	0	0	1	0	0	0	9797	1087	38	1	619	1	MRPL22	5	154346429	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	15157197	154346429	26568831	33	13031										
NUP153	9972	hgsc.bcm.edu	37	chr6	17640200	17640200	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cagaatatctagaacacttcCttctttcaggatttctgcag	6	10	4	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr6:17640200C>G	ENST00000262077.2	-	15	1815	c.1816G>C	c.(1816-1818)Gga>Cga	p.G606R	NUP153_ENST00000537253.1_Missense_Mutation_p.G637R	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	606					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			AGAACACTTCCTTCTTTCAGG	0.348																																					p.G606R		Atlas-SNP	.											.	NUP153	116	.	0			c.G1816C						.						107	110	109					6																	17640200		2203	4300	6503	SO:0001583	missense	9972	exon15			CACTTCCTTCTTT	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"nucleoporin 153kD"			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.1816G>C	chr6.hg19:g.17640200C>G	ENSP00000262077:p.Gly606Arg	92.0	0.0		78.0	24.0	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	hg19	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.880581	0.91740	.	.	ENSG00000124789	ENST00000262077;ENST00000537253	T;T	0.40476	1.03;1.03	5.42	5.42	0.78866	Nucleoporin, Nup153-like (1);	0.000000	0.50627	D	0.000107	T	0.62877	0.2464	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.65998	-0.6032	10	0.72032	D	0.01	-3.6872	19.5755	0.95441	0.0:1.0:0.0:0.0	.	637;606	F6QR24;P49790	.;NU153_HUMAN	R	606;637	ENSP00000262077:G606R;ENSP00000444029:G637R	ENSP00000262077:G606R	G	-	1	0	NUP153	17748179	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.774000	0.75012	2.700000	0.92200	0.585000	0.79938	GGA	.	.		0.348	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			G	17640200	C	G	17640200	3	3	94	1	0	0	0	0	1	0	0	0	10764	690	24	4	2643	4	NUP153	6	17640200	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10		17640200	153474867	34	13032										
OR2J3	442186	hgsc.bcm.edu	37	chr6	29080221	29080221	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tcactttttctgtgaagttcCagcacttctgcgattatcgt	7	10	3	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr6:29080221C>A	ENST00000377169.1	+	1	554	c.554C>A	c.(553-555)cCa>cAa	p.P185Q		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	185						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						TGTGAAGTTCCAGCACTTCTG	0.458																																					p.P185Q		Atlas-SNP	.											.	OR2J3	53	.	0			c.C554A						.						103	113	110					6																	29080221		1304	2585	3889	SO:0001583	missense	442186	exon1			AAGTTCCAGCACT		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"GPCR / Class A : Olfactory receptors"	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.554C>A	chr6.hg19:g.29080221C>A	ENSP00000366374:p.Pro185Gln	328.0	0.0		301.0	85.0	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	hg19	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.962058	0.34659	.	.	ENSG00000204701	ENST00000377169	T	0.00211	8.54	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00300	0.0009	M	0.86864	2.845	0.33794	D	0.625804	D	0.63880	0.993	D	0.74023	0.982	T	0.50092	-0.8868	9	0.87932	D	0	.	7.8712	0.29567	0.0:0.8763:0.0:0.1237	.	185	O76001	OR2J3_HUMAN	Q	185	ENSP00000366374:P185Q	ENSP00000366374:P185Q	P	+	2	0	OR2J3	29188200	0.000000	0.05858	0.999000	0.59377	0.286000	0.27126	-0.162000	0.10012	1.549000	0.49425	0.436000	0.28706	CCA	.	.		0.458	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			A	29080221	C	A	29080221	3	1	94	1	0	0	0	0	1	0	0	0	11013	594	21	3	556	3	OR2J3	6	29080221	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	11440021	29080221	142034846	35	13033										
PPP2R5D	5528	hgsc.bcm.edu	37	chr6	42975774	42975774	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ttggggctccgggcttatatCcgtaggcagatcaaccacat	11	11	1	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr6:42975774C>T	ENST00000485511.1	+	7	1007	c.828C>T	c.(826-828)atC>atT	p.I276I	PPP2R5D_ENST00000461010.1_Silent_p.I170I|PPP2R5D_ENST00000472118.1_Silent_p.I268I|PPP2R5D_ENST00000394110.3_Silent_p.I244I	NM_001270476.1|NM_006245.3	NP_001257405.1|NP_006236.1	Q14738	2A5D_HUMAN	protein phosphatase 2, regulatory subunit B', delta	276					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of catalytic activity (GO:0050790)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	25			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			GGGCTTATATCCGTAGGCAGA	0.542																																					p.I276I	Melanoma(63;587 1613 29742 31770)	Atlas-SNP	.											.	PPP2R5D	47	.	0			c.C828T						.						101	100	100					6																	42975774		2203	4300	6503	SO:0001819	synonymous_variant	5528	exon7			TTATATCCGTAGG	L76702	CCDS4878.1, CCDS43464.1, CCDS55002.1	6p21.1	2010-06-18	2010-04-14		ENSG00000112640	ENSG00000112640		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9312	protein-coding gene	gene with protein product		601646	"protein phosphatase 2, regulatory subunit B (B56), delta isoform", "protein phosphatase 2, regulatory subunit B', delta isoform"			7592815	Standard	NM_006245		Approved	B56D	uc003oth.4	Q14738	OTTHUMG00000014716	ENST00000485511.1:c.828C>T	chr6.hg19:g.42975774C>T		109.0	0.0		126.0	70.0	NM_006245	A8K3I9|B5BUA6|O00494|O00696|Q15171|Q5TC39	Silent	SNP	ENST00000485511.1	hg19	CCDS4878.1	.	.	.	.	.	.	.	.	.	.	C	8.759	0.923119	0.18056	.	.	ENSG00000112640	ENST00000470467	.	.	.	5.84	-1.0	0.10196	.	.	.	.	.	T	0.22322	0.0538	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27434	-1.0074	4	.	.	.	-22.2167	0.9127	0.01298	0.3292:0.3139:0.0988:0.2582	.	.	.	.	S	196	.	.	P	+	1	0	PPP2R5D	43083752	0.967000	0.33354	0.994000	0.49952	0.995000	0.86356	0.071000	0.14594	-0.187000	0.10516	-0.302000	0.09304	CCG	.	.		0.542	PPP2R5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040573.3	NM_006245		T	42975774	C	T	42975774	2	4	94	1	0	0	0	0	0	0	0	1	12407	845	30	3		3	PPP2R5D	6	42975774	Silent	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	13895553	42975774	128139293	36	13034										
TRDN	10345	hgsc.bcm.edu	37	chr6	123825006	123825006	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cctttcacttcctttttagtCttttcttcactcttttctgc	2	13	6	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr6:123825006C>A	ENST00000398178.3	-	8	672	c.651G>T	c.(649-651)aaG>aaT	p.K217N	TRDN_ENST00000546248.1_Missense_Mutation_p.K217N|TRDN_ENST00000334268.4_Missense_Mutation_p.K217N	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	217					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		CCTTTTTAGTCTTTTCTTCAC	0.323																																					p.K217N		Atlas-SNP	.											.	TRDN	88	.	0			c.G651T						.						174	149	157					6																	123825006		1828	4081	5909	SO:0001583	missense	10345	exon8			TTTAGTCTTTTCT	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.651G>T	chr6.hg19:g.123825006C>A	ENSP00000381240:p.Lys217Asn	510.0	0.0		248.0	209.0	NM_001256020	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	hg19	CCDS55053.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.81|13.81	2.348001|2.348001	0.41599|0.41599	.|.	.|.	ENSG00000186439|ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268;ENST00000542014;ENST00000543022;ENST00000546248;ENST00000333613|ENST00000361029	T;T;D|.	0.97575|.	-0.09;-0.09;-4.44|.	5.3|5.3	4.43|4.43	0.53597|0.53597	Aspartyl beta-hydroxylase/Triadin domain (1);|.	0.222762|.	0.39834|.	N|.	0.001257|.	T|T	0.54143|0.54143	0.1840|0.1840	M|M	0.75447|0.75447	2.3|2.3	0.58432|0.58432	D|D	0.999998|0.999998	D;D;D;D|.	0.89917|.	0.99;0.999;0.999;1.0|.	P;D;D;D|.	0.72982|.	0.814;0.969;0.969;0.979|.	T|T	0.58278|0.58278	-0.7664|-0.7664	10|5	0.72032|.	D|.	0.01|.	-8.974|-8.974	8.1933|8.1933	0.31381|0.31381	0.0:0.8163:0.0:0.1837|0.0:0.8163:0.0:0.1837	.|.	217;217;217;217|.	F5H2W7;Q5SWK9;Q8IVK2;Q13061|.	.;.;.;TRDN_HUMAN|.	N|I	217;217;217;217;217;217;122|56	ENSP00000381240:K217N;ENSP00000333984:K217N;ENSP00000439281:K217N|.	ENSP00000329278:K122N|.	K|R	-|-	3|2	2|0	TRDN|TRDN	123866705|123866705	0.917000|0.917000	0.31117|0.31117	0.950000|0.950000	0.38849|0.38849	0.930000|0.930000	0.56654|0.56654	1.573000|1.573000	0.36472|0.36472	1.215000|1.215000	0.43411|0.43411	0.467000|0.467000	0.42956|0.42956	AAG|AGA	.	.		0.323	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	123825006	C	A	123825006	3	1	94	1	0	0	0	0	1	0	0	0	16483	912	32	3	1674	3	TRDN	6	123825006	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	80849232	123825006	47290061	37	13035										
RNF216	54476	hgsc.bcm.edu	37	chr7	5662625	5662625	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cggggctgggataggccccaTgttgagtgggaagttgttga	18	6	0	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr7:5662625T>C	ENST00000425013.2	-	17	2691	c.2467A>G	c.(2467-2469)Atg>Gtg	p.M823V	RNF216_ENST00000469375.1_5'UTR|RNF216_ENST00000389902.3_Missense_Mutation_p.M880V	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	823	Pro-rich.				apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		ATAGGCCCCATGTTGAGTGGG	0.632																																					p.M880V		Atlas-SNP	.											.	RNF216	71	.	0			c.A2638G						.						90	94	93					7																	5662625		2203	4300	6503	SO:0001583	missense	54476	exon17			GCCCCATGTTGAG	AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"RING-type (C3HC4) zinc fingers"	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.2467A>G	chr7.hg19:g.5662625T>C	ENSP00000404602:p.Met823Val	115.0	0.0		63.0	17.0	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Missense_Mutation	SNP	ENST00000425013.2	hg19	CCDS34595.1	.	.	.	.	.	.	.	.	.	.	T	7.905	0.735170	0.15574	.	.	ENSG00000011275	ENST00000425013;ENST00000389902;ENST00000458425	T;T	0.41758	0.99;1.0	5.04	0.817	0.18773	.	0.264571	0.41938	D	0.000795	T	0.25975	0.0633	L	0.29908	0.895	0.27953	N	0.937071	B;B	0.12013	0.004;0.005	B;B	0.10450	0.003;0.005	T	0.12578	-1.0542	10	0.42905	T	0.14	-6.3676	6.4203	0.21740	0.3737:0.0:0.1296:0.4967	.	823;880	Q9NWF9;Q9NWF9-1	RN216_HUMAN;.	V	823;880;635	ENSP00000404602:M823V;ENSP00000374552:M880V	ENSP00000374552:M880V	M	-	1	0	RNF216	5629151	1.000000	0.71417	1.000000	0.80357	0.123000	0.20343	1.296000	0.33389	0.292000	0.22492	0.459000	0.35465	ATG	.	.		0.632	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		C	5662625	T	C	5662625	3	2	94	1	0	0	0	0	1	0	0	0	13495	1464	51	2	137	2	RNF216	7	5662625	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10		5662625	153476038	38	13036										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48467402	48467402	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	aagattccaacaagaaatctCacattgccctggggactgag	9	10	1	3	rs547117792		TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr7:48467402C>T	ENST00000435803.1	+	42	12523	c.12499C>T	c.(12499-12501)Cac>Tac	p.H4167Y		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4167					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CAAGAAATCTCACATTGCCCT	0.423																																					p.H4167Y		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C12499T						.						59	56	57					7																	48467402		1866	4123	5989	SO:0001583	missense	154664	exon42			AAATCTCACATTG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.12499C>T	chr7.hg19:g.48467402C>T	ENSP00000411096:p.His4167Tyr	151.0	0.0		106.0	52.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	0.291	-0.979834	0.02197	.	.	ENSG00000179869	ENST00000435803	D	0.86297	-2.1	4.74	0.727	0.18254	.	0.603419	0.14587	N	0.310535	T	0.62441	0.2428	N	0.02011	-0.69	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.53180	-0.8475	10	0.05436	T	0.98	.	8.5673	0.33547	0.0:0.2977:0.5957:0.1066	.	1869;4167	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	Y	4167	ENSP00000411096:H4167Y	ENSP00000411096:H4167Y	H	+	1	0	ABCA13	48437948	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.394000	0.07296	0.017000	0.15025	-0.150000	0.13652	CAC	.	.		0.423	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48467402	C	T	48467402	3	4	94	1	0	0	0	0	1	0	0	0	31	826	29	3	12494	3	ABCA13	7	48467402	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	42804777	48467402	110671261	39	13037										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88966173	88966173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tgccccctacagcatttattCctacattgtttggtcctcac	5	14	1	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr7:88966173C>T	ENST00000333190.4	+	4	4486	c.3877C>T	c.(3877-3879)Cct>Tct	p.P1293S		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1293							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AGCATTTATTCCTACATTGTT	0.453										HNSCC(36;0.09)																											p.P1293S		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C3877T						.						207	191	197					7																	88966173		2203	4300	6503	SO:0001583	missense	219578	exon4			TTTATTCCTACAT	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.3877C>T	chr7.hg19:g.88966173C>T	ENSP00000329638:p.Pro1293Ser	211.0	0.0		127.0	62.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	C	19.17	3.776524	0.70107	.	.	ENSG00000182348	ENST00000333190	T	0.14766	2.48	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000006	T	0.42063	0.1186	M	0.77103	2.36	0.52099	D	0.999945	D	0.89917	1.0	D	0.91635	0.999	T	0.25502	-1.0130	10	0.72032	D	0.01	-15.2313	19.3813	0.94536	0.0:1.0:0.0:0.0	.	1293	A4D1E1	Z804B_HUMAN	S	1293	ENSP00000329638:P1293S	ENSP00000329638:P1293S	P	+	1	0	ZNF804B	88804109	1.000000	0.71417	0.998000	0.56505	0.489000	0.33432	6.985000	0.76193	2.798000	0.96311	0.655000	0.94253	CCT	.	.		0.453	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88966173	C	T	88966173	3	4	94	1	0	0	0	0	1	0	0	0	18186	855	30	3	3891	3	ZNF804B	7	88966173	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	40498771	88966173	70172490	40	13038										
ASNS	440	hgsc.bcm.edu	37	chr7	97481701	97481701	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	aatggcgttcaaagacttgaCggtagtaatatccttctttg	9	7	2	2	rs568570377		TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr7:97481701C>T	ENST00000394309.3	-	13	2027	c.1556G>A	c.(1555-1557)cGt>cAt	p.R519H	ASNS_ENST00000437628.1_Missense_Mutation_p.R436H|ASNS_ENST00000175506.4_Missense_Mutation_p.R519H|ASNS_ENST00000455086.1_Missense_Mutation_p.R436H|ASNS_ENST00000394308.3_Missense_Mutation_p.R519H|ASNS_ENST00000422745.1_Missense_Mutation_p.R498H|ASNS_ENST00000444334.1_Missense_Mutation_p.R498H	NM_133436.3	NP_597680.2	P08243	ASNS_HUMAN	asparagine synthetase (glutamine-hydrolyzing)	519	Asparagine synthetase.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|asparagine biosynthetic process (GO:0006529)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular protein metabolic process (GO:0044267)|cellular response to glucose starvation (GO:0042149)|cellular response to hormone stimulus (GO:0032870)|endoplasmic reticulum unfolded protein response (GO:0030968)|glutamine metabolic process (GO:0006541)|L-asparagine biosynthetic process (GO:0070981)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|positive regulation of mitotic cell cycle (GO:0045931)|response to amino acid (GO:0043200)|response to follicle-stimulating hormone (GO:0032354)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)|ATP binding (GO:0005524)|cofactor binding (GO:0048037)			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	AAAGACTTGACGGTAGTAATA	0.478																																					p.R519H	Melanoma(70;6 1280 3108 3799 51123)|GBM(6;275 291 425 9929 27738)	Atlas-SNP	.											.	ASNS	97	.	0			c.G1556A						.						154	148	150					7																	97481701		2203	4300	6503	SO:0001583	missense	440	exon13			ACTTGACGGTAGT	M27396	CCDS5652.1, CCDS55131.1, CCDS55132.1	7q21.3	2012-10-02	2010-05-07		ENSG00000070669	ENSG00000070669	6.3.5.4		753	protein-coding gene	gene with protein product		108370	"asparagine synthetase"				Standard	NM_001673		Approved		uc003uov.4	P08243	OTTHUMG00000022892	ENST00000394309.3:c.1556G>A	chr7.hg19:g.97481701C>T	ENSP00000377846:p.Arg519His	135.0	0.0		125.0	50.0	NM_133436	A4D1I8|B4DXZ1|B7ZAA9|D6W5R3|E9PCI3|E9PCX6|P08184|Q15666|Q549T9|Q96HD0	Missense_Mutation	SNP	ENST00000394309.3	hg19	CCDS5652.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.039046	0.93630	.	.	ENSG00000070669	ENST00000175506;ENST00000394309;ENST00000437628;ENST00000394308;ENST00000422745;ENST00000455086;ENST00000444334	T;T;T;T;T;T;T	0.53640	0.62;0.62;0.61;0.62;0.63;0.61;0.63	5.23	5.23	0.72850	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.75803	0.3899	M	0.92459	3.31	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.82186	-0.0582	10	0.87932	D	0	-6.9268	16.6738	0.85273	0.0:1.0:0.0:0.0	.	519	P08243	ASNS_HUMAN	H	519;519;436;519;498;436;498	ENSP00000175506:R519H;ENSP00000377846:R519H;ENSP00000414379:R436H;ENSP00000377845:R519H;ENSP00000414901:R498H;ENSP00000408472:R436H;ENSP00000406994:R498H	ENSP00000175506:R519H	R	-	2	0	ASNS	97319637	1.000000	0.71417	0.996000	0.52242	0.975000	0.68041	5.580000	0.67464	2.609000	0.88269	0.561000	0.74099	CGT	.	.		0.478	ASNS-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333645.1	NM_001673, NM_183356		T	97481701	C	T	97481701	3	4	94	1	0	0	0	0	1	0	0	0	1048	536	19	1	133	1	ASNS	7	97481701	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	8515528	97481701	61656962	41	13039										
ALKBH4	54784	hgsc.bcm.edu	37	chr7	102100057	102100057	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cagggccggtctacctgcttCctccgtccagactgggagag	13	14	1	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr7:102100057C>A	ENST00000292566.3	-	2	354	c.315G>T	c.(313-315)agG>agT	p.R105S		NM_017621.3	NP_060091.1	Q9NXW9	ALKB4_HUMAN	alkB, alkylation repair homolog 4 (E. coli)	105					actomyosin structure organization (GO:0031032)|cleavage furrow ingression (GO:0036090)|protein demethylation (GO:0006482)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	contractile ring (GO:0070938)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)	actin binding (GO:0003779)|demethylase activity (GO:0032451)|metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			kidney(1)|lung(5)|skin(2)	8						CTACCTGCTTCCTCCGTCCAG	0.642																																					p.R105S		Atlas-SNP	.											.	ALKBH4	21	.	0			c.G315T						.						94	88	90					7																	102100057		2203	4300	6503	SO:0001583	missense	54784	exon2			CTGCTTCCTCCGT	BC017096	CCDS5723.1	7q22.1	2006-02-09			ENSG00000160993	ENSG00000160993		"Alkylation repair homologs"	21900	protein-coding gene	gene with protein product		613302					Standard	NM_017621		Approved	FLJ20013	uc003uzl.3	Q9NXW9	OTTHUMG00000157720	ENST00000292566.3:c.315G>T	chr7.hg19:g.102100057C>A	ENSP00000292566:p.Arg105Ser	56.0	0.0		29.0	12.0	NM_017621	Q53H92|Q9H6A4	Missense_Mutation	SNP	ENST00000292566.3	hg19	CCDS5723.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.827971	0.50845	.	.	ENSG00000160993	ENST00000292566	T	0.40756	1.02	4.51	2.7	0.31948	.	0.098436	0.64402	D	0.000002	T	0.46889	0.1416	M	0.86740	2.835	0.53688	D	0.999979	P	0.51653	0.947	B	0.41723	0.365	T	0.54057	-0.8350	10	0.72032	D	0.01	-18.5777	9.7796	0.40640	0.0:0.8308:0.0:0.1692	.	105	Q9NXW9	ALKB4_HUMAN	S	105	ENSP00000292566:R105S	ENSP00000292566:R105S	R	-	3	2	ALKBH4	101887062	1.000000	0.71417	0.997000	0.53966	0.721000	0.41392	2.531000	0.45650	0.355000	0.24131	-0.258000	0.10820	AGG	.	.		0.642	ALKBH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349503.1	NM_017621		A	102100057	C	A	102100057	3	1	94	1	0	0	0	0	1	0	0	0	529	854	30	3	601	3	ALKBH4	7	102100057	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	4618356	102100057	57038606	42	13040										
PREX2	80243	hgsc.bcm.edu	37	chr8	69021775	69021775	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ctaaaagaagaagacttagaAacccaagacatctatcagaa	6	8	2	6			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr8:69021775A>T	ENST00000288368.4	+	25	3340	c.3063A>T	c.(3061-3063)gaA>gaT	p.E1021D		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1021					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AAGACTTAGAAACCCAAGACA	0.463																																					p.E1021D		Atlas-SNP	.											.	PREX2	614	.	0			c.A3063T						.						128	125	126					8																	69021775		2203	4300	6503	SO:0001583	missense	80243	exon25			CTTAGAAACCCAA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3063A>T	chr8.hg19:g.69021775A>T	ENSP00000288368:p.Glu1021Asp	93.0	0.0		102.0	29.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.302048	0.60195	.	.	ENSG00000046889	ENST00000288368	T	0.41400	1.0	5.72	4.57	0.56435	.	.	.	.	.	T	0.36468	0.0968	L	0.43923	1.385	0.40182	D	0.977305	B	0.14805	0.011	B	0.18871	0.023	T	0.18840	-1.0324	9	0.62326	D	0.03	.	11.4392	0.50086	0.9299:0.0:0.0701:0.0	.	1021	Q70Z35	PREX2_HUMAN	D	1021	ENSP00000288368:E1021D	ENSP00000288368:E1021D	E	+	3	2	PREX2	69184329	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.397000	0.44477	1.012000	0.39366	0.533000	0.62120	GAA	.	.		0.463	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	69021775	A	T	69021775	3	4	94	1	0	0	0	0	1	0	0	0	12489	11	1	4	3390	4	PREX2	8	69021775	Missense_Mutation	SNP	A	TCGA-DD-A11C-01A-11D-A12Z-10		69021775	77342247	43	13041										
RGS22	26166	hgsc.bcm.edu	37	chr8	101118126	101118126	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ctgtggggccgccacctaccCgcggtgagcctcttctcggg	14	16	2	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr8:101118126C>A	ENST00000360863.6	-	1	218	c.24G>T	c.(22-24)gcG>gcT	p.A8A	RGS22_ENST00000523287.1_5'Flank|RGS22_ENST00000523437.1_Splice_Site_p.A8A	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	8					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			GCCACCTACCCGCGGTGAGCC	0.751																																					p.A8A		Atlas-SNP	.											.	RGS22	319	.	0			c.G24T						.						7	15	12					8																	101118126		1344	2930	4274	SO:0001630	splice_region_variant	26166	exon1			CCTACCCGCGGTG	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.25+1G>T	chr8.hg19:g.101118126C>A		40.0	0.0		60.0	34.0	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Silent	SNP	ENST00000360863.6	hg19	CCDS43758.1																																																																																			.	.		0.751	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668	Silent	A	101118126	C	A	101118126	5	1	94	1	0	0	0	0	0	0	1	0	13320	666	23	1	3878	1	RGS22	8	101118126	Splice_Site	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	32096351	101118126	45245896	44	13042										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5920263	5920263	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tttggattagtagatataagGagaacatggctgccagctcc	11	7	0	2	rs535663249		TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr9:5920263G>T	ENST00000399933.3	-	8	5732	c.5733C>A	c.(5731-5733)ctC>ctA	p.L1911L	KIAA2026_ENST00000381461.2_Silent_p.L1881L	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1911								p.L1086L(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TAGATATAAGGAGAACATGGC	0.443													G|||	1	0.000199681	0	0	5008	,	,		19171	0		0	False		,,,				2504	0.001				p.L1911L		Atlas-SNP	.											KIAA2026,NS,carcinoma,0,1	KIAA2026	231	.	1	Substitution - coding silent(1)	breast(1)	c.C5733A						.						135	135	135					9																	5920263		1888	4109	5997	SO:0001819	synonymous_variant	158358	exon8			TATAAGGAGAACA	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.5733C>A	chr9.hg19:g.5920263G>T		72.0	0.0		53.0	31.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	hg19																																																																																				.	.		0.443	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		T	5920263	G	T	5920263	2	4	94	1	0	0	0	0	0	0	0	1	8279	1161	41	3		3	KIAA2026	9	5920263	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10		5920263	135293168	45	13043										
C5	727	hgsc.bcm.edu	37	chr9	123792742	123792742	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gaaattatattctggctcgaTtgagacagaaaaatgtggca	10	5	1	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr9:123792742T>C	ENST00000223642.1	-	7	720	c.691A>G	c.(691-693)Atc>Gtc	p.I231V		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	231					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	TCTGGCTCGATTGAGACAGAA	0.284																																					p.I231V		Atlas-SNP	.											.	C5	124	.	0			c.A691G						.						18	19	18					9																	123792742		2136	4159	6295	SO:0001583	missense	727	exon7			GCTCGATTGAGAC	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.691A>G	chr9.hg19:g.123792742T>C	ENSP00000223642:p.Ile231Val	389.0	0.0		186.0	88.0	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	hg19	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	T	4.450	0.083274	0.08533	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	T	0.30714	1.52	5.75	1.96	0.26148	.	0.162190	0.56097	N	0.000036	T	0.20170	0.0485	L	0.49699	1.58	0.24121	N	0.995801	P;B	0.40144	0.704;0.001	B;B	0.28638	0.092;0.004	T	0.11251	-1.0595	10	0.45353	T	0.12	.	7.5761	0.27937	0.1082:0.1314:0.0:0.7604	.	302;231	Q59GS8;P01031	.;CO5_HUMAN	V	231;302	ENSP00000223642:I231V	ENSP00000223642:I231V	I	-	1	0	C5	122832563	1.000000	0.71417	0.300000	0.25030	0.314000	0.28054	1.333000	0.33816	0.115000	0.18071	-1.139000	0.01908	ATC	.	.		0.284	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		C	123792742	T	C	123792742	3	2	94	1	0	0	0	0	1	0	0	0	2282	1493	52	2	4479	2	C5	9	123792742	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	117872479	123792742	17420689	46	13044										
CSGALNACT2	55454	hgsc.bcm.edu	37	chr10	43650967	43650967	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ctagtgatcttttagagtttCttcattcccaaattgacaaa	5	8	3	3			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr10:43650967C>T	ENST00000374466.3	+	2	705	c.370C>T	c.(370-372)Ctt>Ttt	p.L124F	CSGALNACT2_ENST00000374464.1_Missense_Mutation_p.L124F	NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	124					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)			endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TTTAGAGTTTCTTCATTCCCA	0.418																																					p.L124F		Atlas-SNP	.											.	CSGALNACT2	67	.	0			c.C370T						.						90	78	82					10																	43650967		2203	4300	6503	SO:0001583	missense	55454	exon2			GAGTTTCTTCATT	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"Beta 4-glycosyltransferases"	24292	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.370C>T	chr10.hg19:g.43650967C>T	ENSP00000363590:p.Leu124Phe	97.0	0.0		66.0	33.0	NM_018590	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Missense_Mutation	SNP	ENST00000374466.3	hg19	CCDS7201.1	.	.	.	.	.	.	.	.	.	.	C	19.93	3.917611	0.73098	.	.	ENSG00000169826	ENST00000374466;ENST00000374464	T;T	0.36520	1.36;1.25	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.61553	0.2356	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.63391	-0.6648	10	0.59425	D	0.04	-18.9168	13.4372	0.61090	0.0:0.9283:0.0:0.0717	.	124;124	Q8N6G5;Q8N6G5-2	CGAT2_HUMAN;.	F	124	ENSP00000363590:L124F;ENSP00000363588:L124F	ENSP00000363588:L124F	L	+	1	0	CSGALNACT2	42970973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.728000	0.54991	2.861000	0.98227	0.650000	0.86243	CTT	.	.		0.418	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		T	43650967	C	T	43650967	3	4	94	1	0	0	0	0	1	0	0	0	3941	913	32	3	372	3	CSGALNACT2	10	43650967	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10		43650967	91883780	47	13045										
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72324191	72324191	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ctgcagtacttggagcgctaTgtctgcctgattctcttcaa	9	11	3	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr10:72324191T>C	ENST00000263563.6	+	19	2602	c.2334T>C	c.(2332-2334)taT>taC	p.Y778Y		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	778						cytosol (GO:0005829)											TGGAGCGCTATGTCTGCCTGA	0.622																																					p.Y778Y		Atlas-SNP	.											.	.	.	.	0			c.T2334C						.						123	118	120					10																	72324191		2203	4300	6503	SO:0001819	synonymous_variant	27143	exon19			GCGCTATGTCTGC	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"paladin", "KIAA1274"	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.2334T>C	chr10.hg19:g.72324191T>C		168.0	0.0		79.0	20.0	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Silent	SNP	ENST00000263563.6	hg19	CCDS31215.1	.	.	.	.	.	.	.	.	.	.	T	1.598	-0.527231	0.04141	.	.	ENSG00000107719	ENST00000426268	.	.	.	5.21	1.26	0.21427	.	.	.	.	.	T	0.57227	0.2039	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49899	-0.8890	4	.	.	.	-24.9332	8.8717	0.35320	0.0:0.6022:0.0:0.3978	.	.	.	.	R	159	.	.	C	+	1	0	KIAA1274	71994197	0.964000	0.33143	0.326000	0.25389	0.187000	0.23431	0.760000	0.26475	0.203000	0.20529	-0.375000	0.07067	TGT	.	.		0.622	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		C	72324191	T	C	72324191	2	2	94	1	0	0	0	0	0	0	0	1	8229	1471	51	2		2	KIAA1274	10	72324191	Silent	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	28673224	72324191	63210556	48	13046										
VCL	7414	hgsc.bcm.edu	37	chr10	75830792	75830792	+	Frame_Shift_Del	DEL	G	G	-													0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tatcttacagtggcagaggtGgtggagactatggaagattt							TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr10:75830792delG	ENST00000211998.4	+	4	544	c.450delG	c.(448-450)gtgfs	p.V151fs	VCL_ENST00000417648.2_Intron|VCL_ENST00000478896.2_Intron|VCL_ENST00000372755.3_Frame_Shift_Del_p.V151fs	NM_014000.2	NP_054706.1	P18206	VINC_HUMAN	vinculin	151	N-terminal globular head.				adherens junction assembly (GO:0034333)|apical junction assembly (GO:0043297)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|epithelial cell-cell adhesion (GO:0090136)|lamellipodium assembly (GO:0030032)|morphogenesis of an epithelium (GO:0002009)|muscle contraction (GO:0006936)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|protein localization to cell surface (GO:0034394)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cell-substrate junction (GO:0030055)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	actin binding (GO:0003779)|alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)		VCL/ALK(4)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Prostate(51;0.0112)					TGGCAGAGGTGGTGGAGACTA	0.358																																					p.V150fs		Atlas-Indel,Pindel	.											.	VCL	77	.	0			c.449delT						.						114	118	116					10																	75830792		2203	4300	6503	SO:0001589	frameshift_variant	7414	exon4			.	M33308	CCDS7340.1, CCDS7341.1	10q22.1-q23	2014-09-17			ENSG00000035403	ENSG00000035403			12665	protein-coding gene	gene with protein product	"metavinculin"	193065				1339348	Standard	NM_014000		Approved		uc001jwd.3	P18206	OTTHUMG00000018498	ENST00000211998.4:c.450delG	chr10.hg19:g.75830792delG	ENSP00000211998:p.Val151fs	201.0	0.0		105.0	61.0	NM_003373	Q16450|Q5SWX2|Q7Z3B8|Q8IXU7	Frame_Shift_Del	DEL	ENST00000211998.4	hg19	CCDS7341.1																																																																																			.	.		0.358	VCL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003373, NM_014000		-	75830792	G	-	75830792	7	5	94	1	0	1	0	1	0	0	0	0	17154	1335	47	0	464	0	VCL	10	75830792	Frame_Shift_Del	DEL	G	TCGA-DD-A11C-01A-11D-A12Z-10	3506601	75830792	59703955	49	13047										
C10orf57	80195	hgsc.bcm.edu	37	chr10	81850592	81850592	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ggtcgggctcagctactctgGttcctacagactttcttctt	9	12	4	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr10:81850592G>C	ENST00000372281.3	+	4	321	c.291G>C	c.(289-291)tgG>tgC	p.W97C	TMEM254_ENST00000372275.1_3'UTR|TMEM254_ENST00000372274.1_3'UTR|TMEM254_ENST00000467529.1_3'UTR	NM_001270372.1|NM_025125.3	NP_001257301.1|NP_079401.2	Q8TBM7	TM254_HUMAN	transmembrane protein 254	97						integral component of membrane (GO:0016021)											AGCTACTCTGGTTCCTACAGA	0.403																																					p.W121C		Atlas-SNP	.											.	TMEM254	1	.	0			c.G363C						.						161	146	151					10																	81850592		2203	4300	6503	SO:0001583	missense	80195	exon4			ACTCTGGTTCCTA	BC022252	CCDS7363.1, CCDS58086.1, CCDS58087.1, CCDS73157.1	10q23.1	2012-11-06	2012-11-06	2012-11-06	ENSG00000133678	ENSG00000133678			25804	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 57"	C10orf57		14702039	Standard	NM_025125		Approved	FLJ13263, bA369J21.6	uc010qlw.3	Q8TBM7	OTTHUMG00000018602	ENST00000372281.3:c.291G>C	chr10.hg19:g.81850592G>C	ENSP00000361355:p.Trp97Cys	186.0	0.0		89.0	31.0	NM_001270367	D3DWC8|Q53HP4|Q5JTC0|Q5JTC1|Q6IA45|Q9H8S6	Missense_Mutation	SNP	ENST00000372281.3	hg19	CCDS7363.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	16.74|16.74|16.74	3.207456|3.207456|3.207456	0.58343|0.58343|0.58343	.|.|.	.|.|.	ENSG00000133678|ENSG00000133678|ENSG00000133678	ENST00000372273|ENST00000450179|ENST00000372281	.|.|.	.|.|.	.|.|.	4.07|4.07|4.07	4.07|4.07|4.07	0.47477|0.47477|0.47477	.|.|.	.|.|0.000000	.|.|0.85682	.|.|D	.|.|0.000000	T|T|T	0.80221|0.80221|0.80221	0.4583|0.4583|0.4583	M|M|M	0.86420|0.86420|0.86420	2.815|2.815|2.815	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D	.|.|0.89917	.|.|1.0;1.0	.|.|D;D	.|.|0.91635	.|.|0.999;0.999	D|D|D	0.83751|0.83751|0.83751	0.0209|0.0209|0.0209	5|5|9	.|.|0.87932	.|.|D	.|.|0	-15.4804|-15.4804|-15.4804	12.4851|12.4851|12.4851	0.55868|0.55868|0.55868	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|.|121;97	.|.|E7ERB9;Q8TBM7	.|.|.;CJ057_HUMAN	A|L|C	118|75|97	.|.|.	.|.|ENSP00000361355:W97C	G|V|W	+|+|+	2|1|3	0|0|0	C10orf57|C10orf57|C10orf57	81840572|81840572|81840572	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.953000|0.953000|0.953000	0.61014|0.61014|0.61014	3.985000|3.985000|3.985000	0.56930|0.56930|0.56930	2.224000|2.224000|2.224000	0.72417|0.72417|0.72417	0.557000|0.557000|0.557000	0.71058|0.71058|0.71058	GGT|GTT|TGG	.	.		0.403	TMEM254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049030.1	NM_025125		C	81850592	G	C	81850592	3	2	94	1	0	0	0	0	1	0	0	0	1611	1270	44	4	305	4	C10orf57	10	81850592	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	6019800	81850592	53684155	50	13048										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105162878	105162878	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cactttttctcttctagtccCtgtgtgagggaatgcgtatt	9	9	2	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr10:105162878C>T	ENST00000369797.3	+	4	332	c.238C>T	c.(238-240)Ctg>Ttg	p.L80L		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	80					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CTTCTAGTCCCTGTGTGAGGG	0.443																																					p.L80L		Atlas-SNP	.											.	PDCD11	160	.	0			c.C238T						.						188	187	187					10																	105162878		2203	4300	6503	SO:0001819	synonymous_variant	22984	exon4			TAGTCCCTGTGTG	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.238C>T	chr10.hg19:g.105162878C>T		348.0	0.0		216.0	59.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	hg19	CCDS31276.1																																																																																			.	.		0.443	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			T	105162878	C	T	105162878	2	4	94	1	0	0	0	0	0	0	0	1	11626	680	24	3		3	PDCD11	10	105162878	Silent	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	23312286	105162878	30371869	51	13049										
CASP7	840	hgsc.bcm.edu	37	chr10	115457351	115457351	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gaccggtcctcgtttgtaccGtccctcttcaggtaagtttg	10	12	2	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr10:115457351G>A	ENST00000345633.4	+	3	483	c.99G>A	c.(97-99)ccG>ccA	p.P33P	CASP7_ENST00000369315.1_Silent_p.P33P|CASP7_ENST00000369321.2_Silent_p.P66P|CASP7_ENST00000369318.3_Silent_p.P33P|CASP7_ENST00000369331.4_Silent_p.P33P	NM_033339.4	NP_203125.1	P55210	CASP7_HUMAN	caspase 7, apoptosis-related cysteine peptidase	33					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway (GO:0097193)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)	8		Colorectal(252;0.0946)|Breast(234;0.188)		Epithelial(162;0.012)|all cancers(201;0.014)		CGTTTGTACCGTCCCTCTTCA	0.547																																					p.R108H		Atlas-SNP	.											.	CASP7	21	.	0			c.G323A						.						178	141	154					10																	115457351		2203	4300	6503	SO:0001819	synonymous_variant	840	exon2			TGTACCGTCCCTC	U37448	CCDS7580.1, CCDS7581.1, CCDS7582.1, CCDS58096.1, CCDS73200.1	10q25	2006-02-17	2005-08-17		ENSG00000165806	ENSG00000165806		"Caspases"	1508	protein-coding gene	gene with protein product		601761	"caspase 7, apoptosis-related cysteine protease"			8521391, 8576161	Standard	NM_033338		Approved	MCH3, CMH-1, ICE-LAP3	uc010qsa.3	P55210	OTTHUMG00000019076	ENST00000345633.4:c.99G>A	chr10.hg19:g.115457351G>A		127.0	0.0		75.0	17.0	NM_001267057	B4DQU7|B5BU45|D3DRB8|Q13364|Q53YD5|Q5SVL0|Q5SVL3|Q96BA0	Missense_Mutation	SNP	ENST00000345633.4	hg19	CCDS7581.1																																																																																			.	.		0.547	CASP7-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050439.1	NM_033338		A	115457351	G	A	115457351	2	1	94	1	0	0	0	0	0	0	0	1	2678	1132	40	1		1	CASP7	10	115457351	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	10294473	115457351	20077396	52	13050										
ZNF214	7761	hgsc.bcm.edu	37	chr11	7021165	7021165	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cccttataatattcacggcaTttgtaaggtttctctcctgc	6	11	2	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr11:7021165T>G	ENST00000278314.4	-	3	2064	c.1749A>C	c.(1747-1749)aaA>aaC	p.K583N	ZNF214_ENST00000536068.1_Missense_Mutation_p.K583N|ZNF214_ENST00000531083.1_5'Flank	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	583					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		ATTCACGGCATTTGTAAGGTT	0.343																																					p.K583N	Ovarian(22;251 657 736 21522 46864)	Atlas-SNP	.											.	ZNF214	65	.	0			c.A1749C						.						75	79	78					11																	7021165		2200	4295	6495	SO:0001583	missense	7761	exon3			ACGGCATTTGTAA	AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"Zinc fingers, C2H2-type", "-"	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.1749A>C	chr11.hg19:g.7021165T>G	ENSP00000278314:p.Lys583Asn	111.0	0.0		66.0	22.0	NM_013249	B2R8Q1	Missense_Mutation	SNP	ENST00000278314.4	hg19	CCDS31418.1	.	.	.	.	.	.	.	.	.	.	T	6.273	0.418459	0.11870	.	.	ENSG00000149050	ENST00000278314;ENST00000536068	T;T	0.61859	0.07;0.07	3.84	2.72	0.32119	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47852	D	0.000208	T	0.54319	0.1851	M	0.61387	1.9	0.09310	N	1	P	0.48016	0.904	P	0.45167	0.472	T	0.51276	-0.8726	10	0.66056	D	0.02	.	7.5285	0.27668	0.0:0.1056:0.0:0.8944	.	583	Q9UL59	ZN214_HUMAN	N	583	ENSP00000278314:K583N;ENSP00000445373:K583N	ENSP00000278314:K583N	K	-	3	2	ZNF214	6977741	0.000000	0.05858	0.323000	0.25347	0.670000	0.39368	-0.570000	0.05895	0.845000	0.35118	0.454000	0.30748	AAA	.	.		0.343	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1			G	7021165	T	G	7021165	3	3	94	1	0	0	0	0	1	0	0	0	17785	1490	52	5	75	5	ZNF214	11	7021165	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10		7021165	127985351	53	13051										
CALCA	796	hgsc.bcm.edu	37	chr11	14990439	14990439	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ttccaggtgctccaaccccaAttgcagtttgggggaacgtg	12	11	0	0	rs377551213		TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr11:14990439A>T	ENST00000486207.1	-	3	236				CALCA_ENST00000359642.3_Missense_Mutation_p.I111N|CALCA_ENST00000396372.2_Missense_Mutation_p.I111N|CALCA_ENST00000361010.3_Intron|CALCB_ENST00000523376.1_Intron|CALCA_ENST00000331587.4_Missense_Mutation_p.I111N			P06881	CALCA_HUMAN	calcitonin-related polypeptide alpha						activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|cytosolic calcium ion homeostasis (GO:0051480)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|G-protein coupled receptor internalization (GO:0002031)|leukocyte cell-cell adhesion (GO:0007159)|negative regulation of blood pressure (GO:0045776)|negative regulation of bone resorption (GO:0045779)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of osteoclast differentiation (GO:0045671)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of vasodilation (GO:0045909)|protein phosphorylation (GO:0006468)|receptor internalization (GO:0031623)|regulation of blood pressure (GO:0008217)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	protein complex binding (GO:0032403)|receptor binding (GO:0005102)			central_nervous_system(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	8						TCCAACCCCAATTGCAGTTTG	0.517																																					p.I111N		Atlas-SNP	.											.	CALCA	30	.	0			c.T332A						.						221	181	195					11																	14990439		2200	4294	6494	SO:0001627	intron_variant	796	exon4			ACCCCAATTGCAG	X00356, M64486	CCDS7819.1, CCDS31432.1	11p15.2	2014-09-17	2008-02-20		ENSG00000110680	ENSG00000110680		"Endogenous ligands"	1437	protein-coding gene	gene with protein product	"calcitonin"	114130	"calcitonin 1"	CALC1		6546550	Standard	NM_001033953		Approved		uc001mlw.1	P01258	OTTHUMG00000159731	ENST00000486207.1:c.228-1039T>A	chr11.hg19:g.14990439A>T		190.0	0.0		130.0	64.0	NM_001741	Q93048|Q9UCP0	Missense_Mutation	SNP	ENST00000486207.1	hg19	CCDS31432.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.216046	0.39201	.	.	ENSG00000110680	ENST00000359642;ENST00000331587;ENST00000396372	T;T;T	0.31247	1.5;1.5;1.5	4.61	2.26	0.28386	Calcitonin peptide-like (1);	0.227204	0.44902	D	0.000413	T	0.29882	0.0747	L	0.44542	1.39	0.34839	D	0.740528	P	0.50369	0.934	P	0.47402	0.546	T	0.42120	-0.9470	10	0.87932	D	0	-16.9073	8.635	0.33941	0.8373:0.0:0.1627:0.0	.	111	P01258	CALC_HUMAN	N	111	ENSP00000352663:I111N;ENSP00000331746:I111N;ENSP00000379657:I111N	ENSP00000331746:I111N	I	-	2	0	CALCA	14947015	1.000000	0.71417	0.780000	0.31762	0.466000	0.32739	5.577000	0.67444	0.370000	0.24538	-0.290000	0.09829	ATT	.	.		0.517	CALCA-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357068.1	NM_001741		T	14990439	A	T	14990439	1	4	94	0	1	0	0	0	0	0	0	0	2577	101	4	4		4	CALCA	11	14990439	Intron	SNP	A	TCGA-DD-A11C-01A-11D-A12Z-10	7969274	14990439	120016077	54	13052										
LRRC4C	57689	hgsc.bcm.edu	37	chr11	40137651	40137651	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ggaacctcacgcaggtttttCcgaacacaaatcaccttgct	7	13	2	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr11:40137651C>T	ENST00000278198.2	-	2	2155	c.192G>A	c.(190-192)cgG>cgA	p.R64R	LRRC4C_ENST00000528697.1_Silent_p.R64R|LRRC4C_ENST00000527150.1_Silent_p.R64R|LRRC4C_ENST00000530763.1_Silent_p.R64R			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	64	LRRNT.				regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				GCAGGTTTTTCCGAACACAAA	0.532																																					p.R64R		Atlas-SNP	.											.	LRRC4C	190	.	0			c.G192A						.						88	75	79					11																	40137651		2203	4300	6503	SO:0001819	synonymous_variant	57689	exon7			GTTTTTCCGAACA	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.192G>A	chr11.hg19:g.40137651C>T		97.0	0.0		92.0	39.0	NM_001258419	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	hg19	CCDS31464.1																																																																																			.	.		0.532	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		T	40137651	C	T	40137651	2	4	94	1	0	0	0	0	0	0	0	1	9017	842	30	3		3	LRRC4C	11	40137651	Silent	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	25147212	40137651	94868865	55	13053										
ALKBH3	221120	hgsc.bcm.edu	37	chr11	43923153	43923153	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tactctgcaatctttatcgcAatgagaaggacagcgtggac	10	9	2	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr11:43923153A>T	ENST00000302708.4	+	8	958	c.547A>T	c.(547-549)Aat>Tat	p.N183Y	ALKBH3_ENST00000532410.1_Intron	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	183	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)			endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	TCTTTATCGCAATGAGAAGGA	0.502								Direct reversal of damage																													p.N183Y		Atlas-SNP	.											.	ALKBH3	33	.	0			c.A547T						.						170	140	150					11																	43923153		2203	4300	6503	SO:0001583	missense	221120	exon8			TATCGCAATGAGA	AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199		"Alkylation repair homologs"	30141	protein-coding gene	gene with protein product		610603				22055184	Standard	NM_139178		Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.547A>T	chr11.hg19:g.43923153A>T	ENSP00000302232:p.Asn183Tyr	104.0	0.0		65.0	26.0	NM_139178	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	Missense_Mutation	SNP	ENST00000302708.4	hg19	CCDS7906.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.85|16.85	3.237268|3.237268	0.58886|0.58886	.|.	.|.	ENSG00000166199|ENSG00000166199	ENST00000302708;ENST00000529366|ENST00000532129	T;T|.	0.14516|.	2.5;2.5|.	5.67|5.67	1.56|1.56	0.23342|0.23342	Oxoglutarate/iron-dependent oxygenase (2);|.	0.190738|.	0.56097|.	D|.	0.000039|.	T|T	0.53786|0.53786	0.1818|0.1818	M|M	0.80847|0.80847	2.515|2.515	0.24941|0.24941	N|N	0.991851|0.991851	P|.	0.46064|.	0.872|.	P|.	0.56514|.	0.8|.	T|T	0.48681|0.48681	-0.9014|-0.9014	10|5	0.72032|.	D|.	0.01|.	-5.7296|-5.7296	5.0171|5.0171	0.14343|0.14343	0.5765:0.145:0.2785:0.0|0.5765:0.145:0.2785:0.0	.|.	183|.	Q96Q83|.	ALKB3_HUMAN|.	Y|L	183;182|52	ENSP00000302232:N183Y;ENSP00000435848:N182Y|.	ENSP00000302232:N183Y|.	N|Q	+|+	1|2	0|0	ALKBH3|ALKBH3	43879729|43879729	0.906000|0.906000	0.30813|0.30813	0.003000|0.003000	0.11579|0.11579	0.900000|0.900000	0.52787|0.52787	1.880000|1.880000	0.39628|0.39628	0.012000|0.012000	0.14892|0.14892	0.533000|0.533000	0.62120|0.62120	AAT|CAA	.	.		0.502	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389693.1	NM_139178		T	43923153	A	T	43923153	3	4	94	1	0	0	0	0	1	0	0	0	528	130	5	4	573	4	ALKBH3	11	43923153	Missense_Mutation	SNP	A	TCGA-DD-A11C-01A-11D-A12Z-10	3785502	43923153	91083363	56	13054										
CTNND1	1500	hgsc.bcm.edu	37	chr11	57569523	57569523	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	catcccaaaaaggaagtgcaCcttggagcctgtggagctct	11	11	1	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr11:57569523C>T	ENST00000399050.4	+	7	1811	c.1275C>T	c.(1273-1275)caC>caT	p.H425H	CTNND1_ENST00000428599.2_Silent_p.H425H|CTNND1_ENST00000399039.4_Silent_p.H425H|CTNND1_ENST00000529919.1_Silent_p.H425H|CTNND1_ENST00000532463.1_Silent_p.H324H|CTNND1_ENST00000532844.1_Silent_p.H371H|CTNND1_ENST00000532649.1_Silent_p.H371H|CTNND1_ENST00000530094.1_Silent_p.H324H|CTNND1_ENST00000524630.1_Silent_p.H425H|CTNND1_ENST00000526772.1_Silent_p.H102H|CTNND1_ENST00000358694.6_Silent_p.H425H|CTNND1_ENST00000529986.1_Silent_p.H324H|CTNND1_ENST00000361796.4_Silent_p.H425H|CTNND1_ENST00000532787.1_Silent_p.H324H|CTNND1_ENST00000530748.1_Silent_p.H371H|CTNND1_ENST00000534579.1_Silent_p.H371H|CTNND1_ENST00000527467.1_Silent_p.H102H|CTNND1_ENST00000529526.1_Silent_p.H371H|CTNND1_ENST00000529873.1_Silent_p.H371H|CTNND1_ENST00000361332.4_Silent_p.H425H|CTNND1_ENST00000533667.1_Silent_p.H102H|CTNND1_ENST00000525902.1_Silent_p.H102H|CTNND1_ENST00000426142.2_Silent_p.H324H|CTNND1_ENST00000360682.6_Silent_p.H425H|CTNND1_ENST00000528621.1_Silent_p.H371H|CTNND1_ENST00000532245.1_Silent_p.H324H|CTNND1_ENST00000531014.1_Silent_p.H102H|CTNND1_ENST00000526938.1_Silent_p.H425H|CTNND1_ENST00000361391.6_Silent_p.H425H|CTNND1_ENST00000526357.1_Silent_p.H371H|CTNND1_ENST00000528232.1_Silent_p.H324H|CTNND1_ENST00000415361.2_Silent_p.H324H	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	425					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				AGGAAGTGCACCTTGGAGCCT	0.488																																					p.H425H		Atlas-SNP	.											.	CTNND1	203	.	0			c.C1275T						.						167	168	167					11																	57569523		1976	4164	6140	SO:0001819	synonymous_variant	1500	exon7			AGTGCACCTTGGA	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"Armadillo repeat containing"	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.1275C>T	chr11.hg19:g.57569523C>T		128.0	0.0		77.0	36.0	NM_001085461	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Silent	SNP	ENST00000399050.4	hg19	CCDS44604.1																																																																																			.	.		0.488	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331		T	57569523	C	T	57569523	2	4	94	1	0	0	0	0	0	0	0	1	4021	506	18	3		3	CTNND1	11	57569523	Silent	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	13646370	57569523	77436993	57	13055										
GAL3ST3	89792	hgsc.bcm.edu	37	chr11	65810617	65810617	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cccgccaggtaggcggcgtcGtcgcgcgggctgcgctcatt	16	15	1	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr11:65810617G>A	ENST00000312006.4	-	3	938	c.657C>T	c.(655-657)gaC>gaT	p.D219D	GAL3ST3_ENST00000527878.1_Silent_p.D219D	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	219					monosaccharide metabolic process (GO:0005996)|oligosaccharide metabolic process (GO:0009311)|poly-N-acetyllactosamine metabolic process (GO:0030309)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|carbohydrate binding (GO:0030246)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			kidney(1)|lung(9)|ovary(2)|skin(2)	14						AGGCGGCGTCGTCGCGCGGGC	0.667																																					p.D219D		Atlas-SNP	.											GAL3ST3,NS,carcinoma,0,1	GAL3ST3	40	.	0			c.C657T						.						33	38	36					11																	65810617		2199	4292	6491	SO:0001819	synonymous_variant	89792	exon3			GGCGTCGTCGCGC	AY026481	CCDS8128.1	11q13.1	2014-08-12			ENSG00000175229	ENSG00000175229		"Sulfotransferases, membrane-bound"	24144	protein-coding gene	gene with protein product		608234				11323440, 11356829	Standard	NM_033036		Approved	GAL3ST2	uc001ogw.3	Q96A11	OTTHUMG00000166667	ENST00000312006.4:c.657C>T	chr11.hg19:g.65810617G>A		49.0	0.0		40.0	20.0	NM_033036	Q14D05	Silent	SNP	ENST00000312006.4	hg19	CCDS8128.1																																																																																			.	.		0.667	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391052.1	NM_033036		A	65810617	G	A	65810617	2	1	94	1	0	0	0	0	0	0	0	1	6207	1136	40	1		1	GAL3ST3	11	65810617	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	8241094	65810617	69195899	58	13056										
GRM5	2915	hgsc.bcm.edu	37	chr11	88583097	88583097	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cccagaagcagaaattctccCgctagacccaggcgcctcat	8	16	2	3			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr11:88583097C>T	ENST00000305447.4	-	2	1037	c.888G>A	c.(886-888)gcG>gcA	p.A296A	GRM5_ENST00000393297.1_Silent_p.A296A|GRM5_ENST00000455756.2_Silent_p.A296A|GRM5_ENST00000418177.2_Silent_p.A296A|GRM5_ENST00000305432.5_Silent_p.A296A	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	296					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	GAAATTCTCCCGCTAGACCCA	0.517																																					p.A296A		Atlas-SNP	.											GRM5_ENST00000418177,caecum,carcinoma,0,2	GRM5	414	.	0			c.G888A						.						61	68	66					11																	88583097		2201	4299	6500	SO:0001819	synonymous_variant	2915	exon3			TTCTCCCGCTAGA	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.888G>A	chr11.hg19:g.88583097C>T		193.0	0.0		146.0	78.0	NM_000842	Q6J164	Silent	SNP	ENST00000305447.4	hg19	CCDS44694.1																																																																																			.	.		0.517	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		T	88583097	C	T	88583097	2	4	94	1	0	0	0	0	0	0	0	1	6809	639	23	1		1	GRM5	11	88583097	Silent	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	22772480	88583097	46423419	59	13057										
SORL1	6653	hgsc.bcm.edu	37	chr11	121383718	121383718	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ctcttccttggcagcatctcTtgggcagtgaacagcagtct	10	12	3	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr11:121383718T>C	ENST00000260197.7	+	7	1075	c.946T>C	c.(946-948)Ttg>Ctg	p.L316L	SORL1_ENST00000532451.1_3'UTR	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	316					cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		GCAGCATCTCTTGGGCAGTGA	0.443																																					p.L316L		Atlas-SNP	.											.	SORL1	218	.	0			c.T946C						.						70	69	70					11																	121383718		2203	4299	6502	SO:0001819	synonymous_variant	6653	exon7			CATCTCTTGGGCA	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.946T>C	chr11.hg19:g.121383718T>C		97.0	0.0		90.0	32.0	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	hg19	CCDS8436.1																																																																																			.	.		0.443	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		C	121383718	T	C	121383718	2	2	94	1	0	0	0	0	0	0	0	1	14949	1606	56	2		2	SORL1	11	121383718	Silent	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	32800621	121383718	13622798	60	13058										
TMEM225	338661	hgsc.bcm.edu	37	chr11	123753908	123753908	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	agggaattcacagtgtgtgcAcggacaatgctacgaggcat	13	8	1	0	rs369698336		TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr11:123753908A>T	ENST00000375026.2	-	4	831	c.615T>A	c.(613-615)cgT>cgA	p.R205R		NM_001013743.1	NP_001013765.1	Q6GV28	TM225_HUMAN	transmembrane protein 225	205					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	28						CAGTGTGTGCACGGACAATGC	0.398																																					p.R205R		Atlas-SNP	.											.	TMEM225	56	.	0			c.T615A						.						180	164	170					11																	123753908		2202	4299	6501	SO:0001819	synonymous_variant	338661	exon4			GTGTGCACGGACA	AY634366	CCDS31697.1	11q24.1	2014-06-13			ENSG00000204300	ENSG00000204300			32390	protein-coding gene	gene with protein product	"PMP22 claudin domain containing", "protein phosphatase 1, regulatory subunit 154"						Standard	XM_006718832		Approved	PMP22CD, PPP1R154	uc001pzi.3	Q6GV28	OTTHUMG00000165959	ENST00000375026.2:c.615T>A	chr11.hg19:g.123753908A>T		201.0	0.0		206.0	94.0	NM_001013743		Silent	SNP	ENST00000375026.2	hg19	CCDS31697.1																																																																																			.	.		0.398	TMEM225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387260.1	NM_001013743		T	123753908	A	T	123753908	2	4	94	1	0	0	0	0	0	0	0	1	16162	146	6	4		4	TMEM225	11	123753908	Silent	SNP	A	TCGA-DD-A11C-01A-11D-A12Z-10	2370190	123753908	11252608	61	13059										
LRP1	4035	hgsc.bcm.edu	37	chr12	57556190	57556190	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ctgagtatcggagtggcagtGtctaccgcttggaacggggt	16	8	1	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr12:57556190G>T	ENST00000243077.3	+	14	2759	c.2293G>T	c.(2293-2295)Gtc>Ttc	p.V765F		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	765					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GAGTGGCAGTGTCTACCGCTT	0.572																																					p.V765F		Atlas-SNP	.											.	LRP1	428	.	0			c.G2293T						.						199	159	173					12																	57556190		2203	4300	6503	SO:0001583	missense	4035	exon14			GGCAGTGTCTACC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.2293G>T	chr12.hg19:g.57556190G>T	ENSP00000243077:p.Val765Phe	105.0	0.0		72.0	30.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201835	0.58234	.	.	ENSG00000123384	ENST00000243077	D	0.94457	-3.43	4.87	4.87	0.63330	Six-bladed beta-propeller, TolB-like (1);	0.082006	0.48286	D	0.000181	D	0.91219	0.7233	M	0.70787	2.145	0.80722	D	1	P	0.41313	0.745	B	0.33295	0.161	D	0.90526	0.4492	10	0.66056	D	0.02	.	7.5064	0.27547	0.1761:0.0:0.8239:0.0	.	765	Q07954	LRP1_HUMAN	F	765	ENSP00000243077:V765F	ENSP00000243077:V765F	V	+	1	0	LRP1	55842457	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	6.058000	0.71126	2.709000	0.92574	0.563000	0.77884	GTC	.	.		0.572	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57556190	G	T	57556190	3	4	94	1	0	0	0	0	1	0	0	0	8960	1377	48	3	2347	3	LRP1	12	57556190	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10		57556190	76295705	62	13060										
MAB21L1	4081	hgsc.bcm.edu	37	chr13	36049572	36049572	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gcagtctgttctctgcctccGcgaactgcagcacccaggcg	11	16	2	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr13:36049572G>A	ENST00000379919.4	-	1	1260	c.704C>T	c.(703-705)gCg>gTg	p.A235V	NBEA_ENST00000537702.1_5'Flank|NBEA_ENST00000379939.2_Intron|NBEA_ENST00000310336.4_Intron|NBEA_ENST00000540320.1_Intron|NBEA_ENST00000400445.3_Intron	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)	235					anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		CTCTGCCTCCGCGAACTGCAG	0.602																																					p.A235V		Atlas-SNP	.											.	MAB21L1	52	.	0			c.C704T						.						57	63	61					13																	36049572		2203	4300	6503	SO:0001583	missense	4081	exon1			GCCTCCGCGAACT	BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"mab-21 (C. elegans)-like 1"			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.704C>T	chr13.hg19:g.36049572G>A	ENSP00000369251:p.Ala235Val	52.0	0.0		21.0	18.0	NM_005584	Q6I9T5	Missense_Mutation	SNP	ENST00000379919.4	hg19	CCDS9353.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.979676	0.34942	.	.	ENSG00000180660	ENST00000379919	T	0.07908	3.15	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.08758	0.0217	L	0.29908	0.895	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.33879	-0.9851	10	0.19147	T	0.46	-27.0942	19.9576	0.97228	0.0:0.0:1.0:0.0	.	235	Q13394	MB211_HUMAN	V	235	ENSP00000369251:A235V	ENSP00000369251:A235V	A	-	2	0	MAB21L1	34947572	1.000000	0.71417	0.998000	0.56505	0.934000	0.57294	9.869000	0.99810	2.736000	0.93811	0.655000	0.94253	GCG	.	.		0.602	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584		A	36049572	G	A	36049572	3	1	94	1	0	0	0	0	1	0	0	0	9150	1087	38	1	379	1	MAB21L1	13	36049572	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10		36049572	79120306	63	13061										
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24884257	24884257	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ctccttcttcatgggcttcaTggactcccacagggatgcca	9	14	3	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr14:24884257T>C	ENST00000382554.3	+	9	3620	c.3302T>C	c.(3301-3303)aTg>aCg	p.M1101T		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1101					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						ATGGGCTTCATGGACTCCCAC	0.612																																					p.M1101T		Atlas-SNP	.											.	NYNRIN	120	.	0			c.T3302C						.						63	66	65					14																	24884257		2014	4197	6211	SO:0001583	missense	57523	exon9			GCTTCATGGACTC	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.3302T>C	chr14.hg19:g.24884257T>C	ENSP00000371994:p.Met1101Thr	89.0	0.0		76.0	27.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	T	6.859	0.527851	0.13127	.	.	ENSG00000205978	ENST00000382554	T	0.39787	1.06	4.45	3.29	0.37713	.	.	.	.	.	T	0.22781	0.0550	N	0.11201	0.11	0.27869	N	0.9401	B	0.06786	0.001	B	0.04013	0.001	T	0.14699	-1.0463	9	0.46703	T	0.11	.	6.6051	0.22721	0.0:0.1088:0.0:0.8912	.	1101	Q9P2P1	NYNRI_HUMAN	T	1101	ENSP00000371994:M1101T	ENSP00000371994:M1101T	M	+	2	0	NYNRIN	23954097	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	1.810000	0.38932	0.739000	0.32628	0.459000	0.35465	ATG	.	.		0.612	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			C	24884257	T	C	24884257	3	2	94	1	0	0	0	0	1	0	0	0	10805	1464	51	2	3332	2	NYNRIN	14	24884257	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10		24884257	82465283	64	13062										
KIAA0317	9870	hgsc.bcm.edu	37	chr14	75140804	75140804	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tcttcaggtagaactccttcActgagaattgctggaggacc	10	10	3	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr14:75140804A>T	ENST00000356357.4	-	9	1606	c.1091T>A	c.(1090-1092)gTg>gAg	p.V364E	AREL1_ENST00000557401.1_5'UTR	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	364					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GAACTCCTTCACTGAGAATTG	0.408																																					p.V364E		Atlas-SNP	.											.	KIAA0317	68	.	0			c.T1091A						.						73	71	72					14																	75140804		1881	4122	6003	SO:0001583	missense	9870	exon9			TCCTTCACTGAGA	AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"KIAA0317"	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.1091T>A	chr14.hg19:g.75140804A>T	ENSP00000348714:p.Val364Glu	105.0	0.0		50.0	14.0	NM_001039479	B4E2C7|Q7LDY1|Q8IYY9	Missense_Mutation	SNP	ENST00000356357.4	hg19	CCDS41971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.7|26.7	4.758454|4.758454	0.89843|0.89843	.|.	.|.	ENSG00000119682|ENSG00000119682	ENST00000356357;ENST00000543377;ENST00000556202|ENST00000490805	T;T|.	0.52526|.	0.66;0.66|.	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	0.168253|.	0.52532|.	D|.	0.000075|.	T|.	0.59555|.	0.2202|.	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	D|D	1|1	P;P|.	0.48503|.	0.557;0.911|.	B;P|.	0.51385|.	0.279;0.668|.	T|.	0.56938|.	-0.7896|.	10|.	0.72032|.	D|.	0.01|.	.|.	13.7014|13.7014	0.62611|0.62611	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	364;364|.	O15033-2;O15033|.	.;K0317_HUMAN|.	E|R	364;203;203|98	ENSP00000348714:V364E;ENSP00000452101:V203E|.	ENSP00000348714:V364E|.	V|X	-|-	2|1	0|0	KIAA0317|KIAA0317	74210557|74210557	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	8.782000|8.782000	0.91809|0.91809	2.159000|2.159000	0.67721|0.67721	0.477000|0.477000	0.44152|0.44152	GTG|TGA	.	.		0.408	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821		T	75140804	A	T	75140804	3	4	94	1	0	0	0	0	1	0	0	0	8176	159	6	4	1428	4	KIAA0317	14	75140804	Missense_Mutation	SNP	A	TCGA-DD-A11C-01A-11D-A12Z-10	50256547	75140804	32208736	65	13063										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96795907	96795907	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cccaatggacatatcagtacTaaaatatcgggaagctgatc	8	9	1	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr14:96795907T>G	ENST00000359933.4	-	12	2688	c.1795A>C	c.(1795-1797)Agt>Cgt	p.S599R		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	599					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		ATATCAGTACTAAAATATCGG	0.323																																					p.S599R		Atlas-SNP	.											.	ATG2B	169	.	0			c.A1795C						.						115	114	114					14																	96795907		1813	4074	5887	SO:0001583	missense	55102	exon12			CAGTACTAAAATA	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.1795A>C	chr14.hg19:g.96795907T>G	ENSP00000353010:p.Ser599Arg	166.0	0.0		85.0	50.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	T	20.3	3.973215	0.74246	.	.	ENSG00000066739	ENST00000359933	T	0.11385	2.78	5.68	4.41	0.53225	.	0.061259	0.64402	U	0.000007	T	0.13586	0.0329	L	0.60455	1.87	0.44117	D	0.996893	P	0.38250	0.624	B	0.37943	0.261	T	0.01528	-1.1332	10	0.62326	D	0.03	.	11.5336	0.50624	0.0:0.0756:0.0:0.9244	.	599	Q96BY7	ATG2B_HUMAN	R	599	ENSP00000353010:S599R	ENSP00000353010:S599R	S	-	1	0	ATG2B	95865660	1.000000	0.71417	0.851000	0.33527	0.868000	0.49771	4.022000	0.57203	0.962000	0.38057	0.482000	0.46254	AGT	.	.		0.323	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96795907	T	G	96795907	3	3	94	1	0	0	0	0	1	0	0	0	1094	1522	53	5	4565	5	ATG2B	14	96795907	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	21655103	96795907	10553633	66	13064										
ACTC1	70	hgsc.bcm.edu	37	chr15	35085586	35085586	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gcggggcctctgtgagcaggGtggggtgctcctcgggagcc	20	11	1	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr15:35085586G>A	ENST00000290378.4	-	3	969	c.314C>T	c.(313-315)aCc>aTc	p.T105I	RP11-814P5.1_ENST00000503496.1_RNA|ACTC1_ENST00000557860.1_5'Flank	NM_005159.4	NP_005150.1	P68032	ACTC_HUMAN	actin, alpha, cardiac muscle 1	105					actin filament-based movement (GO:0030048)|actin-myosin filament sliding (GO:0033275)|actomyosin structure organization (GO:0031032)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|heart contraction (GO:0060047)|muscle filament sliding (GO:0030049)|negative regulation of apoptotic process (GO:0043066)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|skeletal muscle thin filament assembly (GO:0030240)	actin filament (GO:0005884)|actomyosin, actin portion (GO:0042643)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|I band (GO:0031674)|membrane (GO:0016020)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|myosin binding (GO:0017022)			central_nervous_system(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	31		all_lung(180;2.3e-08)		all cancers(64;5.83e-19)|GBM - Glioblastoma multiforme(113;1.98e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		TGTGAGCAGGGTGGGGTGCTC	0.572																																					p.T105I		Atlas-SNP	.											.	ACTC1	75	.	0			c.C314T						.						86	85	86					15																	35085586		2201	4298	6499	SO:0001583	missense	70	exon3			AGCAGGGTGGGGT	BC009978	CCDS10041.1	15q14	2014-09-17	2006-08-24	2006-08-24	ENSG00000159251	ENSG00000159251			143	protein-coding gene	gene with protein product		102540	"actin, alpha, cardiac muscle"	ACTC		1639426	Standard	NM_005159		Approved	CMD1R	uc001ziu.1	P68032	OTTHUMG00000129675	ENST00000290378.4:c.314C>T	chr15.hg19:g.35085586G>A	ENSP00000290378:p.Thr105Ile	155.0	0.0		88.0	62.0	NM_005159	P04270	Missense_Mutation	SNP	ENST00000290378.4	hg19	CCDS10041.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.118132	0.56505	.	.	ENSG00000159251	ENST00000290378	D	0.93247	-3.19	5.63	5.63	0.86233	.	0.000000	0.53938	U	0.000052	D	0.87537	0.6202	N	0.00092	-2.175	0.80722	D	1	D	0.54772	0.968	D	0.87578	0.998	D	0.94287	0.7525	10	0.87932	D	0	.	20.0442	0.97604	0.0:0.0:1.0:0.0	.	105	P68032	ACTC_HUMAN	I	105	ENSP00000290378:T105I	ENSP00000290378:T105I	T	-	2	0	ACTC1	32872878	1.000000	0.71417	0.988000	0.46212	0.984000	0.73092	8.062000	0.89475	2.814000	0.96858	0.655000	0.94253	ACC	.	.		0.572	ACTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251876.3	NM_005159		A	35085586	G	A	35085586	3	1	94	1	0	0	0	0	1	0	0	0	195	1261	44	3	839	3	ACTC1	15	35085586	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10		35085586	67445806	67	13065										
PPIP5K1	9677	hgsc.bcm.edu	37	chr15	43827486	43827486	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tggttcaaaaagctcttgctCcccttctatggagagctctt	8	11	4	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr15:43827486C>G	ENST00000396923.3	-	30	3809	c.3688G>C	c.(3688-3690)Gag>Cag	p.E1230Q	PPIP5K1_ENST00000381879.4_Missense_Mutation_p.E1206Q|PPIP5K1_ENST00000360135.4_Missense_Mutation_p.E1203Q|PPIP5K1_ENST00000334933.4_Missense_Mutation_p.E1205Q|PPIP5K1_ENST00000381885.1_Missense_Mutation_p.E1226Q|PPIP5K1_ENST00000420765.1_Missense_Mutation_p.E1230Q|PPIP5K1_ENST00000360301.4_Missense_Mutation_p.E1205Q|PPIP5K1_ENST00000348806.6_Missense_Mutation_p.E1203Q			Q6PFW1	VIP1_HUMAN	diphosphoinositol pentakisphosphate kinase 1	1230					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			large_intestine(1)	1						AGCTCTTGCTCCCCTTCTATG	0.557																																					p.E1230Q		Atlas-SNP	.											.	PPIP5K1	34	.	0			c.G3688C						.						94	92	92					15																	43827486		2201	4298	6499	SO:0001583	missense	9677	exon31			CTTGCTCCCCTTC	AF502586	CCDS32215.1, CCDS45252.1, CCDS53937.1	15q15.3	2010-01-27	2010-01-26	2010-01-26	ENSG00000168781	ENSG00000168781	2.7.4.24		29023	protein-coding gene	gene with protein product		610979	"histidine acid phosphatase domain containing 2A"	HISPPD2A		17412958, 17690096, 18981179	Standard	NM_001190214		Approved	KIAA0377, IPS1, VIP1	uc001zrw.3	Q6PFW1	OTTHUMG00000059758	ENST00000396923.3:c.3688G>C	chr15.hg19:g.43827486C>G	ENSP00000380129:p.Glu1230Gln	262.0	0.0		215.0	84.0	NM_001130858	O15082|Q5HYF8|Q7Z3A7|Q86TE7|Q86UV3|Q86UV4|Q86XW8|Q8IZN0	Missense_Mutation	SNP	ENST00000396923.3	hg19	CCDS45252.1	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.603608	0.00849	.	.	ENSG00000168781	ENST00000381885;ENST00000360301;ENST00000360135;ENST00000334933;ENST00000396923;ENST00000304953;ENST00000381878;ENST00000420765;ENST00000381879;ENST00000348806	T;T;T;T;T;T;T;T	0.22743	1.95;1.95;2.52;1.95;1.95;1.95;1.94;2.52	5.14	-1.33	0.09172	.	1.800900	0.02664	N	0.107860	T	0.08179	0.0204	N	0.01705	-0.755	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.25152	-1.0140	10	0.18276	T	0.48	0.7387	6.5571	0.22466	0.0:0.4178:0.2624:0.3198	.	1203;1230;1205	Q6PFW1-7;Q6PFW1;Q6PFW1-3	.;VIP1_HUMAN;.	Q	1226;1205;1203;1205;1230;1230;1205;1230;1206;1203	ENSP00000371309:E1226Q;ENSP00000353446:E1205Q;ENSP00000353253:E1203Q;ENSP00000334779:E1205Q;ENSP00000380129:E1230Q;ENSP00000400887:E1230Q;ENSP00000371303:E1206Q;ENSP00000308773:E1203Q	ENSP00000304750:E1230Q	E	-	1	0	PPIP5K1	41614778	.	.	0.001000	0.08648	0.038000	0.13279	.	.	-0.705000	0.05035	-1.945000	0.00491	GAG	.	.		0.557	PPIP5K1-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132907.1	NM_014659		G	43827486	C	G	43827486	3	3	94	1	0	0	0	0	1	0	0	0	12344	864	30	4	617	4	PPIP5K1	15	43827486	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	8741900	43827486	58703906	68	13066										
RHBDF1	64285	hgsc.bcm.edu	37	chr16	111695	111695	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gccagtaggtgaagaagggcCtgcggggtggagcgtcagcg	20	8	1	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr16:111695C>T	ENST00000262316.6	-	9	1351		c.e9-1		RHBDF1_ENST00000454039.2_Splice_Site	NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)						cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				GAAGAAGGGCCTGCGGGGTGG	0.677																																					.		Atlas-SNP	.											.	RHBDF1	54	.	0			c.1209-1G>A						.						54	53	53					16																	111695		2203	4300	6503	SO:0001630	splice_region_variant	64285	exon10			AAGGGCCTGCGGG	BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"chromosome 16 open reading frame 8", "rhomboid family 1 (Drosophila)"	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.1209-1G>A	chr16.hg19:g.111695C>T		45.0	0.0		45.0	21.0	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Splice_Site	SNP	ENST00000262316.6	hg19	CCDS32344.1	.	.	.	.	.	.	.	.	.	.	c	15.27	2.784646	0.49997	.	.	ENSG00000007384	ENST00000262316;ENST00000454039	.	.	.	4.43	4.43	0.53597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5704	0.84611	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RHBDF1	51695	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.312000	0.78968	2.448000	0.82819	0.462000	0.41574	.	.	.		0.677	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450	Intron	T	111695	C	T	111695	5	4	94	1	0	0	0	0	0	0	1	0	13334	695	24	3	1399	3	RHBDF1	16	111695	Splice_Site	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10		111695	90243058	69	13067										
ASPHD1	253982	hgsc.bcm.edu	37	chr16	29912566	29912566	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gggccctcacttccctgttcCtctggtactgctaccgcctg	9	17	2	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr16:29912566C>T	ENST00000308748.5	+	1	526	c.274C>T	c.(274-276)Ctc>Ttc	p.L92F	SEZ6L2_ENST00000346932.5_5'Flank|ASPHD1_ENST00000483405.1_Intron|SEZ6L2_ENST00000350527.3_5'Flank|SEZ6L2_ENST00000537485.1_5'Flank|SEZ6L2_ENST00000308713.5_5'Flank	NM_181718.3	NP_859069.2	Q5U4P2	ASPH1_HUMAN	aspartate beta-hydroxylase domain containing 1	92					peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)	dioxygenase activity (GO:0051213)			endometrium(4)|large_intestine(2)|lung(1)|prostate(1)	8						TTCCCTGTTCCTCTGGTACTG	0.677																																					p.L92F		Atlas-SNP	.											.	ASPHD1	28	.	0			c.C274T						.						54	59	57					16																	29912566		2196	4299	6495	SO:0001583	missense	253982	exon1			CTGTTCCTCTGGT	AF070642	CCDS10660.1	16p11.2	2008-02-05			ENSG00000174939	ENSG00000174939			27380	protein-coding gene	gene with protein product							Standard	NM_181718		Approved		uc002dut.3	Q5U4P2	OTTHUMG00000132121	ENST00000308748.5:c.274C>T	chr16.hg19:g.29912566C>T	ENSP00000311447:p.Leu92Phe	92.0	0.0		110.0	22.0	NM_181718	A0AVE3|B7ZLZ3|Q8IW63|Q8N316|Q96H00	Missense_Mutation	SNP	ENST00000308748.5	hg19	CCDS10660.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.102295	0.76983	.	.	ENSG00000174939	ENST00000414952;ENST00000308748	T;T	0.56611	0.45;0.45	4.28	3.33	0.38152	.	0.000000	0.56097	D	0.000026	T	0.43255	0.1239	L	0.44542	1.39	0.44908	D	0.997928	B	0.17038	0.02	B	0.17433	0.018	T	0.42999	-0.9418	10	0.72032	D	0.01	-15.8544	9.5322	0.39200	0.0:0.8982:0.0:0.1018	.	92	Q5U4P2	ASPH1_HUMAN	F	92	ENSP00000388036:L92F;ENSP00000311447:L92F	ENSP00000311447:L92F	L	+	1	0	ASPHD1	29820067	0.998000	0.40836	1.000000	0.80357	0.929000	0.56500	1.601000	0.36773	1.151000	0.42436	0.462000	0.41574	CTC	.	.		0.677	ASPHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255163.2	NM_181718		T	29912566	C	T	29912566	3	4	94	1	0	0	0	0	1	0	0	0	1054	681	24	3	276	3	ASPHD1	16	29912566	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	29800871	29912566	60442187	70	13068										
GPR114	221188	hgsc.bcm.edu	37	chr16	57596061	57596061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ccttctgactttgcagaatgCaacaacaggtaagggggctc	11	10	1	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr16:57596061C>T	ENST00000340339.4	+	2	579	c.56C>T	c.(55-57)gCa>gTa	p.A19V	GPR114_ENST00000394361.4_3'UTR|GPR114_ENST00000349457.3_Missense_Mutation_p.A19V	NM_153837.1	NP_722579.1	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	19					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(5)|ovary(2)|stomach(1)|urinary_tract(1)	23						TTGCAGAATGCAACAACAGGT	0.562																																					p.A19V		Atlas-SNP	.											.	GPR114	52	.	0			c.C56T						.						68	64	65					16																	57596061		2198	4300	6498	SO:0001583	missense	221188	exon2			AGAATGCAACAAC	AY140956	CCDS10785.1	16q13	2014-08-08			ENSG00000159618	ENSG00000159618		"-", "GPCR / Class B : Orphans"	19010	protein-coding gene	gene with protein product						12435584	Standard	NM_153837		Approved	PGR27	uc002ely.3	Q8IZF4	OTTHUMG00000133461	ENST00000340339.4:c.56C>T	chr16.hg19:g.57596061C>T	ENSP00000342981:p.Ala19Val	68.0	0.0		47.0	23.0	NM_153837	B3KXZ5|Q6ZMH7|Q6ZML4|Q86SL8|Q8IZ14	Missense_Mutation	SNP	ENST00000340339.4	hg19	CCDS10785.1	.	.	.	.	.	.	.	.	.	.	C	8.768	0.925292	0.18056	.	.	ENSG00000159618	ENST00000394361;ENST00000340339;ENST00000349457	T;T	0.28069	1.63;1.63	4.15	-3.43	0.04810	.	2.191750	0.02573	N	0.098001	T	0.13670	0.0331	N	0.12182	0.205	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.08269	-1.0730	10	0.21014	T	0.42	.	0.4945	0.00569	0.205:0.2823:0.2186:0.2941	.	19;19	B4E148;Q8IZF4	.;GP114_HUMAN	V	19	ENSP00000342981:A19V;ENSP00000290823:A19V	ENSP00000342981:A19V	A	+	2	0	GPR114	56153562	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.017000	0.12590	-0.615000	0.05679	-0.367000	0.07326	GCA	.	.		0.562	GPR114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257336.3	NM_153837		T	57596061	C	T	57596061	3	4	94	1	0	0	0	0	1	0	0	0	6639	710	25	3	58	3	GPR114	16	57596061	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	27683495	57596061	32758692	71	13069										
ACLY	47	hgsc.bcm.edu	37	chr17	40024989	40024989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ccccatactccttcccagcaCaaagatgccattgagggctc	7	16	0	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr17:40024989C>T	ENST00000352035.2	-	28	3314	c.3184G>A	c.(3184-3186)Gtg>Atg	p.V1062M	ACLY_ENST00000590151.1_Missense_Mutation_p.V1062M|ACLY_ENST00000537919.1_Missense_Mutation_p.V791M|ACLY_ENST00000353196.1_Missense_Mutation_p.V1052M|ACLY_ENST00000588779.1_5'UTR|ACLY_ENST00000393896.2_Missense_Mutation_p.V1052M	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	1062					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				CTTCCCAGCACAAAGATGCCA	0.448																																					p.V1062M	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.G3184A						.						171	148	156					17																	40024989		2203	4300	6503	SO:0001583	missense	47	exon28			CCAGCACAAAGAT	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.3184G>A	chr17.hg19:g.40024989C>T	ENSP00000253792:p.Val1062Met	76.0	0.0		48.0	19.0	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	ENST00000352035.2	hg19	CCDS11412.1	.	.	.	.	.	.	.	.	.	.	c	32	5.173660	0.94807	.	.	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000537919;ENST00000393896	D;D;D;D	0.90620	-1.74;-1.74;-2.7;-1.74	5.53	5.53	0.82687	Citrate synthase-like, core (1);	0.059404	0.64402	D	0.000002	D	0.95701	0.8602	M	0.83384	2.64	0.80722	D	1	P;D;D;D;D	0.69078	0.942;0.991;0.991;0.997;0.968	P;P;P;D;P	0.71184	0.776;0.906;0.906;0.972;0.837	D	0.95660	0.8714	10	0.87932	D	0	.	19.6556	0.95837	0.0:1.0:0.0:0.0	.	791;1106;1116;1052;1062	B4E3P0;B4DIM0;E7ENH9;G3XAI4;P53396	.;.;.;.;ACLY_HUMAN	M	1062;1116;1052;791;1052	ENSP00000253792:V1062M;ENSP00000345398:V1052M;ENSP00000445349:V791M;ENSP00000377474:V1052M	ENSP00000253792:V1062M	V	-	1	0	ACLY	37278515	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.182000	0.77689	2.882000	0.98803	0.655000	0.94253	GTG	.	.		0.448	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		T	40024989	C	T	40024989	3	4	94	1	0	0	0	0	1	0	0	0	143	478	17	3	129	3	ACLY	17	40024989	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10		40024989	41170221	72	13070										
GNGT2	2793	hgsc.bcm.edu	37	chr17	47284179	47284179	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ttgtcctcagggatgcctttGagaaaaggatcgtttcctgc	11	9	1	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr17:47284179G>A	ENST00000511277.1	-	4	329	c.150C>T	c.(148-150)ctC>ctT	p.L50L	GNGT2_ENST00000515635.1_Silent_p.L50L|GNGT2_ENST00000300406.2_Silent_p.L50L|GNGT2_ENST00000503070.1_Silent_p.L50L|GNGT2_ENST00000511673.1_Silent_p.L50L|GNGT2_ENST00000507680.1_Silent_p.L50L	NM_001198756.1	NP_001185685.1	O14610	GBGT2_HUMAN	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	50					G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|phototransduction (GO:0007602)|synaptic transmission (GO:0007268)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)	p.L50L(1)		endometrium(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			GGATGCCTTTGAGAAAAGGAT	0.493																																					p.L50L		Atlas-SNP	.											GNGT2,bladder,carcinoma,0,1	GNGT2	12	.	1	Substitution - coding silent(1)	urinary_tract(1)	c.C150T						.						172	149	157					17																	47284179		2203	4300	6503	SO:0001819	synonymous_variant	2793	exon4			GCCTTTGAGAAAA		CCDS11545.1	17q21	2003-12-17				ENSG00000167083			4412	protein-coding gene	gene with protein product		139391				9286705	Standard	NM_031498		Approved	GNG9	uc021tzq.1	O14610		ENST00000511277.1:c.150C>T	chr17.hg19:g.47284179G>A		247.0	0.0		160.0	64.0	NM_031498	B2R746|D3DTW5	Silent	SNP	ENST00000511277.1	hg19	CCDS11545.1																																																																																			.	.		0.493	GNGT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364482.1	NM_031498		A	47284179	G	A	47284179	2	1	94	1	0	0	0	0	0	0	0	1	6542	1277	45	3		3	GNGT2	17	47284179	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	7259190	47284179	33911031	73	13071										
CUEDC1	404093	hgsc.bcm.edu	37	chr17	55945598	55945598	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	caagttcaaacagtttcctcCgggtggctgggggcagagag	15	9	1	1	rs34800498	byFrequency	TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr17:55945598C>G	ENST00000577830.1	-	8	1360	c.947G>C	c.(946-948)cGg>cCg	p.R316P	CUEDC1_ENST00000360238.2_Missense_Mutation_p.R316P|CUEDC1_ENST00000407144.2_Missense_Mutation_p.R316P|CUEDC1_ENST00000577840.1_Missense_Mutation_p.R179P|CUEDC1_ENST00000578357.1_5'UTR	NM_001271875.1	NP_001258804.1	Q9NWM3	CUED1_HUMAN	CUE domain containing 1	316			R -> Q (in dbSNP:rs34800498).							endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12						CAGTTTCCTCCGGGTGGCTGG	0.547																																					p.R316P		Atlas-SNP	.											.	CUEDC1	37	.	0			c.G947C						.						103	86	91					17																	55945598		2203	4300	6503	SO:0001583	missense	404093	exon8			TTCCTCCGGGTGG	AK000746	CCDS11599.1	17q23.2	2004-03-16				ENSG00000180891			31350	protein-coding gene	gene with protein product							Standard	NM_001271875		Approved		uc002ive.2	Q9NWM3		ENST00000577830.1:c.947G>C	chr17.hg19:g.55945598C>G	ENSP00000462717:p.Arg316Pro	102.0	0.0		76.0	43.0	NM_001271875	D3DTZ2|Q9NWD0	Missense_Mutation	SNP	ENST00000577830.1	hg19	CCDS11599.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.963464	0.74016	.	.	ENSG00000180891	ENST00000407144;ENST00000360238	T;T	0.37411	1.2;1.2	4.5	3.52	0.40303	.	0.000000	0.85682	D	0.000000	T	0.51007	0.1649	M	0.61703	1.905	0.58432	D	0.999999	D	0.58970	0.984	P	0.59546	0.859	T	0.54050	-0.8351	10	0.87932	D	0	-6.8965	12.0482	0.53491	0.0:0.9155:0.0:0.0845	.	316	Q9NWM3	CUED1_HUMAN	P	316	ENSP00000384712:R316P;ENSP00000353373:R316P	ENSP00000353373:R316P	R	-	2	0	CUEDC1	53300597	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.413000	0.59795	0.875000	0.35847	0.462000	0.41574	CGG	.	C|0.958;T|0.042		0.547	CUEDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443305.1	NM_017949		G	55945598	C	G	55945598	3	3	94	1	0	0	0	0	1	0	0	0	4054	652	23	4	225	4	CUEDC1	17	55945598	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	8661419	55945598	25249612	74	13072										
OR4D2	124538	hgsc.bcm.edu	37	chr17	56247344	56247344	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tcttccactttttgggaggtGccatggtcttcttcctctca	8	12	4	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr17:56247344G>T	ENST00000545221.1	+	1	328	c.328G>T	c.(328-330)Gcc>Tcc	p.A110S		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						TTTGGGAGGTGCCATGGTCTT	0.542																																					p.A110S		Atlas-SNP	.											.	OR4D2	48	.	0			c.G328T						.						92	85	88					17																	56247344		2203	4300	6503	SO:0001583	missense	124538	exon1			GGAGGTGCCATGG		CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"GPCR / Class A : Olfactory receptors"	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.328G>T	chr17.hg19:g.56247344G>T	ENSP00000441354:p.Ala110Ser	103.0	0.0		56.0	15.0	NM_001004707	Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	hg19	CCDS32688.1	.	.	.	.	.	.	.	.	.	.	G	4.915	0.169998	0.09339	.	.	ENSG00000255713	ENST00000545221	T	0.00882	5.58	5.71	4.74	0.60224	GPCR, rhodopsin-like superfamily (1);	0.242082	0.28612	N	0.014734	T	0.00784	0.0026	N	0.14661	0.345	0.09310	N	1	B	0.20368	0.044	B	0.20767	0.031	T	0.49634	-0.8919	10	0.40728	T	0.16	-23.9432	7.8601	0.29506	0.0806:0.0:0.7571:0.1622	.	110	P58180	OR4D2_HUMAN	S	110	ENSP00000441354:A110S	ENSP00000441354:A110S	A	+	1	0	OR4D2	53602343	0.000000	0.05858	0.988000	0.46212	0.208000	0.24298	-0.009000	0.12765	1.552000	0.49463	0.609000	0.83330	GCC	.	.		0.542	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1			T	56247344	G	T	56247344	3	4	94	1	0	0	0	0	1	0	0	0	11065	1319	46	3	330	3	OR4D2	17	56247344	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	301746	56247344	24947866	75	13073										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9255525	9255525	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ttaaagaggaacgagacaagAttaaaaaggaaagcgagaaa	11	3	0	4			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr18:9255525A>T	ENST00000262126.4	+	9	2500	c.2260A>T	c.(2260-2262)Att>Ttt	p.I754F	ANKRD12_ENST00000400020.3_Missense_Mutation_p.I731F|ANKRD12_ENST00000383440.2_Missense_Mutation_p.I731F	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	754						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						ACGAGACAAGATTAAAAAGGA	0.308																																					p.I754F		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A2260T						.						49	51	50					18																	9255525		2200	4291	6491	SO:0001583	missense	23253	exon9			GACAAGATTAAAA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.2260A>T	chr18.hg19:g.9255525A>T	ENSP00000262126:p.Ile754Phe	64.0	0.0		24.0	11.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	0.090	-1.169146	0.01660	.	.	ENSG00000101745	ENST00000383440;ENST00000262126;ENST00000400020	T;T	0.44083	0.93;0.93	5.1	-1.93	0.07594	.	0.624489	0.15199	N	0.275134	T	0.18841	0.0452	N	0.08118	0	0.20821	N	0.999844	B;B;B	0.24882	0.113;0.091;0.028	B;B;B	0.28232	0.034;0.087;0.015	T	0.14783	-1.0460	10	0.56958	D	0.05	-30.356	4.1483	0.10225	0.5513:0.0:0.2181:0.2306	.	381;731;754	Q9NXU3;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	F	731;754;49	ENSP00000372932:I731F;ENSP00000262126:I754F	ENSP00000262126:I754F	I	+	1	0	ANKRD12	9245525	0.020000	0.18652	0.829000	0.32907	0.680000	0.39746	0.404000	0.20999	-0.230000	0.09840	-0.756000	0.03474	ATT	.	.		0.308	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		T	9255525	A	T	9255525	3	4	94	1	0	0	0	0	1	0	0	0	640	333	12	4	2290	4	ANKRD12	18	9255525	Missense_Mutation	SNP	A	TCGA-DD-A11C-01A-11D-A12Z-10		9255525	68821723	76	13074										
ZBTB7C	201501	hgsc.bcm.edu	37	chr18	45555810	45555810	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ctcagcctccagctgcgcgcGcccgaacagcttcatctgtg	10	17	3	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr18:45555810G>A	ENST00000588982.1	-	4	2182	c.1681C>T	c.(1681-1683)Cgc>Tgc	p.R561C	ZBTB7C_ENST00000535628.2_Missense_Mutation_p.R561C|ZBTB7C_ENST00000586438.1_Missense_Mutation_p.R561C|ZBTB7C_ENST00000332053.2_Missense_Mutation_p.R561C|ZBTB7C_ENST00000590800.1_Missense_Mutation_p.R561C			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	561							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						AGCTGCGCGCGCCCGAACAGC	0.721																																					p.R561C		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.C1681T						.						10	11	11					18																	45555810		2188	4265	6453	SO:0001583	missense	201501	exon3			GCGCGCGCCCGAA	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	31700	protein-coding gene	gene with protein product			"zinc finger and BTB domain containing 36"	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.1681C>T	chr18.hg19:g.45555810G>A	ENSP00000468782:p.Arg561Cys	33.0	0.0		26.0	10.0	NM_001039360	O73453	Missense_Mutation	SNP	ENST00000588982.1	hg19	CCDS32830.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.761613	0.49468	.	.	ENSG00000184828	ENST00000535628;ENST00000332053	T;T	0.11604	2.76;2.76	4.51	2.45	0.29901	.	0.659005	0.12970	N	0.424205	T	0.06690	0.0171	N	0.14661	0.345	0.43852	D	0.996445	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18209	-1.0344	10	0.87932	D	0	.	7.5778	0.27946	0.0966:0.0:0.6156:0.2878	.	561;561	B2RG49;A1YPR0	.;ZBT7C_HUMAN	C	561	ENSP00000439781:R561C;ENSP00000328732:R561C	ENSP00000328732:R561C	R	-	1	0	ZBTB7C	43809808	1.000000	0.71417	0.994000	0.49952	0.977000	0.68977	3.350000	0.52224	0.886000	0.36113	0.555000	0.69702	CGC	.	.		0.721	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360		A	45555810	G	A	45555810	3	1	94	1	0	0	0	0	1	0	0	0	17570	1087	38	1	182	1	ZBTB7C	18	45555810	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	36300285	45555810	32521438	77	13075										
EMR1	2015	hgsc.bcm.edu	37	chr19	6919616	6919616	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ggaatcggttttaaatgagcGcttcttcaaagaccaccagg	10	9	2	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr19:6919616G>A	ENST00000312053.4	+	13	1515	c.1478G>A	c.(1477-1479)cGc>cAc	p.R493H	EMR1_ENST00000381407.5_Missense_Mutation_p.R352H|EMR1_ENST00000450315.3_Missense_Mutation_p.R316H|EMR1_ENST00000250572.8_Missense_Mutation_p.R493H|EMR1_ENST00000381404.4_Missense_Mutation_p.R441H	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	493	Ser/Thr-rich.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					TTAAATGAGCGCTTCTTCAAA	0.473																																					p.R493H		Atlas-SNP	.											EMR1,right_upper_lobe,carcinoma,+1,1	EMR1	153	.	0			c.G1478A						.						140	128	132					19																	6919616		2203	4300	6503	SO:0001583	missense	2015	exon13			ATGAGCGCTTCTT	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.1478G>A	chr19.hg19:g.6919616G>A	ENSP00000311545:p.Arg493His	188.0	0.0		133.0	60.0	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	hg19	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	G	7.865	0.726947	0.15439	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.78707	-1.14;-1.17;-1.2;0.01;0.33	3.99	0.387	0.16259	.	.	.	.	.	T	0.68943	0.3056	L	0.59436	1.845	0.09310	N	1	B;B;B;B;B	0.16603	0.018;0.006;0.007;0.004;0.002	B;B;B;B;B	0.10450	0.004;0.003;0.005;0.001;0.002	T	0.60414	-0.7268	9	0.56958	D	0.05	.	3.8521	0.08959	0.2285:0.202:0.5695:0.0	.	316;352;493;441;493	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	H	493;493;441;493;352;316	ENSP00000311545:R493H;ENSP00000370811:R441H;ENSP00000250572:R493H;ENSP00000370814:R352H;ENSP00000405974:R316H	ENSP00000250572:R493H	R	+	2	0	EMR1	6870616	0.075000	0.21258	0.060000	0.19600	0.001000	0.01503	0.811000	0.27198	0.471000	0.27319	-1.141000	0.01876	CGC	.	.		0.473	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			A	6919616	G	A	6919616	3	1	94	1	0	0	0	0	1	0	0	0	5106	1087	38	1	1528	1	EMR1	19	6919616	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10		6919616	52209367	78	13076										
SLC44A2	57153	hgsc.bcm.edu	37	chr19	10753056	10753056	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	tgcccagacggtgatcgttgGctcctacttgattgcacacg	11	12	0	3			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr19:10753056G>A	ENST00000335757.5	+	21	2319	c.1943G>A	c.(1942-1944)gGc>gAc	p.G648D	SLC44A2_ENST00000407327.4_Missense_Mutation_p.G646D|SLC44A2_ENST00000588214.1_3'UTR|SLC44A2_ENST00000586078.1_Missense_Mutation_p.G648D			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	648					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	GTGATCGTTGGCTCCTACTTG	0.577																																					p.G648D		Atlas-SNP	.											.	SLC44A2	56	.	0			c.G1943A						.						317	201	240					19																	10753056		2203	4300	6503	SO:0001583	missense	57153	exon21			TCGTTGGCTCCTA	AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"Solute carriers"	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000335757.5:c.1943G>A	chr19.hg19:g.10753056G>A	ENSP00000336888:p.Gly648Asp	310.0	0.0		205.0	82.0	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Missense_Mutation	SNP	ENST00000335757.5	hg19	CCDS12245.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382023	0.82792	.	.	ENSG00000129353	ENST00000407327;ENST00000335757;ENST00000380614	T;T	0.24350	1.86;1.86	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.63462	0.2513	M	0.93375	3.41	0.80722	D	1	D;D;D	0.71674	0.998;0.996;0.995	D;D;D	0.78314	0.991;0.953;0.985	T	0.72478	-0.4281	10	0.62326	D	0.03	-3.4702	18.5195	0.90947	0.0:0.0:1.0:0.0	.	648;648;646	Q8IWA5-2;Q8IWA5;Q8IWA5-3	.;CTL2_HUMAN;.	D	646;648;648	ENSP00000385135:G646D;ENSP00000336888:G648D	ENSP00000336888:G648D	G	+	2	0	SLC44A2	10614056	1.000000	0.71417	0.995000	0.50966	0.480000	0.33159	9.300000	0.96151	2.668000	0.90789	0.655000	0.94253	GGC	.	.		0.577	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1			A	10753056	G	A	10753056	3	1	94	1	0	0	0	0	1	0	0	0	14651	1203	42	3	2060	3	SLC44A2	19	10753056	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	3833440	10753056	48375927	79	13077										
IL12RB1	3594	hgsc.bcm.edu	37	chr19	18188364	18188364	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gggtgtccggtgccggaactGcacctcagcaccaacctggt	13	14	1	0			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr19:18188364G>A	ENST00000600835.2	-	6	809	c.511C>T	c.(511-513)Cag>Tag	p.Q171*	IL12RB1_ENST00000322153.7_Nonsense_Mutation_p.Q171*|IL12RB1_ENST00000593993.2_Nonsense_Mutation_p.Q171*			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	171	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						TGCCGGAACTGCACCTCAGCA	0.592																																					p.Q171X		Atlas-SNP	.											.	IL12RB1	92	.	0			c.C511T						.						72	56	61					19																	18188364		2203	4300	6503	SO:0001587	stop_gained	3594	exon5			GGAACTGCACCTC	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.511C>T	chr19.hg19:g.18188364G>A	ENSP00000470788:p.Gln171*	71.0	0.0		58.0	22.0	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Nonsense_Mutation	SNP	ENST00000600835.2	hg19	CCDS54232.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.364002	0.61513	.	.	ENSG00000096996	ENST00000430026;ENST00000322153	.	.	.	3.76	2.55	0.30701	.	0.147877	0.30329	N	0.009879	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-23.4185	8.2813	0.31902	0.0:0.3301:0.6699:0.0	.	.	.	.	X	171	.	ENSP00000314425:Q171X	Q	-	1	0	IL12RB1	18049364	0.946000	0.32159	0.454000	0.27019	0.006000	0.05464	2.529000	0.45632	1.844000	0.53588	0.484000	0.47621	CAG	.	.		0.592	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3			A	18188364	G	A	18188364	4	1	94	1	0	0	0	0	0	1	0	0	7635	1328	46	3	1658	3	IL12RB1	19	18188364	Nonsense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	7435308	18188364	40940619	80	13078										
HAUS5	23354	hgsc.bcm.edu	37	chr19	36106172	36106172	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	cagcacactcaagacacccaGcgtcgagctctcctcctccg	7	19	2	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr19:36106172G>A	ENST00000203166.5	+	6	394	c.369G>A	c.(367-369)caG>caA	p.Q123Q	AC002115.9_ENST00000589603.1_lincRNA|HAUS5_ENST00000379045.2_Silent_p.Q123Q	NM_015302.1	NP_056117.1	O94927	HAUS5_HUMAN	HAUS augmin-like complex, subunit 5	123					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				NS(1)|breast(2)|cervix(3)|endometrium(1)|large_intestine(2)|lung(5)|skin(2)	16						AAGACACCCAGCGTCGAGCTC	0.642																																					p.Q123Q		Atlas-SNP	.											.	HAUS5	41	.	0			c.G369A						.						29	34	32					19																	36106172		2140	4258	6398	SO:0001819	synonymous_variant	23354	exon6			CACCCAGCGTCGA	AB020648	CCDS42550.1	19q13.12	2012-02-22	2009-04-20	2009-04-20	ENSG00000249115	ENSG00000249115		"HAUS augmin-like complex subunits"	29130	protein-coding gene	gene with protein product		613432	"KIAA0841"	KIAA0841		10048485, 19427217	Standard	NM_015302		Approved	dgt5	uc002oam.1	O94927	OTTHUMG00000048110	ENST00000203166.5:c.369G>A	chr19.hg19:g.36106172G>A		61.0	0.0		42.0	22.0	NM_015302	B2RXK1|Q6P2P7|Q7L3D5|Q96CT8	Silent	SNP	ENST00000203166.5	hg19	CCDS42550.1																																																																																			.	.		0.642	HAUS5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459055.2			A	36106172	G	A	36106172	2	1	94	1	0	0	0	0	0	0	0	1	6978	962	34	3		3	HAUS5	19	36106172	Silent	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10	17917808	36106172	23022811	81	13079										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40714481	40714481	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	ggaggtcttctcaggccagtActgcatacagaactgagata	11	9	2	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr20:40714481A>G	ENST00000373187.1	-	28	3858	c.3859T>C	c.(3859-3861)Tac>Cac	p.Y1287H	PTPRT_ENST00000356100.2_Missense_Mutation_p.Y1296H|PTPRT_ENST00000373193.3_Missense_Mutation_p.Y1290H|PTPRT_ENST00000373184.1_Missense_Mutation_p.Y1297H|PTPRT_ENST00000373201.1_Missense_Mutation_p.Y1277H|PTPRT_ENST00000373190.1_Missense_Mutation_p.Y1286H|PTPRT_ENST00000373198.4_Missense_Mutation_p.Y1306H			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1287	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TCAGGCCAGTACTGCATACAG	0.498																																					p.Y1306H		Atlas-SNP	.											.	PTPRT	372	.	0			c.T3916C						.						66	67	67					20																	40714481		1933	4138	6071	SO:0001583	missense	11122	exon29			GCCAGTACTGCAT	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.3859T>C	chr20.hg19:g.40714481A>G	ENSP00000362283:p.Tyr1287His	82.0	0.0		102.0	30.0	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.834450	0.91036	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	D;D;D;D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27	5.31	5.31	0.75309	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.136624	0.51477	D	0.000097	D	0.98317	0.9442	H	0.99379	4.54	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.983;0.99	D	0.99694	1.1002	10	0.87932	D	0	.	15.4285	0.75072	1.0:0.0:0.0:0.0	.	1309;1287	O14522-1;O14522	.;PTPRT_HUMAN	H	1286;1287;1290;1296;1309;1297;1277	ENSP00000362286:Y1286H;ENSP00000362283:Y1287H;ENSP00000362289:Y1290H;ENSP00000348408:Y1296H;ENSP00000362294:Y1309H;ENSP00000362280:Y1297H;ENSP00000362297:Y1277H	ENSP00000348408:Y1296H	Y	-	1	0	PTPRT	40147895	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.040000	0.93783	2.232000	0.73038	0.533000	0.62120	TAC	.	.		0.498	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			G	40714481	A	G	40714481	3	3	94	1	0	0	0	0	1	0	0	0	12827	391	14	2	482	2	PTPRT	20	40714481	Missense_Mutation	SNP	A	TCGA-DD-A11C-01A-11D-A12Z-10		40714481	22311039	82	13080										
TTPAL	79183	hgsc.bcm.edu	37	chr20	43108685	43108685	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gaaccagcccttctgtggccTcactctctgaaaatgagctg	9	13	3	2			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr20:43108685T>G	ENST00000372904.3	+	3	189	c.46T>G	c.(46-48)Tca>Gca	p.S16A	TTPAL_ENST00000262605.4_Missense_Mutation_p.S16A|TTPAL_ENST00000372906.2_Missense_Mutation_p.S16A	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	16						intracellular (GO:0005622)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|skin(5)	18						TTCTGTGGCCTCACTCTCTGA	0.537																																					p.S16A		Atlas-SNP	.											.	TTPAL	31	.	0			c.T46G						.						67	66	66					20																	43108685		2203	4300	6503	SO:0001583	missense	79183	exon2			GTGGCCTCACTCT	BC003071	CCDS13332.2	20q13.12	2008-06-23	2008-06-23	2008-06-23	ENSG00000124120	ENSG00000124120			16114	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 121"	C20orf121			Standard	NM_024331		Approved	dJ179M20.3	uc002xmd.2	Q9BTX7	OTTHUMG00000032536	ENST00000372904.3:c.46T>G	chr20.hg19:g.43108685T>G	ENSP00000361995:p.Ser16Ala	59.0	0.0		60.0	35.0	NM_001039199	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Missense_Mutation	SNP	ENST00000372904.3	hg19	CCDS13332.2	.	.	.	.	.	.	.	.	.	.	T	13.33	2.205585	0.39003	.	.	ENSG00000124120	ENST00000262605;ENST00000372904;ENST00000372906;ENST00000456317	T;T;D;D	0.94184	-1.21;-1.21;-3.37;-2.19	5.18	5.18	0.71444	.	0.350651	0.30168	N	0.010255	D	0.85124	0.5625	N	0.14661	0.345	0.28410	N	0.918245	B	0.29378	0.243	B	0.27380	0.079	T	0.76740	-0.2848	10	0.25106	T	0.35	-14.1751	10.4353	0.44433	0.1453:0.0:0.0:0.8547	.	16	Q9BTX7	TTPAL_HUMAN	A	16	ENSP00000262605:S16A;ENSP00000361995:S16A;ENSP00000361997:S16A;ENSP00000412720:S16A	ENSP00000262605:S16A	S	+	1	0	TTPAL	42542099	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	3.034000	0.49751	2.164000	0.68074	0.533000	0.62120	TCA	.	.		0.537	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331		G	43108685	T	G	43108685	3	3	94	1	0	0	0	0	1	0	0	0	16752	1551	54	5	48	5	TTPAL	20	43108685	Missense_Mutation	SNP	T	TCGA-DD-A11C-01A-11D-A12Z-10	2394204	43108685	19916835	83	13081										
TTC3	7267	hgsc.bcm.edu	37	chr21	38572587	38572587	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	aggtgttcaaatcaaaaaacGtgcgtgtgctcaaatgtggg	12	6	3	0	rs200071342		TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr21:38572587G>A	ENST00000399017.2	+	45	8652	c.5905G>A	c.(5905-5907)Gtg>Atg	p.V1969M	TTC3_ENST00000355666.1_Missense_Mutation_p.V1969M|TTC3_ENST00000354749.2_Missense_Mutation_p.V1969M|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1969					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				ATCAAAAAACGTGCGTGTGCT	0.413																																					p.V1969M	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.G5905A						.						90	78	82					21																	38572587		2203	4300	6503	SO:0001583	missense	7267	exon45			AAAAACGTGCGTG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5905G>A	chr21.hg19:g.38572587G>A	ENSP00000381981:p.Val1969Met	210.0	0.0		138.0	57.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.29|13.29	2.192723|2.192723	0.38707|0.38707	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000428693|ENST00000355666;ENST00000399017;ENST00000354749	.|T;T;T	.|0.71817	.|-0.6;-0.6;-0.6	5.58|5.58	-2.2|-2.2	0.06994|0.06994	.|Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	.|1.130140	.|0.06565	.|N	.|0.747410	T|T	0.55940|0.55940	0.1952|0.1952	L|L	0.59436|0.59436	1.845|1.845	0.09310|0.09310	N|N	1|1	.|P	.|0.39404	.|0.672	.|B	.|0.30943	.|0.122	T|T	0.42447|0.42447	-0.9451|-0.9451	5|10	.|0.19147	.|T	.|0.46	-1.4936|-1.4936	4.8143|4.8143	0.13358|0.13358	0.4155:0.2861:0.2984:0.0|0.4155:0.2861:0.2984:0.0	.|.	.|1969	.|P53804	.|TTC3_HUMAN	H|M	260|1969	.|ENSP00000347889:V1969M;ENSP00000381981:V1969M;ENSP00000346791:V1969M	.|ENSP00000346791:V1969M	R|V	+|+	2|1	0|0	TTC3|TTC3	37494457|37494457	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.975000|0.975000	0.68041|0.68041	-0.537000|-0.537000	0.06128|0.06128	-0.233000|-0.233000	0.09797|0.09797	0.655000|0.655000	0.94253|0.94253	CGT|GTG	.	G|0.999;A|0.001		0.413	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			A	38572587	G	A	38572587	3	1	94	1	0	0	0	0	1	0	0	0	16712	1145	40	1	6079	1	TTC3	21	38572587	Missense_Mutation	SNP	G	TCGA-DD-A11C-01A-11D-A12Z-10		38572587	9557308	84	13082										
RRP1B	23076	hgsc.bcm.edu	37	chr21	45089836	45089836	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	4	1	0.612903225806452	0	0.722911497105046	0.0476190476190476	0.422902494331066	0	gcatgtgggtgcaggatgaaCcccttctacaggtaacatgc	12	10	1	1			TCGA-DD-A11C-01A-11D-A12Z-10	TCGA-DD-A11C-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9cde9a5-c0ff-4c01-8182-81c9ef3920e6	d5d8c783-db2c-487c-9cce-1b76137ddc15	g.chr21:45089836C>A	ENST00000340648.4	+	2	319	c.202C>A	c.(202-204)Ccc>Acc	p.P68T		NM_015056.2	NP_055871.1	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1B	68					negative regulation of phosphatase activity (GO:0010923)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome, small subunit precursor (GO:0030688)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(1)	21				STAD - Stomach adenocarcinoma(101;0.178)		GCAGGATGAACCCCTTCTACA	0.483																																					p.P68T		Atlas-SNP	.											.	RRP1B	51	.	0			c.C202A						.						112	108	109					21																	45089836		2203	4300	6503	SO:0001583	missense	23076	exon2			GATGAACCCCTTC	AK124620	CCDS33577.1	21q22.3	2014-06-13	2013-07-02	2007-03-26	ENSG00000160208	ENSG00000160208			23818	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 136"	610654	"KIAA0179", "ribosomal RNA processing 1 homolog B (S. cerevisiae)"	KIAA0179			Standard	NM_015056		Approved	Nnp1, RRP1, PPP1R136	uc002zdk.3	Q14684	OTTHUMG00000086872	ENST00000340648.4:c.202C>A	chr21.hg19:g.45089836C>A	ENSP00000339145:p.Pro68Thr	310.0	0.0		192.0	103.0	NM_015056	Q8TBZ4	Missense_Mutation	SNP	ENST00000340648.4	hg19	CCDS33577.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.371033	0.61624	.	.	ENSG00000160208	ENST00000340648	T	0.52295	0.67	5.84	4.01	0.46588	.	0.048335	0.85682	D	0.000000	T	0.66287	0.2774	M	0.92507	3.315	0.58432	D	0.999997	P	0.47604	0.898	P	0.51974	0.686	T	0.74034	-0.3794	10	0.87932	D	0	-0.1797	10.3306	0.43820	0.0:0.7944:0.1334:0.0723	.	68	Q14684	RRP1B_HUMAN	T	68	ENSP00000339145:P68T	ENSP00000339145:P68T	P	+	1	0	RRP1B	43914264	1.000000	0.71417	0.972000	0.41901	0.813000	0.45954	2.301000	0.43628	1.473000	0.48159	-0.150000	0.13652	CCC	.	.		0.483	RRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195651.1	NM_015056		A	45089836	C	A	45089836	3	1	94	1	0	0	0	0	1	0	0	0	13703	507	18	3	208	3	RRP1B	21	45089836	Missense_Mutation	SNP	C	TCGA-DD-A11C-01A-11D-A12Z-10	6517249	45089836	3040059	85	13083										
ERRFI1	54206	hgsc.bcm.edu	37	chr1	8074176	8074182	+	Frame_Shift_Del	DEL	GGCTTCA	GGCTTCA	-													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tctgtgtcatccagagagagGgcttcagagattggcaacgg							TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	GGCTTCA	GGCTTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr1:8074176_8074182delGGCTTCA	ENST00000377482.5	-	4	700_706	c.477_483delTGAAGCC	c.(475-483)tctgaagccfs	p.SEA159fs	ERRFI1_ENST00000474874.1_Intron|ERRFI1_ENST00000469499.1_3'UTR|ERRFI1_ENST00000467067.1_3'UTR	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	159					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		CCAGAGAGAGGGCTTCAGAGATTGGCA	0.483																																					p.160_162del		Atlas-Indel,Pindel	.											.	ERRFI1	42	.	0			c.478_484del						.																																			SO:0001589	frameshift_variant	54206	exon4			.	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.477_483delTGAAGCC	chr1.hg19:g.8074176_8074182delGGCTTCA	ENSP00000366702:p.Ser159fs	136.0	0.0		40.0	18.0	NM_018948	B2RDX9|Q9NTG9|Q9UD05	Frame_Shift_Del	DEL	ENST00000377482.5	hg19	CCDS94.1																																																																																			.	.		0.483	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948		-	8074182	GGCTTCA	-	8074176	7	5	95	1	0	1	0	1	0	0	0	0	5246	1219	43	0	909	0	ERRFI1	1	8074176	Frame_Shift_Del	DEL	GGCTTCA	TCGA-DD-A11D-01A-11D-A12Z-10		8074176	241176445	1	13084										
ACTL8	81569	hgsc.bcm.edu	37	chr1	18152300	18152300	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	catgtcccatcggtcctcctGgccgaccagctgcagatgtc	10	16	0	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr1:18152300G>C	ENST00000375406.1	+	3	603	c.387G>C	c.(385-387)ctG>ctC	p.L129L		NM_030812.2	NP_110439.2	Q9H568	ACTL8_HUMAN	actin-like 8	129					epithelial cell differentiation (GO:0030855)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	28		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)		CGGTCCTCCTGGCCGACCAGC	0.587											OREG0013157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L129L		Atlas-SNP	.											.	ACTL8	58	.	0			c.G387C						.						91	76	81					1																	18152300		2203	4300	6503	SO:0001819	synonymous_variant	81569	exon3			CCTCCTGGCCGAC	AK057339	CCDS183.1	1p36.2-p35	2009-03-25			ENSG00000117148	ENSG00000117148			24018	protein-coding gene	gene with protein product	"cancer/testis antigen 57"						Standard	NM_030812		Approved	CT57	uc001bat.3	Q9H568	OTTHUMG00000002512	ENST00000375406.1:c.387G>C	chr1.hg19:g.18152300G>C		120.0	0.0	723	123.0	52.0	NM_030812	Q13104|Q96M75	Silent	SNP	ENST00000375406.1	hg19	CCDS183.1																																																																																			.	.		0.587	ACTL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007143.1	NM_030812		C	18152300	G	C	18152300	2	2	95	1	0	0	0	0	0	0	0	1	202	1335	47	4		4	ACTL8	1	18152300	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	10078124	18152300	231098321	2	13085										
LRRC8D	55144	hgsc.bcm.edu	37	chr1	90399468	90399468	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	caatcctggataaaaaggatGgagagcaggccaaagccctg	12	9	0	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr1:90399468G>A	ENST00000337338.5	+	3	1248	c.841G>A	c.(841-843)Gga>Aga	p.G281R	LRRC8D_ENST00000394593.3_Missense_Mutation_p.G281R	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	281					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		TAAAAAGGATGGAGAGCAGGC	0.428																																					p.G281R		Atlas-SNP	.											.	LRRC8D	78	.	0			c.G841A						.						40	40	40					1																	90399468		2203	4300	6503	SO:0001583	missense	55144	exon3			AAGGATGGAGAGC	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.841G>A	chr1.hg19:g.90399468G>A	ENSP00000338887:p.Gly281Arg	75.0	0.0		52.0	17.0	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	hg19	CCDS726.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.782792	0.70222	.	.	ENSG00000171492	ENST00000337338;ENST00000394593	T;T	0.39406	1.08;1.08	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.48277	0.1491	L	0.49778	1.585	0.80722	D	1	D	0.54772	0.968	P	0.58013	0.831	T	0.19418	-1.0306	9	.	.	.	.	20.2422	0.98381	0.0:0.0:1.0:0.0	.	281	Q7L1W4	LRC8D_HUMAN	R	281	ENSP00000338887:G281R;ENSP00000378093:G281R	.	G	+	1	0	LRRC8D	90172056	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	9.869000	0.99810	2.782000	0.95742	0.655000	0.94253	GGA	.	.		0.428	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		A	90399468	G	A	90399468	3	1	95	1	0	0	0	0	1	0	0	0	9033	1349	47	3	843	3	LRRC8D	1	90399468	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	72247168	90399468	158851153	3	13086										
RFX5	5993	hgsc.bcm.edu	37	chr1	151314816	151314816	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ttctgctgcccttgatgacaCtcacttttgaggggaccaag	10	11	2	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr1:151314816C>A	ENST00000290524.4	-	11	1875	c.1697G>T	c.(1696-1698)aGt>aTt	p.S566I	RP11-126K1.8_ENST00000422153.1_RNA|RFX5_ENST00000478564.1_5'Flank|RFX5_ENST00000368870.2_Missense_Mutation_p.S566I|RFX5_ENST00000452513.2_Missense_Mutation_p.S526I|RFX5_ENST00000452671.2_Missense_Mutation_p.S566I	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	566					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CTTGATGACACTCACTTTTGA	0.498																																					p.S566I		Atlas-SNP	.											.	RFX5	69	.	0			c.G1697T						.						135	128	130					1																	151314816		2203	4300	6503	SO:0001583	missense	5993	exon11			ATGACACTCACTT		CCDS994.1	1q21	2014-09-17			ENSG00000143390	ENSG00000143390			9986	protein-coding gene	gene with protein product		601863				9401005	Standard	XM_005245405		Approved		uc001exw.1	P48382	OTTHUMG00000012495	ENST00000290524.4:c.1697G>T	chr1.hg19:g.151314816C>A	ENSP00000290524:p.Ser566Ile	465.0	0.0		489.0	33.0	NM_000449	B7Z848|D3DV19|E9PFU4|Q5VWC3	Missense_Mutation	SNP	ENST00000290524.4	hg19	CCDS994.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.343206	0.61073	.	.	ENSG00000143390	ENST00000290524;ENST00000368870;ENST00000452671;ENST00000452513;ENST00000392746	T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89	5.15	5.15	0.70609	.	0.147419	0.48767	D	0.000171	T	0.53642	0.1809	M	0.64997	1.995	0.42570	D	0.993179	D;D	0.71674	0.995;0.998	D;D	0.78314	0.986;0.991	T	0.56481	-0.7972	10	0.87932	D	0	-11.928	13.999	0.64421	0.0:1.0:0.0:0.0	.	526;566	B7Z848;P48382	.;RFX5_HUMAN	I	566;566;566;526;566	ENSP00000290524:S566I;ENSP00000357864:S566I;ENSP00000389130:S566I;ENSP00000398388:S526I;ENSP00000376502:S566I	ENSP00000290524:S566I	S	-	2	0	RFX5	149581440	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	3.540000	0.53611	2.689000	0.91719	0.591000	0.81541	AGT	.	.		0.498	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449		A	151314816	C	A	151314816	3	1	95	1	0	0	0	0	1	0	0	0	13281	565	20	3	157	3	RFX5	1	151314816	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	60915348	151314816	97935805	4	13087										
RCSD1	92241	hgsc.bcm.edu	37	chr1	167663459	167663459	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ccagcagccctggtgtgcgaTctaggcccagcgaggcagag	15	13	1	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr1:167663459T>A	ENST00000367854.3	+	5	725	c.394T>A	c.(394-396)Tct>Act	p.S132T	RCSD1_ENST00000537350.1_Missense_Mutation_p.S102T	NM_052862.3	NP_443094.3	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	132					cellular hyperosmotic response (GO:0071474)|skeletal muscle contraction (GO:0003009)	actin filament (GO:0005884)	actin filament binding (GO:0051015)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	24	all_hematologic(923;0.215)					TGGTGTGCGATCTAGGCCCAG	0.582																																					p.S132T		Atlas-SNP	.											.	RCSD1	64	.	0			c.T394A						.						67	63	65					1																	167663459		2203	4300	6503	SO:0001583	missense	92241	exon5			GTGCGATCTAGGC	BC072399	CCDS1263.1	1q24.2	2008-02-05			ENSG00000198771	ENSG00000198771			28310	protein-coding gene	gene with protein product		610579				12477932	Standard	NM_052862		Approved	MK2S4, MGC21854	uc001gem.3	Q6JBY9	OTTHUMG00000035318	ENST00000367854.3:c.394T>A	chr1.hg19:g.167663459T>A	ENSP00000356828:p.Ser132Thr	102.0	0.0		161.0	47.0	NM_052862	B1AK48|Q4G0E7|Q6IN93|Q8IZM2|Q96DX0|Q9NST4	Missense_Mutation	SNP	ENST00000367854.3	hg19	CCDS1263.1	.	.	.	.	.	.	.	.	.	.	T	11.95	1.790947	0.31685	.	.	ENSG00000198771	ENST00000367854;ENST00000361496;ENST00000537350	T;T	0.54675	0.61;0.56	5.18	0.256	0.15567	.	0.320614	0.33092	N	0.005294	T	0.33411	0.0862	L	0.40543	1.245	0.23923	N	0.99646	P;D	0.56521	0.89;0.976	B;P	0.50049	0.318;0.629	T	0.28427	-1.0044	9	0.56958	D	0.05	-1.5821	10.6741	0.45776	0.0:0.4197:0.0:0.5803	.	102;132	B7ZKW8;Q6JBY9	.;CPZIP_HUMAN	T	132;108;102	ENSP00000356828:S132T;ENSP00000439409:S102T	ENSP00000355291:S108T	S	+	1	0	RCSD1	165930083	0.001000	0.12720	0.000000	0.03702	0.100000	0.18952	-0.044000	0.12023	-0.137000	0.11455	-0.256000	0.11100	TCT	.	.		0.582	RCSD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085451.1	NM_052862		A	167663459	T	A	167663459	3	1	95	1	0	0	0	0	1	0	0	0	13200	1435	50	4	412	4	RCSD1	1	167663459	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	16348643	167663459	81587162	5	13088										
ATP2B4	493	hgsc.bcm.edu	37	chr1	203667458	203667481	+	Splice_Site	DEL	CGCCCTGCTGGTGAAGAAAATGAA	CGCCCTGCTGGTGAAGAAAATGAA	-													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ccctggtcctgtccttttatCgccctgctggtgaagaaaat					rs114358697|rs372768311	byFrequency	TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	CGCCCTGCTGGTGAAGAAAATGAA	CGCCCTGCTGGTGAAGAAAATGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr1:203667458_203667481delCGCCCTGCTGGTGAAGAAAATGAA	ENST00000357681.5	+	3	1490_1513	c.367_390delCGCCCTGCTGGTGAAGAAAATGAA	c.(367-390)cgccctgctggtgaagaaaatgaadel	p.RPAGEENE123del	ATP2B4_ENST00000367219.3_Splice_Site_p.RPAGEENE123del|ATP2B4_ENST00000367218.3_Splice_Site_p.RPAGEENE123del|ATP2B4_ENST00000391954.2_Splice_Site_p.RPAGEENE123del|ATP2B4_ENST00000341360.2_Splice_Site_p.RPAGEENE123del	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	123					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)	p.E127E(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GTCCTTTTATCGCCCTGCTGGTGAAGAAAATGAACGTGAGTGTC	0.473																																					p.122_130del		Pindel	.											.	ATP2B4	226	.	2	Substitution - coding silent(2)	urinary_tract(2)	c.366_389del						.																																			SO:0001630	splice_region_variant	493	exon3			.	M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"ATPases / P-type"	817	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 4"	108732	"matrix-remodelling associated 1"	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.391+1CGCCCTGCTGGTGAAGAAAATGAA>-	chr1.hg19:g.203667458_203667481delCGCCCTGCTGGTGAAGAAAATGAA		250.0	0.0		223.0	29.0	NM_001001396	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	In_Frame_Del	DEL	ENST00000357681.5	hg19	CCDS1440.1																																																																																			.	.		0.473	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396	In_Frame_Del	-	203667481	CGCCCTGCTGGTGAAGAAAATGAA	-	203667458	8	5	95	1	0	1	0	1	0	0	1	0	1142	884	31	0	373	0	ATP2B4	1	203667458	Splice_Site	DEL	CGCCCTGCTGGTGAAGAAAATGAA	TCGA-DD-A11D-01A-11D-A12Z-10	36003999	203667458	45583163	6	13089										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247588697	247588697	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aagggccatggactatttccCcaagattgagatcaatctct	8	10	2	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr1:247588697C>A	ENST00000336119.3	+	3	2698	c.1952C>A	c.(1951-1953)cCc>cAc	p.P651H	NLRP3_ENST00000366496.2_Missense_Mutation_p.P651H|NLRP3_ENST00000366497.2_Missense_Mutation_p.P651H|NLRP3_ENST00000391827.2_Missense_Mutation_p.P651H|NLRP3_ENST00000391828.3_Missense_Mutation_p.P651H|NLRP3_ENST00000348069.2_Missense_Mutation_p.P651H|NLRP3_ENST00000474792.1_3'UTR	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	651					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			GACTATTTCCCCAAGATTGAG	0.498																																					p.P651H		Atlas-SNP	.											.	NLRP3	286	.	0			c.C1952A						.						94	80	85					1																	247588697		2203	4300	6503	SO:0001583	missense	114548	exon3			ATTTCCCCAAGAT	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1952C>A	chr1.hg19:g.247588697C>A	ENSP00000337383:p.Pro651His	243.0	0.0		261.0	85.0	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.125165	0.56721	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	D;D;D;D;D;D	0.89552	-2.53;-2.53;-2.53;-2.53;-2.53;-2.53	3.96	3.96	0.45880	.	0.000000	0.48767	D	0.000163	D	0.88887	0.6559	L	0.27053	0.805	0.44843	D	0.997853	B;B;D;B;B	0.69078	0.167;0.278;0.997;0.198;0.23	B;B;D;B;B	0.66716	0.099;0.201;0.946;0.257;0.131	D	0.87909	0.2696	10	0.44086	T	0.13	.	11.8199	0.52232	0.0:1.0:0.0:0.0	.	651;651;651;651;651	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	H	651	ENSP00000375704:P651H;ENSP00000355453:P651H;ENSP00000337383:P651H;ENSP00000294752:P651H;ENSP00000355452:P651H;ENSP00000375703:P651H	ENSP00000337383:P651H	P	+	2	0	NLRP3	245655320	0.035000	0.19736	0.999000	0.59377	0.888000	0.51559	0.459000	0.21908	2.502000	0.84385	0.655000	0.94253	CCC	.	.		0.498	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		A	247588697	C	A	247588697	3	1	95	1	0	0	0	0	1	0	0	0	10487	623	22	3	1962	3	NLRP3	1	247588697	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	43921239	247588697	1661924	7	13090										
OR2L3	391192	hgsc.bcm.edu	37	chr1	248224574	248224574	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	acctgggtctatgagggcacAgtgtttttgagcaccaccat	11	10	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr1:248224574A>T	ENST00000359959.3	+	1	591	c.591A>T	c.(589-591)acA>acT	p.T197T	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			ATGAGGGCACAGTGTTTTTGA	0.478																																					p.T197T		Atlas-SNP	.											.	OR2L3	97	.	0			c.A591T						.						172	191	185					1																	248224574		2196	4300	6496	SO:0001819	synonymous_variant	391192	exon1			GGGCACAGTGTTT	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"GPCR / Class A : Olfactory receptors"	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.591A>T	chr1.hg19:g.248224574A>T		1021.0	0.0		1251.0	67.0	NM_001004687	B9EH44	Silent	SNP	ENST00000359959.3	hg19	CCDS31104.1																																																																																			.	.		0.478	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		T	248224574	A	T	248224574	2	4	95	1	0	0	0	0	0	0	0	1	11017	175	7	4		4	OR2L3	1	248224574	Silent	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	635877	248224574	1026047	8	13091										
HTRA2	27429	hgsc.bcm.edu	37	chr2	74757336	74757336	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gtctgttggggtcactgaacCccgagcatgcctgacgtctg	13	12	3	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr2:74757336C>G	ENST00000258080.3	+	1	833	c.203C>G	c.(202-204)cCc>cGc	p.P68R	AUP1_ENST00000377526.3_5'Flank|HTRA2_ENST00000467961.1_Intron|HTRA2_ENST00000352222.3_Missense_Mutation_p.P68R	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN	HtrA serine peptidase 2	68					adult walking behavior (GO:0007628)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|ceramide metabolic process (GO:0006672)|execution phase of apoptosis (GO:0097194)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitochondrion organization (GO:0007005)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|pentacyclic triterpenoid metabolic process (GO:0019742)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell death (GO:0010942)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of mitochondrion degradation (GO:1903146)|regulation of multicellular organism growth (GO:0040014)|response to herbicide (GO:0009635)	CD40 receptor complex (GO:0035631)|chromatin (GO:0000785)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)|unfolded protein binding (GO:0051082)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12						GTCACTGAACCCCGAGCATGC	0.662																																					p.P68R		Atlas-SNP	.											.	HTRA2	22	.	0			c.C203G						.						12	14	14					2																	74757336		2190	4287	6477	SO:0001583	missense	27429	exon1			CTGAACCCCGAGC		CCDS1951.1, CCDS1952.1	2p13.1	2011-07-21	2005-08-19	2005-08-19	ENSG00000115317	ENSG00000115317		"Serine peptidases / Serine peptidases", "Parkinson disease"	14348	protein-coding gene	gene with protein product		606441	"protease, serine, 25"	PRSS25		10644717, 10971580	Standard	XM_005264266		Approved	OMI, PARK13	uc002smi.1	O43464	OTTHUMG00000129957	ENST00000258080.3:c.203C>G	chr2.hg19:g.74757336C>G	ENSP00000258080:p.Pro68Arg	73.0	0.0		77.0	31.0	NM_013247	Q9HBZ4|Q9P0Y3|Q9P0Y4	Missense_Mutation	SNP	ENST00000258080.3	hg19	CCDS1951.1	.	.	.	.	.	.	.	.	.	.	c	0.011	-1.697609	0.00725	.	.	ENSG00000115317	ENST00000258080;ENST00000352222;ENST00000437202	T;T;T	0.15952	2.38;2.38;2.38	5.0	3.21	0.36854	.	1.090900	0.07058	N	0.833151	T	0.12433	0.0302	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.28324	0.132;0.207;0.207;0.132	B;B;B;B	0.30646	0.055;0.118;0.118;0.055	T	0.37079	-0.9721	10	0.38643	T	0.18	0.2023	6.3613	0.21431	0.1799:0.7281:0.0:0.0919	.	68;68;68;68	A8K7G2;O43464-3;O43464-2;O43464	.;.;.;HTRA2_HUMAN	R	68;68;55	ENSP00000258080:P68R;ENSP00000312893:P68R;ENSP00000399166:P55R	ENSP00000258080:P68R	P	+	2	0	HTRA2	74610844	0.004000	0.15560	0.003000	0.11579	0.139000	0.21198	1.101000	0.31037	0.701000	0.31803	-0.379000	0.06801	CCC	.	.		0.662	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247		G	74757336	C	G	74757336	3	3	95	1	0	0	0	0	1	0	0	0	7463	623	22	4	205	4	HTRA2	2	74757336	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10		74757336	168442037	9	13092										
GTDC1	79712	hgsc.bcm.edu	37	chr2	144903285	144903285	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gccagttcggtcaggttaagCactgaacttgcaaagagggt	13	8	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr2:144903285C>A	ENST00000392869.2	-	4	353	c.201G>T	c.(199-201)gtG>gtT	p.V67V	GTDC1_ENST00000241391.5_Silent_p.V67V|GTDC1_ENST00000463875.2_5'UTR|GTDC1_ENST00000542155.1_Silent_p.V67V|GTDC1_ENST00000392867.3_Silent_p.V67V|GTDC1_ENST00000409298.1_Silent_p.V67V|GTDC1_ENST00000344850.4_Silent_p.V67V|GTDC1_ENST00000409214.1_Silent_p.V67V	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	67					biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		TCAGGTTAAGCACTGAACTTG	0.438																																					p.V67V		Atlas-SNP	.											.	GTDC1	61	.	0			c.G201T						.						100	96	98					2																	144903285		2203	4300	6503	SO:0001819	synonymous_variant	79712	exon5			GTTAAGCACTGAA	AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			ENSG00000121964	ENSG00000121964		"Glycosyltransferase group 1 domain containing"	20887	protein-coding gene	gene with protein product	"mannosyltransferase-like"	610165				15068588, 21821951	Standard	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	Q4AE62	OTTHUMG00000131835	ENST00000392869.2:c.201G>T	chr2.hg19:g.144903285C>A		103.0	0.0		66.0	19.0	NM_001006636	A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Silent	SNP	ENST00000392869.2	hg19	CCDS33300.1																																																																																			.	.		0.438	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2	NM_024659		A	144903285	C	A	144903285	2	1	95	1	0	0	0	0	0	0	0	1	6860	697	25	3		3	GTDC1	2	144903285	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	70145949	144903285	98296088	10	13093										
GAD1	2571	hgsc.bcm.edu	37	chr2	171715379	171715379	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aggggtgtgccagacagcccTcaacgacgggaaaagctaca	13	11	1	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr2:171715379T>A	ENST00000358196.3	+	16	2137	c.1587T>A	c.(1585-1587)ccT>ccA	p.P529P		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	529					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CAGACAGCCCTCAACGACGGG	0.443																																					p.P529P		Atlas-SNP	.											.	GAD1	79	.	0			c.T1587A						.						84	86	85					2																	171715379		2203	4300	6503	SO:0001819	synonymous_variant	2571	exon16			CAGCCCTCAACGA		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1587T>A	chr2.hg19:g.171715379T>A		217.0	0.0		152.0	61.0	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Silent	SNP	ENST00000358196.3	hg19	CCDS2239.1																																																																																			.	.		0.443	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			A	171715379	T	A	171715379	2	1	95	1	0	0	0	0	0	0	0	1	6187	1538	54	4		4	GAD1	2	171715379	Silent	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	26812094	171715379	71483994	11	13094										
TTN	7273	hgsc.bcm.edu	37	chr2	179434262	179434262	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tgtaggacgaccttttatagGaacaaataaccttaaggagc	9	7	0	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr2:179434262G>T	ENST00000591111.1	-	276	71898	c.71674C>A	c.(71674-71676)Cct>Act	p.P23892T	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P16468T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P25533T|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P22965T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P16660T|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P16593T			Q8WZ42	TITIN_HUMAN	titin	23892	Ig-like 120.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTTTTATAGGAACAAATAAC	0.388																																					p.P25533T		Atlas-SNP	.											.	TTN	18412	.	0			c.C76597A						.						88	78	81					2																	179434262		1877	4108	5985	SO:0001583	missense	7273	exon326			TTATAGGAACAAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.71674C>A	chr2.hg19:g.179434262G>T	ENSP00000465570:p.Pro23892Thr	270.0	0.0		246.0	91.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.90	3.502267	0.64298	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.55	5.55	0.83447	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72045	0.3412	L	0.31420	0.93	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.74970	-0.3482	9	0.87932	D	0	.	19.4973	0.95079	0.0:0.0:1.0:0.0	.	16468;16593;16660;23892	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	22965;16468;16660;16593;16466	ENSP00000343764:P22965T;ENSP00000434586:P16468T;ENSP00000340554:P16660T;ENSP00000352154:P16593T	ENSP00000340554:P16660T	P	-	1	0	TTN	179142508	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	9.869000	0.99810	2.608000	0.88229	0.655000	0.94253	CCT	.	.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179434262	G	T	179434262	3	4	95	1	0	0	0	0	1	0	0	0	16750	1174	41	3	31530	3	TTN	2	179434262	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	7718883	179434262	63765111	12	13095										
PECR	55825	hgsc.bcm.edu	37	chr2	216930060	216930060	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ttgcacatgtagaaggtaccCgtcaggttggtctcaagcac	11	10	2	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr2:216930060C>G	ENST00000265322.7	-	3	473	c.399G>C	c.(397-399)acG>acC	p.T133T	PECR_ENST00000497889.1_5'UTR	NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	133					fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)	p.T133T(1)		endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	AGAAGGTACCCGTCAGGTTGG	0.458																																					p.T133T		Atlas-SNP	.											.	PECR	22	.	1	Substitution - coding silent(1)	lung(1)	c.G399C						.						139	132	134					2																	216930060		2203	4300	6503	SO:0001819	synonymous_variant	55825	exon3			GGTACCCGTCAGG	AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18281	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 29C, member 1"	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.399G>C	chr2.hg19:g.216930060C>G		157.0	0.0		126.0	55.0	NM_018441	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	Silent	SNP	ENST00000265322.7	hg19	CCDS33375.1																																																																																			.	.		0.458	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441		G	216930060	C	G	216930060	2	3	95	1	0	0	0	0	0	0	0	1	11726	639	23	4		4	PECR	2	216930060	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	37495798	216930060	26269313	13	13096										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225721666	225721666	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ggtgaaaatcttgagtctctGtccacatttccctggttgtc	9	10	2	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr2:225721666G>C	ENST00000258390.7	-	15	1786	c.1719C>G	c.(1717-1719)gaC>gaG	p.D573E	DOCK10_ENST00000409592.3_Missense_Mutation_p.D567E	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	573					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TTGAGTCTCTGTCCACATTTC	0.318																																					p.D573E		Atlas-SNP	.											.	DOCK10	308	.	0			c.C1719G						.						101	96	97					2																	225721666		1826	4082	5908	SO:0001583	missense	55619	exon15			GTCTCTGTCCACA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.1719C>G	chr2.hg19:g.225721666G>C	ENSP00000258390:p.Asp573Glu	230.0	0.0		161.0	61.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	G	19.19	3.780652	0.70222	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.04194	3.68;3.68	5.53	3.72	0.42706	.	0.000000	0.85682	D	0.000000	T	0.15089	0.0364	L	0.60455	1.87	0.34539	D	0.710089	D;D	0.89917	1.0;0.997	D;D	0.83275	0.996;0.937	T	0.08638	-1.0712	10	0.87932	D	0	.	8.837	0.35117	0.2865:0.0:0.7135:0.0	.	573;567	Q96BY6;B3FL70	DOC10_HUMAN;.	E	567;573	ENSP00000386694:D567E;ENSP00000258390:D573E	ENSP00000258390:D573E	D	-	3	2	DOCK10	225429910	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.912000	0.56386	1.334000	0.45468	-0.245000	0.11935	GAC	.	.		0.318	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			C	225721666	G	C	225721666	3	2	95	1	0	0	0	0	1	0	0	0	4687	1368	48	4	5009	4	DOCK10	2	225721666	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	8791606	225721666	17477707	14	13097										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266124	41266124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gaatccattctggtgccactAccacagctccttctctgagt	7	14	2	1	rs121913412		TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr3:41266124A>G	ENST00000349496.5	+	3	401	c.121A>G	c.(121-123)Acc>Gcc	p.T41A	CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41A|CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41A|CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	41			T -> A (in hepatoblastoma and hepatocellular carcinoma; also in a desmoid tumor; strongly reduces phosphorylation and degradation; abolishes phosphorylation on Ser-33 and Ser-37 and enhances transactivation of target genes). {ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10398436, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10655994, ECO:0000269|PubMed:9927029}.|T -> I (in PTR, hepatocellular carcinoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T41A(550)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41P(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.A39_T42del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGTGCCACTACCACAGCTCC	0.507	T41A(CCK81_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.T41A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	681	Substitution - Missense(559)|Deletion - In frame(96)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)	soft_tissue(387)|liver(158)|large_intestine(61)|endometrium(17)|kidney(11)|stomach(8)|biliary_tract(7)|ovary(6)|small_intestine(4)|lung(4)|prostate(4)|adrenal_gland(3)|haematopoietic_and_lymphoid_tissue(3)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|salivary_gland(1)|pituitary(1)|pancreas(1)	c.A121G						.						89	77	81					3																	41266124		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCCACTACCACAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.121A>G	chr3.hg19:g.41266124A>G	ENSP00000344456:p.Thr41Ala	239.0	1.0		200.0	13.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449381	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.63117	0.2484	M	0.79258	2.445	0.80722	D	1	P	0.50943	0.94	P	0.52267	0.694	T	0.68561	-0.5376	10	0.87932	D	0	-8.9189	16.3453	0.83126	1.0:0.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	A	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34A;ENSP00000385604:T41A;ENSP00000412219:T41A;ENSP00000379486:T41A;ENSP00000344456:T41A;ENSP00000411226:T34A;ENSP00000379488:T41A;ENSP00000409302:T41A;ENSP00000401599:T41A	ENSP00000344456:T41A	T	+	1	0	CTNNB1	41241128	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	ACC	.	.		0.507	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266124	A	G	41266124	3	3	95	1	0	0	0	0	1	0	0	0	4018	391	14	2	127	2	CTNNB1	3	41266124	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10		41266124	156756306	15	13098										
RNF123	63891	hgsc.bcm.edu	37	chr3	49738946	49738946	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tcgacgtgctccgctccgtcGtcttcttttacatcaagagc	8	14	3	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr3:49738946G>T	ENST00000327697.6	+	16	1444	c.1300G>T	c.(1300-1302)Gtc>Ttc	p.V434F	RNF123_ENST00000432042.1_Missense_Mutation_p.V288F	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	434					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.V434I(1)		NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		CCGCTCCGTCGTCTTCTTTTA	0.632											OREG0015570	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V434F		Atlas-SNP	.											RNF123,colon,carcinoma,0,1	RNF123	100	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1300T						.						52	56	54					3																	49738946		2203	4300	6503	SO:0001583	missense	63891	exon16			TCCGTCGTCTTCT	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1300G>T	chr3.hg19:g.49738946G>T	ENSP00000328287:p.Val434Phe	126.0	0.0	964	101.0	53.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	G	9.384	1.073650	0.20147	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.75938	-0.69;-0.98	5.71	4.84	0.62591	.	0.063441	0.64402	D	0.000009	T	0.59321	0.2185	N	0.24115	0.695	0.80722	D	1	P;P	0.46656	0.882;0.675	B;B	0.41691	0.364;0.364	T	0.57242	-0.7845	10	0.10111	T	0.7	-33.9587	13.5769	0.61879	0.0741:0.0:0.9259:0.0	.	288;434	C9J266;Q5XPI4	.;RN123_HUMAN	F	434;434;288	ENSP00000328287:V434F;ENSP00000392443:V288F	ENSP00000328287:V434F	V	+	1	0	RNF123	49713950	1.000000	0.71417	0.865000	0.33974	0.367000	0.29736	7.329000	0.79170	1.423000	0.47198	0.561000	0.74099	GTC	.	.		0.632	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		T	49738946	G	T	49738946	3	4	95	1	0	0	0	0	1	0	0	0	13448	1145	40	1	1358	1	RNF123	3	49738946	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	8472822	49738946	148283484	16	13099										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52394057	52394057	+	Frame_Shift_Del	DEL	G	G	-													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aagctaatccaggagaacgtGgtcagcgtgaatgacttcca							TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr3:52394057delG	ENST00000420323.2	+	27	4794	c.4533delG	c.(4531-4533)gtgfs	p.V1512fs		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1512	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGGAGAACGTGGTCAGCGTGA	0.612																																					p.V1511fs		Atlas-Indel,Pindel	.											.	DNAH1	534	.	0			c.4532delT						.						134	137	136					3																	52394057		2148	4259	6407	SO:0001589	frameshift_variant	25981	exon27			.	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.4533delG	chr3.hg19:g.52394057delG	ENSP00000401514:p.Val1512fs	98.0	0.0		92.0	20.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Frame_Shift_Del	DEL	ENST00000420323.2	hg19	CCDS46842.1																																																																																			.	.		0.612	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		-	52394057	G	-	52394057	7	5	95	1	0	1	0	1	0	0	0	0	4599	1335	47	0	4635	0	DNAH1	3	52394057	Frame_Shift_Del	DEL	G	TCGA-DD-A11D-01A-11D-A12Z-10	2655111	52394057	145628373	17	13100										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126708420	126708420	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cgtgccctggcccaccagctGggcctggctgaggacgagga	16	14	0	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr3:126708420G>A	ENST00000393409.2	+	1	984	c.984G>A	c.(982-984)ctG>ctA	p.L328L	PLXNA1_ENST00000251772.4_Silent_p.L305L	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	328	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CCCACCAGCTGGGCCTGGCTG	0.657																																					p.L328L		Atlas-SNP	.											.	PLXNA1	185	.	0			c.G984A						.						74	81	79					3																	126708420		2203	4300	6503	SO:0001819	synonymous_variant	5361	exon1			CCAGCTGGGCCTG	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.984G>A	chr3.hg19:g.126708420G>A		83.0	0.0		66.0	24.0	NM_032242		Silent	SNP	ENST00000393409.2	hg19	CCDS33847.2																																																																																			.	.		0.657	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		A	126708420	G	A	126708420	2	1	95	1	0	0	0	0	0	0	0	1	12128	1335	47	3		3	PLXNA1	3	126708420	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	74314363	126708420	71314010	18	13101										
TMEM108	66000	hgsc.bcm.edu	37	chr3	133099005	133099005	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	acaaagccaccgggggccacCagccgccccaccacagcgcc	10	21	0	0	rs368132206		TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr3:133099005C>T	ENST00000321871.6	+	4	660	c.450C>T	c.(448-450)acC>acT	p.T150T	TMEM108_ENST00000393130.3_Silent_p.T150T|TMEM108_ENST00000508711.1_Intron|TMEM108_ENST00000515826.1_Silent_p.T150T	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	150	Pro-rich.					integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CGGGGGCCACCAGCCGCCCCA	0.701																																					p.T150T		Atlas-SNP	.											.	TMEM108	67	.	0			c.C450T						.		,	0,4384		0,0,2192	13	17	16		450,450	3.6	1	3		16	1,8573		0,1,4286	no	coding-synonymous,coding-synonymous	TMEM108	NM_001136469.1,NM_023943.2	,	0,1,6478	TT,TC,CC		0.0117,0.0,0.0077	,	150/576,150/576	133099005	1,12957	2192	4287	6479	SO:0001819	synonymous_variant	66000	exon4			GGCCACCAGCCGC	AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"cancer/testis antigen 124"					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.450C>T	chr3.hg19:g.133099005C>T		41.0	0.0		52.0	24.0	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Silent	SNP	ENST00000321871.6	hg19	CCDS33858.1																																																																																			.	.		0.701	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		T	133099005	C	T	133099005	2	4	95	1	0	0	0	0	0	0	0	1	16039	581	21	3		3	TMEM108	3	133099005	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	6390585	133099005	64923425	19	13102										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140178531	140178531	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cctgaccgatcagttcaccaTcaccatgtggatgaaacacg	8	13	3	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr3:140178531T>C	ENST00000458420.3	+	7	1332	c.1142T>C	c.(1141-1143)aTc>aCc	p.I381T	RP11-68L1.1_ENST00000483759.2_RNA|RP11-68L1.2_ENST00000503357.1_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	381					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						CAGTTCACCATCACCATGTGG	0.562										HNSCC(16;0.037)																											p.I381T	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.T1142C						.						91	76	81					3																	140178531		2203	4300	6503	SO:0001583	missense	64084	exon7			TCACCATCACCAT	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1142T>C	chr3.hg19:g.140178531T>C	ENSP00000402460:p.Ile381Thr	84.0	0.0		90.0	39.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.368726	0.82463	.	.	ENSG00000158258	ENST00000458420	T	0.77620	-1.11	5.41	5.41	0.78517	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.057864	0.64402	D	0.000003	D	0.86389	0.5921	M	0.79693	2.465	0.80722	D	1	D	0.56968	0.978	P	0.60236	0.871	D	0.88363	0.2989	10	0.87932	D	0	-30.4199	13.4033	0.60896	0.0:0.0:0.0:1.0	.	381	Q9H4D0	CSTN2_HUMAN	T	381	ENSP00000402460:I381T	ENSP00000402460:I381T	I	+	2	0	CLSTN2	141661221	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.040000	0.89188	2.064000	0.61679	0.533000	0.62120	ATC	.	.		0.562	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		C	140178531	T	C	140178531	3	2	95	1	0	0	0	0	1	0	0	0	3564	1435	50	2	1168	2	CLSTN2	3	140178531	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	7079526	140178531	57843899	20	13103										
HTT	3064	hgsc.bcm.edu	37	chr4	3209018	3209019	+	Frame_Shift_Ins	INS	-	-	A													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gtctattagagcagcatggcINSccagttgccaatggaagaac					rs540936636	byFrequency	TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr4:3209018_3209019insA	ENST00000355072.5	+	45	6231_6232	c.6086_6087insA	c.(6085-6090)gcccagfs	p.Q2030fs		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2030					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AGCAGCATGGCCCAGTTGCCAA	0.441																																					p.A2029fs		Atlas-INDEL	.											.	HTT	221	.	0			c.6086_6087insA						.																																			SO:0001589	frameshift_variant	3064	exon45			.	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	Exception_encountered	chr4.hg19:g.3209018_3209019insA	ENSP00000347184:p.Gln2030fs	93.0	0.0		65.0	19.0	NM_002111	Q9UQB7	Frame_Shift_Ins	INS	ENST00000355072.5	hg19	CCDS43206.1																																																																																			.	.		0.441	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3209019	-	A	3209018	7	5	95	1	0	1	1	0	0	0	0	0	7466	739	26	0	6264	0	HTT	4	3209018	Frame_Shift_Ins	INS	-	TCGA-DD-A11D-01A-11D-A12Z-10		3209018	187945258	21	13104	55	2								
HTT	3064	hgsc.bcm.edu	37	chr4	3209019	3209019	+	Frame_Shift_Del	DEL	C	C	-													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gtctattagagcagcatggcCcagttgccaatggaagaact							TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr4:3209019delC	ENST00000355072.5	+	45	6232	c.6087delC	c.(6085-6087)gccfs	p.A2029fs		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2029					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GCAGCATGGCCCAGTTGCCAA	0.438																																					p.A2029fs		Pindel	.											.	HTT	221	.	0			c.6086delC						.						112	105	107					4																	3209019		1955	4143	6098	SO:0001589	frameshift_variant	3064	exon45			.	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.6087delC	chr4.hg19:g.3209019delC	ENSP00000347184:p.Ala2029fs	93.0	0.0		65.0	16.0	NM_002111	Q9UQB7	Frame_Shift_Del	DEL	ENST00000355072.5	hg19	CCDS43206.1																																																																																			.	.		0.438	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		-	3209019	C	-	3209019	7	5	95	1	0	1	0	1	0	0	0	0	7466	610	22	0	6265	0	HTT	4	3209019	Frame_Shift_Del	DEL	C	TCGA-DD-A11D-01A-11D-A12Z-10	1	3209019	187945257	22	13105	55	2								
KIT	3815	hgsc.bcm.edu	37	chr4	55598063	55598063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	acatagaaagagatgtgactCccgccatcatggaggatgac	11	9	1	4			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr4:55598063C>T	ENST00000288135.5	+	16	2357	c.2260C>T	c.(2260-2262)Ccc>Tcc	p.P754S		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	754	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGATGTGACTCCCGCCATCAT	0.468		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.P754S		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT	7396	.	0			c.C2260T						.						111	98	102					4																	55598063		2203	4299	6502	SO:0001583	missense	3815	exon16	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	GTGACTCCCGCCA	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2260C>T	chr4.hg19:g.55598063C>T	ENSP00000288135:p.Pro754Ser	182.0	0.0		138.0	51.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.920177	0.00498	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.88586	-2.4;-2.4	5.96	3.12	0.35913	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.323928	0.27064	N	0.021105	T	0.71745	0.3376	N	0.11131	0.1	0.09310	N	1	B;B	0.24483	0.003;0.104	B;B	0.26864	0.004;0.074	T	0.58758	-0.7580	10	0.06099	T	0.92	.	5.5127	0.16890	0.1751:0.5564:0.1958:0.0726	.	750;754	P10721-2;P10721	.;KIT_HUMAN	S	754;750	ENSP00000288135:P754S;ENSP00000390987:P750S	ENSP00000288135:P754S	P	+	1	0	KIT	55292820	0.013000	0.17824	0.253000	0.24343	0.001000	0.01503	1.001000	0.29783	1.538000	0.49270	-0.140000	0.14226	CCC	.	.		0.468	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55598063	C	T	55598063	3	4	95	1	0	0	0	0	1	0	0	0	8338	855	30	3	2322	3	KIT	4	55598063	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	52389044	55598063	135556213	23	13106										
HSD17B11	51170	hgsc.bcm.edu	37	chr4	88293884	88293884	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	taagccagtaagaaggggacCgagacatgtccagctgccga	13	10	0	2	rs114331860	byFrequency	TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr4:88293884C>A	ENST00000358290.4	-	4	849	c.534G>T	c.(532-534)tcG>tcT	p.S178S	HSD17B11_ENST00000507286.1_Silent_p.S134S|HSD17B11_ENST00000507518.1_5'UTR	NM_016245.3	NP_057329.2	Q8NBQ5	DHB11_HUMAN	hydroxysteroid (17-beta) dehydrogenase 11	178					androgen catabolic process (GO:0006710)|steroid biosynthetic process (GO:0006694)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|lipid particle (GO:0005811)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|steroid dehydrogenase activity (GO:0016229)			cervix(1)|endometrium(4)|kidney(2)|lung(2)|ovary(2)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000339)		AGAAGGGGACCGAGACATGTC	0.418																																					p.S178S		Atlas-SNP	.											.	HSD17B11	28	.	0			c.G534T						.						158	129	139					4																	88293884		2203	4300	6503	SO:0001819	synonymous_variant	51170	exon4			GGGGACCGAGACA	AF126780	CCDS3619.1	4q22.1	2011-09-20	2006-11-22	2006-11-22	ENSG00000198189	ENSG00000198189	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	22960	protein-coding gene	gene with protein product	"retinal short-chain dehydrogenase/reductase 2", "short chain dehydrogenase/reductase family 16C, member 2"	612831	"dehydrogenase/reductase (SDR family) member 8"	DHRS8		11165019, 12697717, 19027726	Standard	XM_006714232		Approved	RetSDR2, 17-BETA-HSD11, 17-BETA-HSDXI, PAN1B, SDR16C2	uc003hqp.2	Q8NBQ5	OTTHUMG00000130594	ENST00000358290.4:c.534G>T	chr4.hg19:g.88293884C>A		186.0	0.0		131.0	60.0	NM_016245	Q96HF6|Q9UKU4	Silent	SNP	ENST00000358290.4	hg19	CCDS3619.1																																																																																			.	C|0.995;T|0.005		0.418	HSD17B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253041.1	NM_016245		A	88293884	C	A	88293884	2	1	95	1	0	0	0	0	0	0	0	1	7389	639	23	1		1	HSD17B11	4	88293884	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	32695821	88293884	102860392	24	13107										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155156800	155156800	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gagtatcagaaacactaaaaAggagaccaccaggctgattg	10	8	1	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr4:155156800A>C	ENST00000357232.4	-	25	7638	c.7639T>G	c.(7639-7641)Ttt>Gtt	p.F2547V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2547					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AACACTAAAAAGGAGACCACC	0.383																																					p.F2547V		Atlas-SNP	.											DCHS2,caecum,carcinoma,0,1	DCHS2	594	.	0			c.T7639G						.						59	61	60					4																	155156800		2202	4300	6502	SO:0001583	missense	54798	exon25			CTAAAAAGGAGAC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.7639T>G	chr4.hg19:g.155156800A>C	ENSP00000349768:p.Phe2547Val	192.0	0.0		157.0	61.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	A	0.184	-1.059221	0.01950	.	.	ENSG00000197410	ENST00000357232	T	0.54866	0.55	5.53	0.931	0.19460	.	0.552403	0.18120	N	0.151079	T	0.28830	0.0715	L	0.29908	0.895	0.09310	N	0.999998	B	0.14805	0.011	B	0.08055	0.003	T	0.12656	-1.0539	10	0.08599	T	0.76	.	2.4251	0.04457	0.5111:0.2142:0.0775:0.1971	.	2547	Q6V1P9	PCD23_HUMAN	V	2547	ENSP00000349768:F2547V	ENSP00000349768:F2547V	F	-	1	0	DCHS2	155376250	0.126000	0.22350	0.534000	0.28014	0.286000	0.27126	1.187000	0.32090	0.343000	0.23821	0.383000	0.25322	TTT	.	.		0.383	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		C	155156800	A	C	155156800	3	2	95	1	0	0	0	0	1	0	0	0	4290	72	3	5	1115	5	DCHS2	4	155156800	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	66862916	155156800	35997476	25	13108										
TRIML2	205860	hgsc.bcm.edu	37	chr4	189026083	189026083	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gttcaatatttcctggaataActtctatagagaaagcacag	7	7	2	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr4:189026083A>G	ENST00000512729.1	-	2	417	c.43T>C	c.(43-45)Tta>Cta	p.L15L	TRIML2_ENST00000536972.1_Silent_p.L65L|TRIML2_ENST00000502707.1_5'Flank|TRIML2_ENST00000326754.3_Silent_p.L15L	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	15					protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)	p.L15I(1)		central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		TCCTGGAATAACTTCTATAGA	0.378																																					p.L15L		Atlas-SNP	.											TRIML2,brain,glioma,0,1	TRIML2	80	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.T43C						.						143	137	139					4																	189026083		2203	4299	6502	SO:0001819	synonymous_variant	205860	exon2			GGAATAACTTCTA	AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"SPRY domain containing 6"						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.43T>C	chr4.hg19:g.189026083A>G		216.0	1.0		164.0	45.0	NM_173553	B7Z6J6	Silent	SNP	ENST00000512729.1	hg19	CCDS3850.1																																																																																			.	.		0.378	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553		G	189026083	A	G	189026083	2	3	95	1	0	0	0	0	0	0	0	1	16566	40	2	2		2	TRIML2	4	189026083	Silent	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	33869283	189026083	2128193	26	13109										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71491564	71491564	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gaaggcaaggccgcagaggcTgtcgctgcagctgtcggcac	16	12	0	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr5:71491564T>A	ENST00000296755.7	+	5	2680	c.2382T>A	c.(2380-2382)gcT>gcA	p.A794A		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	794					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CCGCAGAGGCTGTCGCTGCAG	0.537																																					p.A794A	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T2382A						.						43	46	45					5																	71491564		2203	4299	6502	SO:0001819	synonymous_variant	4131	exon5			AGAGGCTGTCGCT	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.2382T>A	chr5.hg19:g.71491564T>A		66.0	0.0		77.0	42.0	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	hg19	CCDS4012.1																																																																																			.	.		0.537	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71491564	T	A	71491564	2	1	95	1	0	0	0	0	0	0	0	1	9237	1567	55	4		4	MAP1B	5	71491564	Silent	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10		71491564	109423696	27	13110										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71494133	71494133	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	caatgtctattgaatttggcCaagaatctcctgagcaatcc	7	10	2	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr5:71494133C>A	ENST00000296755.7	+	5	5249	c.4951C>A	c.(4951-4953)Caa>Aaa	p.Q1651K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1651					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TGAATTTGGCCAAGAATCTCC	0.483																																					p.Q1651K	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.C4951A						.						115	119	118					5																	71494133		2203	4300	6503	SO:0001583	missense	4131	exon5			TTTGGCCAAGAAT	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4951C>A	chr5.hg19:g.71494133C>A	ENSP00000296755:p.Gln1651Lys	128.0	0.0		138.0	33.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.011916	0.54468	.	.	ENSG00000131711	ENST00000296755	T	0.04015	3.73	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000015	T	0.03477	0.0100	N	0.08118	0	0.58432	D	0.999997	P;P	0.42456	0.78;0.78	B;B	0.34931	0.192;0.192	T	0.55655	-0.8107	10	0.62326	D	0.03	-17.1043	18.7095	0.91651	0.0:1.0:0.0:0.0	.	1525;1651	A2BDK6;P46821	.;MAP1B_HUMAN	K	1651	ENSP00000296755:Q1651K	ENSP00000296755:Q1651K	Q	+	1	0	MAP1B	71529889	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.487000	0.81328	2.435000	0.82474	0.313000	0.20887	CAA	.	.		0.483	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71494133	C	A	71494133	3	1	95	1	0	0	0	0	1	0	0	0	9237	595	21	3	4969	3	MAP1B	5	71494133	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	2569	71494133	109421127	28	13111										
UTP15	84135	hgsc.bcm.edu	37	chr5	72866457	72866457	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tttgatgcacgaacgagtgaGagtgttctctccgttgagca	12	8	1	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr5:72866457G>T	ENST00000296792.4	+	6	849	c.594G>T	c.(592-594)gaG>gaT	p.E198D	UTP15_ENST00000543251.1_Missense_Mutation_p.E8D|UTP15_ENST00000508491.1_Missense_Mutation_p.E179D	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	198					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		GAACGAGTGAGAGTGTTCTCT	0.398																																					p.E198D		Atlas-SNP	.											.	UTP15	30	.	0			c.G594T						.						158	145	150					5																	72866457		2203	4300	6503	SO:0001583	missense	84135	exon6			GAGTGAGAGTGTT	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"WD repeat domain containing"	25758	protein-coding gene	gene with protein product			"UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.594G>T	chr5.hg19:g.72866457G>T	ENSP00000296792:p.Glu198Asp	227.0	0.0		246.0	67.0	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Missense_Mutation	SNP	ENST00000296792.4	hg19	CCDS34186.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.744|7.744	0.701806|0.701806	0.15172|0.15172	.|.	.|.	ENSG00000164338|ENSG00000164338	ENST00000296792;ENST00000543251;ENST00000508491|ENST00000509005	T;T;T|.	0.45276|.	2.14;0.9;2.14|.	5.85|5.85	0.397|0.397	0.16314|0.16314	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.727609|.	0.14378|.	N|.	0.323303|.	T|T	0.23688|0.23688	0.0573|0.0573	L|L	0.31065|0.31065	0.9|0.9	0.09310|0.09310	N|N	0.999999|0.999999	B;B|.	0.10296|.	0.003;0.001|.	B;B|.	0.11329|.	0.006;0.004|.	T|T	0.24548|0.24548	-1.0157|-1.0157	10|5	0.36615|.	T|.	0.2|.	.|.	3.824|3.824	0.08846|0.08846	0.3754:0.0986:0.4256:0.1003|0.3754:0.0986:0.4256:0.1003	.|.	179;198|.	B4DXK8;Q8TED0|.	.;UTP15_HUMAN|.	D|I	198;8;179|225	ENSP00000296792:E198D;ENSP00000440796:E8D;ENSP00000424609:E179D|.	ENSP00000296792:E198D|.	E|R	+|+	3|2	2|0	UTP15|UTP15	72902213|72902213	0.955000|0.955000	0.32602|0.32602	0.119000|0.119000	0.21687|0.21687	0.554000|0.554000	0.35429|0.35429	0.323000|0.323000	0.19593|0.19593	0.105000|0.105000	0.17753|0.17753	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.		0.398	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175		T	72866457	G	T	72866457	3	4	95	1	0	0	0	0	1	0	0	0	17112	933	33	3	612	3	UTP15	5	72866457	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	1372324	72866457	108048803	29	13112										
CKMT2	1160	hgsc.bcm.edu	37	chr5	80548514	80548514	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ctgccctcctccccacacagCgcagactacccagacctgcg	7	21	0	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr5:80548514C>A	ENST00000424301.2	+	4	391	c.153C>A	c.(151-153)agC>agA	p.S51R	CKMT2-AS1_ENST00000501927.2_RNA|CKMT2-AS1_ENST00000512287.1_RNA|CKMT2_ENST00000254035.4_Splice_Site_p.S51R|CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000505295.1_RNA|CKMT2_ENST00000437669.1_Splice_Site_p.S51R|CKMT2-AS1_ENST00000502041.2_RNA|CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000500148.2_RNA	NM_001825.2	NP_001816.2	P17540	KCRS_HUMAN	creatine kinase, mitochondrial 2 (sarcomeric)	51	Cardiolipin-binding. {ECO:0000250}.|Phosphagen kinase N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00842}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.S51S(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(4)|urinary_tract(1)	17		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	CCCCACACAGCGCAGACTACC	0.602																																					p.S51R		Atlas-SNP	.											CKMT2,NS,carcinoma,0,1	CKMT2	44	.	1	Substitution - coding silent(1)	endometrium(1)	c.C153A						.						67	61	63					5																	80548514		2203	4300	6503	SO:0001630	splice_region_variant	1160	exon4			ACACAGCGCAGAC		CCDS4053.1	5q14.1	2013-09-20			ENSG00000131730	ENSG00000131730	2.7.3.2		1996	protein-coding gene	gene with protein product		123295				2324105	Standard	NM_001825		Approved	SMTCK	uc003khd.4	P17540	OTTHUMG00000119013	ENST00000424301.2:c.153-1C>A	chr5.hg19:g.80548514C>A		42.0	0.0		51.0	36.0	NM_001825	Q6ICS8|Q8N1E1	Missense_Mutation	SNP	ENST00000424301.2	hg19	CCDS4053.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.895581	0.91962	.	.	ENSG00000131730	ENST00000254035;ENST00000511719;ENST00000437669;ENST00000424301;ENST00000505060	T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0	6.04	-8.5	0.00927	ATP:guanido phosphotransferase, N-terminal (3);	0.125812	0.64402	D	0.000001	T	0.73737	0.3625	M	0.80422	2.495	0.51767	D	0.999938	D	0.89917	1.0	D	0.72982	0.979	T	0.83162	-0.0098	9	.	.	.	.	17.4362	0.87553	0.0:0.5501:0.0:0.4499	.	51	P17540	KCRS_HUMAN	R	51	ENSP00000254035:S51R;ENSP00000423264:S51R;ENSP00000410289:S51R;ENSP00000404203:S51R;ENSP00000427635:S51R	.	S	+	3	2	CKMT2	80584270	0.000000	0.05858	0.019000	0.16419	0.872000	0.50106	-3.327000	0.00511	-1.967000	0.01008	-0.224000	0.12420	AGC	.	.		0.602	CKMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369600.1	NM_001825	Missense_Mutation	A	80548514	C	A	80548514	5	1	95	1	0	0	0	0	0	0	1	0	3453	782	27	1	159	1	CKMT2	5	80548514	Splice_Site	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	7682057	80548514	100366746	30	13113										
RGMB	285704	hgsc.bcm.edu	37	chr5	98115463	98115463	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gccgtggcaacctggtatacCattctgccgtgttgggtatc	12	11	1	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr5:98115463C>G	ENST00000513185.1	+	2	752	c.316C>G	c.(316-318)Cat>Gat	p.H106D	RGMB_ENST00000504776.1_3'UTR|RGMB_ENST00000308234.7_Missense_Mutation_p.H147D			Q6NW40	RGMB_HUMAN	repulsive guidance molecule family member b	106					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell adhesion (GO:0007155)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)	identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	10		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		CCTGGTATACCATTCTGCCGT	0.542																																					p.H147D		Atlas-SNP	.											.	RGMB	29	.	0			c.C439G						.						65	67	66					5																	98115463		1976	4162	6138	SO:0001583	missense	285704	exon4			GTATACCATTCTG	AK074887	CCDS47251.1	5q21.1	2013-11-06	2013-11-06		ENSG00000174136	ENSG00000174136			26896	protein-coding gene	gene with protein product		612687	"RGM domain family, member B"			19324014	Standard	NM_001012761		Approved	FLJ90406, DRAGON	uc003knc.3	Q6NW40	OTTHUMG00000162745	ENST00000513185.1:c.316C>G	chr5.hg19:g.98115463C>G	ENSP00000423256:p.His106Asp	94.0	0.0		86.0	50.0	NM_001012761	D6R9A0|Q8NC92	Missense_Mutation	SNP	ENST00000513185.1	hg19		.	.	.	.	.	.	.	.	.	.	C	27.4	4.827997	0.90955	.	.	ENSG00000174136	ENST00000308234;ENST00000513185	D;D	0.97906	-4.6;-4.6	5.4	5.4	0.78164	Repulsive guidance molecule, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98848	0.9611	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99679	1.0998	10	0.72032	D	0.01	-18.147	19.5247	0.95199	0.0:1.0:0.0:0.0	.	106	Q6NW40	RGMB_HUMAN	D	147;106	ENSP00000308219:H147D;ENSP00000423256:H106D	ENSP00000308219:H147D	H	+	1	0	RGMB	98143363	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.445000	0.80570	2.689000	0.91719	0.563000	0.77884	CAT	.	.		0.542	RGMB-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370308.1	NM_173670		G	98115463	C	G	98115463	3	3	95	1	0	0	0	0	1	0	0	0	13296	594	21	4	449	4	RGMB	5	98115463	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	17566949	98115463	82799797	31	13114										
RGMB	285704	hgsc.bcm.edu	37	chr5	98129453	98129453	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cttgatccttatcgtgttttTgtaggggttgtcttttgttt	10	5	1	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr5:98129453T>A	ENST00000513185.1	+	3	1746	c.1310T>A	c.(1309-1311)tTg>tAg	p.L437*	RGMB_ENST00000308234.7_Nonsense_Mutation_p.L478*			Q6NW40	RGMB_HUMAN	repulsive guidance molecule family member b	437					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell adhesion (GO:0007155)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)	identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	10		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		ATCGTGTTTTTGTAGGGGTTG	0.363																																					p.L478X		Atlas-SNP	.											.	RGMB	29	.	0			c.T1433A						.						134	125	128					5																	98129453		1857	4088	5945	SO:0001587	stop_gained	285704	exon5			TGTTTTTGTAGGG	AK074887	CCDS47251.1	5q21.1	2013-11-06	2013-11-06		ENSG00000174136	ENSG00000174136			26896	protein-coding gene	gene with protein product		612687	"RGM domain family, member B"			19324014	Standard	NM_001012761		Approved	FLJ90406, DRAGON	uc003knc.3	Q6NW40	OTTHUMG00000162745	ENST00000513185.1:c.1310T>A	chr5.hg19:g.98129453T>A	ENSP00000423256:p.Leu437*	204.0	0.0		247.0	135.0	NM_001012761	D6R9A0|Q8NC92	Nonsense_Mutation	SNP	ENST00000513185.1	hg19		.	.	.	.	.	.	.	.	.	.	T	38	6.881023	0.97908	.	.	ENSG00000174136	ENST00000308234;ENST00000513185	.	.	.	5.62	3.05	0.35203	.	0.307281	0.27375	N	0.019656	.	.	.	.	.	.	0.34302	D	0.684425	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6986	0.34312	0.1274:0.0:0.1335:0.7391	.	.	.	.	X	478;437	.	ENSP00000308219:L478X	L	+	2	0	RGMB	98157353	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	3.650000	0.54424	0.937000	0.37394	0.533000	0.62120	TTG	.	.		0.363	RGMB-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370308.1	NM_173670		A	98129453	T	A	98129453	4	1	95	1	0	0	0	0	0	1	0	0	13296	1821	63	4	1447	4	RGMB	5	98129453	Nonsense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	13990	98129453	82785807	32	13115										
FER	2241	hgsc.bcm.edu	37	chr5	108203627	108203627	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tctggactccttacaaaagaTgcaagaagaaatgataaaag	8	6	1	4			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr5:108203627T>C	ENST00000281092.4	+	6	1025	c.641T>C	c.(640-642)aTg>aCg	p.M214T	FER_ENST00000536402.1_Missense_Mutation_p.M214T|FER_ENST00000438717.2_Missense_Mutation_p.M39T	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	214	Important for interaction with membranes containing phosphoinositides.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		TTACAAAAGATGCAAGAAGAA	0.353																																					p.M214T	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.T641C						.						95	87	89					5																	108203627		2202	4300	6502	SO:0001583	missense	2241	exon6			AAAAGATGCAAGA	J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	3655	protein-coding gene	gene with protein product	"phosphoprotein NCP94", "protein phosphatase 1, regulatory subunit 74"	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.641T>C	chr5.hg19:g.108203627T>C	ENSP00000281092:p.Met214Thr	237.0	0.0		237.0	126.0	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	hg19	CCDS4098.1	.	.	.	.	.	.	.	.	.	.	T	19.98	3.926950	0.73327	.	.	ENSG00000151422	ENST00000281092;ENST00000536402;ENST00000438717	T;T;T	0.44482	0.92;0.92;2.5	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.60353	0.2262	M	0.63428	1.95	0.80722	D	1	D	0.55800	0.973	P	0.61201	0.885	T	0.63323	-0.6663	10	0.87932	D	0	-20.9734	16.3197	0.82945	0.0:0.0:0.0:1.0	.	214	P16591	FER_HUMAN	T	214;214;39	ENSP00000281092:M214T;ENSP00000442627:M214T;ENSP00000394297:M39T	ENSP00000281092:M214T	M	+	2	0	FER	108231526	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.525000	0.81892	2.302000	0.77476	0.533000	0.62120	ATG	.	.		0.353	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246		C	108203627	T	C	108203627	3	2	95	1	0	0	0	0	1	0	0	0	5821	1464	51	2	655	2	FER	5	108203627	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	10074174	108203627	72711633	33	13116										
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140167846	140167846	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gtgaaggatcacggtgagccGgcgctgacagccacggccac	15	13	1	3	rs376407441		TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr5:140167846G>A	ENST00000504120.2	+	1	1971	c.1971G>A	c.(1969-1971)ccG>ccA	p.P657P	PCDHA1_ENST00000378133.3_Silent_p.P657P|PCDHA1_ENST00000394633.3_Intron	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	657	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGTGAGCCGGCGCTGACAG	0.662													.|||	1	0.000199681	8e-04	0	5008	,	,		15980	0		0	False		,,,				2504	0				p.P657P		Atlas-SNP	.											.	PCDHA1	387	.	0			c.G1971A						.	G	,,	1,4405	2.1+/-5.4	0,1,2202	45	51	49		1971,1971,	-4.9	0.5	5		49	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,intron	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	657/951,657/808,	140167846	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	56147	exon1			TGAGCCGGCGCTG	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"Cadherins / Protocadherins : Clustered"	8663	other	complex locus constituent	"KIAA0345-like 13"	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1971G>A	chr5.hg19:g.140167846G>A		163.0	0.0		175.0	102.0	NM_031410	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	hg19	CCDS54913.1																																																																																			.	.		0.662	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		A	140167846	G	A	140167846	2	1	95	1	0	0	0	0	0	0	0	1	11528	1103	39	1		1	PCDHA1	5	140167846	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	31964219	140167846	40747414	34	13117										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140209428	140209428	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	agcgagctggtgccgcggtcActgggtgcaggccaagtggt	18	10	1	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr5:140209428A>T	ENST00000529310.1	+	1	1866	c.1752A>T	c.(1750-1752)tcA>tcT	p.S584S	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	584	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCCGCGGTCACTGGGTGCAG	0.672																																					p.S584S		Atlas-SNP	.											.	PCDHA6	442	.	0			c.A1752T						.						86	86	86					5																	140209428		2203	4299	6502	SO:0001819	synonymous_variant	56142	exon1			GCGGTCACTGGGT	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1752A>T	chr5.hg19:g.140209428A>T		284.0	0.0		376.0	19.0	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	hg19	CCDS47281.1																																																																																			.	.		0.672	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		T	140209428	A	T	140209428	2	4	95	1	0	0	0	0	0	0	0	1	11537	146	6	4		4	PCDHA6	5	140209428	Silent	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	41582	140209428	40705832	35	13118										
KIF13A	63971	hgsc.bcm.edu	37	chr6	17828535	17828535	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aatgtcaatctcacagtgctGaggctgaattcctatgccaa	8	10	2	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:17828535G>C	ENST00000259711.6	-	14	1573	c.1468C>G	c.(1468-1470)Cag>Gag	p.Q490E	KIF13A_ENST00000378826.2_Missense_Mutation_p.Q490E|KIF13A_ENST00000378814.5_Missense_Mutation_p.Q490E|KIF13A_ENST00000378816.5_Missense_Mutation_p.Q490E|KIF13A_ENST00000378843.2_Missense_Mutation_p.Q490E	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	490	FHA.				ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TCACAGTGCTGAGGCTGAATT	0.423																																					p.Q490E		Atlas-SNP	.											.	KIF13A	276	.	0			c.C1468G						.						70	66	67					6																	17828535		1915	4131	6046	SO:0001583	missense	63971	exon14			AGTGCTGAGGCTG	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.1468C>G	chr6.hg19:g.17828535G>C	ENSP00000259711:p.Gln490Glu	268.0	0.0		192.0	54.0	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	hg19	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	G	6.051	0.377705	0.11466	.	.	ENSG00000137177	ENST00000378814;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	D;D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19;-2.19	6.04	5.18	0.71444	Forkhead-associated (FHA) domain (3);SMAD/FHA domain (1);	0.107001	0.64402	N	0.000007	T	0.41259	0.1151	N	0.00453	-1.485	0.31583	N	0.654868	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.001;0.0	T	0.19289	-1.0310	10	0.02654	T	1	.	17.6519	0.88167	0.0:0.8768:0.1232:0.0	.	461;490;490;490;490	E7ER65;Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;.;KI13A_HUMAN;.	E	490	ENSP00000368091:Q490E;ENSP00000259711:Q490E;ENSP00000368103:Q490E;ENSP00000368120:Q490E;ENSP00000368093:Q490E	ENSP00000259711:Q490E	Q	-	1	0	KIF13A	17936514	0.999000	0.42202	1.000000	0.80357	0.987000	0.75469	4.022000	0.57203	1.579000	0.49836	-0.226000	0.12346	CAG	.	.		0.423	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			C	17828535	G	C	17828535	3	2	95	1	0	0	0	0	1	0	0	0	8283	1299	45	4	4078	4	KIF13A	6	17828535	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10		17828535	153286532	36	13119										
MBOAT1	154141	hgsc.bcm.edu	37	chr6	20151445	20151445	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ttggatacactagcagtgacCatgattgcatagcacattaa	8	8	0	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:20151445C>A	ENST00000324607.7	-	3	458	c.294G>T	c.(292-294)atG>atT	p.M98I	MBOAT1_ENST00000541730.1_5'UTR|MBOAT1_ENST00000536798.1_Missense_Mutation_p.M98I	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	98					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			TAGCAGTGACCATGATTGCAT	0.343																																					p.M98I		Atlas-SNP	.											.	MBOAT1	48	.	0			c.G294T						.						149	130	137					6																	20151445		2203	4300	6503	SO:0001583	missense	154141	exon3			AGTGACCATGATT	AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197			21579	protein-coding gene	gene with protein product	"lysophosphatidylethanolamine acyltransferase 1"	611732	"O-acyltransferase (membrane bound) domain containing 1"	OACT1		18287005	Standard	NM_001080480		Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.294G>T	chr6.hg19:g.20151445C>A	ENSP00000324944:p.Met98Ile	128.0	0.0		75.0	32.0	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Missense_Mutation	SNP	ENST00000324607.7	hg19	CCDS34346.1	.	.	.	.	.	.	.	.	.	.	C	12.71	2.020038	0.35606	.	.	ENSG00000172197	ENST00000324607;ENST00000536798	T;T	0.24151	2.74;1.87	5.69	4.79	0.61399	.	0.214010	0.53938	D	0.000055	T	0.14270	0.0345	L	0.58428	1.81	0.50313	D	0.999868	B	0.16396	0.017	B	0.17098	0.017	T	0.03384	-1.1042	10	0.17832	T	0.49	-14.4912	15.6825	0.77381	0.0:0.8632:0.1368:0.0	.	98	Q6ZNC8	MBOA1_HUMAN	I	98	ENSP00000324944:M98I;ENSP00000439814:M98I	ENSP00000324944:M98I	M	-	3	0	MBOAT1	20259424	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	1.794000	0.38774	2.661000	0.90470	0.650000	0.86243	ATG	.	.		0.343	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1			A	20151445	C	A	20151445	3	1	95	1	0	0	0	0	1	0	0	0	9365	594	21	3	1237	3	MBOAT1	6	20151445	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	2322910	20151445	150963622	37	13120										
CLPS	1208	hgsc.bcm.edu	37	chr6	35762977	35762977	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ccaaagttggtgttggtgatGgagcccacgatggtcttgtc	14	8	1	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:35762977G>A	ENST00000259938.2	-	3	307	c.285C>T	c.(283-285)tcC>tcT	p.S95S		NM_001832.3	NP_001823.1	P04118	COL_HUMAN	colipase, pancreatic	95					lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme activator activity (GO:0008047)			large_intestine(2)|lung(2)|prostate(1)	5						TGTTGGTGATGGAGCCCACGA	0.572																																					p.S95S	Melanoma(167;2962 3494 37796)	Atlas-SNP	.											.	CLPS	15	.	0			c.C285T						.						287	187	221					6																	35762977		2203	4300	6503	SO:0001819	synonymous_variant	1208	exon3			GGTGATGGAGCCC		CCDS4811.1, CCDS75437.1, CCDS75438.1	6p21.31	2012-02-06			ENSG00000137392	ENSG00000137392			2085	protein-coding gene	gene with protein product		120105				2045105	Standard	NM_001832		Approved		uc003ole.2	P04118	OTTHUMG00000014578	ENST00000259938.2:c.285C>T	chr6.hg19:g.35762977G>A		248.0	0.0		192.0	49.0	NM_001832	Q5T9G7|Q5U809	Silent	SNP	ENST00000259938.2	hg19	CCDS4811.1																																																																																			.	.		0.572	CLPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040312.1	NM_001832		A	35762977	G	A	35762977	2	1	95	1	0	0	0	0	0	0	0	1	3555	1335	47	3		3	CLPS	6	35762977	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	15611532	35762977	135352090	38	13121										
GLO1	2739	hgsc.bcm.edu	37	chr6	38650599	38650599	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cttaccgaatcctcgagggtCtgaattgccattgtggtaac	10	10	1	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:38650599C>G	ENST00000373365.4	-	4	447	c.361G>C	c.(361-363)Gac>Cac	p.D121H	GLO1_ENST00000470973.1_5'UTR	NM_006708.2	NP_006699.2	Q04760	LGUL_HUMAN	glyoxalase I	121					carbohydrate metabolic process (GO:0005975)|glutathione metabolic process (GO:0006749)|methylglyoxal metabolic process (GO:0009438)|negative regulation of apoptotic process (GO:0043066)|osteoclast differentiation (GO:0030316)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lactoylglutathione lyase activity (GO:0004462)|zinc ion binding (GO:0008270)			lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	6					Glutathione(DB00143)|Indomethacin(DB00328)	CCTCGAGGGTCTGAATTGCCA	0.343																																					p.D121H		Atlas-SNP	.											.	GLO1	12	.	0			c.G361C						.						159	132	141					6																	38650599		2203	4300	6503	SO:0001583	missense	2739	exon4			GAGGGTCTGAATT	L07837	CCDS4837.1	6p21.3-p21.1	2012-10-02			ENSG00000124767	ENSG00000124767	4.4.1.5		4323	protein-coding gene	gene with protein product	"glyoxalase domain containing 1"	138750				8449929, 7684374	Standard	NM_006708		Approved	GLOD1	uc003ooc.3	Q04760	OTTHUMG00000014636	ENST00000373365.4:c.361G>C	chr6.hg19:g.38650599C>G	ENSP00000362463:p.Asp121His	135.0	0.0		120.0	17.0	NM_006708	B2R6P7|B4DDV0|P78375|Q59EL0|Q5TZW3|Q96FC0|Q96J41	Missense_Mutation	SNP	ENST00000373365.4	hg19	CCDS4837.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.813910	0.90790	.	.	ENSG00000124767	ENST00000373365	T	0.29397	1.57	5.95	5.95	0.96441	Glyoxalase/fosfomycin resistance/dioxygenase (1);Glyoxalase I, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.56140	0.1965	M	0.85630	2.765	0.80722	D	1	D	0.65815	0.995	D	0.67725	0.953	T	0.60850	-0.7181	10	0.87932	D	0	-26.3725	20.0036	0.97427	0.0:1.0:0.0:0.0	.	121	Q04760	LGUL_HUMAN	H	121	ENSP00000362463:D121H	ENSP00000362463:D121H	D	-	1	0	GLO1	38758577	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.280000	0.65603	2.824000	0.97209	0.655000	0.94253	GAC	.	.		0.343	GLO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040438.2	NM_006708		G	38650599	C	G	38650599	3	3	95	1	0	0	0	0	1	0	0	0	6457	913	32	4	205	4	GLO1	6	38650599	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	2887622	38650599	132464468	39	13122										
GLO1	2739	hgsc.bcm.edu	37	chr6	38650627	38650627	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ccattgtggtaactctgggtCtcatcatcttcagtgcccca	8	13	5	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:38650627C>T	ENST00000373365.4	-	4	419	c.333G>A	c.(331-333)gaG>gaA	p.E111E	GLO1_ENST00000470973.1_5'UTR	NM_006708.2	NP_006699.2	Q04760	LGUL_HUMAN	glyoxalase I	111			E -> A (in dbSNP:rs4746). {ECO:0000269|PubMed:10564821, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7684374, ECO:0000269|PubMed:8449929}.		carbohydrate metabolic process (GO:0005975)|glutathione metabolic process (GO:0006749)|methylglyoxal metabolic process (GO:0009438)|negative regulation of apoptotic process (GO:0043066)|osteoclast differentiation (GO:0030316)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lactoylglutathione lyase activity (GO:0004462)|zinc ion binding (GO:0008270)			lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	6					Glutathione(DB00143)|Indomethacin(DB00328)	AACTCTGGGTCTCATCATCTT	0.368																																					p.E111E		Atlas-SNP	.											.	GLO1	12	.	0			c.G333A						.						161	132	142					6																	38650627		2203	4300	6503	SO:0001819	synonymous_variant	2739	exon4			CTGGGTCTCATCA	L07837	CCDS4837.1	6p21.3-p21.1	2012-10-02			ENSG00000124767	ENSG00000124767	4.4.1.5		4323	protein-coding gene	gene with protein product	"glyoxalase domain containing 1"	138750				8449929, 7684374	Standard	NM_006708		Approved	GLOD1	uc003ooc.3	Q04760	OTTHUMG00000014636	ENST00000373365.4:c.333G>A	chr6.hg19:g.38650627C>T		151.0	0.0		119.0	11.0	NM_006708	B2R6P7|B4DDV0|P78375|Q59EL0|Q5TZW3|Q96FC0|Q96J41	Silent	SNP	ENST00000373365.4	hg19	CCDS4837.1																																																																																			.	.		0.368	GLO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040438.2	NM_006708		T	38650627	C	T	38650627	2	4	95	1	0	0	0	0	0	0	0	1	6457	912	32	3		3	GLO1	6	38650627	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	28	38650627	132464440	40	13123										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38738285	38738285	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aaaaatcttttgaggtttcaGaaatgtatatatttggaaaa	7	2	2	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:38738285G>A	ENST00000359357.3	+	10	1317	c.1063G>A	c.(1063-1065)Gaa>Aaa	p.E355K	DNAH8_ENST00000449981.2_Missense_Mutation_p.E572K|DNAH8_ENST00000441566.1_Missense_Mutation_p.E355K			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	355					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGAGGTTTCAGAAATGTATAT	0.363																																					p.E572K		Atlas-SNP	.											DNAH8_ENST00000359357,right_upper_lobe,carcinoma,0,2	DNAH8	1239	.	0			c.G1714A						.						39	40	40					6																	38738285		2203	4299	6502	SO:0001583	missense	1769	exon12			GTTTCAGAAATGT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.1063G>A	chr6.hg19:g.38738285G>A	ENSP00000352312:p.Glu355Lys	102.0	0.0		112.0	11.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	G	29.3	4.992739	0.93167	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.56275	0.47;0.47;0.47	5.45	5.45	0.79879	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	T	0.68842	0.3045	M	0.87097	2.86	0.80722	D	1	P	0.46578	0.88	P	0.59546	0.859	T	0.68625	-0.5359	10	0.39692	T	0.17	.	17.4237	0.87521	0.0:0.0:1.0:0.0	.	355	Q96JB1	DYH8_HUMAN	K	560;560;355;355	ENSP00000333363:E560K;ENSP00000352312:E355K;ENSP00000402294:E355K	ENSP00000333363:E560K	E	+	1	0	DNAH8	38846263	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.481000	0.81124	2.726000	0.93360	0.643000	0.83706	GAA	.	.		0.363	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38738285	G	A	38738285	3	1	95	1	0	0	0	0	1	0	0	0	4609	943	33	3	1093	3	DNAH8	6	38738285	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	87658	38738285	132376782	41	13124										
NFYA	4800	hgsc.bcm.edu	37	chr6	41051832	41051832	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gtcagtggaggccagctaatCacatcaactggccaacccat	9	13	3	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:41051832C>G	ENST00000341376.6	+	4	411	c.210C>G	c.(208-210)atC>atG	p.I70M	NFYA_ENST00000353205.5_Missense_Mutation_p.I41M|OARD1_ENST00000480585.1_Intron	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	70	Gln-rich.				cellular lipid metabolic process (GO:0044255)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	9	Ovarian(28;0.0418)|Colorectal(47;0.196)					GCCAGCTAATCACATCAACTG	0.453																																					p.I70M		Atlas-SNP	.											.	NFYA	33	.	0			c.C210G						.						105	80	88					6																	41051832		2203	4300	6503	SO:0001583	missense	4800	exon4			GCTAATCACATCA		CCDS4849.1, CCDS4850.1	6p21.3	2008-11-11			ENSG00000001167	ENSG00000001167			7804	protein-coding gene	gene with protein product		189903				1774067, 9612081	Standard	NM_002505		Approved	HAP2, CBF-B, NF-YA	uc003opo.3	P23511	OTTHUMG00000014669	ENST00000341376.6:c.210C>G	chr6.hg19:g.41051832C>G	ENSP00000345702:p.Ile70Met	143.0	0.0		126.0	49.0	NM_002505	Q8IXU0	Missense_Mutation	SNP	ENST00000341376.6	hg19	CCDS4849.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.239746	0.58995	.	.	ENSG00000001167	ENST00000341376;ENST00000353205	.	.	.	5.76	3.61	0.41365	.	0.000000	0.85682	D	0.000000	T	0.55210	0.1906	L	0.56769	1.78	0.49798	D	0.999824	D;P	0.54397	0.966;0.943	P;P	0.58721	0.844;0.703	T	0.60110	-0.7327	9	0.72032	D	0.01	-9.5961	9.9989	0.41916	0.0:0.8072:0.0:0.1928	.	41;70	P23511-2;P23511	.;NFYA_HUMAN	M	70;41	.	ENSP00000345702:I70M	I	+	3	3	NFYA	41159810	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.206000	0.51098	0.641000	0.30601	0.650000	0.86243	ATC	.	.		0.453	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040496.1			G	41051832	C	G	41051832	3	3	95	1	0	0	0	0	1	0	0	0	10398	816	29	4	220	4	NFYA	6	41051832	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	2313547	41051832	130063235	42	13125										
UBR2	23304	hgsc.bcm.edu	37	chr6	42619803	42619803	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tgaaaagacaaaatagagaaGatacaggtatttttaatctt	7	3	1	4			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:42619803G>C	ENST00000372899.1	+	24	2866	c.2608G>C	c.(2608-2610)Gat>Cat	p.D870H	UBR2_ENST00000372883.3_Missense_Mutation_p.D374H|UBR2_ENST00000372901.1_Missense_Mutation_p.D870H	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	870					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			AAATAGAGAAGATACAGGTAT	0.353																																					p.D870H		Atlas-SNP	.											.	UBR2	134	.	0			c.G2608C						.						129	142	137					6																	42619803		2203	4300	6503	SO:0001583	missense	23304	exon24			AGAGAAGATACAG	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.2608G>C	chr6.hg19:g.42619803G>C	ENSP00000361990:p.Asp870His	234.0	0.0		174.0	13.0	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	hg19	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419643	0.83559	.	.	ENSG00000024048	ENST00000372899;ENST00000372901;ENST00000372883	T;T;T	0.49432	0.78;0.78;0.78	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.61874	0.2382	L	0.61218	1.895	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.94	T	0.60865	-0.7178	10	0.51188	T	0.08	-24.4855	19.4613	0.94918	0.0:0.0:1.0:0.0	.	870;870	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	H	870;870;374	ENSP00000361990:D870H;ENSP00000361992:D870H;ENSP00000361974:D374H	ENSP00000361974:D374H	D	+	1	0	UBR2	42727781	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.581000	0.90788	2.677000	0.91161	0.557000	0.71058	GAT	.	.		0.353	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		C	42619803	G	C	42619803	3	2	95	1	0	0	0	0	1	0	0	0	16917	942	33	4	2848	4	UBR2	6	42619803	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	1567971	42619803	128495264	43	13126										
OGFRL1	79627	hgsc.bcm.edu	37	chr6	72003250	72003250	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tagcagaacttcaaagatatCcgatatcaaaatgacttgag	7	7	2	4			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:72003250C>G	ENST00000370435.4	+	3	470	c.336C>G	c.(334-336)atC>atG	p.I112M	RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|OGFRL1_ENST00000467503.1_3'UTR|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	112						membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						TCAAAGATATCCGATATCAAA	0.333																																					p.I112M		Atlas-SNP	.											.	OGFRL1	44	.	0			c.C336G						.						57	58	57					6																	72003250		2202	4298	6500	SO:0001583	missense	79627	exon3			AGATATCCGATAT		CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.336C>G	chr6.hg19:g.72003250C>G	ENSP00000359464:p.Ile112Met	232.0	0.0		216.0	16.0	NM_024576	Q2TAC1|Q8NEQ4|Q9H7B5	Missense_Mutation	SNP	ENST00000370435.4	hg19	CCDS34482.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.464741	0.43736	.	.	ENSG00000119900	ENST00000370435	T	0.44482	0.92	5.96	4.11	0.48088	Opioid growth factor receptor (OGFr) conserved domain (1);	0.190794	0.47093	D	0.000259	T	0.14700	0.0355	N	0.08118	0	0.30283	N	0.791097	P	0.45634	0.863	P	0.50405	0.64	T	0.03863	-1.0997	10	0.45353	T	0.12	-6.8875	5.2802	0.15670	0.0:0.5576:0.1449:0.2976	.	112	Q5TC84	OGRL1_HUMAN	M	112	ENSP00000359464:I112M	ENSP00000359464:I112M	I	+	3	3	OGFRL1	72059971	0.992000	0.36948	1.000000	0.80357	0.998000	0.95712	0.244000	0.18124	1.444000	0.47605	0.655000	0.94253	ATC	.	.		0.333	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		G	72003250	C	G	72003250	3	3	95	1	0	0	0	0	1	0	0	0	10853	845	30	4	346	4	OGFRL1	6	72003250	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	29383447	72003250	99111817	44	13127										
POU3F2	5454	hgsc.bcm.edu	37	chr6	99283990	99283990	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gaaagagaaaaggatgacccCtcccggagggactctgccgg	14	11	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:99283990C>T	ENST00000328345.5	+	1	1411	c.1241C>T	c.(1240-1242)cCt>cTt	p.P414L		NM_005604.3	NP_005595.2	P20265	PO3F2_HUMAN	POU class 3 homeobox 2	414					astrocyte development (GO:0014002)|cellular response to organic substance (GO:0071310)|cerebral cortex radially oriented cell migration (GO:0021799)|epidermis development (GO:0008544)|forebrain ventricular zone progenitor cell division (GO:0021869)|hypothalamus cell differentiation (GO:0021979)|myelination in peripheral nervous system (GO:0022011)|neurohypophysis development (GO:0021985)|neuron differentiation (GO:0030182)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of axonogenesis (GO:0050770)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	identical protein binding (GO:0042802)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(5)	10		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0355)		AGGATGACCCCTCCCGGAGGG	0.607																																					p.P414L		Atlas-SNP	.											.	POU3F2	33	.	0			c.C1241T						.						44	55	51					6																	99283990		2202	4298	6500	SO:0001583	missense	5454	exon1			TGACCCCTCCCGG	Z11933	CCDS5040.1	6q16.2	2011-06-20	2007-07-13		ENSG00000184486	ENSG00000184486		"Homeoboxes / POU class"	9215	protein-coding gene	gene with protein product		600494	"POU domain class 3, transcription factor 2"	OTF7		8441633	Standard	NM_005604		Approved	POUF3, BRN2, OCT7	uc003ppe.3	P20265	OTTHUMG00000015258	ENST00000328345.5:c.1241C>T	chr6.hg19:g.99283990C>T	ENSP00000329170:p.Pro414Leu	56.0	0.0		35.0	19.0	NM_005604	Q14960|Q86V54|Q9UJL0	Missense_Mutation	SNP	ENST00000328345.5	hg19	CCDS5040.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951662	0.73787	.	.	ENSG00000184486	ENST00000328345;ENST00000425116	D	0.87491	-2.26	4.51	4.51	0.55191	Homeobox (1);Homeodomain-like (1);	.	.	.	.	D	0.89938	0.6860	L	0.57536	1.79	0.80722	D	1	D	0.76494	0.999	D	0.65323	0.934	D	0.91226	0.5010	9	0.87932	D	0	.	16.1405	0.81519	0.0:1.0:0.0:0.0	.	414	P20265	PO3F2_HUMAN	L	414;347	ENSP00000329170:P414L	ENSP00000329170:P414L	P	+	2	0	POU3F2	99390711	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.555000	0.60767	2.330000	0.79161	0.555000	0.69702	CCT	.	.		0.607	POU3F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041586.2			T	99283990	C	T	99283990	3	4	95	1	0	0	0	0	1	0	0	0	12284	681	24	3	1243	3	POU3F2	6	99283990	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	27280740	99283990	71831077	45	13128										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102516324	102516324	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cagttattgtgaaaacagaaGaagttatcaacatgcacaca	7	7	1	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:102516324G>A	ENST00000421544.1	+	16	3155	c.2665G>A	c.(2665-2667)Gaa>Aaa	p.E889K	GRIK2_ENST00000369134.4_Missense_Mutation_p.E840K|GRIK2_ENST00000369137.3_Missense_Mutation_p.E813K|GRIK2_ENST00000413795.1_3'UTR|GRIK2_ENST00000369138.1_3'UTR	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	889					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GAAAACAGAAGAAGTTATCAA	0.463																																					p.E889K		Atlas-SNP	.											.	GRIK2	487	.	0			c.G2665A						.						111	99	103					6																	102516324		2203	4300	6503	SO:0001583	missense	2898	exon16			ACAGAAGAAGTTA		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2665G>A	chr6.hg19:g.102516324G>A	ENSP00000397026:p.Glu889Lys	161.0	0.0		161.0	14.0	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	hg19	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007574	0.75046	.	.	ENSG00000164418	ENST00000421544;ENST00000369137;ENST00000369134	T;T;T	0.12039	2.72;2.92;2.73	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.07683	0.0193	L	0.36672	1.1	0.58432	D	0.999997	B	0.22211	0.066	B	0.20184	0.028	T	0.13361	-1.0512	10	0.35671	T	0.21	.	20.0361	0.97558	0.0:0.0:1.0:0.0	.	889	Q13002	GRIK2_HUMAN	K	889;813;840	ENSP00000397026:E889K;ENSP00000358133:E813K;ENSP00000358130:E840K	ENSP00000358130:E840K	E	+	1	0	GRIK2	102623017	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.444000	0.97578	2.745000	0.94114	0.462000	0.41574	GAA	.	.		0.463	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			A	102516324	G	A	102516324	3	1	95	1	0	0	0	0	1	0	0	0	6783	943	33	3	2900	3	GRIK2	6	102516324	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	3232334	102516324	68598743	46	13129										
IL20RA	53832	hgsc.bcm.edu	37	chr6	137323493	137323493	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tcatttccataaatcaaaatCtataaagagaaaagagaatg	5	5	3	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:137323493C>G	ENST00000316649.5	-	7	1100		c.e7-1		IL20RA_ENST00000367748.1_Splice_Site|IL20RA_ENST00000468393.1_5'Flank|RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000541547.1_Splice_Site	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha						cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		AAATCAAAATCTATAAAGAGA	0.313																																					.		Atlas-SNP	.											.	IL20RA	54	.	0			c.865-1G>C						.						20	23	22					6																	137323493		2119	4168	6287	SO:0001630	splice_region_variant	53832	exon8			CAAAATCTATAAA	AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"Interleukins and interleukin receptors"	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.865-1G>C	chr6.hg19:g.137323493C>G		61.0	0.0		49.0	7.0	NM_014432	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Splice_Site	SNP	ENST00000316649.5	hg19	CCDS5181.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.353316	0.24512	.	.	ENSG00000016402	ENST00000316649;ENST00000367748;ENST00000541547	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7927	0.85593	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IL20RA	137365186	1.000000	0.71417	0.977000	0.42913	0.018000	0.09664	4.394000	0.59671	2.745000	0.94114	0.655000	0.94253	.	.	.		0.313	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432	Intron	G	137323493	C	G	137323493	5	3	95	1	0	0	0	0	0	0	1	0	7677	927	32	4	801	4	IL20RA	6	137323493	Splice_Site	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	34807169	137323493	33791574	47	13130										
HEBP2	23593	hgsc.bcm.edu	37	chr6	138734131	138734131	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aaggtttactacactgcaggCtacaacagtcctgtcaaatt	7	10	1	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:138734131C>T	ENST00000607197.1	+	4	811	c.534C>T	c.(532-534)ggC>ggT	p.G178G	HEBP2_ENST00000367697.3_3'UTR|HEBP2_ENST00000448741.1_3'UTR	NM_014320.2	NP_055135.1	Q9Y5Z4	HEBP2_HUMAN	heme binding protein 2	178					negative regulation of mitochondrial membrane potential (GO:0010917)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of necrotic cell death (GO:0010940)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(3)	5	Breast(32;0.0933)			GBM - Glioblastoma multiforme(68;0.000732)|OV - Ovarian serous cystadenocarcinoma(155;0.00171)		ACACTGCAGGCTACAACAGTC	0.348																																					p.G178G		Atlas-SNP	.											.	HEBP2	12	.	0			c.C534T						.						143	147	146					6																	138734131		2203	4300	6503	SO:0001819	synonymous_variant	23593	exon4			TGCAGGCTACAAC	AF117616	CCDS5191.1	6q24	2008-08-29	2002-09-23	2002-09-27	ENSG00000051620	ENSG00000051620			15716	protein-coding gene	gene with protein product		605825	"chromosome 6 open reading frame 34"	C6orf34		10640688, 17098234	Standard	NM_014320		Approved	SOUL	uc003qhw.1	Q9Y5Z4	OTTHUMG00000015671	ENST00000607197.1:c.534C>T	chr6.hg19:g.138734131C>T		166.0	0.0		133.0	33.0	NM_014320	Q96P57	Silent	SNP	ENST00000607197.1	hg19	CCDS5191.1																																																																																			.	.		0.348	HEBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042426.2			T	138734131	C	T	138734131	2	4	95	1	0	0	0	0	0	0	0	1	7046	784	28	3		3	HEBP2	6	138734131	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	1410638	138734131	32380936	48	13131										
ACAT2	39	hgsc.bcm.edu	37	chr6	160196246	160196246	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aagtgagtagagaagatcagGacaaggttgcagttctgtcc	13	6	2	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:160196246G>C	ENST00000367048.4	+	5	2295	c.535G>C	c.(535-537)Gac>Cac	p.D179H	ACAT2_ENST00000541436.1_Missense_Mutation_p.D208H	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	179					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		AGAAGATCAGGACAAGGTTGC	0.403																																					p.D179H		Atlas-SNP	.											.	ACAT2	32	.	0			c.G535C						.						97	88	91					6																	160196246		2203	4300	6503	SO:0001583	missense	39	exon5			GATCAGGACAAGG	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	100678	"acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)", "acetyl-Coenzyme A acetyltransferase 2"			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.535G>C	chr6.hg19:g.160196246G>C	ENSP00000356015:p.Asp179His	70.0	0.0		118.0	73.0	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Missense_Mutation	SNP	ENST00000367048.4	hg19	CCDS5268.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.037509	0.93630	.	.	ENSG00000120437	ENST00000367048;ENST00000541436	D;D	0.97232	-4.3;-4.3	5.8	5.8	0.92144	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	D	0.99351	0.9772	H	0.99299	4.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98532	1.0628	10	0.87932	D	0	6.2818	20.0693	0.97712	0.0:0.0:1.0:0.0	.	208;179	B7Z233;Q9BWD1	.;THIC_HUMAN	H	179;208	ENSP00000356015:D179H;ENSP00000437850:D208H	ENSP00000356015:D179H	D	+	1	0	ACAT2	160116236	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	9.188000	0.94921	2.758000	0.94735	0.563000	0.77884	GAC	.	.		0.403	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891		C	160196246	G	C	160196246	3	2	95	1	0	0	0	0	1	0	0	0	122	1174	41	4	553	4	ACAT2	6	160196246	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	21462115	160196246	10918821	49	13132										
RNASET2	8635	hgsc.bcm.edu	37	chr6	167366035	167366035	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ttttttccactcatggttgtCactgttaaaacataagaaac	5	8	2	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr6:167366035C>T	ENST00000508775.1	-	2	607	c.88G>A	c.(88-90)Gac>Aac	p.D30N	RNASET2_ENST00000496851.2_5'Flank|RP11-514O12.4_ENST00000507747.1_Splice_Site_p.V10V|RNASET2_ENST00000476238.2_Splice_Site_p.D30N|RNASET2_ENST00000366855.6_5'UTR	NM_003730.4	NP_003721.2	O00584	RNT2_HUMAN	ribonuclease T2	30					RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	ribonuclease activity (GO:0004540)|ribonuclease T2 activity (GO:0033897)|RNA binding (GO:0003723)			large_intestine(4)|lung(4)	8		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)		TCATGGTTGTCACTGTTAAAA	0.423																																					p.D30N		Atlas-SNP	.											.	RNASET2	18	.	0			c.G88A						.						97	89	92					6																	167366035		2203	4300	6503	SO:0001630	splice_region_variant	8635	exon2			GGTTGTCACTGTT	AJ419866	CCDS5295.1	6q27	2014-05-20			ENSG00000026297	ENSG00000026297			21686	protein-coding gene	gene with protein product		612944				9192857	Standard	NM_003730		Approved	RNASE6PL, FLJ10907, bA514O12.3	uc003qve.3	O00584	OTTHUMG00000016009	ENST00000508775.1:c.87-1G>A	chr6.hg19:g.167366035C>T		265.0	0.0		231.0	27.0	NM_003730	B2RDA7|E1P5C3|Q5T8Q0|Q8TCU2|Q9BZ46|Q9BZ47	Missense_Mutation	SNP	ENST00000508775.1	hg19	CCDS5295.1	.	.	.	.	.	.	.	.	.	.	C	13.03	2.116263	0.37339	.	.	ENSG00000026297	ENST00000508775;ENST00000428859;ENST00000476238;ENST00000478180;ENST00000310843;ENST00000425007	T;T;T	0.64085	-0.08;-0.08;-0.07	4.35	2.53	0.30540	.	0.863021	0.10121	N	0.713457	T	0.11324	0.0276	N	0.08118	0	0.24296	N	0.995147	B	0.33694	0.421	B	0.26864	0.074	T	0.30060	-0.9991	10	0.05525	T	0.97	-8.9063	5.7466	0.18124	0.0:0.6945:0.1981:0.1074	.	30	O00584	RNT2_HUMAN	N	30	ENSP00000426455:D30N;ENSP00000422846:D30N;ENSP00000426059:D30N	ENSP00000028008:D30N	D	-	1	0	RNASET2	167286025	0.118000	0.22208	0.541000	0.28102	0.336000	0.28762	0.563000	0.23547	0.444000	0.26612	0.655000	0.94253	GAC	.	.		0.423	RNASET2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043089.2	NM_003730	Missense_Mutation	T	167366035	C	T	167366035	5	4	95	1	0	0	0	0	0	0	1	0	13433	840	29	3	714	3	RNASET2	6	167366035	Splice_Site	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	7169789	167366035	3749032	50	13133										
CYP2W1	54905	hgsc.bcm.edu	37	chr7	1026794	1026794	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ccaacgcggtggcctgcaccCtggacatggtcatggccggg	15	14	1	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr7:1026794C>A	ENST00000308919.7	+	6	884	c.871C>A	c.(871-873)Ctg>Atg	p.L291M	CYP2W1_ENST00000340150.6_Missense_Mutation_p.L235M	NM_017781.2	NP_060251.2	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W, polypeptide 1	291					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		GGCCTGCACCCTGGACATGGT	0.706																																					p.L291M		Atlas-SNP	.											.	CYP2W1	28	.	0			c.C871A						.						17	18	18					7																	1026794		2171	4276	6447	SO:0001583	missense	54905	exon6			TGCACCCTGGACA	AK000366	CCDS5319.2	7p22.3	2004-07-05			ENSG00000073067	ENSG00000073067		"Cytochrome P450s"	20243	protein-coding gene	gene with protein product		615967					Standard	XM_005249792		Approved	FLJ20359, MGC34287	uc003sjq.1	Q8TAV3	OTTHUMG00000074071	ENST00000308919.7:c.871C>A	chr7.hg19:g.1026794C>A	ENSP00000310149:p.Leu291Met	86.0	0.0		80.0	34.0	NM_017781		Missense_Mutation	SNP	ENST00000308919.7	hg19	CCDS5319.2	.	.	.	.	.	.	.	.	.	.	C	12.27	1.889001	0.33348	.	.	ENSG00000073067	ENST00000308919;ENST00000340150;ENST00000415893	T;T;T	0.80566	-1.39;-1.39;-1.39	5.32	3.52	0.40303	.	0.505958	0.21484	N	0.073782	T	0.79064	0.4383	L	0.39514	1.22	0.27182	N	0.960644	B;P	0.47253	0.236;0.892	B;P	0.52031	0.262;0.688	T	0.69213	-0.5204	10	0.33940	T	0.23	.	10.6798	0.45809	0.0:0.8457:0.0:0.1543	.	235;291	A6NJ10;Q8TAV3	.;CP2W1_HUMAN	M	291;235;65	ENSP00000310149:L291M;ENSP00000344178:L235M;ENSP00000392581:L65M	ENSP00000310149:L291M	L	+	1	2	CYP2W1	993320	0.384000	0.25164	0.460000	0.27093	0.709000	0.40893	1.311000	0.33562	0.638000	0.30545	0.561000	0.74099	CTG	.	.		0.706	CYP2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157249.1	NM_017781		A	1026794	C	A	1026794	3	1	95	1	0	0	0	0	1	0	0	0	4178	680	24	3	893	3	CYP2W1	7	1026794	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10		1026794	158111869	51	13134										
INTS1	26173	hgsc.bcm.edu	37	chr7	1539152	1539152	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cggcccgcctccccctgcagCagcacgctcctggggggcat	13	19	0	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr7:1539152C>A	ENST00000404767.3	-	6	886	c.801G>T	c.(799-801)ctG>ctT	p.L267L	INTS1_ENST00000493531.1_5'Flank|INTS1_ENST00000389470.4_Silent_p.L395L	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	267					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		CCCCCTGCAGCAGCACGCTCC	0.682																																					p.L267L		Atlas-SNP	.											.	INTS1	145	.	0			c.G801T						.						33	40	38					7																	1539152		1967	4154	6121	SO:0001819	synonymous_variant	26173	exon6			CTGCAGCAGCACG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.801G>T	chr7.hg19:g.1539152C>A		51.0	0.0		55.0	38.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	hg19	CCDS47526.1																																																																																			.	.		0.682	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			A	1539152	C	A	1539152	2	1	95	1	0	0	0	0	0	0	0	1	7784	697	25	3		3	INTS1	7	1539152	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	512358	1539152	157599511	52	13135										
ZDHHC4	55146	hgsc.bcm.edu	37	chr7	6624765	6624765	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ttgaccttgacggcctcggcTgccaccgtcgccattgtgag	12	14	0	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr7:6624765T>G	ENST00000396706.2	+	7	1058	c.615T>G	c.(613-615)gcT>gcG	p.A205A	ZDHHC4_ENST00000405731.3_Silent_p.A205A|ZDHHC4_ENST00000396713.2_Silent_p.A205A|ZDHHC4_ENST00000396707.2_Silent_p.A205A|ZDHHC4_ENST00000396709.1_Silent_p.A205A|AC079742.4_ENST00000434951.1_RNA|ZDHHC4_ENST00000335965.6_Silent_p.A205A			Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	205						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)		CGGCCTCGGCTGCCACCGTCG	0.527																																					p.A205A		Atlas-SNP	.											.	ZDHHC4	36	.	0			c.T615G						.						167	114	132					7																	6624765		2203	4300	6503	SO:0001819	synonymous_variant	55146	exon7			CTCGGCTGCCACC	AF201931	CCDS5352.1	7p22.1	2011-01-11			ENSG00000136247	ENSG00000136247		"Zinc fingers, DHHC-type"	18471	protein-coding gene	gene with protein product							Standard	NM_018106		Approved	FLJ10479, ZNF374	uc003sqj.3	Q9NPG8	OTTHUMG00000023579	ENST00000396706.2:c.615T>G	chr7.hg19:g.6624765T>G		255.0	1.0		349.0	175.0	NM_018106	A4D2N9|Q53EV7|Q6FIB5|Q9H0R9	Silent	SNP	ENST00000396706.2	hg19	CCDS5352.1																																																																																			.	.		0.527	ZDHHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207477.3	NM_018106		G	6624765	T	G	6624765	2	3	95	1	0	0	0	0	0	0	0	1	17632	1567	55	5		5	ZDHHC4	7	6624765	Silent	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	5085613	6624765	152513898	53	13136										
MACC1	346389	hgsc.bcm.edu	37	chr7	20199316	20199316	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	attcaggtaattgtactgacCctccttgatggtttactttg	8	8	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr7:20199316C>A	ENST00000400331.5	-	5	976	c.668G>T	c.(667-669)gGg>gTg	p.G223V	MACC1_ENST00000589011.1_Missense_Mutation_p.G223V|MACC1_ENST00000332878.4_Missense_Mutation_p.G223V	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	223					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						TTGTACTGACCCTCCTTGATG	0.488																																					p.G223V		Atlas-SNP	.											.	MACC1	99	.	0			c.G668T						.						108	96	100					7																	20199316		2203	4300	6503	SO:0001583	missense	346389	exon5			ACTGACCCTCCTT		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.668G>T	chr7.hg19:g.20199316C>A	ENSP00000383185:p.Gly223Val	225.0	0.0		257.0	74.0	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	hg19	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.198378	0.58126	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.39592	1.07;1.07	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.68384	0.2995	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70930	-0.4738	10	0.87932	D	0	-11.593	19.8516	0.96743	0.0:1.0:0.0:0.0	.	223	Q6ZN28	MACC1_HUMAN	V	223	ENSP00000383185:G223V;ENSP00000328410:G223V	ENSP00000328410:G223V	G	-	2	0	MACC1	20165841	1.000000	0.71417	0.988000	0.46212	0.438000	0.31896	7.818000	0.86416	2.685000	0.91497	0.585000	0.79938	GGG	.	.		0.488	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		A	20199316	C	A	20199316	3	1	95	1	0	0	0	0	1	0	0	0	9152	623	22	3	1902	3	MACC1	7	20199316	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	13574551	20199316	138939347	54	13137										
BMPER	168667	hgsc.bcm.edu	37	chr7	34097695	34097695	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gagagatgtggtcctctatcAattgtaccatctgtgcttgt	10	8	3	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr7:34097695A>T	ENST00000297161.2	+	11	1326	c.952A>T	c.(952-954)Aat>Tat	p.N318Y	BMPER_ENST00000426693.1_Missense_Mutation_p.N318Y	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	318	VWFC 5. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)		p.N318H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GTCCTCTATCAATTGTACCAT	0.507																																					p.N318Y		Atlas-SNP	.											BMPER,NS,carcinoma,0,1	BMPER	131	.	1	Substitution - Missense(1)	breast(1)	c.A952T						.						272	203	227					7																	34097695		2203	4300	6503	SO:0001583	missense	168667	exon11			TCTATCAATTGTA		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"crossveinless-2"	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.952A>T	chr7.hg19:g.34097695A>T	ENSP00000297161:p.Asn318Tyr	346.0	0.0		422.0	125.0	NM_133468	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	hg19	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.395377	0.83011	.	.	ENSG00000164619	ENST00000297161;ENST00000426693	T;T	0.64991	-0.13;-0.13	5.63	5.63	0.86233	von Willebrand factor, type C (3);	0.085057	0.85682	D	0.000000	T	0.73666	0.3616	L	0.45698	1.435	0.58432	D	0.999999	D	0.71674	0.998	D	0.71184	0.972	T	0.76033	-0.3107	10	0.72032	D	0.01	.	16.1307	0.81436	1.0:0.0:0.0:0.0	.	318	Q8N8U9	BMPER_HUMAN	Y	318	ENSP00000297161:N318Y;ENSP00000393950:N318Y	ENSP00000297161:N318Y	N	+	1	0	BMPER	34064220	1.000000	0.71417	0.966000	0.40874	0.992000	0.81027	8.268000	0.89876	2.263000	0.75096	0.533000	0.62120	AAT	.	.		0.507	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		T	34097695	A	T	34097695	3	4	95	1	0	0	0	0	1	0	0	0	1468	130	5	4	990	4	BMPER	7	34097695	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	13898379	34097695	125040968	55	13138										
TFPI2	7980	hgsc.bcm.edu	37	chr7	93516721	93516721	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gagcacagtccctcatctttTggactgtagcaaaatgatgg	10	9	2	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr7:93516721T>C	ENST00000222543.5	-	4	795	c.483A>G	c.(481-483)ccA>ccG	p.P161P	TFPI2_ENST00000545378.1_Intron|GNGT1_ENST00000455502.1_Intron	NM_001271003.1|NM_001271004.1|NM_006528.3	NP_001257932.1|NP_001257933.1|NP_006519.1	P48307	TFPI2_HUMAN	tissue factor pathway inhibitor 2	161	BPTI/Kunitz inhibitor 3. {ECO:0000255|PROSITE-ProRule:PRU00031}.				blood coagulation (GO:0007596)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(5)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	all_cancers(62;4.45e-10)|all_epithelial(64;2.92e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			CCTCATCTTTTGGACTGTAGC	0.348																																					p.P161P		Atlas-SNP	.											.	TFPI2	37	.	0			c.A483G						.						64	64	64					7																	93516721		2203	4300	6503	SO:0001819	synonymous_variant	7980	exon4			ATCTTTTGGACTG	L27624	CCDS5632.1	7q	2008-07-18			ENSG00000105825	ENSG00000105825			11761	protein-coding gene	gene with protein product		600033				7896752, 8945635	Standard	NM_006528		Approved	PP5, TFPI-2, REF1	uc003umy.2	P48307	OTTHUMG00000022963	ENST00000222543.5:c.483A>G	chr7.hg19:g.93516721T>C		102.0	0.0		118.0	70.0	NM_006528	Q66ME8|Q8NAK6|Q9UC86	Silent	SNP	ENST00000222543.5	hg19	CCDS5632.1																																																																																			.	.		0.348	TFPI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254720.2	NM_006528		C	93516721	T	C	93516721	2	2	95	1	0	0	0	0	0	0	0	1	15824	1799	63	2		2	TFPI2	7	93516721	Silent	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	59419026	93516721	65621942	56	13139										
ANKRD7	56311	hgsc.bcm.edu	37	chr7	117865018	117865018	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gaagaagctgaaggaataccTtcagatcaagaaatatgatg	10	5	2	5			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr7:117865018T>C	ENST00000265224.4	+	1	289	c.134T>C	c.(133-135)cTt>cCt	p.L45P	ANKRD7_ENST00000477532.1_Intron|ANKRD7_ENST00000433239.1_5'UTR|ANKRD7_ENST00000357099.4_Missense_Mutation_p.L45P|ANKRD7_ENST00000417525.1_5'UTR	NM_019644.3	NP_062618.2	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	45					male gonad development (GO:0008584)	nucleus (GO:0005634)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)	29						AAGGAATACCTTCAGATCAAG	0.478																																					p.L45P		Atlas-SNP	.											.	ANKRD7	44	.	0			c.T134C						.						77	78	78					7																	117865018		1845	4086	5931	SO:0001583	missense	56311	exon1			AATACCTTCAGAT	D78334	CCDS43638.1	7q31	2013-01-10			ENSG00000106013	ENSG00000106013		"Ankyrin repeat domain containing"	18588	protein-coding gene	gene with protein product	"testis-specific ankyrin motif containing protein"	610731				8812458	Standard	NM_019644		Approved	TSA806	uc003vji.3	Q92527	OTTHUMG00000156960	ENST00000265224.4:c.134T>C	chr7.hg19:g.117865018T>C	ENSP00000265224:p.Leu45Pro	177.0	0.0		187.0	8.0	NM_019644	B4DYF5|Q96QN1|Q9UDM3	Missense_Mutation	SNP	ENST00000265224.4	hg19	CCDS43638.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.322376	0.41096	.	.	ENSG00000106013	ENST00000357099;ENST00000265224;ENST00000486422	T;T;T	0.72725	-0.68;-0.68;-0.68	4.01	4.01	0.46588	Ankyrin repeat-containing domain (4);	0.000000	0.28482	U	0.015187	D	0.88040	0.6330	H	0.97682	4.055	0.20489	N	0.999895	D	0.89917	1.0	D	0.77557	0.99	T	0.80743	-0.1246	10	0.87932	D	0	-5.6919	9.5654	0.39396	0.0:0.0:0.0:1.0	.	45	Q92527	ANKR7_HUMAN	P	45	ENSP00000349612:L45P;ENSP00000265224:L45P;ENSP00000417353:L45P	ENSP00000265224:L45P	L	+	2	0	ANKRD7	117652254	0.045000	0.20229	0.009000	0.14445	0.002000	0.02628	2.949000	0.49074	1.834000	0.53371	0.444000	0.29173	CTT	.	.		0.478	ANKRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346826.1	NM_001077708		C	117865018	T	C	117865018	3	2	95	1	0	0	0	0	1	0	0	0	686	1609	56	2	136	2	ANKRD7	7	117865018	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	24348297	117865018	41273645	57	13140										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3565967	3565967	+	Frame_Shift_Del	DEL	G	G	-													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ttatggcttccatccttgctGggcagcatcttgactcctct							TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr8:3565967delG	ENST00000520002.1	-	7	1533	c.978delC	c.(976-978)cccfs	p.P326fs	CSMD1_ENST00000602723.1_Frame_Shift_Del_p.P326fs|CSMD1_ENST00000602557.1_Frame_Shift_Del_p.P326fs|CSMD1_ENST00000539096.1_Frame_Shift_Del_p.P326fs|CSMD1_ENST00000400186.3_Frame_Shift_Del_p.P326fs|CSMD1_ENST00000542608.1_Frame_Shift_Del_p.P326fs|CSMD1_ENST00000537824.1_Frame_Shift_Del_p.P326fs			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	326						integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CATCCTTGCTGGGCAGCATCT	0.443																																					p.S327fs		Atlas-Indel,Pindel	.											.	CSMD1	1469	.	0			c.979delA						.						100	100	100					8																	3565967		1987	4178	6165	SO:0001589	frameshift_variant	64478	exon7			.			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.978delC	chr8.hg19:g.3565967delG	ENSP00000430733:p.Pro326fs	171.0	0.0		157.0	56.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Frame_Shift_Del	DEL	ENST00000520002.1	hg19																																																																																				.	.		0.443	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		-	3565967	G	-	3565967	7	5	95	1	0	1	0	1	0	0	0	0	3946	1335	47	0	9785	0	CSMD1	8	3565967	Frame_Shift_Del	DEL	G	TCGA-DD-A11D-01A-11D-A12Z-10		3565967	142798055	58	13141										
ADAM2	2515	hgsc.bcm.edu	37	chr8	39644537	39644537	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tgcatcacacatcttcccttGaaaggttgcaccaacataat	5	12	2	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr8:39644537G>T	ENST00000265708.4	-	10	950	c.847C>A	c.(847-849)Caa>Aaa	p.Q283K	ADAM2_ENST00000347580.4_Missense_Mutation_p.Q264K|ADAM2_ENST00000521880.1_Missense_Mutation_p.Q283K|ADAM2_ENST00000379853.2_Intron	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	283	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		ATCTTCCCTTGAAAGGTTGCA	0.294																																					p.Q283K		Atlas-SNP	.											.	ADAM2	124	.	0			c.C847A						.						121	105	110					8																	39644537		2203	4300	6503	SO:0001583	missense	2515	exon10			TCCCTTGAAAGGT	U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"ADAM metallopeptidase domain containing"	198	protein-coding gene	gene with protein product	"cancer/testis antigen 15"	601533	"fertilin beta"	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.847C>A	chr8.hg19:g.39644537G>T	ENSP00000265708:p.Gln283Lys	392.0	0.0		308.0	110.0	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	hg19	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.558849	0.27827	.	.	ENSG00000104755	ENST00000347580;ENST00000265708;ENST00000521880	T;T;T	0.09445	2.98;2.98;2.98	5.11	2.17	0.27698	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	T	0.09423	0.0232	L	0.43923	1.385	0.26343	N	0.977337	B;B;B	0.29909	0.041;0.22;0.261	B;B;B	0.29663	0.098;0.064;0.105	T	0.32188	-0.9916	8	.	.	.	.	7.7227	0.28742	0.0:0.1607:0.5071:0.3321	.	283;264;283	B4DWY7;Q99965-2;Q99965	.;.;ADAM2_HUMAN	K	264;283;283	ENSP00000343854:Q264K;ENSP00000265708:Q283K;ENSP00000429352:Q283K	.	Q	-	1	0	ADAM2	39763694	0.999000	0.42202	0.876000	0.34364	0.557000	0.35523	0.411000	0.21115	0.130000	0.18549	0.585000	0.79938	CAA	.	.		0.294	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		T	39644537	G	T	39644537	3	4	95	1	0	0	0	0	1	0	0	0	241	1299	45	3	1404	3	ADAM2	8	39644537	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	36078570	39644537	106719485	59	13142										
ANK1	286	hgsc.bcm.edu	37	chr8	41559138	41559138	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	attcgatgcttatcactgacTaactaaaacgagaaaaagca	6	8	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr8:41559138T>C	ENST00000347528.4	-	22	2474	c.2391A>G	c.(2389-2391)ttA>ttG	p.L797L	ANK1_ENST00000379758.2_Silent_p.L797L|ANK1_ENST00000289734.7_Silent_p.L797L|ANK1_ENST00000352337.4_Silent_p.L797L|ANK1_ENST00000396945.1_Silent_p.L797L|ANK1_ENST00000265709.8_Silent_p.L830L|ANK1_ENST00000396942.1_Silent_p.L797L	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	797	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			TATCACTGACTAACTAAAACG	0.478											OREG0018740	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L830L		Atlas-SNP	.											.	ANK1	497	.	0			c.A2490G						.						105	98	100					8																	41559138		2203	4300	6503	SO:0001819	synonymous_variant	286	exon22			ACTGACTAACTAA	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2391A>G	chr8.hg19:g.41559138T>C		148.0	0.0	902	85.0	31.0	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	hg19	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	T	12.85	2.060377	0.36373	.	.	ENSG00000029534	ENST00000520299	.	.	.	5.97	2.28	0.28536	.	.	.	.	.	T	0.57695	0.2071	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48969	-0.8987	4	.	.	.	.	8.8554	0.35225	0.0:0.2289:0.0:0.7711	.	.	.	.	G	111	.	.	S	-	1	0	ANK1	41678295	0.443000	0.25641	0.994000	0.49952	0.842000	0.47809	-0.045000	0.12003	0.152000	0.19188	0.533000	0.62120	AGT	.	.		0.478	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		C	41559138	T	C	41559138	2	2	95	1	0	0	0	0	0	0	0	1	620	1519	53	2		2	ANK1	8	41559138	Silent	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	1914601	41559138	104804884	60	13143										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110454292	110454292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	taaatgtgtctgtgggggacAcagtggcatggcattggcaa	15	6	1	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr8:110454292A>G	ENST00000378402.5	+	35	4365	c.4261A>G	c.(4261-4263)Aca>Gca	p.T1421A		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1421	IPT/TIG 7.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TGTGGGGGACACAGTGGCATG	0.418										HNSCC(38;0.096)																											p.T1421A		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A4261G						.						115	117	116					8																	110454292		1866	4108	5974	SO:0001583	missense	93035	exon35			GGGGACACAGTGG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.4261A>G	chr8.hg19:g.110454292A>G	ENSP00000367655:p.Thr1421Ala	245.0	0.0		200.0	76.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	A	11.70	1.718217	0.30503	.	.	ENSG00000205038	ENST00000378402	D	0.85411	-1.98	5.82	4.6	0.57074	Cupredoxin (1);	0.202657	0.42053	D	0.000771	T	0.81074	0.4747	M	0.63428	1.95	0.23673	N	0.99715	B	0.27117	0.168	B	0.20577	0.03	T	0.71269	-0.4643	10	0.37606	T	0.19	.	10.8656	0.46853	0.8422:0.1577:0.0:0.0	.	1421	Q86WI1	PKHL1_HUMAN	A	1421	ENSP00000367655:T1421A	ENSP00000367655:T1421A	T	+	1	0	PKHD1L1	110523468	1.000000	0.71417	0.995000	0.50966	0.421000	0.31385	3.696000	0.54757	2.218000	0.71995	0.482000	0.46254	ACA	.	.		0.418	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		G	110454292	A	G	110454292	3	3	95	1	0	0	0	0	1	0	0	0	11981	159	6	2	4399	2	PKHD1L1	8	110454292	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	68895154	110454292	35909730	61	13144										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87570246	87570246	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gctgagggcaacccgcccacGgaactgacgcagtcgcagat	13	14	0	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr9:87570246G>T	ENST00000323115.4	+	15	2291	c.1938G>T	c.(1936-1938)acG>acT	p.T646T	NTRK2_ENST00000376213.1_Silent_p.T646T|NTRK2_ENST00000277120.3_Silent_p.T662T|NTRK2_ENST00000376214.1_Silent_p.T662T			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	646	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	ACCCGCCCACGGAACTGACGC	0.627										TSP Lung(25;0.17)																											p.T662T		Atlas-SNP	.											NTRK2_ENST00000376214,caecum,carcinoma,0,2	NTRK2	331	.	0			c.G1986T						.						31	26	28					9																	87570246		2203	4300	6503	SO:0001819	synonymous_variant	4915	exon19			GCCCACGGAACTG	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.1938G>T	chr9.hg19:g.87570246G>T		41.0	0.0		38.0	14.0	NM_006180	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Silent	SNP	ENST00000323115.4	hg19	CCDS35050.1																																																																																			.	.		0.627	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			T	87570246	G	T	87570246	2	4	95	1	0	0	0	0	0	0	0	1	10716	1103	39	1		1	NTRK2	9	87570246	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10		87570246	53643185	62	13145										
C9orf4	23732	hgsc.bcm.edu	37	chr9	111899753	111899753	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ggttagggggttcccatcaaTaggtagaaggtcagagcaac	14	7	2	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr9:111899753T>C	ENST00000561981.2	-	5	1016	c.1017A>G	c.(1015-1017)ctA>ctG	p.L339L		NM_014334.2	NP_055149.2	Q9P0K9	FRS1L_HUMAN	ferric-chelate reductase 1-like	339						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)											TTCCCATCAATAGGTAGAAGG	0.368																																					p.L339L		Atlas-SNP	.											.	.	.	.	0			c.A1017G						.						96	95	95					9																	111899753		2203	4300	6503	SO:0001819	synonymous_variant	23732	exon5			CATCAATAGGTAG	AF155065	CCDS35098.1	9q31.3	2014-07-16	2012-03-06	2012-03-06	ENSG00000260230	ENSG00000260230			1362	protein-coding gene	gene with protein product		604574	"chromosome 9 open reading frame 4"	C9orf4		10603000	Standard	NM_014334		Approved	CG-6	uc004bdw.1	Q9P0K9	OTTHUMG00000020468	ENST00000561981.2:c.1017A>G	chr9.hg19:g.111899753T>C		141.0	0.0		91.0	34.0	NM_014334	Q5T4G4	Silent	SNP	ENST00000561981.2	hg19	CCDS35098.1																																																																																			.	.		0.368	FRRS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053586.2	NM_014334		C	111899753	T	C	111899753	2	2	95	1	0	0	0	0	0	0	0	1	2482	1393	49	2		2	C9orf4	9	111899753	Silent	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	24329507	111899753	29313678	63	13146										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114213731	114213731	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	acgtactccttcttgggtgcTagagagtttgagcaaaacag	11	8	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr9:114213731T>C	ENST00000338205.5	-	2	346	c.127A>G	c.(127-129)Agc>Ggc	p.S43G	KIAA0368_ENST00000259335.4_Missense_Mutation_p.S221G			Q5VYK3	ECM29_HUMAN	KIAA0368	49					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TCTTGGGTGCTAGAGAGTTTG	0.373																																					p.S221G		Atlas-SNP	.											.	KIAA0368	144	.	0			c.A661G						.						65	59	61					9																	114213731		1849	4105	5954	SO:0001583	missense	23392	exon4			GGGTGCTAGAGAG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.127A>G	chr9.hg19:g.114213731T>C	ENSP00000339889:p.Ser43Gly	243.0	0.0		165.0	66.0	NM_001080398	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	hg19		.	.	.	.	.	.	.	.	.	.	T	25.0	4.593025	0.86953	.	.	ENSG00000136813	ENST00000338205;ENST00000259335	T	0.70986	-0.53	5.55	5.55	0.83447	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.83764	0.5325	M	0.78456	2.415	0.80722	D	1	D	0.53885	0.963	D	0.67231	0.95	D	0.86020	0.1506	10	0.87932	D	0	.	15.6977	0.77512	0.0:0.0:0.0:1.0	.	49	Q5VYK3	ECM29_HUMAN	G	43;221	ENSP00000259335:S221G	ENSP00000259335:S221G	S	-	1	0	KIAA0368	113253552	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	7.665000	0.83852	2.107000	0.64212	0.482000	0.46254	AGC	.	.		0.373	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		C	114213731	T	C	114213731	3	2	95	1	0	0	0	0	1	0	0	0	8180	1522	53	2	5584	2	KIAA0368	9	114213731	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	2313978	114213731	26999700	64	13147										
LCN8	389812	hgsc.bcm.edu	37	chr9	139651621	139651621	+	IGR	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tccctccagaatcctccaatCtagagagatacggagcctgg	9	13	1	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr9:139651621C>A	ENST00000316144.5	-	0	762				LCN15_ENST00000482511.1_5'Flank|LCN8_ENST00000482893.1_5'UTR|LCN8_ENST00000371688.3_Splice_Site	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15						lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						ATCCTCCAATCTAGAGAGATA	0.642																																					.		Atlas-SNP	.											.	LCN8	14	.	0			c.25-1G>T						.						39	37	38					9																	139651621		2203	4300	6503	SO:0001628	intergenic_variant	138307	exon3			TCCAATCTAGAGA		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"Lipocalins"	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943		chr9.hg19:g.139651621C>A		79.0	0.0		52.0	21.0	NM_178469		Splice_Site	SNP	ENST00000316144.5	hg19	CCDS7006.1	.	.	.	.	.	.	.	.	.	.	C	6.568	0.473124	0.12461	.	.	ENSG00000204001	ENST00000371688	.	.	.	3.47	3.47	0.39725	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7394	0.46145	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LCN8	138771442	0.634000	0.27190	0.883000	0.34634	0.032000	0.12392	2.823000	0.48081	2.257000	0.74773	0.561000	0.74099	.	.	.		0.642	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347		A	139651621	C	A	139651621	1	1	95	0	1	0	0	0	0	0	0	0	8695	927	32	3		3	LCN8	9	139651621	IGR	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	25437890	139651621	1561810	65	13148										
USP6NL	9712	hgsc.bcm.edu	37	chr10	11532861	11532861	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	atagaataggcagcaagcacAtggaataaggattgttgcct	11	6	0	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr10:11532861A>T	ENST00000609104.1	-	9	907	c.513T>A	c.(511-513)caT>caA	p.H171Q	USP6NL_ENST00000277575.5_Missense_Mutation_p.H188Q|USP6NL_ENST00000379237.2_Missense_Mutation_p.H194Q	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	171	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						CAGCAAGCACATGGAATAAGG	0.348																																					p.H188Q		Atlas-SNP	.											.	USP6NL	57	.	0			c.T564A						.						33	32	32					10																	11532861		1801	4049	5850	SO:0001583	missense	9712	exon8			AAGCACATGGAAT	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"related to the N terminus of tre"	605405	"USP6NL intronic transcript 1 (non-protein coding)"	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.513T>A	chr10.hg19:g.11532861A>T	ENSP00000476462:p.His171Gln	203.0	0.0		152.0	64.0	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	hg19	CCDS53492.1	.	.	.	.	.	.	.	.	.	.	A	19.25	3.791682	0.70452	.	.	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.04083	3.71;3.71	5.58	1.91	0.25777	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.11750	0.0286	L	0.48260	1.515	0.58432	D	0.999994	D;P	0.55172	0.97;0.925	P;P	0.62813	0.907;0.804	T	0.00745	-1.1584	10	0.66056	D	0.02	.	9.6228	0.39732	0.7138:0.0:0.2862:0.0	.	171;188	Q92738;Q92738-2	US6NL_HUMAN;.	Q	171;188;171	ENSP00000277575:H188Q;ENSP00000368539:H171Q	ENSP00000277575:H188Q	H	-	3	2	USP6NL	11572867	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.683000	0.25349	0.133000	0.18654	0.533000	0.62120	CAT	.	.		0.348	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688		T	11532861	A	T	11532861	3	4	95	1	0	0	0	0	1	0	0	0	17102	214	8	4	2001	4	USP6NL	10	11532861	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10		11532861	124001886	66	13149										
DHTKD1	55526	hgsc.bcm.edu	37	chr10	12131171	12131171	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ccgtggccgtgggcaaaactCgcggcaggcagcagtctcgc	15	14	1	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr10:12131171C>T	ENST00000263035.4	+	5	966	c.904C>T	c.(904-906)Cgc>Tgc	p.R302C	DHTKD1_ENST00000465617.1_Intron	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	302					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			GGGCAAAACTCGCGGCAGGCA	0.602																																					p.R302C		Atlas-SNP	.											.	DHTKD1	104	.	0			c.C904T						.						76	69	71					10																	12131171		2203	4300	6503	SO:0001583	missense	55526	exon5			AAAACTCGCGGCA	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.904C>T	chr10.hg19:g.12131171C>T	ENSP00000263035:p.Arg302Cys	58.0	0.0		49.0	12.0	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	hg19	CCDS7087.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.532131	0.45073	.	.	ENSG00000181192	ENST00000263035;ENST00000437298	T;T	0.16196	2.36;2.36	5.43	5.43	0.79202	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	T	0.59824	0.2222	H	0.98388	4.22	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75961	-0.3133	10	0.87932	D	0	-9.1937	14.8998	0.70670	0.1439:0.8561:0.0:0.0	.	302	Q96HY7	DHTK1_HUMAN	C	302;237	ENSP00000263035:R302C;ENSP00000388163:R237C	ENSP00000263035:R302C	R	+	1	0	DHTKD1	12171177	0.977000	0.34250	0.031000	0.17742	0.008000	0.06430	2.402000	0.44521	2.543000	0.85770	0.563000	0.77884	CGC	.	.		0.602	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		T	12131171	C	T	12131171	3	4	95	1	0	0	0	0	1	0	0	0	4502	884	31	1	922	1	DHTKD1	10	12131171	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	598310	12131171	123403576	67	13150										
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38343322	38343322	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gaagtctggacagctgatcaCctgaaagagaggagccaaga	13	8	2	4			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr10:38343322C>T	ENST00000458705.2	+	5	425	c.267C>T	c.(265-267)caC>caT	p.H89H	ZNF33A_ENST00000374618.3_Silent_p.H90H|ZNF33A_ENST00000432900.2_Silent_p.H96H|ZNF33A_ENST00000469037.2_Silent_p.H90H|ZNF33A_ENST00000307441.9_Silent_p.H89H			Q06730	ZN33A_HUMAN	zinc finger protein 33A	89					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						CAGCTGATCACCTGAAAGAGA	0.358																																					p.H90H		Atlas-SNP	.											.	ZNF33A	103	.	0			c.C270T						.						76	77	77					10																	38343322		2203	4300	6503	SO:0001819	synonymous_variant	7581	exon5			TGATCACCTGAAA	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.267C>T	chr10.hg19:g.38343322C>T		181.0	0.0		110.0	52.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	hg19	CCDS31182.1																																																																																			.	.		0.358	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		T	38343322	C	T	38343322	2	4	95	1	0	0	0	0	0	0	0	1	17869	506	18	3		3	ZNF33A	10	38343322	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	26212151	38343322	97191425	68	13151										
ZNF239	8187	hgsc.bcm.edu	37	chr10	44052345	44052346	+	Frame_Shift_Del	DEL	TG	TG	-													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cttctctccagtgtggactcTgagatggatgcgaagatccg							TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr10:44052345_44052346delTG	ENST00000306006.6	-	2	1834_1835	c.1182_1183delCA	c.(1180-1185)ctcagafs	p.R395fs	ZNF239_ENST00000535642.1_Frame_Shift_Del_p.R395fs|ZNF239_ENST00000426961.1_Frame_Shift_Del_p.R395fs|ZNF239_ENST00000374446.2_Frame_Shift_Del_p.R395fs|ZNF239_ENST00000491188.1_5'Flank	NM_005674.2	NP_005665.2	Q16600	ZN239_HUMAN	zinc finger protein 239	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						GTGTGGACTCTGAGATGGATGC	0.515																																					p.395_395del		Atlas-Indel,Pindel	.											.	ZNF239	45	.	0			c.1183_1184del						.																																			SO:0001589	frameshift_variant	8187	exon3			.	X82125	CCDS41502.1	10q11.22-q11.23	2013-01-08			ENSG00000196793	ENSG00000196793		"Zinc fingers, C2H2-type"	13031	protein-coding gene	gene with protein product		601069				8903737, 8587123	Standard	NM_005674		Approved	MOK2, HOK-2	uc009xmk.3	Q16600	OTTHUMG00000018033	ENST00000306006.6:c.1182_1183delCA	chr10.hg19:g.44052345_44052346delTG	ENSP00000307774:p.Arg395fs	283.0	0.0		224.0	65.0	NM_001099284	Q5T1G9|Q8TAS5	Frame_Shift_Del	DEL	ENST00000306006.6	hg19	CCDS41502.1																																																																																			.	.		0.515	ZNF239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047710.1			-	44052346	TG	-	44052345	7	5	95	1	0	1	0	1	0	0	0	0	17806	1588	55	0	197	0	ZNF239	10	44052345	Frame_Shift_Del	DEL	TG	TCGA-DD-A11D-01A-11D-A12Z-10	5709023	44052345	91482402	69	13152	56	2								
ZNF239	8187	hgsc.bcm.edu	37	chr10	44052346	44052346	+	Silent	SNP	G	G	C													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ttctctccagtgtggactctGagatggatgcgaagatccga							TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr10:44052346G>C	ENST00000306006.6	-	2	1834	c.1182C>G	c.(1180-1182)ctC>ctG	p.L394L	ZNF239_ENST00000535642.1_Silent_p.L394L|ZNF239_ENST00000426961.1_Silent_p.L394L|ZNF239_ENST00000374446.2_Silent_p.L394L|ZNF239_ENST00000491188.1_5'Flank	NM_005674.2	NP_005665.2	Q16600	ZN239_HUMAN	zinc finger protein 239	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						TGTGGACTCTGAGATGGATGC	0.517																																					p.L394L		Atlas-SNP	.											.	ZNF239	45	.	0			c.C1182G						.						91	99	96					10																	44052346		2184	4296	6480	SO:0001819	synonymous_variant	8187	exon2			GACTCTGAGATGG	X82125	CCDS41502.1	10q11.22-q11.23	2013-01-08			ENSG00000196793	ENSG00000196793		"Zinc fingers, C2H2-type"	13031	protein-coding gene	gene with protein product		601069				8903737, 8587123	Standard	NM_005674		Approved	MOK2, HOK-2	uc009xmk.3	Q16600	OTTHUMG00000018033	ENST00000306006.6:c.1182C>G	chr10.hg19:g.44052346G>C		289.0	0.0		161.0	10.0	NM_001099283	Q5T1G9|Q8TAS5	Silent	SNP	ENST00000306006.6	hg19	CCDS41502.1																																																																																			.	.		0.517	ZNF239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047710.1			C	44052346	G	C	44052346	2	2	95	1	0	0	0	0	0	0	0	1	17806	1277	45	4		4	ZNF239	10	44052346	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	1	44052346	91482401	70	13153	56	2								
OR51T1	401665	hgsc.bcm.edu	37	chr11	4903945	4903945	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ctcttccactccaccccaagGgtgctctgtagcactttggc	8	16	2	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:4903945G>T	ENST00000322049.1	+	1	816	c.816G>T	c.(814-816)agG>agT	p.R272S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron|OR51T1_ENST00000380378.1_Missense_Mutation_p.R299S			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		CCACCCCAAGGGTGCTCTGTA	0.493																																					p.R299S		Atlas-SNP	.											.	OR51T1	92	.	0			c.G897T						.						118	105	109					11																	4903945		2201	4298	6499	SO:0001583	missense	401665	exon1			CCCAAGGGTGCTC	BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"GPCR / Class A : Olfactory receptors"	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.816G>T	chr11.hg19:g.4903945G>T	ENSP00000322679:p.Arg272Ser	238.0	0.0		178.0	69.0	NM_001004759	Q6IFH9	Missense_Mutation	SNP	ENST00000322049.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.44	1.351761	0.24512	.	.	ENSG00000176900	ENST00000380378;ENST00000322049	T;T	0.35421	1.31;1.31	4.97	-5.93	0.02254	GPCR, rhodopsin-like superfamily (1);	0.509628	0.16622	N	0.206431	T	0.16128	0.0388	N	0.20986	0.625	0.09310	N	1	B	0.21071	0.051	B	0.17433	0.018	T	0.06197	-1.0840	10	0.52906	T	0.07	.	3.03	0.06103	0.5324:0.0951:0.1682:0.2043	.	272	Q8NGJ9	O51T1_HUMAN	S	299;272	ENSP00000369738:R299S;ENSP00000322679:R272S	ENSP00000322679:R272S	R	+	3	2	OR51T1	4860521	0.000000	0.05858	0.075000	0.20258	0.932000	0.56968	-2.939000	0.00684	-1.095000	0.03050	0.491000	0.48974	AGG	.	.		0.493	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759		T	4903945	G	T	4903945	3	4	95	1	0	0	0	0	1	0	0	0	11115	1223	43	3	899	3	OR51T1	11	4903945	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10		4903945	130102571	71	13154										
OR5P3	120066	hgsc.bcm.edu	37	chr11	7846818	7846818	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	caggtggagaaggccttgtgGcggcccttggtggagtgcat	18	8	0	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:7846818G>T	ENST00000328375.1	-	1	701	c.702C>A	c.(700-702)cgC>cgA	p.R234R	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153445.1	NP_703146.1	Q8WZ94	OR5P3_HUMAN	olfactory receptor, family 5, subfamily P, member 3	234						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	15				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGGCCTTGTGGCGGCCCTTGG	0.498																																					p.R234R		Atlas-SNP	.											.	OR5P3	44	.	0			c.C702A						.						118	99	106					11																	7846818		2188	4296	6484	SO:0001819	synonymous_variant	120066	exon1			CTTGTGGCGGCCC	AF158377	CCDS7783.1	11p15.4	2012-08-09			ENSG00000182334	ENSG00000182334		"GPCR / Class A : Olfactory receptors"	14784	protein-coding gene	gene with protein product							Standard	NM_153445		Approved	JCG1	uc010rbg.2	Q8WZ94	OTTHUMG00000165669	ENST00000328375.1:c.702C>A	chr11.hg19:g.7846818G>T		179.0	0.0		144.0	63.0	NM_153445	Q6IFE1|Q8NGM2	Silent	SNP	ENST00000328375.1	hg19	CCDS7783.1																																																																																			.	.		0.498	OR5P3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385697.1	NM_153445		T	7846818	G	T	7846818	2	4	95	1	0	0	0	0	0	0	0	1	11188	1190	42	3		3	OR5P3	11	7846818	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	2942873	7846818	127159698	72	13155										
C11orf16	56673	hgsc.bcm.edu	37	chr11	8947426	8947426	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ggtggcagagagggcacaggAatggagcatccggaggaagc	19	7	0	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:8947426A>G	ENST00000326053.5	-	5	894	c.788T>C	c.(787-789)tTc>tCc	p.F263S	C11orf16_ENST00000525780.1_Missense_Mutation_p.F263S|C11orf16_ENST00000528998.1_5'Flank	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	263										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	22				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		AGGGCACAGGAATGGAGCATC	0.632																																					p.F263S		Atlas-SNP	.											.	C11orf16	43	.	0			c.T788C						.						75	74	74					11																	8947426		2201	4296	6497	SO:0001583	missense	56673	exon5			CACAGGAATGGAG	AJ400877	CCDS7794.1	11p15.3	2008-06-25			ENSG00000176029	ENSG00000176029			1169	protein-coding gene	gene with protein product						11528127	Standard	NM_020643		Approved		uc001mhb.4	Q9NQ32	OTTHUMG00000165654	ENST00000326053.5:c.788T>C	chr11.hg19:g.8947426A>G	ENSP00000318999:p.Phe263Ser	66.0	0.0		49.0	19.0	NM_020643	Q53FB2|Q8N6Y9	Missense_Mutation	SNP	ENST00000326053.5	hg19	CCDS7794.1	.	.	.	.	.	.	.	.	.	.	A	12.08	1.831224	0.32329	.	.	ENSG00000176029	ENST00000525780;ENST00000326053	T;T	0.38401	1.2;1.14	6.07	3.75	0.43078	.	0.630079	0.16603	N	0.207279	T	0.31009	0.0783	M	0.61703	1.905	0.09310	N	1	B;P	0.43287	0.383;0.802	B;B	0.36719	0.095;0.231	T	0.27905	-1.0060	10	0.59425	D	0.04	-33.0708	6.0536	0.19799	0.7227:0.1369:0.1404:0.0	.	263;263	Q9NQ32-2;Q9NQ32	.;CK016_HUMAN	S	263	ENSP00000436818:F263S;ENSP00000318999:F263S	ENSP00000318999:F263S	F	-	2	0	C11orf16	8904002	0.922000	0.31269	0.002000	0.10522	0.005000	0.04900	1.693000	0.37742	0.530000	0.28619	-0.290000	0.09829	TTC	.	.		0.632	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643		G	8947426	A	G	8947426	3	3	95	1	0	0	0	0	1	0	0	0	1633	246	9	2	623	2	C11orf16	11	8947426	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	1100608	8947426	126059090	73	13156										
PDHX	8050	hgsc.bcm.edu	37	chr11	35016491	35016491	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ttggggatgtttggcatcgaCgaatttactgcagtgattaa	12	5	0	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:35016491C>T	ENST00000227868.4	+	11	1362	c.1278C>T	c.(1276-1278)gaC>gaT	p.D426D	PDHX_ENST00000448838.3_Silent_p.D411D|PDHX_ENST00000430469.2_Silent_p.D199D|PDHX_ENST00000477173.3_Intron			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	426					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			TTGGCATCGACGAATTTACTG	0.488																																					p.D426D		Atlas-SNP	.											.	PDHX	40	.	0			c.C1278T						.						117	117	117					11																	35016491		2202	4298	6500	SO:0001819	synonymous_variant	8050	exon11			CATCGACGAATTT	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.1278C>T	chr11.hg19:g.35016491C>T		182.0	0.0		143.0	9.0	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Silent	SNP	ENST00000227868.4	hg19	CCDS7896.1	.	.	.	.	.	.	.	.	.	.	C	5.116	0.206948	0.09704	.	.	ENSG00000110435	ENST00000526309	.	.	.	6.04	-1.72	0.08107	.	.	.	.	.	T	0.58104	0.2099	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55842	-0.8077	4	.	.	.	-25.8974	11.9285	0.52833	0.0:0.5073:0.0:0.4927	.	.	.	.	M	114	.	.	T	+	2	0	PDHX	34973067	0.611000	0.26992	0.959000	0.39883	0.626000	0.37791	-0.211000	0.09332	-0.273000	0.09246	-1.012000	0.02466	ACG	.	.		0.488	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477		T	35016491	C	T	35016491	2	4	95	1	0	0	0	0	0	0	0	1	11676	535	19	1		1	PDHX	11	35016491	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	26069065	35016491	99990025	74	13157										
ZNF408	79797	hgsc.bcm.edu	37	chr11	46726465	46726465	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	catatgctgggccaccgtggGgtgcggcccttcccctgtcc	13	16	0	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:46726465G>T	ENST00000311764.2	+	5	1445	c.1215G>T	c.(1213-1215)ggG>ggT	p.G405G		NM_001184751.1|NM_024741.2	NP_001171680.1|NP_079017.1	Q9H9D4	ZN408_HUMAN	zinc finger protein 408	405					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCCACCGTGGGGTGCGGCCCT	0.582																																					p.G405G	Pancreas(79;698 1390 6545 18745 34127)|Esophageal Squamous(120;1014 1625 12837 24601 49525)	Atlas-SNP	.											.	ZNF408	70	.	0			c.G1215T						.						61	61	61					11																	46726465		2201	4299	6500	SO:0001819	synonymous_variant	79797	exon5			CCGTGGGGTGCGG	AF346626	CCDS7923.1	11p11.2	2008-02-05			ENSG00000175213	ENSG00000175213		"Zinc fingers, C2H2-type"	20041	protein-coding gene	gene with protein product						15231747	Standard	NM_024741		Approved	FLJ12827	uc010rgw.2	Q9H9D4	OTTHUMG00000166568	ENST00000311764.2:c.1215G>T	chr11.hg19:g.46726465G>T		140.0	0.0		91.0	12.0	NM_024741		Silent	SNP	ENST00000311764.2	hg19	CCDS7923.1																																																																																			.	.		0.582	ZNF408-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390485.2	NM_024741		T	46726465	G	T	46726465	2	4	95	1	0	0	0	0	0	0	0	1	17903	1219	43	3		3	ZNF408	11	46726465	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	11709974	46726465	88280051	75	13158										
CELF1	10658	hgsc.bcm.edu	37	chr11	47504291	47504291	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	atttagaccagcaaggtttcCccacacagatgctgcgctga	9	12	0	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:47504291C>A	ENST00000358597.3	-	6	642	c.643G>T	c.(643-645)Gga>Tga	p.G215*	CELF1_ENST00000310513.5_Nonsense_Mutation_p.G215*|CELF1_ENST00000361904.3_Nonsense_Mutation_p.G215*|CELF1_ENST00000395292.2_Nonsense_Mutation_p.G215*|CELF1_ENST00000395290.2_Nonsense_Mutation_p.G214*|CELF1_ENST00000532048.1_Nonsense_Mutation_p.G241*|CELF1_ENST00000531165.1_Nonsense_Mutation_p.G242*			Q92879	CELF1_HUMAN	CUGBP, Elav-like family member 1	215					embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of translation (GO:0017148)|positive regulation of multicellular organism growth (GO:0040018)|regulation of RNA splicing (GO:0043484)|RNA interference (GO:0016246)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation repressor activity, nucleic acid binding (GO:0000900)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(2)	18						GCAAGGTTTCCCCACACAGAT	0.488																																					p.G241X	Pancreas(163;1949 1966 9906 43218 43785)	Atlas-SNP	.											.	CELF1	43	.	0			c.G721T						.						129	116	120					11																	47504291		2201	4298	6499	SO:0001587	stop_gained	10658	exon9			GGTTTCCCCACAC	U63289	CCDS7938.1, CCDS7939.1, CCDS31482.1, CCDS53622.1, CCDS53623.1	11p11	2013-02-12	2010-02-19	2010-02-19				"RNA binding motif (RRM) containing"	2549	protein-coding gene	gene with protein product	"CUG RNA-binding protein", "nuclear polyadenylated RNA-binding protein, 50-kD", "bruno-like 2", "embryo deadenylation element binding protein"	601074	"CUG triplet repeat, RNA-binding protein 1", "CUG triplet repeat, RNA binding protein 1"	CUGBP1		8948631, 9371827	Standard	NM_006560		Approved	CUG-BP, hNab50, BRUNOL2, NAB50, CUGBP, NAPOR, EDEN-BP	uc001nfl.3	Q92879		ENST00000358597.3:c.643G>T	chr11.hg19:g.47504291C>A	ENSP00000351409:p.Gly215*	274.0	0.0		206.0	89.0	NM_001172639	B4E2U5|D3DQS0|F8W940|Q4LE52|Q9NP83|Q9NR06	Nonsense_Mutation	SNP	ENST00000358597.3	hg19	CCDS31482.1	.	.	.	.	.	.	.	.	.	.	c	33	5.290516	0.95546	.	.	ENSG00000149187	ENST00000395290;ENST00000358597;ENST00000395292;ENST00000310513;ENST00000361904;ENST00000531165;ENST00000532048	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	-7.4391	19.7714	0.96367	0.0:1.0:0.0:0.0	.	.	.	.	X	214;215;215;215;215;242;241	.	ENSP00000308386:G215X	G	-	1	0	CELF1	47460867	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.728000	0.84847	2.661000	0.90470	0.651000	0.88453	GGA	.	.		0.488	CELF1-024	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398352.1	NM_006560		A	47504291	C	A	47504291	4	1	95	1	0	0	0	0	0	1	0	0	3217	632	22	3	848	3	CELF1	11	47504291	Nonsense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	777826	47504291	87502225	76	13159										
OR8J1	219477	hgsc.bcm.edu	37	chr11	56127796	56127796	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tagctgtccagagctccagaTtcccctcttcctggtctttc	7	15	2	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:56127796T>C	ENST00000303039.3	+	1	106	c.74T>C	c.(73-75)aTt>aCt	p.I25T		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					GAGCTCCAGATTCCCCTCTTC	0.498																																					p.I25T		Atlas-SNP	.											.	OR8J1	87	.	0			c.T74C						.						109	108	108					11																	56127796		2201	4296	6497	SO:0001583	missense	219477	exon1			TCCAGATTCCCCT	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"GPCR / Class A : Olfactory receptors"	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.74T>C	chr11.hg19:g.56127796T>C	ENSP00000304060:p.Ile25Thr	167.0	0.0		173.0	71.0	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	hg19	CCDS31529.1	.	.	.	.	.	.	.	.	.	.	T	4.133	0.022923	0.08006	.	.	ENSG00000172487	ENST00000303039	T	0.00587	6.38	4.57	3.34	0.38264	.	1.064010	0.07249	N	0.865549	T	0.00666	0.0022	L	0.38953	1.18	0.09310	N	1	B	0.20988	0.05	B	0.25405	0.06	T	0.46735	-0.9170	10	0.40728	T	0.16	.	5.648	0.17600	0.0:0.0946:0.1744:0.731	.	25	Q8NGP2	OR8J1_HUMAN	T	25	ENSP00000304060:I25T	ENSP00000304060:I25T	I	+	2	0	OR8J1	55884372	0.000000	0.05858	0.059000	0.19551	0.366000	0.29705	0.641000	0.24720	1.828000	0.53243	0.523000	0.50628	ATT	.	.		0.498	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205		C	56127796	T	C	56127796	3	2	95	1	0	0	0	0	1	0	0	0	11250	1493	52	2	76	2	OR8J1	11	56127796	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	8623505	56127796	78878720	77	13160										
POLR2G	5436	hgsc.bcm.edu	37	chr11	62532653	62532653	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gatcactcattttttttctaGgttggactcttcacagaaat	6	8	5	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:62532653G>T	ENST00000301788.7	+	4	387		c.e4-1			NM_002696.2	NP_002687.1	P62487	RPB7_HUMAN	polymerase (RNA) II (DNA directed) polypeptide G						7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, exonucleolytic (GO:0000291)|nucleotide-excision repair (GO:0006289)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translational initiation (GO:0045948)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)|translation initiation factor binding (GO:0031369)			lung(3)	3						TTTTTTTCTAGGTTGGACTCT	0.532																																					.		Atlas-SNP	.											.	POLR2G	6	.	0			c.283-1G>T						.						144	132	136					11																	62532653		2202	4299	6501	SO:0001630	splice_region_variant	5436	exon4			TTTCTAGGTTGGA	U20659	CCDS31585.1	11q13.1	2013-01-21			ENSG00000168002	ENSG00000168002		"RNA polymerase subunits"	9194	protein-coding gene	gene with protein product		602013				7579693, 9256063	Standard	NM_002696		Approved	hRPB19, hsRPB7, RPB7	uc001nva.3	P62487	OTTHUMG00000167609	ENST00000301788.7:c.283-1G>T	chr11.hg19:g.62532653G>T		264.0	0.0		191.0	13.0	NM_002696	B2R5C0|P52433|Q2M1Z4	Splice_Site	SNP	ENST00000301788.7	hg19	CCDS31585.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.793127	0.90453	.	.	ENSG00000168002	ENST00000301788	.	.	.	6.04	6.04	0.98038	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0887	0.89466	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	POLR2G	62289229	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	8.440000	0.90311	2.873000	0.98535	0.563000	0.77884	.	.	.		0.532	POLR2G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395344.1	NM_002696	Intron	T	62532653	G	T	62532653	5	4	95	1	0	0	0	0	0	0	1	0	12229	1014	35	3	296	3	POLR2G	11	62532653	Splice_Site	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	6404857	62532653	72473863	78	13161										
PYGM	5837	hgsc.bcm.edu	37	chr11	64520562	64520562	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cacctcagcaatgacctctgCcagcccggggttacacagaa	9	15	2	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:64520562C>A	ENST00000164139.3	-	12	1899	c.1501G>T	c.(1501-1503)Gca>Tca	p.A501S	PYGM_ENST00000377432.3_Missense_Mutation_p.A413S|PYGM_ENST00000462303.1_5'Flank	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	501					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ATGACCTCTGCCAGCCCGGGG	0.567																																					p.A501S		Atlas-SNP	.											.	PYGM	77	.	0			c.G1501T						.						195	222	213					11																	64520562		2201	4297	6498	SO:0001583	missense	5837	exon12			CCTCTGCCAGCCC		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.1501G>T	chr11.hg19:g.64520562C>A	ENSP00000164139:p.Ala501Ser	195.0	0.0		134.0	50.0	NM_005609	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	hg19	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.015598	0.35511	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.92911	-3.13;-3.13	5.82	5.82	0.92795	.	0.000000	0.56097	D	0.000028	D	0.87071	0.6086	N	0.11064	0.09	0.80722	D	1	B;B	0.17465	0.009;0.022	B;B	0.40038	0.105;0.317	T	0.79262	-0.1876	10	0.05833	T	0.94	-12.0263	17.579	0.87960	0.0:1.0:0.0:0.0	.	413;501	A6NDY6;P11217	.;PYGM_HUMAN	S	413;501;482	ENSP00000366650:A413S;ENSP00000164139:A501S	ENSP00000164139:A501S	A	-	1	0	PYGM	64277138	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.748000	0.85085	2.756000	0.94617	0.561000	0.74099	GCA	.	.		0.567	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		A	64520562	C	A	64520562	3	1	95	1	0	0	0	0	1	0	0	0	12877	739	26	3	1063	3	PYGM	11	64520562	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	1987909	64520562	70485954	79	13162										
CD248	57124	hgsc.bcm.edu	37	chr11	66082959	66082959	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tttggttgagatcataggggGctggtgggcaggaggctgtg	20	4	1	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:66082959G>C	ENST00000311330.3	-	1	1556	c.1540C>G	c.(1540-1542)Ccc>Gcc	p.P514A	RP11-867G23.13_ENST00000534065.1_RNA	NM_020404.2	NP_065137.1	Q9HCU0	CD248_HUMAN	CD248 molecule, endosialin	514	Pro-rich.				anatomical structure regression (GO:0060033)|cell migration (GO:0016477)|lymph node development (GO:0048535)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	26						ATCATAGGGGGCTGGTGGGCA	0.577																																					p.P514A		Atlas-SNP	.											.	CD248	69	.	0			c.C1540G						.						78	82	80					11																	66082959		2200	4295	6495	SO:0001583	missense	57124	exon1			TAGGGGGCTGGTG	AF279142	CCDS8134.1	11q13	2006-04-12	2006-03-28	2005-02-11	ENSG00000174807	ENSG00000174807		"CD molecules"	18219	protein-coding gene	gene with protein product	"endosialin", "tumor endothelial marker 1"	606064	"CD164 sialomucin-like 1", "CD248 antigen, endosialin"	CD164L1		10947988, 11084048	Standard	NM_020404		Approved	TEM1	uc001ohm.1	Q9HCU0	OTTHUMG00000167073	ENST00000311330.3:c.1540C>G	chr11.hg19:g.66082959G>C	ENSP00000308117:p.Pro514Ala	189.0	0.0		160.0	68.0	NM_020404	Q2M2V5|Q3SX55|Q96KB6	Missense_Mutation	SNP	ENST00000311330.3	hg19	CCDS8134.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.002839	0.35320	.	.	ENSG00000174807	ENST00000311330	D	0.92752	-3.1	4.44	2.46	0.29980	.	.	.	.	.	D	0.84897	0.5574	L	0.27053	0.805	0.09310	N	1	B	0.18461	0.028	B	0.14023	0.01	T	0.69684	-0.5079	9	0.22706	T	0.39	-10.6789	10.0404	0.42155	0.0:0.0:0.4632:0.5368	.	514	Q9HCU0	CD248_HUMAN	A	514	ENSP00000308117:P514A	ENSP00000308117:P514A	P	-	1	0	CD248	65839535	0.994000	0.37717	0.870000	0.34147	0.420000	0.31355	3.687000	0.54692	0.446000	0.26666	-0.535000	0.04281	CCC	.	.		0.577	CD248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392922.2	NM_020404		C	66082959	G	C	66082959	3	2	95	1	0	0	0	0	1	0	0	0	2991	1203	42	4	737	4	CD248	11	66082959	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	1562397	66082959	68923557	80	13163										
XRRA1	143570	hgsc.bcm.edu	37	chr11	74617459	74617459	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tgaacttgctgtaggtatggGatcctgataatcctgttttc	10	7	0	2	rs369421169		TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:74617459G>T	ENST00000340360.6	-	10	1135	c.804C>A	c.(802-804)atC>atA	p.I268I	XRRA1_ENST00000527087.1_Silent_p.I268I|RP11-147I3.1_ENST00000533875.1_RNA|XRRA1_ENST00000321448.8_Silent_p.I35I	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						GTAGGTATGGGATCCTGATAA	0.423																																					p.I268I		Atlas-SNP	.											.	XRRA1	46	.	0			c.C804A						.						98	95	96					11																	74617459		1922	4116	6038	SO:0001819	synonymous_variant	143570	exon10			GTATGGGATCCTG	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.804C>A	chr11.hg19:g.74617459G>T		355.0	0.0		251.0	116.0	NM_182969		Silent	SNP	ENST00000340360.6	hg19	CCDS44680.1																																																																																			.	.		0.423	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969		T	74617459	G	T	74617459	2	4	95	1	0	0	0	0	0	0	0	1	17476	1164	41	3		3	XRRA1	11	74617459	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	8534500	74617459	60389057	81	13164										
PGR	5241	hgsc.bcm.edu	37	chr11	100998683	100998683	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aagtcgctatagagagggtaCgcgtcgtccttgggctcggc	15	10	0	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:100998683C>T	ENST00000325455.5	-	1	2572	c.1119G>A	c.(1117-1119)gcG>gcA	p.A373A	PGR_ENST00000263463.5_Silent_p.A373A|PGR_ENST00000534013.1_Intron	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	373	Modulating, Pro-Rich.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	AGAGAGGGTACGCGTCGTCCT	0.687																																					p.A373A	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.G1119A						.						19	23	22					11																	100998683		2094	4150	6244	SO:0001819	synonymous_variant	5241	exon1			AGGGTACGCGTCG	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"Nuclear hormone receptors"	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.1119G>A	chr11.hg19:g.100998683C>T		148.0	0.0		111.0	42.0	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Silent	SNP	ENST00000325455.5	hg19	CCDS8310.1																																																																																			.	.		0.687	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			T	100998683	C	T	100998683	2	4	95	1	0	0	0	0	0	0	0	1	11814	523	19	1		1	PGR	11	100998683	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	26381224	100998683	34007833	82	13165										
SCN3B	55800	hgsc.bcm.edu	37	chr11	123516374	123516374	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cctcctctctcttcatgcagGagatgcagcgcagcttcatg	9	14	4	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr11:123516374G>A	ENST00000392770.2	-	2	942	c.140C>T	c.(139-141)tCc>tTc	p.S47F	SCN3B_ENST00000530277.1_Missense_Mutation_p.S47F|SCN3B_ENST00000299333.3_Missense_Mutation_p.S47F	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	47	Ig-like C2-type.				atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	CTTCATGCAGGAGATGCAGCG	0.577																																					p.S47F		Atlas-SNP	.											SCN3B,colon,carcinoma,0,1	SCN3B	53	.	0			c.C140T						.						126	121	123					11																	123516374		2202	4299	6501	SO:0001583	missense	55800	exon2			ATGCAGGAGATGC	AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing"	20665	protein-coding gene	gene with protein product		608214	"sodium channel, voltage-gated, type III, beta"			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.140C>T	chr11.hg19:g.123516374G>A	ENSP00000376523:p.Ser47Phe	122.0	0.0		105.0	42.0	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Missense_Mutation	SNP	ENST00000392770.2	hg19	CCDS8442.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.041137	0.93685	.	.	ENSG00000166257	ENST00000392770;ENST00000299333;ENST00000530277;ENST00000527836;ENST00000528267	D;D;D;D;T	0.94092	-3.35;-3.35;-3.35;-3.35;-0.03	5.96	5.96	0.96718	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.095583	0.85682	D	0.000000	D	0.92906	0.7743	L	0.31526	0.94	0.58432	D	0.999997	D	0.55385	0.971	P	0.53224	0.721	D	0.91496	0.5215	10	0.33940	T	0.23	-4.9537	20.4182	0.99029	0.0:0.0:1.0:0.0	.	47	Q9NY72	SCN3B_HUMAN	F	47	ENSP00000376523:S47F;ENSP00000299333:S47F;ENSP00000432785:S47F;ENSP00000435554:S47F;ENSP00000434363:S47F	ENSP00000299333:S47F	S	-	2	0	SCN3B	123021584	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.258000	0.72487	2.820000	0.97059	0.609000	0.83330	TCC	.	.		0.577	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400		A	123516374	G	A	123516374	3	1	95	1	0	0	0	0	1	0	0	0	13934	1174	41	3	523	3	SCN3B	11	123516374	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	22517691	123516374	11490142	83	13166										
MAGOHB	55110	hgsc.bcm.edu	37	chr12	10766087	10766087	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tcgtgcccaaacttgcccttGtgccctacgtagtagcgcag	10	14	0	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr12:10766087G>A	ENST00000320756.2	-	1	135	c.45C>T	c.(43-45)caC>caT	p.H15H	MAGOHB_ENST00000381881.2_Silent_p.H15H|MAGOHB_ENST00000539554.1_Intron	NM_018048.3	NP_060518.1	Q96A72	MGN2_HUMAN	mago-nashi homolog B (Drosophila)	15					mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|large_intestine(2)	4						ACTTGCCCTTGTGCCCTACGT	0.617																																					p.H15H		Atlas-SNP	.											.	MAGOHB	17	.	0			c.C45T						.						110	105	107					12																	10766087		2203	4300	6503	SO:0001819	synonymous_variant	55110	exon1			GCCCTTGTGCCCT		CCDS8628.1	12p13.2	2014-02-12	2008-01-24		ENSG00000111196	ENSG00000111196			25504	protein-coding gene	gene with protein product							Standard	NM_018048		Approved	FLJ10292, MGN2	uc001qyq.2	Q96A72	OTTHUMG00000168407	ENST00000320756.2:c.45C>T	chr12.hg19:g.10766087G>A		88.0	0.0		74.0	32.0	NM_018048		Silent	SNP	ENST00000320756.2	hg19	CCDS8628.1																																																																																			.	.		0.617	MAGOHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399616.1	NM_018048		A	10766087	G	A	10766087	2	1	95	1	0	0	0	0	0	0	0	1	9204	1368	48	3		3	MAGOHB	12	10766087	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10		10766087	123085808	84	13167										
SCYL2	55681	hgsc.bcm.edu	37	chr12	100728028	100728028	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aactggagcaacttcatataAtgcaagaacagcagaagtaa	8	7	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr12:100728028A>G	ENST00000360820.2	+	14	2283	c.1846A>G	c.(1846-1848)Atg>Gtg	p.M616V		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	616					endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						ACTTCATATAATGCAAGAACA	0.333																																					p.M616V		Atlas-SNP	.											.	SCYL2	99	.	0			c.A1846G						.						111	106	108					12																	100728028		2203	4297	6500	SO:0001583	missense	55681	exon14			CATATAATGCAAG	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.1846A>G	chr12.hg19:g.100728028A>G	ENSP00000354061:p.Met616Val	55.0	0.0		36.0	20.0	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	hg19	CCDS9076.1	.	.	.	.	.	.	.	.	.	.	A	13.86	2.362435	0.41902	.	.	ENSG00000136021	ENST00000549687;ENST00000360820	T;T	0.29917	1.94;1.55	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.31979	0.0814	L	0.55481	1.735	0.80722	D	1	B	0.22003	0.063	B	0.24006	0.05	T	0.06041	-1.0849	10	0.28530	T	0.3	.	15.6868	0.77418	1.0:0.0:0.0:0.0	.	616	Q6P3W7	SCYL2_HUMAN	V	616	ENSP00000448366:M616V;ENSP00000354061:M616V	ENSP00000354061:M616V	M	+	1	0	SCYL2	99252159	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.109000	0.77062	2.153000	0.67306	0.477000	0.44152	ATG	.	.		0.333	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		G	100728028	A	G	100728028	3	3	95	1	0	0	0	0	1	0	0	0	13963	101	4	2	1896	2	SCYL2	12	100728028	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	89961941	100728028	33123867	85	13168										
PIWIL1	9271	hgsc.bcm.edu	37	chr12	130842075	130842075	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	acttaagagtcttacagcaaAaggtcacagcagacacccag	8	11	2	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr12:130842075A>G	ENST00000245255.3	+	14	1914	c.1642A>G	c.(1642-1644)Aag>Gag	p.K548E		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	548	RNA-binding. {ECO:0000250}.				gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		CTTACAGCAAAAGGTCACAGC	0.408																																					p.K548E		Atlas-SNP	.											.	PIWIL1	157	.	0			c.A1642G						.						146	128	134					12																	130842075		2203	4300	6503	SO:0001583	missense	9271	exon14			CAGCAAAAGGTCA	AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.1642A>G	chr12.hg19:g.130842075A>G	ENSP00000245255:p.Lys548Glu	225.0	0.0		185.0	25.0	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	hg19	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	A	15.45	2.838127	0.50951	.	.	ENSG00000125207	ENST00000245255	T	0.13196	2.61	5.59	4.43	0.53597	Ribonuclease H-like (1);	0.177411	0.64402	D	0.000012	T	0.11793	0.0287	L	0.41236	1.265	0.40541	D	0.981025	B;B	0.14438	0.01;0.001	B;B	0.11329	0.004;0.006	T	0.09684	-1.0663	10	0.18710	T	0.47	-1.6065	12.1143	0.53856	0.8564:0.1436:0.0:0.0	.	548;548	Q96J94;Q96J94-2	PIWL1_HUMAN;.	E	548	ENSP00000245255:K548E	ENSP00000245255:K548E	K	+	1	0	PIWIL1	129408028	1.000000	0.71417	0.742000	0.31022	0.986000	0.74619	5.912000	0.69948	0.924000	0.37069	0.533000	0.62120	AAG	.	.		0.408	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			G	130842075	A	G	130842075	3	3	95	1	0	0	0	0	1	0	0	0	11966	15	1	2	1692	2	PIWIL1	12	130842075	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	30114047	130842075	3009820	86	13169										
HTR2A	3356	hgsc.bcm.edu	37	chr13	47409332	47409332	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ccaatgacatcctcattgcaGgactctttgcagatgacggc	9	12	2	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr13:47409332G>A	ENST00000378688.4	-	3	1187	c.1056C>T	c.(1054-1056)tcC>tcT	p.S352S	HTR2A_ENST00000542664.1_Silent_p.S352S|HTR2A_ENST00000543956.1_Silent_p.S268S			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	352					activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CCTCATTGCAGGACTCTTTGC	0.478																																					p.S352S		Atlas-SNP	.											.	HTR2A	98	.	0			c.C1056T						.						136	118	124					13																	47409332		2203	4300	6503	SO:0001819	synonymous_variant	3356	exon4			ATTGCAGGACTCT	X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5293	protein-coding gene	gene with protein product		182135	"5-hydroxytryptamine (serotonin) receptor 2A"	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.1056C>T	chr13.hg19:g.47409332G>A		202.0	0.0		154.0	48.0	NM_000621	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Silent	SNP	ENST00000378688.4	hg19	CCDS9405.1																																																																																			.	.		0.478	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		A	47409332	G	A	47409332	2	1	95	1	0	0	0	0	0	0	0	1	7450	987	35	3		3	HTR2A	13	47409332	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10		47409332	67760546	87	13170										
FANCM	57697	hgsc.bcm.edu	37	chr14	45665463	45665463	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tgggacacatacttctcttaGacttccgcaggaaggaaaag	10	9	1	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr14:45665463G>T	ENST00000267430.5	+	21	5514	c.5429G>T	c.(5428-5430)aGa>aTa	p.R1810I	FANCM_ENST00000542564.2_Missense_Mutation_p.R1784I	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1810	Interaction with FAAP24 and EME1.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						ACTTCTCTTAGACTTCCGCAG	0.438								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R1810I		Atlas-SNP	.											.	FANCM	225	.	0			c.G5429T						.						129	126	127					14																	45665463		2203	4300	6503	SO:0001583	missense	57697	exon21	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTCTTAGACTTCC	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.5429G>T	chr14.hg19:g.45665463G>T	ENSP00000267430:p.Arg1810Ile	195.0	0.0		134.0	62.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.30|18.30	3.594617|3.594617	0.66219|0.66219	.|.	.|.	ENSG00000187790|ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250|ENST00000554809	T;T;T|.	0.18810|.	2.78;2.78;2.19|.	4.75|4.75	2.88|2.88	0.33553|0.33553	.|.	0.957926|.	0.08693|.	N|.	0.907600|.	T|.	0.38134|.	0.1029|.	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	1|1	P;P|.	0.49961|.	0.93;0.855|.	B;B|.	0.41571|.	0.36;0.36|.	T|.	0.26677|.	-1.0096|.	10|.	0.87932|.	D|.	0|.	.|.	4.2487|4.2487	0.10684|0.10684	0.1933:0.0:0.6242:0.1825|0.1933:0.0:0.6242:0.1825	.|.	1784;1810|.	B2RTQ9;Q8IYD8|.	.;FANCM_HUMAN|.	I|Y	1810;1784;1326|777	ENSP00000267430:R1810I;ENSP00000442493:R1784I;ENSP00000452033:R1326I|.	ENSP00000267430:R1810I|.	R|X	+|+	2|3	0|2	FANCM|FANCM	44735213|44735213	0.000000|0.000000	0.05858|0.05858	0.012000|0.012000	0.15200|0.15200	0.497000|0.497000	0.33675|0.33675	-0.014000|-0.014000	0.12656|0.12656	1.228000|1.228000	0.43614|0.43614	0.563000|0.563000	0.77884|0.77884	AGA|TAG	.	.		0.438	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45665463	G	T	45665463	3	4	95	1	0	0	0	0	1	0	0	0	5679	942	33	3	5511	3	FANCM	14	45665463	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10		45665463	61684077	88	13171										
SAV1	60485	hgsc.bcm.edu	37	chr14	51107527	51107527	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	atttctgcagtatgatatggAtttgcaggtaccagaaggga	12	5	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr14:51107527A>T	ENST00000324679.4	-	4	1254	c.891T>A	c.(889-891)aaT>aaA	p.N297K	RN7SL452P_ENST00000482923.2_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	297					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					TATGATATGGATTTGCAGGTA	0.443																																					p.N297K		Atlas-SNP	.											.	SAV1	18	.	0			c.T891A						.						199	186	190					14																	51107527		2203	4300	6503	SO:0001583	missense	60485	exon4			ATATGGATTTGCA	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.891T>A	chr14.hg19:g.51107527A>T	ENSP00000324729:p.Asn297Lys	333.0	0.0		258.0	84.0	NM_021818	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Missense_Mutation	SNP	ENST00000324679.4	hg19	CCDS9701.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.469845	0.84533	.	.	ENSG00000151748	ENST00000555720;ENST00000324679;ENST00000535862	T;T	0.50813	0.78;0.73	5.79	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.63850	0.2546	M	0.71206	2.165	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.65129	-0.6243	10	0.72032	D	0.01	-18.0655	8.7019	0.34332	0.8365:0.0:0.1635:0.0	.	297	Q9H4B6	SAV1_HUMAN	K	229;297;264	ENSP00000451492:N229K;ENSP00000324729:N297K	ENSP00000324729:N297K	N	-	3	2	SAV1	50177277	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.320000	0.43797	0.974000	0.38366	0.533000	0.62120	AAT	.	.		0.443	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			T	51107527	A	T	51107527	3	4	95	1	0	0	0	0	1	0	0	0	13871	330	12	4	268	4	SAV1	14	51107527	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	5442064	51107527	56242013	89	13172										
DACT1	51339	hgsc.bcm.edu	37	chr14	59112430	59112430	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aaaccaagaaccagcgtgaaCgctgaccccacgaaagggct	10	13	0	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr14:59112430C>G	ENST00000335867.4	+	4	1113	c.1089C>G	c.(1087-1089)aaC>aaG	p.N363K	DACT1_ENST00000541264.2_Missense_Mutation_p.N82K|DACT1_ENST00000395153.3_Missense_Mutation_p.N326K|DACT1_ENST00000556859.1_Missense_Mutation_p.N82K			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	363					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						CCAGCGTGAACGCTGACCCCA	0.522																																					p.N363K		Atlas-SNP	.											.	DACT1	119	.	0			c.C1089G						.						60	61	60					14																	59112430		2203	4300	6503	SO:0001583	missense	51339	exon4			CGTGAACGCTGAC	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"dapper homolog 1, antagonist of beta-catenin (xenopus)", "dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.1089C>G	chr14.hg19:g.59112430C>G	ENSP00000337439:p.Asn363Lys	72.0	0.0		75.0	29.0	NM_016651	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	hg19	CCDS9736.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.787717	0.49997	.	.	ENSG00000165617	ENST00000556859;ENST00000421793;ENST00000395151;ENST00000395153;ENST00000335867;ENST00000541264	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	5.46	-6.63	0.01807	.	0.240791	0.47852	N	0.000220	T	0.44456	0.1294	M	0.67953	2.075	0.38146	D	0.938598	P;P	0.45396	0.857;0.857	P;P	0.52109	0.669;0.69	T	0.56007	-0.8050	10	0.45353	T	0.12	-9.4124	10.926	0.47191	0.0:0.3207:0.0901:0.5893	.	326;363	A8MYJ2;Q9NYF0	.;DACT1_HUMAN	K	82;82;82;326;363;82	ENSP00000451598:N82K;ENSP00000404297:N82K;ENSP00000378581:N82K;ENSP00000378582:N326K;ENSP00000337439:N363K;ENSP00000442850:N82K	ENSP00000337439:N363K	N	+	3	2	DACT1	58182183	0.130000	0.22417	0.042000	0.18584	0.857000	0.48899	-0.488000	0.06497	-1.382000	0.02109	-0.471000	0.05019	AAC	.	.		0.522	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651		G	59112430	C	G	59112430	3	3	95	1	0	0	0	0	1	0	0	0	4224	535	19	4	1103	4	DACT1	14	59112430	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	8004903	59112430	48237110	90	13173										
TGFB3	7043	hgsc.bcm.edu	37	chr14	76437499	76437499	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cagccactcacgcacagtgtCagtgacatcaaaggacagcc	9	14	3	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr14:76437499C>G	ENST00000238682.3	-	3	913	c.616G>C	c.(616-618)Gac>Cac	p.D206H	TGFB3_ENST00000556285.1_Missense_Mutation_p.D206H|RP11-270M14.5_ENST00000553732.1_lincRNA	NM_003239.2	NP_003230.1	P10600	TGFB3_HUMAN	transforming growth factor, beta 3	206					activation of MAPK activity (GO:0000187)|aging (GO:0007568)|blood coagulation (GO:0007596)|cell growth (GO:0016049)|cell-cell junction organization (GO:0045216)|detection of hypoxia (GO:0070483)|digestive tract development (GO:0048565)|embryonic neurocranium morphogenesis (GO:0048702)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|female pregnancy (GO:0007565)|frontal suture morphogenesis (GO:0060364)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|mammary gland development (GO:0030879)|menstrual cycle phase (GO:0022601)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of macrophage cytokine production (GO:0010936)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|odontogenesis (GO:0042476)|ossification involved in bone remodeling (GO:0043932)|palate development (GO:0060021)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell division (GO:0051781)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to laminar fluid shear stress (GO:0034616)|response to progesterone (GO:0032570)|salivary gland morphogenesis (GO:0007435)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|T-tubule (GO:0030315)	identical protein binding (GO:0042802)|transforming growth factor beta binding (GO:0050431)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			NS(1)|breast(1)|endometrium(4)|kidney(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	11				BRCA - Breast invasive adenocarcinoma(234;0.0169)		CGCACAGTGTCAGTGACATCA	0.532																																					p.D206H		Atlas-SNP	.											.	TGFB3	25	.	0			c.G616C						.						111	96	101					14																	76437499		2203	4300	6503	SO:0001583	missense	7043	exon3			CAGTGTCAGTGAC		CCDS9846.1	14q24	2014-09-17				ENSG00000119699		"Endogenous ligands"	11769	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-3"	190230	"arrhythmogenic right ventricular dysplasia 1"	ARVD1, ARVD		16549496, 15639475	Standard	XM_005268028		Approved		uc001xsc.2	P10600		ENST00000238682.3:c.616G>C	chr14.hg19:g.76437499C>G	ENSP00000238682:p.Asp206His	62.0	0.0		42.0	10.0	NM_003239	Q8WV88	Missense_Mutation	SNP	ENST00000238682.3	hg19	CCDS9846.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.245418	0.80024	.	.	ENSG00000119699	ENST00000238682;ENST00000556285	T;T	0.65916	-0.18;-0.18	5.55	5.55	0.83447	Transforming growth factor-beta, N-terminal (1);	0.100619	0.64402	D	0.000002	T	0.67002	0.2847	L	0.48642	1.525	0.50813	D	0.999899	P	0.45531	0.86	P	0.53266	0.722	T	0.68526	-0.5385	10	0.62326	D	0.03	-9.7812	12.8047	0.57607	0.0:0.9252:0.0:0.0748	.	206	P10600	TGFB3_HUMAN	H	206	ENSP00000238682:D206H;ENSP00000451110:D206H	ENSP00000238682:D206H	D	-	1	0	TGFB3	75507252	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	5.782000	0.68973	2.627000	0.88993	0.561000	0.74099	GAC	.	.		0.532	TGFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413685.1	NM_003239		G	76437499	C	G	76437499	3	3	95	1	0	0	0	0	1	0	0	0	15834	826	29	4	642	4	TGFB3	14	76437499	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	17325069	76437499	30912041	91	13174										
PAK6	56924	hgsc.bcm.edu	37	chr15	40565801	40565801	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tcagatcagcaaagacgtccCtaagaggaagtccctggtgg	12	10	2	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr15:40565801C>A	ENST00000542403.2	+	7	1778	c.1667C>A	c.(1666-1668)cCt>cAt	p.P556H	PAK6_ENST00000441369.1_Missense_Mutation_p.P556H|PAK6_ENST00000260404.4_Missense_Mutation_p.P556H|PAK6_ENST00000455577.2_Missense_Mutation_p.P556H|RP11-133K1.2_ENST00000558658.1_3'UTR|PAK6_ENST00000560346.1_Missense_Mutation_p.P556H|PAK6_ENST00000453867.1_Missense_Mutation_p.P556H	NM_001276717.1	NP_001263646.1	Q9NQU5	PAK6_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 6	556	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cytoskeleton organization (GO:0007010)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(2)	24		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)		AAAGACGTCCCTAAGAGGAAG	0.567																																					p.W556X		Atlas-SNP	.											.	PAK6	49	.	0			c.G1667A						.						87	80	83					15																	40565801		2203	4300	6503	SO:0001583	missense	56924	exon9			ACGTCCCTAAGAG	AF276893	CCDS10054.1, CCDS61590.1	15q14	2008-06-17	2008-06-17		ENSG00000137843	ENSG00000137843			16061	protein-coding gene	gene with protein product		608110	"p21(CDKN1A)-activated kinase 6"			11278661	Standard	NM_020168		Approved	PAK5	uc001zlb.3	Q9NQU5	OTTHUMG00000129921	ENST00000542403.2:c.1667C>A	chr15.hg19:g.40565801C>A	ENSP00000439597:p.Pro556His	243.0	0.0		198.0	57.0	NM_020168	A8K2G2|B3KYB0|G5E9R2	Nonsense_Mutation	SNP	ENST00000542403.2	hg19	CCDS10054.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.114770	0.77210	.	.	ENSG00000137843	ENST00000441369;ENST00000453867;ENST00000455577;ENST00000260404;ENST00000542403	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	5.16	3.23	0.37069	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70684	0.3252	L	0.44542	1.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.71262	-0.4645	10	0.87932	D	0	.	11.9326	0.52855	0.1378:0.7298:0.1324:0.0	.	556;556	Q9NQU5;G5E9R2	PAK6_HUMAN;.	H	556	ENSP00000406873:P556H;ENSP00000401153:P556H;ENSP00000409465:P556H;ENSP00000260404:P556H;ENSP00000439597:P556H	ENSP00000260404:P556H	P	+	2	0	PAK6	38353093	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	6.030000	0.70903	0.538000	0.28769	0.462000	0.41574	CCT	.	.		0.567	PAK6-004	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000418355.1			A	40565801	C	A	40565801	3	1	95	1	0	0	0	0	1	0	0	0	11413	681	24	3	1689	3	PAK6	15	40565801	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10		40565801	61965591	92	13175										
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15103555	15103555	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	caggatgttgccttcctggaGaaactgattaaagatgatat	10	6	0	4			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr16:15103555G>A	ENST00000396410.4	+	8	763	c.666G>A	c.(664-666)gaG>gaA	p.E222E	PDXDC1_ENST00000455313.2_Silent_p.E199E|PDXDC1_ENST00000535621.2_Silent_p.E222E|PDXDC1_ENST00000325823.7_Silent_p.E207E|MIR1972-1_ENST00000459337.1_RNA|PDXDC1_ENST00000563679.1_Silent_p.E240E|PDXDC1_ENST00000450288.2_Silent_p.E194E|PDXDC1_ENST00000447912.2_Silent_p.E131E|PDXDC1_ENST00000569715.1_Silent_p.E195E	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	222					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CCTTCCTGGAGAAACTGATTA	0.368																																					p.E222E		Atlas-SNP	.											.	PDXDC1	59	.	0			c.G666A						.						61	73	69					16																	15103555		2197	4297	6494	SO:0001819	synonymous_variant	23042	exon8			CCTGGAGAAACTG	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.666G>A	chr16.hg19:g.15103555G>A		582.0	0.0		410.0	85.0	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	hg19	CCDS32393.1																																																																																			.	.		0.368	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		A	15103555	G	A	15103555	2	1	95	1	0	0	0	0	0	0	0	1	11705	933	33	3		3	PDXDC1	16	15103555	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10		15103555	75251198	93	13176										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31926035	31926035	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	caccagcaaatactttcttcTtgtgccaaaagctataactt	4	11	2	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr16:31926035T>G	ENST00000300870.10	+	4	674	c.465T>G	c.(463-465)tcT>tcG	p.S155S	ZNF267_ENST00000394846.3_3'UTR	NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	155					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						TACTTTCTTCTTGTGCCAAAA	0.328																																					p.S155S		Atlas-SNP	.											.	ZNF267	94	.	0			c.T465G						.						68	70	70					16																	31926035		2197	4300	6497	SO:0001819	synonymous_variant	10308	exon4			TTCTTCTTGTGCC	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.465T>G	chr16.hg19:g.31926035T>G		214.0	0.0		209.0	76.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Silent	SNP	ENST00000300870.10	hg19	CCDS32440.1																																																																																			.	.		0.328	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		G	31926035	T	G	31926035	2	3	95	1	0	0	0	0	0	0	0	1	17821	1596	56	5		5	ZNF267	16	31926035	Silent	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	16822480	31926035	58428718	94	13177										
CMTM2	146225	hgsc.bcm.edu	37	chr16	66613710	66613710	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	cgaagtgggcacgaggagggGgtgtcgccgctaccggtggg	21	9	0	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr16:66613710G>T	ENST00000268595.2	+	1	351	c.200G>T	c.(199-201)gGg>gTg	p.G67V	CMTM2_ENST00000379486.2_Missense_Mutation_p.G67V|RP11-403P17.2_ENST00000568430.1_RNA	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	67					chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.068)|Epithelial(162;0.212)		ACGAGGAGGGGGTGTCGCCGC	0.547																																					p.G67V		Atlas-SNP	.											.	CMTM2	33	.	0			c.G200T						.						55	56	56					16																	66613710		2201	4300	6501	SO:0001583	missense	146225	exon1			GGAGGGGGTGTCG	BC025354	CCDS10814.1, CCDS56001.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000140932	ENSG00000140932			19173	protein-coding gene	gene with protein product		607885	"chemokine-like factor super family 2", "chemokine-like factor superfamily 2"	CKLFSF2			Standard	NM_001199317		Approved	MGC39436, FLJ25732	uc002ept.3	Q8TAZ6	OTTHUMG00000137501	ENST00000268595.2:c.200G>T	chr16.hg19:g.66613710G>T	ENSP00000268595:p.Gly67Val	111.0	0.0		95.0	41.0	NM_001199317	Q5I2A4|Q8N7E5	Missense_Mutation	SNP	ENST00000268595.2	hg19	CCDS10814.1	.	.	.	.	.	.	.	.	.	.	G	14.45	2.538351	0.45176	.	.	ENSG00000140932	ENST00000379486;ENST00000268595	T;T	0.74526	-0.85;-0.02	4.14	3.15	0.36227	.	0.595626	0.15482	N	0.260037	T	0.79358	0.4432	L	0.54323	1.7	0.19775	N	0.999952	D;D	0.67145	0.996;0.992	D;D	0.67548	0.952;0.914	T	0.66650	-0.5870	10	0.87932	D	0	.	6.2226	0.20689	0.1483:0.0:0.8517:0.0	.	67;67	Q5I2A4;Q8TAZ6	.;CKLF2_HUMAN	V	67	ENSP00000368800:G67V;ENSP00000268595:G67V	ENSP00000268595:G67V	G	+	2	0	CMTM2	65171211	0.721000	0.28007	0.006000	0.13384	0.683000	0.39861	2.248000	0.43160	1.238000	0.43771	0.561000	0.74099	GGG	.	.		0.547	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1			T	66613710	G	T	66613710	3	4	95	1	0	0	0	0	1	0	0	0	3585	1232	43	3	202	3	CMTM2	16	66613710	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	34687675	66613710	23741043	95	13178										
FAM65A	79567	hgsc.bcm.edu	37	chr16	67572365	67572365	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	actctatgatgtccctgtcgGtgcggccgcagcgccgtctg	13	14	2	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr16:67572365G>A	ENST00000379312.3	+	2	137	c.16G>A	c.(16-18)Gtg>Atg	p.V6M	FAM65A_ENST00000428437.2_Missense_Mutation_p.V20M|FAM65A_ENST00000540839.3_Missense_Mutation_p.V26M|FAM65A_ENST00000042381.4_Missense_Mutation_p.V6M|CTD-2012K14.2_ENST00000567122.1_RNA|FAM65A_ENST00000422602.2_Missense_Mutation_p.V26M|FAM65A_ENST00000566522.1_Intron	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	6						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		GTCCCTGTCGGTGCGGCCGCA	0.716																																					p.V26M		Atlas-SNP	.											.	FAM65A	104	.	0			c.G76A						.						7	9	8					16																	67572365		2074	4105	6179	SO:0001583	missense	79567	exon2			CTGTCGGTGCGGC	AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.16G>A	chr16.hg19:g.67572365G>A	ENSP00000368614:p.Val6Met	156.0	0.0		128.0	59.0	NM_001193523	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	hg19	CCDS54028.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.364472	0.82463	.	.	ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	T;T;T	0.20200	2.12;2.11;2.09	5.05	5.05	0.67936	.	0.064495	0.64402	D	0.000010	T	0.41558	0.1164	L	0.56769	1.78	0.50632	D	0.999883	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.71184	0.956;0.956;0.956;0.972	T	0.25537	-1.0129	10	0.72032	D	0.01	-12.4677	13.8889	0.63726	0.0:0.1519:0.8481:0.0	.	20;26;6;26	B4DIM2;E9PBS3;Q6ZS17;B4DEQ9	.;.;FA65A_HUMAN;.	M	6;6;26;20	ENSP00000368614:V6M;ENSP00000042381:V6M;ENSP00000400099:V26M	ENSP00000042381:V6M	V	+	1	0	FAM65A	66129866	0.999000	0.42202	1.000000	0.80357	0.596000	0.36781	3.110000	0.50352	2.349000	0.79799	0.491000	0.48974	GTG	.	.		0.716	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		A	67572365	G	A	67572365	3	1	95	1	0	0	0	0	1	0	0	0	5607	1261	44	3	18	3	FAM65A	16	67572365	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	958655	67572365	22782388	96	13179										
HPR	3250	hgsc.bcm.edu	37	chr16	72110626	72110626	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ggctggggacaaagtgacaaCtttaaacttactgaccatct	9	9	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr16:72110626C>T	ENST00000540303.2	+	5	725	c.693C>T	c.(691-693)aaC>aaT	p.N231N	HPR_ENST00000356967.5_Silent_p.N231N|HPR_ENST00000561690.1_Intron|HPR_ENST00000228226.8_Silent_p.N268N	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	231	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|spherical high-density lipoprotein particle (GO:0034366)	hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|stomach(1)|urinary_tract(2)	20		Ovarian(137;0.125)				AAAGTGACAACTTTAAACTTA	0.468																																					p.N231N		Atlas-SNP	.											.	HPR	43	.	0			c.C693T						.						181	135	150					16																	72110626		2081	4191	6272	SO:0001819	synonymous_variant	3250	exon5			TGACAACTTTAAA	BC160066	CCDS42193.1	16q22.2	2012-10-03			ENSG00000261701	ENSG00000261701			5156	protein-coding gene	gene with protein product		140210				2987228, 16778136	Standard	NM_020995		Approved		uc002fby.3	P00739	OTTHUMG00000173010	ENST00000540303.2:c.693C>T	chr16.hg19:g.72110626C>T		229.0	0.0		148.0	70.0	NM_020995	Q7LE20|Q92658|Q92659|Q9ULB0	Silent	SNP	ENST00000540303.2	hg19	CCDS42193.1																																																																																			.	.		0.468	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421696.1	NM_020995		T	72110626	C	T	72110626	2	4	95	1	0	0	0	0	0	0	0	1	7346	564	20	3		3	HPR	16	72110626	Silent	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	4538261	72110626	18244127	97	13180										
MON1B	22879	hgsc.bcm.edu	37	chr16	77228415	77228415	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gcagaactatgacctccgccGcctgctggctggttcagagc	12	14	1	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr16:77228415G>A	ENST00000248248.3	+	4	1009	c.659G>A	c.(658-660)cGc>cAc	p.R220H	MON1B_ENST00000439557.2_Missense_Mutation_p.R111H|MON1B_ENST00000545553.1_Missense_Mutation_p.R74H|MON1B_ENST00000320859.6_Intron	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	220										breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						GACCTCCGCCGCCTGCTGGCT	0.627																																					p.R220H		Atlas-SNP	.											MON1B,NS,carcinoma,0,1	MON1B	55	.	0			c.G659A						.						76	71	72					16																	77228415		2198	4300	6498	SO:0001583	missense	22879	exon4			TCCGCCGCCTGCT	BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"MON1 homolog B (yeast)"			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.659G>A	chr16.hg19:g.77228415G>A	ENSP00000248248:p.Arg220His	111.0	0.0		94.0	34.0	NM_014940	B4DDZ0|O94949	Missense_Mutation	SNP	ENST00000248248.3	hg19	CCDS10925.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059274	0.93846	.	.	ENSG00000103111	ENST00000248248;ENST00000439557;ENST00000545553	.	.	.	4.49	4.49	0.54785	.	0.054301	0.64402	D	0.000001	D	0.83982	0.5372	M	0.88979	2.995	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.95;1.0;1.0;0.999	D	0.87256	0.2276	9	0.72032	D	0.01	.	15.4783	0.75504	0.0:0.0:1.0:0.0	.	74;111;100;220	B4DDZ0;E7EW32;Q6ZR87;Q7L1V2	.;.;.;MON1B_HUMAN	H	220;111;74	.	ENSP00000248248:R220H	R	+	2	0	MON1B	75785916	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.428000	0.82296	0.561000	0.74099	CGC	.	.		0.627	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940		A	77228415	G	A	77228415	3	1	95	1	0	0	0	0	1	0	0	0	9708	1087	38	1	669	1	MON1B	16	77228415	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	5117789	77228415	13126338	98	13181										
MBTPS1	8720	hgsc.bcm.edu	37	chr16	84124541	84124541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tacattgttagctgttaattCccacacctacaaaaggagca	6	10	0	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr16:84124541C>T	ENST00000343411.3	-	8	1465	c.970G>A	c.(970-972)Gaa>Aaa	p.E324K	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	324	Peptidase S8.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GCTGTTAATTCCCACACCTAC	0.363																																					p.E324K		Atlas-SNP	.											.	MBTPS1	85	.	0			c.G970A						.						120	111	114					16																	84124541		2200	4300	6500	SO:0001583	missense	8720	exon8			TTAATTCCCACAC	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"membrane-bound transcription factor protease, site 1"			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.970G>A	chr16.hg19:g.84124541C>T	ENSP00000344223:p.Glu324Lys	189.0	0.0		151.0	66.0	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	hg19	CCDS10941.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892897	0.91889	.	.	ENSG00000140943	ENST00000343411	T	0.44083	0.93	5.91	5.91	0.95273	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	T	0.60353	0.2262	L	0.46670	1.46	0.80722	D	1	D	0.55800	0.973	D	0.69479	0.964	T	0.55464	-0.8137	10	0.49607	T	0.09	-28.6816	20.3053	0.98627	0.0:1.0:0.0:0.0	.	324	Q14703	MBTP1_HUMAN	K	324	ENSP00000344223:E324K	ENSP00000344223:E324K	E	-	1	0	MBTPS1	82682042	1.000000	0.71417	0.999000	0.59377	0.608000	0.37181	7.610000	0.82949	2.808000	0.96608	0.655000	0.94253	GAA	.	.		0.363	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		T	84124541	C	T	84124541	3	4	95	1	0	0	0	0	1	0	0	0	9370	864	30	3	2252	3	MBTPS1	16	84124541	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	6896126	84124541	6230212	99	13182										
C17orf57	124989	hgsc.bcm.edu	37	chr17	45479563	45479563	+	Frame_Shift_Del	DEL	T	T	-													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	atatgcgtgatgctgccaggTtagaaggtaagtactgaatt							TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr17:45479563delT	ENST00000331493.2	+	18	2422	c.2011delT	c.(2011-2013)ttafs	p.L671fs	EFCAB13_ENST00000517484.1_Frame_Shift_Del_p.L575fs	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	671						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TGCTGCCAGGTTAGAAGGTAA	0.323																																					p.R670fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.2010delG						.						112	118	116					17																	45479563		2203	4300	6503	SO:0001589	frameshift_variant	124989	exon18			.	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.2011delT	chr17.hg19:g.45479563delT	ENSP00000332111:p.Leu671fs	118.0	0.0		95.0	39.0	NM_152347	G3V128|Q49AG9	Frame_Shift_Del	DEL	ENST00000331493.2	hg19	CCDS11512.1																																																																																			.	.		0.323	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		-	45479563	T	-	45479563	7	5	95	1	0	1	0	1	0	0	0	0	1867	1722	60	0	2069	0	C17orf57	17	45479563	Frame_Shift_Del	DEL	T	TCGA-DD-A11D-01A-11D-A12Z-10		45479563	35715647	100	13183										
ACSF2	80221	hgsc.bcm.edu	37	chr17	48551103	48551103	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tatgatcatccggggtggtgAgaacatctaccccgcagagc	12	11	2	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr17:48551103A>G	ENST00000300441.4	+	13	1657	c.1553A>G	c.(1552-1554)gAg>gGg	p.E518G	ACSF2_ENST00000502667.1_Missense_Mutation_p.E505G|ACSF2_ENST00000506085.1_3'UTR|ACSF2_ENST00000427954.2_Missense_Mutation_p.E543G|ACSF2_ENST00000504392.1_Missense_Mutation_p.E475G|ACSF2_ENST00000541920.1_Missense_Mutation_p.E358G	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	518					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CGGGGTGGTGAGAACATCTAC	0.557																																					p.E518G		Atlas-SNP	.											.	ACSF2	46	.	0			c.A1553G						.						121	111	115					17																	48551103		2203	4300	6503	SO:0001583	missense	80221	exon13			GTGGTGAGAACAT	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1553A>G	chr17.hg19:g.48551103A>G	ENSP00000300441:p.Glu518Gly	109.0	0.0		96.0	40.0	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.846154	0.91277	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53	5.1	5.1	0.69264	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	D	0.82898	0.5137	H	0.98682	4.3	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.89623	0.3850	10	0.87932	D	0	-31.4005	14.5483	0.68047	1.0:0.0:0.0:0.0	.	505;543;475;518	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	G	518;358;475;543;505	ENSP00000300441:E518G;ENSP00000437987:E358G;ENSP00000425964:E475G;ENSP00000401831:E543G;ENSP00000421884:E505G	ENSP00000300441:E518G	E	+	2	0	ACSF2	45906102	1.000000	0.71417	0.994000	0.49952	0.966000	0.64601	7.134000	0.77268	1.918000	0.55548	0.402000	0.26972	GAG	.	.		0.557	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149		G	48551103	A	G	48551103	3	3	95	1	0	0	0	0	1	0	0	0	175	304	11	2	1603	2	ACSF2	17	48551103	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	3071540	48551103	32644107	101	13184										
TBX4	9496	hgsc.bcm.edu	37	chr17	59560737	59560737	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gagagcgcggcctcccccaaGggtgtgagaggaagccaccc	15	14	0	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr17:59560737G>A	ENST00000240335.1	+	8	1543	c.1498G>A	c.(1498-1500)Ggg>Agg	p.G500R	TBX4_ENST00000393853.4_Missense_Mutation_p.G501R	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	500					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CCTCCCCCAAGGGTGTGAGAG	0.552																																					p.G500R		Atlas-SNP	.											.	TBX4	69	.	0			c.G1498A						.						63	64	63					17																	59560737		2203	4300	6503	SO:0001583	missense	9496	exon8			CCCCAAGGGTGTG	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"T-boxes"	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1498G>A	chr17.hg19:g.59560737G>A	ENSP00000240335:p.Gly500Arg	120.0	0.0		82.0	29.0	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Missense_Mutation	SNP	ENST00000240335.1	hg19	CCDS11629.1	.	.	.	.	.	.	.	.	.	.	G	4.713	0.132535	0.09032	.	.	ENSG00000121075	ENST00000393853;ENST00000240335	D;D	0.85411	-1.98;-1.98	5.14	1.96	0.26148	.	1.172590	0.06049	N	0.656267	T	0.75162	0.3812	N	0.22421	0.69	0.09310	N	1	B;B	0.28026	0.198;0.01	B;B	0.30251	0.113;0.004	T	0.59705	-0.7404	9	.	.	.	.	5.727	0.18018	0.2362:0.1402:0.6236:0.0	.	501;500	A5PKU7;P57082	.;TBX4_HUMAN	R	501;500	ENSP00000377435:G501R;ENSP00000240335:G500R	.	G	+	1	0	TBX4	56915519	0.997000	0.39634	0.014000	0.15608	0.036000	0.12997	2.447000	0.44917	0.165000	0.19558	0.655000	0.94253	GGG	.	.		0.552	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488		A	59560737	G	A	59560737	3	1	95	1	0	0	0	0	1	0	0	0	15675	1000	35	3	1528	3	TBX4	17	59560737	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	11009634	59560737	21634473	102	13185										
RGS9	8787	hgsc.bcm.edu	37	chr17	63198195	63198195	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ggagaaagcagaggagatttAcaagtgagcatcagccaggg	15	6	1	4			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr17:63198195A>T	ENST00000262406.9	+	14	1128	c.1061A>T	c.(1060-1062)tAc>tTc	p.Y354F	RGS9_ENST00000443584.3_Missense_Mutation_p.Y351F|RGS9_ENST00000449996.3_Missense_Mutation_p.Y351F	NM_003835.3	NP_003826.2	O75916	RGS9_HUMAN	regulator of G-protein signaling 9	354	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				dopamine receptor signaling pathway (GO:0007212)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to estrogen (GO:0043627)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(8)|liver(2)|lung(12)|ovary(2)|prostate(3)|skin(3)	41						GAGGAGATTTACAAGTGAGCA	0.517																																					p.Y354F		Atlas-SNP	.											.	RGS9	82	.	0			c.A1061T						.						74	75	74					17																	63198195		1962	4158	6120	SO:0001583	missense	8787	exon14			AGATTTACAAGTG	AF071476	CCDS42373.1, CCDS45764.1	17q24	2008-07-18	2007-08-14			ENSG00000108370		"Regulators of G-protein signaling"	10004	protein-coding gene	gene with protein product	"regulator of G protein signalling 9", "regulator of G protein signalling 9L", "regulator of G-protein signaling 9L"	604067	"regulator of G-protein signalling 9"			9765512	Standard	NM_003835		Approved	PERRS, RGS9L, MGC26458, MGC111763	uc002jfe.3	O75916		ENST00000262406.9:c.1061A>T	chr17.hg19:g.63198195A>T	ENSP00000262406:p.Tyr354Phe	97.0	0.0		85.0	23.0	NM_003835	A8K3C0|O75573|Q696R2|Q8TD64|Q8TD65|Q9HC32|Q9HC33	Missense_Mutation	SNP	ENST00000262406.9	hg19	CCDS42373.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.533611	0.45073	.	.	ENSG00000108370	ENST00000262406;ENST00000449996;ENST00000443584	T;T	0.02812	4.15;4.15	5.81	4.72	0.59763	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.184175	0.49916	D	0.000136	T	0.05181	0.0138	L	0.46819	1.47	0.58432	D	0.999998	B;B;B	0.33171	0.4;0.012;0.01	B;B;B	0.39660	0.306;0.033;0.019	T	0.45644	-0.9247	10	0.36615	T	0.2	.	13.2064	0.59798	0.867:0.1329:0.0:0.0	.	354;354;351	A8K1G1;O75916;O75916-5	.;RGS9_HUMAN;.	F	354;351;354	ENSP00000262406:Y354F;ENSP00000396329:Y351F	ENSP00000262406:Y354F	Y	+	2	0	RGS9	60628657	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	7.219000	0.78000	1.005000	0.39183	0.533000	0.62120	TAC	.	.		0.517	RGS9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445885.1	NM_003835		T	63198195	A	T	63198195	3	4	95	1	0	0	0	0	1	0	0	0	13328	391	14	4	1115	4	RGS9	17	63198195	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	3637458	63198195	17997015	103	13186										
MGAT5B	146664	hgsc.bcm.edu	37	chr17	74936580	74936580	+	Frame_Shift_Del	DEL	C	C	-													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	agtcccgcttcagcccgcccCacagctccctcaaccacgag							TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr17:74936580delC	ENST00000569840.2	+	14	2255	c.1681delC	c.(1681-1683)cacfs	p.H561fs	MGAT5B_ENST00000301618.4_Frame_Shift_Del_p.H559fs|MGAT5B_ENST00000428789.2_Frame_Shift_Del_p.H570fs	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	561					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CAGCCCGCCCCACAGCTCCCT	0.647																																					p.P569fs		Pindel	.											.	MGAT5B	98	.	0			c.1707delC						.						74	68	70					17																	74936580		2203	4300	6503	SO:0001589	frameshift_variant	146664	exon12			.	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	24140	protein-coding gene	gene with protein product		612441	"mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1681delC	chr17.hg19:g.74936580delC	ENSP00000456037:p.His561fs	121.0	0.0		90.0	27.0	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Frame_Shift_Del	DEL	ENST00000569840.2	hg19	CCDS59299.1																																																																																			.	.		0.647	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677		-	74936580	C	-	74936580	7	5	95	1	0	1	0	1	0	0	0	0	9558	594	21	0	1826	0	MGAT5B	17	74936580	Frame_Shift_Del	DEL	C	TCGA-DD-A11D-01A-11D-A12Z-10	11738385	74936580	6258630	104	13187										
C19orf21	126353	hgsc.bcm.edu	37	chr19	758698	758699	+	Missense_Mutation	DNP	GA	GA	TG													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ccagatgagaactctgaccaGaactccaggagctcctccca							TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr19:758698_758699GA>TG	ENST00000215582.6	+	2	1855_1856	c.1752_1753GA>TG	c.(1750-1755)caGAac>caTGac	p.584_585QN>HD		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	584					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											ACTCTGACCAGAACTCCAGGAG	0.629																																					p.Q584H|p.N585D		Atlas-SNP	.											.	C19orf21	56	.	0			c.G1752T|c.A1753G						.																																			SO:0001583	missense	126353	exon2			TGACCAGAACTCC|GACCAGAACTCCA	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	Exception_encountered	chr19.hg19:g.758698_758699delinsTG	ENSP00000215582:p.Q584_N585delinsHD	116.0|115.0	0.0		100.0	26.0	NM_173481		Missense_Mutation	SNP	ENST00000215582.6	hg19	CCDS12042.1																																																																																			.	.		0.629	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		TG	758699	GA	TG	758698	3	4	95	1	0	0	0	0	1	0	0	0	1915	933	33	3	1754	3	C19orf21	19	758698	Missense_Mutation	DNP	GA	TCGA-DD-A11D-01A-11D-A12Z-10		758698	58370285	105	13188										
ADAMTS10	81794	hgsc.bcm.edu	37	chr19	8651042	8651042	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ccgtgttgcaggcgcgctgcCttttgggcagcttgctgtgg	16	11	0	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr19:8651042C>T	ENST00000597188.1	-	22	2894	c.2624G>A	c.(2623-2625)aGg>aAg	p.R875K	ADAMTS10_ENST00000595838.1_Missense_Mutation_p.R362K|ADAMTS10_ENST00000270328.4_Missense_Mutation_p.R875K	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	875	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						GGCGCGCTGCCTTTTGGGCAG	0.662											OREG0025221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R875K		Atlas-SNP	.											.	ADAMTS10	132	.	0			c.G2624A						.						27	27	27					19																	8651042		2202	4293	6495	SO:0001583	missense	81794	exon22			CGCTGCCTTTTGG	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"ADAM metallopeptidases with thrombospondin type 1 motif"	13201	protein-coding gene	gene with protein product		608990	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.2624G>A	chr19.hg19:g.8651042C>T	ENSP00000471851:p.Arg875Lys	71.0	0.0	81	63.0	22.0	NM_030957	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	hg19	CCDS12206.1	.	.	.	.	.	.	.	.	.	.	C	13.69	2.312787	0.40895	.	.	ENSG00000142303	ENST00000270328;ENST00000393912	T	0.60171	0.21	4.14	4.14	0.48551	.	0.076752	0.52532	U	0.000067	T	0.32041	0.0816	N	0.11892	0.195	0.43364	D	0.995444	B;B;B	0.15719	0.004;0.003;0.014	B;B;B	0.16289	0.013;0.015;0.014	T	0.16364	-1.0405	10	0.06099	T	0.92	.	9.3885	0.38359	0.0:0.9019:0.0:0.0981	.	629;875;362	Q59FE5;Q9H324;E9PCI6	.;ATS10_HUMAN;.	K	875;629	ENSP00000270328:R875K	ENSP00000270328:R875K	R	-	2	0	ADAMTS10	8557042	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	2.313000	0.43735	2.132000	0.65825	0.561000	0.74099	AGG	.	.		0.662	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957		T	8651042	C	T	8651042	3	4	95	1	0	0	0	0	1	0	0	0	256	681	24	3	707	3	ADAMTS10	19	8651042	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	7892344	8651042	50477941	106	13189										
ZNF177	7730	hgsc.bcm.edu	37	chr19	9492041	9492041	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	accctatgactgtaaggaatGtgggaaggctttcactgttc	11	8	1	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr19:9492041G>A	ENST00000589262.1	+	6	1100	c.1034G>A	c.(1033-1035)tGt>tAt	p.C345Y	ZNF177_ENST00000602856.1_3'UTR|ZNF177_ENST00000602738.1_Missense_Mutation_p.C185Y|ZNF177_ENST00000343499.4_Missense_Mutation_p.C185Y|ZNF177_ENST00000541595.2_Missense_Mutation_p.C185Y|ZNF177_ENST00000434737.2_Missense_Mutation_p.C345Y|ZNF177_ENST00000590616.1_Intron|ZNF177_ENST00000446085.4_3'UTR	NM_001172651.1	NP_001166122.1	Q13360	ZN177_HUMAN	zinc finger protein 177	345					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|stomach(2)	13						TGTAAGGAATGTGGGAAGGCT	0.448																																					p.C345Y		Atlas-SNP	.											.	ZNF177	57	.	0			c.G1034A						.						104	103	103					19																	9492041		2203	4300	6503	SO:0001583	missense	7730	exon6			AGGAATGTGGGAA	U37263, BC012012	CCDS12212.1, CCDS54214.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type", "-"	12966	protein-coding gene	gene with protein product		601276					Standard	NM_003451		Approved		uc021uon.1	Q13360		ENST00000589262.1:c.1034G>A	chr19.hg19:g.9492041G>A	ENSP00000468531:p.Cys345Tyr	125.0	0.0		71.0	30.0	NM_001172651	B4DY57|E9PDG0|I3L0I4|Q96ER2	Missense_Mutation	SNP	ENST00000589262.1	hg19	CCDS54214.1	.	.	.	.	.	.	.	.	.	.	G	17.13	3.311928	0.60414	.	.	ENSG00000188629	ENST00000541595;ENST00000343499;ENST00000434737	D;D;D	0.85861	-2.04;-2.04;-2.04	2.64	2.64	0.31445	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94231	0.8148	H	0.97051	3.93	0.27048	N	0.963847	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.96359	0.9264	8	0.87932	D	0	.	11.4554	0.50179	0.0:0.0:1.0:0.0	.	345;185	B4DY57;Q13360	.;ZN177_HUMAN	Y	185;185;345	ENSP00000445323:C185Y;ENSP00000341497:C185Y;ENSP00000415070:C345Y	ENSP00000341497:C185Y	C	+	2	0	ZNF177	9353041	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.905000	0.87416	1.803000	0.52742	0.563000	0.77884	TGT	.	.		0.448	ZNF177-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449028.1	NM_003451		A	9492041	G	A	9492041	3	1	95	1	0	0	0	0	1	0	0	0	17761	1377	48	3	1052	3	ZNF177	19	9492041	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	840999	9492041	49636942	107	13190										
MAP3K10	4294	hgsc.bcm.edu	37	chr19	40704415	40704415	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	acctacgcctggatggcgccGgaggttatccgtctctccct	11	15	1	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr19:40704415G>A	ENST00000253055.3	+	2	1104	c.816G>A	c.(814-816)ccG>ccA	p.P272P	MAP3K10_ENST00000593906.1_3'UTR	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	272	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GGATGGCGCCGGAGGTTATCC	0.632																																					p.P272P		Atlas-SNP	.											.	MAP3K10	70	.	0			c.G816A						.						72	64	67					19																	40704415		2203	4300	6503	SO:0001819	synonymous_variant	4294	exon2			GGCGCCGGAGGTT	X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6849	protein-coding gene	gene with protein product	"MKN28 kinase", "mixed lineage kinase 2", "MKN28 derived nonreceptor_type serine/threonine kinase"	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.816G>A	chr19.hg19:g.40704415G>A		111.0	0.0		63.0	20.0	NM_002446	Q12761|Q14871	Silent	SNP	ENST00000253055.3	hg19	CCDS12549.1																																																																																			.	.		0.632	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446		A	40704415	G	A	40704415	2	1	95	1	0	0	0	0	0	0	0	1	9253	1103	39	1		1	MAP3K10	19	40704415	Silent	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	31212374	40704415	18424568	108	13191										
HIF3A	64344	hgsc.bcm.edu	37	chr19	46832675	46832675	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gagtgacccccggctgagctGctccagcccttccagagggg	14	15	0	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr19:46832675G>T	ENST00000377670.4	+	12	1683	c.1652G>T	c.(1651-1653)tGc>tTc	p.C551F	HIF3A_ENST00000300862.3_Missense_Mutation_p.C549F|HIF3A_ENST00000244303.6_Missense_Mutation_p.C482F|HIF3A_ENST00000472815.1_Intron|HIF3A_ENST00000339613.2_Missense_Mutation_p.C495F|HIF3A_ENST00000420102.2_Missense_Mutation_p.C500F|HIF3A_ENST00000600383.1_Missense_Mutation_p.C482F|AC007193.10_ENST00000596807.1_RNA	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	551	ODD.				cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.C549Y(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		CGGCTGAGCTGCTCCAGCCCT	0.682																																					p.C551F		Atlas-SNP	.											HIF3A,brain,glioma,0,1	HIF3A	154	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G1652T						.						17	17	17					19																	46832675		2202	4296	6498	SO:0001583	missense	64344	exon12			TGAGCTGCTCCAG	AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"Basic helix-loop-helix proteins"	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1652G>T	chr19.hg19:g.46832675G>T	ENSP00000366898:p.Cys551Phe	59.0	0.0		56.0	25.0	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Missense_Mutation	SNP	ENST00000377670.4	hg19	CCDS12681.2	.	.	.	.	.	.	.	.	.	.	G	12.96	2.094184	0.36952	.	.	ENSG00000124440	ENST00000244302;ENST00000377670;ENST00000244303;ENST00000339613;ENST00000291300;ENST00000300862;ENST00000420102	T;T;T;T;T	0.64085	0.66;-0.07;0.54;0.66;-0.08	4.68	4.68	0.58851	.	0.882388	0.09593	N	0.781335	T	0.59059	0.2166	L	0.27053	0.805	0.35029	D	0.758647	D;B;B;B;B;B	0.55605	0.972;0.075;0.047;0.028;0.028;0.028	P;B;B;B;B;B	0.49085	0.6;0.006;0.009;0.004;0.004;0.004	T	0.62854	-0.6766	10	0.44086	T	0.13	.	13.4928	0.61407	0.0:0.0:1.0:0.0	.	500;482;549;495;551;551	F5H884;B4DNA2;Q9Y2N7-2;A8MPQ1;Q9Y2N7;B0M185	.;.;.;.;HIF3A_HUMAN;.	F	551;551;482;495;495;549;500	ENSP00000366898:C551F;ENSP00000244303:C482F;ENSP00000341877:C495F;ENSP00000300862:C549F;ENSP00000407771:C500F	ENSP00000244302:C551F	C	+	2	0	HIF3A	51524515	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.055000	0.30467	2.340000	0.79590	0.655000	0.94253	TGC	.	.		0.682	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3			T	46832675	G	T	46832675	3	4	95	1	0	0	0	0	1	0	0	0	7114	1319	46	3	1722	3	HIF3A	19	46832675	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	6128260	46832675	12296308	109	13192										
ZNF772	400720	hgsc.bcm.edu	37	chr19	57987070	57987075	+	In_Frame_Del	DEL	GGTACA	GGTACA	-													0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gttctccagcatcacatcacGgtacaggagcctctgagcct					rs374022798		TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	GGTACA	GGTACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr19:57987070_57987075delGGTACA	ENST00000343280.4	-	3	412_417	c.152_157delTGTACC	c.(151-159)ctgtaccgt>cgt	p.LY51del	AC004076.9_ENST00000415705.3_Intron|ZNF772_ENST00000601768.1_Intron|AC004076.9_ENST00000596831.1_In_Frame_Del_p.LY51del|ZNF772_ENST00000600175.1_Intron|ZNF772_ENST00000356584.3_In_Frame_Del_p.LY51del|ZNF772_ENST00000427512.2_Intron|AC003005.2_ENST00000595422.1_lincRNA|ZNF772_ENST00000425074.3_Intron	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)	9		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		ATCACATCACGGTACAGGAGCCTCTG	0.558																																					p.51_53del	Melanoma(5;289 436 14293 15924 30817)	Atlas-Indel,Pindel	.											.	ZNF772	42	.	0			c.153_158del						.																																			SO:0001651	inframe_deletion	400720	exon3			.	BX647068	CCDS33133.1, CCDS46210.1	19q13.43	2013-01-08				ENSG00000197128		"Zinc fingers, C2H2-type", "-"	33106	protein-coding gene	gene with protein product							Standard	NM_001024596		Approved	DKFZp686I1569	uc002qot.3	Q68DY9		ENST00000343280.4:c.152_157delTGTACC	chr19.hg19:g.57987070_57987075delGGTACA	ENSP00000341165:p.Leu51_Tyr52del	323.0	0.0		186.0	34.0	NM_001144068	A6NJK9|B4DH56|B4DYS0	In_Frame_Del	DEL	ENST00000343280.4	hg19	CCDS33133.1																																																																																			.	.		0.558	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596		-	57987075	GGTACA	-	57987070	7	5	95	1	0	1	0	1	0	0	0	0	18160	1116	39	0	1324	0	ZNF772	19	57987070	In_Frame_Del	DEL	GGTACA	TCGA-DD-A11D-01A-11D-A12Z-10	11154395	57987070	1141913	110	13193										
A1BG	1	hgsc.bcm.edu	37	chr19	58864542	58864542	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gtgattcggactctgcccacAggctgggctgcgtctcataa	12	12	2	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr19:58864542A>T	ENST00000263100.3	-	3	153	c.92T>A	c.(91-93)cTg>cAg	p.L31Q	A1BG-AS1_ENST00000594950.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|A1BG-AS1_ENST00000595302.1_RNA|A1BG-AS1_ENST00000599728.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000600379.1_RNA	NM_130786.3	NP_570602.2	P04217	A1BG_HUMAN	alpha-1-B glycoprotein	31	Ig-like V-type 1.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)	15		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)		CTCTGCCCACAGGCTGGGCTG	0.617																																					p.L31Q		Atlas-SNP	.											.	A1BG	40	.	0			c.T92A						.						98	99	98					19																	58864542		2203	4300	6503	SO:0001583	missense	1	exon3			GCCCACAGGCTGG		CCDS12976.1	19q13.43	2013-10-15			ENSG00000121410	ENSG00000121410		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5	protein-coding gene	gene with protein product		138670				2591067	Standard	NM_130786		Approved		uc002qsd.4	P04217	OTTHUMG00000183507	ENST00000263100.3:c.92T>A	chr19.hg19:g.58864542A>T	ENSP00000263100:p.Leu31Gln	104.0	0.0		73.0	39.0	NM_130786	A8K052|Q68CK0|Q8IYJ6|Q96P39	Missense_Mutation	SNP	ENST00000263100.3	hg19	CCDS12976.1	.	.	.	.	.	.	.	.	.	.	A	16.38	3.108224	0.56291	.	.	ENSG00000121410	ENST00000263100	T	0.01379	4.96	3.17	3.17	0.36434	Immunoglobulin-like fold (1);	0.254751	0.20647	N	0.088285	T	0.10252	0.0251	M	0.93978	3.48	0.30286	N	0.790812	D	0.89917	1.0	D	0.97110	1.0	T	0.01476	-1.1345	10	0.87932	D	0	.	8.0905	0.30797	1.0:0.0:0.0:0.0	.	31	P04217	A1BG_HUMAN	Q	31	ENSP00000263100:L31Q	ENSP00000263100:L31Q	L	-	2	0	A1BG	63556354	0.031000	0.19500	0.558000	0.28319	0.155000	0.21991	2.184000	0.42575	1.685000	0.51034	0.460000	0.39030	CTG	.	.		0.617	A1BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466930.1	NM_130786		T	58864542	A	T	58864542	3	4	95	1	0	0	0	0	1	0	0	0	1	188	7	4	1419	4	A1BG	19	58864542	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	877472	58864542	264441	111	13194										
ProSAPiP1	9762	hgsc.bcm.edu	37	chr20	3146846	3146846	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tcccactcccacccgctggaGtcatggtccgagacttgtcc	9	17	1	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr20:3146846G>A	ENST00000329152.3	-	2	2017	c.620C>T	c.(619-621)aCt>aTt	p.T207I	LZTS3_ENST00000360342.3_Missense_Mutation_p.T207I|LZTS3_ENST00000337576.5_Missense_Mutation_p.T207I			O60299	LZTS3_HUMAN		207						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)											ACCCGCTGGAGTCATGGTCCG	0.642																																					p.T207I		Atlas-SNP	.											.	.	.	.	0			c.C620T						.						58	49	52					20																	3146846		2203	4300	6503	SO:0001583	missense	0	exon2			GCTGGAGTCATGG																												ENST00000329152.3:c.620C>T	chr20.hg19:g.3146846G>A	ENSP00000332123:p.Thr207Ile	131.0	0.0		108.0	41.0	NM_014731	A2A2Q7|D3DVX6|Q8IXX8	Missense_Mutation	SNP	ENST00000329152.3	hg19	CCDS13049.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124702	0.56613	.	.	ENSG00000088899	ENST00000329152;ENST00000360342;ENST00000337576	T;T;T	0.32515	1.45;1.48;1.48	5.26	4.25	0.50352	.	0.564326	0.19422	N	0.114671	T	0.28366	0.0701	N	0.22421	0.69	0.32461	N	0.544154	P;P	0.52061	0.95;0.917	P;B	0.50708	0.648;0.445	T	0.10314	-1.0635	10	0.22109	T	0.4	-22.6717	13.1811	0.59655	0.0:0.0:0.7598:0.2402	.	207;207	O60299-2;O60299	.;PRIP1_HUMAN	I	207	ENSP00000332123:T207I;ENSP00000353496:T207I;ENSP00000338166:T207I	ENSP00000332123:T207I	T	-	2	0	RP5-1187M17.10	3094846	1.000000	0.71417	1.000000	0.80357	0.726000	0.41606	2.377000	0.44300	2.450000	0.82876	0.561000	0.74099	ACT	.	.		0.642	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2			A	3146846	G	A	3146846	3	1	95	1	0	0	0	0	1	0	0	0	12885	1029	36	3	1409	3	ProSAPiP1	20	3146846	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10		3146846	59878674	112	13195										
ProSAPiP1	9762	hgsc.bcm.edu	37	chr20	3147349	3147349	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gtctcaggccctgcggactgAcctggtctagcttgccagag	13	13	2	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr20:3147349A>G	ENST00000329152.3	-	1	1857		c.e1+1		LZTS3_ENST00000360342.3_Splice_Site|LZTS3_ENST00000337576.5_Splice_Site			O60299	LZTS3_HUMAN								cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)											CTGCGGACTGACCTGGTCTAG	0.632																																					.		Atlas-SNP	.											.	.	.	.	0			c.459+2T>C						.						64	65	65					20																	3147349		2203	4300	6503	SO:0001630	splice_region_variant	0	exon2			GGACTGACCTGGT																												ENST00000329152.3:c.459+1T>C	chr20.hg19:g.3147349A>G		95.0	0.0		70.0	23.0	NM_014731	A2A2Q7|D3DVX6|Q8IXX8	Splice_Site	SNP	ENST00000329152.3	hg19	CCDS13049.1	.	.	.	.	.	.	.	.	.	.	A	18.64	3.667640	0.67814	.	.	ENSG00000088899	ENST00000329152;ENST00000360342;ENST00000337576	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5784	0.68268	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RP5-1187M17.10	3095349	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.623000	0.54224	1.915000	0.55452	0.459000	0.35465	.	.	.		0.632	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2		Intron	G	3147349	A	G	3147349	5	3	95	1	0	0	0	0	0	0	1	0	12885	289	10	2	1572	2	ProSAPiP1	20	3147349	Splice_Site	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	503	3147349	59878171	113	13196										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57829455	57829455	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tccactggagtcaactgaaaAaactcatcttgaaataccag	6	10	3	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr20:57829455A>C	ENST00000371030.2	+	5	4691	c.4691A>C	c.(4690-4692)aAa>aCa	p.K1564T		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1564							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					TCAACTGAAAAAACTCATCTT	0.478																																					p.K1564T		Atlas-SNP	.											.	ZNF831	287	.	0			c.A4691C						.						49	50	50					20																	57829455		1906	4131	6037	SO:0001583	missense	128611	exon5			CTGAAAAAACTCA	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.4691A>C	chr20.hg19:g.57829455A>C	ENSP00000360069:p.Lys1564Thr	159.0	0.0		128.0	45.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	A	8.170	0.791427	0.16258	.	.	ENSG00000124203	ENST00000371030	T	0.05717	3.4	5.66	4.5	0.54988	.	0.235838	0.29572	N	0.011766	T	0.07773	0.0195	L	0.45581	1.43	0.09310	N	1	D	0.53312	0.959	B	0.43623	0.425	T	0.23119	-1.0197	10	0.72032	D	0.01	-5.8619	9.1128	0.36739	0.8156:0.1844:0.0:0.0	.	1564	Q5JPB2	ZN831_HUMAN	T	1564	ENSP00000360069:K1564T	ENSP00000360069:K1564T	K	+	2	0	ZNF831	57262850	0.007000	0.16637	0.073000	0.20177	0.063000	0.16089	1.997000	0.40786	2.160000	0.67779	0.528000	0.53228	AAA	.	.		0.478	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		C	57829455	A	C	57829455	3	2	95	1	0	0	0	0	1	0	0	0	18200	14	1	5	4709	5	ZNF831	20	57829455	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	54682106	57829455	5196065	114	13197										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41725559	41725559	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tgttgtccttcagccagcggTaatctggctcagggtgcccg	13	12	3	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr21:41725559T>C	ENST00000400454.1	-	5	1244	c.767A>G	c.(766-768)tAc>tGc	p.Y256C		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	256	Ig-like C2-type 3.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CAGCCAGCGGTAATCTGGCTC	0.597																																					p.Y256C	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.A767G						.						43	42	42					21																	41725559		1926	4127	6053	SO:0001583	missense	1826	exon5			CAGCGGTAATCTG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.767A>G	chr21.hg19:g.41725559T>C	ENSP00000383303:p.Tyr256Cys	74.0	0.0		56.0	24.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.850741	0.71719	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.66638	-0.22;-0.22	5.31	4.16	0.48862	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75443	0.3850	L	0.52126	1.63	0.52501	D	0.999958	D	0.76494	0.999	D	0.81914	0.995	T	0.76077	-0.3091	10	0.66056	D	0.02	.	11.2924	0.49258	0.0:0.0722:0.0:0.9278	.	256	O60469	DSCAM_HUMAN	C	256;8	ENSP00000383303:Y256C;ENSP00000385342:Y8C	ENSP00000383303:Y256C	Y	-	2	0	DSCAM	40647429	1.000000	0.71417	0.987000	0.45799	0.999000	0.98932	7.560000	0.82277	0.954000	0.37851	0.528000	0.53228	TAC	.	.		0.597	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		C	41725559	T	C	41725559	3	2	95	1	0	0	0	0	1	0	0	0	4770	1638	57	2	5387	2	DSCAM	21	41725559	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10		41725559	6404336	115	13198										
ZNF280B	140883	hgsc.bcm.edu	37	chr22	22842866	22842866	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tgctgtccatagtaaaagtcActaagtaacacaatgggatt	8	7	1	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr22:22842866A>G	ENST00000406426.1	-	4	1600	c.858T>C	c.(856-858)agT>agC	p.S286S	ZNF280B_ENST00000360412.2_Silent_p.S286S			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	286					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		AGTAAAAGTCACTAAGTAACA	0.383																																					p.S286S		Atlas-SNP	.											.	ZNF280B	67	.	0			c.T858C						.						121	113	115					22																	22842866		2203	4300	6503	SO:0001819	synonymous_variant	140883	exon4			AAAGTCACTAAGT	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"zinc finger protein 279", "suppressor of hairy wing homolog 2 (Drosophila)"	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.858T>C	chr22.hg19:g.22842866A>G		174.0	0.0		180.0	51.0	NM_080764		Silent	SNP	ENST00000406426.1	hg19	CCDS13799.1																																																																																			.	.		0.383	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764		G	22842866	A	G	22842866	2	3	95	1	0	0	0	0	0	0	0	1	17830	156	6	2		2	ZNF280B	22	22842866	Silent	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10		22842866	28461700	116	13199										
ISX	91464	hgsc.bcm.edu	37	chr22	35463259	35463259	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tgaagagggccccggagaagCtgcggcctcaggctctgggc	17	12	2	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr22:35463259C>T	ENST00000308700.6	+	1	1131	c.179C>T	c.(178-180)gCt>gTt	p.A60V	RP1-272J12.1_ENST00000448318.4_RNA|ISX_ENST00000404699.2_Missense_Mutation_p.A60V	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	60					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						CCCGGAGAAGCTGCGGCCTCA	0.567																																					p.A60V		Atlas-SNP	.											.	ISX	62	.	0			c.C179T						.						31	34	33					22																	35463259		2199	4296	6495	SO:0001583	missense	91464	exon1			GAGAAGCTGCGGC	AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"Homeoboxes / PRD class"	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.179C>T	chr22.hg19:g.35463259C>T	ENSP00000311492:p.Ala60Val	83.0	0.0		101.0	37.0	NM_001008494	Q68DJ5	Missense_Mutation	SNP	ENST00000308700.6	hg19	CCDS33640.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.870421	0.33069	.	.	ENSG00000175329	ENST00000308700;ENST00000404699	D;D	0.90732	-2.72;-2.72	4.9	-0.435	0.12279	.	0.487974	0.17243	N	0.181460	T	0.80325	0.4602	L	0.32530	0.975	0.09310	N	1	B	0.14805	0.011	B	0.14023	0.01	T	0.64214	-0.6460	10	0.30078	T	0.28	.	2.7101	0.05173	0.1391:0.5209:0.1536:0.1865	.	60	Q2M1V0	ISX_HUMAN	V	60	ENSP00000311492:A60V;ENSP00000386037:A60V	ENSP00000311492:A60V	A	+	2	0	ISX	33793259	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.660000	0.25009	0.124000	0.18369	-0.742000	0.03525	GCT	.	.		0.567	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494		T	35463259	C	T	35463259	3	4	95	1	0	0	0	0	1	0	0	0	7874	797	28	3	181	3	ISX	22	35463259	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	12620393	35463259	15841307	117	13200										
TST	7263	hgsc.bcm.edu	37	chr22	37414432	37414432	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tggccaaacacacggaacatCcaccagacccggggagcata	10	14	0	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chr22:37414432C>A	ENST00000403892.3	-	1	1076	c.342G>T	c.(340-342)tgG>tgT	p.W114C	MPST_ENST00000397129.1_5'Flank|MPST_ENST00000429360.2_5'Flank|MPST_ENST00000404802.3_5'Flank|MPST_ENST00000404393.1_5'Flank|MPST_ENST00000401419.3_5'Flank|MPST_ENST00000341116.3_5'Flank|TST_ENST00000249042.3_Missense_Mutation_p.W114C	NM_001270483.1	NP_001257412.1	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase (rhodanese)	114	Rhodanese 1. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cellular nitrogen compound metabolic process (GO:0034641)|cyanate catabolic process (GO:0009440)|epithelial cell differentiation (GO:0030855)|rRNA import into mitochondrion (GO:0035928)|rRNA transport (GO:0051029)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|thiosulfate sulfurtransferase activity (GO:0004792)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	7						CACGGAACATCCACCAGACCC	0.622																																					p.W114C		Atlas-SNP	.											.	TST	22	.	0			c.G342T						.						86	68	74					22																	37414432		2203	4300	6503	SO:0001583	missense	7263	exon2			GAACATCCACCAG	Z73420	CCDS13938.1	22q13.1	2002-02-05			ENSG00000128311	ENSG00000128311	2.8.1.1		12388	protein-coding gene	gene with protein product		180370				1953758	Standard	NM_003312		Approved	RDS	uc003aqh.4	Q16762	OTTHUMG00000150533	ENST00000403892.3:c.342G>T	chr22.hg19:g.37414432C>A	ENSP00000385828:p.Trp114Cys	96.0	0.0		96.0	22.0	NM_003312	B3KRM1|Q6IB06	Missense_Mutation	SNP	ENST00000403892.3	hg19	CCDS13938.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.431273	0.83776	.	.	ENSG00000128311	ENST00000403892;ENST00000249042;ENST00000413912;ENST00000438203	T;T;T	0.51817	0.69;0.69;0.69	5.09	5.09	0.68999	Rhodanese-like (5);	0.000000	0.85682	D	0.000000	D	0.83788	0.5330	H	0.99726	4.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91807	0.5456	10	0.87932	D	0	-3.0902	18.5155	0.90934	0.0:1.0:0.0:0.0	.	114	Q16762	THTR_HUMAN	C	114	ENSP00000385828:W114C;ENSP00000249042:W114C;ENSP00000400764:W114C	ENSP00000249042:W114C	W	-	3	0	TST	35744378	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.801000	0.85960	2.355000	0.79922	0.561000	0.74099	TGG	.	.		0.622	TST-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318790.1			A	37414432	C	A	37414432	3	1	95	1	0	0	0	0	1	0	0	0	16688	856	30	3	559	3	TST	22	37414432	Missense_Mutation	SNP	C	TCGA-DD-A11D-01A-11D-A12Z-10	1951173	37414432	13890134	118	13201										
IL1RAPL1	11141	hgsc.bcm.edu	37	chrX	29973331	29973331	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	atctttgagctggaaaccagActtcgaaatatgcttgtgac	9	8	1	3			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chrX:29973331A>T	ENST00000378993.1	+	11	2158	c.1485A>T	c.(1483-1485)agA>agT	p.R495S	IL1RAPL1_ENST00000302196.4_Missense_Mutation_p.R495S	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	495	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						TGGAAACCAGACTTCGAAATA	0.438																																					p.R495S		Atlas-SNP	.											.	IL1RAPL1	311	.	0			c.A1485T						.						98	89	92					X																	29973331		2202	4300	6502	SO:0001583	missense	11141	exon11			AACCAGACTTCGA	AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.1485A>T	chrX.hg19:g.29973331A>T	ENSP00000368278:p.Arg495Ser	340.0	0.0		243.0	91.0	NM_014271	A0AVG4|Q9UJ53	Missense_Mutation	SNP	ENST00000378993.1	hg19	CCDS14218.1	.	.	.	.	.	.	.	.	.	.	A	13.02	2.112983	0.37242	.	.	ENSG00000169306	ENST00000378993;ENST00000302196	T;T	0.07216	3.21;3.21	5.87	2.02	0.26589	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.85682	D	0.000000	T	0.16300	0.0392	M	0.70595	2.14	0.50467	D	0.999878	D	0.55385	0.971	P	0.59546	0.859	T	0.05305	-1.0893	9	.	.	.	.	1.2665	0.02012	0.4731:0.1407:0.2472:0.1389	.	495	Q9NZN1	IRPL1_HUMAN	S	495	ENSP00000368278:R495S;ENSP00000305200:R495S	.	R	+	3	2	IL1RAPL1	29883252	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	0.401000	0.20948	0.333000	0.23563	-0.314000	0.08810	AGA	.	.		0.438	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		T	29973331	A	T	29973331	3	4	95	1	0	0	0	0	1	0	0	0	7670	272	10	4	1523	4	IL1RAPL1	23	29973331	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10		29973331	125297229	119	13202										
EDA	1896	hgsc.bcm.edu	37	chrX	69249366	69249366	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ttttgcaggtgctgctgataAagctggaactcgagaaaacc	11	8	0	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chrX:69249366A>T	ENST00000374552.4	+	5	961	c.719A>T	c.(718-720)aAa>aTa	p.K240I	EDA_ENST00000524573.1_Missense_Mutation_p.K240I|EDA_ENST00000374553.2_Missense_Mutation_p.K240I	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A	240					cell differentiation (GO:0030154)|cell-matrix adhesion (GO:0007160)|ectoderm development (GO:0007398)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|immune response (GO:0006955)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|salivary gland cavitation (GO:0060662)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	apical part of cell (GO:0045177)|collagen trimer (GO:0005581)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						GCTGCTGATAAAGCTGGAACT	0.483											OREG0019846	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K240I		Atlas-SNP	.											.	EDA	61	.	0			c.A719T						.						166	130	142					X																	69249366		2203	4300	6503	SO:0001583	missense	1896	exon5			CTGATAAAGCTGG	U59227	CCDS14394.1, CCDS35318.1, CCDS35319.1, CCDS43966.1, CCDS35318.2, CCDS35319.2, CCDS55436.1	Xq12-q13.1	2013-05-22	2004-08-09	2004-08-12	ENSG00000158813	ENSG00000158813		"Tumor necrosis factor (ligand) superfamily"	3157	protein-coding gene	gene with protein product		300451	"ectodermal dysplasia 1, anhidrotic", "oligodontia 1"	ED1, EDA2, ODT1		8696334, 18657636, 16583127	Standard	NM_001005612		Approved	EDA1, XLHED, HED, XHED, ED1-A1, ED1-A2, EDA-A1, EDA-A2	uc004dxs.3	Q92838	OTTHUMG00000021764	ENST00000374552.4:c.719A>T	chrX.hg19:g.69249366A>T	ENSP00000363680:p.Lys240Ile	216.0	0.0	1113	143.0	56.0	NM_001399	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	Missense_Mutation	SNP	ENST00000374552.4	hg19	CCDS14394.1	.	.	.	.	.	.	.	.	.	.	A	17.65	3.441193	0.63067	.	.	ENSG00000158813	ENST00000374552;ENST00000374553;ENST00000524573;ENST00000503592	D;D;D;D	0.93859	-3.3;-3.3;-3.3;-3.02	4.59	4.59	0.56863	.	0.057403	0.64402	D	0.000002	D	0.94548	0.8244	L	0.42245	1.32	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.81914	0.991;0.995;0.991	D	0.94709	0.7890	10	0.62326	D	0.03	-3.7523	12.4982	0.55940	1.0:0.0:0.0:0.0	.	240;240;240	Q92838-9;Q92838;Q92838-3	.;EDA_HUMAN;.	I	240;240;240;108	ENSP00000363680:K240I;ENSP00000363681:K240I;ENSP00000432585:K240I;ENSP00000423037:K108I	ENSP00000363680:K240I	K	+	2	0	EDA	69166091	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	6.056000	0.71111	1.811000	0.52892	0.486000	0.48141	AAA	.	.		0.483	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057048.2	NM_001399		T	69249366	A	T	69249366	3	4	95	1	0	0	0	0	1	0	0	0	4905	14	1	4	873	4	EDA	23	69249366	Missense_Mutation	SNP	A	TCGA-DD-A11D-01A-11D-A12Z-10	39276035	69249366	86021194	120	13203										
PHKA1	5255	hgsc.bcm.edu	37	chrX	71855112	71855112	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	gcatttccactatcatcttgTtgtccagagccaggtagaac	8	11	2	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chrX:71855112T>C	ENST00000373542.4	-	16	1766	c.1607A>G	c.(1606-1608)aAc>aGc	p.N536S	PHKA1_ENST00000373539.3_Missense_Mutation_p.N536S|PHKA1_ENST00000373545.3_Missense_Mutation_p.N536S|PHKA1_ENST00000541944.1_Missense_Mutation_p.N536S|PHKA1_ENST00000339490.3_Missense_Mutation_p.N536S	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	536					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					TATCATCTTGTTGTCCAGAGC	0.418																																					p.N536S		Atlas-SNP	.											.	PHKA1	129	.	0			c.A1607G						.						117	91	100					X																	71855112		2203	4300	6503	SO:0001583	missense	5255	exon16			ATCTTGTTGTCCA		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.1607A>G	chrX.hg19:g.71855112T>C	ENSP00000362643:p.Asn536Ser	189.0	0.0		160.0	70.0	NM_001172436	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	T	10.69	1.422106	0.25639	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.90844	-2.72;-2.74;-2.71;-2.73;-2.73	4.47	4.47	0.54385	Glycoside hydrolase 15-related (1);	0.050069	0.85682	D	0.000000	D	0.86912	0.6047	L	0.51422	1.61	0.54753	D	0.999989	B;B;B	0.25521	0.128;0.032;0.08	B;B;B	0.30716	0.078;0.034;0.119	T	0.81858	-0.0739	10	0.20519	T	0.43	-11.7535	11.0389	0.47818	0.0:0.0:0.0:1.0	.	536;536;536	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	S	536	ENSP00000362646:N536S;ENSP00000362643:N536S;ENSP00000441251:N536S;ENSP00000342469:N536S;ENSP00000362640:N536S	ENSP00000342469:N536S	N	-	2	0	PHKA1	71771837	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.136000	0.58004	1.572000	0.49736	0.339000	0.21740	AAC	.	.		0.418	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			C	71855112	T	C	71855112	3	2	95	1	0	0	0	0	1	0	0	0	11852	1725	60	2	2132	2	PHKA1	23	71855112	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	2605746	71855112	83415448	121	13204										
ATP7A	538	hgsc.bcm.edu	37	chrX	77243771	77243771	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	aaaaaaatgcaactattattTatgaccctaaactacagact	3	8	0	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chrX:77243771T>A	ENST00000341514.6	+	3	309	c.154T>A	c.(154-156)Tat>Aat	p.Y52N	ATP7A_ENST00000343533.5_Missense_Mutation_p.Y52N|ATP7A_ENST00000350425.4_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	52	HMA 1. {ECO:0000255|PROSITE- ProRule:PRU00280}.				blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	AACTATTATTTATGACCCTAA	0.348																																					p.Y52N		Atlas-SNP	.											.	ATP7A	248	.	0			c.T154A						.						179	170	173					X																	77243771		2203	4296	6499	SO:0001583	missense	538	exon3			ATTATTTATGACC	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.154T>A	chrX.hg19:g.77243771T>A	ENSP00000345728:p.Tyr52Asn	292.0	0.0		232.0	66.0	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	hg19	CCDS35339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.37|18.37	3.609328|3.609328	0.66558|0.66558	.|.	.|.	ENSG00000165240|ENSG00000165240	ENST00000343912|ENST00000343533;ENST00000341514;ENST00000400860;ENST00000355691	.|D;D	.|0.86497	.|-2.13;-2.13	5.59|5.59	5.59|5.59	0.84812|0.84812	.|Heavy metal-associated domain, HMA (3);Heavy metal-associated domain, copper ion-binding (1);	.|0.072596	.|0.56097	.|D	.|0.000023	.|D	.|0.94653	.|0.8276	M|M	0.91196|0.91196	3.185|3.185	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.997;1.0	.|D;D	.|0.79784	.|0.987;0.993	.|D	.|0.95666	.|0.8719	.|10	.|0.87932	.|D	.|0	.|-10.4763	14.835|14.835	0.70175|0.70175	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|52;62	.|Q04656;Q59HD1	.|ATP7A_HUMAN;.	.|N	-1|52;52;52;62	.|ENSP00000343026:Y52N;ENSP00000345728:Y52N	.|ENSP00000345728:Y52N	.|Y	+|+	.|1	.|0	ATP7A|ATP7A	77130427|77130427	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.499000|7.499000	0.81566|0.81566	1.885000|1.885000	0.54596|0.54596	0.430000|0.430000	0.28490|0.28490	.|TAT	.	.		0.348	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		A	77243771	T	A	77243771	3	1	95	1	0	0	0	0	1	0	0	0	1190	1754	61	4	160	4	ATP7A	23	77243771	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	5388659	77243771	78026789	122	13205										
GRIA3	2892	hgsc.bcm.edu	37	chrX	122616686	122616686	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	tgagcctgagcaatgtggcaGgcgttttctatatacttgtc	11	8	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chrX:122616686G>A	ENST00000371251.1	+	15	2528	c.2476G>A	c.(2476-2478)Ggc>Agc	p.G826S	GRIA3_ENST00000542149.1_3'UTR|GRIA3_ENST00000371256.5_Missense_Mutation_p.G826S|GRIA3_ENST00000264357.5_Missense_Mutation_p.G826S			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	826					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	CAATGTGGCAGGCGTTTTCTA	0.448																																					p.G826S		Atlas-SNP	.											.	GRIA3	386	.	0			c.G2476A						.						110	106	107					X																	122616686		2203	4300	6503	SO:0001583	missense	2892	exon15			GTGGCAGGCGTTT	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.2476G>A	chrX.hg19:g.122616686G>A	ENSP00000360297:p.Gly826Ser	216.0	0.0		171.0	73.0	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	hg19	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.828626	0.90955	.	.	ENSG00000125675	ENST00000264357;ENST00000371256;ENST00000371251	T;T;T	0.62364	0.03;0.03;0.03	5.81	5.81	0.92471	Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.82577	0.5067	M	0.87381	2.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	D	0.85515	0.1200	10	0.87932	D	0	.	17.8613	0.88781	0.0:0.0:1.0:0.0	.	826;826	P42263;P42263-2	GRIA3_HUMAN;.	S	826	ENSP00000264357:G826S;ENSP00000360302:G826S;ENSP00000360297:G826S	ENSP00000264357:G826S	G	+	1	0	GRIA3	122444367	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.436000	0.82500	0.600000	0.82982	GGC	.	.		0.448	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		A	122616686	G	A	122616686	3	1	95	1	0	0	0	0	1	0	0	0	6778	1000	35	3	2653	3	GRIA3	23	122616686	Missense_Mutation	SNP	G	TCGA-DD-A11D-01A-11D-A12Z-10	45372915	122616686	32653874	123	13206										
SLC9A6	10479	hgsc.bcm.edu	37	chrX	135080330	135080330	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ctatcatattttatgcaggtTatagcctgaaaagggtaagt	9	5	1	1			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chrX:135080330T>A	ENST00000370698.3	+	3	528	c.493T>A	c.(493-495)Tat>Aat	p.Y165N	SLC9A6_ENST00000370695.4_Missense_Mutation_p.Y197N|SLC9A6_ENST00000370701.1_Missense_Mutation_p.Y145N	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	165					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					TTATGCAGGTTATAGCCTGAA	0.313																																					p.Y197N		Atlas-SNP	.											.	SLC9A6	64	.	0			c.T589A						.						67	69	68					X																	135080330		2203	4297	6500	SO:0001583	missense	10479	exon3			GCAGGTTATAGCC	AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"Solute carriers"	11079	protein-coding gene	gene with protein product		300231	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 6", "solute carrier family 9 (sodium/hydrogen exchanger), member 6"			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.493T>A	chrX.hg19:g.135080330T>A	ENSP00000359732:p.Tyr165Asn	576.0	0.0		436.0	164.0	NM_001042537	A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Missense_Mutation	SNP	ENST00000370698.3	hg19	CCDS14654.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.445438	0.63178	.	.	ENSG00000198689	ENST00000370701;ENST00000370698;ENST00000370695	T;T;T	0.17528	2.27;2.27;2.27	4.77	4.77	0.60923	Cation/H+ exchanger (1);	0.122953	0.64402	D	0.000019	T	0.55000	0.1893	H	0.96833	3.89	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.79784	0.993;0.988;0.993	T	0.70561	-0.4838	10	0.87932	D	0	.	12.8214	0.57696	0.0:0.0:0.0:1.0	.	145;197;165	B4DU30;Q92581-2;Q92581	.;.;SL9A6_HUMAN	N	145;165;197	ENSP00000359735:Y145N;ENSP00000359732:Y165N;ENSP00000359729:Y197N	ENSP00000359729:Y197N	Y	+	1	0	SLC9A6	134907996	1.000000	0.71417	0.988000	0.46212	0.976000	0.68499	7.608000	0.82898	1.687000	0.51057	0.345000	0.21793	TAT	.	.		0.313	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	NM_006359		A	135080330	T	A	135080330	3	1	95	1	0	0	0	0	1	0	0	0	14733	1754	61	4	599	4	SLC9A6	23	135080330	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	12463644	135080330	20190230	124	13207										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140993822	140993822	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ctccttctcctccactttatTgagtattttccagagttccc	4	14	1	2			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chrX:140993822T>C	ENST00000285879.4	+	4	918	c.632T>C	c.(631-633)tTg>tCg	p.L211S	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	211										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					TCCACTTTATTGAGTATTTTC	0.502										HNSCC(15;0.026)																											p.L211S		Atlas-SNP	.											.	MAGEC1	317	.	0			c.T632C						.						128	136	133					X																	140993822		2203	4299	6502	SO:0001583	missense	9947	exon4			CTTTATTGAGTAT	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.632T>C	chrX.hg19:g.140993822T>C	ENSP00000285879:p.Leu211Ser	998.0	1.0		780.0	108.0	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	hg19	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	-	5.768	0.326142	0.10900	.	.	ENSG00000155495	ENST00000285879	T	0.03035	4.07	.	.	.	.	.	.	.	.	T	0.02767	0.0083	N	0.08118	0	0.31656	N	0.646166	P	0.44006	0.824	P	0.48704	0.587	T	0.47674	-0.9099	8	0.28530	T	0.3	.	4.4859	0.11790	0.0:7.0E-4:0.0:0.9993	.	211	O60732	MAGC1_HUMAN	S	211	ENSP00000285879:L211S	ENSP00000285879:L211S	L	+	2	0	MAGEC1	140821488	0.996000	0.38824	0.201000	0.23476	0.201000	0.24016	0.766000	0.26560	0.046000	0.15833	0.046000	0.15203	TTG	.	.		0.502	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		C	140993822	T	C	140993822	3	2	95	1	0	0	0	0	1	0	0	0	9189	1821	63	2	638	2	MAGEC1	23	140993822	Missense_Mutation	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	5913492	140993822	14276738	125	13208										
GABRA3	2556	hgsc.bcm.edu	37	chrX	151424438	151424438	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0887096774193548	11	1	1.71628149889019	2.87087087087087	1.15760922212535	1	1	0	ttcagtctttcatcatgccaTgtctgccgaaaaaatacatc	5	11	5	0			TCGA-DD-A11D-01A-11D-A12Z-10	TCGA-DD-A11D-11A-12D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef36ae28-ea74-4d7d-9fe3-df3b7ee12a58	6509e096-9af2-4933-9691-7463020c7f8d	g.chrX:151424438T>A	ENST00000370314.4	-	5	601	c.363A>T	c.(361-363)acA>acT	p.T121T	GABRA3_ENST00000535043.1_Silent_p.T121T	NM_000808.3	NP_000799.1	P34903	GBRA3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 3	121					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(6)	37	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	CATCATGCCATGTCTGCCGAA	0.443																																					p.T121T	NSCLC(142;2578 2613 10251 16743)	Atlas-SNP	.											.	GABRA3	97	.	0			c.A363T						.						125	103	110					X																	151424438		2203	4300	6503	SO:0001819	synonymous_variant	2556	exon5			ATGCCATGTCTGC		CCDS14706.1	Xq28	2012-06-22			ENSG00000011677	ENSG00000011677		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4077	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 3"	305660					Standard	NM_000808		Approved		uc010ntk.1	P34903	OTTHUMG00000024183	ENST00000370314.4:c.363A>T	chrX.hg19:g.151424438T>A		191.0	0.0		139.0	10.0	NM_000808	Q8TAF9	Silent	SNP	ENST00000370314.4	hg19	CCDS14706.1																																																																																			.	.		0.443	GABRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060921.1	NM_000808		A	151424438	T	A	151424438	2	1	95	1	0	0	0	0	0	0	0	1	6170	1451	51	4		4	GABRA3	23	151424438	Silent	SNP	T	TCGA-DD-A11D-01A-11D-A12Z-10	10430616	151424438	3846122	126	13209										
WDR8	49856	hgsc.bcm.edu	37	chr1	3548777	3548777	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	cctgcgtcagcacaactgacCgttccttgtcgccaggaagt	10	14	1	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr1:3548777C>T	ENST00000270708.7	-	10	1121	c.1048G>A	c.(1048-1050)Gac>Aac	p.D350N	WRAP73_ENST00000378322.3_Splice_Site_p.D350N	NM_017818.3	NP_060288.3	Q9P2S5	WRP73_HUMAN	WD repeat containing, antisense to TP73	350						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)	12						CACAACTGACCGTTCCTTGTC	0.512																																					p.D350N		Atlas-SNP	.											.	WRAP73	43	.	0			c.G1048A						.						237	218	224					1																	3548777		2203	4300	6503	SO:0001630	splice_region_variant	49856	exon10			ACTGACCGTTCCT	AB034912, EF494669	CCDS48.1	1p36.3	2013-05-21	2011-04-13	2011-04-13	ENSG00000116213	ENSG00000116213		"WD repeat domain containing"	12759	protein-coding gene	gene with protein product		606040	"WD repeat domain 8"	WDR8			Standard	NM_017818		Approved		uc001ako.3	Q9P2S5	OTTHUMG00000000612	ENST00000270708.7:c.1048+1G>A	chr1.hg19:g.3548777C>T		86.0	0.0		110.0	18.0	NM_017818	Q5T0D6|Q9BUH7|Q9NTK7|Q9NX56	Missense_Mutation	SNP	ENST00000270708.7	hg19	CCDS48.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760264	0.69763	.	.	ENSG00000116213	ENST00000270708;ENST00000378322	T;T	0.39592	2.91;1.07	4.94	4.94	0.65067	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.48554	0.1506	M	0.83012	2.62	0.80722	D	1	D	0.58970	0.984	B	0.40825	0.341	T	0.59736	-0.7398	10	0.40728	T	0.16	-48.1724	17.1488	0.86773	0.0:1.0:0.0:0.0	.	350	Q9P2S5	WRP73_HUMAN	N	350	ENSP00000270708:D350N;ENSP00000367573:D350N	ENSP00000270708:D350N	D	-	1	0	WRAP73	3538637	1.000000	0.71417	0.450000	0.26969	0.093000	0.18481	6.835000	0.75344	2.291000	0.77112	0.655000	0.94253	GAC	.	.		0.512	WRAP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001470.1		Missense_Mutation	T	3548777	C	T	3548777	5	4	96	1	0	0	0	0	0	0	1	0	17344	666	23	1	346	1	WDR8	1	3548777	Splice_Site	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10		3548777	245701844	1	13210										
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94652058	94652058	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tcaggtaaatacaataccagTttctgaaggggaaggtggct	12	6	2	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr1:94652058T>G	ENST00000260526.6	-	16	1959	c.1777A>C	c.(1777-1779)Act>Cct	p.T593P	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	593					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		ACAATACCAGTTTCTGAAGGG	0.378																																					p.T593P		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.A1777C						.						170	166	167					1																	94652058		2203	4300	6503	SO:0001583	missense	9411	exon16			TACCAGTTTCTGA		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.1777A>C	chr1.hg19:g.94652058T>G	ENSP00000260526:p.Thr593Pro	146.0	0.0		108.0	16.0	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	hg19	CCDS748.1	.	.	.	.	.	.	.	.	.	.	T	11.94	1.787748	0.31593	.	.	ENSG00000137962	ENST00000260526	T	0.22539	1.95	5.98	1.37	0.22104	.	0.732715	0.11319	N	0.576290	T	0.04003	0.0112	L	0.29908	0.895	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.41466	-0.9507	10	0.22706	T	0.39	.	0.7096	0.00922	0.3486:0.297:0.1218:0.2326	.	593;593	F8VWZ8;Q52LW3	.;RHG29_HUMAN	P	593	ENSP00000260526:T593P	ENSP00000260526:T593P	T	-	1	0	ARHGAP29	94424646	0.994000	0.37717	1.000000	0.80357	0.978000	0.69477	1.380000	0.34351	0.837000	0.34925	-0.177000	0.13119	ACT	.	.		0.378	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		G	94652058	T	G	94652058	3	3	96	1	0	0	0	0	1	0	0	0	878	1725	60	5	2040	5	ARHGAP29	1	94652058	Missense_Mutation	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10	91103281	94652058	154598563	2	13211										
DBT	1629	hgsc.bcm.edu	37	chr1	100672083	100672083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	cagagcccaatttctggaggCggttcagttcagtggcgatg	14	9	3	1	rs150934375		TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr1:100672083C>T	ENST00000370132.4	-	9	1140	c.1127G>A	c.(1126-1128)cGc>cAc	p.R376H		NM_001918.3	NP_001909.3	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase E2	376					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity (GO:0043754)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(1)	19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		TTTCTGGAGGCGGTTCAGTTC	0.423																																					p.R376H		Atlas-SNP	.											.	DBT	39	.	0			c.G1127A						.	C	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	194	200	198		1127	5.8	1	1	dbSNP_134	198	0,8600		0,0,4300	no	missense	DBT	NM_001918.2	29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	376/483	100672083	2,13004	2203	4300	6503	SO:0001583	missense	1629	exon9			TGGAGGCGGTTCA	BC016675	CCDS767.1	1p31	2008-02-05	2004-11-15		ENSG00000137992	ENSG00000137992			2698	protein-coding gene	gene with protein product		248610	"dihydrolipoamide branched chain transacylase (E2 component of branched chain keto acid dehydrogenase complex; maple syrup urine disease)"			1420314, 1429740	Standard	NM_001918		Approved		uc001dta.3	P11182	OTTHUMG00000010921	ENST00000370132.4:c.1127G>A	chr1.hg19:g.100672083C>T	ENSP00000359151:p.Arg376His	87.0	0.0		84.0	24.0	NM_001918	B2R811|Q5VVL8	Missense_Mutation	SNP	ENST00000370132.4	hg19	CCDS767.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.942921	0.92526	4.54E-4	0.0	ENSG00000137992	ENST00000543138;ENST00000370132	T	0.46819	0.86	5.84	5.84	0.93424	2-oxoacid dehydrogenase acyltransferase, catalytic domain (1);Chloramphenicol acetyltransferase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.73737	0.3625	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.981;0.993	T	0.78945	-0.2004	10	0.87932	D	0	-4.8811	20.1386	0.98045	0.0:1.0:0.0:0.0	.	195;376	F5H1F9;P11182	.;ODB2_HUMAN	H	195;376	ENSP00000359151:R376H	ENSP00000359151:R376H	R	-	2	0	DBT	100444671	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	7.389000	0.79806	2.767000	0.95098	0.561000	0.74099	CGC	.	C|1.000;T|0.000		0.423	DBT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030101.2	NM_001918		T	100672083	C	T	100672083	3	4	96	1	0	0	0	0	1	0	0	0	4260	768	27	1	333	1	DBT	1	100672083	Missense_Mutation	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	6020025	100672083	148578538	3	13212										
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150531572	150531572	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	ccaacaggaagccggcccccTgacatgcgcgcctgcagcct	11	18	0	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr1:150531572T>C	ENST00000369038.2	+	14	2895	c.2694T>C	c.(2692-2694)ccT>ccC	p.P898P	ADAMTSL4_ENST00000369039.5_Silent_p.P921P|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Silent_p.P898P			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	898	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GCCGGCCCCCTGACATGCGCG	0.677																																					p.P898P		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.T2694C						.						15	19	18					1																	150531572		2196	4294	6490	SO:0001819	synonymous_variant	54507	exon16			GCCCCCTGACATG	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.2694T>C	chr1.hg19:g.150531572T>C		71.0	0.0		90.0	45.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Silent	SNP	ENST00000369038.2	hg19	CCDS955.1																																																																																			.	.		0.677	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		C	150531572	T	C	150531572	2	2	96	1	0	0	0	0	0	0	0	1	277	1567	55	2		2	ADAMTSL4	1	150531572	Silent	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10	49859489	150531572	98719049	4	13213										
HRNR	388697	hgsc.bcm.edu	37	chr1	152185637	152185637	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tgagaaaatatgagccagaaCttcccccatcatggttactt	7	10	1	3	rs150101773	byFrequency	TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr1:152185637C>A	ENST00000368801.2	-	3	8543	c.8468G>T	c.(8467-8469)aGt>aTt	p.S2823I	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2823					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGAGCCAGAACTTCCCCCATC	0.423																																					p.S2823I		Atlas-SNP	.											.	HRNR	403	.	0			c.G8468T						.						71	74	73					1																	152185637		2203	4300	6503	SO:0001583	missense	388697	exon3			CCAGAACTTCCCC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.8468G>T	chr1.hg19:g.152185637C>A	ENSP00000357791:p.Ser2823Ile	358.0	0.0		551.0	54.0	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	hg19	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	C	6.177	0.400926	0.11696	.	.	ENSG00000197915	ENST00000368801	T	0.02085	4.46	4.56	-2.24	0.06909	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	D	0.56968	0.978	P	0.52267	0.694	T	0.48399	-0.9039	9	0.48119	T	0.1	.	5.1577	0.15044	0.0:0.3176:0.1591:0.5233	.	2823	Q86YZ3	HORN_HUMAN	I	2823	ENSP00000357791:S2823I	ENSP00000357791:S2823I	S	-	2	0	HRNR	150452261	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.759000	0.04761	-0.556000	0.06134	-0.258000	0.10820	AGT	.	C|1.000;T|0.000		0.423	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		A	152185637	C	A	152185637	3	1	96	1	0	0	0	0	1	0	0	0	7368	565	20	3	88	3	HRNR	1	152185637	Missense_Mutation	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	1654065	152185637	97064984	5	13214										
LY9	4063	hgsc.bcm.edu	37	chr1	160769681	160769681	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tggtcccaaaaatgctcttgCtttcgcacgtcccaaagaaa	7	12	1	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr1:160769681C>A	ENST00000263285.6	+	2	293	c.263C>A	c.(262-264)gCt>gAt	p.A88D	LY9_ENST00000368039.2_Missense_Mutation_p.A88D|LY9_ENST00000471816.1_3'UTR|LY9_ENST00000368040.1_5'UTR|LY9_ENST00000392203.4_Missense_Mutation_p.A88D|LY9_ENST00000368037.5_Missense_Mutation_p.A88D|LY9_ENST00000368041.2_Missense_Mutation_p.A48D|LY9_ENST00000341032.4_Missense_Mutation_p.A88D			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9	88	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			AATGCTCTTGCTTTCGCACGT	0.488																																					p.A88D		Atlas-SNP	.											.	LY9	115	.	0			c.C263A						.						99	95	96					1																	160769681		2203	4300	6503	SO:0001583	missense	4063	exon2			CTCTTGCTTTCGC	L42621	CCDS30916.1, CCDS30917.1, CCDS65695.1, CCDS65696.1	1q23.3	2013-01-11			ENSG00000122224	ENSG00000122224		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6730	protein-coding gene	gene with protein product		600684				8537117, 7797269	Standard	NM_001261457		Approved	CD229, mLY9, SLAMF3, hly9	uc001fwu.4	Q9HBG7	OTTHUMG00000024007	ENST00000263285.6:c.263C>A	chr1.hg19:g.160769681C>A	ENSP00000263285:p.Ala88Asp	113.0	0.0		200.0	13.0	NM_001261457	A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Missense_Mutation	SNP	ENST00000263285.6	hg19	CCDS30916.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.511901	0.44660	.	.	ENSG00000122224	ENST00000368041;ENST00000341032;ENST00000263285;ENST00000542780;ENST00000368039;ENST00000392203;ENST00000368037	T;T;T	0.69040	1.94;1.94;-0.37	4.04	-3.83	0.04269	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	2.728910	0.01644	N	0.024208	T	0.74658	0.3745	M	0.88842	2.985	0.09310	N	0.999996	D;D;D;D;D;D	0.89917	0.999;0.971;0.997;0.999;1.0;0.999	D;B;D;D;D;D	0.72338	0.974;0.445;0.916;0.952;0.963;0.977	T	0.64058	-0.6496	10	0.72032	D	0.01	0.1092	9.8667	0.41148	0.0:0.3566:0.0:0.6434	.	88;48;88;88;88;88	B4E0J5;Q5VYH9;E7EME5;Q9HBG7-2;Q9HBG7;Q6P2J4	.;.;.;.;LY9_HUMAN;.	D	88;88;88;88;88;48;48	ENSP00000342921:A88D;ENSP00000263285:A88D;ENSP00000357018:A88D	ENSP00000263285:A88D	A	+	2	0	LY9	159036305	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.516000	0.02250	-1.036000	0.03287	-0.253000	0.11424	GCT	.	.		0.488	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348		A	160769681	C	A	160769681	3	1	96	1	0	0	0	0	1	0	0	0	9110	797	28	3	269	3	LY9	1	160769681	Missense_Mutation	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	8584044	160769681	88480940	6	13215										
DARS2	55157	hgsc.bcm.edu	37	chr1	173825830	173825830	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	gtgaaaatgctctcccatctGctccaggctttagattatgg	9	10	2	2			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr1:173825830G>A	ENST00000361951.4	+	16	2428	c.1701G>A	c.(1699-1701)ctG>ctA	p.L567L	DARS2_ENST00000239457.5_Silent_p.L112L|DARS2_ENST00000471476.1_3'UTR	NM_018122.4	NP_060592.2	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial	567					gene expression (GO:0010467)|mitochondrial asparaginyl-tRNA aminoacylation (GO:0070145)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aspartate-tRNA ligase activity (GO:0004815)|aspartate-tRNA(Asn) ligase activity (GO:0050560)|ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)			breast(4)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	30					L-Aspartic Acid(DB00128)	TCTCCCATCTGCTCCAGGCTT	0.393																																					p.L567L		Atlas-SNP	.											.	DARS2	61	.	0			c.G1701A						.						86	87	87					1																	173825830		2203	4300	6503	SO:0001819	synonymous_variant	55157	exon16			CCATCTGCTCCAG	AK022754	CCDS1311.1	1q25.1	2011-07-01	2007-02-23		ENSG00000117593	ENSG00000117593	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	25538	protein-coding gene	gene with protein product	"aspartate tRNA ligase 2, mitochondrial"	610956				15779907	Standard	NM_018122		Approved	FLJ10514	uc001gjh.2	Q6PI48	OTTHUMG00000034803	ENST00000361951.4:c.1701G>A	chr1.hg19:g.173825830G>A		58.0	0.0		107.0	8.0	NM_018122		Silent	SNP	ENST00000361951.4	hg19	CCDS1311.1																																																																																			.	.		0.393	DARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084220.1	NM_018122		A	173825830	G	A	173825830	2	1	96	1	0	0	0	0	0	0	0	1	4244	1306	46	3		3	DARS2	1	173825830	Silent	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	13056149	173825830	75424791	7	13216										
NUAK2	81788	hgsc.bcm.edu	37	chr1	205290713	205290713	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	gccgggctagctctgcggccGagggagtggggccggagcgc	21	12	1	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr1:205290713G>A	ENST00000367157.3	-	1	170	c.44C>T	c.(43-45)tCg>tTg	p.S15L		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CTCTGCGGCCGAGGGAGTGGG	0.677																																					p.S15L		Atlas-SNP	.											.	NUAK2	107	.	0			c.C44T						.						20	25	23					1																	205290713		2202	4299	6501	SO:0001583	missense	81788	exon1			GCGGCCGAGGGAG	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"SNF1/AMP activated protein kinase"	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.44C>T	chr1.hg19:g.205290713G>A	ENSP00000356125:p.Ser15Leu	55.0	0.0		81.0	21.0	NM_030952		Missense_Mutation	SNP	ENST00000367157.3	hg19	CCDS1453.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.205675	0.58234	.	.	ENSG00000163545	ENST00000367157	T	0.72394	-0.65	4.68	3.76	0.43208	.	0.730137	0.11212	N	0.587637	T	0.57315	0.2045	L	0.27053	0.805	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.51276	-0.8726	10	0.62326	D	0.03	.	8.4669	0.32962	0.1051:0.0:0.8949:0.0	.	15	Q9H093	NUAK2_HUMAN	L	15	ENSP00000356125:S15L	ENSP00000356125:S15L	S	-	2	0	NUAK2	203557336	0.255000	0.24002	0.617000	0.29091	0.224000	0.24922	1.438000	0.35002	1.197000	0.43143	0.561000	0.74099	TCG	.	.		0.677	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		A	205290713	G	A	205290713	3	1	96	1	0	0	0	0	1	0	0	0	10722	1059	37	1	1870	1	NUAK2	1	205290713	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	31464883	205290713	43959908	8	13217										
RYR2	6262	hgsc.bcm.edu	37	chr1	237893654	237893654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	ataaactgatagaagatttaGcagtatgtttttagtggggc	11	3	0	3			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr1:237893654G>A	ENST00000366574.2	+	77	11250	c.10933G>A	c.(10933-10935)Gca>Aca	p.A3645T	RYR2_ENST00000542537.1_Missense_Mutation_p.A3629T|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Missense_Mutation_p.A3643T	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3645					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGAAGATTTAGCAGTATGTTT	0.378																																					p.A3645T		Atlas-SNP	.											RYR2,NS,chondrosarcoma,0,1	RYR2	1273	.	0			c.G10933A						.						53	51	51					1																	237893654		1842	4098	5940	SO:0001583	missense	6262	exon77			GATTTAGCAGTAT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.10933G>A	chr1.hg19:g.237893654G>A	ENSP00000355533:p.Ala3645Thr	91.0	0.0		144.0	17.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	11.32	1.605009	0.28623	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.96427	-4.01;-4.0;-4.0	5.52	5.52	0.82312	.	0.188612	0.32015	N	0.006710	D	0.89832	0.6829	N	0.11789	0.175	0.80722	D	1	B;B	0.23540	0.005;0.087	B;B	0.25884	0.004;0.064	D	0.85251	0.1044	10	0.02654	T	1	-16.0419	14.6196	0.68574	0.0:0.0:0.8542:0.1458	.	600;3645	B4DGV4;Q92736	.;RYR2_HUMAN	T	3645;3643;3629;600	ENSP00000355533:A3645T;ENSP00000353174:A3643T;ENSP00000443798:A3629T	ENSP00000353174:A3643T	A	+	1	0	RYR2	235960277	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.755000	0.85180	2.757000	0.94681	0.585000	0.79938	GCA	.	.		0.378	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237893654	G	A	237893654	3	1	96	1	0	0	0	0	1	0	0	0	13784	971	34	3	11239	3	RYR2	1	237893654	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	32602941	237893654	11356967	9	13218										
MSH2	4436	hgsc.bcm.edu	37	chr2	47707967	47707993	+	In_Frame_Del	DEL	ATATCATGGAACCAGCAGCAAAGAAGT	ATATCATGGAACCAGCAGCAAAGAAGT	-													0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tggagaatcgcaaggatatgAtatcatggaaccagcagcaa					rs587780686|rs63750709|rs549759248|rs587782214|rs587779151|rs63751400|rs63750795|rs547695133	byFrequency	TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	ATATCATGGAACCAGCAGCAAAGAAGT	ATATCATGGAACCAGCAGCAAAGAAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr2:47707967_47707993delATATCATGGAACCAGCAGCAAAGAAGT	ENST00000233146.2	+	15	2814_2840	c.2591_2617delATATCATGGAACCAGCAGCAAAGAAGT	c.(2590-2619)gatatcatggaaccagcagcaaagaagtgc>ggc	p.864_873DIMEPAAKKC>G	MSH2_ENST00000543555.1_In_Frame_Del_p.798_807DIMEPAAKKC>G|MSH2_ENST00000461394.1_3'UTR|MSH2_ENST00000406134.1_In_Frame_Del_p.864_873DIMEPAAKKC>G	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	864			A -> G (in gastric cancer; unknown pathological significance). {ECO:0000269|PubMed:12132870}.|C -> G (in gastric cancer; unknown pathological significance). {ECO:0000269|PubMed:12132870}.|P -> A (in gastric cancer; unknown pathological significance). {ECO:0000269|PubMed:12132870}.		ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)|p.E867E(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CAAGGATATGATATCATGGAACCAGCAGCAAAGAAGTGCTATCTGGA	0.374			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.864_872del		Atlas-Indel,Pindel	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	5	Whole gene deletion(2)|Unknown(2)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)|kidney(1)	c.2590_2616del	GRCh37	CD011643|CM015041|CM015042|CM015043	MSH2	D|M		.																																			SO:0001651	inframe_deletion	4436	exon15	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	.	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.2591_2617delATATCATGGAACCAGCAGCAAAGAAGT	chr2.hg19:g.47707967_47707993delATATCATGGAACCAGCAGCAAAGAAGT	ENSP00000233146:p.Asp864_Cys873delinsGly	183.0	0.0		147.0	18.0	NM_000251	B4E2Z2|O75488	In_Frame_Del	DEL	ENST00000233146.2	hg19	CCDS1834.1																																																																																			.	.		0.374	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			-	47707993	ATATCATGGAACCAGCAGCAAAGAAGT	-	47707967	7	5	96	1	0	1	0	1	0	0	0	0	9879	333	12	0	2649	0	MSH2	2	47707967	In_Frame_Del	DEL	ATATCATGGAACCAGCAGCAAAGAAGT	TCGA-DD-A1E9-01A-21D-A152-10		47707967	195491406	10	13219										
INO80B	83444	hgsc.bcm.edu	37	chr2	74683301	74683301	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tagggggtcaggaggaagagGaggaacagaggtggctggat	21	3	1	2			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr2:74683301G>A	ENST00000233331.7	+	4	536	c.442G>A	c.(442-444)Gag>Aag	p.E148K	WBP1_ENST00000233615.2_5'Flank|WBP1_ENST00000393972.3_5'Flank|INO80B_ENST00000469849.1_3'UTR|INO80B_ENST00000409917.1_Missense_Mutation_p.E148K|WBP1_ENST00000409737.1_5'Flank	NM_031288.3	NP_112578.2	Q9C086	IN80B_HUMAN	INO80 complex subunit B	148	Poly-Glu.				chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	13						GGAGGAAGAGGAGGAACAGAG	0.532																																					p.E148K		Atlas-SNP	.											.	INO80B	37	.	0			c.G442A						.						117	110	113					2																	74683301		2203	4300	6503	SO:0001583	missense	83444	exon4			GAAGAGGAGGAAC	AB054538	CCDS1942.2	2p13.1	2011-07-06	2008-08-07	2008-08-07	ENSG00000115274	ENSG00000115274		"Zinc fingers, HIT-type", "INO80 complex subunits"	13324	protein-coding gene	gene with protein product	"PAP-1 binding protein", "IES2 homolog (S. cerevisiae)"		"high mobility group AT-hook 1-like 4", "zinc finger, HIT type 4"	HMGA1L4, ZNHIT4		16230350	Standard	NM_031288		Approved	HMGIYL4, PAPA-1, hIes2, PAP-1BP, IES2	uc002slg.3	Q9C086	OTTHUMG00000129959	ENST00000233331.7:c.442G>A	chr2.hg19:g.74683301G>A	ENSP00000233331:p.Glu148Lys	240.0	0.0		257.0	19.0	NM_031288		Missense_Mutation	SNP	ENST00000233331.7	hg19	CCDS1942.2	.	.	.	.	.	.	.	.	.	.	G	35	5.460970	0.96240	.	.	ENSG00000115274	ENST00000233331;ENST00000431187;ENST00000409917;ENST00000409493	T;T;T;T	0.58797	0.54;0.38;0.31;0.37	5.65	5.65	0.86999	.	0.000000	0.56097	D	0.000028	T	0.71995	0.3406	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.69078	0.997;0.993;0.993;0.988	D;D;D;D	0.75020	0.985;0.968;0.956;0.981	T	0.68830	-0.5305	10	0.33940	T	0.23	-32.2379	15.2215	0.73313	0.0:0.0:1.0:0.0	.	166;133;148;148	B4DJ31;B4DJ22;Q9C086;B8ZZ93	.;.;IN80B_HUMAN;.	K	148;133;148;153	ENSP00000233331:E148K;ENSP00000389887:E133K;ENSP00000387267:E148K;ENSP00000386937:E153K	ENSP00000233331:E148K	E	+	1	0	INO80B	74536809	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.964000	0.93389	2.666000	0.90696	0.555000	0.69702	GAG	.	.		0.532	INO80B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252223.2	NM_031288		A	74683301	G	A	74683301	3	1	96	1	0	0	0	0	1	0	0	0	7756	1175	41	3	456	3	INO80B	2	74683301	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	26975334	74683301	168516072	11	13220										
IWS1	55677	hgsc.bcm.edu	37	chr2	128247508	128247508	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	ggtaagaccaaatataggccTagaccactcatctgtagtaa	8	9	2	2			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr2:128247508T>A	ENST00000295321.4	-	11	2318	c.2059A>T	c.(2059-2061)Agg>Tgg	p.R687W	AC010976.2_ENST00000599001.1_RNA|AC010976.2_ENST00000454503.2_RNA|AC010976.2_ENST00000595561.1_RNA|AC010976.2_ENST00000596439.1_RNA|AC010976.2_ENST00000598065.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	687	Interaction with SUPT6H and ALYREF.|TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		AATATAGGCCTAGACCACTCA	0.373																																					p.R687W		Atlas-SNP	.											.	IWS1	61	.	0			c.A2059T						.						283	259	267					2																	128247508		2203	4300	6503	SO:0001583	missense	55677	exon11			TAGGCCTAGACCA	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.2059A>T	chr2.hg19:g.128247508T>A	ENSP00000295321:p.Arg687Trp	357.0	0.0		391.0	50.0	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	hg19	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	T	19.15	3.771756	0.69992	.	.	ENSG00000163166	ENST00000295321;ENST00000433551	T	0.70164	-0.46	5.03	4.14	0.48551	Transcription factor IIS, N-terminal (3);	0.000000	0.85682	D	0.000000	D	0.83839	0.5341	M	0.89163	3.01	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87064	0.2155	10	0.87932	D	0	-6.0033	14.5147	0.67811	0.0:0.0:0.8461:0.1539	.	687	Q96ST2	IWS1_HUMAN	W	687;640	ENSP00000295321:R687W	ENSP00000295321:R687W	R	-	1	2	IWS1	127963978	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	3.041000	0.49807	1.088000	0.41272	-0.445000	0.05633	AGG	.	.		0.373	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		A	128247508	T	A	128247508	3	1	96	1	0	0	0	0	1	0	0	0	7940	1521	53	4	416	4	IWS1	2	128247508	Missense_Mutation	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10	53564207	128247508	114951865	12	13221										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160194151	160194151	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	ggggttgtcactcttccgttCtagtgcatgtgcactgcttt	11	10	3	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr2:160194151C>G	ENST00000392783.2	-	32	6082	c.5587G>C	c.(5587-5589)Gaa>Caa	p.E1863Q	BAZ2B_ENST00000392782.1_Missense_Mutation_p.E1827Q|BAZ2B_ENST00000355831.2_Missense_Mutation_p.E1829Q|BAZ2B_ENST00000343439.5_Missense_Mutation_p.E1763Q	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1863					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CTCTTCCGTTCTAGTGCATGT	0.438																																					p.E1863Q		Atlas-SNP	.											.	BAZ2B	196	.	0			c.G5587C						.						180	179	179					2																	160194151		1941	4145	6086	SO:0001583	missense	29994	exon32			TCCGTTCTAGTGC	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.5587G>C	chr2.hg19:g.160194151C>G	ENSP00000376534:p.Glu1863Gln	169.0	0.0		185.0	28.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	14.14	2.445224	0.43429	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000426648	T;T;T;T	0.58652	0.41;0.38;0.41;0.32	5.78	5.78	0.91487	.	0.201250	0.23906	U	0.043384	T	0.49541	0.1563	L	0.43152	1.355	0.48341	D	0.999637	B;P	0.45531	0.277;0.86	B;B	0.35813	0.122;0.211	T	0.47459	-0.9116	10	0.24483	T	0.36	-5.0357	20.0022	0.97423	0.0:1.0:0.0:0.0	.	1827;1863	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	Q	1827;1863;1829;1763;81	ENSP00000376533:E1827Q;ENSP00000376534:E1863Q;ENSP00000348087:E1829Q;ENSP00000339670:E1763Q	ENSP00000339670:E1763Q	E	-	1	0	BAZ2B	159902397	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	2.462000	0.45049	2.738000	0.93877	0.655000	0.94253	GAA	.	.		0.438	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			G	160194151	C	G	160194151	3	3	96	1	0	0	0	0	1	0	0	0	1332	922	32	4	943	4	BAZ2B	2	160194151	Missense_Mutation	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	31946643	160194151	83005222	13	13222										
PLCD4	84812	hgsc.bcm.edu	37	chr2	219501200	219501200	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	cctgccccttccaggttaccGccacattcacctgctgtcca	6	19	1	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr2:219501200G>A	ENST00000450993.2	+	16	2528	c.2189G>A	c.(2188-2190)cGc>cAc	p.R730H	RP11-548H3.1_ENST00000607946.1_RNA|PLCD4_ENST00000417849.1_Missense_Mutation_p.R730H|PLCD4_ENST00000432688.1_Missense_Mutation_p.R762H	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	730					acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CCAGGTTACCGCCACATTCAC	0.582																																					p.R730H		Atlas-SNP	.											.	PLCD4	51	.	0			c.G2189A						.						77	82	80					2																	219501200		2058	4188	6246	SO:0001583	missense	84812	exon16			GTTACCGCCACAT	AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"EF-hand domain containing"	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.2189G>A	chr2.hg19:g.219501200G>A	ENSP00000388631:p.Arg730His	117.0	0.0		112.0	31.0	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	hg19	CCDS46516.1	.	.	.	.	.	.	.	.	.	.	G	33	5.262612	0.95399	.	.	ENSG00000115556	ENST00000450993;ENST00000417849;ENST00000432688	T;T;T	0.15256	2.44;2.44;2.44	5.17	5.17	0.71159	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.48607	0.1509	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.50988	-0.8762	10	0.51188	T	0.08	.	18.8753	0.92332	0.0:0.0:1.0:0.0	.	730	Q9BRC7	PLCD4_HUMAN	H	730;730;762	ENSP00000388631:R730H;ENSP00000396942:R730H;ENSP00000396185:R762H	ENSP00000396942:R730H	R	+	2	0	PLCD4	219209444	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.541000	0.98083	2.692000	0.91855	0.655000	0.94253	CGC	.	.		0.582	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1			A	219501200	G	A	219501200	3	1	96	1	0	0	0	0	1	0	0	0	12042	1087	38	1	2247	1	PLCD4	2	219501200	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	59307049	219501200	23698173	14	13223										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129286593	129286593	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	atctcctccatctgcagcagCgtcttctgccagtaacgctc	7	16	4	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr3:129286593C>A	ENST00000324093.4	-	21	4099	c.3921G>T	c.(3919-3921)acG>acT	p.T1307T	PLXND1_ENST00000393239.1_Silent_p.T1307T	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1307					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						TCTGCAGCAGCGTCTTCTGCC	0.602																																					p.T1307T	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.G3921T						.						67	59	61					3																	129286593		2203	4300	6503	SO:0001819	synonymous_variant	23129	exon21			CAGCAGCGTCTTC	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.3921G>T	chr3.hg19:g.129286593C>A		64.0	0.0		35.0	5.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	hg19	CCDS33854.1																																																																																			.	.		0.602	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		A	129286593	C	A	129286593	2	1	96	1	0	0	0	0	0	0	0	1	12136	755	27	1		1	PLXND1	3	129286593	Silent	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10		129286593	68735837	15	13224										
ALB	213	hgsc.bcm.edu	37	chr4	74283866	74283866	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	aacgccagtaagtgacagagTcaccaaatgctgcacagaat	9	10	1	3			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr4:74283866T>A	ENST00000503124.1	+	10	1247	c.1040T>A	c.(1039-1041)gTc>gAc	p.V347D	ALB_ENST00000401494.3_Missense_Mutation_p.V382D|ALB_ENST00000415165.2_Missense_Mutation_p.V305D|ALB_ENST00000295897.4_Missense_Mutation_p.V497D|ALB_ENST00000509063.1_Missense_Mutation_p.V497D|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGTGACAGAGTCACCAAATGC	0.453																																					p.V497D		Atlas-SNP	.											.	ALB	132	.	0			c.T1490A						.						108	101	103					4																	74283866		2203	4300	6503	SO:0001583	missense	213	exon12			ACAGAGTCACCAA	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1040T>A	chr4.hg19:g.74283866T>A	ENSP00000421027:p.Val347Asp	90.0	0.0		104.0	24.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.42|16.42	3.118606|3.118606	0.56505|0.56505	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000511370|ENST00000295897;ENST00000415165;ENST00000329326;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202	.|T;T;T;T;T	.|0.74526	.|-0.85;-0.85;-0.85;-0.85;-0.85	5.94|5.94	5.94|5.94	0.96194|0.96194	.|Serum albumin-like (1);Serum albumin, N-terminal (3);	.|0.258665	.|0.32430	.|N	.|0.006101	D|D	0.88269|0.88269	0.6391|0.6391	M|M	0.88979|0.88979	2.995|2.995	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|0.999;1.0;0.999;1.0;1.0	D|D	0.90320|0.90320	0.4344|0.4344	5|10	.|0.87932	.|D	.|0	-11.5788|-11.5788	15.2238|15.2238	0.73333|0.73333	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|382;305;347;497;497	.|B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768	.|.;.;.;.;ALBU_HUMAN	R|D	341|497;305;284;347;497;382;506	.|ENSP00000295897:V497D;ENSP00000401820:V305D;ENSP00000421027:V347D;ENSP00000422784:V497D;ENSP00000384695:V382D	.|ENSP00000295897:V497D	S|V	+|+	3|2	2|0	ALB|ALB	74502730|74502730	0.966000|0.966000	0.33281|0.33281	0.857000|0.857000	0.33713|0.33713	0.194000|0.194000	0.23727|0.23727	4.628000|4.628000	0.61282|0.61282	2.275000|2.275000	0.75901|0.75901	0.528000|0.528000	0.53228|0.53228	AGT|GTC	.	.		0.453	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		A	74283866	T	A	74283866	3	1	96	1	0	0	0	0	1	0	0	0	486	1667	58	4	1536	4	ALB	4	74283866	Missense_Mutation	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10		74283866	116870410	16	13225										
USP38	84640	hgsc.bcm.edu	37	chr4	144107245	144107245	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	gccgagcctgccacactactGccttccctgcaagaagtttt	8	15	0	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr4:144107245G>A	ENST00000307017.4	+	1	1148	c.642G>A	c.(640-642)ctG>ctA	p.L214L	RP11-284M14.1_ENST00000507826.1_RNA|USP38_ENST00000510377.1_Silent_p.L214L|RP11-284M14.1_ENST00000507486.1_RNA	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	214					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					CCACACTACTGCCTTCCCTGC	0.458																																					p.L214L		Atlas-SNP	.											.	USP38	92	.	0			c.G642A						.						64	68	67					4																	144107245		2203	4300	6503	SO:0001819	synonymous_variant	84640	exon1			ACTACTGCCTTCC	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.642G>A	chr4.hg19:g.144107245G>A		124.0	0.0		126.0	33.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Silent	SNP	ENST00000307017.4	hg19	CCDS3758.1																																																																																			.	.		0.458	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		A	144107245	G	A	144107245	2	1	96	1	0	0	0	0	0	0	0	1	17084	1306	46	3		3	USP38	4	144107245	Silent	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	69823379	144107245	47047031	17	13226										
NR3C2	4306	hgsc.bcm.edu	37	chr4	149357349	149357349	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tgggctgtgcactggaaaacTgccaaagctggctgtggtgg	16	8	0	0	rs374672844		TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr4:149357349T>A	ENST00000358102.3	-	2	1026	c.664A>T	c.(664-666)Agt>Tgt	p.S222C	NR3C2_ENST00000355292.3_Missense_Mutation_p.S222C|NR3C2_ENST00000344721.4_Missense_Mutation_p.S222C|NR3C2_ENST00000511528.1_Missense_Mutation_p.S222C|NR3C2_ENST00000512865.1_Missense_Mutation_p.S222C	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	222	Modulating.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	ACTGGAAAACTGCCAAAGCTG	0.542																																					p.S222C	Melanoma(27;428 957 40335 51025 51111)	Atlas-SNP	.											.	NR3C2	94	.	0			c.A664T						.	T	CYS/SER,CYS/SER	0,4406		0,0,2203	52	55	54		664,664	4.9	1	4		54	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	NR3C2	NM_001166104.1,NM_000901.4	112,112	0,1,6502	AA,AT,TT		0.0116,0.0,0.0077	benign,benign	222/868,222/985	149357349	1,13005	2203	4300	6503	SO:0001583	missense	4306	exon2			GAAAACTGCCAAA	M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.664A>T	chr4.hg19:g.149357349T>A	ENSP00000350815:p.Ser222Cys	60.0	0.0		68.0	13.0	NM_001166104	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Missense_Mutation	SNP	ENST00000358102.3	hg19	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	T	7.106	0.575095	0.13623	0.0	1.16E-4	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000544252;ENST00000342437;ENST00000511528	D;D;D;D;D;D	0.90004	-2.6;-2.6;-2.6;-2.19;-2.2;-2.6	4.86	4.86	0.63082	.	0.851640	0.11115	N	0.598089	T	0.81254	0.4784	N	0.19112	0.55	0.21697	N	0.999583	P;B	0.40000	0.698;0.153	B;B	0.35073	0.159;0.195	T	0.70153	-0.4950	9	.	.	.	.	14.7379	0.69430	0.0:0.0:0.0:1.0	.	222;222	B0ZBF5;B0ZBF6	.;.	C	222	ENSP00000341390:S222C;ENSP00000347441:S222C;ENSP00000350815:S222C;ENSP00000423510:S222C;ENSP00000343907:S222C;ENSP00000421481:S222C	.	S	-	1	0	NR3C2	149576799	1.000000	0.71417	0.970000	0.41538	0.914000	0.54420	2.595000	0.46197	1.937000	0.56155	0.482000	0.46254	AGT	.	.		0.542	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			A	149357349	T	A	149357349	3	1	96	1	0	0	0	0	1	0	0	0	10640	1580	55	4	2322	4	NR3C2	4	149357349	Missense_Mutation	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10	5250104	149357349	41796927	18	13227										
PRR16	51334	hgsc.bcm.edu	37	chr5	120021723	120021723	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	actgacagctccaaaacggaCacgctgaatagtagctcaag	9	11	1	2			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr5:120021723C>A	ENST00000407149.2	+	2	443	c.234C>A	c.(232-234)gaC>gaA	p.D78E	PRR16_ENST00000505123.1_Missense_Mutation_p.D8E|PRR16_ENST00000379551.2_Missense_Mutation_p.D55E|PRR16_ENST00000446965.1_Missense_Mutation_p.D8E			Q569H4	LARGN_HUMAN	proline rich 16	78					positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CCAAAACGGACACGCTGAATA	0.507																																					p.D55E		Atlas-SNP	.											.	PRR16	71	.	0			c.C165A						.						112	102	105					5																	120021723		2203	4300	6503	SO:0001583	missense	51334	exon3			AACGGACACGCTG	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.234C>A	chr5.hg19:g.120021723C>A	ENSP00000385118:p.Asp78Glu	71.0	0.0		97.0	24.0	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Missense_Mutation	SNP	ENST00000407149.2	hg19		.	.	.	.	.	.	.	.	.	.	C	18.03	3.531268	0.64972	.	.	ENSG00000184838	ENST00000407149;ENST00000379551;ENST00000509923;ENST00000505123;ENST00000446965	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	5.46	3.31	0.37934	.	0.000000	0.85682	D	0.000000	T	0.62962	0.2471	M	0.61703	1.905	0.50313	D	0.999869	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.63238	-0.6682	9	.	.	.	-0.035	12.4978	0.55937	0.0:0.8316:0.0:0.1684	.	78;55	Q569H4;Q569H4-3	PRR16_HUMAN;.	E	78;55;8;8;8	ENSP00000385118:D78E;ENSP00000368869:D55E;ENSP00000421256:D8E;ENSP00000423446:D8E;ENSP00000405491:D8E	.	D	+	3	2	PRR16	120049622	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.999000	0.49473	1.276000	0.44395	0.555000	0.69702	GAC	.	.		0.507	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644		A	120021723	C	A	120021723	3	1	96	1	0	0	0	0	1	0	0	0	12601	477	17	3	171	3	PRR16	5	120021723	Missense_Mutation	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10		120021723	60893537	19	13228										
GFOD1	54438	hgsc.bcm.edu	37	chr6	13365402	13365402	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	cggctgagcccaccacagtgAcatcctgcttgaactcgccg	10	16	0	3			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr6:13365402A>G	ENST00000379287.3	-	2	1410	c.746T>C	c.(745-747)gTc>gCc	p.V249A	GFOD1_ENST00000379284.1_Missense_Mutation_p.V146A	NM_018988.3	NP_061861.1	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain containing 1	249						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)	18	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)			CACCACAGTGACATCCTGCTT	0.672																																					p.V249A		Atlas-SNP	.											.	GFOD1	38	.	0			c.T746C						.						37	37	37					6																	13365402		2203	4300	6503	SO:0001583	missense	54438	exon2			ACAGTGACATCCT	AK000337	CCDS4524.1, CCDS56397.1, CCDS64351.1	6p24.1-p23	2013-09-19			ENSG00000145990	ENSG00000145990			21096	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 114"	C6orf114			Standard	NM_018988		Approved	FLJ20330, ADG-90	uc003nat.2	Q9NXC2	OTTHUMG00000014276	ENST00000379287.3:c.746T>C	chr6.hg19:g.13365402A>G	ENSP00000368589:p.Val249Ala	38.0	0.0		38.0	10.0	NM_018988	A8E4L6|Q5T058|Q96JD4|Q9H5K2	Missense_Mutation	SNP	ENST00000379287.3	hg19	CCDS4524.1	.	.	.	.	.	.	.	.	.	.	A	18.66	3.672251	0.67928	.	.	ENSG00000145990	ENST00000379287;ENST00000379284	T;T	0.44881	0.91;0.91	5.73	5.73	0.89815	.	0.120685	0.53938	D	0.000044	T	0.31702	0.0805	M	0.66297	2.02	0.80722	D	1	B	0.30634	0.288	B	0.30716	0.119	T	0.27839	-1.0062	10	0.56958	D	0.05	-28.9863	15.2091	0.73206	1.0:0.0:0.0:0.0	.	249	Q9NXC2	GFOD1_HUMAN	A	249;146	ENSP00000368589:V249A;ENSP00000368586:V146A	ENSP00000368586:V146A	V	-	2	0	GFOD1	13473381	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.335000	0.96500	2.173000	0.68751	0.528000	0.53228	GTC	.	.		0.672	GFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039902.1	NM_018988		G	13365402	A	G	13365402	3	3	96	1	0	0	0	0	1	0	0	0	6351	275	10	2	430	2	GFOD1	6	13365402	Missense_Mutation	SNP	A	TCGA-DD-A1E9-01A-21D-A152-10		13365402	157749665	20	13229										
C6orf62	81688	hgsc.bcm.edu	37	chr6	24714631	24714631	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	caatatcattccgaggccaaAgaatgaaatccatctcctga	6	11	2	3			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr6:24714631A>C	ENST00000378119.4	-	3	2511	c.344T>G	c.(343-345)cTt>cGt	p.L115R	C6orf62_ENST00000540769.1_Missense_Mutation_p.L57R|C6orf62_ENST00000378102.3_Missense_Mutation_p.L86R	NM_030939.4	NP_112201.1	Q9GZU0	CF062_HUMAN	chromosome 6 open reading frame 62	115						intracellular (GO:0005622)				endometrium(2)|kidney(3)|large_intestine(2)|lung(3)	10						CCGAGGCCAAAGAATGAAATC	0.348																																					p.L115R		Atlas-SNP	.											.	C6orf62	18	.	0			c.T344G						.						74	76	76					6																	24714631		2203	4300	6503	SO:0001583	missense	81688	exon3			GGCCAAAGAATGA	AL136632	CCDS4559.1	6p22.1	2011-12-13			ENSG00000112308	ENSG00000112308			20998	protein-coding gene	gene with protein product	"HBV X-transactivated protein 12"					11230166	Standard	NM_030939		Approved	FLJ12619, DKFZP564G182, XTP12	uc003nel.3	Q9GZU0	OTTHUMG00000014361	ENST00000378119.4:c.344T>G	chr6.hg19:g.24714631A>C	ENSP00000367359:p.Leu115Arg	187.0	0.0		143.0	29.0	NM_030939	Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2	Missense_Mutation	SNP	ENST00000378119.4	hg19	CCDS4559.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.981413	0.93044	.	.	ENSG00000112308	ENST00000378119;ENST00000540769;ENST00000378102	T;T;T	0.45668	0.89;0.89;0.89	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.41696	0.1170	N	0.19112	0.55	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.51537	-0.8693	10	0.87932	D	0	-7.733	16.1413	0.81528	1.0:0.0:0.0:0.0	.	115	Q9GZU0	CF062_HUMAN	R	115;57;86	ENSP00000367359:L115R;ENSP00000446225:L57R;ENSP00000367342:L86R	ENSP00000367342:L86R	L	-	2	0	C6orf62	24822610	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.244000	0.95423	2.270000	0.75569	0.482000	0.46254	CTT	.	.		0.348	C6orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040017.1	NM_030939		C	24714631	A	C	24714631	3	2	96	1	0	0	0	0	1	0	0	0	2370	72	3	5	357	5	C6orf62	6	24714631	Missense_Mutation	SNP	A	TCGA-DD-A1E9-01A-21D-A152-10	11349229	24714631	146400436	21	13230										
LRFN2	57497	hgsc.bcm.edu	37	chr6	40400289	40400289	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tctgcaaaggtgccctcggcGatgtgatccagcaggttgtg	14	10	1	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr6:40400289G>A	ENST00000338305.6	-	2	1106	c.564C>T	c.(562-564)atC>atT	p.I188I		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	188						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					TGCCCTCGGCGATGTGATCCA	0.622																																					p.I188I		Atlas-SNP	.											.	LRFN2	133	.	0			c.C564T						.						87	88	88					6																	40400289		2203	4300	6503	SO:0001819	synonymous_variant	57497	exon2			CTCGGCGATGTGA	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	21226	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 2"	612808	"KIAA1246"	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.564C>T	chr6.hg19:g.40400289G>A		101.0	0.0		76.0	13.0	NM_020737	A5PKU3|Q5SYP9	Silent	SNP	ENST00000338305.6	hg19	CCDS34443.1																																																																																			.	.		0.622	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		A	40400289	G	A	40400289	2	1	96	1	0	0	0	0	0	0	0	1	8947	1048	37	1		1	LRFN2	6	40400289	Silent	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	15685658	40400289	130714778	22	13231										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7571282	7571282	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	gagaaggtaccttgccctatTaaattcatagacttgacctt	7	9	1	3			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr7:7571282T>A	ENST00000399429.3	-	3	518	c.378A>T	c.(376-378)ttA>ttT	p.L126F		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	126	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CTTGCCCTATTAAATTCATAG	0.438																																					p.L126F		Atlas-SNP	.											.	COL28A1	113	.	0			c.A378T						.						77	70	72					7																	7571282		1885	4113	5998	SO:0001583	missense	340267	exon3			CCCTATTAAATTC	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.378A>T	chr7.hg19:g.7571282T>A	ENSP00000382356:p.Leu126Phe	106.0	0.0		168.0	59.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	hg19	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	T	7.535	0.659402	0.14645	.	.	ENSG00000215018	ENST00000399429;ENST00000399419;ENST00000448652	T	0.55234	0.53	4.2	-3.54	0.04653	von Willebrand factor, type A (3);	0.539313	0.17218	N	0.182452	T	0.19685	0.0473	N	0.02539	-0.55	0.26904	N	0.967057	B	0.02656	0.0	B	0.04013	0.001	T	0.14420	-1.0473	10	0.25751	T	0.34	5.6329	7.0137	0.24877	0.0768:0.0892:0.5766:0.2574	.	126	Q2UY09	COSA1_HUMAN	F	126	ENSP00000382356:L126F	ENSP00000382347:L126F	L	-	3	2	COL28A1	7537807	0.987000	0.35691	0.909000	0.35828	0.763000	0.43281	0.418000	0.21230	-0.874000	0.04027	-0.313000	0.08912	TTA	.	.		0.438	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		A	7571282	T	A	7571282	3	1	96	1	0	0	0	0	1	0	0	0	3688	1751	61	4	3131	4	COL28A1	7	7571282	Missense_Mutation	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10		7571282	151567381	23	13232										
COBL	23242	hgsc.bcm.edu	37	chr7	51095517	51095517	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	acaacaggtttgaattttttCttcggcccaaaaatgctggg	9	8	1	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr7:51095517C>T	ENST00000265136.7	-	10	3441	c.3276G>A	c.(3274-3276)aaG>aaA	p.K1092K	COBL_ENST00000395542.2_Silent_p.K1174K	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1092					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TGAATTTTTTCTTCGGCCCAA	0.488																																					p.K1092K	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.G3276A						.						170	156	160					7																	51095517		2203	4300	6503	SO:0001819	synonymous_variant	23242	exon10			TTTTTTCTTCGGC	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3276G>A	chr7.hg19:g.51095517C>T		397.0	1.0		346.0	116.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	hg19	CCDS34637.1																																																																																			.	.		0.488	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		T	51095517	C	T	51095517	2	4	96	1	0	0	0	0	0	0	0	1	3655	912	32	3		3	COBL	7	51095517	Silent	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	43524235	51095517	108043146	24	13233										
PCLO	27445	hgsc.bcm.edu	37	chr7	82595462	82595462	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	attagttttttttcttcaggGagtggctttttttcttgaag	9	4	3	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr7:82595462G>A	ENST00000333891.9	-	4	3979	c.3642C>T	c.(3640-3642)ctC>ctT	p.L1214L	PCLO_ENST00000423517.2_Silent_p.L1214L	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTTCTTCAGGGAGTGGCTTTT	0.368																																					p.L1214L		Atlas-SNP	.											.	PCLO	1506	.	0			c.C3642T						.						166	157	160					7																	82595462		1798	4072	5870	SO:0001819	synonymous_variant	27445	exon4			TTCAGGGAGTGGC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.3642C>T	chr7.hg19:g.82595462G>A		785.0	2.0		843.0	325.0	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.368	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82595462	G	A	82595462	2	1	96	1	0	0	0	0	0	0	0	1	11592	1161	41	3		3	PCLO	7	82595462	Silent	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	31499945	82595462	76543201	25	13234										
PTCD1	26024	hgsc.bcm.edu	37	chr7	99030913	99030913	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	acatgcacctggttgtagagGttgaaggccttcttcaggta	12	8	2	2			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr7:99030913G>C	ENST00000292478.4	-	3	832	c.582C>G	c.(580-582)aaC>aaG	p.N194K	ATP5J2-PTCD1_ENST00000437572.1_5'Flank|PTCD1_ENST00000555673.1_Missense_Mutation_p.N243K|PTCD1_ENST00000485746.1_5'UTR|ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.N243K	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	194					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			GGTTGTAGAGGTTGAAGGCCT	0.607																																					p.N243K		Atlas-SNP	.											.	.	.	.	0			c.C729G						.						140	134	136					7																	99030913		2203	4300	6503	SO:0001583	missense	100526740	exon4			GTAGAGGTTGAAG	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.582C>G	chr7.hg19:g.99030913G>C	ENSP00000292478:p.Asn194Lys	78.0	0.0		81.0	34.0	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	hg19	CCDS34691.1	.	.	.	.	.	.	.	.	.	.	G	0.055	-1.240335	0.01493	.	.	ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000555673;ENST00000413834	T;T;T	0.61627	0.09;0.1;0.1	5.23	0.251	0.15540	.	0.983767	0.08319	N	0.964237	T	0.24812	0.0602	N	0.03209	-0.39	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24083	-1.0170	10	0.06757	T	0.87	-1.4307	2.5943	0.04850	0.1076:0.452:0.2122:0.2283	.	243;194	G3V325;O75127	.;PTCD1_HUMAN	K	194;243;243	ENSP00000292478:N194K;ENSP00000450995:N243K;ENSP00000400168:N243K	ENSP00000400168:N243K	N	-	3	2	ATP5J2-PTCD1;PTCD1	98868849	0.000000	0.05858	0.298000	0.25002	0.043000	0.13939	-0.111000	0.10807	0.215000	0.20761	-0.891000	0.02926	AAC	.	.		0.607	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		C	99030913	G	C	99030913	3	2	96	1	0	0	0	0	1	0	0	0	12739	1252	44	4	1544	4	PTCD1	7	99030913	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	16435451	99030913	60107750	26	13235										
HAS2	3037	hgsc.bcm.edu	37	chr8	122641077	122641077	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	accaattgcgttacgtgttgCgagctttctttatgtgactc	9	9	1	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr8:122641077C>T	ENST00000303924.4	-	2	1041	c.504G>A	c.(502-504)tcG>tcA	p.S168S		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	168					atrioventricular canal development (GO:0036302)|bone morphogenesis (GO:0060349)|cellular response to fluid shear stress (GO:0071498)|cellular response to interleukin-1 (GO:0071347)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|endocardial cushion to mesenchymal transition (GO:0090500)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|hyaluronan biosynthetic process (GO:0030213)|kidney development (GO:0001822)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	hyaluronan synthase activity (GO:0050501)		HAS2/PLAG1(10)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			TTACGTGTTGCGAGCTTTCTT	0.453																																					p.S168S		Atlas-SNP	.											.	HAS2	87	.	0			c.G504A						.						376	326	343					8																	122641077		2203	4300	6503	SO:0001819	synonymous_variant	3037	exon2			GTGTTGCGAGCTT	U54804	CCDS6335.1	8q24.12	2013-02-22			ENSG00000170961	ENSG00000170961	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4819	protein-coding gene	gene with protein product		601636				9169154	Standard	NM_005328		Approved		uc003yph.2	Q92819	OTTHUMG00000164953	ENST00000303924.4:c.504G>A	chr8.hg19:g.122641077C>T		128.0	0.0		307.0	174.0	NM_005328	Q32MM3	Silent	SNP	ENST00000303924.4	hg19	CCDS6335.1																																																																																			.	.		0.453	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328		T	122641077	C	T	122641077	2	4	96	1	0	0	0	0	0	0	0	1	6971	755	27	1		1	HAS2	8	122641077	Silent	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10		122641077	23722945	27	13236										
AKR1C1	1645	hgsc.bcm.edu	37	chr10	5005692	5005692	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tggtcacttcatgcctgtccTgggatttggcacctatgcgc	11	12	2	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr10:5005692T>G	ENST00000380872.4	+	1	248	c.56T>G	c.(55-57)cTg>cGg	p.L19R	AKR1C1_ENST00000434459.2_Missense_Mutation_p.L19R|U8_ENST00000459095.1_RNA|AKR1C1_ENST00000477661.1_3'UTR|AKR1C1_ENST00000380859.1_5'Flank	NM_001353.5	NP_001344.2	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	19					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|cholesterol homeostasis (GO:0042632)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|intestinal cholesterol absorption (GO:0030299)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|progesterone metabolic process (GO:0042448)|protein homooligomerization (GO:0051260)|response to organophosphorus (GO:0046683)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase (B-specific) activity (GO:0047042)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|indanol dehydrogenase activity (GO:0047718)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(2)|ovary(3)|prostate(1)	13					Acetylsalicylic acid(DB00945)|Salicylic acid(DB00936)	ATGCCTGTCCTGGGATTTGGC	0.458																																					p.L19R	Colon(130;2054 2316 13360 15380)	Atlas-SNP	.											.	AKR1C1	39	.	0			c.T56G						.						152	134	140					10																	5005692		2203	4300	6503	SO:0001583	missense	1645	exon1			CTGTCCTGGGATT	D26124	CCDS7061.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000187134	ENSG00000187134	1.3.1.20, 1.1.1.149, 1.1.1.112	"Aldo-keto reductases"	384	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase"	600449	"aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)"	DDH1		8011662	Standard	NM_001353		Approved	DDH, MBAB, DD1, HAKRC		Q04828	OTTHUMG00000017580	ENST00000380872.4:c.56T>G	chr10.hg19:g.5005692T>G	ENSP00000370254:p.Leu19Arg	222.0	0.0		180.0	16.0	NM_001353	P52896|Q5SR15|Q7M4N2|Q9UCX2	Missense_Mutation	SNP	ENST00000380872.4	hg19	CCDS7061.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.67|18.67	3.673679|3.673679	0.67928|0.67928	.|.	.|.	ENSG00000187134|ENSG00000187134	ENST00000434459;ENST00000380872|ENST00000442997	T;T|.	0.34859|.	1.34;1.34|.	2.46|2.46	2.46|2.46	0.29980|0.29980	NADP-dependent oxidoreductase domain (3);|.	0.165908|.	0.28595|.	N|.	0.014798|.	T|T	0.66297|0.66297	0.2775|0.2775	M|M	0.81239|0.81239	2.535|2.535	0.42971|0.42971	D|D	0.99443|0.99443	D;D;D|.	0.89917|.	1.0;0.999;1.0|.	D;D;D|.	0.91635|.	0.999;0.984;0.992|.	T|T	0.66093|0.66093	-0.6009|-0.6009	10|5	0.87932|.	D|.	0|.	.|.	6.7142|6.7142	0.23294|0.23294	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	19;19;19|.	B4E0M1;Q2XPP3;Q04828|.	.;.;AK1C1_HUMAN|.	R|G	19|18	ENSP00000412248:L19R;ENSP00000370254:L19R|.	ENSP00000370254:L19R|.	L|W	+|+	2|1	0|0	AKR1C1|AKR1C1	4995692|4995692	0.533000|0.533000	0.26354|0.26354	0.163000|0.163000	0.22734|0.22734	0.471000|0.471000	0.32888|0.32888	2.373000|2.373000	0.44266|0.44266	1.131000|1.131000	0.42111|0.42111	0.254000|0.254000	0.18369|0.18369	CTG|TGG	.	.		0.458	AKR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046523.2	NM_001353		G	5005692	T	G	5005692	3	3	96	1	0	0	0	0	1	0	0	0	469	1580	55	5	58	5	AKR1C1	10	5005692	Missense_Mutation	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10		5005692	130529055	28	13237										
MKI67	4288	hgsc.bcm.edu	37	chr10	129901194	129901194	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	gtgcttaccacgtctcccacGggttctactttaggggcccg	11	14	2	0	rs371689181		TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr10:129901194G>A	ENST00000368654.3	-	13	9285	c.8910C>T	c.(8908-8910)ccC>ccT	p.P2970P	MKI67_ENST00000368653.3_Silent_p.P2610P	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2970					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CGTCTCCCACGGGTTCTACTT	0.502																																					p.P2970P		Atlas-SNP	.											.	MKI67	363	.	0			c.C8910T						.	A	,	1,4405	2.1+/-5.4	0,1,2202	90	90	90		7830,8910	-2.3	0	10		90	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	,	2610/2897,2970/3257	129901194	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	4288	exon13			TCCCACGGGTTCT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.8910C>T	chr10.hg19:g.129901194G>A		88.0	0.0		98.0	26.0	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	hg19	CCDS7659.1																																																																																			.	.		0.502	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		A	129901194	G	A	129901194	2	1	96	1	0	0	0	0	0	0	0	1	9607	1103	39	1		1	MKI67	10	129901194	Silent	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	124895502	129901194	5633553	29	13238										
SSH3	54961	hgsc.bcm.edu	37	chr11	67077797	67077797	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	ggagagcacctcagagaccaGtgacatgccagaggtgaggc	15	10	1	5			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr11:67077797G>T	ENST00000308127.4	+	13	1848	c.1670G>T	c.(1669-1671)aGt>aTt	p.S557I	SSH3_ENST00000308298.7_Missense_Mutation_p.S292I|SSH3_ENST00000376757.5_3'UTR	NM_017857.3	NP_060327.3	Q8TE77	SSH3_HUMAN	slingshot protein phosphatase 3	557					protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|DNA binding (GO:0003677)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			TCAGAGACCAGTGACATGCCA	0.617																																					p.S557I		Atlas-SNP	.											.	SSH3	54	.	0			c.G1670T						.						41	46	44					11																	67077797		2200	4295	6495	SO:0001583	missense	54961	exon13			AGACCAGTGACAT	AF085851	CCDS8157.1	11q13	2013-03-05	2013-03-05		ENSG00000172830	ENSG00000172830		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30581	protein-coding gene	gene with protein product		606780	"slingshot homolog 3 (Drosophila)"			11832213	Standard	NM_017857		Approved	FLJ20515, FLJ10928	uc001okj.3	Q8TE77	OTTHUMG00000167105	ENST00000308127.4:c.1670G>T	chr11.hg19:g.67077797G>T	ENSP00000312081:p.Ser557Ile	80.0	0.0		74.0	15.0	NM_017857	Q6PK42|Q76I75|Q8N9L8|Q8WYL0|Q9NV45|Q9NWZ7	Missense_Mutation	SNP	ENST00000308127.4	hg19	CCDS8157.1	.	.	.	.	.	.	.	.	.	.	G	10.17	1.275638	0.23307	.	.	ENSG00000172830	ENST00000308127;ENST00000308298	T;T	0.29917	3.8;1.55	4.13	-1.32	0.09201	.	2.138560	0.02449	N	0.085412	T	0.20333	0.0489	N	0.19112	0.55	0.09310	N	1	B;B	0.32467	0.372;0.255	B;B	0.33890	0.172;0.083	T	0.14448	-1.0472	10	0.44086	T	0.13	4.549	4.3278	0.11048	0.2847:0.3177:0.3976:0.0	.	411;557	Q8TE77-3;Q8TE77	.;SSH3_HUMAN	I	557;292	ENSP00000312081:S557I;ENSP00000310055:S292I	ENSP00000312081:S557I	S	+	2	0	SSH3	66834373	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	-0.265000	0.08644	-0.336000	0.08438	0.555000	0.69702	AGT	.	.		0.617	SSH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393167.1	NM_018276		T	67077797	G	T	67077797	3	4	96	1	0	0	0	0	1	0	0	0	15201	1029	36	3	1720	3	SSH3	11	67077797	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10		67077797	67928719	30	13239										
FAT3	120114	hgsc.bcm.edu	37	chr11	92534030	92534030	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	gcagatgttggaaggggccaCttggtcactcaagttcaagc	13	9	3	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr11:92534030C>T	ENST00000298047.6	+	9	7868	c.7851C>T	c.(7849-7851)caC>caT	p.H2617H	FAT3_ENST00000525166.1_Silent_p.H2467H|FAT3_ENST00000409404.2_Silent_p.H2617H			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2617	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GAAGGGGCCACTTGGTCACTC	0.488										TCGA Ovarian(4;0.039)																											p.H2617H		Atlas-SNP	.											.	FAT3	1822	.	0			c.C7851T						.						49	48	49					11																	92534030		1966	4158	6124	SO:0001819	synonymous_variant	120114	exon9			GGGCCACTTGGTC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.7851C>T	chr11.hg19:g.92534030C>T		77.0	0.0		58.0	12.0	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	hg19																																																																																				.	.		0.488	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92534030	C	T	92534030	2	4	96	1	0	0	0	0	0	0	0	1	5699	564	20	3		3	FAT3	11	92534030	Silent	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	25456233	92534030	42472486	31	13240										
ETS1	2113	hgsc.bcm.edu	37	chr11	128426289	128426289	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	taattggactggaaaccacaGttcattcgaggatcttcata	8	8	3	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr11:128426289G>C	ENST00000392668.4	-	3	195	c.111C>G	c.(109-111)aaC>aaG	p.N37K	ETS1_ENST00000525404.1_5'UTR	NM_001143820.1	NP_001137292.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	0					angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		GGAAACCACAGTTCATTCGAG	0.423																																					p.N37K		Atlas-SNP	.											.	ETS1	123	.	0			c.C111G						.						150	129	135					11																	128426289		1566	3579	5145	SO:0001583	missense	2113	exon3			ACCACAGTTCATT		CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1", "ets protein"	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000392668.4:c.111C>G	chr11.hg19:g.128426289G>C	ENSP00000376436:p.Asn37Lys	147.0	0.0		164.0	38.0	NM_001143820	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Missense_Mutation	SNP	ENST00000392668.4	hg19	CCDS44767.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.834984	0.32421	.	.	ENSG00000134954	ENST00000392668	T	0.10960	2.82	5.89	4.98	0.66077	.	0.478249	0.20633	N	0.088545	T	0.07818	0.0196	.	.	.	0.80722	D	1	B	0.11235	0.004	B	0.08055	0.003	T	0.23655	-1.0182	9	0.30078	T	0.28	.	9.221	0.37377	0.0781:0.1479:0.774:0.0	.	37	Q6N087	.	K	37	ENSP00000376436:N37K	ENSP00000376436:N37K	N	-	3	2	ETS1	127931499	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.271000	0.33098	2.797000	0.96272	0.563000	0.77884	AAC	.	.		0.423	ETS1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386267.2	NM_005238		C	128426289	G	C	128426289	3	2	96	1	0	0	0	0	1	0	0	0	5277	1020	36	4	1464	4	ETS1	11	128426289	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	35892259	128426289	6580227	32	13241										
USP5	8078	hgsc.bcm.edu	37	chr12	6974387	6974387	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	ctaccatgtgtggtcactacGtctgccacatcaagaaagaa	8	11	3	2			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr12:6974387G>A	ENST00000229268.8	+	19	2510	c.2458G>A	c.(2458-2460)Gtc>Atc	p.V820I	USP5_ENST00000389231.5_Missense_Mutation_p.V797I|TPI1_ENST00000229270.4_5'Flank|TPI1_ENST00000488464.2_5'Flank|TPI1_ENST00000396705.5_5'Flank|TPI1_ENST00000535434.1_5'Flank	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	820	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						TGGTCACTACGTCTGCCACAT	0.507																																					p.V820I		Atlas-SNP	.											.	USP5	124	.	0			c.G2458A						.						94	81	86					12																	6974387		2203	4300	6503	SO:0001583	missense	8078	exon19			CACTACGTCTGCC	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"Ubiquitin-specific peptidases"	12628	protein-coding gene	gene with protein product		601447	"ubiquitin specific protease 5 (isopeptidase T)"			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.2458G>A	chr12.hg19:g.6974387G>A	ENSP00000229268:p.Val820Ile	114.0	0.0		131.0	13.0	NM_001098536	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	hg19	CCDS41743.1	.	.	.	.	.	.	.	.	.	.	G	35	5.478063	0.96291	.	.	ENSG00000111667	ENST00000229268;ENST00000389231	T;T	0.32023	1.47;1.47	5.27	5.27	0.74061	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.52354	0.1729	M	0.78223	2.4	0.80722	D	1	P;D	0.69078	0.948;0.997	P;P	0.55545	0.591;0.778	T	0.54153	-0.8336	10	0.49607	T	0.09	-9.8578	19.0978	0.93260	0.0:0.0:1.0:0.0	.	820;797	P45974;P45974-2	UBP5_HUMAN;.	I	820;797	ENSP00000229268:V820I;ENSP00000373883:V797I	ENSP00000229268:V820I	V	+	1	0	USP5	6844648	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.657000	0.98554	2.735000	0.93741	0.655000	0.94253	GTC	.	.		0.507	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1			A	6974387	G	A	6974387	3	1	96	1	0	0	0	0	1	0	0	0	17096	1145	40	1	2532	1	USP5	12	6974387	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10		6974387	126877508	33	13242										
PZP	5858	hgsc.bcm.edu	37	chr12	9344850	9344850	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	acgatgactcccttagccatGatctgaaatgaaaaaacagt	7	9	1	4			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr12:9344850G>T	ENST00000261336.2	-	13	1513	c.1485C>A	c.(1483-1485)atC>atA	p.I495I	PZP_ENST00000381997.2_Silent_p.I364I	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	495					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CCTTAGCCATGATCTGAAATG	0.473																																					p.I495I	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.C1485A						.						90	81	84					12																	9344850		2203	4300	6503	SO:0001819	synonymous_variant	5858	exon13			AGCCATGATCTGA	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.1485C>A	chr12.hg19:g.9344850G>T		77.0	0.0		90.0	7.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Silent	SNP	ENST00000261336.2	hg19	CCDS8600.1																																																																																			.	.		0.473	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		T	9344850	G	T	9344850	2	4	96	1	0	0	0	0	0	0	0	1	12884	1280	45	3		3	PZP	12	9344850	Silent	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	2370463	9344850	124507045	34	13243										
TAS2R46	259292	hgsc.bcm.edu	37	chr12	11214459	11214459	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	atctgattcatgtttatcacAaaaagatgacaaaccaaaaa	4	7	3	3			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr12:11214459A>C	ENST00000533467.1	-	1	434	c.435T>G	c.(433-435)ttT>ttG	p.F145L	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	145					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)	p.?(1)|p.F145L(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TGTTTATCACAAAAAGATGAC	0.348																																					p.F145L		Atlas-SNP	.											TAS2R46,NS,carcinoma,0,1	TAS2R46	43	.	2	Substitution - Missense(1)|Unknown(1)	lung(2)	c.T435G						.						108	114	112					12																	11214459		2067	4259	6326	SO:0001583	missense	259292	exon1			TATCACAAAAAGA	AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18877	protein-coding gene	gene with protein product		612774				12379855	Standard	NM_176887		Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.435T>G	chr12.hg19:g.11214459A>C	ENSP00000436450:p.Phe145Leu	256.0	0.0		275.0	13.0	NM_176887	P59548|Q645X6	Missense_Mutation	SNP	ENST00000533467.1	hg19	CCDS53748.1	.	.	.	.	.	.	.	.	.	.	A	4.145	0.025222	0.08054	.	.	ENSG00000226761	ENST00000533467	T	0.36340	1.26	2.37	-3.71	0.04424	.	.	.	.	.	T	0.10465	0.0256	N	0.02315	-0.6	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.33369	-0.9871	9	0.11485	T	0.65	.	3.4805	0.07601	0.3727:0.0:0.3609:0.2664	.	145	P59540	T2R46_HUMAN	L	145	ENSP00000436450:F145L	ENSP00000436450:F145L	F	-	3	2	TAS2R46	11105726	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-2.787000	0.00769	-0.280000	0.09154	0.163000	0.16589	TTT	.	.		0.348	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887		C	11214459	A	C	11214459	3	2	96	1	0	0	0	0	1	0	0	0	15597	127	5	5	498	5	TAS2R46	12	11214459	Missense_Mutation	SNP	A	TCGA-DD-A1E9-01A-21D-A152-10	1869609	11214459	122637436	35	13244			1	14		4	4	298	N	T_C_A	2.293327e-11
TAS2R46	259292	hgsc.bcm.edu	37	chr12	11214707	11214707	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	agttgcataccaatttaataCtaatacccagagtaaaccaa	4	9	0	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr12:11214707C>A	ENST00000533467.1	-	1	186	c.187G>T	c.(187-189)Gta>Tta	p.V63L	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	63					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		CAATTTAATACTAATACCCAG	0.383																																					p.V63L		Atlas-SNP	.											.	TAS2R46	43	.	0			c.G187T						.						57	56	56					12																	11214707		1962	4191	6153	SO:0001583	missense	259292	exon1			TTAATACTAATAC	AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18877	protein-coding gene	gene with protein product		612774				12379855	Standard	NM_176887		Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.187G>T	chr12.hg19:g.11214707C>A	ENSP00000436450:p.Val63Leu	236.0	0.0		280.0	20.0	NM_176887	P59548|Q645X6	Missense_Mutation	SNP	ENST00000533467.1	hg19	CCDS53748.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.927156	0.00493	.	.	ENSG00000226761	ENST00000533467	T	0.36699	1.24	2.54	-0.426	0.12314	.	.	.	.	.	T	0.05960	0.0155	N	0.00128	-2.045	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33727	-0.9857	9	0.02654	T	1	.	5.7688	0.18241	0.2913:0.5338:0.0:0.1749	.	63	P59540	T2R46_HUMAN	L	63	ENSP00000436450:V63L	ENSP00000436450:V63L	V	-	1	0	TAS2R46	11105974	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-2.384000	0.01063	-0.633000	0.05545	-1.227000	0.01581	GTA	.	.		0.383	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887		A	11214707	C	A	11214707	3	1	96	1	0	0	0	0	1	0	0	0	15597	565	20	3	746	3	TAS2R46	12	11214707	Missense_Mutation	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	248	11214707	122637188	36	13245			1	14		4	4	298	N	T_C_A	2.293327e-11
TAS2R46	259292	hgsc.bcm.edu	37	chr12	11214720	11214720	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tttaatactaatacccagagTaaaccaactctggagactgc	6	10	1	2			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr12:11214720T>C	ENST00000533467.1	-	1	173	c.174A>G	c.(172-174)ttA>ttG	p.L58L	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	58					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		ATACCCAGAGTAAACCAACTC	0.383																																					p.L58L		Atlas-SNP	.											.	TAS2R46	43	.	0			c.A174G						.						55	54	54					12																	11214720		1979	4201	6180	SO:0001819	synonymous_variant	259292	exon1			CCAGAGTAAACCA	AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18877	protein-coding gene	gene with protein product		612774				12379855	Standard	NM_176887		Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.174A>G	chr12.hg19:g.11214720T>C		279.0	0.0		297.0	19.0	NM_176887	P59548|Q645X6	Silent	SNP	ENST00000533467.1	hg19	CCDS53748.1																																																																																			.	.		0.383	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887		C	11214720	T	C	11214720	2	2	96	1	0	0	0	0	0	0	0	1	15597	1635	57	2		2	TAS2R46	12	11214720	Silent	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10	13	11214720	122637175	37	13246			1	14		4	4	298	N	T_C_A	2.293327e-11
TAS2R46	259292	hgsc.bcm.edu	37	chr12	11214756	11214756	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	actgccagagcagtgagaatTtggtcagcaaaagagatctt	11	7	2	3	rs375315747		TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr12:11214756T>C	ENST00000533467.1	-	1	137	c.138A>G	c.(136-138)caA>caG	p.Q46Q	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	46					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		CAGTGAGAATTTGGTCAGCAA	0.373																																					p.Q46Q		Atlas-SNP	.											.	TAS2R46	43	.	0			c.A138G						.	T		1,3949		0,1,1974	54	53	53		138	-2.3	0	12		53	0,8442		0,0,4221	no	coding-synonymous	TAS2R46	NM_176887.2		0,1,6195	CC,CT,TT		0.0,0.0253,0.0081		46/310	11214756	1,12391	1975	4221	6196	SO:0001819	synonymous_variant	259292	exon1			GAGAATTTGGTCA	AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18877	protein-coding gene	gene with protein product		612774				12379855	Standard	NM_176887		Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.138A>G	chr12.hg19:g.11214756T>C		308.0	0.0		343.0	20.0	NM_176887	P59548|Q645X6	Silent	SNP	ENST00000533467.1	hg19	CCDS53748.1																																																																																			.	.		0.373	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887		C	11214756	T	C	11214756	2	2	96	1	0	0	0	0	0	0	0	1	15597	1838	64	2		2	TAS2R46	12	11214756	Silent	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10	36	11214756	122637139	38	13247			1	14		4	4	298	N	T_C_A	2.293327e-11
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50185782	50185782	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	cgaaaggtgggccctggggcGtaggggacgggcggctgggc	23	9	0	0	rs372382126	byFrequency	TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr12:50185782G>A	ENST00000335999.6	-	13	4046	c.3845C>T	c.(3844-3846)aCg>aTg	p.T1282M		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	1278	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						GCCCTGGGGCGTAGGGGACGG	0.721													G|||	5	0.000998403	0	0	5008	,	,		14103	0		0	False		,,,				2504	0.0051				p.T1282M		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.C3845T						.	G	MET/THR	1,3865		0,1,1932	12	16	14		3845	2.6	0	12		14	0,8230		0,0,4115	no	missense	NCKAP5L	NM_001037806.3	81	0,1,6047	AA,AG,GG		0.0,0.0259,0.0083	probably-damaging	1282/1335	50185782	1,12095	1933	4115	6048	SO:0001583	missense	57701	exon13			TGGGGCGTAGGGG	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.3845C>T	chr12.hg19:g.50185782G>A	ENSP00000337998:p.Thr1282Met	38.0	0.0		65.0	19.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Missense_Mutation	SNP	ENST00000335999.6	hg19	CCDS41781.2	.	.	.	.	.	.	.	.	.	.	G	1.799	-0.477609	0.04414	2.59E-4	0.0	ENSG00000167566	ENST00000335999;ENST00000354423	T	0.45668	0.89	4.46	2.57	0.30868	.	.	.	.	.	T	0.22282	0.0537	N	0.08118	0	0.09310	N	1	B;B	0.14805	0.011;0.005	B;B	0.16289	0.015;0.004	T	0.19192	-1.0313	9	0.45353	T	0.12	2.118	7.3365	0.26613	0.1744:0.1414:0.6842:0.0	.	1256;1278	E2QRB5;Q9HCH0	.;NCK5L_HUMAN	M	1282;1256	ENSP00000337998:T1282M	ENSP00000337998:T1282M	T	-	2	0	NCKAP5L	48472049	0.052000	0.20516	0.003000	0.11579	0.338000	0.28826	0.916000	0.28651	0.238000	0.21222	-1.203000	0.01651	ACG	.	.		0.721	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		A	50185782	G	A	50185782	3	1	96	1	0	0	0	0	1	0	0	0	10233	1145	40	1	163	1	NCKAP5L	12	50185782	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10	38971026	50185782	83666113	39	13248										
NR4A1	3164	hgsc.bcm.edu	37	chr12	52448249	52448249	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	ccccgaggcagcccccgctgCccccactgccctgcccagct	9	24	0	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr12:52448249C>T	ENST00000243050.1	+	3	451	c.137C>T	c.(136-138)gCc>gTc	p.A46V	NR4A1_ENST00000545748.1_Missense_Mutation_p.A100V|NR4A1_ENST00000550082.1_Missense_Mutation_p.A59V|NR4A1_ENST00000394824.2_Missense_Mutation_p.A46V|NR4A1_ENST00000360284.3_Missense_Mutation_p.A59V|NR4A1_ENST00000547206.1_3'UTR|NR4A1_ENST00000394825.1_Missense_Mutation_p.A46V|NR4A1_ENST00000548232.1_Missense_Mutation_p.A46V	NM_002135.4	NP_002126.2	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	46					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell chemotaxis (GO:0035767)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)	16				BRCA - Breast invasive adenocarcinoma(357;0.0967)		GCCCCCGCTGCCCCCACTGCC	0.657																																					p.A59V		Atlas-SNP	.											.	NR4A1	77	.	0			c.C176T						.						79	77	78					12																	52448249		2203	4300	6503	SO:0001583	missense	3164	exon3			CCGCTGCCCCCAC	L13740	CCDS8818.1, CCDS55828.1, CCDS73471.1	12q13	2013-01-16			ENSG00000123358	ENSG00000123358		"Nuclear hormone receptors"	7980	protein-coding gene	gene with protein product		139139		HMR, GFRP1		2626032	Standard	NM_002135		Approved	TR3, N10, NAK-1, NGFIB, NUR77	uc001rzt.3	P22736	OTTHUMG00000150393	ENST00000243050.1:c.137C>T	chr12.hg19:g.52448249C>T	ENSP00000243050:p.Ala46Val	74.0	0.0		56.0	7.0	NM_001202233	B4DML7|Q15627|Q53Y00|Q6IBU8	Missense_Mutation	SNP	ENST00000243050.1	hg19	CCDS8818.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344410	0.61073	.	.	ENSG00000123358	ENST00000360284;ENST00000545748;ENST00000550082;ENST00000243050;ENST00000394825;ENST00000550763;ENST00000394824;ENST00000548232	D;D;D;D;D;T;D;D	0.96651	-3.82;-3.92;-3.82;-3.79;-3.79;0.01;-3.79;-4.08	4.59	3.68	0.42216	.	0.766780	0.12212	N	0.489206	D	0.93132	0.7813	L	0.35644	1.08	0.52501	D	0.99995	B;B;B	0.20052	0.001;0.002;0.041	B;B;B	0.17098	0.003;0.003;0.017	D	0.89744	0.3935	10	0.56958	D	0.05	.	11.2533	0.49039	0.0:0.9053:0.0:0.0947	.	59;46;46	B4DML7;P22736;Q15627	.;NR4A1_HUMAN;.	V	59;100;59;46;46;46;46;46	ENSP00000353427:A59V;ENSP00000440864:A100V;ENSP00000449539:A59V;ENSP00000243050:A46V;ENSP00000378302:A46V;ENSP00000449858:A46V;ENSP00000378301:A46V;ENSP00000449587:A46V	ENSP00000243050:A46V	A	+	2	0	NR4A1	50734516	0.997000	0.39634	0.995000	0.50966	0.882000	0.50991	4.726000	0.61986	1.250000	0.43966	0.561000	0.74099	GCC	.	.		0.657	NR4A1-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317922.2			T	52448249	C	T	52448249	3	4	96	1	0	0	0	0	1	0	0	0	10641	739	26	3	139	3	NR4A1	12	52448249	Missense_Mutation	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	2262467	52448249	81403646	40	13249										
OLFM4	10562	hgsc.bcm.edu	37	chr13	53617269	53617269	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	atgactctcttggtagagaaGcttgagacactagacaaaaa	9	7	1	4			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr13:53617269G>A	ENST00000219022.2	+	4	678	c.600G>A	c.(598-600)aaG>aaA	p.K200K		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	200					cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		TGGTAGAGAAGCTTGAGACAC	0.383																																					p.K200K		Atlas-SNP	.											.	OLFM4	94	.	0			c.G600A						.						101	99	100					13																	53617269		2203	4300	6503	SO:0001819	synonymous_variant	10562	exon4			AGAGAAGCTTGAG	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.600G>A	chr13.hg19:g.53617269G>A		104.0	0.0		119.0	13.0	NM_006418	O95362|Q5VWG0|Q86T22	Silent	SNP	ENST00000219022.2	hg19	CCDS9440.1																																																																																			.	.		0.383	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418		A	53617269	G	A	53617269	2	1	96	1	0	0	0	0	0	0	0	1	10864	962	34	3		3	OLFM4	13	53617269	Silent	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10		53617269	61552609	41	13250										
PABPN1	8106	hgsc.bcm.edu	37	chr14	23793427	23793427	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	gcccgctaccgcgcccggacCaccaactacaacagctcccg	8	21	0	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr14:23793427C>T	ENST00000216727.4	+	6	991	c.810C>T	c.(808-810)acC>acT	p.T270T	BCL2L2-PABPN1_ENST00000553781.1_Silent_p.T297T|PABPN1_ENST00000397276.2_Silent_p.T270T|BCL2L2-PABPN1_ENST00000557008.1_Silent_p.T297T|PABPN1_ENST00000557702.1_Silent_p.T142T|AL049829.1_ENST00000594872.1_5'Flank|PABPN1_ENST00000556821.1_Silent_p.T142T	NM_004643.3	NP_004634.1	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1	270	Necessary for homooligomerization.				gene expression (GO:0010467)|modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|muscle contraction (GO:0006936)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			large_intestine(1)|lung(1)|ovary(2)	4	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GCGCCCGGACCACCAACTACA	0.567																																					p.T297T		Atlas-SNP	.											.	.	.	.	0			c.C891T						.						80	81	81					14																	23793427		2203	4300	6503	SO:0001819	synonymous_variant	100529063	exon8			CCGGACCACCAAC	AF026029	CCDS9592.1	14q11.2	2013-02-12	2001-11-28		ENSG00000100836	ENSG00000100836		"RNA binding motif (RRM) containing"	8565	protein-coding gene	gene with protein product		602279	"poly(A)-binding protein, nuclear 1"	OPMD, PABP2		7795598	Standard	NM_004643		Approved	PAB2		Q86U42	OTTHUMG00000028739	ENST00000216727.4:c.810C>T	chr14.hg19:g.23793427C>T		104.0	0.0		88.0	9.0	NM_001199864	D3DS49|O43484	Silent	SNP	ENST00000216727.4	hg19	CCDS9592.1	.	.	.	.	.	.	.	.	.	.	C	6.111	0.388659	0.11581	.	.	ENSG00000100836	ENST00000555295	.	.	.	5.47	0.998	0.19857	.	.	.	.	.	T	0.42832	0.1220	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23976	-1.0173	4	.	.	.	-10.4575	2.026	0.03519	0.1279:0.4064:0.1253:0.3404	.	.	.	.	Y	70	.	.	H	+	1	0	PABPN1	22863267	0.971000	0.33674	1.000000	0.80357	0.989000	0.77384	0.324000	0.19610	0.276000	0.22118	-0.150000	0.13652	CAC	.	.		0.567	PABPN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071767.4	NM_004643		T	23793427	C	T	23793427	2	4	96	1	0	0	0	0	0	0	0	1	11377	581	21	3		3	PABPN1	14	23793427	Silent	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10		23793427	83556113	42	13251										
WHAMM	123720	hgsc.bcm.edu	37	chr15	83491939	83491939	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tgtggtggggctgcaggatgAtaagaatttggaagtgaaag	17	2	0	3			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr15:83491939A>G	ENST00000286760.4	+	6	1457	c.1358A>G	c.(1357-1359)gAt>gGt	p.D453G		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	453	Mediates interaction with microtubules. {ECO:0000269|PubMed:23027905}.				actin filament organization (GO:0007015)|actin filament reorganization (GO:0090527)|ER to Golgi vesicle-mediated transport (GO:0006888)|focal adhesion assembly (GO:0048041)|lamellipodium assembly (GO:0030032)|membrane tubulation (GO:0097320)|positive regulation of actin nucleation (GO:0051127)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|Golgi membrane (GO:0000139)	Arp2/3 complex binding (GO:0071933)|GTP-Rho binding (GO:0017049)|microtubule binding (GO:0008017)			endometrium(6)|large_intestine(5)|lung(1)|prostate(1)	13						CTGCAGGATGATAAGAATTTG	0.438																																					p.D453G		Atlas-SNP	.											.	WHAMM	63	.	0			c.A1358G						.						40	39	39					15																	83491939		1908	4134	6042	SO:0001583	missense	123720	exon6			AGGATGATAAGAA	AK126887	CCDS45333.1	15q25.2	2009-02-18	2009-02-18	2009-02-18	ENSG00000156232	ENSG00000156232			30493	protein-coding gene	gene with protein product		612393	"WAS protein homology region 2 domain containing 1"	WHDC1		11853319, 18226259, 18614018, 18812086	Standard	XM_005272422		Approved	KIAA1971	uc002bje.3	Q8TF30		ENST00000286760.4:c.1358A>G	chr15.hg19:g.83491939A>G	ENSP00000286760:p.Asp453Gly	295.0	0.0		230.0	45.0	NM_001080435	Q8N1J9	Missense_Mutation	SNP	ENST00000286760.4	hg19	CCDS45333.1	.	.	.	.	.	.	.	.	.	.	A	9.868	1.198128	0.22037	.	.	ENSG00000156232	ENST00000286760;ENST00000234505	T	0.40756	1.02	4.97	-5.53	0.02552	.	2.108940	0.01699	N	0.027094	T	0.12050	0.0293	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.08785	-1.0705	10	0.23302	T	0.38	.	0.6067	0.00753	0.3247:0.2919:0.1766:0.2069	.	453	Q8TF30	WHAMM_HUMAN	G	453	ENSP00000286760:D453G	ENSP00000234505:D453G	D	+	2	0	WHAMM	81288993	0.000000	0.05858	0.000000	0.03702	0.162000	0.22319	-0.620000	0.05565	-0.789000	0.04498	0.260000	0.18958	GAT	.	.		0.438	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1			G	83491939	A	G	83491939	3	3	96	1	0	0	0	0	1	0	0	0	17376	333	12	2	1380	2	WHAMM	15	83491939	Missense_Mutation	SNP	A	TCGA-DD-A1E9-01A-21D-A152-10		83491939	19039453	43	13252										
KIF7	374654	hgsc.bcm.edu	37	chr15	90189142	90189142	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	acctgcgcaggtgtaaggtcCgcctgggcggctcctcctcc	13	16	0	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr15:90189142C>T	ENST00000394412.3	-	8	1980	c.1904G>A	c.(1903-1905)cGg>cAg	p.R635Q		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	635	Sufficient for interaction with NPHP1.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			GTGTAAGGTCCGCCTGGGCGG	0.647																																					p.R635Q		Atlas-SNP	.											.	KIF7	130	.	0			c.G1904A						.						70	67	68					15																	90189142		2200	4299	6499	SO:0001583	missense	374654	exon8			AAGGTCCGCCTGG	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"Kinesins"	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.1904G>A	chr15.hg19:g.90189142C>T	ENSP00000377934:p.Arg635Gln	48.0	0.0		36.0	5.0	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	hg19	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	c	1.109	-0.658648	0.03454	.	.	ENSG00000166813	ENST00000394412	T	0.70631	-0.5	3.84	1.92	0.25849	.	1.363710	0.05123	N	0.491022	T	0.60702	0.2289	L	0.41236	1.265	0.21499	N	0.999665	B;B	0.24533	0.012;0.105	B;B	0.10450	0.002;0.005	T	0.43081	-0.9413	10	0.33141	T	0.24	.	6.976	0.24674	0.0:0.7844:0.0:0.2156	.	122;635	B7ZKY4;Q2M1P5	.;KIF7_HUMAN	Q	635	ENSP00000377934:R635Q	ENSP00000377934:R635Q	R	-	2	0	KIF7	87990146	0.000000	0.05858	0.087000	0.20705	0.057000	0.15508	-0.688000	0.05150	0.381000	0.24851	-0.511000	0.04467	CGG	.	.		0.647	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		T	90189142	C	T	90189142	3	4	96	1	0	0	0	0	1	0	0	0	8318	652	23	1	2175	1	KIF7	15	90189142	Missense_Mutation	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	6697203	90189142	12342250	44	13253										
SALL1	6299	hgsc.bcm.edu	37	chr16	51173341	51173341	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	actcctgcgtgctgttggacGgggacagagcctgcatggaa	15	10	0	1	rs140924793		TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr16:51173341G>T	ENST00000251020.4	-	2	2825	c.2792C>A	c.(2791-2793)cCg>cAg	p.P931Q	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.P834Q	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	931					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GCTGTTGGACGGGGACAGAGC	0.557																																					p.P931Q	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C2792A						.						92	76	81					16																	51173341		2198	4300	6498	SO:0001583	missense	6299	exon2			TTGGACGGGGACA	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2792C>A	chr16.hg19:g.51173341G>T	ENSP00000251020:p.Pro931Gln	122.0	0.0		125.0	5.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.833382	0.71258	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.79940	-1.32;-1.32	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.89777	0.6813	M	0.81682	2.555	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86891	0.2048	10	0.21014	T	0.42	.	19.3096	0.94182	0.0:0.0:1.0:0.0	.	931	Q9NSC2	SALL1_HUMAN	Q	931;834;895	ENSP00000251020:P931Q;ENSP00000407914:P834Q	ENSP00000251020:P931Q	P	-	2	0	SALL1	49730842	1.000000	0.71417	0.959000	0.39883	0.996000	0.88848	9.869000	0.99810	2.557000	0.86248	0.455000	0.32223	CCG	.	G|1.000;A|0.000		0.557	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		T	51173341	G	T	51173341	3	4	96	1	0	0	0	0	1	0	0	0	13825	1116	39	1	1190	1	SALL1	16	51173341	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10		51173341	39181412	45	13254										
PRPF8	10594	hgsc.bcm.edu	37	chr17	1564062	1564062	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	gaatctggttcagtcctgatCgctgagcattagttagcttc	10	9	2	2			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr17:1564062C>A	ENST00000572621.1	-	28	4833	c.4568G>T	c.(4567-4569)cGa>cTa	p.R1523L	PRPF8_ENST00000304992.6_Missense_Mutation_p.R1523L			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	1523	Important for branch point selection. {ECO:0000250}.|Linker.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CAGTCCTGATCGCTGAGCATT	0.507																																					p.R1523L		Atlas-SNP	.											.	PRPF8	169	.	0			c.G4568T						.						141	125	130					17																	1564062		2203	4300	6503	SO:0001583	missense	10594	exon29			CCTGATCGCTGAG	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.4568G>T	chr17.hg19:g.1564062C>A	ENSP00000460348:p.Arg1523Leu	112.0	0.0		128.0	22.0	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	c	21.0	4.077009	0.76415	.	.	ENSG00000174231	ENST00000304992;ENST00000540177	D	0.82433	-1.61	6.17	6.17	0.99709	Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.92795	0.7709	M	0.87456	2.885	0.80722	D	1	D	0.69078	0.997	D	0.72075	0.976	D	0.92691	0.6166	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1523	Q6P2Q9	PRP8_HUMAN	L	1523;50	ENSP00000304350:R1523L	ENSP00000304350:R1523L	R	-	2	0	PRPF8	1510812	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.712000	0.84684	2.941000	0.99782	0.655000	0.94253	CGA	.	.		0.507	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			A	1564062	C	A	1564062	3	1	96	1	0	0	0	0	1	0	0	0	12587	884	31	1	2499	1	PRPF8	17	1564062	Missense_Mutation	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10		1564062	79631148	46	13255										
CYP2A13	1553	hgsc.bcm.edu	37	chr19	41600227	41600227	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	aggaccgggccaagatgcccTacacagaggcagtgatccac	12	13	0	3			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr19:41600227T>C	ENST00000330436.3	+	7	1051	c.1051T>C	c.(1051-1053)Tac>Cac	p.Y351H		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	351					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	CAAGATGCCCTACACAGAGGC	0.547																																					p.Y351H		Atlas-SNP	.											.	CYP2A13	90	.	0			c.T1051C						.						130	114	119					19																	41600227		2203	4300	6503	SO:0001583	missense	1553	exon7			ATGCCCTACACAG	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"Cytochrome P450s"	2608	protein-coding gene	gene with protein product		608055	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.1051T>C	chr19.hg19:g.41600227T>C	ENSP00000332679:p.Tyr351His	215.0	0.0		212.0	39.0	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	hg19	CCDS12571.1	.	.	.	.	.	.	.	.	.	.	.	18.14	3.556936	0.65425	.	.	ENSG00000197838	ENST00000330436	T	0.76186	-1.0	4.19	4.19	0.49359	.	0.070853	0.64402	U	0.000019	D	0.88894	0.6561	H	0.94582	3.555	0.37014	D	0.895864	D	0.89917	1.0	D	0.79784	0.993	D	0.93053	0.6467	10	0.87932	D	0	.	12.4075	0.55449	0.0:0.0:0.0:1.0	.	351	Q16696	CP2AD_HUMAN	H	351	ENSP00000332679:Y351H	ENSP00000332679:Y351H	Y	+	1	0	CYP2A13	46292067	1.000000	0.71417	1.000000	0.80357	0.539000	0.34962	7.644000	0.83416	1.783000	0.52377	0.254000	0.18369	TAC	.	.		0.547	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		C	41600227	T	C	41600227	3	2	96	1	0	0	0	0	1	0	0	0	4163	1522	53	2	1077	2	CYP2A13	19	41600227	Missense_Mutation	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10		41600227	17528756	47	13256										
AP2A1	160	hgsc.bcm.edu	37	chr19	50302171	50302171	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tccaacgccaagaacgccatCctcttcgagaccatcagcct	6	17	2	2			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr19:50302171C>T	ENST00000359032.5	+	8	927	c.927C>T	c.(925-927)atC>atT	p.I309I	AP2A1_ENST00000354293.5_Silent_p.I309I	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	309					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		AGAACGCCATCCTCTTCGAGA	0.607																																					p.I309I		Atlas-SNP	.											.	AP2A1	108	.	0			c.C927T						.						31	34	33					19																	50302171		2037	4167	6204	SO:0001819	synonymous_variant	160	exon8			CGCCATCCTCTTC	AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.927C>T	chr19.hg19:g.50302171C>T		104.0	0.0		90.0	17.0	NM_130787	Q96CI7|Q96PP6|Q96PP7|Q9H070	Silent	SNP	ENST00000359032.5	hg19	CCDS46148.1																																																																																			.	.		0.607	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1			T	50302171	C	T	50302171	2	4	96	1	0	0	0	0	0	0	0	1	739	845	30	3		3	AP2A1	19	50302171	Silent	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	8701944	50302171	8826812	48	13257										
SNRPB	6628	hgsc.bcm.edu	37	chr20	2443295	2443295	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	cacttacctcgcatcccaggGggaggaggccgcattcccgg	13	15	0	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr20:2443295G>C	ENST00000438552.2	-	6	834	c.672C>G	c.(670-672)ccC>ccG	p.P224P	SNRPB_ENST00000339610.6_Silent_p.P145P|SNRPB_ENST00000381342.2_Silent_p.P224P|SNORD119_ENST00000515997.1_RNA	NM_198216.1	NP_937859.1	P14678	RSMB_HUMAN	small nuclear ribonucleoprotein polypeptides B and B1	224	Repeat-rich region.				gene expression (GO:0010467)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)|U7 snRNP (GO:0005683)	histone pre-mRNA DCP binding (GO:0071208)|poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	10						GCATCCCAGGGGGAGGAGGCC	0.572																																					p.P224P		Atlas-SNP	.											.	SNRPB	29	.	0			c.C672G						.						53	55	54					20																	2443295		2192	4284	6476	SO:0001819	synonymous_variant	6628	exon6			CCCAGGGGGAGGA		CCDS13026.1, CCDS13027.1	20p13	2011-10-11			ENSG00000125835	ENSG00000125835			11153	protein-coding gene	gene with protein product		182282		SNRPB1		1376292	Standard	NM_003091		Approved	COD, SmB/SmB', Sm-B/B', snRNP-B	uc002wfz.1	P14678	OTTHUMG00000031694	ENST00000438552.2:c.672C>G	chr20.hg19:g.2443295G>C		114.0	0.0		86.0	10.0	NM_003091	Q15490|Q6IB35|Q9UIS5	Silent	SNP	ENST00000438552.2	hg19	CCDS13026.1																																																																																			.	.		0.572	SNRPB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077585.2			C	2443295	G	C	2443295	2	2	96	1	0	0	0	0	0	0	0	1	14876	1219	43	4		4	SNRPB	20	2443295	Silent	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10		2443295	60582225	49	13258										
WFDC8	90199	hgsc.bcm.edu	37	chr20	44181869	44181869	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	ctgtgacatgaaggtggacaCtccttacgttcagtgaaagg	12	8	1	3			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr20:44181869C>T	ENST00000357199.4	-	5	570	c.492G>A	c.(490-492)gaG>gaA	p.E164E	WFDC8_ENST00000289953.2_Silent_p.E164E	NM_181510.2	NP_852611.2	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8	164	WAP 2. {ECO:0000255|PROSITE- ProRule:PRU00722}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|stomach(1)|upper_aerodigestive_tract(1)	15		Myeloproliferative disorder(115;0.0122)				AAGGTGGACACTCCTTACGTT	0.498																																					p.E164E		Atlas-SNP	.											.	WFDC8	28	.	0			c.G492A						.						137	110	119					20																	44181869		2203	4300	6503	SO:0001819	synonymous_variant	90199	exon5			TGGACACTCCTTA	AL031663	CCDS13361.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000158901	ENSG00000158901		"WAP four-disulfide core domain containing"	16163	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 170"	C20orf170		12206714	Standard	NM_130896		Approved	dJ461P17.1, WAP8	uc002xow.3	Q8IUA0	OTTHUMG00000046342	ENST00000357199.4:c.492G>A	chr20.hg19:g.44181869C>T		108.0	0.0		91.0	9.0	NM_181510	E1P623|Q5TDV2|Q96A34	Silent	SNP	ENST00000357199.4	hg19	CCDS13361.1																																																																																			.	.		0.498	WFDC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106958.1			T	44181869	C	T	44181869	2	4	96	1	0	0	0	0	0	0	0	1	17371	564	20	3		3	WFDC8	20	44181869	Silent	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10	41738574	44181869	18843651	50	13259										
RBM9	23543	hgsc.bcm.edu	37	chr22	36164375	36164375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	gtctgcatcagcactattctCgaaagttacgaacccgaatc	7	12	3	0	rs199852787		TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr22:36164375C>T	ENST00000438146.2	-	6	684	c.685G>A	c.(685-687)Gag>Aag	p.E229K	RBFOX2_ENST00000262829.7_Missense_Mutation_p.E140K|RBFOX2_ENST00000359369.4_Missense_Mutation_p.E138K|RBFOX2_ENST00000449924.2_Missense_Mutation_p.E158K|RBFOX2_ENST00000416721.2_Missense_Mutation_p.E158K|RBFOX2_ENST00000414461.2_Missense_Mutation_p.E158K|RBFOX2_ENST00000405409.2_Missense_Mutation_p.E159K|RBFOX2_ENST00000397303.2_Missense_Mutation_p.E139K	NM_001082578.1|NM_001082579.1	NP_001076047|NP_001076048.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	168					dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(7)|lung(7)	18						GCACTATTCTCGAAAGTTACG	0.448																																					p.E229K		Atlas-SNP	.											RBFOX2_ENST00000438146,NS,carcinoma,0,2	RBFOX2	62	.	0			c.G685A						.						151	135	140					22																	36164375		2203	4300	6503	SO:0001583	missense	23543	exon6			TATTCTCGAAAGT	AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"RNA binding motif (RRM) containing"	9906	protein-coding gene	gene with protein product	"hexaribonucleotide binding protein 2"	612149	"RNA binding motif protein 9"	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000438146.2:c.685G>A	chr22.hg19:g.36164375C>T	ENSP00000413035:p.Glu229Lys	111.0	0.0		90.0	8.0	NM_001082578	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Missense_Mutation	SNP	ENST00000438146.2	hg19	CCDS43013.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946211	0.73672	.	.	ENSG00000100320	ENST00000405409;ENST00000338644;ENST00000414461;ENST00000449924;ENST00000262829;ENST00000397303;ENST00000359369;ENST00000416721;ENST00000438146;ENST00000408983	T;T;T;T;T;T;T;T;T	0.17213	2.29;2.29;2.29;2.29;2.29;2.29;2.29;2.29;2.29	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.27524	0.0676	N	0.12471	0.22	0.80722	D	1	D;D;D;D;P;B;B;B;B	0.76494	0.998;0.999;0.981;0.995;0.89;0.22;0.127;0.325;0.244	P;D;B;D;B;B;B;B;B	0.69142	0.838;0.962;0.379;0.956;0.258;0.119;0.039;0.119;0.104	T	0.16571	-1.0398	10	0.87932	D	0	.	20.3544	0.98835	0.0:1.0:0.0:0.0	.	138;228;229;140;158;159;158;158;139	B0QYY4;O43251-6;O43251-8;O43251-3;O43251-5;O43251-9;O43251-10;O43251-4;B0QYV1	.;.;.;.;.;.;.;.;.	K	159;168;158;158;140;139;138;158;229;181	ENSP00000384944:E159K;ENSP00000407855:E158K;ENSP00000391670:E158K;ENSP00000262829:E140K;ENSP00000380470:E139K;ENSP00000352328:E138K;ENSP00000405651:E158K;ENSP00000413035:E229K;ENSP00000386177:E181K	ENSP00000262829:E140K	E	-	1	0	RBFOX2	34494321	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.773000	0.85462	2.817000	0.96982	0.655000	0.94253	GAG	.	C|1.000;G|0.000		0.448	RBFOX2-005	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319299.3			T	36164375	C	T	36164375	3	4	96	1	0	0	0	0	1	0	0	0	13162	893	31	1	716	1	RBM9	22	36164375	Missense_Mutation	SNP	C	TCGA-DD-A1E9-01A-21D-A152-10		36164375	15140191	51	13260										
XRCC6	2547	hgsc.bcm.edu	37	chr22	42042966	42042966	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	tataatctggtccagaaggcTctcaagcctcctccaataaa	6	12	2	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chr22:42042966T>A	ENST00000359308.4	+	6	1495	c.840T>A	c.(838-840)gcT>gcA	p.A280A	XRCC6_ENST00000405878.1_Silent_p.A280A|XRCC6_ENST00000405506.1_Silent_p.A230A|XRCC6_ENST00000402580.3_Silent_p.A239A|XRCC6_ENST00000428575.2_Silent_p.A147A|Y_RNA_ENST00000363462.1_RNA|XRCC6_ENST00000360079.3_Silent_p.A280A			P12956	XRCC6_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 6	280	Ku.				brain development (GO:0007420)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA ligation (GO:0006266)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	5'-deoxyribose-5-phosphate lyase activity (GO:0051575)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	31						TCCAGAAGGCTCTCAAGCCTC	0.428								Non-homologous end-joining																													p.A280A		Atlas-SNP	.											.	XRCC6	64	.	0			c.T840A						.						119	129	126					22																	42042966		2203	4300	6503	SO:0001819	synonymous_variant	2547	exon7			GAAGGCTCTCAAG	J04607	CCDS14021.1, CCDS74870.1, CCDS74871.1	22q13.2	2011-09-12	2008-07-31	2005-05-06	ENSG00000196419	ENSG00000196419			4055	protein-coding gene	gene with protein product	"Ku autoantigen, 70kDa"	152690	"thyroid autoantigen 70kD (Ku antigen)", "thyroid autoantigen 70kDa (Ku antigen)"	G22P1		9200330, 9223317	Standard	NM_001469		Approved	D22S731, D22S671, KU70, ML8	uc003bao.1	P12956	OTTHUMG00000151190	ENST00000359308.4:c.840T>A	chr22.hg19:g.42042966T>A		137.0	0.0		153.0	47.0	NM_001469	B1AHC8|Q6FG89|Q9UCQ2|Q9UCQ3	Silent	SNP	ENST00000359308.4	hg19	CCDS14021.1																																																																																			.	.		0.428	XRCC6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321688.1	NM_001469		A	42042966	T	A	42042966	2	1	96	1	0	0	0	0	0	0	0	1	17472	1538	54	4		4	XRCC6	22	42042966	Silent	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10	5878591	42042966	9261600	52	13261										
PCDH19	57526	hgsc.bcm.edu	37	chrX	99662112	99662112	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	caggcatgtcccgcacctgcGacggcacgatctggtaggag	14	13	1	0			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chrX:99662112G>A	ENST00000373034.4	-	1	3159	c.1484C>T	c.(1483-1485)tCg>tTg	p.S495L	PCDH19_ENST00000255531.7_Missense_Mutation_p.S495L|PCDH19_ENST00000420881.2_Missense_Mutation_p.S495L	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	495	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						CCGCACCTGCGACGGCACGAT	0.597																																					p.S495L		Atlas-SNP	.											.	PCDH19	269	.	0			c.C1484T						.						86	87	87					X																	99662112		2129	4226	6355	SO:0001583	missense	57526	exon1			ACCTGCGACGGCA	AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.1484C>T	chrX.hg19:g.99662112G>A	ENSP00000362125:p.Ser495Leu	94.0	0.0		101.0	47.0	NM_001184880	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	hg19	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.543562	0.65198	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.52526	0.66;0.66;0.66	5.64	5.64	0.86602	Cadherin (4);Cadherin-like (1);	0.128926	0.53938	D	0.000058	T	0.65144	0.2663	L	0.56124	1.755	0.58432	D	0.999999	D;D;D	0.76494	0.994;0.999;0.999	P;D;D	0.69479	0.891;0.939;0.964	T	0.64984	-0.6278	10	0.51188	T	0.08	.	18.6745	0.91524	0.0:0.0:1.0:0.0	.	495;495;495	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	L	495	ENSP00000400327:S495L;ENSP00000362125:S495L;ENSP00000255531:S495L	ENSP00000255531:S495L	S	-	2	0	PCDH19	99548768	1.000000	0.71417	0.714000	0.30535	0.992000	0.81027	6.216000	0.72212	2.354000	0.79902	0.513000	0.50165	TCG	.	.		0.597	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		A	99662112	G	A	99662112	3	1	96	1	0	0	0	0	1	0	0	0	11523	1059	37	1	1986	1	PCDH19	23	99662112	Missense_Mutation	SNP	G	TCGA-DD-A1E9-01A-21D-A152-10		99662112	55608448	53	13262										
MMGT1	93380	hgsc.bcm.edu	37	chrX	135049605	135049605	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.543436293436293	1.90202702702703	0.317004504504505	1	1	0	aactctcctgcaatatgaacTataccgtaacaggtaactgc	6	11	1	1			TCGA-DD-A1E9-01A-21D-A152-10	TCGA-DD-A1E9-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a0bc36-9f29-4b23-aee1-bf5ff71f697b	f37fe995-4af3-489f-988e-ca04430e4e57	g.chrX:135049605T>G	ENST00000305963.2	-	3	567	c.180A>C	c.(178-180)atA>atC	p.I60I	MMGT1_ENST00000433339.2_Silent_p.I125I	NM_173470.1	NP_775741.1	Q8N4V1	MMGT1_HUMAN	membrane magnesium transporter 1	60					magnesium ion transport (GO:0015693)	early endosome (GO:0005769)|ER membrane protein complex (GO:0072546)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(1)|endometrium(1)|kidney(1)	3						CAATATGAACTATACCGTAAC	0.323																																					p.I60I		Atlas-SNP	.											.	MMGT1	14	.	0			c.A180C						.						135	127	130					X																	135049605		2203	4300	6503	SO:0001819	synonymous_variant	93380	exon3			ATGAACTATACCG	AL157477	CCDS14653.1	Xq26.3	2012-05-23	2008-11-21	2008-11-21	ENSG00000169446	ENSG00000169446			28100	protein-coding gene	gene with protein product	"ER membrane protein complex subunit 5"		"transmembrane protein 32"	TMEM32		18057121, 22119785	Standard	NM_173470		Approved	EMC5	uc004ezi.1	Q8N4V1	OTTHUMG00000022499	ENST00000305963.2:c.180A>C	chrX.hg19:g.135049605T>G		193.0	0.0		220.0	106.0	NM_173470	B2R625|B4DIY3|D3DWG7|Q5JPP7	Silent	SNP	ENST00000305963.2	hg19	CCDS14653.1																																																																																			.	.		0.323	MMGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058453.3	NM_173470		G	135049605	T	G	135049605	2	3	96	1	0	0	0	0	0	0	0	1	9656	1512	53	5		5	MMGT1	23	135049605	Silent	SNP	T	TCGA-DD-A1E9-01A-21D-A152-10	35387493	135049605	20220955	54	13263										
H6PD	9563	hgsc.bcm.edu	37	chr1	9305494	9305494	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cggccaggcccgggcgcctgGctgcgggttgtccttgagaa	17	13	0	1	rs559063919		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:9305494G>A	ENST00000377403.2	+	2	803	c.501G>A	c.(499-501)tgG>tgA	p.W167*	H6PD_ENST00000602477.1_Nonsense_Mutation_p.W178*	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	167	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		CGGGCGCCTGGCTGCGGGTTG	0.597																																					p.W167X		Atlas-SNP	.											.	H6PD	71	.	0			c.G501A						.						46	55	52					1																	9305494		2203	4300	6503	SO:0001587	stop_gained	9563	exon2			CGCCTGGCTGCGG	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"glucose dehyrogenase"	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.501G>A	chr1.hg19:g.9305494G>A	ENSP00000366620:p.Trp167*	30.0	0.0		42.0	20.0	NM_004285	Q4TT33|Q66I35|Q68DT3	Nonsense_Mutation	SNP	ENST00000377403.2	hg19	CCDS101.1	.	.	.	.	.	.	.	.	.	.	G	40	8.156138	0.98680	.	.	ENSG00000049239	ENST00000377403	.	.	.	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.7585	18.3309	0.90268	0.0:0.0:1.0:0.0	.	.	.	.	X	167	.	ENSP00000366620:W167X	W	+	3	0	H6PD	9228081	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.358000	0.97109	2.641000	0.89580	0.591000	0.81541	TGG	.	.		0.597	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		A	9305494	G	A	9305494	4	1	97	1	0	0	0	0	0	1	0	0	6945	1212	42	3	503	3	H6PD	1	9305494	Nonsense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10		9305494	239945127	1	13264										
CLSTN1	22883	hgsc.bcm.edu	37	chr1	9795606	9795606	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ggtacgagatgtgctgcatgGccttatccaattccccgagg	12	11	0	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:9795606G>T	ENST00000377298.4	-	13	2594	c.1802C>A	c.(1801-1803)gCc>gAc	p.A601D	CLSTN1_ENST00000361311.4_Missense_Mutation_p.A591D|CLSTN1_ENST00000477264.1_5'Flank|CLSTN1_ENST00000377288.3_Missense_Mutation_p.A582D	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	601					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		GTGCTGCATGGCCTTATCCAA	0.517																																					p.A601D		Atlas-SNP	.											.	CLSTN1	88	.	0			c.C1802A						.						164	154	157					1																	9795606		2203	4300	6503	SO:0001583	missense	22883	exon13			TGCATGGCCTTAT	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"Cadherins / Cadherin-related"	17447	protein-coding gene	gene with protein product	"cadherin-related family member 12"	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.1802C>A	chr1.hg19:g.9795606G>T	ENSP00000366513:p.Ala601Asp	98.0	0.0		215.0	92.0	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	hg19	CCDS30580.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.354559	0.61293	.	.	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	5.91	5.91	0.95273	.	0.053126	0.85682	D	0.000000	T	0.63780	0.2540	M	0.78049	2.395	0.58432	D	0.999996	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.68943	0.914;0.961;0.914	T	0.64748	-0.6334	10	0.66056	D	0.02	-49.4122	20.2985	0.98592	0.0:0.0:1.0:0.0	.	582;591;601	B4E3Q1;O94985-2;O94985	.;.;CSTN1_HUMAN	D	601;591;402;582;582	ENSP00000366513:A601D;ENSP00000354997:A591D;ENSP00000401934:A402D;ENSP00000366502:A582D	ENSP00000354997:A591D	A	-	2	0	CLSTN1	9718193	1.000000	0.71417	0.994000	0.49952	0.089000	0.18198	4.609000	0.61148	2.793000	0.96121	0.655000	0.94253	GCC	.	.		0.517	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1			T	9795606	G	T	9795606	3	4	97	1	0	0	0	0	1	0	0	0	3563	1203	42	3	1171	3	CLSTN1	1	9795606	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	490112	9795606	239455015	2	13265										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67861669	67861669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ggagcctcagcacatctcccTttctgttttcccctcaagtt	6	15	4	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:67861669T>C	ENST00000262345.1	+	16	3126	c.2486T>C	c.(2485-2487)cTt>cCt	p.L829P	IL12RB2_ENST00000544434.1_Missense_Mutation_p.L743P|IL12RB2_ENST00000371000.1_3'UTR	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	829					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						CACATCTCCCTTTCTGTTTTC	0.512																																					p.L829P		Atlas-SNP	.											.	IL12RB2	94	.	0			c.T2486C						.						310	295	300					1																	67861669		2203	4300	6503	SO:0001583	missense	3595	exon16			TCTCCCTTTCTGT	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.2486T>C	chr1.hg19:g.67861669T>C	ENSP00000262345:p.Leu829Pro	130.0	0.0		335.0	124.0	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	hg19	CCDS638.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.085356	0.36758	.	.	ENSG00000081985	ENST00000262345;ENST00000544434	T;T	0.49139	0.79;1.71	5.29	4.15	0.48705	.	0.892298	0.09923	N	0.738230	T	0.16769	0.0403	L	0.27053	0.805	0.20196	N	0.999927	B;B	0.33637	0.42;0.028	B;B	0.29176	0.099;0.014	T	0.10132	-1.0643	10	0.66056	D	0.02	-6.8301	7.2723	0.26264	0.0:0.0981:0.0:0.9019	.	743;829	F5H7L6;Q99665	.;I12R2_HUMAN	P	829;743	ENSP00000262345:L829P;ENSP00000442443:L743P	ENSP00000262345:L829P	L	+	2	0	IL12RB2	67634257	0.013000	0.17824	0.012000	0.15200	0.388000	0.30384	2.086000	0.41643	2.135000	0.66039	0.482000	0.46254	CTT	.	.		0.512	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		C	67861669	T	C	67861669	3	2	97	1	0	0	0	0	1	0	0	0	7636	1609	56	2	2544	2	IL12RB2	1	67861669	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	58066063	67861669	181388952	3	13266										
AMY2A	279	hgsc.bcm.edu	37	chr1	104160673	104160673	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	taaattatgcacaagatctgGaaatgaagatgaatttagaa	8	3	1	5			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:104160673G>C	ENST00000414303.2	+	2	330	c.266G>C	c.(265-267)gGa>gCa	p.G89A		NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)	89					carbohydrate catabolic process (GO:0016052)|carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|calcium ion binding (GO:0005509)|chloride ion binding (GO:0031404)			endometrium(3)|kidney(1)|large_intestine(5)|liver(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491)	ACAAGATCTGGAAATGAAGAT	0.353																																					p.G89A		Atlas-SNP	.											.	AMY2A	36	.	0			c.G266C						.						131	122	125					1																	104160673		2201	4275	6476	SO:0001583	missense	279	exon2			GATCTGGAAATGA	BC007060	CCDS783.1	1p21.1	2012-10-02	2007-05-03		ENSG00000243480	ENSG00000243480	3.2.1.1		477	protein-coding gene	gene with protein product		104650	"amylase, alpha 2A; pancreatic"	AMY2		3260028	Standard	NM_000699		Approved		uc001dut.3	P04746	OTTHUMG00000011023	ENST00000414303.2:c.266G>C	chr1.hg19:g.104160673G>C	ENSP00000397582:p.Gly89Ala	189.0	0.0		1043.0	374.0	NM_000699	B9EJG1|Q9UBH3	Missense_Mutation	SNP	ENST00000414303.2	hg19	CCDS783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	20.8|20.8	4.045045|4.045045	0.75846|0.75846	.|.	.|.	ENSG00000243480|ENSG00000243480	ENST00000414303;ENST00000393932|ENST00000423678	D|.	0.99929|.	-8.14|.	3.47|3.47	3.47|3.47	0.39725|0.39725	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87728|0.87728	0.6250|0.6250	H|H	0.99104|0.99104	4.43|4.43	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.92796|0.92796	0.6252|0.6252	10|5	0.87932|.	D|.	0|.	.|.	15.0729|15.0729	0.72053|0.72053	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	89;89|.	B9EJG1;P04746|.	.;AMYP_HUMAN|.	A|C	89|87	ENSP00000397582:G89A|.	ENSP00000377509:G89A|.	G|W	+|+	2|3	0|0	AMY2A|AMY2A	103962196|103962196	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.163000|9.163000	0.94750|0.94750	1.927000|1.927000	0.55829|0.55829	0.455000|0.455000	0.32223|0.32223	GGA|TGG	.	.		0.353	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	NM_000699		C	104160673	G	C	104160673	3	2	97	1	0	0	0	0	1	0	0	0	594	1174	41	4	272	4	AMY2A	1	104160673	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	36299004	104160673	145089948	4	13267										
FNDC7	163479	hgsc.bcm.edu	37	chr1	109270564	109270564	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	acaacatggttgagtgcaatGacactactcctgcgtgcacc	9	12	0	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:109270564G>A	ENST00000370017.3	+	7	1523	c.1246G>A	c.(1246-1248)Gac>Aac	p.D416N	FNDC7_ENST00000271311.2_Missense_Mutation_p.D417N	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	416	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		TGAGTGCAATGACACTACTCC	0.488																																					p.D416N		Atlas-SNP	.											.	FNDC7	113	.	0			c.G1246A						.						288	244	259					1																	109270564		2203	4300	6503	SO:0001583	missense	163479	exon7			TGCAATGACACTA		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"Fibronectin type III domain containing"	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.1246G>A	chr1.hg19:g.109270564G>A	ENSP00000359034:p.Asp416Asn	96.0	0.0		200.0	91.0	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	hg19	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.933047	0.92458	.	.	ENSG00000143107	ENST00000370017;ENST00000271311	T;T	0.23950	1.88;1.88	5.73	5.73	0.89815	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.041024	0.85682	D	0.000000	T	0.41073	0.1143	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.03875	-1.0996	10	0.19147	T	0.46	-16.3329	19.9068	0.97010	0.0:0.0:1.0:0.0	.	417;416	Q5VTL7;E9PAZ5	FNDC7_HUMAN;.	N	416;417	ENSP00000359034:D416N;ENSP00000271311:D417N	ENSP00000271311:D417N	D	+	1	0	FNDC7	109072087	1.000000	0.71417	1.000000	0.80357	0.619000	0.37552	9.068000	0.93961	2.710000	0.92621	0.561000	0.74099	GAC	.	.		0.488	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532		A	109270564	G	A	109270564	3	1	97	1	0	0	0	0	1	0	0	0	5981	1290	45	3	1272	3	FNDC7	1	109270564	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	5109891	109270564	139980057	5	13268										
ATP1A1	476	hgsc.bcm.edu	37	chr1	116933025	116933025	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tgaagctgatacgacagagaAtcagagtggtaaggccaggg	15	6	1	4			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:116933025A>C	ENST00000295598.5	+	9	1466	c.1214A>C	c.(1213-1215)aAt>aCt	p.N405T	ATP1A1_ENST00000369496.4_Missense_Mutation_p.N374T|ATP1A1_ENST00000537345.1_Missense_Mutation_p.N405T	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	405					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	ACGACAGAGAATCAGAGTGGT	0.423																																					p.N405T		Atlas-SNP	.											.	ATP1A1	87	.	0			c.A1214C						.						59	58	58					1																	116933025		2203	4300	6503	SO:0001583	missense	476	exon9			CAGAGAATCAGAG	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1214A>C	chr1.hg19:g.116933025A>C	ENSP00000295598:p.Asn405Thr	88.0	0.0		191.0	66.0	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	A	18.43	3.622723	0.66787	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	T;T;T	0.78816	-1.21;-1.21;-1.21	4.87	4.87	0.63330	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.59252	0.2180	N	0.20881	0.62	0.80722	D	1	B;B	0.14805	0.009;0.011	B;B	0.33960	0.108;0.173	T	0.61753	-0.6998	10	0.45353	T	0.12	.	14.6423	0.68734	1.0:0.0:0.0:0.0	.	405;405	F5H3A1;P05023	.;AT1A1_HUMAN	T	405;405;404;374	ENSP00000295598:N405T;ENSP00000445306:N405T;ENSP00000358508:N374T	ENSP00000295598:N405T	N	+	2	0	ATP1A1	116734548	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.126000	0.94411	2.068000	0.61886	0.528000	0.53228	AAT	.	.		0.423	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		C	116933025	A	C	116933025	3	2	97	1	0	0	0	0	1	0	0	0	1128	101	4	5	1264	5	ATP1A1	1	116933025	Missense_Mutation	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	7662461	116933025	132317596	6	13269										
TRIM46	80128	hgsc.bcm.edu	37	chr1	155151089	155151089	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cagagcttaacttcctgcgaGgtaaggagatggccaggccc	13	11	0	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:155151089G>T	ENST00000334634.4	+	7	1285	c.1285G>T	c.(1285-1287)Gtg>Ttg	p.V429L	TRIM46_ENST00000368382.1_Splice_Site_p.V406L|TRIM46_ENST00000392451.2_Splice_Site_p.G429C|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000368383.3_Splice_Site_p.V429L|TRIM46_ENST00000545012.1_Splice_Site_p.V303L|TRIM46_ENST00000543729.1_Splice_Site_p.G436C|TRIM46_ENST00000368385.4_Splice_Site_p.V429L|RP11-201K10.3_ENST00000473363.2_Intron	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	429	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CTTCCTGCGAGGTAAGGAGAT	0.657																																					p.V429L		Atlas-SNP	.											.	TRIM46	79	.	0			c.G1285T						.						77	69	72					1																	155151089		2203	4300	6503	SO:0001630	splice_region_variant	80128	exon7			CTGCGAGGTAAGG		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19019	protein-coding gene	gene with protein product		600986	"tripartite motif-containing 46"				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.1285+1G>T	chr1.hg19:g.155151089G>T		22.0	0.0		81.0	19.0	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	hg19	CCDS1097.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.82|13.82	2.351221|2.351221	0.41700|0.41700	.|.	.|.	ENSG00000163462|ENSG00000163462	ENST00000543729;ENST00000392451|ENST00000430513;ENST00000368385;ENST00000545012;ENST00000368383;ENST00000368382;ENST00000334634	T;T|T;T;T;T;T	0.50548|0.43294	0.8;0.74|0.95;0.95;0.95;0.95;0.95	3.51|3.51	3.51|3.51	0.40186|0.40186	.|Fibronectin, type III (1);	.|0.168925	.|0.37955	.|U	.|0.001863	T|T	0.11367|0.11367	0.0277|0.0277	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|B;B;B;P	.|0.37500	.|0.329;0.143;0.176;0.597	.|B;B;B;B	.|0.34779	.|0.148;0.039;0.096;0.189	T|T	0.08106|0.08106	-1.0738|-1.0738	7|10	0.72032|0.51188	D|T	0.01|0.08	.|.	10.7031|10.7031	0.45939|0.45939	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|429;406;429;429	.|Q5VT61;B1AVQ4;Q7Z4K8;Q7Z4K8-2	.|.;.;TRI46_HUMAN;.	C|L	436;429|387;429;303;429;406;429	ENSP00000442719:G436C;ENSP00000376245:G429C|ENSP00000357369:V429L;ENSP00000440254:V303L;ENSP00000357367:V429L;ENSP00000357366:V406L;ENSP00000334657:V429L	ENSP00000376245:G429C|ENSP00000334657:V429L	G|V	+|+	1|1	0|0	TRIM46|TRIM46	153417713|153417713	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.944000|0.944000	0.59088|0.59088	6.194000|6.194000	0.72082|0.72082	1.952000|1.952000	0.56665|0.56665	0.313000|0.313000	0.20887|0.20887	GGC|GTG	.	.		0.657	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058	Missense_Mutation	T	155151089	G	T	155151089	5	4	97	1	0	0	0	0	0	0	1	0	16536	1014	35	3	1311	3	TRIM46	1	155151089	Splice_Site	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	38218064	155151089	94099532	7	13270										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196309631	196309631	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tctgtagaattcataatgtaTcgaggacctggattcagcaa	9	7	3	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:196309631T>C	ENST00000294725.9	-	16	2538	c.1623A>G	c.(1621-1623)cgA>cgG	p.R541R	KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000367431.4_Silent_p.R491R|KCNT2_ENST00000451324.2_Silent_p.R152R|KCNT2_ENST00000367433.5_Silent_p.R541R|KCNT2_ENST00000609185.1_Silent_p.R491R			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	541	RCK N-terminal.				potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						TCATAATGTATCGAGGACCTG	0.328																																					p.R541R		Atlas-SNP	.											.	KCNT2	243	.	0			c.A1623G						.						73	73	73					1																	196309631		2203	4299	6502	SO:0001819	synonymous_variant	343450	exon16			AATGTATCGAGGA	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.1623A>G	chr1.hg19:g.196309631T>C		70.0	0.0		199.0	42.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	hg19	CCDS1384.1																																																																																			.	.		0.328	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		C	196309631	T	C	196309631	2	2	97	1	0	0	0	0	0	0	0	1	8101	1422	50	2		2	KCNT2	1	196309631	Silent	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	41158542	196309631	52940990	8	13271										
DDX59	83479	hgsc.bcm.edu	37	chr1	200635118	200635118	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	aaaagcagctgtttttcctgAgccagtatctgcactggcca	9	11	1	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:200635118A>T	ENST00000331314.6	-	2	964	c.751T>A	c.(751-753)Tca>Aca	p.S251T	DDX59_ENST00000447706.2_Missense_Mutation_p.S251T|DDX59_ENST00000367348.3_Missense_Mutation_p.S251T	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	251	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						GTTTTTCCTGAGCCAGTATCT	0.418																																					p.S251T		Atlas-SNP	.											.	DDX59	117	.	0			c.T751A						.						90	90	90					1																	200635118		2203	4300	6503	SO:0001583	missense	83479	exon2			TTCCTGAGCCAGT	BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"Zinc fingers, HIT-type", "DEAD-boxes"	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.751T>A	chr1.hg19:g.200635118A>T	ENSP00000330460:p.Ser251Thr	114.0	0.0		442.0	102.0	NM_001031725	Q6PJL2|Q8IVW3|Q9H0W3	Missense_Mutation	SNP	ENST00000331314.6	hg19	CCDS30964.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.724387	0.89298	.	.	ENSG00000118197	ENST00000447706;ENST00000367348;ENST00000331314	T;T;T	0.51574	0.7;0.7;0.7	5.33	5.33	0.75918	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.56217	0.1970	L	0.27944	0.81	0.80722	D	1	D;D	0.65815	0.995;0.995	D;D	0.71656	0.974;0.974	T	0.61491	-0.7052	10	0.87932	D	0	-18.7333	15.3466	0.74343	1.0:0.0:0.0:0.0	.	251;251	B7Z5N6;Q5T1V6	.;DDX59_HUMAN	T	251	ENSP00000394367:S251T;ENSP00000356317:S251T;ENSP00000330460:S251T	ENSP00000330460:S251T	S	-	1	0	DDX59	198901741	1.000000	0.71417	0.990000	0.47175	0.976000	0.68499	9.320000	0.96346	2.021000	0.59480	0.529000	0.55759	TCA	.	.		0.418	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4		T	200635118	A	T	200635118	3	4	97	1	0	0	0	0	1	0	0	0	4378	304	11	4	1136	4	DDX59	1	200635118	Missense_Mutation	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	4325487	200635118	48615503	9	13272										
DYRK3	8444	hgsc.bcm.edu	37	chr1	206820946	206820946	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	aatccaacagttcatccaagGcacccaaagtggtgcctctg	8	13	2	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:206820946G>T	ENST00000367109.2	+	3	571	c.403G>T	c.(403-405)Gca>Tca	p.A135S	DYRK3_ENST00000367106.1_Missense_Mutation_p.A115S|DYRK3_ENST00000489878.1_Intron|DYRK3_ENST00000367108.3_Missense_Mutation_p.A115S	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	135					erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			TTCATCCAAGGCACCCAAAGT	0.413																																					p.A135S	Melanoma(164;427 2622 26826 51707)	Atlas-SNP	.											.	DYRK3	146	.	0			c.G403T						.						79	79	79					1																	206820946		2203	4300	6503	SO:0001583	missense	8444	exon3			TCCAAGGCACCCA	Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"regulatory erythroid kinase", "dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5", "protein kinase Dyrk3"	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.403G>T	chr1.hg19:g.206820946G>T	ENSP00000356076:p.Ala135Ser	79.0	0.0		287.0	177.0	NM_003582	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Missense_Mutation	SNP	ENST00000367109.2	hg19	CCDS30999.1	.	.	.	.	.	.	.	.	.	.	G	0.108	-1.142325	0.01728	.	.	ENSG00000143479	ENST00000367109;ENST00000367108;ENST00000441486;ENST00000367106	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.09	0.837	0.18896	.	0.946011	0.09044	N	0.856863	T	0.20618	0.0496	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.23190	-1.0195	10	0.12430	T	0.62	.	1.6353	0.02740	0.1512:0.1642:0.3442:0.3405	.	135;115	O43781;O43781-2	DYRK3_HUMAN;.	S	135;115;115;115	ENSP00000356076:A135S;ENSP00000356075:A115S;ENSP00000410187:A115S;ENSP00000356073:A115S	ENSP00000356073:A115S	A	+	1	0	DYRK3	204887569	0.007000	0.16637	0.004000	0.12327	0.759000	0.43091	-0.275000	0.08525	-0.005000	0.14395	0.579000	0.79373	GCA	.	.		0.413	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1	NM_003582		T	206820946	G	T	206820946	3	4	97	1	0	0	0	0	1	0	0	0	4859	1203	42	3	434	3	DYRK3	1	206820946	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	6185828	206820946	42429675	10	13273										
CHRM3	1131	hgsc.bcm.edu	37	chr1	240071370	240071370	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gggctcctgccatcttgttcTggcaatactttgttggaaag	11	9	2	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:240071370T>A	ENST00000255380.4	+	5	1398	c.619T>A	c.(619-621)Tgg>Agg	p.W207R		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	207					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CATCTTGTTCTGGCAATACTT	0.517																																					p.W207R		Atlas-SNP	.											.	CHRM3	118	.	0			c.T619A						.						186	191	189					1																	240071370		2203	4300	6503	SO:0001583	missense	1131	exon5			TTGTTCTGGCAAT	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.619T>A	chr1.hg19:g.240071370T>A	ENSP00000255380:p.Trp207Arg	124.0	0.0		570.0	352.0	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	hg19	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.892572	0.72524	.	.	ENSG00000133019	ENST00000255380	T	0.37915	1.17	5.79	5.79	0.91817	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.61776	0.2374	M	0.73753	2.245	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65853	-0.6067	10	0.87932	D	0	-8.7528	16.1388	0.81509	0.0:0.0:0.0:1.0	.	207	P20309	ACM3_HUMAN	R	207	ENSP00000255380:W207R	ENSP00000255380:W207R	W	+	1	0	CHRM3	238137993	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.040000	0.89188	2.205000	0.71048	0.528000	0.53228	TGG	.	.		0.517	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		A	240071370	T	A	240071370	3	1	97	1	0	0	0	0	1	0	0	0	3380	1580	55	4	621	4	CHRM3	1	240071370	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	33250424	240071370	9179251	11	13274										
ZNF672	79894	hgsc.bcm.edu	37	chr1	249142604	249142604	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gagtgcagcaaggccttcagCgtcgcctccaagcttgcact	11	14	1	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:249142604C>T	ENST00000306562.3	+	4	1877	c.1131C>T	c.(1129-1131)agC>agT	p.S377S		NM_024836.1	NP_079112.1	Q499Z4	ZN672_HUMAN	zinc finger protein 672	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(1)	5	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			AGGCCTTCAGCGTCGCCTCCA	0.647																																					p.S377S		Atlas-SNP	.											.	ZNF672	32	.	0			c.C1131T						.						40	37	38					1																	249142604		2201	4300	6501	SO:0001819	synonymous_variant	79894	exon4			CTTCAGCGTCGCC	AK027476	CCDS1638.1	1q44	2013-01-08			ENSG00000171161	ENSG00000171161		"Zinc fingers, C2H2-type"	26179	protein-coding gene	gene with protein product	"hypothetical protein FLJ22301"					12477932	Standard	NM_024836		Approved	FLJ22301	uc001iex.3	Q499Z4	OTTHUMG00000040377	ENST00000306562.3:c.1131C>T	chr1.hg19:g.249142604C>T		5.0	0.0		30.0	18.0	NM_024836	Q96H65|Q96IM3|Q9H6G5	Silent	SNP	ENST00000306562.3	hg19	CCDS1638.1																																																																																			.	.		0.647	ZNF672-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097125.2	NM_024836		T	249142604	C	T	249142604	2	4	97	1	0	0	0	0	0	0	0	1	18094	767	27	1		1	ZNF672	1	249142604	Silent	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	9071234	249142604	108017	12	13275										
APOB	338	hgsc.bcm.edu	37	chr2	21231053	21231053	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gactagagaagtccagtttgGggatgttcaatttgtggaag	14	4	1	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr2:21231053G>A	ENST00000233242.1	-	26	8814	c.8687C>T	c.(8686-8688)cCc>cTc	p.P2896L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2896					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTCCAGTTTGGGGATGTTCAA	0.433																																					p.P2896L		Atlas-SNP	.											.	APOB	761	.	0			c.C8687T						.						176	173	174					2																	21231053		2203	4299	6502	SO:0001583	missense	338	exon26			AGTTTGGGGATGT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8687C>T	chr2.hg19:g.21231053G>A	ENSP00000233242:p.Pro2896Leu	110.0	0.0		232.0	100.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.677007	0.88445	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01527	4.8	5.73	5.73	0.89815	.	0.000000	0.51477	D	0.000088	T	0.11623	0.0283	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00061	-1.2161	10	0.87932	D	0	.	19.5098	0.95137	0.0:0.0:1.0:0.0	.	2896	P04114	APOB_HUMAN	L	2896	ENSP00000233242:P2896L	ENSP00000233242:P2896L	P	-	2	0	APOB	21084558	1.000000	0.71417	0.975000	0.42487	0.996000	0.88848	9.803000	0.99136	2.707000	0.92482	0.555000	0.69702	CCC	.	.		0.433	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21231053	G	A	21231053	3	1	97	1	0	0	0	0	1	0	0	0	785	1232	43	3	5020	3	APOB	2	21231053	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10		21231053	221968320	13	13276										
APOB	338	hgsc.bcm.edu	37	chr2	21245890	21245891	+	Frame_Shift_Ins	INS	-	-	T													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	aactccacagacacggagggINSttttgccaccagttcagcct							TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr2:21245890_21245891insT	ENST00000233242.1	-	18	2755_2756	c.2628_2629insA	c.(2626-2631)aaacccfs	p.P877fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	877			P -> L (in dbSNP:rs12714097).		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.P877S(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GACACGGAGGGTTTTGCCACCA	0.475																																					p.P877fs		Atlas-Indel,Pindel	.											APOB,NS,malignant_melanoma,0,1	APOB	761	.	1	Substitution - Missense(1)	NS(1)	c.2629_2630insA						.																																			SO:0001589	frameshift_variant	338	exon18			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.2629dupA	chr2.hg19:g.21245894_21245894dupT	ENSP00000233242:p.Pro877fs	79.0	0.0		137.0	51.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.475	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21245891	-	T	21245890	7	5	97	1	0	1	1	0	0	0	0	0	785	1261	44	0	11110	0	APOB	2	21245890	Frame_Shift_Ins	INS	-	TCGA-DD-A1EA-01A-11D-A12Z-10	14837	21245890	221953483	14	13277										
MEIS1	4211	hgsc.bcm.edu	37	chr2	66667100	66667100	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gtcattcaatgaagatatagCcgtgttcgccaaacaggtca	9	9	3	2	rs561384504		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr2:66667100C>A	ENST00000272369.9	+	3	822	c.365C>A	c.(364-366)gCc>gAc	p.A122D	MEIS1-AS1_ENST00000454595.1_RNA|MEIS1_ENST00000488550.1_Missense_Mutation_p.A122D|MEIS1_ENST00000495021.2_Missense_Mutation_p.A57D|MEIS1_ENST00000398506.2_Missense_Mutation_p.A120D|MEIS1-AS2_ENST00000439433.1_RNA|MEIS1_ENST00000444274.2_Missense_Mutation_p.A90D|MEIS1_ENST00000407092.2_Missense_Mutation_p.A122D|MEIS1_ENST00000560281.2_Missense_Mutation_p.A122D	NM_002398.2	NP_002389.1	O00470	MEIS1_HUMAN	Meis homeobox 1	122					angiogenesis (GO:0001525)|definitive hemopoiesis (GO:0060216)|lens morphogenesis in camera-type eye (GO:0002089)|megakaryocyte development (GO:0035855)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron differentiation (GO:0045665)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	24						GAAGATATAGCCGTGTTCGCC	0.532																																					p.A122D		Atlas-SNP	.											.	MEIS1	52	.	0			c.C365A						.						40	38	38					2																	66667100		1836	4082	5918	SO:0001583	missense	4211	exon3			ATATAGCCGTGTT		CCDS46309.1	2p14	2011-06-20	2007-02-15		ENSG00000143995	ENSG00000143995		"Homeoboxes / TALE class"	7000	protein-coding gene	gene with protein product		601739	"Meis1 (mouse) homolog", "Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)"			7565694	Standard	NM_002398		Approved		uc002sdu.3	O00470	OTTHUMG00000150714	ENST00000272369.9:c.365C>A	chr2.hg19:g.66667100C>A	ENSP00000272369:p.Ala122Asp	45.0	0.0		87.0	26.0	NM_002398	A8MV50	Missense_Mutation	SNP	ENST00000272369.9	hg19	CCDS46309.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650991	0.67472	.	.	ENSG00000143995	ENST00000272369;ENST00000407092;ENST00000398506;ENST00000444274;ENST00000495021	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.49253	0.1546	L	0.49571	1.57	0.80722	D	1	B;D;P;D	0.63046	0.016;0.992;0.895;0.984	B;D;P;D	0.65140	0.017;0.932;0.652;0.917	T	0.26950	-1.0088	9	.	.	.	.	18.7057	0.91637	0.0:1.0:0.0:0.0	.	57;120;122;122	F5GYS8;O00470-2;O00470;F8W8U3	.;.;MEIS1_HUMAN;.	D	122;122;120;90;57	ENSP00000272369:A122D;ENSP00000384461:A122D;ENSP00000381518:A120D;ENSP00000403206:A90D;ENSP00000440571:A57D	.	A	+	2	0	MEIS1	66520604	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.623000	0.83113	2.735000	0.93741	0.655000	0.94253	GCC	.	.		0.532	MEIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319725.4	NM_002398		A	66667100	C	A	66667100	3	1	97	1	0	0	0	0	1	0	0	0	9476	739	26	3	375	3	MEIS1	2	66667100	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	45421210	66667100	176532273	15	13278										
C2orf29	55571	hgsc.bcm.edu	37	chr2	101885756	101885756	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ttaatgtacaggatttgtttAtagaagtgcaggcattctgt	10	4	1	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr2:101885756A>T	ENST00000289382.3	+	7	1577	c.1414A>T	c.(1414-1416)Ata>Tta	p.I472L	RNF149_ENST00000485752.1_5'Flank	NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	472					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											GGATTTGTTTATAGAAGTGCA	0.383																																					p.I472L		Atlas-SNP	.											.	.	.	.	0			c.A1414T						.						87	90	89					2																	101885756		2203	4300	6503	SO:0001583	missense	55571	exon7			TTGTTTATAGAAG	AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 29"	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.1414A>T	chr2.hg19:g.101885756A>T	ENSP00000289382:p.Ile472Leu	94.0	0.0		188.0	74.0	NM_017546	Q6P2M9|Q8N681	Missense_Mutation	SNP	ENST00000289382.3	hg19	CCDS2050.1	.	.	.	.	.	.	.	.	.	.	A	34	5.383985	0.95967	.	.	ENSG00000158435	ENST00000289382	.	.	.	5.96	5.96	0.96718	.	0.087263	0.85682	D	0.000000	D	0.84234	0.5427	M	0.88310	2.945	0.80722	D	1	D	0.67145	0.996	D	0.68353	0.957	D	0.87008	0.2121	9	0.66056	D	0.02	-26.6738	16.4484	0.83959	1.0:0.0:0.0:0.0	.	472	Q9UKZ1	CB029_HUMAN	L	472	.	ENSP00000289382:I472L	I	+	1	0	C2orf29	101252188	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.210000	0.95106	2.285000	0.76669	0.533000	0.62120	ATA	.	.		0.383	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546		T	101885756	A	T	101885756	3	4	97	1	0	0	0	0	1	0	0	0	2163	449	16	4	1440	4	C2orf29	2	101885756	Missense_Mutation	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	35218656	101885756	141313617	16	13279										
CAB39	51719	hgsc.bcm.edu	37	chr2	231624746	231624746	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ccgtttgggaagtctcacaaAtctccagcagacattgtgaa	9	10	2	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr2:231624746A>G	ENST00000258418.5	+	2	459	c.30A>G	c.(28-30)aaA>aaG	p.K10K	CAB39_ENST00000410084.3_Silent_p.K10K|CAB39_ENST00000409788.3_Silent_p.K10K	NM_016289.3	NP_057373.1	Q9Y376	CAB39_HUMAN	calcium binding protein 39	10					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cellular hypotonic response (GO:0071476)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein heterooligomerization (GO:0051291)|signal transduction by phosphorylation (GO:0023014)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activator activity (GO:0043539)			central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)		AGTCTCACAAATCTCCAGCAG	0.498																																					p.K10K		Atlas-SNP	.											.	CAB39	30	.	0			c.A30G						.						89	92	91					2																	231624746		2203	4300	6503	SO:0001819	synonymous_variant	51719	exon2			TCACAAATCTCCA	AF113536	CCDS2478.1	2q37.1	2008-02-05			ENSG00000135932	ENSG00000135932			20292	protein-coding gene	gene with protein product		612174					Standard	NM_016289		Approved	CGI-66, MO25	uc002vqx.3	Q9Y376	OTTHUMG00000133220	ENST00000258418.5:c.30A>G	chr2.hg19:g.231624746A>G		100.0	0.0		267.0	114.0	NM_001130849	A8K8L7	Silent	SNP	ENST00000258418.5	hg19	CCDS2478.1																																																																																			.	.		0.498	CAB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256955.2	NM_016289		G	231624746	A	G	231624746	2	3	97	1	0	0	0	0	0	0	0	1	2527	98	4	2		2	CAB39	2	231624746	Silent	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	129738990	231624746	11574627	17	13280										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10443888	10443888	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gctcgatgcggctctgcaggCcccggaactgtttctctttg	12	13	2	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:10443888C>A	ENST00000352432.4	-	3	611	c.542G>T	c.(541-543)gGc>gTc	p.G181V	ATP2B2_ENST00000397077.1_Missense_Mutation_p.G181V|ATP2B2_ENST00000383800.4_Missense_Mutation_p.G181V|ATP2B2_ENST00000360273.2_Missense_Mutation_p.G181V|ATP2B2_ENST00000343816.4_Missense_Mutation_p.G181V			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	181					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						GCTCTGCAGGCCCCGGAACTG	0.592																																					p.G181V	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.G542T						.						131	142	138					3																	10443888		2203	4300	6503	SO:0001583	missense	491	exon4			TGCAGGCCCCGGA	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.542G>T	chr3.hg19:g.10443888C>A	ENSP00000324172:p.Gly181Val	45.0	0.0		95.0	40.0	NM_001683	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.013607	0.93404	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	5.44	5.44	0.79542	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.92935	0.7752	L	0.47078	1.49	0.80722	D	1	D;D;P	0.89917	1.0;0.991;0.946	D;D;P	0.97110	1.0;0.937;0.672	D	0.93482	0.6828	10	0.87932	D	0	-36.5231	19.2768	0.94034	0.0:1.0:0.0:0.0	.	181;193;181	Q01814-7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	V	181;181;181;181;181;147;68;181	ENSP00000324172:G181V;ENSP00000373311:G181V;ENSP00000380267:G181V;ENSP00000353414:G181V;ENSP00000344677:G181V;ENSP00000414854:G68V	ENSP00000342954:G181V	G	-	2	0	ATP2B2	10418888	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.550000	0.86006	0.467000	0.42956	GGC	.	.		0.592	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10443888	C	A	10443888	3	1	97	1	0	0	0	0	1	0	0	0	1140	739	26	3	3269	3	ATP2B2	3	10443888	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10		10443888	187578542	18	13281										
DAZL	1618	hgsc.bcm.edu	37	chr3	16639045	16639045	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ttaaaaaatgaaacaaatccAtagctataaaggcagataaa	5	5	0	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:16639045A>G	ENST00000399444.2	-	4	539	c.246T>C	c.(244-246)taT>taC	p.Y82Y	DAZL_ENST00000250863.8_Silent_p.Y102Y	NM_001351.3	NP_001342.2	Q92904	DAZL_HUMAN	deleted in azoospermia-like	82	Homodimerization. {ECO:0000250}.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				female meiosis II (GO:0007147)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|oocyte maturation (GO:0001556)|positive regulation of meiosis (GO:0045836)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494)		RAF1/DAZL(2)	endometrium(1)|large_intestine(3)|lung(4)|prostate(3)	11						AAACAAATCCATAGCTATAAA	0.289																																					p.Y102Y		Atlas-SNP	.											.	DAZL	23	.	0			c.T306C						.						215	175	187					3																	16639045		1829	4082	5911	SO:0001819	synonymous_variant	1618	exon4			AAATCCATAGCTA	BC027595	CCDS43059.1, CCDS54556.1	3p24	2013-02-12			ENSG00000092345	ENSG00000092345		"RNA binding motif (RRM) containing"	2685	protein-coding gene	gene with protein product		601486		DAZLA		8896558	Standard	NM_001351		Approved	DAZH, SPGYLA, MGC26406, DAZL1	uc003cbb.3	Q92904	OTTHUMG00000157050	ENST00000399444.2:c.246T>C	chr3.hg19:g.16639045A>G		112.0	0.0		198.0	68.0	NM_001190811	O15396|Q5HYB4|Q92909	Silent	SNP	ENST00000399444.2	hg19	CCDS43059.1																																																																																			.	.		0.289	DAZL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347261.2	NM_001351		G	16639045	A	G	16639045	2	3	97	1	0	0	0	0	0	0	0	1	4248	224	8	2		2	DAZL	3	16639045	Silent	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	6195157	16639045	181383385	19	13282										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266093	41266107	+	In_Frame_Del	DEL	CCTGGACTCTGGAAT	CCTGGACTCTGGAAT	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cactggcagcaacagtcttaCctggactctggaatccattc					rs28931589|rs121913396|rs121913416|rs121913417|rs121913399|rs121913400|rs28931588		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CCTGGACTCTGGAAT	CCTGGACTCTGGAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:41266093_41266107delCCTGGACTCTGGAAT	ENST00000349496.5	+	3	370_384	c.90_104delCCTGGACTCTGGAAT	c.(88-105)tacctggactctggaatc>tac	p.LDSGI31del	CTNNB1_ENST00000453024.1_In_Frame_Del_p.LDSGI24del|CTNNB1_ENST00000396183.3_In_Frame_Del_p.LDSGI31del|CTNNB1_ENST00000396185.3_In_Frame_Del_p.LDSGI31del|CTNNB1_ENST00000405570.1_In_Frame_Del_p.LDSGI31del	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	31			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.D32Y(128)|p.S33F(97)|p.G34R(87)|p.D32N(82)|p.G34E(73)|p.G34V(72)|p.D32G(65)|p.S33Y(60)|p.A5_A80del(53)|p.S33P(47)|p.D32H(40)|p.D32V(33)|p.I35S(20)|p.S33A(16)|p.D32A(16)|p.I35T(13)|p.A5_A80>D(7)|p.A5_Q143del(7)|p.WQQQSYLD25?(5)|p.Q28_H134del(5)|p.S33L(4)|p.W25_D32del(4)|p.L31L(4)|p.?(4)|p.W25_I140del(3)|p.V22_G38del(3)|p.T3_A126del(2)|p.S33N(2)|p.M5_N141>D(2)|p.D32_S47del(2)|p.Y30_S33del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5_Y142>D(2)|p.A5fs*7(2)|p.D32E(2)|p.Y30*(2)|p.L10_N141del(2)|p.Q28_Q61del(1)|p.S33T(1)|p.S33S(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S29_H36del(1)|p.H24_L31del(1)|p.Y30_A97del(1)|p.A20_A80del(1)|p.Q28_A43del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.W25_I35del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.A13_R151del(1)|p.D32del(1)|p.M1_A87del(1)|p.I35_T41del(1)|p.I35K(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.S23_A39del(1)|p.A21_A80del(1)|p.I35_S37>T(1)|p.I35_K170del(1)|p.M14_S45del(1)|p.D32_H36>D(1)|p.S33_G34insGTS(1)|p.P16_K133del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.M8_A80del(1)|p.S33_S37del(1)|p.D32_S33insS(1)|p.Y30_T40del(1)|p.S33_G34insGI(1)|p.A5_Q143>E(1)|p.I35_G38del(1)|p.L31M(1)|p.Q28_D32>H(1)|p.L31Q(1)|p.Y30_A80del(1)|p.L31W(1)|p.D32fs*9(1)|p.Y30Y(1)|p.Q28fs*20(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S23_I35del(1)|p.V22_S71>A(1)|p.V22_Y64del(1)|p.I35N(1)|p.A20_S111del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		AACAGTCTTACCTGGACTCTGGAATCCATTCTGGT	0.484	D32N(KE39_STOMACH)|D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)|G34E(AGS_STOMACH)|S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.30_35del	Colon(6;3 56 14213 18255)	Atlas-Indel,Pindel	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	1197	Substitution - Missense(1031)|Deletion - In frame(126)|Complex - deletion inframe(18)|Unknown(7)|Substitution - coding silent(6)|Insertion - In frame(3)|Deletion - Frameshift(3)|Substitution - Nonsense(2)|Complex - frameshift(1)	liver(384)|central_nervous_system(201)|endometrium(138)|stomach(88)|pancreas(86)|pituitary(59)|large_intestine(58)|skin(44)|ovary(41)|soft_tissue(14)|lung(12)|salivary_gland(12)|prostate(11)|biliary_tract(9)|bone(9)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|NS(4)|breast(4)|adrenal_gland(4)|urinary_tract(3)|parathyroid(2)|small_intestine(2)|thyroid(1)|cervix(1)	c.89_103del						.																																			SO:0001651	inframe_deletion	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	.	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.90_104delCCTGGACTCTGGAAT	chr3.hg19:g.41266093_41266107delCCTGGACTCTGGAAT	ENSP00000344456:p.Leu31_Ile35del	107.0	0.0		193.0	27.0	NM_001098210	A8K1L7|Q8NEW9|Q8NI94|Q9H391	In_Frame_Del	DEL	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.484	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		-	41266107	CCTGGACTCTGGAAT	-	41266093	7	5	97	1	0	1	0	1	0	0	0	0	4018	518	18	0	96	0	CTNNB1	3	41266093	In_Frame_Del	DEL	CCTGGACTCTGGAAT	TCGA-DD-A1EA-01A-11D-A12Z-10	24627048	41266093	156756337	20	13283										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52662939	52662939	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ttgctgcaattttagaactcGcttgtagatggctgaattgg	11	6	0	3			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:52662939G>A	ENST00000296302.7	-	12	1415	c.1414C>T	c.(1414-1416)Cga>Tga	p.R472*	PBRM1_ENST00000409767.1_Nonsense_Mutation_p.R472*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.R472*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.R472*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.R440*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.R472*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.R472*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.R472*			Q86U86	PB1_HUMAN	polybromo 1	472					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTTAGAACTCGCTTGTAGATG	0.318			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.R472X		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.C1414T						.						101	95	97					3																	52662939		2203	4300	6503	SO:0001587	stop_gained	55193	exon13			GAACTCGCTTGTA	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1414C>T	chr3.hg19:g.52662939G>A	ENSP00000296302:p.Arg472*	79.0	0.0		104.0	60.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	G	37	6.182101	0.97352	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.4	1.45	0.22620	.	0.136047	0.50627	D	0.000116	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-21.0362	11.5495	0.50713	0.0:0.1018:0.3723:0.5259	.	.	.	.	X	440;472;472;472;472;472;472;472;472;416	.	ENSP00000296302:R472X	R	-	1	2	PBRM1	52637979	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	2.206000	0.42779	-0.016000	0.14127	-0.309000	0.09137	CGA	.	.		0.318	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		A	52662939	G	A	52662939	4	1	97	1	0	0	0	0	0	1	0	0	11500	1095	38	1	3562	1	PBRM1	3	52662939	Nonsense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	11396846	52662939	145359491	21	13284										
MCM2	4171	hgsc.bcm.edu	37	chr3	127323584	127323585	+	Missense_Mutation	DNP	GC	GC	AT													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tgcggcagcgtgaccgggagGctggccggggcctgggccgc							TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:127323584_127323585GC>AT	ENST00000265056.7	+	3	614_615	c.370_371GC>AT	c.(370-372)GCt>ATt	p.A124I		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	124	Interaction with KAT7. {ECO:0000250}.				cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						TGACCGGGAGGCTGGCCGGGGC	0.683																																					p.A124T|p.A124V		Atlas-SNP	.											.	MCM2	79	.	0			c.G370A|c.C371T						.																																			SO:0001583	missense	4171	exon3			CGGGAGGCTGGCC|GGGAGGCTGGCCG	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"mitotin"	116945	"minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)", "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	Exception_encountered	chr3.hg19:g.127323584_127323585delinsAT	ENSP00000265056:p.Ala124Ile	8.0|6.0	0.0		51.0	20.0|21.0	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	hg19	CCDS3043.1																																																																																			.	.		0.683	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			AT	127323585	GC	AT	127323584	3	1	97	1	0	0	0	0	1	0	0	0	9395	1203	42	3	380	3	MCM2	3	127323584	Missense_Mutation	DNP	GC	TCGA-DD-A1EA-01A-11D-A12Z-10	74660645	127323584	70698846	22	13285	57	2								
MCM2	4171	hgsc.bcm.edu	37	chr3	127323589	127323589	+	Silent	SNP	C	C	A													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cagcgtgaccgggaggctggCcggggcctgggccgcatgcg							TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:127323589C>A	ENST00000265056.7	+	3	619	c.375C>A	c.(373-375)ggC>ggA	p.G125G		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	125	Interaction with KAT7. {ECO:0000250}.				cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						GGGAGGCTGGCCGGGGCCTGG	0.682																																					p.G125G		Atlas-SNP	.											.	MCM2	79	.	0			c.C375A						.						15	18	17					3																	127323589		2196	4293	6489	SO:0001819	synonymous_variant	4171	exon3			GGCTGGCCGGGGC	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"mitotin"	116945	"minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)", "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.375C>A	chr3.hg19:g.127323589C>A		8.0	0.0		55.0	21.0	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Silent	SNP	ENST00000265056.7	hg19	CCDS3043.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.329669	0.24167	.	.	ENSG00000073111	ENST00000539922	.	.	.	5.29	3.48	0.39840	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.167	0.03840	0.1366:0.4895:0.1999:0.174	.	.	.	.	.	-1	.	.	.	+	.	.	MCM2	128806279	0.993000	0.37304	1.000000	0.80357	0.873000	0.50193	0.310000	0.19356	1.224000	0.43551	0.591000	0.81541	.	.	.		0.682	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			A	127323589	C	A	127323589	2	1	97	1	0	0	0	0	0	0	0	1	9395	726	26	3		3	MCM2	3	127323589	Silent	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	5	127323589	70698841	23	13286	57	2								
COL6A5	256076	hgsc.bcm.edu	37	chr3	130113755	130113755	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tgtcatcttcaggaagctgaCgtgattttcctttgcgatgg	11	8	3	2	rs541531354		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:130113755C>T	ENST00000432398.2	+	8	3509	c.3015C>T	c.(3013-3015)gaC>gaT	p.D1005D	COL6A5_ENST00000265379.6_Silent_p.D1005D	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1005	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						AGGAAGCTGACGTGATTTTCC	0.333																																					p.D1005D		Atlas-SNP	.											.	COL6A5	205	.	0			c.C3015T						.						72	58	62					3																	130113755		692	1591	2283	SO:0001819	synonymous_variant	256076	exon8			AGCTGACGTGATT	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.3015C>T	chr3.hg19:g.130113755C>T		73.0	0.0		124.0	47.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	hg19																																																																																				.	.		0.333	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		T	130113755	C	T	130113755	2	4	97	1	0	0	0	0	0	0	0	1	3704	535	19	1		1	COL6A5	3	130113755	Silent	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	2790166	130113755	67908675	24	13287										
MRPS22	56945	hgsc.bcm.edu	37	chr3	139062911	139062911	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tattgctgtggagcctcttgAggagttctccgggcgtggaa	15	8	2	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:139062911A>T	ENST00000495075.1	+	3	475	c.43A>T	c.(43-45)Agg>Tgg	p.R15W	MRPS22_ENST00000310776.4_Missense_Mutation_p.R15W|MRPS22_ENST00000465056.1_Missense_Mutation_p.R15W|MRPS22_ENST00000478464.1_5'Flank			P82650	RT22_HUMAN	mitochondrial ribosomal protein S22	15						mitochondrial ribosome (GO:0005761)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12						GAGCCTCTTGAGGAGTTCTCC	0.602																																					p.R15W		Atlas-SNP	.											.	MRPS22	40	.	0			c.A43T						.						51	51	51					3																	139062911		2203	4300	6503	SO:0001583	missense	56945	exon1			CTCTTGAGGAGTT	AF226045	CCDS3107.1	3q23	2012-09-13			ENSG00000175110	ENSG00000175110		"Mitochondrial ribosomal proteins / small subunits"	14508	protein-coding gene	gene with protein product		605810				11175783	Standard	NM_020191		Approved	MRP-S22, GK002, C3orf5, GIBT	uc003etb.3	P82650	OTTHUMG00000159910	ENST00000495075.1:c.43A>T	chr3.hg19:g.139062911A>T	ENSP00000418008:p.Arg15Trp	26.0	0.0		64.0	18.0	NM_020191	Q9H3I1	Missense_Mutation	SNP	ENST00000495075.1	hg19	CCDS3107.1	.	.	.	.	.	.	.	.	.	.	A	14.19	2.461464	0.43736	.	.	ENSG00000175110	ENST00000495075;ENST00000310776;ENST00000465056;ENST00000465373	D;D;D;T	0.82984	-1.67;-1.67;-1.67;-1.09	4.01	1.49	0.22878	.	3.538940	0.00815	N	0.001535	T	0.70168	0.3193	N	0.14661	0.345	0.09310	N	1	P;P	0.47106	0.89;0.824	B;B	0.40285	0.325;0.173	T	0.63341	-0.6659	10	0.59425	D	0.04	8.1781	2.9878	0.05973	0.6673:0.0:0.1186:0.2141	.	15;15	G5E9V5;P82650	.;RT22_HUMAN	W	15;15;15;11	ENSP00000418008:R15W;ENSP00000310785:R15W;ENSP00000418233:R15W;ENSP00000419920:R11W	ENSP00000310785:R15W	R	+	1	2	MRPS22	140545601	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.067000	0.11579	0.197000	0.20387	0.482000	0.46254	AGG	.	.		0.602	MRPS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358120.1	NM_020191		T	139062911	A	T	139062911	3	4	97	1	0	0	0	0	1	0	0	0	9842	295	11	4	45	4	MRPS22	3	139062911	Missense_Mutation	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	8949156	139062911	58959519	25	13288										
EIF4A2	1974	hgsc.bcm.edu	37	chr3	186504304	186504304	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ttttaaggttgtgttgctttCtgccacaatgccaactgatg	9	8	1	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:186504304C>T	ENST00000323963.5	+	7	705	c.641C>T	c.(640-642)tCt>tTt	p.S214F	EIF4A2_ENST00000440191.2_Missense_Mutation_p.S215F|RP11-573D15.9_ENST00000577781.1_RNA|SNORA63_ENST00000363548.1_RNA|SNORA63_ENST00000363450.1_RNA|EIF4A2_ENST00000356531.5_Missense_Mutation_p.S119F|SNORD2_ENST00000459163.1_RNA|SNORA81_ENST00000408493.2_RNA|SNORA4_ENST00000584302.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	214	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)	p.S214C(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		GTGTTGCTTTCTGCCACAATG	0.378			T	BCL6	NHL																																p.S214F		Atlas-SNP	.		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	EIF4A2,NS,carcinoma,0,1	EIF4A2	55	.	1	Substitution - Missense(1)	lung(1)	c.C641T						.						102	104	103					3																	186504304		2203	4299	6502	SO:0001583	missense	1974	exon7			TGCTTTCTGCCAC	D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"DEAD-boxes"	3284	protein-coding gene	gene with protein product		601102	"eukaryotic translation initiation factor 4A, isoform 2"	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.641C>T	chr3.hg19:g.186504304C>T	ENSP00000326381:p.Ser214Phe	138.0	0.0		405.0	154.0	NM_001967	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	hg19	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.911871	0.72983	.	.	ENSG00000156976	ENST00000323963;ENST00000440191;ENST00000356531	T;T;T	0.12774	2.65;2.65;2.65	5.13	5.13	0.70059	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.56688	0.2002	H	0.98786	4.33	0.80722	D	1	D;D;D;D	0.76494	0.995;0.999;0.999;0.999	D;D;D;D	0.79108	0.943;0.992;0.946;0.968	T	0.74763	-0.3555	10	0.87932	D	0	-27.6825	16.4642	0.84073	0.0:1.0:0.0:0.0	.	70;119;215;214	B4DJX6;Q9NZE6;Q14240-2;Q14240	.;.;.;IF4A2_HUMAN	F	214;215;119	ENSP00000326381:S214F;ENSP00000398370:S215F;ENSP00000348925:S119F	ENSP00000326381:S214F	S	+	2	0	EIF4A2	187986998	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.075000	0.76798	2.827000	0.97445	0.650000	0.86243	TCT	.	.		0.378	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		T	186504304	C	T	186504304	3	4	97	1	0	0	0	0	1	0	0	0	5027	913	32	3	667	3	EIF4A2	3	186504304	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	47441393	186504304	11518126	26	13289										
ATP13A3	79572	hgsc.bcm.edu	37	chr3	194126804	194126804	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gtcttctttctacagcccagGgcccagggtaagcagcattt	10	12	3	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:194126804G>A	ENST00000439040.1	-	33	4316	c.3525C>T	c.(3523-3525)gcC>gcT	p.A1175A	ATP13A3_ENST00000256031.4_Silent_p.A1175A			Q9H7F0	AT133_HUMAN	ATPase type 13A3	1175						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		TACAGCCCAGGGCCCAGGGTA	0.463																																					p.A1175A		Atlas-SNP	.											.	ATP13A3	94	.	0			c.C3525T						.						122	115	117					3																	194126804		2023	4196	6219	SO:0001819	synonymous_variant	79572	exon32			GCCCAGGGCCCAG	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"ATPases / P-type"	24113	protein-coding gene	gene with protein product	"ATPase family homolog up regulated in senescence cells"	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.3525C>T	chr3.hg19:g.194126804G>A		96.0	0.0		198.0	79.0	NM_024524	Q8NC11|Q96KS1	Silent	SNP	ENST00000439040.1	hg19	CCDS43187.1	.	.	.	.	.	.	.	.	.	.	G	4.813	0.151232	0.09185	.	.	ENSG00000133657	ENST00000429136	.	.	.	5.79	1.76	0.24704	.	.	.	.	.	T	0.53850	0.1822	.	.	.	0.42295	D	0.992155	.	.	.	.	.	.	T	0.44436	-0.9328	4	.	.	.	-12.1813	6.4084	0.21678	0.0796:0.3519:0.47:0.0985	.	.	.	.	S	111	.	.	P	-	1	0	ATP13A3	195608093	1.000000	0.71417	0.342000	0.25602	0.488000	0.33401	2.473000	0.45145	0.337000	0.23665	0.650000	0.86243	CCT	.	.		0.463	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524		A	194126804	G	A	194126804	2	1	97	1	0	0	0	0	0	0	0	1	1125	1219	43	3		3	ATP13A3	3	194126804	Silent	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	7622500	194126804	3895626	27	13290										
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69962823	69962825	+	In_Frame_Del	DEL	TGT	TGT	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ttccctccttcctacgtaccTgttgttatgtcagaattaac							TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:69962823_69962825delTGT	ENST00000508661.1	+	1	612_614	c.585_587delTGT	c.(583-588)cctgtt>cct	p.V197del	UGT2B7_ENST00000305231.7_In_Frame_Del_p.V197del|UGT2B7_ENST00000509763.1_Intron			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	197					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)	p.V196I(1)		autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CCTACGTACCTGTTGTTATGTCA	0.365																																					p.195_196del		Atlas-Indel,Pindel	.											.	UGT2B7	79	.	1	Substitution - Missense(1)	lung(1)	c.584_586del						.																																			SO:0001651	inframe_deletion	7364	exon1			.	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"UDP glucuronosyltransferases"	12554	protein-coding gene	gene with protein product		600068	"UDP glycosyltransferase 2 family, polypeptide B7"			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.585_587delTGT	chr4.hg19:g.69962826_69962828delTGT	ENSP00000427659:p.Val197del	104.0	0.0		304.0	98.0	NM_001074	B2R810|Q6GTW0	In_Frame_Del	DEL	ENST00000508661.1	hg19																																																																																				.	.		0.365	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		-	69962825	TGT	-	69962823	7	5	97	1	0	1	0	1	0	0	0	0	16977	1567	55	0	587	0	UGT2B7	4	69962823	In_Frame_Del	DEL	TGT	TCGA-DD-A1EA-01A-11D-A12Z-10		69962823	121191453	28	13291										
C4orf40	401137	hgsc.bcm.edu	37	chr4	71024317	71024318	+	Frame_Shift_Ins	INS	-	-	T													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cgtttgtccctccttcaaggINStttttttcagcagctgcagc					rs148239542		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:71024317_71024318insT	ENST00000344526.5	+	3	537_538	c.348_349insT	c.(349-351)tttfs	p.F117fs	C4orf40_ENST00000502441.2_3'UTR|C4orf40_ENST00000502294.1_Frame_Shift_Ins_p.F117fs	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		117	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						CTCCTTCAAGGTTTTTTTCAGC	0.55																																					p.R116fs		Atlas-Indel,Pindel	.											.	C4orf40	19	.	0			c.348_349insT						.																																			SO:0001589	frameshift_variant	401137	exon3			.																												ENST00000344526.5:c.355dupT	chr4.hg19:g.71024324_71024324dupT	ENSP00000343172:p.Phe117fs	46.0	0.0		108.0	31.0	NM_214711	A8MXP0|Q6MZR6	Frame_Shift_Ins	INS	ENST00000344526.5	hg19	CCDS3535.1																																																																																			.	.		0.55	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1			T	71024318	-	T	71024317	7	5	97	1	0	1	1	0	0	0	0	0	2271	1252	44	0	358	0	C4orf40	4	71024317	Frame_Shift_Ins	INS	-	TCGA-DD-A1EA-01A-11D-A12Z-10	1061494	71024317	120129959	29	13292										
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90170546	90170546	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ctgaacatccagattctctaGttagaggtttacaggacctc	8	10	1	3			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:90170546G>A	ENST00000609438.1	-	2	1234	c.716C>T	c.(715-717)aCt>aTt	p.T239I	GPRIN3_ENST00000333209.4_Missense_Mutation_p.T239I	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	239								p.T239N(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		AGATTCTCTAGTTAGAGGTTT	0.552																																					p.T239I		Atlas-SNP	.											GPRIN3,NS,carcinoma,0,1	GPRIN3	90	.	1	Substitution - Missense(1)	kidney(1)	c.C716T						.						50	55	53					4																	90170546		2203	4300	6503	SO:0001583	missense	285513	exon2			TCTCTAGTTAGAG	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.716C>T	chr4.hg19:g.90170546G>A	ENSP00000476603:p.Thr239Ile	59.0	0.0		101.0	39.0	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	hg19	CCDS34030.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.318807	0.23994	.	.	ENSG00000185477	ENST00000333209	T	0.10860	2.83	4.93	0.83	0.18854	.	0.807286	0.10088	N	0.717539	T	0.04452	0.0122	N	0.14661	0.345	0.09310	N	1	B	0.30824	0.296	B	0.20955	0.032	T	0.40270	-0.9572	10	0.27785	T	0.31	0.635	1.468	0.02410	0.1827:0.1254:0.4522:0.2398	.	239	Q6ZVF9	GRIN3_HUMAN	I	239	ENSP00000328672:T239I	ENSP00000328672:T239I	T	-	2	0	GPRIN3	90389569	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.754000	0.26390	0.311000	0.23014	-0.142000	0.14014	ACT	.	.		0.552	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		A	90170546	G	A	90170546	3	1	97	1	0	0	0	0	1	0	0	0	6740	1029	36	3	1618	3	GPRIN3	4	90170546	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	19146229	90170546	100983730	30	13293										
TBCK	93627	hgsc.bcm.edu	37	chr4	107092414	107092414	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	atagattctctcacacagcgTtcaatgtcaatttctagata	5	9	5	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:107092414T>C	ENST00000273980.5	-	24	2520	c.2073A>G	c.(2071-2073)gaA>gaG	p.E691E	TBCK_ENST00000394708.2_Silent_p.E691E|TBCK_ENST00000432496.2_Silent_p.E691E|TBCK_ENST00000361687.4_Silent_p.E628E|TBCK_ENST00000514689.1_5'UTR|TBCK_ENST00000394706.3_Silent_p.E652E					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TCACACAGCGTTCAATGTCAA	0.353																																					p.E691E		Atlas-SNP	.											.	TBCK	89	.	0			c.A2073G						.						116	115	116					4																	107092414		2203	4300	6503	SO:0001819	synonymous_variant	93627	exon23			ACAGCGTTCAATG		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.2073A>G	chr4.hg19:g.107092414T>C		112.0	0.0		255.0	96.0	NM_001163436		Silent	SNP	ENST00000273980.5	hg19	CCDS54788.1																																																																																			.	.		0.353	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		C	107092414	T	C	107092414	2	2	97	1	0	0	0	0	0	0	0	1	15651	1722	60	2		2	TBCK	4	107092414	Silent	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	16921868	107092414	84061862	31	13294										
DKK2	27123	hgsc.bcm.edu	37	chr4	107845310	107845310	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tccagaaatgacgagcacagCaaaacccttcaatgcagtct	7	12	2	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:107845310C>T	ENST00000285311.3	-	4	1286	c.581G>A	c.(580-582)tGc>tAc	p.C194Y	DKK2_ENST00000510463.1_Missense_Mutation_p.C148Y|DKK2_ENST00000513208.1_Missense_Mutation_p.C94Y	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	194	DKK-type Cys-2.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.C194F(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		ACGAGCACAGCAAAACCCTTC	0.473																																					p.C194Y		Atlas-SNP	.											DKK2,NS,neuroblastoma,0,1	DKK2	96	.	1	Substitution - Missense(1)	autonomic_ganglia(1)	c.G581A						.						118	109	112					4																	107845310		2203	4300	6503	SO:0001583	missense	27123	exon4			GCACAGCAAAACC	AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"dickkopf (Xenopus laevis) homolog 2", "dickkopf 2 homolog (Xenopus laevis)"			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.581G>A	chr4.hg19:g.107845310C>T	ENSP00000285311:p.Cys194Tyr	84.0	0.0		179.0	79.0	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Missense_Mutation	SNP	ENST00000285311.3	hg19	CCDS3675.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.610495	0.87258	.	.	ENSG00000155011	ENST00000285311;ENST00000513208;ENST00000510463	D;T;T	0.81821	-1.54;-0.61;-1.14	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.90807	0.7113	M	0.82823	2.61	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	D	0.91523	0.5236	10	0.87932	D	0	-8.7032	19.6876	0.95986	0.0:1.0:0.0:0.0	.	194	Q9UBU2	DKK2_HUMAN	Y	194;94;148	ENSP00000285311:C194Y;ENSP00000421255:C94Y;ENSP00000423797:C148Y	ENSP00000285311:C194Y	C	-	2	0	DKK2	108064759	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.487000	0.81328	2.657000	0.90304	0.585000	0.79938	TGC	.	.		0.473	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4			T	107845310	C	T	107845310	3	4	97	1	0	0	0	0	1	0	0	0	4547	710	25	3	202	3	DKK2	4	107845310	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	752896	107845310	83308966	32	13295										
GYPE	2996	hgsc.bcm.edu	37	chr4	144801632	144801632	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	aagtgtgcattgccacaccaGtggtacttgatgctgatatg	11	8	0	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:144801632G>T	ENST00000358615.4	-	2	119	c.68C>A	c.(67-69)aCt>aAt	p.T23N	GYPE_ENST00000437468.2_Missense_Mutation_p.T23N	NM_198682.2	NP_941391.2	P15421	GLPE_HUMAN	glycophorin E (MNS blood group)	23						integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_hematologic(180;0.158)					TGCCACACCAGTGGTACTTGA	0.378																																					p.T23N		Atlas-SNP	.											.	GYPE	21	.	0			c.C68A						.						214	223	220					4																	144801632		2203	4300	6503	SO:0001583	missense	2996	exon2			ACACCAGTGGTAC		CCDS47138.1	4q31.21	2010-01-19	2010-01-19		ENSG00000197465	ENSG00000197465		"Blood group antigens"	4705	protein-coding gene	gene with protein product		138590	"glycophorin E"				Standard	NM_198682		Approved	GPE, MNS	uc003ijj.3	P15421	OTTHUMG00000161402	ENST00000358615.4:c.68C>A	chr4.hg19:g.144801632G>T	ENSP00000351430:p.Thr23Asn	188.0	0.0		1165.0	214.0	NM_198682	D3DNZ5	Missense_Mutation	SNP	ENST00000358615.4	hg19	CCDS47138.1	.	.	.	.	.	.	.	.	.	.	G	10.43	1.348990	0.24426	.	.	ENSG00000197465	ENST00000358615;ENST00000437468;ENST00000428604	T;T	0.06371	3.31;3.31	1.75	-1.39	0.08997	.	.	.	.	.	T	0.09024	0.0223	.	.	.	0.09310	N	1	D	0.62365	0.991	P	0.50136	0.632	T	0.19811	-1.0294	8	0.87932	D	0	.	5.159	0.15050	0.5471:0.0:0.4529:0.0	.	23	P15421	GLPE_HUMAN	N	23	ENSP00000351430:T23N;ENSP00000400698:T23N	ENSP00000351430:T23N	T	-	2	0	GYPE	145021082	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.369000	0.07533	-0.448000	0.07128	0.134000	0.15878	ACT	.	.		0.378	GYPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364780.1	NM_002102		T	144801632	G	T	144801632	3	4	97	1	0	0	0	0	1	0	0	0	6920	1029	36	3	176	3	GYPE	4	144801632	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	36956322	144801632	46352644	33	13296										
NPY2R	4887	hgsc.bcm.edu	37	chr4	156135578	156135578	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tagagagcaagatctccaagCgaatcagcttcctgattatt	8	9	2	3			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:156135578C>G	ENST00000329476.3	+	2	976	c.487C>G	c.(487-489)Cga>Gga	p.R163G	NPY2R_ENST00000506608.1_Missense_Mutation_p.R163G	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	163					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	GATCTCCAAGCGAATCAGCTT	0.552																																					p.R163G		Atlas-SNP	.											NPY2R,right_upper_lobe,carcinoma,0,1	NPY2R	87	.	0			c.C487G						.						55	51	52					4																	156135578		2203	4300	6503	SO:0001583	missense	4887	exon2			TCCAAGCGAATCA	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"GPCR / Class A : Neuropeptide receptors : Y"	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.487C>G	chr4.hg19:g.156135578C>G	ENSP00000332591:p.Arg163Gly	14.0	0.0		48.0	19.0	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation	SNP	ENST00000329476.3	hg19	CCDS3791.1	.	.	.	.	.	.	.	.	.	.	C	8.336	0.827495	0.16749	.	.	ENSG00000185149	ENST00000329476;ENST00000506608	T;T	0.42131	0.98;0.98	5.74	1.05	0.20165	GPCR, rhodopsin-like superfamily (1);	0.627067	0.16311	N	0.220016	T	0.44993	0.1320	M	0.67953	2.075	0.09310	N	1	B	0.22683	0.073	B	0.28553	0.091	T	0.47935	-0.9078	10	0.46703	T	0.11	.	16.4727	0.84115	0.5564:0.4436:0.0:0.0	.	163	P49146	NPY2R_HUMAN	G	163	ENSP00000332591:R163G;ENSP00000426366:R163G	ENSP00000332591:R163G	R	+	1	2	NPY2R	156355028	0.035000	0.19736	0.221000	0.23827	0.744000	0.42396	0.458000	0.21892	0.190000	0.20209	0.643000	0.83706	CGA	.	.		0.552	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910		G	156135578	C	G	156135578	3	3	97	1	0	0	0	0	1	0	0	0	10618	760	27	4	489	4	NPY2R	4	156135578	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	11333946	156135578	35018698	34	13297										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54635850	54635850	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	atttgtaggtatgccattgcAttggccttaagggaaaagca	11	6	0	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr5:54635850A>G	ENST00000230640.5	+	6	782	c.528A>G	c.(526-528)gcA>gcG	p.A176A	SKIV2L2_ENST00000545714.1_Silent_p.A75A	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	176	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				ATGCCATTGCATTGGCCTTAA	0.308																																					p.A176A	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.A528G						.						106	101	103					5																	54635850		2203	4300	6503	SO:0001819	synonymous_variant	23517	exon6			CATTGCATTGGCC	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.528A>G	chr5.hg19:g.54635850A>G		71.0	0.0		198.0	108.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	hg19	CCDS3967.1																																																																																			.	.		0.308	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			G	54635850	A	G	54635850	2	3	97	1	0	0	0	0	0	0	0	1	14375	204	8	2		2	SKIV2L2	5	54635850	Silent	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10		54635850	126279410	35	13298										
PAM	5066	hgsc.bcm.edu	37	chr5	102203011	102203011	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ccagaccattttccaatgaaTgtcttggtaccaccagaccc	6	14	1	3			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr5:102203011T>A	ENST00000438793.3	+	2	594	c.124T>A	c.(124-126)Tgt>Agt	p.C42S	PAM_ENST00000348126.2_Missense_Mutation_p.C42S|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000346918.2_Missense_Mutation_p.C42S|PAM_ENST00000274392.9_5'UTR|PAM_ENST00000304400.7_Missense_Mutation_p.C42S|PAM_ENST00000455264.2_Missense_Mutation_p.C42S|PAM_ENST00000513648.1_3'UTR	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	42	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	TTCCAATGAATGTCTTGGTAC	0.383																																					p.C42S		Atlas-SNP	.											.	PAM	180	.	0			c.T124A						.						143	128	133					5																	102203011		2203	4300	6503	SO:0001583	missense	5066	exon2			AATGAATGTCTTG	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.124T>A	chr5.hg19:g.102203011T>A	ENSP00000396493:p.Cys42Ser	78.0	0.0		237.0	66.0	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	hg19	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	T	19.53	3.845756	0.71603	.	.	ENSG00000145730	ENST00000511839;ENST00000511477;ENST00000509832;ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000455264	T;T;T;T;T;T;T	0.71579	-0.56;-0.58;0.93;0.81;0.85;0.93;0.82	5.68	5.68	0.88126	PHM/PNGase F domain (1);	0.000000	0.85682	D	0.000000	T	0.77678	0.4166	L	0.34521	1.04	0.80722	D	1	D;D;D;D;D	0.76494	0.998;0.999;0.999;0.999;0.999	D;D;D;D;D	0.81914	0.988;0.995;0.995;0.995;0.993	T	0.80169	-0.1494	10	0.72032	D	0.01	.	15.9313	0.79663	0.0:0.0:0.0:1.0	.	42;42;42;42;42	P19021;P19021-4;P19021-3;P19021-5;P19021-2	AMD_HUMAN;.;.;.;.	S	42	ENSP00000426448:C42S;ENSP00000423763:C42S;ENSP00000396493:C42S;ENSP00000282992:C42S;ENSP00000314638:C42S;ENSP00000306100:C42S;ENSP00000403461:C42S	ENSP00000306100:C42S	C	+	1	0	PAM	102230910	1.000000	0.71417	1.000000	0.80357	0.443000	0.32047	5.804000	0.69135	2.163000	0.67991	0.402000	0.26972	TGT	.	.		0.383	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		A	102203011	T	A	102203011	3	1	97	1	0	0	0	0	1	0	0	0	11421	1464	51	4	130	4	PAM	5	102203011	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	47567161	102203011	78712249	36	13299										
FEM1C	56929	hgsc.bcm.edu	37	chr5	114861063	114861063	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tgcctttttccagtatttcaAagccccaagcagatctcttt	5	12	2	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr5:114861063A>C	ENST00000274457.3	-	3	1357	c.796T>G	c.(796-798)Ttg>Gtg	p.L266V		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	266					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		CAGTATTTCAAAGCCCCAAGC	0.398																																					p.L266V		Atlas-SNP	.											.	FEM1C	50	.	0			c.T796G						.						122	118	119					5																	114861063		2202	4300	6502	SO:0001583	missense	56929	exon3			ATTTCAAAGCCCC		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"Ankyrin repeat domain containing"	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.796T>G	chr5.hg19:g.114861063A>C	ENSP00000274457:p.Leu266Val	95.0	0.0		223.0	64.0	NM_020177	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Missense_Mutation	SNP	ENST00000274457.3	hg19	CCDS4118.1	.	.	.	.	.	.	.	.	.	.	A	6.694	0.496617	0.12762	.	.	ENSG00000145780	ENST00000274457	T	0.74947	-0.89	5.76	2.16	0.27623	.	0.000000	0.64402	D	0.000001	T	0.62551	0.2437	L	0.53617	1.68	0.42902	D	0.994231	P	0.39940	0.696	B	0.32022	0.139	T	0.60073	-0.7334	10	0.46703	T	0.11	-11.6108	8.9579	0.35829	0.7232:0.0:0.2768:0.0	.	266	Q96JP0	FEM1C_HUMAN	V	266	ENSP00000274457:L266V	ENSP00000274457:L266V	L	-	1	2	FEM1C	114888962	0.989000	0.36119	0.999000	0.59377	0.519000	0.34347	1.705000	0.37867	0.456000	0.26937	0.528000	0.53228	TTG	.	.		0.398	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177		C	114861063	A	C	114861063	3	2	97	1	0	0	0	0	1	0	0	0	5819	11	1	5	1061	5	FEM1C	5	114861063	Missense_Mutation	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	12658052	114861063	66054197	37	13300										
PCDHGC5	26025	hgsc.bcm.edu	37	chr5	140871440	140871440	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gcgcgaaaccagagtggccgAttaagggatggggctccgag	17	9	0	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr5:140871440A>T	ENST00000252085.3	+	2	2566				PCDHGA10_ENST00000398610.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGC5_ENST00000252087.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGTGGCCGATTAAGGGATG	0.652																																					p.D878V		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.A2633T						.						11	15	13					5																	140871440		1085	2153	3238	SO:0001627	intron_variant	56097	exon1			TGGCCGATTAAGG	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.2425-2934A>T	chr5.hg19:g.140871440A>T		40.0	0.0		141.0	28.0	NM_032407	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	hg19	CCDS4260.1																																																																																			.	.		0.652	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		T	140871440	A	T	140871440	1	4	97	0	1	0	0	0	0	0	0	0	11580	333	12	4		4	PCDHGC5	5	140871440	Intron	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	26010377	140871440	40043820	38	13301										
HLA-DPB1	3115	hgsc.bcm.edu	37	chr6	33053994	33054040	+	Stop_Codon_Del	DEL	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	aacctttcgtctttcatttcAgttcaacgaggatctgcata					rs201552902|rs150818884|rs67523850	byFrequency	TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr6:33053994_33054040delTTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	ENST00000418931.2	+	0	873_897					NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)	p.R255P(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CTTTCATTTCAGTTCAACGAGGATCTGCATAAACAGGTAATATTCCTGCTTTGATTTCCTTGTGGGG	0.429																																					p.253_259del		Pindel	.											.	HLA-DPB1	28	.	1	Substitution - Missense(1)	cervix(1)	c.758_775del						.																																			SO:0001567	stop_retained_variant	3115	exon5			.		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	Exception_encountered	chr6.hg19:g.33053994_33054040delTTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA		0.0	0.0		278.0	23.0	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	In_Frame_Del	DEL	ENST00000418931.2	hg19	CCDS4765.1																																																																																			.	.		0.429	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121		-	33054040	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	-	33053994	7	5	97	1	0	1	0	1	0	0	0	0	7212	202	7	0	774	0	HLA-DPB1	6	33053994	Stop_Codon_Del	DEL	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	TCGA-DD-A1EA-01A-11D-A12Z-10		33053994	138061073	39	13302										
USP49	25862	hgsc.bcm.edu	37	chr6	41773689	41773689	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	actcggctccttgttctggaTgagctccagactccgactaa	9	13	1	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr6:41773689T>G	ENST00000394253.3	-	3	1362	c.1033A>C	c.(1033-1035)Atc>Ctc	p.I345L	USP49_ENST00000373009.3_Missense_Mutation_p.I345L|USP49_ENST00000373010.1_Missense_Mutation_p.I345L|USP49_ENST00000297229.2_Missense_Mutation_p.I345L|USP49_ENST00000373006.1_Missense_Mutation_p.I345L			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	345	USP.				histone H2B conserved C-terminal lysine deubiquitination (GO:0035616)|mRNA splicing, via spliceosome (GO:0000398)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)|skin(2)	23	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TTGTTCTGGATGAGCTCCAGA	0.607																																					p.I345L		Atlas-SNP	.											.	USP49	58	.	0			c.A1033C						.						44	46	45					6																	41773689		2203	4300	6503	SO:0001583	missense	25862	exon4			TCTGGATGAGCTC	AJ586139	CCDS4861.1, CCDS69111.1	6p12.1	2008-02-05	2005-08-08		ENSG00000164663	ENSG00000164663		"Ubiquitin-specific peptidases"	20078	protein-coding gene	gene with protein product			"ubiquitin specific protease 49"			14715245	Standard	NM_018561		Approved	MGC20741	uc003ori.3	Q70CQ1	OTTHUMG00000014688	ENST00000394253.3:c.1033A>C	chr6.hg19:g.41773689T>G	ENSP00000377797:p.Ile345Leu	15.0	0.0		34.0	13.0	NM_018561	Q5T3D9|Q5T3E0|Q96CK4	Missense_Mutation	SNP	ENST00000394253.3	hg19		.	.	.	.	.	.	.	.	.	.	T	16.64	3.180024	0.57800	.	.	ENSG00000164663	ENST00000394253;ENST00000373010;ENST00000373009;ENST00000373006;ENST00000297229	T;T;T;T;T	0.73575	3.76;3.27;3.76;-0.76;-0.76	5.1	5.1	0.69264	.	0.128325	0.64402	D	0.000007	T	0.50240	0.1604	N	0.26130	0.795	0.35841	D	0.826048	P	0.36330	0.548	B	0.41466	0.358	T	0.53387	-0.8446	10	0.11485	T	0.65	-17.1117	14.8356	0.70180	0.0:0.0:0.0:1.0	.	345	Q70CQ1-2	.	L	345	ENSP00000377797:I345L;ENSP00000362101:I345L;ENSP00000362100:I345L;ENSP00000362097:I345L;ENSP00000297229:I345L	ENSP00000297229:I345L	I	-	1	0	USP49	41881667	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.898000	0.63238	2.039000	0.60335	0.533000	0.62120	ATC	.	.		0.607	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000316513.3	NM_018561		G	41773689	T	G	41773689	3	3	97	1	0	0	0	0	1	0	0	0	17095	1464	51	5	905	5	USP49	6	41773689	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	8719695	41773689	129341378	40	13303										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75884785	75884785	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gttccttcaccaaagagggcGtctccagccccagacgcata	9	15	2	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr6:75884785G>T	ENST00000322507.8	-	13	2988	c.2679C>A	c.(2677-2679)gaC>gaA	p.D893E	COL12A1_ENST00000416123.2_Missense_Mutation_p.D893E|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Missense_Mutation_p.D893E	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	893	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CAAAGAGGGCGTCTCCAGCCC	0.468																																					p.D893E		Atlas-SNP	.											.	COL12A1	385	.	0			c.C2679A						.						190	186	187					6																	75884785		1983	4159	6142	SO:0001583	missense	1303	exon13			GAGGGCGTCTCCA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2679C>A	chr6.hg19:g.75884785G>T	ENSP00000325146:p.Asp893Glu	75.0	0.0		170.0	69.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	0.018	-1.482005	0.01027	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.51817	0.69;0.69;0.69	5.94	-8.61	0.00885	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.463941	0.21967	N	0.066519	T	0.02304	0.0071	N	0.02011	-0.69	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.32771	-0.9894	10	0.05436	T	0.98	.	0.6516	0.00828	0.2097:0.1677:0.2157:0.4069	.	893	Q99715	COCA1_HUMAN	E	893	ENSP00000325146:D893E;ENSP00000412864:D893E;ENSP00000421216:D893E	ENSP00000325146:D893E	D	-	3	2	COL12A1	75941505	0.000000	0.05858	0.397000	0.26308	0.387000	0.30353	-3.514000	0.00445	-1.602000	0.01599	-2.049000	0.00408	GAC	.	.		0.468	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75884785	G	T	75884785	3	4	97	1	0	0	0	0	1	0	0	0	3671	1136	40	1	6728	1	COL12A1	6	75884785	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	34111096	75884785	95230282	41	13304										
PHF10	55274	hgsc.bcm.edu	37	chr6	170105298	170105298	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	acacatatcacagaacatcaTttcttcttcatggtggggtt	7	9	5	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr6:170105298T>C	ENST00000339209.4	-	11	1465	c.1342A>G	c.(1342-1344)Atg>Gtg	p.M448V	C6orf120_ENST00000332290.2_3'UTR|PHF10_ENST00000366780.4_Missense_Mutation_p.M446V	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	448					nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		CAGAACATCATTTCTTCTTCA	0.373																																					p.M448V		Atlas-SNP	.											.	PHF10	76	.	0			c.A1342G						.						186	161	169					6																	170105298		2203	4300	6503	SO:0001583	missense	55274	exon11			ACATCATTTCTTC	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"Zinc fingers, PHD-type"	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.1342A>G	chr6.hg19:g.170105298T>C	ENSP00000341805:p.Met448Val	81.0	0.0		160.0	54.0	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Missense_Mutation	SNP	ENST00000339209.4	hg19	CCDS5308.2	.	.	.	.	.	.	.	.	.	.	T	18.57	3.652033	0.67472	.	.	ENSG00000130024	ENST00000366780;ENST00000339209	D;D	0.88664	-2.41;-2.41	5.91	5.91	0.95273	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.035139	0.85682	D	0.000000	D	0.89996	0.6877	M	0.80332	2.49	0.58432	D	0.999998	P;B	0.46064	0.872;0.392	P;P	0.48304	0.522;0.573	D	0.91696	0.5370	10	0.87932	D	0	-27.6999	15.5248	0.75894	0.0:0.0:0.0:1.0	.	446;448	Q8WUB8-2;Q8WUB8	.;PHF10_HUMAN	V	446;448	ENSP00000355743:M446V;ENSP00000341805:M448V	ENSP00000341805:M448V	M	-	1	0	PHF10	169847223	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.457000	0.80775	2.269000	0.75478	0.533000	0.62120	ATG	.	.		0.373	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		C	170105298	T	C	170105298	3	2	97	1	0	0	0	0	1	0	0	0	11830	1493	52	2	162	2	PHF10	6	170105298	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	94220513	170105298	1009769	42	13305										
ZNF735	0	hgsc.bcm.edu	37	chr7	63680468	63680468	+	IGR	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ttaagacacataagataattCatactggagagaaaccctac	6	8	1	3			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr7:63680468C>A								GUSBP6 (69369 upstream) : ZNF679 (8383 downstream)																							TAAGATAATTCATACTGGAGA	0.408																																					p.H347N		Atlas-SNP	.											.	.	.	.	0			c.C1039A						.						47	53	51					7																	63680468		692	1591	2283	SO:0001628	intergenic_variant	730291	exon4			ATAATTCATACTG																													chr7.hg19:g.63680468C>A		22.0	0.0		31.0	9.0	NM_001159524		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.408									A	63680468	C	A	63680468	1	1	97	0	1	0	0	0	0	0	0	0	18139	826	29	3		3	ZNF735	7	63680468	IGR	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10		63680468	95458195	43	13306										
SRCRB4D	136853	hgsc.bcm.edu	37	chr7	76029847	76029847	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tcacagacgctgccccaggaGccaccgtgcatgacttccag	10	16	1	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr7:76029847G>T	ENST00000275560.3	-	4	578	c.231C>A	c.(229-231)ggC>ggA	p.G77G	ZP3_ENST00000336517.4_Intron	NM_080744.1	NP_542782.1														autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(9)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21						TGCCCCAGGAGCCACCGTGCA	0.701																																					p.G77G		Atlas-SNP	.											.	SRCRB4D	47	.	0			c.C231A						.						11	9	10					7																	76029847		2123	4163	6286	SO:0001819	synonymous_variant	136853	exon4			CCAGGAGCCACCG																												ENST00000275560.3:c.231C>A	chr7.hg19:g.76029847G>T		14.0	0.0		45.0	18.0	NM_080744		Silent	SNP	ENST00000275560.3	hg19	CCDS5585.1																																																																																			.	.		0.701	SRCRB4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253001.3			T	76029847	G	T	76029847	2	4	97	1	0	0	0	0	0	0	0	1	15152	958	34	3		3	SRCRB4D	7	76029847	Silent	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	12349379	76029847	83108816	44	13307										
CCDC146	57639	hgsc.bcm.edu	37	chr7	76909777	76909777	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	attccatgctgaaacacgccAacaatgttaccatcagagag	7	11	1	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr7:76909777A>G	ENST00000285871.4	+	14	1853	c.1726A>G	c.(1726-1728)Aac>Gac	p.N576D	CCDC146_ENST00000431197.1_Missense_Mutation_p.N290D|CCDC146_ENST00000415740.2_3'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	576										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				GAAACACGCCAACAATGTTAC	0.323																																					p.N576D		Atlas-SNP	.											.	CCDC146	87	.	0			c.A1726G						.						49	43	45					7																	76909777		2203	4300	6503	SO:0001583	missense	57639	exon14			CACGCCAACAATG	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.1726A>G	chr7.hg19:g.76909777A>G	ENSP00000285871:p.Asn576Asp	92.0	0.0		126.0	50.0	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	hg19	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	A	19.43	3.825269	0.71143	.	.	ENSG00000135205	ENST00000285871;ENST00000431197	T;T	0.29655	1.56;1.56	6.17	6.17	0.99709	.	0.043557	0.85682	D	0.000000	T	0.50871	0.1641	M	0.61703	1.905	0.48632	D	0.999688	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.982	T	0.40459	-0.9562	10	0.13108	T	0.6	-22.5428	16.4837	0.84171	1.0:0.0:0.0:0.0	.	290;576	Q8IYE0-2;Q8IYE0	.;CC146_HUMAN	D	576;290	ENSP00000285871:N576D;ENSP00000413885:N290D	ENSP00000285871:N576D	N	+	1	0	AC007000.1	76747713	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.619000	0.61218	2.371000	0.80710	0.533000	0.62120	AAC	.	.		0.323	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		G	76909777	A	G	76909777	3	3	97	1	0	0	0	0	1	0	0	0	2782	130	5	2	1776	2	CCDC146	7	76909777	Missense_Mutation	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	879930	76909777	82228886	45	13308										
PEG10	23089	hgsc.bcm.edu	37	chr7	94293700	94293700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ccgagccggtgggaggtgccCgcatgcgcctgacgcaggaa	17	13	0	1	rs376581536		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr7:94293700C>T	ENST00000482108.1	+	2	1311	c.832C>T	c.(832-834)Cgc>Tgc	p.R278C	PEG10_ENST00000488574.1_Missense_Mutation_p.R278C	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	278					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GGGAGGTGCCCGCATGCGCCT	0.597																																					p.R354C		Atlas-SNP	.											.	PEG10	36	.	0			c.C1060T						.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,3974		0,0,1987	18	24	22		832,1060,1060,934,934,832	4.3	1	7		22	1,8303		0,1,4151	no	missense,missense,missense,missense,missense,missense	PEG10	NM_001040152.1,NM_001172437.1,NM_001172438.1,NM_001184961.1,NM_001184962.1,NM_015068.3	180,180,180,180,180,180	0,1,6138	TT,TC,CC		0.012,0.0,0.0081	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	278/326,354/785,354/402,312/743,312/360,278/709	94293700	1,12277	1987	4152	6139	SO:0001583	missense	23089	exon2			GGTGCCCGCATGC	AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.832C>T	chr7.hg19:g.94293700C>T	ENSP00000417587:p.Arg278Cys	16.0	0.0		50.0	18.0	NM_001172438	Q96A68|Q9UPV1	Missense_Mutation	SNP	ENST00000482108.1	hg19	CCDS55126.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.927626	0.73327	0.0	1.2E-4	ENSG00000242265	ENST00000482108;ENST00000488574	T;T	0.15139	2.45;2.45	4.34	4.34	0.51931	.	.	.	.	.	T	0.29652	0.0740	L	0.34521	1.04	0.40084	D	0.976172	D;D	0.89917	1.0;1.0	D;D	0.69654	0.965;0.948	T	0.03619	-1.1019	9	0.56958	D	0.05	.	14.7868	0.69810	0.0:1.0:0.0:0.0	.	354;278	B4DSP0;Q86TG7	.;PEG10_HUMAN	C	278	ENSP00000417587:R278C;ENSP00000418944:R278C	ENSP00000417587:R278C	R	+	1	0	PEG10	94131636	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.330000	0.43885	2.429000	0.82318	0.555000	0.69702	CGC	.	.		0.597	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340751.1	NM_015068		T	94293700	C	T	94293700	3	4	97	1	0	0	0	0	1	0	0	0	11728	652	23	1	1066	1	PEG10	7	94293700	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	17383923	94293700	64844963	46	13309										
ARMC10	83787	hgsc.bcm.edu	37	chr7	102738867	102738867	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	agaaggccatttagctgtgcAgcctactttcactgaaggtt	10	9	1	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr7:102738867A>G	ENST00000323716.3	+	7	1291	c.899A>G	c.(898-900)cAg>cGg	p.Q300R	ARMC10_ENST00000441711.2_Missense_Mutation_p.Q265R|ARMC10_ENST00000541300.1_Missense_Mutation_p.Q182R|ARMC10_ENST00000454559.1_Missense_Mutation_p.Q206R|ARMC10_ENST00000428183.2_Missense_Mutation_p.Q241R|ARMC10_ENST00000425331.1_Missense_Mutation_p.Q241R	NM_031905.4	NP_114111.2	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	300					regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						TTAGCTGTGCAGCCTACTTTC	0.403																																					p.Q300R		Atlas-SNP	.											.	ARMC10	25	.	0			c.A899G						.						77	73	74					7																	102738867		2203	4298	6501	SO:0001583	missense	83787	exon7			CTGTGCAGCCTAC	AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632		"Armadillo repeat containing"	21706	protein-coding gene	gene with protein product	"specific Splicing Variant involved in Hepatocarcinogenesis"	611864				12839973	Standard	NM_031905		Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000323716.3:c.899A>G	chr7.hg19:g.102738867A>G	ENSP00000319412:p.Gln300Arg	175.0	0.0		612.0	166.0	NM_031905	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	Missense_Mutation	SNP	ENST00000323716.3	hg19	CCDS5728.1	.	.	.	.	.	.	.	.	.	.	A	3.673	-0.067130	0.07273	.	.	ENSG00000170632	ENST00000323716;ENST00000428183;ENST00000441711;ENST00000454559;ENST00000425331;ENST00000541300;ENST00000434153;ENST00000431642	T;T;T;T;T;T;T;T	0.53423	1.52;1.52;1.52;1.52;1.52;1.52;0.62;1.52	5.68	-0.724	0.11177	Armadillo-type fold (1);	0.554134	0.21062	N	0.080809	T	0.38427	0.1040	L	0.58669	1.825	0.09310	N	1	B;B;B;B;B;B;B	0.30236	0.004;0.004;0.274;0.116;0.004;0.008;0.008	B;B;B;B;B;B;B	0.27887	0.02;0.006;0.084;0.057;0.008;0.019;0.022	T	0.26155	-1.0111	10	0.30854	T	0.27	1.5325	10.9007	0.47049	0.6685:0.0:0.3315:0.0	.	241;182;206;228;241;265;300	B4DWJ8;F5GX65;Q8N2F6-4;C9J5N7;Q8N2F6-3;Q8N2F6-2;Q8N2F6	.;.;.;.;.;.;ARM10_HUMAN	R	300;241;265;206;241;182;228;142	ENSP00000319412:Q300R;ENSP00000396654:Q241R;ENSP00000413619:Q265R;ENSP00000405612:Q206R;ENSP00000397969:Q241R;ENSP00000440463:Q182R;ENSP00000398201:Q228R;ENSP00000406840:Q142R	ENSP00000319412:Q300R	Q	+	2	0	ARMC10	102526103	0.001000	0.12720	0.000000	0.03702	0.377000	0.30045	0.539000	0.23175	-0.070000	0.12908	0.482000	0.46254	CAG	.	.		0.403	ARMC10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347882.1	NM_031905		G	102738867	A	G	102738867	3	3	97	1	0	0	0	0	1	0	0	0	950	188	7	2	925	2	ARMC10	7	102738867	Missense_Mutation	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	8445167	102738867	56399796	47	13310										
TCEA1	6917	hgsc.bcm.edu	37	chr8	54912542	54912542	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gatttgatgagagactttgcCaaagatgtaacttcctcatc	8	8	1	4			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr8:54912542C>A	ENST00000521604.2	-	3	598	c.195G>T	c.(193-195)ttG>ttT	p.L65F	TCEA1_ENST00000520534.1_Missense_Mutation_p.L65F|TCEA1_ENST00000521086.2_5'UTR|TCEA1_ENST00000396401.3_Missense_Mutation_p.L44F|TCEA1_ENST00000518784.1_Missense_Mutation_p.L65F|TCEA1_ENST00000522635.1_Intron	NM_006756.2	NP_006747.1	P23193	TCEA1_HUMAN	transcription elongation factor A (SII), 1	65	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				DNA repair (GO:0006281)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|regulation of DNA-templated transcription, elongation (GO:0032784)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(1)|lung(1)|skin(1)	4		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			GAGACTTTGCCAAAGATGTAA	0.323			T	PLAG1	salivary adenoma																																p.L65F		Atlas-SNP	.		Dom	yes		8	8q11.2	6917	"transcription elongation factor A (SII), 1"		E	.	TCEA1	30	.	0			c.G195T						.						96	88	91					8																	54912542		1824	4074	5898	SO:0001583	missense	6917	exon3			CTTTGCCAAAGAT	X62585	CCDS47857.1, CCDS47858.1	8q11.2	2011-01-25			ENSG00000187735	ENSG00000187735		"General transcription factors"	11612	protein-coding gene	gene with protein product		601425		TCEA, GTF2S		8812434, 8112616	Standard	NM_006756		Approved	SII, TF2S, TFIIS	uc003xru.3	P23193	OTTHUMG00000164262	ENST00000521604.2:c.195G>T	chr8.hg19:g.54912542C>A	ENSP00000428426:p.Leu65Phe	151.0	0.0		392.0	141.0	NM_006756	A6NF25|A8K339|Q15563|Q6FG87	Missense_Mutation	SNP	ENST00000521604.2	hg19	CCDS47858.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.504383	0.44558	.	.	ENSG00000187735	ENST00000396401;ENST00000521604;ENST00000520534;ENST00000518784	.	.	.	5.63	3.28	0.37604	Transcription factor IIS, N-terminal (4);Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type (1);	0.000000	0.64402	D	0.000003	T	0.75968	0.3922	M	0.78049	2.395	0.54753	D	0.999983	D;D	0.89917	1.0;0.997	D;D	0.78314	0.991;0.99	T	0.75216	-0.3396	9	0.72032	D	0.01	-7.9292	9.0457	0.36345	0.0:0.154:0.0:0.846	.	44;65	P23193-2;P23193	.;TCEA1_HUMAN	F	44;65;65;65	.	ENSP00000395483:L44F	L	-	3	2	TCEA1	55075095	1.000000	0.71417	1.000000	0.80357	0.344000	0.29017	0.479000	0.22228	0.433000	0.26313	-0.312000	0.09012	TTG	.	.		0.323	TCEA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377975.2	NM_006756		A	54912542	C	A	54912542	3	1	97	1	0	0	0	0	1	0	0	0	15682	593	21	3	742	3	TCEA1	8	54912542	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10		54912542	91451480	48	13311										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73848335	73848335	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	catggtttaccatggagtacCttttgcgattcttatcctca	7	10	2	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr8:73848335C>G	ENST00000523207.1	+	3	1333	c.745C>G	c.(745-747)Ctt>Gtt	p.L249V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	249					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	CATGGAGTACCTTTTGCGATT	0.458																																					p.L249V		Atlas-SNP	.											.	KCNB2	228	.	0			c.C745G						.						195	168	177					8																	73848335		2203	4300	6503	SO:0001583	missense	9312	exon3			GAGTACCTTTTGC	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.745C>G	chr8.hg19:g.73848335C>G	ENSP00000430846:p.Leu249Val	124.0	0.0		294.0	111.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760784	0.69763	.	.	ENSG00000182674	ENST00000523207	D	0.98419	-4.92	5.93	5.93	0.95920	Ion transport (1);	0.000000	0.40818	N	0.001009	D	0.97654	0.9231	N	0.17631	0.505	0.80722	D	1	P	0.49696	0.927	P	0.61397	0.888	D	0.97710	1.0190	10	0.39692	T	0.17	.	20.3507	0.98813	0.0:1.0:0.0:0.0	.	249	Q92953	KCNB2_HUMAN	V	249	ENSP00000430846:L249V	ENSP00000430846:L249V	L	+	1	0	KCNB2	74010889	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	7.818000	0.86416	2.808000	0.96608	0.655000	0.94253	CTT	.	.		0.458	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		G	73848335	C	G	73848335	3	3	97	1	0	0	0	0	1	0	0	0	8022	681	24	4	751	4	KCNB2	8	73848335	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	18935793	73848335	72515687	49	13312										
LRP12	29967	hgsc.bcm.edu	37	chr8	105510097	105510097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cggggaggcaagtgtaaactTtggtaaaacgggataaacac	13	6	0	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr8:105510097T>C	ENST00000276654.5	-	5	791	c.683A>G	c.(682-684)aAa>aGa	p.K228R	LRP12_ENST00000424843.2_Missense_Mutation_p.K209R|LRP12_ENST00000518375.1_5'Flank	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	228	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			AGTGTAAACTTTGGTAAAACG	0.453																																					p.K228R		Atlas-SNP	.											.	LRP12	124	.	0			c.A683G						.						141	130	134					8																	105510097		2203	4300	6503	SO:0001583	missense	29967	exon5			TAAACTTTGGTAA	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.683A>G	chr8.hg19:g.105510097T>C	ENSP00000276654:p.Lys228Arg	110.0	0.0		221.0	105.0	NM_013437	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000276654.5	hg19	CCDS6303.1	.	.	.	.	.	.	.	.	.	.	T	9.298	1.052444	0.19907	.	.	ENSG00000147650	ENST00000424843;ENST00000276654	D;D	0.83591	-1.74;-1.67	5.66	5.66	0.87406	.	0.049986	0.85682	D	0.000000	T	0.63721	0.2535	N	0.04508	-0.205	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.62728	-0.6793	10	0.02654	T	1	-29.6762	15.9017	0.79384	0.0:0.0:0.0:1.0	.	209;228	Q9Y561-2;Q9Y561	.;LRP12_HUMAN	R	209;228	ENSP00000399148:K209R;ENSP00000276654:K228R	ENSP00000276654:K228R	K	-	2	0	LRP12	105579273	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.365000	0.59486	2.153000	0.67306	0.460000	0.39030	AAA	.	.		0.453	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		C	105510097	T	C	105510097	3	2	97	1	0	0	0	0	1	0	0	0	8963	1841	64	2	1908	2	LRP12	8	105510097	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	31661762	105510097	40853925	50	13313										
IFNA8	3445	hgsc.bcm.edu	37	chr9	21409564	21409564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gatgcaggaagtgggggtgaTagagtctcccctgatgtacg	16	7	1	3	rs28383787		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr9:21409564T>C	ENST00000380205.1	+	1	419	c.389T>C	c.(388-390)aTa>aCa	p.I130T		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	130					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		GTGGGGGTGATAGAGTCTCCC	0.478																																					p.I130T		Atlas-SNP	.											.	IFNA8	19	.	0			c.T389C						.						144	142	142					9																	21409564		2203	4300	6503	SO:0001583	missense	3445	exon1			GGGTGATAGAGTC		CCDS6507.1	9p22	2010-08-24			ENSG00000120242	ENSG00000120242		"Interferons"	5429	protein-coding gene	gene with protein product	"interferon alpha-B''", "interferon alpha type 201"	147568				1385305	Standard	NM_002170		Approved	IFN-alphaB	uc003zpc.1	P32881	OTTHUMG00000019677	ENST00000380205.1:c.389T>C	chr9.hg19:g.21409564T>C	ENSP00000369553:p.Ile130Thr	102.0	0.0		258.0	110.0	NM_002170	P01565|P09236|Q5VWV7|Q5VYQ3	Missense_Mutation	SNP	ENST00000380205.1	hg19	CCDS6507.1	.	.	.	.	.	.	.	.	.	.	T	5.842	0.339510	0.11069	.	.	ENSG00000120242	ENST00000380205	T	0.05081	3.5	3.48	-2.49	0.06403	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	2.002250	0.01939	N	0.041792	T	0.01661	0.0053	N	0.00347	-1.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38436	-0.9661	10	0.40728	T	0.16	.	1.2648	0.02009	0.3469:0.3593:0.1167:0.1771	.	130	P32881	IFNA8_HUMAN	T	130	ENSP00000369553:I130T	ENSP00000369553:I130T	I	+	2	0	IFNA8	21399564	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.378000	0.07446	-0.568000	0.06038	-2.123000	0.00347	ATA	.	.		0.478	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1	NM_002170		C	21409564	T	C	21409564	3	2	97	1	0	0	0	0	1	0	0	0	7552	1406	49	2	391	2	IFNA8	9	21409564	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10		21409564	119803867	51	13314										
COL15A1	1306	hgsc.bcm.edu	37	chr9	101749575	101749575	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tgatccgtctcttttccccaGggctccctccagcagctcac	7	18	2	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr9:101749575G>A	ENST00000375001.3	+	4	1071		c.e4-1			NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1						angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CTTTTCCCCAGGGCTCCCTCC	0.567																																					.		Atlas-SNP	.											.	COL15A1	211	.	0			c.649-1G>A						.						185	169	174					9																	101749575		2203	4300	6503	SO:0001630	splice_region_variant	1306	exon4			TCCCCAGGGCTCC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.649-1G>A	chr9.hg19:g.101749575G>A		25.0	0.0		65.0	27.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Splice_Site	SNP	ENST00000375001.3	hg19	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.403198	0.83230	.	.	ENSG00000204291	ENST00000375001;ENST00000536083	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3894	0.66968	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL15A1	100789396	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.435000	0.80391	2.524000	0.85096	0.655000	0.94253	.	.	.		0.567	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	Intron	A	101749575	G	A	101749575	5	1	97	1	0	0	0	0	0	0	1	0	3674	1014	35	3	662	3	COL15A1	9	101749575	Splice_Site	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	80340011	101749575	39463856	52	13315										
PTPN3	5774	hgsc.bcm.edu	37	chr9	112200499	112200499	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gatgatgtatggaagaattaTagtctccaaaatgagctatc	9	5	1	3			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr9:112200499T>C	ENST00000374541.2	-	8	586	c.482A>G	c.(481-483)tAt>tGt	p.Y161C	PTPN3_ENST00000446349.1_Missense_Mutation_p.Y30C|PTPN3_ENST00000412145.1_Missense_Mutation_p.Y30C|PTPN3_ENST00000262539.3_Missense_Mutation_p.Y52C	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	161	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						GGAAGAATTATAGTCTCCAAA	0.353																																					p.Y161C		Atlas-SNP	.											.	PTPN3	106	.	0			c.A482G						.						71	75	74					9																	112200499		2203	4300	6503	SO:0001583	missense	5774	exon8			GAATTATAGTCTC		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.482A>G	chr9.hg19:g.112200499T>C	ENSP00000363667:p.Tyr161Cys	24.0	0.0		35.0	11.0	NM_001145368	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	hg19	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.038533	0.55003	.	.	ENSG00000070159	ENST00000394831;ENST00000412145;ENST00000446349;ENST00000374541;ENST00000262539	T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9	5.96	4.81	0.61882	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.290359	0.38663	N	0.001618	D	0.84215	0.5423	M	0.78344	2.41	0.80722	D	1	P;D;D	0.59357	0.932;0.985;0.974	P;D;D	0.67103	0.714;0.949;0.925	D	0.85094	0.0953	10	0.87932	D	0	.	10.6503	0.45645	0.1684:0.0:0.0:0.8316	.	52;161;161	B7Z3H5;B7Z9V1;P26045	.;.;PTN3_HUMAN	C	161;30;30;161;52	ENSP00000416654:Y30C;ENSP00000395384:Y30C;ENSP00000363667:Y161C;ENSP00000262539:Y52C	ENSP00000262539:Y52C	Y	-	2	0	PTPN3	111240320	0.952000	0.32445	0.759000	0.31340	0.554000	0.35429	1.687000	0.37680	1.047000	0.40274	0.533000	0.62120	TAT	.	.		0.353	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			C	112200499	T	C	112200499	3	2	97	1	0	0	0	0	1	0	0	0	12804	1406	49	2	2335	2	PTPN3	9	112200499	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	10450924	112200499	29012932	53	13316										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140880982	140880982	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ttcgccctgctggggatgcaGctgtttgggggacagtaagt	16	8	0	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr9:140880982G>T	ENST00000371372.1	+	14	2032	c.1887G>T	c.(1885-1887)caG>caT	p.Q629H	CACNA1B_ENST00000277551.2_Missense_Mutation_p.Q629H|CACNA1B_ENST00000371355.4_Missense_Mutation_p.Q630H|CACNA1B_ENST00000371363.1_Missense_Mutation_p.Q629H|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371357.1_Missense_Mutation_p.Q630H	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	629					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGGGATGCAGCTGTTTGGGG	0.612																																					p.Q629H		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G1887T						.						47	49	49					9																	140880982		2080	4229	6309	SO:0001583	missense	774	exon14			GATGCAGCTGTTT	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1887G>T	chr9.hg19:g.140880982G>T	ENSP00000360423:p.Gln629His	109.0	0.0		298.0	110.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.221756	0.58560	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.98996	-5.31;-5.31;-5.31;-5.31;-5.31	4.35	3.44	0.39384	.	0.000000	0.85682	D	0.000000	D	0.99205	0.9724	M	0.85710	2.77	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	D	0.99486	1.0949	10	0.87932	D	0	.	12.7997	0.57578	0.0816:0.0:0.9184:0.0	.	629;629	B1AQK4;B1AQK6	.;.	H	629;629;629;630;630	ENSP00000360423:Q629H;ENSP00000277551:Q629H;ENSP00000360414:Q629H;ENSP00000360408:Q630H;ENSP00000360406:Q630H	ENSP00000277551:Q629H	Q	+	3	2	CACNA1B	140000803	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.487000	0.60293	0.913000	0.36797	0.462000	0.41574	CAG	.	.		0.612	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		T	140880982	G	T	140880982	3	4	97	1	0	0	0	0	1	0	0	0	2541	962	34	3	1941	3	CACNA1B	9	140880982	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	28680483	140880982	332449	54	13317										
DIP2C	22982	hgsc.bcm.edu	37	chr10	390969	390969	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gatgaggggccacgtcctgaCgtccacagccgccgccgcct	13	17	0	2	rs200340134		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr10:390969C>A	ENST00000280886.6	-	27	3400	c.3313G>T	c.(3313-3315)Gtc>Ttc	p.V1105F		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1105						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CACGTCCTGACGTCCACAGCC	0.592																																					p.V1105F		Atlas-SNP	.											.	DIP2C	195	.	0			c.G3313T						.						72	59	63					10																	390969		2203	4300	6503	SO:0001583	missense	22982	exon27			TCCTGACGTCCAC	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3313G>T	chr10.hg19:g.390969C>A	ENSP00000280886:p.Val1105Phe	29.0	0.0		54.0	23.0	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	C	8.495	0.862866	0.17178	.	.	ENSG00000151240	ENST00000280886;ENST00000535541	T	0.10668	2.85	5.59	4.69	0.59074	AMP-dependent synthetase/ligase (1);	0.188095	0.46145	D	0.000316	T	0.08670	0.0215	N	0.25380	0.74	0.80722	D	1	B	0.13594	0.008	B	0.28305	0.088	T	0.25572	-1.0128	10	0.23891	T	0.37	-31.7464	9.4456	0.38695	0.0:0.7807:0.0:0.2193	.	1105	Q9Y2E4	DIP2C_HUMAN	F	1105;30	ENSP00000280886:V1105F	ENSP00000280886:V1105F	V	-	1	0	DIP2C	380969	0.006000	0.16342	0.885000	0.34714	0.399000	0.30720	0.029000	0.13666	1.368000	0.46115	0.655000	0.94253	GTC	.	C|1.000;T|0.000		0.592	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		A	390969	C	A	390969	3	1	97	1	0	0	0	0	1	0	0	0	4531	536	19	1	1401	1	DIP2C	10	390969	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10		390969	135143778	55	13318										
OGDHL	55753	hgsc.bcm.edu	37	chr10	50947868	50947868	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ggcattggggctggccatggCatagcccagctcaaagccta	13	12	1	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr10:50947868C>A	ENST00000374103.4	-	17	2243	c.2158G>T	c.(2158-2160)Gcc>Tcc	p.A720S	OGDHL_ENST00000490844.1_5'Flank|OGDHL_ENST00000432695.1_Missense_Mutation_p.A511S|OGDHL_ENST00000419399.1_Missense_Mutation_p.A663S	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	720					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CTGGCCATGGCATAGCCCAGC	0.547																																					p.A720S		Atlas-SNP	.											.	OGDHL	149	.	0			c.G2158T						.						65	59	61					10																	50947868		2203	4300	6503	SO:0001583	missense	55753	exon17			CCATGGCATAGCC	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.2158G>T	chr10.hg19:g.50947868C>A	ENSP00000363216:p.Ala720Ser	33.0	0.0		67.0	29.0	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	hg19	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	C	6.641	0.486774	0.12641	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	D;D;D	0.96491	-4.03;-4.03;-4.03	4.61	3.71	0.42584	Transketolase-like, pyrimidine-binding domain (2);	0.057465	0.64402	D	0.000002	D	0.85414	0.5691	N	0.01289	-0.905	0.80722	D	1	B;B;B	0.10296	0.002;0.001;0.003	B;B;B	0.23018	0.025;0.006;0.043	T	0.79825	-0.1640	10	0.02654	T	1	.	12.479	0.55831	0.0:0.9183:0.0:0.0817	.	663;511;720	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	S	720;663;511	ENSP00000363216:A720S;ENSP00000401356:A663S;ENSP00000390240:A511S	ENSP00000363216:A720S	A	-	1	0	OGDHL	50617874	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	7.811000	0.86092	0.950000	0.37743	0.446000	0.29264	GCC	.	.		0.547	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		A	50947868	C	A	50947868	3	1	97	1	0	0	0	0	1	0	0	0	10849	710	25	3	902	3	OGDHL	10	50947868	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	50556899	50947868	84586879	56	13319										
DGAT2	84649	hgsc.bcm.edu	37	chr11	75508294	75508294	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	atcgtggtcgggggtgcggcTgagtctctgagctccatgcc	16	11	1	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr11:75508294T>G	ENST00000228027.7	+	6	986	c.726T>G	c.(724-726)gcT>gcG	p.A242A	DGAT2_ENST00000376262.3_Silent_p.A199A	NM_032564.4	NP_115953.2	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2	242					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|cellular response to oleic acid (GO:0071400)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|diacylglycerol metabolic process (GO:0046339)|fat pad development (GO:0060613)|fatty acid homeostasis (GO:0055089)|glycerol metabolic process (GO:0006071)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)|protein homodimerization activity (GO:0042803)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(5)|lung(5)|prostate(2)|skin(2)	17	Ovarian(111;0.103)					GGGGTGCGGCTGAGTCTCTGA	0.567																																					p.A242A	Melanoma(35;811 1096 8354 24009 39363)	Atlas-SNP	.											.	DGAT2	37	.	0			c.T726G						.						145	125	132					11																	75508294		2200	4293	6493	SO:0001819	synonymous_variant	84649	exon6			TGCGGCTGAGTCT		CCDS31642.1, CCDS58162.1	11q13.3	2010-06-24	2010-06-24		ENSG00000062282	ENSG00000062282			16940	protein-coding gene	gene with protein product		606983	"diacylglycerol O-acyltransferase homolog 2 (mouse)"			11481335, 14970677	Standard	NM_032564		Approved		uc001oxa.3	Q96PD7	OTTHUMG00000165338	ENST00000228027.7:c.726T>G	chr11.hg19:g.75508294T>G		40.0	0.0		101.0	36.0	NM_032564	A6ND76|Q5U810|Q68CL3|Q68DJ0|Q8NDB7|Q96BS0|Q9BYE5	Silent	SNP	ENST00000228027.7	hg19	CCDS31642.1																																																																																			.	.		0.567	DGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383506.1	NM_032564		G	75508294	T	G	75508294	2	3	97	1	0	0	0	0	0	0	0	1	4460	1567	55	5		5	DGAT2	11	75508294	Silent	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10		75508294	59498222	57	13320										
NCAM1	4684	hgsc.bcm.edu	37	chr11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ccctcccagccagcagattaCaatgctgccaaactaaggat					rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				RP11-629G13.1_ENST00000532002.1_RNA|RP11-629G13.1_ENST00000500537.2_RNA|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		0.0	0.0		80.0	24.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		-	112832363	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	112832332	6	5	97	0	1	1	0	1	0	0	0	0	10211	493	17	0		0	NCAM1	11	112832332	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	TCGA-DD-A1EA-01A-11D-A12Z-10	37324038	112832332	22174184	58	13321										
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18534747	18534747	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cagcatgacattacagagtgAgcctcccgtagaaatgataa	9	9	0	5			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr12:18534747A>T	ENST00000266497.5	+	12	1843	c.1805A>T	c.(1804-1806)gAg>gTg	p.E602V	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.E602V|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.E643V			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	602	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TTACAGAGTGAGCCTCCCGTA	0.473																																					p.E602V		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A1805T						.						136	129	131					12																	18534747		1917	4132	6049	SO:0001583	missense	5288	exon13			AGAGTGAGCCTCC	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1805A>T	chr12.hg19:g.18534747A>T	ENSP00000266497:p.Glu602Val	60.0	0.0		120.0	51.0	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.535389	0.45176	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.71341	-0.56;-0.56;-0.56	4.35	3.17	0.36434	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.871539	0.10193	N	0.704434	T	0.78541	0.4299	M	0.65975	2.015	0.33065	D	0.534569	D;D;D	0.58620	0.983;0.978;0.965	P;P;P	0.62382	0.901;0.84;0.83	T	0.75213	-0.3397	10	0.32370	T	0.25	-12.1363	7.9803	0.30179	0.7924:0.2076:0.0:0.0	.	642;643;602	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	V	602;602;643	ENSP00000404845:E602V;ENSP00000266497:E602V;ENSP00000445381:E643V	ENSP00000266497:E602V	E	+	2	0	PIK3C2G	18426014	0.996000	0.38824	1.000000	0.80357	0.650000	0.38633	1.407000	0.34657	0.957000	0.37930	0.460000	0.39030	GAG	.	.		0.473	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		T	18534747	A	T	18534747	3	4	97	1	0	0	0	0	1	0	0	0	11920	304	11	4	1851	4	PIK3C2G	12	18534747	Missense_Mutation	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10		18534747	115317148	59	13322										
CELA1	1990	hgsc.bcm.edu	37	chr12	51740405	51740433	+	Start_Codon_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cgactggaccatatccacttAccataaaggaccagcatgtt					rs150350903|rs573952082|rs201074609|rs141305161|rs117443541|rs377599213|rs143199509|rs61761206|rs148235680|rs370927847|rs148270827|rs116944010|rs386762976|rs149358345|rs55827519	byFrequency	TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr12:51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC	ENST00000293636.1	-	0	30_57					NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1						exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)|p.L4P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ATATCCACTTACCATAAAGGACCAGCATGTTGCCGATGGAGTAGACCAC	0.524																																					p.3_6del		Pindel	.											.	CELA1	39	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.8_16del						.																																			SO:0001582	initiator_codon_variant	1990	exon1			.		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"elastase 1, pancreatic"	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523		chr12.hg19:g.51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC		0.0	0.0		110.0	20.0	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	In_Frame_Del	DEL	ENST00000293636.1	hg19	CCDS8812.1																																																																																			.	-|0.574;CACCAGGAAGCG|0.426		0.524	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971		-	51740433	CTGGACCATATCCACTTACCATAAAGGAC	-	51740405	7	5	97	1	0	1	0	1	0	0	0	0	3212	405	14	0	790	0	CELA1	12	51740405	Start_Codon_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	TCGA-DD-A1EA-01A-11D-A12Z-10	33205658	51740405	82111490	60	13323										
MMP19	4327	hgsc.bcm.edu	37	chr12	56231749	56231750	+	Frame_Shift_Del	DEL	CA	CA	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gtcctgaatctgatacagtcCacacatagtcccccttgaaa							TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr12:56231749_56231750delCA	ENST00000322569.4	-	7	1028_1029	c.937_938delTG	c.(937-939)tggfs	p.W313fs	MMP19_ENST00000548629.1_Frame_Shift_Del_p.W290fs|TMEM198B_ENST00000478241.1_RNA|MMP19_ENST00000394182.1_Frame_Shift_Del_p.W27fs|MMP19_ENST00000409200.3_Frame_Shift_Del_p.V266fs	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	313					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	TGATACAGTCCACACATAGTCC	0.545																																					p.313_313del		Atlas-Indel,Pindel	.											.	MMP19	61	.	0			c.938_939del						.																																			SO:0001589	frameshift_variant	4327	exon7			.	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"matrix metalloproteinase 19"	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.937_938delTG	chr12.hg19:g.56231753_56231754delCA	ENSP00000313437:p.Trp313fs	53.0	0.0		82.0	33.0	NM_002429	B4E030|O15278|O95606|Q99580	Frame_Shift_Del	DEL	ENST00000322569.4	hg19	CCDS8895.1																																																																																			.	.		0.545	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429		-	56231750	CA	-	56231749	7	5	97	1	0	1	0	1	0	0	0	0	9666	595	21	0	600	0	MMP19	12	56231749	Frame_Shift_Del	DEL	CA	TCGA-DD-A1EA-01A-11D-A12Z-10	4491344	56231749	77620146	61	13324										
MED13L	23389	hgsc.bcm.edu	37	chr12	116429410	116429410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	aaagatattcatcacggaatCggagagaatcagggtaacat	10	6	3	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr12:116429410C>T	ENST00000281928.3	-	17	3555	c.3349G>A	c.(3349-3351)Gat>Aat	p.D1117N		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1117						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		ATCACGGAATCGGAGAGAATC	0.527																																					p.D1117N		Atlas-SNP	.											.	MED13L	193	.	0			c.G3349A						.						61	60	61					12																	116429410		2203	4300	6503	SO:0001583	missense	23389	exon17			CGGAATCGGAGAG	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.3349G>A	chr12.hg19:g.116429410C>T	ENSP00000281928:p.Asp1117Asn	57.0	0.0		128.0	48.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.708388	0.68615	.	.	ENSG00000123066	ENST00000281928	D	0.86097	-2.07	5.18	5.18	0.71444	.	0.140018	0.64402	D	0.000006	D	0.83312	0.5227	M	0.64997	1.995	0.80722	D	1	P	0.39551	0.678	B	0.33339	0.162	D	0.86056	0.1529	10	0.87932	D	0	.	18.8897	0.92395	0.0:1.0:0.0:0.0	.	1117	Q71F56	MD13L_HUMAN	N	1117	ENSP00000281928:D1117N	ENSP00000281928:D1117N	D	-	1	0	MED13L	114913793	1.000000	0.71417	0.935000	0.37517	0.843000	0.47879	7.320000	0.79064	2.699000	0.92147	0.460000	0.39030	GAT	.	.		0.527	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			T	116429410	C	T	116429410	3	4	97	1	0	0	0	0	1	0	0	0	9440	884	31	1	3343	1	MED13L	12	116429410	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	60197661	116429410	17422485	62	13325										
RFXAP	5994	hgsc.bcm.edu	37	chr13	37399580	37399580	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cccaggaaagtgcagataacAtactctccattgttaaacaa	6	10	1	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:37399580A>G	ENST00000255476.2	+	2	750	c.616A>G	c.(616-618)Ata>Gta	p.I206V	RFXAP_ENST00000472888.1_3'UTR	NM_000538.3	NP_000529.1	O00287	RFXAP_HUMAN	regulatory factor X-associated protein	206					positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)	4		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;3.5e-07)|Epithelial(112;1.27e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.0069)|BRCA - Breast invasive adenocarcinoma(63;0.0116)|GBM - Glioblastoma multiforme(144;0.0405)		TGCAGATAACATACTCTCCAT	0.323																																					p.I206V		Atlas-SNP	.											.	RFXAP	14	.	0			c.A616G						.						96	97	97					13																	37399580		2203	4298	6501	SO:0001583	missense	5994	exon2			GATAACATACTCT	Y12812	CCDS9359.1	13q14	2014-09-17			ENSG00000133111	ENSG00000133111			9988	protein-coding gene	gene with protein product		601861				9118943	Standard	NM_000538		Approved		uc001uvu.1	O00287	OTTHUMG00000016738	ENST00000255476.2:c.616A>G	chr13.hg19:g.37399580A>G	ENSP00000255476:p.Ile206Val	35.0	0.0		72.0	19.0	NM_000538	B2R9T8|Q5VZM6|Q8TC40	Missense_Mutation	SNP	ENST00000255476.2	hg19	CCDS9359.1	.	.	.	.	.	.	.	.	.	.	A	2.616	-0.289716	0.05568	.	.	ENSG00000133111	ENST00000255476	.	.	.	5.92	-1.86	0.07760	.	0.310059	0.35262	N	0.003335	T	0.17746	0.0426	L	0.36672	1.1	0.09310	N	0.999997	B	0.29988	0.264	B	0.28011	0.085	T	0.36286	-0.9754	9	0.02654	T	1	-6.2063	6.5682	0.22523	0.3427:0.1933:0.0:0.464	.	206	O00287	RFXAP_HUMAN	V	206	.	ENSP00000255476:I206V	I	+	1	0	RFXAP	36297580	0.797000	0.28877	0.260000	0.24451	0.993000	0.82548	0.430000	0.21428	-0.108000	0.12066	0.533000	0.62120	ATA	.	.		0.323	RFXAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044521.1	NM_000538		G	37399580	A	G	37399580	3	3	97	1	0	0	0	0	1	0	0	0	13285	217	8	2	622	2	RFXAP	13	37399580	Missense_Mutation	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10		37399580	77770298	63	13326										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42877120	42877120	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	caaggaactgttaatgttttCaaacaaagagcaccaccaag	7	9	1	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:42877120C>A	ENST00000025301.2	+	8	4413	c.4238C>A	c.(4237-4239)tCa>tAa	p.S1413*		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1413					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TTAATGTTTTCAAACAAAGAG	0.383																																					p.S1413X		Atlas-SNP	.											.	AKAP11	146	.	0			c.C4238A						.						48	51	50					13																	42877120		2203	4300	6503	SO:0001587	stop_gained	11215	exon8			TGTTTTCAAACAA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.4238C>A	chr13.hg19:g.42877120C>A	ENSP00000025301:p.Ser1413*	54.0	0.0		56.0	17.0	NM_016248	O75124|Q9NUK7	Nonsense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	C	38	6.961113	0.97964	.	.	ENSG00000023516	ENST00000025301	.	.	.	5.58	4.55	0.56014	.	0.437976	0.20911	N	0.083466	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	3.6947	0.08360	0.0:0.1427:0.2294:0.628	.	.	.	.	X	1413	.	ENSP00000025301:S1413X	S	+	2	0	AKAP11	41775120	0.001000	0.12720	0.159000	0.22649	0.077000	0.17291	0.934000	0.28910	1.138000	0.42230	0.557000	0.71058	TCA	.	.		0.383	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		A	42877120	C	A	42877120	4	1	97	1	0	0	0	0	0	1	0	0	447	838	29	3	4260	3	AKAP11	13	42877120	Nonsense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	5477540	42877120	72292758	64	13327										
COG3	83548	hgsc.bcm.edu	37	chr13	46077399	46077409	+	Frame_Shift_Del	DEL	AGATGAACAGA	AGATGAACAGA	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cagattgcacagagtttgaaAgatgaacagaagaaggtacc					rs370937289		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	AGATGAACAGA	AGATGAACAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:46077399_46077409delAGATGAACAGA	ENST00000349995.5	+	14	1621_1631	c.1509_1519delAGATGAACAGA	c.(1507-1521)aaagatgaacagaagfs	p.KDEQK503fs	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	503					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AGAGTTTGAAAGATGAACAGAAGAAGGTACC	0.365																																					p.503_506del	Ovarian(150;1048 1859 18083 21577 42700)	Pindel	.											.	COG3	52	.	0			c.1508_1518del						.																																			SO:0001589	frameshift_variant	83548	exon14			.	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1509_1519delAGATGAACAGA	chr13.hg19:g.46077399_46077409delAGATGAACAGA	ENSP00000258654:p.Lys503fs	0.0	0.0		113.0	13.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Frame_Shift_Del	DEL	ENST00000349995.5	hg19	CCDS9398.1																																																																																			.	.		0.365	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			-	46077409	AGATGAACAGA	-	46077399	7	5	97	1	0	1	0	1	0	0	0	0	3661	69	3	0	1563	0	COG3	13	46077399	Frame_Shift_Del	DEL	AGATGAACAGA	TCGA-DD-A1EA-01A-11D-A12Z-10	3200279	46077399	69092479	65	13328	58	3								
COG3	83548	hgsc.bcm.edu	37	chr13	46077404	46077405	+	Missense_Mutation	DNP	AA	AA	TT													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tgcacagagtttgaaagatgAacagaagaaggtaccttcag							TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:46077404_46077405AA>TT	ENST00000349995.5	+	14	1626_1627	c.1514_1515AA>TT	c.(1513-1515)gAA>gTT	p.E505V	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	505					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		TTGAAAGATGAACAGAAGAAGG	0.361																																					p.E505V|p.E505D	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.A1514T|c.A1515T						.																																			SO:0001583	missense	83548	exon14			AAGATGAACAGAA|AGATGAACAGAAG	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	Exception_encountered	chr13.hg19:g.46077404_46077405delinsTT	ENSP00000258654:p.Glu505Val	77.0|78.0	0.0		109.0|111.0	15.0|18.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1																																																																																			.	.		0.361	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			TT	46077405	AA	TT	46077404	3	4	97	1	0	0	0	0	1	0	0	0	3661	246	9	4	1568	4	COG3	13	46077404	Missense_Mutation	DNP	AA	TCGA-DD-A1EA-01A-11D-A12Z-10	5	46077404	69092474	66	13329	58	3								
COG3	83548	hgsc.bcm.edu	37	chr13	46077408	46077408	+	Frame_Shift_Del	DEL	G	G	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cagagtttgaaagatgaacaGaagaaggtaccttcagaagc							TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:46077408delG	ENST00000349995.5	+	14	1630	c.1518delG	c.(1516-1518)cagfs	p.Q506fs	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	506					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AAGATGAACAGAAGAAGGTAC	0.373																																					p.Q506fs	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-INDEL	.											.	COG3	52	.	0			c.1517delA						.						108	105	106					13																	46077408		2203	4300	6503	SO:0001589	frameshift_variant	83548	exon14			.	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1518delG	chr13.hg19:g.46077408delG	ENSP00000258654:p.Gln506fs	80.0	0.0		118.0	18.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Frame_Shift_Del	DEL	ENST00000349995.5	hg19	CCDS9398.1																																																																																			.	.		0.373	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			-	46077408	G	-	46077408	7	5	97	1	0	1	0	1	0	0	0	0	3661	933	33	0	1572	0	COG3	13	46077408	Frame_Shift_Del	DEL	G	TCGA-DD-A1EA-01A-11D-A12Z-10	4	46077408	69092470	67	13330	58	3								
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84454266	84454266	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gtgcccgggaggatgagctgGatagcgttgtactccacgtt	15	9	0	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:84454266G>A	ENST00000377084.2	-	1	2262	c.1377C>T	c.(1375-1377)atC>atT	p.I459I		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	459					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		GGATGAGCTGGATAGCGTTGT	0.542																																					p.I459I		Atlas-SNP	.											.	SLITRK1	196	.	0			c.C1377T						.						92	82	86					13																	84454266		2203	4300	6503	SO:0001819	synonymous_variant	114798	exon1			GAGCTGGATAGCG	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1377C>T	chr13.hg19:g.84454266G>A		65.0	0.0		153.0	51.0	NM_052910	Q5U5I6|Q96SF9	Silent	SNP	ENST00000377084.2	hg19	CCDS9464.1																																																																																			.	.		0.542	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84454266	G	A	84454266	2	1	97	1	0	0	0	0	0	0	0	1	14757	1164	41	3		3	SLITRK1	13	84454266	Silent	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	38376858	84454266	30715612	68	13331										
DHRS4	10901	hgsc.bcm.edu	37	chr14	24435604	24435604	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ctgcctagcacctggacttaTcaagactagcttcagcagga	9	12	2	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:24435604T>G	ENST00000313250.5	+	6	847	c.644T>G	c.(643-645)aTc>aGc	p.I215S	DHRS4_ENST00000397074.3_Intron|DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000397075.3_Intron|DHRS4_ENST00000543741.2_Intron|DHRS4_ENST00000397073.2_Intron|DHRS4_ENST00000558581.1_Missense_Mutation_p.I181S|DHRS4_ENST00000558263.1_Intron|DHRS4_ENST00000308178.8_Intron|DHRS4_ENST00000421831.1_Missense_Mutation_p.I163S|DHRS4_ENST00000382761.3_Intron	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	215					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CCTGGACTTATCAAGACTAGC	0.527																																					p.I215S		Atlas-SNP	.											.	DHRS4	22	.	0			c.T644G						.						113	96	102					14																	24435604		2201	4297	6498	SO:0001583	missense	10901	exon6			GACTTATCAAGAC	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	16985	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 25C, member 2"	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.644T>G	chr14.hg19:g.24435604T>G	ENSP00000326219:p.Ile215Ser	182.0	0.0		1253.0	258.0	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	hg19	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.988233	0.53934	.	.	ENSG00000157326	ENST00000313250;ENST00000421831	D;D	0.93307	-3.2;-3.2	3.53	3.53	0.40419	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.96445	0.8840	M	0.86343	2.81	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.97110	0.902;1.0	D	0.96377	0.9278	10	0.87932	D	0	.	10.3596	0.43984	0.0:0.0:0.0:1.0	.	181;215	Q9BTZ2-4;Q9BTZ2	.;DHRS4_HUMAN	S	215;163	ENSP00000326219:I215S;ENSP00000404147:I163S	ENSP00000326219:I215S	I	+	2	0	DHRS4	23505444	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.861000	0.75478	1.379000	0.46325	0.473000	0.43528	ATC	.	.		0.527	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3			G	24435604	T	G	24435604	3	3	97	1	0	0	0	0	1	0	0	0	4494	1435	50	5	666	5	DHRS4	14	24435604	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10		24435604	82913936	69	13332										
FOXG1	2290	hgsc.bcm.edu	37	chr14	29237348	29237348	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ggccaagctggccttcaagcGcggtgcgcgcctcacctcca	12	17	2	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:29237348G>A	ENST00000313071.4	+	1	1062	c.863G>A	c.(862-864)cGc>cAc	p.R288H	RP11-966I7.1_ENST00000549487.1_RNA|RP11-966I7.1_ENST00000551395.1_RNA|RP11-966I7.1_ENST00000546560.1_RNA|FOXG1_ENST00000382535.3_Missense_Mutation_p.R288H	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	288				FKRGAR -> AFRWCA (in Ref. 1; CAA52241). {ECO:0000305}.	aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		GCCTTCAAGCGCGGTGCGCGC	0.716																																					p.R288H		Atlas-SNP	.											.	FOXG1	92	.	0			c.G863A						.						32	39	37					14																	29237348		2202	4299	6501	SO:0001583	missense	2290	exon1			TCAAGCGCGGTGC		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.863G>A	chr14.hg19:g.29237348G>A	ENSP00000339004:p.Arg288His	9.0	0.0		37.0	16.0	NM_005249	A6NFY2|P55315|Q14488|Q86XT7	Missense_Mutation	SNP	ENST00000313071.4	hg19	CCDS9636.1	.	.	.	.	.	.	.	.	.	.	G	32	5.174455	0.94807	.	.	ENSG00000176165	ENST00000382535;ENST00000313071	D;D	0.94687	-3.49;-3.49	4.05	4.05	0.47172	.	0.265561	0.30850	U	0.008757	D	0.95121	0.8419	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.96016	0.9005	10	0.87932	D	0	.	15.7834	0.78281	0.0:0.0:1.0:0.0	.	288	P55316	FOXG1_HUMAN	H	288	ENSP00000371975:R288H;ENSP00000339004:R288H	ENSP00000339004:R288H	R	+	2	0	FOXG1	28307099	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.725000	0.84808	1.777000	0.52277	0.313000	0.20887	CGC	.	.		0.716	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			A	29237348	G	A	29237348	3	1	97	1	0	0	0	0	1	0	0	0	6015	1087	38	1	865	1	FOXG1	14	29237348	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	4801744	29237348	78112192	70	13333										
DAAM1	23002	hgsc.bcm.edu	37	chr14	59820665	59820665	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tgcagagcgtgtggcagaagTgaaacctaaagtggaaggta	15	5	0	3			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:59820665T>A	ENST00000395125.1	+	19	2392	c.2369T>A	c.(2368-2370)gTg>gAg	p.V790E	DAAM1_ENST00000351081.1_Missense_Mutation_p.V790E|DAAM1_ENST00000553966.1_Intron|DAAM1_ENST00000360909.3_Missense_Mutation_p.V780E	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	790	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		GTGGCAGAAGTGAAACCTAAA	0.363																																					p.V790E		Atlas-SNP	.											.	DAAM1	95	.	0			c.T2369A						.						98	87	91					14																	59820665		2203	4300	6503	SO:0001583	missense	23002	exon19			CAGAAGTGAAACC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.2369T>A	chr14.hg19:g.59820665T>A	ENSP00000378557:p.Val790Glu	69.0	0.0		112.0	46.0	NM_014992	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	hg19	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	t	22.9	4.347348	0.82022	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000395125	T;T;T	0.19532	2.14;2.14;2.14	6.03	6.03	0.97812	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.050329	0.85682	D	0.000000	T	0.49949	0.1587	M	0.81802	2.56	0.58432	D	0.999995	D;D	0.69078	0.994;0.997	D;D	0.70227	0.949;0.968	T	0.54166	-0.8334	10	0.87932	D	0	.	16.5808	0.84714	0.0:0.0:0.0:1.0	.	780;790	Q9Y4D1-2;Q9Y4D1	.;DAAM1_HUMAN	E	780;790;790	ENSP00000354162:V780E;ENSP00000247170:V790E;ENSP00000378557:V790E	ENSP00000247170:V790E	V	+	2	0	DAAM1	58890418	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.183000	0.72002	2.317000	0.78254	0.524000	0.50904	GTG	.	.		0.363	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		A	59820665	T	A	59820665	3	1	97	1	0	0	0	0	1	0	0	0	4217	1696	59	4	2443	4	DAAM1	14	59820665	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	30583317	59820665	47528875	71	13334										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68274238	68274238	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gctgagcagccgctcctcccGcaggggactcccctcggtcc	12	19	0	1	rs267604034		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:68274238G>A	ENST00000347230.4	-	5	901	c.763C>T	c.(763-765)Cgg>Tgg	p.R255W	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.R255W	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	255					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CGCTCCTCCCGCAGGGGACTC	0.627																																					p.R255W		Atlas-SNP	.											ZFYVE26,NS,carcinoma,0,1	ZFYVE26	223	.	0			c.C763T						.						32	34	33					14																	68274238		2203	4300	6503	SO:0001583	missense	23503	exon5			CCTCCCGCAGGGG	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.763C>T	chr14.hg19:g.68274238G>A	ENSP00000251119:p.Arg255Trp	38.0	0.0		64.0	21.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960569	0.53400	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.30714	1.67;1.52	5.43	2.48	0.30137	.	0.598447	0.16810	N	0.198585	T	0.38585	0.1046	L	0.40543	1.245	0.09310	N	1	D;D;D	0.76494	0.999;0.998;0.978	P;P;B	0.53861	0.736;0.736;0.425	T	0.32508	-0.9904	10	0.72032	D	0.01	-0.1957	14.9491	0.71057	0.0:0.0:0.3349:0.6651	.	255;255;255	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	W	255;234;255	ENSP00000251119:R255W;ENSP00000450603:R255W	ENSP00000251119:R255W	R	-	1	2	ZFYVE26	67343991	0.064000	0.20934	0.177000	0.23020	0.681000	0.39784	1.485000	0.35519	0.215000	0.20761	0.491000	0.48974	CGG	.	.		0.627	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68274238	G	A	68274238	3	1	97	1	0	0	0	0	1	0	0	0	17683	1086	38	1	7008	1	ZFYVE26	14	68274238	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	8453573	68274238	39075302	72	13335										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72190408	72190408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cagcccagtggttttcaccaGtgcccggagttcacctaaag	10	13	2	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:72190408G>A	ENST00000555818.1	+	16	4664	c.4316G>A	c.(4315-4317)aGt>aAt	p.S1439N	SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.S1418N|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.S1418N|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.S893N	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1439	Ser-rich.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GTTTTCACCAGTGCCCGGAGT	0.537																																					p.S1439N		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.G4316A						.						135	111	119					14																	72190408		2203	4300	6503	SO:0001583	missense	26037	exon16			TCACCAGTGCCCG	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.4316G>A	chr14.hg19:g.72190408G>A	ENSP00000450832:p.Ser1439Asn	68.0	0.0		124.0	41.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	hg19	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.674277	0.88445	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;D	0.85484	-1.17;-1.2;-1.17;-1.99	5.54	5.54	0.83059	.	0.170379	0.64402	D	0.000004	D	0.86029	0.5835	N	0.19112	0.55	0.58432	D	0.999999	D;P;D;D;D	0.65815	0.995;0.895;0.989;0.974;0.988	P;B;P;P;P	0.61070	0.836;0.264;0.854;0.796;0.883	D	0.85171	0.0998	10	0.35671	T	0.21	-16.5037	19.8379	0.96666	0.0:0.0:1.0:0.0	.	893;1439;893;1418;1439	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	N	1418;1439;1418;893	ENSP00000370630:S1418N;ENSP00000450832:S1439N;ENSP00000351352:S1418N;ENSP00000440682:S893N	ENSP00000351352:S1439N	S	+	2	0	SIPA1L1	71260161	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.938000	0.70170	2.765000	0.95021	0.655000	0.94253	AGT	.	.		0.537	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		A	72190408	G	A	72190408	3	1	97	1	0	0	0	0	1	0	0	0	14344	1029	36	3	4374	3	SIPA1L1	14	72190408	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	3916170	72190408	35159132	73	13336										
DPF3	8110	hgsc.bcm.edu	37	chr14	73159816	73159816	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	catttctgtggttgggtgggGaccgagtctcctggtcttga	15	8	3	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:73159816G>A	ENST00000556509.1	-	7	709	c.710C>T	c.(709-711)tCc>tTc	p.S237F	DPF3_ENST00000541685.1_Missense_Mutation_p.S237F|DPF3_ENST00000546183.1_Missense_Mutation_p.S247F|DPF3_ENST00000557704.1_5'UTR	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	237					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GTTGGGTGGGGACCGAGTCTC	0.582																																					p.S237F		Atlas-SNP	.											.	DPF3	117	.	0			c.C710T						.						203	204	204					14																	73159816		2067	4214	6281	SO:0001583	missense	8110	exon7			GGTGGGGACCGAG	U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"Zinc fingers, PHD-type"	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.710C>T	chr14.hg19:g.73159816G>A	ENSP00000450518:p.Ser237Phe	159.0	0.0		462.0	175.0	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	hg19		.	.	.	.	.	.	.	.	.	.	G	26.9	4.783260	0.90282	.	.	ENSG00000205683	ENST00000556509;ENST00000398816;ENST00000541685;ENST00000546183	D;T;T	0.90900	-2.75;-0.25;-0.2	5.36	5.36	0.76844	.	.	.	.	.	D	0.92071	0.7487	L	0.47716	1.5	0.80722	D	1	P;D;D	0.61080	0.936;0.978;0.989	P;P;P	0.53912	0.729;0.729;0.737	D	0.92906	0.6343	9	0.87932	D	0	.	19.0841	0.93196	0.0:0.0:1.0:0.0	.	247;237;237	F5H575;Q92784-2;Q92784	.;.;DPF3_HUMAN	F	237;236;237;247	ENSP00000450518:S237F;ENSP00000441640:S237F;ENSP00000444662:S247F	ENSP00000381791:S292F	S	-	2	0	DPF3	72229569	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	9.335000	0.96500	2.504000	0.84457	0.462000	0.41574	TCC	.	.		0.582	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2			A	73159816	G	A	73159816	3	1	97	1	0	0	0	0	1	0	0	0	4720	1174	41	3	375	3	DPF3	14	73159816	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	969408	73159816	34189724	74	13337										
LTBP2	4053	hgsc.bcm.edu	37	chr14	74976564	74976565	+	Splice_Site	INS	-	-	GAAATAGGGCATTGCATTCTGTGTG													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tggcacactcatccacatctINSgaaatagggcattgcattct							TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:74976564_74976565insGAAATAGGGCATTGCATTCTGTGTG	ENST00000261978.4	-	21	3538		c.e21-2		LTBP2_ENST00000556690.1_Splice_Site	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2						protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CATCCACATCTGAAATAGGGCA	0.624																																					.		Pindel	.											.	LTBP2	158	.	0			c.3152-2->CACACAGAATGCAATGCCCTATTTC						.																																			SO:0001630	splice_region_variant	4053	exon22			.		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.3152-2->CACACAGAATGCAATGCCCTATTTC	chr14.hg19:g.74976564_74976565insGAAATAGGGCATTGCATTCTGTGTG		0.0	0.0		58.0	11.0	NM_000428	Q99907|Q9NS51	Splice_Site	INS	ENST00000261978.4	hg19	CCDS9831.1																																																																																			.	.		0.624	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	Intron	GAAATAGGGCATTGCATTCTGTGTG	74976565	-	GAAATAGGGCATTGCATTCTGTGTG	74976564	8	5	97	1	0	1	1	0	0	0	1	0	9083	1594	55	0	2379	0	LTBP2	14	74976564	Splice_Site	INS	-	TCGA-DD-A1EA-01A-11D-A12Z-10	1816748	74976564	32372976	75	13338										
PROX2	283571	hgsc.bcm.edu	37	chr14	75330524	75330524	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gctgaggagaaagcaagatgGagtttggatccatcccaggc	14	8	0	3			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:75330524G>T	ENST00000445876.1	-	1	13	c.14C>A	c.(13-15)tCc>tAc	p.S5Y	PROX2_ENST00000556489.2_Missense_Mutation_p.S5Y|PROX2_ENST00000556084.2_Missense_Mutation_p.S5Y			Q3B8N5	PROX2_HUMAN	prospero homeobox 2	5					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(3)	6			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)		AAGCAAGATGGAGTTTGGATC	0.552																																					p.S5Y		Atlas-SNP	.											PROX2_ENST00000445876,NS,carcinoma,0,2	PROX2	44	.	0			c.C14A						.						66	68	67					14																	75330524		1986	4153	6139	SO:0001583	missense	283571	exon1			AAGATGGAGTTTG		CCDS45136.1, CCDS45136.2, CCDS73663.1	14q24.3	2012-10-02			ENSG00000119608	ENSG00000119608		"Homeoboxes / PROS class"	26715	protein-coding gene	gene with protein product		615094					Standard	NM_001080408		Approved	FLJ36749	uc031qpi.1	Q3B8N5	OTTHUMG00000171481	ENST00000445876.1:c.14C>A	chr14.hg19:g.75330524G>T	ENSP00000405932:p.Ser5Tyr	10.0	0.0		21.0	9.0	NM_001080408	C9J5W1|Q8N9Q3	Missense_Mutation	SNP	ENST00000445876.1	hg19	CCDS45136.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.84|17.84	3.488935|3.488935	0.64074|0.64074	.|.	.|.	ENSG00000119608|ENSG00000119608	ENST00000556084|ENST00000556489;ENST00000389664;ENST00000424024;ENST00000445876	.|T;T	.|0.47177	.|0.85;0.85	4.76|4.76	1.83|1.83	0.25207|0.25207	.|.	.|1.400140	.|0.04728	.|N	.|0.420662	T|T	0.32346|0.32346	0.0826|0.0826	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	.|P	.|0.40398	.|0.716	.|B	.|0.34242	.|0.178	T|T	0.22871|0.22871	-1.0204|-1.0204	5|10	.|0.29301	.|T	.|0.29	-1.0645|-1.0645	2.3974|2.3974	0.04393|0.04393	0.2244:0.1309:0.5105:0.1342|0.2244:0.1309:0.5105:0.1342	.|.	.|5	.|G3V3G0	.|.	T|Y	5|5	.|ENSP00000451223:S5Y;ENSP00000405932:S5Y	.|ENSP00000374315:S5Y	P|S	-|-	1|2	0|0	PROX2|PROX2	74400277|74400277	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.970000|0.970000	0.65996|0.65996	0.616000|0.616000	0.24344|0.24344	0.607000|0.607000	0.29982|0.29982	0.561000|0.561000	0.74099|0.74099	CCA|TCC	.	.		0.552	PROX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	75330524	G	T	75330524	3	4	97	1	0	0	0	0	1	0	0	0	12573	1174	41	3	1780	3	PROX2	14	75330524	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	353960	75330524	32019016	76	13339										
RPS6KL1	83694	hgsc.bcm.edu	37	chr14	75376302	75376303	+	Frame_Shift_Ins	INS	-	-	C													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ccggcacagcaccccctgctINScgtgcagcgcctccagcgct							TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:75376302_75376303insC	ENST00000555647.1	-	8	1500_1501	c.1213_1214insG	c.(1213-1215)gagfs	p.E405fs	RPS6KL1_ENST00000354625.2_Frame_Shift_Ins_p.E374fs|RPS6KL1_ENST00000554900.1_5'Flank|RPS6KL1_ENST00000358328.4_Frame_Shift_Ins_p.E405fs|RPS6KL1_ENST00000557413.1_Frame_Shift_Ins_p.E405fs			Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	405	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					ribosome (GO:0005840)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(234;0.00658)		CACCCCCTGCTCGTGCAGCGCC	0.703																																					p.E405fs		Atlas-Indel,Pindel	.											.	RPS6KL1	35	.	0			c.1214_1215insG						.																																			SO:0001589	frameshift_variant	83694	exon7			.	BC004540	CCDS9834.1, CCDS9834.2	14q24.2	2011-04-05				ENSG00000198208			20222	protein-coding gene	gene with protein product							Standard	NM_031464		Approved	MGC11287	uc010tux.2	Q9Y6S9		ENST00000555647.1:c.1214dupG	chr14.hg19:g.75376303_75376303dupC	ENSP00000452027:p.Glu405fs	35.0	0.0		81.0	36.0	NM_031464	A6NGM9|Q69YT9|Q6ZMQ6|Q96NR9|Q9BSU9	Frame_Shift_Ins	INS	ENST00000555647.1	hg19	CCDS9834.2																																																																																			.	.		0.703	RPS6KL1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413732.1			C	75376303	-	C	75376302	7	5	97	1	0	1	1	0	0	0	0	0	13674	1551	54	0	528	0	RPS6KL1	14	75376302	Frame_Shift_Ins	INS	-	TCGA-DD-A1EA-01A-11D-A12Z-10	45778	75376302	31973238	77	13340										
HERC2	8924	hgsc.bcm.edu	37	chr15	28446674	28446674	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gctcgttttttgtacgtctgGctctccgtcacaacagcacc	8	14	3	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr15:28446674G>C	ENST00000261609.7	-	48	7752	c.7644C>G	c.(7642-7644)agC>agG	p.S2548R		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TGTACGTCTGGCTCTCCGTCA	0.368																																					p.S2548R		Atlas-SNP	.											.	HERC2	501	.	0			c.C7644G						.						125	114	118					15																	28446674		2203	4300	6503	SO:0001583	missense	8924	exon48			CGTCTGGCTCTCC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.7644C>G	chr15.hg19:g.28446674G>C	ENSP00000261609:p.Ser2548Arg	135.0	0.0		378.0	146.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.263445	0.59431	.	.	ENSG00000128731	ENST00000261609	T	0.38887	1.11	5.18	3.3	0.37823	.	0.043831	0.85682	D	0.000000	T	0.55800	0.1943	L	0.56769	1.78	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.75484	0.986;0.979	T	0.49532	-0.8930	10	0.25106	T	0.35	.	11.6869	0.51492	0.1348:0.0:0.8652:0.0	.	15;2548	A8KAQ8;O95714	.;HERC2_HUMAN	R	2548	ENSP00000261609:S2548R	ENSP00000261609:S2548R	S	-	3	2	HERC2	26120269	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.798000	0.38814	0.691000	0.31592	0.561000	0.74099	AGC	.	.		0.368	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		C	28446674	G	C	28446674	3	2	97	1	0	0	0	0	1	0	0	0	7067	1194	42	4	7044	4	HERC2	15	28446674	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10		28446674	74084718	78	13341										
AQR	9716	hgsc.bcm.edu	37	chr15	35198872	35198872	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	agtgccataaggttttgtggGacgtacggtaattaaaaagc	12	5	0	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr15:35198872G>T	ENST00000156471.5	-	18	1930	c.1705C>A	c.(1705-1707)Ccc>Acc	p.P569T		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	569					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		GGTTTTGTGGGACGTACGGTA	0.388																																					p.P569T		Atlas-SNP	.											.	AQR	139	.	0			c.C1705A						.						126	113	117					15																	35198872		1901	4133	6034	SO:0001583	missense	9716	exon18			TTGTGGGACGTAC	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.1705C>A	chr15.hg19:g.35198872G>T	ENSP00000156471:p.Pro569Thr	58.0	0.0		100.0	39.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	hg19	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962361	0.74016	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.94232	-3.38	5.44	4.51	0.55191	.	0.047946	0.85682	N	0.000000	D	0.96917	0.8993	M	0.93763	3.455	0.48087	D	0.999589	D	0.69078	0.997	P	0.58210	0.835	D	0.97610	1.0129	10	0.72032	D	0.01	-11.5427	15.454	0.75299	0.0:0.0:0.8602:0.1398	.	569	O60306	AQR_HUMAN	T	569	ENSP00000156471:P569T	ENSP00000156471:P569T	P	-	1	0	AQR	32986164	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.416000	0.97383	1.252000	0.44001	0.591000	0.81541	CCC	.	.		0.388	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		T	35198872	G	T	35198872	3	4	97	1	0	0	0	0	1	0	0	0	835	1174	41	3	2824	3	AQR	15	35198872	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	6752198	35198872	67332520	79	13342										
SGK269	79834	hgsc.bcm.edu	37	chr15	77425574	77425574	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gattttacccactacttcctCccgattctcaagtcctcgat	4	15	1	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr15:77425574C>A	ENST00000560626.2	-	6	4325	c.3850G>T	c.(3850-3852)Gag>Tag	p.E1284*	PEAK1_ENST00000312493.4_Nonsense_Mutation_p.E1284*			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1284					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ACTACTTCCTCCCGATTCTCA	0.532																																					p.E1284X		Atlas-SNP	.											.	.	.	.	0			c.G3850T						.						147	143	144					15																	77425574		1877	4106	5983	SO:0001587	stop_gained	0	exon7			CTTCCTCCCGATT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3850G>T	chr15.hg19:g.77425574C>A	ENSP00000452796:p.Glu1284*	103.0	0.0		234.0	85.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Nonsense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	46	12.343992	0.99659	.	.	ENSG00000173517	ENST00000312493	.	.	.	5.61	5.61	0.85477	.	0.107611	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-9.2526	12.908	0.58164	0.0:0.9258:0.0:0.0742	.	.	.	.	X	1284	.	ENSP00000309230:E1284X	E	-	1	0	AC087465.1	75212629	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.091000	0.71406	2.642000	0.89623	0.655000	0.94253	GAG	.	.		0.532	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			A	77425574	C	A	77425574	4	1	97	1	0	0	0	0	0	1	0	0	14226	864	30	3	1398	3	SGK269	15	77425574	Nonsense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	42226702	77425574	25105818	80	13343										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3778620	3778620	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gcacgccagcctgcatggcaTtcaggttctgcaggctgggc	14	13	2	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:3778620T>C	ENST00000262367.5	-	31	7237	c.6428A>G	c.(6427-6429)aAt>aGt	p.N2143S	CREBBP_ENST00000382070.3_Missense_Mutation_p.N2105S	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2143					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CTGCATGGCATTCAGGTTCTG	0.682			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.N2143S		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.A6428G						.						56	60	58					16																	3778620		2197	4298	6495	SO:0001583	missense	1387	exon31			ATGGCATTCAGGT	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.6428A>G	chr16.hg19:g.3778620T>C	ENSP00000262367:p.Asn2143Ser	23.0	0.0		63.0	18.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	t	4.459	0.084939	0.08583	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.83163	-1.69;-1.58	5.11	3.99	0.46301	.	0.195425	0.44483	N	0.000447	T	0.60117	0.2244	N	0.08118	0	0.33369	D	0.573358	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.57894	-0.7732	10	0.10111	T	0.7	-9.9425	5.7003	0.17879	0.0:0.2769:0.0:0.7231	.	2173;2143	Q4LE28;Q92793	.;CBP_HUMAN	S	2143;2173;2105;678	ENSP00000262367:N2143S;ENSP00000371502:N2105S	ENSP00000262367:N2143S	N	-	2	0	CREBBP	3718621	0.098000	0.21812	0.904000	0.35570	0.512000	0.34134	1.013000	0.29937	1.934000	0.56057	0.533000	0.62120	AAT	.	.		0.682	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		C	3778620	T	C	3778620	3	2	97	1	0	0	0	0	1	0	0	0	3863	1493	52	2	904	2	CREBBP	16	3778620	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10		3778620	86576133	81	13344										
GGA2	23062	hgsc.bcm.edu	37	chr16	23489767	23489767	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ggttctgaacaccaccgcctGgcagcgtgctggaggaggga	16	11	1	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:23489767G>A	ENST00000309859.4	-	13	1296	c.1214C>T	c.(1213-1215)cCa>cTa	p.P405L	GGA2_ENST00000567468.1_Intron|GGA2_ENST00000569182.1_5'UTR	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	405	Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		ACCACCGCCTGGCAGCGTGCT	0.532																																					p.P405L		Atlas-SNP	.											.	GGA2	49	.	0			c.C1214T						.						110	99	103					16																	23489767		2197	4300	6497	SO:0001583	missense	23062	exon13			CCGCCTGGCAGCG	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.1214C>T	chr16.hg19:g.23489767G>A	ENSP00000311962:p.Pro405Leu	58.0	0.0		101.0	44.0	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	hg19	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	G	9.964	1.223606	0.22457	.	.	ENSG00000103365	ENST00000309859	T	0.14893	2.47	4.11	2.0	0.26442	.	487.764000	0.00166	N	0.000000	T	0.19208	0.0461	L	0.54323	1.7	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19614	-1.0300	10	0.34782	T	0.22	-0.0382	5.4904	0.16773	0.2876:0.0:0.7124:0.0	.	405	Q9UJY4	GGA2_HUMAN	L	405	ENSP00000311962:P405L	ENSP00000311962:P405L	P	-	2	0	GGA2	23397268	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.371000	0.20450	0.403000	0.25479	-0.345000	0.07892	CCA	.	.		0.532	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1			A	23489767	G	A	23489767	3	1	97	1	0	0	0	0	1	0	0	0	6361	1348	47	3	647	3	GGA2	16	23489767	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	19711147	23489767	66864986	82	13345										
IL21R	50615	hgsc.bcm.edu	37	chr16	27460101	27460101	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	aggagagggatcggccatacGgcctggtgtccattgacaca	14	10	0	2	rs36031126		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:27460101G>T	ENST00000337929.3	+	9	1587	c.1114G>T	c.(1114-1116)Ggc>Tgc	p.G372C	IL21R_ENST00000395754.4_Missense_Mutation_p.G372C|IL21R_ENST00000564089.1_Missense_Mutation_p.G372C|IL21R_ENST00000395755.1_Missense_Mutation_p.G372C|IL21R-AS1_ENST00000563191.1_RNA	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	372					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						TCGGCCATACGGCCTGGTGTC	0.627			T	BCL6	NHL																																p.G394C		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.G1180T						.						65	62	63					16																	27460101		2197	4300	6497	SO:0001583	missense	50615	exon10			CCATACGGCCTGG	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1114G>T	chr16.hg19:g.27460101G>T	ENSP00000338010:p.Gly372Cys	19.0	0.0		56.0	19.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	hg19	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.337208	0.41398	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.44083	0.93;0.93;0.93	5.19	5.19	0.71726	.	7.212420	0.00166	N	0.000004	T	0.69851	0.3157	M	0.69823	2.125	0.29219	N	0.874075	D	0.89917	1.0	D	0.97110	1.0	T	0.54118	-0.8341	10	0.72032	D	0.01	-25.7504	14.2483	0.66001	0.0:0.0:1.0:0.0	.	372	Q9HBE5	IL21R_HUMAN	C	372	ENSP00000338010:G372C;ENSP00000379104:G372C;ENSP00000379103:G372C	ENSP00000338010:G372C	G	+	1	0	IL21R	27367602	0.997000	0.39634	0.040000	0.18447	0.036000	0.12997	3.922000	0.56462	2.426000	0.82243	0.561000	0.74099	GGC	.	G|0.986;A|0.014		0.627	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		T	27460101	G	T	27460101	3	4	97	1	0	0	0	0	1	0	0	0	7680	1116	39	1	1144	1	IL21R	16	27460101	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	3970334	27460101	62894652	83	13346										
SIAH1	6477	hgsc.bcm.edu	37	chr16	48395633	48395644	+	In_Frame_Del	DEL	CAAGTCAATCGT	CAAGTCAATCGT	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tagatcgaggagtcgcttccCaagtcaatcgtcgcctatga					rs112217260	byFrequency	TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CAAGTCAATCGT	CAAGTCAATCGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:48395633_48395644delCAAGTCAATCGT	ENST00000380006.2	-	1	2149_2160	c.696_707delACGATTGACTTG	c.(694-708)cgacgattgacttgg>cgg	p.RLTW233del	LONP2_ENST00000564259.1_3'UTR|SIAH1_ENST00000356721.3_In_Frame_Del_p.RLTW264del|SIAH1_ENST00000394725.2_In_Frame_Del_p.RLTW233del			Q8IUQ4	SIAH1_HUMAN	siah E3 ubiquitin protein ligase 1	233	SBD.				anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell cycle (GO:0007049)|nervous system development (GO:0007399)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein catabolic process (GO:0030163)|protein destabilization (GO:0031648)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	beta-catenin destruction complex (GO:0030877)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|stomach(1)	7		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)				AGTCGCTTCCCAAGTCAATCGTCGCCTATGAC	0.453																																					p.264_267del		Atlas-Indel,Pindel	.											.	SIAH1	33	.	0			c.790_801del						.																																			SO:0001651	inframe_deletion	6477	exon2			.	U76247	CCDS10735.1, CCDS32444.1	16q12.1	2013-06-03	2012-02-23		ENSG00000196470	ENSG00000196470			10857	protein-coding gene	gene with protein product		602212	"seven in absentia homolog 1 (Drosophila)"			9403064, 9334332	Standard	NM_001006610		Approved	hSIAH1	uc002efo.1	Q8IUQ4	OTTHUMG00000175417	ENST00000380006.2:c.696_707delACGATTGACTTG	chr16.hg19:g.48395633_48395644delCAAGTCAATCGT	ENSP00000369343:p.Arg233_Trp236del	71.0	0.0		162.0	16.0	NM_001006610	A0FKF3|O43269|Q49A58|Q92880	In_Frame_Del	DEL	ENST00000380006.2	hg19	CCDS10735.1																																																																																			.	.		0.453	SIAH1-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256842.12			-	48395644	CAAGTCAATCGT	-	48395633	7	5	97	1	0	1	0	1	0	0	0	0	14314	595	21	0	145	0	SIAH1	16	48395633	In_Frame_Del	DEL	CAAGTCAATCGT	TCGA-DD-A1EA-01A-11D-A12Z-10	20935532	48395633	41959120	84	13347										
CES8	283848	hgsc.bcm.edu	37	chr16	67038121	67038121	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ctggaattcaattggctcttGccttatgtaagtgagtagga	11	6	2	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:67038121G>T	ENST00000326686.5	+	9	1074	c.1074G>T	c.(1072-1074)ttG>ttT	p.L358F	CES4A_ENST00000338718.4_Missense_Mutation_p.L381F|CES4A_ENST00000535696.1_Missense_Mutation_p.L264F|CES4A_ENST00000540947.2_Missense_Mutation_p.L358F|CES4A_ENST00000541479.1_Missense_Mutation_p.L381F|CES4A_ENST00000540579.1_Missense_Mutation_p.L260F|CES4A_ENST00000398354.1_Missense_Mutation_p.L358F			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	358						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						ATTGGCTCTTGCCTTATGTAA	0.517																																					p.L358F		Atlas-SNP	.											.	CES4A	24	.	0			c.G1074T						.						149	141	144					16																	67038121		1981	4172	6153	SO:0001583	missense	283848	exon9			GCTCTTGCCTTAT	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"Carboxylesterases"	26741	protein-coding gene	gene with protein product			"carboxylesterase 8 (putative)"	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.1074G>T	chr16.hg19:g.67038121G>T	ENSP00000314145:p.Leu358Phe	79.0	0.0		210.0	76.0	NM_173815	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Missense_Mutation	SNP	ENST00000326686.5	hg19		.	.	.	.	.	.	.	.	.	.	g	7.020	0.558476	0.13436	.	.	ENSG00000172824	ENST00000540947;ENST00000541479;ENST00000338718;ENST00000398354;ENST00000326686;ENST00000538199;ENST00000540579;ENST00000535696	T;T;T;T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45	4.63	1.3	0.21679	Carboxylesterase, type B (1);	0.000000	0.35772	N	0.002995	T	0.69251	0.3090	L	0.56199	1.76	0.51767	D	0.999931	B;D;B;B	0.59767	0.026;0.986;0.0;0.001	B;P;B;B	0.59221	0.018;0.854;0.021;0.01	T	0.67684	-0.5607	10	0.87932	D	0	.	6.5077	0.22204	0.205:0.1878:0.6072:0.0	.	264;381;358;381	Q5XG92-7;F8WEE9;Q5XG92;F5H5S4	.;.;EST4A_HUMAN;.	F	358;381;381;358;358;321;260;264	ENSP00000444052:L358F;ENSP00000443175:L381F;ENSP00000340714:L381F;ENSP00000381397:L358F;ENSP00000314145:L358F;ENSP00000441103:L321F;ENSP00000441907:L260F;ENSP00000441644:L264F	ENSP00000314145:L358F	L	+	3	2	CES4A	65595622	0.910000	0.30920	0.908000	0.35775	0.142000	0.21351	-0.083000	0.11286	0.372000	0.24591	0.486000	0.48141	TTG	.	.		0.517	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173815		T	67038121	G	T	67038121	3	4	97	1	0	0	0	0	1	0	0	0	3275	1310	46	3	1189	3	CES8	16	67038121	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	18642488	67038121	23316632	85	13348										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89349770	89349770	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ttatgtttttccttggtatcTtttttctctttaaaacattt	3	6	2	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:89349770T>C	ENST00000301030.4	-	9	3640	c.3180A>G	c.(3178-3180)aaA>aaG	p.K1060K	ANKRD11_ENST00000378330.2_Silent_p.K1060K	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1060	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CCTTGGTATCTTTTTTCTCTT	0.378																																					p.K1060K		Atlas-SNP	.											.	ANKRD11	195	.	0			c.A3180G						.						125	133	131					16																	89349770		2198	4300	6498	SO:0001819	synonymous_variant	29123	exon9			GGTATCTTTTTTC	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.3180A>G	chr16.hg19:g.89349770T>C		124.0	0.0		277.0	115.0	NM_001256183	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	T	9.261	1.043111	0.19748	.	.	ENSG00000167522	ENST00000330736	.	.	.	5.39	-2.32	0.06745	.	0.000000	0.85682	D	0.000000	T	0.69672	0.3137	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73056	-0.4103	6	0.87932	D	0	.	13.4948	0.61419	0.0:0.4567:0.0:0.5433	.	.	.	.	R	611	.	ENSP00000330815:K611R	K	-	2	0	ANKRD11	87877271	0.989000	0.36119	0.884000	0.34674	0.989000	0.77384	0.225000	0.17757	-0.377000	0.07930	0.533000	0.62120	AAG	.	.		0.378	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		C	89349770	T	C	89349770	2	2	97	1	0	0	0	0	0	0	0	1	639	1606	56	2		2	ANKRD11	16	89349770	Silent	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	22311649	89349770	1004983	86	13349										
CDC27	996	hgsc.bcm.edu	37	chr17	45234594	45234729	+	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cactagaatataagacacttAcaattgtgtcctggggtgtt					rs149474782|rs113608268|rs370849730|rs78395997|rs76624491|rs370261409|rs75353677|rs368304141|rs376818791|rs372212798|rs375653477|rs374472811|rs76359747|rs147617501|rs374614181|rs78108688|rs142987740|rs143453365|rs75990396|rs144985864|rs367644695|rs202182614|rs139751753|rs11570485|rs372926889|rs140171160|rs368750026|rs201098929|rs199899451|rs75175938|rs200340309|rs537990668	byFrequency	TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr17:45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	ENST00000066544.3	-	6	590_724	c.497_631delAGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG	c.(496-633)cagttcttacggaaacaccccaggacacaattgtaagtgtcttatattctagtgttcaaaatattatgaaaactacaaagaatgatctgaactaaataatatattgtgaatgacttggtagaaattttctgtttcaga>cga	p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	CDC27_ENST00000446365.2_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF105fs|CDC27_ENST00000527547.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000531206.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000528748.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.T167T(7)|p.T171T(3)|p.V201I(2)|p.E199E(2)|p.T200T(2)|p.L173S(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACTGTCTCAGGCTGTCTGTGAGATAAACTATGATTAGGTACTTGTGTTGTGCAAGAGTTGGGCAGACAGTTGCTAAAGTTCTGTAAAGATGTGAATTTAAATGTTTGGTCAGGATC	0.342																																					p.201_211del		Pindel	.											.	CDC27	337	.	17	Substitution - coding silent(14)|Substitution - Missense(3)	large_intestine(6)|prostate(6)|kidney(4)|NS(1)	c.601_631del						.																																			SO:0001630	splice_region_variant	996	exon6			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.631-104AGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG>-	chr17.hg19:g.45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT		0.0	0.0		173.0	12.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.342	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Frame_Shift_Del	-	45234729	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	45234594	8	5	97	1	0	1	0	1	0	0	1	0	3068	405	14	0	1916	0	CDC27	17	45234594	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	TCGA-DD-A1EA-01A-11D-A12Z-10		45234594	35960616	87	13350										
MED13	9969	hgsc.bcm.edu	37	chr17	60088347	60088347	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tgctacatcattagttcggaTatttgaaaatctcacttgac	6	8	2	2			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr17:60088347T>C	ENST00000397786.2	-	9	1607	c.1531A>G	c.(1531-1533)Atc>Gtc	p.I511V		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	511					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTAGTTCGGATATTTGAAAAT	0.473																																					p.I511V		Atlas-SNP	.											.	MED13	181	.	0			c.A1531G						.						174	169	171					17																	60088347		1998	4172	6170	SO:0001583	missense	9969	exon9			TTCGGATATTTGA	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.1531A>G	chr17.hg19:g.60088347T>C	ENSP00000380888:p.Ile511Val	155.0	0.0		539.0	148.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	9.364	1.068753	0.20147	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.73469	-0.75	6.16	5.07	0.68467	.	0.182595	0.56097	D	0.000025	T	0.65144	0.2663	L	0.44542	1.39	0.45733	D	0.998636	B;B	0.30193	0.069;0.272	B;B	0.26864	0.068;0.074	T	0.59700	-0.7405	10	0.25751	T	0.34	-6.9427	12.7623	0.57372	0.0:0.0:0.2583:0.7417	.	24;511	Q9P0Q5;Q9UHV7	.;MED13_HUMAN	V	511;510	ENSP00000380888:I511V	ENSP00000262436:I510V	I	-	1	0	MED13	57443129	1.000000	0.71417	0.998000	0.56505	0.943000	0.58893	2.423000	0.44705	1.117000	0.41842	0.528000	0.53228	ATC	.	.		0.473	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		C	60088347	T	C	60088347	3	2	97	1	0	0	0	0	1	0	0	0	9439	1406	49	2	5081	2	MED13	17	60088347	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	14853753	60088347	21106863	88	13351										
TYMS	7298	hgsc.bcm.edu	37	chr18	671451	671451	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	atcgagccactgaaaattcaGgtaagaattagatgttatac	8	6	1	3			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr18:671451G>A	ENST00000323274.10	+	6	943	c.804G>A	c.(802-804)caG>caA	p.Q268Q	TYMS_ENST00000323250.5_Splice_Site_p.Q185Q|TYMS_ENST00000581920.1_3'UTR|ENOSF1_ENST00000583973.1_5'Flank|TYMS_ENST00000323224.7_Splice_Site_p.Q234Q	NM_001071.2	NP_001062.1	P04818	TYSY_HUMAN	thymidylate synthetase	268					aging (GO:0007568)|cartilage development (GO:0051216)|circadian rhythm (GO:0007623)|deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|developmental growth (GO:0048589)|dTMP biosynthetic process (GO:0006231)|dTTP biosynthetic process (GO:0006235)|dUMP metabolic process (GO:0046078)|G1/S transition of mitotic cell cycle (GO:0000082)|immortalization of host cell by virus (GO:0019088)|intestinal epithelial cell maturation (GO:0060574)|mitotic cell cycle (GO:0000278)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|organ regeneration (GO:0031100)|polysaccharide metabolic process (GO:0005976)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to organophosphorus (GO:0046683)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|response to vitamin A (GO:0033189)|small molecule metabolic process (GO:0044281)|tetrahydrofolate metabolic process (GO:0046653)|uracil metabolic process (GO:0019860)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cofactor binding (GO:0048037)|drug binding (GO:0008144)|folic acid binding (GO:0005542)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|thymidylate synthase activity (GO:0004799)			endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(2)	8					Capecitabine(DB01101)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Leucovorin(DB00650)|Methotrexate(DB00563)|Pemetrexed(DB00642)|Pralatrexate(DB06813)|Raltitrexed(DB00293)|Trifluridine(DB00432)|Trimethoprim(DB00440)	TGAAAATTCAGGTAAGAATTA	0.413																																					p.Q268Q		Atlas-SNP	.											.	TYMS	27	.	0			c.G804A						.						101	99	100					18																	671451		2203	4300	6503	SO:0001630	splice_region_variant	7298	exon6			AATTCAGGTAAGA	X02308	CCDS11821.1	18p11.31-p11.21	2014-09-17			ENSG00000176890	ENSG00000176890	2.1.1.45		12441	protein-coding gene	gene with protein product		188350		TS			Standard	NM_001071		Approved	Tsase, TMS, HsT422	uc010dka.1	P04818	OTTHUMG00000131473	ENST00000323274.10:c.804+1G>A	chr18.hg19:g.671451G>A		72.0	0.0		151.0	57.0	NM_001071	Q8WYK3|Q8WYK4	Silent	SNP	ENST00000323274.10	hg19	CCDS11821.1																																																																																			.	.		0.413	TYMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254316.1	NM_001071	Silent	A	671451	G	A	671451	5	1	97	1	0	0	0	0	0	0	1	0	16827	1014	35	3	826	3	TYMS	18	671451	Splice_Site	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10		671451	77405797	89	13352										
VPS4B	9525	hgsc.bcm.edu	37	chr18	61067824	61067824	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	gaaacaagatcagaggaagaTattgaaaaaaatgttgagtt	10	2	1	5			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr18:61067824T>C	ENST00000238497.5	-	6	800	c.597A>G	c.(595-597)atA>atG	p.I199M	VPS4B_ENST00000591383.1_5'UTR	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	199					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						CAGAGGAAGATATTGAAAAAA	0.373																																					p.I199M		Atlas-SNP	.											.	VPS4B	33	.	0			c.A597G						.						115	115	115					18																	61067824		2203	4300	6503	SO:0001583	missense	9525	exon6			GGAAGATATTGAA	AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"ATPases / AAA-type"	10895	protein-coding gene	gene with protein product		609983	"suppressor of K+ transport defect 1", "vacuolar protein sorting 4B (yeast)"	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.597A>G	chr18.hg19:g.61067824T>C	ENSP00000238497:p.Ile199Met	99.0	0.0		211.0	88.0	NM_004869	Q69HW4|Q9GZS7	Missense_Mutation	SNP	ENST00000238497.5	hg19	CCDS11983.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529046	0.64860	.	.	ENSG00000119541	ENST00000238497	D	0.95853	-3.83	6.11	4.95	0.65309	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.173761	0.64402	D	0.000009	D	0.96383	0.8820	M	0.64567	1.98	0.80722	D	1	B;B;P	0.34837	0.295;0.295;0.472	P;P;P	0.51385	0.668;0.668;0.668	D	0.95892	0.8908	10	0.87932	D	0	-15.9957	12.4617	0.55734	0.0:0.0653:0.0:0.9347	.	199;199;199	A8K5D8;A8K4G7;O75351	.;.;VPS4B_HUMAN	M	199	ENSP00000238497:I199M	ENSP00000238497:I199M	I	-	3	3	VPS4B	59218804	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.712000	0.37940	1.119000	0.41883	0.533000	0.62120	ATA	.	.		0.373	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869		C	61067824	T	C	61067824	3	2	97	1	0	0	0	0	1	0	0	0	17228	1396	49	2	761	2	VPS4B	18	61067824	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	60396373	61067824	17009424	90	13353										
ATCAY	85300	hgsc.bcm.edu	37	chr19	3910853	3910853	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	tccacccctcgtggttcattCggactgtgctggccatctct	9	15	2	0	rs376658701		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr19:3910853C>T	ENST00000450849.2	+	8	1299	c.832C>T	c.(832-834)Cgg>Tgg	p.R278W	ATCAY_ENST00000301260.6_Missense_Mutation_p.R278W|ATCAY_ENST00000398448.3_Missense_Mutation_p.R284W|ATCAY_ENST00000600960.1_Missense_Mutation_p.R278W	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	278	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Mediates interaction with GLS.				apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)	p.R278W(1)		breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		GTGGTTCATTCGGACTGTGCT	0.592																																					p.R278W		Atlas-SNP	.											ATCAY_ENST00000450849,rectum,carcinoma,0,1	ATCAY	84	.	1	Substitution - Missense(1)	large_intestine(1)	c.C832T						.	C	TRP/ARG	0,4270		0,0,2135	119	127	124		832	4.3	1	19		124	1,8483		0,1,4241	no	missense	ATCAY	NM_033064.4	101	0,1,6376	TT,TC,CC		0.0118,0.0,0.0078	probably-damaging	278/372	3910853	1,12753	2135	4242	6377	SO:0001583	missense	85300	exon8			TTCATTCGGACTG		CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"Cayman ataxia", "caytaxin"	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.832C>T	chr19.hg19:g.3910853C>T	ENSP00000390941:p.Arg278Trp	64.0	0.0		137.0	63.0	NM_033064	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Missense_Mutation	SNP	ENST00000450849.2	hg19	CCDS45923.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.366995	0.82463	0.0	1.18E-4	ENSG00000167654	ENST00000450849;ENST00000301260;ENST00000357694;ENST00000398448;ENST00000539301	T;T;T	0.67523	-0.27;-0.27;-0.27	4.35	4.35	0.52113	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.063315	0.64402	D	0.000008	D	0.84174	0.5414	M	0.91717	3.235	0.50813	D	0.999898	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.87653	0.2529	10	0.87932	D	0	-2.6229	12.7004	0.57029	0.165:0.835:0.0:0.0	.	284;278;278	B4DS11;Q86WG3-3;Q86WG3	.;.;ATCAY_HUMAN	W	278;278;278;284;256	ENSP00000390941:R278W;ENSP00000301260:R278W;ENSP00000381466:R284W	ENSP00000301260:R278W	R	+	1	2	ATCAY	3861853	0.998000	0.40836	0.999000	0.59377	0.977000	0.68977	3.866000	0.56040	1.970000	0.57323	0.456000	0.33151	CGG	.	.		0.592	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457872.2			T	3910853	C	T	3910853	3	4	97	1	0	0	0	0	1	0	0	0	1077	875	31	1	858	1	ATCAY	19	3910853	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10		3910853	55218130	91	13354										
ZNF441	126068	hgsc.bcm.edu	37	chr19	11888443	11888443	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	caggactcagtggcatttgaGgatgtggctataaacttcac	11	8	2	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr19:11888443G>A	ENST00000357901.4	+	2	123	c.21G>A	c.(19-21)gaG>gaA	p.E7E	ZNF441_ENST00000454339.2_5'UTR	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	7	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGGCATTTGAGGATGTGGCTA	0.438																																					p.E7E		Atlas-SNP	.											.	ZNF441	123	.	0			c.G21A						.						112	94	100					19																	11888443		692	1591	2283	SO:0001819	synonymous_variant	126068	exon2			ATTTGAGGATGTG	AK095956	CCDS12266.2	19p13.13	2013-01-08			ENSG00000197044	ENSG00000197044		"Zinc fingers, C2H2-type", "-"	20875	protein-coding gene	gene with protein product							Standard	NM_152355		Approved	FLJ38637	uc010dyj.3	Q8N8Z8	OTTHUMG00000154449	ENST00000357901.4:c.21G>A	chr19.hg19:g.11888443G>A		104.0	0.0		223.0	78.0	NM_152355		Silent	SNP	ENST00000357901.4	hg19	CCDS12266.2																																																																																			.	.		0.438	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355		A	11888443	G	A	11888443	2	1	97	1	0	0	0	0	0	0	0	1	17929	991	35	3		3	ZNF441	19	11888443	Silent	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	7977590	11888443	47240540	92	13355										
FUZ	80199	hgsc.bcm.edu	37	chr19	50314913	50314913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	agtccttcttcagtctctccAcgttgcggatattggtcagt	9	11	4	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr19:50314913A>G	ENST00000313777.4	-	4	525	c.362T>C	c.(361-363)gTg>gCg	p.V121A	AC006942.4_ENST00000600669.1_RNA|FUZ_ENST00000445575.2_Missense_Mutation_p.V121A|FUZ_ENST00000533418.1_Missense_Mutation_p.V71A|FUZ_ENST00000534008.1_5'UTR|FUZ_ENST00000528094.1_Missense_Mutation_p.V85A|FUZ_ENST00000526575.1_3'UTR	NM_025129.4	NP_079405.2	Q9BT04	FUZZY_HUMAN	fuzzy planar cell polarity protein	121					cilium assembly (GO:0042384)|embryonic body morphogenesis (GO:0010172)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of planar polarity (GO:0001736)|hair follicle development (GO:0001942)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)|negative regulation of neural crest formation (GO:0090301)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|positive regulation of cilium assembly (GO:0045724)|protein transport (GO:0015031)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(3)	4		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00793)|GBM - Glioblastoma multiforme(134;0.0116)		CAGTCTCTCCACGTTGCGGAT	0.527																																					p.V121A		Atlas-SNP	.											.	FUZ	18	.	0			c.T362C						.						379	343	355					19																	50314913		2203	4300	6503	SO:0001583	missense	80199	exon4			CTCTCCACGTTGC	BC016793	CCDS12781.1, CCDS54293.1	19q13.33	2013-03-05	2013-03-05			ENSG00000010361			26219	protein-coding gene	gene with protein product		610622	"fuzzy homolog (Drosophila)"			21761479	Standard	NM_001171937		Approved	FLJ22688, Fy	uc002ppq.2	Q9BT04		ENST00000313777.4:c.362T>C	chr19.hg19:g.50314913A>G	ENSP00000313309:p.Val121Ala	102.0	0.0		195.0	73.0	NM_025129	B2RD86|B5MDH0|Q6PJY0|Q9H613	Missense_Mutation	SNP	ENST00000313777.4	hg19	CCDS12781.1	.	.	.	.	.	.	.	.	.	.	A	17.40	3.380908	0.61845	.	.	ENSG00000010361	ENST00000528094;ENST00000533418;ENST00000529634;ENST00000313777;ENST00000377092;ENST00000445575;ENST00000529004;ENST00000421740	T;T;T;T;T	0.72942	2.21;2.21;2.21;-0.7;2.21	4.83	4.83	0.62350	.	0.233514	0.33875	N	0.004474	T	0.69305	0.3096	L	0.49350	1.555	0.48341	D	0.999632	P;P;B	0.49961	0.93;0.787;0.202	P;B;B	0.47915	0.561;0.359;0.059	T	0.73360	-0.4007	10	0.87932	D	0	-11.0074	10.7112	0.45984	1.0:0.0:0.0:0.0	.	121;85;121	B4DHF8;Q9BT04-3;Q9BT04	.;.;FUZZY_HUMAN	A	85;71;121;121;21;121;71;121	ENSP00000435177:V85A;ENSP00000431731:V71A;ENSP00000313309:V121A;ENSP00000366296:V21A;ENSP00000408018:V121A	ENSP00000313309:V121A	V	-	2	0	FUZ	55006725	0.713000	0.27926	0.988000	0.46212	0.970000	0.65996	5.556000	0.67307	2.026000	0.59711	0.379000	0.24179	GTG	.	.		0.527	FUZ-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393986.1	NM_025129		G	50314913	A	G	50314913	3	3	97	1	0	0	0	0	1	0	0	0	6120	159	6	2	926	2	FUZ	19	50314913	Missense_Mutation	SNP	A	TCGA-DD-A1EA-01A-11D-A12Z-10	38426470	50314913	8814070	93	13356										
ZSCAN1	284312	hgsc.bcm.edu	37	chr19	58565348	58565348	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ccttccagtgtagcgtctgcGggaaggccttcccctggatg	13	13	1	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr19:58565348G>A	ENST00000282326.1	+	6	1403	c.1156G>A	c.(1156-1158)Ggg>Agg	p.G386R		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	386					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		TAGCGTCTGCGGGAAGGCCTT	0.692																																					p.G386R		Atlas-SNP	.											ZSCAN1,NS,carcinoma,0,1	ZSCAN1	102	.	0			c.G1156A						.						23	26	25					19																	58565348		2201	4298	6499	SO:0001583	missense	284312	exon6			GTCTGCGGGAAGG	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"-", "Zinc fingers, C2H2-type"	23712	protein-coding gene	gene with protein product			"zinc finger with SCAN domain 1"			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.1156G>A	chr19.hg19:g.58565348G>A	ENSP00000282326:p.Gly386Arg	31.0	0.0		43.0	10.0	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	hg19	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.506740	0.64410	.	.	ENSG00000152467	ENST00000282326	T	0.59224	0.28	0.993	0.993	0.19825	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.67239	0.2872	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67309	-0.5703	9	0.87932	D	0	.	7.8299	0.29336	0.0:0.0:1.0:0.0	.	386	Q8NBB4	ZSCA1_HUMAN	R	386	ENSP00000282326:G386R	ENSP00000282326:G386R	G	+	1	0	ZSCAN1	63257160	0.996000	0.38824	0.016000	0.15963	0.376000	0.30014	1.137000	0.31479	0.835000	0.34877	0.313000	0.20887	GGG	.	.		0.692	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		A	58565348	G	A	58565348	3	1	97	1	0	0	0	0	1	0	0	0	18241	1116	39	1	1170	1	ZSCAN1	19	58565348	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10	8250435	58565348	563635	94	13357										
TBC1D10A	83874	hgsc.bcm.edu	37	chr22	30688449	30688463	+	In_Frame_Del	DEL	GGGGCTGAGTCCTTG	GGGGCTGAGTCCTTG	-													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cctggggagccaaatcctgaGgggctgagtccttgggggct					rs530980848|rs36125665		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	GGGGCTGAGTCCTTG	GGGGCTGAGTCCTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr22:30688449_30688463delGGGGCTGAGTCCTTG	ENST00000215790.7	-	9	1592_1606	c.1428_1442delCAAGGACTCAGCCCC	c.(1426-1443)cccaaggactcagcccct>cct	p.476_481PKDSAP>P	TBC1D10A_ENST00000403362.1_In_Frame_Del_p.388_393PKDSAP>P|GATSL3_ENST00000404953.3_5'Flank|GATSL3_ENST00000407689.3_5'Flank|RP1-130H16.18_ENST00000447976.1_Intron|TBC1D10A_ENST00000403477.3_In_Frame_Del_p.483_488PKDSAP>P	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	476					activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)			cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						CAAATCCTGAGGGGCTGAGTCCTTGGGGGCTGAGT	0.628																																					p.484_488del		Atlas-Indel,Pindel	.											.	TBC1D10A	49	.	0			c.1450_1464del						.																																			SO:0001651	inframe_deletion	83874	exon9			.	AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"EBP50-PDZ interactor of 64 kD"	610020	"TBC1 domain family, member 10"	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.1428_1442delCAAGGACTCAGCCCC	chr22.hg19:g.30688449_30688463delGGGGCTGAGTCCTTG	ENSP00000215790:p.Pro476_Ala480del	28.0	0.0		81.0	25.0	NM_001204240	B3KXT8|O76053|Q20WK7|Q543A2	In_Frame_Del	DEL	ENST00000215790.7	hg19	CCDS13874.1																																																																																			.	.		0.628	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937		-	30688463	GGGGCTGAGTCCTTG	-	30688449	7	5	97	1	0	1	0	1	0	0	0	0	15613	1000	35	0	88	0	TBC1D10A	22	30688449	In_Frame_Del	DEL	GGGGCTGAGTCCTTG	TCGA-DD-A1EA-01A-11D-A12Z-10		30688449	20616117	95	13358										
SYNGR1	9145	hgsc.bcm.edu	37	chr22	39777778	39777778	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ttctcccaggactacatggaCcccagccaggactccagcat	8	16	1	0			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr22:39777778C>A	ENST00000328933.5	+	4	576	c.561C>A	c.(559-561)gaC>gaA	p.D187E		NM_004711.4	NP_004702.2	O43759	SNG1_HUMAN	synaptogyrin 1	187					protein targeting (GO:0006605)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle membrane (GO:0030672)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	7	Melanoma(58;0.04)					ACTACATGGACCCCAGCCAGG	0.687																																					p.D187E		Atlas-SNP	.											.	SYNGR1	19	.	0			c.C561A						.						49	50	50					22																	39777778		2203	4300	6503	SO:0001583	missense	9145	exon4			CATGGACCCCAGC	AJ002303	CCDS13989.1, CCDS13990.1, CCDS13991.1	22q13	2008-06-10			ENSG00000100321	ENSG00000100321			11498	protein-coding gene	gene with protein product		603925				9760194, 10595519	Standard	NM_004711		Approved			O43759	OTTHUMG00000030978	ENST00000328933.5:c.561C>A	chr22.hg19:g.39777778C>A	ENSP00000332287:p.Asp187Glu	27.0	0.0		97.0	36.0	NM_004711	A6NP69|A8K0E2|O43757|O43758|Q53Y02|Q96J56|Q9UGZ4	Missense_Mutation	SNP	ENST00000328933.5	hg19	CCDS13989.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.155681	0.57259	.	.	ENSG00000100321	ENST00000328933	T	0.65732	-0.17	4.52	-0.00232	0.14030	.	0.047898	0.85682	D	0.000000	T	0.54351	0.1853	M	0.74647	2.275	0.80722	D	1	P	0.48089	0.905	B	0.39152	0.292	T	0.52939	-0.8508	10	0.33141	T	0.24	.	9.3548	0.38159	0.0:0.7044:0.0:0.2956	.	187	O43759	SNG1_HUMAN	E	187	ENSP00000332287:D187E	ENSP00000332287:D187E	D	+	3	2	SYNGR1	38107724	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	2.340000	0.43974	-0.063000	0.13065	0.462000	0.41574	GAC	.	.		0.687	SYNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075866.2	NM_004711		A	39777778	C	A	39777778	3	1	97	1	0	0	0	0	1	0	0	0	15463	506	18	3	778	3	SYNGR1	22	39777778	Missense_Mutation	SNP	C	TCGA-DD-A1EA-01A-11D-A12Z-10	9089329	39777778	11526788	96	13359										
CNKSR2	22866	hgsc.bcm.edu	37	chrX	21545015	21545015	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	ctagaagtcccacaagcagcGttgccacgccttccagcacc	8	17	0	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chrX:21545015G>A	ENST00000379510.3	+	10	1024	c.988G>A	c.(988-990)Gtt>Att	p.V330I	CNKSR2_ENST00000279451.4_Missense_Mutation_p.V330I|CNKSR2_ENST00000425654.2_Missense_Mutation_p.V330I|CNKSR2_ENST00000543067.1_Missense_Mutation_p.V281I	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	330					regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						CACAAGCAGCGTTGCCACGCC	0.453													G|||	1	0.000264901	0	0	3775	,	,		7043	0		0	False		,,,				2504	0.001				p.V330I		Atlas-SNP	.											.	CNKSR2	158	.	0			c.G988A						.						222	211	215					X																	21545015		2203	4300	6503	SO:0001583	missense	22866	exon10			AGCAGCGTTGCCA	AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.988G>A	chrX.hg19:g.21545015G>A	ENSP00000368824:p.Val330Ile	60.0	0.0		177.0	163.0	NM_001168647	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Missense_Mutation	SNP	ENST00000379510.3	hg19	CCDS14198.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.384359	0.42308	.	.	ENSG00000149970	ENST00000425654;ENST00000543067;ENST00000279451;ENST00000379510	T;T;T;T	0.18502	2.5;2.25;2.21;2.48	5.58	4.66	0.58398	.	0.196899	0.43416	D	0.000563	T	0.06826	0.0174	N	0.02011	-0.69	0.24045	N	0.996062	B;B;B	0.20988	0.029;0.05;0.007	B;B;B	0.12156	0.007;0.003;0.002	T	0.29852	-0.9998	10	0.17832	T	0.49	-9.6134	14.3431	0.66641	0.0:0.0:0.8514:0.1485	.	330;281;330	B7ZLJ1;B4DGR4;Q8WXI2	.;.;CNKR2_HUMAN	I	330;281;330;330	ENSP00000397906:V330I;ENSP00000444633:V281I;ENSP00000279451:V330I;ENSP00000368824:V330I	ENSP00000279451:V330I	V	+	1	0	CNKSR2	21454936	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.870000	0.63035	2.338000	0.79540	0.544000	0.68410	GTT	.	.		0.453	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927		A	21545015	G	A	21545015	3	1	97	1	0	0	0	0	1	0	0	0	3609	1145	40	1	1026	1	CNKSR2	23	21545015	Missense_Mutation	SNP	G	TCGA-DD-A1EA-01A-11D-A12Z-10		21545015	133725545	97	13360										
TAF7L	54457	hgsc.bcm.edu	37	chrX	100547906	100547906	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	caatgtcggcgctgctttcaTaggtggtttcagacccacgg	12	11	2	1			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chrX:100547906T>A	ENST00000372907.3	-	1	139	c.128A>T	c.(127-129)tAt>tTt	p.Y43F	TAF7L_ENST00000356784.1_5'Flank|TAF7L_ENST00000372905.2_5'UTR	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	43					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						GCTGCTTTCATAGGTGGTTTC	0.527																																					p.Y43F	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.A128T						.						175	172	173					X																	100547906		2203	4300	6503	SO:0001583	missense	54457	exon1			CTTTCATAGGTGG	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"cancer/testis antigen 40"	300314	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.128A>T	chrX.hg19:g.100547906T>A	ENSP00000361998:p.Tyr43Phe	69.0	0.0		236.0	213.0	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	hg19	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	T	1.946	-0.442518	0.04604	.	.	ENSG00000102387	ENST00000372907	T	0.13901	2.55	3.67	0.913	0.19354	.	1.853500	0.03176	N	0.171455	T	0.06872	0.0175	N	0.08118	0	0.09310	N	0.999998	B	0.14012	0.009	B	0.12156	0.007	T	0.32322	-0.9911	10	0.10111	T	0.7	6.0409	5.3638	0.16103	0.0:0.5947:0.0:0.4053	.	43	Q5H9L4	TAF7L_HUMAN	F	43	ENSP00000361998:Y43F	ENSP00000361998:Y43F	Y	-	2	0	TAF7L	100434562	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-1.444000	0.02403	0.060000	0.16281	-0.183000	0.12914	TAT	.	.		0.527	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2			A	100547906	T	A	100547906	3	1	97	1	0	0	0	0	1	0	0	0	15548	1406	49	4	1312	4	TAF7L	23	100547906	Missense_Mutation	SNP	T	TCGA-DD-A1EA-01A-11D-A12Z-10	79002891	100547906	54722654	98	13361										
AFF2	2334	hgsc.bcm.edu	37	chrX	148038047	148038048	+	Frame_Shift_Ins	INS	-	-	A													0.0208333333333333	2	1	0.523062139654068	0	0.610239162929746	0.428571428571429	1	0	cactccatgcagcacctgccINSaagccagaccacaaggagac							TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chrX:148038047_148038048insA	ENST00000370460.2	+	11	2951_2952	c.2472_2473insA	c.(2473-2475)aagfs	p.K825fs	AFF2_ENST00000286437.5_Frame_Shift_Ins_p.K466fs|AFF2_ENST00000370457.5_Frame_Shift_Ins_p.K792fs|AFF2_ENST00000342251.3_Frame_Shift_Ins_p.K792fs	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	825					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					CAGCACCTGCCAAGCCAGACCA	0.525																																					p.A824fs		Atlas-INDEL	.											.	AFF2	679	.	0			c.2472_2473insA						.																																			SO:0001589	frameshift_variant	2334	exon11			.	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.2474dupA	chrX.hg19:g.148038049_148038049dupA	ENSP00000359489:p.Lys825fs	27.0	0.0		116.0	11.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Frame_Shift_Ins	INS	ENST00000370460.2	hg19	CCDS14684.1																																																																																			.	.		0.525	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		A	148038048	-	A	148038047	7	5	97	1	0	1	1	0	0	0	0	0	357	581	21	0	2569	0	AFF2	23	148038047	Frame_Shift_Ins	INS	-	TCGA-DD-A1EA-01A-11D-A12Z-10	47490141	148038047	7232513	99	13362										
USP48	84196	hgsc.bcm.edu	37	chr1	22016544	22016544	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	atcacttaaaatctttccatCaattgacaaattctggtcaa	3	9	5	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:22016544C>T	ENST00000308271.9	-	24	3580	c.2932G>A	c.(2932-2934)Gat>Aat	p.D978N	USP48_ENST00000374732.3_Missense_Mutation_p.D464N|USP48_ENST00000529637.1_Missense_Mutation_p.D990N|USP48_ENST00000400301.1_Missense_Mutation_p.D926N	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	978	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		ATCTTTCCATCAATTGACAAA	0.388																																					p.D978N		Atlas-SNP	.											.	USP48	91	.	0			c.G2932A						.						92	90	91					1																	22016544		2203	4300	6503	SO:0001583	missense	84196	exon24			TTCCATCAATTGA	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2932G>A	chr1.hg19:g.22016544C>T	ENSP00000309262:p.Asp978Asn	96.0	0.0		301.0	107.0	NM_032236	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	hg19	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	C	16.82	3.229593	0.58777	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000374732;ENST00000529637	T;T;T;T	0.40476	1.03;1.09;1.03;1.09	5.61	5.61	0.85477	Ubiquitin supergroup (1);	0.042619	0.85682	D	0.000000	T	0.37625	0.1010	L	0.45137	1.4	0.80722	D	1	B;B;B;B;B;B	0.14805	0.008;0.0;0.011;0.001;0.001;0.011	B;B;B;B;B;B	0.17433	0.012;0.001;0.018;0.002;0.003;0.018	T	0.16012	-1.0417	10	0.15066	T	0.55	.	18.2065	0.89857	0.0:1.0:0.0:0.0	.	990;978;103;926;978;464	B7ZKS7;B7ZKS3;Q86UV5-6;Q86UV5-2;Q86UV5;Q86UV5-5	.;.;.;.;UBP48_HUMAN;.	N	926;978;464;990	ENSP00000383157:D926N;ENSP00000309262:D978N;ENSP00000363864:D464N;ENSP00000431949:D990N	ENSP00000309262:D978N	D	-	1	0	USP48	21889131	0.999000	0.42202	1.000000	0.80357	0.978000	0.69477	4.236000	0.58675	2.650000	0.89964	0.655000	0.94253	GAT	.	.		0.388	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		T	22016544	C	T	22016544	3	4	98	1	0	0	0	0	1	0	0	0	17094	826	29	3	191	3	USP48	1	22016544	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10		22016544	227234077	1	13363										
PARS2	25973	hgsc.bcm.edu	37	chr1	55223846	55223846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tttcagccagggttggtttgCcacagacattggtaaactgg	12	8	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:55223846C>T	ENST00000371279.3	-	2	1071	c.989G>A	c.(988-990)gGc>gAc	p.G330D		NM_152268.3	NP_689481.2	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase 2, mitochondrial (putative)	330					gene expression (GO:0010467)|prolyl-tRNA aminoacylation (GO:0006433)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|proline-tRNA ligase activity (GO:0004827)			breast(1)|endometrium(3)|kidney(2)|lung(4)|ovary(2)|prostate(2)|skin(1)	15					L-Proline(DB00172)	GGTTGGTTTGCCACAGACATT	0.507																																					p.G330D		Atlas-SNP	.											.	PARS2	29	.	0			c.G989A						.						100	101	101					1																	55223846		2203	4300	6503	SO:0001583	missense	25973	exon2			GGTTTGCCACAGA	AK025585	CCDS597.1	1p32.2	2011-07-01	2007-02-23		ENSG00000162396	ENSG00000162396	6.1.1.15	"Aminoacyl tRNA synthetases / Class II"	30563	protein-coding gene	gene with protein product	"proline tRNA ligase 2, mitochondrial (putative)"	612036				15779907	Standard	NM_152268		Approved	DKFZp727A071	uc001cxy.3	Q7L3T8	OTTHUMG00000009915	ENST00000371279.3:c.989G>A	chr1.hg19:g.55223846C>T	ENSP00000360327:p.Gly330Asp	54.0	0.0		165.0	66.0	NM_152268	A8K0W4|Q9H6S5|Q9UFT1	Missense_Mutation	SNP	ENST00000371279.3	hg19	CCDS597.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.061515	0.36373	.	.	ENSG00000162396	ENST00000371279	D	0.82167	-1.58	5.66	5.66	0.87406	Aminoacyl-tRNA synthetase, class II (1);	0.163532	0.51477	D	0.000085	D	0.89301	0.6676	M	0.91300	3.195	0.48901	D	0.999725	D	0.58268	0.982	P	0.54664	0.758	D	0.90315	0.4340	10	0.66056	D	0.02	-21.6053	7.4017	0.26967	0.0:0.8011:0.0:0.1989	.	330	Q7L3T8	SYPM_HUMAN	D	330	ENSP00000360327:G330D	ENSP00000360327:G330D	G	-	2	0	PARS2	54996434	1.000000	0.71417	0.048000	0.18961	0.019000	0.09904	4.858000	0.62947	2.665000	0.90641	0.655000	0.94253	GGC	.	.		0.507	PARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027436.1	NM_152268		T	55223846	C	T	55223846	3	4	98	1	0	0	0	0	1	0	0	0	11476	739	26	3	442	3	PARS2	1	55223846	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	33207302	55223846	194026775	2	13364										
JAK1	3716	hgsc.bcm.edu	37	chr1	65316546	65316547	+	Frame_Shift_Ins	INS	-	-	C													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tggctcatggggtagacgggINSctgccactcctgggctttct							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:65316546_65316547insC	ENST00000342505.4	-	12	1943_1944	c.1695_1696insG	c.(1693-1698)cagcccfs	p.P566fs	JAK1_ENST00000465376.1_5'Flank	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	566					cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGGTAGACGGGCTGCCACTCCT	0.584			Mis		ALL																																p.P566fs		Atlas-INDEL	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.1696_1697insG						.																																			SO:0001589	frameshift_variant	3716	exon12			.	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.1696dupG	chr1.hg19:g.65316547_65316547dupC	ENSP00000343204:p.Pro566fs	38.0	0.0		127.0	12.0	NM_002227	Q59GQ2|Q9UD26	Frame_Shift_Ins	INS	ENST00000342505.4	hg19	CCDS41346.1																																																																																			.	.		0.584	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		C	65316547	-	C	65316546	7	5	98	1	0	1	1	0	0	0	0	0	7946	1203	42	0	1824	0	JAK1	1	65316546	Frame_Shift_Ins	INS	-	TCGA-DD-A1EB-01A-11D-A12Z-10	10092700	65316546	183934075	3	13365										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144852472	144852472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	caagggtcacaaggctggagTacatggcagagcccttaggg	15	9	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:144852472T>C	ENST00000369354.3	-	44	7216	c.7027A>G	c.(7027-7029)Act>Gct	p.T2343A	PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.T2479A|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.T2428A|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.T2237A			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2343					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AAGGCTGGAGTACATGGCAGA	0.512			T	PDGFRB	MPD																																p.T2343A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A7027G						.						54	53	53					1																	144852472		2203	4293	6496	SO:0001583	missense	9659	exon44			CTGGAGTACATGG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.7027A>G	chr1.hg19:g.144852472T>C	ENSP00000358360:p.Thr2343Ala	63.0	0.0		180.0	36.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	.	8.960	0.970237	0.18659	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000530740;ENST00000369359	T;T;T;T	0.01685	4.69;4.79;4.79;4.79	4.47	-1.12	0.09808	.	.	.	.	.	T	0.00666	0.0022	L	0.47716	1.5	0.48511	D	0.999669	B;B	0.11235	0.004;0.0	B;B	0.09377	0.004;0.001	T	0.43327	-0.9398	9	0.49607	T	0.09	.	4.0432	0.09761	0.0:0.3064:0.1814:0.5122	.	2237;2343	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	A	2237;2343;2428;2479	ENSP00000327209:T2237A;ENSP00000358360:T2343A;ENSP00000435654:T2428A;ENSP00000358366:T2479A	ENSP00000327209:T2237A	T	-	1	0	PDE4DIP	143563829	0.204000	0.23447	0.722000	0.30670	0.403000	0.30841	-0.491000	0.06474	-0.050000	0.13356	0.449000	0.29647	ACT	.	.		0.512	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144852472	T	C	144852472	3	2	98	1	0	0	0	0	1	0	0	0	11652	1638	57	2	17	2	PDE4DIP	1	144852472	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	79535926	144852472	104398149	4	13366										
ITGA10	8515	hgsc.bcm.edu	37	chr1	145528004	145528004	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	atcgctgccctgtaggggggGcccacaatgccccatgtgcc	13	15	0	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:145528004G>C	ENST00000369304.3	+	3	416	c.241G>C	c.(241-243)Gcc>Ccc	p.A81P	ITGA10_ENST00000538811.1_Intron|ITGA10_ENST00000539363.1_Intron	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	81					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TGTAGGGGGGGCCCACAATGC	0.592																																					p.A81P		Atlas-SNP	.											.	ITGA10	131	.	0			c.G241C						.						8	10	10					1																	145528004		2172	4279	6451	SO:0001583	missense	8515	exon3			GGGGGGGCCCACA	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.241G>C	chr1.hg19:g.145528004G>C	ENSP00000358310:p.Ala81Pro	50.0	0.0		253.0	156.0	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	10.10	1.256782	0.22965	.	.	ENSG00000143127	ENST00000369304;ENST00000543043	T	0.71934	-0.61	5.61	-6.68	0.01778	.	1.143750	0.06345	N	0.708697	T	0.23649	0.0572	N	0.08118	0	0.09310	N	0.999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.0	T	0.31943	-0.9925	10	0.52906	T	0.07	.	7.6532	0.28360	0.0:0.1924:0.4447:0.363	.	47;81;81	F5H3T9;O75578;O75578-2	.;ITA10_HUMAN;.	P	81;47	ENSP00000358310:A81P	ENSP00000358310:A81P	A	+	1	0	ITGA10	144239361	0.000000	0.05858	0.000000	0.03702	0.707000	0.40811	-0.339000	0.07832	-1.187000	0.02709	-0.344000	0.07964	GCC	.	.		0.592	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		C	145528004	G	C	145528004	3	2	98	1	0	0	0	0	1	0	0	0	7882	1203	42	4	251	4	ITGA10	1	145528004	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	675532	145528004	103722617	5	13367										
CHD1L	9557	hgsc.bcm.edu	37	chr1	146714372	146714372	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cgatggagcgcgcgggcgctActagccgcgggggccaagcg	19	13	0	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:146714372A>G	ENST00000369258.4	+	1	39	c.19A>G	c.(19-21)Act>Gct	p.T7A	CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000431239.1_Missense_Mutation_p.T7A|RP11-337C18.10_ENST00000606856.1_RNA|CHD1L_ENST00000361293.5_5'UTR|CHD1L_ENST00000369259.3_Missense_Mutation_p.T7A	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	7					ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					CGCGGGCGCTACTAGCCGCGG	0.746																																					p.T7A		Atlas-SNP	.											.	CHD1L	72	.	0			c.A19G						.						4	7	6					1																	146714372		1931	3882	5813	SO:0001583	missense	9557	exon1			GGCGCTACTAGCC	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.19A>G	chr1.hg19:g.146714372A>G	ENSP00000358262:p.Thr7Ala	9.0	0.0		38.0	14.0	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	hg19	CCDS927.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.921404	0.33908	.	.	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258	D;T;D	0.88509	-2.39;-1.25;-2.29	2.18	0.152	0.14893	.	1.259300	0.06027	N	0.652309	T	0.50137	0.1598	N	0.08118	0	0.09310	N	0.999996	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43147	-0.9409	10	0.10111	T	0.7	.	2.8512	0.05558	0.3183:0.2455:0.4362:0.0	.	7;7;7	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	A	7	ENSP00000389031:T7A;ENSP00000358263:T7A;ENSP00000358262:T7A	ENSP00000358262:T7A	T	+	1	0	CHD1L	145180996	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.032000	0.13732	-0.244000	0.09639	-0.493000	0.04662	ACT	.	.		0.746	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		G	146714372	A	G	146714372	3	3	98	1	0	0	0	0	1	0	0	0	3326	391	14	2	21	2	CHD1L	1	146714372	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	1186368	146714372	102536249	6	13368										
KIAA0907	22889	hgsc.bcm.edu	37	chr1	155899509	155899509	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	caatgcctcctcacctcgtcTtgagtctgtcctcgagtcag	8	15	4	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:155899509T>G	ENST00000368321.3	-	3	401	c.378A>C	c.(376-378)caA>caC	p.Q126H	KIAA0907_ENST00000368319.3_Missense_Mutation_p.Q126H|KIAA0907_ENST00000482337.1_5'UTR|KIAA0907_ENST00000368320.3_Missense_Mutation_p.Q126H	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	126							RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			TCACCTCGTCTTGAGTCTGTC	0.453																																					p.Q126H		Atlas-SNP	.											.	KIAA0907	58	.	0			c.A378C						.						144	127	133					1																	155899509		2203	4300	6503	SO:0001583	missense	22889	exon3			CTCGTCTTGAGTC	BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.378A>C	chr1.hg19:g.155899509T>G	ENSP00000357304:p.Gln126His	59.0	0.0		219.0	68.0	NM_014949	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Missense_Mutation	SNP	ENST00000368321.3	hg19	CCDS30885.1	.	.	.	.	.	.	.	.	.	.	T	19.86	3.904848	0.72868	.	.	ENSG00000132680	ENST00000368321;ENST00000368320;ENST00000368319	T;T;T	0.42513	0.97;0.97;0.97	5.02	-1.31	0.09230	.	0.000000	0.85682	D	0.000000	T	0.51635	0.1686	M	0.84219	2.685	0.53005	D	0.999965	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.997;0.997	D;D;D;D;D;D	0.91635	0.998;0.999;0.996;0.999;0.995;0.995	T	0.60821	-0.7187	10	0.62326	D	0.03	-9.3075	11.1425	0.48411	0.0:0.662:0.0:0.338	.	126;126;126;126;126;126	D3DVA4;Q7Z7F0-4;A8K1I7;Q7Z7F0-3;Q7Z7F0-2;Q7Z7F0	.;.;.;.;.;K0907_HUMAN	H	126	ENSP00000357304:Q126H;ENSP00000357303:Q126H;ENSP00000357302:Q126H	ENSP00000357302:Q126H	Q	-	3	2	KIAA0907	154166133	0.994000	0.37717	0.997000	0.53966	0.846000	0.48090	0.343000	0.19944	-0.101000	0.12219	0.460000	0.39030	CAA	.	.		0.453	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		G	155899509	T	G	155899509	3	3	98	1	0	0	0	0	1	0	0	0	8208	1606	56	5	1514	5	KIAA0907	1	155899509	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	9185137	155899509	93351112	7	13369										
SSR2	6746	hgsc.bcm.edu	37	chr1	155988138	155988138	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ggagggaaggaatcatcagaTagttccacgtctaatgcagc	12	8	3	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:155988138T>C	ENST00000295702.4	-	3	248	c.177A>G	c.(175-177)ctA>ctG	p.L59L	SSR2_ENST00000529008.1_Silent_p.L59L|SSR2_ENST00000496742.1_Intron|SSR2_ENST00000480567.1_Silent_p.L59L	NM_003145.3	NP_003136.1	P43308	SSRB_HUMAN	signal sequence receptor, beta (translocon-associated protein beta)	59					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|stomach(1)	10	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					AATCATCAGATAGTTCCACGT	0.468																																					p.L59L		Atlas-SNP	.											.	SSR2	20	.	0			c.A177G						.						108	100	103					1																	155988138		2203	4300	6503	SO:0001819	synonymous_variant	6746	exon3			ATCAGATAGTTCC	BC000341	CCDS1126.1	1q21-q23	2008-02-05			ENSG00000163479	ENSG00000163479			11324	protein-coding gene	gene with protein product		600867				7789174	Standard	NM_003145		Approved	TLAP, TRAPB	uc001fmx.3	P43308	OTTHUMG00000017456	ENST00000295702.4:c.177A>G	chr1.hg19:g.155988138T>C		30.0	0.0		94.0	33.0	NM_003145	B2R9K9|D3DVA7|Q53HI0|Q5VY95|Q5VY96|Q6IB31|Q9BWE4	Silent	SNP	ENST00000295702.4	hg19	CCDS1126.1																																																																																			.	.		0.468	SSR2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046172.2	NM_003145		C	155988138	T	C	155988138	2	2	98	1	0	0	0	0	0	0	0	1	15206	1393	49	2		2	SSR2	1	155988138	Silent	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	88629	155988138	93262483	8	13370										
NES	10763	hgsc.bcm.edu	37	chr1	156640645	156640645	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cctcttccctggtcagatggCctgggtcccccagccctccc	9	20	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:156640645C>A	ENST00000368223.3	-	4	3467	c.3335G>T	c.(3334-3336)gGc>gTc	p.G1112V		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1112	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGTCAGATGGCCTGGGTCCCC	0.637																																					p.G1112V		Atlas-SNP	.											.	NES	196	.	0			c.G3335T						.						33	34	34					1																	156640645		2202	4299	6501	SO:0001583	missense	10763	exon4			AGATGGCCTGGGT	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3335G>T	chr1.hg19:g.156640645C>A	ENSP00000357206:p.Gly1112Val	37.0	0.0		141.0	43.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	C	14.60	2.582779	0.46006	.	.	ENSG00000132688	ENST00000368223	D	0.85955	-2.05	4.82	-1.18	0.09617	.	0.524091	0.14422	N	0.320573	T	0.70675	0.3251	L	0.56769	1.78	0.09310	N	0.999995	D	0.54964	0.969	P	0.45506	0.483	T	0.64554	-0.6380	10	0.66056	D	0.02	.	6.4028	0.21648	0.0:0.5142:0.1307:0.3552	.	1112	P48681	NEST_HUMAN	V	1112	ENSP00000357206:G1112V	ENSP00000357206:G1112V	G	-	2	0	NES	154907269	0.000000	0.05858	0.001000	0.08648	0.103000	0.19146	-0.250000	0.08830	0.102000	0.17638	0.557000	0.71058	GGC	.	.		0.637	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		A	156640645	C	A	156640645	3	1	98	1	0	0	0	0	1	0	0	0	10346	739	26	3	1534	3	NES	1	156640645	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	652507	156640645	92609976	9	13371										
DDR2	4921	hgsc.bcm.edu	37	chr1	162731029	162731029	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	caacaacatgtttgctaaagGtgtgaagatctttaaggagg	11	5	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:162731029G>T	ENST00000367922.3	+	10	1322	c.884G>T	c.(883-885)gGt>gTt	p.G295V	DDR2_ENST00000367921.3_Missense_Mutation_p.G295V	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	295					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	TTTGCTAAAGGTGTGAAGATC	0.507																																					p.G295V	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											.	DDR2	228	.	0			c.G884T						.						169	123	139					1																	162731029		2203	4300	6503	SO:0001583	missense	4921	exon10			CTAAAGGTGTGAA	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"discoidin domain receptor family, member 2"	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.884G>T	chr1.hg19:g.162731029G>T	ENSP00000356899:p.Gly295Val	83.0	0.0		307.0	71.0	NM_001014796	Q7Z730	Missense_Mutation	SNP	ENST00000367922.3	hg19	CCDS1241.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.258986	0.80246	.	.	ENSG00000162733	ENST00000367922;ENST00000367921	T;T	0.70869	-0.52;-0.52	5.89	5.89	0.94794	.	0.106287	0.64402	D	0.000005	T	0.80182	0.4576	M	0.76574	2.34	0.37495	D	0.916527	D	0.60575	0.988	P	0.60345	0.873	T	0.81686	-0.0820	9	0.87932	D	0	.	18.8112	0.92058	0.0:0.0:1.0:0.0	.	295	Q16832	DDR2_HUMAN	V	295	ENSP00000356899:G295V;ENSP00000356898:G295V	ENSP00000356898:G295V	G	+	2	0	DDR2	160997653	1.000000	0.71417	0.975000	0.42487	0.997000	0.91878	5.841000	0.69409	2.763000	0.94921	0.655000	0.94253	GGT	.	.		0.507	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		T	162731029	G	T	162731029	3	4	98	1	0	0	0	0	1	0	0	0	4339	1261	44	3	910	3	DDR2	1	162731029	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	6090384	162731029	86519592	10	13372										
PBX1	5087	hgsc.bcm.edu	37	chr1	164768965	164768965	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gagttcaccacccacgtgatGaatctcctgcgagagcaaag	10	12	2	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:164768965G>T	ENST00000420696.2	+	4	728	c.540G>T	c.(538-540)atG>atT	p.M180I	PBX1_ENST00000401534.1_Missense_Mutation_p.M180I|PBX1_ENST00000540236.1_Missense_Mutation_p.M180I|PBX1_ENST00000540246.1_Missense_Mutation_p.M75I|PBX1_ENST00000559240.1_Missense_Mutation_p.M180I|PBX1_ENST00000367897.1_Missense_Mutation_p.M180I|PBX1_ENST00000560641.1_Missense_Mutation_p.M75I	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	180					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						CCCACGTGATGAATCTCCTGC	0.542			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.M180I		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1	60	.	0			c.G540T						.						89	81	84					1																	164768965		2203	4300	6503	SO:0001583	missense	5087	exon4			CGTGATGAATCTC	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"Homeoboxes / TALE class"	8632	protein-coding gene	gene with protein product		176310	"pre-B-cell leukemia transcription factor 1"				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.540G>T	chr1.hg19:g.164768965G>T	ENSP00000405890:p.Met180Ile	56.0	0.0		211.0	68.0	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	hg19	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.919683	0.92249	.	.	ENSG00000185630	ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	5.76	5.76	0.90799	PBX (1);	0.000000	0.85682	D	0.000000	T	0.29093	0.0723	M	0.70275	2.135	0.80722	D	1	B;B;B;B	0.33549	0.011;0.109;0.417;0.041	B;B;B;B	0.37943	0.038;0.064;0.261;0.055	T	0.04413	-1.0953	10	0.33141	T	0.24	-15.6208	19.571	0.95419	0.0:0.0:1.0:0.0	.	75;180;180;180	B7Z774;F5H4U9;P40424;Q53YC7	.;.;PBX1_HUMAN;.	I	180;180;180;180;75	ENSP00000405890:M180I;ENSP00000356872:M180I;ENSP00000439943:M180I;ENSP00000384856:M180I;ENSP00000440869:M75I	ENSP00000356872:M180I	M	+	3	0	PBX1	163035589	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.338000	0.96553	2.713000	0.92767	0.655000	0.94253	ATG	.	.		0.542	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		T	164768965	G	T	164768965	3	4	98	1	0	0	0	0	1	0	0	0	11501	1290	45	3	554	3	PBX1	1	164768965	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	2037936	164768965	84481656	11	13373										
MAEL	84944	hgsc.bcm.edu	37	chr1	166974345	166974345	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	accagagtcaactggtgtttGaagcatatggcaaaggcatc	11	8	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:166974345G>A	ENST00000367872.4	+	7	925	c.681G>A	c.(679-681)ttG>ttA	p.L227L	MAEL_ENST00000367870.2_Silent_p.L196L|RNA5SP65_ENST00000363166.1_RNA|MAEL_ENST00000491055.1_3'UTR	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	227					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						ACTGGTGTTTGAAGCATATGG	0.358																																					p.L227L		Atlas-SNP	.											.	MAEL	95	.	0			c.G681A						.						66	67	67					1																	166974345		2203	4300	6503	SO:0001819	synonymous_variant	84944	exon7			GTGTTTGAAGCAT	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"cancer/testis antigen 128", "spermatogenesis associated 35"	611368	"maelstrom homolog (Drosophila)"			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.681G>A	chr1.hg19:g.166974345G>A		113.0	0.0		398.0	104.0	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Silent	SNP	ENST00000367872.4	hg19	CCDS1257.1																																																																																			.	.		0.358	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858		A	166974345	G	A	166974345	2	1	98	1	0	0	0	0	0	0	0	1	9163	1281	45	3		3	MAEL	1	166974345	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	2205380	166974345	82276276	12	13374										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172557990	172557990	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	attgtacagttagttcaagaGgaggaagaggaggcaagtcc	14	5	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:172557990G>C	ENST00000263688.3	+	18	1968	c.1749G>C	c.(1747-1749)gaG>gaC	p.E583D	SUCO_ENST00000608151.1_Missense_Mutation_p.E735D|SUCO_ENST00000367723.4_Missense_Mutation_p.E734D|SUCO_ENST00000610051.1_Missense_Mutation_p.E546D	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	583					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											TAGTTCAAGAGGAGGAAGAGG	0.453																																					p.E583D		Atlas-SNP	.											.	.	.	.	0			c.G1749C						.						75	65	68					1																	172557990		2203	4300	6503	SO:0001583	missense	51430	exon18			TCAAGAGGAGGAA	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1749G>C	chr1.hg19:g.172557990G>C	ENSP00000263688:p.Glu583Asp	69.0	0.0		262.0	75.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	hg19	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.052312	0.36181	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.44	1.97	0.26223	.	0.146153	0.64402	D	0.000013	T	0.29817	0.0745	L	0.58669	1.825	0.44570	D	0.997538	B;B;B;B	0.27068	0.024;0.167;0.167;0.167	B;B;B;B	0.25987	0.012;0.038;0.065;0.038	T	0.11084	-1.0602	9	0.34782	T	0.22	-13.8134	5.2296	0.15414	0.3303:0.1513:0.5183:0.0	.	546;583;735;583	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	D	735;583	.	ENSP00000263688:E583D	E	+	3	2	C1orf9	170824613	0.995000	0.38212	1.000000	0.80357	0.991000	0.79684	0.192000	0.17096	0.586000	0.29626	0.557000	0.71058	GAG	.	.		0.453	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		C	172557990	G	C	172557990	3	2	98	1	0	0	0	0	1	0	0	0	2069	991	35	4	1819	4	C1orf9	1	172557990	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	5583645	172557990	76692631	13	13375										
C1orf49	84066	hgsc.bcm.edu	37	chr1	178489807	178489807	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tccctggccctcctcccccaGtccccttagaagagcaccaa	6	20	0	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:178489807G>C	ENST00000319416.2	+	7	453		c.e7-1		TEX35_ENST00000367641.3_Splice_Site|TEX35_ENST00000367643.3_Splice_Site|TEX35_ENST00000258298.2_Splice_Site|TEX35_ENST00000367642.3_3'UTR|TEX35_ENST00000367639.1_Splice_Site	NM_032126.4	NP_115502.2			testis expressed 35																		TCCTCCCCCAGTCCCCTTAGA	0.562																																					.		Atlas-SNP	.											.	TEX35	15	.	0			c.342-1G>C						.						29	31	30					1																	178489807		2203	4300	6503	SO:0001630	splice_region_variant	84066	exon7			CCCCCAGTCCCCT	AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"Testis-Specific Conserved gene 24kDa"		"chromosome 1 open reading frame 49"	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000319416.2:c.342-1G>C	chr1.hg19:g.178489807G>C		38.0	0.0		105.0	22.0	NM_001170724		Splice_Site	SNP	ENST00000319416.2	hg19	CCDS1323.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669926	0.47677	.	.	ENSG00000240021	ENST00000319416;ENST00000258298;ENST00000367643;ENST00000367641;ENST00000367639	.	.	.	4.09	4.09	0.47781	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.0039	0.53248	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C1orf49	176756430	0.795000	0.28851	0.996000	0.52242	0.413000	0.31143	2.432000	0.44784	2.284000	0.76573	0.536000	0.68110	.	.	.		0.562	TEX35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084917.1	NM_032126	Intron	C	178489807	G	C	178489807	5	2	98	1	0	0	0	0	0	0	1	0	2043	1043	36	4	391	4	C1orf49	1	178489807	Splice_Site	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	5931817	178489807	70760814	14	13376										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185950141	185950141	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agtgataaaggaacctatatTtgtgaagctgaaaaccagtt	9	5	0	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:185950141T>G	ENST00000271588.4	+	17	2827	c.2598T>G	c.(2596-2598)atT>atG	p.I866M	HMCN1_ENST00000367492.2_Missense_Mutation_p.I866M|HMCN1_ENST00000485744.1_3'UTR	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	866	Ig-like C2-type 5.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GAACCTATATTTGTGAAGCTG	0.388																																					p.I866M		Atlas-SNP	.											.	HMCN1	797	.	0			c.T2598G						.						156	163	161					1																	185950141		2203	4300	6503	SO:0001583	missense	83872	exon17			CTATATTTGTGAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.2598T>G	chr1.hg19:g.185950141T>G	ENSP00000271588:p.Ile866Met	64.0	0.0		204.0	51.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	19.29	3.798796	0.70567	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.30182	1.54;1.54	5.81	1.03	0.20045	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.228696	0.44483	D	0.000459	T	0.33265	0.0857	L	0.31294	0.92	0.37495	D	0.916531	P;D	0.76494	0.906;0.999	P;D	0.83275	0.704;0.996	T	0.31916	-0.9926	10	0.46703	T	0.11	.	2.5891	0.04838	0.1401:0.4117:0.1451:0.303	.	250;866	Q96RW7-3;Q96RW7	.;HMCN1_HUMAN	M	866	ENSP00000271588:I866M;ENSP00000356462:I866M	ENSP00000271588:I866M	I	+	3	3	HMCN1	184216764	0.985000	0.35326	0.997000	0.53966	0.997000	0.91878	0.162000	0.16501	0.144000	0.18951	0.533000	0.62120	ATT	.	.		0.388	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	185950141	T	G	185950141	3	3	98	1	0	0	0	0	1	0	0	0	7229	1829	64	5	2664	5	HMCN1	1	185950141	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	7460334	185950141	63300480	15	13377										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204408086	204408086	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctcatactcgtcctccccagGgttgtgtttctgcagccagt	9	14	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:204408086G>C	ENST00000367187.3	-	24	4049	c.3493C>G	c.(3493-3495)Cct>Gct	p.P1165A	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.P1137A	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1165	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TCCTCCCCAGGGTTGTGTTTC	0.592																																					p.P1165A		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C3493G						.						132	94	107					1																	204408086		2203	4300	6503	SO:0001583	missense	5287	exon24			CCCCAGGGTTGTG	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.3493C>G	chr1.hg19:g.204408086G>C	ENSP00000356155:p.Pro1165Ala	43.0	0.0		111.0	22.0	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	hg19	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	G	32	5.147449	0.94603	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.77229	-1.08;-1.08	5.5	5.5	0.81552	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.054940	0.85682	D	0.000000	D	0.86159	0.5866	L	0.54323	1.7	0.58432	D	0.999997	P;D	0.89917	0.863;1.0	P;D	0.87578	0.493;0.998	D	0.85599	0.1251	10	0.48119	T	0.1	.	18.9895	0.92786	0.0:0.0:1.0:0.0	.	1137;1165	F5GWN5;O00750	.;P3C2B_HUMAN	A	1165;1137	ENSP00000356155:P1165A;ENSP00000400561:P1137A	ENSP00000356155:P1165A	P	-	1	0	PIK3C2B	202674709	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.832000	0.99423	2.582000	0.87167	0.563000	0.77884	CCT	.	.		0.592	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		C	204408086	G	C	204408086	3	2	98	1	0	0	0	0	1	0	0	0	11919	1232	43	4	1455	4	PIK3C2B	1	204408086	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	18457945	204408086	44842535	16	13378										
DSTYK	25778	hgsc.bcm.edu	37	chr1	205180511	205180511	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gagcacttgatgtcgcggaaGaacttctgggtctcgcgcag	14	10	2	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:205180511G>A	ENST00000367162.3	-	1	183	c.153C>T	c.(151-153)ttC>ttT	p.F51F	DSTYK_ENST00000367160.4_Silent_p.F51F|DSTYK_ENST00000367161.3_Silent_p.F51F	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	51					cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						TGTCGCGGAAGAACTTCTGGG	0.701																																					p.F51F		Atlas-SNP	.											.	DSTYK	87	.	0			c.C153T						.						35	32	33					1																	205180511		2203	4300	6503	SO:0001819	synonymous_variant	25778	exon1			GCGGAAGAACTTC	AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"receptor interacting protein kinase 5"	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.153C>T	chr1.hg19:g.205180511G>A		8.0	0.0		30.0	12.0	NM_199462	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Silent	SNP	ENST00000367162.3	hg19	CCDS1451.1																																																																																			.	.		0.701	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375		A	205180511	G	A	205180511	2	1	98	1	0	0	0	0	0	0	0	1	4787	933	33	3		3	DSTYK	1	205180511	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	772425	205180511	44070110	17	13379										
RYR2	6262	hgsc.bcm.edu	37	chr1	237580423	237580423	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	actagagacgctaagagttgCgtaagtagaacttctaaaca	9	7	1	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:237580423C>T	ENST00000366574.2	+	11	1165	c.848C>T	c.(847-849)gCg>gTg	p.A283V	RYR2_ENST00000542537.1_Splice_Site_p.A267V|RYR2_ENST00000360064.6_Splice_Site_p.A281V	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	283					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CTAAGAGTTGCGTAAGTAGAA	0.453																																					p.A283V		Atlas-SNP	.											.	RYR2	1273	.	0			c.C848T						.						113	111	111					1																	237580423		2056	4222	6278	SO:0001630	splice_region_variant	6262	exon11			GAGTTGCGTAAGT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.848+1C>T	chr1.hg19:g.237580423C>T		57.0	0.0		177.0	68.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.786594	0.49997	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.87571	-2.27;-2.27;-2.27	5.98	5.98	0.97165	MIR (2);	0.090634	0.44097	D	0.000498	T	0.69797	0.3151	N	0.00926	-1.1	0.80722	D	1	B	0.15473	0.013	B	0.12156	0.007	T	0.67385	-0.5684	10	0.41790	T	0.15	.	15.8847	0.79238	0.0:0.8654:0.1346:0.0	.	283	Q92736	RYR2_HUMAN	V	283;281;267	ENSP00000355533:A283V;ENSP00000353174:A281V;ENSP00000443798:A267V	ENSP00000353174:A281V	A	+	2	0	RYR2	235647046	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	2.252000	0.43196	2.835000	0.97688	0.650000	0.86243	GCG	.	.		0.453	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	Missense_Mutation	T	237580423	C	T	237580423	5	4	98	1	0	0	0	0	0	0	1	0	13784	782	27	1	890	1	RYR2	1	237580423	Splice_Site	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	32399912	237580423	11670198	18	13380										
RYR2	6262	hgsc.bcm.edu	37	chr1	237972285	237972285	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ttttccgaaaattctacaatAaaagtgaagatggtgataca	7	5	1	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr1:237972285A>G	ENST00000366574.2	+	100	14700	c.14383A>G	c.(14383-14385)Aaa>Gaa	p.K4795E	RYR2_ENST00000542537.1_Missense_Mutation_p.K4779E|RYR2_ENST00000360064.6_Missense_Mutation_p.K4801E	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4795					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATTCTACAATAAAAGTGAAGA	0.353																																					p.K4795E		Atlas-SNP	.											.	RYR2	1273	.	0			c.A14383G						.						244	238	240					1																	237972285		1845	4084	5929	SO:0001583	missense	6262	exon100			TACAATAAAAGTG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.14383A>G	chr1.hg19:g.237972285A>G	ENSP00000355533:p.Lys4795Glu	101.0	0.0		308.0	133.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.323155	0.81580	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000536033	D;D;D	0.92397	-3.03;-3.03;-3.03	4.88	4.88	0.63580	Ion transport (1);	0.000000	0.64402	U	0.000016	D	0.93475	0.7918	L	0.37630	1.12	0.54753	D	0.999983	P;D	0.69078	0.904;0.997	P;D	0.77004	0.615;0.989	D	0.93994	0.7269	10	0.56958	D	0.05	.	14.7797	0.69756	1.0:0.0:0.0:0.0	.	228;4795	F5H3C7;Q92736	.;RYR2_HUMAN	E	4795;4801;4779;228	ENSP00000355533:K4795E;ENSP00000353174:K4801E;ENSP00000443798:K4779E	ENSP00000353174:K4801E	K	+	1	0	RYR2	236038908	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.287000	0.95975	1.953000	0.56701	0.460000	0.39030	AAA	.	.		0.353	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237972285	A	G	237972285	3	3	98	1	0	0	0	0	1	0	0	0	13784	363	13	2	14781	2	RYR2	1	237972285	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	391862	237972285	11278336	19	13381										
ASAP2	8853	hgsc.bcm.edu	37	chr2	9528600	9528601	+	Frame_Shift_Ins	INS	-	-	G													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cggagccctcctgagtggcaINSgcccacctcccgcccagcct							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr2:9528600_9528601insG	ENST00000281419.3	+	22	2648_2649	c.2308_2309insG	c.(2308-2310)agcfs	p.S770fs	ASAP2_ENST00000315273.4_Frame_Shift_Ins_p.S770fs|ASAP2_ENST00000491413.1_3'UTR	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	770					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						CCTGAGTGGCAGCCCACCTCCC	0.604																																					p.S770fs		Atlas-INDEL	.											.	ASAP2	91	.	0			c.2308_2309insG						.																																			SO:0001589	frameshift_variant	8853	exon22			.	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2309dupG	chr2.hg19:g.9528601_9528601dupG	ENSP00000281419:p.Ser770fs	43.0	0.0		129.0	12.0	NM_001135191	D6W4Y8	Frame_Shift_Ins	INS	ENST00000281419.3	hg19	CCDS1661.1																																																																																			.	.		0.604	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		G	9528601	-	G	9528600	7	5	98	1	0	1	1	0	0	0	0	0	1011	188	7	0	2394	0	ASAP2	2	9528600	Frame_Shift_Ins	INS	-	TCGA-DD-A1EB-01A-11D-A12Z-10		9528600	233670773	20	13382										
PREB	10113	hgsc.bcm.edu	37	chr2	27355507	27355507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ggtaaggtgtgctggaaaagGtgggtccattttcttgccag	15	6	1	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr2:27355507G>A	ENST00000260643.2	-	5	969	c.716C>T	c.(715-717)aCc>aTc	p.T239I	PREB_ENST00000416802.1_5'Flank|PREB_ENST00000406567.3_Missense_Mutation_p.T239I	NM_013388.4	NP_037520.1	Q9HCU5	PREB_HUMAN	prolactin regulatory element binding	239					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTGGAAAAGGTGGGTCCATT	0.557																																					p.T239I		Atlas-SNP	.											.	PREB	37	.	0			c.C716T						.						111	104	106					2																	27355507		2203	4300	6503	SO:0001583	missense	10113	exon5			GAAAAGGTGGGTC		CCDS1738.1	2p23	2013-01-10			ENSG00000138073	ENSG00000138073		"WD repeat domain containing"	9356	protein-coding gene	gene with protein product		606395				10194769, 12735795	Standard	NM_013388		Approved	SEC12	uc002rix.1	Q9HCU5	OTTHUMG00000097076	ENST00000260643.2:c.716C>T	chr2.hg19:g.27355507G>A	ENSP00000260643:p.Thr239Ile	62.0	0.0		191.0	61.0	NM_013388	Q53SZ8|Q9UH94	Missense_Mutation	SNP	ENST00000260643.2	hg19	CCDS1738.1	.	.	.	.	.	.	.	.	.	.	G	6.445	0.450330	0.12223	.	.	ENSG00000138073	ENST00000260643;ENST00000406567;ENST00000546336	T;T	0.79749	1.6;-1.3	5.76	3.91	0.45181	Quinonprotein alcohol dehydrogenase-like (1);	0.367176	0.32068	N	0.006631	T	0.65831	0.2729	N	0.19112	0.55	0.09310	N	1	B;B	0.23735	0.09;0.09	B;B	0.16289	0.015;0.015	T	0.57335	-0.7829	10	0.52906	T	0.07	-6.3764	9.2763	0.37700	0.0:0.1586:0.6765:0.1649	.	239;239	B5MC98;Q9HCU5	.;PREB_HUMAN	I	239	ENSP00000260643:T239I;ENSP00000384032:T239I	ENSP00000260643:T239I	T	-	2	0	PREB	27209011	0.717000	0.27966	0.950000	0.38849	0.501000	0.33797	0.779000	0.26746	0.739000	0.32628	0.655000	0.94253	ACC	.	.		0.557	PREB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214195.1	NM_013388		A	27355507	G	A	27355507	3	1	98	1	0	0	0	0	1	0	0	0	12482	1261	44	3	557	3	PREB	2	27355507	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	17826907	27355507	215843866	21	13383										
RBKS	64080	hgsc.bcm.edu	37	chr2	28065967	28065967	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ggccattgttagggcttccaAagaagttgctggagttattt	12	6	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr2:28065967A>G	ENST00000302188.3	-	5	1233	c.481T>C	c.(481-483)Ttg>Ctg	p.L161L	RBKS_ENST00000444339.2_Silent_p.L161L	NM_022128.1	NP_071411.1	Q9H477	RBSK_HUMAN	ribokinase	161					D-ribose catabolic process (GO:0019303)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ribokinase activity (GO:0004747)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(172;0.155)					AGGGCTTCCAAAGAAGTTGCT	0.403																																					p.L161L		Atlas-SNP	.											.	RBKS	23	.	0			c.T481C						.						85	85	85					2																	28065967		2203	4300	6503	SO:0001819	synonymous_variant	64080	exon5			CTTCCAAAGAAGT	BC017425	CCDS1762.1	2p23.3	2008-02-05			ENSG00000171174	ENSG00000171174	2.7.1.15		30325	protein-coding gene	gene with protein product		611132				8382990	Standard	NM_022128		Approved	DKFZp686G13268, RBSK	uc002rlo.1	Q9H477	OTTHUMG00000097833	ENST00000302188.3:c.481T>C	chr2.hg19:g.28065967A>G		56.0	0.0		151.0	44.0	NM_022128	A9UK04|B4DV96	Silent	SNP	ENST00000302188.3	hg19	CCDS1762.1	.	.	.	.	.	.	.	.	.	.	A	9.462	1.093234	0.20471	.	.	ENSG00000171174	ENST00000458185	.	.	.	5.87	-2.38	0.06622	.	.	.	.	.	T	0.58264	0.2110	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58064	-0.7702	4	.	.	.	-10.3574	12.4755	0.55811	0.3923:0.0:0.6077:0.0	.	.	.	.	S	21	.	.	F	-	2	0	RBKS	27919471	1.000000	0.71417	0.993000	0.49108	0.966000	0.64601	0.780000	0.26760	-0.226000	0.09899	-1.003000	0.02500	TTT	.	.		0.403	RBKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215118.1	NM_022128		G	28065967	A	G	28065967	2	3	98	1	0	0	0	0	0	0	0	1	13123	11	1	2		2	RBKS	2	28065967	Silent	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	710460	28065967	215133406	22	13384										
NPAS2	4862	hgsc.bcm.edu	37	chr2	101554302	101554302	+	Frame_Shift_Del	DEL	C	C	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cgcctctccttgggcatttaCcggtgagtttccactccaat							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr2:101554302delC	ENST00000335681.5	+	5	646	c.361delC	c.(361-363)ccgfs	p.P121fs	NPAS2_ENST00000486017.1_3'UTR|NPAS2_ENST00000542504.1_Frame_Shift_Del_p.P186fs	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	121	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TGGGCATTTACCGGTGAGTTT	0.488																																					p.L120fs		Atlas-Indel,Pindel	.											.	NPAS2	88	.	0			c.360delA						.						219	189	199					2																	101554302		2203	4300	6503	SO:0001589	frameshift_variant	4862	exon5			.	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"Basic helix-loop-helix proteins"	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.361delC	chr2.hg19:g.101554302delC	ENSP00000338283:p.Pro121fs	71.0	0.0		222.0	97.0	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Frame_Shift_Del	DEL	ENST00000335681.5	hg19	CCDS2048.1																																																																																			.	.		0.488	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3			-	101554302	C	-	101554302	7	5	98	1	0	1	0	1	0	0	0	0	10572	507	18	0	375	0	NPAS2	2	101554302	Frame_Shift_Del	DEL	C	TCGA-DD-A1EB-01A-11D-A12Z-10	73488335	101554302	141645071	23	13385										
TTN	7273	hgsc.bcm.edu	37	chr2	179475909	179475909	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	atgccaactaacagttggaaCtgggacagctctgaagggaa	12	8	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr2:179475909C>G	ENST00000591111.1	-	220	46248	c.46024G>C	c.(46024-46026)Gtt>Ctt	p.V15342L	TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V8043L|TTN_ENST00000460472.2_Missense_Mutation_p.V7918L|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V16983L|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V14415L|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V8110L|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15342	Ig-like 97.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACAGTTGGAACTGGGACAGCT	0.393																																					p.V16983L		Atlas-SNP	.											.	TTN	18412	.	0			c.G50947C						.						107	104	105					2																	179475909		1888	4117	6005	SO:0001583	missense	7273	exon270			TTGGAACTGGGAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.46024G>C	chr2.hg19:g.179475909C>G	ENSP00000465570:p.Val15342Leu	64.0	0.0		151.0	77.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.559	1.118017	0.20877	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.56	3.64	0.41730	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.45296	0.1335	N	0.04746	-0.17	0.25892	N	0.983461	B;B;B;B	0.16802	0.019;0.019;0.019;0.019	B;B;B;B	0.22152	0.038;0.038;0.038;0.038	T	0.33240	-0.9876	9	0.87932	D	0	.	8.6238	0.33877	0.223:0.6945:0.0:0.0824	.	7918;8043;8110;15342	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	14415;7918;8110;8043;7918	ENSP00000343764:V14415L;ENSP00000434586:V7918L;ENSP00000340554:V8110L;ENSP00000352154:V8043L	ENSP00000340554:V8110L	V	-	1	0	TTN	179184154	0.905000	0.30787	1.000000	0.80357	0.986000	0.74619	0.430000	0.21428	2.777000	0.95525	0.591000	0.81541	GTT	.	.		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179475909	C	G	179475909	3	3	98	1	0	0	0	0	1	0	0	0	16750	565	20	4	57118	4	TTN	2	179475909	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	77921607	179475909	63723464	24	13386										
EOMES	8320	hgsc.bcm.edu	37	chr3	27758974	27758974	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctgaaggggcaaggatttaaTgccatatgggagcaatgtgc	14	6	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr3:27758974T>A	ENST00000295743.4	-	6	1851	c.1648A>T	c.(1648-1650)Att>Ttt	p.I550F	EOMES_ENST00000537516.1_Missense_Mutation_p.I274F|EOMES_ENST00000461503.1_5'Flank|EOMES_ENST00000449599.1_Missense_Mutation_p.I569F			O95936	EOMES_HUMAN	eomesodermin	550					brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						AAGGATTTAATGCCATATGGG	0.517																																					p.I550F		Atlas-SNP	.											.	EOMES	65	.	0			c.A1648T						.						104	108	106					3																	27758974		2203	4300	6503	SO:0001583	missense	8320	exon6			ATTTAATGCCATA	BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"T-boxes"	3372	protein-coding gene	gene with protein product	"T-box brain2"	604615	"eomesodermin (Xenopus laevis) homolog"			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.1648A>T	chr3.hg19:g.27758974T>A	ENSP00000295743:p.Ile550Phe	66.0	0.0		187.0	67.0	NM_005442	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Missense_Mutation	SNP	ENST00000295743.4	hg19	CCDS2646.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.818918	0.32145	.	.	ENSG00000163508	ENST00000295743;ENST00000449599;ENST00000537516;ENST00000535713	D;D;D	0.86230	-2.04;-2.09;-1.78	4.72	3.57	0.40892	.	0.165611	0.52532	D	0.000069	T	0.79364	0.4433	L	0.31065	0.9	0.58432	D	0.999999	B;B;B	0.23058	0.001;0.079;0.047	B;B;B	0.25884	0.004;0.064;0.029	T	0.72896	-0.4153	10	0.37606	T	0.19	.	10.5323	0.44983	0.0:0.0778:0.0:0.9222	.	283;569;550	B7Z4I2;G3XAI5;O95936	.;.;EOMES_HUMAN	F	550;569;274;434	ENSP00000295743:I550F;ENSP00000388620:I569F;ENSP00000442097:I274F	ENSP00000295743:I550F	I	-	1	0	EOMES	27733978	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	5.895000	0.69814	0.915000	0.36847	0.383000	0.25322	ATT	.	.		0.517	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442		A	27758974	T	A	27758974	3	1	98	1	0	0	0	0	1	0	0	0	5149	1464	51	4	416	4	EOMES	3	27758974	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10		27758974	170263456	25	13387										
APPL1	26060	hgsc.bcm.edu	37	chr3	57283493	57283493	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gtagcaggaggcctggccatGgacatagacaactgttcagt	13	9	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr3:57283493G>T	ENST00000288266.3	+	11	1116	c.969G>T	c.(967-969)atG>atT	p.M323I		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	323	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.|Required for RAB5A binding.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)			breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		GCCTGGCCATGGACATAGACA	0.458																																					p.M323I		Atlas-SNP	.											.	APPL1	59	.	0			c.G969T						.						155	141	146					3																	57283493		2203	4300	6503	SO:0001583	missense	26060	exon11			GGCCATGGACATA	AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"Pleckstrin homology (PH) domain containing"	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.969G>T	chr3.hg19:g.57283493G>T	ENSP00000288266:p.Met323Ile	77.0	0.0		162.0	66.0	NM_012096	Q9P2B9	Missense_Mutation	SNP	ENST00000288266.3	hg19	CCDS2882.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.536840	0.45176	.	.	ENSG00000157500	ENST00000288266	T	0.33654	1.4	6.06	6.06	0.98353	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.038358	0.85682	D	0.000000	T	0.37265	0.0997	L	0.49126	1.545	0.58432	D	0.999998	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.002	T	0.10847	-1.0612	10	0.21540	T	0.41	.	20.6397	0.99537	0.0:0.0:1.0:0.0	.	306;323	B4DQX8;Q9UKG1	.;DP13A_HUMAN	I	323	ENSP00000288266:M323I	ENSP00000288266:M323I	M	+	3	0	APPL1	57258533	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.565000	0.67365	2.880000	0.98712	0.650000	0.86243	ATG	.	.		0.458	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096		T	57283493	G	T	57283493	3	4	98	1	0	0	0	0	1	0	0	0	817	1348	47	3	1011	3	APPL1	3	57283493	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	29524519	57283493	140738937	26	13388										
OSBPL11	114885	hgsc.bcm.edu	37	chr3	125295107	125295107	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ttgcagtttggaatgtccaaCattaaaaaaagaaatggcat	8	5	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr3:125295107C>A	ENST00000296220.5	-	5	881	c.592G>T	c.(592-594)Gtt>Ttt	p.V198F		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	198					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						GAATGTCCAACATTAAAAAAA	0.378																																					p.V198F		Atlas-SNP	.											.	OSBPL11	64	.	0			c.G592T						.						127	131	130					3																	125295107		2203	4300	6503	SO:0001583	missense	114885	exon5			GTCCAACATTAAA	AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.592G>T	chr3.hg19:g.125295107C>A	ENSP00000296220:p.Val198Phe	84.0	0.0		196.0	74.0	NM_022776	A8K9I7	Missense_Mutation	SNP	ENST00000296220.5	hg19	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.925542	0.52759	.	.	ENSG00000144909	ENST00000296220	T	0.46819	0.86	5.06	5.06	0.68205	.	0.555483	0.18719	N	0.133080	T	0.35098	0.0920	L	0.48642	1.525	0.46654	D	0.999146	P	0.45902	0.868	B	0.30251	0.113	T	0.25745	-1.0123	10	0.29301	T	0.29	-17.4662	14.3282	0.66534	0.0:0.8519:0.1481:0.0	.	198	Q9BXB4	OSB11_HUMAN	F	198	ENSP00000296220:V198F	ENSP00000296220:V198F	V	-	1	0	OSBPL11	126777797	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.424000	0.59868	2.645000	0.89757	0.552000	0.68991	GTT	.	.		0.378	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		A	125295107	C	A	125295107	3	1	98	1	0	0	0	0	1	0	0	0	11285	478	17	3	1687	3	OSBPL11	3	125295107	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	68011614	125295107	72727323	27	13389										
PLOD2	5352	hgsc.bcm.edu	37	chr3	145828234	145828234	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	accagcaaatatgacatcaaAgctgttcaatgaggaaaaaa	7	7	2	2	rs376517611		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr3:145828234A>G	ENST00000360060.3	-	4	517	c.340T>C	c.(340-342)Ttt>Ctt	p.F114L	PLOD2_ENST00000494950.1_Splice_Site_p.F59L|PLOD2_ENST00000282903.5_Splice_Site_p.F114L	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	114					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	ATGACATCAAAGCTGTTCAAT	0.358																																					p.F114L		Atlas-SNP	.											.	PLOD2	81	.	0			c.T340C						.						77	77	77					3																	145828234		2203	4300	6503	SO:0001630	splice_region_variant	5352	exon4			CATCAAAGCTGTT	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"lysyl hydroxlase 2"	601865	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.339-1T>C	chr3.hg19:g.145828234A>G		61.0	0.0		109.0	47.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	hg19	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	A	19.50	3.839074	0.71373	.	.	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000494950;ENST00000469350	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	5.0	5.0	0.66597	.	0.058788	0.64402	D	0.000001	T	0.14227	0.0344	L	0.34521	1.04	0.48696	D	0.999693	B;B;B	0.22909	0.055;0.077;0.064	B;B;B	0.28916	0.033;0.066;0.096	T	0.04413	-1.0953	10	0.72032	D	0.01	-41.3085	14.7082	0.69208	1.0:0.0:0.0:0.0	.	59;114;114	E7ETU9;O00469;O00469-2	.;PLOD2_HUMAN;.	L	114;114;59;86	ENSP00000282903:F114L;ENSP00000353170:F114L;ENSP00000420094:F59L;ENSP00000419963:F86L	ENSP00000282903:F114L	F	-	1	0	PLOD2	147310924	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	8.597000	0.90847	1.872000	0.54250	0.377000	0.23210	TTT	.	.		0.358	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	Missense_Mutation	G	145828234	A	G	145828234	5	3	98	1	0	0	0	0	0	0	1	0	12111	86	3	2	2004	2	PLOD2	3	145828234	Splice_Site	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	20533127	145828234	52194196	28	13390										
MLF1	4291	hgsc.bcm.edu	37	chr3	158322940	158322940	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ggaaggagatcaaatgttttGggggacaaactccacatcaa	11	7	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr3:158322940G>C	ENST00000355893.5	+	7	894	c.756G>C	c.(754-756)ttG>ttC	p.L252F	MLF1_ENST00000469452.1_Missense_Mutation_p.L184F|MLF1_ENST00000359117.5_Missense_Mutation_p.L227F|MLF1_ENST00000471745.1_Missense_Mutation_p.L242F|MLF1_ENST00000484955.1_Missense_Mutation_p.L227F|MLF1_ENST00000482628.1_Missense_Mutation_p.L227F|MLF1_ENST00000478894.2_Missense_Mutation_p.L242F|MLF1_ENST00000497004.1_3'UTR|MLF1_ENST00000392822.3_Missense_Mutation_p.L283F	NM_022443.4	NP_071888.1	P58340	MLF1_HUMAN	myeloid leukemia factor 1	252					cell cycle arrest (GO:0007050)|myeloid progenitor cell differentiation (GO:0002318)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)			large_intestine(3)	3		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)			CAAATGTTTTGGGGGACAAAC	0.333			T	NPM1	AML																																p.L283F		Atlas-SNP	.		Dom	yes		3	3q25.1	4291	myeloid leukemia factor 1		L	.	MLF1	62	.	0			c.G849C						.						69	73	72					3																	158322940		2203	4300	6503	SO:0001583	missense	4291	exon9			TGTTTTGGGGGAC	L49054	CCDS3182.1, CCDS46945.1, CCDS56286.1, CCDS56287.1, CCDS56288.1	3q25	2008-07-18			ENSG00000178053	ENSG00000178053			7125	protein-coding gene	gene with protein product	"myeloid leukemia factor 1 variant 1", "myeloid leukemia factor 1 variant 2", "myeloid leukemia factor 1 variant 3"	601402				8570204	Standard	NM_022443		Approved		uc003fcb.3	P58340	OTTHUMG00000158775	ENST00000355893.5:c.756G>C	chr3.hg19:g.158322940G>C	ENSP00000348157:p.Leu252Phe	102.0	0.0		267.0	119.0	NM_001195432	E9PEU9|Q2TLE3|Q2TLE5|Q8N8F8|Q96MH1	Missense_Mutation	SNP	ENST00000355893.5	hg19	CCDS3182.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.560334	0.00910	.	.	ENSG00000178053	ENST00000491767;ENST00000355893;ENST00000484955;ENST00000359117;ENST00000471745;ENST00000469452;ENST00000482628;ENST00000478894;ENST00000392822	T;T;T;T;T;T;T;T;T	0.43688	1.0;1.02;1.02;1.02;1.01;1.02;1.02;1.01;0.94	5.47	3.1	0.35709	.	0.617004	0.15501	N	0.259020	T	0.14141	0.0342	N	0.01874	-0.695	0.21473	N	0.999671	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.30621	-0.9972	10	0.08179	T	0.78	-1.7527	6.4442	0.21867	0.0:0.0832:0.1659:0.7509	.	184;283;252	Q2TLE5;Q8N8F8;P58340	.;.;MLF1_HUMAN	F	178;252;227;227;242;184;227;242;283	ENSP00000420410:L178F;ENSP00000348157:L252F;ENSP00000417835:L227F;ENSP00000352025:L227F;ENSP00000420134:L242F;ENSP00000418595:L184F;ENSP00000417141:L227F;ENSP00000417777:L242F;ENSP00000376568:L283F	ENSP00000348157:L252F	L	+	3	2	MLF1	159805634	0.998000	0.40836	0.468000	0.27192	0.013000	0.08279	1.858000	0.39408	0.386000	0.24997	-0.485000	0.04761	TTG	.	.		0.333	MLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352164.3	NM_022443		C	158322940	G	C	158322940	3	2	98	1	0	0	0	0	1	0	0	0	9623	1339	47	4	782	4	MLF1	3	158322940	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	12494706	158322940	39699490	29	13391										
IL12A	3592	hgsc.bcm.edu	37	chr3	159708075	159708075	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cactcccaaaacctgctgagGgccgtcagcaacatgctcca	8	16	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr3:159708075G>T	ENST00000305579.2	+	2	547	c.240G>T	c.(238-240)agG>agT	p.R80S	IL12A_ENST00000466512.1_Missense_Mutation_p.R80S|IL12A-AS1_ENST00000497452.1_RNA|IL12A_ENST00000480787.1_Missense_Mutation_p.R80S	NM_000882.3	NP_000873.2	P29459	IL12A_HUMAN	interleukin 12A	46					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cell adhesion (GO:0045785)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|response to lipopolysaccharide (GO:0032496)|response to UV-B (GO:0010224)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)	interleukin-12 beta subunit binding (GO:0042163)|interleukin-12 receptor binding (GO:0005143)|interleukin-27 binding (GO:0045513)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)	9			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ACCTGCTGAGGGCCGTCAGCA	0.602																																					p.R80S		Atlas-SNP	.											.	IL12A	23	.	0			c.G240T						.						108	97	101					3																	159708075		2203	4300	6503	SO:0001583	missense	3592	exon2			GCTGAGGGCCGTC	M65271	CCDS3187.1	3q25.33	2014-04-04	2014-04-04		ENSG00000168811	ENSG00000168811		"Interleukins and interleukin receptors"	5969	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor 1, 35 kD subunit", "cytotoxic lymphocyte maturation factor 1, p35", "interleukin 12, p35", "IL-12, subunit p35", "NF cell stimulatory factor chain 1", "interleukin-12 alpha chain", "IL35 subunit"	161560	"interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35)"	NKSF1		1673147	Standard	NM_000882		Approved	CLMF, IL-12A, p35, NFSK	uc003fcx.3	P29459	OTTHUMG00000158942	ENST00000305579.2:c.240G>T	chr3.hg19:g.159708075G>T	ENSP00000303231:p.Arg80Ser	45.0	0.0		142.0	40.0	NM_000882	Q96QZ1	Missense_Mutation	SNP	ENST00000305579.2	hg19	CCDS3187.1	.	.	.	.	.	.	.	.	.	.	G	11.23	1.578661	0.28180	.	.	ENSG00000168811	ENST00000305579;ENST00000480787;ENST00000466512	.	.	.	4.72	-3.89	0.04193	.	1.413900	0.03810	N	0.265822	T	0.30103	0.0754	L	0.43152	1.355	0.09310	N	1	B	0.30114	0.269	B	0.22601	0.04	T	0.11717	-1.0576	9	0.35671	T	0.21	0.0114	5.4577	0.16600	0.4687:0.2656:0.2657:0.0	.	80	O60595	.	S	80	.	ENSP00000303231:R80S	R	+	3	2	IL12A	161190769	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.410000	0.07151	-0.981000	0.03520	-0.291000	0.09656	AGG	.	.		0.602	IL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352602.2	NM_000882		T	159708075	G	T	159708075	3	4	98	1	0	0	0	0	1	0	0	0	7633	1223	43	3	246	3	IL12A	3	159708075	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	1385135	159708075	38314355	30	13392										
TTC14	151613	hgsc.bcm.edu	37	chr3	180325533	180325533	+	Frame_Shift_Del	DEL	A	A	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	atgcagaggatgctttgcagAaacttcataaatatatgcag							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr3:180325533delA	ENST00000296015.4	+	10	1402	c.1270delA	c.(1270-1272)aaafs	p.K424fs	TTC14_ENST00000382584.4_Frame_Shift_Del_p.K424fs|TTC14_ENST00000412756.2_Frame_Shift_Del_p.K424fs	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	424							RNA binding (GO:0003723)			endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TGCTTTGCAGAAACTTCATAA	0.308																																					p.Q423fs		Atlas-Indel,Pindel	.											.	TTC14	112	.	0			c.1269delG						.						70	78	75					3																	180325533		2202	4295	6497	SO:0001589	frameshift_variant	151613	exon10			.	AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"Tetratricopeptide (TTC) repeat domain containing"	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.1270delA	chr3.hg19:g.180325533delA	ENSP00000296015:p.Lys424fs	97.0	0.0		238.0	102.0	NM_001042601	G5E9X0|Q6UWJ7|Q8TF22	Frame_Shift_Del	DEL	ENST00000296015.4	hg19	CCDS3237.1																																																																																			.	.		0.308	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462		-	180325533	A	-	180325533	7	5	98	1	0	1	0	1	0	0	0	0	16696	247	9	0	1308	0	TTC14	3	180325533	Frame_Shift_Del	DEL	A	TCGA-DD-A1EB-01A-11D-A12Z-10	20617458	180325533	17696897	31	13393										
MCCC1	56922	hgsc.bcm.edu	37	chr3	182756877	182756877	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tggcgatctgctgcccacacGaccagcttcgcaatcatggg	11	14	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr3:182756877G>C	ENST00000265594.4	-	12	1460	c.1314C>G	c.(1312-1314)gtC>gtG	p.V438V	MCCC1_ENST00000489909.1_5'Flank|MCCC1_ENST00000539926.1_Silent_p.V303V|MCCC1_ENST00000492597.1_Silent_p.V329V	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	438	Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	CTGCCCACACGACCAGCTTCG	0.483																																					p.V438V		Atlas-SNP	.											.	MCCC1	87	.	0			c.C1314G						.						130	110	117					3																	182756877		2203	4300	6503	SO:0001819	synonymous_variant	56922	exon12			CCACACGACCAGC	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1314C>G	chr3.hg19:g.182756877G>C		70.0	0.0		194.0	89.0	NM_020166	Q59ES4|Q9H959|Q9NS97	Silent	SNP	ENST00000265594.4	hg19	CCDS3241.1																																																																																			.	.		0.483	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		C	182756877	G	C	182756877	2	2	98	1	0	0	0	0	0	0	0	1	9383	1045	37	4		4	MCCC1	3	182756877	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	2431344	182756877	15265553	32	13394										
CLDN1	9076	hgsc.bcm.edu	37	chr3	190030689	190030689	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agaaatatcgcacccccaatGacagccatcctcatcttctg	5	15	3	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr3:190030689G>T	ENST00000295522.3	-	2	628	c.360C>A	c.(358-360)gtC>gtA	p.V120V		NM_021101.4	NP_066924.1	O95832	CLD1_HUMAN	claudin 1	120					calcium-independent cell-cell adhesion (GO:0016338)|cell adhesion (GO:0007155)|cell-cell junction organization (GO:0045216)|establishment of skin barrier (GO:0061436)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			lung(9)	9	all_cancers(143;2.95e-10)|Ovarian(172;0.0512)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.015)		CACCCCCAATGACAGCCATCC	0.478																																					p.V120V		Atlas-SNP	.											.	CLDN1	23	.	0			c.C360A						.						244	201	216					3																	190030689		2203	4300	6503	SO:0001819	synonymous_variant	9076	exon2			CCCAATGACAGCC	AF101051	CCDS3295.1	3q28-q29	2008-07-18			ENSG00000163347	ENSG00000163347		"Claudins"	2032	protein-coding gene	gene with protein product	"senescence-associated epithelial membrane protein 1"	603718				10828592, 9892664	Standard	NM_021101		Approved	SEMP1, ILVASC	uc003fsh.3	O95832	OTTHUMG00000156214	ENST00000295522.3:c.360C>A	chr3.hg19:g.190030689G>T		67.0	0.0		155.0	53.0	NM_021101		Silent	SNP	ENST00000295522.3	hg19	CCDS3295.1																																																																																			.	.		0.478	CLDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343516.2	NM_021101		T	190030689	G	T	190030689	2	4	98	1	0	0	0	0	0	0	0	1	3473	1277	45	3		3	CLDN1	3	190030689	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	7273812	190030689	7991741	33	13395										
LRCH3	84859	hgsc.bcm.edu	37	chr3	197592314	197592314	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agtgatgacagacctaatgcTctattaagttcacctgcaac	7	10	2	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr3:197592314T>C	ENST00000425562.2	+	16	1737	c.1737T>C	c.(1735-1737)gcT>gcC	p.A579A	LRCH3_ENST00000334859.4_Silent_p.A579A|LRCH3_ENST00000414675.2_Silent_p.A527A|LRCH3_ENST00000441090.2_Silent_p.A425A|LRCH3_ENST00000438796.2_Silent_p.A579A|LRCH3_ENST00000536618.1_Silent_p.A174A			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	579						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		GACCTAATGCTCTATTAAGTT	0.264																																					p.A579A		Atlas-SNP	.											.	LRCH3	96	.	0			c.T1737C						.						39	38	39					3																	197592314		2203	4300	6503	SO:0001819	synonymous_variant	84859	exon16			TAATGCTCTATTA	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1737T>C	chr3.hg19:g.197592314T>C		107.0	0.0		253.0	93.0	NM_032773	B4E0T7|Q96FP9|Q9NT52	Silent	SNP	ENST00000425562.2	hg19																																																																																				.	.		0.264	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773		C	197592314	T	C	197592314	2	2	98	1	0	0	0	0	0	0	0	1	8943	1538	54	2		2	LRCH3	3	197592314	Silent	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	7561625	197592314	430116	34	13396										
KCTD8	386617	hgsc.bcm.edu	37	chr4	44176879	44176879	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ggaaaataatctggaatgtgGatttttttaaaatcctgaat	8	3	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr4:44176879G>A	ENST00000360029.3	-	2	1633	c.1350C>T	c.(1348-1350)atC>atT	p.I450I		NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	450					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						CTGGAATGTGGATTTTTTTAA	0.378										HNSCC(17;0.042)																											p.I450I		Atlas-SNP	.											.	KCTD8	96	.	0			c.C1350T						.						125	133	130					4																	44176879		2203	4300	6503	SO:0001819	synonymous_variant	386617	exon2			AATGTGGATTTTT	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.1350C>T	chr4.hg19:g.44176879G>A		93.0	0.0		210.0	98.0	NM_198353	A2RU39	Silent	SNP	ENST00000360029.3	hg19	CCDS3467.1																																																																																			.	.		0.378	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			A	44176879	G	A	44176879	2	1	98	1	0	0	0	0	0	0	0	1	8124	1164	41	3		3	KCTD8	4	44176879	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10		44176879	146977397	35	13397										
GABRA4	2557	hgsc.bcm.edu	37	chr4	46967062	46967062	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgagggggctttgatgtcttCcttttggctttttccatttg	11	7	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr4:46967062C>A	ENST00000264318.3	-	8	2041	c.1059G>T	c.(1057-1059)agG>agT	p.R353S		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	353					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TTGATGTCTTCCTTTTGGCTT	0.458																																					p.R353S	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											.	GABRA4	129	.	0			c.G1059T						.						113	115	114					4																	46967062		2203	4299	6502	SO:0001583	missense	2557	exon8			TGTCTTCCTTTTG		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4078	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 4"	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.1059G>T	chr4.hg19:g.46967062C>A	ENSP00000264318:p.Arg353Ser	165.0	0.0		620.0	230.0	NM_000809	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	hg19	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.569578	0.65765	.	.	ENSG00000109158	ENST00000264318	D	0.86366	-2.11	4.81	3.95	0.45737	Neurotransmitter-gated ion-channel transmembrane domain (2);	2.432470	0.01856	N	0.036295	D	0.86694	0.5994	L	0.37800	1.135	0.43199	D	0.995048	B	0.30361	0.277	B	0.38655	0.278	T	0.67217	-0.5726	10	0.38643	T	0.18	.	12.5658	0.56308	0.0:0.918:0.0:0.082	.	353	P48169	GBRA4_HUMAN	S	353	ENSP00000264318:R353S	ENSP00000264318:R353S	R	-	3	2	GABRA4	46661819	0.995000	0.38212	0.998000	0.56505	0.851000	0.48451	3.224000	0.51238	2.481000	0.83766	0.591000	0.81541	AGG	.	.		0.458	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			A	46967062	C	A	46967062	3	1	98	1	0	0	0	0	1	0	0	0	6171	854	30	3	613	3	GABRA4	4	46967062	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	2790183	46967062	144187214	36	13398										
CORIN	10699	hgsc.bcm.edu	37	chr4	47746441	47746441	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgctttccgttttcctgctgAggtgagaagcaaattctgct	10	9	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr4:47746441A>C	ENST00000273857.4	-	5	776	c.777T>G	c.(775-777)ccT>ccG	p.P259P	CORIN_ENST00000502252.1_Silent_p.P192P|CORIN_ENST00000505909.1_Silent_p.P259P|CORIN_ENST00000508498.1_Silent_p.P120P|CORIN_ENST00000504584.1_Silent_p.P259P	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	259	FZ 1. {ECO:0000255|PROSITE- ProRule:PRU00090}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						TTTCCTGCTGAGGTGAGAAGC	0.393																																					p.P259P		Atlas-SNP	.											.	CORIN	154	.	0			c.T777G						.						166	167	166					4																	47746441		2203	4300	6503	SO:0001819	synonymous_variant	10699	exon5			CTGCTGAGGTGAG	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"Serine peptidases / Transmembrane"	19012	protein-coding gene	gene with protein product		605236	"corin, serine protease"			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.777T>G	chr4.hg19:g.47746441A>C		61.0	0.0		127.0	41.0	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Silent	SNP	ENST00000273857.4	hg19	CCDS3477.1																																																																																			.	.		0.393	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2			C	47746441	A	C	47746441	2	2	98	1	0	0	0	0	0	0	0	1	3754	291	11	5		5	CORIN	4	47746441	Silent	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	779379	47746441	143407835	37	13399										
SMR3A	26952	hgsc.bcm.edu	37	chr4	71232505	71232505	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cagggagatttccaccacccCtttctccaccctatggtcca	6	17	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr4:71232505C>A	ENST00000226460.4	+	3	295	c.199C>A	c.(199-201)Ctt>Att	p.L67I		NM_012390.3	NP_036522.3	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3A	67	Pro-rich.					extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)	15		all_hematologic(202;0.196)				TCCACCACCCCTTTCTCCACC	0.552																																					p.L67I		Atlas-SNP	.											.	SMR3A	35	.	0			c.C199A						.						158	147	151					4																	71232505		2203	4300	6503	SO:0001583	missense	26952	exon3			CCACCCCTTTCTC	D89501	CCDS34000.1	4q13.3	2009-04-17	2008-02-27	2005-02-07	ENSG00000109208	ENSG00000109208			19216	protein-coding gene	gene with protein product			"proline rich 5 (salivary)", "submaxillary gland androgen regulated protein 3 homolog A (mouse)"	PROL5		9354371, 17512016	Standard	NM_012390		Approved	PBI, PRL5	uc003hfg.1	Q99954	OTTHUMG00000160839	ENST00000226460.4:c.199C>A	chr4.hg19:g.71232505C>A	ENSP00000226460:p.Leu67Ile	105.0	0.0		307.0	119.0	NM_012390		Missense_Mutation	SNP	ENST00000226460.4	hg19	CCDS34000.1	.	.	.	.	.	.	.	.	.	.	C	4.157	0.027601	0.08054	.	.	ENSG00000109208	ENST00000226460	T	0.29917	1.55	2.58	1.69	0.24217	.	.	.	.	.	T	0.13628	0.0330	N	0.08118	0	0.09310	N	1	B	0.29716	0.255	B	0.26416	0.069	T	0.25152	-1.0140	9	0.25106	T	0.35	.	7.2636	0.26217	0.0:0.7239:0.2761:0.0	.	67	Q99954	SMR3A_HUMAN	I	67	ENSP00000226460:L67I	ENSP00000226460:L67I	L	+	1	0	SMR3A	71267094	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.341000	0.19909	0.634000	0.30469	0.313000	0.20887	CTT	.	.		0.552	SMR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362574.1	NM_012390		A	71232505	C	A	71232505	3	1	98	1	0	0	0	0	1	0	0	0	14826	681	24	3	205	3	SMR3A	4	71232505	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	23486064	71232505	119921771	38	13400										
C4orf26	152816	hgsc.bcm.edu	37	chr4	76489342	76489342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	aggacaagaagaggtatttaCgcctcctggagattcacaaa	10	8	1	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr4:76489342C>T	ENST00000311623.4	+	2	121	c.86C>T	c.(85-87)aCg>aTg	p.T29M	C4orf26_ENST00000435974.2_Missense_Mutation_p.R44C	NM_001257072.1|NM_178497.3	NP_001244001.1|NP_848592.2	Q17RF5	CD026_HUMAN	chromosome 4 open reading frame 26	29						extracellular region (GO:0005576)				kidney(1)|large_intestine(4)|stomach(1)	6			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			GAGGTATTTACGCCTCCTGGA	0.527																																					p.R44C		Atlas-SNP	.											C4orf26_ENST00000435974,rectum,carcinoma,-1,2	C4orf26	24	.	0			c.C130T						.						67	71	70					4																	76489342		2203	4300	6503	SO:0001583	missense	152816	exon3			TATTTACGCCTCC	AK074237	CCDS3569.1, CCDS56334.1, CCDS75142.1	4q21.1	2012-10-31			ENSG00000174792	ENSG00000174792			26300	protein-coding gene	gene with protein product		614829				22901946	Standard	NM_001206981		Approved	FLJ23657	uc011cbo.2	Q17RF5	OTTHUMG00000130104	ENST00000311623.4:c.86C>T	chr4.hg19:g.76489342C>T	ENSP00000311307:p.Thr29Met	46.0	0.0		71.0	36.0	NM_001206981	B4DTI3|E7ETQ0|Q8TEC3	Missense_Mutation	SNP	ENST00000311623.4	hg19	CCDS3569.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.382|7.382	0.628915|0.628915	0.14257|0.14257	.|.	.|.	ENSG00000174792|ENSG00000174792	ENST00000435974|ENST00000311623	T|T	0.50813|0.39592	0.73|1.07	4.6|4.6	1.05|1.05	0.20165|0.20165	.|.	.|0.365474	.|0.21557	.|N	.|0.072634	T|T	0.39384|0.39384	0.1076|0.1076	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	B|D	0.06786|0.89917	0.001|1.0	B|P	0.04013|0.58660	0.001|0.843	T|T	0.19418|0.19418	-1.0306|-1.0306	9|10	0.87932|0.87932	D|D	0|0	.|.	4.1083|4.1083	0.10047|0.10047	0.181:0.61:0.0:0.209|0.181:0.61:0.0:0.209	.|.	44|29	E7ETQ0|Q17RF5	.|CD026_HUMAN	C|M	44|29	ENSP00000406925:R44C|ENSP00000311307:T29M	ENSP00000406925:R44C|ENSP00000311307:T29M	R|T	+|+	1|2	0|0	C4orf26|C4orf26	76708366|76708366	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.212000|0.212000	0.24457|0.24457	-0.328000|-0.328000	0.07945|0.07945	0.054000|0.054000	0.16065|0.16065	0.551000|0.551000	0.68910|0.68910	CGC|ACG	.	.		0.527	C4orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252410.1	NM_178497		T	76489342	C	T	76489342	3	4	98	1	0	0	0	0	1	0	0	0	2259	536	19	1	92	1	C4orf26	4	76489342	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	5256837	76489342	114664934	39	13401										
CENPE	1062	hgsc.bcm.edu	37	chr4	104060948	104060948	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ggaagactctgaactcactcTagctatcatttcccttaagg	7	11	4	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr4:104060948T>C	ENST00000265148.3	-	38	6291	c.6202A>G	c.(6202-6204)Aga>Gga	p.R2068G	CENPE_ENST00000380026.3_Intron	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2068					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		GAACTCACTCTAGCTATCATT	0.318																																					p.R2068G		Atlas-SNP	.											.	CENPE	253	.	0			c.A6202G						.						123	122	122					4																	104060948		2203	4300	6503	SO:0001583	missense	1062	exon38			TCACTCTAGCTAT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.6202A>G	chr4.hg19:g.104060948T>C	ENSP00000265148:p.Arg2068Gly	114.0	0.0		227.0	153.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	T	8.637	0.895010	0.17613	.	.	ENSG00000138778	ENST00000265148;ENST00000394771	T	0.70869	-0.52	5.16	-0.361	0.12564	.	.	.	.	.	T	0.54532	0.1864	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35574	-0.9783	9	0.21540	T	0.41	.	5.6326	0.17518	0.0:0.2301:0.1344:0.6355	.	2068	Q02224	CENPE_HUMAN	G	2068	ENSP00000265148:R2068G	ENSP00000265148:R2068G	R	-	1	2	CENPE	104280397	0.000000	0.05858	0.346000	0.25655	0.957000	0.61999	0.072000	0.14617	0.281000	0.22233	0.450000	0.29827	AGA	.	.		0.318	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	104060948	T	C	104060948	3	2	98	1	0	0	0	0	1	0	0	0	3232	1530	53	2	1951	2	CENPE	4	104060948	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	27571606	104060948	87093328	40	13402										
ANK2	287	hgsc.bcm.edu	37	chr4	114278315	114278315	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agtgaaagcttttcatcttcAtcctctttgcctcattgttt	5	10	5	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr4:114278315A>T	ENST00000357077.4	+	38	8594	c.8541A>T	c.(8539-8541)tcA>tcT	p.S2847S	ANK2_ENST00000264366.6_Silent_p.S2814S|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2847					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TTTCATCTTCATCCTCTTTGC	0.403																																					p.S2847S		Atlas-SNP	.											.	ANK2	576	.	0			c.A8541T						.						108	107	108					4																	114278315		2203	4300	6503	SO:0001819	synonymous_variant	287	exon38			ATCTTCATCCTCT	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.8541A>T	chr4.hg19:g.114278315A>T		67.0	0.0		212.0	76.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.		0.403	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114278315	A	T	114278315	2	4	98	1	0	0	0	0	0	0	0	1	621	204	8	4		4	ANK2	4	114278315	Silent	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	10217367	114278315	76875961	41	13403										
NAA15	80155	hgsc.bcm.edu	37	chr4	140272693	140272693	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gaatgtttggataagttcctAaggatgaatttcagcaaggg	12	4	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr4:140272693A>G	ENST00000296543.5	+	9	1265	c.942A>G	c.(940-942)ctA>ctG	p.L314L	NAA15_ENST00000398947.1_Silent_p.L314L|NAA15_ENST00000480277.2_3'UTR	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	314					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						ATAAGTTCCTAAGGATGAATT	0.303																																					p.L314L		Atlas-SNP	.											.	NAA15	88	.	0			c.A942G						.						106	104	105					4																	140272693		1803	4074	5877	SO:0001819	synonymous_variant	80155	exon9			GTTCCTAAGGATG	AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"N(alpha)-acetyltransferase subunits"	30782	protein-coding gene	gene with protein product		608000	"NMDA receptor regulated 1"	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.942A>G	chr4.hg19:g.140272693A>G		86.0	0.0		216.0	96.0	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Silent	SNP	ENST00000296543.5	hg19	CCDS43270.1																																																																																			.	.		0.303	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175		G	140272693	A	G	140272693	2	3	98	1	0	0	0	0	0	0	0	1	10127	349	13	2		2	NAA15	4	140272693	Silent	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	25994378	140272693	50881583	42	13404										
ING2	3622	hgsc.bcm.edu	37	chr4	184431731	184431731	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gaagaccccgcaggcagcggAccagtgaaagccgtgattta	13	11	0	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr4:184431731A>G	ENST00000302327.3	+	2	671	c.469A>G	c.(469-471)Acc>Gcc	p.T157A	ING2_ENST00000434682.2_Missense_Mutation_p.T117A	NM_001564.2	NP_001555.1	Q9H160	ING2_HUMAN	inhibitor of growth family, member 2	157					chromatin modification (GO:0016568)|male germ-line stem cell asymmetric division (GO:0048133)|male meiosis I (GO:0007141)|negative regulation of cell proliferation (GO:0008285)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cellular senescence (GO:2000772)|regulation of growth (GO:0040008)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|seminiferous tubule development (GO:0072520)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleus (GO:0005634)|Sin3 complex (GO:0016580)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)	p.T157S(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)	7		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|all_hematologic(60;0.0207)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		CAGGCAGCGGACCAGTGAAAG	0.448																																					p.T157A		Atlas-SNP	.											ING2,NS,carcinoma,0,1	ING2	20	.	1	Substitution - Missense(1)	lung(1)	c.A469G						.						58	60	59					4																	184431731		2203	4300	6503	SO:0001583	missense	3622	exon2			CAGCGGACCAGTG	AB012853	CCDS3833.1	4q35.1	2013-01-28	2005-02-10	2005-02-11	ENSG00000168556	ENSG00000168556		"Zinc fingers, PHD-type"	6063	protein-coding gene	gene with protein product		604215	"inhibitor of growth family, member 1-like"	ING1L		10072587	Standard	XM_005262982		Approved	p33ING2	uc003ivs.1	Q9H160	OTTHUMG00000150502	ENST00000302327.3:c.469A>G	chr4.hg19:g.184431731A>G	ENSP00000307183:p.Thr157Ala	75.0	0.0		211.0	79.0	NM_001564	B6ZDS1|O95698	Missense_Mutation	SNP	ENST00000302327.3	hg19	CCDS3833.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.559034	0.45590	.	.	ENSG00000168556	ENST00000302327;ENST00000412117;ENST00000434682	.	.	.	5.55	5.55	0.83447	.	0.224702	0.43919	D	0.000506	T	0.48537	0.1505	L	0.43923	1.385	0.36952	D	0.892894	B;B	0.29037	0.231;0.231	B;B	0.29785	0.107;0.107	T	0.50268	-0.8848	9	0.08179	T	0.78	-24.9453	15.8583	0.79000	1.0:0.0:0.0:0.0	.	117;157	B6ZDS1;Q9H160	.;ING2_HUMAN	A	157;117;117	.	ENSP00000307183:T157A	T	+	1	0	ING2	184668725	1.000000	0.71417	0.987000	0.45799	0.967000	0.64934	8.722000	0.91452	2.326000	0.78906	0.533000	0.62120	ACC	.	.		0.448	ING2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318652.1	NM_001564		G	184431731	A	G	184431731	3	3	98	1	0	0	0	0	1	0	0	0	7745	275	10	2	475	2	ING2	4	184431731	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	44159038	184431731	6722545	43	13405										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186533094	186533094	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctgggattttaccttcatacCagttttgatcaactctttta	5	9	3	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr4:186533094C>T	ENST00000284776.7	-	18	3433	c.2924G>A	c.(2923-2925)tGg>tAg	p.W975*	SORBS2_ENST00000437304.2_Nonsense_Mutation_p.W699*|SORBS2_ENST00000393528.3_Nonsense_Mutation_p.W541*|SORBS2_ENST00000449407.2_Nonsense_Mutation_p.W519*|SORBS2_ENST00000431808.1_Nonsense_Mutation_p.W975*|SORBS2_ENST00000319471.9_Nonsense_Mutation_p.W606*|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000418609.1_Nonsense_Mutation_p.W879*|SORBS2_ENST00000355634.5_Nonsense_Mutation_p.W1075*|SORBS2_ENST00000448662.2_Nonsense_Mutation_p.W536*	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	975	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		ACCTTCATACCAGTTTTGATC	0.368																																					p.W1075X	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.G3224A						.						162	148	152					4																	186533094		2203	4300	6503	SO:0001587	stop_gained	8470	exon21			TCATACCAGTTTT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.2924G>A	chr4.hg19:g.186533094C>T	ENSP00000284776:p.Trp975*	113.0	0.0		351.0	22.0	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Nonsense_Mutation	SNP	ENST00000284776.7	hg19	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	C	46	12.545387	0.99676	.	.	ENSG00000154556	ENST00000284776;ENST00000448662;ENST00000431808;ENST00000418609;ENST00000437304;ENST00000319471;ENST00000449407;ENST00000355634;ENST00000393528;ENST00000319454	.	.	.	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.2526	19.0851	0.93200	0.0:1.0:0.0:0.0	.	.	.	.	X	975;536;975;879;699;606;519;1075;541;566	.	ENSP00000284776:W975X	W	-	2	0	SORBS2	186770088	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.736000	0.93811	0.591000	0.81541	TGG	.	.		0.368	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		T	186533094	C	T	186533094	4	4	98	1	0	0	0	0	0	1	0	0	14943	595	21	3	394	3	SORBS2	4	186533094	Nonsense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	2101363	186533094	4621182	44	13406										
CDH18	1016	hgsc.bcm.edu	37	chr5	19612615	19612615	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgttgtagatcctgaaagccCtccaacttgcccagccatgt	8	13	0	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:19612615C>A	ENST00000507958.1	-	8	1729	c.739G>T	c.(739-741)Ggg>Tgg	p.G247W	CDH18_ENST00000502796.1_Missense_Mutation_p.G247W|CDH18_ENST00000382275.1_Missense_Mutation_p.G247W|CDH18_ENST00000511273.1_Missense_Mutation_p.G247W|CDH18_ENST00000506372.1_Missense_Mutation_p.G247W|CDH18_ENST00000274170.4_Missense_Mutation_p.G247W			Q13634	CAD18_HUMAN	cadherin 18, type 2	247	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CCTGAAAGCCCTCCAACTTGC	0.433																																					p.G247W		Atlas-SNP	.											.	CDH18	561	.	0			c.G739T						.						163	147	153					5																	19612615		2203	4300	6503	SO:0001583	missense	1016	exon6			AAAGCCCTCCAAC	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.739G>T	chr5.hg19:g.19612615C>A	ENSP00000425093:p.Gly247Trp	91.0	0.0		375.0	203.0	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.559048	0.86335	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55;0.55	5.95	5.95	0.96441	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.78407	0.4278	M	0.89214	3.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80571	-0.1323	9	.	.	.	.	18.9386	0.92597	0.0:1.0:0.0:0.0	.	247;247	B4DHG6;Q13634	.;CAD18_HUMAN	W	247;247;247;247;247;247;193;247	ENSP00000371710:G247W;ENSP00000425093:G247W;ENSP00000274170:G247W;ENSP00000424931:G247W;ENSP00000422138:G247W;ENSP00000427383:G193W;ENSP00000425854:G247W	.	G	-	1	0	CDH18	19648372	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	7.672000	0.83956	2.817000	0.96982	0.563000	0.77884	GGG	.	.		0.433	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		A	19612615	C	A	19612615	3	1	98	1	0	0	0	0	1	0	0	0	3105	681	24	3	1665	3	CDH18	5	19612615	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10		19612615	161302645	45	13407										
CDH9	1007	hgsc.bcm.edu	37	chr5	26906920	26906920	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agttggcgtcatctgcatctGttgcagttacttgtataaca	9	8	3	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:26906920G>A	ENST00000231021.4	-	4	723	c.551C>T	c.(550-552)aCa>aTa	p.T184I		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	184	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						ATCTGCATCTGTTGCAGTTAC	0.388																																					p.T184I	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.C551T						.						130	115	120					5																	26906920		2203	4300	6503	SO:0001583	missense	1007	exon4			GCATCTGTTGCAG	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.551C>T	chr5.hg19:g.26906920G>A	ENSP00000231021:p.Thr184Ile	67.0	0.0		228.0	121.0	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.224327	0.39300	.	.	ENSG00000113100	ENST00000231021	T	0.55588	0.51	5.69	5.69	0.88448	Cadherin (5);Cadherin-like (1);	0.226724	0.44097	D	0.000494	T	0.53190	0.1781	L	0.58101	1.795	0.09310	N	1	B	0.22746	0.074	B	0.35813	0.211	T	0.46582	-0.9181	9	.	.	.	.	11.8036	0.52141	0.0804:0.0:0.9196:0.0	.	184	Q9ULB4	CADH9_HUMAN	I	184	ENSP00000231021:T184I	.	T	-	2	0	CDH9	26942677	0.998000	0.40836	0.359000	0.25824	0.958000	0.62258	2.649000	0.46656	2.677000	0.91161	0.655000	0.94253	ACA	.	.		0.388	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26906920	G	A	26906920	3	1	98	1	0	0	0	0	1	0	0	0	3119	1377	48	3	1854	3	CDH9	5	26906920	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	7294305	26906920	154008340	46	13408										
PLCXD3	345557	hgsc.bcm.edu	37	chr5	41381972	41381972	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ccacttgccacccctttgacCacagtgctagctttgggggt	10	14	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:41381972C>T	ENST00000377801.3	-	2	842	c.768G>A	c.(766-768)gtG>gtA	p.V256V	PLCXD3_ENST00000328457.3_Silent_p.V256V			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	256					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						CCCCTTTGACCACAGTGCTAG	0.413																																					p.V256V		Atlas-SNP	.											.	PLCXD3	86	.	0			c.G768A						.						81	86	84					5																	41381972		2203	4300	6503	SO:0001819	synonymous_variant	345557	exon2			TTTGACCACAGTG		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.768G>A	chr5.hg19:g.41381972C>T		72.0	0.0		290.0	162.0	NM_001005473	A6NL04	Silent	SNP	ENST00000377801.3	hg19	CCDS34150.1																																																																																			.	.		0.413	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875		T	41381972	C	T	41381972	2	4	98	1	0	0	0	0	0	0	0	1	12052	581	21	3		3	PLCXD3	5	41381972	Silent	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	14475052	41381972	139533288	47	13409										
ERCC8	1161	hgsc.bcm.edu	37	chr5	60200656	60200656	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ttggtggagactggagacatAtgatgactataaactgtttc	11	5	0	4			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:60200656A>G	ENST00000265038.5	-	5	486	c.444T>C	c.(442-444)caT>caC	p.H148H	ERCC8_ENST00000462279.1_5'UTR|ERCC8_ENST00000543101.1_Intron|ERCC8_ENST00000426742.2_Silent_p.H90H	NM_000082.3	NP_000073.1	Q13216	ERCC8_HUMAN	excision repair cross-complementation group 8	148					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|positive regulation of DNA repair (GO:0045739)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|transcription-coupled nucleotide-excision repair (GO:0006283)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|protein complex (GO:0043234)	protein complex binding (GO:0032403)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)				CTGGAGACATATGATGACTAT	0.313																																					p.H148H		Atlas-SNP	.											.	ERCC8	31	.	0			c.T444C						.						116	117	117					5																	60200656		2203	4297	6500	SO:0001819	synonymous_variant	1161	exon5			AGACATATGATGA	U28413	CCDS3978.1	5q12.1	2014-09-17	2014-03-07		ENSG00000049167	ENSG00000049167		"WD repeat domain containing"	3439	protein-coding gene	gene with protein product		609412	"Cockayne syndrome 1 (classical)", "excision repair cross-complementing rodent repair deficiency, complementation group 8"	CKN1		8596535	Standard	NM_000082		Approved	CSA	uc003jsm.3	Q13216	OTTHUMG00000097741	ENST00000265038.5:c.444T>C	chr5.hg19:g.60200656A>G		108.0	0.0		322.0	130.0	NM_000082	B2RB64|Q6FHX5|Q96GB9	Silent	SNP	ENST00000265038.5	hg19	CCDS3978.1																																																																																			.	.		0.313	ERCC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214971.2	NM_000082		G	60200656	A	G	60200656	2	3	98	1	0	0	0	0	0	0	0	1	5221	446	16	2		2	ERCC8	5	60200656	Silent	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	18818684	60200656	120714604	48	13410										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79027939	79027953	+	In_Frame_Del	DEL	ATATTTAGAGCCTGA	ATATTTAGAGCCTGA	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cagaagcagaaaactcaagcAtatttagagcctgagtctga					rs200267723		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	ATATTTAGAGCCTGA	ATATTTAGAGCCTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:79027939_79027953delATATTTAGAGCCTGA	ENST00000446378.2	+	2	3382_3396	c.3351_3365delATATTTAGAGCCTGA	c.(3349-3366)gcatatttagagcctgag>gcg	p.YLEPE1118del		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1118					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.E1122V(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AAACTCAAGCATATTTAGAGCCTGAGTCTGAAGAC	0.414																																					p.1117_1122del		Atlas-Indel,Pindel	.											.	CMYA5	643	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.3350_3364del						.																																			SO:0001651	inframe_deletion	202333	exon2			.	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.3351_3365delATATTTAGAGCCTGA	chr5.hg19:g.79027939_79027953delATATTTAGAGCCTGA	ENSP00000394770:p.Tyr1118_Glu1122del	90.0	0.0		176.0	28.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	In_Frame_Del	DEL	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.		0.414	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		-	79027953	ATATTTAGAGCCTGA	-	79027939	7	5	98	1	0	1	0	1	0	0	0	0	3592	204	8	0	3357	0	CMYA5	5	79027939	In_Frame_Del	DEL	ATATTTAGAGCCTGA	TCGA-DD-A1EB-01A-11D-A12Z-10	18827283	79027939	101887321	49	13411										
MEF2C	4208	hgsc.bcm.edu	37	chr5	88025144	88025144	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gccaatgactgagccgactgGgagttatttatcctttgatt	10	8	0	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:88025144G>T	ENST00000437473.2	-	9	1272	c.855C>A	c.(853-855)tcC>tcA	p.S285S	MEF2C_ENST00000506554.1_Silent_p.S285S|MEF2C_ENST00000514015.1_Silent_p.S285S|MEF2C_ENST00000424173.2_Silent_p.S275S|MEF2C_ENST00000504921.2_Silent_p.S285S|MEF2C_ENST00000340208.5_Silent_p.S295S|MEF2C_ENST00000503554.1_5'Flank|MEF2C_ENST00000539796.1_Silent_p.S229S|MEF2C_ENST00000510942.1_Silent_p.S277S|MEF2C_ENST00000514028.1_Silent_p.S285S|MEF2C_ENST00000508569.1_Silent_p.S277S	NM_001193350.1|NM_002397.4	NP_001180279.1|NP_002388.2	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C	285					apoptotic process (GO:0006915)|B cell homeostasis (GO:0001782)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac ventricle formation (GO:0003211)|cartilage morphogenesis (GO:0060536)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to fluid shear stress (GO:0071498)|cellular response to glucose stimulus (GO:0071333)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to trichostatin A (GO:0035984)|chondrocyte differentiation (GO:0002062)|dentate gyrus development (GO:0021542)|embryonic viscerocranium morphogenesis (GO:0048703)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|germinal center formation (GO:0002467)|glomerulus morphogenesis (GO:0072102)|heart development (GO:0007507)|heart looping (GO:0001947)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|MAPK cascade (GO:0000165)|melanocyte differentiation (GO:0030318)|monocyte differentiation (GO:0030224)|muscle cell differentiation (GO:0042692)|muscle cell fate determination (GO:0007521)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myotube differentiation (GO:0014902)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nephron tubule epithelial cell differentiation (GO:0072160)|nervous system development (GO:0007399)|neural crest cell differentiation (GO:0014033)|neuron development (GO:0048666)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|platelet formation (GO:0030220)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primary heart field specification (GO:0003138)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of dendritic spine development (GO:0060998)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of germinal center formation (GO:0002634)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron apoptotic process (GO:0043523)|regulation of neurotransmitter secretion (GO:0046928)|regulation of sarcomere organization (GO:0060297)|regulation of synapse assembly (GO:0051963)|regulation of synaptic activity (GO:0060025)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|renal tubule morphogenesis (GO:0061333)|response to ischemia (GO:0002931)|response to virus (GO:0009615)|response to vitamin E (GO:0033197)|secondary heart field specification (GO:0003139)|sinoatrial valve morphogenesis (GO:0003185)|skeletal muscle tissue development (GO:0007519)|smooth muscle cell differentiation (GO:0051145)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|sarcomere (GO:0030017)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|miRNA binding (GO:0035198)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	40		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		GAGCCGACTGGGAGTTATTTA	0.343										HNSCC(66;0.2)																											p.S295S		Atlas-SNP	.											.	MEF2C	184	.	0			c.C885A						.						58	63	61					5																	88025144		1810	4074	5884	SO:0001819	synonymous_variant	4208	exon10			CGACTGGGAGTTA	AL833268	CCDS47244.1, CCDS47245.1, CCDS54877.1, CCDS54878.1	5q14.3	2013-07-03	2007-04-24		ENSG00000081189	ENSG00000081189		"Myocyte enhancer factors"	6996	protein-coding gene	gene with protein product		600662				8455629	Standard	NM_002397		Approved		uc003kjl.3	Q06413	OTTHUMG00000162634	ENST00000437473.2:c.855C>A	chr5.hg19:g.88025144G>T		54.0	0.0		119.0	43.0	NM_001193347	C9JMZ0|D7F7N5|F8W7V7	Silent	SNP	ENST00000437473.2	hg19	CCDS47245.1																																																																																			.	.		0.343	MEF2C-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369817.1	NM_002397		T	88025144	G	T	88025144	2	4	98	1	0	0	0	0	0	0	0	1	9466	1219	43	3		3	MEF2C	5	88025144	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	8997205	88025144	92890116	50	13412										
ZNF474	133923	hgsc.bcm.edu	37	chr5	121487810	121487810	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgactcctattctagcctttCcccagaaacagagagtgtta	7	11	1	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:121487810C>T	ENST00000296600.4	+	2	508	c.125C>T	c.(124-126)tCc>tTc	p.S42F	ZNF474_ENST00000514925.1_Intron|CTC-441N14.1_ENST00000505209.1_RNA|CTC-441N14.2_ENST00000504829.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	42							metal ion binding (GO:0046872)	p.S42F(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		TCTAGCCTTTCCCCAGAAACA	0.388																																					p.S42F		Atlas-SNP	.											ZNF474,rectum,carcinoma,0,1	ZNF474	43	.	1	Substitution - Missense(1)	large_intestine(1)	c.C125T						.						94	102	99					5																	121487810		2203	4300	6503	SO:0001583	missense	133923	exon2			GCCTTTCCCCAGA	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"Zinc fingers, C2H2-type"	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.125C>T	chr5.hg19:g.121487810C>T	ENSP00000296600:p.Ser42Phe	90.0	0.0		242.0	111.0	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	hg19	CCDS4130.1	.	.	.	.	.	.	.	.	.	.	C	3.023	-0.201249	0.06219	.	.	ENSG00000164185	ENST00000296600;ENST00000504912	T	0.48836	0.8	5.58	-4.06	0.03986	.	3.371230	0.01961	U	0.043330	T	0.30541	0.0768	N	0.19112	0.55	0.09310	N	1	B	0.18461	0.028	B	0.13407	0.009	T	0.14172	-1.0482	10	0.29301	T	0.29	4.1434	7.1515	0.25614	0.0:0.4522:0.3502:0.1976	.	42	Q6S9Z5	ZN474_HUMAN	F	42	ENSP00000296600:S42F	ENSP00000296600:S42F	S	+	2	0	ZNF474	121515709	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.680000	0.05197	-0.586000	0.05898	-1.004000	0.02495	TCC	.	.		0.388	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317		T	121487810	C	T	121487810	3	4	98	1	0	0	0	0	1	0	0	0	17947	855	30	3	127	3	ZNF474	5	121487810	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	33462666	121487810	59427450	51	13413										
SLC27A6	28965	hgsc.bcm.edu	37	chr5	128368891	128368891	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	aaaatttctgaaccactttaCttcatggataacttgaaaaa	4	7	2	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:128368891C>A	ENST00000262462.4	+	10	2786	c.1776C>A	c.(1774-1776)taC>taA	p.Y592*	SLC27A6_ENST00000395266.1_Nonsense_Mutation_p.Y592*|SLC27A6_ENST00000506176.1_Nonsense_Mutation_p.Y592*			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	592					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		AACCACTTTACTTCATGGATA	0.318																																					p.Y592X		Atlas-SNP	.											.	SLC27A6	112	.	0			c.C1776A						.						63	62	62					5																	128368891		2201	4295	6496	SO:0001587	stop_gained	28965	exon10			ACTTTACTTCATG	AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"Acyl-CoA synthetase family", "Solute carriers"	11000	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 2"	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.1776C>A	chr5.hg19:g.128368891C>A	ENSP00000262462:p.Tyr592*	123.0	0.0		422.0	160.0	NM_001017372	Q6IAM5|Q7Z6E6|Q86YF6	Nonsense_Mutation	SNP	ENST00000262462.4	hg19	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	C	38	7.270356	0.98179	.	.	ENSG00000113396	ENST00000262462;ENST00000395266;ENST00000506176	.	.	.	3.95	3.04	0.35103	.	0.220594	0.39909	N	0.001224	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.8007	4.8991	0.13766	0.0:0.5993:0.0:0.4007	.	.	.	.	X	592	.	.	Y	+	3	2	SLC27A6	128396790	0.988000	0.35896	1.000000	0.80357	0.947000	0.59692	0.159000	0.16442	1.193000	0.43086	0.585000	0.79938	TAC	.	.		0.318	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031		A	128368891	C	A	128368891	4	1	98	1	0	0	0	0	0	1	0	0	14545	576	20	3	1814	3	SLC27A6	5	128368891	Nonsense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	6881081	128368891	52546369	52	13414										
SIL1	64374	hgsc.bcm.edu	37	chr5	138287486	138287486	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tggaaacacaccttcttcttTgcagtgagcggctgctccgt	10	12	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:138287486T>C	ENST00000394817.2	-	8	994	c.855A>G	c.(853-855)gcA>gcG	p.A285A	SIL1_ENST00000515008.1_5'UTR|SIL1_ENST00000265195.5_Silent_p.A285A|SIL1_ENST00000509534.1_Silent_p.A292A	NM_022464.4	NP_071909.1	Q9H173	SIL1_HUMAN	SIL1 nucleotide exchange factor	285					intracellular protein transport (GO:0006886)|protein folding (GO:0006457)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CCTTCTTCTTTGCAGTGAGCG	0.612									Marinesco-Sjgren syndrome																												p.A285A		Atlas-SNP	.											.	SIL1	31	.	0			c.A855G						.						126	106	113					5																	138287486		2203	4300	6503	SO:0001819	synonymous_variant	64374	exon9	Familial Cancer Database	Marinesco-Sjogren syndrome	CTTCTTTGCAGTG	AK075177	CCDS4209.1	5q31	2013-08-21	2013-08-21		ENSG00000120725	ENSG00000120725			24624	protein-coding gene	gene with protein product		608005	"Marinesco-Sjogren syndrome", "SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae)"	MSS		11101517, 12356756, 16282977	Standard	XM_006714671		Approved	BAP, ULG5	uc003ldp.3	Q9H173	OTTHUMG00000129226	ENST00000394817.2:c.855A>G	chr5.hg19:g.138287486T>C		17.0	0.0		64.0	22.0	NM_001037633	D3DQC2|Q8N2L3	Silent	SNP	ENST00000394817.2	hg19	CCDS4209.1																																																																																			.	.		0.612	SIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251319.1	NM_022464		C	138287486	T	C	138287486	2	2	98	1	0	0	0	0	0	0	0	1	14336	1799	63	2		2	SIL1	5	138287486	Silent	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	9918595	138287486	42627774	53	13415										
PCDHB11	56125	hgsc.bcm.edu	37	chr5	140580796	140580796	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gacagagactcaggcaccaaCgcccaggtcaactactcgct	9	15	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:140580796C>T	ENST00000354757.3	+	1	1449	c.1449C>T	c.(1447-1449)aaC>aaT	p.N483N	PCDHB11_ENST00000536699.1_Silent_p.N118N	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	483	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGGCACCAACGCCCAGGTCA	0.627																																					p.N483N		Atlas-SNP	.											.	PCDHB11	162	.	0			c.C1449T						.						139	135	137					5																	140580796		2203	4300	6503	SO:0001819	synonymous_variant	56125	exon1			CACCAACGCCCAG	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"Cadherins / Protocadherins : Clustered"	8682	other	protocadherin	"cadherin ME2"	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.1449C>T	chr5.hg19:g.140580796C>T		64.0	0.0		171.0	65.0	NM_018931	B4DSF7|Q2M223	Silent	SNP	ENST00000354757.3	hg19	CCDS4253.1																																																																																			.	.		0.627	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931		T	140580796	C	T	140580796	2	4	98	1	0	0	0	0	0	0	0	1	11545	535	19	1		1	PCDHB11	5	140580796	Silent	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	2293310	140580796	40334464	54	13416										
CDHR2	54825	hgsc.bcm.edu	37	chr5	176003023	176003023	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctgggtgacagtgagagtgaTggacgtcaatgaccacaaac	13	8	1	4			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:176003023T>C	ENST00000510636.1	+	12	1305	c.1031T>C	c.(1030-1032)aTg>aCg	p.M344T	CDHR2_ENST00000261944.5_Missense_Mutation_p.M344T|CDHR2_ENST00000506348.1_Missense_Mutation_p.M344T	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	344	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						GTGAGAGTGATGGACGTCAAT	0.582																																					p.M344T		Atlas-SNP	.											.	CDHR2	152	.	0			c.T1031C						.						139	115	124					5																	176003023		2203	4300	6503	SO:0001583	missense	54825	exon12			GAGTGATGGACGT	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.1031T>C	chr5.hg19:g.176003023T>C	ENSP00000424565:p.Met344Thr	42.0	0.0		110.0	34.0	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	hg19	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.364629	0.00015	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.59364	0.27;0.27;0.27	4.54	0.571	0.17352	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.23289	0.0563	N	0.00985	-1.075	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24764	-1.0151	9	0.16420	T	0.52	0.0026	8.0838	0.30760	0.0:0.6847:0.0:0.3153	.	344	Q9BYE9	CDHR2_HUMAN	T	344	ENSP00000424565:M344T;ENSP00000261944:M344T;ENSP00000421078:M344T	ENSP00000261944:M344T	M	+	2	0	CDHR2	175935629	0.004000	0.15560	0.002000	0.10522	0.003000	0.03518	0.036000	0.13819	-0.049000	0.13379	-1.182000	0.01712	ATG	.	.		0.582	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		C	176003023	T	C	176003023	3	2	98	1	0	0	0	0	1	0	0	0	3121	1464	51	2	1073	2	CDHR2	5	176003023	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	35422227	176003023	4912237	55	13417										
DBN1	1627	hgsc.bcm.edu	37	chr5	176887553	176887553	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctgggcaataatagctgctgCctcctgagggcacgaggaaa	13	10	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:176887553C>T	ENST00000309007.5	-	10	1054	c.835G>A	c.(835-837)Gca>Aca	p.A279T	DBN1_ENST00000512501.1_Missense_Mutation_p.A11T|DBN1_ENST00000292385.5_Missense_Mutation_p.A281T|DBN1_ENST00000393563.4_Missense_Mutation_p.A11T|DBN1_ENST00000393565.1_Missense_Mutation_p.A279T	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	279					actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATAGCTGCTGCCTCCTGAGGG	0.617																																					p.A281T		Atlas-SNP	.											.	DBN1	122	.	0			c.G841A						.						157	149	152					5																	176887553		2203	4300	6503	SO:0001583	missense	1627	exon11			CTGCTGCCTCCTG		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.835G>A	chr5.hg19:g.176887553C>T	ENSP00000308532:p.Ala279Thr	53.0	0.0		144.0	69.0	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	hg19	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.881097	0.91740	.	.	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000512501;ENST00000393563;ENST00000477391	T;T;T;T;T	0.62639	1.07;1.09;1.58;0.01;0.43	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.74831	0.3768	L	0.55834	1.745	0.54753	D	0.999988	D;D;D;D	0.89917	0.998;1.0;1.0;1.0	D;D;D;D	0.87578	0.995;0.998;0.996;0.998	T	0.75616	-0.3256	10	0.48119	T	0.1	-7.3028	16.2304	0.82332	0.0:1.0:0.0:0.0	.	229;279;279;281	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	T	279;281;279;11;11;278	ENSP00000308532:A279T;ENSP00000292385:A281T;ENSP00000377195:A279T;ENSP00000423208:A11T;ENSP00000377193:A11T	ENSP00000292385:A281T	A	-	1	0	DBN1	176820159	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	6.514000	0.73746	2.368000	0.80403	0.561000	0.74099	GCA	.	.		0.617	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		T	176887553	C	T	176887553	3	4	98	1	0	0	0	0	1	0	0	0	4254	739	26	3	1134	3	DBN1	5	176887553	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	884530	176887553	4027707	56	13418										
ZFP2	80108	hgsc.bcm.edu	37	chr5	178358877	178358877	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cggagagaaaccctatcagtGtaaagagtgtggcaaagcct	12	8	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr5:178358877G>T	ENST00000361362.2	+	5	1093	c.563G>T	c.(562-564)tGt>tTt	p.C188F	ZFP2_ENST00000523286.1_Missense_Mutation_p.C188F|ZFP2_ENST00000520301.1_Missense_Mutation_p.C188F|ZFP2_ENST00000503510.2_Missense_Mutation_p.C188F	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	188					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		CCCTATCAGTGTAAAGAGTGT	0.393																																					p.C188F		Atlas-SNP	.											.	ZFP2	70	.	0			c.G563T						.						48	46	47					5																	178358877		2203	4300	6503	SO:0001583	missense	80108	exon5			ATCAGTGTAAAGA	AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"Zinc fingers, C2H2-type"	26138	protein-coding gene	gene with protein product			"zinc finger protein 2 homolog (mouse)"				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.563G>T	chr5.hg19:g.178358877G>T	ENSP00000354453:p.Cys188Phe	29.0	0.0		52.0	19.0	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Missense_Mutation	SNP	ENST00000361362.2	hg19	CCDS4440.1	.	.	.	.	.	.	.	.	.	.	g	18.13	3.554976	0.65425	.	.	ENSG00000198939	ENST00000361362;ENST00000520301;ENST00000523286;ENST00000503510	D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94	4.7	4.7	0.59300	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34879	N	0.003606	D	0.95066	0.8402	H	0.97611	4.04	0.52099	D	0.999942	D	0.89917	1.0	D	0.97110	1.0	D	0.96623	0.9461	10	0.87932	D	0	-6.0403	15.1771	0.72920	0.0:0.0:1.0:0.0	.	188	Q6ZN57	ZFP2_HUMAN	F	188	ENSP00000354453:C188F;ENSP00000430980:C188F;ENSP00000430531:C188F;ENSP00000438114:C188F	ENSP00000354453:C188F	C	+	2	0	ZFP2	178291483	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.596000	0.82721	2.421000	0.82119	0.585000	0.79938	TGT	.	.		0.393	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613		T	178358877	G	T	178358877	3	4	98	1	0	0	0	0	1	0	0	0	17656	1377	48	3	565	3	ZFP2	5	178358877	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	1471324	178358877	2556383	57	13419										
ZNF322A	79692	hgsc.bcm.edu	37	chr6	26637760	26637762	+	In_Frame_Del	DEL	TTC	TTC	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cctctgtttgagttctcattTtctgttgggcaacaaagtcc							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:26637760_26637762delTTC	ENST00000415922.2	-	4	1665_1667	c.1020_1022delGAA	c.(1018-1023)cagaaa>caa	p.K341del	RP11-457M11.2_ENST00000456172.1_RNA|ZNF322_ENST00000471278.1_In_Frame_Del_p.K341del|ZNF322_ENST00000461899.1_5'Flank	NM_024639.4	NP_078915.2	Q6U7Q0	ZN322_HUMAN	zinc finger protein 322	341					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AGTTCTCATTTTCTGTTGGGCAA	0.419																																					p.341_341del		Atlas-INDEL	.											.	.	.	.	0			c.1021_1023del						.																																			SO:0001651	inframe_deletion	79692	exon5			.	AY376736	CCDS4617.1	6p22.1	2013-01-08	2011-07-29	2011-07-29	ENSG00000181315	ENSG00000181315		"Zinc fingers, C2H2-type"	23640	protein-coding gene	gene with protein product		610847	"zinc finger protein 489", "HLA complex group 12", "zinc finger protein 322A"	ZNF489, ZNF388, HCG12, ZNF322A		15555580	Standard	NM_024639		Approved	bA457M11.3, bA457M11.2	uc021yny.1	Q6U7Q0	OTTHUMG00000014460	ENST00000415922.2:c.1020_1022delGAA	chr6.hg19:g.26637760_26637762delTTC	ENSP00000418897:p.Lys341del	191.0	0.0		1977.0	240.0	NM_001242797	A8K1X3|Q0VDH6|Q6B0G2|Q86W72|Q9H5I9	In_Frame_Del	DEL	ENST00000415922.2	hg19	CCDS4617.1																																																																																			.	.		0.419	ZNF322-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040126.2	NM_024639		-	26637762	TTC	-	26637760	7	5	98	1	0	1	0	1	0	0	0	0	17856	1841	64	0	190	0	ZNF322A	6	26637760	In_Frame_Del	DEL	TTC	TCGA-DD-A1EB-01A-11D-A12Z-10		26637760	144477307	58	13420										
KCNK16	83795	hgsc.bcm.edu	37	chr6	39286869	39286870	+	Frame_Shift_Del	DEL	CC	CC	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgctggggttggtagagttgCctttggggttcacacctttc					rs146890431		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:39286869_39286870delCC	ENST00000373229.5	-	2	266_267	c.253_254delGG	c.(253-255)ggcfs	p.G85fs	KCNK16_ENST00000425054.2_Frame_Shift_Del_p.G85fs|KCNK16_ENST00000507712.1_Frame_Shift_Del_p.G20fs|KCNK16_ENST00000437525.2_Frame_Shift_Del_p.G85fs|KCNK16_ENST00000373227.4_Frame_Shift_Del_p.G85fs	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	85					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						GGTAGAGTTGCCTTTGGGGTTC	0.545																																					p.85_85del		Atlas-INDEL	.											.	KCNK16	59	.	0			c.254_255del						.																																			SO:0001589	frameshift_variant	83795	exon2			.	AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.253_254delGG	chr6.hg19:g.39286869_39286870delCC	ENSP00000362326:p.Gly85fs	29.0	0.0		80.0	25.0	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Frame_Shift_Del	DEL	ENST00000373229.5	hg19	CCDS4843.1																																																																																			.	.		0.545	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115		-	39286870	CC	-	39286869	7	5	98	1	0	1	0	1	0	0	0	0	8072	739	26	0	1080	0	KCNK16	6	39286869	Frame_Shift_Del	DEL	CC	TCGA-DD-A1EB-01A-11D-A12Z-10	12649109	39286869	131828198	59	13421										
CUL9	23113	hgsc.bcm.edu	37	chr6	43153266	43153266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gcacatggattttgacagtcGctatacattgctggagctgt	11	8	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:43153266G>A	ENST00000252050.4	+	3	752	c.668G>A	c.(667-669)cGc>cAc	p.R223H	CUL9_ENST00000354495.3_Missense_Mutation_p.R223H|CUL9_ENST00000372647.2_Missense_Mutation_p.R223H	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	223					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						TTTGACAGTCGCTATACATTG	0.502																																					p.R223H		Atlas-SNP	.											.	CUL9	248	.	0			c.G668A						.						144	118	127					6																	43153266		2203	4300	6503	SO:0001583	missense	23113	exon3			ACAGTCGCTATAC	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.668G>A	chr6.hg19:g.43153266G>A	ENSP00000252050:p.Arg223His	37.0	0.0		121.0	52.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.843852	0.71488	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.49432	0.78;0.78;0.78	4.36	4.36	0.52297	.	0.198282	0.43919	D	0.000502	T	0.62295	0.2416	M	0.71036	2.16	0.38358	D	0.944525	D;D;D	0.89917	1.0;1.0;1.0	P;P;D	0.91635	0.877;0.877;0.999	T	0.68926	-0.5280	10	0.87932	D	0	-8.5472	17.0698	0.86570	0.0:0.0:1.0:0.0	.	223;223;223	E9PEZ1;Q8IWT3;Q05C85	.;CUL9_HUMAN;.	H	223	ENSP00000252050:R223H;ENSP00000346490:R223H;ENSP00000361730:R223H	ENSP00000252050:R223H	R	+	2	0	CUL9	43261244	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.612000	0.98347	2.262000	0.75019	0.462000	0.41574	CGC	.	.		0.502	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43153266	G	A	43153266	3	1	98	1	0	0	0	0	1	0	0	0	4063	1087	38	1	674	1	CUL9	6	43153266	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	3866397	43153266	127961801	60	13422										
CRIP3	401262	hgsc.bcm.edu	37	chr6	43273593	43273593	+	3'UTR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgggtcatagatgtagcagcCcacatcgccaatgttcacac	9	12	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:43273593C>G	ENST00000274990.4	-	0	769				CRIP3_ENST00000372569.3_Missense_Mutation_p.G192R|ZNF318_ENST00000607252.1_5'Flank			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3						T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			ATGTAGCAGCCCACATCGCCA	0.537																																					p.G192R		Atlas-SNP	.											.	CRIP3	30	.	0			c.G574C						.						85	90	88					6																	43273593		2185	4290	6475	SO:0001624	3_prime_UTR_variant	401262	exon8			AGCAGCCCACATC	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.*111G>C	chr6.hg19:g.43273593C>G		74.0	0.0		178.0	56.0	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	hg19		.	.	.	.	.	.	.	.	.	.	C	26.0	4.693798	0.88735	.	.	ENSG00000146215	ENST00000372569	D	0.92495	-3.05	5.66	5.66	0.87406	.	.	.	.	.	D	0.95806	0.8635	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95910	0.8922	8	0.72032	D	0.01	.	17.2419	0.87015	0.0:1.0:0.0:0.0	.	192	Q6Q6R5-3	.	R	192	ENSP00000361650:G192R	ENSP00000361650:G192R	G	-	1	0	CRIP3	43381571	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.469000	0.73555	2.668000	0.90789	0.655000	0.94253	GGC	.	.		0.537	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			G	43273593	C	G	43273593	1	3	98	0	1	0	0	0	0	0	0	0	3878	623	22	4		4	CRIP3	6	43273593	3'UTR	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	120327	43273593	127841474	61	13423										
PHIP	55023	hgsc.bcm.edu	37	chr6	79688429	79688429	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agttctcccacagccaatctCtgacaaaatttaagtaataa	4	10	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:79688429C>A	ENST00000275034.4	-	24	2937		c.e24-1		PHIP_ENST00000479165.1_Splice_Site	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein						cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		CAGCCAATCTCTGACAAAATT	0.308																																					.		Atlas-SNP	.											.	PHIP	177	.	0			c.2770-1G>T						.						57	57	57					6																	79688429		2203	4300	6503	SO:0001630	splice_region_variant	55023	exon25			CAATCTCTGACAA	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2770-1G>T	chr6.hg19:g.79688429C>A		61.0	0.0		151.0	61.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Splice_Site	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.979471	0.53827	.	.	ENSG00000146247	ENST00000275034	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3848	0.83501	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PHIP	79745148	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	5.024000	0.64090	2.527000	0.85204	0.655000	0.94253	.	.	.		0.308	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		Intron	A	79688429	C	A	79688429	5	1	98	1	0	0	0	0	0	0	1	0	11851	927	32	3	2764	3	PHIP	6	79688429	Splice_Site	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	36414836	79688429	91426638	62	13424										
GABRR2	2570	hgsc.bcm.edu	37	chr6	90009577	90009577	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cacatcaaggttcttcttatAtaagtgactgtgaagacaag	8	7	3	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:90009577A>G	ENST00000402938.3	-	2	254	c.121T>C	c.(121-123)Tat>Cat	p.Y41H	GABRR2_ENST00000602808.1_5'UTR|GABRR2_ENST00000602399.1_Missense_Mutation_p.Y66H	NM_002043.3	NP_002034.3	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 2	41					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(10)|prostate(2)|urinary_tract(1)	21		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	TTCTTCTTATATAAGTGACTG	0.473																																					p.Y41H		Atlas-SNP	.											.	GABRR2	41	.	0			c.T121C						.						107	97	100					6																	90009577		2203	4300	6503	SO:0001583	missense	2570	exon2			TCTTATATAAGTG		CCDS5020.2, CCDS5020.3	6q15	2012-06-22	2012-02-03		ENSG00000111886	ENSG00000111886		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4091	protein-coding gene	gene with protein product	"GABA(A) receptor, rho 2"	137162	"gamma-aminobutyric acid (GABA) receptor, rho 2"			1315307	Standard	NM_002043		Approved		uc003pnb.3	P28476	OTTHUMG00000015198	ENST00000402938.3:c.121T>C	chr6.hg19:g.90009577A>G	ENSP00000386029:p.Tyr41His	74.0	0.0		190.0	79.0	NM_002043	A2BDE4|Q9H153	Missense_Mutation	SNP	ENST00000402938.3	hg19	CCDS5020.3	.	.	.	.	.	.	.	.	.	.	A	1.614	-0.523251	0.04141	.	.	ENSG00000111886	ENST00000402938	.	.	.	5.42	1.69	0.24217	.	0.544065	0.20224	N	0.096628	T	0.09379	0.0231	L	0.36672	1.1	0.09310	N	1	B	0.32543	0.375	B	0.32624	0.149	T	0.26121	-1.0112	8	.	.	.	.	5.6197	0.17450	0.7324:0.0:0.141:0.1267	.	66	P28476	GBRR2_HUMAN	H	66	.	.	Y	-	1	0	GABRR2	90066296	0.007000	0.16637	0.000000	0.03702	0.024000	0.10985	2.324000	0.43831	0.052000	0.16007	-0.360000	0.07572	TAT	.	.		0.473	GABRR2-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041482.3			G	90009577	A	G	90009577	3	3	98	1	0	0	0	0	1	0	0	0	6185	449	16	2	1308	2	GABRR2	6	90009577	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	10321148	90009577	81105490	63	13425										
BEND3	57673	hgsc.bcm.edu	37	chr6	107391941	107391941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cttctcaaagagctcgtacaCgtttagcaggtcccccgagg	10	13	1	1	rs142662918	byFrequency	TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:107391941C>T	ENST00000369042.1	-	4	644	c.454G>A	c.(454-456)Gtg>Atg	p.V152M	BEND3_ENST00000429433.2_Missense_Mutation_p.V152M			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	152										central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						AGCTCGTACACGTTTAGCAGG	0.582																																					p.V152M		Atlas-SNP	.											BEND3,NS,carcinoma,0,1	BEND3	70	.	0			c.G454A						.						128	123	124					6																	107391941		2203	4300	6503	SO:0001583	missense	57673	exon5			CGTACACGTTTAG	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"BEN domain containing"	23040	protein-coding gene	gene with protein product			"KIAA1553"	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.454G>A	chr6.hg19:g.107391941C>T	ENSP00000358038:p.Val152Met	54.0	0.0		144.0	59.0	NM_001080450	A2RRH2|Q9HCL9	Missense_Mutation	SNP	ENST00000369042.1	hg19	CCDS34507.1	.	.	.	.	.	.	.	.	.	.	T	1.798	-0.477781	0.04414	.	.	ENSG00000178409	ENST00000369042;ENST00000429433	.	.	.	4.88	-0.588	0.11687	.	0.828604	0.10973	N	0.613676	T	0.04182	0.0116	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39482	-0.9612	9	0.33141	T	0.24	-3.1766	0.5191	0.00609	0.1837:0.2269:0.1882:0.4012	.	152	Q5T5X7	BEND3_HUMAN	M	152	.	ENSP00000358038:V152M	V	-	1	0	BEND3	107498634	0.001000	0.12720	0.002000	0.10522	0.032000	0.12392	0.243000	0.18106	-0.951000	0.03654	-3.115000	0.00062	GTG	.	C|1.000;G|0.000		0.582	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913		T	107391941	C	T	107391941	3	4	98	1	0	0	0	0	1	0	0	0	1399	536	19	1	2036	1	BEND3	6	107391941	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	17382364	107391941	63723126	64	13426										
PDSS2	57107	hgsc.bcm.edu	37	chr6	107475922	107475922	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tccagtgccttgtttccatgGtaacgacacaggtcaatagc	9	11	1	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:107475922G>C	ENST00000369037.4	-	8	1378	c.1101C>G	c.(1099-1101)taC>taG	p.Y367*	PDSS2_ENST00000453874.2_Nonsense_Mutation_p.Y265*	NM_020381.3	NP_065114.3	Q86YH6	DLP1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 2	367					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|regulation of body fluid levels (GO:0050878)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(3)	19	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)		TGTTTCCATGGTAACGACACA	0.443																																					p.Y367X		Atlas-SNP	.											.	PDSS2	37	.	0			c.C1101G						.						80	75	77					6																	107475922		2203	4300	6503	SO:0001587	stop_gained	57107	exon8			TCCATGGTAACGA	AF254956	CCDS5059.1	6q21	2006-02-14	2006-02-14	2006-02-14	ENSG00000164494	ENSG00000164494			23041	protein-coding gene	gene with protein product		610564	"chromosome 6 open reading frame 210"	C6orf210		16262699	Standard	NM_020381		Approved	bA59I9.3	uc003prt.2	Q86YH6	OTTHUMG00000059359	ENST00000369037.4:c.1101C>G	chr6.hg19:g.107475922G>C	ENSP00000358033:p.Tyr367*	51.0	0.0		122.0	53.0	NM_020381	Q33DR4|Q4G158|Q5VU38|Q5VU39|Q9NR58	Nonsense_Mutation	SNP	ENST00000369037.4	hg19	CCDS5059.1	.	.	.	.	.	.	.	.	.	.	G	37	6.102109	0.97286	.	.	ENSG00000164494	ENST00000369037;ENST00000453874	.	.	.	5.53	5.53	0.82687	.	0.423542	0.28606	N	0.014745	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	19.4936	0.95062	0.0:0.0:1.0:0.0	.	.	.	.	X	367;265	.	ENSP00000358033:Y367X	Y	-	3	2	PDSS2	107582615	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.009000	0.88606	2.605000	0.88082	0.655000	0.94253	TAC	.	.		0.443	PDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131954.1	NM_020381		C	107475922	G	C	107475922	4	2	98	1	0	0	0	0	0	1	0	0	11703	1256	44	4	102	4	PDSS2	6	107475922	Nonsense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	83981	107475922	63639145	65	13427										
COL10A1	1300	hgsc.bcm.edu	37	chr6	116441243	116441244	+	Missense_Mutation	DNP	GG	GG	TT													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gctctgtgtgtactcacattGgagccactaggaatcctgag					rs138831203		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:116441243_116441244GG>TT	ENST00000327673.4	-	2	2442_2443	c.2035_2036CC>AA	c.(2035-2037)CCa>AAa	p.P679K	COL10A1_ENST00000243222.4_Missense_Mutation_p.P679K|NT5DC1_ENST00000319550.4_Intron|AL121963.1_ENST00000430695.1_5'Flank			Q03692	COAA1_HUMAN	collagen, type X, alpha 1	679	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Nonhelical region (NC1).				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	cell cortex (GO:0005938)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	13		all_cancers(87;0.0176)|all_epithelial(87;0.0263)|Colorectal(196;0.234)		all cancers(137;0.0157)|OV - Ovarian serous cystadenocarcinoma(136;0.0325)|GBM - Glioblastoma multiforme(226;0.0446)|Epithelial(106;0.0711)		TACTCACATTGGAGCCACTAGG	0.455																																					p.P679Q|p.P679T		Atlas-SNP	.											.	COL10A1	51	.	0			c.C2036A|c.C2035A						.																																			SO:0001583	missense	1300	exon3			CACATTGGAGCCA|ACATTGGAGCCAC		CCDS5105.1	6q21-q22	2013-01-16	2008-07-29		ENSG00000123500	ENSG00000123500		"Collagens"	2185	protein-coding gene	gene with protein product	"Schmid metaphyseal chondrodysplasia"	120110				2037056	Standard	XM_006715332		Approved		uc003pwm.3	Q03692	OTTHUMG00000015426	ENST00000327673.4:c.2035_2036delinsTT	chr6.hg19:g.116441243_116441244delinsTT	ENSP00000327368:p.Pro679Lys	38.0	0.0		97.0|96.0	43.0|42.0	NM_000493	A1L4P2	Missense_Mutation	SNP	ENST00000327673.4	hg19	CCDS5105.1																																																																																			.	.|G|1.000;T|0.000		0.455	COL10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041926.1			TT	116441244	GG	TT	116441243	3	4	98	1	0	0	0	0	1	0	0	0	3668	1348	47	3	10	3	COL10A1	6	116441243	Missense_Mutation	DNP	GG	TCGA-DD-A1EB-01A-11D-A12Z-10	8965321	116441243	54673824	66	13428										
ZUFSP	221302	hgsc.bcm.edu	37	chr6	116987856	116987857	+	Missense_Mutation	DNP	TC	TC	AA													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tcacatgagtttccatatctTcactgtgctcctctattttt							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:116987856_116987857TC>AA	ENST00000368576.3	-	2	742_743	c.499_500GA>TT	c.(499-501)GAa>TTa	p.E167L	ZUFSP_ENST00000471919.1_5'UTR|ZUFSP_ENST00000368573.1_Missense_Mutation_p.E167L	NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	167							metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		TTCCATATCTTCACTGTGCTCC	0.356																																					p.E167V|p.E167X		Atlas-SNP	.											.	ZUFSP	46	.	0			c.A500T|c.G499T						.																																			SO:0001583	missense	221302	exon2			ATATCTTCACTGT|TATCTTCACTGTG	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"Zinc fingers, C2H2-type"	21224	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 113"	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.499_500delinsAA	chr6.hg19:g.116987856_116987857delinsAA	ENSP00000357565:p.Glu167Leu	95.0	0.0		284.0|286.0	25.0|26.0	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000368576.3	hg19	CCDS5110.1																																																																																			.	.		0.356	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062		AA	116987857	TC	AA	116987856	3	1	98	1	0	0	0	0	1	0	0	0	18261	1783	62	4	1272	4	ZUFSP	6	116987856	Missense_Mutation	DNP	TC	TCGA-DD-A1EB-01A-11D-A12Z-10	546613	116987856	54127211	67	13429										
VGLL2	245806	hgsc.bcm.edu	37	chr6	117589420	117589421	+	Frame_Shift_Ins	INS	-	-	C													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cagcagtggcagcggcagctINScctcattttccagccaaacc							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:117589420_117589421insC	ENST00000326274.5	+	2	347_348	c.157_158insC	c.(157-159)tccfs	p.S53fs	VGLL2_ENST00000352536.3_Frame_Shift_Ins_p.S53fs	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	53					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|kidney(1)|lung(3)	5				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)		CAGCGGCAGCTCCTCATTTTCC	0.54																																					p.S53fs		Atlas-INDEL	.											.	VGLL2	18	.	0			c.157_158insC						.																																			SO:0001589	frameshift_variant	245806	exon2			.	AY056583	CCDS5114.1, CCDS5115.1	6q22.31	2014-03-03	2014-03-03		ENSG00000170162	ENSG00000170162			20232	protein-coding gene	gene with protein product		609979	"vestigial like 2 (Drosophila)"			12376544	Standard	NM_153453		Approved		uc003pxn.3	Q8N8G2	OTTHUMG00000015451	ENST00000326274.5:c.159dupC	chr6.hg19:g.117589422_117589422dupC	ENSP00000320957:p.Ser53fs	34.0	0.0		120.0	11.0	NM_182645	Q8WWX1	Frame_Shift_Ins	INS	ENST00000326274.5	hg19	CCDS5115.1																																																																																			.	.		0.54	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453		C	117589421	-	C	117589420	7	5	98	1	0	1	1	0	0	0	0	0	17174	1551	54	0	163	0	VGLL2	6	117589420	Frame_Shift_Ins	INS	-	TCGA-DD-A1EB-01A-11D-A12Z-10	601564	117589420	53525647	68	13430										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136582246	136582439	+	Stop_Codon_Del	DEL	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ttgtaatcttacttcatattTattattcctaaaagagagag					rs376948280|rs537502804|rs562481221|rs527483217|rs62431283|rs112744301|rs62431282|rs370252607|rs570210520|rs111800140|rs193167212|rs375440569	byFrequency	TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:136582246_136582439delTGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	ENST00000531224.1	-	0	2973_3017				BCLAF1_ENST00000031135.9_Stop_Codon_Del|BCLAF1_ENST00000392348.2_Stop_Codon_Del|BCLAF1_ENST00000530767.1_Stop_Codon_Del|BCLAF1_ENST00000527759.1_Stop_Codon_Del|BCLAF1_ENST00000353331.4_Stop_Codon_Del|BCLAF1_ENST00000527536.1_Stop_Codon_Del|BCLAF1_ENST00000529917.1_5'UTR	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1						apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		ACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATTTTATACCTTTTCTTCCTTGCGTCTGTCCTTCTTTTCTTCATTATTTTCCATGG	0.315																																					p.920_921del	Colon(142;1534 1789 5427 7063 28491)	Pindel	.											.	BCLAF1	203	.	0			c.2758_3016del						.																																			SO:0001567	stop_retained_variant	9774	exon13			.	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	Exception_encountered	chr6.hg19:g.136582246_136582439delTGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	Exception_encountered	0.0	0.0		10.0	10.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Frame_Shift_Del	DEL	ENST00000531224.1	hg19	CCDS5177.1																																																																																			.	.		0.315	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		-	136582439	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	-	136582246	7	5	98	1	0	1	0	1	0	0	0	0	1383	1769	61	0	1	0	BCLAF1	6	136582246	Stop_Codon_Del	DEL	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TCGA-DD-A1EB-01A-11D-A12Z-10	18992826	136582246	34532821	69	13431										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136589325	136589325	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ttcctcgtggtcggctaactCctgcaaagcctgagtattct	9	12	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:136589325C>A	ENST00000531224.1	-	10	2624	c.2372G>T	c.(2371-2373)gGa>gTa	p.G791V	BCLAF1_ENST00000031135.9_Missense_Mutation_p.G9V|BCLAF1_ENST00000392348.2_Missense_Mutation_p.G789V|BCLAF1_ENST00000530767.1_Missense_Mutation_p.G618V|BCLAF1_ENST00000527759.1_Missense_Mutation_p.G789V|BCLAF1_ENST00000353331.4_Missense_Mutation_p.G789V|BCLAF1_ENST00000527536.1_Missense_Mutation_p.G791V|BCLAF1_ENST00000529917.1_5'UTR	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	791					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		TCGGCTAACTCCTGCAAAGCC	0.378																																					p.G791V	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											BCLAF1_ENST00000531224,right_upper_lobe,carcinoma,0,1	BCLAF1	203	.	0			c.G2372T						.						195	182	186					6																	136589325		2203	4300	6503	SO:0001583	missense	9774	exon10			CTAACTCCTGCAA	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.2372G>T	chr6.hg19:g.136589325C>A	ENSP00000435210:p.Gly791Val	106.0	0.0		333.0	37.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.12|19.12	3.765070|3.765070	0.69878|0.69878	.|.	.|.	ENSG00000029363|ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000031135;ENST00000392348|ENST00000534762	T;T;T;T;T;T;T|.	0.46819|.	2.9;2.79;2.79;2.49;2.9;0.86;2.79|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	0.000000|.	0.64402|.	D|.	0.000014|.	T|T	0.47284|0.47284	0.1437|0.1437	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	0.999;1.0;0.999;0.999;1.0|.	D;D;D;D;D|.	0.87578|.	0.964;0.993;0.964;0.964;0.998|.	T|T	0.40961|0.40961	-0.9535|-0.9535	10|5	0.52906|.	T|.	0.07|.	-12.0323|-12.0323	18.9333|18.9333	0.92576|0.92576	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	789;119;789;791;618|.	Q9NYF8-2;B7Z8J9;Q9NYF8-3;Q9NYF8;Q9NYF8-4|.	.;.;.;BCLF1_HUMAN;.|.	V|S	791;789;791;618;789;9;789|57	ENSP00000435210:G791V;ENSP00000229446:G789V;ENSP00000435441:G791V;ENSP00000436501:G618V;ENSP00000434826:G789V;ENSP00000031135:G9V;ENSP00000376159:G789V|.	ENSP00000031135:G9V|.	G|R	-|-	2|3	0|2	BCLAF1|BCLAF1	136631018|136631018	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	4.211000|4.211000	0.58507|0.58507	2.492000|2.492000	0.84095|0.84095	0.484000|0.484000	0.47621|0.47621	GGA|AGG	.	.		0.378	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		A	136589325	C	A	136589325	3	1	98	1	0	0	0	0	1	0	0	0	1383	855	30	3	406	3	BCLAF1	6	136589325	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	7079	136589325	34525742	70	13432										
RPS6KA2	6196	hgsc.bcm.edu	37	chr6	166944752	166944752	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctttcttaaggaccttcatgGcgtagagctgcccagcgtcg	11	12	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr6:166944752G>A	ENST00000265678.4	-	3	489	c.266C>T	c.(265-267)gCc>gTc	p.A89V	RPS6KA2_ENST00000481261.2_5'UTR|RPS6KA2_ENST00000366863.2_5'UTR|Z98049.1_ENST00000598601.1_5'Flank|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.A114V|RPS6KA2_ENST00000503859.1_Missense_Mutation_p.A97V|RPS6KA2_ENST00000405189.3_5'UTR	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	89	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		GACCTTCATGGCGTAGAGCTG	0.507																																					p.A97V		Atlas-SNP	.											.	RPS6KA2	212	.	0			c.C290T						.						104	110	108					6																	166944752		2203	4300	6503	SO:0001583	missense	6196	exon4			TTCATGGCGTAGA	L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"ribosomal protein S6 kinase, 90kD, polypeptide 2"			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.266C>T	chr6.hg19:g.166944752G>A	ENSP00000265678:p.Ala89Val	47.0	0.0		108.0	34.0	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Missense_Mutation	SNP	ENST00000265678.4	hg19	CCDS5294.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.960598	0.74016	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000507371;ENST00000506565	T;T;T;T;T	0.76186	0.14;0.14;0.14;-1.0;-1.0	4.4	4.4	0.53042	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.82875	0.5132	M	0.76002	2.32	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.993	D;D;P	0.75020	0.985;0.974;0.835	D	0.85252	0.1045	10	0.87932	D	0	.	16.0683	0.80903	0.0:0.0:1.0:0.0	.	114;97;89	F2Z2J1;Q15349-3;Q15349	.;.;KS6A2_HUMAN	V	89;114;97;73;114	ENSP00000265678:A89V;ENSP00000422435:A114V;ENSP00000427015:A97V;ENSP00000423114:A73V;ENSP00000425148:A114V	ENSP00000265678:A89V	A	-	2	0	RPS6KA2	166864742	1.000000	0.71417	0.951000	0.38953	0.279000	0.26890	8.425000	0.90270	2.440000	0.82611	0.563000	0.77884	GCC	.	.		0.507	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135		A	166944752	G	A	166944752	3	1	98	1	0	0	0	0	1	0	0	0	13666	1203	42	3	2011	3	RPS6KA2	6	166944752	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	30355427	166944752	4170315	71	13433										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11464348	11464348	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ttttcgggtttgcacgccctCtccacagttctcccgcatat	7	15	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr7:11464348C>G	ENST00000423059.4	-	16	3609	c.3358G>C	c.(3358-3360)Gag>Cag	p.E1120Q	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1120	TSP type-1 11. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TGCACGCCCTCTCCACAGTTC	0.488										HNSCC(18;0.044)																											p.E1120Q		Atlas-SNP	.											.	THSD7A	219	.	0			c.G3358C						.						240	226	231					7																	11464348		1984	4170	6154	SO:0001583	missense	221981	exon15			CGCCCTCTCCACA		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.3358G>C	chr7.hg19:g.11464348C>G	ENSP00000406482:p.Glu1120Gln	57.0	0.0		153.0	14.0	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	hg19	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.000125	0.93227	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.60797	0.16	5.85	5.85	0.93711	.	0.045982	0.85682	D	0.000000	T	0.70002	0.3174	L	0.49778	1.585	0.80722	D	1	D	0.53745	0.962	D	0.65987	0.94	T	0.60459	-0.7259	10	0.15066	T	0.55	.	20.1577	0.98120	0.0:1.0:0.0:0.0	.	1120	Q9UPZ6	THS7A_HUMAN	Q	1120	ENSP00000406482:E1120Q	ENSP00000262042:E1120Q	E	-	1	0	THSD7A	11430873	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.247000	0.78257	2.767000	0.95098	0.655000	0.94253	GAG	.	.		0.488	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		G	11464348	C	G	11464348	3	3	98	1	0	0	0	0	1	0	0	0	15894	922	32	4	1667	4	THSD7A	7	11464348	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10		11464348	147674315	72	13434										
CCDC129	223075	hgsc.bcm.edu	37	chr7	31691634	31691634	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gaatttcagttaggagaccgGgctcagcaaatcagagaagg	13	7	3	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr7:31691634G>T	ENST00000407970.3	+	13	2831	c.2793G>T	c.(2791-2793)cgG>cgT	p.R931R	CCDC129_ENST00000319386.3_Silent_p.R783R|CCDC129_ENST00000451887.2_Silent_p.R957R|CCDC129_ENST00000409210.1_Silent_p.R839R	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	931										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TAGGAGACCGGGCTCAGCAAA	0.493																																					p.R957R		Atlas-SNP	.											.	CCDC129	127	.	0			c.G2871T						.						73	60	64					7																	31691634		2203	4300	6503	SO:0001819	synonymous_variant	223075	exon13			AGACCGGGCTCAG	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.2793G>T	chr7.hg19:g.31691634G>T		113.0	0.0		444.0	210.0	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Silent	SNP	ENST00000407970.3	hg19	CCDS5435.2																																																																																			.	.		0.493	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		T	31691634	G	T	31691634	2	4	98	1	0	0	0	0	0	0	0	1	2766	1219	43	3		3	CCDC129	7	31691634	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	20227286	31691634	127447029	73	13435										
UPP1	7378	hgsc.bcm.edu	37	chr7	48147819	48147819	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tctttgtcctttgcagcggcCgtggtgtgtgtcaccctcct	11	13	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr7:48147819C>T	ENST00000331803.4	+	10	1421	c.798C>T	c.(796-798)gcC>gcT	p.A266A	UPP1_ENST00000395564.4_Silent_p.A266A|UPP1_ENST00000429491.2_Silent_p.A129A|UPP1_ENST00000482015.1_3'UTR|UPP1_ENST00000341253.4_Silent_p.A266A			Q16831	UPP1_HUMAN	uridine phosphorylase 1	266					cellular response to glucose starvation (GO:0042149)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)	uridine phosphorylase activity (GO:0004850)			breast(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	18					Fluorouracil(DB00544)	TTGCAGCGGCCGTGGTGTGTG	0.612																																					p.A266A		Atlas-SNP	.											.	UPP1	35	.	0			c.C798T						.						93	87	89					7																	48147819		2203	4300	6503	SO:0001819	synonymous_variant	7378	exon9			AGCGGCCGTGGTG	AK096167	CCDS5507.1	7p12.3	2012-10-02	2003-08-28	2003-08-29	ENSG00000183696	ENSG00000183696	2.4.2.3		12576	protein-coding gene	gene with protein product		191730	"uridine phosphorylase"	UP		752472, 11807789	Standard	NM_003364		Approved	UPASE, UPP, UDRPASE	uc003toj.3	Q16831	OTTHUMG00000129253	ENST00000331803.4:c.798C>T	chr7.hg19:g.48147819C>T		20.0	0.0		58.0	27.0	NM_003364	D3DVM4|Q15362	Silent	SNP	ENST00000331803.4	hg19	CCDS5507.1																																																																																			.	.		0.612	UPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251360.1	NM_003364		T	48147819	C	T	48147819	2	4	98	1	0	0	0	0	0	0	0	1	17027	639	23	1		1	UPP1	7	48147819	Silent	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	16456185	48147819	110990844	74	13436										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48559835	48559835	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgcaactggcctcgcagggcAcagtacttctcctcttgagg	11	13	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr7:48559835A>G	ENST00000435803.1	+	53	14020	c.13996A>G	c.(13996-13998)Aca>Gca	p.T4666A	ABCA13_ENST00000544596.1_Missense_Mutation_p.T396A	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4666					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTCGCAGGGCACAGTACTTCT	0.522																																					p.T4666A		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A13996G						.						74	69	71					7																	48559835		1944	4151	6095	SO:0001583	missense	154664	exon53			CAGGGCACAGTAC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.13996A>G	chr7.hg19:g.48559835A>G	ENSP00000411096:p.Thr4666Ala	98.0	0.0		275.0	92.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.339449	0.41398	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.85629	-2.01;-2.01;-2.01	5.32	4.15	0.48705	.	0.132497	0.34268	N	0.004104	D	0.84179	0.5415	L	0.45470	1.425	0.35129	D	0.76778	B;P;D	0.58970	0.187;0.459;0.984	B;B;P	0.54706	0.074;0.225;0.759	T	0.83121	-0.0118	10	0.16896	T	0.51	.	9.6005	0.39601	0.8441:0.0:0.0:0.1559	.	396;2368;4666	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	A	4666;439;396	ENSP00000411096:T4666A;ENSP00000391042:T439A;ENSP00000442634:T396A	ENSP00000391042:T439A	T	+	1	0	ABCA13	48530381	0.994000	0.37717	0.907000	0.35723	0.137000	0.21094	2.250000	0.43178	0.845000	0.35118	0.533000	0.62120	ACA	.	.		0.522	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48559835	A	G	48559835	3	3	98	1	0	0	0	0	1	0	0	0	31	159	6	2	14035	2	ABCA13	7	48559835	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	412016	48559835	110578828	75	13437										
ELN	2006	hgsc.bcm.edu	37	chr7	73474235	73474235	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gggttagttcctggtgtcggCgtggctcctggagttggcgt	18	8	0	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr7:73474235C>T	ENST00000252034.7	+	23	1833	c.1434C>T	c.(1432-1434)ggC>ggT	p.G478G	ELN_ENST00000320492.7_Silent_p.G397G|ELN_ENST00000414324.1_Silent_p.G454G|ELN_ENST00000445912.1_Silent_p.G478G|ELN_ENST00000458204.1_Silent_p.G468G|ELN_ENST00000358929.4_Silent_p.G513G|ELN_ENST00000357036.5_Silent_p.G483G|ELN_ENST00000380553.4_Silent_p.G342G|ELN_ENST00000320399.6_Silent_p.G478G|ELN_ENST00000380584.4_Silent_p.G445G|ELN_ENST00000380575.4_Silent_p.G449G|ELN_ENST00000380562.4_Silent_p.G484G|ELN_ENST00000380576.5_Silent_p.G459G|ELN_ENST00000429192.1_Silent_p.G464G|CTB-51J22.1_ENST00000435932.1_RNA	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				CTGGTGTCGGCGTGGCTCCTG	0.572			T	PAX5	B-ALL		"Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"																														p.G483G		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN	81	.	0			c.C1449T						.						247	236	239					7																	73474235		2203	4300	6503	SO:0001819	synonymous_variant	2006	exon23			TGTCGGCGTGGCT		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"tropoelastin", "supravalvular aortic stenosis", "Williams-Beuren syndrome"	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1434C>T	chr7.hg19:g.73474235C>T		108.0	0.0		507.0	29.0	NM_001081754	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Silent	SNP	ENST00000252034.7	hg19	CCDS5562.2																																																																																			.	.		0.572	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501		T	73474235	C	T	73474235	2	4	98	1	0	0	0	0	0	0	0	1	5073	755	27	1		1	ELN	7	73474235	Silent	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	24914400	73474235	85664428	76	13438										
TFEC	22797	hgsc.bcm.edu	37	chr7	115624439	115624439	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	acaagaggcccaccacttggCactgcaggttgtgaccattt	10	12	0	2	rs34738022	byFrequency	TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr7:115624439C>A	ENST00000265440.7	-	2	237	c.57G>T	c.(55-57)gtG>gtT	p.V19V	TFEC_ENST00000393485.1_Silent_p.V19V|TFEC_ENST00000320239.7_Silent_p.V19V|TFEC_ENST00000484212.1_Silent_p.V109V	NM_012252.3	NP_036384.1	O14948	TFEC_HUMAN	transcription factor EC	19	Necessary for transcriptional transactivation.				cellular response to heat (GO:0034605)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|kidney(1)|large_intestine(5)|lung(13)|prostate(2)|skin(1)|urinary_tract(2)	25			STAD - Stomach adenocarcinoma(10;0.00878)			CACCACTTGGCACTGCAGGTT	0.483																																					p.V19V		Atlas-SNP	.											.	TFEC	51	.	0			c.G57T						.						187	166	173					7																	115624439		2203	4300	6503	SO:0001819	synonymous_variant	22797	exon2			ACTTGGCACTGCA	D43945	CCDS5762.1, CCDS34738.1, CCDS59076.1	7q31.2	2013-05-21			ENSG00000105967	ENSG00000105967		"Basic helix-loop-helix proteins"	11754	protein-coding gene	gene with protein product		604732				9256061	Standard	NM_012252		Approved	TCFEC, TFECL, bHLHe34	uc003vhj.2	O14948	OTTHUMG00000023518	ENST00000265440.7:c.57G>T	chr7.hg19:g.115624439C>A		127.0	0.0		393.0	158.0	NM_001018058	B2R8X5|Q5H9U8|Q709A4|Q8N6J9	Silent	SNP	ENST00000265440.7	hg19	CCDS5762.1																																																																																			.	C|0.983;T|0.017		0.483	TFEC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059839.4	NM_012252		A	115624439	C	A	115624439	2	1	98	1	0	0	0	0	0	0	0	1	15817	697	25	3		3	TFEC	7	115624439	Silent	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	42150204	115624439	43514224	77	13439										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117375351	117375351	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	aaagtgcaggggctttcagtGctgcgattttcaagaggtgc	14	7	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr7:117375351G>T	ENST00000160373.3	-	15	3751	c.3660C>A	c.(3658-3660)agC>agA	p.S1220R		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1220					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		GGCTTTCAGTGCTGCGATTTT	0.388																																					p.S1220R		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.C3660A						.						68	74	72					7																	117375351		2203	4300	6503	SO:0001583	missense	83992	exon15			TTCAGTGCTGCGA		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.3660C>A	chr7.hg19:g.117375351G>T	ENSP00000160373:p.Ser1220Arg	72.0	0.0		151.0	67.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.18|17.18	3.323752|3.323752	0.60634|0.60634	.|.	.|.	ENSG00000077063|ENSG00000077063	ENST00000446636|ENST00000160373	.|T	.|0.48522	.|0.81	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|0.242732	.|0.56097	.|D	.|0.000039	T|T	0.48352|0.48352	0.1495|0.1495	M|M	0.81802|0.81802	2.56|2.56	0.40475|0.40475	D|D	0.980382|0.980382	.|P	.|0.39717	.|0.684	.|B	.|0.32393	.|0.145	T|T	0.59794|0.59794	-0.7387|-0.7387	5|10	.|0.72032	.|D	.|0.01	-1.2748|-1.2748	13.5357|13.5357	0.61646|0.61646	0.0809:0.0:0.9191:0.0|0.0809:0.0:0.9191:0.0	.|.	.|1220	.|Q8WZ74	.|CTTB2_HUMAN	N|R	708|1220	.|ENSP00000160373:S1220R	.|ENSP00000160373:S1220R	H|S	-|-	1|3	0|2	CTTNBP2|CTTNBP2	117162587|117162587	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	2.355000|2.355000	0.44107|0.44107	2.745000|2.745000	0.94114|0.94114	0.655000|0.655000	0.94253|0.94253	CAC|AGC	.	.		0.388	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		T	117375351	G	T	117375351	3	4	98	1	0	0	0	0	1	0	0	0	4047	1310	46	3	1367	3	CTTNBP2	7	117375351	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	1750912	117375351	41763312	78	13440										
KLHDC10	23008	hgsc.bcm.edu	37	chr7	129760678	129760679	+	Nonsense_Mutation	DNP	GT	GT	TA													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	atgacgtccatgtgtgtaatGtgaagtataagagatgggct							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr7:129760678_129760679GT>TA	ENST00000335420.5	+	4	699_700	c.565_566GT>TA	c.(565-567)GTg>TAg	p.V189*		NM_014997.3	NP_055812.1	Q6PID8	KLD10_HUMAN	kelch domain containing 10	189						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|liver(2)|lung(10)|prostate(1)	17						TGTGTGTAATGTGAAGTATAAG	0.475																																					p.V189L|p.V189E		Atlas-SNP	.											.	KLHDC10	36	.	0			c.G565T|c.T566A						.																																			SO:0001587	stop_gained	23008	exon4			TGTAATGTGAAGT|GTAATGTGAAGTA		CCDS5815.1	7q32.2	2008-08-20			ENSG00000128607	ENSG00000128607			22194	protein-coding gene	gene with protein product	"scruin like at the midline homolog (Drosophila)"	615152					Standard	NM_014997		Approved	KIAA0265, slim	uc003vpj.2	Q6PID8	OTTHUMG00000157654	Exception_encountered	chr7.hg19:g.129760678_129760679delinsTA	ENSP00000334140:p.Val189*	74.0|75.0	0.0		325.0|323.0	76.0|72.0	NM_014997	Q86Y99|Q92554	Missense_Mutation	SNP	ENST00000335420.5	hg19	CCDS5815.1																																																																																			.	.		0.475	KLHDC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349347.2			TA	129760679	GT	TA	129760678	4	4	98	1	0	0	0	0	0	1	0	0	8364	1377	48	3	579	3	KLHDC10	7	129760678	Nonsense_Mutation	DNP	GT	TCGA-DD-A1EB-01A-11D-A12Z-10	12385327	129760678	29377985	79	13441										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131883315	131883315	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	accttgacatgggaggcgatGtcgcgaaattccaggcccag	13	11	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr7:131883315G>T	ENST00000359827.3	-	13	3629	c.2667C>A	c.(2665-2667)gaC>gaA	p.D889E	PLXNA4_ENST00000321063.4_Missense_Mutation_p.D889E			Q9HCM2	PLXA4_HUMAN	plexin A4	889	IPT/TIG 1.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						GGGAGGCGATGTCGCGAAATT	0.572																																					p.D889E		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C2667A						.						76	78	77					7																	131883315		1979	4170	6149	SO:0001583	missense	91584	exon13			GGCGATGTCGCGA	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2667C>A	chr7.hg19:g.131883315G>T	ENSP00000352882:p.Asp889Glu	23.0	0.0		41.0	10.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	8.524	0.869477	0.17322	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.76709	-1.04;-1.04	5.94	5.07	0.68467	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.050751	0.85682	D	0.000000	T	0.59851	0.2224	N	0.13235	0.315	0.47214	D	0.999352	B	0.06786	0.001	B	0.13407	0.009	T	0.55062	-0.8199	10	0.34782	T	0.22	.	7.9778	0.30166	0.1355:0.0:0.7345:0.13	.	889	Q9HCM2	PLXA4_HUMAN	E	889	ENSP00000323194:D889E;ENSP00000352882:D889E	ENSP00000323194:D889E	D	-	3	2	PLXNA4	131533855	1.000000	0.71417	1.000000	0.80357	0.307000	0.27823	1.079000	0.30766	1.521000	0.48983	0.650000	0.86243	GAC	.	.		0.572	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131883315	G	T	131883315	3	4	98	1	0	0	0	0	1	0	0	0	12131	1368	48	3	3097	3	PLXNA4	7	131883315	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	2122637	131883315	27255348	80	13442										
FAM180A	389558	hgsc.bcm.edu	37	chr7	135418945	135418945	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agccggcggatgtctgggatGctcttggggatgacgttgtt	17	7	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr7:135418945G>T	ENST00000338588.3	-	3	565	c.300C>A	c.(298-300)agC>agA	p.S100R	FAM180A_ENST00000435869.1_Intron|FAM180A_ENST00000415751.1_Missense_Mutation_p.S100R	NM_205855.3	NP_995327.1	Q6UWF9	F180A_HUMAN	family with sequence similarity 180, member A	100						extracellular region (GO:0005576)				endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)	14						TGTCTGGGATGCTCTTGGGGA	0.597																																					p.S100R		Atlas-SNP	.											.	FAM180A	32	.	0			c.C300A						.						131	120	124					7																	135418945		2203	4300	6503	SO:0001583	missense	389558	exon3			TGGGATGCTCTTG	AC091736, AK290250, AK310180, AY358803	CCDS5841.1	7q33	2008-07-25			ENSG00000189320	ENSG00000189320			33773	protein-coding gene	gene with protein product						12975309, 12690205	Standard	NM_205855		Approved	HWKM1940, UNQ1940	uc003vtd.3	Q6UWF9	OTTHUMG00000155537	ENST00000338588.3:c.300C>A	chr7.hg19:g.135418945G>T	ENSP00000342336:p.Ser100Arg	41.0	0.0		92.0	41.0	NM_205855	B2RP85	Missense_Mutation	SNP	ENST00000338588.3	hg19	CCDS5841.1	.	.	.	.	.	.	.	.	.	.	G	7.017	0.557989	0.13436	.	.	ENSG00000189320	ENST00000338588;ENST00000415751	T;T	0.30182	1.54;1.54	5.44	4.55	0.56014	.	0.544661	0.23063	N	0.052359	T	0.19846	0.0477	N	0.22421	0.69	0.34191	D	0.672043	B	0.06786	0.001	B	0.04013	0.001	T	0.19976	-1.0289	10	0.21014	T	0.42	2.6297	11.0861	0.48089	0.0915:0.0:0.9084:0.0	.	100	Q6UWF9	F180A_HUMAN	R	100	ENSP00000342336:S100R;ENSP00000395467:S100R	ENSP00000342336:S100R	S	-	3	2	FAM180A	135069485	1.000000	0.71417	0.995000	0.50966	0.463000	0.32649	2.834000	0.48167	1.278000	0.44430	0.561000	0.74099	AGC	.	.		0.597	FAM180A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340554.2	NM_205855		T	135418945	G	T	135418945	3	4	98	1	0	0	0	0	1	0	0	0	5512	1310	46	3	225	3	FAM180A	7	135418945	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	3535630	135418945	23719718	81	13443										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2976080	2976080	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gtacccattctgaaatggggGtggatctggacagttctgta	13	7	3	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr8:2976080G>T	ENST00000520002.1	-	43	6829	c.6274C>A	c.(6274-6276)Ccc>Acc	p.P2092T	CSMD1_ENST00000602557.1_Missense_Mutation_p.P2092T|CSMD1_ENST00000537824.1_Missense_Mutation_p.P2091T|CSMD1_ENST00000602723.1_Missense_Mutation_p.P2092T|CSMD1_ENST00000542608.1_Missense_Mutation_p.P2091T|CSMD1_ENST00000400186.3_Missense_Mutation_p.P2092T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2092	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TGAAATGGGGGTGGATCTGGA	0.408																																					p.P2091T		Atlas-SNP	.											CSMD1_ENST00000537824,right_upper_lobe,carcinoma,0,2	CSMD1	1469	.	0			c.C6271A						.						125	120	121					8																	2976080		1951	4136	6087	SO:0001583	missense	64478	exon42			ATGGGGGTGGATC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.6274C>A	chr8.hg19:g.2976080G>T	ENSP00000430733:p.Pro2092Thr	57.0	0.0		140.0	55.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.18|11.18	1.563363|1.563363	0.27915|0.27915	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	T;T;T;T|.	0.66995|.	-0.24;-0.24;-0.24;-0.24|.	5.03|5.03	5.03|5.03	0.67393|0.67393	Complement control module (2);Sushi/SCR/CCP (3);|.	0.144744|.	0.46758|.	D|.	0.000261|.	T|T	0.50274|0.50274	0.1606|0.1606	L|L	0.38531|0.38531	1.155|1.155	0.21527|0.21527	N|N	0.999656|0.999656	D;B;B|.	0.57257|.	0.979;0.047;0.321|.	P;B;B|.	0.57846|.	0.828;0.216;0.205|.	T|T	0.44559|0.44559	-0.9320|-0.9320	10|5	0.52906|.	T|.	0.07|.	.|.	18.734|18.734	0.91748|0.91748	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	2092;2092;2091|.	E5RIG2;Q96PZ7;F5H2I8|.	.;CSMD1_HUMAN;.|.	T|N	2092;2092;1953;2091;2091|1571	ENSP00000383047:P2092T;ENSP00000430733:P2092T;ENSP00000441462:P2091T;ENSP00000446243:P2091T|.	ENSP00000320445:P1953T|.	P|T	-|-	1|2	0|0	CSMD1|CSMD1	2963487|2963487	0.891000|0.891000	0.30450|0.30450	0.111000|0.111000	0.21465|0.21465	0.976000|0.976000	0.68499|0.68499	3.294000|3.294000	0.51787|0.51787	2.481000|2.481000	0.83766|0.83766	0.563000|0.563000	0.77884|0.77884	CCC|ACC	.	.		0.408	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	2976080	G	T	2976080	3	4	98	1	0	0	0	0	1	0	0	0	3946	1261	44	3	4539	3	CSMD1	8	2976080	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10		2976080	143387942	82	13444										
SGCZ	137868	hgsc.bcm.edu	37	chr8	13965672	13965672	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gtataagaggaagcccttacCtgagatcttgggatggctct	12	8	2	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr8:13965672C>T	ENST00000382080.1	-	6	1335	c.620G>A	c.(619-621)aGg>aAg	p.R207K	SGCZ_ENST00000421524.2_Splice_Site_p.R160K	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	194					membrane organization (GO:0061024)|muscle cell cellular homeostasis (GO:0046716)|muscle cell development (GO:0055001)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|sarcoglycan complex (GO:0016012)				NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		AAGCCCTTACCTGAGATCTTG	0.448																																					p.R207K		Atlas-SNP	.											SGCZ,NS,malignant_melanoma,0,1	SGCZ	96	.	0			c.G620A						.						98	87	91					8																	13965672		2203	4300	6503	SO:0001630	splice_region_variant	137868	exon6			CCTTACCTGAGAT	AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053			14075	protein-coding gene	gene with protein product		608113				12189167	Standard	XM_006716287		Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.620+1G>A	chr8.hg19:g.13965672C>T		76.0	0.0		178.0	64.0	NM_139167	Q6REU0	Missense_Mutation	SNP	ENST00000382080.1	hg19	CCDS5992.2	.	.	.	.	.	.	.	.	.	.	C	10.95	1.497027	0.26861	.	.	ENSG00000185053	ENST00000382080;ENST00000421524	D;D	0.94613	-3.47;-3.47	5.39	3.11	0.35812	.	0.178901	0.64402	N	0.000015	D	0.85115	0.5623	N	0.12853	0.265	0.42529	D	0.993038	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.77405	-0.2600	9	.	.	.	.	7.5185	0.27614	0.0:0.7315:0.0:0.2685	.	160;207	Q08AT0;Q96LD1-2	.;.	K	207;160	ENSP00000371512:R207K;ENSP00000405224:R160K	.	R	-	2	0	SGCZ	14010043	1.000000	0.71417	1.000000	0.80357	0.586000	0.36452	1.534000	0.36051	1.337000	0.45525	0.655000	0.94253	AGG	.	.		0.448	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207636.2	NM_139167	Missense_Mutation	T	13965672	C	T	13965672	5	4	98	1	0	0	0	0	0	0	1	0	14219	695	24	3	330	3	SGCZ	8	13965672	Splice_Site	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	10989592	13965672	132398350	83	13445										
MMP16	4325	hgsc.bcm.edu	37	chr8	89339405	89339405	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	atgatgcacgaaatccaaccGtcttccagtgctgaatgtga	9	10	1	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr8:89339405G>C	ENST00000286614.6	-	1	312	c.31C>G	c.(31-33)Cgg>Ggg	p.R11G	MMP16_ENST00000544227.1_5'UTR|RP11-586K2.1_ENST00000520849.1_RNA|RP11-586K2.1_ENST00000521433.1_RNA|RP11-586K2.1_ENST00000523254.1_RNA	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	11					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	AAATCCAACCGTCTTCCAGTG	0.488																																					p.R11G		Atlas-SNP	.											.	MMP16	176	.	0			c.C31G						.						182	159	167					8																	89339405		2203	4300	6503	SO:0001583	missense	4325	exon1			CCAACCGTCTTCC	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.31C>G	chr8.hg19:g.89339405G>C	ENSP00000286614:p.Arg11Gly	65.0	0.0		113.0	32.0	NM_005941	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	hg19	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.288698	0.40494	.	.	ENSG00000156103	ENST00000286614;ENST00000522726	T;T	0.52983	2.34;0.64	5.44	3.6	0.41247	.	0.359425	0.26590	N	0.023524	T	0.27798	0.0684	N	0.08118	0	0.43729	D	0.996214	B;B	0.29253	0.239;0.001	B;B	0.32211	0.142;0.006	T	0.10428	-1.0630	10	0.66056	D	0.02	.	8.543	0.33404	0.0776:0.0:0.7657:0.1567	.	11;11	P51512-2;P51512	.;MMP16_HUMAN	G	11;28	ENSP00000286614:R11G;ENSP00000429147:R28G	ENSP00000286614:R11G	R	-	1	2	MMP16	89408521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.630000	0.54273	0.613000	0.30089	0.563000	0.77884	CGG	.	.		0.488	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		C	89339405	G	C	89339405	3	2	98	1	0	0	0	0	1	0	0	0	9664	1144	40	4	1988	4	MMP16	8	89339405	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	75373733	89339405	57024617	84	13446										
MTBP	27085	hgsc.bcm.edu	37	chr8	121530146	121530146	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctcagacaactggtaatagtAatcactatcatcatcatgtg	6	9	5	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr8:121530146A>G	ENST00000305949.1	+	19	2347	c.2302A>G	c.(2302-2304)Aat>Gat	p.N768D		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	768	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TGGTAATAGTAATCACTATCA	0.393																																					p.N768D		Atlas-SNP	.											.	MTBP	77	.	0			c.A2302G						.						99	79	86					8																	121530146		2203	4299	6502	SO:0001583	missense	27085	exon19			AATAGTAATCACT		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"MDM2 (mouse double minute 2)-binding protein, 104kD", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.2302A>G	chr8.hg19:g.121530146A>G	ENSP00000303398:p.Asn768Asp	34.0	0.0		108.0	46.0	NM_022045	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	hg19	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	a	10.38	1.334468	0.24253	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.32	-5.81	0.02340	.	1.054780	0.07326	N	0.878357	T	0.28001	0.0690	L	0.44542	1.39	0.09310	N	1	B	0.29037	0.231	B	0.26969	0.075	T	0.25433	-1.0132	9	0.19590	T	0.45	-1.2426	8.2711	0.31844	0.2955:0.4052:0.2992:0.0	.	768	Q96DY7	MTBP_HUMAN	D	768	.	ENSP00000303398:N768D	N	+	1	0	MTBP	121599327	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.143000	0.10296	-0.820000	0.04318	-1.479000	0.00991	AAT	.	.		0.393	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		G	121530146	A	G	121530146	3	3	98	1	0	0	0	0	1	0	0	0	9921	362	13	2	2376	2	MTBP	8	121530146	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	32190741	121530146	24833876	85	13447										
KDM4C	23081	hgsc.bcm.edu	37	chr9	6981046	6981046	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	caccattgatcacacgaagcCtactccagcatccacccctg	5	18	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr9:6981046C>T	ENST00000381309.3	+	9	1608	c.1043C>T	c.(1042-1044)cCt>cTt	p.P348L	KDM4C_ENST00000543771.1_Missense_Mutation_p.P348L|KDM4C_ENST00000536108.1_Missense_Mutation_p.P167L|KDM4C_ENST00000381306.3_Missense_Mutation_p.P348L|RP11-403H13.1_ENST00000445708.1_RNA|KDM4C_ENST00000428870.2_Missense_Mutation_p.P35L|KDM4C_ENST00000442236.2_Missense_Mutation_p.P167L|KDM4C_ENST00000535193.1_Missense_Mutation_p.P370L	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	348					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						CACACGAAGCCTACTCCAGCA	0.458																																					p.P370L		Atlas-SNP	.											.	KDM4C	186	.	0			c.C1109T						.						118	108	111					9																	6981046		2203	4300	6503	SO:0001583	missense	23081	exon9			CGAAGCCTACTCC	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	17071	protein-coding gene	gene with protein product	"tudor domain containing 14C"	605469	"jumonji domain containing 2C"	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.1043C>T	chr9.hg19:g.6981046C>T	ENSP00000370710:p.Pro348Leu	38.0	0.0		92.0	45.0	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	hg19	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.696839	0.88830	.	.	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870	T;T;T;T;T;T;T	0.19938	2.28;2.28;2.46;2.37;2.63;2.11;3.35	5.54	5.54	0.83059	.	0.370310	0.27792	N	0.017829	T	0.47340	0.1440	M	0.63428	1.95	0.80722	D	1	D;D;P;P;D	0.89917	0.999;1.0;0.956;0.93;0.979	D;D;P;P;P	0.83275	0.927;0.996;0.822;0.647;0.887	T	0.42137	-0.9469	10	0.87932	D	0	-7.4993	19.4631	0.94927	0.0:1.0:0.0:0.0	.	167;348;370;348;348	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	L	370;348;348;348;167;167;35	ENSP00000442382:P370L;ENSP00000445427:P348L;ENSP00000370710:P348L;ENSP00000370707:P348L;ENSP00000409353:P167L;ENSP00000440656:P167L;ENSP00000405739:P35L	ENSP00000370707:P348L	P	+	2	0	KDM4C	6971046	0.998000	0.40836	0.994000	0.49952	0.984000	0.73092	6.010000	0.70753	2.594000	0.87642	0.585000	0.79938	CCT	.	.		0.458	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		T	6981046	C	T	6981046	3	4	98	1	0	0	0	0	1	0	0	0	8139	681	24	3	1143	3	KDM4C	9	6981046	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10		6981046	134232385	86	13448										
PLAA	9373	hgsc.bcm.edu	37	chr9	26923264	26923264	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gaatcaatggttgcgtgagaCagttctttttcaaaagcctt	9	7	3	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr9:26923264C>A	ENST00000397292.3	-	7	1368	c.951G>T	c.(949-951)ctG>ctT	p.L317L	PLAA_ENST00000520884.1_Silent_p.L317L	NM_001031689.2	NP_001026859.1	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	317					inflammatory response (GO:0006954)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	phospholipase A2 activator activity (GO:0016005)			breast(1)|endometrium(7)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	17		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		TTGCGTGAGACAGTTCTTTTT	0.388																																					p.L317L	Melanoma(175;2670 2735 14091 35526)	Atlas-SNP	.											.	PLAA	48	.	0			c.G951T						.						191	172	179					9																	26923264		2203	4300	6503	SO:0001819	synonymous_variant	9373	exon7			GTGAGACAGTTCT	AF083395	CCDS35000.1	9p21	2013-01-10			ENSG00000137055	ENSG00000137055		"WD repeat domain containing"	9043	protein-coding gene	gene with protein product	"DOA1 homolog (S. cerevisiae)"	603873				9931468, 10644453	Standard	NM_001031689		Approved	PLAP, PLA2P, FLJ11281, FLJ12699, DOA1	uc003zqd.3	Q9Y263	OTTHUMG00000019708	ENST00000397292.3:c.951G>T	chr9.hg19:g.26923264C>A		111.0	0.0		343.0	122.0	NM_001031689	Q53EU5|Q5VY33|Q9NUL8|Q9NVE9|Q9UF53|Q9Y5L1	Silent	SNP	ENST00000397292.3	hg19	CCDS35000.1																																																																																			.	.		0.388	PLAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051958.2	NM_001031689		A	26923264	C	A	26923264	2	1	98	1	0	0	0	0	0	0	0	1	12020	465	17	3		3	PLAA	9	26923264	Silent	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	19942218	26923264	114290167	87	13449										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35382500	35382500	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tcgctttgcagcctccaactTtggggtaagtatcatgtaaa	9	9	1	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr9:35382500T>G	ENST00000378495.3	+	20	2777	c.2555T>G	c.(2554-2556)tTt>tGt	p.F852C	UNC13B_ENST00000396787.1_Missense_Mutation_p.F864C|UNC13B_ENST00000378496.4_Missense_Mutation_p.F852C	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	852					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GCCTCCAACTTTGGGGTAAGT	0.413																																					p.F852C		Atlas-SNP	.											.	UNC13B	153	.	0			c.T2555G						.						181	152	161					9																	35382500		2203	4300	6503	SO:0001583	missense	10497	exon20			CCAACTTTGGGGT	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.2555T>G	chr9.hg19:g.35382500T>G	ENSP00000367756:p.Phe852Cys	73.0	0.0		233.0	26.0	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	hg19	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.664918	0.88251	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	D;D;D	0.86164	-1.95;-1.88;-2.08	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.93949	0.8063	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.991;0.998	D	0.94855	0.8017	10	0.87932	D	0	-13.7557	15.5777	0.76404	0.0:0.0:0.0:1.0	.	852;852	F8W8M9;O14795	.;UN13B_HUMAN	C	864;852;852;439	ENSP00000380006:F864C;ENSP00000367756:F852C;ENSP00000367757:F852C	ENSP00000367756:F852C	F	+	2	0	UNC13B	35372500	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.680000	0.84062	2.077000	0.62373	0.482000	0.46254	TTT	.	.		0.413	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		G	35382500	T	G	35382500	3	3	98	1	0	0	0	0	1	0	0	0	17000	1841	64	5	2633	5	UNC13B	9	35382500	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	8459236	35382500	105830931	88	13450										
APBA1	320	hgsc.bcm.edu	37	chr9	72064664	72064664	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gatggatccccagccagactCcacaatcaccacacctagga	7	16	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr9:72064664C>A	ENST00000265381.4	-	10	2239	c.2017G>T	c.(2017-2019)Gag>Tag	p.E673*		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	673	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						CAGCCAGACTCCACAATCACC	0.493																																					p.E673X		Atlas-SNP	.											.	APBA1	96	.	0			c.G2017T						.						87	79	82					9																	72064664		2203	4300	6503	SO:0001587	stop_gained	320	exon10			CAGACTCCACAAT	AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.2017G>T	chr9.hg19:g.72064664C>A	ENSP00000265381:p.Glu673*	48.0	0.0		98.0	38.0	NM_001163	O14914|O60570|Q5VYR8	Nonsense_Mutation	SNP	ENST00000265381.4	hg19	CCDS6630.1	.	.	.	.	.	.	.	.	.	.	C	41	9.140791	0.99078	.	.	ENSG00000107282	ENST00000265381	.	.	.	5.78	5.78	0.91487	.	0.052003	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-22.4807	20.0124	0.97464	0.0:1.0:0.0:0.0	.	.	.	.	X	673	.	ENSP00000265381:E673X	E	-	1	0	APBA1	71254484	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.818000	0.86416	2.749000	0.94314	0.655000	0.94253	GAG	.	.		0.493	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		A	72064664	C	A	72064664	4	1	98	1	0	0	0	0	0	1	0	0	756	864	30	3	512	3	APBA1	9	72064664	Nonsense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	36682164	72064664	69148767	89	13451										
SMC5	23137	hgsc.bcm.edu	37	chr9	72879327	72879327	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgccatttgccttggtttagCtggaaaacctgctttcatgg	10	9	1	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr9:72879327C>G	ENST00000361138.5	+	2	351	c.293C>G	c.(292-294)gCt>gGt	p.A98G		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	98					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						CTTGGTTTAGCTGGAAAACCT	0.378																																					p.A98G		Atlas-SNP	.											.	SMC5	96	.	0			c.C293G						.						155	148	151					9																	72879327		2203	4300	6503	SO:0001583	missense	23137	exon2			GTTTAGCTGGAAA	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"Structural maintenance of chromosomes proteins"	20465	protein-coding gene	gene with protein product		609386	"SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.293C>G	chr9.hg19:g.72879327C>G	ENSP00000354957:p.Ala98Gly	92.0	0.0		331.0	155.0	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	hg19	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.044858	0.55110	.	.	ENSG00000198887	ENST00000361138	T	0.49139	0.79	5.77	4.82	0.62117	RecF/RecN/SMC (1);	0.051736	0.85682	D	0.000000	T	0.26955	0.0660	N	0.10837	0.055	0.80722	D	1	P	0.49447	0.924	B	0.41764	0.366	T	0.16748	-1.0392	10	0.02654	T	1	-21.2983	16.2955	0.82768	0.0:0.8676:0.1324:0.0	.	98	Q8IY18	SMC5_HUMAN	G	98	ENSP00000354957:A98G	ENSP00000354957:A98G	A	+	2	0	SMC5	72069147	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.475000	0.60210	2.885000	0.99019	0.655000	0.94253	GCT	.	.		0.378	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		G	72879327	C	G	72879327	3	3	98	1	0	0	0	0	1	0	0	0	14801	797	28	4	299	4	SMC5	9	72879327	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	814663	72879327	68334104	90	13452										
KIF27	55582	hgsc.bcm.edu	37	chr9	86457172	86457172	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	actctgatggtgctagttgcCgccgaattgcttcccctacc	9	14	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr9:86457172C>T	ENST00000297814.2	-	17	3844	c.3701G>A	c.(3700-3702)cGg>cAg	p.R1234Q	RP11-575L7.4_ENST00000591217.1_RNA|KIF27_ENST00000413982.1_Missense_Mutation_p.R1168Q|KIF27_ENST00000334204.2_Missense_Mutation_p.R1137Q	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	1234					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						TGCTAGTTGCCGCCGAATTGC	0.408																																					p.R1234Q		Atlas-SNP	.											.	KIF27	103	.	0			c.G3701A						.						77	68	71					9																	86457172		2203	4300	6503	SO:0001583	missense	55582	exon17			AGTTGCCGCCGAA	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"Kinesins"	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.3701G>A	chr9.hg19:g.86457172C>T	ENSP00000297814:p.Arg1234Gln	138.0	0.0		603.0	245.0	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	hg19	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.793026	0.31685	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.69040	-0.37;-0.33;-0.2	4.24	2.22	0.28083	.	1.256500	0.05800	N	0.611956	T	0.49236	0.1545	L	0.28274	0.84	0.09310	N	1	B;B;B	0.18166	0.017;0.026;0.026	B;B;B	0.06405	0.001;0.002;0.001	T	0.33292	-0.9874	10	0.26408	T	0.33	.	2.9014	0.05707	0.0:0.4491:0.2395:0.3114	.	1137;1168;1234	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	Q	1234;1168;1137	ENSP00000297814:R1234Q;ENSP00000401688:R1168Q;ENSP00000333928:R1137Q	ENSP00000297814:R1234Q	R	-	2	0	KIF27	85646992	0.150000	0.22732	0.055000	0.19348	0.831000	0.47069	0.349000	0.20055	1.011000	0.39340	-0.385000	0.06624	CGG	.	.		0.408	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		T	86457172	C	T	86457172	3	4	98	1	0	0	0	0	1	0	0	0	8305	652	23	1	512	1	KIF27	9	86457172	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	13577845	86457172	54756259	91	13453										
RALGDS	5900	hgsc.bcm.edu	37	chr9	135984101	135984101	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gttccgagtgctccagctggGccaggagaaggtgggcacgg	18	10	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr9:135984101G>A	ENST00000372050.3	-	5	758	c.737C>T	c.(736-738)gCc>gTc	p.A246V	RALGDS_ENST00000542690.1_Missense_Mutation_p.A317V|RALGDS_ENST00000469972.1_5'UTR|RALGDS_ENST00000372062.3_Missense_Mutation_p.A217V|RALGDS_ENST00000393157.3_Missense_Mutation_p.A245V|RALGDS_ENST00000372047.3_Missense_Mutation_p.A234V|RALGDS_ENST00000393160.3_Missense_Mutation_p.A191V	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	246	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		CTCCAGCTGGGCCAGGAGAAG	0.647			T	CIITA	"PMBL, Hodgkin Lymphona, "																																p.A246V	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.C737T						.						65	61	62					9																	135984101		2203	4300	6503	SO:0001583	missense	5900	exon5			AGCTGGGCCAGGA	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.737C>T	chr9.hg19:g.135984101G>A	ENSP00000361120:p.Ala246Val	33.0	0.0		50.0	32.0	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Missense_Mutation	SNP	ENST00000372050.3	hg19	CCDS6959.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.387448	0.82902	.	.	ENSG00000160271	ENST00000372050;ENST00000372047;ENST00000393160;ENST00000372051;ENST00000393157;ENST00000542690;ENST00000372062	T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58	5.67	4.75	0.60458	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (2);	0.175728	0.40302	N	0.001124	T	0.47266	0.1436	L	0.44542	1.39	0.35272	D	0.780525	D;D;D;P;P;P;P;P	0.69078	0.997;0.961;0.986;0.919;0.851;0.919;0.919;0.919	D;P;P;B;B;B;B;B	0.73380	0.98;0.572;0.843;0.253;0.253;0.253;0.253;0.253	T	0.60125	-0.7324	10	0.56958	D	0.05	.	14.8459	0.70259	0.0:0.0:0.8554:0.1446	.	317;217;246;234;191;245;234;246	F5H6M6;E7ER93;Q12967-2;Q8TEK9;Q6KH11;E7ERZ0;Q6PCE1;Q12967	.;.;.;.;.;.;.;GNDS_HUMAN	V	246;234;191;15;245;317;217	ENSP00000361120:A246V;ENSP00000361117:A234V;ENSP00000376867:A191V;ENSP00000376864:A245V;ENSP00000437518:A317V;ENSP00000361132:A217V	ENSP00000361117:A234V	A	-	2	0	RALGDS	134973922	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	5.409000	0.66374	1.349000	0.45751	0.655000	0.94253	GCC	.	.		0.647	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266		A	135984101	G	A	135984101	3	1	98	1	0	0	0	0	1	0	0	0	13031	1203	42	3	2063	3	RALGDS	9	135984101	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	49526929	135984101	5229330	92	13454										
CTNNA3	29119	hgsc.bcm.edu	37	chr10	67829142	67829142	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gatgtcgttgcttgtatcatCccatatctcaatctcagcat	6	11	3	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr10:67829142C>A	ENST00000433211.2	-	15	2257	c.2083G>T	c.(2083-2085)Gat>Tat	p.D695Y	CTNNA3_ENST00000373744.4_Missense_Mutation_p.D695Y|CTNNA3_ENST00000373735.1_5'UTR	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						CTTGTATCATCCCATATCTCA	0.403																																					p.D695Y		Atlas-SNP	.											.	CTNNA3	401	.	0			c.G2083T						.						281	236	251					10																	67829142		2203	4300	6503	SO:0001583	missense	29119	exon15			TATCATCCCATAT	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.2083G>T	chr10.hg19:g.67829142C>A	ENSP00000389714:p.Asp695Tyr	121.0	0.0		354.0	140.0	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	hg19	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.288651	0.80914	.	.	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000373735	T;T;T	0.44083	0.93;0.93;0.93	5.29	5.29	0.74685	.	0.000000	0.56097	D	0.000035	T	0.71307	0.3324	M	0.89968	3.075	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78125	-0.2326	10	0.87932	D	0	-16.2886	16.4194	0.83753	0.0:1.0:0.0:0.0	.	695	Q9UI47	CTNA3_HUMAN	Y	695;695;34	ENSP00000389714:D695Y;ENSP00000362849:D695Y;ENSP00000362840:D34Y	ENSP00000362840:D34Y	D	-	1	0	CTNNA3	67499148	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.529000	0.81952	2.483000	0.83821	0.591000	0.81541	GAT	.	.		0.403	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		A	67829142	C	A	67829142	3	1	98	1	0	0	0	0	1	0	0	0	4016	855	30	3	620	3	CTNNA3	10	67829142	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10		67829142	67705605	93	13455										
ITPRIP	85450	hgsc.bcm.edu	37	chr10	106075119	106075119	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gcgatccaggggcactgagcGgccggagcaccagagctctg	16	13	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr10:106075119G>A	ENST00000337478.1	-	2	862	c.691C>T	c.(691-693)Cgc>Tgc	p.R231C	ITPRIP_ENST00000358187.2_Missense_Mutation_p.R231C|RP11-127L20.5_ENST00000472915.2_RNA|ITPRIP_ENST00000278071.2_Missense_Mutation_p.R231C	NM_001272013.1	NP_001258942.1	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein	231						membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(9)|upper_aerodigestive_tract(1)	20						GGCACTGAGCGGCCGGAGCAC	0.657																																					p.R231C		Atlas-SNP	.											.	ITPRIP	44	.	0			c.C691T						.						38	41	40					10																	106075119		2203	4300	6503	SO:0001583	missense	85450	exon2			CTGAGCGGCCGGA	AB051541	CCDS7557.1	10q25.1	2011-04-28	2011-04-28	2008-08-11	ENSG00000148841	ENSG00000148841			29370	protein-coding gene	gene with protein product			"KIAA1754", "inositol 1,4,5-triphosphate receptor interacting protein"	KIAA1754		11214970, 16990268	Standard	NM_001272012		Approved	bA127L20.2, DANGER	uc001kye.4	Q8IWB1	OTTHUMG00000019003	ENST00000337478.1:c.691C>T	chr10.hg19:g.106075119G>A	ENSP00000337178:p.Arg231Cys	38.0	0.0		77.0	43.0	NM_001272013	D3DRA5|Q5JU17|Q96MS8|Q9C0A9	Missense_Mutation	SNP	ENST00000337478.1	hg19	CCDS7557.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.811038	0.32053	.	.	ENSG00000148841	ENST00000337478;ENST00000278071;ENST00000358187	T;T;T	0.24538	1.85;1.85;1.85	5.25	4.22	0.49857	.	0.878856	0.10244	N	0.698087	T	0.24470	0.0593	L	0.46157	1.445	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.05289	-1.0894	10	0.56958	D	0.05	-16.0835	9.5846	0.39508	0.0:0.1709:0.6579:0.1713	.	231	Q8IWB1	IPRI_HUMAN	C	231	ENSP00000337178:R231C;ENSP00000278071:R231C;ENSP00000350915:R231C	ENSP00000278071:R231C	R	-	1	0	ITPRIP	106065109	0.005000	0.15991	0.869000	0.34112	0.849000	0.48306	1.705000	0.37867	2.601000	0.87937	0.467000	0.42956	CGC	.	.		0.657	ITPRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050204.1	NM_033397		A	106075119	G	A	106075119	3	1	98	1	0	0	0	0	1	0	0	0	7932	1116	39	1	956	1	ITPRIP	10	106075119	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	38245977	106075119	29459628	94	13456										
ITPRIP	85450	hgsc.bcm.edu	37	chr10	106075611	106075611	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cgccacctgctccagtgcctCcttttcggccgccagccgag	10	19	0	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr10:106075611C>G	ENST00000337478.1	-	2	370	c.199G>C	c.(199-201)Gag>Cag	p.E67Q	ITPRIP_ENST00000358187.2_Missense_Mutation_p.E67Q|RP11-127L20.5_ENST00000472915.2_RNA|ITPRIP_ENST00000278071.2_Missense_Mutation_p.E67Q	NM_001272013.1	NP_001258942.1	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein	67						membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(9)|upper_aerodigestive_tract(1)	20						TCCAGTGCCTCCTTTTCGGCC	0.642																																					p.E67Q		Atlas-SNP	.											.	ITPRIP	44	.	0			c.G199C						.						69	67	68					10																	106075611		2203	4300	6503	SO:0001583	missense	85450	exon2			GTGCCTCCTTTTC	AB051541	CCDS7557.1	10q25.1	2011-04-28	2011-04-28	2008-08-11	ENSG00000148841	ENSG00000148841			29370	protein-coding gene	gene with protein product			"KIAA1754", "inositol 1,4,5-triphosphate receptor interacting protein"	KIAA1754		11214970, 16990268	Standard	NM_001272012		Approved	bA127L20.2, DANGER	uc001kye.4	Q8IWB1	OTTHUMG00000019003	ENST00000337478.1:c.199G>C	chr10.hg19:g.106075611C>G	ENSP00000337178:p.Glu67Gln	30.0	0.0		80.0	25.0	NM_001272013	D3DRA5|Q5JU17|Q96MS8|Q9C0A9	Missense_Mutation	SNP	ENST00000337478.1	hg19	CCDS7557.1	.	.	.	.	.	.	.	.	.	.	C	7.020	0.558557	0.13436	.	.	ENSG00000148841	ENST00000337478;ENST00000278071;ENST00000358187;ENST00000458723	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	5.44	4.53	0.55603	.	0.556674	0.19045	N	0.124184	T	0.05181	0.0138	N	0.14661	0.345	0.24609	N	0.99373	P	0.50272	0.933	B	0.44108	0.441	T	0.25047	-1.0143	10	0.02654	T	1	-19.7616	5.153	0.15019	0.0:0.7158:0.0:0.2842	.	67	Q8IWB1	IPRI_HUMAN	Q	67	ENSP00000337178:E67Q;ENSP00000278071:E67Q;ENSP00000350915:E67Q;ENSP00000414141:E67Q	ENSP00000278071:E67Q	E	-	1	0	ITPRIP	106065601	1.000000	0.71417	1.000000	0.80357	0.293000	0.27360	2.633000	0.46519	2.560000	0.86352	0.563000	0.77884	GAG	.	.		0.642	ITPRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050204.1	NM_033397		G	106075611	C	G	106075611	3	3	98	1	0	0	0	0	1	0	0	0	7932	864	30	4	1448	4	ITPRIP	10	106075611	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	492	106075611	29459136	95	13457										
TECTB	6975	hgsc.bcm.edu	37	chr10	114046139	114046139	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgagagccaactgtctctcaActtctacactgtaagtggtc	8	11	3	1	rs538658987		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr10:114046139A>G	ENST00000369422.3	+	4	473	c.473A>G	c.(472-474)aAc>aGc	p.N158S		NM_058222.1	NP_478129.1	Q96PL2	TECTB_HUMAN	tectorin beta	158	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.198)		Epithelial(162;0.0143)|all cancers(201;0.0242)		CTGTCTCTCAACTTCTACACT	0.493																																					p.N158S		Atlas-SNP	.											.	TECTB	35	.	0			c.A473G						.						133	104	113					10																	114046139		2203	4300	6503	SO:0001583	missense	6975	exon4			CTCTCAACTTCTA	AF312827	CCDS7571.1	10q25-q26	2005-06-09			ENSG00000119913	ENSG00000119913			11721	protein-coding gene	gene with protein product		602653				9079715	Standard	NM_058222		Approved		uc001kzr.1	Q96PL2	OTTHUMG00000019056	ENST00000369422.3:c.473A>G	chr10.hg19:g.114046139A>G	ENSP00000358430:p.Asn158Ser	66.0	0.0		142.0	55.0	NM_058222	Q5VW53	Missense_Mutation	SNP	ENST00000369422.3	hg19	CCDS7571.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.776326	0.49786	.	.	ENSG00000119913	ENST00000369422	D	0.81739	-1.53	6.17	5.03	0.67393	Zona pellucida sperm-binding protein (3);	0.000000	0.85682	D	0.000000	D	0.85111	0.5622	L	0.57536	1.79	0.58432	D	0.999997	D	0.71674	0.998	D	0.71656	0.974	T	0.81621	-0.0850	10	0.09084	T	0.74	.	13.7445	0.62868	0.8716:0.1283:0.0:0.0	.	158	Q96PL2	TECTB_HUMAN	S	158	ENSP00000358430:N158S	ENSP00000358430:N158S	N	+	2	0	TECTB	114036129	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	1.137000	0.42214	0.533000	0.62120	AAC	.	.		0.493	TECTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050381.1	NM_058222		G	114046139	A	G	114046139	3	3	98	1	0	0	0	0	1	0	0	0	15763	43	2	2	487	2	TECTB	10	114046139	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	7970528	114046139	21488608	96	13458										
TACC2	10579	hgsc.bcm.edu	37	chr10	123846536	123846536	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gcagggctgacctgggagcgGaacttgccaggtgccggtgt	18	10	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr10:123846536G>T	ENST00000369005.1	+	4	4861	c.4521G>T	c.(4519-4521)cgG>cgT	p.R1507R	TACC2_ENST00000334433.3_Silent_p.R1507R|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Silent_p.R1507R|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Silent_p.R1507R|TACC2_ENST00000453444.2_Silent_p.R1507R	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1507					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CCTGGGAGCGGAACTTGCCAG	0.627																																					p.R1507R		Atlas-SNP	.											.	TACC2	271	.	0			c.G4521T						.						46	47	47					10																	123846536		2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			GGAGCGGAACTTG	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.4521G>T	chr10.hg19:g.123846536G>T		27.0	0.0		53.0	17.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.627	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123846536	G	T	123846536	2	4	98	1	0	0	0	0	0	0	0	1	15517	1161	41	3		3	TACC2	10	123846536	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	9800397	123846536	11688211	97	13459										
SPTY2D1	144108	hgsc.bcm.edu	37	chr11	18638422	18638422	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ataaggctatagatacatacCttttcgtctcagctcctctt	5	11	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:18638422C>G	ENST00000336349.5	-	2	410	c.175G>C	c.(175-177)Gcc>Ccc	p.A59P	SPTY2D1_ENST00000543776.1_5'UTR	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	59										breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						AGATACATACCTTTTCGTCTC	0.398																																					p.A59P		Atlas-SNP	.											.	SPTY2D1	72	.	0			c.G175C						.						144	132	136					11																	18638422		2198	4293	6491	SO:0001630	splice_region_variant	144108	exon2			ACATACCTTTTCG	BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.175+1G>C	chr11.hg19:g.18638422C>G		103.0	0.0		255.0	107.0	NM_194285	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Missense_Mutation	SNP	ENST00000336349.5	hg19	CCDS31441.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.085053	0.76642	.	.	ENSG00000179119	ENST00000336349;ENST00000333429	T	0.26373	1.74	5.54	3.47	0.39725	.	0.127779	0.52532	D	0.000072	T	0.29976	0.0750	M	0.66939	2.045	0.43000	D	0.994511	P	0.43169	0.8	B	0.41860	0.368	T	0.05162	-1.0902	9	.	.	.	-1.5863	13.0466	0.58931	0.0:0.8895:0.0:0.1105	.	59	Q68D10	SPT2_HUMAN	P	59	ENSP00000337991:A59P	.	A	-	1	0	SPTY2D1	18594998	1.000000	0.71417	0.997000	0.53966	0.799000	0.45148	1.843000	0.39259	0.565000	0.29255	0.655000	0.94253	GCC	.	.		0.398	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285	Missense_Mutation	G	18638422	C	G	18638422	5	3	98	1	0	0	0	0	0	0	1	0	15141	695	24	4	1902	4	SPTY2D1	11	18638422	Splice_Site	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10		18638422	116368094	98	13460										
MPEG1	219972	hgsc.bcm.edu	37	chr11	58979138	58979139	+	Frame_Shift_Ins	INS	-	-	G													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gtgagtggattcttctgctcINScaacttttggcagaggagga					rs528545112		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:58979138_58979139insG	ENST00000361050.3	-	1	1285_1286	c.1200_1201insC	c.(1198-1203)ttggagfs	p.E401fs	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	401						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				TTCTTCTGCTCCAACTTTTGGC	0.54																																					p.E401fs		Atlas-Indel,Pindel	.											.	MPEG1	72	.	0			c.1201_1202insC						.																																			SO:0001589	frameshift_variant	219972	exon1			.	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"macrophage expressed gene 1"	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.1200_1201insC	chr11.hg19:g.58979138_58979139insG	ENSP00000354335:p.Glu401fs	55.0	0.0		127.0	38.0	NM_001039396	Q2M1T6|Q8TEF8	Frame_Shift_Ins	INS	ENST00000361050.3	hg19	CCDS41650.1																																																																																			.	.		0.54	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		G	58979139	-	G	58979138	7	5	98	1	0	1	1	0	0	0	0	0	9732	864	30	0	953	0	MPEG1	11	58979138	Frame_Shift_Ins	INS	-	TCGA-DD-A1EB-01A-11D-A12Z-10	40340716	58979138	76027378	99	13461										
C11orf66	220004	hgsc.bcm.edu	37	chr11	61249803	61249803	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gtcgggaggatttcaagcccCgtgtgggcagtcacgtaggc	16	10	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:61249803C>T	ENST00000338608.2	+	3	255	c.130C>T	c.(130-132)Cgt>Tgt	p.R44C	RP11-286N22.8_ENST00000544880.1_Intron|PPP1R32_ENST00000432063.2_Missense_Mutation_p.R44C|RP11-286N22.8_ENST00000543044.1_3'UTR	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	44							phosphatase binding (GO:0019902)										TTTCAAGCCCCGTGTGGGCAG	0.617											OREG0021002	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R44C		Atlas-SNP	.											.	.	.	.	0			c.C130T						.						59	59	59					11																	61249803		2202	4299	6501	SO:0001583	missense	220004	exon3			AAGCCCCGTGTGG	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	28869	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 66"	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.130C>T	chr11.hg19:g.61249803C>T	ENSP00000344140:p.Arg44Cys	31.0	0.0	1052	71.0	22.0	NM_001170753	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	hg19	CCDS8008.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.818735	0.50633	.	.	ENSG00000162148	ENST00000432063;ENST00000338608	T;T	0.54071	0.59;1.17	5.04	4.1	0.47936	.	0.670270	0.13266	N	0.400890	T	0.66896	0.2836	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.65773	0.911;0.938	T	0.66364	-0.5942	10	0.87932	D	0	-6.7839	12.1234	0.53903	0.1722:0.8278:0.0:0.0	.	44;44	Q7Z5V6-2;Q7Z5V6	.;PPR32_HUMAN	C	44	ENSP00000391560:R44C;ENSP00000344140:R44C	ENSP00000344140:R44C	R	+	1	0	C11orf66	61006379	0.886000	0.30341	0.655000	0.29622	0.241000	0.25554	1.704000	0.37857	1.207000	0.43291	0.655000	0.94253	CGT	.	.		0.617	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017		T	61249803	C	T	61249803	3	4	98	1	0	0	0	0	1	0	0	0	1658	652	23	1	136	1	C11orf66	11	61249803	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	2270665	61249803	73756713	100	13462										
GANAB	23193	hgsc.bcm.edu	37	chr11	62407128	62407128	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gaactctcttcacaggtcttAaagttgcttctatccacagc	6	12	4	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:62407128A>G	ENST00000356638.3	-	2	130	c.114T>C	c.(112-114)ttT>ttC	p.F38F	GANAB_ENST00000540933.1_5'UTR|GANAB_ENST00000346178.4_Silent_p.F38F|GANAB_ENST00000534779.1_Intron|GANAB_ENST00000534422.1_5'Flank	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	38					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	CACAGGTCTTAAAGTTGCTTC	0.463																																					p.F38F	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											.	GANAB	110	.	0			c.T114C						.						84	83	84					11																	62407128		2202	4299	6501	SO:0001819	synonymous_variant	23193	exon2			GGTCTTAAAGTTG	AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.114T>C	chr11.hg19:g.62407128A>G		90.0	0.0		194.0	86.0	NM_198334	A6NC20|Q8WTS9|Q9P0X0	Silent	SNP	ENST00000356638.3	hg19	CCDS8026.1																																																																																			.	.		0.463	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334		G	62407128	A	G	62407128	2	3	98	1	0	0	0	0	0	0	0	1	6241	359	13	2		2	GANAB	11	62407128	Silent	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	1157325	62407128	72599388	101	13463										
KAT5	10524	hgsc.bcm.edu	37	chr11	65479799	65479799	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gggagccaggggaggtgggtAgagcccgaggccccccagta	19	11	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:65479799A>G	ENST00000377046.3	+	1	284				KAT5_ENST00000530446.1_Missense_Mutation_p.R21G|KAT5_ENST00000534650.1_5'Flank|KAT5_ENST00000341318.4_Missense_Mutation_p.R21G|KAT5_ENST00000352980.4_Intron	NM_006388.3	NP_006379.2	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5						androgen receptor signaling pathway (GO:0030521)|cellular response to estradiol stimulus (GO:0071392)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|double-strand break repair (GO:0006302)|histone acetylation (GO:0016573)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of growth (GO:0040008)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|repressing transcription factor binding (GO:0070491)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)	21						GGAGGTGGGTAGAGCCCGAGG	0.721																																					p.R21G		Atlas-SNP	.											.	KAT5	36	.	0			c.A61G						.						12	15	14					11																	65479799		2184	4281	6465	SO:0001627	intron_variant	10524	exon1			GTGGGTAGAGCCC	U74667	CCDS8109.1, CCDS8110.1, CCDS31610.1, CCDS55771.1	11q13	2013-01-10	2008-07-04	2008-07-04	ENSG00000172977	ENSG00000172977		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	5275	protein-coding gene	gene with protein product	"Tat interacting protein, 60kDa", "K-acetyltransferase 5"	601409	"HIV-1 Tat interactive protein, 60kDa"	HTATIP		8607265	Standard	NM_006388		Approved	TIP60, PLIP, cPLA2, HTATIP1, ESA1, ZC2HC5	uc001ofk.3	Q92993	OTTHUMG00000166617	ENST00000377046.3:c.12+49A>G	chr11.hg19:g.65479799A>G		56.0	0.0		104.0	37.0	NM_182710	B4E3C7|C9JL99|O95624|Q13430|Q17RW5|Q561W3|Q6GSE8|Q9BWK7	Missense_Mutation	SNP	ENST00000377046.3	hg19	CCDS31610.1	.	.	.	.	.	.	.	.	.	.	A	14.84	2.655700	0.47467	.	.	ENSG00000172977	ENST00000341318;ENST00000530446	T;T	0.43294	0.97;0.95	4.78	3.64	0.41730	.	0.295993	0.28499	N	0.015121	T	0.25827	0.0629	.	.	.	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.05716	-1.0868	9	0.22706	T	0.39	-2.548	7.1587	0.25652	0.8984:0.0:0.1016:0.0	.	21;21	B4E3C7;Q92993-3	.;.	G	21	ENSP00000340330:R21G;ENSP00000434765:R21G	ENSP00000340330:R21G	R	+	1	2	KAT5	65236375	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.646000	0.37249	0.961000	0.38030	0.459000	0.35465	AGA	.	.		0.721	KAT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390866.2	NM_006388		G	65479799	A	G	65479799	1	3	98	0	1	0	0	0	0	0	0	0	7992	412	15	2		2	KAT5	11	65479799	Intron	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	3072671	65479799	69526717	102	13464										
KDM2A	22992	hgsc.bcm.edu	37	chr11	66975117	66975117	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	aatgtcatcagcctcgagttTagccacaccaggctggagaa	10	11	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:66975117T>A	ENST00000529006.2	+	6	890	c.444T>A	c.(442-444)ttT>ttA	p.F148L	KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000398645.2_Missense_Mutation_p.F148L	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	148	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						GCCTCGAGTTTAGCCACACCA	0.478																																					p.F148L		Atlas-SNP	.											.	KDM2A	80	.	0			c.T444A						.						63	66	65					11																	66975117		1978	4146	6124	SO:0001583	missense	22992	exon6			CGAGTTTAGCCAC	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13606	protein-coding gene	gene with protein product	"F-box protein FBL11", "jumonji C domain-containing histone demethylase 1A"	605657	"F-box and leucine-rich repeat protein 11"	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.444T>A	chr11.hg19:g.66975117T>A	ENSP00000432786:p.Phe148Leu	42.0	0.0		125.0	50.0	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Missense_Mutation	SNP	ENST00000529006.2	hg19	CCDS44657.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.742863	0.89573	.	.	ENSG00000173120	ENST00000398645;ENST00000529006	T;T	0.69806	-0.43;-0.43	5.34	0.0679	0.14368	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	T	0.81564	0.4849	H	0.94582	3.555	0.80722	D	1	D	0.69078	0.997	P	0.61533	0.89	T	0.81391	-0.0954	10	0.59425	D	0.04	-9.7026	9.1103	0.36723	0.0:0.5684:0.0:0.4316	.	148	Q9Y2K7	KDM2A_HUMAN	L	148	ENSP00000381640:F148L;ENSP00000432786:F148L	ENSP00000381640:F148L	F	+	3	2	KDM2A	66731693	0.997000	0.39634	0.999000	0.59377	0.974000	0.67602	0.528000	0.23002	0.023000	0.15187	0.533000	0.62120	TTT	.	.		0.478	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308		A	66975117	T	A	66975117	3	1	98	1	0	0	0	0	1	0	0	0	8133	1751	61	4	462	4	KDM2A	11	66975117	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	1495318	66975117	68031399	103	13465										
KDM2A	22992	hgsc.bcm.edu	37	chr11	66986855	66986855	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tatgcagttaaaaatatacaAcattgaagatcggacacggg	9	6	0	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:66986855A>G	ENST00000529006.2	+	10	1384	c.938A>G	c.(937-939)aAc>aGc	p.N313S	KDM2A_ENST00000526258.1_3'UTR|snoU13_ENST00000459034.1_RNA|KDM2A_ENST00000398645.2_Missense_Mutation_p.N313S	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	313	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						AAAATATACAACATTGAAGAT	0.383																																					p.N313S		Atlas-SNP	.											.	KDM2A	80	.	0			c.A938G						.						64	63	63					11																	66986855		1860	4098	5958	SO:0001583	missense	22992	exon10			TATACAACATTGA	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13606	protein-coding gene	gene with protein product	"F-box protein FBL11", "jumonji C domain-containing histone demethylase 1A"	605657	"F-box and leucine-rich repeat protein 11"	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.938A>G	chr11.hg19:g.66986855A>G	ENSP00000432786:p.Asn313Ser	58.0	0.0		153.0	65.0	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Missense_Mutation	SNP	ENST00000529006.2	hg19	CCDS44657.1	.	.	.	.	.	.	.	.	.	.	A	8.080	0.772219	0.16051	.	.	ENSG00000173120	ENST00000398645;ENST00000529006	T;T	0.71222	-0.55;-0.55	5.65	3.21	0.36854	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.175408	0.64402	N	0.000012	T	0.48095	0.1481	N	0.16368	0.405	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	10	0.30078	T	0.28	-11.8304	4.8899	0.13722	0.66:0.1616:0.1783:0.0	.	313	Q9Y2K7	KDM2A_HUMAN	S	313	ENSP00000381640:N313S;ENSP00000432786:N313S	ENSP00000381640:N313S	N	+	2	0	KDM2A	66743431	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.869000	0.27996	1.100000	0.41517	0.528000	0.53228	AAC	.	.		0.383	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308		G	66986855	A	G	66986855	3	3	98	1	0	0	0	0	1	0	0	0	8133	43	2	2	972	2	KDM2A	11	66986855	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	11738	66986855	68019661	104	13466										
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249121	71249121	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	catgggctgctgtggctgctCtggaggctgtggctccggct	17	11	1	0	rs200585722		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:71249121C>G	ENST00000398534.3	+	1	51	c.20C>G	c.(19-21)tCt>tGt	p.S7C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	7						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						TGTGGCTGCTCTGGAGGCTGT	0.657																																					p.S7C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.C20G						.						47	66	60					11																	71249121		2189	4282	6471	SO:0001583	missense	57830	exon1			GCTGCTCTGGAGG	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"Keratin associated proteins"	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.20C>G	chr11.hg19:g.71249121C>G	ENSP00000420723:p.Ser7Cys	72.0	0.0		324.0	17.0	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	hg19	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	c	3.358	-0.131059	0.06753	.	.	ENSG00000241233	ENST00000398534	T	0.01527	4.8	1.57	1.57	0.23409	.	.	.	.	.	T	0.03564	0.0102	M	0.74389	2.26	0.09310	N	1	P	0.39094	0.659	B	0.43225	0.412	T	0.34204	-0.9838	9	0.62326	D	0.03	.	3.9595	0.09404	0.0:0.775:0.0:0.225	.	7	O75690	KRA58_HUMAN	C	7	ENSP00000420723:S7C	ENSP00000420723:S7C	S	+	2	0	KRTAP5-8	70926769	0.030000	0.19436	0.804000	0.32291	0.223000	0.24884	-0.589000	0.05767	1.182000	0.42928	0.514000	0.50259	TCT	.	.		0.657	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046		G	71249121	C	G	71249121	3	3	98	1	0	0	0	0	1	0	0	0	8576	913	32	4	22	4	KRTAP5-8	11	71249121	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	4262266	71249121	63757395	105	13467										
MAML2	84441	hgsc.bcm.edu	37	chr11	95825206	95825206	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ggctgagaagatggttgttgCtgctgctgctgctgctgttg	16	7	0	2	rs547023702|rs149006316	byFrequency	TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:95825206C>T	ENST00000524717.1	-	2	3273	c.1989G>A	c.(1987-1989)caG>caA	p.Q663Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	663					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				atggttgttgctgctgctgct	0.517			T	"MECT1, CRTC3"	salivary gland mucoepidermoid								C|||	2	0.000399361	0	0	5008	,	,		18052	0		0	False		,,,				2504	0.002				p.Q663Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.G1989A						.						44	50	48					11																	95825206		2191	4282	6473	SO:0001819	synonymous_variant	84441	exon2			TTGTTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1989G>A	chr11.hg19:g.95825206C>T		57.0	0.0		240.0	25.0	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.		0.517	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825206	C	T	95825206	2	4	98	1	0	0	0	0	0	0	0	1	9215	796	28	3		3	MAML2	11	95825206	Silent	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	24576085	95825206	39181310	106	13468										
PDGFD	80310	hgsc.bcm.edu	37	chr11	103870889	103870889	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gtcaggagcaggttcctgggGtagctgttcgggaatctagg	17	7	2	0	rs200239592		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:103870889G>A	ENST00000393158.2	-	2	398	c.219C>T	c.(217-219)taC>taT	p.Y73Y	PDGFD_ENST00000302251.5_Silent_p.Y67Y			Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D	73	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cellular response to amino acid stimulus (GO:0071230)|multicellular organismal development (GO:0007275)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		GGTTCCTGGGGTAGCTGTTCG	0.488																																					p.Y73Y		Atlas-SNP	.											.	PDGFD	125	.	0			c.C219T						.						196	179	185					11																	103870889		2202	4299	6501	SO:0001819	synonymous_variant	80310	exon2			CCTGGGGTAGCTG	AF113216	CCDS8326.1, CCDS41703.1	11q22.3	2008-02-05			ENSG00000170962	ENSG00000170962			30620	protein-coding gene	gene with protein product	"spinal cord derived growth factor B"	609673				11162582, 11980634	Standard	NM_033135		Approved	SCDGF-B, MSTP036, IEGF	uc001phq.3	Q9GZP0	OTTHUMG00000165953	ENST00000393158.2:c.219C>T	chr11.hg19:g.103870889G>A		113.0	0.0		423.0	163.0	NM_025208	A8K9T6|Q9BWV5	Silent	SNP	ENST00000393158.2	hg19	CCDS41703.1																																																																																			.	G|1.000;C|0.000		0.488	PDGFD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387231.2	NM_025208		A	103870889	G	A	103870889	2	1	98	1	0	0	0	0	0	0	0	1	11669	1256	44	3		3	PDGFD	11	103870889	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	8045683	103870889	31135627	107	13469										
NCAM1	4684	hgsc.bcm.edu	37	chr11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ccctcccagccagcagattaCaatgctgccaaactaaggat					rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				RP11-629G13.1_ENST00000500537.2_RNA|RP11-629G13.1_ENST00000532002.1_RNA|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		0.0	0.0		31.0	31.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		-	112832363	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	112832332	6	5	98	0	1	1	0	1	0	0	0	0	10211	493	17	0		0	NCAM1	11	112832332	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	TCGA-DD-A1EB-01A-11D-A12Z-10	8961443	112832332	22174184	108	13470										
TMEM25	84866	hgsc.bcm.edu	37	chr11	118402863	118402994	+	Splice_Site	DEL	CTCCTGCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAG	CTCCTGCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAG	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gaggcctcctgctgtgttccAggttggggggagttggagcc					rs200390061|rs572377333|rs11553524|rs367682925|rs377348449|rs551854493|rs570450435|rs45558732|rs370682545|rs35915434	byFrequency	TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	CTCCTGCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAG	CTCCTGCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:118402863_118402994delCTCCTGCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAG	ENST00000313236.5	+	3	123_253	c.70_200delCTCCTGCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAG	c.(70-201)ctcctgctgtgttccaggttggggggagttggagccacaaatagatggtcagacctgggctgagcgggcacttcgggagaatgaacgccacgccttcacctgccgggtggcaggggggcctggcacccccag>g	p.LLLCSRLGGVGATNRWSDLG*AGTSGE*TPRLHLPGGRGAWHPQ24del	TMEM25_ENST00000354064.7_Intron|TMEM25_ENST00000524725.1_Splice_Site_p.LLLCSRLGGVGATNRWSDLG*AGTSGE*TPRLHLPGGRGAWHPQ24del|TMEM25_ENST00000533102.1_Splice_Site_p.LLLCSRLGGVGATNRWSDLG*AGTSGE*TPRLHLPGGRGAWHPQ24del|RP11-770J1.3_ENST00000532597.1_RNA|TMEM25_ENST00000529001.1_3'UTR|TMEM25_ENST00000354284.4_Splice_Site_p.LLLCSRLGGVGATNRWSDLG*AGTSGE*TPRLHLPGGRGAWHPQ24del|RP11-770J1.3_ENST00000556583.1_RNA|TMEM25_ENST00000359862.4_Splice_Site_p.LLLCSRLGGVGATNRWSDLG*AGTSGE*TPRLHLPGGRGAWHPQ24del|TMEM25_ENST00000442938.2_Splice_Site_p.LLLCSRLGGVGATNRWSDLG*AGTSGE*TPRLHLPGGRGAWHPQ24del|TMEM25_ENST00000544878.1_Splice_Site_p.LLLCSRLGGVGATNRWSDLG*AGTSGE*TPRLHLPGGRGAWHPQ24del|TMEM25_ENST00000411589.2_Splice_Site_p.LLLCSRLGGVGATNRWSDLG*AGTSGE*TPRLHLPGGRGAWHPQ24del|RP11-770J1.3_ENST00000525992.2_RNA|RP11-770J1.3_ENST00000554407.1_RNA|RP11-770J1.3_ENST00000528578.1_RNA	NM_032780.3	NP_116169.2	Q86YD3	TMM25_HUMAN	transmembrane protein 25	24						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P58fs*23(1)|p.R53L(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|stomach(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		GCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAGATTGGCCTGGTATCTGGATGGACAG	0.623																																					p.24_62del		Pindel	.											.	TMEM25	24	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|kidney(1)	c.71_184del						.																																			SO:0001630	splice_region_variant	84866	exon3			.	AK075437	CCDS8398.1, CCDS44745.1, CCDS44746.1, CCDS44747.1, CCDS44748.1	11q23.3	2013-01-11			ENSG00000149582	ENSG00000149582		"Immunoglobulin superfamily / C2-set domain containing"	25890	protein-coding gene	gene with protein product		613934				15254712, 12975309	Standard	NM_001144034		Approved	FLJ14399	uc010rye.2	Q86YD3	OTTHUMG00000166339	ENST00000313236.5:c.71-1CTCCTGCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAG>-	chr11.hg19:g.118402863_118402994delCTCCTGCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAG		0.0	0.0		12.0	12.0	NM_001144038	A8K8J4|B0YJA6|B0YJA7|B0YJA9|G5E9U4|Q6UW89|Q86UA7|Q8NBL5|Q96KA6|Q96MW9	In_Frame_Del	DEL	ENST00000313236.5	hg19	CCDS8398.1																																																																																			.	.		0.623	TMEM25-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389266.1	NM_032780	In_Frame_Del	-	118402994	CTCCTGCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAG	-	118402863	8	5	98	1	0	1	0	1	0	0	1	0	16165	202	7	0	75	0	TMEM25	11	118402863	Splice_Site	DEL	CTCCTGCTGTGTTCCAGGTTGGGGGGAGTTGGAGCCACAAATAGATGGTCAGACCTGGGCTGAGCGGGCACTTCGGGAGAATGAACGCCACGCCTTCACCTGCCGGGTGGCAGGGGGGCCTGGCACCCCCAG	TCGA-DD-A1EB-01A-11D-A12Z-10	5570531	118402863	16603653	109	13471										
SPATA19	219938	hgsc.bcm.edu	37	chr11	133714431	133714431	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctggtcacgtggatgtcctgGccatgggtgggaggggagtc	19	8	1	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr11:133714431G>T	ENST00000299140.3	-	3	294	c.240C>A	c.(238-240)ggC>ggA	p.G80G	SPATA19_ENST00000532889.1_Silent_p.G80G	NM_174927.1	NP_777587.1	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	80					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	mitochondrial outer membrane (GO:0005741)				cervix(1)|endometrium(2)|large_intestine(2)|lung(5)|prostate(1)	11	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		GGATGTCCTGGCCATGGGTGG	0.557																																					p.G80G		Atlas-SNP	.											.	SPATA19	36	.	0			c.C240A						.						142	131	135					11																	133714431		2201	4297	6498	SO:0001819	synonymous_variant	219938	exon3			GTCCTGGCCATGG	AK098717	CCDS8493.1	11q25	2010-04-23				ENSG00000166118			30614	protein-coding gene	gene with protein product	"spergen 1", "cancer/testis antigen 132"	609805				12477932	Standard	XM_005271448		Approved	FLJ25851, spergen1, SPAS1, CT132	uc001qgv.1	Q7Z5L4		ENST00000299140.3:c.240C>A	chr11.hg19:g.133714431G>T		78.0	0.0		219.0	91.0	NM_174927	Q8N7A9	Silent	SNP	ENST00000299140.3	hg19	CCDS8493.1																																																																																			.	.		0.557	SPATA19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393281.1	NM_174927		T	133714431	G	T	133714431	2	4	98	1	0	0	0	0	0	0	0	1	15019	1190	42	3		3	SPATA19	11	133714431	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	15311568	133714431	1292085	110	13472										
GRIN2B	2904	hgsc.bcm.edu	37	chr12	13720174	13720174	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	acaaatgccagtgagccagaGagcttccagttcttccatct	8	12	2	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:13720174G>A	ENST00000609686.1	-	12	2592	c.2383C>T	c.(2383-2385)Ctc>Ttc	p.L795F		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	795					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GTGAGCCAGAGAGCTTCCAGT	0.502																																					p.L795F		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C2383T						.						72	70	71					12																	13720174		2203	4300	6503	SO:0001583	missense	2904	exon12			GCCAGAGAGCTTC		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.2383C>T	chr12.hg19:g.13720174G>A	ENSP00000477455:p.Leu795Phe	61.0	0.0		172.0	69.0	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	hg19	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.217128	0.79352	.	.	ENSG00000150086	ENST00000279593	T	0.27256	1.68	5.59	5.59	0.84812	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.30978	0.0782	N	0.03324	-0.35	0.80722	D	1	D	0.71674	0.998	D	0.72982	0.979	T	0.52320	-0.8591	10	0.66056	D	0.02	.	19.5854	0.95488	0.0:0.0:1.0:0.0	.	795	Q13224	NMDE2_HUMAN	F	795	ENSP00000279593:L795F	ENSP00000279593:L795F	L	-	1	0	GRIN2B	13611441	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.634000	0.74290	2.630000	0.89119	0.650000	0.86243	CTC	.	.		0.502	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			A	13720174	G	A	13720174	3	1	98	1	0	0	0	0	1	0	0	0	6789	942	33	3	2079	3	GRIN2B	12	13720174	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10		13720174	120131721	111	13473										
BCAT1	586	hgsc.bcm.edu	37	chr12	24989464	24989464	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cccactgatgtgccaggtccAgaatgcaccgccttgtcact	9	15	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:24989464A>G	ENST00000261192.7	-	8	1410	c.884T>C	c.(883-885)cTg>cCg	p.L295P	BCAT1_ENST00000342945.5_Missense_Mutation_p.L234P|BCAT1_ENST00000538118.1_Missense_Mutation_p.L294P|BCAT1_ENST00000539780.1_Missense_Mutation_p.L258P|BCAT1_ENST00000539282.1_Missense_Mutation_p.L307P|BCAT1_ENST00000544418.1_5'UTR|RP11-625L16.3_ENST00000545410.1_RNA	NM_001178091.1|NM_005504.6	NP_001171562.1|NP_005495.2	P54687	BCAT1_HUMAN	branched chain amino-acid transaminase 1, cytosolic	295					branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cell proliferation (GO:0008283)|cellular nitrogen compound metabolic process (GO:0034641)|G1/S transition of mitotic cell cycle (GO:0000082)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)			breast(1)|large_intestine(1)|lung(3)|prostate(2)	7	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)	TGCCAGGTCCAGAATGCACCG	0.413																																					p.L307P		Atlas-SNP	.											.	BCAT1	44	.	0			c.T920C						.						69	66	67					12																	24989464		1916	4122	6038	SO:0001583	missense	586	exon8			AGGTCCAGAATGC		CCDS44845.1, CCDS53760.1, CCDS53761.1, CCDS53762.1, CCDS53763.1	12p12.1	2012-10-02	2010-05-07		ENSG00000060982	ENSG00000060982	2.6.1.42		976	protein-coding gene	gene with protein product		113520	"branched chain aminotransferase 1, cytosolic"	BCT1		9165094	Standard	NM_005504		Approved		uc010six.2	P54687	OTTHUMG00000169053	ENST00000261192.7:c.884T>C	chr12.hg19:g.24989464A>G	ENSP00000261192:p.Leu295Pro	80.0	0.0		171.0	67.0	NM_001178093	B3KY27|B7Z2M5|B7Z5L0|F5H5E4|Q68DQ7|Q96MY9	Missense_Mutation	SNP	ENST00000261192.7	hg19	CCDS44845.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.059333	0.76074	.	.	ENSG00000060982	ENST00000261192;ENST00000538118;ENST00000342945;ENST00000539282;ENST00000539780	T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42	5.11	5.11	0.69529	.	0.083454	0.49916	D	0.000134	T	0.71592	0.3358	H	0.98314	4.2	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.995;0.996;0.995;0.998;0.998	D	0.83931	0.0306	10	0.87932	D	0	-25.8717	15.2341	0.73416	1.0:0.0:0.0:0.0	.	258;307;234;295;294	B7Z5L0;F5H5E4;B3KY27;P54687;Q68DQ7	.;.;.;BCAT1_HUMAN;.	P	295;294;234;307;258	ENSP00000261192:L295P;ENSP00000440817:L294P;ENSP00000339805:L234P;ENSP00000443459:L307P;ENSP00000440827:L258P	ENSP00000261192:L295P	L	-	2	0	BCAT1	24880731	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.840000	0.86819	2.054000	0.61138	0.528000	0.53228	CTG	.	.		0.413	BCAT1-001	KNOWN	upstream_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402080.1	NM_005504		G	24989464	A	G	24989464	3	3	98	1	0	0	0	0	1	0	0	0	1354	188	7	2	292	2	BCAT1	12	24989464	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	11269290	24989464	108862431	112	13474										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70970186	70970186	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ccgctcttggctgaaggagtGattttcatacttgccactcc	9	12	2	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:70970186G>T	ENST00000261266.5	-	9	2193	c.2164C>A	c.(2164-2166)Cac>Aac	p.H722N	PTPRB_ENST00000550358.1_Intron|PTPRB_ENST00000550857.1_Missense_Mutation_p.H632N|PTPRB_ENST00000538708.1_Missense_Mutation_p.H722N|PTPRB_ENST00000551525.1_Missense_Mutation_p.H939N|PTPRB_ENST00000334414.6_Missense_Mutation_p.H940N|PTPRB_ENST00000451516.2_Missense_Mutation_p.H632N	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	722	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CTGAAGGAGTGATTTTCATAC	0.517																																					p.H940N		Atlas-SNP	.											.	PTPRB	676	.	0			c.C2818A						.						63	64	64					12																	70970186		2010	4185	6195	SO:0001583	missense	5787	exon11			AGGAGTGATTTTC	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.2164C>A	chr12.hg19:g.70970186G>T	ENSP00000261266:p.His722Asn	88.0	0.0		234.0	81.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	G	10.18	1.280305	0.23392	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T	0.04156	4.2;4.22;4.25;4.22;4.25;3.69;3.73	5.98	4.14	0.48551	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.551006	0.21078	N	0.080530	T	0.10252	0.0251	L	0.60455	1.87	0.29608	N	0.84713	P;P;P;B;P;P	0.47604	0.696;0.696;0.898;0.275;0.696;0.741	P;P;P;B;P;P	0.53809	0.457;0.457;0.735;0.117;0.535;0.593	T	0.02950	-1.1090	10	0.12430	T	0.62	.	10.6081	0.45406	0.2049:0.0:0.7951:0.0	.	632;722;819;939;940;722	P23467-2;F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467	.;.;.;.;.;PTPRB_HUMAN	N	940;632;722;632;722;939;819	ENSP00000334928:H940N;ENSP00000393028:H632N;ENSP00000438927:H722N;ENSP00000447302:H632N;ENSP00000261266:H722N;ENSP00000448349:H939N;ENSP00000446982:H819N	ENSP00000261266:H722N	H	-	1	0	PTPRB	69256453	1.000000	0.71417	0.181000	0.23098	0.301000	0.27625	2.579000	0.46059	1.529000	0.49120	0.650000	0.86243	CAC	.	.		0.517	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70970186	G	T	70970186	3	4	98	1	0	0	0	0	1	0	0	0	12811	1290	45	3	3925	3	PTPRB	12	70970186	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	45980722	70970186	62881709	113	13475										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80761993	80761993	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cattatatgcagcaccaggtAtatactccatccccaagtga	6	12	0	1	rs370122451		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:80761993A>G	ENST00000547103.1	+	54	6462	c.6456A>G	c.(6454-6456)gtA>gtG	p.V2152V	OTOGL_ENST00000458043.2_Silent_p.V2164V|OTOGL_ENST00000546620.1_Silent_p.V183V			Q3ZCN5	OTOGL_HUMAN	otogelin-like	2152					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						AGCACCAGGTATATACTCCAT	0.353																																					p.V2164V		Atlas-SNP	.											.	OTOGL	235	.	0			c.A6492G						.	A		0,4406		0,0,2203	131	117	122		6492	-4.3	0.1	12		122	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OTOGL	NM_173591.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		2164/2345	80761993	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	283310	exon54			CCAGGTATATACT	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.6456A>G	chr12.hg19:g.80761993A>G		90.0	0.0		207.0	74.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Silent	SNP	ENST00000547103.1	hg19		.	.	.	.	.	.	.	.	.	.	A	7.554	0.663357	0.14710	0.0	1.16E-4	ENSG00000165899	ENST00000298820	.	.	.	5.47	-4.34	0.03666	.	.	.	.	.	T	0.51126	0.1656	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49799	-0.8901	4	.	.	.	.	8.5452	0.33417	0.4137:0.0:0.474:0.1123	.	.	.	.	C	572	.	.	Y	+	2	0	OTOGL	79286124	0.000000	0.05858	0.082000	0.20525	0.898000	0.52572	-2.168000	0.01270	-0.885000	0.03971	-0.386000	0.06593	TAT	.	.		0.353	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		G	80761993	A	G	80761993	2	3	98	1	0	0	0	0	0	0	0	1	1709	436	16	2		2	C12orf64	12	80761993	Silent	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	9791807	80761993	53089902	114	13476										
TMTC2	160335	hgsc.bcm.edu	37	chr12	83250884	83250885	+	Frame_Shift_Ins	INS	-	-	C													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	actcttctaacccacagtggINScagccacaagtcctaccggc							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:83250884_83250885insC	ENST00000321196.3	+	2	886_887	c.179_180insC	c.(178-183)ggcagcfs	p.S61fs	TMTC2_ENST00000549919.1_Frame_Shift_Ins_p.S55fs|TMTC2_ENST00000548305.1_Frame_Shift_Ins_p.S61fs	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	61					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						ACCCACAGTGGCAGCCACAAGT	0.49																																					p.G60fs		Atlas-INDEL	.											.	TMTC2	100	.	0			c.179_180insC						.																																			SO:0001589	frameshift_variant	160335	exon2			.	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.180dupC	chr12.hg19:g.83250885_83250885dupC	ENSP00000322300:p.Ser61fs	62.0	0.0		216.0	15.0	NM_152588	B2RCU7|Q8N2K8	Frame_Shift_Ins	INS	ENST00000321196.3	hg19	CCDS9025.1																																																																																			.	.		0.49	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		C	83250885	-	C	83250884	7	5	98	1	0	1	1	0	0	0	0	0	16276	1203	42	0	185	0	TMTC2	12	83250884	Frame_Shift_Ins	INS	-	TCGA-DD-A1EB-01A-11D-A12Z-10	2488891	83250884	50601011	115	13477										
MGAT4C	25834	hgsc.bcm.edu	37	chr12	86374008	86374008	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tataaccattaatcttcctgCaataatatggtgcgcaaatt	5	8	1	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:86374008C>A	ENST00000604798.1	-	8	1700	c.496G>T	c.(496-498)Gca>Tca	p.A166S	MGAT4C_ENST00000552435.2_Intron|MGAT4C_ENST00000393205.2_Missense_Mutation_p.A195S|MGAT4C_ENST00000552808.2_Missense_Mutation_p.A166S|MGAT4C_ENST00000549405.2_Missense_Mutation_p.A166S|MGAT4C_ENST00000332156.1_Missense_Mutation_p.A166S|MGAT4C_ENST00000548651.1_Missense_Mutation_p.A166S			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	166					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						AATCTTCCTGCAATAATATGG	0.398																																					p.A166S		Atlas-SNP	.											.	MGAT4C	110	.	0			c.G496T						.						99	97	98					12																	86374008		2203	4300	6503	SO:0001583	missense	25834	exon7			TTCCTGCAATAAT		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	30871	protein-coding gene	gene with protein product		607385	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.496G>T	chr12.hg19:g.86374008C>A	ENSP00000474896:p.Ala166Ser	44.0	0.0		109.0	48.0	NM_013244	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	hg19	CCDS9030.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.360069	0.41801	.	.	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225	T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18	5.58	5.58	0.84498	.	0.061260	0.64402	D	0.000005	T	0.34861	0.0912	N	0.19112	0.55	0.54753	D	0.999982	D;D	0.58970	0.984;0.984	P;P	0.54140	0.743;0.676	T	0.03957	-1.0989	10	0.02654	T	1	-21.5613	19.5899	0.95506	0.0:1.0:0.0:0.0	.	195;166	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	S	166;195;166;166;166;166;166	ENSP00000331664:A166S;ENSP00000376900:A195S;ENSP00000449022:A166S;ENSP00000446647:A166S;ENSP00000447253:A166S;ENSP00000449172:A166S	ENSP00000331664:A166S	A	-	1	0	MGAT4C	84898139	1.000000	0.71417	0.996000	0.52242	0.025000	0.11179	4.772000	0.62324	2.612000	0.88384	0.655000	0.94253	GCA	.	.		0.398	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		A	86374008	C	A	86374008	3	1	98	1	0	0	0	0	1	0	0	0	9556	710	25	3	944	3	MGAT4C	12	86374008	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	3123124	86374008	47477887	116	13478										
CEP290	80184	hgsc.bcm.edu	37	chr12	88486497	88486497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gttccatttcattcttctctAattctagaatccgttgccta	4	11	4	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:88486497A>G	ENST00000552810.1	-	29	3765	c.3422T>C	c.(3421-3423)tTa>tCa	p.L1141S	CEP290_ENST00000547691.2_Missense_Mutation_p.L201S|CEP290_ENST00000397838.3_Missense_Mutation_p.L201S|CEP290_ENST00000309041.7_Missense_Mutation_p.L1143S	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1141					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						ATTCTTCTCTAATTCTAGAAT	0.348																																					p.L1141S		Atlas-SNP	.											.	CEP290	195	.	0			c.T3422C						.						190	176	181					12																	88486497		1906	4140	6046	SO:0001583	missense	80184	exon29			TTCTCTAATTCTA	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.3422T>C	chr12.hg19:g.88486497A>G	ENSP00000448012:p.Leu1141Ser	119.0	0.0		366.0	150.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.204154	0.79127	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.75260	-0.38;-0.92;-0.91;-0.38	5.83	5.83	0.93111	.	0.065233	0.64402	D	0.000007	D	0.84356	0.5454	M	0.71581	2.175	0.44359	D	0.997257	D	0.76494	0.999	D	0.72338	0.977	T	0.82092	-0.0628	10	0.24483	T	0.36	.	16.192	0.81996	1.0:0.0:0.0:0.0	.	1141	O15078	CE290_HUMAN	S	201;1141;1143;201	ENSP00000446905:L201S;ENSP00000448012:L1141S;ENSP00000308021:L1143S;ENSP00000380938:L201S	ENSP00000308021:L1143S	L	-	2	0	CEP290	87010628	1.000000	0.71417	0.998000	0.56505	0.719000	0.41307	8.548000	0.90669	2.229000	0.72834	0.482000	0.46254	TTA	.	.		0.348	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		G	88486497	A	G	88486497	3	3	98	1	0	0	0	0	1	0	0	0	3255	372	13	2	4121	2	CEP290	12	88486497	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	2112489	88486497	45365398	117	13479										
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94542869	94542869	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cgcggacgagcccgtgtggcGgtcggagcaagccatcggag	18	12	0	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:94542869G>T	ENST00000258526.4	+	1	371	c.122G>T	c.(121-123)cGg>cTg	p.R41L		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	41	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CCCGTGTGGCGGTCGGAGCAA	0.756																																					p.R41L		Atlas-SNP	.											.	PLXNC1	135	.	0			c.G122T						.						8	9	9					12																	94542869		1938	3905	5843	SO:0001583	missense	10154	exon1			TGTGGCGGTCGGA	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.122G>T	chr12.hg19:g.94542869G>T	ENSP00000258526:p.Arg41Leu	0.0	0.0		18.0	10.0	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	G	17.10	3.302322	0.60195	.	.	ENSG00000136040	ENST00000258526	T	0.04317	3.65	3.95	3.95	0.45737	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	0.200531	0.26951	N	0.021662	T	0.05686	0.0149	L	0.57536	1.79	0.80722	D	1	B	0.21753	0.06	B	0.12156	0.007	T	0.20371	-1.0277	10	0.66056	D	0.02	.	4.9789	0.14155	0.1097:0.0:0.6624:0.2279	.	41	O60486	PLXC1_HUMAN	L	41	ENSP00000258526:R41L	ENSP00000258526:R41L	R	+	2	0	PLXNC1	93067000	1.000000	0.71417	0.879000	0.34478	0.935000	0.57460	3.914000	0.56401	2.022000	0.59522	0.455000	0.32223	CGG	.	.		0.756	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			T	94542869	G	T	94542869	3	4	98	1	0	0	0	0	1	0	0	0	12135	1116	39	1	124	1	PLXNC1	12	94542869	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	6056372	94542869	39309026	118	13480										
SIRT4	23409	hgsc.bcm.edu	37	chr12	120741415	120741415	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tcagcaaaaggccgttggatCgcaaaccccagccagccgtg	11	14	1	0	rs199859894		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:120741415C>T	ENST00000202967.4	+	2	110	c.51C>T	c.(49-51)atC>atT	p.I17I		NM_012240.2	NP_036372.1			sirtuin 4											haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCCGTTGGATCGCAAACCCCA	0.483																																					p.I17I		Atlas-SNP	.											.	SIRT4	29	.	0			c.C51T						.						94	98	97					12																	120741415		2203	4300	6503	SO:0001819	synonymous_variant	23409	exon2			TTGGATCGCAAAC	AF083109	CCDS9194.1	12q24.31	2010-06-25	2010-06-25		ENSG00000089163	ENSG00000089163			14932	protein-coding gene	gene with protein product		604482	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 4", "sirtuin (silent mating type information regulation 2 homolog) 4 (S. cerevisiae)"			10381378	Standard	NM_012240		Approved	SIR2L4	uc001tyc.3	Q9Y6E7	OTTHUMG00000169028	ENST00000202967.4:c.51C>T	chr12.hg19:g.120741415C>T		40.0	0.0		86.0	25.0	NM_012240		Silent	SNP	ENST00000202967.4	hg19	CCDS9194.1																																																																																			.	.		0.483	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240		T	120741415	C	T	120741415	2	4	98	1	0	0	0	0	0	0	0	1	14355	874	31	1		1	SIRT4	12	120741415	Silent	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	26198546	120741415	13110480	119	13481										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121416711	121416714	+	Frame_Shift_Del	DEL	GGGA	GGGA	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agaaggccccctggacaaggGggagtcctgcggcggcggtc							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	GGGA	GGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:121416711_121416714delGGGA	ENST00000257555.6	+	1	366_369	c.140_143delGGGA	c.(139-144)ggggagfs	p.GE47fs	HNF1A-AS1_ENST00000537361.1_RNA|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A-AS1_ENST00000535301.1_RNA|HNF1A_ENST00000543427.1_Intron|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_Frame_Shift_Del_p.GE47fs|HNF1A_ENST00000402929.1_Frame_Shift_Del_p.GE47fs|HNF1A_ENST00000400024.2_Frame_Shift_Del_p.GE47fs|HNF1A_ENST00000541395.1_Frame_Shift_Del_p.GE47fs			P20823	HNF1A_HUMAN	HNF1 homeobox A	47					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.D45fs*9(1)|p.D45fs*102(1)|p.Y36fs*107(1)|p.?(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CTGGACAAGGGGGAGTCCTGCGGC	0.691									Hepatic Adenoma, Familial Clustering of																												p.47_48del		Atlas-Indel,Pindel	.											.	HNF1A	302	.	4	Deletion - Frameshift(2)|Unknown(1)|Complex - frameshift(1)	liver(3)|endometrium(1)	c.139_142del	GRCh37	CD013206|CM030524|CM981895	HNF1A	D|M		.																																			SO:0001589	frameshift_variant	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	.	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.140_143delGGGA	chr12.hg19:g.121416711_121416714delGGGA	ENSP00000257555:p.Gly47fs	42.0	0.0		96.0	33.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Frame_Shift_Del	DEL	ENST00000257555.6	hg19	CCDS9209.1																																																																																			.	.		0.691	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		-	121416714	GGGA	-	121416711	7	5	98	1	0	1	0	1	0	0	0	0	7260	1232	43	0	142	0	HNF1A	12	121416711	Frame_Shift_Del	DEL	GGGA	TCGA-DD-A1EB-01A-11D-A12Z-10	675296	121416711	12435184	120	13482										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121432014	121432014	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cccatcacaggcacaggggcTgggctccaacctcgtcacgg	12	16	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr12:121432014T>A	ENST00000257555.6	+	4	987	c.761T>A	c.(760-762)cTg>cAg	p.L254Q	HNF1A_ENST00000543427.1_Missense_Mutation_p.L137Q|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_Missense_Mutation_p.L254Q|HNF1A_ENST00000402929.1_Missense_Mutation_p.L254Q|HNF1A_ENST00000400024.2_Missense_Mutation_p.L254Q|HNF1A_ENST00000541395.1_Missense_Mutation_p.L254Q			P20823	HNF1A_HUMAN	HNF1 homeobox A	254			L -> M (in late-onset NIDDM; low penetrance; unknown pathological significance). {ECO:0000269|PubMed:9287055}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.Q250_G255del(2)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GCACAGGGGCTGGGCTCCAAC	0.612									Hepatic Adenoma, Familial Clustering of																												p.L254Q		Atlas-SNP	.											.	HNF1A	302	.	2	Deletion - In frame(2)	liver(2)	c.T761A						.						40	40	40					12																	121432014		2203	4300	6503	SO:0001583	missense	6927	exon4	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	AGGGGCTGGGCTC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.761T>A	chr12.hg19:g.121432014T>A	ENSP00000257555:p.Leu254Gln	34.0	0.0		71.0	21.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.585079	0.86748	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D;D	0.95788	-3.81;-3.81;-3.81;-3.81	4.84	4.84	0.62591	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.50627	D	0.000101	D	0.97259	0.9104	M	0.73598	2.24	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.91635	0.999;0.999;0.999;0.994	D	0.97877	1.0289	10	0.87932	D	0	-15.4213	13.6279	0.62178	0.0:0.0:0.0:1.0	.	254;254;254;254	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	Q	254;254;254;254;254;137;254;254;254;254;254	ENSP00000257555:L254Q;ENSP00000439721:L137Q;ENSP00000443112:L254Q;ENSP00000438804:L254Q	ENSP00000257555:L254Q	L	+	2	0	HNF1A	119916397	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.630000	0.83225	1.820000	0.53075	0.335000	0.21663	CTG	.	.		0.612	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		A	121432014	T	A	121432014	3	1	98	1	0	0	0	0	1	0	0	0	7260	1580	55	4	775	4	HNF1A	12	121432014	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	15303	121432014	12419881	121	13483										
NBEA	26960	hgsc.bcm.edu	37	chr13	35672500	35672500	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gccatgcaagaacagatgctGggtggaaaaggctttttagt	13	6	0	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr13:35672500G>T	ENST00000400445.3	+	11	2172	c.1638G>T	c.(1636-1638)ctG>ctT	p.L546L	NBEA_ENST00000310336.4_Silent_p.L546L|NBEA_ENST00000379939.2_Silent_p.L546L|NBEA_ENST00000540320.1_Silent_p.L546L	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	546					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AACAGATGCTGGGTGGAAAAG	0.383																																					p.L546L		Atlas-SNP	.											.	NBEA	340	.	0			c.G1638T						.						94	85	87					13																	35672500		1877	4124	6001	SO:0001819	synonymous_variant	26960	exon11			GATGCTGGGTGGA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.1638G>T	chr13.hg19:g.35672500G>T		70.0	0.0		178.0	64.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.383	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35672500	G	T	35672500	2	4	98	1	0	0	0	0	0	0	0	1	10196	1335	47	3		3	NBEA	13	35672500	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10		35672500	79497378	122	13484										
CSNK1A1L	122011	hgsc.bcm.edu	37	chr13	37678916	37678916	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gtctctgtactttttggccaAaccaaaatcaataaggaaca	6	9	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr13:37678916A>T	ENST00000379800.3	-	1	887	c.478T>A	c.(478-480)Ttg>Atg	p.L160M		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	160	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		TTTTTGGCCAAACCAAAATCA	0.428																																					p.L160M		Atlas-SNP	.											.	CSNK1A1L	69	.	0			c.T478A						.						223	204	211					13																	37678916		2203	4300	6503	SO:0001583	missense	122011	exon1			TGGCCAAACCAAA	BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.478T>A	chr13.hg19:g.37678916A>T	ENSP00000369126:p.Leu160Met	152.0	0.0		743.0	336.0	NM_145203	Q5T2N2	Missense_Mutation	SNP	ENST00000379800.3	hg19	CCDS9363.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.793775	0.50102	.	.	ENSG00000180138	ENST00000379800	T	0.13089	2.62	1.08	1.08	0.20341	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.41419	0.1158	H	0.94423	3.535	0.38146	D	0.938581	D	0.89917	1.0	D	0.97110	1.0	T	0.46952	-0.9154	10	0.87932	D	0	.	6.2671	0.20932	1.0:0.0:0.0:0.0	.	160	Q8N752	KC1AL_HUMAN	M	160	ENSP00000369126:L160M	ENSP00000369126:L160M	L	-	1	2	CSNK1A1L	36576916	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	3.407000	0.52644	0.725000	0.32318	0.459000	0.35465	TTG	.	.		0.428	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203		T	37678916	A	T	37678916	3	4	98	1	0	0	0	0	1	0	0	0	3953	11	1	4	539	4	CSNK1A1L	13	37678916	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	2006416	37678916	77490962	123	13485										
SUGT1	10910	hgsc.bcm.edu	37	chr13	53254291	53254291	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gtgccatgaacaaatcctttGtaagaatataaacttaaaga	6	6	0	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr13:53254291G>T	ENST00000343788.6	+	13	1078		c.e13+1		SUGT1_ENST00000535397.1_Splice_Site|SUGT1_ENST00000310528.8_Splice_Site	NM_001130912.1	NP_001124384.1	Q9Y2Z0	SUGT1_HUMAN	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)						innate immune response (GO:0045087)|mitotic nuclear division (GO:0007067)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				kidney(3)|large_intestine(3)|lung(2)	8		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		CAAATCCTTTGTAAGAATATA	0.333																																					.		Atlas-SNP	.											.	SUGT1	37	.	0			c.996+1G>T						.						68	74	72					13																	53254291		2203	4300	6503	SO:0001630	splice_region_variant	10910	exon13			TCCTTTGTAAGAA	AF068289	CCDS9436.1, CCDS45050.1	13q14.3	2014-03-20			ENSG00000165416	ENSG00000165416			16987	protein-coding gene	gene with protein product		604098				10445024	Standard	NM_006704		Approved	SGT1	uc001vhc.2	Q9Y2Z0	OTTHUMG00000016977	ENST00000343788.6:c.996+1G>T	chr13.hg19:g.53254291G>T		76.0	0.0		142.0	44.0	NM_001130912	A2A303|Q5JAK5|Q5TAM6|Q6VXY6	Splice_Site	SNP	ENST00000343788.6	hg19	CCDS45050.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.253380	0.80135	.	.	ENSG00000165416	ENST00000343788;ENST00000535397;ENST00000310528	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.149	0.93481	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SUGT1	52152292	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	9.420000	0.97426	2.592000	0.87571	0.467000	0.42956	.	.	.		0.333	SUGT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045104.2		Intron	T	53254291	G	T	53254291	5	4	98	1	0	0	0	0	0	0	1	0	15384	1391	48	3	1047	3	SUGT1	13	53254291	Splice_Site	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	15575375	53254291	61915587	124	13486										
TBC1D4	9882	hgsc.bcm.edu	37	chr13	76055603	76055603	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cggactagtgccccccgaggCcccagcgcccggcgcgggga	16	18	0	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr13:76055603C>T	ENST00000377636.3	-	1	647	c.301G>A	c.(301-303)Gcc>Acc	p.A101T	TBC1D4_ENST00000377625.2_Missense_Mutation_p.A101T|TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000431480.2_Missense_Mutation_p.A101T	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	101	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		CCCCCCGAGGCCCCAGCGCCC	0.716																																					p.A101T		Atlas-SNP	.											.	TBC1D4	142	.	0			c.G301A						.						39	46	44					13																	76055603		1962	4147	6109	SO:0001583	missense	9882	exon1			CCGAGGCCCCAGC	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.301G>A	chr13.hg19:g.76055603C>T	ENSP00000366863:p.Ala101Thr	26.0	0.0		80.0	39.0	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	hg19	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.964745	0.34659	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625	T;T;T	0.03152	4.04;4.04;4.03	4.03	4.03	0.46877	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	1.455410	0.05029	N	0.474285	T	0.02610	0.0079	N	0.08118	0	0.80722	D	1	B;B;B	0.25609	0.001;0.13;0.079	B;B;B	0.18561	0.003;0.022;0.01	T	0.32745	-0.9895	10	0.05833	T	0.94	-2.0177	13.6942	0.62567	0.0:1.0:0.0:0.0	.	101;101;101	O60343-2;O60343-3;O60343	.;.;TBCD4_HUMAN	T	101	ENSP00000366863:A101T;ENSP00000395986:A101T;ENSP00000366852:A101T	ENSP00000366852:A101T	A	-	1	0	TBC1D4	74953604	.	.	0.810000	0.32431	0.720000	0.41350	.	.	2.062000	0.61559	0.462000	0.41574	GCC	.	.		0.716	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		T	76055603	C	T	76055603	3	4	98	1	0	0	0	0	1	0	0	0	15637	739	26	3	3679	3	TBC1D4	13	76055603	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	22801312	76055603	39114275	125	13487										
MYO16	23026	hgsc.bcm.edu	37	chr13	109540788	109540788	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	acacctcacctgcagggctgGcgccagcagggccacactgg	13	16	1	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr13:109540788G>T	ENST00000357550.2	+	13	1597	c.1556G>T	c.(1555-1557)gGc>gTc	p.G519V	MYO16_ENST00000251041.5_Missense_Mutation_p.G519V|MYO16_ENST00000356711.2_Missense_Mutation_p.G519V|MYO16_ENST00000457511.2_Missense_Mutation_p.G31V	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TGCAGGGCTGGCGCCAGCAGG	0.433																																					p.G541V		Atlas-SNP	.											.	MYO16	285	.	0			c.G1622T						.						72	79	77					13																	109540788		2203	4300	6503	SO:0001583	missense	23026	exon14			GGGCTGGCGCCAG		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.1556G>T	chr13.hg19:g.109540788G>T	ENSP00000350160:p.Gly519Val	69.0	0.0		202.0	81.0	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	hg19	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	G	9.038	0.989015	0.18966	.	.	ENSG00000041515	ENST00000356711;ENST00000397258;ENST00000357550;ENST00000251041;ENST00000375857;ENST00000457511	D;D;D;D	0.87809	-2.3;-2.3;-2.3;-2.3	5.18	1.2	0.21068	Myosin head, motor domain (2);	0.977084	0.08301	U	0.966834	D	0.88232	0.6381	M	0.79805	2.47	0.09310	N	1	P;B;P	0.40360	0.666;0.061;0.714	B;B;B	0.40982	0.311;0.1;0.345	T	0.76206	-0.3044	9	.	.	.	.	12.0628	0.53572	0.0711:0.3319:0.5969:0.0	.	31;519;519	F8W883;Q9Y6X6-2;Q9Y6X6	.;.;MYO16_HUMAN	V	519;519;519;519;307;31	ENSP00000349145:G519V;ENSP00000350160:G519V;ENSP00000251041:G519V;ENSP00000401633:G31V	.	G	+	2	0	MYO16	108338789	0.024000	0.19004	0.000000	0.03702	0.002000	0.02628	0.810000	0.27183	0.027000	0.15297	-0.795000	0.03280	GGC	.	.		0.433	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		T	109540788	G	T	109540788	3	4	98	1	0	0	0	0	1	0	0	0	10073	1203	42	3	1606	3	MYO16	13	109540788	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	33485185	109540788	5629090	126	13488										
OR4K2	390431	hgsc.bcm.edu	37	chr14	20344661	20344661	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctcttgcttctttcgccaccCcaaagatgattacagattac	5	13	2	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr14:20344661C>A	ENST00000298642.2	+	1	271	c.235C>A	c.(235-237)Cca>Aca	p.P79T		NM_001005501.1	NP_001005501.1	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K, member 2	79						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(16)|ovary(2)|skin(9)|upper_aerodigestive_tract(2)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTCGCCACCCCAAAGATGAT	0.413																																					p.P79T		Atlas-SNP	.											.	OR4K2	97	.	0			c.C235A						.						270	264	266					14																	20344661		2203	4300	6503	SO:0001583	missense	390431	exon1			GCCACCCCAAAGA		CCDS32023.1	14q11.2	2013-09-23			ENSG00000165762	ENSG00000165762		"GPCR / Class A : Olfactory receptors"	14728	protein-coding gene	gene with protein product							Standard	NM_001005501		Approved		uc001vwh.1	Q8NGD2	OTTHUMG00000170624	ENST00000298642.2:c.235C>A	chr14.hg19:g.20344661C>A	ENSP00000298642:p.Pro79Thr	124.0	0.0		413.0	119.0	NM_001005501	B2RNK8|Q6IFA5	Missense_Mutation	SNP	ENST00000298642.2	hg19	CCDS32023.1	.	.	.	.	.	.	.	.	.	.	.	20.9	4.070178	0.76301	.	.	ENSG00000165762	ENST00000298642	T	0.01854	4.6	5.27	5.27	0.74061	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000151	T	0.28962	0.0719	H	0.99650	4.68	0.53005	D	0.999963	D	0.89917	1.0	D	0.83275	0.996	T	0.57493	-0.7802	10	0.87932	D	0	.	16.4283	0.83832	0.0:1.0:0.0:0.0	.	79	Q8NGD2	OR4K2_HUMAN	T	79	ENSP00000298642:P79T	ENSP00000298642:P79T	P	+	1	0	OR4K2	19414501	0.998000	0.40836	1.000000	0.80357	0.943000	0.58893	4.477000	0.60223	2.740000	0.93945	0.563000	0.77884	CCA	.	.		0.413	OR4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409864.1			A	20344661	C	A	20344661	3	1	98	1	0	0	0	0	1	0	0	0	11081	623	22	3	237	3	OR4K2	14	20344661	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10		20344661	87004879	127	13489										
OR4K1	79544	hgsc.bcm.edu	37	chr14	20404418	20404418	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tacatatgaaatggaaattaTgaccctaacgaacagtggcc	8	8	0	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr14:20404418T>G	ENST00000285600.4	+	1	652	c.593T>G	c.(592-594)aTg>aGg	p.M198R		NM_001004063.2	NP_001004063.2	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K, member 1	198						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(24)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		ATGGAAATTATGACCCTAACG	0.453																																					p.M198R		Atlas-SNP	.											.	OR4K1	108	.	0			c.T593G						.						159	161	160					14																	20404418		2203	4300	6503	SO:0001583	missense	79544	exon1			AAATTATGACCCT		CCDS32025.1	14q11.2	2013-09-23			ENSG00000155249	ENSG00000155249		"GPCR / Class A : Olfactory receptors"	14726	protein-coding gene	gene with protein product							Standard	NM_001004063		Approved		uc001vwj.2	Q8NGD4	OTTHUMG00000170633	ENST00000285600.4:c.593T>G	chr14.hg19:g.20404418T>G	ENSP00000285600:p.Met198Arg	132.0	0.0		284.0	74.0	NM_001004063	B9EKV9|Q8NGD6|Q96R73	Missense_Mutation	SNP	ENST00000285600.4	hg19	CCDS32025.1	.	.	.	.	.	.	.	.	.	.	.	7.015	0.557492	0.13436	.	.	ENSG00000155249	ENST00000285600	T	0.37235	1.21	4.82	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.340024	0.26170	N	0.025939	T	0.50446	0.1616	M	0.84511	2.7	0.09310	N	1	B	0.30542	0.284	B	0.40038	0.317	T	0.54118	-0.8341	10	0.87932	D	0	.	12.3562	0.55176	0.0:0.0:0.0:1.0	.	198	Q8NGD4	OR4K1_HUMAN	R	198	ENSP00000285600:M198R	ENSP00000285600:M198R	M	+	2	0	OR4K1	19474258	0.866000	0.29940	0.125000	0.21846	0.350000	0.29205	4.403000	0.59729	2.011000	0.59026	0.460000	0.39030	ATG	.	.		0.453	OR4K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409881.1			G	20404418	T	G	20404418	3	3	98	1	0	0	0	0	1	0	0	0	11076	1464	51	5	595	5	OR4K1	14	20404418	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	59757	20404418	86945122	128	13490										
MYH7	4625	hgsc.bcm.edu	37	chr14	23897841	23897841	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	aagaactgctgcagcttctcGttggtgaagttgatgcagag	13	7	1	4			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr14:23897841G>A	ENST00000355349.3	-	15	1608	c.1446C>T	c.(1444-1446)aaC>aaT	p.N482N		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	482	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		GCAGCTTCTCGTTGGTGAAGT	0.537																																					p.N482N		Atlas-SNP	.											MYH7,caecum,carcinoma,0,1	MYH7	349	.	0			c.C1446T						.						129	102	111					14																	23897841		2203	4300	6503	SO:0001819	synonymous_variant	4625	exon15			CTTCTCGTTGGTG	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.1446C>T	chr14.hg19:g.23897841G>A		96.0	0.0		381.0	19.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	hg19	CCDS9601.1																																																																																			.	.		0.537	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23897841	G	A	23897841	2	1	98	1	0	0	0	0	0	0	0	1	10048	1136	40	1		1	MYH7	14	23897841	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	3493423	23897841	83451699	129	13491										
RTN1	6252	hgsc.bcm.edu	37	chr14	60074128	60074128	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	acgctcaccacgctgaactgGgtcagggagaagagcagcag	14	11	2	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr14:60074128G>T	ENST00000267484.5	-	4	2183	c.1848C>A	c.(1846-1848)acC>acA	p.T616T	RTN1_ENST00000557422.1_5'UTR|RTN1_ENST00000395090.1_Silent_p.T33T|RTN1_ENST00000342503.4_Silent_p.T48T	NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	616	Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		CGCTGAACTGGGTCAGGGAGA	0.557																																					p.T616T		Atlas-SNP	.											.	RTN1	139	.	0			c.C1848A						.						71	64	66					14																	60074128		2203	4300	6503	SO:0001819	synonymous_variant	6252	exon4			GAACTGGGTCAGG	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.1848C>A	chr14.hg19:g.60074128G>T		18.0	0.0		78.0	33.0	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Silent	SNP	ENST00000267484.5	hg19	CCDS9740.1																																																																																			.	.		0.557	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			T	60074128	G	T	60074128	2	4	98	1	0	0	0	0	0	0	0	1	13740	1219	43	3		3	RTN1	14	60074128	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	36176287	60074128	47275412	130	13492										
RTN1	6252	hgsc.bcm.edu	37	chr14	60097163	60097163	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctactgaaataaagagaataCcctgacttttccagttgctc	6	10	0	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr14:60097163C>A	ENST00000267484.5	-	4	2101				RTN1_ENST00000557422.1_Splice_Site|RTN1_ENST00000395090.1_Splice_Site|RTN1_ENST00000342503.4_Splice_Site	NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1						neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		AAAGAGAATACCCTGACTTTT	0.582																																					.		Atlas-SNP	.											.	RTN1	139	.	0			c.61+1G>T						.						138	146	143					14																	60097163		2203	4300	6503	SO:0001627	intron_variant	6252	exon2			AGAATACCCTGAC	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.1766-22953G>T	chr14.hg19:g.60097163C>A		31.0	0.0		78.0	23.0	NM_206852	Q16800|Q16801|Q5BKZ4|Q9BQ59	Splice_Site	SNP	ENST00000267484.5	hg19	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.673967	0.47781	.	.	ENSG00000139970	ENST00000342503	.	.	.	4.34	3.44	0.39384	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.687	0.56954	0.166:0.834:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RTN1	59166916	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.971000	0.63749	1.012000	0.39366	-0.182000	0.12963	.	.	.		0.582	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			A	60097163	C	A	60097163	1	1	98	0	1	0	0	0	0	0	0	0	13740	521	18	3		3	RTN1	14	60097163	Intron	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	23035	60097163	47252377	131	13493										
POMT2	29954	hgsc.bcm.edu	37	chr14	77751296	77751296	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	aaagtgacctcactcacactTgggattgatatggtcctcca	8	11	2	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr14:77751296T>A	ENST00000261534.4	-	14	1775	c.1573A>T	c.(1573-1575)Aag>Tag	p.K525*		NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	525						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		CACTCACACTTGGGATTGATA	0.463																																					p.K525X		Atlas-SNP	.											.	POMT2	47	.	0			c.A1573T						.						106	96	99					14																	77751296		2203	4300	6503	SO:0001587	stop_gained	29954	exon14			CACACTTGGGATT	AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.1573A>T	chr14.hg19:g.77751296T>A	ENSP00000261534:p.Lys525*	52.0	0.0		126.0	50.0	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Nonsense_Mutation	SNP	ENST00000261534.4	hg19	CCDS9857.1	.	.	.	.	.	.	.	.	.	.	T	39	7.682920	0.98431	.	.	ENSG00000009830	ENST00000261534	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0609	0.71951	0.0:0.0:0.0:1.0	.	.	.	.	X	525	.	ENSP00000261534:K525X	K	-	1	0	POMT2	76821049	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.628000	0.83189	2.026000	0.59711	0.533000	0.62120	AAG	.	.		0.463	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382		A	77751296	T	A	77751296	4	1	98	1	0	0	0	0	0	1	0	0	12255	1821	63	4	711	4	POMT2	14	77751296	Nonsense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	17654133	77751296	29598244	132	13494										
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105351860	105351860	+	Frame_Shift_Del	DEL	C	C	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctcccggccactgggtgcggCcccccaggcggagcaccagg							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr14:105351860delC	ENST00000414716.3	+	10	2153	c.1925delC	c.(1924-1926)gccfs	p.A642fs	CEP170B_ENST00000418279.1_Frame_Shift_Del_p.A572fs|CEP170B_ENST00000453495.1_Frame_Shift_Del_p.A643fs|CEP170B_ENST00000556508.1_Frame_Shift_Del_p.A572fs	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	642						cytoplasm (GO:0005737)|microtubule (GO:0005874)											CTGGGTGCGGCCCCCCAGGCG	0.697																																					p.A642fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1924delG						.						11	13	12					14																	105351860		1897	4093	5990	SO:0001589	frameshift_variant	283638	exon10			.	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.1925delC	chr14.hg19:g.105351860delC	ENSP00000404151:p.Ala642fs	8.0	0.0		32.0	16.0	NM_001112726	Q2KHR7|Q86TI7	Frame_Shift_Del	DEL	ENST00000414716.3	hg19	CCDS45175.1																																																																																			.	.		0.697	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		-	105351860	C	-	105351860	7	5	98	1	0	1	0	1	0	0	0	0	8175	739	26	0	1959	0	KIAA0284	14	105351860	Frame_Shift_Del	DEL	C	TCGA-DD-A1EB-01A-11D-A12Z-10	27600564	105351860	1997680	133	13495										
MEIS2	4212	hgsc.bcm.edu	37	chr15	37329148	37329148	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	caggtgaagctacactgttgTctaaaccatcccctagtaga	8	11	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr15:37329148T>A	ENST00000561208.1	-	8	1185	c.767A>T	c.(766-768)gAc>gTc	p.D256V	MEIS2_ENST00000424352.2_Missense_Mutation_p.D256V|MEIS2_ENST00000559085.1_Missense_Mutation_p.D243V|MEIS2_ENST00000338564.5_Missense_Mutation_p.D256V|MEIS2_ENST00000397624.3_Missense_Mutation_p.D168V|MEIS2_ENST00000397620.2_Missense_Mutation_p.D168V|MEIS2_ENST00000340545.5_Missense_Mutation_p.D243V|MEIS2_ENST00000444725.1_Missense_Mutation_p.D256V|MEIS2_ENST00000219869.9_Missense_Mutation_p.D110V|MEIS2_ENST00000559561.1_Missense_Mutation_p.D256V|MEIS2_ENST00000557796.2_Missense_Mutation_p.D243V|MEIS2_ENST00000382766.2_Missense_Mutation_p.D256V			O14770	MEIS2_HUMAN	Meis homeobox 2	256	Asp/Glu-rich (acidic).				eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		TACACTGTTGTCTAAACCATC	0.413																																					p.D256V		Atlas-SNP	.											.	MEIS2	99	.	0			c.A767T						.						142	126	131					15																	37329148		2201	4297	6498	SO:0001583	missense	4212	exon8			CTGTTGTCTAAAC	AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"Homeoboxes / TALE class"	7001	protein-coding gene	gene with protein product		601740	"Meis (mouse) homolog 2", "Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.767A>T	chr15.hg19:g.37329148T>A	ENSP00000453793:p.Asp256Val	83.0	0.0		236.0	114.0	NM_170676	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Missense_Mutation	SNP	ENST00000561208.1	hg19	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	T	15.47	2.843516	0.51057	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766;ENST00000424352;ENST00000444725;ENST00000340545;ENST00000397624;ENST00000397620;ENST00000219869	T;D;D;D;D;D;D;D	0.89617	1.83;-2.28;-2.28;-2.19;-2.25;-2.25;-2.25;-2.54	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.93828	0.8026	M	0.75264	2.295	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.997;1.0;0.998;0.999;0.994;0.996;0.999;0.991	P;D;D;D;P;D;D;D	0.87578	0.898;0.991;0.969;0.991;0.869;0.944;0.998;0.944	D	0.93904	0.7191	10	0.49607	T	0.09	-11.808	15.2495	0.73532	0.0:0.0:0.0:1.0	.	243;256;256;256;256;110;168;243	Q96DI2;O14770-4;O14770;O14770-3;O14770-2;B3KP81;B3KPQ6;B3KP98	.;.;MEIS2_HUMAN;.;.;.;.;.	V	256;256;256;256;256;243;243;168;110	ENSP00000326296:D256V;ENSP00000341400:D256V;ENSP00000372216:D256V;ENSP00000404185:D256V;ENSP00000391887:D256V;ENSP00000339549:D243V;ENSP00000380745:D168V;ENSP00000219869:D110V	ENSP00000219869:D110V	D	-	2	0	MEIS2	35116440	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.068000	0.61886	0.528000	0.53228	GAC	.	.		0.413	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677		A	37329148	T	A	37329148	3	1	98	1	0	0	0	0	1	0	0	0	9477	1667	58	4	749	4	MEIS2	15	37329148	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10		37329148	65202244	134	13496										
MGA	23269	hgsc.bcm.edu	37	chr15	42059127	42059127	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	aaagctattgatggagggaaGaatacttctggcctccctgc	11	9	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr15:42059127G>A	ENST00000570161.1	+	23	8847	c.8847G>A	c.(8845-8847)aaG>aaA	p.K2949K	MGA_ENST00000389936.4_Silent_p.K2910K|MGA_ENST00000219905.7_Silent_p.K2949K|MGA_ENST00000566586.1_Silent_p.K2740K|MGA_ENST00000545763.1_Silent_p.K2740K			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ATGGAGGGAAGAATACTTCTG	0.483																																					p.K2949K		Atlas-SNP	.											.	MGA	264	.	0			c.G8847A						.						54	55	55					15																	42059127		1924	4116	6040	SO:0001819	synonymous_variant	23269	exon24			AGGGAAGAATACT	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.8847G>A	chr15.hg19:g.42059127G>A		49.0	0.0		80.0	26.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.483	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42059127	G	A	42059127	2	1	98	1	0	0	0	0	0	0	0	1	9549	933	33	3		3	MGA	15	42059127	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	4729979	42059127	60472265	135	13497										
FBN1	2200	hgsc.bcm.edu	37	chr15	48780612	48780612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gagcaaagccgctgtcacacCtgcacttaaagctgccaatg	9	13	1	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr15:48780612C>T	ENST00000316623.5	-	26	3616	c.3161G>A	c.(3160-3162)aGg>aAg	p.R1054K		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1054	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GCTGTCACACCTGCACTTAAA	0.468																																					p.R1054K		Atlas-SNP	.											.	FBN1	310	.	0			c.G3161A						.						91	85	87					15																	48780612		2198	4296	6494	SO:0001583	missense	2200	exon26			TCACACCTGCACT	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.3161G>A	chr15.hg19:g.48780612C>T	ENSP00000325527:p.Arg1054Lys	40.0	0.0		123.0	52.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789568	0.70337	.	.	ENSG00000166147	ENST00000316623	D	0.92149	-2.98	6.17	6.17	0.99709	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.85513	0.5714	N	0.17564	0.495	0.80722	D	1	B	0.12013	0.005	B	0.19946	0.027	T	0.79291	-0.1864	10	0.26408	T	0.33	.	14.6223	0.68594	0.0:0.9304:0.0:0.0696	.	1054	P35555	FBN1_HUMAN	K	1054	ENSP00000325527:R1054K	ENSP00000325527:R1054K	R	-	2	0	FBN1	46567904	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.590000	0.46154	2.941000	0.99782	0.655000	0.94253	AGG	.	.		0.468	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48780612	C	T	48780612	3	4	98	1	0	0	0	0	1	0	0	0	5710	681	24	3	5618	3	FBN1	15	48780612	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	6721485	48780612	53750780	136	13498										
PDCD7	10081	hgsc.bcm.edu	37	chr15	65426109	65426109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gaccctggccgaagaatggtGgcagggccatgttcacgacg	15	11	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr15:65426109G>A	ENST00000204549.4	-	1	65	c.11C>T	c.(10-12)cCa>cTa	p.P4L		NM_005707.1	NP_005698.1	Q8N8D1	PDCD7_HUMAN	programmed cell death 7	4	Pro-rich.				apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of T cell apoptotic process (GO:0070234)|response to glucocorticoid (GO:0051384)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)				endometrium(4)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	7						GAAGAATGGTGGCAGGGCCAT	0.657																																					p.P4L		Atlas-SNP	.											.	PDCD7	22	.	0			c.C11T						.						7	8	7					15																	65426109		2020	4140	6160	SO:0001583	missense	10081	exon1			AATGGTGGCAGGG	AF083930	CCDS10201.1	15q22.2	2012-06-07			ENSG00000090470	ENSG00000090470			8767	protein-coding gene	gene with protein product	"U11/U12 snRNP 59K"	608138				10037816	Standard	NM_005707		Approved	HES18, ES18	uc002aol.3	Q8N8D1	OTTHUMG00000133117	ENST00000204549.4:c.11C>T	chr15.hg19:g.65426109G>A	ENSP00000204549:p.Pro4Leu	26.0	0.0		71.0	29.0	NM_005707	Q96AK8|Q9Y6D7	Missense_Mutation	SNP	ENST00000204549.4	hg19	CCDS10201.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.432041	0.43122	.	.	ENSG00000090470	ENST00000204549	.	.	.	4.49	4.49	0.54785	.	0.080527	0.48286	D	0.000184	T	0.53753	0.1816	N	0.19112	0.55	0.51482	D	0.999923	D	0.65815	0.995	P	0.58721	0.844	T	0.61163	-0.7118	9	0.87932	D	0	-3.5192	15.043	0.71805	0.0:0.0:1.0:0.0	.	4	Q8N8D1	PDCD7_HUMAN	L	4	.	ENSP00000204549:P4L	P	-	2	0	PDCD7	63213162	1.000000	0.71417	0.995000	0.50966	0.094000	0.18550	3.034000	0.49751	2.201000	0.70794	0.491000	0.48974	CCA	.	.		0.657	PDCD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256784.2	NM_005707		A	65426109	G	A	65426109	3	1	98	1	0	0	0	0	1	0	0	0	11634	1348	47	3	1466	3	PDCD7	15	65426109	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	16645497	65426109	37105283	137	13499										
IDH3A	3419	hgsc.bcm.edu	37	chr15	78454584	78454584	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cctgtcttgcagattgttgaTggagtcgtgcagagtatcaa	12	7	2	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr15:78454584T>C	ENST00000299518.2	+	6	569	c.486T>C	c.(484-486)gaT>gaC	p.D162D	IDH3A_ENST00000441490.2_Silent_p.D53D|IDH3A_ENST00000558535.1_3'UTR|IDH3A_ENST00000558554.1_Silent_p.D127D|IDH3A_ENST00000559205.1_Intron|IDH3A_ENST00000561366.1_5'Flank	NM_005530.2	NP_005521.1	P50213	IDH3A_HUMAN	isocitrate dehydrogenase 3 (NAD+) alpha	162					carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	12						AGATTGTTGATGGAGTCGTGC	0.542																																					p.D162D		Atlas-SNP	.											.	IDH3A	24	.	0			c.T486C						.						127	100	109					15																	78454584		2196	4293	6489	SO:0001819	synonymous_variant	3419	exon6			TGTTGATGGAGTC		CCDS10297.1	15q25.1-q25.2	2008-07-18			ENSG00000166411	ENSG00000166411	1.1.1.41		5384	protein-coding gene	gene with protein product	"H-IDH alpha", "isocitric dehydrogenase", "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "NAD+-specific ICDH", "NAD(H)-specific isocitrate dehydrogenase alpha subunit", "isocitrate dehydrogenase (NAD+) alpha chain"	601149				8833160	Standard	NM_005530		Approved		uc002bdd.3	P50213	OTTHUMG00000143732	ENST00000299518.2:c.486T>C	chr15.hg19:g.78454584T>C		26.0	0.0		106.0	64.0	NM_005530	D3DW83|Q9H3X0	Silent	SNP	ENST00000299518.2	hg19	CCDS10297.1																																																																																			.	.		0.542	IDH3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289799.4	NM_005530		C	78454584	T	C	78454584	2	2	98	1	0	0	0	0	0	0	0	1	7505	1461	51	2		2	IDH3A	15	78454584	Silent	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	13028475	78454584	24076808	138	13500										
UNKL	64718	hgsc.bcm.edu	37	chr16	1420138	1420138	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agccggcactcacctaggggGctgtaggatgaggctgcaga	16	10	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr16:1420138G>A	ENST00000389221.4	-	12	1568	c.1569C>T	c.(1567-1569)agC>agT	p.S523S	UNKL_ENST00000391893.2_5'Flank|UNKL_ENST00000248104.7_5'UTR|UNKL_ENST00000402641.2_Silent_p.S25S|UNKL_ENST00000403703.1_Silent_p.S25S|UNKL_ENST00000508903.2_Silent_p.S526S|UNKL_ENST00000397464.1_Silent_p.S25S	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	523	Ser-rich.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Hepatocellular(780;0.0893)				CACCTAGGGGGCTGTAGGATG	0.692																																					p.S526S		Atlas-SNP	.											.	UNKL	46	.	0			c.C1578T						.						20	24	23					16																	1420138		1812	3419	5231	SO:0001819	synonymous_variant	64718	exon12			TAGGGGGCTGTAG	BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145		"Zinc fingers, CCCH-type domain containing"	14184	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 28", "unkempt homolog (Drosophila)-like"	C16orf28		20148946	Standard	NM_001193389		Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000389221.4:c.1569C>T	chr16.hg19:g.1420138G>A		11.0	0.0		33.0	13.0	NM_001193388	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Silent	SNP	ENST00000389221.4	hg19	CCDS53981.1																																																																																			.	.		0.692	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125		A	1420138	G	A	1420138	2	1	98	1	0	0	0	0	0	0	0	1	17016	1194	42	3		3	UNKL	16	1420138	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10		1420138	88934615	139	13501										
ZNF434	54925	hgsc.bcm.edu	37	chr16	3433548	3433548	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tcactctcccctggagaattTctacattgccttcttgatgt	6	12	4	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr16:3433548T>G	ENST00000396852.4	-	7	1705	c.1398A>C	c.(1396-1398)agA>agC	p.R466S	NAA60_ENST00000576906.1_Intron|ZSCAN32_ENST00000439568.2_Missense_Mutation_p.R177S|ZSCAN32_ENST00000304926.3_Missense_Mutation_p.R254S|ZSCAN32_ENST00000396846.3_Missense_Mutation_p.R466S	NM_001284527.1|NM_001284529.1	NP_001271456.1|NP_001271458.1	Q9NX65	ZSC32_HUMAN	zinc finger and SCAN domain containing 32	466					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)										CTGGAGAATTTCTACATTGCC	0.458																																					p.R254S		Atlas-SNP	.											.	.	.	.	0			c.A762C						.						110	103	105					16																	3433548		2197	4300	6497	SO:0001583	missense	54925	exon6			AGAATTTCTACAT	AK000424	CCDS10503.1, CCDS66920.1, CCDS66921.1	16p13.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000140987	ENSG00000140987		"-", "Zinc fingers, C2H2-type"	20812	protein-coding gene	gene with protein product			"zinc finger protein 434"	ZNF434			Standard	XM_005255402		Approved	FLJ20417	uc002cux.4	Q9NX65	OTTHUMG00000129357	ENST00000396852.4:c.1398A>C	chr16.hg19:g.3433548T>G	ENSP00000380061:p.Arg466Ser	112.0	0.0		307.0	121.0	NM_017810	B4DWL5|C9JB03|Q6WMU8|Q7Z6G2|Q8NFX8|Q9BU74	Missense_Mutation	SNP	ENST00000396852.4	hg19		.	.	.	.	.	.	.	.	.	.	T	11.90	1.777261	0.31411	.	.	ENSG00000140987	ENST00000304926;ENST00000396852;ENST00000396846;ENST00000439568	T;T;T;T	0.08458	3.09;3.16;3.16;3.13	3.45	2.29	0.28610	.	.	.	.	.	T	0.08268	0.0206	L	0.52905	1.665	0.09310	N	1	B;B	0.25486	0.127;0.127	B;B	0.19946	0.014;0.027	T	0.36212	-0.9757	9	0.27082	T	0.32	.	6.4586	0.21944	0.0:0.0:0.2518:0.7482	.	254;466	Q9NX65;Q6WMU8	ZN434_HUMAN;.	S	254;466;466;177	ENSP00000302502:R254S;ENSP00000380061:R466S;ENSP00000380057:R466S;ENSP00000391787:R177S	ENSP00000302502:R254S	R	-	3	2	ZNF434	3373549	0.000000	0.05858	0.001000	0.08648	0.550000	0.35303	0.132000	0.15891	0.230000	0.21059	0.459000	0.35465	AGA	.	.		0.458	ZSCAN32-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251509.2	NM_017810		G	3433548	T	G	3433548	3	3	98	1	0	0	0	0	1	0	0	0	17923	1780	62	5	699	5	ZNF434	16	3433548	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	2013410	3433548	86921205	140	13502										
XPO6	23214	hgsc.bcm.edu	37	chr16	28112968	28112968	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tggaccaggacctggagcagCacgttcacaaactggaacag	12	11	1	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr16:28112968C>A	ENST00000304658.5	-	23	3587	c.3087G>T	c.(3085-3087)gtG>gtT	p.V1029V	XPO6_ENST00000565698.1_Silent_p.V1015V	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	1029			V -> L (in dbSNP:rs14672).		protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						CCTGGAGCAGCACGTTCACAA	0.582																																					p.V1029V		Atlas-SNP	.											.	XPO6	177	.	0			c.G3087T						.						70	76	74					16																	28112968		2086	4222	6308	SO:0001819	synonymous_variant	23214	exon23			GAGCAGCACGTTC	AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"Exportins"	19733	protein-coding gene	gene with protein product		608411	"RAN binding protein 20"	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.3087G>T	chr16.hg19:g.28112968C>A		24.0	0.0		40.0	16.0	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Silent	SNP	ENST00000304658.5	hg19	CCDS42135.1																																																																																			.	.		0.582	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		A	28112968	C	A	28112968	2	1	98	1	0	0	0	0	0	0	0	1	17463	697	25	3		3	XPO6	16	28112968	Silent	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	24679420	28112968	62241785	141	13503										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30750324	30750324	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gctagtttgtcccactgctaCtgttgccaacactgtcacca	7	14	1	0	rs369907818		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr16:30750324C>T	ENST00000262518.4	+	34	9348	c.8963C>T	c.(8962-8964)aCt>aTt	p.T2988I	SRCAP_ENST00000395059.2_Missense_Mutation_p.T2926I|SRCAP_ENST00000344771.4_Missense_Mutation_p.T2830I|RP11-2C24.4_ENST00000483578.1_lincRNA	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2988	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CCCACTGCTACTGTTGCCAAC	0.597																																					p.T2988I		Atlas-SNP	.											.	SRCAP	298	.	0			c.C8963T						.	C	ILE/THR	0,4394		0,0,2197	155	113	127		8963	4.2	1	16		127	1,8599	1.2+/-3.3	0,1,4299	no	missense	SRCAP	NM_006662.2	89	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	benign	2988/3231	30750324	1,12993	2197	4300	6497	SO:0001583	missense	10847	exon34			CTGCTACTGTTGC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.8963C>T	chr16.hg19:g.30750324C>T	ENSP00000262518:p.Thr2988Ile	40.0	0.0		91.0	35.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	6.871	0.530105	0.13127	0.0	1.16E-4	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91237	-2.79;-2.81;-2.8	5.18	4.22	0.49857	.	0.531483	0.15849	N	0.241628	T	0.80660	0.4665	N	0.08118	0	0.25338	N	0.98897	B;B	0.25609	0.13;0.023	B;B	0.21360	0.034;0.015	T	0.72984	-0.4125	10	0.54805	T	0.06	-0.6423	11.9673	0.53042	0.0:0.8259:0.174:0.0	.	2926;2988	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	I	2988;2926;2830	ENSP00000262518:T2988I;ENSP00000378499:T2926I;ENSP00000343042:T2830I	ENSP00000262518:T2988I	T	+	2	0	SRCAP	30657825	0.968000	0.33430	0.994000	0.49952	0.943000	0.58893	2.014000	0.40951	1.536000	0.49237	0.655000	0.94253	ACT	.	.		0.597	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30750324	C	T	30750324	3	4	98	1	0	0	0	0	1	0	0	0	15150	565	20	3	9089	3	SRCAP	16	30750324	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	2637356	30750324	59604429	142	13504										
PDPR	55066	hgsc.bcm.edu	37	chr16	70190496	70190496	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cctagacctttggccttggtGgggagagcccatttaccgga	13	11	0	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr16:70190496G>T	ENST00000288050.4	+	19	3311	c.2354G>T	c.(2353-2355)tGg>tTg	p.W785L	RP11-296I10.3_ENST00000502126.1_RNA|PDPR_ENST00000542659.1_Missense_Mutation_p.W130L|RP11-296I10.3_ENST00000566989.1_RNA|PDPR_ENST00000398122.3_Missense_Mutation_p.W685L|PDPR_ENST00000567046.1_Missense_Mutation_p.W143L|PDPR_ENST00000568530.1_Missense_Mutation_p.W785L|PDPR_ENST00000562100.1_3'UTR	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	785					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		TGGCCTTGGTGGGGAGAGCCC	0.567																																					p.W785L		Atlas-SNP	.											.	PDPR	66	.	0			c.G2354T						.						232	255	247					16																	70190496		2088	4212	6300	SO:0001583	missense	55066	exon19			CTTGGTGGGGAGA		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.2354G>T	chr16.hg19:g.70190496G>T	ENSP00000288050:p.Trp785Leu	65.0	0.0		176.0	24.0	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	hg19	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	G	34	5.406594	0.96051	.	.	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055;ENST00000542659	T;T;T	0.75938	-0.98;-0.98;-0.98	6.03	6.03	0.97812	Glycine cleavage T-protein, C-terminal barrel (1);	0.062767	0.64402	D	0.000001	T	0.81389	0.4812	L	0.36672	1.1	0.80722	D	1	D;D	0.71674	0.998;0.984	D;P	0.68039	0.955;0.845	T	0.80867	-0.1190	10	0.54805	T	0.06	.	19.5634	0.95382	0.0:0.0:1.0:0.0	.	452;785	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	L	785;685;452;130	ENSP00000288050:W785L;ENSP00000381190:W685L;ENSP00000441690:W130L	ENSP00000205055:W452L	W	+	2	0	PDPR	68747997	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.793000	0.99091	2.868000	0.98415	0.557000	0.71058	TGG	.	.		0.567	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990		T	70190496	G	T	70190496	3	4	98	1	0	0	0	0	1	0	0	0	11698	1357	47	3	2420	3	PDPR	16	70190496	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	39440172	70190496	20164257	143	13505										
TCF25	22980	hgsc.bcm.edu	37	chr16	89960138	89960138	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agcactctcccctcccaggtCtgtccatgcggctgctggaa	10	16	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr16:89960138C>G	ENST00000263346.8	+	7	756	c.700C>G	c.(700-702)Ctg>Gtg	p.L234V	TCF25_ENST00000263347.7_5'UTR	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	234					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		CCTCCCAGGTCTGTCCATGCG	0.607																																					p.L234V		Atlas-SNP	.											.	TCF25	61	.	0			c.C700G						.						67	62	64					16																	89960138		2198	4300	6498	SO:0001583	missense	22980	exon7			CCAGGTCTGTCCA	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.700C>G	chr16.hg19:g.89960138C>G	ENSP00000263346:p.Leu234Val	30.0	0.0		153.0	42.0	NM_014972	Q2MK75|Q9UPV3	Missense_Mutation	SNP	ENST00000263346.8	hg19	CCDS10987.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.414671	0.42817	.	.	ENSG00000141002	ENST00000263346	.	.	.	5.42	2.15	0.27550	.	0.055782	0.64402	D	0.000001	T	0.34803	0.0910	L	0.39898	1.24	0.80722	D	1	B	0.33379	0.41	B	0.25884	0.064	T	0.19289	-1.0310	9	0.66056	D	0.02	.	4.4948	0.11831	0.3378:0.4669:0.0:0.1953	.	234	Q9BQ70	TCF25_HUMAN	V	234	.	ENSP00000263346:L234V	L	+	1	2	TCF25	88487639	1.000000	0.71417	0.973000	0.42090	0.970000	0.65996	3.148000	0.50647	0.659000	0.30945	0.561000	0.74099	CTG	.	.		0.607	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972		G	89960138	C	G	89960138	3	3	98	1	0	0	0	0	1	0	0	0	15708	912	32	4	726	4	TCF25	16	89960138	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	19769642	89960138	394615	144	13506										
TP53	7157	hgsc.bcm.edu	37	chr17	7578554	7578554	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cttgttgagggcaggggagtActgtaggaagaggaaggaga	19	3	0	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr17:7578554A>C	ENST00000269305.4	-	5	565	c.376T>G	c.(376-378)Tac>Gac	p.Y126D	TP53_ENST00000445888.2_Splice_Site_p.Y126D|TP53_ENST00000413465.2_Splice_Site_p.Y126D|TP53_ENST00000420246.2_Splice_Site_p.Y126D|TP53_ENST00000455263.2_Splice_Site_p.Y126D|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Splice_Site_p.Y126D	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	126	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> G (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y126D(9)|p.0?(8)|p.Y126N(6)|p.Y126_K132delYSPALNK(6)|p.Y126_N131delYSPALN(3)|p.Y33D(2)|p.V73fs*9(1)|p.?(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)|p.Y126fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAGGGGAGTACTGTAGGAAG	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y126D	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	40	Substitution - Missense(17)|Deletion - In frame(9)|Whole gene deletion(8)|Deletion - Frameshift(4)|Insertion - In frame(1)|Unknown(1)	central_nervous_system(6)|haematopoietic_and_lymphoid_tissue(6)|upper_aerodigestive_tract(4)|large_intestine(4)|lung(4)|prostate(4)|bone(4)|breast(3)|ovary(2)|stomach(1)|liver(1)|oesophagus(1)	c.T376G	GRCh37	CI004819	TP53	I		.						42	43	43					17																	7578554		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGGAGTACTGTAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.376-1T>G	chr17.hg19:g.7578554A>C		17.0	0.0		21.0	14.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443641	0.83993	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	5.48	5.48	0.80851	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99869	0.9938	M	0.90483	3.12	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.999;0.999;1.0;0.971;1.0;1.0;1.0	D	0.96375	0.9277	10	0.87932	D	0	-28.2517	13.8301	0.63375	1.0:0.0:0.0:0.0	.	87;126;126;33;126;126;126	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	D	126;126;126;126;126;126;115;33;33;126;126	ENSP00000410739:Y126D;ENSP00000352610:Y126D;ENSP00000269305:Y126D;ENSP00000398846:Y126D;ENSP00000391127:Y126D;ENSP00000391478:Y126D;ENSP00000423862:Y33D;ENSP00000424104:Y126D;ENSP00000426252:Y126D	ENSP00000269305:Y126D	Y	-	1	0	TP53	7519279	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	9.240000	0.95396	2.206000	0.71126	0.533000	0.62120	TAC	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Missense_Mutation	C	7578554	A	C	7578554	5	2	98	1	0	0	0	0	0	0	1	0	16396	405	14	5	922	5	TP53	17	7578554	Splice_Site	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10		7578554	73616656	145	13507										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27493801	27493801	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ggcgcgtcttggattcacgcTtggaggagcggttcaggttg	17	8	3	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr17:27493801T>C	ENST00000527372.1	-	2	338	c.158A>G	c.(157-159)aAg>aGg	p.K53R	MYO18A_ENST00000533112.1_Missense_Mutation_p.K53R|MYO18A_ENST00000354329.4_Missense_Mutation_p.K53R|MYO18A_ENST00000531253.1_Missense_Mutation_p.K53R	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	53	Mediates nucleotide-independent binding to F-actin and interaction with GOLPH3.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			GGATTCACGCTTGGAGGAGCG	0.567																																					p.K53R	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.A158G						.						46	54	51					17																	27493801		2164	4271	6435	SO:0001583	missense	399687	exon2			TCACGCTTGGAGG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.158A>G	chr17.hg19:g.27493801T>C	ENSP00000437073:p.Lys53Arg	79.0	0.0		225.0	81.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433922	0.83776	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372	D;D;D;D	0.90261	-2.52;-2.64;-2.52;-2.52	4.94	4.94	0.65067	.	0.056975	0.64402	N	0.000003	D	0.92231	0.7536	L	0.32530	0.975	0.46609	D	0.999121	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.80764	0.994;0.994;0.985	D	0.93333	0.6703	10	0.87932	D	0	.	14.7704	0.69671	0.0:0.0:0.0:1.0	.	53;53;53	Q92614-3;Q92614-4;Q92614	.;.;MY18A_HUMAN	R	53	ENSP00000346291:K53R;ENSP00000435932:K53R;ENSP00000434228:K53R;ENSP00000437073:K53R	ENSP00000346291:K53R	K	-	2	0	MYO18A	24517927	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.630000	0.67805	2.084000	0.62774	0.383000	0.25322	AAG	.	.		0.567	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		C	27493801	T	C	27493801	3	2	98	1	0	0	0	0	1	0	0	0	10074	1609	56	2	6170	2	MYO18A	17	27493801	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	19915247	27493801	53701409	146	13508										
GPR179	440435	hgsc.bcm.edu	37	chr17	36483358	36483358	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ttttccatcctgccttgacaCccctttgacagggattcttt	6	13	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr17:36483358C>A	ENST00000342292.4	-	11	6114	c.6094G>T	c.(6094-6096)Gtg>Ttg	p.V2032L	GPR179_ENST00000584976.1_Intron	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	2032					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TGCCTTGACACCCCTTTGACA	0.502																																					p.V2032L		Atlas-SNP	.											.	GPR179	170	.	0			c.G6094T						.						115	109	111					17																	36483358		1938	4150	6088	SO:0001583	missense	440435	exon11			TTGACACCCCTTT		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.6094G>T	chr17.hg19:g.36483358C>A	ENSP00000345060:p.Val2032Leu	70.0	0.0		142.0	57.0	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	C	6.818	0.519989	0.13005	.	.	ENSG00000188888	ENST00000342292	T	0.49139	0.79	4.88	-1.29	0.09288	.	0.965211	0.08475	N	0.940342	T	0.30198	0.0757	L	0.29908	0.895	0.09310	N	1	B	0.18013	0.025	B	0.14023	0.01	T	0.22452	-1.0216	10	0.25751	T	0.34	-0.3936	5.4542	0.16582	0.0:0.401:0.1444:0.4546	.	2032	Q6PRD1	GP179_HUMAN	L	2032	ENSP00000345060:V2032L	ENSP00000345060:V2032L	V	-	1	0	GPR179	33736884	0.000000	0.05858	0.000000	0.03702	0.096000	0.18686	-0.211000	0.09332	-0.043000	0.13513	-0.291000	0.09656	GTG	.	.		0.502	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36483358	C	A	36483358	3	1	98	1	0	0	0	0	1	0	0	0	6682	507	18	3	1013	3	GPR179	17	36483358	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	8989557	36483358	44711852	147	13509										
G6PC3	92579	hgsc.bcm.edu	37	chr17	42152763	42152763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ttgactgcactggccctcatGctaggcaccagcctcatcta	8	15	3	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr17:42152763G>A	ENST00000269097.4	+	5	852	c.621G>A	c.(619-621)atG>atA	p.M207I		NM_138387.3	NP_612396.1	Q9BUM1	G6PC3_HUMAN	glucose 6 phosphatase, catalytic, 3	207					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucose-6-phosphatase activity (GO:0004346)			endometrium(2)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	11		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.113)		TGGCCCTCATGCTAGGCACCA	0.577																																					p.M207I		Atlas-SNP	.											.	G6PC3	26	.	0			c.G621A						.						174	146	156					17																	42152763		2203	4300	6503	SO:0001583	missense	92579	exon5			CCTCATGCTAGGC	BC021574	CCDS11476.1	17q21.31	2014-09-17				ENSG00000141349			24861	protein-coding gene	gene with protein product		611045				12370122, 12965222	Standard	NM_138387		Approved	UGRP	uc002iex.3	Q9BUM1		ENST00000269097.4:c.621G>A	chr17.hg19:g.42152763G>A	ENSP00000269097:p.Met207Ile	93.0	0.0		286.0	99.0	NM_138387	Q8WU15	Missense_Mutation	SNP	ENST00000269097.4	hg19	CCDS11476.1	.	.	.	.	.	.	.	.	.	.	G	9.508	1.105100	0.20632	.	.	ENSG00000141349	ENST00000269097	T	0.74632	-0.86	5.27	3.3	0.37823	.	0.277563	0.35067	N	0.003464	T	0.60157	0.2247	L	0.29908	0.895	0.30631	N	0.757485	B	0.06786	0.001	B	0.04013	0.001	T	0.56902	-0.7902	10	0.37606	T	0.19	-17.7143	9.6863	0.40100	0.1524:0.0:0.8476:0.0	.	207	Q9BUM1	G6PC3_HUMAN	I	207	ENSP00000269097:M207I	ENSP00000269097:M207I	M	+	3	0	G6PC3	39508289	1.000000	0.71417	0.998000	0.56505	0.108000	0.19459	2.196000	0.42686	0.815000	0.34398	0.563000	0.77884	ATG	.	.		0.577	G6PC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457675.1	NM_138387		A	42152763	G	A	42152763	3	1	98	1	0	0	0	0	1	0	0	0	6153	1319	46	3	639	3	G6PC3	17	42152763	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	5669405	42152763	39042447	148	13510										
CDC27	996	hgsc.bcm.edu	37	chr17	45234594	45234729	+	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cactagaatataagacacttAcaattgtgtcctggggtgtt					rs149474782|rs113608268|rs370849730|rs78395997|rs76624491|rs370261409|rs75353677|rs368304141|rs376818791|rs372212798|rs375653477|rs374472811|rs76359747|rs147617501|rs374614181|rs78108688|rs142987740|rs143453365|rs75990396|rs144985864|rs367644695|rs202182614|rs139751753|rs11570485|rs372926889|rs140171160|rs368750026|rs201098929|rs199899451|rs75175938|rs200340309|rs537990668	byFrequency	TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr17:45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	ENST00000066544.3	-	6	590_724	c.497_631delAGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG	c.(496-633)cagttcttacggaaacaccccaggacacaattgtaagtgtcttatattctagtgttcaaaatattatgaaaactacaaagaatgatctgaactaaataatatattgtgaatgacttggtagaaattttctgtttcaga>cga	p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000531206.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000527547.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000446365.2_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF105fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.T167T(7)|p.T171T(3)|p.V201I(2)|p.E199E(2)|p.T200T(2)|p.L173S(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACTGTCTCAGGCTGTCTGTGAGATAAACTATGATTAGGTACTTGTGTTGTGCAAGAGTTGGGCAGACAGTTGCTAAAGTTCTGTAAAGATGTGAATTTAAATGTTTGGTCAGGATC	0.342																																					p.201_211del		Pindel	.											.	CDC27	337	.	17	Substitution - coding silent(14)|Substitution - Missense(3)	large_intestine(6)|prostate(6)|kidney(4)|NS(1)	c.601_631del						.																																			SO:0001630	splice_region_variant	996	exon6			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.631-104AGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG>-	chr17.hg19:g.45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT		0.0	0.0		15.0	15.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.342	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Frame_Shift_Del	-	45234729	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	45234594	8	5	98	1	0	1	0	1	0	0	1	0	3068	405	14	0	1916	0	CDC27	17	45234594	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	TCGA-DD-A1EB-01A-11D-A12Z-10	3081831	45234594	35960616	149	13511										
SFRS1	6426	hgsc.bcm.edu	37	chr17	56083127	56083127	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gttaagaccactgtatccaaTtctggtcaaagaaaagaata	7	7	2	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr17:56083127T>C	ENST00000258962.4	-	3	761				SRSF1_ENST00000585096.1_Intron|RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000584773.1_Intron|SRSF1_ENST00000581497.1_5'Flank|SRSF1_ENST00000582730.2_Missense_Mutation_p.N196S	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1						cardiac muscle contraction (GO:0060048)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA 3'-end processing (GO:0031124)|mRNA 5'-splice site recognition (GO:0000395)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CTGTATCCAATTCTGGTCAAA	0.368																																					p.N196S		Atlas-SNP	.											.	SRSF1	41	.	0			c.A587G						.						95	85	88					17																	56083127		2203	4300	6503	SO:0001627	intron_variant	6426	exon3			ATCCAATTCTGGT		CCDS11600.1, CCDS58580.1	17q22	2013-02-12	2010-06-22	2010-06-22	ENSG00000136450	ENSG00000136450		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10780	protein-coding gene	gene with protein product	"splicing factor 2", "pre-mRNA-splicing factor SF2, P33 subunit", "alternate splicing factor", "SR splicing factor 1"	600812	"splicing factor, arginine/serine-rich 1"	SFRS1		8530103, 20516191	Standard	NM_006924		Approved	ASF, SF2, SRp30a, SF2p33, MGC5228	uc002ivi.3	Q07955		ENST00000258962.4:c.552+34A>G	chr17.hg19:g.56083127T>C		58.0	0.0		117.0	39.0	NM_001078166	B2R6Z7|D3DTZ3|Q13809	Missense_Mutation	SNP	ENST00000258962.4	hg19	CCDS11600.1																																																																																			.	.		0.368	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924		C	56083127	T	C	56083127	1	2	98	0	1	0	0	0	0	0	0	0	14180	1493	52	2		2	SFRS1	17	56083127	Intron	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	10848533	56083127	25112083	150	13512										
UNC13D	201294	hgsc.bcm.edu	37	chr17	73836847	73836847	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gccctgcaacacgaacctgcGaagcccatgcagatccgtga	10	15	0	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr17:73836847G>T	ENST00000207549.4	-	8	1058	c.679C>A	c.(679-681)Cgc>Agc	p.R227S	UNC13D_ENST00000587504.1_5'UTR|UNC13D_ENST00000412096.2_Missense_Mutation_p.R227S	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	227					defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			ACGAACCTGCGAAGCCCATGC	0.597									Familial Hemophagocytic Lymphohistiocytosis																												p.R227S		Atlas-SNP	.											.	UNC13D	68	.	0			c.C679A						.						139	129	132					17																	73836847		2203	4300	6503	SO:0001583	missense	201294	exon8	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	ACCTGCGAAGCCC	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.679C>A	chr17.hg19:g.73836847G>T	ENSP00000207549:p.Arg227Ser	53.0	0.0		251.0	68.0	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.804067	0.31869	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.70986	-0.51;-0.53	4.49	2.43	0.29744	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.183733	0.33199	N	0.005174	T	0.59224	0.2178	L	0.38175	1.15	0.09310	N	1	D;P	0.56035	0.974;0.945	P;P	0.49999	0.628;0.472	T	0.52094	-0.8621	10	0.07990	T	0.79	.	6.3405	0.21321	0.0936:0.0:0.3916:0.5148	.	227;227	B4DTQ6;Q70J99	.;UN13D_HUMAN	S	227	ENSP00000207549:R227S;ENSP00000388093:R227S	ENSP00000207549:R227S	R	-	1	0	UNC13D	71348442	0.991000	0.36638	0.912000	0.35992	0.433000	0.31745	3.825000	0.55730	0.852000	0.35287	0.551000	0.68910	CGC	.	.		0.597	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		T	73836847	G	T	73836847	3	4	98	1	0	0	0	0	1	0	0	0	17002	1058	37	1	2693	1	UNC13D	17	73836847	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	17753720	73836847	7358363	151	13513										
EVPL	2125	hgsc.bcm.edu	37	chr17	74003252	74003252	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gtacccctccagtgccgctgGcaggagcagcaggccgctca	13	16	1	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr17:74003252G>T	ENST00000301607.3	-	22	6287	c.6034C>A	c.(6034-6036)Cca>Aca	p.P2012T	EVPL_ENST00000586740.1_Missense_Mutation_p.P2034T|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	2012	Globular 2.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						AGTGCCGCTGGCAGGAGCAGC	0.677																																					p.P2012T		Atlas-SNP	.											.	EVPL	155	.	0			c.C6034A						.						38	42	41					17																	74003252		2201	4297	6498	SO:0001583	missense	2125	exon22			CCGCTGGCAGGAG	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.6034C>A	chr17.hg19:g.74003252G>T	ENSP00000301607:p.Pro2012Thr	6.0	0.0		72.0	11.0	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	hg19	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551735	0.65311	.	.	ENSG00000167880	ENST00000301607	T	0.71698	-0.59	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	D	0.82609	0.5074	M	0.61703	1.905	0.43517	D	0.995785	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	D	0.83939	0.0310	10	0.72032	D	0.01	-18.0196	17.5417	0.87850	0.0:0.0:1.0:0.0	.	2034;2012	B7ZLH8;Q92817	.;EVPL_HUMAN	T	2012	ENSP00000301607:P2012T	ENSP00000301607:P2012T	P	-	1	0	EVPL	71514847	1.000000	0.71417	0.924000	0.36721	0.060000	0.15804	9.469000	0.97679	2.564000	0.86499	0.561000	0.74099	CCA	.	.		0.677	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		T	74003252	G	T	74003252	3	4	98	1	0	0	0	0	1	0	0	0	5294	1203	42	3	71	3	EVPL	17	74003252	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	166405	74003252	7191958	152	13514										
ZNF407	55628	hgsc.bcm.edu	37	chr18	72346946	72346946	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	atttattttggaggaggatgGcccagcttctgatagcacag	12	7	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr18:72346946G>A	ENST00000299687.5	+	1	3971	c.3971G>A	c.(3970-3972)gGc>gAc	p.G1324D	ZNF407_ENST00000577538.1_Missense_Mutation_p.G1324D|ZNF407_ENST00000582337.1_Missense_Mutation_p.G1324D|ZNF407_ENST00000309902.6_Missense_Mutation_p.G1324D	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1324					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAGGAGGATGGCCCAGCTTCT	0.393																																					p.G1324D		Atlas-SNP	.											.	ZNF407	231	.	0			c.G3971A						.						52	53	53					18																	72346946		1899	4120	6019	SO:0001583	missense	55628	exon1			AGGATGGCCCAGC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.3971G>A	chr18.hg19:g.72346946G>A	ENSP00000299687:p.Gly1324Asp	48.0	0.0		104.0	48.0	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	G	8.708	0.911378	0.17833	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.11063	2.81;3.2	5.14	2.28	0.28536	.	0.511871	0.20538	N	0.090377	T	0.07954	0.0199	L	0.34521	1.04	0.22378	N	0.999152	B;B;B	0.27140	0.169;0.169;0.105	B;B;B	0.28553	0.091;0.091;0.042	T	0.31138	-0.9954	10	0.48119	T	0.1	.	5.2563	0.15548	0.0738:0.2793:0.5108:0.1361	.	1324;1324;1324	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	D	1324	ENSP00000299687:G1324D;ENSP00000310359:G1324D	ENSP00000299687:G1324D	G	+	2	0	ZNF407	70475934	0.501000	0.26099	0.098000	0.21074	0.601000	0.36947	1.431000	0.34925	-0.100000	0.12241	0.655000	0.94253	GGC	.	.		0.393	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		A	72346946	G	A	72346946	3	1	98	1	0	0	0	0	1	0	0	0	17902	1203	42	3	3973	3	ZNF407	18	72346946	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10		72346946	5730302	153	13515										
AKAP8L	26993	hgsc.bcm.edu	37	chr19	15512065	15512065	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gcccgggaaggcgcccccacCtcgcatgccctggaacatgc	12	18	0	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr19:15512065C>T	ENST00000397410.5	-	5	842	c.712G>A	c.(712-714)Ggt>Agt	p.G238S	AKAP8L_ENST00000595879.1_5'UTR|AKAP8L_ENST00000595465.2_Missense_Mutation_p.G177S	NM_014371.2	NP_055186.2	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like	238						cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(4)|kidney(2)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	11						GCGCCCCCACCTCGCATGCCC	0.647																																					p.G238S		Atlas-SNP	.											.	AKAP8L	64	.	0			c.G712A						.						87	101	97					19																	15512065		1947	4138	6085	SO:0001583	missense	26993	exon5			CCCCACCTCGCAT	BC000713	CCDS46005.1	19p13.12	2013-10-16			ENSG00000011243	ENSG00000011243			29857	protein-coding gene	gene with protein product	"neighbor of A kinase anchoring protein 95"	609475				10748171, 10761695	Standard	XM_005259854		Approved	NAKAP95, HAP95	uc002naw.1	Q9ULX6	OTTHUMG00000182446	ENST00000397410.5:c.712G>A	chr19.hg19:g.15512065C>T	ENSP00000380557:p.Gly238Ser	19.0	0.0		22.0	17.0	NM_014371	B4DJ74|B5BU90|O94792|Q96J58|Q9NRQ0|Q9UGM0	Missense_Mutation	SNP	ENST00000397410.5	hg19	CCDS46005.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.678657	0.68042	.	.	ENSG00000011243	ENST00000397410	T	0.58652	0.32	4.74	4.74	0.60224	.	0.061125	0.64402	D	0.000005	T	0.69797	0.3151	L	0.49778	1.585	0.34874	D	0.743843	D;D;D;D	0.89917	0.996;1.0;0.995;0.996	D;D;D;P	0.87578	0.933;0.998;0.922;0.875	T	0.76785	-0.2831	10	0.42905	T	0.14	-11.5322	14.6587	0.68852	0.0:1.0:0.0:0.0	.	177;8;238;238	B4DJ74;Q9UF73;B3KMD4;Q9ULX6	.;.;.;AKP8L_HUMAN	S	238	ENSP00000380557:G238S	ENSP00000380557:G238S	G	-	1	0	AKAP8L	15373065	1.000000	0.71417	0.814000	0.32528	0.670000	0.39368	5.810000	0.69179	2.194000	0.70268	0.491000	0.48974	GGT	.	.		0.647	AKAP8L-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461301.2	NM_014371		T	15512065	C	T	15512065	3	4	98	1	0	0	0	0	1	0	0	0	458	681	24	3	1268	3	AKAP8L	19	15512065	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10		15512065	43616918	154	13516										
HRC	3270	hgsc.bcm.edu	37	chr19	49657886	49657886	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ccatactcagtggaggcctcCtcttcctcctcctcctcctc	5	20	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr19:49657886C>T	ENST00000252825.4	-	1	795	c.609G>A	c.(607-609)gaG>gaA	p.E203E	HRC_ENST00000595625.1_Silent_p.E203E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	203	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		TGGAGGcctcctcttcctcct	0.572																																					p.E203E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G609A						.						123	91	102					19																	49657886		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			GGCCTCCTCTTCC		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.609G>A	chr19.hg19:g.49657886C>T		79.0	0.0		219.0	9.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.572	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		T	49657886	C	T	49657886	2	4	98	1	0	0	0	0	0	0	0	1	7361	680	24	3		3	HRC	19	49657886	Silent	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	34145821	49657886	9471097	155	13517										
HRC	3270	hgsc.bcm.edu	37	chr19	49657916	49657916	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tcctcctcctcctcctcctcTtctccttcatcatcttcccc	0	23	5	0	rs7409255		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr19:49657916T>C	ENST00000252825.4	-	1	765	c.579A>G	c.(577-579)gaA>gaG	p.E193E	HRC_ENST00000595625.1_Silent_p.E193E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	193	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cctcctcctcttcTCCTTCAT	0.557																																					p.E193E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A579G						.						119	95	103					19																	49657916		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCTCCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.579A>G	chr19.hg19:g.49657916T>C		84.0	0.0		238.0	14.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.557	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657916	T	C	49657916	2	2	98	1	0	0	0	0	0	0	0	1	7361	1606	56	2		2	HRC	19	49657916	Silent	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	30	49657916	9471067	156	13518										
ZNF808	388558	hgsc.bcm.edu	37	chr19	53057994	53057994	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	aagtttttggtcagaaatcaGctcttgagtcacataagaga	9	6	4	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr19:53057994G>T	ENST00000359798.4	+	5	2005	c.1825G>T	c.(1825-1827)Gct>Tct	p.A609S		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	609					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		TCAGAAATCAGCTCTTGAGTC	0.398																																					p.A609S		Atlas-SNP	.											.	ZNF808	81	.	0			c.G1825T						.						53	57	56					19																	53057994		2198	4298	6496	SO:0001583	missense	388558	exon5			AAATCAGCTCTTG	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.1825G>T	chr19.hg19:g.53057994G>T	ENSP00000352846:p.Ala609Ser	39.0	0.0		77.0	30.0	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	hg19	CCDS46167.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.592478	0.00126	.	.	ENSG00000198482	ENST00000359798	T	0.03524	3.9	1.41	-2.83	0.05769	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01454	0.0047	N	0.03209	-0.39	0.09310	N	1	B	0.02656	0.0	B	0.17979	0.02	T	0.37641	-0.9697	9	0.17369	T	0.5	.	2.4606	0.04540	0.2016:0.3472:0.3328:0.1183	.	609	Q8N4W9	ZN808_HUMAN	S	609	ENSP00000352846:A609S	ENSP00000352846:A609S	A	+	1	0	ZNF808	57749806	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.923000	0.28757	-3.625000	0.00130	-2.619000	0.00157	GCT	.	.		0.398	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		T	53057994	G	T	53057994	3	4	98	1	0	0	0	0	1	0	0	0	18188	971	34	3	1835	3	ZNF808	19	53057994	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	3400078	53057994	6070989	157	13519										
ZNF611	81856	hgsc.bcm.edu	37	chr19	53209133	53209133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgtatggtttctctccagtaTgaattctcttatgtgtctca	7	8	3	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr19:53209133T>C	ENST00000319783.1	-	7	1491	c.1175A>G	c.(1174-1176)cAt>cGt	p.H392R	ZNF611_ENST00000540744.1_Missense_Mutation_p.H392R|ZNF611_ENST00000453741.2_Missense_Mutation_p.H323R|ZNF611_ENST00000602162.1_Missense_Mutation_p.H323R|ZNF611_ENST00000595798.1_Missense_Mutation_p.H323R|ZNF611_ENST00000543227.1_Missense_Mutation_p.H392R|ZNF611_ENST00000602046.1_5'Flank	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	392					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		CTCTCCAGTATGAATTCTCTT	0.383																																					p.H392R		Atlas-SNP	.											.	ZNF611	72	.	0			c.A1175G						.						62	62	62					19																	53209133		2203	4300	6503	SO:0001583	missense	81856	exon7			CCAGTATGAATTC	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"Zinc fingers, C2H2-type", "-"	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.1175A>G	chr19.hg19:g.53209133T>C	ENSP00000322427:p.His392Arg	60.0	0.0		107.0	41.0	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	hg19	CCDS12855.1	.	.	.	.	.	.	.	.	.	.	.	15.95	2.983092	0.53827	.	.	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	1.62	1.62	0.23740	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.83482	0.5264	M	0.93594	3.435	0.27689	N	0.946178	D	0.89917	1.0	D	0.79108	0.992	T	0.72323	-0.4328	9	0.87932	D	0	.	8.0771	0.30722	0.0:0.0:0.0:1.0	.	392	Q8N823	ZN611_HUMAN	R	392;392;323;392	ENSP00000437616:H392R;ENSP00000439211:H392R;ENSP00000443505:H323R;ENSP00000322427:H392R	ENSP00000322427:H392R	H	-	2	0	ZNF611	57900945	1.000000	0.71417	0.011000	0.14972	0.164000	0.22412	6.180000	0.71981	0.745000	0.32763	0.163000	0.16589	CAT	.	.		0.383	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972		C	53209133	T	C	53209133	3	2	98	1	0	0	0	0	1	0	0	0	18052	1464	51	2	946	2	ZNF611	19	53209133	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	151139	53209133	5919850	158	13520										
PCNA	5111	hgsc.bcm.edu	37	chr20	5096123	5096123	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	acatctgcagacatactgagTgtcaccgttgaagagagtgg	12	8	2	4			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr20:5096123T>C	ENST00000379160.3	-	6	920	c.678A>G	c.(676-678)acA>acG	p.T226T	TMEM230_ENST00000202834.7_5'Flank|TMEM230_ENST00000379286.2_5'Flank|TMEM230_ENST00000342308.5_5'Flank|TMEM230_ENST00000379283.2_5'Flank|TMEM230_ENST00000379277.2_5'Flank|TMEM230_ENST00000492419.1_5'Flank|TMEM230_ENST00000379279.2_5'Flank|PCNA_ENST00000379143.5_Silent_p.T226T|Y_RNA_ENST00000516558.1_RNA	NM_002592.2	NP_002583.1	P12004	PCNA_HUMAN	proliferating cell nuclear antigen	226					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|epithelial cell differentiation (GO:0030855)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|leading strand elongation (GO:0006272)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of deoxyribonuclease activity (GO:0032077)|regulation of DNA replication (GO:0006275)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cadmium ion (GO:0046686)|response to lipid (GO:0033993)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)|translesion synthesis (GO:0019985)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|nuclear replication fork (GO:0043596)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA complex (GO:0043626)|PCNA-p21 complex (GO:0070557)	dinucleotide insertion or deletion binding (GO:0032139)|DNA polymerase binding (GO:0070182)|DNA polymerase processivity factor activity (GO:0030337)|identical protein binding (GO:0042802)|MutLalpha complex binding (GO:0032405)|purine-specific mismatch base pair DNA N-glycosylase activity (GO:0000701)|receptor tyrosine kinase binding (GO:0030971)			endometrium(2)|kidney(1)|large_intestine(4)|lung(2)	9						ACATACTGAGTGTCACCGTTG	0.388								DNA polymerases (catalytic subunits)																													p.T226T		Atlas-SNP	.											.	PCNA	17	.	0			c.A678G						.						192	181	185					20																	5096123		2203	4300	6503	SO:0001819	synonymous_variant	5111	exon6			ACTGAGTGTCACC	J04718	CCDS13087.1	20p13-p12.3	2013-09-19			ENSG00000132646	ENSG00000132646			8729	protein-coding gene	gene with protein product		176740				2565339	Standard	NM_002592		Approved		uc002wlp.3	P12004	OTTHUMG00000031798	ENST00000379160.3:c.678A>G	chr20.hg19:g.5096123T>C		93.0	0.0		239.0	104.0	NM_002592	B2R897|D3DW02	Silent	SNP	ENST00000379160.3	hg19	CCDS13087.1																																																																																			.	.		0.388	PCNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077852.2			C	5096123	T	C	5096123	2	2	98	1	0	0	0	0	0	0	0	1	11597	1683	59	2		2	PCNA	20	5096123	Silent	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10		5096123	57929397	159	13521										
PLUNC	51297	hgsc.bcm.edu	37	chr20	31825880	31825880	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gccctcagcaatggcctgctGtctgggggcctgttgggcat	15	12	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr20:31825880G>T	ENST00000354297.4	+	3	251	c.180G>T	c.(178-180)ctG>ctT	p.L60L	BPIFA1_ENST00000375422.2_Silent_p.L60L|BPIFA1_ENST00000375413.4_Silent_p.L60L	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	60					antibacterial humoral response (GO:0019731)|innate immune response (GO:0045087)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|regulation of liquid surface tension (GO:0050828)|regulation of sodium ion transmembrane transport (GO:1902305)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)										ATGGCCTGCTGTCTGGGGGCC	0.597																																					p.L60L		Atlas-SNP	.											.	.	.	.	0			c.G180T						.						49	50	50					20																	31825880		2203	4300	6503	SO:0001819	synonymous_variant	51297	exon3			CCTGCTGTCTGGG	AB024937	CCDS13217.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000198183	ENSG00000198183		"BPI fold containing"	15749	protein-coding gene	gene with protein product		607412	"palate, lung and nasal epithelium carcinoma associated", "palate, lung and nasal epithelium associated"	PLUNC		11018263, 11251963, 21787333	Standard	NM_130852		Approved	LUNX, bA49G10.5, SPLUNC1	uc002wyv.3	Q9NP55	OTTHUMG00000032243	ENST00000354297.4:c.180G>T	chr20.hg19:g.31825880G>T		37.0	0.0		95.0	38.0	NM_016583	A8K9R3|E1P5M9|Q9NZT0	Silent	SNP	ENST00000354297.4	hg19	CCDS13217.1																																																																																			.	.		0.597	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		T	31825880	G	T	31825880	2	4	98	1	0	0	0	0	0	0	0	1	12124	1364	48	3		3	PLUNC	20	31825880	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	26729757	31825880	31199640	160	13522										
PREX1	57580	hgsc.bcm.edu	37	chr20	47269916	47269916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	taccagggcctcttcgcgccGactccggaatgcctggaagt	12	14	1	0	rs371398821		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr20:47269916G>A	ENST00000371941.3	-	20	2351	c.2329C>T	c.(2329-2331)Cgg>Tgg	p.R777W	PREX1_ENST00000396220.1_Missense_Mutation_p.R777W	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	777					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TCTTCGCGCCGACTCCGGAAT	0.582																																					p.R777W		Atlas-SNP	.											.	PREX1	441	.	0			c.C2329T						.	G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	84	86	85		2329	3	0.2	20		85	0,8600		0,0,4300	no	missense	PREX1	NM_020820.3	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	777/1660	47269916	1,13005	2203	4300	6503	SO:0001583	missense	57580	exon20			CGCGCCGACTCCG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2329C>T	chr20.hg19:g.47269916G>A	ENSP00000361009:p.Arg777Trp	22.0	0.0		55.0	27.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.709441	0.48517	2.27E-4	0.0	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.38560	1.13;1.13	5.12	2.95	0.34219	PDZ/DHR/GLGF (1);	1.252740	0.06178	U	0.678964	T	0.49609	0.1567	L	0.42245	1.32	0.22142	N	0.999336	P;D	0.63046	0.918;0.992	B;P	0.52710	0.368;0.707	T	0.46735	-0.9170	10	0.87932	D	0	.	11.6856	0.51483	0.0:0.0:0.6956:0.3044	.	777;74	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	W	777	ENSP00000361009:R777W;ENSP00000379522:R777W	ENSP00000361009:R777W	R	-	1	2	PREX1	46703323	0.578000	0.26717	0.188000	0.23233	0.355000	0.29361	1.778000	0.38614	2.386000	0.81285	0.462000	0.41574	CGG	.	.		0.582	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47269916	G	A	47269916	3	1	98	1	0	0	0	0	1	0	0	0	12488	1057	37	1	2734	1	PREX1	20	47269916	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	15444036	47269916	15755604	161	13523										
CABLES2	81928	hgsc.bcm.edu	37	chr20	60968622	60968622	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gtcactcttgtgtgtgaccaGggcgttggtgggatacagga	16	7	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr20:60968622G>T	ENST00000279101.5	-	6	762	c.754C>A	c.(754-756)Ctg>Atg	p.L252M		NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	252					cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TGTGTGACCAGGGCGTTGGTG	0.597																																					p.L252M		Atlas-SNP	.											.	CABLES2	30	.	0			c.C754A						.						113	112	112					20																	60968622		2203	4300	6503	SO:0001583	missense	81928	exon6			TGACCAGGGCGTT	BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679			16143	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 150"	C20orf150		12477932	Standard	NM_031215		Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.754C>A	chr20.hg19:g.60968622G>T	ENSP00000279101:p.Leu252Met	52.0	0.0		120.0	57.0	NM_031215	Q5JWL0|Q9BYK0	Missense_Mutation	SNP	ENST00000279101.5	hg19	CCDS33503.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247863	0.59103	.	.	ENSG00000149679	ENST00000370560;ENST00000279101	T	0.52057	0.68	5.42	2.35	0.29111	.	0.000000	0.85682	D	0.000000	T	0.48205	0.1487	M	0.63428	1.95	0.53005	D	0.999966	P	0.50710	0.938	P	0.47162	0.54	T	0.44205	-0.9343	10	0.54805	T	0.06	-25.2009	9.534	0.39211	0.2245:0.0:0.7755:0.0	.	252	Q9BTV7	CABL2_HUMAN	M	40;252	ENSP00000279101:L252M	ENSP00000279101:L252M	L	-	1	2	CABLES2	60402017	0.987000	0.35691	0.997000	0.53966	0.901000	0.52897	1.159000	0.31749	0.245000	0.21373	0.563000	0.77884	CTG	.	.		0.597	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080027.2	XM_037265		T	60968622	G	T	60968622	3	4	98	1	0	0	0	0	1	0	0	0	2532	991	35	3	702	3	CABLES2	20	60968622	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	13698706	60968622	2056898	162	13524										
GART	2618	hgsc.bcm.edu	37	chr21	34876612	34876612	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gcaaaataatctgtccagcaTccacatcttcctggaaaagt	6	11	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr21:34876612T>A	ENST00000381831.3	-	22	3115	c.2852A>T	c.(2851-2853)gAt>gTt	p.D951V	GART_ENST00000381815.4_Missense_Mutation_p.D951V|GART_ENST00000381839.3_Missense_Mutation_p.D951V|GART_ENST00000543717.1_Missense_Mutation_p.D503V	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	951	10-formyltetrahydrofolate binding.|GART.	Raises pKa of active site His. {ECO:0000250}.			'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	CTGTCCAGCATCCACATCTTC	0.358																																					p.D951V		Atlas-SNP	.											.	GART	81	.	0			c.A2852T						.						60	60	60					21																	34876612		2203	4300	6503	SO:0001583	missense	2618	exon22			CCAGCATCCACAT	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2852A>T	chr21.hg19:g.34876612T>A	ENSP00000371253:p.Asp951Val	46.0	0.0		99.0	35.0	NM_001136005	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	hg19	CCDS13627.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.489056	0.84962	.	.	ENSG00000159131	ENST00000381815;ENST00000381831;ENST00000381839;ENST00000543717	D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63	5.76	5.76	0.90799	Formyl transferase, N-terminal (3);	0.105526	0.64402	D	0.000005	D	0.98617	0.9537	H	0.99325	4.515	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99741	1.1015	10	0.87932	D	0	-36.3836	16.3634	0.83296	0.0:0.0:0.0:1.0	.	951	P22102	PUR2_HUMAN	V	951;951;951;503	ENSP00000371236:D951V;ENSP00000371253:D951V;ENSP00000371261:D951V;ENSP00000443579:D503V	ENSP00000371236:D951V	D	-	2	0	GART	33798482	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	7.466000	0.80914	2.324000	0.78689	0.533000	0.62120	GAT	.	.		0.358	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819		A	34876612	T	A	34876612	3	1	98	1	0	0	0	0	1	0	0	0	6251	1435	50	4	184	4	GART	21	34876612	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10		34876612	13253283	163	13525										
KRTAP10-6	386674	hgsc.bcm.edu	37	chr21	46011435	46011435	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gcagcaggtggacttgcacaCagggtggcagaggagggaca	18	8	0	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr21:46011435C>A	ENST00000400368.1	-	1	951	c.931G>T	c.(931-933)Gtg>Ttg	p.V311L	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	311	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						GACTTGCACACAGGGTGGCAG	0.672																																					p.V311L		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.G931T						.						72	83	80					21																	46011435		2203	4299	6502	SO:0001583	missense	386674	exon1			TGCACACAGGGTG	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"Keratin associated proteins"	20523	protein-coding gene	gene with protein product			"keratin associated protein 18-6"	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.931G>T	chr21.hg19:g.46011435C>A	ENSP00000383219:p.Val311Leu	95.0	0.0		306.0	119.0	NM_198688		Missense_Mutation	SNP	ENST00000400368.1	hg19	CCDS42959.1	.	.	.	.	.	.	.	.	.	.	c	12.41	1.928713	0.34002	.	.	ENSG00000188155	ENST00000400368	T	0.01422	4.91	2.8	2.8	0.32819	.	.	.	.	.	T	0.06280	0.0162	M	0.72576	2.205	0.27005	N	0.964812	D	0.64830	0.994	D	0.71656	0.974	T	0.10989	-1.0606	9	0.52906	T	0.07	.	9.205	0.37285	0.0:1.0:0.0:0.0	.	311	P60371	KR106_HUMAN	L	311	ENSP00000383219:V311L	ENSP00000383219:V311L	V	-	1	0	KRTAP10-6	44835863	.	.	1.000000	0.80357	0.028000	0.11728	.	.	1.583000	0.49898	0.194000	0.17425	GTG	.	.		0.672	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688		A	46011435	C	A	46011435	3	1	98	1	0	0	0	0	1	0	0	0	8522	478	17	3	170	3	KRTAP10-6	21	46011435	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	11134823	46011435	2118460	164	13526										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18273818	18273818	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cagtcgactctgccggtcttCcagctccagctcccgggcac	10	18	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr22:18273818C>T	ENST00000441493.2	-	31	6122	c.5770G>A	c.(5770-5772)Gaa>Aaa	p.E1924K	XXbac-B461K10.4_ENST00000476405.1_RNA|MICAL3_ENST00000580469.1_5'UTR	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1924					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		TGCCGGTCTTCCAGCTCCAGC	0.652																																					p.E1924K		Atlas-SNP	.											.	MICAL3	53	.	0			c.G5770A						.						35	42	39					22																	18273818		2109	4230	6339	SO:0001583	missense	57553	exon31			GGTCTTCCAGCTC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.5770G>A	chr22.hg19:g.18273818C>T	ENSP00000416015:p.Glu1924Lys	21.0	0.0		52.0	21.0	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.40|18.40	3.616072|3.616072	0.66672|0.66672	.|.	.|.	ENSG00000093100|ENSG00000093100	ENST00000441493|ENST00000252134	T|.	0.58060|.	0.36|.	5.34|5.34	5.34|5.34	0.76211|0.76211	Domain of unknown function DUF3585 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.84674|.	0.5524|.	M|M	0.89414|0.89414	3.03|3.03	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.83275|.	0.996|.	D|.	0.87007|.	0.2120|.	10|.	0.87932|.	D|.	0|.	.|.	19.0447|19.0447	0.93015|0.93015	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1924|.	Q7RTP6|.	MICA3_HUMAN|.	K|X	1924|905	ENSP00000416015:E1924K|.	ENSP00000416015:E1924K|.	E|W	-|-	1|3	0|0	XXbac-B461K10.4|XXbac-B461K10.4	16653818|16653818	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.813000|7.813000	0.86123|0.86123	2.510000|2.510000	0.84645|0.84645	0.591000|0.591000	0.81541|0.81541	GAA|TGG	.	.		0.652	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18273818	C	T	18273818	3	4	98	1	0	0	0	0	1	0	0	0	9580	864	30	3	246	3	MICAL3	22	18273818	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10		18273818	33030748	165	13527										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26423608	26423608	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	acggggaggaaagacgacgaTgttgcgagcataatgaagaa	15	5	0	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr22:26423608T>C	ENST00000407587.2	+	43	7840	c.7671T>C	c.(7669-7671)gaT>gaC	p.D2557D	MYO18B_ENST00000335473.7_Silent_p.D2556D|MYO18B_ENST00000536101.1_Silent_p.D2556D			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2556						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AAGACGACGATGTTGCGAGCA	0.552																																					p.D2556D		Atlas-SNP	.											.	MYO18B	322	.	0			c.T7668C						.						54	53	53					22																	26423608		1959	4139	6098	SO:0001819	synonymous_variant	84700	exon43			CGACGATGTTGCG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7671T>C	chr22.hg19:g.26423608T>C		39.0	0.0		93.0	35.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	T	0.490	-0.875937	0.02550	.	.	ENSG00000133454	ENST00000543971	.	.	.	4.44	-7.16	0.01516	.	.	.	.	.	T	0.58906	0.2155	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62798	-0.6778	4	.	.	.	.	12.7127	0.57098	0.0:0.3476:0.0:0.6524	.	.	.	.	T	506	.	.	M	+	2	0	MYO18B	24753608	0.000000	0.05858	0.015000	0.15790	0.005000	0.04900	-4.219000	0.00272	-1.303000	0.02332	-0.366000	0.07423	ATG	.	.		0.552	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		C	26423608	T	C	26423608	2	2	98	1	0	0	0	0	0	0	0	1	10075	1461	51	2		2	MYO18B	22	26423608	Silent	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	8149790	26423608	24880958	166	13528										
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26706636	26706636	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ctctctgctcccactgccagGatgacggttcacagcgggca	11	15	2	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr22:26706636G>A	ENST00000248933.6	+	7	1610	c.1515G>A	c.(1513-1515)agG>agA	p.R505R	SEZ6L_ENST00000529632.2_Splice_Site_p.R505R|SEZ6L_ENST00000343706.4_Splice_Site_p.R505R|SEZ6L_ENST00000403121.1_Splice_Site_p.R278R|SEZ6L_ENST00000360929.3_Splice_Site_p.R505R|SEZ6L_ENST00000404234.3_Splice_Site_p.R505R|SEZ6L_ENST00000402979.1_Splice_Site_p.R278R			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	505	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						CCACTGCCAGGATGACGGTTC	0.562																																					p.R505R		Atlas-SNP	.											.	SEZ6L	174	.	0			c.G1515A						.						129	100	110					22																	26706636		2203	4300	6503	SO:0001630	splice_region_variant	23544	exon7			TGCCAGGATGACG	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1515-1G>A	chr22.hg19:g.26706636G>A		44.0	0.0		102.0	36.0	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	hg19	CCDS13833.1																																																																																			.	.		0.562	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		Silent	A	26706636	G	A	26706636	5	1	98	1	0	0	0	0	0	0	1	0	14158	1188	41	3	1541	3	SEZ6L	22	26706636	Splice_Site	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	283028	26706636	24597930	167	13529										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38119757	38119757	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tctcccaacagaaccactcaAcgagagaattccagaacatc	5	14	2	3	rs71322688|rs67890459|rs199535040|rs55745992	byFrequency	TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr22:38119757A>T	ENST00000406386.3	+	7	1449	c.1194A>T	c.(1192-1194)caA>caT	p.Q398H		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	398					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GAACCACTCAACGAGAGAATT	0.547																																					p.Q398H		Atlas-SNP	.											.	TRIOBP	262	.	0			c.A1194T						.						118	99	106					22																	38119757		1848	3567	5415	SO:0001583	missense	11078	exon7			CACTCAACGAGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1194A>T	chr22.hg19:g.38119757A>T	ENSP00000384312:p.Gln398His	36.0	0.0		116.0	10.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.346788	0.41599	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.34275	1.37	2.47	-1.65	0.08291	.	.	.	.	.	T	0.42177	0.1191	L	0.44542	1.39	0.09310	N	0.999998	D	0.54964	0.969	P	0.62382	0.901	T	0.32402	-0.9908	9	0.49607	T	0.09	.	6.5071	0.22202	0.6093:0.0:0.3907:0.0	.	398	Q9H2D6	TARA_HUMAN	H	398	ENSP00000384312:Q398H	ENSP00000384312:Q398H	Q	+	3	2	TRIOBP	36449703	.	.	0.034000	0.17996	0.078000	0.17371	.	.	-0.503000	0.06586	0.113000	0.15668	CAA	.	.		0.547	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			T	38119757	A	T	38119757	3	4	98	1	0	0	0	0	1	0	0	0	16568	40	2	4	1212	4	TRIOBP	22	38119757	Missense_Mutation	SNP	A	TCGA-DD-A1EB-01A-11D-A12Z-10	11413121	38119757	13184809	168	13530										
TRMU	55687	hgsc.bcm.edu	37	chr22	46751486	46751486	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	ccgccaccagatggcactagGtgactgacgggagggctcct	14	13	0	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chr22:46751486G>A	ENST00000290846.4	+	9	1358		c.e9+1		TRMU_ENST00000381019.3_Splice_Site	NM_018006.4	NP_060476.2	O75648	MTU1_HUMAN	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase						tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|sulfurtransferase activity (GO:0016783)|tRNA binding (GO:0000049)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)	10		Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00449)|LUAD - Lung adenocarcinoma(64;0.248)		ATGGCACTAGGTGACTGACGG	0.637											OREG0026654	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	TRMU	23	.	0			c.1018+1G>A						.						47	45	45					22																	46751486		2203	4300	6503	SO:0001630	splice_region_variant	55687	exon9			CACTAGGTGACTG	AY062123	CCDS14075.1, CCDS63510.1	22q13	2005-08-11	2005-08-11	2005-08-11	ENSG00000100416	ENSG00000100416	2.1.1.61		25481	protein-coding gene	gene with protein product		610230	"tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase "	TRMT		14746906	Standard	XM_005261678		Approved	FLJ10140, MTO2	uc003bhp.3	O75648	OTTHUMG00000150424	ENST00000290846.4:c.1018+1G>A	chr22.hg19:g.46751486G>A		27.0	0.0	941	53.0	39.0	NM_018006	A8K3U7|Q05C99|Q5W9C8|Q66K31|Q6ICC3|Q9NWC1	Splice_Site	SNP	ENST00000290846.4	hg19	CCDS14075.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.553422	0.86127	.	.	ENSG00000100416	ENST00000290846;ENST00000381019	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7114	0.91658	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TRMU	45130150	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.096000	0.94182	2.597000	0.87782	0.563000	0.77884	.	.	.		0.637	TRMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318042.2	NM_018006	Intron	A	46751486	G	A	46751486	5	1	98	1	0	0	0	0	0	0	1	0	16586	1275	44	3	1053	3	TRMU	22	46751486	Splice_Site	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	8631729	46751486	4553080	169	13531										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3240505	3240505	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tggagtgtgtggggtctcccTctagcatatttcctccctgt	11	11	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:3240505T>A	ENST00000217939.6	-	5	3375	c.3221A>T	c.(3220-3222)gAg>gTg	p.E1074V		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1074						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GGGGTCTCCCTCTAGCATATT	0.453																																					p.E1074V		Atlas-SNP	.											.	MXRA5	815	.	0			c.A3221T						.						138	114	122					X																	3240505		2203	4300	6503	SO:0001583	missense	25878	exon5			TCTCCCTCTAGCA	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.3221A>T	chrX.hg19:g.3240505T>A	ENSP00000217939:p.Glu1074Val	132.0	0.0		520.0	190.0	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	t	7.332	0.619181	0.14129	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.66638	-0.22	3.14	-3.12	0.05282	.	0.652332	0.12390	U	0.473099	T	0.44705	0.1306	N	0.24115	0.695	0.09310	N	1	D	0.54964	0.969	B	0.41135	0.348	T	0.44003	-0.9356	10	0.45353	T	0.12	.	5.8116	0.18469	0.0:0.2541:0.1321:0.6138	.	1074	Q9NR99	MXRA5_HUMAN	V	1074	ENSP00000217939:E1074V	ENSP00000217939:E1074V	E	-	2	0	MXRA5	3250505	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.071000	0.11505	-1.909000	0.01085	-3.202000	0.00054	GAG	.	.		0.453	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3240505	T	A	3240505	3	1	98	1	0	0	0	0	1	0	0	0	10012	1551	54	4	5277	4	MXRA5	23	3240505	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10		3240505	152030055	170	13532										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12712563	12712563	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tccagttgctttcgagtatcTctatgttcaggtatgttaaa	8	7	2	0			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:12712563T>C	ENST00000380682.1	+	9	1429	c.923T>C	c.(922-924)cTc>cCc	p.L308P		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	308	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TTCGAGTATCTCTATGTTCAG	0.373																																					p.L308P		Atlas-SNP	.											.	FRMPD4	214	.	0			c.T923C						.						106	91	96					X																	12712563		2203	4300	6503	SO:0001583	missense	9758	exon9			AGTATCTCTATGT	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.923T>C	chrX.hg19:g.12712563T>C	ENSP00000370057:p.Leu308Pro	103.0	0.0		328.0	132.0	NM_014728	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	hg19	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.105780	0.77096	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.53857	0.6	5.02	5.02	0.67125	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.64402	D	0.000003	T	0.73281	0.3567	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.77963	-0.2390	10	0.87932	D	0	.	14.1021	0.65062	0.0:0.0:0.0:1.0	.	300;308	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	P	308;299;297	ENSP00000370057:L308P	ENSP00000304583:L297P	L	+	2	0	FRMPD4	12622484	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.578000	0.82498	1.775000	0.52247	0.417000	0.27973	CTC	.	.		0.373	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		C	12712563	T	C	12712563	3	2	98	1	0	0	0	0	1	0	0	0	6067	1551	54	2	957	2	FRMPD4	23	12712563	Missense_Mutation	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	9472058	12712563	142557997	171	13533										
ATXN3L	92552	hgsc.bcm.edu	37	chrX	13337139	13337139	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tcgtgtaggtatgaactgtgGcccggcagatctgactgttg	14	8	1	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:13337139G>T	ENST00000380622.2	-	1	1379	c.915C>A	c.(913-915)ggC>ggA	p.G305G	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	305					protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						ATGAACTGTGGCCCGGCAGAT	0.468																																					p.G305G		Atlas-SNP	.											.	ATXN3L	64	.	0			c.C915A						.						193	155	166					X																	13337139		1568	3582	5150	SO:0001819	synonymous_variant	92552	exon1			ACTGTGGCCCGGC		CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.915C>A	chrX.hg19:g.13337139G>T		141.0	0.0		457.0	213.0	NM_001135995	B2RNY8	Silent	SNP	ENST00000380622.2	hg19	CCDS48080.1																																																																																			.	.		0.468	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995		T	13337139	G	T	13337139	2	4	98	1	0	0	0	0	0	0	0	1	1214	1190	42	3		3	ATXN3L	23	13337139	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	624576	13337139	141933421	172	13534										
SCML1	6322	hgsc.bcm.edu	37	chrX	17768332	17768332	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	caacgtatggttcttcttcaGggctctgccttggcaaccct	9	13	4	0	rs199560760		TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:17768332G>T	ENST00000380041.3	+	6	950	c.622G>T	c.(622-624)Ggg>Tgg	p.G208W	SCML1_ENST00000380043.3_Missense_Mutation_p.G181W|SCML1_ENST00000380045.3_Missense_Mutation_p.G87W|SCML1_ENST00000398080.1_Missense_Mutation_p.G87W	NM_001037540.1	NP_001032629.1	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 (Drosophila)	208					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)	10	Hepatocellular(33;0.183)					TTCTTCTTCAGGGCTCTGCCT	0.537																																					p.G208W		Atlas-SNP	.											.	SCML1	55	.	0			c.G622T						.						115	90	98					X																	17768332		2203	4300	6503	SO:0001583	missense	6322	exon6			TCTTCAGGGCTCT		CCDS14182.2, CCDS35210.1, CCDS35211.1	Xp22	2013-01-10	2001-11-28		ENSG00000047634	ENSG00000047634		"Sterile alpha motif (SAM) domain containing"	10580	protein-coding gene	gene with protein product		300227	"sex comb on midleg (Drosophila)-like 1"			9570953	Standard	XM_005274578		Approved		uc004cyc.3	Q9UN30	OTTHUMG00000021206	ENST00000380041.3:c.622G>T	chrX.hg19:g.17768332G>T	ENSP00000369380:p.Gly208Trp	77.0	0.0		173.0	58.0	NM_001037540	B0FZN6|B2RA08|Q5H968|Q5H969	Missense_Mutation	SNP	ENST00000380041.3	hg19	CCDS35210.1	.	.	.	.	.	.	.	.	.	.	G	10.12	1.261749	0.23051	.	.	ENSG00000047634	ENST00000380045;ENST00000380041;ENST00000380043;ENST00000398080	.	.	.	3.03	-6.07	0.02158	.	1.937890	0.02845	N	0.128439	T	0.19886	0.0478	N	0.08118	0	0.09310	N	1	D;P	0.54047	0.964;0.939	P;B	0.49387	0.609;0.405	T	0.28138	-1.0053	9	0.40728	T	0.16	-0.0138	6.1285	0.20192	0.2717:0.3744:0.3539:0.0	.	181;208	Q9UN30-2;Q9UN30	.;SCML1_HUMAN	W	87;208;181;87	.	ENSP00000369380:G208W	G	+	1	0	SCML1	17678253	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.683000	0.00199	-2.254000	0.00697	-1.028000	0.02416	GGG	.	G|1.000;A|0.000		0.537	SCML1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060495.5	NM_006746		T	17768332	G	T	17768332	3	4	98	1	0	0	0	0	1	0	0	0	13924	1000	35	3	643	3	SCML1	23	17768332	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	4431193	17768332	137502228	173	13535										
DCAF8L1	139425	hgsc.bcm.edu	37	chrX	27998516	27998516	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tcttgcctgaggtcaatggtGaacacaacggcatcttcacc	9	12	4	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:27998516G>A	ENST00000441525.1	-	1	1050	c.936C>T	c.(934-936)ttC>ttT	p.F312F		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	312										NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						GGTCAATGGTGAACACAACGG	0.493																																					p.F312F		Atlas-SNP	.											.	DCAF8L1	121	.	0			c.C936T						.						86	75	79					X																	27998516		2202	4300	6502	SO:0001819	synonymous_variant	139425	exon1			AATGGTGAACACA		CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"WD repeat domain containing"	31810	protein-coding gene	gene with protein product			"WD repeat domain 42B"	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.936C>T	chrX.hg19:g.27998516G>A		64.0	0.0		183.0	59.0	NM_001017930	B3KXX1	Silent	SNP	ENST00000441525.1	hg19	CCDS35222.1																																																																																			.	.		0.493	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690		A	27998516	G	A	27998516	2	1	98	1	0	0	0	0	0	0	0	1	4279	1281	45	3		3	DCAF8L1	23	27998516	Silent	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	10230184	27998516	127272044	174	13536										
DMD	1756	hgsc.bcm.edu	37	chrX	31200854	31200854	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tttttttttggttcctaataCctgaatccaatgattggaca	6	7	0	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:31200854C>A	ENST00000357033.4	-	68	10181		c.e68+1		DMD_ENST00000378677.2_Splice_Site|DMD_ENST00000361471.4_Splice_Site|DMD_ENST00000474231.1_Splice_Site|DMD_ENST00000343523.2_Splice_Site|DMD_ENST00000378723.3_Splice_Site|DMD_ENST00000541735.1_Splice_Site|DMD_ENST00000378702.4_Splice_Site|DMD_ENST00000378707.3_Splice_Site|DMD_ENST00000359836.1_Splice_Site|DMD_ENST00000378680.2_Splice_Site	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin						cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GTTCCTAATACCTGAATCCAA	0.418																																					.		Atlas-SNP	.											.	DMD	2127	.	0			c.770+1G>T	GRCh37	CS071228	DMD	S		.						92	85	87					X																	31200854		2202	4300	6502	SO:0001630	splice_region_variant	1756	exon8			CTAATACCTGAAT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.9974+1G>T	chrX.hg19:g.31200854C>A		75.0	0.0		153.0	58.0	NM_004016	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Splice_Site	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.871204	0.72065	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378723;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000378702;ENST00000465285;ENST00000474231;ENST00000361471;ENST00000378680;ENST00000378705	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2593	0.90030	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DMD	31110775	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.651000	0.83577	2.506000	0.84524	0.600000	0.82982	.	.	.		0.418	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	Intron	A	31200854	C	A	31200854	5	1	98	1	0	0	0	0	0	0	1	0	4582	521	18	3	1220	3	DMD	23	31200854	Splice_Site	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	3202338	31200854	124069706	175	13537										
CASK	8573	hgsc.bcm.edu	37	chrX	41428985	41428985	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	caatgatttagttcattcatTtttaaagtgattccctgtta	5	6	2	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:41428985T>C	ENST00000378163.1	-	16	1992	c.1518A>G	c.(1516-1518)aaA>aaG	p.K506K	CASK_ENST00000472704.1_5'UTR|CASK_ENST00000378154.1_Silent_p.K506K|CASK_ENST00000361962.4_Silent_p.K506K|CASK_ENST00000378166.4_Silent_p.K506K|CASK_ENST00000442742.2_Silent_p.K506K|CASK_ENST00000421587.2_Silent_p.K500K|RNU6-1321P_ENST00000390905.1_RNA|CASK_ENST00000378158.1_Silent_p.K506K|CASK_ENST00000318588.9_Silent_p.K506K			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	506	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						GTTCATTCATTTTTAAAGTGA	0.303																																					p.K506K	NSCLC(42;104 1086 3090 27189 35040)	Atlas-SNP	.											.	CASK	93	.	0			c.A1518G						.						90	87	88					X																	41428985		2202	4300	6502	SO:0001819	synonymous_variant	8573	exon16			ATTCATTTTTAAA	AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"trinucleotide repeat containing 8"	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.1518A>G	chrX.hg19:g.41428985T>C		137.0	0.0		411.0	162.0	NM_001126054	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Silent	SNP	ENST00000378163.1	hg19																																																																																				.	.		0.303	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688		C	41428985	T	C	41428985	2	2	98	1	0	0	0	0	0	0	0	1	2667	1838	64	2		2	CASK	23	41428985	Silent	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	10228131	41428985	113841575	176	13538										
MAOB	4129	hgsc.bcm.edu	37	chrX	43652777	43652777	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tggcagagggggattgaagtGaatcttcatgcccagagtag	15	6	2	4			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:43652777G>T	ENST00000378069.4	-	8	964	c.817C>A	c.(817-819)Cac>Aac	p.H273N	MAOB_ENST00000538942.1_Missense_Mutation_p.H257N|MAOB_ENST00000536181.1_Missense_Mutation_p.H257N	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	273					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	GGATTGAAGTGAATCTTCATG	0.398																																					p.H273N		Atlas-SNP	.											.	MAOB	52	.	0			c.C817A						.						135	112	120					X																	43652777		2203	4300	6503	SO:0001583	missense	4129	exon8			TGAAGTGAATCTT		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.817C>A	chrX.hg19:g.43652777G>T	ENSP00000367309:p.His273Asn	142.0	0.0		461.0	152.0	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.599667	0.87055	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	D;D;D	0.92149	-2.98;-2.98;-2.98	5.97	5.97	0.96955	Amine oxidase (1);	0.000000	0.85682	D	0.000000	D	0.94918	0.8357	M	0.69358	2.11	0.80722	D	1	D;D	0.63880	0.993;0.986	D;D	0.63703	0.917;0.913	D	0.92601	0.6091	10	0.18276	T	0.48	-20.7527	19.371	0.94484	0.0:0.0:1.0:0.0	.	257;273	B7Z5H3;P27338	.;AOFB_HUMAN	N	273;257;257	ENSP00000367309:H273N;ENSP00000441613:H257N;ENSP00000442240:H257N	ENSP00000367309:H273N	H	-	1	0	MAOB	43537721	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.265000	0.95647	2.527000	0.85204	0.600000	0.82982	CAC	.	.		0.398	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		T	43652777	G	T	43652777	3	4	98	1	0	0	0	0	1	0	0	0	9235	1290	45	3	777	3	MAOB	23	43652777	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	2223792	43652777	111617783	177	13539										
ARHGEF9	23229	hgsc.bcm.edu	37	chrX	62926264	62926264	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cagaggcagtctgaattgggGtccaggtgtccgttctgcac	14	10	2	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:62926264G>T	ENST00000253401.6	-	3	1055	c.255C>A	c.(253-255)gaC>gaA	p.D85E	ARHGEF9_ENST00000495564.1_5'UTR|ARHGEF9_ENST00000374878.1_Missense_Mutation_p.D83E|ARHGEF9_ENST00000374870.4_5'UTR|ARHGEF9_ENST00000374872.1_Missense_Mutation_p.D64E|ARHGEF9_ENST00000437457.2_Missense_Mutation_p.D32E	NM_015185.2	NP_056000.1	O43307	ARHG9_HUMAN	Cdc42 guanine nucleotide exchange factor (GEF) 9	85					apoptotic signaling pathway (GO:0097190)|ion transmembrane transport (GO:0034220)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|skin(1)	35						CTGAATTGGGGTCCAGGTGTC	0.547																																					p.D85E		Atlas-SNP	.											.	ARHGEF9	117	.	0			c.C255A						.						99	70	80					X																	62926264		2203	4299	6502	SO:0001583	missense	23229	exon3			ATTGGGGTCCAGG	AB007884	CCDS35315.1, CCDS55429.1, CCDS55430.1	Xq11.1	2013-01-10			ENSG00000131089	ENSG00000131089		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14561	protein-coding gene	gene with protein product	"collybistin"	300429				10559246, 9455477	Standard	NM_015185		Approved	KIAA0424, PEM-2	uc011mot.2	O43307	OTTHUMG00000021700	ENST00000253401.6:c.255C>A	chrX.hg19:g.62926264G>T	ENSP00000253401:p.Asp85Glu	49.0	0.0		102.0	45.0	NM_015185	A8K1S8|B4DHC7|F8W7P8|Q5JSL6	Missense_Mutation	SNP	ENST00000253401.6	hg19	CCDS35315.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.806466	0.31961	.	.	ENSG00000131089	ENST00000253401;ENST00000374878;ENST00000437457;ENST00000374872	T;T;T;T	0.72282	1.0;1.0;-0.64;1.0	5.73	1.97	0.26223	Src homology-3 domain (1);	0.051722	0.85682	D	0.000000	T	0.41971	0.1182	N	0.04959	-0.14	0.80722	D	1	B;B;B	0.13594	0.002;0.008;0.001	B;B;B	0.17722	0.003;0.019;0.003	T	0.04565	-1.0942	10	0.17369	T	0.5	.	5.1822	0.15165	0.3076:0.0:0.5572:0.1352	.	32;83;85	B4DHC7;B1AMR4;O43307	.;.;ARHG9_HUMAN	E	85;83;32;64	ENSP00000253401:D85E;ENSP00000364012:D83E;ENSP00000399994:D32E;ENSP00000364006:D64E	ENSP00000253401:D85E	D	-	3	2	ARHGEF9	62842989	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	0.945000	0.29056	-0.036000	0.13669	-0.176000	0.13171	GAC	.	.		0.547	ARHGEF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056937.1			T	62926264	G	T	62926264	3	4	98	1	0	0	0	0	1	0	0	0	912	1252	44	3	1327	3	ARHGEF9	23	62926264	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	19273487	62926264	92344296	178	13540										
FOXO4	4303	hgsc.bcm.edu	37	chrX	70316754	70316754	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	agaagcgactgacacttgccCagatctacgagtggatggtc	12	10	1	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:70316754C>G	ENST00000374259.3	+	1	708	c.376C>G	c.(376-378)Cag>Gag	p.Q126E	FOXO4_ENST00000466874.1_3'UTR|FOXO4_ENST00000341558.3_Missense_Mutation_p.Q71E	NM_001170931.1|NM_005938.3	NP_001164402.1|NP_005929.2	P98177	FOXO4_HUMAN	forkhead box O4	126					cell cycle arrest (GO:0007050)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mitotic G2 DNA damage checkpoint (GO:0007095)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of smooth muscle cell differentiation (GO:0051151)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)	18	Renal(35;0.156)					GACACTTGCCCAGATCTACGA	0.542																																					p.Q126E		Atlas-SNP	.											.	FOXO4	60	.	0			c.C376G						.						61	59	60					X																	70316754		2188	4296	6484	SO:0001583	missense	4303	exon1			CTTGCCCAGATCT		CCDS43969.1, CCDS55440.1	Xq13.1	2008-02-05	2007-05-02	2007-05-02	ENSG00000184481	ENSG00000184481		"Forkhead boxes"	7139	protein-coding gene	gene with protein product		300033	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 7", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7"	MLLT7		7529552	Standard	NM_005938		Approved	AFX1	uc004dys.2	P98177	OTTHUMG00000021789	ENST00000374259.3:c.376C>G	chrX.hg19:g.70316754C>G	ENSP00000363377:p.Gln126Glu	91.0	0.0		283.0	115.0	NM_005938	B7WPJ7|O43821|Q13720|Q3KPF1|Q8TDK9	Missense_Mutation	SNP	ENST00000374259.3	hg19	CCDS43969.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.023877	0.75390	.	.	ENSG00000184481	ENST00000374259;ENST00000341558	D;D	0.94650	-3.48;-3.48	5.02	5.02	0.67125	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	D	0.000000	D	0.93520	0.7932	N	0.13235	0.315	0.80722	D	1	B;P;P	0.46395	0.272;0.877;0.844	B;B;D	0.63113	0.332;0.38;0.911	D	0.92885	0.6326	10	0.28530	T	0.3	-27.8271	15.999	0.80275	0.0:1.0:0.0:0.0	.	126;71;126	B4DTB6;P98177-2;P98177	.;.;FOXO4_HUMAN	E	126;71	ENSP00000363377:Q126E;ENSP00000342209:Q71E	ENSP00000342209:Q71E	Q	+	1	0	FOXO4	70233479	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.388000	0.79795	2.077000	0.62373	0.523000	0.50628	CAG	.	.		0.542	FOXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057115.1	NM_005938		G	70316754	C	G	70316754	3	3	98	1	0	0	0	0	1	0	0	0	6033	595	21	4	378	4	FOXO4	23	70316754	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	7390490	70316754	84953806	179	13541										
TGIF2LX	90316	hgsc.bcm.edu	37	chrX	89177576	89177576	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cccctgtggcccttgccaaaGggccagatgtcaagagagaa	12	12	1	3			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:89177576G>T	ENST00000561129.2	+	1	622	c.492G>T	c.(490-492)aaG>aaT	p.K164N	TGIF2LX_ENST00000283891.5_Missense_Mutation_p.K164N			Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	164					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(29)|ovary(1)|skin(3)|urinary_tract(1)	40						CCTTGCCAAAGGGCCAGATGT	0.592																																					p.K164N		Atlas-SNP	.											.	TGIF2LX	84	.	0			c.G492T						.						34	39	37					X																	89177576		2203	4296	6499	SO:0001583	missense	90316	exon2			GCCAAAGGGCCAG	AF497480	CCDS14459.1	Xq21.31	2014-05-14	2007-02-07		ENSG00000153779	ENSG00000153779		"Homeoboxes / TALE class"	18570	protein-coding gene	gene with protein product		300411	"TGFB-induced factor 2-like, X-linked"				Standard	NM_138960		Approved		uc004efe.3	Q8IUE1	OTTHUMG00000021954	ENST00000561129.2:c.492G>T	chrX.hg19:g.89177576G>T	ENSP00000453704:p.Lys164Asn	68.0	0.0		165.0	65.0	NM_138960	Q5JRM9|Q8TD48	Missense_Mutation	SNP	ENST00000561129.2	hg19	CCDS14459.1	.	.	.	.	.	.	.	.	.	.	G	1.707	-0.500112	0.04291	.	.	ENSG00000153779	ENST00000283891	T	0.63744	-0.06	2.8	-1.23	0.09465	.	.	.	.	.	T	0.45895	0.1365	L	0.51422	1.61	0.09310	N	1	P	0.34462	0.454	B	0.23275	0.045	T	0.16571	-1.0398	8	.	.	.	-18.4385	6.378	0.21519	0.5672:0.0:0.4328:0.0	.	164	Q8IUE1	TF2LX_HUMAN	N	164	ENSP00000355119:K164N	.	K	+	3	2	TGIF2LX	89064232	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.146000	0.16180	-0.472000	0.06881	-0.287000	0.09952	AAG	.	.		0.592	TGIF2LX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417911.2	NM_138960		T	89177576	G	T	89177576	3	4	98	1	0	0	0	0	1	0	0	0	15842	991	35	3	494	3	TGIF2LX	23	89177576	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	18860822	89177576	66092984	180	13542										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107807134	107807134	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgatgatggaattccagggcCaccaggaccaaaaggaatca	11	9	1	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:107807134C>A	ENST00000361603.2	+	4	498	c.254C>A	c.(253-255)cCa>cAa	p.P85Q	COL4A5_ENST00000328300.6_Missense_Mutation_p.P85Q	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	85	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						ATTCCAGGGCCACCAGGACCA	0.328									Alport syndrome with Diffuse Leiomyomatosis																												p.P85Q		Atlas-SNP	.											.	COL4A5	262	.	0			c.C254A						.						66	65	65					X																	107807134		2203	4300	6503	SO:0001583	missense	1287	exon4	Familial Cancer Database		CAGGGCCACCAGG	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.254C>A	chrX.hg19:g.107807134C>A	ENSP00000354505:p.Pro85Gln	148.0	0.0		498.0	220.0	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	hg19	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837414	0.50951	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.96716	-4.1;-4.1	5.67	4.8	0.61643	.	0.129886	0.52532	D	0.000072	D	0.95564	0.8558	L	0.48260	1.515	0.36193	D	0.850221	D;D	0.53462	0.96;0.96	P;P	0.55455	0.776;0.776	D	0.94553	0.7755	10	0.13108	T	0.6	.	12.6549	0.56782	0.0:0.9169:0.0:0.0831	.	85;85	E7EVY4;P29400	.;CO4A5_HUMAN	Q	85	ENSP00000331902:P85Q;ENSP00000354505:P85Q	ENSP00000331902:P85Q	P	+	2	0	COL4A5	107693790	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	4.049000	0.57397	1.153000	0.42468	0.600000	0.82982	CCA	.	.		0.328	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			A	107807134	C	A	107807134	3	1	98	1	0	0	0	0	1	0	0	0	3696	594	21	3	268	3	COL4A5	23	107807134	Missense_Mutation	SNP	C	TCGA-DD-A1EB-01A-11D-A12Z-10	18629558	107807134	47463426	181	13543										
GPR112	139378	hgsc.bcm.edu	37	chrX	135487872	135487872	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	tgttggattaaagatgattcTatcttttacatctcagtggt	8	5	3	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:135487872T>C	ENST00000394143.1	+	23	8967	c.8676T>C	c.(8674-8676)tcT>tcC	p.S2892S	GPR112_ENST00000412101.1_Silent_p.S2687S|GPR112_ENST00000287534.4_Silent_p.S2645S|GPR112_ENST00000370652.1_Silent_p.S2892S|GPR112_ENST00000394141.1_Silent_p.S2687S	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2892					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					AAGATGATTCTATCTTTTACA	0.358																																					p.S2892S		Atlas-SNP	.											.	GPR112	459	.	0			c.T8676C						.						175	138	151					X																	135487872		2203	4300	6503	SO:0001819	synonymous_variant	139378	exon23			TGATTCTATCTTT	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.8676T>C	chrX.hg19:g.135487872T>C		143.0	0.0		487.0	173.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	hg19	CCDS35409.1																																																																																			.	.		0.358	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			C	135487872	T	C	135487872	2	2	98	1	0	0	0	0	0	0	0	1	6637	1509	53	2		2	GPR112	23	135487872	Silent	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	27680738	135487872	19782688	182	13544										
HTATSF1	27336	hgsc.bcm.edu	37	chrX	135582923	135582923	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gaagaatttaaggtcaaactTtacaaagataatcaaggaaa	7	4	2	2			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:135582923T>G	ENST00000218364.4	+	4	690	c.516T>G	c.(514-516)ctT>ctG	p.L172L	HTATSF1_ENST00000535601.1_Silent_p.L172L	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	172	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					AGGTCAAACTTTACAAAGATA	0.318																																					p.L172L		Atlas-SNP	.											.	HTATSF1	66	.	0			c.T516G						.						100	104	103					X																	135582923		2203	4293	6496	SO:0001819	synonymous_variant	27336	exon5			CAAACTTTACAAA	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"RNA binding motif (RRM) containing"	5276	protein-coding gene	gene with protein product		300346	"HIV TAT specific factor 1"			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.516T>G	chrX.hg19:g.135582923T>G		155.0	0.0		579.0	246.0	NM_001163280	D3DWG9|Q59G06|Q99730	Silent	SNP	ENST00000218364.4	hg19	CCDS14657.1																																																																																			.	.		0.318	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		G	135582923	T	G	135582923	2	3	98	1	0	0	0	0	0	0	0	1	7442	1828	64	5		5	HTATSF1	23	135582923	Silent	SNP	T	TCGA-DD-A1EB-01A-11D-A12Z-10	95051	135582923	19687637	183	13545										
ARHGEF6	9459	hgsc.bcm.edu	37	chrX	135767930	135767930	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cccatgcctgaataggttcgGacagtatctgtaactccagc	9	12	1	1			TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:135767930G>C	ENST00000250617.6	-	12	2503	c.1298C>G	c.(1297-1299)tCc>tGc	p.S433C	ARHGEF6_ENST00000370620.1_Missense_Mutation_p.S279C|ARHGEF6_ENST00000535227.1_Missense_Mutation_p.S306C|ARHGEF6_ENST00000370622.1_Missense_Mutation_p.S279C	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	433					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					AATAGGTTCGGACAGTATCTG	0.393																																					p.S433C		Atlas-SNP	.											.	ARHGEF6	111	.	0			c.C1298G						.						160	128	139					X																	135767930		2203	4300	6503	SO:0001583	missense	9459	exon12			GGTTCGGACAGTA	D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	685	protein-coding gene	gene with protein product	"Rac/Cdc42 guanine exchange factor (GEF) 6", "PAK-interacting exchange factor, alpha", "rho guanine nucleotide exchange factor 6"	300267	"mental retardation, X-linked 46"	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.1298C>G	chrX.hg19:g.135767930G>C	ENSP00000250617:p.Ser433Cys	103.0	0.0		320.0	118.0	NM_004840	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Missense_Mutation	SNP	ENST00000250617.6	hg19	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	g	16.81	3.225349	0.58668	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.36	5.36	0.76844	Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.58509	0.2127	M	0.62723	1.935	0.58432	D	0.999999	D;D	0.57257	0.979;0.979	P;P	0.57204	0.643;0.815	T	0.61530	-0.7044	10	0.59425	D	0.04	.	18.1967	0.89825	0.0:0.0:1.0:0.0	.	306;433	B7Z3C7;Q15052	.;ARHG6_HUMAN	C	433;279;279;279;306	ENSP00000250617:S433C;ENSP00000359654:S279C;ENSP00000359656:S279C;ENSP00000439483:S306C	ENSP00000250617:S433C	S	-	2	0	ARHGEF6	135595596	1.000000	0.71417	0.865000	0.33974	0.090000	0.18270	9.866000	0.99616	2.235000	0.73313	0.519000	0.50382	TCC	.	.		0.393	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840		C	135767930	G	C	135767930	3	2	98	1	0	0	0	0	1	0	0	0	910	1174	41	4	1076	4	ARHGEF6	23	135767930	Missense_Mutation	SNP	G	TCGA-DD-A1EB-01A-11D-A12Z-10	185007	135767930	19502630	184	13546										
MAGEA6	4105	hgsc.bcm.edu	37	chrX	151869343	151869343	+	Frame_Shift_Del	DEL	G	G	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	cagaggagtcagcactgcaaGcctgaagaaggccttgaggc							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:151869343delG	ENST00000329342.5	+	3	258	c.33delG	c.(31-33)aagfs	p.K11fs		NM_005363.2	NP_005354.1	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	11										breast(1)|endometrium(3)|large_intestine(3)|lung(16)|prostate(3)|skin(1)|urinary_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					AGCACTGCAAGCCTGAAGAAG	0.637																																					p.K11fs		Atlas-INDEL	.											.	MAGEA6	53	.	0			c.32delA						.						1	1	1					X																	151869343		403	1084	1487	SO:0001589	frameshift_variant	4105	exon3			.		CCDS76050.1	Xq28	2009-03-13			ENSG00000197172	ENSG00000197172			6804	protein-coding gene	gene with protein product	"MAGE-6 antigen", "melanoma-associated antigen 6", "melanoma antigen family A 6", "cancer/testis antigen family 1, member 6"	300176		MAGE6		8575766	Standard	NM_005363		Approved	CT1.6	uc004ffq.1	P43360	OTTHUMG00000022642	ENST00000329342.5:c.33delG	chrX.hg19:g.151869343delG	ENSP00000329199:p.Lys11fs	111.0	0.0		237.0	25.0	NM_005363	A8IF93|Q6NW44	Frame_Shift_Del	DEL	ENST00000329342.5	hg19	CCDS14708.1																																																																																			.	.		0.637	MAGEA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058747.2	NM_005363		-	151869343	G	-	151869343	7	5	98	1	0	1	0	1	0	0	0	0	9179	962	34	0	35	0	MAGEA6	23	151869343	Frame_Shift_Del	DEL	G	TCGA-DD-A1EB-01A-11D-A12Z-10	16101413	151869343	3401217	185	13547										
MAGEA3	4102	hgsc.bcm.edu	37	chrX	151936132	151936132	+	Frame_Shift_Del	DEL	G	G	-													0.0483870967741935	9	1	1.04711246200608	1.22163120567376	0.977304964539007	0.419710144927536	1	0	gggcctcaaggccttcttcaGgcttgcagtgctgactcctc							TCGA-DD-A1EB-01A-11D-A12Z-10	TCGA-DD-A1EB-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90611290-e44c-438e-91aa-f3b83dae3b71	239524f2-0ff6-4bc9-b813-0bb78ff48919	g.chrX:151936132delG	ENST00000393902.3	-	3	602	c.35delC	c.(34-36)cctfs	p.P12fs	MAGEA3_ENST00000370278.3_Frame_Shift_Del_p.P12fs			P43357	MAGA3_HUMAN	melanoma antigen family A, 3	12										endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	15	Acute lymphoblastic leukemia(192;6.56e-05)					GCCTTCTTCAGGCTTGCAGTG	0.632																																					p.P12fs		Atlas-INDEL	.											.	MAGEA3	36	.	0			c.36delT						.						1	1	1					X																	151936132		716	1500	2216	SO:0001589	frameshift_variant	4102	exon3			.		CCDS76045.1	Xq28	2009-03-13			ENSG00000221867	ENSG00000221867			6801	protein-coding gene	gene with protein product	"melanoma-associated antigen 3", "antigen MZ2-D", "MAGE-3 antigen", "cancer/testis antigen family 1, member 3"	300174		MAGE3		1840703, 8575766	Standard	NM_005362		Approved	HYPD, HIP8, MGC14613, CT1.3	uc004fgp.3	P43357	OTTHUMG00000022640	ENST00000393902.3:c.35delC	chrX.hg19:g.151936132delG	ENSP00000377480:p.Pro12fs	118.0	0.0		224.0	23.0	NM_005362	Q6FHI6	Frame_Shift_Del	DEL	ENST00000393902.3	hg19	CCDS14715.1																																																																																			.	.		0.632	MAGEA3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058744.1	NM_005362		-	151936132	G	-	151936132	7	5	98	1	0	1	0	1	0	0	0	0	9176	1000	35	0	913	0	MAGEA3	23	151936132	Frame_Shift_Del	DEL	G	TCGA-DD-A1EB-01A-11D-A12Z-10	66789	151936132	3334428	186	13548										
GPN2	54707	hgsc.bcm.edu	37	chr1	27210697	27210697	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	tgcggcagacatcatggcttCcaagcttcgctgctcttggg	12	12	2	1			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr1:27210697C>A	ENST00000374135.4	-	4	1014	c.814G>T	c.(814-816)Gaa>Taa	p.E272*	GPN2_ENST00000461282.1_5'Flank|GPN2_ENST00000374133.3_Nonsense_Mutation_p.E93*	NM_018066.3	NP_060536.3			GPN-loop GTPase 2											endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9						ATCATGGCTTCCAAGCTTCGC	0.547																																					p.E272X		Atlas-SNP	.											.	GPN2	18	.	0			c.G814T						.						89	74	79					1																	27210697		2203	4300	6503	SO:0001587	stop_gained	54707	exon4			TGGCTTCCAAGCT	AK001211	CCDS289.1	1p36.11	2008-04-30	2008-04-30	2008-04-30	ENSG00000142751	ENSG00000142751		"GPN-loop GTPases"	25513	protein-coding gene	gene with protein product			"ATP binding domain 1 family, member B"	ATPBD1B		12975309	Standard	NM_018066		Approved	FLJ10349	uc001bnd.1	Q9H9Y4	OTTHUMG00000004227	ENST00000374135.4:c.814G>T	chr1.hg19:g.27210697C>A	ENSP00000363250:p.Glu272*	137.0	0.0		127.0	17.0	NM_018066		Nonsense_Mutation	SNP	ENST00000374135.4	hg19	CCDS289.1	.	.	.	.	.	.	.	.	.	.	C	37	6.442196	0.97572	.	.	ENSG00000142751	ENST00000374135;ENST00000374133	.	.	.	5.41	5.41	0.78517	.	0.113746	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-26.9871	18.8009	0.92016	0.0:1.0:0.0:0.0	.	.	.	.	X	272;93	.	ENSP00000363248:E93X	E	-	1	0	GPN2	27083284	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	4.984000	0.63838	2.536000	0.85505	0.491000	0.48974	GAA	.	.		0.547	GPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012175.2	NM_018066		A	27210697	C	A	27210697	4	1	99	1	0	0	0	0	0	1	0	0	6626	864	30	3	126	3	GPN2	1	27210697	Nonsense_Mutation	SNP	C	TCGA-DD-A1EC-01A-21D-A12Z-10		27210697	222039924	1	13549										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67795378	67795378	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	ggtactgcttaatcgactcaGatatcggcccagtaacagca	9	11	1	1			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr1:67795378G>C	ENST00000262345.1	+	6	1413	c.773G>C	c.(772-774)aGa>aCa	p.R258T	IL12RB2_ENST00000544434.1_Missense_Mutation_p.R258T|IL12RB2_ENST00000371000.1_Missense_Mutation_p.R258T|IL12RB2_ENST00000541374.1_Missense_Mutation_p.R258T	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	258	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						AATCGACTCAGATATCGGCCC	0.428																																					p.R258T		Atlas-SNP	.											.	IL12RB2	94	.	0			c.G773C						.						127	121	123					1																	67795378		2203	4300	6503	SO:0001583	missense	3595	exon6			GACTCAGATATCG	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.773G>C	chr1.hg19:g.67795378G>C	ENSP00000262345:p.Arg258Thr	150.0	0.0		142.0	23.0	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	hg19	CCDS638.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.31|14.31	2.495951|2.495951	0.44352|0.44352	.|.	.|.	ENSG00000081985|ENSG00000081985	ENST00000441640|ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	.|T;T;T;T	.|0.56444	.|0.46;0.46;0.46;0.46	5.2|5.2	2.04|2.04	0.26737|0.26737	.|Fibronectin, type III (3);Immunoglobulin-like fold (1);	.|0.213014	.|0.49916	.|D	.|0.000125	T|T	0.52208|0.52208	0.1720|0.1720	M|M	0.78637|0.78637	2.42|2.42	0.37417|0.37417	D|D	0.913466|0.913466	.|P;D;P;D	.|0.60575	.|0.547;0.988;0.946;0.961	.|B;P;P;P	.|0.58721	.|0.276;0.844;0.754;0.617	T|T	0.56226|0.56226	-0.8014|-0.8014	5|10	.|0.56958	.|D	.|0.05	-11.6493|-11.6493	7.2644|7.2644	0.26222|0.26222	0.3292:0.0:0.6708:0.0|0.3292:0.0:0.6708:0.0	.|.	.|258;258;258;258	.|B4DGA4;F5H7L6;Q99665-2;Q99665	.|.;.;.;I12R2_HUMAN	H|T	125|258	.|ENSP00000262345:R258T;ENSP00000360039:R258T;ENSP00000445276:R258T;ENSP00000442443:R258T	.|ENSP00000262345:R258T	Q|R	+|+	3|2	2|0	IL12RB2|IL12RB2	67567966|67567966	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.290000|0.290000	0.27261|0.27261	1.499000|1.499000	0.35671|0.35671	0.587000|0.587000	0.29643|0.29643	0.561000|0.561000	0.74099|0.74099	CAG|AGA	.	.		0.428	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		C	67795378	G	C	67795378	3	2	99	1	0	0	0	0	1	0	0	0	7636	942	33	4	791	4	IL12RB2	1	67795378	Missense_Mutation	SNP	G	TCGA-DD-A1EC-01A-21D-A12Z-10	40584681	67795378	181455243	2	13550										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144859947	144859947	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	ctcgtacctctgccaccaggTggctcaggtcactgctcaaa	9	15	4	0			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr1:144859947T>C	ENST00000369354.3	-	38	6326	c.6137A>G	c.(6136-6138)cAc>cGc	p.H2046R	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.H2131R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.H1940R|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.H2046R|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.H2182R|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2046					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGCCACCAGGTGGCTCAGGTC	0.547			T	PDGFRB	MPD																																p.H2046R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6137G						.						102	97	98					1																	144859947		2203	4297	6500	SO:0001583	missense	9659	exon38			ACCAGGTGGCTCA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6137A>G	chr1.hg19:g.144859947T>C	ENSP00000358360:p.His2046Arg	242.0	0.0		305.0	29.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	3.859	-0.030327	0.07543	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01516	4.81;4.89;4.89;4.91;4.89	5.1	-1.38	0.09027	.	.	.	.	.	T	0.00666	0.0022	M	0.61703	1.905	0.18873	N	0.999982	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42531	-0.9446	9	0.22109	T	0.4	.	5.581	0.17250	0.0:0.3664:0.1494:0.4842	.	1940;2046	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	R	1940;2046;2046;2131;2182	ENSP00000327209:H1940R;ENSP00000358360:H2046R;ENSP00000358363:H2046R;ENSP00000435654:H2131R;ENSP00000358366:H2182R	ENSP00000327209:H1940R	H	-	2	0	PDE4DIP	143571304	0.963000	0.33076	0.914000	0.36105	0.085000	0.17905	0.421000	0.21280	0.067000	0.16545	0.528000	0.53228	CAC	.	.		0.547	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144859947	T	C	144859947	3	2	99	1	0	0	0	0	1	0	0	0	11652	1696	59	2	931	2	PDE4DIP	1	144859947	Missense_Mutation	SNP	T	TCGA-DD-A1EC-01A-21D-A12Z-10	77064569	144859947	104390674	3	13551										
RASSF5	83593	hgsc.bcm.edu	37	chr1	206730943	206730943	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	agcagtgggtactgcagcctGgacgaggaactggaagactg	16	8	0	1			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr1:206730943G>T	ENST00000355294.4	+	2	636				RASSF5_ENST00000367117.3_Intron|RASSF5_ENST00000304534.8_Silent_p.L14L	NM_182663.2	NP_872604.1	Q8WWW0	RASF5_HUMAN	Ras association (RalGDS/AF-6) domain family member 5						apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein localization to nucleus (GO:1900180)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	8	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			ACTGCAGCCTGGACGAGGAAC	0.542																																					p.L14L	GBM(162;656 1984 11916 22872 31529)	Atlas-SNP	.											.	RASSF5	54	.	0			c.G42T						.						98	92	94					1																	206730943		2203	4300	6503	SO:0001627	intron_variant	83593	exon1			CAGCCTGGACGAG	BC004270	CCDS1463.1, CCDS1464.1, CCDS30998.1	1q31	2014-04-10	2008-02-22		ENSG00000136653	ENSG00000266094			17609	protein-coding gene	gene with protein product		607020				11978988, 11965544	Standard	NM_182663		Approved	Maxp1, NORE1, RAPL	uc001hed.3	Q8WWW0	OTTHUMG00000184616	ENST00000355294.4:c.579+19321G>T	chr1.hg19:g.206730943G>T		97.0	0.0		122.0	18.0	NM_182665	A8K1E6|Q5SY32|Q8WWV9|Q8WXF4|Q9BT99	Silent	SNP	ENST00000355294.4	hg19	CCDS30998.1																																																																																			.	.		0.542	RASSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088469.1	NM_031437		T	206730943	G	T	206730943	1	4	99	0	1	0	0	0	0	0	0	0	13104	1335	47	3		3	RASSF5	1	206730943	Intron	SNP	G	TCGA-DD-A1EC-01A-21D-A12Z-10	61870996	206730943	42519678	4	13552										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32692803	32692803	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	acctcccgtgtgcagattcaTgaaggtaaagaactttaaga	9	8	1	4			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr2:32692803T>C	ENST00000421745.2	+	27	5701	c.5567T>C	c.(5566-5568)aTg>aCg	p.M1856T		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1856					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TGCAGATTCATGAAGGTAAAG	0.333																																					p.M1856T	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T5567C						.						53	49	50					2																	32692803		2203	4300	6503	SO:0001583	missense	57448	exon27			GATTCATGAAGGT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.5567T>C	chr2.hg19:g.32692803T>C	ENSP00000393596:p.Met1856Thr	129.0	0.0		123.0	22.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	17.40	3.378901	0.61735	.	.	ENSG00000115760	ENST00000421745	T	0.75477	-0.94	5.61	5.61	0.85477	.	0.090659	0.64402	D	0.000001	T	0.69869	0.3159	L	0.50333	1.59	0.58432	D	0.999992	P	0.37864	0.61	B	0.34824	0.19	T	0.74250	-0.3726	10	0.87932	D	0	.	15.8638	0.79047	0.0:0.0:0.0:1.0	.	1856	Q9NR09	BIRC6_HUMAN	T	1856	ENSP00000393596:M1856T	ENSP00000393596:M1856T	M	+	2	0	BIRC6	32546307	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	7.717000	0.84732	2.162000	0.67917	0.456000	0.33151	ATG	.	.		0.333	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32692803	T	C	32692803	3	2	99	1	0	0	0	0	1	0	0	0	1438	1464	51	2	5673	2	BIRC6	2	32692803	Missense_Mutation	SNP	T	TCGA-DD-A1EC-01A-21D-A12Z-10		32692803	210506570	5	13553										
LONRF2	164832	hgsc.bcm.edu	37	chr2	100906810	100906810	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	aaccgactgatgccaatcgcGtctacaacagaacttccatc	6	14	1	2			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr2:100906810G>A	ENST00000393437.3	-	10	2469	c.1830C>T	c.(1828-1830)gaC>gaT	p.D610D	LONRF2_ENST00000409647.1_Silent_p.D367D	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	610	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						TGCCAATCGCGTCTACAACAG	0.458																																					p.D610D		Atlas-SNP	.											.	LONRF2	62	.	0			c.C1830T						.						146	131	136					2																	100906810		2203	4300	6503	SO:0001819	synonymous_variant	164832	exon10			AATCGCGTCTACA	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"RING-type (C3HC4) zinc fingers"	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1830C>T	chr2.hg19:g.100906810G>A		170.0	0.0		165.0	29.0	NM_198461	B9A006|Q6ZSR4	Silent	SNP	ENST00000393437.3	hg19	CCDS2046.2																																																																																			.	.		0.458	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461		A	100906810	G	A	100906810	2	1	99	1	0	0	0	0	0	0	0	1	8904	1136	40	1		1	LONRF2	2	100906810	Silent	SNP	G	TCGA-DD-A1EC-01A-21D-A12Z-10	68214007	100906810	142292563	6	13554										
FARSB	10056	hgsc.bcm.edu	37	chr2	223505623	223505623	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	tggatttttccatcaggcatTacccgtttatacactggagc	8	10	1	0			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr2:223505623T>A	ENST00000281828.6	-	4	560	c.297A>T	c.(295-297)gtA>gtT	p.V99V	FARSB_ENST00000536361.1_5'UTR	NM_005687.3	NP_005678.3	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	99					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|RNA binding (GO:0003723)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	24		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	CATCAGGCATTACCCGTTTAT	0.254																																					p.V99V		Atlas-SNP	.											.	FARSB	49	.	0			c.A297T						.						37	39	39					2																	223505623		2201	4297	6498	SO:0001819	synonymous_variant	10056	exon4			AGGCATTACCCGT	AF042346	CCDS2454.1	2q36.2	2011-07-01	2007-02-23	2007-02-23	ENSG00000116120	ENSG00000116120	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	17800	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 1, beta, cytoplasmic"	609690	"phenylalanyl-tRNA synthetase-like, beta subunit"	FARSLB		10049785	Standard	NM_005687		Approved	PheHB, FRSB	uc002vne.1	Q9NSD9	OTTHUMG00000133155	ENST00000281828.6:c.297A>T	chr2.hg19:g.223505623T>A		633.0	0.0		329.0	54.0	NM_005687	B4DFM0|O95708|Q4ZFX1|Q57ZJ5|Q9NZZ6	Silent	SNP	ENST00000281828.6	hg19	CCDS2454.1																																																																																			.	.		0.254	FARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256855.2	NM_005687		A	223505623	T	A	223505623	2	1	99	1	0	0	0	0	0	0	0	1	5688	1741	61	4		4	FARSB	2	223505623	Silent	SNP	T	TCGA-DD-A1EC-01A-21D-A12Z-10	122598813	223505623	19693750	7	13555										
CADPS	8618	hgsc.bcm.edu	37	chr3	62484884	62484884	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	aagaacttcaatgactagttCagcaagacgtattgtatctt	7	7	3	3			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr3:62484884C>T	ENST00000383710.4	-	18	3008	c.2659G>A	c.(2659-2661)Gaa>Aaa	p.E887K	CADPS_ENST00000283269.9_Missense_Mutation_p.E904K|CADPS_ENST00000357948.3_Missense_Mutation_p.E864K	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	887	Interaction with DRD2.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		ATGACTAGTTCAGCAAGACGT	0.448																																					p.E904K		Atlas-SNP	.											CADPS_ENST00000383710,NS,haematopoietic_neoplasm,0,4	CADPS	387	.	0			c.G2710A						.						162	138	146					3																	62484884		2203	4300	6503	SO:0001583	missense	8618	exon18			CTAGTTCAGCAAG	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.2659G>A	chr3.hg19:g.62484884C>T	ENSP00000373215:p.Glu887Lys	272.0	1.0		294.0	75.0	NM_183394	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.992910	0.93167	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269	T;T;T	0.56611	0.48;0.47;0.45	5.89	5.89	0.94794	Calcium-dependent secretion activator (1);	0.000000	0.85682	D	0.000000	T	0.75982	0.3924	M	0.80616	2.505	0.80722	D	1	P;D;D;D	0.63880	0.911;0.99;0.969;0.993	P;D;P;P	0.72982	0.674;0.979;0.735;0.864	T	0.77566	-0.2540	10	0.87932	D	0	.	20.2562	0.98421	0.0:1.0:0.0:0.0	.	864;904;887;887	Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4	.;.;CAPS1_HUMAN;.	K	887;887;864;904	ENSP00000373215:E887K;ENSP00000350632:E864K;ENSP00000283269:E904K	ENSP00000283269:E904K	E	-	1	0	CADPS	62459924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.797000	0.96272	0.563000	0.77884	GAA	.	.		0.448	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		T	62484884	C	T	62484884	3	4	99	1	0	0	0	0	1	0	0	0	2572	835	29	3	1454	3	CADPS	3	62484884	Missense_Mutation	SNP	C	TCGA-DD-A1EC-01A-21D-A12Z-10		62484884	135537546	8	13556										
RAPGEF2	9693	hgsc.bcm.edu	37	chr4	160225597	160225597	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	tagtatcactagtgattctgGgagcagcagtctttctgata	10	7	4	2			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr4:160225597G>C	ENST00000264431.4	+	2	583	c.164G>C	c.(163-165)gGg>gCg	p.G55A	RAPGEF2_ENST00000504604.1_3'UTR	NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	55					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		AGTGATTCTGGGAGCAGCAGT	0.413																																					p.G55A		Atlas-SNP	.											.	RAPGEF2	171	.	0			c.G164C						.						167	157	160					4																	160225597		1915	4127	6042	SO:0001583	missense	9693	exon2			ATTCTGGGAGCAG	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.164G>C	chr4.hg19:g.160225597G>C	ENSP00000264431:p.Gly55Ala	423.0	0.0		389.0	51.0	NM_014247	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	hg19	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.781279	0.90282	.	.	ENSG00000109756	ENST00000505478;ENST00000510510;ENST00000264431;ENST00000514565	T	0.50548	0.74	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.70011	0.3175	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69658	-0.5086	10	0.52906	T	0.07	.	19.8097	0.96542	0.0:0.0:1.0:0.0	.	55	Q9Y4G8	RPGF2_HUMAN	A	211;53;55;36	ENSP00000264431:G55A	ENSP00000264431:G55A	G	+	2	0	RAPGEF2	160445047	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.476000	0.97823	2.685000	0.91497	0.484000	0.47621	GGG	.	.		0.413	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		C	160225597	G	C	160225597	3	2	99	1	0	0	0	0	1	0	0	0	13059	1232	43	4	170	4	RAPGEF2	4	160225597	Missense_Mutation	SNP	G	TCGA-DD-A1EC-01A-21D-A12Z-10		160225597	30928679	9	13557										
FOXK1	221937	hgsc.bcm.edu	37	chr7	4799104	4799104	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	ggcccccaccgtcaccatggTcagggtggtcaccacatctg	11	16	4	0			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr7:4799104T>G	ENST00000328914.4	+	7	1574	c.1574T>G	c.(1573-1575)gTc>gGc	p.V525G	FOXK1_ENST00000446823.1_Missense_Mutation_p.V362G	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GTCACCATGGTCAGGGTGGTC	0.697																																					p.V525G		Atlas-SNP	.											.	FOXK1	64	.	0			c.T1574G						.						37	29	32					7																	4799104		2192	4297	6489	SO:0001583	missense	221937	exon7			CCATGGTCAGGGT	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.1574T>G	chr7.hg19:g.4799104T>G	ENSP00000328720:p.Val525Gly	29.0	0.0		74.0	10.0	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	hg19	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.159664	0.78226	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.96136	-3.54;-3.92	5.65	5.65	0.86999	.	0.061247	0.64402	D	0.000004	D	0.94686	0.8286	L	0.46157	1.445	0.80722	D	1	D;B	0.54047	0.964;0.449	P;B	0.49140	0.601;0.329	D	0.94630	0.7821	10	0.51188	T	0.08	.	15.3584	0.74448	0.0:0.0:0.0:1.0	.	525;362	P85037;P85037-2	FOXK1_HUMAN;.	G	362;281;525;408	ENSP00000394442:V362G;ENSP00000328720:V525G	ENSP00000328720:V525G	V	+	2	0	FOXK1	4765630	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	7.556000	0.82233	2.279000	0.76181	0.533000	0.62120	GTC	.	.		0.697	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			G	4799104	T	G	4799104	3	3	99	1	0	0	0	0	1	0	0	0	6022	1667	58	5	1600	5	FOXK1	7	4799104	Missense_Mutation	SNP	T	TCGA-DD-A1EC-01A-21D-A12Z-10		4799104	154339559	10	13558										
SUPV3L1	6832	hgsc.bcm.edu	37	chr10	70951452	70951452	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	acaggtgaagagcgtgtgacAgttcagccaaatgggaaaca	13	7	1	3			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr10:70951452A>G	ENST00000359655.4	+	6	843	c.783A>G	c.(781-783)acA>acG	p.T261T	SUPV3L1_ENST00000483572.1_3'UTR	NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	261	Helicase ATP-binding.				ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGCGTGTGACAGTTCAGCCAA	0.378																																					p.T261T		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.A783G						.						219	181	194					10																	70951452		2203	4300	6503	SO:0001819	synonymous_variant	6832	exon6			TGTGACAGTTCAG	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"suppressor of var1 (S.cerevisiae) 3-like 1"			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.783A>G	chr10.hg19:g.70951452A>G		451.0	0.0		336.0	53.0	NM_003171	A8K301|O43630	Silent	SNP	ENST00000359655.4	hg19	CCDS7287.1																																																																																			.	.		0.378	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171		G	70951452	A	G	70951452	2	3	99	1	0	0	0	0	0	0	0	1	15417	175	7	2		2	SUPV3L1	10	70951452	Silent	SNP	A	TCGA-DD-A1EC-01A-21D-A12Z-10		70951452	64583295	11	13559										
CEP290	80184	hgsc.bcm.edu	37	chr12	88508195	88508195	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	taacatgaaaaaaataacttAcattaactagtctttcaagg	4	6	2	1			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr12:88508195A>C	ENST00000552810.1	-	20	2396		c.e20+1		CEP290_ENST00000309041.7_Splice_Site|CEP290_ENST00000397838.3_Splice_Site	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						aaaataacTTACATTAACTAG	0.318																																					.		Atlas-SNP	.											.	CEP290	195	.	0			c.2052+2T>G						.						146	129	134					12																	88508195		1475	3267	4742	SO:0001630	splice_region_variant	80184	exon21			TAACTTACATTAA	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.2052+1T>G	chr12.hg19:g.88508195A>C		201.0	0.0		109.0	31.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Splice_Site	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.440396	0.83993	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6245	0.84952	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CEP290	87032326	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.744000	0.85034	2.323000	0.78572	0.528000	0.53228	.	.	.		0.318	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	Intron	C	88508195	A	C	88508195	5	2	99	1	0	0	0	0	0	0	1	0	3255	405	14	5	5525	5	CEP290	12	88508195	Splice_Site	SNP	A	TCGA-DD-A1EC-01A-21D-A12Z-10		88508195	45343700	12	13560										
BRCA2	675	hgsc.bcm.edu	37	chr13	32912486	32912486	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	ctgctgccagtagaaattctCataacttagaatttgatggc	8	8	1	3			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr13:32912486C>T	ENST00000380152.3	+	11	4227	c.3994C>T	c.(3994-3996)Cat>Tat	p.H1332Y	BRCA2_ENST00000544455.1_Missense_Mutation_p.H1332Y			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1332					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TAGAAATTCTCATAACTTAGA	0.308			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.H1332Y	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2	812	.	0			c.C3994T						.						24	24	24					13																	32912486		2202	4289	6491	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	AATTCTCATAACT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.3994C>T	chr13.hg19:g.32912486C>T	ENSP00000369497:p.His1332Tyr	160.0	0.0		124.0	26.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	0.001	-3.113434	0.00032	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00678	5.87;5.87	5.44	-0.395	0.12431	.	1.264310	0.05114	N	0.489382	T	0.00440	0.0014	N	0.10874	0.06	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45469	-0.9259	10	0.02654	T	1	.	0.2365	0.00187	0.2378:0.2012:0.1562:0.4049	.	1332	P51587	BRCA2_HUMAN	Y	1332	ENSP00000369497:H1332Y;ENSP00000439902:H1332Y	ENSP00000369497:H1332Y	H	+	1	0	BRCA2	31810486	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.239000	0.08965	0.374000	0.24650	-0.484000	0.04775	CAT	.	.		0.308	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		T	32912486	C	T	32912486	3	4	99	1	0	0	0	0	1	0	0	0	1501	826	29	3	4032	3	BRCA2	13	32912486	Missense_Mutation	SNP	C	TCGA-DD-A1EC-01A-21D-A12Z-10		32912486	82257392	13	13561										
IPO5	3843	hgsc.bcm.edu	37	chr13	98670928	98670928	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	tgggagtcatggcacagtacGgtggagataattatcgccct	13	8	1	1			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr13:98670928G>A	ENST00000490680.1	+	23	2871	c.2806G>A	c.(2806-2808)Ggt>Agt	p.G936S	IPO5_ENST00000261574.5_Missense_Mutation_p.G954S|IPO5_ENST00000539640.1_Missense_Mutation_p.G811S			O00410	IPO5_HUMAN	importin 5	936					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						GGCACAGTACGGTGGAGATAA	0.443																																					p.G954S		Atlas-SNP	.											.	IPO5	90	.	0			c.G2860A						.						183	130	148					13																	98670928		2203	4300	6503	SO:0001583	missense	3843	exon26			CAGTACGGTGGAG	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"Importins"	6402	protein-coding gene	gene with protein product		602008	"karyopherin (importin) beta 3", "RAN binding protein 5"	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.2806G>A	chr13.hg19:g.98670928G>A	ENSP00000418393:p.Gly936Ser	151.0	0.0		184.0	38.0	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Missense_Mutation	SNP	ENST00000490680.1	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.481160	0.96307	.	.	ENSG00000065150	ENST00000261574;ENST00000357602;ENST00000490680;ENST00000539640	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.82	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.78868	0.4351	M	0.77820	2.39	0.80722	D	1	D	0.76494	0.999	P	0.58331	0.837	T	0.81807	-0.0763	10	0.62326	D	0.03	-9.9941	14.6536	0.68817	0.0694:0.0:0.9306:0.0	.	954	O00410-3	.	S	954;936;936;811	ENSP00000261574:G954S;ENSP00000350219:G936S;ENSP00000418393:G936S;ENSP00000445126:G811S	ENSP00000261574:G954S	G	+	1	0	IPO5	97468929	1.000000	0.71417	0.805000	0.32314	0.995000	0.86356	9.581000	0.98210	1.469000	0.48083	0.650000	0.86243	GGT	.	.		0.443	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271		A	98670928	G	A	98670928	3	1	99	1	0	0	0	0	1	0	0	0	7805	1116	39	1	2954	1	IPO5	13	98670928	Missense_Mutation	SNP	G	TCGA-DD-A1EC-01A-21D-A12Z-10	65758442	98670928	16498950	14	13562										
TDRD9	122402	hgsc.bcm.edu	37	chr14	104473004	104473005	+	Frame_Shift_Ins	INS	-	-	T													0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	gcagctctttctttgaagaaINStttttttgcaatgcctttcc							TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr14:104473004_104473005insT	ENST00000409874.4	+	17	1949_1950	c.1901_1902insT	c.(1900-1905)aattttfs	p.NF634fs	TDRD9_ENST00000339063.5_Frame_Shift_Ins_p.NF634fs	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	634					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TCTTTGAAGAATTTTTTTGCAA	0.332																																					p.N634fs		Pindel	.											.	TDRD9	175	.	0			c.1901_1902insT						.																																			SO:0001589	frameshift_variant	122402	exon17			.	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1908dupT	chr14.hg19:g.104473011_104473011dupT	ENSP00000387303:p.Asn634fs	299.0	0.0		235.0	14.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Frame_Shift_Ins	INS	ENST00000409874.4	hg19	CCDS9987.2																																																																																			.	.		0.332	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		T	104473005	-	T	104473004	7	5	99	1	0	1	1	0	0	0	0	0	15751	101	4	0	1967	0	TDRD9	14	104473004	Frame_Shift_Ins	INS	-	TCGA-DD-A1EC-01A-21D-A12Z-10		104473004	2876536	15	13563										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31925948	31925948	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	gaggagtgtgaagggcacaaTggatgttatgatgaaaagac	15	3	0	4			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr16:31925948T>C	ENST00000300870.10	+	4	587	c.378T>C	c.(376-378)aaT>aaC	p.N126N	ZNF267_ENST00000394846.3_3'UTR	NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	126					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						AAGGGCACAATGGATGTTATG	0.363																																					p.N126N		Atlas-SNP	.											.	ZNF267	94	.	0			c.T378C						.						123	122	122					16																	31925948		2197	4300	6497	SO:0001819	synonymous_variant	10308	exon4			GCACAATGGATGT	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.378T>C	chr16.hg19:g.31925948T>C		158.0	0.0		148.0	28.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Silent	SNP	ENST00000300870.10	hg19	CCDS32440.1																																																																																			.	.		0.363	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		C	31925948	T	C	31925948	2	2	99	1	0	0	0	0	0	0	0	1	17821	1461	51	2		2	ZNF267	16	31925948	Silent	SNP	T	TCGA-DD-A1EC-01A-21D-A12Z-10		31925948	58428805	16	13564										
SKAP1	8631	hgsc.bcm.edu	37	chr17	46262096	46262096	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	gcgtcctacctcatagctgcGcctatcctgggaggtcagtt	11	13	2	0			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr17:46262096G>A	ENST00000336915.6	-	7	625	c.556C>T	c.(556-558)Cgc>Tgc	p.R186C	RP11-456D7.1_ENST00000582246.1_RNA|SKAP1_ENST00000584924.1_Missense_Mutation_p.R186C	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	186	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(1)|lung(10)|prostate(2)|skin(4)|urinary_tract(1)	18						TCATAGCTGCGCCTATCCTGG	0.522																																					p.R186C		Atlas-SNP	.											.	SKAP1	41	.	0			c.C556T						.						210	193	199					17																	46262096		2203	4300	6503	SO:0001583	missense	8631	exon7			AGCTGCGCCTATC	Y11215	CCDS32674.1	17q21.32	2013-01-10	2006-09-28	2006-09-28		ENSG00000141293		"Pleckstrin homology (PH) domain containing"	15605	protein-coding gene	gene with protein product		604969	"src family associated phosphoprotein 1"	SCAP1		9195899	Standard	NM_003726		Approved	SKAP55	uc002ini.1	Q86WV1		ENST00000336915.6:c.556C>T	chr17.hg19:g.46262096G>A	ENSP00000338171:p.Arg186Cys	138.0	0.0		128.0	26.0	NM_003726	D3DTV1|O15268	Missense_Mutation	SNP	ENST00000336915.6	hg19	CCDS32674.1	.	.	.	.	.	.	.	.	.	.	G	13.74	2.326383	0.41197	.	.	ENSG00000141293	ENST00000336915	T	0.18502	2.21	5.55	5.55	0.83447	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.061153	0.64402	D	0.000002	T	0.54303	0.1850	M	0.93283	3.4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.991	T	0.66416	-0.5929	10	0.87932	D	0	-54.9613	17.2809	0.87128	0.0:0.0:1.0:0.0	.	186;186	Q86WV1-2;Q86WV1	.;SKAP1_HUMAN	C	186	ENSP00000338171:R186C	ENSP00000338171:R186C	R	-	1	0	SKAP1	43617095	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.764000	0.74960	2.612000	0.88384	0.557000	0.71058	CGC	.	.		0.522	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726		A	46262096	G	A	46262096	3	1	99	1	0	0	0	0	1	0	0	0	14370	1087	38	1	547	1	SKAP1	17	46262096	Missense_Mutation	SNP	G	TCGA-DD-A1EC-01A-21D-A12Z-10		46262096	34933114	17	13565										
GPR142	350383	hgsc.bcm.edu	37	chr17	72367888	72367888	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	tcagcctcctgaccgcagtgGccctggcgcgccttgccacc	11	19	1	1			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr17:72367888G>A	ENST00000335666.4	+	4	586	c.538G>A	c.(538-540)Gcc>Acc	p.A180T		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	180						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A180T(1)		central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						GACCGCAGTGGCCCTGGCGCG	0.622																																					p.A180T		Atlas-SNP	.											GPR142,NS,carcinoma,0,1	GPR142	74	.	1	Substitution - Missense(1)	lung(1)	c.G538A						.						45	40	42					17																	72367888		2203	4300	6503	SO:0001583	missense	350383	exon4			GCAGTGGCCCTGG	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"GPCR / Class A : Orphans"	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.538G>A	chr17.hg19:g.72367888G>A	ENSP00000335158:p.Ala180Thr	44.0	0.0		47.0	10.0	NM_181790	A4CYJ8|Q86SL3	Missense_Mutation	SNP	ENST00000335666.4	hg19	CCDS11698.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.762461	0.31228	.	.	ENSG00000257008	ENST00000335666	T	0.38560	1.13	4.68	3.71	0.42584	GPCR, rhodopsin-like superfamily (1);	0.175229	0.49916	N	0.000129	T	0.44052	0.1275	L	0.50919	1.6	0.40575	D	0.981335	P;P	0.47484	0.896;0.476	P;B	0.47118	0.538;0.219	T	0.48614	-0.9020	10	0.56958	D	0.05	-3.3935	12.8413	0.57805	0.0831:0.0:0.9169:0.0	.	180;1142	Q7Z601;Q8NGB0	GP142_HUMAN;.	T	180	ENSP00000335158:A180T	ENSP00000335158:A180T	A	+	1	0	GPR142	69879483	1.000000	0.71417	0.892000	0.35008	0.219000	0.24729	3.189000	0.50965	1.283000	0.44513	0.558000	0.71614	GCC	.	.		0.622	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790		A	72367888	G	A	72367888	3	1	99	1	0	0	0	0	1	0	0	0	6658	1203	42	3	552	3	GPR142	17	72367888	Missense_Mutation	SNP	G	TCGA-DD-A1EC-01A-21D-A12Z-10	26105792	72367888	8827322	18	13566										
FBF1	85302	hgsc.bcm.edu	37	chr17	73918105	73918105	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	agcagctgcgtgctcaagccCttgtgtgctggtgagaggtt	15	9	1	1			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr17:73918105C>G	ENST00000586717.1	-	14	1678	c.1405G>C	c.(1405-1407)Ggg>Cgg	p.G469R	FBF1_ENST00000319129.5_Missense_Mutation_p.G468R|FBF1_ENST00000389570.4_Missense_Mutation_p.G469R			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	469					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TGCTCAAGCCCTTGTGTGCTG	0.622																																					p.G468R		Atlas-SNP	.											.	FBF1	48	.	0			c.G1402C						.						41	47	45					17																	73918105		2071	3986	6057	SO:0001583	missense	85302	exon14			CAAGCCCTTGTGT	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.1405G>C	chr17.hg19:g.73918105C>G	ENSP00000465132:p.Gly469Arg	120.0	0.0		108.0	20.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.75	1.437176	0.25900	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.17370	2.28;2.28	5.45	3.43	0.39272	.	.	.	.	.	T	0.12817	0.0311	L	0.44542	1.39	0.09310	N	1	B;B;B	0.31548	0.328;0.029;0.102	B;B;B	0.29598	0.104;0.021;0.063	T	0.22626	-1.0211	9	0.11485	T	0.65	-8.5154	8.9107	0.35552	0.0:0.8223:0.0:0.1777	.	483;469;468	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	R	469;469;468;482	ENSP00000374221:G469R;ENSP00000324292:G468R	ENSP00000324292:G468R	G	-	1	0	FBF1	71429700	0.001000	0.12720	0.005000	0.12908	0.002000	0.02628	1.370000	0.34238	1.287000	0.44583	0.655000	0.94253	GGG	.	.		0.622	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		G	73918105	C	G	73918105	3	3	99	1	0	0	0	0	1	0	0	0	5703	681	24	4	2063	4	FBF1	17	73918105	Missense_Mutation	SNP	C	TCGA-DD-A1EC-01A-21D-A12Z-10	1550217	73918105	7277105	19	13567										
POLD1	5424	hgsc.bcm.edu	37	chr19	50912834	50912834	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	ggcgccaggtcctggatggaCggcagctggcgctgaaggtg	19	10	0	1			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr19:50912834C>T	ENST00000440232.2	+	17	2118	c.2065C>T	c.(2065-2067)Cgg>Tgg	p.R689W	POLD1_ENST00000595904.1_Missense_Mutation_p.R715W|POLD1_ENST00000599857.1_Missense_Mutation_p.R689W	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	689					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CCTGGATGGACGGCAGCTGGC	0.672								DNA polymerases (catalytic subunits)																													p.R689W		Atlas-SNP	.											POLD1_ENST00000440232,colon,carcinoma,0,2	POLD1	174	.	0			c.C2065T						.						58	65	62					19																	50912834		2203	4299	6502	SO:0001583	missense	5424	exon17			GATGGACGGCAGC		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2065C>T	chr19.hg19:g.50912834C>T	ENSP00000406046:p.Arg689Trp	138.0	0.0		154.0	27.0	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	hg19	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.471484	0.84533	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.19806	2.12	4.38	4.38	0.52667	DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.000000	0.85682	D	0.000000	T	0.64659	0.2618	H	0.99156	4.45	0.80722	D	1	D;D	0.60160	0.987;0.987	P;D	0.66979	0.887;0.948	T	0.81986	-0.0681	10	0.87932	D	0	-33.0089	16.0916	0.81094	0.0:1.0:0.0:0.0	.	715;689	E7EVW0;P28340	.;DPOD1_HUMAN	W	689;690	ENSP00000406046:R689W	ENSP00000366129:R690W	R	+	1	2	POLD1	55604646	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.126000	0.64721	2.190000	0.69967	0.561000	0.74099	CGG	.	.		0.672	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			T	50912834	C	T	50912834	3	4	99	1	0	0	0	0	1	0	0	0	12199	527	19	1	2127	1	POLD1	19	50912834	Missense_Mutation	SNP	C	TCGA-DD-A1EC-01A-21D-A12Z-10		50912834	8216149	20	13568										
XKR7	343702	hgsc.bcm.edu	37	chr20	30585125	30585125	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.142857142857143	3	1	1.84310850439883	2.25268817204301	1.68951612903226	1	1	0	cgcaagaagtacccggcctgGgatgctcattttattgaccg	11	11	1	2			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr20:30585125G>A	ENST00000562532.2	+	3	1779	c.1605G>A	c.(1603-1605)tgG>tgA	p.W535*		NM_001011718.1	NP_001011718.1	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related family, member 7	535						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			ACCCGGCCTGGGATGCTCATT	0.632																																					p.W535X		Atlas-SNP	.											.	XKR7	62	.	0			c.G1605A						.						50	57	55					20																	30585125		2203	4300	6503	SO:0001587	stop_gained	343702	exon3			GGCCTGGGATGCT	AY534245	CCDS33459.1	20q11.21	2014-07-16	2006-01-12		ENSG00000260903	ENSG00000260903			23062	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 7", "chromosome 20 open reading frame 159"	C20orf159			Standard	NM_001011718		Approved	dJ310O13.4	uc002wxe.3	Q5GH72	OTTHUMG00000032198	ENST00000562532.2:c.1605G>A	chr20.hg19:g.30585125G>A	ENSP00000477059:p.Trp535*	37.0	0.0		22.0	7.0	NM_001011718	Q9NUG5	Nonsense_Mutation	SNP	ENST00000562532.2	hg19	CCDS33459.1	.	.	.	.	.	.	.	.	.	.	G	37	6.445175	0.97572	.	.	ENSG00000101321	ENST00000217299	.	.	.	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.5108	16.7017	0.85351	0.0:0.0:1.0:0.0	.	.	.	.	X	535	.	ENSP00000217299:W535X	W	+	3	0	XKR7	30048786	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.657000	0.98554	2.518000	0.84900	0.561000	0.74099	TGG	.	.		0.632	XKR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078597.3	NM_001011718		A	30585125	G	A	30585125	4	1	99	1	0	0	0	0	0	1	0	0	17451	1241	43	3	1615	3	XKR7	20	30585125	Nonsense_Mutation	SNP	G	TCGA-DD-A1EC-01A-21D-A12Z-10		30585125	32440395	21	13569										
SKI	6497	hgsc.bcm.edu	37	chr1	2234733	2234733	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tttctcgacagagcctgggcTgtgttcaccctcgccagcgc	11	15	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:2234733T>C	ENST00000378536.4	+	3	1177	c.1105T>C	c.(1105-1107)Tgt>Cgt	p.C369R	SKI_ENST00000478223.2_3'UTR	NM_003036.3	NP_003027.1	P12755	SKI_HUMAN	SKI proto-oncogene	369					anterior/posterior axis specification (GO:0009948)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|gene expression (GO:0010467)|lens morphogenesis in camera-type eye (GO:0002089)|myelination in peripheral nervous system (GO:0022011)|myotube differentiation (GO:0014902)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neural tube closure (GO:0001843)|nose morphogenesis (GO:0043585)|olfactory bulb development (GO:0021772)|palate development (GO:0060021)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|retina development in camera-type eye (GO:0060041)|skeletal muscle fiber development (GO:0048741)|SMAD protein signal transduction (GO:0060395)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase inhibitor activity (GO:0046811)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|repressing transcription factor binding (GO:0070491)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(2)|lung(5)|prostate(1)|stomach(1)	10	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)		GAGCCTGGGCTGTGTTCACCC	0.617																																					p.C369R	Ovarian(177;144 1678 13697 20086 27838 40755)	Atlas-SNP	.											.	SKI	33	.	0			c.T1105C						.						145	146	145					1																	2234733		2203	4300	6503	SO:0001583	missense	6497	exon3			CTGGGCTGTGTTC	X15218	CCDS39.1	1p36.33	2014-06-25	2014-06-25		ENSG00000157933	ENSG00000157933		"SKI transcriptional corepressors"	10896	protein-coding gene	gene with protein product		164780	"v-ski avian sarcoma viral oncogene homolog"			2762147	Standard	NM_003036		Approved		uc001aja.4	P12755	OTTHUMG00000001407	ENST00000378536.4:c.1105T>C	chr1.hg19:g.2234733T>C	ENSP00000367797:p.Cys369Arg	108.0	0.0		62.0	4.0	NM_003036	Q5SYT7	Missense_Mutation	SNP	ENST00000378536.4	hg19	CCDS39.1	.	.	.	.	.	.	.	.	.	.	t	6.330	0.428917	0.11987	.	.	ENSG00000157933	ENST00000378536	D	0.95690	-3.78	4.42	4.42	0.53409	.	0.217731	0.48767	D	0.000170	D	0.91720	0.7382	L	0.54323	1.7	0.53688	D	0.999974	P	0.34462	0.454	B	0.27262	0.078	D	0.89751	0.3940	10	0.15499	T	0.54	-14.4652	13.1714	0.59599	0.0:0.0:0.0:1.0	.	369	P12755	SKI_HUMAN	R	369	ENSP00000367797:C369R	ENSP00000367797:C369R	C	+	1	0	SKI	2224593	1.000000	0.71417	0.769000	0.31535	0.205000	0.24178	2.348000	0.44045	1.767000	0.52121	0.454000	0.30748	TGT	.	.		0.617	SKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004070.1	NM_003036		C	2234733	T	C	2234733	3	2	100	1	0	0	0	0	1	0	0	0	14372	1580	55	2	1115	2	SKI	1	2234733	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10		2234733	247015888	1	13570										
CASZ1	54897	hgsc.bcm.edu	37	chr1	10707949	10707949	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cgaggcgggcaggtgaggcaCtgacgctgggatctgaggca	19	9	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:10707949C>T	ENST00000377022.3	-	16	3723	c.3406G>A	c.(3406-3408)Gtg>Atg	p.V1136M	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Missense_Mutation_p.V1136M	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1136	Pro-rich.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		AGGTGAGGCACTGACGCTGGG	0.657																																					p.V1136M		Atlas-SNP	.											.	CASZ1	150	.	0			c.G3406A						.						72	77	75					1																	10707949		2203	4300	6503	SO:0001583	missense	54897	exon16			GAGGCACTGACGC	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.3406G>A	chr1.hg19:g.10707949C>T	ENSP00000366221:p.Val1136Met	96.0	0.0		57.0	4.0	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	hg19	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.929587	0.34096	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	5.65	5.65	0.86999	.	0.047698	0.85682	D	0.000000	T	0.50429	0.1615	L	0.39898	1.24	0.35386	D	0.790363	B;B	0.33940	0.433;0.264	B;B	0.27887	0.084;0.04	T	0.59495	-0.7444	9	0.42905	T	0.14	-24.7409	19.7244	0.96157	0.0:1.0:0.0:0.0	.	1136;1136	Q86V15-2;Q86V15	.;CASZ1_HUMAN	M	1136	.	ENSP00000339445:V1136M	V	-	1	0	CASZ1	10630536	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.836000	0.55813	2.659000	0.90383	0.655000	0.94253	GTG	.	.		0.657	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		T	10707949	C	T	10707949	3	4	100	1	0	0	0	0	1	0	0	0	2687	565	20	3	1901	3	CASZ1	1	10707949	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	8473216	10707949	238542672	2	13571										
CASZ1	54897	hgsc.bcm.edu	37	chr1	10711116	10711116	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cggggggaacctggctggggTgacctgctgcccgcttcctg	17	13	0	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:10711116T>C	ENST00000377022.3	-	12	3015	c.2698A>G	c.(2698-2700)Acc>Gcc	p.T900A	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Missense_Mutation_p.T900A	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	900					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		CTGGCTGGGGTGACCTGCTGC	0.716																																					p.T900A		Atlas-SNP	.											.	CASZ1	150	.	0			c.A2698G						.						7	9	8					1																	10711116		2134	4255	6389	SO:0001583	missense	54897	exon12			CTGGGGTGACCTG	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.2698A>G	chr1.hg19:g.10711116T>C	ENSP00000366221:p.Thr900Ala	47.0	0.0		24.0	5.0	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	hg19	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	T	0.201	-1.044952	0.01997	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.75	-4.81	0.03180	.	0.580004	0.18783	N	0.131266	T	0.18593	0.0446	N	0.14661	0.345	0.22034	N	0.999405	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.11867	-1.0570	9	0.28530	T	0.3	-9.8464	7.8164	0.29263	0.0:0.3252:0.4187:0.2561	.	900;900	Q86V15-2;Q86V15	.;CASZ1_HUMAN	A	900	.	ENSP00000339445:T900A	T	-	1	0	CASZ1	10633703	0.362000	0.24980	0.881000	0.34555	0.881000	0.50899	-0.157000	0.10085	-0.651000	0.05415	0.482000	0.46254	ACC	.	.		0.716	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		C	10711116	T	C	10711116	3	2	100	1	0	0	0	0	1	0	0	0	2687	1696	59	2	2625	2	CASZ1	1	10711116	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	3167	10711116	238539505	3	13572										
PADI3	51702	hgsc.bcm.edu	37	chr1	17606886	17606886	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tctccatcaaccaggtgctcTccaataaagacctcatcaac	4	15	5	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:17606886T>C	ENST00000375460.3	+	14	1637	c.1597T>C	c.(1597-1599)Tcc>Ccc	p.S533P	MIR3972_ENST00000582732.1_RNA	NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	533					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CCAGGTGCTCTCCAATAAAGA	0.522																																					p.S533P		Atlas-SNP	.											.	PADI3	81	.	0			c.T1597C						.						146	134	138					1																	17606886		2203	4300	6503	SO:0001583	missense	51702	exon14			GTGCTCTCCAATA	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"Peptidyl arginine deiminases"	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.1597T>C	chr1.hg19:g.17606886T>C	ENSP00000364609:p.Ser533Pro	183.0	0.0		80.0	5.0	NM_016233	Q58EY7|Q70SX5	Missense_Mutation	SNP	ENST00000375460.3	hg19	CCDS179.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.689416	0.48097	.	.	ENSG00000142619	ENST00000375460	T	0.27104	1.69	4.43	1.88	0.25563	Protein-arginine deiminase, C-terminal (1);	0.818839	0.11392	N	0.568715	T	0.27241	0.0668	M	0.68317	2.08	0.25143	N	0.990484	P	0.47484	0.896	B	0.42827	0.399	T	0.15321	-1.0441	10	0.59425	D	0.04	-20.6483	5.7136	0.17948	0.1682:0.0:0.1752:0.6566	.	533	Q9ULW8	PADI3_HUMAN	P	533	ENSP00000364609:S533P	ENSP00000364609:S533P	S	+	1	0	PADI3	17479473	0.554000	0.26522	0.992000	0.48379	0.633000	0.38033	0.133000	0.15912	0.138000	0.18790	0.383000	0.25322	TCC	.	.		0.522	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1			C	17606886	T	C	17606886	3	2	100	1	0	0	0	0	1	0	0	0	11388	1551	54	2	1651	2	PADI3	1	17606886	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	6895770	17606886	231643735	4	13573										
SRRM1	10250	hgsc.bcm.edu	37	chr1	24995725	24995725	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aagagaagaacggcttcaccTcctccccctcctaaacgaag	7	15	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:24995725T>C	ENST00000323848.9	+	14	2166	c.1851T>C	c.(1849-1851)ccT>ccC	p.P617P	SRRM1_ENST00000447431.2_Silent_p.P629P|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000374389.4_Silent_p.P626P|SRRM1_ENST00000479034.1_3'UTR	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	617	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CGGCTTCACCTCCTCCCCCTC	0.552																																					p.P617P	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.T1851C						.						101	101	101					1																	24995725		2203	4300	6503	SO:0001819	synonymous_variant	10250	exon14			TTCACCTCCTCCC	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1851T>C	chr1.hg19:g.24995725T>C		196.0	0.0		124.0	5.0	NM_005839	O60585|Q5VVN4	Silent	SNP	ENST00000323848.9	hg19	CCDS255.1																																																																																			.	.		0.552	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		C	24995725	T	C	24995725	2	2	100	1	0	0	0	0	0	0	0	1	15183	1538	54	2		2	SRRM1	1	24995725	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	7388839	24995725	224254896	5	13574										
GRIK3	2899	hgsc.bcm.edu	37	chr1	37291209	37291209	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aaggaattgccttacctggcGatgacgaagaggacacagct	12	9	0	2	rs138685291	byFrequency	TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:37291209G>T	ENST00000373091.3	-	11	1765	c.1749C>A	c.(1747-1749)atC>atA	p.I583I	GRIK3_ENST00000373093.4_Silent_p.I583I	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	583					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.I583I(1)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CTTACCTGGCGATGACGAAGA	0.582																																					p.I583I		Atlas-SNP	.											GRIK3,caecum,carcinoma,0,2	GRIK3	195	.	1	Substitution - coding silent(1)	lung(1)	c.C1749A						.						65	62	63					1																	37291209		2203	4300	6503	SO:0001819	synonymous_variant	2899	exon11			CCTGGCGATGACG	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.1749C>A	chr1.hg19:g.37291209G>T		74.0	0.0		37.0	2.0	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	hg19	CCDS416.1																																																																																			.	G|1.000;A|0.000		0.582	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		T	37291209	G	T	37291209	2	4	100	1	0	0	0	0	0	0	0	1	6784	1048	37	1		1	GRIK3	1	37291209	Silent	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	12295484	37291209	211959412	6	13575										
MACF1	23499	hgsc.bcm.edu	37	chr1	39934403	39934403	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtgaaaaatgatccctgccgAggtaaggaaccattctaagc	10	9	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:39934403A>G	ENST00000372915.3	+	94	21654	c.21567A>G	c.(21565-21567)cgA>cgG	p.R7189R	MACF1_ENST00000567887.1_Splice_Site_p.R7333R|MACF1_ENST00000564288.1_Splice_Site_p.R7296R|MACF1_ENST00000539005.1_Splice_Site_p.R5101R|MACF1_ENST00000545844.1_Splice_Site_p.R5231R|MACF1_ENST00000289893.4_Splice_Site_p.R5739R|MACF1_ENST00000361689.2_Splice_Site_p.R5231R|MACF1_ENST00000317713.7_Splice_Site_p.R5231R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	7189	C-terminal tail. {ECO:0000250}.|GAR. {ECO:0000255|PROSITE- ProRule:PRU00792}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ATCCCTGCCGAGGTAAGGAAC	0.483																																					p.R5231R		Atlas-SNP	.											.	MACF1	909	.	0			c.A15693G						.						105	99	101					1																	39934403		2203	4300	6503	SO:0001630	splice_region_variant	23499	exon92			CTGCCGAGGTAAG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.21568+1A>G	chr1.hg19:g.39934403A>G		148.0	0.0		93.0	4.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.52|17.52	3.410202|3.410202	0.62399|0.62399	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000360115;ENST00000442046|ENST00000372925;ENST00000446276	.|.	.|.	.|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	.|.	.|.	.|.	.|.	T|T	0.73869|0.73869	0.3642|0.3642	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.72530|0.72530	-0.4265|-0.4265	4|4	.|.	.|.	.|.	.|.	16.8222|16.8222	0.85835|0.85835	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	G|G	344;132|4235;219	.|.	.|.	E|S	+|+	2|1	0|0	MACF1|MACF1	39706990|39706990	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	5.212000|5.212000	0.65225|0.65225	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	GAG|AGC	.	.		0.483	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	Silent	G	39934403	A	G	39934403	5	3	100	1	0	0	0	0	0	0	1	0	9153	318	11	2	22228	2	MACF1	1	39934403	Splice_Site	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	2643194	39934403	209316218	7	13576										
HECTD3	79654	hgsc.bcm.edu	37	chr1	45469991	45469991	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tctccaactcttgccaggtcAgcaagtccagcacagcctgt	8	15	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:45469991A>G	ENST00000372172.4	-	17	2272	c.2201T>C	c.(2200-2202)cTg>cCg	p.L734P	HECTD3_ENST00000486132.1_5'UTR|HECTD3_ENST00000372168.3_Missense_Mutation_p.L344P	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	734	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					TTGCCAGGTCAGCAAGTCCAG	0.592																																					p.L734P		Atlas-SNP	.											.	HECTD3	158	.	0			c.T2201C						.						119	120	119					1																	45469991		2122	4259	6381	SO:0001583	missense	79654	exon17			CAGGTCAGCAAGT	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.2201T>C	chr1.hg19:g.45469991A>G	ENSP00000361245:p.Leu734Pro	143.0	0.0		74.0	4.0	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Missense_Mutation	SNP	ENST00000372172.4	hg19	CCDS41318.1	.	.	.	.	.	.	.	.	.	.	.	25.1	4.602233	0.87055	.	.	ENSG00000126107	ENST00000372172;ENST00000372168	T;T	0.62364	0.03;0.03	5.78	5.78	0.91487	HECT (4);	0.066178	0.64402	D	0.000007	D	0.82572	0.5066	M	0.88241	2.94	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.98	D	0.86111	0.1562	10	0.87932	D	0	.	16.1213	0.81359	1.0:0.0:0.0:0.0	.	734;344	Q5T447;Q5T447-2	HECD3_HUMAN;.	P	734;344	ENSP00000361245:L734P;ENSP00000361241:L344P	ENSP00000361241:L344P	L	-	2	0	HECTD3	45242578	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.070000	0.93974	2.202000	0.70862	0.523000	0.50628	CTG	.	.		0.592	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		G	45469991	A	G	45469991	3	3	100	1	0	0	0	0	1	0	0	0	7050	188	7	2	404	2	HECTD3	1	45469991	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	5535588	45469991	203780630	8	13577										
LDLRAD1	388633	hgsc.bcm.edu	37	chr1	54474701	54474701	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cggaccagtcggagcagtgcTgtacatggtcgcggcagaga	16	10	0	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:54474701T>G	ENST00000371360.1	-	6	589	c.572A>C	c.(571-573)cAg>cCg	p.Q191P	LDLRAD1_ENST00000545928.1_Missense_Mutation_p.Q148P|LDLRAD1_ENST00000420619.1_Missense_Mutation_p.Q152P|LDLRAD1_ENST00000371362.3_Missense_Mutation_p.Q102P	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1	191	LDL-receptor class A 3; atypical. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						GGAGCAGTGCTGTACATGGTC	0.602																																					p.Q191P		Atlas-SNP	.											.	LDLRAD1	22	.	0			c.A572C						.						123	117	119					1																	54474701		2203	4300	6503	SO:0001583	missense	388633	exon6			CAGTGCTGTACAT		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"low density lipoprotein receptor A domain containing 1"				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.572A>C	chr1.hg19:g.54474701T>G	ENSP00000360411:p.Gln191Pro	176.0	0.0		100.0	4.0	NM_001010978	A0PJY0|B7ZME3|Q5T6Z9	Missense_Mutation	SNP	ENST00000371360.1	hg19	CCDS30725.1	.	.	.	.	.	.	.	.	.	.	T	17.26	3.344125	0.61073	.	.	ENSG00000203985	ENST00000371362;ENST00000371360;ENST00000545928;ENST00000420619	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	4.25	4.25	0.50352	.	0.000000	0.53938	D	0.000048	D	0.91646	0.7360	M	0.71581	2.175	0.46774	D	0.999193	D;D	0.89917	0.997;1.0	P;D	0.85130	0.849;0.997	D	0.90151	0.4221	10	0.29301	T	0.29	-17.6216	12.5085	0.55995	0.0:0.0:0.0:1.0	.	148;191	B7ZME3;Q5T700	.;LRAD1_HUMAN	P	102;191;148;152	ENSP00000360413:Q102P;ENSP00000360411:Q191P;ENSP00000445871:Q148P;ENSP00000411017:Q152P	ENSP00000360411:Q191P	Q	-	2	0	LDLRAD1	54247289	1.000000	0.71417	0.995000	0.50966	0.689000	0.40095	5.221000	0.65272	1.788000	0.52465	0.533000	0.62120	CAG	.	.		0.602	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978		G	54474701	T	G	54474701	3	3	100	1	0	0	0	0	1	0	0	0	8714	1580	55	5	49	5	LDLRAD1	1	54474701	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	9004710	54474701	194775920	9	13578										
TTC4	7268	hgsc.bcm.edu	37	chr1	55182348	55182348	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gggagaatcctgacttggctTgtctccagtcaattattttt	9	8	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:55182348T>C	ENST00000371281.3	+	2	274	c.187T>C	c.(187-189)Tgt>Cgt	p.C63R	MROH7-TTC4_ENST00000414150.2_Silent_p.L1298L|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	63										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						TGACTTGGCTTGTCTCCAGTC	0.388																																					p.C63R		Atlas-SNP	.											.	TTC4	21	.	0			c.T187C						.						98	94	95					1																	55182348		2203	4300	6503	SO:0001583	missense	7268	exon2			TTGGCTTGTCTCC		CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"Tetratricopeptide (TTC) repeat domain containing"	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.187T>C	chr1.hg19:g.55182348T>C	ENSP00000360329:p.Cys63Arg	75.0	0.0		46.0	5.0	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Missense_Mutation	SNP	ENST00000371281.3	hg19	CCDS596.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.240330	0.79912	.	.	ENSG00000243725	ENST00000371281;ENST00000371284	T	0.13901	2.55	4.92	3.75	0.43078	.	.	.	.	.	T	0.28234	0.0697	M	0.78049	2.395	0.80722	D	1	P;D	0.56035	0.918;0.974	P;P	0.53861	0.451;0.736	T	0.03315	-1.1049	9	0.72032	D	0.01	-3.1047	10.0705	0.42330	0.0:0.0:0.1693:0.8307	.	63;74	O95801;Q5TA95	TTC4_HUMAN;.	R	63;74	ENSP00000360329:C63R	ENSP00000360329:C63R	C	+	1	0	TTC4	54954936	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	6.593000	0.74100	0.958000	0.37956	0.533000	0.62120	TGT	.	.		0.388	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623		C	55182348	T	C	55182348	3	2	100	1	0	0	0	0	1	0	0	0	16725	1812	63	2	193	2	TTC4	1	55182348	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	707647	55182348	194068273	10	13579										
CLCA1	1179	hgsc.bcm.edu	37	chr1	86961308	86961308	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	taacgcagccagacggagagTgataccccagcagagtggag	14	10	0	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:86961308T>C	ENST00000234701.3	+	13	2414	c.2063T>C	c.(2062-2064)gTg>gCg	p.V688A	CLCA1_ENST00000394711.1_Missense_Mutation_p.V688A			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	688					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		AGACGGAGAGTGATACCCCAG	0.458																																					p.V688A		Atlas-SNP	.											.	CLCA1	109	.	0			c.T2063C						.						92	89	90					1																	86961308		2203	4300	6503	SO:0001583	missense	1179	exon12			GGAGAGTGATACC		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.2063T>C	chr1.hg19:g.86961308T>C	ENSP00000234701:p.Val688Ala	125.0	0.0		91.0	4.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	hg19	CCDS709.1	.	.	.	.	.	.	.	.	.	.	T	5.685	0.310944	0.10733	.	.	ENSG00000016490	ENST00000234701;ENST00000394711	T;T	0.02763	4.17;4.17	5.45	-10.9	0.00192	.	1.930170	0.02560	N	0.096619	T	0.00300	0.0009	N	0.03324	-0.35	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48592	-0.9022	10	0.13108	T	0.6	8.9942	1.4137	0.02297	0.1544:0.2764:0.2308:0.3384	.	688	A8K7I4	CLCA1_HUMAN	A	688	ENSP00000234701:V688A;ENSP00000378200:V688A	ENSP00000234701:V688A	V	+	2	0	CLCA1	86733896	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.417000	0.02464	-2.033000	0.00925	-0.798000	0.03219	GTG	.	.		0.458	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		C	86961308	T	C	86961308	3	2	100	1	0	0	0	0	1	0	0	0	3459	1696	59	2	2109	2	CLCA1	1	86961308	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	31778960	86961308	162289313	11	13580										
ABCD3	5825	hgsc.bcm.edu	37	chr1	94965076	94965076	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gaaggaatacttagacaatgTccagttgggtcatatccttg	10	7	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:94965076T>C	ENST00000370214.4	+	20	1670	c.1646T>C	c.(1645-1647)gTc>gCc	p.V549A	ABCD3_ENST00000484213.1_3'UTR|ABCD3_ENST00000536817.1_Missense_Mutation_p.V476A|ABCD3_ENST00000394233.2_Missense_Mutation_p.V439A|ABCD3_ENST00000454898.2_Missense_Mutation_p.V573A	NM_002858.3	NP_002849.1	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D (ALD), member 3	549	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|fatty acid beta-oxidation (GO:0006635)|peroxisome organization (GO:0007031)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(2)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		TTAGACAATGTCCAGTTGGGT	0.373																																					p.V549A		Atlas-SNP	.											.	ABCD3	62	.	0			c.T1646C						.						147	125	132					1																	94965076		2203	4300	6503	SO:0001583	missense	5825	exon20			ACAATGTCCAGTT	M81182	CCDS749.1, CCDS44175.1	1p21.3	2012-05-16			ENSG00000117528	ENSG00000117528		"ATP binding cassette transporters / subfamily D"	67	protein-coding gene	gene with protein product		170995		PXMP1		1301993, 8449508	Standard	NM_002858		Approved	PMP70, ZWS2	uc001dqn.4	P28288	OTTHUMG00000010717	ENST00000370214.4:c.1646T>C	chr1.hg19:g.94965076T>C	ENSP00000359233:p.Val549Ala	132.0	0.0		87.0	4.0	NM_002858	D3DT46|Q15271|Q6NUN5|Q96DA3|Q9H529	Missense_Mutation	SNP	ENST00000370214.4	hg19	CCDS749.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.947829	0.92593	.	.	ENSG00000117528	ENST00000394233;ENST00000454898;ENST00000536817;ENST00000370214	D;D;D;D	0.94576	-3.46;-3.46;-3.46;-3.46	5.98	5.98	0.97165	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.94968	0.8372	L	0.38953	1.18	0.80722	D	1	D;D;D	0.89917	1.0;0.996;1.0	D;D;D	0.97110	1.0;0.987;1.0	D	0.96174	0.9125	10	0.87932	D	0	-15.1185	16.4578	0.84025	0.0:0.0:0.0:1.0	.	573;439;549	E7EUE1;P28288-2;P28288	.;.;ABCD3_HUMAN	A	439;573;476;549	ENSP00000377780:V439A;ENSP00000403357:V573A;ENSP00000440692:V476A;ENSP00000359233:V549A	ENSP00000359233:V549A	V	+	2	0	ABCD3	94737664	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.635000	0.83286	2.288000	0.76882	0.482000	0.46254	GTC	.	.		0.373	ABCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029597.1	NM_002858		C	94965076	T	C	94965076	3	2	100	1	0	0	0	0	1	0	0	0	62	1667	58	2	1755	2	ABCD3	1	94965076	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	8003768	94965076	154285545	12	13581										
ALG14	199857	hgsc.bcm.edu	37	chr1	95448789	95448789	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cgtagacaatgatcactttcTttattcctagtatcccaagg	6	10	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:95448789T>C	ENST00000370205.5	-	4	540	c.494A>G	c.(493-495)aAg>aGg	p.K165R		NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	165					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	6		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		GATCACTTTCTTTATTCCTAG	0.408																																					p.K165R		Atlas-SNP	.											.	ALG14	13	.	0			c.A494G						.						102	89	93					1																	95448789		2203	4300	6503	SO:0001583	missense	199857	exon4			ACTTTCTTTATTC		CCDS752.1	1p21.3	2013-02-21	2013-02-21		ENSG00000172339	ENSG00000172339			28287	protein-coding gene	gene with protein product		612866	"asparagine-linked glycosylation 14 homolog (yeast)", "asparagine-linked glycosylation 14 homolog (S. cerevisiae)"			15615718	Standard	NM_144988		Approved	MGC19780	uc001dra.2	Q96F25	OTTHUMG00000010781	ENST00000370205.5:c.494A>G	chr1.hg19:g.95448789T>C	ENSP00000359224:p.Lys165Arg	167.0	0.0		107.0	5.0	NM_144988	A8K030	Missense_Mutation	SNP	ENST00000370205.5	hg19	CCDS752.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.375919	0.61735	.	.	ENSG00000172339	ENST00000370205	T	0.44482	0.92	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.17874	0.0429	L	0.33485	1.01	0.58432	D	0.999999	B	0.28470	0.213	B	0.30401	0.115	T	0.06552	-1.0820	10	0.09084	T	0.74	-16.3264	16.2473	0.82450	0.0:0.0:0.0:1.0	.	165	Q96F25	ALG14_HUMAN	R	165	ENSP00000359224:K165R	ENSP00000359224:K165R	K	-	2	0	ALG14	95221377	1.000000	0.71417	0.996000	0.52242	0.999000	0.98932	5.790000	0.69038	2.238000	0.73509	0.533000	0.62120	AAG	.	.		0.408	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029699.2	NM_144988		C	95448789	T	C	95448789	3	2	100	1	0	0	0	0	1	0	0	0	516	1609	56	2	160	2	ALG14	1	95448789	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	483713	95448789	153801832	13	13582										
AHCYL1	10768	hgsc.bcm.edu	37	chr1	110559004	110559004	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agctgggaagctctgtgttcCggccatgaacgtcaatgatt	12	9	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:110559004C>T	ENST00000369799.5	+	8	1188	c.821C>T	c.(820-822)cCg>cTg	p.P274L	AHCYL1_ENST00000393614.4_Missense_Mutation_p.P227L|AHCYL1_ENST00000359172.3_Missense_Mutation_p.P227L	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	274					mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		CTCTGTGTTCCGGCCATGAAC	0.403																																					p.P274L		Atlas-SNP	.											.	AHCYL1	49	.	0			c.C821T						.						93	99	97					1																	110559004		2203	4300	6503	SO:0001583	missense	10768	exon8			GTGTTCCGGCCAT	U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"inositol 1,4,5-trisphosphate receptor-binding protein", "protein phosphatase 1, regulatory subunit 78"	607826	"S-adenosylhomocysteine hydrolase-like 1"			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.821C>T	chr1.hg19:g.110559004C>T	ENSP00000358814:p.Pro274Leu	160.0	0.0		95.0	4.0	NM_006621	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Missense_Mutation	SNP	ENST00000369799.5	hg19	CCDS818.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.733762	0.89482	.	.	ENSG00000168710	ENST00000369799;ENST00000359172;ENST00000393614	D;D;D	0.89746	-2.56;-2.56;-2.56	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.97256	0.9103	H	0.98996	4.395	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98336	1.0536	10	0.87932	D	0	-22.0931	20.1649	0.98147	0.0:1.0:0.0:0.0	.	274	O43865	SAHH2_HUMAN	L	274;227;227	ENSP00000358814:P274L;ENSP00000352092:P227L;ENSP00000377238:P227L	ENSP00000352092:P227L	P	+	2	0	AHCYL1	110360527	1.000000	0.71417	0.991000	0.47740	0.990000	0.78478	7.818000	0.86416	2.753000	0.94483	0.655000	0.94253	CCG	.	.		0.403	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1			T	110559004	C	T	110559004	3	4	100	1	0	0	0	0	1	0	0	0	410	652	23	1	851	1	AHCYL1	1	110559004	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	15110215	110559004	138691617	14	13583										
CEPT1	10390	hgsc.bcm.edu	37	chr1	111702071	111702071	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agtctttggatgctattgatGggaaacaggcaagaagaacc	12	6	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:111702071G>T	ENST00000545121.1	+	3	617	c.409G>T	c.(409-411)Ggg>Tgg	p.G137W	CEPT1_ENST00000357172.4_Missense_Mutation_p.G137W	NM_001007794.1	NP_001007795.1	Q9Y6K0	CEPT1_HUMAN	choline/ethanolamine phosphotransferase 1	137					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	diacylglycerol cholinephosphotransferase activity (GO:0004142)|ethanolaminephosphotransferase activity (GO:0004307)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	8		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)	TGCTATTGATGGGAAACAGGC	0.388																																					p.G137W		Atlas-SNP	.											.	CEPT1	25	.	0			c.G409T						.						170	171	170					1																	111702071		2203	4300	6503	SO:0001583	missense	10390	exon3			ATTGATGGGAAAC	AF068302	CCDS830.1	1p13	2010-07-08			ENSG00000134255	ENSG00000134255	2.7.8.1, 2.7.8.2		24289	protein-coding gene	gene with protein product						10191259, 12216837	Standard	XM_005270353		Approved		uc001eah.1	Q9Y6K0	OTTHUMG00000012357	ENST00000545121.1:c.409G>T	chr1.hg19:g.111702071G>T	ENSP00000441980:p.Gly137Trp	345.0	0.0		273.0	11.0	NM_006090	Q69YJ9|Q9P0Y8	Missense_Mutation	SNP	ENST00000545121.1	hg19	CCDS830.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516943	0.85495	.	.	ENSG00000134255	ENST00000545121;ENST00000357172	D;D	0.95342	-3.68;-3.68	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.98046	0.9356	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99257	1.0889	10	0.87932	D	0	-18.579	16.3671	0.83335	0.0:0.0:1.0:0.0	.	137;137	Q9Y6K0;B3KN25	CEPT1_HUMAN;.	W	137	ENSP00000441980:G137W;ENSP00000349696:G137W	ENSP00000349696:G137W	G	+	1	0	CEPT1	111503594	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.476000	0.97823	2.450000	0.82876	0.655000	0.94253	GGG	.	.		0.388	CEPT1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034462.2	NM_006090		T	111702071	G	T	111702071	3	4	100	1	0	0	0	0	1	0	0	0	3266	1348	47	3	415	3	CEPT1	1	111702071	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	1143067	111702071	137548550	15	13584										
CHD1L	9557	hgsc.bcm.edu	37	chr1	146731569	146731569	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctgctgcataagaccttgtcAgaggtaaacttacagtgtag	10	8	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:146731569A>G	ENST00000369258.4	+	6	593	c.573A>G	c.(571-573)tcA>tcG	p.S191S	CHD1L_ENST00000369259.3_Intron|CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000361293.5_5'UTR|CHD1L_ENST00000431239.1_Silent_p.S191S	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	191	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					AGACCTTGTCAGAGGTAAACT	0.353																																					p.S191S		Atlas-SNP	.											.	CHD1L	72	.	0			c.A573G						.						149	155	153					1																	146731569		2203	4300	6503	SO:0001819	synonymous_variant	9557	exon6			CTTGTCAGAGGTA	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.573A>G	chr1.hg19:g.146731569A>G		54.0	0.0		40.0	4.0	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Silent	SNP	ENST00000369258.4	hg19	CCDS927.1																																																																																			.	.		0.353	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		G	146731569	A	G	146731569	2	3	100	1	0	0	0	0	0	0	0	1	3326	175	7	2		2	CHD1L	1	146731569	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	35029498	146731569	102519052	16	13585										
PGLYRP4	57115	hgsc.bcm.edu	37	chr1	153317834	153317834	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cccatgccttgcgagagaccGtggtggagacatctgtggga	15	10	1	2	rs200715095		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:153317834G>A	ENST00000359650.5	-	4	228	c.164C>T	c.(163-165)aCg>aTg	p.T55M	PGLYRP4_ENST00000368739.3_Missense_Mutation_p.T51M|PGLYRP4_ENST00000490266.1_5'UTR	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	55					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.T55M(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCGAGAGACCGTGGTGGAGAC	0.587																																					p.T55M		Atlas-SNP	.											PGLYRP4,colon,carcinoma,-1,1	PGLYRP4	45	.	1	Substitution - Missense(1)	ovary(1)	c.C164T						.						127	98	108					1																	153317834		2203	4300	6503	SO:0001583	missense	57115	exon4			GAGACCGTGGTGG	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I beta precursor"	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.164C>T	chr1.hg19:g.153317834G>A	ENSP00000352672:p.Thr55Met	85.0	0.0		45.0	2.0	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	hg19	CCDS30871.1	.	.	.	.	.	.	.	.	.	.	G	0.539	-0.854573	0.02630	.	.	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.04603	3.61;3.59	3.2	-1.57	0.08506	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (2);	.	.	.	.	T	0.00468	0.0015	N	0.01576	-0.805	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.45848	-0.9233	9	0.24483	T	0.36	-17.5147	2.2658	0.04078	0.4913:0.0:0.2841:0.2246	.	51;55	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	M	51;55	ENSP00000357728:T51M;ENSP00000352672:T55M	ENSP00000352672:T55M	T	-	2	0	PGLYRP4	151584458	0.000000	0.05858	0.204000	0.23530	0.070000	0.16714	0.510000	0.22723	0.026000	0.15269	-0.657000	0.03884	ACG	.	.		0.587	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393		A	153317834	G	A	153317834	3	1	100	1	0	0	0	0	1	0	0	0	11805	1145	40	1	981	1	PGLYRP4	1	153317834	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	6586265	153317834	95932787	17	13586										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155307890	155307890	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttcttcttaccattttttccAgggattttttcaaggagatt	6	7	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:155307890A>G	ENST00000368346.3	-	27	9447	c.8808T>C	c.(8806-8808)ccT>ccC	p.P2936P	ASH1L_ENST00000392403.3_Silent_p.P2931P			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2936					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CATTTTTTCCAGGGATTTTTT	0.418																																					p.P2931P		Atlas-SNP	.											.	ASH1L	279	.	0			c.T8793C						.						90	84	86					1																	155307890		2203	4300	6503	SO:0001819	synonymous_variant	55870	exon27			TTTTCCAGGGATT	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.8808T>C	chr1.hg19:g.155307890A>G		146.0	0.0		75.0	4.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.		0.418	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		G	155307890	A	G	155307890	2	3	100	1	0	0	0	0	0	0	0	1	1041	175	7	2		2	ASH1L	1	155307890	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1990056	155307890	93942731	18	13587										
GPATCH4	54865	hgsc.bcm.edu	37	chr1	156565484	156565484	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgtagcttcttcctcctcttTctgcctccttttctttttct	3	14	5	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:156565484T>C	ENST00000438976.2	-	8	679	c.649A>G	c.(649-651)Aaa>Gaa	p.K217E	GPATCH4_ENST00000497287.1_5'UTR|GPATCH4_ENST00000368232.4_Missense_Mutation_p.K212E			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	212							poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(3)|stomach(1)	17	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TCCTCCTCTTTCTGCCTCCTT	0.498																																					p.K217E		Atlas-SNP	.											.	GPATCH4	34	.	0			c.A649G						.						161	150	154					1																	156565484		2203	4300	6503	SO:0001583	missense	54865	exon8			CCTCTTTCTGCCT	BC056904	CCDS1146.1, CCDS44245.1	1q22	2013-01-28		2006-12-13	ENSG00000160818	ENSG00000160818		"G patch domain containing"	25982	protein-coding gene	gene with protein product				GPATC4		12477932	Standard	NM_015590		Approved	FLJ20249, DKFZP434F1735	uc001fpl.3	Q5T3I0	OTTHUMG00000033203	ENST00000438976.2:c.649A>G	chr1.hg19:g.156565484T>C	ENSP00000396441:p.Lys217Glu	137.0	0.0		77.0	4.0	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Missense_Mutation	SNP	ENST00000438976.2	hg19	CCDS44245.1	.	.	.	.	.	.	.	.	.	.	T	8.561	0.877881	0.17395	.	.	ENSG00000160818	ENST00000368232;ENST00000368229;ENST00000438976;ENST00000415314	T;T;T	0.47177	0.85;0.85;0.85	5.8	2.25	0.28309	.	0.426017	0.24620	N	0.036961	T	0.13114	0.0318	N	0.19112	0.55	0.40805	D	0.983374	B;B	0.25521	0.128;0.049	B;B	0.20577	0.03;0.018	T	0.06338	-1.0832	10	0.66056	D	0.02	-24.1852	4.8958	0.13749	0.1271:0.2178:0.0:0.6551	.	217;212	E9PAV9;Q5T3I0	.;GPTC4_HUMAN	E	212;212;217;183	ENSP00000357215:K212E;ENSP00000396441:K217E;ENSP00000412620:K183E	ENSP00000357212:K212E	K	-	1	0	GPATCH4	154832108	0.000000	0.05858	0.961000	0.40146	0.274000	0.26718	0.097000	0.15168	0.137000	0.18759	-0.256000	0.11100	AAA	.	.		0.498	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725		C	156565484	T	C	156565484	3	2	100	1	0	0	0	0	1	0	0	0	6601	1792	62	2	482	2	GPATCH4	1	156565484	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1257594	156565484	92685137	19	13588										
ILDR2	387597	hgsc.bcm.edu	37	chr1	166891985	166891985	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttgcttctcatctgatggaaAgactggcggaaattgctgtc	11	8	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:166891985A>G	ENST00000271417.3	-	8	1111	c.1056T>C	c.(1054-1056)tcT>tcC	p.S352S	ILDR2_ENST00000528703.1_Silent_p.S293S|ILDR2_ENST00000525740.1_Silent_p.S225S|ILDR2_ENST00000469934.2_Silent_p.S352S|ILDR2_ENST00000526687.1_Silent_p.S244S|ILDR2_ENST00000529071.1_Silent_p.S333S|ILDR2_ENST00000529387.1_Intron	NM_199351.2	NP_955383.1	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor 2	352					cell differentiation (GO:0030154)|homeostasis of number of cells within a tissue (GO:0048873)|insulin secretion (GO:0030073)|pancreas development (GO:0031016)|response to glucose (GO:0009749)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(3)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	22						TCTGATGGAAAGACTGGCGGA	0.507																																					p.S352S		Atlas-SNP	.											.	ILDR2	79	.	0			c.T1056C						.						160	151	154					1																	166891985		2203	4300	6503	SO:0001819	synonymous_variant	387597	exon8			ATGGAAAGACTGG	AF503509	CCDS1256.1	1q24.1	2008-12-18	2008-12-18	2008-12-18	ENSG00000143195	ENSG00000143195			18131	protein-coding gene	gene with protein product	"LISCH-like"		"chromosome 1 open reading frame 32"	C1orf32			Standard	NM_199351		Approved		uc001gdx.2	Q71H61	OTTHUMG00000034320	ENST00000271417.3:c.1056T>C	chr1.hg19:g.166891985A>G		148.0	0.0		95.0	4.0	NM_199351		Silent	SNP	ENST00000271417.3	hg19	CCDS1256.1																																																																																			.	.		0.507	ILDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082880.2	NM_199351		G	166891985	A	G	166891985	2	3	100	1	0	0	0	0	0	0	0	1	7719	59	3	2		2	ILDR2	1	166891985	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	10326501	166891985	82358636	20	13589										
GPR161	23432	hgsc.bcm.edu	37	chr1	168066409	168066409	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccagatgtagacaagtgccaTcacagcccggttccctgtga	10	13	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:168066409T>C	ENST00000367838.1	-	5	749	c.436A>G	c.(436-438)Atg>Gtg	p.M146V	GPR161_ENST00000271357.5_Missense_Mutation_p.M146V|GPR161_ENST00000361697.2_Missense_Mutation_p.M146V|GPR161_ENST00000537209.1_Missense_Mutation_p.M166V|GPR161_ENST00000367835.1_Missense_Mutation_p.M146V|GPR161_ENST00000367836.1_Missense_Mutation_p.M14V|GPR161_ENST00000539777.1_Missense_Mutation_p.M68V|GPR161_ENST00000546300.1_Missense_Mutation_p.M32V	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	146					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					ACAAGTGCCATCACAGCCCGG	0.532																																					p.M166V		Atlas-SNP	.											.	GPR161	56	.	0			c.A496G						.						82	69	74					1																	168066409		2203	4300	6503	SO:0001583	missense	23432	exon4			GTGCCATCACAGC	AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"GPCR / Class A : Orphans"	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.436A>G	chr1.hg19:g.168066409T>C	ENSP00000356812:p.Met146Val	102.0	0.0		72.0	4.0	NM_001267609	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Missense_Mutation	SNP	ENST00000367838.1	hg19	CCDS1268.1	.	.	.	.	.	.	.	.	.	.	T	7.511	0.654590	0.14580	.	.	ENSG00000143147	ENST00000367838;ENST00000271357;ENST00000367836;ENST00000367835;ENST00000546300;ENST00000539777;ENST00000537209;ENST00000361697	T;T;T;T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37;-0.37;-0.37;-0.37	4.92	0.165	0.14995	GPCR, rhodopsin-like superfamily (1);	0.292632	0.37530	N	0.002045	T	0.14830	0.0358	N	0.03071	-0.42	0.28415	N	0.91801	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.002;0.001;0.001;0.0;0.0;0.001	T	0.10109	-1.0644	9	0.19147	T	0.46	-29.3646	6.4485	0.21890	0.0:0.2759:0.4948:0.2293	.	166;32;68;166;146;146	F5GXD6;B7Z5E8;F5H6J7;B7Z5Z6;Q8N6U8-2;Q8N6U8	.;.;.;.;.;GP161_HUMAN	V	146;146;14;146;32;68;166;146	ENSP00000356812:M146V;ENSP00000271357:M146V;ENSP00000356810:M14V;ENSP00000356809:M146V;ENSP00000444348:M32V;ENSP00000437576:M68V;ENSP00000441039:M166V;ENSP00000355194:M146V	ENSP00000271357:M146V	M	-	1	0	GPR161	166333033	0.188000	0.23250	0.710000	0.30468	0.960000	0.62799	0.109000	0.15417	0.210000	0.20664	0.459000	0.35465	ATG	.	.		0.532	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369		C	168066409	T	C	168066409	3	2	100	1	0	0	0	0	1	0	0	0	6673	1435	50	2	1169	2	GPR161	1	168066409	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1174424	168066409	81184212	21	13590										
CEP350	9857	hgsc.bcm.edu	37	chr1	180062484	180062484	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctctcagtcttgcagagataAgccacagccaatgaggagct	10	11	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:180062484A>G	ENST00000367607.3	+	34	7662	c.7244A>G	c.(7243-7245)aAg>aGg	p.K2415R	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	2415					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TGCAGAGATAAGCCACAGCCA	0.418																																					p.K2415R		Atlas-SNP	.											.	CEP350	418	.	0			c.A7244G						.						30	28	29					1																	180062484		2203	4300	6503	SO:0001583	missense	9857	exon34			GAGATAAGCCACA	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.7244A>G	chr1.hg19:g.180062484A>G	ENSP00000356579:p.Lys2415Arg	214.0	0.0		149.0	6.0	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	A	7.515	0.655519	0.14580	.	.	ENSG00000135837	ENST00000367607	T	0.57752	0.38	5.38	3.01	0.34805	.	0.304180	0.23105	N	0.051869	T	0.38108	0.1028	L	0.36672	1.1	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.20371	-1.0277	9	.	.	.	.	8.4496	0.32862	0.845:0.0:0.155:0.0	.	2415;2415	E7EU22;Q5VT06	.;CE350_HUMAN	R	2415	ENSP00000356579:K2415R	.	K	+	2	0	CEP350	178329107	1.000000	0.71417	0.712000	0.30502	0.761000	0.43186	2.011000	0.40922	0.341000	0.23771	0.528000	0.53228	AAG	.	.		0.418	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		G	180062484	A	G	180062484	3	3	100	1	0	0	0	0	1	0	0	0	3256	72	3	2	7374	2	CEP350	1	180062484	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	11996075	180062484	69188137	22	13591										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181759582	181759582	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atttgacattgcttttcaggAgtggccggagtggataccct	12	8	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:181759582A>G	ENST00000367573.2	+	44	5788	c.5788A>G	c.(5788-5790)Agt>Ggt	p.S1930G	CACNA1E_ENST00000367570.1_Splice_Site_p.S1930G|CACNA1E_ENST00000360108.3_Splice_Site_p.S1911G|CACNA1E_ENST00000526775.1_Splice_Site_p.S1911G|CACNA1E_ENST00000357570.5_Splice_Site_p.S1881G|CACNA1E_ENST00000358338.5_Splice_Site_p.S1862G|CACNA1E_ENST00000367567.4_Splice_Site_p.S1537G	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1930					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GCTTTTCAGGAGTGGCCGGAG	0.532																																					p.S1930G		Atlas-SNP	.											.	CACNA1E	778	.	0			c.A5788G						.						73	81	78					1																	181759582		1966	4148	6114	SO:0001630	splice_region_variant	777	exon44			TTCAGGAGTGGCC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5787-1A>G	chr1.hg19:g.181759582A>G		143.0	0.0		95.0	4.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.348531	0.41599	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96300	-3.92;-3.92;-3.94;-3.91;-3.97;-3.95;-3.94	5.54	4.4	0.53042	.	0.648009	0.17406	N	0.175366	D	0.91047	0.7183	N	0.19112	0.55	0.44852	D	0.997869	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	D	0.85512	0.1198	10	0.38643	T	0.18	.	8.6952	0.34291	0.9072:0.0:0.0928:0.0	.	1911;1930	Q15878-2;Q15878-3	.;.	G	1930;1911;1881;1862;1537;1911;1930	ENSP00000356542:S1930G;ENSP00000434814:S1911G;ENSP00000350183:S1881G;ENSP00000351101:S1862G;ENSP00000356539:S1537G;ENSP00000353222:S1911G;ENSP00000356545:S1930G	ENSP00000350183:S1881G	S	+	1	0	CACNA1E	180026205	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.239000	0.51360	0.919000	0.36945	0.533000	0.62120	AGT	.	.		0.532	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	Missense_Mutation	G	181759582	A	G	181759582	5	3	100	1	0	0	0	0	0	0	1	0	2544	318	11	2	5962	2	CACNA1E	1	181759582	Splice_Site	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1697098	181759582	67491039	23	13592										
KIF14	9928	hgsc.bcm.edu	37	chr1	200572973	200572973	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agcattccatttacctttagTcgatctccattagtgtgagc	7	10	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:200572973T>C	ENST00000367350.4	-	9	2295	c.1857A>G	c.(1855-1857)cgA>cgG	p.R619R		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	619	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						TTACCTTTAGTCGATCTCCAT	0.398																																					p.R619R		Atlas-SNP	.											.	KIF14	156	.	0			c.A1857G						.						117	106	110					1																	200572973		2203	4300	6503	SO:0001819	synonymous_variant	9928	exon9			CTTTAGTCGATCT	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.1857A>G	chr1.hg19:g.200572973T>C		148.0	0.0		94.0	4.0	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	hg19	CCDS30963.1																																																																																			.	.		0.398	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		C	200572973	T	C	200572973	2	2	100	1	0	0	0	0	0	0	0	1	8285	1654	58	2		2	KIF14	1	200572973	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	18813391	200572973	48677648	24	13593										
C1orf131	128061	hgsc.bcm.edu	37	chr1	231360124	231360124	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	acctgtccaatccgtccattTgacaaaatactgggagcgga	9	11	0	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:231360124T>C	ENST00000366649.2	-	7	808	c.783A>G	c.(781-783)tcA>tcG	p.S261S	C1orf131_ENST00000366651.3_Silent_p.S260S|C1orf131_ENST00000318906.2_3'UTR			Q8NDD1	CA131_HUMAN	chromosome 1 open reading frame 131	262							poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	8	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				TCCGTCCATTTGACAAAATAC	0.373																																					p.S261S		Atlas-SNP	.											.	C1orf131	30	.	0			c.A783G						.						78	77	77					1																	231360124		2203	4300	6503	SO:0001819	synonymous_variant	128061	exon7			TCCATTTGACAAA	BC062353	CCDS1591.2, CCDS73049.1	1q42.2	2012-06-27			ENSG00000143633	ENSG00000143633			25332	protein-coding gene	gene with protein product						12975309	Standard	XM_005273051		Approved	DKFZp547B1713	uc001hul.3	Q8NDD1	OTTHUMG00000038023	ENST00000366649.2:c.783A>G	chr1.hg19:g.231360124T>C		220.0	0.0		165.0	9.0	NM_152379	Q5TBI0|Q5TBI1|Q6P6B4|Q7Z6H5|Q8N432|Q96NM6	Silent	SNP	ENST00000366649.2	hg19	CCDS1591.2																																																																																			.	.		0.373	C1orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092864.1	NM_152379		C	231360124	T	C	231360124	2	2	100	1	0	0	0	0	0	0	0	1	2000	1799	63	2		2	C1orf131	1	231360124	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	30787151	231360124	17890497	25	13594										
C1orf57	84284	hgsc.bcm.edu	37	chr1	233105712	233105712	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tcatcgatgagattgggaagAtggagctcttcagtcagctt	12	7	4	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:233105712A>G	ENST00000366628.5	+	4	439	c.352A>G	c.(352-354)Atg>Gtg	p.M118V	NTPCR_ENST00000490098.1_3'UTR|NTPCR_ENST00000366627.4_Missense_Mutation_p.M118V	NM_032324.1	NP_115700.1	Q9BSD7	NTPCR_HUMAN	nucleoside-triphosphatase, cancer-related	118						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|nucleoside-triphosphatase activity (GO:0017111)|nucleotide phosphatase activity, acting on free nucleotides (GO:0098519)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(1)|ovary(1)	4						GATTGGGAAGATGGAGCTCTT	0.502																																					p.M118V		Atlas-SNP	.											.	NTPCR	15	.	0			c.A352G						.						150	132	138					1																	233105712		2203	4300	6503	SO:0001583	missense	84284	exon4			GGGAAGATGGAGC	BC005102	CCDS1597.1	1q42.2	2010-12-20	2010-12-20	2010-12-20	ENSG00000135778	ENSG00000135778	3.6.1.15		28204	protein-coding gene	gene with protein product	"human cancer-related NTPase"		"chromosome 1 open reading frame 57"	C1orf57		17291528	Standard	NM_032324		Approved	MGC13186, HCR-NTPase	uc001hvj.1	Q9BSD7	OTTHUMG00000037822	ENST00000366628.5:c.352A>G	chr1.hg19:g.233105712A>G	ENSP00000355587:p.Met118Val	130.0	0.0		73.0	4.0	NM_032324		Missense_Mutation	SNP	ENST00000366628.5	hg19	CCDS1597.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.385276	0.82792	.	.	ENSG00000135778	ENST00000366628;ENST00000366627	T;T	0.60171	0.21;0.21	4.59	4.59	0.56863	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.82724	0.5099	H	0.96080	3.765	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.81914	0.995;0.994	D	0.88473	0.3063	10	0.87932	D	0	5.5874	14.4307	0.67249	1.0:0.0:0.0:0.0	.	118;118	Q9BSD7;Q5TDF0	NTPCR_HUMAN;.	V	118	ENSP00000355587:M118V;ENSP00000355586:M118V	ENSP00000355586:M118V	M	+	1	0	NTPCR	231172335	1.000000	0.71417	0.989000	0.46669	0.988000	0.76386	9.136000	0.94489	2.055000	0.61198	0.533000	0.62120	ATG	.	.		0.502	NTPCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092324.2	NM_032324		G	233105712	A	G	233105712	3	3	100	1	0	0	0	0	1	0	0	0	2051	333	12	2	366	2	C1orf57	1	233105712	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1745588	233105712	16144909	26	13595										
RYR2	6262	hgsc.bcm.edu	37	chr1	237789001	237789001	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gggtctctggatggaaacagTgatttaacaattagagggcg	14	5	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:237789001T>C	ENST00000366574.2	+	40	6380	c.6063T>C	c.(6061-6063)agT>agC	p.S2021S	RYR2_ENST00000542537.1_Silent_p.S2005S|RYR2_ENST00000360064.6_Silent_p.S2019S	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2021	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATGGAAACAGTGATTTAACAA	0.378																																					p.S2021S		Atlas-SNP	.											.	RYR2	1273	.	0			c.T6063C						.						130	121	124					1																	237789001		1836	4091	5927	SO:0001819	synonymous_variant	6262	exon40			AAACAGTGATTTA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.6063T>C	chr1.hg19:g.237789001T>C		179.0	0.0		114.0	5.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.378	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237789001	T	C	237789001	2	2	100	1	0	0	0	0	0	0	0	1	13784	1693	59	2		2	RYR2	1	237789001	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	4683289	237789001	11461620	27	13596										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247588783	247588783	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtcatcgggtggagtcactgTccctggggtttctccataac	12	11	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr1:247588783T>C	ENST00000336119.3	+	3	2784	c.2038T>C	c.(2038-2040)Tcc>Ccc	p.S680P	NLRP3_ENST00000391828.3_Missense_Mutation_p.S680P|NLRP3_ENST00000391827.2_Missense_Mutation_p.S680P|NLRP3_ENST00000366497.2_Missense_Mutation_p.S680P|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000366496.2_Missense_Mutation_p.S680P|NLRP3_ENST00000348069.2_Missense_Mutation_p.S680P	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	680					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			GGAGTCACTGTCCCTGGGGTT	0.502																																					p.S680P		Atlas-SNP	.											.	NLRP3	286	.	0			c.T2038C						.						95	84	88					1																	247588783		2203	4300	6503	SO:0001583	missense	114548	exon3			TCACTGTCCCTGG	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.2038T>C	chr1.hg19:g.247588783T>C	ENSP00000337383:p.Ser680Pro	136.0	0.0		85.0	4.0	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	T	12.15	1.850912	0.32699	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	D;D;D;T;D;T	0.89343	-2.5;-2.5;-2.5;0.51;-2.5;0.51	3.96	3.96	0.45880	.	0.000000	0.48767	D	0.000177	D	0.92120	0.7502	M	0.72894	2.215	0.33278	D	0.561852	D;D;D;D;D	0.76494	0.987;0.999;0.998;0.958;0.979	P;D;D;P;P	0.71184	0.732;0.972;0.947;0.815;0.658	D	0.92446	0.5966	10	0.34782	T	0.22	.	9.5208	0.39133	0.0:0.0:0.0:1.0	.	680;680;680;680;680	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	P	680	ENSP00000375704:S680P;ENSP00000355453:S680P;ENSP00000337383:S680P;ENSP00000294752:S680P;ENSP00000355452:S680P;ENSP00000375703:S680P	ENSP00000337383:S680P	S	+	1	0	NLRP3	245655406	0.000000	0.05858	0.974000	0.42286	0.353000	0.29299	0.378000	0.20569	2.024000	0.59613	0.533000	0.62120	TCC	.	.		0.502	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		C	247588783	T	C	247588783	3	2	100	1	0	0	0	0	1	0	0	0	10487	1667	58	2	2048	2	NLRP3	1	247588783	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	9799782	247588783	1661838	28	13597										
MFSD2B	388931	hgsc.bcm.edu	37	chr2	24236185	24236185	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccggtcgcctctcattctgtAcaaaggtgtgctatggcatt	10	11	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:24236185A>G	ENST00000406420.3	+	2	143	c.127A>G	c.(127-129)Aca>Gca	p.T43A	MFSD2B_ENST00000338315.4_Missense_Mutation_p.T43A	NM_001080473.1	NP_001073942.1	A6NFX1	MFS2B_HUMAN	major facilitator superfamily domain containing 2B	43					transport (GO:0006810)	integral component of membrane (GO:0016021)				cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10						CTCATTCTGTACAAAGGTGTG	0.542																																					p.T43A		Atlas-SNP	.											.	MFSD2B	45	.	0			c.A127G						.						59	59	59					2																	24236185		1948	4148	6096	SO:0001583	missense	388931	exon2			TTCTGTACAAAGG		CCDS46228.1	2p23.3	2010-05-11			ENSG00000205639	ENSG00000205639			37207	protein-coding gene	gene with protein product						18694395	Standard	NM_001080473		Approved		uc002reo.2	A6NFX1	OTTHUMG00000090819	ENST00000406420.3:c.127A>G	chr2.hg19:g.24236185A>G	ENSP00000385527:p.Thr43Ala	75.0	0.0		41.0	4.0	NM_001080473	B5MC32	Missense_Mutation	SNP	ENST00000406420.3	hg19	CCDS46228.1	.	.	.	.	.	.	.	.	.	.	A	15.95	2.984662	0.53934	.	.	ENSG00000205639	ENST00000406420;ENST00000338315	T;T	0.18502	2.21;2.21	5.49	4.27	0.50696	Major facilitator superfamily domain, general substrate transporter (1);	0.466367	0.23137	U	0.051510	T	0.16171	0.0389	L	0.44542	1.39	0.31522	N	0.662257	B	0.28258	0.205	B	0.32393	0.145	T	0.06427	-1.0827	10	0.35671	T	0.21	-4.5516	10.6471	0.45626	0.8564:0.0:0.0:0.1436	.	43	A6NFX1	MFS2B_HUMAN	A	43	ENSP00000385527:T43A;ENSP00000342501:T43A	ENSP00000342501:T43A	T	+	1	0	MFSD2B	24089689	0.998000	0.40836	0.857000	0.33713	0.695000	0.40330	3.599000	0.54045	2.225000	0.72522	0.379000	0.24179	ACA	.	.		0.542	MFSD2B-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000324307.1	NM_001080473		G	24236185	A	G	24236185	3	3	100	1	0	0	0	0	1	0	0	0	9540	391	14	2	133	2	MFSD2B	2	24236185	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		24236185	218963188	29	13598										
ABHD1	84696	hgsc.bcm.edu	37	chr2	27351823	27351823	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccaaaaccagtgacatcctcCaaacaccagatggaggccag	8	14	0	2	rs370556895		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:27351823C>A	ENST00000316470.4	+	3	400	c.286C>A	c.(286-288)Caa>Aaa	p.Q96K		NM_032604.3	NP_115993	Q96SE0	ABHD1_HUMAN	abhydrolase domain containing 1	96						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			endometrium(1)|kidney(1)|lung(3)	5	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGACATCCTCCAAACACCAGA	0.517																																					p.Q96K		Atlas-SNP	.											.	ABHD1	18	.	0			c.C286A						.						85	84	84					2																	27351823		2203	4300	6503	SO:0001583	missense	84696	exon3			ATCCTCCAAACAC	AK093447	CCDS1736.1	2p23.3	2011-01-21			ENSG00000143994	ENSG00000143994		"Abhydrolase domain containing"	17553	protein-coding gene	gene with protein product		612195				11922611	Standard	NM_032604		Approved	LABH1, FLJ36128	uc002rit.3	Q96SE0	OTTHUMG00000097072	ENST00000316470.4:c.286C>A	chr2.hg19:g.27351823C>A	ENSP00000326491:p.Gln96Lys	103.0	0.0		71.0	8.0	NM_032604	B3KSF6|E9PDR9|Q05BY3|Q53SZ1|Q8IXQ7	Missense_Mutation	SNP	ENST00000316470.4	hg19	CCDS1736.1	.	.	.	.	.	.	.	.	.	.	C	0.681	-0.798159	0.02862	.	.	ENSG00000143994	ENST00000316470;ENST00000416071	T;T	0.41758	3.11;0.99	4.82	3.93	0.45458	.	0.644473	0.15463	N	0.261009	T	0.30510	0.0767	L	0.38175	1.15	0.28692	N	0.904561	B	0.09022	0.002	B	0.09377	0.004	T	0.19549	-1.0302	10	0.12766	T	0.61	8.6033	11.0174	0.47698	0.0:0.7959:0.2041:0.0	.	96	Q96SE0	ABHD1_HUMAN	K	96;33	ENSP00000326491:Q96K;ENSP00000397522:Q33K	ENSP00000326491:Q96K	Q	+	1	0	ABHD1	27205327	0.019000	0.18553	0.972000	0.41901	0.497000	0.33675	0.433000	0.21477	1.221000	0.43506	0.561000	0.74099	CAA	.	.		0.517	ABHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214188.1	NM_032604		A	27351823	C	A	27351823	3	1	100	1	0	0	0	0	1	0	0	0	73	595	21	3	296	3	ABHD1	2	27351823	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	3115638	27351823	215847550	30	13599										
PROKR1	10887	hgsc.bcm.edu	37	chr2	68873336	68873336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctactatgtggtgcgccagcTctcctgggagcacggccacg	13	14	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:68873336T>C	ENST00000303786.3	+	2	803	c.383T>C	c.(382-384)cTc>cCc	p.L128P	PROKR1_ENST00000394342.2_Missense_Mutation_p.L128P			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	128					negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			endometrium(3)|kidney(2)|large_intestine(14)|lung(9)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						GTGCGCCAGCTCTCCTGGGAG	0.582																																					p.L128P		Atlas-SNP	.											.	PROKR1	69	.	0			c.T383C						.						157	140	145					2																	68873336		2203	4300	6503	SO:0001583	missense	10887	exon1			GCCAGCTCTCCTG	AF506287	CCDS1889.1	2p14	2012-08-08	2006-02-15	2006-02-15	ENSG00000169618	ENSG00000169618		"GPCR / Class A : Prokineticin receptors"	4524	protein-coding gene	gene with protein product		607122	"G protein-coupled receptor 73"	GPR73		10760605	Standard	NM_138964		Approved	PKR1, ZAQ, GPR73a	uc010yqj.2	Q8TCW9	OTTHUMG00000129567	ENST00000303786.3:c.383T>C	chr2.hg19:g.68873336T>C	ENSP00000303775:p.Leu128Pro	230.0	0.0		119.0	5.0	NM_138964	A5JUU2|Q53QT9|Q8NFJ7	Missense_Mutation	SNP	ENST00000303786.3	hg19	CCDS1889.1	.	.	.	.	.	.	.	.	.	.	T	16.98	3.270980	0.59540	.	.	ENSG00000169618	ENST00000303786;ENST00000394342	T;T	0.71934	-0.61;-0.61	5.21	5.21	0.72293	GPCR, rhodopsin-like superfamily (1);	0.058640	0.64402	D	0.000001	T	0.76666	0.4019	L	0.42008	1.315	0.80722	D	1	D	0.69078	0.997	D	0.67725	0.953	T	0.74954	-0.3488	10	0.35671	T	0.21	.	13.3807	0.60766	0.0:0.0:0.0:1.0	.	128	Q8TCW9	PKR1_HUMAN	P	128	ENSP00000303775:L128P;ENSP00000377874:L128P	ENSP00000303775:L128P	L	+	2	0	PROKR1	68726840	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.753000	0.68736	2.330000	0.79161	0.528000	0.53228	CTC	.	.		0.582	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2			C	68873336	T	C	68873336	3	2	100	1	0	0	0	0	1	0	0	0	12564	1551	54	2	385	2	PROKR1	2	68873336	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	41521513	68873336	174326037	31	13600										
C2orf78	388960	hgsc.bcm.edu	37	chr2	74042293	74042293	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctccagaattctccaagtccTtcagtagcagaaatacccag	6	13	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:74042293T>C	ENST00000409561.1	+	3	1064	c.943T>C	c.(943-945)Ttc>Ctc	p.F315L		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	315										cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						CTCCAAGTCCTTCAGTAGCAG	0.463																																					p.F315L		Atlas-SNP	.											.	C2orf78	150	.	0			c.T943C						.						89	83	84					2																	74042293		1865	4106	5971	SO:0001583	missense	388960	exon3			AAGTCCTTCAGTA	AC092653, AC136006, AK125975	CCDS46338.1	2p13.2	2008-07-18			ENSG00000187833	ENSG00000187833			34349	protein-coding gene	gene with protein product							Standard	NM_001080474		Approved	FLJ43987, hCG1989538, COG5373	uc002sjr.1	A6NCI8	OTTHUMG00000152819	ENST00000409561.1:c.943T>C	chr2.hg19:g.74042293T>C	ENSP00000387124:p.Phe315Leu	141.0	0.0		86.0	4.0	NM_001080474		Missense_Mutation	SNP	ENST00000409561.1	hg19	CCDS46338.1	.	.	.	.	.	.	.	.	.	.	T	8.104	0.777320	0.16120	.	.	ENSG00000187833	ENST00000409561;ENST00000342345	.	.	.	5.47	4.28	0.50868	.	0.248011	0.28641	N	0.014623	T	0.25754	0.0627	N	0.14661	0.345	0.09310	N	1	B	0.19935	0.04	B	0.17722	0.019	T	0.17289	-1.0374	9	0.49607	T	0.09	-3.2008	9.6473	0.39875	0.0:0.0:0.1754:0.8246	.	315	A6NCI8	CB078_HUMAN	L	315	.	ENSP00000340692:F315L	F	+	1	0	C2orf78	73895801	0.090000	0.21635	0.003000	0.11579	0.009000	0.06853	0.306000	0.19279	0.979000	0.38497	0.528000	0.53228	TTC	.	.		0.463	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474		C	74042293	T	C	74042293	3	2	100	1	0	0	0	0	1	0	0	0	2197	1609	56	2	953	2	C2orf78	2	74042293	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	5168957	74042293	169157080	32	13601										
DQX1	165545	hgsc.bcm.edu	37	chr2	74751206	74751206	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tctctgggtatatgcacaatAggaggattgccccagaaagc	11	9	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:74751206A>G	ENST00000404568.3	-	4	879	c.660T>C	c.(658-660)ccT>ccC	p.P220P	DQX1_ENST00000495597.1_5'UTR|DQX1_ENST00000393951.2_Silent_p.P220P	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	220	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						TATGCACAATAGGAGGATTGC	0.562																																					p.P220P		Atlas-SNP	.											.	DQX1	95	.	0			c.T660C						.						79	79	79					2																	74751206		2203	4300	6503	SO:0001819	synonymous_variant	165545	exon4			CACAATAGGAGGA	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.660T>C	chr2.hg19:g.74751206A>G		166.0	0.0		81.0	4.0	NM_133637	Q6B017|Q8NAM8	Silent	SNP	ENST00000404568.3	hg19	CCDS1949.2																																																																																			.	.		0.562	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		G	74751206	A	G	74751206	2	3	100	1	0	0	0	0	0	0	0	1	4753	407	15	2		2	DQX1	2	74751206	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	708913	74751206	168448167	33	13602										
ZNF2	7549	hgsc.bcm.edu	37	chr2	95843262	95843262	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cgaagacgttgccgtggtttTcacagatgaagagtggagtc	14	7	1	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:95843262T>C	ENST00000340539.5	+	3	530	c.68T>C	c.(67-69)tTc>tCc	p.F23S	ZNF2_ENST00000453539.2_Missense_Mutation_p.F23S|ZNF2_ENST00000425369.1_5'UTR|ZNF2_ENST00000295210.6_Missense_Mutation_p.F23S|ZNF2_ENST00000398107.2_5'UTR	NM_021088.2	NP_066574	Q9BSG1	ZNF2_HUMAN	zinc finger protein 2	23	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	12		Ovarian(717;0.00768)		READ - Rectum adenocarcinoma(193;0.0222)		GCCGTGGTTTTCACAGATGAA	0.453																																					p.F23S		Atlas-SNP	.											.	ZNF2	21	.	0			c.T68C						.						167	164	165					2																	95843262		1998	4193	6191	SO:0001583	missense	7549	exon3			TGGTTTTCACAGA	X60152	CCDS42712.1, CCDS42713.1, CCDS62957.1	2q11.1	2013-09-24	2005-02-07		ENSG00000163067	ENSG00000275111		"Zinc fingers, C2H2-type", "-"	12991	protein-coding gene	gene with protein product		194500	"zinc finger protein 2 (A1-5)"			8183940, 1945843	Standard	NM_021088		Approved	A1-5, ZNF661, Zfp661	uc002suf.3	Q9BSG1	OTTHUMG00000155150	ENST00000340539.5:c.68T>C	chr2.hg19:g.95843262T>C	ENSP00000345392:p.Phe23Ser	153.0	0.0		80.0	5.0	NM_021088	A8MWV7|B4DIR4|Q4ZFY6|Q96G44|Q9UMC5	Missense_Mutation	SNP	ENST00000340539.5	hg19	CCDS42712.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.345149	0.82022	.	.	ENSG00000163067	ENST00000340539;ENST00000295210;ENST00000453539	T;T;T	0.14766	2.48;2.48;2.48	5.07	5.07	0.68467	Krueppel-associated box (4);	0.000000	0.49916	D	0.000135	T	0.50888	0.1642	H	0.97077	3.935	0.37024	D	0.896359	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.71649	-0.4529	10	0.87932	D	0	-18.5907	12.8268	0.57725	0.0:0.0:0.0:1.0	.	23;23	B4DIR4;Q9BSG1	.;ZNF2_HUMAN	S	23	ENSP00000345392:F23S;ENSP00000295210:F23S;ENSP00000411051:F23S	ENSP00000295210:F23S	F	+	2	0	ZNF2	95206989	1.000000	0.71417	0.993000	0.49108	0.921000	0.55340	4.955000	0.63638	2.120000	0.65058	0.496000	0.49642	TTC	.	.		0.453	ZNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338595.2	NM_021088		C	95843262	T	C	95843262	3	2	100	1	0	0	0	0	1	0	0	0	17775	1783	62	2	74	2	ZNF2	2	95843262	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	21092056	95843262	147356111	34	13603										
SNRNP200	23020	hgsc.bcm.edu	37	chr2	96949561	96949561	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgggtcctacctggatgtgcAgctccaaggggacgggacgc	16	11	0	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:96949561A>G	ENST00000323853.5	-	32	4651	c.4574T>C	c.(4573-4575)cTg>cCg	p.L1525P	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1525					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						CTGGATGTGCAGCTCCAAGGG	0.572																																					p.L1525P		Atlas-SNP	.											.	SNRNP200	195	.	0			c.T4574C						.						61	55	57					2																	96949561		2203	4300	6503	SO:0001583	missense	23020	exon32			ATGTGCAGCTCCA	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.4574T>C	chr2.hg19:g.96949561A>G	ENSP00000317123:p.Leu1525Pro	132.0	0.0		95.0	4.0	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	hg19	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.189244	0.78789	.	.	ENSG00000144028	ENST00000323853;ENST00000543553	D	0.92965	-3.14	4.69	4.69	0.59074	DEAD-like helicase (1);ATPase, AAA+ type, core (1);	0.000000	0.64402	D	0.000004	D	0.96244	0.8775	M	0.91818	3.245	0.80722	D	1	D;D	0.63880	0.993;0.989	D;P	0.63033	0.91;0.862	D	0.97012	0.9737	10	0.87932	D	0	-12.3455	13.5638	0.61806	1.0:0.0:0.0:0.0	.	1276;1525	A4FU77;O75643	.;U520_HUMAN	P	1525;108	ENSP00000317123:L1525P	ENSP00000317123:L1525P	L	-	2	0	SNRNP200	96313288	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.651000	0.91078	2.111000	0.64477	0.533000	0.62120	CTG	.	.		0.572	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		G	96949561	A	G	96949561	3	3	100	1	0	0	0	0	1	0	0	0	14867	188	7	2	1892	2	SNRNP200	2	96949561	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1106299	96949561	146249812	35	13604										
C2orf64	493753	hgsc.bcm.edu	37	chr2	99217252	99217252	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctctgaatcttgccctgttaTccaactgaaaataaatatac	4	10	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:99217252T>C	ENST00000328709.3	-	3	274	c.188A>G	c.(187-189)gAt>gGt	p.D63G	COA5_ENST00000483527.1_5'UTR	NM_001008215.2	NP_001008216.1	Q86WW8	COA5_HUMAN	cytochrome c oxidase assembly factor 5	63						mitochondrion (GO:0005739)											TGCCCTGTTATCCAACTGAAA	0.318																																					p.D63G		Atlas-SNP	.											.	.	.	.	0			c.A188G						.						89	79	82					2																	99217252		2200	4297	6497	SO:0001583	missense	493753	exon3			CTGTTATCCAACT		CCDS33257.1	2q11.2	2012-10-15	2012-10-15	2011-07-19	ENSG00000183513	ENSG00000183513		"Mitochondrial respiratory chain complex assembly factors"	33848	protein-coding gene	gene with protein product		613920	"chromosome 2 open reading frame 64"	C2orf64		21457908	Standard	NM_001008215		Approved	MGC52110, FLJ27524, Pet191	uc002syz.3	Q86WW8	OTTHUMG00000153101	ENST00000328709.3:c.188A>G	chr2.hg19:g.99217252T>C	ENSP00000330730:p.Asp63Gly	120.0	0.0		81.0	4.0	NM_001008215		Missense_Mutation	SNP	ENST00000328709.3	hg19	CCDS33257.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.868991	0.72065	.	.	ENSG00000183513	ENST00000328709	D	0.82803	-1.65	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	D	0.87124	0.6099	.	.	.	0.80722	D	1	P	0.43938	0.822	P	0.51055	0.657	D	0.88748	0.3248	9	0.87932	D	0	-15.5939	14.3354	0.66586	0.0:0.0:0.0:1.0	.	63	Q86WW8	COA5_HUMAN	G	63	ENSP00000330730:D63G	ENSP00000330730:D63G	D	-	2	0	COA5	98583684	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	5.629000	0.67798	2.173000	0.68751	0.533000	0.62120	GAT	.	.		0.318	COA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329529.2	NM_001008215		C	99217252	T	C	99217252	3	2	100	1	0	0	0	0	1	0	0	0	2185	1435	50	2	40	2	C2orf64	2	99217252	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2267691	99217252	143982121	36	13605										
ZSWIM2	151112	hgsc.bcm.edu	37	chr2	187693106	187693106	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tggtattttcccaaatgacaCagtgggtaaatcttgaagat	9	6	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:187693106C>A	ENST00000295131.2	-	9	1546	c.1507G>T	c.(1507-1509)Gtg>Ttg	p.V503L		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	503					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			CCAAATGACACAGTGGGTAAA	0.338																																					p.V503L		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.G1507T						.						63	63	63					2																	187693106		2203	4300	6503	SO:0001583	missense	151112	exon9			ATGACACAGTGGG	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1507G>T	chr2.hg19:g.187693106C>A	ENSP00000295131:p.Val503Leu	238.0	0.0		188.0	25.0	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	hg19	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	C	0.438	-0.900198	0.02472	.	.	ENSG00000163012	ENST00000295131	T	0.22336	1.96	5.6	-2.76	0.05896	.	1.923360	0.02246	N	0.066233	T	0.10895	0.0266	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.25222	-1.0138	10	0.31617	T	0.26	1.1578	6.8641	0.24084	0.1214:0.3205:0.0:0.5581	.	503	Q8NEG5	ZSWM2_HUMAN	L	503	ENSP00000295131:V503L	ENSP00000295131:V503L	V	-	1	0	ZSWIM2	187401351	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.799000	0.04560	-0.434000	0.07275	-0.907000	0.02831	GTG	.	.		0.338	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		A	187693106	C	A	187693106	3	1	100	1	0	0	0	0	1	0	0	0	18256	478	17	3	398	3	ZSWIM2	2	187693106	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	88475854	187693106	55506267	37	13606										
INHA	3623	hgsc.bcm.edu	37	chr2	220439447	220439447	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gaggacaagtcagctgccagAgggctggcccaggaggctga	17	10	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:220439447A>G	ENST00000243786.2	+	2	480	c.300A>G	c.(298-300)agA>agG	p.R100R	INHA_ENST00000489456.1_3'UTR|OBSL1_ENST00000491370.1_5'Flank	NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	100					cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|erythrocyte differentiation (GO:0030218)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|ovarian follicle development (GO:0001541)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|regulation of cell cycle (GO:0051726)|regulation of cell proliferation (GO:0042127)|response to external stimulus (GO:0009605)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|inhibin A complex (GO:0043512)|inhibin-betaglycan-ActRII complex (GO:0034673)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|receptor binding (GO:0005102)			large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10		Renal(207;0.0183)		Epithelial(149;4.58e-07)|all cancers(144;4.31e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CAGCTGCCAGAGGGCTGGCCC	0.622																																					p.R100R		Atlas-SNP	.											.	INHA	30	.	0			c.A300G						.						18	20	19					2																	220439447		2200	4299	6499	SO:0001819	synonymous_variant	3623	exon2			TGCCAGAGGGCTG		CCDS2444.1	2q35	2013-09-19			ENSG00000123999	ENSG00000123999			6065	protein-coding gene	gene with protein product		147380				3345731	Standard	NM_002191		Approved		uc002vmk.2	P05111	OTTHUMG00000059237	ENST00000243786.2:c.300A>G	chr2.hg19:g.220439447A>G		113.0	0.0		78.0	4.0	NM_002191	A8K8H5	Silent	SNP	ENST00000243786.2	hg19	CCDS2444.1																																																																																			.	.		0.622	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1			G	220439447	A	G	220439447	2	3	100	1	0	0	0	0	0	0	0	1	7749	301	11	2		2	INHA	2	220439447	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	32746341	220439447	22759926	38	13607										
PAX3	5077	hgsc.bcm.edu	37	chr2	223086014	223086014	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aaggtcggcatggcagtgggAgggaaccccccgggaatgag	18	9	0	1	rs199847426		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:223086014A>G	ENST00000350526.4	-	6	1021	c.885T>C	c.(883-885)ccT>ccC	p.P295P	PAX3_ENST00000392069.2_Silent_p.P295P|PAX3_ENST00000392070.2_Silent_p.P295P|PAX3_ENST00000409551.3_Silent_p.P294P|PAX3_ENST00000344493.4_Silent_p.P295P|PAX3_ENST00000464706.1_5'UTR|PAX3_ENST00000336840.6_Silent_p.P295P	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	295					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGGCAGTGGGAGGGAACCCCC	0.547			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.P295P		Atlas-SNP	.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	PAX3	106	.	0			c.T885C						.						172	179	177					2																	223086014		2203	4300	6503	SO:0001819	synonymous_variant	5077	exon6			AGTGGGAGGGAAC		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.885T>C	chr2.hg19:g.223086014A>G		127.0	0.0		110.0	7.0	NM_181457	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Silent	SNP	ENST00000350526.4	hg19	CCDS42826.1																																																																																			.	.		0.547	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			G	223086014	A	G	223086014	2	3	100	1	0	0	0	0	0	0	0	1	11489	291	11	2		2	PAX3	2	223086014	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	2646567	223086014	20113359	39	13608										
PID1	55022	hgsc.bcm.edu	37	chr2	229890580	229890580	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cgaagatgttggggctcacgTtgtggtcggcggtgcagtag	18	7	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:229890580T>C	ENST00000354069.6	-	3	551	c.521A>G	c.(520-522)aAc>aGc	p.N174S	PID1_ENST00000409462.1_Missense_Mutation_p.N92S|PID1_ENST00000392055.3_Missense_Mutation_p.N141S|PID1_ENST00000392054.3_Missense_Mutation_p.N172S|PID1_ENST00000482518.2_Intron			Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1	174	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to cytokine stimulus (GO:0071345)|cellular response to fatty acid (GO:0071398)|cellular response to interleukin-6 (GO:0071354)|cellular response to leptin stimulus (GO:0044320)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|mitochondrion morphogenesis (GO:0070584)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of mitochondrial DNA replication (GO:0090298)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of fat cell proliferation (GO:0070346)|positive regulation of gene expression (GO:0010628)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of mitochondrial fusion (GO:0010635)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(4)|endometrium(3)|large_intestine(5)|lung(8)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)		GGGGCTCACGTTGTGGTCGGC	0.587																																					p.N172S		Atlas-SNP	.											.	PID1	43	.	0			c.A515G						.						149	133	138					2																	229890580		2203	4300	6503	SO:0001583	missense	55022	exon4			CTCACGTTGTGGT	AK096636	CCDS2471.1, CCDS42830.1	2q36.3	2007-02-02			ENSG00000153823	ENSG00000153823			26084	protein-coding gene	gene with protein product		612930				17124247, 16815647, 15221005	Standard	NM_001100818		Approved	NYGGF4, FLJ20701	uc002vps.4	Q7Z2X4	OTTHUMG00000133191	ENST00000354069.6:c.521A>G	chr2.hg19:g.229890580T>C	ENSP00000283937:p.Asn174Ser	208.0	0.0		99.0	4.0	NM_017933	B3KU82|Q68CJ2|Q6ZUS3|Q8IXL0|Q9NWP6	Missense_Mutation	SNP	ENST00000354069.6	hg19		.	.	.	.	.	.	.	.	.	.	T	11.59	1.682572	0.29872	.	.	ENSG00000153823	ENST00000392054;ENST00000409462;ENST00000392055;ENST00000542363;ENST00000354069	.	.	.	5.85	4.72	0.59763	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.229457	0.52532	D	0.000073	T	0.38427	0.1040	N	0.14661	0.345	0.37010	D	0.895689	B;B;B;B	0.10296	0.0;0.0;0.003;0.003	B;B;B;B	0.10450	0.001;0.0;0.005;0.004	T	0.28933	-1.0028	8	.	.	.	-39.7963	12.161	0.54103	0.0:0.0:0.1601:0.8399	.	92;141;172;174	Q7Z2X4-3;Q7Z2X4-4;Q7Z2X4-2;Q7Z2X4	.;.;.;PCLI1_HUMAN	S	172;92;141;174;174	.	.	N	-	2	0	PID1	229598824	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	4.669000	0.61575	1.068000	0.40764	0.533000	0.62120	AAC	.	.		0.587	PID1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000331810.2	NM_017933		C	229890580	T	C	229890580	3	2	100	1	0	0	0	0	1	0	0	0	11891	1725	60	2	235	2	PID1	2	229890580	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	6804566	229890580	13308793	40	13609										
IQCA1	79781	hgsc.bcm.edu	37	chr2	237405864	237405864	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aatggaactccgtgagttccAgctccaccatctcgttcttc	7	14	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr2:237405864A>G	ENST00000409907.3	-	2	552	c.278T>C	c.(277-279)cTg>cCg	p.L93P	IQCA1_ENST00000309507.5_Missense_Mutation_p.L89P|IQCA1_ENST00000431676.2_Missense_Mutation_p.L93P	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	93							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						CGTGAGTTCCAGCTCCACCAT	0.493																																					p.L100P		Atlas-SNP	.											.	IQCA1	170	.	0			c.T299C						.						43	43	43					2																	237405864		1953	4141	6094	SO:0001583	missense	79781	exon2			AGTTCCAGCTCCA	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"ATPases / AAA-type"	26195	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 11"		"IQ motif containing with AAA domain"	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.278T>C	chr2.hg19:g.237405864A>G	ENSP00000387347:p.Leu93Pro	159.0	0.0		104.0	5.0	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	hg19	CCDS46549.1	.	.	.	.	.	.	.	.	.	.	A	14.88	2.667448	0.47677	.	.	ENSG00000132321	ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437	D;D;D	0.95069	-3.46;-3.47;-3.6	5.51	5.51	0.81932	.	0.000000	0.47852	D	0.000217	D	0.97105	0.9054	M	0.83953	2.67	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.997	D;D;D	0.68943	0.947;0.961;0.947	D	0.97337	0.9954	10	0.52906	T	0.07	.	15.6604	0.77182	1.0:0.0:0.0:0.0	.	93;100;93	E7EWQ0;E9PH78;Q86XH1	.;.;IQCA1_HUMAN	P	93;100;89;93;89	ENSP00000387347:L93P;ENSP00000311951:L89P;ENSP00000407213:L93P	ENSP00000254653:L93P	L	-	2	0	IQCA1	237070603	0.993000	0.37304	0.867000	0.34043	0.375000	0.29983	3.832000	0.55783	2.095000	0.63458	0.528000	0.53228	CTG	.	.		0.493	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		G	237405864	A	G	237405864	3	3	100	1	0	0	0	0	1	0	0	0	7811	188	7	2	2262	2	IQCA1	2	237405864	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	7515284	237405864	5793509	41	13610										
THUMPD3	25917	hgsc.bcm.edu	37	chr3	9425958	9425958	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cctacgggagatgagccgtgTctgcacacctaccacaggcc	11	15	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:9425958T>C	ENST00000345094.3	+	9	1632	c.1298T>C	c.(1297-1299)gTc>gCc	p.V433A	SETD5-AS1_ENST00000520629.1_RNA|SETD5-AS1_ENST00000468186.1_RNA|SETD5-AS1_ENST00000521609.1_RNA|THUMPD3_ENST00000515662.2_Missense_Mutation_p.V433A|SETD5-AS1_ENST00000523354.1_RNA|SETD5-AS1_ENST00000519043.1_RNA|THUMPD3_ENST00000452837.2_Missense_Mutation_p.V433A	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	433						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		ATGAGCCGTGTCTGCACACCT	0.458																																					p.V433A		Atlas-SNP	.											.	THUMPD3	46	.	0			c.T1298C						.						195	201	199					3																	9425958		2203	4300	6503	SO:0001583	missense	25917	exon9			GCCGTGTCTGCAC	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.1298T>C	chr3.hg19:g.9425958T>C	ENSP00000339532:p.Val433Ala	145.0	0.0		82.0	4.0	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Missense_Mutation	SNP	ENST00000345094.3	hg19	CCDS2573.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.506860	0.85282	.	.	ENSG00000134077	ENST00000452837;ENST00000345094;ENST00000515662	T;T;T	0.34072	1.38;1.38;1.38	5.66	5.66	0.87406	Putative RNA methylase (1);	0.107605	0.64402	D	0.000007	T	0.64929	0.2643	M	0.86573	2.825	0.58432	D	0.999994	D	0.65815	0.995	D	0.68765	0.96	T	0.71718	-0.4508	10	0.72032	D	0.01	-8.377	15.5607	0.76244	0.0:0.0:0.0:1.0	.	433	Q9BV44	THUM3_HUMAN	A	433	ENSP00000395893:V433A;ENSP00000339532:V433A;ENSP00000424064:V433A	ENSP00000339532:V433A	V	+	2	0	THUMPD3	9400958	1.000000	0.71417	0.961000	0.40146	0.690000	0.40134	7.856000	0.86956	2.175000	0.68902	0.528000	0.53228	GTC	.	.		0.458	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453		C	9425958	T	C	9425958	3	2	100	1	0	0	0	0	1	0	0	0	15899	1667	58	2	1328	2	THUMPD3	3	9425958	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10		9425958	188596472	42	13611										
SLC6A1	6529	hgsc.bcm.edu	37	chr3	11072874	11072874	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atcttgcaggggggtatttaTgtcttcaaactctttgacta	9	7	4	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:11072874T>C	ENST00000287766.4	+	13	1756	c.1335T>C	c.(1333-1335)taT>taC	p.Y445Y	SLC6A1_ENST00000536032.1_Silent_p.Y267Y	NM_003042.3	NP_003033.3	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 1	445					gamma-aminobutyric acid import (GO:0051939)|learning (GO:0007612)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neurotransmitter secretion (GO:0007269)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|protein homooligomerization (GO:0051260)|response to calcium ion (GO:0051592)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to lead ion (GO:0010288)|response to purine-containing compound (GO:0014074)|response to sucrose (GO:0009744)|response to toxic substance (GO:0009636)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	26		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Clobazam(DB00349)|Tiagabine(DB00906)	GGGGTATTTATGTCTTCAAAC	0.493																																					p.Y445Y		Atlas-SNP	.											.	SLC6A1	88	.	0			c.T1335C						.						272	252	259					3																	11072874		2203	4300	6503	SO:0001819	synonymous_variant	6529	exon13			TATTTATGTCTTC		CCDS2603.1	3p25.3	2013-07-19	2013-07-19		ENSG00000157103	ENSG00000157103		"Solute carriers"	11042	protein-coding gene	gene with protein product	"GABA transporter 1"	137165	"solute carrier family 6 (neurotransmitter transporter, GABA), member 1"			8530094	Standard	NM_003042		Approved	GAT1, GABATR, GABATHG	uc010hdq.3	P30531	OTTHUMG00000044208	ENST00000287766.4:c.1335T>C	chr3.hg19:g.11072874T>C		144.0	0.0		92.0	5.0	NM_003042	Q8N4K8	Silent	SNP	ENST00000287766.4	hg19	CCDS2603.1																																																																																			.	.		0.493	SLC6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102767.2	NM_003042		C	11072874	T	C	11072874	2	2	100	1	0	0	0	0	0	0	0	1	14688	1471	51	2		2	SLC6A1	3	11072874	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1646916	11072874	186949556	43	13612										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266610	41266610	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	acagatgctgaaacatgcagTtgtaaacttgattaactatc	7	7	0	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:41266610T>C	ENST00000349496.5	+	4	687	c.407T>C	c.(406-408)gTt>gCt	p.V136A	CTNNB1_ENST00000396185.3_Missense_Mutation_p.V136A|CTNNB1_ENST00000453024.1_Missense_Mutation_p.V129A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.V136A|CTNNB1_ENST00000405570.1_Missense_Mutation_p.V136A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	136					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_Q143del(7)|p.W25_I140del(3)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.M5_N141>D(2)|p.M1_V173del(1)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.I35_K170del(1)|p.E15_I140>V(1)|p.A20_N141del(1)|p.D11_Y142>H(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		AAACATGCAGTTGTAAACTTG	0.448		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.V136A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	23	Deletion - In frame(16)|Complex - deletion inframe(7)	liver(22)|skin(1)	c.T407C						.						147	128	134					3																	41266610		2203	4300	6503	SO:0001583	missense	1499	exon4	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ATGCAGTTGTAAA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.407T>C	chr3.hg19:g.41266610T>C	ENSP00000344456:p.Val136Ala	77.0	0.0		69.0	12.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.766195	0.69878	.	.	ENSG00000168036	ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T;T	0.66638	-0.22;0.96;-0.22;-0.22;-0.22;-0.22	5.4	5.4	0.78164	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.70919	0.3279	L	0.58810	1.83	0.80722	D	1	B;B	0.32425	0.171;0.371	B;P	0.44447	0.202;0.45	T	0.67086	-0.5759	10	0.24483	T	0.36	-2.7182	15.7251	0.77751	0.0:0.0:0.0:1.0	.	64;136	B4DSW9;P35222	.;CTNB1_HUMAN	A	136;136;136;136;129;136	ENSP00000385604:V136A;ENSP00000412219:V136A;ENSP00000379486:V136A;ENSP00000344456:V136A;ENSP00000411226:V129A;ENSP00000379488:V136A	ENSP00000344456:V136A	V	+	2	0	CTNNB1	41241614	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.997000	0.88414	2.175000	0.68902	0.533000	0.62120	GTT	.	.		0.448	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266610	T	C	41266610	3	2	100	1	0	0	0	0	1	0	0	0	4018	1725	60	2	417	2	CTNNB1	3	41266610	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	30193736	41266610	156755820	44	13613										
SACM1L	22908	hgsc.bcm.edu	37	chr3	45744960	45744960	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cctgaaaaattttatgtggaAgcttgtgatgatggagcaga	12	4	0	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:45744960A>G	ENST00000389061.5	+	2	267	c.63A>G	c.(61-63)gaA>gaG	p.E21E	SACM1L_ENST00000541314.1_Missense_Mutation_p.K3R|SACM1L_ENST00000418611.1_5'UTR|SACM1L_ENST00000464524.1_3'UTR	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	21					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		TTTATGTGGAAGCTTGTGATG	0.358																																					p.E21E		Atlas-SNP	.											.	SACM1L	38	.	0			c.A63G						.						127	125	125					3																	45744960		2203	4300	6503	SO:0001819	synonymous_variant	22908	exon2			TGTGGAAGCTTGT	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.63A>G	chr3.hg19:g.45744960A>G		137.0	0.0		81.0	4.0	NM_014016	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Silent	SNP	ENST00000389061.5	hg19	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	A	16.66	3.185734	0.57909	.	.	ENSG00000211456	ENST00000438671;ENST00000541314	T	0.44881	0.91	5.33	2.5	0.30297	.	.	.	.	.	T	0.46776	0.1410	.	.	.	0.21740	N	0.99956	.	.	.	.	.	.	T	0.40534	-0.9558	6	0.87932	D	0	-14.8707	10.7129	0.45995	0.8459:0.0:0.1541:0.0	.	.	.	.	R	3	ENSP00000443373:K3R	ENSP00000411966:K3R	K	+	2	0	SACM1L	45719964	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.370000	0.44240	0.817000	0.34445	0.482000	0.46254	AAG	.	.		0.358	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016		G	45744960	A	G	45744960	2	3	100	1	0	0	0	0	0	0	0	1	13818	69	3	2		2	SACM1L	3	45744960	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	4478350	45744960	152277470	45	13614										
APEH	327	hgsc.bcm.edu	37	chr3	49712710	49712710	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gactcagtggtgtttgcaggAcctgcaggcaacagtgtgga	15	8	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:49712710A>G	ENST00000296456.5	+	3	640	c.240A>G	c.(238-240)ggA>ggG	p.G80G	APEH_ENST00000438011.1_Silent_p.G80G	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	80					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TGTTTGCAGGACCTGCAGGCA	0.567																																					p.G80G		Atlas-SNP	.											.	APEH	45	.	0			c.A240G						.						97	83	88					3																	49712710		2203	4300	6503	SO:0001819	synonymous_variant	327	exon3			TGCAGGACCTGCA	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.240A>G	chr3.hg19:g.49712710A>G		129.0	0.0		71.0	4.0	NM_001640	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	hg19	CCDS2801.1																																																																																			.	.		0.567	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			G	49712710	A	G	49712710	2	3	100	1	0	0	0	0	0	0	0	1	768	262	10	2		2	APEH	3	49712710	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	3967750	49712710	148309720	46	13615										
ARF4	378	hgsc.bcm.edu	37	chr3	57563094	57563094	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	attctttcacgatcgttgctAtctaccacaaaaataagacc	4	11	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:57563094A>G	ENST00000303436.6	-	4	546	c.279T>C	c.(277-279)gaT>gaC	p.D93D	ARF4_ENST00000496292.1_Silent_p.D66D|ARF4_ENST00000489843.1_5'UTR	NM_001660.3	NP_001651.1	P18085	ARF4_HUMAN	ADP-ribosylation factor 4	93					activation of phospholipase D activity (GO:0031584)|brain development (GO:0007420)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein transport (GO:0015031)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to axon injury (GO:0048678)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	epidermal growth factor receptor binding (GO:0005154)|GTP binding (GO:0005525)			large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0449)|Kidney(284;0.0561)		GATCGTTGCTATCTACCACAA	0.353																																					p.D93D		Atlas-SNP	.											.	ARF4	14	.	0			c.T279C						.						114	129	124					3																	57563094		2203	4300	6503	SO:0001819	synonymous_variant	378	exon4			GTTGCTATCTACC	M36341	CCDS2884.1	3p21.2-p21.1	2007-03-19			ENSG00000168374	ENSG00000168374		"ADP-ribosylation factors"	655	protein-coding gene	gene with protein product		601177	"ADP-ribosylation factor 2"	ARF2		2107548	Standard	NM_001660		Approved		uc003dix.4	P18085	OTTHUMG00000158601	ENST00000303436.6:c.279T>C	chr3.hg19:g.57563094A>G		175.0	0.0		90.0	4.0	NM_001660	B2R7J7|P21371	Silent	SNP	ENST00000303436.6	hg19	CCDS2884.1																																																																																			.	.		0.353	ARF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351443.1	NM_001660		G	57563094	A	G	57563094	2	3	100	1	0	0	0	0	0	0	0	1	846	446	16	2		2	ARF4	3	57563094	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	7850384	57563094	140459336	47	13616										
PTPRG	5793	hgsc.bcm.edu	37	chr3	62278152	62278152	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	taccaccctgtcccagcaacTggagaatgaaaatgctgtgg	10	11	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:62278152T>C	ENST00000474889.1	+	29	4489	c.4112T>C	c.(4111-4113)cTg>cCg	p.L1371P	PTPRG-AS1_ENST00000466893.1_RNA|PTPRG-AS1_ENST00000498655.1_RNA|PTPRG-AS1_ENST00000474795.1_RNA|PTPRG-AS1_ENST00000479018.1_RNA|PTPRG-AS1_ENST00000495542.1_RNA|PTPRG_ENST00000295874.10_Missense_Mutation_p.L1342P|PTPRG-AS1_ENST00000462497.1_RNA|PTPRG-AS1_ENST00000490916.1_RNA|PTPRG-AS1_ENST00000475371.1_RNA	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	1371	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TCCCAGCAACTGGAGAATGAA	0.418																																					p.L1371P		Atlas-SNP	.											.	PTPRG	153	.	0			c.T4112C						.						143	140	141					3																	62278152		2203	4300	6503	SO:0001583	missense	5793	exon29			AGCAACTGGAGAA	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.4112T>C	chr3.hg19:g.62278152T>C	ENSP00000418112:p.Leu1371Pro	121.0	0.0		75.0	4.0	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	hg19	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.160427	0.78226	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	D;D	0.85955	-2.05;-2.05	4.76	4.76	0.60689	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.64402	D	0.000001	D	0.94430	0.8208	H	0.95645	3.7	0.80722	D	1	D;D;D	0.89917	0.998;0.999;1.0	D;D;D	0.91635	0.967;0.995;0.999	D	0.95937	0.8943	10	0.87932	D	0	.	14.4326	0.67261	0.0:0.0:0.0:1.0	.	617;1342;1371	B7Z3T1;P23470-2;P23470	.;.;PTPRG_HUMAN	P	1371;1342	ENSP00000418112:L1371P;ENSP00000295874:L1342P	ENSP00000295874:L1342P	L	+	2	0	PTPRG	62253192	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.868000	0.87116	2.006000	0.58801	0.477000	0.44152	CTG	.	.		0.418	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		C	62278152	T	C	62278152	3	2	100	1	0	0	0	0	1	0	0	0	12817	1580	55	2	4226	2	PTPRG	3	62278152	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	4715058	62278152	135744278	48	13617										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89499441	89499441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	acaggaacaacagacccaagTttgagcagattgttagtatt	9	7	0	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:89499441T>C	ENST00000336596.2	+	15	2836	c.2611T>C	c.(2611-2613)Ttt>Ctt	p.F871L	EPHA3_ENST00000494014.1_Missense_Mutation_p.F871L	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	871	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.F871V(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CAGACCCAAGTTTGAGCAGAT	0.512										TSP Lung(6;0.00050)																											p.F871L		Atlas-SNP	.											EPHA3,NS,carcinoma,0,1	EPHA3	501	.	1	Substitution - Missense(1)	ovary(1)	c.T2611C						.						94	83	87					3																	89499441		2203	4300	6503	SO:0001583	missense	2042	exon15			CCCAAGTTTGAGC	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2611T>C	chr3.hg19:g.89499441T>C	ENSP00000337451:p.Phe871Leu	218.0	1.0		104.0	5.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	T	32	5.115970	0.94339	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	D;D	0.87103	-2.21;-2.21	5.66	5.66	0.87406	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94112	0.8112	M	0.87617	2.895	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.94720	0.7900	9	.	.	.	.	15.9043	0.79412	0.0:0.0:0.0:1.0	.	871	P29320	EPHA3_HUMAN	L	871	ENSP00000337451:F871L;ENSP00000419190:F871L	.	F	+	1	0	EPHA3	89582131	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	8.040000	0.89188	2.160000	0.67779	0.528000	0.53228	TTT	.	.		0.512	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		C	89499441	T	C	89499441	3	2	100	1	0	0	0	0	1	0	0	0	5170	1725	60	2	2695	2	EPHA3	3	89499441	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	27221289	89499441	108522989	49	13618										
CEP97	79598	hgsc.bcm.edu	37	chr3	101445525	101445525	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tattcacactttgattctggAtaaaaatcagattattaaat	4	5	3	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:101445525A>G	ENST00000341893.3	+	2	883	c.131A>G	c.(130-132)gAt>gGt	p.D44G	CEP97_ENST00000494050.1_Missense_Mutation_p.D44G|CEP97_ENST00000327230.4_Missense_Mutation_p.D44G			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	44					cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						TTGATTCTGGATAAAAATCAG	0.348																																					p.D44G		Atlas-SNP	.											.	CEP97	122	.	0			c.A131G						.						65	68	67					3																	101445525		2203	4300	6503	SO:0001583	missense	79598	exon2			TTCTGGATAAAAA	AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504			26244	protein-coding gene	gene with protein product		615864	"leucine-rich repeats and IQ motif containing 2"	LRRIQ2		17719545, 18068367	Standard	NM_024548		Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.131A>G	chr3.hg19:g.101445525A>G	ENSP00000342510:p.Asp44Gly	95.0	0.0		73.0	4.0	NM_024548	B5MDY8|Q8NA71|Q9H5T9	Missense_Mutation	SNP	ENST00000341893.3	hg19	CCDS2944.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.195015	0.78902	.	.	ENSG00000182504	ENST00000341893;ENST00000327230;ENST00000494050	T;T;T	0.24350	1.86;1.86;2.26	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.38295	0.1035	N	0.25992	0.78	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.992;0.996;0.987	T	0.31503	-0.9941	10	0.72032	D	0.01	-20.1694	14.7073	0.69200	1.0:0.0:0.0:0.0	.	44;44;44	E9PG22;Q8IW35-2;Q8IW35	.;.;CEP97_HUMAN	G	44	ENSP00000342510:D44G;ENSP00000325881:D44G;ENSP00000418185:D44G	ENSP00000325881:D44G	D	+	2	0	CEP97	102928215	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.056000	0.89455	1.928000	0.55862	0.533000	0.62120	GAT	.	.		0.348	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548		G	101445525	A	G	101445525	3	3	100	1	0	0	0	0	1	0	0	0	3265	333	12	2	137	2	CEP97	3	101445525	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	11946084	101445525	96576905	50	13619										
PARP9	83666	hgsc.bcm.edu	37	chr3	122274538	122274538	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atccaccgaggcccaacagcAtggatgatctgtttgcaggg	12	11	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:122274538A>G	ENST00000360356.2	-	4	812	c.585T>C	c.(583-585)caT>caC	p.H195H	PARP9_ENST00000462315.1_Silent_p.H160H|PARP9_ENST00000492382.1_Intron|PARP9_ENST00000471785.1_Silent_p.H160H|PARP9_ENST00000477522.2_Silent_p.H160H	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	195	Macro 1. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		GCCCAACAGCATGGATGATCT	0.458																																					p.H195H		Atlas-SNP	.											.	PARP9	72	.	0			c.T585C						.						65	61	62					3																	122274538		2203	4300	6503	SO:0001819	synonymous_variant	83666	exon4			AACAGCATGGATG	AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"Poly (ADP-ribose) polymerases"	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.585T>C	chr3.hg19:g.122274538A>G		125.0	0.0		84.0	4.0	NM_031458	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Silent	SNP	ENST00000360356.2	hg19	CCDS3014.1																																																																																			.	.		0.458	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		G	122274538	A	G	122274538	2	3	100	1	0	0	0	0	0	0	0	1	11475	214	8	2		2	PARP9	3	122274538	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	20829013	122274538	75747892	51	13620										
TMCC1	23023	hgsc.bcm.edu	37	chr3	129370465	129370465	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agggggaccacacagttggcTacagtggagacaaagaccaa	13	9	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:129370465T>C	ENST00000393238.3	-	6	2161	c.1821A>G	c.(1819-1821)gtA>gtG	p.V607V	TMCC1_ENST00000426664.2_Silent_p.V493V|TMCC1_ENST00000432054.2_Silent_p.V283V|TMCC1_ENST00000329333.5_Silent_p.V428V	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	607						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						CACAGTTGGCTACAGTGGAGA	0.522																																					p.V607V		Atlas-SNP	.											.	TMCC1	105	.	0			c.A1821G						.						162	143	150					3																	129370465		2203	4300	6503	SO:0001819	synonymous_variant	23023	exon6			GTTGGCTACAGTG	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.1821A>G	chr3.hg19:g.129370465T>C		197.0	0.0		97.0	4.0	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Silent	SNP	ENST00000393238.3	hg19	CCDS33855.1																																																																																			.	.		0.522	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		C	129370465	T	C	129370465	2	2	100	1	0	0	0	0	0	0	0	1	16007	1509	53	2		2	TMCC1	3	129370465	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	7095927	129370465	68651965	52	13621										
TMCC1	23023	hgsc.bcm.edu	37	chr3	129546875	129546875	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tatgcaagcttgtccctctcTtcatcttgggtggcactcga	9	12	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:129546875T>C	ENST00000393238.3	-	3	687	c.347A>G	c.(346-348)aAg>aGg	p.K116R	TMCC1_ENST00000426664.2_Missense_Mutation_p.K2R	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	116						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						TGTCCCTCTCTTCATCTTGGG	0.552																																					p.K116R		Atlas-SNP	.											.	TMCC1	105	.	0			c.A347G						.						95	89	91					3																	129546875		2203	4300	6503	SO:0001583	missense	23023	exon3			CCTCTCTTCATCT	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.347A>G	chr3.hg19:g.129546875T>C	ENSP00000376930:p.Lys116Arg	144.0	0.0		77.0	4.0	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Missense_Mutation	SNP	ENST00000393238.3	hg19	CCDS33855.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.620336	0.87460	.	.	ENSG00000172765	ENST00000393238;ENST00000426664;ENST00000505616;ENST00000513411	T;T;T	0.61274	0.66;0.9;0.12	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.73140	0.3549	L	0.61218	1.895	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.75202	-0.3401	10	0.62326	D	0.03	-25.8093	16.2237	0.82280	0.0:0.0:0.0:1.0	.	116	O94876	TMCC1_HUMAN	R	116;2;2;2	ENSP00000376930:K116R;ENSP00000389892:K2R;ENSP00000422544:K2R	ENSP00000376930:K116R	K	-	2	0	TMCC1	131029565	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.610000	0.82949	2.289000	0.77006	0.482000	0.46254	AAG	.	.		0.552	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		C	129546875	T	C	129546875	3	2	100	1	0	0	0	0	1	0	0	0	16007	1609	56	2	1630	2	TMCC1	3	129546875	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	176410	129546875	68475555	53	13622										
ASTE1	28990	hgsc.bcm.edu	37	chr3	130733158	130733158	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cttagcctcaggacatatgcTcaggagactttctacagagg	10	10	3	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:130733158T>C	ENST00000264992.3	-	6	2224	c.1783A>G	c.(1783-1785)Agc>Ggc	p.S595G	ATP2C1_ENST00000504381.1_Intron|ASTE1_ENST00000514044.1_Missense_Mutation_p.S620G|ATP2C1_ENST00000513801.1_Intron|ATP2C1_ENST00000393221.4_Intron|ATP2C1_ENST00000533801.2_Intron|ATP2C1_ENST00000328560.8_Intron|ATP2C1_ENST00000359644.3_Intron|ATP2C1_ENST00000507488.2_Intron|ATP2C1_ENST00000422190.2_Intron	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	595					DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						GGACATATGCTCAGGAGACTT	0.433																																					p.S595G		Atlas-SNP	.											.	ASTE1	67	.	0			c.A1783G						.						79	80	80					3																	130733158		2203	4300	6503	SO:0001583	missense	28990	exon6			ATATGCTCAGGAG	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.1783A>G	chr3.hg19:g.130733158T>C	ENSP00000264992:p.Ser595Gly	225.0	0.0		121.0	5.0	NM_014065	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Missense_Mutation	SNP	ENST00000264992.3	hg19	CCDS3068.1	.	.	.	.	.	.	.	.	.	.	T	9.905	1.207903	0.22205	.	.	ENSG00000034533	ENST00000514044;ENST00000264992	.	.	.	5.81	3.46	0.39613	.	0.332927	0.38778	N	0.001564	T	0.41673	0.1169	L	0.50333	1.59	0.32860	D	0.507849	B;B	0.28713	0.22;0.1	B;B	0.22386	0.039;0.024	T	0.49437	-0.8940	9	0.48119	T	0.1	-2.2679	6.87	0.24115	0.0:0.0796:0.1627:0.7578	.	620;595	D6RG30;Q2TB18	.;ASTE1_HUMAN	G	620;595	.	ENSP00000264992:S595G	S	-	1	0	ASTE1	132215848	0.000000	0.05858	0.713000	0.30519	0.288000	0.27193	0.044000	0.13992	0.485000	0.27652	0.455000	0.32223	AGC	.	.		0.433	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		C	130733158	T	C	130733158	3	2	100	1	0	0	0	0	1	0	0	0	1062	1551	54	2	260	2	ASTE1	3	130733158	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1186283	130733158	67289272	54	13623										
CEP63	80254	hgsc.bcm.edu	37	chr3	134270832	134270832	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tctttctgaaatggtgatgaAattggaattgggtttacatg	11	3	2	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:134270832A>G	ENST00000337090.3	+	12	1618	c.1445A>G	c.(1444-1446)aAa>aGa	p.K482R	CEP63_ENST00000383229.3_Missense_Mutation_p.K482R|CEP63_ENST00000332047.5_Missense_Mutation_p.K436R|CEP63_ENST00000513612.2_Missense_Mutation_p.K482R|CEP63_ENST00000354446.3_Missense_Mutation_p.K436R|CEP63_ENST00000606977.1_Missense_Mutation_p.K482R			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	482					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						ATGGTGATGAAATTGGAATTG	0.289																																					p.K482R		Atlas-SNP	.											.	CEP63	56	.	0			c.A1445G						.						77	88	84					3																	134270832		2203	4295	6498	SO:0001583	missense	80254	exon13			TGATGAAATTGGA	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1445A>G	chr3.hg19:g.134270832A>G	ENSP00000336524:p.Lys482Arg	90.0	0.0		56.0	4.0	NM_025180	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	hg19	CCDS3086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.10|12.10	1.836635|1.836635	0.32421|0.32421	.|.	.|.	ENSG00000182923|ENSG00000182923	ENST00000332047;ENST00000354446;ENST00000337090;ENST00000383229;ENST00000513612;ENST00000514678|ENST00000504929	T;T;T;T;T;T|.	0.33438|.	1.48;1.89;2.22;1.49;2.22;1.41|.	4.94|4.94	3.74|3.74	0.42951|0.42951	.|.	0.247017|.	0.38778|.	N|.	0.001575|.	T|T	0.47002|0.47002	0.1422|0.1422	L|L	0.45581|0.45581	1.43|1.43	0.29859|0.29859	N|N	0.827813|0.827813	D;B;B;P|.	0.65815|.	0.995;0.114;0.136;0.844|.	P;B;B;P|.	0.61477|.	0.889;0.084;0.05;0.503|.	T|T	0.44221|0.44221	-0.9342|-0.9342	10|5	0.30854|.	T|.	0.27|.	-18.0577|-18.0577	10.7337|10.7337	0.46111|0.46111	0.8403:0.1597:0.0:0.0|0.8403:0.1597:0.0:0.0	.|.	482;482;436;436|.	Q96MT8;Q96MT8-2;Q96MT8-4;Q96MT8-3|.	CEP63_HUMAN;.;.;.|.	R|D	436;436;482;482;482;155|171	ENSP00000328382:K436R;ENSP00000346432:K436R;ENSP00000336524:K482R;ENSP00000372716:K482R;ENSP00000426129:K482R;ENSP00000427526:K155R|.	ENSP00000328382:K436R|.	K|N	+|+	2|1	0|0	CEP63|CEP63	135753522|135753522	0.997000|0.997000	0.39634|0.39634	0.821000|0.821000	0.32701|0.32701	0.749000|0.749000	0.42624|0.42624	4.001000|4.001000	0.57046|0.57046	0.976000|0.976000	0.38417|0.38417	0.477000|0.477000	0.44152|0.44152	AAA|AAT	.	.		0.289	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180		G	134270832	A	G	134270832	3	3	100	1	0	0	0	0	1	0	0	0	3259	14	1	2	1487	2	CEP63	3	134270832	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	3537674	134270832	63751598	55	13624										
SLC7A14	57709	hgsc.bcm.edu	37	chr3	170198199	170198199	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	caaggggccatgtagggcagCttcttggggttctctggctg	16	9	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:170198199C>T	ENST00000231706.5	-	7	2187	c.1872G>A	c.(1870-1872)aaG>aaA	p.K624K	CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	624					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			TGTAGGGCAGCTTCTTGGGGT	0.557																																					p.K624K		Atlas-SNP	.											.	SLC7A14	110	.	0			c.G1872A						.						112	116	115					3																	170198199		2203	4300	6503	SO:0001819	synonymous_variant	57709	exon7			GGGCAGCTTCTTG	BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"Solute carriers"	29326	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 142"	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.1872G>A	chr3.hg19:g.170198199C>T		93.0	0.0		76.0	4.0	NM_020949	B3KV33|Q9HCF9	Silent	SNP	ENST00000231706.5	hg19	CCDS33892.1																																																																																			.	.		0.557	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		T	170198199	C	T	170198199	2	4	100	1	0	0	0	0	0	0	0	1	14711	796	28	3		3	SLC7A14	3	170198199	Silent	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	35927367	170198199	27824231	56	13625										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178943817	178943817	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aatatctggcaaaatcaaggTcttgatcttcggtaggtaac	9	7	4	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:178943817T>C	ENST00000263967.3	+	17	2641	c.2484T>C	c.(2482-2484)ggT>ggC	p.G828G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	828	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AAAATCAAGGTCTTGATCTTC	0.308		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.G828G	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	.	PIK3CA	8460	.	0			c.T2484C						.						94	88	90					3																	178943817		1841	4090	5931	SO:0001819	synonymous_variant	5290	exon17			TCAAGGTCTTGAT		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2484T>C	chr3.hg19:g.178943817T>C		142.0	0.0		75.0	4.0	NM_006218	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	hg19	CCDS43171.1																																																																																			.	.		0.308	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178943817	T	C	178943817	2	2	100	1	0	0	0	0	0	0	0	1	11922	1654	58	2		2	PIK3CA	3	178943817	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	8745618	178943817	19078613	57	13626										
ZNF639	51193	hgsc.bcm.edu	37	chr3	179051221	179051221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	attatgatatagagacagaaAacaattcctctgagagtctc	7	7	2	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:179051221A>G	ENST00000326361.3	+	7	914	c.469A>G	c.(469-471)Aac>Gac	p.N157D	ZNF639_ENST00000484866.1_Missense_Mutation_p.N157D|ZNF639_ENST00000466663.1_3'UTR|ZNF639_ENST00000496856.1_Missense_Mutation_p.N157D	NM_016331.1	NP_057415.1	Q9UID6	ZN639_HUMAN	zinc finger protein 639	157					negative regulation by host of viral transcription (GO:0043922)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|transcription, DNA-templated (GO:0006351)|viral entry into host cell (GO:0046718)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein self-association (GO:0043621)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(10)|urinary_tract(1)	16	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			AGAGACAGAAAACAATTCCTC	0.418																																					p.N157D		Atlas-SNP	.											.	ZNF639	45	.	0			c.A469G						.						69	70	70					3																	179051221		2203	4300	6503	SO:0001583	missense	51193	exon7			ACAGAAAACAATT	BC020500	CCDS3227.1	3q27.1	2010-03-26			ENSG00000121864	ENSG00000121864		"Zinc fingers, C2H2-type"	30950	protein-coding gene	gene with protein product	"zinc finger amplified in esophageal squamous cell carcinomas 1"					14522885	Standard	NM_016331		Approved	ANC-2H01, ZASC1	uc003fjr.1	Q9UID6	OTTHUMG00000157439	ENST00000326361.3:c.469A>G	chr3.hg19:g.179051221A>G	ENSP00000325634:p.Asn157Asp	230.0	0.0		152.0	7.0	NM_016331	A9X3Z9|D3DNR3	Missense_Mutation	SNP	ENST00000326361.3	hg19	CCDS3227.1	.	.	.	.	.	.	.	.	.	.	A	18.85	3.712109	0.68730	.	.	ENSG00000121864	ENST00000496856;ENST00000491818;ENST00000326361;ENST00000466264;ENST00000484866	T;T;T;T	0.03689	3.84;3.84;4.47;3.84	5.87	5.87	0.94306	.	0.191571	0.46442	N	0.000292	T	0.09379	0.0231	L	0.29908	0.895	0.29633	N	0.845314	D	0.63880	0.993	D	0.70935	0.971	T	0.04268	-1.0964	10	0.56958	D	0.05	.	10.8542	0.46789	0.9299:0.0:0.0701:0.0	.	157	Q9UID6	ZN639_HUMAN	D	157	ENSP00000417740:N157D;ENSP00000325634:N157D;ENSP00000419650:N157D;ENSP00000418766:N157D	ENSP00000325634:N157D	N	+	1	0	ZNF639	180533915	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.603000	0.61105	2.371000	0.80710	0.533000	0.62120	AAC	.	.		0.418	ZNF639-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348855.1	NM_016331		G	179051221	A	G	179051221	3	3	100	1	0	0	0	0	1	0	0	0	18071	14	1	2	483	2	ZNF639	3	179051221	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	107404	179051221	18971209	58	13627										
TNK2	10188	hgsc.bcm.edu	37	chr3	195611685	195611685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aggacacagagagctcaccgTcttccctgagggcgcgtccc	12	15	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr3:195611685T>C	ENST00000333602.6	-	4	1071	c.454A>G	c.(454-456)Acg>Gcg	p.T152A	TNK2_ENST00000316664.3_Missense_Mutation_p.T152A|TNK2_ENST00000392400.1_Missense_Mutation_p.T152A|TNK2_ENST00000381916.2_Missense_Mutation_p.T215A|TNK2_ENST00000468819.1_5'UTR|TNK2_ENST00000428187.1_Missense_Mutation_p.T184A	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	152	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		T -> M (in dbSNP:rs56161912). {ECO:0000269|PubMed:17344846}.		cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	GAGCTCACCGTCTTCCCTGAG	0.657																																					p.T215A		Atlas-SNP	.											.	TNK2	246	.	0			c.A643G						.						25	25	25					3																	195611685		2200	4298	6498	SO:0001583	missense	10188	exon4			TCACCGTCTTCCC	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"activated Cdc42-associated kinase 1"	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.454A>G	chr3.hg19:g.195611685T>C	ENSP00000329425:p.Thr152Ala	143.0	0.0		62.0	4.0	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Missense_Mutation	SNP	ENST00000333602.6	hg19	CCDS33928.1	.	.	.	.	.	.	.	.	.	.	T	8.760	0.923378	0.18056	.	.	ENSG00000061938	ENST00000333602;ENST00000381916;ENST00000428187;ENST00000392400;ENST00000316664	D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61	5.12	2.72	0.32119	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.531595	0.20189	N	0.097348	T	0.65365	0.2684	N	0.26092	0.79	0.80722	D	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.49093	-0.8975	10	0.08179	T	0.78	.	4.1861	0.10398	0.149:0.1653:0.0:0.6857	.	152;152;215;184	Q07912-2;Q07912;Q07912-3;C9J1X3	.;ACK1_HUMAN;.;.	A	152;215;184;152;152	ENSP00000329425:T152A;ENSP00000371341:T215A;ENSP00000392546:T184A;ENSP00000376201:T152A;ENSP00000323216:T152A	ENSP00000323216:T152A	T	-	1	0	TNK2	197096082	1.000000	0.71417	1.000000	0.80357	0.061000	0.15899	3.432000	0.52824	0.376000	0.24707	-0.473000	0.04963	ACG	.	.		0.657	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781		C	195611685	T	C	195611685	3	2	100	1	0	0	0	0	1	0	0	0	16333	1667	58	2	2759	2	TNK2	3	195611685	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	16560464	195611685	2410745	59	13628										
PDE6B	5158	hgsc.bcm.edu	37	chr4	629718	629718	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gttgtacctgaagatctatcAcctgagctacctccacaact	6	13	2	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:629718A>G	ENST00000496514.1	+	3	692	c.671A>G	c.(670-672)cAc>cGc	p.H224R	PDE6B_ENST00000255622.6_Missense_Mutation_p.H224R			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	224					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	AAGATCTATCACCTGAGCTAC	0.537																																					p.H224R	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.A671G						.						128	117	121					4																	629718		2203	4300	6503	SO:0001583	missense	5158	exon3			TCTATCACCTGAG	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"Phosphodiesterases"	8786	protein-coding gene	gene with protein product	"congenital stationary night blindness 3, autosomal dominant"	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.671A>G	chr4.hg19:g.629718A>G	ENSP00000420295:p.His224Arg	124.0	0.0		90.0	5.0	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	hg19	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.844052	0.51164	.	.	ENSG00000133256	ENST00000255622;ENST00000496514	T;T	0.64438	-0.1;-0.1	4.25	4.25	0.50352	GAF (1);	0.000000	0.85682	D	0.000000	T	0.62998	0.2474	M	0.67397	2.05	0.80722	D	1	B;B	0.29481	0.159;0.245	B;B	0.36335	0.111;0.222	T	0.65932	-0.6048	10	0.56958	D	0.05	.	11.5849	0.50912	1.0:0.0:0.0:0.0	.	224;224	P35913;P35913-2	PDE6B_HUMAN;.	R	224	ENSP00000255622:H224R;ENSP00000420295:H224R	ENSP00000255622:H224R	H	+	2	0	PDE6B	619718	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.389000	0.90172	1.694000	0.51137	0.402000	0.26972	CAC	.	.		0.537	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		G	629718	A	G	629718	3	3	100	1	0	0	0	0	1	0	0	0	11655	159	6	2	681	2	PDE6B	4	629718	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		629718	190524558	60	13629										
BEND4	389206	hgsc.bcm.edu	37	chr4	42119674	42119674	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtcgggcgtgaccgacagcgTcgctgaacactttgtttatc	12	11	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:42119674T>C	ENST00000502486.1	-	6	2045	c.1466A>G	c.(1465-1467)gAc>gGc	p.D489G	BEND4_ENST00000504360.1_3'UTR	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	489	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.									NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						ACCGACAGCGTCGCTGAACAC	0.522																																					p.D489G		Atlas-SNP	.											.	BEND4	67	.	0			c.A1466G						.						36	36	36					4																	42119674		1852	4091	5943	SO:0001583	missense	389206	exon6			ACAGCGTCGCTGA	AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"BEN domain containing"	23815	protein-coding gene	gene with protein product			"coiled-coil domain containing 4"	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.1466A>G	chr4.hg19:g.42119674T>C	ENSP00000421169:p.Asp489Gly	143.0	0.0		100.0	4.0	NM_207406	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Missense_Mutation	SNP	ENST00000502486.1	hg19	CCDS47048.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.872737	0.91587	.	.	ENSG00000188848	ENST00000411720;ENST00000502486	T	0.43688	0.94	5.41	5.41	0.78517	BEN domain (2);	0.053177	0.64402	D	0.000001	T	0.40932	0.1137	N	0.08118	0	0.80722	D	1	P	0.49783	0.928	P	0.56916	0.809	T	0.52419	-0.8578	10	0.87932	D	0	-12.636	15.7384	0.77866	0.0:0.0:0.0:1.0	.	489	Q6ZU67	BEND4_HUMAN	G	360;489	ENSP00000421169:D489G	ENSP00000412495:D360G	D	-	2	0	BEND4	41814431	1.000000	0.71417	0.956000	0.39512	0.880000	0.50808	7.655000	0.83696	2.174000	0.68829	0.459000	0.35465	GAC	.	.		0.522	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406		C	42119674	T	C	42119674	3	2	100	1	0	0	0	0	1	0	0	0	1400	1667	58	2	142	2	BEND4	4	42119674	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	41489956	42119674	149034602	61	13630										
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54265995	54265995	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tctttgttcaagactgggctTccaccgagcaggttagttac	10	10	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:54265995T>C	ENST00000337488.6	+	10	998	c.804T>C	c.(802-804)ctT>ctC	p.L268L	FIP1L1_ENST00000507166.1_Silent_p.L268L|FIP1L1_ENST00000306932.6_Silent_p.L230L|FIP1L1_ENST00000358575.5_Silent_p.L253L|FIP1L1_ENST00000507922.1_Silent_p.L253L	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	268	Necessary for stimulating PAPOLA activity.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			AGACTGGGCTTCCACCGAGCA	0.388			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.L268L		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.T804C						.						145	140	142					4																	54265995		2203	4300	6503	SO:0001819	synonymous_variant	81608	exon10			TGGGCTTCCACCG	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.804T>C	chr4.hg19:g.54265995T>C		139.0	0.0		102.0	5.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Silent	SNP	ENST00000337488.6	hg19	CCDS3491.1																																																																																			.	.		0.388	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		C	54265995	T	C	54265995	2	2	100	1	0	0	0	0	0	0	0	1	5904	1770	62	2		2	FIP1L1	4	54265995	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	12146321	54265995	136888281	62	13631										
SULT1E1	6783	hgsc.bcm.edu	37	chr4	70719946	70719946	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tctggttaccttacaatcctTttcccaaaatgaggcaggaa	7	10	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:70719946T>C	ENST00000226444.3	-	4	470	c.358A>G	c.(358-360)Aag>Gag	p.K120E		NM_005420.2	NP_005411.1	P49888	ST1E1_HUMAN	sulfotransferase family 1E, estrogen-preferring, member 1	120					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	estrone sulfotransferase activity (GO:0004304)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid binding (GO:0005496)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	10					Acetaminophen(DB00316)|Cyclizine(DB01176)	TTACAATCCTTTTCCCAAAAT	0.338																																					p.K120E		Atlas-SNP	.											.	SULT1E1	44	.	0			c.A358G						.						94	91	92					4																	70719946		2203	4300	6503	SO:0001583	missense	6783	exon4			AATCCTTTTCCCA	BC027956	CCDS3531.1	4q13.1	2008-02-05	2004-02-06	2004-02-04	ENSG00000109193	ENSG00000109193	2.8.2.4	"Sulfotransferases, cytosolic"	11377	protein-coding gene	gene with protein product		600043	"sulfotransferase, estrogen-preferring"	STE		7961757	Standard	NM_005420		Approved	EST	uc003heo.3	P49888	OTTHUMG00000129403	ENST00000226444.3:c.358A>G	chr4.hg19:g.70719946T>C	ENSP00000226444:p.Lys120Glu	167.0	0.0		91.0	4.0	NM_005420	Q8N6X5	Missense_Mutation	SNP	ENST00000226444.3	hg19	CCDS3531.1	.	.	.	.	.	.	.	.	.	.	T	8.025	0.760428	0.15914	.	.	ENSG00000109193	ENST00000226444	T	0.01787	4.64	4.7	3.51	0.40186	Sulfotransferase domain (1);	0.146210	0.46442	D	0.000292	T	0.02119	0.0066	L	0.58925	1.835	0.24431	N	0.994578	B;B	0.30179	0.271;0.271	B;B	0.30105	0.111;0.111	T	0.42899	-0.9424	10	0.22109	T	0.4	.	5.0602	0.14553	0.0:0.0946:0.1836:0.7218	.	120;120	Q53X91;P49888	.;ST1E1_HUMAN	E	120	ENSP00000226444:K120E	ENSP00000226444:K120E	K	-	1	0	SULT1E1	70754535	0.987000	0.35691	0.777000	0.31699	0.799000	0.45148	0.741000	0.26202	0.940000	0.37473	0.533000	0.62120	AAG	.	.		0.338	SULT1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251559.1	NM_005420		C	70719946	T	C	70719946	3	2	100	1	0	0	0	0	1	0	0	0	15395	1850	64	2	546	2	SULT1E1	4	70719946	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	16453951	70719946	120434330	63	13632										
PPEF2	5470	hgsc.bcm.edu	37	chr4	76797575	76797575	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cggcaccgctctagctccagTtccacggagctccgcacctg	10	18	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:76797575T>C	ENST00000286719.7	-	11	1541	c.1185A>G	c.(1183-1185)gaA>gaG	p.E395E		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	395	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			CTAGCTCCAGTTCCACGGAGC	0.662																																					p.E395E	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.A1185G						.						27	29	29					4																	76797575		2203	4299	6502	SO:0001819	synonymous_variant	5470	exon11			CTCCAGTTCCACG	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9244	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, beta isozyme"	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.1185A>G	chr4.hg19:g.76797575T>C		70.0	0.0		62.0	5.0	NM_006239	O14831	Silent	SNP	ENST00000286719.7	hg19	CCDS34013.1																																																																																			.	.		0.662	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		C	76797575	T	C	76797575	2	2	100	1	0	0	0	0	0	0	0	1	12317	1722	60	2		2	PPEF2	4	76797575	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	6077629	76797575	114356701	64	13633										
INPP4B	8821	hgsc.bcm.edu	37	chr4	143045901	143045901	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ggatgaggggatacaactgtTcataccagtcctctggggga	14	8	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:143045901T>C	ENST00000513000.1	-	20	2166	c.1733A>G	c.(1732-1734)gAa>gGa	p.E578G	INPP4B_ENST00000308502.4_Missense_Mutation_p.E578G|INPP4B_ENST00000508116.1_Missense_Mutation_p.E578G|INPP4B_ENST00000509777.1_Missense_Mutation_p.E578G|INPP4B_ENST00000262992.4_Missense_Mutation_p.E578G	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	578					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					ATACAACTGTTCATACCAGTC	0.468																																					p.E578G		Atlas-SNP	.											.	INPP4B	132	.	0			c.A1733G						.						55	43	47					4																	143045901		2203	4300	6503	SO:0001583	missense	8821	exon20			AACTGTTCATACC	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.1733A>G	chr4.hg19:g.143045901T>C	ENSP00000425487:p.Glu578Gly	102.0	0.0		94.0	4.0	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	hg19	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185880	0.78789	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.79	4.58	0.56647	.	0.052908	0.64402	D	0.000001	T	0.64091	0.2567	M	0.65975	2.015	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.983	T	0.61217	-0.7107	10	0.29301	T	0.29	.	12.9879	0.58602	0.0:0.0:0.135:0.865	.	449;578	B7Z6T2;O15327	.;INP4B_HUMAN	G	578;578;578;449;578;578;393;393;578;449	ENSP00000425487:E578G;ENSP00000262992:E578G;ENSP00000308441:E578G;ENSP00000423954:E578G;ENSP00000422793:E578G;ENSP00000426207:E393G;ENSP00000427250:E578G;ENSP00000421065:E449G	ENSP00000262992:E578G	E	-	2	0	INPP4B	143265351	1.000000	0.71417	0.524000	0.27887	0.980000	0.70556	5.961000	0.70356	0.984000	0.38629	0.533000	0.62120	GAA	.	.		0.468	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		C	143045901	T	C	143045901	3	2	100	1	0	0	0	0	1	0	0	0	7762	1783	62	2	1073	2	INPP4B	4	143045901	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	66248326	143045901	48108375	65	13634										
HHIP	64399	hgsc.bcm.edu	37	chr4	145636456	145636456	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tatgtttctgttgtaggaatTtcctaactctccagcaaagt	7	8	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:145636456T>C	ENST00000296575.3	+	10	2207	c.1552T>C	c.(1552-1554)Ttc>Ctc	p.F518L		NM_022475.2	NP_071920.1	Q96QV1	HHIP_HUMAN	hedgehog interacting protein	518					carbohydrate metabolic process (GO:0005975)|dorsal/ventral pattern formation (GO:0009953)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|negative regulation of signal transduction (GO:0009968)|negative regulation of smoothened signaling pathway (GO:0045879)|neuroblast proliferation (GO:0007405)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|skeletal system morphogenesis (GO:0048705)|smoothened signaling pathway (GO:0007224)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	hedgehog family protein binding (GO:0097108)|oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		TTGTAGGAATTTCCTAACTCT	0.373																																					p.F518L		Atlas-SNP	.											.	HHIP	100	.	0			c.T1552C						.						91	87	88					4																	145636456		2203	4300	6503	SO:0001583	missense	64399	exon10			AGGAATTTCCTAA	AK024645	CCDS3762.1	4q31.21-q31.3	2008-08-29	2001-11-29		ENSG00000164161	ENSG00000164161			14866	protein-coding gene	gene with protein product		606178	"hedgehog-interacting protein"			11435703, 11731473	Standard	NM_022475		Approved	HIP, FLJ20992	uc003ijs.2	Q96QV1	OTTHUMG00000161428	ENST00000296575.3:c.1552T>C	chr4.hg19:g.145636456T>C	ENSP00000296575:p.Phe518Leu	131.0	0.0		95.0	5.0	NM_022475	Q6PK09|Q8NCI7|Q9BXK3|Q9H1J4|Q9H7E7	Missense_Mutation	SNP	ENST00000296575.3	hg19	CCDS3762.1	.	.	.	.	.	.	.	.	.	.	T	8.653	0.898663	0.17686	.	.	ENSG00000164161	ENST00000296575	T	0.04406	3.63	6.06	6.06	0.98353	Six-bladed beta-propeller, TolB-like (1);	0.049365	0.85682	D	0.000000	T	0.02418	0.0074	N	0.02854	-0.475	0.80722	D	1	B	0.13145	0.007	B	0.08055	0.003	T	0.36866	-0.9730	10	0.02654	T	1	-22.1949	16.6127	0.84892	0.0:0.0:0.0:1.0	.	518	Q96QV1	HHIP_HUMAN	L	518	ENSP00000296575:F518L	ENSP00000296575:F518L	F	+	1	0	HHIP	145855906	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.305000	0.51873	2.322000	0.78497	0.528000	0.53228	TTC	.	.		0.373	HHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364887.2			C	145636456	T	C	145636456	3	2	100	1	0	0	0	0	1	0	0	0	7101	1841	64	2	1590	2	HHIP	4	145636456	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2590555	145636456	45517820	66	13635										
ABCE1	6059	hgsc.bcm.edu	37	chr4	146030345	146030345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gaactaatggtattggaaagTcaactgctttaaaaatttta	7	4	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:146030345T>C	ENST00000296577.4	+	5	864	c.349T>C	c.(349-351)Tca>Cca	p.S117P	OTUD4_ENST00000455611.2_5'Flank|ABCE1_ENST00000502803.1_Intron	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	117	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					TATTGGAAAGTCAACTGCTTT	0.328																																					p.S117P		Atlas-SNP	.											.	ABCE1	47	.	0			c.T349C						.						107	108	108					4																	146030345		2203	4300	6503	SO:0001583	missense	6059	exon5			GGAAAGTCAACTG	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"ATP binding cassette transporters / subfamily E"	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.349T>C	chr4.hg19:g.146030345T>C	ENSP00000296577:p.Ser117Pro	109.0	0.0		57.0	4.0	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Missense_Mutation	SNP	ENST00000296577.4	hg19	CCDS34071.1	.	.	.	.	.	.	.	.	.	.	T	32	5.113348	0.94339	.	.	ENSG00000164163	ENST00000296577;ENST00000502586	D;D	0.97870	-4.31;-4.58	5.86	5.86	0.93980	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.99369	0.9778	H	0.99312	4.51	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98325	1.0530	10	0.87932	D	0	-33.4121	16.5602	0.84551	0.0:0.0:0.0:1.0	.	117	P61221	ABCE1_HUMAN	P	117	ENSP00000296577:S117P;ENSP00000421250:S117P	ENSP00000296577:S117P	S	+	1	0	ABCE1	146249795	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.832000	0.86757	2.367000	0.80283	0.528000	0.53228	TCA	.	.		0.328	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940		C	146030345	T	C	146030345	3	2	100	1	0	0	0	0	1	0	0	0	64	1667	58	2	363	2	ABCE1	4	146030345	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	393889	146030345	45123931	67	13636										
LRBA	987	hgsc.bcm.edu	37	chr4	151773447	151773447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cagtttttcaccggcttcagAtgcagctggagacaaactgt	10	10	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:151773447A>G	ENST00000357115.3	-	23	3658	c.3415T>C	c.(3415-3417)Tct>Cct	p.S1139P	LRBA_ENST00000507224.1_Missense_Mutation_p.S1139P|LRBA_ENST00000535741.1_Missense_Mutation_p.S1139P|LRBA_ENST00000510413.1_Missense_Mutation_p.S1139P	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1139						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					CCGGCTTCAGATGCAGCTGGA	0.398																																					p.S1139P		Atlas-SNP	.											.	LRBA	253	.	0			c.T3415C						.						97	95	96					4																	151773447		2203	4300	6503	SO:0001583	missense	987	exon23			CTTCAGATGCAGC	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.3415T>C	chr4.hg19:g.151773447A>G	ENSP00000349629:p.Ser1139Pro	186.0	0.0		141.0	6.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.361289	0.24684	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.57752	0.8;0.95;0.8;0.38	5.87	1.99	0.26369	.	0.562244	0.17496	N	0.172173	T	0.32041	0.0816	L	0.27053	0.805	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.14035	-1.0487	10	0.40728	T	0.16	.	2.1804	0.03873	0.5606:0.1258:0.1896:0.1239	.	1139;1139	P50851;P50851-2	LRBA_HUMAN;.	P	1139	ENSP00000446299:S1139P;ENSP00000421552:S1139P;ENSP00000349629:S1139P;ENSP00000422180:S1139P	ENSP00000349629:S1139P	S	-	1	0	LRBA	151992897	0.001000	0.12720	0.801000	0.32222	0.463000	0.32649	0.092000	0.15066	0.517000	0.28361	0.533000	0.62120	TCT	.	.		0.398	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			G	151773447	A	G	151773447	3	3	100	1	0	0	0	0	1	0	0	0	8940	333	12	2	5320	2	LRBA	4	151773447	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	5743102	151773447	39380829	68	13637										
SFRP2	6423	hgsc.bcm.edu	37	chr4	154709740	154709740	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccgggtggcactgcttcatgAccagcgggatccaagcgccg	14	14	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:154709740A>G	ENST00000274063.4	-	1	532	c.248T>C	c.(247-249)gTc>gCc	p.V83A		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	83	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				bone morphogenesis (GO:0060349)|brain development (GO:0007420)|cardiac left ventricle morphogenesis (GO:0003214)|cell-cell signaling (GO:0007267)|cellular response to extracellular stimulus (GO:0031668)|cellular response to X-ray (GO:0071481)|chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|embryonic digit morphogenesis (GO:0042733)|gonad development (GO:0008406)|hematopoietic stem cell proliferation (GO:0071425)|male gonad development (GO:0008584)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dermatome development (GO:0061185)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of gene expression (GO:0010629)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-anal tail morphogenesis (GO:0036342)|regulation of stem cell division (GO:2000035)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|sclerotome development (GO:0061056)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase activator activity (GO:0061133)|fibronectin binding (GO:0001968)|integrin binding (GO:0005178)|metalloenzyme activator activity (GO:0010577)|PDZ domain binding (GO:0030165)|receptor agonist activity (GO:0048018)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.V83A(2)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	16	all_hematologic(180;0.093)	Renal(120;0.117)				CTGCTTCATGACCAGCGGGAT	0.627																																					p.V83A		Atlas-SNP	.											SFRP2,NS,carcinoma,0,1	SFRP2	45	.	2	Substitution - Missense(2)	prostate(2)	c.T248C						.						98	109	106					4																	154709740		2203	4300	6503	SO:0001583	missense	6423	exon1			TTCATGACCAGCG	AF017986	CCDS34082.1	4q31.3	2008-08-29			ENSG00000145423	ENSG00000145423		"Secreted frizzled-related proteins"	10777	protein-coding gene	gene with protein product		604157				9391078	Standard	NM_003013		Approved	SARP1, SDF-5, FRP-2	uc003inv.1	Q96HF1	OTTHUMG00000161559	ENST00000274063.4:c.248T>C	chr4.hg19:g.154709740A>G	ENSP00000274063:p.Val83Ala	131.0	0.0		78.0	5.0	NM_003013	B3KQR2|O14778|Q9HAP5	Missense_Mutation	SNP	ENST00000274063.4	hg19	CCDS34082.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.405560	0.83230	.	.	ENSG00000145423	ENST00000274063	T	0.56444	0.46	4.77	3.53	0.40419	Frizzled domain (5);	0.111099	0.64402	D	0.000010	T	0.51398	0.1672	L	0.48986	1.54	0.58432	D	0.999998	B	0.33379	0.41	B	0.41135	0.348	T	0.51505	-0.8697	10	0.56958	D	0.05	.	10.6521	0.45655	0.8561:0.0:0.0:0.1439	.	83	Q96HF1	SFRP2_HUMAN	A	83	ENSP00000274063:V83A	ENSP00000274063:V83A	V	-	2	0	SFRP2	154929190	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.177000	0.94849	0.715000	0.32103	0.533000	0.62120	GTC	.	.		0.627	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1			G	154709740	A	G	154709740	3	3	100	1	0	0	0	0	1	0	0	0	14177	275	10	2	651	2	SFRP2	4	154709740	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	2936293	154709740	36444536	69	13638										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175898801	175898801	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aaccaataaaaaagcagcaaGatgttcaaactccatctgca	5	10	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:175898801G>A	ENST00000359240.3	+	5	2795	c.2125G>A	c.(2125-2127)Gat>Aat	p.D709N	RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.D709N|ADAM29_ENST00000404450.4_Missense_Mutation_p.D709N|ADAM29_ENST00000445694.1_Missense_Mutation_p.D709N	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	709					spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		AAAGCAGCAAGATGTTCAAAC	0.363																																					p.D709N	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.G2125A						.						53	55	54					4																	175898801		2203	4300	6503	SO:0001583	missense	11086	exon4			CAGCAAGATGTTC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2125G>A	chr4.hg19:g.175898801G>A	ENSP00000352177:p.Asp709Asn	97.0	0.0		55.0	4.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	hg19	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	G	3.572	-0.087491	0.07097	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01821	4.62;4.62;4.62;4.62	2.46	-3.86	0.04230	.	.	.	.	.	T	0.01061	0.0035	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47724	-0.9095	8	.	.	.	.	5.4277	0.16436	0.2376:0.2036:0.5588:0.0	.	709	Q9UKF5	ADA29_HUMAN	N	709	ENSP00000352177:D709N;ENSP00000414544:D709N;ENSP00000384229:D709N;ENSP00000423517:D709N	.	D	+	1	0	ADAM29	176135376	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.018000	0.13422	-0.901000	0.03891	-0.323000	0.08544	GAT	.	.		0.363	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				A	175898801	G	A	175898801	3	1	100	1	0	0	0	0	1	0	0	0	247	942	33	3	2127	3	ADAM29	4	175898801	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	21189061	175898801	15255475	70	13639										
WWC2	80014	hgsc.bcm.edu	37	chr4	184129212	184129212	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gccctccggacacagaaggaActgtaccatgtgaaggagca	12	11	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:184129212A>G	ENST00000403733.3	+	3	547	c.348A>G	c.(346-348)gaA>gaG	p.E116E	WWC2_ENST00000513834.1_Silent_p.E116E|WWC2_ENST00000378925.3_Silent_p.E18E|WWC2_ENST00000504005.1_5'Flank|WWC2_ENST00000448232.2_Silent_p.E116E	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	116					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		CACAGAAGGAACTGTACCATG	0.502																																					p.E116E		Atlas-SNP	.											.	WWC2	78	.	0			c.A348G						.						65	71	69					4																	184129212		2091	4229	6320	SO:0001819	synonymous_variant	80014	exon3			GAAGGAACTGTAC	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.348A>G	chr4.hg19:g.184129212A>G		89.0	0.0		57.0	4.0	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Silent	SNP	ENST00000403733.3	hg19	CCDS34109.2																																																																																			.	.		0.502	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		G	184129212	A	G	184129212	2	3	100	1	0	0	0	0	0	0	0	1	17427	40	2	2		2	WWC2	4	184129212	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	8230411	184129212	7025064	71	13640										
SLC25A4	291	hgsc.bcm.edu	37	chr4	186066951	186066951	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agaacgtgcacatttttgtgAgctggatgattgcccagagt	12	7	0	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr4:186066951A>G	ENST00000281456.6	+	3	769	c.637A>G	c.(637-639)Agc>Ggc	p.S213G		NM_001151.3	NP_001142.2	P12235	ADT1_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4	213					adenine transport (GO:0015853)|apoptotic mitochondrial changes (GO:0008637)|energy reserve metabolic process (GO:0006112)|generation of precursor metabolites and energy (GO:0006091)|mitochondrial genome maintenance (GO:0000002)|negative regulation of necroptotic process (GO:0060546)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)			endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)	10		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;4.48e-44)|Epithelial(43;2.1e-41)|all cancers(43;1.37e-36)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)	Adenosine triphosphate(DB00171)|Clodronate(DB00720)	CATTTTTGTGAGCTGGATGAT	0.562																																					p.S213G		Atlas-SNP	.											.	SLC25A4	27	.	0			c.A637G						.						110	86	94					4																	186066951		2203	4300	6503	SO:0001583	missense	291	exon3			TTTGTGAGCTGGA	BC008664	CCDS34114.1	4q35	2014-09-17			ENSG00000151729	ENSG00000151729		"Solute carriers"	10990	protein-coding gene	gene with protein product		103220		PEO3, PEO2, ANT1		1582253	Standard	NM_001151		Approved	T1	uc003ixd.3	P12235	OTTHUMG00000134299	ENST00000281456.6:c.637A>G	chr4.hg19:g.186066951A>G	ENSP00000281456:p.Ser213Gly	130.0	0.0		79.0	4.0	NM_001151	D3DP59	Missense_Mutation	SNP	ENST00000281456.6	hg19	CCDS34114.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.069903	0.76301	.	.	ENSG00000151729	ENST00000281456	T	0.80304	-1.36	5.54	5.54	0.83059	Mitochondrial carrier domain (2);	0.037658	0.85682	D	0.000000	D	0.84759	0.5543	M	0.88704	2.975	0.80722	D	1	B	0.21688	0.059	B	0.26202	0.067	D	0.84106	0.0398	10	0.87932	D	0	-11.4116	15.8465	0.78895	1.0:0.0:0.0:0.0	.	213	P12235	ADT1_HUMAN	G	213	ENSP00000281456:S213G	ENSP00000281456:S213G	S	+	1	0	SLC25A4	186303945	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.123000	0.94387	2.326000	0.78906	0.533000	0.62120	AGC	.	.		0.562	SLC25A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259170.3	NM_001151		G	186066951	A	G	186066951	3	3	100	1	0	0	0	0	1	0	0	0	14519	304	11	2	647	2	SLC25A4	4	186066951	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1937739	186066951	5087325	72	13641										
CLPTM1L	81037	hgsc.bcm.edu	37	chr5	1341797	1341797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gaccctcacctgtgtatcagActccccggtgagcaggttga	11	13	2	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:1341797A>G	ENST00000320895.5	-	3	699	c.442T>C	c.(442-444)Tct>Cct	p.S148P	CLPTM1L_ENST00000507807.1_Missense_Mutation_p.S15P|CLPTM1L_ENST00000320927.6_Missense_Mutation_p.S148P	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	148					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		TGTGTATCAGACTCCCCGGTG	0.572																																					p.S148P		Atlas-SNP	.											.	CLPTM1L	60	.	0			c.T442C						.						113	103	107					5																	1341797		2203	4300	6503	SO:0001583	missense	81037	exon3			TATCAGACTCCCC	AK027306	CCDS3862.1	5p15.33	2008-02-05			ENSG00000049656	ENSG00000049656			24308	protein-coding gene	gene with protein product	"cisplatin resistance related protein"	612585				11162647	Standard	NM_030782		Approved	FLJ14400, CRR9	uc003jch.3	Q96KA5	OTTHUMG00000131015	ENST00000320895.5:c.442T>C	chr5.hg19:g.1341797A>G	ENSP00000313854:p.Ser148Pro	134.0	0.0		95.0	5.0	NM_030782	D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Missense_Mutation	SNP	ENST00000320895.5	hg19	CCDS3862.1	.	.	.	.	.	.	.	.	.	.	A	9.927	1.213881	0.22289	.	.	ENSG00000049656	ENST00000320895;ENST00000507807;ENST00000320927	T;T;T	0.48201	0.85;0.87;0.82	5.03	-2.0	0.07433	.	0.516798	0.22188	N	0.063410	T	0.21761	0.0524	N	0.17345	0.48	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.05084	-1.0907	10	0.33940	T	0.23	-3.9941	1.852	0.03171	0.4432:0.1301:0.3013:0.1255	.	148;15	Q96KA5;G5E9Z2	CLP1L_HUMAN;.	P	148;15;148	ENSP00000313854:S148P;ENSP00000423321:S15P;ENSP00000315196:S148P	ENSP00000313854:S148P	S	-	1	0	CLPTM1L	1394797	0.308000	0.24509	0.000000	0.03702	0.003000	0.03518	1.031000	0.30165	-0.530000	0.06349	-0.408000	0.06270	TCT	.	.		0.572	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2	NM_030782		G	1341797	A	G	1341797	3	3	100	1	0	0	0	0	1	0	0	0	3557	275	10	2	1234	2	CLPTM1L	5	1341797	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		1341797	179573463	73	13642										
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5303777	5303777	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gcgcagctgctgcccgacgcTgtctgcacctccgagcccaa	11	18	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:5303777T>C	ENST00000274181.7	+	20	3222	c.3084T>C	c.(3082-3084)gcT>gcC	p.A1028A		NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	1028	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						TGCCCGACGCTGTCTGCACCT	0.652																																					p.A1028A		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.T3084C						.						37	45	42					5																	5303777		2145	4264	6409	SO:0001819	synonymous_variant	170690	exon20			CGACGCTGTCTGC	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.3084T>C	chr5.hg19:g.5303777T>C		110.0	0.0		94.0	4.0	NM_139056	C6G490|Q8IVE2	Silent	SNP	ENST00000274181.7	hg19	CCDS43299.1																																																																																			.	.		0.652	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		C	5303777	T	C	5303777	2	2	100	1	0	0	0	0	0	0	0	1	261	1567	55	2		2	ADAMTS16	5	5303777	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	3961980	5303777	175611483	74	13643										
CARD6	84674	hgsc.bcm.edu	37	chr5	40843572	40843572	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aaaagatggacagagatatgAggagctagatgattctttat	11	3	1	5			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:40843572A>G	ENST00000254691.5	+	2	801	c.602A>G	c.(601-603)gAg>gGg	p.E201G	CARD6_ENST00000381677.3_Missense_Mutation_p.E201G	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	201	Asp/Glu-rich.				apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						CAGAGATATGAGGAGCTAGAT	0.378																																					p.E201G		Atlas-SNP	.											CARD6,NS,carcinoma,0,1	CARD6	141	.	0			c.A602G						.						43	47	45					5																	40843572		2203	4300	6503	SO:0001583	missense	84674	exon2			GATATGAGGAGCT	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.602A>G	chr5.hg19:g.40843572A>G	ENSP00000254691:p.Glu201Gly	75.0	0.0		73.0	3.0	NM_032587	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	hg19	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	A	19.16	3.774576	0.70107	.	.	ENSG00000132357	ENST00000254691;ENST00000381677;ENST00000444789;ENST00000509771	T;T	0.54675	1.81;0.56	5.23	5.23	0.72850	.	0.255180	0.27831	N	0.017670	T	0.56232	0.1971	L	0.36672	1.1	0.33773	D	0.623322	D	0.60160	0.987	P	0.56865	0.808	T	0.69439	-0.5145	10	0.72032	D	0.01	-7.3434	11.4306	0.50038	1.0:0.0:0.0:0.0	.	201	Q9BX69	CARD6_HUMAN	G	201	ENSP00000254691:E201G;ENSP00000371093:E201G	ENSP00000254691:E201G	E	+	2	0	CARD6	40879329	0.812000	0.29077	0.998000	0.56505	0.948000	0.59901	2.439000	0.44846	2.197000	0.70478	0.533000	0.62120	GAG	.	.		0.378	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			G	40843572	A	G	40843572	3	3	100	1	0	0	0	0	1	0	0	0	2652	304	11	2	608	2	CARD6	5	40843572	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	35539795	40843572	140071688	75	13644										
MOCS2	4338	hgsc.bcm.edu	37	chr5	52402917	52402917	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tctcacatacctagatggctCaaaagcactatcctccacta	4	14	2	1	rs34034664		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:52402917C>A	ENST00000396954.3	-	3	765	c.88G>T	c.(88-90)Gag>Tag	p.E30*	MOCS2_ENST00000508922.1_3'UTR|MOCS2_ENST00000527216.1_3'UTR|CTD-2366F13.1_ENST00000502171.2_RNA|MOCS2_ENST00000361377.4_3'UTR|CTD-2366F13.1_ENST00000499459.2_RNA|MOCS2_ENST00000584946.1_3'UTR|MOCS2_ENST00000582677.1_3'UTR|CTD-2366F13.1_ENST00000512301.1_RNA|MOCS2_ENST00000450852.3_3'UTR|MOCS2_ENST00000510818.2_3'UTR	NM_004531.3	NP_004522.1			molybdenum cofactor synthesis 2											endometrium(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(810;3.08e-05)|Breast(144;0.0848)				CTAGATGGCTCAAAAGCACTA	0.433																																					p.E30X		Atlas-SNP	.											.	MOCS2	28	.	0			c.G88T						.						96	82	87					5																	52402917		2203	4300	6503	SO:0001587	stop_gained	4338	exon3			ATGGCTCAAAAGC	AF117815	CCDS3958.1, CCDS47205.1	5q11	2008-02-05			ENSG00000164172	ENSG00000164172			7193	protein-coding gene	gene with protein product		603708				10053004, 9889283	Standard	NM_004531		Approved	MOCO1	uc003joz.3	O96007	OTTHUMG00000096981	ENST00000396954.3:c.88G>T	chr5.hg19:g.52402917C>A	ENSP00000380157:p.Glu30*	91.0	0.0		58.0	12.0	NM_004531		Nonsense_Mutation	SNP	ENST00000396954.3	hg19	CCDS3958.1	.	.	.	.	.	.	.	.	.	.	C	41	8.846833	0.98976	.	.	ENSG00000164172	ENST00000396954;ENST00000527216	.	.	.	5.92	4.1	0.47936	.	0.624751	0.16259	N	0.222307	.	.	.	.	.	.	0.20307	N	0.999912	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-13.4529	10.2954	0.43620	0.0:0.6788:0.2524:0.0688	.	.	.	.	X	30	.	ENSP00000380157:E30X	E	-	1	0	MOCS2	52438674	0.001000	0.12720	0.004000	0.12327	0.178000	0.23041	0.690000	0.25451	0.803000	0.34113	0.655000	0.94253	GAG	.	.		0.433	MOCS2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214053.3	NM_183418		A	52402917	C	A	52402917	4	1	100	1	0	0	0	0	0	1	0	0	9700	835	29	3	498	3	MOCS2	5	52402917	Nonsense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	11559345	52402917	128512343	76	13645										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55260061	55260075	+	In_Frame_Del	DEL	AATACACAGTAGAAT	AATACACAGTAGAAT	-													0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccagacttcaatgttgacaaAatacacagtagaataatcaa							TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	AATACACAGTAGAAT	AATACACAGTAGAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:55260061_55260075delAATACACAGTAGAAT	ENST00000381298.2	-	6	869_883	c.557_571delATTCTACTGTGTATT	c.(556-573)tattctactgtgtatttt>ttt	p.YSTVY186del	IL6ST_ENST00000577363.1_5'UTR|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000381294.3_In_Frame_Del_p.YSTVY186del|IL6ST_ENST00000396816.1_In_Frame_Del_p.ILLCI44del|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000536319.1_In_Frame_Del_p.YSTVY186del|IL6ST_ENST00000381287.4_In_Frame_Del_p.YSTVY186del|IL6ST_ENST00000522633.2_In_Frame_Del_p.YSTVY186del|IL6ST_ENST00000502326.3_In_Frame_Del_p.YSTVY186del|IL6ST_ENST00000336909.5_In_Frame_Del_p.YSTVY186del	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	186	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)	p.Y186_Y190delYSTVY(1)		breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				ATGTTGACAAAATACACAGTAGAATAATCAACAGT	0.367			O		hepatocellular ca																																p.186_191del		Pindel	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	1	Deletion - In frame(1)	liver(1)	c.558_572del						.																																			SO:0001651	inframe_deletion	3572	exon6			.	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.557_571delATTCTACTGTGTATT	chr5.hg19:g.55260061_55260075delAATACACAGTAGAAT	ENSP00000370698:p.Tyr186_Tyr190del	315.0	0.0		194.0	13.0	NM_002184	A0N0L4|Q5FC04|Q9UQ41	In_Frame_Del	DEL	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.		0.367	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		-	55260075	AATACACAGTAGAAT	-	55260061	7	5	100	1	0	1	0	1	0	0	0	0	7712	14	1	0	2233	0	IL6ST	5	55260061	In_Frame_Del	DEL	AATACACAGTAGAAT	TCGA-DD-A1ED-01A-11D-A152-10	2857144	55260061	125655199	77	13646										
SV2C	22987	hgsc.bcm.edu	37	chr5	75587051	75587051	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgtttctctctacaggtaaaCaaaataaaaactcctaaaca	3	9	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:75587051C>T	ENST00000502798.2	+	7	1585	c.1143C>T	c.(1141-1143)aaC>aaT	p.N381N	SV2C_ENST00000322285.7_Silent_p.N381N|RP11-466P24.6_ENST00000502589.1_RNA	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	381					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		TACAGGTAAACAAAATAAAAA	0.398																																					p.N381N		Atlas-SNP	.											.	SV2C	97	.	0			c.C1143T						.						88	88	88					5																	75587051		2022	4226	6248	SO:0001819	synonymous_variant	22987	exon7			GGTAAACAAAATA	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.1143C>T	chr5.hg19:g.75587051C>T		152.0	0.0		113.0	5.0	NM_014979	Q496K1|Q9UPU8	Silent	SNP	ENST00000502798.2	hg19	CCDS43331.1																																																																																			.	.		0.398	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4			T	75587051	C	T	75587051	2	4	100	1	0	0	0	0	0	0	0	1	15434	477	17	3		3	SV2C	5	75587051	Silent	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	20326990	75587051	105328209	78	13647										
POU5F2	134187	hgsc.bcm.edu	37	chr5	93076777	93076777	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctgctgggcctcgaagcggcAgatggtcgtctggctaagca	15	11	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:93076777A>C	ENST00000510627.4	-	1	566	c.493T>G	c.(493-495)Tgc>Ggc	p.C165G	FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000395965.3_Intron|FAM172A_ENST00000509739.1_Intron|RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000505869.1_Intron|POU5F2_ENST00000606183.1_5'UTR	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	165	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		TCGAAGCGGCAGATGGTCGTC	0.582																																					p.C165G		Atlas-SNP	.											.	POU5F2	10	.	0			c.T493G						.						88	92	91					5																	93076777		2169	4284	6453	SO:0001583	missense	134187	exon1			AGCGGCAGATGGT		CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.493T>G	chr5.hg19:g.93076777A>C	ENSP00000464890:p.Cys165Gly	71.0	0.0		45.0	7.0	NM_153216	Q15169|Q6MZL7|Q8N748	Missense_Mutation	SNP	ENST00000510627.4	hg19	CCDS59489.1																																																																																			.	.		0.582	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		C	93076777	A	C	93076777	3	2	100	1	0	0	0	0	1	0	0	0	12292	188	7	5	497	5	POU5F2	5	93076777	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	17489726	93076777	87838483	79	13648										
ANKRD32	84250	hgsc.bcm.edu	37	chr5	93964624	93964624	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tagattgcacttttattaagAgtgaggtaagaaacttatca	8	4	1	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:93964624A>G	ENST00000265140.5	+	2	528	c.109A>G	c.(109-111)Agt>Ggt	p.S37G		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	37	BRCT 1.					centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		TTTTATTAAGAGTGAGGTAAG	0.303																																					p.S37G		Atlas-SNP	.											.	ANKRD32	117	.	0			c.A109G						.						94	84	87					5																	93964624		692	1588	2280	SO:0001583	missense	84250	exon2			ATTAAGAGTGAGG	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"Ankyrin repeat domain containing"	25408	protein-coding gene	gene with protein product			"BRCT domain containing 1"	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.109A>G	chr5.hg19:g.93964624A>G	ENSP00000265140:p.Ser37Gly	103.0	0.0		83.0	4.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Missense_Mutation	SNP	ENST00000265140.5	hg19	CCDS4071.2	.	.	.	.	.	.	.	.	.	.	A	16.45	3.126518	0.56721	.	.	ENSG00000133302	ENST00000265140;ENST00000504099	T;T	0.66815	-0.23;-0.23	5.47	5.47	0.80525	BRCT (2);	0.757107	0.11780	N	0.530310	T	0.61035	0.2315	L	0.42245	1.32	0.32350	N	0.558555	P	0.44006	0.824	B	0.37015	0.239	T	0.70525	-0.4848	10	0.72032	D	0.01	.	15.5395	0.76031	1.0:0.0:0.0:0.0	.	37	Q9BQI6	ANR32_HUMAN	G	37	ENSP00000265140:S37G;ENSP00000425022:S37G	ENSP00000265140:S37G	S	+	1	0	ANKRD32	93990380	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.188000	0.72045	2.089000	0.63090	0.533000	0.62120	AGT	.	.		0.303	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290		G	93964624	A	G	93964624	3	3	100	1	0	0	0	0	1	0	0	0	660	304	11	2	111	2	ANKRD32	5	93964624	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	887847	93964624	86950636	80	13649										
FBN2	2201	hgsc.bcm.edu	37	chr5	127712455	127712455	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cgcccatttggagccaagacAaatcctggtttgcagatgca	10	11	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:127712455A>G	ENST00000508053.1	-	20	2915	c.1941T>C	c.(1939-1941)ttT>ttC	p.F647F	FBN2_ENST00000508989.1_Silent_p.F614F|FBN2_ENST00000262464.4_Silent_p.F647F|FBN2_ENST00000511489.1_5'UTR			P35556	FBN2_HUMAN	fibrillin 2	647	EGF-like 9; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GAGCCAAGACAAATCCTGGTT	0.413																																					p.F647F		Atlas-SNP	.											.	FBN2	858	.	0			c.T1941C						.						248	211	223					5																	127712455		2203	4300	6503	SO:0001819	synonymous_variant	2201	exon14			CAAGACAAATCCT	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.1941T>C	chr5.hg19:g.127712455A>G		160.0	0.0		85.0	4.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	.		0.413	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		G	127712455	A	G	127712455	2	3	100	1	0	0	0	0	0	0	0	1	5711	127	5	2		2	FBN2	5	127712455	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	33747831	127712455	53202805	81	13650										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130769307	130769307	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agaaatctcactatggctggAgtcagacaagttgtcagatt	10	7	3	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:130769307A>G	ENST00000509018.1	-	25	3995	c.3790T>C	c.(3790-3792)Tcc>Ccc	p.S1264P	RAPGEF6_ENST00000507093.1_Missense_Mutation_p.S1272P|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.S1314P|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.S1272P|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.S1277P	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1264	Ser-rich.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		CTATGGCTGGAGTCAGACAAG	0.453																																					p.S1277P	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.T3829C						.						109	100	103					5																	130769307		2203	4300	6503	SO:0001583	missense	51735	exon27			GGCTGGAGTCAGA	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3790T>C	chr5.hg19:g.130769307A>G	ENSP00000421684:p.Ser1264Pro	101.0	0.0		74.0	4.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.823101	0.90873	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000514667	T;T;T;T;T	0.33865	1.49;1.39;1.41;1.49;1.59	5.83	5.83	0.93111	.	0.110074	0.64402	D	0.000005	T	0.61438	0.2347	M	0.74258	2.255	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;0.999	D;D;D;D;D	0.91635	0.998;0.979;0.979;0.999;0.979	T	0.63440	-0.6637	10	0.52906	T	0.07	.	16.214	0.82191	1.0:0.0:0.0:0.0	.	1272;1272;1314;1277;1264	A3KN82;B7ZML2;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;RPGF6_HUMAN	P	1264;1277;1272;1272;1277;1314	ENSP00000421684:S1264P;ENSP00000309298:S1277P;ENSP00000426081:S1272P;ENSP00000296859:S1272P;ENSP00000426948:S1314P	ENSP00000426948:S1314P	S	-	1	0	RAPGEF6;FNIP1	130797206	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.330000	0.90019	2.224000	0.72417	0.528000	0.53228	TCC	.	.		0.453	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		G	130769307	A	G	130769307	3	3	100	1	0	0	0	0	1	0	0	0	13063	304	11	2	1031	2	RAPGEF6	5	130769307	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	3056852	130769307	50145953	82	13651										
AFF4	27125	hgsc.bcm.edu	37	chr5	132222022	132222022	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cttcaggtgctctgtcagtgTctttgagtacttcagagcat	10	9	5	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:132222022T>C	ENST00000265343.5	-	18	3458	c.3079A>G	c.(3079-3081)Aca>Gca	p.T1027A		NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	1027					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTGTCAGTGTCTTTGAGTAC	0.478																																					p.T1027A	Ovarian(126;889 1733 2942 10745 11605)	Atlas-SNP	.											.	AFF4	120	.	0			c.A3079G						.						167	153	158					5																	132222022		2203	4300	6503	SO:0001583	missense	27125	exon18			TCAGTGTCTTTGA	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.3079A>G	chr5.hg19:g.132222022T>C	ENSP00000265343:p.Thr1027Ala	224.0	0.0		118.0	5.0	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	hg19	CCDS4164.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.098562	0.56183	.	.	ENSG00000072364	ENST00000265343	T	0.65916	-0.18	5.48	4.3	0.51218	.	0.102374	0.64402	D	0.000002	T	0.50326	0.1609	L	0.35644	1.08	0.80722	D	1	B	0.23650	0.089	B	0.28638	0.092	T	0.35968	-0.9767	10	0.13853	T	0.58	-4.6048	12.0849	0.53691	0.129:0.0:0.0:0.871	.	1027	Q9UHB7	AFF4_HUMAN	A	1027	ENSP00000265343:T1027A	ENSP00000265343:T1027A	T	-	1	0	AFF4	132249921	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.006000	0.57083	1.005000	0.39183	0.528000	0.53228	ACA	.	.		0.478	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		C	132222022	T	C	132222022	3	2	100	1	0	0	0	0	1	0	0	0	359	1667	58	2	428	2	AFF4	5	132222022	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1452715	132222022	48693238	83	13652										
JAKMIP2	9832	hgsc.bcm.edu	37	chr5	147040867	147040867	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctcgtgctgcttgataaggtTctccctcacagcctgcagct	9	14	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:147040867T>C	ENST00000265272.5	-	3	738	c.271A>G	c.(271-273)Aac>Gac	p.N91D	JAKMIP2_ENST00000333010.6_Missense_Mutation_p.N49D|JAKMIP2_ENST00000507386.1_Missense_Mutation_p.N91D	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	91						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGATAAGGTTCTCCCTCACA	0.557																																					p.N91D		Atlas-SNP	.											.	JAKMIP2	154	.	0			c.A271G						.						190	174	180					5																	147040867		2203	4300	6503	SO:0001583	missense	9832	exon3			TAAGGTTCTCCCT	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.271A>G	chr5.hg19:g.147040867T>C	ENSP00000265272:p.Asn91Asp	163.0	0.0		100.0	4.0	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	hg19	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	T	8.356	0.831957	0.16820	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	T;T;T	0.08102	3.13;3.13;3.13	4.67	4.67	0.58626	.	0.209202	0.47852	D	0.000205	T	0.07773	0.0195	L	0.50333	1.59	0.40265	D	0.978223	P;B;B;B	0.35872	0.525;0.058;0.058;0.058	B;B;B;B	0.27608	0.081;0.025;0.025;0.025	T	0.27773	-1.0064	10	0.11794	T	0.64	.	14.8123	0.70006	0.0:0.0:0.0:1.0	.	49;91;91;91	B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8	.;.;.;JKIP2_HUMAN	D	91;91;49;91	ENSP00000421398:N91D;ENSP00000265272:N91D;ENSP00000328989:N49D	ENSP00000265272:N91D	N	-	1	0	JAKMIP2	147021060	1.000000	0.71417	0.985000	0.45067	0.623000	0.37688	3.128000	0.50492	2.046000	0.60703	0.460000	0.39030	AAC	.	.		0.557	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790		C	147040867	T	C	147040867	3	2	100	1	0	0	0	0	1	0	0	0	7950	1783	62	2	2237	2	JAKMIP2	5	147040867	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	14818845	147040867	33874393	84	13653										
LMAN2	10960	hgsc.bcm.edu	37	chr5	176778206	176778206	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gatagagccctctttgctgcGctcgtcaggggtcagacgta	13	11	3	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:176778206G>A	ENST00000303127.7	-	2	487	c.283C>T	c.(283-285)Cgc>Tgc	p.R95C	LMAN2_ENST00000506310.1_5'UTR|LMAN2_ENST00000515209.1_Missense_Mutation_p.R95C	NM_006816.2	NP_006807.1	Q12907	LMAN2_HUMAN	lectin, mannose-binding 2	95	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.				positive regulation of phagocytosis (GO:0050766)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|heat shock protein binding (GO:0031072)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCTTTGCTGCGCTCGTCAGGG	0.602																																					p.R95C		Atlas-SNP	.											.	LMAN2	35	.	0			c.C283T						.						124	114	117					5																	176778206		2203	4300	6503	SO:0001583	missense	10960	exon2			TGCTGCGCTCGTC	U10362	CCDS4417.1	5q35	2008-02-05		2003-07-04	ENSG00000169223	ENSG00000169223			16986	protein-coding gene	gene with protein product		609551	"chromosome 5 open reading frame 8"	C5orf8		12609988	Standard	NM_006816		Approved	GP36B, VIP36	uc003mge.3	Q12907	OTTHUMG00000130860	ENST00000303127.7:c.283C>T	chr5.hg19:g.176778206G>A	ENSP00000303366:p.Arg95Cys	106.0	0.0		49.0	4.0	NM_006816	Q53HH1	Missense_Mutation	SNP	ENST00000303127.7	hg19	CCDS4417.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.365489	0.82463	.	.	ENSG00000169223	ENST00000303127;ENST00000539488;ENST00000515209;ENST00000514458;ENST00000502560;ENST00000513877	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.67	5.67	0.87782	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.101632	0.64402	D	0.000010	T	0.76133	0.3945	M	0.80616	2.505	0.80722	D	1	D;D	0.76494	0.997;0.999	P;P	0.58660	0.765;0.843	T	0.79291	-0.1864	10	0.72032	D	0.01	-16.7678	13.5517	0.61736	0.0:0.0:0.8441:0.1559	.	95;95	Q12907;D6RBV2	LMAN2_HUMAN;.	C	95;24;95;95;95;24	ENSP00000303366:R95C;ENSP00000423998:R95C;ENSP00000424132:R95C;ENSP00000425229:R95C;ENSP00000427377:R24C	ENSP00000303366:R95C	R	-	1	0	LMAN2	176710812	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.802000	0.62539	2.685000	0.91497	0.644000	0.83932	CGC	.	.		0.602	LMAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253434.1	NM_006816		A	176778206	G	A	176778206	3	1	100	1	0	0	0	0	1	0	0	0	8847	1087	38	1	815	1	LMAN2	5	176778206	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	29737339	176778206	4137054	85	13654										
F12	2161	hgsc.bcm.edu	37	chr5	176829426	176829426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgagccggcgctctgcagctTggtcctcacacaccagcggg	13	15	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr5:176829426T>C	ENST00000253496.3	-	14	1763	c.1715A>G	c.(1714-1716)cAa>cGa	p.Q572R	PFN3_ENST00000358571.2_5'Flank|F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	572	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	CTCTGCAGCTTGGTCCTCACA	0.637									Hereditary Angioedema																												p.Q572R		Atlas-SNP	.											F12,NS,carcinoma,0,1	F12	35	.	0			c.A1715G						.						44	38	40					5																	176829426		2203	4300	6503	SO:0001583	missense	2161	exon14	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	GCAGCTTGGTCCT	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.1715A>G	chr5.hg19:g.176829426T>C	ENSP00000253496:p.Gln572Arg	75.0	0.0		42.0	2.0	NM_000505	P78339	Missense_Mutation	SNP	ENST00000253496.3	hg19	CCDS34302.1	.	.	.	.	.	.	.	.	.	.	T	10.58	1.390570	0.25118	.	.	ENSG00000131187	ENST00000253496	D	0.88896	-2.44	4.03	0.376	0.16193	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.242130	0.05783	N	0.608976	T	0.79695	0.4490	N	0.16130	0.375	0.09310	N	1	B	0.27416	0.178	B	0.28385	0.089	T	0.67585	-0.5633	10	0.49607	T	0.09	.	6.5787	0.22581	0.0:0.3635:0.0:0.6365	.	572	P00748	FA12_HUMAN	R	572	ENSP00000253496:Q572R	ENSP00000253496:Q572R	Q	-	2	0	F12	176762032	0.000000	0.05858	0.000000	0.03702	0.742000	0.42306	-0.325000	0.07976	0.065000	0.16485	0.459000	0.35465	CAA	.	.		0.637	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			C	176829426	T	C	176829426	3	2	100	1	0	0	0	0	1	0	0	0	5341	1812	63	2	136	2	F12	5	176829426	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	51220	176829426	4085834	86	13655										
RIPK1	8737	hgsc.bcm.edu	37	chr6	3105913	3105913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cgaaacagcagcccagacagAatgtggcttacaacagagag	11	10	0	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr6:3105913A>G	ENST00000259808.4	+	9	1502	c.1204A>G	c.(1204-1206)Aat>Gat	p.N402D	RIPK1_ENST00000479389.1_3'UTR|RIPK1_ENST00000380409.2_Missense_Mutation_p.N402D|RIPK1_ENST00000541791.1_Missense_Mutation_p.N356D			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	402	Interaction with SQSTM1.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				GCCCAGACAGAATGTGGCTTA	0.502																																					p.N402D		Atlas-SNP	.											.	RIPK1	56	.	0			c.A1204G						.						69	73	72					6																	3105913		2203	4300	6503	SO:0001583	missense	8737	exon8			AGACAGAATGTGG	U25994	CCDS4482.1	6p25.2	2008-02-05			ENSG00000137275	ENSG00000137275			10019	protein-coding gene	gene with protein product		603453				7538908, 8612133	Standard	XM_005249458		Approved	RIP	uc003mux.3	Q13546	OTTHUMG00000014134	ENST00000259808.4:c.1204A>G	chr6.hg19:g.3105913A>G	ENSP00000259808:p.Asn402Asp	171.0	0.0		114.0	5.0	NM_003804	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	Missense_Mutation	SNP	ENST00000259808.4	hg19	CCDS4482.1	.	.	.	.	.	.	.	.	.	.	A	12.42	1.934090	0.34096	.	.	ENSG00000137275	ENST00000259808;ENST00000541791;ENST00000380409	T;T;T	0.77098	-1.07;-0.56;-1.07	5.6	0.295	0.15752	.	1.461890	0.03202	N	0.174871	T	0.51449	0.1675	L	0.53249	1.67	0.09310	N	1	P;P	0.36535	0.557;0.514	B;B	0.31101	0.124;0.039	T	0.43360	-0.9396	10	0.44086	T	0.13	-2.7032	5.528	0.16968	0.6328:0.1354:0.2318:0.0	.	356;402	Q13546-2;Q13546	.;RIPK1_HUMAN	D	402;356;402	ENSP00000259808:N402D;ENSP00000442294:N356D;ENSP00000369773:N402D	ENSP00000259808:N402D	N	+	1	0	RIPK1	3050912	0.000000	0.05858	0.000000	0.03702	0.912000	0.54170	0.066000	0.14489	0.077000	0.16863	0.533000	0.62120	AAT	.	.		0.502	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039659.2	NM_003804		G	3105913	A	G	3105913	3	3	100	1	0	0	0	0	1	0	0	0	13395	246	9	2	1234	2	RIPK1	6	3105913	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		3105913	168009154	87	13656										
GFOD1	54438	hgsc.bcm.edu	37	chr6	13487004	13487004	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tcatctccttggccagctccTccgcttcttcctgcgtgcgg	9	17	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr6:13487004T>C	ENST00000379287.3	-	1	783	c.119A>G	c.(118-120)gAg>gGg	p.E40G	GFOD1-AS1_ENST00000446001.1_RNA|GFOD1_ENST00000379278.3_5'Flank|AL583828.1_ENST00000558378.1_5'Flank|GFOD1_ENST00000603223.1_Missense_Mutation_p.E40G	NM_018988.3	NP_061861.1	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain containing 1	40						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)	18	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)			GGCCAGCTCCTCCGCTTCTTC	0.622																																					p.E40G		Atlas-SNP	.											.	GFOD1	38	.	0			c.A119G						.						153	124	134					6																	13487004		2203	4300	6503	SO:0001583	missense	54438	exon1			AGCTCCTCCGCTT	AK000337	CCDS4524.1, CCDS56397.1, CCDS64351.1	6p24.1-p23	2013-09-19			ENSG00000145990	ENSG00000145990			21096	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 114"	C6orf114			Standard	NM_018988		Approved	FLJ20330, ADG-90	uc003nat.2	Q9NXC2	OTTHUMG00000014276	ENST00000379287.3:c.119A>G	chr6.hg19:g.13487004T>C	ENSP00000368589:p.Glu40Gly	83.0	0.0		78.0	4.0	NM_018988	A8E4L6|Q5T058|Q96JD4|Q9H5K2	Missense_Mutation	SNP	ENST00000379287.3	hg19	CCDS4524.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.862194	0.71949	.	.	ENSG00000145990	ENST00000379287	T	0.25749	1.78	4.39	4.39	0.52855	Oxidoreductase, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.18045	0.0433	M	0.64997	1.995	0.80722	D	1	B	0.22276	0.067	B	0.30646	0.118	T	0.06972	-1.0797	10	0.56958	D	0.05	-0.6489	12.9312	0.58288	0.0:0.0:0.0:1.0	.	40	Q9NXC2	GFOD1_HUMAN	G	40	ENSP00000368589:E40G	ENSP00000368589:E40G	E	-	2	0	GFOD1	13594983	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.706000	0.84615	1.841000	0.53522	0.438000	0.28831	GAG	.	.		0.622	GFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039902.1	NM_018988		C	13487004	T	C	13487004	3	2	100	1	0	0	0	0	1	0	0	0	6351	1551	54	2	1061	2	GFOD1	6	13487004	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	10381091	13487004	157628063	88	13657										
BAT2	7916	hgsc.bcm.edu	37	chr6	31603241	31603241	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gctaacagcatcagtcactgAggtaagtgggagtaagagtt	13	6	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr6:31603241A>G	ENST00000376033.2	+	23	5606	c.5372A>G	c.(5371-5373)gAg>gGg	p.E1791G	PRRC2A_ENST00000376007.4_Splice_Site_p.E1791G	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1791	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TCAGTCACTGAGGTAAGTGGG	0.522																																					p.E1791G		Atlas-SNP	.											.	PRRC2A	152	.	0			c.A5372G						.						113	111	112					6																	31603241		1511	2709	4220	SO:0001630	splice_region_variant	7916	exon23			TCACTGAGGTAAG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5373+1A>G	chr6.hg19:g.31603241A>G		168.0	0.0		98.0	4.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	hg19	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	A	11.06	1.527599	0.27299	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01981	4.52;4.52	4.94	2.36	0.29203	.	0.207947	0.34268	N	0.004101	T	0.00496	0.0016	N	0.08118	0	0.35216	D	0.775561	B	0.02656	0.0	B	0.04013	0.001	T	0.46898	-0.9158	10	0.87932	D	0	-6.4453	2.8996	0.05701	0.6118:0.0:0.2061:0.1822	.	1791	P48634	PRC2A_HUMAN	G	1785;1774;1791;1791;1016	ENSP00000365175:E1791G;ENSP00000365201:E1791G	ENSP00000365175:E1791G	E	+	2	0	PRRC2A	31711220	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	2.076000	0.41548	1.008000	0.39264	0.459000	0.35465	GAG	.	.		0.522	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	Missense_Mutation	G	31603241	A	G	31603241	5	3	100	1	0	0	0	0	0	0	1	0	1319	318	11	2	5458	2	BAT2	6	31603241	Splice_Site	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	18116237	31603241	139511826	89	13658										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72960073	72960073	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agtgggacaccagctgattgTaaatgttctgcaagcaacag	11	8	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr6:72960073T>C	ENST00000521978.1	+	13	2282	c.2282T>C	c.(2281-2283)gTa>gCa	p.V761A	RIMS1_ENST00000401910.3_Missense_Mutation_p.V235A|RIMS1_ENST00000522291.1_Missense_Mutation_p.V761A|RIMS1_ENST00000523963.1_Missense_Mutation_p.V235A|RIMS1_ENST00000425662.2_Missense_Mutation_p.V154A|RIMS1_ENST00000491071.2_Missense_Mutation_p.V761A|RIMS1_ENST00000520567.1_Missense_Mutation_p.V761A|RIMS1_ENST00000517960.1_Missense_Mutation_p.V761A|RIMS1_ENST00000538414.1_5'Flank|RIMS1_ENST00000264839.7_Missense_Mutation_p.V761A|RIMS1_ENST00000348717.5_Missense_Mutation_p.V761A|RIMS1_ENST00000518273.1_Missense_Mutation_p.V761A|RIMS1_ENST00000517827.1_Missense_Mutation_p.V220A	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	761	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				CAGCTGATTGTAAATGTTCTG	0.368																																					p.V761A		Atlas-SNP	.											.	RIMS1	278	.	0			c.T2282C						.						83	81	82					6																	72960073		1857	4101	5958	SO:0001583	missense	22999	exon13			TGATTGTAAATGT	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2282T>C	chr6.hg19:g.72960073T>C	ENSP00000428417:p.Val761Ala	174.0	0.0		95.0	4.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.342893	0.82022	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827	D;D;D;D;D;D;D;D;D;D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82	5.28	4.07	0.47477	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.093937	0.44902	D	0.000419	D	0.91818	0.7411	M	0.91972	3.26	0.80722	D	1	D;B;D;D;D;D;D	0.89917	0.982;0.028;0.995;0.995;1.0;0.997;0.995	D;B;D;D;D;D;D	0.97110	0.995;0.215;0.998;0.998;1.0;0.998;0.998	D	0.93054	0.6468	10	0.87932	D	0	-15.1989	12.354	0.55165	0.0:0.0:0.1412:0.8588	.	220;235;761;220;235;761;761	B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;C9JNW6;Q86UR5	.;.;.;.;.;.;RIMS1_HUMAN	A	761;761;761;761;761;761;761;761;761;761;761;761;235;235;154;154;220	ENSP00000430101:V761A;ENSP00000275037:V761A;ENSP00000264839:V761A;ENSP00000429959:V761A;ENSP00000430408:V761A;ENSP00000430502:V761A;ENSP00000430932:V761A;ENSP00000428417:V761A;ENSP00000385649:V235A;ENSP00000428328:V235A;ENSP00000411235:V154A;ENSP00000389503:V154A;ENSP00000428367:V220A	ENSP00000264839:V761A	V	+	2	0	RIMS1	73016794	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	7.993000	0.88291	0.889000	0.36185	0.477000	0.44152	GTA	.	.		0.368	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			C	72960073	T	C	72960073	3	2	100	1	0	0	0	0	1	0	0	0	13382	1638	57	2	2495	2	RIMS1	6	72960073	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	41356832	72960073	98154994	90	13659										
C6orf167	253714	hgsc.bcm.edu	37	chr6	97627437	97627437	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aagtgcttcacataatgtgcTgtagaaacaaattgacaaat	7	6	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr6:97627437T>C	ENST00000275053.4	-	17	2650		c.e17-2		MMS22L_ENST00000369251.2_Splice_Site	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein						double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						CATAATGTGCTGTAGAAACAA	0.318																																					.		Atlas-SNP	.											.	MMS22L	102	.	0			c.2385-2A>G						.						44	43	43					6																	97627437		2203	4299	6502	SO:0001630	splice_region_variant	253714	exon18			ATGTGCTGTAGAA		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"chromosome 6 open reading frame 167"	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.2385-2A>G	chr6.hg19:g.97627437T>C		61.0	0.0		55.0	4.0	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Splice_Site	SNP	ENST00000275053.4	hg19	CCDS5039.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.094512	0.76870	.	.	ENSG00000146263	ENST00000275053;ENST00000369251	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9664	0.71198	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MMS22L	97734158	1.000000	0.71417	0.999000	0.59377	0.907000	0.53573	4.896000	0.63222	2.272000	0.75746	0.524000	0.50904	.	.	.		0.318	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468	Intron	C	97627437	T	C	97627437	5	2	100	1	0	0	0	0	0	0	1	0	2344	1594	55	2	1384	2	C6orf167	6	97627437	Splice_Site	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	24667364	97627437	73487630	91	13660										
ROS1	6098	hgsc.bcm.edu	37	chr6	117718268	117718268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aatattcctaatcaaaggtgCagtttcaggaactggaagag	10	6	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr6:117718268C>T	ENST00000368508.3	-	7	787	c.589G>A	c.(589-591)Gca>Aca	p.A197T	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.A206T	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	197	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		ATCAAAGGTGCAGTTTCAGGA	0.383			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.A197T		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.G589A						.						77	77	77					6																	117718268		2203	4300	6503	SO:0001583	missense	6098	exon7			AAGGTGCAGTTTC	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.589G>A	chr6.hg19:g.117718268C>T	ENSP00000357494:p.Ala197Thr	158.0	0.0		96.0	4.0	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	hg19	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.203963	0.79127	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.56776	0.44;0.44	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000003	T	0.68063	0.2960	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67260	-0.5715	10	0.51188	T	0.08	.	18.8227	0.92103	0.0:1.0:0.0:0.0	.	197	P08922	ROS1_HUMAN	T	197;206	ENSP00000357494:A197T;ENSP00000357493:A206T	ENSP00000357493:A206T	A	-	1	0	ROS1	117824961	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	2.223000	0.42936	2.762000	0.94881	0.650000	0.86243	GCA	.	.		0.383	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			T	117718268	C	T	117718268	3	4	100	1	0	0	0	0	1	0	0	0	13546	710	25	3	6602	3	ROS1	6	117718268	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	20090831	117718268	53396799	92	13661										
AIMP2	7965	hgsc.bcm.edu	37	chr7	6063115	6063115	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gagggaagcagtaaagaaaaAgccgctgttttccgctccat	11	9	0	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:6063115A>G	ENST00000223029.3	+	4	875	c.756A>G	c.(754-756)aaA>aaG	p.K252K	EIF2AK1_ENST00000199389.6_3'UTR|AIMP2_ENST00000400479.2_Silent_p.K174K|AIMP2_ENST00000395236.2_Silent_p.K183K	NM_006303.3	NP_006294.2	Q13155	AIMP2_HUMAN	aminoacyl tRNA synthetase complex-interacting multifunctional protein 2	252	GST C-terminal.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|tRNA aminoacylation for protein translation (GO:0006418)|Type II pneumocyte differentiation (GO:0060510)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						GTAAAGAAAAAGCCGCTGTTT	0.488																																					p.K252K		Atlas-SNP	.											.	AIMP2	32	.	0			c.A756G						.						81	77	79					7																	6063115		2203	4300	6503	SO:0001819	synonymous_variant	7965	exon4			AGAAAAAGCCGCT	U24169	CCDS5344.1	7p22.1	2009-05-29			ENSG00000106305	ENSG00000106305			20609	protein-coding gene	gene with protein product		600859				8666379, 18695251	Standard	NM_006303		Approved	p38, PRO0992, JTV-1, JTV1	uc003spo.3	Q13155	OTTHUMG00000122077	ENST00000223029.3:c.756A>G	chr7.hg19:g.6063115A>G		174.0	0.0		94.0	6.0	NM_006303	Q75MR1|Q96CZ5|Q9P1L2	Silent	SNP	ENST00000223029.3	hg19	CCDS5344.1																																																																																			.	.		0.488	AIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242834.2	NM_006303		G	6063115	A	G	6063115	2	3	100	1	0	0	0	0	0	0	0	1	434	69	3	2		2	AIMP2	7	6063115	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		6063115	153075548	93	13662										
OSBPL3	26031	hgsc.bcm.edu	37	chr7	24849448	24849448	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gctctccatacacaggcagaAgaggagccgccgccacagta	11	14	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:24849448A>G	ENST00000313367.2	-	20	2746	c.2295T>C	c.(2293-2295)tcT>tcC	p.S765S	OSBPL3_ENST00000487020.1_5'UTR|OSBPL3_ENST00000396429.1_Silent_p.S729S|OSBPL3_ENST00000353930.1_Silent_p.S729S|OSBPL3_ENST00000396431.1_Silent_p.S734S|OSBPL3_ENST00000352860.1_Silent_p.S734S|OSBPL3_ENST00000409069.1_Silent_p.S698S|OSBPL3_ENST00000431825.2_Silent_p.S698S	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	765					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						CACAGGCAGAAGAGGAGCCGC	0.547																																					p.S765S		Atlas-SNP	.											.	OSBPL3	100	.	0			c.T2295C						.						90	80	83					7																	24849448		2203	4300	6503	SO:0001819	synonymous_variant	26031	exon20			GGCAGAAGAGGAG	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.2295T>C	chr7.hg19:g.24849448A>G		125.0	0.0		70.0	4.0	NM_015550	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Silent	SNP	ENST00000313367.2	hg19	CCDS5390.1																																																																																			.	.		0.547	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2			G	24849448	A	G	24849448	2	3	100	1	0	0	0	0	0	0	0	1	11288	59	3	2		2	OSBPL3	7	24849448	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	18786333	24849448	134289215	94	13663										
CCDC129	223075	hgsc.bcm.edu	37	chr7	31683097	31683097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttcctctaaatactggcagcTccaggtctgtaatgacccag	8	12	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:31683097T>C	ENST00000407970.3	+	11	2151	c.2113T>C	c.(2113-2115)Tcc>Ccc	p.S705P	CCDC129_ENST00000319386.3_Missense_Mutation_p.S557P|CCDC129_ENST00000409210.1_Missense_Mutation_p.S613P|CCDC129_ENST00000451887.2_Missense_Mutation_p.S731P	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	705										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TACTGGCAGCTCCAGGTCTGT	0.537																																					p.S731P		Atlas-SNP	.											.	CCDC129	127	.	0			c.T2191C						.						60	62	61					7																	31683097		2203	4300	6503	SO:0001583	missense	223075	exon11			GGCAGCTCCAGGT	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.2113T>C	chr7.hg19:g.31683097T>C	ENSP00000384416:p.Ser705Pro	149.0	0.0		98.0	5.0	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	hg19	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	T	15.88	2.963296	0.53507	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.24538	1.85;2.13;2.12;1.86	5.81	0.31	0.15825	.	0.376195	0.23307	N	0.049620	T	0.34366	0.0895	M	0.64997	1.995	0.09310	N	1	D;D;D;D	0.63880	0.993;0.985;0.985;0.985	P;P;P;P	0.62298	0.9;0.838;0.838;0.838	T	0.12400	-1.0549	10	0.51188	T	0.08	-0.1602	2.2277	0.03988	0.151:0.0836:0.3134:0.4519	.	731;715;705;557	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	P	557;705;731;715;613	ENSP00000313062:S557P;ENSP00000384416:S705P;ENSP00000395835:S731P;ENSP00000387214:S613P	ENSP00000313062:S557P	S	+	1	0	CCDC129	31649622	0.046000	0.20272	0.000000	0.03702	0.016000	0.09150	0.318000	0.19504	0.104000	0.17725	0.533000	0.62120	TCC	.	.		0.537	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		C	31683097	T	C	31683097	3	2	100	1	0	0	0	0	1	0	0	0	2766	1551	54	2	2151	2	CCDC129	7	31683097	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	6833649	31683097	127455566	95	13664										
CAMK2B	816	hgsc.bcm.edu	37	chr7	44279251	44279251	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cattgtggccggagcggtggTctgtctgcccactgttagca	14	11	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:44279251T>C	ENST00000395749.2	-	13	1034	c.958A>G	c.(958-960)Acc>Gcc	p.T320A	CAMK2B_ENST00000502837.2_Missense_Mutation_p.T191A|CAMK2B_ENST00000395747.2_Intron|CAMK2B_ENST00000440254.2_Missense_Mutation_p.T320A|CAMK2B_ENST00000346990.4_Intron|CAMK2B_ENST00000350811.3_Missense_Mutation_p.T320A|CAMK2B_ENST00000457475.1_Intron|CAMK2B_ENST00000358707.3_Intron|CAMK2B_ENST00000353625.4_Intron|CAMK2B_ENST00000347193.4_Missense_Mutation_p.T320A|CAMK2B_ENST00000258682.6_Intron	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	320					activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						GGAGCGGTGGTCTGTCTGCCC	0.647																																					p.T320A		Atlas-SNP	.											.	CAMK2B	56	.	0			c.A958G						.						63	44	50					7																	44279251		1878	3632	5510	SO:0001583	missense	816	exon13			CGGTGGTCTGTCT	U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"CaM-kinase II beta chain", "calcium/calmodulin-dependent protein kinase type II beta chain", "CaM kinase II beta subunit", "proline rich calmodulin-dependent protein kinase"	607707	"calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.958A>G	chr7.hg19:g.44279251T>C	ENSP00000379098:p.Thr320Ala	69.0	0.0		35.0	4.0	NM_172082	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Missense_Mutation	SNP	ENST00000395749.2	hg19	CCDS5483.1	.	.	.	.	.	.	.	.	.	.	T	13.98	2.398827	0.42512	.	.	ENSG00000058404	ENST00000350811;ENST00000395749;ENST00000502837;ENST00000440254;ENST00000347193	T;T;T;T;T	0.66280	-0.18;-0.2;0.53;-0.18;-0.19	4.68	4.68	0.58851	Protein kinase-like domain (1);	.	.	.	.	T	0.67636	0.2914	L	0.43152	1.355	0.51482	D	0.99992	D;P;B	0.56035	0.974;0.905;0.001	D;B;B	0.67725	0.953;0.202;0.001	T	0.62062	-0.6933	9	0.11182	T	0.66	.	13.2445	0.60016	0.0:0.0:0.0:1.0	.	320;320;320	Q13554-6;Q13554;Q13554-2	.;KCC2B_HUMAN;.	A	320;320;191;320;320	ENSP00000326375:T320A;ENSP00000379098:T320A;ENSP00000422416:T191A;ENSP00000397937:T320A;ENSP00000326544:T320A	ENSP00000326544:T320A	T	-	1	0	CAMK2B	44245776	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.902000	0.75699	1.982000	0.57802	0.455000	0.32223	ACC	.	.		0.647	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084		C	44279251	T	C	44279251	3	2	100	1	0	0	0	0	1	0	0	0	2602	1667	58	2	1089	2	CAMK2B	7	44279251	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	12596154	44279251	114859412	96	13665										
EGFR	1956	hgsc.bcm.edu	37	chr7	55249014	55249014	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cgtgatggccagcgtggacaAcccccacgtgtgccgcctgc	13	16	0	1	rs397517113|rs121913445		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:55249014A>G	ENST00000275493.2	+	20	2489	c.2312A>G	c.(2311-2313)aAc>aGc	p.N771S	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Missense_Mutation_p.N726S|EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000454757.2_Missense_Mutation_p.N718S	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	771	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.D770_N771insSVD(7)|p.N771_P772>SVDNR(1)|p.N771_P772insRH(1)|p.N771>TH(1)|p.D770_N771>AGG(1)|p.N771>SH(1)|p.N771>GF(1)|p.D770_N771insMATP(1)|p.D770_P772>ASVDNR(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	AGCGTGGACAACCCCCACGTG	0.647		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.N771S		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	.,3	EGFR	20426	.	15	Insertion - In frame(9)|Complex - insertion inframe(6)	lung(15)	c.A2312G						.						105	96	99					7																	55249014		2203	4300	6503	SO:0001583	missense	1956	exon20	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	TGGACAACCCCCA		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2312A>G	chr7.hg19:g.55249014A>G	ENSP00000275493:p.Asn771Ser	76.0	0.0		48.0	3.0	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	hg19	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.498959	0.64298	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	T;T;T	0.61510	0.1;0.1;0.1	5.85	4.7	0.59300	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.085206	0.85682	D	0.000000	T	0.35480	0.0933	N	0.12831	0.26	0.47584	D	0.999469	B;B	0.27791	0.189;0.169	B;B	0.22601	0.003;0.04	T	0.11542	-1.0583	10	0.19590	T	0.45	.	10.9301	0.47213	0.9258:0.0:0.0742:0.0	.	726;771	Q504U8;P00533	.;EGFR_HUMAN	S	726;641;771;718	ENSP00000415559:N726S;ENSP00000275493:N771S;ENSP00000395243:N718S	ENSP00000275493:N771S	N	+	2	0	EGFR	55216508	1.000000	0.71417	0.990000	0.47175	0.995000	0.86356	6.264000	0.72527	1.030000	0.39839	0.533000	0.62120	AAC	.	.		0.647	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55249014	A	G	55249014	3	3	100	1	0	0	0	0	1	0	0	0	4969	43	2	2	2654	2	EGFR	7	55249014	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	10969763	55249014	103889649	97	13666										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	71142270	71142270	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cacacagcaatattgtatccGtgccatggctggggaccaca	10	12	0	0	rs145007893		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:71142270G>A	ENST00000333538.5	+	9	2113	c.1479G>A	c.(1477-1479)ccG>ccA	p.P493P	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	493	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				TATTGTATCCGTGCCATGGCT	0.537																																					p.P493P		Atlas-SNP	.											WBSCR17,rectum,carcinoma,+2,1	WBSCR17	208	.	0			c.G1479A						.	G		1,4405	2.1+/-5.4	0,1,2202	181	180	180		1479	-7.2	0.8	7	dbSNP_134	180	0,8600		0,0,4300	no	coding-synonymous	WBSCR17	NM_022479.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		493/599	71142270	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	64409	exon9			GTATCCGTGCCAT	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1479G>A	chr7.hg19:g.71142270G>A		77.0	0.0		50.0	3.0	NM_022479	Q8NFV9|Q9NTA8	Silent	SNP	ENST00000333538.5	hg19	CCDS5540.1																																																																																			.	G|1.000;A|0.000		0.537	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		A	71142270	G	A	71142270	2	1	100	1	0	0	0	0	0	0	0	1	17279	1132	40	1		1	WBSCR17	7	71142270	Silent	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	15893256	71142270	87996393	98	13667										
CCL24	6369	hgsc.bcm.edu	37	chr7	75442715	75442715	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cttggaaacaaagaacatgcAgcagggagaggggatgacca	14	7	0	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:75442715A>G	ENST00000416943.1	-	3	193	c.100T>C	c.(100-102)Tgc>Cgc	p.C34R	CCL24_ENST00000222902.2_Missense_Mutation_p.C34R	NM_002991.2	NP_002982.2	O00175	CCL24_HUMAN	chemokine (C-C motif) ligand 24	34					cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of inflammatory response (GO:0050729)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(1)|lung(2)	3						AAGAACATGCAGCAGGGAGAG	0.552																																					p.C34R		Atlas-SNP	.											.	CCL24	11	.	0			c.T100C						.						69	71	70					7																	75442715		2203	4300	6503	SO:0001583	missense	6369	exon2			ACATGCAGCAGGG	U85768	CCDS34670.1	7q11.23	2013-02-25	2002-08-22	2002-08-23	ENSG00000106178	ENSG00000106178		"Chemokine ligands", "Endogenous ligands"	10623	protein-coding gene	gene with protein product	"CK-beta-6", "myeloid progenitor inhibitory factor 2", "eotaxin-2"	602495	"small inducible cytokine subfamily A (Cys-Cys), member 24"	SCYA24		9104803, 9598329	Standard	NM_002991		Approved	Ckb-6, MPIF-2, eotaxin-2, MPIF2	uc011kga.2	O00175	OTTHUMG00000156635	ENST00000416943.1:c.100T>C	chr7.hg19:g.75442715A>G	ENSP00000400533:p.Cys34Arg	55.0	0.0		31.0	4.0	NM_002991	B2R5K2	Missense_Mutation	SNP	ENST00000416943.1	hg19	CCDS34670.1	.	.	.	.	.	.	.	.	.	.	.	12.79	2.044754	0.36085	.	.	ENSG00000106178	ENST00000222902;ENST00000416943	D;D	0.85556	-2.0;-2.0	4.14	4.14	0.48551	Chemokine interleukin-8-like domain (3);	0.000000	0.53938	D	0.000054	D	0.94565	0.8249	H	0.98027	4.13	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95008	0.8149	10	0.87932	D	0	.	9.7462	0.40448	1.0:0.0:0.0:0.0	.	34	O00175	CCL24_HUMAN	R	34	ENSP00000222902:C34R;ENSP00000400533:C34R	ENSP00000222902:C34R	C	-	1	0	CCL24	75280651	0.999000	0.42202	0.997000	0.53966	0.187000	0.23431	3.605000	0.54088	1.868000	0.54150	0.533000	0.62120	TGC	.	.		0.552	CCL24-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344886.1	NM_002991		G	75442715	A	G	75442715	3	3	100	1	0	0	0	0	1	0	0	0	2898	188	7	2	265	2	CCL24	7	75442715	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	4300445	75442715	83695948	99	13668										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83610694	83610694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	catcccaagcacagtaagggTctcgggcgaggcaacactca	11	13	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:83610694T>C	ENST00000265362.4	-	14	1909	c.1595A>G	c.(1594-1596)gAc>gGc	p.D532G	SEMA3A_ENST00000436949.1_Missense_Mutation_p.D532G	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	532					apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						ACAGTAAGGGTCTCGGGCGAG	0.453																																					p.D532G		Atlas-SNP	.											.	SEMA3A	121	.	0			c.A1595G						.						77	70	73					7																	83610694		2203	4300	6503	SO:0001583	missense	10371	exon14			TAAGGGTCTCGGG	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1595A>G	chr7.hg19:g.83610694T>C	ENSP00000265362:p.Asp532Gly	120.0	0.0		88.0	5.0	NM_006080		Missense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	T	19.21	3.784242	0.70222	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.52057	0.68;0.68	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.69296	0.3095	H	0.94771	3.58	0.80722	D	1	P	0.50617	0.937	P	0.49301	0.606	T	0.79928	-0.1596	10	0.87932	D	0	.	15.9869	0.80160	0.0:0.0:0.0:1.0	.	532	Q14563	SEM3A_HUMAN	G	532	ENSP00000265362:D532G;ENSP00000415260:D532G	ENSP00000265362:D532G	D	-	2	0	SEMA3A	83448630	1.000000	0.71417	0.998000	0.56505	0.235000	0.25334	7.991000	0.88244	2.171000	0.68590	0.533000	0.62120	GAC	.	.		0.453	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		C	83610694	T	C	83610694	3	2	100	1	0	0	0	0	1	0	0	0	14039	1667	58	2	736	2	SEMA3A	7	83610694	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	8167979	83610694	75527969	100	13669										
RINT1	60561	hgsc.bcm.edu	37	chr7	105205724	105205724	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	taaaaatgtgttttttccagAtggttgtccttgccatctca	7	8	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:105205724A>G	ENST00000257700.2	+	13	2118	c.1887A>G	c.(1885-1887)agA>agG	p.R629R	EFCAB10_ENST00000480514.1_3'UTR|EFCAB10_ENST00000485614.1_3'UTR|EFCAB10_ENST00000490493.1_5'Flank	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	629	RINT1/TIP20. {ECO:0000255|PROSITE- ProRule:PRU00717}.				G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TTTTTTCCAGATGGTTGTCCT	0.403																																					p.R629R		Atlas-SNP	.											.	RINT1	65	.	0			c.A1887G						.						77	71	73					7																	105205724		2203	4300	6503	SO:0001630	splice_region_variant	60561	exon13			TTCCAGATGGTTG	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.1887-1A>G	chr7.hg19:g.105205724A>G		126.0	0.0		101.0	5.0	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Silent	SNP	ENST00000257700.2	hg19	CCDS34726.1																																																																																			.	.		0.403	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930	Silent	G	105205724	A	G	105205724	5	3	100	1	0	0	0	0	0	0	1	0	13391	347	12	2	1937	2	RINT1	7	105205724	Splice_Site	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	21595030	105205724	53932939	101	13670										
HBP1	26959	hgsc.bcm.edu	37	chr7	106836396	106836396	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	caagactttgcaagatctggAttcagtaaaaactgtggctc	9	8	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:106836396A>G	ENST00000222574.4	+	9	1371	c.1185A>G	c.(1183-1185)ggA>ggG	p.G395G	CTA-363E19.2_ENST00000607036.1_RNA|HBP1_ENST00000485846.1_Silent_p.G395G|HBP1_ENST00000468410.1_Silent_p.G395G|HBP1_ENST00000461963.1_3'UTR	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	395					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						CAAGATCTGGATTCAGTAAAA	0.463																																					p.G405G		Atlas-SNP	.											.	HBP1	31	.	0			c.A1215G						.						133	125	128					7																	106836396		2203	4300	6503	SO:0001819	synonymous_variant	26959	exon9			ATCTGGATTCAGT	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.1185A>G	chr7.hg19:g.106836396A>G		186.0	0.0		123.0	5.0	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Silent	SNP	ENST00000222574.4	hg19	CCDS5741.1																																																																																			.	.		0.463	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		G	106836396	A	G	106836396	2	3	100	1	0	0	0	0	0	0	0	1	6994	320	12	2		2	HBP1	7	106836396	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1630672	106836396	52302267	102	13671										
FAM40B	57464	hgsc.bcm.edu	37	chr7	129079892	129079892	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gactgtcccactctggagttTgagtatggagatgcagatgg	14	7	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:129079892T>C	ENST00000249344.2	+	2	199	c.159T>C	c.(157-159)ttT>ttC	p.F53F	STRIP2_ENST00000435494.2_Silent_p.F53F	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	53					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											CTCTGGAGTTTGAGTATGGAG	0.517																																					p.F53F		Atlas-SNP	.											.	.	.	.	0			c.T159C						.						119	109	112					7																	129079892		2203	4300	6503	SO:0001819	synonymous_variant	57464	exon2			GGAGTTTGAGTAT	AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog B (yeast)"		"family with sequence similarity 40, member B"	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.159T>C	chr7.hg19:g.129079892T>C		267.0	0.0		169.0	7.0	NM_020704	Q8WUZ4	Silent	SNP	ENST00000249344.2	hg19	CCDS34752.1																																																																																			.	.		0.517	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336		C	129079892	T	C	129079892	2	2	100	1	0	0	0	0	0	0	0	1	5569	1809	63	2		2	FAM40B	7	129079892	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	22243496	129079892	30058771	103	13672										
EZH2	2146	hgsc.bcm.edu	37	chr7	148507486	148507486	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tacactttccctcttctgtcAgcttcatcttgagaaataat	4	11	5	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:148507486A>G	ENST00000460911.1	-	17	2041	c.1953T>C	c.(1951-1953)gcT>gcC	p.A651A	EZH2_ENST00000483967.1_Silent_p.A642A|EZH2_ENST00000320356.2_Silent_p.A656A|EZH2_ENST00000350995.2_Silent_p.A612A|EZH2_ENST00000476773.1_Silent_p.A600A|EZH2_ENST00000541220.1_Silent_p.A600A|EZH2_ENST00000478654.1_Silent_p.A600A			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	651	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			CTCTTCTGTCAGCTTCATCTT	0.403			Mis		DLBCL																																p.A656A		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,colon,carcinoma,0,2	EZH2	823	.	0			c.T1968C						.						85	74	78					7																	148507486		2202	4300	6502	SO:0001819	synonymous_variant	2146	exon17			TCTGTCAGCTTCA		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"Chromatin-modifying enzymes / K-methyltransferases"	3527	protein-coding gene	gene with protein product		601573	"enhancer of zeste (Drosophila) homolog 2", "enhancer of zeste homolog 2 (Drosophila)"			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.1953T>C	chr7.hg19:g.148507486A>G		53.0	0.0		42.0	2.0	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Silent	SNP	ENST00000460911.1	hg19	CCDS56516.1																																																																																			.	.		0.403	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		G	148507486	A	G	148507486	2	3	100	1	0	0	0	0	0	0	0	1	5336	175	7	2		2	EZH2	7	148507486	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	19427594	148507486	10631177	104	13673										
SSPO	23145	hgsc.bcm.edu	37	chr7	149500388	149500388	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtgcccccatgcccaccctcCtgcctggatcccaaggccaa	8	20	0	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:149500388C>T	ENST00000378016.2	+	0	7914							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GCCCACCCTCCTGCCTGGATC	0.652																																					p.S2638S		Atlas-SNP	.											.	.	.	.	0			c.C7914T						.						40	51	47					7																	149500388		2110	4235	6345			23145	exon53			ACCCTCCTGCCTG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149500388C>T		48.0	0.0		39.0	5.0	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149500388	C	T	149500388	1	4	100	0	1	0	0	0	0	0	0	0	15204	668	24	3		3	SSPO	7	149500388	RNA	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	992902	149500388	9638275	105	13674										
ACCN3	9311	hgsc.bcm.edu	37	chr7	150748946	150748946	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttgaggccctcaactatgagAccgtggagcagaagaaggcc	13	10	1	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr7:150748946A>G	ENST00000349064.5	+	7	1462	c.1264A>G	c.(1264-1266)Acc>Gcc	p.T422A	ASIC3_ENST00000297512.8_Missense_Mutation_p.T422A|ASIC3_ENST00000357922.4_Missense_Mutation_p.T422A	NM_004769.3|NM_020321.3	NP_004760.1|NP_064717.1	Q9UHC3	ASIC3_HUMAN	acid-sensing (proton-gated) ion channel 3	422					cation transmembrane transport (GO:0098655)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ion transmembrane transport (GO:0034220)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|response to heat (GO:0009408)|sensory perception (GO:0007600)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|enterobactin transporter activity (GO:0042931)|ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)										CAACTATGAGACCGTGGAGCA	0.607																																					p.T422A		Atlas-SNP	.											.	.	.	.	0			c.A1264G						.						111	101	105					7																	150748946		2203	4300	6503	SO:0001583	missense	9311	exon7			TATGAGACCGTGG	AB010575	CCDS5914.1, CCDS5915.1, CCDS5916.1	7q35	2012-02-23	2012-02-22	2012-02-22	ENSG00000213199	ENSG00000213199		"Ion channels / Acid-sensing (proton-gated) ion channels"	101	protein-coding gene	gene with protein product	"testis sodium channel 1"	611741	"amiloride-sensitive cation channel 3, testis", "amiloride-sensitive cation channel 3"	ACCN3		9571199, 9744806	Standard	NM_004769		Approved	TNaC1, DRASIC	uc003wio.3	Q9UHC3	OTTHUMG00000158685	ENST00000349064.5:c.1264A>G	chr7.hg19:g.150748946A>G	ENSP00000344838:p.Thr422Ala	144.0	0.0		89.0	5.0	NM_020322	B2R9V0|O60263|O75906|Q59FN9|Q9UER8|Q9UHC4	Missense_Mutation	SNP	ENST00000349064.5	hg19	CCDS5916.1	.	.	.	.	.	.	.	.	.	.	a	10.90	1.482432	0.26598	.	.	ENSG00000213199	ENST00000357922;ENST00000349064;ENST00000297512;ENST00000490540	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	4.7	0.683	0.17998	.	0.435766	0.16264	N	0.222087	T	0.45296	0.1335	L	0.39514	1.22	0.09310	N	1	B;B;B	0.11235	0.003;0.004;0.002	B;B;B	0.21708	0.036;0.007;0.011	T	0.27872	-1.0061	10	0.34782	T	0.22	-2.0045	2.1938	0.03906	0.5923:0.1603:0.0928:0.1545	.	422;422;422	Q9UHC3-2;Q9UHC3-3;Q9UHC3	.;.;ACCN3_HUMAN	A	422;422;422;53	ENSP00000350600:T422A;ENSP00000344838:T422A;ENSP00000297512:T422A;ENSP00000418361:T53A	ENSP00000297512:T422A	T	+	1	0	ACCN3	150379879	0.046000	0.20272	0.020000	0.16555	0.685000	0.39939	0.715000	0.25822	0.179000	0.19938	0.478000	0.44815	ACC	.	.		0.607	ASIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351725.1	NM_004769		G	150748946	A	G	150748946	3	3	100	1	0	0	0	0	1	0	0	0	130	275	10	2	1290	2	ACCN3	7	150748946	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1248558	150748946	8389717	106	13675										
ANGPT2	285	hgsc.bcm.edu	37	chr8	6420324	6420324	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tccatctctggcaggaggaaAgtgtagctgcaggacccatg	13	10	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr8:6420324A>G	ENST00000325203.5	-	1	606	c.132T>C	c.(130-132)acT>acC	p.T44T	MCPH1_ENST00000344683.5_Intron|ANGPT2_ENST00000338312.6_Silent_p.T44T|ANGPT2_ENST00000523120.1_Silent_p.T44T|ANGPT2_ENST00000415216.1_Silent_p.T44T			O15123	ANGP2_HUMAN	angiopoietin 2	44					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		GCAGGAGGAAAGTGTAGCTGC	0.552																																					p.T44T		Atlas-SNP	.											.	ANGPT2	126	.	0			c.T132C						.						127	102	111					8																	6420324		2203	4300	6503	SO:0001819	synonymous_variant	285	exon1			GAGGAAAGTGTAG	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"Fibrinogen C domain containing"	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.132T>C	chr8.hg19:g.6420324A>G		195.0	0.0		92.0	4.0	NM_001118888	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Silent	SNP	ENST00000325203.5	hg19	CCDS5958.1																																																																																			.	.		0.552	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147		G	6420324	A	G	6420324	2	3	100	1	0	0	0	0	0	0	0	1	611	59	3	2		2	ANGPT2	8	6420324	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		6420324	139943698	107	13676										
MTUS1	57509	hgsc.bcm.edu	37	chr8	17579296	17579296	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cacgaccagcagtgtcaataAggtagcatcatagtgcctct	9	11	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr8:17579296A>G	ENST00000262102.6	-	4	2674				MTUS1_ENST00000381861.3_Silent_p.L39L|MTUS1_ENST00000381869.3_Intron|MTUS1_ENST00000544260.1_Intron|MTUS1_ENST00000519263.1_Intron	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1						cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		AGTGTCAATAAGGTAGCATCA	0.418																																					p.L39L		Atlas-SNP	.											.	MTUS1	144	.	0			c.T115C						.						85	84	84					8																	17579296		1904	4109	6013	SO:0001627	intron_variant	57509	exon1			TCAATAAGGTAGC	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2449+1884T>C	chr8.hg19:g.17579296A>G		168.0	0.0		97.0	4.0	NM_001001931	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	hg19	CCDS43717.1																																																																																			.	.		0.418	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		G	17579296	A	G	17579296	1	3	100	0	1	0	0	0	0	0	0	0	9974	69	3	2		2	MTUS1	8	17579296	Intron	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	11158972	17579296	128784726	108	13677										
SLC39A14	23516	hgsc.bcm.edu	37	chr8	22273319	22273319	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccattatgcctctgagtcgcTtccctccaagaaggaccagg	9	14	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr8:22273319T>C	ENST00000381237.1	+	6	907	c.788T>C	c.(787-789)cTt>cCt	p.L263P	SLC39A14_ENST00000240095.6_Missense_Mutation_p.L263P|SLC39A14_ENST00000359741.5_Missense_Mutation_p.L263P|SLC39A14_ENST00000289952.5_Missense_Mutation_p.L263P	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	263					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		TCTGAGTCGCTTCCCTCCAAG	0.557																																					p.L263P		Atlas-SNP	.											.	SLC39A14	59	.	0			c.T788C						.						79	66	70					8																	22273319		2203	4300	6503	SO:0001583	missense	23516	exon6			AGTCGCTTCCCTC	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"Solute carriers"	20858	protein-coding gene	gene with protein product		608736	"solute carrier family 39 (metal ion transporter), member 14"			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.788T>C	chr8.hg19:g.22273319T>C	ENSP00000370635:p.Leu263Pro	66.0	0.0		58.0	4.0	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Missense_Mutation	SNP	ENST00000381237.1	hg19	CCDS47823.1	.	.	.	.	.	.	.	.	.	.	T	10.58	1.389319	0.25118	.	.	ENSG00000104635	ENST00000359741;ENST00000240095;ENST00000381237;ENST00000289952;ENST00000517370	T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84	5.75	3.31	0.37934	.	0.910923	0.09683	N	0.769478	T	0.41026	0.1141	L	0.28556	0.865	0.37406	D	0.91306	P;B;P	0.43788	0.817;0.003;0.753	P;B;B	0.45343	0.477;0.014;0.442	T	0.10613	-1.0622	10	0.29301	T	0.29	-10.9615	9.5118	0.39082	0.2731:0.0:0.0:0.7269	.	263;263;263	Q15043-2;Q15043;B6EU88	.;S39AE_HUMAN;.	P	263;263;263;263;86	ENSP00000352779:L263P;ENSP00000240095:L263P;ENSP00000370635:L263P;ENSP00000289952:L263P;ENSP00000427981:L86P	ENSP00000240095:L263P	L	+	2	0	SLC39A14	22329264	0.492000	0.26027	0.008000	0.14137	0.181000	0.23173	2.369000	0.44231	0.397000	0.25310	0.460000	0.39030	CTT	.	.		0.557	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677		C	22273319	T	C	22273319	3	2	100	1	0	0	0	0	1	0	0	0	14632	1609	56	2	980	2	SLC39A14	8	22273319	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	4694023	22273319	124090703	109	13678										
LRRCC1	85444	hgsc.bcm.edu	37	chr8	86022370	86022370	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gacttgaagaactaattaatCtgactagactaaatgtatct	6	6	2	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr8:86022370C>T	ENST00000360375.3	+	3	480	c.331C>T	c.(331-333)Ctg>Ttg	p.L111L	LRRCC1_ENST00000414626.2_Silent_p.L91L	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	111					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						ACTAATTAATCTGACTAGACT	0.249																																					p.L111L		Atlas-SNP	.											.	LRRCC1	212	.	0			c.C331T						.						95	86	89					8																	86022370		1808	4064	5872	SO:0001819	synonymous_variant	85444	exon3			ATTAATCTGACTA	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.331C>T	chr8.hg19:g.86022370C>T		123.0	0.0		107.0	22.0	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Silent	SNP	ENST00000360375.3	hg19	CCDS43750.1																																																																																			.	.		0.249	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		T	86022370	C	T	86022370	2	4	100	1	0	0	0	0	0	0	0	1	9035	912	32	3		3	LRRCC1	8	86022370	Silent	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	63749051	86022370	60341652	110	13679										
TSPYL5	85453	hgsc.bcm.edu	37	chr8	98288873	98288873	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tccattggctgctttcctggAccttgcctgccttctttttc	7	14	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr8:98288873A>G	ENST00000322128.3	-	1	1303	c.1200T>C	c.(1198-1200)ggT>ggC	p.G400G		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	400					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					GCTTTCCTGGACCTTGCCTGC	0.517																																					p.G400G		Atlas-SNP	.											.	TSPYL5	48	.	0			c.T1200C						.						180	181	181					8																	98288873		2203	4300	6503	SO:0001819	synonymous_variant	85453	exon1			TCCTGGACCTTGC	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.1200T>C	chr8.hg19:g.98288873A>G		219.0	0.0		157.0	7.0	NM_033512	B3KRF0|Q9C0B3	Silent	SNP	ENST00000322128.3	hg19	CCDS34927.1																																																																																			.	.		0.517	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512		G	98288873	A	G	98288873	2	3	100	1	0	0	0	0	0	0	0	1	16677	262	10	2		2	TSPYL5	8	98288873	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	12266503	98288873	48075149	111	13680										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125094661	125094661	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gagaaccgcttctacagcaaAcaccgagccatctgtggctt	9	13	2	1	rs540398915		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr8:125094661A>G	ENST00000522917.1	+	33	4559	c.4353A>G	c.(4351-4353)aaA>aaG	p.K1451K	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6_ENST00000399018.1_Silent_p.K1451K	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1451						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TCTACAGCAAACACCGAGCCA	0.502													A|||	1	0.000199681	0	0.0014	5008	,	,		21004	0		0	False		,,,				2504	0				p.K1451K		Atlas-SNP	.											.	FER1L6	268	.	0			c.A4353G						.						172	184	180					8																	125094661		2203	4300	6503	SO:0001819	synonymous_variant	654463	exon33			CAGCAAACACCGA	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.4353A>G	chr8.hg19:g.125094661A>G		100.0	0.0		71.0	4.0	NM_001039112		Silent	SNP	ENST00000522917.1	hg19	CCDS43767.1																																																																																			.	.		0.502	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		G	125094661	A	G	125094661	2	3	100	1	0	0	0	0	0	0	0	1	5823	40	2	2		2	FER1L6	8	125094661	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	26805788	125094661	21269361	112	13681										
C9orf68	55064	hgsc.bcm.edu	37	chr9	4604223	4604223	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtgagtatttcttcagagggTagcttggtctttcaatgata	11	5	4	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:4604223T>C	ENST00000454239.2	-	12	1381	c.1136A>G	c.(1135-1137)tAc>tGc	p.Y379C	SPATA6L_ENST00000381895.5_Missense_Mutation_p.Y256C|SPATA6L_ENST00000475086.1_Missense_Mutation_p.Y321C|SPATA6L_ENST00000381890.5_Intron			Q8N4H0	SPA6L_HUMAN	spermatogenesis associated 6-like	379																	CTTCAGAGGGTAGCTTGGTCT	0.338																																					p.Y321C		Atlas-SNP	.											.	SPATA6L	3	.	0			c.A962G						.						145	136	139					9																	4604223		1813	4084	5897	SO:0001583	missense	55064	exon10			AGAGGGTAGCTTG	AK000920	CCDS43785.1, CCDS43785.2	9p24.2	2012-03-15	2012-03-15	2012-03-15	ENSG00000106686	ENSG00000106686			25472	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 68"	C9orf68			Standard	NM_001039395		Approved	FLJ10058	uc011llz.2	Q8N4H0	OTTHUMG00000019469	ENST00000454239.2:c.1136A>G	chr9.hg19:g.4604223T>C	ENSP00000404277:p.Tyr379Cys	155.0	0.0		111.0	6.0	NM_001039395	B4DIY4|Q5JVJ5|Q8IY90	Missense_Mutation	SNP	ENST00000454239.2	hg19		.	.	.	.	.	.	.	.	.	.	T	0.739	-0.777003	0.02929	.	.	ENSG00000106686	ENST00000454239;ENST00000475086;ENST00000381895	T;T;T	0.25579	1.87;1.85;1.79	4.99	-7.07	0.01563	.	.	.	.	.	T	0.14141	0.0342	L	0.29908	0.895	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.08055	0.0;0.0;0.003	T	0.31971	-0.9924	9	0.41790	T	0.15	-7.8174	6.9088	0.24323	0.0:0.388:0.227:0.3851	.	321;256;379	B4DIY4;E7ENB5;Q8N4H0	.;.;CI068_HUMAN	C	379;321;256	ENSP00000404277:Y379C;ENSP00000417063:Y321C;ENSP00000371319:Y256C	ENSP00000371319:Y256C	Y	-	2	0	C9orf68	4594223	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.240000	0.08952	-1.072000	0.03141	-2.352000	0.00242	TAC	.	.		0.338	SPATA6L-202	KNOWN	basic	protein_coding	protein_coding		NM_017985		C	4604223	T	C	4604223	3	2	100	1	0	0	0	0	1	0	0	0	2493	1638	57	2	46	2	C9orf68	9	4604223	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10		4604223	136609208	113	13682										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13150535	13150535	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cgattctatctccaggtttcAaggttccatttttgccagct	7	11	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:13150535A>G	ENST00000319217.7	-	25	3852	c.3605T>C	c.(3604-3606)tTg>tCg	p.L1202S	MPDZ_ENST00000447879.1_Missense_Mutation_p.L1202S|MPDZ_ENST00000381015.4_Missense_Mutation_p.L1202S|MPDZ_ENST00000546205.1_Missense_Mutation_p.L1216S|MPDZ_ENST00000536827.1_Missense_Mutation_p.L1202S|MPDZ_ENST00000381022.2_Missense_Mutation_p.L1202S|MPDZ_ENST00000541718.1_Missense_Mutation_p.L1202S|MPDZ_ENST00000538841.1_Missense_Mutation_p.L94S	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1202	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TCCAGGTTTCAAGGTTCCATT	0.383																																					p.L1202S		Atlas-SNP	.											.	MPDZ	324	.	0			c.T3605C						.						164	162	163					9																	13150535		1848	4092	5940	SO:0001583	missense	8777	exon25			GGTTTCAAGGTTC	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.3605T>C	chr9.hg19:g.13150535A>G	ENSP00000320006:p.Leu1202Ser	157.0	0.0		89.0	5.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	A	16.39	3.109717	0.56398	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205;ENST00000433359;ENST00000542239	T;T;T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.95	5.95	0.96441	.	0.000000	0.36591	N	0.002513	T	0.80497	0.4634	H	0.97291	3.975	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.999;1.0	D	0.87530	0.2452	10	0.87932	D	0	.	16.4159	0.83738	1.0:0.0:0.0:0.0	.	1202;94;1202;1152;1202	B7ZMI4;B7ZB24;O75970-3;E7EPZ1;O75970-2	.;.;.;.;.	S	1202;1202;1202;208;94;1202;1202;1202;1152;1216;94;94	ENSP00000320006:L1202S;ENSP00000439807:L1202S;ENSP00000370410:L1202S;ENSP00000444230:L208S;ENSP00000444717:L94S;ENSP00000444151:L1202S;ENSP00000415208:L1202S;ENSP00000370403:L1202S;ENSP00000446358:L1216S;ENSP00000389705:L94S;ENSP00000443672:L94S	ENSP00000320006:L1202S	L	-	2	0	MPDZ	13140535	1.000000	0.71417	1.000000	0.80357	0.115000	0.19883	8.962000	0.93254	2.279000	0.76181	0.533000	0.62120	TTG	.	.		0.383	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		G	13150535	A	G	13150535	3	3	100	1	0	0	0	0	1	0	0	0	9731	131	5	2	2608	2	MPDZ	9	13150535	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	8546312	13150535	128062896	114	13683										
TMC1	117531	hgsc.bcm.edu	37	chr9	75403363	75403363	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atcggcaatcctgaaacagcAgacaacaaatttaattctat	5	9	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:75403363A>G	ENST00000297784.5	+	14	1533	c.993A>G	c.(991-993)gcA>gcG	p.A331A	TMC1_ENST00000340019.3_Silent_p.A331A|TMC1_ENST00000396237.3_Silent_p.A331A	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	331					auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						CTGAAACAGCAGACAACAAAT	0.398																																					p.A331A	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.A993G						.						79	74	76					9																	75403363		2203	4300	6503	SO:0001819	synonymous_variant	117531	exon14			AACAGCAGACAAC	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"transmembrane, cochlear expressed, 1"	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.993A>G	chr9.hg19:g.75403363A>G		122.0	0.0		90.0	4.0	NM_138691	A8MVZ2|B1AM91	Silent	SNP	ENST00000297784.5	hg19	CCDS6643.1																																																																																			.	.		0.398	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1			G	75403363	A	G	75403363	2	3	100	1	0	0	0	0	0	0	0	1	15999	175	7	2		2	TMC1	9	75403363	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	62252828	75403363	65810068	115	13684										
PHF2	5253	hgsc.bcm.edu	37	chr9	96429513	96429513	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ggttggcgcgctggagtacaAccccagcaggtgggccccac	15	14	0	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:96429513A>G	ENST00000359246.4	+	17	2706	c.2339A>G	c.(2338-2340)aAc>aGc	p.N780S	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	780					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		CTGGAGTACAACCCCAGCAGG	0.692																																					p.N780S		Atlas-SNP	.											.	PHF2	113	.	0			c.A2339G						.						29	29	29					9																	96429513		2199	4298	6497	SO:0001583	missense	5253	exon17			AGTACAACCCCAG	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	8920	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1E", "centromere protein 35"	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.2339A>G	chr9.hg19:g.96429513A>G	ENSP00000352185:p.Asn780Ser	80.0	0.0		46.0	5.0	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	hg19	CCDS35069.1	.	.	.	.	.	.	.	.	.	.	a	3.179	-0.168250	0.06461	.	.	ENSG00000197724	ENST00000359246	T	0.16597	2.33	4.99	3.81	0.43845	.	0.099233	0.64402	D	0.000002	T	0.20700	0.0498	N	0.16903	0.455	0.80722	D	1	D;B	0.71674	0.998;0.15	D;B	0.76071	0.987;0.027	T	0.03483	-1.1032	10	0.09338	T	0.73	-34.6457	11.745	0.51815	0.8523:0.1477:0.0:0.0	.	199;780	Q8N359;O75151	.;PHF2_HUMAN	S	780	ENSP00000352185:N780S	ENSP00000352185:N780S	N	+	2	0	PHF2	95469334	1.000000	0.71417	1.000000	0.80357	0.393000	0.30537	3.574000	0.53863	0.702000	0.31825	0.248000	0.18094	AAC	.	.		0.692	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		G	96429513	A	G	96429513	3	3	100	1	0	0	0	0	1	0	0	0	11839	43	2	2	2405	2	PHF2	9	96429513	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	21026150	96429513	44783918	116	13685										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114184313	114184313	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cttgaatagcaagtcgagtcTcaggctcttcctataaagat	8	9	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:114184313T>C	ENST00000338205.5	-	14	1562	c.1343A>G	c.(1342-1344)gAg>gGg	p.E448G	KIAA0368_ENST00000259335.4_Missense_Mutation_p.E626G			Q5VYK3	ECM29_HUMAN	KIAA0368	454					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						AAGTCGAGTCTCAGGCTCTTC	0.453																																					p.E626G		Atlas-SNP	.											.	KIAA0368	144	.	0			c.A1877G						.						86	79	81					9																	114184313		1864	4102	5966	SO:0001583	missense	23392	exon16			CGAGTCTCAGGCT	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1343A>G	chr9.hg19:g.114184313T>C	ENSP00000339889:p.Glu448Gly	113.0	0.0		79.0	4.0	NM_001080398	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	hg19		.	.	.	.	.	.	.	.	.	.	T	19.14	3.770297	0.69992	.	.	ENSG00000136813	ENST00000338205;ENST00000259335	T	0.47869	0.83	5.56	5.56	0.83823	Armadillo-like helical (1);Armadillo-type fold (1);	0.053115	0.64402	D	0.000001	T	0.43456	0.1248	L	0.43923	1.385	0.80722	D	1	B	0.22541	0.071	B	0.19391	0.025	T	0.31475	-0.9942	10	0.51188	T	0.08	.	16.021	0.80493	0.0:0.0:0.0:1.0	.	454	Q5VYK3	ECM29_HUMAN	G	448;626	ENSP00000259335:E626G	ENSP00000259335:E626G	E	-	2	0	KIAA0368	113224134	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.655000	0.83696	2.240000	0.73641	0.533000	0.62120	GAG	.	.		0.453	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		C	114184313	T	C	114184313	3	2	100	1	0	0	0	0	1	0	0	0	8180	1551	54	2	4320	2	KIAA0368	9	114184313	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	17754800	114184313	27029118	117	13686										
FKBP15	23307	hgsc.bcm.edu	37	chr9	115931901	115931901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tctgtgggatgggatgcaagAcagttcgggtggaagggaac	18	5	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:115931901A>G	ENST00000238256.3	-	26	3205	c.3088T>C	c.(3088-3090)Tct>Cct	p.S1030P		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1030					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GGGATGCAAGACAGTTCGGGT	0.552																																					p.S1030P		Atlas-SNP	.											.	FKBP15	128	.	0			c.T3088C						.						91	98	96					9																	115931901		1966	4152	6118	SO:0001583	missense	23307	exon26			TGCAAGACAGTTC	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23397	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 76", "WASP and FKBP-like protein"		"KIAA0674"	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.3088T>C	chr9.hg19:g.115931901A>G	ENSP00000238256:p.Ser1030Pro	155.0	0.0		82.0	4.0	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	hg19	CCDS48007.1	.	.	.	.	.	.	.	.	.	.	A	4.004	-0.001983	0.07819	.	.	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.23950	1.88;1.9	5.08	-2.19	0.07015	.	.	.	.	.	T	0.13500	0.0327	L	0.29908	0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31503	-0.9941	9	0.48119	T	0.1	-0.664	0.1722	0.00114	0.2797:0.2777:0.1856:0.2569	.	611;1030	B4DVS2;Q5T1M5	.;FKB15_HUMAN	P	1055;1030	ENSP00000416158:S1055P;ENSP00000238256:S1030P	ENSP00000238256:S1030P	S	-	1	0	FKBP15	114971722	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.925000	0.03992	-0.422000	0.07405	-1.464000	0.01018	TCT	.	.		0.552	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258		G	115931901	A	G	115931901	3	3	100	1	0	0	0	0	1	0	0	0	5913	275	10	2	583	2	FKBP15	9	115931901	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1747588	115931901	25281530	118	13687										
PRPF4	9128	hgsc.bcm.edu	37	chr9	116053283	116053283	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	catcagaacttagtgactggTgtcaagtttgagcgtaagct	11	7	2	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:116053283T>C	ENST00000374198.4	+	13	1464	c.1362T>C	c.(1360-1362)ggT>ggC	p.G454G	PRPF4_ENST00000374199.4_Silent_p.G453G	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	454					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						TAGTGACTGGTGTCAAGTTTG	0.493																																					p.G454G		Atlas-SNP	.											.	PRPF4	56	.	0			c.T1362C						.						211	173	186					9																	116053283		2203	4300	6503	SO:0001819	synonymous_variant	9128	exon13			GACTGGTGTCAAG	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"WD repeat domain containing"	17349	protein-coding gene	gene with protein product	"PRP4/STK/WD splicing factor", "U4/U6 small nuclear ribonucleoprotein Prp4"	607795	"PRP4 pre-mRNA processing factor 4 homolog (yeast)"			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.1362T>C	chr9.hg19:g.116053283T>C		170.0	0.0		89.0	4.0	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Silent	SNP	ENST00000374198.4	hg19	CCDS6791.1																																																																																			.	.		0.493	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697		C	116053283	T	C	116053283	2	2	100	1	0	0	0	0	0	0	0	1	12582	1683	59	2		2	PRPF4	9	116053283	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	121382	116053283	25160148	119	13688										
ASTN2	23245	hgsc.bcm.edu	37	chr9	119625906	119625906	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccggtcagacacacacttgaAgttgcgagtgcagcccccat	10	14	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:119625906A>G	ENST00000313400.4	-	11	2096	c.1996T>C	c.(1996-1998)Ttc>Ctc	p.F666L	ASTN2_ENST00000373996.3_Missense_Mutation_p.F662L|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000361209.2_Missense_Mutation_p.F615L			O75129	ASTN2_HUMAN	astrotactin 2	666	EGF-like 2.				negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						ACACACTTGAAGTTGCGAGTG	0.577																																					p.F615L		Atlas-SNP	.											.	ASTN2	307	.	0			c.T1843C						.						120	101	107					9																	119625906		2203	4300	6503	SO:0001583	missense	23245	exon10			ACTTGAAGTTGCG	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1996T>C	chr9.hg19:g.119625906A>G	ENSP00000314038:p.Phe666Leu	119.0	0.0		82.0	6.0	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	hg19		.	.	.	.	.	.	.	.	.	.	A	24.4	4.527409	0.85706	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	T;T;T;T	0.13901	2.71;2.71;2.55;2.75	5.71	5.71	0.89125	.	0.142736	0.50627	D	0.000108	T	0.26955	0.0660	L	0.32530	0.975	0.80722	D	1	D;D;D	0.71674	0.998;0.982;0.997	D;D;D	0.76071	0.987;0.952;0.978	T	0.01390	-1.1367	9	.	.	.	-27.9909	15.966	0.79970	1.0:0.0:0.0:0.0	.	615;666;662	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	L	666;662;389;615	ENSP00000314038:F666L;ENSP00000363108:F662L;ENSP00000363098:F389L;ENSP00000354504:F615L	.	F	-	1	0	ASTN2	118665727	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.918000	0.92759	2.172000	0.68678	0.533000	0.62120	TTC	.	.		0.577	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		G	119625906	A	G	119625906	3	3	100	1	0	0	0	0	1	0	0	0	1065	72	3	2	2307	2	ASTN2	9	119625906	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	3572623	119625906	21587525	120	13689										
CEP110	11064	hgsc.bcm.edu	37	chr9	123874744	123874744	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	attgggccaatagctaaaacAgaagaccatagaattaacac	7	8	0	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:123874744A>G	ENST00000373855.1	+	9	1270	c.1010A>G	c.(1009-1011)cAg>cGg	p.Q337R	CNTRL_ENST00000373865.2_Missense_Mutation_p.Q337R|CNTRL_ENST00000238341.5_Missense_Mutation_p.Q337R			Q7Z7A1	CNTRL_HUMAN	centriolin	337					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						TAGCTAAAACAGAAGACCATA	0.338																																					p.Q337R		Atlas-SNP	.											.	CNTRL	161	.	0			c.A1010G						.						104	98	100					9																	123874744		2203	4300	6503	SO:0001583	missense	11064	exon7			TAAAACAGAAGAC	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.1010A>G	chr9.hg19:g.123874744A>G	ENSP00000362962:p.Gln337Arg	133.0	0.0		76.0	4.0	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.072744	0.36566	.	.	ENSG00000119397	ENST00000373865;ENST00000373855;ENST00000238341;ENST00000454238	T;T	0.26223	1.75;1.75	5.78	4.65	0.58169	.	.	.	.	.	T	0.22360	0.0539	L	0.47716	1.5	0.34699	D	0.726492	B	0.10296	0.003	B	0.06405	0.002	T	0.15407	-1.0438	9	0.35671	T	0.21	.	9.2543	0.37573	0.918:0.0:0.082:0.0	.	337	Q7Z7A1	CNTRL_HUMAN	R	337	ENSP00000362962:Q337R;ENSP00000238341:Q337R	ENSP00000238341:Q337R	Q	+	2	0	CNTRL	122914565	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	4.452000	0.60054	1.028000	0.39785	0.460000	0.39030	CAG	.	.		0.338	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123874744	A	G	123874744	3	3	100	1	0	0	0	0	1	0	0	0	3247	188	7	2	1036	2	CEP110	9	123874744	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	4248838	123874744	17338687	121	13690										
ASS1	445	hgsc.bcm.edu	37	chr9	133364729	133364729	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aaaatggctaggtatctacgAgaccccagcaggcaccatcc	9	13	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:133364729A>G	ENST00000372394.1	+	13	1329	c.848A>G	c.(847-849)gAg>gGg	p.E283G	ASS1_ENST00000352480.5_Missense_Mutation_p.E283G|ASS1_ENST00000493984.2_3'UTR|ASS1_ENST00000372393.3_Missense_Mutation_p.E283G			P00966	ASSY_HUMAN	argininosuccinate synthase 1	283			E -> K (in CTLN1). {ECO:0000269|PubMed:12815590, ECO:0000269|PubMed:16475226}.		acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	GGTATCTACGAGACCCCAGCA	0.453																																					p.E283G		Atlas-SNP	.											.	ASS1	37	.	0			c.A848G						.						88	95	93					9																	133364729		2203	4300	6503	SO:0001583	missense	445	exon12			TCTACGAGACCCC	X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"argininosuccinate synthetase"	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.848A>G	chr9.hg19:g.133364729A>G	ENSP00000361471:p.Glu283Gly	104.0	0.0		59.0	5.0	NM_054012	Q6LDL2|Q86UZ0|Q96GT4	Missense_Mutation	SNP	ENST00000372394.1	hg19	CCDS6933.1	.	.	.	.	.	.	.	.	.	.	A	19.03	3.747165	0.69418	.	.	ENSG00000130707	ENST00000334909;ENST00000352480;ENST00000372394;ENST00000372393;ENST00000372386	D;D;D;D	0.99574	-6.2;-6.2;-6.2;-5.87	4.5	4.5	0.54988	Argininosuccinate synthetase, catalytic/multimerisation domain body (1);	0.000000	0.85682	U	0.000000	D	0.99597	0.9854	H	0.95470	3.675	0.80722	D	1	P;D;D;P;P	0.56746	0.724;0.977;0.977;0.724;0.724	P;P;P;P;P	0.55112	0.578;0.769;0.769;0.578;0.578	D	0.97864	1.0282	10	0.87932	D	0	.	13.3017	0.60328	1.0:0.0:0.0:0.0	.	283;166;166;283;283	A8KAP9;B4E395;E9PDT0;Q5T6L4;P00966	.;.;.;.;ASSY_HUMAN	G	283;283;283;283;40	ENSP00000253004:E283G;ENSP00000361471:E283G;ENSP00000361469:E283G;ENSP00000361461:E40G	ENSP00000361470:E283G	E	+	2	0	ASS1	132354550	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.684000	0.91242	1.802000	0.52723	0.379000	0.24179	GAG	.	.		0.453	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050		G	133364729	A	G	133364729	3	3	100	1	0	0	0	0	1	0	0	0	1061	304	11	2	890	2	ASS1	9	133364729	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	9489985	133364729	7848702	122	13691										
NUP214	8021	hgsc.bcm.edu	37	chr9	134020110	134020110	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agccctccttcccaccctcaAcctctgctgtcaaagtcaac	4	19	4	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:134020110A>G	ENST00000359428.5	+	12	1882	c.1738A>G	c.(1738-1740)Acc>Gcc	p.T580A	RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000588378.1_RNA|NUP214_ENST00000451030.1_Missense_Mutation_p.T580A|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000587408.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.T580A|RP11-544A12.4_ENST00000589540.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	580	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		CCCACCCTCAACCTCTGCTGT	0.418			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.T580A	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.A1738G						.						50	47	48					9																	134020110		2203	4299	6502	SO:0001583	missense	8021	exon12			CCCTCAACCTCTG	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.1738A>G	chr9.hg19:g.134020110A>G	ENSP00000352400:p.Thr580Ala	201.0	0.0		99.0	5.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.294|0.294	-0.977970|-0.977970	0.02197|0.02197	.|.	.|.	ENSG00000126883|ENSG00000126883	ENST00000530863|ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605	.|T;T;T	.|0.30182	.|1.69;1.54;1.66	5.56|5.56	-2.91|-2.91	0.05631|0.05631	.|.	.|0.932418	.|0.08874	.|N	.|0.881118	T|T	0.09949|0.09949	0.0244|0.0244	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.001;0.001;0.001	T|T	0.32877|0.32877	-0.9890|-0.9890	5|10	.|0.06494	.|T	.|0.89	-2.224|-2.224	2.0126|2.0126	0.03491|0.03491	0.2388:0.1002:0.4363:0.2247|0.2388:0.1002:0.4363:0.2247	.|.	.|173;580;580	.|Q5JUP9;P35658-4;P35658	.|.;.;NU214_HUMAN	S|A	155|580;580;580;580;173;9	.|ENSP00000352400:T580A;ENSP00000396576:T580A;ENSP00000405014:T580A	.|ENSP00000352400:T580A	N|T	+|+	2|1	0|0	NUP214|NUP214	133009931|133009931	0.044000|0.044000	0.20184|0.20184	0.004000|0.004000	0.12327|0.12327	0.616000|0.616000	0.37450|0.37450	0.367000|0.367000	0.20382|0.20382	-0.337000|-0.337000	0.08426|0.08426	-1.317000|-1.317000	0.01298|0.01298	AAC|ACC	.	.		0.418	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		G	134020110	A	G	134020110	3	3	100	1	0	0	0	0	1	0	0	0	10771	43	2	2	1784	2	NUP214	9	134020110	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	655381	134020110	7193321	123	13692										
NDOR1	27158	hgsc.bcm.edu	37	chr9	140110580	140110580	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgtgcagcaccggctccgggAgctggggtcgcttgtgtggg	19	10	0	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr9:140110580A>G	ENST00000344894.5	+	13	1672	c.1589A>G	c.(1588-1590)gAg>gGg	p.E530G	NDOR1_ENST00000458322.2_Missense_Mutation_p.E523G|NDOR1_ENST00000371521.4_Missense_Mutation_p.E539G|NDOR1_ENST00000427047.2_Missense_Mutation_p.E496G	NM_001144028.1|NM_014434.2	NP_001137500.1|NP_055249.1			NADPH dependent diflavin oxidoreductase 1											breast(1)|endometrium(5)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		CGGCTCCGGGAGCTGGGGTCG	0.657																																					p.E539G		Atlas-SNP	.											.	NDOR1	71	.	0			c.A1616G						.						49	54	53					9																	140110580		2203	4300	6503	SO:0001583	missense	27158	exon13			TCCGGGAGCTGGG	BC015735	CCDS7036.1, CCDS48061.1, CCDS48062.1, CCDS48063.1	9q34.3	2008-02-05			ENSG00000188566	ENSG00000188566			29838	protein-coding gene	gene with protein product	"NADPH dependent FMN and FAD containing oxidoreductase"	606073				10625700, 12631275	Standard	XM_005266066		Approved	NR1, bA350O14.9	uc004clx.3	Q9UHB4	OTTHUMG00000020986	ENST00000344894.5:c.1589A>G	chr9.hg19:g.140110580A>G	ENSP00000343344:p.Glu530Gly	95.0	0.0		53.0	4.0	NM_001144026		Missense_Mutation	SNP	ENST00000344894.5	hg19	CCDS7036.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.303276	0.60195	.	.	ENSG00000188566	ENST00000458322;ENST00000427047;ENST00000371521;ENST00000344894	D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32	4.06	4.06	0.47325	Oxidoreductase FAD/NAD(P)-binding (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.000000	0.85682	D	0.000000	D	0.93370	0.7886	M	0.92367	3.3	0.80722	D	1	D;B;P;B	0.53312	0.959;0.226;0.949;0.125	P;B;P;B	0.59825	0.864;0.213;0.786;0.32	D	0.94255	0.7497	10	0.87932	D	0	-9.9853	10.9983	0.47589	1.0:0.0:0.0:0.0	.	523;496;539;530	D3YTG6;D3YTH9;Q9UHB4-2;Q9UHB4	.;.;.;NDOR1_HUMAN	G	523;496;539;530	ENSP00000389905:E523G;ENSP00000394309:E496G;ENSP00000360576:E539G;ENSP00000343344:E530G	ENSP00000343344:E530G	E	+	2	0	NDOR1	139230401	1.000000	0.71417	0.960000	0.40013	0.624000	0.37722	3.698000	0.54771	1.713000	0.51359	0.459000	0.35465	GAG	.	.		0.657	NDOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254704.1	NM_014434		G	140110580	A	G	140110580	3	3	100	1	0	0	0	0	1	0	0	0	10258	304	11	2	1666	2	NDOR1	9	140110580	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	6090470	140110580	1102851	124	13693										
KLF6	1316	hgsc.bcm.edu	37	chr10	3824046	3824046	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cagttgagaaggttccctgcTcagttccggagaagatggag	14	8	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:3824046T>C	ENST00000497571.1	-	2	723	c.463A>G	c.(463-465)Agc>Ggc	p.S155G	KLF6_ENST00000469435.1_Missense_Mutation_p.S155G|KLF6_ENST00000542957.1_Missense_Mutation_p.S155G|KLF6_ENST00000173785.4_5'UTR	NM_001160124.1|NM_001300.5	NP_001153596.1|NP_001291.3	Q99612	KLF6_HUMAN	Kruppel-like factor 6	155			S -> R (found in gastric cancer samples; somatic mutation). {ECO:0000269|PubMed:15824733}.		B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				Colorectal(1;0.238)		GGTTCCCTGCTCAGTTCCGGA	0.607											OREG0019980	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S155G		Atlas-SNP	.											.	KLF6	38	.	0			c.A463G						.						69	68	69					10																	3824046		2203	4300	6503	SO:0001583	missense	1316	exon2			CCCTGCTCAGTTC	U51869	CCDS7060.1, CCDS53490.1	10p15	2013-01-08	2004-11-29	2004-12-01	ENSG00000067082	ENSG00000067082		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	2235	protein-coding gene	gene with protein product	"GC-rich binding factor"	602053	"core promoter element binding protein"	BCD1, ST12, COPEB		9503030, 9685731	Standard	NM_001300		Approved	CPBP, GBF, Zf9, PAC1	uc001iha.3	Q99612	OTTHUMG00000017567	ENST00000497571.1:c.463A>G	chr10.hg19:g.3824046T>C	ENSP00000419923:p.Ser155Gly	87.0	0.0	614	68.0	4.0	NM_001160125	B2RE86|B4DDN0|D3DRR1|F5H3M5|Q5VUT7|Q5VUT8|Q9BT79	Missense_Mutation	SNP	ENST00000497571.1	hg19	CCDS7060.1	.	.	.	.	.	.	.	.	.	.	T	8.735	0.917524	0.17982	.	.	ENSG00000067082	ENST00000497571;ENST00000542957;ENST00000469435	T;T;T	0.53640	3.18;0.61;0.84	4.99	2.29	0.28610	.	0.470516	0.26213	N	0.025679	T	0.22820	0.0551	N	0.05259	-0.085	0.27472	N	0.952831	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.09377	0.0;0.002;0.004;0.0	T	0.15321	-1.0441	10	0.22109	T	0.4	.	9.2466	0.37529	0.0:0.1777:0.0:0.8223	.	155;155;155;155	D3GC14;F5H3M5;Q99612-2;Q99612	.;.;.;KLF6_HUMAN	G	155	ENSP00000419923:S155G;ENSP00000445301:S155G;ENSP00000419079:S155G	ENSP00000419079:S155G	S	-	1	0	KLF6	3814046	0.998000	0.40836	0.998000	0.56505	0.956000	0.61745	0.801000	0.27055	0.758000	0.33059	0.459000	0.35465	AGC	.	.		0.607	KLF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046495.1			C	3824046	T	C	3824046	3	2	100	1	0	0	0	0	1	0	0	0	8359	1551	54	2	400	2	KLF6	10	3824046	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10		3824046	131710701	125	13694										
BEND7	222389	hgsc.bcm.edu	37	chr10	13541881	13541881	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ggcggtagctcattccacacAccacgtgaagacgggtggag	14	11	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:13541881A>G	ENST00000396900.2	-	3	344	c.345T>C	c.(343-345)ggT>ggC	p.G115G	BEND7_ENST00000378605.3_Silent_p.G63G|BEND7_ENST00000396898.2_Silent_p.G115G|BEND7_ENST00000341083.3_Silent_p.G63G			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	115						extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						CATTCCACACACCACGTGAAG	0.572																																					p.G63G		Atlas-SNP	.											.	BEND7	85	.	0			c.T189C						.						79	81	80					10																	13541881		2203	4300	6503	SO:0001819	synonymous_variant	222389	exon2			CCACACACCACGT	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"BEN domain containing"	23514	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 30"	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.345T>C	chr10.hg19:g.13541881A>G		188.0	0.0		118.0	7.0	NM_001100912	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	hg19																																																																																				.	.		0.572	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751		G	13541881	A	G	13541881	2	3	100	1	0	0	0	0	0	0	0	1	1403	146	6	2		2	BEND7	10	13541881	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	9717835	13541881	121992866	126	13695										
CUBN	8029	hgsc.bcm.edu	37	chr10	17024537	17024537	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tcagtgaagttcaagagaacAcgatgatttctgtcaacccg	9	9	4	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:17024537A>G	ENST00000377833.4	-	31	4706	c.4641T>C	c.(4639-4641)cgT>cgC	p.R1547R		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1547	CUB 10. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TCAAGAGAACACGATGATTTC	0.433																																					p.R1547R		Atlas-SNP	.											.	CUBN	515	.	0			c.T4641C						.						131	107	115					10																	17024537		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon31			GAGAACACGATGA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.4641T>C	chr10.hg19:g.17024537A>G		87.0	0.0		58.0	7.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.		0.433	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17024537	A	G	17024537	2	3	100	1	0	0	0	0	0	0	0	1	4053	146	6	2		2	CUBN	10	17024537	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	3482656	17024537	118510210	127	13696										
CUBN	8029	hgsc.bcm.edu	37	chr10	17153015	17153015	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttatttatctcacattcattGatatcttcgcaaatatatcc	2	9	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:17153015G>C	ENST00000377833.4	-	9	983	c.918C>G	c.(916-918)atC>atG	p.I306M		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	306	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CACATTCATTGATATCTTCGC	0.453																																					p.I306M		Atlas-SNP	.											.	CUBN	515	.	0			c.C918G						.						104	100	101					10																	17153015		2203	4300	6503	SO:0001583	missense	8029	exon9			TTCATTGATATCT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.918C>G	chr10.hg19:g.17153015G>C	ENSP00000367064:p.Ile306Met	109.0	0.0		65.0	11.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.795638	0.50208	.	.	ENSG00000107611	ENST00000377833	D	0.93547	-3.24	5.83	2.74	0.32292	Growth factor, receptor (1);EGF-like calcium-binding (1);	0.289804	0.24640	N	0.036817	D	0.92355	0.7574	M	0.79614	2.46	0.80722	D	1	P	0.39717	0.684	P	0.45099	0.469	D	0.89301	0.3626	10	0.51188	T	0.08	.	3.7944	0.08733	0.4027:0.1787:0.4186:0.0	.	306	O60494	CUBN_HUMAN	M	306	ENSP00000367064:I306M	ENSP00000367064:I306M	I	-	3	3	CUBN	17193021	0.966000	0.33281	0.981000	0.43875	0.794000	0.44872	0.900000	0.28431	0.767000	0.33267	0.650000	0.86243	ATC	.	.		0.453	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	17153015	G	C	17153015	3	2	100	1	0	0	0	0	1	0	0	0	4053	1280	45	4	10189	4	CUBN	10	17153015	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	128478	17153015	118381732	128	13697										
C10orf71	118461	hgsc.bcm.edu	37	chr10	50530756	50530756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atgactcctatctggctgtgTccccggatatcacccgacag	9	14	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:50530756T>C	ENST00000374144.3	+	3	454	c.166T>C	c.(166-168)Tcc>Ccc	p.S56P	C10orf71_ENST00000323868.4_Missense_Mutation_p.S56P			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	56										endometrium(1)	1						TCTGGCTGTGTCCCCGGATAT	0.557																																					p.S56P		Atlas-SNP	.											.	C10orf71	179	.	0			c.T166C						.						48	51	50					10																	50530756		2050	4187	6237	SO:0001583	missense	118461	exon3			GCTGTGTCCCCGG	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.166T>C	chr10.hg19:g.50530756T>C	ENSP00000363259:p.Ser56Pro	135.0	0.0		94.0	4.0	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	hg19	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.596257	0.46318	.	.	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.27720	1.65;2.85	5.13	5.13	0.70059	.	0.000000	0.48767	D	0.000171	T	0.43853	0.1266	M	0.70275	2.135	0.39751	D	0.971895	D	0.56521	0.976	P	0.53006	0.715	T	0.51044	-0.8755	10	0.87932	D	0	.	10.2112	0.43141	0.0:0.0783:0.0:0.9217	.	56	Q711Q0-3	.	P	56	ENSP00000318713:S56P;ENSP00000363259:S56P	ENSP00000318713:S56P	S	+	1	0	C10orf71	50200762	0.997000	0.39634	1.000000	0.80357	0.086000	0.17979	2.596000	0.46205	1.940000	0.56252	0.455000	0.32223	TCC	.	.		0.557	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		C	50530756	T	C	50530756	3	2	100	1	0	0	0	0	1	0	0	0	1616	1667	58	2	168	2	C10orf71	10	50530756	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	33377741	50530756	85003991	129	13698										
NCOA4	8031	hgsc.bcm.edu	37	chr10	51582886	51582886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atcaagctccttacatacccAgcaccgacccccaggactgg	7	17	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:51582886A>G	ENST00000443446.1	+	7	890	c.661A>G	c.(661-663)Agc>Ggc	p.S221G	NCOA4_ENST00000374082.1_Missense_Mutation_p.S221G|NCOA4_ENST00000438493.1_Missense_Mutation_p.S237G|NCOA4_ENST00000374087.4_Missense_Mutation_p.S221G|NCOA4_ENST00000414907.2_Missense_Mutation_p.S55G|NCOA4_ENST00000344348.6_Missense_Mutation_p.S221G|NCOA4_ENST00000498586.1_3'UTR|NCOA4_ENST00000452682.1_Missense_Mutation_p.S237G|NCOA4_ENST00000430396.2_Missense_Mutation_p.S121G	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	221					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)	p.S237G(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						TTACATACCCAGCACCGACCC	0.493			T	RET	papillary thyroid																																p.S237G		Atlas-SNP	.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	NCOA4_ENST00000452682,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	NCOA4	58	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.A709G						.						82	73	76					10																	51582886		2203	4300	6503	SO:0001583	missense	8031	exon8			ATACCCAGCACCG	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.661A>G	chr10.hg19:g.51582886A>G	ENSP00000390713:p.Ser221Gly	96.0	0.0		47.0	2.0	NM_001145261	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Missense_Mutation	SNP	ENST00000443446.1	hg19	CCDS7237.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.10|17.10	3.302602|3.302602	0.60195|0.60195	.|.	.|.	ENSG00000138293|ENSG00000138293	ENST00000431200|ENST00000438493;ENST00000452682;ENST00000430396;ENST00000374087;ENST00000330923;ENST00000414907;ENST00000344348;ENST00000374082;ENST00000443446	.|T;T;T;T;T;T;T;T	.|0.39229	.|1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.66636|0.66636	0.2809|0.2809	M|M	0.78801|0.78801	2.425|2.425	0.51233|0.51233	D|D	0.999911|0.999911	.|D;D;D;D	.|0.89917	.|0.999;0.999;0.999;1.0	.|D;D;D;D	.|0.87578	.|0.997;0.997;0.997;0.998	T|T	0.70193|0.70193	-0.4939|-0.4939	5|10	.|0.66056	.|D	.|0.02	-14.98|-14.98	16.0574|16.0574	0.80816|0.80816	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|121;237;237;221	.|B4DF87;B4E260;E9PAV7;Q13772	.|.;.;.;NCOA4_HUMAN	R|G	136|237;237;121;221;221;55;221;221;221	.|ENSP00000405146:S237G;ENSP00000395465:S237G;ENSP00000393053:S121G;ENSP00000363200:S221G;ENSP00000411018:S55G;ENSP00000344552:S221G;ENSP00000363195:S221G;ENSP00000390713:S221G	.|ENSP00000332421:S221G	Q|S	+|+	2|1	0|0	NCOA4|NCOA4	51252892|51252892	1.000000|1.000000	0.71417|0.71417	0.929000|0.929000	0.37066|0.37066	0.030000|0.030000	0.12068|0.12068	6.865000|6.865000	0.75500|0.75500	2.258000|2.258000	0.74832|0.74832	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.493	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		G	51582886	A	G	51582886	3	3	100	1	0	0	0	0	1	0	0	0	10240	188	7	2	735	2	NCOA4	10	51582886	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1052130	51582886	83951861	130	13699										
SGMS1	259230	hgsc.bcm.edu	37	chr10	52071024	52071024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gaagtcttttagacttacacTctttgataaataagtaggta	7	5	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:52071024T>C	ENST00000361781.2	-	9	1852	c.893A>G	c.(892-894)gAg>gGg	p.E298G	SGMS1_ENST00000429490.1_Missense_Mutation_p.E129G	NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	304					apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						AGACTTACACTCTTTGATAAA	0.443																																					p.E298G		Atlas-SNP	.											.	SGMS1	40	.	0			c.A893G						.						118	104	109					10																	52071024		2203	4300	6503	SO:0001583	missense	259230	exon9			TTACACTCTTTGA	AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	2.7.8.27	"Sterile alpha motif (SAM) domain containing"	29799	protein-coding gene	gene with protein product		611573	"transmembrane protein 23"	TMEM23		11841947, 14976195	Standard	NM_147156		Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.893A>G	chr10.hg19:g.52071024T>C	ENSP00000354829:p.Glu298Gly	89.0	0.0		57.0	4.0	NM_147156	Q68U43|Q6EKK0|Q75SP1	Missense_Mutation	SNP	ENST00000361781.2	hg19	CCDS7240.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.807270	0.90623	.	.	ENSG00000198964	ENST00000412547;ENST00000361781;ENST00000429490	T;T	0.75260	0.56;-0.92	5.87	5.87	0.94306	.	0.046562	0.85682	D	0.000000	D	0.88793	0.6533	M	0.91406	3.205	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91012	0.4850	10	0.87932	D	0	-14.2433	14.5226	0.67863	0.0:0.0:0.0:1.0	.	129;304	B4DJU2;Q86VZ5	.;SMS1_HUMAN	G	98;298;129	ENSP00000354829:E298G;ENSP00000406795:E129G	ENSP00000354829:E298G	E	-	2	0	SGMS1	51741030	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.975000	0.88055	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.443	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048074.2	NM_147156		C	52071024	T	C	52071024	3	2	100	1	0	0	0	0	1	0	0	0	14229	1551	54	2	360	2	SGMS1	10	52071024	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	488138	52071024	83463723	131	13700										
HK1	3098	hgsc.bcm.edu	37	chr10	71144583	71144583	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cattgtctcctgcatctctgActtcttggactacatgggga	9	11	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:71144583A>G	ENST00000359426.6	+	12	1855	c.1751A>G	c.(1750-1752)gAc>gGc	p.D584G	HK1_ENST00000404387.2_Missense_Mutation_p.D588G|HK1_ENST00000360289.2_Missense_Mutation_p.D572G|HK1_ENST00000298649.3_Missense_Mutation_p.D583G|HK1_ENST00000494253.1_3'UTR|HK1_ENST00000448642.2_Missense_Mutation_p.D619G	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	584	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						TGCATCTCTGACTTCTTGGAC	0.512																																					p.D588G		Atlas-SNP	.											.	HK1	170	.	0			c.A1763G						.						229	230	230					10																	71144583		2203	4300	6503	SO:0001583	missense	3098	exon15			TCTCTGACTTCTT	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.1751A>G	chr10.hg19:g.71144583A>G	ENSP00000352398:p.Asp584Gly	144.0	0.0		78.0	4.0	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	hg19	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.001403	0.93227	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	D;D;D;D;D	0.99014	-5.33;-5.33;-5.33;-5.33;-5.33	5.68	5.68	0.88126	Hexokinase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99193	0.9720	M	0.76938	2.355	0.80722	D	1	P;P;P;D;D;D	0.76494	0.756;0.918;0.935;0.99;0.988;0.999	P;P;P;D;D;D	0.78314	0.611;0.907;0.87;0.982;0.928;0.991	D	0.99585	1.0974	10	0.72032	D	0.01	.	15.5796	0.76422	1.0:0.0:0.0:0.0	.	584;584;583;619;588;572	A8K7J7;P19367;P19367-2;E7ENR4;P19367-3;P19367-4	.;HXK1_HUMAN;.;.;.;.	G	572;619;588;583;584;584	ENSP00000353433:D572G;ENSP00000402103:D619G;ENSP00000384774:D588G;ENSP00000298649:D583G;ENSP00000352398:D584G	ENSP00000298649:D583G	D	+	2	0	HK1	70814589	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.168000	0.68352	0.482000	0.46254	GAC	.	.		0.512	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		G	71144583	A	G	71144583	3	3	100	1	0	0	0	0	1	0	0	0	7199	275	10	2	1975	2	HK1	10	71144583	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	19073559	71144583	64390164	132	13701										
TSPAN15	23555	hgsc.bcm.edu	37	chr10	71255355	71255355	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tctccttttgaatagaccatTgacttcctgaacgacaacat	5	11	1	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:71255355T>C	ENST00000373290.2	+	4	485	c.363T>C	c.(361-363)atT>atC	p.I121I	TSPAN15_ENST00000459981.1_3'UTR	NM_012339.3	NP_036471.1	O95858	TSN15_HUMAN	tetraspanin 15	121					establishment of protein localization to plasma membrane (GO:0090002)|protein maturation (GO:0051604)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	9						AATAGACCATTGACTTCCTGA	0.428																																					p.I121I		Atlas-SNP	.											.	TSPAN15	22	.	0			c.T363C						.						121	111	114					10																	71255355		2203	4300	6503	SO:0001819	synonymous_variant	23555	exon4			GACCATTGACTTC	AY358934	CCDS7294.1	10q22.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000099282	ENSG00000099282		"Tetraspanins"	23298	protein-coding gene	gene with protein product		613140	"transmembrane 4 superfamily member 15"	TM4SF15		11739647, 10719184	Standard	NM_012339		Approved	NET-7	uc001jpo.1	O95858	OTTHUMG00000018381	ENST00000373290.2:c.363T>C	chr10.hg19:g.71255355T>C		152.0	0.0		86.0	4.0	NM_012339	Q6UW79	Silent	SNP	ENST00000373290.2	hg19	CCDS7294.1																																																																																			.	.		0.428	TSPAN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048444.1	NM_012339		C	71255355	T	C	71255355	2	2	100	1	0	0	0	0	0	0	0	1	16654	1800	63	2		2	TSPAN15	10	71255355	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	110772	71255355	64279392	133	13702										
CDH23	64072	hgsc.bcm.edu	37	chr10	73375278	73375278	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cagggaataccaacagcatcTttgccctggactacatcagc	8	13	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:73375278T>C	ENST00000224721.6	+	9	870	c.865T>C	c.(865-867)Ttt>Ctt	p.F289L	CDH23_ENST00000398842.3_Missense_Mutation_p.F284L|CDH23_ENST00000398809.4_Missense_Mutation_p.F284L|CDH23_ENST00000461841.3_Missense_Mutation_p.F329L|CDH23_ENST00000299366.7_Missense_Mutation_p.F329L	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	284	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CAACAGCATCTTTGCCCTGGA	0.602																																					p.F284L		Atlas-SNP	.											.	CDH23	365	.	0			c.T850C						.						84	86	85					10																	73375278		2029	4175	6204	SO:0001583	missense	64072	exon10			AGCATCTTTGCCC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.865T>C	chr10.hg19:g.73375278T>C	ENSP00000224721:p.Phe289Leu	117.0	0.0		72.0	4.0	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	T	24.0	4.487407	0.84854	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721;ENST00000416060	T;T	0.70749	-0.51;-0.51	4.22	4.22	0.49857	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000002	D	0.84991	0.5595	M	0.86343	2.81	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.974	D;D;D	0.97110	1.0;0.994;0.969	D	0.87498	0.2431	10	0.62326	D	0.03	.	13.4567	0.61204	0.0:0.0:0.0:1.0	.	284;284;284	A5D6V9;Q9H251;Q9H251-5	.;CAD23_HUMAN;.	L	291;284;284;284;284;289;289;201	ENSP00000381789:F284L;ENSP00000381822:F284L	ENSP00000224721:F291L	F	+	1	0	CDH23	73045284	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.431000	0.80335	1.771000	0.52183	0.455000	0.32223	TTT	.	.		0.602	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		C	73375278	T	C	73375278	3	2	100	1	0	0	0	0	1	0	0	0	3110	1609	56	2	884	2	CDH23	10	73375278	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2119923	73375278	62159469	134	13703										
BTAF1	9044	hgsc.bcm.edu	37	chr10	93718881	93718881	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aaagctcatgggaaaagtggTggtaaaatgggtgacagcac	14	5	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:93718881T>C	ENST00000265990.6	+	9	1268	c.960T>C	c.(958-960)ggT>ggC	p.G320G	BTAF1_ENST00000471217.1_3'UTR	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	320					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				GGAAAAGTGGTGGTAAAATGG	0.373																																					p.G320G		Atlas-SNP	.											.	BTAF1	148	.	0			c.T960C						.						152	146	148					10																	93718881		2203	4300	6503	SO:0001819	synonymous_variant	9044	exon9			AAGTGGTGGTAAA	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.960T>C	chr10.hg19:g.93718881T>C		183.0	0.0		90.0	4.0	NM_003972	B4E0W6|O43578	Silent	SNP	ENST00000265990.6	hg19	CCDS7419.1																																																																																			.	.		0.373	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		C	93718881	T	C	93718881	2	2	100	1	0	0	0	0	0	0	0	1	1538	1683	59	2		2	BTAF1	10	93718881	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	20343603	93718881	41815866	135	13704										
PLCE1	51196	hgsc.bcm.edu	37	chr10	96076426	96076426	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccattccagagagccattggTccagaagaggagatcatgca	11	10	1	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:96076426T>C	ENST00000371380.3	+	28	6490	c.6255T>C	c.(6253-6255)ggT>ggC	p.G2085G	RP11-76P2.4_ENST00000609123.1_RNA|PLCE1_ENST00000371385.3_Silent_p.G1777G|PLCE1_ENST00000260766.3_Silent_p.G2085G|PLCE1_ENST00000371375.1_Silent_p.G1777G|NOC3L_ENST00000543788.1_Intron			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	2085	Ras-associating 1. {ECO:0000255|PROSITE- ProRule:PRU00166}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				GAGCCATTGGTCCAGAAGAGG	0.383																																					p.G2085G		Atlas-SNP	.											.	PLCE1	543	.	0			c.T6255C						.						93	90	91					10																	96076426		1854	4091	5945	SO:0001819	synonymous_variant	51196	exon29			CATTGGTCCAGAA		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.6255T>C	chr10.hg19:g.96076426T>C		118.0	0.0		100.0	4.0	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	hg19	CCDS41552.1																																																																																			.	.		0.383	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		C	96076426	T	C	96076426	2	2	100	1	0	0	0	0	0	0	0	1	12043	1654	58	2		2	PLCE1	10	96076426	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2357545	96076426	39458321	136	13705										
DNMBP	23268	hgsc.bcm.edu	37	chr10	101668878	101668878	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gaaggggccaccagtgatgaAgactgggaggagaggagcgt	19	6	0	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr10:101668878A>G	ENST00000324109.4	-	5	2377	c.2286T>C	c.(2284-2286)tcT>tcC	p.S762S	DNMBP_ENST00000342239.3_Silent_p.S762S|DNMBP_ENST00000543621.1_Silent_p.S8S	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	762					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		CCAGTGATGAAGACTGGGAGG	0.507																																					p.S762S		Atlas-SNP	.											.	DNMBP	173	.	0			c.T2286C						.						59	54	56					10																	101668878		2203	4300	6503	SO:0001819	synonymous_variant	23268	exon5			TGATGAAGACTGG	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"Rho guanine nucleotide exchange factors"	30373	protein-coding gene	gene with protein product	"scaffold protein TUBA"	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.2286T>C	chr10.hg19:g.101668878A>G		121.0	0.0		84.0	4.0	NM_015221	Q8IVY3|Q9Y2L3	Silent	SNP	ENST00000324109.4	hg19	CCDS7485.1																																																																																			.	.		0.507	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221		G	101668878	A	G	101668878	2	3	100	1	0	0	0	0	0	0	0	1	4676	59	3	2		2	DNMBP	10	101668878	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	5592452	101668878	33865869	137	13706										
TRPM5	29850	hgsc.bcm.edu	37	chr11	2438955	2438955	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgcccaccctgcccgccctcAcctttcaccagcgccttcag	6	22	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:2438955A>G	ENST00000155858.6	-	7	1018		c.e7+1		TRPM5_ENST00000528453.1_Splice_Site|TRPM5_ENST00000452833.1_Splice_Site|TRPM5_ENST00000533060.1_Splice_Site	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		GCCCGCCCTCACCTTTCACCA	0.627																																					.	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.1009+2T>C						.						21	20	21					11																	2438955		2190	4293	6483	SO:0001630	splice_region_variant	29850	exon8			GCCCTCACCTTTC	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"Voltage-gated ion channels / Transient receptor potential cation channels"	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.1009+1T>C	chr11.hg19:g.2438955A>G		94.0	0.0		63.0	4.0	NM_014555		Splice_Site	SNP	ENST00000155858.6	hg19	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	A	18.31	3.594831	0.66219	.	.	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	.	.	.	4.05	4.05	0.47172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0364	0.47804	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TRPM5	2395531	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	8.017000	0.88712	1.608000	0.50180	0.260000	0.18958	.	.	.		0.627	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	Intron	G	2438955	A	G	2438955	5	3	100	1	0	0	0	0	0	0	1	0	16604	173	6	2	2558	2	TRPM5	11	2438955	Splice_Site	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		2438955	132567561	138	13707										
CHRNA10	57053	hgsc.bcm.edu	37	chr11	3687610	3687610	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ggagataactcaggtggcctGgactgcccacagggctcccc	13	14	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:3687610G>A	ENST00000250699.2	-	5	1151	c.1080C>T	c.(1078-1080)tcC>tcT	p.S360S	CHRNA10_ENST00000534359.1_3'UTR|Y_RNA_ENST00000363331.1_RNA|Y_RNA_ENST00000364409.1_RNA|CHRNA10_ENST00000493827.2_5'Flank	NM_020402.2	NP_065135.2	Q9GZZ6	ACH10_HUMAN	cholinergic receptor, nicotinic, alpha 10 (neuronal)	360					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|inner ear morphogenesis (GO:0042472)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of cell proliferation (GO:0042127)|synaptic transmission, cholinergic (GO:0007271)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perikaryon (GO:0043204)|postsynaptic membrane (GO:0045211)	acetylcholine-activated cation-selective channel activity (GO:0004889)|calcium channel activity (GO:0005262)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(3)|ovary(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0164)|all_neural(188;0.0577)		BRCA - Breast invasive adenocarcinoma(625;0.0344)|LUSC - Lung squamous cell carcinoma(625;0.192)	Chloroprocaine(DB01161)|Galantamine(DB00674)|Methadone(DB00333)|Nicotine(DB00184)|Pentolinium(DB01090)|Succinylcholine(DB00202)|Trimethaphan(DB01116)	CAGGTGGCCTGGACTGCCCAC	0.701																																					p.S360S	Melanoma(153;17 1869 2949 7120 36888)	Atlas-SNP	.											CHRNA10,colon,carcinoma,0,1	CHRNA10	31	.	0			c.C1080T						.						53	56	55					11																	3687610		2201	4297	6498	SO:0001819	synonymous_variant	57053	exon5			TGGCCTGGACTGC	AF199235	CCDS7745.1	11p15.5	2012-02-11	2012-02-07		ENSG00000129749	ENSG00000129749		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	13800	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 10 (neuronal)"	606372	"cholinergic receptor, nicotinic, alpha polypeptide 10"				Standard	NM_020402		Approved		uc001lyf.3	Q9GZZ6	OTTHUMG00000011844	ENST00000250699.2:c.1080C>T	chr11.hg19:g.3687610G>A		48.0	0.0		32.0	2.0	NM_020402		Silent	SNP	ENST00000250699.2	hg19	CCDS7745.1																																																																																			.	.		0.701	CHRNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032763.2			A	3687610	G	A	3687610	2	1	100	1	0	0	0	0	0	0	0	1	3384	1335	47	3		3	CHRNA10	11	3687610	Silent	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	1248655	3687610	131318906	139	13708										
NUP98	4928	hgsc.bcm.edu	37	chr11	3720345	3720345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cagagagcaggcctcactgaTccttttgcctgtgaggtagc	12	11	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:3720345T>C	ENST00000324932.7	-	25	4396	c.3976A>G	c.(3976-3978)Atc>Gtc	p.I1326V	NUP98_ENST00000355260.3_Missense_Mutation_p.I1326V|NUP98_ENST00000359171.4_Missense_Mutation_p.I1326V|NUP98_ENST00000488828.1_5'Flank	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1343					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		GCCTCACTGATCCTTTTGCCT	0.552			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																p.I1326V		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.A3976G						.						168	164	165					11																	3720345		2201	4298	6499	SO:0001583	missense	4928	exon25			CACTGATCCTTTT	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.3976A>G	chr11.hg19:g.3720345T>C	ENSP00000316032:p.Ile1326Val	139.0	0.0		94.0	8.0	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	hg19	CCDS7746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.46|19.46	3.832340|3.832340	0.71258|0.71258	.|.	.|.	ENSG00000110713|ENSG00000110713	ENST00000429801|ENST00000324932;ENST00000359171;ENST00000355260	.|.	.|.	.|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.62925|0.62925	0.2468|0.2468	L|L	0.28776|0.28776	0.89|0.89	0.43364|0.43364	D|D	0.995441|0.995441	.|D;P;D	.|0.69078	.|0.997;0.596;0.991	.|D;P;D	.|0.77557	.|0.99;0.495;0.978	T|T	0.56637|0.56637	-0.7946|-0.7946	5|9	.|0.12430	.|T	.|0.62	-15.952|-15.952	15.3831|15.3831	0.74676|0.74676	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1326;1326;1240	.|P52948-2;P52948-5;P52948-6	.|.;.;.	G|V	278|1326	.|.	.|ENSP00000316032:I1326V	D|I	-|-	2|1	0|0	NUP98|NUP98	3676921|3676921	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	7.201000|7.201000	0.77847|0.77847	2.285000|2.285000	0.76669|0.76669	0.533000|0.533000	0.62120|0.62120	GAT|ATC	.	.		0.552	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		C	3720345	T	C	3720345	3	2	100	1	0	0	0	0	1	0	0	0	10782	1435	50	2	1462	2	NUP98	11	3720345	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	32735	3720345	131286171	140	13709										
NUP98	4928	hgsc.bcm.edu	37	chr11	3746442	3746442	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cttcaaaaccaacttcttaaTgctcttcctataaacaagaa	2	11	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:3746442T>C	ENST00000324932.7	-	15	2158	c.1738A>G	c.(1738-1740)Att>Gtt	p.I580V	NUP98_ENST00000397007.4_Missense_Mutation_p.I597V|NUP98_ENST00000397004.4_Missense_Mutation_p.I580V|NUP98_ENST00000355260.3_Missense_Mutation_p.I580V|NUP98_ENST00000359171.4_Missense_Mutation_p.I580V	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	597					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		AACTTCTTAATGCTCTTCCTA	0.338			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																p.I597V		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.A1789G						.						70	73	72					11																	3746442		2200	4293	6493	SO:0001583	missense	4928	exon15			TCTTAATGCTCTT	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.1738A>G	chr11.hg19:g.3746442T>C	ENSP00000316032:p.Ile580Val	117.0	0.0		88.0	4.0	NM_005387	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	hg19	CCDS7746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.34|16.34	3.095892|3.095892	0.56075|0.56075	.|.	.|.	ENSG00000110713|ENSG00000110713	ENST00000527104|ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007	.|.	.|.	.|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.64907|0.64907	0.2641|0.2641	L|L	0.39898|0.39898	1.24|1.24	0.48135|0.48135	D|D	0.999592|0.999592	.|D;B;D;D	.|0.69078	.|0.978;0.311;0.993;0.997	.|D;B;D;D	.|0.77557	.|0.968;0.303;0.986;0.99	T|T	0.59096|0.59096	-0.7518|-0.7518	5|9	.|0.10377	.|T	.|0.69	.|.	14.7666|14.7666	0.69642|0.69642	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|597;580;580;580	.|P52948-3;P52948-4;P52948-2;P52948-5	.|.;.;.;.	R|V	199|580;580;580;580;597	.|.	.|ENSP00000316032:I580V	H|I	-|-	2|1	0|0	NUP98|NUP98	3703018|3703018	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	7.412000|7.412000	0.80091|0.80091	2.093000|2.093000	0.63338|0.63338	0.377000|0.377000	0.23210|0.23210	CAT|ATT	.	.		0.338	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		C	3746442	T	C	3746442	3	2	100	1	0	0	0	0	1	0	0	0	10782	1464	51	2	3761	2	NUP98	11	3746442	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	26097	3746442	131260074	141	13710										
ANO3	63982	hgsc.bcm.edu	37	chr11	26656592	26656592	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cccaggaaaatacaataaacTttttgaccggtggagactgg	10	8	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:26656592T>C	ENST00000256737.3	+	20	2870	c.2018T>C	c.(2017-2019)cTt>cCt	p.L673P	ANO3_ENST00000537978.1_Missense_Mutation_p.L657P|ANO3_ENST00000525139.1_Missense_Mutation_p.L657P|ANO3_ENST00000531568.1_Missense_Mutation_p.L527P	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	673					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						TACAATAAACTTTTTGACCGG	0.458																																					p.L673P		Atlas-SNP	.											.	ANO3	145	.	0			c.T2018C						.						136	123	127					11																	26656592		2203	4299	6502	SO:0001583	missense	63982	exon20			ATAAACTTTTTGA	AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	14004	protein-coding gene	gene with protein product	"transmembrane protein 16C (eight membrane-spanning domains)"	610110	"chromosome 11 open reading frame 25", "transmembrane protein 16C"	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.2018T>C	chr11.hg19:g.26656592T>C	ENSP00000256737:p.Leu673Pro	212.0	0.0		112.0	5.0	NM_031418	B7Z3F5	Missense_Mutation	SNP	ENST00000256737.3	hg19	CCDS31447.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.608922	0.87258	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	T;T;T;T	0.74315	-0.82;-0.82;-0.83;-0.71	6.03	6.03	0.97812	.	0.111684	0.64402	D	0.000006	D	0.86628	0.5978	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.992;0.996	D	0.87160	0.2214	10	0.49607	T	0.09	.	15.7467	0.77949	0.0:0.0:0.0:1.0	.	575;673	B7Z7Y6;Q9BYT9	.;ANO3_HUMAN	P	657;657;673;575;527	ENSP00000440737:L657P;ENSP00000432576:L657P;ENSP00000256737:L673P;ENSP00000432394:L527P	ENSP00000256737:L673P	L	+	2	0	ANO3	26613168	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.928000	0.87587	2.302000	0.77476	0.533000	0.62120	CTT	.	.		0.458	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		C	26656592	T	C	26656592	3	2	100	1	0	0	0	0	1	0	0	0	698	1609	56	2	2096	2	ANO3	11	26656592	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	22910150	26656592	108349924	142	13711										
OR5M9	390162	hgsc.bcm.edu	37	chr11	56230291	56230291	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttccagcaataacaatcattGtgatttctttgatgtgcact	6	8	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:56230291G>A	ENST00000279791.1	-	1	586	c.587C>T	c.(586-588)aCa>aTa	p.T196I		NM_001004743.1	NP_001004743.1	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M, member 9	196						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	36	Esophageal squamous(21;0.00448)					AACAATCATTGTGATTTCTTT	0.448																																					p.T196I		Atlas-SNP	.											.	OR5M9	75	.	0			c.C587T						.						86	90	88					11																	56230291		2201	4296	6497	SO:0001583	missense	390162	exon1			ATCATTGTGATTT	AB065747	CCDS31531.1	11q11	2012-08-09			ENSG00000150269	ENSG00000150269		"GPCR / Class A : Olfactory receptors"	15294	protein-coding gene	gene with protein product							Standard	NM_001004743		Approved		uc010rjj.2	Q8NGP3	OTTHUMG00000166874	ENST00000279791.1:c.587C>T	chr11.hg19:g.56230291G>A	ENSP00000279791:p.Thr196Ile	106.0	0.0		79.0	4.0	NM_001004743	Q6IEW5|Q96RB9	Missense_Mutation	SNP	ENST00000279791.1	hg19	CCDS31531.1	.	.	.	.	.	.	.	.	.	.	G	3.241	-0.155326	0.06544	.	.	ENSG00000150269	ENST00000279791	T	0.35605	1.3	4.39	1.25	0.21368	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45606	D	0.000351	T	0.28466	0.0704	N	0.11201	0.11	0.09310	N	1	D	0.54601	0.967	P	0.61592	0.891	T	0.07083	-1.0791	10	0.28530	T	0.3	-15.8863	5.5424	0.17045	0.2025:0.1688:0.6287:0.0	.	196	Q8NGP3	OR5M9_HUMAN	I	196	ENSP00000279791:T196I	ENSP00000279791:T196I	T	-	2	0	OR5M9	55986867	0.000000	0.05858	0.893000	0.35052	0.238000	0.25445	0.286000	0.18902	0.972000	0.38314	0.542000	0.68232	ACA	.	.		0.448	OR5M9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391638.1	NM_001004743		A	56230291	G	A	56230291	3	1	100	1	0	0	0	0	1	0	0	0	11186	1377	48	3	347	3	OR5M9	11	56230291	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	29573699	56230291	78776225	143	13712										
OR5B2	390190	hgsc.bcm.edu	37	chr11	58190477	58190477	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttgtaggagatgaccttgtcTcctctaaggaacccagccat	9	11	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:58190477T>C	ENST00000302581.2	-	1	309	c.258A>G	c.(256-258)ggA>ggG	p.G86G		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TGACCTTGTCTCCTCTAAGGA	0.493																																					p.G86G		Atlas-SNP	.											.	OR5B2	75	.	0			c.A258G						.						136	118	124					11																	58190477		2201	4295	6496	SO:0001819	synonymous_variant	390190	exon1			CTTGTCTCCTCTA	AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"GPCR / Class A : Olfactory receptors"	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.258A>G	chr11.hg19:g.58190477T>C		136.0	0.0		89.0	6.0	NM_001005566	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Silent	SNP	ENST00000302581.2	hg19	CCDS31550.1																																																																																			.	.		0.493	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566		C	58190477	T	C	58190477	2	2	100	1	0	0	0	0	0	0	0	1	11159	1538	54	2		2	OR5B2	11	58190477	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1960186	58190477	76816039	144	13713										
METTL12	751071	hgsc.bcm.edu	37	chr11	62434058	62434058	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctggatgtgggctgtgggacTtccagcctatgtacaggcct	14	10	0	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:62434058T>C	ENST00000532971.1	+	3	515	c.258T>C	c.(256-258)acT>acC	p.T86T	C11orf48_ENST00000532208.1_Intron|C11orf48_ENST00000354588.3_Intron|C11orf48_ENST00000431002.2_Intron|C11orf48_ENST00000525675.1_5'Flank|RP11-831H9.11_ENST00000528405.1_5'Flank|C11orf48_ENST00000524958.1_5'Flank|METTL12_ENST00000398922.2_3'UTR|SNORA57_ENST00000383870.1_RNA	NM_001043229.1	NP_001036694.1	A8MUP2	MET12_HUMAN	methyltransferase like 12	86						mitochondrion (GO:0005739)	methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	6						GCTGTGGGACTTCCAGCCTAT	0.582																																					p.T86T		Atlas-SNP	.											.	METTL12	11	.	0			c.T258C						.						57	65	62					11																	62434058		2002	4160	6162	SO:0001819	synonymous_variant	751071	exon3			TGGGACTTCCAGC	BC041359	CCDS41657.1	11q12.3	2013-09-30			ENSG00000214756	ENSG00000214756			33113	protein-coding gene	gene with protein product							Standard	NM_001043229		Approved	U99HG	uc001nuh.3	A8MUP2	OTTHUMG00000167545	ENST00000532971.1:c.258T>C	chr11.hg19:g.62434058T>C		87.0	0.0		77.0	5.0	NM_001043229	B7Z4C1	Silent	SNP	ENST00000532971.1	hg19	CCDS41657.1																																																																																			.	.		0.582	METTL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394990.1	NM_001043229		C	62434058	T	C	62434058	2	2	100	1	0	0	0	0	0	0	0	1	9505	1596	56	2		2	METTL12	11	62434058	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	4243581	62434058	72572458	145	13714										
SLC25A45	283130	hgsc.bcm.edu	37	chr11	65147388	65147388	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atcaacgatgccccggtaggTggtctgggtctgcagcctca	13	12	4	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:65147388T>C	ENST00000527174.1	-	3	158	c.103A>G	c.(103-105)Acc>Gcc	p.T35A	SLC25A45_ENST00000526432.1_Missense_Mutation_p.T35A|SLC25A45_ENST00000398802.1_Missense_Mutation_p.T35A|SLC25A45_ENST00000377152.2_5'UTR|SLC25A45_ENST00000534028.1_Intron|SLC25A45_ENST00000294187.6_5'UTR|SLC25A45_ENST00000360662.3_Intron|SLC25A45_ENST00000417511.2_5'UTR			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	35					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14						CCCCGGTAGGTGGTCTGGGTC	0.627																																					p.T35A		Atlas-SNP	.											.	SLC25A45	23	.	0			c.A103G						.						60	68	65					11																	65147388		2065	4195	6260	SO:0001583	missense	283130	exon4			GGTAGGTGGTCTG	BC041100	CCDS41670.1, CCDS41671.1, CCDS60850.1	11q13.1	2013-05-22			ENSG00000162241	ENSG00000162241		"Solute carriers"	27442	protein-coding gene	gene with protein product		610825				16949250	Standard	XM_006718507		Approved		uc001odr.1	Q8N413	OTTHUMG00000166255	ENST00000527174.1:c.103A>G	chr11.hg19:g.65147388T>C	ENSP00000435489:p.Thr35Ala	102.0	0.0		63.0	4.0	NM_182556	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	hg19	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	T	4.906	0.168366	0.09339	.	.	ENSG00000162241	ENST00000527174;ENST00000398802;ENST00000526432;ENST00000530936	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	4.38	0.541	0.17168	Mitochondrial carrier domain (2);	.	.	.	.	T	0.49983	0.1589	N	0.05280	-0.08	0.09310	N	0.999998	B;B	0.14438	0.01;0.001	B;B	0.12837	0.006;0.008	T	0.34179	-0.9839	9	0.10636	T	0.68	.	4.6237	0.12467	0.0:0.1882:0.1641:0.6477	.	35;35	E9PJQ3;Q8N413	.;S2545_HUMAN	A	35	ENSP00000435489:T35A;ENSP00000381782:T35A;ENSP00000435547:T35A;ENSP00000431642:T35A	ENSP00000381782:T35A	T	-	1	0	SLC25A45	64903964	0.516000	0.26218	0.108000	0.21378	0.842000	0.47809	0.553000	0.23391	0.247000	0.21414	0.459000	0.35465	ACC	.	.		0.627	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556		C	65147388	T	C	65147388	3	2	100	1	0	0	0	0	1	0	0	0	14525	1696	59	2	779	2	SLC25A45	11	65147388	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2713330	65147388	69859128	146	13715										
FCHSD2	9873	hgsc.bcm.edu	37	chr11	72551945	72551945	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tcgcagtttgccatatgaggTctcaggagtatgccttgatg	12	8	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:72551945T>C	ENST00000409418.4	-	19	2499	c.2116A>G	c.(2116-2118)Acc>Gcc	p.T706A	FCHSD2_ENST00000458644.2_Missense_Mutation_p.T570A|FCHSD2_ENST00000409263.1_Missense_Mutation_p.T67A|FCHSD2_ENST00000311172.7_Missense_Mutation_p.T650A|ATG16L2_ENST00000534905.1_Intron|FCHSD2_ENST00000409314.1_Missense_Mutation_p.T730A	NM_014824.2	NP_055639.2	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	706										endometrium(2)|large_intestine(11)|lung(5)|ovary(2)|prostate(1)|skin(1)	22			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			CCATATGAGGTCTCAGGAGTA	0.418																																					p.T706A		Atlas-SNP	.											.	FCHSD2	106	.	0			c.A2116G						.						115	103	107					11																	72551945		2200	4293	6493	SO:0001583	missense	9873	exon19			ATGAGGTCTCAGG	AB018312	CCDS8218.2	11q13.3	2008-02-05	2004-04-14	2004-04-16	ENSG00000137478	ENSG00000137478			29114	protein-coding gene	gene with protein product			"SH3 multiple domains 3"	SH3MD3		9872452, 15067381	Standard	NM_014824		Approved	KIAA0769	uc009ytl.3	O94868	OTTHUMG00000153082	ENST00000409418.4:c.2116A>G	chr11.hg19:g.72551945T>C	ENSP00000386722:p.Thr706Ala	105.0	0.0		61.0	5.0	NM_014824	B4DNI3|Q7L8J9|Q8WVM2|Q96FV7|Q9UF77	Missense_Mutation	SNP	ENST00000409418.4	hg19	CCDS8218.2	.	.	.	.	.	.	.	.	.	.	T	13.87	2.367561	0.42003	.	.	ENSG00000137478	ENST00000311172;ENST00000409314;ENST00000409418;ENST00000409263;ENST00000458644	T;T;T;T	0.14144	2.53;2.65;2.65;2.53	5.3	4.11	0.48088	.	0.426091	0.23863	N	0.043824	T	0.07052	0.0179	N	0.12182	0.205	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20806	-1.0264	10	0.09338	T	0.73	-13.8225	11.7994	0.52118	0.0:0.0:0.1461:0.8539	.	570;706	E7ENZ2;O94868	.;FCSD2_HUMAN	A	650;730;706;67;570	ENSP00000308978:T650A;ENSP00000386987:T730A;ENSP00000386722:T706A;ENSP00000402972:T570A	ENSP00000308978:T650A	T	-	1	0	FCHSD2	72229593	0.999000	0.42202	1.000000	0.80357	0.605000	0.37080	1.692000	0.37731	2.225000	0.72522	0.460000	0.39030	ACC	.	.		0.418	FCHSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329429.2	NM_014824		C	72551945	T	C	72551945	3	2	100	1	0	0	0	0	1	0	0	0	5798	1667	58	2	114	2	FCHSD2	11	72551945	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	7404557	72551945	62454571	147	13716										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73073127	73073127	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgaacagctgcccggagcccTcgcctgaggtatgggtctgc	14	13	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:73073127T>C	ENST00000263674.3	+	13	4887	c.4537T>C	c.(4537-4539)Tcg>Ccg	p.S1513P		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1513					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CCCGGAGCCCTCGCCTGAGGT	0.662																																					p.S1513P		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.T4537C						.						29	31	30					11																	73073127		2200	4292	6492	SO:0001583	missense	9828	exon13			GAGCCCTCGCCTG	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.4537T>C	chr11.hg19:g.73073127T>C	ENSP00000263674:p.Ser1513Pro	113.0	0.0		51.0	5.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.138391	0.56936	.	.	ENSG00000110237	ENST00000263674	T	0.58506	0.33	5.31	-6.75	0.01738	.	0.848702	0.10855	N	0.626767	T	0.32645	0.0836	N	0.14661	0.345	0.09310	N	1	B	0.27068	0.167	B	0.20384	0.029	T	0.17561	-1.0365	10	0.56958	D	0.05	0.0042	10.1721	0.42915	0.0979:0.0:0.4841:0.4179	.	1513	Q96PE2	ARHGH_HUMAN	P	1513	ENSP00000263674:S1513P	ENSP00000263674:S1513P	S	+	1	0	ARHGEF17	72750775	0.506000	0.26139	0.003000	0.11579	0.940000	0.58332	0.257000	0.18369	-1.177000	0.02744	0.533000	0.62120	TCG	.	.		0.662	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		C	73073127	T	C	73073127	3	2	100	1	0	0	0	0	1	0	0	0	900	1551	54	2	4587	2	ARHGEF17	11	73073127	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	521182	73073127	61933389	148	13717										
ESAM	90952	hgsc.bcm.edu	37	chr11	124624658	124624658	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cttaaagacccacggatgacAtctgtggacacaatttagcc	8	11	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:124624658A>G	ENST00000278927.5	-	5	738	c.609T>C	c.(607-609)gaT>gaC	p.D203D	VSIG2_ENST00000403470.1_5'Flank|ESAM_ENST00000442070.2_Splice_Site_p.D24D|VSIG2_ENST00000326621.5_5'Flank	NM_138961.2	NP_620411.2	Q96AP7	ESAM_HUMAN	endothelial cell adhesion molecule	203	Ig-like C2-type.				blood coagulation (GO:0007596)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)|single organismal cell-cell adhesion (GO:0016337)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.022)		CACGGATGACATCTGTGGACA	0.483																																					p.D203D		Atlas-SNP	.											.	ESAM	31	.	0			c.T609C						.						171	162	165					11																	124624658		2201	4299	6500	SO:0001630	splice_region_variant	90952	exon5			GATGACATCTGTG	AK075396	CCDS8453.1	11q24.2	2013-01-29			ENSG00000149564	ENSG00000149564		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17474	protein-coding gene	gene with protein product		614281				11279107, 11906820	Standard	NM_138961		Approved	W117m	uc001qav.4	Q96AP7	OTTHUMG00000151986	ENST00000278927.5:c.608-1T>C	chr11.hg19:g.124624658A>G		124.0	0.0		88.0	5.0	NM_138961	B4DVN8|Q96T50	Silent	SNP	ENST00000278927.5	hg19	CCDS8453.1																																																																																			.	.		0.483	ESAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324686.1	NM_138961	Silent	G	124624658	A	G	124624658	5	3	100	1	0	0	0	0	0	0	1	0	5249	231	8	2	575	2	ESAM	11	124624658	Splice_Site	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	51551531	124624658	10381858	149	13718										
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126318909	126318909	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	caccactgcactcacagtagAcgtcaaccgtgcggctgagg	11	14	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr11:126318909A>G	ENST00000525144.2	-	8	1241	c.992T>C	c.(991-993)gTc>gCc	p.V331A	KIRREL3_ENST00000529097.2_Missense_Mutation_p.V331A|KIRREL3_ENST00000525704.2_Missense_Mutation_p.V331A	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	331					hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		CTCACAGTAGACGTCAACCGT	0.577																																					p.V331A		Atlas-SNP	.											.	KIRREL3	183	.	0			c.T992C						.						60	66	64					11																	126318909		2094	4225	6319	SO:0001583	missense	84623	exon8			CAGTAGACGTCAA	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.992T>C	chr11.hg19:g.126318909A>G	ENSP00000435466:p.Val331Ala	68.0	0.0		54.0	4.0	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Missense_Mutation	SNP	ENST00000525144.2	hg19	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.811738	0.90707	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000525704	T;T;T	0.22134	1.97;1.97;1.97	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000001	T	0.47525	0.1450	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	0.996;0.963;1.0	D;D;D	0.85130	0.987;0.973;0.997	T	0.51204	-0.8735	10	0.87932	D	0	.	14.9562	0.71116	1.0:0.0:0.0:0.0	.	331;331;331	Q8IZU9-2;E9PRX9;Q8IZU9	.;.;KIRR3_HUMAN	A	331	ENSP00000435466:V331A;ENSP00000434081:V331A;ENSP00000435094:V331A	ENSP00000435466:V331A	V	-	2	0	KIRREL3	125824119	1.000000	0.71417	0.968000	0.41197	0.951000	0.60555	8.962000	0.93254	2.013000	0.59113	0.523000	0.50628	GTC	.	.		0.577	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		G	126318909	A	G	126318909	3	3	100	1	0	0	0	0	1	0	0	0	8335	275	10	2	1491	2	KIRREL3	11	126318909	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1694251	126318909	8687607	150	13719										
NTF3	4908	hgsc.bcm.edu	37	chr12	5603792	5603792	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	acagaacatcacggcggaaaCggtacgcggagcataagagt	13	9	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:5603792C>T	ENST00000331010.6	+	1	495	c.412C>T	c.(412-414)Cgg>Tgg	p.R138W	NTF3_ENST00000423158.3_Missense_Mutation_p.R151W|NTF3_ENST00000535299.1_Intron	NM_002527.4	NP_002518.1	P20783	NTF3_HUMAN	neurotrophin 3	138					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell-cell signaling (GO:0007267)|enteric nervous system development (GO:0048484)|epidermis development (GO:0008544)|glial cell fate determination (GO:0007403)|induction of positive chemotaxis (GO:0050930)|mechanoreceptor differentiation (GO:0042490)|myelination (GO:0042552)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive chemotaxis (GO:0050918)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of synaptic transmission (GO:0050804)|signal transduction (GO:0007165)|smooth muscle cell differentiation (GO:0051145)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular region (GO:0005576)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)	p.R138W(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(3)|upper_aerodigestive_tract(1)	22						ACGGCGGAAACGGTACGCGGA	0.602																																					p.R151W	GBM(194;1104 2182 8339 9578 18493)	Atlas-SNP	.											NTF3,NS,carcinoma,-1,2	NTF3	50	.	1	Substitution - Missense(1)	pancreas(1)	c.C451T						.						90	85	87					12																	5603792		2203	4300	6503	SO:0001583	missense	4908	exon2			CGGAAACGGTACG		CCDS8538.1, CCDS44806.1	12p13	2014-01-30			ENSG00000185652	ENSG00000185652		"Endogenous ligands"	8023	protein-coding gene	gene with protein product		162660				1889806	Standard	NM_002527		Approved	NGF2	uc001qnk.4	P20783	OTTHUMG00000168649	ENST00000331010.6:c.412C>T	chr12.hg19:g.5603792C>T	ENSP00000328738:p.Arg138Trp	70.0	0.0		41.0	2.0	NM_001102654	B7Z1T5|Q6FH50	Missense_Mutation	SNP	ENST00000331010.6	hg19	CCDS8538.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.402300	0.62288	.	.	ENSG00000185652	ENST00000423158;ENST00000331010	T;T	0.71461	-0.57;-0.57	5.52	0.544	0.17185	.	0.000000	0.85682	D	0.000000	D	0.82972	0.5153	M	0.89601	3.045	0.49483	D	0.999797	D;D	0.76494	0.997;0.999	P;P	0.57720	0.826;0.826	D	0.87975	0.2739	10	0.87932	D	0	-11.5385	15.2584	0.73603	0.3181:0.6819:0.0:0.0	.	138;151	P20783;B7Z1T5	NTF3_HUMAN;.	W	151;138	ENSP00000397297:R151W;ENSP00000328738:R138W	ENSP00000328738:R138W	R	+	1	2	NTF3	5474053	1.000000	0.71417	0.995000	0.50966	0.950000	0.60333	2.989000	0.49393	0.516000	0.28340	0.591000	0.81541	CGG	.	.		0.602	NTF3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400486.1			T	5603792	C	T	5603792	3	4	100	1	0	0	0	0	1	0	0	0	10705	527	19	1	457	1	NTF3	12	5603792	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10		5603792	128248103	151	13720										
PTPRO	5800	hgsc.bcm.edu	37	chr12	15654901	15654901	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cagagaagtcaacatcaggcTctttctcctttttccctgtg	7	12	4	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:15654901T>C	ENST00000281171.4	+	5	1339	c.1009T>C	c.(1009-1011)Tct>Cct	p.S337P	PTPRO_ENST00000348962.2_Missense_Mutation_p.S337P|PTPRO_ENST00000543886.1_Missense_Mutation_p.S337P	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	337	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				AACATCAGGCTCTTTCTCCTT	0.428																																					p.S337P		Atlas-SNP	.											.	PTPRO	148	.	0			c.T1009C						.						100	84	90					12																	15654901		2203	4300	6503	SO:0001583	missense	5800	exon5			TCAGGCTCTTTCT	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9678	protein-coding gene	gene with protein product	"osteoclastic transmembrane protein-tyrosine phosphatase"	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.1009T>C	chr12.hg19:g.15654901T>C	ENSP00000281171:p.Ser337Pro	129.0	0.0		95.0	4.0	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	hg19	CCDS8675.1	.	.	.	.	.	.	.	.	.	.	T	0.288	-0.981860	0.02197	.	.	ENSG00000151490	ENST00000281171;ENST00000543886;ENST00000348962	T;T	0.03772	3.81;3.83	4.29	-0.718	0.11205	Fibronectin, type III (1);	0.443298	0.17231	N	0.181942	T	0.01387	0.0045	N	0.01576	-0.805	0.34781	D	0.734711	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.50118	-0.8865	10	0.02654	T	1	.	8.6781	0.34191	0.0:0.5646:0.0:0.4354	.	337;337;337	Q16827-2;Q16827;Q8IYG3	.;PTPRO_HUMAN;.	P	337	ENSP00000281171:S337P;ENSP00000343434:S337P	ENSP00000281171:S337P	S	+	1	0	PTPRO	15546168	0.028000	0.19301	0.007000	0.13788	0.981000	0.71138	0.341000	0.19909	-0.036000	0.13669	0.533000	0.62120	TCT	.	.		0.428	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			C	15654901	T	C	15654901	3	2	100	1	0	0	0	0	1	0	0	0	12824	1551	54	2	1027	2	PTPRO	12	15654901	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	10051109	15654901	118196994	152	13721										
REP15	387849	hgsc.bcm.edu	37	chr12	27849605	27849605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgcagctcagaaactgaaggAgtaccttggatttgaatatc	10	7	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:27849605A>G	ENST00000310791.2	+	1	178	c.110A>G	c.(109-111)gAg>gGg	p.E37G	RP11-1060J15.4_ENST00000542660.1_RNA|RP11-1060J15.4_ENST00000536922.1_RNA|RP11-1060J15.4_ENST00000536317.1_RNA	NM_001029874.1	NP_001025045.1	Q6BDI9	REP15_HUMAN	RAB15 effector protein	37					receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	endosome membrane (GO:0010008)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)				breast(1)|cervix(1)|large_intestine(2)|lung(4)|ovary(1)	9	Lung SC(9;0.0873)					AAACTGAAGGAGTACCTTGGA	0.453																																					p.E37G		Atlas-SNP	.											REP15,right_upper_lobe,carcinoma,0,1	REP15	13	.	0			c.A110G						.						97	87	90					12																	27849605		2203	4300	6503	SO:0001583	missense	387849	exon1			TGAAGGAGTACCT	BC140921	CCDS31762.1	12p11.22	2010-09-02			ENSG00000174236	ENSG00000174236			33748	protein-coding gene	gene with protein product		610848				16195351	Standard	NM_001029874		Approved	RAB15EP	uc001rig.1	Q6BDI9		ENST00000310791.2:c.110A>G	chr12.hg19:g.27849605A>G	ENSP00000310335:p.Glu37Gly	82.0	0.0		73.0	3.0	NM_001029874	B2RU16	Missense_Mutation	SNP	ENST00000310791.2	hg19	CCDS31762.1	.	.	.	.	.	.	.	.	.	.	A	14.76	2.632340	0.46944	.	.	ENSG00000174236	ENST00000310791	T	0.39787	1.06	5.11	2.72	0.32119	.	0.249234	0.31210	N	0.008043	T	0.36496	0.0969	L	0.59436	1.845	0.33875	D	0.635396	B	0.17268	0.021	B	0.16289	0.015	T	0.42899	-0.9424	10	0.72032	D	0.01	-0.5657	7.7418	0.28845	0.7869:0.1398:0.0733:0.0	.	37	Q6BDI9	REP15_HUMAN	G	37	ENSP00000310335:E37G	ENSP00000310335:E37G	E	+	2	0	REP15	27740872	1.000000	0.71417	0.955000	0.39395	0.866000	0.49608	3.367000	0.52350	0.407000	0.25591	0.528000	0.53228	GAG	.	.		0.453	REP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402894.1	NM_001029874		G	27849605	A	G	27849605	3	3	100	1	0	0	0	0	1	0	0	0	13241	304	11	2	112	2	REP15	12	27849605	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	12194704	27849605	106002290	153	13722										
DENND5B	160518	hgsc.bcm.edu	37	chr12	31604973	31604973	+	Frame_Shift_Del	DEL	A	A	-													0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	taatctgcaaacatctgtgtAaaacggttagcaaagacctc							TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:31604973delA	ENST00000389082.5	-	5	1794	c.1530delT	c.(1528-1530)tttfs	p.F510fs	DENND5B_ENST00000306833.6_Frame_Shift_Del_p.F545fs|DENND5B_ENST00000354285.4_Frame_Shift_Del_p.F532fs|DENND5B_ENST00000536562.1_Frame_Shift_Del_p.F545fs|snoU13_ENST00000458765.1_RNA	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	510	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						ACATCTGTGTAAAACGGTTAG	0.453																																					p.T511fs		Atlas-INDEL	.											.	DENND5B	114	.	0			c.1531delA						.						136	134	135					12																	31604973		1924	4145	6069	SO:0001589	frameshift_variant	160518	exon5			.	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.1530delT	chr12.hg19:g.31604973delA	ENSP00000373734:p.Phe510fs	212.0	0.0		126.0	12.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Frame_Shift_Del	DEL	ENST00000389082.5	hg19	CCDS44857.1																																																																																			.	.		0.453	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		-	31604973	A	-	31604973	7	5	100	1	0	1	0	1	0	0	0	0	4439	359	13	0	2362	0	DENND5B	12	31604973	Frame_Shift_Del	DEL	A	TCGA-DD-A1ED-01A-11D-A152-10	3755368	31604973	102246922	154	13723										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41967381	41967381	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cagacgatgacaccatgagcGagatgaaaatggggcgctac	13	9	0	5			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:41967381G>T	ENST00000402685.2	+	10	2808	c.2800G>T	c.(2800-2802)Gag>Tag	p.E934*	PDZRN4_ENST00000298919.7_Nonsense_Mutation_p.E674*|PDZRN4_ENST00000539469.2_Nonsense_Mutation_p.E676*	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	934							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E676K(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				CACCATGAGCGAGATGAAAAT	0.547																																					p.E934X		Atlas-SNP	.											PDZRN4,colon,carcinoma,0,1	PDZRN4	346	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2800T						.						95	90	92					12																	41967381		2203	4300	6503	SO:0001587	stop_gained	29951	exon10			ATGAGCGAGATGA	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2800G>T	chr12.hg19:g.41967381G>T	ENSP00000384197:p.Glu934*	82.0	0.0		44.0	2.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Nonsense_Mutation	SNP	ENST00000402685.2	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	G	41	8.917515	0.99002	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	.	.	.	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-37.6407	19.7189	0.96135	0.0:0.0:1.0:0.0	.	.	.	.	X	934;676;674	.	ENSP00000298919:E674X	E	+	1	0	PDZRN4	40253648	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.834000	0.97654	0.650000	0.86243	GAG	.	.		0.547	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		T	41967381	G	T	41967381	4	4	100	1	0	0	0	0	0	1	0	0	11719	1059	37	1	2911	1	PDZRN4	12	41967381	Nonsense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	10362408	41967381	91884514	155	13724										
ADCY6	112	hgsc.bcm.edu	37	chr12	49177177	49177177	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	caccccaggctgttttccgtTcatccactttagggaccagg	9	14	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:49177177T>C	ENST00000307885.4	-	1	735	c.41A>G	c.(40-42)gAa>gGa	p.E14G	ADCY6_ENST00000550422.1_Missense_Mutation_p.E14G|ADCY6_ENST00000357869.3_Missense_Mutation_p.E14G	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	14					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						TGTTTTCCGTTCATCCACTTT	0.552																																					p.E14G		Atlas-SNP	.											.	ADCY6	81	.	0			c.A41G						.						77	69	71					12																	49177177		2203	4300	6503	SO:0001583	missense	112	exon2			TTCCGTTCATCCA		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"Adenylate cyclases"	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.41A>G	chr12.hg19:g.49177177T>C	ENSP00000311405:p.Glu14Gly	113.0	0.0		66.0	4.0	NM_020983	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	hg19	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	T	17.93	3.508973	0.64410	.	.	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.80304	-1.36;-1.36;-1.36	5.09	5.09	0.68999	.	0.260319	0.37857	N	0.001920	T	0.80053	0.4553	L	0.48642	1.525	0.47819	D	0.999523	P;P	0.44139	0.827;0.734	P;B	0.46758	0.526;0.326	T	0.82516	-0.0418	10	0.72032	D	0.01	.	13.9768	0.64277	0.0:0.0:0.0:1.0	.	14;14	O43306-2;O43306	.;ADCY6_HUMAN	G	14	ENSP00000350536:E14G;ENSP00000446730:E14G;ENSP00000311405:E14G	ENSP00000311405:E14G	E	-	2	0	ADCY6	47463444	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.300000	0.78841	2.142000	0.66516	0.459000	0.35465	GAA	.	.		0.552	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		C	49177177	T	C	49177177	3	2	100	1	0	0	0	0	1	0	0	0	298	1783	62	2	3549	2	ADCY6	12	49177177	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	7209796	49177177	84674718	156	13725										
TUBA1B	10376	hgsc.bcm.edu	37	chr12	49522077	49522077	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	caccaatccacaaactggatGctgcgcttggttttgatggt	10	10	0	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:49522077G>A	ENST00000336023.5	-	4	1114	c.1020C>T	c.(1018-1020)agC>agT	p.S340S	RP11-386G11.10_ENST00000548149.1_RNA|RP11-386G11.10_ENST00000552893.1_RNA|RP11-386G11.10_ENST00000547712.1_RNA|RP11-386G11.10_ENST00000547387.1_RNA	NM_006082.2	NP_006073.2	P68363	TBA1B_HUMAN	tubulin, alpha 1b	340				S -> T (in Ref. 1; AAA91576). {ECO:0000305}.	'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(4)	12						CAAACTGGATGCTGCGCTTGG	0.547																																					p.S340S		Atlas-SNP	.											.	TUBA1B	24	.	0			c.C1020T						.						92	80	84					12																	49522077		2203	4300	6503	SO:0001819	synonymous_variant	10376	exon4			CTGGATGCTGCGC	AF081484	CCDS31792.1	12q13.12	2007-02-12				ENSG00000123416		"Tubulins"	18809	protein-coding gene	gene with protein product	"tubulin, alpha, ubiquitous"	602530				12054644, 6646120	Standard	NM_006082		Approved	K-ALPHA-1	uc001rtm.3	P68363	OTTHUMG00000170410	ENST00000336023.5:c.1020C>T	chr12.hg19:g.49522077G>A		282.0	0.0		182.0	32.0	NM_006082	P04687|P05209|Q27I68|Q8WU19	Silent	SNP	ENST00000336023.5	hg19	CCDS31792.1																																																																																			.	.		0.547	TUBA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409005.1	NM_006082		A	49522077	G	A	49522077	2	1	100	1	0	0	0	0	0	0	0	1	16759	1310	46	3		3	TUBA1B	12	49522077	Silent	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	344900	49522077	84329818	157	13726										
SCN8A	6334	hgsc.bcm.edu	37	chr12	52056675	52056675	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccctgagtcactggcaaacaTtgagaggcgcattgctgaga	12	10	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:52056675T>G	ENST00000354534.6	+	2	252	c.74T>G	c.(73-75)aTt>aGt	p.I25S	SCN8A_ENST00000550891.1_Missense_Mutation_p.I25S|SCN8A_ENST00000545061.1_Missense_Mutation_p.I25S	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	25					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	CTGGCAAACATTGAGAGGCGC	0.562																																					p.I25S		Atlas-SNP	.											.	SCN8A	331	.	0			c.T74G						.						110	110	110					12																	52056675		2027	4202	6229	SO:0001583	missense	6334	exon2			CAAACATTGAGAG	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10596	protein-coding gene	gene with protein product		600702	"sodium channel, voltage gated, type VIII, alpha polypeptide"	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.74T>G	chr12.hg19:g.52056675T>G	ENSP00000346534:p.Ile25Ser	66.0	0.0		52.0	4.0	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	hg19	CCDS44891.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.707309	0.89018	.	.	ENSG00000196876	ENST00000550891;ENST00000354534;ENST00000545061;ENST00000355133	D;D;D;D	0.97850	-4.51;-4.57;-4.54;-4.42	4.97	4.97	0.65823	.	.	.	.	.	D	0.97977	0.9334	H	0.95679	3.705	0.58432	D	0.999999	P	0.39391	0.671	B	0.37943	0.261	D	0.99609	1.0980	9	0.87932	D	0	.	15.1227	0.72457	0.0:0.0:0.0:1.0	.	25	Q9UQD0	SCN8A_HUMAN	S	25	ENSP00000448415:I25S;ENSP00000346534:I25S;ENSP00000440360:I25S;ENSP00000347255:I25S	ENSP00000346534:I25S	I	+	2	0	SCN8A	50342942	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	7.868000	0.87116	2.228000	0.72767	0.533000	0.62120	ATT	.	.		0.562	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		G	52056675	T	G	52056675	3	3	100	1	0	0	0	0	1	0	0	0	13939	1493	52	5	76	5	SCN8A	12	52056675	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2534598	52056675	81795220	158	13727										
EIF4B	1975	hgsc.bcm.edu	37	chr12	53413702	53413702	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttattccttcagatcagtgcAgtgcgtttaccacgtgaacc	8	11	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:53413702A>G	ENST00000262056.9	+	4	695	c.369A>G	c.(367-369)gcA>gcG	p.A123A	EIF4B_ENST00000551527.1_3'UTR|EIF4B_ENST00000416762.3_Intron|RP11-983P16.4_ENST00000552905.1_RNA|EIF4B_ENST00000420463.3_Silent_p.A123A|RP11-983P16.4_ENST00000549388.1_RNA	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	123	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						AGATCAGTGCAGTGCGTTTAC	0.428																																					p.A123A		Atlas-SNP	.											.	EIF4B	38	.	0			c.A369G						.						120	113	115					12																	53413702		1861	4107	5968	SO:0001819	synonymous_variant	1975	exon4			CAGTGCAGTGCGT	X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"RNA binding motif (RRM) containing"	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.369A>G	chr12.hg19:g.53413702A>G		156.0	0.0		97.0	4.0	NM_001417	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Silent	SNP	ENST00000262056.9	hg19	CCDS41788.1																																																																																			.	.		0.428	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404852.2	NM_001417		G	53413702	A	G	53413702	2	3	100	1	0	0	0	0	0	0	0	1	5029	175	7	2		2	EIF4B	12	53413702	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1357027	53413702	80438193	159	13728										
CD63	967	hgsc.bcm.edu	37	chr12	56120684	56120684	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccctgcttaccttatctctaAacacatagccagcaatggct	5	14	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:56120684A>G	ENST00000549117.1	-	4	756	c.320T>C	c.(319-321)tTt>tCt	p.F107S	CD63_ENST00000420846.3_Missense_Mutation_p.F107S|CD63_ENST00000257857.4_Missense_Mutation_p.F107S|RP11-644F5.11_ENST00000552576.1_RNA|CD63_ENST00000546939.1_Missense_Mutation_p.F25S|CD63_ENST00000550776.1_Missense_Mutation_p.F25S|CD63_ENST00000548898.1_Missense_Mutation_p.F14S|CD63_ENST00000552067.1_Missense_Mutation_p.F14S|CD63_ENST00000552692.1_Missense_Mutation_p.F107S|CD63_ENST00000548160.1_Missense_Mutation_p.F14S|CD63_ENST00000552754.1_Missense_Mutation_p.F84S	NM_001257389.1	NP_001244318.1	P08962	CD63_HUMAN	CD63 molecule	107					blood coagulation (GO:0007596)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular protein localization (GO:0034613)|endosome to melanosome transport (GO:0035646)|pigment granule maturation (GO:0048757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of receptor internalization (GO:0002092)|protein transport (GO:0015031)|regulation of rubidium ion transport (GO:2000680)|regulation of vascular endothelial growth factor signaling pathway (GO:1900746)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|multivesicular body, internal vesicle (GO:0097487)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)				kidney(1)|large_intestine(3)|lung(2)|ovary(1)	7						CTTATCTCTAAACACATAGCC	0.522																																					p.F107S	Pancreas(123;1459 1747 6717 18841 37380)	Atlas-SNP	.											.	CD63	13	.	0			c.T320C						.						154	167	162					12																	56120684		2203	4300	6503	SO:0001583	missense	967	exon4			TCTCTAAACACAT	M58485	CCDS8890.1, CCDS58242.1, CCDS58243.1	12q12-q13	2013-02-14	2006-03-28					"CD molecules", "Tetraspanins"	1692	protein-coding gene	gene with protein product		155740	"CD63 antigen (melanoma 1 antigen)"	MLA1			Standard	NM_001780		Approved	ME491, TSPAN30	uc031qhv.1	P08962		ENST00000549117.1:c.320T>C	chr12.hg19:g.56120684A>G	ENSP00000447730:p.Phe107Ser	127.0	0.0		91.0	4.0	NM_001257390	F8VZE2|Q5TZP3|Q8N6Z9|Q9UCG6	Missense_Mutation	SNP	ENST00000549117.1	hg19	CCDS8890.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880324	0.72294	.	.	ENSG00000135404	ENST00000548898;ENST00000552067;ENST00000420846;ENST00000548160;ENST00000546939;ENST00000552692;ENST00000549117;ENST00000257857;ENST00000552754;ENST00000550776;ENST00000552164;ENST00000551173;ENST00000546457	T;T;T;T;T;T;T;T;T;T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29	5.2	5.2	0.72013	Tetraspanin, EC2 domain (1);	0.173065	0.50627	D	0.000108	D	0.86146	0.5863	M	0.71920	2.185	0.53688	D	0.999973	D;P;P	0.64830	0.994;0.736;0.578	D;P;P	0.63033	0.91;0.718;0.648	D	0.87047	0.2144	10	0.72032	D	0.01	.	8.7558	0.34645	0.8313:0.0:0.0:0.1687	.	84;107;107	Q8N6Z9;C9JV86;P08962	.;.;CD63_HUMAN	S	14;14;107;14;25;107;107;107;84;25;107;107;107	ENSP00000447938:F14S;ENSP00000449684:F14S;ENSP00000393502:F107S;ENSP00000449654:F14S;ENSP00000447356:F25S;ENSP00000449337:F107S;ENSP00000447730:F107S;ENSP00000257857:F107S;ENSP00000446807:F84S;ENSP00000448091:F25S;ENSP00000449281:F107S;ENSP00000446752:F107S;ENSP00000450191:F107S	ENSP00000257857:F107S	F	-	2	0	CD63	54406951	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.617000	0.54181	2.113000	0.64589	0.482000	0.46254	TTT	.	.		0.522	CD63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409234.1			G	56120684	A	G	56120684	3	3	100	1	0	0	0	0	1	0	0	0	3031	14	1	2	416	2	CD63	12	56120684	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	2706982	56120684	77731211	160	13729										
DGKA	1606	hgsc.bcm.edu	37	chr12	56345833	56345833	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctccaggatgcctctattgcTcatcgattccacatcatgcg	7	14	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:56345833T>C	ENST00000331886.5	+	19	2056	c.1602T>C	c.(1600-1602)gcT>gcC	p.A534A	DGKA_ENST00000549079.2_3'UTR|DGKA_ENST00000394147.1_Silent_p.A534A|DGKA_ENST00000551156.1_Silent_p.A534A	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	534					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	CCTCTATTGCTCATCGATTCC	0.547																																					p.A534A		Atlas-SNP	.											.	DGKA	70	.	0			c.T1602C						.						106	96	100					12																	56345833		2203	4300	6503	SO:0001819	synonymous_variant	1606	exon19			TATTGCTCATCGA	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"EF-hand domain containing"	2849	protein-coding gene	gene with protein product		125855	"diacylglycerol kinase, alpha (80kD)"	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.1602T>C	chr12.hg19:g.56345833T>C		121.0	0.0		73.0	5.0	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Silent	SNP	ENST00000331886.5	hg19	CCDS8896.1																																																																																			.	.		0.547	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1			C	56345833	T	C	56345833	2	2	100	1	0	0	0	0	0	0	0	1	4467	1538	54	2		2	DGKA	12	56345833	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	225149	56345833	77506062	161	13730										
SILV	6490	hgsc.bcm.edu	37	chr12	56355450	56355450	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cttctgtccactctggatacAgctgcctgttccaggctttg	9	13	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:56355450A>G	ENST00000548747.1	-	2	805	c.143T>C	c.(142-144)cTg>cCg	p.L48P	PMEL_ENST00000550464.1_Intron|PMEL_ENST00000550447.1_Intron|PMEL_ENST00000552882.1_Missense_Mutation_p.L48P|PMEL_ENST00000548689.1_5'UTR|PMEL_ENST00000536427.1_Missense_Mutation_p.L48P|PMEL_ENST00000539511.1_Intron|PMEL_ENST00000360714.4_Missense_Mutation_p.L48P|PMEL_ENST00000449260.2_Missense_Mutation_p.L48P|PMEL_ENST00000548493.1_Missense_Mutation_p.L48P			P40967	PMEL_HUMAN	premelanosome protein	48					melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTCTGGATACAGCTGCCTGTT	0.532																																					p.L48P		Atlas-SNP	.											.	PMEL	60	.	0			c.T143C						.						121	120	120					12																	56355450		2203	4300	6503	SO:0001583	missense	6490	exon2			GGATACAGCTGCC	AK092881	CCDS8897.1, CCDS55833.1, CCDS55834.1	12q13-q14	2010-12-17	2010-12-17	2010-12-17	ENSG00000185664	ENSG00000185664			10880	protein-coding gene	gene with protein product		155550	"silver (mouse homolog) like", "silver homolog (mouse)"	SIL, SILV		8739560	Standard	NM_001200053		Approved	D12S53E, SI, Pmel17, gp100	uc001siq.3	P40967		ENST00000548747.1:c.143T>C	chr12.hg19:g.56355450A>G	ENSP00000448828:p.Leu48Pro	125.0	0.0		88.0	4.0	NM_001200054	B3KS57|B7Z6D7|Q12763|Q14448|Q14817|Q16565	Missense_Mutation	SNP	ENST00000548747.1	hg19	CCDS8897.1	.	.	.	.	.	.	.	.	.	.	a	17.96	3.515174	0.64634	.	.	ENSG00000185664	ENST00000449260;ENST00000552882;ENST00000548747;ENST00000548493;ENST00000360714;ENST00000536427;ENST00000548803;ENST00000547137;ENST00000546543;ENST00000549418;ENST00000549233	T;T;T;T;T;T;T;T;T	0.51574	2.39;2.38;2.38;2.38;2.4;2.09;0.7;1.59;2.2	4.74	4.74	0.60224	.	0.000000	0.41097	D	0.000956	T	0.67590	0.2909	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.71590	-0.4547	10	0.66056	D	0.02	-7.2432	12.158	0.54087	1.0:0.0:0.0:0.0	.	48;48	P40967-2;P40967	.;PMEL_HUMAN	P	48;48;48;48;48;48;48;48;48;48;51	ENSP00000402758:L48P;ENSP00000449690:L48P;ENSP00000448828:L48P;ENSP00000447374:L48P;ENSP00000353940:L48P;ENSP00000438695:L48P;ENSP00000447732:L48P;ENSP00000448849:L48P;ENSP00000446662:L48P	ENSP00000353940:L48P	L	-	2	0	PMEL	54641717	0.997000	0.39634	0.969000	0.41365	0.752000	0.42762	4.955000	0.63638	2.124000	0.65301	0.523000	0.50628	CTG	.	.		0.532	PMEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409626.1	NM_006928		G	56355450	A	G	56355450	3	3	100	1	0	0	0	0	1	0	0	0	14337	188	7	2	1882	2	SILV	12	56355450	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	9617	56355450	77496445	162	13731										
GLI1	2735	hgsc.bcm.edu	37	chr12	57865654	57865654	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ggactctcttgatcttgacaAcactcagctggactttgtgg	10	10	3	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:57865654A>G	ENST00000228682.2	+	12	3222	c.3131A>G	c.(3130-3132)aAc>aGc	p.N1044S	GLI1_ENST00000543426.1_Missense_Mutation_p.N916S|GLI1_ENST00000546141.1_Missense_Mutation_p.N1003S	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	1044	Asp/Glu-rich (acidic).				cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			GATCTTGACAACACTCAGCTG	0.592																																					p.N1044S	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.A3131G						.						159	151	154					12																	57865654		2203	4300	6503	SO:0001583	missense	2735	exon12			TTGACAACACTCA		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.3131A>G	chr12.hg19:g.57865654A>G	ENSP00000228682:p.Asn1044Ser	120.0	0.0		77.0	4.0	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	hg19	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	A	13.82	2.350417	0.41599	.	.	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	T;T;T;T	0.26067	1.82;1.76;1.85;1.85	5.04	5.04	0.67666	.	0.000000	0.50627	D	0.000110	T	0.43255	0.1239	L	0.50333	1.59	0.49213	D	0.999764	D	0.76494	0.999	D	0.78314	0.991	T	0.12167	-1.0558	10	0.30078	T	0.28	.	14.2029	0.65716	1.0:0.0:0.0:0.0	.	1044	P08151	GLI1_HUMAN	S	916;1044;1003;1003;512	ENSP00000437607:N916S;ENSP00000228682:N1044S;ENSP00000441006:N1003S;ENSP00000434408:N1003S	ENSP00000228682:N1044S	N	+	2	0	GLI1	56151921	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.195000	0.51013	2.254000	0.74563	0.533000	0.62120	AAC	.	.		0.592	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		G	57865654	A	G	57865654	3	3	100	1	0	0	0	0	1	0	0	0	6445	43	2	2	3173	2	GLI1	12	57865654	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1510204	57865654	75986241	163	13732										
PTPRB	5787	hgsc.bcm.edu	37	chr12	71016408	71016408	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttctagtgctcctcaccgaaActtctgctcccaggccagct	7	16	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:71016408A>G	ENST00000550358.1	-	3	495	c.470T>C	c.(469-471)gTt>gCt	p.V157A	PTPRB_ENST00000551525.1_Missense_Mutation_p.V156A|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Missense_Mutation_p.V157A			P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	0	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CCTCACCGAAACTTCTGCTCC	0.403																																					p.V157A		Atlas-SNP	.											.	PTPRB	676	.	0			c.T470C						.						29	31	31					12																	71016408		1838	4090	5928	SO:0001583	missense	5787	exon3			ACCGAAACTTCTG	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000550358.1:c.470T>C	chr12.hg19:g.71016408A>G	ENSP00000448058:p.Val157Ala	124.0	0.0		85.0	4.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000550358.1	hg19		.	.	.	.	.	.	.	.	.	.	A	7.880	0.730041	0.15507	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000551525	T;T;T	0.04862	4.07;4.04;3.54	5.42	3.02	0.34903	.	.	.	.	.	T	0.03348	0.0097	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.15141	0.012;0.001;0.003;0.003	B;B;B;B	0.11329	0.006;0.006;0.003;0.003	T	0.42103	-0.9471	9	0.13108	T	0.6	.	6.7107	0.23276	0.7283:0.0:0.2717:0.0	.	157;156;157;157	Q6ZTX7;F8VSD5;P23467-3;F8VU56	.;.;.;.	A	157;157;157;156	ENSP00000334928:V157A;ENSP00000448058:V157A;ENSP00000448349:V156A	ENSP00000334928:V157A	V	-	2	0	PTPRB	69302675	0.876000	0.30132	0.929000	0.37066	0.438000	0.31896	1.130000	0.31393	0.981000	0.38548	0.533000	0.62120	GTT	.	.		0.403	PTPRB-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404436.1			G	71016408	A	G	71016408	3	3	100	1	0	0	0	0	1	0	0	0	12811	43	2	2	6363	2	PTPRB	12	71016408	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	13150754	71016408	62835487	164	13733										
PWP1	11137	hgsc.bcm.edu	37	chr12	108105903	108105903	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tttagtaaatgaagcatttgGaagacgagagaggcttgttc	12	4	0	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:108105903G>A	ENST00000412830.3	+	15	1580	c.1412G>A	c.(1411-1413)gGa>gAa	p.G471E	PWP1_ENST00000541166.1_Missense_Mutation_p.G409E	NM_007062.1	NP_008993.1	Q13610	PWP1_HUMAN	PWP1 homolog (S. cerevisiae)	471					transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(3)|endometrium(4)|kidney(1)|large_intestine(8)|lung(6)|urinary_tract(1)	23						GAAGCATTTGGAAGACGAGAG	0.373																																					p.G471E		Atlas-SNP	.											.	PWP1	43	.	0			c.G1412A						.						122	122	122					12																	108105903		2203	4300	6503	SO:0001583	missense	11137	exon15			CATTTGGAAGACG	BC000067	CCDS9114.1	12q23.3	2013-06-10				ENSG00000136045		"WD repeat domain containing"	17015	protein-coding gene	gene with protein product	"endonuclein"					7828893, 11850830	Standard	NM_007062		Approved	IEF-SSP-9502	uc001tmo.1	Q13610	OTTHUMG00000169913	ENST00000412830.3:c.1412G>A	chr12.hg19:g.108105903G>A	ENSP00000387365:p.Gly471Glu	130.0	0.0		94.0	4.0	NM_007062	A8K3R6|Q7Z3X9	Missense_Mutation	SNP	ENST00000412830.3	hg19	CCDS9114.1	.	.	.	.	.	.	.	.	.	.	G	17.26	3.344645	0.61073	.	.	ENSG00000136045	ENST00000412830;ENST00000541166	T;T	0.70516	-0.49;1.89	5.86	5.86	0.93980	.	0.091121	0.85682	D	0.000000	T	0.70046	0.3179	M	0.62154	1.92	0.80722	D	1	P	0.49961	0.93	B	0.40982	0.345	T	0.68796	-0.5314	10	0.29301	T	0.29	.	20.1581	0.98126	0.0:0.0:1.0:0.0	.	471	Q13610	PWP1_HUMAN	E	471;409	ENSP00000387365:G471E;ENSP00000445249:G409E	ENSP00000387365:G471E	G	+	2	0	PWP1	106630033	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.987000	0.70571	2.937000	0.99478	0.650000	0.86243	GGA	.	.		0.373	PWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406539.1	NM_007062		A	108105903	G	A	108105903	3	1	100	1	0	0	0	0	1	0	0	0	12858	1174	41	3	1470	3	PWP1	12	108105903	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	37089495	108105903	25745992	165	13734										
USP30	84749	hgsc.bcm.edu	37	chr12	109522828	109522828	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgctccccatctttattgccAacgctgtcagcgccgatgcc	8	16	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:109522828A>G	ENST00000257548.5	+	12	1332	c.1239A>G	c.(1237-1239)ccA>ccG	p.P413P	USP30_ENST00000392784.2_Silent_p.P382P	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	413	USP.				mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(7)|kidney(1)|large_intestine(1)|liver(2)|lung(11)|prostate(1)|skin(3)|stomach(2)	28						CTTTATTGCCAACGCTGTCAG	0.527																																					p.P413P		Atlas-SNP	.											.	USP30	48	.	0			c.A1239G						.						184	201	195					12																	109522828		2203	4300	6503	SO:0001819	synonymous_variant	84749	exon12			ATTGCCAACGCTG	BC022094	CCDS9123.2	12q23.3	2006-01-20	2005-08-08		ENSG00000135093	ENSG00000135093		"Ubiquitin-specific peptidases"	20065	protein-coding gene	gene with protein product		612492	"ubiquitin specific protease 30"			12838346	Standard	XM_005253962		Approved	MGC10702, FLJ40511	uc010sxi.2	Q70CQ3	OTTHUMG00000133613	ENST00000257548.5:c.1239A>G	chr12.hg19:g.109522828A>G		67.0	0.0		49.0	5.0	NM_032663	Q8WTU7|Q96JX4|Q9BSS3	Silent	SNP	ENST00000257548.5	hg19	CCDS9123.2																																																																																			.	.		0.527	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663		G	109522828	A	G	109522828	2	3	100	1	0	0	0	0	0	0	0	1	17076	117	5	2		2	USP30	12	109522828	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1416925	109522828	24329067	166	13735										
ATP2A2	488	hgsc.bcm.edu	37	chr12	110784133	110784133	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctacctggaacctggtaaagAgtgtgtgcagcctgccacca	11	12	0	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:110784133A>G	ENST00000539276.2	+	20	3096	c.2987A>G	c.(2986-2988)gAg>gGg	p.E996G	ATP2A2_ENST00000395494.2_Missense_Mutation_p.E969G|ATP2A2_ENST00000308664.6_Intron			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	996					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						CCTGGTAAAGAGTGTGTGCAG	0.552																																					p.E996G		Atlas-SNP	.											.	ATP2A2	78	.	0			c.A2987G						.						91	73	79					12																	110784133		2203	4300	6503	SO:0001583	missense	488	exon20			GTAAAGAGTGTGT		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.2987A>G	chr12.hg19:g.110784133A>G	ENSP00000440045:p.Glu996Gly	153.0	0.0		80.0	4.0	NM_170665	A6NDN7|B4DF05|P16614|Q86VJ2	Missense_Mutation	SNP	ENST00000539276.2	hg19	CCDS9144.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.095280	0.56075	.	.	ENSG00000174437	ENST00000395494;ENST00000539276	D;D	0.95001	-3.58;-3.55	6.17	6.17	0.99709	.	0.556756	0.19304	N	0.117568	D	0.88426	0.6433	N	0.11756	0.17	0.53688	D	0.999979	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	D	0.83846	0.0260	9	.	.	.	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	969;996	P16615-4;P16615	.;AT2A2_HUMAN	G	969;996	ENSP00000378872:E969G;ENSP00000440045:E996G	.	E	+	2	0	ATP2A2	109268516	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.495000	0.81514	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.552	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		G	110784133	A	G	110784133	3	3	100	1	0	0	0	0	1	0	0	0	1137	304	11	2	3065	2	ATP2A2	12	110784133	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1261305	110784133	23067762	167	13736										
MED13L	23389	hgsc.bcm.edu	37	chr12	116413459	116413459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtatttctggctcgcctcacCaaacgtctctcccagctctg	7	16	4	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:116413459C>T	ENST00000281928.3	-	24	5655	c.5449G>A	c.(5449-5451)Ggt>Agt	p.G1817S		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1817						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		CTCGCCTCACCAAACGTCTCT	0.522																																					p.G1817S		Atlas-SNP	.											.	MED13L	193	.	0			c.G5449A						.						105	105	105					12																	116413459		2203	4300	6503	SO:0001583	missense	23389	exon24			CCTCACCAAACGT	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.5449G>A	chr12.hg19:g.116413459C>T	ENSP00000281928:p.Gly1817Ser	138.0	0.0		75.0	4.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.586455|5.586455	0.96578|0.96578	.|.	.|.	ENSG00000123066|ENSG00000123066	ENST00000281928|ENST00000552447	D|.	0.82081|.	-1.57|.	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	0.049130|.	0.85682|.	D|.	0.000000|.	T|.	0.76227|.	0.3958|.	M|M	0.69358|0.69358	2.11|2.11	0.80722|0.80722	D|D	1|1	D|.	0.67145|.	0.996|.	P|.	0.61070|.	0.883|.	T|.	0.72915|.	-0.4147|.	10|.	0.52906|.	T|.	0.07|.	-16.747|-16.747	20.3473|20.3473	0.98799|0.98799	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1817|.	Q71F56|.	MD13L_HUMAN|.	S|X	1817|9	ENSP00000281928:G1817S|.	ENSP00000281928:G1817S|.	G|W	-|-	1|2	0|0	MED13L|MED13L	114897842|114897842	1.000000|1.000000	0.71417|0.71417	0.907000|0.907000	0.35723|0.35723	0.998000|0.998000	0.95712|0.95712	4.527000|4.527000	0.60573|0.60573	2.884000|2.884000	0.98904|0.98904	0.655000|0.655000	0.94253|0.94253	GGT|TGG	.	.		0.522	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			T	116413459	C	T	116413459	3	4	100	1	0	0	0	0	1	0	0	0	9440	594	21	3	1215	3	MED13L	12	116413459	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	5629326	116413459	17438436	168	13737										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130184598	130184598	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cattgcttctcctcgcgtctTccctgacgcagtcccctctc	6	19	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:130184598T>C	ENST00000422113.2	-	2	1051	c.725A>G	c.(724-726)gAa>gGa	p.E242G	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	242					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CCTCGCGTCTTCCCTGACGCA	0.632																																					p.E242G		Atlas-SNP	.											.	TMEM132D	299	.	0			c.A725G						.						90	80	83					12																	130184598		2203	4300	6503	SO:0001583	missense	121256	exon2			GCGTCTTCCCTGA	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.725A>G	chr12.hg19:g.130184598T>C	ENSP00000408581:p.Glu242Gly	124.0	0.0		93.0	4.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	T	10.22	1.290766	0.23564	.	.	ENSG00000151952	ENST00000422113	T	0.12039	2.72	5.29	-3.75	0.04372	.	1.097200	0.07090	N	0.838620	T	0.08088	0.0202	N	0.25380	0.74	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.41288	-0.9517	9	.	.	.	-1.9471	5.654	0.17633	0.0:0.3141:0.2502:0.4357	.	242	Q14C87	T132D_HUMAN	G	242	ENSP00000408581:E242G	.	E	-	2	0	TMEM132D	128750551	0.854000	0.29725	0.000000	0.03702	0.000000	0.00434	2.051000	0.41307	-1.033000	0.03299	-1.133000	0.01973	GAA	.	.		0.632	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		C	130184598	T	C	130184598	3	2	100	1	0	0	0	0	1	0	0	0	16062	1783	62	2	2606	2	TMEM132D	12	130184598	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	13771139	130184598	3667297	169	13738										
ULK1	8408	hgsc.bcm.edu	37	chr12	132404542	132404542	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agtggtgcgcaggctgaatgAgctgtacaaggccagcgtgg	17	8	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr12:132404542A>G	ENST00000321867.4	+	26	3173	c.2822A>G	c.(2821-2823)gAg>gGg	p.E941G	ULK1_ENST00000540647.1_Missense_Mutation_p.E186G	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	941					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		AGGCTGAATGAGCTGTACAAG	0.647																																					p.E941G		Atlas-SNP	.											.	ULK1	92	.	0			c.A2822G						.						56	59	58					12																	132404542		2203	4299	6502	SO:0001583	missense	8408	exon26			TGAATGAGCTGTA	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"ATG1 autophagy related 1 homolog (S. cerevisiae)"	603168	"unc-51 (C. elegans)-like kinase 1", "unc-51-like kinase 1 (C. elegans)"			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.2822A>G	chr12.hg19:g.132404542A>G	ENSP00000324560:p.Glu941Gly	127.0	0.0		91.0	4.0	NM_003565	Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	hg19	CCDS9274.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.182495|4.182495	0.78677|0.78677	.|.	.|.	ENSG00000177169|ENSG00000177169	ENST00000321867;ENST00000540647|ENST00000542419	T;T|.	0.49139|.	0.79;0.79|.	5.13|5.13	3.99|3.99	0.46301|0.46301	Serine/threonine-protein kinase, C-terminal (1);|.	0.062539|.	0.64402|.	D|.	0.000008|.	T|T	0.59729|0.59729	0.2215|0.2215	M|M	0.79475|0.79475	2.455|2.455	0.23546|0.23546	N|N	0.997446|0.997446	P|.	0.46277|.	0.875|.	P|.	0.50378|.	0.639|.	T|T	0.52155|0.52155	-0.8613|-0.8613	10|5	0.72032|.	D|.	0.01|.	-23.676|-23.676	11.8019|11.8019	0.52133|0.52133	0.8396:0.1604:0.0:0.0|0.8396:0.1604:0.0:0.0	.|.	941|.	O75385|.	ULK1_HUMAN|.	G|G	941;186|2	ENSP00000324560:E941G;ENSP00000441794:E186G|.	ENSP00000324560:E941G|.	E|S	+|+	2|1	0|0	ULK1|ULK1	130970495|130970495	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.704000|0.704000	0.40688|0.40688	5.890000|5.890000	0.69774|0.69774	0.788000|0.788000	0.33755|0.33755	0.459000|0.459000	0.35465|0.35465	GAG|AGC	.	.		0.647	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			G	132404542	A	G	132404542	3	3	100	1	0	0	0	0	1	0	0	0	16990	304	11	2	2924	2	ULK1	12	132404542	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	2219944	132404542	1447353	170	13739										
B3GALTL	145173	hgsc.bcm.edu	37	chr13	31850851	31850851	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttttttagagaaagccagtgAagaagaaggatatttttgtt	10	2	0	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr13:31850851A>G	ENST00000343307.4	+	10	942	c.793A>G	c.(793-795)Aag>Gag	p.K265E	B3GALTL_ENST00000461652.2_3'UTR	NM_194318.3	NP_919299.3	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	265					fucose metabolic process (GO:0006004)|protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		AAAGCCAGTGAAGAAGAAGGA	0.343																																					p.K265E		Atlas-SNP	.											.	B3GALTL	48	.	0			c.A793G						.						120	130	127					13																	31850851		2203	4300	6503	SO:0001583	missense	145173	exon10			CCAGTGAAGAAGA	AB101481	CCDS9341.1	13q12.3	2014-03-24			ENSG00000187676	ENSG00000187676		"Beta 3-glycosyltransferases"	20207	protein-coding gene	gene with protein product		610308				12943678, 16899492, 17032646	Standard	NM_194318		Approved	B3GTL, B3Glc-T	uc010aaz.3	Q6Y288	OTTHUMG00000016688	ENST00000343307.4:c.793A>G	chr13.hg19:g.31850851A>G	ENSP00000343002:p.Lys265Glu	91.0	0.0		62.0	4.0	NM_194318	A8K5F8|Q5W0H2|Q6NUI3	Missense_Mutation	SNP	ENST00000343307.4	hg19	CCDS9341.1	.	.	.	.	.	.	.	.	.	.	A	8.939	0.965388	0.18583	.	.	ENSG00000187676	ENST00000343307	T	0.61274	0.12	5.93	4.77	0.60923	.	0.310682	0.38272	N	0.001742	T	0.33818	0.0876	N	0.12746	0.255	0.47308	D	0.999386	B	0.14012	0.009	B	0.14023	0.01	T	0.18713	-1.0328	10	0.21540	T	0.41	-26.5674	6.7295	0.23375	0.7671:0.155:0.0779:0.0	.	265	Q6Y288	B3GLT_HUMAN	E	265	ENSP00000343002:K265E	ENSP00000343002:K265E	K	+	1	0	B3GALTL	30748851	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.232000	0.51302	2.268000	0.75426	0.455000	0.32223	AAG	.	.		0.343	B3GALTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044396.3	NM_194318		G	31850851	A	G	31850851	3	3	100	1	0	0	0	0	1	0	0	0	1252	247	9	2	831	2	B3GALTL	13	31850851	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		31850851	83319027	171	13740										
N4BP2L2	10443	hgsc.bcm.edu	37	chr13	33111159	33111159	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttaccttcaatttcaccataAgacatctgagaaataaataa	3	8	3	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr13:33111159A>G	ENST00000267068.3	-	2	170	c.6T>C	c.(4-6)tcT>tcC	p.S2S	N4BP2L2_ENST00000399396.3_Silent_p.S2S|N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000446957.2_Silent_p.S2S	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	2					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TTTCACCATAAGACATCTGAG	0.289																																					p.S2S		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.T6C						.						57	53	54					13																	33111159		2203	4300	6503	SO:0001819	synonymous_variant	10443	exon2			ACCATAAGACATC	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"phosphonoformate immuno-associated protein 5"	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.6T>C	chr13.hg19:g.33111159A>G		78.0	0.0		50.0	4.0	NM_033111	A3KME8	Silent	SNP	ENST00000267068.3	hg19	CCDS9346.1																																																																																			.	.		0.289	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887		G	33111159	A	G	33111159	2	3	100	1	0	0	0	0	0	0	0	1	10121	59	3	2		2	N4BP2L2	13	33111159	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1260308	33111159	82058719	172	13741										
ALG5	29880	hgsc.bcm.edu	37	chr13	37524168	37524168	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtctttacccatttgtagccAgctccagaatggaactaatt	7	10	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr13:37524168A>G	ENST00000239891.3	-	10	952	c.886T>C	c.(886-888)Tgg>Cgg	p.W296R	ALG5_ENST00000443765.1_Missense_Mutation_p.W266R|ALG5_ENST00000413537.2_3'UTR	NM_013338.4	NP_037470.1	Q9Y673	ALG5_HUMAN	ALG5, dolichyl-phosphate beta-glucosyltransferase	296					cellular protein metabolic process (GO:0044267)|determination of left/right symmetry (GO:0007368)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dolichyl-phosphate beta-glucosyltransferase activity (GO:0004581)|oligosaccharyl transferase activity (GO:0004576)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;5.79e-07)|Epithelial(112;1.81e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00785)|BRCA - Breast invasive adenocarcinoma(63;0.0127)|GBM - Glioblastoma multiforme(144;0.0472)		ATTTGTAGCCAGCTCCAGAAT	0.348																																					p.W296R		Atlas-SNP	.											.	ALG5	28	.	0			c.T886C						.						65	64	65					13																	37524168		2203	4300	6503	SO:0001583	missense	29880	exon10			GTAGCCAGCTCCA	AF088028	CCDS9361.1, CCDS45033.1	13q13.1	2013-02-22	2013-02-21		ENSG00000120697	ENSG00000120697	2.4.1.117	"Glycosyltransferase family 2 domain containing"	20266	protein-coding gene	gene with protein product		604565	"asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate beta-glucosyltransferase)", "asparagine-linked glycosylation 5, dolichyl-phosphate beta-glucosyltransferase homolog (S. cerevisiae)"			10359825	Standard	NM_013338		Approved	bA421P11.2	uc001uvy.3	Q9Y673	OTTHUMG00000016741	ENST00000239891.3:c.886T>C	chr13.hg19:g.37524168A>G	ENSP00000239891:p.Trp296Arg	52.0	0.0		56.0	4.0	NM_013338	B4DR37|Q5TBA6	Missense_Mutation	SNP	ENST00000239891.3	hg19	CCDS9361.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.471282	0.84533	.	.	ENSG00000120697	ENST00000443765;ENST00000239891	T;T	0.54675	0.56;0.56	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.74306	0.3699	M	0.86953	2.85	0.80722	D	1	D;D	0.65815	0.995;0.992	D;P	0.66847	0.947;0.887	T	0.74411	-0.3674	10	0.25751	T	0.34	.	16.2429	0.82424	1.0:0.0:0.0:0.0	.	266;296	Q9Y673-2;Q9Y673	.;ALG5_HUMAN	R	266;296	ENSP00000390533:W266R;ENSP00000239891:W296R	ENSP00000239891:W296R	W	-	1	0	ALG5	36422168	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.681000	0.91228	2.238000	0.73509	0.533000	0.62120	TGG	.	.		0.348	ALG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044528.2	NM_013338		G	37524168	A	G	37524168	3	3	100	1	0	0	0	0	1	0	0	0	521	188	7	2	92	2	ALG5	13	37524168	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	4413009	37524168	77645710	173	13742										
SUGT1	10910	hgsc.bcm.edu	37	chr13	53237230	53237230	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttcctttttatgttttaataGgctcagaatctgaggtggta	9	5	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr13:53237230G>C	ENST00000343788.6	+	8	560		c.e8-1		SUGT1_ENST00000483074.1_Splice_Site|SUGT1_ENST00000310528.8_Splice_Site|SUGT1_ENST00000535397.1_Splice_Site	NM_001130912.1	NP_001124384.1	Q9Y2Z0	SUGT1_HUMAN	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)						innate immune response (GO:0045087)|mitotic nuclear division (GO:0007067)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				kidney(3)|large_intestine(3)|lung(2)	8		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		TGTTTTAATAGGCTCAGAATC	0.303																																					.		Atlas-SNP	.											.	SUGT1	37	.	0			c.479-1G>C						.						114	110	112					13																	53237230		2202	4297	6499	SO:0001630	splice_region_variant	10910	exon8			TTAATAGGCTCAG	AF068289	CCDS9436.1, CCDS45050.1	13q14.3	2014-03-20			ENSG00000165416	ENSG00000165416			16987	protein-coding gene	gene with protein product		604098				10445024	Standard	NM_006704		Approved	SGT1	uc001vhc.2	Q9Y2Z0	OTTHUMG00000016977	ENST00000343788.6:c.479-1G>C	chr13.hg19:g.53237230G>C		278.0	0.0		187.0	16.0	NM_001130912	A2A303|Q5JAK5|Q5TAM6|Q6VXY6	Splice_Site	SNP	ENST00000343788.6	hg19	CCDS45050.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.254771	0.59212	.	.	ENSG00000165416	ENST00000343788;ENST00000535397;ENST00000310528	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9866	0.64339	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SUGT1	52135231	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	4.262000	0.58847	2.438000	0.82558	0.555000	0.69702	.	.	.		0.303	SUGT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045104.2		Intron	C	53237230	G	C	53237230	5	2	100	1	0	0	0	0	0	0	1	0	15384	1014	35	4	508	4	SUGT1	13	53237230	Splice_Site	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	15713062	53237230	61932648	174	13743										
TDRD3	81550	hgsc.bcm.edu	37	chr13	61102826	61102826	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	acttcatatcctttaggttcTcagcatagtgatggtgcttt	8	8	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr13:61102826T>C	ENST00000196169.3	+	11	1976	c.1188T>C	c.(1186-1188)tcT>tcC	p.S396S	TDRD3_ENST00000535286.1_Silent_p.S489S|TDRD3_ENST00000377881.2_Silent_p.S396S|TDRD3_ENST00000377894.2_Silent_p.S396S	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	396					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		CTTTAGGTTCTCAGCATAGTG	0.383																																					p.S489S	Colon(36;164 906 35820 50723)	Atlas-SNP	.											.	TDRD3	123	.	0			c.T1467C						.						77	83	81					13																	61102826		2203	4300	6503	SO:0001819	synonymous_variant	81550	exon11			AGGTTCTCAGCAT	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.1188T>C	chr13.hg19:g.61102826T>C		115.0	0.0		85.0	4.0	NM_001146070	B2MWP9|Q53XA6|Q6P992	Silent	SNP	ENST00000196169.3	hg19	CCDS9441.1																																																																																			.	.		0.383	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		C	61102826	T	C	61102826	2	2	100	1	0	0	0	0	0	0	0	1	15747	1538	54	2		2	TDRD3	13	61102826	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	7865596	61102826	54067052	175	13744										
IPO5	3843	hgsc.bcm.edu	37	chr13	98637853	98637853	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgatattgcggcagaactggCcaggaatttaataggtgtgt	13	5	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr13:98637853C>T	ENST00000490680.1	+	3	415	c.350C>T	c.(349-351)gCc>gTc	p.A117V	IPO5_ENST00000539640.1_Intron|IPO5_ENST00000261574.5_Missense_Mutation_p.A135V			O00410	IPO5_HUMAN	importin 5	117					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						GCAGAACTGGCCAGGAATTTA	0.373																																					p.A135V		Atlas-SNP	.											.	IPO5	90	.	0			c.C404T						.						93	90	91					13																	98637853		2203	4300	6503	SO:0001583	missense	3843	exon6			AACTGGCCAGGAA	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"Importins"	6402	protein-coding gene	gene with protein product		602008	"karyopherin (importin) beta 3", "RAN binding protein 5"	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.350C>T	chr13.hg19:g.98637853C>T	ENSP00000418393:p.Ala117Val	156.0	0.0		124.0	5.0	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Missense_Mutation	SNP	ENST00000490680.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.5|23.5	4.428780|4.428780	0.83667|0.83667	.|.	.|.	ENSG00000065150|ENSG00000065150	ENST00000460070;ENST00000261574;ENST00000357602;ENST00000475420;ENST00000480641;ENST00000490680;ENST00000389591;ENST00000403772;ENST00000473582|ENST00000469360	T;T;T;T;T;T;T;T|.	0.71222|.	-0.55;-0.55;-0.55;-0.55;3.2;-0.55;-0.55;3.2|.	5.74|5.74	4.87|4.87	0.63330|0.63330	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.155685|.	0.56097|.	D|.	0.000024|.	T|T	0.74160|0.74160	0.3680|0.3680	M|M	0.72576|0.72576	2.205|2.205	0.80722|0.80722	D|D	1|1	D;P|.	0.53312|.	0.959;0.891|.	B;P|.	0.48425|.	0.383;0.577|.	T|T	0.74657|0.74657	-0.3592|-0.3592	10|5	0.62326|.	D|.	0.03|.	-1.4843|-1.4843	16.5418|16.5418	0.84386|0.84386	0.0:0.8692:0.1308:0.0|0.0:0.8692:0.1308:0.0	.|.	117;135|.	O00410;O00410-3|.	IPO5_HUMAN;.|.	V|S	135;135;117;117;57;117;90;88;98|119	ENSP00000420284:A135V;ENSP00000261574:A135V;ENSP00000350219:A117V;ENSP00000420079:A117V;ENSP00000419003:A57V;ENSP00000418393:A117V;ENSP00000385938:A88V;ENSP00000420491:A98V|.	ENSP00000261574:A135V|.	A|P	+|+	2|1	0|0	IPO5|IPO5	97435854|97435854	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.630000|5.630000	0.67805|0.67805	1.365000|1.365000	0.46057|0.46057	0.563000|0.563000	0.77884|0.77884	GCC|CCA	.	.		0.373	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271		T	98637853	C	T	98637853	3	4	100	1	0	0	0	0	1	0	0	0	7805	739	26	3	418	3	IPO5	13	98637853	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	37535027	98637853	16532025	176	13745										
FARP1	10160	hgsc.bcm.edu	37	chr13	99063059	99063059	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gagcgaacatatctgaaggaTctcgaagttatcacttcggt	10	8	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr13:99063059T>C	ENST00000319562.6	+	15	1939	c.1674T>C	c.(1672-1674)gaT>gaC	p.D558D	FARP1_ENST00000595437.1_Silent_p.D558D|FARP1_ENST00000376586.2_Silent_p.D558D	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	558	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			ATCTGAAGGATCTCGAAGTTA	0.433																																					p.D558D		Atlas-SNP	.											.	FARP1	207	.	0			c.T1674C						.						131	115	120					13																	99063059		2202	4299	6501	SO:0001819	synonymous_variant	10160	exon15			GAAGGATCTCGAA	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.1674T>C	chr13.hg19:g.99063059T>C		224.0	0.0		148.0	6.0	NM_005766	Q5JVI9|Q6IQ29	Silent	SNP	ENST00000319562.6	hg19	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	T	6.218	0.408279	0.11754	.	.	ENSG00000152767	ENST00000457029	.	.	.	5.66	-1.08	0.09936	.	.	.	.	.	T	0.65059	0.2655	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61456	-0.7059	4	.	.	.	.	13.382	0.60773	0.0:0.6488:0.0:0.3512	.	.	.	.	T	87	.	.	I	+	2	0	FARP1	97861060	0.988000	0.35896	0.905000	0.35620	0.598000	0.36846	0.253000	0.18296	-0.402000	0.07633	0.460000	0.39030	ATC	.	.		0.433	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		C	99063059	T	C	99063059	2	2	100	1	0	0	0	0	0	0	0	1	5684	1432	50	2		2	FARP1	13	99063059	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	425206	99063059	16106819	177	13746										
ZNF828	283489	hgsc.bcm.edu	37	chr13	115089644	115089644	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	acagatcctgtgaaaagcccTcctcttcctgaacaccagaa	6	14	1	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr13:115089644T>C	ENST00000361283.1	+	3	636	c.327T>C	c.(325-327)ccT>ccC	p.P109P		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	109	Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										TGAAAAGCCCTCCTCTTCCTG	0.398																																					p.P109P		Atlas-SNP	.											.	.	.	.	0			c.T327C						.						81	84	83					13																	115089644		2203	4300	6503	SO:0001819	synonymous_variant	283489	exon3			AAGCCCTCCTCTT	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"Zinc fingers, C2H2-type"	20311	protein-coding gene	gene with protein product	"chromosome alignment-maintaining phosphoprotein"		"chromosome 13 open reading frame 8", "zinc finger protein 828"	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.327T>C	chr13.hg19:g.115089644T>C		268.0	0.0		158.0	24.0	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Silent	SNP	ENST00000361283.1	hg19	CCDS9545.1																																																																																			.	.		0.398	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		C	115089644	T	C	115089644	2	2	100	1	0	0	0	0	0	0	0	1	18196	1538	54	2		2	ZNF828	13	115089644	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	16026585	115089644	80234	178	13747										
MYH6	4624	hgsc.bcm.edu	37	chr14	23862189	23862189	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atgctctcctgggtcagcttCaggtcgccctccagtttccg	10	15	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr14:23862189C>T	ENST00000356287.3	-	23	3212	c.3183G>A	c.(3181-3183)ctG>ctA	p.L1061L	MYH6_ENST00000405093.3_Silent_p.L1061L			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1061					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		GGGTCAGCTTCAGGTCGCCCT	0.527																																					p.L1061L		Atlas-SNP	.											.	MYH6	274	.	0			c.G3183A						.						133	116	122					14																	23862189		2203	4300	6503	SO:0001819	synonymous_variant	4624	exon24			CAGCTTCAGGTCG	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.3183G>A	chr14.hg19:g.23862189C>T		121.0	0.0		93.0	4.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	hg19	CCDS9600.1																																																																																			.	.		0.527	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23862189	C	T	23862189	2	4	100	1	0	0	0	0	0	0	0	1	10047	813	29	3		3	MYH6	14	23862189	Silent	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10		23862189	83487351	179	13748										
EIF2S1	1965	hgsc.bcm.edu	37	chr14	67841207	67841207	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tatattgatttgtcaaaaagAagagtttctccagaggaagc	9	5	2	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr14:67841207A>G	ENST00000256383.4	+	3	725	c.264A>G	c.(262-264)agA>agG	p.R88R	EIF2S1_ENST00000466499.2_Silent_p.R88R	NM_004094.4	NP_004085.1	P05198	IF2A_HUMAN	eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa	88	S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|protein autophosphorylation (GO:0046777)|regulation of translational initiation in response to stress (GO:0043558)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9				all cancers(60;0.000683)|OV - Ovarian serous cystadenocarcinoma(108;0.00579)|BRCA - Breast invasive adenocarcinoma(234;0.00937)		TGTCAAAAAGAAGAGTTTCTC	0.333																																					p.R88R		Atlas-SNP	.											.	EIF2S1	17	.	0			c.A264G						.						91	94	93					14																	67841207		2203	4298	6501	SO:0001819	synonymous_variant	1965	exon3			AAAAAGAAGAGTT	J02645	CCDS9781.1	14q21.3	2011-01-07	2002-08-29		ENSG00000134001	ENSG00000134001			3265	protein-coding gene	gene with protein product		603907	"eukaryotic translation initiation factor 2, subunit 1 (alpha, 35kD )"	EIF2		2948954	Standard	NM_004094		Approved	EIF-2alpha, EIF2A	uc001xjg.3	P05198	OTTHUMG00000029800	ENST00000256383.4:c.264A>G	chr14.hg19:g.67841207A>G		196.0	0.0		97.0	4.0	NM_004094		Silent	SNP	ENST00000256383.4	hg19	CCDS9781.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.95|10.95	1.494834|1.494834	0.26774|0.26774	.|.	.|.	ENSG00000134001|ENSG00000134001	ENST00000437108|ENST00000555876	.|.	.|.	.|.	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	.|.	.|.	.|.	.|.	.|T	.|0.63438	.|0.2511	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.62680	.|-0.6803	.|4	.|.	.|.	.|.	.|-14.6773	10.8862|10.8862	0.46968|0.46968	0.9304:0.0:0.0696:0.0|0.9304:0.0:0.0696:0.0	.|.	.|.	.|.	.|.	.|G	-1|45	.|.	.|.	.|E	+|+	.|2	.|0	EIF2S1|EIF2S1	66910960|66910960	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.164000|6.164000	0.71885|0.71885	2.323000|2.323000	0.78572|0.78572	0.528000|0.528000	0.53228|0.53228	.|GAA	.	.		0.333	EIF2S1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074342.3	NM_004094		G	67841207	A	G	67841207	2	3	100	1	0	0	0	0	0	0	0	1	5011	243	9	2		2	EIF2S1	14	67841207	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	43979018	67841207	39508333	180	13749										
RBM25	58517	hgsc.bcm.edu	37	chr14	73569996	73569996	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agcgtgaaagggaacgagaaAggcgagaacgggaacgagaa	17	5	0	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr14:73569996A>C	ENST00000261973.7	+	10	1249	c.964A>C	c.(964-966)Agg>Cgg	p.R322R	RBM25_ENST00000527432.1_Silent_p.R322R	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	322	Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		ggaacgagaaaggcgagaacg	0.483																																					p.R322R		Atlas-SNP	.											.	RBM25	81	.	0			c.A964C						.						146	119	128					14																	73569996		2199	4299	6498	SO:0001819	synonymous_variant	58517	exon10			CGAGAAAGGCGAG	BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"RNA binding motif (RRM) containing"	23244	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 94"	612427	"RNA-binding region (RNP1, RRM) containing 7"	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.964A>C	chr14.hg19:g.73569996A>C		194.0	0.0		94.0	4.0	NM_021239	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Silent	SNP	ENST00000261973.7	hg19	CCDS32113.1																																																																																			.	.		0.483	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		C	73569996	A	C	73569996	2	2	100	1	0	0	0	0	0	0	0	1	13140	63	3	5		5	RBM25	14	73569996	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	5728789	73569996	33779544	181	13750										
CPSF2	53981	hgsc.bcm.edu	37	chr14	92621560	92621560	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	catgacttgatgatgaaaggTgaaggcagtcgtaaaggaag	14	4	0	5			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr14:92621560T>C	ENST00000298875.4	+	11	1620	c.1335T>C	c.(1333-1335)ggT>ggC	p.G445G		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	445					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		TGATGAAAGGTGAAGGCAGTC	0.408																																					p.G445G	Ovarian(78;28 1788 18702 44111)	Atlas-SNP	.											.	CPSF2	63	.	0			c.T1335C						.						117	106	110					14																	92621560		2203	4300	6503	SO:0001819	synonymous_variant	53981	exon11			GAAAGGTGAAGGC	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"cleavage and polyadenylation specific factor 2, 100kD subunit"			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.1335T>C	chr14.hg19:g.92621560T>C		135.0	0.0		117.0	5.0	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Silent	SNP	ENST00000298875.4	hg19	CCDS9902.1	.	.	.	.	.	.	.	.	.	.	T	11.42	1.633546	0.29068	.	.	ENSG00000165934	ENST00000555244	.	.	.	5.81	-9.09	0.00717	.	.	.	.	.	T	0.42630	0.1211	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47837	-0.9086	4	.	.	.	.	4.9248	0.13887	0.0862:0.2897:0.4208:0.2034	.	.	.	.	A	13	.	.	V	+	2	0	CPSF2	91691313	0.495000	0.26051	0.725000	0.30721	0.993000	0.82548	-0.336000	0.07863	-1.802000	0.01244	0.379000	0.24179	GTG	.	.		0.408	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1			C	92621560	T	C	92621560	2	2	100	1	0	0	0	0	0	0	0	1	3827	1683	59	2		2	CPSF2	14	92621560	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	19051564	92621560	14727980	182	13751										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94038391	94038391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ggaagccatcagaacagaagTcccagataatcagttaaaag	9	8	2	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr14:94038391T>C	ENST00000393151.2	+	15	1907	c.1907T>C	c.(1906-1908)gTc>gCc	p.V636A	UNC79_ENST00000256339.4_Missense_Mutation_p.V459A|UNC79_ENST00000555664.1_Missense_Mutation_p.V636A|UNC79_ENST00000553484.1_Missense_Mutation_p.V636A			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	636					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AGAACAGAAGTCCCAGATAAT	0.403																																					p.V459A		Atlas-SNP	.											.	UNC79	366	.	0			c.T1376C						.						62	63	63					14																	94038391		2203	4300	6503	SO:0001583	missense	57578	exon15			CAGAAGTCCCAGA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.1907T>C	chr14.hg19:g.94038391T>C	ENSP00000376858:p.Val636Ala	75.0	0.0		46.0	4.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	T	26.0	4.699267	0.88830	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.26373	1.74;1.74;1.74;1.74	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000002	T	0.46229	0.1382	L	0.49778	1.585	0.54753	D	0.999989	D	0.58268	0.982	D	0.70227	0.968	T	0.41395	-0.9511	10	0.87932	D	0	-7.1544	16.0095	0.80391	0.0:0.0:0.0:1.0	.	636	C9JQL1	.	A	459;636;636;636;636	ENSP00000256339:V459A;ENSP00000450868:V636A;ENSP00000451360:V636A;ENSP00000376858:V636A	ENSP00000256339:V459A	V	+	2	0	KIAA1409	93108144	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.713000	0.84693	2.189000	0.69895	0.528000	0.53228	GTC	.	.		0.403	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		C	94038391	T	C	94038391	3	2	100	1	0	0	0	0	1	0	0	0	8239	1667	58	2	1422	2	KIAA1409	14	94038391	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1416831	94038391	13311149	183	13752										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94088335	94088335	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cagaggttaggttaaactgtAtggagactttcgaggtgaaa	13	4	0	3	rs149602204		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr14:94088335A>G	ENST00000393151.2	+	30	4756	c.4756A>G	c.(4756-4758)Atg>Gtg	p.M1586V	UNC79_ENST00000256339.4_Missense_Mutation_p.M1409V|UNC79_ENST00000555664.1_Missense_Mutation_p.M1586V|UNC79_ENST00000553484.1_Missense_Mutation_p.M1608V			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1586					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						GTTAAACTGTATGGAGACTTT	0.488																																					p.M1409V		Atlas-SNP	.											UNC79,NS,carcinoma,0,2	UNC79	366	.	0			c.A4225G						.	A	VAL/MET	0,4406		0,0,2203	71	75	74		4225	6	1	14	dbSNP_134	74	1,8599	1.2+/-3.3	0,1,4299	no	missense	UNC79	NM_020818.3	21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	possibly-damaging	1409/2459	94088335	1,13005	2203	4300	6503	SO:0001583	missense	57578	exon30			AACTGTATGGAGA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4756A>G	chr14.hg19:g.94088335A>G	ENSP00000376858:p.Met1586Val	165.0	0.0		95.0	4.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	A	13.50	2.255981	0.39896	0.0	1.16E-4	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.23950	1.92;1.88;1.93;1.92	5.98	5.98	0.97165	.	0.036664	0.85682	D	0.000000	T	0.39064	0.1064	L	0.32530	0.975	0.47037	D	0.999293	P	0.48911	0.917	D	0.63488	0.915	T	0.04565	-1.0942	10	0.30078	T	0.28	-21.1065	16.4728	0.84119	1.0:0.0:0.0:0.0	.	1608	C9JQL1	.	V	1409;1586;1608;1586;1608	ENSP00000256339:M1409V;ENSP00000450868:M1586V;ENSP00000451360:M1608V;ENSP00000376858:M1586V	ENSP00000256339:M1409V	M	+	1	0	KIAA1409	93158088	1.000000	0.71417	1.000000	0.80357	0.184000	0.23303	7.166000	0.77553	2.296000	0.77279	0.482000	0.46254	ATG	.	A|1.000;G|0.000		0.488	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		G	94088335	A	G	94088335	3	3	100	1	0	0	0	0	1	0	0	0	8239	449	16	2	4331	2	KIAA1409	14	94088335	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	49944	94088335	13261205	184	13753										
DDX24	57062	hgsc.bcm.edu	37	chr14	94528810	94528810	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ggcaatgcatcagactcagcTtcagccttgcctggtgatct	10	12	4	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr14:94528810T>C	ENST00000330836.5	-	3	1007	c.876A>G	c.(874-876)gaA>gaG	p.E292E	DDX24_ENST00000555054.1_Silent_p.E249E|DDX24_ENST00000544005.1_Silent_p.E42E	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	292	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		CAGACTCAGCTTCAGCCTTGC	0.547																																					p.E292E		Atlas-SNP	.											.	DDX24	82	.	0			c.A876G						.						137	112	120					14																	94528810		2203	4300	6503	SO:0001819	synonymous_variant	57062	exon3			CTCAGCTTCAGCC	AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"DEAD-boxes"	13266	protein-coding gene	gene with protein product		606181	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.876A>G	chr14.hg19:g.94528810T>C		126.0	0.0		86.0	4.0	NM_020414	E7EMJ4|Q4V9L5	Silent	SNP	ENST00000330836.5	hg19	CCDS9918.1																																																																																			.	.		0.547	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		C	94528810	T	C	94528810	2	2	100	1	0	0	0	0	0	0	0	1	4353	1606	56	2		2	DDX24	14	94528810	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	440475	94528810	12820730	185	13754										
RCOR1	23186	hgsc.bcm.edu	37	chr14	103173693	103173693	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atatcatttttgtaggctctTgggatgctcttctggcataa	9	7	4	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr14:103173693T>C	ENST00000570597.1	+	5	495	c.495T>C	c.(493-495)ctT>ctC	p.L165L	RCOR1_ENST00000262241.6_Silent_p.L168L			Q9UKL0	RCOR1_HUMAN	REST corepressor 1	165	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interaction with HDAC1.				blood coagulation (GO:0007596)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	12						TGTAGGCTCTTGGGATGCTCT	0.348																																					p.L168L		Atlas-SNP	.											.	RCOR1	39	.	0			c.T504C						.						106	107	106					14																	103173693		2203	4300	6503	SO:0001819	synonymous_variant	23186	exon5			GGCTCTTGGGATG	AF155595	CCDS9974.1, CCDS9974.2	14q32.33	2004-04-16	2004-04-16	2004-04-16		ENSG00000089902			17441	protein-coding gene	gene with protein product		607675	"REST corepressor"	RCOR		10449787	Standard	NM_015156		Approved	COREST, KIAA0071	uc001ymb.4	Q9UKL0		ENST00000570597.1:c.495T>C	chr14.hg19:g.103173693T>C		141.0	0.0		83.0	4.0	NM_015156	Q15044|Q6P2I9|Q86VG5	Silent	SNP	ENST00000570597.1	hg19																																																																																				.	.		0.348	RCOR1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015156		C	103173693	T	C	103173693	2	2	100	1	0	0	0	0	0	0	0	1	13197	1799	63	2		2	RCOR1	14	103173693	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	8644883	103173693	4175847	186	13755										
CDC42BPB	9578	hgsc.bcm.edu	37	chr14	103438401	103438401	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gctctgccatgcgctcgttcAgctccgagaactcctgcagg	11	15	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr14:103438401A>G	ENST00000361246.2	-	13	2027	c.1739T>C	c.(1738-1740)cTg>cCg	p.L580P		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		GCGCTCGTTCAGCTCCGAGAA	0.602																																					p.L580P		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.T1739C						.						99	92	94					14																	103438401		2203	4300	6503	SO:0001583	missense	9578	exon13			TCGTTCAGCTCCG	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"CDC42-binding protein kinase beta (DMPK-like)"			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.1739T>C	chr14.hg19:g.103438401A>G	ENSP00000355237:p.Leu580Pro	168.0	0.0		73.0	4.0	NM_006035		Missense_Mutation	SNP	ENST00000361246.2	hg19	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	A	19.50	3.840273	0.71488	.	.	ENSG00000198752	ENST00000361246	D	0.85702	-2.02	5.31	5.31	0.75309	.	0.065036	0.64402	D	0.000005	D	0.91188	0.7224	M	0.77103	2.36	0.80722	D	1	D	0.54964	0.969	P	0.61070	0.883	D	0.92315	0.5861	10	0.72032	D	0.01	.	15.2521	0.73556	1.0:0.0:0.0:0.0	.	580	Q9Y5S2	MRCKB_HUMAN	P	580	ENSP00000355237:L580P	ENSP00000355237:L580P	L	-	2	0	CDC42BPB	102508154	1.000000	0.71417	1.000000	0.80357	0.525000	0.34531	9.262000	0.95591	2.017000	0.59298	0.460000	0.39030	CTG	.	.		0.602	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		G	103438401	A	G	103438401	3	3	100	1	0	0	0	0	1	0	0	0	3075	188	7	2	3496	2	CDC42BPB	14	103438401	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	264708	103438401	3911139	187	13756										
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105344813	105344813	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgtgctggagcgtgtgcagcAccgagtcccggaggaggcac	17	11	0	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr14:105344813A>G	ENST00000414716.3	+	5	536	c.308A>G	c.(307-309)cAc>cGc	p.H103R	CEP170B_ENST00000453495.1_Missense_Mutation_p.H103R|CEP170B_ENST00000556508.1_Missense_Mutation_p.H33R|CEP170B_ENST00000418279.1_Missense_Mutation_p.H33R	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	103						cytoplasm (GO:0005737)|microtubule (GO:0005874)											CGTGTGCAGCACCGAGTCCCG	0.637																																					p.H103R		Atlas-SNP	.											.	.	.	.	0			c.A308G						.						102	111	108					14																	105344813		2123	4233	6356	SO:0001583	missense	283638	exon5			TGCAGCACCGAGT	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.308A>G	chr14.hg19:g.105344813A>G	ENSP00000404151:p.His103Arg	66.0	0.0		51.0	4.0	NM_001112726	Q2KHR7|Q86TI7	Missense_Mutation	SNP	ENST00000414716.3	hg19	CCDS45175.1	.	.	.	.	.	.	.	.	.	.	A	18.92	3.725786	0.69074	.	.	ENSG00000099814	ENST00000556508;ENST00000414716;ENST00000453495;ENST00000418279	T;T;T;T	0.36340	1.26;1.26;1.26;1.26	4.14	4.14	0.48551	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	0.080156	0.47455	D	0.000228	T	0.44912	0.1316	L	0.49455	1.56	0.45330	D	0.998324	D;B;P	0.53151	0.958;0.296;0.82	P;B;P	0.56163	0.793;0.046;0.502	T	0.24693	-1.0153	10	0.25106	T	0.35	-24.6896	12.9586	0.58444	1.0:0.0:0.0:0.0	.	103;103;33	Q9Y4F5-2;Q9Y4F5;E9PFC1	.;K0284_HUMAN;.	R	33;103;103;33	ENSP00000451249:H33R;ENSP00000404151:H103R;ENSP00000407238:H103R;ENSP00000415006:H33R	ENSP00000404151:H103R	H	+	2	0	KIAA0284	104415858	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	5.082000	0.64450	1.732000	0.51606	0.260000	0.18958	CAC	.	.		0.637	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		G	105344813	A	G	105344813	3	3	100	1	0	0	0	0	1	0	0	0	8175	159	6	2	322	2	KIAA0284	14	105344813	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	1906412	105344813	2004727	188	13757										
RYR3	6263	hgsc.bcm.edu	37	chr15	34130147	34130147	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gttccatgagccagccaaggAcatagggtttaatgtggctg	13	8	0	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:34130147A>G	ENST00000389232.4	+	89	12036	c.11966A>G	c.(11965-11967)gAc>gGc	p.D3989G	RYR3_ENST00000415757.3_Missense_Mutation_p.D3984G	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3989					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CCAGCCAAGGACATAGGGTTT	0.448																																					p.D3989G		Atlas-SNP	.											.	RYR3	760	.	0			c.A11966G						.						127	126	127					15																	34130147		1950	4154	6104	SO:0001583	missense	6263	exon89			CCAAGGACATAGG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.11966A>G	chr15.hg19:g.34130147A>G	ENSP00000373884:p.Asp3989Gly	184.0	0.0		137.0	6.0	NM_001036	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	A	19.32	3.805558	0.70682	.	.	ENSG00000198838	ENST00000389232;ENST00000361728	D	0.97710	-4.5	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.98201	0.9405	M	0.62723	1.935	0.80722	D	1	D;D	0.65815	0.987;0.995	P;D	0.67548	0.882;0.952	D	0.99376	1.0921	10	0.87932	D	0	.	15.5941	0.76566	1.0:0.0:0.0:0.0	.	3984;3989	Q15413-2;Q15413	.;RYR3_HUMAN	G	3989;3985	ENSP00000373884:D3989G	ENSP00000354735:D3985G	D	+	2	0	RYR3	31917439	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.020000	0.93667	2.272000	0.75746	0.450000	0.29827	GAC	.	.		0.448	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			G	34130147	A	G	34130147	3	3	100	1	0	0	0	0	1	0	0	0	13785	275	10	2	12320	2	RYR3	15	34130147	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		34130147	68401245	189	13758										
FBN1	2200	hgsc.bcm.edu	37	chr15	48712988	48712988	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gctggcagcggtggttacccTcacactcgtccacgtctgaa	11	14	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:48712988T>C	ENST00000316623.5	-	63	8170	c.7715A>G	c.(7714-7716)gAg>gGg	p.E2572G		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2572	EGF-like 45; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GTGGTTACCCTCACACTCGTC	0.542																																					p.E2572G		Atlas-SNP	.											.	FBN1	310	.	0			c.A7715G						.						76	66	69					15																	48712988		2198	4296	6494	SO:0001583	missense	2200	exon63			TTACCCTCACACT	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.7715A>G	chr15.hg19:g.48712988T>C	ENSP00000325527:p.Glu2572Gly	46.0	0.0		41.0	4.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	T	15.74	2.922841	0.52653	.	.	ENSG00000166147	ENST00000316623	D	0.92249	-3.0	5.99	5.99	0.97316	EGF-like calcium-binding, conserved site (1);Growth factor, receptor (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.099912	0.64402	D	0.000003	D	0.87079	0.6088	L	0.31065	0.9	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.82331	-0.0510	10	0.20519	T	0.43	.	16.1557	0.81666	0.0:0.0:0.0:1.0	.	2572	P35555	FBN1_HUMAN	G	2572	ENSP00000325527:E2572G	ENSP00000325527:E2572G	E	-	2	0	FBN1	46500280	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.048000	0.57390	2.291000	0.77112	0.533000	0.62120	GAG	.	.		0.542	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			C	48712988	T	C	48712988	3	2	100	1	0	0	0	0	1	0	0	0	5710	1551	54	2	916	2	FBN1	15	48712988	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	14582841	48712988	53818404	190	13759										
FBN1	2200	hgsc.bcm.edu	37	chr15	48752514	48752514	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cacagagtgtagcaaactcaTctgcaatgattaaacaaagg	8	8	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:48752514T>C	ENST00000316623.5	-	43	5680	c.5225A>G	c.(5224-5226)gAt>gGt	p.D1742G		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1742	TB 7.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		AGCAAACTCATCTGCAATGAT	0.403																																					p.D1742G		Atlas-SNP	.											.	FBN1	310	.	0			c.A5225G						.						75	67	70					15																	48752514		2198	4296	6494	SO:0001630	splice_region_variant	2200	exon43			AACTCATCTGCAA	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5225-1A>G	chr15.hg19:g.48752514T>C		87.0	0.0		72.0	5.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	T	11.94	1.787891	0.31593	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.92858	-3.12	6.16	6.16	0.99307	Matrix fibril-associated (3);TGF-beta binding (1);	0.090906	0.85682	D	0.000000	D	0.93507	0.7928	L	0.46614	1.455	0.80722	D	1	D	0.63046	0.992	D	0.72338	0.977	D	0.91451	0.5181	10	0.23302	T	0.38	.	12.3343	0.55058	0.0:0.0:0.1408:0.8592	.	1742	P35555	FBN1_HUMAN	G	1742;310;632	ENSP00000325527:D1742G	ENSP00000325527:D1742G	D	-	2	0	FBN1	46539806	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.989000	0.56958	2.367000	0.80283	0.528000	0.53228	GAT	.	.		0.403	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		Missense_Mutation	C	48752514	T	C	48752514	5	2	100	1	0	0	0	0	0	0	1	0	5710	1449	50	2	3486	2	FBN1	15	48752514	Splice_Site	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	39526	48752514	53778878	191	13760										
USP50	373509	hgsc.bcm.edu	37	chr15	50833284	50833284	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tttggatggaatggggagtgAgaagacagtgaagacttcgt	16	3	0	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:50833284A>G	ENST00000532404.1	-	4	795	c.622T>C	c.(622-624)Tca>Cca	p.S208P	USP50_ENST00000530218.1_Intron	NM_203494.4	NP_987090.2	Q70EL3	UBP50_HUMAN	ubiquitin specific peptidase 50	213	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(5)	13				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)		ATGGGGAGTGAGAAGACAGTG	0.453																																					p.S208P		Atlas-SNP	.											.	USP50	24	.	0			c.T622C						.						132	125	127					15																	50833284		1930	4142	6072	SO:0001583	missense	373509	exon4			GGAGTGAGAAGAC	AI990110	CCDS53944.1	15q21.1	2008-02-05	2005-08-08			ENSG00000170236		"Ubiquitin-specific peptidases"	20079	protein-coding gene	gene with protein product			"ubiquitin specific protease 50"			12838346	Standard	NM_203494		Approved		uc021sky.1	Q70EL3		ENST00000532404.1:c.622T>C	chr15.hg19:g.50833284A>G	ENSP00000434676:p.Ser208Pro	164.0	0.0		103.0	5.0	NM_203494	E9PP86	Missense_Mutation	SNP	ENST00000532404.1	hg19	CCDS53944.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744512	0.49151	.	.	ENSG00000170236	ENST00000532404	T	0.36699	1.24	5.45	4.32	0.51571	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.068855	0.64402	D	0.000012	T	0.45175	0.1329	M	0.83852	2.665	0.34738	D	0.730491	B	0.24576	0.106	B	0.34385	0.181	T	0.56974	-0.7890	10	0.72032	D	0.01	-8.2452	8.9374	0.35708	0.9144:0.0:0.0856:0.0	.	213	Q70EL3	UBP50_HUMAN	P	208	ENSP00000434676:S208P	ENSP00000434676:S208P	S	-	1	0	USP50	48620576	1.000000	0.71417	0.970000	0.41538	0.854000	0.48673	3.367000	0.52350	0.898000	0.36418	0.459000	0.35465	TCA	.	.		0.453	USP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395249.1			G	50833284	A	G	50833284	3	3	100	1	0	0	0	0	1	0	0	0	17097	304	11	2	398	2	USP50	15	50833284	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	2080770	50833284	51698108	192	13761										
NARG2	79664	hgsc.bcm.edu	37	chr15	60742037	60742037	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gcactcgttgacttcacaggAcatcttatgtaaataaattg	7	8	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:60742037A>G	ENST00000261520.4	-	10	1363	c.1129T>C	c.(1129-1131)Tcc>Ccc	p.S377P	NARG2_ENST00000439632.1_Missense_Mutation_p.S240P	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						ACTTCACAGGACATCTTATGT	0.358																																					p.S377P		Atlas-SNP	.											.	NARG2	82	.	0			c.T1129C						.						54	58	57					15																	60742037		2198	4276	6474	SO:0001583	missense	79664	exon10			CACAGGACATCTT																												ENST00000261520.4:c.1129T>C	chr15.hg19:g.60742037A>G	ENSP00000261520:p.Ser377Pro	77.0	0.0		56.0	4.0	NM_024611		Missense_Mutation	SNP	ENST00000261520.4	hg19	CCDS10176.1	.	.	.	.	.	.	.	.	.	.	A	5.055	0.195731	0.09599	.	.	ENSG00000128915	ENST00000261520;ENST00000439632	.	.	.	5.45	-1.17	0.09648	.	0.489229	0.24587	N	0.037252	T	0.19927	0.0479	N	0.17474	0.49	0.09310	N	1	B;B	0.15930	0.015;0.002	B;B	0.11329	0.006;0.001	T	0.12477	-1.0546	9	0.24483	T	0.36	-1.9507	5.7089	0.17923	0.5039:0.0:0.3686:0.1275	.	45;377	B3KXT2;Q659A1	.;NARG2_HUMAN	P	377;240	.	ENSP00000261520:S377P	S	-	1	0	NARG2	58529329	0.021000	0.18746	0.003000	0.11579	0.223000	0.24884	0.197000	0.17197	-0.098000	0.12285	0.477000	0.44152	TCC	.	.		0.358	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			G	60742037	A	G	60742037	3	3	100	1	0	0	0	0	1	0	0	0	10178	275	10	2	1847	2	NARG2	15	60742037	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	9908753	60742037	41789355	193	13762										
CYP1A2	1544	hgsc.bcm.edu	37	chr15	75047231	75047231	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agtgagaagatgatgctgttTggcatgggcaagcgccggtg	17	6	0	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:75047231T>C	ENST00000343932.4	+	7	1416	c.1353T>C	c.(1351-1353)ttT>ttC	p.F451F		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	451				LF -> MLV (in Ref. 10; AAA52154). {ECO:0000305}.	alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"	TGATGCTGTTTGGCATGGGCA	0.597																																					p.F451F		Atlas-SNP	.											.	CYP1A2	70	.	0			c.T1353C						.						121	108	112					15																	75047231		2197	4296	6493	SO:0001819	synonymous_variant	1544	exon7			GCTGTTTGGCATG	AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"Cytochrome P450s"	2596	protein-coding gene	gene with protein product		124060	"cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.1353T>C	chr15.hg19:g.75047231T>C		151.0	0.0		64.0	8.0	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Silent	SNP	ENST00000343932.4	hg19	CCDS32293.1																																																																																			.	.		0.597	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761		C	75047231	T	C	75047231	2	2	100	1	0	0	0	0	0	0	0	1	4152	1809	63	2		2	CYP1A2	15	75047231	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	14305194	75047231	27484161	194	13763										
SNX33	257364	hgsc.bcm.edu	37	chr15	75941871	75941871	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	caccaacgggcaccctccccTcaacctctcctaccctggtg	6	21	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:75941871T>C	ENST00000308527.5	+	1	1625	c.428T>C	c.(427-429)cTc>cCc	p.L143P	IMP3_ENST00000565349.1_5'Flank|IMP3_ENST00000314852.2_5'Flank	NM_153271.1	NP_695003.1	Q8WV41	SNX33_HUMAN	sorting nexin 33	143					cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|macropinocytosis (GO:0044351)|membrane tubulation (GO:0097320)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|negative regulation of endocytosis (GO:0045806)|negative regulation of protein localization to cell surface (GO:2000009)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein localization to cell surface (GO:2000010)|protein import (GO:0017038)	cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|soft_tissue(1)|urinary_tract(2)	19						CACCCTCCCCTCAACCTCTCC	0.657																																					p.L143P		Atlas-SNP	.											.	SNX33	43	.	0			c.T428C						.						55	55	55					15																	75941871		2197	4293	6490	SO:0001583	missense	257364	exon1			CTCCCCTCAACCT	AK091291	CCDS10283.1	15q23	2008-04-18	2008-03-25	2008-03-25	ENSG00000173548	ENSG00000173548			28468	protein-coding gene	gene with protein product			"SH3 and PX domain containing 3"	SH3PX3		16374509, 16782399, 18353773	Standard	NM_153271		Approved	MGC32065, SH3PXD3C, SNX30	uc002bau.3	Q8WV41	OTTHUMG00000142835	ENST00000308527.5:c.428T>C	chr15.hg19:g.75941871T>C	ENSP00000311427:p.Leu143Pro	104.0	0.0		78.0	6.0	NM_153271	B1NM17	Missense_Mutation	SNP	ENST00000308527.5	hg19	CCDS10283.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.813817	0.32053	.	.	ENSG00000173548	ENST00000308527	T	0.65364	-0.15	4.83	4.83	0.62350	.	0.639639	0.16138	N	0.227857	T	0.37865	0.1019	N	0.08118	0	0.58432	D	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.28138	-1.0053	10	0.35671	T	0.21	-1.7839	5.9195	0.19073	0.0:0.1792:0.0:0.8208	.	143	Q8WV41	SNX33_HUMAN	P	143	ENSP00000311427:L143P	ENSP00000311427:L143P	L	+	2	0	SNX33	73728926	0.965000	0.33210	0.993000	0.49108	0.984000	0.73092	2.496000	0.45346	2.027000	0.59764	0.528000	0.53228	CTC	.	.		0.657	SNX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286471.1	NM_153271		C	75941871	T	C	75941871	3	2	100	1	0	0	0	0	1	0	0	0	14918	1551	54	2	430	2	SNX33	15	75941871	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	894640	75941871	26589521	195	13764										
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79307690	79307690	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgatcatctgcggcacagtgAccttggaattttcttcaaat	8	9	4	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:79307690A>G	ENST00000419573.3	-	13	2079	c.1805T>C	c.(1804-1806)gTc>gCc	p.V602A	RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000558480.2_Missense_Mutation_p.V602A	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	602					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CGGCACAGTGACCTTGGAATT	0.512																																					p.V602A		Atlas-SNP	.											.	RASGRF1	168	.	0			c.T1805C						.						179	146	157					15																	79307690		2196	4293	6489	SO:0001583	missense	5923	exon13			ACAGTGACCTTGG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.1805T>C	chr15.hg19:g.79307690A>G	ENSP00000405963:p.Val602Ala	124.0	0.0		79.0	6.0	NM_001145648	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.042910	0.75732	.	.	ENSG00000058335	ENST00000419573;ENST00000394741	T	0.56776	0.44	3.68	3.68	0.42216	.	0.000000	0.64402	D	0.000006	T	0.65428	0.2690	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;0.998;0.998;0.999	D;D;D;D;D	0.81914	0.995;0.935;0.93;0.952;0.978	T	0.64651	-0.6357	10	0.10377	T	0.69	.	10.3632	0.44008	1.0:0.0:0.0:0.0	.	11;602;602;602;602	B7Z6Z6;A8K270;Q8IUU5;Q13972;F8VPA5	.;.;.;RGRF1_HUMAN;.	A	602	ENSP00000405963:V602A	ENSP00000378224:V602A	V	-	2	0	RASGRF1	77094745	1.000000	0.71417	0.998000	0.56505	0.940000	0.58332	8.812000	0.91959	1.528000	0.49103	0.397000	0.26171	GTC	.	.		0.512	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		G	79307690	A	G	79307690	3	3	100	1	0	0	0	0	1	0	0	0	13087	275	10	2	2080	2	RASGRF1	15	79307690	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	3365819	79307690	23223702	196	13765										
ACAN	176	hgsc.bcm.edu	37	chr15	89402123	89402123	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tcccagaatctagcagtgagAcgtccgcctatcctgaagct	9	13	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:89402123A>G	ENST00000561243.1	+	11	6307	c.6307A>G	c.(6307-6309)Acg>Gcg	p.T2103A	ACAN_ENST00000559004.1_Missense_Mutation_p.T2103A|ACAN_ENST00000439576.2_Missense_Mutation_p.T2103A|ACAN_ENST00000352105.7_Missense_Mutation_p.T2103A			P16112	PGCA_HUMAN	aggrecan	1988	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TAGCAGTGAGACGTCCGCCTA	0.562																																					p.T2103A		Atlas-SNP	.											AGC1,NS,carcinoma,0,2	ACAN	220	.	0			c.A6307G						.						41	42	41					15																	89402123		1907	4112	6019	SO:0001583	missense	176	exon12			AGTGAGACGTCCG	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.6307A>G	chr15.hg19:g.89402123A>G	ENSP00000453342:p.Thr2103Ala	62.0	0.0		43.0	3.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	hg19	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	A	11.17	1.560900	0.27827	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02236	4.61;4.38	5.18	-4.59	0.03400	.	1.118760	0.07130	N	0.845433	T	0.01627	0.0052	L	0.50333	1.59	0.09310	N	1	P;P	0.46220	0.874;0.861	B;B	0.39339	0.297;0.297	T	0.45614	-0.9249	10	0.07175	T	0.84	2.7281	0.4911	0.00564	0.3941:0.2005:0.1471:0.2582	.	2103;2103	E7ENV9;E7EX88	.;.	A	2103;2103;1989	ENSP00000387356:T2103A;ENSP00000341615:T2103A	ENSP00000268134:T1989A	T	+	1	0	ACAN	87203127	0.011000	0.17503	0.001000	0.08648	0.490000	0.33462	0.939000	0.28978	-0.357000	0.08175	0.454000	0.30748	ACG	.	.		0.562	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		G	89402123	A	G	89402123	3	3	100	1	0	0	0	0	1	0	0	0	117	275	10	2	6349	2	ACAN	15	89402123	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	10094433	89402123	13129269	197	13766										
PLIN1	5346	hgsc.bcm.edu	37	chr15	90210343	90210343	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgtcacagccgagatggtggTctggagggtcttctgcaggg	17	8	4	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:90210343T>C	ENST00000300055.5	-	8	1198	c.1033A>G	c.(1033-1035)Acc>Gcc	p.T345A	PLIN1_ENST00000430628.2_Missense_Mutation_p.T345A	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	345					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						GAGATGGTGGTCTGGAGGGTC	0.657																																					p.T345A		Atlas-SNP	.											.	PLIN1	36	.	0			c.A1033G						.						97	86	90					15																	90210343		2200	4299	6499	SO:0001583	missense	5346	exon8			TGGTGGTCTGGAG	AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"Perilipins"	9076	protein-coding gene	gene with protein product		170290	"perilipin"	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.1033A>G	chr15.hg19:g.90210343T>C	ENSP00000300055:p.Thr345Ala	126.0	0.0		97.0	4.0	NM_001145311	Q8N5Y6	Missense_Mutation	SNP	ENST00000300055.5	hg19	CCDS10353.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.498012	0.26861	.	.	ENSG00000166819	ENST00000300055;ENST00000430628	T;T	0.05025	3.51;3.51	5.35	-1.12	0.09808	.	1.732160	0.03257	N	0.182673	T	0.06371	0.0164	L	0.36672	1.1	0.09310	N	1	B	0.20671	0.047	B	0.19391	0.025	T	0.40942	-0.9536	10	0.62326	D	0.03	-5.3931	3.8252	0.08852	0.2822:0.3172:0.0:0.4006	.	345	O60240	PLIN1_HUMAN	A	345	ENSP00000300055:T345A;ENSP00000402167:T345A	ENSP00000300055:T345A	T	-	1	0	PLIN1	88011347	0.000000	0.05858	0.000000	0.03702	0.656000	0.38851	-0.125000	0.10579	-0.487000	0.06735	-0.516000	0.04426	ACC	.	.		0.657	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313424.2	NM_002666		C	90210343	T	C	90210343	3	2	100	1	0	0	0	0	1	0	0	0	12098	1667	58	2	543	2	PLIN1	15	90210343	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	808220	90210343	12321049	198	13767										
IDH2	3418	hgsc.bcm.edu	37	chr15	90628063	90628063	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cgcacttgctgaggccgtgaAtgcagcccgccaggtccttg	13	14	0	2	rs554169929		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr15:90628063A>G	ENST00000330062.3	-	10	1369	c.1256T>C	c.(1255-1257)aTt>aCt	p.I419T	RP11-617F23.1_ENST00000558334.1_RNA|IDH2_ENST00000540499.2_Missense_Mutation_p.I367T|IDH2_ENST00000539790.1_Missense_Mutation_p.I289T|IDH2_ENST00000559482.1_Intron	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	419					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			GAGGCCGTGAATGCAGCCCGC	0.627			M		GBM								A|||	1	0.000199681	8e-04	0	5008	,	,		19294	0		0	False		,,,				2504	0				p.I419T		Atlas-SNP	.		Dom	yes		15	15q26.1	3418	"socitrate dehydrogenase 2 (NADP+), mitochondrial "		M	.	IDH2	1372	.	0			c.T1256C						.						105	107	106					15																	90628063		2200	4298	6498	SO:0001583	missense	3418	exon10			CCGTGAATGCAGC		CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.1256T>C	chr15.hg19:g.90628063A>G	ENSP00000331897:p.Ile419Thr	87.0	0.0		69.0	4.0	NM_002168	B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	hg19	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.664260	0.47572	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	T;T;T	0.77098	-1.07;-1.07;-1.07	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.82761	0.5107	M	0.62209	1.925	0.80722	D	1	D	0.52996	0.957	P	0.54889	0.763	D	0.84890	0.0836	10	0.87932	D	0	.	13.6826	0.62496	1.0:0.0:0.0:0.0	.	419	P48735	IDHP_HUMAN	T	419;289;367	ENSP00000331897:I419T;ENSP00000438457:I289T;ENSP00000446147:I367T	ENSP00000331897:I419T	I	-	2	0	IDH2	88429067	1.000000	0.71417	1.000000	0.80357	0.269000	0.26545	7.469000	0.80959	2.117000	0.64856	0.459000	0.35465	ATT	.	.		0.627	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			G	90628063	A	G	90628063	3	3	100	1	0	0	0	0	1	0	0	0	7504	101	4	2	110	2	IDH2	15	90628063	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	417720	90628063	11903329	199	13768										
TPSG1	8912	hgsc.bcm.edu	37	chr16	1271981	1271981	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tccagttcacgtaggcagggAcacgagtgtagactcccggc	13	12	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:1271981A>G	ENST00000348261.5	+	0	8084				TPSG1_ENST00000234798.4_Missense_Mutation_p.V258A	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit						aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GTAGGCAGGGACACGAGTGTA	0.672																																					p.V258A		Atlas-SNP	.											.	TPSG1	19	.	0			c.T773C						.						29	39	36					16																	1271981		2196	4297	6493	SO:0001628	intergenic_variant	25823	exon6			GCAGGGACACGAG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180			chr16.hg19:g.1271981A>G		146.0	0.0		80.0	7.0	NM_012467	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	a	16.76	3.211574	0.58343	.	.	ENSG00000116176	ENST00000234798	D	0.96774	-4.12	4.28	3.18	0.36537	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.98002	0.9342	M	0.89904	3.07	0.09310	N	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.92688	0.6164	9	0.59425	D	0.04	.	7.9097	0.29782	0.8966:0.0:0.1034:0.0	.	258	Q9NRR2	TRYG1_HUMAN	A	258	ENSP00000234798:V258A	ENSP00000234798:V258A	V	-	2	0	TPSG1	1211982	0.032000	0.19561	0.001000	0.08648	0.003000	0.03518	3.236000	0.51336	0.599000	0.29845	0.524000	0.50904	GTC	.	.		0.672	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		G	1271981	A	G	1271981	1	3	100	0	1	0	0	0	0	0	0	0	16441	275	10	2		2	TPSG1	16	1271981	IGR	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		1271981	89082772	200	13769										
ABCC6	368	hgsc.bcm.edu	37	chr16	16308279	16308279	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	caggcataggtaggtggacaGgtggcggacagggtcgctct	18	8	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:16308279G>C	ENST00000205557.7	-	5	531	c.502C>G	c.(502-504)Ctg>Gtg	p.L168V	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	168					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	TAGGTGGACAGGTGGCGGACA	0.572																																					p.L168V		Atlas-SNP	.											.	ABCC6	110	.	0			c.C502G						.						6	7	6					16																	16308279		1961	3880	5841	SO:0001583	missense	368	exon5			TGGACAGGTGGCG	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.502C>G	chr16.hg19:g.16308279G>C	ENSP00000205557:p.Leu168Val	277.0	0.0		159.0	7.0	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	hg19	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	.	0.007	-1.992607	0.00439	.	.	ENSG00000091262	ENST00000205557;ENST00000456970;ENST00000546056	T;T	0.49720	0.77;0.77	3.89	2.83	0.33086	.	0.428472	0.16828	U	0.197845	T	0.23370	0.0565	N	0.25890	0.77	0.80722	D	1	P;B	0.35401	0.499;0.298	B;B	0.29440	0.102;0.064	T	0.15838	-1.0423	10	0.02654	T	1	.	6.3836	0.21548	0.0:0.1999:0.5947:0.2054	.	180;168	F5GWQ0;O95255	.;MRP6_HUMAN	V	168;168;180	ENSP00000205557:L168V;ENSP00000405002:L168V	ENSP00000205557:L168V	L	-	1	2	ABCC6	16215780	1.000000	0.71417	1.000000	0.80357	0.185000	0.23345	1.275000	0.33144	1.919000	0.55581	0.306000	0.20318	CTG	.	.		0.572	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			C	16308279	G	C	16308279	3	2	100	1	0	0	0	0	1	0	0	0	57	991	35	4	4117	4	ABCC6	16	16308279	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	15036298	16308279	74046474	201	13770										
TMC5	79838	hgsc.bcm.edu	37	chr16	19505602	19505602	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aggagggcaaagataaaatgTtcctgatagaaaaattgatc	10	4	0	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:19505602T>C	ENST00000396229.2	+	20	3594	c.2845T>C	c.(2845-2847)Ttc>Ctc	p.F949L	TMC5_ENST00000542583.2_Missense_Mutation_p.F949L|TMC5_ENST00000219821.5_Missense_Mutation_p.F703L|TMC5_ENST00000564959.1_Missense_Mutation_p.F632L|TMC5_ENST00000561503.1_Missense_Mutation_p.F590L|TMC5_ENST00000541464.1_Missense_Mutation_p.F897L|TMC5_ENST00000381414.4_Missense_Mutation_p.F891L	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	949					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						AGATAAAATGTTCCTGATAGA	0.408																																					p.F949L		Atlas-SNP	.											.	TMC5	169	.	0			c.T2845C						.						119	128	125					16																	19505602		2197	4300	6497	SO:0001583	missense	79838	exon20			AAAATGTTCCTGA	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.2845T>C	chr16.hg19:g.19505602T>C	ENSP00000379531:p.Phe949Leu	194.0	0.0		84.0	5.0	NM_001105248	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	hg19	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.843527	0.91197	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.79653	-0.97;-1.29;-1.16;-1.16;-1.28	5.57	5.57	0.84162	.	1.702360	0.02414	N	0.082006	D	0.92224	0.7534	M	0.85462	2.755	0.49915	D	0.999834	D;D;D;D;D	0.89917	1.0;0.998;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.918;0.999;0.997;0.999	T	0.78863	-0.2036	10	0.49607	T	0.09	-27.6758	14.2507	0.66019	0.0:0.0:0.0:1.0	.	897;632;703;949;891	F5GYU8;E7EU57;Q6UXY8-3;Q6UXY8;Q6UXY8-2	.;.;.;TMC5_HUMAN;.	L	897;891;949;949;703;632	ENSP00000441227:F897L;ENSP00000370822:F891L;ENSP00000379531:F949L;ENSP00000446274:F949L;ENSP00000219821:F703L	ENSP00000219821:F703L	F	+	1	0	TMC5	19413103	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.135000	0.64777	2.243000	0.73865	0.533000	0.62120	TTC	.	.		0.408	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		C	19505602	T	C	19505602	3	2	100	1	0	0	0	0	1	0	0	0	16003	1725	60	2	3229	2	TMC5	16	19505602	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	3197323	19505602	70849151	202	13771										
CP110	9738	hgsc.bcm.edu	37	chr16	19556463	19556463	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gacatattctttgtaatggaTgcagctgaaagaatgtctat	9	5	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:19556463T>C	ENST00000381396.5	+	10	2881	c.2634T>C	c.(2632-2634)gaT>gaC	p.D878D	CCP110_ENST00000396208.2_Silent_p.D878D|CCP110_ENST00000396212.2_Silent_p.D878D	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	878					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						TTGTAATGGATGCAGCTGAAA	0.348																																					p.D878D		Atlas-SNP	.											.	CCP110	57	.	0			c.T2634C						.						134	120	125					16																	19556463		2196	4300	6496	SO:0001819	synonymous_variant	9738	exon10			AATGGATGCAGCT	AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.2634T>C	chr16.hg19:g.19556463T>C		118.0	0.0		78.0	4.0	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Silent	SNP	ENST00000381396.5	hg19	CCDS55992.1																																																																																			.	.		0.348	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		C	19556463	T	C	19556463	2	2	100	1	0	0	0	0	0	0	0	1	3790	1461	51	2		2	CP110	16	19556463	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	50861	19556463	70798290	203	13772										
ZNF720	124411	hgsc.bcm.edu	37	chr16	31734663	31734663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gaagagtgcagagacagtagCcatccagccaggtaggtggg	16	8	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:31734663C>T	ENST00000316491.9	+	3	414	c.215C>T	c.(214-216)gCc>gTc	p.A72V	ZNF720_ENST00000531864.2_Intron|ZNF720_ENST00000399681.3_5'UTR|ZNF720_ENST00000534369.1_Intron|ZNF720_ENST00000398696.3_Intron|ZNF720_ENST00000539915.1_Intron	NM_001130913.1	NP_001124385.1	Q7Z2F6	ZN720_HUMAN	zinc finger protein 720	72	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)|lung(1)|stomach(1)	4						GAGACAGTAGCCATCCAGCCA	0.478																																					p.A72V		Atlas-SNP	.											.	ZNF720	15	.	0			c.C215T						.						81	78	79					16																	31734663		692	1591	2283	SO:0001583	missense	124411	exon3			CAGTAGCCATCCA	AK128671	CCDS45473.1	16p11.2	2013-01-08				ENSG00000197302		"Zinc fingers, C2H2-type", "-"	26987	protein-coding gene	gene with protein product							Standard	NM_001130913		Approved		uc002ecq.3	Q7Z2F6		ENST00000316491.9:c.215C>T	chr16.hg19:g.31734663C>T	ENSP00000319222:p.Ala72Val	121.0	0.0		77.0	4.0	NM_001130913	Q6ZQX1	Missense_Mutation	SNP	ENST00000316491.9	hg19	CCDS45473.1	.	.	.	.	.	.	.	.	.	.	c	11.11	1.541691	0.27563	.	.	ENSG00000197302	ENST00000316491;ENST00000530881;ENST00000529515	T;T;T	0.00672	5.97;5.89;6.0	1.51	0.182	0.15077	Krueppel-associated box (1);	.	.	.	.	T	0.00845	0.0028	L	0.33245	0.995	0.09310	N	0.999994	P	0.36587	0.559	B	0.40066	0.318	T	0.50566	-0.8813	9	0.59425	D	0.04	.	4.8837	0.13692	0.0:0.6046:0.3954:0.0	.	72	Q7Z2F6	ZN720_HUMAN	V	72;113;72	ENSP00000319222:A72V;ENSP00000435171:A113V;ENSP00000437310:A72V	ENSP00000319222:A72V	A	+	2	0	ZNF720	31642164	0.000000	0.05858	0.102000	0.21198	0.377000	0.30045	-0.209000	0.09358	0.837000	0.34925	0.313000	0.20887	GCC	.	.		0.478	ZNF720-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394883.3	NM_001004300		T	31734663	C	T	31734663	3	4	100	1	0	0	0	0	1	0	0	0	18136	739	26	3	225	3	ZNF720	16	31734663	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	12178200	31734663	58620090	204	13773										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31926978	31926978	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tttacaaatgtaaagtatgtAgcaaatcttatgctcgttct	6	6	2	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:31926978A>G	ENST00000300870.10	+	4	1617	c.1408A>G	c.(1408-1410)Agc>Ggc	p.S470G		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	470					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						TAAAGTATGTAGCAAATCTTA	0.343																																					p.S470G		Atlas-SNP	.											.	ZNF267	94	.	0			c.A1408G						.						69	77	74					16																	31926978		2197	4298	6495	SO:0001583	missense	10308	exon4			GTATGTAGCAAAT	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.1408A>G	chr16.hg19:g.31926978A>G	ENSP00000300870:p.Ser470Gly	118.0	0.0		85.0	4.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Missense_Mutation	SNP	ENST00000300870.10	hg19	CCDS32440.1	.	.	.	.	.	.	.	.	.	.	.	3.395	-0.123397	0.06795	.	.	ENSG00000185947	ENST00000300870	T	0.01998	4.51	0.458	-0.707	0.11245	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00580	0.0019	N	0.00450	-1.49	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.46498	-0.9187	9	0.02654	T	1	.	4.3506	0.11153	0.3743:0.0:0.6257:0.0	.	470	Q14586	ZN267_HUMAN	G	470	ENSP00000300870:S470G	ENSP00000300870:S470G	S	+	1	0	ZNF267	31834479	1.000000	0.71417	0.162000	0.22713	0.138000	0.21146	1.453000	0.35167	-0.417000	0.07461	-0.425000	0.05940	AGC	.	.		0.343	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		G	31926978	A	G	31926978	3	3	100	1	0	0	0	0	1	0	0	0	17821	420	15	2	1422	2	ZNF267	16	31926978	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	192315	31926978	58427775	205	13774										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48596262	48596262	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctgaatcaagcttttcagaaAcaggctctctgccccaacaa	6	13	3	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:48596262A>G	ENST00000262384.3	-	2	528	c.292T>C	c.(292-294)Ttt>Ctt	p.F98L	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	98					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				CTTTTCAGAAACAGGCTCTCT	0.448																																					p.F98L		Atlas-SNP	.											.	N4BP1	121	.	0			c.T292C						.						55	56	56					16																	48596262		1948	4133	6081	SO:0001583	missense	9683	exon2			TCAGAAACAGGCT	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.292T>C	chr16.hg19:g.48596262A>G	ENSP00000262384:p.Phe98Leu	162.0	0.0		99.0	4.0	NM_153029	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	hg19	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.451091	0.84209	.	.	ENSG00000102921	ENST00000262384	T	0.39592	1.07	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.64260	0.2582	M	0.70595	2.14	0.54753	D	0.999989	D	0.76494	0.999	D	0.80764	0.994	T	0.67956	-0.5536	10	0.72032	D	0.01	-22.7416	15.8164	0.78604	1.0:0.0:0.0:0.0	.	98	O75113	N4BP1_HUMAN	L	98	ENSP00000262384:F98L	ENSP00000262384:F98L	F	-	1	0	N4BP1	47153763	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.749000	0.91619	2.195000	0.70347	0.533000	0.62120	TTT	.	.		0.448	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		G	48596262	A	G	48596262	3	3	100	1	0	0	0	0	1	0	0	0	10118	43	2	2	2422	2	N4BP1	16	48596262	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	16669284	48596262	41758491	206	13775										
NUP93	9688	hgsc.bcm.edu	37	chr16	56852599	56852599	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agctacatcagtgatgtgggAccccctggtcgaagctctct	11	12	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:56852599A>G	ENST00000308159.5	+	6	634	c.513A>G	c.(511-513)ggA>ggG	p.G171G	NUP93_ENST00000569842.1_Silent_p.G171G|NUP93_ENST00000542526.1_Silent_p.G48G|NUP93_ENST00000564887.1_Silent_p.G48G	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	171					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						GTGATGTGGGACCCCCTGGTC	0.443																																					p.G171G	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.A513G						.						128	122	124					16																	56852599		2198	4300	6498	SO:0001819	synonymous_variant	9688	exon6			TGTGGGACCCCCT	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.513A>G	chr16.hg19:g.56852599A>G		155.0	0.0		86.0	5.0	NM_014669	B3KPQ8|Q14705	Silent	SNP	ENST00000308159.5	hg19	CCDS10769.1																																																																																			.	.		0.443	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669		G	56852599	A	G	56852599	2	3	100	1	0	0	0	0	0	0	0	1	10781	262	10	2		2	NUP93	16	56852599	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	8256337	56852599	33502154	207	13776										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58576414	58576414	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agcaagccaactcacaattgTcctgagctaattgagcagct	8	11	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:58576414T>C	ENST00000317147.5	-	32	4825	c.4493A>G	c.(4492-4494)gAc>gGc	p.D1498G	CNOT1_ENST00000569240.1_Missense_Mutation_p.D1493G|CNOT1_ENST00000245138.4_Missense_Mutation_p.D349G	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1498	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CTCACAATTGTCCTGAGCTAA	0.458																																					p.D1498G		Atlas-SNP	.											.	CNOT1	359	.	0			c.A4493G						.						183	200	194					16																	58576414		2198	4300	6498	SO:0001583	missense	23019	exon32			CAATTGTCCTGAG	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4493A>G	chr16.hg19:g.58576414T>C	ENSP00000320949:p.Asp1498Gly	248.0	0.0		125.0	5.0	NM_016284	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.380911	0.82792	.	.	ENSG00000125107	ENST00000317147;ENST00000245138;ENST00000394200	T	0.57107	0.42	5.8	4.7	0.59300	CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 (1);	0.000000	0.85682	D	0.000000	T	0.75170	0.3813	M	0.88377	2.95	0.80722	D	1	D;D;D	0.71674	0.995;0.998;0.997	P;D;D	0.70227	0.884;0.968;0.946	T	0.79581	-0.1744	10	0.72032	D	0.01	-27.1022	13.1748	0.59619	0.0:0.0:0.1333:0.8667	.	349;1498;1493	B5MDN3;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	G	1498;349;1493	ENSP00000320949:D1498G	ENSP00000245138:D349G	D	-	2	0	CNOT1	57133915	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.273000	0.72581	0.999000	0.39023	0.533000	0.62120	GAC	.	.		0.458	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		C	58576414	T	C	58576414	3	2	100	1	0	0	0	0	1	0	0	0	3619	1667	58	2	2709	2	CNOT1	16	58576414	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1723815	58576414	31778339	208	13777										
COG8	84342	hgsc.bcm.edu	37	chr16	69368967	69368967	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tcctcgtctgagaagatggcAcggtactgggtgatgatatc	13	8	1	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:69368967A>G	ENST00000306875.4	-	3	984	c.870T>C	c.(868-870)cgT>cgC	p.R290R	COG8_ENST00000562081.1_Silent_p.R290R|RP11-343C2.12_ENST00000562949.1_5'Flank	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	290					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						AGAAGATGGCACGGTACTGGG	0.517																																					p.R290R		Atlas-SNP	.											.	COG8	32	.	0			c.T870C						.						83	69	74					16																	69368967		2198	4300	6498	SO:0001819	synonymous_variant	84342	exon3			GATGGCACGGTAC	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"Components of oligomeric golgi complex"	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.870T>C	chr16.hg19:g.69368967A>G		172.0	0.0		96.0	4.0	NM_032382	Q0VAK2|Q8WVV6|Q9H6F8	Silent	SNP	ENST00000306875.4	hg19	CCDS10876.1																																																																																			.	.		0.517	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382		G	69368967	A	G	69368967	2	3	100	1	0	0	0	0	0	0	0	1	3666	146	6	2		2	COG8	16	69368967	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	10792553	69368967	20985786	209	13778										
TXNL4B	54957	hgsc.bcm.edu	37	chr16	72120695	72120695	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cccacaaacttagtgtgatcTggagatctagacagcataga	9	9	2	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:72120695T>C	ENST00000268483.3	-	4	612	c.291A>G	c.(289-291)ccA>ccG	p.P97P	TXNL4B_ENST00000426362.2_Silent_p.P97P|RP11-384M15.3_ENST00000561827.1_RNA|TXNL4B_ENST00000423037.1_Silent_p.P97P	NM_001142318.1|NM_017853.2	NP_001135790.1|NP_060323.1	Q9NX01	TXN4B_HUMAN	thioredoxin-like 4B	97					mitotic nuclear division (GO:0007067)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)				cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)	8						TAGTGTGATCTGGAGATCTAG	0.373																																					p.P97P		Atlas-SNP	.											.	TXNL4B	17	.	0			c.A291G						.						69	66	67					16																	72120695		2198	4300	6498	SO:0001819	synonymous_variant	54957	exon4			GTGATCTGGAGAT	BC009646	CCDS10906.1	16q22.2	2012-11-19			ENSG00000140830	ENSG00000140830			26041	protein-coding gene	gene with protein product						15161931	Standard	NM_017853		Approved	FLJ20511, DLP, Dim2	uc010vmn.2	Q9NX01	OTTHUMG00000173453	ENST00000268483.3:c.291A>G	chr16.hg19:g.72120695T>C		157.0	0.0		109.0	5.0	NM_001142318	D3DWS6	Silent	SNP	ENST00000268483.3	hg19	CCDS10906.1																																																																																			.	.		0.373	TXNL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269007.2	NM_017853		C	72120695	T	C	72120695	2	2	100	1	0	0	0	0	0	0	0	1	16821	1567	55	2		2	TXNL4B	16	72120695	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2751728	72120695	18234058	210	13779										
DHX38	9785	hgsc.bcm.edu	37	chr16	72135463	72135463	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tataatgggcgtcaagaaggAggaagagccagataaagctg	14	5	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:72135463A>G	ENST00000268482.3	+	11	1960	c.1451A>G	c.(1450-1452)gAg>gGg	p.E484G	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	484					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				GTCAAGAAGGAGGAAGAGCCA	0.562																																					p.E484G	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											.	DHX38	91	.	0			c.A1451G						.						79	55	64					16																	72135463		2123	4147	6270	SO:0001583	missense	9785	exon11			AGAAGGAGGAAGA	AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"DEAH-boxes"	17211	protein-coding gene	gene with protein product		605584	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.1451A>G	chr16.hg19:g.72135463A>G	ENSP00000268482:p.Glu484Gly	119.0	0.0		74.0	5.0	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	hg19	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.942821	0.53079	.	.	ENSG00000140829	ENST00000268482	D	0.86030	-2.06	5.06	5.06	0.68205	.	0.120396	0.56097	D	0.000039	D	0.85093	0.5618	M	0.78049	2.395	0.80722	D	1	B	0.29378	0.243	B	0.25987	0.065	D	0.84828	0.0800	10	0.56958	D	0.05	.	14.85	0.70289	1.0:0.0:0.0:0.0	.	484	Q92620	PRP16_HUMAN	G	484	ENSP00000268482:E484G	ENSP00000268482:E484G	E	+	2	0	DHX38	70692964	0.999000	0.42202	1.000000	0.80357	0.817000	0.46193	4.195000	0.58400	1.909000	0.55274	0.533000	0.62120	GAG	.	.		0.562	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		G	72135463	A	G	72135463	3	3	100	1	0	0	0	0	1	0	0	0	4513	304	11	2	1489	2	DHX38	16	72135463	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	14768	72135463	18219290	211	13780										
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88666240	88666240	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cgaaaagaacaggagcctgaTtttgaagagaaaaggtttac	11	5	0	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr16:88666240T>C	ENST00000301011.5	+	6	1172	c.972T>C	c.(970-972)gaT>gaC	p.D324D	ZC3H18_ENST00000452588.2_Silent_p.D348D	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	324						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		AGGAGCCTGATTTTGAAGAGA	0.413																																					p.D324D	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.T972C						.						141	162	155					16																	88666240		2198	4300	6498	SO:0001819	synonymous_variant	124245	exon6			GCCTGATTTTGAA	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.972T>C	chr16.hg19:g.88666240T>C		106.0	0.0		64.0	4.0	NM_144604	Q96DG4|Q96MP7	Silent	SNP	ENST00000301011.5	hg19	CCDS10967.1																																																																																			.	.		0.413	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		C	88666240	T	C	88666240	2	2	100	1	0	0	0	0	0	0	0	1	17583	1490	52	2		2	ZC3H18	16	88666240	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	16530777	88666240	1688513	212	13781										
FBXO39	162517	hgsc.bcm.edu	37	chr17	6690124	6690124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aacttgtgaattcaacaacaAccatgagtcactcgacgagg	8	10	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:6690124A>G	ENST00000321535.4	+	3	1179	c.1049A>G	c.(1048-1050)aAc>aGc	p.N350S		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	350										NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	26						TTCAACAACAACCATGAGTCA	0.448																																					p.N350S		Atlas-SNP	.											.	FBXO39	50	.	0			c.A1049G						.						93	80	85					17																	6690124		2203	4300	6503	SO:0001583	missense	162517	exon3			ACAACAACCATGA	BC034782	CCDS11082.1	17p13.2	2014-01-21			ENSG00000177294	ENSG00000177294		"F-boxes /  "other""	28565	protein-coding gene	gene with protein product		609106				12477932	Standard	NM_153230		Approved	MGC35179, Fbx39, CT144	uc010vtg.2	Q8N4B4	OTTHUMG00000102062	ENST00000321535.4:c.1049A>G	chr17.hg19:g.6690124A>G	ENSP00000321386:p.Asn350Ser	177.0	0.0		114.0	5.0	NM_153230		Missense_Mutation	SNP	ENST00000321535.4	hg19	CCDS11082.1	.	.	.	.	.	.	.	.	.	.	A	11.39	1.625680	0.28889	.	.	ENSG00000177294	ENST00000321535	T	0.52526	0.66	5.36	5.36	0.76844	.	0.082472	0.51477	D	0.000082	T	0.49064	0.1535	N	0.19112	0.55	0.31606	N	0.652053	D	0.63880	0.993	D	0.68192	0.956	T	0.50558	-0.8814	10	0.19590	T	0.45	-28.0565	12.0193	0.53333	1.0:0.0:0.0:0.0	.	350	Q8N4B4	FBX39_HUMAN	S	350	ENSP00000321386:N350S	ENSP00000321386:N350S	N	+	2	0	FBXO39	6630848	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	1.315000	0.33608	2.163000	0.67991	0.528000	0.53228	AAC	.	.		0.448	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230		G	6690124	A	G	6690124	3	3	100	1	0	0	0	0	1	0	0	0	5755	43	2	2	1055	2	FBXO39	17	6690124	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		6690124	74505086	213	13782										
ALOXE3	59344	hgsc.bcm.edu	37	chr17	8006758	8006758	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtggtccccttggtctggggTgggggctgcctcatggatga	18	9	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:8006758T>C	ENST00000448843.2	-	15	2179	c.1839A>G	c.(1837-1839)ccA>ccG	p.P613P	ALOXE3_ENST00000380149.1_Silent_p.P769P|ALOXE3_ENST00000318227.3_Silent_p.P745P	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3	613	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|fat cell differentiation (GO:0045444)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|sensory perception of pain (GO:0019233)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)	hepoxilin A3 synthase activity (GO:0051120)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	31						TGGTCTGGGGTGGGGGCTGCC	0.577																																					p.P745P		Atlas-SNP	.											.	ALOXE3	145	.	0			c.A2235G						.						104	93	97					17																	8006758		2203	4300	6503	SO:0001819	synonymous_variant	59344	exon15			CTGGGGTGGGGGC	AJ269499	CCDS11130.1, CCDS54084.1	17p13.1	2009-07-10			ENSG00000179148	ENSG00000179148	1.13.11.-	"Arachidonate lipoxygenases"	13743	protein-coding gene	gene with protein product		607206					Standard	NM_021628		Approved	eLOX3, E-LOX	uc010vuo.2	Q9BYJ1	OTTHUMG00000108179	ENST00000448843.2:c.1839A>G	chr17.hg19:g.8006758T>C		167.0	0.0		117.0	5.0	NM_001165960	B2R981|B7Z3W0|Q3ZB74|Q9H4F2|Q9HC22	Silent	SNP	ENST00000448843.2	hg19	CCDS11130.1																																																																																			.	.		0.577	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1			C	8006758	T	C	8006758	2	2	100	1	0	0	0	0	0	0	0	1	542	1683	59	2		2	ALOXE3	17	8006758	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1316634	8006758	73188452	214	13783										
ULK2	9706	hgsc.bcm.edu	37	chr17	19705089	19705089	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctgtttttaaactctacttaCccaaaggggaaggtgagtaa	9	7	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:19705089C>A	ENST00000395544.4	-	16	1941		c.e16+1		ULK2_ENST00000361658.2_Splice_Site|ULK2_ENST00000580130.1_Splice_Site	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2						autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					ACTCTACTTACCCAAAGGGGA	0.463																																					.		Atlas-SNP	.											.	ULK2	142	.	0			c.1441+1G>T						.						123	124	124					17																	19705089		2203	4300	6503	SO:0001630	splice_region_variant	9706	exon17			TACTTACCCAAAG	AB014523	CCDS11213.1	17p11.2	2014-02-12	2013-07-02		ENSG00000083290	ENSG00000083290	2.7.11.1		13480	protein-coding gene	gene with protein product		608650	"unc-51 (C. elegans)-like kinase 2", "unc-51-like kinase 2 (C. elegans)"			10557072	Standard	NM_014683		Approved	KIAA0623, Unc51.2, ATG1B	uc002gwn.3	Q8IYT8	OTTHUMG00000059511	ENST00000395544.4:c.1441+1G>T	chr17.hg19:g.19705089C>A		98.0	0.0		71.0	8.0	NM_014683	A8MY69|O75119	Splice_Site	SNP	ENST00000395544.4	hg19	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.993195	0.74703	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	.	.	.	5.6	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9996	0.71462	0.1434:0.8566:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ULK2	19645681	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.261000	0.78400	1.354000	0.45846	0.655000	0.94253	.	.	.		0.463	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683	Intron	A	19705089	C	A	19705089	5	1	100	1	0	0	0	0	0	0	1	0	16991	521	18	3	1716	3	ULK2	17	19705089	Splice_Site	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	11698331	19705089	61490121	215	13784										
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28378143	28378143	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cttctttgcttaggtagggtTtttggatcggcagaggacat	13	6	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:28378143T>C	ENST00000394835.3	+	9	1400	c.1208T>C	c.(1207-1209)tTt>tCt	p.F403S	EFCAB5_ENST00000378738.3_Missense_Mutation_p.F403S|EFCAB5_ENST00000536908.2_Missense_Mutation_p.F347S|EFCAB5_ENST00000320856.5_Missense_Mutation_p.F403S|EFCAB5_ENST00000394832.2_Missense_Mutation_p.F403S|EFCAB5_ENST00000541045.1_Missense_Mutation_p.F60S	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	403							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TAGGTAGGGTTTTTGGATCGG	0.398																																					p.F403S		Atlas-SNP	.											EFCAB5,colon,carcinoma,0,1	EFCAB5	122	.	0			c.T1208C						.						103	90	94					17																	28378143		1862	4093	5955	SO:0001583	missense	374786	exon9			TAGGGTTTTTGGA	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.1208T>C	chr17.hg19:g.28378143T>C	ENSP00000378312:p.Phe403Ser	140.0	0.0		68.0	3.0	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	hg19	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	T	15.76	2.927781	0.52759	.	.	ENSG00000176927	ENST00000536908;ENST00000534836;ENST00000541045;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598;ENST00000419434	T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.48	3.23	0.37069	.	0.933792	0.08894	N	0.878280	T	0.54902	0.1887	M	0.66939	2.045	0.22050	N	0.999396	P;P;D;D;B;P	0.59767	0.842;0.902;0.986;0.986;0.225;0.763	B;B;P;P;B;B	0.53035	0.185;0.342;0.59;0.716;0.048;0.387	T	0.35201	-0.9798	10	0.35671	T	0.21	-1.0477	6.1085	0.20087	0.0:0.088:0.1643:0.7477	.	347;347;403;403;403;403	B4DS75;F5GYL2;A8MSY9;B5MEA3;E7EVS9;A4FU69	.;.;.;.;.;EFCB5_HUMAN	S	347;146;60;403;403;403;403;347;209	ENSP00000440619:F347S;ENSP00000445575:F60S;ENSP00000378312:F403S;ENSP00000322003:F403S;ENSP00000378309:F403S;ENSP00000368012:F403S;ENSP00000417009:F209S	ENSP00000322003:F403S	F	+	2	0	EFCAB5	25402269	1.000000	0.71417	0.507000	0.27676	0.699000	0.40488	2.519000	0.45546	0.364000	0.24374	0.533000	0.62120	TTT	.	.		0.398	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		C	28378143	T	C	28378143	3	2	100	1	0	0	0	0	1	0	0	0	4940	1841	64	2	1242	2	EFCAB5	17	28378143	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	8673054	28378143	52817067	216	13785										
TCAP	8557	hgsc.bcm.edu	37	chr17	37822111	37822111	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgcaggagtaccagctgcccTaccagcgggtactgccgctg	13	14	0	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:37822111T>C	ENST00000309889.2	+	2	1426	c.253T>C	c.(253-255)Tac>Cac	p.Y85H	PNMT_ENST00000269582.2_5'Flank|PNMT_ENST00000581428.1_5'Flank|TCAP_ENST00000578283.1_Missense_Mutation_p.Y61H|PNMT_ENST00000394246.1_5'Flank			O15273	TELT_HUMAN	titin-cap	85					adult heart development (GO:0007512)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of mechanical stimulus (GO:0050982)|detection of muscle stretch (GO:0035995)|muscle filament sliding (GO:0030049)|otic vesicle formation (GO:0030916)|protein complex assembly (GO:0006461)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle contraction (GO:0003009)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)	cytosol (GO:0005829)|I band (GO:0031674)|Z disc (GO:0030018)	FATZ binding (GO:0051373)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			kidney(1)|lung(1)	2	all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCAGCTGCCCTACCAGCGGGT	0.677																																					p.Y85H		Atlas-SNP	.											.	TCAP	12	.	0			c.T253C						.						20	20	20					17																	37822111		2198	4292	6490	SO:0001583	missense	8557	exon2			CTGCCCTACCAGC	AJ000491	CCDS11342.1	17q12	2014-09-17	2012-09-20		ENSG00000173991	ENSG00000173991			11610	protein-coding gene	gene with protein product	"19 kDa sarcomeric protein"	604488	"limb girdle muscular dystrophy 2G (autosomal recessive)", "titin-cap (telethonin)"	LGMD2G		9350988, 9817758	Standard	NM_003673		Approved	T-cap, TELE, telethonin, CMD1N	uc002hsh.3	O15273	OTTHUMG00000133215	ENST00000309889.2:c.253T>C	chr17.hg19:g.37822111T>C	ENSP00000312624:p.Tyr85His	56.0	0.0		43.0	8.0	NM_003673	Q96L27	Missense_Mutation	SNP	ENST00000309889.2	hg19	CCDS11342.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.234409	0.39498	.	.	ENSG00000173991	ENST00000309889	D	0.88201	-2.35	5.71	5.71	0.89125	.	0.125315	0.53938	D	0.000047	D	0.90817	0.7116	L	0.29908	0.895	0.51482	D	0.999924	D	0.76494	0.999	D	0.72338	0.977	D	0.92096	0.5684	10	0.87932	D	0	-27.7638	14.9524	0.71086	0.0:0.0:0.0:1.0	.	85	O15273	TELT_HUMAN	H	85	ENSP00000312624:Y85H	ENSP00000312624:Y85H	Y	+	1	0	TCAP	35075637	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.142000	0.64820	2.176000	0.68965	0.379000	0.24179	TAC	.	.		0.677	TCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256942.1	NM_003673		C	37822111	T	C	37822111	3	2	100	1	0	0	0	0	1	0	0	0	15681	1522	53	2	259	2	TCAP	17	37822111	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	9443968	37822111	43373099	217	13786										
BRCA1	672	hgsc.bcm.edu	37	chr17	41228506	41228506	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttacattgatgtttcttaccTttccactcctggttctttat	4	10	2	1	rs80357854		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:41228506T>C	ENST00000357654.3	-	13	4601	c.4483A>G	c.(4483-4485)Agg>Ggg	p.R1495G	BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000352993.3_Splice_Site_p.R353G|BRCA1_ENST00000471181.2_Splice_Site_p.R1516G|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000346315.3_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000354071.3_Intron|BRCA1_ENST00000351666.3_Splice_Site_p.R312G|BRCA1_ENST00000309486.4_Splice_Site_p.R1199G|BRCA1_ENST00000468300.1_Splice_Site_p.R391G|BRCA1_ENST00000493795.1_Splice_Site_p.R1448G|BRCA1_ENST00000491747.2_Splice_Site_p.R391G	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1495			R -> M (in BC; unknown pathological significance). {ECO:0000269|PubMed:17924331}.		androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GTTTCTTACCTTTCCACTCCT	0.353			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.R1516G		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.A4546G	GRCh37	CD984132	BRCA1	D	rs80357854	.						121	111	114					17																	41228506		2202	4300	6502	SO:0001630	splice_region_variant	672	exon14	Familial Cancer Database		CTTACCTTTCCAC	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.4484+1A>G	chr17.hg19:g.41228506T>C		161.0	0.0		84.0	4.0	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	hg19	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	T	9.996	1.232259	0.22626	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000352993;ENST00000351666;ENST00000309486;ENST00000468300;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747;ENST00000478531;ENST00000484087;ENST00000493919	D;D;D;D;D;D;D;D;D;D	0.90324	-2.26;-2.33;-2.47;-2.16;-2.23;-2.65;-2.38;-2.11;-1.88;-2.3	4.97	1.4	0.22301	.	0.486738	0.19146	N	0.121561	D	0.89164	0.6637	L	0.36672	1.1	0.30091	N	0.808308	D;P;B;B;B;B;B;B	0.54601	0.967;0.688;0.024;0.043;0.024;0.024;0.094;0.09	D;B;B;B;B;B;B;B	0.63597	0.916;0.138;0.012;0.021;0.012;0.012;0.049;0.046	T	0.82259	-0.0546	10	0.42905	T	0.14	-0.4238	3.3868	0.07274	0.0:0.2164:0.2066:0.577	.	391;344;390;392;391;1517;1495;1495	E7EUM2;B4DES0;E7ETR2;P38398-3;Q6IN79;E9PFC7;P38398;P38398-2	.;.;.;.;.;.;BRCA1_HUMAN;.	G	1495;1516;353;312;1199;391;344;1517;1448;390;391;266;345	ENSP00000350283:R1495G;ENSP00000312236:R353G;ENSP00000338007:R312G;ENSP00000310938:R1199G;ENSP00000417148:R391G;ENSP00000377294:R344G;ENSP00000418775:R1448G;ENSP00000420412:R391G;ENSP00000419481:R266G;ENSP00000418819:R345G	ENSP00000310938:R1199G	R	-	1	2	BRCA1	38482032	0.985000	0.35326	0.941000	0.38009	0.421000	0.31385	0.494000	0.22467	0.366000	0.24427	0.459000	0.35465	AGG	.	.		0.353	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	Missense_Mutation	C	41228506	T	C	41228506	5	2	100	1	0	0	0	0	0	0	1	0	1500	1623	56	2	1152	2	BRCA1	17	41228506	Splice_Site	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	3406395	41228506	39966704	218	13787										
STXBP4	252983	hgsc.bcm.edu	37	chr17	53155463	53155463	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtgttcaggatttaaaaaagAgaatcatggtactcgactgc	10	6	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:53155463A>G	ENST00000376352.2	+	14	1420	c.1213A>G	c.(1213-1215)Aga>Gga	p.R405G	STXBP4_ENST00000434978.2_Missense_Mutation_p.R383G	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	405					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						TTTAAAAAAGAGAATCATGGT	0.348																																					p.R405G		Atlas-SNP	.											.	STXBP4	41	.	0			c.A1213G						.						82	84	83					17																	53155463		2203	4300	6503	SO:0001583	missense	252983	exon14			AAAAAGAGAATCA	BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.1213A>G	chr17.hg19:g.53155463A>G	ENSP00000365530:p.Arg405Gly	154.0	0.0		121.0	5.0	NM_178509	Q8IVZ5	Missense_Mutation	SNP	ENST00000376352.2	hg19	CCDS11584.2	.	.	.	.	.	.	.	.	.	.	A	21.6	4.166225	0.78339	.	.	ENSG00000166263	ENST00000376352;ENST00000434978	T;T	0.54866	0.55;0.55	5.33	4.24	0.50183	.	0.042741	0.85682	D	0.000000	T	0.72095	0.3418	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.962	T	0.75263	-0.3379	10	0.87932	D	0	-18.8204	12.0609	0.53562	0.8559:0.1441:0.0:0.0	.	383;405	E7EPP7;Q6ZWJ1	.;STXB4_HUMAN	G	405;383	ENSP00000365530:R405G;ENSP00000391087:R383G	ENSP00000365530:R405G	R	+	1	2	STXBP4	50510462	1.000000	0.71417	0.998000	0.56505	0.882000	0.50991	6.265000	0.72534	0.948000	0.37687	0.533000	0.62120	AGA	.	.		0.348	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509		G	53155463	A	G	53155463	3	3	100	1	0	0	0	0	1	0	0	0	15370	296	11	2	1259	2	STXBP4	17	53155463	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	11926957	53155463	28039747	219	13788										
ANKFN1	162282	hgsc.bcm.edu	37	chr17	54428134	54428134	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttcctcttcttaggaattgtCgtgtgaaaatgacgcaacaa	8	8	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:54428134C>T	ENST00000318698.2	+	4	240	c.205C>T	c.(205-207)Cgt>Tgt	p.R69C	ANKFN1_ENST00000566473.2_Missense_Mutation_p.R69C	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	69								p.R69C(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						TAGGAATTGTCGTGTGAAAAT	0.383																																					p.R69C		Atlas-SNP	.											ANKFN1,rectum,carcinoma,0,1	ANKFN1	115	.	1	Substitution - Missense(1)	large_intestine(1)	c.C205T						.						89	89	89					17																	54428134		2203	4300	6503	SO:0001583	missense	162282	exon4			AATTGTCGTGTGA	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.205C>T	chr17.hg19:g.54428134C>T	ENSP00000321627:p.Arg69Cys	106.0	0.0		49.0	2.0	NM_153228		Missense_Mutation	SNP	ENST00000318698.2	hg19	CCDS32686.1	.	.	.	.	.	.	.	.	.	.	c	7.864	0.726604	0.15439	.	.	ENSG00000153930	ENST00000318698	T	0.23348	1.91	5.57	-6.12	0.02124	.	1.490830	0.03541	N	0.223895	T	0.19644	0.0472	L	0.29908	0.895	0.27876	N	0.939853	B	0.02656	0.0	B	0.01281	0.0	T	0.20042	-1.0287	10	0.46703	T	0.11	.	12.1817	0.54216	0.0:0.3146:0.0821:0.6034	.	69	Q8N957	ANKF1_HUMAN	C	69	ENSP00000321627:R69C	ENSP00000321627:R69C	R	+	1	0	ANKFN1	51783133	0.000000	0.05858	0.002000	0.10522	0.547000	0.35210	-1.502000	0.02279	-2.206000	0.00741	-1.739000	0.00688	CGT	.	.		0.383	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		T	54428134	C	T	54428134	3	4	100	1	0	0	0	0	1	0	0	0	625	884	31	1	219	1	ANKFN1	17	54428134	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	1272671	54428134	26767076	220	13789										
SEPT4	5414	hgsc.bcm.edu	37	chr17	56598359	56598359	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtcctggcttctggtcatacTtgcgattccgttccttcacc	8	14	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:56598359T>C	ENST00000317268.3	-	10	1453	c.1277A>G	c.(1276-1278)aAc>aGc	p.N426S	SEPT4_ENST00000426861.1_3'UTR|SEPT4_ENST00000412945.3_Splice_Site_p.N418S|SEPT4_ENST00000457347.2_Splice_Site_p.N441S|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000579371.1_Splice_Site_p.K327R|SEPT4_ENST00000317256.6_Splice_Site_p.N407S|SEPT4_ENST00000393086.1_Splice_Site_p.N407S|SEPT4_ENST00000583114.1_Splice_Site_p.N279S|SEPT4_ENST00000580844.1_Splice_Site_p.N327S	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	426					apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTGGTCATACTTGCGATTCCG	0.557											OREG0024614	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N441S		Atlas-SNP	.											.	SEPT4	48	.	0			c.A1322G						.						151	133	139					17																	56598359		2203	4300	6503	SO:0001630	splice_region_variant	5414	exon11			TCATACTTGCGAT	AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"Septins"	9165	protein-coding gene	gene with protein product	"bradeoin", "septin-M"	603696	"peanut-like 2 (Drosophila)"	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.1277+1A>G	chr17.hg19:g.56598359T>C		152.0	0.0	1016	94.0	5.0	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Missense_Mutation	SNP	ENST00000317268.3	hg19	CCDS11610.1	.	.	.	.	.	.	.	.	.	.	T	11.01	1.513060	0.27123	.	.	ENSG00000108387	ENST00000412945;ENST00000457347;ENST00000317256;ENST00000317268;ENST00000393086	T;T;T;T	0.50548	0.74;0.75;0.74;0.75	5.59	5.59	0.84812	.	0.094954	0.64402	D	0.000001	T	0.38904	0.1058	L	0.33189	0.99	0.58432	D	0.999992	B;P;B;B;B	0.44429	0.002;0.835;0.002;0.003;0.001	B;B;B;B;B	0.41271	0.011;0.352;0.011;0.006;0.005	T	0.17198	-1.0377	9	.	.	.	.	14.0047	0.64456	0.0:0.0:0.0:1.0	.	418;441;407;279;426	O43236-3;O43236-4;O43236-2;O43236-5;O43236	.;.;.;.;SEPT4_HUMAN	S	418;440;407;426;407	ENSP00000414779:N418S;ENSP00000321071:N407S;ENSP00000321674:N426S;ENSP00000376801:N407S	.	N	-	2	0	SEPT4	53953358	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.151000	0.58105	2.231000	0.72958	0.533000	0.62120	AAC	.	.		0.557	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417	Missense_Mutation	C	56598359	T	C	56598359	5	2	100	1	0	0	0	0	0	0	1	0	14081	1623	56	2	171	2	SEPT4	17	56598359	Splice_Site	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2170225	56598359	24596851	221	13790										
SLC39A11	201266	hgsc.bcm.edu	37	chr17	71027829	71027829	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aactgctggggccagaagagAccaataggaagctgccaaca	12	10	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:71027829A>G	ENST00000542342.2	-	4	260	c.172T>C	c.(172-174)Tct>Cct	p.S58P	SLC39A11_ENST00000255559.3_Missense_Mutation_p.S58P|SLC39A11_ENST00000579732.1_Missense_Mutation_p.S58P	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	58					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			endometrium(1)|large_intestine(4)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						GCCAGAAGAGACCAATAGGAA	0.537																																					p.S58P	NSCLC(95;736 1527 12296 39625 41839)	Atlas-SNP	.											.	SLC39A11	32	.	0			c.T172C						.						125	110	115					17																	71027829		2203	4300	6503	SO:0001583	missense	201266	exon4			GAAGAGACCAATA	AF331643	CCDS11690.1, CCDS54160.1	17q24.3-q25.1	2014-08-12	2013-07-17	2003-10-24	ENSG00000133195	ENSG00000133195		"Solute carriers"	14463	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 26"	C17orf26		11707075	Standard	NM_139177		Approved		uc002jjb.3	Q8N1S5	OTTHUMG00000178306	ENST00000542342.2:c.172T>C	chr17.hg19:g.71027829A>G	ENSP00000445829:p.Ser58Pro	125.0	0.0		64.0	5.0	NM_001159770	B2R8H7|Q8WZ81	Missense_Mutation	SNP	ENST00000542342.2	hg19	CCDS54160.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.572696	0.86542	.	.	ENSG00000133195	ENST00000542342;ENST00000255559	T;T	0.50277	0.75;0.75	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.76471	0.3992	H	0.94658	3.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83588	0.0121	10	0.87932	D	0	.	13.7113	0.62670	1.0:0.0:0.0:0.0	.	58;58	Q8N1S5;Q8N1S5-2	S39AB_HUMAN;.	P	58	ENSP00000445829:S58P;ENSP00000255559:S58P	ENSP00000255559:S58P	S	-	1	0	SLC39A11	68539424	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	8.105000	0.89553	1.923000	0.55706	0.533000	0.62120	TCT	.	.		0.537	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1			G	71027829	A	G	71027829	3	3	100	1	0	0	0	0	1	0	0	0	14629	275	10	2	884	2	SLC39A11	17	71027829	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	14429470	71027829	10167381	222	13791										
OTOP3	347741	hgsc.bcm.edu	37	chr17	72939421	72939421	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctgcaaagactgtgttcgggTccagaccaacttcactaggt	10	11	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:72939421T>C	ENST00000328801.4	+	4	668	c.668T>C	c.(667-669)gTc>gCc	p.V223A		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	223						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					TGTGTTCGGGTCCAGACCAAC	0.597																																					p.V223A		Atlas-SNP	.											.	OTOP3	64	.	0			c.T668C						.						142	135	137					17																	72939421		2203	4300	6503	SO:0001583	missense	347741	exon4			TTCGGGTCCAGAC	BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.668T>C	chr17.hg19:g.72939421T>C	ENSP00000328090:p.Val223Ala	137.0	0.0		100.0	4.0	NM_178233		Missense_Mutation	SNP	ENST00000328801.4	hg19	CCDS11709.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.609288	0.46527	.	.	ENSG00000182938	ENST00000328801	T	0.08546	3.08	5.27	5.27	0.74061	.	0.508988	0.18406	N	0.142192	T	0.08891	0.0220	L	0.50333	1.59	0.37078	D	0.898867	P	0.40909	0.732	B	0.33846	0.171	T	0.16928	-1.0386	10	0.52906	T	0.07	-7.4115	11.5673	0.50813	0.0:0.0:0.0:1.0	.	223	Q7RTS5	OTOP3_HUMAN	A	223	ENSP00000328090:V223A	ENSP00000328090:V223A	V	+	2	0	OTOP3	70451016	1.000000	0.71417	0.996000	0.52242	0.928000	0.56348	3.577000	0.53885	1.987000	0.57996	0.460000	0.39030	GTC	.	.		0.597	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233		C	72939421	T	C	72939421	3	2	100	1	0	0	0	0	1	0	0	0	11316	1667	58	2	682	2	OTOP3	17	72939421	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1911592	72939421	8255789	223	13792										
UNK	85451	hgsc.bcm.edu	37	chr17	73820373	73820373	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	acatgcagtcggtgaaatgcCttaagtgtcaggaacagaag	12	7	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:73820373C>T	ENST00000589666.1	+	16	2418	c.2308C>T	c.(2308-2310)Ctt>Ttt	p.L770F	UNK_ENST00000293218.3_Missense_Mutation_p.L846F	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	770							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.L846I(1)|p.L770I(1)		cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGTGAAATGCCTTAAGTGTCA	0.617																																					p.L770F		Atlas-SNP	.											UNK_ENST00000293218,NS,carcinoma,0,2	UNK	87	.	2	Substitution - Missense(2)	endometrium(2)	c.C2308T						.						41	42	41					17																	73820373		2125	4243	6368	SO:0001583	missense	85451	exon16			AAATGCCTTAAGT	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"Zinc fingers, CCCH-type domain containing"	29369	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 5", "zinc finger CCCH-type containing 5", "unkempt homolog (Drosophila)"	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.2308C>T	chr17.hg19:g.73820373C>T	ENSP00000464893:p.Leu770Phe	54.0	0.0		37.0	3.0	NM_001080419		Missense_Mutation	SNP	ENST00000589666.1	hg19	CCDS45778.2	.	.	.	.	.	.	.	.	.	.	C	21.2	4.107085	0.77096	.	.	ENSG00000132478	ENST00000293218	.	.	.	4.91	4.91	0.64330	Zinc finger, RING-type (1);	0.296899	0.31859	N	0.006956	T	0.53948	0.1828	L	0.51422	1.61	0.42428	D	0.992668	P	0.44578	0.838	B	0.38562	0.276	T	0.62609	-0.6818	9	0.59425	D	0.04	-4.3399	18.3073	0.90187	0.0:1.0:0.0:0.0	.	770	Q9C0B0	UNK_HUMAN	F	846	.	ENSP00000293218:L846F	L	+	1	0	UNK	71331968	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.602000	0.54066	2.561000	0.86390	0.563000	0.77884	CTT	.	.		0.617	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		T	73820373	C	T	73820373	3	4	100	1	0	0	0	0	1	0	0	0	17015	681	24	3	2602	3	UNK	17	73820373	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	880952	73820373	7374837	224	13793										
TMC8	147138	hgsc.bcm.edu	37	chr17	76134220	76134220	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cctcttctactgccccctgcTgcccctgctgaatagcgtct	7	18	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:76134220T>C	ENST00000318430.5	+	12	1858	c.1484T>C	c.(1483-1485)cTg>cCg	p.L495P	TMC8_ENST00000589691.1_Missense_Mutation_p.L272P	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	495					ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			TGCCCCCTGCTGCCCCTGCTG	0.617																																					p.L495P		Atlas-SNP	.											.	TMC8	44	.	0			c.T1484C						.						91	91	91					17																	76134220		2203	4300	6503	SO:0001583	missense	147138	exon12			CCCTGCTGCCCCT	AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"epidermodysplasia verruciformis 2"	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.1484T>C	chr17.hg19:g.76134220T>C	ENSP00000325561:p.Leu495Pro	162.0	0.0		112.0	5.0	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Missense_Mutation	SNP	ENST00000318430.5	hg19	CCDS32749.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.403403	0.83230	.	.	ENSG00000167895	ENST00000318430	T	0.79845	-1.31	4.57	4.57	0.56435	.	0.000000	0.64402	D	0.000001	D	0.90789	0.7108	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92549	0.6048	10	0.87932	D	0	-16.866	13.1778	0.59637	0.0:0.0:0.0:1.0	.	495	Q8IU68	TMC8_HUMAN	P	495	ENSP00000325561:L495P	ENSP00000325561:L495P	L	+	2	0	TMC8	73645815	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.948000	0.75965	1.814000	0.52955	0.460000	0.39030	CTG	.	.		0.617	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3			C	76134220	T	C	76134220	3	2	100	1	0	0	0	0	1	0	0	0	16006	1580	55	2	1526	2	TMC8	17	76134220	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2313847	76134220	5060990	225	13794										
LRRC45	201255	hgsc.bcm.edu	37	chr17	79986334	79986334	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gctgttccagaccaggcaggAgatgaccagcatgtcagctg	13	11	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr17:79986334A>G	ENST00000306688.3	+	11	1529	c.1187A>G	c.(1186-1188)gAg>gGg	p.E396G		NM_144999.2	NP_659436.1	Q96CN5	LRC45_HUMAN	leucine rich repeat containing 45	396						centrosome (GO:0005813)				lung(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	5	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			ACCAGGCAGGAGATGACCAGC	0.662																																					p.E396G		Atlas-SNP	.											.	LRRC45	22	.	0			c.A1187G						.						39	42	41					17																	79986334		2195	4297	6492	SO:0001583	missense	201255	exon11			GGCAGGAGATGAC	BC014109	CCDS11797.1	17q25.3	2005-08-09				ENSG00000169683			28302	protein-coding gene	gene with protein product						12477932	Standard	NM_144999		Approved	MGC20806	uc002kde.3	Q96CN5		ENST00000306688.3:c.1187A>G	chr17.hg19:g.79986334A>G	ENSP00000306760:p.Glu396Gly	148.0	0.0		85.0	4.0	NM_144999		Missense_Mutation	SNP	ENST00000306688.3	hg19	CCDS11797.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.830009	0.71258	.	.	ENSG00000169683	ENST00000306688	T	0.45668	0.89	3.93	3.93	0.45458	.	0.225630	0.37623	N	0.002019	T	0.45115	0.1326	M	0.71581	2.175	0.51233	D	0.999912	P	0.46395	0.877	B	0.43360	0.417	T	0.49457	-0.8938	9	.	.	.	-23.238	12.9226	0.58241	1.0:0.0:0.0:0.0	.	396	Q96CN5	LRC45_HUMAN	G	396	ENSP00000306760:E396G	.	E	+	2	0	LRRC45	77579623	1.000000	0.71417	1.000000	0.80357	0.582000	0.36321	8.767000	0.91732	1.641000	0.50575	0.459000	0.35465	GAG	.	.		0.662	LRRC45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442058.1	NM_144999		G	79986334	A	G	79986334	3	3	100	1	0	0	0	0	1	0	0	0	9011	304	11	2	1229	2	LRRC45	17	79986334	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	3852114	79986334	1208876	226	13795										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2728556	2728556	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aagttttagatgaatcagacAacataacagcacaaccaaaa	5	8	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr18:2728556A>G	ENST00000320876.6	+	23	3213	c.2875A>G	c.(2875-2877)Aac>Gac	p.N959D	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.N959D|SMCHD1_ENST00000609587.1_3'UTR	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	959					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TGAATCAGACAACATAACAGC	0.348																																					p.N959D		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A2875G						.						106	101	103					18																	2728556		1858	4098	5956	SO:0001583	missense	23347	exon23			TCAGACAACATAA	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.2875A>G	chr18.hg19:g.2728556A>G	ENSP00000326603:p.Asn959Asp	124.0	0.0		81.0	5.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.567745	0.86439	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.46451	0.87;0.9	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.62612	0.2442	M	0.63843	1.955	0.38022	D	0.934897	D	0.69078	0.997	D	0.73380	0.98	T	0.68796	-0.5314	10	0.72032	D	0.01	-20.6615	16.226	0.82293	1.0:0.0:0.0:0.0	.	959	A6NHR9	SMHD1_HUMAN	D	959	ENSP00000326603:N959D;ENSP00000261598:N959D	ENSP00000261598:N959D	N	+	1	0	SMCHD1	2718556	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.748000	0.74877	2.230000	0.72887	0.528000	0.53228	AAC	.	.		0.348	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			G	2728556	A	G	2728556	3	3	100	1	0	0	0	0	1	0	0	0	14803	130	5	2	2965	2	SMCHD1	18	2728556	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		2728556	75348692	227	13796										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7016513	7016513	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tacagctaccatcctggtagGcgtagaagccatgggcacac	11	12	0	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr18:7016513G>T	ENST00000389658.3	-	21	3059	c.2966C>A	c.(2965-2967)gCc>gAc	p.A989D		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	989	Laminin EGF-like 10. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				ATCCTGGTAGGCGTAGAAGCC	0.542																																					p.A989D		Atlas-SNP	.											.	LAMA1	458	.	0			c.C2966A						.						143	99	114					18																	7016513		2203	4300	6503	SO:0001583	missense	284217	exon21			TGGTAGGCGTAGA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2966C>A	chr18.hg19:g.7016513G>T	ENSP00000374309:p.Ala989Asp	66.0	0.0		56.0	10.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	G	4.633	0.117620	0.08881	.	.	ENSG00000101680	ENST00000389658	T	0.61158	0.13	5.8	-0.853	0.10709	EGF-like, laminin (4);	0.296144	0.30732	N	0.008998	T	0.32734	0.0839	N	0.05608	-0.0099999999999999	0.09310	N	1	B	0.32653	0.379	B	0.34536	0.185	T	0.28933	-1.0028	10	0.59425	D	0.04	.	8.7892	0.34841	0.0587:0.4137:0.4202:0.1074	.	989	P25391	LAMA1_HUMAN	D	989	ENSP00000374309:A989D	ENSP00000374309:A989D	A	-	2	0	LAMA1	7006513	0.000000	0.05858	0.000000	0.03702	0.194000	0.23727	0.480000	0.22244	-0.143000	0.11334	-0.149000	0.13747	GCC	.	.		0.542	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	7016513	G	T	7016513	3	4	100	1	0	0	0	0	1	0	0	0	8614	1203	42	3	6433	3	LAMA1	18	7016513	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	4287957	7016513	71060735	228	13797										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8718551	8718551	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aaaactgccgaatcctgcagTaccgtcttcggaaagccgag	10	12	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr18:8718551T>C	ENST00000306329.11	+	2	1183	c.1183T>C	c.(1183-1185)Tac>Cac	p.Y395H	Y_RNA_ENST00000516510.1_RNA|SOGA2_ENST00000400050.3_Missense_Mutation_p.Y35H|SOGA2_ENST00000517570.1_Missense_Mutation_p.Y35H|SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000359865.3_Missense_Mutation_p.Y35H																							AATCCTGCAGTACCGTCTTCG	0.512																																					p.Y35H		Atlas-SNP	.											.	.	.	.	0			c.T103C						.						110	99	102					18																	8718551		2203	4300	6503	SO:0001583	missense	23255	exon3			CTGCAGTACCGTC																												ENST00000306329.11:c.1183T>C	chr18.hg19:g.8718551T>C	ENSP00000305027:p.Tyr395His	119.0	0.0		81.0	5.0	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	hg19		.	.	.	.	.	.	.	.	.	.	T	28.7	4.944215	0.92593	.	.	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050	T;T;T	0.77620	-1.11;-1.11;-1.11	5.01	5.01	0.66863	.	0.000000	0.43747	D	0.000536	D	0.85243	0.5652	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83306	-0.0025	10	0.27082	T	0.32	-28.2908	14.8775	0.70504	0.0:0.0:0.0:1.0	.	35	Q9Y4B5-3	.	H	56;35;35;35	ENSP00000429556:Y35H;ENSP00000352927:Y35H;ENSP00000382924:Y35H	ENSP00000305027:Y56H	Y	+	1	0	CCDC165	8708551	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.868000	0.87116	2.100000	0.63781	0.460000	0.39030	TAC	.	.		0.512	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			C	8718551	T	C	8718551	3	2	100	1	0	0	0	0	1	0	0	0	8203	1638	57	2	105	2	KIAA0802	18	8718551	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1702038	8718551	69358697	229	13798										
IMPACT	55364	hgsc.bcm.edu	37	chr18	22029801	22029801	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agattttgaatgtgaagaatGtcatggtggtagtatcacgc	12	4	2	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr18:22029801G>A	ENST00000284202.4	+	10	919	c.778G>A	c.(778-780)Gtc>Atc	p.V260I		NM_018439.3	NP_060909	Q9P2X3	IMPCT_HUMAN	impact RWD domain protein	260					negative regulation of protein phosphorylation (GO:0001933)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(2)	16	all_cancers(21;0.00018)|all_epithelial(16;1.5e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)					TGTGAAGAATGTCATGGTGGT	0.348																																					p.V260I		Atlas-SNP	.											.	IMPACT	37	.	0			c.G778A						.						101	91	94					18																	22029801		2203	4300	6503	SO:0001583	missense	55364	exon10			AAGAATGTCATGG	AB026264	CCDS11886.1	18q11.2-q12.1	2012-12-07	2012-12-07		ENSG00000154059	ENSG00000154059			20387	protein-coding gene	gene with protein product	"RWD domain containing 5"	615319	"Impact homolog (mouse)"			11116084	Standard	NM_018439		Approved	RWDD5	uc002kvh.4	Q9P2X3	OTTHUMG00000131943	ENST00000284202.4:c.778G>A	chr18.hg19:g.22029801G>A	ENSP00000284202:p.Val260Ile	123.0	0.0		93.0	11.0	NM_018439	A8MXG0|Q49AM0|Q9H2X4	Missense_Mutation	SNP	ENST00000284202.4	hg19	CCDS11886.1	.	.	.	.	.	.	.	.	.	.	G	17.10	3.301790	0.60195	.	.	ENSG00000154059	ENST00000284202	T	0.46063	0.88	5.93	5.93	0.95920	Ribosomal protein S5 domain 2-type fold (1);Impact, N-terminal (2);Uncharacterised protein family UPF0029, Impact, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.53899	0.1825	M	0.62016	1.91	0.80722	D	1	P	0.44877	0.845	P	0.48654	0.585	T	0.53690	-0.8403	10	0.62326	D	0.03	.	19.1136	0.93328	0.0:0.0:1.0:0.0	.	260	Q9P2X3	IMPCT_HUMAN	I	260	ENSP00000284202:V260I	ENSP00000284202:V260I	V	+	1	0	IMPACT	20283799	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.250000	0.95477	2.810000	0.96702	0.655000	0.94253	GTC	.	.		0.348	IMPACT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254901.1	NM_018439		A	22029801	G	A	22029801	3	1	100	1	0	0	0	0	1	0	0	0	7733	1377	48	3	816	3	IMPACT	18	22029801	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	13311250	22029801	56047447	230	13799										
DSG3	1830	hgsc.bcm.edu	37	chr18	29045290	29045290	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttatgaaacagatatgtcatGggacgtaacgatggtggata	12	4	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr18:29045290G>C	ENST00000257189.4	+	10	1364	c.1281G>C	c.(1279-1281)atG>atC	p.M427I		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	427	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GATATGTCATGGGACGTAACG	0.264																																					p.M427I		Atlas-SNP	.											.	DSG3	172	.	0			c.G1281C						.						67	73	71					18																	29045290		2203	4300	6503	SO:0001583	missense	1830	exon10			TGTCATGGGACGT	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.1281G>C	chr18.hg19:g.29045290G>C	ENSP00000257189:p.Met427Ile	277.0	0.0		179.0	12.0	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	hg19	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	G	3.256	-0.152135	0.06585	.	.	ENSG00000134757	ENST00000257189	T	0.54479	0.57	5.82	4.94	0.65067	Cadherin (3);Cadherin-like (1);	0.234251	0.29722	N	0.011370	T	0.20861	0.0502	N	0.03000	-0.44	0.26889	N	0.967371	B	0.11235	0.004	B	0.10450	0.005	T	0.31194	-0.9952	10	0.02654	T	1	.	5.5788	0.17238	0.1735:0.1736:0.653:0.0	.	427	P32926	DSG3_HUMAN	I	427	ENSP00000257189:M427I	ENSP00000257189:M427I	M	+	3	0	DSG3	27299288	1.000000	0.71417	0.993000	0.49108	0.033000	0.12548	1.963000	0.40452	1.436000	0.47453	0.467000	0.42956	ATG	.	.		0.264	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		C	29045290	G	C	29045290	3	2	100	1	0	0	0	0	1	0	0	0	4780	1348	47	4	1319	4	DSG3	18	29045290	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	7015489	29045290	49031958	231	13800										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31320168	31320168	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aagggagtacacagagtcggTtagaaacctcacatacttcc	9	10	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr18:31320168T>C	ENST00000269197.5	+	11	2800	c.2800T>C	c.(2800-2802)Tta>Cta	p.L934L		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	934					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						ACAGAGTCGGTTAGAAACCTC	0.393																																					p.L934L		Atlas-SNP	.											ASXL3_ENST00000269197,caecum,carcinoma,0,2	ASXL3	405	.	0			c.T2800C						.						78	72	74					18																	31320168		1860	4096	5956	SO:0001819	synonymous_variant	80816	exon11			AGTCGGTTAGAAA	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.2800T>C	chr18.hg19:g.31320168T>C		137.0	1.0		120.0	6.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Silent	SNP	ENST00000269197.5	hg19	CCDS45847.1																																																																																			.	.		0.393	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			C	31320168	T	C	31320168	2	2	100	1	0	0	0	0	0	0	0	1	1068	1722	60	2		2	ASXL3	18	31320168	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2274878	31320168	46757080	232	13801										
SETBP1	26040	hgsc.bcm.edu	37	chr18	42281540	42281540	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	attccaactccaacgcggacAgtgagaaatgggtggcagga	13	9	0	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr18:42281540A>G	ENST00000282030.5	+	2	525	c.229A>G	c.(229-231)Agt>Ggt	p.S77G	SETBP1_ENST00000426838.4_Missense_Mutation_p.S77G	NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	77						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		CAACGCGGACAGTGAGAAATG	0.547									Schinzel-Giedion syndrome																												p.S77G		Atlas-SNP	.											.	SETBP1	577	.	0			c.A229G						.						104	91	96					18																	42281540		2203	4300	6503	SO:0001583	missense	26040	exon2	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	GCGGACAGTGAGA	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.229A>G	chr18.hg19:g.42281540A>G	ENSP00000282030:p.Ser77Gly	183.0	0.0		108.0	5.0	NM_001130110	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	hg19	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	A	18.72	3.685010	0.68157	.	.	ENSG00000152217	ENST00000426838;ENST00000282030;ENST00000552979	T	0.69435	-0.4	5.7	5.7	0.88788	.	0.049723	0.85682	D	0.000000	T	0.73984	0.3657	L	0.44542	1.39	0.36532	D	0.870788	P;D	0.69078	0.952;0.997	P;D	0.64042	0.57;0.921	T	0.76266	-0.3022	10	0.31617	T	0.26	.	15.9644	0.79956	1.0:0.0:0.0:0.0	.	77;77	Q9Y6X0;Q9Y6X0-2	SETBP_HUMAN;.	G	77	ENSP00000282030:S77G	ENSP00000282030:S77G	S	+	1	0	SETBP1	40535538	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.280000	0.65603	2.170000	0.68504	0.482000	0.46254	AGT	.	.		0.547	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		G	42281540	A	G	42281540	3	3	100	1	0	0	0	0	1	0	0	0	14144	188	7	2	231	2	SETBP1	18	42281540	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	10961372	42281540	35795708	233	13802										
PHLPP1	23239	hgsc.bcm.edu	37	chr18	60625874	60625874	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tttttcagtgtgtggacctgAgctgtaatgagctaagtgaa	12	5	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr18:60625874A>G	ENST00000262719.5	+	13	3571	c.3337A>G	c.(3337-3339)Agc>Ggc	p.S1113G	PHLPP1_ENST00000400316.4_Missense_Mutation_p.S601G			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	1113					apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						TGTGGACCTGAGCTGTAATGA	0.453																																					p.S1113G		Atlas-SNP	.											PHLPP1_ENST00000262719,colon,carcinoma,0,3	PHLPP1	164	.	0			c.A3337G						.						142	135	137					18																	60625874		1914	4128	6042	SO:0001583	missense	23239	exon13			GACCTGAGCTGTA	AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.3337A>G	chr18.hg19:g.60625874A>G	ENSP00000262719:p.Ser1113Gly	105.0	0.0		61.0	3.0	NM_194449	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Missense_Mutation	SNP	ENST00000262719.5	hg19	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	A	23.3	4.405207	0.83230	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	T;T	0.21932	1.98;1.98	5.36	5.36	0.76844	.	.	.	.	.	T	0.39091	0.1065	L	0.58101	1.795	0.80722	D	1	D	0.69078	0.997	D	0.70716	0.97	T	0.11108	-1.0601	9	0.12430	T	0.62	-20.9905	15.5239	0.75887	1.0:0.0:0.0:0.0	.	1113	O60346	PHLP1_HUMAN	G	601;1113	ENSP00000383170:S601G;ENSP00000262719:S1113G	ENSP00000262719:S1113G	S	+	1	0	PHLPP1	58776854	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.096000	0.94182	2.259000	0.74868	0.528000	0.53228	AGC	.	.		0.453	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		G	60625874	A	G	60625874	3	3	100	1	0	0	0	0	1	0	0	0	11863	304	11	2	3387	2	PHLPP1	18	60625874	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	18344334	60625874	17451374	234	13803										
SHD	56961	hgsc.bcm.edu	37	chr19	4280256	4280256	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gccctggggactccaagaacCccggagatgccaagtatggt	13	12	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:4280256C>T	ENST00000543264.2	+	1	1659	c.196C>T	c.(196-198)Ccc>Tcc	p.P66S	SHD_ENST00000599689.1_Missense_Mutation_p.P66S	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	66										breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCCAAGAACCCCGGAGATGC	0.672																																					p.P66S		Atlas-SNP	.											SHD,NS,carcinoma,0,1	SHD	33	.	0			c.C196T						.						18	21	20					19																	4280256		2200	4297	6497	SO:0001583	missense	56961	exon1			AAGAACCCCGGAG	BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"SH2 domain containing"	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.196C>T	chr19.hg19:g.4280256C>T	ENSP00000446058:p.Pro66Ser	71.0	0.0		42.0	2.0	NM_020209	Q96NC2	Missense_Mutation	SNP	ENST00000543264.2	hg19	CCDS12125.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.436504	0.01108	.	.	ENSG00000105251	ENST00000543264	T	0.29397	1.57	2.97	0.604	0.17547	.	1.227080	0.05750	N	0.602889	T	0.14056	0.0340	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20974	-1.0259	10	0.02654	T	1	-0.8873	8.849	0.35188	0.0:0.5465:0.4535:0.0	.	66	Q96IW2	SHD_HUMAN	S	66	ENSP00000446058:P66S	ENSP00000446058:P66S	P	+	1	0	SHD	4231256	0.000000	0.05858	0.013000	0.15412	0.089000	0.18198	0.235000	0.17948	0.085000	0.17107	-0.458000	0.05436	CCC	.	.		0.672	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209		T	4280256	C	T	4280256	3	4	100	1	0	0	0	0	1	0	0	0	14290	623	22	3	198	3	SHD	19	4280256	Missense_Mutation	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10		4280256	54848727	235	13804										
FEM1A	55527	hgsc.bcm.edu	37	chr19	4792763	4792763	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agccgggaagctgccgtggaAgccttggaattgctgggagc	17	9	0	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:4792763A>G	ENST00000269856.3	+	1	1036	c.897A>G	c.(895-897)gaA>gaG	p.E299E	AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000601192.1_RNA|AC005523.2_ENST00000596170.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	299					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		CTGCCGTGGAAGCCTTGGAAT	0.607																																					p.E299E		Atlas-SNP	.											.	FEM1A	41	.	0			c.A897G						.						57	61	60					19																	4792763		2203	4300	6503	SO:0001819	synonymous_variant	55527	exon1			CGTGGAAGCCTTG	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"Ankyrin repeat domain containing"	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.897A>G	chr19.hg19:g.4792763A>G		153.0	0.0		71.0	4.0	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Silent	SNP	ENST00000269856.3	hg19	CCDS12135.1																																																																																			.	.		0.607	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1			G	4792763	A	G	4792763	2	3	100	1	0	0	0	0	0	0	0	1	5817	69	3	2		2	FEM1A	19	4792763	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	512507	4792763	54336220	236	13805										
MUC16	94025	hgsc.bcm.edu	37	chr19	9048766	9048766	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtggtctctggttcaccaagAgaaaaagtcagaattggaat	11	6	3	2	rs370340214		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:9048766A>G	ENST00000397910.4	-	5	33068	c.32865T>C	c.(32863-32865)tcT>tcC	p.S10955S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10957	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTTCACCAAGAGAAAAAGTCA	0.493																																					p.S10955S		Atlas-SNP	.											.	MUC16	4315	.	0			c.T32865C						.						141	130	133					19																	9048766		1913	4125	6038	SO:0001819	synonymous_variant	94025	exon5			ACCAAGAGAAAAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.32865T>C	chr19.hg19:g.9048766A>G		158.0	0.0		93.0	4.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9048766	A	G	9048766	2	3	100	1	0	0	0	0	0	0	0	1	9982	291	11	2		2	MUC16	19	9048766	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	4256003	9048766	50080217	237	13806										
MUC16	94025	hgsc.bcm.edu	37	chr19	9070574	9070574	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccagagctggtttcttccacAgggggagttgtcatccatga	12	10	2	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:9070574A>G	ENST00000397910.4	-	3	17075	c.16872T>C	c.(16870-16872)ccT>ccC	p.P5624P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5626	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTTCTTCCACAGGGGGAGTTG	0.537																																					p.P5624P		Atlas-SNP	.											.	MUC16	4315	.	0			c.T16872C						.						65	65	65					19																	9070574		1915	4119	6034	SO:0001819	synonymous_variant	94025	exon3			TTCCACAGGGGGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.16872T>C	chr19.hg19:g.9070574A>G		111.0	0.0		99.0	4.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.537	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9070574	A	G	9070574	2	3	100	1	0	0	0	0	0	0	0	1	9982	175	7	2		2	MUC16	19	9070574	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	21808	9070574	50058409	238	13807										
KLF1	10661	hgsc.bcm.edu	37	chr19	12995833	12995833	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctcgtccgagcgcgcgaatcTccagccgcagccttcccacg	10	19	1	0	rs397514445		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:12995833T>C	ENST00000264834.4	-	3	995	c.955A>G	c.(955-957)Aga>Gga	p.R319G	CTD-2265O21.7_ENST00000592400.1_RNA	NM_006563.3	NP_006554.1	Q13351	KLF1_HUMAN	Kruppel-like factor 1 (erythroid)	319					cellular response to peptide (GO:1901653)|chromatin remodeling (GO:0006338)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|large_intestine(1)|skin(1)	5		Hepatocellular(1079;0.137)		GBM - Glioblastoma multiforme(1328;0.00016)|Lung(535;0.171)|STAD - Stomach adenocarcinoma(1328;0.18)		CGCGCGAATCTCCAGCCGCAG	0.657																																					p.R319G		Atlas-SNP	.											KLF1,NS,carcinoma,0,1	KLF1	15	.	0			c.A955G	GRCh37	CI084287	KLF1	I		.						36	40	38					19																	12995833		2203	4299	6502	SO:0001583	missense	10661	exon3			CGAATCTCCAGCC	U37106	CCDS12285.1	19p13.2	2014-07-18			ENSG00000105610	ENSG00000105610		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6345	protein-coding gene	gene with protein product	"erythroid Kruppel-like factor"	600599				8924208, 9119377	Standard	NM_006563		Approved	EKLF	uc002mvo.3	Q13351	OTTHUMG00000180536	ENST00000264834.4:c.955A>G	chr19.hg19:g.12995833T>C	ENSP00000264834:p.Arg319Gly	46.0	1.0		30.0	2.0	NM_006563	Q6PIJ5|Q92899	Missense_Mutation	SNP	ENST00000264834.4	hg19	CCDS12285.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.932773	0.92458	.	.	ENSG00000105610	ENST00000264834	T	0.53423	0.62	4.9	2.75	0.32379	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.531595	0.15694	N	0.249297	T	0.42743	0.1216	N	0.05608	-0.01	0.43156	D	0.994938	P	0.47604	0.898	P	0.58620	0.842	T	0.42932	-0.9422	10	0.87932	D	0	.	10.1104	0.42559	0.0:0.0:0.3235:0.6765	.	319	Q13351	KLF1_HUMAN	G	319	ENSP00000264834:R319G	ENSP00000264834:R319G	R	-	1	2	KLF1	12856833	1.000000	0.71417	0.947000	0.38551	0.982000	0.71751	3.265000	0.51561	0.334000	0.23590	0.459000	0.35465	AGA	.	.		0.657	KLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451794.1	NM_006563		C	12995833	T	C	12995833	3	2	100	1	0	0	0	0	1	0	0	0	8346	1559	54	2	137	2	KLF1	19	12995833	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	3925259	12995833	46133150	239	13808										
ZNF493	284443	hgsc.bcm.edu	37	chr19	21607389	21607389	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agcttttaagcggtcctcacAcctcgctgggcacaagcaaa	9	13	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:21607389A>G	ENST00000355504.4	+	2	1810	c.1544A>G	c.(1543-1545)cAc>cGc	p.H515R	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.H643R	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	515					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						CGGTCCTCACACCTCGCTGGG	0.373																																					p.H643R		Atlas-SNP	.											.	ZNF493	178	.	0			c.A1928G						.						44	48	47					19																	21607389		2199	4294	6493	SO:0001583	missense	284443	exon4			CCTCACACCTCGC	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1544A>G	chr19.hg19:g.21607389A>G	ENSP00000347691:p.His515Arg	154.0	0.0		113.0	5.0	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	hg19	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	0.024	-1.387956	0.01194	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.12984	2.63;2.63	0.361	-0.721	0.11189	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06735	0.0172	N	0.25094	0.71	0.09310	N	0.999999	B;B	0.31383	0.014;0.321	B;B	0.21917	0.022;0.037	T	0.38415	-0.9662	9	0.23891	T	0.37	.	5.3335	0.15945	0.7069:0.2931:0.0:0.0	.	515;643	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	R	643;515	ENSP00000376110:H643R;ENSP00000347691:H515R	ENSP00000347691:H515R	H	+	2	0	ZNF493	21399229	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.581000	0.00906	-0.660000	0.05352	-0.695000	0.03696	CAC	.	.		0.373	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		G	21607389	A	G	21607389	3	3	100	1	0	0	0	0	1	0	0	0	17959	159	6	2	2005	2	ZNF493	19	21607389	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	8611556	21607389	37521594	240	13809										
GPATCH1	55094	hgsc.bcm.edu	37	chr19	33579153	33579153	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gtttctctgctggatacttcAatactgttggctcaaaagaa	8	8	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:33579153A>G	ENST00000170564.2	+	2	501	c.187A>G	c.(187-189)Aat>Gat	p.N63D		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	63					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					TGGATACTTCAATACTGTTGG	0.388																																					p.N63D	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.A187G						.						103	107	105					19																	33579153		2203	4300	6503	SO:0001583	missense	55094	exon2			TACTTCAATACTG	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"G patch domain containing"	24658	protein-coding gene	gene with protein product	"evolutionarily conserved G patch domain containing"			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.187A>G	chr19.hg19:g.33579153A>G	ENSP00000170564:p.Asn63Asp	200.0	0.0		100.0	4.0	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Missense_Mutation	SNP	ENST00000170564.2	hg19	CCDS12428.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.196296	0.78902	.	.	ENSG00000076650	ENST00000170564	T	0.44482	0.92	5.43	5.43	0.79202	Domain of unknown function DUF1604 (1);	0.000000	0.85682	D	0.000000	T	0.70701	0.3254	M	0.89658	3.05	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77653	-0.2507	10	0.72032	D	0.01	-30.4861	14.9395	0.70983	1.0:0.0:0.0:0.0	.	63	Q9BRR8	GPTC1_HUMAN	D	63	ENSP00000170564:N63D	ENSP00000170564:N63D	N	+	1	0	GPATCH1	38270993	1.000000	0.71417	0.997000	0.53966	0.548000	0.35241	8.595000	0.90840	2.190000	0.69967	0.533000	0.62120	AAT	.	.		0.388	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		G	33579153	A	G	33579153	3	3	100	1	0	0	0	0	1	0	0	0	6598	130	5	2	193	2	GPATCH1	19	33579153	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	11971764	33579153	25549830	241	13810										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36350514	36350514	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cccacaggaagagacacagcTatcacactgagcctgcagtg	10	13	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:36350514T>C	ENST00000360202.5	+	5	852	c.654T>C	c.(652-654)gcT>gcC	p.A218A	KIRREL2_ENST00000262625.7_Silent_p.A218A|KIRREL2_ENST00000592409.1_Silent_p.A218A|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Silent_p.A168A	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	218	Ig-like C2-type 2.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GAGACACAGCTATCACACTGA	0.622																																					p.A218A		Atlas-SNP	.											.	KIRREL2	170	.	0			c.T654C						.						53	52	53					19																	36350514		2203	4300	6503	SO:0001819	synonymous_variant	84063	exon5			CACAGCTATCACA	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.654T>C	chr19.hg19:g.36350514T>C		40.0	0.0		40.0	4.0	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	hg19	CCDS12481.1																																																																																			.	.		0.622	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		C	36350514	T	C	36350514	2	2	100	1	0	0	0	0	0	0	0	1	8334	1509	53	2		2	KIRREL2	19	36350514	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2771361	36350514	22778469	242	13811										
ZNF383	163087	hgsc.bcm.edu	37	chr19	37733879	37733879	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ctttctcaacatcagagaatCcataccggtaagaaacccta	5	12	2	2	rs367688274		TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:37733879C>T	ENST00000589413.1	+	8	1324	c.741C>T	c.(739-741)atC>atT	p.I247I	ZNF383_ENST00000352998.3_Silent_p.I247I|ZNF383_ENST00000590503.1_Silent_p.I247I			Q8NA42	ZN383_HUMAN	zinc finger protein 383	247					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I247I(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)	15			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATCAGAGAATCCATACCGGTA	0.408																																					p.I247I		Atlas-SNP	.											ZNF383,NS,NS,0,1	ZNF383	42	.	1	Substitution - coding silent(1)	NS(1)	c.C741T						.						67	65	66					19																	37733879		2203	4300	6503	SO:0001819	synonymous_variant	163087	exon5			GAGAATCCATACC	AY438646	CCDS12501.1	19q13.13	2013-01-08				ENSG00000188283		"Zinc fingers, C2H2-type", "-"	18609	protein-coding gene	gene with protein product							Standard	NM_152604		Approved	FLJ35863	uc002ofu.1	Q8NA42		ENST00000589413.1:c.741C>T	chr19.hg19:g.37733879C>T		87.0	1.0		66.0	3.0	NM_152604	Q6X2C7	Silent	SNP	ENST00000589413.1	hg19	CCDS12501.1																																																																																			.	.		0.408	ZNF383-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458141.1	NM_152604		T	37733879	C	T	37733879	2	4	100	1	0	0	0	0	0	0	0	1	17889	845	30	3		3	ZNF383	19	37733879	Silent	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	1383365	37733879	21395104	243	13812										
CYP2F1	1572	hgsc.bcm.edu	37	chr19	41622142	41622142	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tcctgctcctggctctcgtcTgtctgctcctgaccctaagc	8	17	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:41622142T>C	ENST00000331105.2	+	2	121	c.49T>C	c.(49-51)Tgt>Cgt	p.C17R		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	17					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						GGCTCTCGTCTGTCTGCTCCT	0.577																																					p.C17R		Atlas-SNP	.											.	CYP2F1	60	.	0			c.T49C						.						159	140	147					19																	41622142		2203	4300	6503	SO:0001583	missense	1572	exon2			CTCGTCTGTCTGC	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"Cytochrome P450s"	2632	protein-coding gene	gene with protein product		124070	"cytochrome P450, subfamily IIF, polypeptide 1"	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.49T>C	chr19.hg19:g.41622142T>C	ENSP00000333534:p.Cys17Arg	148.0	0.0		76.0	4.0	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	hg19	CCDS12572.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.471423	0.43942	.	.	ENSG00000197446	ENST00000331105	T	0.69561	-0.41	3.86	3.86	0.44501	.	1.762820	0.02983	U	0.145829	T	0.52741	0.1753	N	0.08118	0	0.35299	D	0.782843	B;B	0.23650	0.089;0.022	B;B	0.19946	0.027;0.015	T	0.39941	-0.9589	10	0.66056	D	0.02	.	11.8244	0.52259	0.0:0.0:0.0:1.0	.	17;17	Q32MN5;P24903	.;CP2F1_HUMAN	R	17	ENSP00000333534:C17R	ENSP00000333534:C17R	C	+	1	0	CYP2F1	46313982	0.011000	0.17503	0.083000	0.20561	0.779000	0.44077	1.626000	0.37039	1.617000	0.50277	0.445000	0.29226	TGT	.	.		0.577	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2			C	41622142	T	C	41622142	3	2	100	1	0	0	0	0	1	0	0	0	4173	1580	55	2	51	2	CYP2F1	19	41622142	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	3888263	41622142	17506841	244	13813										
CIC	23152	hgsc.bcm.edu	37	chr19	42793506	42793506	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gccagtgaggacatgacgagTgatgaggagcgcatggtcat	16	7	1	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:42793506T>C	ENST00000575354.2	+	8	1348	c.1308T>C	c.(1306-1308)agT>agC	p.S436S	CIC_ENST00000160740.3_Silent_p.S436S|CIC_ENST00000572681.2_Silent_p.S1345S	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	436					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				ACATGACGAGTGATGAGGAGC	0.637			"Mis, F, S"		oligodendroglioma																																p.S436S		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.T1308C						.						68	54	59					19																	42793506		2203	4300	6503	SO:0001819	synonymous_variant	23152	exon8			GACGAGTGATGAG	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"capicua (Drosophila) homolog", "capicua homolog (Drosophila)"			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.1308T>C	chr19.hg19:g.42793506T>C		143.0	0.0		72.0	4.0	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Silent	SNP	ENST00000575354.2	hg19	CCDS12601.1																																																																																			.	.		0.637	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			C	42793506	T	C	42793506	2	2	100	1	0	0	0	0	0	0	0	1	3426	1693	59	2		2	CIC	19	42793506	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1171364	42793506	16335477	245	13814										
TMEM145	284339	hgsc.bcm.edu	37	chr19	42818606	42818606	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	acatctctggtctgcaggccAagtgctgtcagaacatcctc	9	13	3	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:42818606A>G	ENST00000301204.3	+	3	240	c.199A>G	c.(199-201)Aag>Gag	p.K67E	TMEM145_ENST00000598766.1_Missense_Mutation_p.K77E|TMEM145_ENST00000601020.1_3'UTR	NM_173633.2	NP_775904.2	Q8NBT3	TM145_HUMAN	transmembrane protein 145	67					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	27		Prostate(69;0.00682)				TCTGCAGGCCAAGTGCTGTCA	0.602																																					p.K67E		Atlas-SNP	.											.	TMEM145	55	.	0			c.A199G						.						157	147	150					19																	42818606		2203	4300	6503	SO:0001583	missense	284339	exon3			CAGGCCAAGTGCT	AK075286	CCDS12603.1	19q13.2	2008-02-05				ENSG00000167619			26912	protein-coding gene	gene with protein product							Standard	NM_173633		Approved	FLJ90805	uc002otk.1	Q8NBT3		ENST00000301204.3:c.199A>G	chr19.hg19:g.42818606A>G	ENSP00000301204:p.Lys67Glu	103.0	0.0		61.0	4.0	NM_173633		Missense_Mutation	SNP	ENST00000301204.3	hg19	CCDS12603.1	.	.	.	.	.	.	.	.	.	.	A	8.315	0.823101	0.16678	.	.	ENSG00000167619	ENST00000301204	T	0.41065	1.01	4.76	4.76	0.60689	.	0.152029	0.43919	D	0.000509	T	0.25232	0.0613	L	0.28274	0.84	0.38794	D	0.95505	B	0.25105	0.118	B	0.17098	0.017	T	0.09596	-1.0667	10	0.02654	T	1	-22.5791	12.535	0.56137	1.0:0.0:0.0:0.0	.	67	Q8NBT3	TM145_HUMAN	E	67	ENSP00000301204:K67E	ENSP00000301204:K67E	K	+	1	0	TMEM145	47510446	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.853000	0.62911	1.930000	0.55929	0.460000	0.39030	AAG	.	.		0.602	TMEM145-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463737.1	NM_173633		G	42818606	A	G	42818606	3	3	100	1	0	0	0	0	1	0	0	0	16074	131	5	2	209	2	TMEM145	19	42818606	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	25100	42818606	16310377	246	13815										
TEX101	83639	hgsc.bcm.edu	37	chr19	43920572	43920572	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agggctgcatcccggaagggGaggaggccataacaattgtc	15	9	0	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:43920572G>A	ENST00000598265.1	+	4	422	c.256G>A	c.(256-258)Gag>Aag	p.E86K	TEX101_ENST00000601707.1_3'UTR|TEX101_ENST00000253435.7_Missense_Mutation_p.E104K|TEX101_ENST00000602198.1_Missense_Mutation_p.E104K	NM_001130011.1	NP_001123483.1	Q9BY14	TX101_HUMAN	testis expressed 101	86						acrosomal membrane (GO:0002080)|anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				large_intestine(1)|lung(12)|ovary(1)|skin(1)	15		Prostate(69;0.0199)				CCCGGAAGGGGAGGAGGCCAT	0.532																																					p.E104K		Atlas-SNP	.											.	TEX101	28	.	0			c.G310A						.						151	140	144					19																	43920572		2203	4300	6503	SO:0001583	missense	83639	exon7			GAAGGGGAGGAGG	AF241268	CCDS12619.1, CCDS59393.1	19q13.31	2013-06-06	2007-03-13			ENSG00000131126			30722	protein-coding gene	gene with protein product	"cancer/testis antigen 131", "spermatogenesis associated 44"	612665	"testis expressed sequence 101"			16388701, 16516155	Standard	NM_031451		Approved	MGC4766, SGRG, CT131, SPATA44	uc010xwo.2	Q9BY14		ENST00000598265.1:c.256G>A	chr19.hg19:g.43920572G>A	ENSP00000472769:p.Glu86Lys	138.0	0.0		108.0	17.0	NM_031451	Q7L5R2|Q9BPY7	Missense_Mutation	SNP	ENST00000598265.1	hg19	CCDS59393.1	.	.	.	.	.	.	.	.	.	.	G	1.389	-0.581187	0.03854	.	.	ENSG00000131126	ENST00000253435;ENST00000407156	T	0.69685	-0.42	4.26	-6.51	0.01878	.	3.000930	0.00951	N	0.002973	T	0.35740	0.0942	N	0.08118	0	0.09310	N	1	B;B	0.15930	0.009;0.015	B;B	0.20577	0.01;0.03	T	0.44190	-0.9344	10	0.06099	T	0.92	0.5252	1.9355	0.03336	0.2081:0.1253:0.4201:0.2465	.	86;104	Q9BY14;Q9BY14-2	TX101_HUMAN;.	K	104;99	ENSP00000253435:E104K	ENSP00000253435:E104K	E	+	1	0	TEX101	48612412	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.072000	0.03434	-1.574000	0.01657	-1.108000	0.02087	GAG	.	.		0.532	TEX101-004	KNOWN	non_canonical_other|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000463176.1	NM_031451		A	43920572	G	A	43920572	3	1	100	1	0	0	0	0	1	0	0	0	15788	1175	41	3	324	3	TEX101	19	43920572	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	1101966	43920572	15208411	247	13816										
RASIP1	54922	hgsc.bcm.edu	37	chr19	49238547	49238547	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	actgatcgaagtccccggggTctgcagttccgatttgggcg	14	11	1	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:49238547T>C	ENST00000222145.4	-	4	1289	c.1085A>G	c.(1084-1086)gAc>gGc	p.D362G	RASIP1_ENST00000594232.1_5'UTR	NM_017805.2	NP_060275.2	Q5U651	RAIN_HUMAN	Ras interacting protein 1	362					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|negative regulation of autophagy (GO:0010507)|regulation of Rho GTPase activity (GO:0032319)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	Golgi apparatus (GO:0005794)				central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	21		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000272)|Epithelial(262;0.0155)|GBM - Glioblastoma multiforme(486;0.0222)		GTCCCCGGGGTCTGCAGTTCC	0.667																																					p.D362G		Atlas-SNP	.											.	RASIP1	80	.	0			c.A1085G						.						42	43	42					19																	49238547		2203	4300	6503	SO:0001583	missense	54922	exon4			CCGGGGTCTGCAG	BC028614	CCDS12731.1	19q13.33	2008-02-05				ENSG00000105538			24716	protein-coding gene	gene with protein product		609623				15031288	Standard	NM_017805		Approved	FLJ20401, RAIN	uc002pki.3	Q5U651		ENST00000222145.4:c.1085A>G	chr19.hg19:g.49238547T>C	ENSP00000222145:p.Asp362Gly	147.0	0.0		115.0	6.0	NM_017805	Q6U676	Missense_Mutation	SNP	ENST00000222145.4	hg19	CCDS12731.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.446769	0.63178	.	.	ENSG00000105538	ENST00000222145	T	0.08102	3.13	5.27	4.24	0.50183	.	0.329639	0.28736	N	0.014312	T	0.05823	0.0152	N	0.21097	0.63	0.38450	D	0.946925	B	0.10296	0.003	B	0.04013	0.001	T	0.22695	-1.0209	10	0.49607	T	0.09	-0.0601	7.2395	0.26088	0.0:0.098:0.0:0.902	.	362	Q5U651	RAIN_HUMAN	G	362	ENSP00000222145:D362G	ENSP00000222145:D362G	D	-	2	0	RASIP1	53930359	0.998000	0.40836	0.955000	0.39395	0.969000	0.65631	2.107000	0.41844	2.126000	0.65437	0.459000	0.35465	GAC	.	.		0.667	RASIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466185.1	NM_017805		C	49238547	T	C	49238547	3	2	100	1	0	0	0	0	1	0	0	0	13093	1667	58	2	1842	2	RASIP1	19	49238547	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	5317975	49238547	9890436	248	13817										
DHDH	27294	hgsc.bcm.edu	37	chr19	49442937	49442937	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	agccagagaagatttctgtcGtgggaaggcgtcatgaaaca	13	7	2	3	rs35453148	byFrequency	TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:49442937G>T	ENST00000221403.2	+	4	638	c.598G>T	c.(598-600)Gtg>Ttg	p.V200L	DHDH_ENST00000522614.1_Missense_Mutation_p.V200L|DHDH_ENST00000523250.1_Intron	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	200			V -> M (in dbSNP:rs35453148).		carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)	p.V200M(1)		central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		GATTTCTGTCGTGGGAAGGCG	0.542																																					p.V200L		Atlas-SNP	.											DHDH,brainstem,primitive_neuroectodermal_tumour-medulloblastoma,0,1	DHDH	35	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G598T						.						106	109	108					19																	49442937		2203	4300	6503	SO:0001583	missense	27294	exon4			TCTGTCGTGGGAA	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.598G>T	chr19.hg19:g.49442937G>T	ENSP00000221403:p.Val200Leu	52.0	0.0		32.0	4.0	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	hg19	CCDS12741.1	.	.	.	.	.	.	.	.	.	.	G	8.545	0.874201	0.17395	.	.	ENSG00000104808	ENST00000221403;ENST00000522614	T;T	0.21191	2.02;2.02	5.12	-1.8	0.07907	.	0.904653	0.09763	N	0.758985	T	0.16896	0.0406	L	0.45581	1.43	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.34153	-0.9840	10	0.24483	T	0.36	-6.9556	9.9213	0.41466	0.461:0.0:0.539:0.0	.	200	Q9UQ10	DHDH_HUMAN	L	200	ENSP00000221403:V200L;ENSP00000428672:V200L	ENSP00000221403:V200L	V	+	1	0	DHDH	54134749	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.091000	0.11146	-0.183000	0.10585	-0.340000	0.08031	GTG	.	G|0.997;A|0.003		0.542	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475		T	49442937	G	T	49442937	3	4	100	1	0	0	0	0	1	0	0	0	4481	1145	40	1	612	1	DHDH	19	49442937	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	204390	49442937	9686046	249	13818										
ZNF320	162967	hgsc.bcm.edu	37	chr19	53384285	53384285	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gacgtgaatcactccggaaaGccttgtcacaaaccttacat	7	12	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:53384285G>A	ENST00000595635.1	-	8	1595	c.1094C>T	c.(1093-1095)gCt>gTt	p.A365V	ZNF320_ENST00000391781.2_Missense_Mutation_p.A365V|ZNF320_ENST00000597909.1_Intron|ZNF320_ENST00000600930.1_Intron	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	365					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		ACTCCGGAAAGCCTTGTCACA	0.408																																					p.A365V		Atlas-SNP	.											.	ZNF320	67	.	0			c.C1094T						.						129	122	124					19																	53384285		2203	4300	6503	SO:0001583	missense	162967	exon4			CGGAAAGCCTTGT	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"Zinc fingers, C2H2-type", "-"	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.1094C>T	chr19.hg19:g.53384285G>A	ENSP00000473091:p.Ala365Val	157.0	0.0		111.0	5.0	NM_207333	Q8NDR6	Missense_Mutation	SNP	ENST00000595635.1	hg19	CCDS33095.1	.	.	.	.	.	.	.	.	.	.	-	0.659	-0.806637	0.02819	.	.	ENSG00000182986	ENST00000391781	T	0.13778	2.56	1.74	-0.844	0.10741	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11750	0.0286	L	0.35249	1.045	0.19300	N	0.99997	P	0.50617	0.937	P	0.49276	0.605	T	0.18840	-1.0324	9	0.33141	T	0.24	.	3.7473	0.08552	0.2968:0.2043:0.4988:0.0	.	365	A2RRD8	ZN320_HUMAN	V	365	ENSP00000375660:A365V	ENSP00000375660:A365V	A	-	2	0	ZNF320	58076097	0.000000	0.05858	0.008000	0.14137	0.208000	0.24298	-2.623000	0.00876	-0.339000	0.08401	0.184000	0.17185	GCT	.	.		0.408	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333		A	53384285	G	A	53384285	3	1	100	1	0	0	0	0	1	0	0	0	17854	971	34	3	439	3	ZNF320	19	53384285	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	3941348	53384285	5744698	250	13819										
CACNG7	59284	hgsc.bcm.edu	37	chr19	54418669	54418669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tggtcagcctcttcctcgtgTtcacggccttcgtcatcagc	9	15	5	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:54418669T>C	ENST00000391767.1	+	4	546	c.334T>C	c.(334-336)Ttc>Ctc	p.F112L	CACNG7_ENST00000222212.2_Missense_Mutation_p.F112L|CACNG7_ENST00000468076.1_3'UTR|CACNG7_ENST00000391766.1_Missense_Mutation_p.F112L			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	112					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		CTTCCTCGTGTTCACGGCCTT	0.602																																					p.F112L		Atlas-SNP	.											CACNG7,NS,carcinoma,0,1	CACNG7	58	.	0			c.T334C						.						107	90	96					19																	54418669		2203	4300	6503	SO:0001583	missense	59284	exon3			CTCGTGTTCACGG	AF288387	CCDS12868.1	19q13.4	2008-05-02			ENSG00000105605	ENSG00000105605		"Calcium channel subunits"	13626	protein-coding gene	gene with protein product		606899				11170751	Standard	NM_031896		Approved		uc002qcr.2	P62955	OTTHUMG00000064852	ENST00000391767.1:c.334T>C	chr19.hg19:g.54418669T>C	ENSP00000375647:p.Phe112Leu	185.0	0.0		90.0	4.0	NM_031896	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Missense_Mutation	SNP	ENST00000391767.1	hg19	CCDS12868.1	.	.	.	.	.	.	.	.	.	.	T	12.85	2.061669	0.36373	.	.	ENSG00000105605	ENST00000391767;ENST00000222212;ENST00000391766	D;D;D	0.87966	-2.32;-2.32;-2.32	3.77	3.77	0.43336	.	0.000000	0.85682	D	0.000000	T	0.73521	0.3597	N	0.20845	0.615	0.80722	D	1	B	0.17852	0.024	B	0.18263	0.021	T	0.65615	-0.6125	10	0.02654	T	1	-29.2668	11.1063	0.48205	0.0:0.0:0.0:1.0	.	112	P62955	CCG7_HUMAN	L	112	ENSP00000375647:F112L;ENSP00000222212:F112L;ENSP00000375646:F112L	ENSP00000222212:F112L	F	+	1	0	CACNG7	59110481	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.381000	0.79718	1.928000	0.55862	0.460000	0.39030	TTC	.	.		0.602	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2			C	54418669	T	C	54418669	3	2	100	1	0	0	0	0	1	0	0	0	2564	1725	60	2	344	2	CACNG7	19	54418669	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	1034384	54418669	4710314	251	13820										
ZNF471	57573	hgsc.bcm.edu	37	chr19	57027722	57027722	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tgaaccctgctcagaagcgtTtatacaggagtatgatgttg	11	7	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr19:57027722T>G	ENST00000308031.5	+	3	245	c.112T>G	c.(112-114)Tta>Gta	p.L38V	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_Missense_Mutation_p.L38V	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	38	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		TCAGAAGCGTTTATACAGGAG	0.403																																					p.L38V	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.T112G						.						166	152	157					19																	57027722		2203	4300	6503	SO:0001583	missense	57573	exon3			AAGCGTTTATACA	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.112T>G	chr19.hg19:g.57027722T>G	ENSP00000309161:p.Leu38Val	255.0	0.0		163.0	16.0	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	hg19	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.480783	0.26598	.	.	ENSG00000196263	ENST00000308031	T	0.05081	3.5	3.77	-1.3	0.09259	Krueppel-associated box (4);	.	.	.	.	T	0.28333	0.0700	H	0.94542	3.55	0.09310	N	1	D	0.76494	0.999	D	0.87578	0.998	T	0.03993	-1.0986	9	0.72032	D	0.01	.	5.9946	0.19487	0.0:0.5124:0.1813:0.3063	.	38	Q9BX82	ZN471_HUMAN	V	38	ENSP00000309161:L38V	ENSP00000309161:L38V	L	+	1	2	ZNF471	61719534	0.000000	0.05858	0.009000	0.14445	0.308000	0.27856	-0.447000	0.06828	-0.179000	0.10654	0.528000	0.53228	TTA	.	.		0.403	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		G	57027722	T	G	57027722	3	3	100	1	0	0	0	0	1	0	0	0	17945	1838	64	5	118	5	ZNF471	19	57027722	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	2609053	57027722	2101261	252	13821										
TPX2	22974	hgsc.bcm.edu	37	chr20	30365314	30365314	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	acctgtgaagaaatcagtgaGccaggtcaccaaatcagttg	10	9	3	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr20:30365314G>T	ENST00000300403.6	+	9	1283	c.755G>T	c.(754-756)aGc>aTc	p.S252I	TPX2_ENST00000340513.4_Missense_Mutation_p.S252I	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	252					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			AAATCAGTGAGCCAGGTCACC	0.428																																					p.S252I		Atlas-SNP	.											.	TPX2	61	.	0			c.G755T						.						130	114	119					20																	30365314		2203	4300	6503	SO:0001583	missense	22974	exon9			CAGTGAGCCAGGT	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"chromosome 20 open reading frame 1", "TPX2, microtubule-associated, homolog (Xenopus laevis)"	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.755G>T	chr20.hg19:g.30365314G>T	ENSP00000300403:p.Ser252Ile	145.0	0.0		81.0	8.0	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	hg19	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.928142	0.34002	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.32515	1.45	5.36	3.36	0.38483	.	0.319078	0.35151	N	0.003412	T	0.19846	0.0477	N	0.22421	0.69	0.29470	N	0.857132	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.12142	-1.0559	10	0.20046	T	0.44	-0.961	12.8578	0.57894	0.0:0.0:0.5725:0.4275	.	252;252	Q96RR5;Q9ULW0	.;TPX2_HUMAN	I	252	ENSP00000341145:S252I	ENSP00000300403:S252I	S	+	2	0	TPX2	29828975	0.494000	0.26043	1.000000	0.80357	0.993000	0.82548	0.640000	0.24705	0.706000	0.31912	0.655000	0.94253	AGC	.	.		0.428	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2			T	30365314	G	T	30365314	3	4	100	1	0	0	0	0	1	0	0	0	16447	971	34	3	781	3	TPX2	20	30365314	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10		30365314	32660206	253	13822										
PHACTR3	116154	hgsc.bcm.edu	37	chr20	58342290	58342290	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gaagcagacgctggcagcctCctgcccaccaccaatgagct	10	16	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr20:58342290C>A	ENST00000371015.1	+	5	1058	c.591C>A	c.(589-591)ctC>ctA	p.L197L	PHACTR3_ENST00000355648.4_Silent_p.L156L|PHACTR3_ENST00000395639.4_Intron|PHACTR3_ENST00000361300.4_Intron|PHACTR3_ENST00000359926.3_Silent_p.L194L|PHACTR3_ENST00000395636.2_Silent_p.L156L|PHACTR3_ENST00000541461.1_Silent_p.L156L	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	197						nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			CTGGCAGCCTCCTGCCCACCA	0.577																																					p.L197L		Atlas-SNP	.											.	PHACTR3	104	.	0			c.C591A						.						53	49	51					20																	58342290		2203	4300	6503	SO:0001819	synonymous_variant	116154	exon5			CAGCCTCCTGCCC	AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"Phosphatase and actin regulators"	15833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 123"	608725	"chromosome 20 open reading frame 101"	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.591C>A	chr20.hg19:g.58342290C>A		145.0	0.0		103.0	7.0	NM_080672	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Silent	SNP	ENST00000371015.1	hg19	CCDS13480.1																																																																																			.	.		0.577	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		A	58342290	C	A	58342290	2	1	100	1	0	0	0	0	0	0	0	1	11820	842	30	3		3	PHACTR3	20	58342290	Silent	SNP	C	TCGA-DD-A1ED-01A-11D-A152-10	27976976	58342290	4683230	254	13823										
OPRL1	4987	hgsc.bcm.edu	37	chr20	62730031	62730031	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gaacttcaaggcctgcttccGcaagttctgctgtgcatctg	10	12	3	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr20:62730031G>A	ENST00000349451.3	+	6	1404	c.992G>A	c.(991-993)cGc>cAc	p.R331H	OPRL1_ENST00000336866.2_Missense_Mutation_p.R331H|OPRL1_ENST00000355631.4_Missense_Mutation_p.R331H	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	331					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavior (GO:0007610)|opioid receptor signaling pathway (GO:0038003)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|nociceptin receptor activity (GO:0001626)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					GCCTGCTTCCGCAAGTTCTGC	0.627																																					p.R331H		Atlas-SNP	.											OPRL1,NS,carcinoma,0,1	OPRL1	47	.	0			c.G992A						.						95	85	88					20																	62730031		2202	4297	6499	SO:0001583	missense	4987	exon4			GCTTCCGCAAGTT		CCDS13556.1	20q13.33	2012-08-08			ENSG00000125510	ENSG00000125510		"GPCR / Class A : Opioid receptors"	8155	protein-coding gene	gene with protein product	"LC132 receptor-like", "orphanin FQ receptor", "kappa3-related opioid receptor"	602548				8137918	Standard	NM_000913		Approved	NOCIR, ORL1, OOR, KOR-3	uc021wgs.1	P41146	OTTHUMG00000033027	ENST00000349451.3:c.992G>A	chr20.hg19:g.62730031G>A	ENSP00000336764:p.Arg331His	110.0	0.0		64.0	3.0	NM_000913	Q8TD34|Q8WYH9|Q9H4K4	Missense_Mutation	SNP	ENST00000349451.3	hg19	CCDS13556.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.862400	0.51482	.	.	ENSG00000125510	ENST00000336866;ENST00000355631;ENST00000349451	T;T;T	0.40476	1.03;1.03;1.03	5.05	4.1	0.47936	.	0.168029	0.42053	D	0.000771	T	0.45736	0.1357	L	0.55990	1.75	0.42819	D	0.993987	D;B	0.64830	0.994;0.246	P;B	0.54706	0.759;0.013	T	0.48843	-0.8999	10	0.66056	D	0.02	.	4.8144	0.13360	0.3115:0.0:0.6885:0.0	.	326;331	P41146-2;P41146	.;OPRX_HUMAN	H	331	ENSP00000336843:R331H;ENSP00000347848:R331H;ENSP00000336764:R331H	ENSP00000336843:R331H	R	+	2	0	OPRL1	62200475	1.000000	0.71417	0.967000	0.41034	0.876000	0.50452	2.259000	0.43259	2.346000	0.79739	0.500000	0.49745	CGC	.	.		0.627	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647		A	62730031	G	A	62730031	3	1	100	1	0	0	0	0	1	0	0	0	10895	1087	38	1	1002	1	OPRL1	20	62730031	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10	4387741	62730031	295489	255	13824										
PIWIL3	440822	hgsc.bcm.edu	37	chr22	25153964	25153964	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	caatccttctctcctgcaagGgcgctgtatgcaacccagcc	8	16	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr22:25153964G>A	ENST00000332271.5	-	4	682	c.266C>T	c.(265-267)cCc>cTc	p.P89L	PIWIL3_ENST00000533313.1_5'UTR|PIWIL3_ENST00000527701.1_5'UTR|PIWIL3_ENST00000532537.2_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	89					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						CTCCTGCAAGGGCGCTGTATG	0.443																																					p.P89L		Atlas-SNP	.											.	PIWIL3	115	.	0			c.C266T						.						201	209	206					22																	25153964		2203	4300	6503	SO:0001583	missense	440822	exon4			TGCAAGGGCGCTG	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.266C>T	chr22.hg19:g.25153964G>A	ENSP00000330031:p.Pro89Leu	177.0	0.0		95.0	20.0	NM_001008496		Missense_Mutation	SNP	ENST00000332271.5	hg19	CCDS33623.1	.	.	.	.	.	.	.	.	.	.	G	0.080	-1.184821	0.01620	.	.	ENSG00000184571	ENST00000332271	T	0.04275	3.66	2.21	1.18	0.20946	.	1.020570	0.07843	U	0.963402	T	0.02807	0.0084	N	0.08118	0	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.46442	-0.9191	10	0.30854	T	0.27	0.0061	6.8309	0.23909	0.1555:0.0:0.8445:0.0	.	89;89	B4DYF7;Q7Z3Z3	.;PIWL3_HUMAN	L	89	ENSP00000330031:P89L	ENSP00000330031:P89L	P	-	2	0	PIWIL3	23483964	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.157000	0.16402	0.504000	0.28082	0.455000	0.32223	CCC	.	.		0.443	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		A	25153964	G	A	25153964	3	1	100	1	0	0	0	0	1	0	0	0	11968	1232	43	3	2454	3	PIWIL3	22	25153964	Missense_Mutation	SNP	G	TCGA-DD-A1ED-01A-11D-A152-10		25153964	26150602	256	13825										
SLC5A4	6527	hgsc.bcm.edu	37	chr22	32643496	32643496	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	cttgagatattccggcatggTcatcacctgcagagacagac	10	11	2	3	rs551408084	byFrequency	TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chr22:32643496T>C	ENST00000266086.4	-	5	390	c.379A>G	c.(379-381)Acc>Gcc	p.T127A	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	127					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TCCGGCATGGTCATCACCTGC	0.483													T|||	7	0.00139776	0	0	5008	,	,		20055	0		0	False		,,,				2504	0.0072				p.T127A		Atlas-SNP	.											.	SLC5A4	82	.	0			c.A379G						.						92	74	80					22																	32643496		2203	4300	6503	SO:0001583	missense	6527	exon5			GCATGGTCATCAC	U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"Solute carriers"	11039	protein-coding gene	gene with protein product			"solute carrier family 5 (low affinity glucose cotransporter), member 4"			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.379A>G	chr22.hg19:g.32643496T>C	ENSP00000266086:p.Thr127Ala	149.0	0.0		86.0	4.0	NM_014227	O15279	Missense_Mutation	SNP	ENST00000266086.4	hg19	CCDS13903.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.407566	0.83340	.	.	ENSG00000100191	ENST00000266086	D	0.94966	-3.57	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	D	0.98185	0.9400	H	0.97365	3.99	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.99153	1.0859	10	0.87932	D	0	.	13.0161	0.58757	0.0:0.0:0.0:1.0	.	127	Q9NY91	SC5A4_HUMAN	A	127	ENSP00000266086:T127A	ENSP00000266086:T127A	T	-	1	0	SLC5A4	30973496	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	7.404000	0.79996	2.174000	0.68829	0.533000	0.62120	ACC	.	.		0.483	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227		C	32643496	T	C	32643496	3	2	100	1	0	0	0	0	1	0	0	0	14682	1667	58	2	1644	2	SLC5A4	22	32643496	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	7489532	32643496	18661070	257	13826										
PRKX	5613	hgsc.bcm.edu	37	chrX	3573330	3573330	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atggcacagatgatctctgcAgagtagaagagccccgtggt	13	9	1	5			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:3573330A>G	ENST00000262848.5	-	3	813	c.459T>C	c.(457-459)tcT>tcC	p.S153S	PRKX_ENST00000425240.1_5'UTR	NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	153	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				TGATCTCTGCAGAGTAGAAGA	0.572																																					p.S153S		Atlas-SNP	.											.	PRKX	29	.	0			c.T459C						.						105	93	97					X																	3573330		2203	4300	6503	SO:0001819	synonymous_variant	5613	exon3			CTCTGCAGAGTAG		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.459T>C	chrX.hg19:g.3573330A>G		119.0	0.0		82.0	4.0	NM_005044		Silent	SNP	ENST00000262848.5	hg19	CCDS14125.1																																																																																			.	.		0.572	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044		G	3573330	A	G	3573330	2	3	100	1	0	0	0	0	0	0	0	1	12539	175	7	2		2	PRKX	23	3573330	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10		3573330	151697230	258	13827										
CNKSR2	22866	hgsc.bcm.edu	37	chrX	21458842	21458842	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gctgctgtgacagactattcAgttacaagaaataatgtcat	8	7	2	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:21458842A>G	ENST00000379510.3	+	4	498	c.462A>G	c.(460-462)tcA>tcG	p.S154S	CNKSR2_ENST00000425654.2_Silent_p.S154S|CNKSR2_ENST00000279451.4_Silent_p.S154S|CNKSR2_ENST00000543067.1_Silent_p.S154S	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	154	CRIC. {ECO:0000255|PROSITE- ProRule:PRU00621}.				regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						CAGACTATTCAGTTACAAGAA	0.348																																					p.S154S		Atlas-SNP	.											.	CNKSR2	158	.	0			c.A462G						.						91	77	82					X																	21458842		2203	4299	6502	SO:0001819	synonymous_variant	22866	exon4			CTATTCAGTTACA	AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.462A>G	chrX.hg19:g.21458842A>G		60.0	0.0		55.0	4.0	NM_001168647	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Silent	SNP	ENST00000379510.3	hg19	CCDS14198.1																																																																																			.	.		0.348	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927		G	21458842	A	G	21458842	2	3	100	1	0	0	0	0	0	0	0	1	3609	175	7	2		2	CNKSR2	23	21458842	Silent	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	17885512	21458842	133811718	259	13828										
CXorf22	170063	hgsc.bcm.edu	37	chrX	35966467	35966467	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ataccacggccaattacccaTcctcatttttccaactagtg	4	14	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:35966467T>C	ENST00000297866.5	+	4	620	c.554T>C	c.(553-555)aTc>aCc	p.I185T		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	185										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						CAATTACCCATCCTCATTTTT	0.408																																					p.I185T		Atlas-SNP	.											.	CXorf22	272	.	0			c.T554C						.						207	163	178					X																	35966467		2202	4300	6502	SO:0001583	missense	170063	exon4			TACCCATCCTCAT	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.554T>C	chrX.hg19:g.35966467T>C	ENSP00000297866:p.Ile185Thr	78.0	0.0		52.0	5.0	NM_152632	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	hg19	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	T	12.07	1.828867	0.32329	.	.	ENSG00000165164	ENST00000297866	T	0.42900	0.96	4.91	4.91	0.64330	.	0.297149	0.36628	N	0.002483	T	0.53530	0.1802	M	0.70275	2.135	0.09310	N	0.999999	P	0.51240	0.943	P	0.51777	0.679	T	0.53251	-0.8465	10	0.62326	D	0.03	-0.5245	13.0394	0.58891	0.0:0.0:0.0:1.0	.	185	Q6ZTR5	CX022_HUMAN	T	185	ENSP00000297866:I185T	ENSP00000297866:I185T	I	+	2	0	CXorf22	35876388	0.998000	0.40836	0.398000	0.26321	0.084000	0.17831	3.518000	0.53451	1.739000	0.51704	0.433000	0.28618	ATC	.	.		0.408	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		C	35966467	T	C	35966467	3	2	100	1	0	0	0	0	1	0	0	0	4104	1435	50	2	568	2	CXorf22	23	35966467	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	14507625	35966467	119304093	260	13829										
SUV39H1	6839	hgsc.bcm.edu	37	chrX	48558562	48558562	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ccacggcagaatctcaagtgTgtgcgtatcctcaagcagtt	10	11	2	1			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:48558562T>C	ENST00000376687.3	+	3	436	c.246T>C	c.(244-246)tgT>tgC	p.C82C	SUV39H1_ENST00000453214.2_Missense_Mutation_p.C20R|AF196970.3_ENST00000416061.1_RNA|SUV39H1_ENST00000337852.6_Silent_p.C93C	NM_003173.2	NP_003164.1	O43463	SUV91_HUMAN	suppressor of variegation 3-9 homolog 1 (Drosophila)	82	Chromo. {ECO:0000255|PROSITE- ProRule:PRU00053}.|Interaction with SIRT1.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chromatin organization (GO:0006325)|chromatin silencing at rDNA (GO:0000183)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin silencing complex (GO:0005677)|chromosome, centromeric region (GO:0000775)|condensed nuclear chromosome (GO:0000794)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|rDNA heterochromatin (GO:0033553)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|protein N-terminus binding (GO:0047485)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14						ATCTCAAGTGTGTGCGTATCC	0.582																																					p.C82C		Atlas-SNP	.											.	SUV39H1	36	.	0			c.T246C						.						28	20	23					X																	48558562		2200	4297	6497	SO:0001819	synonymous_variant	6839	exon3			CAAGTGTGTGCGT	AF019968	CCDS14304.1, CCDS65252.1	Xp11.23	2011-07-01	2001-11-28		ENSG00000101945	ENSG00000101945		"Chromatin-modifying enzymes / K-methyltransferases"	11479	protein-coding gene	gene with protein product		300254	"suppressor of variegation 3-9 (Drosophila) homolog 1"	SUV39H		10202156	Standard	NM_001282166		Approved	KMT1A	uc004dkn.3	O43463	OTTHUMG00000022701	ENST00000376687.3:c.246T>C	chrX.hg19:g.48558562T>C		83.0	0.0		71.0	5.0	NM_003173	B2R6E8|B4DST0|Q53G60|Q6FHK6	Silent	SNP	ENST00000376687.3	hg19	CCDS14304.1	.	.	.	.	.	.	.	.	.	.	T	9.572	1.121393	0.20877	.	.	ENSG00000101945	ENST00000448548;ENST00000453214	.	.	.	4.82	2.45	0.29901	.	0.000000	0.85682	D	0.000000	T	0.38799	0.1054	.	.	.	0.41190	D	0.986292	.	.	.	.	.	.	T	0.08126	-1.0737	6	0.13470	T	0.59	.	6.0384	0.19720	0.0:0.3262:0.0:0.6738	.	.	.	.	R	82;20	.	ENSP00000410043:C82R	C	+	1	0	SUV39H1	48443506	0.001000	0.12720	0.763000	0.31416	0.491000	0.33493	-0.159000	0.10056	0.119000	0.18210	0.409000	0.27619	TGT	.	.		0.582	SUV39H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058909.1	NM_003173		C	48558562	T	C	48558562	2	2	100	1	0	0	0	0	0	0	0	1	15427	1702	59	2		2	SUV39H1	23	48558562	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	12592095	48558562	106711998	261	13830										
TSPYL2	64061	hgsc.bcm.edu	37	chrX	53114958	53114958	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	tcatggagaccaccgactacTtcgagaccactgacaatgag	9	12	1	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:53114958T>C	ENST00000375442.4	+	6	1516	c.1384T>C	c.(1384-1386)Ttc>Ctc	p.F462L		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	462					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						CACCGACTACTTCGAGACCAC	0.443																																					p.F462L		Atlas-SNP	.											.	TSPYL2	53	.	0			c.T1384C						.						201	161	175					X																	53114958		2203	4300	6503	SO:0001583	missense	64061	exon6			GACTACTTCGAGA	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.1384T>C	chrX.hg19:g.53114958T>C	ENSP00000364591:p.Phe462Leu	94.0	0.0		82.0	4.0	NM_022117	O94799|Q96DG7|Q9BZW6	Missense_Mutation	SNP	ENST00000375442.4	hg19	CCDS14350.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.068313	0.36470	.	.	ENSG00000184205	ENST00000375442	T	0.30448	1.53	2.63	1.39	0.22231	.	0.000000	0.33854	U	0.004489	T	0.30947	0.0781	L	0.29908	0.895	0.25560	N	0.987002	P;P	0.49447	0.659;0.924	B;P	0.57776	0.32;0.827	T	0.07252	-1.0782	10	0.72032	D	0.01	-4.9966	4.3252	0.11036	0.3033:0.0:0.0:0.6967	.	102;462	Q59GC7;Q9H2G4	.;TSYL2_HUMAN	L	462	ENSP00000364591:F462L	ENSP00000364591:F462L	F	+	1	0	TSPYL2	53131683	1.000000	0.71417	0.970000	0.41538	0.135000	0.20990	1.666000	0.37460	0.279000	0.22186	0.231000	0.17811	TTC	.	.		0.443	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		C	53114958	T	C	53114958	3	2	100	1	0	0	0	0	1	0	0	0	16675	1609	56	2	1406	2	TSPYL2	23	53114958	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	4556396	53114958	102155602	262	13831										
ATRX	546	hgsc.bcm.edu	37	chrX	76972657	76972657	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ggagaacttgtttcttcagaTtcttctgatgagtgtgcaag	11	6	4	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:76972657T>C	ENST00000373344.5	-	2	298	c.84A>G	c.(82-84)gaA>gaG	p.E28E	ATRX_ENST00000395603.3_Silent_p.E28E|ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000373341.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	28					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TTTCTTCAGATTCTTCTGATG	0.328			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.E28E		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.A84G						.						172	159	163					X																	76972657		2203	4296	6499	SO:0001819	synonymous_variant	546	exon2			TTCAGATTCTTCT	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.84A>G	chrX.hg19:g.76972657T>C		84.0	0.0		55.0	7.0	NM_138270	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Silent	SNP	ENST00000373344.5	hg19	CCDS14434.1																																																																																			.	.		0.328	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		C	76972657	T	C	76972657	2	2	100	1	0	0	0	0	0	0	0	1	1208	1490	52	2		2	ATRX	23	76972657	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	23857699	76972657	78297903	263	13832										
PCDH19	57526	hgsc.bcm.edu	37	chrX	99657571	99657571	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ggtcaggctgctggggccccTggctgttgaaagagtgatgg	18	8	1	3			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:99657571T>C	ENST00000373034.4	-	3	4242	c.2567A>G	c.(2566-2568)cAg>cGg	p.Q856R	PCDH19_ENST00000255531.7_Missense_Mutation_p.Q809R|PCDH19_ENST00000420881.2_Missense_Mutation_p.Q809R	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	856					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						CTGGGGCCCCTGGCTGTTGAA	0.557																																					p.Q856R		Atlas-SNP	.											.	PCDH19	269	.	0			c.A2567G						.						101	94	96					X																	99657571		2022	4170	6192	SO:0001583	missense	57526	exon3			GGCCCCTGGCTGT	AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.2567A>G	chrX.hg19:g.99657571T>C	ENSP00000362125:p.Gln856Arg	139.0	0.0		69.0	4.0	NM_001184880	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	hg19	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	t	16.77	3.215336	0.58452	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.53640	0.61;0.64;0.61	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	L	0.43152	1.355	0.58432	D	0.999999	P;P;B	0.42827	0.791;0.572;0.437	B;B;B	0.38755	0.212;0.281;0.146	T	0.20306	-1.0279	10	0.22706	T	0.39	.	14.8534	0.70316	0.0:0.0:0.0:1.0	.	856;809;809	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	R	809;856;809	ENSP00000400327:Q809R;ENSP00000362125:Q856R;ENSP00000255531:Q809R	ENSP00000255531:Q809R	Q	-	2	0	PCDH19	99544227	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.448000	0.80631	1.889000	0.54706	0.481000	0.45027	CAG	.	.		0.557	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		C	99657571	T	C	99657571	3	2	100	1	0	0	0	0	1	0	0	0	11523	1580	55	2	895	2	PCDH19	23	99657571	Missense_Mutation	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	22684914	99657571	55612989	264	13833										
CXorf57	55086	hgsc.bcm.edu	37	chrX	105876229	105876229	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	gccttttagtttttgtaggaAgggtccagcggtcaaaaaag	12	6	1	0			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:105876229A>G	ENST00000372548.4	+	5	1265	c.1156A>G	c.(1156-1158)Agg>Ggg	p.R386G	CXorf57_ENST00000372544.2_Missense_Mutation_p.R386G	NM_018015.5	NP_060485.4	Q6NSI4	CX057_HUMAN	chromosome X open reading frame 57	386							poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	31						TTTTGTAGGAAGGGTCCAGCG	0.294																																					p.R386G		Atlas-SNP	.											.	CXorf57	107	.	0			c.A1156G						.						89	91	90					X																	105876229		2203	4298	6501	SO:0001583	missense	55086	exon5			GTAGGAAGGGTCC	AK024253	CCDS14519.1, CCDS55470.1	Xq22.3	2008-02-05			ENSG00000147231	ENSG00000147231			25486	protein-coding gene	gene with protein product							Standard	NM_018015		Approved	FLJ14191, FLJ10178	uc004emi.4	Q6NSI4	OTTHUMG00000022150	ENST00000372548.4:c.1156A>G	chrX.hg19:g.105876229A>G	ENSP00000361628:p.Arg386Gly	238.0	0.0		186.0	8.0	NM_018015	H7BY89|Q4G0L7|Q5JQS1|Q5JRF9|Q6PHY5|Q6PII9|Q6PJU8|Q9H7W5|Q9NWA6	Missense_Mutation	SNP	ENST00000372548.4	hg19	CCDS14519.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.826405	0.50739	.	.	ENSG00000147231	ENST00000372544;ENST00000372548;ENST00000421550	T;T;T	0.66460	-0.21;-0.15;-0.04	4.53	4.53	0.55603	.	0.045750	0.85682	D	0.000000	T	0.78868	0.4351	M	0.66939	2.045	0.38835	D	0.955925	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.998;0.996	T	0.82151	-0.0599	10	0.66056	D	0.02	-16.1492	12.3285	0.55024	1.0:0.0:0.0:0.0	.	386;386;386	A8K6R5;Q6NSI4;Q6NSI4-2	.;CX057_HUMAN;.	G	386;386;194	ENSP00000361623:R386G;ENSP00000361628:R386G;ENSP00000405866:R194G	ENSP00000361623:R386G	R	+	1	2	CXorf57	105762885	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	4.361000	0.59461	1.746000	0.51805	0.481000	0.45027	AGG	.	.		0.294	CXorf57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057800.2	NM_018015		G	105876229	A	G	105876229	3	3	100	1	0	0	0	0	1	0	0	0	4115	63	3	2	1174	2	CXorf57	23	105876229	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	6218658	105876229	49394331	265	13834										
LUZP4	51213	hgsc.bcm.edu	37	chrX	114540807	114540807	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	ttatgaggcccaagcagagaAgaatcaaggccagtcagagg	13	8	2	4			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:114540807A>G	ENST00000371920.3	+	4	387	c.380A>G	c.(379-381)aAg>aGg	p.K127R	LUZP4_ENST00000451986.2_Missense_Mutation_p.K45R	NM_016383.3	NP_057467.1	Q9P127	LUZP4_HUMAN	leucine zipper protein 4	127						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	14						CAAGCAGAGAAGAATCAAGGC	0.408																																					p.K127R		Atlas-SNP	.											.	LUZP4	51	.	0			c.A380G						.						71	69	70					X																	114540807		2203	4300	6503	SO:0001583	missense	51213	exon4			CAGAGAAGAATCA	AF124430	CCDS14567.1	Xq24	2009-03-25			ENSG00000102021	ENSG00000102021			24971	protein-coding gene	gene with protein product	"cancer/testis antigen 28"	300616				12032826, 11051238	Standard	XM_005268343		Approved	HOM-TES-85, CT-8, CT28	uc004eqa.3	Q9P127	OTTHUMG00000022234	ENST00000371920.3:c.380A>G	chrX.hg19:g.114540807A>G	ENSP00000360988:p.Lys127Arg	157.0	0.0		112.0	5.0	NM_016383	B3KSD6	Missense_Mutation	SNP	ENST00000371920.3	hg19	CCDS14567.1	.	.	.	.	.	.	.	.	.	.	A	10.71	1.428057	0.25726	.	.	ENSG00000102021	ENST00000451986;ENST00000371920	T;T	0.53423	0.62;1.33	3.01	-4.19	0.03835	.	.	.	.	.	T	0.19525	0.0469	N	0.12182	0.205	0.09310	N	1	B;B	0.17038	0.02;0.02	B;B	0.15484	0.008;0.013	T	0.19418	-1.0306	9	0.17832	T	0.49	.	0.7359	0.00965	0.3859:0.1638:0.2857:0.1646	.	45;127	B3KSD6;Q9P127	.;LUZP4_HUMAN	R	45;127	ENSP00000411212:K45R;ENSP00000360988:K127R	ENSP00000360988:K127R	K	+	2	0	LUZP4	114447063	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	-0.550000	0.06034	-0.912000	0.03837	0.376000	0.23039	AAG	.	.		0.408	LUZP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057972.1	NM_016383		G	114540807	A	G	114540807	3	3	100	1	0	0	0	0	1	0	0	0	9097	72	3	2	394	2	LUZP4	23	114540807	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	8664578	114540807	40729753	266	13835										
NKRF	55922	hgsc.bcm.edu	37	chrX	118724383	118724383	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	atgacaaaattggtccagtgTttggcagaagcattaaaaat	9	5	0	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:118724383T>C	ENST00000371527.1	-	2	1657	c.1005A>G	c.(1003-1005)aaA>aaG	p.K335K	NKRF_ENST00000542113.1_Silent_p.K350K|NKRF_ENST00000304449.5_Silent_p.K335K|NKRF_ENST00000487600.1_Intron	NM_001173488.1	NP_001166959.1	O15226	NKRF_HUMAN	NFKB repressing factor	335					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	30						TGGTCCAGTGTTTGGCAGAAG	0.413																																					p.K350K		Atlas-SNP	.											.	NKRF	121	.	0			c.A1050G						.						100	99	99					X																	118724383		2203	4300	6503	SO:0001819	synonymous_variant	55922	exon4			CCAGTGTTTGGCA	AJ011812	CCDS35375.1, CCDS55486.1	Xq24	2013-01-28	2008-03-26		ENSG00000186416	ENSG00000186416		"G patch domain containing"	19374	protein-coding gene	gene with protein product		300440	"NF-kappaB repressing factor"			10562553	Standard	NM_017544		Approved	ITBA4, NRF	uc022cdk.1	O15226	OTTHUMG00000022277	ENST00000371527.1:c.1005A>G	chrX.hg19:g.118724383T>C		123.0	0.0		86.0	4.0	NM_001173487	G3V1N1|Q4VC41|Q9UJ91	Silent	SNP	ENST00000371527.1	hg19	CCDS35375.1																																																																																			.	.		0.413	NKRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058044.1	NM_017544		C	118724383	T	C	118724383	2	2	100	1	0	0	0	0	0	0	0	1	10456	1722	60	2		2	NKRF	23	118724383	Silent	SNP	T	TCGA-DD-A1ED-01A-11D-A152-10	4183576	118724383	36546177	267	13836										
STAG2	10735	hgsc.bcm.edu	37	chrX	123200272	123200272	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0149253731343284	4	1	0.77037037037037	1.58888888888889	0.657471264367816	0.523809523809524	1	0	aacttgctaagataactgaaAgcagctctacaaaggtttgt	8	7	1	2			TCGA-DD-A1ED-01A-11D-A152-10	TCGA-DD-A1ED-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c3eda94-56f4-46d3-8c88-50d476e773f6	09455f77-1bc1-4f4b-9b75-dd79fd3237c3	g.chrX:123200272A>G	ENST00000371160.1	+	23	2541	c.2251A>G	c.(2251-2253)Agc>Ggc	p.S751G	STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.S751G|STAG2_ENST00000371157.3_Missense_Mutation_p.S751G|STAG2_ENST00000371144.3_Missense_Mutation_p.S751G|STAG2_ENST00000371145.3_Missense_Mutation_p.S751G|STAG2_ENST00000354548.5_Missense_Mutation_p.S682G	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	751					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GATAACTGAAAGCAGCTCTAC	0.328																																					p.S751G		Atlas-SNP	.											.	STAG2	309	.	0			c.A2251G						.						90	72	78					X																	123200272		2203	4300	6503	SO:0001583	missense	10735	exon23			ACTGAAAGCAGCT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.2251A>G	chrX.hg19:g.123200272A>G	ENSP00000360202:p.Ser751Gly	182.0	0.0		93.0	5.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	6.955	0.546148	0.13312	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46;1.46	5.32	5.32	0.75619	Armadillo-type fold (1);	0.088399	0.85682	D	0.000000	T	0.11537	0.0281	N	0.01277	-0.915	0.46901	D	0.999248	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.16988	-1.0384	10	0.11794	T	0.64	-17.6528	14.5796	0.68278	1.0:0.0:0.0:0.0	.	751;751	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	G	751;682;751;751;751;751	ENSP00000218089:S751G;ENSP00000346555:S682G;ENSP00000360202:S751G;ENSP00000360199:S751G;ENSP00000360187:S751G;ENSP00000360186:S751G	ENSP00000218089:S751G	S	+	1	0	STAG2	123027953	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.218000	0.72224	1.891000	0.54761	0.486000	0.48141	AGC	.	.		0.328	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		G	123200272	A	G	123200272	3	3	100	1	0	0	0	0	1	0	0	0	15258	72	3	2	2333	2	STAG2	23	123200272	Missense_Mutation	SNP	A	TCGA-DD-A1ED-01A-11D-A152-10	4475889	123200272	32070288	268	13837										
C1orf93	127281	hgsc.bcm.edu	37	chr1	2520399	2520399	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgcatttcgtccagaagtccCcaggcgactacgtccccaag	9	15	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:2520399C>G	ENST00000378425.5	+	6	575	c.499C>G	c.(499-501)Cca>Gca	p.P167A	FAM213B_ENST00000419916.2_Missense_Mutation_p.P197A|FAM213B_ENST00000378424.4_Missense_Mutation_p.P204R|FAM213B_ENST00000484099.1_3'UTR|FAM213B_ENST00000537325.1_Missense_Mutation_p.P160A|FAM213B_ENST00000444521.2_Missense_Mutation_p.P185A			Q8TBF2	PGFS_HUMAN	family with sequence similarity 213, member B	167					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|myelin sheath (GO:0043209)	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|prostaglandin-F synthase activity (GO:0047017)	p.P167T(1)									CCAGAAGTCCCCAGGCGACTA	0.652																																					p.P215A		Atlas-SNP	.											C1orf93,caecum,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C643G						.						62	62	62					1																	2520399		2203	4300	6503	SO:0001583	missense	127281	exon6			AAGTCCCCAGGCG	AK075273	CCDS44.1, CCDS44.2, CCDS55564.1, CCDS72690.1, CCDS72691.1	1p36.32	2011-12-08	2011-11-24	2011-11-24	ENSG00000157870	ENSG00000157870	1.11.1.20		28390	protein-coding gene	gene with protein product	"prostamide/prostaglandin F synthase"		"chromosome 1 open reading frame 93"	C1orf93		18006499	Standard	NM_152371		Approved	MGC26818	uc001ajv.2	Q8TBF2	OTTHUMG00000000847	ENST00000378425.5:c.499C>G	chr1.hg19:g.2520399C>G	ENSP00000367682:p.Pro167Ala	46.0	1.0		169.0	34.0	NM_001195736	A8K793|B3KPY3|B4DQR9|B4E0S5|B7ZAC8|B9DI90|B9DI92|J3KQD0|Q8N2H0	Missense_Mutation	SNP	ENST00000378425.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.352|6.352	0.433117|0.433117	0.12045|0.12045	.|.	.|.	ENSG00000157870|ENSG00000157870	ENST00000419916;ENST00000537325;ENST00000378425;ENST00000444521|ENST00000378424	T;T;T;T|T	0.50548|0.50548	0.99;0.74;1.01;0.89|0.74	4.44|4.44	4.44|4.44	0.53790|0.53790	.|.	1.149570|1.149570	0.06726|0.06726	N|N	0.775697|0.775697	T|T	0.42381|0.42381	0.1200|0.1200	.|.	.|.	.|.	0.50632|0.50632	D|D	0.99988|0.99988	D;D;D;D;P|P	0.89917|0.36837	1.0;0.982;0.98;0.98;0.929|0.571	D;P;P;P;B|B	0.91635|0.33254	0.999;0.831;0.79;0.838;0.408|0.16	T|T	0.33033|0.33033	-0.9884|-0.9884	9|9	0.15952|0.56958	T|D	0.53|0.05	-3.3791|-3.3791	12.413|12.413	0.55478|0.55478	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	160;131;193;185;167|156	Q8TBF2-5;Q8TBF2-4;Q8TBF2-6;Q8TBF2-3;Q8TBF2|Q8TBF2-2	.;.;.;.;PGFS_HUMAN|.	A|R	197;160;167;185|204	ENSP00000394405:P197A;ENSP00000443605:P160A;ENSP00000367682:P167A;ENSP00000413218:P185A|ENSP00000367681:P204R	ENSP00000367682:P167A|ENSP00000367681:P204R	P|P	+|+	1|2	0|0	C1orf93|C1orf93	2510259|2510259	0.975000|0.975000	0.34042|0.34042	0.701000|0.701000	0.30321|0.30321	0.011000|0.011000	0.07611|0.07611	5.228000|5.228000	0.65310|0.65310	2.301000|2.301000	0.77427|0.77427	0.313000|0.313000	0.20887|0.20887	CCA|CCC	.	.		0.652	FAM213B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152371		G	2520399	C	G	2520399	3	3	101	1	0	0	0	0	1	0	0	0	2072	623	22	4	521	4	C1orf93	1	2520399	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10		2520399	246730222	1	13838										
MMEL1	79258	hgsc.bcm.edu	37	chr1	2535696	2535696	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caacgtggccactgacaccaTgaactgcaggtaggcttccc	10	14	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:2535696T>C	ENST00000378412.3	-	10	1002	c.841A>G	c.(841-843)Atg>Gtg	p.M281V	MMEL1_ENST00000288709.6_Missense_Mutation_p.M272V|MMEL1_ENST00000502556.1_Intron			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	281						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		ACTGACACCATGAACTGCAGG	0.652																																					p.M281V		Atlas-SNP	.											.	MMEL1	64	.	0			c.A841G						.						63	65	64					1																	2535696		2202	4299	6501	SO:0001583	missense	79258	exon10			ACACCATGAACTG	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"membrane metallo-endopeptidase-like 2"	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.841A>G	chr1.hg19:g.2535696T>C	ENSP00000367668:p.Met281Val	76.0	0.0		235.0	28.0	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	hg19	CCDS30569.2	.	.	.	.	.	.	.	.	.	.	T	18.27	3.585868	0.66105	.	.	ENSG00000142606	ENST00000288709;ENST00000378412	T;T	0.75050	-0.9;-0.9	4.43	4.43	0.53597	Peptidase M13 (1);	0.000000	0.85682	D	0.000000	D	0.85639	0.5743	M	0.82823	2.61	0.80722	D	1	D	0.76494	0.999	D	0.69654	0.965	D	0.87970	0.2736	10	0.87932	D	0	-31.6286	13.1682	0.59583	0.0:0.0:0.0:1.0	.	281	Q495T6	MMEL1_HUMAN	V	272;281	ENSP00000288709:M272V;ENSP00000367668:M281V	ENSP00000288709:M272V	M	-	1	0	MMEL1	2525556	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	3.567000	0.53813	1.741000	0.51731	0.397000	0.26171	ATG	.	.		0.652	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467		C	2535696	T	C	2535696	3	2	101	1	0	0	0	0	1	0	0	0	9655	1464	51	2	1558	2	MMEL1	1	2535696	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	15297	2535696	246714925	2	13839										
ACTRT2	140625	hgsc.bcm.edu	37	chr1	2938475	2938475	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctgcagctgcactcccctttCgagcgtggcctgatcacagg	11	15	1	1	rs144521527		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:2938475C>T	ENST00000378404.2	+	1	430	c.225C>T	c.(223-225)ttC>ttT	p.F75F		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	75						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		ACTCCCCTTTCGAGCGTGGCC	0.597																																					p.F75F		Atlas-SNP	.											.	ACTRT2	69	.	0			c.C225T						.	C		1,4405	2.1+/-5.4	0,1,2202	73	73	73		225	-1.3	1	1	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ACTRT2	NM_080431.4		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		75/378	2938475	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	140625	exon1			CCCTTTCGAGCGT	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.225C>T	chr1.hg19:g.2938475C>T		48.0	0.0		93.0	11.0	NM_080431	B1AN52|Q8NHS6|Q8TDG1	Silent	SNP	ENST00000378404.2	hg19	CCDS45.1																																																																																			.	C|1.000;T|0.000		0.597	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431		T	2938475	C	T	2938475	2	4	101	1	0	0	0	0	0	0	0	1	219	883	31	1		1	ACTRT2	1	2938475	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	402779	2938475	246312146	3	13840										
H6PD	9563	hgsc.bcm.edu	37	chr1	9305494	9305494	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cggccaggcccgggcgcctgGctgcgggttgtccttgagaa	17	13	0	1	rs559063919		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:9305494G>A	ENST00000377403.2	+	2	803	c.501G>A	c.(499-501)tgG>tgA	p.W167*	H6PD_ENST00000602477.1_Nonsense_Mutation_p.W178*	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	167	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		CGGGCGCCTGGCTGCGGGTTG	0.597																																					p.W167X		Atlas-SNP	.											.	H6PD	71	.	0			c.G501A						.						46	55	52					1																	9305494		2203	4300	6503	SO:0001587	stop_gained	9563	exon2			CGCCTGGCTGCGG	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"glucose dehyrogenase"	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.501G>A	chr1.hg19:g.9305494G>A	ENSP00000366620:p.Trp167*	16.0	0.0		63.0	11.0	NM_004285	Q4TT33|Q66I35|Q68DT3	Nonsense_Mutation	SNP	ENST00000377403.2	hg19	CCDS101.1	.	.	.	.	.	.	.	.	.	.	G	40	8.156138	0.98680	.	.	ENSG00000049239	ENST00000377403	.	.	.	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.7585	18.3309	0.90268	0.0:0.0:1.0:0.0	.	.	.	.	X	167	.	ENSP00000366620:W167X	W	+	3	0	H6PD	9228081	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.358000	0.97109	2.641000	0.89580	0.591000	0.81541	TGG	.	.		0.597	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		A	9305494	G	A	9305494	4	1	101	1	0	0	0	0	0	1	0	0	6945	1212	42	3	503	3	H6PD	1	9305494	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6367019	9305494	239945127	4	13841										
SRM	6723	hgsc.bcm.edu	37	chr1	11119332	11119332	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caggttggcgatcatctcctGgtaggagaactcgtctctct	11	11	4	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:11119332G>A	ENST00000376957.2	-	2	318	c.238C>T	c.(238-240)Cag>Tag	p.Q80*		NM_003132.2	NP_003123.2	P19623	SPEE_HUMAN	spermidine synthase	80	PABS.				cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)|spermidine synthase activity (GO:0004766)			large_intestine(1)|lung(1)|urinary_tract(1)	3	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.228)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)	S-Adenosylmethionine(DB00118)	ATCATCTCCTGGTAGGAGAAC	0.637																																					p.Q80X		Atlas-SNP	.											.	SRM	18	.	0			c.C238T						.						116	101	106					1																	11119332		2203	4300	6503	SO:0001587	stop_gained	6723	exon2			TCTCCTGGTAGGA	BC033106	CCDS125.1	1p36-p22	2010-11-08			ENSG00000116649	ENSG00000116649	2.5.1.16		11296	protein-coding gene	gene with protein product		182891		SRML1		2344393	Standard	NM_003132		Approved	SPS1	uc001arz.1	P19623	OTTHUMG00000002119	ENST00000376957.2:c.238C>T	chr1.hg19:g.11119332G>A	ENSP00000366156:p.Gln80*	71.0	0.0		178.0	8.0	NM_003132	B1AKP9|Q15511	Nonsense_Mutation	SNP	ENST00000376957.2	hg19	CCDS125.1	.	.	.	.	.	.	.	.	.	.	G	37	6.242829	0.97408	.	.	ENSG00000116649	ENST00000376957	.	.	.	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.289	0.66265	0.0:0.0:1.0:0.0	.	.	.	.	X	80	.	ENSP00000366156:Q80X	Q	-	1	0	SRM	11041919	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.865000	0.92300	2.191000	0.70037	0.448000	0.29417	CAG	.	.		0.637	SRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006056.1	NM_003132		A	11119332	G	A	11119332	4	1	101	1	0	0	0	0	0	1	0	0	15166	1357	47	3	698	3	SRM	1	11119332	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1813838	11119332	238131289	5	13842										
DHRS3	9249	hgsc.bcm.edu	37	chr1	12677249	12677249	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggacgttctcccgcgacagGtcccgcagcttggcgggcag	15	14	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:12677249G>T	ENST00000376223.2	-	1	488	c.105C>A	c.(103-105)gaC>gaA	p.D35E	RP11-474O21.5_ENST00000606790.1_lincRNA|DHRS3_ENST00000482265.1_5'Flank	NM_004753.4	NP_004744.2	O75911	DHRS3_HUMAN	dehydrogenase/reductase (SDR family) member 3	35					bone morphogenesis (GO:0060349)|cardiac septum morphogenesis (GO:0060411)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|phototransduction, visible light (GO:0007603)|regulation of ossification (GO:0030278)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|photoreceptor outer segment membrane (GO:0042622)	electron carrier activity (GO:0009055)|NADP-retinol dehydrogenase activity (GO:0052650)|nucleotide binding (GO:0000166)|retinol dehydrogenase activity (GO:0004745)			cervix(1)|large_intestine(4)|lung(2)|prostate(1)|skin(1)	9	Ovarian(185;0.249)	Lung NSC(185;4.11e-05)|all_lung(284;4.58e-05)|Renal(390;0.000147)|Colorectal(325;0.000585)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;9.25e-07)|COAD - Colon adenocarcinoma(227;0.000326)|BRCA - Breast invasive adenocarcinoma(304;0.000344)|Kidney(185;0.00235)|KIRC - Kidney renal clear cell carcinoma(229;0.00656)|STAD - Stomach adenocarcinoma(313;0.00798)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	CCCGCGACAGGTCCCGCAGCT	0.662																																					p.D35E		Atlas-SNP	.											.	DHRS3	18	.	0			c.C105A						.						61	65	64					1																	12677249		2203	4298	6501	SO:0001583	missense	9249	exon1			CGACAGGTCCCGC	AF061741	CCDS146.1	1p36.1	2011-09-20			ENSG00000162496	ENSG00000162496	1.1.-.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	17693	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 16C, member 1"	612830				9705317, 12226107, 19027726	Standard	XM_005263533		Approved	retSDR1, Rsdr1, SDR1, RDH17, SDR16C1	uc001auc.3	O75911	OTTHUMG00000001885	ENST00000376223.2:c.105C>A	chr1.hg19:g.12677249G>T	ENSP00000365397:p.Asp35Glu	42.0	0.0		120.0	45.0	NM_004753	B2R7F3|Q5VUY3|Q6UY38|Q9BUC8	Missense_Mutation	SNP	ENST00000376223.2	hg19	CCDS146.1	.	.	.	.	.	.	.	.	.	.	G	18.66	3.671885	0.67928	.	.	ENSG00000162496	ENST00000376223	D	0.90133	-2.62	5.05	4.12	0.48240	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.81955	0.4932	N	0.08118	0	0.52099	D	0.999943	P;B;P	0.46395	0.877;0.34;0.877	B;B;B	0.43194	0.411;0.171;0.411	T	0.82145	-0.0602	10	0.38643	T	0.18	.	13.7562	0.62937	0.0:0.0:0.8449:0.1551	.	35;35;35	B2R7F3;O75911-2;O75911	.;.;DHRS3_HUMAN	E	35	ENSP00000365397:D35E	ENSP00000365397:D35E	D	-	3	2	DHRS3	12599836	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.051000	0.57412	1.066000	0.40716	0.561000	0.74099	GAC	.	.		0.662	DHRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005318.1	NM_004753		T	12677249	G	T	12677249	3	4	101	1	0	0	0	0	1	0	0	0	4493	1252	44	3	827	3	DHRS3	1	12677249	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1557917	12677249	236573372	6	13843										
TMEM82	388595	hgsc.bcm.edu	37	chr1	16073479	16073479	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctggacctgctgggcatccTtgtctccctactgggcgagc	13	14	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:16073479T>A	ENST00000375782.1	+	5	1013	c.875T>A	c.(874-876)cTt>cAt	p.L292H	RP11-169K16.4_ENST00000418525.1_RNA	NM_001013641.1	NP_001013663.1	A0PJX8	TMM82_HUMAN	transmembrane protein 82	292	Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|lung(5)|prostate(1)|skin(1)	13		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGGCATCCTTGTCTCCCTA	0.672																																					p.L292H		Atlas-SNP	.											.	TMEM82	30	.	0			c.T875A						.						99	87	91					1																	16073479		2203	4300	6503	SO:0001583	missense	388595	exon5			GCATCCTTGTCTC		CCDS30608.1	1p36.13	2008-02-05				ENSG00000162460			32350	protein-coding gene	gene with protein product							Standard	NM_001013641		Approved		uc001axc.4	A0PJX8		ENST00000375782.1:c.875T>A	chr1.hg19:g.16073479T>A	ENSP00000364938:p.Leu292His	72.0	0.0		187.0	19.0	NM_001013641	B2RP27|Q5VVD4	Missense_Mutation	SNP	ENST00000375782.1	hg19	CCDS30608.1	.	.	.	.	.	.	.	.	.	.	T	14.68	2.608396	0.46527	.	.	ENSG00000162460	ENST00000375782	T	0.54279	0.58	4.8	3.67	0.42095	.	0.709482	0.13524	N	0.381498	T	0.58892	0.2154	L	0.38175	1.15	0.21627	N	0.999612	D	0.71674	0.998	D	0.63192	0.912	T	0.48559	-0.9025	10	0.72032	D	0.01	-4.3264	9.972	0.41761	0.0:0.0812:0.0:0.9188	.	292	A0PJX8	TMM82_HUMAN	H	292	ENSP00000364938:L292H	ENSP00000364938:L292H	L	+	2	0	TMEM82	15946066	0.439000	0.25610	0.002000	0.10522	0.114000	0.19823	4.145000	0.58065	0.862000	0.35528	0.379000	0.24179	CTT	.	.		0.672	TMEM82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008471.2	NM_001013641		A	16073479	T	A	16073479	3	1	101	1	0	0	0	0	1	0	0	0	16221	1609	56	4	893	4	TMEM82	1	16073479	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	3396230	16073479	233177142	7	13844										
SYF2	25949	hgsc.bcm.edu	37	chr1	25558651	25558651	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctgttcgcgcttctgagcggCcagctccgccgccgcagcga	13	17	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:25558651C>A	ENST00000236273.4	-	2	101	c.76G>T	c.(76-78)Gcc>Tcc	p.A26S	SYF2_ENST00000354361.3_Missense_Mutation_p.A26S|SYF2_ENST00000476231.1_5'UTR	NM_015484.4	NP_056299.1	O95926	SYF2_HUMAN	SYF2 pre-mRNA-splicing factor	26					embryonic organ development (GO:0048568)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|mitotic G2 DNA damage checkpoint (GO:0007095)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(4)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-26)|Colorectal(126;2.54e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000455)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00145)|GBM - Glioblastoma multiforme(114;0.00443)|READ - Rectum adenocarcinoma(331;0.0936)|Lung(427;0.201)		TTCTGAGCGGCCAGCTCCGCC	0.647																																					p.A26S		Atlas-SNP	.											.	SYF2	13	.	0			c.G76T						.						21	25	24					1																	25558651		2203	4300	6503	SO:0001583	missense	25949	exon2			GAGCGGCCAGCTC	AF273089	CCDS258.1, CCDS259.1	1p36.11	2013-08-21	2013-08-21	2005-09-14	ENSG00000117614	ENSG00000117614			19824	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 29"	607090	"CCNDBP1 interactor", "SYF2 homolog, RNA splicing factor (S. cerevisiae)"	CBPIN		11118353	Standard	NM_207170		Approved	p29, DKFZp564O2082, NTC31, fSAP29	uc001bjt.1	O95926	OTTHUMG00000043610	ENST00000236273.4:c.76G>T	chr1.hg19:g.25558651C>A	ENSP00000236273:p.Ala26Ser	48.0	0.0		110.0	21.0	NM_207170	Q5TH73	Missense_Mutation	SNP	ENST00000236273.4	hg19	CCDS259.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.204648	0.79127	.	.	ENSG00000117614	ENST00000236273;ENST00000354361	T;T	0.47869	0.88;0.83	5.42	3.54	0.40534	.	0.104346	0.64402	N	0.000002	T	0.33847	0.0877	L	0.41236	1.265	0.54753	D	0.99998	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.08330	-1.0727	10	0.13470	T	0.59	-11.5655	9.2119	0.37324	0.146:0.7773:0.0:0.0768	.	26;26;26	B4E0Y8;B2RBX8;O95926	.;.;SYF2_HUMAN	S	26	ENSP00000236273:A26S;ENSP00000346330:A26S	ENSP00000236273:A26S	A	-	1	0	SYF2	25431238	1.000000	0.71417	0.992000	0.48379	0.806000	0.45545	2.272000	0.43373	0.651000	0.30788	0.561000	0.74099	GCC	.	.		0.647	SYF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000101962.1	NM_015484		A	25558651	C	A	25558651	3	1	101	1	0	0	0	0	1	0	0	0	15452	739	26	3	679	3	SYF2	1	25558651	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	9485172	25558651	223691970	8	13845										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27087894	27087898	+	Frame_Shift_Del	DEL	GCCAC	GCCAC	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggcaaccagatgccacctcgGccacccagtggccagtcgga							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	GCCAC	GCCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:27087894_27087898delGCCAC	ENST00000324856.7	+	6	2552_2556	c.2181_2185delGCCAC	c.(2179-2187)cggccacccfs	p.PP728fs	ARID1A_ENST00000457599.2_Frame_Shift_Del_p.PP728fs|RN7SL501P_ENST00000578818.1_RNA|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.PP345fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	728					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.R727fs*12(1)|p.P728fs(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TGCCACCTCGGCCACCCAGTGGCCA	0.522			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.727_728del		Atlas-Indel,Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.,1	ARID1A	842	.	2	Deletion - Frameshift(1)|Complex(1)	ovary(1)|liver(1)	c.2180_2184del						.																																			SO:0001589	frameshift_variant	8289	exon6			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2181_2185delGCCAC	chr1.hg19:g.27087894_27087898delGCCAC	ENSP00000320485:p.Pro728fs	119.0	0.0		280.0	26.0	NM_139135	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.522	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27087898	GCCAC	-	27087894	7	5	101	1	0	1	0	1	0	0	0	0	913	1190	42	0	2203	0	ARID1A	1	27087894	Frame_Shift_Del	DEL	GCCAC	TCGA-DD-A1EE-01A-11D-A12Z-10	1529243	27087894	222162727	9	13846										
PHACTR4	65979	hgsc.bcm.edu	37	chr1	28800595	28800595	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctttttgaaaacagtgacagCttttctgaggacagcagtac	9	8	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:28800595C>G	ENST00000373839.3	+	7	1614	c.1353C>G	c.(1351-1353)agC>agG	p.S451R	PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Missense_Mutation_p.S461R	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	451					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		ACAGTGACAGCTTTTCTGAGG	0.468																																					p.S461R		Atlas-SNP	.											.	PHACTR4	64	.	0			c.C1383G						.						120	121	121					1																	28800595		1970	4162	6132	SO:0001583	missense	65979	exon6			TGACAGCTTTTCT	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1353C>G	chr1.hg19:g.28800595C>G	ENSP00000362945:p.Ser451Arg	59.0	0.0		150.0	11.0	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	hg19	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	C	1.196	-0.633920	0.03584	.	.	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.23348	1.91;1.91	5.75	4.83	0.62350	.	1.347100	0.04068	N	0.307570	T	0.20659	0.0497	N	0.25647	0.755	0.19575	N	0.999967	B;B	0.31383	0.321;0.112	B;B	0.32465	0.146;0.068	T	0.29243	-1.0018	10	0.16420	T	0.52	-0.0126	7.5436	0.27753	0.0:0.7135:0.1374:0.1491	.	461;451	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	R	451;461;450	ENSP00000362945:S451R;ENSP00000362942:S461R	ENSP00000362942:S461R	S	+	3	2	PHACTR4	28673182	0.332000	0.24722	0.921000	0.36526	0.059000	0.15707	0.877000	0.28106	1.424000	0.47217	0.655000	0.94253	AGC	.	.		0.468	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		G	28800595	C	G	28800595	3	3	101	1	0	0	0	0	1	0	0	0	11821	796	28	4	1425	4	PHACTR4	1	28800595	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1712701	28800595	220450026	10	13847										
FAM176B	55194	hgsc.bcm.edu	37	chr1	36788575	36788575	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccggcgcccgccctcaccgcGgatgtgcgcgtaggcagcca	14	18	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:36788575G>C	ENST00000270824.1	-	2	355	c.64C>G	c.(64-66)Cgc>Ggc	p.R22G	RP11-268J15.5_ENST00000373137.2_5'Flank|SH3D21_ENST00000474766.1_Intron|EVA1B_ENST00000490466.1_5'UTR	NM_018166.1	NP_060636.1	Q9NVM1	EVA1B_HUMAN	eva-1 homolog B (C. elegans)	22						integral component of membrane (GO:0016021)											CCCTCACCGCGGATGTGCGCG	0.701																																					p.R22G		Atlas-SNP	.											.	.	.	.	0			c.C64G						.						40	45	44					1																	36788575		2203	4300	6503	SO:0001583	missense	55194	exon2			CACCGCGGATGTG	AK001509	CCDS406.1	1p34.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000142694	ENSG00000142694			25558	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 78", "family with sequence similarity 176, member B"	C1orf78, FAM176B		14702039	Standard	XM_005270998		Approved	FLJ10647	uc001caj.1	Q9NVM1	OTTHUMG00000007867	ENST00000270824.1:c.64C>G	chr1.hg19:g.36788575G>C	ENSP00000270824:p.Arg22Gly	94.0	0.0		244.0	21.0	NM_018166	D3DPS7	Missense_Mutation	SNP	ENST00000270824.1	hg19	CCDS406.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158435	0.78114	.	.	ENSG00000142694	ENST00000270824	T	0.48201	0.82	4.59	2.53	0.30540	.	0.066949	0.64402	D	0.000017	T	0.48370	0.1496	L	0.57536	1.79	0.48901	D	0.999725	P	0.52170	0.951	P	0.47744	0.556	T	0.52503	-0.8567	10	0.72032	D	0.01	.	10.318	0.43749	0.0:0.0:0.6473:0.3527	.	22	Q9NVM1	F176B_HUMAN	G	22	ENSP00000270824:R22G	ENSP00000270824:R22G	R	-	1	0	FAM176B	36561162	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	0.961000	0.29267	0.889000	0.36185	0.462000	0.41574	CGC	.	.		0.701	EVA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021689.1	NM_018166		C	36788575	G	C	36788575	3	2	101	1	0	0	0	0	1	0	0	0	5505	1116	39	4	441	4	FAM176B	1	36788575	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	7987980	36788575	212462046	11	13848										
SF3A3	10946	hgsc.bcm.edu	37	chr1	38453345	38453345	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tggcattgagctcctcctttCgtaatctgcaatttcaggaa	8	10	2	1	rs372195588		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:38453345C>T	ENST00000373019.4	-	4	1158	c.203G>A	c.(202-204)cGa>cAa	p.R68Q	SF3A3_ENST00000489537.1_5'UTR|SF3A3_ENST00000448721.2_Intron	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	68					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CTCCTCCTTTCGTAATCTGCA	0.423																																					p.R68Q		Atlas-SNP	.											.	SF3A3	37	.	0			c.G203A						.	C	GLN/ARG	0,4406		0,0,2203	104	105	105		203	5.6	1	1		105	1,8599	1.2+/-3.3	0,1,4299	no	missense	SF3A3	NM_006802.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	68/502	38453345	1,13005	2203	4300	6503	SO:0001583	missense	10946	exon4			TCCTTTCGTAATC	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"splicing factor 3a, subunit 3, 60kD"			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.203G>A	chr1.hg19:g.38453345C>T	ENSP00000362110:p.Arg68Gln	80.0	0.0		162.0	11.0	NM_006802	D3DPT5|Q15460|Q5VT87	Missense_Mutation	SNP	ENST00000373019.4	hg19	CCDS428.1	.	.	.	.	.	.	.	.	.	.	C	36	5.708777	0.96821	0.0	1.16E-4	ENSG00000183431	ENST00000373019	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.86351	0.5912	M	0.92604	3.325	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.88495	0.3078	9	0.56958	D	0.05	-7.9523	19.6316	0.95708	0.0:1.0:0.0:0.0	.	68	Q12874	SF3A3_HUMAN	Q	68	.	ENSP00000362110:R68Q	R	-	2	0	SF3A3	38225932	1.000000	0.71417	0.995000	0.50966	0.936000	0.57629	7.684000	0.84104	2.642000	0.89623	0.557000	0.71058	CGA	.	.		0.423	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802		T	38453345	C	T	38453345	3	4	101	1	0	0	0	0	1	0	0	0	14163	884	31	1	1358	1	SF3A3	1	38453345	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1664770	38453345	210797276	12	13849										
NRD1	114883	hgsc.bcm.edu	37	chr1	52254983	52254983	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atatcagtaatggggatgatAcaatctgccagcagaggaga	12	6	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:52254983A>G	ENST00000428468.1	+	0	2893				NRD1_ENST00000352171.7_Silent_p.C1127C|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000354831.7_Silent_p.C1195C|NRD1_ENST00000539524.1_Silent_p.C1063C			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9						lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						TGGGGATGATACAATCTGCCA	0.448																																					p.C1195C		Atlas-SNP	.											.	NRD1	89	.	0			c.T3585C						.						161	147	152					1																	52254983		2203	4300	6503	SO:0001628	intergenic_variant	4898	exon33			GATGATACAATCT	AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16386	protein-coding gene	gene with protein product		606737					Standard	NM_148904		Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234		chr1.hg19:g.52254983A>G		77.0	0.0		143.0	48.0	NM_002525	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	Silent	SNP	ENST00000428468.1	hg19	CCDS41332.3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.020|6.020	0.372102|0.372102	0.11409|0.11409	.|.	.|.	ENSG00000078618|ENSG00000078618	ENST00000546169|ENST00000440943	.|.	.|.	.|.	5.75|5.75	-4.65|-4.65	0.03339|0.03339	.|.	.|.	.|.	.|.	.|.	T|T	0.20536|0.20536	0.0494|0.0494	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999995|0.999995	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.30909|0.30909	-0.9962|-0.9962	5|4	0.05620|.	T|.	0.96|.	-1.2614|-1.2614	4.5853|4.5853	0.12279|0.12279	0.3672:0.1033:0.4277:0.1019|0.3672:0.1033:0.4277:0.1019	.|.	.|.	.|.	.|.	A|H	1127|514	.|.	ENSP00000437424:V1127A|.	V|Y	-|-	2|1	0|0	NRD1|NRD1	52027571|52027571	0.000000|0.000000	0.05858|0.05858	0.047000|0.047000	0.18901|0.18901	0.859000|0.859000	0.49053|0.49053	-2.449000|-2.449000	0.01008|0.01008	-0.751000|-0.751000	0.04734|0.04734	-0.263000|-0.263000	0.10527|0.10527	GTA|TAT	.	.		0.448	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022584.4			G	52254983	A	G	52254983	1	3	101	0	1	0	0	0	0	0	0	0	10654	389	14	2		2	NRD1	1	52254983	IGR	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	13801638	52254983	196995638	13	13850										
C8A	731	hgsc.bcm.edu	37	chr1	57349332	57349339	+	Frame_Shift_Del	DEL	AATTAAAC	AATTAAAC	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agacacttcattcttgaacgAattaaacaagtataatgaga							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	AATTAAAC	AATTAAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:57349332_57349339delAATTAAAC	ENST00000361249.3	+	6	929_936	c.833_840delAATTAAAC	c.(832-840)gaattaaacfs	p.ELN278fs		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	278	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						TTCTTGAACGAATTAAACAAGTATAATG	0.399																																					p.278_280del		Atlas-Indel,Pindel	.											C8A,NS,malignant_melanoma,0,3	C8A	103	.	0			c.832_839del						.																																			SO:0001589	frameshift_variant	731	exon6			.	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"Complement system"	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.833_840delAATTAAAC	chr1.hg19:g.57349332_57349339delAATTAAAC	ENSP00000354458:p.Glu278fs	32.0	0.0		63.0	16.0	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Frame_Shift_Del	DEL	ENST00000361249.3	hg19	CCDS606.1																																																																																			.	.		0.399	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		-	57349339	AATTAAAC	-	57349332	7	5	101	1	0	1	0	1	0	0	0	0	2418	246	9	0	855	0	C8A	1	57349332	Frame_Shift_Del	DEL	AATTAAAC	TCGA-DD-A1EE-01A-11D-A12Z-10	5094349	57349332	191901289	14	13851										
PDE4B	5142	hgsc.bcm.edu	37	chr1	66723358	66723358	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atgacttgattgtaactcctTttgcccaggtatgtattatg	8	7	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:66723358T>G	ENST00000329654.4	+	5	692	c.505T>G	c.(505-507)Ttt>Gtt	p.F169V	PDE4B_ENST00000423207.2_Missense_Mutation_p.F154V|PDE4B_ENST00000371049.3_Missense_Mutation_p.F169V|PDE4B_ENST00000371048.3_3'UTR	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	169					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	TGTAACTCCTTTTGCCCAGGT	0.383																																					p.F169V		Atlas-SNP	.											.	PDE4B	231	.	0			c.T505G						.						262	254	257					1																	66723358		2203	4300	6503	SO:0001583	missense	5142	exon5			ACTCCTTTTGCCC	L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"Phosphodiesterases"	8781	protein-coding gene	gene with protein product	"phosphodiesterase E4 dunce homolog (Drosophila)"	600127	"phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)", "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.505T>G	chr1.hg19:g.66723358T>G	ENSP00000332116:p.Phe169Val	117.0	0.0		261.0	23.0	NM_001037341	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	hg19	CCDS632.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.7|23.7	4.447079|4.447079	0.84101|0.84101	.|.	.|.	ENSG00000184588|ENSG00000184588	ENST00000491340|ENST00000329654;ENST00000341517;ENST00000371049;ENST00000423207;ENST00000412480	.|T;T;T;T;D	.|0.87491	.|-1.42;-1.42;-1.42;-1.43;-2.26	5.07|5.07	5.07|5.07	0.68467|0.68467	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.89876|0.89876	0.6842|0.6842	M|M	0.79123|0.79123	2.44|2.44	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.48230	.|0.907;0.85;0.85	.|P;P;P	.|0.55055	.|0.767;0.589;0.589	D|D	0.91466|0.91466	0.5193|0.5193	6|10	.|0.87932	.|D	.|0	.|.	14.4679|14.4679	0.67497|0.67497	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|154;159;169	.|Q07343-3;Q59GM8;Q07343	.|.;.;PDE4B_HUMAN	C|V	10|169;169;169;154;77	.|ENSP00000332116:F169V;ENSP00000342637:F169V;ENSP00000360088:F169V;ENSP00000392947:F154V;ENSP00000397548:F77V	.|ENSP00000332116:F169V	F|F	+|+	2|1	0|0	PDE4B|PDE4B	66495946|66495946	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.881000|0.881000	0.50899|0.50899	7.093000|7.093000	0.76937|0.76937	2.251000|2.251000	0.74343|0.74343	0.528000|0.528000	0.53228|0.53228	TTT|TTT	.	.		0.383	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		G	66723358	T	G	66723358	3	3	101	1	0	0	0	0	1	0	0	0	11649	1841	64	5	759	5	PDE4B	1	66723358	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	9374026	66723358	182527263	15	13852										
FPGT	8790	hgsc.bcm.edu	37	chr1	74671212	74671212	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaagttacttcaattctttgGagtctgtttcctgtcatgct	7	8	4	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:74671212G>T	ENST00000609362.1	+	4	1518	c.1481G>T	c.(1480-1482)gGa>gTa	p.G494V	FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT_ENST00000534056.1_Missense_Mutation_p.G240V|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT_ENST00000370894.5_3'UTR|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron|TNNI3K_ENST00000370891.2_Intron|FPGT_ENST00000524915.1_Intron|FPGT_ENST00000370898.3_Missense_Mutation_p.G507V	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	494					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)			breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						CAATTCTTTGGAGTCTGTTTC	0.368																																					p.G494V		Atlas-SNP	.											.	FPGT	77	.	0			c.G1481T						.						102	95	97					1																	74671212		2203	4300	6503	SO:0001583	missense	8790	exon4			TCTTTGGAGTCTG	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.1481G>T	chr1.hg19:g.74671212G>T	ENSP00000476680:p.Gly494Val	79.0	0.0		181.0	10.0	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Missense_Mutation	SNP	ENST00000609362.1	hg19	CCDS663.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.276437	0.59649	.	.	ENSG00000254685	ENST00000370898;ENST00000534056	T;T	0.45668	0.89;0.89	5.1	5.1	0.69264	L-fucokinase (1);	.	.	.	.	T	0.61123	0.2322	M	0.77616	2.38	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.65294	-0.6203	9	0.56958	D	0.05	.	18.5201	0.90948	0.0:0.0:1.0:0.0	.	240;119;494	E9PNQ2;B4E2Y7;O14772	.;.;FPGT_HUMAN	V	494;240	ENSP00000359935:G494V;ENSP00000432819:G240V	ENSP00000359935:G494V	G	+	2	0	TNNI3K	74443800	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.434000	0.97515	2.351000	0.79841	0.563000	0.77884	GGA	.	.		0.368	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	74671212	G	T	74671212	3	4	101	1	0	0	0	0	1	0	0	0	6045	1174	41	3	1495	3	FPGT	1	74671212	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	7947854	74671212	174579409	16	13853										
STXBP3	6814	hgsc.bcm.edu	37	chr1	109339272	109339272	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agaaaatttggacaggttgaTccagaatgtaaagatagaaa	10	3	0	5			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:109339272T>A	ENST00000370008.3	+	15	1330	c.1280T>A	c.(1279-1281)aTc>aAc	p.I427N		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	427					blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		GACAGGTTGATCCAGAATGTA	0.358																																					p.I427N		Atlas-SNP	.											.	STXBP3	44	.	0			c.T1280A						.						137	134	135					1																	109339272		2203	4300	6503	SO:0001583	missense	6814	exon15			GGTTGATCCAGAA	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1280T>A	chr1.hg19:g.109339272T>A	ENSP00000359025:p.Ile427Asn	76.0	0.0		203.0	9.0	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	hg19	CCDS790.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.422713	0.83559	.	.	ENSG00000116266	ENST00000370008	T	0.79141	-1.24	5.44	5.44	0.79542	.	0.149746	0.64402	D	0.000017	T	0.77758	0.4178	M	0.78049	2.395	0.58432	D	0.999996	B	0.27765	0.188	B	0.40101	0.319	T	0.80462	-0.1372	10	0.72032	D	0.01	-1.0014	15.4851	0.75560	0.0:0.0:0.0:1.0	.	427	O00186	STXB3_HUMAN	N	427	ENSP00000359025:I427N	ENSP00000359025:I427N	I	+	2	0	STXBP3	109140795	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.999000	0.76283	2.060000	0.61445	0.383000	0.25322	ATC	.	.		0.358	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		A	109339272	T	A	109339272	3	1	101	1	0	0	0	0	1	0	0	0	15369	1435	50	4	1338	4	STXBP3	1	109339272	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	34668060	109339272	139911349	17	13854										
ATP1A1	476	hgsc.bcm.edu	37	chr1	116933025	116933025	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgaagctgatacgacagagaAtcagagtggtaaggccaggg	15	6	1	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:116933025A>C	ENST00000295598.5	+	9	1466	c.1214A>C	c.(1213-1215)aAt>aCt	p.N405T	ATP1A1_ENST00000369496.4_Missense_Mutation_p.N374T|ATP1A1_ENST00000537345.1_Missense_Mutation_p.N405T	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	405					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	ACGACAGAGAATCAGAGTGGT	0.423																																					p.N405T		Atlas-SNP	.											.	ATP1A1	87	.	0			c.A1214C						.						59	58	58					1																	116933025		2203	4300	6503	SO:0001583	missense	476	exon9			CAGAGAATCAGAG	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1214A>C	chr1.hg19:g.116933025A>C	ENSP00000295598:p.Asn405Thr	70.0	0.0		229.0	25.0	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	A	18.43	3.622723	0.66787	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	T;T;T	0.78816	-1.21;-1.21;-1.21	4.87	4.87	0.63330	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.59252	0.2180	N	0.20881	0.62	0.80722	D	1	B;B	0.14805	0.009;0.011	B;B	0.33960	0.108;0.173	T	0.61753	-0.6998	10	0.45353	T	0.12	.	14.6423	0.68734	1.0:0.0:0.0:0.0	.	405;405	F5H3A1;P05023	.;AT1A1_HUMAN	T	405;405;404;374	ENSP00000295598:N405T;ENSP00000445306:N405T;ENSP00000358508:N374T	ENSP00000295598:N405T	N	+	2	0	ATP1A1	116734548	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.126000	0.94411	2.068000	0.61886	0.528000	0.53228	AAT	.	.		0.423	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		C	116933025	A	C	116933025	3	2	101	1	0	0	0	0	1	0	0	0	1128	101	4	5	1264	5	ATP1A1	1	116933025	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	7593753	116933025	132317596	18	13855										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120461966	120461966	+	Frame_Shift_Del	DEL	G	G	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttgggcatcagctgccactGcagcatggagtggacagcgg							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:120461966delG	ENST00000256646.2	-	31	5969	c.5750delC	c.(5749-5751)gcafs	p.A1917fs		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1917					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGCTGCCACTGCAGCATGGAG	0.502			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.A1917fs		Atlas-INDEL	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.5751delA						.						63	60	61					1																	120461966		2203	4300	6503	SO:0001589	frameshift_variant	4853	exon31	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	.	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.5750delC	chr1.hg19:g.120461966delG	ENSP00000256646:p.Ala1917fs	29.0	0.0		65.0	17.0	NM_024408	Q5T3X7|Q99734|Q9H240	Frame_Shift_Del	DEL	ENST00000256646.2	hg19	CCDS908.1																																																																																			.	.		0.502	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		-	120461966	G	-	120461966	7	5	101	1	0	1	0	1	0	0	0	0	10557	1319	46	0	1681	0	NOTCH2	1	120461966	Frame_Shift_Del	DEL	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3528941	120461966	128788655	19	13856										
HIST2H2AC	8338	hgsc.bcm.edu	37	chr1	149858545	149858545	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atgtctggtcgtggcaaacaAggaggcaaggcccgcgccaa	14	11	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:149858545A>T	ENST00000331380.2	+	1	21	c.21A>T	c.(19-21)caA>caT	p.Q7H	HIST2H2BE_ENST00000369155.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	7						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|ovary(1)|skin(1)	20	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			GTGGCAAACAAGGAGGCAAGG	0.562																																					p.Q7H		Atlas-SNP	.											.	HIST2H2AC	75	.	0			c.A21T						.						82	90	87					1																	149858545		2203	4300	6503	SO:0001583	missense	8338	exon1			CAAACAAGGAGGC	AY131973	CCDS937.1	1q21.2	2011-01-27	2006-10-11	2003-02-21	ENSG00000184260	ENSG00000184260		"Histones / Replication-dependent"	4738	protein-coding gene	gene with protein product		602797	"H2A histone family, member Q", "histone 2, H2ac"	H2A, H2AFQ		1469070, 9439656, 12408966	Standard	NM_003517		Approved	H2A/q	uc001etd.3	Q16777	OTTHUMG00000035825	ENST00000331380.2:c.21A>T	chr1.hg19:g.149858545A>T	ENSP00000332194:p.Gln7His	53.0	0.0		191.0	49.0	NM_003517	Q6DRA7|Q8IUE5	Missense_Mutation	SNP	ENST00000331380.2	hg19	CCDS937.1	.	.	.	.	.	.	.	.	.	.	A	10.54	1.377615	0.24944	.	.	ENSG00000184260	ENST00000331380	T	0.42900	0.96	5.81	-7.0	0.01599	Histone-fold (2);Histone H2A (1);	0.000000	0.42548	D	0.000696	T	0.10809	0.0264	N	0.17474	0.49	0.31702	N	0.640667	B	0.23937	0.094	B	0.20384	0.029	T	0.01484	-1.1343	10	0.66056	D	0.02	.	16.9467	0.86232	0.3794:0.0:0.6206:0.0	.	7	Q16777	H2A2C_HUMAN	H	7	ENSP00000332194:Q7H	ENSP00000332194:Q7H	Q	+	3	2	HIST2H2AC	148125169	0.001000	0.12720	0.253000	0.24343	0.817000	0.46193	-1.370000	0.02575	-1.576000	0.01652	-0.408000	0.06270	CAA	.	.		0.562	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087128.1	NM_003517		T	149858545	A	T	149858545	3	4	101	1	0	0	0	0	1	0	0	0	7187	69	3	4	23	4	HIST2H2AC	1	149858545	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	29396579	149858545	99392076	20	13857										
CGN	57530	hgsc.bcm.edu	37	chr1	151499552	151499552	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcaggcccgagctagtgctgGagatactcgccaggttgagg	16	10	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:151499552G>T	ENST00000271636.7	+	10	1998	c.1865G>T	c.(1864-1866)gGa>gTa	p.G622V	SNORA44_ENST00000517031.1_RNA	NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	616	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCTAGTGCTGGAGATACTCGC	0.542																																					p.G622V		Atlas-SNP	.											.	CGN	106	.	0			c.G1865T						.						117	107	111					1																	151499552		2203	4300	6503	SO:0001583	missense	57530	exon10			GTGCTGGAGATAC	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.1865G>T	chr1.hg19:g.151499552G>T	ENSP00000271636:p.Gly622Val	68.0	0.0		315.0	29.0	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	hg19	CCDS999.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.309784	0.23821	.	.	ENSG00000143375	ENST00000271636	T	0.62364	0.03	5.54	3.27	0.37495	.	0.748757	0.13601	N	0.375871	T	0.24431	0.0592	N	0.25647	0.755	0.27275	N	0.958263	B	0.10296	0.003	B	0.09377	0.004	T	0.07986	-1.0744	10	0.31617	T	0.26	-1.8441	5.9002	0.18962	0.1227:0.4023:0.4749:0.0	.	616	Q9P2M7	CING_HUMAN	V	622	ENSP00000271636:G622V	ENSP00000271636:G622V	G	+	2	0	CGN	149766176	0.766000	0.28496	0.614000	0.29051	0.983000	0.72400	0.482000	0.22276	1.457000	0.47850	0.650000	0.86243	GGA	.	.		0.542	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		T	151499552	G	T	151499552	3	4	101	1	0	0	0	0	1	0	0	0	3305	1174	41	3	1899	3	CGN	1	151499552	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1641007	151499552	97751069	21	13858										
TCHHL1	126637	hgsc.bcm.edu	37	chr1	152057483	152057486	+	Frame_Shift_Del	DEL	CTCT	CTCT	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cctccctttgtagtaccagcCtctctctctgagggtgacct							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	CTCT	CTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:152057483_152057486delCTCT	ENST00000368806.1	-	3	2736_2739	c.2672_2675delAGAG	c.(2671-2676)gagaggfs	p.ER891fs		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	891							calcium ion binding (GO:0005509)			breast(4)|endometrium(1)|kidney(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(1)|skin(7)|stomach(1)	60	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			TAGTACCAGCCTCTCTCTCTGAGG	0.505																																					p.891_892del		Atlas-Indel,Pindel	.											.	TCHHL1	132	.	0			c.2673_2676del						.																																			SO:0001589	frameshift_variant	126637	exon3			.		CCDS30857.1	1q21.3	2011-10-11	2004-10-05	2006-01-27	ENSG00000182898	ENSG00000182898		"S100 calcium binding proteins"	31796	protein-coding gene	gene with protein product			"S100 calcium binding protein A17"	S100A17, THHL1			Standard	NM_001008536		Approved		uc001ezo.1	Q5QJ38	OTTHUMG00000013058	ENST00000368806.1:c.2672_2675delAGAG	chr1.hg19:g.152057487_152057490delCTCT	ENSP00000357796:p.Glu891fs	108.0	0.0		402.0	76.0	NM_001008536	B2RPK8|Q5VTJ9	Frame_Shift_Del	DEL	ENST00000368806.1	hg19	CCDS30857.1																																																																																			.	.		0.505	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104		-	152057486	CTCT	-	152057483	7	5	101	1	0	1	0	1	0	0	0	0	15716	681	24	0	43	0	TCHHL1	1	152057483	Frame_Shift_Del	DEL	CTCT	TCGA-DD-A1EE-01A-11D-A12Z-10	557931	152057483	97193138	22	13859										
PGLYRP4	57115	hgsc.bcm.edu	37	chr1	153314164	153314164	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcgcctttcccaagaagtggCtgaacataactggatgacag	10	10	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:153314164C>A	ENST00000359650.5	-	6	628	c.564G>T	c.(562-564)caG>caT	p.Q188H	PGLYRP4_ENST00000368739.3_Missense_Mutation_p.Q184H	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	188					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAAGAAGTGGCTGAACATAAC	0.572																																					p.Q188H		Atlas-SNP	.											.	PGLYRP4	45	.	0			c.G564T						.						122	116	118					1																	153314164		2203	4300	6503	SO:0001583	missense	57115	exon6			AAGTGGCTGAACA	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I beta precursor"	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.564G>T	chr1.hg19:g.153314164C>A	ENSP00000352672:p.Gln188His	44.0	0.0		180.0	21.0	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	hg19	CCDS30871.1	.	.	.	.	.	.	.	.	.	.	C	11.27	1.588345	0.28357	.	.	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.05319	3.46;3.46	4.2	1.05	0.20165	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.000000	0.44483	D	0.000451	T	0.09774	0.0240	M	0.76838	2.35	0.27729	N	0.944877	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.03981	-1.0987	10	0.62326	D	0.03	-42.2259	5.3818	0.16196	0.0:0.6116:0.0:0.3884	.	184;188	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	H	184;188	ENSP00000357728:Q184H;ENSP00000352672:Q188H	ENSP00000352672:Q188H	Q	-	3	2	PGLYRP4	151580788	1.000000	0.71417	0.985000	0.45067	0.031000	0.12232	0.559000	0.23485	0.421000	0.25980	-0.194000	0.12790	CAG	.	.		0.572	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393		A	153314164	C	A	153314164	3	1	101	1	0	0	0	0	1	0	0	0	11805	796	28	3	573	3	PGLYRP4	1	153314164	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1256681	153314164	95936457	23	13860										
ZBTB7B	51043	hgsc.bcm.edu	37	chr1	154988092	154988092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgacctgatggcctacctaaGctccctgcaccaggacaacc	8	16	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:154988092G>A	ENST00000368426.3	+	3	1093	c.956G>A	c.(955-957)aGc>aAc	p.S319N	ZBTB7B_ENST00000292176.2_Missense_Mutation_p.S319N|ZBTB7B_ENST00000417934.2_Missense_Mutation_p.S353N|ZBTB7B_ENST00000535420.1_Missense_Mutation_p.S319N	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	319					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCCTACCTAAGCTCCCTGCAC	0.657																																					p.S353N		Atlas-SNP	.											.	ZBTB7B	69	.	0			c.G1058A						.						44	43	43					1																	154988092		2203	4300	6503	SO:0001583	missense	51043	exon4			ACCTAAGCTCCCT	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	18668	protein-coding gene	gene with protein product	"zinc finger and BTB domain containing 15"	607646	"zinc finger protein 67 homolog (mouse)"	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.956G>A	chr1.hg19:g.154988092G>A	ENSP00000357411:p.Ser319Asn	38.0	0.0		267.0	14.0	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	hg19	CCDS1081.1	.	.	.	.	.	.	.	.	.	.	g	14.18	2.459273	0.43634	.	.	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.10477	2.89;2.89;2.87;2.89	4.08	4.08	0.47627	.	0.187911	0.30969	N	0.008506	T	0.02119	0.0066	N	0.14661	0.345	0.28989	N	0.888149	B;B;B	0.21225	0.053;0.053;0.053	B;B;B	0.17722	0.019;0.01;0.019	T	0.38286	-0.9668	10	0.44086	T	0.13	.	7.6015	0.28079	0.115:0.0:0.885:0.0	.	319;319;353	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	N	319;319;353;319	ENSP00000438647:S319N;ENSP00000357411:S319N;ENSP00000406286:S353N;ENSP00000292176:S319N	ENSP00000292176:S319N	S	+	2	0	ZBTB7B	153254716	0.953000	0.32496	0.988000	0.46212	0.972000	0.66771	2.260000	0.43267	2.109000	0.64355	0.462000	0.41574	AGC	.	.		0.657	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872		A	154988092	G	A	154988092	3	1	101	1	0	0	0	0	1	0	0	0	17569	971	34	3	958	3	ZBTB7B	1	154988092	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1673928	154988092	94262529	24	13861										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156939122	156939122	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccagagtccaagccactgtcCccctcctgggaatccagaga	9	16	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:156939122C>A	ENST00000361409.2	-	9	1399	c.657G>T	c.(655-657)ggG>ggT	p.G219G	ARHGEF11_ENST00000368194.3_Silent_p.G259G	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	219					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AGCCACTGTCCCCCTCCTGGG	0.552																																					p.G259G		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G777T						.						37	32	34					1																	156939122		2202	4299	6501	SO:0001819	synonymous_variant	9826	exon10			ACTGTCCCCCTCC	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.657G>T	chr1.hg19:g.156939122C>A		30.0	0.0		138.0	69.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Silent	SNP	ENST00000361409.2	hg19	CCDS1162.1																																																																																			.	.		0.552	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		A	156939122	C	A	156939122	2	1	101	1	0	0	0	0	0	0	0	1	896	610	22	3		3	ARHGEF11	1	156939122	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1951030	156939122	92311499	25	13862										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158605719	158605719	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcaccgggccttggccaactCtttgagcttctcccagtgtt	9	14	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:158605719C>G	ENST00000368147.4	-	38	5596	c.5416G>C	c.(5416-5418)Gag>Cag	p.E1806Q		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1806					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTGGCCAACTCTTTGAGCTTC	0.537																																					p.E1806Q		Atlas-SNP	.											.	SPTA1	720	.	0			c.G5416C						.						90	93	92					1																	158605719		1942	4139	6081	SO:0001583	missense	6708	exon38			CCAACTCTTTGAG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5416G>C	chr1.hg19:g.158605719C>G	ENSP00000357129:p.Glu1806Gln	49.0	0.0		214.0	9.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.536202	0.27475	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.51574	0.7;0.7	5.65	3.8	0.43715	.	0.266274	0.19779	N	0.106267	T	0.19765	0.0475	L	0.59967	1.855	0.32110	N	0.589433	B	0.30973	0.302	B	0.30401	0.115	T	0.09228	-1.0684	10	0.12766	T	0.61	.	7.8794	0.29614	0.0:0.7181:0.1338:0.1481	.	1806	P02549	SPTA1_HUMAN	Q	1806	ENSP00000357130:E1806Q;ENSP00000357129:E1806Q	ENSP00000357129:E1806Q	E	-	1	0	SPTA1	156872343	0.998000	0.40836	0.998000	0.56505	0.993000	0.82548	3.002000	0.49496	0.944000	0.37579	0.655000	0.94253	GAG	.	.		0.537	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		G	158605719	C	G	158605719	3	3	101	1	0	0	0	0	1	0	0	0	15131	922	32	4	1903	4	SPTA1	1	158605719	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1666597	158605719	90644902	26	13863										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158651408	158651408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	actggtcacccttctccaggGtcagctctaacagcaggtcc	9	15	4	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:158651408G>A	ENST00000368147.4	-	4	620	c.440C>T	c.(439-441)aCc>aTc	p.T147I		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	147					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CTTCTCCAGGGTCAGCTCTAA	0.547																																					p.T147I		Atlas-SNP	.											.	SPTA1	720	.	0			c.C440T						.						132	135	134					1																	158651408		2011	4166	6177	SO:0001583	missense	6708	exon4			TCCAGGGTCAGCT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.440C>T	chr1.hg19:g.158651408G>A	ENSP00000357129:p.Thr147Ile	80.0	0.0		344.0	138.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	9.380	1.072843	0.20147	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48836	0.8;0.8	5.15	3.25	0.37280	.	.	.	.	.	T	0.24470	0.0593	M	0.65677	2.01	0.35854	D	0.826973	B	0.10296	0.003	B	0.18561	0.022	T	0.06881	-1.0802	9	0.23302	T	0.38	.	6.9641	0.24613	0.3221:0.0:0.6779:0.0	.	147	P02549	SPTA1_HUMAN	I	147	ENSP00000357130:T147I;ENSP00000357129:T147I	ENSP00000357129:T147I	T	-	2	0	SPTA1	156918032	0.999000	0.42202	0.960000	0.40013	0.347000	0.29111	3.240000	0.51368	1.401000	0.46761	0.563000	0.77884	ACC	.	.		0.547	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158651408	G	A	158651408	3	1	101	1	0	0	0	0	1	0	0	0	15131	1261	44	3	7015	3	SPTA1	1	158651408	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	45689	158651408	90599213	27	13864										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167086745	167086745	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggttcaggatcgccaagaggCgccctggaatgaggtggatg	17	8	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:167086745C>T	ENST00000361200.2	+	4	552	c.386C>T	c.(385-387)gCg>gTg	p.A129V	DUSP27_ENST00000271385.5_Missense_Mutation_p.A129V|DUSP27_ENST00000443333.1_Missense_Mutation_p.A129V			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	129					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CGCCAAGAGGCGCCCTGGAAT	0.547																																					p.A129V		Atlas-SNP	.											DUSP27,NS,carcinoma,0,1	DUSP27	235	.	0			c.C386T						.						79	66	70					1																	167086745		2203	4300	6503	SO:0001583	missense	92235	exon3			AAGAGGCGCCCTG	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.386C>T	chr1.hg19:g.167086745C>T	ENSP00000354483:p.Ala129Val	53.0	0.0		226.0	34.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.561321	0.45590	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.59906	0.23;0.23;0.23	4.93	4.02	0.46733	.	0.464667	0.22997	N	0.053138	T	0.28333	0.0700	L	0.32530	0.975	0.38538	D	0.949141	P	0.42161	0.772	B	0.32583	0.148	T	0.30238	-0.9985	10	0.66056	D	0.02	-8.4801	13.1155	0.59297	0.0:0.9231:0.0:0.0769	.	129	Q5VZP5	DUS27_HUMAN	V	129	ENSP00000354483:A129V;ENSP00000271385:A129V;ENSP00000404874:A129V	ENSP00000271385:A129V	A	+	2	0	DUSP27	165353369	1.000000	0.71417	0.568000	0.28447	0.164000	0.22412	5.622000	0.67750	1.297000	0.44761	0.655000	0.94253	GCG	.	.		0.547	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		T	167086745	C	T	167086745	3	4	101	1	0	0	0	0	1	0	0	0	4826	768	27	1	396	1	DUSP27	1	167086745	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	8435337	167086745	82163876	28	13865										
RFWD2	64326	hgsc.bcm.edu	37	chr1	175956209	175956209	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aagtcttagaaagtcctttaTagtacaggtagagagagtta	10	4	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:175956209T>C	ENST00000367669.3	-	18	2517	c.2003A>G	c.(2002-2004)tAt>tGt	p.Y668C	RFWD2_ENST00000308769.8_Missense_Mutation_p.Y644C	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	668					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						AAGTCCTTTATAGTACAGGTA	0.299																																					p.Y668C	Ovarian(134;1413 1765 5706 35534 51541)	Atlas-SNP	.											.	RFWD2	67	.	0			c.A2003G						.						59	59	59					1																	175956209		2203	4300	6503	SO:0001583	missense	64326	exon18			CCTTTATAGTACA	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	17440	protein-coding gene	gene with protein product		608067	"ring finger and WD repeat domain 2"			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.2003A>G	chr1.hg19:g.175956209T>C	ENSP00000356641:p.Tyr668Cys	56.0	0.0		300.0	15.0	NM_022457	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Missense_Mutation	SNP	ENST00000367669.3	hg19	CCDS30944.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962913	0.53507	.	.	ENSG00000143207	ENST00000367665;ENST00000367669;ENST00000367666;ENST00000308769	T;T;T	0.70399	-0.48;-0.48;-0.48	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.85969	0.5821	M	0.87269	2.87	0.80722	D	1	B;D;B;D;D	0.76494	0.067;0.98;0.169;0.999;0.98	B;D;B;D;D	0.77557	0.114;0.941;0.091;0.99;0.941	D	0.88357	0.2985	10	0.72032	D	0.01	-15.7895	15.8017	0.78456	0.0:0.0:0.0:1.0	.	443;428;644;668;668	Q8NHY2-3;B1AMD2;Q8NHY2-2;Q8NHY2;Q504W6	.;.;.;RFWD2_HUMAN;.	C	443;668;503;644	ENSP00000356641:Y668C;ENSP00000356638:Y503C;ENSP00000310943:Y644C	ENSP00000310943:Y644C	Y	-	2	0	RFWD2	174222832	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.268000	0.78473	2.261000	0.74972	0.533000	0.62120	TAT	.	.		0.299	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457		C	175956209	T	C	175956209	3	2	101	1	0	0	0	0	1	0	0	0	13275	1406	49	2	204	2	RFWD2	1	175956209	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	8869464	175956209	73294412	29	13866										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179561759	179561759	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctgtagggcacaatgtctgaAcaagagcgtatacaggaatg	12	7	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:179561759A>G	ENST00000367614.1	+	2	368	c.9A>G	c.(7-9)gaA>gaG	p.E3E	TDRD5_ENST00000294848.8_Silent_p.E3E|RP11-545A16.4_ENST00000567150.1_RNA|TDRD5_ENST00000444136.1_Silent_p.E3E	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	3					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						CAATGTCTGAACAAGAGCGTA	0.443																																					p.E3E		Atlas-SNP	.											.	TDRD5	149	.	0			c.A9G						.						125	121	122					1																	179561759		2203	4300	6503	SO:0001819	synonymous_variant	163589	exon2			GTCTGAACAAGAG	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.9A>G	chr1.hg19:g.179561759A>G		29.0	0.0		102.0	41.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.		0.443	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		G	179561759	A	G	179561759	2	3	101	1	0	0	0	0	0	0	0	1	15748	40	2	2		2	TDRD5	1	179561759	Silent	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	3605550	179561759	69688862	30	13867										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179603595	179603595	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cggaaatttgtgtttagttcAgtcagataagaaaatagaag	10	3	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:179603595A>T	ENST00000367614.1	+	8	1489	c.1130A>T	c.(1129-1131)cAg>cTg	p.Q377L	TDRD5_ENST00000294848.8_Missense_Mutation_p.Q377L|TDRD5_ENST00000444136.1_Missense_Mutation_p.Q377L	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	377					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						TGTTTAGTTCAGTCAGATAAG	0.383																																					p.Q377L		Atlas-SNP	.											.	TDRD5	149	.	0			c.A1130T						.						101	101	101					1																	179603595		2203	4300	6503	SO:0001583	missense	163589	exon8			TAGTTCAGTCAGA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1130A>T	chr1.hg19:g.179603595A>T	ENSP00000356586:p.Gln377Leu	74.0	0.0		324.0	16.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	A	9.612	1.131531	0.21041	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.12774	2.65;2.65;2.83	5.24	2.72	0.32119	.	0.626135	0.16158	N	0.226908	T	0.12689	0.0308	L	0.54323	1.7	0.29136	N	0.879299	B;B	0.12013	0.005;0.002	B;B	0.09377	0.004;0.002	T	0.12344	-1.0551	10	0.27785	T	0.31	-2.8607	8.2597	0.31777	0.687:0.0:0.0:0.313	.	377;377	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	L	377	ENSP00000356586:Q377L;ENSP00000294848:Q377L;ENSP00000406052:Q377L	ENSP00000294848:Q377L	Q	+	2	0	TDRD5	177870218	0.997000	0.39634	0.996000	0.52242	0.864000	0.49448	1.718000	0.38001	0.910000	0.36722	0.533000	0.62120	CAG	.	.		0.383	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		T	179603595	A	T	179603595	3	4	101	1	0	0	0	0	1	0	0	0	15748	188	7	4	1156	4	TDRD5	1	179603595	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	41836	179603595	69647026	31	13868										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181548355	181548355	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcgagcatgcttcatgaacaAttcaggtagggtcgttcttt	10	8	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:181548355A>T	ENST00000367573.2	+	5	764	c.764A>T	c.(763-765)aAt>aTt	p.N255I	CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000358338.5_Missense_Mutation_p.N206I|CACNA1E_ENST00000357570.5_Missense_Mutation_p.N206I|CACNA1E_ENST00000526775.1_Missense_Mutation_p.N255I|CACNA1E_ENST00000367570.1_Missense_Mutation_p.N255I|CACNA1E_ENST00000360108.3_Missense_Mutation_p.N255I	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	255					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TTCATGAACAATTCAGGTAGG	0.453																																					p.N255I		Atlas-SNP	.											.	CACNA1E	778	.	0			c.A764T						.						303	277	285					1																	181548355		1934	4151	6085	SO:0001583	missense	777	exon5			TGAACAATTCAGG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.764A>T	chr1.hg19:g.181548355A>T	ENSP00000356545:p.Asn255Ile	127.0	0.0		400.0	16.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.570357	0.45798	.	.	ENSG00000198216	ENST00000524607;ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.97430	-4.38;-4.0;-3.99;-4.01;-3.99;-3.99;-4.0	4.88	4.88	0.63580	.	11.845600	0.00166	N	0.000006	D	0.95370	0.8497	L	0.33245	0.995	0.80722	D	1	B;B	0.14012	0.009;0.009	B;B	0.15484	0.013;0.013	T	0.72626	-0.4236	10	0.33141	T	0.24	.	14.4515	0.67389	1.0:0.0:0.0:0.0	.	255;255	Q15878-2;Q15878-3	.;.	I	255;255;255;206;206;255;255	ENSP00000432038:N255I;ENSP00000356542:N255I;ENSP00000434814:N255I;ENSP00000350183:N206I;ENSP00000351101:N206I;ENSP00000353222:N255I;ENSP00000356545:N255I	ENSP00000350183:N206I	N	+	2	0	CACNA1E	179814978	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.016000	0.49607	1.951000	0.56629	0.459000	0.35465	AAT	.	.		0.453	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181548355	A	T	181548355	3	4	101	1	0	0	0	0	1	0	0	0	2544	101	4	4	782	4	CACNA1E	1	181548355	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1944760	181548355	67702266	32	13869										
DHX9	1660	hgsc.bcm.edu	37	chr1	182823304	182823304	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtacacccaagtgggtcctgAtcacaacaggtttgcttgtt	10	10	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:182823304A>G	ENST00000367549.3	+	6	727	c.617A>G	c.(616-618)gAt>gGt	p.D206G		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	206	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.|Interaction with CREBBP.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						GTGGGTCCTGATCACAACAGG	0.363																																					p.D206G	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.A617G						.						72	71	71					1																	182823304		1845	4085	5930	SO:0001583	missense	1660	exon6			GTCCTGATCACAA	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.617A>G	chr1.hg19:g.182823304A>G	ENSP00000356520:p.Asp206Gly	83.0	0.0		367.0	16.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.703563	0.88924	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	T	0.77098	-1.07	5.39	5.39	0.77823	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.90215	0.6941	M	0.92219	3.285	0.80722	D	1	P	0.46952	0.887	D	0.64042	0.921	D	0.92387	0.5918	10	0.87932	D	0	.	15.0812	0.72117	1.0:0.0:0.0:0.0	.	206	Q08211	DHX9_HUMAN	G	206	ENSP00000356520:D206G	ENSP00000356520:D206G	D	+	2	0	DHX9	181089927	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.661000	0.91125	2.045000	0.60652	0.533000	0.62120	GAT	.	.		0.363	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		G	182823304	A	G	182823304	3	3	101	1	0	0	0	0	1	0	0	0	4518	333	12	2	635	2	DHX9	1	182823304	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1274949	182823304	66427317	33	13870										
DHX9	1660	hgsc.bcm.edu	37	chr1	182852382	182852382	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caatgtatgctatcataaggAaaagaggaagattctcacca	8	7	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:182852382A>T	ENST00000367549.3	+	25	3133	c.3023A>T	c.(3022-3024)gAa>gTa	p.E1008V	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	1008					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						TATCATAAGGAAAAGAGGAAG	0.413																																					p.E1008V	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.A3023T						.						155	132	139					1																	182852382		1900	4120	6020	SO:0001583	missense	1660	exon25			ATAAGGAAAAGAG	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.3023A>T	chr1.hg19:g.182852382A>T	ENSP00000356520:p.Glu1008Val	103.0	0.0		348.0	17.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.848970	0.91277	.	.	ENSG00000135829	ENST00000367549	T	0.04275	3.66	5.39	5.39	0.77823	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.18964	0.0455	M	0.85197	2.74	0.80722	D	1	P;P	0.47604	0.898;0.885	P;P	0.53722	0.733;0.665	T	0.00728	-1.1591	10	0.48119	T	0.1	.	15.4176	0.74983	1.0:0.0:0.0:0.0	.	287;1008	B3KU66;Q08211	.;DHX9_HUMAN	V	1008	ENSP00000356520:E1008V	ENSP00000356520:E1008V	E	+	2	0	DHX9	181119005	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.699000	0.91316	2.027000	0.59764	0.533000	0.62120	GAA	.	.		0.413	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		T	182852382	A	T	182852382	3	4	101	1	0	0	0	0	1	0	0	0	4518	246	9	4	3117	4	DHX9	1	182852382	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	29078	182852382	66398239	34	13871										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186007150	186007150	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acagctggagtgtaaggcagCtggaaatcctgtgcctggta	14	8	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:186007150C>A	ENST00000271588.4	+	37	6063	c.5834C>A	c.(5833-5835)gCt>gAt	p.A1945D	HMCN1_ENST00000367492.2_Missense_Mutation_p.A1945D	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1945	Ig-like C2-type 17.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGTAAGGCAGCTGGAAATCCT	0.398																																					p.A1945D		Atlas-SNP	.											.	HMCN1	797	.	0			c.C5834A						.						140	134	136					1																	186007150		2203	4300	6503	SO:0001583	missense	83872	exon37			AGGCAGCTGGAAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.5834C>A	chr1.hg19:g.186007150C>A	ENSP00000271588:p.Ala1945Asp	76.0	0.0		244.0	99.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.568365	0.28003	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.67345	-0.26;-0.26	5.52	5.52	0.82312	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.406062	0.28192	N	0.016246	T	0.52175	0.1718	N	0.03238	-0.38	0.29889	N	0.825357	P	0.49253	0.921	P	0.51193	0.662	T	0.52396	-0.8581	10	0.24483	T	0.36	.	13.7184	0.62712	0.0:0.9241:0.0:0.0758	.	1945	Q96RW7	HMCN1_HUMAN	D	1945	ENSP00000271588:A1945D;ENSP00000356462:A1945D	ENSP00000271588:A1945D	A	+	2	0	HMCN1	184273773	0.224000	0.23674	0.372000	0.25991	0.191000	0.23601	2.161000	0.42358	2.597000	0.87782	0.555000	0.69702	GCT	.	.		0.398	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186007150	C	A	186007150	3	1	101	1	0	0	0	0	1	0	0	0	7229	797	28	3	5980	3	HMCN1	1	186007150	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3154768	186007150	63243471	35	13872										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200946358	200946358	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acctgctaagctcccagatgCggacggcattgcccgaggcg	13	14	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:200946358C>A	ENST00000422435.2	-	31	4623	c.4307G>T	c.(4306-4308)cGc>cTc	p.R1436L	KIF21B_ENST00000332129.2_Missense_Mutation_p.R1423L|KIF21B_ENST00000360529.5_Missense_Mutation_p.R1423L|KIF21B_ENST00000461742.2_Missense_Mutation_p.R1436L	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1436					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CTCCCAGATGCGGACGGCATT	0.642																																					p.R1436L		Atlas-SNP	.											KIF21B,NS,carcinoma,0,1	KIF21B	208	.	0			c.G4307T						.						114	107	110					1																	200946358		2203	4300	6503	SO:0001583	missense	23046	exon31			CAGATGCGGACGG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.4307G>T	chr1.hg19:g.200946358C>A	ENSP00000411831:p.Arg1436Leu	30.0	0.0		137.0	10.0	NM_001252102	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	hg19	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630802	0.67015	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.07567	3.18;3.18;3.18;3.18	4.88	4.88	0.63580	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.35970	0.0950	M	0.86953	2.85	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;0.999;0.998	D;D;D;D	0.91635	0.997;0.999;0.997;0.994	T	0.41448	-0.9508	10	0.87932	D	0	.	18.0342	0.89294	0.0:1.0:0.0:0.0	.	1423;1436;1436;1423	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	L	1423;1423;1436;1436;1436	ENSP00000328494:R1423L;ENSP00000353724:R1423L;ENSP00000433808:R1436L;ENSP00000411831:R1436L	ENSP00000328494:R1423L	R	-	2	0	KIF21B	199212981	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	5.761000	0.68801	2.249000	0.74217	0.561000	0.74099	CGC	.	.		0.642	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200946358	C	A	200946358	3	1	101	1	0	0	0	0	1	0	0	0	8298	768	27	1	626	1	KIF21B	1	200946358	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	14939208	200946358	48304263	36	13873										
DYRK3	8444	hgsc.bcm.edu	37	chr1	206820946	206820946	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aatccaacagttcatccaagGcacccaaagtggtgcctctg	8	13	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:206820946G>T	ENST00000367109.2	+	3	571	c.403G>T	c.(403-405)Gca>Tca	p.A135S	DYRK3_ENST00000367108.3_Missense_Mutation_p.A115S|DYRK3_ENST00000489878.1_Intron|DYRK3_ENST00000367106.1_Missense_Mutation_p.A115S	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	135					erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			TTCATCCAAGGCACCCAAAGT	0.413																																					p.A135S	Melanoma(164;427 2622 26826 51707)	Atlas-SNP	.											.	DYRK3	146	.	0			c.G403T						.						79	79	79					1																	206820946		2203	4300	6503	SO:0001583	missense	8444	exon3			TCCAAGGCACCCA	Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"regulatory erythroid kinase", "dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5", "protein kinase Dyrk3"	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.403G>T	chr1.hg19:g.206820946G>T	ENSP00000356076:p.Ala135Ser	79.0	0.0		432.0	35.0	NM_003582	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Missense_Mutation	SNP	ENST00000367109.2	hg19	CCDS30999.1	.	.	.	.	.	.	.	.	.	.	G	0.108	-1.142325	0.01728	.	.	ENSG00000143479	ENST00000367109;ENST00000367108;ENST00000441486;ENST00000367106	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.09	0.837	0.18896	.	0.946011	0.09044	N	0.856863	T	0.20618	0.0496	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.23190	-1.0195	10	0.12430	T	0.62	.	1.6353	0.02740	0.1512:0.1642:0.3442:0.3405	.	135;115	O43781;O43781-2	DYRK3_HUMAN;.	S	135;115;115;115	ENSP00000356076:A135S;ENSP00000356075:A115S;ENSP00000410187:A115S;ENSP00000356073:A115S	ENSP00000356073:A115S	A	+	1	0	DYRK3	204887569	0.007000	0.16637	0.004000	0.12327	0.759000	0.43091	-0.275000	0.08525	-0.005000	0.14395	0.579000	0.79373	GCA	.	.		0.413	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1	NM_003582		T	206820946	G	T	206820946	3	4	101	1	0	0	0	0	1	0	0	0	4859	1203	42	3	434	3	DYRK3	1	206820946	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	5874588	206820946	42429675	37	13874										
LAMB3	3914	hgsc.bcm.edu	37	chr1	209789918	209789918	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctcacccagcatggaactctGacccaaccggtccttcaact	6	17	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:209789918G>A	ENST00000356082.4	-	22	3414	c.3280C>T	c.(3280-3282)Cag>Tag	p.Q1094*	LAMB3_ENST00000367030.3_Nonsense_Mutation_p.Q1094*|LAMB3_ENST00000391911.1_Nonsense_Mutation_p.Q1094*	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	1094	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		ATGGAACTCTGACCCAACCGG	0.488																																					p.Q1094X		Atlas-SNP	.											.	LAMB3	136	.	0			c.C3280T						.						157	149	151					1																	209789918		2203	4300	6503	SO:0001587	stop_gained	3914	exon22			AACTCTGACCCAA	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.3280C>T	chr1.hg19:g.209789918G>A	ENSP00000348384:p.Gln1094*	89.0	0.0		357.0	20.0	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Nonsense_Mutation	SNP	ENST00000356082.4	hg19	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	G	31	5.094827	0.94197	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	.	.	.	3.91	2.95	0.34219	.	1.007520	0.07981	U	0.985576	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.4611	0.21956	0.0:0.2041:0.5857:0.2102	.	.	.	.	X	1094	.	ENSP00000348384:Q1094X	Q	-	1	0	LAMB3	207856541	0.028000	0.19301	0.007000	0.13788	0.185000	0.23345	2.092000	0.41700	0.810000	0.34279	0.449000	0.29647	CAG	.	.		0.488	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		A	209789918	G	A	209789918	4	1	101	1	0	0	0	0	0	1	0	0	8621	1299	45	3	246	3	LAMB3	1	209789918	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2968972	209789918	39460703	38	13875										
SLC30A10	55532	hgsc.bcm.edu	37	chr1	220091827	220091827	+	Frame_Shift_Del	DEL	A	A	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gggcatctcccatcacatgcAaaagtacacctgccaggaag							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:220091827delA	ENST00000366926.3	-	3	889	c.728delT	c.(727-729)ttgfs	p.L243fs	SLC30A10_ENST00000484079.1_5'UTR|SLC30A10_ENST00000536446.1_5'UTR	NM_018713.2	NP_061183.2	Q6XR72	ZNT10_HUMAN	solute carrier family 30, member 10	243					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	13				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)		CATCACATGCAAAAGTACACC	0.517																																					p.L243fs	Colon(76;360 1614 43677 51136)	Atlas-Indel,Pindel	.											.	SLC30A10	58	.	0			c.729delG						.						116	108	111					1																	220091827		2203	4300	6503	SO:0001589	frameshift_variant	55532	exon3			.	AY212919	CCDS31026.1	1q41	2013-05-22			ENSG00000196660	ENSG00000196660		"Solute carriers"	25355	protein-coding gene	gene with protein product	"zinc transporter 8"	611146				15154973	Standard	NR_046437		Approved	DKFZp547M236, ZnT-10, ZRC1, ZNT8	uc001hlw.3	Q6XR72	OTTHUMG00000037434	ENST00000366926.3:c.728delT	chr1.hg19:g.220091827delA	ENSP00000355893:p.Leu243fs	24.0	0.0		116.0	72.0	NM_018713	Q49AL9|Q9NPW0	Frame_Shift_Del	DEL	ENST00000366926.3	hg19	CCDS31026.1																																																																																			.	.		0.517	SLC30A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357709.1	NM_018713		-	220091827	A	-	220091827	7	5	101	1	0	1	0	1	0	0	0	0	14569	131	5	0	737	0	SLC30A10	1	220091827	Frame_Shift_Del	DEL	A	TCGA-DD-A1EE-01A-11D-A12Z-10	10301909	220091827	29158794	39	13876										
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222705320	222705320	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tttgttacctgcttcatcttCagcaaaggagatgatgaact	8	8	3	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:222705320C>G	ENST00000343410.6	-	6	1769	c.1711G>C	c.(1711-1713)Gaa>Caa	p.E571Q		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	571					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		GCTTCATCTTCAGCAAAGGAG	0.433																																					p.E571Q		Atlas-SNP	.											.	HHIPL2	122	.	0			c.G1711C						.						84	81	82					1																	222705320		2203	4300	6503	SO:0001583	missense	79802	exon6			CATCTTCAGCAAA	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"KIAA1822-like"	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1711G>C	chr1.hg19:g.222705320C>G	ENSP00000342118:p.Glu571Gln	40.0	0.0		225.0	19.0	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	hg19	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999179	0.74818	.	.	ENSG00000143512	ENST00000343410	T	0.11169	2.8	5.0	4.09	0.47781	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.052062	0.64402	D	0.000001	T	0.23688	0.0573	L	0.43757	1.38	0.52099	D	0.999942	D	0.89917	1.0	D	0.97110	1.0	T	0.00581	-1.1660	10	0.39692	T	0.17	-18.8979	12.8232	0.57704	0.0:0.9204:0.0:0.0796	.	571	Q6UWX4	HIPL2_HUMAN	Q	571	ENSP00000342118:E571Q	ENSP00000342118:E571Q	E	-	1	0	HHIPL2	220771943	1.000000	0.71417	0.994000	0.49952	0.982000	0.71751	5.694000	0.68272	1.091000	0.41335	0.591000	0.81541	GAA	.	.		0.433	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		G	222705320	C	G	222705320	3	3	101	1	0	0	0	0	1	0	0	0	7103	835	29	4	479	4	HHIPL2	1	222705320	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2613493	222705320	26545301	40	13877										
C1orf65	164127	hgsc.bcm.edu	37	chr1	223568584	223568584	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttccaggagttccagaagctCcctcaggcctccaggagaga	11	13	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:223568584C>T	ENST00000366875.3	+	1	1870	c.1767C>T	c.(1765-1767)ctC>ctT	p.L589L		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		589										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		TCCAGAAGCTCCCTCAGGCCT	0.557																																					p.L589L		Atlas-SNP	.											.	C1orf65	71	.	0			c.C1767T						.						65	64	64					1																	223568584		2203	4300	6503	SO:0001819	synonymous_variant	164127	exon1			GAAGCTCCCTCAG																												ENST00000366875.3:c.1767C>T	chr1.hg19:g.223568584C>T		50.0	0.0		207.0	61.0	NM_152610	Q8N746|Q8NA93	Silent	SNP	ENST00000366875.3	hg19	CCDS1537.1																																																																																			.	.		0.557	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			T	223568584	C	T	223568584	2	4	101	1	0	0	0	0	0	0	0	1	2057	842	30	3		3	C1orf65	1	223568584	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	863264	223568584	25682037	41	13878										
WDR26	80232	hgsc.bcm.edu	37	chr1	224619473	224619473	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgactcttgcatgaggagatCaacagtctggctgcaggaaa	12	8	3	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:224619473C>A	ENST00000414423.2	-	2	626	c.433G>T	c.(433-435)Gat>Tat	p.D145Y	WDR26_ENST00000295024.6_5'UTR|WDR26_ENST00000366852.2_Missense_Mutation_p.D145Y	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	145	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		ATGAGGAGATCAACAGTCTGG	0.403																																					p.D145Y		Atlas-SNP	.											.	WDR26	104	.	0			c.G433T						.						72	61	64					1																	224619473		2203	4300	6503	SO:0001583	missense	80232	exon2			GGAGATCAACAGT	AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"WD repeat domain containing"	21208	protein-coding gene	gene with protein product	"GID complex subunit 7 homolog (S. cerevisiae)"						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.433G>T	chr1.hg19:g.224619473C>A	ENSP00000408108:p.Asp145Tyr	63.0	0.0		218.0	9.0	NM_001115113	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Missense_Mutation	SNP	ENST00000414423.2	hg19	CCDS31037.2	.	.	.	.	.	.	.	.	.	.	C	23.2	4.389394	0.82902	.	.	ENSG00000162923	ENST00000414423;ENST00000366852	D;D	0.84070	-1.8;-1.8	5.69	5.69	0.88448	.	.	.	.	.	D	0.89174	0.6640	M	0.62723	1.935	0.80722	D	1	.	.	.	.	.	.	D	0.89395	0.3691	7	0.72032	D	0.01	.	19.8145	0.96560	0.0:1.0:0.0:0.0	.	.	.	.	Y	145	ENSP00000408108:D145Y;ENSP00000355817:D145Y	ENSP00000355817:D145Y	D	-	1	0	WDR26	222686096	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.683000	0.91414	0.563000	0.77884	GAT	.	.		0.403	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160		A	224619473	C	A	224619473	3	1	101	1	0	0	0	0	1	0	0	0	17298	826	29	3	1604	3	WDR26	1	224619473	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1050889	224619473	24631148	42	13879										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227216748	227216748	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cacacacaggcatgtgagagCtccatggcgcacctttccag	10	14	0	1	rs375342151		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:227216748C>G	ENST00000366769.3	-	29	5228	c.3937G>C	c.(3937-3939)Gct>Cct	p.A1313P	CDC42BPA_ENST00000366766.2_Missense_Mutation_p.A1348P|CDC42BPA_ENST00000366767.3_Missense_Mutation_p.A1232P|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.A1285P|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.A1313P|CDC42BPA_ENST00000366765.3_Missense_Mutation_p.A1326P|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.A1293P	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				CATGTGAGAGCTCCATGGCGC	0.448																																					p.A1313P		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.G3937C						.						72	60	64					1																	227216748		2203	4300	6503	SO:0001583	missense	8476	exon29			TGAGAGCTCCATG	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.3937G>C	chr1.hg19:g.227216748C>G	ENSP00000355731:p.Ala1313Pro	18.0	0.0		103.0	10.0	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	hg19	CCDS1558.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.44|10.44	1.349882|1.349882	0.24426|0.24426	.|.	.|.	ENSG00000143776|ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765|ENST00000448940;ENST00000442054;ENST00000429440;ENST00000441725	T;T;T;T;T;T;T|.	0.05319|.	3.46;3.46;3.46;3.46;3.46;3.46;3.46|.	5.32|5.32	3.43|3.43	0.39272|0.39272	.|.	0.210090|.	0.50627|.	D|.	0.000116|.	T|T	0.55386|0.55386	0.1917|0.1917	L|L	0.41710|0.41710	1.295|1.295	0.44201|0.44201	D|D	0.997023|0.997023	P;B;B;B;P;B;B;P|.	0.49253|.	0.507;0.0;0.03;0.001;0.699;0.0;0.0;0.921|.	B;B;B;B;P;B;B;P|.	0.56474|.	0.28;0.001;0.145;0.008;0.625;0.003;0.005;0.799|.	T|T	0.51505|0.51505	-0.8697|-0.8697	10|5	0.21014|.	T|.	0.42|.	.|.	11.4823|11.4823	0.50333|0.50333	0.0:0.8543:0.0:0.1457|0.0:0.8543:0.0:0.1457	.|.	1293;1285;628;210;1232;1313;1348;515|.	F5H5N0;Q5VT25-4;E9PEF7;Q5T7A7;Q5VT25-3;Q5VT25-5;Q5VT25-2;Q5T799|.	.;.;.;.;.;.;.;.|.	P|T	1313;1232;1313;1348;1285;628;1293;1326|515;641;210;537	ENSP00000355731:A1313P;ENSP00000355729:A1232P;ENSP00000335341:A1313P;ENSP00000355728:A1348P;ENSP00000355726:A1285P;ENSP00000443275:A1293P;ENSP00000355727:A1326P|.	ENSP00000335341:A1313P|.	A|S	-|-	1|2	0|0	CDC42BPA|CDC42BPA	225283371|225283371	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	1.565000|1.565000	0.36386|0.36386	1.391000|1.391000	0.46566|0.46566	0.585000|0.585000	0.79938|0.79938	GCT|AGC	.	.		0.448	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		G	227216748	C	G	227216748	3	3	101	1	0	0	0	0	1	0	0	0	3074	797	28	4	1254	4	CDC42BPA	1	227216748	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2597275	227216748	22033873	43	13880										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228474524	228474524	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagatgccaccatcacagagGgtgaggacttgaccctggtg	13	11	1	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:228474524G>T	ENST00000422127.1	+	35	9372	c.9328G>T	c.(9328-9330)Ggt>Tgt	p.G3110C	OBSCN_ENST00000359599.6_Missense_Mutation_p.G1957C|OBSCN_ENST00000366707.4_Missense_Mutation_p.G229C|OBSCN_ENST00000366709.4_Missense_Mutation_p.G229C|OBSCN_ENST00000570156.2_Missense_Mutation_p.G3539C|OBSCN_ENST00000284548.11_Missense_Mutation_p.G3110C	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3110	Ig-like 31.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CATCACAGAGGGTGAGGACTT	0.622																																					p.G3539C		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G10615T						.						66	76	72					1																	228474524		2106	4239	6345	SO:0001583	missense	84033	exon40			ACAGAGGGTGAGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.9328G>T	chr1.hg19:g.228474524G>T	ENSP00000409493:p.Gly3110Cys	41.0	0.0		249.0	29.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.339114	0.81911	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5	4.81	4.81	0.61882	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94341	0.8181	H	0.99104	4.43	0.53005	D	0.999969	D;D	0.89917	0.999;1.0	D;D	0.97110	0.999;1.0	D	0.96799	0.9588	10	0.87932	D	0	.	17.0384	0.86482	0.0:0.0:1.0:0.0	.	3110;3110	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	C	3110;3110;229;229;1957	ENSP00000284548:G3110C;ENSP00000409493:G3110C;ENSP00000355668:G229C;ENSP00000355670:G229C;ENSP00000352613:G1957C	ENSP00000284548:G3110C	G	+	1	0	OBSCN	226541147	1.000000	0.71417	1.000000	0.80357	0.597000	0.36814	8.169000	0.89672	2.484000	0.83849	0.491000	0.48974	GGT	.	.		0.622	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228474524	G	T	228474524	3	4	101	1	0	0	0	0	1	0	0	0	10821	1232	43	3	9462	3	OBSCN	1	228474524	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1257776	228474524	20776097	44	13881										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228474710	228474710	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acaagtgtgaggctgggggcGcctgcagcagctccattgtc	15	11	0	1	rs558072959		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:228474710G>T	ENST00000422127.1	+	35	9558	c.9514G>T	c.(9514-9516)Gcc>Tcc	p.A3172S	OBSCN_ENST00000359599.6_Missense_Mutation_p.A2019S|OBSCN_ENST00000366707.4_Missense_Mutation_p.A291S|OBSCN_ENST00000366709.4_Missense_Mutation_p.A291S|OBSCN_ENST00000570156.2_Missense_Mutation_p.A3601S|OBSCN_ENST00000284548.11_Missense_Mutation_p.A3172S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3172	Ig-like 31.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGCTGGGGGCGCCTGCAGCAG	0.662																																					p.A3601S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G10801T						.						10	12	12					1																	228474710		2006	4171	6177	SO:0001583	missense	84033	exon40			GGGGGCGCCTGCA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.9514G>T	chr1.hg19:g.228474710G>T	ENSP00000409493:p.Ala3172Ser	20.0	0.0		191.0	26.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.462369	0.43736	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.05382	3.45;3.45;3.45;3.45;3.45	5.09	1.06	0.20224	Immunoglobulin subtype 2 (1);	0.367653	0.26467	N	0.024211	T	0.08447	0.0210	L	0.39147	1.195	0.09310	N	1	B;D	0.64830	0.13;0.994	B;P	0.58172	0.173;0.834	T	0.21415	-1.0246	10	0.09590	T	0.72	.	5.6767	0.17753	0.1333:0.0:0.4468:0.4199	.	3172;3172	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	3172;3172;291;291;2019	ENSP00000284548:A3172S;ENSP00000409493:A3172S;ENSP00000355668:A291S;ENSP00000355670:A291S;ENSP00000352613:A2019S	ENSP00000284548:A3172S	A	+	1	0	OBSCN	226541333	0.000000	0.05858	0.224000	0.23877	0.043000	0.13939	-0.225000	0.09151	0.034000	0.15491	0.561000	0.74099	GCC	.	.		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228474710	G	T	228474710	3	4	101	1	0	0	0	0	1	0	0	0	10821	1087	38	1	9648	1	OBSCN	1	228474710	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	186	228474710	20775911	45	13882										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228495849	228495849	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtacgggggctggttgatgcGgaggtgacggccgatgagga	21	6	0	3	rs562134549		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:228495849G>T	ENST00000422127.1	+	47	12548	c.12504G>T	c.(12502-12504)gcG>gcT	p.A4168A	OBSCN_ENST00000366707.4_Silent_p.A1802A|OBSCN_ENST00000366709.4_Silent_p.A1287A|OBSCN_ENST00000570156.2_Silent_p.A5125A|OBSCN_ENST00000284548.11_Silent_p.A4168A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4168					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGGTTGATGCGGAGGTGACGG	0.602																																					p.A5125A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G15375T						.						88	101	97					1																	228495849		2160	4257	6417	SO:0001819	synonymous_variant	84033	exon58			TGATGCGGAGGTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.12504G>T	chr1.hg19:g.228495849G>T		75.0	0.0		261.0	113.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.602	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228495849	G	T	228495849	2	4	101	1	0	0	0	0	0	0	0	1	10821	1103	39	1		1	OBSCN	1	228495849	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	21139	228495849	20754772	46	13883										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232650005	232650005	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agtctgggatgctgcagatgCcccagtggttatgtttttcc	12	9	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:232650005C>A	ENST00000366630.1	-	2	1439	c.1081G>T	c.(1081-1083)Gca>Tca	p.A361S	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.A361S			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	361					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GCTGCAGATGCCCCAGTGGTT	0.488																																					p.A361S		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G1081T						.						101	103	103					1																	232650005		1952	4136	6088	SO:0001583	missense	57568	exon1			CAGATGCCCCAGT	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.1081G>T	chr1.hg19:g.232650005C>A	ENSP00000355589:p.Ala361Ser	40.0	0.0		140.0	6.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.694733	0.88830	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	D;D	0.91577	-2.87;-2.87	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.95472	0.8529	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95411	0.8498	10	0.72032	D	0.01	-26.4199	19.3561	0.94414	0.0:1.0:0.0:0.0	.	361	Q9P2F8	SI1L2_HUMAN	S	361	ENSP00000355589:A361S;ENSP00000262861:A361S	ENSP00000262861:A361S	A	-	1	0	SIPA1L2	230716628	1.000000	0.71417	0.938000	0.37757	0.992000	0.81027	7.651000	0.83577	2.810000	0.96702	0.650000	0.86243	GCA	.	.		0.488	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232650005	C	A	232650005	3	1	101	1	0	0	0	0	1	0	0	0	14345	739	26	3	4171	3	SIPA1L2	1	232650005	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4154156	232650005	16600616	47	13884										
RBM34	23029	hgsc.bcm.edu	37	chr1	235318339	235318339	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aagtatttttctatctgctaCtttaacaccaggttgagaat	6	7	2	1	rs200657743		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:235318339C>A	ENST00000408888.3	-	4	684	c.454G>T	c.(454-456)Gta>Tta	p.V152L	RBM34_ENST00000366606.3_Missense_Mutation_p.V147L			P42696	RBM34_HUMAN	RNA binding motif protein 34	152						nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			CTATCTGCTACTTTAACACCA	0.368																																					p.V152L		Atlas-SNP	.											.	RBM34	41	.	0			c.G454T						.						188	159	168					1																	235318339		1819	4089	5908	SO:0001583	missense	23029	exon4			CTGCTACTTTAAC		CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739		"RNA binding motif (RRM) containing"	28965	protein-coding gene	gene with protein product						7788527, 15134903	Standard	NM_015014		Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.454G>T	chr1.hg19:g.235318339C>A	ENSP00000386226:p.Val152Leu	155.0	0.0		751.0	57.0	NM_001161533	A8K8J7|Q8N2Z8|Q9H5A1	Missense_Mutation	SNP	ENST00000408888.3	hg19	CCDS41477.2	.	.	.	.	.	.	.	.	.	.	C	1.089	-0.664488	0.03428	.	.	ENSG00000188739	ENST00000408888;ENST00000366606;ENST00000400947;ENST00000447801;ENST00000429912	T;T;T	0.14391	2.51;2.51;2.63	5.67	0.267	0.15622	.	1.363850	0.04381	N	0.360761	T	0.15003	0.0362	M	0.64997	1.995	0.09310	N	1	B;B	0.33171	0.4;0.01	B;B	0.26969	0.075;0.005	T	0.35201	-0.9798	10	0.27785	T	0.31	-1.4571	8.9883	0.36008	0.0:0.5752:0.0:0.4248	.	152;152	P42696-2;P42696	.;RBM34_HUMAN	L	152;147;181;150;181	ENSP00000386226:V152L;ENSP00000355565:V147L;ENSP00000400000:V150L	ENSP00000355565:V147L	V	-	1	0	RBM34	233384962	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.038000	0.12144	0.091000	0.17302	0.655000	0.94253	GTA	.	.		0.368	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100146.1	NM_015014		A	235318339	C	A	235318339	3	1	101	1	0	0	0	0	1	0	0	0	13146	565	20	3	891	3	RBM34	1	235318339	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2668334	235318339	13932282	48	13885										
ZP4	57829	hgsc.bcm.edu	37	chr1	238048491	238048491	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cctgagggcctgtttctccaCtgtagggttcacaaagctga	11	11	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:238048491C>A	ENST00000366570.4	-	9	1443	c.1285G>T	c.(1285-1287)Gtg>Ttg	p.V429L	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	429	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)	p.V429L(1)		breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			TGTTTCTCCACTGTAGGGTTC	0.532																																					p.V429L	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											ZP4,NS,carcinoma,0,1	ZP4	161	.	1	Substitution - Missense(1)	kidney(1)	c.G1285T						.						88	91	90					1																	238048491		2203	4300	6503	SO:0001583	missense	57829	exon9			TCTCCACTGTAGG	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"Zona pellucida glycoproteins"	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.1285G>T	chr1.hg19:g.238048491C>A	ENSP00000355529:p.Val429Leu	83.0	0.0		291.0	74.0	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	hg19	CCDS1615.1	.	.	.	.	.	.	.	.	.	.	C	5.632	0.301343	0.10678	.	.	ENSG00000116996	ENST00000366570	T	0.74209	-0.82	5.09	-7.04	0.01578	Zona pellucida sperm-binding protein (3);	2.733670	0.01388	N	0.013174	T	0.60958	0.2309	L	0.46741	1.465	0.09310	N	1	B	0.10296	0.003	B	0.16722	0.016	T	0.38243	-0.9670	10	0.25751	T	0.34	.	2.9815	0.05955	0.1038:0.1418:0.3069:0.4474	.	429	Q12836	ZP4_HUMAN	L	429	ENSP00000355529:V429L	ENSP00000355529:V429L	V	-	1	0	ZP4	236115114	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.298000	0.02756	-0.982000	0.03515	-0.840000	0.03056	GTG	.	.		0.532	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			A	238048491	C	A	238048491	3	1	101	1	0	0	0	0	1	0	0	0	18233	565	20	3	353	3	ZP4	1	238048491	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2730152	238048491	11202130	49	13886										
CHRM3	1131	hgsc.bcm.edu	37	chr1	240071656	240071656	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcaacagcaaagcatgaaacGctccaacaggaggaagtatg	10	9	1	1	rs202097685		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:240071656G>T	ENST00000255380.4	+	5	1684	c.905G>T	c.(904-906)cGc>cTc	p.R302L		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	302					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	AGCATGAAACGCTCCAACAGG	0.547																																					p.R302L		Atlas-SNP	.											.	CHRM3	118	.	0			c.G905T						.						42	45	44					1																	240071656		2203	4300	6503	SO:0001583	missense	1131	exon5			TGAAACGCTCCAA	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.905G>T	chr1.hg19:g.240071656G>T	ENSP00000255380:p.Arg302Leu	35.0	0.0		195.0	31.0	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	hg19	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434483	0.25813	.	.	ENSG00000133019	ENST00000255380	T	0.59772	0.24	5.88	3.0	0.34707	GPCR, rhodopsin-like superfamily (1);	0.485395	0.21374	N	0.075600	T	0.32971	0.0847	N	0.08118	0	0.22811	N	0.998705	B	0.23540	0.087	B	0.30179	0.112	T	0.22138	-1.0225	10	0.19590	T	0.45	-4.1978	6.22	0.20675	0.2031:0.0:0.6668:0.1301	.	302	P20309	ACM3_HUMAN	L	302	ENSP00000255380:R302L	ENSP00000255380:R302L	R	+	2	0	CHRM3	238138279	0.330000	0.24705	0.016000	0.15963	0.880000	0.50808	1.231000	0.32624	0.391000	0.25143	0.591000	0.81541	CGC	.	.		0.547	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		T	240071656	G	T	240071656	3	4	101	1	0	0	0	0	1	0	0	0	3380	1087	38	1	907	1	CHRM3	1	240071656	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2023165	240071656	9178965	50	13887										
CEP170	9859	hgsc.bcm.edu	37	chr1	243327863	243327876	+	Frame_Shift_Del	DEL	AGAACTTGTTGTGG	AGAACTTGTTGTGG	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cctgtgggaggttttgatgtAgaacttgttgtggatacttc							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	AGAACTTGTTGTGG	AGAACTTGTTGTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr1:243327863_243327876delAGAACTTGTTGTGG	ENST00000366542.1	-	13	3437_3450	c.3386_3399delCCACAACAAGTTCT	c.(3385-3399)tccacaacaagttctfs	p.STTSS1129fs	RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000366543.1_Frame_Shift_Del_p.STTSS1031fs|CEP170_ENST00000490813.1_5'Flank|CEP170_ENST00000366544.1_Frame_Shift_Del_p.STTSS1031fs|RP11-261C10.4_ENST00000437499.1_RNA	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	1129	Targeting to centrosomes.|Targeting to microtubules.					centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GTTTTGATGTAGAACTTGTTGTGGATACTTCAGA	0.491																																					p.1129_1134del		Atlas-Indel,Pindel	.											.	CEP170	153	.	0			c.3387_3400del						.																																			SO:0001589	frameshift_variant	9859	exon13			.	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.3386_3399delCCACAACAAGTTCT	chr1.hg19:g.243327863_243327876delAGAACTTGTTGTGG	ENSP00000355500:p.Ser1129fs	151.0	0.0		655.0	44.0	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Frame_Shift_Del	DEL	ENST00000366542.1	hg19	CCDS44339.1																																																																																			.	.		0.491	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		-	243327876	AGAACTTGTTGTGG	-	243327863	7	5	101	1	0	1	0	1	0	0	0	0	3252	407	15	0	1417	0	CEP170	1	243327863	Frame_Shift_Del	DEL	AGAACTTGTTGTGG	TCGA-DD-A1EE-01A-11D-A12Z-10	3256207	243327863	5922758	51	13888										
TPO	7173	hgsc.bcm.edu	37	chr2	1497607	1497607	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gagggagttctgcggcctgcCtcgcctggagacccccgctg	15	15	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:1497607C>A	ENST00000345913.4	+	11	1893	c.1802C>A	c.(1801-1803)cCt>cAt	p.P601H	TPO_ENST00000349624.3_Missense_Mutation_p.P428H|TPO_ENST00000382198.1_Missense_Mutation_p.P428H|TPO_ENST00000346956.3_Missense_Mutation_p.P601H|TPO_ENST00000329066.4_Missense_Mutation_p.P601H|TPO_ENST00000382201.3_Missense_Mutation_p.P544H|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000337415.3_Missense_Mutation_p.P601H	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	601					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TGCGGCCTGCCTCGCCTGGAG	0.572																																					p.P601H		Atlas-SNP	.											.	TPO	224	.	0			c.C1802A						.						53	49	50					2																	1497607		2203	4300	6503	SO:0001583	missense	7173	exon11			GCCTGCCTCGCCT		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.1802C>A	chr2.hg19:g.1497607C>A	ENSP00000318820:p.Pro601His	32.0	0.0		103.0	12.0	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.11|11.11	1.542287|1.542287	0.27563|0.27563	.|.	.|.	ENSG00000115705|ENSG00000115705	ENST00000446278|ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607	.|T;T;T;T;T;T;T;T;T	.|0.69435	.|-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4	4.84|4.84	0.334|0.334	0.15948|0.15948	.|.	.|0.964866	.|0.08705	.|N	.|0.905723	T|T	0.77994|0.77994	0.4214|0.4214	M|M	0.81112|0.81112	2.525|2.525	0.09310|0.09310	N|N	1|1	.|P;D;P;P	.|0.57571	.|0.941;0.98;0.941;0.952	.|P;P;P;P	.|0.57776	.|0.735;0.804;0.735;0.827	T|T	0.66015|0.66015	-0.6028|-0.6028	5|10	.|0.87932	.|D	.|0	-9.514|-9.514	10.2455|10.2455	0.43339|0.43339	0.2471:0.5131:0.2398:0.0|0.2471:0.5131:0.2398:0.0	.|.	.|601;428;544;601	.|P07202-4;P07202-5;P07202-2;P07202	.|.;.;.;PERT_HUMAN	I|H	76|601;601;601;428;601;544;428;530;75	.|ENSP00000337263:P601H;ENSP00000318820:P601H;ENSP00000263886:P601H;ENSP00000332044:P428H;ENSP00000329869:P601H;ENSP00000371636:P544H;ENSP00000371633:P428H;ENSP00000405788:P530H;ENSP00000419461:P75H	.|ENSP00000329869:P601H	L|P	+|+	1|2	0|0	TPO|TPO	1476614|1476614	0.003000|0.003000	0.15002|0.15002	0.000000|0.000000	0.03702|0.03702	0.070000|0.070000	0.16714|0.16714	0.521000|0.521000	0.22893|0.22893	0.129000|0.129000	0.18514|0.18514	0.561000|0.561000	0.74099|0.74099	CTC|CCT	.	.		0.572	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		A	1497607	C	A	1497607	3	1	101	1	0	0	0	0	1	0	0	0	16425	681	24	3	1840	3	TPO	2	1497607	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10		1497607	241701766	52	13889										
KCNF1	3754	hgsc.bcm.edu	37	chr2	11053359	11053359	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atcctccccttctacgtgagCctcacgctcacgcacctggg	8	18	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:11053359C>T	ENST00000295082.1	+	1	1297	c.807C>T	c.(805-807)agC>agT	p.S269S		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	269					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		TCTACGTGAGCCTCACGCTCA	0.617																																					p.S269S		Atlas-SNP	.											KCNF1,right_lower_lobe,carcinoma,0,1	KCNF1	70	.	0			c.C807T						.						62	52	55					2																	11053359		2203	4300	6503	SO:0001819	synonymous_variant	3754	exon1			CGTGAGCCTCACG	AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.807C>T	chr2.hg19:g.11053359C>T		51.0	0.0		71.0	5.0	NM_002236	O43527|Q585L3	Silent	SNP	ENST00000295082.1	hg19	CCDS1676.1																																																																																			.	.		0.617	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236		T	11053359	C	T	11053359	2	4	101	1	0	0	0	0	0	0	0	1	8035	738	26	3		3	KCNF1	2	11053359	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	9555752	11053359	232146014	53	13890										
KCNF1	3754	hgsc.bcm.edu	37	chr2	11053487	11053487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccactcctcgggcctgcagaCcctcacctatgccctcaagc	7	20	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:11053487C>T	ENST00000295082.1	+	1	1425	c.935C>T	c.(934-936)aCc>aTc	p.T312I		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	312					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		GGCCTGCAGACCCTCACCTAT	0.622																																					p.T312I		Atlas-SNP	.											.	KCNF1	70	.	0			c.C935T						.						61	59	60					2																	11053487		2203	4300	6503	SO:0001583	missense	3754	exon1			TGCAGACCCTCAC	AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.935C>T	chr2.hg19:g.11053487C>T	ENSP00000295082:p.Thr312Ile	36.0	0.0		160.0	8.0	NM_002236	O43527|Q585L3	Missense_Mutation	SNP	ENST00000295082.1	hg19	CCDS1676.1	.	.	.	.	.	.	.	.	.	.	c	17.50	3.404087	0.62288	.	.	ENSG00000162975	ENST00000295082	D	0.98684	-5.07	4.74	4.74	0.60224	Ion transport (1);	0.105772	0.64402	D	0.000005	D	0.96642	0.8904	N	0.11427	0.14	0.80722	D	1	D	0.55605	0.972	P	0.57620	0.824	D	0.94414	0.7634	10	0.02654	T	1	.	18.1029	0.89512	0.0:1.0:0.0:0.0	.	312	Q9H3M0	KCNF1_HUMAN	I	312	ENSP00000295082:T312I	ENSP00000295082:T312I	T	+	2	0	KCNF1	10970938	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.348000	0.79779	0.556000	0.70494	ACC	.	.		0.622	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236		T	11053487	C	T	11053487	3	4	101	1	0	0	0	0	1	0	0	0	8035	507	18	3	937	3	KCNF1	2	11053487	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	128	11053487	232145886	54	13891										
APOB	338	hgsc.bcm.edu	37	chr2	21230944	21230945	+	Frame_Shift_Ins	INS	-	-	T													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	catctgagaatctggggcagINSgcccatttccatgacccttt							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:21230944_21230945insT	ENST00000233242.1	-	26	8922_8923	c.8795_8796insA	c.(8794-8796)gccfs	p.A2932fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2932					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATCTGGGGCAGGCCCATTTCCA	0.47																																					p.A2932fs		Atlas-INDEL	.											.	APOB	761	.	0			c.8796_8797insA						.																																			SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8795_8796insA	chr2.hg19:g.21230944_21230945insT	ENSP00000233242:p.Ala2932fs	135.0	0.0		298.0	27.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.47	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21230945	-	T	21230944	7	5	101	1	0	1	1	0	0	0	0	0	785	987	35	0	4911	0	APOB	2	21230944	Frame_Shift_Ins	INS	-	TCGA-DD-A1EE-01A-11D-A12Z-10	10177457	21230944	221968429	55	13892										
APOB	338	hgsc.bcm.edu	37	chr2	21231053	21231053	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gactagagaagtccagtttgGggatgttcaatttgtggaag	14	4	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:21231053G>A	ENST00000233242.1	-	26	8814	c.8687C>T	c.(8686-8688)cCc>cTc	p.P2896L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2896					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTCCAGTTTGGGGATGTTCAA	0.433																																					p.P2896L		Atlas-SNP	.											.	APOB	761	.	0			c.C8687T						.						176	173	174					2																	21231053		2203	4299	6502	SO:0001583	missense	338	exon26			AGTTTGGGGATGT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8687C>T	chr2.hg19:g.21231053G>A	ENSP00000233242:p.Pro2896Leu	117.0	0.0		230.0	12.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.677007	0.88445	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01527	4.8	5.73	5.73	0.89815	.	0.000000	0.51477	D	0.000088	T	0.11623	0.0283	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00061	-1.2161	10	0.87932	D	0	.	19.5098	0.95137	0.0:0.0:1.0:0.0	.	2896	P04114	APOB_HUMAN	L	2896	ENSP00000233242:P2896L	ENSP00000233242:P2896L	P	-	2	0	APOB	21084558	1.000000	0.71417	0.975000	0.42487	0.996000	0.88848	9.803000	0.99136	2.707000	0.92482	0.555000	0.69702	CCC	.	.		0.433	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21231053	G	A	21231053	3	1	101	1	0	0	0	0	1	0	0	0	785	1232	43	3	5020	3	APOB	2	21231053	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	109	21231053	221968320	56	13893										
UBXN2A	165324	hgsc.bcm.edu	37	chr2	24194229	24194229	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttttgttgatagcctttttgAggaagctcagaaggttagtt	11	4	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:24194229A>T	ENST00000309033.4	+	3	369	c.125A>T	c.(124-126)gAg>gTg	p.E42V	UBXN2A_ENST00000446425.2_3'UTR|UBXN2A_ENST00000404924.1_Missense_Mutation_p.E42V|UBXN2A_ENST00000535786.1_Missense_Mutation_p.E42V	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	42					regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						AGCCTTTTTGAGGAAGCTCAG	0.333																																					p.E42V		Atlas-SNP	.											.	UBXN2A	20	.	0			c.A125T						.						128	135	133					2																	24194229		2203	4300	6503	SO:0001583	missense	165324	exon3			TTTTTGAGGAAGC	BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960		"UBX domain containing"	27265	protein-coding gene	gene with protein product			"UBX domain containing 4"	UBXD4		12477932	Standard	NM_181713		Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.125A>T	chr2.hg19:g.24194229A>T	ENSP00000312107:p.Glu42Val	70.0	0.0		113.0	13.0	NM_181713	A8K577|B7ZKP8|Q569G8	Missense_Mutation	SNP	ENST00000309033.4	hg19	CCDS1704.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.948036	0.73787	.	.	ENSG00000173960	ENST00000404924;ENST00000309033;ENST00000535786	T;T;T	0.51574	0.75;0.75;0.7	4.53	4.53	0.55603	.	0.096452	0.64402	D	0.000001	T	0.54951	0.1890	L	0.32530	0.975	0.41646	D	0.989103	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.957	T	0.52533	-0.8563	10	0.33940	T	0.23	-0.4989	12.105	0.53807	1.0:0.0:0.0:0.0	.	42;42	B7ZKP8;P68543	.;UBX2A_HUMAN	V	42	ENSP00000385525:E42V;ENSP00000312107:E42V;ENSP00000440533:E42V	ENSP00000312107:E42V	E	+	2	0	UBXN2A	24047733	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.240000	0.65378	2.011000	0.59026	0.524000	0.50904	GAG	.	.		0.333	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246824.2	NM_181713		T	24194229	A	T	24194229	3	4	101	1	0	0	0	0	1	0	0	0	16929	304	11	4	131	4	UBXN2A	2	24194229	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	2963176	24194229	219005144	57	13894										
TRIM54	57159	hgsc.bcm.edu	37	chr2	27528584	27528584	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agaagctgcagcgcgtccgcGgcctcatccgtcagtatggc	13	14	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:27528584G>C	ENST00000380075.2	+	5	1082	c.742G>C	c.(742-744)Ggc>Cgc	p.G248R	TRIM54_ENST00000296098.4_Missense_Mutation_p.G290R	NM_187841.2	NP_912730.2	Q9BYV2	TRI54_HUMAN	tripartite motif containing 54	248					cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|negative regulation of microtubule depolymerization (GO:0007026)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCGCGTCCGCGGCCTCATCCG	0.632																																					p.G290R		Atlas-SNP	.											.	TRIM54	35	.	0			c.G868C						.						34	32	33					2																	27528584		2202	4300	6502	SO:0001583	missense	57159	exon6			GTCCGCGGCCTCA	AJ291714	CCDS1745.2, CCDS1746.2	2p23.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000138100	ENSG00000138100		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16008	protein-coding gene	gene with protein product		606474	"ring finger protein 30", "tripartite motif-containing 54"	RNF30		11243782	Standard	NM_032546		Approved	MURF, MURF-3	uc002rjn.3	Q9BYV2	OTTHUMG00000097078	ENST00000380075.2:c.742G>C	chr2.hg19:g.27528584G>C	ENSP00000369415:p.Gly248Arg	36.0	0.0		165.0	33.0	NM_032546	A5D8T7|Q53SY4|Q9BYV3	Missense_Mutation	SNP	ENST00000380075.2	hg19	CCDS1746.2	.	.	.	.	.	.	.	.	.	.	G	15.64	2.894559	0.52121	.	.	ENSG00000138100	ENST00000380075;ENST00000380073;ENST00000296098	T;T	0.40225	1.24;1.04	4.85	3.04	0.35103	.	0.386929	0.26867	N	0.022083	T	0.43478	0.1249	L	0.46157	1.445	0.18873	N	0.999989	P;P	0.41366	0.488;0.747	B;P	0.52823	0.357;0.71	T	0.20438	-1.0275	10	0.33141	T	0.24	-14.4805	4.6928	0.12788	0.1859:0.0:0.6429:0.1711	.	248;290	Q9BYV2;Q9BYV2-2	TRI54_HUMAN;.	R	248;69;290	ENSP00000369415:G248R;ENSP00000296098:G290R	ENSP00000296098:G290R	G	+	1	0	TRIM54	27382088	0.002000	0.14202	0.852000	0.33557	0.858000	0.48976	0.624000	0.24462	0.461000	0.27071	-0.291000	0.09656	GGC	.	.		0.632	TRIM54-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214199.2	NM_187841		C	27528584	G	C	27528584	3	2	101	1	0	0	0	0	1	0	0	0	16543	1116	39	4	890	4	TRIM54	2	27528584	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3334355	27528584	215670789	58	13895										
TRMT61B	55006	hgsc.bcm.edu	37	chr2	29075273	29075273	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaaaacagttatattactcaCtttactacatatacagcaca	2	9	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:29075273C>T	ENST00000306108.5	-	4	1109		c.e4+1		TRMT61B_ENST00000484060.1_Splice_Site	NM_017910.3	NP_060380.3	Q9BVS5	TR61B_HUMAN	tRNA methyltransferase 61 homolog B (S. cerevisiae)						mitochondrial tRNA methylation (GO:0070901)|protein homooligomerization (GO:0051260)	mitochondrion (GO:0005739)|tRNA (m1A) methyltransferase complex (GO:0031515)	tRNA (adenine-N1-)-methyltransferase activity (GO:0016429)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	13						ATATTACTCACTTTACTACAT	0.294																																					.		Atlas-SNP	.											.	TRMT61B	28	.	0			c.1085+1G>A						.						79	76	77					2																	29075273		2203	4300	6503	SO:0001630	splice_region_variant	55006	exon5			TACTCACTTTACT	BC010365	CCDS1768.1	2p23.2	2009-01-09			ENSG00000171103	ENSG00000171103			26070	protein-coding gene	gene with protein product						11230166	Standard	NM_017910		Approved	FLJ20628	uc002rmm.3	Q9BVS5	OTTHUMG00000128433	ENST00000306108.5:c.1085+1G>A	chr2.hg19:g.29075273C>T		85.0	0.0		158.0	12.0	NM_017910	Q9H0Q9|Q9NWS7	Splice_Site	SNP	ENST00000306108.5	hg19	CCDS1768.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.866656	0.32977	.	.	ENSG00000171103	ENST00000306108	.	.	.	5.43	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.562	0.68148	0.0:0.9286:0.0:0.0714	.	.	.	.	.	-1	.	.	.	-	.	.	TRMT61B	28928777	1.000000	0.71417	1.000000	0.80357	0.238000	0.25445	3.754000	0.55189	1.268000	0.44264	0.655000	0.94253	.	.	.		0.294	TRMT61B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250224.1	NM_017910	Intron	T	29075273	C	T	29075273	5	4	101	1	0	0	0	0	0	0	1	0	16585	579	20	3	363	3	TRMT61B	2	29075273	Splice_Site	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1546689	29075273	214124100	59	13896										
GALNT14	79623	hgsc.bcm.edu	37	chr2	31165150	31165151	+	Missense_Mutation	DNP	CC	CC	AA													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctttgtcgatcacgaagagcCctccagctatgataggagtc							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:31165150_31165151CC>AA	ENST00000349752.5	-	9	1486_1487	c.847_848GG>TT	c.(847-849)GGg>TTg	p.G283L	GALNT14_ENST00000356174.3_Missense_Mutation_p.G250L|GALNT14_ENST00000406653.1_Missense_Mutation_p.G263L|GALNT14_ENST00000420311.2_Missense_Mutation_p.G248L|GALNT14_ENST00000324589.5_Missense_Mutation_p.G288L|GALNT14_ENST00000486564.1_5'UTR	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	283	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					CACGAAGAGCCCTCCAGCTATG	0.49																																					p.G288V|p.G288W		Atlas-SNP	.											.	GALNT14	103	.	0			c.G863T|c.G862T						.																																			SO:0001583	missense	79623	exon10			AAGAGCCCTCCAG|AGAGCCCTCCAGC	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"Glycosyltransferase family 2 domain containing"	22946	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 14"	608225	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.847_848delinsAA	chr2.hg19:g.31165150_31165151delinsAA	ENSP00000288988:p.Gly283Leu	39.0|38.0	0.0		45.0|44.0	17.0|16.0	NM_001253826	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	hg19	CCDS1773.2																																																																																			.	.		0.49	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572		AA	31165151	CC	AA	31165150	3	1	101	1	0	0	0	0	1	0	0	0	6220	623	22	3	838	3	GALNT14	2	31165150	Missense_Mutation	DNP	CC	TCGA-DD-A1EE-01A-11D-A12Z-10	2089877	31165150	212034223	60	13897										
XDH	7498	hgsc.bcm.edu	37	chr2	31591490	31591490	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtgtgttccggggtgtcagCaaccacagcaccaatgatat	11	10	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:31591490C>A	ENST00000379416.3	-	19	2065	c.2017G>T	c.(2017-2019)Gct>Tct	p.A673S		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	673					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GGGGTGTCAGCAACCACAGCA	0.458																																					p.A673S	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.G2017T						.						122	112	115					2																	31591490		2203	4300	6503	SO:0001583	missense	7498	exon19			TGTCAGCAACCAC	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.2017G>T	chr2.hg19:g.31591490C>A	ENSP00000368727:p.Ala673Ser	90.0	0.0		135.0	6.0	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	hg19	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159438	0.78226	.	.	ENSG00000158125	ENST00000379416	T	0.42131	0.98	6.17	-4.47	0.03525	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead (3);	0.332151	0.36628	N	0.002484	T	0.60830	0.2299	M	0.92970	3.365	0.58432	D	0.999997	B	0.24092	0.097	B	0.40444	0.329	T	0.69269	-0.5189	10	0.87932	D	0	.	19.8172	0.96573	0.0:0.8549:0.0:0.1451	.	673	P47989	XDH_HUMAN	S	673	ENSP00000368727:A673S	ENSP00000368727:A673S	A	-	1	0	XDH	31444994	0.272000	0.24172	0.004000	0.12327	0.927000	0.56198	0.902000	0.28459	-0.747000	0.04759	0.655000	0.94253	GCT	.	.		0.458	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		A	31591490	C	A	31591490	3	1	101	1	0	0	0	0	1	0	0	0	17441	710	25	3	2056	3	XDH	2	31591490	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	426340	31591490	211607883	61	13898										
SFRS7	6432	hgsc.bcm.edu	37	chr2	38976737	38976737	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtcccttttcgccacactcaTagcatctatcatttggatca	5	13	4	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:38976737T>C	ENST00000313117.6	-	3	557	c.320A>G	c.(319-321)tAt>tGt	p.Y107C	SRSF7_ENST00000409276.1_Missense_Mutation_p.Y107C|SRSF7_ENST00000446327.2_Missense_Mutation_p.Y107C|GEMIN6_ENST00000409011.1_5'Flank	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	107					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GCCACACTCATAGCATCTATC	0.458																																					p.Y107C		Atlas-SNP	.											.	SRSF7	29	.	0			c.A320G						.						149	141	144					2																	38976737		2203	4300	6503	SO:0001583	missense	6432	exon3			CACTCATAGCATC	L41887	CCDS33183.1, CCDS56115.1	2p22.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000115875	ENSG00000115875		"Zinc fingers, CCHC domain containing", "Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10789	protein-coding gene	gene with protein product	"SR splicing factor 7"	600572	"splicing factor, arginine/serine-rich 7 (35kD)", "splicing factor, arginine/serine-rich 7, 35kDa"	SFRS7		8013463, 20516191	Standard	NM_001031684		Approved	9G8, ZCRB2, HSSG1, AAG3, RBM37, ZCCHC20	uc002rqz.3	Q16629	OTTHUMG00000102076	ENST00000313117.6:c.320A>G	chr2.hg19:g.38976737T>C	ENSP00000325905:p.Tyr107Cys	101.0	0.0		299.0	17.0	NM_001195446	B4DLU6|G5E9M3|Q564D3	Missense_Mutation	SNP	ENST00000313117.6	hg19	CCDS33183.1	.	.	.	.	.	.	.	.	.	.	T	18.42	3.621157	0.66787	.	.	ENSG00000115875	ENST00000313117;ENST00000446327;ENST00000409276	T;T;T	0.78003	-1.14;-1.14;-1.14	5.93	4.75	0.60458	Zinc finger, CCHC retroviral-type (1);Zinc finger, CCHC-type (2);	0.000000	0.64402	D	0.000004	D	0.89047	0.6604	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.90120	0.4198	10	0.87932	D	0	.	12.3223	0.54991	0.1269:0.0:0.0:0.8731	.	107;107	G5E9M3;Q16629	.;SRSF7_HUMAN	C	107	ENSP00000325905:Y107C;ENSP00000402264:Y107C;ENSP00000386806:Y107C	ENSP00000325905:Y107C	Y	-	2	0	SRSF7	38830241	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.677000	0.84024	1.024000	0.39682	0.533000	0.62120	TAT	.	.		0.458	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684		C	38976737	T	C	38976737	3	2	101	1	0	0	0	0	1	0	0	0	14197	1406	49	2	420	2	SFRS7	2	38976737	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	7385247	38976737	204222636	62	13899										
ABCG5	64240	hgsc.bcm.edu	37	chr2	44053584	44053584	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	attcggttcctgcgagccagTtccaccaggaggacgacaat	11	12	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:44053584T>G	ENST00000260645.1	-	6	850	c.711A>C	c.(709-711)gaA>gaC	p.E237D	ABCG5_ENST00000543989.1_Intron|ABCG5_ENST00000405322.1_Intron	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	237	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	TGCGAGCCAGTTCCACCAGGA	0.532																																					p.E237D		Atlas-SNP	.											.	ABCG5	72	.	0			c.A711C						.						146	126	133					2																	44053584		2203	4300	6503	SO:0001583	missense	64240	exon6			AGCCAGTTCCACC	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"ATP binding cassette transporters / subfamily G"	13886	protein-coding gene	gene with protein product	"sterolin 1"	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.711A>C	chr2.hg19:g.44053584T>G	ENSP00000260645:p.Glu237Asp	58.0	0.0		146.0	10.0	NM_022436	Q2T9G2|Q96QZ2|Q96QZ3	Missense_Mutation	SNP	ENST00000260645.1	hg19	CCDS1814.1	.	.	.	.	.	.	.	.	.	.	T	11.50	1.657373	0.29425	.	.	ENSG00000138075	ENST00000260645	T	0.42131	0.98	5.56	2.31	0.28768	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.300661	0.40222	N	0.001146	T	0.25344	0.0616	N	0.20845	0.615	0.80722	D	1	P	0.46395	0.877	B	0.43194	0.411	T	0.02560	-1.1141	10	0.13853	T	0.58	.	9.2504	0.37551	0.0:0.6013:0.0:0.3987	.	237	Q9H222	ABCG5_HUMAN	D	237	ENSP00000260645:E237D	ENSP00000260645:E237D	E	-	3	2	ABCG5	43907088	1.000000	0.71417	0.985000	0.45067	0.195000	0.23768	1.080000	0.30779	0.689000	0.31550	-0.242000	0.12053	GAA	.	.		0.532	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436		G	44053584	T	G	44053584	3	3	101	1	0	0	0	0	1	0	0	0	71	1722	60	5	1276	5	ABCG5	2	44053584	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	5076847	44053584	199145789	63	13900										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54855371	54855371	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aatgcctccgcccagaagttCgcaacagacggggaaggtaa	12	11	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:54855371C>G	ENST00000356805.4	+	13	2063	c.1782C>G	c.(1780-1782)ttC>ttG	p.F594L	SPTBN1_ENST00000333896.5_Missense_Mutation_p.F581L	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	594					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CCCAGAAGTTCGCAACAGACG	0.512																																					p.F594L		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C1782G						.						93	80	85					2																	54855371		2203	4300	6503	SO:0001583	missense	6711	exon13			GAAGTTCGCAACA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.1782C>G	chr2.hg19:g.54855371C>G	ENSP00000349259:p.Phe594Leu	39.0	0.0		63.0	6.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.313326	0.81358	.	.	ENSG00000115306	ENST00000356805;ENST00000389980;ENST00000333896	T;T;T	0.28069	1.63;1.63;1.63	5.72	-0.858	0.10689	.	0.105784	0.64402	D	0.000003	T	0.44746	0.1308	L	0.59967	1.855	0.41608	D	0.988894	D;D	0.76494	0.997;0.999	D;D	0.72625	0.963;0.978	T	0.26916	-1.0089	10	0.56958	D	0.05	.	10.1497	0.42784	0.0:0.3365:0.0:0.6635	.	581;594	Q01082-3;Q01082	.;SPTB2_HUMAN	L	594;594;581	ENSP00000349259:F594L;ENSP00000374630:F594L;ENSP00000334156:F581L	ENSP00000334156:F581L	F	+	3	2	SPTBN1	54708875	0.984000	0.35163	0.978000	0.43139	0.990000	0.78478	0.137000	0.15995	-0.376000	0.07943	-0.334000	0.08254	TTC	.	.		0.512	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			G	54855371	C	G	54855371	3	3	101	1	0	0	0	0	1	0	0	0	15134	883	31	4	1941	4	SPTBN1	2	54855371	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	10801787	54855371	188344002	64	13901										
MDH1	4190	hgsc.bcm.edu	37	chr2	63824634	63824634	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaggcatggagagaaaagatTtactgaaagcaaatgtgaaa	11	3	0	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:63824634T>A	ENST00000233114.8	+	4	736	c.301T>A	c.(301-303)Tta>Ata	p.L101I	MDH1_ENST00000409476.1_Intron|MDH1_ENST00000394423.1_Missense_Mutation_p.L101I|MDH1_ENST00000539945.1_Missense_Mutation_p.L119I|MDH1_ENST00000409908.1_Intron|MDH1_ENST00000544381.1_Missense_Mutation_p.L12I	NM_005917.3	NP_005908.1	P40925	MDHC_HUMAN	malate dehydrogenase 1, NAD (soluble)	101					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	diiodophenylpyruvate reductase activity (GO:0047860)|L-malate dehydrogenase activity (GO:0030060)|malic enzyme activity (GO:0004470)|NAD binding (GO:0051287)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(4)	13						GAGAAAAGATTTACTGAAAGC	0.433																																					p.L119I		Atlas-SNP	.											.	MDH1	29	.	0			c.T355A						.						77	76	76					2																	63824634		2203	4300	6503	SO:0001583	missense	4190	exon4			AAAGATTTACTGA		CCDS1874.1, CCDS56121.1, CCDS56122.1	2p23	2012-10-02			ENSG00000014641	ENSG00000014641	1.1.1.37		6970	protein-coding gene	gene with protein product		154200					Standard	NM_005917		Approved		uc010ypv.2	P40925	OTTHUMG00000129512	ENST00000233114.8:c.301T>A	chr2.hg19:g.63824634T>A	ENSP00000233114:p.Leu101Ile	119.0	0.0		266.0	106.0	NM_001199111	B2R5V5|B4DUN2|B7Z3I7|F5H098|Q6I9V0	Missense_Mutation	SNP	ENST00000233114.8	hg19	CCDS1874.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.355747	0.82243	.	.	ENSG00000014641	ENST00000233114;ENST00000436321;ENST00000454035;ENST00000432309;ENST00000539945;ENST00000544381;ENST00000394423	D;D;D;D;D;D;D	0.96522	-4.04;-4.04;-4.04;-4.04;-4.04;-4.04;-4.04	5.42	3.05	0.35203	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.98413	0.9472	H	0.96518	3.835	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.91635	0.998;0.999	D	0.97583	1.0112	10	0.87932	D	0	-19.6791	8.5945	0.33707	0.0:0.2253:0.0:0.7747	.	119;101	F5H098;P40925	.;MDHC_HUMAN	I	101;56;102;119;119;12;101	ENSP00000233114:L101I;ENSP00000394504:L56I;ENSP00000409027:L102I;ENSP00000410073:L119I;ENSP00000438144:L119I;ENSP00000446395:L12I;ENSP00000377945:L101I	ENSP00000233114:L101I	L	+	1	2	MDH1	63678138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.952000	0.40343	0.451000	0.26802	0.533000	0.62120	TTA	.	.		0.433	MDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251687.1			A	63824634	T	A	63824634	3	1	101	1	0	0	0	0	1	0	0	0	9417	1838	64	4	315	4	MDH1	2	63824634	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	8969263	63824634	179374739	65	13902										
C2orf42	54980	hgsc.bcm.edu	37	chr2	70408657	70408657	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cctgcattgcattcaggaccGagctcttcagggtcagaggg	13	11	4	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:70408657G>A	ENST00000264434.2	-	3	840	c.461C>T	c.(460-462)tCg>tTg	p.S154L	C2orf42_ENST00000420306.1_Missense_Mutation_p.S154L|C2orf42_ENST00000470096.1_5'Flank	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	154										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						ATTCAGGACCGAGCTCTTCAG	0.567																																					p.S154L		Atlas-SNP	.											.	C2orf42	30	.	0			c.C461T						.						64	62	63					2																	70408657		2203	4300	6503	SO:0001583	missense	54980	exon3			AGGACCGAGCTCT	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.461C>T	chr2.hg19:g.70408657G>A	ENSP00000264434:p.Ser154Leu	19.0	0.0		49.0	27.0	NM_017880	D6W5G3|Q9H629	Missense_Mutation	SNP	ENST00000264434.2	hg19	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	G	32	5.142084	0.94560	.	.	ENSG00000115998	ENST00000264434;ENST00000420306;ENST00000447804;ENST00000417865	T;T	0.51325	0.71;0.71	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.66366	0.2782	L	0.61218	1.895	0.58432	D	0.999998	D	0.71674	0.998	D	0.72982	0.979	T	0.69423	-0.5149	10	0.87932	D	0	-21.4195	16.994	0.86361	0.0:0.0:1.0:0.0	.	154	Q9NWW7	CB042_HUMAN	L	154	ENSP00000264434:S154L;ENSP00000404515:S154L	ENSP00000264434:S154L	S	-	2	0	C2orf42	70262161	1.000000	0.71417	0.994000	0.49952	0.931000	0.56810	9.083000	0.94067	2.576000	0.86940	0.485000	0.47835	TCG	.	.		0.567	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880		A	70408657	G	A	70408657	3	1	101	1	0	0	0	0	1	0	0	0	2168	1059	37	1	1295	1	C2orf42	2	70408657	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6584023	70408657	172790716	66	13903										
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71047619	71047619	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggggtgcagggagacacactGgttatctgtgcagaagcgga	17	7	1	2	rs575554427		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:71047619G>T	ENST00000272367.2	-	1	113	c.37C>A	c.(37-39)Cag>Aag	p.Q13K	CLEC4F_ENST00000426626.1_Missense_Mutation_p.Q13K	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	13					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						GAGACACACTGGTTATCTGTG	0.617																																					p.Q13K	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.C37A						.						109	78	89					2																	71047619		2203	4299	6502	SO:0001583	missense	165530	exon1			CACACTGGTTATC	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.37C>A	chr2.hg19:g.71047619G>T	ENSP00000272367:p.Gln13Lys	56.0	0.0		141.0	20.0	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	hg19	CCDS1910.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.734209	0.48939	.	.	ENSG00000152672	ENST00000272367;ENST00000426626	T;T	0.03330	3.99;3.97	3.36	2.44	0.29823	.	.	.	.	.	T	0.05547	0.0146	L	0.52573	1.65	0.09310	N	0.999999	P;P	0.51057	0.941;0.941	B;B	0.44224	0.444;0.444	T	0.33650	-0.9860	9	0.87932	D	0	.	8.4551	0.32895	0.0:0.2405:0.7595:0.0	.	13;13	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	K	13	ENSP00000272367:Q13K;ENSP00000390581:Q13K	ENSP00000272367:Q13K	Q	-	1	0	CLEC4F	70901127	0.418000	0.25440	0.167000	0.22817	0.294000	0.27393	2.075000	0.41538	0.954000	0.37851	0.467000	0.42956	CAG	.	.		0.617	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		T	71047619	G	T	71047619	3	4	101	1	0	0	0	0	1	0	0	0	3518	1357	47	3	1760	3	CLEC4F	2	71047619	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	638962	71047619	172151754	67	13904										
POLR1A	25885	hgsc.bcm.edu	37	chr2	86259502	86259502	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttcctcatcaccctcctgctCtccctgtggtttgtgggcaa	8	15	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:86259502C>A	ENST00000263857.6	-	29	4543	c.4165G>T	c.(4165-4167)Gag>Tag	p.E1389*	POLR1A_ENST00000409681.1_Nonsense_Mutation_p.E1389*			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1389					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						CCCTCCTGCTCTCCCTGTGGT	0.537																																					p.E1389X		Atlas-SNP	.											.	POLR1A	137	.	0			c.G4165T						.						141	148	146					2																	86259502		2100	4220	6320	SO:0001587	stop_gained	25885	exon29			CCTGCTCTCCCTG	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.4165G>T	chr2.hg19:g.86259502C>A	ENSP00000263857:p.Glu1389*	94.0	0.0		118.0	32.0	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Nonsense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	43	10.425248	0.99403	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	.	.	.	4.21	3.32	0.38043	.	1.177410	0.05873	N	0.625014	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	-24.0561	6.3892	0.21577	0.0:0.6875:0.0:0.3125	.	.	.	.	X	1389	.	ENSP00000263857:E1389X	E	-	1	0	POLR1A	86113013	0.503000	0.26115	1.000000	0.80357	0.633000	0.38033	1.477000	0.35431	2.311000	0.77944	0.462000	0.41574	GAG	.	.		0.537	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		A	86259502	C	A	86259502	4	1	101	1	0	0	0	0	0	1	0	0	12218	922	32	3	1021	3	POLR1A	2	86259502	Nonsense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	15211883	86259502	156939871	68	13905										
C2orf29	55571	hgsc.bcm.edu	37	chr2	101885756	101885756	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttaatgtacaggatttgtttAtagaagtgcaggcattctgt	10	4	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:101885756A>T	ENST00000289382.3	+	7	1577	c.1414A>T	c.(1414-1416)Ata>Tta	p.I472L	RNF149_ENST00000485752.1_5'Flank	NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	472					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											GGATTTGTTTATAGAAGTGCA	0.383																																					p.I472L		Atlas-SNP	.											.	.	.	.	0			c.A1414T						.						87	90	89					2																	101885756		2203	4300	6503	SO:0001583	missense	55571	exon7			TTGTTTATAGAAG	AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 29"	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.1414A>T	chr2.hg19:g.101885756A>T	ENSP00000289382:p.Ile472Leu	103.0	0.0		223.0	21.0	NM_017546	Q6P2M9|Q8N681	Missense_Mutation	SNP	ENST00000289382.3	hg19	CCDS2050.1	.	.	.	.	.	.	.	.	.	.	A	34	5.383985	0.95967	.	.	ENSG00000158435	ENST00000289382	.	.	.	5.96	5.96	0.96718	.	0.087263	0.85682	D	0.000000	D	0.84234	0.5427	M	0.88310	2.945	0.80722	D	1	D	0.67145	0.996	D	0.68353	0.957	D	0.87008	0.2121	9	0.66056	D	0.02	-26.6738	16.4484	0.83959	1.0:0.0:0.0:0.0	.	472	Q9UKZ1	CB029_HUMAN	L	472	.	ENSP00000289382:I472L	I	+	1	0	C2orf29	101252188	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.210000	0.95106	2.285000	0.76669	0.533000	0.62120	ATA	.	.		0.383	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546		T	101885756	A	T	101885756	3	4	101	1	0	0	0	0	1	0	0	0	2163	449	16	4	1440	4	C2orf29	2	101885756	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	15626254	101885756	141313617	69	13906										
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105924415	105924415	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acgtggctgcccccttgatgCgggcccccgaaggcactggc	14	16	0	1	rs369840873		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:105924415C>A	ENST00000393359.2	-	2	770	c.344G>T	c.(343-345)cGc>cTc	p.R115L	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.R115L			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	115	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						CCCCTTGATGCGGGCCCCCGA	0.582																																					p.R115L	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.G344T						.						57	63	61					2																	105924415		2203	4300	6503	SO:0001583	missense	9392	exon2			TTGATGCGGGCCC	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.344G>T	chr2.hg19:g.105924415C>A	ENSP00000377027:p.Arg115Leu	17.0	0.0		128.0	16.0	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	hg19	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168629	0.78339	.	.	ENSG00000135966	ENST00000393359;ENST00000258449	T;T	0.04706	3.57;3.57	5.02	5.02	0.67125	Citron-like (2);	0.055423	0.64402	D	0.000001	T	0.05456	0.0144	L	0.44542	1.39	0.45930	D	0.998766	B	0.34214	0.442	B	0.31614	0.133	T	0.40813	-0.9543	10	0.36615	T	0.2	-30.6776	12.2513	0.54599	0.0:0.9224:0.0:0.0776	.	115	Q8WUH2	TGFA1_HUMAN	L	115	ENSP00000377027:R115L;ENSP00000258449:R115L	ENSP00000258449:R115L	R	-	2	0	TGFBRAP1	105290847	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	4.578000	0.60929	2.760000	0.94817	0.655000	0.94253	CGC	.	.		0.582	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		A	105924415	C	A	105924415	3	1	101	1	0	0	0	0	1	0	0	0	15839	768	27	1	2282	1	TGFBRAP1	2	105924415	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4038659	105924415	137274958	70	13907										
SLC5A7	60482	hgsc.bcm.edu	37	chr2	108622601	108622601	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtccttcctggcagctttcGggtgcctggtgatggccatc	13	12	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:108622601G>A	ENST00000264047.2	+	7	1114	c.838G>A	c.(838-840)Ggg>Agg	p.G280R	SLC5A7_ENST00000409059.1_Missense_Mutation_p.G280R|SLC5A7_ENST00000540517.1_Missense_Mutation_p.G175R	NM_021815.2	NP_068587.1	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (sodium/choline cotransporter), member 7	280					acetylcholine biosynthetic process (GO:0008292)|cell death (GO:0008219)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	choline binding (GO:0033265)|choline transmembrane transporter activity (GO:0015220)|choline:sodium symporter activity (GO:0005307)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	49					Choline(DB00122)	GGCAGCTTTCGGGTGCCTGGT	0.522																																					p.G280R		Atlas-SNP	.											.	SLC5A7	109	.	0			c.G838A						.						109	94	99					2																	108622601		2203	4300	6503	SO:0001583	missense	60482	exon7			GCTTTCGGGTGCC	AF276871	CCDS2074.1	2q12	2013-07-19	2013-07-19		ENSG00000115665	ENSG00000115665		"Solute carriers"	14025	protein-coding gene	gene with protein product		608761	"solute carrier family 5 (choline transporter), member 7"			11027560	Standard	NM_021815		Approved	hCHT, CHT1	uc002tdv.3	Q9GZV3	OTTHUMG00000130959	ENST00000264047.2:c.838G>A	chr2.hg19:g.108622601G>A	ENSP00000264047:p.Gly280Arg	37.0	0.0		149.0	23.0	NM_021815	Q53TF2	Missense_Mutation	SNP	ENST00000264047.2	hg19	CCDS2074.1	.	.	.	.	.	.	.	.	.	.	G	33	5.207259	0.95033	.	.	ENSG00000115665	ENST00000409059;ENST00000540517;ENST00000264047	D;D;D	0.88201	-2.35;-2.35;-2.35	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.95934	0.8676	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.96084	0.9056	10	0.66056	D	0.02	-14.1517	19.8703	0.96847	0.0:0.0:1.0:0.0	.	280	Q9GZV3	SC5A7_HUMAN	R	280;175;280	ENSP00000387346:G280R;ENSP00000445351:G175R;ENSP00000264047:G280R	ENSP00000264047:G280R	G	+	1	0	SLC5A7	107989033	1.000000	0.71417	0.993000	0.49108	0.896000	0.52359	9.810000	0.99221	2.770000	0.95276	0.650000	0.86243	GGG	.	.		0.522	SLC5A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253562.1			A	108622601	G	A	108622601	3	1	101	1	0	0	0	0	1	0	0	0	14685	1116	39	1	860	1	SLC5A7	2	108622601	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2698186	108622601	134576772	71	13908										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109381074	109381074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtcttggtggcattgtaacaGctgctcattaaagaatgctt	10	7	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:109381074G>A	ENST00000283195.6	+	20	4205	c.4079G>A	c.(4078-4080)aGc>aAc	p.S1360N		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1360					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CATTGTAACAGCTGCTCATTA	0.388																																					p.S1360N		Atlas-SNP	.											.	RANBP2	488	.	0			c.G4079A						.						88	89	89					2																	109381074		2203	4300	6503	SO:0001583	missense	5903	exon20			GTAACAGCTGCTC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.4079G>A	chr2.hg19:g.109381074G>A	ENSP00000283195:p.Ser1360Asn	60.0	0.0		217.0	22.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	G	5.864	0.343570	0.11126	.	.	ENSG00000153201	ENST00000283195	T	0.57595	0.39	5.48	5.48	0.80851	Zinc finger, RanBP2-type (4);	.	.	.	.	T	0.46737	0.1408	L	0.47716	1.5	0.20196	N	0.999923	B	0.32010	0.351	B	0.34038	0.174	T	0.37174	-0.9717	9	0.29301	T	0.29	-5.1313	11.2651	0.49106	0.0:0.1352:0.7251:0.1397	.	1360	P49792	RBP2_HUMAN	N	1360	ENSP00000283195:S1360N	ENSP00000283195:S1360N	S	+	2	0	RANBP2	108747506	0.890000	0.30428	0.998000	0.56505	0.992000	0.81027	1.266000	0.33039	2.554000	0.86153	0.655000	0.94253	AGC	.	.		0.388	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		A	109381074	G	A	109381074	3	1	101	1	0	0	0	0	1	0	0	0	13043	971	34	3	4157	3	RANBP2	2	109381074	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	758473	109381074	133818299	72	13909										
WDR33	55339	hgsc.bcm.edu	37	chr2	128474768	128474768	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttgtccggggttcagaggggGaatgcgaccttgtgctccct	15	10	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:128474768G>T	ENST00000322313.4	-	17	2988	c.2830C>A	c.(2830-2832)Ccc>Acc	p.P944T		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	944					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TTCAGAGGGGGAATGCGACCT	0.488																																					p.P944T		Atlas-SNP	.											WDR33,scalp,malignant_melanoma,0,1	WDR33	136	.	0			c.C2830A						.						42	40	41					2																	128474768		2203	4300	6503	SO:0001583	missense	55339	exon17			GAGGGGGAATGCG		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.2830C>A	chr2.hg19:g.128474768G>T	ENSP00000325377:p.Pro944Thr	77.0	0.0		181.0	23.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.564656	0.45694	.	.	ENSG00000136709	ENST00000322313	D	0.89343	-2.5	5.27	5.27	0.74061	.	0.200449	0.35970	N	0.002871	T	0.78451	0.4285	N	0.08118	0	0.80722	D	1	B	0.27498	0.18	B	0.17098	0.017	T	0.78074	-0.2346	10	0.72032	D	0.01	-4.998	14.8293	0.70135	0.0:0.1867:0.8133:0.0	.	944	Q9C0J8	WDR33_HUMAN	T	944	ENSP00000325377:P944T	ENSP00000325377:P944T	P	-	1	0	WDR33	128191238	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.230000	0.58632	2.473000	0.83533	0.563000	0.77884	CCC	.	.		0.488	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		T	128474768	G	T	128474768	3	4	101	1	0	0	0	0	1	0	0	0	17302	1174	41	3	1204	3	WDR33	2	128474768	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	19093694	128474768	114724605	73	13910										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133547663	133547663	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tggagtactcgctgcaggtgCttgaaagagacagttcactg	13	8	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:133547663C>A	ENST00000409261.1	-	13	1398	c.1025G>T	c.(1024-1026)aGc>aTc	p.S342I	NCKAP5_ENST00000317721.6_Missense_Mutation_p.S342I|NCKAP5_ENST00000409213.1_Missense_Mutation_p.S342I|NCKAP5_ENST00000405974.3_Missense_Mutation_p.S342I	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	342	Ser-rich.									NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						GCTGCAGGTGCTTGAAAGAGA	0.532																																					p.S342I		Atlas-SNP	.											.	NCKAP5	322	.	0			c.G1025T						.						75	81	79					2																	133547663		2072	4213	6285	SO:0001583	missense	344148	exon13			CAGGTGCTTGAAA	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.1025G>T	chr2.hg19:g.133547663C>A	ENSP00000387128:p.Ser342Ile	60.0	0.0		185.0	16.0	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	hg19	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.628812	0.87560	.	.	ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661	T;T;T;T	0.56941	1.79;0.43;1.79;0.43	5.12	5.12	0.69794	.	0.000000	0.37623	U	0.002008	T	0.62889	0.2465	L	0.29908	0.895	0.38970	D	0.958732	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.67952	-0.5537	10	0.87932	D	0	.	16.9089	0.86135	0.0:1.0:0.0:0.0	.	342;342	O14513-2;O14513	.;NCKP5_HUMAN	I	342	ENSP00000387128:S342I;ENSP00000386952:S342I;ENSP00000380603:S342I;ENSP00000385692:S342I	ENSP00000380603:S342I	S	-	2	0	NCKAP5	133264133	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.426000	0.73374	2.658000	0.90341	0.650000	0.86243	AGC	.	.		0.532	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		A	133547663	C	A	133547663	3	1	101	1	0	0	0	0	1	0	0	0	10232	797	28	3	4736	3	NCKAP5	2	133547663	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	5072895	133547663	109651710	74	13911										
CACNB4	785	hgsc.bcm.edu	37	chr2	152732958	152732958	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	accctccgtgaaaacgtcctCttttttgttcttgctggatc	7	12	2	1	rs376364352		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:152732958C>G	ENST00000539935.1	-	5	570	c.503G>C	c.(502-504)aGa>aCa	p.R168T	CACNB4_ENST00000397327.2_Missense_Mutation_p.R121T|CACNB4_ENST00000201943.5_Missense_Mutation_p.R168T|CACNB4_ENST00000360283.6_Missense_Mutation_p.R134T|CACNB4_ENST00000427385.1_Missense_Mutation_p.R150T|CACNB4_ENST00000534999.1_Missense_Mutation_p.R134T	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	168					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AAAACGTCCTCTTTTTTGTTC	0.418																																					p.R168T		Atlas-SNP	.											.	CACNB4	108	.	0			c.G503C						.	C	THR/ARG,THR/ARG,THR/ARG,THR/ARG	1,3793		0,1,1896	139	131	134		503,449,401,503	5.6	1	2		134	0,8242		0,0,4121	no	missense,missense,missense,missense	CACNB4	NM_000726.3,NM_001005746.2,NM_001005747.2,NM_001145798.1	71,71,71,71	0,1,6017	GG,GC,CC		0.0,0.0264,0.0083	benign,benign,benign,benign	168/521,150/503,134/487,168/459	152732958	1,12035	1897	4121	6018	SO:0001583	missense	785	exon5			CGTCCTCTTTTTT	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"Calcium channel subunits"	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.503G>C	chr2.hg19:g.152732958C>G	ENSP00000438949:p.Arg168Thr	84.0	0.0		149.0	15.0	NM_001145798	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Missense_Mutation	SNP	ENST00000539935.1	hg19	CCDS46426.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.731069	0.48939	2.64E-4	0.0	ENSG00000182389	ENST00000539935;ENST00000360283;ENST00000543269;ENST00000439467;ENST00000534999;ENST00000397327;ENST00000427385;ENST00000201943;ENST00000339254	D;D;D;D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57;-1.57;-1.57	5.63	5.63	0.86233	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	T	0.76343	0.3974	L	0.28115	0.83	0.58432	D	0.999999	P;B;P;B;P	0.38922	0.651;0.129;0.561;0.418;0.554	B;B;B;B;B	0.39419	0.212;0.071;0.157;0.157;0.299	T	0.72228	-0.4354	10	0.15952	T	0.53	-17.4098	20.0499	0.97621	0.0:1.0:0.0:0.0	.	168;134;168;150;134	A7BJ74;E7DBM8;O00305;B4DG40;O00305-2	.;.;CACB4_HUMAN;.;.	T	168;134;125;163;134;121;150;168;168	ENSP00000438949:R168T;ENSP00000353425:R134T;ENSP00000390161:R163T;ENSP00000443893:R134T;ENSP00000380490:R121T;ENSP00000410978:R150T;ENSP00000201943:R168T	ENSP00000201943:R168T	R	-	2	0	CACNB4	152441204	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.847000	0.69451	2.798000	0.96311	0.655000	0.94253	AGA	.	.		0.418	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3		G	152732958	C	G	152732958	3	3	101	1	0	0	0	0	1	0	0	0	2557	913	32	4	1099	4	CACNB4	2	152732958	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	19185295	152732958	90466415	75	13912										
PRPF40A	151188	hgsc.bcm.edu	37	chr2	153573934	153573934	+	5'Flank	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggctcagactgctccgccggCggccactgccgctacacata	11	17	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:153573934C>A	ENST00000326446.5	+	0	0				PRPF40A_ENST00000410080.1_Missense_Mutation_p.R7L|PRPF40A_ENST00000486100.1_5'UTR	NM_152522.5	NP_689735.1	Q8N6S5	AR6P6_HUMAN	ADP-ribosylation factor-like 6 interacting protein 6							integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|pancreas(1)	5						GCTCCGCCGGCGGCCACTGCC	0.647																																					p.R7L		Atlas-SNP	.											.	PRPF40A	149	.	0			c.G20T						.						30	37	35					2																	153573934		1934	4137	6071	SO:0001631	upstream_gene_variant	55660	exon1			CGCCGGCGGCCAC	AK023109	CCDS2197.1	2q23	2014-05-12	2014-05-12		ENSG00000177917	ENSG00000177917			24048	protein-coding gene	gene with protein product							Standard	NM_152522		Approved	MGC33864	uc002tyn.3	Q8N6S5	OTTHUMG00000131901		chr2.hg19:g.153573934C>A	Exception_encountered	25.0	0.0		189.0	31.0	NM_017892	B2RDS6|Q7Z4G7	Missense_Mutation	SNP	ENST00000326446.5	hg19	CCDS2197.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344018	0.61073	.	.	ENSG00000196504	ENST00000410080;ENST00000359961;ENST00000448428	T	0.34859	1.34	4.87	4.87	0.63330	.	.	.	.	.	T	0.19846	0.0477	N	0.08118	0	0.25132	N	0.990568	B	0.11235	0.004	B	0.06405	0.002	T	0.07731	-1.0757	9	0.14656	T	0.56	.	13.3945	0.60843	0.0:1.0:0.0:0.0	.	7	E9PFS0	.	L	7;7;13	ENSP00000386458:R7L	ENSP00000353046:R7L	R	-	2	0	PRPF40A	153282180	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.309000	0.51903	2.518000	0.84900	0.655000	0.94253	CGC	.	.		0.647	ARL6IP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254852.3	NM_152522		A	153573934	C	A	153573934	1	1	101	0	1	0	0	0	0	0	0	0	12583	768	27	1		1	PRPF40A	2	153573934	5'Flank	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	840976	153573934	89625439	76	13913										
NR4A2	4929	hgsc.bcm.edu	37	chr2	157186659	157186659	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctgagaagcggggctggctcCttgaggcgaggacccatact	15	11	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:157186659C>T	ENST00000339562.4	-	3	402	c.40G>A	c.(40-42)Gga>Aga	p.G14R	NR4A2_ENST00000409572.1_Missense_Mutation_p.G14R|NR4A2_ENST00000539077.1_Missense_Mutation_p.G25R|NR4A2_ENST00000426264.1_Intron|NR4A2_ENST00000429376.1_Intron|NR4A2_ENST00000409108.2_Missense_Mutation_p.G14R	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	14					adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						GGGCTGGCTCCTTGAGGCGAG	0.517																																					p.G14R		Atlas-SNP	.											.	NR4A2	82	.	0			c.G40A						.						48	51	50					2																	157186659		2203	4300	6503	SO:0001583	missense	4929	exon3			TGGCTCCTTGAGG	X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"Nuclear hormone receptors"	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.40G>A	chr2.hg19:g.157186659C>T	ENSP00000344479:p.Gly14Arg	61.0	0.0		155.0	17.0	NM_006186	Q16311|Q53RZ2|Q6NXU0	Missense_Mutation	SNP	ENST00000339562.4	hg19	CCDS2201.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.003131	0.74932	.	.	ENSG00000153234	ENST00000339562;ENST00000409572;ENST00000539077;ENST00000409108;ENST00000424077	D;D;D;D;D	0.93859	-3.04;-3.04;-3.02;-3.3;-1.75	5.43	5.43	0.79202	.	0.214284	0.48286	D	0.000187	D	0.95007	0.8384	L	0.42245	1.32	0.80722	D	1	D	0.63880	0.993	D	0.64237	0.923	D	0.95066	0.8200	10	0.66056	D	0.02	.	19.0129	0.92881	0.0:1.0:0.0:0.0	.	14	P43354	NR4A2_HUMAN	R	14;14;25;14;14	ENSP00000344479:G14R;ENSP00000386747:G14R;ENSP00000444925:G25R;ENSP00000386993:G14R;ENSP00000406808:G14R	ENSP00000344479:G14R	G	-	1	0	NR4A2	156894905	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.825000	0.97269	0.655000	0.94253	GGA	.	.		0.517	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2			T	157186659	C	T	157186659	3	4	101	1	0	0	0	0	1	0	0	0	10642	690	24	3	1780	3	NR4A2	2	157186659	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3612725	157186659	86012714	77	13914										
LY75	4065	hgsc.bcm.edu	37	chr2	160737645	160737646	+	Missense_Mutation	DNP	CT	CT	AA													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttattgtagggaacatttggCtcattctcatcccaatatgt							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:160737645_160737646CT>AA	ENST00000263636.4	-	8	1379_1380	c.1352_1353AG>TT	c.(1351-1353)gAG>gTT	p.E451V	LY75-CD302_ENST00000504764.1_Missense_Mutation_p.E451V|LY75_ENST00000554112.1_Missense_Mutation_p.E451V|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.E451V|LY75_ENST00000553424.1_Missense_Mutation_p.E451V	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	451	C-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GAACATTTGGCTCATTCTCATC	0.386																																					p.E451D|p.E451V		Atlas-SNP	.											.	LY75	151	.	0			c.G1353T|c.A1352T						.																																			SO:0001583	missense	4065	exon8			ATTTGGCTCATTC|TTTGGCTCATTCT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.1352_1353delinsAA	chr2.hg19:g.160737645_160737646delinsAA	ENSP00000263636:p.Glu451Val	87.0	0.0		258.0|259.0	18.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1																																																																																			.	.		0.386	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			AA	160737646	CT	AA	160737645	3	1	101	1	0	0	0	0	1	0	0	0	9108	796	28	3	3927	3	LY75	2	160737645	Missense_Mutation	DNP	CT	TCGA-DD-A1EE-01A-11D-A12Z-10	3550986	160737645	82461728	78	13915										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160833216	160833216	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cgtactggtaccagaacggaAtcttgggtttcacatctgca	10	10	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:160833216A>G	ENST00000283243.7	-	16	2623	c.2417T>C	c.(2416-2418)aTt>aCt	p.I806T	PLA2R1_ENST00000392771.1_Missense_Mutation_p.I806T	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	806					cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CCAGAACGGAATCTTGGGTTT	0.353																																					p.I806T		Atlas-SNP	.											.	PLA2R1	153	.	0			c.T2417C						.						88	81	84					2																	160833216		2203	4300	6503	SO:0001583	missense	22925	exon16			AACGGAATCTTGG	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.2417T>C	chr2.hg19:g.160833216A>G	ENSP00000283243:p.Ile806Thr	96.0	0.0		291.0	21.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	hg19	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	A	1.441	-0.567640	0.03910	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.06218	3.37;3.33	4.77	3.62	0.41486	.	0.335919	0.30528	N	0.009440	T	0.06554	0.0168	L	0.60455	1.87	0.28249	N	0.925339	B;P;B	0.36959	0.004;0.575;0.265	B;B;B	0.33620	0.011;0.167;0.116	T	0.21245	-1.0251	10	0.14252	T	0.57	.	9.3311	0.38023	0.913:0.0:0.087:0.0	.	806;806;806	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	T	806	ENSP00000283243:I806T;ENSP00000376524:I806T	ENSP00000283243:I806T	I	-	2	0	PLA2R1	160541462	0.985000	0.35326	0.894000	0.35097	0.968000	0.65278	1.144000	0.31565	0.798000	0.33994	0.459000	0.35465	ATT	.	.		0.353	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			G	160833216	A	G	160833216	3	3	101	1	0	0	0	0	1	0	0	0	12019	101	4	2	2042	2	PLA2R1	2	160833216	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	95571	160833216	82366157	79	13916										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166211045	166211045	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtagaaaaatatgtcgtggAtgaaagtgattacatgtcat	10	3	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:166211045A>G	ENST00000375437.2	+	17	3553	c.3263A>G	c.(3262-3264)gAt>gGt	p.D1088G	SCN2A_ENST00000375427.2_Missense_Mutation_p.D1088G|SCN2A_ENST00000357398.3_Missense_Mutation_p.D1088G|SCN2A_ENST00000283256.6_Missense_Mutation_p.D1088G	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1088					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TATGTCGTGGATGAAAGTGAT	0.373																																					p.D1088G		Atlas-SNP	.											.	SCN2A	589	.	0			c.A3263G						.						113	111	112					2																	166211045		2203	4300	6503	SO:0001583	missense	6326	exon16			TCGTGGATGAAAG	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.3263A>G	chr2.hg19:g.166211045A>G	ENSP00000364586:p.Asp1088Gly	102.0	0.0		267.0	15.0	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	hg19	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.193601	0.38707	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	5.26	5.26	0.73747	Sodium ion transport-associated (1);	0.172626	0.41001	D	0.000972	D	0.88239	0.6383	M	0.77616	2.38	0.34725	D	0.729149	B;P	0.47545	0.01;0.897	B;P	0.53760	0.015;0.734	D	0.91929	0.5553	10	0.40728	T	0.16	.	15.1655	0.72821	1.0:0.0:0.0:0.0	.	1088;1088	Q99250-2;Q99250	.;SCN2A_HUMAN	G	1088	ENSP00000364586:D1088G;ENSP00000349973:D1088G;ENSP00000283256:D1088G;ENSP00000364576:D1088G	ENSP00000283256:D1088G	D	+	2	0	SCN2A	165919291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.903000	0.56318	1.981000	0.57761	0.482000	0.46254	GAT	.	.		0.373	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		G	166211045	A	G	166211045	3	3	101	1	0	0	0	0	1	0	0	0	13931	333	12	2	3421	2	SCN2A	2	166211045	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	5377829	166211045	76988328	80	13917										
CSRNP3	80034	hgsc.bcm.edu	37	chr2	166514403	166514403	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agggggaagcaccctggggaTgtccagccgccataacagcg	15	12	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:166514403T>A	ENST00000342316.4	+	3	553	c.281T>A	c.(280-282)aTg>aAg	p.M94K	CSRNP3_ENST00000314499.7_Missense_Mutation_p.M94K|CSRNP3_ENST00000409420.1_Missense_Mutation_p.M126K	NM_024969.3	NP_079245.2	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	94					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						ACCCTGGGGATGTCCAGCCGC	0.547																																					p.M94K		Atlas-SNP	.											.	CSRNP3	73	.	0			c.T281A						.						51	44	47					2																	166514403		2203	4300	6503	SO:0001583	missense	80034	exon5			TGGGGATGTCCAG	AB063300	CCDS2225.1	2q24.3	2012-04-17	2009-01-07	2009-01-07	ENSG00000178662	ENSG00000178662		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30729	protein-coding gene	gene with protein product	"TGF beta induced apotosis protein 2", "protein phosphatase 1, regulatory subunit 73"		"family with sequence similarity 130, member A2"	FAM130A2		17726538	Standard	NM_024969		Approved	FLJ32093, TAIP-2, PPP1R73	uc002udg.3	Q8WYN3	OTTHUMG00000132145	ENST00000342316.4:c.281T>A	chr2.hg19:g.166514403T>A	ENSP00000344042:p.Met94Lys	40.0	0.0		133.0	46.0	NM_001172173	B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9	Missense_Mutation	SNP	ENST00000342316.4	hg19	CCDS2225.1	.	.	.	.	.	.	.	.	.	.	T	31	5.086010	0.94100	.	.	ENSG00000178662	ENST00000421875;ENST00000431452;ENST00000314499;ENST00000409664;ENST00000342316;ENST00000409420	T;T;T;T;T	0.14893	2.47;2.47;2.47;2.47;2.47	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.46698	0.1406	M	0.87456	2.885	0.80722	D	1	D	0.57899	0.981	D	0.66351	0.943	T	0.55604	-0.8115	10	0.87932	D	0	-18.9762	15.4469	0.75238	0.0:0.0:0.0:1.0	.	94	Q8WYN3	CSRN3_HUMAN	K	94;101;94;94;94;126	ENSP00000412081:M94K;ENSP00000318258:M94K;ENSP00000386278:M94K;ENSP00000344042:M94K;ENSP00000387195:M126K	ENSP00000318258:M94K	M	+	2	0	CSRNP3	166222649	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.997000	0.88414	2.104000	0.64026	0.460000	0.39030	ATG	.	.		0.547	CSRNP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255191.2	NM_024969		A	166514403	T	A	166514403	3	1	101	1	0	0	0	0	1	0	0	0	3967	1464	51	4	287	4	CSRNP3	2	166514403	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	303358	166514403	76684970	81	13918										
BBS5	129880	hgsc.bcm.edu	37	chr2	170344622	170344622	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acttctgtgatggcagtacaCaggtatagtaatactttatg	9	6	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:170344622C>A	ENST00000295240.3	+	5	760	c.384C>A	c.(382-384)caC>caA	p.H128Q	BBS5_ENST00000392663.2_Missense_Mutation_p.H128Q|BBS5_ENST00000554017.1_Missense_Mutation_p.H128Q|RP11-724O16.1_ENST00000513963.1_Missense_Mutation_p.H128Q	NM_152384.2	NP_689597.1	Q8N3I7	BBS5_HUMAN	Bardet-Biedl syndrome 5	128					cilium assembly (GO:0042384)|heart looping (GO:0001947)|melanosome transport (GO:0032402)|motile cilium assembly (GO:0044458)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphate binding (GO:0032266)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TGGCAGTACACAGGTATAGTA	0.343									Bardet-Biedl syndrome																												p.H128Q		Atlas-SNP	.											.	BBS5	27	.	0			c.C384A						.						52	58	56					2																	170344622		2202	4299	6501	SO:0001583	missense	129880	exon5	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AGTACACAGGTAT	AY604003	CCDS2233.1	2q31	2011-08-02			ENSG00000163093	ENSG00000163093			970	protein-coding gene	gene with protein product		603650				9888993, 10053027	Standard	NM_152384		Approved	DKFZp762I194		Q8N3I7	OTTHUMG00000132207	ENST00000295240.3:c.384C>A	chr2.hg19:g.170344622C>A	ENSP00000295240:p.His128Gln	117.0	0.0		237.0	79.0	NM_152384	D3DPC3|Q6PKN0	Missense_Mutation	SNP	ENST00000295240.3	hg19	CCDS2233.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.982609	0.74474	.	.	ENSG00000163093;ENSG00000163093;ENSG00000163093;ENSG00000251569	ENST00000295240;ENST00000554017;ENST00000392663;ENST00000513963	T;T;T;T	0.73681	-0.77;-0.77;-0.77;-0.77	5.38	3.58	0.41010	.	0.000000	0.85682	D	0.000000	T	0.79269	0.4417	L	0.46741	1.465	0.80722	D	1	D;P;P	0.69078	0.997;0.911;0.927	D;P;P	0.65874	0.939;0.563;0.602	T	0.77027	-0.2740	10	0.44086	T	0.13	-10.4498	11.5199	0.50545	0.0:0.8549:0.0:0.1451	.	128;128;128	E9PBE3;Q8N3I7-2;Q8N3I7	.;.;BBS5_HUMAN	Q	128	ENSP00000295240:H128Q;ENSP00000452313:H128Q;ENSP00000376431:H128Q;ENSP00000424363:H128Q	ENSP00000295240:H128Q	H	+	3	2	BBS5;RP11-724O16.1	170052868	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.978000	0.63799	0.649000	0.30751	0.655000	0.94253	CAC	.	.		0.343	BBS5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255265.2	NM_152384		A	170344622	C	A	170344622	3	1	101	1	0	0	0	0	1	0	0	0	1340	477	17	3	402	3	BBS5	2	170344622	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3830219	170344622	72854751	82	13919										
UBR3	130507	hgsc.bcm.edu	37	chr2	170806152	170806152	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agttttcagtttagtagcagAacgtagaaagaaatttcagg	10	4	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:170806152A>G	ENST00000272793.5	+	23	3172	c.3122A>G	c.(3121-3123)gAa>gGa	p.E1041G	UBR3_ENST00000418381.1_Missense_Mutation_p.E1041G			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1041					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						TTAGTAGCAGAACGTAGAAAG	0.358																																					p.E1041G		Atlas-SNP	.											.	UBR3	182	.	0			c.A3122G						.						47	39	41					2																	170806152		692	1590	2282	SO:0001583	missense	130507	exon23			TAGCAGAACGTAG	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.3122A>G	chr2.hg19:g.170806152A>G	ENSP00000272793:p.Glu1041Gly	48.0	0.0		101.0	5.0	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.7|27.7	4.854316|4.854316	0.91355|0.91355	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381|ENST00000392632	T;T|.	0.56275|.	0.47;0.47|.	5.28|5.28	5.28|5.28	0.74379|0.74379	.|.	.|.	.|.	.|.	.|.	T|T	0.57873|0.57873	0.2083|0.2083	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	D|.	0.71674|.	0.998|.	D|.	0.72982|.	0.979|.	T|T	0.54768|0.54768	-0.8244|-0.8244	9|5	0.33141|.	T|.	0.24|.	.|.	15.2668|15.2668	0.73669|0.73669	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1041|.	Q6ZT12|.	UBR3_HUMAN|.	G|D	1041|99	ENSP00000272793:E1041G;ENSP00000396068:E1041G|.	ENSP00000272793:E1041G|.	E|N	+|+	2|1	0|0	UBR3|UBR3	170514398|170514398	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	9.336000|9.336000	0.96533|0.96533	2.021000|2.021000	0.59480|0.59480	0.524000|0.524000	0.50904|0.50904	GAA|AAC	.	.		0.358	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		G	170806152	A	G	170806152	3	3	101	1	0	0	0	0	1	0	0	0	16918	246	9	2	3212	2	UBR3	2	170806152	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	461530	170806152	72393221	83	13920										
CHRNA1	1134	hgsc.bcm.edu	37	chr2	175624066	175624066	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctggctaagttacctgtttcAgacgcacattggttgtcacg	10	10	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:175624066A>T	ENST00000261007.5	-	3	293	c.227T>A	c.(226-228)cTg>cAg	p.L76Q	CHRNA1_ENST00000409542.1_Missense_Mutation_p.L76Q|CHRNA1_ENST00000409219.1_Missense_Mutation_p.L76Q|CHRNA1_ENST00000348749.5_Missense_Mutation_p.L76Q|CHRNA1_ENST00000409323.1_Missense_Mutation_p.L76Q|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	76					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	TACCTGTTTCAGACGCACATT	0.428																																					p.L76Q		Atlas-SNP	.											.	CHRNA1	92	.	0			c.T227A						.						106	101	102					2																	175624066		2203	4300	6503	SO:0001583	missense	1134	exon3			TGTTTCAGACGCA	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1955	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 1 (muscle)"	100690	"cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.227T>A	chr2.hg19:g.175624066A>T	ENSP00000261007:p.Leu76Gln	65.0	0.0		198.0	13.0	NM_001039523	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	hg19	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.883238	0.91740	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219;ENST00000409323	D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58	5.95	5.95	0.96441	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.93245	0.7848	M	0.92738	3.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.997;1.0	D	0.94649	0.7837	10	0.87932	D	0	.	16.4101	0.83708	1.0:0.0:0.0:0.0	.	76;76;76	G5E9G9;Q53SH4;P02708	.;.;ACHA_HUMAN	Q	76	ENSP00000261008:L76Q;ENSP00000261007:L76Q;ENSP00000387026:L76Q;ENSP00000386611:L76Q;ENSP00000386684:L76Q	ENSP00000261007:L76Q	L	-	2	0	CHRNA1	175332312	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.277000	0.95755	2.280000	0.76307	0.460000	0.39030	CTG	.	.		0.428	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			T	175624066	A	T	175624066	3	4	101	1	0	0	0	0	1	0	0	0	3383	188	7	4	1253	4	CHRNA1	2	175624066	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	4817914	175624066	67575307	84	13921										
HOXD4	3233	hgsc.bcm.edu	37	chr2	177017653	177017653	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tggccaaagaccaccacacgGacctgacgaccttatagaag	9	13	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:177017653G>C	ENST00000306324.3	+	2	1163	c.751G>C	c.(751-753)Gac>Cac	p.D251H	HOXD3_ENST00000468418.3_5'UTR|MIR10B_ENST00000385011.1_RNA	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	251					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		CCACCACACGGACCTGACGAC	0.627																																					p.D251H		Atlas-SNP	.											.	HOXD4	32	.	0			c.G751C						.						70	77	75					2																	177017653		2203	4300	6503	SO:0001583	missense	3233	exon2			CACACGGACCTGA		CCDS2269.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170166	ENSG00000170166		"Homeoboxes / ANTP class : HOXL subclass"	5138	protein-coding gene	gene with protein product		142981	"homeo box D4"	HOX4B, HOX4		1973146, 1358459	Standard	NM_014621		Approved		uc002uks.3	P09016	OTTHUMG00000132515	ENST00000306324.3:c.751G>C	chr2.hg19:g.177017653G>C	ENSP00000302548:p.Asp251His	43.0	0.0		170.0	18.0	NM_014621	B2R9R3|Q96AU0	Missense_Mutation	SNP	ENST00000306324.3	hg19	CCDS2269.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.988556	0.74589	.	.	ENSG00000170166	ENST00000306324	D	0.91011	-2.77	5.67	5.67	0.87782	.	1.924890	0.02868	N	0.131199	D	0.95529	0.8547	L	0.60455	1.87	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	D	0.85832	0.1392	10	0.87932	D	0	.	19.7626	0.96329	0.0:0.0:1.0:0.0	.	251	P09016	HXD4_HUMAN	H	251	ENSP00000302548:D251H	ENSP00000302548:D251H	D	+	1	0	HOXD4	176725899	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.914000	0.87478	2.676000	0.91093	0.561000	0.74099	GAC	.	.		0.627	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2			C	177017653	G	C	177017653	3	2	101	1	0	0	0	0	1	0	0	0	7333	1174	41	4	757	4	HOXD4	2	177017653	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1393587	177017653	66181720	85	13922										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098961	178098963	+	In_Frame_Del	DEL	TAT	TAT	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctcgacttactccaagatcTatatcttgcctccaaagtat							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	TAT	TAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:178098961_178098963delTAT	ENST00000397062.3	-	2	636_638	c.82_84delATA	c.(82-84)atadel	p.I28del	NFE2L2_ENST00000423513.1_In_Frame_Del_p.I12del|NFE2L2_ENST00000397063.4_In_Frame_Del_p.I12del|NFE2L2_ENST00000464747.1_In_Frame_Del_p.I12del|NFE2L2_ENST00000446151.2_In_Frame_Del_p.I12del	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	28					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I28T(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			CTCCAAGATCTATATCTTGCCTC	0.36			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.28_29del		Atlas-Indel,Pindel	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,bladder,carcinoma,0,18	NFE2L2	225	.	1	Substitution - Missense(1)	lung(1)	c.83_85del						.																																			SO:0001651	inframe_deletion	4780	exon2			.		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.82_84delATA	chr2.hg19:g.178098961_178098963delTAT	ENSP00000380252:p.Ile28del	78.0	0.0		92.0	30.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	In_Frame_Del	DEL	ENST00000397062.3	hg19	CCDS42782.1																																																																																			.	.		0.36	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		-	178098963	TAT	-	178098961	7	5	101	1	0	1	0	1	0	0	0	0	10377	1512	53	0	1749	0	NFE2L2	2	178098961	In_Frame_Del	DEL	TAT	TCGA-DD-A1EE-01A-11D-A12Z-10	1081308	178098961	65100412	86	13923										
HIBCH	26275	hgsc.bcm.edu	37	chr2	191155206	191155206	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttttgccttttcagcttccgAgatcactaggaaggaaagat	9	8	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:191155206A>C	ENST00000359678.5	-	5	604	c.310T>G	c.(310-312)Tcg>Gcg	p.S104A	HIBCH_ENST00000392332.3_Missense_Mutation_p.S104A	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	104					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			TCAGCTTCCGAGATCACTAGG	0.323																																					p.S104A		Atlas-SNP	.											.	HIBCH	28	.	0			c.T310G						.						72	68	70					2																	191155206		2203	4300	6503	SO:0001583	missense	26275	exon5			CTTCCGAGATCAC	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"3-hydroxyisobutyryl-Coenzyme A hydrolase"			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.310T>G	chr2.hg19:g.191155206A>C	ENSP00000352706:p.Ser104Ala	64.0	0.0		122.0	17.0	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Missense_Mutation	SNP	ENST00000359678.5	hg19	CCDS2304.1	.	.	.	.	.	.	.	.	.	.	A	0.017	-1.494319	0.01009	.	.	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000409934	T;T;T	0.70282	-0.14;-0.47;-0.14	5.42	-0.0735	0.13735	Crotonase, core (1);	.	.	.	.	T	0.33381	0.0861	N	0.01289	-0.905	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.38564	-0.9655	9	0.05620	T	0.96	0.7649	9.0984	0.36653	0.3045:0.5681:0.0:0.1274	.	104;104	Q6NVY1-2;Q6NVY1	.;HIBCH_HUMAN	A	104;104;158	ENSP00000376144:S104A;ENSP00000352706:S104A;ENSP00000387247:S158A	ENSP00000352706:S104A	S	-	1	0	HIBCH	190863451	0.985000	0.35326	0.903000	0.35520	0.007000	0.05969	0.560000	0.23500	0.111000	0.17947	-0.461000	0.05368	TCG	.	.		0.323	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1			C	191155206	A	C	191155206	3	2	101	1	0	0	0	0	1	0	0	0	7109	304	11	5	890	5	HIBCH	2	191155206	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	13056245	191155206	52044167	87	13924										
MYO1B	4430	hgsc.bcm.edu	37	chr2	192160953	192160953	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tatgaactgagccctcacatGtaagtactgtactaaagcat	7	9	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:192160953G>T	ENST00000392318.3	+	3	498		c.e3+1		MYO1B_ENST00000304164.4_Splice_Site|MYO1B_ENST00000339514.4_Splice_Site|MYO1B_ENST00000392316.1_Splice_Site	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB						actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			GCCCTCACATGTAAGTACTGT	0.363																																					.		Atlas-SNP	.											.	MYO1B	160	.	0			c.251+1G>T						.						78	73	75					2																	192160953		2203	4300	6503	SO:0001630	splice_region_variant	4430	exon3			TCACATGTAAGTA	L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.251+1G>T	chr2.hg19:g.192160953G>T		58.0	0.0		146.0	61.0	NM_012223	O43794|Q7Z6L5	Splice_Site	SNP	ENST00000392318.3	hg19	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.752989	0.89753	.	.	ENSG00000128641	ENST00000418908;ENST00000339514;ENST00000439452;ENST00000392318;ENST00000304164;ENST00000438652;ENST00000451437;ENST00000392316	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8567	0.96761	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MYO1B	191869198	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.613000	0.98350	2.706000	0.92434	0.579000	0.79373	.	.	.		0.363	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223	Intron	T	192160953	G	T	192160953	5	4	101	1	0	0	0	0	0	0	1	0	10078	1391	48	3	258	3	MYO1B	2	192160953	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1005747	192160953	51038420	88	13925										
SLC39A10	57181	hgsc.bcm.edu	37	chr2	196593015	196593015	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcagtatgccaataacatcaCactttggatctttgcagtca	6	10	4	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:196593015C>A	ENST00000409086.3	+	9	2554	c.2279C>A	c.(2278-2280)aCa>aAa	p.T760K	SLC39A10_ENST00000359634.5_Missense_Mutation_p.T760K|SLC39A10_ENST00000541054.1_Missense_Mutation_p.T310K	NM_001127257.1	NP_001120729.1	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter), member 10	760					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(16)|pancreas(1)|prostate(1)|skin(2)	34			OV - Ovarian serous cystadenocarcinoma(117;0.221)			AATAACATCACACTTTGGATC	0.408																																					p.T760K		Atlas-SNP	.											.	SLC39A10	89	.	0			c.C2279A						.						253	216	229					2																	196593015		2203	4300	6503	SO:0001583	missense	57181	exon9			ACATCACACTTTG		CCDS33353.1	2q33.1	2013-05-22			ENSG00000196950	ENSG00000196950		"Solute carriers"	20861	protein-coding gene	gene with protein product		608733	"solute carrier family 39 (metal ion transporter), member 10"			12659941	Standard	NM_020342		Approved	KIAA1265, FLJ90515, DKFZp564L2123	uc002utg.4	Q9ULF5	OTTHUMG00000154380	ENST00000409086.3:c.2279C>A	chr2.hg19:g.196593015C>A	ENSP00000386766:p.Thr760Lys	150.0	0.0		387.0	53.0	NM_020342	A8K5C6|B4DGU0|Q3MJA4|Q68CR5|Q6DKH6|Q9Y3Z1	Missense_Mutation	SNP	ENST00000409086.3	hg19	CCDS33353.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480599	0.84747	.	.	ENSG00000196950	ENST00000409086;ENST00000359634;ENST00000541054	T;T;T	0.50548	0.74;0.74;0.74	5.4	4.53	0.55603	.	0.045219	0.85682	D	0.000000	T	0.63343	0.2503	L	0.59967	1.855	0.80722	D	1	D	0.67145	0.996	D	0.72338	0.977	T	0.64158	-0.6473	10	0.45353	T	0.12	.	14.1635	0.65461	0.0:0.9285:0.0:0.0715	.	760	Q9ULF5	S39AA_HUMAN	K	760;760;310	ENSP00000386766:T760K;ENSP00000352655:T760K;ENSP00000437787:T310K	ENSP00000352655:T760K	T	+	2	0	SLC39A10	196301260	1.000000	0.71417	0.981000	0.43875	0.992000	0.81027	7.604000	0.82830	1.527000	0.49086	0.655000	0.94253	ACA	.	.		0.408	SLC39A10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335186.1	XM_047707		A	196593015	C	A	196593015	3	1	101	1	0	0	0	0	1	0	0	0	14628	478	17	3	2309	3	SLC39A10	2	196593015	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4432062	196593015	46606358	89	13926										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196825086	196825086	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaatttcatcaactgatgccAaaataaatgtcccagtttct	5	9	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:196825086A>G	ENST00000312428.6	-	18	2889	c.2789T>C	c.(2788-2790)tTg>tCg	p.L930S		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	930	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AACTGATGCCAAAATAAATGT	0.348																																					p.L930S		Atlas-SNP	.											.	DNAH7	512	.	0			c.T2789C						.						117	116	116					2																	196825086		1856	4101	5957	SO:0001583	missense	56171	exon18			GATGCCAAAATAA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.2789T>C	chr2.hg19:g.196825086A>G	ENSP00000311273:p.Leu930Ser	53.0	0.0		86.0	10.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018893	0.75275	.	.	ENSG00000118997	ENST00000312428	T	0.69561	-0.41	5.64	5.64	0.86602	Dynein heavy chain, domain-2 (1);	0.000000	0.35151	U	0.003404	D	0.89441	0.6716	H	0.99090	4.425	0.80722	D	1	D	0.56287	0.975	D	0.68483	0.958	D	0.93764	0.7069	10	0.87932	D	0	.	15.8646	0.79055	1.0:0.0:0.0:0.0	.	930	Q8WXX0	DYH7_HUMAN	S	930	ENSP00000311273:L930S	ENSP00000311273:L930S	L	-	2	0	DNAH7	196533331	1.000000	0.71417	0.805000	0.32314	0.845000	0.48019	7.403000	0.79983	2.149000	0.67028	0.477000	0.44152	TTG	.	.		0.348	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		G	196825086	A	G	196825086	3	3	101	1	0	0	0	0	1	0	0	0	4608	131	5	2	9477	2	DNAH7	2	196825086	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	232071	196825086	46374287	90	13927										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196825220	196825220	+	Frame_Shift_Del	DEL	T	T	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctaataccttcaaatcggtcTatatatggttccagattcat							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:196825220delT	ENST00000312428.6	-	18	2755	c.2655delA	c.(2653-2655)atafs	p.I885fs		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	885	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CAAATCGGTCTATATATGGTT	0.438																																					p.D886fs		Atlas-INDEL	.											.	DNAH7	512	.	0			c.2656delG						.						109	106	107					2																	196825220		1864	4110	5974	SO:0001589	frameshift_variant	56171	exon18			.	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.2655delA	chr2.hg19:g.196825220delT	ENSP00000311273:p.Ile885fs	75.0	0.0		216.0	17.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Frame_Shift_Del	DEL	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.438	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		-	196825220	T	-	196825220	7	5	101	1	0	1	0	1	0	0	0	0	4608	1512	53	0	9611	0	DNAH7	2	196825220	Frame_Shift_Del	DEL	T	TCGA-DD-A1EE-01A-11D-A12Z-10	134	196825220	46374153	91	13928										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198267360	198267360	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tagctatctgttgtacaatcTtaataccagtgtgtctcgct	7	9	3	0	rs374250186		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:198267360T>G	ENST00000335508.6	-	14	2088	c.1997A>C	c.(1996-1998)aAg>aCg	p.K666T	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	666					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.K666R(7)|p.K666T(6)|p.K666M(6)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TTGTACAATCTTAATACCAGT	0.413			Mis		myelodysplastic syndrome																																p.K666T		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	SF3B1,NS,malignant_melanoma,0,27	SF3B1	1038	.	19	Substitution - Missense(19)	haematopoietic_and_lymphoid_tissue(18)|NS(1)	c.A1997C						.						116	116	116					2																	198267360		2203	4300	6503	SO:0001583	missense	23451	exon14			ACAATCTTAATAC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1997A>C	chr2.hg19:g.198267360T>G	ENSP00000335321:p.Lys666Thr	99.0	0.0		242.0	20.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736206	0.89482	.	.	ENSG00000115524	ENST00000335508	T	0.65549	-0.16	5.68	5.68	0.88126	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85208	0.5644	H	0.95645	3.7	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.89754	0.3942	10	0.87932	D	0	.	15.938	0.79729	0.0:0.0:0.0:1.0	.	666	O75533	SF3B1_HUMAN	T	666	ENSP00000335321:K666T	ENSP00000335321:K666T	K	-	2	0	SF3B1	197975605	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.877000	0.87225	2.167000	0.68274	0.459000	0.35465	AAG	.	.		0.413	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			G	198267360	T	G	198267360	3	3	101	1	0	0	0	0	1	0	0	0	14164	1609	56	5	1965	5	SF3B1	2	198267360	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	1442140	198267360	44932013	92	13929										
DYTN	391475	hgsc.bcm.edu	37	chr2	207530732	207530732	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgcaacttgtctttgtattgGtttaactgttttttaaggag	9	4	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:207530732G>T	ENST00000452335.2	-	10	1118	c.1002C>A	c.(1000-1002)aaC>aaA	p.N334K		NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	334						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		CTTTGTATTGGTTTAACTGTT	0.403																																					p.N334K		Atlas-SNP	.											.	DYTN	168	.	0			c.C1002A						.						174	154	161					2																	207530732		1826	4080	5906	SO:0001583	missense	391475	exon10			GTATTGGTTTAAC	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.1002C>A	chr2.hg19:g.207530732G>T	ENSP00000396593:p.Asn334Lys	114.0	0.0		220.0	21.0	NM_001093730		Missense_Mutation	SNP	ENST00000452335.2	hg19	CCDS46502.1	.	.	.	.	.	.	.	.	.	.	G	8.469	0.857115	0.17106	.	.	ENSG00000232125	ENST00000452335	T	0.15718	2.4	4.89	0.962	0.19643	.	.	.	.	.	T	0.07548	0.0190	N	0.24115	0.695	0.09310	N	1	P	0.39282	0.666	B	0.33339	0.162	T	0.24119	-1.0169	9	0.22109	T	0.4	-1.6294	1.7438	0.02958	0.1824:0.162:0.4882:0.1675	.	334	A2CJ06	DYTN_HUMAN	K	334	ENSP00000396593:N334K	ENSP00000396593:N334K	N	-	3	2	DYTN	207238977	0.026000	0.19158	0.013000	0.15412	0.517000	0.34286	-0.050000	0.11904	0.061000	0.16311	0.561000	0.74099	AAC	.	.		0.403	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			T	207530732	G	T	207530732	3	4	101	1	0	0	0	0	1	0	0	0	4863	1252	44	3	746	3	DYTN	2	207530732	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	9263372	207530732	35668641	93	13930										
IDH1	3417	hgsc.bcm.edu	37	chr2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttgatccccataagcatgacGacctatgatgataggtttta	8	8	0	4	rs121913499		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000446179.1_Missense_Mutation_p.R132C|IDH1_ENST00000345146.2_Missense_Mutation_p.R132C	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																p.R132C	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	IDH1,NS,haematopoietic_neoplasm,0,788	IDH1	6310	.	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)	c.C394T						.						81	74	76					2																	209113113		2203	4300	6503	SO:0001583	missense	3417	exon4			CATGACGACCTAT		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>T	chr2.hg19:g.209113113G>A	ENSP00000390265:p.Arg132Cys	91.0	0.0		267.0	17.0	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	hg19	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT	.	.		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			A	209113113	G	A	209113113	3	1	101	1	0	0	0	0	1	0	0	0	7503	1058	37	1	878	1	IDH1	2	209113113	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1582381	209113113	34086260	94	13931										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212615384	212615384	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aagtctggcaatgattttctGtgggtccccagcaacggcca	11	11	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:212615384G>T	ENST00000342788.4	-	5	912	c.602C>A	c.(601-603)aCa>aAa	p.T201K	ERBB4_ENST00000484474.1_5'UTR|ERBB4_ENST00000402597.1_Missense_Mutation_p.T201K|ERBB4_ENST00000436443.1_Missense_Mutation_p.T201K	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	201	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T201K(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ATGATTTTCTGTGGGTCCCCA	0.458										TSP Lung(8;0.080)																											p.T201K		Atlas-SNP	.											ERBB4,NS,carcinoma,0,1	ERBB4	480	.	1	Substitution - Missense(1)	endometrium(1)	c.C602A						.						136	113	121					2																	212615384		2203	4300	6503	SO:0001583	missense	2066	exon5			TTTTCTGTGGGTC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.602C>A	chr2.hg19:g.212615384G>T	ENSP00000342235:p.Thr201Lys	54.0	0.0		124.0	15.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.73|17.73	3.462532|3.462532	0.63513|0.63513	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000260943|ENST00000342788;ENST00000436443;ENST00000402597	.|D;D;D	.|0.82081	.|-1.57;-1.57;-1.57	5.58|5.58	5.58|5.58	0.84498|0.84498	.|Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	.|0.211367	.|0.49916	.|D	.|0.000132	T|T	0.69557|0.69557	0.3124|0.3124	N|N	0.08118|0.08118	0|0	0.43559|0.43559	D|D	0.995878|0.995878	.|B;B;B;B;B	.|0.06786	.|0.0;0.001;0.0;0.0;0.0	.|B;B;B;B;B	.|0.09377	.|0.001;0.004;0.001;0.001;0.0	T|T	0.64041|0.64041	-0.6500|-0.6500	5|9	.|.	.|.	.|.	.|.	19.6257|19.6257	0.95677|0.95677	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|201;201;60;201;201	.|Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.|.;.;.;.;ERBB4_HUMAN	K|K	201|201	.|ENSP00000342235:T201K;ENSP00000403204:T201K;ENSP00000385565:T201K	.|.	Q|T	-|-	1|2	0|0	ERBB4|ERBB4	212323629|212323629	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	5.303000|5.303000	0.65738|0.65738	2.625000|2.625000	0.88918|0.88918	0.650000|0.650000	0.86243|0.86243	CAG|ACA	.	.		0.458	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212615384	G	T	212615384	3	4	101	1	0	0	0	0	1	0	0	0	5211	1377	48	3	3420	3	ERBB4	2	212615384	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3502271	212615384	30583989	95	13932										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215823013	215823013	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttactcaccatgtcataaatGaagtttgttacccagtagca	6	9	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:215823013G>T	ENST00000272895.7	-	41	6324	c.6105C>A	c.(6103-6105)ttC>ttA	p.F2035L	AC072062.1_ENST00000420134.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.F1717L|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2035					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TGTCATAAATGAAGTTTGTTA	0.383																																					p.F2035L	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C6105A						.						203	180	188					2																	215823013		2203	4300	6503	SO:0001583	missense	26154	exon41			ATAAATGAAGTTT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.6105C>A	chr2.hg19:g.215823013G>T	ENSP00000272895:p.Phe2035Leu	71.0	0.0		139.0	16.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.949949	0.73787	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.87809	-2.3;-2.3	5.52	4.65	0.58169	.	0.000000	0.64402	D	0.000001	D	0.90930	0.7149	M	0.82923	2.615	0.80722	D	1	P;P	0.35944	0.501;0.529	P;B	0.48063	0.565;0.331	D	0.91174	0.4971	10	0.62326	D	0.03	.	11.5673	0.50813	0.0684:0.125:0.8066:0.0	.	2035;1717	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	L	2035;1717	ENSP00000272895:F2035L;ENSP00000374312:F1717L	ENSP00000272895:F2035L	F	-	3	2	ABCA12	215531258	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.670000	0.68088	1.483000	0.48342	0.650000	0.86243	TTC	.	.		0.383	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215823013	G	T	215823013	3	4	101	1	0	0	0	0	1	0	0	0	30	1281	45	3	1734	3	ABCA12	2	215823013	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3207629	215823013	27376360	96	13933										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215843664	215843664	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaagtacataaacaagctctCccccaatatcctccttgagg	6	13	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:215843664C>T	ENST00000272895.7	-	32	5060	c.4841G>A	c.(4840-4842)gGa>gAa	p.G1614E	ABCA12_ENST00000389661.4_Missense_Mutation_p.G1296E	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1614					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AACAAGCTCTCCCCCAATATC	0.498																																					p.G1614E	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.G4841A						.						158	139	145					2																	215843664		2203	4300	6503	SO:0001583	missense	26154	exon32			AGCTCTCCCCCAA	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.4841G>A	chr2.hg19:g.215843664C>T	ENSP00000272895:p.Gly1614Glu	106.0	0.0		320.0	21.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304121	0.81136	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	T;T	0.62639	0.01;0.01	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000002	T	0.74152	0.3679	L	0.43554	1.36	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77004	0.989;0.979	T	0.72944	-0.4138	10	0.45353	T	0.12	.	19.4492	0.94860	0.0:1.0:0.0:0.0	.	1614;1296	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	E	1614;1296	ENSP00000272895:G1614E;ENSP00000374312:G1296E	ENSP00000272895:G1614E	G	-	2	0	ABCA12	215551909	0.995000	0.38212	0.998000	0.56505	0.901000	0.52897	4.063000	0.57499	2.669000	0.90835	0.655000	0.94253	GGA	.	.		0.498	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215843664	C	T	215843664	3	4	101	1	0	0	0	0	1	0	0	0	30	855	30	3	3034	3	ABCA12	2	215843664	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	20651	215843664	27355709	97	13934										
FAM124B	79843	hgsc.bcm.edu	37	chr2	225266346	225266346	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agtatttcacaggactggccCgttcagacacctgaaagagc	10	11	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:225266346C>G	ENST00000409685.3	-	1	405	c.140G>C	c.(139-141)cGg>cCg	p.R47P	FAM124B_ENST00000243806.2_Missense_Mutation_p.R47P|FAM124B_ENST00000389874.3_Missense_Mutation_p.R47P	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	47										endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		AGGACTGGCCCGTTCAGACAC	0.572																																					p.R47P		Atlas-SNP	.											FAM124B_ENST00000409685,NS,carcinoma,0,2	FAM124B	71	.	0			c.G140C						.						47	49	49					2																	225266346		2203	4300	6503	SO:0001583	missense	79843	exon1			CTGGCCCGTTCAG	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.140G>C	chr2.hg19:g.225266346C>G	ENSP00000386895:p.Arg47Pro	36.0	0.0		118.0	27.0	NM_024785	A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	hg19	CCDS46527.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695087	0.68386	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	T;T;T	0.55052	0.54;0.54;0.54	5.81	5.81	0.92471	.	0.052994	0.64402	D	0.000001	T	0.76637	0.4015	M	0.83603	2.65	0.58432	D	0.999998	D;D	0.89917	0.986;1.0	D;D	0.79784	0.927;0.993	T	0.78398	-0.2219	10	0.66056	D	0.02	-33.1611	20.0628	0.97684	0.0:1.0:0.0:0.0	.	47;47	Q9H5Z6;Q9H5Z6-2	F124B_HUMAN;.	P	47	ENSP00000374524:R47P;ENSP00000386895:R47P;ENSP00000243806:R47P	ENSP00000243806:R47P	R	-	2	0	FAM124B	224974590	0.968000	0.33430	0.386000	0.26170	0.075000	0.17131	7.294000	0.78760	2.745000	0.94114	0.655000	0.94253	CGG	.	.		0.572	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		G	225266346	C	G	225266346	3	3	101	1	0	0	0	0	1	0	0	0	5431	652	23	4	1326	4	FAM124B	2	225266346	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	9422682	225266346	17933027	98	13935										
SLC19A3	80704	hgsc.bcm.edu	37	chr2	228560620	228560620	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttacactgctatggttataAgaagcatatagctggacttg	9	7	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:228560620A>G	ENST00000258403.3	-	4	1228	c.1157T>C	c.(1156-1158)cTt>cCt	p.L386P	SLC19A3_ENST00000541617.1_Missense_Mutation_p.L382P|SLC19A3_ENST00000409287.1_Intron	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	386					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)			breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	TATGGTTATAAGAAGCATATA	0.388																																					p.L386P		Atlas-SNP	.											.	SLC19A3	62	.	0			c.T1157C						.						68	72	71					2																	228560620		2203	4300	6503	SO:0001583	missense	80704	exon4			GTTATAAGAAGCA	AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"Solute carriers"	16266	protein-coding gene	gene with protein product	"thiamine transporter 2"	606152	"solute carrier family 19, member 3"			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.1157T>C	chr2.hg19:g.228560620A>G	ENSP00000258403:p.Leu386Pro	55.0	0.0		87.0	36.0	NM_025243		Missense_Mutation	SNP	ENST00000258403.3	hg19	CCDS2468.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.057777	0.76074	.	.	ENSG00000135917	ENST00000258403;ENST00000541617	D;D	0.89196	-2.48;-2.48	5.03	5.03	0.67393	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.95598	0.8569	M	0.93016	3.37	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.96558	0.9413	10	0.72032	D	0.01	-20.1456	14.927	0.70887	1.0:0.0:0.0:0.0	.	382;386	F5H2M8;Q9BZV2	.;S19A3_HUMAN	P	386;382	ENSP00000258403:L386P;ENSP00000445519:L382P	ENSP00000258403:L386P	L	-	2	0	SLC19A3	228268864	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	8.630000	0.90987	2.111000	0.64477	0.533000	0.62120	CTT	.	.		0.388	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			G	228560620	A	G	228560620	3	3	101	1	0	0	0	0	1	0	0	0	14445	72	3	2	345	2	SLC19A3	2	228560620	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	3294274	228560620	14638753	99	13936										
USP40	55230	hgsc.bcm.edu	37	chr2	234394446	234394446	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggaagccactcgaacttttcGggaaagtatttggcaatttc	10	8	0	0	rs542793420		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:234394446G>A	ENST00000427112.2	-	28	3407	c.3372C>T	c.(3370-3372)ccC>ccT	p.P1124P	USP40_ENST00000251722.6_Silent_p.P1124P|USP40_ENST00000450966.1_Silent_p.P1136P|USP40_ENST00000496298.1_5'UTR			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1124					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CGAACTTTTCGGGAAAGTATT	0.512													G|||	1	0.000199681	0	0	5008	,	,		18876	0.001		0	False		,,,				2504	0				p.P1136P		Atlas-SNP	.											.	USP40	174	.	0			c.C3408T						.						24	27	26					2																	234394446		1875	4098	5973	SO:0001819	synonymous_variant	55230	exon28			CTTTTCGGGAAAG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3372C>T	chr2.hg19:g.234394446G>A		113.0	0.0		266.0	107.0	NM_018218	Q6NX38|Q70EL0	Silent	SNP	ENST00000427112.2	hg19	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312564	0.23908	.	.	ENSG00000085982	ENST00000454354	T	0.34072	1.38	5.75	-2.8	0.05823	.	0.636347	0.17268	N	0.180514	T	0.36853	0.0982	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33574	-0.9863	7	0.62326	D	0.03	.	4.7274	0.12948	0.4326:0.0:0.3385:0.2289	.	.	.	.	L	92	ENSP00000394133:P92L	ENSP00000394133:P92L	P	-	2	0	USP40	234059185	0.357000	0.24938	0.954000	0.39281	0.965000	0.64279	-0.372000	0.07504	-0.444000	0.07170	-1.000000	0.02509	CCG	.	.		0.512	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		A	234394446	G	A	234394446	2	1	101	1	0	0	0	0	0	0	0	1	17087	1103	39	1		1	USP40	2	234394446	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	5833826	234394446	8804927	100	13937										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238249117	238249117	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctgacgaaggatggcaacagCctcccgaagcgcatcaaagg	12	12	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr2:238249117C>T	ENST00000295550.4	-	38	8894	c.8442G>A	c.(8440-8442)agG>agA	p.R2814R	COL6A3_ENST00000409809.1_Silent_p.R2608R|COL6A3_ENST00000472056.1_Silent_p.R2207R|COL6A3_ENST00000347401.3_Silent_p.R2613R|COL6A3_ENST00000353578.4_Silent_p.R2608R|COL6A3_ENST00000346358.4_Silent_p.R2614R	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2814	Nonhelical region.|VWFA 12. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		ATGGCAACAGCCTCCCGAAGC	0.552																																					p.R2814R		Atlas-SNP	.											.	COL6A3	608	.	0			c.G8442A						.						73	66	68					2																	238249117		2203	4300	6503	SO:0001819	synonymous_variant	1293	exon38			CAACAGCCTCCCG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8442G>A	chr2.hg19:g.238249117C>T		19.0	0.0		46.0	20.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.		0.552	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238249117	C	T	238249117	2	4	101	1	0	0	0	0	0	0	0	1	3703	738	26	3		3	COL6A3	2	238249117	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3854671	238249117	4950256	101	13938										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1371531	1371532	+	Missense_Mutation	DNP	GA	GA	AT													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttttgttcaagttggtgggGatattgttatcggatgcaaa							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:1371531_1371532GA>AT	ENST00000446702.2	+	11	1903_1904	c.1276_1277GA>AT	c.(1276-1278)GAt>ATt	p.D426I	CNTN6_ENST00000539053.1_Missense_Mutation_p.D354I|CNTN6_ENST00000350110.2_Missense_Mutation_p.D426I			Q9UQ52	CNTN6_HUMAN	contactin 6	426	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.D426N(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AGTTGGTGGGGATATTGTTATC	0.371																																					p.D426N|p.D426V		Atlas-SNP	.											CNTN6,colon,carcinoma,0,1|.	CNTN6	245	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1276A|c.A1277T						.																																			SO:0001583	missense	27255	exon11			GGTGGGGATATTG|GTGGGGATATTGT	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	Exception_encountered	chr3.hg19:g.1371531_1371532delinsAT	ENSP00000407822:p.Asp426Ile	142.0|143.0	1.0|0.0		436.0|442.0	26.0	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	hg19	CCDS2557.1																																																																																			.	.		0.371	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		AT	1371532	GA	AT	1371531	3	1	101	1	0	0	0	0	1	0	0	0	3647	1174	41	3	1314	3	CNTN6	3	1371531	Missense_Mutation	DNP	GA	TCGA-DD-A1EE-01A-11D-A12Z-10		1371531	196650899	102	13939										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4732940	4732940	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctgcatagagactcacggtcGgaatgtccagtatataaagt	10	8	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:4732940G>A	ENST00000443694.2	+	29	3896	c.3896G>A	c.(3895-3897)cGg>cAg	p.R1299Q	ITPR1_ENST00000423119.2_Missense_Mutation_p.R1305Q|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.R1314Q|ITPR1_ENST00000302640.8_Missense_Mutation_p.R1299Q|ITPR1_ENST00000357086.4_Missense_Mutation_p.R1305Q|ITPR1_ENST00000456211.2_Missense_Mutation_p.R1290Q			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1314					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	ACTCACGGTCGGAATGTCCAG	0.408																																					p.R1305Q		Atlas-SNP	.											.	ITPR1	659	.	0			c.G3914A						.						89	87	88					3																	4732940		1917	4149	6066	SO:0001583	missense	3708	exon32			ACGGTCGGAATGT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.3896G>A	chr3.hg19:g.4732940G>A	ENSP00000401671:p.Arg1299Gln	97.0	0.0		319.0	23.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	34	5.351730	0.95830	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13;-4.13;-4.13	5.24	5.24	0.73138	Intracellular calcium-release channel (1);	0.000000	0.85682	D	0.000000	D	0.98229	0.9414	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72982	0.968;0.979	D	0.98763	1.0725	10	0.56958	D	0.05	.	18.8583	0.92262	0.0:0.0:1.0:0.0	.	1314;1305	Q14643;G5E9P1	ITPR1_HUMAN;.	Q	1314;1299;1314;1305;1305;1290;1299	ENSP00000306253:R1299Q;ENSP00000346595:R1314Q;ENSP00000405934:R1305Q;ENSP00000349597:R1305Q;ENSP00000397885:R1290Q;ENSP00000401671:R1299Q	ENSP00000306253:R1299Q	R	+	2	0	ITPR1	4707940	1.000000	0.71417	0.849000	0.33467	0.941000	0.58515	9.778000	0.99011	2.437000	0.82529	0.655000	0.94253	CGG	.	.		0.408	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4732940	G	A	4732940	3	1	101	1	0	0	0	0	1	0	0	0	7929	1116	39	1	4059	1	ITPR1	3	4732940	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3361409	4732940	193289490	103	13940										
BRPF1	7862	hgsc.bcm.edu	37	chr3	9776191	9776191	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tggatgtggtgtcagaggatGaggaagcccccgaggaggcc	18	8	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:9776191G>A	ENST00000457855.1	+	1	378	c.367G>A	c.(367-369)Gag>Aag	p.E123K	BRPF1_ENST00000433861.2_Missense_Mutation_p.E123K|BRPF1_ENST00000424362.1_Missense_Mutation_p.E123K|BRPF1_ENST00000383829.2_Missense_Mutation_p.E123K|BRPF1_ENST00000302054.3_Missense_Mutation_p.E123K			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	123	Interaction with KAT6A and KAT6B.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					GTCAGAGGATGAGGAAGCCCC	0.562																																					p.E123K		Atlas-SNP	.											.	BRPF1	104	.	0			c.G367A						.						82	85	84					3																	9776191		2203	4300	6503	SO:0001583	missense	7862	exon2			GAGGATGAGGAAG	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"peregrin", "bromodomain-containing protein, 140kD"	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.367G>A	chr3.hg19:g.9776191G>A	ENSP00000410210:p.Glu123Lys	65.0	0.0		154.0	20.0	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	hg19	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	G	34	5.350093	0.95830	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.73	5.73	0.89815	Enhancer of polycomb-like, N-terminal (1);	0.145914	0.64402	D	0.000007	T	0.61148	0.2324	L	0.48362	1.52	0.80722	D	1	P;B;B;P	0.48016	0.904;0.384;0.226;0.582	P;B;B;P	0.57548	0.823;0.419;0.343;0.7	T	0.60622	-0.7227	10	0.66056	D	0.02	.	19.4877	0.95037	0.0:0.0:1.0:0.0	.	123;123;123;123	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	K	123	ENSP00000402485:E123K;ENSP00000398863:E123K;ENSP00000373340:E123K;ENSP00000306297:E123K;ENSP00000410210:E123K	ENSP00000306297:E123K	E	+	1	0	BRPF1	9751191	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.476000	0.97823	2.709000	0.92574	0.563000	0.77884	GAG	.	.		0.562	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		A	9776191	G	A	9776191	3	1	101	1	0	0	0	0	1	0	0	0	1522	1291	45	3	369	3	BRPF1	3	9776191	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	5043251	9776191	188246239	104	13941										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10401567	10401567	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgccctgcccagcgcttactTcttgagcacgatctcagaag	9	14	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:10401567T>C	ENST00000352432.4	-	12	1969	c.1900A>G	c.(1900-1902)Aag>Gag	p.K634E	ATP2B2_ENST00000360273.2_Splice_Site_p.K634E|ATP2B2_ENST00000397077.1_Splice_Site_p.K589E|ATP2B2_ENST00000383800.4_Splice_Site_p.K589E|ATP2B2_ENST00000343816.4_Splice_Site_p.K620E			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	634					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						AGCGCTTACTTCTTGAGCACG	0.622																																					p.K634E	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A1900G						.						65	61	62					3																	10401567		2203	4300	6503	SO:0001630	splice_region_variant	491	exon13			CTTACTTCTTGAG	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.1901+1A>G	chr3.hg19:g.10401567T>C		40.0	0.0		80.0	5.0	NM_001001331	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.940928	0.92526	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	T;T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49;-0.49	4.86	4.86	0.63082	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.82949	0.5148	M	0.74467	2.265	0.80722	D	1	D;P;P	0.63046	0.992;0.863;0.784	D;P;P	0.74674	0.984;0.589;0.672	D	0.85330	0.1089	10	0.72032	D	0.01	-27.9035	14.4662	0.67485	0.0:0.0:0.0:1.0	.	569;601;634	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	E	634;589;589;634;620;569;490;634	ENSP00000324172:K634E;ENSP00000373311:K589E;ENSP00000380267:K589E;ENSP00000353414:K634E;ENSP00000344677:K620E;ENSP00000414854:K490E	ENSP00000342954:K634E	K	-	1	0	ATP2B2	10376567	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	8.026000	0.88783	1.816000	0.52996	0.443000	0.29094	AAG	.	.		0.622	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	Missense_Mutation	C	10401567	T	C	10401567	5	2	101	1	0	0	0	0	0	0	1	0	1140	1797	62	2	1875	2	ATP2B2	3	10401567	Splice_Site	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	625376	10401567	187620863	105	13942										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10443888	10443888	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctcgatgcggctctgcaggCcccggaactgtttctctttg	12	13	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:10443888C>A	ENST00000352432.4	-	3	611	c.542G>T	c.(541-543)gGc>gTc	p.G181V	ATP2B2_ENST00000360273.2_Missense_Mutation_p.G181V|ATP2B2_ENST00000397077.1_Missense_Mutation_p.G181V|ATP2B2_ENST00000383800.4_Missense_Mutation_p.G181V|ATP2B2_ENST00000343816.4_Missense_Mutation_p.G181V			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	181					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						GCTCTGCAGGCCCCGGAACTG	0.592																																					p.G181V	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.G542T						.						131	142	138					3																	10443888		2203	4300	6503	SO:0001583	missense	491	exon4			TGCAGGCCCCGGA	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.542G>T	chr3.hg19:g.10443888C>A	ENSP00000324172:p.Gly181Val	34.0	0.0		99.0	14.0	NM_001683	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.013607	0.93404	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	5.44	5.44	0.79542	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.92935	0.7752	L	0.47078	1.49	0.80722	D	1	D;D;P	0.89917	1.0;0.991;0.946	D;D;P	0.97110	1.0;0.937;0.672	D	0.93482	0.6828	10	0.87932	D	0	-36.5231	19.2768	0.94034	0.0:1.0:0.0:0.0	.	181;193;181	Q01814-7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	V	181;181;181;181;181;147;68;181	ENSP00000324172:G181V;ENSP00000373311:G181V;ENSP00000380267:G181V;ENSP00000353414:G181V;ENSP00000344677:G181V;ENSP00000414854:G68V	ENSP00000342954:G181V	G	-	2	0	ATP2B2	10418888	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.550000	0.86006	0.467000	0.42956	GGC	.	.		0.592	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10443888	C	A	10443888	3	1	101	1	0	0	0	0	1	0	0	0	1140	739	26	3	3269	3	ATP2B2	3	10443888	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	42321	10443888	187578542	106	13943										
RFTN1	23180	hgsc.bcm.edu	37	chr3	16368288	16368288	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgttattgttacctggtagtCttgacgacgggagttggtag	14	5	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:16368288C>T	ENST00000334133.4	-	8	1514	c.1242G>A	c.(1240-1242)aaG>aaA	p.K414K	RFTN1_ENST00000432519.1_Silent_p.K378K|OXNAD1_ENST00000605932.1_Intron|OXNAD1_ENST00000435829.2_Intron|OXNAD1_ENST00000606098.1_Intron|RFTN1_ENST00000483671.1_5'UTR|OXNAD1_ENST00000544043.1_Intron	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	414					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						ACCTGGTAGTCTTGACGACGG	0.488																																					p.K414K		Atlas-SNP	.											.	RFTN1	79	.	0			c.G1242A						.						63	54	57					3																	16368288		2203	4300	6503	SO:0001819	synonymous_variant	23180	exon8			GGTAGTCTTGACG	D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"raft-linking protein"					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.1242G>A	chr3.hg19:g.16368288C>T		28.0	0.0		61.0	4.0	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Silent	SNP	ENST00000334133.4	hg19	CCDS33712.1																																																																																			.	.		0.488	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150		T	16368288	C	T	16368288	2	4	101	1	0	0	0	0	0	0	0	1	13273	912	32	3		3	RFTN1	3	16368288	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	5924400	16368288	181654142	107	13944										
TRIM71	131405	hgsc.bcm.edu	37	chr3	32915309	32915309	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtaccctctcttgtccccaGgtgctgcacctgtactgtga	9	14	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:32915309G>A	ENST00000383763.5	+	2	915		c.e2-1			NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase						fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CTTGTCCCCAGGTGCTGCACC	0.592																																					.		Atlas-SNP	.											.	TRIM71	73	.	0			c.853-1G>A						.						301	312	308					3																	32915309		2116	4231	6347	SO:0001630	splice_region_variant	131405	exon2			TCCCCAGGTGCTG		CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32669	protein-coding gene	gene with protein product			"tripartite motif-containing 71", "tripartite motif containing 71"				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.853-1G>A	chr3.hg19:g.32915309G>A		103.0	0.0		214.0	13.0	NM_001039111		Splice_Site	SNP	ENST00000383763.5	hg19	CCDS43060.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.606327	0.87157	.	.	ENSG00000206557	ENST00000383763	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3848	0.90463	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TRIM71	32890313	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	9.751000	0.98889	2.769000	0.95229	0.655000	0.94253	.	.	.		0.592	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111	Intron	A	32915309	G	A	32915309	5	1	101	1	0	0	0	0	0	0	1	0	16559	1014	35	3	858	3	TRIM71	3	32915309	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	16547021	32915309	165107121	108	13945										
GLB1	2720	hgsc.bcm.edu	37	chr3	33106973	33106973	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acctgcactgttataactggCcctccattctgatagaggag	9	11	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:33106973C>T	ENST00000307377.8	-	3	382	c.322G>A	c.(322-324)Gcc>Acc	p.A108T	GLB1_ENST00000445488.2_Silent_p.G226G|GLB1_ENST00000307363.5_Silent_p.G178G|GLB1_ENST00000399402.3_Silent_p.G148G	NM_001135602.1	NP_001129074	P16278	BGAL_HUMAN	galactosidase, beta 1	0					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)	beta-galactosidase activity (GO:0004565)|galactoside binding (GO:0016936)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	21		Melanoma(143;0.104)				TTATAACTGGCCCTCCATTCT	0.468																																					p.A108T		Atlas-SNP	.											.	GLB1	51	.	0			c.G322A						.						57	63	61					3																	33106973		1941	4117	6058	SO:0001583	missense	2720	exon3			AACTGGCCCTCCA	M22590	CCDS43061.1, CCDS43062.1, CCDS46785.1	3p22.3	2012-10-02			ENSG00000170266	ENSG00000170266	3.2.1.23		4298	protein-coding gene	gene with protein product		611458	"elastin receptor 1, 67kDa", "elastin receptor 1 (67kD)"	ELNR1		110522, 3143362	Standard	NM_000404		Approved	EBP	uc003cfi.1	P16278	OTTHUMG00000155781	ENST00000307377.8:c.322G>A	chr3.hg19:g.33106973C>T	ENSP00000305920:p.Ala108Thr	122.0	0.0		339.0	42.0	NM_001135602	B2R7H8|B7Z6B0|P16279	Missense_Mutation	SNP	ENST00000307377.8	hg19	CCDS46785.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.500002	0.44455	.	.	ENSG00000170266	ENST00000307377	D	0.97924	-4.61	6.01	-1.38	0.09027	.	.	.	.	.	D	0.93419	0.7901	.	.	.	0.80722	D	1	B	0.21071	0.051	B	0.19946	0.027	T	0.82786	-0.0285	8	0.54805	T	0.06	-19.1601	1.3747	0.02218	0.1315:0.2644:0.2826:0.3215	.	108	E7EQ29	.	T	108	ENSP00000305920:A108T	ENSP00000305920:A108T	A	-	1	0	GLB1	33081977	0.003000	0.15002	0.825000	0.32803	0.980000	0.70556	-1.147000	0.03188	-0.611000	0.05709	0.650000	0.86243	GCC	.	.		0.468	GLB1-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341571.1	NM_000404		T	33106973	C	T	33106973	3	4	101	1	0	0	0	0	1	0	0	0	6435	739	26	3	1547	3	GLB1	3	33106973	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	191664	33106973	164915457	109	13946										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38135225	38135225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcctgaaaaccttcggtccaCggctaggaagcagctgatta	11	11	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:38135225C>T	ENST00000308059.6	+	12	1907	c.1886C>T	c.(1885-1887)aCg>aTg	p.T629M	DLEC1_ENST00000452631.2_Missense_Mutation_p.T629M|DLEC1_ENST00000346219.3_Missense_Mutation_p.T629M					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CTTCGGTCCACGGCTAGGAAG	0.502																																					p.T629M		Atlas-SNP	.											.	DLEC1	278	.	0			c.C1886T						.						123	124	123					3																	38135225		1909	4135	6044	SO:0001583	missense	9940	exon12			GGTCCACGGCTAG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1886C>T	chr3.hg19:g.38135225C>T	ENSP00000308597:p.Thr629Met	70.0	0.0		184.0	18.0	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	13.25	2.180990	0.38511	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05996	3.37;3.36;3.6	5.08	3.25	0.37280	.	0.239343	0.42420	D	0.000702	T	0.07548	0.0190	L	0.53249	1.67	0.09310	N	0.999999	D;D;D	0.56521	0.976;0.976;0.976	P;B;P	0.44673	0.457;0.356;0.457	T	0.25745	-1.0123	10	0.34782	T	0.22	-12.8453	6.5019	0.22174	0.0:0.7237:0.0:0.2763	.	629;629;629	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	M	629	ENSP00000308597:T629M;ENSP00000315914:T629M;ENSP00000410427:T629M	ENSP00000308597:T629M	T	+	2	0	DLEC1	38110229	0.020000	0.18652	0.645000	0.29479	0.974000	0.67602	1.115000	0.31209	1.096000	0.41439	0.655000	0.94253	ACG	.	.		0.502	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38135225	C	T	38135225	3	4	101	1	0	0	0	0	1	0	0	0	4554	536	19	1	1932	1	DLEC1	3	38135225	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	5028252	38135225	159887205	110	13947										
TTC21A	199223	hgsc.bcm.edu	37	chr3	39171742	39171742	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gacactttccccaccagcccGagaaggccctggaggtctat	10	15	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:39171742G>T	ENST00000431162.2	+	17	2367	c.2233G>T	c.(2233-2235)Gag>Tag	p.E745*	TTC21A_ENST00000301819.6_Nonsense_Mutation_p.E746*|TTC21A_ENST00000440121.1_Nonsense_Mutation_p.E697*			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	745										NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CCACCAGCCCGAGAAGGCCCT	0.582																																					p.E745X		Atlas-SNP	.											.	TTC21A	96	.	0			c.G2233T						.						44	45	45					3																	39171742		1914	4118	6032	SO:0001587	stop_gained	199223	exon17			CAGCCCGAGAAGG	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"Tetratricopeptide (TTC) repeat domain containing"	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.2233G>T	chr3.hg19:g.39171742G>T	ENSP00000398211:p.Glu745*	49.0	0.0		128.0	25.0	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Nonsense_Mutation	SNP	ENST00000431162.2	hg19	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	38	7.162369	0.98107	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	.	.	.	4.85	4.85	0.62838	.	0.159354	0.38217	N	0.001765	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-28.9477	17.1263	0.86715	0.0:0.0:1.0:0.0	.	.	.	.	X	746;728;745;697	.	ENSP00000301819:E746X	E	+	1	0	TTC21A	39146746	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.872000	0.75536	2.414000	0.81942	0.563000	0.77884	GAG	.	.		0.582	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		T	39171742	G	T	39171742	4	4	101	1	0	0	0	0	0	1	0	0	16702	1059	37	1	2302	1	TTC21A	3	39171742	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1036517	39171742	158850688	111	13948										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41268766	41268766	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaggacctatacttacgaaaAactactgtggaccacaagca	8	10	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:41268766A>T	ENST00000349496.5	+	7	1284	c.1004A>T	c.(1003-1005)aAa>aTa	p.K335I	CTNNB1_ENST00000453024.1_Missense_Mutation_p.K328I|CTNNB1_ENST00000396183.3_Missense_Mutation_p.K335I|CTNNB1_ENST00000405570.1_Missense_Mutation_p.K335I|CTNNB1_ENST00000396185.3_Missense_Mutation_p.K335I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	335					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.K335I(8)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACTTACGAAAAACTACTGTGG	0.383		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.K335I	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,colon,carcinoma,-1,11	CTNNB1	4904	.	8	Substitution - Missense(8)	liver(7)|kidney(1)	c.A1004T						.						110	108	109					3																	41268766		2203	4300	6503	SO:0001583	missense	1499	exon7	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACGAAAAACTACT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1004A>T	chr3.hg19:g.41268766A>T	ENSP00000344456:p.Lys335Ile	68.0	0.0		138.0	10.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.040885	0.93685	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.82148	0.4974	M	0.89287	3.02	0.80722	D	1	D;D	0.71674	0.995;0.998	D;D	0.75484	0.97;0.986	D	0.85830	0.1391	10	0.72032	D	0.01	-3.7939	15.5934	0.76558	1.0:0.0:0.0:0.0	.	263;335	B4DSW9;P35222	.;CTNB1_HUMAN	I	335;335;335;328;335	ENSP00000385604:K335I;ENSP00000379486:K335I;ENSP00000344456:K335I;ENSP00000411226:K328I;ENSP00000379488:K335I	ENSP00000344456:K335I	K	+	2	0	CTNNB1	41243770	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	9.339000	0.96797	2.094000	0.63399	0.482000	0.46254	AAA	.	.		0.383	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41268766	A	T	41268766	3	4	101	1	0	0	0	0	1	0	0	0	4018	14	1	4	1026	4	CTNNB1	3	41268766	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	2097024	41268766	156753664	112	13949										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41275047	41275047	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tggaaggtctccttgggactCttgttcagcttctgggttca	12	9	5	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:41275047C>T	ENST00000349496.5	+	9	1493	c.1213C>T	c.(1213-1215)Ctt>Ttt	p.L405F	CTNNB1_ENST00000453024.1_Missense_Mutation_p.L398F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.L405F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.L405F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.L405F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	405					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CCTTGGGACTCTTGTTCAGCT	0.418		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.L405F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	0			c.C1213T						.						150	143	146					3																	41275047		2203	4300	6503	SO:0001583	missense	1499	exon9	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GGGACTCTTGTTC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1213C>T	chr3.hg19:g.41275047C>T	ENSP00000344456:p.Leu405Phe	51.0	0.0		110.0	6.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.939289	0.92526	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14	5.86	5.86	0.93980	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.91236	0.7238	M	0.91090	3.175	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	D	0.92265	0.5820	10	0.87932	D	0	-0.542	20.1865	0.98220	0.0:1.0:0.0:0.0	.	333;398;405	B4DSW9;B4DGU4;P35222	.;.;CTNB1_HUMAN	F	405;405;405;398;405	ENSP00000385604:L405F;ENSP00000379486:L405F;ENSP00000344456:L405F;ENSP00000411226:L398F;ENSP00000379488:L405F	ENSP00000344456:L405F	L	+	1	0	CTNNB1	41250051	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.775000	0.95449	0.655000	0.94253	CTT	.	.		0.418	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41275047	C	T	41275047	3	4	101	1	0	0	0	0	1	0	0	0	4018	913	32	3	1243	3	CTNNB1	3	41275047	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	6281	41275047	156747383	113	13950										
CDCP1	64866	hgsc.bcm.edu	37	chr3	45153871	45153871	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agatgaaagttctgttgaggGtaggcaacaacgatgtcgag	14	5	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:45153871G>C	ENST00000296129.1	-	3	493	c.359C>G	c.(358-360)aCc>aGc	p.T120S	CDCP1_ENST00000490471.1_5'UTR|CDCP1_ENST00000425231.2_Missense_Mutation_p.T120S	NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	120						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		TCTGTTGAGGGTAGGCAACAA	0.498																																					p.T120S		Atlas-SNP	.											.	CDCP1	61	.	0			c.C359G						.						177	184	181					3																	45153871		2203	4300	6503	SO:0001583	missense	64866	exon3			TTGAGGGTAGGCA	AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"CD molecules"	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.359C>G	chr3.hg19:g.45153871G>C	ENSP00000296129:p.Thr120Ser	64.0	0.0		121.0	57.0	NM_178181	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Missense_Mutation	SNP	ENST00000296129.1	hg19	CCDS2727.1	.	.	.	.	.	.	.	.	.	.	G	0.023	-1.396493	0.01175	.	.	ENSG00000163814	ENST00000296129;ENST00000425231	T;T	0.40756	2.05;1.02	5.6	1.62	0.23740	.	1.693290	0.02601	N	0.101072	T	0.24547	0.0595	N	0.16478	0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12941	-1.0528	10	0.08381	T	0.77	.	3.7598	0.08599	0.154:0.3891:0.347:0.11	.	120;120	Q9H5V8-3;Q9H5V8	.;CDCP1_HUMAN	S	120	ENSP00000296129:T120S;ENSP00000399342:T120S	ENSP00000296129:T120S	T	-	2	0	CDCP1	45128875	0.586000	0.26782	0.006000	0.13384	0.089000	0.18198	1.019000	0.30014	0.010000	0.14839	0.563000	0.77884	ACC	.	.		0.498	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842		C	45153871	G	C	45153871	3	2	101	1	0	0	0	0	1	0	0	0	3095	1261	44	4	2187	4	CDCP1	3	45153871	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3878824	45153871	152868559	114	13951										
TRAIP	10293	hgsc.bcm.edu	37	chr3	49867199	49867199	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acccagtgagagctgggactCctgcagggaagaccccaggg	15	12	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:49867199C>T	ENST00000331456.2	-	13	1200	c.1087G>A	c.(1087-1089)Gag>Aag	p.E363K	TRAIP_ENST00000469027.1_Splice_Site_p.E208K	NM_005879.2	NP_005870.2	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	363	Interaction with CYLD.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|receptor signaling protein activity (GO:0005057)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AGCTGGGACTCCTGCAGGGAA	0.567																																					p.E363K		Atlas-SNP	.											.	TRAIP	47	.	0			c.G1087A						.						31	31	31					3																	49867199		2203	4300	6503	SO:0001630	splice_region_variant	10293	exon13			GGGACTCCTGCAG	BC019283	CCDS2806.1	3p21.31	2013-01-09			ENSG00000183763	ENSG00000183763		"RING-type (C3HC4) zinc fingers"	30764	protein-coding gene	gene with protein product	"ring finger protein 206"	605958				9104814	Standard	NM_005879		Approved	TRIP, RNF206	uc003cxs.1	Q9BWF2	OTTHUMG00000158269	ENST00000331456.2:c.1087-1G>A	chr3.hg19:g.49867199C>T		31.0	0.0		95.0	9.0	NM_005879	B5BU84|B5BUL3|O00467	Missense_Mutation	SNP	ENST00000331456.2	hg19	CCDS2806.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.844797	0.32606	.	.	ENSG00000183763	ENST00000331456;ENST00000469027	T	0.44881	0.91	5.08	4.21	0.49690	.	0.512387	0.20570	N	0.089742	T	0.31071	0.0785	L	0.51422	1.61	0.35350	D	0.787276	B;B	0.18610	0.001;0.029	B;B	0.14023	0.002;0.01	T	0.24835	-1.0149	10	0.06236	T	0.91	-14.4236	9.2917	0.37791	0.0:0.9033:0.0:0.0967	.	363;363	A8K807;Q9BWF2	.;TRAIP_HUMAN	K	363;208	ENSP00000420085:E208K	ENSP00000328203:E363K	E	-	1	0	TRAIP	49842203	0.998000	0.40836	0.993000	0.49108	0.134000	0.20937	1.262000	0.32992	1.376000	0.46267	0.561000	0.74099	GAG	.	.		0.567	TRAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350518.1	NM_005879	Missense_Mutation	T	49867199	C	T	49867199	5	4	101	1	0	0	0	0	0	0	1	0	16463	869	30	3	334	3	TRAIP	3	49867199	Splice_Site	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4713328	49867199	148155231	115	13952										
NAT6	24142	hgsc.bcm.edu	37	chr3	50334446	50334446	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgaggcggcggccaaagccaCggcccctcagggcccgggcc	16	17	1	1	rs587623768		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:50334446C>A	ENST00000443842.1	-	2	1256	c.449G>T	c.(448-450)cGt>cTt	p.R150L	NAT6_ENST00000443094.2_Missense_Mutation_p.R150L|HYAL3_ENST00000513170.1_Intron|HYAL3_ENST00000415204.1_Intron|HYAL3_ENST00000336307.1_Intron|NAT6_ENST00000354862.4_Missense_Mutation_p.R172L|HYAL3_ENST00000359051.3_Intron|NAT6_ENST00000417393.1_Missense_Mutation_p.R150L|HYAL3_ENST00000450982.1_Intron			Q93015	NAT6_HUMAN	N-acetyltransferase 6 (GCN5-related)	150	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.					cytoplasm (GO:0005737)	N-acetyltransferase activity (GO:0008080)			endometrium(3)|lung(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GCCAAAGCCACGGCCCCTCAG	0.672																																					p.R172L		Atlas-SNP	.											.	NAT6	14	.	0			c.G515T						.						9	11	11					3																	50334446		1766	3964	5730	SO:0001583	missense	24142	exon2			AAGCCACGGCCCC	AF040705	CCDS43095.1, CCDS56258.1	3p21.3	2011-11-16	2008-09-24		ENSG00000243477	ENSG00000243477	2.3.1.-		30252	protein-coding gene	gene with protein product		607073	"N-acetyltransferase 6"			11929860, 11085536	Standard	NM_012191		Approved	FUS2		Q93015	OTTHUMG00000156939	ENST00000443842.1:c.449G>T	chr3.hg19:g.50334446C>A	ENSP00000400559:p.Arg150Leu	9.0	0.0		30.0	10.0	NM_012191	Q93014	Missense_Mutation	SNP	ENST00000443842.1	hg19	CCDS56258.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.224609	0.79576	.	.	ENSG00000243477	ENST00000354862;ENST00000417393;ENST00000443094;ENST00000443842	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	5.8	2.65	0.31530	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.420201	0.17152	U	0.185023	T	0.32645	0.0836	L	0.46614	1.455	0.33569	D	0.598331	D;D	0.63046	0.99;0.992	P;P	0.59948	0.79;0.866	T	0.46582	-0.9181	10	0.66056	D	0.02	0.8591	3.2491	0.06807	0.0:0.4812:0.2117:0.3071	.	172;150	Q93015-2;Q93015	.;NAT6_HUMAN	L	172;150;150;150	ENSP00000346927:R172L;ENSP00000391893:R150L;ENSP00000410610:R150L;ENSP00000400559:R150L	ENSP00000346927:R172L	R	-	2	0	NAT6	50309450	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.079000	0.30766	0.798000	0.33994	0.655000	0.94253	CGT	.	.		0.672	NAT6-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346681.1	NM_012191		A	50334446	C	A	50334446	3	1	101	1	0	0	0	0	1	0	0	0	10187	536	19	1	415	1	NAT6	3	50334446	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	467247	50334446	147687984	116	13953										
TMEM115	11070	hgsc.bcm.edu	37	chr3	50395815	50395815	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctgcaggatctcagggaagAaagtggcgaaagcaaagtgg	16	6	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:50395815A>T	ENST00000266025.3	-	1	1226	c.680T>A	c.(679-681)tTc>tAc	p.F227Y	XXcos-LUCA11.5_ENST00000606589.1_Intron	NM_007024.4	NP_008955.1	Q12893	TM115_HUMAN	transmembrane protein 115	227					negative regulation of cell proliferation (GO:0008285)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(1)|lung(1)|prostate(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CTCAGGGAAGAAAGTGGCGAA	0.567																																					p.F227Y		Atlas-SNP	.											.	TMEM115	20	.	0			c.T680A						.						98	95	96					3																	50395815		2203	4300	6503	SO:0001583	missense	11070	exon1			GGGAAGAAAGTGG	BC011948	CCDS2828.1	3p21.31	2008-11-04			ENSG00000126062	ENSG00000126062			30055	protein-coding gene	gene with protein product	"placental protein 6"	607069				11085536	Standard	NM_007024		Approved	PL6	uc003dan.1	Q12893	OTTHUMG00000044212	ENST00000266025.3:c.680T>A	chr3.hg19:g.50395815A>T	ENSP00000266025:p.Phe227Tyr	55.0	0.0		121.0	9.0	NM_007024	A2IDB7|O14568|Q6IAY4|Q9UIX3	Missense_Mutation	SNP	ENST00000266025.3	hg19	CCDS2828.1	.	.	.	.	.	.	.	.	.	.	A	30	5.053497	0.93793	.	.	ENSG00000126062	ENST00000266025	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.78291	0.4260	M	0.71581	2.175	0.80722	D	1	D	0.63880	0.993	D	0.74674	0.984	T	0.80756	-0.1240	9	0.87932	D	0	1.0E-4	15.788	0.78322	1.0:0.0:0.0:0.0	.	227	Q12893	TM115_HUMAN	Y	227	.	ENSP00000266025:F227Y	F	-	2	0	TMEM115	50370819	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.069000	0.93967	2.200000	0.70718	0.460000	0.39030	TTC	.	.		0.567	TMEM115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102784.3	NM_007024		T	50395815	A	T	50395815	3	4	101	1	0	0	0	0	1	0	0	0	16044	246	9	4	383	4	TMEM115	3	50395815	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	61369	50395815	147626615	117	13954										
STAB1	23166	hgsc.bcm.edu	37	chr3	52549455	52549455	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccaggacacacccaggaagaGctgtgtctaccgatctggct	11	13	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:52549455G>T	ENST00000321725.6	+	37	3957	c.3881G>T	c.(3880-3882)aGc>aTc	p.S1294I		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1294					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CCCAGGAAGAGCTGTGTCTAC	0.607																																					p.S1294I		Atlas-SNP	.											.	STAB1	178	.	0			c.G3881T						.						76	71	73					3																	52549455		2202	4300	6502	SO:0001583	missense	23166	exon37			GGAAGAGCTGTGT	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.3881G>T	chr3.hg19:g.52549455G>T	ENSP00000312946:p.Ser1294Ile	39.0	0.0		106.0	16.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.281890	0.59758	.	.	ENSG00000010327	ENST00000321725	T	0.03152	4.03	4.71	3.83	0.44106	.	0.269718	0.34879	N	0.003614	T	0.05593	0.0147	N	0.17474	0.49	0.39755	D	0.971946	D	0.69078	0.997	P	0.62014	0.897	T	0.56890	-0.7904	10	0.20046	T	0.44	-28.4682	8.8676	0.35296	0.1024:0.0:0.8976:0.0	.	1294	Q9NY15	STAB1_HUMAN	I	1294	ENSP00000312946:S1294I	ENSP00000312946:S1294I	S	+	2	0	STAB1	52524495	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	3.320000	0.51991	1.327000	0.45338	0.563000	0.77884	AGC	.	.		0.607	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52549455	G	T	52549455	3	4	101	1	0	0	0	0	1	0	0	0	15252	971	34	3	4027	3	STAB1	3	52549455	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2153640	52549455	145472975	118	13955										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52588770	52588770	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gatgcccgggaggccaggcaCacctggcggaagatggtggg	19	10	0	1	rs143564112	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:52588770C>A	ENST00000296302.7	-	27	4580	c.4579G>T	c.(4579-4581)Gtg>Ttg	p.V1527L	RNU6-856P_ENST00000516959.1_RNA|PBRM1_ENST00000337303.4_Intron|PBRM1_ENST00000410007.1_Missense_Mutation_p.V1447L|PBRM1_ENST00000409114.3_Intron|PBRM1_ENST00000409767.1_Intron|PBRM1_ENST00000409057.1_Missense_Mutation_p.V1472L|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000394830.3_Missense_Mutation_p.V1420L|PBRM1_ENST00000356770.4_Missense_Mutation_p.V1440L			Q86U86	PB1_HUMAN	polybromo 1	1527	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AGGCCAGGCACACCTGGCGGA	0.557			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.V1420L		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	PBRM1_ENST00000356770,NS,lymphoid_neoplasm,0,1	PBRM1	1252	.	0			c.G4258T						.						45	44	45					3																	52588770		2203	4300	6503	SO:0001583	missense	55193	exon27			CAGGCACACCTGG	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4579G>T	chr3.hg19:g.52588770C>A	ENSP00000296302:p.Val1527Leu	82.0	0.0		250.0	12.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	C	13.52	2.262476	0.39995	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000409057;ENST00000410007	T;T;T;T;T	0.33216	1.42;1.42;1.46;1.43;1.42	5.62	3.58	0.41010	.	0.353225	0.30850	N	0.008759	T	0.13884	0.0336	N	0.08118	0	0.80722	D	1	B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001	B;B;B;B;B	0.17722	0.005;0.003;0.005;0.001;0.019	T	0.06516	-1.0822	10	0.49607	T	0.09	-7.5268	4.2397	0.10642	0.0:0.6107:0.0:0.3893	.	1447;1420;1472;1527;1440	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86;Q86U86-3	.;.;.;PB1_HUMAN;.	L	1440;1420;1527;1472;1447	ENSP00000349213:V1440L;ENSP00000378307:V1420L;ENSP00000296302:V1527L;ENSP00000386593:V1472L;ENSP00000386529:V1447L	ENSP00000296302:V1527L	V	-	1	0	PBRM1	52563810	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.917000	0.56424	1.348000	0.45733	0.563000	0.77884	GTG	.	C|0.999;T|0.001		0.557	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		A	52588770	C	A	52588770	3	1	101	1	0	0	0	0	1	0	0	0	11500	478	17	3	506	3	PBRM1	3	52588770	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	39315	52588770	145433660	119	13956										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52662939	52662939	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttgctgcaattttagaactcGcttgtagatggctgaattgg	11	6	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:52662939G>A	ENST00000296302.7	-	12	1415	c.1414C>T	c.(1414-1416)Cga>Tga	p.R472*	PBRM1_ENST00000337303.4_Nonsense_Mutation_p.R472*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.R472*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.R472*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.R472*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.R472*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.R472*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.R440*			Q86U86	PB1_HUMAN	polybromo 1	472					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTTAGAACTCGCTTGTAGATG	0.318			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.R472X		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.C1414T						.						101	95	97					3																	52662939		2203	4300	6503	SO:0001587	stop_gained	55193	exon13			GAACTCGCTTGTA	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1414C>T	chr3.hg19:g.52662939G>A	ENSP00000296302:p.Arg472*	75.0	0.0		138.0	8.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	G	37	6.182101	0.97352	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.4	1.45	0.22620	.	0.136047	0.50627	D	0.000116	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-21.0362	11.5495	0.50713	0.0:0.1018:0.3723:0.5259	.	.	.	.	X	440;472;472;472;472;472;472;472;472;416	.	ENSP00000296302:R472X	R	-	1	2	PBRM1	52637979	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	2.206000	0.42779	-0.016000	0.14127	-0.309000	0.09137	CGA	.	.		0.318	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		A	52662939	G	A	52662939	4	1	101	1	0	0	0	0	0	1	0	0	11500	1095	38	1	3562	1	PBRM1	3	52662939	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	74169	52662939	145359491	120	13957										
PTPRG	5793	hgsc.bcm.edu	37	chr3	61975392	61975392	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tttagaccagtatgcgcgtgTtggggaagaataccaggaac	13	7	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:61975392T>C	ENST00000474889.1	+	3	661	c.284T>C	c.(283-285)gTt>gCt	p.V95A	PTPRG_ENST00000295874.10_Missense_Mutation_p.V95A	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	95	Alpha-carbonic anhydrase.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TATGCGCGTGTTGGGGAAGAA	0.493																																					p.V95A		Atlas-SNP	.											.	PTPRG	153	.	0			c.T284C						.						119	109	112					3																	61975392		2203	4300	6503	SO:0001583	missense	5793	exon3			CGCGTGTTGGGGA	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.284T>C	chr3.hg19:g.61975392T>C	ENSP00000418112:p.Val95Ala	81.0	0.0		124.0	18.0	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	hg19	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	T	18.83	3.707702	0.68615	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.67171	-0.25;-0.25	5.92	5.92	0.95590	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.359047	0.29300	N	0.012560	T	0.66934	0.2840	L	0.52011	1.625	0.52501	D	0.999954	P;P	0.44429	0.835;0.517	B;B	0.43889	0.435;0.226	T	0.71237	-0.4652	10	0.87932	D	0	.	16.3413	0.83082	0.0:0.0:0.0:1.0	.	95;95	P23470-2;P23470	.;PTPRG_HUMAN	A	95	ENSP00000418112:V95A;ENSP00000295874:V95A	ENSP00000295874:V95A	V	+	2	0	PTPRG	61950432	1.000000	0.71417	0.107000	0.21349	0.943000	0.58893	7.642000	0.83385	2.257000	0.74773	0.533000	0.62120	GTT	.	.		0.493	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		C	61975392	T	C	61975392	3	2	101	1	0	0	0	0	1	0	0	0	12817	1725	60	2	294	2	PTPRG	3	61975392	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	9312453	61975392	136047038	121	13958										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77614146	77614146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcagaccgtggcaaaccatgTaaagaccaccctctatactg	8	13	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:77614146T>C	ENST00000461745.1	+	12	2624	c.1724T>C	c.(1723-1725)gTa>gCa	p.V575A	ROBO2_ENST00000487694.3_Missense_Mutation_p.V591A|ROBO2_ENST00000332191.8_Missense_Mutation_p.V575A	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	575	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GCAAACCATGTAAAGACCACC	0.463																																					p.V575A		Atlas-SNP	.											.	ROBO2	527	.	0			c.T1724C						.						78	76	77					3																	77614146		1976	4165	6141	SO:0001583	missense	6092	exon12			ACCATGTAAAGAC	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.1724T>C	chr3.hg19:g.77614146T>C	ENSP00000417164:p.Val575Ala	33.0	0.0		68.0	18.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	T	17.39	3.378492	0.61735	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.54866	0.55;0.55;0.55	6.02	6.02	0.97574	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41294	D	0.000907	T	0.70360	0.3215	M	0.79926	2.475	0.46416	D	0.999038	B;B;B	0.31256	0.316;0.098;0.316	P;P;P	0.47430	0.547;0.535;0.547	T	0.74163	-0.3754	9	0.87932	D	0	.	16.542	0.84395	0.0:0.0:0.0:1.0	.	591;575;575	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	A	591;591;595;575;575;296	ENSP00000417335:V591A;ENSP00000417164:V575A;ENSP00000327536:V575A	ENSP00000327536:V575A	V	+	2	0	ROBO2	77696836	1.000000	0.71417	0.668000	0.29813	0.394000	0.30568	6.258000	0.72487	2.304000	0.77564	0.528000	0.53228	GTA	.	.		0.463	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		C	77614146	T	C	77614146	3	2	101	1	0	0	0	0	1	0	0	0	13529	1638	57	2	1772	2	ROBO2	3	77614146	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	15638754	77614146	120408284	122	13959										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77629195	77629195	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tggattattcccaggtattcAataccgggtagaggttgcag	12	7	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:77629195A>C	ENST00000461745.1	+	16	3326	c.2426A>C	c.(2425-2427)cAa>cCa	p.Q809P	ROBO2_ENST00000487694.3_Missense_Mutation_p.Q825P|ROBO2_ENST00000332191.8_Missense_Mutation_p.Q809P	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	809	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CCAGGTATTCAATACCGGGTA	0.448																																					p.Q809P		Atlas-SNP	.											.	ROBO2	527	.	0			c.A2426C						.						124	122	122					3																	77629195		1888	4118	6006	SO:0001583	missense	6092	exon16			GTATTCAATACCG	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.2426A>C	chr3.hg19:g.77629195A>C	ENSP00000417164:p.Gln809Pro	78.0	0.0		191.0	37.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.790591	0.31685	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.57436	0.4;0.4;0.4	5.53	5.53	0.82687	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.38492	U	0.001662	T	0.43500	0.1250	L	0.35414	1.06	0.42344	D	0.992343	B;B;B	0.11235	0.002;0.004;0.002	B;B;B	0.16289	0.007;0.015;0.007	T	0.48115	-0.9063	9	0.30078	T	0.28	.	15.3169	0.74089	1.0:0.0:0.0:0.0	.	825;809;809	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	P	825;825;829;809;809;530	ENSP00000417335:Q825P;ENSP00000417164:Q809P;ENSP00000327536:Q809P	ENSP00000327536:Q809P	Q	+	2	0	ROBO2	77711885	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	3.750000	0.55157	2.095000	0.63458	0.460000	0.39030	CAA	.	.		0.448	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		C	77629195	A	C	77629195	3	2	101	1	0	0	0	0	1	0	0	0	13529	130	5	5	2490	5	ROBO2	3	77629195	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	15049	77629195	120393235	123	13960										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77651546	77651546	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcatacatgaattggctgtcGatctgcctgatccacaatgg	10	10	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:77651546G>A	ENST00000461745.1	+	20	3940	c.3040G>A	c.(3040-3042)Gat>Aat	p.D1014N	ROBO2_ENST00000487694.3_Missense_Mutation_p.D1030N|ROBO2_ENST00000332191.8_Missense_Mutation_p.D1014N	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1014					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		ATTGGCTGTCGATCTGCCTGA	0.423																																					p.D1014N		Atlas-SNP	.											ROBO2_ENST00000487694,NS,carcinoma,0,6	ROBO2	527	.	0			c.G3040A						.						116	108	110					3																	77651546		1964	4162	6126	SO:0001583	missense	6092	exon20			GCTGTCGATCTGC	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3040G>A	chr3.hg19:g.77651546G>A	ENSP00000417164:p.Asp1014Asn	87.0	0.0		269.0	12.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.8|29.8	5.040614|5.040614	0.93630|0.93630	.|.	.|.	ENSG00000185008|ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191|ENST00000471893	T;T;T|.	0.64991|.	-0.13;-0.09;-0.08|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	0.000000|.	0.47455|.	D|.	0.000232|.	T|T	0.69178|0.69178	0.3082|0.3082	L|L	0.42245|0.42245	1.32|1.32	0.29415|.	N|.	0.860951|.	D;D;D|.	0.76494|.	0.998;0.999;0.997|.	P;P;P|.	0.62184|.	0.825;0.899;0.649|.	T|T	0.62756|0.62756	-0.6787|-0.6787	9|4	0.48119|.	T|.	0.1|.	.|.	20.1432|20.1432	0.98067|0.98067	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1030;1014;1014|.	Q19AB5;F8W703;Q9HCK4|.	.;.;ROBO2_HUMAN|.	N|Q	1030;1030;1034;1014;1014|88	ENSP00000417335:D1030N;ENSP00000417164:D1014N;ENSP00000327536:D1014N|.	ENSP00000327536:D1014N|.	D|R	+|+	1|2	0|0	ROBO2|ROBO2	77734236|77734236	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.476000|9.476000	0.97823|0.97823	2.769000|2.769000	0.95229|0.95229	0.561000|0.561000	0.74099|0.74099	GAT|CGA	.	.		0.423	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		A	77651546	G	A	77651546	3	1	101	1	0	0	0	0	1	0	0	0	13529	1058	37	1	3120	1	ROBO2	3	77651546	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	22351	77651546	120370884	124	13961										
CADM2	253559	hgsc.bcm.edu	37	chr3	85984981	85984981	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaaggacagcctttaattttGacttgtgaatccaaaggaaa	9	6	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:85984981G>T	ENST00000407528.2	+	6	800	c.738G>T	c.(736-738)ttG>ttT	p.L246F	CADM2_ENST00000383699.3_Missense_Mutation_p.L255F|CADM2_ENST00000405615.2_Missense_Mutation_p.L248F	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	246	Ig-like C2-type 2.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		CTTTAATTTTGACTTGTGAAT	0.308																																					p.L255F		Atlas-SNP	.											.	CADM2	195	.	0			c.G765T						.						96	102	100					3																	85984981		2203	4297	6500	SO:0001583	missense	253559	exon7			AATTTTGACTTGT	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.738G>T	chr3.hg19:g.85984981G>T	ENSP00000384575:p.Leu246Phe	126.0	0.0		393.0	34.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155619	0.78114	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	D;T;T	0.89415	-2.51;-1.48;-1.48	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92280	0.7551	L	0.43554	1.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	D	0.89344	0.3656	10	0.23302	T	0.38	.	19.9785	0.97317	0.0:0.0:1.0:0.0	.	248;255;246	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	F	255;246;248	ENSP00000373200:L255F;ENSP00000384575:L246F;ENSP00000384193:L248F	ENSP00000373200:L255F	L	+	3	2	CADM2	86067671	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.778000	0.75043	2.724000	0.93272	0.650000	0.86243	TTG	.	.		0.308	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		T	85984981	G	T	85984981	3	4	101	1	0	0	0	0	1	0	0	0	2569	1281	45	3	831	3	CADM2	3	85984981	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	8333435	85984981	112037449	125	13962										
CADM2	253559	hgsc.bcm.edu	37	chr3	86114753	86114753	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aatattttcctgtcttttccAgatcctaatgctttggctgg	7	9	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:86114753A>G	ENST00000407528.2	+	9	1125		c.e9-1		CADM2_ENST00000383699.3_Splice_Site|CADM2_ENST00000405615.2_Splice_Site	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2						adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		TGTCTTTTCCAGATCCTAATG	0.368																																					.		Atlas-SNP	.											.	CADM2	195	.	0			c.1064-2A>G						.						134	122	126					3																	86114753		2203	4300	6503	SO:0001630	splice_region_variant	253559	exon9			TTTTCCAGATCCT	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.1064-1A>G	chr3.hg19:g.86114753A>G		86.0	0.0		210.0	13.0	NM_001167674	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Splice_Site	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.622329	0.87460	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0708	0.80928	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CADM2	86197443	1.000000	0.71417	0.960000	0.40013	0.941000	0.58515	9.339000	0.96797	2.197000	0.70478	0.528000	0.53228	.	.	.		0.368	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184	Intron	G	86114753	A	G	86114753	5	3	101	1	0	0	0	0	0	0	1	0	2569	202	7	2	1167	2	CADM2	3	86114753	Splice_Site	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	129772	86114753	111907677	126	13963										
EPHA6	285220	hgsc.bcm.edu	37	chr3	97202883	97202883	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgatccctcaagaattcgtaTtgagagagtcattggggcag	12	7	2	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:97202883T>C	ENST00000514100.1	+	7	598	c.356T>C	c.(355-357)aTt>aCt	p.I119T	EPHA6_ENST00000502694.1_Missense_Mutation_p.I119T|EPHA6_ENST00000389672.5_Missense_Mutation_p.I727T|EPHA6_ENST00000442602.2_Missense_Mutation_p.I93T	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	633	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						AGAATTCGTATTGAGAGAGTC	0.358																																					p.I727T		Atlas-SNP	.											.	EPHA6	439	.	0			c.T2180C						.						95	95	95					3																	97202883		1851	4110	5961	SO:0001583	missense	285220	exon10			TTCGTATTGAGAG	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000514100.1:c.356T>C	chr3.hg19:g.97202883T>C	ENSP00000421711:p.Ile119Thr	76.0	0.0		177.0	11.0	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000514100.1	hg19		.	.	.	.	.	.	.	.	.	.	T	21.8	4.198363	0.79015	.	.	ENSG00000080224	ENST00000389672;ENST00000514100;ENST00000502694;ENST00000442602	D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67	5.42	5.42	0.78866	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.89389	0.6701	L	0.59967	1.855	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.996;1.0	D;D;D;D	0.91635	0.999;0.999;0.99;0.999	D	0.90503	0.4475	9	0.87932	D	0	.	15.5233	0.75881	0.0:0.0:0.0:1.0	.	93;632;119;119	B4DXQ6;Q9UF33;Q9UF33-2;D6RAL5	.;EPHA6_HUMAN;.;.	T	727;119;119;93	ENSP00000374323:I727T;ENSP00000421711:I119T;ENSP00000423950:I119T;ENSP00000403100:I93T	ENSP00000374323:I727T	I	+	2	0	EPHA6	98685573	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.695000	0.84257	2.071000	0.62044	0.454000	0.30748	ATT	.	.		0.358	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448		C	97202883	T	C	97202883	3	2	101	1	0	0	0	0	1	0	0	0	5173	1493	52	2	2286	2	EPHA6	3	97202883	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	11088130	97202883	100819547	127	13964										
RG9MTD1	54931	hgsc.bcm.edu	37	chr3	101283884	101283884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caacaatctcaagcagtaagGatgaagatcctctagctgcc	8	11	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:101283884G>A	ENST00000309922.6	+	2	413	c.259G>A	c.(259-261)Gat>Aat	p.D87N		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	87					mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										AAGCAGTAAGGATGAAGATCC	0.438																																					p.D87N		Atlas-SNP	.											.	.	.	.	0			c.G259A						.						117	108	111					3																	101283884		1907	4127	6034	SO:0001583	missense	54931	exon2			AGTAAGGATGAAG	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 1"	615423	"RNA (guanine-9-) methyltransferase domain containing 1"	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.259G>A	chr3.hg19:g.101283884G>A	ENSP00000312356:p.Asp87Asn	58.0	0.0		153.0	15.0	NM_017819	Q9NRG5|Q9NX54|Q9Y596	Missense_Mutation	SNP	ENST00000309922.6	hg19	CCDS43122.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.673703	0.29693	.	.	ENSG00000174173	ENST00000309922;ENST00000495642	T;T	0.54866	0.55;0.55	5.45	5.45	0.79879	.	0.854822	0.10779	N	0.635072	T	0.54598	0.1868	L	0.57536	1.79	0.32643	N	0.520404	B	0.27559	0.181	B	0.20767	0.031	T	0.57768	-0.7754	10	0.39692	T	0.17	-2.6616	20.1745	0.98175	0.0:0.0:1.0:0.0	.	87	Q7L0Y3	MRRP1_HUMAN	N	87	ENSP00000312356:D87N;ENSP00000419389:D87N	ENSP00000312356:D87N	D	+	1	0	RG9MTD1	102766574	1.000000	0.71417	0.943000	0.38184	0.644000	0.38419	3.148000	0.50647	2.941000	0.99782	0.655000	0.94253	GAT	.	.		0.438	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819		A	101283884	G	A	101283884	3	1	101	1	0	0	0	0	1	0	0	0	13286	1174	41	3	261	3	RG9MTD1	3	101283884	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	4081001	101283884	96738546	128	13965										
IFT57	55081	hgsc.bcm.edu	37	chr3	107937444	107937444	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aagcaatcaagaacatagcaTacatgttctccataacctga	5	10	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:107937444T>C	ENST00000264538.3	-	3	679	c.432A>G	c.(430-432)gtA>gtG	p.V144V		NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	144					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			GAACATAGCATACATGTTCTC	0.338																																					p.V144V		Atlas-SNP	.											.	IFT57	44	.	0			c.A432G						.						69	70	69					3																	107937444		2203	4300	6503	SO:0001819	synonymous_variant	55081	exon3			ATAGCATACATGT	AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"Intraflagellar transport homologs"	17367	protein-coding gene	gene with protein product		606621	"estrogen-related receptor beta like 1", "intraflagellar transport 57 homolog (Chlamydomonas)"	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.432A>G	chr3.hg19:g.107937444T>C		104.0	0.0		226.0	99.0	NM_018010	Q96DA9	Silent	SNP	ENST00000264538.3	hg19	CCDS2951.1																																																																																			.	.		0.338	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010		C	107937444	T	C	107937444	2	2	101	1	0	0	0	0	0	0	0	1	7571	1393	49	2		2	IFT57	3	107937444	Silent	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	6653560	107937444	90084986	129	13966										
TMPRSS7	344805	hgsc.bcm.edu	37	chr3	111797619	111797619	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctccctcgttctgcagcaagCggaggtagagctcattgatc	11	12	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:111797619C>T	ENST00000452346.2	+	17	2258	c.2255C>T	c.(2254-2256)gCg>gTg	p.A752V	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.A626V			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	752	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CTGCAGCAAGCGGAGGTAGAG	0.463																																					p.A626V		Atlas-SNP	.											.	TMPRSS7	126	.	0			c.C1877T						.						112	111	112					3																	111797619		1942	4131	6073	SO:0001583	missense	344805	exon15			AGCAAGCGGAGGT	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.2255C>T	chr3.hg19:g.111797619C>T	ENSP00000398236:p.Ala752Val	74.0	0.0		233.0	14.0	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	hg19		.	.	.	.	.	.	.	.	.	.	C	35	5.518493	0.96416	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	T;T	0.58940	0.3;0.3	5.79	5.79	0.91817	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	T	0.54647	0.1871	N	0.02765	-0.5	0.58432	D	0.999997	D;D	0.89917	1.0;0.996	D;P	0.80764	0.994;0.794	T	0.64968	-0.6282	10	0.39692	T	0.17	.	16.9482	0.86236	0.0:1.0:0.0:0.0	.	752;626	Q7RTY8;Q7RTY8-2	TMPS7_HUMAN;.	V	752;740;726;626	ENSP00000398236:A752V;ENSP00000411645:A626V	ENSP00000411645:A626V	A	+	2	0	TMPRSS7	113280309	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.884000	0.75600	2.716000	0.92895	0.655000	0.94253	GCG	.	.		0.463	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		T	111797619	C	T	111797619	3	4	101	1	0	0	0	0	1	0	0	0	16267	768	27	1	1931	1	TMPRSS7	3	111797619	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3860175	111797619	86224811	130	13967										
ADPRH	141	hgsc.bcm.edu	37	chr3	119305482	119305482	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctactttgtagaggaaaatCttcaacactggtgagtctgt	10	7	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:119305482C>T	ENST00000478399.1	+	3	2054	c.649C>T	c.(649-651)Ctt>Ttt	p.L217F	ADPRH_ENST00000465513.1_Missense_Mutation_p.L217F|ADPRH_ENST00000357003.3_Missense_Mutation_p.L217F|ADPRH_ENST00000471850.1_3'UTR|ADPRH_ENST00000478927.1_Missense_Mutation_p.L217F			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	217					cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		AGAGGAAAATCTTCAACACTG	0.463																																					p.L217F	GBM(133;579 1804 5989 9967 40052)	Atlas-SNP	.											ADPRH,right_upper_lobe,carcinoma,0,1	ADPRH	33	.	0			c.C649T						.						75	76	75					3																	119305482		2203	4300	6503	SO:0001583	missense	141	exon4			GAAAATCTTCAAC	L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843			269	protein-coding gene	gene with protein product		603081				8349667, 12070318	Standard	NM_001125		Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.649C>T	chr3.hg19:g.119305482C>T	ENSP00000420200:p.Leu217Phe	19.0	0.0		42.0	2.0	NM_001125	B2R8H1|D3DN83	Missense_Mutation	SNP	ENST00000478399.1	hg19	CCDS2990.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.061701	0.76187	.	.	ENSG00000144843	ENST00000478399;ENST00000478927;ENST00000357003;ENST00000465513	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.54	5.54	0.83059	.	0.206931	0.42172	D	0.000744	T	0.47116	0.1428	L	0.59436	1.845	0.50313	D	0.999864	P	0.48694	0.914	P	0.45071	0.468	T	0.46735	-0.9170	10	0.54805	T	0.06	-12.9773	17.0271	0.86450	0.0:1.0:0.0:0.0	.	217	P54922	ADPRH_HUMAN	F	217	ENSP00000420200:L217F;ENSP00000417528:L217F;ENSP00000349496:L217F;ENSP00000417430:L217F	ENSP00000349496:L217F	L	+	1	0	ADPRH	120788172	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	1.413000	0.34725	2.884000	0.98904	0.655000	0.94253	CTT	.	.		0.463	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355199.1	NM_001125		T	119305482	C	T	119305482	3	4	101	1	0	0	0	0	1	0	0	0	331	913	32	3	655	3	ADPRH	3	119305482	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	7507863	119305482	78716948	131	13968										
GTF2E1	2960	hgsc.bcm.edu	37	chr3	120469757	120469757	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaattgagaccgatgagagaGattcgaccaaccgggcttcc	12	10	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:120469757G>A	ENST00000283875.5	+	2	451	c.358G>A	c.(358-360)Gat>Aat	p.D120N		NM_005513.2	NP_005504.2	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1, alpha 56kDa	120					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)	22				GBM - Glioblastoma multiforme(114;0.159)		CGATGAGAGAGATTCGACCAA	0.403																																					p.D120N		Atlas-SNP	.											.	GTF2E1	52	.	0			c.G358A						.						81	82	82					3																	120469757		2203	4300	6503	SO:0001583	missense	2960	exon2			GAGAGAGATTCGA	S67859	CCDS3002.1	3q21-q24	2010-03-23	2002-08-29		ENSG00000153767	ENSG00000153767		"General transcription factors"	4650	protein-coding gene	gene with protein product		189962	"general transcription factor IIE, polypeptide 1 (alpha subunit, 56kD)"			1454543, 8162052	Standard	NM_005513		Approved	TFIIE-A, FE	uc003edz.4	P29083	OTTHUMG00000159667	ENST00000283875.5:c.358G>A	chr3.hg19:g.120469757G>A	ENSP00000283875:p.Asp120Asn	64.0	0.0		175.0	14.0	NM_005513	Q16103	Missense_Mutation	SNP	ENST00000283875.5	hg19	CCDS3002.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.973662	0.53720	.	.	ENSG00000153767	ENST00000283875;ENST00000492959	T	0.47528	0.84	6.06	5.18	0.71444	Zinc finger, RING/FYVE/PHD-type (1);TFIIEalpha/SarR/Rpc3 HTH domain (1);	0.042733	0.85682	N	0.000000	T	0.49115	0.1538	M	0.68593	2.085	0.80722	D	1	B;B	0.16166	0.002;0.016	B;B	0.29077	0.047;0.098	T	0.43130	-0.9410	9	.	.	.	-8.7497	13.5627	0.61799	0.075:0.0:0.925:0.0	.	120;120	P29083;Q53F88	T2EA_HUMAN;.	N	120	ENSP00000283875:D120N	.	D	+	1	0	GTF2E1	121952447	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	7.905000	0.87416	1.547000	0.49401	0.655000	0.94253	GAT	.	.		0.403	GTF2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356770.1	NM_005513		A	120469757	G	A	120469757	3	1	101	1	0	0	0	0	1	0	0	0	6865	942	33	3	360	3	GTF2E1	3	120469757	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1164275	120469757	77552673	132	13969										
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122629075	122629075	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggcttgggtagtaagtagtcGtgtacacattggtctgctgc	14	7	1	0	rs369693926		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:122629075G>A	ENST00000357599.3	-	23	3757	c.3371C>T	c.(3370-3372)aCg>aTg	p.T1124M	SEMA5B_ENST00000451055.2_Missense_Mutation_p.T1178M|SEMA5B_ENST00000195173.4_3'UTR	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	1124					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GTAAGTAGTCGTGTACACATT	0.542																																					p.T1178M		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C3533T						.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	206	173	184		3371	5.1	1	3		184	0,8600		0,0,4300	no	missense	SEMA5B	NM_001031702.2	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1124/1152	122629075	1,13005	2203	4300	6503	SO:0001583	missense	54437	exon23			GTAGTCGTGTACA	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.3371C>T	chr3.hg19:g.122629075G>A	ENSP00000350215:p.Thr1124Met	145.0	0.0		529.0	27.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	hg19	CCDS35491.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.7|22.7	4.323460|4.323460	0.81580|0.81580	2.27E-4|2.27E-4	0.0|0.0	ENSG00000082684|ENSG00000082684	ENST00000451541|ENST00000357599;ENST00000418793;ENST00000451055	.|T;T	.|0.37584	.|1.19;1.23	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	.|0.052354	.|0.85682	.|D	.|0.000000	.|T	.|0.48786	.|0.1519	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.72338	.|0.977;0.95	.|T	.|0.46693	.|-0.9173	.|10	.|0.52906	.|T	.|0.07	.|.	17.1675|17.1675	0.86820|0.86820	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1030;1124	.|D3YTI7;Q9P283	.|.;SEM5B_HUMAN	X|M	170|1124;1030;1178	.|ENSP00000350215:T1124M;ENSP00000389588:T1178M	.|ENSP00000350215:T1124M	R|T	-|-	1|2	2|0	SEMA5B|SEMA5B	124111765|124111765	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.981000|0.981000	0.71138|0.71138	9.263000|9.263000	0.95617|0.95617	2.643000|2.643000	0.89663|0.89663	0.650000|0.650000	0.86243|0.86243	CGA|ACG	.	.		0.542	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		A	122629075	G	A	122629075	3	1	101	1	0	0	0	0	1	0	0	0	14053	1145	40	1	88	1	SEMA5B	3	122629075	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2159318	122629075	75393355	133	13970										
KALRN	8997	hgsc.bcm.edu	37	chr3	124165646	124165646	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aagaaacaggtgaattttacCtctcaacacatacctccact	4	12	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:124165646C>G	ENST00000240874.3	+	21	3617	c.3460C>G	c.(3460-3462)Ctc>Gtc	p.L1154V	KALRN_ENST00000360013.3_Missense_Mutation_p.L1154V|KALRN_ENST00000460856.1_Missense_Mutation_p.L1145V	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1154					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TGAATTTTACCTCTCAACACA	0.488																																					p.L1154V		Atlas-SNP	.											.	KALRN	556	.	0			c.C3460G						.						125	127	127					3																	124165646		2203	4300	6503	SO:0001583	missense	8997	exon21			TTTTACCTCTCAA	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.3460C>G	chr3.hg19:g.124165646C>G	ENSP00000240874:p.Leu1154Val	51.0	0.0		116.0	12.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	hg19	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.972333	0.92919	.	.	ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013	T;T;T	0.54071	0.59;0.59;0.59	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000001	T	0.72590	0.3479	M	0.73217	2.22	0.80722	D	1	P;P;D;P	0.69078	0.933;0.921;0.997;0.918	P;P;D;P	0.79108	0.718;0.901;0.992;0.596	T	0.70945	-0.4734	10	0.44086	T	0.13	.	19.3628	0.94448	0.0:1.0:0.0:0.0	.	1145;500;1154;1154	C9IZQ6;F2Z3Q6;O60229;O60229-2	.;.;KALRN_HUMAN;.	V	1145;1154;1154	ENSP00000418611:L1145V;ENSP00000240874:L1154V;ENSP00000353109:L1154V	ENSP00000240874:L1154V	L	+	1	0	KALRN	125648336	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.782000	0.62396	2.802000	0.96397	0.561000	0.74099	CTC	.	.		0.488	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		G	124165646	C	G	124165646	3	3	101	1	0	0	0	0	1	0	0	0	7984	681	24	4	3542	4	KALRN	3	124165646	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1536571	124165646	73856784	134	13971										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129275500	129275500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cgtacttataaatctctgccAtggccacattggtgttgaac	8	10	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:129275500A>G	ENST00000324093.4	-	35	5799	c.5621T>C	c.(5620-5622)aTg>aCg	p.M1874T	PLXND1_ENST00000393239.1_3'UTR|PLXND1_ENST00000504689.1_Missense_Mutation_p.M30T	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1874					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						AATCTCTGCCATGGCCACATT	0.552																																					p.M1874T	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.T5621C						.						158	142	147					3																	129275500		2203	4300	6503	SO:0001583	missense	23129	exon35			TCTGCCATGGCCA	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.5621T>C	chr3.hg19:g.129275500A>G	ENSP00000317128:p.Met1874Thr	83.0	0.0		291.0	27.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.636703	0.47049	.	.	ENSG00000004399	ENST00000324093;ENST00000504689	T;T	0.11930	2.73;2.73	5.11	3.96	0.45880	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.103102	0.64402	D	0.000004	T	0.09905	0.0243	N	0.14661	0.345	0.80722	D	1	B;P	0.38677	0.017;0.642	B;B	0.39971	0.018;0.315	T	0.14559	-1.0468	10	0.87932	D	0	.	10.902	0.47058	0.9258:0.0:0.0742:0.0	.	470;1874	B4DRU3;Q9Y4D7	.;PLXD1_HUMAN	T	1874;30	ENSP00000317128:M1874T;ENSP00000426162:M30T	ENSP00000317128:M1874T	M	-	2	0	PLXND1	130758190	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	5.168000	0.64978	0.786000	0.33708	-0.609000	0.04063	ATG	.	.		0.552	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		G	129275500	A	G	129275500	3	3	101	1	0	0	0	0	1	0	0	0	12136	217	8	2	164	2	PLXND1	3	129275500	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	5109854	129275500	68746930	135	13972										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130286897	130286897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tttttcctatgcagcttgcaAagagatgaaagctgacatca	8	8	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:130286897A>G	ENST00000358511.6	+	5	1881	c.1850A>G	c.(1849-1851)aAa>aGa	p.K617R	COL6A6_ENST00000453409.2_Missense_Mutation_p.K617R	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	617	Nonhelical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GCAGCTTGCAAAGAGATGAAA	0.343																																					p.K617R		Atlas-SNP	.											.	COL6A6	497	.	0			c.A1850G						.						50	48	49					3																	130286897		1828	4101	5929	SO:0001583	missense	131873	exon5			CTTGCAAAGAGAT	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1850A>G	chr3.hg19:g.130286897A>G	ENSP00000351310:p.Lys617Arg	52.0	0.0		149.0	11.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	A	8.783	0.928789	0.18131	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.78246	-1.16;-1.16	5.32	0.312	0.15837	.	0.095602	0.45867	N	0.000322	T	0.57417	0.2052	N	0.20304	0.555	0.25997	N	0.982165	B	0.18310	0.027	B	0.15052	0.012	T	0.38866	-0.9641	10	0.19147	T	0.46	.	8.7651	0.34698	0.6943:0.0:0.3057:0.0	.	617	A6NMZ7	CO6A6_HUMAN	R	617	ENSP00000351310:K617R;ENSP00000399236:K617R	ENSP00000351310:K617R	K	+	2	0	COL6A6	131769587	1.000000	0.71417	0.985000	0.45067	0.538000	0.34931	3.306000	0.51881	-0.161000	0.10983	-0.250000	0.11733	AAA	.	.		0.343	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		G	130286897	A	G	130286897	3	3	101	1	0	0	0	0	1	0	0	0	3705	14	1	2	1868	2	COL6A6	3	130286897	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1011397	130286897	67735533	136	13973										
KY	339855	hgsc.bcm.edu	37	chr3	134348537	134348537	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttccacagtcagttgtgtcCctacaaaggaaaaggagatg	10	9	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:134348537C>A	ENST00000423778.2	-	4	324	c.263G>T	c.(262-264)gGg>gTg	p.G88V	KY_ENST00000508041.1_5'Flank|KY_ENST00000503669.1_Splice_Site_p.G88V|KY_ENST00000508956.1_Splice_Site_p.G67V	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	88					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						CAGTTGTGTCCCTACAAAGGA	0.443																																					p.G88V		Atlas-SNP	.											.	KY	92	.	0			c.G263T						.						68	68	68					3																	134348537		1987	4200	6187	SO:0001630	splice_region_variant	339855	exon4			TGTGTCCCTACAA	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.263-1G>T	chr3.hg19:g.134348537C>A		63.0	0.0		162.0	12.0	NM_178554	B7Z1S4|Q6ZT15	Missense_Mutation	SNP	ENST00000423778.2	hg19	CCDS46920.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.129807	0.56721	.	.	ENSG00000174611	ENST00000508956;ENST00000423778;ENST00000503669;ENST00000310263	.	.	.	5.58	5.58	0.84498	.	0.069279	0.56097	D	0.000026	T	0.63486	0.2515	L	0.59436	1.845	0.80722	D	1	P;D;P;D	0.63046	0.947;0.972;0.867;0.992	P;P;B;P	0.51415	0.656;0.669;0.44;0.656	T	0.59526	-0.7438	9	0.25751	T	0.34	.	16.4916	0.84202	0.0:1.0:0.0:0.0	.	67;88;88;49	Q8NBH2-3;B4DGA7;Q8NBH2-4;Q8NBH2-2	.;.;.;.	V	67;88;88;88	.	ENSP00000309520:G88V	G	-	2	0	KY	135831227	1.000000	0.71417	0.998000	0.56505	0.406000	0.30931	4.312000	0.59154	2.622000	0.88805	0.557000	0.71058	GGG	.	.		0.443	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	Missense_Mutation	A	134348537	C	A	134348537	5	1	101	1	0	0	0	0	0	0	1	0	8595	637	22	3	1754	3	KY	3	134348537	Splice_Site	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4061640	134348537	63673893	137	13974										
CEP70	80321	hgsc.bcm.edu	37	chr3	138219253	138219253	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtcatcacctaattctaagaGttcttggaggtttctcacag	8	9	5	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:138219253G>A	ENST00000264982.3	-	15	1791	c.1525C>T	c.(1525-1527)Ctc>Ttc	p.L509F	CEP70_ENST00000489254.1_Missense_Mutation_p.L357F|CEP70_ENST00000484888.1_Missense_Mutation_p.L509F|CEP70_ENST00000542237.1_Missense_Mutation_p.L489F|CEP70_ENST00000481834.1_Missense_Mutation_p.L509F	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	509					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						AATTCTAAGAGTTCTTGGAGG	0.318																																					p.L509F		Atlas-SNP	.											.	CEP70	51	.	0			c.C1525T						.						100	112	108					3																	138219253		2203	4300	6503	SO:0001583	missense	80321	exon15			CTAAGAGTTCTTG	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.1525C>T	chr3.hg19:g.138219253G>A	ENSP00000264982:p.Leu509Phe	116.0	0.0		366.0	28.0	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	hg19	CCDS3102.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100107	0.56183	.	.	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000489254;ENST00000484888;ENST00000474781;ENST00000481834	T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62	4.88	3.93	0.45458	Tetratricopeptide repeat-containing (1);	0.326421	0.29838	N	0.011079	T	0.50103	0.1596	M	0.66939	2.045	0.42564	D	0.993153	D;P;D;P	0.69078	0.96;0.904;0.997;0.904	P;P;D;P	0.68192	0.663;0.625;0.956;0.625	T	0.52866	-0.8518	10	0.72032	D	0.01	-0.9042	12.1533	0.54062	0.0:0.0:0.8187:0.1813	.	357;489;509;509	B7Z2D2;F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;.;CEP70_HUMAN	F	509;489;357;509;491;509	ENSP00000264982:L509F;ENSP00000444128:L489F;ENSP00000417821:L357F;ENSP00000419231:L509F;ENSP00000419833:L491F;ENSP00000417465:L509F	ENSP00000264982:L509F	L	-	1	0	CEP70	139701943	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.310000	0.43708	2.552000	0.86080	0.655000	0.94253	CTC	.	.		0.318	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491		A	138219253	G	A	138219253	3	1	101	1	0	0	0	0	1	0	0	0	3261	1029	36	3	284	3	CEP70	3	138219253	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3870716	138219253	59803177	138	13975										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140281020	140281020	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaggaaatgcttcataacttAgatttctgtgacattttggt	9	5	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:140281020A>T	ENST00000458420.3	+	13	2272	c.2082A>T	c.(2080-2082)ttA>ttT	p.L694F		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	694					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						TTCATAACTTAGATTTCTGTG	0.498										HNSCC(16;0.037)																											p.L694F	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.A2082T						.						102	98	99					3																	140281020		2203	4300	6503	SO:0001583	missense	64084	exon13			TAACTTAGATTTC	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2082A>T	chr3.hg19:g.140281020A>T	ENSP00000402460:p.Leu694Phe	47.0	0.0		144.0	16.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.228156	0.79576	.	.	ENSG00000158258	ENST00000458420	T	0.34072	1.38	5.43	-1.16	0.09678	.	0.000000	0.85682	D	0.000000	T	0.54806	0.1881	M	0.85630	2.765	0.46774	D	0.999195	D	0.76494	0.999	D	0.85130	0.997	T	0.54516	-0.8282	9	.	.	.	-32.6169	6.295	0.21081	0.2692:0.0:0.5783:0.1525	.	694	Q9H4D0	CSTN2_HUMAN	F	694	ENSP00000402460:L694F	.	L	+	3	2	CLSTN2	141763710	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	2.414000	0.44627	0.125000	0.18397	0.533000	0.62120	TTA	.	.		0.498	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		T	140281020	A	T	140281020	3	4	101	1	0	0	0	0	1	0	0	0	3564	417	15	4	2132	4	CLSTN2	3	140281020	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	2061767	140281020	57741410	139	13976										
TFDP2	7029	hgsc.bcm.edu	37	chr3	141678612	141678613	+	Nonsense_Mutation	DNP	CC	CC	AA													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctccaggccaaacgacattcCcatccgctttagtacttcta							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:141678612_141678613CC>AA	ENST00000489671.1	-	11	1384_1385	c.954_955GG>TT	c.(952-957)atGGga>atTTga	p.318_319MG>I*	TFDP2_ENST00000495310.1_Nonsense_Mutation_p.221_222MG>I*|TFDP2_ENST00000317104.7_Nonsense_Mutation_p.242_243MG>I*|TFDP2_ENST00000467072.1_Nonsense_Mutation_p.258_259MG>I*|TFDP2_ENST00000310282.6_Nonsense_Mutation_p.258_259MG>I*|TFDP2_ENST00000499676.2_Nonsense_Mutation_p.258_259MG>I*|TFDP2_ENST00000397991.4_Nonsense_Mutation_p.290_291MG>I*|TFDP2_ENST00000477292.1_Nonsense_Mutation_p.182_183MG>I*|TFDP2_ENST00000479040.1_Nonsense_Mutation_p.257_258MG>I*|TFDP2_ENST00000486111.1_Nonsense_Mutation_p.258_259MG>I*			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	318	DCB2.				gene expression (GO:0010467)|heart development (GO:0007507)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			kidney(1)|upper_aerodigestive_tract(2)	3						AACGACATTCCCATCCGCTTTA	0.421																																					p.G319X|p.M318I		Atlas-SNP	.											.	TFDP2	44	.	0			c.G955T|c.G954T						.																																			SO:0001587	stop_gained	7029	exon11			ACATTCCCATCCG|CATTCCCATCCGC	U18422	CCDS43159.1, CCDS54647.1, CCDS54648.1, CCDS54649.1, CCDS54650.1	3q23	2011-05-24			ENSG00000114126	ENSG00000114126			11751	protein-coding gene	gene with protein product		602160				7784053, 9027491	Standard	NM_001178138		Approved	Dp-2	uc003eun.4	Q14188	OTTHUMG00000164975	ENST00000489671.1:c.954_955delinsAA	chr3.hg19:g.141678612_141678613delinsAA	ENSP00000420616:p.M318_G319delinsI*	61.0	0.0		157.0|159.0	14.0|15.0	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000489671.1	hg19	CCDS54650.1																																																																																			.	.		0.421	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286		AA	141678613	CC	AA	141678612	4	1	101	1	0	0	0	0	0	1	0	0	15813	632	22	3	397	3	TFDP2	3	141678612	Nonsense_Mutation	DNP	CC	TCGA-DD-A1EE-01A-11D-A12Z-10	1397592	141678612	56343818	140	13977										
CPB1	1360	hgsc.bcm.edu	37	chr3	148559613	148559613	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccttttgtttgcaataggttGgcaaagctggacaaaataag	10	6	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:148559613G>A	ENST00000491148.1	+	7	812	c.478G>A	c.(478-480)Ggc>Agc	p.G160S	CPB1_ENST00000282957.4_Missense_Mutation_p.G160S			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	160						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			GCAATAGGTTGGCAAAGCTGG	0.453																																					p.G160S		Atlas-SNP	.											.	CPB1	74	.	0			c.G478A						.						150	138	142					3																	148559613		2203	4300	6503	SO:0001583	missense	1360	exon6			TAGGTTGGCAAAG	AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase B", "tissue carboxypeptidase B", "protaminase"	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.478G>A	chr3.hg19:g.148559613G>A	ENSP00000417222:p.Gly160Ser	98.0	0.0		224.0	21.0	NM_001871	O60834|Q53XJ0|Q96BQ8	Missense_Mutation	SNP	ENST00000491148.1	hg19	CCDS33874.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.958321	0.92726	.	.	ENSG00000153002	ENST00000491148;ENST00000282957;ENST00000468341	T;T;T	0.30714	1.52;1.52;2.89	5.28	5.28	0.74379	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.43523	0.1251	L	0.33668	1.02	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.08848	-1.0702	10	0.09338	T	0.73	.	19.2751	0.94029	0.0:0.0:1.0:0.0	.	160	P15086	CBPB1_HUMAN	S	160;160;126	ENSP00000417222:G160S;ENSP00000282957:G160S;ENSP00000419427:G126S	ENSP00000282957:G160S	G	+	1	0	CPB1	150042303	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.583000	0.74053	2.644000	0.89710	0.655000	0.94253	GGC	.	.		0.453	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871		A	148559613	G	A	148559613	3	1	101	1	0	0	0	0	1	0	0	0	3798	1348	47	3	500	3	CPB1	3	148559613	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6881001	148559613	49462817	141	13978										
SUCNR1	56670	hgsc.bcm.edu	37	chr3	151598552	151598552	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctctgacttagcttttctgtGcaccctccccatgctgataa	6	14	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:151598552G>T	ENST00000362032.5	+	3	326	c.221G>T	c.(220-222)tGc>tTc	p.C74F	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_033050.4	NP_149039.2	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	74						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)	GCTTTTCTGTGCACCCTCCCC	0.423																																					p.C74F		Atlas-SNP	.											.	SUCNR1	31	.	0			c.G221T						.						152	149	150					3																	151598552		2203	4300	6503	SO:0001583	missense	56670	exon3			TTCTGTGCACCCT	AF348078	CCDS3162.1	3q25.1	2012-08-21	2004-07-08	2004-07-09	ENSG00000198829	ENSG00000198829		"GPCR / Class A : Orphans"	4542	protein-coding gene	gene with protein product		606381	"G protein-coupled receptor 91"	GPR91		11273702, 15141213, 17192395	Standard	NM_033050		Approved		uc003ezf.2	Q9BXA5	OTTHUMG00000159880	ENST00000362032.5:c.221G>T	chr3.hg19:g.151598552G>T	ENSP00000355156:p.Cys74Phe	103.0	0.0		305.0	34.0	NM_033050	A8K305|Q8TDQ8	Missense_Mutation	SNP	ENST00000362032.5	hg19	CCDS3162.1	.	.	.	.	.	.	.	.	.	.	G	11.32	1.603049	0.28534	.	.	ENSG00000198829	ENST00000362032	T	0.35789	1.29	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	L	0.33624	1.015	0.47441	D	0.999423	D	0.76494	0.999	D	0.79784	0.993	T	0.39603	-0.9606	10	0.34782	T	0.22	.	19.2413	0.93886	0.0:0.0:1.0:0.0	.	74	Q9BXA5	SUCR1_HUMAN	F	74	ENSP00000355156:C74F	ENSP00000355156:C74F	C	+	2	0	SUCNR1	153081242	1.000000	0.71417	0.999000	0.59377	0.058000	0.15608	4.301000	0.59086	2.625000	0.88918	0.655000	0.94253	TGC	.	.		0.423	SUCNR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357897.2	NM_033050		T	151598552	G	T	151598552	3	4	101	1	0	0	0	0	1	0	0	0	15381	1319	46	3	227	3	SUCNR1	3	151598552	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3038939	151598552	46423878	142	13979										
GMPS	8833	hgsc.bcm.edu	37	chr3	155643090	155643090	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aagaggatcaggagaagctgAtgcaaattaccagtctgcat	11	7	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:155643090A>T	ENST00000496455.2	+	12	1830	c.1495A>T	c.(1495-1497)Atg>Ttg	p.M499L	GMPS_ENST00000295920.7_Missense_Mutation_p.M400L	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase	499					glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|GMP synthase (glutamine-hydrolyzing) activity (GO:0003922)|GMP synthase activity (GO:0003921)|pyrophosphatase activity (GO:0016462)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamine(DB00130)	GGAGAAGCTGATGCAAATTAC	0.408			T	MLL	AML																																p.M499L	Ovarian(153;896 1876 4149 15499 28134)	Atlas-SNP	.		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	.	GMPS	70	.	0			c.A1495T						.						111	111	111					3																	155643090		1913	4133	6046	SO:0001583	missense	8833	exon12			AAGCTGATGCAAA	U10860	CCDS46941.1	3q25.31	2013-06-18	2013-06-18		ENSG00000163655	ENSG00000163655	6.3.5.2		4378	protein-coding gene	gene with protein product	"GMP synthase"	600358	"guanine monphosphate synthetase"			8089153, 9195163	Standard	NM_003875		Approved		uc003faq.3	P49915	OTTHUMG00000158551	ENST00000496455.2:c.1495A>T	chr3.hg19:g.155643090A>T	ENSP00000419851:p.Met499Leu	159.0	0.0		624.0	73.0	NM_003875	A8K639|B4DXV7|F8W720	Missense_Mutation	SNP	ENST00000496455.2	hg19	CCDS46941.1	.	.	.	.	.	.	.	.	.	.	A	12.17	1.858086	0.32791	.	.	ENSG00000163655	ENST00000496455;ENST00000295920;ENST00000537975;ENST00000541628	.	.	.	5.76	4.61	0.57282	GMP synthase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.27933	0.0688	N	0.05306	-0.075	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07616	-1.0763	9	0.09338	T	0.73	-17.9133	11.5552	0.50743	0.9307:0.0:0.0693:0.0	.	400;499	F8W720;P49915	.;GUAA_HUMAN	L	499;400;448;499	.	ENSP00000295920:M400L	M	+	1	0	GMPS	157125784	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.210000	0.95106	1.018000	0.39521	0.533000	0.62120	ATG	.	.		0.408	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351260.2			T	155643090	A	T	155643090	3	4	101	1	0	0	0	0	1	0	0	0	6506	333	12	4	1541	4	GMPS	3	155643090	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	4044538	155643090	42379340	143	13980										
SHOX2	6474	hgsc.bcm.edu	37	chr3	157820591	157820591	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gttccagggtgaaattggtcCgacttcgcctctgcttgatt	11	10	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:157820591C>T	ENST00000425436.3	-	2	456	c.431G>A	c.(430-432)cGg>cAg	p.R144Q	SHOX2_ENST00000554685.1_5'UTR|SHOX2_ENST00000389589.4_Missense_Mutation_p.R168Q|SHOX2_ENST00000490689.2_Missense_Mutation_p.R15Q|SHOX2_ENST00000441443.2_Missense_Mutation_p.R15Q|SHOX2_ENST00000483851.2_Missense_Mutation_p.R144Q	NM_001163678.1|NM_006884.3	NP_001157150.1|NP_006875.2	O60902	SHOX2_HUMAN	short stature homeobox 2	144					cardiac atrium morphogenesis (GO:0003209)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte development (GO:0002063)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|heart development (GO:0007507)|heart valve development (GO:0003170)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of axonogenesis (GO:0050772)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of chondrocyte differentiation (GO:0032330)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(10)|skin(3)|upper_aerodigestive_tract(1)	20			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)			GAAATTGGTCCGACTTCGCCT	0.567																																					p.R168Q		Atlas-SNP	.											.	SHOX2	84	.	0			c.G503A						.						185	150	162					3																	157820591		2203	4300	6503	SO:0001583	missense	6474	exon3			TTGGTCCGACTTC	AJ002368	CCDS33884.1, CCDS43164.1, CCDS33884.2, CCDS54664.1	3q25.32	2011-06-20			ENSG00000168779	ENSG00000168779		"Homeoboxes / PRD class"	10854	protein-coding gene	gene with protein product		602504				9482898, 9466998	Standard	NM_006884		Approved	SHOT, OG12X, OG12	uc003fbs.3	O60902	OTTHUMG00000158755	ENST00000425436.3:c.431G>A	chr3.hg19:g.157820591C>T	ENSP00000398704:p.Arg144Gln	123.0	0.0		218.0	11.0	NM_003030	O60465|O60467|O60903	Missense_Mutation	SNP	ENST00000425436.3	hg19	CCDS43164.1	.	.	.	.	.	.	.	.	.	.	C	36	5.790320	0.96945	.	.	ENSG00000168779;ENSG00000168779;ENSG00000168779;ENSG00000168779;ENSG00000168779;ENSG00000258518	ENST00000425436;ENST00000490689;ENST00000389589;ENST00000313019;ENST00000441443;ENST00000483851	D;D;D;D;D	0.99150	-5.49;-5.49;-5.49;-5.49;-5.49	5.49	5.49	0.81192	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000001	D	0.99664	0.9875	H	0.98833	4.345	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.97110	0.986;0.999;1.0	D	0.97355	0.9966	10	0.87932	D	0	.	19.3594	0.94431	0.0:1.0:0.0:0.0	.	144;168;144	O60902-2;O60902-3;O60902	.;.;SHOX2_HUMAN	Q	168;15;144;15;15;144	ENSP00000398704:R168Q;ENSP00000451888:R15Q;ENSP00000374240:R144Q;ENSP00000397099:R15Q;ENSP00000419362:R144Q	ENSP00000327294:R15Q	R	-	2	0	SHOX2;AC112502.1	159303285	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.576000	0.86940	0.655000	0.94253	CGG	.	.		0.567	SHOX2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352057.2			T	157820591	C	T	157820591	3	4	101	1	0	0	0	0	1	0	0	0	14304	652	23	1	580	1	SHOX2	3	157820591	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2177501	157820591	40201839	144	13981										
SI	6476	hgsc.bcm.edu	37	chr3	164750329	164750329	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cctggttagaagcatcataaGtgaaattggaatgagcgttc	11	6	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:164750329G>A	ENST00000264382.3	-	24	2779	c.2717C>T	c.(2716-2718)aCt>aTt	p.T906I		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	906	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	AGCATCATAAGTGAAATTGGA	0.313										HNSCC(35;0.089)																											p.T906I		Atlas-SNP	.											.	SI	500	.	0			c.C2717T						.						136	132	133					3																	164750329		2202	4300	6502	SO:0001583	missense	6476	exon24			TCATAAGTGAAAT	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.2717C>T	chr3.hg19:g.164750329G>A	ENSP00000264382:p.Thr906Ile	60.0	0.0		115.0	7.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	hg19	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	G	9.509	1.105222	0.20632	.	.	ENSG00000090402	ENST00000264382	T	0.13901	2.55	4.88	1.8	0.24995	.	0.881571	0.10133	N	0.711840	T	0.21347	0.0514	M	0.85197	2.74	0.23930	N	0.996436	B	0.18863	0.031	B	0.16289	0.015	T	0.22591	-1.0212	10	0.72032	D	0.01	.	9.0727	0.36502	0.0:0.4573:0.3861:0.1566	.	906	P14410	SUIS_HUMAN	I	906	ENSP00000264382:T906I	ENSP00000264382:T906I	T	-	2	0	SI	166233023	0.996000	0.38824	0.364000	0.25888	0.701000	0.40568	0.488000	0.22371	0.720000	0.32209	0.655000	0.94253	ACT	.	.		0.313	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		A	164750329	G	A	164750329	3	1	101	1	0	0	0	0	1	0	0	0	14312	1029	36	3	2866	3	SI	3	164750329	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6929738	164750329	33272101	145	13982										
WDR49	151790	hgsc.bcm.edu	37	chr3	167250760	167250760	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tagaacaatttctccatcatAactccctacacaagacagga	4	12	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:167250760A>C	ENST00000308378.3	-	8	1209	c.904T>G	c.(904-906)Tat>Gat	p.Y302D	WDR49_ENST00000453925.2_Missense_Mutation_p.Y366D|WDR49_ENST00000479765.1_Intron|WDR49_ENST00000476376.1_Missense_Mutation_p.Y127D	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	302										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						TCTCCATCATAACTCCCTACA	0.368																																					p.Y302D		Atlas-SNP	.											.	WDR49	188	.	0			c.T904G						.						95	83	87					3																	167250760		2203	4299	6502	SO:0001583	missense	151790	exon8			CATCATAACTCCC	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.904T>G	chr3.hg19:g.167250760A>C	ENSP00000311343:p.Tyr302Asp	56.0	0.0		125.0	41.0	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	hg19	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.803325	0.70682	.	.	ENSG00000174776	ENST00000308378;ENST00000476376;ENST00000453925	T;T;T	0.58797	0.31;0.31;0.31	5.82	5.82	0.92795	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.301359	0.37761	N	0.001953	T	0.68183	0.2973	L	0.42581	1.335	0.37360	D	0.911182	D;D	0.76494	0.998;0.999	D;D	0.73708	0.969;0.981	T	0.69924	-0.5013	10	0.33940	T	0.23	.	15.1777	0.72927	1.0:0.0:0.0:0.0	.	366;302	E7EQK3;Q8IV35	.;WDR49_HUMAN	D	302;127;366	ENSP00000311343:Y302D;ENSP00000420508:Y127D;ENSP00000410863:Y366D	ENSP00000311343:Y302D	Y	-	1	0	WDR49	168733454	1.000000	0.71417	0.998000	0.56505	0.914000	0.54420	5.828000	0.69307	2.228000	0.72767	0.460000	0.39030	TAT	.	.		0.368	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		C	167250760	A	C	167250760	3	2	101	1	0	0	0	0	1	0	0	0	17317	362	13	5	1221	5	WDR49	3	167250760	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	2500431	167250760	30771670	146	13983										
WDR49	151790	hgsc.bcm.edu	37	chr3	167293931	167293931	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tggtgttgaatatcccagagTctcaaaacctggatgaaaag	10	7	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:167293931T>A	ENST00000308378.3	-	4	566	c.261A>T	c.(259-261)agA>agT	p.R87S	WDR49_ENST00000453925.2_Missense_Mutation_p.R140S|WDR49_ENST00000479765.1_Missense_Mutation_p.R428S|WDR49_ENST00000476376.1_5'Flank	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	87										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						TATCCCAGAGTCTCAAAACCT	0.393																																					p.R87S		Atlas-SNP	.											.	WDR49	188	.	0			c.A261T						.						59	57	58					3																	167293931		2203	4300	6503	SO:0001583	missense	151790	exon4			CCAGAGTCTCAAA	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.261A>T	chr3.hg19:g.167293931T>A	ENSP00000311343:p.Arg87Ser	54.0	0.0		115.0	54.0	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	hg19	CCDS3201.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.48|18.48	3.633155|3.633155	0.67015|0.67015	.|.	.|.	ENSG00000174776|ENSG00000174776	ENST00000472600|ENST00000308378;ENST00000479765;ENST00000453925	.|T;T;T	.|0.67345	.|-0.26;-0.26;-0.26	5.76|5.76	3.43|3.43	0.39272|0.39272	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.269257	.|0.42420	.|D	.|0.000709	T|T	0.77054|0.77054	0.4074|0.4074	M|M	0.78049|0.78049	2.395|2.395	0.22366|0.22366	N|N	0.999164|0.999164	.|D;D;D	.|0.69078	.|0.984;0.997;0.981	.|P;D;P	.|0.65140	.|0.896;0.932;0.756	T|T	0.67252|0.67252	-0.5717|-0.5717	5|10	.|0.87932	.|D	.|0	.|.	7.4604|7.4604	0.27291|0.27291	0.0:0.229:0.0:0.771|0.0:0.229:0.0:0.771	.|.	.|140;428;87	.|E7EQK3;E9PDB0;Q8IV35	.|.;.;WDR49_HUMAN	V|S	152|87;428;140	.|ENSP00000311343:R87S;ENSP00000419749:R428S;ENSP00000410863:R140S	.|ENSP00000311343:R87S	D|R	-|-	2|3	0|2	WDR49|WDR49	168776625|168776625	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.810000|0.810000	0.45777|0.45777	0.880000|0.880000	0.28159|0.28159	1.036000|1.036000	0.39998|0.39998	0.529000|0.529000	0.55759|0.55759	GAC|AGA	.	.		0.393	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		A	167293931	T	A	167293931	3	1	101	1	0	0	0	0	1	0	0	0	17317	1664	58	4	1880	4	WDR49	3	167293931	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	43171	167293931	30728499	147	13984										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173322666	173322666	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agccccaccaacaggggaacGtcgttttcagcctccagaac	9	15	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:173322666G>T	ENST00000457714.1	+	3	707	c.278G>T	c.(277-279)cGt>cTt	p.R93L	NLGN1_ENST00000361589.4_Missense_Mutation_p.R93L|NLGN1_ENST00000401917.3_Missense_Mutation_p.R93L|NLGN1_ENST00000545397.1_Missense_Mutation_p.R93L	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	93					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)	p.R93L(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			ACAGGGGAACGTCGTTTTCAG	0.453																																					p.R93L		Atlas-SNP	.											NLGN1,caecum,adenoma,0,3	NLGN1	209	.	2	Substitution - Missense(2)	lung(2)	c.G278T						.						130	129	129					3																	173322666		2203	4300	6503	SO:0001583	missense	22871	exon3			GGGAACGTCGTTT	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.278G>T	chr3.hg19:g.173322666G>T	ENSP00000392500:p.Arg93Leu	86.0	0.0		149.0	20.0	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	hg19	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	G	6.574	0.474179	0.12521	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000415045;ENST00000545397;ENST00000401917	T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3	5.62	3.23	0.37069	.	0.229124	0.34314	N	0.004077	T	0.22666	0.0547	N	0.01410	-0.885	0.32782	N	0.502396	B;B	0.26195	0.004;0.144	B;B	0.18561	0.022;0.016	T	0.16630	-1.0396	10	0.23891	T	0.37	.	6.2449	0.20811	0.6324:0.0:0.3676:0.0	.	93;93	D2X2H5;Q8N2Q7-2	.;.	L	93	ENSP00000392500:R93L;ENSP00000354541:R93L;ENSP00000410374:R93L;ENSP00000441108:R93L;ENSP00000385750:R93L	ENSP00000354541:R93L	R	+	2	0	NLGN1	174805360	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	2.321000	0.43805	1.069000	0.40788	-0.373000	0.07131	CGT	.	.		0.453	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		T	173322666	G	T	173322666	3	4	101	1	0	0	0	0	1	0	0	0	10470	1145	40	1	280	1	NLGN1	3	173322666	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6028735	173322666	24699764	148	13985										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173525610	173525610	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcatcacagtcaactatcgaCttggagtactcggtaagaag	9	9	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:173525610C>A	ENST00000457714.1	+	4	1063	c.634C>A	c.(634-636)Ctt>Att	p.L212I	NLGN1_ENST00000361589.4_Missense_Mutation_p.L212I|NLGN1_ENST00000401917.3_Missense_Mutation_p.L252I|NLGN1_ENST00000545397.1_Missense_Mutation_p.L212I	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	229					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			CAACTATCGACTTGGAGTACT	0.388																																					p.L212I		Atlas-SNP	.											.	NLGN1	209	.	0			c.C634A						.						140	132	135					3																	173525610		2203	4300	6503	SO:0001583	missense	22871	exon4			TATCGACTTGGAG	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.634C>A	chr3.hg19:g.173525610C>A	ENSP00000392500:p.Leu212Ile	74.0	0.0		194.0	17.0	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	hg19	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.987790	0.93106	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000415045;ENST00000545397;ENST00000401917	T;T;T;T;T	0.74947	-0.6;-0.6;-0.89;-0.6;-0.6	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000001	D	0.85128	0.5626	M	0.88377	2.95	0.80722	D	1	P;P	0.50066	0.931;0.605	P;P	0.50934	0.654;0.619	D	0.87424	0.2384	10	0.62326	D	0.03	.	19.6981	0.96039	0.0:1.0:0.0:0.0	.	252;212	D2X2H5;Q8N2Q7-2	.;.	I	212;212;252;212;252	ENSP00000392500:L212I;ENSP00000354541:L212I;ENSP00000410374:L252I;ENSP00000441108:L212I;ENSP00000385750:L252I	ENSP00000354541:L212I	L	+	1	0	NLGN1	175008304	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.085000	0.71343	2.665000	0.90641	0.557000	0.71058	CTT	.	.		0.388	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		A	173525610	C	A	173525610	3	1	101	1	0	0	0	0	1	0	0	0	10470	565	20	3	640	3	NLGN1	3	173525610	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	202944	173525610	24496820	149	13986										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916692	178916692	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcctagtagaatgtttactaCcaaatggaatgatagtgact	8	6	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:178916692C>A	ENST00000263967.3	+	2	236	c.79C>A	c.(79-81)Cca>Aca	p.P27T		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	27	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATGTTTACTACCAAATGGAAT	0.413		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.P27T	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	.	PIK3CA	8460	.	0			c.C79A						.						67	66	66					3																	178916692		1853	4089	5942	SO:0001583	missense	5290	exon2			TTACTACCAAATG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.79C>A	chr3.hg19:g.178916692C>A	ENSP00000263967:p.Pro27Thr	42.0	0.0		143.0	14.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364380	0.82463	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	D;D	0.91740	-1.97;-2.9	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.96516	0.8863	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96326	0.9240	9	.	.	.	-18.5061	19.267	0.93990	0.0:1.0:0.0:0.0	.	27	P42336	PK3CA_HUMAN	T	27	ENSP00000263967:P27T;ENSP00000417479:P27T	.	P	+	1	0	PIK3CA	180399386	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.394000	0.79862	2.616000	0.88540	0.650000	0.86243	CCA	.	.		0.413	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178916692	C	A	178916692	3	1	101	1	0	0	0	0	1	0	0	0	11922	507	18	3	81	3	PIK3CA	3	178916692	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	5391082	178916692	19105738	150	13987										
EIF4A2	1974	hgsc.bcm.edu	37	chr3	186504304	186504304	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttttaaggttgtgttgctttCtgccacaatgccaactgatg	9	8	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:186504304C>T	ENST00000323963.5	+	7	705	c.641C>T	c.(640-642)tCt>tTt	p.S214F	SNORA81_ENST00000408493.2_RNA|SNORA63_ENST00000363450.1_RNA|SNORD2_ENST00000459163.1_RNA|EIF4A2_ENST00000440191.2_Missense_Mutation_p.S215F|RP11-573D15.9_ENST00000577781.1_RNA|SNORA63_ENST00000363548.1_RNA|EIF4A2_ENST00000356531.5_Missense_Mutation_p.S119F|SNORA4_ENST00000584302.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	214	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)	p.S214C(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		GTGTTGCTTTCTGCCACAATG	0.378			T	BCL6	NHL																																p.S214F		Atlas-SNP	.		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	EIF4A2,NS,carcinoma,0,1	EIF4A2	55	.	1	Substitution - Missense(1)	lung(1)	c.C641T						.						102	104	103					3																	186504304		2203	4299	6502	SO:0001583	missense	1974	exon7			TGCTTTCTGCCAC	D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"DEAD-boxes"	3284	protein-coding gene	gene with protein product		601102	"eukaryotic translation initiation factor 4A, isoform 2"	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.641C>T	chr3.hg19:g.186504304C>T	ENSP00000326381:p.Ser214Phe	139.0	0.0		363.0	27.0	NM_001967	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	hg19	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.911871	0.72983	.	.	ENSG00000156976	ENST00000323963;ENST00000440191;ENST00000356531	T;T;T	0.12774	2.65;2.65;2.65	5.13	5.13	0.70059	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.56688	0.2002	H	0.98786	4.33	0.80722	D	1	D;D;D;D	0.76494	0.995;0.999;0.999;0.999	D;D;D;D	0.79108	0.943;0.992;0.946;0.968	T	0.74763	-0.3555	10	0.87932	D	0	-27.6825	16.4642	0.84073	0.0:1.0:0.0:0.0	.	70;119;215;214	B4DJX6;Q9NZE6;Q14240-2;Q14240	.;.;.;IF4A2_HUMAN	F	214;215;119	ENSP00000326381:S214F;ENSP00000398370:S215F;ENSP00000348925:S119F	ENSP00000326381:S214F	S	+	2	0	EIF4A2	187986998	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.075000	0.76798	2.827000	0.97445	0.650000	0.86243	TCT	.	.		0.378	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		T	186504304	C	T	186504304	3	4	101	1	0	0	0	0	1	0	0	0	5027	913	32	3	667	3	EIF4A2	3	186504304	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	7587612	186504304	11518126	151	13988										
C3orf59	151963	hgsc.bcm.edu	37	chr3	192516472	192516472	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agcttccgggcgtgaagcatGactgtctcctcagacagatg	12	11	2	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:192516472G>T	ENST00000392452.2	-	2	1499	c.1179C>A	c.(1177-1179)gtC>gtA	p.V393V		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	393							protein complex binding (GO:0032403)			endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						CGTGAAGCATGACTGTCTCCT	0.562																																					p.V393V		Atlas-SNP	.											.	MB21D2	75	.	0			c.C1179A						.						58	48	51					3																	192516472		2203	4300	6503	SO:0001819	synonymous_variant	151963	exon2			AAGCATGACTGTC	AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 59"	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.1179C>A	chr3.hg19:g.192516472G>T		23.0	0.0		42.0	20.0	NM_178496	Q86VD8	Silent	SNP	ENST00000392452.2	hg19	CCDS3302.2																																																																																			.	.		0.562	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496		T	192516472	G	T	192516472	2	4	101	1	0	0	0	0	0	0	0	1	2239	1277	45	3		3	C3orf59	3	192516472	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6012168	192516472	5505958	152	13989										
ZDHHC19	131540	hgsc.bcm.edu	37	chr3	195935366	195935366	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cacagggacaggacaagcagCatgaagaagcggaagttgcg	15	8	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr3:195935366C>T	ENST00000296326.3	-	4	553	c.474G>A	c.(472-474)atG>atA	p.M158I	ZDHHC19_ENST00000488508.1_5'UTR	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	158						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		GGACAAGCAGCATGAAGAAGC	0.597																																					p.M158I		Atlas-SNP	.											.	ZDHHC19	25	.	0			c.G474A						.						126	146	139					3																	195935366		2192	4282	6474	SO:0001583	missense	131540	exon4			AAGCAGCATGAAG	BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958		"Zinc fingers, DHHC-type"	20713	protein-coding gene	gene with protein product							Standard	XR_246038		Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.474G>A	chr3.hg19:g.195935366C>T	ENSP00000296326:p.Met158Ile	78.0	0.0		241.0	30.0	NM_001039617	A8MSY6|B3KVI1	Missense_Mutation	SNP	ENST00000296326.3	hg19	CCDS43190.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485295	0.63962	.	.	ENSG00000163958	ENST00000296326	T	0.20881	2.04	5.61	4.68	0.58851	Zinc finger, DHHC-type, palmitoyltransferase (2);	0.368313	0.26635	N	0.023291	T	0.11324	0.0276	N	0.11845	0.185	0.31438	N	0.672257	P	0.35656	0.514	B	0.31016	0.123	T	0.06427	-1.0827	10	0.48119	T	0.1	-23.8633	11.6545	0.51309	0.0:0.8214:0.1786:0.0	.	158	Q8WVZ1	ZDH19_HUMAN	I	158	ENSP00000296326:M158I	ENSP00000296326:M158I	M	-	3	0	ZDHHC19	197419763	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.782000	0.47758	2.638000	0.89438	0.561000	0.74099	ATG	.	.		0.597	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341533.1	NM_144637		T	195935366	C	T	195935366	3	4	101	1	0	0	0	0	1	0	0	0	17624	710	25	3	471	3	ZDHHC19	3	195935366	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3418894	195935366	2087064	153	13990										
WHSC1	7468	hgsc.bcm.edu	37	chr4	1957858	1957858	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gagtgttcccgtacatggagGgggaccggggcagccgctac	17	11	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:1957858G>T	ENST00000382895.3	+	17	3255	c.2824G>T	c.(2824-2826)Ggg>Tgg	p.G942W	WHSC1_ENST00000508803.1_Missense_Mutation_p.G942W|WHSC1_ENST00000382892.2_Missense_Mutation_p.G942W|WHSC1_ENST00000382888.3_Missense_Mutation_p.G290W|WHSC1_ENST00000382891.5_Missense_Mutation_p.G942W|WHSC1_ENST00000482415.2_3'UTR	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	942	PWWP 2. {ECO:0000255|PROSITE- ProRule:PRU00162}.				anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		GTACATGGAGGGGGACCGGGG	0.512			T	IGH@	MM																																p.G942W		Atlas-SNP	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.G2824T						.						79	98	91					4																	1957858		2203	4300	6503	SO:0001583	missense	7468	exon15			ATGGAGGGGGACC	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"Zinc fingers, PHD-type"	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.2824G>T	chr4.hg19:g.1957858G>T	ENSP00000372351:p.Gly942Trp	42.0	0.0		180.0	14.0	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	hg19	CCDS33940.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.3|24.3	4.517268|4.517268	0.85495|0.85495	.|.	.|.	ENSG00000109685|ENSG00000109685	ENST00000514329|ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895;ENST00000382888	.|T;T;T;T;T	.|0.33438	.|1.41;1.41;1.41;1.41;1.41	5.76|5.76	4.92|4.92	0.64577|0.64577	.|PWWP (2);	0.101187|0.101187	0.43919|0.43919	D|D	0.000517|0.000517	T|T	0.60104|0.60104	0.2243|0.2243	M|M	0.85197|0.85197	2.74|2.74	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.995;0.999	T|T	0.67803|0.67803	-0.5576|-0.5576	6|10	.|0.87932	.|D	.|0	.|.	14.6702|14.6702	0.68937|0.68937	0.0696:0.0:0.9304:0.0|0.0696:0.0:0.9304:0.0	.|.	.|290;942	.|A2A2T2;O96028	.|.;NSD2_HUMAN	V|W	265|942;942;942;942;290	.|ENSP00000423972:G942W;ENSP00000372347:G942W;ENSP00000372348:G942W;ENSP00000372351:G942W;ENSP00000372344:G290W	.|ENSP00000372344:G290W	G|G	+|+	2|1	0|0	WHSC1|WHSC1	1927656|1927656	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.661000|9.661000	0.98601|0.98601	1.432000|1.432000	0.47375|0.47375	0.655000|0.655000	0.94253|0.94253	GGG|GGG	.	.		0.512	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		T	1957858	G	T	1957858	3	4	101	1	0	0	0	0	1	0	0	0	17377	1232	43	3	2954	3	WHSC1	4	1957858	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10		1957858	189196418	154	13991										
FAM193A	8603	hgsc.bcm.edu	37	chr4	2717767	2717767	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagatgatgtctttctacctAaagatattgacctagacagt	7	8	2	5			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:2717767A>G	ENST00000324666.5	+	19	3991	c.3640A>G	c.(3640-3642)Aaa>Gaa	p.K1214E	FAM193A_ENST00000505311.1_Missense_Mutation_p.K1173E|FAM193A_ENST00000502458.1_Missense_Mutation_p.K1195E|FAM193A_ENST00000382839.3_Missense_Mutation_p.K1173E|FAM193A_ENST00000545951.1_Missense_Mutation_p.K1173E	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	1214										NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						CTTTCTACCTAAAGATATTGA	0.408																																					p.K1214E		Atlas-SNP	.											.	FAM193A	103	.	0			c.A3640G						.						207	196	200					4																	2717767		2203	4300	6503	SO:0001583	missense	8603	exon19			CTACCTAAAGATA	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 8"	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.3640A>G	chr4.hg19:g.2717767A>G	ENSP00000324587:p.Lys1214Glu	147.0	0.0		187.0	74.0	NM_001256666	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	hg19	CCDS58875.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.638692	0.87760	.	.	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458	T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.81588	0.4854	L	0.42245	1.32	0.80722	D	1	D;P;D;D;D	0.76494	0.992;0.855;0.999;0.999;0.998	D;P;D;D;D	0.87578	0.984;0.615;0.998;0.997;0.998	T	0.82855	-0.0251	10	0.59425	D	0.04	-23.2818	14.4897	0.67642	1.0:0.0:0.0:0.0	.	1173;1195;1214;1195;1173	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	E	1173;1214;1173;1195	ENSP00000372290:K1173E;ENSP00000324587:K1214E;ENSP00000443617:K1173E;ENSP00000427505:K1195E	ENSP00000324587:K1214E	K	+	1	0	FAM193A	2687565	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.011000	0.88624	2.105000	0.64084	0.482000	0.46254	AAA	.	.		0.408	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		G	2717767	A	G	2717767	3	3	101	1	0	0	0	0	1	0	0	0	5529	363	13	2	3579	2	FAM193A	4	2717767	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	759909	2717767	188436509	155	13992										
HS3ST1	9957	hgsc.bcm.edu	37	chr4	11400952	11400952	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctctcgaccttttggatctcAgggaaggggtccctgatgag	13	10	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:11400952A>T	ENST00000002596.5	-	2	1852	c.678T>A	c.(676-678)ccT>ccA	p.P226P		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	226					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						TTTGGATCTCAGGGAAGGGGT	0.552																																					p.P226P		Atlas-SNP	.											.	HS3ST1	41	.	0			c.T678A						.						35	36	36					4																	11400952		2203	4300	6503	SO:0001819	synonymous_variant	9957	exon2			GATCTCAGGGAAG	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"Sulfotransferases, membrane-bound"	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.678T>A	chr4.hg19:g.11400952A>T		19.0	0.0		66.0	34.0	NM_005114	B3KUA6|Q6PEY8	Silent	SNP	ENST00000002596.5	hg19	CCDS3408.1																																																																																			.	.		0.552	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114		T	11400952	A	T	11400952	2	4	101	1	0	0	0	0	0	0	0	1	7372	175	7	4		4	HS3ST1	4	11400952	Silent	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	8683185	11400952	179753324	156	13993										
CD38	952	hgsc.bcm.edu	37	chr4	15839760	15839760	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tccatgtgatgctcaatggaTcccgcagtaaaatctttgac	8	10	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:15839760T>C	ENST00000226279.3	+	5	768	c.631T>C	c.(631-633)Tcc>Ccc	p.S211P		NM_001775.2	NP_001766.2	P28907	CD38_HUMAN	CD38 molecule	211					apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|female pregnancy (GO:0007565)|long term synaptic depression (GO:0060292)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone resorption (GO:0045779)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hydroperoxide (GO:0033194)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|phosphorus-oxygen lyase activity (GO:0016849)|transferase activity (GO:0016740)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|stomach(1)	14						GCTCAATGGATCCCGCAGTAA	0.383																																					p.S211P		Atlas-SNP	.											.	CD38	36	.	0			c.T631C						.						143	133	136					4																	15839760		2203	4300	6503	SO:0001583	missense	952	exon5			AATGGATCCCGCA	D84276	CCDS3417.1	4p15.32	2010-05-04	2006-03-28		ENSG00000004468	ENSG00000004468	3.2.2.5	"CD molecules"	1667	protein-coding gene	gene with protein product	"ADP-ribosyl cyclase 1", "NAD(+) nucleosidase"	107270	"CD38 antigen (p45)"			9074508, 2319135	Standard	NM_001775		Approved		uc003gol.1	P28907	OTTHUMG00000048206	ENST00000226279.3:c.631T>C	chr4.hg19:g.15839760T>C	ENSP00000226279:p.Ser211Pro	53.0	0.0		86.0	11.0	NM_001775	O00121|O00122|Q96HY4	Missense_Mutation	SNP	ENST00000226279.3	hg19	CCDS3417.1	.	.	.	.	.	.	.	.	.	.	T	13.69	2.312152	0.40895	.	.	ENSG00000004468	ENST00000226279;ENST00000510674	T;T	0.53857	0.6;0.6	5.4	5.4	0.78164	NAD(P)-binding domain (1);	0.112478	0.64402	D	0.000007	T	0.74703	0.3751	M	0.87381	2.88	0.40730	D	0.982734	D	0.89917	1.0	D	0.91635	0.999	T	0.80169	-0.1494	10	0.87932	D	0	-28.9521	12.0932	0.53739	0.0:0.0:0.0:1.0	.	211	P28907	CD38_HUMAN	P	211;99	ENSP00000226279:S211P;ENSP00000423047:S99P	ENSP00000226279:S211P	S	+	1	0	CD38	15448858	0.010000	0.17322	0.355000	0.25773	0.161000	0.22273	0.907000	0.28531	2.178000	0.69098	0.533000	0.62120	TCC	.	.		0.383	CD38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250322.2	NM_001775		C	15839760	T	C	15839760	3	2	101	1	0	0	0	0	1	0	0	0	3011	1435	50	2	649	2	CD38	4	15839760	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	4438808	15839760	175314516	157	13994										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30724910	30724910	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atccccgtgctgcagggcagCactacggtgattgtgcaggt	14	11	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:30724910C>A	ENST00000361762.2	+	1	2874	c.1866C>A	c.(1864-1866)agC>agA	p.S622R	PCDH7_ENST00000543491.1_Missense_Mutation_p.S622R	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	622	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						TGCAGGGCAGCACTACGGTGA	0.488																																					p.S622R		Atlas-SNP	.											.	PCDH7	215	.	0			c.C1866A						.						92	97	95					4																	30724910		2203	4300	6503	SO:0001583	missense	5099	exon1			GGGCAGCACTACG	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1866C>A	chr4.hg19:g.30724910C>A	ENSP00000355243:p.Ser622Arg	32.0	0.0		100.0	18.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.82|13.82	2.352629|2.352629	0.41700|0.41700	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000511884|ENST00000361762;ENST00000543491;ENST00000333135	.|T;T	.|0.50813	.|0.73;0.73	5.37|5.37	3.65|3.65	0.41850|0.41850	.|Cadherin (5);Cadherin-like (1);	.|.	.|.	.|.	.|.	T|T	0.45054|0.45054	0.1323|0.1323	N|N	0.25957|0.25957	0.775|0.775	0.48975|0.48975	D|D	0.99973|0.99973	.|D;D;P	.|0.55800	.|0.973;0.973;0.872	.|P;P;P	.|0.55871	.|0.786;0.786;0.756	T|T	0.41342|0.41342	-0.9514|-0.9514	5|9	.|0.72032	.|D	.|0.01	.|.	6.8325|6.8325	0.23917|0.23917	0.1414:0.7145:0.0:0.1441|0.1414:0.7145:0.0:0.1441	.|.	.|622;575;622	.|F5GWJ1;O60245-3;O60245	.|.;.;PCDH7_HUMAN	N|R	312|622;622;575	.|ENSP00000355243:S622R;ENSP00000441802:S622R	.|ENSP00000330302:S575R	H|S	+|+	1|3	0|2	PCDH7|PCDH7	30334008|30334008	0.845000|0.845000	0.29573|0.29573	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	-0.058000|-0.058000	0.11750|0.11750	0.839000|0.839000	0.34971|0.34971	0.655000|0.655000	0.94253|0.94253	CAC|AGC	.	.		0.488	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		A	30724910	C	A	30724910	3	1	101	1	0	0	0	0	1	0	0	0	11525	709	25	3	1868	3	PCDH7	4	30724910	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	14885150	30724910	160429366	158	13995										
RFC1	5981	hgsc.bcm.edu	37	chr4	39310299	39310299	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctcttttgccagtttcggagCcagcgtaggagtttgttggc	13	9	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:39310299C>A	ENST00000381897.1	-	13	1975	c.1842G>T	c.(1840-1842)tgG>tgT	p.W614C	RFC1_ENST00000349703.2_Missense_Mutation_p.W614C	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	614					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						AGTTTCGGAGCCAGCGTAGGA	0.428																																					p.W614C	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.G1842T						.						159	166	164					4																	39310299		2203	4300	6503	SO:0001583	missense	5981	exon13			TCGGAGCCAGCGT	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.1842G>T	chr4.hg19:g.39310299C>A	ENSP00000371321:p.Trp614Cys	139.0	0.0		352.0	33.0	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	hg19	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611366	0.87258	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.17854	2.25;2.25	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.54398	0.1856	M	0.90922	3.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62548	-0.6831	10	0.87932	D	0	-6.9473	20.3053	0.98627	0.0:1.0:0.0:0.0	.	614;614	P35251;P35251-2	RFC1_HUMAN;.	C	614	ENSP00000371321:W614C;ENSP00000261424:W614C	ENSP00000261424:W614C	W	-	3	0	RFC1	38986694	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.502000	0.81614	2.808000	0.96608	0.655000	0.94253	TGG	.	.		0.428	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		A	39310299	C	A	39310299	3	1	101	1	0	0	0	0	1	0	0	0	13259	740	26	3	1653	3	RFC1	4	39310299	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	8585389	39310299	151843977	159	13996										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46053503	46053503	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcctttttggttgctggtaaAataatgcaaggttccatatt	8	6	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:46053503A>T	ENST00000295452.4	-	8	1236	c.1069T>A	c.(1069-1071)Ttt>Att	p.F357I		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	357					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTGCTGGTAAAATAATGCAAG	0.323																																					p.F357I		Atlas-SNP	.											.	GABRG1	172	.	0			c.T1069A						.						77	71	73					4																	46053503		2203	4299	6502	SO:0001583	missense	2565	exon8			TGGTAAAATAATG	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.1069T>A	chr4.hg19:g.46053503A>T	ENSP00000295452:p.Phe357Ile	79.0	0.0		80.0	31.0	NM_173536	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.875245	0.91664	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	D	0.85339	-1.97	5.64	5.64	0.86602	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.84252	0.5431	N	0.20807	0.61	0.58432	D	0.999994	P	0.52316	0.952	P	0.57720	0.826	D	0.83888	0.0283	10	0.33141	T	0.24	.	15.0509	0.71867	1.0:0.0:0.0:0.0	.	357	Q8N1C3	GBRG1_HUMAN	I	357	ENSP00000295452:F357I	ENSP00000295452:F357I	F	-	1	0	GABRG1	45748260	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	8.962000	0.93254	2.152000	0.67230	0.533000	0.62120	TTT	.	.		0.323	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		T	46053503	A	T	46053503	3	4	101	1	0	0	0	0	1	0	0	0	6179	14	1	4	336	4	GABRG1	4	46053503	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	6743204	46053503	145100773	160	13997										
GABRA2	2555	hgsc.bcm.edu	37	chr4	46390679	46390679	+	Frame_Shift_Del	DEL	A	A	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gggtcccacaccaagaaaacAaaaagcaggaactgcatgtt							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:46390679delA	ENST00000510861.1	-	2	218	c.45delT	c.(43-45)tttfs	p.F15fs	RP11-436F23.1_ENST00000502455.1_RNA|GABRA2_ENST00000381620.4_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000507460.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000540012.1_5'UTR|GABRA2_ENST00000507069.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000356504.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000509716.1_5'UTR|GABRA2_ENST00000515082.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000514090.1_Frame_Shift_Del_p.F15fs			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	15					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	CCAAGAAAACAAAAAGCAGGA	0.373																																					p.V16fs		Atlas-Indel,Pindel	.											.	GABRA2	134	.	0			c.46delG						.						157	155	156					4																	46390679		2203	4300	6503	SO:0001589	frameshift_variant	2555	exon1			.		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.45delT	chr4.hg19:g.46390679delA	ENSP00000421828:p.Phe15fs	143.0	0.0		499.0	38.0	NM_001114175	A8K0U7|B7Z1H8|Q59G14	Frame_Shift_Del	DEL	ENST00000510861.1	hg19	CCDS3471.1																																																																																			.	.		0.373	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			-	46390679	A	-	46390679	7	5	101	1	0	1	0	1	0	0	0	0	6169	127	5	0	1346	0	GABRA2	4	46390679	Frame_Shift_Del	DEL	A	TCGA-DD-A1EE-01A-11D-A12Z-10	337176	46390679	144763597	161	13998	59	2								
GABRA2	2555	hgsc.bcm.edu	37	chr4	46390684	46390684	+	Missense_Mutation	SNP	G	G	T													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccacaccaagaaaacaaaaaGcaggaactgcatgttgtaga							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:46390684G>T	ENST00000510861.1	-	2	213	c.40C>A	c.(40-42)Ctt>Att	p.L14I	RP11-436F23.1_ENST00000502455.1_RNA|GABRA2_ENST00000381620.4_Missense_Mutation_p.L14I|GABRA2_ENST00000507460.1_Missense_Mutation_p.L14I|GABRA2_ENST00000540012.1_5'UTR|GABRA2_ENST00000507069.1_Missense_Mutation_p.L14I|GABRA2_ENST00000356504.1_Missense_Mutation_p.L14I|GABRA2_ENST00000509716.1_5'UTR|GABRA2_ENST00000515082.1_Missense_Mutation_p.L14I|GABRA2_ENST00000514090.1_Missense_Mutation_p.L14I			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	14					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	AAAACAAAAAGCAGGAACTGC	0.378																																					p.L14I		Atlas-SNP	.											.	GABRA2	134	.	0			c.C40A						.						159	157	158					4																	46390684		2203	4300	6503	SO:0001583	missense	2555	exon2			CAAAAAGCAGGAA		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.40C>A	chr4.hg19:g.46390684G>T	ENSP00000421828:p.Leu14Ile	142.0	0.0		490.0	38.0	NM_000807	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	hg19	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.315639	0.60524	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000507069;ENST00000515082;ENST00000503806;ENST00000506961;ENST00000507460	T;T;T;T;T;D;T;T	0.81908	-1.34;-1.34;-1.34;-1.34;-1.49;-1.55;-1.17;-1.17	5.0	5.0	0.66597	.	1.271310	0.05211	N	0.506821	D	0.87621	0.6223	N	0.24115	0.695	0.26319	N	0.9777	D;P;P	0.67145	0.996;0.927;0.458	D;D;P	0.80764	0.994;0.953;0.745	T	0.79650	-0.1715	10	0.72032	D	0.01	.	15.9563	0.79889	0.0:0.0:1.0:0.0	.	14;14;14	D6RAA9;G5E9Z6;P47869	.;.;GBRA2_HUMAN	I	14	ENSP00000421828:L14I;ENSP00000421300:L14I;ENSP00000371033:L14I;ENSP00000348897:L14I;ENSP00000427603:L14I;ENSP00000423840:L14I;ENSP00000424362:L14I;ENSP00000424093:L14I	ENSP00000348897:L14I	L	-	1	0	GABRA2	46085441	0.998000	0.40836	0.269000	0.24586	0.582000	0.36321	2.893000	0.48633	2.746000	0.94184	0.561000	0.74099	CTT	.	.		0.378	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			T	46390684	G	T	46390684	3	4	101	1	0	0	0	0	1	0	0	0	6169	971	34	3	1351	3	GABRA2	4	46390684	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	5	46390684	144763592	162	13999	59	2								
GABRA4	2557	hgsc.bcm.edu	37	chr4	46930408	46930408	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccgatggaggaggagtagctGacaacttcccagtagcccct	12	12	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:46930408G>T	ENST00000264318.3	-	9	2481	c.1499C>A	c.(1498-1500)tCa>tAa	p.S500*		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	500					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	AGGAGTAGCTGACAACTTCCC	0.468																																					p.S500X	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											.	GABRA4	129	.	0			c.C1499A						.						166	155	158					4																	46930408		2203	4300	6503	SO:0001587	stop_gained	2557	exon9			GTAGCTGACAACT		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4078	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 4"	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.1499C>A	chr4.hg19:g.46930408G>T	ENSP00000264318:p.Ser500*	101.0	0.0		230.0	18.0	NM_000809	Q8IYR7	Nonsense_Mutation	SNP	ENST00000264318.3	hg19	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	G	42	9.806889	0.99268	.	.	ENSG00000109158	ENST00000264318	.	.	.	5.82	5.82	0.92795	.	1.208420	0.05585	N	0.573544	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	17.2702	0.87099	0.0:0.0:1.0:0.0	.	.	.	.	X	500	.	ENSP00000264318:S500X	S	-	2	0	GABRA4	46625165	1.000000	0.71417	0.016000	0.15963	0.002000	0.02628	5.713000	0.68415	2.765000	0.95021	0.650000	0.86243	TCA	.	.		0.468	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			T	46930408	G	T	46930408	4	4	101	1	0	0	0	0	0	1	0	0	6171	1294	45	3	169	3	GABRA4	4	46930408	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	539724	46930408	144223868	163	14000										
EXOC1	55763	hgsc.bcm.edu	37	chr4	56750089	56750089	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cacaactaaagaaagcaagaAgtttggtaagcttaggcatg	10	6	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:56750089A>C	ENST00000381295.2	+	10	1673	c.1325A>C	c.(1324-1326)aAg>aCg	p.K442T	EXOC1_ENST00000346134.7_Missense_Mutation_p.K442T|RNU6-652P_ENST00000365488.1_RNA|EXOC1_ENST00000349598.6_Missense_Mutation_p.K442T	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	442					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					GAAAGCAAGAAGTTTGGTAAG	0.318																																					p.K442T		Atlas-SNP	.											.	EXOC1	103	.	0			c.A1325C						.						60	63	62					4																	56750089		2203	4299	6502	SO:0001583	missense	55763	exon10			GCAAGAAGTTTGG	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"SEC3-like 1 (S. cerevisiae)"	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.1325A>C	chr4.hg19:g.56750089A>C	ENSP00000370695:p.Lys442Thr	146.0	0.0		430.0	44.0	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	hg19	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	A	14.79	2.640414	0.47153	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.91	5.91	0.95273	.	0.041576	0.85682	D	0.000000	T	0.51449	0.1675	L	0.32530	0.975	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.46176	-0.9210	9	0.16896	T	0.51	.	16.3432	0.83101	1.0:0.0:0.0:0.0	.	442;442	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	T	442	.	ENSP00000326514:K442T	K	+	2	0	EXOC1	56444846	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.962000	0.93254	2.263000	0.75096	0.377000	0.23210	AAG	.	.		0.318	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		C	56750089	A	C	56750089	3	2	101	1	0	0	0	0	1	0	0	0	5303	72	3	5	1359	5	EXOC1	4	56750089	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	9819681	56750089	134404187	164	14001										
CEP135	9662	hgsc.bcm.edu	37	chr4	56846403	56846403	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaaatatatggaagatatacAgtccaatgttaaattattga	6	3	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:56846403A>T	ENST00000257287.4	+	12	1692	c.1568A>T	c.(1567-1569)cAg>cTg	p.Q523L		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	523					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					GAAGATATACAGTCCAATGTT	0.289																																					p.Q523L		Atlas-SNP	.											.	CEP135	115	.	0			c.A1568T						.						71	74	73					4																	56846403		2203	4296	6499	SO:0001583	missense	9662	exon12			ATATACAGTCCAA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.1568A>T	chr4.hg19:g.56846403A>T	ENSP00000257287:p.Gln523Leu	129.0	0.0		401.0	24.0	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	hg19	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.387832	0.82902	.	.	ENSG00000174799	ENST00000257287	T	0.57273	0.41	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.73187	0.3555	M	0.78801	2.425	0.58432	D	0.999995	D	0.89917	1.0	D	0.80764	0.994	T	0.74553	-0.3627	10	0.46703	T	0.11	.	16.2813	0.82687	1.0:0.0:0.0:0.0	.	523	Q66GS9	CP135_HUMAN	L	523	ENSP00000257287:Q523L	ENSP00000257287:Q523L	Q	+	2	0	CEP135	56541160	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.121000	0.71602	2.244000	0.73946	0.533000	0.62120	CAG	.	.		0.289	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		T	56846403	A	T	56846403	3	4	101	1	0	0	0	0	1	0	0	0	3249	188	7	4	1610	4	CEP135	4	56846403	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	96314	56846403	134307873	165	14002										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62849309	62849309	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agtagactacaggagttatgGaacagataaagtgtaagttt	11	3	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:62849309G>T	ENST00000514591.1	+	18	3349	c.3020G>T	c.(3019-3021)gGa>gTa	p.G1007V	LPHN3_ENST00000545650.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000514157.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000514996.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000506746.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000508946.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000506720.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000509896.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000506700.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000507164.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000512091.2_Missense_Mutation_p.G1007V|LPHN3_ENST00000507625.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000511324.1_Missense_Mutation_p.G1075V|LPHN3_ENST00000504896.1_Missense_Mutation_p.G1007V|LPHN3_ENST00000508693.1_Missense_Mutation_p.G1075V			Q9HAR2	LPHN3_HUMAN	latrophilin 3	994					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						AGGAGTTATGGAACAGATAAA	0.383																																					p.G1007V		Atlas-SNP	.											.	LPHN3	800	.	0			c.G3020T						.						179	172	174					4																	62849309		1865	4120	5985	SO:0001583	missense	23284	exon16			GTTATGGAACAGA	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.3020G>T	chr4.hg19:g.62849309G>T	ENSP00000422533:p.Gly1007Val	80.0	0.0		254.0	22.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.5|25.5	4.645391|4.645391	0.87859|0.87859	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996|ENST00000502815	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.47869|.	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83|.	5.82|5.82	5.82|5.82	0.92795|0.92795	GPCR, family 2-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84270|0.84270	0.5435|0.5435	M|M	0.86502|0.86502	2.82|2.82	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	D|D	0.85057|0.85057	0.0932|0.0932	10|5	0.87932|.	D|.	0|.	.|.	20.099|20.099	0.97865|0.97865	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1007;994;1007|.	E9PE04;Q9HAR2;Q9HAR2-2|.	.;LPHN3_HUMAN;.|.	V|C	1007;1007;1075;1075;1007;1007;994;1007;1075;1075;1075;1007;1007;1007;1075;1075;1007|464	ENSP00000423388:G1007V;ENSP00000422533:G1007V;ENSP00000423787:G1075V;ENSP00000425033:G1075V;ENSP00000424120:G1007V;ENSP00000439831:G1007V;ENSP00000421476:G1075V;ENSP00000424030:G1075V;ENSP00000421372:G1075V;ENSP00000425201:G1007V;ENSP00000423434:G1007V;ENSP00000421627:G1007V;ENSP00000420931:G1075V;ENSP00000425884:G1075V;ENSP00000424258:G1007V|.	ENSP00000280009:G1007V|.	G|W	+|+	2|3	0|0	LPHN3|LPHN3	62531904|62531904	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	9.869000|9.869000	0.99810|0.99810	2.752000|2.752000	0.94435|0.94435	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.	.		0.383	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			T	62849309	G	T	62849309	3	4	101	1	0	0	0	0	1	0	0	0	8926	1174	41	3	3082	3	LPHN3	4	62849309	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6002906	62849309	128304967	166	14003										
TECRL	253017	hgsc.bcm.edu	37	chr4	65240898	65240898	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tataaaacttacatgctttgTgaaacttttgcttaacatca	4	7	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:65240898T>C	ENST00000381210.3	-	2	388	c.278A>G	c.(277-279)cAc>cGc	p.H93R	TECRL_ENST00000507440.1_Missense_Mutation_p.H93R	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	93					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(2)|kidney(5)|large_intestine(7)|lung(30)|prostate(1)|skin(1)|stomach(1)	47						ACATGCTTTGTGAAACTTTTG	0.234																																					p.H93R		Atlas-SNP	.											.	TECRL	106	.	0			c.A278G						.						9	10	10					4																	65240898		2077	4122	6199	SO:0001583	missense	253017	exon2			GCTTTGTGAAACT	AL833108	CCDS33990.1	4q13.1	2009-07-21			ENSG00000205678	ENSG00000205678			27365	protein-coding gene	gene with protein product	"glycoprotein, synaptic 2-like"					12477932	Standard	NM_001010874		Approved	GPSN2L, SRD5A2L2, DKFZp313D0829, DKFZp313B2333, TERL	uc003hcv.3	Q5HYJ1	OTTHUMG00000160680	ENST00000381210.3:c.278A>G	chr4.hg19:g.65240898T>C	ENSP00000370607:p.His93Arg	103.0	0.0		209.0	68.0	NM_001010874		Missense_Mutation	SNP	ENST00000381210.3	hg19	CCDS33990.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.053500	0.36181	.	.	ENSG00000205678	ENST00000507440;ENST00000381210;ENST00000509536	T;T;T	0.41758	0.99;0.99;0.99	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.65460	0.2693	M	0.87097	2.86	0.46749	D	0.999181	D;D	0.69078	0.997;0.995	D;P	0.63793	0.918;0.878	T	0.70633	-0.4818	10	0.52906	T	0.07	-5.0281	12.1533	0.54062	0.0:0.0:0.0:1.0	.	93;93	Q6IN47;Q5HYJ1	.;TECRL_HUMAN	R	93	ENSP00000426043:H93R;ENSP00000370607:H93R;ENSP00000422497:H93R	ENSP00000370607:H93R	H	-	2	0	TECRL	64923493	1.000000	0.71417	1.000000	0.80357	0.539000	0.34962	4.204000	0.58460	2.131000	0.65755	0.477000	0.44152	CAC	.	.		0.234	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874		C	65240898	T	C	65240898	3	2	101	1	0	0	0	0	1	0	0	0	15761	1696	59	2	857	2	TECRL	4	65240898	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2391589	65240898	125913378	167	14004										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66218783	66218783	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caaaaatgtatctaaagagcCattctccatatactctgtca	4	10	4	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:66218783C>T	ENST00000273854.3	-	13	2875	c.2275G>A	c.(2275-2277)Ggc>Agc	p.G759S	EPHA5_ENST00000511294.1_Missense_Mutation_p.G760S|EPHA5_ENST00000432638.2_Missense_Mutation_p.G596S|EPHA5_ENST00000354839.4_Missense_Mutation_p.G737S	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	759	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						TCTAAAGAGCCATTCTCCATA	0.358										TSP Lung(17;0.13)																											p.G759S		Atlas-SNP	.											.	EPHA5	315	.	0			c.G2275A						.						113	103	107					4																	66218783		2203	4300	6503	SO:0001583	missense	2044	exon13			AAGAGCCATTCTC	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.2275G>A	chr4.hg19:g.66218783C>T	ENSP00000273854:p.Gly759Ser	95.0	0.0		211.0	98.0	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	hg19	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	C	36	5.674796	0.96764	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	D;D;D;D	0.89746	-2.56;-2.56;-2.56;-2.56	5.73	5.73	0.89815	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.104377	0.42294	D	0.000735	D	0.96411	0.8829	H	0.94306	3.52	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96959	0.9700	10	0.87932	D	0	.	19.907	0.97012	0.0:1.0:0.0:0.0	.	738;760;737;759	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	S	759;596;737;760	ENSP00000273854:G759S;ENSP00000389208:G596S;ENSP00000346899:G737S;ENSP00000427638:G760S	ENSP00000273854:G759S	G	-	1	0	EPHA5	65901378	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.814000	0.86154	2.718000	0.92993	0.585000	0.79938	GGC	.	.		0.358	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		T	66218783	C	T	66218783	3	4	101	1	0	0	0	0	1	0	0	0	5172	594	21	3	862	3	EPHA5	4	66218783	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	977885	66218783	124935493	168	14005										
UGT2A1	10941	hgsc.bcm.edu	37	chr4	70455333	70455333	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggctttacaggttgatcatgGtgaattcttgataacctcat	9	7	3	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:70455333G>T	ENST00000503640.1	-	6	1396	c.1341C>A	c.(1339-1341)caC>caA	p.H447Q	UGT2A1_ENST00000514019.1_Missense_Mutation_p.H613Q|UGT2A1_ENST00000286604.4_Missense_Mutation_p.H447Q|UGT2A1_ENST00000502343.1_5'UTR|UGT2A2_ENST00000457664.2_Missense_Mutation_p.H456Q|UGT2A1_ENST00000512704.1_Missense_Mutation_p.H403Q	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	447					cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						GTTGATCATGGTGAATTCTTG	0.398																																					p.H613Q		Atlas-SNP	.											.	UGT2A1	131	.	0			c.C1839A						.						99	104	103					4																	70455333		2203	4300	6503	SO:0001583	missense	10941	exon7			ATCATGGTGAATT	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"UDP glucuronosyltransferases"	12542	protein-coding gene	gene with protein product		604716	"UDP glycosyltransferase 2 family, polypeptide A1", "UDP glucuronosyltransferase 2 family, polypeptide A1"			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.1341C>A	chr4.hg19:g.70455333G>T	ENSP00000424478:p.His447Gln	106.0	0.0		311.0	30.0	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	hg19	CCDS3529.1	.	.	.	.	.	.	.	.	.	.	G	16.04	3.009498	0.54361	.	.	ENSG00000173610	ENST00000457664;ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57;-0.57	4.65	-2.05	0.07321	.	0.050572	0.85682	N	0.000000	T	0.75953	0.3920	M	0.69358	2.11	.	.	.	P;D;D;D;B	0.89917	0.476;0.988;1.0;0.999;0.134	B;P;D;D;B	0.87578	0.159;0.863;0.998;0.994;0.112	T	0.74645	-0.3596	9	0.49607	T	0.09	.	5.8441	0.18652	0.5368:0.0:0.3295:0.1337	.	613;613;403;456;447	E9PDM7;B4E2F4;D6RFW5;Q9Y4X1-2;Q9Y4X1	.;.;.;.;UD2A1_HUMAN	Q	456;447;403;613;447	ENSP00000387888:H456Q;ENSP00000424478:H447Q;ENSP00000421432:H403Q;ENSP00000425497:H613Q;ENSP00000286604:H447Q	ENSP00000286604:H447Q	H	-	3	2	UGT2A1	70489922	0.999000	0.42202	0.946000	0.38457	0.956000	0.61745	0.520000	0.22878	-0.616000	0.05671	0.579000	0.79373	CAC	.	.		0.398	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798		T	70455333	G	T	70455333	3	4	101	1	0	0	0	0	1	0	0	0	16968	1252	44	3	246	3	UGT2A1	4	70455333	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	4236550	70455333	120698943	169	14006										
C4orf40	401137	hgsc.bcm.edu	37	chr4	71024516	71024516	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctgagcctgctgcagaggcaCctgttggagtggagccagct	15	11	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:71024516C>A	ENST00000344526.5	+	3	736	c.547C>A	c.(547-549)Cct>Act	p.P183T	C4orf40_ENST00000502294.1_Missense_Mutation_p.P183T	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		183	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						TGCAGAGGCACCTGTTGGAGT	0.622																																					p.P183T		Atlas-SNP	.											.	C4orf40	19	.	0			c.C547A						.						48	45	46					4																	71024516		2203	4299	6502	SO:0001583	missense	401137	exon3			GAGGCACCTGTTG																												ENST00000344526.5:c.547C>A	chr4.hg19:g.71024516C>A	ENSP00000343172:p.Pro183Thr	93.0	0.0		250.0	16.0	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	hg19	CCDS3535.1	.	.	.	.	.	.	.	.	.	.	C	9.866	1.197693	0.22037	.	.	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.39997	1.05;1.05	3.02	3.02	0.34903	.	.	.	.	.	T	0.47710	0.1460	N	0.24115	0.695	0.22562	N	0.998984	D	0.89917	1.0	D	0.74674	0.984	T	0.33954	-0.9848	9	0.40728	T	0.16	-11.9068	11.8918	0.52633	0.0:1.0:0.0:0.0	.	183	Q6MZM9	CD040_HUMAN	T	183	ENSP00000426249:P183T;ENSP00000343172:P183T	ENSP00000343172:P183T	P	+	1	0	C4orf40	71059105	0.678000	0.27586	0.002000	0.10522	0.008000	0.06430	0.890000	0.28295	1.425000	0.47237	0.400000	0.26472	CCT	.	.		0.622	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1			A	71024516	C	A	71024516	3	1	101	1	0	0	0	0	1	0	0	0	2271	507	18	3	557	3	C4orf40	4	71024516	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	569183	71024516	120129760	170	14007										
MUC7	4589	hgsc.bcm.edu	37	chr4	71346814	71346814	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tccatctgtgactttcccatCagcttccaccaaaattacta	3	14	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:71346814C>T	ENST00000304887.5	+	3	543	c.353C>T	c.(352-354)tCa>tTa	p.S118L	MUC7_ENST00000456088.1_Missense_Mutation_p.S118L|MUC7_ENST00000514512.1_3'UTR|MUC7_ENST00000413702.1_Missense_Mutation_p.S118L	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	118	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			ACTTTCCCATCAGCTTCCACC	0.428																																					p.S118L		Atlas-SNP	.											.	MUC7	91	.	0			c.C353T						.						122	115	118					4																	71346814		2203	4300	6503	SO:0001583	missense	4589	exon4			TCCCATCAGCTTC	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"Mucins"	7518	protein-coding gene	gene with protein product		158375	"mucin 7, salivary"			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.353C>T	chr4.hg19:g.71346814C>T	ENSP00000302021:p.Ser118Leu	65.0	0.0		211.0	12.0	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	hg19	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.704882	0.30232	.	.	ENSG00000171195	ENST00000413702;ENST00000505411;ENST00000456088;ENST00000304887	T;T;T;T	0.54479	0.58;0.57;0.58;0.58	3.44	2.57	0.30868	.	.	.	.	.	T	0.52256	0.1723	N	0.24115	0.695	0.09310	N	1	D	0.65815	0.995	P	0.61003	0.882	T	0.39035	-0.9633	9	0.37606	T	0.19	-2.6315	10.1996	0.43075	0.2007:0.7993:0.0:0.0	.	118	Q8TAX7	MUC7_HUMAN	L	118	ENSP00000407422:S118L;ENSP00000427594:S118L;ENSP00000400585:S118L;ENSP00000302021:S118L	ENSP00000302021:S118L	S	+	2	0	MUC7	71381403	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	1.245000	0.32790	0.991000	0.38814	-0.181000	0.13052	TCA	.	.		0.428	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		T	71346814	C	T	71346814	3	4	101	1	0	0	0	0	1	0	0	0	9990	838	29	3	359	3	MUC7	4	71346814	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	322298	71346814	119807462	171	14008										
ALB	213	hgsc.bcm.edu	37	chr4	74274521	74274524	+	Splice_Site	DEL	AAGT	AAGT	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atgaagagacatttttgaaaAagtaagtaatcagatgttta					rs17853494		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:74274521_74274524delAAGT	ENST00000295897.4	+	4	570_571	c.481_482delAAGT	c.(481-483)aag>g	p.K161fs	ALB_ENST00000509063.1_Splice_Site_p.K161fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Intron|ALB_ENST00000415165.2_Intron|ALB_ENST00000503124.1_Intron	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATTTTTGAAAAAGTAAGTAATCAG	0.348																																					p.160_161del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.480_482del						.																																			SO:0001630	splice_region_variant	213	exon4			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.482+1AAGT>-	chr4.hg19:g.74274525_74274528delAAGT		55.0	0.0		86.0	32.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	In_Frame_Del	DEL	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.348	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477	Frame_Shift_Del	-	74274524	AAGT	-	74274521	8	5	101	1	0	1	0	1	0	0	1	0	486	28	1	0	495	0	ALB	4	74274521	Splice_Site	DEL	AAGT	TCGA-DD-A1EE-01A-11D-A12Z-10	2927707	74274521	116879755	172	14009										
ALB	213	hgsc.bcm.edu	37	chr4	74283297	74283298	+	Frame_Shift_Ins	INS	-	-	T													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccaagtgtcaactccaactcINSttgtagaggtctcaagaaac							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:74283297_74283298insT	ENST00000503124.1	+	9	1096_1097	c.889_890insT	c.(889-891)cttfs	p.L297fs	ALB_ENST00000295897.4_Frame_Shift_Ins_p.L447fs|ALB_ENST00000509063.1_Frame_Shift_Ins_p.L447fs|ALB_ENST00000505649.1_Intron|ALB_ENST00000401494.3_Frame_Shift_Ins_p.L332fs|ALB_ENST00000415165.2_Frame_Shift_Ins_p.L255fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AACTCCAACTCTTGTAGAGGTC	0.401																																					p.L447fs		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.1339_1340insT						.																																			SO:0001589	frameshift_variant	213	exon11			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.891dupT	chr4.hg19:g.74283299_74283299dupT	ENSP00000421027:p.Leu297fs	77.0	0.0		217.0	33.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Ins	INS	ENST00000503124.1	hg19																																																																																				.	.		0.401	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		T	74283298	-	T	74283297	7	5	101	1	0	1	1	0	0	0	0	0	486	913	32	0	1381	0	ALB	4	74283297	Frame_Shift_Ins	INS	-	TCGA-DD-A1EE-01A-11D-A12Z-10	8776	74283297	116870979	173	14010										
STBD1	100631383	hgsc.bcm.edu	37	chr4	77230589	77230589	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcagctacatgttttgcagaGaagttgccttctagcaacct	9	10	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:77230589G>T	ENST00000237642.6	+	2	1257	c.513G>T	c.(511-513)gaG>gaT	p.E171D	FAM47E_ENST00000515604.1_3'UTR|FAM47E-STBD1_ENST00000539752.1_Missense_Mutation_p.E22D	NM_003943.4	NP_003934.1			FAM47E-STBD1 readthrough																		GTTTTGCAGAGAAGTTGCCTT	0.443																																					p.E171D		Atlas-SNP	.											.	STBD1	22	.	0			c.G513T						.						52	54	54					4																	77230589		2203	4300	6503	SO:0001583	missense	8987	exon2			TGCAGAGAAGTTG		CCDS58908.1	4q21.1	2013-04-23			ENSG00000118804	ENSG00000118804			44667	other	readthrough							Standard	NM_001242939		Approved				OTTHUMG00000160966	ENST00000237642.6:c.513G>T	chr4.hg19:g.77230589G>T	ENSP00000237642:p.Glu171Asp	65.0	0.0		137.0	15.0	NM_003943		Missense_Mutation	SNP	ENST00000237642.6	hg19	CCDS3578.1	.	.	.	.	.	.	.	.	.	.	G	2.139	-0.397246	0.04899	.	.	ENSG00000118804	ENST00000539752;ENST00000237642	.	.	.	4.73	-1.64	0.08318	.	0.933364	0.08922	N	0.874297	T	0.23926	0.0579	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.21930	-1.0231	9	0.30078	T	0.28	-0.6048	1.7559	0.02982	0.3423:0.1295:0.3961:0.132	.	171	O95210	STBD1_HUMAN	D	22;171	.	ENSP00000237642:E171D	E	+	3	2	STBD1	77449613	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-0.073000	0.11468	-0.250000	0.09555	-0.165000	0.13383	GAG	.	.		0.443	FAM47E-STBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252415.2			T	77230589	G	T	77230589	3	4	101	1	0	0	0	0	1	0	0	0	15289	933	33	3	519	3	STBD1	4	77230589	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2947292	77230589	113923687	174	14011										
STBD1	100631383	hgsc.bcm.edu	37	chr4	77230700	77230700	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gagtgggaaatggtgcctagGcactcatcttggggggatgt	17	6	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:77230700G>T	ENST00000237642.6	+	2	1368	c.624G>T	c.(622-624)agG>agT	p.R208S	FAM47E_ENST00000515604.1_3'UTR|FAM47E-STBD1_ENST00000539752.1_Missense_Mutation_p.R59S	NM_003943.4	NP_003934.1			FAM47E-STBD1 readthrough																		TGGTGCCTAGGCACTCATCTT	0.502																																					p.R208S		Atlas-SNP	.											.	STBD1	22	.	0			c.G624T						.						76	73	74					4																	77230700		2203	4300	6503	SO:0001583	missense	8987	exon2			GCCTAGGCACTCA		CCDS58908.1	4q21.1	2013-04-23			ENSG00000118804	ENSG00000118804			44667	other	readthrough							Standard	NM_001242939		Approved				OTTHUMG00000160966	ENST00000237642.6:c.624G>T	chr4.hg19:g.77230700G>T	ENSP00000237642:p.Arg208Ser	72.0	0.0		124.0	11.0	NM_003943		Missense_Mutation	SNP	ENST00000237642.6	hg19	CCDS3578.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.080052	0.55753	.	.	ENSG00000118804	ENST00000539752;ENST00000237642	.	.	.	4.98	3.22	0.36961	.	0.000000	0.53938	D	0.000050	T	0.60702	0.2289	L	0.54323	1.7	0.34174	D	0.670185	D	0.69078	0.997	P	0.60789	0.879	T	0.70967	-0.4728	9	0.49607	T	0.09	-21.8029	10.2488	0.43356	0.1572:0.0:0.8428:0.0	.	208	O95210	STBD1_HUMAN	S	59;208	.	ENSP00000237642:R208S	R	+	3	2	STBD1	77449724	1.000000	0.71417	1.000000	0.80357	0.431000	0.31685	1.565000	0.36386	1.322000	0.45245	0.655000	0.94253	AGG	.	.		0.502	FAM47E-STBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252415.2			T	77230700	G	T	77230700	3	4	101	1	0	0	0	0	1	0	0	0	15289	1194	42	3	630	3	STBD1	4	77230700	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	111	77230700	113923576	175	14012										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79455713	79455713	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaaggtgttcctaatggatcCcaatacatctgatatgtcac	8	9	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:79455713C>T	ENST00000264895.6	+	71	11476	c.11036C>T	c.(11035-11037)cCc>cTc	p.P3679L		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3675					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CTAATGGATCCCAATACATCT	0.453																																					p.P3679L		Atlas-SNP	.											.	FRAS1	779	.	0			c.C11036T						.						131	118	122					4																	79455713		1896	4124	6020	SO:0001583	missense	80144	exon71			TGGATCCCAATAC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11036C>T	chr4.hg19:g.79455713C>T	ENSP00000264895:p.Pro3679Leu	59.0	0.0		199.0	8.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.401489	0.83120	.	.	ENSG00000138759	ENST00000264895	T	0.14516	2.5	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.39332	0.1074	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.28106	-1.0054	10	0.87932	D	0	.	18.4025	0.90522	0.0:1.0:0.0:0.0	.	3679	E9PHH6	.	L	3679	ENSP00000264895:P3679L	ENSP00000264895:P3679L	P	+	2	0	FRAS1	79674737	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	7.667000	0.83888	2.336000	0.79503	0.591000	0.81541	CCC	.	.		0.453	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79455713	C	T	79455713	3	4	101	1	0	0	0	0	1	0	0	0	6050	623	22	3	11393	3	FRAS1	4	79455713	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2225013	79455713	111698563	176	14013										
ANXA3	306	hgsc.bcm.edu	37	chr4	79503384	79503384	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggccactttgagcatctcatGgtggccctagtgactccacc	10	14	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:79503384G>A	ENST00000264908.6	+	5	631	c.252G>A	c.(250-252)atG>atA	p.M84I	ANXA3_ENST00000503570.2_Missense_Mutation_p.M45I|ANXA3_ENST00000512884.1_Missense_Mutation_p.M45I	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	84					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						AGCATCTCATGGTGGCCCTAG	0.453																																					p.M84I	GBM(2;126 157 27790 28920 42492)	Atlas-SNP	.											.	ANXA3	35	.	0			c.G252A						.						87	84	85					4																	79503384		2203	4300	6503	SO:0001583	missense	306	exon5			TCTCATGGTGGCC	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"Annexins"	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.252G>A	chr4.hg19:g.79503384G>A	ENSP00000264908:p.Met84Ile	103.0	0.0		219.0	15.0	NM_005139	B2R9W6|Q6LET2	Missense_Mutation	SNP	ENST00000264908.6	hg19	CCDS3584.1	.	.	.	.	.	.	.	.	.	.	G	8.570	0.879933	0.17467	.	.	ENSG00000138772	ENST00000264908;ENST00000512884;ENST00000503570;ENST00000512373;ENST00000514171;ENST00000508214	T;T;T;T;T;T	0.03181	4.02;4.02;4.02;4.02;4.02;4.02	5.16	5.16	0.70880	Annexin repeat, conserved site (1);	0.146214	0.64402	D	0.000009	T	0.03220	0.0094	N	0.16066	0.365	0.51233	D	0.999914	B	0.27117	0.168	B	0.34346	0.18	T	0.32268	-0.9913	10	0.02654	T	1	.	17.5603	0.87905	0.0:0.0:1.0:0.0	.	84	P12429	ANXA3_HUMAN	I	84;45;45;84;84;84	ENSP00000264908:M84I;ENSP00000423068:M45I;ENSP00000421015:M45I;ENSP00000424584:M84I;ENSP00000421512:M84I;ENSP00000422281:M84I	ENSP00000264908:M84I	M	+	3	0	ANXA3	79722408	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	1.792000	0.38754	2.674000	0.91012	0.591000	0.81541	ATG	.	.		0.453	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139		A	79503384	G	A	79503384	3	1	101	1	0	0	0	0	1	0	0	0	719	1348	47	3	266	3	ANXA3	4	79503384	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	47671	79503384	111650892	177	14014										
FGF5	2250	hgsc.bcm.edu	37	chr4	81207740	81207740	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctgaaaagaaaaagccacctAgccctatcaagccaaagatt	6	11	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:81207740A>C	ENST00000312465.7	+	3	947	c.721A>C	c.(721-723)Agc>Cgc	p.S241R	FGF5_ENST00000456523.3_3'UTR|FGF5_ENST00000503413.1_3'UTR	NM_004464.3	NP_004455.2	P12034	FGF5_HUMAN	fibroblast growth factor 5	241					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell differentiation (GO:0010001)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction involved in regulation of gene expression (GO:0023019)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	fibroblast growth factor receptor binding (GO:0005104)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22						AAAGCCACCTAGCCCTATCAA	0.448																																					p.S241R		Atlas-SNP	.											.	FGF5	49	.	0			c.A721C						.						73	71	72					4																	81207740		2203	4300	6503	SO:0001583	missense	2250	exon3			CCACCTAGCCCTA	M23534	CCDS3586.1, CCDS34021.1	4q21	2014-01-30			ENSG00000138675	ENSG00000138675		"Endogenous ligands"	3683	protein-coding gene	gene with protein product		165190				3211147, 2577873	Standard	NM_001291812		Approved		uc003hmd.3	P12034	OTTHUMG00000130288	ENST00000312465.7:c.721A>C	chr4.hg19:g.81207740A>C	ENSP00000311697:p.Ser241Arg	61.0	0.0		114.0	10.0	NM_004464	B2R554|O75846|Q3Y8M3|Q8NF90	Missense_Mutation	SNP	ENST00000312465.7	hg19	CCDS34021.1	.	.	.	.	.	.	.	.	.	.	A	1.674	-0.508240	0.04231	.	.	ENSG00000138675	ENST00000312465	T	0.74842	-0.88	5.6	1.31	0.21738	.	1.463330	0.03457	N	0.211570	T	0.53706	0.1813	N	0.12182	0.205	0.09310	N	0.999999	B	0.18166	0.026	B	0.16289	0.015	T	0.44360	-0.9333	10	0.28530	T	0.3	.	1.7714	0.03012	0.5301:0.1387:0.0846:0.2466	.	241	P12034	FGF5_HUMAN	R	241	ENSP00000311697:S241R	ENSP00000311697:S241R	S	+	1	0	FGF5	81426764	0.001000	0.12720	0.010000	0.14722	0.093000	0.18481	1.395000	0.34520	0.966000	0.38159	-0.250000	0.11733	AGC	.	.		0.448	FGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252627.2			C	81207740	A	C	81207740	3	2	101	1	0	0	0	0	1	0	0	0	5863	420	15	5	731	5	FGF5	4	81207740	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1704356	81207740	109946536	178	14015										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87643424	87643424	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcaagagatcatgctaaaacGgcaagaggaagaactgatgc	11	7	2	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:87643424G>A	ENST00000411767.2	+	10	1508	c.1445G>A	c.(1444-1446)cGg>cAg	p.R482Q	PTPN13_ENST00000316707.6_Missense_Mutation_p.R482Q|PTPN13_ENST00000436978.1_Missense_Mutation_p.R482Q|PTPN13_ENST00000511467.1_Missense_Mutation_p.R482Q|PTPN13_ENST00000427191.2_Missense_Mutation_p.R482Q			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	482					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		ATGCTAAAACGGCAAGAGGAA	0.433																																					p.R482Q		Atlas-SNP	.											.	PTPN13	203	.	0			c.G1445A						.						101	93	96					4																	87643424		1907	4124	6031	SO:0001583	missense	5783	exon10			TAAAACGGCAAGA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.1445G>A	chr4.hg19:g.87643424G>A	ENSP00000407249:p.Arg482Gln	116.0	0.0		268.0	111.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.077198	0.76415	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	4.92	4.92	0.64577	.	0.000000	0.43747	D	0.000534	T	0.53351	0.1791	L	0.56769	1.78	0.45056	D	0.998072	D;D;D;D	0.89917	0.998;1.0;1.0;1.0	D;D;D;D	0.72625	0.928;0.965;0.951;0.978	T	0.56300	-0.8002	10	0.72032	D	0.01	.	18.4798	0.90807	0.0:0.0:1.0:0.0	.	482;482;482;482	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	Q	482;482;482;482;482;450	ENSP00000408368:R482Q;ENSP00000394794:R482Q;ENSP00000322675:R482Q;ENSP00000407249:R482Q;ENSP00000426626:R482Q	ENSP00000322675:R482Q	R	+	2	0	PTPN13	87862448	1.000000	0.71417	0.999000	0.59377	0.542000	0.35054	5.399000	0.66314	2.444000	0.82710	0.655000	0.94253	CGG	.	.		0.433	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87643424	G	A	87643424	3	1	101	1	0	0	0	0	1	0	0	0	12795	1116	39	1	1479	1	PTPN13	4	87643424	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6435684	87643424	103510852	179	14016										
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90170546	90170546	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctgaacatccagattctctaGttagaggtttacaggacctc	8	10	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:90170546G>A	ENST00000609438.1	-	2	1234	c.716C>T	c.(715-717)aCt>aTt	p.T239I	GPRIN3_ENST00000333209.4_Missense_Mutation_p.T239I	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	239								p.T239N(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		AGATTCTCTAGTTAGAGGTTT	0.552																																					p.T239I		Atlas-SNP	.											GPRIN3,NS,carcinoma,0,1	GPRIN3	90	.	1	Substitution - Missense(1)	kidney(1)	c.C716T						.						50	55	53					4																	90170546		2203	4300	6503	SO:0001583	missense	285513	exon2			TCTCTAGTTAGAG	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.716C>T	chr4.hg19:g.90170546G>A	ENSP00000476603:p.Thr239Ile	50.0	0.0		93.0	9.0	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	hg19	CCDS34030.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.318807	0.23994	.	.	ENSG00000185477	ENST00000333209	T	0.10860	2.83	4.93	0.83	0.18854	.	0.807286	0.10088	N	0.717539	T	0.04452	0.0122	N	0.14661	0.345	0.09310	N	1	B	0.30824	0.296	B	0.20955	0.032	T	0.40270	-0.9572	10	0.27785	T	0.31	0.635	1.468	0.02410	0.1827:0.1254:0.4522:0.2398	.	239	Q6ZVF9	GRIN3_HUMAN	I	239	ENSP00000328672:T239I	ENSP00000328672:T239I	T	-	2	0	GPRIN3	90389569	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.754000	0.26390	0.311000	0.23014	-0.142000	0.14014	ACT	.	.		0.552	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		A	90170546	G	A	90170546	3	1	101	1	0	0	0	0	1	0	0	0	6740	1029	36	3	1618	3	GPRIN3	4	90170546	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2527122	90170546	100983730	180	14017										
ADH6	130	hgsc.bcm.edu	37	chr4	100134799	100134799	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tactccttctccaatactctCaacgattccagccccttcat	2	17	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:100134799C>T	ENST00000237653.7	-	3	610	c.226G>A	c.(226-228)Gag>Aag	p.E76K	ADH6_ENST00000394899.2_Missense_Mutation_p.E76K|RP11-696N14.1_ENST00000500358.2_RNA|RP11-696N14.1_ENST00000506454.1_RNA|ADH6_ENST00000407820.2_Intron|ADH6_ENST00000394897.1_Missense_Mutation_p.E76K|RP11-696N14.1_ENST00000506160.1_RNA	NM_000672.3	NP_000663	P28332	ADH6_HUMAN	alcohol dehydrogenase 6 (class V)	76					ethanol oxidation (GO:0006069)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|ethanol binding (GO:0035276)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)	20				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)	CCAATACTCTCAACGATTCCA	0.473																																					p.E76K		Atlas-SNP	.											.	ADH6	74	.	0			c.G226A						.						157	132	140					4																	100134799		2203	4300	6503	SO:0001583	missense	130	exon3			TACTCTCAACGAT	AK092768	CCDS3647.1, CCDS43255.1	4q23	2008-02-05			ENSG00000172955	ENSG00000172955	1.1.1.1	"Alcohol dehydrogenases"	255	protein-coding gene	gene with protein product		103735				1881901	Standard	NM_000672		Approved	ADH-5	uc003huo.2	P28332	OTTHUMG00000131024	ENST00000237653.7:c.226G>A	chr4.hg19:g.100134799C>T	ENSP00000237653:p.Glu76Lys	81.0	0.0		143.0	8.0	NM_000672	B3KS45|Q58F53	Missense_Mutation	SNP	ENST00000237653.7	hg19	CCDS3647.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.356288	0.41700	.	.	ENSG00000172955	ENST00000394897;ENST00000394899;ENST00000237653;ENST00000508558	T;T;T;T	0.04156	3.69;3.69;3.69;3.69	4.61	1.82	0.25136	GroES-like (1);Alcohol dehydrogenase GroES-like (1);Alcohol dehydrogenase, zinc-type, conserved site (1);	0.099974	0.64402	D	0.000002	T	0.24275	0.0588	M	0.86805	2.84	0.80722	D	1	P;D;D	0.89917	0.954;0.982;1.0	P;P;D	0.91635	0.908;0.852;0.999	T	0.04855	-1.0922	10	0.87932	D	0	-14.4268	15.0639	0.71977	0.0:0.5945:0.4055:0.0	.	76;76;76	E9PBI1;P28332;P28332-2	.;ADH6_HUMAN;.	K	76	ENSP00000378358:E76K;ENSP00000378359:E76K;ENSP00000237653:E76K;ENSP00000426187:E76K	ENSP00000237653:E76K	E	-	1	0	ADH6	100353822	0.998000	0.40836	0.012000	0.15200	0.054000	0.15201	4.067000	0.57527	0.034000	0.15491	-0.802000	0.03209	GAG	.	.		0.473	ADH6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253665.1	NM_000672		T	100134799	C	T	100134799	3	4	101	1	0	0	0	0	1	0	0	0	312	835	29	3	933	3	ADH6	4	100134799	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	9964253	100134799	91019477	181	14018										
DKK2	27123	hgsc.bcm.edu	37	chr4	107845310	107845310	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tccagaaatgacgagcacagCaaaacccttcaatgcagtct	7	12	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:107845310C>T	ENST00000285311.3	-	4	1286	c.581G>A	c.(580-582)tGc>tAc	p.C194Y	DKK2_ENST00000510463.1_Missense_Mutation_p.C148Y|DKK2_ENST00000513208.1_Missense_Mutation_p.C94Y	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	194	DKK-type Cys-2.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.C194F(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		ACGAGCACAGCAAAACCCTTC	0.473																																					p.C194Y		Atlas-SNP	.											DKK2,NS,neuroblastoma,0,1	DKK2	96	.	1	Substitution - Missense(1)	autonomic_ganglia(1)	c.G581A						.						118	109	112					4																	107845310		2203	4300	6503	SO:0001583	missense	27123	exon4			GCACAGCAAAACC	AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"dickkopf (Xenopus laevis) homolog 2", "dickkopf 2 homolog (Xenopus laevis)"			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.581G>A	chr4.hg19:g.107845310C>T	ENSP00000285311:p.Cys194Tyr	69.0	0.0		191.0	16.0	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Missense_Mutation	SNP	ENST00000285311.3	hg19	CCDS3675.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.610495	0.87258	.	.	ENSG00000155011	ENST00000285311;ENST00000513208;ENST00000510463	D;T;T	0.81821	-1.54;-0.61;-1.14	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.90807	0.7113	M	0.82823	2.61	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	D	0.91523	0.5236	10	0.87932	D	0	-8.7032	19.6876	0.95986	0.0:1.0:0.0:0.0	.	194	Q9UBU2	DKK2_HUMAN	Y	194;94;148	ENSP00000285311:C194Y;ENSP00000421255:C94Y;ENSP00000423797:C148Y	ENSP00000285311:C194Y	C	-	2	0	DKK2	108064759	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.487000	0.81328	2.657000	0.90304	0.585000	0.79938	TGC	.	.		0.473	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4			T	107845310	C	T	107845310	3	4	101	1	0	0	0	0	1	0	0	0	4547	710	25	3	202	3	DKK2	4	107845310	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	7710511	107845310	83308966	182	14019										
ANK2	287	hgsc.bcm.edu	37	chr4	114274329	114274329	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aagatttgatcaaaatgaccGccatcttgaccacagatgtg	8	9	2	5	rs200920714		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:114274329G>A	ENST00000357077.4	+	38	4608	c.4555G>A	c.(4555-4557)Gcc>Acc	p.A1519T	ANK2_ENST00000264366.6_Missense_Mutation_p.A1486T|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1519	Death 1. {ECO:0000255|PROSITE- ProRule:PRU00064}.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.A1519T(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CAAAATGACCGCCATCTTGAC	0.453																																					p.A1519T		Atlas-SNP	.											ANK2,caecum,carcinoma,0,1	ANK2	576	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4555A						.						73	74	74					4																	114274329		2203	4300	6503	SO:0001583	missense	287	exon38			ATGACCGCCATCT	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.4555G>A	chr4.hg19:g.114274329G>A	ENSP00000349588:p.Ala1519Thr	49.0	0.0		92.0	6.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.810005	0.90707	.	.	ENSG00000145362	ENST00000503423;ENST00000504454;ENST00000357077;ENST00000264366	T;T;T;T	0.73575	1.87;1.87;-0.76;-0.67	5.83	5.83	0.93111	.	0.000000	0.53938	D	0.000045	D	0.86251	0.5888	M	0.74647	2.275	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.71656	0.92;0.974	D	0.84583	0.0662	10	0.41790	T	0.15	.	20.1195	0.97955	0.0:0.0:1.0:0.0	.	1486;1519	Q01484;Q01484-4	ANK2_HUMAN;.	T	1432;1534;1519;1486	ENSP00000421011:A1432T;ENSP00000424722:A1534T;ENSP00000349588:A1519T;ENSP00000264366:A1486T	ENSP00000264366:A1486T	A	+	1	0	ANK2	114493778	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	6.662000	0.74426	2.759000	0.94783	0.650000	0.86243	GCC	.	G|0.999;T|0.001		0.453	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114274329	G	A	114274329	3	1	101	1	0	0	0	0	1	0	0	0	621	1087	38	1	4770	1	ANK2	4	114274329	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6429019	114274329	76879947	183	14020										
SMARCA5	8467	hgsc.bcm.edu	37	chr4	144467138	144467138	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaaaagaagaacagcttaaaAttgatgaagctgaatccctt	7	6	0	5			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:144467138A>G	ENST00000283131.3	+	19	2920	c.2458A>G	c.(2458-2460)Att>Gtt	p.I820V		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	820					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					ACAGCTTAAAATTGATGAAGC	0.348																																					p.I820V		Atlas-SNP	.											.	SMARCA5	73	.	0			c.A2458G						.						86	90	88					4																	144467138		2203	4300	6503	SO:0001583	missense	8467	exon19			CTTAAAATTGATG	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.2458A>G	chr4.hg19:g.144467138A>G	ENSP00000283131:p.Ile820Val	89.0	0.0		300.0	17.0	NM_003601		Missense_Mutation	SNP	ENST00000283131.3	hg19	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.354537	0.61293	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.91464	-2.85	5.3	5.3	0.74995	ATPase, nucleosome remodelling ISWI, HAND domain (2);	0.000000	0.85682	D	0.000000	D	0.88912	0.6566	L	0.56769	1.78	0.58432	D	0.999999	B	0.20368	0.044	B	0.22152	0.038	D	0.85626	0.1267	10	0.37606	T	0.19	-19.4602	15.5566	0.76200	1.0:0.0:0.0:0.0	.	820	O60264	SMCA5_HUMAN	V	820;763;763	ENSP00000283131:I820V	ENSP00000283131:I820V	I	+	1	0	SMARCA5	144686588	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.680000	0.91225	2.136000	0.66102	0.533000	0.62120	ATT	.	.		0.348	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			G	144467138	A	G	144467138	3	3	101	1	0	0	0	0	1	0	0	0	14786	101	4	2	2532	2	SMARCA5	4	144467138	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	30192809	144467138	46687138	184	14021										
GYPA	2994	hgsc.bcm.edu	37	chr4	145039884	145039884	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tacctggttcagagaaatgaTgggcaagttgtaccctttct	10	8	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:145039884T>A	ENST00000283126.7	-	1	93				GYPA_ENST00000535709.1_Missense_Mutation_p.H59L|GYPA_ENST00000512064.1_Intron|GYPA_ENST00000360771.4_Missense_Mutation_p.H85L|GYPA_ENST00000504786.1_Missense_Mutation_p.H53L|RP11-673E1.4_ENST00000506982.1_RNA|GYPA_ENST00000512789.1_Missense_Mutation_p.H20L|GYPA_ENST00000503627.1_Intron|GYPA_ENST00000324022.10_Missense_Mutation_p.H52L			P06028	GLPB_HUMAN	glycophorin B (MNS blood group)							integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|skin(1)	4	all_hematologic(180;0.158)					AGAGAAATGATGGGCAAGTTG	0.313																																					p.H85L		Atlas-SNP	.											GYPA,right_upper_lobe,carcinoma,0,1	GYPA	27	.	0			c.A254T						.						109	109	109					4																	145039884		2203	4300	6503	SO:0001627	intron_variant	2993	exon4			AAATGATGGGCAA		CCDS54809.1	4q31.21	2014-09-17	2006-02-23			ENSG00000250361		"CD molecules", "Blood group antigens"	4703	protein-coding gene	gene with protein product		111740	"glycophorin B (includes Ss blood group)", "glycophorin B (Ss blood group)"	MNS			Standard	NM_002100		Approved	GPB, SS, CD235b		P06028		ENST00000283126.7:c.37+21867A>T	chr4.hg19:g.145039884T>A		170.0	0.0		662.0	43.0	NM_002099	B8Q174|E2QBW7|Q0VAF4|Q58HE9|Q58HF0|Q58HF1|Q9UCH7	Missense_Mutation	SNP	ENST00000283126.7	hg19		.	.	.	.	.	.	.	.	.	.	T	9.261	1.043323	0.19748	.	.	ENSG00000170180	ENST00000360771;ENST00000324022;ENST00000535709;ENST00000512789;ENST00000504786;ENST00000394119	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	3.94	1.33	0.21861	.	0.000000	0.42682	D	0.000668	T	0.35711	0.0941	M	0.68952	2.095	0.09310	N	1	D;D;D;B;D	0.89917	0.996;0.992;0.999;0.007;1.0	D;D;D;B;D	0.72338	0.934;0.912;0.955;0.022;0.977	T	0.08743	-1.0707	10	0.87932	D	0	-13.6461	4.5091	0.11903	0.1971:0.0:0.2052:0.5976	.	52;20;53;85;85	B8Q185;Q13030;E7EQF3;P02724;Q16336	.;.;.;GLPA_HUMAN;.	L	85;52;59;20;53;53	ENSP00000354003:H85L;ENSP00000324483:H52L;ENSP00000445398:H59L;ENSP00000425193:H20L;ENSP00000425549:H53L	ENSP00000324483:H52L	H	-	2	0	GYPA	145259334	0.029000	0.19370	0.000000	0.03702	0.001000	0.01503	1.046000	0.30354	0.288000	0.22398	0.482000	0.46254	CAT	.	.		0.313	GYPB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002100		A	145039884	T	A	145039884	1	1	101	0	1	0	0	0	0	0	0	0	6917	1464	51	4		4	GYPA	4	145039884	Intron	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	572746	145039884	46114392	185	14022										
ZNF827	152485	hgsc.bcm.edu	37	chr4	146824067	146824068	+	Missense_Mutation	DNP	GA	GA	TT													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgctgctcaggggcttgttgGagcctgggtcatcgtcacac							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:146824067_146824068GA>TT	ENST00000508784.1	-	2	570_571	c.343_344TC>AA	c.(343-345)TCc>AAc	p.S115N	ZNF827_ENST00000379448.4_Missense_Mutation_p.S115N|ZNF827_ENST00000513320.1_Intron			Q17R98	ZN827_HUMAN	zinc finger protein 827	115					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					GGGCTTGTTGGAGCCTGGGTCA	0.589																																					p.S115Y|p.S115T		Atlas-SNP	.											.	ZNF827	102	.	0			c.C344A|c.T343A						.																																			SO:0001583	missense	152485	exon2			TTGTTGGAGCCTG|TGTTGGAGCCTGG	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.343_344delinsTT	chr4.hg19:g.146824067_146824068delinsTT	ENSP00000421863:p.Ser115Asn	32.0	0.0		70.0|69.0	5.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	hg19																																																																																				.	.		0.589	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		TT	146824068	GA	TT	146824067	3	4	101	1	0	0	0	0	1	0	0	0	18195	1174	41	3	2937	3	ZNF827	4	146824067	Missense_Mutation	DNP	GA	TCGA-DD-A1EE-01A-11D-A12Z-10	1784183	146824067	44330209	186	14023										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148886196	148886196	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aagcggcagcccagaatctcGtgttaatgcgatccatttct	9	11	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:148886196G>A	ENST00000336498.3	+	17	1711	c.1472G>A	c.(1471-1473)cGt>cAt	p.R491H	ARHGAP10_ENST00000414545.2_Missense_Mutation_p.R140H	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	1254					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		CCAGAATCTCGTGTTAATGCG	0.308																																					p.R491H		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.G1472A						.						78	76	77					4																	148886196		2203	4300	6503	SO:0001583	missense	79658	exon17			AATCTCGTGTTAA	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.1472G>A	chr4.hg19:g.148886196G>A	ENSP00000336923:p.Arg491His	117.0	0.0		353.0	155.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.634973	0.67130	.	.	ENSG00000071205	ENST00000336498;ENST00000414545	T;T	0.22743	1.94;1.94	5.55	5.55	0.83447	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.64907	0.2641	H	0.97465	4.01	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.991;0.996	T	0.78548	-0.2162	10	0.87932	D	0	.	19.5156	0.95162	0.0:0.0:1.0:0.0	.	72;140;491	Q86T21;E7EUW5;A1A4S6	.;.;RHG10_HUMAN	H	491;140	ENSP00000336923:R491H;ENSP00000406624:R140H	ENSP00000336923:R491H	R	+	2	0	ARHGAP10	149105646	1.000000	0.71417	0.961000	0.40146	0.122000	0.20287	9.059000	0.93902	2.611000	0.88343	0.561000	0.74099	CGT	.	.		0.308	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		A	148886196	G	A	148886196	3	1	101	1	0	0	0	0	1	0	0	0	862	1145	40	1	1538	1	ARHGAP10	4	148886196	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2062129	148886196	42268080	187	14024										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155278437	155278437	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttccttgtctgctgaaaagTtgacagcactcagaatttct	7	10	3	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:155278437T>C	ENST00000357232.4	-	6	733	c.734A>G	c.(733-735)aAc>aGc	p.N245S	DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	245	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		tgctgaaaagttgacagcact	0.433																																					p.N245S		Atlas-SNP	.											.	DCHS2	594	.	0			c.A734G						.						117	122	120					4																	155278437		2203	4300	6503	SO:0001583	missense	54798	exon6			GAAAAGTTGACAG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.734A>G	chr4.hg19:g.155278437T>C	ENSP00000349768:p.Asn245Ser	47.0	0.0		66.0	4.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.575094	0.00131	.	.	ENSG00000197410	ENST00000357232	T	0.55413	0.52	0.772	-0.951	0.10369	Cadherin (1);	.	.	.	.	T	0.28034	0.0691	N	0.22421	0.69	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.21415	-1.0246	9	0.09338	T	0.73	.	3.0531	0.06175	0.0:0.3566:0.0:0.6434	.	245	Q6V1P9	PCD23_HUMAN	S	245	ENSP00000349768:N245S	ENSP00000349768:N245S	N	-	2	0	DCHS2	155497887	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-1.189000	0.03061	-0.333000	0.08476	-0.495000	0.04643	AAC	.	.		0.433	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		C	155278437	T	C	155278437	3	2	101	1	0	0	0	0	1	0	0	0	4290	1725	60	2	8192	2	DCHS2	4	155278437	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	6392241	155278437	35875839	188	14025										
NPY2R	4887	hgsc.bcm.edu	37	chr4	156135578	156135578	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tagagagcaagatctccaagCgaatcagcttcctgattatt	8	9	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:156135578C>G	ENST00000329476.3	+	2	976	c.487C>G	c.(487-489)Cga>Gga	p.R163G	NPY2R_ENST00000506608.1_Missense_Mutation_p.R163G	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	163					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	GATCTCCAAGCGAATCAGCTT	0.552																																					p.R163G		Atlas-SNP	.											NPY2R,right_upper_lobe,carcinoma,0,1	NPY2R	87	.	0			c.C487G						.						55	51	52					4																	156135578		2203	4300	6503	SO:0001583	missense	4887	exon2			TCCAAGCGAATCA	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"GPCR / Class A : Neuropeptide receptors : Y"	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.487C>G	chr4.hg19:g.156135578C>G	ENSP00000332591:p.Arg163Gly	14.0	0.0		70.0	8.0	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation	SNP	ENST00000329476.3	hg19	CCDS3791.1	.	.	.	.	.	.	.	.	.	.	C	8.336	0.827495	0.16749	.	.	ENSG00000185149	ENST00000329476;ENST00000506608	T;T	0.42131	0.98;0.98	5.74	1.05	0.20165	GPCR, rhodopsin-like superfamily (1);	0.627067	0.16311	N	0.220016	T	0.44993	0.1320	M	0.67953	2.075	0.09310	N	1	B	0.22683	0.073	B	0.28553	0.091	T	0.47935	-0.9078	10	0.46703	T	0.11	.	16.4727	0.84115	0.5564:0.4436:0.0:0.0	.	163	P49146	NPY2R_HUMAN	G	163	ENSP00000332591:R163G;ENSP00000426366:R163G	ENSP00000332591:R163G	R	+	1	2	NPY2R	156355028	0.035000	0.19736	0.221000	0.23827	0.744000	0.42396	0.458000	0.21892	0.190000	0.20209	0.643000	0.83706	CGA	.	.		0.552	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910		G	156135578	C	G	156135578	3	3	101	1	0	0	0	0	1	0	0	0	10618	760	27	4	489	4	NPY2R	4	156135578	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	857141	156135578	35018698	189	14026										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158262498	158262499	+	Missense_Mutation	DNP	GC	GC	AA													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cctacacggctaacttagctGccttcctgactgtagagagg							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:158262498_158262499GC>AA	ENST00000264426.9	+	12	2206_2207	c.1927_1928GC>AA	c.(1927-1929)GCc>AAc	p.A643N	GRIA2_ENST00000296526.7_Missense_Mutation_p.A643N|GRIA2_ENST00000393815.2_Missense_Mutation_p.A596N|GRIA2_ENST00000449365.1_Missense_Mutation_p.A596N|GRIA2_ENST00000507898.1_Missense_Mutation_p.A596N	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	643					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TAACTTAGCTGCCTTCCTGACT	0.455																																					p.A643T|p.A643D		Atlas-SNP	.											.	GRIA2	358	.	0			c.G1927A|c.C1928A						.																																			SO:0001583	missense	2891	exon12			TTAGCTGCCTTCC|TAGCTGCCTTCCT		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	Exception_encountered	chr4.hg19:g.158262498_158262499delinsAA	ENSP00000264426:p.Ala643Asn	163.0|162.0	0.0		385.0|380.0	36.0|35.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1																																																																																			.	.		0.455	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			AA	158262499	GC	AA	158262498	3	1	101	1	0	0	0	0	1	0	0	0	6777	1319	46	3	1973	3	GRIA2	4	158262498	Missense_Mutation	DNP	GC	TCGA-DD-A1EE-01A-11D-A12Z-10	2126920	158262498	32891778	190	14027										
FNIP2	57600	hgsc.bcm.edu	37	chr4	159790073	159790073	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgatgtggctcaggacccgcAggtttctaggagccctttta	12	10	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:159790073A>T	ENST00000264433.6	+	13	2360	c.2285A>T	c.(2284-2286)cAg>cTg	p.Q762L	FNIP2_ENST00000379346.3_Missense_Mutation_p.Q785L	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	762	Interaction with PRKAA1.				intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		CAGGACCCGCAGGTTTCTAGG	0.532																																					p.Q762L		Atlas-SNP	.											.	FNIP2	90	.	0			c.A2285T						.						45	50	49					4																	159790073		1933	4140	6073	SO:0001583	missense	57600	exon13			ACCCGCAGGTTTC	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"O6-methylguanine-induced apoptosis 1"	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.2285A>T	chr4.hg19:g.159790073A>T	ENSP00000264433:p.Gln762Leu	32.0	0.0		103.0	7.0	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	hg19	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	A	13.31	2.199874	0.38905	.	.	ENSG00000052795	ENST00000264433;ENST00000379346	T;T	0.24908	1.83;1.83	5.55	-4.96	0.03038	.	1.330380	0.04524	N	0.385205	T	0.22820	0.0551	M	0.74258	2.255	0.09310	N	1	B	0.28933	0.228	B	0.24394	0.053	T	0.25882	-1.0119	9	.	.	.	.	2.2785	0.04108	0.3484:0.2244:0.3184:0.1087	.	762	Q9P278	FNIP2_HUMAN	L	762;785	ENSP00000264433:Q762L;ENSP00000368651:Q785L	.	Q	+	2	0	FNIP2	160009523	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.484000	0.22308	-0.736000	0.04831	-1.127000	0.01993	CAG	.	.		0.532	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		T	159790073	A	T	159790073	3	4	101	1	0	0	0	0	1	0	0	0	5984	188	7	4	2335	4	FNIP2	4	159790073	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1527575	159790073	31364203	191	14028										
NPY5R	4889	hgsc.bcm.edu	37	chr4	164272591	164272591	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gccactacaccttttccatgTggtaactgattttaatgaca	6	10	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr4:164272591T>A	ENST00000515560.1	+	4	2688	c.1166T>A	c.(1165-1167)gTg>gAg	p.V389E	NPY5R_ENST00000506953.1_Missense_Mutation_p.V389E|NPY5R_ENST00000338566.3_Missense_Mutation_p.V389E			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	389					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				CTTTTCCATGTGGTAACTGAT	0.348																																					p.V389E	Melanoma(139;1287 1774 9781 19750 25599)	Atlas-SNP	.											.	NPY5R	101	.	0			c.T1166A						.						160	152	155					4																	164272591		2203	4300	6503	SO:0001583	missense	4889	exon4			TCCATGTGGTAAC	BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"GPCR / Class A : Neuropeptide receptors : Y"	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.1166T>A	chr4.hg19:g.164272591T>A	ENSP00000423917:p.Val389Glu	77.0	0.0		135.0	13.0	NM_006174	Q6GTR7|Q92916	Missense_Mutation	SNP	ENST00000515560.1	hg19	CCDS3804.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.453285	0.63290	.	.	ENSG00000164129	ENST00000338566;ENST00000515560;ENST00000506953	T;T;T	0.55930	0.49;0.49;0.49	4.9	3.7	0.42460	GPCR, rhodopsin-like superfamily (1);	0.283599	0.24294	N	0.039799	T	0.63331	0.2502	M	0.68317	2.08	0.35343	D	0.786634	D	0.61080	0.989	P	0.58172	0.834	T	0.74349	-0.3694	10	0.62326	D	0.03	.	11.1021	0.48182	0.0:0.0772:0.0:0.9228	.	389	Q15761	NPY5R_HUMAN	E	389	ENSP00000339377:V389E;ENSP00000423917:V389E;ENSP00000423474:V389E	ENSP00000339377:V389E	V	+	2	0	NPY5R	164492041	1.000000	0.71417	0.999000	0.59377	0.854000	0.48673	5.294000	0.65687	1.966000	0.57179	0.377000	0.23210	GTG	.	.		0.348	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174		A	164272591	T	A	164272591	3	1	101	1	0	0	0	0	1	0	0	0	10619	1696	59	4	1168	4	NPY5R	4	164272591	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	4482518	164272591	26881685	192	14029										
IRX1	79192	hgsc.bcm.edu	37	chr5	3599577	3599577	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	catcaccaagatgaccctcaCgcaggtctccacctggttcg	8	16	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:3599577C>A	ENST00000302006.3	+	2	567	c.515C>A	c.(514-516)aCg>aAg	p.T172K	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	172					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						ATGACCCTCACGCAGGTCTCC	0.617																																					p.T172K		Atlas-SNP	.											.	IRX1	106	.	0			c.C515A						.						154	119	131					5																	3599577		2203	4300	6503	SO:0001583	missense	79192	exon2			CCCTCACGCAGGT	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.515C>A	chr5.hg19:g.3599577C>A	ENSP00000305244:p.Thr172Lys	97.0	0.0		200.0	31.0	NM_024337	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	hg19	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.936665	0.92458	.	.	ENSG00000170549	ENST00000302006	D	0.90324	-2.65	4.81	4.81	0.61882	Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1);Homeobox, conserved site (1);	0.049539	0.85682	D	0.000000	D	0.92280	0.7551	L	0.36672	1.1	0.80722	D	1	D	0.54964	0.969	P	0.62560	0.904	D	0.93527	0.6866	10	0.87932	D	0	-25.1634	17.5082	0.87753	0.0:1.0:0.0:0.0	.	172	P78414	IRX1_HUMAN	K	172	ENSP00000305244:T172K	ENSP00000305244:T172K	T	+	2	0	IRX1	3652577	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.547000	0.82146	2.173000	0.68751	0.655000	0.94253	ACG	.	.		0.617	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		A	3599577	C	A	3599577	3	1	101	1	0	0	0	0	1	0	0	0	7852	536	19	1	521	1	IRX1	5	3599577	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10		3599577	177315683	193	14030										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11082847	11082847	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gacgtccaaggccatgttccGcagcgcagtggccaccgcgc	13	16	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:11082847G>A	ENST00000304623.8	-	16	2938	c.2749C>T	c.(2749-2751)Cgg>Tgg	p.R917W	CTNND2_ENST00000503622.1_Missense_Mutation_p.R580W|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000511377.1_Missense_Mutation_p.R826W|CTNND2_ENST00000458100.2_Missense_Mutation_p.R484W|CTNND2_ENST00000359640.2_Missense_Mutation_p.R859W	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	917					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GCCATGTTCCGCAGCGCAGTG	0.522																																					p.R917W		Atlas-SNP	.											CTNND2,NS,carcinoma,0,1	CTNND2	289	.	0			c.C2749T						.						133	116	121					5																	11082847		2203	4300	6503	SO:0001583	missense	1501	exon16			TGTTCCGCAGCGC	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.2749C>T	chr5.hg19:g.11082847G>A	ENSP00000307134:p.Arg917Trp	43.0	0.0		110.0	9.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281706	0.80692	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377;ENST00000538638;ENST00000458100;ENST00000503622	T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49	5.04	5.04	0.67666	Armadillo-like helical (1);Armadillo-type fold (1);	0.209202	0.40554	N	0.001070	D	0.87485	0.6189	M	0.90542	3.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.997	D	0.90094	0.4179	10	0.87932	D	0	-22.3756	18.7557	0.91832	0.0:0.0:1.0:0.0	.	580;509;917	B4DRK2;B4DG58;Q9UQB3	.;.;CTND2_HUMAN	W	917;859;826;12;484;580	ENSP00000307134:R917W;ENSP00000352661:R859W;ENSP00000426510:R826W;ENSP00000391155:R484W;ENSP00000426887:R580W	ENSP00000307134:R917W	R	-	1	2	CTNND2	11135847	1.000000	0.71417	0.997000	0.53966	0.955000	0.61496	3.392000	0.52537	2.505000	0.84491	0.563000	0.77884	CGG	.	.		0.522	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11082847	G	A	11082847	3	1	101	1	0	0	0	0	1	0	0	0	4022	1086	38	1	956	1	CTNND2	5	11082847	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	7483270	11082847	169832413	194	14031										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13770967	13770967	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtgggtagaacgtcggaatcTctgaaaataatcaacacact	9	8	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:13770967T>C	ENST00000265104.4	-	56	9600	c.9496A>G	c.(9496-9498)Aga>Gga	p.R3166G	DNAH5_ENST00000504001.3_5'UTR	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3166	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CGTCGGAATCTCTGAAAATAA	0.468									Kartagener syndrome																												p.R3166G		Atlas-SNP	.											.	DNAH5	868	.	0			c.A9496G						.						137	132	134					5																	13770967		2203	4300	6503	SO:0001583	missense	1767	exon56	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGAATCTCTGAAA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.9496A>G	chr5.hg19:g.13770967T>C	ENSP00000265104:p.Arg3166Gly	71.0	0.0		236.0	18.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	19.49	3.838286	0.71373	.	.	ENSG00000039139	ENST00000265104	T	0.41400	1.0	5.71	4.51	0.55191	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.85682	D	0.000000	T	0.70465	0.3227	M	0.92649	3.33	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.76650	-0.2881	10	0.87932	D	0	.	12.0222	0.53350	0.0:0.0:0.2733:0.7267	.	3166	Q8TE73	DYH5_HUMAN	G	3166	ENSP00000265104:R3166G	ENSP00000265104:R3166G	R	-	1	2	DNAH5	13823967	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.820000	0.48057	0.933000	0.37291	0.533000	0.62120	AGA	.	.		0.468	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13770967	T	C	13770967	3	2	101	1	0	0	0	0	1	0	0	0	4606	1559	54	2	4474	2	DNAH5	5	13770967	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2688120	13770967	167144293	195	14032										
PRLR	5618	hgsc.bcm.edu	37	chr5	35089695	35089695	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaaaagtagcagagtgaaaaCggttgcagatgccacatttt	10	6	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:35089695C>T	ENST00000382002.5	-	3	454	c.28G>A	c.(28-30)Gtt>Att	p.V10I	PRLR_ENST00000231423.3_Missense_Mutation_p.V10I|PRLR_ENST00000348262.3_Missense_Mutation_p.V10I|PRLR_ENST00000542609.1_Missense_Mutation_p.V10I|PRLR_ENST00000397391.3_5'UTR|PRLR_ENST00000310101.5_Missense_Mutation_p.V10I|PRLR_ENST00000511486.1_Missense_Mutation_p.V10I|PRLR_ENST00000513753.1_Missense_Mutation_p.V10I|PRLR_ENST00000342362.5_Missense_Mutation_p.V10I	NM_000949.5	NP_000940.1	P16471	PRLR_HUMAN	prolactin receptor	10					activation of JAK2 kinase activity (GO:0042977)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell surface receptor signaling pathway (GO:0007166)|embryo implantation (GO:0007566)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|prolactin signaling pathway (GO:0038161)|steroid biosynthetic process (GO:0006694)|T cell activation (GO:0042110)	cell surface (GO:0009986)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|ornithine decarboxylase activator activity (GO:0042978)|peptide hormone binding (GO:0017046)|prolactin receptor activity (GO:0004925)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Fluoxymesterone(DB01185)|Somatropin recombinant(DB00052)	AGAGTGAAAACGGTTGCAGAT	0.458																																					p.V10I		Atlas-SNP	.											.	PRLR	90	.	0			c.G28A						.						143	130	134					5																	35089695		2203	4300	6503	SO:0001583	missense	5618	exon3			TGAAAACGGTTGC		CCDS3909.1, CCDS56358.1, CCDS56359.1, CCDS56360.1, CCDS56361.1, CCDS56362.1	5p14-p13	2013-02-27			ENSG00000113494	ENSG00000113494			9446	protein-coding gene	gene with protein product		176761					Standard	NM_001204315		Approved		uc003jjm.3	P16471	OTTHUMG00000090789	ENST00000382002.5:c.28G>A	chr5.hg19:g.35089695C>T	ENSP00000371432:p.Val10Ile	64.0	0.0		86.0	13.0	NM_000949	B2R882|D1MDP1|Q16354|Q8TD75|Q8TD78|Q96P35|Q96P36|Q9BX87|Q9UHJ5	Missense_Mutation	SNP	ENST00000382002.5	hg19	CCDS3909.1	.	.	.	.	.	.	.	.	.	.	C	2.780	-0.253654	0.05829	.	.	ENSG00000113494	ENST00000231423;ENST00000513753;ENST00000348262;ENST00000542609;ENST00000342362;ENST00000382002;ENST00000511486;ENST00000310101;ENST00000514206;ENST00000509839;ENST00000503330;ENST00000504500;ENST00000515839	T;T;T;T;D;T;D;T;T;T;T;T;T	0.88354	0.04;0.04;0.04;0.04;-2.37;0.04;-2.37;0.04;0.04;0.04;0.04;0.04;0.04	5.62	1.77	0.24775	.	1.017420	0.07830	N	0.961153	D	0.86045	0.5839	M	0.73962	2.25	0.09310	N	1	P;B;P;P;P	0.50156	0.685;0.022;0.932;0.827;0.827	B;B;B;B;B	0.38020	0.089;0.005;0.263;0.169;0.169	T	0.72054	-0.4406	10	0.27785	T	0.31	-1.1959	8.3729	0.32425	0.0:0.5864:0.0:0.4136	.	10;10;10;10;10	P16471;P16471-2;P16471-7;P16471-6;P16471-4	PRLR_HUMAN;.;.;.;.	I	10	ENSP00000231423:V10I;ENSP00000424841:V10I;ENSP00000311613:V10I;ENSP00000441813:V10I;ENSP00000339213:V10I;ENSP00000371432:V10I;ENSP00000422556:V10I;ENSP00000309008:V10I;ENSP00000423493:V10I;ENSP00000427060:V10I;ENSP00000422385:V10I;ENSP00000422867:V10I;ENSP00000421864:V10I	ENSP00000231423:V10I	V	-	1	0	PRLR	35125452	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.939000	0.03933	0.310000	0.22990	-0.727000	0.03589	GTT	.	.		0.458	PRLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207575.2			T	35089695	C	T	35089695	3	4	101	1	0	0	0	0	1	0	0	0	12543	536	19	1	1872	1	PRLR	5	35089695	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	21318728	35089695	145825565	196	14033										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38370498	38370498	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ataccaactaccagtttgccGtgagggcaatgaattcccat	8	11	0	2	rs369204325		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:38370498G>T	ENST00000354891.3	+	6	992	c.646G>T	c.(646-648)Gtg>Ttg	p.V216L	EGFLAM_ENST00000322350.5_Missense_Mutation_p.V216L	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	216	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					CCAGTTTGCCGTGAGGGCAAT	0.567																																					p.V216L	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.G646T						.						69	64	66					5																	38370498		2203	4300	6503	SO:0001583	missense	133584	exon6			TTTGCCGTGAGGG	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.646G>T	chr5.hg19:g.38370498G>T	ENSP00000346964:p.Val216Leu	38.0	0.0		154.0	22.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	hg19	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.597961	0.66332	.	.	ENSG00000164318	ENST00000354891;ENST00000322350	T;T	0.72282	-0.64;-0.64	5.82	5.82	0.92795	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.058756	0.64402	D	0.000002	T	0.72087	0.3417	M	0.62723	1.935	0.80722	D	1	B;B	0.22909	0.077;0.063	B;B	0.26969	0.075;0.045	T	0.67749	-0.5590	10	0.49607	T	0.09	-0.1892	19.688	0.95987	0.0:0.0:1.0:0.0	.	216;216	Q63HQ2;Q63HQ2-2	EGFLA_HUMAN;.	L	216	ENSP00000346964:V216L;ENSP00000313084:V216L	ENSP00000313084:V216L	V	+	1	0	EGFLAM	38406255	1.000000	0.71417	0.950000	0.38849	0.988000	0.76386	3.223000	0.51231	2.756000	0.94617	0.561000	0.74099	GTG	.	.		0.567	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		T	38370498	G	T	38370498	3	4	101	1	0	0	0	0	1	0	0	0	4968	1145	40	1	668	1	EGFLAM	5	38370498	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3280803	38370498	142544762	197	14034										
SEPP1	100129792	hgsc.bcm.edu	37	chr5	42804757	42804757	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaaaataattcagaaaaataCcgtgagagagcagtttccac	7	7	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:42804757C>A	ENST00000361970.5	+	0	3431				SEPP1_ENST00000507920.1_Intron|SEPP1_ENST00000506577.1_Splice_Site|SEPP1_ENST00000509276.1_Splice_Site|CTD-2325A15.5_ENST00000606056.1_RNA|SEPP1_ENST00000514985.1_Splice_Site|SEPP1_ENST00000511224.1_Splice_Site	NM_001134848.1	NP_001128320.1	Q4G0S7	CC152_HUMAN	coiled-coil domain containing 152											endometrium(1)	1						CAGAAAAATACCGTGAGAGAG	0.343																																					.		Atlas-SNP	.											.	SEPP1	33	.	0			c.534+1G>T						.						86	82	83					5																	42804757		1800	4072	5872	SO:0001628	intergenic_variant	6414	exon5			AAAATACCGTGAG		CCDS47203.1	5p12	2008-07-14			ENSG00000198865	ENSG00000198865			34438	protein-coding gene	gene with protein product							Standard	NM_001134848		Approved	LOC100129792	uc003jmx.3	Q4G0S7	OTTHUMG00000162141		chr5.hg19:g.42804757C>A		107.0	0.0		295.0	17.0	NM_005410	B3KXI4|B4E0P7|Q5BLP6	Splice_Site	SNP	ENST00000361970.5	hg19	CCDS47203.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.572417	0.65765	.	.	ENSG00000250722	ENST00000514985;ENST00000511224;ENST00000506577;ENST00000514218;ENST00000510965	.	.	.	5.53	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2261	0.82293	0.0:0.8668:0.1332:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEPP1	42840514	1.000000	0.71417	0.696000	0.30242	0.986000	0.74619	6.174000	0.71943	1.276000	0.44395	0.557000	0.71058	.	.	.		0.343	CCDC152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367497.1	XM_001717416		A	42804757	C	A	42804757	1	1	101	0	1	0	0	0	0	0	0	0	14072	521	18	3		3	SEPP1	5	42804757	IGR	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4434259	42804757	138110503	198	14035										
PDE4D	5144	hgsc.bcm.edu	37	chr5	58882174	58882174	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccatatccaggaatgccttcTaaagggaaaattattcacgt	7	9	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:58882174T>C	ENST00000340635.6	-	1	631				PDE4D_ENST00000502484.2_Intron|PDE4D_ENST00000502575.1_Intron|PDE4D_ENST00000546160.1_Intron|PDE4D_ENST00000507116.1_Intron|PDE4D_ENST00000360047.5_Missense_Mutation_p.R10G	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific						adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	GAATGCCTTCTAAAGGGAAAA	0.353																																					p.R10G		Atlas-SNP	.											.	PDE4D	345	.	0			c.A28G						.						258	253	254					5																	58882174		1864	4103	5967	SO:0001627	intron_variant	5144	exon1			GCCTTCTAAAGGG		CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"Phosphodiesterases"	8783	protein-coding gene	gene with protein product	"phosphodiesterase E3 dunce homolog (Drosophila)"	600129	"phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.455+306820A>G	chr5.hg19:g.58882174T>C		88.0	0.0		210.0	13.0	NM_006203	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Missense_Mutation	SNP	ENST00000340635.6	hg19	CCDS47213.1	.	.	.	.	.	.	.	.	.	.	T	9.961	1.222890	0.22457	.	.	ENSG00000113448	ENST00000360047	T	0.67865	-0.29	5.64	5.64	0.86602	.	.	.	.	.	T	0.73745	0.3626	.	.	.	0.80722	D	1	P	0.43662	0.814	P	0.51701	0.677	T	0.76119	-0.3076	8	0.62326	D	0.03	.	11.9443	0.52920	0.0:0.0:0.1448:0.8552	.	9	Q08499-2	.	G	10	ENSP00000353152:R10G	ENSP00000353152:R10G	R	-	1	2	PDE4D	58917931	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.288000	0.43514	2.367000	0.80283	0.528000	0.53228	AGA	.	.		0.353	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3			C	58882174	T	C	58882174	1	2	101	0	1	0	0	0	0	0	0	0	11651	1530	53	2		2	PDE4D	5	58882174	Intron	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	16077417	58882174	122033086	199	14036										
SGTB	54557	hgsc.bcm.edu	37	chr5	64976616	64976616	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atttattcaaggcagtgaggGccagcctgaagggaatagaa	13	6	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:64976616G>A	ENST00000381007.4	-	7	720	c.485C>T	c.(484-486)gCc>gTc	p.A162V		NM_019072.2	NP_061945.1	Q96EQ0	SGTB_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, beta	162										large_intestine(3)|lung(3)|skin(3)	9		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)		GGCAGTGAGGGCCAGCCTGAA	0.353																																					p.A162V		Atlas-SNP	.											.	SGTB	22	.	0			c.C485T						.						71	69	70					5																	64976616		2203	4300	6503	SO:0001583	missense	54557	exon7			GTGAGGGCCAGCC	AK096321	CCDS3988.1	5q12.3	2013-01-10			ENSG00000197860	ENSG00000197860		"Tetratricopeptide (TTC) repeat domain containing"	23567	protein-coding gene	gene with protein product						12477932	Standard	XM_005248548		Approved	Sgt2, FLJ39002	uc003jud.3	Q96EQ0	OTTHUMG00000097801	ENST00000381007.4:c.485C>T	chr5.hg19:g.64976616G>A	ENSP00000370395:p.Ala162Val	55.0	0.0		136.0	68.0	NM_019072		Missense_Mutation	SNP	ENST00000381007.4	hg19	CCDS3988.1	.	.	.	.	.	.	.	.	.	.	G	34	5.356958	0.95854	.	.	ENSG00000197860	ENST00000381007;ENST00000506816	T;T	0.67171	-0.25;-0.25	5.31	5.31	0.75309	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.114435	0.64402	D	0.000014	D	0.82504	0.5051	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.83842	0.0258	10	0.56958	D	0.05	-26.1574	18.9824	0.92760	0.0:0.0:1.0:0.0	.	162	Q96EQ0	SGTB_HUMAN	V	162	ENSP00000370395:A162V;ENSP00000421447:A162V	ENSP00000370395:A162V	A	-	2	0	SGTB	65012372	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.444000	0.97578	2.496000	0.84212	0.557000	0.71058	GCC	.	.		0.353	SGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215057.2	NM_019072		A	64976616	G	A	64976616	3	1	101	1	0	0	0	0	1	0	0	0	14241	1203	42	3	449	3	SGTB	5	64976616	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6094442	64976616	115938644	200	14037										
FCHO2	115548	hgsc.bcm.edu	37	chr5	72348291	72348292	+	Frame_Shift_Ins	INS	-	-	A													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atggcttctttggatgaattINSaaaagtatctatagggaata							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:72348291_72348292insA	ENST00000430046.2	+	13	1246_1247	c.1130_1131insA	c.(1129-1134)ttaaaafs	p.LK377fs	FCHO2_ENST00000512348.1_Frame_Shift_Ins_p.LK344fs|FCHO2_ENST00000341845.6_Frame_Shift_Ins_p.LK377fs	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	377					clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		TTGGATGAATTAAAAGTATCTA	0.342																																					p.L377fs		Atlas-Indel,Pindel	.											.	FCHO2	96	.	0			c.1130_1131insA						.																																			SO:0001589	frameshift_variant	115548	exon13			.	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.1134dupA	chr5.hg19:g.72348295_72348295dupA	ENSP00000393776:p.Leu377fs	100.0	0.0		315.0	101.0	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Frame_Shift_Ins	INS	ENST00000430046.2	hg19	CCDS47230.1																																																																																			.	.		0.342	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		A	72348292	-	A	72348291	7	5	101	1	0	1	1	0	0	0	0	0	5796	1764	61	0	1180	0	FCHO2	5	72348291	Frame_Shift_Ins	INS	-	TCGA-DD-A1EE-01A-11D-A12Z-10	7371675	72348291	108566969	201	14038										
AGGF1	55109	hgsc.bcm.edu	37	chr5	76342270	76342270	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaaaagaaggccaaaataggCattcatcacaaaaatagtcc	6	8	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:76342270C>T	ENST00000312916.7	+	6	1351	c.969C>T	c.(967-969)ggC>ggT	p.G323G		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	323					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		CCAAAATAGGCATTCATCACA	0.363																																					p.G323G		Atlas-SNP	.											.	AGGF1	71	.	0			c.C969T						.						112	120	117					5																	76342270		2203	4300	6503	SO:0001819	synonymous_variant	55109	exon6			AATAGGCATTCAT	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"G patch domain containing"	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.969C>T	chr5.hg19:g.76342270C>T		84.0	0.0		213.0	17.0	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Silent	SNP	ENST00000312916.7	hg19	CCDS4035.1																																																																																			.	.		0.363	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046		T	76342270	C	T	76342270	2	4	101	1	0	0	0	0	0	0	0	1	382	697	25	3		3	AGGF1	5	76342270	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3993979	76342270	104572990	202	14039										
GPR98	84059	hgsc.bcm.edu	37	chr5	89910835	89910835	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaatgttactgcaattgtatCggtaagaaattattatagct	7	4	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:89910835C>A	ENST00000405460.2	+	2	302	c.206C>A	c.(205-207)tCg>tAg	p.S69*		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	69	Calx-beta 1. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GCAATTGTATCGGTAAGAAAT	0.308																																					p.S69X		Atlas-SNP	.											.	GPR98	605	.	0			c.C206A						.						46	41	43					5																	89910835		1804	4056	5860	SO:0001630	splice_region_variant	84059	exon2			TTGTATCGGTAAG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.207+1C>A	chr5.hg19:g.89910835C>A		65.0	0.0		208.0	16.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Nonsense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.034704	0.93575	.	.	ENSG00000164199	ENST00000508842;ENST00000405460;ENST00000296619;ENST00000399043	.	.	.	5.98	5.98	0.97165	.	0.167402	0.48286	D	0.000194	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	15.2005	0.73132	0.1408:0.8592:0.0:0.0	.	.	.	.	X	73;69;69;69	.	ENSP00000296619:S69X	S	+	2	0	GPR98	89946591	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.714000	0.47202	2.838000	0.97847	0.591000	0.81541	TCG	.	.		0.308	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	Nonsense_Mutation	A	89910835	C	A	89910835	5	1	101	1	0	0	0	0	0	0	1	0	6730	898	31	1	212	1	GPR98	5	89910835	Splice_Site	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	13568565	89910835	91004425	203	14040										
ELL2	22936	hgsc.bcm.edu	37	chr5	95226823	95226823	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttacctgatactcttttgagCctggagaaaggcgctttctt	9	9	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:95226823C>A	ENST00000237853.4	-	10	2094	c.1745G>T	c.(1744-1746)gGc>gTc	p.G582V	ELL2_ENST00000431061.2_Missense_Mutation_p.G332V	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	582					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		CTCTTTTGAGCCTGGAGAAAG	0.428																																					p.G582V		Atlas-SNP	.											.	ELL2	63	.	0			c.G1745T						.						198	195	196					5																	95226823		2203	4300	6503	SO:0001583	missense	22936	exon10			TTTGAGCCTGGAG	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1745G>T	chr5.hg19:g.95226823C>A	ENSP00000237853:p.Gly582Val	91.0	0.0		172.0	15.0	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	hg19	CCDS4080.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.1|28.1	4.888928|4.888928	0.91814|0.91814	.|.	.|.	ENSG00000118985|ENSG00000118985	ENST00000508757|ENST00000237853;ENST00000431061	.|T;T	.|0.26223	.|1.75;1.75	6.16|6.16	6.16|6.16	0.99307|0.99307	.|Occludin/RNA polymerase II elongation factor, ELL domain (1);	.|0.043393	.|0.85682	.|D	.|0.000000	T|T	0.62490|0.62490	0.2432|0.2432	M|M	0.90369|0.90369	3.11|3.11	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	T|T	0.67225|0.67225	-0.5724|-0.5724	5|10	.|0.87932	.|D	.|0	-1.8572|-1.8572	20.4549|20.4549	0.99139|0.99139	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|582	.|O00472	.|ELL2_HUMAN	S|V	100|582;332	.|ENSP00000237853:G582V;ENSP00000399704:G332V	.|ENSP00000237853:G582V	A|G	-|-	1|2	0|0	ELL2|ELL2	95252579|95252579	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.989000|0.989000	0.77384|0.77384	6.066000|6.066000	0.71185|0.71185	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GCT|GGC	.	.		0.428	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		A	95226823	C	A	95226823	3	1	101	1	0	0	0	0	1	0	0	0	5065	739	26	3	189	3	ELL2	5	95226823	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	5315988	95226823	85688437	204	14041										
ELL2	22936	hgsc.bcm.edu	37	chr5	95226961	95226961	+	Missense_Mutation	SNP	A	A	T													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctggcgttgctcataggagAcgatagcgatatattttcta							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:95226961A>T	ENST00000237853.4	-	10	1956	c.1607T>A	c.(1606-1608)gTc>gAc	p.V536D	ELL2_ENST00000431061.2_Missense_Mutation_p.V286D	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	536					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		CTCATAGGAGACGATAGCGAT	0.363																																					p.V536D		Atlas-SNP	.											ELL2,caecum,carcinoma,0,1	ELL2	63	.	0			c.T1607A						.						115	109	111					5																	95226961		2203	4300	6503	SO:0001583	missense	22936	exon10			TAGGAGACGATAG	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1607T>A	chr5.hg19:g.95226961A>T	ENSP00000237853:p.Val536Asp	50.0	0.0		86.0	11.0	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	hg19	CCDS4080.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.7|20.7	4.040378|4.040378	0.75732|0.75732	.|.	.|.	ENSG00000118985|ENSG00000118985	ENST00000508757|ENST00000237853;ENST00000431061	.|T;T	.|0.23552	.|1.9;1.9	5.7|5.7	5.7|5.7	0.88788|0.88788	.|Occludin/RNA polymerase II elongation factor, ELL domain (1);	.|0.166029	.|0.53938	.|D	.|0.000056	T|T	0.48333|0.48333	0.1494|0.1494	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|D	.|0.72625	.|0.978	T|T	0.41716|0.41716	-0.9493|-0.9493	5|10	.|0.46703	.|T	.|0.11	-0.2399|-0.2399	15.6217|15.6217	0.76810|0.76810	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|536	.|O00472	.|ELL2_HUMAN	T|D	54|536;286	.|ENSP00000237853:V536D;ENSP00000399704:V286D	.|ENSP00000237853:V536D	S|V	-|-	1|2	0|0	ELL2|ELL2	95252717|95252717	0.999000|0.999000	0.42202|0.42202	0.998000|0.998000	0.56505|0.56505	0.932000|0.932000	0.56968|0.56968	2.556000|2.556000	0.45862|0.45862	2.168000|2.168000	0.68352|0.68352	0.528000|0.528000	0.53228|0.53228	TCT|GTC	.	.		0.363	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		T	95226961	A	T	95226961	3	4	101	1	0	0	0	0	1	0	0	0	5065	275	10	4	327	4	ELL2	5	95226961	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	138	95226961	85688299	205	14042	60	2								
ELL2	22936	hgsc.bcm.edu	37	chr5	95226963	95226963	+	Frame_Shift_Del	DEL	G	G	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tggcgttgctcataggagacGatagcgatatattttctaat							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:95226963delG	ENST00000237853.4	-	10	1954	c.1605delC	c.(1603-1605)atcfs	p.I535fs	ELL2_ENST00000431061.2_Frame_Shift_Del_p.I285fs	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	535					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		CATAGGAGACGATAGCGATAT	0.363																																					p.V536fs		Atlas-INDEL	.											.	ELL2	63	.	0			c.1606delG						.						107	102	104					5																	95226963		2203	4300	6503	SO:0001589	frameshift_variant	22936	exon10			.	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1605delC	chr5.hg19:g.95226963delG	ENSP00000237853:p.Ile535fs	49.0	0.0		82.0	11.0	NM_012081	B4DNK7	Frame_Shift_Del	DEL	ENST00000237853.4	hg19	CCDS4080.1																																																																																			.	.		0.363	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		-	95226963	G	-	95226963	7	5	101	1	0	1	0	1	0	0	0	0	5065	1048	37	0	329	0	ELL2	5	95226963	Frame_Shift_Del	DEL	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2	95226963	85688297	206	14043	60	2								
REEP5	7905	hgsc.bcm.edu	37	chr5	112238112	112238112	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaaggggaaccatgacaggaAgatatcagagaagaattcag	13	5	2	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:112238112A>G	ENST00000379638.4	-	3	664	c.316T>C	c.(316-318)Ttc>Ctc	p.F106L	REEP5_ENST00000474542.2_5'UTR|REEP5_ENST00000513339.1_Missense_Mutation_p.F106L|REEP5_ENST00000545426.1_Missense_Mutation_p.F106L|REEP5_ENST00000504247.1_Intron	NM_005669.4	NP_005660.4	Q00765	REEP5_HUMAN	receptor accessory protein 5	106						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		Epithelial(69;1.3e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.26e-08)|all cancers(49;3.56e-07)|Colorectal(14;0.00778)|COAD - Colon adenocarcinoma(37;0.013)		CATGACAGGAAGATATCAGAG	0.418																																					p.F106L		Atlas-SNP	.											.	REEP5	12	.	0			c.T316C						.						162	141	148					5																	112238112		2202	4300	6502	SO:0001583	missense	7905	exon3			ACAGGAAGATATC	BC000232	CCDS4109.2	5q22-q23	2008-02-05	2006-02-07	2006-02-07	ENSG00000129625	ENSG00000129625		"Receptor accessory proteins"	30077	protein-coding gene	gene with protein product	"deleted in polyposis 1", "polyposis locus protein 1", "polyposis coli region hypothetical protein DP1"	125265	"chromosome 5 open reading frame 18"	C5orf18		16271481, 15550249	Standard	NM_005669		Approved	DP1, TB2, D5S346	uc003kqe.1	Q00765	OTTHUMG00000128807	ENST00000379638.4:c.316T>C	chr5.hg19:g.112238112A>G	ENSP00000368959:p.Phe106Leu	66.0	0.0		196.0	17.0	NM_005669	B7Z681|D3DT04|Q04198|Q5QGT0|Q9BWH9	Missense_Mutation	SNP	ENST00000379638.4	hg19	CCDS4109.2	.	.	.	.	.	.	.	.	.	.	A	9.689	1.151291	0.21371	.	.	ENSG00000129625	ENST00000379638;ENST00000513339;ENST00000545426;ENST00000261482	D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89	5.73	5.73	0.89815	.	0.043741	0.85682	D	0.000000	T	0.80270	0.4592	N	0.03948	-0.315	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.13407	0.009;0.009;0.006	T	0.76206	-0.3044	10	0.02654	T	1	-14.5387	16.0233	0.80516	1.0:0.0:0.0:0.0	.	106;79;106	B7Z510;B7Z2A3;Q00765	.;.;REEP5_HUMAN	L	106;106;106;97	ENSP00000368959:F106L;ENSP00000425901:F106L;ENSP00000442940:F106L;ENSP00000261482:F97L	ENSP00000261482:F97L	F	-	1	0	REEP5	112266011	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.401000	0.79962	2.186000	0.69663	0.533000	0.62120	TTC	.	.		0.418	REEP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250739.2	NM_005669		G	112238112	A	G	112238112	3	3	101	1	0	0	0	0	1	0	0	0	13223	72	3	2	265	2	REEP5	5	112238112	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	17011149	112238112	68677148	207	14044										
FEM1C	56929	hgsc.bcm.edu	37	chr5	114861063	114861063	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgcctttttccagtatttcaAagccccaagcagatctcttt	5	12	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:114861063A>C	ENST00000274457.3	-	3	1357	c.796T>G	c.(796-798)Ttg>Gtg	p.L266V		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	266					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		CAGTATTTCAAAGCCCCAAGC	0.398																																					p.L266V		Atlas-SNP	.											.	FEM1C	50	.	0			c.T796G						.						122	118	119					5																	114861063		2202	4300	6502	SO:0001583	missense	56929	exon3			ATTTCAAAGCCCC		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"Ankyrin repeat domain containing"	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.796T>G	chr5.hg19:g.114861063A>C	ENSP00000274457:p.Leu266Val	99.0	0.0		282.0	12.0	NM_020177	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Missense_Mutation	SNP	ENST00000274457.3	hg19	CCDS4118.1	.	.	.	.	.	.	.	.	.	.	A	6.694	0.496617	0.12762	.	.	ENSG00000145780	ENST00000274457	T	0.74947	-0.89	5.76	2.16	0.27623	.	0.000000	0.64402	D	0.000001	T	0.62551	0.2437	L	0.53617	1.68	0.42902	D	0.994231	P	0.39940	0.696	B	0.32022	0.139	T	0.60073	-0.7334	10	0.46703	T	0.11	-11.6108	8.9579	0.35829	0.7232:0.0:0.2768:0.0	.	266	Q96JP0	FEM1C_HUMAN	V	266	ENSP00000274457:L266V	ENSP00000274457:L266V	L	-	1	2	FEM1C	114888962	0.989000	0.36119	0.999000	0.59377	0.519000	0.34347	1.705000	0.37867	0.456000	0.26937	0.528000	0.53228	TTG	.	.		0.398	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177		C	114861063	A	C	114861063	3	2	101	1	0	0	0	0	1	0	0	0	5819	11	1	5	1061	5	FEM1C	5	114861063	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	2622951	114861063	66054197	208	14045										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118485268	118485268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	accatcttctaaacaagaacCtgttataacagattcgtaca	4	10	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:118485268C>T	ENST00000311085.8	+	18	3826	c.3746C>T	c.(3745-3747)cCt>cTt	p.P1249L	DMXL1_ENST00000539542.1_Missense_Mutation_p.P1249L	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1249										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AAACAAGAACCTGTTATAACA	0.423																																					p.P1249L		Atlas-SNP	.											.	DMXL1	268	.	0			c.C3746T						.						85	79	81					5																	118485268		2202	4300	6502	SO:0001583	missense	1657	exon18			AAGAACCTGTTAT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.3746C>T	chr5.hg19:g.118485268C>T	ENSP00000309690:p.Pro1249Leu	45.0	0.0		108.0	8.0	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	C	1.114	-0.657206	0.03480	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.09350	2.99;2.99	5.39	3.61	0.41365	.	0.469142	0.25487	N	0.030325	T	0.07683	0.0193	N	0.25647	0.755	0.34149	D	0.667335	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.17592	-1.0364	10	0.27785	T	0.31	-4.4666	9.6826	0.40078	0.0:0.7593:0.0:0.2407	.	1249;1249	F5H269;Q9Y485	.;DMXL1_HUMAN	L	1249	ENSP00000309690:P1249L;ENSP00000439479:P1249L	ENSP00000309690:P1249L	P	+	2	0	DMXL1	118513167	0.001000	0.12720	0.922000	0.36590	0.995000	0.86356	1.124000	0.31320	0.773000	0.33404	0.655000	0.94253	CCT	.	.		0.423	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		T	118485268	C	T	118485268	3	4	101	1	0	0	0	0	1	0	0	0	4596	681	24	3	3816	3	DMXL1	5	118485268	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3624205	118485268	62429992	209	14046										
PRR16	51334	hgsc.bcm.edu	37	chr5	120021691	120021691	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgacctctgacctacagctgGaggatgagatgactgacagc	12	10	1	5			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:120021691G>C	ENST00000407149.2	+	2	411	c.202G>C	c.(202-204)Gag>Cag	p.E68Q	PRR16_ENST00000505123.1_5'UTR|PRR16_ENST00000379551.2_Missense_Mutation_p.E45Q|PRR16_ENST00000446965.1_5'UTR			Q569H4	LARGN_HUMAN	proline rich 16	68					positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CCTACAGCTGGAGGATGAGAT	0.468																																					p.E45Q		Atlas-SNP	.											.	PRR16	71	.	0			c.G133C						.						101	92	95					5																	120021691		2203	4300	6503	SO:0001583	missense	51334	exon3			CAGCTGGAGGATG	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.202G>C	chr5.hg19:g.120021691G>C	ENSP00000385118:p.Glu68Gln	35.0	0.0		39.0	19.0	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Missense_Mutation	SNP	ENST00000407149.2	hg19		.	.	.	.	.	.	.	.	.	.	G	23.1	4.370371	0.82573	.	.	ENSG00000184838	ENST00000407149;ENST00000379551	T;T	0.57436	0.4;0.4	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.68622	0.3021	L	0.55990	1.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.66622	-0.5877	9	.	.	.	-4.021	17.7817	0.88526	0.0:0.0:1.0:0.0	.	68;45	Q569H4;Q569H4-3	PRR16_HUMAN;.	Q	68;45	ENSP00000385118:E68Q;ENSP00000368869:E45Q	.	E	+	1	0	PRR16	120049590	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.338000	0.96553	2.568000	0.86640	0.555000	0.69702	GAG	.	.		0.468	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644		C	120021691	G	C	120021691	3	2	101	1	0	0	0	0	1	0	0	0	12601	1175	41	4	139	4	PRR16	5	120021691	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1536423	120021691	60893569	210	14047										
FAM53C	51307	hgsc.bcm.edu	37	chr5	137681062	137681062	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtcaccttgcccacctcagCgccgcttctccctgtcaccc	6	21	4	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:137681062C>T	ENST00000239906.5	+	4	1113	c.685C>T	c.(685-687)Cgc>Tgc	p.R229C	FAM53C_ENST00000507506.1_3'UTR|FAM53C_ENST00000513056.1_Intron|FAM53C_ENST00000434981.2_Missense_Mutation_p.R229C|RP11-256P1.1_ENST00000504539.1_RNA	NM_016605.2	NP_057689.1	Q9NYF3	FA53C_HUMAN	family with sequence similarity 53, member C	229										breast(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CCCACCTCAGCGCCGCTTCTC	0.677																																					p.R229C		Atlas-SNP	.											.	FAM53C	35	.	0			c.C685T						.						85	97	93					5																	137681062		2203	4300	6503	SO:0001583	missense	51307	exon4			CCTCAGCGCCGCT	AF251040	CCDS4204.1	5q31	2008-02-05	2004-11-24	2004-11-26	ENSG00000120709	ENSG00000120709			1336	protein-coding gene	gene with protein product		609372	"chromosome 5 open reading frame 6"	C5orf6		11087669, 11161817	Standard	NM_001135647		Approved		uc003lcv.3	Q9NYF3	OTTHUMG00000129201	ENST00000239906.5:c.685C>T	chr5.hg19:g.137681062C>T	ENSP00000239906:p.Arg229Cys	25.0	0.0		71.0	5.0	NM_001135647	B2RDJ5|D3DQB9	Missense_Mutation	SNP	ENST00000239906.5	hg19	CCDS4204.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.929458	0.73327	.	.	ENSG00000120709	ENST00000434981;ENST00000239906	T;T	0.57907	0.37;0.37	5.55	5.55	0.83447	.	0.252298	0.39834	N	0.001253	T	0.70937	0.3281	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	P	0.62298	0.9	T	0.70156	-0.4949	9	.	.	.	-9.4919	18.4386	0.90656	0.0:1.0:0.0:0.0	.	229	Q9NYF3	FA53C_HUMAN	C	229	ENSP00000403705:R229C;ENSP00000239906:R229C	.	R	+	1	0	FAM53C	137708961	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.135000	0.50546	2.894000	0.99253	0.655000	0.94253	CGC	.	.		0.677	FAM53C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251278.2	NM_016605		T	137681062	C	T	137681062	3	4	101	1	0	0	0	0	1	0	0	0	5589	768	27	1	695	1	FAM53C	5	137681062	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	17659371	137681062	43234198	211	14048										
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140347607	140347607	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaatggctttggaaactcctAtacactggtggtgagcggcc	13	9	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:140347607A>G	ENST00000289269.5	+	1	1788	c.1256A>G	c.(1255-1257)tAt>tGt	p.Y419C	PCDHA4_ENST00000512229.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	419	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAAACTCCTATACACTGGTG	0.577																																					p.Y419C	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.A1256G						.						90	89	89					5																	140347607		2203	4300	6503	SO:0001583	missense	56134	exon1			ACTCCTATACACT	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"Cadherins / Protocadherins : Clustered"	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1256A>G	chr5.hg19:g.140347607A>G	ENSP00000289269:p.Tyr419Cys	22.0	0.0		75.0	11.0	NM_031883	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	hg19	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	A	10.47	1.358951	0.24598	.	.	ENSG00000243232	ENST00000289269	T	0.68181	-0.31	5.82	5.82	0.92795	Cadherin (4);Cadherin-like (1);	0.000000	0.38164	N	0.001799	D	0.88115	0.6350	H	0.97077	3.935	0.58432	D	0.999995	D;D	0.89917	0.999;1.0	D;D	0.97110	0.97;1.0	D	0.92032	0.5634	10	0.87932	D	0	.	16.1728	0.81831	1.0:0.0:0.0:0.0	.	419;419	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	C	419	ENSP00000289269:Y419C	ENSP00000289269:Y419C	Y	+	2	0	PCDHAC2	140327791	1.000000	0.71417	0.978000	0.43139	0.029000	0.11900	5.199000	0.65152	2.228000	0.72767	0.533000	0.62120	TAT	.	.		0.577	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		G	140347607	A	G	140347607	3	3	101	1	0	0	0	0	1	0	0	0	11542	449	16	2	1258	2	PCDHAC2	5	140347607	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	2666545	140347607	40567653	212	14049										
PCDHGC5	56097	hgsc.bcm.edu	37	chr5	140871119	140871119	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcggcccacagactcgcagaGccactgctacaggacgtgct	12	15	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:140871119G>A	ENST00000252087.1	+	1	2312	c.2312G>A	c.(2311-2313)aGc>aAc	p.S771N	PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	771					homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACTCGCAGAGCCACTGCTAC	0.612																																					p.S771N		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.G2312A						.						43	43	43					5																	140871119		2203	4300	6503	SO:0001583	missense	56097	exon1			CGCAGAGCCACTG	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"Cadherins / Protocadherins : Clustered"	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.2312G>A	chr5.hg19:g.140871119G>A	ENSP00000252087:p.Ser771Asn	42.0	0.0		84.0	24.0	NM_018929	Q9Y5C2	Missense_Mutation	SNP	ENST00000252087.1	hg19	CCDS4263.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.609920	0.46527	.	.	ENSG00000240764	ENST00000252087	T	0.48836	0.8	5.07	4.2	0.49525	.	0.000000	0.64402	D	0.000011	T	0.44767	0.1309	L	0.60067	1.865	0.34479	D	0.703668	P;B	0.35272	0.493;0.046	B;B	0.36186	0.219;0.019	T	0.57545	-0.7793	10	0.29301	T	0.29	.	13.4065	0.60915	0.0:0.1588:0.8412:0.0	.	771;771	Q9Y5F6-2;Q9Y5F6	.;PCDGM_HUMAN	N	771	ENSP00000252087:S771N	ENSP00000252087:S771N	S	+	2	0	PCDHGC5	140851303	0.964000	0.33143	0.960000	0.40013	0.813000	0.45954	1.808000	0.38912	1.355000	0.45865	0.555000	0.69702	AGC	.	.		0.612	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929		A	140871119	G	A	140871119	3	1	101	1	0	0	0	0	1	0	0	0	11580	971	34	3	2314	3	PCDHGC5	5	140871119	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	523512	140871119	40044141	213	14050										
FBXO38	81545	hgsc.bcm.edu	37	chr5	147819259	147819259	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atttagtggtccctacccctAtcacatctgtattatccatg	5	12	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:147819259A>G	ENST00000340253.5	+	19	3242	c.3074A>G	c.(3073-3075)tAt>tGt	p.Y1025C	FBXO38_ENST00000296701.6_Missense_Mutation_p.Y780C|FBXO38_ENST00000394370.3_Missense_Mutation_p.Y950C|FBXO38_ENST00000513826.1_Missense_Mutation_p.Y780C			Q6PIJ6	FBX38_HUMAN	F-box protein 38	1025					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)			ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCTACCCCTATCACATCTGT	0.428																																					p.Y950C		Atlas-SNP	.											.	FBXO38	115	.	0			c.A2849G						.						128	121	123					5																	147819259		2203	4300	6503	SO:0001583	missense	81545	exon19			ACCCCTATCACAT	BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.3074A>G	chr5.hg19:g.147819259A>G	ENSP00000342023:p.Tyr1025Cys	83.0	0.0		186.0	57.0	NM_030793	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	ENST00000340253.5	hg19		.	.	.	.	.	.	.	.	.	.	A	23.2	4.383309	0.82792	.	.	ENSG00000145868	ENST00000340253;ENST00000296701;ENST00000394370;ENST00000513826	T;T;T;T	0.40476	1.03;1.19;1.14;1.19	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.53753	0.1816	L	0.34521	1.04	0.34301	D	0.684307	D;D;D	0.76494	0.999;0.996;0.997	D;P;D	0.79784	0.993;0.8;0.912	T	0.66724	-0.5851	10	0.72032	D	0.01	-16.9523	14.7245	0.69332	1.0:0.0:0.0:0.0	.	780;950;1025	Q6PIJ6-3;Q6PIJ6-2;Q6PIJ6	.;.;FBX38_HUMAN	C	1025;780;950;780	ENSP00000342023:Y1025C;ENSP00000296701:Y780C;ENSP00000377895:Y950C;ENSP00000426410:Y780C	ENSP00000296701:Y780C	Y	+	2	0	FBXO38	147799452	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.696000	0.91302	2.213000	0.71641	0.528000	0.53228	TAT	.	.		0.428	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		G	147819259	A	G	147819259	3	3	101	1	0	0	0	0	1	0	0	0	5754	449	16	2	3144	2	FBXO38	5	147819259	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	6948140	147819259	33096001	214	14051										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148406879	148406879	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggcctggctggctaagagatAggcccatgccaggcagagag	16	10	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:148406879A>G	ENST00000515425.1	-	11	2517	c.2416T>C	c.(2416-2418)Tat>Cat	p.Y806H	SH3TC2_ENST00000394358.2_Missense_Mutation_p.Y691H|SH3TC2_ENST00000512049.1_Missense_Mutation_p.Y799H|SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000538184.1_Missense_Mutation_p.Y353H	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	806					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTAAGAGATAGGCCCATGCC	0.562																																					p.Y806H		Atlas-SNP	.											.	SH3TC2	178	.	0			c.T2416C						.						57	61	60					5																	148406879		2203	4300	6503	SO:0001583	missense	79628	exon11			AGAGATAGGCCCA	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.2416T>C	chr5.hg19:g.148406879A>G	ENSP00000423660:p.Tyr806His	36.0	0.0		91.0	4.0	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	A	0.444	-0.897252	0.02472	.	.	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049;ENST00000394358	T;T;T;T	0.79940	-0.05;-1.32;-1.32;-0.05	6.16	2.51	0.30379	Tetratricopeptide-like helical (1);	0.323596	0.30704	N	0.009058	T	0.72606	0.3481	L	0.59436	1.845	0.28519	N	0.913187	B;B;B;B	0.34181	0.256;0.44;0.139;0.44	B;B;B;B	0.27500	0.043;0.08;0.025;0.08	T	0.63368	-0.6653	10	0.41790	T	0.15	-4.4206	10.2947	0.43616	0.6913:0.0:0.3087:0.0	.	691;799;806;806	C9JLC3;Q14CC0;E9PDF1;Q8TF17	.;.;.;S3TC2_HUMAN	H	353;806;799;691	ENSP00000441427:Y353H;ENSP00000423660:Y806H;ENSP00000421860:Y799H;ENSP00000377886:Y691H	ENSP00000377886:Y691H	Y	-	1	0	SH3TC2	148387072	1.000000	0.71417	0.992000	0.48379	0.084000	0.17831	1.894000	0.39768	0.207000	0.20607	-0.911000	0.02809	TAT	.	.		0.562	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		G	148406879	A	G	148406879	3	3	101	1	0	0	0	0	1	0	0	0	14277	420	15	2	1478	2	SH3TC2	5	148406879	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	587620	148406879	32508381	215	14052										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148411195	148411195	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctcagtctgcttatcacttcCcagggccaacagggagcatc	9	14	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:148411195C>A	ENST00000515425.1	-	9	1158	c.1057G>T	c.(1057-1059)Gga>Tga	p.G353*	SH3TC2_ENST00000394358.2_Nonsense_Mutation_p.G238*|SH3TC2_ENST00000512049.1_Nonsense_Mutation_p.G346*|SH3TC2_ENST00000513340.1_5'UTR|SH3TC2_ENST00000538184.1_5'UTR	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	353					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTATCACTTCCCAGGGCCAAC	0.527																																					p.G353X		Atlas-SNP	.											.	SH3TC2	178	.	0			c.G1057T						.						160	128	139					5																	148411195		2203	4300	6503	SO:0001587	stop_gained	79628	exon9			CACTTCCCAGGGC	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.1057G>T	chr5.hg19:g.148411195C>A	ENSP00000423660:p.Gly353*	56.0	0.0		138.0	15.0	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Nonsense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.865918	0.91511	.	.	ENSG00000169247	ENST00000515425;ENST00000512049;ENST00000394358	.	.	.	5.53	4.66	0.58398	.	0.208186	0.44097	D	0.000488	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	9.565	0.39394	0.1737:0.7505:0.0:0.0758	.	.	.	.	X	353;346;238	.	ENSP00000377886:G238X	G	-	1	0	SH3TC2	148391388	0.677000	0.27577	0.719000	0.30619	0.397000	0.30659	1.260000	0.32968	1.468000	0.48064	0.563000	0.77884	GGA	.	.		0.527	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		A	148411195	C	A	148411195	4	1	101	1	0	0	0	0	0	1	0	0	14277	632	22	3	2845	3	SH3TC2	5	148411195	Nonsense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4316	148411195	32504065	216	14053										
PDGFRB	5159	hgsc.bcm.edu	37	chr5	149497264	149497264	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agggggatgatatagtcgttGtcaccctcattgggctgcac	13	9	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:149497264G>T	ENST00000261799.4	-	22	3523	c.3054C>A	c.(3052-3054)gaC>gaA	p.D1018E		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	1018					adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TATAGTCGTTGTCACCCTCAT	0.637			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"																																p.D1018E		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	.	PDGFRB	142	.	0			c.C3054A						.						103	100	101					5																	149497264		2203	4300	6503	SO:0001583	missense	5159	exon22			GTCGTTGTCACCC	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.3054C>A	chr5.hg19:g.149497264G>T	ENSP00000261799:p.Asp1018Glu	35.0	0.0		50.0	19.0	NM_002609	B5A957|Q8N5L4	Missense_Mutation	SNP	ENST00000261799.4	hg19	CCDS4303.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.421141	0.42918	.	.	ENSG00000113721	ENST00000261799;ENST00000544453	T	0.75260	-0.92	5.26	4.33	0.51752	.	0.000000	0.53938	D	0.000055	T	0.50531	0.1621	N	0.08118	0	0.31525	N	0.661856	B;B	0.32245	0.361;0.036	B;B	0.28784	0.094;0.012	T	0.57860	-0.7738	10	0.38643	T	0.18	.	9.0691	0.36482	0.0819:0.248:0.6701:0.0	.	1018;1018	A8KAM8;P09619	.;PGFRB_HUMAN	E	1018;688	ENSP00000261799:D1018E	ENSP00000261799:D1018E	D	-	3	2	PDGFRB	149477457	1.000000	0.71417	0.994000	0.49952	0.884000	0.51177	2.350000	0.44063	2.465000	0.83290	0.655000	0.94253	GAC	.	.		0.637	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		T	149497264	G	T	149497264	3	4	101	1	0	0	0	0	1	0	0	0	11671	1368	48	3	274	3	PDGFRB	5	149497264	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1086069	149497264	31417996	217	14054										
WWC1	23286	hgsc.bcm.edu	37	chr5	167891765	167891765	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caagtcgctgcgctccgagcGtctgatccgtacctcgctgg	12	15	1	1	rs139653620		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:167891765G>A	ENST00000265293.4	+	21	3450	c.2948G>A	c.(2947-2949)cGt>cAt	p.R983H	WWC1_ENST00000521089.1_Missense_Mutation_p.R989H|WWC1_ENST00000522140.1_3'UTR	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	983	Interaction with PRKCZ.|Interaction with histone H3.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)	p.R983H(1)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		CGCTCCGAGCGTCTGATCCGT	0.602																																					p.R989H		Atlas-SNP	.											WWC1,colon,carcinoma,0,2	WWC1	98	.	1	Substitution - Missense(1)	ovary(1)	c.G2966A						.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	54	53	53		2966,2966,2948	4.1	1	5	dbSNP_134	53	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	WWC1	NM_001161661.1,NM_001161662.1,NM_015238.2	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	989/1120,989/1119,983/1114	167891765	1,13005	2203	4300	6503	SO:0001583	missense	23286	exon21			CCGAGCGTCTGAT	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2948G>A	chr5.hg19:g.167891765G>A	ENSP00000265293:p.Arg983His	42.0	0.0		130.0	6.0	NM_001161662	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	hg19	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.760611	0.31137	0.0	1.16E-4	ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000524038	T;T;T	0.42131	0.98;0.98;0.98	4.99	4.12	0.48240	.	0.129675	0.56097	D	0.000032	T	0.30947	0.0781	L	0.33485	1.01	0.50632	D	0.999882	B;B	0.21821	0.061;0.01	B;B	0.16722	0.016;0.005	T	0.05971	-1.0853	10	0.18276	T	0.48	.	13.4327	0.61064	0.076:0.0:0.924:0.0	.	989;983	Q8IX03-2;Q8IX03	.;KIBRA_HUMAN	H	983;989;315	ENSP00000265293:R983H;ENSP00000427772:R989H;ENSP00000428084:R315H	ENSP00000265293:R983H	R	+	2	0	WWC1	167824343	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	5.504000	0.66968	1.106000	0.41623	0.442000	0.29010	CGT	.	G|1.000;A|0.000		0.602	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		A	167891765	G	A	167891765	3	1	101	1	0	0	0	0	1	0	0	0	17426	1145	40	1	3048	1	WWC1	5	167891765	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	18394501	167891765	13023495	218	14055										
FOXI1	2299	hgsc.bcm.edu	37	chr5	169535204	169535204	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agcagtctcccggtggacagCcccaagaccacggagcctca	11	16	2	1	rs35678180	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:169535204C>A	ENST00000306268.6	+	2	787	c.726C>A	c.(724-726)agC>agA	p.S242R	FOXI1_ENST00000449804.2_Intron			Q12951	FOXI1_HUMAN	forkhead box I1	242					embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGGTGGACAGCCCCAAGACCA	0.592									Pendred syndrome																												p.S242R		Atlas-SNP	.											.	FOXI1	70	.	0			c.C726A						.						56	62	60					5																	169535204		2203	4300	6503	SO:0001583	missense	2299	exon2	Familial Cancer Database	Goiter-Deafness syndrome	GGACAGCCCCAAG	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.726C>A	chr5.hg19:g.169535204C>A	ENSP00000304286:p.Ser242Arg	39.0	0.0		157.0	8.0	NM_012188	Q14518|Q66SR7|Q8N6L8	Missense_Mutation	SNP	ENST00000306268.6	hg19	CCDS4372.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.949135	0.34377	.	.	ENSG00000168269	ENST00000306268	D	0.94280	-3.39	4.91	3.01	0.34805	.	0.246213	0.41605	D	0.000858	D	0.94997	0.8381	M	0.81682	2.555	0.80722	D	1	D	0.59357	0.985	P	0.58077	0.832	D	0.93602	0.6931	10	0.41790	T	0.15	.	10.1849	0.42991	0.0:0.826:0.0:0.174	.	242	Q12951	FOXI1_HUMAN	R	242	ENSP00000304286:S242R	ENSP00000304286:S242R	S	+	3	2	FOXI1	169467782	1.000000	0.71417	0.997000	0.53966	0.015000	0.08874	1.094000	0.30951	0.987000	0.38709	0.455000	0.32223	AGC	.	C|0.995;T|0.005		0.592	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		A	169535204	C	A	169535204	3	1	101	1	0	0	0	0	1	0	0	0	6017	738	26	3	732	3	FOXI1	5	169535204	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1643439	169535204	11380056	219	14056										
LCP2	3937	hgsc.bcm.edu	37	chr5	169685155	169685155	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaagtagtgctggctggggcAaaggtctctgatgcactgtg	16	7	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:169685155A>G	ENST00000046794.5	-	16	1601	c.986T>C	c.(985-987)tTg>tCg	p.L329S	LCP2_ENST00000521416.1_Missense_Mutation_p.L124S	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	329					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TGGCTGGGGCAAAGGTCTCTG	0.498																																					p.L329S		Atlas-SNP	.											.	LCP2	133	.	0			c.T986C						.						175	173	174					5																	169685155		1945	4144	6089	SO:0001583	missense	3937	exon16			TGGGGCAAAGGTC		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.986T>C	chr5.hg19:g.169685155A>G	ENSP00000046794:p.Leu329Ser	54.0	0.0		156.0	13.0	NM_005565	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	hg19	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.620395	0.46736	.	.	ENSG00000043462	ENST00000046794;ENST00000521416;ENST00000520344	T;T	0.48836	0.82;0.8	5.72	4.56	0.56223	.	0.301944	0.29073	N	0.013231	T	0.42494	0.1205	L	0.50333	1.59	0.36232	D	0.852709	P;P	0.44776	0.843;0.469	B;B	0.42653	0.394;0.209	T	0.50988	-0.8762	9	.	.	.	-5.6214	9.5973	0.39582	0.92:0.0:0.08:0.0	.	124;329	E7ESF6;Q13094	.;LCP2_HUMAN	S	329;124;96	ENSP00000046794:L329S;ENSP00000428871:L124S	.	L	-	2	0	LCP2	169617733	0.999000	0.42202	0.984000	0.44739	0.744000	0.42396	2.971000	0.49248	1.108000	0.41662	0.533000	0.62120	TTG	.	.		0.498	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		G	169685155	A	G	169685155	3	3	101	1	0	0	0	0	1	0	0	0	8701	131	5	2	639	2	LCP2	5	169685155	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	149951	169685155	11230105	220	14057										
DBN1	1627	hgsc.bcm.edu	37	chr5	176895871	176895871	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atgctgcaagcttgaggtcaTcggagccatcttcatatgtg	11	9	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:176895871T>A	ENST00000309007.5	-	2	335	c.116A>T	c.(115-117)gAt>gTt	p.D39V	DBN1_ENST00000393565.1_Missense_Mutation_p.D39V|DBN1_ENST00000292385.5_Missense_Mutation_p.D41V	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	39	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTTGAGGTCATCGGAGCCATC	0.607																																					p.D41V		Atlas-SNP	.											.	DBN1	122	.	0			c.A122T						.						183	159	167					5																	176895871		2203	4300	6503	SO:0001583	missense	1627	exon3			AGGTCATCGGAGC		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.116A>T	chr5.hg19:g.176895871T>A	ENSP00000308532:p.Asp39Val	53.0	0.0		143.0	11.0	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	hg19	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.098996	0.76870	.	.	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000477391;ENST00000514833	T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16	3.76	3.76	0.43208	Actin-binding, cofilin/tropomyosin type (3);	0.137801	0.47093	D	0.000241	T	0.56790	0.2009	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.987	T	0.62220	-0.6900	10	0.87932	D	0	-21.9146	12.4455	0.55649	0.0:0.0:0.0:1.0	.	39;41	Q16643;Q16643-2	DREB_HUMAN;.	V	39;41;39;39;39	ENSP00000308532:D39V;ENSP00000292385:D41V;ENSP00000377195:D39V;ENSP00000422854:D39V;ENSP00000421465:D39V	ENSP00000292385:D41V	D	-	2	0	DBN1	176828477	1.000000	0.71417	0.994000	0.49952	0.827000	0.46813	5.052000	0.64263	1.941000	0.56285	0.450000	0.29827	GAT	.	.		0.607	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		A	176895871	T	A	176895871	3	1	101	1	0	0	0	0	1	0	0	0	4254	1435	50	4	1885	4	DBN1	5	176895871	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	7210716	176895871	4019389	221	14058										
PDLIM7	9260	hgsc.bcm.edu	37	chr5	176916422	176916422	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttgtggcactggtgacacaCgggagtcttgccgttgttgc	14	10	1	1	rs35410317		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:176916422C>T	ENST00000355841.2	-	9	907	c.841G>A	c.(841-843)Gtg>Atg	p.V281M	PDLIM7_ENST00000359895.2_Missense_Mutation_p.V247M|PDLIM7_ENST00000356618.4_Missense_Mutation_p.R260H|PDLIM7_ENST00000393551.1_Missense_Mutation_p.R260H	NM_005451.3	NP_005442.2	Q9NR12	PDLI7_HUMAN	PDZ and LIM domain 7 (enigma)	281	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|receptor-mediated endocytosis (GO:0006898)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ruffle (GO:0001726)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGGTGACACACGGGAGTCTTG	0.682																																					p.V281M		Atlas-SNP	.											.	PDLIM7	32	.	0			c.G841A						.						26	34	31					5																	176916422		2198	4294	6492	SO:0001583	missense	9260	exon9			GACACACGGGAGT	BC001093	CCDS4422.1, CCDS4423.1, CCDS4424.1	5q35.3	2008-02-05			ENSG00000196923	ENSG00000196923			22958	protein-coding gene	gene with protein product		605903				11874232	Standard	NM_005451		Approved	ENIGMA	uc003mhc.1	Q9NR12	OTTHUMG00000130853	ENST00000355841.2:c.841G>A	chr5.hg19:g.176916422C>T	ENSP00000348099:p.Val281Met	56.0	0.0		66.0	26.0	NM_005451	Q14250|Q5XG82|Q6NVZ5|Q96C91|Q9BXB8|Q9BXB9	Missense_Mutation	SNP	ENST00000355841.2	hg19	CCDS4422.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.40|11.40	1.626733|1.626733	0.28978|0.28978	.|.	.|.	ENSG00000196923|ENSG00000196923	ENST00000356618;ENST00000393551|ENST00000359895;ENST00000355841	T;T|T;T	0.16457|0.50548	2.34;2.34|0.86;0.74	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Zinc finger, LIM-type (3);	.|0.000000	.|0.52532	.|D	.|0.000064	T|T	0.41534|0.41534	0.1163|0.1163	L|L	0.45744|0.45744	1.44|1.44	0.26193|0.26193	N|N	0.979551|0.979551	B|D;D	0.10296|0.61697	0.003|0.99;0.985	B|P;P	0.06405|0.49421	0.002|0.61;0.522	T|T	0.39210|0.39210	-0.9625|-0.9625	9|10	0.38643|0.02654	T|T	0.18|1	.|.	9.5492|9.5492	0.39299|0.39299	0.0:0.7763:0.1452:0.0784|0.0:0.7763:0.1452:0.0784	.|.	260|281;247	Q9NR12-4|Q9NR12;Q9NR12-2	.|PDLI7_HUMAN;.	H|M	260|247;281	ENSP00000349030:R260H;ENSP00000377182:R260H|ENSP00000352964:V247M;ENSP00000348099:V281M	ENSP00000349030:R260H|ENSP00000348099:V281M	R|V	-|-	2|1	0|0	PDLIM7|PDLIM7	176849028|176849028	0.512000|0.512000	0.26186|0.26186	0.963000|0.963000	0.40424|0.40424	0.872000|0.872000	0.50106|0.50106	1.033000|1.033000	0.30191|0.30191	2.505000|2.505000	0.84491|0.84491	0.655000|0.655000	0.94253|0.94253	CGT|GTG	.	.		0.682	PDLIM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253423.1	NM_005451		T	176916422	C	T	176916422	3	4	101	1	0	0	0	0	1	0	0	0	11693	536	19	1	552	1	PDLIM7	5	176916422	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	20551	176916422	3998838	222	14059										
BTNL3	10917	hgsc.bcm.edu	37	chr5	180432823	180432823	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tatccagcatgcgatgtatgAcgaggaaaaggggactccca	12	9	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr5:180432823A>C	ENST00000342868.6	+	8	1536	c.1352A>C	c.(1351-1353)gAc>gCc	p.D451A	RNU6-1036P_ENST00000383959.1_RNA	NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3	451	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			GCGATGTATGACGAGGAAAAG	0.483																																					p.D451A		Atlas-SNP	.											.	BTNL3	55	.	0			c.A1352C						.						68	63	65					5																	180432823		1941	4146	6087	SO:0001583	missense	10917	exon8			TGTATGACGAGGA	AB020625	CCDS47358.1	5q35	2014-01-14			ENSG00000168903	ENSG00000168903		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1143	protein-coding gene	gene with protein product	"butyrophilin-like receptor"	606192				10429365	Standard	NM_197975		Approved	BTNLR, BTN9.1	uc003mmr.3	Q6UXE8	OTTHUMG00000162091	ENST00000342868.6:c.1352A>C	chr5.hg19:g.180432823A>C	ENSP00000341787:p.Asp451Ala	67.0	0.0		245.0	14.0	NM_197975	Q496L7|Q9Y2C7	Missense_Mutation	SNP	ENST00000342868.6	hg19	CCDS47358.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.811989	0.32053	.	.	ENSG00000168903	ENST00000342868;ENST00000376852	T	0.60797	0.16	2.37	-0.711	0.11230	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.45276	0.1334	L	0.52126	1.63	0.09310	N	1	B;B	0.23650	0.089;0.0	B;B	0.25614	0.062;0.0	T	0.43861	-0.9365	9	0.66056	D	0.02	.	2.1176	0.03718	0.5797:0.0:0.1676:0.2527	.	417;451	C9JDC2;Q6UXE8	.;BTNL3_HUMAN	A	451;417	ENSP00000341787:D451A	ENSP00000341787:D451A	D	+	2	0	BTNL3	180365429	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.006000	0.12833	-0.467000	0.06932	0.164000	0.16699	GAC	.	.		0.483	BTNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367176.2	NM_197975		C	180432823	A	C	180432823	3	2	101	1	0	0	0	0	1	0	0	0	1568	275	10	5	1382	5	BTNL3	5	180432823	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	3516401	180432823	482437	223	14060										
JARID2	3720	hgsc.bcm.edu	37	chr6	15507624	15507624	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caataacacagggtccatccTgcgtcacctcggtgctgtgc	10	14	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:15507624T>A	ENST00000341776.2	+	11	2952	c.2708T>A	c.(2707-2709)cTg>cAg	p.L903Q	JARID2_ENST00000397311.3_Missense_Mutation_p.L731Q|JARID2_ENST00000541660.1_Missense_Mutation_p.L865Q|JARID2_ENST00000474854.1_3'UTR	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	903	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				GGGTCCATCCTGCGTCACCTC	0.587																																					p.L903Q		Atlas-SNP	.											.	JARID2	135	.	0			c.T2708A						.						154	127	136					6																	15507624		2203	4300	6503	SO:0001583	missense	3720	exon11			CCATCCTGCGTCA	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.2708T>A	chr6.hg19:g.15507624T>A	ENSP00000341280:p.Leu903Gln	46.0	0.0		119.0	7.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	hg19	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.945874	0.92593	.	.	ENSG00000008083	ENST00000341776;ENST00000397311;ENST00000541660	T;T;T	0.57752	0.38;0.38;0.38	5.36	5.36	0.76844	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	T	0.69433	0.3110	M	0.83012	2.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.76024	-0.3110	10	0.87932	D	0	-10.9955	15.3324	0.74223	0.0:0.0:0.0:1.0	.	865;903	F5H590;Q92833	.;JARD2_HUMAN	Q	903;731;865	ENSP00000341280:L903Q;ENSP00000380478:L731Q;ENSP00000444623:L865Q	ENSP00000341280:L903Q	L	+	2	0	JARID2	15615603	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.930000	0.87610	2.028000	0.59812	0.477000	0.44152	CTG	.	.		0.587	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		A	15507624	T	A	15507624	3	1	101	1	0	0	0	0	1	0	0	0	7954	1580	55	4	2750	4	JARID2	6	15507624	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10		15507624	155607443	224	14061										
PRL	5617	hgsc.bcm.edu	37	chr6	22294684	22294684	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggttatggatgtagtgggacAggacgacggcgcggtcaaac	17	7	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:22294684A>T	ENST00000306482.1	-	2	676	c.158T>A	c.(157-159)cTg>cAg	p.L53Q	RP3-404K8.2_ENST00000561912.1_RNA	NM_000948.5|NM_001163558.2	NP_000939.1|NP_001157030.1	P01236	PRL_HUMAN	prolactin	53					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|circadian rhythm (GO:0007623)|female pregnancy (GO:0007565)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|multicellular organismal response to stress (GO:0033555)|ovulation cycle (GO:0042698)|parturition (GO:0007567)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of JAK-STAT cascade (GO:0046427)|regulation of multicellular organism growth (GO:0040014)|regulation of ossification (GO:0030278)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	prolactin receptor binding (GO:0005148)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)|prostate(1)	16	Ovarian(93;0.163)					GTAGTGGGACAGGACGACGGC	0.587																																					p.L53Q		Atlas-SNP	.											.	PRL	41	.	0			c.T158A						.						103	93	96					6																	22294684		2203	4300	6503	SO:0001583	missense	5617	exon2			TGGGACAGGACGA	D00411	CCDS4548.1	6p22.3	2013-09-16			ENSG00000172179	ENSG00000172179			9445	protein-coding gene	gene with protein product		176760					Standard	NM_000948		Approved		uc003ndq.3	P01236	OTTHUMG00000016111	ENST00000306482.1:c.158T>A	chr6.hg19:g.22294684A>T	ENSP00000302150:p.Leu53Gln	79.0	0.0		360.0	16.0	NM_000948	Q15199|Q92996	Missense_Mutation	SNP	ENST00000306482.1	hg19	CCDS4548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.1|22.1	4.242959|4.242959	0.79912|0.79912	.|.	.|.	ENSG00000172179|ENSG00000172179	ENST00000438606|ENST00000306482	.|D	.|0.89939	.|-2.59	6.04|6.04	4.86|4.86	0.63082|0.63082	.|Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	.|0.256840	.|0.40222	.|N	.|0.001143	.|D	.|0.92652	.|0.7665	M|M	0.82323|0.82323	2.585|2.585	0.54753|0.54753	D|D	0.999985|0.999985	.|B;D	.|0.89917	.|0.222;1.0	.|P;D	.|0.81914	.|0.814;0.995	.|D	.|0.92698	.|0.6172	.|10	.|0.49607	.|T	.|0.09	.|-0.0438	12.5677|12.5677	0.56318|0.56318	0.8753:0.0:0.0:0.1247|0.8753:0.0:0.0:0.1247	.|.	.|53;54	.|P01236;Q5I0G2	.|PRL_HUMAN;.	.|Q	-1|53	.|ENSP00000302150:L53Q	.|ENSP00000302150:L53Q	.|L	-|-	.|2	.|0	PRL|PRL	22402663|22402663	0.999000|0.999000	0.42202|0.42202	0.943000|0.943000	0.38184|0.38184	0.954000|0.954000	0.61252|0.61252	4.588000|4.588000	0.60999|0.60999	1.068000|1.068000	0.40764|0.40764	0.460000|0.460000	0.39030|0.39030	.|CTG	.	.		0.587	PRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043327.1	NM_000948		T	22294684	A	T	22294684	3	4	101	1	0	0	0	0	1	0	0	0	12540	188	7	4	541	4	PRL	6	22294684	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	6787060	22294684	148820383	225	14062										
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156943	26156943	+	Nonsense_Mutation	SNP	A	A	T													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cgggttccttcaaactcaacAagaaggcggcctctggggaa							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:26156943A>T	ENST00000304218.3	+	1	385	c.325A>T	c.(325-327)Aag>Tag	p.K109*	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	109	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						CAAACTCAACAAGAAGGCGGC	0.617																																					p.K109X		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.A325T						.						33	40	38					6																	26156943		2203	4300	6503	SO:0001587	stop_gained	3008	exon1			CTCAACAAGAAGG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"Histones / Replication-dependent"	4718	protein-coding gene	gene with protein product		142220	"H1 histone family, member 4", "histone 1, H1e"	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.325A>T	chr6.hg19:g.26156943A>T	ENSP00000307705:p.Lys109*	55.0	0.0		217.0	19.0	NM_005321	Q4VB25	Nonsense_Mutation	SNP	ENST00000304218.3	hg19	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	35	5.588280	0.96590	.	.	ENSG00000168298	ENST00000304218	.	.	.	5.35	5.35	0.76521	.	0.105304	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2553	14.7974	0.69886	1.0:0.0:0.0:0.0	.	.	.	.	X	109	.	ENSP00000307705:K109X	K	+	1	0	HIST1H1E	26264922	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.448000	0.80631	2.146000	0.66826	0.459000	0.35465	AAG	.	.		0.617	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		T	26156943	A	T	26156943	4	4	101	1	0	0	0	0	0	1	0	0	7135	131	5	4	327	4	HIST1H1E	6	26156943	Nonsense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	3862259	26156943	144958124	226	14063	61	2								
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156946	26156946	+	Nonsense_Mutation	SNP	A	A	T													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gttccttcaaactcaacaagAaggcggcctctggggaagcc							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:26156946A>T	ENST00000304218.3	+	1	388	c.328A>T	c.(328-330)Aag>Tag	p.K110*	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	110					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						ACTCAACAAGAAGGCGGCCTC	0.627																																					p.K110X		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.A328T						.						33	39	37					6																	26156946		2203	4300	6503	SO:0001587	stop_gained	3008	exon1			AACAAGAAGGCGG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"Histones / Replication-dependent"	4718	protein-coding gene	gene with protein product		142220	"H1 histone family, member 4", "histone 1, H1e"	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.328A>T	chr6.hg19:g.26156946A>T	ENSP00000307705:p.Lys110*	55.0	0.0		219.0	18.0	NM_005321	Q4VB25	Nonsense_Mutation	SNP	ENST00000304218.3	hg19	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	35	5.574334	0.96553	.	.	ENSG00000168298	ENST00000304218	.	.	.	5.35	5.35	0.76521	.	0.152047	0.41194	D	0.000922	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.1063	14.7974	0.69886	1.0:0.0:0.0:0.0	.	.	.	.	X	110	.	ENSP00000307705:K110X	K	+	1	0	HIST1H1E	26264925	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	6.134000	0.71689	2.146000	0.66826	0.459000	0.35465	AAG	.	.		0.627	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		T	26156946	A	T	26156946	4	4	101	1	0	0	0	0	0	1	0	0	7135	247	9	4	330	4	HIST1H1E	6	26156946	Nonsense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	3	26156946	144958121	227	14064	61	2								
PGBD1	84547	hgsc.bcm.edu	37	chr6	28268674	28268674	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agggagaaaaaaagacaaagCtcgagtgagtgaactgctcc	12	7	0	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:28268674C>T	ENST00000405948.2	+	7	1463	c.1043C>T	c.(1042-1044)gCt>gTt	p.A348V	PGBD1_ENST00000259883.3_Missense_Mutation_p.A348V	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	348						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A348D(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						AAAGACAAAGCTCGAGTGAGT	0.483																																					p.A348V		Atlas-SNP	.											PGBD1,NS,carcinoma,0,1	PGBD1	106	.	1	Substitution - Missense(1)	endometrium(1)	c.C1043T						.						89	92	91					6																	28268674		2203	4300	6503	SO:0001583	missense	84547	exon7			ACAAAGCTCGAGT	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"-"	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1043C>T	chr6.hg19:g.28268674C>T	ENSP00000385213:p.Ala348Val	62.0	0.0		157.0	12.0	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	hg19	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	C	12.36	1.915317	0.33815	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.01388	4.95;4.95	4.54	3.66	0.41972	.	0.984994	0.08254	N	0.974212	T	0.00384	0.0012	N	0.14661	0.345	0.24096	N	0.995897	B	0.34214	0.442	B	0.26969	0.075	T	0.40553	-0.9557	10	0.25751	T	0.34	-10.3144	9.0861	0.36581	0.0:0.8974:0.0:0.1026	.	348	Q96JS3	PGBD1_HUMAN	V	348	ENSP00000385213:A348V;ENSP00000259883:A348V	ENSP00000259883:A348V	A	+	2	0	PGBD1	28376653	0.985000	0.35326	1.000000	0.80357	0.997000	0.91878	0.968000	0.29357	1.238000	0.43771	0.655000	0.94253	GCT	.	.		0.483	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			T	28268674	C	T	28268674	3	4	101	1	0	0	0	0	1	0	0	0	11789	797	28	3	1065	3	PGBD1	6	28268674	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2111728	28268674	142846393	228	14065			1	15		3	3	383	N	G_C	3.094091e-05
PGBD1	84547	hgsc.bcm.edu	37	chr6	28268801	28268801	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtttcccagaaaagagttgGaccaaaagagacattaaacc	8	8	0	3	rs143874020		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:28268801G>C	ENST00000405948.2	+	7	1590	c.1170G>C	c.(1168-1170)tgG>tgC	p.W390C	PGBD1_ENST00000259883.3_Missense_Mutation_p.W390C	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	390						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						AAAAGAGTTGGACCAAAAGAG	0.413																																					p.W390C		Atlas-SNP	.											.	PGBD1	106	.	0			c.G1170C						.	G	CYS/TRP,CYS/TRP	1,4405	2.1+/-5.4	0,1,2202	65	69	68		1170,1170	4.5	1	6	dbSNP_134	68	0,8600		0,0,4300	no	missense,missense	PGBD1	NM_001184743.1,NM_032507.3	215,215	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	390/810,390/810	28268801	1,13005	2203	4300	6503	SO:0001583	missense	84547	exon7			GAGTTGGACCAAA	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"-"	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1170G>C	chr6.hg19:g.28268801G>C	ENSP00000385213:p.Trp390Cys	34.0	0.0		129.0	10.0	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	hg19	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.612478	0.46631	2.27E-4	0.0	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.02369	4.32;4.32	4.54	4.54	0.55810	.	0.195133	0.25836	N	0.027990	T	0.04724	0.0128	L	0.32530	0.975	0.58432	D	0.999993	D	0.89917	1.0	D	0.75020	0.985	T	0.42799	-0.9430	10	0.87932	D	0	-16.3181	12.9975	0.58654	0.0:0.0:1.0:0.0	.	390	Q96JS3	PGBD1_HUMAN	C	390	ENSP00000385213:W390C;ENSP00000259883:W390C	ENSP00000259883:W390C	W	+	3	0	PGBD1	28376780	0.998000	0.40836	0.976000	0.42696	0.862000	0.49288	4.406000	0.59748	2.521000	0.84997	0.655000	0.94253	TGG	.	G|1.000;C|0.000		0.413	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			C	28268801	G	C	28268801	3	2	101	1	0	0	0	0	1	0	0	0	11789	1183	41	4	1192	4	PGBD1	6	28268801	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	127	28268801	142846266	229	14066			1	15		3	3	383	N	G_C	3.094091e-05
PGBD1	84547	hgsc.bcm.edu	37	chr6	28269056	28269056	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tttatgaggcatcctagaagGgaaatgtattgggaagtctc	12	5	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:28269056G>T	ENST00000405948.2	+	7	1845	c.1425G>T	c.(1423-1425)agG>agT	p.R475S	PGBD1_ENST00000259883.3_Missense_Mutation_p.R475S	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	475						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						ATCCTAGAAGGGAAATGTATT	0.418																																					p.R475S		Atlas-SNP	.											.	PGBD1	106	.	0			c.G1425T						.						158	156	156					6																	28269056		2203	4300	6503	SO:0001583	missense	84547	exon7			TAGAAGGGAAATG	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"-"	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1425G>T	chr6.hg19:g.28269056G>T	ENSP00000385213:p.Arg475Ser	107.0	0.0		338.0	17.0	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	hg19	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.432087	0.25813	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.17854	2.25;2.25	4.66	0.887	0.19200	.	0.140189	0.33253	N	0.005116	T	0.05914	0.0154	L	0.60455	1.87	0.23809	N	0.996784	B	0.22146	0.065	B	0.32211	0.142	T	0.39901	-0.9591	10	0.22109	T	0.4	-6.7987	6.3282	0.21255	0.414:0.0:0.586:0.0	.	475	Q96JS3	PGBD1_HUMAN	S	475	ENSP00000385213:R475S;ENSP00000259883:R475S	ENSP00000259883:R475S	R	+	3	2	PGBD1	28377035	0.860000	0.29831	0.970000	0.41538	0.987000	0.75469	0.262000	0.18460	0.292000	0.22492	0.655000	0.94253	AGG	.	.		0.418	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			T	28269056	G	T	28269056	3	4	101	1	0	0	0	0	1	0	0	0	11789	1223	43	3	1447	3	PGBD1	6	28269056	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	255	28269056	142846011	230	14067			1	15		3	3	383	N	G_C	3.094091e-05
OR11A1	26531	hgsc.bcm.edu	37	chr6	29395051	29395051	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggtagcaaattgccaggtagCggtcatatgccatgacagcc	12	10	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:29395051C>T	ENST00000377149.1	-	5	840	c.368G>A	c.(367-369)cGc>cAc	p.R123H	OR11A1_ENST00000377147.2_Missense_Mutation_p.R123H|OR11A1_ENST00000377148.1_Missense_Mutation_p.R123H|OR5V1_ENST00000377154.1_Intron			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						TGCCAGGTAGCGGTCATATGC	0.537																																					p.R123H		Atlas-SNP	.											.	OR11A1	30	.	0			c.G368A						.						64	70	68					6																	29395051		1510	2709	4219	SO:0001583	missense	26531	exon1			AGGTAGCGGTCAT		CCDS34363.1	6p22.2-p21.31	2014-02-19	2002-02-28		ENSG00000204694	ENSG00000204694		"GPCR / Class A : Olfactory receptors"	8176	protein-coding gene	gene with protein product			"olfactory receptor, family 11, subfamily A, member 2"	OR11A2			Standard	XM_005249001		Approved	hs6M1-18	uc003nmg.3	Q9GZK7	OTTHUMG00000031225	ENST00000377149.1:c.368G>A	chr6.hg19:g.29395051C>T	ENSP00000366354:p.Arg123His	58.0	0.0		231.0	13.0	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	hg19	CCDS34363.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638066	0.47153	.	.	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.77489	-1.1;-1.1;-1.1	3.78	2.9	0.33743	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38436	N	0.001686	D	0.84969	0.5590	M	0.88906	2.99	0.35989	D	0.836566	D	0.89917	1.0	D	0.87578	0.998	D	0.86849	0.2022	10	0.87932	D	0	-20.52	10.1326	0.42687	0.0:0.8986:0.0:0.1014	.	123	Q9GZK7	O11A1_HUMAN	H	123	ENSP00000366353:R123H;ENSP00000366354:R123H;ENSP00000366352:R123H	ENSP00000366352:R123H	R	-	2	0	OR11A1	29503030	0.966000	0.33281	0.949000	0.38748	0.086000	0.17979	5.138000	0.64795	0.785000	0.33685	0.405000	0.27470	CGC	.	.		0.537	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1			T	29395051	C	T	29395051	3	4	101	1	0	0	0	0	1	0	0	0	10933	768	27	1	583	1	OR11A1	6	29395051	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1125995	29395051	141720016	231	14068										
PPT2	9374	hgsc.bcm.edu	37	chr6	32123651	32123651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgccattcgcttgccagacaCggactacttgaagtggctgt	11	11	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:32123651C>T	ENST00000324816.6	+	5	1005	c.437C>T	c.(436-438)aCg>aTg	p.T146M	PPT2_ENST00000375137.2_Missense_Mutation_p.T146M|PPT2_ENST00000395523.1_Missense_Mutation_p.T146M|PRRT1_ENST00000375150.2_5'Flank|PPT2_ENST00000437001.2_Missense_Mutation_p.T23M|PPT2_ENST00000445576.2_Missense_Mutation_p.T146M|PPT2-EGFL8_ENST00000422437.1_Missense_Mutation_p.T146M|PPT2-EGFL8_ENST00000453656.2_3'UTR|PPT2_ENST00000493548.1_3'UTR|PPT2_ENST00000375143.2_Missense_Mutation_p.T146M|PPT2_ENST00000361568.2_Missense_Mutation_p.T152M			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	146					cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						TTGCCAGACACGGACTACTTG	0.527																																					p.T152M		Atlas-SNP	.											.	PPT2	19	.	0			c.C455T						.						159	130	140					6																	32123651		1511	2709	4220	SO:0001583	missense	9374	exon5			CAGACACGGACTA	AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	3.1.2.22		9326	protein-coding gene	gene with protein product		603298				9341199, 10051407	Standard	NM_138717		Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.437C>T	chr6.hg19:g.32123651C>T	ENSP00000320528:p.Thr146Met	109.0	0.0		433.0	19.0	NM_138717	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	Missense_Mutation	SNP	ENST00000324816.6	hg19	CCDS4742.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.780951	0.90282	.	.	ENSG00000221988	ENST00000414204;ENST00000361568;ENST00000395523;ENST00000445576;ENST00000324816;ENST00000437001;ENST00000375137;ENST00000375143;ENST00000424499;ENST00000436118	T;D;D;D;D;D;D;D;D	0.96232	-0.25;-3.95;-3.95;-3.95;-3.95;-3.38;-3.95;-3.95;-3.38	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.97666	0.9235	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.985;0.992;0.992	D	0.98139	1.0435	10	0.62326	D	0.03	-4.8314	16.689	0.85316	0.0:1.0:0.0:0.0	.	146;146;152	Q9UMR5-2;Q9UMR5;B0S872	.;PPT2_HUMAN;.	M	146;152;146;146;146;23;146;146;68;146	ENSP00000398847:T146M;ENSP00000354608:T152M;ENSP00000378894:T146M;ENSP00000412381:T146M;ENSP00000320528:T146M;ENSP00000415350:T23M;ENSP00000364279:T146M;ENSP00000364285:T146M;ENSP00000409877:T68M	ENSP00000320528:T146M	T	+	2	0	PPT2	32231629	1.000000	0.71417	0.995000	0.50966	0.949000	0.60115	6.997000	0.76270	2.527000	0.85204	0.557000	0.71058	ACG	.	.		0.527	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076552.4	NM_138717		T	32123651	C	T	32123651	3	4	101	1	0	0	0	0	1	0	0	0	12424	536	19	1	473	1	PPT2	6	32123651	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2728600	32123651	138991416	232	14069										
RXRB	6257	hgsc.bcm.edu	37	chr6	33166198	33166198	+	Frame_Shift_Del	DEL	G	G	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctggtggcttcacatcttcaGgggggccagacccaccccca							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:33166198delG	ENST00000374680.3	-	3	738	c.527delC	c.(526-528)cctfs	p.P176fs	RXRB_ENST00000544186.1_Intron|SLC39A7_ENST00000374675.3_5'Flank|RXRB_ENST00000413614.2_Frame_Shift_Del_p.P80fs|RXRB_ENST00000374685.4_Frame_Shift_Del_p.P176fs|SLC39A7_ENST00000374677.3_5'Flank|RNY4P10_ENST00000365571.1_RNA	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	176	Modulating. {ECO:0000250}.|Pro-rich.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	CACATCTTCAGGGGGGCCAGA	0.592																																					p.P176fs		Atlas-INDEL	.											.	RXRB	34	.	0			c.528delT						.						94	114	107					6																	33166198		1508	2707	4215	SO:0001589	frameshift_variant	6257	exon3			.	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"Nuclear hormone receptors"	10478	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 2"	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.527delC	chr6.hg19:g.33166198delG	ENSP00000363812:p.Pro176fs	25.0	0.0		112.0	10.0	NM_001270401	P28703|Q59G65|Q5JP92|Q5STQ1	Frame_Shift_Del	DEL	ENST00000374680.3	hg19	CCDS4768.1																																																																																			.	.		0.592	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		-	33166198	G	-	33166198	7	5	101	1	0	1	0	1	0	0	0	0	13779	1000	35	0	1106	0	RXRB	6	33166198	Frame_Shift_Del	DEL	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1042547	33166198	137948869	233	14070										
ZBTB9	221504	hgsc.bcm.edu	37	chr6	33423961	33423961	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagggggtggaggacctgggGgagcaggccaggccgtgcat	21	9	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:33423961G>A	ENST00000395064.2	+	2	1352	c.1084G>A	c.(1084-1086)Gga>Aga	p.G362R		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	362	Gly-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						AGGACCTGGGGGAGCAGGCCA	0.612																																					p.G362R		Atlas-SNP	.											.	ZBTB9	23	.	0			c.G1084A						.						22	22	22					6																	33423961		2203	4300	6503	SO:0001583	missense	221504	exon2			CCTGGGGGAGCAG	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.1084G>A	chr6.hg19:g.33423961G>A	ENSP00000378503:p.Gly362Arg	26.0	0.0		81.0	25.0	NM_152735	A2AB19	Missense_Mutation	SNP	ENST00000395064.2	hg19	CCDS4780.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.168838	0.57584	.	.	ENSG00000213588	ENST00000395064	T	0.08193	3.12	4.99	4.99	0.66335	.	0.507304	0.15055	U	0.283080	T	0.02649	0.0080	L	0.32530	0.975	0.30017	N	0.814695	B	0.31435	0.323	B	0.31101	0.124	T	0.39683	-0.9602	10	0.14252	T	0.57	.	13.6367	0.62227	0.0:0.0:1.0:0.0	.	362	Q96C00	ZBTB9_HUMAN	R	362	ENSP00000378503:G362R	ENSP00000378503:G362R	G	+	1	0	ZBTB9	33531939	1.000000	0.71417	0.915000	0.36163	0.944000	0.59088	4.348000	0.59379	2.594000	0.87642	0.655000	0.94253	GGA	.	.		0.612	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735		A	33423961	G	A	33423961	3	1	101	1	0	0	0	0	1	0	0	0	17573	1233	43	3	1086	3	ZBTB9	6	33423961	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	257763	33423961	137691106	234	14071										
C6orf106	64771	hgsc.bcm.edu	37	chr6	34574641	34574641	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agctgctgcgttactcctaaAagtccacccacctccacact	5	17	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:34574641A>C	ENST00000374023.3	-	4	795	c.552T>G	c.(550-552)ctT>ctG	p.L184L	C6orf106_ENST00000374021.1_Silent_p.L110L|C6orf106_ENST00000374026.3_Silent_p.L118L	NM_024294.2	NP_077270.1	Q9H6K1	CF106_HUMAN	chromosome 6 open reading frame 106	184										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10						TTACTCCTAAAAGTCCACCCA	0.468																																					p.L184L		Atlas-SNP	.											.	C6orf106	29	.	0			c.T552G						.						73	65	68					6																	34574641		2203	4300	6503	SO:0001819	synonymous_variant	64771	exon4			TCCTAAAAGTCCA	AF052106	CCDS4795.1, CCDS4796.1	6p21.31	2012-01-27			ENSG00000196821	ENSG00000196821			21215	protein-coding gene	gene with protein product		612217					Standard	XM_005249298		Approved	FLJ22195, dJ391O22.4	uc003ojr.2	Q9H6K1	OTTHUMG00000014553	ENST00000374023.3:c.552T>G	chr6.hg19:g.34574641A>C		26.0	0.0		50.0	15.0	NM_024294	B2R8K7|Q5VV77|Q96MG5|Q9BUR9	Silent	SNP	ENST00000374023.3	hg19	CCDS4796.1																																																																																			.	.		0.468	C6orf106-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040251.1	NM_022758		C	34574641	A	C	34574641	2	2	101	1	0	0	0	0	0	0	0	1	2321	1	1	5		5	C6orf106	6	34574641	Silent	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1150680	34574641	136540426	235	14072										
UHRF1BP1	54887	hgsc.bcm.edu	37	chr6	34802105	34802105	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcttttgaattgtggcagctCcagggctatagtgtcaaccc	10	10	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:34802105C>A	ENST00000192788.5	+	5	621	c.450C>A	c.(448-450)ctC>ctA	p.L150L	UHRF1BP1_ENST00000452449.2_Silent_p.L150L	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	150							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						TGTGGCAGCTCCAGGGCTATA	0.517																																					p.L150L		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C450A						.						66	64	65					6																	34802105		1983	4154	6137	SO:0001819	synonymous_variant	54887	exon5			GCAGCTCCAGGGC	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 107"	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.450C>A	chr6.hg19:g.34802105C>A		82.0	0.0		278.0	163.0	NM_017754	Q9NXE0	Silent	SNP	ENST00000192788.5	hg19	CCDS43455.1																																																																																			.	.		0.517	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		A	34802105	C	A	34802105	2	1	101	1	0	0	0	0	0	0	0	1	16983	842	30	3		3	UHRF1BP1	6	34802105	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	227464	34802105	136312962	236	14073										
RPL10A	4736	hgsc.bcm.edu	37	chr6	35436589	35436589	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cccgcagcagcaaagtctctCgcgacaccctgtacgaggcg	11	16	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:35436589C>G	ENST00000322203.6	+	2	46	c.19C>G	c.(19-21)Cgc>Ggc	p.R7G	RPL10A_ENST00000467020.1_3'UTR	NM_007104.4	NP_009035.3	P62906	RL10A_HUMAN	ribosomal protein L10a	7					anatomical structure morphogenesis (GO:0009653)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|large_intestine(2)|ovary(1)	4						CAAAGTCTCTCGCGACACCCT	0.692																																					p.R7G		Atlas-SNP	.											.	RPL10A	13	.	0			c.C19G						.						11	12	11					6																	35436589		2196	4293	6489	SO:0001583	missense	4736	exon2			GTCTCTCGCGACA	U12404	CCDS4806.1	6p21.31	2011-04-06			ENSG00000198755	ENSG00000198755		"L ribosomal proteins"	10299	protein-coding gene	gene with protein product		615660		NEDD6		7609734, 9647638	Standard	NM_007104		Approved	Csa-19, L10A	uc003okp.1	P62906	OTTHUMG00000014566	ENST00000322203.6:c.19C>G	chr6.hg19:g.35436589C>G	ENSP00000363018:p.Arg7Gly	24.0	0.0		52.0	19.0	NM_007104	B2R801|P52859|P53025|Q5TZT6|Q8J013	Missense_Mutation	SNP	ENST00000322203.6	hg19	CCDS4806.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.919415	0.52653	.	.	ENSG00000198755	ENST00000322203	T	0.44482	0.92	5.24	5.24	0.73138	Ribosomal protein L1, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.32763	0.0840	M	0.72353	2.195	0.80722	D	1	B	0.06786	0.001	B	0.16289	0.015	T	0.16928	-1.0386	10	0.40728	T	0.16	.	17.4093	0.87481	0.0:1.0:0.0:0.0	.	7	P62906	RL10A_HUMAN	G	7	ENSP00000363018:R7G	ENSP00000363018:R7G	R	+	1	0	RPL10A	35544567	1.000000	0.71417	0.998000	0.56505	0.889000	0.51656	4.559000	0.60796	2.436000	0.82500	0.491000	0.48974	CGC	.	.		0.692	RPL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040283.1	NM_007104		G	35436589	C	G	35436589	3	3	101	1	0	0	0	0	1	0	0	0	13570	884	31	4	25	4	RPL10A	6	35436589	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	634484	35436589	135678478	237	14074										
KCTD20	222658	hgsc.bcm.edu	37	chr6	36447368	36447368	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcttcctaatctatttacagGattattacaaaaccggtatc	4	9	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:36447368G>T	ENST00000373731.2	+	5	929	c.538G>T	c.(538-540)Gat>Tat	p.D180Y	KCTD20_ENST00000536244.1_Splice_Site_p.D35Y|KCTD20_ENST00000449081.2_Intron|KCTD20_ENST00000544295.1_Intron|KCTD20_ENST00000474988.1_Intron	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	180	BTB.				protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						CTATTTACAGGATTATTACAA	0.353																																					p.D180Y		Atlas-SNP	.											.	KCTD20	37	.	0			c.G538T						.						109	106	107					6																	36447368		2203	4300	6503	SO:0001630	splice_region_variant	222658	exon5			TTACAGGATTATT	BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"chromosome 6 open reading frame 69", "potassium channel tetramerisation domain containing 20"	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.538-1G>T	chr6.hg19:g.36447368G>T		37.0	0.0		84.0	6.0	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	hg19	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170316	0.78452	.	.	ENSG00000112078	ENST00000373731;ENST00000536244	D;D	0.82433	-1.61;-1.61	5.01	5.01	0.66863	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.90338	0.6977	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89978	0.4098	9	.	.	.	-26.3868	18.5249	0.90968	0.0:0.0:1.0:0.0	.	180	Q7Z5Y7	KCD20_HUMAN	Y	180;35	ENSP00000362836:D180Y;ENSP00000439118:D35Y	.	D	+	1	0	KCTD20	36555346	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	9.657000	0.98554	2.602000	0.87976	0.591000	0.81541	GAT	.	.		0.353	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562	Missense_Mutation	T	36447368	G	T	36447368	5	4	101	1	0	0	0	0	0	0	1	0	8117	1188	41	3	552	3	KCTD20	6	36447368	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1010779	36447368	134667699	238	14075										
PGC	5225	hgsc.bcm.edu	37	chr6	41707607	41707607	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtactgctggggcacagtgAgcagagaggtgcctgtgtcc	16	9	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:41707607A>G	ENST00000373025.3	-	7	907	c.845T>C	c.(844-846)cTc>cCc	p.L282P		NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	282					digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|skin(1)	16	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			GGGCACAGTGAGCAGAGAGGT	0.617																																					p.L282P		Atlas-SNP	.											.	PGC	56	.	0			c.T845C						.						95	89	91					6																	41707607		2203	4300	6503	SO:0001583	missense	5225	exon7			ACAGTGAGCAGAG		CCDS4859.1, CCDS55000.1	6p21.1	2012-10-02			ENSG00000096088	ENSG00000096088	3.4.23.3		8890	protein-coding gene	gene with protein product		169740					Standard	NM_002630		Approved		uc003ora.2	P20142	OTTHUMG00000014683	ENST00000373025.3:c.845T>C	chr6.hg19:g.41707607A>G	ENSP00000362116:p.Leu282Pro	50.0	0.0		180.0	8.0	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Missense_Mutation	SNP	ENST00000373025.3	hg19	CCDS4859.1	.	.	.	.	.	.	.	.	.	.	A	17.76	3.469891	0.63625	.	.	ENSG00000096088	ENST00000373025	T	0.62232	0.04	5.14	5.14	0.70334	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.000000	0.64402	D	0.000001	D	0.86176	0.5870	H	0.99169	4.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91880	0.5515	10	0.87932	D	0	.	14.8424	0.70235	1.0:0.0:0.0:0.0	.	282	P20142	PEPC_HUMAN	P	282	ENSP00000362116:L282P	ENSP00000362116:L282P	L	-	2	0	PGC	41815585	1.000000	0.71417	1.000000	0.80357	0.341000	0.28922	8.218000	0.89768	2.169000	0.68431	0.454000	0.30748	CTC	.	.		0.617	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2			G	41707607	A	G	41707607	3	3	101	1	0	0	0	0	1	0	0	0	11794	304	11	2	333	2	PGC	6	41707607	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	5260239	41707607	129407460	239	14076										
USP49	25862	hgsc.bcm.edu	37	chr6	41773689	41773689	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	actcggctccttgttctggaTgagctccagactccgactaa	9	13	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:41773689T>G	ENST00000394253.3	-	3	1362	c.1033A>C	c.(1033-1035)Atc>Ctc	p.I345L	USP49_ENST00000373006.1_Missense_Mutation_p.I345L|USP49_ENST00000297229.2_Missense_Mutation_p.I345L|USP49_ENST00000373010.1_Missense_Mutation_p.I345L|USP49_ENST00000373009.3_Missense_Mutation_p.I345L			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	345	USP.				histone H2B conserved C-terminal lysine deubiquitination (GO:0035616)|mRNA splicing, via spliceosome (GO:0000398)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)|skin(2)	23	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TTGTTCTGGATGAGCTCCAGA	0.607																																					p.I345L		Atlas-SNP	.											.	USP49	58	.	0			c.A1033C						.						44	46	45					6																	41773689		2203	4300	6503	SO:0001583	missense	25862	exon4			TCTGGATGAGCTC	AJ586139	CCDS4861.1, CCDS69111.1	6p12.1	2008-02-05	2005-08-08		ENSG00000164663	ENSG00000164663		"Ubiquitin-specific peptidases"	20078	protein-coding gene	gene with protein product			"ubiquitin specific protease 49"			14715245	Standard	NM_018561		Approved	MGC20741	uc003ori.3	Q70CQ1	OTTHUMG00000014688	ENST00000394253.3:c.1033A>C	chr6.hg19:g.41773689T>G	ENSP00000377797:p.Ile345Leu	14.0	0.0		101.0	16.0	NM_018561	Q5T3D9|Q5T3E0|Q96CK4	Missense_Mutation	SNP	ENST00000394253.3	hg19		.	.	.	.	.	.	.	.	.	.	T	16.64	3.180024	0.57800	.	.	ENSG00000164663	ENST00000394253;ENST00000373010;ENST00000373009;ENST00000373006;ENST00000297229	T;T;T;T;T	0.73575	3.76;3.27;3.76;-0.76;-0.76	5.1	5.1	0.69264	.	0.128325	0.64402	D	0.000007	T	0.50240	0.1604	N	0.26130	0.795	0.35841	D	0.826048	P	0.36330	0.548	B	0.41466	0.358	T	0.53387	-0.8446	10	0.11485	T	0.65	-17.1117	14.8356	0.70180	0.0:0.0:0.0:1.0	.	345	Q70CQ1-2	.	L	345	ENSP00000377797:I345L;ENSP00000362101:I345L;ENSP00000362100:I345L;ENSP00000362097:I345L;ENSP00000297229:I345L	ENSP00000297229:I345L	I	-	1	0	USP49	41881667	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.898000	0.63238	2.039000	0.60335	0.533000	0.62120	ATC	.	.		0.607	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000316513.3	NM_018561		G	41773689	T	G	41773689	3	3	101	1	0	0	0	0	1	0	0	0	17095	1464	51	5	905	5	USP49	6	41773689	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	66082	41773689	129341378	240	14077										
PPP2R5D	5528	hgsc.bcm.edu	37	chr6	42978962	42978962	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cccaggacgtgtacaccatcAaggcactggaggcgcacaag	12	13	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:42978962A>C	ENST00000485511.1	+	16	1926	c.1747A>C	c.(1747-1749)Aag>Cag	p.K583Q	KLHDC3_ENST00000326974.4_5'Flank|PPP2R5D_ENST00000461010.1_Missense_Mutation_p.K477Q|PPP2R5D_ENST00000472118.1_Missense_Mutation_p.K575Q|PPP2R5D_ENST00000394110.3_Missense_Mutation_p.K551Q	NM_001270476.1|NM_006245.3	NP_001257405.1|NP_006236.1	Q14738	2A5D_HUMAN	protein phosphatase 2, regulatory subunit B', delta	583					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of catalytic activity (GO:0050790)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	25			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			GTACACCATCAAGGCACTGGA	0.577																																					p.K583Q	Melanoma(63;587 1613 29742 31770)	Atlas-SNP	.											.	PPP2R5D	47	.	0			c.A1747C						.						98	95	96					6																	42978962		2203	4300	6503	SO:0001583	missense	5528	exon16			ACCATCAAGGCAC	L76702	CCDS4878.1, CCDS43464.1, CCDS55002.1	6p21.1	2010-06-18	2010-04-14		ENSG00000112640	ENSG00000112640		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9312	protein-coding gene	gene with protein product		601646	"protein phosphatase 2, regulatory subunit B (B56), delta isoform", "protein phosphatase 2, regulatory subunit B', delta isoform"			7592815	Standard	NM_006245		Approved	B56D	uc003oth.4	Q14738	OTTHUMG00000014716	ENST00000485511.1:c.1747A>C	chr6.hg19:g.42978962A>C	ENSP00000417963:p.Lys583Gln	62.0	0.0		246.0	29.0	NM_006245	A8K3I9|B5BUA6|O00494|O00696|Q15171|Q5TC39	Missense_Mutation	SNP	ENST00000485511.1	hg19	CCDS4878.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.53|14.53	2.563151|2.563151	0.45694|0.45694	.|.	.|.	ENSG00000112640|ENSG00000112640	ENST00000485511;ENST00000394110;ENST00000472118;ENST00000541610;ENST00000461010|ENST00000470467	T;T;T;T|.	0.51071|.	0.74;0.73;0.72;0.76|.	5.49|5.49	5.49|5.49	0.81192|0.81192	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68054|0.68054	0.2959|0.2959	M|M	0.74881|0.74881	2.28|2.28	0.50467|0.50467	D|D	0.99987|0.99987	B;B;B;B|.	0.23249|.	0.016;0.082;0.049;0.082|.	B;B;B;B|.	0.28139|.	0.041;0.059;0.027;0.086|.	T|T	0.69796|0.69796	-0.5048|-0.5048	10|5	0.46703|.	T|.	0.11|.	-30.3757|-30.3757	15.2607|15.2607	0.73621|0.73621	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	477;565;583;551|.	Q14738-3;F5GYS1;Q14738;Q14738-2|.	.;.;2A5D_HUMAN;.|.	Q|P	583;551;575;565;477|484	ENSP00000417963:K583Q;ENSP00000377669:K551Q;ENSP00000420550:K575Q;ENSP00000420674:K477Q|.	ENSP00000377669:K551Q|.	K|Q	+|+	1|2	0|0	PPP2R5D|PPP2R5D	43086940|43086940	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	7.310000|7.310000	0.78947|0.78947	2.089000|2.089000	0.63090|0.63090	0.533000|0.533000	0.62120|0.62120	AAG|CAA	.	.		0.577	PPP2R5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040573.3	NM_006245		C	42978962	A	C	42978962	3	2	101	1	0	0	0	0	1	0	0	0	12407	131	5	5	1809	5	PPP2R5D	6	42978962	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1205273	42978962	128136105	241	14078										
CRIP3	401262	hgsc.bcm.edu	37	chr6	43274043	43274043	+	Missense_Mutation	SNP	C	C	T													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atttctgcctaatgacatcaCcttctcagctggtggtggaa							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:43274043C>T	ENST00000274990.4	-	6	413	c.409G>A	c.(409-411)Gtg>Atg	p.V137M	CRIP3_ENST00000372569.3_Missense_Mutation_p.V137M|ZNF318_ENST00000607252.1_5'Flank			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	137	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			AATGACATCACCTTCTCAGCT	0.572																																					p.V137M		Atlas-SNP	.											.	CRIP3	30	.	0			c.G409A						.						99	92	95					6																	43274043		2203	4300	6503	SO:0001583	missense	401262	exon6			ACATCACCTTCTC	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.409G>A	chr6.hg19:g.43274043C>T	ENSP00000274990:p.Val137Met	41.0	0.0		173.0	24.0	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.9|22.9	4.343643|4.343643	0.82022|0.82022	.|.	.|.	ENSG00000146215|ENSG00000146215	ENST00000416431|ENST00000372569;ENST00000451294;ENST00000274990	.|D;D;D	.|0.89050	.|-2.46;-2.46;-2.46	4.94|4.94	4.94|4.94	0.65067|0.65067	.|Zinc finger, LIM-type (5);	.|0.000000	.|0.64402	.|D	.|0.000009	D|D	0.91942|0.91942	0.7448|0.7448	M|M	0.68952|0.68952	2.095|2.095	0.54753|0.54753	D|D	0.999985|0.999985	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.999	D|D	0.90761|0.90761	0.4665|0.4665	5|10	.|0.34782	.|T	.|0.22	-0.8605|-0.8605	15.6476|15.6476	0.77068|0.77068	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|137;137	.|Q6Q6R5;Q6Q6R5-3	.|CRIP3_HUMAN;.	D|M	60|137;9;137	.|ENSP00000361650:V137M;ENSP00000397775:V9M;ENSP00000274990:V137M	.|ENSP00000274990:V137M	G|V	-|-	2|1	0|0	CRIP3|CRIP3	43382021|43382021	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	6.947000|6.947000	0.75959|0.75959	2.283000|2.283000	0.76528|0.76528	0.561000|0.561000	0.74099|0.74099	GGT|GTG	.	.		0.572	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			T	43274043	C	T	43274043	3	4	101	1	0	0	0	0	1	0	0	0	3878	507	18	3	217	3	CRIP3	6	43274043	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	295081	43274043	127841024	242	14079	62	2								
CRIP3	401262	hgsc.bcm.edu	37	chr6	43274045	43274046	+	Missense_Mutation	DNP	TT	TT	AC													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttctgcctaatgacatcaccTtctcagctggtggtggaaag							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:43274045_43274046TT>AC	ENST00000274990.4	-	6	410_411	c.406_407AA>GT	c.(406-408)AAg>GTg	p.K136V	CRIP3_ENST00000372569.3_Missense_Mutation_p.K136V|ZNF318_ENST00000607252.1_5'Flank			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	136	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			TGACATCACCTTCTCAGCTGGT	0.569																																					p.K136M|p.K136E		Atlas-SNP	.											.	CRIP3	30	.	0			c.A407T|c.A406G						.																																			SO:0001583	missense	401262	exon6			ATCACCTTCTCAG|TCACCTTCTCAGC	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.406_407delinsAC	chr6.hg19:g.43274045_43274046delinsAC	ENSP00000274990:p.Lys136Val	41.0|40.0	0.0		175.0|170.0	26.0|22.0	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	hg19																																																																																				.	.		0.569	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			AC	43274046	TT	AC	43274045	3	1	101	1	0	0	0	0	1	0	0	0	3878	1609	56	4	219	4	CRIP3	6	43274045	Missense_Mutation	DNP	TT	TCGA-DD-A1EE-01A-11D-A12Z-10	2	43274045	127841022	243	14080	62	2								
CLIC5	53405	hgsc.bcm.edu	37	chr6	45922898	45922898	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agatccacagtggtgacattGaacacgactcctttcagcca	8	12	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:45922898G>A	ENST00000185206.6	-	2	776	c.624C>T	c.(622-624)ttC>ttT	p.F208F	CLIC5_ENST00000544153.1_Silent_p.F49F|CLIC5_ENST00000339561.6_Silent_p.F49F	NM_001114086.1	NP_001107558.1	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5	208					auditory receptor cell stereocilium organization (GO:0060088)|chloride transport (GO:0006821)|diet induced thermogenesis (GO:0002024)|female pregnancy (GO:0007565)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	actin cytoskeleton (GO:0015629)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|stereocilium (GO:0032420)	voltage-gated chloride channel activity (GO:0005247)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						TGGTGACATTGAACACGACTC	0.473																																					p.F208F		Atlas-SNP	.											.	CLIC5	48	.	0			c.C624T						.						124	103	110					6																	45922898		2203	4300	6503	SO:0001819	synonymous_variant	53405	exon2			GACATTGAACACG	AF216941	CCDS4914.1, CCDS47438.1, CCDS59022.1	6p12.3	2014-03-14			ENSG00000112782	ENSG00000112782		"Ion channels / Chloride channels : Intracellular"	13517	protein-coding gene	gene with protein product		607293				10793131	Standard	NM_001114086		Approved		uc003oxv.3	Q9NZA1	OTTHUMG00000014775	ENST00000185206.6:c.624C>T	chr6.hg19:g.45922898G>A		42.0	0.0		198.0	20.0	NM_001114086	B3KUF1|Q5T4Z0|Q8NBY3|Q96JT5|Q9BWZ0	Silent	SNP	ENST00000185206.6	hg19	CCDS47438.1																																																																																			.	.		0.473	CLIC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040761.1			A	45922898	G	A	45922898	2	1	101	1	0	0	0	0	0	0	0	1	3531	1281	45	3		3	CLIC5	6	45922898	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2648853	45922898	125192169	244	14081										
PLA2G7	7941	hgsc.bcm.edu	37	chr6	46672428	46672428	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccactgatcaaaatctttatGaagtcctataaaatataaag	4	7	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:46672428G>C	ENST00000274793.7	-	12	1391	c.1195C>G	c.(1195-1197)Cat>Gat	p.H399D	PLA2G7_ENST00000537365.1_Missense_Mutation_p.H399D	NM_005084.3	NP_005075.3	Q13093	PAFA_HUMAN	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	399					cellular protein metabolic process (GO:0044267)|lipid catabolic process (GO:0016042)|lipid oxidation (GO:0034440)|low-density lipoprotein particle remodeling (GO:0034374)|plasma lipoprotein particle oxidation (GO:0034441)|positive regulation of inflammatory response (GO:0050729)|positive regulation of monocyte chemotaxis (GO:0090026)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|low-density lipoprotein particle (GO:0034362)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|skin(1)|soft_tissue(1)	14			Lung(136;0.192)			AAATCTTTATGAAGTCCTATA	0.338																																					p.H399D		Atlas-SNP	.											.	PLA2G7	49	.	0			c.C1195G						.						72	67	69					6																	46672428		2202	4298	6500	SO:0001583	missense	7941	exon12			CTTTATGAAGTCC	U20157	CCDS4917.1	6p21.2-p12	2008-09-19			ENSG00000146070	ENSG00000146070	3.1.1.4		9040	protein-coding gene	gene with protein product		601690				7700381, 8624782	Standard	NM_005084		Approved	PAFAH, LDL-PLA2	uc021zae.1	Q13093	OTTHUMG00000014789	ENST00000274793.7:c.1195C>G	chr6.hg19:g.46672428G>C	ENSP00000274793:p.His399Asp	92.0	0.0		306.0	26.0	NM_005084	A5HTT5|Q15692|Q5VTT1|Q8IVA2	Missense_Mutation	SNP	ENST00000274793.7	hg19	CCDS4917.1	.	.	.	.	.	.	.	.	.	.	G	9.263	1.043790	0.19748	.	.	ENSG00000146070	ENST00000274793;ENST00000537365	T;T	0.39406	1.08;1.08	5.5	2.48	0.30137	.	0.960419	0.08735	N	0.901426	T	0.09598	0.0236	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31447	-0.9943	10	0.13853	T	0.58	.	9.9133	0.41419	0.0:0.1357:0.5908:0.2735	.	399	Q13093	PAFA_HUMAN	D	399	ENSP00000274793:H399D;ENSP00000445666:H399D	ENSP00000274793:H399D	H	-	1	0	PLA2G7	46780387	0.995000	0.38212	0.982000	0.44146	0.966000	0.64601	0.383000	0.20651	0.254000	0.21573	0.561000	0.74099	CAT	.	.		0.338	PLA2G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040802.1			C	46672428	G	C	46672428	3	2	101	1	0	0	0	0	1	0	0	0	12018	1290	45	4	134	4	PLA2G7	6	46672428	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	749530	46672428	124442639	245	14082										
GPR110	266977	hgsc.bcm.edu	37	chr6	46976681	46976681	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gttattgttactgttctcacCtggaatgcattgagtaaagc	9	7	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:46976681C>G	ENST00000371253.2	-	11	2705	c.2490G>C	c.(2488-2490)caG>caC	p.Q830H	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Splice_Site_p.Q633H	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	830					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						CTGTTCTCACCTGGAATGCAT	0.443																																					p.Q830H		Atlas-SNP	.											.	GPR110	102	.	0			c.G2490C						.						50	55	54					6																	46976681		2203	4300	6503	SO:0001630	splice_region_variant	266977	exon11			TCTCACCTGGAAT	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.2490+1G>C	chr6.hg19:g.46976681C>G		67.0	0.0		226.0	19.0	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	hg19	CCDS34471.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.412312	0.83340	.	.	ENSG00000153292	ENST00000371253;ENST00000283297	T;T	0.60424	0.19;0.19	5.9	5.9	0.94986	GPCR, family 2-like (1);	0.000000	0.56097	D	0.000025	T	0.80347	0.4606	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82837	-0.0260	9	.	.	.	-16.5137	20.2789	0.98501	0.0:1.0:0.0:0.0	.	830	Q5T601	GP110_HUMAN	H	830;633	ENSP00000360299:Q830H;ENSP00000283297:Q633H	.	Q	-	3	2	GPR110	47084640	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.852000	0.69488	2.788000	0.95919	0.650000	0.86243	CAG	.	.		0.443	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	Missense_Mutation	G	46976681	C	G	46976681	5	3	101	1	0	0	0	0	0	0	1	0	6635	695	24	4	262	4	GPR110	6	46976681	Splice_Site	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	304253	46976681	124138386	246	14083										
PGK2	5232	hgsc.bcm.edu	37	chr6	49753721	49753721	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tagactggcaccgcctccagTgctgacatggctgactttat	10	12	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:49753721T>A	ENST00000304801.3	-	1	1332	c.1180A>T	c.(1180-1182)Act>Tct	p.T394S		NM_138733.4	NP_620061.2	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	394					glycolytic process (GO:0006096)|phosphorylation (GO:0016310)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	ATP binding (GO:0005524)|phosphoglycerate kinase activity (GO:0004618)			autonomic_ganglia(1)|endometrium(3)|large_intestine(12)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	47	Lung NSC(77;0.0402)					CCGCCTCCAGTGCTGACATGG	0.483																																					p.T394S		Atlas-SNP	.											.	PGK2	87	.	0			c.A1180T						.						114	110	112					6																	49753721		2203	4300	6503	SO:0001583	missense	5232	exon1			CTCCAGTGCTGAC	K03019	CCDS4930.1	6p12.3	2012-09-20		2002-04-19	ENSG00000170950	ENSG00000170950			8898	protein-coding gene	gene with protein product		172270				3839763, 3453121	Standard	NM_138733		Approved	PGKPS, PGK-2	uc003ozu.3	P07205	OTTHUMG00000014824	ENST00000304801.3:c.1180A>T	chr6.hg19:g.49753721T>A	ENSP00000305995:p.Thr394Ser	50.0	0.0		187.0	8.0	NM_138733	B2R6Y8|Q9H107	Missense_Mutation	SNP	ENST00000304801.3	hg19	CCDS4930.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.388149	0.82902	.	.	ENSG00000170950	ENST00000304801	D	0.94330	-3.4	4.19	4.19	0.49359	Phosphoglycerate kinase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96337	0.8805	M	0.92691	3.335	0.58432	D	0.999997	P	0.51537	0.946	P	0.61275	0.886	D	0.96806	0.9593	10	0.72032	D	0.01	-20.2441	11.8373	0.52333	0.0:0.0:0.0:1.0	.	394	P07205	PGK2_HUMAN	S	394	ENSP00000305995:T394S	ENSP00000305995:T394S	T	-	1	0	PGK2	49861680	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.565000	0.67365	2.115000	0.64714	0.477000	0.44152	ACT	.	.		0.483	PGK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040872.1			A	49753721	T	A	49753721	3	1	101	1	0	0	0	0	1	0	0	0	11800	1696	59	4	77	4	PGK2	6	49753721	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2777040	49753721	121361346	247	14084										
IL17F	112744	hgsc.bcm.edu	37	chr6	52101936	52101936	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cactgggcctgtacaacttcCgaggggtaccggttggggtc	15	11	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:52101936C>T	ENST00000336123.4	-	3	392	c.285G>A	c.(283-285)tcG>tcA	p.S95S		NM_052872.3	NP_443104.1	Q96PD4	IL17F_HUMAN	interleukin 17F	95			S -> L (in CANDF6). {ECO:0000269|PubMed:21350122}.		cartilage development (GO:0051216)|cytokine biosynthetic process (GO:0042089)|inflammatory response (GO:0006954)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045423)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of interleukin-8 biosynthetic process (GO:0045414)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine binding (GO:0019955)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)	14	Lung NSC(77;0.116)					GTACAACTTCCGAGGGGTACC	0.557																																					p.S95S		Atlas-SNP	.											.	IL17F	28	.	0			c.G285A						.						53	49	51					6																	52101936		2203	4300	6503	SO:0001819	synonymous_variant	112744	exon3			AACTTCCGAGGGG	AF384857	CCDS4938.1	6p12	2014-09-17			ENSG00000112116	ENSG00000112116		"Interleukins and interleukin receptors"	16404	protein-coding gene	gene with protein product		606496				11591732, 11591768	Standard	NM_052872		Approved	IL-17F, ML-1, ML1	uc003pam.1	Q96PD4	OTTHUMG00000014845	ENST00000336123.4:c.285G>A	chr6.hg19:g.52101936C>T		30.0	0.0		96.0	8.0	NM_052872	Q6NSI0|Q7Z6P4|Q96PI8|Q9NUE6	Silent	SNP	ENST00000336123.4	hg19	CCDS4938.1																																																																																			.	.		0.557	IL17F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040901.3	NM_052872		T	52101936	C	T	52101936	2	4	101	1	0	0	0	0	0	0	0	1	7647	639	23	1		1	IL17F	6	52101936	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2348215	52101936	119013131	248	14085										
COL9A1	1297	hgsc.bcm.edu	37	chr6	70993489	70993489	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tttctctcctgggccgcaggGggtcacaatggatcagcatc	12	12	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:70993489G>T	ENST00000357250.6	-	6	889	c.731C>A	c.(730-732)cCc>cAc	p.P244H	COL9A1_ENST00000370499.4_5'Flank|COL9A1_ENST00000320755.7_5'Flank|COL9A1_ENST00000370496.3_Missense_Mutation_p.P244H	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	244	Laminin G-like.|Nonhelical region (NC4).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						GGGCCGCAGGGGGTCACAATG	0.512																																					p.P244H		Atlas-SNP	.											.	COL9A1	228	.	0			c.C731A						.						105	86	92					6																	70993489		2203	4300	6503	SO:0001583	missense	1297	exon6			CGCAGGGGGTCAC		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.731C>A	chr6.hg19:g.70993489G>T	ENSP00000349790:p.Pro244His	61.0	0.0		170.0	26.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	hg19	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.204529	0.79127	.	.	ENSG00000112280	ENST00000357250;ENST00000370496	T;T	0.02525	4.26;4.26	5.56	5.56	0.83823	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.148765	0.47852	D	0.000213	T	0.14013	0.0339	M	0.87547	2.89	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00804	-1.1559	10	0.87932	D	0	.	18.5065	0.90900	0.0:0.0:1.0:0.0	.	244	P20849	CO9A1_HUMAN	H	244	ENSP00000349790:P244H;ENSP00000359527:P244H	ENSP00000349790:P244H	P	-	2	0	COL9A1	71050210	1.000000	0.71417	0.992000	0.48379	0.861000	0.49209	7.215000	0.77966	2.633000	0.89246	0.655000	0.94253	CCC	.	.		0.512	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			T	70993489	G	T	70993489	3	4	101	1	0	0	0	0	1	0	0	0	3709	1232	43	3	2242	3	COL9A1	6	70993489	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	18891553	70993489	100121578	249	14086										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75884785	75884785	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gttccttcaccaaagagggcGtctccagccccagacgcata	9	15	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:75884785G>T	ENST00000322507.8	-	13	2988	c.2679C>A	c.(2677-2679)gaC>gaA	p.D893E	COL12A1_ENST00000416123.2_Missense_Mutation_p.D893E|COL12A1_ENST00000483888.2_Missense_Mutation_p.D893E|COL12A1_ENST00000345356.6_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	893	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CAAAGAGGGCGTCTCCAGCCC	0.468																																					p.D893E		Atlas-SNP	.											.	COL12A1	385	.	0			c.C2679A						.						190	186	187					6																	75884785		1983	4159	6142	SO:0001583	missense	1303	exon13			GAGGGCGTCTCCA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2679C>A	chr6.hg19:g.75884785G>T	ENSP00000325146:p.Asp893Glu	66.0	0.0		108.0	5.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	0.018	-1.482005	0.01027	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.51817	0.69;0.69;0.69	5.94	-8.61	0.00885	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.463941	0.21967	N	0.066519	T	0.02304	0.0071	N	0.02011	-0.69	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.32771	-0.9894	10	0.05436	T	0.98	.	0.6516	0.00828	0.2097:0.1677:0.2157:0.4069	.	893	Q99715	COCA1_HUMAN	E	893	ENSP00000325146:D893E;ENSP00000412864:D893E;ENSP00000421216:D893E	ENSP00000325146:D893E	D	-	3	2	COL12A1	75941505	0.000000	0.05858	0.397000	0.26308	0.387000	0.30353	-3.514000	0.00445	-1.602000	0.01599	-2.049000	0.00408	GAC	.	.		0.468	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75884785	G	T	75884785	3	4	101	1	0	0	0	0	1	0	0	0	3671	1136	40	1	6728	1	COL12A1	6	75884785	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	4891296	75884785	95230282	250	14087										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76024218	76024218	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggtgcactcagatttactctTgctaaatgcttcttccaatt	6	10	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:76024218T>A	ENST00000237172.7	-	5	1660	c.1330A>T	c.(1330-1332)Aag>Tag	p.K444*	FILIP1_ENST00000393004.2_Nonsense_Mutation_p.K444*|FILIP1_ENST00000370020.1_Nonsense_Mutation_p.K345*|FILIP1_ENST00000498523.1_5'UTR	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	444										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GATTTACTCTTGCTAAATGCT	0.408																																					p.K444X		Atlas-SNP	.											.	FILIP1	173	.	0			c.A1330T						.						141	142	142					6																	76024218		2203	4300	6503	SO:0001587	stop_gained	27145	exon5			TACTCTTGCTAAA	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.1330A>T	chr6.hg19:g.76024218T>A	ENSP00000237172:p.Lys444*	148.0	0.0		236.0	36.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Nonsense_Mutation	SNP	ENST00000237172.7	hg19	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	T	38	6.803656	0.97849	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	.	.	.	5.65	3.07	0.35406	.	0.221173	0.45867	D	0.000329	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.2141	12.2983	0.54860	0.0:0.0:0.2768:0.7232	.	.	.	.	X	444;444;345	.	ENSP00000237172:K444X	K	-	1	0	FILIP1	76080938	0.800000	0.28916	1.000000	0.80357	0.942000	0.58702	0.942000	0.29017	1.057000	0.40506	0.533000	0.62120	AAG	.	.		0.408	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76024218	T	A	76024218	4	1	101	1	0	0	0	0	0	1	0	0	5902	1821	63	4	2319	4	FILIP1	6	76024218	Nonsense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	139433	76024218	95090849	251	14088										
ME1	4199	hgsc.bcm.edu	37	chr6	84117526	84117526	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gatgctcgaaattttttactActctaagaacctggatctcc	6	10	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:84117526A>T	ENST00000369705.3	-	2	289	c.173T>A	c.(172-174)gTa>gAa	p.V58E	ME1_ENST00000541327.1_Intron|ME1_ENST00000543031.1_Intron	NM_002395.4	NP_002386.1	P48163	MAOX_HUMAN	malic enzyme 1, NADP(+)-dependent, cytosolic	58					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|malate metabolic process (GO:0006108)|NADP biosynthetic process (GO:0006741)|protein tetramerization (GO:0051262)|response to carbohydrate (GO:0009743)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|manganese ion binding (GO:0030145)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|oxaloacetate decarboxylase activity (GO:0008948)			NS(2)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)		ATTTTTTACTACTCTAAGAAC	0.388																																					p.V58E		Atlas-SNP	.											.	ME1	68	.	0			c.T173A						.						132	136	134					6																	84117526		2203	4300	6503	SO:0001583	missense	4199	exon2			TTTACTACTCTAA	X77244	CCDS34492.1	6q12	2012-10-02			ENSG00000065833	ENSG00000065833	1.1.1.40		6983	protein-coding gene	gene with protein product		154250				8187880	Standard	NM_002395		Approved		uc003pjy.3	P48163	OTTHUMG00000015111	ENST00000369705.3:c.173T>A	chr6.hg19:g.84117526A>T	ENSP00000358719:p.Val58Glu	61.0	0.0		85.0	12.0	NM_002395	B4DZ70|Q16797|Q16855|Q53F72|Q5VWA2|Q9BWX8|Q9H1W3|Q9UIY4	Missense_Mutation	SNP	ENST00000369705.3	hg19	CCDS34492.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.997740	0.54147	.	.	ENSG00000065833	ENST00000369705	T	0.23950	1.88	5.43	5.43	0.79202	.	0.312221	0.33895	N	0.004458	T	0.43055	0.1230	M	0.84326	2.69	0.80722	D	1	D	0.56968	0.978	P	0.61477	0.889	T	0.49143	-0.8970	10	0.56958	D	0.05	-7.0144	15.4817	0.75534	1.0:0.0:0.0:0.0	.	58	P48163	MAOX_HUMAN	E	58	ENSP00000358719:V58E	ENSP00000358719:V58E	V	-	2	0	ME1	84174245	0.987000	0.35691	0.061000	0.19648	0.003000	0.03518	9.009000	0.93606	2.054000	0.61138	0.528000	0.53228	GTA	.	.		0.388	ME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041350.1			T	84117526	A	T	84117526	3	4	101	1	0	0	0	0	1	0	0	0	9426	391	14	4	1597	4	ME1	6	84117526	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	8093308	84117526	86997541	252	14089										
GPR63	81491	hgsc.bcm.edu	37	chr6	97246970	97246970	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggtcggggtttcctacggctAaaggaaaagctacacaaaag	12	8	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:97246970A>G	ENST00000229955.3	-	2	983	c.638T>C	c.(637-639)tTa>tCa	p.L213S	GPR63_ENST00000417980.1_Missense_Mutation_p.L213S	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		TCCTACGGCTAAAGGAAAAGC	0.458																																					p.L213S		Atlas-SNP	.											.	GPR63	60	.	0			c.T638C						.						75	75	75					6																	97246970		2203	4300	6503	SO:0001583	missense	81491	exon2			ACGGCTAAAGGAA	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.638T>C	chr6.hg19:g.97246970A>G	ENSP00000229955:p.Leu213Ser	62.0	0.0		86.0	25.0	NM_030784	Q9UJH3	Missense_Mutation	SNP	ENST00000229955.3	hg19	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	A	11.24	1.580195	0.28180	.	.	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	T;T;T	0.38560	1.13;1.13;1.13	5.3	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000010	T	0.10337	0.0253	N	0.12422	0.21	0.54753	D	0.999985	B	0.32526	0.374	B	0.28991	0.097	T	0.08889	-1.0700	10	0.22109	T	0.4	-0.8812	11.3705	0.49697	0.9282:0.0:0.0718:0.0	.	213	Q9BZJ6	GPR63_HUMAN	S	237;213;213;213	ENSP00000393170:L213S;ENSP00000229955:L213S;ENSP00000358273:L213S	ENSP00000229955:L213S	L	-	2	0	GPR63	97353691	1.000000	0.71417	0.840000	0.33206	0.724000	0.41520	8.910000	0.92685	0.957000	0.37930	0.528000	0.53228	TTA	.	.		0.458	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			G	97246970	A	G	97246970	3	3	101	1	0	0	0	0	1	0	0	0	6712	372	13	2	625	2	GPR63	6	97246970	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	13129444	97246970	73868097	253	14090										
FBXL4	26235	hgsc.bcm.edu	37	chr6	99322272	99322272	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtaaagaaagatctttacaaGattccaggagttttcttaag	8	5	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:99322272G>T	ENST00000369244.2	-	10	2176	c.1748C>A	c.(1747-1749)tCt>tAt	p.S583Y	FBXL4_ENST00000229971.1_Missense_Mutation_p.S583Y	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	583					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		ATCTTTACAAGATTCCAGGAG	0.343																																					p.S583Y		Atlas-SNP	.											.	FBXL4	54	.	0			c.C1748A						.						119	123	122					6																	99322272		2203	4300	6503	SO:0001583	missense	26235	exon9			TTACAAGATTCCA	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"F-boxes / Leucine-rich repeats"	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.1748C>A	chr6.hg19:g.99322272G>T	ENSP00000358247:p.Ser583Tyr	91.0	0.0		164.0	13.0	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	hg19	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783913	0.49891	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.19105	2.17;2.17	5.95	5.08	0.68730	.	0.166936	0.53938	D	0.000042	T	0.11707	0.0285	L	0.40543	1.245	0.45867	D	0.998725	P	0.36789	0.57	B	0.40101	0.319	T	0.04796	-1.0926	10	0.30854	T	0.27	.	15.774	0.78193	0.0:0.3814:0.6186:0.0	.	583	Q9UKA2	FBXL4_HUMAN	Y	583	ENSP00000358247:S583Y;ENSP00000229971:S583Y	ENSP00000229971:S583Y	S	-	2	0	FBXL4	99428993	1.000000	0.71417	0.990000	0.47175	0.999000	0.98932	4.331000	0.59273	1.504000	0.48704	0.655000	0.94253	TCT	.	.		0.343	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			T	99322272	G	T	99322272	3	4	101	1	0	0	0	0	1	0	0	0	5729	942	33	3	121	3	FBXL4	6	99322272	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2075302	99322272	71792795	254	14091										
REV3L	5980	hgsc.bcm.edu	37	chr6	111678241	111678241	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttattatatttgcaatttcaTgaaaaagtgccttctcatca	4	7	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:111678241T>A	ENST00000358835.3	-	19	7614	c.7160A>T	c.(7159-7161)cAt>cTt	p.H2387L	REV3L_ENST00000368805.1_Missense_Mutation_p.H2387L|REV3L_ENST00000368802.3_Missense_Mutation_p.H2387L|REV3L_ENST00000435970.1_Missense_Mutation_p.H2309L			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2387					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TGCAATTTCATGAAAAAGTGC	0.323								DNA polymerases (catalytic subunits)																													p.H2387L		Atlas-SNP	.											.	REV3L	386	.	0			c.A7160T						.						90	99	96					6																	111678241		2203	4300	6503	SO:0001583	missense	5980	exon18			ATTTCATGAAAAA	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.7160A>T	chr6.hg19:g.111678241T>A	ENSP00000351697:p.His2387Leu	93.0	0.0		165.0	27.0	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	T	16.23	3.065852	0.55539	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	T;T;T;T	0.08720	3.06;3.06;3.06;3.06	5.93	5.93	0.95920	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.188610	0.47455	D	0.000229	T	0.01800	0.0057	N	0.02247	-0.625	0.39361	D	0.965926	B	0.06786	0.001	B	0.01281	0.0	T	0.49312	-0.8953	10	0.44086	T	0.13	-0.8613	16.3766	0.83401	0.0:0.0:0.0:1.0	.	2387	O60673	DPOLZ_HUMAN	L	2387;2387;2387;2309;460	ENSP00000357792:H2387L;ENSP00000357795:H2387L;ENSP00000351697:H2387L;ENSP00000402003:H2309L	ENSP00000351697:H2387L	H	-	2	0	REV3L	111784934	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.213000	0.77950	2.263000	0.75096	0.533000	0.62120	CAT	.	.		0.323	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111678241	T	A	111678241	3	1	101	1	0	0	0	0	1	0	0	0	13255	1464	51	4	2292	4	REV3L	6	111678241	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	12355969	111678241	59436826	255	14092										
HDAC2	3066	hgsc.bcm.edu	37	chr6	114264582	114264582	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttctttgctcctttcttatgAtcagccacatttcttcgacc	4	13	4	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:114264582A>T	ENST00000519065.1	-	12	1687	c.1311T>A	c.(1309-1311)gaT>gaA	p.D437E	HDAC2_ENST00000398283.2_Missense_Mutation_p.D531E|HDAC2_ENST00000368632.2_Missense_Mutation_p.D407E|HDAC2_ENST00000519108.1_Missense_Mutation_p.D407E			Q92769	HDAC2_HUMAN	histone deacetylase 2	437					ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	ctttcttATGATCAGCCACAT	0.378																																					p.D437E		Atlas-SNP	.											.	HDAC2	102	.	0			c.T1311A						.						168	156	160					6																	114264582		1866	4104	5970	SO:0001583	missense	3066	exon12			CTTATGATCAGCC	U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.1311T>A	chr6.hg19:g.114264582A>T	ENSP00000430432:p.Asp437Glu	71.0	0.0		72.0	11.0	NM_001527	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Missense_Mutation	SNP	ENST00000519065.1	hg19	CCDS43493.2	.	.	.	.	.	.	.	.	.	.	A	14.99	2.700563	0.48307	.	.	ENSG00000196591	ENST00000519065;ENST00000398283;ENST00000519108;ENST00000368632	T;T;T;T	0.73047	-0.69;-0.71;-0.69;-0.69	6.16	3.79	0.43588	.	0.073236	0.56097	N	0.000032	T	0.30198	0.0757	N	0.16098	0.37	0.42098	D	0.99132	B;B	0.19583	0.0;0.037	B;B	0.18263	0.001;0.021	T	0.09773	-1.0659	10	0.14656	T	0.56	-45.4507	10.4506	0.44520	0.8697:0.0:0.1303:0.0	.	407;437	B3KRS5;Q92769	.;HDAC2_HUMAN	E	437;531;407;407	ENSP00000430432:D437E;ENSP00000381331:D531E;ENSP00000430008:D407E;ENSP00000357621:D407E	ENSP00000357621:D407E	D	-	3	2	HDAC2	114371275	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.696000	0.47052	0.567000	0.29293	-0.256000	0.11100	GAT	.	.		0.378	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2			T	114264582	A	T	114264582	3	4	101	1	0	0	0	0	1	0	0	0	7016	330	12	4	167	4	HDAC2	6	114264582	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	2586341	114264582	56850485	256	14093										
TPD52L1	7164	hgsc.bcm.edu	37	chr6	125584076	125584076	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agagcttggcaggaggctccCggcggaccaaggaggaggag	19	9	0	1	rs559154046		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:125584076C>T	ENST00000534000.1	+	7	879	c.583C>T	c.(583-585)Cgg>Tgg	p.R195W	HDDC2_ENST00000608456.1_Intron|TPD52L1_ENST00000524679.1_3'UTR|TPD52L1_ENST00000530868.1_3'UTR|TPD52L1_ENST00000392482.2_3'UTR|TPD52L1_ENST00000527711.1_Missense_Mutation_p.R182W|TPD52L1_ENST00000368402.5_3'UTR|TPD52L1_ENST00000368388.2_3'UTR|TPD52L1_ENST00000304877.13_Missense_Mutation_p.R200W|TPD52L1_ENST00000528193.1_3'UTR|TPD52L1_ENST00000532429.1_Missense_Mutation_p.R166W|TPD52L1_ENST00000534199.1_3'UTR	NM_003287.2	NP_003278.1	Q16890	TPD53_HUMAN	tumor protein D52-like 1	195					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|prostate(1)	5			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)		AGGAGGCTCCCGGCGGACCAA	0.612													C|||	1	0.000199681	8e-04	0	5008	,	,		14409	0		0	False		,,,				2504	0				p.R195W		Atlas-SNP	.											.	TPD52L1	14	.	0			c.C583T						.						37	35	36					6																	125584076		2203	4300	6503	SO:0001583	missense	7164	exon7			GGCTCCCGGCGGA	U44427	CCDS5130.1, CCDS34527.1, CCDS34528.1, CCDS43502.1, CCDS75513.1, CCDS75514.1	6q22-q23	2008-07-29			ENSG00000111907	ENSG00000111907			12006	protein-coding gene	gene with protein product		604069				8812487, 16112108	Standard	NM_003287		Approved	D53, hD53	uc003pzu.1	Q16890	OTTHUMG00000015505	ENST00000534000.1:c.583C>T	chr6.hg19:g.125584076C>T	ENSP00000434142:p.Arg195Trp	22.0	0.0		51.0	15.0	NM_003287	A8K757|A8K772|A8MUD2|A8MUJ7|A8MW70|F6V707|O43397|Q5TC99|Q5TDQ0|Q9BUQ6|Q9C054	Missense_Mutation	SNP	ENST00000534000.1	hg19	CCDS5130.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.896287	0.33442	.	.	ENSG00000111907	ENST00000304877;ENST00000534000;ENST00000527711;ENST00000532429;ENST00000392484	T;T;T;T	0.48201	1.4;1.39;1.77;0.82	5.53	2.67	0.31697	.	1.108680	0.06628	N	0.758775	T	0.10981	0.0268	N	0.08118	0	0.22666	N	0.998871	B	0.02656	0.0	B	0.01281	0.0	T	0.31806	-0.9930	10	0.66056	D	0.02	-3.2296	5.1614	0.15064	0.1497:0.627:0.1444:0.0789	.	195	Q16890	TPD53_HUMAN	W	200;195;182;166;195	ENSP00000306285:R200W;ENSP00000434142:R195W;ENSP00000436953:R182W;ENSP00000435447:R166W	ENSP00000306285:R200W	R	+	1	2	TPD52L1	125625775	0.004000	0.15560	0.012000	0.15200	0.850000	0.48378	1.103000	0.31062	0.253000	0.21552	-0.133000	0.14855	CGG	.	.		0.612	TPD52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042065.2			T	125584076	C	T	125584076	3	4	101	1	0	0	0	0	1	0	0	0	16413	643	23	1	609	1	TPD52L1	6	125584076	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	11319494	125584076	45530991	257	14094										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151161944	151161944	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgacaaactgaatgactatcTttggagggggccatctccca	10	10	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:151161944T>G	ENST00000358517.2	+	16	4281	c.4070T>G	c.(4069-4071)cTt>cGt	p.L1357R	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.L1357R			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	1357							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		AATGACTATCTTTGGAGGGGG	0.408																																					p.L1357R		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.T4070G						.						86	87	86					6																	151161944		2203	4300	6503	SO:0001583	missense	57480	exon17			ACTATCTTTGGAG	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.4070T>G	chr6.hg19:g.151161944T>G	ENSP00000351318:p.Leu1357Arg	67.0	0.0		77.0	8.0	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	hg19	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.366450	0.82463	.	.	ENSG00000120278	ENST00000367328;ENST00000358517	T;T	0.71934	-0.61;-0.61	5.7	5.7	0.88788	.	0.175401	0.51477	D	0.000093	T	0.79516	0.4459	M	0.66939	2.045	0.48571	D	0.99967	D;D	0.89917	1.0;0.998	D;D	0.76575	0.988;0.915	T	0.82540	-0.0406	10	0.87932	D	0	.	15.9568	0.79893	0.0:0.0:0.0:1.0	.	1164;1357	Q5EBL9;Q9ULL1	.;PKHG1_HUMAN	R	1357	ENSP00000356297:L1357R;ENSP00000351318:L1357R	ENSP00000351318:L1357R	L	+	2	0	PLEKHG1	151203637	1.000000	0.71417	0.992000	0.48379	0.984000	0.73092	7.170000	0.77587	2.160000	0.67779	0.533000	0.62120	CTT	.	.		0.408	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			G	151161944	T	G	151161944	3	3	101	1	0	0	0	0	1	0	0	0	12077	1609	56	5	4128	5	PLEKHG1	6	151161944	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	25577868	151161944	19953123	258	14095										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152583243	152583243	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	attcttgatgtaggctttccCatttcattctcatctggtct	6	10	5	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:152583243C>A	ENST00000367255.5	-	101	19497	c.18896G>T	c.(18895-18897)tGg>tTg	p.W6299L	SYNE1_ENST00000448038.1_Missense_Mutation_p.W6228L|SYNE1_ENST00000341594.5_Missense_Mutation_p.W5911L|SYNE1_ENST00000356820.4_Missense_Mutation_p.W823L|SYNE1_ENST00000265368.4_Missense_Mutation_p.W6299L|SYNE1_ENST00000423061.1_Missense_Mutation_p.W6228L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6299					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TAGGCTTTCCCATTTCATTCT	0.373										HNSCC(10;0.0054)																											p.W6299L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G18896T						.						157	144	148					6																	152583243		2203	4300	6503	SO:0001583	missense	23345	exon101			CTTTCCCATTTCA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.18896G>T	chr6.hg19:g.152583243C>A	ENSP00000356224:p.Trp6299Leu	123.0	0.0		147.0	18.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	29.2	4.982397	0.93044	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	D;D;D;D;D;T	0.86865	-2.09;-2.12;-2.18;-2.1;-1.56;0.05	5.96	5.96	0.96718	.	0.000000	0.56097	D	0.000035	D	0.92198	0.7526	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.89072	0.3470	10	0.32370	T	0.25	.	20.4192	0.99033	0.0:1.0:0.0:0.0	.	6299;6299;6228	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	L	6299;6228;6299;6228;5911;823	ENSP00000356224:W6299L;ENSP00000396024:W6228L;ENSP00000265368:W6299L;ENSP00000390975:W6228L;ENSP00000341887:W5911L;ENSP00000349276:W823L	ENSP00000265368:W6299L	W	-	2	0	SYNE1	152624936	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.439000	0.73430	2.831000	0.97527	0.650000	0.86243	TGG	.	.		0.373	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152583243	C	A	152583243	3	1	101	1	0	0	0	0	1	0	0	0	15460	595	21	3	7754	3	SYNE1	6	152583243	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1421299	152583243	18531824	259	14096										
PDE10A	10846	hgsc.bcm.edu	37	chr6	165846593	165846593	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acgagtccctgattccagtcCagtacctcttggaaatcgtt	8	12	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:165846593C>G	ENST00000366882.1	-	8	686	c.532G>C	c.(532-534)Gga>Cga	p.G178R	PDE10A_ENST00000539869.2_Missense_Mutation_p.G188R|PDE10A_ENST00000354448.4_Missense_Mutation_p.G178R			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	178	GAF 1.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	GATTCCAGTCCAGTACCTCTT	0.388																																					p.G188R	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											.	PDE10A	154	.	0			c.G562C						.						94	90	91					6																	165846593		2203	4300	6503	SO:0001583	missense	10846	exon7			CCAGTCCAGTACC	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.532G>C	chr6.hg19:g.165846593C>G	ENSP00000355847:p.Gly178Arg	88.0	0.0		160.0	10.0	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	hg19		.	.	.	.	.	.	.	.	.	.	C	27.8	4.867217	0.91511	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.69435	-0.4;-0.4	5.89	5.89	0.94794	GAF (2);	0.000000	0.85682	D	0.000000	T	0.79364	0.4433	M	0.68952	2.095	0.80722	D	1	D;P	0.89917	1.0;0.86	D;P	0.97110	1.0;0.643	T	0.79475	-0.1788	10	0.72032	D	0.01	.	20.2508	0.98407	0.0:1.0:0.0:0.0	.	188;178	Q9ULW9;Q9Y233	.;PDE10_HUMAN	R	178;206;188;178;177	ENSP00000355847:G178R;ENSP00000346435:G178R	ENSP00000341187:G188R	G	-	1	0	PDE10A	165766583	1.000000	0.71417	0.927000	0.36925	0.842000	0.47809	7.538000	0.82048	2.788000	0.95919	0.585000	0.79938	GGA	.	.		0.388	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			G	165846593	C	G	165846593	3	3	101	1	0	0	0	0	1	0	0	0	11639	603	21	4	1871	4	PDE10A	6	165846593	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	13263350	165846593	5268474	260	14097										
PHF10	55274	hgsc.bcm.edu	37	chr6	170105298	170105298	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acacatatcacagaacatcaTttcttcttcatggtggggtt	7	9	5	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr6:170105298T>C	ENST00000339209.4	-	11	1465	c.1342A>G	c.(1342-1344)Atg>Gtg	p.M448V	PHF10_ENST00000366780.4_Missense_Mutation_p.M446V|C6orf120_ENST00000332290.2_3'UTR	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	448					nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		CAGAACATCATTTCTTCTTCA	0.373																																					p.M448V		Atlas-SNP	.											.	PHF10	76	.	0			c.A1342G						.						186	161	169					6																	170105298		2203	4300	6503	SO:0001583	missense	55274	exon11			ACATCATTTCTTC	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"Zinc fingers, PHD-type"	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.1342A>G	chr6.hg19:g.170105298T>C	ENSP00000341805:p.Met448Val	72.0	0.0		97.0	18.0	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Missense_Mutation	SNP	ENST00000339209.4	hg19	CCDS5308.2	.	.	.	.	.	.	.	.	.	.	T	18.57	3.652033	0.67472	.	.	ENSG00000130024	ENST00000366780;ENST00000339209	D;D	0.88664	-2.41;-2.41	5.91	5.91	0.95273	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.035139	0.85682	D	0.000000	D	0.89996	0.6877	M	0.80332	2.49	0.58432	D	0.999998	P;B	0.46064	0.872;0.392	P;P	0.48304	0.522;0.573	D	0.91696	0.5370	10	0.87932	D	0	-27.6999	15.5248	0.75894	0.0:0.0:0.0:1.0	.	446;448	Q8WUB8-2;Q8WUB8	.;PHF10_HUMAN	V	446;448	ENSP00000355743:M446V;ENSP00000341805:M448V	ENSP00000341805:M448V	M	-	1	0	PHF10	169847223	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.457000	0.80775	2.269000	0.75478	0.533000	0.62120	ATG	.	.		0.373	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		C	170105298	T	C	170105298	3	2	101	1	0	0	0	0	1	0	0	0	11830	1493	52	2	162	2	PHF10	6	170105298	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	4258705	170105298	1009769	261	14098										
FSCN1	6624	hgsc.bcm.edu	37	chr7	5643546	5643546	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaccgccccatcatcgtgttCcgcggggagcatggcttcat	11	14	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:5643546C>T	ENST00000382361.3	+	4	1278	c.1164C>T	c.(1162-1164)ttC>ttT	p.F388F	FSCN1_ENST00000340250.6_Silent_p.F367F	NM_003088.3	NP_003079.1	Q16658	FSCN1_HUMAN	fascin actin-bundling protein 1	388					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|cell motility (GO:0048870)|cell proliferation (GO:0008283)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|invadopodium (GO:0071437)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|drug binding (GO:0008144)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)		TCATCGTGTTCCGCGGGGAGC	0.622																																					p.F388F		Atlas-SNP	.											.	FSCN1	29	.	0			c.C1164T						.						65	63	64					7																	5643546		2203	4300	6503	SO:0001819	synonymous_variant	6624	exon4			CGTGTTCCGCGGG	U03057	CCDS5342.1	7p22	2014-02-03	2014-02-03	2002-09-20	ENSG00000075618	ENSG00000075618		"Fascins"	11148	protein-coding gene	gene with protein product	"Singed, drosophila, homolog-like", "actin bundling protein"	602689	"singed (Drosophila)-like (sea urchin fascin homolog like)", "fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus)"	SNL		8068206, 10783262	Standard	NM_003088		Approved	p55, FLJ38511	uc003sou.3	Q16658	OTTHUMG00000090599	ENST00000382361.3:c.1164C>T	chr7.hg19:g.5643546C>T		26.0	0.0		89.0	59.0	NM_003088	A6NI89|B2RE97|Q96IC5|Q96IH1|Q9BRF1	Silent	SNP	ENST00000382361.3	hg19	CCDS5342.1																																																																																			.	.		0.622	FSCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207153.3	NM_003088		T	5643546	C	T	5643546	2	4	101	1	0	0	0	0	0	0	0	1	6075	854	30	3		3	FSCN1	7	5643546	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10		5643546	153495117	262	14099										
MPP6	51678	hgsc.bcm.edu	37	chr7	24705683	24705683	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agcaaaaaaaagaaaaagatGatgtatctcacaaccagaaa	6	6	1	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:24705683G>C	ENST00000222644.5	+	8	1177	c.927G>C	c.(925-927)atG>atC	p.M309I	MPP6_ENST00000409761.1_Missense_Mutation_p.M197I|MPP6_ENST00000396475.2_Missense_Mutation_p.M309I			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.M309I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						AGAAAAAGATGATGTATCTCA	0.303																																					p.M309I		Atlas-SNP	.											.	MPP6	62	.	1	Substitution - Missense(1)	lung(1)	c.G927C						.						92	107	102					7																	24705683		2197	4293	6490	SO:0001583	missense	51678	exon9			AAAGATGATGTAT	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.927G>C	chr7.hg19:g.24705683G>C	ENSP00000222644:p.Met309Ile	69.0	0.0		176.0	8.0	NM_016447	B2RAF0	Missense_Mutation	SNP	ENST00000222644.5	hg19	CCDS5388.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.624452	0.46840	.	.	ENSG00000105926	ENST00000222644;ENST00000409761;ENST00000396475	D;D;D	0.82167	-1.58;-1.58;-1.58	5.32	5.32	0.75619	Src homology-3 domain (1);	0.000000	0.64402	D	0.000002	T	0.73877	0.3643	N	0.16743	0.435	0.80722	D	1	B	0.17268	0.021	B	0.12156	0.007	T	0.67707	-0.5601	10	0.36615	T	0.2	.	18.9769	0.92740	0.0:0.0:1.0:0.0	.	309	Q9NZW5	MPP6_HUMAN	I	309;197;309	ENSP00000222644:M309I;ENSP00000386262:M197I;ENSP00000379737:M309I	ENSP00000222644:M309I	M	+	3	0	MPP6	24672208	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.794000	0.85869	2.477000	0.83638	0.591000	0.81541	ATG	.	.		0.303	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4			C	24705683	G	C	24705683	3	2	101	1	0	0	0	0	1	0	0	0	9747	1290	45	4	953	4	MPP6	7	24705683	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	19062137	24705683	134432980	263	14100										
HECW1	23072	hgsc.bcm.edu	37	chr7	43484350	43484350	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcaggctgcagctgcgggccTcggtgaagagaaaaagcagg	17	9	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:43484350T>A	ENST00000395891.2	+	11	2184	c.1579T>A	c.(1579-1581)Tcg>Acg	p.S527T	HECW1_ENST00000453890.1_Missense_Mutation_p.S527T	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	527					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						GCTGCGGGCCTCGGTGAAGAG	0.652																																					p.S527T		Atlas-SNP	.											.	HECW1	540	.	0			c.T1579A						.						26	34	31					7																	43484350		2132	4229	6361	SO:0001583	missense	23072	exon11			CGGGCCTCGGTGA	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.1579T>A	chr7.hg19:g.43484350T>A	ENSP00000379228:p.Ser527Thr	42.0	0.0		155.0	24.0	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	hg19	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	T	2.333	-0.353009	0.05173	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.30448	1.53;1.54	5.32	4.15	0.48705	.	.	.	.	.	T	0.19644	0.0472	L	0.27053	0.805	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20505	-1.0273	9	0.30854	T	0.27	.	5.9688	0.19340	0.2829:0.0:0.1247:0.5924	.	527;527	B4DH42;Q76N89	.;HECW1_HUMAN	T	527	ENSP00000379228:S527T;ENSP00000407774:S527T	ENSP00000265522:S527T	S	+	1	0	HECW1	43450875	0.002000	0.14202	0.029000	0.17559	0.126000	0.20510	0.651000	0.24873	0.838000	0.34948	0.533000	0.62120	TCG	.	.		0.652	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43484350	T	A	43484350	3	1	101	1	0	0	0	0	1	0	0	0	7051	1551	54	4	1613	4	HECW1	7	43484350	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	18778667	43484350	115654313	264	14101										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47876625	47876625	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcaggtagcggctggaggagGgcctgctgtacaccgacagc	17	11	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:47876625G>A	ENST00000289672.2	-	37	5887	c.5837C>T	c.(5836-5838)cCc>cTc	p.P1946L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1946					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GCTGGAGGAGGGCCTGCTGTA	0.582																																					p.P1946L		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C5837T						.						60	53	55					7																	47876625		2203	4300	6503	SO:0001583	missense	168507	exon37			GAGGAGGGCCTGC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5837C>T	chr7.hg19:g.47876625G>A	ENSP00000289672:p.Pro1946Leu	34.0	0.0		149.0	71.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354085	0.82243	.	.	ENSG00000158683	ENST00000289672	T	0.28895	1.59	5.1	4.22	0.49857	.	0.000000	0.64402	D	0.000005	T	0.58481	0.2125	M	0.87381	2.88	0.49687	D	0.999811	D	0.89917	1.0	D	0.87578	0.998	T	0.64360	-0.6426	10	0.72032	D	0.01	-33.0327	11.2105	0.48795	0.0904:0.0:0.9096:0.0	.	1946	Q8TDX9	PK1L1_HUMAN	L	1946	ENSP00000289672:P1946L	ENSP00000289672:P1946L	P	-	2	0	PKD1L1	47843150	1.000000	0.71417	0.890000	0.34922	0.996000	0.88848	6.472000	0.73567	1.134000	0.42165	0.655000	0.94253	CCC	.	.		0.582	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47876625	G	A	47876625	3	1	101	1	0	0	0	0	1	0	0	0	11973	1232	43	3	2796	3	PKD1L1	7	47876625	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	4392275	47876625	111262038	265	14102										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48443391	48443391	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctttcatgggcatgtcgagGaccgtggttctggatgagcc	15	9	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:48443391G>T	ENST00000435803.1	+	39	12009	c.11985G>T	c.(11983-11985)agG>agT	p.R3995S		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3995	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GCATGTCGAGGACCGTGGTTC	0.572																																					p.R3995S		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G11985T						.						91	92	92					7																	48443391		2008	4168	6176	SO:0001583	missense	154664	exon39			GTCGAGGACCGTG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11985G>T	chr7.hg19:g.48443391G>T	ENSP00000411096:p.Arg3995Ser	61.0	0.0		115.0	11.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	9.789	1.177279	0.21787	.	.	ENSG00000179869	ENST00000435803	D	0.93307	-3.2	6.17	1.96	0.26148	ATPase, AAA+ type, core (1);ABC transporter-like (2);	1.053980	0.07446	N	0.898305	D	0.85767	0.5773	N	0.17764	0.52	0.09310	N	1	B;B	0.30146	0.27;0.097	B;B	0.26693	0.072;0.032	T	0.76580	-0.2907	10	0.56958	D	0.05	.	3.9532	0.09379	0.1998:0.1068:0.5712:0.1222	.	1697;3995	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	S	3995	ENSP00000411096:R3995S	ENSP00000411096:R3995S	R	+	3	2	ABCA13	48413937	0.001000	0.12720	0.198000	0.23420	0.316000	0.28119	-0.199000	0.09491	0.484000	0.27630	-0.176000	0.13171	AGG	.	.		0.572	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48443391	G	T	48443391	3	4	101	1	0	0	0	0	1	0	0	0	31	1165	41	3	11968	3	ABCA13	7	48443391	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	566766	48443391	110695272	266	14103										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48559659	48559659	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tttacagaatatctatgatgTcctcaagtgggtctttacta	7	7	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:48559659T>C	ENST00000435803.1	+	53	13844	c.13820T>C	c.(13819-13821)gTc>gCc	p.V4607A	ABCA13_ENST00000544596.1_Missense_Mutation_p.V337A	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4607					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATCTATGATGTCCTCAAGTGG	0.328																																					p.V4607A		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T13820C						.						101	89	93					7																	48559659		1833	4073	5906	SO:0001583	missense	154664	exon53			ATGATGTCCTCAA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.13820T>C	chr7.hg19:g.48559659T>C	ENSP00000411096:p.Val4607Ala	56.0	0.0		177.0	97.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.520975	0.44866	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.86694	-2.16;-2.16;-2.16	5.35	1.61	0.23674	.	0.474755	0.17696	N	0.165083	D	0.82586	0.5069	L	0.41824	1.3	0.19300	N	0.99998	B;P;P	0.51791	0.321;0.459;0.948	B;B;P	0.49799	0.205;0.173;0.622	T	0.72849	-0.4168	10	0.52906	T	0.07	.	4.1499	0.10234	0.1492:0.1619:0.0:0.6889	.	337;2309;4607	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	A	4607;380;337	ENSP00000411096:V4607A;ENSP00000391042:V380A;ENSP00000442634:V337A	ENSP00000391042:V380A	V	+	2	0	ABCA13	48530205	0.954000	0.32549	0.038000	0.18304	0.982000	0.71751	2.503000	0.45407	0.036000	0.15547	0.528000	0.53228	GTC	.	.		0.328	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48559659	T	C	48559659	3	2	101	1	0	0	0	0	1	0	0	0	31	1667	58	2	13859	2	ABCA13	7	48559659	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	116268	48559659	110579004	267	14104										
GUSB	2990	hgsc.bcm.edu	37	chr7	65440043	65440043	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cacaggccccagtgacgtctGtgcagtcagctgcacctatg	11	14	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:65440043G>A	ENST00000304895.4	-	6	1058	c.928C>T	c.(928-930)Cag>Tag	p.Q310*	GUSB_ENST00000421103.1_Nonsense_Mutation_p.Q164*|GUSB_ENST00000345660.6_Intron|GUSB_ENST00000476486.1_5'UTR	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	310					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						AGTGACGTCTGTGCAGTCAGC	0.607																																					p.Q310X		Atlas-SNP	.											.	GUSB	52	.	0			c.C928T						.						70	64	66					7																	65440043		2203	4300	6503	SO:0001587	stop_gained	2990	exon6			ACGTCTGTGCAGT	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.928C>T	chr7.hg19:g.65440043G>A	ENSP00000302728:p.Gln310*	25.0	0.0		110.0	65.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Nonsense_Mutation	SNP	ENST00000304895.4	hg19	CCDS5530.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376815	0.82682	.	.	ENSG00000169919	ENST00000304895;ENST00000421103	.	.	.	4.99	1.04	0.20106	.	0.888310	0.09996	N	0.729024	.	.	.	.	.	.	0.38947	D	0.958264	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	9.8986	0.41334	0.0:0.3697:0.3767:0.2536	.	.	.	.	X	310;164	.	ENSP00000302728:Q310X	Q	-	1	0	GUSB	65077478	0.937000	0.31787	0.003000	0.11579	0.219000	0.24729	1.931000	0.40134	0.005000	0.14708	0.511000	0.50034	CAG	.	.		0.607	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		A	65440043	G	A	65440043	4	1	101	1	0	0	0	0	0	1	0	0	6911	1386	48	3	1055	3	GUSB	7	65440043	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	16880384	65440043	93698620	268	14105										
TPST1	8460	hgsc.bcm.edu	37	chr7	65751568	65751568	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tatcaaaatgggttgggaagAtaccgccagatgttttacaa	10	6	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:65751568A>G	ENST00000304842.5	+	3	1341	c.916A>G	c.(916-918)Ata>Gta	p.I306V	TPST1_ENST00000480281.1_3'UTR	NM_003596.3	NP_003587.1	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1	306					inflammatory response (GO:0006954)|peptidyl-tyrosine sulfation (GO:0006478)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			NS(1)|biliary_tract(1)|breast(1)|kidney(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						GGTTGGGAAGATACCGCCAGA	0.413																																					p.I306V		Atlas-SNP	.											.	TPST1	25	.	0			c.A916G						.						140	124	130					7																	65751568		2203	4300	6503	SO:0001583	missense	8460	exon3			GGGAAGATACCGC	AF038009	CCDS5533.1	7q11.21	2012-12-13			ENSG00000169902	ENSG00000169902	2.8.2.20	"Sulfotransferases, membrane-bound"	12020	protein-coding gene	gene with protein product	"transport and golgi organization 13 homolog A (Drosophila)"	603125				9501187	Standard	NM_003596		Approved	TANGO13A	uc003tuw.3	O60507	OTTHUMG00000023871	ENST00000304842.5:c.916A>G	chr7.hg19:g.65751568A>G	ENSP00000302413:p.Ile306Val	56.0	0.0		92.0	8.0	NM_003596	A4D2M0|Q6FGM7	Missense_Mutation	SNP	ENST00000304842.5	hg19	CCDS5533.1	.	.	.	.	.	.	.	.	.	.	A	17.36	3.370232	0.61624	.	.	ENSG00000169902	ENST00000304842;ENST00000544114	T	0.45276	0.9	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.55033	0.1895	M	0.86740	2.835	0.80722	D	1	P;P	0.40834	0.73;0.467	B;B	0.43445	0.42;0.175	T	0.61108	-0.7129	10	0.42905	T	0.14	-21.5617	14.8826	0.70545	1.0:0.0:0.0:0.0	.	306;306	F5H7U7;O60507	.;TPST1_HUMAN	V	306	ENSP00000302413:I306V	ENSP00000302413:I306V	I	+	1	0	TPST1	65389003	1.000000	0.71417	0.997000	0.53966	0.900000	0.52787	8.266000	0.89871	2.123000	0.65237	0.383000	0.25322	ATA	.	.		0.413	TPST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251705.2	NM_003596		G	65751568	A	G	65751568	3	3	101	1	0	0	0	0	1	0	0	0	16442	333	12	2	922	2	TPST1	7	65751568	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	311525	65751568	93387095	269	14106										
UPK3B	80761	hgsc.bcm.edu	37	chr7	76142448	76142448	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gggctcacccagggctgagaCcaagtggtcagaccccatca	12	14	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:76142448C>A	ENST00000257632.5	+	3	754				UPK3B_ENST00000334348.3_Missense_Mutation_p.T170N|UPK3B_ENST00000448265.3_Intron|UPK3B_ENST00000419923.2_Intron|UPK3B_ENST00000443097.2_Missense_Mutation_p.T170N|UPK3B_ENST00000394849.1_Intron			Q9BT76	UPK3B_HUMAN	uroplakin 3B						negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				AGGGCTGAGACCAAGTGGTCA	0.657																																					p.T170N		Atlas-SNP	.											.	UPK3B	15	.	0			c.C509A						.						61	44	50					7																	76142448		2203	4300	6503	SO:0001627	intron_variant	80761	exon4			CTGAGACCAAGTG	BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566			21444	protein-coding gene	gene with protein product	"uroplakin IIIb"	611887				12446744	Standard	XM_005250612		Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000257632.5:c.627-816C>A	chr7.hg19:g.76142448C>A		88.0	0.0		201.0	42.0	NM_182684	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Missense_Mutation	SNP	ENST00000257632.5	hg19	CCDS5588.1	.	.	.	.	.	.	.	.	.	.	.	16.59	3.164810	0.57476	.	.	ENSG00000243566	ENST00000334348;ENST00000443097	T;T	0.70869	-0.52;-0.52	5.21	5.21	0.72293	.	.	.	.	.	D	0.84215	0.5423	M	0.81802	2.56	0.36151	D	0.847449	D	0.89917	1.0	D	0.74674	0.984	D	0.89240	0.3583	9	0.87932	D	0	.	15.522	0.75874	0.0:1.0:0.0:0.0	.	170	A6NHH5	.	N	170	ENSP00000334938:T170N;ENSP00000444585:T170N	ENSP00000334938:T170N	T	+	2	0	UPK3B	75980384	0.630000	0.27155	0.997000	0.53966	0.169000	0.22640	0.953000	0.29162	2.436000	0.82500	0.563000	0.77884	ACC	.	.		0.657	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570		A	76142448	C	A	76142448	1	1	101	0	1	0	0	0	0	0	0	0	17026	507	18	3		3	UPK3B	7	76142448	Intron	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	10390880	76142448	82996215	270	14107										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77569480	77569480	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	actcacagcacattctgcttCagaactttatgtgattgcat	6	10	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:77569480C>A	ENST00000248550.7	+	13	1677	c.1601C>A	c.(1600-1602)tCa>tAa	p.S534*	PHTF2_ENST00000416283.2_Nonsense_Mutation_p.S500*|PHTF2_ENST00000275575.7_Nonsense_Mutation_p.S496*|PHTF2_ENST00000424760.1_Nonsense_Mutation_p.S496*|PHTF2_ENST00000307305.8_Nonsense_Mutation_p.S496*|PHTF2_ENST00000422959.2_Nonsense_Mutation_p.S500*			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	534					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						CATTCTGCTTCAGAACTTTAT	0.373																																					p.S500X		Atlas-SNP	.											.	PHTF2	104	.	0			c.C1499A						.						126	116	119					7																	77569480		1862	4106	5968	SO:0001587	stop_gained	57157	exon12			CTGCTTCAGAACT	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1601C>A	chr7.hg19:g.77569480C>A	ENSP00000248550:p.Ser534*	133.0	0.0		367.0	38.0	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Nonsense_Mutation	SNP	ENST00000248550.7	hg19		.	.	.	.	.	.	.	.	.	.	C	38	6.899107	0.97920	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000275575;ENST00000416283;ENST00000248550	.	.	.	5.67	5.67	0.87782	.	0.344882	0.27482	N	0.019166	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.3448	13.9903	0.64362	0.0:0.9275:0.0:0.0725	.	.	.	.	X	500;500;496;496;496;500;534	.	ENSP00000248550:S534X	S	+	2	0	PHTF2	77407416	0.990000	0.36364	0.995000	0.50966	0.969000	0.65631	1.485000	0.35519	2.665000	0.90641	0.557000	0.71058	TCA	.	.		0.373	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		A	77569480	C	A	77569480	4	1	101	1	0	0	0	0	0	1	0	0	11872	838	29	3	1599	3	PHTF2	7	77569480	Nonsense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1427032	77569480	81569183	271	14108										
PCLO	27445	hgsc.bcm.edu	37	chr7	82585390	82585390	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtcttcatcatgccatgagtGacgtcttcctgcatcttcat	7	12	6	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:82585390G>A	ENST00000333891.9	-	5	5216	c.4879C>T	c.(4879-4881)Cac>Tac	p.H1627Y	PCLO_ENST00000423517.2_Missense_Mutation_p.H1627Y	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGCCATGAGTGACGTCTTCCT	0.403																																					p.H1627Y		Atlas-SNP	.											.	PCLO	1506	.	0			c.C4879T						.						318	305	310					7																	82585390		2067	4192	6259	SO:0001583	missense	27445	exon5			ATGAGTGACGTCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.4879C>T	chr7.hg19:g.82585390G>A	ENSP00000334319:p.His1627Tyr	92.0	0.0		197.0	52.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.793628	0.31685	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17054	2.3;2.3	5.15	5.15	0.70609	.	.	.	.	.	T	0.38983	0.1061	L	0.51422	1.61	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.16482	-1.0401	9	0.87932	D	0	.	18.629	0.91352	0.0:0.0:1.0:0.0	.	1627;1627	Q9Y6V0-5;Q9Y6V0-6	.;.	Y	1558;1627;1627	ENSP00000334319:H1627Y;ENSP00000388393:H1627Y	ENSP00000334319:H1627Y	H	-	1	0	PCLO	82423326	1.000000	0.71417	0.928000	0.36995	0.975000	0.68041	6.805000	0.75191	2.400000	0.81607	0.655000	0.94253	CAC	.	.		0.403	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82585390	G	A	82585390	3	1	101	1	0	0	0	0	1	0	0	0	11592	1290	45	3	10650	3	PCLO	7	82585390	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	5015910	82585390	76553273	272	14109										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83590805	83590805	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tatgtcctggcctttgccgaCgttgttttcggtcccttttc	9	12	0	0	rs318240753		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:83590805C>A	ENST00000265362.4	-	17	2512	c.2198G>T	c.(2197-2199)cGt>cTt	p.R733L	SEMA3A_ENST00000436949.1_Missense_Mutation_p.R733L	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	733	Arg/Lys-rich (basic).		R -> H (in HH16; phenotype consistent with Kallmann syndrome; dbSNP:rs318240753). {ECO:0000269|PubMed:22927827}.		apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CCTTTGCCGACGTTGTTTTCG	0.458																																					p.R733L		Atlas-SNP	.											.	SEMA3A	121	.	0			c.G2198T						.						222	197	206					7																	83590805		2203	4300	6503	SO:0001583	missense	10371	exon17			TGCCGACGTTGTT	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.2198G>T	chr7.hg19:g.83590805C>A	ENSP00000265362:p.Arg733Leu	148.0	0.0		385.0	21.0	NM_006080		Missense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.537539	0.45176	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.28255	1.62;1.62	6.08	6.08	0.98989	.	0.048367	0.85682	D	0.000000	T	0.23649	0.0572	N	0.13235	0.315	0.58432	D	0.999996	B	0.30563	0.285	B	0.28385	0.089	T	0.03739	-1.1008	10	0.44086	T	0.13	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	733	Q14563	SEM3A_HUMAN	L	733	ENSP00000265362:R733L;ENSP00000415260:R733L	ENSP00000265362:R733L	R	-	2	0	SEMA3A	83428741	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	4.589000	0.61006	2.894000	0.99253	0.655000	0.94253	CGT	.	.		0.458	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		A	83590805	C	A	83590805	3	1	101	1	0	0	0	0	1	0	0	0	14039	536	19	1	121	1	SEMA3A	7	83590805	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1005415	83590805	75547858	273	14110										
PEG10	23089	hgsc.bcm.edu	37	chr7	94293700	94293700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccgagccggtgggaggtgccCgcatgcgcctgacgcaggaa	17	13	0	1	rs376581536		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:94293700C>T	ENST00000482108.1	+	2	1311	c.832C>T	c.(832-834)Cgc>Tgc	p.R278C	PEG10_ENST00000488574.1_Missense_Mutation_p.R278C	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	278					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GGGAGGTGCCCGCATGCGCCT	0.597																																					p.R354C		Atlas-SNP	.											.	PEG10	36	.	0			c.C1060T						.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,3974		0,0,1987	18	24	22		832,1060,1060,934,934,832	4.3	1	7		22	1,8303		0,1,4151	no	missense,missense,missense,missense,missense,missense	PEG10	NM_001040152.1,NM_001172437.1,NM_001172438.1,NM_001184961.1,NM_001184962.1,NM_015068.3	180,180,180,180,180,180	0,1,6138	TT,TC,CC		0.012,0.0,0.0081	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	278/326,354/785,354/402,312/743,312/360,278/709	94293700	1,12277	1987	4152	6139	SO:0001583	missense	23089	exon2			GGTGCCCGCATGC	AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.832C>T	chr7.hg19:g.94293700C>T	ENSP00000417587:p.Arg278Cys	20.0	0.0		112.0	7.0	NM_001172438	Q96A68|Q9UPV1	Missense_Mutation	SNP	ENST00000482108.1	hg19	CCDS55126.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.927626	0.73327	0.0	1.2E-4	ENSG00000242265	ENST00000482108;ENST00000488574	T;T	0.15139	2.45;2.45	4.34	4.34	0.51931	.	.	.	.	.	T	0.29652	0.0740	L	0.34521	1.04	0.40084	D	0.976172	D;D	0.89917	1.0;1.0	D;D	0.69654	0.965;0.948	T	0.03619	-1.1019	9	0.56958	D	0.05	.	14.7868	0.69810	0.0:1.0:0.0:0.0	.	354;278	B4DSP0;Q86TG7	.;PEG10_HUMAN	C	278	ENSP00000417587:R278C;ENSP00000418944:R278C	ENSP00000417587:R278C	R	+	1	0	PEG10	94131636	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.330000	0.43885	2.429000	0.82318	0.555000	0.69702	CGC	.	.		0.597	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340751.1	NM_015068		T	94293700	C	T	94293700	3	4	101	1	0	0	0	0	1	0	0	0	11728	652	23	1	1066	1	PEG10	7	94293700	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	10702895	94293700	64844963	274	14111										
MCM7	4176	hgsc.bcm.edu	37	chr7	99693701	99693701	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agccagcaccagggccccacCctctaaggtcagttctccac	8	18	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:99693701C>A	ENST00000303887.5	-	11	1936	c.1291G>T	c.(1291-1293)Ggt>Tgt	p.G431C	MIR25_ENST00000384816.1_RNA|MCM7_ENST00000343023.6_Intron|MIR93_ENST00000385024.1_RNA|MIR106B_ENST00000385301.1_RNA|MCM7_ENST00000354230.3_Missense_Mutation_p.G255C	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	431	MCM.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGGGCCCCACCCTCTAAGGTC	0.607																																					p.G431C		Atlas-SNP	.											.	MCM7	136	.	0			c.G1291T						.						57	54	55					7																	99693701		2203	4300	6503	SO:0001583	missense	4176	exon11			CCCCACCCTCTAA		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.1291G>T	chr7.hg19:g.99693701C>A	ENSP00000307288:p.Gly431Cys	25.0	0.0		160.0	11.0	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	hg19	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.254289	0.80135	.	.	ENSG00000166508	ENST00000303887;ENST00000542483;ENST00000362082;ENST00000354230	T;T	0.11495	2.77;2.77	5.02	4.13	0.48395	ATPase, AAA+ type, core (1);	0.109029	0.64402	D	0.000007	T	0.48909	0.1526	H	0.98370	4.215	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67821	-0.5571	10	0.87932	D	0	-23.2828	12.4978	0.55937	0.1682:0.8318:0.0:0.0	.	431	P33993	MCM7_HUMAN	C	431;368;324;255	ENSP00000307288:G431C;ENSP00000346171:G255C	ENSP00000307288:G431C	G	-	1	0	MCM7	99531637	1.000000	0.71417	0.988000	0.46212	0.914000	0.54420	7.604000	0.82830	1.302000	0.44855	0.655000	0.94253	GGT	.	.		0.607	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			A	99693701	C	A	99693701	3	1	101	1	0	0	0	0	1	0	0	0	9401	623	22	3	888	3	MCM7	7	99693701	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	5400001	99693701	59444962	275	14112										
MCM7	4176	hgsc.bcm.edu	37	chr7	99697309	99697309	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaattgagtccaccaactcgGggtcatcctcggctacgtcg	10	13	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:99697309G>C	ENST00000303887.5	-	3	824	c.179C>G	c.(178-180)cCc>cGc	p.P60R	AP4M1_ENST00000422582.1_5'Flank|AP4M1_ENST00000429084.1_5'Flank|AP4M1_ENST00000359593.4_5'Flank|MCM7_ENST00000343023.6_Missense_Mutation_p.P60R|AP4M1_ENST00000421755.1_5'Flank|MCM7_ENST00000354230.3_5'UTR	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	60					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CACCAACTCGGGGTCATCCTC	0.562																																					p.P60R		Atlas-SNP	.											.	MCM7	136	.	0			c.C179G						.						132	124	126					7																	99697309		2203	4300	6503	SO:0001583	missense	4176	exon3			AACTCGGGGTCAT		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.179C>G	chr7.hg19:g.99697309G>C	ENSP00000307288:p.Pro60Arg	17.0	0.0		93.0	13.0	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	hg19	CCDS5683.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.31|13.31	2.197802|2.197802	0.38806|0.38806	.|.	.|.	ENSG00000166508|ENSG00000166508	ENST00000542483|ENST00000343023;ENST00000303887	.|T;T	.|0.10763	.|2.84;2.84	4.5|4.5	4.5|4.5	0.54988|0.54988	.|Nucleic acid-binding, OB-fold-like (1);	0.199666|0.199666	0.41823|0.41823	D|D	0.000812|0.000812	T|T	0.10337|0.10337	0.0253|0.0253	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|B	.|0.29862	.|0.259	.|B	.|0.30029	.|0.11	T|T	0.18241|0.18241	-1.0343|-1.0343	7|10	0.87932|0.28530	D|T	0|0.3	.|.	14.7626|14.7626	0.69617|0.69617	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|60	.|P33993	.|MCM7_HUMAN	A|R	3|60	.|ENSP00000344006:P60R;ENSP00000307288:P60R	ENSP00000445904:P18A|ENSP00000307288:P60R	P|P	-|-	1|2	0|0	MCM7|MCM7	99535245|99535245	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	7.148000|7.148000	0.77389|0.77389	2.314000|2.314000	0.78098|0.78098	0.557000|0.557000	0.71058|0.71058	CCG|CCC	.	.		0.562	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			C	99697309	G	C	99697309	3	2	101	1	0	0	0	0	1	0	0	0	9401	1232	43	4	2032	4	MCM7	7	99697309	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3608	99697309	59441354	276	14113										
PVRIG	79037	hgsc.bcm.edu	37	chr7	99818613	99818613	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gccactatcaacaccagctgCcgcccagctactttggacac	7	17	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:99818613C>A	ENST00000317271.2	+	6	1083	c.720C>A	c.(718-720)tgC>tgA	p.C240*	AC005071.1_ENST00000410550.1_RNA|GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA	NM_024070.3	NP_076975.2	Q6DKI7	PVRIG_HUMAN	poliovirus receptor related immunoglobulin domain containing	240						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)	11	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACACCAGCTGCCGCCCAGCTA	0.677																																					p.C240X		Atlas-SNP	.											.	PVRIG	20	.	0			c.C720A						.						65	70	68					7																	99818613		2203	4300	6503	SO:0001587	stop_gained	79037	exon6			CAGCTGCCGCCCA	BC001129	CCDS5690.1	7q22.1	2013-06-26			ENSG00000213413	ENSG00000213413			32190	protein-coding gene	gene with protein product						16926269	Standard	NM_024070		Approved	MGC2463, C7orf15	uc003uuf.1	Q6DKI7	OTTHUMG00000156798	ENST00000317271.2:c.720C>A	chr7.hg19:g.99818613C>A	ENSP00000316675:p.Cys240*	66.0	0.0		173.0	14.0	NM_024070	D6W5U9|Q9BVK3	Nonsense_Mutation	SNP	ENST00000317271.2	hg19	CCDS5690.1	.	.	.	.	.	.	.	.	.	.	c	26.9	4.780649	0.90195	.	.	ENSG00000213413	ENST00000317271	.	.	.	3.01	3.01	0.34805	.	.	.	.	.	.	.	.	.	.	.	0.35377	D	0.789556	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	9.7879	0.40688	0.0:1.0:0.0:0.0	.	.	.	.	X	240	.	ENSP00000316675:C240X	C	+	3	2	PVRIG	99656549	0.001000	0.12720	0.004000	0.12327	0.149000	0.21700	0.819000	0.27308	2.010000	0.58986	0.505000	0.49811	TGC	.	.		0.677	PVRIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345870.2	NM_024070		A	99818613	C	A	99818613	4	1	101	1	0	0	0	0	0	1	0	0	12853	747	26	3	738	3	PVRIG	7	99818613	Nonsense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	121304	99818613	59320050	277	14114										
GNB2	2783	hgsc.bcm.edu	37	chr7	100274386	100274386	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaccctccgtgggcacctggCaaagatctatgccatgcact	10	14	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:100274386C>A	ENST00000303210.4	+	4	649	c.167C>A	c.(166-168)gCa>gAa	p.A56E	GNB2_ENST00000436220.1_Missense_Mutation_p.A12E|GNB2_ENST00000427895.1_Intron|GNB2_ENST00000419828.1_Intron|GNB2_ENST00000424361.1_Missense_Mutation_p.A12E|GNB2_ENST00000393924.1_Missense_Mutation_p.A56E|GNB2_ENST00000393926.1_Missense_Mutation_p.A56E	NM_005273.3	NP_005264.2	P62879	GBB2_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2	56					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|lung(3)|ovary(2)|prostate(1)	7	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)	Ovarian(593;0.238)				GGGCACCTGGCAAAGATCTAT	0.637																																					p.A56E		Atlas-SNP	.											.	GNB2	29	.	0			c.C167A						.						70	35	46					7																	100274386		2200	4299	6499	SO:0001583	missense	2783	exon4			ACCTGGCAAAGAT	M16514	CCDS5703.1	7q21.3-q22.1	2013-01-10			ENSG00000172354	ENSG00000172354		"WD repeat domain containing"	4398	protein-coding gene	gene with protein product	"G protein, beta-2 subunit", "guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 2", "signal-transducing guanine nucleotide-binding regulatory protein beta subunit", "transducin beta chain 2"	139390				9799793	Standard	NM_005273		Approved		uc003uwb.3	P62879	OTTHUMG00000137419	ENST00000303210.4:c.167C>A	chr7.hg19:g.100274386C>A	ENSP00000305260:p.Ala56Glu	28.0	0.0		78.0	23.0	NM_005273	B3KPU1|P11016|P54312	Missense_Mutation	SNP	ENST00000303210.4	hg19	CCDS5703.1	.	.	.	.	.	.	.	.	.	.	.	27.1	4.795965	0.90453	.	.	ENSG00000172354	ENST00000303210;ENST00000451587;ENST00000436220;ENST00000424361;ENST00000393926;ENST00000431068;ENST00000412215;ENST00000393924	T;T;T;T;T;T;T;T	0.80824	5.06;5.06;-1.42;-1.42;5.06;5.06;5.06;5.06	4.96	4.08	0.47627	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);G-protein, beta subunit (1);	0.000000	0.85682	D	0.000000	T	0.79581	0.4470	N	0.20483	0.58	0.58432	D	0.999998	P	0.52061	0.95	P	0.61592	0.891	T	0.81304	-0.0993	10	0.72032	D	0.01	-1.2442	10.9761	0.47467	0.0:0.9091:0.0:0.0909	.	56	P62879	GBB2_HUMAN	E	56;56;12;12;56;56;56;56	ENSP00000305260:A56E;ENSP00000399904:A56E;ENSP00000401873:A12E;ENSP00000389391:A12E;ENSP00000377503:A56E;ENSP00000390077:A56E;ENSP00000413219:A56E;ENSP00000377501:A56E	ENSP00000305260:A56E	A	+	2	0	GNB2	100112322	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.651000	0.83577	1.303000	0.44873	0.561000	0.74099	GCA	.	.		0.637	GNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268391.2	NM_005273		A	100274386	C	A	100274386	3	1	101	1	0	0	0	0	1	0	0	0	6525	710	25	3	177	3	GNB2	7	100274386	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	455773	100274386	58864277	278	14115										
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100452001	100452001	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agttgtttttctgaggattgGtgagtgggtcctggggcggg	19	4	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:100452001G>T	ENST00000354161.3	+	2	306		c.e2+1		SLC12A9_ENST00000540482.1_Splice_Site|SLC12A9_ENST00000415287.1_Splice_Site|RP11-126L15.4_ENST00000412754.1_RNA|SLC12A9_ENST00000275729.3_Splice_Site|SLC12A9_ENST00000428758.1_Splice_Site	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CTGAGGATTGGTGAGTGGGTC	0.577																																					.		Atlas-SNP	.											.	SLC12A9	81	.	0			c.181+1G>T						.						120	119	120					7																	100452001		2203	4300	6503	SO:0001630	splice_region_variant	56996	exon2			GGATTGGTGAGTG	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"Solute carriers"	17435	protein-coding gene	gene with protein product	"cation-chloride cotransporter-interacting protein"					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.181+1G>T	chr7.hg19:g.100452001G>T		145.0	0.0		395.0	18.0	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Splice_Site	SNP	ENST00000354161.3	hg19	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.655266	0.67472	.	.	ENSG00000146828	ENST00000540482;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161;ENST00000416675;ENST00000434158	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7812	0.69769	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A9	100289937	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	7.406000	0.80017	2.340000	0.79590	0.407000	0.27541	.	.	.		0.577	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	Intron	T	100452001	G	T	100452001	5	4	101	1	0	0	0	0	0	0	1	0	14405	1275	44	3	184	3	SLC12A9	7	100452001	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	177615	100452001	58686662	279	14116										
RELN	5649	hgsc.bcm.edu	37	chr7	103276844	103276844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agagcctggaactgccaaagCtttcagaaataaacattggg	10	8	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:103276844C>T	ENST00000428762.1	-	18	2300	c.2141G>A	c.(2140-2142)aGc>aAc	p.S714N	RELN_ENST00000424685.2_Missense_Mutation_p.S714N|RELN_ENST00000343529.5_Missense_Mutation_p.S714N	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	714					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ACTGCCAAAGCTTTCAGAAAT	0.458																																					p.S714N	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.G2141A						.						60	62	61					7																	103276844		2203	4300	6503	SO:0001583	missense	5649	exon18			CCAAAGCTTTCAG		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.2141G>A	chr7.hg19:g.103276844C>T	ENSP00000392423:p.Ser714Asn	73.0	0.0		220.0	10.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.436206	0.43224	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.22945	1.93;1.93;1.93	5.76	5.76	0.90799	.	0.043835	0.85682	D	0.000000	T	0.30541	0.0768	N	0.12182	0.205	0.50632	D	0.999887	D;D	0.60160	0.96;0.987	P;D	0.63381	0.577;0.914	T	0.07424	-1.0773	10	0.11485	T	0.65	.	19.9658	0.97266	0.0:1.0:0.0:0.0	.	714;714	P78509-2;P78509	.;RELN_HUMAN	N	714	ENSP00000392423:S714N;ENSP00000345694:S714N;ENSP00000388446:S714N	ENSP00000345694:S714N	S	-	2	0	RELN	103064080	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.295000	0.78780	2.721000	0.93114	0.591000	0.81541	AGC	.	.		0.458	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103276844	C	T	103276844	3	4	101	1	0	0	0	0	1	0	0	0	13235	797	28	3	8433	3	RELN	7	103276844	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2824843	103276844	55861819	280	14117										
PNPLA8	50640	hgsc.bcm.edu	37	chr7	108155899	108155899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acttcttgcattactaaggaGgtaaatatatatatctacag	6	6	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:108155899G>A	ENST00000422087.1	-	4	443	c.37C>T	c.(37-39)Ctc>Ttc	p.L13F	PNPLA8_ENST00000453144.1_Intron|PNPLA8_ENST00000257694.8_Missense_Mutation_p.L13F|PNPLA8_ENST00000388728.5_Missense_Mutation_p.L13F|PNPLA8_ENST00000436062.1_Missense_Mutation_p.L13F|PNPLA8_ENST00000426128.2_Missense_Mutation_p.L13F|PNPLA8_ENST00000483879.1_Intron	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	13					arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						TTACTAAGGAGGTAAATATAT	0.338																																					p.L13F		Atlas-SNP	.											.	PNPLA8	82	.	0			c.C37T						.						60	56	58					7																	108155899		2202	4300	6502	SO:0001583	missense	50640	exon2			TAAGGAGGTAAAT	AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"Patatin-like phospholipase domain containing"	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.37C>T	chr7.hg19:g.108155899G>A	ENSP00000410804:p.Leu13Phe	48.0	0.0		119.0	8.0	NM_001256008	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Missense_Mutation	SNP	ENST00000422087.1	hg19	CCDS34733.1	.	.	.	.	.	.	.	.	.	.	G	9.319	1.057455	0.19907	.	.	ENSG00000135241	ENST00000426128;ENST00000257694;ENST00000388728;ENST00000422087;ENST00000436062;ENST00000427008;ENST00000415498	D;D;D;D;D	0.98493	-3.77;-4.96;-3.77;-4.96;-4.96	5.26	2.4	0.29515	.	0.649498	0.14456	N	0.318482	D	0.94676	0.8283	L	0.46157	1.445	0.25488	N	0.987675	B	0.11235	0.004	B	0.09377	0.004	D	0.85450	0.1160	10	0.12430	T	0.62	.	4.4129	0.11441	0.4079:0.0:0.4435:0.1486	.	13	Q9NP80	PLPL8_HUMAN	F	13	ENSP00000394988:L13F;ENSP00000257694:L13F;ENSP00000373380:L13F;ENSP00000410804:L13F;ENSP00000406779:L13F	ENSP00000257694:L13F	L	-	1	0	PNPLA8	107943135	0.993000	0.37304	1.000000	0.80357	0.977000	0.68977	0.170000	0.16663	0.565000	0.29255	0.460000	0.39030	CTC	.	.		0.338	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		A	108155899	G	A	108155899	3	1	101	1	0	0	0	0	1	0	0	0	12180	1000	35	3	2347	3	PNPLA8	7	108155899	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	4879055	108155899	50982764	281	14118										
KCND2	3751	hgsc.bcm.edu	37	chr7	119914945	119914945	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctcagcagtatttctttgacCgtgacccagacatcttccgc	7	14	3	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:119914945C>A	ENST00000331113.4	+	1	1224	c.259C>A	c.(259-261)Cgt>Agt	p.R87S		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	87	Interaction with KCNIP1. {ECO:0000250}.				action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	TTTCTTTGACCGTGACCCAGA	0.527																																					p.R87S		Atlas-SNP	.											.	KCND2	194	.	0			c.C259A						.						134	137	136					7																	119914945		2203	4300	6503	SO:0001583	missense	3751	exon1			TTTGACCGTGACC	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.259C>A	chr7.hg19:g.119914945C>A	ENSP00000333496:p.Arg87Ser	48.0	0.0		138.0	11.0	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	hg19	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049908	0.75846	.	.	ENSG00000184408	ENST00000331113	D	0.90133	-2.62	5.51	5.51	0.81932	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.97235	0.9096	H	0.98646	4.29	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.98281	1.0508	9	.	.	.	.	14.2875	0.66256	0.1486:0.8514:0.0:0.0	.	87	Q9NZV8	KCND2_HUMAN	S	87	ENSP00000333496:R87S	.	R	+	1	0	KCND2	119702181	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.930000	0.70104	2.603000	0.88011	0.655000	0.94253	CGT	.	.		0.527	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		A	119914945	C	A	119914945	3	1	101	1	0	0	0	0	1	0	0	0	8028	652	23	1	261	1	KCND2	7	119914945	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	11759046	119914945	39223718	282	14119										
KCND2	3751	hgsc.bcm.edu	37	chr7	119915059	119915059	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aactggccttctttggcctcAtcccggaaatcatcggcgac	9	14	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:119915059A>G	ENST00000331113.4	+	1	1338	c.373A>G	c.(373-375)Atc>Gtc	p.I125V		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	125					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	CTTTGGCCTCATCCCGGAAAT	0.577																																					p.I125V		Atlas-SNP	.											KCND2,NS,carcinoma,0,1	KCND2	194	.	0			c.A373G						.						132	134	133					7																	119915059		2203	4300	6503	SO:0001583	missense	3751	exon1			GGCCTCATCCCGG	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.373A>G	chr7.hg19:g.119915059A>G	ENSP00000333496:p.Ile125Val	34.0	0.0		128.0	17.0	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	hg19	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	A	8.909	0.958135	0.18507	.	.	ENSG00000184408	ENST00000331113	T	0.75821	-0.97	5.71	5.71	0.89125	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	T	0.55481	0.1923	N	0.05574	-0.02	0.49299	D	0.999776	B	0.02656	0.0	B	0.04013	0.001	T	0.52939	-0.8508	9	.	.	.	.	15.9958	0.80243	1.0:0.0:0.0:0.0	.	125	Q9NZV8	KCND2_HUMAN	V	125	ENSP00000333496:I125V	.	I	+	1	0	KCND2	119702295	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.512000	0.53407	2.188000	0.69820	0.533000	0.62120	ATC	.	.		0.577	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		G	119915059	A	G	119915059	3	3	101	1	0	0	0	0	1	0	0	0	8028	217	8	2	375	2	KCND2	7	119915059	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	114	119915059	39223604	283	14120										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121684477	121684477	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	attgtcattgttttgccaggAgcaatatgtcttcattcatg	8	7	4	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:121684477A>G	ENST00000393386.2	+	23	6350	c.5939A>G	c.(5938-5940)gAg>gGg	p.E1980G	PTPRZ1_ENST00000449182.1_Splice_Site_p.E1113G	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1980	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TTTTGCCAGGAGCAATATGTC	0.383																																					p.E1980G		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.A5939G						.						183	169	174					7																	121684477		2203	4300	6503	SO:0001630	splice_region_variant	5803	exon23			GCCAGGAGCAATA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.5938-1A>G	chr7.hg19:g.121684477A>G		135.0	0.0		373.0	183.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.584806	0.86748	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	D;D	0.85013	-1.93;-1.93	5.65	5.65	0.86999	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.64402	D	0.000003	D	0.92264	0.7546	M	0.77313	2.365	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	0.999;0.993;1.0	D	0.93199	0.6590	10	0.87932	D	0	.	15.8828	0.79216	1.0:0.0:0.0:0.0	.	1119;1113;1980	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	G	1980;1113	ENSP00000377047:E1980G;ENSP00000410000:E1113G	ENSP00000377047:E1980G	E	+	2	0	PTPRZ1	121471713	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	9.339000	0.96797	2.152000	0.67230	0.533000	0.62120	GAG	.	.		0.383	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	Missense_Mutation	G	121684477	A	G	121684477	5	3	101	1	0	0	0	0	0	0	1	0	12829	318	11	2	6029	2	PTPRZ1	7	121684477	Splice_Site	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1769418	121684477	37454186	284	14121										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128449544	128449544	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	actgacagaattgcaggaaaAgtacaaggccagccagaagg	12	8	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:128449544A>T	ENST00000297788.4	+	11	2013	c.1646A>T	c.(1645-1647)aAg>aTg	p.K549M	CCDC136_ENST00000378685.4_Intron|CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000487361.1_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	549						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						TTGCAGGAAAAGTACAAGGCC	0.587																																					p.K549M		Atlas-SNP	.											.	CCDC136	170	.	0			c.A1646T						.						21	24	23					7																	128449544		2027	4107	6134	SO:0001583	missense	64753	exon11			AGGAAAAGTACAA		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.1646A>T	chr7.hg19:g.128449544A>T	ENSP00000297788:p.Lys549Met	110.0	0.0		528.0	25.0	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.61|18.61	3.660929|3.660929	0.67700|0.67700	.|.	.|.	ENSG00000128596|ENSG00000128596	ENST00000297788;ENST00000397697;ENST00000320524;ENST00000464672|ENST00000494552	T;T|.	0.35789|.	1.29;1.29|.	5.95|5.95	2.06|2.06	0.26882|0.26882	.|.	0.737577|.	0.12983|.	N|.	0.423081|.	T|T	0.24314|0.24314	0.0589|0.0589	L|L	0.34521|0.34521	1.04|1.04	0.20703|0.20703	N|N	0.999869|0.999869	B;B|.	0.33171|.	0.206;0.4|.	B;B|.	0.30855|.	0.085;0.121|.	T|T	0.21484|0.21484	-1.0244|-1.0244	10|5	0.62326|.	D|.	0.03|.	-19.2775|-19.2775	1.5329|1.5329	0.02539|0.02539	0.5498:0.1492:0.0917:0.2092|0.5498:0.1492:0.0917:0.2092	.|.	549;549|.	Q96JN2-2;Q96JN2|.	.;CC136_HUMAN|.	M|C	549;549;549;140|426	ENSP00000297788:K549M;ENSP00000417991:K140M|.	ENSP00000297788:K549M|.	K|S	+|+	2|1	0|0	CCDC136|CCDC136	128236780|128236780	0.332000|0.332000	0.24722|0.24722	0.785000|0.785000	0.31869|0.31869	0.968000|0.968000	0.65278|0.65278	0.640000|0.640000	0.24705|0.24705	0.499000|0.499000	0.27970|0.27970	0.533000|0.533000	0.62120|0.62120	AAG|AGT	.	.		0.587	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		T	128449544	A	T	128449544	3	4	101	1	0	0	0	0	1	0	0	0	2772	72	3	4	1688	4	CCDC136	7	128449544	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	6765067	128449544	30689119	285	14122										
CNOT4	4850	hgsc.bcm.edu	37	chr7	135047915	135047915	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atcttgaagagagtctaaacTgtttcctgaagacgctggaa	10	7	2	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:135047915T>C	ENST00000451834.1	-	12	2138	c.1855A>G	c.(1855-1857)Agt>Ggt	p.S619G	CNOT4_ENST00000361528.4_Missense_Mutation_p.S548G|CNOT4_ENST00000541284.1_Missense_Mutation_p.S622G|CNOT4_ENST00000473470.1_5'UTR|CNOT4_ENST00000423368.2_Missense_Mutation_p.S551G			O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	0					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						GAGTCTAAACTGTTTCCTGAA	0.453																																					p.S622G	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.A1864G						.						118	120	119					7																	135047915		1925	4142	6067	SO:0001583	missense	4850	exon12			CTAAACTGTTTCC	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"RNA binding motif (RRM) containing"	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000451834.1:c.1855A>G	chr7.hg19:g.135047915T>C	ENSP00000388491:p.Ser619Gly	40.0	0.0		90.0	60.0	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000451834.1	hg19	CCDS55167.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.822152	0.32237	.	.	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528	T;T;T;T	0.58060	0.69;0.69;0.37;0.36	5.85	5.85	0.93711	.	0.112857	0.85682	D	0.000000	T	0.32763	0.0840	N	0.17082	0.46	0.80722	D	1	B;B;B;B	0.10296	0.0;0.001;0.0;0.003	B;B;B;B	0.13407	0.0;0.0;0.0;0.009	T	0.19353	-1.0308	10	0.09084	T	0.74	-2.5711	10.5619	0.45150	0.0:0.0715:0.0:0.9284	.	619;622;551;548	E7ET38;F8VQP3;O95628-4;O95628-8	.;.;.;.	G	622;619;551;622;548	ENSP00000445508:S622G;ENSP00000388491:S619G;ENSP00000406777:S551G;ENSP00000354673:S548G	ENSP00000262563:S622G	S	-	1	0	CNOT4	134698455	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.849000	0.62882	2.233000	0.73108	0.455000	0.32223	AGT	.	.		0.453	CNOT4-003	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340670.1	NM_013316		C	135047915	T	C	135047915	3	2	101	1	0	0	0	0	1	0	0	0	3623	1580	55	2	281	2	CNOT4	7	135047915	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	6598371	135047915	24090748	286	14123										
CLCN1	1180	hgsc.bcm.edu	37	chr7	143039472	143039472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctccctccatagcaaatatAccatctttgttgaggacatc	5	12	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:143039472A>G	ENST00000343257.2	+	16	1891	c.1804A>G	c.(1804-1806)Acc>Gcc	p.T602A		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	602					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					TAGCAAATATACCATCTTTGT	0.463																																					p.T602A		Atlas-SNP	.											.	CLCN1	141	.	0			c.A1804G						.						147	114	125					7																	143039472		2203	4300	6503	SO:0001583	missense	1180	exon16			AAATATACCATCT	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.1804A>G	chr7.hg19:g.143039472A>G	ENSP00000339867:p.Thr602Ala	74.0	0.0		210.0	10.0	NM_000083	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	hg19	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.714293	0.68730	.	.	ENSG00000188037	ENST00000343257	D	0.87966	-2.32	5.82	5.82	0.92795	.	0.147273	0.64402	D	0.000020	T	0.81688	0.4875	N	0.24115	0.695	0.50171	D	0.999857	P	0.42296	0.775	B	0.42851	0.4	T	0.80632	-0.1296	10	0.27082	T	0.32	.	16.1771	0.81858	1.0:0.0:0.0:0.0	.	602	P35523	CLCN1_HUMAN	A	602	ENSP00000339867:T602A	ENSP00000339867:T602A	T	+	1	0	CLCN1	142749594	1.000000	0.71417	0.994000	0.49952	0.883000	0.51084	9.331000	0.96430	2.225000	0.72522	0.523000	0.50628	ACC	.	.		0.463	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		G	143039472	A	G	143039472	3	3	101	1	0	0	0	0	1	0	0	0	3464	391	14	2	1866	2	CLCN1	7	143039472	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	7991557	143039472	16099191	287	14124										
CHPF2	54480	hgsc.bcm.edu	37	chr7	150934562	150934562	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caccacactctcgctttgagGtgctgggctgggactacttc	11	13	1	1	rs139379425	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr7:150934562G>A	ENST00000035307.2	+	4	2627	c.1114G>A	c.(1114-1116)Gtg>Atg	p.V372M	MIR671_ENST00000390183.1_RNA|CHPF2_ENST00000495645.1_Missense_Mutation_p.V364M|RP4-548D19.3_ENST00000607902.1_RNA	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	372					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						TCGCTTTGAGGTGCTGGGCTG	0.637																																					p.V372M		Atlas-SNP	.											.	CHPF2	52	.	0			c.G1114A						.						81	81	81					7																	150934562		2203	4300	6503	SO:0001583	missense	54480	exon4			TTTGAGGTGCTGG	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.1114G>A	chr7.hg19:g.150934562G>A	ENSP00000035307:p.Val372Met	44.0	0.0		159.0	9.0	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	hg19	CCDS34779.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025532	0.75390	.	.	ENSG00000033100	ENST00000495645;ENST00000035307;ENST00000377851	T;T	0.25579	1.79;1.79	5.63	5.63	0.86233	.	0.058009	0.64402	D	0.000002	T	0.49047	0.1534	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.81914	0.995;0.925	T	0.45381	-0.9265	10	0.62326	D	0.03	-22.7659	14.3202	0.66482	0.0:0.1479:0.8521:0.0	.	372;364	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	M	364;372;372	ENSP00000418914:V364M;ENSP00000035307:V372M	ENSP00000035307:V372M	V	+	1	0	CHPF2	150565495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.884000	0.87274	2.652000	0.90054	0.655000	0.94253	GTG	.	G|1.000;T|0.000		0.637	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015		A	150934562	G	A	150934562	3	1	101	1	0	0	0	0	1	0	0	0	3371	1261	44	3	1128	3	CHPF2	7	150934562	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	7895090	150934562	8204101	288	14125										
DLGAP2	9228	hgsc.bcm.edu	37	chr8	1616828	1616828	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctcctcaagagccgctgctCctccatcgggattcaggtag	11	14	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:1616828C>T	ENST00000421627.2	+	6	2038	c.1904C>T	c.(1903-1905)tCc>tTc	p.S635F		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	714					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		AGCCGCTGCTCCTCCATCGGG	0.637																																					p.S635F		Atlas-SNP	.											DLGAP2_ENST00000356067,NS,carcinoma,0,2	DLGAP2	292	.	0			c.C1904T						.						15	20	19					8																	1616828		2033	4168	6201	SO:0001583	missense	9228	exon6			GCTGCTCCTCCAT	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"discs, large (Drosophila) homolog-associated protein 2"			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.1904C>T	chr8.hg19:g.1616828C>T	ENSP00000400258:p.Ser635Phe	23.0	0.0		49.0	2.0	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	hg19	CCDS47760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.90|16.90	3.250705|3.250705	0.59212|0.59212	.|.	.|.	ENSG00000198010|ENSG00000198010	ENST00000520901|ENST00000356067;ENST00000421627	.|T	.|0.19532	.|2.14	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	.|0.198058	.|0.56097	.|D	.|0.000033	T|T	0.44095|0.44095	0.1277|0.1277	M|M	0.80422|0.80422	2.495|2.495	0.41790|0.41790	D|D	0.989869|0.989869	.|P;P	.|0.45986	.|0.842;0.87	.|P;P	.|0.52672	.|0.581;0.706	T|T	0.29761|0.29761	-1.0001|-1.0001	5|10	.|0.39692	.|T	.|0.17	-12.2698|-12.2698	19.557|19.557	0.95354|0.95354	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|714;714	.|Q9P1A6-2;Q9P1A6	.|.;DLGP2_HUMAN	S|F	652|680;635	.|ENSP00000400258:S635F	.|ENSP00000348366:S680F	P|S	+|+	1|2	0|0	DLGAP2|DLGAP2	1604235|1604235	1.000000|1.000000	0.71417|0.71417	0.867000|0.867000	0.34043|0.34043	0.727000|0.727000	0.41649|0.41649	5.698000|5.698000	0.68302|0.68302	2.609000|2.609000	0.88269|0.88269	0.650000|0.650000	0.86243|0.86243	CCT|TCC	.	.		0.637	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		T	1616828	C	T	1616828	3	4	101	1	0	0	0	0	1	0	0	0	4562	855	30	3	1922	3	DLGAP2	8	1616828	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10		1616828	144747194	289	14126										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10470139	10470139	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctccagctttccgctcagccCctatctgggcagaggggctg	12	15	2	1	rs578108515		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:10470139C>A	ENST00000382483.3	-	4	1692	c.1469G>T	c.(1468-1470)gGg>gTg	p.G490V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	490					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CCGCTCAGCCCCTATCTGGGC	0.711																																					p.G490V		Atlas-SNP	.											RP1L1,bladder,carcinoma,-1,1	RP1L1	453	.	0			c.G1469T						.						27	31	29					8																	10470139		1911	4119	6030	SO:0001583	missense	94137	exon4			TCAGCCCCTATCT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1469G>T	chr8.hg19:g.10470139C>A	ENSP00000371923:p.Gly490Val	30.0	0.0		30.0	5.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	12.05	1.822299	0.32237	.	.	ENSG00000183638	ENST00000382483	T	0.04015	3.73	4.41	-2.38	0.06622	.	1.713650	0.04054	U	0.305219	T	0.04003	0.0112	L	0.27053	0.805	0.09310	N	1	P	0.38827	0.649	B	0.36186	0.219	T	0.37033	-0.9723	10	0.72032	D	0.01	2.6844	5.0251	0.14381	0.1409:0.4006:0.0:0.4585	.	490	A6NKC6	.	V	490	ENSP00000371923:G490V	ENSP00000371923:G490V	G	-	2	0	RP1L1	10507549	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.099000	0.15210	-0.466000	0.06943	0.561000	0.74099	GGG	.	.		0.711	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10470139	C	A	10470139	3	1	101	1	0	0	0	0	1	0	0	0	13548	623	22	3	5737	3	RP1L1	8	10470139	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	8853311	10470139	135893883	290	14127										
FGF20	26281	hgsc.bcm.edu	37	chr8	16853235	16853235	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cacacctctaatactgaccaGtcccactgccacactgatga	5	16	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:16853235G>T	ENST00000180166.5	-	2	467	c.319C>A	c.(319-321)Ctg>Atg	p.L107M		NM_019851.2	NP_062825.1	Q9NP95	FGF20_HUMAN	fibroblast growth factor 20	107					cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of cardiac muscle cell proliferation (GO:0060043)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	11				Colorectal(111;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		ATACTGACCAGTCCCACTGCC	0.338																																					p.L107M		Atlas-SNP	.											.	FGF20	16	.	0			c.C319A						.						113	107	109					8																	16853235		2203	4300	6503	SO:0001583	missense	26281	exon2			TGACCAGTCCCAC	AB030648	CCDS5998.1	8p22	2008-05-15			ENSG00000078579	ENSG00000078579			3677	protein-coding gene	gene with protein product		605558				10913340	Standard	NM_019851		Approved		uc003wxc.1	Q9NP95	OTTHUMG00000096964	ENST00000180166.5:c.319C>A	chr8.hg19:g.16853235G>T	ENSP00000180166:p.Leu107Met	69.0	0.0		97.0	21.0	NM_019851	B2RPH5	Missense_Mutation	SNP	ENST00000180166.5	hg19	CCDS5998.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.97|17.97	3.518782|3.518782	0.64634|0.64634	.|.	.|.	ENSG00000078579|ENSG00000078579	ENST00000180166|ENST00000381981	T|.	0.68479|.	-0.33|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67088|0.67088	0.2856|0.2856	L|L	0.58302|0.58302	1.8|1.8	0.58432|0.58432	D|D	0.999998|0.999998	B|.	0.32693|.	0.38|.	B|.	0.39971|.	0.315|.	T|T	0.68511|0.68511	-0.5389|-0.5389	10|6	0.66056|0.87932	D|D	0.02|0	.|.	13.4923|13.4923	0.61402|0.61402	0.0714:0.0:0.9286:0.0|0.0714:0.0:0.9286:0.0	.|.	107|.	Q9NP95|.	FGF20_HUMAN|.	M|N	107|75	ENSP00000180166:L107M|.	ENSP00000180166:L107M|ENSP00000371411:T75N	L|T	-|-	1|2	2|0	FGF20|FGF20	16897606|16897606	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	3.808000|3.808000	0.55598|0.55598	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	CTG|ACT	.	.		0.338	FGF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214030.1			T	16853235	G	T	16853235	3	4	101	1	0	0	0	0	1	0	0	0	5857	1020	36	3	324	3	FGF20	8	16853235	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6383096	16853235	129510787	291	14128										
MTMR7	9108	hgsc.bcm.edu	37	chr8	17198903	17198903	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtcaacgacataaacgaagTcacttcctggattggctttc	8	10	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:17198903T>C	ENST00000180173.5	-	6	735	c.701A>G	c.(700-702)gAc>gGc	p.D234G	MTMR7_ENST00000521857.1_Missense_Mutation_p.D234G|MTMR7_ENST00000523571.1_5'UTR	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	234	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		ATAAACGAAGTCACTTCCTGG	0.557																																					p.D234G		Atlas-SNP	.											.	MTMR7	75	.	0			c.A701G						.						177	110	133					8																	17198903		2203	4300	6503	SO:0001583	missense	9108	exon6			ACGAAGTCACTTC	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.701A>G	chr8.hg19:g.17198903T>C	ENSP00000180173:p.Asp234Gly	46.0	0.0		73.0	8.0	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	hg19	CCDS34851.1	.	.	.	.	.	.	.	.	.	.	T	13.28	2.191393	0.38707	.	.	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.90197	-2.63;-2.63	4.94	3.78	0.43462	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.220883	0.49916	N	0.000131	D	0.83801	0.5333	L	0.29908	0.895	0.80722	D	1	P;B	0.35139	0.486;0.01	B;B	0.35550	0.205;0.02	T	0.80176	-0.1491	10	0.33940	T	0.23	.	10.9107	0.47108	0.0:0.0741:0.0:0.9259	.	234;234	Q9Y216-2;Q9Y216	.;MTMR7_HUMAN	G	234	ENSP00000180173:D234G;ENSP00000429733:D234G	ENSP00000180173:D234G	D	-	2	0	MTMR7	17243274	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	3.252000	0.51461	1.017000	0.39495	0.460000	0.39030	GAC	.	.		0.557	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686		C	17198903	T	C	17198903	3	2	101	1	0	0	0	0	1	0	0	0	9957	1667	58	2	1317	2	MTMR7	8	17198903	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	345668	17198903	129165119	292	14129										
PPP2CB	5516	hgsc.bcm.edu	37	chr8	30643819	30643819	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acgaggcgctgggtcaaattGaaggctgtaaatggcaaaaa	13	6	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:30643819G>A	ENST00000221138.4	-	7	1312	c.862C>T	c.(862-864)Caa>Taa	p.Q288*	PPP2CB_ENST00000518564.1_Intron	NM_001009552.1	NP_001009552.1	P62714	PP2AB_HUMAN	protein phosphatase 2, catalytic subunit, beta isozyme	288					apoptotic mitochondrial changes (GO:0008637)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of Ras protein signal transduction (GO:0046580)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|regulation of gene expression (GO:0010468)|response to antibiotic (GO:0046677)|response to endoplasmic reticulum stress (GO:0034976)|response to hydrogen peroxide (GO:0042542)	chromosome, centromeric region (GO:0000775)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	9				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)	GGGTCAAATTGAAGGCTGTAA	0.438																																					p.Q288X		Atlas-SNP	.											.	PPP2CB	27	.	0			c.C862T						.						44	43	43					8																	30643819		2199	4297	6496	SO:0001587	stop_gained	5516	exon7			CAAATTGAAGGCT		CCDS6079.1	8p12	2011-05-24	2010-03-05		ENSG00000104695	ENSG00000104695	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9300	protein-coding gene	gene with protein product	"protein phosphatase 2A catalytic subunit, beta isoform"	176916	"protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform"			8383590	Standard	NM_001009552		Approved	PP2Abeta	uc003xik.3	P62714	OTTHUMG00000163949	ENST00000221138.4:c.862C>T	chr8.hg19:g.30643819G>A	ENSP00000221138:p.Gln288*	25.0	0.0		34.0	5.0	NM_001009552	D3DSV4|P11082|Q6FHK5	Nonsense_Mutation	SNP	ENST00000221138.4	hg19	CCDS6079.1	.	.	.	.	.	.	.	.	.	.	G	39	7.904227	0.98554	.	.	ENSG00000104695	ENST00000221138;ENST00000406655	.	.	.	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-8.8029	17.9622	0.89089	0.0:0.0:1.0:0.0	.	.	.	.	X	288	.	ENSP00000221138:Q288X	Q	-	1	0	PPP2CB	30763361	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	9.476000	0.97823	2.400000	0.81607	0.563000	0.77884	CAA	.	.		0.438	PPP2CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376527.2	NM_001009552		A	30643819	G	A	30643819	4	1	101	1	0	0	0	0	0	1	0	0	12393	1299	45	3	71	3	PPP2CB	8	30643819	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	13444916	30643819	115720203	293	14130										
ZMAT4	79698	hgsc.bcm.edu	37	chr8	40683185	40683185	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ataaatcctgatcaatatcgGaggacttcatcaggctacaa	7	9	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:40683185G>A	ENST00000297737.6	-	2	157	c.11C>T	c.(10-12)tCc>tTc	p.S4F	ZMAT4_ENST00000523823.1_5'UTR|ZMAT4_ENST00000315769.7_Missense_Mutation_p.S4F	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	4						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			ATCAATATCGGAGGACTTCAT	0.443																																					p.S4F		Atlas-SNP	.											.	ZMAT4	47	.	0			c.C11T						.						44	37	39					8																	40683185		2186	4262	6448	SO:0001583	missense	79698	exon2			ATATCGGAGGACT	AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061		"Zinc fingers, matrin-type"	25844	protein-coding gene	gene with protein product						12477932	Standard	NM_024645		Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.11C>T	chr8.hg19:g.40683185G>A	ENSP00000297737:p.Ser4Phe	28.0	0.0		78.0	8.0	NM_024645	Q8WUT8	Missense_Mutation	SNP	ENST00000297737.6	hg19	CCDS34885.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.428304	0.43122	.	.	ENSG00000165061	ENST00000315769;ENST00000297737;ENST00000519406	T;T;T	0.46819	0.86;0.87;0.87	5.37	5.37	0.77165	.	0.174304	0.50627	D	0.000101	T	0.48169	0.1485	N	0.08118	0	0.46376	D	0.999019	P;P	0.48694	0.914;0.855	D;B	0.63703	0.917;0.36	T	0.57142	-0.7862	10	0.72032	D	0.01	-16.5024	14.9923	0.71399	0.0:0.0:1.0:0.0	.	4;4	Q9H898-2;Q9H898	.;ZMAT4_HUMAN	F	4	ENSP00000319785:S4F;ENSP00000297737:S4F;ENSP00000428423:S4F	ENSP00000297737:S4F	S	-	2	0	ZMAT4	40802342	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.339000	0.72969	2.692000	0.91855	0.591000	0.81541	TCC	.	.		0.443	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376950.1	NM_024645		A	40683185	G	A	40683185	3	1	101	1	0	0	0	0	1	0	0	0	17709	1174	41	3	702	3	ZMAT4	8	40683185	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	10039366	40683185	105680837	294	14131										
HGSNAT	138050	hgsc.bcm.edu	37	chr8	43033222	43033222	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctagattctttttaggtttgTatttattatgggatcttcca	7	5	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:43033222T>A	ENST00000458501.2	+	10	941	c.941T>A	c.(940-942)gTa>gAa	p.V314E	HGSNAT_ENST00000297798.7_5'Flank|HGSNAT_ENST00000521576.1_5'Flank|HGSNAT_ENST00000379644.4_Missense_Mutation_p.V286E			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	314					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			TTTAGGTTTGTATTTATTATG	0.333																																					p.V286E		Atlas-SNP	.											.	HGSNAT	85	.	0			c.T857A						.						115	116	116					8																	43033222		1792	4062	5854	SO:0001583	missense	138050	exon10			GGTTTGTATTTAT		CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"transmembrane protein 76"	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.941T>A	chr8.hg19:g.43033222T>A	ENSP00000389524:p.Val314Glu	101.0	0.0		225.0	17.0	NM_152419	B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	hg19		.	.	.	.	.	.	.	.	.	.	T	22.2	4.255759	0.80135	.	.	ENSG00000165102	ENST00000458501;ENST00000379644;ENST00000522082	D;D;D	0.91068	-2.78;-2.78;-1.89	5.68	5.68	0.88126	.	0.144593	0.46442	D	0.000287	D	0.95204	0.8445	M	0.85373	2.75	0.80722	D	1	D	0.63880	0.993	D	0.65573	0.936	D	0.95751	0.8792	10	0.87932	D	0	-10.7461	13.9256	0.63961	0.0:0.0:0.0:1.0	.	314	Q68CP4	HGNAT_HUMAN	E	314;286;33	ENSP00000389524:V314E;ENSP00000368965:V286E;ENSP00000430151:V33E	ENSP00000368965:V286E	V	+	2	0	HGSNAT	43152379	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	6.332000	0.72934	2.179000	0.69175	0.529000	0.55759	GTA	.	.		0.333	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038		A	43033222	T	A	43033222	3	1	101	1	0	0	0	0	1	0	0	0	7097	1638	57	4	895	4	HGSNAT	8	43033222	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2350037	43033222	103330800	295	14132										
OPRK1	4986	hgsc.bcm.edu	37	chr8	54147486	54147486	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccacgctcatcatggtcaagGtgaagatgctggtgaacatg	12	9	3	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:54147486G>C	ENST00000265572.3	-	3	740	c.443C>G	c.(442-444)aCc>aGc	p.T148S	RP11-162D9.3_ENST00000524425.1_RNA|OPRK1_ENST00000520287.1_Missense_Mutation_p.T148S|OPRK1_ENST00000524278.1_Missense_Mutation_p.T59S	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	148					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)			NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CATGGTCAAGGTGAAGATGCT	0.483																																					p.T148S		Atlas-SNP	.											.	OPRK1	90	.	0			c.C443G						.						140	113	122					8																	54147486		2203	4300	6503	SO:0001583	missense	4986	exon3			GTCAAGGTGAAGA		CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"GPCR / Class A : Opioid receptors"	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.443C>G	chr8.hg19:g.54147486G>C	ENSP00000265572:p.Thr148Ser	62.0	0.0		189.0	12.0	NM_000912	E5RHC9|Q499G4	Missense_Mutation	SNP	ENST00000265572.3	hg19	CCDS6152.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.379661	0.82682	.	.	ENSG00000082556	ENST00000265572;ENST00000524278;ENST00000520287;ENST00000396798	T;T;T	0.19532	2.14;2.14;2.14	5.95	5.95	0.96441	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.49270	0.1547	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.35847	-0.9772	10	0.12430	T	0.62	.	20.3732	0.98896	0.0:0.0:1.0:0.0	.	148	P41145	OPRK_HUMAN	S	148;59;148;134	ENSP00000265572:T148S;ENSP00000430923:T59S;ENSP00000429706:T148S	ENSP00000265572:T148S	T	-	2	0	OPRK1	54310039	1.000000	0.71417	0.990000	0.47175	0.997000	0.91878	9.711000	0.98735	2.809000	0.96659	0.650000	0.86243	ACC	.	.		0.483	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1			C	54147486	G	C	54147486	3	2	101	1	0	0	0	0	1	0	0	0	10894	1261	44	4	707	4	OPRK1	8	54147486	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	11114264	54147486	92216536	296	14133										
TRIM55	84675	hgsc.bcm.edu	37	chr8	67067941	67067941	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagtgcttgatttttactttAatgggtaggaaatattttct	8	4	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:67067941A>C	ENST00000315962.4	+	9	1897				TRIM55_ENST00000353317.5_Intron|TRIM55_ENST00000276573.7_Missense_Mutation_p.L536F|TRIM55_ENST00000350034.4_Intron	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55						signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			TTTTTACTTTAATGGGTAGGA	0.363																																					p.L536F		Atlas-SNP	.											.	TRIM55	91	.	0			c.A1608C						.						146	130	135					8																	67067941		2203	4299	6502	SO:0001627	intron_variant	84675	exon10			TACTTTAATGGGT	AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	14215	protein-coding gene	gene with protein product		606469	"ring finger protein 29", "tripartite motif-containing 55"	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.1524+1372A>C	chr8.hg19:g.67067941A>C		136.0	0.0		288.0	26.0	NM_033058	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	hg19	CCDS6184.1	.	.	.	.	.	.	.	.	.	.	A	17.21	3.330611	0.60743	.	.	ENSG00000147573	ENST00000276573	T	0.35048	1.33	5.8	3.04	0.35103	.	.	.	.	.	T	0.17959	0.0431	N	0.08118	0	0.80722	D	1	B	0.20671	0.047	B	0.19946	0.027	T	0.04991	-1.0913	9	0.31617	T	0.26	.	8.5873	0.33666	0.5693:0.3543:0.0763:0.0	.	536	Q9BYV6-3	.	F	536	ENSP00000276573:L536F	ENSP00000276573:L536F	L	+	3	2	TRIM55	67230495	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.539000	0.23175	1.000000	0.39049	0.529000	0.55759	TTA	.	.		0.363	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		C	67067941	A	C	67067941	1	2	101	0	1	0	0	0	0	0	0	0	16544	359	13	5		5	TRIM55	8	67067941	Intron	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	12920455	67067941	79296081	297	14134										
PREX2	80243	hgsc.bcm.edu	37	chr8	68934295	68934295	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acaagtttcgtatctatgatGaatattgtagtaaccatgag	8	5	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:68934295G>C	ENST00000288368.4	+	4	638	c.361G>C	c.(361-363)Gaa>Caa	p.E121Q	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	121	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TATCTATGATGAATATTGTAG	0.294																																					p.E121Q		Atlas-SNP	.											.	PREX2	614	.	0			c.G361C						.						108	106	107					8																	68934295		2202	4300	6502	SO:0001583	missense	80243	exon4			TATGATGAATATT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.361G>C	chr8.hg19:g.68934295G>C	ENSP00000288368:p.Glu121Gln	40.0	0.0		93.0	7.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	31	5.067046	0.93898	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.64085	-0.08	6.04	6.04	0.98038	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.75781	0.3896	L	0.45051	1.395	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.999	D;D;D	0.91635	0.999;0.981;0.979	T	0.75739	-0.3212	10	0.87932	D	0	.	20.5948	0.99439	0.0:0.0:1.0:0.0	.	121;121;121	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	Q	121	ENSP00000288368:E121Q	ENSP00000288368:E121Q	E	+	1	0	PREX2	69096849	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.452000	0.97615	2.873000	0.98535	0.563000	0.77884	GAA	.	.		0.294	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		C	68934295	G	C	68934295	3	2	101	1	0	0	0	0	1	0	0	0	12489	1291	45	4	375	4	PREX2	8	68934295	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1866354	68934295	77429727	298	14135										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73848335	73848335	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	catggtttaccatggagtacCttttgcgattcttatcctca	7	10	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:73848335C>G	ENST00000523207.1	+	3	1333	c.745C>G	c.(745-747)Ctt>Gtt	p.L249V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	249					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	CATGGAGTACCTTTTGCGATT	0.458																																					p.L249V		Atlas-SNP	.											.	KCNB2	228	.	0			c.C745G						.						195	168	177					8																	73848335		2203	4300	6503	SO:0001583	missense	9312	exon3			GAGTACCTTTTGC	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.745C>G	chr8.hg19:g.73848335C>G	ENSP00000430846:p.Leu249Val	134.0	0.0		405.0	34.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760784	0.69763	.	.	ENSG00000182674	ENST00000523207	D	0.98419	-4.92	5.93	5.93	0.95920	Ion transport (1);	0.000000	0.40818	N	0.001009	D	0.97654	0.9231	N	0.17631	0.505	0.80722	D	1	P	0.49696	0.927	P	0.61397	0.888	D	0.97710	1.0190	10	0.39692	T	0.17	.	20.3507	0.98813	0.0:1.0:0.0:0.0	.	249	Q92953	KCNB2_HUMAN	V	249	ENSP00000430846:L249V	ENSP00000430846:L249V	L	+	1	0	KCNB2	74010889	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	7.818000	0.86416	2.808000	0.96608	0.655000	0.94253	CTT	.	.		0.458	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		G	73848335	C	G	73848335	3	3	101	1	0	0	0	0	1	0	0	0	8022	681	24	4	751	4	KCNB2	8	73848335	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4914040	73848335	72515687	299	14136										
LRRCC1	85444	hgsc.bcm.edu	37	chr8	86057622	86057622	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	taaaatttacatgtcgatttAggtccatcaaattgaaaaag	6	5	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:86057622A>T	ENST00000360375.3	+	19	3125		c.e19-1		LRRCC1_ENST00000414626.2_Splice_Site	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1						mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.?(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						ATGTCGATTTAGGTCCATCAA	0.264																																					.		Atlas-SNP	.											LRRCC1_ENST00000414626,NS,carcinoma,0,2	LRRCC1	212	.	2	Unknown(2)	lung(2)	c.2977-2A>T						.						37	34	35					8																	86057622		1785	4056	5841	SO:0001630	splice_region_variant	85444	exon19			CGATTTAGGTCCA	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.2977-1A>T	chr8.hg19:g.86057622A>T		109.0	0.0		300.0	141.0	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Splice_Site	SNP	ENST00000360375.3	hg19	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	A	10.56	1.384971	0.25031	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9715	0.71238	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LRRCC1	86244874	1.000000	0.71417	0.972000	0.41901	0.023000	0.10783	7.483000	0.81158	2.112000	0.64535	0.459000	0.35465	.	.	.		0.264	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	Intron	T	86057622	A	T	86057622	5	4	101	1	0	0	0	0	0	0	1	0	9035	434	15	4	3049	4	LRRCC1	8	86057622	Splice_Site	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	12209287	86057622	60306400	300	14137										
STK3	6788	hgsc.bcm.edu	37	chr8	99560362	99560362	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctccacactagtcttcaccaTggtgtgggaatccagctcat	8	13	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:99560362T>A	ENST00000419617.2	-	9	1116	c.976A>T	c.(976-978)Atg>Ttg	p.M326L	STK3_ENST00000523601.1_Missense_Mutation_p.M354L	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	326					apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		GTCTTCACCATGGTGTGGGAA	0.463																																					p.M354L		Atlas-SNP	.											.	STK3	47	.	0			c.A1060T						.						57	54	55					8																	99560362		1937	4146	6083	SO:0001583	missense	6788	exon11			TCACCATGGTGTG	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"serine/threonine kinase 3 (Ste20, yeast homolog)"			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.976A>T	chr8.hg19:g.99560362T>A	ENSP00000390500:p.Met326Leu	61.0	0.0		212.0	9.0	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Missense_Mutation	SNP	ENST00000419617.2	hg19	CCDS47900.1	.	.	.	.	.	.	.	.	.	.	T	18.55	3.648917	0.67358	.	.	ENSG00000104375	ENST00000419617;ENST00000523601;ENST00000518165	T;T;T	0.71222	-0.55;-0.54;0.27	5.74	5.74	0.90152	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.72827	0.3509	L	0.49455	1.56	0.80722	D	1	B;B;B	0.27068	0.167;0.011;0.026	B;B;B	0.41332	0.354;0.02;0.02	T	0.68349	-0.5432	10	0.27082	T	0.32	.	16.0502	0.80755	0.0:0.0:0.0:1.0	.	215;326;354	E5RFQ9;Q13188;B3KYA7	.;STK3_HUMAN;.	L	326;354;215	ENSP00000390500:M326L;ENSP00000429744:M354L;ENSP00000428014:M215L	ENSP00000390500:M326L	M	-	1	0	STK3	99629538	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.625000	0.83145	2.197000	0.70478	0.528000	0.53228	ATG	.	.		0.463	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281		A	99560362	T	A	99560362	3	1	101	1	0	0	0	0	1	0	0	0	15310	1464	51	4	511	4	STK3	8	99560362	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	13502740	99560362	46803660	301	14138										
TM7SF4	81501	hgsc.bcm.edu	37	chr8	105360964	105360964	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgccatcaatcatagcggccGctgcctcctggattatcacg	9	14	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:105360964G>A	ENST00000297581.2	+	2	233	c.184G>A	c.(184-186)Gct>Act	p.A62T	DPYS_ENST00000521601.1_Intron|DCSTAMP_ENST00000517991.1_Missense_Mutation_p.A62T	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	62	Poly-Ala. {ECO:0000255}.				cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											CATAGCGGCCGCTGCCTCCTG	0.507																																					p.A62T		Atlas-SNP	.											.	.	.	.	0			c.G184A						.						131	120	124					8																	105360964		2203	4300	6503	SO:0001583	missense	81501	exon2			GCGGCCGCTGCCT	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"Dendritic cells (DC)-specific transmembrane protein", "IL-Four INDuced"	605933	"transmembrane 7 superfamily member 4"	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.184G>A	chr8.hg19:g.105360964G>A	ENSP00000297581:p.Ala62Thr	106.0	0.0		298.0	88.0	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	hg19	CCDS6301.1	.	.	.	.	.	.	.	.	.	.	G	7.740	0.701009	0.15172	.	.	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.30182	1.54	5.84	-11.7	0.00046	.	1.847400	0.01832	N	0.034757	T	0.12347	0.0300	N	0.12182	0.205	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.06338	-1.0832	9	.	.	.	2.7823	5.6546	0.17635	0.5878:0.146:0.178:0.0883	.	62	Q9H295	TM7S4_HUMAN	T	62	ENSP00000297581:A62T	.	A	+	1	0	TM7SF4	105430140	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.120000	0.03273	-2.683000	0.00407	-0.302000	0.09304	GCT	.	.		0.507	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		A	105360964	G	A	105360964	3	1	101	1	0	0	0	0	1	0	0	0	15991	1087	38	1	186	1	TM7SF4	8	105360964	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	5800602	105360964	41003058	302	14139										
TM7SF4	81501	hgsc.bcm.edu	37	chr8	105361088	105361088	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgctttgattgcagctggcaCagggatcgtcatcttgggac	13	9	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:105361088C>A	ENST00000297581.2	+	2	357	c.308C>A	c.(307-309)aCa>aAa	p.T103K	DPYS_ENST00000521601.1_Intron|DCSTAMP_ENST00000517991.1_Missense_Mutation_p.T103K	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	103					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											GCAGCTGGCACAGGGATCGTC	0.443																																					p.T103K		Atlas-SNP	.											.	.	.	.	0			c.C308A						.						65	63	64					8																	105361088		2203	4300	6503	SO:0001583	missense	81501	exon2			CTGGCACAGGGAT	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"Dendritic cells (DC)-specific transmembrane protein", "IL-Four INDuced"	605933	"transmembrane 7 superfamily member 4"	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.308C>A	chr8.hg19:g.105361088C>A	ENSP00000297581:p.Thr103Lys	103.0	0.0		344.0	20.0	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	hg19	CCDS6301.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.481689	0.84747	.	.	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.34859	1.34	5.84	5.84	0.93424	.	0.097167	0.64402	D	0.000001	T	0.59945	0.2231	M	0.66939	2.045	0.58432	D	0.999997	D	0.89917	1.0	D	0.77004	0.989	T	0.55679	-0.8103	9	.	.	.	-18.0528	18.3185	0.90229	0.0:1.0:0.0:0.0	.	103	Q9H295	TM7S4_HUMAN	K	103	ENSP00000297581:T103K	.	T	+	2	0	TM7SF4	105430264	0.991000	0.36638	0.993000	0.49108	0.993000	0.82548	2.937000	0.48979	2.779000	0.95612	0.655000	0.94253	ACA	.	.		0.443	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		A	105361088	C	A	105361088	3	1	101	1	0	0	0	0	1	0	0	0	15991	478	17	3	310	3	TM7SF4	8	105361088	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	124	105361088	41002934	303	14140										
ABRA	137735	hgsc.bcm.edu	37	chr8	107782232	107782232	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agggggtgtgattggtttagGagcttgaggtgagtcctggg	20	3	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:107782232G>C	ENST00000311955.3	-	1	241	c.187C>G	c.(187-189)Cct>Gct	p.P63A		NM_139166.4	NP_631905.1			actin-binding Rho activating protein									p.P63T(1)		breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			ATTGGTTTAGGAGCTTGAGGT	0.607																																					p.P63A		Atlas-SNP	.											ABRA,NS,carcinoma,0,1	ABRA	57	.	1	Substitution - Missense(1)	ovary(1)	c.C187G						.						89	90	90					8																	107782232		2203	4300	6503	SO:0001583	missense	137735	exon1			GTTTAGGAGCTTG	AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"striated muscle activator of Rho-dependent signaling"	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.187C>G	chr8.hg19:g.107782232G>C	ENSP00000311436:p.Pro63Ala	127.0	0.0		451.0	292.0	NM_139166		Missense_Mutation	SNP	ENST00000311955.3	hg19	CCDS6305.1	.	.	.	.	.	.	.	.	.	.	G	1.608	-0.524884	0.04141	.	.	ENSG00000174429	ENST00000311955	D	0.92446	-3.04	5.66	0.368	0.16146	.	0.804396	0.11835	N	0.524850	D	0.85124	0.5625	L	0.50333	1.59	0.09310	N	1	B	0.27068	0.167	B	0.24269	0.052	T	0.71269	-0.4643	10	0.31617	T	0.26	0.172	0.8137	0.01098	0.3794:0.1161:0.2683:0.2362	.	63	Q8N0Z2	ABRA_HUMAN	A	63	ENSP00000311436:P63A	ENSP00000311436:P63A	P	-	1	0	ABRA	107851408	0.000000	0.05858	0.008000	0.14137	0.330000	0.28571	0.103000	0.15292	0.030000	0.15379	-0.150000	0.13652	CCT	.	.		0.607	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166		C	107782232	G	C	107782232	3	2	101	1	0	0	0	0	1	0	0	0	100	1174	41	4	966	4	ABRA	8	107782232	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2421144	107782232	38581790	304	14141										
OC90	729330	hgsc.bcm.edu	37	chr8	133053841	133053841	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaccatagtcttcaaagtctCgggggcagagaccagccaca	10	12	3	1	rs372434452		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:133053841C>A	ENST00000443356.2	-	5	361	c.275G>T	c.(274-276)cGa>cTa	p.R92L	OC90_ENST00000262283.5_Missense_Mutation_p.R288L|OC90_ENST00000603859.1_Missense_Mutation_p.R92L|OC90_ENST00000254627.3_Missense_Mutation_p.R92L			Q02509	OC90_HUMAN	otoconin 90	92	Phospholipase A2-like 1.				lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			TTCAAAGTCTCGGGGGCAGAG	0.527																																					p.R92L		Atlas-SNP	.											.	OC90	163	.	0			c.G275T						.						46	47	47					8																	133053841		1998	4165	6163	SO:0001583	missense	729330	exon5			AAGTCTCGGGGGC	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.275G>T	chr8.hg19:g.133053841C>A	ENSP00000390050:p.Arg92Leu	69.0	0.0		447.0	18.0	NM_001080399	B4DNG8	Missense_Mutation	SNP	ENST00000443356.2	hg19		.	.	.	.	.	.	.	.	.	.	C	20.9	4.073290	0.76415	.	.	ENSG00000253117;ENSG00000253117;ENSG00000258417	ENST00000254627;ENST00000443356;ENST00000262283	T;T;T	0.23552	1.9;1.9;1.9	5.88	4.9	0.64082	Phospholipase A2 (3);	0.204155	0.39909	N	0.001230	T	0.26011	0.0634	N	0.04880	-0.145	0.34035	D	0.654297	D;D	0.89917	1.0;1.0	D;D	0.78314	0.985;0.991	T	0.27331	-1.0077	10	0.35671	T	0.21	-24.1919	10.1278	0.42661	0.0:0.8788:0.0:0.1212	.	92;92	Q02509-2;Q02509	.;OC90_HUMAN	L	92;92;288	ENSP00000254627:R92L;ENSP00000390050:R92L;ENSP00000262283:R288L	ENSP00000254627:R92L	R	-	2	0	RP11-240B13.2;OC90	133123023	0.991000	0.36638	0.998000	0.56505	0.991000	0.79684	2.905000	0.48727	2.790000	0.95986	0.591000	0.81541	CGA	.	.		0.527	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399		A	133053841	C	A	133053841	3	1	101	1	0	0	0	0	1	0	0	0	10823	884	31	1	1198	1	OC90	8	133053841	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	25271609	133053841	13310181	305	14142										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133153576	133153576	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gatccaagagacccagctttTggctacaaaataagcaaaag	8	9	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:133153576T>A	ENST00000388996.4	-	10	1685	c.1265A>T	c.(1264-1266)cAa>cTa	p.Q422L	KCNQ3_ENST00000521134.1_Missense_Mutation_p.Q302L|KCNQ3_ENST00000519445.1_Missense_Mutation_p.Q422L	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	422					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	ACCCAGCTTTTGGCTACAAAA	0.428																																					p.Q422L		Atlas-SNP	.											.	KCNQ3	164	.	0			c.A1265T						.						59	62	61					8																	133153576		2203	4300	6503	SO:0001583	missense	3786	exon10			AGCTTTTGGCTAC	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1265A>T	chr8.hg19:g.133153576T>A	ENSP00000373648:p.Gln422Leu	38.0	0.0		133.0	20.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	hg19	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	T	19.15	3.772611	0.69992	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.99113	-5.43;-5.38;-5.44	5.88	5.88	0.94601	.	0.057631	0.64402	D	0.000001	D	0.98741	0.9577	L	0.41824	1.3	0.58432	D	0.99999	D;D	0.63880	0.993;0.993	D;D	0.72338	0.977;0.977	D	0.99912	1.1208	10	0.72032	D	0.01	-11.0067	15.4686	0.75422	0.0:0.0:0.0:1.0	.	422;422	E7ET42;O43525	.;KCNQ3_HUMAN	L	422;302;422;411;301	ENSP00000373648:Q422L;ENSP00000429799:Q302L;ENSP00000428790:Q422L	ENSP00000373648:Q422L	Q	-	2	0	KCNQ3	133222758	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.480000	0.81109	2.248000	0.74166	0.528000	0.53228	CAA	.	.		0.428	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		A	133153576	T	A	133153576	3	1	101	1	0	0	0	0	1	0	0	0	8093	1812	63	4	1377	4	KCNQ3	8	133153576	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	99735	133153576	13210446	306	14143										
NAPRT1	642475	hgsc.bcm.edu	37	chr8	144657868	144657904	+	5'Flank	DEL	CTGCCCTGGGTGGGGAAGGGGGTGGCCGTGAGCCCAG	CTGCCCTGGGTGGGGAAGGGGGTGGCCGTGAGCCCAG	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgccaatgacattcacctcaCtgccctgggtggggaagggg					rs370919058|rs200834238		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	CTGCCCTGGGTGGGGAAGGGGGTGGCCGTGAGCCCAG	CTGCCCTGGGTGGGGAAGGGGGTGGCCGTGAGCCCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:144657868_144657904delCTGCCCTGGGTGGGGAAGGGGGTGGCCGTGAGCCCAG	ENST00000398882.3	-	0	0				RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000460623.1_5'UTR|NAPRT1_ENST00000426292.3_Splice_Site_p.LG370fs|NAPRT1_ENST00000435154.3_Splice_Site_p.LG370fs|NAPRT1_ENST00000449291.2_Splice_Site_p.LG370fs|NAPRT1_ENST00000276844.7_Splice_Site_p.LG370fs	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6																		ATTCACCTCACTGCCCTGGGTGGGGAAGGGGGTGGCCGTGAGCCCAGCTGCCCTGGG	0.679																																					p.370_371del		Pindel	.											NAPRT1_ENST00000449291,caecum,carcinoma,0,2	NAPRT1	47	.	0			c.1108_1113del						.																																			SO:0001631	upstream_gene_variant	93100	exon9			.	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"maestro heat-like repeat containing"	27814	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 73"	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164		chr8.hg19:g.144657868_144657904delCTGCCCTGGGTGGGGAAGGGGGTGGCCGTGAGCCCAG	Exception_encountered	15.0	0.0		128.0	23.0	NM_145201	A8MWB1	In_Frame_Del	DEL	ENST00000398882.3	hg19	CCDS47928.1																																																																																			.	.		0.679	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		-	144657904	CTGCCCTGGGTGGGGAAGGGGGTGGCCGTGAGCCCAG	-	144657868	6	5	101	0	1	1	0	1	0	0	0	0	10174	565	20	0		0	NAPRT1	8	144657868	5'Flank	DEL	CTGCCCTGGGTGGGGAAGGGGGTGGCCGTGAGCCCAG	TCGA-DD-A1EE-01A-11D-A12Z-10	11504292	144657868	1706154	307	14144										
GPR172A	79581	hgsc.bcm.edu	37	chr8	145584640	145584640	+	Frame_Shift_Del	DEL	A	A	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcatctatcacgtgttccacAgcagaaaggactgtgcagac							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr8:145584640delA	ENST00000532887.1	+	5	1886	c.1303delA	c.(1303-1305)agcfs	p.S435fs	SLC52A2_ENST00000530047.1_Frame_Shift_Del_p.S435fs|SLC52A2_ENST00000329994.2_Frame_Shift_Del_p.S435fs|SLC52A2_ENST00000526752.1_Frame_Shift_Del_p.Q104fs|SLC52A2_ENST00000402965.1_Frame_Shift_Del_p.S435fs|FBXL6_ENST00000331890.5_5'Flank|SLC52A2_ENST00000527078.1_Frame_Shift_Del_p.S435fs|SLC52A2_ENST00000540505.1_Frame_Shift_Del_p.S347fs|FBXL6_ENST00000455319.2_5'Flank			Q9HAB3	S52A2_HUMAN	solute carrier family 52 (riboflavin transporter), member 2	435					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)									Gamma Hydroxybutyric Acid(DB01440)	CGTGTTCCACAGCAGAAAGGA	0.642																																					p.H434fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1302delC						.						118	112	114					8																	145584640		2203	4300	6503	SO:0001589	frameshift_variant	79581	exon5			.	AY070774	CCDS6423.1	8q24.3	2013-07-17	2013-07-17	2012-02-29		ENSG00000185803		"Solute carriers"	30224	protein-coding gene	gene with protein product		607882	"G protein-coupled receptor 172A"	GPR172A		12740431	Standard	NM_024531		Approved	FLJ11856, PAR1, GPCR41, D15Ertd747e, RFVT2, hRFT3	uc003zcd.2	Q9HAB3		ENST00000532887.1:c.1303delA	chr8.hg19:g.145584640delA	ENSP00000436768:p.Ser435fs	50.0	0.0		131.0	32.0	NM_024531	A8K6B6|D3DWL8|G1UCY1|Q86UT1	Frame_Shift_Del	DEL	ENST00000532887.1	hg19	CCDS6423.1																																																																																			.	.		0.642	SLC52A2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382405.1	NM_024531		-	145584640	A	-	145584640	7	5	101	1	0	1	0	1	0	0	0	0	6677	188	7	0	1317	0	GPR172A	8	145584640	Frame_Shift_Del	DEL	A	TCGA-DD-A1EE-01A-11D-A12Z-10	926772	145584640	779382	308	14145										
KANK1	23189	hgsc.bcm.edu	37	chr9	738429	738429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atgtcatcaacttggcagacGgcaacggcaacacagccctc	9	14	2	1	rs374492770		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:738429G>A	ENST00000382303.1	+	12	4130	c.3478G>A	c.(3478-3480)Ggc>Agc	p.G1160S	KANK1_ENST00000382293.3_Missense_Mutation_p.G1002S|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.G1160S	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	1160	Interaction with KIF21A.				negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		CTTGGCAGACGGCAACGGCAA	0.547																																					p.G1160S		Atlas-SNP	.											.	KANK1	231	.	0			c.G3478A						.	G	SER/GLY,SER/GLY	0,4406		0,0,2203	166	123	138		3478,3004	5.4	1	9		138	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	KANK1	NM_015158.2,NM_153186.3	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1160/1353,1002/1195	738429	1,13005	2203	4300	6503	SO:0001583	missense	23189	exon12			GCAGACGGCAACG	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.3478G>A	chr9.hg19:g.738429G>A	ENSP00000371740:p.Gly1160Ser	92.0	0.0		175.0	16.0	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	hg19	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.613308	0.87359	0.0	1.16E-4	ENSG00000107104	ENST00000382303;ENST00000397976;ENST00000382297;ENST00000382293;ENST00000382289;ENST00000382286	T;T;T	0.62788	0.0;0.0;0.0	5.37	5.37	0.77165	Ankyrin repeat-containing domain (3);	0.000000	0.52532	D	0.000076	T	0.73976	0.3656	L	0.54965	1.715	0.80722	D	1	D;D;D	0.76494	0.999;0.994;0.999	D;P;D	0.71414	0.973;0.803;0.972	T	0.66500	-0.5908	10	0.14656	T	0.56	-18.4727	19.4732	0.94971	0.0:0.0:1.0:0.0	.	206;72;1160	F5H7I5;Q5W0W2;Q14678	.;.;KANK1_HUMAN	S	1160;206;1160;1002;138;72	ENSP00000371740:G1160S;ENSP00000371734:G1160S;ENSP00000371730:G1002S	ENSP00000371723:G72S	G	+	1	0	KANK1	728429	1.000000	0.71417	0.987000	0.45799	0.943000	0.58893	9.700000	0.98707	2.680000	0.91292	0.563000	0.77884	GGC	.	.		0.547	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		A	738429	G	A	738429	3	1	101	1	0	0	0	0	1	0	0	0	7985	1116	39	1	3504	1	KANK1	9	738429	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10		738429	140475002	309	14146										
KCNV2	169522	hgsc.bcm.edu	37	chr9	2718262	2718262	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gggtgctgctggtgctcgacGggctgtgtccgcgccgcttc	17	13	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:2718262G>A	ENST00000382082.3	+	1	761	c.523G>A	c.(523-525)Ggg>Agg	p.G175R		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	175					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		GGTGCTCGACGGGCTGTGTCC	0.647																																					p.G175R		Atlas-SNP	.											KCNV2,NS,carcinoma,0,1	KCNV2	72	.	0			c.G523A						.						24	21	22					9																	2718262		2200	4300	6500	SO:0001583	missense	169522	exon1			CTCGACGGGCTGT	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.523G>A	chr9.hg19:g.2718262G>A	ENSP00000371514:p.Gly175Arg	22.0	0.0		55.0	22.0	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	hg19	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.402059	0.25291	.	.	ENSG00000168263	ENST00000423608;ENST00000382082	D	0.94417	-3.42	4.98	4.98	0.66077	BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.155107	0.56097	D	0.000029	D	0.91161	0.7216	L	0.37697	1.125	0.21967	N	0.999442	B	0.26577	0.153	B	0.09377	0.004	D	0.84442	0.0583	10	0.66056	D	0.02	.	18.2717	0.90070	0.0:0.0:1.0:0.0	.	175	Q8TDN2	KCNV2_HUMAN	R	175	ENSP00000371514:G175R	ENSP00000371514:G175R	G	+	1	0	KCNV2	2708262	1.000000	0.71417	0.928000	0.36995	0.024000	0.10985	9.852000	0.99516	2.306000	0.77630	0.462000	0.41574	GGG	.	.		0.647	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		A	2718262	G	A	2718262	3	1	101	1	0	0	0	0	1	0	0	0	8104	1116	39	1	525	1	KCNV2	9	2718262	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1979833	2718262	138495169	310	14147										
RFX3	5991	hgsc.bcm.edu	37	chr9	3346710	3346710	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atcgcttccttccacatactGcacctgagcgggatagacat	8	13	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:3346710G>A	ENST00000382004.3	-	4	483	c.172C>T	c.(172-174)Cag>Tag	p.Q58*	RFX3_ENST00000358730.2_Nonsense_Mutation_p.Q58*|RFX3_ENST00000302303.1_Nonsense_Mutation_p.Q58*|RFX3_ENST00000381984.2_Nonsense_Mutation_p.Q58*	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	58					cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		TCCACATACTGCACCTGAGCG	0.418																																					p.Q58X		Atlas-SNP	.											.	RFX3	156	.	0			c.C172T						.						150	127	135					9																	3346710		2203	4300	6503	SO:0001587	stop_gained	5991	exon4			CATACTGCACCTG	AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.172C>T	chr9.hg19:g.3346710G>A	ENSP00000371434:p.Gln58*	69.0	0.0		137.0	6.0	NM_134428	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Nonsense_Mutation	SNP	ENST00000382004.3	hg19	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	G	37	5.987667	0.97179	.	.	ENSG00000080298	ENST00000382004;ENST00000381992;ENST00000358730;ENST00000302303;ENST00000457373;ENST00000451859;ENST00000442560;ENST00000420720;ENST00000381985;ENST00000449190;ENST00000381984	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-8.7085	18.3614	0.90375	0.0:0.0:1.0:0.0	.	.	.	.	X	58;58;58;58;58;58;19;19;58;58;58	.	ENSP00000303847:Q58X	Q	-	1	0	RFX3	3336710	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.257000	0.89851	2.612000	0.88384	0.655000	0.94253	CAG	.	.		0.418	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		A	3346710	G	A	3346710	4	1	101	1	0	0	0	0	0	1	0	0	13279	1328	46	3	2293	3	RFX3	9	3346710	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	628448	3346710	137866721	311	14148										
PLIN2	123	hgsc.bcm.edu	37	chr9	19121143	19121143	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcttttgccccagtcacagcGcctttggcattggcaacaat	8	13	2	0	rs368424624		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:19121143G>A	ENST00000276914.2	-	5	509	c.330C>T	c.(328-330)ggC>ggT	p.G110G	PLIN2_ENST00000411567.1_Silent_p.G110G	NM_001122.3	NP_001113.2	Q99541	PLIN2_HUMAN	perilipin 2	110					cellular lipid metabolic process (GO:0044255)|lipid storage (GO:0019915)|long-chain fatty acid transport (GO:0015909)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	19						CAGTCACAGCGCCTTTGGCAT	0.512																																					p.G110G		Atlas-SNP	.											.	PLIN2	41	.	0			c.C330T						.						64	55	58					9																	19121143		2203	4300	6503	SO:0001819	synonymous_variant	123	exon5			CACAGCGCCTTTG	X97324	CCDS6490.1	9p22.1	2009-08-12	2009-08-12	2009-08-12	ENSG00000147872	ENSG00000147872		"Perilipins"	248	protein-coding gene	gene with protein product	"adipophilin"	103195	"adipose differentiation-related protein"	ADFP		9003395, 19638644	Standard	NM_001122		Approved	ADRP	uc003zno.3	Q99541	OTTHUMG00000019624	ENST00000276914.2:c.330C>T	chr9.hg19:g.19121143G>A		46.0	0.0		76.0	15.0	NM_001122	Q9BSC3	Silent	SNP	ENST00000276914.2	hg19	CCDS6490.1																																																																																			.	.		0.512	PLIN2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051835.1	NM_001122		A	19121143	G	A	19121143	2	1	101	1	0	0	0	0	0	0	0	1	12099	1074	38	1		1	PLIN2	9	19121143	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	15774433	19121143	122092288	312	14149										
IFNA8	3445	hgsc.bcm.edu	37	chr9	21409564	21409564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gatgcaggaagtgggggtgaTagagtctcccctgatgtacg	16	7	1	3	rs28383787		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:21409564T>C	ENST00000380205.1	+	1	419	c.389T>C	c.(388-390)aTa>aCa	p.I130T		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	130					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		GTGGGGGTGATAGAGTCTCCC	0.478																																					p.I130T		Atlas-SNP	.											.	IFNA8	19	.	0			c.T389C						.						144	142	142					9																	21409564		2203	4300	6503	SO:0001583	missense	3445	exon1			GGGTGATAGAGTC		CCDS6507.1	9p22	2010-08-24			ENSG00000120242	ENSG00000120242		"Interferons"	5429	protein-coding gene	gene with protein product	"interferon alpha-B''", "interferon alpha type 201"	147568				1385305	Standard	NM_002170		Approved	IFN-alphaB	uc003zpc.1	P32881	OTTHUMG00000019677	ENST00000380205.1:c.389T>C	chr9.hg19:g.21409564T>C	ENSP00000369553:p.Ile130Thr	110.0	0.0		236.0	11.0	NM_002170	P01565|P09236|Q5VWV7|Q5VYQ3	Missense_Mutation	SNP	ENST00000380205.1	hg19	CCDS6507.1	.	.	.	.	.	.	.	.	.	.	T	5.842	0.339510	0.11069	.	.	ENSG00000120242	ENST00000380205	T	0.05081	3.5	3.48	-2.49	0.06403	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	2.002250	0.01939	N	0.041792	T	0.01661	0.0053	N	0.00347	-1.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38436	-0.9661	10	0.40728	T	0.16	.	1.2648	0.02009	0.3469:0.3593:0.1167:0.1771	.	130	P32881	IFNA8_HUMAN	T	130	ENSP00000369553:I130T	ENSP00000369553:I130T	I	+	2	0	IFNA8	21399564	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.378000	0.07446	-0.568000	0.06038	-2.123000	0.00347	ATA	.	.		0.478	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1	NM_002170		C	21409564	T	C	21409564	3	2	101	1	0	0	0	0	1	0	0	0	7552	1406	49	2	391	2	IFNA8	9	21409564	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2288421	21409564	119803867	313	14150										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79322715	79322715	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cactgtctatagggacgtccCcaaaatcaagacttcgggga	10	11	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:79322715C>A	ENST00000376718.3	-	8	4598	c.4475G>T	c.(4474-4476)gGg>gTg	p.G1492V	PRUNE2_ENST00000428286.1_Missense_Mutation_p.G1133V	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1492					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AGGGACGTCCCCAAAATCAAG	0.473																																					p.G1492V		Atlas-SNP	.											.	PRUNE2	331	.	0			c.G4475T						.						43	42	42					9																	79322715		1568	3582	5150	SO:0001583	missense	158471	exon8			ACGTCCCCAAAAT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.4475G>T	chr9.hg19:g.79322715C>A	ENSP00000365908:p.Gly1492Val	42.0	0.0		70.0	31.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.827|9.827	1.187396|1.187396	0.21870|0.21870	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.42900|.	0.96;0.96|.	5.49|5.49	1.47|1.47	0.22746|0.22746	.|.	2.023720|.	0.02173|.	N|.	0.059905|.	T|T	0.22589|0.22589	0.0545|0.0545	N|N	0.22421|0.22421	0.69|0.69	0.23981|0.23981	N|N	0.996276|0.996276	B|.	0.23806|.	0.091|.	B|.	0.19148|.	0.024|.	T|T	0.23261|0.23261	-1.0193|-1.0193	10|5	0.44086|.	T|.	0.13|.	8.2657|8.2657	5.2588|5.2588	0.15561|0.15561	0.153:0.6233:0.0:0.2236|0.153:0.6233:0.0:0.2236	.|.	1492|.	Q8WUY3|.	PRUN2_HUMAN|.	V|C	1492;1133;1491|813	ENSP00000365908:G1492V;ENSP00000397425:G1133V|.	ENSP00000365908:G1492V|.	G|W	-|-	2|3	0|0	PRUNE2|PRUNE2	78512535|78512535	0.622000|0.622000	0.27085|0.27085	0.009000|0.009000	0.14445|0.14445	0.004000|0.004000	0.04260|0.04260	0.607000|0.607000	0.24209|0.24209	0.344000|0.344000	0.23847|0.23847	-0.140000|-0.140000	0.14226|0.14226	GGG|TGG	.	.		0.473	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79322715	C	A	79322715	3	1	101	1	0	0	0	0	1	0	0	0	12653	623	22	3	4839	3	PRUNE2	9	79322715	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	57913151	79322715	61890716	314	14151										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79824389	79824389	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttgcagaaaaattagttacaCagatcataaaaaatcttcag	5	6	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:79824389C>T	ENST00000360280.3	+	6	696	c.436C>T	c.(436-438)Cag>Tag	p.Q146*	VPS13A_ENST00000376636.3_Nonsense_Mutation_p.Q146*|VPS13A_ENST00000376634.4_Nonsense_Mutation_p.Q146*|VPS13A_ENST00000357409.5_Nonsense_Mutation_p.Q146*	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	146					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						ATTAGTTACACAGATCATAAA	0.254																																					p.Q146X		Atlas-SNP	.											.	VPS13A	735	.	0			c.C436T						.						38	40	39					9																	79824389		2203	4290	6493	SO:0001587	stop_gained	23230	exon6			GTTACACAGATCA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.436C>T	chr9.hg19:g.79824389C>T	ENSP00000353422:p.Gln146*	99.0	0.0		282.0	23.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Nonsense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	C	38	6.912853	0.97928	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4521	0.94872	0.0:1.0:0.0:0.0	.	.	.	.	X	146	.	ENSP00000349985:Q146X	Q	+	1	0	VPS13A	79014209	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.182000	0.77689	2.703000	0.92315	0.655000	0.94253	CAG	.	.		0.254	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		T	79824389	C	T	79824389	4	4	101	1	0	0	0	0	0	1	0	0	17204	479	17	3	458	3	VPS13A	9	79824389	Nonsense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	501674	79824389	61389042	315	14152										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79867172	79867172	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgataattggagagaagcacGaaaactcagtgtatctaccc	9	8	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:79867172G>A	ENST00000360280.3	+	22	2452	c.2192G>A	c.(2191-2193)cGa>cAa	p.R731Q	VPS13A_ENST00000376636.3_Missense_Mutation_p.R731Q|VPS13A_ENST00000376634.4_Missense_Mutation_p.R731Q|VPS13A_ENST00000357409.5_Missense_Mutation_p.R731Q	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	731					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AGAGAAGCACGAAAACTCAGT	0.353																																					p.R731Q		Atlas-SNP	.											VPS13A_ENST00000376634,caecum,carcinoma,0,3	VPS13A	735	.	0			c.G2192A						.						193	183	186					9																	79867172		2203	4300	6503	SO:0001583	missense	23230	exon22			AAGCACGAAAACT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.2192G>A	chr9.hg19:g.79867172G>A	ENSP00000353422:p.Arg731Gln	77.0	0.0		121.0	7.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	G	31	5.085841	0.94100	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.55588	0.51;0.51;0.51;0.51	5.46	5.46	0.80206	.	0.148405	0.45606	D	0.000352	T	0.73305	0.3570	M	0.81802	2.56	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.95;0.997;1.0;1.0	T	0.69172	-0.5215	10	0.17369	T	0.5	.	18.9119	0.92489	0.0:0.0:1.0:0.0	.	731;731;731;731	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	Q	731	ENSP00000365821:R731Q;ENSP00000365823:R731Q;ENSP00000353422:R731Q;ENSP00000349985:R731Q	ENSP00000349985:R731Q	R	+	2	0	VPS13A	79056992	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.938000	0.87678	2.552000	0.86080	0.561000	0.74099	CGA	.	.		0.353	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		A	79867172	G	A	79867172	3	1	101	1	0	0	0	0	1	0	0	0	17204	1058	37	1	2278	1	VPS13A	9	79867172	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	42783	79867172	61346259	316	14153										
LOC645961	645961	hgsc.bcm.edu	37	chr9	90745601	90745601	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	attgggctcctaagctcctgCtctgctgggtgctgcctgtg	13	12	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:90745601C>A								U6 (132351 upstream) : U3 (243582 downstream)																							TAAGCTCCTGCTCTGCTGGGT	0.577																																					p.S784I		Atlas-SNP	.											.	.	.	.	0			c.G2351T						.						2	3	3					9																	90745601		601	1415	2016	SO:0001628	intergenic_variant	645961	exon4			CTCCTGCTCTGCT																													chr9.hg19:g.90745601C>A		57.0	0.0		163.0	54.0	NM_001166137		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.577									A	90745601	C	A	90745601	1	1	101	0	1	0	0	0	0	0	0	0	8892	797	28	3		3	LOC645961	9	90745601	IGR	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	10878429	90745601	50467830	317	14154										
COL15A1	1306	hgsc.bcm.edu	37	chr9	101749575	101749575	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgatccgtctcttttccccaGggctccctccagcagctcac	7	18	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:101749575G>A	ENST00000375001.3	+	4	1071		c.e4-1			NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1						angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CTTTTCCCCAGGGCTCCCTCC	0.567																																					.		Atlas-SNP	.											.	COL15A1	211	.	0			c.649-1G>A						.						185	169	174					9																	101749575		2203	4300	6503	SO:0001630	splice_region_variant	1306	exon4			TCCCCAGGGCTCC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.649-1G>A	chr9.hg19:g.101749575G>A		38.0	0.0		91.0	16.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Splice_Site	SNP	ENST00000375001.3	hg19	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.403198	0.83230	.	.	ENSG00000204291	ENST00000375001;ENST00000536083	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3894	0.66968	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL15A1	100789396	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.435000	0.80391	2.524000	0.85096	0.655000	0.94253	.	.	.		0.567	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	Intron	A	101749575	G	A	101749575	5	1	101	1	0	0	0	0	0	0	1	0	3674	1014	35	3	662	3	COL15A1	9	101749575	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	11003974	101749575	39463856	318	14155										
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104449365	104449365	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaagtcggtgatgttccagtCttcctggcacagcaacaagc	11	11	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:104449365C>A	ENST00000361820.3	-	2	1417	c.817G>T	c.(817-819)Gac>Tac	p.D273Y		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	273					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	ATGTTCCAGTCTTCCTGGCAC	0.448																																					p.D273Y		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G817T						.						134	122	126					9																	104449365		2203	4300	6503	SO:0001583	missense	116443	exon2			TCCAGTCTTCCTG		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.817G>T	chr9.hg19:g.104449365C>A	ENSP00000355155:p.Asp273Tyr	89.0	0.0		193.0	13.0	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.670461	0.67814	.	.	ENSG00000198785	ENST00000361820	D	0.88896	-2.44	5.82	5.82	0.92795	.	0.350421	0.31821	N	0.007002	D	0.84897	0.5574	L	0.44542	1.39	0.58432	D	0.999999	P	0.34780	0.468	B	0.32864	0.154	T	0.81693	-0.0817	10	0.11182	T	0.66	.	20.1178	0.97943	0.0:1.0:0.0:0.0	.	273	Q8TCU5	NMD3A_HUMAN	Y	273	ENSP00000355155:D273Y	ENSP00000355155:D273Y	D	-	1	0	GRIN3A	103489186	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.495000	0.66912	2.759000	0.94783	0.557000	0.71058	GAC	.	.		0.448	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			A	104449365	C	A	104449365	3	1	101	1	0	0	0	0	1	0	0	0	6792	913	32	3	2562	3	GRIN3A	9	104449365	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2699790	104449365	36764066	319	14156										
SMC2	10592	hgsc.bcm.edu	37	chr9	106894408	106894408	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaatattgcatggcaaaaggTactttttatgtttgttttat	7	3	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:106894408T>G	ENST00000286398.7	+	22	3396		c.e22+2		SMC2_ENST00000303219.8_Splice_Site|SMC2_ENST00000374793.3_Splice_Site|SMC2_ENST00000374787.3_Splice_Site	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2						kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						TGGCAAAAGGTACTTTTTATG	0.303																																					.		Atlas-SNP	.											.	SMC2	127	.	0			c.3108+2T>G						.						67	72	70					9																	106894408		2203	4294	6497	SO:0001630	splice_region_variant	10592	exon22			AAAAGGTACTTTT	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.3108+2T>G	chr9.hg19:g.106894408T>G		144.0	0.0		435.0	47.0	NM_001042551	Q6IEE0|Q9P1P2	Splice_Site	SNP	ENST00000286398.7	hg19	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.106937	0.77096	.	.	ENSG00000136824	ENST00000286398;ENST00000374793;ENST00000303219;ENST00000374787	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1896	0.65630	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMC2	105934229	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	7.971000	0.88012	2.222000	0.72286	0.533000	0.62120	.	.	.		0.303	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1		Intron	G	106894408	T	G	106894408	5	3	101	1	0	0	0	0	0	0	1	0	14798	1652	57	5	3192	5	SMC2	9	106894408	Splice_Site	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2445043	106894408	34319023	320	14157										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114202776	114202776	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agggtatttcatgtgaaaaaGggttggtattaaaagatgca	12	2	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:114202776G>T	ENST00000338205.5	-	5	634	c.415C>A	c.(415-417)Ctt>Att	p.L139I	KIAA0368_ENST00000259335.4_Missense_Mutation_p.L317I			Q5VYK3	ECM29_HUMAN	KIAA0368	145					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						ATGTGAAAAAGGGTTGGTATT	0.323																																					p.L317I		Atlas-SNP	.											.	KIAA0368	144	.	0			c.C949A						.						65	63	64					9																	114202776		1822	4078	5900	SO:0001583	missense	23392	exon7			GAAAAAGGGTTGG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.415C>A	chr9.hg19:g.114202776G>T	ENSP00000339889:p.Leu139Ile	39.0	0.0		86.0	29.0	NM_001080398	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	hg19		.	.	.	.	.	.	.	.	.	.	G	27.2	4.810502	0.90707	.	.	ENSG00000136813	ENST00000338205;ENST00000259335	T	0.46451	0.87	6.02	6.02	0.97574	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58666	0.2138	L	0.41027	1.25	0.80722	D	1	D	0.57257	0.979	D	0.74023	0.982	T	0.50575	-0.8812	10	0.40728	T	0.16	.	20.5373	0.99239	0.0:0.0:1.0:0.0	.	145	Q5VYK3	ECM29_HUMAN	I	139;317	ENSP00000259335:L317I	ENSP00000259335:L317I	L	-	1	0	KIAA0368	113242597	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.269000	0.78482	2.857000	0.98124	0.650000	0.86243	CTT	.	.		0.323	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		T	114202776	G	T	114202776	3	4	101	1	0	0	0	0	1	0	0	0	8180	1000	35	3	5284	3	KIAA0368	9	114202776	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	7308368	114202776	27010655	321	14158										
ALAD	210	hgsc.bcm.edu	37	chr9	116151330	116151330	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gccccggcctgggctccatgCcacagcatggcaaactctcc	10	18	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:116151330C>G	ENST00000409155.3	-	11	1054	c.858G>C	c.(856-858)tgG>tgC	p.W286C	ALAD_ENST00000482001.1_5'Flank|ALAD_ENST00000277315.5_Missense_Mutation_p.W269C	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	286					cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1)	9					Aminolevulinic acid(DB00855)	GGGCTCCATGCCACAGCATGG	0.612																																					p.W286C		Atlas-SNP	.											.	ALAD	36	.	0			c.G858C						.						41	38	39					9																	116151330		2203	4300	6503	SO:0001583	missense	210	exon11			TCCATGCCACAGC	M13928	CCDS6794.2	9q32	2010-04-29	2010-04-29		ENSG00000148218	ENSG00000148218	4.2.1.24		395	protein-coding gene	gene with protein product	"porphobilinogen synthase"	125270	"aminolevulinate, delta-, dehydratase"			6839527, 6378062	Standard	NM_000031		Approved	ALADH, PBGS	uc011lxf.2	P13716	OTTHUMG00000020522	ENST00000409155.3:c.858G>C	chr9.hg19:g.116151330C>G	ENSP00000386284:p.Trp286Cys	47.0	0.0		121.0	11.0	NM_000031	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Missense_Mutation	SNP	ENST00000409155.3	hg19	CCDS6794.2	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815140	0.50527	.	.	ENSG00000148218	ENST00000409155;ENST00000277315	D;D	0.86694	-2.16;-2.16	5.7	5.7	0.88788	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.85071	0.5613	L	0.48935	1.535	0.80722	D	1	B;B;B	0.18610	0.007;0.013;0.029	B;B;B	0.17722	0.007;0.014;0.019	T	0.81013	-0.1125	10	0.66056	D	0.02	-8.9224	18.4109	0.90550	0.0:1.0:0.0:0.0	.	286;269;315	P13716;B7Z3I9;P13716-2	HEM2_HUMAN;.;.	C	286;269	ENSP00000386284:W286C;ENSP00000277315:W269C	ENSP00000277315:W269C	W	-	3	0	ALAD	115191151	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.216000	0.77974	2.688000	0.91661	0.655000	0.94253	TGG	.	.		0.612	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945		G	116151330	C	G	116151330	3	3	101	1	0	0	0	0	1	0	0	0	483	740	26	4	142	4	ALAD	9	116151330	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1948554	116151330	25062101	322	14159										
ZBTB6	10773	hgsc.bcm.edu	37	chr9	125674263	125674263	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttgatacatcacaaaataaaTtctgctgtctcaaaagattc	4	8	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:125674263T>C	ENST00000373659.3	-	2	177	c.89A>G	c.(88-90)aAt>aGt	p.N30S		NM_006626.5	NP_006617.1	Q15916	ZBTB6_HUMAN	zinc finger and BTB domain containing 6	30					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	11						ACAAAATAAATTCTGCTGTCT	0.388																																					p.N30S		Atlas-SNP	.											.	ZBTB6	32	.	0			c.A89G						.						104	113	110					9																	125674263		2203	4300	6503	SO:0001583	missense	10773	exon2			AATAAATTCTGCT	X82018	CCDS6846.1	9q33.1-q33.3	2013-01-08	2006-04-10	2006-04-10	ENSG00000186130	ENSG00000186130		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16764	protein-coding gene	gene with protein product		605976	"zinc finger protein 482"	ZNF482		7958847	Standard	NM_006626		Approved	ZID	uc004bnh.4	Q15916	OTTHUMG00000020628	ENST00000373659.3:c.89A>G	chr9.hg19:g.125674263T>C	ENSP00000362763:p.Asn30Ser	96.0	0.0		241.0	33.0	NM_006626	A8K8N6	Missense_Mutation	SNP	ENST00000373659.3	hg19	CCDS6846.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.186360	0.57909	.	.	ENSG00000186130	ENST00000373659	T	0.70399	-0.48	6.17	6.17	0.99709	BTB/POZ (1);BTB/POZ fold (2);	0.141133	0.64402	D	0.000006	T	0.75554	0.3865	L	0.33710	1.025	0.36865	D	0.888606	D	0.53151	0.958	P	0.60012	0.867	T	0.80625	-0.1299	10	0.62326	D	0.03	.	16.0034	0.80327	0.0:0.0:0.0:1.0	.	30	Q15916	ZBTB6_HUMAN	S	30	ENSP00000362763:N30S	ENSP00000362763:N30S	N	-	2	0	ZBTB6	124714084	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.824000	0.55723	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.388	ZBTB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053962.1	NM_006626		C	125674263	T	C	125674263	3	2	101	1	0	0	0	0	1	0	0	0	17567	1493	52	2	1189	2	ZBTB6	9	125674263	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	9522933	125674263	15539168	323	14160										
OLFML2A	169611	hgsc.bcm.edu	37	chr9	127561615	127561615	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggtggtgaaggacagcgtgCgccacctcagtgagcagttg	16	9	1	2	rs533587628	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:127561615C>A	ENST00000373580.3	+	4	514	c.514C>A	c.(514-516)Cgc>Agc	p.R172S	OLFML2A_ENST00000288815.5_5'Flank	NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	172					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						GGACAGCGTGCGCCACCTCAG	0.597																																					p.R172S		Atlas-SNP	.											.	OLFML2A	61	.	0			c.C514A						.						45	51	49					9																	127561615		2157	4275	6432	SO:0001583	missense	169611	exon4			AGCGTGCGCCACC	AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.514C>A	chr9.hg19:g.127561615C>A	ENSP00000362682:p.Arg172Ser	54.0	0.0		132.0	57.0	NM_182487	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Missense_Mutation	SNP	ENST00000373580.3	hg19	CCDS6857.2	.	.	.	.	.	.	.	.	.	.	C	12.18	1.861208	0.32884	.	.	ENSG00000185585	ENST00000331715;ENST00000425732;ENST00000373580	T;T	0.44083	0.93;0.93	5.67	3.76	0.43208	.	0.489979	0.22803	N	0.055449	T	0.31009	0.0783	L	0.44542	1.39	0.80722	D	1	P;B	0.36392	0.551;0.395	B;B	0.34489	0.184;0.062	T	0.03202	-1.1061	10	0.19147	T	0.46	.	10.8651	0.46851	0.1204:0.661:0.2186:0.0	.	136;172	Q5JTM7;Q68BL7	.;OLM2A_HUMAN	S	136;136;172	ENSP00000336425:R136S;ENSP00000362682:R172S	ENSP00000336425:R136S	R	+	1	0	OLFML2A	126601436	0.683000	0.27633	1.000000	0.80357	0.691000	0.40173	1.032000	0.30178	2.681000	0.91329	0.655000	0.94253	CGC	.	.		0.597	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487		A	127561615	C	A	127561615	3	1	101	1	0	0	0	0	1	0	0	0	10866	768	27	1	528	1	OLFML2A	9	127561615	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1887352	127561615	13651816	324	14161										
CDK9	1025	hgsc.bcm.edu	37	chr9	130550943	130550943	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcaccaactcgccctcatcaGtcagctctgcggctccatca	7	18	5	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:130550943G>T	ENST00000373264.4	+	6	825	c.725G>T	c.(724-726)aGt>aTt	p.S242I	CDK9_ENST00000373265.2_Missense_Mutation_p.S359I|MIR3960_ENST00000583311.1_RNA	NM_001261.3	NP_001252.1	P50750	CDK9_HUMAN	cyclin-dependent kinase 9	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|DNA repair (GO:0006281)|gene expression (GO:0010467)|negative regulation of cell cycle arrest (GO:0071157)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of DNA repair (GO:0006282)|regulation of histone modification (GO:0031056)|replication fork arrest (GO:0043111)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|positive transcription elongation factor complex b (GO:0008024)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|DNA binding (GO:0003677)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			lung(1)	1						GCCCTCATCAGTCAGCTCTGC	0.652																																					p.S242I		Atlas-SNP	.											.	CDK9	22	.	0			c.G725T						.						60	54	56					9																	130550943		2203	4300	6503	SO:0001583	missense	1025	exon6			TCATCAGTCAGCT	L25676	CCDS6879.1	9q34.1	2011-11-08	2007-11-21		ENSG00000136807	ENSG00000136807		"Cyclin-dependent kinases"	1780	protein-coding gene	gene with protein product		603251	"cyclin-dependent kinase 9 (CDC2-related kinase)"	CDC2L4		8170997, 9356449	Standard	NM_001261		Approved	PITALRE, C-2k, TAK	uc004bse.2	P50750	OTTHUMG00000020715	ENST00000373264.4:c.725G>T	chr9.hg19:g.130550943G>T	ENSP00000362361:p.Ser242Ile	95.0	0.0		404.0	96.0	NM_001261	Q5JU24|Q5JU25|Q5U006|Q96TF1	Missense_Mutation	SNP	ENST00000373264.4	hg19	CCDS6879.1	.	.	.	.	.	.	.	.	.	.	G	19.71	3.877895	0.72294	.	.	ENSG00000136807	ENST00000373265;ENST00000373264	T;T	0.40225	1.04;1.04	5.13	5.13	0.70059	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.40423	0.1116	N	0.04508	-0.205	0.80722	D	1	D	0.56521	0.976	D	0.65323	0.934	T	0.44711	-0.9310	10	0.22109	T	0.4	-13.7553	17.5564	0.87890	0.0:0.0:1.0:0.0	.	242	P50750	CDK9_HUMAN	I	359;242	ENSP00000362362:S359I;ENSP00000362361:S242I	ENSP00000362361:S242I	S	+	2	0	CDK9	129590764	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.571000	0.98176	2.385000	0.81259	0.491000	0.48974	AGT	.	.		0.652	CDK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054235.1			T	130550943	G	T	130550943	3	4	101	1	0	0	0	0	1	0	0	0	3153	1029	36	3	747	3	CDK9	9	130550943	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2989328	130550943	10662488	325	14162										
ODF2	4957	hgsc.bcm.edu	37	chr9	131256871	131256871	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cacggaggcgaagctggctgAgtgccaagaccaactgcagg	15	11	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:131256871A>C	ENST00000434106.3	+	17	2198	c.1835A>C	c.(1834-1836)gAg>gCg	p.E612A	ODF2_ENST00000444119.2_Missense_Mutation_p.E588A|ODF2_ENST00000448249.3_Missense_Mutation_p.E531A|ODF2_ENST00000393533.2_Missense_Mutation_p.E612A|ODF2_ENST00000393527.3_Missense_Mutation_p.E588A|ODF2_ENST00000546203.1_Missense_Mutation_p.E593A|ODF2_ENST00000372791.3_Missense_Mutation_p.E593A|ODF2_ENST00000372807.5_Missense_Mutation_p.E607A|ODF2_ENST00000372814.3_Missense_Mutation_p.E656A|ODF2_ENST00000604420.1_Missense_Mutation_p.E612A|ODF2_ENST00000351030.3_Missense_Mutation_p.E607A	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	612					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)	p.E588G(1)|p.E656G(1)|p.E612G(1)		autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						AAGCTGGCTGAGTGCCAAGAC	0.577																																					p.E676A		Atlas-SNP	.											ODF2_ENST00000372814,NS,carcinoma,0,2	ODF2	227	.	3	Substitution - Missense(3)	kidney(3)	c.A2027C						.						75	65	68					9																	131256871		2203	4300	6503	SO:0001583	missense	4957	exon17			TGGCTGAGTGCCA	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"cancer/testis antigen 134"	602015	"outer dense fibre of sperm tails 2"			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1835A>C	chr9.hg19:g.131256871A>C	ENSP00000403453:p.Glu612Ala	58.0	0.0		153.0	26.0	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	hg19	CCDS56588.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107982	0.77096	.	.	ENSG00000136811	ENST00000393533;ENST00000372814;ENST00000351030;ENST00000372796;ENST00000303890;ENST00000448249;ENST00000546203;ENST00000372791	T;D;D;D;D;D;T;T	0.86956	1.05;-2.19;-1.97;-1.97;-1.97;-2.19;1.09;1.1	5.4	5.4	0.78164	.	0.048281	0.85682	D	0.000000	D	0.91680	0.7370	M	0.73217	2.22	0.80722	D	1	D;D;P;D;D;D;D	0.76494	0.972;0.998;0.873;0.978;0.972;0.999;0.999	P;D;B;P;P;D;D	0.68192	0.673;0.921;0.356;0.814;0.673;0.956;0.921	D	0.91885	0.5519	10	0.56958	D	0.05	-27.7591	11.069	0.47993	0.8614:0.0:0.0:0.1386	.	593;607;531;612;593;612;588	Q5BJF6-8;Q5BJF6-4;Q5BJF6-9;B4DX73;Q5BJF6-5;Q5BJF6;Q5BJF6-3	.;.;.;.;.;ODFP2_HUMAN;.	A	612;656;607;612;588;531;593;593	ENSP00000377166:E612A;ENSP00000361901:E656A;ENSP00000342581:E607A;ENSP00000361882:E612A;ENSP00000307781:E588A;ENSP00000396687:E531A;ENSP00000437579:E593A;ENSP00000361877:E593A	ENSP00000307781:E588A	E	+	2	0	ODF2	130296692	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	4.478000	0.60230	2.047000	0.60756	0.459000	0.35465	GAG	.	.		0.577	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			C	131256871	A	C	131256871	3	2	101	1	0	0	0	0	1	0	0	0	10836	304	11	5	1952	5	ODF2	9	131256871	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	705928	131256871	9956560	326	14163										
PPP2R4	5524	hgsc.bcm.edu	37	chr9	131909700	131909700	+	Missense_Mutation	SNP	A	A	G													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccctgtgatccagcacttcaAgttcgggagcctgctgccca							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:131909700A>G	ENST00000337738.1	+	11	1301	c.1034A>G	c.(1033-1035)aAg>aGg	p.K345R	PPP2R4_ENST00000419582.1_Missense_Mutation_p.K48R|PPP2R4_ENST00000423100.1_Missense_Mutation_p.K48R|PPP2R4_ENST00000357197.4_Missense_Mutation_p.K281R|PPP2R4_ENST00000414510.1_Missense_Mutation_p.K48R|PPP2R4_ENST00000393370.2_Missense_Mutation_p.K310R|PPP2R4_ENST00000434095.1_Missense_Mutation_p.K48R|PPP2R4_ENST00000347048.4_Missense_Mutation_p.K91R|PPP2R4_ENST00000358994.4_Missense_Mutation_p.K310R|PPP2R4_ENST00000355007.3_Missense_Mutation_p.K268R|PPP2R4_ENST00000432651.1_Missense_Mutation_p.K48R|PPP2R4_ENST00000348141.5_Missense_Mutation_p.K316R|PPP2R4_ENST00000435132.1_Missense_Mutation_p.K48R	NM_178001.2	NP_821068.1	Q15257	PTPA_HUMAN	protein phosphatase 2A activator, regulatory subunit 4	345					ATP catabolic process (GO:0006200)|mitotic spindle organization in nucleus (GO:0030472)|negative regulation of phosphoprotein phosphatase activity (GO:0032515)|negative regulation of protein dephosphorylation (GO:0035308)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein dephosphorylation (GO:0035307)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of phosphoprotein phosphatase activity (GO:0043666)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	ATP binding (GO:0005524)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein tyrosine phosphatase activator activity (GO:0008160)|receptor binding (GO:0005102)			breast(3)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12		Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		CAGCACTTCAAGTTCGGGAGC	0.632																																					p.K345R	Colon(158;2158 2504 4450 20433)	Atlas-SNP	.											.	PPP2R4	32	.	0			c.A1034G						.						90	71	78					9																	131909700		2203	4300	6503	SO:0001583	missense	5524	exon11			ACTTCAAGTTCGG	X73478	CCDS6920.1, CCDS65156.1, CCDS75917.1	9q34	2010-06-18	2007-01-22		ENSG00000119383	ENSG00000119383		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9308	protein-coding gene	gene with protein product	"phosphotyrosyl phosphatase activator", "PP2A phosphatase activator"	600756	"protein phosphatase 2A, regulatory subunit B' (PR 53)"			8530035	Standard	NM_021131		Approved	PTPA, PR53	uc004bxm.2	Q15257	OTTHUMG00000020774	ENST00000337738.1:c.1034A>G	chr9.hg19:g.131909700A>G	ENSP00000337448:p.Lys345Arg	26.0	0.0		76.0	24.0	NM_178001	A2A347|A9IZU4|B4DXM4|Q15258|Q53GZ3|Q5TZQ2|Q9BUK1|Q9NNZ7|Q9NNZ8|Q9NNZ9	Missense_Mutation	SNP	ENST00000337738.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.87	2.365001	0.41902	.	.	ENSG00000119383	ENST00000358994;ENST00000393370;ENST00000337738;ENST00000348141;ENST00000347048;ENST00000357197;ENST00000355007;ENST00000423100;ENST00000414510;ENST00000419582;ENST00000432651;ENST00000435132;ENST00000434095	T;T;T;T;T;T;T;T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61	5.16	4.02	0.46733	.	0.045098	0.85682	D	0.000000	T	0.19765	0.0475	N	0.17248	0.465	0.80722	D	1	B;B;B;B;B	0.15473	0.0;0.013;0.001;0.001;0.001	B;B;B;B;B	0.28465	0.005;0.09;0.004;0.012;0.002	T	0.05305	-1.0893	10	0.25106	T	0.35	.	9.9436	0.41596	0.9199:0.0:0.0801:0.0	.	281;91;268;345;310	Q15257-3;Q68CR8;Q15257-4;Q15257;Q15257-2	.;.;.;PTPA_HUMAN;.	R	310;310;345;316;91;281;268;48;48;48;48;48;48	ENSP00000351885:K310R;ENSP00000377036:K310R;ENSP00000337448:K345R;ENSP00000335200:K316R;ENSP00000337412:K91R;ENSP00000349726:K281R;ENSP00000347109:K268R;ENSP00000408316:K48R;ENSP00000408726:K48R;ENSP00000394001:K48R;ENSP00000416661:K48R;ENSP00000387726:K48R;ENSP00000411604:K48R	ENSP00000337448:K345R	K	+	2	0	PPP2R4	130949521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.960000	0.76036	0.812000	0.34326	0.459000	0.35465	AAG	.	.		0.632	PPP2R4-201	KNOWN	basic	protein_coding	protein_coding		NM_021131		G	131909700	A	G	131909700	3	3	101	1	0	0	0	0	1	0	0	0	12403	72	3	2	1076	2	PPP2R4	9	131909700	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	652829	131909700	9303731	327	14164	63	2								
PPP2R4	5524	hgsc.bcm.edu	37	chr9	131909703	131909703	+	Missense_Mutation	SNP	T	T	C													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtgatccagcacttcaagtTcgggagcctgctgcccatcc							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:131909703T>C	ENST00000337738.1	+	11	1304	c.1037T>C	c.(1036-1038)tTc>tCc	p.F346S	PPP2R4_ENST00000419582.1_Missense_Mutation_p.F49S|PPP2R4_ENST00000423100.1_Missense_Mutation_p.F49S|PPP2R4_ENST00000357197.4_Missense_Mutation_p.F282S|PPP2R4_ENST00000414510.1_Missense_Mutation_p.F49S|PPP2R4_ENST00000393370.2_Missense_Mutation_p.F311S|PPP2R4_ENST00000434095.1_Missense_Mutation_p.F49S|PPP2R4_ENST00000347048.4_Missense_Mutation_p.F92S|PPP2R4_ENST00000358994.4_Missense_Mutation_p.F311S|PPP2R4_ENST00000355007.3_Missense_Mutation_p.F269S|PPP2R4_ENST00000432651.1_Missense_Mutation_p.F49S|PPP2R4_ENST00000348141.5_Missense_Mutation_p.F317S|PPP2R4_ENST00000435132.1_Missense_Mutation_p.F49S	NM_178001.2	NP_821068.1	Q15257	PTPA_HUMAN	protein phosphatase 2A activator, regulatory subunit 4	346					ATP catabolic process (GO:0006200)|mitotic spindle organization in nucleus (GO:0030472)|negative regulation of phosphoprotein phosphatase activity (GO:0032515)|negative regulation of protein dephosphorylation (GO:0035308)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein dephosphorylation (GO:0035307)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of phosphoprotein phosphatase activity (GO:0043666)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	ATP binding (GO:0005524)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein tyrosine phosphatase activator activity (GO:0008160)|receptor binding (GO:0005102)			breast(3)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12		Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		CACTTCAAGTTCGGGAGCCTG	0.637																																					p.F346S	Colon(158;2158 2504 4450 20433)	Atlas-SNP	.											.	PPP2R4	32	.	0			c.T1037C						.						89	70	76					9																	131909703		2203	4300	6503	SO:0001583	missense	5524	exon11			TCAAGTTCGGGAG	X73478	CCDS6920.1, CCDS65156.1, CCDS75917.1	9q34	2010-06-18	2007-01-22		ENSG00000119383	ENSG00000119383		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9308	protein-coding gene	gene with protein product	"phosphotyrosyl phosphatase activator", "PP2A phosphatase activator"	600756	"protein phosphatase 2A, regulatory subunit B' (PR 53)"			8530035	Standard	NM_021131		Approved	PTPA, PR53	uc004bxm.2	Q15257	OTTHUMG00000020774	ENST00000337738.1:c.1037T>C	chr9.hg19:g.131909703T>C	ENSP00000337448:p.Phe346Ser	25.0	0.0		74.0	25.0	NM_178001	A2A347|A9IZU4|B4DXM4|Q15258|Q53GZ3|Q5TZQ2|Q9BUK1|Q9NNZ7|Q9NNZ8|Q9NNZ9	Missense_Mutation	SNP	ENST00000337738.1	hg19		.	.	.	.	.	.	.	.	.	.	T	33	5.231764	0.95207	.	.	ENSG00000119383	ENST00000358994;ENST00000393370;ENST00000337738;ENST00000348141;ENST00000347048;ENST00000357197;ENST00000355007;ENST00000423100;ENST00000414510;ENST00000419582;ENST00000432651;ENST00000435132;ENST00000434095	T;T;T;T;T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;1.04;0.73;0.73;1.04;1.04;1.04;1.04;1.04;1.04	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.78566	0.4303	H	0.96861	3.895	0.80722	D	1	P;D;P;D;D	0.89917	0.892;0.999;0.938;0.997;1.0	P;D;P;D;D	0.81914	0.883;0.986;0.851;0.992;0.995	D	0.86023	0.1508	10	0.87932	D	0	.	14.1769	0.65546	0.0:0.0:0.0:1.0	.	282;92;269;346;311	Q15257-3;Q68CR8;Q15257-4;Q15257;Q15257-2	.;.;.;PTPA_HUMAN;.	S	311;311;346;317;92;282;269;49;49;49;49;49;49	ENSP00000351885:F311S;ENSP00000377036:F311S;ENSP00000337448:F346S;ENSP00000335200:F317S;ENSP00000337412:F92S;ENSP00000349726:F282S;ENSP00000347109:F269S;ENSP00000408316:F49S;ENSP00000408726:F49S;ENSP00000394001:F49S;ENSP00000416661:F49S;ENSP00000387726:F49S;ENSP00000411604:F49S	ENSP00000337448:F346S	F	+	2	0	PPP2R4	130949524	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.539000	0.82063	1.944000	0.56390	0.459000	0.35465	TTC	.	.		0.637	PPP2R4-201	KNOWN	basic	protein_coding	protein_coding		NM_021131		C	131909703	T	C	131909703	3	2	101	1	0	0	0	0	1	0	0	0	12403	1783	62	2	1079	2	PPP2R4	9	131909703	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	3	131909703	9303728	328	14165	63	2								
C9orf96	169436	hgsc.bcm.edu	37	chr9	136269044	136269044	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agcccggcccctttctgcagGctgcatcaaggagcagcagt	12	14	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:136269044G>T	ENST00000371957.3	+	16	1711	c.1604G>T	c.(1603-1605)gGc>gTc	p.G535V	C9orf96_ENST00000371955.1_Splice_Site_p.G68V	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		535							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CTTTCTGCAGGCTGCATCAAG	0.667																																					p.G535V		Atlas-SNP	.											.	C9orf96	77	.	0			c.G1604T						.						39	43	42					9																	136269044		2203	4300	6503	SO:0001630	splice_region_variant	169436	exon16			CTGCAGGCTGCAT																												ENST00000371957.3:c.1604-1G>T	chr9.hg19:g.136269044G>T		22.0	0.0		93.0	12.0	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	hg19	CCDS35169.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.021670	0.54576	.	.	ENSG00000198870	ENST00000371957;ENST00000371955	T;T	0.51071	0.72;0.76	5.13	4.23	0.50019	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.63780	0.2540	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.63256	-0.6678	9	.	.	.	.	12.6603	0.56809	0.0803:0.0:0.9197:0.0	.	535	Q8NE28	SGK71_HUMAN	V	535;68	ENSP00000361025:G535V;ENSP00000361023:G68V	.	G	+	2	0	C9orf96	135258865	1.000000	0.71417	1.000000	0.80357	0.301000	0.27625	5.846000	0.69444	1.134000	0.42165	0.561000	0.74099	GGC	.	.		0.667	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		Missense_Mutation	T	136269044	G	T	136269044	5	4	101	1	0	0	0	0	0	0	1	0	2510	1217	42	3	1666	3	C9orf96	9	136269044	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	4359341	136269044	4944387	329	14166										
RXRA	6256	hgsc.bcm.edu	37	chr9	137328351	137328351	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccgcctgccggctctgcgctCcatcgggctcaaatgcctgg	12	17	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:137328351C>T	ENST00000481739.1	+	10	1332	c.1280C>T	c.(1279-1281)tCc>tTc	p.S427F	RXRA_ENST00000540193.1_Missense_Mutation_p.S330F|RXRA_ENST00000356384.4_3'UTR	NM_002957.4	NP_002948.1	P19793	RXRA_HUMAN	retinoid X receptor, alpha	427	Ligand-binding.				camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	GCTCTGCGCTCCATCGGGCTC	0.607																																					p.S427F		Atlas-SNP	.											RXRA,bladder,carcinoma,0,5	RXRA	52	.	0			c.C1280T						.						132	117	122					9																	137328351		2203	4300	6503	SO:0001583	missense	6256	exon10			TGCGCTCCATCGG	X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350		"Nuclear hormone receptors"	10477	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 1"	180245				2159111	Standard	XM_005263409		Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000481739.1:c.1280C>T	chr9.hg19:g.137328351C>T	ENSP00000419692:p.Ser427Phe	46.0	0.0		134.0	9.0	NM_002957	B3KY83|Q2NL52|Q2V504	Missense_Mutation	SNP	ENST00000481739.1	hg19	CCDS35172.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.825420	0.90955	.	.	ENSG00000186350	ENST00000481739;ENST00000540193	D;D	0.96940	-4.18;-4.18	4.76	4.76	0.60689	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.98369	0.9458	M	0.88241	2.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99744	1.1016	10	0.87932	D	0	.	17.7817	0.88526	0.0:1.0:0.0:0.0	.	427	P19793	RXRA_HUMAN	F	427;330	ENSP00000419692:S427F;ENSP00000442123:S330F	ENSP00000419692:S427F	S	+	2	0	RXRA	136468172	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.532000	0.81985	2.193000	0.70182	0.591000	0.81541	TCC	.	.		0.607	RXRA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054949.1	NM_002957		T	137328351	C	T	137328351	3	4	101	1	0	0	0	0	1	0	0	0	13778	855	30	3	1318	3	RXRA	9	137328351	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1059307	137328351	3885080	330	14167										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140880982	140880982	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttcgccctgctggggatgcaGctgtttgggggacagtaagt	16	8	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr9:140880982G>T	ENST00000371372.1	+	14	2032	c.1887G>T	c.(1885-1887)caG>caT	p.Q629H	CACNA1B_ENST00000277551.2_Missense_Mutation_p.Q629H|CACNA1B_ENST00000371355.4_Missense_Mutation_p.Q630H|CACNA1B_ENST00000371357.1_Missense_Mutation_p.Q630H|CACNA1B_ENST00000371363.1_Missense_Mutation_p.Q629H|CACNA1B_ENST00000277549.5_5'UTR	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	629					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGGGATGCAGCTGTTTGGGG	0.612																																					p.Q629H		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G1887T						.						47	49	49					9																	140880982		2080	4229	6309	SO:0001583	missense	774	exon14			GATGCAGCTGTTT	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1887G>T	chr9.hg19:g.140880982G>T	ENSP00000360423:p.Gln629His	99.0	0.0		187.0	22.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.221756	0.58560	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.98996	-5.31;-5.31;-5.31;-5.31;-5.31	4.35	3.44	0.39384	.	0.000000	0.85682	D	0.000000	D	0.99205	0.9724	M	0.85710	2.77	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	D	0.99486	1.0949	10	0.87932	D	0	.	12.7997	0.57578	0.0816:0.0:0.9184:0.0	.	629;629	B1AQK4;B1AQK6	.;.	H	629;629;629;630;630	ENSP00000360423:Q629H;ENSP00000277551:Q629H;ENSP00000360414:Q629H;ENSP00000360408:Q630H;ENSP00000360406:Q630H	ENSP00000277551:Q629H	Q	+	3	2	CACNA1B	140000803	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.487000	0.60293	0.913000	0.36797	0.462000	0.41574	CAG	.	.		0.612	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		T	140880982	G	T	140880982	3	4	101	1	0	0	0	0	1	0	0	0	2541	962	34	3	1941	3	CACNA1B	9	140880982	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3552631	140880982	332449	331	14168										
DIP2C	22982	hgsc.bcm.edu	37	chr10	390969	390969	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gatgaggggccacgtcctgaCgtccacagccgccgccgcct	13	17	0	2	rs200340134		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:390969C>A	ENST00000280886.6	-	27	3400	c.3313G>T	c.(3313-3315)Gtc>Ttc	p.V1105F		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1105						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CACGTCCTGACGTCCACAGCC	0.592																																					p.V1105F		Atlas-SNP	.											.	DIP2C	195	.	0			c.G3313T						.						72	59	63					10																	390969		2203	4300	6503	SO:0001583	missense	22982	exon27			TCCTGACGTCCAC	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3313G>T	chr10.hg19:g.390969C>A	ENSP00000280886:p.Val1105Phe	22.0	0.0		68.0	4.0	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	C	8.495	0.862866	0.17178	.	.	ENSG00000151240	ENST00000280886;ENST00000535541	T	0.10668	2.85	5.59	4.69	0.59074	AMP-dependent synthetase/ligase (1);	0.188095	0.46145	D	0.000316	T	0.08670	0.0215	N	0.25380	0.74	0.80722	D	1	B	0.13594	0.008	B	0.28305	0.088	T	0.25572	-1.0128	10	0.23891	T	0.37	-31.7464	9.4456	0.38695	0.0:0.7807:0.0:0.2193	.	1105	Q9Y2E4	DIP2C_HUMAN	F	1105;30	ENSP00000280886:V1105F	ENSP00000280886:V1105F	V	-	1	0	DIP2C	380969	0.006000	0.16342	0.885000	0.34714	0.399000	0.30720	0.029000	0.13666	1.368000	0.46115	0.655000	0.94253	GTC	.	C|1.000;T|0.000		0.592	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		A	390969	C	A	390969	3	1	101	1	0	0	0	0	1	0	0	0	4531	536	19	1	1401	1	DIP2C	10	390969	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10		390969	135143778	332	14169										
PITRM1	10531	hgsc.bcm.edu	37	chr10	3201169	3201169	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggctttgtaaaagggagaaTtgggcccagaagtcaagagt	14	5	1	3	rs373184654		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:3201169T>C	ENST00000224949.4	-	10	1107	c.1073A>G	c.(1072-1074)aAt>aGt	p.N358S	PITRM1_ENST00000380994.1_5'Flank|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000451104.2_Missense_Mutation_p.N326S|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.N358S			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	358					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						AAAGGGAGAATTGGGCCCAGA	0.413																																					p.N358S		Atlas-SNP	.											.	PITRM1	109	.	0			c.A1073G						.	T	SER/ASN,SER/ASN,SER/ASN	0,3788		0,0,1894	87	82	84		1073,977,1073	4.7	1	10		84	1,8225		0,1,4112	no	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	46,46,46	0,1,6006	CC,CT,TT		0.0122,0.0,0.0083	possibly-damaging,possibly-damaging,possibly-damaging	358/1039,326/940,358/1038	3201169	1,12013	1894	4113	6007	SO:0001583	missense	10531	exon10			GGAGAATTGGGCC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1073A>G	chr10.hg19:g.3201169T>C	ENSP00000224949:p.Asn358Ser	107.0	0.0		230.0	73.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	hg19	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	t	18.72	3.684170	0.68157	0.0	1.22E-4	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.07216	3.21;3.21;3.21	5.81	4.67	0.58626	Peptidase M16, C-terminal (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.07954	0.0199	N	0.20807	0.61	0.53005	D	0.999962	B;B;P;P;P;P	0.40834	0.121;0.226;0.73;0.654;0.654;0.654	B;B;B;B;B;B	0.43783	0.019;0.326;0.305;0.431;0.431;0.431	T	0.39035	-0.9633	10	0.35671	T	0.21	-35.4887	11.8314	0.52297	0.0:0.0685:0.0:0.9315	.	351;326;358;358;358;351	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3;B4DH07	.;.;.;.;PREP_HUMAN;.	S	358;351;358;326	ENSP00000224949:N358S;ENSP00000370377:N358S;ENSP00000401201:N326S	ENSP00000224949:N358S	N	-	2	0	PITRM1	3191169	1.000000	0.71417	0.989000	0.46669	0.745000	0.42441	4.492000	0.60334	1.021000	0.39600	0.528000	0.53228	AAT	.	.		0.413	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			C	3201169	T	C	3201169	3	2	101	1	0	0	0	0	1	0	0	0	11962	1493	52	2	2112	2	PITRM1	10	3201169	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2810200	3201169	132333578	333	14170										
MCM10	55388	hgsc.bcm.edu	37	chr10	13239672	13239672	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggccaggttcttacaaaaaCaaacccaaacagcattaaga	6	10	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:13239672C>T	ENST00000484800.2	+	15	2130	c.2027C>T	c.(2026-2028)aCa>aTa	p.T676I	MCM10_ENST00000378694.1_Missense_Mutation_p.T675I|MCM10_ENST00000378714.3_Missense_Mutation_p.T675I			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	676					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						CTTACAAAAACAAACCCAAAC	0.408																																					p.T676I		Atlas-SNP	.											.	MCM10	76	.	0			c.C2027T						.						95	88	90					10																	13239672		2203	4300	6503	SO:0001583	missense	55388	exon15			CAAAAACAAACCC	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.2027C>T	chr10.hg19:g.13239672C>T	ENSP00000418268:p.Thr676Ile	81.0	0.0		151.0	16.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	hg19	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	C	8.838	0.941562	0.18281	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.29655	1.56;1.56;1.56	5.23	2.32	0.28847	Replication factor Mcm10 (1);	0.398558	0.30859	N	0.008728	T	0.19167	0.0460	L	0.34521	1.04	0.26907	N	0.966989	B;B;B	0.12630	0.006;0.004;0.005	B;B;B	0.17098	0.017;0.004;0.007	T	0.14671	-1.0464	10	0.40728	T	0.16	0.2019	4.1158	0.10081	0.1306:0.5994:0.1265:0.1435	.	675;675;676	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	I	675;676;676;675	ENSP00000367986:T675I;ENSP00000418268:T676I;ENSP00000367966:T675I	ENSP00000354945:T676I	T	+	2	0	MCM10	13279678	0.807000	0.29009	0.994000	0.49952	0.761000	0.43186	0.511000	0.22739	0.283000	0.22279	0.655000	0.94253	ACA	.	.		0.408	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		T	13239672	C	T	13239672	3	4	101	1	0	0	0	0	1	0	0	0	9394	478	17	3	2081	3	MCM10	10	13239672	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	10038503	13239672	122295075	334	14171										
SUV39H2	79723	hgsc.bcm.edu	37	chr10	14939003	14939003	+	Frame_Shift_Del	DEL	A	A	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaaggcaaagcaataactccAaaagacaataacaaaacttt							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:14939003delA	ENST00000354919.6	+	3	336	c.336delA	c.(334-336)ccafs	p.P112fs	SUV39H2_ENST00000313519.5_Frame_Shift_Del_p.P52fs|SUV39H2_ENST00000378325.3_Intron	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	112					cell differentiation (GO:0030154)|chromatin assembly or disassembly (GO:0006333)|chromatin remodeling (GO:0006338)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|male meiosis (GO:0007140)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nuclear heterochromatin (GO:0005720)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						CAATAACTCCAAAAGACAATA	0.378																																					p.P112fs		Atlas-Indel,Pindel	.											.	SUV39H2	72	.	0			c.335delC						.						66	65	65					10																	14939003		2203	4300	6503	SO:0001589	frameshift_variant	79723	exon3			.	AK027067	CCDS7104.1, CCDS53493.1, CCDS53494.1	10p13	2011-07-01			ENSG00000152455	ENSG00000152455		"Chromatin-modifying enzymes / K-methyltransferases"	17287	protein-coding gene	gene with protein product		606503				11094092	Standard	NM_001193424		Approved	FLJ23414, KMT1B	uc021png.1	Q9H5I1	OTTHUMG00000017718	ENST00000354919.6:c.336delA	chr10.hg19:g.14939003delA	ENSP00000346997:p.Pro112fs	33.0	0.0		64.0	15.0	NM_001193424	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Frame_Shift_Del	DEL	ENST00000354919.6	hg19	CCDS53494.1																																																																																			.	.		0.378	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670		-	14939003	A	-	14939003	7	5	101	1	0	1	0	1	0	0	0	0	15428	117	5	0	158	0	SUV39H2	10	14939003	Frame_Shift_Del	DEL	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1699331	14939003	120595744	335	14172										
MASTL	84930	hgsc.bcm.edu	37	chr10	27459955	27459955	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atttcgtgtgcctacagtggTtcatatcccatggctataac	8	10	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:27459955T>G	ENST00000375940.4	+	8	2124	c.2067T>G	c.(2065-2067)ggT>ggG	p.G689G	MASTL_ENST00000375946.4_Silent_p.G689G|MASTL_ENST00000342386.6_Silent_p.G689G|MASTL_ENST00000477034.1_3'UTR			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	689	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCTACAGTGGTTCATATCCCA	0.343																																					p.G689G		Atlas-SNP	.											.	MASTL	81	.	0			c.T2067G						.						115	119	118					10																	27459955		2203	4300	6503	SO:0001819	synonymous_variant	84930	exon8			CAGTGGTTCATAT	BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.2067T>G	chr10.hg19:g.27459955T>G		115.0	0.0		332.0	20.0	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Silent	SNP	ENST00000375940.4	hg19	CCDS53502.1																																																																																			.	.		0.343	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		G	27459955	T	G	27459955	2	3	101	1	0	0	0	0	0	0	0	1	9337	1712	60	5		5	MASTL	10	27459955	Silent	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	12520952	27459955	108074792	336	14173										
ASAH2	56624	hgsc.bcm.edu	37	chr10	52008360	52008360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctccaagttagagaaggtgCgtttggccatttcttctcag	10	9	3	1	rs376205298		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:52008360C>T	ENST00000395526.4	-	1	10	c.11G>A	c.(10-12)cGc>cAc	p.R4H	ASAH2_ENST00000447815.1_Missense_Mutation_p.R4H|ASAH2_ENST00000329428.6_5'Flank	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	4					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ceramidase activity (GO:0017040)			large_intestine(1)|lung(9)|urinary_tract(1)	11						AGAGAAGGTGCGTTTGGCCAT	0.438																																					p.R4H		Atlas-SNP	.											.	ASAH2	69	.	0			c.G11A						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	94	91	92		11,11	4.1	0.9	10		92	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ASAH2	NM_001143974.1,NM_019893.2	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	4/746,4/781	52008360	1,13005	2203	4300	6503	SO:0001583	missense	56624	exon1			AAGGTGCGTTTGG	AF250847	CCDS7239.2, CCDS44398.1	10q11.23	2008-08-11			ENSG00000188611	ENSG00000188611			18860	protein-coding gene	gene with protein product		611202				10781606	Standard	NM_019893		Approved		uc001jjd.3	Q9NR71	OTTHUMG00000018223	ENST00000395526.4:c.11G>A	chr10.hg19:g.52008360C>T	ENSP00000378897:p.Arg4His	63.0	0.0		162.0	7.0	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Missense_Mutation	SNP	ENST00000395526.4	hg19	CCDS7239.2	.	.	.	.	.	.	.	.	.	.	C	13.80	2.346638	0.41599	0.0	1.16E-4	ENSG00000188611	ENST00000395526;ENST00000447815	T;T	0.34859	1.38;1.34	5.94	4.1	0.47936	.	0.271361	0.30593	U	0.009284	T	0.26122	0.0637	L	0.31926	0.97	0.58432	D	0.999999	B;B	0.21821	0.061;0.036	B;B	0.13407	0.009;0.004	T	0.04307	-1.0961	10	0.40728	T	0.16	.	9.5095	0.39067	0.0:0.8371:0.0:0.1629	.	4;4	Q9NR71-2;Q9NR71	.;ASAH2_HUMAN	H	4	ENSP00000378897:R4H;ENSP00000388206:R4H	ENSP00000378897:R4H	R	-	2	0	ASAH2	51678366	0.002000	0.14202	0.876000	0.34364	0.987000	0.75469	0.461000	0.21940	0.852000	0.35287	0.563000	0.77884	CGC	.	.		0.438	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893		T	52008360	C	T	52008360	3	4	101	1	0	0	0	0	1	0	0	0	1007	768	27	1	2411	1	ASAH2	10	52008360	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	24548405	52008360	83526387	337	14174										
PCDH15	65217	hgsc.bcm.edu	37	chr10	56106175	56106177	+	In_Frame_Del	DEL	CAT	CAT	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctctatctgtccatttggtcCatcatctatatctgtagctc							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:56106175_56106177delCAT	ENST00000320301.6	-	6	936_938	c.542_544delATG	c.(541-546)gatgga>gga	p.D181del	PCDH15_ENST00000395433.1_In_Frame_Del_p.D159del|PCDH15_ENST00000361849.3_In_Frame_Del_p.D181del|PCDH15_ENST00000395446.1_In_Frame_Del_p.D181del|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000437009.1_In_Frame_Del_p.D181del|PCDH15_ENST00000395432.2_In_Frame_Del_p.D181del|AC013737.1_ENST00000583830.1_RNA|PCDH15_ENST00000373965.2_In_Frame_Del_p.D181del|PCDH15_ENST00000395440.1_In_Frame_Del_p.D181del|PCDH15_ENST00000414778.1_In_Frame_Del_p.D186del|PCDH15_ENST00000395442.1_In_Frame_Del_p.D181del|PCDH15_ENST00000395438.1_In_Frame_Del_p.D181del|PCDH15_ENST00000373957.3_In_Frame_Del_p.D159del|PCDH15_ENST00000395445.1_In_Frame_Del_p.D181del|PCDH15_ENST00000373955.1_In_Frame_Del_p.D181del|PCDH15_ENST00000395430.1_In_Frame_Del_p.D181del	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	181	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CCATTTGGTCCATCATCTATATC	0.315										HNSCC(58;0.16)																											p.186_187del		Atlas-Indel,Pindel	.											.	PCDH15	1715	.	0			c.558_560del						.																																			SO:0001651	inframe_deletion	65217	exon7			.	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.542_544delATG	chr10.hg19:g.56106178_56106180delCAT	ENSP00000322604:p.Asp181del	65.0	0.0		166.0	13.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	In_Frame_Del	DEL	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.		0.315	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		-	56106177	CAT	-	56106175	7	5	101	1	0	1	0	1	0	0	0	0	11520	603	21	0	7079	0	PCDH15	10	56106175	In_Frame_Del	DEL	CAT	TCGA-DD-A1EE-01A-11D-A12Z-10	4097815	56106175	79428572	338	14175										
ANK3	288	hgsc.bcm.edu	37	chr10	61835056	61835056	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgaggctgaggatgtgtctcCgtagtcaatgttttaatggg	14	5	2	2	rs548657898	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:61835056C>T	ENST00000280772.2	-	37	5774	c.5583G>A	c.(5581-5583)acG>acA	p.T1861T	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1861	Ser-rich.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GATGTGTCTCCGTAGTCAATG	0.423													C|||	2	0.000399361	8e-04	0	5008	,	,		21386	0		0	False		,,,				2504	0.001				p.T1861T		Atlas-SNP	.											.	ANK3	703	.	0			c.G5583A						.						154	135	141					10																	61835056		2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			TGTCTCCGTAGTC	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.5583G>A	chr10.hg19:g.61835056C>T		90.0	0.0		175.0	57.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.		0.423	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61835056	C	T	61835056	2	4	101	1	0	0	0	0	0	0	0	1	622	639	23	1		1	ANK3	10	61835056	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	5728881	61835056	73699691	339	14176										
EGR2	1959	hgsc.bcm.edu	37	chr10	64573581	64573581	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cccagcactggggccccccaGggtaaagttacggattgtag	13	12	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:64573581G>A	ENST00000242480.3	-	2	1142	c.817C>T	c.(817-819)Ctg>Ttg	p.L273L	EGR2_ENST00000439032.1_Silent_p.L273L|EGR2_ENST00000411732.1_Silent_p.L223L|EGR2_ENST00000493899.2_5'Flank	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	273					brain development (GO:0007420)|brain segmentation (GO:0035284)|cell death (GO:0008219)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|facial nerve structural organization (GO:0021612)|fat cell differentiation (GO:0045444)|learning or memory (GO:0007611)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein sumoylation (GO:0016925)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ossification (GO:0030278)|response to insulin (GO:0032868)|rhombomere 3 formation (GO:0021660)|rhombomere 5 formation (GO:0021666)|rhythmic behavior (GO:0007622)|Schwann cell differentiation (GO:0014037)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	36	Prostate(12;0.0297)|all_hematologic(501;0.228)					GGGCCCCCCAGGGTAAAGTTA	0.677																																					p.L273L		Atlas-SNP	.											.	EGR2	77	.	0			c.C817T						.						21	26	24					10																	64573581		2188	4268	6456	SO:0001819	synonymous_variant	1959	exon2			CCCCCAGGGTAAA	BC035625	CCDS7267.1, CCDS44409.1	10q21.1	2014-09-17	2009-04-23		ENSG00000122877	ENSG00000122877		"Zinc fingers, C2H2-type"	3239	protein-coding gene	gene with protein product	"Krox-20 homolog, Drosophila"	129010	"early growth response 2 (Krox-20 homolog, Drosophila)"	KROX20			Standard	NM_000399		Approved		uc001jmi.3	P11161	OTTHUMG00000018308	ENST00000242480.3:c.817C>T	chr10.hg19:g.64573581G>A		31.0	0.0		50.0	22.0	NM_000399	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Silent	SNP	ENST00000242480.3	hg19	CCDS7267.1																																																																																			.	.		0.677	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399		A	64573581	G	A	64573581	2	1	101	1	0	0	0	0	0	0	0	1	4974	991	35	3		3	EGR2	10	64573581	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2738525	64573581	70961166	340	14177										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88206050	88206050	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctccttcttatgtttctcttCtgtaccatcagtcttttcag	4	12	6	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:88206050C>T	ENST00000298767.5	-	16	3743	c.3271G>A	c.(3271-3273)Gaa>Aaa	p.E1091K	WAPAL_ENST00000372075.1_Missense_Mutation_p.E303K|WAPAL_ENST00000263070.7_Missense_Mutation_p.E303K|WAPAL_ENST00000484070.1_5'Flank	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	1091	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						TGTTTCTCTTCTGTACCATCA	0.388																																					p.E1091K		Atlas-SNP	.											.	WAPAL	81	.	0			c.G3271A						.						186	185	186					10																	88206050		2203	4300	6503	SO:0001583	missense	23063	exon16			TCTCTTCTGTACC	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.3271G>A	chr10.hg19:g.88206050C>T	ENSP00000298767:p.Glu1091Lys	107.0	0.0		253.0	43.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.300015	0.60195	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076;ENST00000372075;ENST00000263070	T;T;T	0.36520	1.25;1.25;1.25	5.51	5.51	0.81932	Armadillo-type fold (1);	0.269247	0.36628	N	0.002493	T	0.37489	0.1005	L	0.48642	1.525	0.54753	D	0.999989	P;B;P;B	0.37864	0.61;0.06;0.61;0.447	B;B;B;B	0.40982	0.345;0.018;0.345;0.168	T	0.06899	-1.0801	10	0.13853	T	0.58	.	19.4394	0.94811	0.0:1.0:0.0:0.0	.	1085;1129;1091;1128	B2RTX8;E9PH12;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	K	1176;1091;1176;303;303	ENSP00000298767:E1091K;ENSP00000361145:E303K;ENSP00000263070:E303K	ENSP00000263070:E303K	E	-	1	0	WAPAL	88196030	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	3.385000	0.52485	2.581000	0.87130	0.655000	0.94253	GAA	.	.		0.388	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		T	88206050	C	T	88206050	3	4	101	1	0	0	0	0	1	0	0	0	17263	922	32	3	317	3	WAPAL	10	88206050	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	23632469	88206050	47328697	341	14178										
HTR7	3363	hgsc.bcm.edu	37	chr10	92508782	92508782	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agtttgcatagcctagccacAgaaatgtcctctccacccac	6	15	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:92508782A>T	ENST00000336152.3	-	2	1135	c.1109T>A	c.(1108-1110)cTg>cAg	p.L370Q	HTR7_ENST00000277874.6_Missense_Mutation_p.L370Q|HTR7_ENST00000371719.2_Missense_Mutation_p.L370Q|HTR7_ENST00000371721.3_Missense_Mutation_p.L370Q	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	370					blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	GCCTAGCCACAGAAATGTCCT	0.537																																					p.L370Q		Atlas-SNP	.											.	HTR7	122	.	0			c.T1109A						.						115	115	115					10																	92508782		2203	4300	6503	SO:0001583	missense	3363	exon2			AGCCACAGAAATG	BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5302	protein-coding gene	gene with protein product		182137	"5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)"			8226867	Standard	NM_000872		Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000336152.3:c.1109T>A	chr10.hg19:g.92508782A>T	ENSP00000337949:p.Leu370Gln	52.0	0.0		119.0	22.0	NM_019860	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Missense_Mutation	SNP	ENST00000336152.3	hg19	CCDS7408.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880013	0.72294	.	.	ENSG00000148680	ENST00000336152;ENST00000277874;ENST00000371719;ENST00000371721	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	5.33	5.33	0.75918	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.69433	0.3110	M	0.88979	2.995	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.79108	0.989;0.992	T	0.74864	-0.3519	10	0.49607	T	0.09	.	15.2898	0.73857	1.0:0.0:0.0:0.0	.	370;370	P34969;P34969-2	5HT7R_HUMAN;.	Q	370	ENSP00000337949:L370Q;ENSP00000277874:L370Q;ENSP00000360784:L370Q;ENSP00000360786:L370Q	ENSP00000277874:L370Q	L	-	2	0	HTR7	92498762	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.302000	0.78861	2.011000	0.59026	0.528000	0.53228	CTG	.	.		0.537	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1	NM_000872		T	92508782	A	T	92508782	3	4	101	1	0	0	0	0	1	0	0	0	7461	188	7	4	346	4	HTR7	10	92508782	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	4302732	92508782	43025965	342	14179										
HTR7	3363	hgsc.bcm.edu	37	chr10	92508894	92508894	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcacacggtaaaggccccgaCgatgatccccagggtggtgg	15	12	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:92508894C>T	ENST00000336152.3	-	2	1023	c.997G>A	c.(997-999)Gtc>Atc	p.V333I	HTR7_ENST00000277874.6_Missense_Mutation_p.V333I|HTR7_ENST00000371719.2_Missense_Mutation_p.V333I|HTR7_ENST00000371721.3_Missense_Mutation_p.V333I	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	333					blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	AAGGCCCCGACGATGATCCCC	0.537																																					p.V333I		Atlas-SNP	.											.	HTR7	122	.	0			c.G997A						.						81	73	76					10																	92508894		2203	4300	6503	SO:0001583	missense	3363	exon2			CCCCGACGATGAT	BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5302	protein-coding gene	gene with protein product		182137	"5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)"			8226867	Standard	NM_000872		Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000336152.3:c.997G>A	chr10.hg19:g.92508894C>T	ENSP00000337949:p.Val333Ile	83.0	0.0		162.0	11.0	NM_019860	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Missense_Mutation	SNP	ENST00000336152.3	hg19	CCDS7408.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.301775	0.81136	.	.	ENSG00000148680	ENST00000336152;ENST00000277874;ENST00000371719;ENST00000371721	T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82	5.35	5.35	0.76521	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.82033	0.4949	L	0.50993	1.605	0.50467	D	0.999875	D;D	0.76494	0.999;0.996	P;P	0.60886	0.88;0.803	T	0.83054	-0.0151	10	0.59425	D	0.04	.	19.0553	0.93062	0.0:1.0:0.0:0.0	.	333;333	P34969;P34969-2	5HT7R_HUMAN;.	I	333	ENSP00000337949:V333I;ENSP00000277874:V333I;ENSP00000360784:V333I;ENSP00000360786:V333I	ENSP00000277874:V333I	V	-	1	0	HTR7	92498874	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.086000	0.71352	2.499000	0.84300	0.650000	0.86243	GTC	.	.		0.537	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1	NM_000872		T	92508894	C	T	92508894	3	4	101	1	0	0	0	0	1	0	0	0	7461	536	19	1	458	1	HTR7	10	92508894	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	112	92508894	43025853	343	14180										
ANKRD1	27063	hgsc.bcm.edu	37	chr10	92679010	92679011	+	Frame_Shift_Ins	INS	-	-	T													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agctttgatctttgttctagINSttttttctttttgagctaaa							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:92679010_92679011insT	ENST00000371697.3	-	3	470_471	c.222_223insA	c.(220-225)aaactafs	p.L75fs		NM_014391.2	NP_055206.2	Q15327	ANKR1_HUMAN	ankyrin repeat domain 1 (cardiac muscle)	75					cardiac muscle tissue morphogenesis (GO:0055008)|cellular lipid metabolic process (GO:0044255)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|skeletal muscle cell differentiation (GO:0035914)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I band (GO:0031674)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|p53 binding (GO:0002039)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|titin binding (GO:0031432)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|prostate(3)|skin(1)	27		Colorectal(252;0.0475)				CTTTGTTCTAGTTTTTTCTTTT	0.302																																					p.L75fs		Atlas-INDEL	.											ANKRD1,NS,carcinoma,0,1	ANKRD1	50	.	0			c.223_224insA						.			1,4253		0,1,2126						4.9	1			47	1,8245		0,1,4122	no	frameshift	ANKRD1	NM_014391.2		0,2,6248	A1A1,A1R,RR		0.0121,0.0235,0.016				2,12498				SO:0001589	frameshift_variant	27063	exon3			.	X83703	CCDS7412.1	10q23.33	2014-09-17			ENSG00000148677	ENSG00000148677		"Ankyrin repeat domain containing"	15819	protein-coding gene	gene with protein product		609599				7730328	Standard	NM_014391		Approved	C-193, ALRP, CARP, CVARP, MCARP	uc001khe.1	Q15327	OTTHUMG00000018734	ENST00000371697.3:c.223dupA	chr10.hg19:g.92679016_92679016dupT	ENSP00000360762:p.Leu75fs	71.0	0.0		66.0	11.0	NM_014391	Q96LE7	Frame_Shift_Ins	INS	ENST00000371697.3	hg19	CCDS7412.1																																																																																			.	.		0.302	ANKRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049357.1	NM_014391		T	92679011	-	T	92679010	7	5	101	1	0	1	1	0	0	0	0	0	637	1020	36	0	764	0	ANKRD1	10	92679010	Frame_Shift_Ins	INS	-	TCGA-DD-A1EE-01A-11D-A12Z-10	170116	92679010	42855737	344	14181										
IDE	3416	hgsc.bcm.edu	37	chr10	94225544	94225544	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	catgtctgtttggtagtataTctcgatgccacagttattgt	9	7	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:94225544T>C	ENST00000265986.6	-	20	2433	c.2377A>G	c.(2377-2379)Ata>Gta	p.I793V	IDE_ENST00000496903.1_5'UTR|IDE_ENST00000371581.5_Missense_Mutation_p.I238V	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	793					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TGGTAGTATATCTCGATGCCA	0.408																																					p.I793V		Atlas-SNP	.											.	IDE	77	.	0			c.A2377G						.						184	168	174					10																	94225544		2203	4300	6503	SO:0001583	missense	3416	exon20			AGTATATCTCGAT	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.2377A>G	chr10.hg19:g.94225544T>C	ENSP00000265986:p.Ile793Val	116.0	0.0		345.0	19.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	2.951	-0.216720	0.06101	.	.	ENSG00000119912	ENST00000265986;ENST00000371581	T;T	0.08193	3.12;3.12	6.02	6.02	0.97574	Peptidase M16, C-terminal (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.03959	0.0111	N	0.02247	-0.625	0.80722	D	1	B;B	0.18013	0.008;0.025	B;B	0.25987	0.015;0.065	T	0.29088	-1.0023	10	0.02654	T	1	-16.6034	16.5494	0.84464	0.0:0.0:0.0:1.0	.	793;238	P14735;B3KSB8	IDE_HUMAN;.	V	793;238	ENSP00000265986:I793V;ENSP00000360637:I238V	ENSP00000265986:I793V	I	-	1	0	IDE	94215524	1.000000	0.71417	0.985000	0.45067	0.187000	0.23431	7.803000	0.85983	2.299000	0.77371	0.528000	0.53228	ATA	.	.		0.408	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		C	94225544	T	C	94225544	3	2	101	1	0	0	0	0	1	0	0	0	7502	1435	50	2	706	2	IDE	10	94225544	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	1546534	94225544	41309203	345	14182										
C10orf12	26148	hgsc.bcm.edu	37	chr10	98742351	98742351	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagaaaatcagagttccccaAtgggcttggagccccccatg	10	13	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:98742351A>G	ENST00000286067.2	+	1	1311	c.1204A>G	c.(1204-1206)Atg>Gtg	p.M402V		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	402										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		GAGTTCCCCAATGGGCTTGGA	0.517																																					p.M402V		Atlas-SNP	.											.	C10orf12	94	.	0			c.A1204G						.						86	97	93					10																	98742351		2203	4300	6503	SO:0001583	missense	26148	exon1			TCCCCAATGGGCT	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.1204A>G	chr10.hg19:g.98742351A>G	ENSP00000286067:p.Met402Val	26.0	0.0		42.0	15.0	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	hg19	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.520045	0.00010	.	.	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.04360	3.64	5.92	-3.14	0.05250	.	1.164320	0.06741	N	0.778364	T	0.01765	0.0056	N	0.02916	-0.46	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48614	-0.9020	10	0.13108	T	0.6	0.0069	4.6888	0.12771	0.2855:0.0:0.3767:0.3378	.	236;402	A0PJI9;Q8N655	.;CJ012_HUMAN	V	402;236	ENSP00000286067:M402V	ENSP00000286067:M402V	M	+	1	0	C10orf12	98732341	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.071000	0.11505	-0.341000	0.08376	-1.184000	0.01707	ATG	.	.		0.517	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		G	98742351	A	G	98742351	3	3	101	1	0	0	0	0	1	0	0	0	1591	101	4	2	1206	2	C10orf12	10	98742351	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	4516807	98742351	36792396	346	14183										
AVPI1	60370	hgsc.bcm.edu	37	chr10	99437748	99437748	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggctgtctctgtggcactctGtgggttggccagtgcagagt	16	9	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:99437748G>C	ENST00000370626.3	-	3	889	c.322C>G	c.(322-324)Cag>Gag	p.Q108E		NM_021732.2	NP_068378.2	Q5T686	AVPI1_HUMAN	arginine vasopressin-induced 1	108					activation of MAPK activity (GO:0000187)|cell cycle (GO:0007049)					breast(1)|endometrium(1)|large_intestine(2)|skin(1)	5		Colorectal(252;0.162)		Epithelial(162;8.37e-11)|all cancers(201;7.94e-09)		GTGGCACTCTGTGGGTTGGCC	0.522																																					p.Q108E		Atlas-SNP	.											.	AVPI1	16	.	0			c.C322G						.						86	80	82					10																	99437748		2203	4300	6503	SO:0001583	missense	60370	exon3			CACTCTGTGGGTT	AF131791	CCDS7470.1	10q24.2	2004-04-05			ENSG00000119986	ENSG00000119986			30898	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_021732		Approved	VIP32, PP5395, VIT32	uc001koi.2	Q5T686	OTTHUMG00000018864	ENST00000370626.3:c.322C>G	chr10.hg19:g.99437748G>C	ENSP00000359660:p.Gln108Glu	50.0	0.0		97.0	42.0	NM_021732	Q53G32|Q9H2R9|Q9HBN9	Missense_Mutation	SNP	ENST00000370626.3	hg19	CCDS7470.1	.	.	.	.	.	.	.	.	.	.	G	1.804	-0.476238	0.04414	.	.	ENSG00000119986	ENST00000370626	T	0.42513	0.97	5.12	2.21	0.28008	.	.	.	.	.	T	0.22003	0.0530	N	0.24115	0.695	0.09310	N	1	B	0.18166	0.026	B	0.13407	0.009	T	0.28870	-1.0030	9	0.02654	T	1	-2.1518	6.8938	0.24245	0.0913:0.3446:0.5642:0.0	.	108	Q5T686	AVPI1_HUMAN	E	108	ENSP00000359660:Q108E	ENSP00000359660:Q108E	Q	-	1	0	AVPI1	99427738	0.999000	0.42202	0.663000	0.29738	0.094000	0.18550	1.209000	0.32357	0.834000	0.34852	-0.175000	0.13238	CAG	.	.		0.522	AVPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049736.1	NM_021732		C	99437748	G	C	99437748	3	2	101	1	0	0	0	0	1	0	0	0	1230	1386	48	4	125	4	AVPI1	10	99437748	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	695397	99437748	36096999	347	14184										
CPN1	1369	hgsc.bcm.edu	37	chr10	101802222	101802222	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagctgcctcatctccatttCtttctttctggcttggggct	8	13	5	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:101802222C>T	ENST00000370418.3	-	9	1590	c.1339G>A	c.(1339-1341)Gaa>Aaa	p.E447K		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	447					response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		ATCTCCATTTCTTTCTTTCTG	0.552																																					p.E447K		Atlas-SNP	.											.	CPN1	62	.	0			c.G1339A						.						97	86	90					10																	101802222		2203	4300	6503	SO:0001583	missense	1369	exon9			CCATTTCTTTCTT	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"anaphylatoxin inactivator", "arginine carboxypeptidase", "carboxypeptidase K", "kininase I", "lysine carboxypeptidase"	603103	"carboxypeptidase N, polypeptide 1, 50kD"			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.1339G>A	chr10.hg19:g.101802222C>T	ENSP00000359446:p.Glu447Lys	80.0	0.0		171.0	26.0	NM_001308	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	hg19	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	C	7.828	0.719197	0.15372	.	.	ENSG00000120054	ENST00000370418	T	0.16457	2.34	4.02	1.14	0.20703	.	.	.	.	.	T	0.06142	0.0159	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.14578	0.011	T	0.42310	-0.9459	9	0.07990	T	0.79	-13.8138	3.3415	0.07120	0.2046:0.5783:0.0:0.2171	.	447	P15169	CBPN_HUMAN	K	447	ENSP00000359446:E447K	ENSP00000359446:E447K	E	-	1	0	CPN1	101792212	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.022000	0.12480	0.252000	0.21531	-0.145000	0.13849	GAA	.	.		0.552	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		T	101802222	C	T	101802222	3	4	101	1	0	0	0	0	1	0	0	0	3811	922	32	3	41	3	CPN1	10	101802222	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2364474	101802222	33732525	348	14185										
CNNM2	54805	hgsc.bcm.edu	37	chr10	104679587	104679587	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aagacggtggaggacgtgatGaccccactccgggactgctt	14	11	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:104679587G>A	ENST00000369878.4	+	1	1538	c.1350G>A	c.(1348-1350)atG>atA	p.M450I	CNNM2_ENST00000369875.3_Missense_Mutation_p.M450I|CNNM2_ENST00000433628.2_Missense_Mutation_p.M450I	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	450	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		AGGACGTGATGACCCCACTCC	0.587																																					p.M450I		Atlas-SNP	.											.	CNNM2	119	.	0			c.G1350A						.						73	66	68					10																	104679587		2203	4300	6503	SO:0001583	missense	54805	exon1			CGTGATGACCCCA	AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"cyclin M2"	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1350G>A	chr10.hg19:g.104679587G>A	ENSP00000358894:p.Met450Ile	24.0	0.0		66.0	31.0	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Missense_Mutation	SNP	ENST00000369878.4	hg19	CCDS44474.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.128972	0.77549	.	.	ENSG00000148842	ENST00000457502;ENST00000433628;ENST00000369875;ENST00000369878;ENST00000345419;ENST00000541201	D;D;D	0.81659	-1.52;-1.52;-1.52	4.81	4.81	0.61882	Cystathionine beta-synthase, core (1);	0.084446	0.85682	D	0.000000	D	0.93789	0.8014	H	0.98068	4.14	0.80722	D	1	B;B;D	0.65815	0.357;0.427;0.995	B;B;D	0.81914	0.343;0.186;0.995	D	0.96370	0.9273	10	0.87932	D	0	.	17.8745	0.88821	0.0:0.0:1.0:0.0	.	450;450;450	Q9H8M5-2;Q9H8M5;F5H1I3	.;CNNM2_HUMAN;.	I	450	ENSP00000392875:M450I;ENSP00000358891:M450I;ENSP00000358894:M450I	ENSP00000286899:M450I	M	+	3	0	CNNM2	104669577	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.852000	0.99516	2.187000	0.69744	0.555000	0.69702	ATG	.	.		0.587	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		A	104679587	G	A	104679587	3	1	101	1	0	0	0	0	1	0	0	0	3615	1290	45	3	1352	3	CNNM2	10	104679587	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2877365	104679587	30855160	349	14186										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106959776	106959776	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gagtttttggccacttcagcCtccgctccgaatggcaattg	10	12	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:106959776C>T	ENST00000369701.3	+	15	2256	c.2029C>T	c.(2029-2031)Ctc>Ttc	p.L677F	SORCS3_ENST00000369699.4_5'UTR	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	677					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CCACTTCAGCCTCCGCTCCGA	0.498																																					p.L677F	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.C2029T						.						113	101	105					10																	106959776		2203	4300	6503	SO:0001583	missense	22986	exon15			TTCAGCCTCCGCT	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.2029C>T	chr10.hg19:g.106959776C>T	ENSP00000358715:p.Leu677Phe	65.0	0.0		147.0	7.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.842417	0.51057	.	.	ENSG00000156395	ENST00000369701	T	0.29917	1.55	6.07	6.07	0.98685	VPS10 (1);	0.127920	0.53938	D	0.000043	T	0.28632	0.0709	L	0.34521	1.04	0.58432	D	0.999993	B	0.25563	0.129	B	0.26310	0.068	T	0.03773	-1.1005	9	.	.	.	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	677	Q9UPU3	SORC3_HUMAN	F	677	ENSP00000358715:L677F	.	L	+	1	0	SORCS3	106949766	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.630000	0.67805	2.890000	0.99128	0.650000	0.86243	CTC	.	.		0.498	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		T	106959776	C	T	106959776	3	4	101	1	0	0	0	0	1	0	0	0	14947	681	24	3	2087	3	SORCS3	10	106959776	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2280189	106959776	28574971	350	14187										
DCLRE1A	9937	hgsc.bcm.edu	37	chr10	115609989	115609989	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agatttcacagtcactgaagTcattttctggcaatggcaaa	8	8	4	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:115609989T>C	ENST00000361384.2	-	2	1792	c.875A>G	c.(874-876)gAc>gGc	p.D292G	DCLRE1A_ENST00000369305.1_Missense_Mutation_p.D292G	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	292					mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		GTCACTGAAGTCATTTTCTGG	0.368								Other identified genes with known or suspected DNA repair function																													p.D292G		Atlas-SNP	.											.	DCLRE1A	80	.	0			c.A875G						.						123	116	119					10																	115609989		2203	4300	6503	SO:0001583	missense	9937	exon2			CTGAAGTCATTTT		CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	609682	"DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.875A>G	chr10.hg19:g.115609989T>C	ENSP00000355185:p.Asp292Gly	60.0	0.0		143.0	7.0	NM_014881	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Missense_Mutation	SNP	ENST00000361384.2	hg19	CCDS7584.1	.	.	.	.	.	.	.	.	.	.	T	14.93	2.681545	0.47991	.	.	ENSG00000198924	ENST00000361384;ENST00000369305	T;T	0.72051	-0.62;-0.62	5.8	4.64	0.57946	.	0.218930	0.43416	N	0.000580	T	0.63307	0.2500	L	0.49126	1.545	0.35438	D	0.794648	B	0.30664	0.289	B	0.28784	0.094	T	0.68861	-0.5297	10	0.52906	T	0.07	-5.9362	10.7508	0.46209	0.0:0.0727:0.0:0.9273	.	292	Q6PJP8	DCR1A_HUMAN	G	292	ENSP00000355185:D292G;ENSP00000358311:D292G	ENSP00000355185:D292G	D	-	2	0	DCLRE1A	115599979	0.986000	0.35501	0.844000	0.33320	0.989000	0.77384	1.943000	0.40253	0.980000	0.38523	0.528000	0.53228	GAC	.	.		0.368	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881		C	115609989	T	C	115609989	3	2	101	1	0	0	0	0	1	0	0	0	4296	1667	58	2	2279	2	DCLRE1A	10	115609989	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	8650213	115609989	19924758	351	14188										
KCNK18	338567	hgsc.bcm.edu	37	chr10	118960672	118960672	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggtcatgtctttctccagtgGtggaagacagaaaacaggat	12	7	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:118960672G>A	ENST00000334549.1	+	2	226	c.226G>A	c.(226-228)Gtg>Atg	p.V76M		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	76					cellular response to pH (GO:0071467)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41		Colorectal(252;0.19)		all cancers(201;0.0211)		TTCTCCAGTGGTGGAAGACAG	0.517																																					p.V76M		Atlas-SNP	.											.	KCNK18	70	.	0			c.G226A						.						169	169	169					10																	118960672		2203	4300	6503	SO:0001583	missense	338567	exon2			CCAGTGGTGGAAG	AB087138	CCDS7598.1	10q26.11	2012-03-07			ENSG00000186795	ENSG00000186795		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	19439	protein-coding gene	gene with protein product	"TWIK related spinal cord K+ channel"	613655				16382106	Standard	NM_181840		Approved	K2p18.1, TRESK-2, TRESK2, TRESK, TRIK	uc010qsr.2	Q7Z418	OTTHUMG00000019120	ENST00000334549.1:c.226G>A	chr10.hg19:g.118960672G>A	ENSP00000334650:p.Val76Met	28.0	0.0		42.0	4.0	NM_181840	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	hg19	CCDS7598.1	.	.	.	.	.	.	.	.	.	.	G	8.195	0.796956	0.16327	.	.	ENSG00000186795	ENST00000334549	T	0.15372	2.43	4.34	1.2	0.21068	.	1.105970	0.06748	N	0.779507	T	0.09423	0.0232	N	0.14661	0.345	0.09310	N	1	B	0.14012	0.009	B	0.11329	0.006	T	0.37197	-0.9716	10	0.34782	T	0.22	.	3.2515	0.06816	0.2378:0.0:0.562:0.2002	.	76	Q7Z418	KCNKI_HUMAN	M	76	ENSP00000334650:V76M	ENSP00000334650:V76M	V	+	1	0	KCNK18	118950662	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.511000	0.22739	0.252000	0.21531	-0.140000	0.14226	GTG	.	.		0.517	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840		A	118960672	G	A	118960672	3	1	101	1	0	0	0	0	1	0	0	0	8074	1261	44	3	232	3	KCNK18	10	118960672	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3350683	118960672	16574075	352	14189										
CHST15	51363	hgsc.bcm.edu	37	chr10	125769678	125769678	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcagctctcacgtcgtcttcCacgcaaacgcctcatccgcg	7	18	4	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:125769678C>T	ENST00000346248.5	-	8	2315	c.1673G>A	c.(1672-1674)tGg>tAg	p.W558*	CHST15_ENST00000435907.1_Nonsense_Mutation_p.W558*	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	558					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						CGTCGTCTTCCACGCAAACGC	0.562																																					p.W558X		Atlas-SNP	.											.	CHST15	134	.	0			c.G1673A						.						65	65	65					10																	125769678		2203	4300	6503	SO:0001587	stop_gained	51363	exon8			GTCTTCCACGCAA	AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"Sulfotransferases, membrane-bound"	18137	protein-coding gene	gene with protein product	"B cell RAG associated protein", "N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1673G>A	chr10.hg19:g.125769678C>T	ENSP00000333947:p.Trp558*	33.0	0.0		84.0	14.0	NM_015892	O60338|O60474|Q86VM4	Nonsense_Mutation	SNP	ENST00000346248.5	hg19	CCDS7638.1	.	.	.	.	.	.	.	.	.	.	C	43	10.455762	0.99408	.	.	ENSG00000182022	ENST00000346248;ENST00000435907	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.112	19.2238	0.93810	0.0:1.0:0.0:0.0	.	.	.	.	X	558	.	ENSP00000333947:W558X	W	-	2	0	CHST15	125759668	1.000000	0.71417	0.997000	0.53966	0.875000	0.50365	6.984000	0.76186	2.543000	0.85770	0.563000	0.77884	TGG	.	.		0.562	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892		T	125769678	C	T	125769678	4	4	101	1	0	0	0	0	0	1	0	0	3405	595	21	3	16	3	CHST15	10	125769678	Nonsense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	6809006	125769678	9765069	353	14190										
DOCK1	1793	hgsc.bcm.edu	37	chr10	128840966	128840966	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gagacttttgacacgttagtCtttgatgctctggtaagaga	11	6	2	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr10:128840966C>A	ENST00000280333.6	+	20	2134	c.2025C>A	c.(2023-2025)gtC>gtA	p.V675V		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	675					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		ACACGTTAGTCTTTGATGCTC	0.498																																					p.V675V		Atlas-SNP	.											.	DOCK1	188	.	0			c.C2025A						.						188	187	187					10																	128840966		2091	4247	6338	SO:0001819	synonymous_variant	1793	exon20			GTTAGTCTTTGAT	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.2025C>A	chr10.hg19:g.128840966C>A		83.0	0.0		139.0	18.0	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	hg19																																																																																				.	.		0.498	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		A	128840966	C	A	128840966	2	1	101	1	0	0	0	0	0	0	0	1	4686	900	32	3		3	DOCK1	10	128840966	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3071288	128840966	6693781	354	14191										
NLRP6	171389	hgsc.bcm.edu	37	chr11	281055	281055	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acgggccccggttgcagggcGacctgcgcaatctgtgccgc	15	15	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:281055G>C	ENST00000312165.5	+	4	1321	c.1321G>C	c.(1321-1323)Gac>Cac	p.D441H	NLRP6_ENST00000534750.1_Missense_Mutation_p.D441H	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	441	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		GTTGCAGGGCGACCTGCGCAA	0.657																																					p.D441H		Atlas-SNP	.											.	NLRP6	4	.	0			c.G1321C						.						57	65	62					11																	281055		2202	4296	6498	SO:0001583	missense	171389	exon4			CAGGGCGACCTGC	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"Nucleotide-binding domain and leucine rich repeat containing"	22944	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"	609650	"NACHT, leucine rich repeat and PYD containing 6"	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.1321G>C	chr11.hg19:g.281055G>C	ENSP00000309767:p.Asp441His	27.0	0.0		61.0	7.0	NM_138329	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	hg19	CCDS7693.1	.	.	.	.	.	.	.	.	.	.	G	1.891	-0.455583	0.04540	.	.	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.75154	-0.91;-0.9	3.26	1.21	0.21127	NACHT nucleoside triphosphatase (1);	0.195037	0.25338	N	0.031390	T	0.49525	0.1562	N	0.04508	-0.205	0.09310	N	1	B;P	0.45240	0.007;0.854	B;B	0.43274	0.002;0.414	T	0.46638	-0.9177	10	0.30854	T	0.27	.	7.304	0.26436	0.0:0.186:0.6225:0.1915	.	441;441	E9PJZ8;P59044	.;NALP6_HUMAN	H	441	ENSP00000433617:D441H;ENSP00000309767:D441H	ENSP00000309767:D441H	D	+	1	0	NLRP6	271055	0.000000	0.05858	0.068000	0.19968	0.563000	0.35712	0.153000	0.16323	0.327000	0.23409	0.455000	0.32223	GAC	.	.		0.657	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		C	281055	G	C	281055	3	2	101	1	0	0	0	0	1	0	0	0	10490	1058	37	4	1335	4	NLRP6	11	281055	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10		281055	134725461	355	14192										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6643329	6643329	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cgatacggggagctgggggaCatggccgagcttcatccttg	16	10	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:6643329C>A	ENST00000299441.3	-	21	9989	c.9578G>T	c.(9577-9579)tGt>tTt	p.C3193F	TPP1_ENST00000299427.6_5'Flank|RP11-732A19.9_ENST00000545572.1_RNA|TPP1_ENST00000533371.1_5'Flank|TPP1_ENST00000528657.1_5'Flank|RP11-732A19.5_ENST00000526456.1_RNA|TPP1_ENST00000534644.1_5'Flank	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	3193					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGCTGGGGGACATGGCCGAGC	0.617																																					p.C3193F		Atlas-SNP	.											.	DCHS1	277	.	0			c.G9578T						.						43	49	47					11																	6643329		2201	4296	6497	SO:0001583	missense	8642	exon21			GGGGGACATGGCC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.9578G>T	chr11.hg19:g.6643329C>A	ENSP00000299441:p.Cys3193Phe	38.0	0.0		95.0	19.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	8.080	0.772134	0.16051	.	.	ENSG00000166341	ENST00000299441	T	0.53423	0.62	4.88	4.88	0.63580	.	0.000000	0.46145	D	0.000314	T	0.38268	0.1034	N	0.22421	0.69	0.34786	D	0.735252	D	0.56521	0.976	P	0.44518	0.452	T	0.48948	-0.8989	10	0.31617	T	0.26	.	16.7719	0.85539	0.0:1.0:0.0:0.0	.	3193	Q96JQ0	PCD16_HUMAN	F	3193	ENSP00000299441:C3193F	ENSP00000299441:C3193F	C	-	2	0	DCHS1	6599905	0.999000	0.42202	0.990000	0.47175	0.865000	0.49528	3.651000	0.54431	2.531000	0.85337	0.313000	0.20887	TGT	.	.		0.617	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6643329	C	A	6643329	3	1	101	1	0	0	0	0	1	0	0	0	4289	478	17	3	322	3	DCHS1	11	6643329	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	6362274	6643329	128363187	356	14193										
OR10A3	26496	hgsc.bcm.edu	37	chr11	7960259	7960259	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccaatgagatcagtttcttgGtttcgggtgagtagccagat	12	7	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:7960259G>C	ENST00000360759.3	-	1	882	c.809C>G	c.(808-810)aCc>aGc	p.T270S		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	270					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAGTTTCTTGGTTTCGGGTGA	0.453																																					p.T270S		Atlas-SNP	.											.	OR10A3	54	.	0			c.C809G						.						197	179	185					11																	7960259		2201	4296	6497	SO:0001583	missense	26496	exon1			TTCTTGGTTTCGG	BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"GPCR / Class A : Olfactory receptors"	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.809C>G	chr11.hg19:g.7960259G>C	ENSP00000353988:p.Thr270Ser	117.0	0.0		370.0	33.0	NM_001003745	B9EH39|Q6IF58|Q96R11	Missense_Mutation	SNP	ENST00000360759.3	hg19	CCDS31421.1	.	.	.	.	.	.	.	.	.	.	G	0.429	-0.904393	0.02453	.	.	ENSG00000170683	ENST00000360759	T	0.00054	8.8	4.65	1.46	0.22682	GPCR, rhodopsin-like superfamily (1);	0.370076	0.19214	N	0.119853	T	0.00073	0.0002	N	0.04018	-0.295	0.09310	N	1	B	0.09022	0.002	B	0.21708	0.036	T	0.02437	-1.1159	10	0.09084	T	0.74	.	8.9595	0.35838	0.0:0.4598:0.3828:0.1574	.	270	P58181	O10A3_HUMAN	S	270	ENSP00000353988:T270S	ENSP00000353988:T270S	T	-	2	0	OR10A3	7916835	0.000000	0.05858	0.998000	0.56505	0.501000	0.33797	0.019000	0.13444	0.671000	0.31185	-0.234000	0.12200	ACC	.	.		0.453	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745		C	7960259	G	C	7960259	3	2	101	1	0	0	0	0	1	0	0	0	10900	1261	44	4	138	4	OR10A3	11	7960259	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1316930	7960259	127046257	357	14194										
DENND5A	23258	hgsc.bcm.edu	37	chr11	9202573	9202573	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccaatttgttggggaactgtGgcaagtcctctggcaactca	11	10	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:9202573G>T	ENST00000328194.3	-	6	1516	c.1196C>A	c.(1195-1197)cCa>cAa	p.P399Q	DENND5A_ENST00000530044.1_Missense_Mutation_p.P399Q|DENND5A_ENST00000526523.1_5'Flank	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	399					positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GGGGAACTGTGGCAAGTCCTC	0.468																																					p.P399Q		Atlas-SNP	.											.	DENND5A	84	.	0			c.C1196A						.						67	68	68					11																	9202573		2201	4296	6497	SO:0001583	missense	23258	exon6			AACTGTGGCAAGT	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"DENN/MADD domain containing"	19344	protein-coding gene	gene with protein product			"RAB6 interacting protein 1"	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.1196C>A	chr11.hg19:g.9202573G>T	ENSP00000328524:p.Pro399Gln	74.0	0.0		211.0	17.0	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	hg19	CCDS31423.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.808638	0.90707	.	.	ENSG00000184014	ENST00000328194;ENST00000530044	T;T	0.05319	3.46;3.46	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.26557	0.0649	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.00740	-1.1586	10	0.87932	D	0	.	18.9552	0.92655	0.0:0.0:1.0:0.0	.	399;399	E9PS91;Q6IQ26	.;DEN5A_HUMAN	Q	399	ENSP00000328524:P399Q;ENSP00000435866:P399Q	ENSP00000328524:P399Q	P	-	2	0	DENND5A	9159149	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.810000	0.99221	2.550000	0.86006	0.563000	0.77884	CCA	.	.		0.468	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		T	9202573	G	T	9202573	3	4	101	1	0	0	0	0	1	0	0	0	4438	1348	47	3	2739	3	DENND5A	11	9202573	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1242314	9202573	125803943	358	14195										
PRDM11	56981	hgsc.bcm.edu	37	chr11	45246096	45246096	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	catggtgtgcagaatataggCcagacccagggggaggggga	18	7	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:45246096C>T	ENST00000530656.1	+	7	1173	c.1173C>T	c.(1171-1173)ggC>ggT	p.G391G	PRDM11_ENST00000424263.2_Silent_p.G357G|CTD-2560E9.3_ENST00000527450.1_RNA|PRDM11_ENST00000528980.1_Intron|PRDM11_ENST00000263765.4_Silent_p.G391G			Q9NQV5	PRD11_HUMAN	PR domain containing 11	391							methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						AGAATATAGGCCAGACCCAGG	0.567																																					p.G357G	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											.	PRDM11	53	.	0			c.C1071T						.						74	84	80					11																	45246096		2203	4299	6502	SO:0001819	synonymous_variant	56981	exon7			TATAGGCCAGACC	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"PR-domain containing protein 11"						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.1173C>T	chr11.hg19:g.45246096C>T		25.0	0.0		58.0	6.0	NM_001256695	Q8N9F1	Silent	SNP	ENST00000530656.1	hg19																																																																																				.	.		0.567	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229		T	45246096	C	T	45246096	2	4	101	1	0	0	0	0	0	0	0	1	12464	726	26	3		3	PRDM11	11	45246096	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	36043523	45246096	89760420	359	14196										
OR4C46	119749	hgsc.bcm.edu	37	chr11	51516034	51516034	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtcatcttattctttgtgccCtgcatatttgtgtacatgag	8	8	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:51516034C>T	ENST00000328188.1	+	1	753	c.753C>T	c.(751-753)ccC>ccT	p.P251P		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	251						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						TCTTTGTGCCCTGCATATTTG	0.433																																					p.P251P		Atlas-SNP	.											.	OR4C46	96	.	0			c.C753T						.						119	99	106					11																	51516034		2201	4296	6497	SO:0001819	synonymous_variant	119749	exon1			TGTGCCCTGCATA		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"GPCR / Class A : Olfactory receptors"	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.753C>T	chr11.hg19:g.51516034C>T		129.0	0.0		206.0	68.0	NM_001004703		Silent	SNP	ENST00000328188.1	hg19	CCDS31498.1																																																																																			.	.		0.433	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703		T	51516034	C	T	51516034	2	4	101	1	0	0	0	0	0	0	0	1	11060	668	24	3		3	OR4C46	11	51516034	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	6269938	51516034	83490482	360	14197										
OR4C16	219428	hgsc.bcm.edu	37	chr11	55339975	55339975	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gttgaccgctatgtggacatCtgtaagcccctgcactacat	9	12	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:55339975C>A	ENST00000314634.3	+	1	372	c.372C>A	c.(370-372)atC>atA	p.I124I		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				ATGTGGACATCTGTAAGCCCC	0.512																																					p.I124I		Atlas-SNP	.											.	OR4C16	104	.	0			c.C372A						.						190	181	184					11																	55339975		2201	4296	6497	SO:0001819	synonymous_variant	219428	exon1			GGACATCTGTAAG	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"GPCR / Class A : Olfactory receptors"	15172	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily C, member 16"				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.372C>A	chr11.hg19:g.55339975C>A		71.0	0.0		110.0	50.0	NM_001004701	Q6IEV8	Silent	SNP	ENST00000314634.3	hg19	CCDS31502.1																																																																																			.	.		0.512	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701		A	55339975	C	A	55339975	2	1	101	1	0	0	0	0	0	0	0	1	11058	903	32	3		3	OR4C16	11	55339975	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3823941	55339975	79666541	361	14198										
OR5AS1	219447	hgsc.bcm.edu	37	chr11	55798784	55798784	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tagtttcagaaacaaggatgTgaaaaatgctctcaaaaagc	8	6	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:55798784T>A	ENST00000313555.1	+	1	890	c.890T>A	c.(889-891)gTg>gAg	p.V297E		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	297						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					AACAAGGATGTGAAAAATGCT	0.313																																					p.V297E		Atlas-SNP	.											.	OR5AS1	121	.	0			c.T890A						.						47	52	50					11																	55798784		2201	4296	6497	SO:0001583	missense	219447	exon1			AGGATGTGAAAAA	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"GPCR / Class A : Olfactory receptors"	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.890T>A	chr11.hg19:g.55798784T>A	ENSP00000324111:p.Val297Glu	21.0	0.0		37.0	11.0	NM_001001921	Q6IFB8	Missense_Mutation	SNP	ENST00000313555.1	hg19	CCDS31516.1	.	.	.	.	.	.	.	.	.	.	T	11.73	1.727078	0.30593	.	.	ENSG00000181785	ENST00000313555	T	0.39997	1.05	4.76	3.62	0.41486	.	0.000000	0.30593	U	0.009282	T	0.41190	0.1148	L	0.27053	0.805	0.20489	N	0.999894	D	0.63880	0.993	P	0.55161	0.77	T	0.22034	-1.0228	10	0.87932	D	0	.	9.3769	0.38288	0.0:0.0878:0.0:0.9122	.	297	Q8N127	O5AS1_HUMAN	E	297	ENSP00000324111:V297E	ENSP00000324111:V297E	V	+	2	0	OR5AS1	55555360	1.000000	0.71417	0.211000	0.23655	0.056000	0.15407	5.677000	0.68142	0.656000	0.30886	0.472000	0.43445	GTG	.	.		0.313	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921		A	55798784	T	A	55798784	3	1	101	1	0	0	0	0	1	0	0	0	11155	1696	59	4	892	4	OR5AS1	11	55798784	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	458809	55798784	79207732	362	14199										
HNRNPUL2	221092	hgsc.bcm.edu	37	chr11	62491884	62491884	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgctggttttgacttttcacTatcctggtcatctcctacaa	6	11	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:62491884T>G	ENST00000301785.5	-	2	745	c.553A>C	c.(553-555)Agt>Cgt	p.S185R	HNRNPUL2-BSCL2_ENST00000403734.2_Missense_Mutation_p.S185R	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	185	Glu-rich. {ECO:0000255}.					membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GACTTTTCACTATCCTGGTCA	0.458																																					p.S185R		Atlas-SNP	.											.	HNRNPUL2	41	.	0			c.A553C						.						105	103	104					11																	62491884		1875	4120	5995	SO:0001583	missense	221092	exon2			TTTCACTATCCTG		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.553A>C	chr11.hg19:g.62491884T>G	ENSP00000301785:p.Ser185Arg	103.0	0.0		243.0	43.0	NM_001079559	Q8N3B3	Missense_Mutation	SNP	ENST00000301785.5	hg19	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.091707	0.36952	.	.	ENSG00000214753	ENST00000301785	T	0.43294	0.95	5.08	5.08	0.68730	.	0.541134	0.20885	N	0.083924	T	0.22975	0.0555	N	0.14661	0.345	0.36983	D	0.894393	P	0.39551	0.678	B	0.33799	0.17	T	0.18681	-1.0329	10	0.15499	T	0.54	-9.8168	12.8404	0.57800	0.0:0.0:0.0:1.0	.	185	Q1KMD3	HNRL2_HUMAN	R	185	ENSP00000301785:S185R	ENSP00000301785:S185R	S	-	1	0	HNRNPUL2	62248460	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.933000	0.40153	2.140000	0.66376	0.533000	0.62120	AGT	.	.		0.458	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		G	62491884	T	G	62491884	3	3	101	1	0	0	0	0	1	0	0	0	7284	1522	53	5	1742	5	HNRNPUL2	11	62491884	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	6693100	62491884	72514632	363	14200										
ATL3	25923	hgsc.bcm.edu	37	chr11	63396832	63396832	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggatggtcttccaacaactgCatccctcacagtggcctgag	10	13	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:63396832C>A	ENST00000398868.3	-	13	1861	c.1585G>T	c.(1585-1587)Gca>Tca	p.A529S	ATL3_ENST00000332645.4_Missense_Mutation_p.A556S|ATL3_ENST00000538786.1_Missense_Mutation_p.A511S	NM_015459.3	NP_056274.3	Q6DD88	ATLA3_HUMAN	atlastin GTPase 3	529					endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	11						CCAACAACTGCATCCCTCACA	0.388																																					p.A529S		Atlas-SNP	.											.	ATL3	31	.	0			c.G1585T						.						124	117	119					11																	63396832		1905	4120	6025	SO:0001583	missense	25923	exon13			CAACTGCATCCCT		CCDS41663.1, CCDS73309.1	11q13.1	2008-09-17			ENSG00000184743	ENSG00000184743			24526	protein-coding gene	gene with protein product		609369				18270207	Standard	XM_005273891		Approved	DKFZP564J0863	uc001nxk.1	Q6DD88	OTTHUMG00000167854	ENST00000398868.3:c.1585G>T	chr11.hg19:g.63396832C>A	ENSP00000381844:p.Ala529Ser	97.0	0.0		255.0	35.0	NM_015459	Q8N7W5|Q9H8Q5|Q9UFL1	Missense_Mutation	SNP	ENST00000398868.3	hg19	CCDS41663.1	.	.	.	.	.	.	.	.	.	.	C	8.508	0.865783	0.17250	.	.	ENSG00000184743	ENST00000398868;ENST00000332645;ENST00000538786	T;T;T	0.80480	-1.25;-1.38;-1.24	5.63	1.39	0.22231	.	0.572977	0.18801	N	0.130797	T	0.52948	0.1766	N	0.04959	-0.14	0.09310	N	1	B	0.28820	0.224	B	0.24701	0.055	T	0.38564	-0.9655	10	0.29301	T	0.29	-7.3235	1.6857	0.02841	0.1828:0.4839:0.155:0.1782	.	529	Q6DD88	ATLA3_HUMAN	S	529;556;511	ENSP00000381844:A529S;ENSP00000329034:A556S;ENSP00000437593:A511S	ENSP00000329034:A556S	A	-	1	0	ATL3	63153408	0.002000	0.14202	0.425000	0.26659	0.009000	0.06853	0.010000	0.13242	0.298000	0.22638	-0.274000	0.10170	GCA	.	.		0.388	ATL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396637.1	NM_015459		A	63396832	C	A	63396832	3	1	101	1	0	0	0	0	1	0	0	0	1108	710	25	3	44	3	ATL3	11	63396832	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	904948	63396832	71609684	364	14201										
ESRRA	2101	hgsc.bcm.edu	37	chr11	64082291	64082291	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgccatgcctgaccccgcagGccctgatgggcacctcccag	11	18	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:64082291G>T	ENST00000405666.1	+	5	884	c.650G>T	c.(649-651)gGc>gTc	p.G217V	ESRRA_ENST00000406310.1_Missense_Mutation_p.G216V|ESRRA_ENST00000000442.6_Missense_Mutation_p.G217V	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	217	Ligand binding domain.				cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						GACCCCGCAGGCCCTGATGGG	0.577																																					p.G217V		Atlas-SNP	.											.	ESRRA	56	.	0			c.G650T						.						62	63	62					11																	64082291		2060	4218	6278	SO:0001583	missense	2101	exon5			CCGCAGGCCCTGA	X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"Nuclear hormone receptors"	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.650G>T	chr11.hg19:g.64082291G>T	ENSP00000384851:p.Gly217Val	33.0	0.0		74.0	8.0	NM_004451	Q14514	Missense_Mutation	SNP	ENST00000405666.1	hg19	CCDS41667.1	.	.	.	.	.	.	.	.	.	.	G	1.675	-0.507963	0.04231	.	.	ENSG00000173153	ENST00000406310;ENST00000000442;ENST00000539594;ENST00000405666	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	3.99	3.99	0.46301	Nuclear hormone receptor, ligand-binding (2);	0.279419	0.37348	N	0.002138	T	0.14485	0.0350	N	0.02539	-0.55	0.48511	D	0.999663	B;B	0.16802	0.019;0.002	B;B	0.20955	0.032;0.0	T	0.09487	-1.0672	10	0.24483	T	0.36	.	9.2555	0.37581	0.0:0.0:0.7845:0.2155	.	216;217	P11474-2;P11474	.;ERR1_HUMAN	V	216;217;74;217	ENSP00000385971:G216V;ENSP00000000442:G217V;ENSP00000439896:G74V;ENSP00000384851:G217V	ENSP00000000442:G217V	G	+	2	0	ESRRA	63838867	1.000000	0.71417	0.994000	0.49952	0.716000	0.41182	2.988000	0.49386	2.232000	0.73038	0.462000	0.41574	GGC	.	.		0.577	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451		T	64082291	G	T	64082291	3	4	101	1	0	0	0	0	1	0	0	0	5262	1203	42	3	664	3	ESRRA	11	64082291	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	685459	64082291	70924225	365	14202										
C11orf2	738	hgsc.bcm.edu	37	chr11	64878964	64878964	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acgaagaactcgtgcacttgCtgctggacgaagtggtggcc	14	10	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:64878964C>G	ENST00000279281.3	+	10	2346	c.2254C>G	c.(2254-2256)Ctg>Gtg	p.L752V	VPS51_ENST00000527646.1_3'UTR|AP003068.9_ENST00000528887.1_RNA|TM7SF2_ENST00000540748.1_5'Flank|TM7SF2_ENST00000279263.7_5'Flank|TM7SF2_ENST00000345348.5_5'Flank	NM_013265.2	NP_037397.2	Q9UID3	VPS51_HUMAN	vacuolar protein sorting 51 homolog (S. cerevisiae)	752					autophagy (GO:0006914)|lipid transport (GO:0006869)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											CGTGCACTTGCTGCTGGACGA	0.632																																					p.L752V		Atlas-SNP	.											.	.	.	.	0			c.C2254G						.						115	85	95					11																	64878964		2201	4297	6498	SO:0001583	missense	738	exon10			CACTTGCTGCTGG	AF024631	CCDS8093.1	11q13.1	2012-07-19	2012-07-19	2012-07-19	ENSG00000149823	ENSG00000149823			1172	protein-coding gene	gene with protein product	"fat-free homolog (zebrafish)"	615738	"chromosome 11 open reading frame 3", "chromosome 11 open reading frame 2"	C11orf3, C11orf2		9286704, 20685960	Standard	NM_013265		Approved	ANG2, ANG3, FFR	uc001ocr.2	Q9UID3	OTTHUMG00000165600	ENST00000279281.3:c.2254C>G	chr11.hg19:g.64878964C>G	ENSP00000279281:p.Leu752Val	64.0	0.0		202.0	24.0	NM_013265	Q6PJV5|Q7L8A6|Q8WZ35|Q96DF4|Q96GR3	Missense_Mutation	SNP	ENST00000279281.3	hg19	CCDS8093.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393038	0.62066	.	.	ENSG00000149823	ENST00000279281	.	.	.	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000001	T	0.80423	0.4620	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81959	-0.0694	9	0.52906	T	0.07	-13.1403	16.005	0.80357	0.0:1.0:0.0:0.0	.	752	Q9UID3	FFR_HUMAN	V	752	.	ENSP00000279281:L752V	L	+	1	2	C11orf2	64635540	1.000000	0.71417	1.000000	0.80357	0.524000	0.34500	2.909000	0.48758	2.647000	0.89833	0.555000	0.69702	CTG	.	.		0.632	VPS51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385217.1	NM_013265		G	64878964	C	G	64878964	3	3	101	1	0	0	0	0	1	0	0	0	1635	796	28	4	2292	4	C11orf2	11	64878964	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	796673	64878964	70127552	366	14203										
SUV420H1	51111	hgsc.bcm.edu	37	chr11	67957441	67957441	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttcagggtgtccttccccgTgtgctgtaattttgattgat	10	9	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:67957441T>A	ENST00000304363.4	-	2	456	c.103A>T	c.(103-105)Acg>Tcg	p.T35S	SUV420H1_ENST00000405515.1_Missense_Mutation_p.T35S|SUV420H1_ENST00000402185.2_Missense_Mutation_p.T35S|SUV420H1_ENST00000401547.2_Missense_Mutation_p.T35S|SUV420H1_ENST00000402789.1_Missense_Mutation_p.T35S	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	35					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TCCTTCCCCGTGTGCTGTAAT	0.453																																					p.T35S		Atlas-SNP	.											.	SUV420H1	125	.	0			c.A103T						.						370	320	337					11																	67957441		2200	4294	6494	SO:0001583	missense	51111	exon2			TCCCCGTGTGCTG	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.103A>T	chr11.hg19:g.67957441T>A	ENSP00000305899:p.Thr35Ser	144.0	0.0		316.0	21.0	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Missense_Mutation	SNP	ENST00000304363.4	hg19	CCDS31623.1	.	.	.	.	.	.	.	.	.	.	T	5.134	0.210418	0.09757	.	.	ENSG00000110066	ENST00000304363;ENST00000401547;ENST00000405515;ENST00000402789;ENST00000402185;ENST00000434573	T;T;T;T;T;T	0.40476	1.04;1.04;1.04;1.04;1.03;1.04	5.77	-11.5	0.00074	.	1.182760	0.05656	N	0.586013	T	0.19967	0.0480	L	0.29908	0.895	0.18873	N	0.999987	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.002;0.001	T	0.06463	-1.0825	10	0.08179	T	0.78	0.5301	5.4972	0.16809	0.3645:0.3961:0.1218:0.1176	.	35;35;35;35	B7WNX0;B5MCB3;Q4FZB7-2;Q4FZB7	.;.;.;SV421_HUMAN	S	35	ENSP00000305899:T35S;ENSP00000385965:T35S;ENSP00000385640:T35S;ENSP00000385005:T35S;ENSP00000384724:T35S;ENSP00000402921:T35S	ENSP00000305899:T35S	T	-	1	0	SUV420H1	67714017	0.000000	0.05858	0.002000	0.10522	0.950000	0.60333	-3.146000	0.00584	-4.185000	0.00066	-0.386000	0.06593	ACG	.	.		0.453	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		A	67957441	T	A	67957441	3	1	101	1	0	0	0	0	1	0	0	0	15429	1696	59	4	2602	4	SUV420H1	11	67957441	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	3078477	67957441	67049075	367	14204										
LRTOMT	25906	hgsc.bcm.edu	37	chr11	71819726	71819726	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atcagctgagtcgggcagacCtggtgctcctggcacaccgg	14	13	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:71819726C>A	ENST00000227618.4	-	0	886				ANAPC15_ENST00000502597.2_Intron|LRTOMT_ENST00000307198.7_Missense_Mutation_p.L211M|ANAPC15_ENST00000543015.1_5'Flank|LRTOMT_ENST00000435085.1_Missense_Mutation_p.L211M|LRTOMT_ENST00000419228.1_Missense_Mutation_p.L171M|ANAPC15_ENST00000543050.1_Intron|LRTOMT_ENST00000439209.1_3'UTR	NM_001278487.1|NM_001278491.1|NM_014042.2	NP_001265416.1|NP_001265420.1|NP_054761.1	P60006	APC15_HUMAN	anaphase promoting complex subunit 15						mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	anaphase-promoting complex (GO:0005680)|intracellular (GO:0005622)											TCGGGCAGACCTGGTGCTCCT	0.652																																					p.L211M		Atlas-SNP	.											.	LRTOMT	20	.	0			c.C631A						.						54	51	52					11																	71819726		692	1591	2283	SO:0001628	intergenic_variant	220074	exon9			GCAGACCTGGTGC	AL080071	CCDS8210.1, CCDS60880.1	11q13.4	2012-10-17	2012-05-31	2012-05-31	ENSG00000110200	ENSG00000110200		"Anaphase promoting complex subunits"	24531	protein-coding gene	gene with protein product		614717	"chromosome 11 open reading frame 51"	C11orf51		21926987	Standard	NM_014042		Approved	HSPC020, DKFZP564M082, APC15	uc001orw.3	P60006	OTTHUMG00000167865		chr11.hg19:g.71819726C>A		17.0	0.0		56.0	4.0	NM_001145309	G3V1Q3|Q9CXK2|Q9Y269	Missense_Mutation	SNP	ENST00000227618.4	hg19	CCDS8210.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687934	0.29962	.	.	ENSG00000184154	ENST00000419228;ENST00000435085;ENST00000307198	T;T;T	0.29142	1.58;1.58;1.58	5.17	3.21	0.36854	.	.	.	.	.	T	0.39384	0.1076	L	0.44542	1.39	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.75020	0.985;0.974	T	0.14090	-1.0485	9	0.18710	T	0.47	-3.6591	7.6386	0.28280	0.0:0.6301:0.0:0.3699	.	211;171	Q8WZ04;Q8WZ04-2	TOMT_HUMAN;.	M	171;211;211	ENSP00000392233:L171M;ENSP00000409789:L211M;ENSP00000305742:L211M	ENSP00000305742:L171M	L	+	1	2	LRTOMT	71497374	0.483000	0.25956	0.988000	0.46212	0.915000	0.54546	0.730000	0.26043	0.647000	0.30713	-0.144000	0.13903	CTG	.	.		0.652	ANAPC15-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396695.1	NM_014042		A	71819726	C	A	71819726	1	1	101	0	1	0	0	0	0	0	0	0	9055	680	24	3		3	LRTOMT	11	71819726	IGR	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3862285	71819726	63186790	368	14205										
PLEKHB1	58473	hgsc.bcm.edu	37	chr11	73372585	73372585	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cccctctggccatgggcatgCttgcgggagccgccactggg	15	15	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:73372585C>T	ENST00000354190.5	+	8	1101	c.670C>T	c.(670-672)Ctt>Ttt	p.L224F	PLEKHB1_ENST00000535129.1_Missense_Mutation_p.L170F|PLEKHB1_ENST00000543085.1_Missense_Mutation_p.L119F|Y_RNA_ENST00000516923.1_RNA|PLEKHB1_ENST00000398492.4_Missense_Mutation_p.L189F|PLEKHB1_ENST00000398494.4_Missense_Mutation_p.L205F|PLEKHB1_ENST00000227214.6_Missense_Mutation_p.L170F	NM_021200.2	NP_067023.1	Q9UF11	PKHB1_HUMAN	pleckstrin homology domain containing, family B (evectins) member 1	224					multicellular organismal development (GO:0007275)|phototransduction (GO:0007602)|regulation of cell differentiation (GO:0045595)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	7						CATGGGCATGCTTGCGGGAGC	0.687											OREG0021217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L224F		Atlas-SNP	.											.	PLEKHB1	16	.	0			c.C670T						.						40	45	43					11																	73372585		1981	4147	6128	SO:0001583	missense	58473	exon8			GGCATGCTTGCGG	AF081583	CCDS44672.1, CCDS44673.1, CCDS44674.1, CCDS44675.1	11q13.5-q14.1	2013-01-10	2002-11-04	2002-11-08	ENSG00000021300	ENSG00000021300		"Pleckstrin homology (PH) domain containing"	19079	protein-coding gene	gene with protein product		607651	"PH domain containing, retinal 1"	PHRET1		10585447	Standard	NM_021200		Approved	PHR1, KPL1	uc001ouc.3	Q9UF11	OTTHUMG00000168030	ENST00000354190.5:c.670C>T	chr11.hg19:g.73372585C>T	ENSP00000346127:p.Leu224Phe	13.0	0.0	1144	66.0	14.0	NM_021200	A8K0Q5|B2RBP1|B7Z716|Q9UBF5|Q9UI37|Q9UI44	Missense_Mutation	SNP	ENST00000354190.5	hg19	CCDS44672.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.539467	0.85917	.	.	ENSG00000021300	ENST00000354190;ENST00000398492;ENST00000227214;ENST00000398494;ENST00000543085;ENST00000542185;ENST00000535129;ENST00000540431	.	.	.	4.82	3.91	0.45181	.	0.000000	0.85682	D	0.000000	T	0.67505	0.2900	L	0.52573	1.65	0.35813	D	0.824046	D;D;D	0.76494	0.999;0.997;0.999	D;D;D	0.80764	0.994;0.986;0.994	T	0.74509	-0.3642	9	0.87932	D	0	-15.4959	10.5851	0.45278	0.0:0.9061:0.0:0.0939	.	193;189;224	Q59EU5;Q9UF11-2;Q9UF11	.;.;PKHB1_HUMAN	F	224;189;170;205;119;140;170;177	.	ENSP00000227214:L170F	L	+	1	0	PLEKHB1	73050233	1.000000	0.71417	0.997000	0.53966	0.866000	0.49608	2.994000	0.49433	2.677000	0.91161	0.561000	0.74099	CTT	.	.		0.687	PLEKHB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397593.1			T	73372585	C	T	73372585	3	4	101	1	0	0	0	0	1	0	0	0	12073	797	28	3	700	3	PLEKHB1	11	73372585	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1552859	73372585	61633931	369	14206										
RPS3	6188	hgsc.bcm.edu	37	chr11	75110602	75110602	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cggcggcaagatggcagtgcAaatatccaagaagaggaagg	15	7	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:75110602A>G	ENST00000531188.1	+	1	73	c.11A>G	c.(10-12)cAa>cGa	p.Q4R	RPS3_ENST00000278572.6_Missense_Mutation_p.Q4R|RPS3_ENST00000524851.1_Missense_Mutation_p.Q4R|RPS3_ENST00000534440.1_Missense_Mutation_p.Q4R|SNORD15A_ENST00000384214.1_RNA|RPS3_ENST00000530164.1_Missense_Mutation_p.Q4R|RPS3_ENST00000527446.1_Missense_Mutation_p.Q4R|RPS3_ENST00000526608.1_Missense_Mutation_p.Q4R	NM_001005.4|NM_001260506.1|NM_001260507.1	NP_000996.2|NP_001247435.1|NP_001247436.1	P23396	RS3_HUMAN	ribosomal protein S3	4					cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic translation (GO:0002181)|DNA catabolic process, endonucleolytic (GO:0000737)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of DNA repair (GO:0045738)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of DNA N-glycosylase activity (GO:1902546)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ruffle membrane (GO:0032587)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|enzyme binding (GO:0019899)|iron-sulfur cluster binding (GO:0051536)|mRNA binding (GO:0003729)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						ATGGCAGTGCAAATATCCAAG	0.662																																					p.Q4R		Atlas-SNP	.											.	RPS3	20	.	0			c.A11G						.						47	49	48					11																	75110602		2200	4293	6493	SO:0001583	missense	6188	exon1			CAGTGCAAATATC		CCDS8236.1, CCDS58161.1	11q13.3-q13.5	2011-04-05				ENSG00000149273		"S ribosomal proteins"	10420	protein-coding gene	gene with protein product	"IMR-90 ribosomal protein S3", "40S ribosomal protein S3"	600454				1712897, 7789996	Standard	NM_001005		Approved	FLJ26283, FLJ27450, MGC87870, S3	uc031qcs.1	P23396		ENST00000531188.1:c.11A>G	chr11.hg19:g.75110602A>G	ENSP00000434643:p.Gln4Arg	42.0	0.0		157.0	9.0	NM_001256802	B2R7N5|J3KN86|Q498B5|Q8NI95	Missense_Mutation	SNP	ENST00000531188.1	hg19	CCDS8236.1	.	.	.	.	.	.	.	.	.	.	a	14.36	2.513561	0.44763	.	.	ENSG00000149273	ENST00000531188;ENST00000530164;ENST00000530689;ENST00000278572;ENST00000534440;ENST00000527446;ENST00000526608;ENST00000527273;ENST00000524851	.	.	.	5.74	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.60431	0.2268	M	0.62266	1.93	0.58432	D	0.999992	B	0.06786	0.001	B	0.27500	0.08	T	0.62905	-0.6755	9	0.72032	D	0.01	-1.5195	10.7726	0.46332	0.8411:0.1589:0.0:0.0	.	4	P23396	RS3_HUMAN	R	4	.	ENSP00000278572:Q4R	Q	+	2	0	RPS3	74788250	1.000000	0.71417	0.949000	0.38748	0.132000	0.20833	6.324000	0.72896	2.194000	0.70268	0.449000	0.29647	CAA	.	.		0.662	RPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384158.2	NM_001005		G	75110602	A	G	75110602	3	3	101	1	0	0	0	0	1	0	0	0	13658	130	5	2	13	2	RPS3	11	75110602	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1738017	75110602	59895914	370	14207										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76858899	76858899	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caagcctatgcaccccacgtCggtccacggcgtggaggaca	12	15	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:76858899C>G	ENST00000409709.3	+	4	460	c.188C>G	c.(187-189)tCg>tGg	p.S63W	MYO7A_ENST00000409893.1_Missense_Mutation_p.S63W|MYO7A_ENST00000409619.2_Missense_Mutation_p.S52W|MYO7A_ENST00000458637.2_Missense_Mutation_p.S63W	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	63					actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CACCCCACGTCGGTCCACGGC	0.637																																					p.S63W		Atlas-SNP	.											.	MYO7A	164	.	0			c.C188G						.						32	37	35					11																	76858899		2102	4217	6319	SO:0001583	missense	4647	exon4			CCACGTCGGTCCA	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.188C>G	chr11.hg19:g.76858899C>G	ENSP00000386331:p.Ser63Trp	27.0	0.0		128.0	15.0	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	C	33	5.195496	0.94960	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67	4.86	4.86	0.63082	Myosin head, motor domain (1);	0.000000	0.64402	D	0.000001	D	0.86855	0.6033	M	0.88377	2.95	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.89341	0.3654	10	0.72032	D	0.01	.	18.1904	0.89805	0.0:1.0:0.0:0.0	.	63;63;63	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	W	63;63;63;52;62;62;62;62	ENSP00000386331:S63W;ENSP00000386689:S63W;ENSP00000392185:S63W;ENSP00000386635:S52W	ENSP00000345075:S62W	S	+	2	0	MYO7A	76536547	1.000000	0.71417	0.969000	0.41365	0.986000	0.74619	4.730000	0.62015	2.523000	0.85059	0.455000	0.32223	TCG	.	.		0.637	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		G	76858899	C	G	76858899	3	3	101	1	0	0	0	0	1	0	0	0	10091	893	31	4	198	4	MYO7A	11	76858899	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1748297	76858899	58147617	371	14208										
GDPD4	220032	hgsc.bcm.edu	37	chr11	76969478	76969478	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	attcagagtcgataggaaatCccagttgaagaaggcagggt	13	6	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:76969478C>T	ENST00000376217.2	-	10	1067	c.817G>A	c.(817-819)Gat>Aat	p.D273N	GDPD4_ENST00000315938.4_Missense_Mutation_p.D273N			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	273	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						GATAGGAAATCCCAGTTGAAG	0.438																																					p.D273N		Atlas-SNP	.											.	GDPD4	49	.	0			c.G817A						.						149	144	146					11																	76969478		2200	4292	6492	SO:0001583	missense	220032	exon10			GGAAATCCCAGTT	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.817G>A	chr11.hg19:g.76969478C>T	ENSP00000365390:p.Asp273Asn	101.0	0.0		277.0	25.0	NM_182833	Q7Z5B0	Missense_Mutation	SNP	ENST00000376217.2	hg19		.	.	.	.	.	.	.	.	.	.	C	9.854	1.194494	0.22037	.	.	ENSG00000178795	ENST00000376217;ENST00000315938	T;T	0.30448	1.53;1.53	4.84	-9.68	0.00528	.	1.705610	0.02590	N	0.099851	T	0.20292	0.0488	L	0.45228	1.405	0.09310	N	0.999999	B	0.32467	0.372	B	0.30316	0.114	T	0.05037	-1.0910	10	0.21014	T	0.42	0.3622	8.3392	0.32232	0.0:0.1276:0.1973:0.6751	.	273	Q6W3E5-2	.	N	273	ENSP00000365390:D273N;ENSP00000320815:D273N	ENSP00000320815:D273N	D	-	1	0	GDPD4	76647126	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-1.641000	0.02007	-1.708000	0.01401	-0.367000	0.07326	GAT	.	.		0.438	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833		T	76969478	C	T	76969478	3	4	101	1	0	0	0	0	1	0	0	0	6334	855	30	3	773	3	GDPD4	11	76969478	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	110579	76969478	58037038	372	14209										
KBTBD3	143879	hgsc.bcm.edu	37	chr11	105925003	105925003	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaaagtcactgcaagctttgGataggaaggaaacttgaaga	11	5	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:105925003G>C	ENST00000526793.1	-	3	572	c.413C>G	c.(412-414)tCc>tGc	p.S138C	KBTBD3_ENST00000531837.1_Missense_Mutation_p.S138C|KBTBD3_ENST00000534815.1_Missense_Mutation_p.S59C	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	134										NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		GCAAGCTTTGGATAGGAAGGA	0.318																																					p.S138C		Atlas-SNP	.											.	KBTBD3	59	.	0			c.C413G						.						66	70	68					11																	105925003		2200	4298	6498	SO:0001583	missense	143879	exon3			GCTTTGGATAGGA	AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"BTB/POZ domain containing"	22934	protein-coding gene	gene with protein product			"BTB and kelch domain containing 3"	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.413C>G	chr11.hg19:g.105925003G>C	ENSP00000436262:p.Ser138Cys	105.0	0.0		232.0	11.0	NM_152433	Q6N066|Q86X38|Q96NK5	Missense_Mutation	SNP	ENST00000526793.1	hg19	CCDS8334.1	.	.	.	.	.	.	.	.	.	.	G	15.28	2.785454	0.49997	.	.	ENSG00000182359	ENST00000534815;ENST00000526793;ENST00000531837	T;T;T	0.70869	-0.52;-0.52;-0.52	5.36	5.36	0.76844	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.163800	0.56097	D	0.000028	T	0.67869	0.2939	N	0.13098	0.295	0.38045	D	0.935583	B;P	0.42456	0.347;0.78	P;P	0.49999	0.505;0.628	T	0.75263	-0.3379	10	0.72032	D	0.01	.	19.0932	0.93238	0.0:0.0:1.0:0.0	.	138;134	A8K1K0;Q8NAB2	.;KBTB3_HUMAN	C	59;138;138	ENSP00000431910:S59C;ENSP00000436262:S138C;ENSP00000432163:S138C	ENSP00000436262:S138C	S	-	2	0	KBTBD3	105430213	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.923000	0.56469	2.511000	0.84671	0.650000	0.86243	TCC	.	.		0.318	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433		C	105925003	G	C	105925003	3	2	101	1	0	0	0	0	1	0	0	0	8003	1174	41	4	1429	4	KBTBD3	11	105925003	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	28955525	105925003	29081513	373	14210										
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120317715	120317715	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agctgactaaacttgatgcaGagcgagacaaggaccgattg	12	8	0	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:120317715G>C	ENST00000397843.2	+	18	1676	c.1510G>C	c.(1510-1512)Gag>Cag	p.E504Q	ARHGEF12_ENST00000356641.3_Missense_Mutation_p.E485Q|ARHGEF12_ENST00000532993.1_Missense_Mutation_p.E401Q	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	504	RGSL.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		ACTTGATGCAGAGCGAGACAA	0.428			T	MLL	AML																																p.E504Q		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.G1510C						.						127	119	121					11																	120317715		1976	4177	6153	SO:0001583	missense	23365	exon18			GATGCAGAGCGAG	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.1510G>C	chr11.hg19:g.120317715G>C	ENSP00000380942:p.Glu504Gln	73.0	0.0		206.0	20.0	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	hg19	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	G	33	5.252150	0.95336	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	D;D;D	0.85013	-1.93;-1.93;-1.93	5.3	5.3	0.74995	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.000000	0.46758	D	0.000263	D	0.92011	0.7469	M	0.70595	2.14	0.58432	D	0.999995	D;D;D	0.89917	0.994;0.999;1.0	D;D;D	0.79108	0.95;0.979;0.992	D	0.91908	0.5537	10	0.54805	T	0.06	-19.1516	19.3235	0.94252	0.0:0.0:1.0:0.0	.	401;485;504	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	Q	504;485;401	ENSP00000380942:E504Q;ENSP00000349056:E485Q;ENSP00000432984:E401Q	ENSP00000349056:E485Q	E	+	1	0	ARHGEF12	119822925	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.314000	0.96306	2.627000	0.88993	0.650000	0.86243	GAG	.	.		0.428	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		C	120317715	G	C	120317715	3	2	101	1	0	0	0	0	1	0	0	0	897	943	33	4	1580	4	ARHGEF12	11	120317715	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	14392712	120317715	14688801	374	14211										
SCN3B	55800	hgsc.bcm.edu	37	chr11	123513234	123513234	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caaactcaaactcccgggacAcattgcaggtgtagaggcca	10	12	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:123513234A>T	ENST00000392770.2	-	3	1167	c.365T>A	c.(364-366)gTg>gAg	p.V122E	SCN3B_ENST00000299333.3_Missense_Mutation_p.V122E|SCN3B_ENST00000530277.1_Missense_Mutation_p.V122E	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	122	Ig-like C2-type.				atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	CTCCCGGGACACATTGCAGGT	0.602																																					p.V122E		Atlas-SNP	.											.	SCN3B	53	.	0			c.T365A						.						104	96	99					11																	123513234		2202	4299	6501	SO:0001583	missense	55800	exon3			CGGGACACATTGC	AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing"	20665	protein-coding gene	gene with protein product		608214	"sodium channel, voltage-gated, type III, beta"			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.365T>A	chr11.hg19:g.123513234A>T	ENSP00000376523:p.Val122Glu	46.0	0.0		128.0	11.0	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Missense_Mutation	SNP	ENST00000392770.2	hg19	CCDS8442.1	.	.	.	.	.	.	.	.	.	.	A	32	5.160704	0.94727	.	.	ENSG00000166257	ENST00000392770;ENST00000299333;ENST00000530277;ENST00000527836	D;D;D;D	0.95690	-3.78;-3.78;-3.78;-3.78	6.03	6.03	0.97812	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.110193	0.64402	D	0.000008	D	0.97430	0.9159	M	0.79805	2.47	0.80722	D	1	D	0.63046	0.992	P	0.62089	0.898	D	0.97985	1.0351	10	0.87932	D	0	-9.7242	16.5655	0.84588	1.0:0.0:0.0:0.0	.	122	Q9NY72	SCN3B_HUMAN	E	122	ENSP00000376523:V122E;ENSP00000299333:V122E;ENSP00000432785:V122E;ENSP00000435554:V122E	ENSP00000299333:V122E	V	-	2	0	SCN3B	123018444	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.285000	0.89914	2.302000	0.77476	0.533000	0.62120	GTG	.	.		0.602	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400		T	123513234	A	T	123513234	3	4	101	1	0	0	0	0	1	0	0	0	13934	159	6	4	294	4	SCN3B	11	123513234	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	3195519	123513234	11493282	375	14212										
OR8B2	26595	hgsc.bcm.edu	37	chr11	124252995	124252995	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tttttgacacaaagttcattAgcattttgggagtgaaaaca	8	5	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:124252995A>C	ENST00000375013.2	-	1	263	c.245T>G	c.(244-246)cTa>cGa	p.L82R		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		AAAGTTCATTAGCATTTTGGG	0.378																																					p.L82R		Atlas-SNP	.											.	OR8B2	42	.	0			c.T245G						.						133	127	129					11																	124252995		2201	4299	6500	SO:0001583	missense	26595	exon1			TTCATTAGCATTT	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"GPCR / Class A : Olfactory receptors"	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.245T>G	chr11.hg19:g.124252995A>C	ENSP00000364152:p.Leu82Arg	107.0	0.0		276.0	13.0	NM_001005468	Q8NGH2	Missense_Mutation	SNP	ENST00000375013.2	hg19	CCDS31708.1	.	.	.	.	.	.	.	.	.	.	a	12.46	1.943514	0.34283	.	.	ENSG00000204293	ENST00000375013	T	0.00424	7.45	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45606	D	0.000346	T	0.01800	0.0057	H	0.99299	4.505	0.26874	N	0.967685	P	0.52577	0.954	P	0.53450	0.726	T	0.12477	-1.0546	10	0.87932	D	0	.	12.5889	0.56432	1.0:0.0:0.0:0.0	.	82	Q96RD0	OR8B2_HUMAN	R	82	ENSP00000364152:L82R	ENSP00000364152:L82R	L	-	2	0	OR8B2	123758205	0.912000	0.30974	0.465000	0.27155	0.171000	0.22731	6.762000	0.74950	1.911000	0.55334	0.329000	0.21502	CTA	.	.		0.378	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468		C	124252995	A	C	124252995	3	2	101	1	0	0	0	0	1	0	0	0	11236	420	15	5	699	5	OR8B2	11	124252995	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	739761	124252995	10753521	376	14213										
OR8B8	26493	hgsc.bcm.edu	37	chr11	124310110	124310110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgacgtccttattcctcaggCtataaattaatgggttgagc	9	8	1	2	rs147220624	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr11:124310110C>T	ENST00000328064.2	-	1	944	c.872G>A	c.(871-873)aGc>aAc	p.S291N		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	291					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		ATTCCTCAGGCTATAAATTAA	0.408																																					p.S291N		Atlas-SNP	.											.	OR8B8	76	.	0			c.G872A						.						107	98	101					11																	124310110		2201	4299	6500	SO:0001583	missense	26493	exon1			CTCAGGCTATAAA	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"GPCR / Class A : Olfactory receptors"	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.872G>A	chr11.hg19:g.124310110C>T	ENSP00000330280:p.Ser291Asn	49.0	0.0		119.0	10.0	NM_012378	A1L446|Q96RC8	Missense_Mutation	SNP	ENST00000328064.2	hg19	CCDS8446.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.379611	0.42207	.	.	ENSG00000197125	ENST00000328064	T	0.39056	1.1	3.81	3.81	0.43845	.	0.000000	0.56097	D	0.000036	T	0.76870	0.4048	H	0.98559	4.265	0.25578	N	0.98683	D	0.71674	0.998	D	0.66847	0.947	T	0.75889	-0.3158	10	0.87932	D	0	.	16.615	0.84904	0.0:1.0:0.0:0.0	.	291	Q15620	OR8B8_HUMAN	N	291	ENSP00000330280:S291N	ENSP00000330280:S291N	S	-	2	0	OR8B8	123815320	0.017000	0.18338	0.749000	0.31150	0.468000	0.32798	1.191000	0.32138	2.412000	0.81896	0.655000	0.94253	AGC	.	C|0.999;A|0.001		0.408	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378		T	124310110	C	T	124310110	3	4	101	1	0	0	0	0	1	0	0	0	11239	797	28	3	66	3	OR8B8	11	124310110	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	57115	124310110	10696406	377	14214										
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	668557	668557	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caaggagttccgagaccgctGgggcggggaagactgggagc	19	9	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:668557G>A	ENST00000266383.5	+	19	2871	c.2858G>A	c.(2857-2859)tGg>tAg	p.W953*		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	953					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			CGAGACCGCTGGGGCGGGGAA	0.617																																					p.W953X		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G2858A						.						88	94	92					12																	668557		2203	4300	6503	SO:0001587	stop_gained	283358	exon19			ACCGCTGGGGCGG	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.2858G>A	chr12.hg19:g.668557G>A	ENSP00000266383:p.Trp953*	45.0	0.0		102.0	11.0	NM_173593	Q6ZNC1|Q8N7T6	Nonsense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	G	41	8.958160	0.99016	.	.	ENSG00000139044	ENST00000266383	.	.	.	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.6164	18.2881	0.90120	0.0:0.0:1.0:0.0	.	.	.	.	X	953	.	ENSP00000266383:W953X	W	+	2	0	B4GALNT3	538818	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.809000	0.86057	2.383000	0.81215	0.462000	0.41574	TGG	.	.		0.617	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		A	668557	G	A	668557	4	1	101	1	0	0	0	0	0	1	0	0	1268	1357	47	3	2932	3	B4GALNT3	12	668557	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10		668557	133183338	378	14215										
NRIP2	83714	hgsc.bcm.edu	37	chr12	2944113	2944113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctctctttccaacaggaggGtctccacgggagggaaagag	14	10	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:2944113G>A	ENST00000337508.4	-	1	77	c.37C>T	c.(37-39)Ccc>Tcc	p.P13S		NM_031474.2	NP_113662.1	Q9BQI9	NRIP2_HUMAN	nuclear receptor interacting protein 2	13					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	aspartic-type endopeptidase activity (GO:0004190)			central_nervous_system(1)|endometrium(2)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CAACAGGAGGGTCTCCACGGG	0.587																																					p.P13S		Atlas-SNP	.											.	NRIP2	21	.	0			c.C37T						.						48	44	45					12																	2944113		2203	4300	6503	SO:0001583	missense	83714	exon1			AGGAGGGTCTCCA	AK054740	CCDS8514.1	12p13.33	2008-02-05			ENSG00000053702	ENSG00000053702			23078	protein-coding gene	gene with protein product						11230166	Standard	NM_031474		Approved	DKFZP761G1913	uc001qlc.3	Q9BQI9	OTTHUMG00000130616	ENST00000337508.4:c.37C>T	chr12.hg19:g.2944113G>A	ENSP00000337501:p.Pro13Ser	60.0	0.0		137.0	10.0	NM_031474	A2RRE3|B4DV61	Missense_Mutation	SNP	ENST00000337508.4	hg19	CCDS8514.1	.	.	.	.	.	.	.	.	.	.	G	9.806	1.181895	0.21787	.	.	ENSG00000053702	ENST00000337508;ENST00000546074	.	.	.	4.34	4.34	0.51931	.	.	.	.	.	T	0.49695	0.1572	L	0.43152	1.355	0.26649	N	0.972146	D	0.64830	0.994	P	0.56127	0.792	T	0.40979	-0.9534	8	0.87932	D	0	-12.3098	12.2247	0.54453	0.0:0.0:1.0:0.0	.	13	Q9BQI9	NRIP2_HUMAN	S	13	.	ENSP00000337501:P13S	P	-	1	0	NRIP2	2814374	0.998000	0.40836	0.942000	0.38095	0.031000	0.12232	1.929000	0.40114	2.259000	0.74868	0.484000	0.47621	CCC	.	.		0.587	NRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253090.4	NM_031474		A	2944113	G	A	2944113	3	1	101	1	0	0	0	0	1	0	0	0	10662	1261	44	3	832	3	NRIP2	12	2944113	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2275556	2944113	130907782	379	14216										
FGF6	2251	hgsc.bcm.edu	37	chr12	4553334	4553334	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcctttactgttcatggcaaCgaagagggcacttctcactc	8	12	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:4553334C>T	ENST00000228837.2	-	2	458	c.415G>A	c.(415-417)Gtt>Att	p.V139I		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	139					angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)	p.V139I(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			TTCATGGCAACGAAGAGGGCA	0.512																																					p.V139I		Atlas-SNP	.											FGF6,NS,carcinoma,0,1	FGF6	40	.	1	Substitution - Missense(1)	prostate(1)	c.G415A						.						106	81	89					12																	4553334		2203	4300	6503	SO:0001583	missense	2251	exon2			TGGCAACGAAGAG	X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"Endogenous ligands"	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.415G>A	chr12.hg19:g.4553334C>T	ENSP00000228837:p.Val139Ile	43.0	0.0		215.0	24.0	NM_020996	Q0VAE1	Missense_Mutation	SNP	ENST00000228837.2	hg19	CCDS8527.1	.	.	.	.	.	.	.	.	.	.	c	8.440	0.850726	0.17034	.	.	ENSG00000111241	ENST00000543077;ENST00000228837	D;T	0.85861	-2.04;1.5	5.63	-3.46	0.04767	.	0.271169	0.41605	N	0.000859	T	0.77198	0.4095	L	0.43923	1.385	0.40032	D	0.975543	B	0.13594	0.008	B	0.17433	0.018	T	0.55786	-0.8086	10	0.42905	T	0.14	.	13.631	0.62196	0.0:0.4678:0.0:0.5322	.	139	P10767	FGF6_HUMAN	I	18;139	ENSP00000445479:V18I;ENSP00000228837:V139I	ENSP00000228837:V139I	V	-	1	0	FGF6	4423595	0.002000	0.14202	0.017000	0.16124	0.633000	0.38033	-1.160000	0.03147	-1.177000	0.02744	-2.144000	0.00337	GTT	.	.		0.512	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996		T	4553334	C	T	4553334	3	4	101	1	0	0	0	0	1	0	0	0	5864	536	19	1	219	1	FGF6	12	4553334	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1609221	4553334	129298561	380	14217										
VAMP1	6843	hgsc.bcm.edu	37	chr12	6575091	6575091	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcctgcctgcaaggcatcagCtcggtcatccagctctgaca	9	15	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:6575091C>G	ENST00000396308.3	-	3	350	c.205G>C	c.(205-207)Gct>Cct	p.A69P	VAMP1_ENST00000544432.1_5'UTR|TAPBPL_ENST00000545700.1_3'UTR|VAMP1_ENST00000361716.3_Missense_Mutation_p.A69P|VAMP1_ENST00000400911.3_Missense_Mutation_p.A69P|VAMP1_ENST00000535180.1_Missense_Mutation_p.A69P	NM_014231.3|NM_199245.1	NP_055046.1|NP_954740.1	P23763	VAMP1_HUMAN	vesicle-associated membrane protein 1 (synaptobrevin 1)	69	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				neurotransmitter secretion (GO:0007269)|SNARE complex assembly (GO:0035493)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuron projection (GO:0043005)|synapse (GO:0045202)				endometrium(1)|large_intestine(1)|prostate(1)	3					Botulinum Toxin Type B(DB00042)	AAGGCATCAGCTCGGTCATCC	0.512											OREG0021627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A69P		Atlas-SNP	.											.	VAMP1	6	.	0			c.G205C						.						132	108	116					12																	6575091		2203	4300	6503	SO:0001583	missense	6843	exon3			CATCAGCTCGGTC		CCDS31731.1, CCDS41740.1, CCDS44809.1, CCDS73422.1	12p	2013-02-13			ENSG00000139190	ENSG00000139190		"Vesicle-associated membrane proteins"	12642	protein-coding gene	gene with protein product		185880		SYB1		1976629	Standard	XM_006719011		Approved	VAMP-1	uc001qok.3	P23763	OTTHUMG00000168269	ENST00000396308.3:c.205G>C	chr12.hg19:g.6575091C>G	ENSP00000379602:p.Ala69Pro	71.0	0.0	635	157.0	16.0	NM_014231	A8MVP3|D3DUR3|O75468|Q15857|Q6FG94|Q8IVC9	Missense_Mutation	SNP	ENST00000396308.3	hg19	CCDS41740.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.609022	0.87258	.	.	ENSG00000139190	ENST00000400911;ENST00000361716;ENST00000535180;ENST00000355479;ENST00000396308;ENST00000396943;ENST00000539047	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.77	5.77	0.91146	Synaptobrevin (4);	0.000000	0.85682	D	0.000000	T	0.73513	0.3596	H	0.94771	3.58	0.80722	D	1	B;B;B	0.31100	0.2;0.238;0.308	B;B;P	0.44946	0.317;0.445;0.465	T	0.77175	-0.2684	10	0.87932	D	0	.	19.9983	0.97395	0.0:1.0:0.0:0.0	.	69;69;69	P23763-3;P23763;P23763-2	.;VAMP1_HUMAN;.	P	69	ENSP00000383702:A69P;ENSP00000355122:A69P;ENSP00000444181:A69P;ENSP00000379602:A69P	ENSP00000347664:A69P	A	-	1	0	VAMP1	6445352	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.747000	0.85070	2.724000	0.93272	0.561000	0.74099	GCT	.	.		0.512	VAMP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399078.1			G	6575091	C	G	6575091	3	3	101	1	0	0	0	0	1	0	0	0	17127	797	28	4	192	4	VAMP1	12	6575091	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2021757	6575091	127276804	381	14218										
ATN1	1822	hgsc.bcm.edu	37	chr12	7045220	7045220	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctactcccatttcagtatcaAgctctggggctagtggtgct	10	11	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:7045220A>T	ENST00000356654.4	+	5	1027	c.790A>T	c.(790-792)Agc>Tgc	p.S264C	ATN1_ENST00000396684.2_Missense_Mutation_p.S264C	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	264					cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						TTCAGTATCAAGCTCTGGGGC	0.622																																					p.S264C		Atlas-SNP	.											.	ATN1	95	.	0			c.A790T						.						45	43	43					12																	7045220		2203	4300	6503	SO:0001583	missense	1822	exon5			GTATCAAGCTCTG	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"dentatorubral-pallidoluysian atrophy (atrophin-1)"	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.790A>T	chr12.hg19:g.7045220A>T	ENSP00000349076:p.Ser264Cys	20.0	0.0		30.0	12.0	NM_001007026	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	hg19	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	a	13.12	2.142145	0.37825	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325	T;T;T	0.55052	0.54;0.54;0.54	3.51	1.1	0.20463	.	0.187765	0.26000	U	0.026951	T	0.26557	0.0649	N	0.14661	0.345	0.29885	N	0.825662	P;P	0.50369	0.758;0.934	B;B	0.37550	0.171;0.253	T	0.28332	-1.0047	10	0.59425	D	0.04	.	5.1633	0.15073	0.6358:0.0:0.3642:0.0	.	264;264	Q86V38;P54259	.;ATN1_HUMAN	C	264	ENSP00000349076:S264C;ENSP00000379915:S264C;ENSP00000441744:S264C	ENSP00000349076:S264C	S	+	1	0	ATN1	6915481	0.814000	0.29104	1.000000	0.80357	0.714000	0.41099	0.549000	0.23329	0.514000	0.28300	0.473000	0.43528	AGC	.	.		0.622	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		T	7045220	A	T	7045220	3	4	101	1	0	0	0	0	1	0	0	0	1111	72	3	4	804	4	ATN1	12	7045220	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	470129	7045220	126806675	382	14219										
SLC2A3	6515	hgsc.bcm.edu	37	chr12	8086448	8086448	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccagtgttgtagccaaattgGaaagagccgattgtagcaac	11	8	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:8086448G>T	ENST00000075120.7	-	2	306	c.66C>A	c.(64-66)ttC>ttA	p.F22L		NM_006931.2	NP_008862.1	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 3	22					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(14)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				Kidney(36;0.0866)		AGCCAAATTGGAAAGAGCCGA	0.443											OREG0021656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F22L	Colon(96;424 1461 14416 20933 23688)	Atlas-SNP	.											.	SLC2A3	83	.	0			c.C66A						.						97	94	95					12																	8086448		2203	4300	6503	SO:0001583	missense	6515	exon2			AAATTGGAAAGAG	M20681	CCDS8586.1	12p13.3	2013-05-22			ENSG00000059804	ENSG00000059804		"Solute carriers"	11007	protein-coding gene	gene with protein product		138170		GLUT3			Standard	NM_006931		Approved		uc001qtr.3	P11169	OTTHUMG00000133685	ENST00000075120.7:c.66C>A	chr12.hg19:g.8086448G>T	ENSP00000075120:p.Phe22Leu	71.0	0.0	646	159.0	12.0	NM_006931	B2R606|D3DUU6|Q6I9U2|Q9UG15	Missense_Mutation	SNP	ENST00000075120.7	hg19	CCDS8586.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870476	0.72065	.	.	ENSG00000059804	ENST00000075120	D	0.82167	-1.58	4.23	3.33	0.38152	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.062472	0.64402	D	0.000003	T	0.60689	0.2288	N	0.05534	-0.03	0.45216	D	0.998223	B	0.10296	0.003	B	0.20184	0.028	T	0.53989	-0.8360	10	0.12430	T	0.62	.	5.4377	0.16490	0.1094:0.2076:0.6829:0.0	.	22	P11169	GTR3_HUMAN	L	22	ENSP00000075120:F22L	ENSP00000075120:F22L	F	-	3	2	SLC2A3	7977715	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	1.215000	0.32431	2.370000	0.80446	0.543000	0.68304	TTC	.	.		0.443	SLC2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257914.1	NM_006931		T	8086448	G	T	8086448	3	4	101	1	0	0	0	0	1	0	0	0	14560	1165	41	3	1460	3	SLC2A3	12	8086448	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1041228	8086448	125765447	383	14220										
CLEC4E	26253	hgsc.bcm.edu	37	chr12	8692481	8692481	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggtgatgaaacaggcactgaGaaataggatggggatcccag	15	6	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:8692481G>A	ENST00000299663.3	-	2	265	c.100C>T	c.(100-102)Ctc>Ttc	p.L34F	CLEC4E_ENST00000545274.1_Missense_Mutation_p.L34F|CLEC4E_ENST00000446457.2_Missense_Mutation_p.L34F	NM_014358.2	NP_055173.1	Q9ULY5	CLC4E_HUMAN	C-type lectin domain family 4, member E	34					immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12	Lung SC(5;0.184)					CAGGCACTGAGAAATAGGATG	0.423																																					p.L34F		Atlas-SNP	.											.	CLEC4E	30	.	0			c.C100T						.						223	224	223					12																	8692481		2203	4300	6503	SO:0001583	missense	26253	exon2			CACTGAGAAATAG	AB024718	CCDS8594.1	12p13.31	2005-02-09		2005-02-09	ENSG00000166523	ENSG00000166523		"C-type lectin domain containing"	14555	protein-coding gene	gene with protein product		609962	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 9"	CLECSF9		10528209	Standard	NM_014358		Approved	mincle	uc001quo.1	Q9ULY5	OTTHUMG00000168675	ENST00000299663.3:c.100C>T	chr12.hg19:g.8692481G>A	ENSP00000299663:p.Leu34Phe	44.0	0.0		123.0	24.0	NM_014358	B2R6Q6	Missense_Mutation	SNP	ENST00000299663.3	hg19	CCDS8594.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.796740	0.50208	.	.	ENSG00000166523	ENST00000299663;ENST00000446457;ENST00000545274	T;T	0.52057	3.58;0.68	3.98	3.98	0.46160	.	0.000000	0.41294	D	0.000911	T	0.68183	0.2973	M	0.83384	2.64	0.34830	D	0.739567	D	0.89917	1.0	D	0.83275	0.996	T	0.78130	-0.2324	10	0.51188	T	0.08	.	11.7537	0.51863	0.0:0.0:1.0:0.0	.	34	Q9ULY5	CLC4E_HUMAN	F	34	ENSP00000299663:L34F;ENSP00000443034:L34F	ENSP00000299663:L34F	L	-	1	0	CLEC4E	8583748	0.991000	0.36638	0.916000	0.36221	0.417000	0.31264	2.600000	0.46240	2.223000	0.72356	0.655000	0.94253	CTC	.	.		0.423	CLEC4E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400566.1	NM_014358		A	8692481	G	A	8692481	3	1	101	1	0	0	0	0	1	0	0	0	3517	942	33	3	579	3	CLEC4E	12	8692481	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	606033	8692481	125159414	384	14221										
C12orf69	440087	hgsc.bcm.edu	37	chr12	14959587	14959587	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttcccgcctttttgggttctCtgggtaaaggaagtcacttt	10	9	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:14959587C>G	ENST00000316048.2	-	2	100	c.28G>C	c.(28-30)Gag>Cag	p.E10Q	C12orf60_ENST00000527783.1_Intron|C12orf60_ENST00000330828.2_Intron	NM_001013698.2	NP_001013720.2	A2RU48	SMCO3_HUMAN	single-pass membrane protein with coiled-coil domains 3	10						integral component of membrane (GO:0016021)											TTTGGGTTCTCTGGGTAAAGG	0.388																																					p.E10Q		Atlas-SNP	.											.	.	.	.	0			c.G28C						.						81	81	81					12																	14959587		1829	4091	5920	SO:0001583	missense	0	exon2			GGTTCTCTGGGTA		CCDS41759.1	12p12.3	2013-03-11	2013-03-11	2013-03-11	ENSG00000179256	ENSG00000179256			34401	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 69"	C12orf69			Standard	NM_001013698		Approved	LOC440087	uc001rck.1	A2RU48	OTTHUMG00000167474	ENST00000316048.2:c.28G>C	chr12.hg19:g.14959587C>G	ENSP00000381895:p.Glu10Gln	70.0	0.0		122.0	11.0	NM_001013698	Q8NAI5	Missense_Mutation	SNP	ENST00000316048.2	hg19	CCDS41759.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828948	0.32329	.	.	ENSG00000179256	ENST00000316048	T	0.33865	1.39	5.25	4.34	0.51931	.	0.641612	0.12334	N	0.478087	T	0.20901	0.0503	N	0.12182	0.205	0.21256	N	0.999747	B	0.09022	0.002	B	0.08055	0.003	T	0.17018	-1.0383	10	0.15952	T	0.53	-19.9399	11.3905	0.49811	0.0:0.8093:0.1907:0.0	.	10	A2RU48	CL069_HUMAN	Q	10	ENSP00000381895:E10Q	ENSP00000381895:E10Q	E	-	1	0	C12orf69	14850854	1.000000	0.71417	0.990000	0.47175	0.853000	0.48598	2.512000	0.45485	1.398000	0.46701	0.555000	0.69702	GAG	.	.		0.388	SMCO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394738.1	NM_001013698		G	14959587	C	G	14959587	3	3	101	1	0	0	0	0	1	0	0	0	1713	922	32	4	653	4	C12orf69	12	14959587	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	6267106	14959587	118892308	385	14222										
RECQL	5965	hgsc.bcm.edu	37	chr12	21643210	21643210	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	taacaagaaatacctcctttCcagccattgttacgttaata	4	10	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:21643210C>G	ENST00000444129.2	-	4	785	c.317G>C	c.(316-318)gGa>gCa	p.G106A	RECQL_ENST00000421138.2_Missense_Mutation_p.G106A	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	106	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)	membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						TACCTCCTTTCCAGCCATTGT	0.348								Other identified genes with known or suspected DNA repair function																													p.G106A		Atlas-SNP	.											.	RECQL	45	.	0			c.G317C						.						120	121	120					12																	21643210		2203	4300	6503	SO:0001583	missense	5965	exon5			TCCTTTCCAGCCA	D37984	CCDS31756.1	12p12.1	2014-03-07	2014-03-07	2014-03-07	ENSG00000004700	ENSG00000004700			9948	protein-coding gene	gene with protein product	"DNA helicase Q1-like"	600537	"RecQ protein-like (DNA helicase Q1-like)"			7527136, 7961977	Standard	NM_002907		Approved	RecQ1, RecQL1	uc001rex.3	P46063	OTTHUMG00000169131	ENST00000444129.2:c.317G>C	chr12.hg19:g.21643210C>G	ENSP00000416739:p.Gly106Ala	95.0	0.0		171.0	30.0	NM_032941	A8K6G2	Missense_Mutation	SNP	ENST00000444129.2	hg19	CCDS31756.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708568	0.89018	.	.	ENSG00000004700	ENST00000444129;ENST00000421138;ENST00000396093;ENST00000314748;ENST00000542432;ENST00000536240	T;T;T;T;T;T	0.76968	-0.97;-0.97;-0.53;-0.53;-0.53;-1.06	5.29	5.29	0.74685	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.117022	0.64402	D	0.000017	D	0.84790	0.5550	M	0.91038	3.17	0.58432	D	0.999992	P	0.48407	0.91	B	0.43575	0.424	D	0.88762	0.3258	10	0.66056	D	0.02	-1.1318	19.2899	0.94095	0.0:1.0:0.0:0.0	.	106	P46063	RECQ1_HUMAN	A	106	ENSP00000416739:G106A;ENSP00000395449:G106A;ENSP00000379400:G106A;ENSP00000318727:G106A;ENSP00000445555:G106A;ENSP00000439069:G106A	ENSP00000318727:G106A	G	-	2	0	RECQL	21534477	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.570000	0.82390	2.615000	0.88500	0.650000	0.86243	GGA	.	.		0.348	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907		G	21643210	C	G	21643210	3	3	101	1	0	0	0	0	1	0	0	0	13216	855	30	4	1680	4	RECQL	12	21643210	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	6683623	21643210	112208685	386	14223										
TENC1	23371	hgsc.bcm.edu	37	chr12	53446269	53446269	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggcgacgcacagaaaatgtgAagcaaaggtgggtatctgat	14	6	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:53446269A>T	ENST00000314250.6	+	3	505	c.215A>T	c.(214-216)gAa>gTa	p.E72V	RP11-983P16.4_ENST00000550601.1_RNA|TENC1_ENST00000549700.1_Missense_Mutation_p.E72V|TENC1_ENST00000379902.3_De_novo_Start_OutOfFrame|TENC1_ENST00000552570.1_Missense_Mutation_p.E72V|RP11-983P16.4_ENST00000546793.1_RNA|RP11-983P16.4_ENST00000551890.1_RNA|TENC1_ENST00000451358.1_Missense_Mutation_p.E72V|TENC1_ENST00000314276.3_Missense_Mutation_p.E82V|TENC1_ENST00000546602.1_Missense_Mutation_p.E72V	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	72					cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						AGAAAATGTGAAGCAAAGGTG	0.567																																					p.E82V		Atlas-SNP	.											.	TENC1	148	.	0			c.A245T						.						227	213	218					12																	53446269		2203	4300	6503	SO:0001583	missense	23371	exon3			AATGTGAAGCAAA	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	19737	protein-coding gene	gene with protein product	"tensin 2"	607717	"tensin like C1 domain-containing phosphatase"				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.215A>T	chr12.hg19:g.53446269A>T	ENSP00000319684:p.Glu72Val	64.0	0.0		173.0	24.0	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Missense_Mutation	SNP	ENST00000314250.6	hg19	CCDS8843.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.503466	0.85176	.	.	ENSG00000111077	ENST00000314276;ENST00000314250;ENST00000451358;ENST00000443113;ENST00000546602;ENST00000552570;ENST00000549700	D;D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73;-1.73	5.55	4.41	0.53225	Protein kinase C-like, phorbol ester/diacylglycerol binding (3);	0.000000	0.64402	D	0.000003	D	0.87966	0.6311	L	0.61218	1.895	0.40401	D	0.979645	D;D;D;D	0.89917	1.0;0.975;1.0;0.997	D;P;D;D	0.80764	0.963;0.668;0.983;0.994	D	0.88702	0.3216	10	0.87932	D	0	-3.8027	9.2442	0.37515	0.9148:0.0:0.0852:0.0	.	72;72;82;49	Q63HR2;F8W661;Q63HR2-4;Q6ZMJ1	TENC1_HUMAN;.;.;.	V	82;72;72;72;72;72;72	ENSP00000319756:E82V;ENSP00000319684:E72V;ENSP00000393362:E72V;ENSP00000449363:E72V;ENSP00000447021:E72V;ENSP00000449361:E72V	ENSP00000319684:E72V	E	+	2	0	TENC1	51732536	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.667000	0.54547	2.251000	0.74343	0.482000	0.46254	GAA	.	.		0.567	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754		T	53446269	A	T	53446269	3	4	101	1	0	0	0	0	1	0	0	0	15773	246	9	4	334	4	TENC1	12	53446269	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	31803059	53446269	80405626	387	14224										
HOXC4	3221	hgsc.bcm.edu	37	chr12	54447739	54447739	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcgtatttgatggactctaaCtacatcgatccgaaatttcc	6	10	1	1	rs377491433		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:54447739C>A	ENST00000430889.2	+	1	79	c.33C>A	c.(31-33)aaC>aaA	p.N11K	HOXC4_ENST00000609810.1_Missense_Mutation_p.N11K|HOXC4_ENST00000303406.4_Missense_Mutation_p.N11K	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	11					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						TGGACTCTAACTACATCGATC	0.423																																					p.N11K		Atlas-SNP	.											.	HOXC4	29	.	0			c.C33A						.						97	96	96					12																	54447739		2203	4300	6503	SO:0001583	missense	3221	exon3			CTCTAACTACATC		CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"Homeoboxes / ANTP class : HOXL subclass"	5126	protein-coding gene	gene with protein product		142974	"homeo box C4"	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.33C>A	chr12.hg19:g.54447739C>A	ENSP00000399808:p.Asn11Lys	38.0	0.0		135.0	14.0	NM_014620		Missense_Mutation	SNP	ENST00000430889.2	hg19	CCDS8873.1	.	.	.	.	.	.	.	.	.	.	C	12.51	1.960162	0.34565	.	.	ENSG00000198353	ENST00000303406;ENST00000430889	T;T	0.55234	0.53;0.53	3.41	3.41	0.39046	.	0.055508	0.64402	D	0.000002	T	0.62368	0.2422	L	0.46819	1.47	0.80722	D	1	D	0.63880	0.993	D	0.70227	0.968	T	0.57929	-0.7726	10	0.23302	T	0.38	.	14.7795	0.69754	0.0:1.0:0.0:0.0	.	11	P09017	HXC4_HUMAN	K	11	ENSP00000305973:N11K;ENSP00000399808:N11K	ENSP00000305973:N11K	N	+	3	2	HOXC4	52734006	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.319000	0.43788	2.187000	0.69744	0.462000	0.41574	AAC	.	.		0.423	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1			A	54447739	C	A	54447739	3	1	101	1	0	0	0	0	1	0	0	0	7322	564	20	3	35	3	HOXC4	12	54447739	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1001470	54447739	79404156	388	14225										
HOXC4	3221	hgsc.bcm.edu	37	chr12	54447841	54447841	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cggaccagggaatcgggattCcagcatcaccaccaggagct	12	13	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:54447841C>A	ENST00000430889.2	+	1	181	c.135C>A	c.(133-135)ttC>ttA	p.F45L	HOXC4_ENST00000609810.1_Missense_Mutation_p.F45L|HOXC4_ENST00000303406.4_Missense_Mutation_p.F45L	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	45					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						AATCGGGATTCCAGCATCACC	0.567																																					p.F45L		Atlas-SNP	.											.	HOXC4	29	.	0			c.C135A						.						124	132	129					12																	54447841		2203	4300	6503	SO:0001583	missense	3221	exon3			GGGATTCCAGCAT		CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"Homeoboxes / ANTP class : HOXL subclass"	5126	protein-coding gene	gene with protein product		142974	"homeo box C4"	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.135C>A	chr12.hg19:g.54447841C>A	ENSP00000399808:p.Phe45Leu	49.0	0.0		100.0	9.0	NM_014620		Missense_Mutation	SNP	ENST00000430889.2	hg19	CCDS8873.1	.	.	.	.	.	.	.	.	.	.	c	13.63	2.294124	0.40594	.	.	ENSG00000198353	ENST00000303406;ENST00000430889	T;T	0.80653	-1.4;-1.4	3.41	2.53	0.30540	.	0.503896	0.19881	N	0.103975	T	0.71592	0.3358	L	0.52266	1.64	0.46279	D	0.998966	B	0.25667	0.131	B	0.19666	0.026	T	0.67902	-0.5550	10	0.46703	T	0.11	.	7.4489	0.27227	0.0:0.7876:0.0:0.2124	.	45	P09017	HXC4_HUMAN	L	45	ENSP00000305973:F45L;ENSP00000399808:F45L	ENSP00000305973:F45L	F	+	3	2	HOXC4	52734108	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	1.449000	0.35123	1.009000	0.39289	-0.355000	0.07637	TTC	.	.		0.567	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1			A	54447841	C	A	54447841	3	1	101	1	0	0	0	0	1	0	0	0	7322	854	30	3	137	3	HOXC4	12	54447841	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	102	54447841	79404054	389	14226										
OR6C74	254783	hgsc.bcm.edu	37	chr12	55641327	55641327	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttcttgttagtatggcaacaGgtgataagaccatttcttac	8	7	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:55641327G>A	ENST00000343870.4	+	1	346	c.256G>A	c.(256-258)Ggt>Agt	p.G86S		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	86			G -> D (in dbSNP:rs6581025).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	12						TATGGCAACAGGTGATAAGAC	0.393																																					p.G86S		Atlas-SNP	.											.	OR6C74	52	.	0			c.G256A						.						197	199	198					12																	55641327		2203	4300	6503	SO:0001583	missense	254783	exon1			GCAACAGGTGATA		CCDS31816.1	12q13.13	2012-08-09			ENSG00000197706	ENSG00000197706		"GPCR / Class A : Olfactory receptors"	31303	protein-coding gene	gene with protein product							Standard	NM_001005490		Approved		uc010spg.2	A6NCV1	OTTHUMG00000165162	ENST00000343870.4:c.256G>A	chr12.hg19:g.55641327G>A	ENSP00000342836:p.Gly86Ser	92.0	0.0		284.0	30.0	NM_001005490		Missense_Mutation	SNP	ENST00000343870.4	hg19	CCDS31816.1	.	.	.	.	.	.	.	.	.	.	g	15.46	2.841617	0.51057	.	.	ENSG00000197706	ENST00000343870	T	0.02916	4.11	5.36	3.5	0.40072	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000062	T	0.04634	0.0126	L	0.51422	1.61	0.09310	N	1	P	0.39759	0.687	B	0.44133	0.442	T	0.22417	-1.0217	10	0.87932	D	0	.	6.9684	0.24635	0.1567:0.2468:0.5965:0.0	.	86	A6NCV1	O6C74_HUMAN	S	86	ENSP00000342836:G86S	ENSP00000342836:G86S	G	+	1	0	OR6C74	53927594	0.000000	0.05858	0.217000	0.23759	0.954000	0.61252	0.637000	0.24659	1.371000	0.46172	0.551000	0.68910	GGT	.	.		0.393	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1			A	55641327	G	A	55641327	3	1	101	1	0	0	0	0	1	0	0	0	11207	1000	35	3	258	3	OR6C74	12	55641327	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1193486	55641327	78210568	390	14227										
OR6C75	390323	hgsc.bcm.edu	37	chr12	55759521	55759521	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtaacactgatggtcaccttGacattagttattctctccta	6	10	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:55759521G>T	ENST00000343399.3	+	1	627	c.627G>T	c.(625-627)ttG>ttT	p.L209F		NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C, member 75	209						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)	25						TGGTCACCTTGACATTAGTTA	0.408																																					p.L209F		Atlas-SNP	.											.	OR6C75	67	.	0			c.G627T						.						147	129	135					12																	55759521		2203	4300	6503	SO:0001583	missense	390323	exon1			CACCTTGACATTA		CCDS31820.1	12q13.2	2013-09-23			ENSG00000187857	ENSG00000187857		"GPCR / Class A : Olfactory receptors"	31304	protein-coding gene	gene with protein product							Standard	NM_001005497		Approved		uc010spk.2	A6NL08	OTTHUMG00000169886	ENST00000343399.3:c.627G>T	chr12.hg19:g.55759521G>T	ENSP00000368987:p.Leu209Phe	141.0	0.0		371.0	16.0	NM_001005497		Missense_Mutation	SNP	ENST00000343399.3	hg19	CCDS31820.1	.	.	.	.	.	.	.	.	.	.	g	15.12	2.740123	0.49045	.	.	ENSG00000187857	ENST00000343399	T	0.40476	1.03	5.22	-0.481	0.12082	GPCR, rhodopsin-like superfamily (1);	0.201247	0.23896	N	0.043482	T	0.32224	0.0822	L	0.28274	0.84	0.09310	N	0.999996	P	0.45011	0.848	P	0.50825	0.651	T	0.15464	-1.0436	10	0.72032	D	0.01	.	3.0854	0.06276	0.2711:0.4368:0.1802:0.1119	.	209	A6NL08	O6C75_HUMAN	F	209	ENSP00000368987:L209F	ENSP00000368987:L209F	L	+	3	2	OR6C75	54045788	0.000000	0.05858	0.904000	0.35570	0.966000	0.64601	-2.394000	0.01054	-0.010000	0.14271	0.632000	0.83419	TTG	.	.		0.408	OR6C75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406418.1			T	55759521	G	T	55759521	3	4	101	1	0	0	0	0	1	0	0	0	11208	1281	45	3	629	3	OR6C75	12	55759521	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	118194	55759521	78092374	391	14228										
SLC39A5	283375	hgsc.bcm.edu	37	chr12	56628734	56628739	+	In_Frame_Del	DEL	GCTCCG	GCTCCG	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acagccgcgtctgcatcggcGctccggcccctgcaccccca					rs61731625|rs371921611	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	GCTCCG	GCTCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:56628734_56628739delGCTCCG	ENST00000266980.4	+	4	891_896	c.598_603delGCTCCG	c.(598-603)gctccgdel	p.AP204del	ANKRD52_ENST00000548241.1_5'Flank|SLC39A5_ENST00000454355.2_In_Frame_Del_p.AP204del	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	204					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTGCATCGGCGCTCCGGCCCCTGCAC	0.612																																					p.199_201del		Atlas-Indel,Pindel	.											.	SLC39A5	52	.	0			c.597_602del						.		,	3,4261		0,3,2129					,	-0.4	0.2			91	8,8246		0,8,4119	no	coding,coding	SLC39A5	NM_173596.2,NM_001135195.1	,	0,11,6248	A1A1,A1R,RR		0.0969,0.0704,0.0879	,	,		11,12507				SO:0001651	inframe_deletion	283375	exon6			.		CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"Solute carriers"	20502	protein-coding gene	gene with protein product		608730	"solute carrier family 39 (metal ion transporter), member 5"				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.598_603delGCTCCG	chr12.hg19:g.56628734_56628739delGCTCCG	ENSP00000266980:p.Ala204_Pro205del	16.0	0.0		55.0	23.0	NM_173596	B2R808|Q8N6Y3	In_Frame_Del	DEL	ENST00000266980.4	hg19	CCDS8912.2																																																																																			.	.		0.612	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596		-	56628739	GCTCCG	-	56628734	7	5	101	1	0	1	0	1	0	0	0	0	14636	1087	38	0	608	0	SLC39A5	12	56628734	In_Frame_Del	DEL	GCTCCG	TCGA-DD-A1EE-01A-11D-A12Z-10	869213	56628734	77223161	392	14229										
CNPY2	10330	hgsc.bcm.edu	37	chr12	56708752	56708752	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tccaccagagccctgcatgcTggtggaagaggagagaatga	14	9	0	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:56708752T>C	ENST00000273308.4	-	3	629		c.e3-2		RP11-977G19.11_ENST00000549565.1_RNA|RP11-977G19.10_ENST00000549318.1_Splice_Site|PAN2_ENST00000549090.1_5'Flank|RP11-977G19.11_ENST00000549860.1_RNA|CNPY2_ENST00000551720.1_Splice_Site	NM_014255.5	NP_055070.1	Q9Y2B0	CNPY2_HUMAN	canopy FGF signaling regulator 2						negative regulation of gene expression (GO:0010629)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of low-density lipoprotein particle clearance (GO:0010988)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)				large_intestine(2)|lung(2)	4						CCCTGCATGCTGGTGGAAGAG	0.537																																					.		Atlas-SNP	.											.	CNPY2	16	.	0			c.89-2A>G						.						71	66	68					12																	56708752		2203	4300	6503	SO:0001630	splice_region_variant	10330	exon4			GCATGCTGGTGGA	AB015631	CCDS8914.1	12q15	2013-07-23	2013-07-23	2007-10-22		ENSG00000257727			13529	protein-coding gene	gene with protein product		605861	"transmembrane protein 4", "canopy 2 homolog (zebrafish)"	TMEM4		10072769, 15905959	Standard	NM_001190991		Approved	HP10390, ZSIG9, Cnpy2	uc001sku.2	Q9Y2B0	OTTHUMG00000170330	ENST00000273308.4:c.89-2A>G	chr12.hg19:g.56708752T>C		55.0	0.0		144.0	15.0	NM_014255	B2R7B9|Q9UHE9	Splice_Site	SNP	ENST00000273308.4	hg19	CCDS8914.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937588	0.52972	.	.	ENSG00000144785;ENSG00000144785;ENSG00000144785;ENSG00000257727;ENSG00000257727	ENST00000549318;ENST00000547423;ENST00000548360;ENST00000273308;ENST00000551475	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9233	0.70856	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RP11-977G19.10;CNPY2	54995019	1.000000	0.71417	0.999000	0.59377	0.575000	0.36095	7.848000	0.86902	2.231000	0.72958	0.533000	0.62120	.	.	.		0.537	CNPY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408546.1	NM_014255	Intron	C	56708752	T	C	56708752	5	2	101	1	0	0	0	0	0	0	1	0	3630	1594	55	2	477	2	CNPY2	12	56708752	Splice_Site	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	80018	56708752	77143143	393	14230										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56993854	56993854	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cgagggtctggcgccagacaCgaatgcgaggggtgatctca	16	10	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:56993854C>A	ENST00000551812.1	-	25	5118	c.4925G>T	c.(4924-4926)cGt>cTt	p.R1642L	BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000379441.3_Missense_Mutation_p.R1612L|BAZ2A_ENST00000549884.1_Missense_Mutation_p.R1640L|BAZ2A_ENST00000179765.5_Missense_Mutation_p.R1610L	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1642					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R1642H(2)		breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						GCGCCAGACACGAATGCGAGG	0.572																																					p.R1642L		Atlas-SNP	.											BAZ2A_ENST00000551812,colon,carcinoma,0,2	BAZ2A	263	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4925T						.						81	82	82					12																	56993854		2002	4179	6181	SO:0001583	missense	11176	exon25			CAGACACGAATGC	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.4925G>T	chr12.hg19:g.56993854C>A	ENSP00000446880:p.Arg1642Leu	55.0	0.0		198.0	20.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.001011	0.93227	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.71698	-0.34;-0.34;-0.36;-0.59;-0.36	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.80428	0.4621	L	0.47716	1.5	0.80722	D	1	D;P;B;D	0.89917	0.999;0.524;0.272;1.0	D;P;B;D	0.91635	0.996;0.498;0.302;0.999	T	0.77305	-0.2637	10	0.35671	T	0.21	-14.6921	18.5763	0.91155	0.0:1.0:0.0:0.0	.	1640;1638;1642;1615	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	L	1612;1610;1642;574;1640	ENSP00000368754:R1612L;ENSP00000179765:R1610L;ENSP00000446880:R1642L;ENSP00000448760:R574L;ENSP00000447941:R1640L	ENSP00000179765:R1610L	R	-	2	0	BAZ2A	55280121	1.000000	0.71417	0.962000	0.40283	0.989000	0.77384	5.568000	0.67385	2.763000	0.94921	0.650000	0.86243	CGT	.	.		0.572	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		A	56993854	C	A	56993854	3	1	101	1	0	0	0	0	1	0	0	0	1331	536	19	1	812	1	BAZ2A	12	56993854	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	285102	56993854	76858041	394	14231										
LRP1	4035	hgsc.bcm.edu	37	chr12	57571304	57571304	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcaccgtgcaccgggagaccGgctctgggggctggcccaac	16	15	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:57571304G>T	ENST00000243077.3	+	26	4757	c.4291G>T	c.(4291-4293)Ggc>Tgc	p.G1431C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1431					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCGGGAGACCGGCTCTGGGGG	0.667																																					p.G1431C		Atlas-SNP	.											.	LRP1	428	.	0			c.G4291T						.						36	37	37					12																	57571304		2203	4300	6503	SO:0001583	missense	4035	exon26			GAGACCGGCTCTG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.4291G>T	chr12.hg19:g.57571304G>T	ENSP00000243077:p.Gly1431Cys	45.0	0.0		130.0	19.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	18.48	3.632881	0.67015	.	.	ENSG00000123384	ENST00000243077	D	0.93604	-3.25	4.71	4.71	0.59529	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000001	D	0.94291	0.8166	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94669	0.7855	10	0.56958	D	0.05	.	16.9684	0.86293	0.0:0.0:1.0:0.0	.	1431	Q07954	LRP1_HUMAN	C	1431	ENSP00000243077:G1431C	ENSP00000243077:G1431C	G	+	1	0	LRP1	55857571	1.000000	0.71417	0.928000	0.36995	0.670000	0.39368	7.715000	0.84713	2.631000	0.89168	0.462000	0.41574	GGC	.	.		0.667	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57571304	G	T	57571304	3	4	101	1	0	0	0	0	1	0	0	0	8960	1116	39	1	4393	1	LRP1	12	57571304	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	577450	57571304	76280591	395	14232										
TBK1	29110	hgsc.bcm.edu	37	chr12	64882345	64882345	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acattggatttctgtatcagAaacattgaaaaaactgtgaa	7	5	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:64882345A>G	ENST00000331710.5	+	12	1758	c.1419A>G	c.(1417-1419)agA>agG	p.R473R		NM_013254.3	NP_037386.1	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	473					defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of gene expression (GO:0010629)|negative regulation of type I interferon production (GO:0032480)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon production (GO:0032606)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)	ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)	20				GBM - Glioblastoma multiforme(28;0.0386)		TCTGTATCAGAAACATTGAAA	0.274																																					p.R473R		Atlas-SNP	.											.	TBK1	149	.	0			c.A1419G						.						49	50	49					12																	64882345		2196	4299	6495	SO:0001819	synonymous_variant	29110	exon12			TATCAGAAACATT	AF191838	CCDS8968.1	12q14.2	2006-06-10			ENSG00000183735	ENSG00000183735			11584	protein-coding gene	gene with protein product		604834				10581243, 10783893	Standard	NM_013254		Approved	NAK	uc001ssc.2	Q9UHD2	OTTHUMG00000168796	ENST00000331710.5:c.1419A>G	chr12.hg19:g.64882345A>G		116.0	0.0		298.0	116.0	NM_013254	A8K4S4|Q8IYV3|Q9NUJ5	Silent	SNP	ENST00000331710.5	hg19	CCDS8968.1																																																																																			.	.		0.274	TBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401130.1	NM_013254		G	64882345	A	G	64882345	2	3	101	1	0	0	0	0	0	0	0	1	15652	243	9	2		2	TBK1	12	64882345	Silent	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	7311041	64882345	68969550	396	14233										
WIF1	11197	hgsc.bcm.edu	37	chr12	65448938	65448938	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgccaaccttcttgacattgGcatttgttgggttcatggca	10	9	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:65448938G>C	ENST00000286574.4	-	9	1352	c.978C>G	c.(976-978)tgC>tgG	p.C326W		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	326	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		CTTGACATTGGCATTTGTTGG	0.393			T	HMGA2	pleomorphic salivary gland adenoma																																p.C326W	Esophageal Squamous(148;1595 1816 48559 49439 49664)	Atlas-SNP	.		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	WIF1	96	.	0			c.C978G						.						92	87	89					12																	65448938		2203	4300	6503	SO:0001583	missense	11197	exon9			ACATTGGCATTTG	AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.978C>G	chr12.hg19:g.65448938G>C	ENSP00000286574:p.Cys326Trp	69.0	0.0		98.0	7.0	NM_007191	Q6UXI1|Q8WVG4	Missense_Mutation	SNP	ENST00000286574.4	hg19	CCDS8971.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.851565	0.51270	.	.	ENSG00000156076	ENST00000286574;ENST00000543094	D;D	0.99984	-11.36;-6.54	5.71	3.89	0.44902	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99986	0.9997	H	0.95611	3.695	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.96261	0.9191	9	.	.	.	.	9.9417	0.41585	0.2071:0.0:0.7929:0.0	.	326	Q9Y5W5	WIF1_HUMAN	W	326;75	ENSP00000286574:C326W;ENSP00000439024:C75W	.	C	-	3	2	WIF1	63735205	1.000000	0.71417	0.998000	0.56505	0.601000	0.36947	3.540000	0.53611	0.887000	0.36136	0.655000	0.94253	TGC	.	.		0.393	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2			C	65448938	G	C	65448938	3	2	101	1	0	0	0	0	1	0	0	0	17381	1195	42	4	169	4	WIF1	12	65448938	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	566593	65448938	68402957	397	14234										
OSBPL8	114882	hgsc.bcm.edu	37	chr12	76752567	76752567	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttctgttgcctggttggctTatgtttcattttggggacgc	12	8	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:76752567T>A	ENST00000261183.3	-	22	2832	c.2353A>T	c.(2353-2355)Aag>Tag	p.K785*	OSBPL8_ENST00000393250.4_Nonsense_Mutation_p.K743*|OSBPL8_ENST00000393249.2_Nonsense_Mutation_p.K743*	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	785					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						CTGGTTGGCTTATGTTTCATT	0.368																																					p.K785X		Atlas-SNP	.											.	OSBPL8	86	.	0			c.A2353T						.						194	173	180					12																	76752567		2203	4300	6503	SO:0001587	stop_gained	114882	exon22			TTGGCTTATGTTT	AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.2353A>T	chr12.hg19:g.76752567T>A	ENSP00000261183:p.Lys785*	133.0	0.0		219.0	80.0	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Nonsense_Mutation	SNP	ENST00000261183.3	hg19	CCDS31862.1	.	.	.	.	.	.	.	.	.	.	T	44	10.572060	0.99430	.	.	ENSG00000091039	ENST00000393249;ENST00000261183;ENST00000446075;ENST00000393250	.	.	.	5.88	5.88	0.94601	.	0.120578	0.53938	D	0.000051	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.2044	15.9407	0.79750	0.0:0.0:0.0:1.0	.	.	.	.	X	743;785;770;743	.	ENSP00000261183:K785X	K	-	1	0	OSBPL8	75276698	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.264000	0.51553	2.243000	0.73865	0.533000	0.62120	AAG	.	.		0.368	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841		A	76752567	T	A	76752567	4	1	101	1	0	0	0	0	0	1	0	0	11292	1763	61	4	328	4	OSBPL8	12	76752567	Nonsense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	11303629	76752567	57099328	398	14235										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81746949	81746949	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cctgaagcatcatggctagcGtctgggcatcggaatgacca	12	11	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:81746949G>T	ENST00000549396.1	-	17	2103	c.1943C>A	c.(1942-1944)aCg>aAg	p.T648K	PPFIA2_ENST00000550584.2_Missense_Mutation_p.T648K|PPFIA2_ENST00000443686.3_Missense_Mutation_p.T549K|PPFIA2_ENST00000541017.1_5'UTR|PPFIA2_ENST00000541570.2_Missense_Mutation_p.T215K|PPFIA2_ENST00000333447.7_Missense_Mutation_p.T630K|PPFIA2_ENST00000548586.1_Missense_Mutation_p.T648K|PPFIA2_ENST00000407050.4_Missense_Mutation_p.T574K|PPFIA2_ENST00000552948.1_Missense_Mutation_p.T648K|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000549325.1_Missense_Mutation_p.T630K|PPFIA2_ENST00000550359.2_Missense_Mutation_p.T495K	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	648					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						CATGGCTAGCGTCTGGGCATC	0.383																																					p.T648K		Atlas-SNP	.											.	PPFIA2	207	.	0			c.C1943A						.						148	142	144					12																	81746949		1952	4174	6126	SO:0001583	missense	8499	exon16			GCTAGCGTCTGGG	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.1943C>A	chr12.hg19:g.81746949G>T	ENSP00000450337:p.Thr648Lys	85.0	0.0		163.0	7.0	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	hg19	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.043873	0.93685	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000541570;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948;ENST00000553058	T;T;T;T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.56863	0.2014	M	0.83312	2.635	0.80722	D	1	D	0.63880	0.993	D	0.74023	0.982	T	0.61811	-0.6986	10	0.66056	D	0.02	-17.3587	19.2605	0.93966	0.0:0.0:1.0:0.0	.	648	O75334	LIPA2_HUMAN	K	648;630;215;574;659;630;648;549;648;229	ENSP00000450337:T648K;ENSP00000450298:T630K;ENSP00000438337:T215K;ENSP00000385093:T574K;ENSP00000327416:T630K;ENSP00000449338:T648K;ENSP00000388373:T549K;ENSP00000447868:T648K;ENSP00000448941:T229K	ENSP00000327416:T630K	T	-	2	0	PPFIA2	80271080	1.000000	0.71417	0.958000	0.39756	0.960000	0.62799	9.799000	0.99117	2.534000	0.85438	0.585000	0.79938	ACG	.	.		0.383	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			T	81746949	G	T	81746949	3	4	101	1	0	0	0	0	1	0	0	0	12319	1145	40	1	1894	1	PPFIA2	12	81746949	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	4994382	81746949	52104946	399	14236										
ALX1	8092	hgsc.bcm.edu	37	chr12	85674229	85674229	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cccgcgccgagcatcacgtgCgcttggagaggacctcgccc	13	17	1	1	rs145944049	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:85674229C>A	ENST00000316824.3	+	1	345	c.190C>A	c.(190-192)Cgc>Agc	p.R64S		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	64					anterior/posterior pattern specification (GO:0009952)|brain development (GO:0007420)|cartilage condensation (GO:0001502)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|mesenchymal cell development (GO:0014031)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1)	26				GBM - Glioblastoma multiforme(134;0.134)		GCATCACGTGCGCTTGGAGAG	0.637																																					p.R64S		Atlas-SNP	.											.	ALX1	61	.	0			c.C190A						.						32	33	32					12																	85674229		2203	4300	6503	SO:0001583	missense	8092	exon1			CACGTGCGCTTGG	U31986	CCDS9028.1	12q21.31	2011-06-20	2007-07-26	2007-07-26		ENSG00000180318		"Homeoboxes / PRD class"	1494	protein-coding gene	gene with protein product		601527	"cartilage paired-class homeoprotein 1"	CART1		8756334, 7592751	Standard	NM_006982		Approved		uc001tae.4	Q15699	OTTHUMG00000169820	ENST00000316824.3:c.190C>A	chr12.hg19:g.85674229C>A	ENSP00000315417:p.Arg64Ser	20.0	0.0		45.0	24.0	NM_006982	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	hg19	CCDS9028.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.784563	0.49997	.	.	ENSG00000180318	ENST00000316824	D	0.92199	-2.99	5.48	4.51	0.55191	.	0.188276	0.43747	D	0.000540	D	0.88760	0.6524	N	0.08118	0	0.44515	D	0.997462	D	0.53745	0.962	D	0.65010	0.931	D	0.84476	0.0602	10	0.10636	T	0.68	.	13.0251	0.58810	0.2775:0.7225:0.0:0.0	.	64	Q15699	ALX1_HUMAN	S	64	ENSP00000315417:R64S	ENSP00000315417:R64S	R	+	1	0	ALX1	84198360	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.730000	0.38125	2.563000	0.86464	0.655000	0.94253	CGC	.	C|0.997;T|0.003		0.637	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982		A	85674229	C	A	85674229	3	1	101	1	0	0	0	0	1	0	0	0	556	768	27	1	192	1	ALX1	12	85674229	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3927280	85674229	48177666	400	14237										
GALNT4	8693	hgsc.bcm.edu	37	chr12	89916661	89916662	+	Frame_Shift_Ins	INS	-	-	A													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atttgtacatcaggtcggccINSctccggtgtccgataagcac							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:89916661_89916662insA	ENST00000529983.2	-	1	1921_1922	c.1665_1666insT	c.(1663-1668)gagggcfs	p.G556fs	POC1B_ENST00000549504.1_Intron|POC1B_ENST00000549035.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000541909.1_Intron|GALNT4_ENST00000413530.1_Frame_Shift_Ins_p.G384fs|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000313546.3_Intron|POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B-GALNT4_ENST00000548729.1_Frame_Shift_Ins_p.G553fs	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	556	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						TCAGGTCGGCCCTCCGGTGTCC	0.416																																					p.G556fs		Atlas-INDEL	.											.	GALNT4	38	.	0			c.1666_1667insT						.																																			SO:0001589	frameshift_variant	8693	exon1			.	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4126	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 4"	603565	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.1665_1666insT	chr12.hg19:g.89916661_89916662insA	ENSP00000436604:p.Gly556fs	113.0	0.0		196.0	26.0	NM_003774	B2R775|B4DMX6|O00208	Frame_Shift_Ins	INS	ENST00000529983.2	hg19	CCDS53817.1																																																																																			.	.		0.416	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774		A	89916662	-	A	89916661	7	5	101	1	0	1	1	0	0	0	0	0	6223	623	22	0	74	0	GALNT4	12	89916661	Frame_Shift_Ins	INS	-	TCGA-DD-A1EE-01A-11D-A12Z-10	4242432	89916661	43935234	401	14238										
FGD6	55785	hgsc.bcm.edu	37	chr12	95603522	95603522	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccaaaagctcctcggaggcaGcctttttaagcactcctgta	8	13	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:95603522G>C	ENST00000343958.4	-	2	1761	c.1538C>G	c.(1537-1539)gCt>gGt	p.A513G	FGD6_ENST00000549499.1_Missense_Mutation_p.A513G|FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000546711.1_Missense_Mutation_p.A513G	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	513					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						CTCGGAGGCAGCCTTTTTAAG	0.393																																					p.A513G		Atlas-SNP	.											.	FGD6	127	.	0			c.C1538G						.						68	75	73					12																	95603522		2198	4297	6495	SO:0001583	missense	55785	exon2			GAGGCAGCCTTTT	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.1538C>G	chr12.hg19:g.95603522G>C	ENSP00000344446:p.Ala513Gly	79.0	0.0		184.0	8.0	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	hg19	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.016558	0.75161	.	.	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	T;T;T	0.73469	-0.64;-0.75;-0.72	6.04	6.04	0.98038	.	0.000000	0.48767	D	0.000171	D	0.85075	0.5614	M	0.64997	1.995	0.46564	D	0.999101	D	0.76494	0.999	D	0.65443	0.935	D	0.84873	0.0826	10	0.72032	D	0.01	-16.7761	20.5792	0.99380	0.0:0.0:1.0:0.0	.	513	Q6ZV73	FGD6_HUMAN	G	513	ENSP00000344446:A513G;ENSP00000450342:A513G;ENSP00000449005:A513G	ENSP00000344446:A513G	A	-	2	0	FGD6	94127653	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.262000	0.65501	2.873000	0.98535	0.561000	0.74099	GCT	.	.		0.393	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		C	95603522	G	C	95603522	3	2	101	1	0	0	0	0	1	0	0	0	5845	971	34	4	2834	4	FGD6	12	95603522	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	5686861	95603522	38248373	402	14239										
TMPO	7112	hgsc.bcm.edu	37	chr12	98938066	98938066	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aagtggatcttcaaaaggcgGacctctgcaggcattaacta	10	9	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:98938066G>A	ENST00000556029.1	+	5	1078	c.722G>A	c.(721-723)gGa>gAa	p.G241E	TMPO_ENST00000548223.1_3'UTR|TMPO_ENST00000393053.2_Intron|TMPO_ENST00000343315.5_Intron	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	241	NAKAP95-binding N.|Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TCAAAAGGCGGACCTCTGCAG	0.408																																					p.G241E		Atlas-SNP	.											.	TMPO	111	.	0			c.G722A						.						86	87	87					12																	98938066		2203	4300	6503	SO:0001583	missense	7112	exon5			AAGGCGGACCTCT		CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.722G>A	chr12.hg19:g.98938066G>A	ENSP00000450627:p.Gly241Glu	92.0	0.0		261.0	34.0	NM_001032283	A2T926|Q14861	Missense_Mutation	SNP	ENST00000556029.1	hg19	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.187716	0.78789	.	.	ENSG00000120802	ENST00000556029	T	0.71579	-0.58	5.75	5.75	0.90469	.	.	.	.	.	T	0.81735	0.4885	L	0.53249	1.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77167	-0.2687	9	0.28530	T	0.3	.	19.9478	0.97189	0.0:0.0:1.0:0.0	.	241	P42167	LAP2B_HUMAN	E	241	ENSP00000450627:G241E	ENSP00000340251:G241E	G	+	2	0	TMPO	97462197	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.473000	0.73572	2.712000	0.92718	0.591000	0.81541	GGA	.	.		0.408	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		A	98938066	G	A	98938066	3	1	101	1	0	0	0	0	1	0	0	0	16252	1174	41	3	2264	3	TMPO	12	98938066	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3334544	98938066	34913829	403	14240										
ALDH1L2	160428	hgsc.bcm.edu	37	chr12	105431912	105431919	+	Frame_Shift_Del	DEL	TTAAATAT	TTAAATAT	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccttgtcaagttcacagtcaTtaaatattataagtggagac							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	TTAAATAT	TTAAATAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:105431912_105431919delTTAAATAT	ENST00000258494.9	-	18	2247_2254	c.2107_2114delATATTTAA	c.(2107-2115)atatttaatfs	p.IFN703fs	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	703	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						TTCACAGTCATTAAATATTATAAGTGGA	0.423																																					p.703_705del		Atlas-Indel,Pindel	.											.	ALDH1L2	71	.	0			c.2108_2115del						.																																			SO:0001589	frameshift_variant	160428	exon18			.	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2107_2114delATATTTAA	chr12.hg19:g.105431912_105431919delTTAAATAT	ENSP00000258494:p.Ile703fs	56.0	0.0		105.0	34.0	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Frame_Shift_Del	DEL	ENST00000258494.9	hg19	CCDS31891.1																																																																																			.	.		0.423	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		-	105431919	TTAAATAT	-	105431912	7	5	101	1	0	1	0	1	0	0	0	0	495	1493	52	0	681	0	ALDH1L2	12	105431912	Frame_Shift_Del	DEL	TTAAATAT	TCGA-DD-A1EE-01A-11D-A12Z-10	6493846	105431912	28419983	404	14241										
ALDH1L2	160428	hgsc.bcm.edu	37	chr12	105464456	105464456	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgggaatgaactgagtgcagAaagggagcacatttagctct	13	6	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:105464456A>G	ENST00000258494.9	-	3	460	c.320T>C	c.(319-321)tTc>tCc	p.F107S	RP11-61E11.1_ENST00000547750.1_RNA|ALDH1L2_ENST00000424857.2_Missense_Mutation_p.F107S	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	107	GART.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						CTGAGTGCAGAAAGGGAGCAC	0.498																																					p.F107S		Atlas-SNP	.											.	ALDH1L2	71	.	0			c.T320C						.						168	137	147					12																	105464456		2203	4300	6503	SO:0001583	missense	160428	exon3			GTGCAGAAAGGGA	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.320T>C	chr12.hg19:g.105464456A>G	ENSP00000258494:p.Phe107Ser	99.0	0.0		208.0	15.0	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	hg19	CCDS31891.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.683030	0.88542	.	.	ENSG00000136010	ENST00000258494;ENST00000424857	T;T	0.75367	-0.93;-0.93	5.27	5.27	0.74061	Formyl transferase, N-terminal (3);	0.047094	0.85682	D	0.000000	T	0.80607	0.4655	L	0.45470	1.425	0.80722	D	1	D	0.59767	0.986	D	0.72075	0.976	T	0.81924	-0.0710	10	0.72032	D	0.01	.	10.6981	0.45911	0.8576:0.0:0.0:0.1424	.	107	Q3SY69	AL1L2_HUMAN	S	107	ENSP00000258494:F107S;ENSP00000389608:F107S	ENSP00000258494:F107S	F	-	2	0	ALDH1L2	103988586	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.217000	0.77982	2.133000	0.65898	0.533000	0.62120	TTC	.	.		0.498	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		G	105464456	A	G	105464456	3	3	101	1	0	0	0	0	1	0	0	0	495	246	9	2	2535	2	ALDH1L2	12	105464456	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	32544	105464456	28387439	405	14242										
IFT81	28981	hgsc.bcm.edu	37	chr12	110581329	110581331	+	In_Frame_Del	DEL	TCT	TCT	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccagctatgggccattctgaTcttcttgaacttgaatctaa					rs372365248		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:110581329_110581331delTCT	ENST00000242591.5	+	9	1430_1432	c.924_926delTCT	c.(922-927)gatctt>gat	p.L310del	IFT81_ENST00000361948.4_In_Frame_Del_p.L310del|IFT81_ENST00000552912.1_In_Frame_Del_p.L310del|IFT81_ENST00000549009.1_3'UTR	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	310					cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|spermatogenesis (GO:0007283)	centrosome (GO:0005813)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)	tubulin binding (GO:0015631)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)	10						GCCATTCTGATCTTCTTGAACTT	0.305																																					p.308_309del		Atlas-Indel,Pindel	.											.	IFT81	86	.	0			c.923_925del						.																																			SO:0001651	inframe_deletion	28981	exon9			.	AF139540	CCDS9142.1, CCDS41831.1	12q24.13	2014-07-03	2014-07-03	2005-11-02		ENSG00000122970		"Intraflagellar transport homologs"	14313	protein-coding gene	gene with protein product		605489	"carnitine deficiency-associated, expressed in ventricle 1", "intraflagellar transport 81 homolog (Chlamydomonas)"	CDV1		11130971	Standard	NM_014055		Approved	CDV-1R, MGC4027	uc001tqi.3	Q8WYA0	OTTHUMG00000169326	ENST00000242591.5:c.924_926delTCT	chr12.hg19:g.110581332_110581334delTCT	ENSP00000242591:p.Leu310del	85.0	0.0		142.0	45.0	NM_014055	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	In_Frame_Del	DEL	ENST00000242591.5	hg19	CCDS41831.1																																																																																			.	.		0.305	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055		-	110581331	TCT	-	110581329	7	5	101	1	0	1	0	1	0	0	0	0	7574	1432	50	0	954	0	IFT81	12	110581329	In_Frame_Del	DEL	TCT	TCGA-DD-A1EE-01A-11D-A12Z-10	5116873	110581329	23270566	406	14243										
BRAP	8315	hgsc.bcm.edu	37	chr12	112093435	112093435	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtagattcgctgagattccaGctggcttgttagtaaatatg	11	6	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:112093435G>C	ENST00000327551.6	-	10	1296	c.1156C>G	c.(1156-1158)Ctg>Gtg	p.L386V	BRAP_ENST00000419234.4_Missense_Mutation_p.L416V|BRAP_ENST00000539060.1_Missense_Mutation_p.L237V			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	0					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						TGAGATTCCAGCTGGCTTGTT	0.383																																					p.L416V	Pancreas(146;846 1904 7830 25130 26065)	Atlas-SNP	.											.	BRAP	42	.	0			c.C1246G						.						155	134	141					12																	112093435		2203	4300	6503	SO:0001583	missense	8315	exon10			ATTCCAGCTGGCT	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"RING-type (C3HC4) zinc fingers"	1099	protein-coding gene	gene with protein product	"impedes mitogenic signal propagation", "galectin-2-binding protein"	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.1156C>G	chr12.hg19:g.112093435G>C	ENSP00000330813:p.Leu386Val	75.0	0.0		124.0	12.0	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000327551.6	hg19		.	.	.	.	.	.	.	.	.	.	G	19.68	3.873277	0.72180	.	.	ENSG00000089234	ENST00000419234;ENST00000539060;ENST00000327551;ENST00000547043	T;T;T	0.70164	-0.46;-0.46;-0.46	5.16	4.27	0.50696	.	0.000000	0.85682	D	0.000000	D	0.84000	0.5376	M	0.92459	3.31	0.80722	D	1	P;D	0.69078	0.956;0.997	P;D	0.78314	0.899;0.991	D	0.86081	0.1544	10	0.59425	D	0.04	-10.2253	10.9941	0.47565	0.1504:0.0:0.8496:0.0	.	237;416	B4DRM1;Q7Z569	.;BRAP_HUMAN	V	416;237;386;198	ENSP00000403524:L416V;ENSP00000441659:L237V;ENSP00000330813:L386V	ENSP00000330813:L386V	L	-	1	2	BRAP	110577818	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.188000	0.65093	1.181000	0.42912	0.561000	0.74099	CTG	.	.		0.383	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			C	112093435	G	C	112093435	3	2	101	1	0	0	0	0	1	0	0	0	1499	962	34	4	544	4	BRAP	12	112093435	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1512106	112093435	21758460	407	14244										
MED13L	23389	hgsc.bcm.edu	37	chr12	116429410	116429410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaagatattcatcacggaatCggagagaatcagggtaacat	10	6	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:116429410C>T	ENST00000281928.3	-	17	3555	c.3349G>A	c.(3349-3351)Gat>Aat	p.D1117N		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1117						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		ATCACGGAATCGGAGAGAATC	0.527																																					p.D1117N		Atlas-SNP	.											.	MED13L	193	.	0			c.G3349A						.						61	60	61					12																	116429410		2203	4300	6503	SO:0001583	missense	23389	exon17			CGGAATCGGAGAG	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.3349G>A	chr12.hg19:g.116429410C>T	ENSP00000281928:p.Asp1117Asn	47.0	0.0		209.0	21.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.708388	0.68615	.	.	ENSG00000123066	ENST00000281928	D	0.86097	-2.07	5.18	5.18	0.71444	.	0.140018	0.64402	D	0.000006	D	0.83312	0.5227	M	0.64997	1.995	0.80722	D	1	P	0.39551	0.678	B	0.33339	0.162	D	0.86056	0.1529	10	0.87932	D	0	.	18.8897	0.92395	0.0:1.0:0.0:0.0	.	1117	Q71F56	MD13L_HUMAN	N	1117	ENSP00000281928:D1117N	ENSP00000281928:D1117N	D	-	1	0	MED13L	114913793	1.000000	0.71417	0.935000	0.37517	0.843000	0.47879	7.320000	0.79064	2.699000	0.92147	0.460000	0.39030	GAT	.	.		0.527	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			T	116429410	C	T	116429410	3	4	101	1	0	0	0	0	1	0	0	0	9440	884	31	1	3343	1	MED13L	12	116429410	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4335975	116429410	17422485	408	14245										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124305198	124305198	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gccgtcaggaactggctaacGctgagaaacttttcgatctt	10	10	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:124305198G>T	ENST00000409039.3	+	23	3743	c.3718G>T	c.(3718-3720)Gct>Tct	p.A1240S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1240	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		ACTGGCTAACGCTGAGAAACT	0.428																																					p.A1240S		Atlas-SNP	.											.	DNAH10	888	.	0			c.G3718T						.						123	125	125					12																	124305198		1907	4132	6039	SO:0001583	missense	196385	exon23			GCTAACGCTGAGA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.3718G>T	chr12.hg19:g.124305198G>T	ENSP00000386770:p.Ala1240Ser	81.0	0.0		174.0	14.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	14.73	2.622632	0.46840	.	.	ENSG00000197653	ENST00000409039	T	0.22539	1.95	5.18	5.18	0.71444	.	.	.	.	.	T	0.39572	0.1083	M	0.72479	2.2	0.53688	D	0.999971	D	0.53745	0.962	P	0.58013	0.831	T	0.19976	-1.0289	9	0.09843	T	0.71	.	18.6962	0.91601	0.0:0.0:1.0:0.0	.	1240	Q8IVF4	DYH10_HUMAN	S	1240	ENSP00000386770:A1240S	ENSP00000386770:A1240S	A	+	1	0	DNAH10	122871151	1.000000	0.71417	0.819000	0.32651	0.092000	0.18411	5.607000	0.67648	2.409000	0.81822	0.555000	0.69702	GCT	.	.		0.428	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124305198	G	T	124305198	3	4	101	1	0	0	0	0	1	0	0	0	4600	1087	38	1	3808	1	DNAH10	12	124305198	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	7875788	124305198	9546697	409	14246										
DHX37	57647	hgsc.bcm.edu	37	chr12	125453127	125453127	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agaccttccggaagcactcgCcactgtagtcttccagcggt	10	14	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:125453127C>A	ENST00000308736.2	-	10	1459	c.1361G>T	c.(1360-1362)gGc>gTc	p.G454V	DHX37_ENST00000544745.1_Missense_Mutation_p.G241V	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	454							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		GAAGCACTCGCCACTGTAGTC	0.612																																					p.G454V		Atlas-SNP	.											.	DHX37	114	.	0			c.G1361T						.						133	133	133					12																	125453127		2203	4300	6503	SO:0001583	missense	57647	exon10			CACTCGCCACTGT	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.1361G>T	chr12.hg19:g.125453127C>A	ENSP00000311135:p.Gly454Val	15.0	0.0		57.0	7.0	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	hg19	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.756702	0.31137	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.03831	3.79;3.79	4.6	4.6	0.57074	.	0.104012	0.64402	D	0.000003	T	0.07773	0.0195	M	0.63428	1.95	0.80722	D	1	B	0.14438	0.01	B	0.17098	0.017	T	0.12372	-1.0550	10	0.32370	T	0.25	-27.7653	13.9708	0.64240	0.0:0.847:0.153:0.0	.	454	Q8IY37	DHX37_HUMAN	V	454;241	ENSP00000311135:G454V;ENSP00000439009:G241V	ENSP00000311135:G454V	G	-	2	0	DHX37	124019080	0.998000	0.40836	0.770000	0.31555	0.759000	0.43091	3.530000	0.53539	2.263000	0.75096	0.561000	0.74099	GGC	.	.		0.612	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		A	125453127	C	A	125453127	3	1	101	1	0	0	0	0	1	0	0	0	4512	739	26	3	2184	3	DHX37	12	125453127	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1147929	125453127	8398768	410	14247										
ZNF10	7556	hgsc.bcm.edu	37	chr12	133733009	133733009	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcagacagagcacacatctcAttctgcatcagagaacccat	6	13	4	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr12:133733009A>G	ENST00000248211.6	+	5	1399	c.1177A>G	c.(1177-1179)Att>Gtt	p.I393V	ZNF10_ENST00000402932.2_Missense_Mutation_p.I259V|ZNF10_ENST00000426665.2_Missense_Mutation_p.I393V|ZNF268_ENST00000416488.1_Intron|CTD-2140B24.4_ENST00000540096.2_Intron	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CACACATCTCATTCTGCATCA	0.438																																					p.I393V		Atlas-SNP	.											.	ZNF10	58	.	0			c.A1177G						.						161	162	162					12																	133733009		2203	4300	6503	SO:0001583	missense	7556	exon5			CATCTCATTCTGC	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"Zinc fingers, C2H2-type", "-"	12879	protein-coding gene	gene with protein product		194538	"zinc finger protein 10 (KOX 1)"			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.1177A>G	chr12.hg19:g.133733009A>G	ENSP00000248211:p.Ile393Val	80.0	0.0		184.0	13.0	NM_015394	B2RBS1|Q8TC91	Missense_Mutation	SNP	ENST00000248211.6	hg19	CCDS9283.1	.	.	.	.	.	.	.	.	.	.	A	1.364	-0.588059	0.03799	.	.	ENSG00000256223	ENST00000248211;ENST00000426665;ENST00000402932	T;T;T	0.15017	2.46;2.46;2.46	3.73	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	1.021450	0.07856	N	0.965538	T	0.10165	0.0249	N	0.21282	0.65	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40608	-0.9554	9	.	.	.	.	4.1126	0.10065	0.6048:0.1785:0.2168:0.0	.	393	P21506	ZNF10_HUMAN	V	393;393;259	ENSP00000248211:I393V;ENSP00000393814:I393V;ENSP00000384893:I259V	.	I	+	1	0	ZNF10	132243082	0.000000	0.05858	0.992000	0.48379	0.994000	0.84299	-0.455000	0.06762	0.109000	0.17891	0.533000	0.62120	ATT	.	.		0.438	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394		G	133733009	A	G	133733009	3	3	101	1	0	0	0	0	1	0	0	0	17727	217	8	2	1191	2	ZNF10	12	133733009	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	8279882	133733009	118886	411	14248										
NBEA	26960	hgsc.bcm.edu	37	chr13	35731313	35731313	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaagattaccgaaatggtctAcaatatcttccggattcttt	7	8	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:35731313A>G	ENST00000400445.3	+	21	3284	c.2750A>G	c.(2749-2751)tAc>tGc	p.Y917C	NBEA_ENST00000310336.4_Missense_Mutation_p.Y917C|NBEA_ENST00000540320.1_Missense_Mutation_p.Y917C|NBEA_ENST00000379939.2_Missense_Mutation_p.Y917C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	917					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GAAATGGTCTACAATATCTTC	0.408																																					p.Y917C		Atlas-SNP	.											.	NBEA	340	.	0			c.A2750G						.						115	113	114					13																	35731313		1826	4081	5907	SO:0001583	missense	26960	exon21			TGGTCTACAATAT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.2750A>G	chr13.hg19:g.35731313A>G	ENSP00000383295:p.Tyr917Cys	101.0	0.0		193.0	34.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.898496	0.72639	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.77280	0.4107	M	0.69248	2.105	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.79022	-0.1973	10	0.56958	D	0.05	.	15.6702	0.77267	1.0:0.0:0.0:0.0	.	917	Q5T321	.	C	917	ENSP00000440951:Y917C;ENSP00000383295:Y917C;ENSP00000369271:Y917C;ENSP00000308534:Y917C	ENSP00000308534:Y917C	Y	+	2	0	NBEA	34629313	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.171000	0.68590	0.528000	0.53228	TAC	.	.		0.408	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35731313	A	G	35731313	3	3	101	1	0	0	0	0	1	0	0	0	10196	391	14	2	2832	2	NBEA	13	35731313	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10		35731313	79438565	412	14249										
NBEA	26960	hgsc.bcm.edu	37	chr13	35756573	35756573	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctgatggtttccaagtatcGtgacatattagaaccccaga	8	9	1	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:35756573G>A	ENST00000400445.3	+	29	5273	c.4739G>A	c.(4738-4740)cGt>cAt	p.R1580H	NBEA_ENST00000310336.4_Missense_Mutation_p.R1580H|NBEA_ENST00000540320.1_Missense_Mutation_p.R1580H|NBEA_ENST00000379939.2_Missense_Mutation_p.R1577H	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1580					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.R1580H(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TCCAAGTATCGTGACATATTA	0.388																																					p.R1580H		Atlas-SNP	.											NBEA,NS,carcinoma,0,1	NBEA	340	.	1	Substitution - Missense(1)	endometrium(1)	c.G4739A						.						133	122	126					13																	35756573		1833	4088	5921	SO:0001583	missense	26960	exon29			AGTATCGTGACAT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.4739G>A	chr13.hg19:g.35756573G>A	ENSP00000383295:p.Arg1580His	120.0	0.0		262.0	25.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	35	5.424444	0.96111	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.69306	-0.39;-0.38;-0.39;-0.39	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.83248	0.5213	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.84686	0.0720	10	0.87932	D	0	.	19.6933	0.96010	0.0:0.0:1.0:0.0	.	1580;1577	Q8NFP9;Q5T321	NBEA_HUMAN;.	H	1580;1580;1577;1580;239	ENSP00000440951:R1580H;ENSP00000383295:R1580H;ENSP00000369271:R1577H;ENSP00000308534:R1580H	ENSP00000308534:R1580H	R	+	2	0	NBEA	34654573	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	9.869000	0.99810	2.651000	0.90000	0.467000	0.42956	CGT	.	.		0.388	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35756573	G	A	35756573	3	1	101	1	0	0	0	0	1	0	0	0	10196	1145	40	1	4853	1	NBEA	13	35756573	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	25260	35756573	79413305	413	14250										
MAB21L1	4081	hgsc.bcm.edu	37	chr13	36050193	36050193	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agacttcccggatagttttgGcaatggcagctttcctggct	11	10	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:36050193G>T	ENST00000379919.4	-	1	639	c.83C>A	c.(82-84)gCc>gAc	p.A28D	NBEA_ENST00000310336.4_Intron|NBEA_ENST00000537702.1_5'Flank|NBEA_ENST00000540320.1_Intron|NBEA_ENST00000400445.3_Intron|NBEA_ENST00000379939.2_Intron	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)	28					anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		GATAGTTTTGGCAATGGCAGC	0.507																																					p.A28D		Atlas-SNP	.											.	MAB21L1	52	.	0			c.C83A						.						101	104	103					13																	36050193		2203	4300	6503	SO:0001583	missense	4081	exon1			GTTTTGGCAATGG	BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"mab-21 (C. elegans)-like 1"			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.83C>A	chr13.hg19:g.36050193G>T	ENSP00000369251:p.Ala28Asp	51.0	0.0		119.0	14.0	NM_005584	Q6I9T5	Missense_Mutation	SNP	ENST00000379919.4	hg19	CCDS9353.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.706307	0.48412	.	.	ENSG00000180660	ENST00000379919	T	0.18960	2.18	5.76	5.76	0.90799	.	0.155272	0.64402	D	0.000020	T	0.25457	0.0619	M	0.61703	1.905	0.51767	D	0.99993	B	0.26845	0.161	B	0.27608	0.081	T	0.01661	-1.1301	10	0.34782	T	0.22	-3.2857	15.1394	0.72599	0.0695:0.0:0.9305:0.0	.	28	Q13394	MB211_HUMAN	D	28	ENSP00000369251:A28D	ENSP00000369251:A28D	A	-	2	0	MAB21L1	34948193	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.736000	0.93811	0.655000	0.94253	GCC	.	.		0.507	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584		T	36050193	G	T	36050193	3	4	101	1	0	0	0	0	1	0	0	0	9150	1203	42	3	1000	3	MAB21L1	13	36050193	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	293620	36050193	79119685	414	14251										
NBEA	26960	hgsc.bcm.edu	37	chr13	36229035	36229036	+	Frame_Shift_Ins	INS	-	-	C													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggcagatcacagacctcgttINSgaccagagtatacaaatcaa							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:36229035_36229036insC	ENST00000400445.3	+	53	8550_8551	c.8016_8017insC	c.(8017-8019)gacfs	p.D2673fs	NBEA_ENST00000310336.4_Frame_Shift_Ins_p.D2673fs|NBEA_ENST00000379922.3_Frame_Shift_Ins_p.D251fs|NBEA_ENST00000537702.1_Frame_Shift_Ins_p.D466fs|NBEA_ENST00000540320.1_Frame_Shift_Ins_p.D2673fs|NBEA_ENST00000379939.2_Frame_Shift_Ins_p.D2670fs	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2673					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CAGACCTCGTTGACCAGAGTAT	0.366																																					p.V2672fs		Atlas-Indel,Pindel	.											.	NBEA	340	.	0			c.8016_8017insC						.																																			SO:0001589	frameshift_variant	26960	exon53			.	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	Exception_encountered	chr13.hg19:g.36229035_36229036insC	ENSP00000383295:p.Asp2673fs	59.0	0.0		112.0	22.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Frame_Shift_Ins	INS	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.366	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		C	36229036	-	C	36229035	7	5	101	1	0	1	1	0	0	0	0	0	10196	1799	63	0	8226	0	NBEA	13	36229035	Frame_Shift_Ins	INS	-	TCGA-DD-A1EE-01A-11D-A12Z-10	178842	36229035	78940843	415	14252										
FREM2	341640	hgsc.bcm.edu	37	chr13	39265055	39265055	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccaccaatgatgaacagccaGagatgtttatgagagaattt	9	7	0	5			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:39265055G>T	ENST00000280481.7	+	1	3790	c.3574G>T	c.(3574-3576)Gag>Tag	p.E1192*		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1192					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TGAACAGCCAGAGATGTTTAT	0.418																																					p.E1192X		Atlas-SNP	.											.	FREM2	385	.	0			c.G3574T						.						229	219	222					13																	39265055		2203	4300	6503	SO:0001587	stop_gained	341640	exon1			CAGCCAGAGATGT	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.3574G>T	chr13.hg19:g.39265055G>T	ENSP00000280481:p.Glu1192*	128.0	0.0		313.0	40.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Nonsense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	44	11.144798	0.99522	.	.	ENSG00000150893	ENST00000280481	.	.	.	6.07	6.07	0.98685	.	0.199491	0.52532	D	0.000079	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	.	.	.	X	1192	.	ENSP00000280481:E1192X	E	+	1	0	FREM2	38163055	1.000000	0.71417	0.997000	0.53966	0.788000	0.44548	9.864000	0.99589	2.890000	0.99128	0.650000	0.86243	GAG	.	.		0.418	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39265055	G	T	39265055	4	4	101	1	0	0	0	0	0	1	0	0	6053	943	33	3	3576	3	FREM2	13	39265055	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3036020	39265055	75904823	416	14253										
FREM2	341640	hgsc.bcm.edu	37	chr13	39265478	39265478	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tattaatggcaacagatttaGattcagaagacaaatctttg	7	5	2	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:39265478G>C	ENST00000280481.7	+	1	4213	c.3997G>C	c.(3997-3999)Gat>Cat	p.D1333H		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1333					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D1333Y(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AACAGATTTAGATTCAGAAGA	0.353																																					p.D1333H		Atlas-SNP	.											FREM2,rectum,carcinoma,0,1	FREM2	385	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3997C						.						76	80	79					13																	39265478		2203	4300	6503	SO:0001583	missense	341640	exon1			GATTTAGATTCAG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.3997G>C	chr13.hg19:g.39265478G>C	ENSP00000280481:p.Asp1333His	41.0	0.0		188.0	28.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.781469	0.70222	.	.	ENSG00000150893	ENST00000280481	T	0.74106	-0.81	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.92047	0.7480	H	0.97611	4.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93768	0.7072	10	0.87932	D	0	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	1333	Q5SZK8	FREM2_HUMAN	H	1333	ENSP00000280481:D1333H	ENSP00000280481:D1333H	D	+	1	0	FREM2	38163478	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.864000	0.99589	2.894000	0.99253	0.655000	0.94253	GAT	.	.		0.353	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39265478	G	C	39265478	3	2	101	1	0	0	0	0	1	0	0	0	6053	942	33	4	3999	4	FREM2	13	39265478	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	423	39265478	75904400	417	14254										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42877120	42877120	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caaggaactgttaatgttttCaaacaaagagcaccaccaag	7	9	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:42877120C>A	ENST00000025301.2	+	8	4413	c.4238C>A	c.(4237-4239)tCa>tAa	p.S1413*		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1413					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TTAATGTTTTCAAACAAAGAG	0.383																																					p.S1413X		Atlas-SNP	.											.	AKAP11	146	.	0			c.C4238A						.						48	51	50					13																	42877120		2203	4300	6503	SO:0001587	stop_gained	11215	exon8			TGTTTTCAAACAA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.4238C>A	chr13.hg19:g.42877120C>A	ENSP00000025301:p.Ser1413*	39.0	0.0		76.0	7.0	NM_016248	O75124|Q9NUK7	Nonsense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	C	38	6.961113	0.97964	.	.	ENSG00000023516	ENST00000025301	.	.	.	5.58	4.55	0.56014	.	0.437976	0.20911	N	0.083466	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	3.6947	0.08360	0.0:0.1427:0.2294:0.628	.	.	.	.	X	1413	.	ENSP00000025301:S1413X	S	+	2	0	AKAP11	41775120	0.001000	0.12720	0.159000	0.22649	0.077000	0.17291	0.934000	0.28910	1.138000	0.42230	0.557000	0.71058	TCA	.	.		0.383	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		A	42877120	C	A	42877120	4	1	101	1	0	0	0	0	0	1	0	0	447	838	29	3	4260	3	AKAP11	13	42877120	Nonsense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3611642	42877120	72292758	418	14255										
RB1	5925	hgsc.bcm.edu	37	chr13	48947605	48947606	+	Frame_Shift_Ins	INS	-	-	A													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agcaagtgatcaaccttcagINSaaaatctgatttcctatttt							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:48947605_48947606insA	ENST00000267163.4	+	12	1330_1331	c.1192_1193insA	c.(1192-1194)gaafs	p.E398fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	398	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.E398L(2)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TCAACCTTCAGAAAATCTGATT	0.287		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.E398fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.,1	RB1	1068	.	25	Whole gene deletion(15)|Unknown(8)|Substitution - Missense(2)	bone(11)|breast(5)|central_nervous_system(2)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.1192_1193insA						.																																			SO:0001589	frameshift_variant	5925	exon12	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1196dupA	chr13.hg19:g.48947609_48947609dupA	ENSP00000267163:p.Glu398fs	146.0	0.0		609.0	110.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Ins	INS	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.287	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			A	48947606	-	A	48947605	7	5	101	1	0	1	1	0	0	0	0	0	13113	943	33	0	1238	0	RB1	13	48947605	Frame_Shift_Ins	INS	-	TCGA-DD-A1EE-01A-11D-A12Z-10	6070485	48947605	66222273	419	14256										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58207559	58207559	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cctgaccgcgtgcgggagctCttctccatcgaccccaagac	10	17	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:58207559C>T	ENST00000377918.3	+	1	905	c.879C>T	c.(877-879)ctC>ctT	p.L293L		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	293	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		TGCGGGAGCTCTTCTCCATCG	0.582																																					p.L293L	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.C879T						.						56	53	54					13																	58207559		2203	4300	6503	SO:0001819	synonymous_variant	27253	exon1			GGAGCTCTTCTCC	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.879C>T	chr13.hg19:g.58207559C>T		47.0	0.0		89.0	10.0	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	hg19	CCDS31986.1																																																																																			.	.		0.582	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		T	58207559	C	T	58207559	2	4	101	1	0	0	0	0	0	0	0	1	11521	900	32	3		3	PCDH17	13	58207559	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	9259954	58207559	56962319	420	14257										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111082761	111082761	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccattagggtgaacctggagAgcctggattggtcggtttcc	14	9	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:111082761A>G	ENST00000360467.5	+	9	869	c.563A>G	c.(562-564)gAg>gGg	p.E188G	COL4A2_ENST00000462309.1_3'UTR	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	188	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GAACCTGGAGAGCCTGGATTG	0.358																																					p.E188G		Atlas-SNP	.											.	COL4A2	178	.	0			c.A563G						.						86	85	85					13																	111082761		1807	4070	5877	SO:0001583	missense	1284	exon9			CTGGAGAGCCTGG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.563A>G	chr13.hg19:g.111082761A>G	ENSP00000353654:p.Glu188Gly	62.0	0.0		187.0	8.0	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	hg19	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	A	9.789	1.177348	0.21787	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.93906	-3.31	5.19	5.19	0.71726	.	0.504141	0.17796	N	0.161738	D	0.94039	0.8090	M	0.76838	2.35	0.38545	D	0.949315	P	0.41784	0.762	P	0.48063	0.565	D	0.92822	0.6273	10	0.16896	T	0.51	.	13.6015	0.62022	1.0:0.0:0.0:0.0	.	188	P08572	CO4A2_HUMAN	G	188	ENSP00000353654:E188G	ENSP00000257309:E188G	E	+	2	0	COL4A2	109880762	0.899000	0.30636	0.967000	0.41034	0.394000	0.30568	2.243000	0.43115	1.943000	0.56356	0.528000	0.53228	GAG	.	.		0.358	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		G	111082761	A	G	111082761	3	3	101	1	0	0	0	0	1	0	0	0	3692	304	11	2	593	2	COL4A2	13	111082761	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	52875202	111082761	4087117	421	14258										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111117937	111117937	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggccctcctggccccgcaggGaccccaggacaaataggtat	12	15	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr13:111117937G>A	ENST00000360467.5	+	25	2268	c.1962G>A	c.(1960-1962)ggG>ggA	p.G654G	COL4A2-AS2_ENST00000458403.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	654	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GCCCCGCAGGGACCCCAGGAC	0.577																																					p.G654G		Atlas-SNP	.											.	COL4A2	178	.	0			c.G1962A						.						24	28	27					13																	111117937		1884	4103	5987	SO:0001819	synonymous_variant	1284	exon25			CGCAGGGACCCCA	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.1962G>A	chr13.hg19:g.111117937G>A		28.0	0.0		66.0	25.0	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	hg19	CCDS41907.1																																																																																			.	.		0.577	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		A	111117937	G	A	111117937	2	1	101	1	0	0	0	0	0	0	0	1	3692	1161	41	3		3	COL4A2	13	111117937	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	35176	111117937	4051941	422	14259										
POTEM	641455	hgsc.bcm.edu	37	chr14	20000537	20000537	+	Splice_Site	DEL	C	C	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttctggttcttgagacatttCctgcagatgcaaaaacagaa							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:20000537delC	ENST00000551509.1	-	8	1249	c.1198delG	c.(1198-1200)gaa>aa	p.E400fs		NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN	POTE ankyrin domain family, member M	400										endometrium(4)|kidney(1)|lung(4)	9						TGAGACATTTCCTGCAGATGC	0.289																																					p.E400fs		Atlas-Indel,Pindel	.											.	POTEM	51	.	0			c.1199delA						.						1	0	1					14																	20000537		1	0	1	SO:0001630	splice_region_variant	641455	exon8			.		CCDS73609.1	14q11.2	2013-01-10			ENSG00000187537	ENSG00000187537		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	37096	protein-coding gene	gene with protein product	"prostate-specific P704P"					16364570	Standard	NM_001145442		Approved	POTE14beta, P704P, ACT	uc001vwc.3	A6NI47		ENST00000551509.1:c.1198-1G>-	chr14.hg19:g.20000537delC		197.0	0.0		1473.0	239.0	NM_001145442		Frame_Shift_Del	DEL	ENST00000551509.1	hg19	CCDS45076.1																																																																																			.	.		0.289	POTEM-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409490.3	NM_001145442	Frame_Shift_Del	-	20000537	C	-	20000537	8	5	101	1	0	1	0	1	0	0	1	0	12277	869	30	0	340	0	POTEM	14	20000537	Splice_Site	DEL	C	TCGA-DD-A1EE-01A-11D-A12Z-10		20000537	87349003	423	14260										
MYH6	4624	hgsc.bcm.edu	37	chr14	23866803	23866803	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gagccctttttcttgcctccTttgcttttaccactgtcccc	5	16	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:23866803T>A	ENST00000356287.3	-	15	1940	c.1911A>T	c.(1909-1911)aaA>aaT	p.K637N	MYH6_ENST00000405093.3_Missense_Mutation_p.K637N			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	637	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TCTTGCCTCCTTTGCTTTTAC	0.572																																					p.K637N		Atlas-SNP	.											.	MYH6	274	.	0			c.A1911T						.						94	89	91					14																	23866803		2203	4300	6503	SO:0001583	missense	4624	exon16			GCCTCCTTTGCTT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.1911A>T	chr14.hg19:g.23866803T>A	ENSP00000348634:p.Lys637Asn	39.0	0.0		110.0	15.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	.	17.79	3.475098	0.63737	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.88201	-2.35;-2.35	4.27	4.27	0.50696	Myosin head, motor domain (2);	.	.	.	.	D	0.92270	0.7548	M	0.74881	2.28	0.50813	D	0.999891	P	0.44986	0.847	P	0.59056	0.851	D	0.92455	0.5973	9	0.72032	D	0.01	.	9.2762	0.37700	0.0:0.0893:0.0:0.9107	.	637	P13533	MYH6_HUMAN	N	637	ENSP00000386041:K637N;ENSP00000348634:K637N	ENSP00000348634:K637N	K	-	3	2	MYH6	22936643	0.988000	0.35896	1.000000	0.80357	0.917000	0.54804	0.286000	0.18902	1.933000	0.56026	0.533000	0.62120	AAA	.	.		0.572	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23866803	T	A	23866803	3	1	101	1	0	0	0	0	1	0	0	0	10047	1606	56	4	4004	4	MYH6	14	23866803	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	3866266	23866803	83482737	424	14261										
NOVA1	4857	hgsc.bcm.edu	37	chr14	26917704	26917704	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acctaaacctaaagtgttgaGattatatccatagctggcta	7	8	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:26917704G>T	ENST00000539517.2	-	5	1302	c.985C>A	c.(985-987)Ctc>Atc	p.L329I	NOVA1_ENST00000465357.2_Missense_Mutation_p.L305I|NOVA1_ENST00000267422.7_Missense_Mutation_p.L207I	NM_002515.2	NP_002506.2	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	332	Ala-rich.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		AAAGTGTTGAGATTATATCCA	0.502																																					p.L329I		Atlas-SNP	.											.	NOVA1	146	.	0			c.C985A						.						52	48	50					14																	26917704		2203	4300	6503	SO:0001583	missense	4857	exon5			TGTTGAGATTATA	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000539517.2:c.985C>A	chr14.hg19:g.26917704G>T	ENSP00000438875:p.Leu329Ile	26.0	0.0		78.0	8.0	NM_002515	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000539517.2	hg19	CCDS32061.1	.	.	.	.	.	.	.	.	.	.	G	4.892	0.165831	0.09339	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000267422	T;T;T	0.34472	1.37;1.36;1.37	5.93	5.93	0.95920	.	0.168630	0.41712	D	0.000828	T	0.20251	0.0487	N	0.08118	0	0.53005	D	0.999967	B;B;P	0.35872	0.092;0.256;0.525	B;B;B	0.30572	0.018;0.055;0.117	T	0.09530	-1.0670	10	0.10902	T	0.67	-5.7973	20.3363	0.98740	0.0:0.0:1.0:0.0	.	332;305;329	P51513;D3DS81;P51513-4	NOVA1_HUMAN;.;.	I	305;329;207	ENSP00000447391:L305I;ENSP00000438875:L329I;ENSP00000267422:L207I	ENSP00000267422:L207I	L	-	1	0	NOVA1	25987544	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.392000	0.79840	2.814000	0.96858	0.563000	0.77884	CTC	.	.		0.502	NOVA1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000073261.3	NM_006491		T	26917704	G	T	26917704	3	4	101	1	0	0	0	0	1	0	0	0	10563	942	33	3	542	3	NOVA1	14	26917704	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3050901	26917704	80431836	425	14262										
MAP4K5	11183	hgsc.bcm.edu	37	chr14	50915494	50915494	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttaaaaatgaattcttaccaTttcatctcgtgcttctgttt	4	8	4	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:50915494T>C	ENST00000013125.4	-	15	1390	c.1072A>G	c.(1072-1074)Atg>Gtg	p.M358V	RP11-406H23.2_ENST00000555257.1_lincRNA	NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	358					activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					ATTCTTACCATTTCATCTCGT	0.284																																					p.M358V		Atlas-SNP	.											.	MAP4K5	48	.	0			c.A1072G						.						82	76	78					14																	50915494		1801	4063	5864	SO:0001583	missense	11183	exon15			TTACCATTTCATC	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6867	protein-coding gene	gene with protein product	"germinal center kinase-related"	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.1072A>G	chr14.hg19:g.50915494T>C	ENSP00000013125:p.Met358Val	67.0	0.0		141.0	23.0	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	hg19		.	.	.	.	.	.	.	.	.	.	T	10.38	1.334513	0.24253	.	.	ENSG00000012983	ENST00000013125	T	0.12879	2.64	5.79	4.64	0.57946	Protein kinase-like domain (1);	0.091042	0.64402	N	0.000001	T	0.13586	0.0329	L	0.51422	1.61	0.45528	D	0.998486	B;B;B	0.22480	0.0;0.036;0.07	B;B;B	0.22753	0.0;0.041;0.016	T	0.05649	-1.0872	10	0.24483	T	0.36	.	10.9645	0.47403	0.0:0.0742:0.0:0.9258	.	32;358;358	B3KWC4;B2R928;Q9Y4K4	.;.;M4K5_HUMAN	V	358	ENSP00000013125:M358V	ENSP00000013125:M358V	M	-	1	0	MAP4K5	49985244	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.266000	0.51569	0.996000	0.38943	0.533000	0.62120	ATG	.	.		0.284	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575		C	50915494	T	C	50915494	3	2	101	1	0	0	0	0	1	0	0	0	9272	1493	52	2	1540	2	MAP4K5	14	50915494	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	23997790	50915494	56434046	426	14263										
C14orf101	54916	hgsc.bcm.edu	37	chr14	57070549	57070549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcaggctttctggctcatctGctggaggaatccttgctgcg	13	11	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:57070549G>A	ENST00000261556.6	+	4	483	c.361G>A	c.(361-363)Gct>Act	p.A121T	TMEM260_ENST00000536419.1_Intron|TMEM260_ENST00000538838.1_Missense_Mutation_p.A121T	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	121						integral component of membrane (GO:0016021)											TGGCTCATCTGCTGGAGGAAT	0.413																																					p.A121T		Atlas-SNP	.											.	.	.	.	0			c.G361A						.						104	107	106					14																	57070549		2203	4300	6503	SO:0001583	missense	0	exon4			TCATCTGCTGGAG	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 101"	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.361G>A	chr14.hg19:g.57070549G>A	ENSP00000261556:p.Ala121Thr	135.0	0.0		303.0	24.0	NM_017799	A8KAN4|B3KPF5|Q86XE1	Missense_Mutation	SNP	ENST00000261556.6	hg19	CCDS9727.2	.	.	.	.	.	.	.	.	.	.	G	22.3	4.273708	0.80580	.	.	ENSG00000070269	ENST00000261556;ENST00000538838	T;T	0.49432	1.37;0.78	5.88	5.88	0.94601	.	0.054747	0.64402	D	0.000001	T	0.46927	0.1418	L	0.45051	1.395	0.80722	D	1	P	0.43477	0.808	B	0.43082	0.407	T	0.19745	-1.0296	10	0.20046	T	0.44	-11.5948	20.2381	0.98363	0.0:0.0:1.0:0.0	.	121	Q9NX78	CN101_HUMAN	T	121	ENSP00000261556:A121T;ENSP00000441934:A121T	ENSP00000261556:A121T	A	+	1	0	C14orf101	56140302	1.000000	0.71417	0.980000	0.43619	0.994000	0.84299	6.781000	0.75068	2.779000	0.95612	0.650000	0.86243	GCT	.	.		0.413	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799		A	57070549	G	A	57070549	3	1	101	1	0	0	0	0	1	0	0	0	1736	1319	46	3	375	3	C14orf101	14	57070549	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	6155055	57070549	50278991	427	14264										
DAAM1	23002	hgsc.bcm.edu	37	chr14	59820665	59820665	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgcagagcgtgtggcagaagTgaaacctaaagtggaaggta	15	5	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:59820665T>A	ENST00000395125.1	+	19	2392	c.2369T>A	c.(2368-2370)gTg>gAg	p.V790E	DAAM1_ENST00000553966.1_Intron|DAAM1_ENST00000360909.3_Missense_Mutation_p.V780E|DAAM1_ENST00000351081.1_Missense_Mutation_p.V790E	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	790	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		GTGGCAGAAGTGAAACCTAAA	0.363																																					p.V790E		Atlas-SNP	.											.	DAAM1	95	.	0			c.T2369A						.						98	87	91					14																	59820665		2203	4300	6503	SO:0001583	missense	23002	exon19			CAGAAGTGAAACC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.2369T>A	chr14.hg19:g.59820665T>A	ENSP00000378557:p.Val790Glu	71.0	0.0		157.0	11.0	NM_014992	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	hg19	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	t	22.9	4.347348	0.82022	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000395125	T;T;T	0.19532	2.14;2.14;2.14	6.03	6.03	0.97812	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.050329	0.85682	D	0.000000	T	0.49949	0.1587	M	0.81802	2.56	0.58432	D	0.999995	D;D	0.69078	0.994;0.997	D;D	0.70227	0.949;0.968	T	0.54166	-0.8334	10	0.87932	D	0	.	16.5808	0.84714	0.0:0.0:0.0:1.0	.	780;790	Q9Y4D1-2;Q9Y4D1	.;DAAM1_HUMAN	E	780;790;790	ENSP00000354162:V780E;ENSP00000247170:V790E;ENSP00000378557:V790E	ENSP00000247170:V790E	V	+	2	0	DAAM1	58890418	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.183000	0.72002	2.317000	0.78254	0.524000	0.50904	GTG	.	.		0.363	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		A	59820665	T	A	59820665	3	1	101	1	0	0	0	0	1	0	0	0	4217	1696	59	4	2443	4	DAAM1	14	59820665	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2750116	59820665	47528875	428	14265										
C14orf39	317761	hgsc.bcm.edu	37	chr14	60921835	60921835	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggattccttttctgtttgaaCttcaggtactgcatttctat	7	8	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:60921835C>G	ENST00000321731.3	-	16	1546	c.1387G>C	c.(1387-1389)Gtt>Ctt	p.V463L		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	463					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TCTGTTTGAACTTCAGGTACT	0.299																																					p.V463L		Atlas-SNP	.											.	C14orf39	79	.	0			c.G1387C						.						58	63	61					14																	60921835		2201	4291	6492	SO:0001583	missense	317761	exon16			TTTGAACTTCAGG	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1387G>C	chr14.hg19:g.60921835C>G	ENSP00000324920:p.Val463Leu	110.0	0.0		280.0	16.0	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	hg19	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.656197	0.29425	.	.	ENSG00000179008	ENST00000321731	T	0.22336	1.96	5.84	-0.985	0.10256	.	1.016140	0.07853	N	0.965033	T	0.10981	0.0268	N	0.22421	0.69	0.09310	N	1	B	0.19817	0.039	B	0.18871	0.023	T	0.36915	-0.9728	9	.	.	.	2.2271	1.9519	0.03368	0.1248:0.452:0.1214:0.3018	.	463	Q8N1H7	S6OS1_HUMAN	L	463	ENSP00000324920:V463L	.	V	-	1	0	C14orf39	59991588	0.008000	0.16893	0.247000	0.24249	0.990000	0.78478	-0.400000	0.07241	-0.152000	0.11156	0.561000	0.74099	GTT	.	.		0.299	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		G	60921835	C	G	60921835	3	3	101	1	0	0	0	0	1	0	0	0	1774	565	20	4	388	4	C14orf39	14	60921835	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1101170	60921835	46427705	429	14266										
PRKCH	5583	hgsc.bcm.edu	37	chr14	61997206	61997206	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atgagatgctctgtggtcacGcgccttttgaggcagagaac	13	9	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:61997206G>T	ENST00000332981.5	+	12	2039	c.1654G>T	c.(1654-1656)Gcg>Tcg	p.A552S	RP11-47I22.4_ENST00000556347.1_Silent_p.T56T|PRKCH_ENST00000555082.1_Missense_Mutation_p.A391S	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	552	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		CTGTGGTCACGCGCCTTTTGA	0.552																																					p.A552S	Melanoma(135;863 1779 8064 14443 26348)	Atlas-SNP	.											PRKCH,colon,carcinoma,-1,1	PRKCH	89	.	0			c.G1654T						.						225	180	195					14																	61997206		2203	4300	6503	SO:0001583	missense	5583	exon12			GGTCACGCGCCTT	M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.1654G>T	chr14.hg19:g.61997206G>T	ENSP00000329127:p.Ala552Ser	73.0	0.0		137.0	8.0	NM_006255	B4DJN5|Q16246|Q8NE03	Missense_Mutation	SNP	ENST00000332981.5	hg19	CCDS9752.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.588420	0.28357	.	.	ENSG00000027075	ENST00000555185;ENST00000332981;ENST00000555082	T;T;T	0.65549	-0.16;1.88;1.88	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000011	T	0.62877	0.2464	N	0.17345	0.48	0.80722	D	1	D	0.53312	0.959	D	0.67548	0.952	T	0.54364	-0.8305	10	0.02654	T	1	.	19.6972	0.96030	0.0:0.0:1.0:0.0	.	552	P24723	KPCL_HUMAN	S	120;552;391	ENSP00000451871:A120S;ENSP00000329127:A552S;ENSP00000450981:A391S	ENSP00000329127:A552S	A	+	1	0	PRKCH	61066959	1.000000	0.71417	0.268000	0.24571	0.241000	0.25554	4.418000	0.59828	2.663000	0.90544	0.650000	0.86243	GCG	.	.		0.552	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255		T	61997206	G	T	61997206	3	4	101	1	0	0	0	0	1	0	0	0	12525	1087	38	1	1700	1	PRKCH	14	61997206	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1075371	61997206	45352334	430	14267										
HIF1A	3091	hgsc.bcm.edu	37	chr14	62207716	62207716	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caaaagaccgtatggaagacAttaaaatattgattgcatct	7	6	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:62207716A>T	ENST00000337138.4	+	12	2168	c.1903A>T	c.(1903-1905)Att>Ttt	p.I635F	HIF1A-AS2_ENST00000554254.1_lincRNA|HIF1A_ENST00000323441.6_Missense_Mutation_p.I635F|HIF1A_ENST00000394997.1_Missense_Mutation_p.I636F|HIF1A_ENST00000557538.1_Missense_Mutation_p.I576F|HIF1A_ENST00000539097.1_Missense_Mutation_p.I659F|RP11-618G20.1_ENST00000555937.1_RNA	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	635	ID.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	TATGGAAGACATTAAAATATT	0.408																																					p.I659F		Atlas-SNP	.											.	HIF1A	120	.	0			c.A1975T						.						108	100	103					14																	62207716		2203	4300	6503	SO:0001583	missense	3091	exon12			GAAGACATTAAAA	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.1903A>T	chr14.hg19:g.62207716A>T	ENSP00000338018:p.Ile635Phe	71.0	0.0		158.0	62.0	NM_001243084	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Missense_Mutation	SNP	ENST00000337138.4	hg19	CCDS9753.1	.	.	.	.	.	.	.	.	.	.	A	8.810	0.935036	0.18206	.	.	ENSG00000100644	ENST00000539494;ENST00000394988;ENST00000337138;ENST00000394997;ENST00000323441;ENST00000557538;ENST00000539097	T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65	5.72	2.13	0.27403	.	3.176880	0.00628	N	0.000473	T	0.30916	0.0780	N	0.19112	0.55	0.30200	N	0.798702	B;B;B	0.26809	0.16;0.16;0.16	B;B;B	0.26693	0.072;0.072;0.072	T	0.21381	-1.0247	10	0.15952	T	0.53	.	2.0923	0.03660	0.4959:0.1201:0.2679:0.1161	.	636;635;635	A8MYV6;D0VY79;Q16665	.;.;HIF1A_HUMAN	F	386;576;635;636;635;576;659	ENSP00000338018:I635F;ENSP00000378446:I636F;ENSP00000323326:I635F;ENSP00000451696:I576F;ENSP00000437955:I659F	ENSP00000323326:I635F	I	+	1	0	HIF1A	61277469	0.902000	0.30710	0.996000	0.52242	0.898000	0.52572	0.814000	0.27239	0.187000	0.20147	-0.256000	0.11100	ATT	.	.		0.408	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		T	62207716	A	T	62207716	3	4	101	1	0	0	0	0	1	0	0	0	7112	217	8	4	1949	4	HIF1A	14	62207716	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	210510	62207716	45141824	431	14268										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64518635	64518635	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaccaaagcatgattgccttGaccactgacctccaggctac	7	14	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:64518635G>T	ENST00000344113.4	+	48	8216	c.8004G>T	c.(8002-8004)ttG>ttT	p.L2668F	SYNE2_ENST00000554584.1_Missense_Mutation_p.L2701F|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000358025.3_Missense_Mutation_p.L2668F	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2668					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGATTGCCTTGACCACTGACC	0.453																																					p.L2668F		Atlas-SNP	.											.	SYNE2	577	.	0			c.G8004T						.						102	103	103					14																	64518635		1970	4153	6123	SO:0001583	missense	23224	exon48			TGCCTTGACCACT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.8004G>T	chr14.hg19:g.64518635G>T	ENSP00000341781:p.Leu2668Phe	102.0	0.0		225.0	31.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	4.015	0.000139	0.07819	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.59224	0.65;0.66;0.28	5.68	2.39	0.29439	.	0.797647	0.10644	N	0.650623	T	0.51398	0.1672	L	0.27053	0.805	0.18873	N	0.999986	P;P	0.50272	0.933;0.919	P;P	0.48704	0.462;0.587	T	0.40776	-0.9545	10	0.62326	D	0.03	.	9.9368	0.41556	0.2556:0.0:0.7444:0.0	.	2668;2668	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	F	2668;2668;2701;2701	ENSP00000350719:L2668F;ENSP00000341781:L2668F;ENSP00000452570:L2701F	ENSP00000261678:L2701F	L	+	3	2	SYNE2	63588388	0.058000	0.20735	0.032000	0.17829	0.036000	0.12997	1.632000	0.37102	0.730000	0.32425	0.563000	0.77884	TTG	.	.		0.453	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64518635	G	T	64518635	3	4	101	1	0	0	0	0	1	0	0	0	15461	1281	45	3	8190	3	SYNE2	14	64518635	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2310919	64518635	42830905	432	14269										
SLC10A1	6554	hgsc.bcm.edu	37	chr14	70252897	70252897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aatgagaaccaggaccagtgAtatcacgatgcctttatagg	10	8	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:70252897A>G	ENST00000216540.4	-	2	617	c.484T>C	c.(484-486)Tca>Cca	p.S162P		NM_003049.3	NP_003040.1	Q14973	NTCP_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 1	162					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)	14				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)	Bumetanide(DB00887)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Ethinyl Estradiol(DB00977)|Indomethacin(DB00328)|Liothyronine(DB00279)|Liotrix(DB01583)|Pitavastatin(DB08860)|Probenecid(DB01032)|Progesterone(DB00396)|Testosterone(DB00624)|Ursodeoxycholic acid(DB01586)	AGGACCAGTGATATCACGATG	0.517																																					p.S162P		Atlas-SNP	.											.	SLC10A1	32	.	0			c.T484C						.						236	194	208					14																	70252897		2203	4300	6503	SO:0001583	missense	6554	exon2			CCAGTGATATCAC	L21893	CCDS9797.1	14q24.2	2013-07-18	2013-07-18		ENSG00000100652	ENSG00000100652		"Solute carriers"	10905	protein-coding gene	gene with protein product		182396				8132774	Standard	NM_003049		Approved	NTCP	uc001xlr.2	Q14973	OTTHUMG00000171236	ENST00000216540.4:c.484T>C	chr14.hg19:g.70252897A>G	ENSP00000216540:p.Ser162Pro	101.0	0.0		225.0	17.0	NM_003049	B9EGB6|Q2TU29	Missense_Mutation	SNP	ENST00000216540.4	hg19	CCDS9797.1	.	.	.	.	.	.	.	.	.	.	A	11.60	1.687662	0.29962	.	.	ENSG00000100652	ENST00000216540	T	0.12147	2.71	5.01	5.01	0.66863	.	0.203863	0.42821	D	0.000647	T	0.40297	0.1111	M	0.89353	3.025	0.29023	N	0.88618	D	0.89917	1.0	D	0.76071	0.987	T	0.43909	-0.9362	10	0.48119	T	0.1	-11.5151	10.1438	0.42751	0.8509:0.0:0.0:0.1491	.	162	Q14973	NTCP_HUMAN	P	162	ENSP00000216540:S162P	ENSP00000216540:S162P	S	-	1	0	SLC10A1	69322650	0.465000	0.25815	0.222000	0.23844	0.004000	0.04260	1.097000	0.30988	2.227000	0.72691	0.459000	0.35465	TCA	.	.		0.517	SLC10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412464.1			G	70252897	A	G	70252897	3	3	101	1	0	0	0	0	1	0	0	0	14388	333	12	2	581	2	SLC10A1	14	70252897	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	5734262	70252897	37096643	433	14270										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72190408	72190408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagcccagtggttttcaccaGtgcccggagttcacctaaag	10	13	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:72190408G>A	ENST00000555818.1	+	16	4664	c.4316G>A	c.(4315-4317)aGt>aAt	p.S1439N	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.S1418N|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.S893N|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.S1418N	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1439	Ser-rich.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GTTTTCACCAGTGCCCGGAGT	0.537																																					p.S1439N		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.G4316A						.						135	111	119					14																	72190408		2203	4300	6503	SO:0001583	missense	26037	exon16			TCACCAGTGCCCG	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.4316G>A	chr14.hg19:g.72190408G>A	ENSP00000450832:p.Ser1439Asn	50.0	0.0		122.0	19.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	hg19	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.674277	0.88445	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;D	0.85484	-1.17;-1.2;-1.17;-1.99	5.54	5.54	0.83059	.	0.170379	0.64402	D	0.000004	D	0.86029	0.5835	N	0.19112	0.55	0.58432	D	0.999999	D;P;D;D;D	0.65815	0.995;0.895;0.989;0.974;0.988	P;B;P;P;P	0.61070	0.836;0.264;0.854;0.796;0.883	D	0.85171	0.0998	10	0.35671	T	0.21	-16.5037	19.8379	0.96666	0.0:0.0:1.0:0.0	.	893;1439;893;1418;1439	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	N	1418;1439;1418;893	ENSP00000370630:S1418N;ENSP00000450832:S1439N;ENSP00000351352:S1418N;ENSP00000440682:S893N	ENSP00000351352:S1439N	S	+	2	0	SIPA1L1	71260161	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.938000	0.70170	2.765000	0.95021	0.655000	0.94253	AGT	.	.		0.537	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		A	72190408	G	A	72190408	3	1	101	1	0	0	0	0	1	0	0	0	14344	1029	36	3	4374	3	SIPA1L1	14	72190408	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1937511	72190408	35159132	434	14271										
DPF3	8110	hgsc.bcm.edu	37	chr14	73159816	73159816	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	catttctgtggttgggtgggGaccgagtctcctggtcttga	15	8	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:73159816G>A	ENST00000556509.1	-	7	709	c.710C>T	c.(709-711)tCc>tTc	p.S237F	DPF3_ENST00000557704.1_5'UTR|DPF3_ENST00000546183.1_Missense_Mutation_p.S247F|DPF3_ENST00000541685.1_Missense_Mutation_p.S237F	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	237					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GTTGGGTGGGGACCGAGTCTC	0.582																																					p.S237F		Atlas-SNP	.											.	DPF3	117	.	0			c.C710T						.						203	204	204					14																	73159816		2067	4214	6281	SO:0001583	missense	8110	exon7			GGTGGGGACCGAG	U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"Zinc fingers, PHD-type"	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.710C>T	chr14.hg19:g.73159816G>A	ENSP00000450518:p.Ser237Phe	143.0	0.0		300.0	31.0	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	hg19		.	.	.	.	.	.	.	.	.	.	G	26.9	4.783260	0.90282	.	.	ENSG00000205683	ENST00000556509;ENST00000398816;ENST00000541685;ENST00000546183	D;T;T	0.90900	-2.75;-0.25;-0.2	5.36	5.36	0.76844	.	.	.	.	.	D	0.92071	0.7487	L	0.47716	1.5	0.80722	D	1	P;D;D	0.61080	0.936;0.978;0.989	P;P;P	0.53912	0.729;0.729;0.737	D	0.92906	0.6343	9	0.87932	D	0	.	19.0841	0.93196	0.0:0.0:1.0:0.0	.	247;237;237	F5H575;Q92784-2;Q92784	.;.;DPF3_HUMAN	F	237;236;237;247	ENSP00000450518:S237F;ENSP00000441640:S237F;ENSP00000444662:S247F	ENSP00000381791:S292F	S	-	2	0	DPF3	72229569	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	9.335000	0.96500	2.504000	0.84457	0.462000	0.41574	TCC	.	.		0.582	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2			A	73159816	G	A	73159816	3	1	101	1	0	0	0	0	1	0	0	0	4720	1174	41	3	375	3	DPF3	14	73159816	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	969408	73159816	34189724	435	14272										
RPS6KL1	83694	hgsc.bcm.edu	37	chr14	75376302	75376303	+	Frame_Shift_Ins	INS	-	-	C													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccggcacagcaccccctgctINScgtgcagcgcctccagcgct							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:75376302_75376303insC	ENST00000555647.1	-	8	1500_1501	c.1213_1214insG	c.(1213-1215)gagfs	p.E405fs	RPS6KL1_ENST00000554900.1_5'Flank|RPS6KL1_ENST00000557413.1_Frame_Shift_Ins_p.E405fs|RPS6KL1_ENST00000354625.2_Frame_Shift_Ins_p.E374fs|RPS6KL1_ENST00000358328.4_Frame_Shift_Ins_p.E405fs			Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	405	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					ribosome (GO:0005840)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(234;0.00658)		CACCCCCTGCTCGTGCAGCGCC	0.703																																					p.E405fs		Atlas-Indel,Pindel	.											.	RPS6KL1	35	.	0			c.1214_1215insG						.																																			SO:0001589	frameshift_variant	83694	exon7			.	BC004540	CCDS9834.1, CCDS9834.2	14q24.2	2011-04-05				ENSG00000198208			20222	protein-coding gene	gene with protein product							Standard	NM_031464		Approved	MGC11287	uc010tux.2	Q9Y6S9		ENST00000555647.1:c.1214dupG	chr14.hg19:g.75376303_75376303dupC	ENSP00000452027:p.Glu405fs	32.0	0.0		158.0	21.0	NM_031464	A6NGM9|Q69YT9|Q6ZMQ6|Q96NR9|Q9BSU9	Frame_Shift_Ins	INS	ENST00000555647.1	hg19	CCDS9834.2																																																																																			.	.		0.703	RPS6KL1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413732.1			C	75376303	-	C	75376302	7	5	101	1	0	1	1	0	0	0	0	0	13674	1551	54	0	528	0	RPS6KL1	14	75376302	Frame_Shift_Ins	INS	-	TCGA-DD-A1EE-01A-11D-A12Z-10	2216486	75376302	31973238	436	14273										
C14orf118	55668	hgsc.bcm.edu	37	chr14	76668083	76668083	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccagcatcacaagcccccaaAtcacccagctctgagtggtt	7	16	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:76668083A>G	ENST00000261530.7	+	10	1404	c.1338A>G	c.(1336-1338)aaA>aaG	p.K446K	GPATCH2L_ENST00000312858.5_Silent_p.K441K|GPATCH2L_ENST00000556675.1_Intron	NM_017926.2	NP_060396.2	Q9NWQ4	GPT2L_HUMAN	G patch domain containing 2-like	446																	AAGCCCCCAAATCACCCAGCT	0.478																																					p.K446K		Atlas-SNP	.											.	.	.	.	0			c.A1338G						.						85	80	82					14																	76668083		2203	4300	6503	SO:0001819	synonymous_variant	55668	exon10			CCCCAAATCACCC	AK000696	CCDS9848.1, CCDS9849.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000089916	ENSG00000089916			20210	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 118"	C14orf118		10574461	Standard	NM_017926		Approved	FLJ20689, FLJ10033	uc001xsh.3	Q9NWQ4	OTTHUMG00000171490	ENST00000261530.7:c.1338A>G	chr14.hg19:g.76668083A>G		94.0	0.0		191.0	13.0	NM_017926	B3KN42|Q6PEJ7|Q9H3M3|Q9NWH0|Q9ULR8	Silent	SNP	ENST00000261530.7	hg19	CCDS9848.1	.	.	.	.	.	.	.	.	.	.	A	5.361	0.251864	0.10185	.	.	ENSG00000089916	ENST00000336993	.	.	.	5.63	-5.48	0.02592	.	.	.	.	.	T	0.49406	0.1555	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.57814	-0.7746	5	0.87932	D	0	-8.6954	13.884	0.63698	0.4345:0.0:0.5655:0.0	.	.	.	.	S	440	.	ENSP00000337200:N440S	N	+	2	0	C14orf118	75737836	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-0.921000	0.04008	-1.467000	0.01895	-0.264000	0.10439	AAT	.	.		0.478	GPATCH2L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000413698.2	NM_017926		G	76668083	A	G	76668083	2	3	101	1	0	0	0	0	0	0	0	1	1743	98	4	2		2	C14orf118	14	76668083	Silent	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1291781	76668083	30681457	437	14274										
ZDHHC22	283576	hgsc.bcm.edu	37	chr14	77606003	77606003	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctgggcaggaagaggaagaGctgcagcacgaaggtcacca	16	9	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:77606003G>A	ENST00000319374.4	-	2	281	c.79C>T	c.(79-81)Ctc>Ttc	p.L27F	AC007375.1_ENST00000600936.1_5'Flank|RP11-463C8.4_ENST00000557752.1_Intron	NM_174976.2	NP_777636.2	Q8N966	ZDH22_HUMAN	zinc finger, DHHC-type containing 22	27					protein localization to plasma membrane (GO:0072659)|protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)|urinary_tract(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0277)		AAGAGGAAGAGCTGCAGCACG	0.667											OREG0022834	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L27F		Atlas-SNP	.											.	ZDHHC22	30	.	0			c.C79T						.						10	13	12					14																	77606003		2096	4206	6302	SO:0001583	missense	283576	exon2			GGAAGAGCTGCAG	AK095612	CCDS45140.1	14q24.3	2008-08-06	2004-03-05	2004-03-10	ENSG00000177108	ENSG00000177108		"Zinc fingers, DHHC-type"	20106	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 59"	C14orf59			Standard	NM_174976		Approved		uc010asp.3	Q8N966		ENST00000319374.4:c.79C>T	chr14.hg19:g.77606003G>A	ENSP00000318222:p.Leu27Phe	27.0	0.0	1177	54.0	10.0	NM_174976	A6NH02|B7Z2L5|Q149P4	Missense_Mutation	SNP	ENST00000319374.4	hg19	CCDS45140.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.765692	0.49574	.	.	ENSG00000177108	ENST00000319374;ENST00000555389;ENST00000555327	T	0.58652	0.32	5.67	5.67	0.87782	.	0.128302	0.53938	D	0.000046	T	0.36717	0.0977	N	0.08118	0	0.40340	D	0.979024	B	0.17038	0.02	B	0.10450	0.005	T	0.25082	-1.0142	10	0.21540	T	0.41	.	13.8634	0.63574	0.0:0.0:0.8382:0.1617	.	27	Q8N966	ZDH22_HUMAN	F	27	ENSP00000318222:L27F	ENSP00000318222:L27F	L	-	1	0	ZDHHC22	76675756	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.584000	0.53936	2.677000	0.91161	0.561000	0.74099	CTC	.	.		0.667	ZDHHC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414289.1	NM_174976		A	77606003	G	A	77606003	3	1	101	1	0	0	0	0	1	0	0	0	17628	971	34	3	720	3	ZDHHC22	14	77606003	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	937920	77606003	29743537	438	14275										
RPS6KA5	9252	hgsc.bcm.edu	37	chr14	91338575	91338575	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgctgcgcgtctcggtactgGtgctagtctttttcattttt	10	9	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:91338575G>C	ENST00000261991.3	-	17	2425	c.2252C>G	c.(2251-2253)aCc>aGc	p.T751S	RPS6KA5_ENST00000536315.2_Missense_Mutation_p.T672S	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	751					axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		CTCGGTACTGGTGCTAGTCTT	0.483																																					p.T751S		Atlas-SNP	.											.	RPS6KA5	135	.	0			c.C2252G						.						129	114	119					14																	91338575		2203	4300	6503	SO:0001583	missense	9252	exon17			GTACTGGTGCTAG	AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"ribosomal protein S6 kinase, 90kD, polypeptide 5"			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.2252C>G	chr14.hg19:g.91338575G>C	ENSP00000261991:p.Thr751Ser	113.0	0.0		335.0	37.0	NM_004755	O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	hg19	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.354677	0.24512	.	.	ENSG00000100784	ENST00000261991;ENST00000536315	T;T	0.66815	-0.23;-0.23	5.25	5.25	0.73442	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.70290	0.3207	L	0.33485	1.01	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.61959	-0.6955	10	0.05959	T	0.93	.	19.2225	0.93803	0.0:0.0:1.0:0.0	.	751	O75582	KS6A5_HUMAN	S	751;672	ENSP00000261991:T751S;ENSP00000442803:T672S	ENSP00000261991:T751S	T	-	2	0	RPS6KA5	90408328	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.813000	0.99286	2.611000	0.88343	0.655000	0.94253	ACC	.	.		0.483	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		C	91338575	G	C	91338575	3	2	101	1	0	0	0	0	1	0	0	0	13669	1261	44	4	160	4	RPS6KA5	14	91338575	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	13732572	91338575	16010965	439	14276										
RCOR1	23186	hgsc.bcm.edu	37	chr14	103174914	103174914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaaacaaaaacgggagcgggAggagaggtgagcacatggct	17	6	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:103174914A>G	ENST00000570597.1	+	6	764	c.764A>G	c.(763-765)gAg>gGg	p.E255G	RCOR1_ENST00000262241.6_Missense_Mutation_p.E258G			Q9UKL0	RCOR1_HUMAN	REST corepressor 1	255					blood coagulation (GO:0007596)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	12						CGGGAGCGGGAGGAGAGGTGA	0.483																																					p.E258G		Atlas-SNP	.											.	RCOR1	39	.	0			c.A773G						.						97	102	100					14																	103174914		2203	4300	6503	SO:0001583	missense	23186	exon6			AGCGGGAGGAGAG	AF155595	CCDS9974.1, CCDS9974.2	14q32.33	2004-04-16	2004-04-16	2004-04-16		ENSG00000089902			17441	protein-coding gene	gene with protein product		607675	"REST corepressor"	RCOR		10449787	Standard	NM_015156		Approved	COREST, KIAA0071	uc001ymb.4	Q9UKL0		ENST00000570597.1:c.764A>G	chr14.hg19:g.103174914A>G	ENSP00000459789:p.Glu255Gly	39.0	0.0		85.0	10.0	NM_015156	Q15044|Q6P2I9|Q86VG5	Missense_Mutation	SNP	ENST00000570597.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.91	3.253093	0.59212	.	.	ENSG00000089902	ENST00000262241	.	.	.	5.88	5.88	0.94601	.	0.105736	0.64402	D	0.000005	T	0.44850	0.1313	N	0.21142	0.635	0.58432	D	0.999997	B	0.15719	0.014	B	0.15484	0.013	T	0.31668	-0.9935	9	0.21014	T	0.42	-28.233	16.2879	0.82732	1.0:0.0:0.0:0.0	.	255	Q9UKL0	RCOR1_HUMAN	G	255	.	ENSP00000262241:E255G	E	+	2	0	RCOR1	102244667	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	5.846000	0.69444	2.242000	0.73789	0.533000	0.62120	GAG	.	.		0.483	RCOR1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015156		G	103174914	A	G	103174914	3	3	101	1	0	0	0	0	1	0	0	0	13197	304	11	2	786	2	RCOR1	14	103174914	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	11836339	103174914	4174626	440	14277										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105419292	105419292	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttgaacttgggcattttgaaCttgctgtctttggcagtcac	10	8	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr14:105419292C>A	ENST00000333244.5	-	7	2615	c.2496G>T	c.(2494-2496)aaG>aaT	p.K832N	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	832						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCATTTTGAACTTGCTGTCTT	0.622																																					p.K832N		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G2496T						.						236	259	252					14																	105419292		1956	4145	6101	SO:0001583	missense	113146	exon7			TTTGAACTTGCTG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.2496G>T	chr14.hg19:g.105419292C>A	ENSP00000353114:p.Lys832Asn	94.0	0.0		169.0	67.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	8.580	0.882016	0.17467	.	.	ENSG00000185567	ENST00000333244	T	0.01871	4.59	4.02	2.13	0.27403	.	.	.	.	.	T	0.11367	0.0277	M	0.87328	2.875	0.21184	N	0.999764	D	0.76494	0.999	D	0.81914	0.995	T	0.16512	-1.0400	9	0.20519	T	0.43	.	9.0866	0.36586	0.0:0.7193:0.0:0.2807	.	832	Q8IVF2	AHNK2_HUMAN	N	832	ENSP00000353114:K832N	ENSP00000353114:K832N	K	-	3	2	AHNAK2	104490337	0.000000	0.05858	0.558000	0.28319	0.017000	0.09413	-0.608000	0.05641	0.187000	0.20147	-1.579000	0.00862	AAG	.	.		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105419292	C	A	105419292	3	1	101	1	0	0	0	0	1	0	0	0	415	564	20	3	14895	3	AHNAK2	14	105419292	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2244378	105419292	1930248	441	14278										
HERC2	8924	hgsc.bcm.edu	37	chr15	28446674	28446674	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctcgttttttgtacgtctgGctctccgtcacaacagcacc	8	14	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:28446674G>C	ENST00000261609.7	-	48	7752	c.7644C>G	c.(7642-7644)agC>agG	p.S2548R		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TGTACGTCTGGCTCTCCGTCA	0.368																																					p.S2548R		Atlas-SNP	.											.	HERC2	501	.	0			c.C7644G						.						125	114	118					15																	28446674		2203	4300	6503	SO:0001583	missense	8924	exon48			CGTCTGGCTCTCC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.7644C>G	chr15.hg19:g.28446674G>C	ENSP00000261609:p.Ser2548Arg	122.0	0.0		537.0	24.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.263445	0.59431	.	.	ENSG00000128731	ENST00000261609	T	0.38887	1.11	5.18	3.3	0.37823	.	0.043831	0.85682	D	0.000000	T	0.55800	0.1943	L	0.56769	1.78	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.75484	0.986;0.979	T	0.49532	-0.8930	10	0.25106	T	0.35	.	11.6869	0.51492	0.1348:0.0:0.8652:0.0	.	15;2548	A8KAQ8;O95714	.;HERC2_HUMAN	R	2548	ENSP00000261609:S2548R	ENSP00000261609:S2548R	S	-	3	2	HERC2	26120269	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.798000	0.38814	0.691000	0.31592	0.561000	0.74099	AGC	.	.		0.368	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		C	28446674	G	C	28446674	3	2	101	1	0	0	0	0	1	0	0	0	7067	1194	42	4	7044	4	HERC2	15	28446674	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10		28446674	74084718	442	14279										
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32928928	32928928	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaactaatgatttgactataGtagaatcaaaggagaaatat	7	3	1	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:32928928G>A	ENST00000361627.3	+	12	2676	c.1954G>A	c.(1954-1956)Gta>Ata	p.V652I	ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.V463I|ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.V463I	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	652					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		TTTGACTATAGTAGAATCAAA	0.333																																					p.V652I	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.G1954A						.						27	28	28					15																	32928928		2186	4293	6479	SO:0001583	missense	9824	exon12			ACTATAGTAGAAT	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1954G>A	chr15.hg19:g.32928928G>A	ENSP00000355090:p.Val652Ile	78.0	0.0		204.0	92.0	NM_014783	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	hg19	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	1.822	-0.471895	0.04445	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.09630	2.96	5.05	1.17	0.20885	.	0.980375	0.08352	N	0.959089	T	0.03053	0.0090	N	0.01048	-1.04	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.45789	-0.9237	10	0.17832	T	0.49	.	4.6642	0.12657	0.4877:0.3054:0.2069:0.0	.	652	Q6P4F7	RHGBA_HUMAN	I	652;463	ENSP00000355090:V652I	ENSP00000355090:V652I	V	+	1	0	ARHGAP11A	30716220	0.004000	0.15560	0.979000	0.43373	0.870000	0.49936	0.164000	0.16542	0.378000	0.24764	-0.484000	0.04775	GTA	.	.		0.333	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		A	32928928	G	A	32928928	3	1	101	1	0	0	0	0	1	0	0	0	863	1029	36	3	2023	3	ARHGAP11A	15	32928928	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	4482254	32928928	69602464	443	14280										
AQR	9716	hgsc.bcm.edu	37	chr15	35198872	35198872	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agtgccataaggttttgtggGacgtacggtaattaaaaagc	12	5	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:35198872G>T	ENST00000156471.5	-	18	1930	c.1705C>A	c.(1705-1707)Ccc>Acc	p.P569T		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	569					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		GGTTTTGTGGGACGTACGGTA	0.388																																					p.P569T		Atlas-SNP	.											.	AQR	139	.	0			c.C1705A						.						126	113	117					15																	35198872		1901	4133	6034	SO:0001583	missense	9716	exon18			TTGTGGGACGTAC	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.1705C>A	chr15.hg19:g.35198872G>T	ENSP00000156471:p.Pro569Thr	49.0	0.0		139.0	13.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	hg19	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962361	0.74016	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.94232	-3.38	5.44	4.51	0.55191	.	0.047946	0.85682	N	0.000000	D	0.96917	0.8993	M	0.93763	3.455	0.48087	D	0.999589	D	0.69078	0.997	P	0.58210	0.835	D	0.97610	1.0129	10	0.72032	D	0.01	-11.5427	15.454	0.75299	0.0:0.0:0.8602:0.1398	.	569	O60306	AQR_HUMAN	T	569	ENSP00000156471:P569T	ENSP00000156471:P569T	P	-	1	0	AQR	32986164	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.416000	0.97383	1.252000	0.44001	0.591000	0.81541	CCC	.	.		0.388	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		T	35198872	G	T	35198872	3	4	101	1	0	0	0	0	1	0	0	0	835	1174	41	3	2824	3	AQR	15	35198872	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2269944	35198872	67332520	444	14281										
BAHD1	22893	hgsc.bcm.edu	37	chr15	40757537	40757537	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acctgtctccctttgagcccTtgcagaatgaagtgtttgca	9	11	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:40757537T>A	ENST00000416165.1	+	6	2127	c.2056T>A	c.(2056-2058)Ttg>Atg	p.L686M	BAHD1_ENST00000560846.1_Intron|BAHD1_ENST00000561234.1_Missense_Mutation_p.L685M|RP11-64K12.8_ENST00000559730.1_RNA	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	686	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		CTTTGAGCCCTTGCAGAATGA	0.537																																					p.L686M		Atlas-SNP	.											.	BAHD1	68	.	0			c.T2056A						.						166	124	138					15																	40757537		2203	4300	6503	SO:0001583	missense	22893	exon6			GAGCCCTTGCAGA	AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.2056T>A	chr15.hg19:g.40757537T>A	ENSP00000396976:p.Leu686Met	70.0	0.0		119.0	13.0	NM_014952	Q8NDF7|Q9Y2F4	Missense_Mutation	SNP	ENST00000416165.1	hg19	CCDS10058.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.518522	0.64634	.	.	ENSG00000140320	ENST00000416165	T	0.19669	2.13	5.75	5.75	0.90469	Bromo adjacent homology (BAH) domain (3);	0.177862	0.39407	N	0.001364	T	0.35068	0.0919	L	0.50333	1.59	0.80722	D	1	D;D	0.61697	0.99;0.987	P;P	0.62298	0.9;0.838	T	0.03493	-1.1031	10	0.36615	T	0.2	-6.7082	11.1463	0.48432	0.0:0.0:0.1535:0.8465	.	686;685	Q8TBE0;Q8TBE0-2	BAHD1_HUMAN;.	M	686	ENSP00000396976:L686M	ENSP00000396976:L686M	L	+	1	2	BAHD1	38544829	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	2.232000	0.43018	2.191000	0.70037	0.533000	0.62120	TTG	.	.		0.537	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		A	40757537	T	A	40757537	3	1	101	1	0	0	0	0	1	0	0	0	1297	1606	56	4	2074	4	BAHD1	15	40757537	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	5558665	40757537	61773855	445	14282										
MGA	23269	hgsc.bcm.edu	37	chr15	42028515	42028522	+	Frame_Shift_Del	DEL	TTTGAGCA	TTTGAGCA	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaggaagatcggaacaagatTttgagcatcttatcccagca							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	TTTGAGCA	TTTGAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:42028515_42028522delTTTGAGCA	ENST00000570161.1	+	12	4053_4060	c.4053_4060delTTTGAGCA	c.(4051-4062)attttgagcatcfs	p.ILSI1351fs	MGA_ENST00000566586.1_Frame_Shift_Del_p.ILSI1351fs|MGA_ENST00000545763.1_Frame_Shift_Del_p.ILSI1351fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.ILSI1351fs|MGA_ENST00000219905.7_Frame_Shift_Del_p.ILSI1351fs			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.S1353N(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GGAACAAGATTTTGAGCATCTTATCCCA	0.471																																					p.1351_1353del		Atlas-Indel,Pindel	.											.	MGA	264	.	1	Substitution - Missense(1)	endometrium(1)	c.4052_4059del						.																																			SO:0001589	frameshift_variant	23269	exon13			.	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.4053_4060delTTTGAGCA	chr15.hg19:g.42028515_42028522delTTTGAGCA	ENSP00000457035:p.Ile1351fs	87.0	0.0		129.0	39.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.471	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		-	42028522	TTTGAGCA	-	42028515	7	5	101	1	0	1	0	1	0	0	0	0	9549	1829	64	0	4099	0	MGA	15	42028515	Frame_Shift_Del	DEL	TTTGAGCA	TCGA-DD-A1EE-01A-11D-A12Z-10	1270978	42028515	60502877	446	14283										
TGM7	116179	hgsc.bcm.edu	37	chr15	43571883	43571883	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaagggcttctgggtaccacCcccatgcagcagggcctgtg	14	13	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:43571883C>T	ENST00000452443.2	-	10	1622	c.1618G>A	c.(1618-1620)Ggt>Agt	p.G540S		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	540					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	TGGGTACCACCCCCATGCAGC	0.642																																					p.G540S		Atlas-SNP	.											.	TGM7	86	.	0			c.G1618A						.						93	94	94					15																	43571883		2202	4299	6501	SO:0001583	missense	116179	exon10			TACCACCCCCATG	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1618G>A	chr15.hg19:g.43571883C>T	ENSP00000389466:p.Gly540Ser	32.0	0.0		101.0	14.0	NM_052955		Missense_Mutation	SNP	ENST00000452443.2	hg19	CCDS32213.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.607287	0.46527	.	.	ENSG00000159495	ENST00000452443	T	0.68331	-0.32	4.69	4.69	0.59074	Transglutaminase, C-terminal (1);Immunoglobulin-like fold (1);	0.121727	0.56097	D	0.000026	T	0.71702	0.3371	M	0.78801	2.425	0.19300	N	0.999973	D	0.59767	0.986	P	0.48304	0.573	T	0.69323	-0.5175	10	0.59425	D	0.04	-12.9329	13.0102	0.58727	0.0:1.0:0.0:0.0	.	540	Q96PF1	TGM7_HUMAN	S	540	ENSP00000389466:G540S	ENSP00000389466:G540S	G	-	1	0	TGM7	41359175	0.137000	0.22531	0.076000	0.20297	0.693000	0.40251	1.492000	0.35594	2.427000	0.82271	0.655000	0.94253	GGT	.	.		0.642	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		T	43571883	C	T	43571883	3	4	101	1	0	0	0	0	1	0	0	0	15850	623	22	3	530	3	TGM7	15	43571883	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1543368	43571883	58959509	447	14284										
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43749109	43749109	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggatactatcattttcagcaGgaacaaatttagaattgaga	8	5	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:43749109G>C	ENST00000263801.3	-	12	1934	c.1682C>G	c.(1681-1683)cCt>cGt	p.P561R	TP53BP1_ENST00000382039.3_Missense_Mutation_p.P566R|TP53BP1_ENST00000605155.1_5'Flank|TP53BP1_ENST00000450115.2_Missense_Mutation_p.P566R|TP53BP1_ENST00000382044.4_Missense_Mutation_p.P566R	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	561					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		ATTTTCAGCAGGAACAAATTT	0.413								Other conserved DNA damage response genes																													p.P566R		Atlas-SNP	.											.	TP53BP1	157	.	0			c.C1697G						.						147	134	139					15																	43749109		2201	4298	6499	SO:0001583	missense	7158	exon12			TCAGCAGGAACAA	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.1682C>G	chr15.hg19:g.43749109G>C	ENSP00000263801:p.Pro561Arg	88.0	0.0		156.0	7.0	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	hg19	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	G	8.830	0.939737	0.18281	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.16597	2.33;2.33;2.33;2.33;2.33	5.04	3.13	0.36017	.	0.321644	0.29995	N	0.010668	T	0.13200	0.0320	L	0.38838	1.175	0.31601	N	0.652675	B;B;B;B	0.09022	0.002;0.001;0.001;0.001	B;B;B;B	0.09377	0.004;0.001;0.003;0.003	T	0.05971	-1.0853	10	0.51188	T	0.08	-1.3124	8.7541	0.34635	0.0775:0.2843:0.6381:0.0	.	566;561;566;566	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	R	561;566;566;566;566	ENSP00000263801:P561R;ENSP00000371475:P566R;ENSP00000371470:P566R;ENSP00000393497:P566R;ENSP00000388028:P566R	ENSP00000263801:P561R	P	-	2	0	TP53BP1	41536401	0.048000	0.20356	1.000000	0.80357	0.663000	0.39108	1.628000	0.37060	0.609000	0.30018	0.563000	0.77884	CCT	.	.		0.413	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			C	43749109	G	C	43749109	3	2	101	1	0	0	0	0	1	0	0	0	16398	1000	35	4	4304	4	TP53BP1	15	43749109	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	177226	43749109	58782283	448	14285										
DUOXA2	405753	hgsc.bcm.edu	37	chr15	45408389	45408389	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acatcctacaaagccttcagCgcagcgcgcgttacagcccg	9	16	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:45408389C>A	ENST00000323030.5	+	3	558	c.273C>A	c.(271-273)agC>agA	p.S91R	DUOX2_ENST00000389039.6_5'Flank|DUOX2_ENST00000603300.1_5'Flank	NM_207581.3	NP_997464.2	Q1HG44	DOXA2_HUMAN	dual oxidase maturation factor 2	91					hydrogen peroxide metabolic process (GO:0042743)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)							all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		AAGCCTTCAGCGCAGCGCGCG	0.572																																					p.S91R		Atlas-SNP	.											.	DUOXA2	38	.	0			c.C273A						.						139	132	134					15																	45408389		2002	4151	6153	SO:0001583	missense	405753	exon3			CTTCAGCGCAGCG	BX537581	CCDS10118.2	15q21.1	2008-10-30		2006-07-25	ENSG00000140274	ENSG00000140274			32698	protein-coding gene	gene with protein product		612772				16651268	Standard	NM_207581		Approved		uc001zuo.3	Q1HG44	OTTHUMG00000131354	ENST00000323030.5:c.273C>A	chr15.hg19:g.45408389C>A	ENSP00000319705:p.Ser91Arg	36.0	0.0		112.0	13.0	NM_207581	B2RPI9|H0YNQ6	Missense_Mutation	SNP	ENST00000323030.5	hg19	CCDS10118.2	.	.	.	.	.	.	.	.	.	.	C	14.81	2.646005	0.47258	.	.	ENSG00000140274	ENST00000323030	T	0.67865	-0.29	5.41	-9.39	0.00619	.	0.117307	0.85682	D	0.000000	T	0.78742	0.4331	M	0.79123	2.44	0.31474	N	0.668055	D	0.76494	0.999	D	0.71870	0.975	T	0.82678	-0.0338	10	0.72032	D	0.01	-18.1639	23.4889	0.99983	0.0:0.8007:0.0:0.1993	.	91	Q1HG44	DOXA2_HUMAN	R	91	ENSP00000319705:S91R	ENSP00000319705:S91R	S	+	3	2	DUOXA2	43195681	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-0.207000	0.09384	-2.250000	0.00701	-1.267000	0.01435	AGC	.	.		0.572	DUOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254142.1	NM_207581		A	45408389	C	A	45408389	3	1	101	1	0	0	0	0	1	0	0	0	4805	767	27	1	283	1	DUOXA2	15	45408389	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1659280	45408389	57123003	449	14286										
PLDN	26258	hgsc.bcm.edu	37	chr15	45884374	45884374	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atgaagggttaatagaggacTtgactatagaagacaaagca	11	4	0	5			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:45884374T>A	ENST00000220531.3	+	2	445	c.124T>A	c.(124-126)Ttg>Atg	p.L42M	BLOC1S6_ENST00000562384.1_Intron|BLOC1S6_ENST00000565216.1_Intron|BLOC1S6_ENST00000565323.1_Missense_Mutation_p.L47M|RP11-96O20.4_ENST00000564080.1_Intron|BLOC1S6_ENST00000568816.1_5'UTR|Y_RNA_ENST00000363549.1_RNA|BLOC1S6_ENST00000566753.1_Missense_Mutation_p.L42M|BLOC1S6_ENST00000564765.1_5'UTR|BLOC1S6_ENST00000565409.1_5'UTR|BLOC1S6_ENST00000567740.1_Intron|BLOC1S6_ENST00000567461.1_Intron	NM_012388.2	NP_036520.1	Q9UL45	BL1S6_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	42					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|endosome to melanosome transport (GO:0035646)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of pigment cell differentiation (GO:0050942)|post-Golgi vesicle-mediated transport (GO:0006892)|secretion of lysosomal enzymes (GO:0033299)|synaptic vesicle docking involved in exocytosis (GO:0016081)	BLOC-1 complex (GO:0031083)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|transport vesicle (GO:0030133)	actin filament binding (GO:0051015)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)										AATAGAGGACTTGACTATAGA	0.398																																					p.L42M		Atlas-SNP	.											.	.	.	.	0			c.T124A						.						94	93	93					15																	45884374		2198	4298	6496	SO:0001583	missense	26258	exon2			GAGGACTTGACTA	AF080470	CCDS10126.1	15q21.1	2013-09-27	2012-08-07	2012-08-01	ENSG00000104164	ENSG00000104164		"Biogenesis of lysosomal organelles complex-1 subunits"	8549	protein-coding gene	gene with protein product		604310	"pallid (mouse) homolog, pallidin", "pallidin homolog (mouse)"	PA, PLDN		10610180	Standard	NM_012388		Approved	HPS9	uc001zvq.3	Q9UL45	OTTHUMG00000131477	ENST00000220531.3:c.124T>A	chr15.hg19:g.45884374T>A	ENSP00000220531:p.Leu42Met	53.0	0.0		133.0	7.0	NM_012388		Missense_Mutation	SNP	ENST00000220531.3	hg19	CCDS10126.1	.	.	.	.	.	.	.	.	.	.	T	17.76	3.467683	0.63625	.	.	ENSG00000104164	ENST00000220531	.	.	.	5.74	0.369	0.16151	.	0.559941	0.20041	N	0.100502	T	0.47563	0.1452	L	0.47716	1.5	0.58432	D	0.999999	P	0.40875	0.731	P	0.47528	0.549	T	0.39781	-0.9597	9	0.59425	D	0.04	1.1294	4.9159	0.13846	0.0:0.1755:0.295:0.5295	.	42	Q9UL45	PLDN_HUMAN	M	42	.	ENSP00000220531:L42M	L	+	1	2	PLDN	43671666	0.159000	0.22864	0.409000	0.26459	0.884000	0.51177	-0.555000	0.05999	0.085000	0.17107	0.460000	0.39030	TTG	.	.		0.398	BLOC1S6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254320.2	NM_012388		A	45884374	T	A	45884374	3	1	101	1	0	0	0	0	1	0	0	0	12060	1606	56	4	130	4	PLDN	15	45884374	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	475985	45884374	56647018	450	14287										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48063289	48063289	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tacaacacgtctttctcaaaCtccaatgctcacaaagctga	4	13	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:48063289C>A	ENST00000316364.5	+	19	2968	c.2529C>A	c.(2527-2529)aaC>aaA	p.N843K	SEMA6D_ENST00000536845.2_Missense_Mutation_p.N843K|SEMA6D_ENST00000389432.2_Missense_Mutation_p.N800K|SEMA6D_ENST00000537942.1_Missense_Mutation_p.N781K|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000389433.2_Missense_Mutation_p.N824K|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000354744.4_Missense_Mutation_p.N787K|SEMA6D_ENST00000389428.3_Missense_Mutation_p.N768K|SEMA6D_ENST00000358066.4_Missense_Mutation_p.N781K|SEMA6D_ENST00000558014.1_Missense_Mutation_p.N781K	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	843					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CTTTCTCAAACTCCAATGCTC	0.458																																					p.N843K		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C2529A						.						105	96	99					15																	48063289		2198	4297	6495	SO:0001583	missense	80031	exon19			CTCAAACTCCAAT	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.2529C>A	chr15.hg19:g.48063289C>A	ENSP00000324857:p.Asn843Lys	69.0	0.0		210.0	10.0	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	C	11.11	1.543237	0.27563	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428	T;T;T;T;T;T;T;T	0.16897	2.31;2.34;2.34;2.31;2.31;2.31;2.31;2.32	5.58	2.23	0.28157	.	0.601453	0.16987	N	0.191479	T	0.11281	0.0275	N	0.22421	0.69	0.80722	D	1	B;P;B;P	0.47762	0.43;0.9;0.227;0.622	B;B;B;B	0.42522	0.1;0.39;0.138;0.146	T	0.15723	-1.0427	10	0.29301	T	0.29	.	8.8988	0.35481	0.0:0.6408:0.0:0.3592	.	768;787;843;781	Q8NFY4-3;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;SEM6D_HUMAN;.	K	781;843;843;824;800;787;781;768	ENSP00000442040:N781K;ENSP00000446152:N843K;ENSP00000324857:N843K;ENSP00000374084:N824K;ENSP00000374083:N800K;ENSP00000346786:N787K;ENSP00000350770:N781K;ENSP00000374079:N768K	ENSP00000324857:N843K	N	+	3	2	SEMA6D	45850581	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	0.593000	0.23999	0.712000	0.32039	0.563000	0.77884	AAC	.	.		0.458	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48063289	C	A	48063289	3	1	101	1	0	0	0	0	1	0	0	0	14057	564	20	3	2642	3	SEMA6D	15	48063289	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2178915	48063289	54468103	451	14288										
SHC4	399694	hgsc.bcm.edu	37	chr15	49148299	49148299	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atcttctctctcctcggcatGgctatcaatatgcacctcct	5	15	4	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:49148299G>A	ENST00000332408.4	-	8	1521	c.1093C>T	c.(1093-1095)Cat>Tat	p.H365Y	SHC4_ENST00000537958.1_Missense_Mutation_p.H79Y|SHC4_ENST00000396535.3_Missense_Mutation_p.H122Y	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	365	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		TCCTCGGCATGGCTATCAATA	0.448																																					p.H365Y		Atlas-SNP	.											.	SHC4	70	.	0			c.C1093T						.						137	129	132					15																	49148299		2197	4294	6491	SO:0001583	missense	399694	exon8			CGGCATGGCTATC	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"SH2 domain containing"	16743	protein-coding gene	gene with protein product	"rai-like protein"						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.1093C>T	chr15.hg19:g.49148299G>A	ENSP00000329668:p.His365Tyr	79.0	0.0		159.0	10.0	NM_203349	Q6UXQ3|Q8IYW3	Missense_Mutation	SNP	ENST00000332408.4	hg19	CCDS10130.1	.	.	.	.	.	.	.	.	.	.	G	4.357	0.065842	0.08388	.	.	ENSG00000185634	ENST00000332408;ENST00000396535;ENST00000537958	T;T;T	0.30182	3.55;1.54;1.55	5.14	0.673	0.17941	.	1.508310	0.03699	N	0.248252	T	0.15089	0.0364	N	0.08118	0	0.09310	N	1	B;B	0.30709	0.291;0.035	B;B	0.25884	0.064;0.009	T	0.18366	-1.0339	10	0.62326	D	0.03	-6.9214	2.2079	0.03940	0.1485:0.1126:0.3831:0.3559	.	122;365	Q6S5L8-2;Q6S5L8	.;SHC4_HUMAN	Y	365;122;79	ENSP00000329668:H365Y;ENSP00000379786:H122Y;ENSP00000443300:H79Y	ENSP00000329668:H365Y	H	-	1	0	SHC4	46935591	0.003000	0.15002	0.002000	0.10522	0.041000	0.13682	0.523000	0.22925	0.010000	0.14839	0.655000	0.94253	CAT	.	.		0.448	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349		A	49148299	G	A	49148299	3	1	101	1	0	0	0	0	1	0	0	0	14288	1348	47	3	819	3	SHC4	15	49148299	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1085010	49148299	53383093	452	14289										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51791589	51791589	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttcagtgtctccaaatttgaCagcatgcttccactgtgcat	7	11	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:51791589C>G	ENST00000251076.5	-	18	4119	c.3832G>C	c.(3832-3834)Gtc>Ctc	p.V1278L	DMXL2_ENST00000543779.2_Missense_Mutation_p.V1278L|DMXL2_ENST00000449909.3_Intron|RP11-707P17.1_ENST00000561007.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1278						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		CCAAATTTGACAGCATGCTTC	0.413																																					p.V1278L		Atlas-SNP	.											.	DMXL2	262	.	0			c.G3832C						.						183	178	180					15																	51791589		2195	4293	6488	SO:0001583	missense	23312	exon18			ATTTGACAGCATG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.3832G>C	chr15.hg19:g.51791589C>G	ENSP00000251076:p.Val1278Leu	75.0	0.0		171.0	17.0	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	1.984	-0.433474	0.04669	.	.	ENSG00000104093	ENST00000251076;ENST00000543779	T;T	0.20738	2.05;2.05	5.66	4.73	0.59995	.	0.164769	0.53938	D	0.000051	T	0.13970	0.0338	N	0.25647	0.755	0.80722	D	1	B;B	0.18741	0.03;0.017	B;B	0.17433	0.018;0.011	T	0.07404	-1.0774	10	0.27785	T	0.31	.	9.6847	0.40091	0.0:0.7935:0.0:0.2065	.	1278;1278	F5GWF1;Q8TDJ6	.;DMXL2_HUMAN	L	1278	ENSP00000251076:V1278L;ENSP00000441858:V1278L	ENSP00000251076:V1278L	V	-	1	0	DMXL2	49578881	0.999000	0.42202	1.000000	0.80357	0.901000	0.52897	1.791000	0.38744	2.669000	0.90835	0.591000	0.81541	GTC	.	.		0.413	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		G	51791589	C	G	51791589	3	3	101	1	0	0	0	0	1	0	0	0	4597	478	17	4	5385	4	DMXL2	15	51791589	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2643290	51791589	50739803	453	14290										
LEO1	123169	hgsc.bcm.edu	37	chr15	52251010	52251010	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaattcatcttcataatactGaggatcaaaaggtctacaaa	5	7	5	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:52251010G>T	ENST00000299601.5	-	6	1234	c.1174C>A	c.(1174-1176)Cag>Aag	p.Q392K	LEO1_ENST00000315141.5_Intron	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	392					endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		TCATAATACTGAGGATCAAAA	0.269																																					p.Q392K	Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)	Atlas-SNP	.											.	LEO1	46	.	0			c.C1174A						.						77	76	76					15																	52251010		2194	4288	6482	SO:0001583	missense	123169	exon6			AATACTGAGGATC	AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.1174C>A	chr15.hg19:g.52251010G>T	ENSP00000299601:p.Gln392Lys	99.0	0.0		317.0	17.0	NM_138792	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	hg19	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.433155	0.62844	.	.	ENSG00000166477	ENST00000299601;ENST00000538386	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.42966	0.1226	N	0.13168	0.305	0.80722	D	1	B	0.27910	0.193	B	0.27715	0.082	T	0.28522	-1.0041	9	0.18710	T	0.47	.	19.1406	0.93445	0.0:0.0:1.0:0.0	.	392	Q8WVC0	LEO1_HUMAN	K	392;370	.	ENSP00000299601:Q392K	Q	-	1	0	LEO1	50038302	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	9.602000	0.98312	2.619000	0.88677	0.557000	0.71058	CAG	.	.		0.269	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792		T	52251010	G	T	52251010	3	4	101	1	0	0	0	0	1	0	0	0	8735	1299	45	3	854	3	LEO1	15	52251010	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	459421	52251010	50280382	454	14291										
LEO1	123169	hgsc.bcm.edu	37	chr15	52258056	52258056	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctcttcatcagacagctgtGgttgttcttcatcatcagaa	7	10	7	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:52258056G>C	ENST00000299601.5	-	2	764	c.704C>G	c.(703-705)cCa>cGa	p.P235R	LEO1_ENST00000315141.5_Missense_Mutation_p.P235R	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	235	Asp-rich.				endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		AGACAGCTGTGGTTGTTCTTC	0.423																																					p.P235R	Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)	Atlas-SNP	.											.	LEO1	46	.	0			c.C704G						.						246	246	246					15																	52258056		2195	4293	6488	SO:0001583	missense	123169	exon2			AGCTGTGGTTGTT	AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.704C>G	chr15.hg19:g.52258056G>C	ENSP00000299601:p.Pro235Arg	148.0	0.0		477.0	35.0	NM_138792	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	hg19	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.003248	0.35320	.	.	ENSG00000166477	ENST00000299601;ENST00000315141	.	.	.	4.84	4.84	0.62591	.	0.261206	0.40818	N	0.001011	T	0.42517	0.1206	N	0.16478	0.41	0.80722	D	1	B;B	0.11235	0.004;0.001	B;B	0.09377	0.004;0.001	T	0.24835	-1.0149	9	0.18276	T	0.48	.	18.1449	0.89651	0.0:0.0:1.0:0.0	.	235;235	Q8WVC0-2;Q8WVC0	.;LEO1_HUMAN	R	235	.	ENSP00000299601:P235R	P	-	2	0	LEO1	50045348	0.997000	0.39634	0.555000	0.28281	0.965000	0.64279	3.722000	0.54948	2.509000	0.84616	0.655000	0.94253	CCA	.	.		0.423	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792		C	52258056	G	C	52258056	3	2	101	1	0	0	0	0	1	0	0	0	8735	1348	47	4	1340	4	LEO1	15	52258056	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	7046	52258056	50273336	455	14292										
GNB5	10681	hgsc.bcm.edu	37	chr15	52476791	52476791	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agctgagttgttgagacttcTtgaaaactggtctcagagct	11	7	2	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:52476791T>A	ENST00000261837.7	-	2	148	c.83A>T	c.(82-84)aAg>aTg	p.K28M	RP11-430B1.2_ENST00000560518.1_lincRNA	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	28					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		TTGAGACTTCTTGAAAACTGG	0.378																																					p.K28M		Atlas-SNP	.											.	GNB5	28	.	0			c.A83T						.						129	123	125					15																	52476791		2195	4293	6488	SO:0001583	missense	10681	exon2			GACTTCTTGAAAA	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"WD repeat domain containing"	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.83A>T	chr15.hg19:g.52476791T>A	ENSP00000261837:p.Lys28Met	60.0	0.0		112.0	10.0	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Missense_Mutation	SNP	ENST00000261837.7	hg19	CCDS10149.1	.	.	.	.	.	.	.	.	.	.	T	14.42	2.528624	0.44969	.	.	ENSG00000069966	ENST00000261837	T	0.61627	0.09	5.78	4.63	0.57726	.	0.222920	0.29480	N	0.012030	T	0.46308	0.1386	L	0.36672	1.1	0.80722	D	1	B	0.19445	0.036	B	0.17979	0.02	T	0.47235	-0.9133	10	0.59425	D	0.04	-28.8729	10.0548	0.42239	0.2612:0.0:0.0:0.7388	.	28	O14775	GBB5_HUMAN	M	28	ENSP00000261837:K28M	ENSP00000261837:K28M	K	-	2	0	GNB5	50264083	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.474000	0.60203	2.195000	0.70347	0.528000	0.53228	AAG	.	.		0.378	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			A	52476791	T	A	52476791	3	1	101	1	0	0	0	0	1	0	0	0	6529	1609	56	4	1152	4	GNB5	15	52476791	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	218735	52476791	50054601	456	14293										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54592572	54592572	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tccatttatcaagctatgacGtaagtactacagaacattta	5	8	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:54592572G>A	ENST00000260323.11	+	12	4268		c.e12+1		UNC13C_ENST00000545554.1_Splice_Site|UNC13C_ENST00000537900.1_Splice_Site	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)						exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AAGCTATGACGTAAGTACTAC	0.328																																					.		Atlas-SNP	.											.	UNC13C	674	.	0			c.4268+1G>A						.						81	71	74					15																	54592572		1824	4108	5932	SO:0001630	splice_region_variant	440279	exon11			TATGACGTAAGTA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.4268+1G>A	chr15.hg19:g.54592572G>A		66.0	0.0		104.0	6.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Splice_Site	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.754855	0.89843	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6257	0.91336	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UNC13C	52379864	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.799000	0.99117	2.640000	0.89533	0.655000	0.94253	.	.	.		0.328	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	Intron	A	54592572	G	A	54592572	5	1	101	1	0	0	0	0	0	0	1	0	17001	1159	40	1	4311	1	UNC13C	15	54592572	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2115781	54592572	47938820	457	14294										
STOML1	9399	hgsc.bcm.edu	37	chr15	74277722	74277722	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcctcccaggaagtgcagggCcagctgctggagggtgctgt	16	11	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:74277722C>A	ENST00000316900.5	-	5	851	c.727G>T	c.(727-729)Gcc>Tcc	p.A243S	STOML1_ENST00000359750.4_Missense_Mutation_p.A243S|STOML1_ENST00000541638.1_Missense_Mutation_p.A201S|STOML1_ENST00000561656.1_Missense_Mutation_p.A156S|STOML1_ENST00000316911.6_Missense_Mutation_p.A193S|STOML1_ENST00000564777.1_Missense_Mutation_p.A193S	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	243						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						AAGTGCAGGGCCAGCTGCTGG	0.692																																					p.A243S		Atlas-SNP	.											.	STOML1	22	.	0			c.G727T						.						21	19	20					15																	74277722		2198	4297	6495	SO:0001583	missense	9399	exon5			GCAGGGCCAGCTG	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"stomatin-like 1", "stomatin (EBP72)-like 1"	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.727G>T	chr15.hg19:g.74277722C>A	ENSP00000319323:p.Ala243Ser	50.0	0.0		104.0	15.0	NM_001256672	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Missense_Mutation	SNP	ENST00000316900.5	hg19	CCDS10254.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.455809	0.63401	.	.	ENSG00000067221	ENST00000316900;ENST00000316911;ENST00000541638;ENST00000359750	D;D;D;D	0.98221	-3.13;-2.71;-3.1;-4.8	5.22	4.31	0.51392	.	0.107947	0.64402	D	0.000006	D	0.96433	0.8836	L	0.29908	0.895	0.51482	D	0.999928	P;P;P;P;P;P	0.45827	0.791;0.666;0.867;0.666;0.578;0.791	P;B;P;B;B;B	0.50314	0.535;0.194;0.637;0.194;0.272;0.389	D	0.94849	0.8012	10	0.34782	T	0.22	-14.6048	10.6367	0.45569	0.0:0.9109:0.0:0.0891	.	201;243;193;243;243;243	B4DUU5;E7ESC0;Q9UBI4-2;Q4PNR4;Q53HB6;Q9UBI4	.;.;.;.;.;STML1_HUMAN	S	243;193;201;243	ENSP00000319323:A243S;ENSP00000319384:A193S;ENSP00000442478:A201S;ENSP00000352788:A243S	ENSP00000319323:A243S	A	-	1	0	STOML1	72064775	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.057000	0.49931	1.201000	0.43203	0.655000	0.94253	GCC	.	.		0.692	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809		A	74277722	C	A	74277722	3	1	101	1	0	0	0	0	1	0	0	0	15328	739	26	3	481	3	STOML1	15	74277722	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	19685150	74277722	28253670	458	14295										
RCN2	5955	hgsc.bcm.edu	37	chr15	77227917	77227917	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttaagcattatgctatgcaaGaagcaaaacaacagtttgtt	7	6	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:77227917G>A	ENST00000394885.3	+	3	524	c.301G>A	c.(301-303)Gaa>Aaa	p.E101K	RCN2_ENST00000320963.5_Missense_Mutation_p.E101K|RCN2_ENST00000394883.3_Intron	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	101	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						TGCTATGCAAGAAGCAAAACA	0.348																																					p.E101K		Atlas-SNP	.											.	RCN2	16	.	0			c.G301A						.						165	146	153					15																	77227917		2196	4294	6490	SO:0001583	missense	5955	exon3			ATGCAAGAAGCAA	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"EF-hand domain containing"	9935	protein-coding gene	gene with protein product	"Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.301G>A	chr15.hg19:g.77227917G>A	ENSP00000378349:p.Glu101Lys	49.0	0.0		176.0	15.0	NM_002902	A8MTG6|F8WCY5|Q53XN8	Missense_Mutation	SNP	ENST00000394885.3	hg19	CCDS10291.1	.	.	.	.	.	.	.	.	.	.	G	34	5.408127	0.96051	.	.	ENSG00000117906	ENST00000394885;ENST00000320963	T;T	0.74315	-0.83;-0.83	5.47	5.47	0.80525	EF-hand-like domain (1);	0.048133	0.85682	D	0.000000	T	0.81475	0.4830	M	0.80183	2.485	0.80722	D	1	D;P	0.53462	0.96;0.92	P;P	0.47603	0.497;0.551	D	0.84779	0.0772	10	0.72032	D	0.01	-22.0183	19.328	0.94270	0.0:0.0:1.0:0.0	.	101;101	F8WCY5;Q14257	.;RCN2_HUMAN	K	101	ENSP00000378349:E101K;ENSP00000319739:E101K	ENSP00000319739:E101K	E	+	1	0	RCN2	75014972	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.789000	0.91839	2.559000	0.86315	0.591000	0.81541	GAA	.	.		0.348	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902		A	77227917	G	A	77227917	3	1	101	1	0	0	0	0	1	0	0	0	13195	943	33	3	311	3	RCN2	15	77227917	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2950195	77227917	25303475	459	14296										
RCN2	5955	hgsc.bcm.edu	37	chr15	77241537	77241537	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atggcagacagctccatgatGactatttctatcatgatgag	9	8	2	5			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:77241537G>T	ENST00000394885.3	+	7	1151	c.928G>T	c.(928-930)Gac>Tac	p.D310Y	RCN2_ENST00000320963.5_Missense_Mutation_p.D328Y|RCN2_ENST00000394883.3_Missense_Mutation_p.D209Y	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	310						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						GCTCCATGATGACTATTTCTA	0.388																																					p.D328Y		Atlas-SNP	.											.	RCN2	16	.	0			c.G982T						.						101	102	102					15																	77241537		2196	4294	6490	SO:0001583	missense	5955	exon8			CATGATGACTATT	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"EF-hand domain containing"	9935	protein-coding gene	gene with protein product	"Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.928G>T	chr15.hg19:g.77241537G>T	ENSP00000378349:p.Asp310Tyr	41.0	0.0		77.0	4.0	NM_001271837	A8MTG6|F8WCY5|Q53XN8	Missense_Mutation	SNP	ENST00000394885.3	hg19	CCDS10291.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.673307	0.47781	.	.	ENSG00000117906	ENST00000394885;ENST00000320963;ENST00000394883	T;T;T	0.76316	-1.01;-0.05;0.73	5.91	4.02	0.46733	.	0.316616	0.39834	N	0.001243	T	0.62696	0.2449	N	0.12182	0.205	0.38267	D	0.942036	P;P;P	0.52842	0.956;0.904;0.828	P;P;B	0.44811	0.459;0.461;0.34	T	0.70417	-0.4877	10	0.87932	D	0	-16.8327	10.2245	0.43216	0.1882:0.0:0.8118:0.0	.	209;328;310	A8MXP8;F8WCY5;Q14257	.;.;RCN2_HUMAN	Y	310;328;209	ENSP00000378349:D310Y;ENSP00000319739:D328Y;ENSP00000378347:D209Y	ENSP00000319739:D328Y	D	+	1	0	RCN2	75028592	0.997000	0.39634	0.999000	0.59377	0.998000	0.95712	2.133000	0.42093	2.809000	0.96659	0.555000	0.69702	GAC	.	.		0.388	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902		T	77241537	G	T	77241537	3	4	101	1	0	0	0	0	1	0	0	0	13195	1290	45	3	954	3	RCN2	15	77241537	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	13620	77241537	25289855	460	14297										
SGK269	79834	hgsc.bcm.edu	37	chr15	77425574	77425574	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gattttacccactacttcctCccgattctcaagtcctcgat	4	15	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:77425574C>A	ENST00000560626.2	-	6	4325	c.3850G>T	c.(3850-3852)Gag>Tag	p.E1284*	PEAK1_ENST00000312493.4_Nonsense_Mutation_p.E1284*			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1284					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ACTACTTCCTCCCGATTCTCA	0.532																																					p.E1284X		Atlas-SNP	.											.	.	.	.	0			c.G3850T						.						147	143	144					15																	77425574		1877	4106	5983	SO:0001587	stop_gained	0	exon7			CTTCCTCCCGATT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3850G>T	chr15.hg19:g.77425574C>A	ENSP00000452796:p.Glu1284*	100.0	0.0		321.0	33.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Nonsense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	46	12.343992	0.99659	.	.	ENSG00000173517	ENST00000312493	.	.	.	5.61	5.61	0.85477	.	0.107611	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-9.2526	12.908	0.58164	0.0:0.9258:0.0:0.0742	.	.	.	.	X	1284	.	ENSP00000309230:E1284X	E	-	1	0	AC087465.1	75212629	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.091000	0.71406	2.642000	0.89623	0.655000	0.94253	GAG	.	.		0.532	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			A	77425574	C	A	77425574	4	1	101	1	0	0	0	0	0	1	0	0	14226	864	30	3	1398	3	SGK269	15	77425574	Nonsense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	184037	77425574	25105818	461	14298										
LINGO1	84894	hgsc.bcm.edu	37	chr15	77906599	77906599	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agggtcttgatgtcgaagggGaaaggcacagtggcgcgggt	19	6	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:77906599G>T	ENST00000355300.6	-	2	1824	c.1650C>A	c.(1648-1650)ttC>ttA	p.F550L	LINGO1_ENST00000561030.1_Missense_Mutation_p.F544L	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	550					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						TGTCGAAGGGGAAAGGCACAG	0.612																																					p.F550L		Atlas-SNP	.											.	LINGO1	76	.	0			c.C1650A						.						127	133	131					15																	77906599		2166	4258	6424	SO:0001583	missense	84894	exon2			GAAGGGGAAAGGC	AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"Immunoglobulin superfamily / I-set domain containing"	21205	protein-coding gene	gene with protein product		609791	"leucine rich repeat neuronal 6A"	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.1650C>A	chr15.hg19:g.77906599G>T	ENSP00000347451:p.Phe550Leu	59.0	0.0		77.0	30.0	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Missense_Mutation	SNP	ENST00000355300.6	hg19	CCDS45313.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.617318	0.28801	.	.	ENSG00000169783	ENST00000355300	T	0.50548	0.74	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.45357	0.1338	L	0.60845	1.875	0.80722	D	1	B	0.14805	0.011	B	0.15484	0.013	T	0.32375	-0.9909	10	0.33940	T	0.23	.	14.3775	0.66889	0.0732:0.0:0.9268:0.0	.	550	Q96FE5	LIGO1_HUMAN	L	550	ENSP00000347451:F550L	ENSP00000347451:F550L	F	-	3	2	LINGO1	75693654	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.794000	0.62482	2.509000	0.84616	0.561000	0.74099	TTC	.	.		0.612	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808		T	77906599	G	T	77906599	3	4	101	1	0	0	0	0	1	0	0	0	8823	1165	41	3	216	3	LINGO1	15	77906599	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	481025	77906599	24624793	462	14299										
ARNT2	9915	hgsc.bcm.edu	37	chr15	80767490	80767490	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agagtggtttgggagcacacTgtatgaacaggtgcatcctg	14	7	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:80767490T>G	ENST00000303329.4	+	5	713	c.548T>G	c.(547-549)cTg>cGg	p.L183R	ARNT2_ENST00000531595.3_3'UTR|ARNT2_ENST00000527771.1_Missense_Mutation_p.L172R|ARNT2_ENST00000533983.1_Missense_Mutation_p.L172R	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	183	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			GGGAGCACACTGTATGAACAG	0.527																																					p.L183R		Atlas-SNP	.											.	ARNT2	88	.	0			c.T548G						.						120	115	117					15																	80767490		2203	4300	6503	SO:0001583	missense	9915	exon5			GCACACTGTATGA	AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"Basic helix-loop-helix proteins"	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.548T>G	chr15.hg19:g.80767490T>G	ENSP00000307479:p.Leu183Arg	69.0	0.0		162.0	31.0	NM_014862	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	hg19	CCDS32307.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.202645	0.79127	.	.	ENSG00000172379	ENST00000360062;ENST00000303329;ENST00000540859	T	0.19394	2.15	4.5	4.5	0.54988	PAS (2);PAS fold (1);	0.067492	0.56097	D	0.000022	T	0.57257	0.2041	H	0.94925	3.6	0.80722	D	1	D;D	0.89917	1.0;0.979	D;D	0.91635	0.999;0.971	T	0.71041	-0.4707	10	0.87932	D	0	.	13.9888	0.64353	0.0:0.0:0.0:1.0	.	183;183	Q9HBZ2;Q86TN1	ARNT2_HUMAN;.	R	172;183;183	ENSP00000307479:L183R	ENSP00000307479:L183R	L	+	2	0	ARNT2	78554545	1.000000	0.71417	0.815000	0.32552	0.884000	0.51177	7.149000	0.77396	1.883000	0.54544	0.448000	0.29417	CTG	.	.		0.527	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2			G	80767490	T	G	80767490	3	3	101	1	0	0	0	0	1	0	0	0	966	1580	55	5	566	5	ARNT2	15	80767490	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2860891	80767490	21763902	463	14300										
IL16	3603	hgsc.bcm.edu	37	chr15	81589305	81589305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgccactgctgctaccacagGaagacacagcagggagaagc	12	12	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:81589305G>A	ENST00000302987.4	+	12	1939	c.1939G>A	c.(1939-1941)Gaa>Aaa	p.E647K	IL16_ENST00000394652.2_5'UTR|IL16_ENST00000394660.2_Missense_Mutation_p.E647K			Q14005	IL16_HUMAN	interleukin 16	647					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GCTACCACAGGAAGACACAGC	0.602																																					p.E647K		Atlas-SNP	.											.	IL16	254	.	0			c.G1939A						.						35	39	38					15																	81589305		1963	4158	6121	SO:0001583	missense	3603	exon13			CCACAGGAAGACA	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1939G>A	chr15.hg19:g.81589305G>A	ENSP00000302935:p.Glu647Lys	41.0	0.0		195.0	33.0	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.460644	0.43736	.	.	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653	T;T	0.11063	2.81;2.81	4.7	4.7	0.59300	.	0.582759	0.14620	N	0.308470	T	0.15912	0.0383	M	0.65975	2.015	0.80722	D	1	B;B;B;B;B	0.26635	0.089;0.155;0.155;0.016;0.027	B;B;B;B;B	0.32864	0.034;0.043;0.154;0.021;0.047	T	0.07083	-1.0791	10	0.10636	T	0.68	.	15.7839	0.78286	0.0:0.0:1.0:0.0	.	141;184;37;647;647	Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;IL16_HUMAN;.	K	647;479;647;184;37	ENSP00000378155:E647K;ENSP00000302935:E647K	ENSP00000302935:E647K	E	+	1	0	IL16	79376360	1.000000	0.71417	0.985000	0.45067	0.317000	0.28152	2.648000	0.46647	2.305000	0.77605	0.655000	0.94253	GAA	.	.		0.602	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		A	81589305	G	A	81589305	3	1	101	1	0	0	0	0	1	0	0	0	7642	1175	41	3	1985	3	IL16	15	81589305	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	821815	81589305	20942087	464	14301										
STARD5	80765	hgsc.bcm.edu	37	chr15	81615246	81615246	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggcatgcacttacaggttcCctggaaactccacagatggc	10	12	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:81615246C>A	ENST00000302824.6	-	2	168	c.143G>T	c.(142-144)gGg>gTg	p.G48V	RP11-761I4.3_ENST00000559781.1_RNA|STARD5_ENST00000559913.1_5'UTR|RP11-761I4.3_ENST00000560973.1_RNA	NM_181900.2	NP_871629.1	Q9NSY2	STAR5_HUMAN	StAR-related lipid transfer (START) domain containing 5	48	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				C21-steroid hormone biosynthetic process (GO:0006700)|lipid transport (GO:0006869)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)	lipid binding (GO:0008289)			large_intestine(3)|ovary(1)|skin(1)|stomach(1)	6						TTACAGGTTCCCTGGAAACTC	0.483																																					p.G48V		Atlas-SNP	.											.	STARD5	20	.	0			c.G143T						.						76	76	76					15																	81615246		2203	4300	6503	SO:0001583	missense	80765	exon2			AGGTTCCCTGGAA	AF480304	CCDS10318.1	15q26	2011-09-12	2007-08-16		ENSG00000172345	ENSG00000172345		"StAR-related lipid transfer (START) domain containing"	18065	protein-coding gene	gene with protein product		607050	"START domain containing 5"			12011452	Standard	NM_181900		Approved	MGC10327	uc002bgm.3	Q9NSY2	OTTHUMG00000147342	ENST00000302824.6:c.143G>T	chr15.hg19:g.81615246C>A	ENSP00000304032:p.Gly48Val	68.0	0.0		154.0	14.0	NM_181900	P59094	Missense_Mutation	SNP	ENST00000302824.6	hg19	CCDS10318.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.868363	0.91587	.	.	ENSG00000172345	ENST00000302824	T	0.79247	-1.25	5.4	5.4	0.78164	Lipid-binding START (3);START-like domain (1);	0.000000	0.85682	D	0.000000	D	0.88987	0.6587	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86928	0.2071	10	0.25106	T	0.35	-11.9245	18.7698	0.91887	0.0:1.0:0.0:0.0	.	48	Q9NSY2	STAR5_HUMAN	V	48	ENSP00000304032:G48V	ENSP00000304032:G48V	G	-	2	0	STARD5	79402301	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.520000	0.73773	2.542000	0.85734	0.655000	0.94253	GGG	.	.		0.483	STARD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303950.2			A	81615246	C	A	81615246	3	1	101	1	0	0	0	0	1	0	0	0	15275	623	22	3	518	3	STARD5	15	81615246	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	25941	81615246	20916146	465	14302										
RHCG	51458	hgsc.bcm.edu	37	chr15	90023512	90023512	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caatcatggcaaagaggtccGactggtacacagaattctgt	10	9	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:90023512G>T	ENST00000268122.4	-	4	718	c.650C>A	c.(649-651)tCg>tAg	p.S217*	RHCG_ENST00000544600.1_Nonsense_Mutation_p.S217*	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	217					amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					AAAGAGGTCCGACTGGTACAC	0.547																																					p.S217X		Atlas-SNP	.											.	RHCG	49	.	0			c.C650A						.						205	179	188					15																	90023512		2200	4299	6499	SO:0001587	stop_gained	51458	exon4			AGGTCCGACTGGT	AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"Solute carriers"	18140	protein-coding gene	gene with protein product		605381	"chromosome 15 open reading frame 6", "Rhesus blood group, C glycoprotein"	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.650C>A	chr15.hg19:g.90023512G>T	ENSP00000268122:p.Ser217*	68.0	0.0		88.0	7.0	NM_016321	A8K4D4|Q6X3Y4	Nonsense_Mutation	SNP	ENST00000268122.4	hg19	CCDS10351.1	.	.	.	.	.	.	.	.	.	.	G	38	6.998013	0.97990	.	.	ENSG00000140519	ENST00000544600;ENST00000268122;ENST00000536247	.	.	.	5.59	5.59	0.84812	.	0.107977	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.7037	19.6374	0.95740	0.0:0.0:1.0:0.0	.	.	.	.	X	217;217;208	.	.	S	-	2	0	RHCG	87824516	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	9.830000	0.99415	2.647000	0.89833	0.558000	0.71614	TCG	.	.		0.547	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321		T	90023512	G	T	90023512	4	4	101	1	0	0	0	0	0	1	0	0	13341	1059	37	1	817	1	RHCG	15	90023512	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	8408266	90023512	12507880	466	14303										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94901714	94901714	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aactgcatgttttctagacaCtgtgtaagagtgcaaatccg	9	8	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:94901714C>T	ENST00000357742.4	+	9	1174	c.1174C>T	c.(1174-1176)Ctg>Ttg	p.L392L	MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000557742.1_Intron|MCTP2_ENST00000543482.1_Intron|MCTP2_ENST00000451018.3_Silent_p.L392L	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	392	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			TTTCTAGACACTGTGTAAGAG	0.378																																					p.L392L		Atlas-SNP	.											MCTP2,NS,carcinoma,0,1	MCTP2	122	.	0			c.C1174T						.						94	90	91					15																	94901714		2197	4298	6495	SO:0001819	synonymous_variant	55784	exon9			TAGACACTGTGTA	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.1174C>T	chr15.hg19:g.94901714C>T		36.0	0.0		104.0	0.0	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	hg19	CCDS32338.1																																																																																			.	.		0.378	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		T	94901714	C	T	94901714	2	4	101	1	0	0	0	0	0	0	0	1	9410	564	20	3		3	MCTP2	15	94901714	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4878202	94901714	7629678	467	14304										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94901825	94901825	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaaaggacaacaaaaagcatGaggaacgtctgggcacgtga	13	7	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:94901825G>C	ENST00000357742.4	+	9	1285	c.1285G>C	c.(1285-1287)Gag>Cag	p.E429Q	MCTP2_ENST00000331706.4_Missense_Mutation_p.E17Q|MCTP2_ENST00000557742.1_Missense_Mutation_p.E17Q|MCTP2_ENST00000543482.1_3'UTR|MCTP2_ENST00000451018.3_Missense_Mutation_p.E429Q	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	429	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			CAAAAAGCATGAGGAACGTCT	0.507																																					p.E429Q		Atlas-SNP	.											.	MCTP2	122	.	0			c.G1285C						.						114	99	104					15																	94901825		2197	4298	6495	SO:0001583	missense	55784	exon9			AAGCATGAGGAAC	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.1285G>C	chr15.hg19:g.94901825G>C	ENSP00000350377:p.Glu429Gln	49.0	0.0		140.0	20.0	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	hg19	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.593492	0.66219	.	.	ENSG00000140563	ENST00000451018;ENST00000331706;ENST00000357742	T;T;T	0.71579	2.97;-0.58;2.97	5.87	4.95	0.65309	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.093845	0.64402	N	0.000001	T	0.69691	0.3139	L	0.48362	1.52	0.58432	D	0.999997	B;B;B	0.32188	0.023;0.332;0.359	B;B;B	0.39503	0.073;0.135;0.301	T	0.67565	-0.5638	10	0.36615	T	0.2	.	16.6123	0.84886	0.0:0.1405:0.8595:0.0	.	429;17;429	Q6DN12-2;Q6DN12-4;Q6DN12	.;.;MCTP2_HUMAN	Q	429;17;429	ENSP00000395109:E429Q;ENSP00000329646:E17Q;ENSP00000350377:E429Q	ENSP00000329646:E17Q	E	+	1	0	MCTP2	92702829	1.000000	0.71417	0.990000	0.47175	0.914000	0.54420	6.074000	0.71253	1.454000	0.47793	0.650000	0.86243	GAG	.	.		0.507	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		C	94901825	G	C	94901825	3	2	101	1	0	0	0	0	1	0	0	0	9410	1291	45	4	1319	4	MCTP2	15	94901825	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	111	94901825	7629567	468	14305										
FAM169B	283777	hgsc.bcm.edu	37	chr15	99023985	99023985	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtttagaatgaaaagcacaaCcctttccccaaacgactgaa	6	11	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:99023985C>G	ENST00000558256.1	-	4	277	c.28G>C	c.(28-30)Gtt>Ctt	p.V10L	FAM169B_ENST00000332908.4_Missense_Mutation_p.V10L	NM_182562.2	NP_872368.2	Q8N8A8	F169B_HUMAN	family with sequence similarity 169, member B	10										large_intestine(3)|lung(3)|urinary_tract(1)	7						AAAAGCACAACCCTTTCCCCA	0.373																																					p.V10L		Atlas-SNP	.											.	FAM169B	23	.	0			c.G28C						.						72	69	70					15																	99023985		1864	4095	5959	SO:0001583	missense	283777	exon4			GCACAACCCTTTC		CCDS45360.1	15q26.3	2008-08-08			ENSG00000185087	ENSG00000185087			26835	protein-coding gene	gene with protein product							Standard	NM_182562		Approved	FLJ39743, KIAA0888L	uc002buk.1	Q8N8A8		ENST00000558256.1:c.28G>C	chr15.hg19:g.99023985C>G	ENSP00000453554:p.Val10Leu	59.0	0.0		116.0	8.0	NM_182562	B5MDL8	Missense_Mutation	SNP	ENST00000558256.1	hg19	CCDS45360.1	.	.	.	.	.	.	.	.	.	.	C	11.33	1.608089	0.28623	.	.	ENSG00000185087	ENST00000332908	T	0.72282	-0.64	5.27	2.89	0.33648	.	0.290655	0.33110	N	0.005280	T	0.50411	0.1614	N	0.17082	0.46	0.26442	N	0.975758	B	0.02656	0.0	B	0.01281	0.0	T	0.39231	-0.9624	10	0.44086	T	0.13	-9.8168	7.3417	0.26640	0.0:0.0771:0.1438:0.7791	.	10	Q8N8A8	F169B_HUMAN	L	10	ENSP00000332615:V10L	ENSP00000332615:V10L	V	-	1	0	FAM169B	96841508	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.945000	0.40273	0.283000	0.22279	-0.294000	0.09567	GTT	.	.		0.373	FAM169B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415488.1	NM_182562		G	99023985	C	G	99023985	3	3	101	1	0	0	0	0	1	0	0	0	5493	507	18	4	566	4	FAM169B	15	99023985	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4122160	99023985	3507407	469	14306										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101550657	101550657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccttcttctccatcgcaggcTacttgaaattgacatttcca	5	13	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr15:101550657T>C	ENST00000388948.3	+	8	1351	c.992T>C	c.(991-993)cTa>cCa	p.L331P	LRRK1_ENST00000284395.5_Missense_Mutation_p.L328P	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CATCGCAGGCTACTTGAAATT	0.373																																					p.L331P		Atlas-SNP	.											.	LRRK1	310	.	0			c.T992C						.						80	77	78					15																	101550657		1856	4083	5939	SO:0001583	missense	79705	exon8			GCAGGCTACTTGA	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.992T>C	chr15.hg19:g.101550657T>C	ENSP00000373600:p.Leu331Pro	104.0	0.0		198.0	71.0	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	T	17.29	3.352489	0.61293	.	.	ENSG00000154237	ENST00000388948;ENST00000284395	T;T	0.70631	-0.5;-0.5	5.67	4.53	0.55603	.	0.324362	0.25280	N	0.031802	D	0.88640	0.6491	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.90994	0.4837	10	0.87932	D	0	.	12.4414	0.55627	0.0:0.0:0.1403:0.8597	.	331	Q38SD2	LRRK1_HUMAN	P	331;328	ENSP00000373600:L331P;ENSP00000284395:L328P	ENSP00000284395:L328P	L	+	2	0	LRRK1	99368180	1.000000	0.71417	0.759000	0.31340	0.702000	0.40608	6.014000	0.70784	1.055000	0.40461	0.533000	0.62120	CTA	.	.		0.373	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		C	101550657	T	C	101550657	3	2	101	1	0	0	0	0	1	0	0	0	9041	1522	53	2	1018	2	LRRK1	15	101550657	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2526672	101550657	980735	470	14307										
MAPK8IP3	23162	hgsc.bcm.edu	37	chr16	1816311	1816311	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggaggtgccagaccctgggcCcagcgagccagagacagcca	15	14	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:1816311C>G	ENST00000250894.4	+	22	2874	c.2717C>G	c.(2716-2718)cCc>cGc	p.P906R	MAPK8IP3_ENST00000356010.5_Missense_Mutation_p.P900R	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	906					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						GACCCTGGGCCCAGCGAGCCA	0.687																																					p.P906R		Atlas-SNP	.											.	MAPK8IP3	164	.	0			c.C2717G						.						26	38	34					16																	1816311		2100	4233	6333	SO:0001583	missense	23162	exon22			CTGGGCCCAGCGA	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"homolog of Drosophila Sunday driver 2"	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.2717C>G	chr16.hg19:g.1816311C>G	ENSP00000250894:p.Pro906Arg	41.0	0.0		88.0	18.0	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Missense_Mutation	SNP	ENST00000250894.4	hg19	CCDS10442.2	.	.	.	.	.	.	.	.	.	.	C	11.03	1.520322	0.27211	.	.	ENSG00000138834	ENST00000250894;ENST00000356010	T;T	0.29142	1.58;1.58	5.09	5.09	0.68999	.	0.184910	0.47852	D	0.000212	T	0.32133	0.0819	L	0.54323	1.7	0.47547	D	0.999455	B;B;B	0.17667	0.012;0.023;0.023	B;B;B	0.25291	0.049;0.036;0.059	T	0.13629	-1.0502	10	0.66056	D	0.02	-23.231	12.5717	0.56341	0.0:0.9182:0.0:0.0818	.	907;900;906	B7ZMF3;E9PFH7;Q9UPT6	.;.;JIP3_HUMAN	R	906;900	ENSP00000250894:P906R;ENSP00000348290:P900R	ENSP00000250894:P906R	P	+	2	0	MAPK8IP3	1756312	1.000000	0.71417	0.900000	0.35374	0.221000	0.24807	4.671000	0.61590	2.387000	0.81309	0.561000	0.74099	CCC	.	.		0.687	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439		G	1816311	C	G	1816311	3	3	101	1	0	0	0	0	1	0	0	0	9295	623	22	4	2819	4	MAPK8IP3	16	1816311	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10		1816311	88538442	471	14308										
TSC2	7249	hgsc.bcm.edu	37	chr16	2098719	2098719	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccaggtctgcagagggtaaaCagacggagtttatcatcacc	11	10	3	2	rs137854105		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:2098719C>T	ENST00000219476.3	+	2	733	c.103C>T	c.(103-105)Cag>Tag	p.Q35*	TSC2_ENST00000439673.2_Nonsense_Mutation_p.Q35*|TSC2_ENST00000568454.1_Nonsense_Mutation_p.Q46*|TSC2_ENST00000382538.6_Intron|TSC2_ENST00000350773.4_Nonsense_Mutation_p.Q35*|TSC2_ENST00000401874.2_Nonsense_Mutation_p.Q35*|NTHL1_ENST00000219066.1_5'Flank|TSC2_ENST00000353929.4_Nonsense_Mutation_p.Q35*	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	35	Required for interaction with TSC1.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				AGAGGGTAAACAGACGGAGTT	0.493			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.Q35X		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.C103T						.						172	145	154					16																	2098719		2198	4299	6497	SO:0001587	stop_gained	7249	exon2	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GGTAAACAGACGG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.103C>T	chr16.hg19:g.2098719C>T	ENSP00000219476:p.Gln35*	78.0	0.0		184.0	10.0	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Nonsense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.768370	0.90020	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000350773;ENST00000445113	.	.	.	5.16	5.16	0.70880	.	0.211530	0.41294	D	0.000910	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-20.3627	18.6588	0.91465	0.0:1.0:0.0:0.0	.	.	.	.	X	35;35;35;35;35;46	.	ENSP00000219476:Q35X	Q	+	1	0	TSC2	2038720	1.000000	0.71417	0.921000	0.36526	0.909000	0.53808	5.108000	0.64609	2.403000	0.81681	0.563000	0.77884	CAG	.	.		0.493	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		T	2098719	C	T	2098719	4	4	101	1	0	0	0	0	0	1	0	0	16621	479	17	3	105	3	TSC2	16	2098719	Nonsense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	282408	2098719	88256034	472	14309										
RSL1D1	26156	hgsc.bcm.edu	37	chr16	11944139	11944139	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agaaaatcacaacttacaatCtgaccctcagttctttactt	3	11	4	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:11944139C>A	ENST00000571133.1	-	2	314	c.242G>T	c.(241-243)aGa>aTa	p.R81I	RP11-166B2.8_ENST00000574364.1_RNA|RSL1D1_ENST00000542106.1_Intron	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	81					osteoblast differentiation (GO:0001649)|regulation of apoptotic process (GO:0042981)|regulation of cellular senescence (GO:2000772)|regulation of protein localization (GO:0032880)	membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						AACTTACAATCTGACCCTCAG	0.318																																					p.R81I		Atlas-SNP	.											.	RSL1D1	40	.	0			c.G242T						.						86	81	83					16																	11944139		2197	4299	6496	SO:0001583	missense	26156	exon2			TACAATCTGACCC	AY154473	CCDS10551.1	16p13.13	2011-08-12			ENSG00000171490	ENSG00000171490			24534	protein-coding gene	gene with protein product		615874				15334068, 9859858	Standard	NM_015659		Approved	PBK1, L12, DKFZP564M182, CSIG, UTP30	uc002dbp.1	O76021	OTTHUMG00000129824	ENST00000571133.1:c.242G>T	chr16.hg19:g.11944139C>A	ENSP00000460871:p.Arg81Ile	53.0	0.0		63.0	31.0	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Missense_Mutation	SNP	ENST00000571133.1	hg19	CCDS10551.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.001072	0.74818	.	.	ENSG00000171490	ENST00000355674;ENST00000396503	T	0.42900	0.96	5.91	-3.56	0.04626	Ribosomal protein L1, 2-layer alpha/beta-sandwich (1);Ribosomal protein L1, superfamily (1);	0.550375	0.20217	N	0.096790	T	0.55577	0.1929	M	0.83118	2.625	0.21967	N	0.999444	D;D	0.63046	0.992;0.986	P;P	0.61800	0.859;0.894	T	0.52866	-0.8518	10	0.72032	D	0.01	.	8.7755	0.34758	0.0:0.4364:0.0959:0.4677	.	81;81	Q32Q62;O76021	.;RL1D1_HUMAN	I	81	ENSP00000347897:R81I	ENSP00000347897:R81I	R	-	2	0	RSL1D1	11851640	0.535000	0.26370	0.251000	0.24312	0.993000	0.82548	-0.169000	0.09911	-0.581000	0.05937	0.555000	0.69702	AGA	.	.		0.318	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659		A	11944139	C	A	11944139	3	1	101	1	0	0	0	0	1	0	0	0	13715	913	32	3	1262	3	RSL1D1	16	11944139	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	9845420	11944139	78410614	473	14310										
TMC7	79905	hgsc.bcm.edu	37	chr16	19049310	19049310	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtattgttctggctgttttaGgggcatgcttttatgcaata	11	5	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:19049310G>T	ENST00000304381.5	+	8	1250	c.1120G>T	c.(1120-1122)Ggg>Tgg	p.G374W	TMC7_ENST00000561963.1_3'UTR|TMC7_ENST00000421369.3_Missense_Mutation_p.G264W|TMC7_ENST00000569532.1_Missense_Mutation_p.G374W	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	374					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						GGCTGTTTTAGGGGCATGCTT	0.398																																					p.G374W		Atlas-SNP	.											.	TMC7	75	.	0			c.G1120T						.						214	185	195					16																	19049310		2197	4300	6497	SO:0001583	missense	79905	exon8			GTTTTAGGGGCAT	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1120G>T	chr16.hg19:g.19049310G>T	ENSP00000304710:p.Gly374Trp	120.0	0.0		283.0	41.0	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Missense_Mutation	SNP	ENST00000304381.5	hg19	CCDS10573.1	.	.	.	.	.	.	.	.	.	.	G	12.27	1.886793	0.33348	.	.	ENSG00000170537	ENST00000304381;ENST00000421369	T;T	0.53640	0.61;0.61	5.5	3.51	0.40186	.	0.422877	0.25319	N	0.031530	T	0.37293	0.0998	L	0.52126	1.63	0.22601	N	0.998941	B;B	0.33904	0.229;0.431	B;B	0.31290	0.08;0.127	T	0.36040	-0.9764	10	0.59425	D	0.04	.	6.4874	0.22097	0.085:0.0:0.5074:0.4076	.	374;374	Q7Z402;B3KSZ3	TMC7_HUMAN;.	W	374;264	ENSP00000304710:G374W;ENSP00000397081:G264W	ENSP00000304710:G374W	G	+	1	0	TMC7	18956811	0.998000	0.40836	0.051000	0.19133	0.548000	0.35241	4.618000	0.61211	1.284000	0.44531	0.650000	0.86243	GGG	.	.		0.398	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847		T	19049310	G	T	19049310	3	4	101	1	0	0	0	0	1	0	0	0	16005	1000	35	3	1150	3	TMC7	16	19049310	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	7105171	19049310	71305443	474	14311										
GGA2	23062	hgsc.bcm.edu	37	chr16	23489767	23489767	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggttctgaacaccaccgcctGgcagcgtgctggaggaggga	16	11	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:23489767G>A	ENST00000309859.4	-	13	1296	c.1214C>T	c.(1213-1215)cCa>cTa	p.P405L	GGA2_ENST00000569182.1_5'UTR|GGA2_ENST00000567468.1_Intron	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	405	Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		ACCACCGCCTGGCAGCGTGCT	0.532																																					p.P405L		Atlas-SNP	.											.	GGA2	49	.	0			c.C1214T						.						110	99	103					16																	23489767		2197	4300	6497	SO:0001583	missense	23062	exon13			CCGCCTGGCAGCG	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.1214C>T	chr16.hg19:g.23489767G>A	ENSP00000311962:p.Pro405Leu	63.0	0.0		158.0	18.0	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	hg19	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	G	9.964	1.223606	0.22457	.	.	ENSG00000103365	ENST00000309859	T	0.14893	2.47	4.11	2.0	0.26442	.	487.764000	0.00166	N	0.000000	T	0.19208	0.0461	L	0.54323	1.7	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19614	-1.0300	10	0.34782	T	0.22	-0.0382	5.4904	0.16773	0.2876:0.0:0.7124:0.0	.	405	Q9UJY4	GGA2_HUMAN	L	405	ENSP00000311962:P405L	ENSP00000311962:P405L	P	-	2	0	GGA2	23397268	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.371000	0.20450	0.403000	0.25479	-0.345000	0.07892	CCA	.	.		0.532	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1			A	23489767	G	A	23489767	3	1	101	1	0	0	0	0	1	0	0	0	6361	1348	47	3	647	3	GGA2	16	23489767	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	4440457	23489767	66864986	475	14312										
IL21R	50615	hgsc.bcm.edu	37	chr16	27448870	27448870	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcagcctccacaggtcggccCacaatgccacgcatgccacc	9	19	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:27448870C>A	ENST00000337929.3	+	4	687	c.214C>A	c.(214-216)Cac>Aac	p.H72N	IL21R_ENST00000395755.1_Missense_Mutation_p.H72N|IL21R_ENST00000564089.1_Missense_Mutation_p.H72N|IL21R_ENST00000395754.4_Missense_Mutation_p.H72N	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	72	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						CAGGTCGGCCCACAATGCCAC	0.557			T	BCL6	NHL																																p.H94N		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.C280A						.						131	100	111					16																	27448870		2197	4300	6497	SO:0001583	missense	50615	exon5			TCGGCCCACAATG	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.214C>A	chr16.hg19:g.27448870C>A	ENSP00000338010:p.His72Asn	32.0	0.0		80.0	9.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	hg19	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.711849	0.30322	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	D;D;D	0.95885	-3.84;-3.84;-3.84	4.65	4.65	0.58169	Fibronectin, type III (1);	0.407180	0.21333	N	0.076263	D	0.93138	0.7815	M	0.66939	2.045	0.37177	D	0.903308	P	0.37276	0.589	B	0.35813	0.211	D	0.92638	0.6122	10	0.14656	T	0.56	-17.6511	13.3953	0.60849	0.0:1.0:0.0:0.0	.	72	Q9HBE5	IL21R_HUMAN	N	72	ENSP00000338010:H72N;ENSP00000379104:H72N;ENSP00000379103:H72N	ENSP00000338010:H72N	H	+	1	0	IL21R	27356371	0.045000	0.20229	0.811000	0.32455	0.038000	0.13279	0.197000	0.17197	2.271000	0.75665	0.650000	0.86243	CAC	.	.		0.557	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		A	27448870	C	A	27448870	3	1	101	1	0	0	0	0	1	0	0	0	7680	594	21	3	224	3	IL21R	16	27448870	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3959103	27448870	62905883	476	14313										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27517278	27517278	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtcaccactgttgctgtccGcacagtgggagacaaaggac	12	11	1	1	rs140459536		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:27517278G>T	ENST00000356183.4	-	10	1727	c.1712C>A	c.(1711-1713)gCg>gAg	p.A571E	GTF3C1_ENST00000561623.1_Missense_Mutation_p.A571E	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	571					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						GTTGCTGTCCGCACAGTGGGA	0.567																																					p.A571E		Atlas-SNP	.											.	GTF3C1	210	.	0			c.C1712A						.						139	115	123					16																	27517278		2197	4300	6497	SO:0001583	missense	2975	exon10			CTGTCCGCACAGT	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.1712C>A	chr16.hg19:g.27517278G>T	ENSP00000348510:p.Ala571Glu	58.0	0.0		148.0	19.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	G	0.498	-0.872140	0.02570	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.22539	1.95	5.39	2.83	0.33086	.	1.419090	0.03886	N	0.277842	T	0.12050	0.0293	N	0.19112	0.55	0.09310	N	1	B;B	0.18610	0.001;0.029	B;B	0.12156	0.0;0.007	T	0.28427	-1.0044	10	0.02654	T	1	-4.6393	5.1223	0.14867	0.7147:0.0:0.2853:0.0	.	571;571	Q12789;Q12789-3	TF3C1_HUMAN;.	E	571;569	ENSP00000348510:A571E	ENSP00000348510:A571E	A	-	2	0	GTF3C1	27424779	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	0.574000	0.23714	0.984000	0.38629	-0.302000	0.09304	GCG	.	G|1.000;A|0.000		0.567	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		T	27517278	G	T	27517278	3	4	101	1	0	0	0	0	1	0	0	0	6881	1087	38	1	4729	1	GTF3C1	16	27517278	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	68408	27517278	62837475	477	14314										
CD19	930	hgsc.bcm.edu	37	chr16	28946809	28946809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctggtggctggaaggtctcaGctgtgactttggcttatctg	14	8	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:28946809G>A	ENST00000324662.3	+	5	924	c.880G>A	c.(880-882)Gct>Act	p.A294T	CD19_ENST00000567541.1_Missense_Mutation_p.A294T|CD19_ENST00000538922.1_Missense_Mutation_p.A294T			P15391	CD19_HUMAN	CD19 molecule	294					B cell receptor signaling pathway (GO:0050853)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor signaling protein activity (GO:0005057)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(4)|urinary_tract(1)	29						GAAGGTCTCAGCTGTGACTTT	0.547																																					p.A294T		Atlas-SNP	.											.	CD19	65	.	0			c.G880A						.						318	243	269					16																	28946809		2197	4300	6497	SO:0001583	missense	930	exon5			GTCTCAGCTGTGA		CCDS10644.1, CCDS53998.1	16p11.2	2014-09-17	2006-03-28		ENSG00000177455	ENSG00000177455		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1633	protein-coding gene	gene with protein product		107265	"CD19 antigen"				Standard	NM_001770		Approved		uc010byo.2	P15391	OTTHUMG00000097049	ENST00000324662.3:c.880G>A	chr16.hg19:g.28946809G>A	ENSP00000313419:p.Ala294Thr	152.0	0.0		304.0	21.0	NM_001178098	A0N0P9|F5H635|Q96S68|Q9BRD6	Missense_Mutation	SNP	ENST00000324662.3	hg19	CCDS10644.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.287512	0.59976	.	.	ENSG00000177455	ENST00000538922;ENST00000380673;ENST00000324662;ENST00000537306	T;T	0.42131	0.98;0.98	5.05	5.05	0.67936	.	0.982646	0.08269	N	0.971709	T	0.45736	0.1357	L	0.46157	1.445	0.24613	N	0.993711	P;P	0.44139	0.827;0.734	B;B	0.44133	0.442;0.257	T	0.41197	-0.9522	10	0.54805	T	0.06	-0.3878	13.8988	0.63790	0.0:0.0:1.0:0.0	.	294;294	F5H635;P15391	.;CD19_HUMAN	T	294;101;294;143	ENSP00000437940:A294T;ENSP00000313419:A294T	ENSP00000313419:A294T	A	+	1	0	CD19	28854310	0.582000	0.26749	0.093000	0.20910	0.383000	0.30230	2.830000	0.48136	2.337000	0.79520	0.313000	0.20887	GCT	.	.		0.547	CD19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214152.2			A	28946809	G	A	28946809	3	1	101	1	0	0	0	0	1	0	0	0	2975	971	34	3	898	3	CD19	16	28946809	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1429531	28946809	61407944	478	14315										
SETD1A	9739	hgsc.bcm.edu	37	chr16	30977205	30977205	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctccttggagctcatggaccGacttggggctcagtggggag	16	10	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:30977205G>T	ENST00000262519.8	+	8	2689	c.2003G>T	c.(2002-2004)cGa>cTa	p.R668L		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	668					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CTCATGGACCGACTTGGGGCT	0.617																																					p.R668L		Atlas-SNP	.											.	SETD1A	143	.	0			c.G2003T						.						76	73	74					16																	30977205		2197	4300	6497	SO:0001583	missense	9739	exon8			TGGACCGACTTGG	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.2003G>T	chr16.hg19:g.30977205G>T	ENSP00000262519:p.Arg668Leu	90.0	0.0		191.0	25.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.694952	0.30052	.	.	ENSG00000099381	ENST00000262519	D	0.94000	-3.33	4.67	4.67	0.58626	.	0.084306	0.49916	D	0.000124	D	0.92093	0.7494	N	0.19112	0.55	0.46356	D	0.999007	D	0.63880	0.993	D	0.74023	0.982	D	0.87573	0.2479	10	0.02654	T	1	.	16.5112	0.84286	0.0:0.0:1.0:0.0	.	668	O15047	SET1A_HUMAN	L	668	ENSP00000262519:R668L	ENSP00000262519:R668L	R	+	2	0	SETD1A	30884706	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.187000	0.42602	2.434000	0.82447	0.655000	0.94253	CGA	.	.		0.617	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		T	30977205	G	T	30977205	3	4	101	1	0	0	0	0	1	0	0	0	14145	1058	37	1	2029	1	SETD1A	16	30977205	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2030396	30977205	59377548	479	14316										
ZNF668	79759	hgsc.bcm.edu	37	chr16	31072640	31072640	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gggccggagctccgggtgtgAgcgctcgtgccgacgcagca	18	13	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:31072640A>T	ENST00000538906.1	-	3	2393	c.1609T>A	c.(1609-1611)Tca>Aca	p.S537T	ZNF668_ENST00000300849.4_Missense_Mutation_p.S537T|ZNF668_ENST00000539836.3_Missense_Mutation_p.S560T|ZNF668_ENST00000394983.2_Missense_Mutation_p.S537T|ZNF668_ENST00000417110.2_5'Flank|ZNF668_ENST00000426488.2_Missense_Mutation_p.S560T|ZNF668_ENST00000535577.1_Missense_Mutation_p.S537T	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	537					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						TCCGGGTGTGAGCGCTCGTGC	0.667																																					p.S560T	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.T1678A						.						39	39	39					16																	31072640		2197	4300	6497	SO:0001583	missense	79759	exon4			GGTGTGAGCGCTC		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"Zinc fingers, C2H2-type"	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.1609T>A	chr16.hg19:g.31072640A>T	ENSP00000440149:p.Ser537Thr	45.0	0.0		113.0	9.0	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Missense_Mutation	SNP	ENST00000538906.1	hg19	CCDS10701.1	.	.	.	.	.	.	.	.	.	.	A	12.98	2.100316	0.37048	.	.	ENSG00000167394	ENST00000539836;ENST00000535577;ENST00000538906;ENST00000394983;ENST00000300849	T;T;T;T;T	0.16073	2.37;2.37;2.37;2.37;2.37	5.04	3.92	0.45320	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.340229	0.27275	N	0.020117	T	0.08492	0.0211	N	0.10760	0.04	0.28473	N	0.915336	B	0.17268	0.021	B	0.18561	0.022	T	0.19745	-1.0296	10	0.33940	T	0.23	-14.3349	8.5754	0.33595	0.6922:0.0:0.0:0.3078	.	537	Q96K58	ZN668_HUMAN	T	560;537;537;537;537	ENSP00000442573:S560T;ENSP00000441349:S537T;ENSP00000440149:S537T;ENSP00000378434:S537T;ENSP00000300849:S537T	ENSP00000300849:S537T	S	-	1	0	ZNF668	30980141	0.056000	0.20664	1.000000	0.80357	0.970000	0.65996	0.209000	0.17435	0.905000	0.36596	0.459000	0.35465	TCA	.	.		0.667	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706		T	31072640	A	T	31072640	3	4	101	1	0	0	0	0	1	0	0	0	18090	304	11	4	254	4	ZNF668	16	31072640	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	95435	31072640	59282113	480	14317										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31927200	31927200	+	Frame_Shift_Del	DEL	G	G	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgcatgagagaattcatactGgagagaaaccctataaatgt							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:31927200delG	ENST00000300870.10	+	4	1839	c.1630delG	c.(1630-1632)ggafs	p.G544fs		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	544					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						AATTCATACTGGAGAGAAACC	0.338																																					p.T543fs		Atlas-INDEL	.											.	ZNF267	94	.	0			c.1629delT						.						38	42	40					16																	31927200		2196	4299	6495	SO:0001589	frameshift_variant	10308	exon4			.	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.1630delG	chr16.hg19:g.31927200delG	ENSP00000300870:p.Gly544fs	24.0	0.0		65.0	10.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Frame_Shift_Del	DEL	ENST00000300870.10	hg19	CCDS32440.1																																																																																			.	.		0.338	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		-	31927200	G	-	31927200	7	5	101	1	0	1	0	1	0	0	0	0	17821	1349	47	0	1644	0	ZNF267	16	31927200	Frame_Shift_Del	DEL	G	TCGA-DD-A1EE-01A-11D-A12Z-10	854560	31927200	58427553	481	14318										
DNAJA2	10294	hgsc.bcm.edu	37	chr16	46991020	46991020	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tatcattataggcttcacgcCtctgaccacctcctgagcct	6	15	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:46991020C>A	ENST00000317089.5	-	9	1375	c.1160G>T	c.(1159-1161)aGg>aTg	p.R387M		NM_005880.3	NP_005871.1	O60884	DNJA2_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 2	387					positive regulation of cell proliferation (GO:0008284)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	14		all_cancers(37;0.00125)|all_lung(18;0.00338)|all_epithelial(9;0.00358)|Lung NSC(13;0.0309)|Breast(268;0.116)				GGCTTCACGCCTCTGACCACC	0.478																																					p.R387M		Atlas-SNP	.											.	DNAJA2	28	.	0			c.G1160T						.						268	262	264					16																	46991020		2203	4300	6503	SO:0001583	missense	10294	exon9			TCACGCCTCTGAC	AF116720	CCDS10726.1	16q12.1	2011-09-02			ENSG00000069345	ENSG00000069345		"Heat shock proteins / DNAJ (HSP40)"	14884	protein-coding gene	gene with protein product		611322				9710638, 11147971	Standard	NM_005880		Approved	HIRIP4, DNAJ, CPR3, DNJ3	uc002eeo.2	O60884	OTTHUMG00000133104	ENST00000317089.5:c.1160G>T	chr16.hg19:g.46991020C>A	ENSP00000314030:p.Arg387Met	69.0	0.0		166.0	12.0	NM_005880	B2R7L7|O14711	Missense_Mutation	SNP	ENST00000317089.5	hg19	CCDS10726.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.739595	0.89573	.	.	ENSG00000069345	ENST00000317089	T	0.38722	1.12	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.60353	0.2262	M	0.78456	2.415	0.80722	D	1	D	0.57571	0.98	P	0.52672	0.706	T	0.64769	-0.6329	10	0.62326	D	0.03	-18.9488	19.5403	0.95271	0.0:1.0:0.0:0.0	.	387	O60884	DNJA2_HUMAN	M	387	ENSP00000314030:R387M	ENSP00000314030:R387M	R	-	2	0	DNAJA2	45548521	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.610000	0.82949	2.623000	0.88846	0.561000	0.74099	AGG	.	.		0.478	DNAJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256769.2			A	46991020	C	A	46991020	3	1	101	1	0	0	0	0	1	0	0	0	4614	681	24	3	82	3	DNAJA2	16	46991020	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	15063820	46991020	43363733	482	14319										
CHD9	80205	hgsc.bcm.edu	37	chr16	53358701	53358701	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggaactgaaccaagtcctcTcaatgaaaacagcacagatg	8	10	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:53358701T>G	ENST00000398510.3	+	38	8675	c.8588T>G	c.(8587-8589)cTc>cGc	p.L2863R	CHD9_ENST00000564845.1_Missense_Mutation_p.L2847R|CHD9_ENST00000566029.1_Missense_Mutation_p.L2847R|CHD9_ENST00000447540.1_Missense_Mutation_p.L2848R			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2863					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				CCAAGTCCTCTCAATGAAAAC	0.398																																					p.L2847R		Atlas-SNP	.											.	CHD9	203	.	0			c.T8540G						.						35	33	34					16																	53358701		1871	4102	5973	SO:0001583	missense	80205	exon39			GTCCTCTCAATGA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.8588T>G	chr16.hg19:g.53358701T>G	ENSP00000381522:p.Leu2863Arg	97.0	0.0		188.0	59.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	hg19		.	.	.	.	.	.	.	.	.	.	T	6.687	0.495279	0.12762	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	D	0.85171	-1.95	5.06	5.06	0.68205	.	0.000000	0.46758	D	0.000275	T	0.73837	0.3638	N	0.24115	0.695	0.31914	N	0.614243	P;B;B;B	0.51933	0.949;0.0;0.296;0.0	P;B;B;B	0.46585	0.521;0.002;0.066;0.002	T	0.72174	-0.4370	10	0.09843	T	0.71	-5.4299	5.9372	0.19173	0.2551:0.0:0.1334:0.6114	.	929;2848;2863;2847	C9JR69;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	R	2848;2847;929	ENSP00000396345:L2848R	ENSP00000381522:L2847R	L	+	2	0	CHD9	51916202	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.144000	0.50616	2.028000	0.59812	0.533000	0.62120	CTC	.	.		0.398	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		G	53358701	T	G	53358701	3	3	101	1	0	0	0	0	1	0	0	0	3334	1551	54	5	8690	5	CHD9	16	53358701	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	6367681	53358701	36996052	483	14320										
SLC38A7	55238	hgsc.bcm.edu	37	chr16	58706093	58706093	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccatgtcctccgagggatagGacaggagcacgtcaggatcc	13	12	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:58706093G>T	ENST00000570101.1	-	8	1821	c.938C>A	c.(937-939)tCc>tAc	p.S313Y	SLC38A7_ENST00000566953.1_5'UTR|SLC38A7_ENST00000219320.4_Missense_Mutation_p.S313Y|SLC38A7_ENST00000564010.1_Missense_Mutation_p.S224Y|SLC38A7_ENST00000564100.1_Intron			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	313					sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)			endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						CGAGGGATAGGACAGGAGCAC	0.622																																					p.S313Y		Atlas-SNP	.											.	SLC38A7	26	.	0			c.C938A						.						50	40	43					16																	58706093		2187	4289	6476	SO:0001583	missense	55238	exon9			GGATAGGACAGGA	BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042		"Solute carriers"	25582	protein-coding gene	gene with protein product		614236					Standard	XM_006721229		Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000570101.1:c.938C>A	chr16.hg19:g.58706093G>T	ENSP00000454646:p.Ser313Tyr	53.0	0.0		193.0	25.0	NM_018231	Q53GJ9|Q9H9I5	Missense_Mutation	SNP	ENST00000570101.1	hg19	CCDS10800.1	.	.	.	.	.	.	.	.	.	.	G	32	5.151293	0.94645	.	.	ENSG00000103042	ENST00000219320	T	0.02812	4.15	5.36	5.36	0.76844	.	0.110975	0.64402	D	0.000004	T	0.16428	0.0395	M	0.77313	2.365	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.00215	-1.1911	9	.	.	.	.	18.0759	0.89427	0.0:0.0:1.0:0.0	.	313	Q9NVC3	S38A7_HUMAN	Y	313	ENSP00000219320:S313Y	.	S	-	2	0	SLC38A7	57263594	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.360000	0.97119	2.497000	0.84241	0.591000	0.81541	TCC	.	.		0.622	SLC38A7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422206.2	NM_018231		T	58706093	G	T	58706093	3	4	101	1	0	0	0	0	1	0	0	0	14624	1174	41	3	466	3	SLC38A7	16	58706093	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	5347392	58706093	31648660	484	14321										
CES8	283848	hgsc.bcm.edu	37	chr16	67029593	67029593	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaaccctgcaaggaaaacagAtgcatgtggggaagacaccc	12	10	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:67029593A>G	ENST00000326686.5	+	2	121	c.121A>G	c.(121-123)Atg>Gtg	p.M41V	CES4A_ENST00000540947.2_Missense_Mutation_p.M41V|CES4A_ENST00000398354.1_Missense_Mutation_p.M41V|CES4A_ENST00000541479.1_Missense_Mutation_p.M64V|CES4A_ENST00000338718.4_Missense_Mutation_p.M64V			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	41						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						AGGAAAACAGATGCATGTGGG	0.542																																					p.M41V		Atlas-SNP	.											.	CES4A	24	.	0			c.A121G						.						115	114	114					16																	67029593		1905	4134	6039	SO:0001583	missense	283848	exon2			AAACAGATGCATG	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"Carboxylesterases"	26741	protein-coding gene	gene with protein product			"carboxylesterase 8 (putative)"	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.121A>G	chr16.hg19:g.67029593A>G	ENSP00000314145:p.Met41Val	58.0	0.0		95.0	4.0	NM_173815	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Missense_Mutation	SNP	ENST00000326686.5	hg19		.	.	.	.	.	.	.	.	.	.	A	0.017	-1.505528	0.00992	.	.	ENSG00000172824	ENST00000540947;ENST00000541479;ENST00000338718;ENST00000543913;ENST00000398354;ENST00000326686;ENST00000538199	T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;3.31;-0.05	5.01	-2.64	0.06114	Carboxylesterase, type B (1);	.	.	.	.	T	0.25717	0.0626	N	0.00960	-1.095	0.09310	N	1	B;B;B	0.09022	0.0;0.0;0.002	B;B;B	0.06405	0.002;0.001;0.002	T	0.34279	-0.9835	9	0.02654	T	1	.	12.6276	0.56638	0.3867:0.0:0.6133:0.0	.	64;41;64	F8WEE9;Q5XG92;F5H5S4	.;EST4A_HUMAN;.	V	41;64;64;41;41;41;4	ENSP00000444052:M41V;ENSP00000443175:M64V;ENSP00000340714:M64V;ENSP00000381397:M41V;ENSP00000314145:M41V;ENSP00000441103:M4V	ENSP00000314145:M41V	M	+	1	0	CES4A	65587094	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.194000	0.09559	-0.772000	0.04602	-0.256000	0.11100	ATG	.	.		0.542	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173815		G	67029593	A	G	67029593	3	3	101	1	0	0	0	0	1	0	0	0	3275	333	12	2	196	2	CES8	16	67029593	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	8323500	67029593	23325160	485	14322										
CES8	283848	hgsc.bcm.edu	37	chr16	67038121	67038121	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctggaattcaattggctcttGccttatgtaagtgagtagga	11	6	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:67038121G>T	ENST00000326686.5	+	9	1074	c.1074G>T	c.(1072-1074)ttG>ttT	p.L358F	CES4A_ENST00000540947.2_Missense_Mutation_p.L358F|CES4A_ENST00000398354.1_Missense_Mutation_p.L358F|CES4A_ENST00000541479.1_Missense_Mutation_p.L381F|CES4A_ENST00000540579.1_Missense_Mutation_p.L260F|CES4A_ENST00000535696.1_Missense_Mutation_p.L264F|CES4A_ENST00000338718.4_Missense_Mutation_p.L381F			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	358						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						ATTGGCTCTTGCCTTATGTAA	0.517																																					p.L358F		Atlas-SNP	.											.	CES4A	24	.	0			c.G1074T						.						149	141	144					16																	67038121		1981	4172	6153	SO:0001583	missense	283848	exon9			GCTCTTGCCTTAT	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"Carboxylesterases"	26741	protein-coding gene	gene with protein product			"carboxylesterase 8 (putative)"	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.1074G>T	chr16.hg19:g.67038121G>T	ENSP00000314145:p.Leu358Phe	70.0	0.0		166.0	10.0	NM_173815	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Missense_Mutation	SNP	ENST00000326686.5	hg19		.	.	.	.	.	.	.	.	.	.	g	7.020	0.558476	0.13436	.	.	ENSG00000172824	ENST00000540947;ENST00000541479;ENST00000338718;ENST00000398354;ENST00000326686;ENST00000538199;ENST00000540579;ENST00000535696	T;T;T;T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45	4.63	1.3	0.21679	Carboxylesterase, type B (1);	0.000000	0.35772	N	0.002995	T	0.69251	0.3090	L	0.56199	1.76	0.51767	D	0.999931	B;D;B;B	0.59767	0.026;0.986;0.0;0.001	B;P;B;B	0.59221	0.018;0.854;0.021;0.01	T	0.67684	-0.5607	10	0.87932	D	0	.	6.5077	0.22204	0.205:0.1878:0.6072:0.0	.	264;381;358;381	Q5XG92-7;F8WEE9;Q5XG92;F5H5S4	.;.;EST4A_HUMAN;.	F	358;381;381;358;358;321;260;264	ENSP00000444052:L358F;ENSP00000443175:L381F;ENSP00000340714:L381F;ENSP00000381397:L358F;ENSP00000314145:L358F;ENSP00000441103:L321F;ENSP00000441907:L260F;ENSP00000441644:L264F	ENSP00000314145:L358F	L	+	3	2	CES4A	65595622	0.910000	0.30920	0.908000	0.35775	0.142000	0.21351	-0.083000	0.11286	0.372000	0.24591	0.486000	0.48141	TTG	.	.		0.517	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173815		T	67038121	G	T	67038121	3	4	101	1	0	0	0	0	1	0	0	0	3275	1310	46	3	1189	3	CES8	16	67038121	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	8528	67038121	23316632	486	14323										
ZDHHC1	29800	hgsc.bcm.edu	37	chr16	67432171	67432171	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctccctgtgaacccccttggCctcctgtggtgggcggtgct	13	15	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:67432171C>G	ENST00000348579.2	-	8	1212	c.871G>C	c.(871-873)Gcc>Ccc	p.A291P	ZDHHC1_ENST00000566075.1_5'Flank	NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	291					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		ACCCCCTTGGCCTCCTGTGGT	0.637																																					p.A291P		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.G871C						.						121	106	111					16																	67432171		2198	4300	6498	SO:0001583	missense	29800	exon8			CCTTGGCCTCCTG	U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"Zinc fingers, DHHC-type"	17916	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 1"	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.871G>C	chr16.hg19:g.67432171C>G	ENSP00000340299:p.Ala291Pro	57.0	0.0		125.0	23.0	NM_013304	O15461	Missense_Mutation	SNP	ENST00000348579.2	hg19	CCDS10836.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.529073	0.44969	.	.	ENSG00000159714	ENST00000348579	T	0.37752	1.18	5.46	4.49	0.54785	.	1.706460	0.02790	N	0.121901	T	0.28632	0.0709	L	0.27053	0.805	0.32577	N	0.528965	B	0.15473	0.013	B	0.12156	0.007	T	0.30297	-0.9983	10	0.30078	T	0.28	.	5.4746	0.16688	0.1477:0.6332:0.1425:0.0765	.	291	Q8WTX9	ZDHC1_HUMAN	P	291	ENSP00000340299:A291P	ENSP00000340299:A291P	A	-	1	0	ZDHHC1	65989672	0.994000	0.37717	1.000000	0.80357	0.861000	0.49209	0.541000	0.23207	1.260000	0.44134	0.407000	0.27541	GCC	.	.		0.637	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304		G	67432171	C	G	67432171	3	3	101	1	0	0	0	0	1	0	0	0	17615	739	26	4	602	4	ZDHHC1	16	67432171	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	394050	67432171	22922582	487	14324										
CDH1	999	hgsc.bcm.edu	37	chr16	68856129	68856129	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cattcagtacaacgacccaaGtgggtacctgagttttattt	8	9	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:68856129G>A	ENST00000261769.5	+	12	2127		c.e12+1		CDH1_ENST00000562836.1_Splice_Site|CDH1_ENST00000422392.2_Splice_Site|RP11-354M1.2_ENST00000563916.1_RNA	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)						adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		AACGACCCAAGTGGGTACCTG	0.488			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												.		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	CDH1,NS,carcinoma,0,2	CDH1	535	.	0			c.1936+1G>A						.						72	60	64					16																	68856129		2198	4300	6498	SO:0001630	splice_region_variant	999	exon12	Familial Cancer Database	HDGC	ACCCAAGTGGGTA	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1936+1G>A	chr16.hg19:g.68856129G>A		46.0	0.0		100.0	4.0	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Splice_Site	SNP	ENST00000261769.5	hg19	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.025419	0.35701	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000422392	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4194	0.90584	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDH1	67413630	1.000000	0.71417	0.540000	0.28089	0.048000	0.14542	7.958000	0.87877	2.697000	0.92050	0.632000	0.83419	.	.	.		0.488	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	Intron	A	68856129	G	A	68856129	5	1	101	1	0	0	0	0	0	0	1	0	3097	1043	36	3	1983	3	CDH1	16	68856129	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1423958	68856129	21498624	488	14325										
AP1G1	164	hgsc.bcm.edu	37	chr16	71823203	71823203	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtccaaagtgagcagggtaGcccagcatgtgcatatacag	12	9	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:71823203G>A	ENST00000299980.4	-	2	621	c.180C>T	c.(178-180)ggC>ggT	p.G60G	AP1G1_ENST00000423132.2_Silent_p.G60G|AP1G1_ENST00000570297.1_5'Flank|AP1G1_ENST00000433195.2_Silent_p.G83G|AP1G1_ENST00000569748.1_Silent_p.G60G|AP1G1_ENST00000393512.3_Silent_p.G60G	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	60					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				GAGCAGGGTAGCCCAGCATGT	0.453																																					p.G60G		Atlas-SNP	.											.	AP1G1	83	.	0			c.C180T						.						128	105	112					16																	71823203		2198	4300	6498	SO:0001819	synonymous_variant	164	exon2			AGGGTAGCCCAGC	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.180C>T	chr16.hg19:g.71823203G>A		64.0	0.0		147.0	19.0	NM_001030007	O75709|O75842|Q9UG09|Q9Y3U4	Silent	SNP	ENST00000299980.4	hg19	CCDS32480.1																																																																																			.	.		0.453	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			A	71823203	G	A	71823203	2	1	101	1	0	0	0	0	0	0	0	1	732	958	34	3		3	AP1G1	16	71823203	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2967074	71823203	18531550	489	14326										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72984568	72984568	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtacttctgcacgtgcttgtCtgtcttgcagtgcagctgga	12	10	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:72984568C>G	ENST00000268489.5	-	3	3688	c.3016G>C	c.(3016-3018)Gac>Cac	p.D1006H	ZFHX3_ENST00000397992.5_Missense_Mutation_p.D92H	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1006					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				ACGTGCTTGTCTGTCTTGCAG	0.607																																					p.D1006H		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G3016C						.						165	130	142					16																	72984568		2198	4300	6498	SO:0001583	missense	463	exon3			GCTTGTCTGTCTT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.3016G>C	chr16.hg19:g.72984568C>G	ENSP00000268489:p.Asp1006His	88.0	0.0		133.0	52.0	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	hg19	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.519066	0.64634	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.63744	-0.06;-0.06	5.21	5.21	0.72293	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);	0.000000	0.52532	D	0.000067	T	0.62183	0.2407	N	0.03224	-0.385	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75001	-0.3471	10	0.87932	D	0	.	18.7673	0.91878	0.0:1.0:0.0:0.0	.	1006	Q15911	ZFHX3_HUMAN	H	1006;92	ENSP00000268489:D1006H;ENSP00000438926:D92H	ENSP00000268489:D1006H	D	-	1	0	ZFHX3	71542069	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.767000	0.85331	2.415000	0.81967	0.650000	0.86243	GAC	.	.		0.607	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		G	72984568	C	G	72984568	3	3	101	1	0	0	0	0	1	0	0	0	17649	913	32	4	8127	4	ZFHX3	16	72984568	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1161365	72984568	17370185	490	14327										
ADAD2	161931	hgsc.bcm.edu	37	chr16	84229967	84229967	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggatgtggccaccgggcgtgTgaaggccaagtgagaagggc	19	8	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr16:84229967T>A	ENST00000315906.5	+	8	1569	c.1517T>A	c.(1516-1518)gTg>gAg	p.V506E	RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.V588E|RP11-486L19.2_ENST00000561900.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	506	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						ACCGGGCGTGTGAAGGCCAAG	0.657																																					p.V588E		Atlas-SNP	.											.	ADAD2	46	.	0			c.T1763A						.						19	23	22					16																	84229967		2108	4158	6266	SO:0001583	missense	161931	exon9			GGCGTGTGAAGGC	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1517T>A	chr16.hg19:g.84229967T>A	ENSP00000325153:p.Val506Glu	36.0	0.0		90.0	30.0	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	hg19	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	T	12.43	1.936643	0.34189	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	D;D	0.93189	-3.18;-3.18	5.48	4.39	0.52855	Adenosine deaminase/editase (2);	0.074280	0.51477	D	0.000088	D	0.95837	0.8645	M	0.81341	2.54	0.37920	D	0.931675	D;D	0.76494	0.999;0.999	D;D	0.72982	0.979;0.968	D	0.95808	0.8839	10	0.72032	D	0.01	-33.6413	8.1071	0.30892	0.0:0.0912:0.0:0.9088	.	506;588	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	E	506;588	ENSP00000325153:V506E;ENSP00000268624:V588E	ENSP00000268624:V588E	V	+	2	0	ADAD2	82787468	1.000000	0.71417	0.999000	0.59377	0.004000	0.04260	2.456000	0.44997	0.918000	0.36919	-0.250000	0.11733	GTG	.	.		0.657	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		A	84229967	T	A	84229967	3	1	101	1	0	0	0	0	1	0	0	0	232	1696	59	4	1797	4	ADAD2	16	84229967	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	11245399	84229967	6124786	491	14328										
SPNS2	124976	hgsc.bcm.edu	37	chr17	4416595	4416595	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcaaggaccgaggcgccggcCtgctgcagtcaggtgaggcc	16	13	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:4416595C>T	ENST00000329078.3	+	2	634	c.424C>T	c.(424-426)Ctg>Ttg	p.L142L		NM_001124758.1	NP_001118230.1	Q8IVW8	SPNS2_HUMAN	spinster homolog 2 (Drosophila)	142					B cell homeostasis (GO:0001782)|bone development (GO:0060348)|lymph node development (GO:0048535)|lymphocyte migration (GO:0072676)|regulation of eye pigmentation (GO:0048073)|regulation of humoral immune response (GO:0002920)|sphingolipid metabolic process (GO:0006665)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell homeostasis (GO:0043029)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	sphingolipid transporter activity (GO:0046624)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6						AGGCGCCGGCCTGCTGCAGTC	0.662																																					p.L142L		Atlas-SNP	.											.	SPNS2	24	.	0			c.C424T						.						60	62	62					17																	4416595		1568	3582	5150	SO:0001819	synonymous_variant	124976	exon2			GCCGGCCTGCTGC	BC041772	CCDS42237.1	17p13.2	2008-12-15				ENSG00000183018			26992	protein-coding gene	gene with protein product		612584				12815463	Standard	NM_001124758		Approved		uc002fxx.2	Q8IVW8		ENST00000329078.3:c.424C>T	chr17.hg19:g.4416595C>T		38.0	0.0		77.0	4.0	NM_001124758	B9A1T3	Silent	SNP	ENST00000329078.3	hg19	CCDS42237.1																																																																																			.	.		0.662	SPNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438802.1			T	4416595	C	T	4416595	2	4	101	1	0	0	0	0	0	0	0	1	15090	680	24	3		3	SPNS2	17	4416595	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10		4416595	76778615	492	14329										
DLG4	1742	hgsc.bcm.edu	37	chr17	7097812	7097812	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcttgtcgtaatcaaacaggGccctggagggcaagtggcta	13	9	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:7097812G>A	ENST00000399506.2	-	12	1495	c.1304C>T	c.(1303-1305)gCc>gTc	p.A435V	DLG4_ENST00000302955.6_Missense_Mutation_p.A432V|DLG4_ENST00000399510.2_Missense_Mutation_p.A478V			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	435	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	ATCAAACAGGGCCCTGGAGGG	0.597																																					p.A478V		Atlas-SNP	.											.	DLG4	110	.	0			c.C1433T						.						28	32	31					17																	7097812		2041	4198	6239	SO:0001583	missense	1742	exon14			AACAGGGCCCTGG	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.1304C>T	chr17.hg19:g.7097812G>A	ENSP00000382425:p.Ala435Val	25.0	0.0		74.0	11.0	NM_001365	B7Z1S1|G5E939|Q92941|Q9UKK8	Missense_Mutation	SNP	ENST00000399506.2	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.555178	0.96514	.	.	ENSG00000132535	ENST00000399506;ENST00000302955;ENST00000399510;ENST00000293813;ENST00000380912;ENST00000539674	T;T;T	0.80304	-1.36;-1.36;-1.36	5.3	5.3	0.74995	Src homology-3 domain (4);	.	.	.	.	D	0.91358	0.7274	M	0.90309	3.105	0.80722	D	1	D;D;D;D	0.76494	0.995;0.999;0.998;0.989	D;D;D;D	0.79784	0.953;0.972;0.985;0.993	D	0.92680	0.6157	9	0.87932	D	0	.	16.5016	0.84259	0.0:0.0:1.0:0.0	.	475;435;432;478	B9EGL1;P78352;G5E939;P78352-2	.;DLG4_HUMAN;.;.	V	435;432;478;478;375;478	ENSP00000382425:A435V;ENSP00000307471:A432V;ENSP00000382428:A478V	ENSP00000293813:A478V	A	-	2	0	DLG4	7038536	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.601000	0.98297	2.769000	0.95229	0.655000	0.94253	GCC	.	.		0.597	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365		A	7097812	G	A	7097812	3	1	101	1	0	0	0	0	1	0	0	0	4559	1203	42	3	906	3	DLG4	17	7097812	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2681217	7097812	74097398	493	14330										
GPS2	2874	hgsc.bcm.edu	37	chr17	7216697	7216697	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctcctgcatgggatgttatcAcctgtctgagtgggctgaaa	12	9	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:7216697A>G	ENST00000380728.2	-	8	1025		c.e8+1		GPS2_ENST00000389167.5_Splice_Site|RP11-542C16.2_ENST00000575474.1_Splice_Site|GPS2_ENST00000391950.3_Splice_Site			Q13227	GPS2_HUMAN	G protein pathway suppressor 2						cell cycle (GO:0007049)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase inhibitor activity (GO:0005095)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(4)	24		Prostate(122;0.157)				GGATGTTATCACCTGTCTGAG	0.557											OREG0024133	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	GPS2	44	.	0			c.724+2T>C						.						99	102	101					17																	7216697		2203	4300	6503	SO:0001630	splice_region_variant	2874	exon9			GTTATCACCTGTC	U28963	CCDS11100.1	17p13.1	2006-04-29			ENSG00000132522	ENSG00000132522			4550	protein-coding gene	gene with protein product		601935				8943324	Standard	NM_004489		Approved		uc002gfx.1	Q13227	OTTHUMG00000102198	ENST00000380728.2:c.724+1T>C	chr17.hg19:g.7216697A>G		38.0	0.0	640	106.0	12.0	NM_004489	B4DXA1|Q6FHM8	Splice_Site	SNP	ENST00000380728.2	hg19	CCDS11100.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.044178	0.55110	.	.	ENSG00000132522	ENST00000391950;ENST00000380728;ENST00000389167;ENST00000315601	.	.	.	3.67	3.67	0.42095	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6611	0.45702	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GPS2	7157421	0.999000	0.42202	1.000000	0.80357	0.958000	0.62258	4.623000	0.61247	1.899000	0.54978	0.523000	0.50628	.	.	.		0.557	GPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220048.4	NM_004489	Intron	G	7216697	A	G	7216697	5	3	101	1	0	0	0	0	0	0	1	0	6742	173	6	2	273	2	GPS2	17	7216697	Splice_Site	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	118885	7216697	73978513	494	14331										
TMEM102	284114	hgsc.bcm.edu	37	chr17	7339378	7339378	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gggagccgatctcctccgggCcaaggactttgtcttctctt	11	13	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:7339378C>T	ENST00000323206.1	+	2	461	c.188C>T	c.(187-189)gCc>gTc	p.A63V	FGF11_ENST00000293829.4_5'Flank|RP11-104H15.7_ENST00000575310.1_RNA|FGF11_ENST00000575235.1_5'Flank|TMEM102_ENST00000396568.1_Missense_Mutation_p.A63V|RP11-104H15.9_ENST00000570444.1_RNA	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	63					apoptotic process (GO:0006915)|positive regulation of cell adhesion (GO:0045785)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				kidney(1)|lung(3)|skin(1)	5		Prostate(122;0.173)				CTCCTCCGGGCCAAGGACTTT	0.632																																					p.A63V		Atlas-SNP	.											.	TMEM102	11	.	0			c.C188T						.						88	114	105					17																	7339378		2203	4299	6502	SO:0001583	missense	284114	exon2			TCCGGGCCAAGGA	AK094197	CCDS11104.1	17p13.1	2008-04-21			ENSG00000181284	ENSG00000181284			26722	protein-coding gene	gene with protein product		613936				12477932	Standard	NM_178518		Approved	FLJ36878	uc002ggx.1	Q8N9M5	OTTHUMG00000132901	ENST00000323206.1:c.188C>T	chr17.hg19:g.7339378C>T	ENSP00000315387:p.Ala63Val	46.0	0.0		199.0	32.0	NM_178518	D3DTP8	Missense_Mutation	SNP	ENST00000323206.1	hg19	CCDS11104.1	.	.	.	.	.	.	.	.	.	.	C	33	5.232363	0.95207	.	.	ENSG00000181284	ENST00000323206;ENST00000396568	T;T	0.54479	0.57;0.57	5.66	5.66	0.87406	.	0.000000	0.56097	D	0.000039	T	0.72087	0.3417	M	0.72894	2.215	0.51012	D	0.999909	D	0.89917	1.0	D	0.74674	0.984	T	0.74237	-0.3730	10	0.72032	D	0.01	-8.6371	17.2341	0.86994	0.0:1.0:0.0:0.0	.	63	Q8N9M5	TM102_HUMAN	V	63	ENSP00000315387:A63V;ENSP00000379815:A63V	ENSP00000315387:A63V	A	+	2	0	TMEM102	7280102	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.801000	0.62532	2.652000	0.90054	0.655000	0.94253	GCC	.	.		0.632	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518		T	7339378	C	T	7339378	3	4	101	1	0	0	0	0	1	0	0	0	16032	739	26	3	190	3	TMEM102	17	7339378	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	122681	7339378	73855832	495	14332										
TP53	7157	hgsc.bcm.edu	37	chr17	7577107	7577107	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtgcgccggtctctcccaggAcaggcacaaacacgcacctc	10	17	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:7577107A>T	ENST00000269305.4	-	8	1020	c.831T>A	c.(829-831)tgT>tgA	p.C277*	TP53_ENST00000359597.4_Nonsense_Mutation_p.C277*|TP53_ENST00000445888.2_Nonsense_Mutation_p.C277*|TP53_ENST00000420246.2_Nonsense_Mutation_p.C277*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.C277*|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	277	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in an osteosarcoma with no family history; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.C277*(8)|p.C277C(4)|p.?(2)|p.P278fs*28(2)|p.C277W(2)|p.A276_R283delACPGRDRR(1)|p.C275fs*20(1)|p.A276fs*64(1)|p.L265_K305del41(1)|p.F270_D281del12(1)|p.A276_C277delAC(1)|p.V274_P278del(1)|p.C277_P278insXXXXXXX(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTCTCCCAGGACAGGCACAAA	0.547		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.C277X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,-1,2	TP53	33396	.	38	Substitution - Nonsense(8)|Whole gene deletion(8)|Deletion - In frame(7)|Deletion - Frameshift(4)|Substitution - coding silent(4)|Insertion - Frameshift(2)|Unknown(2)|Substitution - Missense(2)|Insertion - In frame(1)	upper_aerodigestive_tract(6)|breast(6)|urinary_tract(5)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|stomach(3)|central_nervous_system(2)|oesophagus(2)|lung(2)|biliary_tract(1)|large_intestine(1)|ovary(1)|prostate(1)	c.T831A	GRCh37	CM065496	TP53	M		.						72	62	65					17																	7577107		2203	4300	6503	SO:0001587	stop_gained	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CCCAGGACAGGCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.831T>A	chr17.hg19:g.7577107A>T	ENSP00000269305:p.Cys277*	35.0	0.0		67.0	10.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	37	6.040834	0.97226	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.13	1.53	0.23141	.	0.044315	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.0792	7.7422	0.28848	0.6581:0.0:0.3419:0.0	.	.	.	.	X	277;277;277;277;277;266;145	.	ENSP00000269305:C277X	C	-	3	2	TP53	7517832	0.987000	0.35691	1.000000	0.80357	0.977000	0.68977	0.281000	0.18810	0.383000	0.24910	0.379000	0.24179	TGT	.	.		0.547	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577107	A	T	7577107	4	4	101	1	0	0	0	0	0	1	0	0	16396	273	10	4	455	4	TP53	17	7577107	Nonsense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	237729	7577107	73618103	496	14333										
TP53	7157	hgsc.bcm.edu	37	chr17	7578271	7578271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttccttccactcggataagaTgctgaggaggggccagacct	12	11	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:7578271T>C	ENST00000269305.4	-	6	767	c.578A>G	c.(577-579)cAt>cGt	p.H193R	TP53_ENST00000359597.4_Missense_Mutation_p.H193R|TP53_ENST00000445888.2_Missense_Mutation_p.H193R|TP53_ENST00000420246.2_Missense_Mutation_p.H193R|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.H193R|TP53_ENST00000413465.2_Missense_Mutation_p.H193R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	193	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7887414}.|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.H193R(80)|p.H193L(42)|p.H193P(18)|p.0?(8)|p.?(6)|p.H61R(4)|p.H100R(4)|p.H100L(4)|p.H61L(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.H193fs*16(3)|p.P191fs*53(2)|p.H61P(2)|p.H100P(2)|p.A189fs*53(1)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P98_E105>Q(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCGGATAAGATGCTGAGGAGG	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.H193R	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	193	Substitution - Missense(160)|Whole gene deletion(8)|Complex - deletion inframe(6)|Unknown(6)|Deletion - In frame(5)|Deletion - Frameshift(4)|Insertion - Frameshift(3)|Complex - frameshift(1)	lung(36)|upper_aerodigestive_tract(26)|ovary(20)|breast(18)|oesophagus(14)|haematopoietic_and_lymphoid_tissue(12)|endometrium(12)|biliary_tract(10)|liver(9)|stomach(7)|central_nervous_system(6)|large_intestine(6)|urinary_tract(5)|skin(5)|bone(4)|pancreas(2)|prostate(1)	c.A578G	GRCh37	CM083194|CM951225	TP53	M		.						97	87	90					17																	7578271		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ATAAGATGCTGAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.578A>G	chr17.hg19:g.7578271T>C	ENSP00000269305:p.His193Arg	64.0	0.0		188.0	23.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.413611	0.42817	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99850	-7.16;-7.16;-7.16;-7.16;-7.16;-7.16;-7.16;-7.16	5.41	4.33	0.51752	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.92738	3.34	0.58432	D	0.999992	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97536	1.0083	10	0.72032	D	0.01	-29.0766	9.707	0.40222	0.0:0.0827:0.0:0.9173	.	154;193;193;100;193;193;193	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	193;193;193;193;193;193;182;100;61;100;61	ENSP00000410739:H193R;ENSP00000352610:H193R;ENSP00000269305:H193R;ENSP00000398846:H193R;ENSP00000391127:H193R;ENSP00000391478:H193R;ENSP00000425104:H61R;ENSP00000423862:H100R	ENSP00000269305:H193R	H	-	2	0	TP53	7518996	1.000000	0.71417	0.814000	0.32528	0.023000	0.10783	7.996000	0.88334	1.001000	0.39076	-0.256000	0.11100	CAT	.	.		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578271	T	C	7578271	3	2	101	1	0	0	0	0	1	0	0	0	16396	1464	51	2	716	2	TP53	17	7578271	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	1164	7578271	73616939	497	14334										
TP53	7157	hgsc.bcm.edu	37	chr17	7578449	7578449	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctgtgactgcttgtagatggCcatggcgcggacgcgggtgc	17	10	0	2	rs193920817		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:7578449C>A	ENST00000269305.4	-	5	670	c.481G>T	c.(481-483)Gcc>Tcc	p.A161S	TP53_ENST00000359597.4_Missense_Mutation_p.A161S|TP53_ENST00000445888.2_Missense_Mutation_p.A161S|TP53_ENST00000420246.2_Missense_Mutation_p.A161S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.A161S|TP53_ENST00000413465.2_Missense_Mutation_p.A161S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	161	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		A -> D (in sporadic cancers; somatic mutation).|A -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|A -> G (in sporadic cancers; somatic mutation).|A -> P (in sporadic cancers; somatic mutation).|A -> S (in sporadic cancers; somatic mutation).|A -> T (in sporadic cancers; somatic mutation).|A -> V (in sporadic cancers; somatic mutation).|MA -> IP (in a sporadic cancer; somatic mutation).|MA -> IS (in sporadic cancers; somatic mutation).|MA -> IT (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.A161T(54)|p.0?(8)|p.A68T(3)|p.A29T(3)|p.A161fs*9(3)|p.R156_I162delRVRAMAI(2)|p.M160fs*10(2)|p.V157_C176del20(1)|p.A161fs*19(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156fs*18(1)|p.A161fs*10(1)|p.R156_A161del(1)|p.V157fs*9(1)|p.A161fs*20(1)|p.M160_A161>IS(1)|p.A161fs*8(1)|p.S149fs*72(1)|p.A161fs*7(1)|p.T155_A161delTRVRAMA(1)|p.R156fs*20(1)|p.A161S(1)|p.A161P(1)|p.V157_I162delVRAMAI(1)|p.A161F(1)|p.A159_Q167delAMAIYKQSQ(1)|p.R158fs*8(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTGTAGATGGCCATGGCGCGG	0.632		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.A161S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,lymphoid_neoplasm,0,1	TP53	33396	.	96	Substitution - Missense(63)|Deletion - Frameshift(10)|Deletion - In frame(9)|Whole gene deletion(8)|Complex - frameshift(3)|Insertion - Frameshift(2)|Complex - compound substitution(1)	lung(15)|large_intestine(13)|urinary_tract(8)|stomach(7)|central_nervous_system(7)|upper_aerodigestive_tract(6)|oesophagus(6)|pancreas(6)|haematopoietic_and_lymphoid_tissue(5)|endometrium(5)|bone(4)|liver(4)|breast(3)|ovary(3)|thyroid(1)|meninges(1)|peritoneum(1)|skin(1)	c.G481T						.						52	53	53					17																	7578449		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGATGGCCATGGC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.481G>T	chr17.hg19:g.7578449C>A	ENSP00000269305:p.Ala161Ser	37.0	0.0		108.0	14.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.832703	0.50845	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99811	-6.87;-6.87;-6.87;-6.87;-6.87;-6.87;-6.87;-6.87;-6.87	5.59	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99711	0.9889	M	0.79805	2.47	0.48696	D	0.999696	D;P;D;D;D;D;D	0.89917	0.998;0.951;0.976;0.998;0.961;0.999;1.0	D;D;D;D;D;D;D	0.97110	0.998;0.989;0.981;0.998;0.994;1.0;1.0	D	0.97397	0.9993	10	0.59425	D	0.04	-25.6622	14.7187	0.69289	0.0:0.8543:0.1457:0.0	.	122;161;161;68;161;161;161	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	S	161;161;161;161;161;161;150;68;29;68;29;161	ENSP00000410739:A161S;ENSP00000352610:A161S;ENSP00000269305:A161S;ENSP00000398846:A161S;ENSP00000391127:A161S;ENSP00000391478:A161S;ENSP00000425104:A29S;ENSP00000423862:A68S;ENSP00000424104:A161S	ENSP00000269305:A161S	A	-	1	0	TP53	7519174	1.000000	0.71417	1.000000	0.80357	0.121000	0.20230	1.014000	0.29950	1.498000	0.48600	0.655000	0.94253	GCC	.	.		0.632	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578449	C	A	7578449	3	1	101	1	0	0	0	0	1	0	0	0	16396	739	26	3	817	3	TP53	17	7578449	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	178	7578449	73616761	498	14335										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7734001	7734001	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agaaaacttgctgagcctctAtctcgatgagtacgaggaga	11	8	2	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:7734001A>G	ENST00000572933.1	+	79	13531	c.12071A>G	c.(12070-12072)tAt>tGt	p.Y4024C	DNAH2_ENST00000389173.2_Missense_Mutation_p.Y4024C			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	4024					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTGAGCCTCTATCTCGATGAG	0.542																																					p.Y4024C		Atlas-SNP	.											.	DNAH2	498	.	0			c.A12071G						.						75	73	74					17																	7734001		2203	4300	6503	SO:0001583	missense	146754	exon78			GCCTCTATCTCGA	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.12071A>G	chr17.hg19:g.7734001A>G	ENSP00000458355:p.Tyr4024Cys	64.0	0.0		161.0	19.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.777868	0.70107	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.13657	2.57	5.84	5.84	0.93424	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.51924	0.1703	H	0.96547	3.84	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.67937	-0.5541	10	0.87932	D	0	.	15.1984	0.73116	1.0:0.0:0.0:0.0	.	3985;4024	Q9P225-2;Q9P225	.;DYH2_HUMAN	C	3985;4024	ENSP00000373825:Y4024C	ENSP00000353818:Y3985C	Y	+	2	0	DNAH2	7674726	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	5.509000	0.67012	2.243000	0.73865	0.533000	0.62120	TAT	.	.		0.542	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		G	7734001	A	G	7734001	3	3	101	1	0	0	0	0	1	0	0	0	4604	449	16	2	12381	2	DNAH2	17	7734001	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	155552	7734001	73461209	499	14336										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11775087	11775087	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggacagaacttggaggccctAcctgagccagctgaaagtac	12	11	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:11775087A>T	ENST00000262442.4	+	52	10294	c.10226A>T	c.(10225-10227)tAc>tTc	p.Y3409F	DNAH9_ENST00000454412.2_Missense_Mutation_p.Y3409F	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3409					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TGGAGGCCCTACCTGAGCCAG	0.488																																					p.Y3409F		Atlas-SNP	.											.	DNAH9	695	.	0			c.A10226T						.						95	104	101					17																	11775087		2203	4300	6503	SO:0001583	missense	1770	exon52			GGCCCTACCTGAG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10226A>T	chr17.hg19:g.11775087A>T	ENSP00000262442:p.Tyr3409Phe	58.0	0.0		154.0	33.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	4.653	0.121327	0.08881	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.75589	-0.95;-0.95	4.82	3.72	0.42706	Dynein heavy chain, coiled coil stalk (1);	0.145258	0.48767	D	0.000178	T	0.43010	0.1228	N	0.01656	-0.775	0.80722	D	1	B	0.06786	0.001	B	0.13407	0.009	T	0.34354	-0.9832	10	0.07482	T	0.82	.	11.1169	0.48266	0.8614:0.0:0.0:0.1386	.	3409	Q9NYC9	DYH9_HUMAN	F	3409;3409;1991	ENSP00000262442:Y3409F;ENSP00000414874:Y3409F	ENSP00000262442:Y3409F	Y	+	2	0	DNAH9	11715812	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	5.868000	0.69605	0.939000	0.37446	0.523000	0.50628	TAC	.	.		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11775087	A	T	11775087	3	4	101	1	0	0	0	0	1	0	0	0	4610	391	14	4	10432	4	DNAH9	17	11775087	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	4041086	11775087	69420123	500	14337										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11786904	11786904	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcttgcttgatatttgcagtCcgatctcacaaagcagcaga	8	10	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:11786904C>A	ENST00000262442.4	+	56	10876	c.10808C>A	c.(10807-10809)tCc>tAc	p.S3603Y	DNAH9_ENST00000454412.2_Splice_Site_p.S3603Y|DNAH9_ENST00000608377.1_5'UTR|DNAH9_ENST00000396001.2_3'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3603	AAA 5. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TATTTGCAGTCCGATCTCACA	0.498																																					p.S3603Y		Atlas-SNP	.											.	DNAH9	695	.	0			c.C10808A						.						112	99	103					17																	11786904		2203	4300	6503	SO:0001630	splice_region_variant	1770	exon56			TGCAGTCCGATCT	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10807-1C>A	chr17.hg19:g.11786904C>A		44.0	0.0		116.0	11.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197228	0.79015	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.27557	1.66;1.66	4.91	4.91	0.64330	.	0.200493	0.45361	D	0.000376	T	0.58708	0.2141	M	0.84948	2.725	0.80722	D	1	P	0.40211	0.707	P	0.55667	0.781	T	0.63323	-0.6663	10	0.72032	D	0.01	.	18.6493	0.91425	0.0:1.0:0.0:0.0	.	3603	Q9NYC9	DYH9_HUMAN	Y	3603;3603;2185	ENSP00000262442:S3603Y;ENSP00000414874:S3603Y	ENSP00000262442:S3603Y	S	+	2	0	DNAH9	11727629	0.998000	0.40836	0.984000	0.44739	0.961000	0.63080	3.923000	0.56469	2.709000	0.92574	0.655000	0.94253	TCC	.	.		0.498	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	Missense_Mutation	A	11786904	C	A	11786904	5	1	101	1	0	0	0	0	0	0	1	0	4610	869	30	3	11030	3	DNAH9	17	11786904	Splice_Site	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	11817	11786904	69408306	501	14338										
RICH2	9912	hgsc.bcm.edu	37	chr17	12819314	12819314	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gagacgtgattgagcccctgTttttgctggcggaggtaagc	15	8	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:12819314T>A	ENST00000379672.5	+	5	673	c.373T>A	c.(373-375)Ttt>Att	p.F125I	ARHGAP44_ENST00000340825.3_Missense_Mutation_p.F125I|ARHGAP44_ENST00000262444.9_Missense_Mutation_p.F125I|MIR1269B_ENST00000580405.1_RNA	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	125	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						TGAGCCCCTGTTTTTGCTGGC	0.522																																					p.F125I		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.T373A						.						80	81	80					17																	12819314		2080	4207	6287	SO:0001583	missense	9912	exon5			CCCCTGTTTTTGC		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"Rho GTPase activating proteins"	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.373T>A	chr17.hg19:g.12819314T>A	ENSP00000368994:p.Phe125Ile	65.0	0.0		194.0	25.0	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Missense_Mutation	SNP	ENST00000379672.5	hg19	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.667102	0.47677	.	.	ENSG00000006740	ENST00000379672;ENST00000340825	T;T	0.63096	-0.02;-0.02	5.92	5.92	0.95590	BAR (3);	0.182798	0.49916	D	0.000131	T	0.51398	0.1672	N	0.22421	0.69	0.41260	D	0.986773	P;B	0.38677	0.642;0.409	B;B	0.41135	0.316;0.348	T	0.50668	-0.8801	10	0.25106	T	0.35	.	14.3183	0.66468	0.0:0.0:0.0:1.0	.	125;125	A6NCP5;Q17R89	.;RHG44_HUMAN	I	125	ENSP00000368994:F125I;ENSP00000342566:F125I	ENSP00000342566:F125I	F	+	1	0	ARHGAP44	12760039	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	5.166000	0.64965	2.274000	0.75844	0.533000	0.62120	TTT	.	.		0.522	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859		A	12819314	T	A	12819314	3	1	101	1	0	0	0	0	1	0	0	0	13372	1725	60	4	391	4	RICH2	17	12819314	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	1032410	12819314	68375896	502	14339										
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319098	21319098	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	accaccatcggctacgggctGcgctgtgtgacggaggagtg	16	11	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:21319098G>T	ENST00000583088.1	+	3	1339	c.444G>T	c.(442-444)ctG>ctT	p.L148L	KCNJ12_ENST00000331718.5_Silent_p.L148L	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	148					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GCTACGGGCTGCGCTGTGTGA	0.637										Prostate(3;0.18)																											p.L148L		Atlas-SNP	.											.	.	.	.	0			c.G444T						.						54	52	53					17																	21319098		2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			CGGGCTGCGCTGT	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.444G>T	chr17.hg19:g.21319098G>T		41.0	0.0		148.0	27.0	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	hg19	CCDS11219.1																																																																																			.	.		0.637	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		T	21319098	G	T	21319098	2	4	101	1	0	0	0	0	0	0	0	1	8055	1306	46	3		3	KCNJ12	17	21319098	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	8499784	21319098	59876112	503	14340										
FOXN1	8456	hgsc.bcm.edu	37	chr17	26851109	26851109	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggctcccctgccccacagaGtgtaagtacccggcatctgg	11	15	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:26851109G>T	ENST00000226247.2	+	1	151	c.122G>T	c.(121-123)aGt>aTt	p.S41I	FOXN1_ENST00000579795.1_Splice_Site_p.S41I	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	41					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					GCCCCACAGAGTGTAAGTACC	0.682																																					p.S41I		Atlas-SNP	.											.	FOXN1	51	.	0			c.G122T						.						10	10	10					17																	26851109		2192	4284	6476	SO:0001630	splice_region_variant	8456	exon1			CACAGAGTGTAAG	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"Forkhead boxes"	12765	protein-coding gene	gene with protein product		600838	"winged-helix nude", "Rowett nude"	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.123+1G>T	chr17.hg19:g.26851109G>T		38.0	0.0		115.0	16.0	NM_003593	B2R9Q7|O15352	Missense_Mutation	SNP	ENST00000226247.2	hg19	CCDS11232.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.268947	0.40095	.	.	ENSG00000109101	ENST00000226247	D	0.93133	-3.17	5.03	0.129	0.14739	.	0.431911	0.24229	N	0.040373	D	0.85080	0.5615	N	0.19112	0.55	0.24096	N	0.99589	B	0.29085	0.232	B	0.28709	0.093	T	0.76250	-0.3028	10	0.66056	D	0.02	.	7.9671	0.30104	0.3666:0.0:0.6334:0.0	.	41	O15353	FOXN1_HUMAN	I	41	ENSP00000226247:S41I	ENSP00000226247:S41I	S	+	2	0	FOXN1	23875236	0.037000	0.19845	0.969000	0.41365	0.619000	0.37552	-0.171000	0.09883	-0.133000	0.11537	0.561000	0.74099	AGT	.	.		0.682	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1		Missense_Mutation	T	26851109	G	T	26851109	5	4	101	1	0	0	0	0	0	0	1	0	6027	1043	36	3	124	3	FOXN1	17	26851109	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	5532011	26851109	54344101	504	14341										
PHF12	57649	hgsc.bcm.edu	37	chr17	27251239	27251239	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctgtccaacaagtcagtgtCactgctgggggatgtagtcc	12	10	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:27251239C>A	ENST00000332830.4	-	4	1213	c.403G>T	c.(403-405)Gac>Tac	p.D135Y	RP11-20B24.5_ENST00000582631.1_RNA|PHF12_ENST00000577226.1_Missense_Mutation_p.D135Y|PHF12_ENST00000268756.3_Missense_Mutation_p.D135Y|RP11-20B24.5_ENST00000580782.1_RNA|PHF12_ENST00000582655.1_5'UTR	NM_001033561.1	NP_001028733.1			PHD finger protein 12											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			AAGTCAGTGTCACTGCTGGGG	0.537																																					p.D135Y		Atlas-SNP	.											.	PHF12	69	.	0			c.G403T						.						153	123	133					17																	27251239		2203	4300	6503	SO:0001583	missense	57649	exon4			CAGTGTCACTGCT	AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"Zinc fingers, PHD-type"	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.403G>T	chr17.hg19:g.27251239C>A	ENSP00000329933:p.Asp135Tyr	72.0	0.0		145.0	6.0	NM_020889		Missense_Mutation	SNP	ENST00000332830.4	hg19	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667068	0.88251	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.94828	-3.5;-3.53;-3.53	5.58	5.58	0.84498	.	0.095435	0.64402	D	0.000001	D	0.95937	0.8677	L	0.44542	1.39	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.976;0.999	D;D;P;D	0.70935	0.936;0.971;0.656;0.936	D	0.96325	0.9239	10	0.72032	D	0.01	-7.893	18.1066	0.89521	0.0:1.0:0.0:0.0	.	117;135;135;135	B4DFE2;Q96QT6-2;Q2TAK2;Q96QT6	.;.;.;PHF12_HUMAN	Y	135	ENSP00000329933:D135Y;ENSP00000368157:D135Y;ENSP00000268756:D135Y	ENSP00000268756:D135Y	D	-	1	0	PHF12	24275365	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.252000	0.78309	2.609000	0.88269	0.655000	0.94253	GAC	.	.		0.537	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889		A	27251239	C	A	27251239	3	1	101	1	0	0	0	0	1	0	0	0	11832	826	29	3	2685	3	PHF12	17	27251239	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	400130	27251239	53943971	505	14342										
TMEM132E	124842	hgsc.bcm.edu	37	chr17	32956067	32956067	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttggagatcttgcagctggaCtttgaaatggagaacttcac	11	7	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:32956067C>A	ENST00000321639.5	+	5	1240	c.912C>A	c.(910-912)gaC>gaA	p.D304E		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	304						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TGCAGCTGGACTTTGAAATGG	0.627																																					p.D304E		Atlas-SNP	.											.	TMEM132E	122	.	0			c.C912A						.						84	84	84					17																	32956067		2203	4300	6503	SO:0001583	missense	124842	exon5			GCTGGACTTTGAA	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.912C>A	chr17.hg19:g.32956067C>A	ENSP00000316532:p.Asp304Glu	55.0	0.0		190.0	9.0	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	hg19	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	c	10.69	1.420108	0.25552	.	.	ENSG00000181291	ENST00000321639	T	0.21361	2.01	4.51	4.51	0.55191	.	0.097095	0.64402	D	0.000002	T	0.19167	0.0460	L	0.52364	1.645	0.44492	D	0.997435	P	0.41393	0.748	B	0.40101	0.319	T	0.01545	-1.1328	10	0.23302	T	0.38	-35.2459	10.179	0.42957	0.0:0.8974:0.0:0.1026	.	304	Q6IEE7	T132E_HUMAN	E	304	ENSP00000316532:D304E	ENSP00000316532:D304E	D	+	3	2	TMEM132E	29980180	1.000000	0.71417	1.000000	0.80357	0.024000	0.10985	2.339000	0.43965	2.502000	0.84385	0.447000	0.29281	GAC	.	.		0.627	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		A	32956067	C	A	32956067	3	1	101	1	0	0	0	0	1	0	0	0	16063	564	20	3	930	3	TMEM132E	17	32956067	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	5704828	32956067	48239143	506	14343										
NLE1	54475	hgsc.bcm.edu	37	chr17	33469091	33469091	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cccagcagctgcccgccctcAtcctggaactgcactagcaa	8	18	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:33469091A>G	ENST00000442241.4	-	2	108	c.69T>C	c.(67-69)gaT>gaC	p.D23D	NLE1_ENST00000593176.1_5'UTR|NLE1_ENST00000586869.1_5'UTR|NLE1_ENST00000360831.5_Silent_p.D23D	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	23					hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				GCCCGCCCTCATCCTGGAACT	0.682																																					p.D23D		Atlas-SNP	.											.	NLE1	42	.	0			c.T69C						.						44	34	37					17																	33469091		2203	4300	6503	SO:0001819	synonymous_variant	54475	exon2			GCCCTCATCCTGG		CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"WD repeat domain containing"	19889	protein-coding gene	gene with protein product	"Notchless gene homolog, (Drosophila)"						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.69T>C	chr17.hg19:g.33469091A>G		36.0	0.0		54.0	16.0	NM_018096	O60868|Q59GJ8|Q9BU54	Silent	SNP	ENST00000442241.4	hg19	CCDS11291.1																																																																																			.	.		0.682	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096		G	33469091	A	G	33469091	2	3	101	1	0	0	0	0	0	0	0	1	10469	214	8	2		2	NLE1	17	33469091	Silent	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	513024	33469091	47726119	507	14344										
MED24	9862	hgsc.bcm.edu	37	chr17	38179422	38179422	+	Frame_Shift_Del	DEL	T	T	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaaccagtagacgccgcccaTgtgcagcagggtgtcaaaga							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:38179422delT	ENST00000394128.2	-	20	2293	c.2212delA	c.(2212-2214)atgfs	p.M738fs	MED24_ENST00000501516.3_Frame_Shift_Del_p.M757fs|MED24_ENST00000394126.1_Frame_Shift_Del_p.M763fs|MED24_ENST00000394127.2_Frame_Shift_Del_p.M725fs|MED24_ENST00000356271.3_Frame_Shift_Del_p.M725fs	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	738					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					ACGCCGCCCATGTGCAGCAGG	0.602																																					p.M738fs		Atlas-INDEL	.											.	MED24	89	.	0			c.2213delT						.						69	64	65					17																	38179422		2203	4300	6503	SO:0001589	frameshift_variant	9862	exon20			.	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2212delA	chr17.hg19:g.38179422delT	ENSP00000377686:p.Met738fs	26.0	0.0		97.0	22.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Frame_Shift_Del	DEL	ENST00000394128.2	hg19	CCDS11359.1																																																																																			.	.		0.602	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		-	38179422	T	-	38179422	7	5	101	1	0	1	0	1	0	0	0	0	9451	1464	51	0	785	0	MED24	17	38179422	Frame_Shift_Del	DEL	T	TCGA-DD-A1EE-01A-11D-A12Z-10	4710331	38179422	43015788	508	14345										
KRTAP3-3	85293	hgsc.bcm.edu	37	chr17	39150290	39150290	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cggcaggatttgtcagaggaGcagatggtggtggcaggccc	18	8	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:39150290G>T	ENST00000391586.1	-	1	95	c.60C>A	c.(58-60)tgC>tgA	p.C20*		NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	20	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			lung(2)|prostate(2)	4		Breast(137;0.00043)				TGTCAGAGGAGCAGATGGTGG	0.567																																					p.C20X		Atlas-SNP	.											.	KRTAP3-3	11	.	0			c.C60A						.						93	92	92					17																	39150290		2203	4296	6499	SO:0001587	stop_gained	85293	exon1			AGAGGAGCAGATG	AJ406933	CCDS32643.1	17q21.2	2013-06-25			ENSG00000212899	ENSG00000212899		"Keratin associated proteins"	18890	protein-coding gene	gene with protein product						11279113	Standard	NM_033185		Approved	KAP3.3	uc002hvr.1	Q9BYR6	OTTHUMG00000133591	ENST00000391586.1:c.60C>A	chr17.hg19:g.39150290G>T	ENSP00000375428:p.Cys20*	50.0	0.0		183.0	9.0	NM_033185	Q52LP0|Q6NTD4	Nonsense_Mutation	SNP	ENST00000391586.1	hg19	CCDS32643.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.957773	0.53400	.	.	ENSG00000212899	ENST00000391586	.	.	.	5.62	4.65	0.58169	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.41	0.44287	0.0894:0.0:0.9106:0.0	.	.	.	.	X	20	.	ENSP00000375428:C20X	C	-	3	2	KRTAP3-3	36403816	1.000000	0.71417	0.998000	0.56505	0.210000	0.24377	2.963000	0.49184	1.380000	0.46344	0.650000	0.86243	TGC	.	.		0.567	KRTAP3-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257695.1			T	39150290	G	T	39150290	4	4	101	1	0	0	0	0	0	1	0	0	8556	963	34	3	240	3	KRTAP3-3	17	39150290	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	970868	39150290	42044920	509	14346										
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40652840	40652840	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acaagtggacggcctatgatGctcatacctctgagaatgca	10	10	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:40652840G>T	ENST00000343619.4	+	16	1918	c.1795G>T	c.(1795-1797)Gct>Tct	p.A599S	ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.A599S|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.A556S|ATP6V0A1_ENST00000544137.1_Missense_Mutation_p.A245S|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.A599S|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.A606S|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.A556S	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	599					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		GGCCTATGATGCTCATACCTC	0.378																																					p.A606S		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.G1816T						.						215	195	202					17																	40652840		2203	4300	6503	SO:0001583	missense	535	exon16			TATGATGCTCATA	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"ATPases / V-type"	865	protein-coding gene	gene with protein product		192130	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 1", "ATPase, H+ transporting, lysosomal V0 subunit A1"	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.1795G>T	chr17.hg19:g.40652840G>T	ENSP00000342951:p.Ala599Ser	177.0	0.0		655.0	63.0	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	hg19	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.083018	0.76642	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728;ENST00000544137	D;D;D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17;-2.17;-2.17	4.91	4.91	0.64330	.	0.147766	0.64402	D	0.000010	D	0.90031	0.6887	L	0.60455	1.87	0.80722	D	1	B;B;B;P;B	0.46512	0.086;0.004;0.078;0.879;0.052	B;B;B;P;B	0.52823	0.156;0.02;0.063;0.71;0.056	D	0.89406	0.3699	10	0.44086	T	0.13	-9.9702	18.6406	0.91394	0.0:0.0:1.0:0.0	.	556;556;606;599;599	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1	.;.;.;VPP1_HUMAN;.	S	599;599;599;606;556;245	ENSP00000342951:A599S;ENSP00000444676:A599S;ENSP00000377415:A599S;ENSP00000264649:A606S;ENSP00000443991:A556S;ENSP00000446377:A245S	ENSP00000264649:A606S	A	+	1	0	ATP6V0A1	37906366	1.000000	0.71417	0.874000	0.34290	0.993000	0.82548	9.601000	0.98297	2.716000	0.92895	0.561000	0.74099	GCT	.	.		0.378	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020		T	40652840	G	T	40652840	3	4	101	1	0	0	0	0	1	0	0	0	1168	1319	46	3	1874	3	ATP6V0A1	17	40652840	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1502550	40652840	40542370	510	14347										
WNK4	65266	hgsc.bcm.edu	37	chr17	40946819	40946819	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agagcagcacctccctggagCacaggagctggacagccttc	12	14	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:40946819C>G	ENST00000246914.5	+	14	2401	c.2380C>G	c.(2380-2382)Cac>Gac	p.H794D		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	794					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CTCCCTGGAGCACAGGAGCTG	0.587																																					p.H794D	Esophageal Squamous(6;201 374 4964 23855 42828)	Atlas-SNP	.											.	WNK4	182	.	0			c.C2380G						.						123	94	104					17																	40946819		2203	4300	6503	SO:0001583	missense	65266	exon14			CTGGAGCACAGGA	AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"protein kinase, lysine deficient 4"	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.2380C>G	chr17.hg19:g.40946819C>G	ENSP00000246914:p.His794Asp	89.0	0.0		155.0	51.0	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Missense_Mutation	SNP	ENST00000246914.5	hg19	CCDS11439.1	.	.	.	.	.	.	.	.	.	.	C	0.224	-1.026490	0.02045	.	.	ENSG00000126562	ENST00000246914;ENST00000316085	T	0.70869	-0.52	5.15	5.15	0.70609	.	0.286819	0.25161	N	0.032664	T	0.46171	0.1379	N	0.08118	0	0.26263	N	0.978546	B;B;B	0.16396	0.017;0.01;0.004	B;B;B	0.11329	0.006;0.003;0.003	T	0.21042	-1.0257	10	0.12430	T	0.62	-6.8088	9.8456	0.41026	0.0:0.9086:0.0:0.0914	.	794;794;794	Q96J92-3;B0LPI0;Q96J92	.;.;WNK4_HUMAN	D	794;566	ENSP00000246914:H794D	ENSP00000246914:H794D	H	+	1	0	WNK4	38200345	0.815000	0.29118	1.000000	0.80357	0.397000	0.30659	1.617000	0.36943	2.837000	0.97791	0.591000	0.81541	CAC	.	.		0.587	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1			G	40946819	C	G	40946819	3	3	101	1	0	0	0	0	1	0	0	0	17395	710	25	4	2434	4	WNK4	17	40946819	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	293979	40946819	40248391	511	14348										
CNTD1	124817	hgsc.bcm.edu	37	chr17	40961398	40961398	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgaaggttgtggggcatttgCagagcatcactggtattgcc	14	7	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:40961398C>A	ENST00000588408.1	+	7	1114	c.838C>A	c.(838-840)Cag>Aag	p.Q280K	CNTD1_ENST00000588527.1_Missense_Mutation_p.Q197K|CNTD1_ENST00000315066.5_3'UTR	NM_173478.2	NP_775749.2	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1	280										central_nervous_system(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		GGGGCATTTGCAGAGCATCAC	0.438																																					p.Q280K		Atlas-SNP	.											.	CNTD1	22	.	0			c.C838A						.						135	128	130					17																	40961398		2203	4300	6503	SO:0001583	missense	124817	exon7			CATTTGCAGAGCA	AK097456	CCDS11440.1	17q21.31	2014-07-03	2006-03-31	2006-03-31	ENSG00000176563	ENSG00000176563			26847	protein-coding gene	gene with protein product			"cyclin N-terminal domain containing"	CNTD		24891606	Standard	NM_173478		Approved	FLJ40137	uc002ibm.4	Q8N815		ENST00000588408.1:c.838C>A	chr17.hg19:g.40961398C>A	ENSP00000465204:p.Gln280Lys	77.0	0.0		188.0	11.0	NM_173478	Q658Q6|Q8NEP1	Missense_Mutation	SNP	ENST00000588408.1	hg19	CCDS11440.1	.	.	.	.	.	.	.	.	.	.	C	5.742	0.321308	0.10845	.	.	ENSG00000176563	ENST00000315066	.	.	.	6.03	6.03	0.97812	.	0.192857	0.56097	D	0.000034	T	0.37679	0.1012	L	0.36672	1.1	0.32552	N	0.532304	B	0.23937	0.094	B	0.19666	0.026	T	0.35525	-0.9785	9	0.02654	T	1	-7.9759	12.2136	0.54394	0.132:0.7405:0.1275:0.0	.	280	Q8N815	CNTD1_HUMAN	K	280	.	ENSP00000316647:Q280K	Q	+	1	0	CNTD1	38214924	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	2.324000	0.43831	2.868000	0.98415	0.555000	0.69702	CAG	.	.		0.438	CNTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452398.1	NM_173478		A	40961398	C	A	40961398	3	1	101	1	0	0	0	0	1	0	0	0	3637	711	25	3	864	3	CNTD1	17	40961398	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	14579	40961398	40233812	512	14349										
CCDC43	124808	hgsc.bcm.edu	37	chr17	42756228	42756228	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atagagtaggccaaggttatCgctttcgctcccctctctgt	9	12	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:42756228C>G	ENST00000315286.8	-	5	679	c.671G>C	c.(670-672)cGa>cCa	p.R224P	CCDC43_ENST00000457422.2_3'UTR|C17orf104_ENST00000588805.1_Intron|RP11-1072C15.4_ENST00000591628.1_RNA|CCDC43_ENST00000588210.1_Missense_Mutation_p.R227P	NM_144609.2	NP_653210.2	Q96MW1	CCD43_HUMAN	coiled-coil domain containing 43	224										lung(2)	2		Prostate(33;0.0322)				CCAAGGTTATCGCTTTCGCTC	0.453																																					p.R224P		Atlas-SNP	.											.	CCDC43	34	.	0			c.G671C						.						78	81	80					17																	42756228		1914	4123	6037	SO:0001583	missense	124808	exon5			GGTTATCGCTTTC	AK056357	CCDS45704.1, CCDS45705.1	17q21.31	2005-12-16							26472	protein-coding gene	gene with protein product						12477932	Standard	NM_001099225		Approved	FLJ31795	uc002ihc.2	Q96MW1		ENST00000315286.8:c.671G>C	chr17.hg19:g.42756228C>G	ENSP00000323782:p.Arg224Pro	155.0	0.0		287.0	18.0	NM_144609	C9JVK9	Missense_Mutation	SNP	ENST00000315286.8	hg19	CCDS45704.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058141	0.76074	.	.	ENSG00000180329	ENST00000315286	.	.	.	6.16	6.16	0.99307	.	0.120163	0.56097	D	0.000024	T	0.79499	0.4456	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79215	-0.1895	9	0.87932	D	0	.	19.6313	0.95704	0.0:1.0:0.0:0.0	.	224	Q96MW1	CCD43_HUMAN	P	224	.	ENSP00000323782:R224P	R	-	2	0	CCDC43	40111754	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.802000	0.75175	2.937000	0.99478	0.650000	0.86243	CGA	.	.		0.453	CCDC43-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457812.1	NM_144609		G	42756228	C	G	42756228	3	3	101	1	0	0	0	0	1	0	0	0	2817	884	31	4	7	4	CCDC43	17	42756228	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1794830	42756228	38438982	513	14350										
CCDC43	124808	hgsc.bcm.edu	37	chr17	42756390	42756391	+	Frame_Shift_Ins	INS	-	-	GT													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggcattaaggacatcttccaINScattggtgtttcggaacaga							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:42756390_42756391insGT	ENST00000315286.8	-	5	516_517	c.508_509insAC	c.(508-510)gtgfs	p.V170fs	CCDC43_ENST00000457422.2_Frame_Shift_Ins_p.C150fs|C17orf104_ENST00000588805.1_3'UTR|RP11-1072C15.4_ENST00000591628.1_RNA|CCDC43_ENST00000588210.1_Frame_Shift_Ins_p.V173fs	NM_144609.2	NP_653210.2	Q96MW1	CCD43_HUMAN	coiled-coil domain containing 43	170										lung(2)	2		Prostate(33;0.0322)				GACATCTTCCACATTGGTGTTT	0.475																																					p.V170fs		Atlas-INDEL	.											.	CCDC43	34	.	0			c.509_510insAC						.																																			SO:0001589	frameshift_variant	124808	exon5			.	AK056357	CCDS45704.1, CCDS45705.1	17q21.31	2005-12-16							26472	protein-coding gene	gene with protein product						12477932	Standard	NM_001099225		Approved	FLJ31795	uc002ihc.2	Q96MW1		ENST00000315286.8:c.508_509insAC	chr17.hg19:g.42756390_42756391insGT	ENSP00000323782:p.Val170fs	97.0	0.0		196.0	30.0	NM_144609	C9JVK9	Frame_Shift_Ins	INS	ENST00000315286.8	hg19	CCDS45704.1																																																																																			.	.		0.475	CCDC43-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457812.1	NM_144609		GT	42756391	-	GT	42756390	7	5	101	1	0	1	1	0	0	0	0	0	2817	160	6	0	169	0	CCDC43	17	42756390	Frame_Shift_Ins	INS	-	TCGA-DD-A1EE-01A-11D-A12Z-10	162	42756390	38438820	514	14351										
GJC1	10052	hgsc.bcm.edu	37	chr17	42883077	42883077	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gatggattctcctcctacagCtgtaaggacgatccggaaga	11	10	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:42883077C>G	ENST00000426548.1	-	3	378	c.109G>C	c.(109-111)Gct>Cct	p.A37P	GJC1_ENST00000592524.1_Missense_Mutation_p.A37P|GJC1_ENST00000330514.4_Missense_Mutation_p.A37P|GJC1_ENST00000590758.1_Missense_Mutation_p.A37P	NM_001080383.1|NM_005497.3	NP_001073852.1|NP_005488.2	P36383	CXG1_HUMAN	gap junction protein, gamma 1, 45kDa	37					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle tissue development (GO:0048738)|cell development (GO:0048468)|cell-cell junction assembly (GO:0007043)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vasculogenesis (GO:0001570)|visual perception (GO:0007601)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion channel activity (GO:0005216)			NS(1)|kidney(1)|large_intestine(5)|liver(1)|lung(10)|prostate(1)	19		Prostate(33;0.0959)				CCTCCTACAGCTGTAAGGACG	0.483																																					p.A37P		Atlas-SNP	.											.	GJC1	45	.	0			c.G109C						.						108	89	95					17																	42883077		2203	4300	6503	SO:0001583	missense	10052	exon3			CTACAGCTGTAAG	U03493	CCDS11487.1	17q21.31	2008-02-04	2007-11-06	2007-11-06		ENSG00000182963		"Ion channels / Gap junction proteins (connexins)"	4280	protein-coding gene	gene with protein product	"connexin 45"	608655	"gap junction protein, alpha 7, 45kDa"	GJA7		7966354	Standard	NM_005497		Approved	CX45	uc002ihl.3	P36383		ENST00000426548.1:c.109G>C	chr17.hg19:g.42883077C>G	ENSP00000411528:p.Ala37Pro	62.0	0.0		223.0	20.0	NM_005497	B3KW68|Q4VAY0	Missense_Mutation	SNP	ENST00000426548.1	hg19	CCDS11487.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.230285	0.79688	.	.	ENSG00000182963	ENST00000426548;ENST00000330514	D;D	0.99194	-5.54;-5.54	5.26	5.26	0.73747	Connexin, N-terminal (1);	0.056597	0.64402	D	0.000001	D	0.99299	0.9755	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99357	1.0916	10	0.66056	D	0.02	.	17.8787	0.88833	0.0:1.0:0.0:0.0	.	37	P36383	CXG1_HUMAN	P	37	ENSP00000411528:A37P;ENSP00000333193:A37P	ENSP00000333193:A37P	A	-	1	0	GJC1	40238603	1.000000	0.71417	0.996000	0.52242	0.971000	0.66376	7.818000	0.86416	2.458000	0.83093	0.455000	0.32223	GCT	.	.		0.483	GJC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448661.1	NM_005497		G	42883077	C	G	42883077	3	3	101	1	0	0	0	0	1	0	0	0	6422	797	28	4	1085	4	GJC1	17	42883077	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	126687	42883077	38312133	515	14352										
NFE2L1	4779	hgsc.bcm.edu	37	chr17	46136906	46136906	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcccagtcagtatgcgctccAgtacgccggggacggcagtg	15	13	1	0	rs141070896		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:46136906A>T	ENST00000362042.3	+	6	2838	c.2222A>T	c.(2221-2223)cAg>cTg	p.Q741L	NFE2L1_ENST00000583378.1_Missense_Mutation_p.Q542L|NFE2L1_ENST00000582155.1_Missense_Mutation_p.Q553L|NFE2L1_ENST00000585291.1_Missense_Mutation_p.Q711L|NFE2L1_ENST00000361665.3_Missense_Mutation_p.Q730L|RP5-890E16.4_ENST00000583349.1_RNA|NFE2L1_ENST00000357480.5_Missense_Mutation_p.Q711L|NFE2L1_ENST00000536222.1_Missense_Mutation_p.Q585L	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	741					anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TATGCGCTCCAGTACGCCGGG	0.642																																					p.Q741L		Atlas-SNP	.											.	NFE2L1	60	.	0			c.A2222T						.						65	68	67					17																	46136906		2203	4300	6503	SO:0001583	missense	4779	exon6			CGCTCCAGTACGC	AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"basic leucine zipper proteins"	7781	protein-coding gene	gene with protein product		163260	"nuclear factor (erythroid-derived 2)-like 1"	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.2222A>T	chr17.hg19:g.46136906A>T	ENSP00000354855:p.Gln741Leu	21.0	0.0		62.0	7.0	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Missense_Mutation	SNP	ENST00000362042.3	hg19	CCDS11524.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.276019	0.80580	.	.	ENSG00000082641	ENST00000362042;ENST00000361665;ENST00000357480;ENST00000536222	T;T	0.28454	1.91;1.61	5.89	5.89	0.94794	.	0.101984	0.64402	D	0.000001	T	0.49474	0.1559	M	0.71206	2.165	0.80722	D	1	D;D;P;D	0.56521	0.976;0.958;0.949;0.973	P;P;P;P	0.55785	0.784;0.613;0.6;0.711	T	0.53121	-0.8483	10	0.87932	D	0	-32.454	15.2935	0.73885	1.0:0.0:0.0:0.0	.	585;553;711;741	F5H1B7;B4DYE1;Q14494-2;Q14494	.;.;.;NF2L1_HUMAN	L	760;741;711;585	ENSP00000350072:Q711L;ENSP00000445811:Q585L	ENSP00000350072:Q711L	Q	+	2	0	NFE2L1	43491905	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.249000	0.95470	2.257000	0.74773	0.460000	0.39030	CAG	.	A|1.000;G|0.000		0.642	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204		T	46136906	A	T	46136906	3	4	101	1	0	0	0	0	1	0	0	0	10376	188	7	4	2240	4	NFE2L1	17	46136906	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	3253829	46136906	35058304	516	14353										
DLX4	1748	hgsc.bcm.edu	37	chr17	48046980	48046980	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccaatttgtcctactccaggCcgtatggccacctcctgtct	7	16	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:48046980C>T	ENST00000240306.3	+	1	443	c.148C>T	c.(148-150)Ccg>Tcg	p.P50S	DLX4_ENST00000505318.2_Missense_Mutation_p.P50S|DLX4_ENST00000503410.1_3'UTR	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4	50				MTSLPCPLPGRDASKAVFPDLAPVPSVAAAYPLGLSPTTAA SPNLSYSRPYGHLLSYPYTEPANPGDSYLSCQQPAALSQPL CGPAEHPQELEA -> GGSLSLPPEPLCARCPTKEGAAPRR PGFWGSLETQAATVWRGRHGHFSCRVRLSRGAARYSRRGQG KPGVTISAARLVFKVLSAGPLTHPAGRSRRLPRGHRLKPLS IALSLCLQCPSSVISRPRLSPGPSLSAPPYPKLAPPPVAEL RPPTAGAAVPWLWPSARFLPRVTGPIRVGAPLGAELRLVSP GAVNVGVETLHAE (in Ref. 9). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(3)	10						CTACTCCAGGCCGTATGGCCA	0.652																																					p.P50S		Atlas-SNP	.											DLX4,caecum,carcinoma,0,1	DLX4	25	.	0			c.C148T						.						99	100	100					17																	48046980		2203	4300	6503	SO:0001583	missense	1748	exon1			TCCAGGCCGTATG		CCDS11555.1, CCDS45728.1	17q21.33	2011-06-20			ENSG00000108813	ENSG00000108813		"Homeoboxes / ANTP class : NKL subclass"	2917	protein-coding gene	gene with protein product		601911		DLX7, DLX9			Standard	NM_138281		Approved	DLX8, BP1	uc002ipv.3	Q92988	OTTHUMG00000161839	ENST00000240306.3:c.148C>T	chr17.hg19:g.48046980C>T	ENSP00000240306:p.Pro50Ser	12.0	0.0		61.0	7.0	NM_138281	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Missense_Mutation	SNP	ENST00000240306.3	hg19	CCDS11555.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.660455	0.29515	.	.	ENSG00000108813	ENST00000240306	D	0.91351	-2.83	3.88	0.596	0.17496	.	.	.	.	.	T	0.75027	0.3794	N	0.14661	0.345	0.09310	N	0.999997	B	0.09022	0.002	B	0.04013	0.001	T	0.61098	-0.7131	9	0.02654	T	1	-0.3069	3.3909	0.07289	0.2023:0.5656:0.0:0.2321	.	50	Q92988	DLX4_HUMAN	S	50	ENSP00000240306:P50S	ENSP00000240306:P50S	P	+	1	0	DLX4	45401979	0.007000	0.16637	0.006000	0.13384	0.898000	0.52572	1.018000	0.30002	0.304000	0.22809	0.313000	0.20887	CCG	.	.		0.652	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1			T	48046980	C	T	48046980	3	4	101	1	0	0	0	0	1	0	0	0	4575	739	26	3	150	3	DLX4	17	48046980	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1910074	48046980	33148230	517	14354										
SGCA	6442	hgsc.bcm.edu	37	chr17	48244792	48244792	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctacacccacttgtgggccGtgtctttgtgcacaccttgg	11	13	1	0	rs371675217		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:48244792G>T	ENST00000262018.3	+	2	137	c.101G>T	c.(100-102)cGt>cTt	p.R34L	SGCA_ENST00000344627.6_Missense_Mutation_p.R34L|SGCA_ENST00000543315.1_Missense_Mutation_p.R34L|SGCA_ENST00000513942.1_Intron|RP11-893F2.14_ENST00000572855.1_RNA|SGCA_ENST00000451235.2_5'UTR	NM_000023.2	NP_000014.1	Q16586	SGCA_HUMAN	sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein)	34			R -> C (in LGMD2D). {ECO:0000269|PubMed:9192266}.|R -> H (in LGMD2D). {ECO:0000269|PubMed:7663524}.		muscle contraction (GO:0006936)|muscle organ development (GO:0007517)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						CTTGTGGGCCGTGTCTTTGTG	0.642																																					p.R34L		Atlas-SNP	.											SGCA,colon,carcinoma,0,1	SGCA	35	.	0			c.G101T	GRCh37	CM951149	SGCA	M		.						104	87	92					17																	48244792		2203	4300	6503	SO:0001583	missense	6442	exon2			TGGGCCGTGTCTT	L34355	CCDS32679.1, CCDS45729.1	17q21	2014-09-17	2002-08-29		ENSG00000108823	ENSG00000108823			10805	protein-coding gene	gene with protein product	"50kD DAG", "Sarcoglycan, alpha (50kD dystrophin-associated glycoprotein; adhalin)", "adhalin (limb girdle muscular dystrophy 2D)"	600119	"sarcoglycan, alpha (50kD dystrophin-associated glycoprotein)"	ADL		7937874	Standard	NM_000023		Approved	SCARMD1, LGMD2D, adhalin, DMDA2, A2	uc002iqi.3	Q16586	OTTHUMG00000162024	ENST00000262018.3:c.101G>T	chr17.hg19:g.48244792G>T	ENSP00000262018:p.Arg34Leu	65.0	0.0		170.0	8.0	NM_001135697	A6NEB8|A8K3K7|Q13710|Q13712	Missense_Mutation	SNP	ENST00000262018.3	hg19	CCDS32679.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857415	0.51376	.	.	ENSG00000108823	ENST00000344627;ENST00000262018;ENST00000543315	D;D;D	0.98531	-4.98;-4.98;-4.98	4.47	4.47	0.54385	Dystroglycan-type cadherin-like (1);Cadherin-like (1);	0.144240	0.43579	D	0.000544	D	0.95990	0.8694	L	0.46157	1.445	0.80722	D	1	B;B	0.28636	0.218;0.004	B;B	0.26864	0.074;0.007	D	0.95008	0.8149	10	0.42905	T	0.14	-15.278	12.9801	0.58559	0.0:0.0:1.0:0.0	.	34;34	Q16586-2;Q16586	.;SGCA_HUMAN	L	34	ENSP00000345522:R34L;ENSP00000262018:R34L;ENSP00000444539:R34L	ENSP00000262018:R34L	R	+	2	0	SGCA	45599791	0.584000	0.26766	0.960000	0.40013	0.753000	0.42808	2.894000	0.48640	2.184000	0.69523	0.407000	0.27541	CGT	.	.		0.642	SGCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366841.1	NM_000023		T	48244792	G	T	48244792	3	4	101	1	0	0	0	0	1	0	0	0	14214	1145	40	1	107	1	SGCA	17	48244792	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	197812	48244792	32950418	518	14355										
EPN3	55040	hgsc.bcm.edu	37	chr17	48614425	48614425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtgggcagctgggcttcagcCgccgctacggcgaggactac	16	13	1	0	rs146173668	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:48614425C>T	ENST00000268933.3	+	2	1087	c.508C>T	c.(508-510)Cgc>Tgc	p.R170C	EPN3_ENST00000537145.1_Missense_Mutation_p.R225C|EPN3_ENST00000541226.1_Missense_Mutation_p.R114C|RP11-94C24.8_ENST00000513017.1_RNA	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	170						clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			GGGCTTCAGCCGCCGCTACGG	0.682													C|||	4	0.000798722	0.0015	0	5008	,	,		15206	0		0.002	False		,,,				2504	0				p.R170C		Atlas-SNP	.											.	EPN3	32	.	0			c.C508T						.	C	CYS/ARG	0,4292		0,0,2146	17	15	16		508	5.2	1	17	dbSNP_134	16	1,8445		0,1,4222	no	missense	EPN3	NM_017957.2	180	0,1,6368	TT,TC,CC		0.0118,0.0,0.0079	probably-damaging	170/633	48614425	1,12737	2146	4223	6369	SO:0001583	missense	55040	exon2			TTCAGCCGCCGCT	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.508C>T	chr17.hg19:g.48614425C>T	ENSP00000268933:p.Arg170Cys	12.0	0.0		127.0	22.0	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	hg19	CCDS11570.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171748	0.78452	0.0	1.18E-4	ENSG00000049283	ENST00000268933;ENST00000442715;ENST00000537145;ENST00000541226;ENST00000411703	T;T;T	0.50813	2.33;2.22;0.73	5.24	5.24	0.73138	.	0.659654	0.11791	N	0.529152	T	0.68210	0.2976	L	0.58810	1.83	0.48901	D	0.999725	D;D;D	0.89917	1.0;1.0;0.961	D;D;P	0.91635	0.972;0.999;0.586	T	0.64799	-0.6322	10	0.49607	T	0.09	-18.696	18.4459	0.90683	0.0:1.0:0.0:0.0	.	225;225;170	B4DK18;F6QWW5;Q9H201	.;.;EPN3_HUMAN	C	170;225;225;114;170	ENSP00000268933:R170C;ENSP00000439512:R225C;ENSP00000440540:R114C	ENSP00000268933:R170C	R	+	1	0	EPN3	45969424	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.620000	0.36976	2.457000	0.83068	0.561000	0.74099	CGC	.	C|1.000;T|0.000		0.682	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957		T	48614425	C	T	48614425	3	4	101	1	0	0	0	0	1	0	0	0	5189	652	23	1	510	1	EPN3	17	48614425	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	369633	48614425	32580785	519	14356										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48695290	48695290	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtgatgcaggccctgccccaGgtagccgggaggtggggggc	20	11	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:48695290G>A	ENST00000359106.5	+	30	5226	c.5226G>A	c.(5224-5226)caG>caA	p.Q1742Q	CACNA1G_ENST00000505165.1_Splice_Site_p.Q1742Q|CACNA1G_ENST00000515765.1_Splice_Site_p.Q1731Q|CACNA1G_ENST00000442258.2_Splice_Site_p.Q1701Q|CACNA1G_ENST00000514079.1_Splice_Site_p.Q1749Q|CACNA1G_ENST00000354983.4_Splice_Site_p.Q1708Q|CACNA1G_ENST00000507609.1_Intron|CACNA1G_ENST00000513689.2_Splice_Site_p.Q1697Q|CACNA1G_ENST00000512389.1_Splice_Site_p.Q1731Q|CACNA1G_ENST00000507336.1_Splice_Site_p.Q1731Q|CACNA1G_ENST00000510366.1_Splice_Site_p.Q1690Q|CACNA1G_ENST00000510115.1_Splice_Site_p.Q1708Q|CACNA1G_ENST00000358244.5_Splice_Site_p.Q1708Q|CACNA1G_ENST00000515411.1_Splice_Site_p.Q1724Q|CACNA1G_ENST00000502264.1_Splice_Site_p.Q1719Q|CACNA1G_ENST00000513964.1_Splice_Site_p.Q1697Q|CACNA1G_ENST00000503485.1_Splice_Site_p.Q1708Q|CACNA1G_ENST00000352832.5_Splice_Site_p.Q1708Q|CACNA1G_ENST00000514181.1_Intron|CACNA1G_ENST00000514717.1_Splice_Site_p.Q1685Q|CACNA1G_ENST00000507510.2_Splice_Site_p.Q1742Q|CACNA1G_ENST00000515165.1_Splice_Site_p.Q1742Q|CACNA1G_ENST00000429973.2_Splice_Site_p.Q1724Q|CACNA1G_ENST00000507896.1_Splice_Site_p.Q1731Q|CACNA1G_ENST00000360761.4_Splice_Site_p.Q1719Q	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1742					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CCCTGCCCCAGGTAGCCGGGA	0.637																																					p.Q1749Q		Atlas-SNP	.											.	CACNA1G	659	.	0			c.G5247A						.						38	41	40					17																	48695290		1880	4107	5987	SO:0001630	splice_region_variant	8913	exon30			GCCCCAGGTAGCC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.5226+1G>A	chr17.hg19:g.48695290G>A		46.0	0.0		120.0	44.0	NM_001256325	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	hg19	CCDS45730.1																																																																																			.	.		0.637	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	Silent	A	48695290	G	A	48695290	5	1	101	1	0	0	0	0	0	0	1	0	2546	1014	35	3	5611	3	CACNA1G	17	48695290	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	80865	48695290	32499920	520	14357										
SPAG9	9043	hgsc.bcm.edu	37	chr17	49067132	49067132	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gacgccagtttgggagatgtCcactgtgtcttcagctgacc	12	11	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:49067132C>T	ENST00000262013.7	-	21	2927	c.2719G>A	c.(2719-2721)Gac>Aac	p.D907N	SPAG9_ENST00000510283.1_Missense_Mutation_p.D750N|SPAG9_ENST00000505279.1_Missense_Mutation_p.D897N|SPAG9_ENST00000357122.4_Missense_Mutation_p.D893N	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	907					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			TGGGAGATGTCCACTGTGTCT	0.468																																					p.D907N		Atlas-SNP	.											.	SPAG9	151	.	0			c.G2719A						.						180	146	157					17																	49067132		2203	4300	6503	SO:0001583	missense	9043	exon21			AGATGTCCACTGT	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2719G>A	chr17.hg19:g.49067132C>T	ENSP00000262013:p.Asp907Asn	139.0	0.0		239.0	95.0	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	hg19	CCDS45740.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.7|20.7	4.037756|4.037756	0.75617|0.75617	.|.	.|.	ENSG00000008294|ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000357791;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445|ENST00000513906	T;T;T;T|.	0.22945|.	1.93;1.93;1.93;1.93|.	5.77|5.77	5.77|5.77	0.91146|0.91146	WD40 repeat-like-containing domain (1);|.	0.142130|.	0.53938|.	D|.	0.000051|.	T|.	0.73321|.	0.3572|.	L|L	0.56769|0.56769	1.78|1.78	0.53688|0.53688	D|D	0.999975|0.999975	D;D;B;B;P;D|.	0.89917|.	1.0;0.964;0.049;0.012;0.58;0.962|.	D;P;B;B;B;P|.	0.91635|.	0.999;0.84;0.021;0.009;0.344;0.528|.	T|.	0.69015|.	-0.5257|.	10|.	0.26408|.	T|.	0.33|.	-19.5081|-19.5081	19.9831|19.9831	0.97336|0.97336	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	893;907;897;907;893;750|.	O60271-5;O60271-3;O60271-2;O60271;O60271-4;E7ENU2|.	.;.;.;JIP4_HUMAN;.;.|.	N|X	907;664;654;444;750;897;893;505|150	ENSP00000262013:D907N;ENSP00000423165:D750N;ENSP00000426900:D897N;ENSP00000349636:D893N|.	ENSP00000262013:D907N|.	D|W	-|-	1|3	0|0	SPAG9|SPAG9	46422131|46422131	0.994000|0.994000	0.37717|0.37717	1.000000|1.000000	0.80357|0.80357	0.834000|0.834000	0.47266|0.47266	4.066000|4.066000	0.57520|0.57520	2.728000|2.728000	0.93425|0.93425	0.650000|0.650000	0.86243|0.86243	GAC|TGG	.	.		0.468	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		T	49067132	C	T	49067132	3	4	101	1	0	0	0	0	1	0	0	0	15000	855	30	3	1286	3	SPAG9	17	49067132	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	371842	49067132	32128078	521	14358										
TOM1L1	10040	hgsc.bcm.edu	37	chr17	52991114	52991114	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atctcttgaattcagacttgGtcacagggcttcccaggagg	11	10	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:52991114G>C	ENST00000575882.1	+	5	731	c.378G>C	c.(376-378)tgG>tgC	p.W126C	TOM1L1_ENST00000540336.1_Missense_Mutation_p.W49C|TOM1L1_ENST00000572158.1_Missense_Mutation_p.W119C|TOM1L1_ENST00000575333.1_Missense_Mutation_p.W126C|TOM1L1_ENST00000536554.1_Missense_Mutation_p.W49C|TOM1L1_ENST00000348161.4_Missense_Mutation_p.W49C|TOM1L1_ENST00000572405.1_Missense_Mutation_p.W91C|TOM1L1_ENST00000445275.2_Missense_Mutation_p.W126C|TOM1L1_ENST00000570371.1_Missense_Mutation_p.W126C	NM_005486.2	NP_005477.2	O75674	TM1L1_HUMAN	target of myb1 (chicken)-like 1	126	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				activation of protein kinase activity (GO:0032147)|intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|positive regulation of protein autophosphorylation (GO:0031954)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	clathrin binding (GO:0030276)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|ubiquitin binding (GO:0043130)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	15						TTCAGACTTGGTCACAGGGCT	0.403																																					p.W126C		Atlas-SNP	.											.	TOM1L1	33	.	0			c.G378C						.						99	96	97					17																	52991114		2203	4300	6503	SO:0001583	missense	10040	exon5			GACTTGGTCACAG	AJ010071	CCDS11582.1	17q23.2	2008-01-03	2007-01-12			ENSG00000141198			11983	protein-coding gene	gene with protein product		604701	"target of myb1 (chicken) homolog-like 1"			10329004, 15611048, 17977829	Standard	NM_005486		Approved	SRCASM	uc002iud.2	O75674		ENST00000575882.1:c.378G>C	chr17.hg19:g.52991114G>C	ENSP00000460823:p.Trp126Cys	63.0	0.0		132.0	8.0	NM_005486	Q53G06|Q8N749	Missense_Mutation	SNP	ENST00000575882.1	hg19	CCDS11582.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.765230	0.49574	.	.	ENSG00000141198	ENST00000445275;ENST00000540336;ENST00000348161;ENST00000536554	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.44	4.48	0.54585	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.000000	0.64402	D	0.000006	T	0.71247	0.3317	M	0.92784	3.345	0.80722	D	1	B;P;P;P;D;P	0.89917	0.44;0.869;0.685;0.869;1.0;0.473	B;P;B;P;D;B	0.97110	0.209;0.621;0.347;0.545;1.0;0.347	T	0.78700	-0.2102	10	0.66056	D	0.02	-6.0111	13.5452	0.61699	0.0:0.0:0.8428:0.1572	.	49;119;49;126;126;49	B4DUW5;B4E1N0;B7Z9E2;O75674;Q8N749;B4E1M9	.;.;.;TM1L1_HUMAN;.;.	C	126;49;49;49	ENSP00000408958:W126C;ENSP00000441242:W49C;ENSP00000343901:W49C;ENSP00000443099:W49C	ENSP00000343901:W49C	W	+	3	0	TOM1L1	50346113	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	4.082000	0.57635	1.305000	0.44909	-0.224000	0.12420	TGG	.	.		0.403	TOM1L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439029.2	NM_005486		C	52991114	G	C	52991114	3	2	101	1	0	0	0	0	1	0	0	0	16367	1270	44	4	396	4	TOM1L1	17	52991114	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3923982	52991114	28204096	522	14359										
C17orf71	55181	hgsc.bcm.edu	37	chr17	57288227	57288227	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccttttcctctttcaactcaAtggagccctcaaggtagaac	6	13	4	1	rs548055635		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:57288227A>G	ENST00000543872.2	+	2	1079	c.815A>G	c.(814-816)aAt>aGt	p.N272S	SMG8_ENST00000578922.1_Missense_Mutation_p.N272S|CTD-2510F5.6_ENST00000577660.1_Intron|SMG8_ENST00000580498.1_Intron|SMG8_ENST00000300917.5_Missense_Mutation_p.N272S			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	272					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						TTTCAACTCAATGGAGCCCTC	0.517													A|||	1	0.000199681	0	0	5008	,	,		20521	0		0	False		,,,				2504	0.001				p.N272S		Atlas-SNP	.											.	SMG8	79	.	0			c.A815G						.						72	82	79					17																	57288227		2203	4300	6503	SO:0001583	missense	55181	exon1			AACTCAATGGAGC	AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"chromosome 17 open reading frame 71", "smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.815A>G	chr17.hg19:g.57288227A>G	ENSP00000438748:p.Asn272Ser	29.0	0.0		120.0	16.0	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	hg19	CCDS11615.1	.	.	.	.	.	.	.	.	.	.	A	8.343	0.829101	0.16749	.	.	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.47528	0.84;0.84	5.46	5.46	0.80206	.	0.122499	0.85682	D	0.000000	T	0.40546	0.1121	L	0.51422	1.61	0.52099	D	0.999947	B	0.33135	0.399	B	0.28916	0.096	T	0.23691	-1.0181	10	0.18276	T	0.48	-24.8098	14.8818	0.70540	1.0:0.0:0.0:0.0	.	272	Q8ND04	SMG8_HUMAN	S	272	ENSP00000300917:N272S;ENSP00000438748:N272S	ENSP00000300917:N272S	N	+	2	0	SMG8	54643009	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.517000	0.81783	2.291000	0.77112	0.533000	0.62120	AAT	.	.		0.517	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		G	57288227	A	G	57288227	3	3	101	1	0	0	0	0	1	0	0	0	1880	101	4	2	817	2	C17orf71	17	57288227	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	4297113	57288227	23906983	523	14360										
RPS6KB1	6198	hgsc.bcm.edu	37	chr17	58013587	58013587	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctttaaagctgctgaaaagAaatgctgcttctcgtctggg	10	8	3	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:58013587A>T	ENST00000225577.4	+	11	1011	c.990A>T	c.(988-990)agA>agT	p.R330S	RPS6KB1_ENST00000393021.3_Missense_Mutation_p.R277S|RPS6KB1_ENST00000406116.3_Missense_Mutation_p.R330S|RPS6KB1_ENST00000443572.2_Missense_Mutation_p.R307S	NM_001272042.1|NM_001272044.1|NM_001272060.1|NM_003161.2	NP_001258971.1|NP_001258973.1|NP_001258989.1|NP_003152.1	P23443	KS6B1_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 1	330	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				aging (GO:0007568)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell development (GO:0007281)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue growth (GO:0048633)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of glucose import (GO:0046324)|response to drug (GO:0042493)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to ethanol (GO:0045471)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to leucine (GO:0043201)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to testosterone (GO:0033574)|response to toxic substance (GO:0009636)|response to tumor necrosis factor (GO:0034612)|response to wounding (GO:0009611)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	all_cancers(5;1.63e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.57e-12)|all cancers(12;6.41e-11)			TGCTGAAAAGAAATGCTGCTT	0.408																																					p.R330S		Atlas-SNP	.											.	RPS6KB1	43	.	0			c.A990T						.						110	110	110					17																	58013587		2203	4300	6503	SO:0001583	missense	6198	exon11			GAAAAGAAATGCT	M60724	CCDS11621.1, CCDS62271.1, CCDS62272.1, CCDS62273.1	17q23.1	2011-04-05	2002-08-29		ENSG00000108443	ENSG00000108443			10436	protein-coding gene	gene with protein product		608938	"ribosomal protein S6 kinase, 70kD, polypeptide 1"	STK14A		1922062	Standard	NM_003161		Approved	S6K1, p70(S6K)-alpha, PS6K	uc002ixy.4	P23443	OTTHUMG00000150642	ENST00000225577.4:c.990A>T	chr17.hg19:g.58013587A>T	ENSP00000225577:p.Arg330Ser	107.0	0.0		201.0	21.0	NM_001272043	B2R779|B4DLT4|B4DTG1|E7ESB8|F6UYM1|Q7Z721	Missense_Mutation	SNP	ENST00000225577.4	hg19	CCDS11621.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716500	0.89205	.	.	ENSG00000108443	ENST00000443572;ENST00000406116;ENST00000225577;ENST00000393021	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.55	3.35	0.38373	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.62648	0.2445	L	0.33710	1.025	0.80722	D	1	D;D;D	0.89917	1.0;0.996;0.999	D;D;D	0.78314	0.991;0.978;0.987	T	0.63849	-0.6544	10	0.87932	D	0	.	9.3291	0.38010	0.8551:0.0:0.1449:0.0	.	307;330;330	F6UYM1;Q7Z721;P23443	.;.;KS6B1_HUMAN	S	307;330;330;277	ENSP00000441993:R307S;ENSP00000384335:R330S;ENSP00000225577:R330S;ENSP00000376744:R277S	ENSP00000225577:R330S	R	+	3	2	RPS6KB1	55368369	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.090000	0.57693	0.941000	0.37499	0.524000	0.50904	AGA	.	.		0.408	RPS6KB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319324.1	NM_003161		T	58013587	A	T	58013587	3	4	101	1	0	0	0	0	1	0	0	0	13671	243	9	4	1032	4	RPS6KB1	17	58013587	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	725360	58013587	23181623	524	14361										
DDX42	11325	hgsc.bcm.edu	37	chr17	61890756	61890756	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttttgctggtgacctggtccGgaacttggaaggagccaatc	13	9	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:61890756G>T	ENST00000578681.1	+	16	2445	c.1844G>T	c.(1843-1845)cGg>cTg	p.R615L	DDX42_ENST00000457800.2_Missense_Mutation_p.R615L|DDX42_ENST00000389924.2_Missense_Mutation_p.R615L|DDX42_ENST00000583590.1_Missense_Mutation_p.R615L|DDX42_ENST00000359353.5_Missense_Mutation_p.R496L	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	615	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						GACCTGGTCCGGAACTTGGAA	0.522																																					p.R615L		Atlas-SNP	.											.	DDX42	86	.	0			c.G1844T						.						117	95	102					17																	61890756		2203	4300	6503	SO:0001583	missense	11325	exon15			TGGTCCGGAACTT	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"DEAD-boxes"	18676	protein-coding gene	gene with protein product	"splicing factor 3b, subunit 8"	613369	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.1844G>T	chr17.hg19:g.61890756G>T	ENSP00000464050:p.Arg615Leu	61.0	0.0		181.0	13.0	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	hg19	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.793936	0.90453	.	.	ENSG00000198231	ENST00000389924;ENST00000457800;ENST00000359353	T;T	0.23147	1.92;1.92	5.52	5.52	0.82312	Helicase, C-terminal (1);	0.207947	0.46758	D	0.000280	T	0.42675	0.1213	L	0.35341	1.055	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.74348	0.983;0.94	T	0.27434	-1.0074	10	0.87932	D	0	-11.7694	18.809	0.92050	0.0:0.0:1.0:0.0	.	161;615	B3KV84;Q86XP3	.;DDX42_HUMAN	L	615;615;332	ENSP00000374574:R615L;ENSP00000390121:R615L	ENSP00000352308:R332L	R	+	2	0	DDX42	59244488	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.841000	0.99482	2.764000	0.94973	0.650000	0.86243	CGG	.	.		0.522	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372		T	61890756	G	T	61890756	3	4	101	1	0	0	0	0	1	0	0	0	4364	1116	39	1	1898	1	DDX42	17	61890756	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3877169	61890756	19304454	525	14362										
PSMC5	5705	hgsc.bcm.edu	37	chr17	61908431	61908431	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gggagctgtttgtcatggcaCgggaacatgctccatctatc	12	10	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:61908431C>T	ENST00000310144.6	+	8	1023	c.715C>T	c.(715-717)Cgg>Tgg	p.R239W	PSMC5_ENST00000581882.1_Missense_Mutation_p.R231W|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000580864.1_Missense_Mutation_p.R231W|PSMC5_ENST00000375812.4_Missense_Mutation_p.R231W	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	239	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						TGTCATGGCACGGGAACATGC	0.567																																					p.R239W		Atlas-SNP	.											.	PSMC5	41	.	0			c.C715T						.						84	81	82					17																	61908431		2203	4300	6503	SO:0001583	missense	5705	exon8			ATGGCACGGGAAC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.715C>T	chr17.hg19:g.61908431C>T	ENSP00000310572:p.Arg239Trp	61.0	0.0		140.0	11.0	NM_002805	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	hg19	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.525518	0.64860	.	.	ENSG00000087191	ENST00000310144;ENST00000375812	D;D	0.93859	-3.3;-3.3	5.64	5.64	0.86602	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.97704	0.9247	H	0.94925	3.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	D	0.98241	1.0488	10	0.87932	D	0	.	17.243	0.87019	0.0:1.0:0.0:0.0	.	231;239	A8K3Z3;P62195	.;PRS8_HUMAN	W	239;231	ENSP00000310572:R239W;ENSP00000364970:R231W	ENSP00000310572:R239W	R	+	1	2	PSMC5	59262163	0.089000	0.21612	0.993000	0.49108	0.817000	0.46193	0.559000	0.23485	2.937000	0.99478	0.650000	0.86243	CGG	.	.		0.567	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		T	61908431	C	T	61908431	3	4	101	1	0	0	0	0	1	0	0	0	12702	527	19	1	745	1	PSMC5	17	61908431	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	17675	61908431	19286779	526	14363										
CSH1	1442	hgsc.bcm.edu	37	chr17	61972411	61972411	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acagctgccctccacagagcGgcactgcaccatgcgcagga	11	16	0	1	rs61764004		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:61972411G>T	ENST00000316193.8	-	5	766	c.625C>A	c.(625-627)Cgc>Agc	p.R209S	CSH1_ENST00000453363.3_Missense_Mutation_p.R114S|CSH1_ENST00000329882.8_3'UTR	NM_001317.5	NP_001308.1	P0DML2	CSH1_HUMAN	chorionic somatomammotropin hormone 1 (placental lactogen)	209						extracellular region (GO:0005576)	metal ion binding (GO:0046872)	p.R209C(1)		central_nervous_system(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						TCCACAGAGCGGCACTGCACC	0.607									Russell-Silver syndrome																												p.R209S		Atlas-SNP	.											CSH1,brain,atypical_teratoid-rhabdoid_tumour,0,1	CSH1	18	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.C625A						.						105	94	98					17																	61972411		2198	4299	6497	SO:0001583	missense	1442	exon5	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	CAGAGCGGCACTG	J00118	CCDS11649.1	17q22-q24	2008-07-18				ENSG00000136488			2440	protein-coding gene	gene with protein product	"chorionic somatomammotropin A", "placental lactogen", "choriomammotropin"	150200				6208192	Standard	NM_001317		Approved	hCS-A, CSA, PL, CSMT, FLJ75407	uc002jcs.2	P0DML2		ENST00000316193.8:c.625C>A	chr17.hg19:g.61972411G>T	ENSP00000316416:p.Arg209Ser	77.0	1.0		209.0	9.0	NM_001317	P01243|Q0VDB1|Q14407	Missense_Mutation	SNP	ENST00000316193.8	hg19	CCDS11649.1	.	.	.	.	.	.	.	.	.	.	g	10.94	1.491692	0.26774	.	.	ENSG00000136488	ENST00000316193;ENST00000453363	D;D	0.92911	-3.13;-3.13	2.56	1.57	0.23409	.	.	.	.	.	D	0.95319	0.8481	M	0.86651	2.83	0.43114	D	0.994825	D;D	0.71674	0.989;0.998	D;D	0.71414	0.973;0.955	D	0.93904	0.7191	9	0.72032	D	0.01	.	8.4239	0.32718	0.1261:0.0:0.8739:0.0	rs61764004	114;209	B1A4H2;Q6PF11	.;.	S	209;114	ENSP00000316416:R209S;ENSP00000402517:R114S	ENSP00000316416:R209S	R	-	1	0	CSH1	59326143	1.000000	0.71417	0.996000	0.52242	0.012000	0.07955	6.449000	0.73473	0.405000	0.25532	-0.671000	0.03813	CGC	.	G|0.993;T|0.007		0.607	CSH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416040.1	NM_001317		T	61972411	G	T	61972411	3	4	101	1	0	0	0	0	1	0	0	0	3942	1116	39	1	32	1	CSH1	17	61972411	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	63980	61972411	19222799	527	14364										
KIF19	124602	hgsc.bcm.edu	37	chr17	72344027	72344027	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acgccggccgggccaagaacAttaagactagggtgagggcc	15	11	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:72344027A>G	ENST00000389916.4	+	9	1174	c.1036A>G	c.(1036-1038)Att>Gtt	p.I346V		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	346	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GGCCAAGAACATTAAGACTAG	0.622																																					p.I346V		Atlas-SNP	.											.	KIF19	102	.	0			c.A1036G						.						41	35	37					17																	72344027		2193	4287	6480	SO:0001583	missense	124602	exon9			AAGAACATTAAGA	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.1036A>G	chr17.hg19:g.72344027A>G	ENSP00000374566:p.Ile346Val	8.0	0.0		67.0	10.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	A	19.62	3.860939	0.71834	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.76968	-1.06;-1.06	5.68	5.68	0.88126	Kinesin, motor domain (3);	.	.	.	.	D	0.87561	0.6208	M	0.76170	2.325	0.58432	D	0.999998	D;D;D;D	0.76494	0.999;0.999;0.994;0.994	D;D;D;D	0.85130	0.99;0.997;0.986;0.986	D	0.88969	0.3399	9	0.87932	D	0	.	14.9658	0.71193	1.0:0.0:0.0:0.0	.	346;304;304;346	Q2TAC6;F8VW50;Q2TAC6-3;Q2TAC6-2	KIF19_HUMAN;.;.;.	V	304;346	ENSP00000449134:I304V;ENSP00000374566:I346V	ENSP00000374566:I346V	I	+	1	0	KIF19	69855622	1.000000	0.71417	1.000000	0.80357	0.434000	0.31775	8.934000	0.92915	2.184000	0.69523	0.454000	0.30748	ATT	.	.		0.622	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		G	72344027	A	G	72344027	3	3	101	1	0	0	0	0	1	0	0	0	8291	217	8	2	1070	2	KIF19	17	72344027	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	10371616	72344027	8851183	528	14365										
CDR2L	30850	hgsc.bcm.edu	37	chr17	72998268	72998268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgctccgggagaagcgggaaCgcaggcgtaccatccacacc	13	14	0	1	rs529209429		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:72998268C>T	ENST00000337231.5	+	4	863	c.451C>T	c.(451-453)Cgc>Tgc	p.R151C		NM_014603.2	NP_055418.2	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like	151												all_lung(278;0.226)					GAAGCGGGAACGCAGGCGTAC	0.642													C|||	1	0.000199681	0	0	5008	,	,		17825	0		0.001	False		,,,				2504	0				p.R151C		Atlas-SNP	.											HUMPPA,NS,carcinoma,0,1	.	.	.	0			c.C451T						.						67	49	56					17																	72998268		2203	4299	6502	SO:0001583	missense	30850	exon4			CGGGAACGCAGGC		CCDS11710.2	17q25.1	2006-03-28			ENSG00000109089	ENSG00000109089			29999	protein-coding gene	gene with protein product	"paraneoplastic antigen"						Standard	NM_014603		Approved	HUMPPA	uc002jml.4	Q86X02	OTTHUMG00000150435	ENST00000337231.5:c.451C>T	chr17.hg19:g.72998268C>T	ENSP00000336587:p.Arg151Cys	18.0	0.0		77.0	7.0	NM_014603	B4DFA7|Q15175	Missense_Mutation	SNP	ENST00000337231.5	hg19	CCDS11710.2	.	.	.	.	.	.	.	.	.	.	C	23.7	4.448746	0.84101	.	.	ENSG00000109089	ENST00000337231	T	0.50813	0.73	5.22	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.67970	0.2950	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71938	-0.4441	10	0.72032	D	0.01	-24.4178	13.7862	0.63110	0.2953:0.7047:0.0:0.0	.	151	Q86X02	CDR2L_HUMAN	C	151	ENSP00000336587:R151C	ENSP00000336587:R151C	R	+	1	0	CDR2L	70509863	0.949000	0.32298	0.984000	0.44739	0.996000	0.88848	1.774000	0.38573	2.609000	0.88269	0.563000	0.77884	CGC	.	.		0.642	CDR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318080.1	NM_014603		T	72998268	C	T	72998268	3	4	101	1	0	0	0	0	1	0	0	0	3175	536	19	1	465	1	CDR2L	17	72998268	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	654241	72998268	8196942	529	14366										
WBP2	23558	hgsc.bcm.edu	37	chr17	73851333	73851333	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttttcacctctcggtgttatTgacgatcactccgccgccct	7	15	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:73851333T>C	ENST00000591399.1	-	2	470	c.46A>G	c.(46-48)Aat>Gat	p.N16D	WBP2_ENST00000585462.1_5'UTR|WBP2_ENST00000433525.2_Missense_Mutation_p.N16D|WBP2_ENST00000590450.1_5'UTR|WBP2_ENST00000590221.1_Missense_Mutation_p.N16D|WBP2_ENST00000254806.3_Missense_Mutation_p.N16D|WBP2_ENST00000344296.4_5'UTR			Q969T9	WBP2_HUMAN	WW domain binding protein 2	16	GRAM.				cellular response to estrogen stimulus (GO:0071391)|establishment of protein localization (GO:0045184)|positive regulation of gene expression, epigenetic (GO:0045815)|positive regulation of histone H3-K14 acetylation (GO:0071442)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nuclear chromatin (GO:0000790)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	7			all cancers(21;2.61e-06)|Epithelial(20;2.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCGGTGTTATTGACGATCACT	0.577																																					p.N16D		Atlas-SNP	.											.	WBP2	17	.	0			c.A46G						.						170	171	170					17																	73851333		2203	4300	6503	SO:0001583	missense	23558	exon1			TGTTATTGACGAT	U79458	CCDS11731.1	17q25	2008-02-01				ENSG00000132471			12738	protein-coding gene	gene with protein product		606962				7644498	Standard	NM_012478		Approved	WBP-2	uc002jps.3	Q969T9		ENST00000591399.1:c.46A>G	chr17.hg19:g.73851333T>C	ENSP00000467579:p.Asn16Asp	98.0	0.0		222.0	51.0	NM_012478	O95638	Missense_Mutation	SNP	ENST00000591399.1	hg19	CCDS11731.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.847164	0.91277	.	.	ENSG00000132471	ENST00000254806;ENST00000433525;ENST00000431190;ENST00000416574	D;D	0.88354	-2.37;-2.37	4.21	4.21	0.49690	GRAM (1);	0.117941	0.64402	D	0.000001	D	0.92364	0.7577	L	0.61036	1.89	0.80722	D	1	D;D;D;D	0.76494	0.988;0.999;0.998;0.998	P;D;D;D	0.71414	0.825;0.973;0.963;0.963	D	0.91452	0.5182	10	0.35671	T	0.21	-19.4032	13.7292	0.62776	0.0:0.0:0.0:1.0	.	16;16;16;16	B4DV07;B4DFG2;Q7Z511;Q969T9	.;.;.;WBP2_HUMAN	D	16	ENSP00000254806:N16D;ENSP00000415251:N16D	ENSP00000254806:N16D	N	-	1	0	WBP2	71362928	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.631000	0.54280	1.891000	0.54761	0.460000	0.39030	AAT	.	.		0.577	WBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448862.1	NM_012478		C	73851333	T	C	73851333	3	2	101	1	0	0	0	0	1	0	0	0	17274	1812	63	2	771	2	WBP2	17	73851333	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	853065	73851333	7343877	530	14367										
FBF1	85302	hgsc.bcm.edu	37	chr17	73916170	73916170	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagctcatgctgggcccgttCtagctccagcttccgcacct	9	17	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:73916170C>G	ENST00000586717.1	-	18	2080	c.1807G>C	c.(1807-1809)Gaa>Caa	p.E603Q	FBF1_ENST00000319129.5_Missense_Mutation_p.E602Q|FBF1_ENST00000389570.4_Missense_Mutation_p.E603Q			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	603					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TGGGCCCGTTCTAGCTCCAGC	0.662																																					p.E602Q		Atlas-SNP	.											.	FBF1	48	.	0			c.G1804C						.						17	20	19					17																	73916170		2025	4177	6202	SO:0001583	missense	85302	exon18			CCCGTTCTAGCTC	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.1807G>C	chr17.hg19:g.73916170C>G	ENSP00000465132:p.Glu603Gln	45.0	0.0		107.0	45.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	C	27.4	4.828670	0.90955	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.32023	1.47;1.47	5.15	5.15	0.70609	.	.	.	.	.	T	0.57519	0.2059	M	0.74258	2.255	0.52501	D	0.999956	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.988;0.999;0.998	T	0.58819	-0.7569	9	0.48119	T	0.1	-30.2077	18.2267	0.89920	0.0:1.0:0.0:0.0	.	617;603;602	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	Q	603;603;602;616	ENSP00000374221:E603Q;ENSP00000324292:E602Q	ENSP00000324292:E602Q	E	-	1	0	FBF1	71427765	1.000000	0.71417	0.980000	0.43619	0.952000	0.60782	6.645000	0.74343	2.409000	0.81822	0.655000	0.94253	GAA	.	.		0.662	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		G	73916170	C	G	73916170	3	3	101	1	0	0	0	0	1	0	0	0	5703	922	32	4	1645	4	FBF1	17	73916170	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	64837	73916170	7279040	531	14368										
SPHK1	8877	hgsc.bcm.edu	37	chr17	74383108	74383109	+	Frame_Shift_Del	DEL	GT	GT	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cactctgggcaccttcctgcGtctggcagccctgcgcacct					rs138977514|rs549579958|rs17850292	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:74383108_74383109delGT	ENST00000545180.1	+	8	1405_1406	c.596_597delGT	c.(595-597)cgtfs	p.R199fs	SPHK1_ENST00000392496.3_Frame_Shift_Del_p.R199fs|SPHK1_ENST00000592299.1_Frame_Shift_Del_p.R199fs|SPHK1_ENST00000590959.1_Frame_Shift_Del_p.R213fs|SPHK1_ENST00000323374.4_Frame_Shift_Del_p.R285fs			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	199					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	ACCTTCCTGCGTCTGGCAGCCC	0.639																																					p.285_285del	GBM(90;966 1307 27369 33775 44498)	Pindel	.											.	SPHK1	24	.	0			c.853_854del						.																																			SO:0001589	frameshift_variant	8877	exon6			.	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.596_597delGT	chr17.hg19:g.74383108_74383109delGT	ENSP00000440970:p.Arg199fs	44.0	0.0		80.0	20.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Frame_Shift_Del	DEL	ENST00000545180.1	hg19	CCDS45785.1																																																																																			.	.		0.639	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		-	74383109	GT	-	74383108	7	5	101	1	0	1	0	1	0	0	0	0	15061	1145	40	0	918	0	SPHK1	17	74383108	Frame_Shift_Del	DEL	GT	TCGA-DD-A1EE-01A-11D-A12Z-10	466938	74383108	6812102	532	14369										
SPHK1	8877	hgsc.bcm.edu	37	chr17	74383503	74383503	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tggtcgccttccgcttggagCccaaggatgggaaaggtgtg	16	9	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:74383503C>G	ENST00000545180.1	+	8	1800	c.991C>G	c.(991-993)Ccc>Gcc	p.P331A	SPHK1_ENST00000392496.3_Missense_Mutation_p.P331A|SPHK1_ENST00000592299.1_Missense_Mutation_p.P331A|SPHK1_ENST00000590959.1_Missense_Mutation_p.P345A|SPHK1_ENST00000323374.4_Missense_Mutation_p.P417A			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	331					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	CCGCTTGGAGCCCAAGGATGG	0.577																																					p.P417A	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.C1249G						.						78	78	78					17																	74383503		2202	4300	6502	SO:0001583	missense	8877	exon6			TTGGAGCCCAAGG	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.991C>G	chr17.hg19:g.74383503C>G	ENSP00000440970:p.Pro331Ala	45.0	0.0		122.0	15.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	hg19	CCDS45785.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.814537	0.50527	.	.	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.13538	2.58;2.58;2.58	5.08	4.11	0.48088	.	2.948360	0.02167	N	0.059323	T	0.47507	0.1449	M	0.85462	2.755	0.52501	D	0.999959	D;D;D	0.67145	0.993;0.987;0.996	P;P;D	0.70716	0.899;0.844;0.97	T	0.00468	-1.1721	10	0.72032	D	0.01	-12.5451	13.3258	0.60459	0.0:0.9235:0.0:0.0765	.	417;345;331	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	A	331;417;331;330	ENSP00000440970:P331A;ENSP00000313681:P417A;ENSP00000376285:P331A	ENSP00000313681:P417A	P	+	1	0	SPHK1	71895098	1.000000	0.71417	0.865000	0.33974	0.086000	0.17979	5.617000	0.67716	1.135000	0.42183	0.456000	0.33151	CCC	.	.		0.577	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		G	74383503	C	G	74383503	3	3	101	1	0	0	0	0	1	0	0	0	15061	739	26	4	1313	4	SPHK1	17	74383503	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	395	74383503	6811707	533	14370										
ENGASE	64772	hgsc.bcm.edu	37	chr17	77077980	77077980	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggtccttgttgcttctcagGgtcttctttgattcctgcga	10	10	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:77077980G>T	ENST00000579016.1	+	7	873	c.873G>T	c.(871-873)agG>agT	p.R291S	ENGASE_ENST00000539857.2_Splice_Site_p.R105S	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	291	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.					cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						TGCTTCTCAGGGTCTTCTTTG	0.607																																					p.R291S		Atlas-SNP	.											.	ENGASE	55	.	0			c.G873T						.						95	105	102					17																	77077980		1951	4141	6092	SO:0001630	splice_region_variant	64772	exon7			TCTCAGGGTCTTC	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.873-1G>T	chr17.hg19:g.77077980G>T		51.0	0.0		125.0	11.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	hg19	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.634643	0.47049	.	.	ENSG00000167280	ENST00000311595;ENST00000545583	.	.	.	4.34	1.27	0.21489	Glycoside hydrolase, family 85 (1);	0.000000	0.85682	D	0.000000	T	0.57695	0.2071	M	0.73217	2.22	0.49687	D	0.999815	P;P;B	0.49185	0.92;0.722;0.067	P;B;B	0.47603	0.551;0.338;0.064	T	0.55095	-0.8194	8	.	.	.	.	8.401	0.32586	0.3253:0.0:0.6747:0.0	.	105;291;291	B4DVK0;Q8NFI3;Q8NFI3-3	.;ENASE_HUMAN;.	S	291	.	.	R	+	3	2	ENGASE	74589575	1.000000	0.71417	0.991000	0.47740	0.475000	0.33008	1.833000	0.39161	0.140000	0.18849	0.313000	0.20887	AGG	.	.		0.607	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	Missense_Mutation	T	77077980	G	T	77077980	5	4	101	1	0	0	0	0	0	0	1	0	5120	1246	43	3	899	3	ENGASE	17	77077980	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2694477	77077980	4117230	534	14371										
GAA	2548	hgsc.bcm.edu	37	chr17	78091993	78091993	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cgtgtccttccctttccaggGccctggcctcacaaccacag	8	18	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:78091993G>T	ENST00000302262.3	+	18	2702	c.2483G>T	c.(2482-2484)gGc>gTc	p.G828V	GAA_ENST00000390015.3_Splice_Site_p.G828V	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	828					cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	CCTTTCCAGGGCCCTGGCCTC	0.667																																					p.G828V		Atlas-SNP	.											.	GAA	66	.	0			c.G2483T						.						44	46	45					17																	78091993		2203	4300	6503	SO:0001630	splice_region_variant	2548	exon19			TCCAGGGCCCTGG		CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"Pompe disease", "glycogen storage disease type II"	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.2482-1G>T	chr17.hg19:g.78091993G>T		34.0	0.0		107.0	19.0	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Missense_Mutation	SNP	ENST00000302262.3	hg19	CCDS32760.1	.	.	.	.	.	.	.	.	.	.	G	9.396	1.076732	0.20227	.	.	ENSG00000171298	ENST00000302262;ENST00000390015	D;D	0.89810	-2.57;-2.57	5.51	1.96	0.26148	.	0.464777	0.24020	N	0.042294	T	0.78635	0.4314	L	0.37850	1.14	0.58432	D	0.999996	B	0.09022	0.002	B	0.09377	0.004	T	0.69888	-0.5023	10	0.34782	T	0.22	-33.8352	2.0092	0.03484	0.1276:0.3792:0.2986:0.1945	.	828	P10253	LYAG_HUMAN	V	828	ENSP00000305692:G828V;ENSP00000374665:G828V	ENSP00000305692:G828V	G	+	2	0	GAA	75706588	0.950000	0.32346	0.985000	0.45067	0.615000	0.37417	1.871000	0.39539	1.267000	0.44247	0.655000	0.94253	GGC	.	.		0.667	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		Missense_Mutation	T	78091993	G	T	78091993	5	4	101	1	0	0	0	0	0	0	1	0	6155	1217	42	3	2549	3	GAA	17	78091993	Splice_Site	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1014013	78091993	3103217	535	14372										
CCDC57	284001	hgsc.bcm.edu	37	chr17	80115731	80115731	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttccccagctcagccacctGcttccgcagctccaaaacct	5	20	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr17:80115731G>A	ENST00000389641.4	-	14	2170	c.2134C>T	c.(2134-2136)Cag>Tag	p.Q712*	RP11-1376P16.1_ENST00000582774.1_RNA|CCDC57_ENST00000392347.1_Nonsense_Mutation_p.Q712*|CCDC57_ENST00000392343.3_Nonsense_Mutation_p.Q712*|CCDC57_ENST00000327026.3_5'UTR			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	712										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			TCAGCCACCTGCTTCCGCAGC	0.682																																					p.Q712X		Atlas-SNP	.											.	CCDC57	102	.	0			c.C2134T						.						25	29	27					17																	80115731		1989	4159	6148	SO:0001587	stop_gained	284001	exon14			CCACCTGCTTCCG	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.2134C>T	chr17.hg19:g.80115731G>A	ENSP00000374292:p.Gln712*	21.0	0.0		80.0	6.0	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Nonsense_Mutation	SNP	ENST00000389641.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.540187|5.540187	0.96474|0.96474	.|.	.|.	ENSG00000176155|ENSG00000176155	ENST00000419322|ENST00000389641;ENST00000392347;ENST00000327026;ENST00000392343	.|.	.|.	.|.	3.19|3.19	2.15|2.15	0.27550|0.27550	.|.	.|0.000000	.|0.38959	.|N	.|0.001517	T|.	0.60932|.	0.2307|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.58918|.	-0.7551|.	4|.	.|0.49607	.|T	.|0.09	-22.0135|-22.0135	8.1007|8.1007	0.30854|0.30854	0.0:0.2506:0.7494:0.0|0.0:0.2506:0.7494:0.0	.|.	.|.	.|.	.|.	V|X	57|712;712;220;712	.|.	.|ENSP00000315967:Q220X	A|Q	-|-	2|1	0|0	CCDC57|CCDC57	77709020|77709020	0.988000|0.988000	0.35896|0.35896	0.645000|0.645000	0.29479|0.29479	0.176000|0.176000	0.22953|0.22953	2.236000|2.236000	0.43052|0.43052	0.612000|0.612000	0.30071|0.30071	0.462000|0.462000	0.41574|0.41574	GCA|CAG	.	.		0.682	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		A	80115731	G	A	80115731	4	1	101	1	0	0	0	0	0	1	0	0	2829	1328	46	3	629	3	CCDC57	17	80115731	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2023738	80115731	1079479	536	14373										
LPIN2	9663	hgsc.bcm.edu	37	chr18	2925247	2925247	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggtctgaggagaggcggagaGacttcttatatgaagttgtg	16	4	2	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr18:2925247G>C	ENST00000261596.4	-	14	2151	c.1913C>G	c.(1912-1914)tCt>tGt	p.S638C		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	638	C-LIP.				cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		GAGGCGGAGAGACTTCTTATA	0.493																																					p.S638C		Atlas-SNP	.											.	LPIN2	75	.	0			c.C1913G						.						98	95	96					18																	2925247		2203	4300	6503	SO:0001583	missense	9663	exon14			CGGAGAGACTTCT	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.1913C>G	chr18.hg19:g.2925247G>C	ENSP00000261596:p.Ser638Cys	89.0	0.0		167.0	9.0	NM_014646	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	hg19	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.998856	0.54147	.	.	ENSG00000101577	ENST00000261596	D	0.82433	-1.61	4.41	4.41	0.53225	.	0.117372	0.64402	D	0.000012	D	0.91690	0.7373	M	0.88775	2.98	0.80722	D	1	D	0.67145	0.996	P	0.62813	0.907	D	0.93294	0.6671	10	0.62326	D	0.03	-17.4867	17.9017	0.88906	0.0:0.0:1.0:0.0	.	638	Q92539	LPIN2_HUMAN	C	638	ENSP00000261596:S638C	ENSP00000261596:S638C	S	-	2	0	LPIN2	2915247	1.000000	0.71417	0.997000	0.53966	0.084000	0.17831	9.214000	0.95140	2.366000	0.80165	0.563000	0.77884	TCT	.	.		0.493	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		C	2925247	G	C	2925247	3	2	101	1	0	0	0	0	1	0	0	0	8928	942	33	4	805	4	LPIN2	18	2925247	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10		2925247	75152001	537	14374										
RAB31	11031	hgsc.bcm.edu	37	chr18	9859227	9859227	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcctcctttttgttgcaggcCgccagatcccacccttggac	9	16	0	1	rs147665641	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr18:9859227C>A	ENST00000578921.1	+	7	734	c.493C>A	c.(493-495)Cgc>Agc	p.R165S	RAB31_ENST00000577284.1_3'UTR	NM_006868.3	NP_006859.2	Q13636	RAB31_HUMAN	RAB31, member RAS oncogene family	164					cellular response to insulin stimulus (GO:0032869)|Golgi to plasma membrane protein transport (GO:0043001)|GTP catabolic process (GO:0006184)|phagosome maturation (GO:0090382)|receptor internalization (GO:0031623)|regulated secretory pathway (GO:0045055)|small GTPase mediated signal transduction (GO:0007264)	early endosome (GO:0005769)|phagocytic vesicle (GO:0045335)|trans-Golgi network membrane (GO:0032588)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(2)|large_intestine(2)|lung(3)|skin(1)	10						TGTTGCAGGCCGCCAGATCCC	0.527																																					p.R165S		Atlas-SNP	.											RAB31,colon,carcinoma,0,1	RAB31	23	.	0			c.C493A						.						43	48	46					18																	9859227		1948	4140	6088	SO:0001583	missense	11031	exon7			GCAGGCCGCCAGA	U59877	CCDS45826.1	18p11.22	2014-03-18			ENSG00000168461	ENSG00000168461		"RAB, member RAS oncogene"	9771	protein-coding gene	gene with protein product		605694				8863739	Standard	NM_006868		Approved	Rab22B	uc002kog.2	Q13636	OTTHUMG00000178513	ENST00000578921.1:c.493C>A	chr18.hg19:g.9859227C>A	ENSP00000461945:p.Arg165Ser	54.0	0.0		141.0	24.0	NM_006868	B2RBT7|Q15770|Q9HC00	Missense_Mutation	SNP	ENST00000578921.1	hg19	CCDS45826.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.308590	0.60305	.	.	ENSG00000168461	ENST00000306096;ENST00000435762	.	.	.	5.73	5.73	0.89815	.	0.302822	0.35525	N	0.003154	T	0.51601	0.1684	L	0.28400	0.85	0.54753	D	0.999986	B	0.13145	0.007	B	0.23419	0.046	T	0.40942	-0.9536	8	.	.	.	1.9938	15.769	0.78149	0.0:1.0:0.0:0.0	.	164	Q13636	RAB31_HUMAN	S	165;156	.	.	R	+	1	0	RAB31	9849227	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	4.220000	0.58567	2.868000	0.98415	0.557000	0.71058	CGC	.	C|0.999;T|0.001		0.527	RAB31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442280.3			A	9859227	C	A	9859227	3	1	101	1	0	0	0	0	1	0	0	0	12935	652	23	1	519	1	RAB31	18	9859227	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	6933980	9859227	68218021	538	14375										
CEP76	79959	hgsc.bcm.edu	37	chr18	12691398	12691398	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtcgtgagttgtgtgagggtCgaatttgcaaatattctctc	12	6	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr18:12691398C>A	ENST00000262127.2	-	7	1118	c.893G>T	c.(892-894)cGa>cTa	p.R298L	PSMG2_ENST00000585331.2_Intron|CEP76_ENST00000423709.2_Missense_Mutation_p.R223L	NM_024899.2	NP_079175.2	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	298					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GTGTGAGGGTCGAATTTGCAA	0.348																																					p.R298L		Atlas-SNP	.											.	CEP76	45	.	0			c.G893T						.						101	102	102					18																	12691398		2203	4300	6503	SO:0001583	missense	79959	exon7			GAGGGTCGAATTT	BC026307	CCDS11861.1, CCDS62390.1	18p11.21	2014-02-20	2005-12-01	2005-12-01	ENSG00000101624	ENSG00000101624			25727	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 9"	C18orf9		14654843	Standard	NM_024899		Approved	HsT1705, FLJ12542	uc002kri.4	Q8TAP6	OTTHUMG00000131701	ENST00000262127.2:c.893G>T	chr18.hg19:g.12691398C>A	ENSP00000262127:p.Arg298Leu	65.0	0.0		127.0	10.0	NM_024899	B0YJB2|B4DXG5|B4DZW1|Q658N5|Q9H9U7	Missense_Mutation	SNP	ENST00000262127.2	hg19	CCDS11861.1	.	.	.	.	.	.	.	.	.	.	C	34	5.373872	0.95923	.	.	ENSG00000101624	ENST00000262127;ENST00000423709	D;T	0.81499	-1.5;-1.45	5.67	5.67	0.87782	.	0.056826	0.64402	D	0.000001	D	0.90253	0.6952	M	0.80183	2.485	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.987	D	0.87685	0.2550	10	0.31617	T	0.26	-9.0197	20.1358	0.98028	0.0:1.0:0.0:0.0	.	223;298;120	Q8TAP6-2;Q8TAP6;Q8TAP6-3	.;CEP76_HUMAN;.	L	298;223	ENSP00000262127:R298L;ENSP00000403074:R223L	ENSP00000262127:R298L	R	-	2	0	CEP76	12681398	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.776000	0.85560	2.833000	0.97629	0.585000	0.79938	CGA	.	.		0.348	CEP76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254611.1	NM_024899		A	12691398	C	A	12691398	3	1	101	1	0	0	0	0	1	0	0	0	3263	884	31	1	1110	1	CEP76	18	12691398	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2832171	12691398	65385850	539	14376										
CEP192	55125	hgsc.bcm.edu	37	chr18	13056654	13056654	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtgccgtctgttggtacaaaCtgtggaattgaaccatggga	13	7	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr18:13056654C>T	ENST00000325971.8	+	17	3870	c.2277C>T	c.(2275-2277)aaC>aaT	p.N759N	CEP192_ENST00000430049.2_Silent_p.N880N|CEP192_ENST00000506447.1_Silent_p.N1355N			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	759					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TTGGTACAAACTGTGGAATTG	0.398																																					p.N1355N		Atlas-SNP	.											.	CEP192	340	.	0			c.C4065T						.						144	149	147					18																	13056654		2203	4300	6503	SO:0001819	synonymous_variant	55125	exon19			TACAAACTGTGGA	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.2277C>T	chr18.hg19:g.13056654C>T		69.0	0.0		111.0	46.0	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	hg19																																																																																				.	.		0.398	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		T	13056654	C	T	13056654	2	4	101	1	0	0	0	0	0	0	0	1	3253	564	20	3		3	CEP192	18	13056654	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	365256	13056654	65020594	540	14377										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31314285	31314285	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctttttaggagagtttaccCcagaaatgcagttgcggata	10	7	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr18:31314285C>T	ENST00000269197.5	+	10	988	c.988C>T	c.(988-990)Cca>Tca	p.P330S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	330					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AGAGTTTACCCCAGAAATGCA	0.308																																					p.P330S		Atlas-SNP	.											.	ASXL3	405	.	0			c.C988T						.						51	50	50					18																	31314285		1798	4059	5857	SO:0001583	missense	80816	exon10			TTTACCCCAGAAA	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.988C>T	chr18.hg19:g.31314285C>T	ENSP00000269197:p.Pro330Ser	111.0	0.0		198.0	8.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566279	0.86439	.	.	ENSG00000141431	ENST00000269197	T	0.25250	1.81	5.71	5.71	0.89125	.	0.227351	0.38492	N	0.001663	T	0.50735	0.1633	M	0.61703	1.905	0.54753	D	0.999986	D	0.89917	1.0	D	0.81914	0.995	T	0.34428	-0.9829	10	0.41790	T	0.15	.	19.8549	0.96755	0.0:1.0:0.0:0.0	.	330	Q9C0F0	ASXL3_HUMAN	S	330	ENSP00000269197:P330S	ENSP00000269197:P330S	P	+	1	0	ASXL3	29568283	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.365000	0.79537	2.699000	0.92147	0.460000	0.39030	CCA	.	.		0.308	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			T	31314285	C	T	31314285	3	4	101	1	0	0	0	0	1	0	0	0	1068	623	22	3	1026	3	ASXL3	18	31314285	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	18257631	31314285	46762963	541	14378										
SYT4	6860	hgsc.bcm.edu	37	chr18	40854035	40854035	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaaagagcttcggggttgcaTtctccagatcagaaggactg	12	8	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr18:40854035T>A	ENST00000255224.3	-	2	727	c.359A>T	c.(358-360)aAt>aTt	p.N120I	SYT4_ENST00000586678.1_Intron|SYT4_ENST00000590752.1_Missense_Mutation_p.N102I	NM_020783.3	NP_065834.1	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	120					exocytosis (GO:0006887)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of vesicle fusion (GO:0031339)|neurotransmitter secretion (GO:0007269)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44						CGGGGTTGCATTCTCCAGATC	0.433																																					p.N120I	NSCLC(85;81 1419 2855 22820 35912)	Atlas-SNP	.											.	SYT4	162	.	0			c.A359T						.						118	116	117					18																	40854035		2203	4298	6501	SO:0001583	missense	6860	exon2			GTTGCATTCTCCA	BC036538	CCDS11922.1	18q12.3	2013-01-21			ENSG00000132872	ENSG00000132872		"Synaptotagmins"	11512	protein-coding gene	gene with protein product		600103				8058779	Standard	NM_020783		Approved	KIAA1342, HsT1192	uc002law.3	Q9H2B2	OTTHUMG00000132610	ENST00000255224.3:c.359A>T	chr18.hg19:g.40854035T>A	ENSP00000255224:p.Asn120Ile	85.0	0.0		188.0	8.0	NM_020783	B4DEU3|Q9P2K4	Missense_Mutation	SNP	ENST00000255224.3	hg19	CCDS11922.1	.	.	.	.	.	.	.	.	.	.	T	7.314	0.615635	0.14129	.	.	ENSG00000132872	ENST00000255224	T	0.37235	1.21	5.87	2.2	0.27929	.	0.335126	0.36002	N	0.002846	T	0.27489	0.0675	L	0.44542	1.39	0.33493	D	0.589003	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.25222	-1.0138	10	0.28530	T	0.3	.	9.812	0.40828	0.0:0.1939:0.0:0.8061	.	102;120	B4DEU3;Q9H2B2	.;SYT4_HUMAN	I	120	ENSP00000255224:N120I	ENSP00000255224:N120I	N	-	2	0	SYT4	39108033	1.000000	0.71417	0.949000	0.38748	0.606000	0.37113	3.844000	0.55873	0.206000	0.20587	0.533000	0.62120	AAT	.	.		0.433	SYT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255851.2	NM_020783		A	40854035	T	A	40854035	3	1	101	1	0	0	0	0	1	0	0	0	15491	1493	52	4	930	4	SYT4	18	40854035	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	9539750	40854035	37223213	542	14379										
RAB27B	5874	hgsc.bcm.edu	37	chr18	52556472	52556472	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tagcataccatattttgaaaCaagtgcagcaactggacaga	8	8	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr18:52556472C>A	ENST00000262094.5	+	6	1006	c.485C>A	c.(484-486)aCa>aAa	p.T162K	RP11-839G9.1_ENST00000588466.1_RNA	NM_004163.4	NP_004154.2	O00194	RB27B_HUMAN	RAB27B, member RAS oncogene family	162					multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|multivesicular body membrane (GO:0032585)|trans-Golgi network transport vesicle (GO:0030140)|zymogen granule membrane (GO:0042589)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein domain specific binding (GO:0019904)			large_intestine(3)|lung(3)|skin(1)	7				Colorectal(16;0.0273)|READ - Rectum adenocarcinoma(59;0.219)		TATTTTGAAACAAGTGCAGCA	0.398																																					p.T162K		Atlas-SNP	.											.	RAB27B	24	.	0			c.C485A						.						94	87	90					18																	52556472		2203	4300	6503	SO:0001583	missense	5874	exon6			TTGAAACAAGTGC	U57093	CCDS11958.1	18q21.2	2006-12-18			ENSG00000041353	ENSG00000041353		"RAB, member RAS oncogene"	9767	protein-coding gene	gene with protein product		603869				9066979	Standard	NM_004163		Approved		uc002lfr.3	O00194	OTTHUMG00000132710	ENST00000262094.5:c.485C>A	chr18.hg19:g.52556472C>A	ENSP00000262094:p.Thr162Lys	40.0	0.0		108.0	7.0	NM_004163	B2RAB0|Q9BZB6	Missense_Mutation	SNP	ENST00000262094.5	hg19	CCDS11958.1	.	.	.	.	.	.	.	.	.	.	C	31	5.072762	0.93950	.	.	ENSG00000041353	ENST00000262094	T	0.77750	-1.12	5.87	5.87	0.94306	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.92841	0.7723	H	0.97491	4.015	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.94500	0.7709	10	0.87932	D	0	-5.786	19.3531	0.94398	0.0:1.0:0.0:0.0	.	162	O00194	RB27B_HUMAN	K	162	ENSP00000262094:T162K	ENSP00000262094:T162K	T	+	2	0	RAB27B	50707470	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.509000	0.81698	2.941000	0.99782	0.655000	0.94253	ACA	.	.		0.398	RAB27B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256008.3	NM_004163		A	52556472	C	A	52556472	3	1	101	1	0	0	0	0	1	0	0	0	12930	478	17	3	503	3	RAB27B	18	52556472	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	11702437	52556472	25520776	543	14380										
VPS4B	9525	hgsc.bcm.edu	37	chr18	61067824	61067824	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaaacaagatcagaggaagaTattgaaaaaaatgttgagtt	10	2	1	5			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr18:61067824T>C	ENST00000238497.5	-	6	800	c.597A>G	c.(595-597)atA>atG	p.I199M	VPS4B_ENST00000591383.1_5'UTR	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	199					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						CAGAGGAAGATATTGAAAAAA	0.373																																					p.I199M		Atlas-SNP	.											.	VPS4B	33	.	0			c.A597G						.						115	115	115					18																	61067824		2203	4300	6503	SO:0001583	missense	9525	exon6			GGAAGATATTGAA	AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"ATPases / AAA-type"	10895	protein-coding gene	gene with protein product		609983	"suppressor of K+ transport defect 1", "vacuolar protein sorting 4B (yeast)"	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.597A>G	chr18.hg19:g.61067824T>C	ENSP00000238497:p.Ile199Met	87.0	0.0		238.0	16.0	NM_004869	Q69HW4|Q9GZS7	Missense_Mutation	SNP	ENST00000238497.5	hg19	CCDS11983.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529046	0.64860	.	.	ENSG00000119541	ENST00000238497	D	0.95853	-3.83	6.11	4.95	0.65309	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.173761	0.64402	D	0.000009	D	0.96383	0.8820	M	0.64567	1.98	0.80722	D	1	B;B;P	0.34837	0.295;0.295;0.472	P;P;P	0.51385	0.668;0.668;0.668	D	0.95892	0.8908	10	0.87932	D	0	-15.9957	12.4617	0.55734	0.0:0.0653:0.0:0.9347	.	199;199;199	A8K5D8;A8K4G7;O75351	.;.;VPS4B_HUMAN	M	199	ENSP00000238497:I199M	ENSP00000238497:I199M	I	-	3	3	VPS4B	59218804	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.712000	0.37940	1.119000	0.41883	0.533000	0.62120	ATA	.	.		0.373	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869		C	61067824	T	C	61067824	3	2	101	1	0	0	0	0	1	0	0	0	17228	1396	49	2	761	2	VPS4B	18	61067824	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	8511352	61067824	17009424	544	14381										
CDH7	1005	hgsc.bcm.edu	37	chr18	63430104	63430104	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gttgggcaaagtggagttctGccattttctgcagctaatag	12	7	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr18:63430104G>T	ENST00000397968.2	+	2	452	c.26G>T	c.(25-27)tGc>tTc	p.C9F	CDH7_ENST00000323011.3_Missense_Mutation_p.C9F|CDH7_ENST00000536984.2_Missense_Mutation_p.C9F	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	9					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				GTGGAGTTCTGCCATTTTCTG	0.408																																					p.C9F		Atlas-SNP	.											.	CDH7	362	.	0			c.G26T						.						114	112	113					18																	63430104		2203	4300	6503	SO:0001583	missense	1005	exon2			AGTTCTGCCATTT	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.26G>T	chr18.hg19:g.63430104G>T	ENSP00000381058:p.Cys9Phe	54.0	0.0		131.0	8.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	hg19	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.399009	0.25291	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.54279	0.58;0.6;0.58	5.83	4.96	0.65561	.	0.073160	0.64402	D	0.000013	T	0.47985	0.1475	L	0.58101	1.795	0.42167	D	0.991626	P;P	0.50943	0.723;0.94	B;B	0.41571	0.173;0.36	T	0.47873	-0.9083	10	0.12766	T	0.61	.	15.2241	0.73336	0.0672:0.0:0.9328:0.0	.	9;9	F5H5X9;Q9ULB5	.;CADH7_HUMAN	F	9	ENSP00000319166:C9F;ENSP00000443030:C9F;ENSP00000381058:C9F	ENSP00000319166:C9F	C	+	2	0	CDH7	61581084	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.450000	0.60041	1.487000	0.48415	-0.127000	0.14921	TGC	.	.		0.408	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		T	63430104	G	T	63430104	3	4	101	1	0	0	0	0	1	0	0	0	3117	1319	46	3	28	3	CDH7	18	63430104	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2362280	63430104	14647144	545	14382										
ABCA7	10347	hgsc.bcm.edu	37	chr19	1051263	1051263	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggatgtggggctggtctccAagcagagtgtgcagactcgc	16	9	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:1051263A>T	ENST00000263094.6	+	20	3025	c.2794A>T	c.(2794-2796)Aag>Tag	p.K932*	ABCA7_ENST00000433129.1_Nonsense_Mutation_p.K932*|ABCA7_ENST00000435683.2_Nonsense_Mutation_p.K794*	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	932	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTGGTCTCCAAGCAGAGTGT	0.642																																					p.K932X		Atlas-SNP	.											.	ABCA7	174	.	0			c.A2794T						.						51	49	50					19																	1051263		2190	4288	6478	SO:0001587	stop_gained	10347	exon20			GTCTCCAAGCAGA	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.2794A>T	chr19.hg19:g.1051263A>T	ENSP00000263094:p.Lys932*	36.0	0.0		120.0	15.0	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Nonsense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	A	43	10.507155	0.99418	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7119	0.51630	1.0:0.0:0.0:0.0	.	.	.	.	X	932	.	ENSP00000263094:K932X	K	+	1	0	ABCA7	1002263	1.000000	0.71417	0.622000	0.29159	0.789000	0.44602	8.712000	0.91403	1.665000	0.50811	0.374000	0.22700	AAG	.	.		0.642	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1051263	A	T	1051263	4	4	101	1	0	0	0	0	0	1	0	0	37	131	5	4	2868	4	ABCA7	19	1051263	Nonsense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10		1051263	58077720	546	14383										
DPP9	91039	hgsc.bcm.edu	37	chr19	4682767	4682767	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcctcatagccgtgctggttGttctcagggacgtccatgta	12	11	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:4682767G>A	ENST00000598800.1	-	21	2833	c.2328C>T	c.(2326-2328)aaC>aaT	p.N776N	DPP9_ENST00000262960.9_Silent_p.N805N|DPP9_ENST00000601173.1_5'Flank|DPP9_ENST00000594671.1_Silent_p.N776N|AC005594.3_ENST00000381796.1_RNA			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	776						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		CGTGCTGGTTGTTCTCAGGGA	0.652																																					p.N805N		Atlas-SNP	.											.	DPP9	59	.	0			c.C2415T						.						62	73	70					19																	4682767		2130	4253	6383	SO:0001819	synonymous_variant	91039	exon20			CTGGTTGTTCTCA	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"dipeptidylpeptidase 9"				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.2328C>T	chr19.hg19:g.4682767G>A		56.0	0.0		119.0	13.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Silent	SNP	ENST00000598800.1	hg19																																																																																				.	.		0.652	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2			A	4682767	G	A	4682767	2	1	101	1	0	0	0	0	0	0	0	1	4735	1368	48	3		3	DPP9	19	4682767	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3631504	4682767	54446216	547	14384										
MUC16	94025	hgsc.bcm.edu	37	chr19	9002558	9002558	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcccagctcagtgatgccgtGggtcagctggctcagcttcc	13	14	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:9002558G>T	ENST00000397910.4	-	51	40461	c.40258C>A	c.(40258-40260)Cac>Aac	p.H13420N	MUC16_ENST00000380951.5_Missense_Mutation_p.H61N	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13422	SEA 9. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGATGCCGTGGGTCAGCTGG	0.587																																					p.H13420N		Atlas-SNP	.											.	MUC16	4315	.	0			c.C40258A						.						187	170	175					19																	9002558		2150	4250	6400	SO:0001583	missense	94025	exon51			TGCCGTGGGTCAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.40258C>A	chr19.hg19:g.9002558G>T	ENSP00000381008:p.His13420Asn	91.0	0.0		210.0	26.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	6.688	0.495604	0.12762	.	.	ENSG00000181143	ENST00000397910;ENST00000380951	T;T	0.35605	1.3;1.3	2.75	1.69	0.24217	SEA (1);	.	.	.	.	T	0.43964	0.1271	L	0.46157	1.445	.	.	.	B;P	0.46859	0.003;0.885	B;P	0.60236	0.005;0.871	T	0.51568	-0.8689	8	0.37606	T	0.19	-0.5084	7.0787	0.25219	0.0:0.0:0.7305:0.2695	.	21065;13420	Q8WXI7;B5ME49	MUC16_HUMAN;.	N	13420;61	ENSP00000381008:H13420N;ENSP00000370338:H61N	ENSP00000370338:H61N	H	-	1	0	MUC16	8863558	0.001000	0.12720	0.250000	0.24296	0.003000	0.03518	0.235000	0.17948	0.737000	0.32582	-0.656000	0.03901	CAC	.	.		0.587	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9002558	G	T	9002558	3	4	101	1	0	0	0	0	1	0	0	0	9982	1348	47	3	3401	3	MUC16	19	9002558	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	4319791	9002558	50126425	548	14385										
MUC16	94025	hgsc.bcm.edu	37	chr19	9086899	9086899	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccagggtgactccactactaCtgctccctgttgttgtgttg	10	12	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:9086899C>G	ENST00000397910.4	-	1	5119	c.4916G>C	c.(4915-4917)aGt>aCt	p.S1639T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1639	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCCACTACTACTGCTCCCTGT	0.493																																					p.S1639T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G4916C						.						203	195	198					19																	9086899		2034	4189	6223	SO:0001583	missense	94025	exon1			CTACTACTGCTCC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4916G>C	chr19.hg19:g.9086899C>G	ENSP00000381008:p.Ser1639Thr	144.0	0.0		317.0	16.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	2.345	-0.350148	0.05173	.	.	ENSG00000181143	ENST00000397910	T	0.02552	4.25	1.33	0.156	0.14910	.	.	.	.	.	T	0.01730	0.0055	N	0.08118	0	.	.	.	D	0.55172	0.97	B	0.42386	0.386	T	0.48281	-0.9049	8	0.87932	D	0	.	5.2179	0.15352	0.0:0.6276:0.3724:0.0	.	1639	B5ME49	.	T	1639	ENSP00000381008:S1639T	ENSP00000381008:S1639T	S	-	2	0	MUC16	8947899	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-0.229000	0.09098	0.088000	0.17205	0.313000	0.20887	AGT	.	.		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9086899	C	G	9086899	3	3	101	1	0	0	0	0	1	0	0	0	9982	565	20	4	38943	4	MUC16	19	9086899	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	84341	9086899	50042084	549	14386										
OR7D4	125958	hgsc.bcm.edu	37	chr19	9324856	9324856	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cattaaggaggagacaatctGagagtaggagaagaggatcc	14	5	1	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:9324856G>T	ENST00000308682.2	-	1	686	c.658C>A	c.(658-660)Cag>Aag	p.Q220K		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						GAGACAATCTGAGAGTAGGAG	0.512																																					p.Q220K		Atlas-SNP	.											.	OR7D4	66	.	0			c.C658A						.						79	74	76					19																	9324856		2203	4300	6503	SO:0001583	missense	125958	exon1			CAATCTGAGAGTA		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"GPCR / Class A : Olfactory receptors"	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.658C>A	chr19.hg19:g.9324856G>T	ENSP00000310488:p.Gln220Lys	65.0	0.0		88.0	7.0	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Missense_Mutation	SNP	ENST00000308682.2	hg19	CCDS32901.1	.	.	.	.	.	.	.	.	.	.	G	0.039	-1.291492	0.01375	.	.	ENSG00000174667	ENST00000308682	T	0.00183	8.6	3.75	-1.99	0.07457	GPCR, rhodopsin-like superfamily (1);	0.778678	0.11432	N	0.564673	T	0.00109	0.0003	N	0.25825	0.765	0.09310	N	1	B	0.14805	0.011	B	0.20577	0.03	T	0.26430	-1.0103	10	0.02654	T	1	.	7.1788	0.25760	0.0893:0.0:0.2881:0.6225	.	220	Q8NG98	OR7D4_HUMAN	K	220	ENSP00000310488:Q220K	ENSP00000310488:Q220K	Q	-	1	0	OR7D4	9185856	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.398000	0.01051	-0.336000	0.08438	0.205000	0.17691	CAG	.	.		0.512	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1			T	9324856	G	T	9324856	3	4	101	1	0	0	0	0	1	0	0	0	11229	1299	45	3	284	3	OR7D4	19	9324856	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	237957	9324856	49804127	550	14387										
OR7D4	125958	hgsc.bcm.edu	37	chr19	9324879	9324879	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agtaggagaagaggatcccaGctacaggaaacacacccagc	11	11	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:9324879G>T	ENST00000308682.2	-	1	663	c.635C>A	c.(634-636)gCt>gAt	p.A212D		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						GAGGATCCCAGCTACAGGAAA	0.522																																					p.A212D		Atlas-SNP	.											OR7D4,right_upper_lobe,carcinoma,0,1	OR7D4	66	.	0			c.C635A						.						88	83	85					19																	9324879		2203	4300	6503	SO:0001583	missense	125958	exon1			ATCCCAGCTACAG		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"GPCR / Class A : Olfactory receptors"	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.635C>A	chr19.hg19:g.9324879G>T	ENSP00000310488:p.Ala212Asp	59.0	0.0		85.0	10.0	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Missense_Mutation	SNP	ENST00000308682.2	hg19	CCDS32901.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.997375	0.35226	.	.	ENSG00000174667	ENST00000308682	T	0.39229	1.09	3.84	-3.0	0.05480	GPCR, rhodopsin-like superfamily (1);	0.686881	0.13725	N	0.367118	T	0.34135	0.0887	M	0.64170	1.965	0.09310	N	1	P	0.34909	0.475	B	0.36335	0.222	T	0.30149	-0.9988	10	0.66056	D	0.02	.	5.0162	0.14337	0.2679:0.2841:0.448:0.0	.	212	Q8NG98	OR7D4_HUMAN	D	212	ENSP00000310488:A212D	ENSP00000310488:A212D	A	-	2	0	OR7D4	9185879	0.004000	0.15560	0.000000	0.03702	0.161000	0.22273	1.376000	0.34306	-0.511000	0.06514	0.205000	0.17691	GCT	.	.		0.522	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1			T	9324879	G	T	9324879	3	4	101	1	0	0	0	0	1	0	0	0	11229	971	34	3	307	3	OR7D4	19	9324879	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	23	9324879	49804104	551	14388										
PIN1	5300	hgsc.bcm.edu	37	chr19	9949168	9949168	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gccagtgggagcggcccagcGgcaacagcagcagtggtggc	18	12	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:9949168G>T	ENST00000247970.4	+	2	137	c.115G>T	c.(115-117)Ggc>Tgc	p.G39C	PIN1_ENST00000588695.1_Missense_Mutation_p.G39C|PIN1_ENST00000380889.6_3'UTR|PIN1_ENST00000587625.1_Missense_Mutation_p.G39C	NM_006221.3	NP_006212.1	Q13526	PIN1_HUMAN	peptidylprolyl cis/trans isomerase, NIMA-interacting 1	39	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cell cycle (GO:0007049)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|negative regulation of cell motility (GO:2000146)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of cytokinesis (GO:0032465)|regulation of mitosis (GO:0007088)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTPase activating protein binding (GO:0032794)|mitogen-activated protein kinase kinase binding (GO:0031434)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)	p.G39C(1)		skin(3)	3						GCGGCCCAGCGGCAACAGCAG	0.652																																					p.G39C		Atlas-SNP	.											PIN1_ENST00000247970,NS,carcinoma,0,1	PIN1	7	.	1	Substitution - Missense(1)	lung(1)	c.G115T						.						17	19	18					19																	9949168		2201	4298	6499	SO:0001583	missense	5300	exon2			CCCAGCGGCAACA		CCDS12220.1	19p13	2014-09-17	2008-03-25		ENSG00000127445	ENSG00000127445			8988	protein-coding gene	gene with protein product		601052	"protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1"			8606777	Standard	NM_006221		Approved	dod	uc002mml.2	Q13526		ENST00000247970.4:c.115G>T	chr19.hg19:g.9949168G>T	ENSP00000247970:p.Gly39Cys	30.0	0.0		96.0	9.0	NM_006221	A8K4V9|Q53X75	Missense_Mutation	SNP	ENST00000247970.4	hg19	CCDS12220.1	.	.	.	.	.	.	.	.	.	.	G	19.07	3.755544	0.69648	.	.	ENSG00000127445	ENST00000247970;ENST00000424497	T	0.76839	-1.05	3.63	2.59	0.31030	WW/Rsp5/WWP (3);	0.327520	0.27851	N	0.017596	T	0.80969	0.4726	M	0.69185	2.1	0.42263	D	0.992026	D;P;D	0.65815	0.995;0.894;0.983	P;P;P	0.58721	0.769;0.649;0.844	T	0.79351	-0.1839	9	.	.	.	-36.7392	6.9465	0.24522	0.1238:0.0:0.8762:0.0	.	39;39;39	B3KUM4;Q13526;E7EQR5	.;PIN1_HUMAN;.	C	39	ENSP00000247970:G39C	.	G	+	1	0	PIN1	9810168	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	5.971000	0.70440	1.125000	0.41998	0.555000	0.69702	GGC	.	.		0.652	PIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451107.1			T	9949168	G	T	9949168	3	4	101	1	0	0	0	0	1	0	0	0	11939	1116	39	1	121	1	PIN1	19	9949168	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	624289	9949168	49179815	552	14389										
ZNF440	126070	hgsc.bcm.edu	37	chr19	11942428	11942428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tggaccaaagccatgtaagtGtcaacaacctaaaaaagcct	7	10	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:11942428G>A	ENST00000304060.5	+	4	601	c.437G>A	c.(436-438)tGt>tAt	p.C146Y		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CCATGTAAGTGTCAACAACCT	0.413																																					p.C146Y		Atlas-SNP	.											.	ZNF440	56	.	0			c.G437A						.						158	157	157					19																	11942428		2203	4300	6503	SO:0001583	missense	126070	exon4			GTAAGTGTCAACA	AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"Zinc fingers, C2H2-type", "-"	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.437G>A	chr19.hg19:g.11942428G>A	ENSP00000305373:p.Cys146Tyr	96.0	0.0		203.0	76.0	NM_152357	Q8N1R9	Missense_Mutation	SNP	ENST00000304060.5	hg19	CCDS42503.1	.	.	.	.	.	.	.	.	.	.	g	8.537	0.872302	0.17322	.	.	ENSG00000171295	ENST00000304060;ENST00000457526;ENST00000427505;ENST00000414255	T;T;T;T	0.58358	0.34;1.3;2.99;5.16	0.91	0.91	0.19337	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.66197	0.2765	M	0.89968	3.075	0.22996	N	0.998452	P	0.48640	0.913	P	0.53450	0.726	T	0.56661	-0.7942	9	0.72032	D	0.01	.	5.1414	0.14961	0.0:0.0:1.0:0.0	.	146	Q8IYI8	ZN440_HUMAN	Y	146;24;149;148	ENSP00000305373:C146Y;ENSP00000404425:C24Y;ENSP00000393489:C149Y;ENSP00000411974:C148Y	ENSP00000305373:C146Y	C	+	2	0	ZNF440	11803428	.	.	0.041000	0.18516	0.009000	0.06853	.	.	0.806000	0.34183	0.205000	0.17691	TGT	.	.		0.413	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357		A	11942428	G	A	11942428	3	1	101	1	0	0	0	0	1	0	0	0	17928	1377	48	3	451	3	ZNF440	19	11942428	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1993260	11942428	47186555	553	14390										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23545393	23545393	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tttgtgcaccttacactcatCcacacttttacaaccttttc	2	14	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:23545393C>A	ENST00000300619.7	-	4	593	c.388G>T	c.(388-390)Gat>Tat	p.D130Y	ZNF91_ENST00000397082.2_Missense_Mutation_p.D98Y|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	130					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TTACACTCATCCACACTTTTA	0.338																																					p.D130Y		Atlas-SNP	.											.	ZNF91	349	.	0			c.G388T						.						76	81	80					19																	23545393		2157	4280	6437	SO:0001583	missense	7644	exon4			ACTCATCCACACT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.388G>T	chr19.hg19:g.23545393C>A	ENSP00000300619:p.Asp130Tyr	95.0	0.0		207.0	22.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	2.880	-0.232000	0.05983	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.05996	3.36;3.36	0.987	-0.984	0.10259	.	.	.	.	.	T	0.15522	0.0374	L	0.61387	1.9	0.09310	N	1	B;D	0.89917	0.291;1.0	B;D	0.74674	0.093;0.984	T	0.12451	-1.0547	9	0.66056	D	0.02	.	3.7254	0.08473	0.0:0.661:0.0:0.339	.	98;130	Q05481-2;Q05481	.;ZNF91_HUMAN	Y	130;98	ENSP00000300619:D130Y;ENSP00000380272:D98Y	ENSP00000300619:D130Y	D	-	1	0	ZNF91	23337233	0.000000	0.05858	0.007000	0.13788	0.322000	0.28314	-0.648000	0.05391	-0.453000	0.07076	0.174000	0.16983	GAT	.	.		0.338	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		A	23545393	C	A	23545393	3	1	101	1	0	0	0	0	1	0	0	0	18215	855	30	3	3191	3	ZNF91	19	23545393	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	11602965	23545393	35583590	554	14391										
ANKRD27	84079	hgsc.bcm.edu	37	chr19	33134347	33134347	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccaccctcacctccactgccTgcttcatcaggttcatctgg	6	18	5	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:33134347T>A	ENST00000306065.4	-	7	787	c.629A>T	c.(628-630)cAg>cTg	p.Q210L	ANKRD27_ENST00000587352.1_Missense_Mutation_p.Q210L	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	210					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					CTCCACTGCCTGCTTCATCAG	0.567																																					p.Q210L		Atlas-SNP	.											.	ANKRD27	86	.	0			c.A629T						.						165	173	171					19																	33134347		2203	4300	6503	SO:0001583	missense	84079	exon7			ACTGCCTGCTTCA	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"Ankyrin repeat domain containing"	25310	protein-coding gene	gene with protein product	"Vps9 domain and ankyrin-repeat-containing protein"					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.629A>T	chr19.hg19:g.33134347T>A	ENSP00000304292:p.Gln210Leu	52.0	0.0		118.0	63.0	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	hg19	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	T	13.77	2.337772	0.41398	.	.	ENSG00000105186	ENST00000306065	T	0.29397	1.57	5.59	5.59	0.84812	.	0.000000	0.56097	D	0.000034	T	0.28499	0.0705	N	0.08118	0	0.41503	D	0.988297	D	0.71674	0.998	P	0.60117	0.869	T	0.09378	-1.0677	10	0.07990	T	0.79	-24.0274	15.8187	0.78624	0.0:0.0:0.0:1.0	.	210	Q96NW4	ANR27_HUMAN	L	210	ENSP00000304292:Q210L	ENSP00000304292:Q210L	Q	-	2	0	ANKRD27	37826187	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.923000	0.75817	2.135000	0.66039	0.363000	0.22086	CAG	.	.		0.567	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		A	33134347	T	A	33134347	3	1	101	1	0	0	0	0	1	0	0	0	655	1580	55	4	2615	4	ANKRD27	19	33134347	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	9588954	33134347	25994636	555	14392										
RGS9BP	388531	hgsc.bcm.edu	37	chr19	33167297	33167297	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcggcaggagctgcaaaagaCgcgccagaaggcgcaggagc	17	11	0	2	rs371159333		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:33167297C>T	ENST00000334176.3	+	1	985	c.128C>T	c.(127-129)aCg>aTg	p.T43M	ANKRD27_ENST00000306065.4_5'Flank|ANKRD27_ENST00000587352.1_5'Flank	NM_207391.2	NP_997274.2	Q6ZS82	R9BP_HUMAN	regulator of G protein signaling 9 binding protein	43					detection of light stimulus involved in visual perception (GO:0050908)|negative regulation of signal transduction (GO:0009968)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	integral component of membrane (GO:0016021)				central_nervous_system(1)|lung(2)	3	Esophageal squamous(110;0.137)					CTGCAAAAGACGCGCCAGAAG	0.701																																					p.T43M		Atlas-SNP	.											.	RGS9BP	9	.	0			c.C128T						.	C	MET/THR	0,4332		0,0,2166	18	16	17		128	3.6	1	19		17	1,8527		0,1,4263	no	missense	RGS9BP	NM_207391.2	81	0,1,6429	TT,TC,CC		0.0117,0.0,0.0078	probably-damaging	43/236	33167297	1,12859	2166	4264	6430	SO:0001583	missense	388531	exon1			AAAAGACGCGCCA	AW302149	CCDS12424.1	19q13.11	2008-02-05	2007-08-14			ENSG00000186326			30304	protein-coding gene	gene with protein product		607814	"regulator of G protein signalling 9 binding protein"			12119397, 8889548	Standard	NM_207391		Approved	FLJ45744, PERRS, R9AP, RGS9	uc002ntp.1	Q6ZS82		ENST00000334176.3:c.128C>T	chr19.hg19:g.33167297C>T	ENSP00000334134:p.Thr43Met	8.0	0.0		18.0	6.0	NM_207391	Q6ZVJ6	Missense_Mutation	SNP	ENST00000334176.3	hg19	CCDS12424.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.191750	0.78902	0.0	1.17E-4	ENSG00000186326	ENST00000334176	T	0.31510	1.49	4.63	3.6	0.41247	.	0.000000	0.85682	U	0.000000	T	0.48314	0.1493	M	0.80847	2.515	0.80722	D	1	D	0.67145	0.996	P	0.54460	0.753	T	0.57254	-0.7843	10	0.87932	D	0	-33.2445	12.5274	0.56093	0.0:0.9194:0.0:0.0806	.	43	Q6ZS82	R9BP_HUMAN	M	43	ENSP00000334134:T43M	ENSP00000334134:T43M	T	+	2	0	RGS9BP	37859137	1.000000	0.71417	1.000000	0.80357	0.635000	0.38103	5.836000	0.69375	1.165000	0.42670	0.305000	0.20034	ACG	.	.		0.701	RGS9BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450337.1	NM_207391		T	33167297	C	T	33167297	3	4	101	1	0	0	0	0	1	0	0	0	13329	536	19	1	130	1	RGS9BP	19	33167297	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	32950	33167297	25961686	556	14393										
KIAA0355	9710	hgsc.bcm.edu	37	chr19	34791740	34791740	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cacacagctcaaagatgtgcAggagcatgtcatggaagcag	12	9	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:34791740A>C	ENST00000299505.6	+	2	1235	c.362A>C	c.(361-363)cAg>cCg	p.Q121P		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	121										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					AAAGATGTGCAGGAGCATGTC	0.512																																					p.Q121P		Atlas-SNP	.											.	KIAA0355	105	.	0			c.A362C						.						55	46	49					19																	34791740		2203	4300	6503	SO:0001583	missense	9710	exon2			ATGTGCAGGAGCA		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.362A>C	chr19.hg19:g.34791740A>C	ENSP00000299505:p.Gln121Pro	48.0	0.0		128.0	15.0	NM_014686	Q2M3W4	Missense_Mutation	SNP	ENST00000299505.6	hg19	CCDS12436.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.980051	0.53827	.	.	ENSG00000166398	ENST00000299505	.	.	.	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.65333	0.2681	L	0.27053	0.805	0.80722	D	1	D	0.64830	0.994	D	0.75484	0.986	T	0.69964	-0.5002	9	0.87932	D	0	-11.3164	15.4502	0.75268	1.0:0.0:0.0:0.0	.	121	O15063	K0355_HUMAN	P	121	.	ENSP00000299505:Q121P	Q	+	2	0	KIAA0355	39483580	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.910000	0.92685	2.107000	0.64212	0.459000	0.35465	CAG	.	.		0.512	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686		C	34791740	A	C	34791740	3	2	101	1	0	0	0	0	1	0	0	0	8179	188	7	5	364	5	KIAA0355	19	34791740	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	1624443	34791740	24337243	557	14394										
SBSN	374897	hgsc.bcm.edu	37	chr19	36019030	36019030	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gattccactgttgatgccatCcagggccttgcccacctctc	8	16	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:36019030C>A	ENST00000452271.2	-	1	182	c.154G>T	c.(154-156)Gat>Tat	p.D52Y	SBSN_ENST00000518157.1_Missense_Mutation_p.D52Y	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	52	Ala/Gly/His-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TTGATGCCATCCAGGGCCTTG	0.567																																					p.D52Y		Atlas-SNP	.											.	SBSN	58	.	0			c.G154T						.						197	169	179					19																	36019030		2203	4300	6503	SO:0001583	missense	374897	exon1			TGCCATCCAGGGC	AY358701	CCDS12464.1, CCDS54253.1	19q13.13	2008-02-05							24950	protein-coding gene	gene with protein product		609969				12228223	Standard	NM_198538		Approved	UNQ698, HLAR698	uc002oad.2	Q6UWP8		ENST00000452271.2:c.154G>T	chr19.hg19:g.36019030C>A	ENSP00000430242:p.Asp52Tyr	81.0	0.0		205.0	44.0	NM_001166034	A8K5J0|E9PBV3	Missense_Mutation	SNP	ENST00000452271.2	hg19	CCDS54253.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.291395	0.59976	.	.	ENSG00000189001	ENST00000452271;ENST00000518157	T;T	0.53206	0.76;0.63	4.71	4.71	0.59529	.	0.402247	0.20878	N	0.084053	T	0.55242	0.1908	L	0.34521	1.04	0.27539	N	0.950856	D;D	0.65815	0.995;0.984	P;D	0.64506	0.807;0.926	T	0.51490	-0.8699	10	0.72032	D	0.01	.	13.1495	0.59482	0.0:1.0:0.0:0.0	.	52;52	Q6UWP8;E9PBV3	SBSN_HUMAN;.	Y	52	ENSP00000430242:D52Y;ENSP00000428771:D52Y	ENSP00000430242:D52Y	D	-	1	0	SBSN	40710870	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	3.545000	0.53648	2.131000	0.65755	0.555000	0.69702	GAT	.	.		0.567	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538		A	36019030	C	A	36019030	3	1	101	1	0	0	0	0	1	0	0	0	13879	855	30	3	1634	3	SBSN	19	36019030	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1227290	36019030	23109953	558	14395										
ZNF527	84503	hgsc.bcm.edu	37	chr19	37879212	37879212	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcttgatatttttcagactgGgagtcttggtgtgaaattga	11	4	3	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:37879212G>T	ENST00000436120.2	+	5	368	c.261G>T	c.(259-261)tgG>tgT	p.W87C	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	87	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTCAGACTGGGAGTCTTGGT	0.383																																					p.W87C		Atlas-SNP	.											.	ZNF527	78	.	0			c.G261T						.						44	42	42					19																	37879212		1822	4086	5908	SO:0001583	missense	84503	exon5			AGACTGGGAGTCT	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"Zinc fingers, C2H2-type", "-"	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.261G>T	chr19.hg19:g.37879212G>T	ENSP00000390179:p.Trp87Cys	70.0	0.0		284.0	23.0	NM_032453	B4DVL5	Missense_Mutation	SNP	ENST00000436120.2	hg19	CCDS42559.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.413878	0.42817	.	.	ENSG00000189164	ENST00000356178;ENST00000317566;ENST00000436120	.	.	.	4.72	3.62	0.41486	.	0.000000	0.30501	N	0.009483	T	0.39306	0.1073	N	0.16862	0.45	0.80722	D	1	B;B	0.20988	0.03;0.05	B;B	0.21151	0.015;0.033	T	0.35226	-0.9797	9	0.51188	T	0.08	.	10.1897	0.43019	0.0:0.0:0.8027:0.1973	.	87;55	Q8NB42;Q8NB42-2	ZN527_HUMAN;.	C	87;55;35	.	ENSP00000325231:W55C	W	+	3	0	ZNF527	42571052	0.786000	0.28738	1.000000	0.80357	0.991000	0.79684	0.462000	0.21956	2.455000	0.83008	0.655000	0.94253	TGG	.	.		0.383	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453		T	37879212	G	T	37879212	3	4	101	1	0	0	0	0	1	0	0	0	17983	1241	43	3	275	3	ZNF527	19	37879212	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1860182	37879212	21249771	559	14396										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40366097	40366097	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acaggctgccacgtaggtagCcactgcaggacagaggcctc	13	13	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:40366097C>T	ENST00000221347.6	-	30	14144	c.14137G>A	c.(14137-14139)Gct>Act	p.A4713T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4713						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			ACGTAGGTAGCCACTGCAGGA	0.667																																					p.A4713T		Atlas-SNP	.											.	FCGBP	416	.	0			c.G14137A						.						35	44	41					19																	40366097		2201	4298	6499	SO:0001583	missense	8857	exon30			AGGTAGCCACTGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.14137G>A	chr19.hg19:g.40366097C>T	ENSP00000221347:p.Ala4713Thr	19.0	0.0		77.0	8.0	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.437238	0.25900	.	.	ENSG00000090920	ENST00000221347	D	0.86030	-2.06	4.47	4.47	0.54385	Uncharacterised domain, cysteine-rich (2);	0.512331	0.17949	U	0.156598	T	0.80919	0.4716	L	0.57130	1.785	0.09310	N	1	B	0.25850	0.136	B	0.25614	0.062	T	0.67776	-0.5583	10	0.26408	T	0.33	.	10.6625	0.45710	0.0:0.9057:0.0:0.0943	.	4713	Q9Y6R7	FCGBP_HUMAN	T	4713	ENSP00000221347:A4713T	ENSP00000221347:A4713T	A	-	1	0	FCGBP	45057937	0.000000	0.05858	0.975000	0.42487	0.581000	0.36288	-0.477000	0.06583	2.467000	0.83353	0.305000	0.20034	GCT	.	.		0.667	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40366097	C	T	40366097	3	4	101	1	0	0	0	0	1	0	0	0	5786	739	26	3	2108	3	FCGBP	19	40366097	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2486885	40366097	18762886	560	14397										
MAP3K10	4294	hgsc.bcm.edu	37	chr19	40715117	40715117	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcatcatcccccggctgaggGccattcgccgtgagtatctc	11	15	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:40715117G>A	ENST00000253055.3	+	6	1831	c.1543G>A	c.(1543-1545)Gcc>Acc	p.A515T		NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	515					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						CCGGCTGAGGGCCATTCGCCG	0.552																																					p.A515T		Atlas-SNP	.											.	MAP3K10	70	.	0			c.G1543A						.						50	57	54					19																	40715117		2203	4300	6503	SO:0001583	missense	4294	exon6			CTGAGGGCCATTC	X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6849	protein-coding gene	gene with protein product	"MKN28 kinase", "mixed lineage kinase 2", "MKN28 derived nonreceptor_type serine/threonine kinase"	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.1543G>A	chr19.hg19:g.40715117G>A	ENSP00000253055:p.Ala515Thr	18.0	0.0		85.0	41.0	NM_002446	Q12761|Q14871	Missense_Mutation	SNP	ENST00000253055.3	hg19	CCDS12549.1	.	.	.	.	.	.	.	.	.	.	G	35	5.461008	0.96240	.	.	ENSG00000130758	ENST00000253055	T	0.12984	2.63	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.32734	0.0839	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.66602	0.945	T	0.01591	-1.1317	10	0.59425	D	0.04	.	16.2537	0.82501	0.0:0.0:1.0:0.0	.	515	Q02779	M3K10_HUMAN	T	515	ENSP00000253055:A515T	ENSP00000253055:A515T	A	+	1	0	MAP3K10	45406957	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.712000	0.98738	2.518000	0.84900	0.555000	0.69702	GCC	.	.		0.552	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446		A	40715117	G	A	40715117	3	1	101	1	0	0	0	0	1	0	0	0	9253	1203	42	3	1565	3	MAP3K10	19	40715117	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	349020	40715117	18413866	561	14398										
CEACAM3	1084	hgsc.bcm.edu	37	chr19	42300660	42300660	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaatgcatcccctggcagggGcttctgctcacaggtgagtg	14	11	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:42300660G>A	ENST00000357396.3	+	1	292	c.51G>A	c.(49-51)ggG>ggA	p.G17G	CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000221999.4_Silent_p.G17G|CEACAM3_ENST00000344550.4_Silent_p.G17G	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	17						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						CCTGGCAGGGGCTTCTGCTCA	0.622																																					p.G17G		Atlas-SNP	.											.	CEACAM3	37	.	0			c.G51A						.						41	41	41					19																	42300660		2203	4300	6503	SO:0001819	synonymous_variant	1084	exon1			GCAGGGGCTTCTG	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.51G>A	chr19.hg19:g.42300660G>A		50.0	0.0		65.0	29.0	NM_001815	G5E978|Q3KPH9	Silent	SNP	ENST00000357396.3	hg19	CCDS12586.2																																																																																			.	.		0.622	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815		A	42300660	G	A	42300660	2	1	101	1	0	0	0	0	0	0	0	1	3195	1190	42	3		3	CEACAM3	19	42300660	Silent	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1585543	42300660	16828323	562	14399										
PHLDB3	653583	hgsc.bcm.edu	37	chr19	43983597	43983597	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcttcctccaggtcttgatgCggccgcccatcttcaccagg	10	16	3	1	rs200179651		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:43983597C>A	ENST00000292140.5	-	14	1994	c.1634G>T	c.(1633-1635)cGc>cTc	p.R545L		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	545	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GGTCTTGATGCGGCCGCCCAT	0.652																																					p.R545L		Atlas-SNP	.											.	PHLDB3	30	.	0			c.G1634T						.						15	18	17					19																	43983597		2039	4169	6208	SO:0001583	missense	653583	exon14			TTGATGCGGCCGC		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"Pleckstrin homology (PH) domain containing"	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1634G>T	chr19.hg19:g.43983597C>A	ENSP00000292140:p.Arg545Leu	37.0	0.0		221.0	19.0	NM_198850	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	hg19	CCDS12621.2	.	.	.	.	.	.	.	.	.	.	C	15.59	2.877146	0.51801	.	.	ENSG00000176531	ENST00000292140	T	0.74002	-0.8	4.59	3.56	0.40772	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.64402	D	0.000002	T	0.80330	0.4603	L	0.46157	1.445	0.50313	D	0.999866	D;D	0.76494	0.997;0.999	D;D	0.75484	0.949;0.986	T	0.81239	-0.1023	10	0.72032	D	0.01	.	11.179	0.48616	0.0:0.9062:0.0:0.0938	.	215;545	B2RXH3;Q6NSJ2	.;PHLB3_HUMAN	L	545	ENSP00000292140:R545L	ENSP00000292140:R545L	R	-	2	0	PHLDB3	48675437	0.996000	0.38824	0.899000	0.35326	0.222000	0.24845	2.367000	0.44213	1.260000	0.44134	-0.236000	0.12185	CGC	.	.		0.652	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2			A	43983597	C	A	43983597	3	1	101	1	0	0	0	0	1	0	0	0	11862	768	27	1	300	1	PHLDB3	19	43983597	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1682937	43983597	15145386	563	14400										
SYMPK	8189	hgsc.bcm.edu	37	chr19	46321291	46321291	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtacatggtcagggactggaTgacggtcctcatgagcagca	14	9	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:46321291T>G	ENST00000245934.7	-	23	3251	c.3007A>C	c.(3007-3009)Atc>Ctc	p.I1003L	RSPH6A_ENST00000221538.3_5'Flank|RSPH6A_ENST00000597055.1_5'Flank|SYMPK_ENST00000598155.1_5'UTR	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	1003					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		AGGGACTGGATGACGGTCCTC	0.632																																					p.I1003L		Atlas-SNP	.											.	SYMPK	104	.	0			c.A3007C						.						54	43	46					19																	46321291		2198	4294	6492	SO:0001583	missense	8189	exon23			ACTGGATGACGGT	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.3007A>C	chr19.hg19:g.46321291T>G	ENSP00000245934:p.Ile1003Leu	41.0	0.0		98.0	49.0	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Missense_Mutation	SNP	ENST00000245934.7	hg19	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	T	26.8	4.775170	0.90108	.	.	ENSG00000125755	ENST00000245934	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.59810	0.2221	L	0.42008	1.315	0.80722	D	1	P	0.39022	0.655	P	0.47786	0.557	T	0.61922	-0.6963	9	0.52906	T	0.07	.	13.295	0.60292	0.0:0.0:0.0:1.0	.	1003	Q92797	SYMPK_HUMAN	L	1003	.	ENSP00000245934:I1003L	I	-	1	0	SYMPK	51013131	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.489000	0.81451	2.039000	0.60335	0.454000	0.30748	ATC	.	.		0.632	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		G	46321291	T	G	46321291	3	3	101	1	0	0	0	0	1	0	0	0	15454	1464	51	5	837	5	SYMPK	19	46321291	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	2337694	46321291	12807692	564	14401										
CCDC8	83987	hgsc.bcm.edu	37	chr19	46914889	46914889	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccctggtcagctggggcctcCgccctctgattatctgcagc	11	16	3	1	rs538950740		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:46914889C>T	ENST00000307522.3	-	1	1952	c.1179G>A	c.(1177-1179)gcG>gcA	p.A393A		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	393					microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;4.66e-05)|all cancers(93;0.000582)|Epithelial(262;0.00428)|GBM - Glioblastoma multiforme(486;0.0421)		CTGGGGCCTCCGCCCTCTGAT	0.582																																					p.A393A		Atlas-SNP	.											.	CCDC8	56	.	0			c.G1179A						.						121	114	116					19																	46914889		2203	4300	6503	SO:0001819	synonymous_variant	83987	exon1			GGCCTCCGCCCTC	BC025243	CCDS12685.1	19q13.33	2012-04-17			ENSG00000169515	ENSG00000169515		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25367	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 20"	614145				11230166	Standard	NM_032040		Approved	DKFZp564K0322, 3M3, PPP1R20	uc002pep.3	Q9H0W5	OTTHUMG00000162348	ENST00000307522.3:c.1179G>A	chr19.hg19:g.46914889C>T		105.0	0.0		131.0	9.0	NM_032040	Q8TB26	Silent	SNP	ENST00000307522.3	hg19	CCDS12685.1	.	.	.	.	.	.	.	.	.	.	C	4.719	0.133637	0.09032	.	.	ENSG00000169515	ENST00000540252	.	.	.	3.03	-0.331	0.12679	.	.	.	.	.	T	0.19485	0.0468	.	.	.	0.18873	N	0.999984	.	.	.	.	.	.	T	0.30736	-0.9968	5	0.16896	T	0.51	.	5.7112	0.17935	0.0:0.4164:0.0:0.5836	.	.	.	.	Q	240	.	ENSP00000441180:R240Q	R	-	2	0	CCDC8	51606729	0.000000	0.05858	0.009000	0.14445	0.012000	0.07955	-0.684000	0.05173	-0.134000	0.11516	-0.811000	0.03165	CGG	.	.		0.582	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	NM_032040		T	46914889	C	T	46914889	2	4	101	1	0	0	0	0	0	0	0	1	2855	639	23	1		1	CCDC8	19	46914889	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	593598	46914889	12214094	565	14402										
KCNA7	3743	hgsc.bcm.edu	37	chr19	49573841	49573841	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttgaagatgcggaagacacGcaccaatcggatgactctca	10	11	1	4	rs546430763		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:49573841G>A	ENST00000221444.1	-	2	1205	c.850C>T	c.(850-852)Cgt>Tgt	p.R284C		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	284					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	CGGAAGACACGCACCAATCGG	0.627																																					p.R284C	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											.	KCNA7	30	.	0			c.C850T						.						84	78	80					19																	49573841		2203	4300	6503	SO:0001583	missense	3743	exon2			AGACACGCACCAA	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.850C>T	chr19.hg19:g.49573841G>A	ENSP00000221444:p.Arg284Cys	28.0	0.0		72.0	9.0	NM_031886	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	hg19	CCDS12755.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.243894	0.58995	.	.	ENSG00000104848	ENST00000221444	D	0.99652	-6.3	4.54	3.47	0.39725	Ion transport (1);	0.102964	0.64402	D	0.000008	D	0.99785	0.9910	H	0.99273	4.495	0.54753	D	0.999986	D	0.89917	1.0	D	0.87578	0.998	D	0.97373	0.9977	10	0.87932	D	0	.	10.7412	0.46154	0.0:0.0:0.5281:0.4719	.	284	Q96RP8	KCNA7_HUMAN	C	284	ENSP00000221444:R284C	ENSP00000221444:R284C	R	-	1	0	KCNA7	54265653	0.133000	0.22466	1.000000	0.80357	0.986000	0.74619	0.466000	0.22019	1.003000	0.39130	0.491000	0.48974	CGT	.	.		0.627	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886		A	49573841	G	A	49573841	3	1	101	1	0	0	0	0	1	0	0	0	8017	1087	38	1	524	1	KCNA7	19	49573841	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2658952	49573841	9555142	566	14403										
VRK3	51231	hgsc.bcm.edu	37	chr19	50482384	50482384	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gggaggccaatggggtcataTggagacacacgcagatcctg	15	9	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:50482384T>C	ENST00000599538.1	-	14	2056	c.1392A>G	c.(1390-1392)ccA>ccG	p.P464P	VRK3_ENST00000377011.2_Silent_p.P414P|VRK3_ENST00000594948.1_Silent_p.P464P|VRK3_ENST00000316763.3_Silent_p.P464P|VRK3_ENST00000601341.1_Silent_p.P414P|VRK3_ENST00000443401.2_Silent_p.P233P			Q8IV63	VRK3_HUMAN	vaccinia related kinase 3	464					negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)|stomach(2)|urinary_tract(1)	23		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)		TGGGGTCATATGGAGACACAC	0.587																																					p.P464P	Pancreas(6;90 181 4352 12603 17050 34726 35237 44094)	Atlas-SNP	.											.	VRK3	49	.	0			c.A1392G						.						151	122	132					19																	50482384		2203	4300	6503	SO:0001819	synonymous_variant	51231	exon14			GTCATATGGAGAC	AB031052	CCDS12791.1, CCDS33076.1	19q13.33	2011-01-14			ENSG00000105053	ENSG00000105053			18996	protein-coding gene	gene with protein product							Standard	XM_005258971		Approved		uc002prh.1	Q8IV63		ENST00000599538.1:c.1392A>G	chr19.hg19:g.50482384T>C		46.0	0.0		103.0	33.0	NM_016440	A6NEG5|A8KA53|Q502Y2|Q9P2V8	Silent	SNP	ENST00000599538.1	hg19	CCDS12791.1																																																																																			.	.		0.587	VRK3-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464815.1	NM_016440		C	50482384	T	C	50482384	2	2	101	1	0	0	0	0	0	0	0	1	17236	1451	51	2		2	VRK3	19	50482384	Silent	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	908543	50482384	8646599	567	14404										
KLK11	11012	hgsc.bcm.edu	37	chr19	51530742	51530742	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgagacctctgcccgatgacTtccagtcccgcagccacctc	8	18	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:51530742T>C	ENST00000594768.1	-	1	217	c.32A>G	c.(31-33)aAg>aGg	p.K11R	KLK11_ENST00000594458.1_5'Flank|KLK11_ENST00000319720.7_Intron|KLK11_ENST00000453757.3_5'Flank|KLK11_ENST00000600362.1_5'Flank|KLK11_ENST00000391804.3_Intron|CTC-518B2.9_ENST00000594910.1_RNA	NM_144947.1	NP_659196.1	Q9UBX7	KLK11_HUMAN	kallikrein-related peptidase 11	11						extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|GBM - Glioblastoma multiforme(134;0.00878)		GCCCGATGACTTCCAGTCCCG	0.607																																					p.K11R		Atlas-SNP	.											.	KLK11	28	.	0			c.A32G						.						91	92	92					19																	51530742		2203	4300	6503	SO:0001583	missense	11012	exon1			GATGACTTCCAGT	AB012917	CCDS12818.1, CCDS12819.1, CCDS54297.1	19q13.33	2011-09-07	2006-10-27			ENSG00000167757		"Kallikreins", "Serine peptidases / Serine peptidases"	6359	protein-coding gene	gene with protein product		604434	"kallikrein 11"	PRSS20		9765601, 10662548, 16800724, 16800723	Standard	NM_006853		Approved	TLSP	uc002pvb.2	Q9UBX7		ENST00000594768.1:c.32A>G	chr19.hg19:g.51530742T>C	ENSP00000473047:p.Lys11Arg	32.0	0.0		83.0	11.0	NM_144947	O75837|Q0WXX5|Q8IXD7|Q9NS65	Missense_Mutation	SNP	ENST00000594768.1	hg19	CCDS12818.1	.	.	.	.	.	.	.	.	.	.	t	11.46	1.646536	0.29246	.	.	ENSG00000167757	ENST00000319756	D	0.87887	-2.31	2.76	2.76	0.32466	.	.	.	.	.	T	0.74313	0.3700	N	0.22421	0.69	0.22842	N	0.998667	P	0.37061	0.58	B	0.29176	0.099	T	0.64901	-0.6298	9	0.42905	T	0.14	.	7.392	0.26915	0.0:0.0:0.0:1.0	.	11	Q9UBX7	KLK11_HUMAN	R	11	ENSP00000324414:K11R	ENSP00000324414:K11R	K	-	2	0	KLK11	56222554	0.013000	0.17824	0.057000	0.19452	0.139000	0.21198	1.126000	0.31344	1.510000	0.48803	0.383000	0.25322	AAG	.	.		0.607	KLK11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464314.2	NM_006853		C	51530742	T	C	51530742	3	2	101	1	0	0	0	0	1	0	0	0	8408	1609	56	2	915	2	KLK11	19	51530742	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	1048358	51530742	7598241	568	14405										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52001391	52001391	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctcgaggcagctccagcaccCcaaggttcgaggactgtgag	13	13	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:52001391C>A	ENST00000291707.3	-	5	1341	c.1286G>T	c.(1285-1287)gGg>gTg	p.G429V	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.G311V	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	429	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CTCCAGCACCCCAAGGTTCGA	0.617																																					p.G429V		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.G1286T						.						50	49	49					19																	52001391		2203	4300	6503	SO:0001583	missense	89858	exon5			AGCACCCCAAGGT	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1286G>T	chr19.hg19:g.52001391C>A	ENSP00000291707:p.Gly429Val	41.0	0.0		104.0	9.0	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	hg19	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	9.204	1.029301	0.19512	.	.	ENSG00000254521	ENST00000291707	T	0.15718	2.4	1.39	-2.77	0.05877	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.198493	0.24779	U	0.035667	T	0.41673	0.1169	H	0.95402	3.665	0.09310	N	0.999998	D;D	0.69078	0.997;0.99	D;D	0.76071	0.987;0.929	T	0.33394	-0.9870	10	0.72032	D	0.01	.	2.2019	0.03926	0.2445:0.4208:0.0:0.3347	.	429;311	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	V	429	ENSP00000291707:G429V	ENSP00000291707:G429V	G	-	2	0	SIGLEC12	56693203	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.240000	0.18042	-0.859000	0.04105	-0.784000	0.03344	GGG	.	.		0.617	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		A	52001391	C	A	52001391	3	1	101	1	0	0	0	0	1	0	0	0	14323	623	22	3	517	3	SIGLEC12	19	52001391	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	470649	52001391	7127592	569	14406										
ZNF613	79898	hgsc.bcm.edu	37	chr19	52443518	52443518	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acttgggaggagtggcagctCctcggccctgctcagaagga	15	11	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:52443518C>G	ENST00000293471.6	+	4	751	c.72C>G	c.(70-72)ctC>ctG	p.L24L	ZNF613_ENST00000391794.4_5'UTR	NM_001031721.3	NP_001026891.2	Q6PF04	ZN613_HUMAN	zinc finger protein 613	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	19		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		AGTGGCAGCTCCTCGGCCCTG	0.517																																					p.L24L		Atlas-SNP	.											.	ZNF613	62	.	0			c.C72G						.						124	119	121					19																	52443518		2203	4300	6503	SO:0001819	synonymous_variant	79898	exon4			GCAGCTCCTCGGC	AK027565	CCDS12844.1, CCDS33089.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	25827	protein-coding gene	gene with protein product						12477932	Standard	NM_001031721		Approved	FLJ13590	uc002pxz.2	Q6PF04		ENST00000293471.6:c.72C>G	chr19.hg19:g.52443518C>G		35.0	0.0		171.0	62.0	NM_001031721	Q96SS9	Silent	SNP	ENST00000293471.6	hg19	CCDS33089.1																																																																																			.	.		0.517	ZNF613-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461104.2	NM_024840		G	52443518	C	G	52443518	2	3	101	1	0	0	0	0	0	0	0	1	18053	842	30	4		4	ZNF613	19	52443518	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	442127	52443518	6685465	570	14407										
VN1R2	317701	hgsc.bcm.edu	37	chr19	53761997	53761997	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggggatacaagccaagatcCacagatttgattctcaggca	10	9	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:53761997C>A	ENST00000341702.3	+	1	453	c.369C>A	c.(367-369)tcC>tcA	p.S123S		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	123					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		AGCCAAGATCCACAGATTTGA	0.403																																					p.S123S		Atlas-SNP	.											VN1R2,NS,carcinoma,0,1	VN1R2	71	.	0			c.C369A						.						85	90	88					19																	53761997		2203	4300	6503	SO:0001819	synonymous_variant	317701	exon1			AAGATCCACAGAT	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.369C>A	chr19.hg19:g.53761997C>A		72.0	0.0		130.0	61.0	NM_173856	A1L411|Q8TDU4	Silent	SNP	ENST00000341702.3	hg19	CCDS12862.1																																																																																			.	.		0.403	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		A	53761997	C	A	53761997	2	1	101	1	0	0	0	0	0	0	0	1	17194	581	21	3		3	VN1R2	19	53761997	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1318479	53761997	5366986	571	14408										
OSCAR	126014	hgsc.bcm.edu	37	chr19	54602893	54602893	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtactcacctataatggccaCtaaggggaatgagaaaagaa	10	7	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:54602893C>A	ENST00000284648.6	-	3	268				OSCAR_ENST00000356532.3_Splice_Site|OSCAR_ENST00000358375.4_Intron|OSCAR_ENST00000391760.1_Intron|OSCAR_ENST00000359649.4_Splice_Site|OSCAR_ENST00000351806.4_Intron|OSCAR_ENST00000391761.1_Intron			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|skin(1)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)					ataatgGCCACTAAGgggaat	0.428																																					.		Atlas-SNP	.											.	OSCAR	22	.	0			c.71-1G>T						.						86	81	83					19																	54602893		2203	4300	6503	SO:0001627	intron_variant	126014	exon4			TGGCCACTAAGGG	AK130199	CCDS12873.1, CCDS12874.1, CCDS12875.1, CCDS12876.1, CCDS62789.1, CCDS74444.1	19q13.42	2013-01-29			ENSG00000170909	ENSG00000170909		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29960	protein-coding gene	gene with protein product		606862				11805147	Standard	NM_206818		Approved		uc002qda.3	Q8IYS5	OTTHUMG00000064966	ENST00000284648.6:c.70+145G>T	chr19.hg19:g.54602893C>A		42.0	0.0		88.0	9.0	NM_130771	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Splice_Site	SNP	ENST00000284648.6	hg19		.	.	.	.	.	.	.	.	.	.	C	5.864	0.343657	0.11126	.	.	ENSG00000170909	ENST00000356532;ENST00000359649	.	.	.	2.17	2.17	0.27698	.	.	.	.	.	.	.	.	.	.	.	0.20403	N	0.99991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.9473	0.29993	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	OSCAR	59294705	0.015000	0.18098	0.013000	0.15412	0.087000	0.18053	0.337000	0.19841	1.558000	0.49541	0.456000	0.33151	.	.	.		0.428	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169		A	54602893	C	A	54602893	1	1	101	0	1	0	0	0	0	0	0	0	11294	579	20	3		3	OSCAR	19	54602893	Intron	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	840896	54602893	4526090	572	14409										
LILRA1	11024	hgsc.bcm.edu	37	chr19	55111991	55111991	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctcaggagcagctaacaccCtcagcccatcacaaaacaag	6	15	3	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:55111991C>A	ENST00000251372.3	+	9	1509	c.1327C>A	c.(1327-1329)Ctc>Atc	p.L443I	LILRB1_ENST00000396321.2_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Missense_Mutation_p.L243I	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	443					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		AGCTAACACCCTCAGCCCATC	0.537																																					p.L443I		Atlas-SNP	.											.	LILRA1	105	.	0			c.C1327A						.						96	96	96					19																	55111991		2203	4300	6503	SO:0001583	missense	11024	exon9			AACACCCTCAGCC	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.1327C>A	chr19.hg19:g.55111991C>A	ENSP00000251372:p.Leu443Ile	63.0	0.0		167.0	20.0	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	hg19	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	C	2.191	-0.385190	0.04966	.	.	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.00531	6.76;6.89	1.75	-3.5	0.04710	.	.	.	.	.	T	0.00356	0.0011	L	0.43152	1.355	0.09310	N	1	B	0.31519	0.327	B	0.19148	0.024	T	0.34254	-0.9836	9	0.20046	T	0.44	.	7.8519	0.29459	0.2912:0.7088:0.0:0.0	.	443	O75019	LIRA1_HUMAN	I	443;243	ENSP00000251372:L443I;ENSP00000413715:L243I	ENSP00000251372:L443I	L	+	1	0	LILRA1	59803803	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.580000	0.02121	-0.674000	0.05253	0.195000	0.17529	CTC	.	.		0.537	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863		A	55111991	C	A	55111991	3	1	101	1	0	0	0	0	1	0	0	0	8793	681	24	3	1357	3	LILRA1	19	55111991	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	509098	55111991	4016992	573	14410										
GP6	51206	hgsc.bcm.edu	37	chr19	55543507	55543507	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tccgatcccccttcctttacCcgtggcaacgagctccagct	7	18	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:55543507C>T	ENST00000417454.1	-	3	352	c.325G>A	c.(325-327)Gga>Aga	p.G109R	GP6_ENST00000333884.2_Splice_Site_p.G109R|CTC-550B14.7_ENST00000593060.1_RNA|CTC-550B14.7_ENST00000586961.1_RNA|CTC-550B14.7_ENST00000586845.1_RNA|CTC-550B14.6_ENST00000585492.1_RNA|GP6_ENST00000310373.3_Splice_Site_p.G109R	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	109					blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.G109*(1)		NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		CTTCCTTTACCCGTGGCAACG	0.622																																					p.G109R		Atlas-SNP	.											GP6,NS,carcinoma,0,1	GP6	55	.	1	Substitution - Nonsense(1)	lung(1)	c.G325A						.						37	40	39					19																	55543507		2035	4175	6210	SO:0001630	splice_region_variant	51206	exon3			CTTTACCCGTGGC	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.325+1G>A	chr19.hg19:g.55543507C>T		10.0	0.0		43.0	2.0	NM_016363	Q9HCN7|Q9UIF2	Missense_Mutation	SNP	ENST00000417454.1	hg19	CCDS46184.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.352143	0.61183	.	.	ENSG00000088053	ENST00000417454;ENST00000310373;ENST00000333884	T;T;T	0.13901	2.55;2.55;2.55	3.83	3.83	0.44106	Immunoglobulin-like fold (1);	.	.	.	.	T	0.39963	0.1098	M	0.85099	2.735	0.30808	N	0.739123	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.992;0.995;0.997	T	0.42498	-0.9448	8	.	.	.	.	11.4045	0.49889	0.0:1.0:0.0:0.0	.	109;109;109	Q9HCN6-2;Q9HCN6-3;Q9HCN6	.;.;GPVI_HUMAN	R	109	ENSP00000394922:G109R;ENSP00000308782:G109R;ENSP00000334552:G109R	.	G	-	1	0	GP6	60235319	0.772000	0.28567	0.367000	0.25926	0.008000	0.06430	1.575000	0.36493	2.142000	0.66516	0.549000	0.68633	GGA	.	.		0.622	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		Missense_Mutation	T	55543507	C	T	55543507	5	4	101	1	0	0	0	0	0	0	1	0	6592	637	22	3	1561	3	GP6	19	55543507	Splice_Site	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	431516	55543507	3585476	574	14411										
PTPRH	5794	hgsc.bcm.edu	37	chr19	55713470	55713470	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gagctgttgattccattcttCcccacccacacggaaaacac	6	15	1	1	rs536291307	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:55713470C>T	ENST00000376350.3	-	6	1129	c.1107G>A	c.(1105-1107)ggG>ggA	p.G369G	PTPRH_ENST00000263434.5_Silent_p.G191G|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	369	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		TTCCATTCTTCCCCACCCACA	0.512													C|||	23	0.00459265	0	0	5008	,	,		20155	0		0	False		,,,				2504	0.0235				p.G369G		Atlas-SNP	.											PTPRH,colon,carcinoma,0,1	PTPRH	139	.	0			c.G1107A						.						148	142	144					19																	55713470		2203	4300	6503	SO:0001819	synonymous_variant	5794	exon6			ATTCTTCCCCACC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.1107G>A	chr19.hg19:g.55713470C>T		96.0	1.0		204.0	22.0	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Silent	SNP	ENST00000376350.3	hg19	CCDS33110.1																																																																																			.	.		0.512	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			T	55713470	C	T	55713470	2	4	101	1	0	0	0	0	0	0	0	1	12818	842	30	3		3	PTPRH	19	55713470	Silent	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	169963	55713470	3415513	575	14412										
PTPRH	5794	hgsc.bcm.edu	37	chr19	55716907	55716907	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggggacctcccaggtcagggCgatggagctgttggtctgag	18	9	2	1	rs144055741	byFrequency	TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:55716907C>A	ENST00000376350.3	-	4	428	c.406G>T	c.(406-408)Gcc>Tcc	p.A136S	PTPRH_ENST00000263434.5_Intron|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	136	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CAGGTCAGGGCGATGGAGCTG	0.592																																					p.A136S		Atlas-SNP	.											.	PTPRH	139	.	0			c.G406T						.						106	86	93					19																	55716907		2203	4300	6503	SO:0001583	missense	5794	exon4			TCAGGGCGATGGA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.406G>T	chr19.hg19:g.55716907C>A	ENSP00000365528:p.Ala136Ser	101.0	0.0		233.0	10.0	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	hg19	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	c	0.017	-1.509536	0.00984	.	.	ENSG00000080031	ENST00000376350	T	0.55413	0.52	4.23	2.09	0.27110	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.265460	0.06178	N	0.678911	T	0.28764	0.0713	N	0.04162	-0.26	0.29679	N	0.841854	B	0.14438	0.01	B	0.10450	0.005	T	0.26780	-1.0093	10	0.08599	T	0.76	.	9.1546	0.36985	0.0:0.1011:0.0:0.8989	.	136	Q9HD43	PTPRH_HUMAN	S	136	ENSP00000365528:A136S	ENSP00000365528:A136S	A	-	1	0	PTPRH	60408719	0.733000	0.28132	0.086000	0.20670	0.000000	0.00434	0.023000	0.13533	0.177000	0.19895	-2.885000	0.00097	GCC	.	C|1.000;T|0.000		0.592	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			A	55716907	C	A	55716907	3	1	101	1	0	0	0	0	1	0	0	0	12818	768	27	1	3009	1	PTPRH	19	55716907	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3437	55716907	3412076	576	14413										
ZNF264	9422	hgsc.bcm.edu	37	chr19	57723451	57723453	+	In_Frame_Del	DEL	GCT	GCT	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agtctttcgacataggccagGctttctccggcactatgttg							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:57723451_57723453delGCT	ENST00000263095.6	+	4	1400_1402	c.986_988delGCT	c.(985-990)ggcttt>gtt	p.329_330GF>V	ZNF264_ENST00000536056.1_In_Frame_Del_p.329_330GF>V	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	329					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	27		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		CATAGGCCAGGCTTTCTCCGGCA	0.488																																					p.329_329del		Atlas-INDEL	.											.	ZNF264	65	.	0			c.985_987del						.																																			SO:0001651	inframe_deletion	9422	exon4			.	AB007872	CCDS33127.1	19q13.4	2013-01-08				ENSG00000083844		"Zinc fingers, C2H2-type", "-"	13057	protein-coding gene	gene with protein product		604668				9455477	Standard	NM_003417		Approved	KIAA0412	uc002qob.3	O43296		ENST00000263095.6:c.986_988delGCT	chr19.hg19:g.57723451_57723453delGCT	ENSP00000263095:p.Gly329_Phe330delinsVal	40.0	0.0		85.0	16.0	NM_003417	A8K8Y9|Q9P1V0	In_Frame_Del	DEL	ENST00000263095.6	hg19	CCDS33127.1																																																																																			.	.		0.488	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1			-	57723453	GCT	-	57723451	7	5	101	1	0	1	0	1	0	0	0	0	17819	1203	42	0	1000	0	ZNF264	19	57723451	In_Frame_Del	DEL	GCT	TCGA-DD-A1EE-01A-11D-A12Z-10	2006544	57723451	1405532	577	14414										
ZNF264	9422	hgsc.bcm.edu	37	chr19	57723567	57723567	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	accagcagactcataccgggGagaagccctatgagtgcagt	12	11	1	3	rs373693955		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:57723567G>T	ENST00000263095.6	+	4	1516	c.1102G>T	c.(1102-1104)Gag>Tag	p.E368*	ZNF264_ENST00000536056.1_Nonsense_Mutation_p.E368*	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	368					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	27		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		TCATACCGGGGAGAAGCCCTA	0.512																																					p.E368X		Atlas-SNP	.											.	ZNF264	65	.	0			c.G1102T						.						78	85	83					19																	57723567		2203	4300	6503	SO:0001587	stop_gained	9422	exon4			ACCGGGGAGAAGC	AB007872	CCDS33127.1	19q13.4	2013-01-08				ENSG00000083844		"Zinc fingers, C2H2-type", "-"	13057	protein-coding gene	gene with protein product		604668				9455477	Standard	NM_003417		Approved	KIAA0412	uc002qob.3	O43296		ENST00000263095.6:c.1102G>T	chr19.hg19:g.57723567G>T	ENSP00000263095:p.Glu368*	73.0	0.0		181.0	24.0	NM_003417	A8K8Y9|Q9P1V0	Nonsense_Mutation	SNP	ENST00000263095.6	hg19	CCDS33127.1	.	.	.	.	.	.	.	.	.	.	G	37	6.267388	0.97426	.	.	ENSG00000083844	ENST00000263095;ENST00000536056	.	.	.	2.35	0.159	0.14968	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	7.162	0.25669	0.2431:0.0:0.7569:0.0	.	.	.	.	X	368	.	ENSP00000263095:E368X	E	+	1	0	ZNF264	62415379	1.000000	0.71417	0.962000	0.40283	0.648000	0.38561	3.351000	0.52232	0.096000	0.17463	0.491000	0.48974	GAG	.	.		0.512	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1			T	57723567	G	T	57723567	4	4	101	1	0	0	0	0	0	1	0	0	17819	1175	41	3	1116	3	ZNF264	19	57723567	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	116	57723567	1405416	578	14415										
ZNF543	125919	hgsc.bcm.edu	37	chr19	57840472	57840472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gaaaggcttttaatcgcggcTcatccctcacacatcatcaa	6	13	4	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr19:57840472T>C	ENST00000321545.4	+	4	1987	c.1642T>C	c.(1642-1644)Tca>Cca	p.S548P		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	548					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TAATCGCGGCTCATCCCTCAC	0.463																																					p.S548P		Atlas-SNP	.											.	ZNF543	61	.	0			c.T1642C						.						96	88	91					19																	57840472		2203	4300	6503	SO:0001583	missense	125919	exon4			CGCGGCTCATCCC	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"Zinc fingers, C2H2-type", "-"	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.1642T>C	chr19.hg19:g.57840472T>C	ENSP00000322545:p.Ser548Pro	71.0	0.0		144.0	6.0	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	hg19	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	T	8.098	0.775921	0.16051	.	.	ENSG00000178229	ENST00000321545	T	0.32988	1.43	2.87	0.481	0.16809	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.50137	0.1598	M	0.79123	2.44	0.09310	N	1	D	0.76494	0.999	D	0.66602	0.945	T	0.36792	-0.9733	9	0.66056	D	0.02	.	8.6472	0.34013	0.0:0.0:0.3628:0.6372	.	548	Q08ER8	ZN543_HUMAN	P	548	ENSP00000322545:S548P	ENSP00000322545:S548P	S	+	1	0	ZNF543	62532284	0.000000	0.05858	0.003000	0.11579	0.016000	0.09150	0.427000	0.21379	-0.088000	0.12506	0.379000	0.24179	TCA	.	.		0.463	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		C	57840472	T	C	57840472	3	2	101	1	0	0	0	0	1	0	0	0	17991	1551	54	2	1656	2	ZNF543	19	57840472	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	116905	57840472	1288511	579	14416										
SIRPD	128646	hgsc.bcm.edu	37	chr20	1532400	1532400	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gatagctcttccttttatgaActtcacgcagtaataggtgc	8	9	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:1532400A>G	ENST00000381623.3	-	2	1547	c.358T>C	c.(358-360)Ttc>Ctc	p.F120L	SIRPD_ENST00000381621.1_Missense_Mutation_p.F120L			Q9H106	SIRPD_HUMAN	signal-regulatory protein delta	120	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)	15						CCTTTTATGAACTTCACGCAG	0.488																																					p.F120L		Atlas-SNP	.											.	SIRPD	34	.	0			c.T358C						.						149	143	145					20																	1532400		2203	4300	6503	SO:0001583	missense	128646	exon2			TTATGAACTTCAC	AL049634	CCDS13018.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000125900	ENSG00000125900		"Signal-regulatory proteins", "Immunoglobulin superfamily / V-set domain containing"	16248	protein-coding gene	gene with protein product			"protein tyrosine phosphatase, non-receptor type substrate 1-like 2"	PTPNS1L2		16339511	Standard	NM_178460		Approved	dJ576H24.4	uc002wfi.3	Q9H106	OTTHUMG00000031674	ENST00000381623.3:c.358T>C	chr20.hg19:g.1532400A>G	ENSP00000371036:p.Phe120Leu	59.0	0.0		161.0	20.0	NM_178460	B3KS88|Q5TFQ6	Missense_Mutation	SNP	ENST00000381623.3	hg19	CCDS13018.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.272461	0.40194	.	.	ENSG00000125900	ENST00000381623;ENST00000381621	T;T	0.64991	-0.13;-0.13	4.02	1.74	0.24563	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.680568	0.12147	N	0.495245	T	0.44973	0.1319	L	0.33753	1.03	0.24203	N	0.995501	P	0.34587	0.458	B	0.29077	0.098	T	0.32188	-0.9916	10	0.59425	D	0.04	.	5.698	0.17867	0.7725:0.0:0.2275:0.0	.	120	Q9H106	SIRPD_HUMAN	L	120	ENSP00000371036:F120L;ENSP00000371034:F120L	ENSP00000371034:F120L	F	-	1	0	SIRPD	1480400	1.000000	0.71417	0.776000	0.31678	0.180000	0.23129	2.564000	0.45931	0.235000	0.21160	-0.394000	0.06481	TTC	.	.		0.488	SIRPD-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077552.1	NM_178460		G	1532400	A	G	1532400	3	3	101	1	0	0	0	0	1	0	0	0	14350	43	2	2	247	2	SIRPD	20	1532400	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10		1532400	61493120	580	14417										
ADRA1D	146	hgsc.bcm.edu	37	chr20	4202228	4202229	+	Missense_Mutation	DNP	GC	GC	TT													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	attcgtaggcctggcaggtgGcgccctcggccacctcgtgt					rs371559421		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:4202228_4202229GC>TT	ENST00000379453.4	-	2	1776_1777	c.1660_1661GC>AA	c.(1660-1662)GCc>AAc	p.A554N		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	554				KPPSAFREWRLLGPFRRPTTQLRAKVSSLSHKIRAGGAQRA EAACAQRSEVEAVSLGVPHEVAEGATCQAYELADYSNLRET DI -> SHPAPSASGGCWGRSGDPRPSCAPKSPACRTRSPP GARSAQRQRAPSAQRWRLCP (in Ref. 1). {ECO:0000305}.	adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			endometrium(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	14					Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	CTGGCAGGTGGCGCCCTCGGCC	0.688																																					p.A554D|p.A554T		Atlas-SNP	.											.	ADRA1D	36	.	0			c.C1661A|c.G1660A						.																																			SO:0001583	missense	146	exon2			CAGGTGGCGCCCT|AGGTGGCGCCCTC	U03864	CCDS13079.1	20p13	2012-08-08	2012-05-09		ENSG00000171873	ENSG00000171873		"GPCR / Class A : Adrenoceptors : alpha"	280	protein-coding gene	gene with protein product		104219	"adrenergic, alpha-1D-, receptor"			8039425	Standard	NM_000678		Approved	ADRA1R, ADRA1A, ADRA1	uc002wkr.2	P25100	OTTHUMG00000031779	ENST00000379453.4:c.1660_1661delinsTT	chr20.hg19:g.4202228_4202229delinsTT	ENSP00000368766:p.Ala554Asn	43.0	0.0		121.0|119.0	18.0|19.0	NM_000678	Q9NPY0	Missense_Mutation	SNP	ENST00000379453.4	hg19	CCDS13079.1																																																																																			.	.		0.688	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678		TT	4202229	GC	TT	4202228	3	4	101	1	0	0	0	0	1	0	0	0	336	1203	42	3	61	3	ADRA1D	20	4202228	Missense_Mutation	DNP	GC	TCGA-DD-A1EE-01A-11D-A12Z-10	2669828	4202228	58823292	581	14418										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9401994	9401994	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaaattggcacctacgtagaGgtggatatgtatgggttgcc	13	6	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:9401994G>T	ENST00000378493.1	+	23	2184	c.2169G>T	c.(2167-2169)gaG>gaT	p.E723D	PLCB4_ENST00000378473.3_Missense_Mutation_p.E735D|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378501.2_Missense_Mutation_p.E723D|PLCB4_ENST00000278655.4_Missense_Mutation_p.E723D|PLCB4_ENST00000334005.3_Missense_Mutation_p.E723D|PLCB4_ENST00000414679.2_Missense_Mutation_p.E735D			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	723	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						CCTACGTAGAGGTGGATATGT	0.418																																					p.E735D		Atlas-SNP	.											.	PLCB4	204	.	0			c.G2205T						.						116	106	109					20																	9401994		2203	4300	6503	SO:0001583	missense	5332	exon26			CGTAGAGGTGGAT		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.2169G>T	chr20.hg19:g.9401994G>T	ENSP00000367754:p.Glu723Asp	60.0	0.0		153.0	14.0	NM_001172646	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	hg19	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.605140	0.66445	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	5.68	2.21	0.28008	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.86301	0.5900	H	0.94658	3.565	0.80722	D	1	D;P;D;D	0.89917	1.0;0.913;0.962;0.983	D;P;D;P	0.91635	0.999;0.549;0.957;0.826	D	0.85773	0.1356	10	0.87932	D	0	.	9.7585	0.40517	0.7336:0.0:0.2664:0.0	.	735;570;723;723	E2QRH8;Q15147-2;Q15147;Q15147-4	.;.;PLCB4_HUMAN;.	D	723;735;723;723;723;571	ENSP00000334105:E723D;ENSP00000367734:E735D;ENSP00000278655:E723D;ENSP00000367754:E723D;ENSP00000367762:E723D;ENSP00000390616:E571D	ENSP00000278655:E723D	E	+	3	2	PLCB4	9349994	1.000000	0.71417	0.998000	0.56505	0.926000	0.56050	1.150000	0.31639	0.119000	0.18210	-0.483000	0.04790	GAG	.	.		0.418	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			T	9401994	G	T	9401994	3	4	101	1	0	0	0	0	1	0	0	0	12039	991	35	3	2299	3	PLCB4	20	9401994	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	5199766	9401994	53623526	582	14419										
KIF16B	55614	hgsc.bcm.edu	37	chr20	16316592	16316592	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tctgcatactttaacttcaaTgttttatgcatttctcgaaa	4	8	3	0	rs370943548		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:16316592T>C	ENST00000354981.2	-	24	3847	c.3690A>G	c.(3688-3690)acA>acG	p.T1230T	KIF16B_ENST00000378003.2_Silent_p.T415T|KIF16B_ENST00000355755.3_Intron	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	1230	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						TTAACTTCAATGTTTTATGCA	0.323																																					p.T1230T		Atlas-SNP	.											.	KIF16B	305	.	0			c.A3690G						.	T	,	1,4405	2.1+/-5.4	0,1,2202	124	113	116		3537,3690	-0.3	1	20		116	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	KIF16B	NM_001199865.1,NM_024704.4	,	0,1,6499	CC,CT,TT		0.0,0.0227,0.0077	,	1179/1267,1230/1318	16316592	1,12999	2203	4297	6500	SO:0001819	synonymous_variant	55614	exon24			CTTCAATGTTTTA	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.3690A>G	chr20.hg19:g.16316592T>C		64.0	0.0		68.0	34.0	NM_024704	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	hg19	CCDS13122.1																																																																																			.	.		0.323	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		C	16316592	T	C	16316592	2	2	101	1	0	0	0	0	0	0	0	1	8287	1451	51	2		2	KIF16B	20	16316592	Silent	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	6914598	16316592	46708928	583	14420										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20056165	20056165	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	taactgtttttgaccaagtgGggaacatcccgtgtctgacg	11	9	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:20056165G>T	ENST00000245957.5	+	6	548	c.472G>T	c.(472-474)Ggg>Tgg	p.G158W	C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000451767.2_Missense_Mutation_p.G158W|C20orf26_ENST00000377306.1_Missense_Mutation_p.G158W	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		158										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		TGACCAAGTGGGGAACATCCC	0.423																																					p.G158W		Atlas-SNP	.											.	C20orf26	188	.	0			c.G472T						.						145	139	141					20																	20056165		2203	4300	6503	SO:0001583	missense	26074	exon6			CAAGTGGGGAACA																												ENST00000245957.5:c.472G>T	chr20.hg19:g.20056165G>T	ENSP00000245957:p.Gly158Trp	77.0	0.0		127.0	9.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	hg19	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.789748	0.70337	.	.	ENSG00000089101	ENST00000340348;ENST00000343997;ENST00000389655;ENST00000245957;ENST00000377306;ENST00000377303;ENST00000451767;ENST00000472660	T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44	5.9	5.9	0.94986	.	0.393691	0.26719	N	0.022852	T	0.51991	0.1707	L	0.53249	1.67	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	1.0;0.97;0.992;1.0	T	0.48433	-0.9036	10	0.72032	D	0.01	.	15.7823	0.78269	0.0:0.0:1.0:0.0	.	158;158;112;158	Q8NHU2-3;F8W6K4;F8W6E2;Q8NHU2	.;.;.;CT026_HUMAN	W	112;158;158;158;158;158;158;54	ENSP00000345553:G112W;ENSP00000245957:G158W;ENSP00000366521:G158W;ENSP00000366518:G158W;ENSP00000414537:G158W;ENSP00000420498:G54W	ENSP00000245957:G158W	G	+	1	0	C20orf26	20004165	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	2.650000	0.46665	2.806000	0.96561	0.655000	0.94253	GGG	.	.		0.423	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			T	20056165	G	T	20056165	3	4	101	1	0	0	0	0	1	0	0	0	2108	1232	43	3	490	3	C20orf26	20	20056165	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3739573	20056165	42969355	584	14421										
GZF1	64412	hgsc.bcm.edu	37	chr20	23345190	23345190	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggcagtgctggctgccaccaGcaagttttttaaggaagtgt	13	8	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:23345190G>A	ENST00000338121.5	+	2	247	c.170G>A	c.(169-171)aGc>aAc	p.S57N	GZF1_ENST00000542987.1_Intron|GZF1_ENST00000544236.1_Intron|GZF1_ENST00000377051.2_Missense_Mutation_p.S57N			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	57	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					GCTGCCACCAGCAAGTTTTTT	0.488																																					p.S57N		Atlas-SNP	.											.	GZF1	61	.	0			c.G170A						.						74	72	73					20																	23345190		2203	4300	6503	SO:0001583	missense	64412	exon1			CCACCAGCAAGTT	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	15808	protein-coding gene	gene with protein product		613842	"zinc finger protein 336"	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.170G>A	chr20.hg19:g.23345190G>A	ENSP00000338290:p.Ser57Asn	57.0	0.0		112.0	15.0	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Missense_Mutation	SNP	ENST00000338121.5	hg19	CCDS13151.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.042489	0.93685	.	.	ENSG00000125812	ENST00000338121;ENST00000377051	D;D	0.85861	-2.04;-2.04	5.33	5.33	0.75918	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.64402	D	0.000001	D	0.94324	0.8176	M	0.92459	3.31	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95447	0.8531	10	0.87932	D	0	.	18.0175	0.89246	0.0:0.0:1.0:0.0	.	57	Q9H116	GZF1_HUMAN	N	57	ENSP00000338290:S57N;ENSP00000366250:S57N	ENSP00000338290:S57N	S	+	2	0	GZF1	23293190	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.790000	0.99075	2.517000	0.84864	0.650000	0.86243	AGC	.	.		0.488	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482		A	23345190	G	A	23345190	3	1	101	1	0	0	0	0	1	0	0	0	6923	971	34	3	172	3	GZF1	20	23345190	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3289025	23345190	39680330	585	14422										
PLUNC	51297	hgsc.bcm.edu	37	chr20	31825552	31825552	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gggcctcattgtcttctacgGgctgttagcccagaccatgg	12	12	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:31825552G>A	ENST00000354297.4	+	2	106	c.35G>A	c.(34-36)gGg>gAg	p.G12E	BPIFA1_ENST00000375422.2_Missense_Mutation_p.G12E|BPIFA1_ENST00000375413.4_Missense_Mutation_p.G12E	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	12					antibacterial humoral response (GO:0019731)|innate immune response (GO:0045087)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|regulation of liquid surface tension (GO:0050828)|regulation of sodium ion transmembrane transport (GO:1902305)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)										GTCTTCTACGGGCTGTTAGCC	0.542																																					p.G12E		Atlas-SNP	.											.	.	.	.	0			c.G35A						.						78	77	78					20																	31825552		2203	4300	6503	SO:0001583	missense	51297	exon2			TCTACGGGCTGTT	AB024937	CCDS13217.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000198183	ENSG00000198183		"BPI fold containing"	15749	protein-coding gene	gene with protein product		607412	"palate, lung and nasal epithelium carcinoma associated", "palate, lung and nasal epithelium associated"	PLUNC		11018263, 11251963, 21787333	Standard	NM_130852		Approved	LUNX, bA49G10.5, SPLUNC1	uc002wyv.3	Q9NP55	OTTHUMG00000032243	ENST00000354297.4:c.35G>A	chr20.hg19:g.31825552G>A	ENSP00000346251:p.Gly12Glu	63.0	0.0		88.0	34.0	NM_016583	A8K9R3|E1P5M9|Q9NZT0	Missense_Mutation	SNP	ENST00000354297.4	hg19	CCDS13217.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.484662	0.44147	.	.	ENSG00000198183	ENST00000375422;ENST00000354297;ENST00000375413;ENST00000544328	T;T;T	0.52057	0.68;0.68;0.68	5.26	4.31	0.51392	.	0.200224	0.35739	N	0.003020	T	0.47783	0.1464	M	0.78801	2.425	0.31295	N	0.689001	P	0.37663	0.604	B	0.35899	0.213	T	0.62882	-0.6760	10	0.87932	D	0	-8.0239	10.1231	0.42632	0.0905:0.0:0.9095:0.0	.	12	Q9NP55	BPIA1_HUMAN	E	12	ENSP00000364571:G12E;ENSP00000346251:G12E;ENSP00000364562:G12E	ENSP00000346251:G12E	G	+	2	0	BPIFA1	31289213	1.000000	0.71417	0.998000	0.56505	0.055000	0.15305	2.710000	0.47169	1.598000	0.50083	-0.150000	0.13652	GGG	.	.		0.542	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		A	31825552	G	A	31825552	3	1	101	1	0	0	0	0	1	0	0	0	12124	1232	43	3	37	3	PLUNC	20	31825552	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	8480362	31825552	31199968	586	14423										
TRPC4AP	26133	hgsc.bcm.edu	37	chr20	33598060	33598060	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gatggcactgagttcattcaGctcctggttgttgagtaaca	11	8	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:33598060G>C	ENST00000252015.2	-	12	1530	c.1441C>G	c.(1441-1443)Ctg>Gtg	p.L481V	TRPC4AP_ENST00000432634.2_Missense_Mutation_p.L442V|TRPC4AP_ENST00000539834.1_Missense_Mutation_p.L83V|TRPC4AP_ENST00000451813.2_Missense_Mutation_p.L473V			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	481					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			AGTTCATTCAGCTCCTGGTTG	0.532																																					p.L481V		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.C1441G						.						234	162	186					20																	33598060		2203	4300	6503	SO:0001583	missense	26133	exon12			CATTCAGCTCCTG	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.1441C>G	chr20.hg19:g.33598060G>C	ENSP00000252015:p.Leu481Val	102.0	0.0		241.0	22.0	NM_015638	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	hg19	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.155652	0.57259	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000539834;ENST00000432634;ENST00000541994	.	.	.	5.67	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.62539	0.2436	M	0.62723	1.935	0.53688	D	0.999975	B;B;B	0.29481	0.245;0.201;0.201	B;B;B	0.35182	0.197;0.138;0.138	T	0.63497	-0.6624	9	0.52906	T	0.07	.	12.8124	0.57647	0.0758:0.0:0.9242:0.0	.	442;473;481	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	V	481;473;83;442;466	.	ENSP00000252015:L481V	L	-	1	2	TRPC4AP	33061721	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.846000	0.62860	1.399000	0.46721	0.555000	0.69702	CTG	.	.		0.532	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		C	33598060	G	C	33598060	3	2	101	1	0	0	0	0	1	0	0	0	16596	962	34	4	984	4	TRPC4AP	20	33598060	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1772508	33598060	29427460	587	14424										
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37154091	37154091	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtaaatccaacagaattgcGaagatcctccattaatatcc	5	10	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:37154091G>C	ENST00000262879.6	+	12	2116	c.1832G>C	c.(1831-1833)cGa>cCa	p.R611P	RALGAPB_ENST00000397040.1_Missense_Mutation_p.R611P|RALGAPB_ENST00000397038.1_Missense_Mutation_p.R389P|RALGAPB_ENST00000397042.3_Missense_Mutation_p.R611P			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	611					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.R611P(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						ACAGAATTGCGAAGATCCTCC	0.328																																					p.R611P		Atlas-SNP	.											RALGAPB,NS,carcinoma,0,1	RALGAPB	134	.	1	Substitution - Missense(1)	lung(1)	c.G1832C						.						133	136	135					20																	37154091		2203	4300	6503	SO:0001583	missense	57148	exon12			AATTGCGAAGATC	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"KIAA1219"	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.1832G>C	chr20.hg19:g.37154091G>C	ENSP00000262879:p.Arg611Pro	140.0	0.0		380.0	16.0	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	hg19	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	G	32	5.164602	0.94727	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000397038;ENST00000397040;ENST00000438490	T;T	0.73363	-0.74;-0.74	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.86138	0.5861	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;0.998	D;D;D;D	0.87578	0.998;0.991;0.997;0.991	D	0.86502	0.1804	10	0.87932	D	0	.	20.0308	0.97536	0.0:0.0:1.0:0.0	.	439;611;611;611	A2A2F0;Q86X10-4;A2A2E9;Q86X10	.;.;.;RLGPB_HUMAN	P	611;611;611;389;611;439	ENSP00000262879:R611P;ENSP00000380233:R611P	ENSP00000262879:R611P	R	+	2	0	RALGAPB	36587505	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.476000	0.97823	2.732000	0.93576	0.585000	0.79938	CGA	.	.		0.328	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		C	37154091	G	C	37154091	3	2	101	1	0	0	0	0	1	0	0	0	13030	1058	37	4	1874	4	RALGAPB	20	37154091	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3556031	37154091	25871429	588	14425										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39792450	39792451	+	Frame_Shift_Ins	INS	-	-	T													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acaaccctctttcccactacINStggatctcctcctcgcacaa							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:39792450_39792451insT	ENST00000373271.1	+	10	1392_1393	c.987_988insT	c.(988-990)tggfs	p.W330fs	PLCG1_ENST00000373272.2_Frame_Shift_Ins_p.W330fs|PLCG1_ENST00000244007.3_Frame_Shift_Ins_p.W330fs	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	330	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				TTTCCCACTACTGGATCTCCTC	0.559																																					p.Y329fs		Atlas-Indel,Pindel	.											.	PLCG1	111	.	0			c.987_988insT						.																																			SO:0001589	frameshift_variant	5335	exon10			.	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.988dupT	chr20.hg19:g.39792451_39792451dupT	ENSP00000362368:p.Trp330fs	63.0	0.0		187.0	22.0	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Frame_Shift_Ins	INS	ENST00000373271.1	hg19	CCDS13314.1																																																																																			.	.		0.559	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		T	39792451	-	T	39792450	7	5	101	1	0	1	1	0	0	0	0	0	12044	576	20	0	1025	0	PLCG1	20	39792450	Frame_Shift_Ins	INS	-	TCGA-DD-A1EE-01A-11D-A12Z-10	2638359	39792450	23233070	589	14426										
ELMO2	63916	hgsc.bcm.edu	37	chr20	45004003	45004003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagttcaaatatgatgtcccTttgagcctgcgaggtgaaac	10	9	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:45004003T>C	ENST00000290246.6	-	13	1131	c.937A>G	c.(937-939)Agg>Ggg	p.R313G	ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000396391.1_Missense_Mutation_p.R313G|ELMO2_ENST00000352077.2_Missense_Mutation_p.R311G|ELMO2_ENST00000454865.2_Missense_Mutation_p.R45G|ELMO2_ENST00000445496.2_Missense_Mutation_p.R130G|ELMO2_ENST00000372176.1_Missense_Mutation_p.R225G|ELMO2_ENST00000439931.2_Missense_Mutation_p.R325G	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	313	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				ATGATGTCCCTTTGAGCCTGC	0.502																																					p.R313G		Atlas-SNP	.											.	ELMO2	51	.	0			c.A937G						.						112	78	90					20																	45004003		2203	4300	6503	SO:0001583	missense	63916	exon12			TGTCCCTTTGAGC	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"Engulfment and cell motility proteins"	17233	protein-coding gene	gene with protein product		606421	"engulfment and cell motility 2 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.937A>G	chr20.hg19:g.45004003T>C	ENSP00000290246:p.Arg313Gly	71.0	0.0		172.0	15.0	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Missense_Mutation	SNP	ENST00000290246.6	hg19	CCDS13398.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.756808	0.69648	.	.	ENSG00000062598	ENST00000290246;ENST00000372176;ENST00000396391;ENST00000439931;ENST00000445496;ENST00000454865;ENST00000352077;ENST00000425546;ENST00000450812	T;T;T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.73	4.81	3.67	0.42095	Terpene synthase-like (1);Engulfment/cell motility, ELMO (2);	0.000000	0.85682	D	0.000000	T	0.53642	0.1809	M	0.62723	1.935	0.80722	D	1	P;D;D;D;P	0.67145	0.785;0.996;0.985;0.974;0.943	P;D;P;P;P	0.72625	0.636;0.978;0.83;0.908;0.867	T	0.54214	-0.8327	10	0.66056	D	0.02	-14.8006	10.8249	0.46627	0.0:0.0:0.1588:0.8412	.	325;45;313;130;313	B4DRL5;B4DZ20;E9PBG2;B7Z1S8;Q96JJ3	.;.;.;.;ELMO2_HUMAN	G	313;225;313;325;130;45;311;101;313	ENSP00000290246:R313G;ENSP00000361249:R225G;ENSP00000379673:R313G;ENSP00000396519:R325G;ENSP00000409920:R130G;ENSP00000415641:R45G;ENSP00000326172:R311G;ENSP00000388962:R101G;ENSP00000416181:R313G	ENSP00000290246:R313G	R	-	1	2	ELMO2	44437410	1.000000	0.71417	0.995000	0.50966	0.776000	0.43924	4.964000	0.63701	0.828000	0.34709	0.454000	0.30748	AGG	.	.		0.502	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086		C	45004003	T	C	45004003	3	2	101	1	0	0	0	0	1	0	0	0	5068	1608	56	2	1265	2	ELMO2	20	45004003	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	5211553	45004003	18021517	590	14427										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50346419	50346419	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acttctgattgttgatgacaTtccgaggatacctctggtct	9	9	3	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:50346419T>A	ENST00000338821.5	-	2	431	c.167A>T	c.(166-168)aAt>aTt	p.N56I	ATP9A_ENST00000402822.1_Missense_Mutation_p.N56I|ATP9A_ENST00000477492.1_5'UTR|ATP9A_ENST00000311637.5_Missense_Mutation_p.N41I	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	56					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GTTGATGACATTCCGAGGATA	0.547																																					p.N56I		Atlas-SNP	.											.	ATP9A	135	.	0			c.A167T						.						155	133	140					20																	50346419		2203	4300	6503	SO:0001583	missense	10079	exon2			ATGACATTCCGAG	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.167A>T	chr20.hg19:g.50346419T>A	ENSP00000342481:p.Asn56Ile	55.0	0.0		134.0	12.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	hg19	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.980823	0.92982	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	D;D;D	0.98762	-5.12;-5.12;-5.12	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.98855	0.9613	M	0.85041	2.73	0.33794	D	0.625851	B;P	0.49862	0.054;0.929	B;P	0.54815	0.055;0.761	D	0.99978	1.2344	10	0.87932	D	0	-20.706	15.4675	0.75412	0.0:0.0:0.0:1.0	.	56;56	O75110-2;O75110	.;ATP9A_HUMAN	I	41;56;56	ENSP00000309086:N41I;ENSP00000342481:N56I;ENSP00000385875:N56I	ENSP00000309086:N41I	N	-	2	0	ATP9A	49779826	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.461000	0.80834	2.107000	0.64212	0.460000	0.39030	AAT	.	.		0.547	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		A	50346419	T	A	50346419	3	1	101	1	0	0	0	0	1	0	0	0	1198	1493	52	4	3084	4	ATP9A	20	50346419	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	5342416	50346419	12679101	591	14428										
BMP7	655	hgsc.bcm.edu	37	chr20	55840845	55840845	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagaggggggccctgggtacTgaagacggccttgtaggggt	19	8	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:55840845T>A	ENST00000395863.3	-	1	839	c.334A>T	c.(334-336)Agt>Tgt	p.S112C	RP4-813D12.3_ENST00000412321.1_lincRNA|BMP7_ENST00000395864.3_Missense_Mutation_p.S112C|BMP7_ENST00000450594.2_Missense_Mutation_p.S112C	NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	112					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of an epithelial tube (GO:0048754)|cartilage development (GO:0051216)|cellular response to hypoxia (GO:0071456)|dendrite development (GO:0016358)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint morphogenesis (GO:0060272)|epithelial cell differentiation (GO:0030855)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|mesenchymal cell differentiation (GO:0048762)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|mesonephros development (GO:0001823)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephros development (GO:0001656)|monocyte aggregation (GO:0070487)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis (GO:0072040)|negative regulation of mitosis (GO:0045839)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of dendrite development (GO:1900006)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of removal of superoxide radicals (GO:2000121)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|steroid hormone mediated signaling pathway (GO:0043401)|ureteric bud development (GO:0001657)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	heparin binding (GO:0008201)			endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			CCCTGGGTACTGAAGACGGCC	0.647																																					p.S112C		Atlas-SNP	.											.	BMP7	60	.	0			c.A334T						.						24	24	24					20																	55840845		2202	4299	6501	SO:0001583	missense	655	exon1			GGGTACTGAAGAC		CCDS13455.1	20q13	2014-01-30	2008-05-22		ENSG00000101144	ENSG00000101144		"Bone morphogenetic proteins", "Endogenous ligands"	1074	protein-coding gene	gene with protein product	"osteogenic protein 1"	112267				1427904	Standard	NM_001719		Approved	OP-1	uc010gip.1	P18075	OTTHUMG00000032812	ENST00000395863.3:c.334A>T	chr20.hg19:g.55840845T>A	ENSP00000379204:p.Ser112Cys	52.0	0.0		112.0	16.0	NM_001719	Q9H512|Q9NTQ7	Missense_Mutation	SNP	ENST00000395863.3	hg19	CCDS13455.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.595492	0.46318	.	.	ENSG00000101144	ENST00000395863;ENST00000395864;ENST00000450594	T;T;T	0.68479	-0.33;-0.33;-0.33	5.04	5.04	0.67666	Transforming growth factor-beta, N-terminal (1);	0.090404	0.85682	D	0.000000	T	0.69958	0.3169	L	0.49126	1.545	0.38758	D	0.954257	D;B;B	0.54601	0.967;0.21;0.049	P;B;B	0.51055	0.657;0.057;0.051	T	0.76321	-0.3002	10	0.72032	D	0.01	.	14.7775	0.69740	0.0:0.0:0.0:1.0	.	112;112;112	B1AKZ9;P18075;B1AL00	.;BMP7_HUMAN;.	C	112	ENSP00000379204:S112C;ENSP00000379205:S112C;ENSP00000398687:S112C	ENSP00000379204:S112C	S	-	1	0	BMP7	55274252	1.000000	0.71417	0.996000	0.52242	0.978000	0.69477	2.865000	0.48412	1.873000	0.54277	0.402000	0.26972	AGT	.	.		0.647	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079831.2			A	55840845	T	A	55840845	3	1	101	1	0	0	0	0	1	0	0	0	1465	1580	55	4	989	4	BMP7	20	55840845	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	5494426	55840845	7184675	592	14429										
STX16	8675	hgsc.bcm.edu	37	chr20	57246217	57246217	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	actgtcttgctagggttttaCagaggaccagttagttctgg	12	7	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:57246217C>A	ENST00000371141.4	+	7	1380	c.656C>A	c.(655-657)aCa>aAa	p.T219K	STX16-NPEPL1_ENST00000530122.1_Missense_Mutation_p.T219K|STX16_ENST00000355957.5_Missense_Mutation_p.T202K|STX16_ENST00000358029.4_Missense_Mutation_p.T215K|STX16_ENST00000371132.4_Missense_Mutation_p.T198K|STX16_ENST00000361830.3_Missense_Mutation_p.T219K|STX16_ENST00000361770.5_Missense_Mutation_p.T202K|STX16_ENST00000359617.4_Missense_Mutation_p.T166K|STX16_ENST00000496003.1_Intron	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	219					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			TAGGGTTTTACAGAGGACCAG	0.418																																					p.T219K		Atlas-SNP	.											.	STX16	36	.	0			c.C656A						.						100	96	98					20																	57246217		2203	4300	6503	SO:0001583	missense	8675	exon7			GTTTTACAGAGGA	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.656C>A	chr20.hg19:g.57246217C>A	ENSP00000360183:p.Thr219Lys	55.0	0.0		125.0	6.0	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Missense_Mutation	SNP	ENST00000371141.4	hg19	CCDS13468.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.254460	0.80135	.	.	ENSG00000124222	ENST00000355957;ENST00000361770;ENST00000312283;ENST00000359617;ENST00000371141;ENST00000371138;ENST00000371132;ENST00000358029;ENST00000361830;ENST00000435446	T;T;T;T;T;T;T;T	0.42900	1.96;1.96;0.96;1.96;1.96;1.96;1.96;1.96	5.69	5.69	0.88448	t-SNARE (1);	0.000000	0.85682	U	0.000000	T	0.61986	0.2391	M	0.74881	2.28	0.80722	D	1	D;P;P;P	0.58970	0.984;0.929;0.894;0.76	P;P;P;B	0.59221	0.854;0.614;0.517;0.443	T	0.58662	-0.7597	10	0.34782	T	0.22	.	18.8116	0.92059	0.0:1.0:0.0:0.0	.	215;202;198;219	Q6GMS8;O14662-4;O14662-2;O14662	.;.;.;STX16_HUMAN	K	202;202;166;166;219;166;198;215;219;33	ENSP00000348229:T202K;ENSP00000355408:T202K;ENSP00000312086:T166K;ENSP00000352634:T166K;ENSP00000360183:T219K;ENSP00000360173:T198K;ENSP00000350723:T215K;ENSP00000354445:T219K	ENSP00000360180:T166K	T	+	2	0	STX16	56679623	1.000000	0.71417	0.248000	0.24265	0.477000	0.33069	7.487000	0.81328	2.674000	0.91012	0.650000	0.86243	ACA	.	.		0.418	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433		A	57246217	C	A	57246217	3	1	101	1	0	0	0	0	1	0	0	0	15354	478	17	3	682	3	STX16	20	57246217	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1405372	57246217	5779303	593	14430										
CDH26	60437	hgsc.bcm.edu	37	chr20	58560154	58560154	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtggatgtgcaagaaggcaaCaaccacaggcctgcatttac	11	10	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:58560154C>A	ENST00000244047.5	+	7	1118	c.807C>A	c.(805-807)aaC>aaA	p.N269K	CDH26_ENST00000348616.4_Missense_Mutation_p.N269K			Q8IXH8	CAD26_HUMAN	cadherin 26	269	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			AAGAAGGCAACAACCACAGGC	0.557																																					p.N269K		Atlas-SNP	.											.	CDH26	229	.	0			c.C807A						.						60	53	55					20																	58560154		2203	4300	6503	SO:0001583	missense	60437	exon7			AGGCAACAACCAC	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"Cadherins / Major cadherins"	15902	protein-coding gene	gene with protein product			"cadherin-like 26"				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.807C>A	chr20.hg19:g.58560154C>A	ENSP00000244047:p.Asn269Lys	16.0	0.0		68.0	9.0	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	hg19		.	.	.	.	.	.	.	.	.	.	C	11.55	1.672713	0.29693	.	.	ENSG00000124215	ENST00000244047;ENST00000348616	T;T	0.75477	-0.94;-0.94	4.44	2.46	0.29980	.	0.103168	0.64402	D	0.000005	D	0.89269	0.6667	H	0.98005	4.125	0.23572	N	0.997382	D	0.89917	1.0	D	0.97110	1.0	T	0.80365	-0.1413	10	0.87932	D	0	.	7.0596	0.25119	0.0:0.7294:0.1739:0.0967	.	269	Q8IXH8-4	.	K	269	ENSP00000244047:N269K;ENSP00000339390:N269K	ENSP00000244047:N269K	N	+	3	2	CDH26	57993549	1.000000	0.71417	0.004000	0.12327	0.035000	0.12851	1.796000	0.38794	0.316000	0.23135	0.591000	0.81541	AAC	.	.		0.557	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980		A	58560154	C	A	58560154	3	1	101	1	0	0	0	0	1	0	0	0	3112	477	17	3	833	3	CDH26	20	58560154	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1313937	58560154	4465366	594	14431										
YTHDF1	54915	hgsc.bcm.edu	37	chr20	61835099	61835099	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	attgagggagtaaggaaatcCaatggacggcgggtaatagc	15	5	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:61835099C>G	ENST00000370339.3	-	4	534	c.193G>C	c.(193-195)Gga>Cga	p.G65R	YTHDF1_ENST00000370334.4_Intron|YTHDF1_ENST00000370333.4_Missense_Mutation_p.G15R	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	65							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						TAAGGAAATCCAATGGACGGC	0.522																																					p.G65R		Atlas-SNP	.											.	YTHDF1	66	.	0			c.G193C						.						80	88	85					20																	61835099		2203	4300	6503	SO:0001583	missense	54915	exon4			GAAATCCAATGGA	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"YTH domain family 1"	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.193G>C	chr20.hg19:g.61835099C>G	ENSP00000359364:p.Gly65Arg	32.0	0.0		84.0	26.0	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Missense_Mutation	SNP	ENST00000370339.3	hg19	CCDS13511.1	.	.	.	.	.	.	.	.	.	.	C	18.50	3.637695	0.67130	.	.	ENSG00000149658	ENST00000370339;ENST00000370333	T;T	0.58940	0.3;0.3	5.24	5.24	0.73138	.	0.049657	0.85682	D	0.000000	T	0.68833	0.3044	M	0.68317	2.08	0.80722	D	1	D	0.55385	0.971	P	0.57468	0.821	T	0.71234	-0.4653	10	0.56958	D	0.05	-8.2765	13.1667	0.59575	0.0:0.9237:0.0:0.0763	.	65	Q9BYJ9	YTHD1_HUMAN	R	65;15	ENSP00000359364:G65R;ENSP00000359358:G15R	ENSP00000359358:G15R	G	-	1	0	YTHDF1	61305544	1.000000	0.71417	0.991000	0.47740	0.945000	0.59286	4.873000	0.63057	2.448000	0.82819	0.561000	0.74099	GGA	.	.		0.522	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798		G	61835099	C	G	61835099	3	3	101	1	0	0	0	0	1	0	0	0	17513	603	21	4	1494	4	YTHDF1	20	61835099	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	3274945	61835099	1190421	595	14432										
COL20A1	57642	hgsc.bcm.edu	37	chr20	61938948	61938948	+	Frame_Shift_Del	DEL	C	C	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttccagcaggtcaaggacttCctggccagtgtcatcgcacc							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:61938948delC	ENST00000358894.6	+	6	703	c.603delC	c.(601-603)ttcfs	p.F201fs	COL20A1_ENST00000422202.1_Frame_Shift_Del_p.F208fs|COL20A1_ENST00000326996.6_Frame_Shift_Del_p.F201fs|COL20A1_ENST00000435874.1_Frame_Shift_Del_p.F208fs	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	201	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					TCAAGGACTTCCTGGCCAGTG	0.657																																					p.F201fs		Atlas-Indel,Pindel	.											.	COL20A1	137	.	0			c.602delT						.			1,3941		0,1,1970	43	49	47			3.9	1	20		47	3,8037		1,1,4018	no	frameshift	COL20A1	NM_020882.2		1,2,5988	A1A1,A1R,RR		0.0373,0.0254,0.0334			61938948	4,11978	2055	4193	6248	SO:0001589	frameshift_variant	57642	exon6			.	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.603delC	chr20.hg19:g.61938948delC	ENSP00000351767:p.Phe201fs	31.0	0.0		62.0	24.0	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Frame_Shift_Del	DEL	ENST00000358894.6	hg19	CCDS46628.1																																																																																			.	.		0.657	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		-	61938948	C	-	61938948	7	5	101	1	0	1	0	1	0	0	0	0	3681	854	30	0	621	0	COL20A1	20	61938948	Frame_Shift_Del	DEL	C	TCGA-DD-A1EE-01A-11D-A12Z-10	103849	61938948	1086572	596	14433										
NPBWR2	2832	hgsc.bcm.edu	37	chr20	62737266	62737266	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggggttcaggcacgagttggCgtagctgaggctggtgatga	19	6	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr20:62737266C>T	ENST00000369768.1	-	1	1258	c.919G>A	c.(919-921)Gcc>Acc	p.A307T		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	307					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					CACGAGTTGGCGTAGCTGAGG	0.597																																					p.A307T		Atlas-SNP	.											.	NPBWR2	36	.	0			c.G919A						.						197	132	154					20																	62737266		2202	4298	6500	SO:0001583	missense	2832	exon1			AGTTGGCGTAGCT	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"GPCR / Class A : Neuropeptide receptors : W/B"	4530	protein-coding gene	gene with protein product		600731	"G protein-coupled receptor 8"	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.919G>A	chr20.hg19:g.62737266C>T	ENSP00000358783:p.Ala307Thr	31.0	0.0		89.0	11.0	NM_005286	Q6NWQ6|Q9H4K3	Missense_Mutation	SNP	ENST00000369768.1	hg19	CCDS13557.1	.	.	.	.	.	.	.	.	.	.	C	6.535	0.467050	0.12402	.	.	ENSG00000125522	ENST00000369768	T	0.37915	1.17	3.43	0.189	0.15119	GPCR, rhodopsin-like superfamily (1);	0.224693	0.35262	N	0.003338	T	0.19525	0.0469	L	0.33137	0.985	0.39667	D	0.970707	B	0.29766	0.256	B	0.26310	0.068	T	0.18366	-1.0339	10	0.06236	T	0.91	.	9.5523	0.39317	0.0:0.7615:0.0:0.2385	.	307	P48146	NPBW2_HUMAN	T	307	ENSP00000358783:A307T	ENSP00000358783:A307T	A	-	1	0	NPBWR2	62207710	0.975000	0.34042	0.272000	0.24630	0.688000	0.40055	1.370000	0.34238	0.104000	0.17725	0.491000	0.48974	GCC	.	.		0.597	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286		T	62737266	C	T	62737266	3	4	101	1	0	0	0	0	1	0	0	0	10578	768	27	1	85	1	NPBWR2	20	62737266	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	798318	62737266	288254	597	14434										
KRTAP13-2	337959	hgsc.bcm.edu	37	chr21	31744410	31744410	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gctggcaggtgctgggagagCagaggtcagtgctgtagacc	18	8	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr21:31744410C>A	ENST00000399889.2	-	1	147	c.122G>T	c.(121-123)tGc>tTc	p.C41F		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	41						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						GCTGGGAGAGCAGAGGTCAGT	0.597																																					p.C41F		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.G122T						.						86	82	83					21																	31744410		2203	4300	6503	SO:0001583	missense	337959	exon1			GGAGAGCAGAGGT	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"Keratin associated proteins"	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.122G>T	chr21.hg19:g.31744410C>A	ENSP00000382777:p.Cys41Phe	73.0	0.0		158.0	10.0	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	hg19	CCDS13589.1	.	.	.	.	.	.	.	.	.	.	C	13.25	2.181048	0.38511	.	.	ENSG00000182816	ENST00000399889	T	0.04454	3.62	4.51	2.16	0.27623	.	1.394900	0.05165	N	0.498547	T	0.16428	0.0395	M	0.72118	2.19	0.09310	N	1	P	0.48911	0.917	P	0.56700	0.804	T	0.14117	-1.0484	10	0.72032	D	0.01	.	7.6607	0.28402	0.0:0.816:0.0:0.184	.	41	Q52LG2	KR132_HUMAN	F	41	ENSP00000382777:C41F	ENSP00000382777:C41F	C	-	2	0	KRTAP13-2	30666281	0.000000	0.05858	0.001000	0.08648	0.979000	0.70002	-0.339000	0.07832	0.305000	0.22832	0.655000	0.94253	TGC	.	.		0.597	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1			A	31744410	C	A	31744410	3	1	101	1	0	0	0	0	1	0	0	0	8532	710	25	3	409	3	KRTAP13-2	21	31744410	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10		31744410	16385485	598	14435										
KRTAP22-1	337979	hgsc.bcm.edu	37	chr21	31973499	31973499	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gccaaaggaggcctgggctgCagctatggctgtggtcttag	16	9	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr21:31973499C>A	ENST00000334680.2	+	1	86	c.60C>A	c.(58-60)tgC>tgA	p.C20*	KRTAP6-2_ENST00000334897.3_5'Flank	NM_181620.1	NP_853651.1	Q3MIV0	KR221_HUMAN	keratin associated protein 22-1	20						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	8						GCCTGGGCTGCAGCTATGGCT	0.483																																					p.C20X		Atlas-SNP	.											.	KRTAP22-1	16	.	0			c.C60A						.						183	168	173					21																	31973499		2203	4300	6503	SO:0001587	stop_gained	337979	exon1			GGGCTGCAGCTAT	AP001708	CCDS13601.1	21q22.1	2011-02-10			ENSG00000186924	ENSG00000186924		"Keratin associated proteins"	18947	protein-coding gene	gene with protein product						12359730	Standard	NM_181620		Approved	KAP22.1	uc011add.2	Q3MIV0	OTTHUMG00000057778	ENST00000334680.2:c.60C>A	chr21.hg19:g.31973499C>A	ENSP00000333887:p.Cys20*	97.0	0.0		184.0	60.0	NM_181620		Nonsense_Mutation	SNP	ENST00000334680.2	hg19	CCDS13601.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.498753	0.44455	.	.	ENSG00000186924	ENST00000334680	.	.	.	4.8	3.65	0.41850	.	0.867451	0.09695	N	0.767763	.	.	.	.	.	.	0.30745	N	0.745793	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.7665	0.23571	0.0:0.1091:0.0:0.8909	.	.	.	.	X	20	.	ENSP00000333887:C20X	C	+	3	2	KRTAP22-1	30895370	0.041000	0.20044	0.019000	0.16419	0.035000	0.12851	0.244000	0.18124	0.973000	0.38340	-0.373000	0.07131	TGC	.	.		0.483	KRTAP22-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128230.2			A	31973499	C	A	31973499	4	1	101	1	0	0	0	0	0	1	0	0	8549	718	25	3	62	3	KRTAP22-1	21	31973499	Nonsense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	229089	31973499	16156396	599	14436										
HUNK	30811	hgsc.bcm.edu	37	chr21	33296847	33296847	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgtcaccaaaaacctgcggcGagagggtcagatccagcaga	12	11	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr21:33296847G>A	ENST00000270112.2	+	2	689	c.329G>A	c.(328-330)cGa>cAa	p.R110Q		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	110	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						AACCTGCGGCGAGAGGGTCAG	0.463																																					p.R110Q		Atlas-SNP	.											.	HUNK	74	.	0			c.G329A						.						58	54	55					21																	33296847		2203	4300	6503	SO:0001583	missense	30811	exon2			TGCGGCGAGAGGG	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"hormonally upregulated Neu-associated kinase"			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.329G>A	chr21.hg19:g.33296847G>A	ENSP00000270112:p.Arg110Gln	52.0	0.0		134.0	19.0	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	hg19	CCDS13610.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573179	0.86542	.	.	ENSG00000142149	ENST00000270112	T	0.27890	1.64	4.86	4.86	0.63082	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.067411	0.64402	D	0.000017	T	0.52773	0.1755	L	0.55017	1.72	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.55496	-0.8132	10	0.87932	D	0	-5.5714	18.1961	0.89822	0.0:0.0:1.0:0.0	.	110	P57058	HUNK_HUMAN	Q	110	ENSP00000270112:R110Q	ENSP00000270112:R110Q	R	+	2	0	HUNK	32218718	1.000000	0.71417	0.996000	0.52242	0.534000	0.34807	9.205000	0.95048	2.513000	0.84729	0.650000	0.86243	CGA	.	.		0.463	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		A	33296847	G	A	33296847	3	1	101	1	0	0	0	0	1	0	0	0	7467	1058	37	1	335	1	HUNK	21	33296847	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1323348	33296847	14833048	600	14437										
SON	6651	hgsc.bcm.edu	37	chr21	34925206	34925206	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caaagtgagatttcggagccTtcagcagtgcctactgatta	10	9	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr21:34925206T>A	ENST00000356577.4	+	3	4144	c.3669T>A	c.(3667-3669)ccT>ccA	p.P1223P	SON_ENST00000290239.6_Silent_p.P1223P|SON_ENST00000300278.4_Silent_p.P1223P|SON_ENST00000381679.4_Silent_p.P1223P|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1223					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						TTTCGGAGCCTTCAGCAGTGC	0.493																																					p.P1223P		Atlas-SNP	.											.	SON	343	.	0			c.T3669A						.						153	156	155					21																	34925206		2203	4300	6503	SO:0001819	synonymous_variant	6651	exon3			GGAGCCTTCAGCA	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.3669T>A	chr21.hg19:g.34925206T>A		88.0	0.0		164.0	69.0	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	hg19	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	5.392	0.257602	0.10239	.	.	ENSG00000159140	ENST00000436227	.	.	.	5.42	4.25	0.50352	.	.	.	.	.	T	0.55016	0.1894	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51044	-0.8755	4	.	.	.	.	5.6107	0.17404	0.0:0.0869:0.1746:0.7385	.	.	.	.	H	218	.	.	L	+	2	0	SON	33847076	0.879000	0.30193	0.882000	0.34594	0.509000	0.34042	1.139000	0.31504	0.875000	0.35847	0.460000	0.39030	CTT	.	.		0.493	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		A	34925206	T	A	34925206	2	1	101	1	0	0	0	0	0	0	0	1	14941	1596	56	4		4	SON	21	34925206	Silent	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	1628359	34925206	13204689	601	14438										
TTC3	7267	hgsc.bcm.edu	37	chr21	38538901	38538901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aacaaacattccacacgtgcAgatggttgccatacaggtaa	8	10	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr21:38538901A>G	ENST00000399017.2	+	33	7132	c.4385A>G	c.(4384-4386)cAg>cGg	p.Q1462R	TTC3_ENST00000355666.1_Missense_Mutation_p.Q1462R|TTC3_ENST00000354749.2_Missense_Mutation_p.Q1462R|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1462					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				CCACACGTGCAGATGGTTGCC	0.348																																					p.Q1462R	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A4385G						.						40	38	38					21																	38538901		2203	4300	6503	SO:0001583	missense	7267	exon33			ACGTGCAGATGGT	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.4385A>G	chr21.hg19:g.38538901A>G	ENSP00000381981:p.Gln1462Arg	85.0	0.0		228.0	22.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	A	3.781	-0.045728	0.07452	.	.	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.07800	3.16;3.16;3.16	4.96	2.15	0.27550	.	0.452951	0.20187	N	0.097386	T	0.04092	0.0114	L	0.31065	0.9	0.09310	N	0.999997	B;P	0.35433	0.201;0.501	B;B	0.25140	0.032;0.058	T	0.36915	-0.9728	9	.	.	.	-3.6352	2.6852	0.05105	0.5413:0.2717:0.187:0.0	.	520;1462	Q5GIT6;P53804	.;TTC3_HUMAN	R	1462	ENSP00000347889:Q1462R;ENSP00000381981:Q1462R;ENSP00000346791:Q1462R	.	Q	+	2	0	TTC3	37460771	0.002000	0.14202	0.010000	0.14722	0.142000	0.21351	1.121000	0.31283	0.796000	0.33947	0.460000	0.39030	CAG	.	.		0.348	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			G	38538901	A	G	38538901	3	3	101	1	0	0	0	0	1	0	0	0	16712	188	7	2	4511	2	TTC3	21	38538901	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	3613695	38538901	9590994	602	14439										
RRP1B	23076	hgsc.bcm.edu	37	chr21	45094517	45094517	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caaaaattgcctttctttagCtgattcgtctggtcctgagg	9	9	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr21:45094517C>A	ENST00000340648.4	+	5	475	c.358C>A	c.(358-360)Ctg>Atg	p.L120M		NM_015056.2	NP_055871.1	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1B	120					negative regulation of phosphatase activity (GO:0010923)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome, small subunit precursor (GO:0030688)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(1)	21				STAD - Stomach adenocarcinoma(101;0.178)		CTTTCTTTAGCTGATTCGTCT	0.353																																					p.L120M		Atlas-SNP	.											.	RRP1B	51	.	0			c.C358A						.						78	71	73					21																	45094517		2203	4300	6503	SO:0001630	splice_region_variant	23076	exon5			CTTTAGCTGATTC	AK124620	CCDS33577.1	21q22.3	2014-06-13	2013-07-02	2007-03-26	ENSG00000160208	ENSG00000160208			23818	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 136"	610654	"KIAA0179", "ribosomal RNA processing 1 homolog B (S. cerevisiae)"	KIAA0179			Standard	NM_015056		Approved	Nnp1, RRP1, PPP1R136	uc002zdk.3	Q14684	OTTHUMG00000086872	ENST00000340648.4:c.358-1C>A	chr21.hg19:g.45094517C>A		54.0	0.0		144.0	9.0	NM_015056	Q8TBZ4	Missense_Mutation	SNP	ENST00000340648.4	hg19	CCDS33577.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.083221	0.36758	.	.	ENSG00000160208	ENST00000340648	T	0.64991	-0.13	5.53	3.33	0.38152	.	0.069267	0.56097	D	0.000021	D	0.82426	0.5034	H	0.96604	3.85	0.53005	D	0.999964	D	0.89917	1.0	D	0.97110	1.0	T	0.82973	-0.0191	9	.	.	.	-9.1608	5.382	0.16196	0.0:0.6875:0.0:0.3124	.	120	Q14684	RRP1B_HUMAN	M	120	ENSP00000339145:L120M	.	L	+	1	2	RRP1B	43918945	1.000000	0.71417	0.993000	0.49108	0.114000	0.19823	1.046000	0.30354	1.466000	0.48025	0.650000	0.86243	CTG	.	.		0.353	RRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195651.1	NM_015056	Missense_Mutation	A	45094517	C	A	45094517	5	1	101	1	0	0	0	0	0	0	1	0	13703	811	28	3	376	3	RRP1B	21	45094517	Splice_Site	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	6555616	45094517	3035378	603	14440										
KRTAP10-1	386677	hgsc.bcm.edu	37	chr21	45959615	45959615	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agcaaacaggcacacagcagGactgctggctggaggaagag	15	9	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr21:45959615G>T	ENST00000400375.1	-	1	463	c.419C>A	c.(418-420)tCc>tAc	p.S140Y	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	140	24 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S140Y(1)		breast(1)|central_nervous_system(1)|endometrium(1)|lung(3)|prostate(4)|skin(1)	11						CACACAGCAGGACTGCTGGCT	0.582																																					p.S140Y		Atlas-SNP	.											KRTAP10-1,NS,carcinoma,0,1	KRTAP10-1	34	.	1	Substitution - Missense(1)	endometrium(1)	c.C419A						.						120	124	122					21																	45959615		2203	4300	6503	SO:0001583	missense	386677	exon1			CAGCAGGACTGCT	AJ566380	CCDS42954.1	21q22.3	2007-10-05			ENSG00000215455	ENSG00000215455		"Keratin associated proteins"	22966	protein-coding gene	gene with protein product				KRTAP18-1			Standard	NM_198691		Approved	KAP10.1, KAP18.1	uc002zfh.1	P60331	OTTHUMG00000057627	ENST00000400375.1:c.419C>A	chr21.hg19:g.45959615G>T	ENSP00000383226:p.Ser140Tyr	114.0	0.0		171.0	11.0	NM_198691	Q0VAR0|Q0VAR1	Missense_Mutation	SNP	ENST00000400375.1	hg19	CCDS42954.1	.	.	.	.	.	.	.	.	.	.	g	0.020	-1.447605	0.01089	.	.	ENSG00000215455	ENST00000400375;ENST00000545982	T	0.01838	4.61	2.39	1.44	0.22558	.	.	.	.	.	T	0.04137	0.0115	M	0.79805	2.47	0.21290	N	0.999737	B	0.25667	0.131	B	0.29862	0.108	T	0.36986	-0.9725	9	0.54805	T	0.06	.	2.9769	0.05941	0.1584:0.0:0.5692:0.2723	.	140	P60331	KR101_HUMAN	Y	140	ENSP00000383226:S140Y	ENSP00000383226:S140Y	S	-	2	0	KRTAP10-1	44784043	0.027000	0.19231	0.537000	0.28052	0.117000	0.20001	0.093000	0.15086	0.308000	0.22923	0.194000	0.17425	TCC	.	.		0.582	KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1			T	45959615	G	T	45959615	3	4	101	1	0	0	0	0	1	0	0	0	8514	1174	41	3	433	3	KRTAP10-1	21	45959615	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	865098	45959615	2170280	604	14441										
KRTAP10-1	386677	hgsc.bcm.edu	37	chr21	45959819	45959819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acgagggcgtgcaggagctgGtgcagcctgattggcagggg	20	8	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr21:45959819G>A	ENST00000400375.1	-	1	259	c.215C>T	c.(214-216)aCc>aTc	p.T72I	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	72	24 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(3)|prostate(4)|skin(1)	11						GCAGGAGCTGGTGCAGCCTGA	0.711																																					p.T72I		Atlas-SNP	.											KRTAP10-1,NS,carcinoma,0,1	KRTAP10-1	34	.	0			c.C215T						.						44	51	49					21																	45959819		2197	4290	6487	SO:0001583	missense	386677	exon1			GAGCTGGTGCAGC	AJ566380	CCDS42954.1	21q22.3	2007-10-05			ENSG00000215455	ENSG00000215455		"Keratin associated proteins"	22966	protein-coding gene	gene with protein product				KRTAP18-1			Standard	NM_198691		Approved	KAP10.1, KAP18.1	uc002zfh.1	P60331	OTTHUMG00000057627	ENST00000400375.1:c.215C>T	chr21.hg19:g.45959819G>A	ENSP00000383226:p.Thr72Ile	48.0	0.0		40.0	3.0	NM_198691	Q0VAR0|Q0VAR1	Missense_Mutation	SNP	ENST00000400375.1	hg19	CCDS42954.1	.	.	.	.	.	.	.	.	.	.	g	2.677	-0.276175	0.05679	.	.	ENSG00000215455	ENST00000400375;ENST00000545982	T	0.00856	5.61	2.87	0.849	0.18972	.	.	.	.	.	T	0.02571	0.0078	M	0.73962	2.25	0.09310	N	1	P	0.50369	0.934	P	0.50314	0.637	T	0.35748	-0.9776	9	0.66056	D	0.02	.	9.5849	0.39510	0.0:0.4182:0.5818:0.0	.	72	P60331	KR101_HUMAN	I	72	ENSP00000383226:T72I	ENSP00000383226:T72I	T	-	2	0	KRTAP10-1	44784247	0.000000	0.05858	0.165000	0.22776	0.527000	0.34593	-0.068000	0.11561	0.064000	0.16427	0.491000	0.48974	ACC	.	.		0.711	KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1			A	45959819	G	A	45959819	3	1	101	1	0	0	0	0	1	0	0	0	8514	1261	44	3	637	3	KRTAP10-1	21	45959819	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	204	45959819	2170076	605	14442										
POTEH	23784	hgsc.bcm.edu	37	chr22	16268181	16268181	+	Splice_Site	DEL	C	C	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttctggttcttgagacatttCctgcagatgcaaaaacagaa							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:16268181delC	ENST00000343518.6	-	8	1360	c.1309delG	c.(1309-1311)gaa>aa	p.E437fs		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	437										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						TGAGACATTTCCTGCAGATGC	0.289																																					p.E437fs		Atlas-Indel,Pindel	.											.	POTEH	114	.	0			c.1310delA						.						1	1	1					22																	16268181		3	7	10	SO:0001630	splice_region_variant	23784	exon8			.	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	133	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 7"	608913	"actin, beta-like 1", "ANKRD26-like family C, member 3"	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.1309-1G>-	chr22.hg19:g.16268181delC		195.0	0.0		1508.0	229.0	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Frame_Shift_Del	DEL	ENST00000343518.6	hg19	CCDS46658.1																																																																																			.	.		0.289	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213	Frame_Shift_Del	-	16268181	C	-	16268181	8	5	101	1	0	1	0	1	0	0	1	0	12276	869	30	0	340	0	POTEH	22	16268181	Splice_Site	DEL	C	TCGA-DD-A1EE-01A-11D-A12Z-10		16268181	35036385	606	14443										
SCARF2	91179	hgsc.bcm.edu	37	chr22	20784723	20784723	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccggggcactcactggggccCgtggacgccagggctgcaca	16	15	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:20784723C>T	ENST00000266214.5	-	6	1299	c.1195G>A	c.(1195-1197)Ggg>Agg	p.G399R	SCARF2_ENST00000405555.3_Missense_Mutation_p.G399R	NM_153334.4	NP_699165.2	Q96GP6	SREC2_HUMAN	scavenger receptor class F, member 2	399	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	10	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			CACTGGGGCCCGTGGACGCCA	0.716																																					p.G399R		Atlas-SNP	.											.	SCARF2	23	.	0			c.G1195A						.						6	7	7					22																	20784723		2139	4207	6346	SO:0001583	missense	91179	exon6			GGGGCCCGTGGAC	AF522196	CCDS13779.1, CCDS46666.1	22q11.21	2011-10-10			ENSG00000244486	ENSG00000244486			19869	protein-coding gene	gene with protein product		613619				12154095	Standard	XM_006724364		Approved	SREC-II, SREC2, HUMZD58C02	uc002zsk.2	Q96GP6	OTTHUMG00000150779	ENST00000266214.5:c.1195G>A	chr22.hg19:g.20784723C>T	ENSP00000266214:p.Gly399Arg	13.0	0.0		24.0	8.0	NM_182895	E5RFB8|Q58A83|Q8IXF3|Q9BW74	Missense_Mutation	SNP	ENST00000266214.5	hg19	CCDS13779.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.556727	0.86231	.	.	ENSG00000244486	ENST00000405555;ENST00000341328;ENST00000266214	T;T	0.72394	-0.65;-0.65	4.45	4.45	0.53987	EGF-like region, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.83138	0.5189	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85718	0.1323	10	0.87932	D	0	-21.5452	14.9433	0.71012	0.0:1.0:0.0:0.0	.	399;399	E5RFB8;Q96GP6	.;SREC2_HUMAN	R	399	ENSP00000385589:G399R;ENSP00000266214:G399R	ENSP00000266214:G399R	G	-	1	0	SCARF2	19114723	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	6.737000	0.74816	2.188000	0.69820	0.561000	0.74099	GGG	.	.		0.716	SCARF2-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320047.1			T	20784723	C	T	20784723	3	4	101	1	0	0	0	0	1	0	0	0	13899	652	23	1	1441	1	SCARF2	22	20784723	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	4516542	20784723	30519843	607	14444										
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26688528	26688528	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ggaagtgctgggcgagctggTgctggatgggaccgcaccct	18	10	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:26688528T>C	ENST00000248933.6	+	2	346	c.251T>C	c.(250-252)gTg>gCg	p.V84A	SEZ6L_ENST00000343706.4_Missense_Mutation_p.V84A|SEZ6L_ENST00000403121.1_5'UTR|SEZ6L_ENST00000404234.3_Missense_Mutation_p.V84A|SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000529632.2_Missense_Mutation_p.V84A|SEZ6L_ENST00000360929.3_Missense_Mutation_p.V84A			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	84					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GGCGAGCTGGTGCTGGATGGG	0.657																																					p.V84A		Atlas-SNP	.											.	SEZ6L	174	.	0			c.T251C						.						62	52	56					22																	26688528		2203	4300	6503	SO:0001583	missense	23544	exon2			AGCTGGTGCTGGA	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.251T>C	chr22.hg19:g.26688528T>C	ENSP00000248933:p.Val84Ala	31.0	0.0		67.0	10.0	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	hg19	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	A	10.21	1.288511	0.23478	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	4.15	-3.41	0.04839	.	1.150010	0.06840	N	0.795474	T	0.12774	0.0310	N	0.08118	0	0.09310	N	0.999999	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.001;0.0;0.0	T	0.31223	-0.9951	10	0.16420	T	0.52	.	6.1891	0.20513	0.1777:0.615:0.0948:0.1125	.	84;84;84;84;84;84	B7ZLJ8;B7ZLJ6;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;SE6L1_HUMAN	A	84	ENSP00000384772:V84A;ENSP00000437037:V84A;ENSP00000354185:V84A;ENSP00000248933:V84A;ENSP00000342661:V84A	ENSP00000248933:V84A	V	+	2	0	SEZ6L	25018528	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.020000	0.12525	-0.792000	0.04480	-0.455000	0.05494	GTG	.	.		0.657	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			C	26688528	T	C	26688528	3	2	101	1	0	0	0	0	1	0	0	0	14158	1696	59	2	257	2	SEZ6L	22	26688528	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	5903805	26688528	24616038	608	14445										
NF2	4771	hgsc.bcm.edu	37	chr22	30069414	30069414	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggaggagaagcgcctgatgGagcagaaggtgctggaagcc	18	7	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:30069414G>T	ENST00000338641.4	+	12	1720	c.1279G>T	c.(1279-1281)Gag>Tag	p.E427*	NF2_ENST00000353887.4_Nonsense_Mutation_p.E344*|NF2_ENST00000361452.4_Nonsense_Mutation_p.E386*|NF2_ENST00000347330.5_Intron|NF2_ENST00000413209.2_Intron|NF2_ENST00000397789.3_Nonsense_Mutation_p.E427*|NF2_ENST00000361166.4_Nonsense_Mutation_p.E427*|NF2_ENST00000403999.3_Nonsense_Mutation_p.E427*|NF2_ENST00000361676.4_Nonsense_Mutation_p.E385*|NF2_ENST00000403435.1_Nonsense_Mutation_p.E398*|NF2_ENST00000334961.7_Nonsense_Mutation_p.E344*	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	427	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						GCGCCTGATGGAGCAGAAGGT	0.632			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.E427X		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2	1312	.	3	Unknown(3)	large_intestine(1)|stomach(1)|central_nervous_system(1)	c.G1279T	GRCh37	CM002818	NF2	M		.						53	46	48					22																	30069414		2203	4300	6503	SO:0001587	stop_gained	4771	exon12	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	CTGATGGAGCAGA	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.1279G>T	chr22.hg19:g.30069414G>T	ENSP00000344666:p.Glu427*	45.0	0.0		123.0	7.0	NM_000268	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Nonsense_Mutation	SNP	ENST00000338641.4	hg19	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	G	42	9.416160	0.99164	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2159	0.98296	0.0:0.0:1.0:0.0	.	.	.	.	X	427;398;386;402;427;344;344;427;385;427	.	.	E	+	1	0	NF2	28399414	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.848000	0.99507	2.882000	0.98803	0.655000	0.94253	GAG	.	.		0.632	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		T	30069414	G	T	30069414	4	4	101	1	0	0	0	0	0	1	0	0	10366	1175	41	3	1325	3	NF2	22	30069414	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	3380886	30069414	21235152	609	14446										
PLA2G3	50487	hgsc.bcm.edu	37	chr22	31533849	31533849	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ccccttccgaaggtgctgctTctgtcgaggcttgggagggg	16	11	1	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:31533849T>A	ENST00000215885.3	-	4	1165	c.913A>T	c.(913-915)Aag>Tag	p.K305*		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	305					acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						AGGTGCTGCTTCTGTCGAGGC	0.652																																					p.K305X		Atlas-SNP	.											.	PLA2G3	85	.	0			c.A913T						.						82	94	90					22																	31533849		2203	4300	6503	SO:0001587	stop_gained	50487	exon4			GCTGCTTCTGTCG	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.913A>T	chr22.hg19:g.31533849T>A	ENSP00000215885:p.Lys305*	83.0	0.0		209.0	23.0	NM_015715	O95768	Nonsense_Mutation	SNP	ENST00000215885.3	hg19	CCDS13889.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.612473	0.87258	.	.	ENSG00000100078	ENST00000215885	.	.	.	3.68	1.48	0.22813	.	0.904173	0.09678	N	0.770218	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.9249	4.5179	0.11945	0.0:0.1107:0.3999:0.4894	.	.	.	.	X	305	.	ENSP00000215885:K305X	K	-	1	0	PLA2G3	29863849	0.001000	0.12720	0.006000	0.13384	0.023000	0.10783	0.169000	0.16641	0.257000	0.21650	0.533000	0.62120	AAG	.	.		0.652	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715		A	31533849	T	A	31533849	4	1	101	1	0	0	0	0	0	1	0	0	12009	1792	62	4	632	4	PLA2G3	22	31533849	Nonsense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	1464435	31533849	19770717	610	14447										
PLA2G3	50487	hgsc.bcm.edu	37	chr22	31534717	31534717	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcggatgccatagttgtactGcaagggtgagatgttctgtg	14	6	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:31534717G>T	ENST00000215885.3	-	2	835	c.583C>A	c.(583-585)Cag>Aag	p.Q195K		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	195	Phospholipase A2-like.				acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						TAGTTGTACTGCAAGGGTGAG	0.597																																					p.Q195K		Atlas-SNP	.											.	PLA2G3	85	.	0			c.C583A						.						309	240	263					22																	31534717		2203	4300	6503	SO:0001583	missense	50487	exon2			TGTACTGCAAGGG	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.583C>A	chr22.hg19:g.31534717G>T	ENSP00000215885:p.Gln195Lys	133.0	0.0		311.0	16.0	NM_015715	O95768	Missense_Mutation	SNP	ENST00000215885.3	hg19	CCDS13889.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.491740	0.64074	.	.	ENSG00000100078	ENST00000215885	T	0.29142	1.58	5.41	4.35	0.52113	Phospholipase A2 (3);	0.370207	0.28871	N	0.013866	T	0.34366	0.0895	L	0.55990	1.75	0.32021	N	0.60077	P	0.47677	0.899	P	0.45610	0.487	T	0.49000	-0.8984	10	0.56958	D	0.05	-17.6393	12.855	0.57880	0.0:0.2879:0.7121:0.0	.	195	Q9NZ20	PA2G3_HUMAN	K	195	ENSP00000215885:Q195K	ENSP00000215885:Q195K	Q	-	1	0	PLA2G3	29864717	1.000000	0.71417	0.998000	0.56505	0.870000	0.49936	1.665000	0.37449	2.546000	0.85860	0.561000	0.74099	CAG	.	.		0.597	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715		T	31534717	G	T	31534717	3	4	101	1	0	0	0	0	1	0	0	0	12009	1328	46	3	970	3	PLA2G3	22	31534717	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	868	31534717	19769849	611	14448										
SLC5A1	6523	hgsc.bcm.edu	37	chr22	32480424	32480440	+	Splice_Site	DEL	TCCAGCTTTTCACGAAG	TCCAGCTTTTCACGAAG	-													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tttctgtaccgatgttttccAgcttttcacgaagtgggagg					rs200105615|rs145490212		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	TCCAGCTTTTCACGAAG	TCCAGCTTTTCACGAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:32480424_32480440delTCCAGCTTTTCACGAAG	ENST00000266088.4	+	8	914_929	c.664_679delTCCAGCTTTTCACGAAG	c.(664-681)tccagcttttcacgaagg>gg	p.SSFSRR222fs	SLC5A1_ENST00000543737.1_Splice_Site_p.SSFSRR95fs	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	222					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	GATGTTTTCCAGCTTTTCACGAAGTGGGAGGCTATGA	0.461																																					p.222_225del		Atlas-Indel,Pindel	.											.	SLC5A1	80	.	0			c.665_675del						.																																			SO:0001630	splice_region_variant	6523	exon8			.		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"Solute carriers"	11036	protein-coding gene	gene with protein product	"sodium/glucose cotransporter 1"	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.665-1TCCAGCTTTTCACGAAG>-	chr22.hg19:g.32480424_32480440delTCCAGCTTTTCACGAAG		41.0	0.0		95.0	22.0	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Frame_Shift_Del	DEL	ENST00000266088.4	hg19	CCDS13902.1																																																																																			.	.		0.461	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343	Frame_Shift_Del	-	32480440	TCCAGCTTTTCACGAAG	-	32480424	8	5	101	1	0	1	0	1	0	0	1	0	14676	202	7	0	693	0	SLC5A1	22	32480424	Splice_Site	DEL	TCCAGCTTTTCACGAAG	TCGA-DD-A1EE-01A-11D-A12Z-10	945707	32480424	18824142	612	14449										
MCM5	4174	hgsc.bcm.edu	37	chr22	35796490	35796490	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagcttcgggggcgacgcccAggccgacgaggggcaggccc	18	15	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:35796490A>G	ENST00000216122.4	+	2	213	c.59A>G	c.(58-60)cAg>cGg	p.Q20R	MCM5_ENST00000382011.5_Missense_Mutation_p.Q20R	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	20					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						GGCGACGCCCAGGCCGACGAG	0.652																																					p.Q20R		Atlas-SNP	.											.	MCM5	54	.	0			c.A59G						.						45	50	48					22																	35796490		2203	4300	6503	SO:0001583	missense	4174	exon2			ACGCCCAGGCCGA		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)", "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.59A>G	chr22.hg19:g.35796490A>G	ENSP00000216122:p.Gln20Arg	61.0	0.0		140.0	8.0	NM_006739	O60785|Q14578|Q9BTJ4|Q9BWL8	Missense_Mutation	SNP	ENST00000216122.4	hg19	CCDS13915.1	.	.	.	.	.	.	.	.	.	.	A	7.342	0.621126	0.14193	.	.	ENSG00000100297	ENST00000216122;ENST00000382011;ENST00000416905	T;T;T	0.31247	4.23;3.89;1.5	5.08	-4.01	0.04045	.	0.784752	0.11702	N	0.537828	T	0.18923	0.0454	L	0.39020	1.185	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.34900	-0.9810	10	0.16420	T	0.52	-6.6021	10.3507	0.43934	0.0687:0.5662:0.283:0.0821	.	20;20	B1AHB1;P33992	.;MCM5_HUMAN	R	20	ENSP00000216122:Q20R;ENSP00000371441:Q20R;ENSP00000393977:Q20R	ENSP00000216122:Q20R	Q	+	2	0	MCM5	34126490	0.000000	0.05858	0.067000	0.19924	0.455000	0.32408	0.009000	0.13219	-0.418000	0.07450	-1.701000	0.00721	CAG	.	.		0.652	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3			G	35796490	A	G	35796490	3	3	101	1	0	0	0	0	1	0	0	0	9399	188	7	2	61	2	MCM5	22	35796490	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	3316066	35796490	15508076	613	14450										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38120914	38120914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcccaggacctcctctcccaAtagagccacacgagacaacc	6	18	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:38120914A>G	ENST00000406386.3	+	7	2606	c.2351A>G	c.(2350-2352)aAt>aGt	p.N784S		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	784					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					TCCTCTCCCAATAGAGCCACA	0.562																																					p.N784S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.A2351G						.						136	147	143					22																	38120914		1980	4156	6136	SO:0001583	missense	11078	exon7			CTCCCAATAGAGC	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.2351A>G	chr22.hg19:g.38120914A>G	ENSP00000384312:p.Asn784Ser	90.0	0.0		161.0	15.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	7.619	0.676520	0.14841	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19394	2.15	3.65	-1.7	0.08159	.	.	.	.	.	T	0.11750	0.0286	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32587	-0.9901	9	0.33940	T	0.23	.	1.5067	0.02488	0.3434:0.3775:0.1108:0.1683	.	784	Q9H2D6	TARA_HUMAN	S	784	ENSP00000384312:N784S	ENSP00000384312:N784S	N	+	2	0	TRIOBP	36450860	0.075000	0.21258	0.003000	0.11579	0.028000	0.11728	-0.418000	0.07080	-0.145000	0.11294	-0.560000	0.04181	AAT	.	.		0.562	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			G	38120914	A	G	38120914	3	3	101	1	0	0	0	0	1	0	0	0	16568	101	4	2	2369	2	TRIOBP	22	38120914	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	2324424	38120914	13183652	614	14451										
EP300	2033	hgsc.bcm.edu	37	chr22	41560092	41560092	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agagtgcggaagaaagatgcAtcagatctgtgtccttcacc	11	9	3	4			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:41560092A>T	ENST00000263253.7	+	22	4983	c.3764A>T	c.(3763-3765)cAt>cTt	p.H1255L		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1255					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AGAAAGATGCATCAGATCTGT	0.388			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.H1255L		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.A3764T						.						229	201	211					22																	41560092		2203	4300	6503	SO:0001583	missense	2033	exon22	Familial Cancer Database	Broad Thumb-Hallux syndrome	AGATGCATCAGAT	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3764A>T	chr22.hg19:g.41560092A>T	ENSP00000263253:p.His1255Leu	127.0	0.0		260.0	24.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.457081	0.84317	.	.	ENSG00000100393	ENST00000263253	D	0.97941	-4.62	5.59	5.59	0.84812	.	0.000000	0.47852	D	0.000207	D	0.99026	0.9667	M	0.93328	3.405	0.54753	D	0.999986	D	0.76494	0.999	D	0.78314	0.991	D	0.99533	1.0961	10	0.87932	D	0	-13.0515	15.7693	0.78152	1.0:0.0:0.0:0.0	.	1255	Q09472	EP300_HUMAN	L	1255	ENSP00000263253:H1255L	ENSP00000263253:H1255L	H	+	2	0	EP300	39890038	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.339000	0.96797	2.125000	0.65367	0.459000	0.35465	CAT	.	.		0.388	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		T	41560092	A	T	41560092	3	4	101	1	0	0	0	0	1	0	0	0	5150	217	8	4	3850	4	EP300	22	41560092	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	3439178	41560092	9744474	615	14452										
POLR3H	171568	hgsc.bcm.edu	37	chr22	41928119	41928119	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	acttggctggctgctgcagtGactctggggggatgagaatg	17	7	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:41928119G>T	ENST00000355209.4	-	4	681	c.338C>A	c.(337-339)tCa>tAa	p.S113*	POLR3H_ENST00000396504.2_Nonsense_Mutation_p.S113*|POLR3H_ENST00000407461.1_Nonsense_Mutation_p.S113*|POLR3H_ENST00000420561.1_5'Flank|POLR3H_ENST00000337566.5_Nonsense_Mutation_p.S84*	NM_001018050.2	NP_001018060.1	Q9Y535	RPC8_HUMAN	polymerase (RNA) III (DNA directed) polypeptide H (22.9kD)	113					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|nucleobase-containing compound metabolic process (GO:0006139)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|lung(5)|skin(1)|urinary_tract(1)	8						CTGCTGCAGTGACTCTGGGGG	0.567																																					p.S113X		Atlas-SNP	.											.	POLR3H	30	.	0			c.C338A						.						98	79	85					22																	41928119		2203	4300	6503	SO:0001587	stop_gained	171568	exon4			TGCAGTGACTCTG	AB051452	CCDS14018.1, CCDS33651.1	22q13	2013-01-21			ENSG00000100413	ENSG00000100413		"RNA polymerase subunits"	30349	protein-coding gene	gene with protein product						11258795, 12391170	Standard	XR_244356		Approved	RPC8, KIAA1665	uc003baf.3	Q9Y535	OTTHUMG00000150971	ENST00000355209.4:c.338C>A	chr22.hg19:g.41928119G>T	ENSP00000347345:p.Ser113*	47.0	0.0		70.0	34.0	NM_001018050	B0QYH9|Q5M7Y8|Q96AE3|Q9BY95	Nonsense_Mutation	SNP	ENST00000355209.4	hg19	CCDS14018.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.797136	0.70567	.	.	ENSG00000100413	ENST00000396504;ENST00000355209;ENST00000337566;ENST00000407461	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	18.4486	0.90695	0.0:0.0:1.0:0.0	.	.	.	.	X	113;113;84;113	.	ENSP00000337627:S84X	S	-	2	0	POLR3H	40258065	1.000000	0.71417	0.937000	0.37676	0.951000	0.60555	9.623000	0.98386	2.602000	0.87976	0.650000	0.86243	TCA	.	.		0.567	POLR3H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320701.1	NM_138338		T	41928119	G	T	41928119	4	4	101	1	0	0	0	0	0	1	0	0	12245	1294	45	3	288	3	POLR3H	22	41928119	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	368027	41928119	9376447	616	14453										
CRELD2	79174	hgsc.bcm.edu	37	chr22	50316298	50316298	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agacgtgctcgggcctgaccAacagagactgcggcgagtgt	15	11	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:50316298A>T	ENST00000328268.4	+	6	705	c.631A>T	c.(631-633)Aac>Tac	p.N211Y	CRELD2_ENST00000444954.1_3'UTR|CRELD2_ENST00000404488.3_Missense_Mutation_p.N260Y|CRELD2_ENST00000407217.3_Missense_Mutation_p.N211Y|CRELD2_ENST00000403427.3_Missense_Mutation_p.N211Y	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	211						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		GGGCCTGACCAACAGAGACTG	0.672																																					p.N260Y		Atlas-SNP	.											.	CRELD2	57	.	0			c.A778T						.						48	34	39					22																	50316298		2187	4287	6474	SO:0001583	missense	79174	exon7			CTGACCAACAGAG	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.631A>T	chr22.hg19:g.50316298A>T	ENSP00000332223:p.Asn211Tyr	51.0	0.0		54.0	27.0	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Missense_Mutation	SNP	ENST00000328268.4	hg19	CCDS14082.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.827080	0.50739	.	.	ENSG00000184164	ENST00000450207;ENST00000404488;ENST00000328268;ENST00000407217;ENST00000403427	T;D;D;D;D	0.88124	2.48;-2.34;-2.34;-2.34;-2.34	4.13	1.83	0.25207	Growth factor, receptor (1);	0.354221	0.30311	N	0.009910	D	0.87881	0.6289	L	0.43701	1.375	0.21473	N	0.999678	D;D;D;P;D;D	0.65815	0.982;0.995;0.992;0.949;0.975;0.989	P;D;P;B;P;P	0.65874	0.814;0.939;0.861;0.269;0.59;0.7	T	0.78239	-0.2281	10	0.59425	D	0.04	.	7.5597	0.27845	0.7607:0.1527:0.0866:0.0	.	211;260;211;211;211;211	Q6UXH1-2;Q6UXH1-5;Q6UXH1-4;A5GZA6;Q6UXH1;Q6UXH1-3	.;.;.;.;CREL2_HUMAN;.	Y	211;260;211;211;211	ENSP00000387769:N211Y;ENSP00000383938:N260Y;ENSP00000332223:N211Y;ENSP00000386034:N211Y;ENSP00000384111:N211Y	ENSP00000332223:N211Y	N	+	1	0	CRELD2	48702302	0.015000	0.18098	0.098000	0.21074	0.926000	0.56050	0.711000	0.25764	0.644000	0.30656	0.528000	0.53228	AAC	.	.		0.672	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324		T	50316298	A	T	50316298	3	4	101	1	0	0	0	0	1	0	0	0	3869	130	5	4	804	4	CRELD2	22	50316298	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	8388179	50316298	988268	617	14454										
IL17REL	400935	hgsc.bcm.edu	37	chr22	50439551	50439551	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cgtacacgcaggagcatcgcGcagccgtcagaggggacaca	14	13	1	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:50439551G>C	ENST00000389983.2	-	4	333	c.69C>G	c.(67-69)tgC>tgG	p.C23W	IL17REL_ENST00000341280.5_Missense_Mutation_p.C23W	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	23										endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GGAGCATCGCGCAGCCGTCAG	0.652																																					p.C23W		Atlas-SNP	.											.	IL17REL	21	.	0			c.C69G						.						41	33	35					22																	50439551		2194	4295	6489	SO:0001583	missense	400935	exon4			CATCGCGCAGCCG	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.69C>G	chr22.hg19:g.50439551G>C	ENSP00000374633:p.Cys23Trp	46.0	0.0		160.0	17.0	NM_001001694	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	hg19	CCDS33679.1	.	.	.	.	.	.	.	.	.	.	g	12.74	2.028950	0.35797	.	.	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.34072	1.38;1.38	3.16	-0.348	0.12613	.	0.155416	0.43747	U	0.000535	T	0.47432	0.1445	L	0.59436	1.845	0.09310	N	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.27157	-1.0082	10	0.87932	D	0	.	5.7491	0.18136	0.4071:0.0:0.5929:0.0	.	23	Q6ZVW7	I17EL_HUMAN	W	23	ENSP00000374633:C23W;ENSP00000342520:C23W	ENSP00000342520:C23W	C	-	3	2	IL17REL	48781678	0.022000	0.18835	0.020000	0.16555	0.006000	0.05464	-0.109000	0.10840	0.093000	0.17368	-0.144000	0.13903	TGC	.	.		0.652	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694		C	50439551	G	C	50439551	3	2	101	1	0	0	0	0	1	0	0	0	7653	1079	38	4	985	4	IL17REL	22	50439551	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	123253	50439551	865015	618	14455										
TRABD	80305	hgsc.bcm.edu	37	chr22	50636557	50636557	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgggcgtcgtgggcatgggcCacgtgcctggcatcgagaag	18	10	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:50636557C>G	ENST00000303434.4	+	9	1017	c.898C>G	c.(898-900)Cac>Gac	p.H300D	RP3-402G11.26_ENST00000608025.1_RNA|TRABD_ENST00000380909.4_Missense_Mutation_p.H300D|TRABD_ENST00000395829.1_Missense_Mutation_p.H300D|TRABD_ENST00000395827.1_Missense_Mutation_p.H300D|SELO_ENST00000380903.2_5'Flank	NM_025204.2	NP_079480.2	Q9H4I3	TRABD_HUMAN	TraB domain containing	300										breast(1)|central_nervous_system(1)|large_intestine(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	7		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)		GGGCATGGGCCACGTGCCTGG	0.662																																					p.H300D		Atlas-SNP	.											.	TRABD	21	.	0			c.C898G						.						58	54	56					22																	50636557		2200	4299	6499	SO:0001583	missense	80305	exon9			ATGGGCCACGTGC	AL449244	CCDS14086.1	22q13.33	2006-07-06			ENSG00000170638	ENSG00000170638			28805	protein-coding gene	gene with protein product						12477932	Standard	NM_025204		Approved	PP2447	uc003bjs.1	Q9H4I3	OTTHUMG00000044644	ENST00000303434.4:c.898C>G	chr22.hg19:g.50636557C>G	ENSP00000305664:p.His300Asp	41.0	0.0		83.0	27.0	NM_025204	Q19CC5|Q96ED8|Q9H7N1|Q9UGX6|Q9UGX7	Missense_Mutation	SNP	ENST00000303434.4	hg19	CCDS14086.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.041436	0.93685	.	.	ENSG00000170638	ENST00000380909;ENST00000303434;ENST00000395827;ENST00000395829	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.07	5.07	0.68467	.	0.101138	0.64402	D	0.000002	D	0.87265	0.6134	H	0.94620	3.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.91072	0.4893	10	0.87932	D	0	-18.7703	18.492	0.90851	0.0:1.0:0.0:0.0	.	254;300	Q9H4I3-2;Q9H4I3	.;TRABD_HUMAN	D	300	ENSP00000370295:H300D;ENSP00000305664:H300D;ENSP00000379171:H300D;ENSP00000379173:H300D	ENSP00000305664:H300D	H	+	1	0	TRABD	48978684	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	6.682000	0.74528	2.364000	0.80123	0.555000	0.69702	CAC	.	.		0.662	TRABD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316987.1	NM_025204		G	50636557	C	G	50636557	3	3	101	1	0	0	0	0	1	0	0	0	16450	594	21	4	928	4	TRABD	22	50636557	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	197006	50636557	668009	619	14456										
SBF1	6305	hgsc.bcm.edu	37	chr22	50898976	50898976	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tccatacctgagggaaggacCcttgtccttggtgactcgcg	12	12	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chr22:50898976C>T	ENST00000390679.3	-	24	3317	c.3133G>A	c.(3133-3135)Ggt>Agt	p.G1045S	SBF1_ENST00000348911.6_Missense_Mutation_p.G1046S|SBF1_ENST00000380817.3_Missense_Mutation_p.G1045S			O95248	MTMR5_HUMAN	SET binding factor 1	1045					cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		AGGGAAGGACCCTTGTCCTTG	0.647																																					p.G1045S		Atlas-SNP	.											.	SBF1	211	.	0			c.G3133A						.						69	79	76					22																	50898976		2128	4217	6345	SO:0001583	missense	6305	exon24			AAGGACCCTTGTC	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.3133G>A	chr22.hg19:g.50898976C>T	ENSP00000375097:p.Gly1045Ser	32.0	0.0		77.0	4.0	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	C	11.45	1.643808	0.29246	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000337034;ENST00000390679	T;T;T	0.01767	4.65;4.65;4.65	3.95	2.84	0.33178	.	0.325676	0.30667	N	0.009140	T	0.00845	0.0028	N	0.03608	-0.345	0.33390	D	0.57606	B;B	0.20052	0.009;0.041	B;B	0.22601	0.016;0.04	T	0.41928	-0.9481	10	0.20046	T	0.44	.	3.5534	0.07855	0.0:0.607:0.0:0.393	.	1045;1045	O95248;O95248-4	MTMR5_HUMAN;.	S	1045;1046;1055;1045	ENSP00000370196:G1045S;ENSP00000252027:G1046S;ENSP00000375097:G1045S	ENSP00000336522:G1055S	G	-	1	0	SBF1	49245842	1.000000	0.71417	0.993000	0.49108	0.446000	0.32137	2.662000	0.46766	2.027000	0.59764	0.467000	0.42956	GGT	.	.		0.647	SBF1-201	KNOWN	basic	protein_coding	protein_coding				T	50898976	C	T	50898976	3	4	101	1	0	0	0	0	1	0	0	0	13873	623	22	3	2620	3	SBF1	22	50898976	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	262419	50898976	405590	620	14457										
WWC3	55841	hgsc.bcm.edu	37	chrX	10085259	10085259	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctccagccggggctccctgaGctcggtcagcttcacggaca	12	16	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:10085259G>A	ENST00000380861.4	+	11	1551	c.1160G>A	c.(1159-1161)aGc>aAc	p.S387N	WWC3_ENST00000454666.1_Missense_Mutation_p.S387N	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	387	Ser-rich.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						GGCTCCCTGAGCTCGGTCAGC	0.662																																					p.S387N		Atlas-SNP	.											.	WWC3	142	.	0			c.G1160A						.						48	52	51					X																	10085259		2203	4299	6502	SO:0001583	missense	55841	exon11			CCCTGAGCTCGGT	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1160G>A	chrX.hg19:g.10085259G>A	ENSP00000370242:p.Ser387Asn	21.0	0.0		92.0	84.0	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	hg19	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.101531	0.56183	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543293;ENST00000398613	T;T	0.43294	0.95;0.95	5.53	5.53	0.82687	.	0.192666	0.64402	D	0.000005	T	0.53045	0.1772	L	0.41824	1.3	0.49483	D	0.999797	D	0.63880	0.993	P	0.60117	0.869	T	0.43686	-0.9376	10	0.30078	T	0.28	-15.4907	18.6465	0.91411	0.0:0.0:1.0:0.0	.	387	Q9ULE0	WWC3_HUMAN	N	387;387;51;387	ENSP00000370242:S387N;ENSP00000399584:S387N	ENSP00000370242:S387N	S	+	2	0	WWC3	10045259	1.000000	0.71417	0.998000	0.56505	0.662000	0.39071	6.390000	0.73204	2.348000	0.79779	0.464000	0.42555	AGC	.	.		0.662	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		A	10085259	G	A	10085259	3	1	101	1	0	0	0	0	1	0	0	0	17428	971	34	3	1198	3	WWC3	23	10085259	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10		10085259	145185301	621	14458										
MAP3K15	389840	hgsc.bcm.edu	37	chrX	19379516	19379516	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ttaagaatatccgaaagtgtAtaaccctcttcaacaatctg	5	9	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:19379516A>G	ENST00000338883.4	-	28	3797	c.3798T>C	c.(3796-3798)taT>taC	p.Y1266Y	PDHA1_ENST00000540249.1_3'UTR|PDHA1_ENST00000379806.5_3'UTR|MAP3K15_ENST00000359173.3_Silent_p.Y701Y|MAP3K15_ENST00000469203.2_Silent_p.Y1098Y|MAP3K15_ENST00000518578.1_5'UTR|PDHA1_ENST00000545074.1_3'UTR|PDHA1_ENST00000422285.2_3'UTR	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	1266							ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					CCGAAAGTGTATAACCCTCTT	0.348																																					p.Y1266Y		Atlas-SNP	.											.	MAP3K15	108	.	0			c.T3798C						.						67	59	61					X																	19379516		2203	4300	6503	SO:0001819	synonymous_variant	389840	exon28			AAGTGTATAACCC	AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.3798T>C	chrX.hg19:g.19379516A>G		70.0	0.0		179.0	18.0	NM_001001671	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Silent	SNP	ENST00000338883.4	hg19																																																																																				.	.		0.348	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671		G	19379516	A	G	19379516	2	3	101	1	0	0	0	0	0	0	0	1	9258	456	16	2		2	MAP3K15	23	19379516	Silent	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	9294257	19379516	135891044	622	14459										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20252926	20252926	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aggttcatccataatttgctGtccattctgtgaaaagcaca	7	9	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:20252926G>A	ENST00000379565.3	-	2	283	c.76C>T	c.(76-78)Cag>Tag	p.Q26*	RPS6KA3_ENST00000540702.1_5'UTR|RPS6KA3_ENST00000544447.1_5'UTR	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	26					axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	ATAATTTGCTGTCCATTCTGT	0.338																																					p.Q26X		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.C76T						.						93	77	83					X																	20252926		2203	4300	6503	SO:0001587	stop_gained	6197	exon2			TTTGCTGTCCATT	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.76C>T	chrX.hg19:g.20252926G>A	ENSP00000368884:p.Gln26*	85.0	0.0		337.0	33.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Nonsense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	G	37	6.183972	0.97357	.	.	ENSG00000177189	ENST00000379565	.	.	.	5.31	5.31	0.75309	.	0.484849	0.20103	N	0.099190	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	.	13.3469	0.60578	0.0:0.0:1.0:0.0	.	.	.	.	X	26	.	ENSP00000368884:Q26X	Q	-	1	0	RPS6KA3	20162847	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.349000	0.66010	2.213000	0.71641	0.594000	0.82650	CAG	.	.		0.338	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		A	20252926	G	A	20252926	4	1	101	1	0	0	0	0	0	1	0	0	13667	1386	48	3	2230	3	RPS6KA3	23	20252926	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	873410	20252926	135017634	623	14460										
CNKSR2	22866	hgsc.bcm.edu	37	chrX	21545015	21545015	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	ctagaagtcccacaagcagcGttgccacgccttccagcacc	8	17	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:21545015G>A	ENST00000379510.3	+	10	1024	c.988G>A	c.(988-990)Gtt>Att	p.V330I	CNKSR2_ENST00000543067.1_Missense_Mutation_p.V281I|CNKSR2_ENST00000279451.4_Missense_Mutation_p.V330I|CNKSR2_ENST00000425654.2_Missense_Mutation_p.V330I	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	330					regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						CACAAGCAGCGTTGCCACGCC	0.453													G|||	1	0.000264901	0	0	3775	,	,		7043	0		0	False		,,,				2504	0.001				p.V330I		Atlas-SNP	.											.	CNKSR2	158	.	0			c.G988A						.						222	211	215					X																	21545015		2203	4300	6503	SO:0001583	missense	22866	exon10			AGCAGCGTTGCCA	AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.988G>A	chrX.hg19:g.21545015G>A	ENSP00000368824:p.Val330Ile	54.0	0.0		200.0	39.0	NM_001168647	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Missense_Mutation	SNP	ENST00000379510.3	hg19	CCDS14198.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.384359	0.42308	.	.	ENSG00000149970	ENST00000425654;ENST00000543067;ENST00000279451;ENST00000379510	T;T;T;T	0.18502	2.5;2.25;2.21;2.48	5.58	4.66	0.58398	.	0.196899	0.43416	D	0.000563	T	0.06826	0.0174	N	0.02011	-0.69	0.24045	N	0.996062	B;B;B	0.20988	0.029;0.05;0.007	B;B;B	0.12156	0.007;0.003;0.002	T	0.29852	-0.9998	10	0.17832	T	0.49	-9.6134	14.3431	0.66641	0.0:0.0:0.8514:0.1485	.	330;281;330	B7ZLJ1;B4DGR4;Q8WXI2	.;.;CNKR2_HUMAN	I	330;281;330;330	ENSP00000397906:V330I;ENSP00000444633:V281I;ENSP00000279451:V330I;ENSP00000368824:V330I	ENSP00000279451:V330I	V	+	1	0	CNKSR2	21454936	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.870000	0.63035	2.338000	0.79540	0.544000	0.68410	GTT	.	.		0.453	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927		A	21545015	G	A	21545015	3	1	101	1	0	0	0	0	1	0	0	0	3609	1145	40	1	1026	1	CNKSR2	23	21545015	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1292089	21545015	133725545	624	14461										
ARAF	369	hgsc.bcm.edu	37	chrX	47428285	47428285	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtggcccggcagactgcccaGggcatggagtgagcctccca	15	14	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:47428285G>T	ENST00000377045.4	+	11	1439	c.1245G>T	c.(1243-1245)caG>caT	p.Q415H		NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	415	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	AGACTGCCCAGGGCATGGAGT	0.657											OREG0019759	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q418H		Atlas-SNP	.											.	ARAF	67	.	0			c.G1254T						.						29	24	26					X																	47428285		2203	4300	6503	SO:0001583	missense	369	exon11			TGCCCAGGGCATG	X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"v-raf murine sarcoma 3611 viral oncogene homolog 1"	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.1245G>T	chrX.hg19:g.47428285G>T	ENSP00000366244:p.Gln415His	38.0	0.0	946	203.0	28.0	NM_001256196	P07557|Q5H9B2|Q5H9B3	Missense_Mutation	SNP	ENST00000377045.4	hg19	CCDS35232.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990746	0.74589	.	.	ENSG00000078061	ENST00000377045	D	0.83163	-1.69	5.33	4.47	0.54385	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85366	0.5680	L	0.41356	1.27	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.84916	0.0851	10	0.87932	D	0	.	7.5126	0.27583	0.1992:0.0:0.8008:0.0	.	415;281	P10398;B4DV85	ARAF_HUMAN;.	H	415	ENSP00000366244:Q415H	ENSP00000366244:Q415H	Q	+	3	2	ARAF	47313229	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.143000	0.64826	1.008000	0.39264	0.422000	0.28245	CAG	.	.		0.657	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1			T	47428285	G	T	47428285	3	4	101	1	0	0	0	0	1	0	0	0	837	991	35	3	1283	3	ARAF	23	47428285	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	25883270	47428285	107842275	625	14462										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63410708	63410708	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caggattctcttcacacttgCcttccccatcccgttccaca	4	18	2	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:63410708C>A	ENST00000330258.3	-	2	2731	c.2459G>T	c.(2458-2460)gGc>gTc	p.G820V	AMER1_ENST00000374869.3_Intron|AMER1_ENST00000403336.1_Intron	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	820					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									TTCACACTTGCCTTCCCCATC	0.502																																					p.G820V		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.G2459T						.						45	43	43					X																	63410708		2200	4296	6496	SO:0001583	missense	139285	exon2			CACTTGCCTTCCC	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.2459G>T	chrX.hg19:g.63410708C>A	ENSP00000329117:p.Gly820Val	25.0	0.0		125.0	34.0	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	hg19	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	17.92	3.507616	0.64410	.	.	ENSG00000184675	ENST00000330258	T	0.75367	-0.93	5.0	5.0	0.66597	.	.	.	.	.	T	0.76786	0.4036	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75542	-0.3281	8	.	.	.	0.4471	16.219	0.82244	0.0:1.0:0.0:0.0	.	820	Q5JTC6	F123B_HUMAN	V	820	ENSP00000329117:G820V	.	G	-	2	0	FAM123B	63327433	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.660000	0.74417	2.484000	0.83849	0.529000	0.55759	GGC	.	.		0.502	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63410708	C	A	63410708	3	1	101	1	0	0	0	0	1	0	0	0	5428	739	26	3	952	3	FAM123B	23	63410708	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	15982423	63410708	91859852	626	14463										
ASB12	142689	hgsc.bcm.edu	37	chrX	63444957	63444957	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gcggaaacagtccaggtgccCgtagactgcggccaaataga	13	11	0	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:63444957C>A	ENST00000396130.2	-	1	546	c.547G>T	c.(547-549)Ggg>Tgg	p.G183W	MTMR8_ENST00000453546.1_Missense_Mutation_p.G567W|ASB12_ENST00000362002.2_Missense_Mutation_p.G192W			Q8WXK4	ASB12_HUMAN	ankyrin repeat and SOCS box containing 12	183					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.0?(2)		endometrium(2)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14						TCCAGGTGCCCGTAGACTGCG	0.572																																					p.G192W		Atlas-SNP	.											.	ASB12	102	.	2	Whole gene deletion(2)	ovary(1)|large_intestine(1)	c.G574T						.						66	60	62					X																	63444957		2203	4300	6503	SO:0001583	missense	142689	exon2			GGTGCCCGTAGAC	AF403030	CCDS14378.1, CCDS14378.2	Xq11.1	2013-01-10	2011-01-25		ENSG00000198881	ENSG00000198881		"Ankyrin repeat domain containing"	19763	protein-coding gene	gene with protein product		300891	"ankyrin repeat and SOCS box-containing 12"			12076535	Standard	NM_130388		Approved	FLJ39577		Q8WXK4	OTTHUMG00000021705	ENST00000396130.2:c.547G>T	chrX.hg19:g.63444957C>A	ENSP00000379435:p.Gly183Trp	24.0	0.0		102.0	5.0	NM_130388	J3KP57|Q2M3D5|Q52LK4|Q6ISF9|Q8N8F5	Missense_Mutation	SNP	ENST00000396130.2	hg19		.	.	.	.	.	.	.	.	.	.	C	16.17	3.047096	0.55110	.	.	ENSG00000198881;ENSG00000198881;ENSG00000198881;ENSG00000102043	ENST00000362002;ENST00000396130;ENST00000361287;ENST00000453546	T;T;T	0.75154	-0.91;-0.91;-0.91	4.0	3.14	0.36123	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	D	0.85822	0.5786	M	0.87971	2.92	0.28421	N	0.917728	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.79531	-0.1765	10	0.87932	D	0	-14.651	9.8685	0.41160	0.0:0.8937:0.0:0.1063	.	567;183	B4DQL0;Q8WXK4	.;ASB12_HUMAN	W	192;183;192;567	ENSP00000355195:G192W;ENSP00000379435:G183W;ENSP00000394003:G567W	ENSP00000354626:G192W	G	-	1	0	ASB12;MTMR8	63361682	1.000000	0.71417	0.966000	0.40874	0.878000	0.50629	4.288000	0.59007	0.838000	0.34948	0.468000	0.43344	GGG	.	.		0.572	ASB12-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				A	63444957	C	A	63444957	3	1	101	1	0	0	0	0	1	0	0	0	1016	652	23	1	390	1	ASB12	23	63444957	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	34249	63444957	91825603	627	14464										
ASB12	142689	hgsc.bcm.edu	37	chrX	63445128	63445128	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agaacagttgttgtagatgcTaccaccaggagaggcaccag	12	9	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:63445128T>C	ENST00000396130.2	-	1	375	c.376A>G	c.(376-378)Agc>Ggc	p.S126G	MTMR8_ENST00000453546.1_Missense_Mutation_p.S510G|ASB12_ENST00000362002.2_Missense_Mutation_p.S135G			Q8WXK4	ASB12_HUMAN	ankyrin repeat and SOCS box containing 12	126					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.0?(2)		endometrium(2)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14						TTGTAGATGCTACCACCAGGA	0.547																																					p.S135G		Atlas-SNP	.											.	ASB12	102	.	2	Whole gene deletion(2)	ovary(1)|large_intestine(1)	c.A403G						.						104	65	78					X																	63445128		2203	4300	6503	SO:0001583	missense	142689	exon2			AGATGCTACCACC	AF403030	CCDS14378.1, CCDS14378.2	Xq11.1	2013-01-10	2011-01-25		ENSG00000198881	ENSG00000198881		"Ankyrin repeat domain containing"	19763	protein-coding gene	gene with protein product		300891	"ankyrin repeat and SOCS box-containing 12"			12076535	Standard	NM_130388		Approved	FLJ39577		Q8WXK4	OTTHUMG00000021705	ENST00000396130.2:c.376A>G	chrX.hg19:g.63445128T>C	ENSP00000379435:p.Ser126Gly	45.0	0.0		214.0	16.0	NM_130388	J3KP57|Q2M3D5|Q52LK4|Q6ISF9|Q8N8F5	Missense_Mutation	SNP	ENST00000396130.2	hg19		.	.	.	.	.	.	.	.	.	.	T	19.39	3.817934	0.71028	.	.	ENSG00000198881;ENSG00000198881;ENSG00000198881;ENSG00000102043	ENST00000362002;ENST00000396130;ENST00000361287;ENST00000453546	T;T;T	0.64618	-0.11;-0.11;-0.11	4.0	4.0	0.46444	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.63070	0.2480	L	0.28192	0.835	0.27853	N	0.940689	D;D	0.69078	0.997;0.997	D;D	0.80764	0.994;0.992	T	0.54390	-0.8301	10	0.14656	T	0.56	-24.6711	11.2485	0.49010	0.0:0.0:0.0:1.0	.	510;126	B4DQL0;Q8WXK4	.;ASB12_HUMAN	G	135;126;135;510	ENSP00000355195:S135G;ENSP00000379435:S126G;ENSP00000394003:S510G	ENSP00000354626:S135G	S	-	1	0	ASB12;MTMR8	63361853	1.000000	0.71417	0.998000	0.56505	0.910000	0.53928	7.194000	0.77789	1.595000	0.50050	0.381000	0.24937	AGC	.	.		0.547	ASB12-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				C	63445128	T	C	63445128	3	2	101	1	0	0	0	0	1	0	0	0	1016	1522	53	2	561	2	ASB12	23	63445128	Missense_Mutation	SNP	T	TCGA-DD-A1EE-01A-11D-A12Z-10	171	63445128	91825432	628	14465										
TAF1	6872	hgsc.bcm.edu	37	chrX	70680629	70680629	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agacggtggggaggcttcccAtggtttggaggatagcaaca	16	7	0	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:70680629A>G	ENST00000373790.4	+	37	5423	c.5372A>G	c.(5371-5373)cAt>cGt	p.H1791R	TAF1_ENST00000276072.3_Missense_Mutation_p.H1812R|TAF1_ENST00000461764.1_3'UTR|TAF1_ENST00000423759.1_Missense_Mutation_p.H1814R|TAF1_ENST00000449580.1_Missense_Mutation_p.H1825R	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1791	Asp/Glu-rich (acidic tail).|Protein kinase 2.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GAGGCTTCCCATGGTTTGGAG	0.507																																					p.H1812R		Atlas-SNP	.											.	TAF1	439	.	0			c.A5435G						.						117	81	93					X																	70680629		2201	4299	6500	SO:0001583	missense	6872	exon37			CTTCCCATGGTTT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.5372A>G	chrX.hg19:g.70680629A>G	ENSP00000362895:p.His1791Arg	68.0	0.0		177.0	36.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.11|10.11	1.259763|1.259763	0.23051|0.23051	.|.	.|.	ENSG00000147133|ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000395779;ENST00000276072|ENST00000437147	T;T;T;T|.	0.08370|.	3.1;3.14;3.16;3.1|.	4.76|4.76	-0.271|-0.271	0.12922|0.12922	.|.	0.662303|.	0.16392|.	N|.	0.216437|.	T|T	0.22704|0.22704	0.0548|0.0548	N|N	0.19112|0.19112	0.55|0.55	0.20873|0.20873	N|N	0.999833|0.999833	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.001;0.0;0.001|.	T|T	0.29701|0.29701	-1.0003|-1.0003	10|5	0.11485|.	T|.	0.65|.	.|.	8.3625|8.3625	0.32367|0.32367	0.6661:0.0:0.3339:0.0|0.6661:0.0:0.3339:0.0	.|.	481;1825;1791;1812|.	A5CVC9;P21675-4;P21675;P21675-2|.	.;.;TAF1_HUMAN;.|.	R|V	1791;1825;1814;533;1812|480	ENSP00000362895:H1791R;ENSP00000389000:H1825R;ENSP00000406549:H1814R;ENSP00000276072:H1812R|.	ENSP00000276072:H1812R|.	H|M	+|+	2|1	0|0	TAF1|TAF1	70597354|70597354	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.997000|0.997000	0.91878|0.91878	1.978000|1.978000	0.40598|0.40598	-0.324000|-0.324000	0.08589|0.08589	0.430000|0.430000	0.28490|0.28490	CAT|ATG	.	.		0.507	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		G	70680629	A	G	70680629	3	3	101	1	0	0	0	0	1	0	0	0	15528	217	8	2	5581	2	TAF1	23	70680629	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	7235501	70680629	84589931	629	14466										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128877	83128877	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agaaatgattcaagaaatttGaagaaagcttcaaagaatga	8	3	2	7			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:83128877G>T	ENST00000329312.4	+	4	1198	c.1161G>T	c.(1159-1161)ttG>ttT	p.L387F		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	387					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						CAAGAAATTTGAAGAAAGCTT	0.353																																					p.L387F		Atlas-SNP	.											.	CYLC1	272	.	0			c.G1161T						.						29	25	27					X																	83128877		2194	4287	6481	SO:0001583	missense	1538	exon4			AAATTTGAAGAAA	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1161G>T	chrX.hg19:g.83128877G>T	ENSP00000331556:p.Leu387Phe	51.0	0.0		157.0	9.0	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	hg19	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	g	0.989	-0.694703	0.03303	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.23348	1.91	3.43	-6.87	0.01671	.	.	.	.	.	T	0.09730	0.0239	N	0.08118	0	0.09310	N	1	B;B	0.18166	0.026;0.026	B;B	0.22753	0.041;0.041	T	0.31888	-0.9927	9	0.56958	D	0.05	.	2.736	0.05240	0.5957:0.1112:0.1291:0.164	.	387;387	P35663;F5H4V5	CYLC1_HUMAN;.	F	387	ENSP00000331556:L387F	ENSP00000331556:L387F	L	+	3	2	CYLC1	83015533	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.359000	0.02602	-1.457000	0.01919	-1.346000	0.01242	TTG	.	.		0.353	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		T	83128877	G	T	83128877	3	4	101	1	0	0	0	0	1	0	0	0	4143	1281	45	3	1175	3	CYLC1	23	83128877	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	12448248	83128877	72141683	630	14467										
CHM	1121	hgsc.bcm.edu	37	chrX	85218969	85218969	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cgtaggcaggaaggcagaatCtgcagcttctgtggagtttg	15	7	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:85218969C>G	ENST00000357749.2	-	5	432	c.403G>C	c.(403-405)Gat>Cat	p.D135H	CHM_ENST00000467744.2_Intron|CHM_ENST00000537751.1_5'UTR	NM_000390.2	NP_000381.1	P24386	RAE1_HUMAN	choroideremia (Rab escort protein 1)	135					blood vessel development (GO:0001568)|protein geranylgeranylation (GO:0018344)|protein targeting to membrane (GO:0006612)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytosol (GO:0005829)|Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|prostate(1)	20		all_lung(315;5.41e-06)				AAGGCAGAATCTGCAGCTTCT	0.453																																					p.D135H		Atlas-SNP	.											.	CHM	57	.	0			c.G403C						.						80	69	73					X																	85218969		2203	4300	6503	SO:0001583	missense	1121	exon5			CAGAATCTGCAGC	X78121	CCDS14454.1, CCDS48139.1	Xq21.1-q21.3	2014-09-17			ENSG00000188419	ENSG00000188419			1940	protein-coding gene	gene with protein product		300390		TCD, DXS540		1373238	Standard	XM_006724615		Approved	REP-1	uc004eet.3	P24386	OTTHUMG00000021937	ENST00000357749.2:c.403G>C	chrX.hg19:g.85218969C>G	ENSP00000350386:p.Asp135His	75.0	0.0		247.0	13.0	NM_000390	A1L4D2|O43732	Missense_Mutation	SNP	ENST00000357749.2	hg19	CCDS14454.1	.	.	.	.	.	.	.	.	.	.	C	2.434	-0.330191	0.05314	.	.	ENSG00000188419	ENST00000357749	T	0.59502	0.26	4.64	0.677	0.17964	.	0.600547	0.17895	N	0.158391	T	0.35508	0.0934	N	0.21448	0.665	0.09310	N	0.999998	B	0.12630	0.006	B	0.14023	0.01	T	0.19484	-1.0304	10	0.54805	T	0.06	-0.0743	2.2676	0.04083	0.1209:0.4594:0.1255:0.2941	.	135	P24386	RAE1_HUMAN	H	135	ENSP00000350386:D135H	ENSP00000350386:D135H	D	-	1	0	CHM	85105625	0.020000	0.18652	0.020000	0.16555	0.108000	0.19459	1.596000	0.36718	-0.245000	0.09625	0.284000	0.19432	GAT	.	.		0.453	CHM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057396.3	NM_000390		G	85218969	C	G	85218969	3	3	101	1	0	0	0	0	1	0	0	0	3352	913	32	4	1602	4	CHM	23	85218969	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	2090092	85218969	70051591	631	14468										
TGIF2LX	90316	hgsc.bcm.edu	37	chrX	89177619	89177620	+	Missense_Mutation	DNP	CC	CC	AG													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaccagatccggagtcggccCctagccagaagctcaccgga							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:89177619_89177620CC>AG	ENST00000561129.2	+	1	665_666	c.535_536CC>AG	c.(535-537)CCt>AGt	p.P179S	TGIF2LX_ENST00000283891.5_Missense_Mutation_p.P179S			Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	179					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(29)|ovary(1)|skin(3)|urinary_tract(1)	40						GGAGTCGGCCCCTAGCCAGAAG	0.574																																					p.P179T|p.P179R		Atlas-SNP	.											.	TGIF2LX	84	.	0			c.C535A|c.C536G						.																																			SO:0001583	missense	90316	exon2			TCGGCCCCTAGCC|CGGCCCCTAGCCA	AF497480	CCDS14459.1	Xq21.31	2014-05-14	2007-02-07		ENSG00000153779	ENSG00000153779		"Homeoboxes / TALE class"	18570	protein-coding gene	gene with protein product		300411	"TGFB-induced factor 2-like, X-linked"				Standard	NM_138960		Approved		uc004efe.3	Q8IUE1	OTTHUMG00000021954	Exception_encountered	chrX.hg19:g.89177619_89177620delinsAG	ENSP00000453704:p.Pro179Ser	53.0|52.0	0.0		339.0|345.0	57.0|59.0	NM_138960	Q5JRM9|Q8TD48	Missense_Mutation	SNP	ENST00000561129.2	hg19	CCDS14459.1																																																																																			.	.		0.574	TGIF2LX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417911.2	NM_138960		AG	89177620	CC	AG	89177619	3	1	101	1	0	0	0	0	1	0	0	0	15842	623	22	3	537	3	TGIF2LX	23	89177619	Missense_Mutation	DNP	CC	TCGA-DD-A1EE-01A-11D-A12Z-10	3958650	89177619	66092941	632	14469										
TGIF2LX	90316	hgsc.bcm.edu	37	chrX	89177754	89177754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tcctgctgctagtcgatgcaGcagtacaaagggctgccgag	13	11	0	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:89177754G>A	ENST00000561129.2	+	1	800	c.670G>A	c.(670-672)Gca>Aca	p.A224T	TGIF2LX_ENST00000283891.5_Missense_Mutation_p.A224T			Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	224					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(29)|ovary(1)|skin(3)|urinary_tract(1)	40						AGTCGATGCAGCAGTACAAAG	0.498																																					p.A224T		Atlas-SNP	.											.	TGIF2LX	84	.	0			c.G670A						.						44	47	46					X																	89177754		2198	4293	6491	SO:0001583	missense	90316	exon2			GATGCAGCAGTAC	AF497480	CCDS14459.1	Xq21.31	2014-05-14	2007-02-07		ENSG00000153779	ENSG00000153779		"Homeoboxes / TALE class"	18570	protein-coding gene	gene with protein product		300411	"TGFB-induced factor 2-like, X-linked"				Standard	NM_138960		Approved		uc004efe.3	Q8IUE1	OTTHUMG00000021954	ENST00000561129.2:c.670G>A	chrX.hg19:g.89177754G>A	ENSP00000453704:p.Ala224Thr	94.0	0.0		551.0	76.0	NM_138960	Q5JRM9|Q8TD48	Missense_Mutation	SNP	ENST00000561129.2	hg19	CCDS14459.1	.	.	.	.	.	.	.	.	.	.	G	11.15	1.553979	0.27739	.	.	ENSG00000153779	ENST00000283891	T	0.76060	-0.99	3.11	2.24	0.28232	.	0.671285	0.12355	N	0.476210	D	0.84051	0.5387	M	0.83483	2.645	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.70029	-0.4984	9	.	.	.	-20.3271	5.5631	0.17154	0.1575:0.0:0.8425:0.0	.	224	Q8IUE1	TF2LX_HUMAN	T	224	ENSP00000355119:A224T	.	A	+	1	0	TGIF2LX	89064410	0.990000	0.36364	0.011000	0.14972	0.004000	0.04260	4.421000	0.59848	0.723000	0.32274	0.415000	0.27848	GCA	.	.		0.498	TGIF2LX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417911.2	NM_138960		A	89177754	G	A	89177754	3	1	101	1	0	0	0	0	1	0	0	0	15842	971	34	3	672	3	TGIF2LX	23	89177754	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	135	89177754	66092806	633	14470										
MORF4L2	9643	hgsc.bcm.edu	37	chrX	102931737	102931737	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	tgcttgttctttctggtcttCctcacggatcctgaaggggg	12	10	4	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:102931737C>A	ENST00000441076.2	-	4	523	c.219G>T	c.(217-219)agG>agT	p.R73S	MORF4L2_ENST00000433176.2_Missense_Mutation_p.R73S|MORF4L2_ENST00000492116.1_5'UTR|MORF4L2_ENST00000360458.1_Missense_Mutation_p.R73S|MORF4L2_ENST00000451301.1_Missense_Mutation_p.R73S|MORF4L2_ENST00000423833.2_Missense_Mutation_p.R73S|MORF4L2_ENST00000422154.2_Missense_Mutation_p.R73S	NM_001142419.1|NM_012286.2	NP_001135891.1|NP_036418.1	Q15014	MO4L2_HUMAN	mortality factor 4 like 2	73					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA repair (GO:0006281)|positive regulation of striated muscle cell differentiation (GO:0051155)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)	13						TTCTGGTCTTCCTCACGGATC	0.567																																					p.R73S		Atlas-SNP	.											.	MORF4L2	35	.	0			c.G219T						.						66	57	60					X																	102931737		2203	4300	6503	SO:0001583	missense	9643	exon5			GGTCTTCCTCACG	AF100620	CCDS14512.1	Xq22	2010-11-24			ENSG00000123562	ENSG00000123562			16849	protein-coding gene	gene with protein product	"MORF-related gene X"	300409				9891081, 7584026	Standard	NM_012286		Approved	KIAA0026, MRGX	uc011msa.2	Q15014	OTTHUMG00000022104	ENST00000441076.2:c.219G>T	chrX.hg19:g.102931737C>A	ENSP00000391969:p.Arg73Ser	33.0	0.0		133.0	31.0	NM_001142422	B3KP92|D3DXA5|Q567V0|Q8J026	Missense_Mutation	SNP	ENST00000441076.2	hg19	CCDS14512.1	.	.	.	.	.	.	.	.	.	.	C	9.773	1.173156	0.21704	.	.	ENSG00000123562	ENST00000360458;ENST00000433176;ENST00000422154;ENST00000451301;ENST00000372619;ENST00000441076;ENST00000423833;ENST00000434230;ENST00000418819;ENST00000442614	T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55	4.52	3.66	0.41972	.	0.109692	0.38837	N	0.001545	T	0.15089	0.0364	N	0.24115	0.695	0.34938	D	0.749982	B	0.26081	0.141	B	0.18263	0.021	T	0.15607	-1.0431	10	0.07482	T	0.82	-16.8622	7.308	0.26459	0.0:0.8813:0.0:0.1187	.	73	Q15014	MO4L2_HUMAN	S	73;73;73;73;55;73;73;73;73;73	ENSP00000353643:R73S;ENSP00000415476:R73S;ENSP00000394417:R73S;ENSP00000410532:R73S;ENSP00000391969:R73S;ENSP00000416120:R73S	ENSP00000353643:R73S	R	-	3	2	MORF4L2	102818393	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.687000	0.46976	1.244000	0.43870	0.600000	0.82982	AGG	.	.		0.567	MORF4L2-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057732.1	NM_012286		A	102931737	C	A	102931737	3	1	101	1	0	0	0	0	1	0	0	0	9716	854	30	3	651	3	MORF4L2	23	102931737	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	13753983	102931737	52338823	634	14471										
PLP1	5354	hgsc.bcm.edu	37	chrX	103041518	103041518	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agatctttggcgactacaagAccaccatctgcggcaagggc	11	12	2	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:103041518A>G	ENST00000303958.2	+	3	462	c.316A>G	c.(316-318)Acc>Gcc	p.T106A	PLP1_ENST00000418604.1_Missense_Mutation_p.T106A|PLP1_ENST00000361621.2_Missense_Mutation_p.T106A	NM_000533.3	NP_000524.3	P60201	MYPR_HUMAN	proteolipid protein 1	106					astrocyte development (GO:0014002)|axon development (GO:0061564)|axon ensheathment (GO:0008366)|cell death (GO:0008219)|cell maturation (GO:0048469)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|long-chain fatty acid biosynthetic process (GO:0042759)|positive regulation of gene expression (GO:0010628)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	structural constituent of myelin sheath (GO:0019911)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	17						CGACTACAAGACCACCATCTG	0.587																																					p.T106A		Atlas-SNP	.											.	PLP1	37	.	0			c.A316G						.						119	106	110					X																	103041518		2203	4300	6503	SO:0001583	missense	5354	exon4			TACAAGACCACCA	M27110	CCDS14513.1, CCDS14514.1	Xq22	2013-05-14	2008-07-28		ENSG00000123560	ENSG00000123560			9086	protein-coding gene	gene with protein product	"Pelizaeus-Merzbacher disease"	300401	"spastic paraplegia 2, uncomplicated"	SPG2, PLP			Standard	NM_001128834		Approved	GPM6C	uc004elk.3	P60201	OTTHUMG00000022111	ENST00000303958.2:c.316A>G	chrX.hg19:g.103041518A>G	ENSP00000305152:p.Thr106Ala	71.0	0.0		387.0	90.0	NM_001128834	P04400|P06905|Q502Y1|Q6FHZ6	Missense_Mutation	SNP	ENST00000303958.2	hg19	CCDS14513.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.564697	0.45694	.	.	ENSG00000123560	ENST00000434483;ENST00000429977;ENST00000455268;ENST00000422393;ENST00000418604;ENST00000443502;ENST00000303958;ENST00000361621	D;D;D;D;D;D;D;D	0.99259	-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64	5.78	5.78	0.91487	.	0.183995	0.64402	D	0.000018	D	0.97284	0.9112	N	0.19112	0.55	0.41067	D	0.985429	B;B;B;B;P	0.35192	0.022;0.003;0.003;0.003;0.489	B;B;B;B;B	0.39465	0.012;0.006;0.008;0.006;0.3	D	0.97617	1.0133	10	0.42905	T	0.14	-4.5431	12.8049	0.57607	1.0:0.0:0.0:0.0	.	51;106;106;106;106	B4DI30;A8K9L3;B1B1G6;P60201;P60201-2	.;.;.;MYPR_HUMAN;.	A	106	ENSP00000403335:T106A;ENSP00000399913:T106A;ENSP00000409802:T106A;ENSP00000413931:T106A;ENSP00000405750:T106A;ENSP00000391853:T106A;ENSP00000305152:T106A;ENSP00000354860:T106A	ENSP00000305152:T106A	T	+	1	0	PLP1	102928174	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.159000	0.77483	1.931000	0.55961	0.486000	0.48141	ACC	.	.		0.587	PLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057743.2			G	103041518	A	G	103041518	3	3	101	1	0	0	0	0	1	0	0	0	12113	275	10	2	326	2	PLP1	23	103041518	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	109781	103041518	52229042	635	14472										
PLP1	5354	hgsc.bcm.edu	37	chrX	103041636	103041636	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	gtgtcattgtttgggaaaatGgctaggacatcccgacaagg	13	7	1	0	rs132630292		TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:103041636G>A	ENST00000303958.2	+	3	580	c.434G>A	c.(433-435)tGg>tAg	p.W145*	PLP1_ENST00000418604.1_Nonsense_Mutation_p.W145*|PLP1_ENST00000361621.2_Intron	NM_000533.3	NP_000524.3	P60201	MYPR_HUMAN	proteolipid protein 1	145			Missing (in HLD1).		astrocyte development (GO:0014002)|axon development (GO:0061564)|axon ensheathment (GO:0008366)|cell death (GO:0008219)|cell maturation (GO:0048469)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|long-chain fatty acid biosynthetic process (GO:0042759)|positive regulation of gene expression (GO:0010628)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	structural constituent of myelin sheath (GO:0019911)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	17						TTGGGAAAATGGCTAGGACAT	0.562																																					p.W145X		Atlas-SNP	.											.	PLP1	37	.	0			c.G434A	GRCh37	CM950965	PLP1	M	rs132630292	.						136	118	124					X																	103041636		2203	4300	6503	SO:0001587	stop_gained	5354	exon4			GAAAATGGCTAGG	M27110	CCDS14513.1, CCDS14514.1	Xq22	2013-05-14	2008-07-28		ENSG00000123560	ENSG00000123560			9086	protein-coding gene	gene with protein product	"Pelizaeus-Merzbacher disease"	300401	"spastic paraplegia 2, uncomplicated"	SPG2, PLP			Standard	NM_001128834		Approved	GPM6C	uc004elk.3	P60201	OTTHUMG00000022111	ENST00000303958.2:c.434G>A	chrX.hg19:g.103041636G>A	ENSP00000305152:p.Trp145*	84.0	0.0		382.0	47.0	NM_001128834	P04400|P06905|Q502Y1|Q6FHZ6	Nonsense_Mutation	SNP	ENST00000303958.2	hg19	CCDS14513.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.783343	0.90282	.	.	ENSG00000123560	ENST00000418604;ENST00000303958;ENST00000428755	.	.	.	5.78	4.9	0.64082	.	0.211332	0.36703	N	0.002450	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	-15.4207	12.6272	0.56636	0.0:0.0:0.8334:0.1666	.	.	.	.	X	145;145;123	.	ENSP00000305152:W145X	W	+	2	0	PLP1	102928292	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.473000	0.73572	1.141000	0.42275	0.600000	0.82982	TGG	.	.		0.562	PLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057743.2			A	103041636	G	A	103041636	4	1	101	1	0	0	0	0	0	1	0	0	12113	1357	47	3	444	3	PLP1	23	103041636	Nonsense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	118	103041636	52228924	636	14473										
OCRL	4952	hgsc.bcm.edu	37	chrX	128722192	128722192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cccctggaatgcaggaagagCtccagcagatcattgattgt	11	10	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:128722192C>T	ENST00000371113.4	+	21	2458	c.2293C>T	c.(2293-2295)Ctc>Ttc	p.L765F	OCRL_ENST00000357121.5_Missense_Mutation_p.L757F	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	765	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						GCAGGAAGAGCTCCAGCAGAT	0.463																																					p.L765F		Atlas-SNP	.											.	OCRL	117	.	0			c.C2293T						.						96	85	89					X																	128722192		2203	4300	6503	SO:0001583	missense	4952	exon21			GAAGAGCTCCAGC	U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.2293C>T	chrX.hg19:g.128722192C>T	ENSP00000360154:p.Leu765Phe	57.0	0.0		173.0	32.0	NM_000276	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	hg19	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	C	6.013	0.370877	0.11409	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	T;T	0.20200	2.09;2.09	5.52	3.16	0.36331	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.070421	0.56097	D	0.000035	T	0.24005	0.0581	L	0.28504	0.86	0.53688	D	0.999978	D;B	0.63046	0.992;0.044	P;B	0.62813	0.907;0.04	T	0.09862	-1.0655	10	0.12430	T	0.62	.	7.4919	0.27466	0.0:0.2692:0.0:0.7308	.	757;765	Q01968-2;Q01968	.;OCRL_HUMAN	F	765;757	ENSP00000360154:L765F;ENSP00000349635:L757F	ENSP00000349635:L757F	L	+	1	0	OCRL	128549873	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	0.664000	0.25068	0.252000	0.21531	-0.340000	0.08031	CTC	.	.		0.463	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		T	128722192	C	T	128722192	3	4	101	1	0	0	0	0	1	0	0	0	10832	797	28	3	2375	3	OCRL	23	128722192	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	25680556	128722192	26548368	637	14474										
FRMD7	90167	hgsc.bcm.edu	37	chrX	131212315	131212315	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cttgaatgttacatacaaatGcatcttccaaatttgggtct	6	8	2	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:131212315G>A	ENST00000298542.4	-	12	1905	c.1730C>T	c.(1729-1731)gCa>gTa	p.A577V	FRMD7_ENST00000370879.1_Missense_Mutation_p.A457V|FRMD7_ENST00000464296.1_Missense_Mutation_p.A562V	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	577					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					ACATACAAATGCATCTTCCAA	0.423																																					p.A577V		Atlas-SNP	.											.	FRMD7	69	.	0			c.C1730T						.						126	113	117					X																	131212315		2203	4300	6503	SO:0001583	missense	90167	exon12			ACAAATGCATCTT	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"nystagmus 1, congenital"	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1730C>T	chrX.hg19:g.131212315G>A	ENSP00000298542:p.Ala577Val	60.0	0.0		242.0	26.0	NM_194277	C0LLJ3|Q5JX99	Missense_Mutation	SNP	ENST00000298542.4	hg19	CCDS35397.1	.	.	.	.	.	.	.	.	.	.	G	3.190	-0.166006	0.06461	.	.	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	D;D;D	0.87809	-2.3;-1.96;-2.06	5.26	2.15	0.27550	.	0.822948	0.10736	N	0.640041	T	0.78329	0.4266	L	0.31752	0.955	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.60255	-0.7299	10	0.21540	T	0.41	.	9.0464	0.36349	0.3562:0.0:0.6438:0.0	.	562;577	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	V	457;577;562	ENSP00000359916:A457V;ENSP00000298542:A577V;ENSP00000417996:A562V	ENSP00000298542:A577V	A	-	2	0	FRMD7	131039996	0.643000	0.27269	0.926000	0.36857	0.064000	0.16182	1.180000	0.32005	0.275000	0.22094	-0.197000	0.12766	GCA	.	.		0.423	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		A	131212315	G	A	131212315	3	1	101	1	0	0	0	0	1	0	0	0	6063	1319	46	3	418	3	FRMD7	23	131212315	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	2490123	131212315	24058245	638	14475										
GPR112	139378	hgsc.bcm.edu	37	chrX	135453612	135453612	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cacaatgtgatgagataagtAtgaacctaactcatgttatg	8	6	1	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:135453612A>G	ENST00000394143.1	+	14	7813	c.7522A>G	c.(7522-7524)Atg>Gtg	p.M2508V	GPR112_ENST00000394141.1_Missense_Mutation_p.M2303V|GPR112_ENST00000370652.1_Missense_Mutation_p.M2508V|GPR112_ENST00000412101.1_Missense_Mutation_p.M2303V|GPR112_ENST00000287534.4_Missense_Mutation_p.M2306V	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2508					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TGAGATAAGTATGAACCTAAC	0.313																																					p.M2508V		Atlas-SNP	.											.	GPR112	459	.	0			c.A7522G						.						65	59	61					X																	135453612		2203	4296	6499	SO:0001583	missense	139378	exon14			ATAAGTATGAACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.7522A>G	chrX.hg19:g.135453612A>G	ENSP00000377699:p.Met2508Val	83.0	0.0		302.0	26.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	a	8.194	0.796709	0.16327	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.27557	1.7;1.7;1.66;1.92;1.66	5.14	2.52	0.30459	.	.	.	.	.	T	0.14787	0.0357	N	0.14661	0.345	0.09310	N	0.999996	B;B	0.17667	0.023;0.002	B;B	0.14023	0.01;0.008	T	0.32375	-0.9909	9	0.14252	T	0.57	.	5.4056	0.16320	0.7028:0.1896:0.1076:0.0	.	2303;2508	Q8IZF6-3;Q8IZF6	.;GP112_HUMAN	V	2508;2508;2303;2306;2303	ENSP00000377699:M2508V;ENSP00000359686:M2508V;ENSP00000416526:M2303V;ENSP00000287534:M2306V;ENSP00000377697:M2303V	ENSP00000287534:M2306V	M	+	1	0	GPR112	135281278	0.986000	0.35501	1.000000	0.80357	0.981000	0.71138	0.168000	0.16622	0.612000	0.30071	0.483000	0.47432	ATG	.	.		0.313	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			G	135453612	A	G	135453612	3	3	101	1	0	0	0	0	1	0	0	0	6637	449	16	2	7564	2	GPR112	23	135453612	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	4241297	135453612	19816948	639	14476										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140985121	140985121	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	caaccactcctatttctttgAagacacattagacctcacct	3	14	2	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:140985121A>G	ENST00000298296.1	+	7	1577	c.1577A>G	c.(1576-1578)gAa>gGa	p.E526G	MAGEC3_ENST00000536088.1_Missense_Mutation_p.E228G|MAGEC3_ENST00000544766.1_Missense_Mutation_p.E228G|MAGEC3_ENST00000409007.1_Missense_Mutation_p.E228G|MAGEC3_ENST00000443323.2_Missense_Mutation_p.E148G	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	526	MAGE 2. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					TATTTCTTTGAAGACACATTA	0.438																																					p.E526G		Atlas-SNP	.											.	MAGEC3	228	.	0			c.A1577G						.						152	144	147					X																	140985121		2203	4300	6503	SO:0001583	missense	139081	exon7			TCTTTGAAGACAC	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1577A>G	chrX.hg19:g.140985121A>G	ENSP00000298296:p.Glu526Gly	29.0	0.0		106.0	8.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	hg19	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	a	5.460	0.269946	0.10349	.	.	ENSG00000165509	ENST00000298296;ENST00000536088;ENST00000443323;ENST00000544766;ENST00000409007	T;T;T;T;T	0.04603	3.59;3.59;3.59;3.59;3.59	1.25	-2.5	0.06384	.	.	.	.	.	T	0.02418	0.0074	N	0.08118	0	0.09310	N	1	P;P	0.49253	0.921;0.49	B;B	0.42188	0.218;0.379	T	0.37865	-0.9687	9	0.59425	D	0.04	.	4.071	0.09882	0.5973:0.0:0.0:0.4027	.	526;228	Q8TD91;Q3SYA7	MAGC3_HUMAN;.	G	526;228;148;228;228	ENSP00000298296:E526G;ENSP00000441107:E228G;ENSP00000438254:E148G;ENSP00000440444:E228G;ENSP00000386566:E228G	ENSP00000298296:E526G	E	+	2	0	MAGEC3	140812787	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.807000	0.04520	-1.029000	0.03317	-1.111000	0.02071	GAA	.	.		0.438	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		G	140985121	A	G	140985121	3	3	101	1	0	0	0	0	1	0	0	0	9191	246	9	2	1832	2	MAGEC3	23	140985121	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	5531509	140985121	14285439	640	14477										
HMGB3	3149	hgsc.bcm.edu	37	chrX	150155724	150155724	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aataatttaaatgacagtgaAaagcagccttacatcactaa	5	7	1	2			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:150155724A>T	ENST00000325307.7	+	4	510	c.414A>T	c.(412-414)gaA>gaT	p.E138D	HMGB3_ENST00000448905.2_Missense_Mutation_p.E138D	NM_005342.2	NP_005333.2	O15347	HMGB3_HUMAN	high mobility group box 3	138					DNA recombination (GO:0006310)|multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(2)|lung(2)|skin(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					ATGACAGTGAAAAGCAGCCTT	0.488																																					p.E138D		Atlas-SNP	.											.	HMGB3	27	.	0			c.A414T						.						47	45	46					X																	150155724		2203	4297	6500	SO:0001583	missense	3149	exon4			CAGTGAAAAGCAG	AF274572	CCDS35428.1	Xq28	2011-07-01	2011-04-05	2002-08-16	ENSG00000029993	ENSG00000029993		"High-mobility group / Canonical"	5004	protein-coding gene	gene with protein product	"non-histone chromosomal protein"	300193	"high-mobility group (nonhistone chromosomal) protein 4", "high-mobility group box 3"	HMG4		9598312	Standard	XM_005274665		Approved	HMG2A, MGC90319	uc004fep.3	O15347	OTTHUMG00000024162	ENST00000325307.7:c.414A>T	chrX.hg19:g.150155724A>T	ENSP00000359393:p.Glu138Asp	43.0	0.0		109.0	101.0	NM_005342	O95556|Q6NS40	Missense_Mutation	SNP	ENST00000325307.7	hg19	CCDS35428.1	.	.	.	.	.	.	.	.	.	.	a	5.724	0.318006	0.10845	.	.	ENSG00000029993	ENST00000419110;ENST00000325307;ENST00000455596;ENST00000448905;ENST00000430118	D;D;D;D;D	0.95342	-3.68;-3.68;-3.68;-3.68;-3.68	5.05	-3.08	0.05347	High mobility group, HMG1/HMG2, subgroup (1);High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.127237	0.52532	D	0.000079	T	0.81341	0.4802	N	0.02192	-0.645	0.41426	D	0.987836	B	0.19200	0.034	B	0.24848	0.056	T	0.66763	-0.5841	10	0.02654	T	1	.	15.3324	0.74223	0.2667:0.0:0.7333:0.0	.	138	O15347	HMGB3_HUMAN	D	138	ENSP00000410354:E138D;ENSP00000359393:E138D;ENSP00000405601:E138D;ENSP00000442758:E138D;ENSP00000417027:E138D	ENSP00000359393:E138D	E	+	3	2	HMGB3	149906382	0.619000	0.27059	0.765000	0.31456	0.990000	0.78478	-0.130000	0.10498	-0.793000	0.04475	0.430000	0.28490	GAA	.	.		0.488	HMGB3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060867.1	NM_005342		T	150155724	A	T	150155724	3	4	101	1	0	0	0	0	1	0	0	0	7236	11	1	4	424	4	HMGB3	23	150155724	Missense_Mutation	SNP	A	TCGA-DD-A1EE-01A-11D-A12Z-10	9170603	150155724	5114836	641	14478										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151821044	151821044	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	agacggagtcagctctctccCcatcaccccagcgcaggccc	9	19	3	1			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:151821044C>A	ENST00000370306.2	+	9	1219	c.1199C>A	c.(1198-1200)cCc>cAc	p.P400H		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	400					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AGCTCTCTCCCCATCACCCCA	0.582																																					p.P400H		Atlas-SNP	.											.	GABRQ	131	.	0			c.C1199A						.						74	68	70					X																	151821044		2203	4300	6503	SO:0001583	missense	55879	exon9			CTCTCCCCATCAC	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1199C>A	chrX.hg19:g.151821044C>A	ENSP00000359329:p.Pro400His	63.0	0.0		293.0	19.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	hg19	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.279283	0.59758	.	.	ENSG00000147402	ENST00000370306	D	0.85629	-2.01	4.59	-0.767	0.11016	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.485053	0.15556	N	0.256196	T	0.74558	0.3732	L	0.46157	1.445	0.09310	N	1	B	0.12013	0.005	B	0.20767	0.031	T	0.62576	-0.6825	10	0.56958	D	0.05	.	0.591	0.00728	0.1747:0.3097:0.1684:0.3472	.	400	Q9UN88	GBRT_HUMAN	H	400	ENSP00000359329:P400H	ENSP00000359329:P400H	P	+	2	0	GABRQ	151571700	0.000000	0.05858	0.000000	0.03702	0.480000	0.33159	0.034000	0.13776	-0.294000	0.08973	0.600000	0.82982	CCC	.	.		0.582	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		A	151821044	C	A	151821044	3	1	101	1	0	0	0	0	1	0	0	0	6183	623	22	3	1233	3	GABRQ	23	151821044	Missense_Mutation	SNP	C	TCGA-DD-A1EE-01A-11D-A12Z-10	1665320	151821044	3449516	642	14479										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153035604	153035604	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	cagatgaatacttccattgtGcgttcggggactatgacagc	11	9	0	3			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:153035604G>A	ENST00000361971.5	+	8	1801	c.1687G>A	c.(1687-1689)Gcg>Acg	p.A563T	PLXNB3_ENST00000538543.1_Missense_Mutation_p.A113T|PLXNB3_ENST00000538282.1_Missense_Mutation_p.A173T|PLXNB3_ENST00000538966.1_Missense_Mutation_p.A586T|PLXNB3_ENST00000538776.1_Missense_Mutation_p.A216T	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	563					axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CTTCCATTGTGCGTTCGGGGA	0.597																																					p.A586T		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G1756A						.						99	89	93					X																	153035604		2203	4300	6503	SO:0001583	missense	5365	exon9			CATTGTGCGTTCG	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.1687G>A	chrX.hg19:g.153035604G>A	ENSP00000355378:p.Ala563Thr	28.0	0.0		86.0	82.0	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	8.755	0.922281	0.17982	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538543;ENST00000538282	T;T;T;T;T	0.68479	5.22;5.19;4.6;1.89;-0.33	5.06	4.19	0.49359	.	0.513595	0.21302	N	0.076798	T	0.50803	0.1637	L	0.31207	0.915	0.27042	N	0.963982	B;P;B;B;B	0.49696	0.058;0.927;0.216;0.081;0.209	B;P;B;B;B	0.45881	0.038;0.496;0.134;0.034;0.055	T	0.41124	-0.9526	10	0.11485	T	0.65	.	5.5958	0.17327	0.1085:0.1988:0.6926:0.0	.	216;245;113;586;563	B7Z3H9;B7Z9A5;F5GZZ4;F5H773;Q9ULL4	.;.;.;.;PLXB3_HUMAN	T	586;563;216;113;173	ENSP00000442736:A586T;ENSP00000355378:A563T;ENSP00000445569:A216T;ENSP00000444086:A113T;ENSP00000441919:A173T	ENSP00000355378:A563T	A	+	1	0	PLXNB3	152688798	0.818000	0.29161	1.000000	0.80357	0.300000	0.27592	0.267000	0.18552	2.090000	0.63153	0.529000	0.55759	GCG	.	.		0.597	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			A	153035604	G	A	153035604	3	1	101	1	0	0	0	0	1	0	0	0	12134	1319	46	3	1831	3	PLXNB3	23	153035604	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	1214560	153035604	2234956	643	14480										
IDH3G	3421	hgsc.bcm.edu	37	chrX	153055245	153055245	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	atcagcattggaactcacgtGcacctcttcaaagtccactg	7	13	4	0			TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrX:153055245G>A	ENST00000217901.5	-	5	464	c.268C>T	c.(268-270)Cac>Tac	p.H90Y	IDH3G_ENST00000370093.1_Missense_Mutation_p.H90Y|IDH3G_ENST00000427365.2_Missense_Mutation_p.H32Y|IDH3G_ENST00000497043.1_5'UTR|IDH3G_ENST00000370092.3_Missense_Mutation_p.H90Y	NM_004135.3	NP_004126.1	P51553	IDH3G_HUMAN	isocitrate dehydrogenase 3 (NAD+) gamma	90					carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)	17	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					GAACTCACGTGCACCTCTTCA	0.647																																					p.H90Y		Atlas-SNP	.											.	IDH3G	36	.	0			c.C268T						.						86	59	68					X																	153055245		2202	4298	6500	SO:0001583	missense	3421	exon5			TCACGTGCACCTC		CCDS14730.1, CCDS44019.1	Xq28	2008-02-05			ENSG00000067829	ENSG00000067829	1.1.1.41		5386	protein-coding gene	gene with protein product		300089				9286695	Standard	NM_004135		Approved		uc004fip.4	P51553	OTTHUMG00000024219	ENST00000217901.5:c.268C>T	chrX.hg19:g.153055245G>A	ENSP00000217901:p.His90Tyr	9.0	0.0		69.0	16.0	NM_004135	E9PDD5|Q9BUU5	Missense_Mutation	SNP	ENST00000217901.5	hg19	CCDS14730.1	.	.	.	.	.	.	.	.	.	.	G	17.42	3.384208	0.61845	.	.	ENSG00000067829	ENST00000370092;ENST00000217901;ENST00000370093;ENST00000427365;ENST00000444450;ENST00000444338	T;T;T;T;T;T	0.66280	0.64;0.64;0.64;0.64;0.64;-0.2	5.34	5.34	0.76211	Isopropylmalate dehydrogenase-like domain (2);	0.281987	0.39020	N	0.001489	T	0.38825	0.1055	N	0.12569	0.235	0.26986	N	0.965255	P;B	0.34800	0.469;0.137	B;B	0.27380	0.079;0.035	T	0.25882	-1.0119	10	0.21014	T	0.42	.	12.0109	0.53286	0.0:0.0:0.8271:0.1729	.	90;90	E9PDD5;P51553	.;IDH3G_HUMAN	Y	90;90;90;32;67;1	ENSP00000359110:H90Y;ENSP00000217901:H90Y;ENSP00000359111:H90Y;ENSP00000408529:H32Y;ENSP00000401862:H67Y;ENSP00000402747:H1Y	ENSP00000217901:H90Y	H	-	1	0	IDH3G	152708439	0.965000	0.33210	1.000000	0.80357	0.955000	0.61496	3.048000	0.49862	2.238000	0.73509	0.529000	0.55759	CAC	.	.		0.647	IDH3G-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061084.27			A	153055245	G	A	153055245	3	1	101	1	0	0	0	0	1	0	0	0	7507	1319	46	3	1012	3	IDH3G	23	153055245	Missense_Mutation	SNP	G	TCGA-DD-A1EE-01A-11D-A12Z-10	19641	153055245	2215315	644	14481										
TGIF2LY	90655	hgsc.bcm.edu	37	chrY	3447819	3447820	+	Missense_Mutation	DNP	CC	CC	AG													0.05	32	1	0.987975404806332	1.51606300457688	0.777369040612125	0.530729918092061	1	0	aaccagatccggagtcggccCctagccagaagctcaccgga							TCGA-DD-A1EE-01A-11D-A12Z-10	TCGA-DD-A1EE-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	65ed0706-a804-4744-a5fb-b473edf78c63	1d47f982-8d2a-4164-bf7a-ed6962fc2b13	g.chrY:3447819_3447820CC>AG	ENST00000559055.2	+	1	664_665	c.534_535CC>AG	c.(532-537)ccCCta>ccAGta	p.L179V	TGIF2LY_ENST00000321217.4_Missense_Mutation_p.L179V			Q8IUE0	TF2LY_HUMAN	TGFB-induced factor homeobox 2-like, Y-linked	179					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|upper_aerodigestive_tract(1)	2						GGAGTCGGCCCCTAGCCAGAAG	0.55																																					p.P178P|p.L179V		Atlas-SNP	.											.	TGIF2LY	6	.	0			c.C534A|c.C535G						.																																			SO:0001583	missense	90655	exon2			TCGGCCCCTAGCC|CGGCCCCTAGCCA	AF332223	CCDS14775.1	Yp11.2	2011-06-20	2007-02-07		ENSG00000176679	ENSG00000176679		"Homeoboxes / TALE class"	18569	protein-coding gene	gene with protein product		400025	"TGFB-induced factor 2-like, Y-linked"				Standard	NM_139214		Approved		uc004fqk.3	Q8IUE0	OTTHUMG00000036153	Exception_encountered	chrY.hg19:g.3447819_3447820delinsAG	ENSP00000453750:p.Leu179Val	50.0|51.0	0.0		143.0|146.0	18.0|19.0	NM_139214	A2VCU1	Silent|Missense_Mutation	SNP	ENST00000559055.2	hg19	CCDS14775.1																																																																																			.	.		0.55	TGIF2LY-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417915.2	NM_139214		AG	3447820	CC	AG	3447819	3	1	101	1	0	0	0	0	1	0	0	0	15843	610	22	3	536	3	TGIF2LY	24	3447819	Missense_Mutation	DNP	CC	TCGA-DD-A1EE-01A-11D-A12Z-10		3447819	55925747	645	14482										
CCNL2	81669	hgsc.bcm.edu	37	chr1	1322749	1322749	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tttcccggattatccgcccgCtcccgtgacctgcttcgaga	9	16	0	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:1322749C>T	ENST00000400809.3	-	11	1430	c.1425G>A	c.(1423-1425)gaG>gaA	p.E475E	CCNL2_ENST00000505849.1_5'UTR|CCNL2_ENST00000408952.5_Silent_p.E253E	NM_030937.4	NP_112199.2	Q96S94	CCNL2_HUMAN	cyclin L2	475					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		TATCCGCCCGCTCCCGTGACC	0.562																																					p.E475E		Atlas-SNP	.											.	CCNL2	54	.	0			c.G1425A						.						110	120	117					1																	1322749		2203	4296	6499	SO:0001819	synonymous_variant	81669	exon11			CGCCCGCTCCCGT	AF251294	CCDS30557.1, CCDS30558.1	1p36.33	2014-07-03			ENSG00000221978	ENSG00000221978			20570	protein-coding gene	gene with protein product	"cyclin S"	613482	"cyclin M"	CCNM		14725631	Standard	NM_030937		Approved	ania-6b, PCEE, SB138, HLA-ISO, CCNS	uc001afi.2	Q96S94	OTTHUMG00000002917	ENST00000400809.3:c.1425G>A	chr1.hg19:g.1322749C>T		56.0	0.0		96.0	31.0	NM_030937	A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00	Silent	SNP	ENST00000400809.3	hg19	CCDS30557.1																																																																																			.	.		0.562	CCNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008146.2	NM_030937		T	1322749	C	T	1322749	2	4	102	1	0	0	0	0	0	0	0	1	2934	796	28	3		3	CCNL2	1	1322749	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10		1322749	247927872	1	14483										
MMEL1	79258	hgsc.bcm.edu	37	chr1	2535696	2535696	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	caacgtggccactgacaccaTgaactgcaggtaggcttccc	10	14	0	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:2535696T>C	ENST00000378412.3	-	10	1002	c.841A>G	c.(841-843)Atg>Gtg	p.M281V	MMEL1_ENST00000502556.1_Intron|MMEL1_ENST00000288709.6_Missense_Mutation_p.M272V			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	281						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		ACTGACACCATGAACTGCAGG	0.652																																					p.M281V		Atlas-SNP	.											.	MMEL1	64	.	0			c.A841G						.						63	65	64					1																	2535696		2202	4299	6501	SO:0001583	missense	79258	exon10			ACACCATGAACTG	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"membrane metallo-endopeptidase-like 2"	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.841A>G	chr1.hg19:g.2535696T>C	ENSP00000367668:p.Met281Val	67.0	0.0		126.0	82.0	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	hg19	CCDS30569.2	.	.	.	.	.	.	.	.	.	.	T	18.27	3.585868	0.66105	.	.	ENSG00000142606	ENST00000288709;ENST00000378412	T;T	0.75050	-0.9;-0.9	4.43	4.43	0.53597	Peptidase M13 (1);	0.000000	0.85682	D	0.000000	D	0.85639	0.5743	M	0.82823	2.61	0.80722	D	1	D	0.76494	0.999	D	0.69654	0.965	D	0.87970	0.2736	10	0.87932	D	0	-31.6286	13.1682	0.59583	0.0:0.0:0.0:1.0	.	281	Q495T6	MMEL1_HUMAN	V	272;281	ENSP00000288709:M272V;ENSP00000367668:M281V	ENSP00000288709:M272V	M	-	1	0	MMEL1	2525556	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	3.567000	0.53813	1.741000	0.51731	0.397000	0.26171	ATG	.	.		0.652	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467		C	2535696	T	C	2535696	3	2	102	1	0	0	0	0	1	0	0	0	9655	1464	51	2	1558	2	MMEL1	1	2535696	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	1212947	2535696	246714925	2	14484										
MTOR	2475	hgsc.bcm.edu	37	chr1	11204794	11204794	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ctcctccagctcggacagcaTgtggcaagaaaccatggcct	10	14	0	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:11204794T>C	ENST00000361445.4	-	34	4859	c.4783A>G	c.(4783-4785)Atg>Gtg	p.M1595V	MTOR-AS1_ENST00000445982.1_RNA|MTOR_ENST00000495435.1_5'UTR|MTOR-AS1_ENST00000420480.1_RNA	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1595	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCGGACAGCATGTGGCAAGAA	0.483																																					p.M1595V		Atlas-SNP	.											.	MTOR	327	.	0			c.A4783G						.						92	83	86					1																	11204794		2203	4300	6503	SO:0001583	missense	2475	exon34			ACAGCATGTGGCA	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.4783A>G	chr1.hg19:g.11204794T>C	ENSP00000354558:p.Met1595Val	28.0	0.0		42.0	28.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.157965	0.78114	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.71579	-0.58	5.6	5.6	0.85130	PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	D	0.85323	0.5670	M	0.93763	3.455	0.80722	D	1	P	0.35542	0.508	P	0.48795	0.59	D	0.87752	0.2592	10	0.72032	D	0.01	-11.5413	15.7961	0.78412	0.0:0.0:0.0:1.0	.	1595	P42345	MTOR_HUMAN	V	1595	ENSP00000354558:M1595V	ENSP00000354558:M1595V	M	-	1	0	MTOR	11127381	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.665000	0.83852	2.131000	0.65755	0.533000	0.62120	ATG	.	.		0.483	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		C	11204794	T	C	11204794	3	2	102	1	0	0	0	0	1	0	0	0	9963	1464	51	2	2966	2	MTOR	1	11204794	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	8669098	11204794	238045827	3	14485										
CELA3A	10136	hgsc.bcm.edu	37	chr1	22332241	22332241	+	Missense_Mutation	SNP	A	A	G													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ggtgatccccatcaactctgAggagctgtttgtgcatccac					rs75527968	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:22332241A>G	ENST00000290122.3	+	4	333	c.314A>G	c.(313-315)gAg>gGg	p.E105G	RN7SL768P_ENST00000584415.1_RNA|CELA3A_ENST00000374663.1_Missense_Mutation_p.E105G	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	105	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						ATCAACTCTGAGGAGCTGTTT	0.592											OREG0013211	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	5	0.000998403	0.0015	0.0014	5008	,	,		21127	0		0	False		,,,				2504	0.002				p.E105G		Atlas-SNP	.											.	CELA3A	35	.	0			c.A314G						.						128	112	118					1																	22332241		2197	4300	6497	SO:0001583	missense	10136	exon4			ACTCTGAGGAGCT	D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"protease E"		"elastase 3A, pancreatic (protease E)", "elastase 3A, pancreatic"	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.314A>G	chr1.hg19:g.22332241A>G	ENSP00000290122:p.Glu105Gly	70.0	0.0	755	133.0	9.0	NM_005747	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	hg19	CCDS220.1	.	.	.	.	.	.	.	.	.	.	A	5.149	0.213076	0.09757	.	.	ENSG00000142789	ENST00000290122;ENST00000374663;ENST00000374661	T;D	0.93547	2.21;-3.24	3.88	-0.633	0.11519	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.86560	0.5962	L	0.38953	1.18	0.09310	N	1	B;B	0.10296	0.003;0.0	B;B	0.16289	0.015;0.005	T	0.71262	-0.4645	9	0.18710	T	0.47	-3.7117	6.9051	0.24305	0.575:0.0:0.425:0.0	.	105;105	B1AQ52;P09093	.;CEL3A_HUMAN	G	105;105;121	ENSP00000290122:E105G;ENSP00000363795:E105G	ENSP00000290122:E105G	E	+	2	0	CELA3A	22204828	0.000000	0.05858	0.003000	0.11579	0.017000	0.09413	-1.034000	0.03567	0.009000	0.14813	-1.727000	0.00703	GAG	.	A|0.500;G|0.500		0.592	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747		G	22332241	A	G	22332241	3	3	102	1	0	0	0	0	1	0	0	0	3215	304	11	2	328	2	CELA3A	1	22332241	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	11127447	22332241	226918380	4	14486	64	2								
CELA3A	10136	hgsc.bcm.edu	37	chr1	22332245	22332245	+	Missense_Mutation	SNP	G	G	C													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	atccccatcaactctgaggaGctgtttgtgcatccactctg					rs74958230	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:22332245G>C	ENST00000290122.3	+	4	337	c.318G>C	c.(316-318)gaG>gaC	p.E106D	RN7SL768P_ENST00000584415.1_RNA|CELA3A_ENST00000374663.1_Missense_Mutation_p.E106D	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	106	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.			Missing (in Ref. 1; AAA66350). {ECO:0000305}.	cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						ACTCTGAGGAGCTGTTTGTGC	0.592													c|||	222	0.0443291	0.0325	0.0749	5008	,	,		19649	0.0357		0.0626	False		,,,				2504	0.0286				p.E106D		Atlas-SNP	.											.	CELA3A	35	.	0			c.G318C						.						130	113	119					1																	22332245		2197	4300	6497	SO:0001583	missense	10136	exon4			TGAGGAGCTGTTT	D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"protease E"		"elastase 3A, pancreatic (protease E)", "elastase 3A, pancreatic"	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.318G>C	chr1.hg19:g.22332245G>C	ENSP00000290122:p.Glu106Asp	69.0	0.0		140.0	10.0	NM_005747	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	hg19	CCDS220.1	.	.	.	.	.	.	.	.	.	.	G	8.422	0.846631	0.16963	.	.	ENSG00000142789	ENST00000290122;ENST00000374663;ENST00000374661	T;D	0.93189	2.26;-3.18	3.88	0.792	0.18625	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.85487	0.5708	N	0.21545	0.675	0.19300	N	0.999971	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.002	T	0.70371	-0.4890	9	0.22706	T	0.39	-20.2782	7.771	0.29008	0.321:0.5221:0.157:0.0	.	106;106	B1AQ52;P09093	.;CEL3A_HUMAN	D	106;106;122	ENSP00000290122:E106D;ENSP00000363795:E106D	ENSP00000290122:E106D	E	+	3	2	CELA3A	22204832	0.909000	0.30893	0.224000	0.23877	0.007000	0.05969	0.262000	0.18460	-0.019000	0.14055	-0.514000	0.04452	GAG	.	G|0.500;C|0.500		0.592	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747		C	22332245	G	C	22332245	3	2	102	1	0	0	0	0	1	0	0	0	3215	962	34	4	332	4	CELA3A	1	22332245	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	4	22332245	226918376	5	14487	64	2								
SLC22A15	55356	hgsc.bcm.edu	37	chr1	116563474	116563474	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ggcctttgtcttgcttaatgAatgtgtgggcaccgcctact	11	10	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:116563474A>G	ENST00000369503.4	+	4	696	c.566A>G	c.(565-567)gAa>gGa	p.E189G	SLC22A15_ENST00000369502.1_Missense_Mutation_p.E189G	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	189					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TTGCTTAATGAATGTGTGGGC	0.488											OREG0013699	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E189G		Atlas-SNP	.											.	SLC22A15	65	.	0			c.A566G						.						106	104	105					1																	116563474		1984	4168	6152	SO:0001583	missense	55356	exon4			TTAATGAATGTGT	AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"Solute carriers"	20301	protein-coding gene	gene with protein product		608275	"solute carrier family 22 (organic cation transporter), member 15"			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.566A>G	chr1.hg19:g.116563474A>G	ENSP00000358515:p.Glu189Gly	136.0	0.0	1474	366.0	151.0	NM_018420	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Missense_Mutation	SNP	ENST00000369503.4	hg19	CCDS44198.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.919801	0.92249	.	.	ENSG00000163393	ENST00000369503;ENST00000369502	D;T	0.86694	-2.16;0.33	5.84	5.84	0.93424	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.95752	0.8618	H	0.98256	4.185	0.58432	D	0.99999	D;D	0.58268	0.974;0.982	D;D	0.70487	0.969;0.959	D	0.97366	0.9973	10	0.87932	D	0	.	16.2254	0.82286	1.0:0.0:0.0:0.0	.	189;189	Q8IZD6;Q8IZD6-2	S22AF_HUMAN;.	G	189	ENSP00000358515:E189G;ENSP00000358514:E189G	ENSP00000358514:E189G	E	+	2	0	SLC22A15	116364997	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.980000	0.88113	2.225000	0.72522	0.528000	0.53228	GAA	.	.		0.488	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420		G	116563474	A	G	116563474	3	3	102	1	0	0	0	0	1	0	0	0	14461	246	9	2	580	2	SLC22A15	1	116563474	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	94231229	116563474	132687147	6	14488										
FAM189B	10712	hgsc.bcm.edu	37	chr1	155224577	155224577	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ccagcgtaagcagggcctgcAgccagggtcggtggaggcgg	19	11	0	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:155224577A>C	ENST00000361361.2	-	1	601	c.92T>G	c.(91-93)cTg>cGg	p.L31R	FAM189B_ENST00000472550.1_5'UTR|FAM189B_ENST00000350210.2_Missense_Mutation_p.L31R|SCAMP3_ENST00000472397.1_5'Flank|FAM189B_ENST00000368368.3_Missense_Mutation_p.L31R	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	31						integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						CAGGGCCTGCAGCCAGGGTCG	0.672																																					p.L31R		Atlas-SNP	.											.	FAM189B	51	.	0			c.T92G						.						43	39	40					1																	155224577		2203	4300	6503	SO:0001583	missense	10712	exon1			GCCTGCAGCCAGG	AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 2"	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.92T>G	chr1.hg19:g.155224577A>C	ENSP00000354958:p.Leu31Arg	47.0	0.0		170.0	19.0	NM_001267608	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	hg19	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	A	19.34	3.809219	0.70797	.	.	ENSG00000160767	ENST00000350210;ENST00000333966;ENST00000368368;ENST00000361361;ENST00000491082	T;T;T;T	0.24350	2.16;2.43;2.42;1.86	4.59	4.59	0.56863	.	0.195943	0.35013	N	0.003501	T	0.13200	0.0320	N	0.08118	0	0.32694	N	0.513739	D;D;D;D	0.65815	0.968;0.995;0.994;0.995	P;D;P;P	0.69142	0.724;0.962;0.81;0.884	T	0.07271	-1.0781	10	0.32370	T	0.25	.	6.958	0.24582	0.8987:0.0:0.1013:0.0	.	31;31;31;31	D6RD59;B1AVS5;P81408-2;P81408	.;.;.;F189B_HUMAN	R	31	ENSP00000307128:L31R;ENSP00000357352:L31R;ENSP00000354958:L31R;ENSP00000427011:L31R	ENSP00000333944:L31R	L	-	2	0	FAM189B	153491201	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.772000	0.55325	2.057000	0.61298	0.533000	0.62120	CTG	.	.		0.672	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589		C	155224577	A	C	155224577	3	2	102	1	0	0	0	0	1	0	0	0	5522	188	7	5	1962	5	FAM189B	1	155224577	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	38661103	155224577	94026044	7	14489										
OR6K6	128371	hgsc.bcm.edu	37	chr1	158725609	158725609	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tggaaggcttttccactatcAgaagagggctggttgggctg	15	7	1	2	rs559439148		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:158725609A>G	ENST00000368144.2	+	1	1100	c.1004A>G	c.(1003-1005)cAg>cGg	p.Q335R		NM_001005184.1	NP_001005184.1	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K, member 6	335						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(17)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0378)					TTCCACTATCAGAAGAGGGCT	0.418													A|||	1	0.000199681	0	0	5008	,	,		19386	0		0	False		,,,				2504	0.001				p.Q335R		Atlas-SNP	.											.	OR6K6	81	.	0			c.A1004G						.						83	87	86					1																	158725609		2203	4300	6503	SO:0001583	missense	128371	exon1			ACTATCAGAAGAG	BK004198	CCDS30904.1	1q23.1	2012-08-09			ENSG00000180433	ENSG00000180433		"GPCR / Class A : Olfactory receptors"	15033	protein-coding gene	gene with protein product							Standard	NM_001005184		Approved		uc001fsw.1	Q8NGW6	OTTHUMG00000022772	ENST00000368144.2:c.1004A>G	chr1.hg19:g.158725609A>G	ENSP00000357126:p.Gln335Arg	118.0	0.0		301.0	46.0	NM_001005184	B9EIM8|Q5VUU9|Q6IFR4	Missense_Mutation	SNP	ENST00000368144.2	hg19	CCDS30904.1	.	.	.	.	.	.	.	.	.	.	A	7.484	0.649280	0.14516	.	.	ENSG00000180433	ENST00000368144	T	0.35048	1.33	5.26	2.92	0.33932	.	0.634090	0.12974	N	0.423879	T	0.05502	0.0145	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41288	-0.9517	10	0.27082	T	0.32	-1.0501	7.7691	0.28997	0.8182:0.0:0.1818:0.0	.	335	Q8NGW6	OR6K6_HUMAN	R	335	ENSP00000357126:Q335R	ENSP00000357126:Q335R	Q	+	2	0	OR6K6	156992233	0.001000	0.12720	0.003000	0.11579	0.005000	0.04900	1.190000	0.32126	0.440000	0.26502	-0.274000	0.10170	CAG	.	.		0.418	OR6K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059065.2	NM_001005184		G	158725609	A	G	158725609	3	3	102	1	0	0	0	0	1	0	0	0	11213	188	7	2	1006	2	OR6K6	1	158725609	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	3501032	158725609	90525012	8	14490										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179621325	179621325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gtcaaaagagagtgagttacGtatcttggtaagagattttt	11	3	2	3	rs375929466		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:179621325G>A	ENST00000367614.1	+	13	2512	c.2153G>A	c.(2152-2154)cGt>cAt	p.R718H	TDRD5_ENST00000444136.1_Missense_Mutation_p.R718H|TDRD5_ENST00000294848.8_Missense_Mutation_p.R718H	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	718					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						AGTGAGTTACGTATCTTGGTA	0.348																																					p.R718H		Atlas-SNP	.											.	TDRD5	149	.	0			c.G2153A						.	A	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	825.9+/-416.6	0,1,2202	81	79	80		2153,818,2153,2153,2153	-0.7	0	1		80	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	TDRD5	NM_173533.3,NM_001199092.1,NM_001199091.1,NM_001199089.1,NM_001199085.1	29,29,29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign	718/982,273/537,718/982,718/1036,718/1036	179621325	1,13005	2203	4300	6503	SO:0001583	missense	163589	exon13			AGTTACGTATCTT	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2153G>A	chr1.hg19:g.179621325G>A	ENSP00000356586:p.Arg718His	106.0	0.0		239.0	23.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.513657	0.27123	2.27E-4	0.0	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.30182	2.76;2.76;2.92;1.54	4.75	-0.711	0.11230	.	1.820450	0.03225	N	0.178189	T	0.13372	0.0324	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.11227	-1.0596	10	0.20519	T	0.43	.	0.2658	0.00225	0.325:0.1442:0.2511:0.2797	.	718;718	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	H	718;718;718;174	ENSP00000356586:R718H;ENSP00000294848:R718H;ENSP00000406052:R718H;ENSP00000410744:R174H	ENSP00000294848:R718H	R	+	2	0	TDRD5	177887948	0.000000	0.05858	0.000000	0.03702	0.383000	0.30230	-0.429000	0.06982	-0.227000	0.09884	-0.381000	0.06696	CGT	.	.		0.348	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		A	179621325	G	A	179621325	3	1	102	1	0	0	0	0	1	0	0	0	15748	1145	40	1	2199	1	TDRD5	1	179621325	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	20895716	179621325	69629296	9	14491										
PTPRC	5788	hgsc.bcm.edu	37	chr1	198721876	198721876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aagggaacaagcatcacaagAgtacacctctactcattcac	6	12	4	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:198721876A>G	ENST00000367376.2	+	31	3649	c.3478A>G	c.(3478-3480)Agt>Ggt	p.S1160G	PTPRC_ENST00000352140.3_Missense_Mutation_p.S1112G|PTPRC_ENST00000348564.6_Missense_Mutation_p.S1001G|PTPRC_ENST00000594404.1_Missense_Mutation_p.S999G|PTPRC_ENST00000442510.2_Missense_Mutation_p.S1162G	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	1160	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						GCATCACAAGAGTACACCTCT	0.433																																					p.S1162G		Atlas-SNP	.											.	PTPRC	229	.	0			c.A3484G						.						66	62	63					1																	198721876		2203	4299	6502	SO:0001583	missense	5788	exon31			CACAAGAGTACAC	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.3478A>G	chr1.hg19:g.198721876A>G	ENSP00000356346:p.Ser1160Gly	36.0	0.0		89.0	13.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	hg19		.	.	.	.	.	.	.	.	.	.	A	11.12	1.543897	0.27563	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000442510;ENST00000348564	D	0.84298	-1.83	6.02	3.7	0.42460	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.685138	0.13231	N	0.403621	T	0.75064	0.3799	N	0.25332	0.735	0.24376	N	0.994813	B;B;B	0.14805	0.011;0.011;0.011	B;B;B	0.19666	0.026;0.026;0.018	T	0.62558	-0.6829	10	0.35671	T	0.21	.	7.2685	0.26244	0.7741:0.1523:0.0736:0.0	.	1001;1112;1160	B1ALS3;E9PC28;P08575	.;.;PTPRC_HUMAN	G	1162;1112;1160;999	ENSP00000193532:S1112G	ENSP00000306782:S999G	S	+	1	0	PTPRC	196988499	0.801000	0.28930	0.250000	0.24296	0.447000	0.32167	1.536000	0.36072	1.078000	0.41014	0.528000	0.53228	AGT	.	.		0.433	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				G	198721876	A	G	198721876	3	3	102	1	0	0	0	0	1	0	0	0	12812	304	11	2	3607	2	PTPRC	1	198721876	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	19100551	198721876	50528745	10	14492										
OPTC	26254	hgsc.bcm.edu	37	chr1	203468895	203468895	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gagaaccagttggaagctctGcccgtgctgcccagtggcat	13	12	1	1	rs114294638	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:203468895G>T	ENST00000367222.2	+	5	764	c.648G>T	c.(646-648)ctG>ctT	p.L216L		NM_014359.3	NP_055174.1	Q9UBM4	OPT_HUMAN	opticin	216					negative regulation of angiogenesis (GO:0016525)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			breast(1)|cervix(1)|kidney(5)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.109)			TGGAAGCTCTGCCCGTGCTGC	0.567																																					p.L216L		Atlas-SNP	.											.	OPTC	50	.	0			c.G648T						.						177	173	175					1																	203468895		2203	4300	6503	SO:0001819	synonymous_variant	26254	exon5			AGCTCTGCCCGTG	AF161702	CCDS1439.1	1q31	2008-02-05			ENSG00000188770	ENSG00000188770			8158	protein-coding gene	gene with protein product	"oculoglycan"	605127				10636917	Standard	NM_014359		Approved		uc001gzu.1	Q9UBM4	OTTHUMG00000036100	ENST00000367222.2:c.648G>T	chr1.hg19:g.203468895G>T		74.0	0.0		188.0	114.0	NM_014359	Q5T2G4	Silent	SNP	ENST00000367222.2	hg19	CCDS1439.1																																																																																			.	G|0.998;A|0.002		0.567	OPTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087964.1	NM_014359		T	203468895	G	T	203468895	2	4	102	1	0	0	0	0	0	0	0	1	10897	1306	46	3		3	OPTC	1	203468895	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	4747019	203468895	45781726	11	14493										
EXO1	9156	hgsc.bcm.edu	37	chr1	242035389	242035389	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tctctttcatttacgaagaaGaccaagaaaaatagctctga	6	8	3	4			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:242035389G>A	ENST00000366548.3	+	12	1916	c.1323G>A	c.(1321-1323)aaG>aaA	p.K441K	EXO1_ENST00000348581.5_Silent_p.K441K|EXO1_ENST00000518483.1_Silent_p.K441K	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	441	Interaction with MLH1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			TTACGAAGAAGACCAAGAAAA	0.358								Editing and processing nucleases																													p.K441K		Atlas-SNP	.											EXO1,colon,carcinoma,0,1	EXO1	103	.	0			c.G1323A						.						44	45	45					1																	242035389		2203	4300	6503	SO:0001819	synonymous_variant	9156	exon10			GAAGAAGACCAAG	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1323G>A	chr1.hg19:g.242035389G>A		140.0	0.0		376.0	32.0	NM_006027	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Silent	SNP	ENST00000366548.3	hg19	CCDS1620.1																																																																																			.	.		0.358	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027		A	242035389	G	A	242035389	2	1	102	1	0	0	0	0	0	0	0	1	5302	933	33	3		3	EXO1	1	242035389	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	38566494	242035389	7215232	12	14494										
ASAP2	8853	hgsc.bcm.edu	37	chr2	9528642	9528643	+	Frame_Shift_Ins	INS	-	-	C													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	agcccccagcaccaccagcgINScccccccgcttcctccacgg					rs376816649		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:9528642_9528643insC	ENST00000281419.3	+	22	2690_2691	c.2350_2351insC	c.(2350-2352)gccfs	p.A784fs	ASAP2_ENST00000315273.4_Frame_Shift_Ins_p.A784fs|ASAP2_ENST00000491413.1_3'UTR	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	784	Pro-rich.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						CACCACCAGCGCCCCCCCGCTT	0.579																																					p.A784fs		Atlas-INDEL	.											.,2	ASAP2	91	.	0			c.2350_2351insC						.		,	9,4257		0,9,2124					,	5.6	1			28	12,8240		0,12,4114	no	frameshift,frameshift	ASAP2	NM_003887.2,NM_001135191.1	,	0,21,6238	A1A1,A1R,RR		0.1454,0.211,0.1678	,	,		21,12497				SO:0001589	frameshift_variant	8853	exon22			.	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2357dupC	chr2.hg19:g.9528649_9528649dupC	ENSP00000281419:p.Ala784fs	33.0	0.0		70.0	11.0	NM_001135191	D6W4Y8	Frame_Shift_Ins	INS	ENST00000281419.3	hg19	CCDS1661.1																																																																																			.	.		0.579	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		C	9528643	-	C	9528642	7	5	102	1	0	1	1	0	0	0	0	0	1011	1087	38	0	2436	0	ASAP2	2	9528642	Frame_Shift_Ins	INS	-	TCGA-DD-A1EF-01A-11D-A12Z-10		9528642	233670731	13	14495										
UBXN2A	165324	hgsc.bcm.edu	37	chr2	24194229	24194229	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttttgttgatagcctttttgAggaagctcagaaggttagtt	11	4	1	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:24194229A>T	ENST00000309033.4	+	3	369	c.125A>T	c.(124-126)gAg>gTg	p.E42V	UBXN2A_ENST00000446425.2_3'UTR|UBXN2A_ENST00000404924.1_Missense_Mutation_p.E42V|UBXN2A_ENST00000535786.1_Missense_Mutation_p.E42V	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	42					regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						AGCCTTTTTGAGGAAGCTCAG	0.333																																					p.E42V		Atlas-SNP	.											.	UBXN2A	20	.	0			c.A125T						.						128	135	133					2																	24194229		2203	4300	6503	SO:0001583	missense	165324	exon3			TTTTTGAGGAAGC	BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960		"UBX domain containing"	27265	protein-coding gene	gene with protein product			"UBX domain containing 4"	UBXD4		12477932	Standard	NM_181713		Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.125A>T	chr2.hg19:g.24194229A>T	ENSP00000312107:p.Glu42Val	69.0	0.0		106.0	64.0	NM_181713	A8K577|B7ZKP8|Q569G8	Missense_Mutation	SNP	ENST00000309033.4	hg19	CCDS1704.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.948036	0.73787	.	.	ENSG00000173960	ENST00000404924;ENST00000309033;ENST00000535786	T;T;T	0.51574	0.75;0.75;0.7	4.53	4.53	0.55603	.	0.096452	0.64402	D	0.000001	T	0.54951	0.1890	L	0.32530	0.975	0.41646	D	0.989103	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.957	T	0.52533	-0.8563	10	0.33940	T	0.23	-0.4989	12.105	0.53807	1.0:0.0:0.0:0.0	.	42;42	B7ZKP8;P68543	.;UBX2A_HUMAN	V	42	ENSP00000385525:E42V;ENSP00000312107:E42V;ENSP00000440533:E42V	ENSP00000312107:E42V	E	+	2	0	UBXN2A	24047733	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.240000	0.65378	2.011000	0.59026	0.524000	0.50904	GAG	.	.		0.333	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246824.2	NM_181713		T	24194229	A	T	24194229	3	4	102	1	0	0	0	0	1	0	0	0	16929	304	11	4	131	4	UBXN2A	2	24194229	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	14665587	24194229	219005144	14	14496										
MTIF2	4528	hgsc.bcm.edu	37	chr2	55473534	55473534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cactggaccattgggatctgCtttcaattctaacatttctg	7	10	4	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:55473534C>T	ENST00000263629.4	-	10	1360	c.1045G>A	c.(1045-1047)Gca>Aca	p.A349T	MTIF2_ENST00000394600.3_Missense_Mutation_p.A349T|MTIF2_ENST00000403721.1_Missense_Mutation_p.A349T	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	349					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						TTGGGATCTGCTTTCAATTCT	0.378																																					p.A349T		Atlas-SNP	.											.	MTIF2	64	.	0			c.G1045A						.						169	155	159					2																	55473534		2203	4300	6503	SO:0001583	missense	4528	exon10			GATCTGCTTTCAA	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1045G>A	chr2.hg19:g.55473534C>T	ENSP00000263629:p.Ala349Thr	125.0	0.0		256.0	24.0	NM_002453	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	hg19	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	C	35	5.553310	0.96501	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823;ENST00000535023	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.33	5.33	0.75918	.	0.110995	0.64402	D	0.000010	T	0.63558	0.2521	M	0.85710	2.77	0.80722	D	1	P	0.38978	0.652	P	0.49829	0.623	T	0.66779	-0.5837	10	0.52906	T	0.07	-15.7217	19.0262	0.92932	0.0:1.0:0.0:0.0	.	349	P46199	IF2M_HUMAN	T	349;349;349;69;349	ENSP00000384481:A349T;ENSP00000263629:A349T;ENSP00000378099:A349T;ENSP00000403492:A69T	ENSP00000263629:A349T	A	-	1	0	MTIF2	55327038	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.268000	0.78473	2.505000	0.84491	0.655000	0.94253	GCA	.	.		0.378	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		T	55473534	C	T	55473534	3	4	102	1	0	0	0	0	1	0	0	0	9943	797	28	3	1166	3	MTIF2	2	55473534	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	31279305	55473534	187725839	15	14497										
WDR33	55339	hgsc.bcm.edu	37	chr2	128474768	128474768	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttgtccggggttcagaggggGaatgcgaccttgtgctccct	15	10	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:128474768G>T	ENST00000322313.4	-	17	2988	c.2830C>A	c.(2830-2832)Ccc>Acc	p.P944T		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	944					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TTCAGAGGGGGAATGCGACCT	0.488																																					p.P944T		Atlas-SNP	.											WDR33,scalp,malignant_melanoma,0,1	WDR33	136	.	0			c.C2830A						.						42	40	41					2																	128474768		2203	4300	6503	SO:0001583	missense	55339	exon17			GAGGGGGAATGCG		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.2830C>A	chr2.hg19:g.128474768G>T	ENSP00000325377:p.Pro944Thr	60.0	0.0		152.0	97.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.564656	0.45694	.	.	ENSG00000136709	ENST00000322313	D	0.89343	-2.5	5.27	5.27	0.74061	.	0.200449	0.35970	N	0.002871	T	0.78451	0.4285	N	0.08118	0	0.80722	D	1	B	0.27498	0.18	B	0.17098	0.017	T	0.78074	-0.2346	10	0.72032	D	0.01	-4.998	14.8293	0.70135	0.0:0.1867:0.8133:0.0	.	944	Q9C0J8	WDR33_HUMAN	T	944	ENSP00000325377:P944T	ENSP00000325377:P944T	P	-	1	0	WDR33	128191238	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.230000	0.58632	2.473000	0.83533	0.563000	0.77884	CCC	.	.		0.488	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		T	128474768	G	T	128474768	3	4	102	1	0	0	0	0	1	0	0	0	17302	1174	41	3	1204	3	WDR33	2	128474768	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	73001234	128474768	114724605	16	14498										
TTN	7273	hgsc.bcm.edu	37	chr2	179548789	179548789	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aactttttcttctgggacagCtctcttcggttcctctggca	8	12	4	0	rs72650032	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:179548789C>T	ENST00000591111.1	-	131	32016	c.31792G>A	c.(31792-31794)Gct>Act	p.A10598T	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A9671T|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A10915T|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTGGGACAGCTCTCTTCGGT	0.363																																					p.A10915T		Atlas-SNP	.											.	TTN	18412	.	0			c.G32743A						.						82	81	81					2																	179548789		1809	4072	5881	SO:0001583	missense	7273	exon133			GGACAGCTCTCTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.31792G>A	chr2.hg19:g.179548789C>T	ENSP00000465570:p.Ala10598Thr	91.0	0.0		181.0	115.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.37	2.217774	0.39201	.	.	ENSG00000155657	ENST00000342992	T	0.64438	-0.1	5.58	2.76	0.32466	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.43500	0.1250	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.35798	-0.9774	9	0.87932	D	0	.	9.9864	0.41843	0.0:0.6767:0.1633:0.16	.	10598	Q8WZ42	TITIN_HUMAN	T	9671	ENSP00000343764:A9671T	ENSP00000343764:A9671T	A	-	1	0	TTN	179257034	0.405000	0.25336	0.999000	0.59377	0.829000	0.46940	0.190000	0.17057	0.744000	0.32741	0.563000	0.77884	GCT	.	C|0.998;G|0.002		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179548789	C	T	179548789	3	4	102	1	0	0	0	0	1	0	0	0	16750	797	28	3	71706	3	TTN	2	179548789	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	51074021	179548789	63650584	17	14499										
TTN	7273	hgsc.bcm.edu	37	chr2	179575865	179575865	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	caggaatactggcctgcaagGctccggtcagttttaaaaat	10	9	1	0	rs374930292		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:179575865G>C	ENST00000591111.1	-	95	27371	c.27147C>G	c.(27145-27147)agC>agG	p.S9049R	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S8122R|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S9366R|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	13187	Ig-like 73.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGCCTGCAAGGCTCCGGTCAG	0.428																																					p.S9366R		Atlas-SNP	.											.	TTN	18412	.	0			c.C28098G						.	G	,,,ARG/SER	1,3677		0,1,1838	121	121	121		,,,24366	2.9	1	2		121	0,8180		0,0,4090	no	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,110	0,1,5928	CC,CG,GG		0.0,0.0272,0.0084	,,,benign	,,,8122/33424	179575865	1,11857	1839	4090	5929	SO:0001583	missense	7273	exon97			TGCAAGGCTCCGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.27147C>G	chr2.hg19:g.179575865G>C	ENSP00000465570:p.Ser9049Arg	70.0	0.0		77.0	13.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.61	1.691391	0.30052	2.72E-4	0.0	ENSG00000155657	ENST00000342992	T	0.46819	0.86	5.76	2.91	0.33838	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.41696	0.1170	L	0.50993	1.605	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.31668	-0.9935	9	0.87932	D	0	.	10.9549	0.47351	0.203:0.0:0.797:0.0	.	9049	Q8WZ42	TITIN_HUMAN	R	8122	ENSP00000343764:S8122R	ENSP00000343764:S8122R	S	-	3	2	TTN	179284110	0.995000	0.38212	0.996000	0.52242	0.989000	0.77384	0.372000	0.20467	0.409000	0.25649	0.655000	0.94253	AGC	.	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179575865	G	C	179575865	3	2	102	1	0	0	0	0	1	0	0	0	16750	1194	42	4	76495	4	TTN	2	179575865	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	27076	179575865	63623508	18	14500										
RAPH1	65059	hgsc.bcm.edu	37	chr2	204326584	204326584	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	atatcacctttttcacttgtGcctctttaattttctctagg	4	10	4	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:204326584G>A	ENST00000319170.5	-	5	1096	c.797C>T	c.(796-798)gCa>gTa	p.A266V	RAPH1_ENST00000308091.4_Missense_Mutation_p.A318V|RAPH1_ENST00000374493.3_Missense_Mutation_p.A318V|RAPH1_ENST00000419464.1_Missense_Mutation_p.A266V|RAPH1_ENST00000439222.1_Missense_Mutation_p.A291V|RAPH1_ENST00000374488.2_Missense_Mutation_p.A291V|RAPH1_ENST00000374489.2_Missense_Mutation_p.A293V|RAPH1_ENST00000453034.1_Missense_Mutation_p.A318V|RAPH1_ENST00000457812.1_Missense_Mutation_p.A266V|RAPH1_ENST00000418114.1_Missense_Mutation_p.A266V|RAPH1_ENST00000423104.1_Missense_Mutation_p.A293V	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	266					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTTCACTTGTGCCTCTTTAAT	0.368																																					p.A318V		Atlas-SNP	.											.	RAPH1	118	.	0			c.C953T						.						132	123	127					2																	204326584		2202	4300	6502	SO:0001583	missense	65059	exon7			ACTTGTGCCTCTT	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.797C>T	chr2.hg19:g.204326584G>A	ENSP00000316543:p.Ala266Val	114.0	0.0		474.0	24.0	NM_203365	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	hg19	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	G	34	5.346929	0.95807	.	.	ENSG00000173166	ENST00000457812;ENST00000319170;ENST00000374493;ENST00000374489;ENST00000374488;ENST00000308091;ENST00000439222;ENST00000419464;ENST00000423104;ENST00000453034;ENST00000432342;ENST00000418114;ENST00000413201	T;T;T;T;T;T;T;T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95;-0.95;-0.95;-0.95;-0.95;-0.95;-0.95;-0.95	5.65	5.65	0.86999	.	0.000000	0.45606	D	0.000345	D	0.83677	0.5306	L	0.48642	1.525	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.999	D;D;D	0.91635	0.999;0.985;0.994	D	0.84257	0.0481	10	0.87932	D	0	-20.7348	19.7068	0.96076	0.0:0.0:1.0:0.0	.	318;318;266	Q70E73-6;C9K0J5;Q70E73	.;.;RAPH1_HUMAN	V	266;266;318;293;291;318;291;266;293;318;291;266;293	ENSP00000392854:A266V;ENSP00000316543:A266V;ENSP00000363617:A318V;ENSP00000363613:A293V;ENSP00000363612:A291V;ENSP00000311293:A318V;ENSP00000411138:A291V;ENSP00000390578:A266V;ENSP00000397751:A293V;ENSP00000406662:A318V;ENSP00000396711:A266V	ENSP00000311293:A318V	A	-	2	0	RAPH1	204034829	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.924000	0.87555	2.824000	0.97209	0.655000	0.94253	GCA	.	.		0.368	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		A	204326584	G	A	204326584	3	1	102	1	0	0	0	0	1	0	0	0	13065	1319	46	3	3002	3	RAPH1	2	204326584	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	24750719	204326584	38872789	19	14501										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228884727	228884727	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tctggagatcgttctgttttAatcaatggtgtgggatattt	11	4	3	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:228884727A>T	ENST00000392056.3	-	7	889	c.843T>A	c.(841-843)atT>atA	p.I281I	SPHKAP_ENST00000344657.5_Silent_p.I281I	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	281						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GTTCTGTTTTAATCAATGGTG	0.443																																					p.I281I		Atlas-SNP	.											.	SPHKAP	750	.	0			c.T843A						.						236	251	246					2																	228884727		2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			TGTTTTAATCAAT		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.843T>A	chr2.hg19:g.228884727A>T		187.0	0.0		1095.0	145.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	hg19	CCDS46537.1																																																																																			.	.		0.443	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228884727	A	T	228884727	2	4	102	1	0	0	0	0	0	0	0	1	15063	358	13	4		4	SPHKAP	2	228884727	Silent	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	24558143	228884727	14314646	20	14502										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4732940	4732940	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ctgcatagagactcacggtcGgaatgtccagtatataaagt	10	8	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:4732940G>A	ENST00000443694.2	+	29	3896	c.3896G>A	c.(3895-3897)cGg>cAg	p.R1299Q	ITPR1_ENST00000354582.6_Missense_Mutation_p.R1314Q|ITPR1_ENST00000423119.2_Missense_Mutation_p.R1305Q|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000302640.8_Missense_Mutation_p.R1299Q|ITPR1_ENST00000357086.4_Missense_Mutation_p.R1305Q|ITPR1_ENST00000456211.2_Missense_Mutation_p.R1290Q			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1314					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	ACTCACGGTCGGAATGTCCAG	0.408																																					p.R1305Q		Atlas-SNP	.											.	ITPR1	659	.	0			c.G3914A						.						89	87	88					3																	4732940		1917	4149	6066	SO:0001583	missense	3708	exon32			ACGGTCGGAATGT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.3896G>A	chr3.hg19:g.4732940G>A	ENSP00000401671:p.Arg1299Gln	106.0	0.0		225.0	68.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	34	5.351730	0.95830	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13;-4.13;-4.13	5.24	5.24	0.73138	Intracellular calcium-release channel (1);	0.000000	0.85682	D	0.000000	D	0.98229	0.9414	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72982	0.968;0.979	D	0.98763	1.0725	10	0.56958	D	0.05	.	18.8583	0.92262	0.0:0.0:1.0:0.0	.	1314;1305	Q14643;G5E9P1	ITPR1_HUMAN;.	Q	1314;1299;1314;1305;1305;1290;1299	ENSP00000306253:R1299Q;ENSP00000346595:R1314Q;ENSP00000405934:R1305Q;ENSP00000349597:R1305Q;ENSP00000397885:R1290Q;ENSP00000401671:R1299Q	ENSP00000306253:R1299Q	R	+	2	0	ITPR1	4707940	1.000000	0.71417	0.849000	0.33467	0.941000	0.58515	9.778000	0.99011	2.437000	0.82529	0.655000	0.94253	CGG	.	.		0.408	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4732940	G	A	4732940	3	1	102	1	0	0	0	0	1	0	0	0	7929	1116	39	1	4059	1	ITPR1	3	4732940	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10		4732940	193289490	21	14503										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38135225	38135225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gcctgaaaaccttcggtccaCggctaggaagcagctgatta	11	11	0	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:38135225C>T	ENST00000308059.6	+	12	1907	c.1886C>T	c.(1885-1887)aCg>aTg	p.T629M	DLEC1_ENST00000452631.2_Missense_Mutation_p.T629M|DLEC1_ENST00000346219.3_Missense_Mutation_p.T629M					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CTTCGGTCCACGGCTAGGAAG	0.502																																					p.T629M		Atlas-SNP	.											.	DLEC1	278	.	0			c.C1886T						.						123	124	123					3																	38135225		1909	4135	6044	SO:0001583	missense	9940	exon12			GGTCCACGGCTAG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1886C>T	chr3.hg19:g.38135225C>T	ENSP00000308597:p.Thr629Met	68.0	0.0		189.0	54.0	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	13.25	2.180990	0.38511	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05996	3.37;3.36;3.6	5.08	3.25	0.37280	.	0.239343	0.42420	D	0.000702	T	0.07548	0.0190	L	0.53249	1.67	0.09310	N	0.999999	D;D;D	0.56521	0.976;0.976;0.976	P;B;P	0.44673	0.457;0.356;0.457	T	0.25745	-1.0123	10	0.34782	T	0.22	-12.8453	6.5019	0.22174	0.0:0.7237:0.0:0.2763	.	629;629;629	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	M	629	ENSP00000308597:T629M;ENSP00000315914:T629M;ENSP00000410427:T629M	ENSP00000308597:T629M	T	+	2	0	DLEC1	38110229	0.020000	0.18652	0.645000	0.29479	0.974000	0.67602	1.115000	0.31209	1.096000	0.41439	0.655000	0.94253	ACG	.	.		0.502	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38135225	C	T	38135225	3	4	102	1	0	0	0	0	1	0	0	0	4554	536	19	1	1932	1	DLEC1	3	38135225	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	33402285	38135225	159887205	22	14504										
BAP1	8314	hgsc.bcm.edu	37	chr3	52440270	52440276	+	Splice_Site	DEL	TGCTGCA	TGCTGCA	-													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aggaagaaagggcacctaccTgctgcagagcctctagtact							TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	TGCTGCA	TGCTGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:52440270_52440276delTGCTGCA	ENST00000460680.1	-	9	1247_1253	c.776_782delTGCAGCA	c.(775-783)ctgcagcag>cg	p.LQQ259fs	BAP1_ENST00000296288.5_Splice_Site_p.LQQ241fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q261*(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GGCACCTACCTGCTGCAGAGCCTCTAG	0.57			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.259_261del	GBM(101;493 1458 7992 21037 25532)	Atlas-INDEL	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	BAP1,NS,carcinoma,-2,1	BAP1	371	.	1	Substitution - Nonsense(1)	breast(1)	c.777_783del						.																																			SO:0001630	splice_region_variant	8314	exon9			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.783+1TGCAGCA>-	chr3.hg19:g.52440270_52440276delTGCTGCA		60.0	0.0		48.0	14.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.57	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		Frame_Shift_Del	-	52440276	TGCTGCA	-	52440270	8	5	102	1	0	1	0	1	0	0	1	0	1311	1594	55	0	1443	0	BAP1	3	52440270	Splice_Site	DEL	TGCTGCA	TCGA-DD-A1EF-01A-11D-A12Z-10	14305045	52440270	145582160	23	14505										
PHLDB2	90102	hgsc.bcm.edu	37	chr3	111688738	111688738	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tttttgatcggaacaagcgaAcattctcttattatgcaggt	8	7	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:111688738A>T	ENST00000431670.2	+	16	3928	c.3517A>T	c.(3517-3519)Aca>Tca	p.T1173S	PHLDB2_ENST00000393925.3_Missense_Mutation_p.T1173S|PHLDB2_ENST00000481953.1_Missense_Mutation_p.T1130S|PHLDB2_ENST00000412622.1_Missense_Mutation_p.T1130S|PHLDB2_ENST00000393923.3_Missense_Mutation_p.T1157S|PHLDB2_ENST00000495180.1_Missense_Mutation_p.T664S	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	1173	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						GAACAAGCGAACATTCTCTTA	0.378																																					p.T1173S		Atlas-SNP	.											.	PHLDB2	449	.	0			c.A3517T						.						130	134	132					3																	111688738		2203	4300	6503	SO:0001583	missense	90102	exon16			AAGCGAACATTCT		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"Pleckstrin homology (PH) domain containing"	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.3517A>T	chr3.hg19:g.111688738A>T	ENSP00000405405:p.Thr1173Ser	72.0	0.0		123.0	39.0	NM_001134439	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Missense_Mutation	SNP	ENST00000431670.2	hg19	CCDS46886.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.049472	0.75846	.	.	ENSG00000144824	ENST00000393923;ENST00000431670;ENST00000412622;ENST00000393925;ENST00000481953;ENST00000495180	T;T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89;-0.89;-0.89	5.09	3.92	0.45320	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.056069	0.64402	D	0.000001	T	0.72574	0.3477	N	0.12443	0.215	0.50813	D	0.999894	D;P;P;D;D	0.76494	0.999;0.558;0.856;0.991;0.991	D;B;P;D;D	0.83275	0.996;0.262;0.722;0.981;0.952	T	0.74061	-0.3786	10	0.52906	T	0.07	.	10.3965	0.44203	0.8532:0.0:0.0:0.1468	.	285;664;1173;1130;1157	Q658P8;E9PGF6;Q86SQ0;Q86SQ0-2;Q86SQ0-3	.;.;PHLB2_HUMAN;.;.	S	1157;1173;1130;1173;1130;664	ENSP00000377500:T1157S;ENSP00000405405:T1173S;ENSP00000405292:T1130S;ENSP00000377502:T1173S;ENSP00000418319:T1130S;ENSP00000420303:T664S	ENSP00000377500:T1157S	T	+	1	0	PHLDB2	113171428	1.000000	0.71417	0.924000	0.36721	0.992000	0.81027	8.718000	0.91430	0.938000	0.37419	0.477000	0.44152	ACA	.	.		0.378	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		T	111688738	A	T	111688738	3	4	102	1	0	0	0	0	1	0	0	0	11861	43	2	4	3660	4	PHLDB2	3	111688738	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	59248468	111688738	86333692	24	14506										
BOC	91653	hgsc.bcm.edu	37	chr3	112969411	112969411	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tcttcctccagacgaggtccCtcaggtcaccgtccagcctg	9	17	3	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:112969411C>T	ENST00000495514.1	+	4	811	c.107C>T	c.(106-108)cCt>cTt	p.P36L	BOC_ENST00000355385.3_Missense_Mutation_p.P36L|BOC_ENST00000484034.1_Missense_Mutation_p.P36L|BOC_ENST00000273395.4_Missense_Mutation_p.P36L|BOC_ENST00000485230.1_Missense_Mutation_p.P36L			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	36	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			GACGAGGTCCCTCAGGTCACC	0.562																																					p.P36L		Atlas-SNP	.											.	BOC	139	.	0			c.C107T						.						94	90	92					3																	112969411		2203	4300	6503	SO:0001583	missense	91653	exon4			AGGTCCCTCAGGT	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.107C>T	chr3.hg19:g.112969411C>T	ENSP00000418663:p.Pro36Leu	47.0	0.0		94.0	7.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	hg19	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	c	18.51	3.638988	0.67130	.	.	ENSG00000144857	ENST00000464546;ENST00000495514;ENST00000485230;ENST00000273395;ENST00000355385;ENST00000484034	D;T;T;T;T;T	0.84223	-1.82;-1.3;-1.3;-1.3;-1.3;-1.3	5.68	5.68	0.88126	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.064498	0.64402	D	0.000007	D	0.89326	0.6683	M	0.75447	2.3	0.58432	D	0.999997	P;B;P;D	0.62365	0.724;0.282;0.529;0.991	B;B;P;P	0.58013	0.274;0.278;0.521;0.831	D	0.88822	0.3299	10	0.46703	T	0.11	.	10.8259	0.46631	0.0:0.8859:0.0:0.1141	.	36;36;36;36	C9J2L7;Q9BWV1-3;Q9BWV1;Q96DN7	.;.;BOC_HUMAN;.	L	36	ENSP00000417362:P36L;ENSP00000418663:P36L;ENSP00000420154:P36L;ENSP00000273395:P36L;ENSP00000347546:P36L;ENSP00000417337:P36L	ENSP00000273395:P36L	P	+	2	0	BOC	114452101	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	5.579000	0.67457	2.672000	0.90937	0.651000	0.88453	CCT	.	.		0.562	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		T	112969411	C	T	112969411	3	4	102	1	0	0	0	0	1	0	0	0	1481	681	24	3	113	3	BOC	3	112969411	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	1280673	112969411	85053019	25	14507										
POLQ	10721	hgsc.bcm.edu	37	chr3	121207657	121207657	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ggtgctgttcagcaggaaaaGgaatgtgacactccttctga	12	8	2	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:121207657G>A	ENST00000264233.5	-	16	4249	c.4121C>T	c.(4120-4122)cCt>cTt	p.P1374L		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1374					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		AGCAGGAAAAGGAATGTGACA	0.443								DNA polymerases (catalytic subunits)																													p.P1374L	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C4121T						.						175	161	166					3																	121207657		2203	4300	6503	SO:0001583	missense	10721	exon16			GGAAAAGGAATGT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.4121C>T	chr3.hg19:g.121207657G>A	ENSP00000264233:p.Pro1374Leu	144.0	0.0		405.0	46.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.452007	0.26074	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.45668	0.89	5.16	-0.725	0.11174	.	1.325950	0.05226	N	0.509359	T	0.20373	0.0490	N	0.08118	0	0.09310	N	1	B;B	0.23442	0.085;0.0	B;B	0.19666	0.026;0.0	T	0.17899	-1.0354	10	0.14252	T	0.57	.	5.9899	0.19454	0.5432:0.0:0.29:0.1668	.	1374;546	O75417;O75417-2	DPOLQ_HUMAN;.	L	997;1374;1510	ENSP00000264233:P1374L	ENSP00000264233:P1374L	P	-	2	0	POLQ	122690347	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.091000	0.11146	-0.048000	0.13401	0.655000	0.94253	CCT	.	.		0.443	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121207657	G	A	121207657	3	1	102	1	0	0	0	0	1	0	0	0	12217	1000	35	3	3711	3	POLQ	3	121207657	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	8238246	121207657	76814773	26	14508										
TMCC1	23023	hgsc.bcm.edu	37	chr3	129389440	129389440	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cttcttcactaccatattttGggctagactgaaagtttgaa	7	8	2	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:129389440G>T	ENST00000393238.3	-	4	1584	c.1244C>A	c.(1243-1245)cCa>cAa	p.P415Q	TMCC1_ENST00000426664.2_Missense_Mutation_p.P301Q|TMCC1_ENST00000432054.2_Missense_Mutation_p.P91Q|TMCC1_ENST00000329333.5_Missense_Mutation_p.P236Q	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	415						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						ACCATATTTTGGGCTAGACTG	0.507																																					p.P415Q		Atlas-SNP	.											.	TMCC1	105	.	0			c.C1244A						.						101	95	97					3																	129389440		2203	4300	6503	SO:0001583	missense	23023	exon4			TATTTTGGGCTAG	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.1244C>A	chr3.hg19:g.129389440G>T	ENSP00000376930:p.Pro415Gln	119.0	0.0		269.0	32.0	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Missense_Mutation	SNP	ENST00000393238.3	hg19	CCDS33855.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934937	0.73442	.	.	ENSG00000172765	ENST00000432054;ENST00000393238;ENST00000426664;ENST00000329333	T;T;T;T	0.51574	0.7;0.7;0.7;0.7	5.21	5.21	0.72293	.	0.093329	0.85682	D	0.000000	T	0.68650	0.3024	M	0.81497	2.545	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.72625	0.978;0.967	T	0.64723	-0.6340	10	0.12430	T	0.62	-16.0998	19.1112	0.93317	0.0:0.0:1.0:0.0	.	236;415	B4DE04;O94876	.;TMCC1_HUMAN	Q	91;415;301;236	ENSP00000404711:P91Q;ENSP00000376930:P415Q;ENSP00000389892:P301Q;ENSP00000327349:P236Q	ENSP00000327349:P236Q	P	-	2	0	TMCC1	130872130	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.301000	0.96167	2.581000	0.87130	0.591000	0.81541	CCA	.	.		0.507	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		T	129389440	G	T	129389440	3	4	102	1	0	0	0	0	1	0	0	0	16007	1348	47	3	729	3	TMCC1	3	129389440	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	8181783	129389440	68632990	27	14509										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140140017	140140017	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	atgacaaacaacaccagtatGagatcctggtgaccgcctac	8	12	0	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:140140017G>C	ENST00000458420.3	+	5	878	c.688G>C	c.(688-690)Gag>Cag	p.E230Q		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	230	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						ACACCAGTATGAGATCCTGGT	0.512										HNSCC(16;0.037)																											p.E230Q	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G688C						.						164	151	155					3																	140140017		2203	4300	6503	SO:0001583	missense	64084	exon5			CAGTATGAGATCC	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.688G>C	chr3.hg19:g.140140017G>C	ENSP00000402460:p.Glu230Gln	47.0	0.0		87.0	8.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.012485	0.35511	.	.	ENSG00000158258	ENST00000458420	T	0.54675	0.56	5.7	5.7	0.88788	Cadherin (5);Cadherin-like (1);	0.260319	0.37809	N	0.001938	T	0.48241	0.1489	L	0.49126	1.545	0.42028	D	0.99101	B	0.17268	0.021	B	0.19391	0.025	T	0.40942	-0.9536	10	0.14252	T	0.57	-4.5927	17.3368	0.87283	0.0:0.0:1.0:0.0	.	230	Q9H4D0	CSTN2_HUMAN	Q	230	ENSP00000402460:E230Q	ENSP00000402460:E230Q	E	+	1	0	CLSTN2	141622707	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.532000	0.45659	2.679000	0.91253	0.655000	0.94253	GAG	.	.		0.512	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		C	140140017	G	C	140140017	3	2	102	1	0	0	0	0	1	0	0	0	3564	1291	45	4	706	4	CLSTN2	3	140140017	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	10750577	140140017	57882413	28	14510										
ATR	545	hgsc.bcm.edu	37	chr3	142215986	142215986	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gaactgtcacctggagaatgCtggaaaagtggtttgatgct	13	6	1	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:142215986C>T	ENST00000350721.4	-	33	5728	c.5607G>A	c.(5605-5607)caG>caA	p.Q1869Q	ATR_ENST00000383101.3_Silent_p.Q1805Q	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1869	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CTGGAGAATGCTGGAAAAGTG	0.413								Other conserved DNA damage response genes																													p.Q1869Q		Atlas-SNP	.											.	ATR	285	.	0			c.G5607A						.						112	120	118					3																	142215986		2203	4300	6503	SO:0001819	synonymous_variant	545	exon33			AGAATGCTGGAAA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5607G>A	chr3.hg19:g.142215986C>T		43.0	0.0		96.0	42.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.413	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142215986	C	T	142215986	2	4	102	1	0	0	0	0	0	0	0	1	1204	796	28	3		3	ATR	3	142215986	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	2075969	142215986	55806444	29	14511										
MED12L	116931	hgsc.bcm.edu	37	chr3	150873991	150873991	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tatcttcgagagcagttggcCaagatttctgacttttacca	8	9	2	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:150873991C>T	ENST00000474524.1	+	5	638	c.600C>T	c.(598-600)gcC>gcT	p.A200A	MED12L_ENST00000273432.4_Silent_p.A200A|MED12L_ENST00000422248.2_Silent_p.A200A|MED12L_ENST00000309237.4_Silent_p.A200A	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	200						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGCAGTTGGCCAAGATTTCTG	0.458																																					p.A200A		Atlas-SNP	.											.	MED12L	271	.	0			c.C600T						.						104	100	101					3																	150873991		2203	4300	6503	SO:0001819	synonymous_variant	116931	exon5			GTTGGCCAAGATT	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.600C>T	chr3.hg19:g.150873991C>T		41.0	0.0		87.0	27.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	hg19	CCDS33876.1																																																																																			.	.		0.458	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		T	150873991	C	T	150873991	2	4	102	1	0	0	0	0	0	0	0	1	9438	581	21	3		3	MED12L	3	150873991	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	8658005	150873991	47148439	30	14512										
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910999	184910999	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ctggtttgcacacagctgagAgttcagcaaagacctgcttc	10	11	1	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:184910999A>C	ENST00000231887.3	-	7	1262	c.1187T>G	c.(1186-1188)cTc>cGc	p.L396R	EHHADH_ENST00000456310.1_Missense_Mutation_p.L300R|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	396	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CACAGCTGAGAGTTCAGCAAA	0.443																																					p.L396R		Atlas-SNP	.											.	EHHADH	73	.	0			c.T1187G						.						183	173	176					3																	184910999		2203	4300	6503	SO:0001583	missense	1962	exon7			GCTGAGAGTTCAG	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1187T>G	chr3.hg19:g.184910999A>C	ENSP00000231887:p.Leu396Arg	98.0	0.0		169.0	64.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.055404	0.75960	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	D;D	0.81821	-1.54;-1.54	6.08	6.08	0.98989	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.93190	0.7831	H	0.96208	3.785	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95085	0.8217	10	0.87932	D	0	-11.8271	16.6512	0.85203	1.0:0.0:0.0:0.0	.	396	Q08426	ECHP_HUMAN	R	396;396;300	ENSP00000231887:L396R;ENSP00000387746:L300R	ENSP00000231887:L396R	L	-	2	0	EHHADH	186393693	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	8.818000	0.91991	2.333000	0.79357	0.482000	0.46254	CTC	.	.		0.443	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			C	184910999	A	C	184910999	3	2	102	1	0	0	0	0	1	0	0	0	4984	304	11	5	988	5	EHHADH	3	184910999	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	34037008	184910999	13111431	31	14513										
LYAR	55646	hgsc.bcm.edu	37	chr4	4275388	4275388	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	catctttttcttcttagaatCtgtttcaactaagtatttgg	5	7	5	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:4275388C>T	ENST00000343470.4	-	8	1081	c.841G>A	c.(841-843)Gat>Aat	p.D281N	LYAR_ENST00000452476.1_Missense_Mutation_p.D281N	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	281	Lys-rich.					nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TTCTTAGAATCTGTTTCAACT	0.403																																					p.D281N		Atlas-SNP	.											.	LYAR	36	.	0			c.G841A						.						78	80	79					4																	4275388		2203	4300	6503	SO:0001583	missense	55646	exon8			TAGAATCTGTTTC	AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"Zinc fingers, C2HC-type containing"	26021	protein-coding gene	gene with protein product			"Ly1 antibody reactive homolog (mouse)"			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.841G>A	chr4.hg19:g.4275388C>T	ENSP00000345917:p.Asp281Asn	76.0	0.0		149.0	40.0	NM_017816	D3DVS4|Q6FI78|Q9NYS1	Missense_Mutation	SNP	ENST00000343470.4	hg19	CCDS3374.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.862908	0.32884	.	.	ENSG00000145220	ENST00000343470;ENST00000452476	T;T	0.32515	1.45;1.45	5.24	1.32	0.21799	.	1.811300	0.01927	N	0.040948	T	0.19604	0.0471	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.12630	-1.0540	10	0.23302	T	0.38	-3.6287	3.4773	0.07589	0.176:0.5217:0.0:0.3022	.	281	Q9NX58	LYAR_HUMAN	N	281	ENSP00000345917:D281N;ENSP00000397367:D281N	ENSP00000345917:D281N	D	-	1	0	LYAR	4326289	0.000000	0.05858	0.000000	0.03702	0.581000	0.36288	0.130000	0.15850	0.245000	0.21373	-0.366000	0.07423	GAT	.	.		0.403	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816		T	4275388	C	T	4275388	3	4	102	1	0	0	0	0	1	0	0	0	9112	913	32	3	310	3	LYAR	4	4275388	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10		4275388	186878888	32	14514										
STK32B	55351	hgsc.bcm.edu	37	chr4	5170120	5170120	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gagggatgaggttcggaatgTtttccgggagctgcagatca	16	6	1	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:5170120T>A	ENST00000282908.5	+	3	625	c.203T>A	c.(202-204)gTt>gAt	p.V68D	STK32B_ENST00000510398.1_Missense_Mutation_p.V21D|STK32B_ENST00000512636.1_Missense_Mutation_p.V21D	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						GTTCGGAATGTTTTCCGGGAG	0.532																																					p.V68D		Atlas-SNP	.											.	STK32B	87	.	0			c.T203A						.						105	94	98					4																	5170120		2203	4300	6503	SO:0001583	missense	55351	exon3			GGAATGTTTTCCG	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.203T>A	chr4.hg19:g.5170120T>A	ENSP00000282908:p.Val68Asp	56.0	0.0		176.0	34.0	NM_018401		Missense_Mutation	SNP	ENST00000282908.5	hg19	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561482	0.65538	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.26518	1.73;1.73;1.73	5.03	5.03	0.67393	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38778	U	0.001569	T	0.58119	0.2100	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68062	-0.5508	10	0.87932	D	0	.	13.9602	0.64175	0.0:0.0:0.0:1.0	.	68	Q9NY57	ST32B_HUMAN	D	68;21;21	ENSP00000282908:V68D;ENSP00000423209:V21D;ENSP00000420984:V21D	ENSP00000282908:V68D	V	+	2	0	STK32B	5221021	1.000000	0.71417	0.988000	0.46212	0.331000	0.28603	7.552000	0.82192	1.890000	0.54733	0.533000	0.62120	GTT	.	.		0.532	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		A	5170120	T	A	5170120	3	1	102	1	0	0	0	0	1	0	0	0	15313	1725	60	4	213	4	STK32B	4	5170120	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	894732	5170120	185984156	33	14515										
PROM1	8842	hgsc.bcm.edu	37	chr4	16035130	16035130	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	atccctgcttcatagtagacAatctgcaattcaaacaaaag	5	10	3	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:16035130A>G	ENST00000510224.1	-	5	554	c.306T>C	c.(304-306)atT>atC	p.I102I	PROM1_ENST00000505450.1_Silent_p.I93I|PROM1_ENST00000543373.1_Silent_p.I93I|PROM1_ENST00000540805.1_Silent_p.I102I|PROM1_ENST00000539194.1_Silent_p.I102I|PROM1_ENST00000502943.1_5'UTR|PROM1_ENST00000447510.2_Silent_p.I102I|PROM1_ENST00000508167.1_Silent_p.I93I			O43490	PROM1_HUMAN	prominin 1	102					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						CATAGTAGACAATCTGCAATT	0.343																																					p.I102I		Atlas-SNP	.											.	PROM1	91	.	0			c.T306C						.						36	33	34					4																	16035130		1866	4111	5977	SO:0001819	synonymous_variant	8842	exon4			GTAGACAATCTGC	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.306T>C	chr4.hg19:g.16035130A>G		75.0	0.0		172.0	46.0	NM_006017	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Silent	SNP	ENST00000510224.1	hg19	CCDS47029.1																																																																																			.	.		0.343	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		G	16035130	A	G	16035130	2	3	102	1	0	0	0	0	0	0	0	1	12567	126	5	2		2	PROM1	4	16035130	Silent	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	10865010	16035130	175119146	34	14516										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79428611	79428611	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttttaaagttgagatcctgtCcaatgaagaccgggaatggc	11	7	0	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:79428611C>T	ENST00000264895.6	+	62	9793	c.9353C>T	c.(9352-9354)tCc>tTc	p.S3118F		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3114	Calx-beta 5.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GAGATCCTGTCCAATGAAGAC	0.473																																					p.S3118F		Atlas-SNP	.											.	FRAS1	779	.	0			c.C9353T						.						110	103	105					4																	79428611		1984	4165	6149	SO:0001583	missense	80144	exon62			TCCTGTCCAATGA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.9353C>T	chr4.hg19:g.79428611C>T	ENSP00000264895:p.Ser3118Phe	99.0	0.0		179.0	51.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.198610	0.38806	.	.	ENSG00000138759	ENST00000264895	T	0.28255	1.62	5.25	5.25	0.73442	.	0.126361	0.56097	D	0.000037	T	0.35711	0.0941	N	0.21097	0.63	0.80722	D	1	D;D	0.59767	0.983;0.986	P;P	0.58331	0.776;0.837	T	0.03335	-1.1047	10	0.10377	T	0.69	.	19.1854	0.93641	0.0:1.0:0.0:0.0	.	3117;3118	Q86XX4-2;E9PHH6	.;.	F	3118	ENSP00000264895:S3118F	ENSP00000264895:S3118F	S	+	2	0	FRAS1	79647635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.648000	0.83479	2.612000	0.88384	0.591000	0.81541	TCC	.	.		0.473	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79428611	C	T	79428611	3	4	102	1	0	0	0	0	1	0	0	0	6050	855	30	3	9674	3	FRAS1	4	79428611	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	63393481	79428611	111725665	35	14517										
ABCG2	9429	hgsc.bcm.edu	37	chr4	89039357	89039357	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gctatcaaacaacttgaagaTggaatatcgaggctgatgaa	10	6	1	4			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:89039357T>C	ENST00000237612.3	-	7	1290	c.745A>G	c.(745-747)Atc>Gtc	p.I249V	ABCG2_ENST00000515655.1_Missense_Mutation_p.I249V	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	249	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	AACTTGAAGATGGAATATCGA	0.423																																					p.I249V		Atlas-SNP	.											.	ABCG2	151	.	0			c.A745G						.						139	125	129					4																	89039357		2203	4300	6503	SO:0001583	missense	9429	exon7			TGAAGATGGAATA	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.745A>G	chr4.hg19:g.89039357T>C	ENSP00000237612:p.Ile249Val	80.0	0.0		109.0	34.0	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	hg19	CCDS3628.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.275027	0.80580	.	.	ENSG00000118777	ENST00000515655;ENST00000237612	T;T	0.43688	0.94;0.94	5.45	4.25	0.50352	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	T	0.44685	0.1305	N	0.21508	0.67	0.50467	D	0.999873	D;D;D	0.62365	0.991;0.969;0.969	D;P;P	0.63877	0.919;0.589;0.589	T	0.21348	-1.0248	10	0.26408	T	0.33	-36.5828	11.6976	0.51553	0.1328:0.0:0.0:0.8672	.	249;249;249	Q9UNQ0-2;Q9UNQ0;Q4W5I3	.;ABCG2_HUMAN;.	V	249	ENSP00000426917:I249V;ENSP00000237612:I249V	ENSP00000237612:I249V	I	-	1	0	ABCG2	89258381	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.666000	0.83877	0.981000	0.38548	0.533000	0.62120	ATC	.	.		0.423	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		C	89039357	T	C	89039357	3	2	102	1	0	0	0	0	1	0	0	0	69	1464	51	2	1262	2	ABCG2	4	89039357	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	9610746	89039357	102114919	36	14518										
SMARCA5	8467	hgsc.bcm.edu	37	chr4	144467138	144467138	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aaaaagaagaacagcttaaaAttgatgaagctgaatccctt	7	6	0	5			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:144467138A>G	ENST00000283131.3	+	19	2920	c.2458A>G	c.(2458-2460)Att>Gtt	p.I820V		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	820					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					ACAGCTTAAAATTGATGAAGC	0.348																																					p.I820V		Atlas-SNP	.											.	SMARCA5	73	.	0			c.A2458G						.						86	90	88					4																	144467138		2203	4300	6503	SO:0001583	missense	8467	exon19			CTTAAAATTGATG	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.2458A>G	chr4.hg19:g.144467138A>G	ENSP00000283131:p.Ile820Val	102.0	0.0		243.0	84.0	NM_003601		Missense_Mutation	SNP	ENST00000283131.3	hg19	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.354537	0.61293	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.91464	-2.85	5.3	5.3	0.74995	ATPase, nucleosome remodelling ISWI, HAND domain (2);	0.000000	0.85682	D	0.000000	D	0.88912	0.6566	L	0.56769	1.78	0.58432	D	0.999999	B	0.20368	0.044	B	0.22152	0.038	D	0.85626	0.1267	10	0.37606	T	0.19	-19.4602	15.5566	0.76200	1.0:0.0:0.0:0.0	.	820	O60264	SMCA5_HUMAN	V	820;763;763	ENSP00000283131:I820V	ENSP00000283131:I820V	I	+	1	0	SMARCA5	144686588	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.680000	0.91225	2.136000	0.66102	0.533000	0.62120	ATT	.	.		0.348	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			G	144467138	A	G	144467138	3	3	102	1	0	0	0	0	1	0	0	0	14786	101	4	2	2532	2	SMARCA5	4	144467138	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	55427781	144467138	46687138	37	14519										
ZNF827	152485	hgsc.bcm.edu	37	chr4	146686272	146686272	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tctgcagatgacgctcaaacAtgttcttcgtcttgcagaca	8	11	4	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:146686272A>T	ENST00000508784.1	-	13	3325	c.3098T>A	c.(3097-3099)aTg>aAg	p.M1033K	ZNF827_ENST00000379448.4_Missense_Mutation_p.M1033K|ZNF827_ENST00000513320.1_Missense_Mutation_p.M683K			Q17R98	ZN827_HUMAN	zinc finger protein 827	1033					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					ACGCTCAAACATGTTCTTCGT	0.522																																					p.M1033K		Atlas-SNP	.											.	ZNF827	102	.	0			c.T3098A						.						87	79	82					4																	146686272		2203	4300	6503	SO:0001583	missense	152485	exon13			TCAAACATGTTCT	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.3098T>A	chr4.hg19:g.146686272A>T	ENSP00000421863:p.Met1033Lys	62.0	0.0		104.0	20.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.3|20.3	3.969817|3.969817	0.74246|0.74246	.|.	.|.	ENSG00000151612|ENSG00000151612	ENST00000511659|ENST00000508784;ENST00000513320;ENST00000379448;ENST00000281318;ENST00000440280	.|T;T;T	.|0.59772	.|0.24;0.24;0.24	4.83|4.83	4.83|4.83	0.62350|0.62350	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.52354|0.52354	0.1729|0.1729	N|N	0.03177|0.03177	-0.4|-0.4	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D;D;P	.|0.54772	.|0.96;0.968;0.96;0.932	.|D;D;D;P	.|0.70487	.|0.948;0.969;0.948;0.888	T|T	0.57539|0.57539	-0.7794|-0.7794	5|10	.|0.23891	.|T	.|0.37	-18.7384|-18.7384	14.7219|14.7219	0.69314|0.69314	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|683;1033;1033;683	.|G5E9Z1;Q17R98;Q17R98-2;E7ESI8	.|.;ZN827_HUMAN;.;.	S|K	134|1033;683;1033;1032;683	.|ENSP00000421863:M1033K;ENSP00000423130:M683K;ENSP00000368761:M1033K	.|ENSP00000281318:M1032K	C|M	-|-	1|2	0|0	ZNF827|ZNF827	146905722|146905722	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	8.910000|8.910000	0.92685|0.92685	1.920000|1.920000	0.55613|0.55613	0.533000|0.533000	0.62120|0.62120	TGT|ATG	.	.		0.522	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		T	146686272	A	T	146686272	3	4	102	1	0	0	0	0	1	0	0	0	18195	217	8	4	139	4	ZNF827	4	146686272	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	2219134	146686272	44468004	38	14520										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155278437	155278437	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cttccttgtctgctgaaaagTtgacagcactcagaatttct	7	10	3	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:155278437T>C	ENST00000357232.4	-	6	733	c.734A>G	c.(733-735)aAc>aGc	p.N245S	DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	245	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		tgctgaaaagttgacagcact	0.433																																					p.N245S		Atlas-SNP	.											.	DCHS2	594	.	0			c.A734G						.						117	122	120					4																	155278437		2203	4300	6503	SO:0001583	missense	54798	exon6			GAAAAGTTGACAG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.734A>G	chr4.hg19:g.155278437T>C	ENSP00000349768:p.Asn245Ser	46.0	0.0		60.0	19.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.575094	0.00131	.	.	ENSG00000197410	ENST00000357232	T	0.55413	0.52	0.772	-0.951	0.10369	Cadherin (1);	.	.	.	.	T	0.28034	0.0691	N	0.22421	0.69	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.21415	-1.0246	9	0.09338	T	0.73	.	3.0531	0.06175	0.0:0.3566:0.0:0.6434	.	245	Q6V1P9	PCD23_HUMAN	S	245	ENSP00000349768:N245S	ENSP00000349768:N245S	N	-	2	0	DCHS2	155497887	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-1.189000	0.03061	-0.333000	0.08476	-0.495000	0.04643	AAC	.	.		0.433	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		C	155278437	T	C	155278437	3	2	102	1	0	0	0	0	1	0	0	0	4290	1725	60	2	8192	2	DCHS2	4	155278437	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	8592165	155278437	35875839	39	14521										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	181677	181677	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gggtataggcaaccagccatTcatggatgtcaagcccagag	12	10	2	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:181677T>C	ENST00000283426.6	+	17	3433	c.3383T>C	c.(3382-3384)tTc>tCc	p.F1128S		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	1128							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		AACCAGCCATTCATGGATGTC	0.527																																					p.F1128S		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.T3383C						.						97	96	96					5																	181677		2203	4300	6503	SO:0001583	missense	153478	exon17			AGCCATTCATGGA	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.3383T>C	chr5.hg19:g.181677T>C	ENSP00000283426:p.Phe1128Ser	49.0	0.0		99.0	25.0	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	hg19	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.879233	0.33162	.	.	ENSG00000153404	ENST00000283426	T	0.35789	1.29	3.64	2.45	0.29901	Pleckstrin homology-type (1);	.	.	.	.	T	0.54549	0.1865	M	0.83223	2.63	0.34532	D	0.709334	D	0.89917	1.0	D	0.72625	0.978	T	0.60994	-0.7152	9	0.20519	T	0.43	.	7.071	0.25179	0.0:0.1158:0.0:0.8842	.	1128	Q96PX9	PKH4B_HUMAN	S	1128	ENSP00000283426:F1128S	ENSP00000283426:F1128S	F	+	2	0	PLEKHG4B	234677	1.000000	0.71417	0.005000	0.12908	0.045000	0.14185	4.841000	0.62824	0.301000	0.22738	0.377000	0.23210	TTC	.	.		0.527	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		C	181677	T	C	181677	3	2	102	1	0	0	0	0	1	0	0	0	12081	1783	62	2	3449	2	PLEKHG4B	5	181677	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10		181677	180733583	40	14522										
DDX4	54514	hgsc.bcm.edu	37	chr5	55083699	55083699	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttttctcctaccaattttggCtcatatgatgcatgatggaa	7	8	2	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:55083699C>T	ENST00000505374.1	+	15	1135	c.1043C>T	c.(1042-1044)gCt>gTt	p.A348V	DDX4_ENST00000353507.5_Missense_Mutation_p.A314V|DDX4_ENST00000511853.1_Missense_Mutation_p.A199V|DDX4_ENST00000354991.5_Missense_Mutation_p.A314V|DDX4_ENST00000514278.2_Missense_Mutation_p.A328V	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	348	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				CCAATTTTGGCTCATATGATG	0.393																																					p.A348V		Atlas-SNP	.											.	DDX4	194	.	0			c.C1043T						.						100	101	101					5																	55083699		2203	4300	6503	SO:0001583	missense	54514	exon15			TTTTGGCTCATAT	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.1043C>T	chr5.hg19:g.55083699C>T	ENSP00000424838:p.Ala348Val	81.0	0.0		128.0	30.0	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Missense_Mutation	SNP	ENST00000505374.1	hg19	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.156592	0.78114	.	.	ENSG00000152670	ENST00000353507;ENST00000514278;ENST00000505374;ENST00000506511;ENST00000354991;ENST00000511853	T;T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;2.41;2.41	5.83	5.83	0.93111	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.175936	0.51477	D	0.000096	T	0.27524	0.0676	L	0.28344	0.845	0.35409	D	0.792272	B;D;P;D	0.76494	0.126;0.974;0.864;0.999	B;P;P;D	0.74023	0.113;0.777;0.713;0.982	T	0.18903	-1.0322	10	0.56958	D	0.05	-17.2683	12.0012	0.53232	0.1349:0.7351:0.13:0.0	.	328;199;314;348	D6RDK4;E9PCD8;Q9NQI0-2;Q9NQI0	.;.;.;DDX4_HUMAN	V	314;328;348;328;314;199	ENSP00000334167:A314V;ENSP00000425359:A328V;ENSP00000424838:A348V;ENSP00000427167:A328V;ENSP00000347087:A314V;ENSP00000423123:A199V	ENSP00000334167:A314V	A	+	2	0	DDX4	55119456	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.937000	0.48979	2.756000	0.94617	0.655000	0.94253	GCT	.	.		0.393	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		T	55083699	C	T	55083699	3	4	102	1	0	0	0	0	1	0	0	0	4362	797	28	3	1138	3	DDX4	5	55083699	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	54902022	55083699	125831561	41	14523										
SRFBP1	153443	hgsc.bcm.edu	37	chr5	121358098	121358098	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	caggctccaaaaacaagatcCctaggtatgtattcatagtt	7	9	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:121358098C>G	ENST00000339397.4	+	7	1173	c.1101C>G	c.(1099-1101)tcC>tcG	p.S367S	SRFBP1_ENST00000504881.1_3'UTR	NM_152546.2	NP_689759.2			serum response factor binding protein 1											central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		AAACAAGATCCCTAGGTATGT	0.303																																					p.S367S		Atlas-SNP	.											.	SRFBP1	47	.	0			c.C1101G						.						64	59	60					5																	121358098		1813	4069	5882	SO:0001819	synonymous_variant	153443	exon7			AAGATCCCTAGGT	AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"BUD22 homolog (S. cerevisiae)"	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.1101C>G	chr5.hg19:g.121358098C>G		93.0	0.0		110.0	35.0	NM_152546		Silent	SNP	ENST00000339397.4	hg19	CCDS43354.1																																																																																			.	.		0.303	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546		G	121358098	C	G	121358098	2	3	102	1	0	0	0	0	0	0	0	1	15159	610	22	4		4	SRFBP1	5	121358098	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	66274399	121358098	59557162	42	14524										
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188279	140188279	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	agcggcgggtaggggagcgcGcgctgtcgagctacgtttcg	19	10	0	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:140188279G>A	ENST00000530339.1	+	1	1507	c.1507G>A	c.(1507-1509)Gcg>Acg	p.A503T	PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.A503T|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.A503T|PCDHA1_ENST00000394633.3_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	503	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGGGAGCGCGCGCTGTCGAG	0.662																																					p.A503T		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G1507A						.						54	55	55					5																	140188279		2203	4300	6503	SO:0001583	missense	56144	exon1			GAGCGCGCGCTGT	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"Cadherins / Protocadherins : Clustered"	8670	other	complex locus constituent	"ortholog of mouse CNR1, KIAA0345-like 10"	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1507G>A	chr5.hg19:g.140188279G>A	ENSP00000435300:p.Ala503Thr	40.0	0.0		112.0	36.0	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	hg19	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	g	10.70	1.422976	0.25639	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.52983	0.7;0.64;0.68	4.18	-1.28	0.09318	Cadherin (4);Cadherin-like (1);	0.515141	0.14366	U	0.324099	T	0.23094	0.0558	N	0.10874	0.06	0.09310	N	1	B;P;B	0.35033	0.362;0.481;0.416	B;B;B	0.37550	0.072;0.253;0.113	T	0.14811	-1.0459	10	0.62326	D	0.03	.	1.7485	0.02967	0.1824:0.4049:0.1981:0.2145	.	503;503;503	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	T	503	ENSP00000423470:A503T;ENSP00000349344:A503T;ENSP00000435300:A503T	ENSP00000349344:A503T	A	+	1	0	PCDHA4	140168463	0.000000	0.05858	0.470000	0.27216	0.651000	0.38670	-0.431000	0.06965	-0.017000	0.14103	0.580000	0.79431	GCG	.	.		0.662	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		A	140188279	G	A	140188279	3	1	102	1	0	0	0	0	1	0	0	0	11535	1087	38	1	1509	1	PCDHA4	5	140188279	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	18830181	140188279	40726981	43	14525										
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140723657	140723657	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ctggccctgctgtgcgcgctCctggggacgctgtgcgaaac	15	14	0	0	rs200693710		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:140723657C>T	ENST00000253812.6	+	1	57	c.57C>T	c.(55-57)ctC>ctT	p.L19L	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	19					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTGCGCGCTCCTGGGGACGC	0.542											OREG0016855	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L19L		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.C57T						.						124	137	133					5																	140723657		2077	4234	6311	SO:0001819	synonymous_variant	56112	exon1			CGCGCTCCTGGGG	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.57C>T	chr5.hg19:g.140723657C>T		47.0	0.0	1658	61.0	17.0	NM_032011	Q9Y5D4	Silent	SNP	ENST00000253812.6	hg19	CCDS47290.1																																																																																			.	C|1.000;G|0.000		0.542	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140723657	C	T	140723657	2	4	102	1	0	0	0	0	0	0	0	1	11564	842	30	3		3	PCDHGA3	5	140723657	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	535378	140723657	40191603	44	14526										
FAT2	2196	hgsc.bcm.edu	37	chr5	150922777	150922777	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttgaccacaccagtgactggGttaatttcaatgacatcttt	7	9	2	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:150922777G>A	ENST00000261800.5	-	9	7923	c.7911C>T	c.(7909-7911)aaC>aaT	p.N2637N		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2637	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAGTGACTGGGTTAATTTCAA	0.478																																					p.N2637N		Atlas-SNP	.											.	FAT2	465	.	0			c.C7911T						.						142	139	140					5																	150922777		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon9			GACTGGGTTAATT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.7911C>T	chr5.hg19:g.150922777G>A		49.0	0.0		53.0	18.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1																																																																																			.	.		0.478	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150922777	G	A	150922777	2	1	102	1	0	0	0	0	0	0	0	1	5698	1252	44	3		3	FAT2	5	150922777	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	10199120	150922777	29992483	45	14527										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169484584	169484584	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	acccctctgcccacggacagTccatgtggattgagagaacc	10	14	1	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:169484584T>C	ENST00000256935.8	+	44	4461	c.4381T>C	c.(4381-4383)Tcc>Ccc	p.S1461P	DOCK2_ENST00000520908.1_Splice_Site_p.S953P|DOCK2_ENST00000540750.1_Splice_Site_p.S522P|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1461	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCACGGACAGTCCATGTGGAT	0.567																																					p.S1461P		Atlas-SNP	.											.	DOCK2	389	.	0			c.T4381C						.						106	88	94					5																	169484584		2203	4300	6503	SO:0001630	splice_region_variant	1794	exon44			GGACAGTCCATGT	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4381-1T>C	chr5.hg19:g.169484584T>C		70.0	0.0		101.0	17.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.943045	0.73672	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.18810	2.19;2.19;2.19	5.47	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.44456	0.1294	M	0.73598	2.24	0.43025	D	0.994583	D;D;D	0.89917	1.0;0.997;1.0	D;D;D	0.91635	0.999;0.968;0.996	T	0.34700	-0.9818	10	0.48119	T	0.1	.	11.4863	0.50356	0.1348:0.0:0.0:0.8652	.	953;17;1461	E7ERW7;B3KY14;Q92608	.;.;DOCK2_HUMAN	P	1461;953;522	ENSP00000256935:S1461P;ENSP00000429283:S953P;ENSP00000438827:S522P	ENSP00000256935:S1461P	S	+	1	0	DOCK2	169417162	1.000000	0.71417	0.961000	0.40146	0.906000	0.53458	2.048000	0.41278	0.845000	0.35118	0.533000	0.62120	TCC	.	.		0.567	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	Missense_Mutation	C	169484584	T	C	169484584	5	2	102	1	0	0	0	0	0	0	1	0	4689	1681	58	2	4555	2	DOCK2	5	169484584	Splice_Site	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	18561807	169484584	11430676	46	14528										
HNRNPH1	3187	hgsc.bcm.edu	37	chr5	179043886	179043886	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttacacaagcccatgcctccCatcatttggctaccataagc	5	15	1	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:179043886C>T	ENST00000356731.5	-	10	2726	c.1191G>A	c.(1189-1191)atG>atA	p.M397I	HNRNPH1_ENST00000511300.2_Intron|HNRNPH1_ENST00000393432.4_Missense_Mutation_p.M397I|HNRNPH1_ENST00000329433.6_Missense_Mutation_p.M397I|HNRNPH1_ENST00000510411.1_Intron|HNRNPH1_ENST00000524180.1_5'Flank|HNRNPH1_ENST00000442819.2_Missense_Mutation_p.M397I			P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1 (H)	397	2 X 16 AA Gly-rich approximate repeats.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1)	14						CCATGCCTCCCATCATTTGGC	0.338																																					p.M397I		Atlas-SNP	.											.	HNRNPH1	62	.	0			c.G1191A						.						103	101	102					5																	179043886		2203	4300	6503	SO:0001583	missense	3187	exon11			GCCTCCCATCATT	BC001348	CCDS4446.1	5q35.3	2013-02-12		2008-04-18	ENSG00000169045	ENSG00000169045		"RNA binding motif (RRM) containing"	5041	protein-coding gene	gene with protein product		601035		HNRPH1		7499401	Standard	NM_005520		Approved	hnRNPH	uc003mkf.5	P31943	OTTHUMG00000130908	ENST00000356731.5:c.1191G>A	chr5.hg19:g.179043886C>T	ENSP00000349168:p.Met397Ile	134.0	0.0		290.0	12.0	NM_001257293	B3KW86|D3DWQ2|Q6IBM4	Missense_Mutation	SNP	ENST00000356731.5	hg19	CCDS4446.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	c|c|c	13.68|13.68|13.68	2.310259|2.310259|2.310259	0.40895|0.40895|0.40895	.|.|.	.|.|.	ENSG00000169045|ENSG00000169045|ENSG00000169045	ENST00000523449;ENST00000523136|ENST00000393432;ENST00000442819;ENST00000356731;ENST00000329433;ENST00000523921|ENST00000521173	.|T;T;T;T;T|.	.|0.12361|.	.|2.69;2.69;2.69;2.69;2.69|.	5.84|5.84|5.84	4.97|4.97|4.97	0.65823|0.65823|0.65823	.|.|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|.	0.67126|0.67126|.	0.2860|0.2860|.	L|L|L	0.47190|0.47190|0.47190	1.495|1.495|1.495	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|B|.	.|0.09022|.	.|0.002|.	.|B|.	.|0.08055|.	.|0.003|.	T|T|.	0.64786|0.64786|.	-0.6325|-0.6325|.	5|10|.	.|0.36615|.	.|T|.	.|0.2|.	-0.6785|-0.6785|-0.6785	16.5635|16.5635|16.5635	0.84573|0.84573|0.84573	0.1317:0.8683:0.0:0.0|0.1317:0.8683:0.0:0.0|0.1317:0.8683:0.0:0.0	.|.|.	.|397|.	.|P31943|.	.|HNRH1_HUMAN|.	R|I|X	65;14|397;397;397;397;191|272	.|ENSP00000377082:M397I;ENSP00000397797:M397I;ENSP00000349168:M397I;ENSP00000327539:M397I;ENSP00000429270:M191I|.	.|ENSP00000327539:M397I|.	G|M|W	-|-|-	1|3|2	0|0|0	HNRNPH1|HNRNPH1|HNRNPH1	178976492|178976492|178976492	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.995000|0.995000|0.995000	0.86356|0.86356|0.86356	2.357000|2.357000|2.357000	0.44125|0.44125|0.44125	1.478000|1.478000|1.478000	0.48253|0.48253|0.48253	-0.127000|-0.127000|-0.127000	0.14921|0.14921|0.14921	GGG|ATG|TGG	.	.		0.338	HNRNPH1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253497.3	NM_005520		T	179043886	C	T	179043886	3	4	102	1	0	0	0	0	1	0	0	0	7275	594	21	3	170	3	HNRNPH1	5	179043886	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	9559302	179043886	1871374	47	14529										
HIST1H3I	8354	hgsc.bcm.edu	37	chr6	27839822	27839822	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cgcaagcctcctgcagcgccAtcaccgccgagctctggaag	11	17	2	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr6:27839822A>G	ENST00000328488.2	-	1	277	c.272T>C	c.(271-273)aTg>aCg	p.M91T		NM_003533.2	NP_003524.1	P68431	H31_HUMAN	histone cluster 1, H3i	91					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CTGCAGCGCCATCACCGCCGA	0.567																																					p.M91T		Atlas-SNP	.											.	HIST1H3I	28	.	0			c.T272C						.						82	88	86					6																	27839822		2203	4300	6503	SO:0001583	missense	8354	exon1			AGCGCCATCACCG	X83550	CCDS4636.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000182572	ENSG00000275379		"Histones / Replication-dependent"	4771	protein-coding gene	gene with protein product		602814	"H3 histone family, member F", "histone 1, H3i"	H3FF		9031620, 9439656, 12408966	Standard	NM_003533		Approved	H3/f, H3.f	uc003njy.3	P68431	OTTHUMG00000016184	ENST00000328488.2:c.272T>C	chr6.hg19:g.27839822A>G	ENSP00000329554:p.Met91Thr	65.0	0.0		180.0	85.0	NM_003533	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000328488.2	hg19	CCDS4636.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.582648	0.28180	.	.	ENSG00000182572	ENST00000328488	T	0.66995	-0.24	4.12	4.12	0.48240	.	.	.	.	.	T	0.64182	0.2575	.	.	.	0.41515	D	0.988361	.	.	.	.	.	.	T	0.65105	-0.6249	6	0.39692	T	0.17	.	13.3331	0.60500	1.0:0.0:0.0:0.0	.	.	.	.	T	91	ENSP00000329554:M91T	ENSP00000329554:M91T	M	-	2	0	HIST1H3I	27947801	1.000000	0.71417	0.995000	0.50966	0.668000	0.39293	4.395000	0.59678	2.086000	0.62901	0.528000	0.53228	ATG	.	.		0.567	HIST1H3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043452.1	NM_003533		G	27839822	A	G	27839822	3	3	102	1	0	0	0	0	1	0	0	0	7172	217	8	2	142	2	HIST1H3I	6	27839822	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10		27839822	143275245	48	14530										
OR2B6	26212	hgsc.bcm.edu	37	chr6	27925139	27925139	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cttacactgtgaccatctttGgcaatctgaccattattcta	5	11	3	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr6:27925139G>A	ENST00000244623.1	+	1	121	c.121G>A	c.(121-123)Ggc>Agc	p.G41S		NM_012367.1	NP_036499.1	P58173	OR2B6_HUMAN	olfactory receptor, family 2, subfamily B, member 6	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GACCATCTTTGGCAATCTGAC	0.428																																					p.G41S		Atlas-SNP	.											.	OR2B6	48	.	0			c.G121A						.						187	175	179					6																	27925139		2203	4300	6503	SO:0001583	missense	26212	exon1			ATCTTTGGCAATC	U86275	CCDS4642.1	6p22.1	2012-08-09			ENSG00000124657	ENSG00000124657		"GPCR / Class A : Olfactory receptors"	8241	protein-coding gene	gene with protein product				OR2B6P, OR2B1, OR2B1P, OR2B5		9500546	Standard	NM_012367		Approved	OR6-31, dJ408B20.2, OR5-40, OR5-41	uc011dkx.2	P58173	OTTHUMG00000014497	ENST00000244623.1:c.121G>A	chr6.hg19:g.27925139G>A	ENSP00000244623:p.Gly41Ser	147.0	0.0		385.0	16.0	NM_012367	O43883|Q6IF89|Q9H5B0	Missense_Mutation	SNP	ENST00000244623.1	hg19	CCDS4642.1	.	.	.	.	.	.	.	.	.	.	g	13.19	2.164266	0.38217	.	.	ENSG00000124657	ENST00000244623	T	0.04275	3.66	3.78	2.91	0.33838	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34088	U	0.004270	T	0.05868	0.0153	M	0.88105	2.93	0.29422	N	0.860477	B	0.26081	0.141	B	0.37508	0.252	T	0.05649	-1.0872	10	0.72032	D	0.01	.	9.8937	0.41304	0.1074:0.0:0.8926:0.0	.	41	P58173	OR2B6_HUMAN	S	41	ENSP00000244623:G41S	ENSP00000244623:G41S	G	+	1	0	OR2B6	28033118	0.036000	0.19791	0.995000	0.50966	0.669000	0.39330	1.997000	0.40786	0.864000	0.35578	-0.244000	0.11960	GGC	.	.		0.428	OR2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040165.1			A	27925139	G	A	27925139	3	1	102	1	0	0	0	0	1	0	0	0	11000	1348	47	3	123	3	OR2B6	6	27925139	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	85317	27925139	143189928	49	14531										
PPT2	9374	hgsc.bcm.edu	37	chr6	32123651	32123651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tgccattcgcttgccagacaCggactacttgaagtggctgt	11	11	0	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr6:32123651C>T	ENST00000324816.6	+	5	1005	c.437C>T	c.(436-438)aCg>aTg	p.T146M	PPT2-EGFL8_ENST00000453656.2_3'UTR|PPT2_ENST00000375143.2_Missense_Mutation_p.T146M|PPT2_ENST00000445576.2_Missense_Mutation_p.T146M|PPT2_ENST00000375137.2_Missense_Mutation_p.T146M|PPT2_ENST00000493548.1_3'UTR|PPT2_ENST00000395523.1_Missense_Mutation_p.T146M|PPT2_ENST00000361568.2_Missense_Mutation_p.T152M|PRRT1_ENST00000375150.2_5'Flank|PPT2_ENST00000437001.2_Missense_Mutation_p.T23M|PPT2-EGFL8_ENST00000422437.1_Missense_Mutation_p.T146M			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	146					cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						TTGCCAGACACGGACTACTTG	0.527																																					p.T152M		Atlas-SNP	.											.	PPT2	19	.	0			c.C455T						.						159	130	140					6																	32123651		1511	2709	4220	SO:0001583	missense	9374	exon5			CAGACACGGACTA	AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	3.1.2.22		9326	protein-coding gene	gene with protein product		603298				9341199, 10051407	Standard	NM_138717		Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.437C>T	chr6.hg19:g.32123651C>T	ENSP00000320528:p.Thr146Met	95.0	0.0		351.0	73.0	NM_138717	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	Missense_Mutation	SNP	ENST00000324816.6	hg19	CCDS4742.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.780951	0.90282	.	.	ENSG00000221988	ENST00000414204;ENST00000361568;ENST00000395523;ENST00000445576;ENST00000324816;ENST00000437001;ENST00000375137;ENST00000375143;ENST00000424499;ENST00000436118	T;D;D;D;D;D;D;D;D	0.96232	-0.25;-3.95;-3.95;-3.95;-3.95;-3.38;-3.95;-3.95;-3.38	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.97666	0.9235	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.985;0.992;0.992	D	0.98139	1.0435	10	0.62326	D	0.03	-4.8314	16.689	0.85316	0.0:1.0:0.0:0.0	.	146;146;152	Q9UMR5-2;Q9UMR5;B0S872	.;PPT2_HUMAN;.	M	146;152;146;146;146;23;146;146;68;146	ENSP00000398847:T146M;ENSP00000354608:T152M;ENSP00000378894:T146M;ENSP00000412381:T146M;ENSP00000320528:T146M;ENSP00000415350:T23M;ENSP00000364279:T146M;ENSP00000364285:T146M;ENSP00000409877:T68M	ENSP00000320528:T146M	T	+	2	0	PPT2	32231629	1.000000	0.71417	0.995000	0.50966	0.949000	0.60115	6.997000	0.76270	2.527000	0.85204	0.557000	0.71058	ACG	.	.		0.527	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076552.4	NM_138717		T	32123651	C	T	32123651	3	4	102	1	0	0	0	0	1	0	0	0	12424	536	19	1	473	1	PPT2	6	32123651	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	4198512	32123651	138991416	50	14532										
BZW2	28969	hgsc.bcm.edu	37	chr7	16720997	16720997	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	actgtgtgttttcagcaaatGaagatcatgaaaccatccga	8	8	2	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:16720997G>T	ENST00000433922.2	+	4	485	c.307G>T	c.(307-309)Gaa>Taa	p.E103*	BZW2_ENST00000405202.1_Nonsense_Mutation_p.E27*|BZW2_ENST00000258761.3_Nonsense_Mutation_p.E103*|BZW2_ENST00000452975.2_Nonsense_Mutation_p.E103*|BZW2_ENST00000432311.1_3'UTR	NM_001159767.1	NP_001153239.1	Q9Y6E2	BZW2_HUMAN	basic leucine zipper and W2 domains 2	103					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	membrane (GO:0016020)		p.E103K(1)		cervix(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	15	Lung NSC(10;0.0367)|all_lung(11;0.0837)			UCEC - Uterine corpus endometrioid carcinoma (126;0.199)		TTCAGCAAATGAAGATCATGA	0.428																																					p.E103X		Atlas-SNP	.											BZW2,NS,carcinoma,0,1	BZW2	35	.	1	Substitution - Missense(1)	cervix(1)	c.G307T						.						137	121	126					7																	16720997		2203	4300	6503	SO:0001587	stop_gained	28969	exon4			GCAAATGAAGATC	AF083246	CCDS5362.1	7p21.3	2008-07-18			ENSG00000136261	ENSG00000136261			18808	protein-coding gene	gene with protein product						11042152	Standard	NM_001159767		Approved	HSPC028, MST017, MSTP017	uc003stj.2	Q9Y6E2	OTTHUMG00000130755	ENST00000433922.2:c.307G>T	chr7.hg19:g.16720997G>T	ENSP00000397249:p.Glu103*	57.0	0.0		107.0	19.0	NM_014038	A4D123|Q3B779|Q96JW5|Q9H3F7	Nonsense_Mutation	SNP	ENST00000433922.2	hg19	CCDS5362.1	.	.	.	.	.	.	.	.	.	.	G	39	7.514962	0.98332	.	.	ENSG00000136261	ENST00000415365;ENST00000258761;ENST00000433922;ENST00000452975;ENST00000405202;ENST00000446596;ENST00000438834;ENST00000430000	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	-12.2543	20.2527	0.98410	0.0:0.0:1.0:0.0	.	.	.	.	X	103;103;103;103;27;103;103;103	.	ENSP00000258761:E103X	E	+	1	0	BZW2	16687522	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.810000	0.99221	2.788000	0.95919	0.557000	0.71058	GAA	.	.		0.428	BZW2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253256.2	NM_014038		T	16720997	G	T	16720997	4	4	102	1	0	0	0	0	0	1	0	0	1581	1291	45	3	317	3	BZW2	7	16720997	Nonsense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10		16720997	142417666	51	14533										
CBX3	11335	hgsc.bcm.edu	37	chr7	26248077	26248077	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aattgattgaagcgtttcttAactctcagaaagctggcaaa	8	7	2	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:26248077A>G	ENST00000337620.4	+	4	660	c.232A>G	c.(232-234)Aac>Gac	p.N78D	CBX3_ENST00000497498.1_3'UTR|CBX3_ENST00000409747.1_Intron|CBX3_ENST00000396386.2_Missense_Mutation_p.N78D	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3	78	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						AGCGTTTCTTAACTCTCAGAA	0.328																																					p.N78D		Atlas-SNP	.											.	CBX3	25	.	0			c.A232G						.						53	60	58					7																	26248077		2202	4300	6502	SO:0001583	missense	11335	exon4			TTTCTTAACTCTC	U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"HP1 gamma homolog (Drosophila)"	604477	"chromobox homolog 3 (Drosophila HP1 gamma)"			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.232A>G	chr7.hg19:g.26248077A>G	ENSP00000336687:p.Asn78Asp	116.0	0.0		248.0	102.0	NM_016587	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Missense_Mutation	SNP	ENST00000337620.4	hg19	CCDS5398.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.087128	0.55968	.	.	ENSG00000122565	ENST00000337620;ENST00000396386	T;T	0.70749	-0.51;-0.51	5.35	5.35	0.76521	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (2);	0.091219	0.85682	D	0.000000	T	0.52354	0.1729	N	0.10629	0.01	0.80722	D	1	B	0.06786	0.001	B	0.14023	0.01	T	0.48317	-0.9046	10	0.31617	T	0.26	.	15.6276	0.76874	1.0:0.0:0.0:0.0	.	78	Q13185	CBX3_HUMAN	D	78	ENSP00000336687:N78D;ENSP00000379670:N78D	ENSP00000336687:N78D	N	+	1	0	CBX3	26214602	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.135000	0.57997	2.150000	0.67090	0.533000	0.62120	AAC	.	.		0.328	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276		G	26248077	A	G	26248077	3	3	102	1	0	0	0	0	1	0	0	0	2721	362	13	2	242	2	CBX3	7	26248077	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	9527080	26248077	132890586	52	14534										
C7orf51	222950	hgsc.bcm.edu	37	chr7	100085893	100085893	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gatgagtcctgccccccaggCccctctcctcgaggggggaa	13	16	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:100085893C>T	ENST00000300179.2	+	4	708	c.549C>T	c.(547-549)ggC>ggT	p.G183G	NYAP1_ENST00000423930.1_Silent_p.G183G|NYAP1_ENST00000454988.1_Silent_p.G126G	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	183	Involved in CYFIP1- and NCKAP1-binding. {ECO:0000250}.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GCCCCCCAGGCCCCTCTCCTC	0.652																																					p.G183G		Atlas-SNP	.											.	.	.	.	0			c.C549T						.						59	68	65					7																	100085893		2203	4300	6503	SO:0001819	synonymous_variant	222950	exon4			CCCAGGCCCCTCT	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.549C>T	chr7.hg19:g.100085893C>T		50.0	0.0		67.0	23.0	NM_173564	Q6U9Y3|Q8N1V0	Silent	SNP	ENST00000300179.2	hg19	CCDS5696.1																																																																																			.	.		0.652	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		T	100085893	C	T	100085893	2	4	102	1	0	0	0	0	0	0	0	1	2402	726	26	3		3	C7orf51	7	100085893	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	73837816	100085893	59052770	53	14535										
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100452001	100452001	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	agttgtttttctgaggattgGtgagtgggtcctggggcggg	19	4	1	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:100452001G>T	ENST00000354161.3	+	2	306		c.e2+1		SLC12A9_ENST00000428758.1_Splice_Site|SLC12A9_ENST00000540482.1_Splice_Site|SLC12A9_ENST00000415287.1_Splice_Site|SLC12A9_ENST00000275729.3_Splice_Site|RP11-126L15.4_ENST00000412754.1_RNA	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CTGAGGATTGGTGAGTGGGTC	0.577																																					.		Atlas-SNP	.											.	SLC12A9	81	.	0			c.181+1G>T						.						120	119	120					7																	100452001		2203	4300	6503	SO:0001630	splice_region_variant	56996	exon2			GGATTGGTGAGTG	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"Solute carriers"	17435	protein-coding gene	gene with protein product	"cation-chloride cotransporter-interacting protein"					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.181+1G>T	chr7.hg19:g.100452001G>T		158.0	0.0		499.0	133.0	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Splice_Site	SNP	ENST00000354161.3	hg19	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.655266	0.67472	.	.	ENSG00000146828	ENST00000540482;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161;ENST00000416675;ENST00000434158	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7812	0.69769	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A9	100289937	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	7.406000	0.80017	2.340000	0.79590	0.407000	0.27541	.	.	.		0.577	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	Intron	T	100452001	G	T	100452001	5	4	102	1	0	0	0	0	0	0	1	0	14405	1275	44	3	184	3	SLC12A9	7	100452001	Splice_Site	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	366108	100452001	58686662	54	14536										
MUC17	140453	hgsc.bcm.edu	37	chr7	100678400	100678400	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	acacgccagtggccagttctGaggctagcaccctttcaaca	9	14	2	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:100678400G>T	ENST00000306151.4	+	3	3767	c.3703G>T	c.(3703-3705)Gag>Tag	p.E1235*		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1235	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GGCCAGTTCTGAGGCTAGCAC	0.517																																					p.E1235X		Atlas-SNP	.											.	MUC17	804	.	0			c.G3703T						.						304	291	296					7																	100678400		2203	4300	6503	SO:0001587	stop_gained	140453	exon3			AGTTCTGAGGCTA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3703G>T	chr7.hg19:g.100678400G>T	ENSP00000302716:p.Glu1235*	67.0	0.0		102.0	21.0	NM_001040105	O14761|Q685J2|Q8TDH7	Nonsense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	38	6.641995	0.97726	.	.	ENSG00000169876	ENST00000306151	.	.	.	0.471	0.471	0.16752	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	.	.	.	.	.	.	.	X	1235	.	ENSP00000302716:E1235X	E	+	1	0	MUC17	100465120	0.000000	0.05858	0.005000	0.12908	0.037000	0.13140	0.216000	0.17585	0.558000	0.29135	0.134000	0.15878	GAG	.	.		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100678400	G	T	100678400	4	4	102	1	0	0	0	0	0	1	0	0	9983	1291	45	3	3713	3	MUC17	7	100678400	Nonsense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	226399	100678400	58460263	55	14537										
GPR22	2845	hgsc.bcm.edu	37	chr7	107115448	107115448	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aaaagagagtcttcaggatgTctttattgattatttctaca	7	5	4	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:107115448T>C	ENST00000304402.4	+	3	2286	c.943T>C	c.(943-945)Tct>Cct	p.S315P	COG5_ENST00000475638.2_Intron|COG5_ENST00000393603.2_Intron|COG5_ENST00000347053.3_Intron|COG5_ENST00000297135.3_Intron	NM_005295.2	NP_005286.2	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	315					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(3)|lung(6)|ovary(2)|stomach(1)	12						CTTCAGGATGTCTTTATTGAT	0.383																																					p.S315P		Atlas-SNP	.											.	GPR22	43	.	0			c.T943C						.						118	120	119					7																	107115448		2203	4300	6503	SO:0001583	missense	2845	exon3			AGGATGTCTTTAT	U66581	CCDS5744.1	7q22-q31.1	2012-08-21			ENSG00000172209	ENSG00000172209		"GPCR / Class A : Orphans"	4477	protein-coding gene	gene with protein product		601910				9073069	Standard	NM_005295		Approved		uc003vef.3	Q99680	OTTHUMG00000154902	ENST00000304402.4:c.943T>C	chr7.hg19:g.107115448T>C	ENSP00000302676:p.Ser315Pro	153.0	0.0		330.0	109.0	NM_005295	O14554	Missense_Mutation	SNP	ENST00000304402.4	hg19	CCDS5744.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.514345	0.64522	.	.	ENSG00000172209	ENST00000304402	T	0.37915	1.17	5.66	5.66	0.87406	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.59432	0.2193	M	0.65498	2.005	0.80722	D	1	D	0.63880	0.993	D	0.79108	0.992	T	0.62900	-0.6756	10	0.87932	D	0	-9.5576	15.8804	0.79201	0.0:0.0:0.0:1.0	.	315	Q99680	GPR22_HUMAN	P	315	ENSP00000302676:S315P	ENSP00000302676:S315P	S	+	1	0	GPR22	106902684	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.040000	0.89188	2.160000	0.67779	0.477000	0.44152	TCT	.	.		0.383	GPR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337598.1			C	107115448	T	C	107115448	3	2	102	1	0	0	0	0	1	0	0	0	6690	1667	58	2	945	2	GPR22	7	107115448	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	6437048	107115448	52023215	56	14538										
SGCZ	137868	hgsc.bcm.edu	37	chr8	13948074	13948074	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tgtctgtcgagaacttgaggAgctgggtgaagaagatgaga	16	4	1	6			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:13948074A>T	ENST00000382080.1	-	8	1532	c.817T>A	c.(817-819)Tcc>Acc	p.S273T	SGCZ_ENST00000421524.2_Missense_Mutation_p.S226T	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	260					membrane organization (GO:0061024)|muscle cell cellular homeostasis (GO:0046716)|muscle cell development (GO:0055001)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|sarcoglycan complex (GO:0016012)				NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		GAACTTGAGGAGCTGGGTGAA	0.433																																					p.S273T		Atlas-SNP	.											.	SGCZ	96	.	0			c.T817A						.						130	121	124					8																	13948074		2203	4300	6503	SO:0001583	missense	137868	exon8			TTGAGGAGCTGGG	AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053			14075	protein-coding gene	gene with protein product		608113				12189167	Standard	XM_006716287		Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.817T>A	chr8.hg19:g.13948074A>T	ENSP00000371512:p.Ser273Thr	52.0	0.0		60.0	26.0	NM_139167	Q6REU0	Missense_Mutation	SNP	ENST00000382080.1	hg19	CCDS5992.2	.	.	.	.	.	.	.	.	.	.	A	8.987	0.976707	0.18812	.	.	ENSG00000185053	ENST00000382080;ENST00000421524	T;T	0.11385	2.78;2.78	5.5	4.33	0.51752	.	0.385763	0.30177	N	0.010225	T	0.06005	0.0156	N	0.20807	0.61	0.31984	N	0.605484	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.001	T	0.27262	-1.0079	10	0.10377	T	0.69	.	7.1543	0.25628	0.7793:0.146:0.0747:0.0	.	226;273	Q08AT0;Q96LD1-2	.;.	T	273;226	ENSP00000371512:S273T;ENSP00000405224:S226T	ENSP00000371512:S273T	S	-	1	0	SGCZ	13992445	0.999000	0.42202	0.998000	0.56505	0.997000	0.91878	2.276000	0.43408	1.028000	0.39785	0.533000	0.62120	TCC	.	.		0.433	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207636.2	NM_139167		T	13948074	A	T	13948074	3	4	102	1	0	0	0	0	1	0	0	0	14219	304	11	4	125	4	SGCZ	8	13948074	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10		13948074	132415948	57	14539										
UBR5	51366	hgsc.bcm.edu	37	chr8	103293516	103293516	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cctcatggcaagaatggataCcttttgcgttctagttgagg	11	8	2	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:103293516C>T	ENST00000520539.1	-	41	6534		c.e41+1		UBR5_ENST00000220959.4_Splice_Site|UBR5_ENST00000521922.1_Splice_Site	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5						cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			AGAATGGATACCTTTTGCGTT	0.368																																					.	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.5927+1G>A						.						95	75	82					8																	103293516		2203	4300	6503	SO:0001630	splice_region_variant	51366	exon42			TGGATACCTTTTG	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.5927+1G>A	chr8.hg19:g.103293516C>T		146.0	0.0		727.0	219.0	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Splice_Site	SNP	ENST00000520539.1	hg19	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.547843	0.86022	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.692	0.88271	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBR5	103362692	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.772000	0.85439	2.152000	0.67230	0.563000	0.77884	.	.	.		0.368	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	Intron	T	103293516	C	T	103293516	5	4	102	1	0	0	0	0	0	0	1	0	16920	521	18	3	2547	3	UBR5	8	103293516	Splice_Site	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	89345442	103293516	43070506	58	14540										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106331179	106331179	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ccgccgccgagatgtcccggCgaaagcaaagcaaaccccgg	12	16	0	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:106331179C>T	ENST00000407775.2	+	1	260	c.10C>T	c.(10-12)Cga>Tga	p.R4*	ZFPM2_ENST00000520492.1_5'Flank	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	4					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GATGTCCCGGCGAAAGCAAAG	0.741																																					p.R4X		Atlas-SNP	.											ZFPM2,colon,carcinoma,0,1	ZFPM2	219	.	0			c.C10T						.						4	5	5					8																	106331179		1410	3262	4672	SO:0001587	stop_gained	23414	exon1			TCCCGGCGAAAGC	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.10C>T	chr8.hg19:g.106331179C>T	ENSP00000384179:p.Arg4*	37.0	0.0		205.0	30.0	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Nonsense_Mutation	SNP	ENST00000407775.2	hg19	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	C	40	7.932149	0.98568	.	.	ENSG00000169946	ENST00000407775	.	.	.	3.5	2.46	0.29980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.6804	0.28509	0.5355:0.4645:0.0:0.0	.	.	.	.	X	4	.	ENSP00000384179:R4X	R	+	1	2	ZFPM2	106400355	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.329000	0.52060	1.491000	0.48482	0.460000	0.39030	CGA	.	.		0.741	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			T	106331179	C	T	106331179	4	4	102	1	0	0	0	0	0	1	0	0	17673	760	27	1	12	1	ZFPM2	8	106331179	Nonsense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	3037663	106331179	40032843	59	14541										
ANGPT1	284	hgsc.bcm.edu	37	chr8	108297062	108297062	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cccagccaatattcaccggaGggatttccaaaaccctggga	9	13	1	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:108297062G>T	ENST00000520734.1	-	6	738	c.453C>A	c.(451-453)ccC>ccA	p.P151P	ANGPT1_ENST00000520052.1_Silent_p.P150P|ANGPT1_ENST00000518386.1_Intron			Q15389	ANGP1_HUMAN	angiopoietin 1	351					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			ATTCACCGGAGGGATTTCCAA	0.378																																					p.P351P		Atlas-SNP	.											.	ANGPT1	111	.	0			c.C1053A						.						56	53	54					8																	108297062		2203	4300	6503	SO:0001819	synonymous_variant	284	exon7			ACCGGAGGGATTT	D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"Fibrinogen C domain containing"	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.453C>A	chr8.hg19:g.108297062G>T		76.0	0.0		278.0	40.0	NM_001146	Q5HYA0	Silent	SNP	ENST00000520734.1	hg19																																																																																				.	.		0.378	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290		T	108297062	G	T	108297062	2	4	102	1	0	0	0	0	0	0	0	1	610	987	35	3		3	ANGPT1	8	108297062	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	1965883	108297062	38066960	60	14542										
ADCY8	114	hgsc.bcm.edu	37	chr8	131797673	131797673	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cacggccatgtaggtgctgcCaatggtcttaatcttttcaa	9	10	3	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:131797673C>T	ENST00000286355.5	-	16	5201	c.3109G>A	c.(3109-3111)Ggc>Agc	p.G1037S	ADCY8_ENST00000377928.3_Missense_Mutation_p.G906S	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	1037					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TAGGTGCTGCCAATGGTCTTA	0.483										HNSCC(32;0.087)																											p.G1037S		Atlas-SNP	.											.	ADCY8	291	.	0			c.G3109A						.						112	99	103					8																	131797673		2203	4300	6503	SO:0001583	missense	114	exon16			TGCTGCCAATGGT	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.3109G>A	chr8.hg19:g.131797673C>T	ENSP00000286355:p.Gly1037Ser	51.0	0.0		109.0	9.0	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	C	36	5.714181	0.96830	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	D;D	0.97811	-4.55;-4.55	5.07	5.07	0.68467	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.98654	0.9549	M	0.79926	2.475	0.50632	D	0.99988	D;D	0.69078	0.997;0.997	D;D	0.75484	0.972;0.986	D	0.99572	1.0971	10	0.62326	D	0.03	.	17.8033	0.88595	0.0:1.0:0.0:0.0	.	906;1037	E7EVL1;P40145	.;ADCY8_HUMAN	S	1037;906	ENSP00000286355:G1037S;ENSP00000367161:G906S	ENSP00000286355:G1037S	G	-	1	0	ADCY8	131866855	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.770000	0.85390	2.535000	0.85469	0.591000	0.81541	GGC	.	.		0.483	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			T	131797673	C	T	131797673	3	4	102	1	0	0	0	0	1	0	0	0	300	594	21	3	658	3	ADCY8	8	131797673	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	23500611	131797673	14566349	61	14543										
TG	7038	hgsc.bcm.edu	37	chr8	133961019	133961019	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tcctacctcttgtgattctcAggtgccatcatctgtgggtt	9	11	4	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:133961019A>G	ENST00000220616.4	+	27	5273		c.e27-1		TG_ENST00000377869.1_Splice_Site|TG_ENST00000542445.1_Splice_Site	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin						hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TGTGATTCTCAGGTGCCATCA	0.498																																					.		Atlas-SNP	.											.	TG	416	.	0			c.5234-2A>G						.						189	173	179					8																	133961019		2203	4300	6503	SO:0001630	splice_region_variant	7038	exon27			ATTCTCAGGTGCC	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.5234-1A>G	chr8.hg19:g.133961019A>G		90.0	0.0		266.0	63.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Splice_Site	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.296961	0.23650	.	.	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000519178;ENST00000542445	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4081	0.55451	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TG	134030201	0.998000	0.40836	0.751000	0.31187	0.003000	0.03518	4.592000	0.61027	2.246000	0.74042	0.533000	0.62120	.	.	.		0.498	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	Intron	G	133961019	A	G	133961019	5	3	102	1	0	0	0	0	0	0	1	0	15828	202	7	2	5338	2	TG	8	133961019	Splice_Site	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	2163346	133961019	12403003	62	14544										
DMRT2	10655	hgsc.bcm.edu	37	chr9	1056606	1056606	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	acagtatcccttgtcctcaaGatttttagtttggcccaagt	7	10	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:1056606G>T	ENST00000358146.2	+	3	1019	c.1019G>T	c.(1018-1020)aGa>aTa	p.R340I	DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000302441.6_Missense_Mutation_p.R340I|DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000382251.3_Missense_Mutation_p.R340I			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	340					embryonic skeletal system development (GO:0048706)|positive regulation of myotome development (GO:2000287)|regulation of somitogenesis (GO:0014807)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(1)|prostate(2)	4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		TTGTCCTCAAGATTTTTAGTT	0.478																																					p.R340I		Atlas-SNP	.											.	DMRT2	70	.	0			c.G1019T						.						100	105	103					9																	1056606		2203	4300	6503	SO:0001583	missense	10655	exon4			CCTCAAGATTTTT	AF130729	CCDS6444.1, CCDS6445.1	9p24.3	2008-07-21			ENSG00000173253	ENSG00000173253			2935	protein-coding gene	gene with protein product	"terra-like protein"	604935				10332030	Standard	NM_181872		Approved		uc003zha.3	Q9Y5R5	OTTHUMG00000019437	ENST00000358146.2:c.1019G>T	chr9.hg19:g.1056606G>T	ENSP00000350865:p.Arg340Ile	66.0	0.0		89.0	22.0	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	hg19	CCDS6444.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725832	0.69074	.	.	ENSG00000173253	ENST00000382251;ENST00000302441;ENST00000358146	T;T;T	0.27557	1.66;1.66;1.66	5.62	5.62	0.85841	.	0.240668	0.40908	D	0.000985	T	0.53077	0.1774	L	0.59436	1.845	0.58432	D	0.999999	D;D	0.67145	0.994;0.996	P;D	0.66497	0.88;0.944	T	0.52366	-0.8585	10	0.72032	D	0.01	-15.4915	19.2806	0.94051	0.0:0.0:1.0:0.0	.	340;184	Q9Y5R5;Q5HYK2	DMRT2_HUMAN;.	I	340	ENSP00000371686:R340I;ENSP00000305785:R340I;ENSP00000350865:R340I	ENSP00000305785:R340I	R	+	2	0	DMRT2	1046606	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	9.153000	0.94687	2.665000	0.90641	0.650000	0.86243	AGA	.	.		0.478	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557		T	1056606	G	T	1056606	3	4	102	1	0	0	0	0	1	0	0	0	4588	942	33	3	1086	3	DMRT2	9	1056606	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10		1056606	140156825	63	14545										
IFNA4	3441	hgsc.bcm.edu	37	chr9	21187344	21187344	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gtggccatcaaactcctcctCggggaatccgaaatcatgtc	9	13	2	0	rs142712065	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:21187344C>G	ENST00000421715.1	-	1	254	c.187G>C	c.(187-189)Gag>Cag	p.E63Q		NM_021068.2	NP_066546.1	P05014	IFNA4_HUMAN	interferon, alpha 4	63					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17				GBM - Glioblastoma multiforme(5;2.69e-202)|Lung(24;2.26e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		AACTCCTCCTCGGGGAATCCG	0.517																																					p.E63Q	NSCLC(154;890 1986 23660 27800 51138)	Atlas-SNP	.											.	IFNA4	34	.	0			c.G187C						.						114	114	114					9																	21187344		2203	4300	6503	SO:0001583	missense	3441	exon1			CCTCCTCGGGGAA		CCDS6498.1	9p22	2010-08-24			ENSG00000236637	ENSG00000236637		"Interferons"	5425	protein-coding gene	gene with protein product		147564				1385305	Standard	NM_021068		Approved	MGC142200, IFN-alpha4a	uc003zon.2	P05014	OTTHUMG00000019660	ENST00000421715.1:c.187G>C	chr9.hg19:g.21187344C>G	ENSP00000412897:p.Glu63Gln	135.0	0.0		326.0	103.0	NM_021068	P13358|Q14CS4|Q5VV15	Missense_Mutation	SNP	ENST00000421715.1	hg19	CCDS6498.1	.	.	.	.	.	.	.	.	.	.	-	0.010	-1.794798	0.00617	.	.	ENSG00000236637	ENST00000421715	T	0.03242	4.0	2.96	-2.48	0.06423	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.591514	0.17433	N	0.174416	T	0.00552	0.0018	N	0.00084	-2.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39502	-0.9611	10	0.02654	T	1	.	2.3247	0.04220	0.1004:0.2772:0.342:0.2804	.	63	P05014	IFNA4_HUMAN	Q	63	ENSP00000412897:E63Q	ENSP00000412897:E63Q	E	-	1	0	IFNA4	21177344	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.618000	0.02049	-0.623000	0.05618	-0.332000	0.08345	GAG	.	.		0.517	IFNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051889.1	NM_021068		G	21187344	C	G	21187344	3	3	102	1	0	0	0	0	1	0	0	0	7548	893	31	4	386	4	IFNA4	9	21187344	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	20130738	21187344	120026087	64	14546										
LOC645961	645961	hgsc.bcm.edu	37	chr9	90746873	90746873	+	IGR	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	caggagataggactgggaaaGaggattgaagatgggcctga	17	4	0	5			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:90746873G>A								U6 (133623 upstream) : U3 (242310 downstream)																							GACTGGGAAAGAGGATTGAAG	0.532																																					p.S360F		Atlas-SNP	.											.	.	.	.	0			c.C1079T						.						14	17	16					9																	90746873		691	1590	2281	SO:0001628	intergenic_variant	645961	exon4			GGGAAAGAGGATT																													chr9.hg19:g.90746873G>A		81.0	0.0		139.0	37.0	NM_001166137		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.532									A	90746873	G	A	90746873	1	1	102	0	1	0	0	0	0	0	0	0	8892	942	33	3		3	LOC645961	9	90746873	IGR	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	69559529	90746873	50466558	65	14547										
ZNF189	7743	hgsc.bcm.edu	37	chr9	104171115	104171115	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tgtggaaaaagtttcagtcgGagctcattccttattgaaca	9	7	2	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:104171115G>A	ENST00000339664.2	+	3	1194	c.1065G>A	c.(1063-1065)cgG>cgA	p.R355R	ZNF189_ENST00000259395.4_Silent_p.R313R|ZNF189_ENST00000374861.3_Silent_p.R341R	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	355					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				GTTTCAGTCGGAGCTCATTCC	0.408																																					p.R355R		Atlas-SNP	.											.	ZNF189	79	.	0			c.G1065A						.						83	89	87					9																	104171115		2203	4300	6503	SO:0001819	synonymous_variant	7743	exon3			CAGTCGGAGCTCA	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"Zinc fingers, C2H2-type", "-"	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.1065G>A	chr9.hg19:g.104171115G>A		52.0	0.0		81.0	19.0	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Silent	SNP	ENST00000339664.2	hg19	CCDS6754.1																																																																																			.	.		0.408	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		A	104171115	G	A	104171115	2	1	102	1	0	0	0	0	0	0	0	1	17769	1161	41	3		3	ZNF189	9	104171115	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	13424242	104171115	37042316	66	14548										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767037	105767037	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cattatggatgtaccgttctTtaatgagaatttctgagaga	9	5	2	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:105767037T>C	ENST00000374798.3	+	4	311	c.241T>C	c.(241-243)Tta>Cta	p.L81L	CYLC2_ENST00000487798.1_Silent_p.L81L	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	81	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				GTACCGTTCTTTAATGAGAAT	0.403																																					p.L81L		Atlas-SNP	.											.	CYLC2	109	.	0			c.T241C						.						86	83	84					9																	105767037		2203	4300	6503	SO:0001819	synonymous_variant	1539	exon4			CGTTCTTTAATGA	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.241T>C	chr9.hg19:g.105767037T>C		76.0	0.0		128.0	35.0	NM_001340	B2R8F4|Q5VVJ9	Silent	SNP	ENST00000374798.3	hg19	CCDS35085.1																																																																																			.	.		0.403	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		C	105767037	T	C	105767037	2	2	102	1	0	0	0	0	0	0	0	1	4144	1838	64	2		2	CYLC2	9	105767037	Silent	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	1595922	105767037	35446394	67	14549										
OR13C9	286362	hgsc.bcm.edu	37	chr9	107379994	107379994	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttcctgcagaaaggcaattgTactacaaatgtagtttgtac	8	7	0	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:107379994T>C	ENST00000259362.1	-	1	491	c.492A>G	c.(490-492)gtA>gtG	p.V164V		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	164						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						AAGGCAATTGTACTACAAATG	0.438																																					p.V164V		Atlas-SNP	.											.	OR13C9	42	.	0			c.A492G						.						121	104	110					9																	107379994		2203	4300	6503	SO:0001819	synonymous_variant	286362	exon1			CAATTGTACTACA		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"GPCR / Class A : Olfactory receptors"	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.492A>G	chr9.hg19:g.107379994T>C		105.0	0.0		206.0	67.0	NM_001001956	Q6IFL2	Silent	SNP	ENST00000259362.1	hg19	CCDS35093.1																																																																																			.	.		0.438	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1			C	107379994	T	C	107379994	2	2	102	1	0	0	0	0	0	0	0	1	10948	1625	57	2		2	OR13C9	9	107379994	Silent	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	1612957	107379994	33833437	68	14550										
SUSD1	64420	hgsc.bcm.edu	37	chr9	114820918	114820918	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gaagcgccttcagaatcacaAgaaaatgtgctttggagggc	12	8	2	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:114820918A>T	ENST00000374270.3	-	14	2071	c.1899T>A	c.(1897-1899)tcT>tcA	p.S633S	SUSD1_ENST00000374263.3_Silent_p.S633S|SUSD1_ENST00000374264.2_Silent_p.S633S	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	633						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						CAGAATCACAAGAAAATGTGC	0.483																																					p.S633S		Atlas-SNP	.											.	SUSD1	51	.	0			c.T1899A						.						96	100	99					9																	114820918		2203	4300	6503	SO:0001819	synonymous_variant	64420	exon14			ATCACAAGAAAAT	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1899T>A	chr9.hg19:g.114820918A>T		55.0	0.0		97.0	28.0	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Silent	SNP	ENST00000374270.3	hg19	CCDS6783.1	.	.	.	.	.	.	.	.	.	.	A	3.405	-0.121499	0.06838	.	.	ENSG00000106868	ENST00000355396	.	.	.	5.44	1.18	0.20946	.	.	.	.	.	T	0.55641	0.1933	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47787	-0.9090	4	.	.	.	-0.135	8.3921	0.32535	0.6833:0.2432:0.0735:0.0	.	.	.	.	M	617	.	.	L	-	1	2	SUSD1	113860739	0.668000	0.27493	0.998000	0.56505	0.165000	0.22458	0.976000	0.29462	0.327000	0.23409	0.459000	0.35465	TTG	.	.		0.483	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		T	114820918	A	T	114820918	2	4	102	1	0	0	0	0	0	0	0	1	15422	59	3	4		4	SUSD1	9	114820918	Silent	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	7440924	114820918	26392513	69	14551										
DIP2C	22982	hgsc.bcm.edu	37	chr10	436697	436697	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tacctttaaactgtgggatcTctcccgttgggctttttgga	10	9	1	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:436697T>A	ENST00000280886.6	-	11	1454	c.1367A>T	c.(1366-1368)gAg>gTg	p.E456V	DIP2C_ENST00000381496.3_Missense_Mutation_p.E349V	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	456						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CTGTGGGATCTCTCCCGTTGG	0.557																																					p.E456V		Atlas-SNP	.											.	DIP2C	195	.	0			c.A1367T						.						210	191	197					10																	436697		2203	4300	6503	SO:0001583	missense	22982	exon11			GGGATCTCTCCCG	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.1367A>T	chr10.hg19:g.436697T>A	ENSP00000280886:p.Glu456Val	54.0	0.0		94.0	23.0	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.394392	0.83011	.	.	ENSG00000151240	ENST00000280886;ENST00000381496	T;T	0.44083	0.93;0.93	5.41	5.41	0.78517	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.62441	0.2428	M	0.67953	2.075	0.58432	D	0.999998	D;B	0.64830	0.994;0.319	D;P	0.71656	0.974;0.513	T	0.64943	-0.6288	10	0.56958	D	0.05	-36.63	15.441	0.75181	0.0:0.0:0.0:1.0	.	349;456	E7EPU2;Q9Y2E4	.;DIP2C_HUMAN	V	456;349	ENSP00000280886:E456V;ENSP00000370907:E349V	ENSP00000280886:E456V	E	-	2	0	DIP2C	426697	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	7.997000	0.88414	2.046000	0.60703	0.254000	0.18369	GAG	.	.		0.557	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		A	436697	T	A	436697	3	1	102	1	0	0	0	0	1	0	0	0	4531	1551	54	4	3411	4	DIP2C	10	436697	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10		436697	135098050	70	14552										
PFKFB3	5209	hgsc.bcm.edu	37	chr10	6258734	6258734	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cttcattttgccaaagaaaaTgactttaaggtgagctgagc	9	7	1	4			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:6258734T>C	ENST00000379775.4	+	5	762	c.432T>C	c.(430-432)aaT>aaC	p.N144N	PFKFB3_ENST00000536985.1_Silent_p.N124N|PFKFB3_ENST00000360521.2_Silent_p.N144N|PFKFB3_ENST00000540253.1_Silent_p.N158N|PFKFB3_ENST00000379782.3_Silent_p.N144N|PFKFB3_ENST00000379789.4_Silent_p.N124N|PFKFB3_ENST00000379785.1_Silent_p.N144N|PFKFB3_ENST00000317350.4_Silent_p.N144N	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	144	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						CCAAAGAAAATGACTTTAAGG	0.498																																					p.N144N		Atlas-SNP	.											.	PFKFB3	82	.	0			c.T432C						.						197	190	193					10																	6258734		2203	4300	6503	SO:0001819	synonymous_variant	5209	exon5			AGAAAATGACTTT		CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.432T>C	chr10.hg19:g.6258734T>C		59.0	0.0		83.0	30.0	NM_004566	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Silent	SNP	ENST00000379775.4	hg19	CCDS7078.1																																																																																			.	.		0.498	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1			C	6258734	T	C	6258734	2	2	102	1	0	0	0	0	0	0	0	1	11771	1461	51	2		2	PFKFB3	10	6258734	Silent	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	5822037	6258734	129276013	71	14553										
CUBN	8029	hgsc.bcm.edu	37	chr10	17130262	17130262	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ctagttacaacaatccagacAcaatctcttcctgggggata	7	11	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:17130262A>G	ENST00000377833.4	-	15	1913	c.1848T>C	c.(1846-1848)tgT>tgC	p.C616C		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	616	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAATCCAGACACAATCTCTTC	0.458																																					p.C616C		Atlas-SNP	.											.	CUBN	515	.	0			c.T1848C						.						100	91	94					10																	17130262		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon15			CCAGACACAATCT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1848T>C	chr10.hg19:g.17130262A>G		52.0	0.0		140.0	28.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.		0.458	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17130262	A	G	17130262	2	3	102	1	0	0	0	0	0	0	0	1	4053	157	6	2		2	CUBN	10	17130262	Silent	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	10871528	17130262	118404485	72	14554										
RBP3	5949	hgsc.bcm.edu	37	chr10	48388579	48388579	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	caccagctgttgccataccaGccgcaccagctgtggcccca	9	18	0	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:48388579G>A	ENST00000224600.4	-	1	2412	c.2299C>T	c.(2299-2301)Ctg>Ttg	p.L767L	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	767	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	TGCCATACCAGCCGCACCAGC	0.632																																					p.L767L		Atlas-SNP	.											.	RBP3	152	.	0			c.C2299T						.						30	29	29					10																	48388579		2202	4300	6502	SO:0001819	synonymous_variant	5949	exon1			ATACCAGCCGCAC	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.2299C>T	chr10.hg19:g.48388579G>A		24.0	0.0		90.0	38.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	hg19	CCDS7218.1																																																																																			.	.		0.632	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		A	48388579	G	A	48388579	2	1	102	1	0	0	0	0	0	0	0	1	13172	962	34	3		3	RBP3	10	48388579	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	31258317	48388579	87146168	73	14555										
ZWINT	11130	hgsc.bcm.edu	37	chr10	58118598	58118598	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tcccgctcctgttctgcctgCtgcttcaggtttccaagttt	8	14	2	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:58118598C>T	ENST00000373944.3	-	6	629	c.591G>A	c.(589-591)caG>caA	p.Q197Q	ZWINT_ENST00000361148.6_Intron|ZWINT_ENST00000318387.2_Silent_p.Q77Q|ZWINT_ENST00000460654.1_5'UTR|ZWINT_ENST00000395405.1_Silent_p.Q197Q			O95229	ZWINT_HUMAN	ZW10 interacting kinetochore protein	197					establishment of localization in cell (GO:0051649)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|kinetochore (GO:0000776)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)	20						GTTCTGCCTGCTGCTTCAGGT	0.537																																					p.Q197Q		Atlas-SNP	.											.	ZWINT	39	.	0			c.G591A						.						136	133	134					10																	58118598		2203	4300	6503	SO:0001819	synonymous_variant	11130	exon6			TGCCTGCTGCTTC	AF067656	CCDS7249.1, CCDS31205.1	10q21-q22	2013-05-01	2013-05-01		ENSG00000122952	ENSG00000122952			13195	protein-coding gene	gene with protein product		609177	"ZW10 interactor"				Standard	XM_005269463		Approved	KNTC2AP	uc001jka.1	O95229	OTTHUMG00000018261	ENST00000373944.3:c.591G>A	chr10.hg19:g.58118598C>T		120.0	0.0		272.0	49.0	NM_007057	A6NNV6|Q0D2I3|Q9BWD0	Silent	SNP	ENST00000373944.3	hg19	CCDS7249.1																																																																																			.	.		0.537	ZWINT-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048132.1			T	58118598	C	T	58118598	2	4	102	1	0	0	0	0	0	0	0	1	18264	796	28	3		3	ZWINT	10	58118598	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	9730019	58118598	77416149	74	14556										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64950774	64950774	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gagccttgttcattattctgGgacacaagaggtgatgttct	11	7	3	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:64950774G>A	ENST00000399262.2	-	17	6389	c.6171C>T	c.(6169-6171)tcC>tcT	p.S2057S	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000542921.1_Silent_p.S1875S|JMJD1C_ENST00000402544.1_Silent_p.S1820S	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2057					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					CATTATTCTGGGACACAAGAG	0.433																																					p.S2057S		Atlas-SNP	.											.	JMJD1C	347	.	0			c.C6171T						.						263	256	258					10																	64950774		1907	4116	6023	SO:0001819	synonymous_variant	221037	exon17			ATTCTGGGACACA	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.6171C>T	chr10.hg19:g.64950774G>A		151.0	0.0		529.0	161.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Silent	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	G	8.568	0.879284	0.17467	.	.	ENSG00000171988	ENST00000327520	.	.	.	5.52	-0.906	0.10524	.	.	.	.	.	T	0.57475	0.2056	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53387	-0.8446	4	.	.	.	-1.3648	10.5664	0.45175	0.5247:0.0:0.4753:0.0	.	.	.	.	L	604	.	.	P	-	2	0	JMJD1C	64620780	0.955000	0.32602	0.764000	0.31436	0.855000	0.48748	-0.005000	0.12855	-0.121000	0.11787	0.650000	0.86243	CCC	.	.		0.433	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		A	64950774	G	A	64950774	2	1	102	1	0	0	0	0	0	0	0	1	7959	1219	43	3		3	JMJD1C	10	64950774	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	6832176	64950774	70583973	75	14557										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64966479	64966479	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aaatcattttgcttctttttGtaagttggcttaggttgtct	8	5	3	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:64966479G>C	ENST00000399262.2	-	10	5168	c.4950C>G	c.(4948-4950)taC>taG	p.Y1650*	JMJD1C_ENST00000399251.1_Nonsense_Mutation_p.Y1431*|JMJD1C_ENST00000542921.1_Nonsense_Mutation_p.Y1468*|JMJD1C_ENST00000402544.1_Nonsense_Mutation_p.Y1431*	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1650					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					GCTTCTTTTTGTAAGTTGGCT	0.378																																					p.Y1650X		Atlas-SNP	.											.	JMJD1C	347	.	0			c.C4950G						.						173	151	158					10																	64966479		1852	4106	5958	SO:0001587	stop_gained	221037	exon10			CTTTTTGTAAGTT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.4950C>G	chr10.hg19:g.64966479G>C	ENSP00000382204:p.Tyr1650*	174.0	0.0		525.0	161.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Nonsense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	49|49	15.123811|15.123811	0.99823|0.99823	.|.	.|.	ENSG00000171988|ENSG00000171988	ENST00000327520|ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	.|.	.|.	.|.	5.62|5.62	-2.44|-2.44	0.06502|0.06502	.|.	.|0.059320	.|0.64402	.|D	.|0.000001	T|.	0.23572|.	0.0570|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.42155|.	-0.9468|.	3|.	.|0.02654	.|T	.|1	-8.1512|-8.1512	13.2443|13.2443	0.60014|0.60014	0.5054:0.0:0.4946:0.0|0.5054:0.0:0.4946:0.0	.|.	.|.	.|.	.|.	R|X	336|1650;1431;1431;1468	.|.	.|ENSP00000382195:Y1431X	T|Y	-|-	2|3	0|2	JMJD1C|JMJD1C	64636485|64636485	0.998000|0.998000	0.40836|0.40836	0.983000|0.983000	0.44433|0.44433	0.986000|0.986000	0.74619|0.74619	0.404000|0.404000	0.20999|0.20999	-0.391000|-0.391000	0.07763|0.07763	-0.225000|-0.225000	0.12378|0.12378	ACA|TAC	.	.		0.378	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		C	64966479	G	C	64966479	4	2	102	1	0	0	0	0	0	1	0	0	7959	1372	48	4	2740	4	JMJD1C	10	64966479	Nonsense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	15705	64966479	70568268	76	14558										
KIF20B	9585	hgsc.bcm.edu	37	chr10	91474892	91474892	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	atctaaattccaaaagagaaAgatgctgcgcctttcccaag	7	10	1	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:91474892A>G	ENST00000371728.3	+	8	958	c.893A>G	c.(892-894)aAg>aGg	p.K298R	KIF20B_ENST00000260753.4_Missense_Mutation_p.K298R|KIF20B_ENST00000394289.2_Missense_Mutation_p.K298R|KIF20B_ENST00000416354.1_Missense_Mutation_p.K298R	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	298	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						CAAAAGAGAAAGATGCTGCGC	0.303																																					p.K298R		Atlas-SNP	.											.	KIF20B	191	.	0			c.A893G						.						44	48	47					10																	91474892		2199	4285	6484	SO:0001583	missense	9585	exon8			AGAGAAAGATGCT	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.893A>G	chr10.hg19:g.91474892A>G	ENSP00000360793:p.Lys298Arg	107.0	0.0		174.0	64.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.39	3.613542	0.66672	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99	5.36	5.36	0.76844	Kinesin, motor domain (4);	0.000000	0.49916	D	0.000125	T	0.70509	0.3232	L	0.28649	0.875	0.43313	D	0.995325	B;B	0.32862	0.387;0.055	B;B	0.44163	0.443;0.273	T	0.71695	-0.4515	10	0.51188	T	0.08	-17.2908	11.6171	0.51096	0.9281:0.0:0.0719:0.0	.	298;298	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	R	298	ENSP00000260753:K298R;ENSP00000411545:K298R;ENSP00000377830:K298R;ENSP00000360793:K298R	ENSP00000260753:K298R	K	+	2	0	KIF20B	91464872	0.521000	0.26258	0.999000	0.59377	0.991000	0.79684	1.162000	0.31786	2.160000	0.67779	0.528000	0.53228	AAG	.	.		0.303	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		G	91474892	A	G	91474892	3	3	102	1	0	0	0	0	1	0	0	0	8296	72	3	2	919	2	KIF20B	10	91474892	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	26508413	91474892	44059855	77	14559										
IDE	3416	hgsc.bcm.edu	37	chr10	94223595	94223595	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gaattgctaatgcctgaatgTgtttttggaaggcctcttct	10	7	2	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:94223595T>A	ENST00000265986.6	-	21	2710	c.2654A>T	c.(2653-2655)cAc>cTc	p.H885L	IDE_ENST00000371581.5_Missense_Mutation_p.H330L|IDE_ENST00000496903.1_5'UTR	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	885					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TGCCTGAATGTGTTTTTGGAA	0.413																																					p.H885L		Atlas-SNP	.											.	IDE	77	.	0			c.A2654T						.						234	227	230					10																	94223595		2203	4300	6503	SO:0001583	missense	3416	exon21			TGAATGTGTTTTT	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.2654A>T	chr10.hg19:g.94223595T>A	ENSP00000265986:p.His885Leu	163.0	0.0		521.0	78.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936385	0.73442	.	.	ENSG00000119912	ENST00000265986;ENST00000371581	T;T	0.06768	3.26;3.26	5.61	5.61	0.85477	Peptidase M16, C-terminal (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.39489	0.1080	M	0.93720	3.45	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.79784	0.96;0.993	T	0.50415	-0.8831	10	0.46703	T	0.11	-16.1168	16.0994	0.81158	0.0:0.0:0.0:1.0	.	885;330	P14735;B3KSB8	IDE_HUMAN;.	L	885;330	ENSP00000265986:H885L;ENSP00000360637:H330L	ENSP00000265986:H885L	H	-	2	0	IDE	94213575	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.760000	0.85248	2.261000	0.74972	0.533000	0.62120	CAC	.	.		0.413	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		A	94223595	T	A	94223595	3	1	102	1	0	0	0	0	1	0	0	0	7502	1696	59	4	425	4	IDE	10	94223595	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	2748703	94223595	41311152	78	14560										
MYOF	26509	hgsc.bcm.edu	37	chr10	95123767	95123767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tccagtcgcccccggggtagCggctctcgttctgatagact	12	14	2	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:95123767C>T	ENST00000359263.4	-	27	2818	c.2819G>A	c.(2818-2820)cGc>cAc	p.R940H	MYOF_ENST00000371502.4_Missense_Mutation_p.R940H|MYOF_ENST00000358334.5_Missense_Mutation_p.R927H|MYOF_ENST00000371501.4_Missense_Mutation_p.R940H	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	940					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						CCCGGGGTAGCGGCTCTCGTT	0.607																																					p.R940H		Atlas-SNP	.											.	MYOF	177	.	0			c.G2819A						.						67	67	67					10																	95123767		1953	4146	6099	SO:0001583	missense	26509	exon27			GGGTAGCGGCTCT	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.2819G>A	chr10.hg19:g.95123767C>T	ENSP00000352208:p.Arg940His	25.0	0.0		48.0	19.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	C	34	5.300298	0.95574	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	D;D;D;D	0.87029	-2.19;-2.18;-2.18;-2.2	5.65	5.65	0.86999	Ferlin/Peroxisome membrane (1);	0.049306	0.85682	N	0.000000	D	0.94673	0.8282	M	0.86502	2.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.94683	0.7867	10	0.87932	D	0	-14.6837	19.9142	0.97043	0.0:1.0:0.0:0.0	.	927;940	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	H	927;940;940;940	ENSP00000351094:R927H;ENSP00000352208:R940H;ENSP00000360556:R940H;ENSP00000360557:R940H	ENSP00000351094:R927H	R	-	2	0	MYOF	95113757	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	7.651000	0.83577	2.941000	0.99782	0.655000	0.94253	CGC	.	.		0.607	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		T	95123767	C	T	95123767	3	4	102	1	0	0	0	0	1	0	0	0	10098	768	27	1	3478	1	MYOF	10	95123767	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	900172	95123767	40410980	79	14561										
DENND5A	23258	hgsc.bcm.edu	37	chr11	9202573	9202573	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ccaatttgttggggaactgtGgcaagtcctctggcaactca	11	10	2	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:9202573G>T	ENST00000328194.3	-	6	1516	c.1196C>A	c.(1195-1197)cCa>cAa	p.P399Q	DENND5A_ENST00000526523.1_5'Flank|DENND5A_ENST00000530044.1_Missense_Mutation_p.P399Q	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	399					positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GGGGAACTGTGGCAAGTCCTC	0.468																																					p.P399Q		Atlas-SNP	.											.	DENND5A	84	.	0			c.C1196A						.						67	68	68					11																	9202573		2201	4296	6497	SO:0001583	missense	23258	exon6			AACTGTGGCAAGT	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"DENN/MADD domain containing"	19344	protein-coding gene	gene with protein product			"RAB6 interacting protein 1"	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.1196C>A	chr11.hg19:g.9202573G>T	ENSP00000328524:p.Pro399Gln	82.0	0.0		161.0	35.0	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	hg19	CCDS31423.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.808638	0.90707	.	.	ENSG00000184014	ENST00000328194;ENST00000530044	T;T	0.05319	3.46;3.46	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.26557	0.0649	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.00740	-1.1586	10	0.87932	D	0	.	18.9552	0.92655	0.0:0.0:1.0:0.0	.	399;399	E9PS91;Q6IQ26	.;DEN5A_HUMAN	Q	399	ENSP00000328524:P399Q;ENSP00000435866:P399Q	ENSP00000328524:P399Q	P	-	2	0	DENND5A	9159149	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.810000	0.99221	2.550000	0.86006	0.563000	0.77884	CCA	.	.		0.468	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		T	9202573	G	T	9202573	3	4	102	1	0	0	0	0	1	0	0	0	4438	1348	47	3	2739	3	DENND5A	11	9202573	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10		9202573	125803943	80	14562										
CPT1A	1374	hgsc.bcm.edu	37	chr11	68530229	68530229	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gaggcaaaacttgcccatgtCctggggaaagagaagtactt	12	8	0	1	rs201706909		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:68530229C>A	ENST00000265641.5	-	15	1895	c.1741G>T	c.(1741-1743)Gac>Tac	p.D581Y	CPT1A_ENST00000537756.2_5'UTR|CPT1A_ENST00000539743.1_Splice_Site_p.D581Y|CPT1A_ENST00000376618.2_Splice_Site_p.D581Y|CPT1A_ENST00000540367.1_Splice_Site_p.D581Y	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	581					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	TTGCCCATGTCCTGGGGAAAG	0.547																																					p.D581Y		Atlas-SNP	.											.	CPT1A	89	.	0			c.G1741T						.						67	59	62					11																	68530229		2200	4294	6494	SO:0001630	splice_region_variant	1374	exon15			CCATGTCCTGGGG	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.1741-1G>T	chr11.hg19:g.68530229C>A		20.0	0.0		39.0	24.0	NM_001876	Q8TCU0|Q9BWK0	Missense_Mutation	SNP	ENST00000265641.5	hg19	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.862602	0.71949	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.89785	3.06	0.80722	D	1	D;D	0.76494	0.977;0.999	D;D	0.70716	0.918;0.97	D	0.86645	0.1894	10	0.02654	T	1	.	19.912	0.97027	0.0:1.0:0.0:0.0	.	581;581	P50416;P50416-2	CPT1A_HUMAN;.	Y	581	ENSP00000439084:D581Y;ENSP00000365803:D581Y;ENSP00000265641:D581Y;ENSP00000446108:D581Y	ENSP00000265641:D581Y	D	-	1	0	CPT1A	68286805	1.000000	0.71417	1.000000	0.80357	0.268000	0.26511	7.364000	0.79526	2.783000	0.95769	0.655000	0.94253	GAC	.	C|0.999;T|0.001		0.547	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876	Missense_Mutation	A	68530229	C	A	68530229	5	1	102	1	0	0	0	0	0	0	1	0	3833	869	30	3	640	3	CPT1A	11	68530229	Splice_Site	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	59327656	68530229	66476287	81	14563										
FDXACB1	91893	hgsc.bcm.edu	37	chr11	111746109	111746109	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	taacactagtggcagatgtgAtaacagacccaataattaga	8	7	0	4			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:111746109A>G	ENST00000260257.4	-	5	1459	c.1412T>C	c.(1411-1413)aTc>aCc	p.I471T	FDXACB1_ENST00000542429.1_Missense_Mutation_p.I322T|ALG9_ENST00000524880.1_Intron|ALG9_ENST00000527377.1_Intron	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	471					phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						GGCAGATGTGATAACAGACCC	0.373																																					p.I471T		Atlas-SNP	.											.	FDXACB1	74	.	0			c.T1412C						.						67	66	66					11																	111746109		1897	4120	6017	SO:0001583	missense	91893	exon5			GATGTGATAACAG		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"hypothetical protein BC006136"						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.1412T>C	chr11.hg19:g.111746109A>G	ENSP00000260257:p.Ile471Thr	69.0	0.0		85.0	48.0	NM_138378	A0PJW7|B4DUU2	Missense_Mutation	SNP	ENST00000260257.4	hg19	CCDS44729.1	.	.	.	.	.	.	.	.	.	.	A	0.024	-1.392498	0.01185	.	.	ENSG00000255561	ENST00000260257;ENST00000542429;ENST00000528274	T;T;T	0.71222	0.45;-0.55;0.99	5.22	-2.09	0.07232	.	1.085210	0.06820	N	0.792008	T	0.45935	0.1367	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20405	-1.0276	10	0.14252	T	0.57	.	1.1115	0.01705	0.4584:0.176:0.1633:0.2023	.	471	Q9BRP7	FDXA1_HUMAN	T	471;322;382	ENSP00000260257:I471T;ENSP00000441304:I322T;ENSP00000435572:I382T	ENSP00000260257:I471T	I	-	2	0	FDXACB1	111251319	0.003000	0.15002	0.520000	0.27837	0.563000	0.35712	-0.004000	0.12878	0.012000	0.14892	-0.132000	0.14878	ATC	.	.		0.373	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378		G	111746109	A	G	111746109	3	3	102	1	0	0	0	0	1	0	0	0	5814	333	12	2	466	2	FDXACB1	11	111746109	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	43215880	111746109	23260407	82	14564										
NCAM1	4684	hgsc.bcm.edu	37	chr11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ccctcccagccagcagattaCaatgctgccaaactaaggat					rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000500537.2_RNA|RP11-629G13.1_ENST00000532002.1_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		0.0	0.0		18.0	18.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		-	112832363	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	112832332	6	5	102	0	1	1	0	1	0	0	0	0	10211	493	17	0		0	NCAM1	11	112832332	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	TCGA-DD-A1EF-01A-11D-A12Z-10	1086223	112832332	22174184	83	14565										
OR6M1	390261	hgsc.bcm.edu	37	chr11	123676275	123676275	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tcataatccagtgaggagttCtgattgggtctcacatacac	9	9	3	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:123676275C>T	ENST00000309154.2	-	1	820	c.783G>A	c.(781-783)caG>caA	p.Q261Q		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		GTGAGGAGTTCTGATTGGGTC	0.502																																					p.Q261Q		Atlas-SNP	.											OR6M1,NS,carcinoma,0,1	OR6M1	60	.	0			c.G783A						.						110	101	104					11																	123676275		2202	4299	6501	SO:0001819	synonymous_variant	390261	exon1			GGAGTTCTGATTG	AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"GPCR / Class A : Olfactory receptors"	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.783G>A	chr11.hg19:g.123676275C>T		84.0	0.0		161.0	81.0	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Silent	SNP	ENST00000309154.2	hg19	CCDS31696.1																																																																																			.	.		0.502	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325		T	123676275	C	T	123676275	2	4	102	1	0	0	0	0	0	0	0	1	11214	912	32	3		3	OR6M1	11	123676275	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	10843943	123676275	11330241	84	14566										
PKNOX2	63876	hgsc.bcm.edu	37	chr11	125237764	125237764	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gacggcaaccgcccagccacCctccaaggcccaggctgtcc	10	20	0	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:125237764C>T	ENST00000298282.9	+	5	381	c.110C>T	c.(109-111)cCc>cTc	p.P37L	PKNOX2_ENST00000542175.1_Intron|PKNOX2_ENST00000530517.1_3'UTR	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	37					regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		GCCCAGCCACCCTCCAAGGCC	0.662																																					p.P37L		Atlas-SNP	.											.	PKNOX2	60	.	0			c.C110T						.						53	65	61					11																	125237764		2090	4202	6292	SO:0001583	missense	63876	exon5			AGCCACCCTCCAA	AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"Homeoboxes / TALE class"	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.110C>T	chr11.hg19:g.125237764C>T	ENSP00000298282:p.Pro37Leu	59.0	0.0		93.0	20.0	NM_022062	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Missense_Mutation	SNP	ENST00000298282.9	hg19	CCDS41730.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.448842	0.63178	.	.	ENSG00000165495	ENST00000530517;ENST00000531116;ENST00000298282;ENST00000527238;ENST00000531212;ENST00000535518	T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66	5.49	5.49	0.81192	.	0.130686	0.52532	D	0.000062	T	0.52141	0.1716	N	0.08118	0	0.80722	D	1	B	0.16603	0.018	B	0.14578	0.011	T	0.48479	-0.9032	10	0.16896	T	0.51	-18.5915	18.1483	0.89665	0.0:1.0:0.0:0.0	.	37	Q96KN3	PKNX2_HUMAN	L	8;8;37;37;37;25	ENSP00000434732:P8L;ENSP00000433971:P8L;ENSP00000298282:P37L;ENSP00000434255:P37L	ENSP00000298282:P37L	P	+	2	0	PKNOX2	124742974	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.210000	0.58500	2.564000	0.86499	0.563000	0.77884	CCC	.	.		0.662	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3			T	125237764	C	T	125237764	3	4	102	1	0	0	0	0	1	0	0	0	11992	623	22	3	116	3	PKNOX2	11	125237764	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	1561489	125237764	9768752	85	14567										
ANO2	57101	hgsc.bcm.edu	37	chr12	5936960	5936960	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gtgttgttggctcgggagcaGgctgtgcgcttcaggatctc	16	9	2	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:5936960G>A	ENST00000356134.5	-	8	929	c.858C>T	c.(856-858)gcC>gcT	p.A286A	ANO2_ENST00000546188.1_Silent_p.A286A|ANO2_ENST00000327087.8_Silent_p.A285A	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	290					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						CTCGGGAGCAGGCTGTGCGCT	0.662																																					p.A285A		Atlas-SNP	.											.	ANO2	309	.	0			c.C855T						.						33	39	37					12																	5936960		2026	4194	6220	SO:0001819	synonymous_variant	57101	exon7			GGAGCAGGCTGTG	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	1183	protein-coding gene	gene with protein product	"transmembrane protein 16B (eight membrane-spanning domains)"	610109	"chromosome 12 open reading frame 3", "transmembrane protein 16B", "anoctamin 2"	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.858C>T	chr12.hg19:g.5936960G>A		33.0	0.0		80.0	31.0	NM_020373	C4N787|Q9H847	Silent	SNP	ENST00000356134.5	hg19																																																																																				.	.		0.662	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		A	5936960	G	A	5936960	2	1	102	1	0	0	0	0	0	0	0	1	697	987	35	3		3	ANO2	12	5936960	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10		5936960	127914935	86	14568										
STRAP	11171	hgsc.bcm.edu	37	chr12	16035698	16035698	+	Frame_Shift_Del	DEL	T	T	-													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cacacgcgacccgtggttgaTttggccttcagtggcatcac							TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:16035698delT	ENST00000419869.2	+	1	370	c.57delT	c.(55-57)gatfs	p.D19fs	STRAP_ENST00000538352.1_5'UTR|STRAP_ENST00000025399.6_Frame_Shift_Del_p.D19fs	NM_007178.3	NP_009109.3	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated protein	19					maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|spliceosomal snRNP assembly (GO:0000387)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	15		Hepatocellular(102;0.121)				CCGTGGTTGATTTGGCCTTCA	0.617																																					p.D19fs		Atlas-Indel,Pindel	.											.	STRAP	33	.	0			c.56delA						.						62	55	57					12																	16035698		2203	4300	6503	SO:0001589	frameshift_variant	11171	exon1			.	AB024327	CCDS8676.1	12p13.1	2013-01-10			ENSG00000023734	ENSG00000023734		"WD repeat domain containing"	30796	protein-coding gene	gene with protein product	"Unr-interacting protein"	605986					Standard	NM_007178		Approved	UNRIP, pt-wd, MAWD	uc001rdc.4	Q9Y3F4	OTTHUMG00000168791	ENST00000419869.2:c.57delT	chr12.hg19:g.16035698delT	ENSP00000392270:p.Asp19fs	33.0	0.0		69.0	28.0	NM_007178	B2R5S5|B4DNJ6|Q5TZT4|Q9NTK0|Q9UQC8	Frame_Shift_Del	DEL	ENST00000419869.2	hg19	CCDS8676.1																																																																																			.	.		0.617	STRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401114.1	NM_007178		-	16035698	T	-	16035698	7	5	102	1	0	1	0	1	0	0	0	0	15341	1490	52	0	59	0	STRAP	12	16035698	Frame_Shift_Del	DEL	T	TCGA-DD-A1EF-01A-11D-A12Z-10	10098738	16035698	117816197	87	14569										
CELA1	1990	hgsc.bcm.edu	37	chr12	51740405	51740433	+	Start_Codon_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cgactggaccatatccacttAccataaaggaccagcatgtt					rs150350903|rs573952082|rs201074609|rs141305161|rs117443541|rs377599213|rs143199509|rs61761206|rs148235680|rs370927847|rs148270827|rs116944010|rs386762976|rs149358345|rs55827519	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC	ENST00000293636.1	-	0	30_57					NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1						exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)|p.L4P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ATATCCACTTACCATAAAGGACCAGCATGTTGCCGATGGAGTAGACCAC	0.524																																					p.3_6del		Pindel	.											.	CELA1	39	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.8_16del						.																																			SO:0001582	initiator_codon_variant	1990	exon1			.		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"elastase 1, pancreatic"	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523		chr12.hg19:g.51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC		0.0	0.0		25.0	25.0	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	In_Frame_Del	DEL	ENST00000293636.1	hg19	CCDS8812.1																																																																																			.	-|0.574;CACCAGGAAGCG|0.426		0.524	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971		-	51740433	CTGGACCATATCCACTTACCATAAAGGAC	-	51740405	7	5	102	1	0	1	0	1	0	0	0	0	3212	405	14	0	790	0	CELA1	12	51740405	Start_Codon_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	TCGA-DD-A1EF-01A-11D-A12Z-10	35704707	51740405	82111490	88	14570										
OR6C74	254783	hgsc.bcm.edu	37	chr12	55641327	55641327	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttcttgttagtatggcaacaGgtgataagaccatttcttac	8	7	2	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:55641327G>A	ENST00000343870.4	+	1	346	c.256G>A	c.(256-258)Ggt>Agt	p.G86S		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	86			G -> D (in dbSNP:rs6581025).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	12						TATGGCAACAGGTGATAAGAC	0.393																																					p.G86S		Atlas-SNP	.											.	OR6C74	52	.	0			c.G256A						.						197	199	198					12																	55641327		2203	4300	6503	SO:0001583	missense	254783	exon1			GCAACAGGTGATA		CCDS31816.1	12q13.13	2012-08-09			ENSG00000197706	ENSG00000197706		"GPCR / Class A : Olfactory receptors"	31303	protein-coding gene	gene with protein product							Standard	NM_001005490		Approved		uc010spg.2	A6NCV1	OTTHUMG00000165162	ENST00000343870.4:c.256G>A	chr12.hg19:g.55641327G>A	ENSP00000342836:p.Gly86Ser	108.0	0.0		260.0	70.0	NM_001005490		Missense_Mutation	SNP	ENST00000343870.4	hg19	CCDS31816.1	.	.	.	.	.	.	.	.	.	.	g	15.46	2.841617	0.51057	.	.	ENSG00000197706	ENST00000343870	T	0.02916	4.11	5.36	3.5	0.40072	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000062	T	0.04634	0.0126	L	0.51422	1.61	0.09310	N	1	P	0.39759	0.687	B	0.44133	0.442	T	0.22417	-1.0217	10	0.87932	D	0	.	6.9684	0.24635	0.1567:0.2468:0.5965:0.0	.	86	A6NCV1	O6C74_HUMAN	S	86	ENSP00000342836:G86S	ENSP00000342836:G86S	G	+	1	0	OR6C74	53927594	0.000000	0.05858	0.217000	0.23759	0.954000	0.61252	0.637000	0.24659	1.371000	0.46172	0.551000	0.68910	GGT	.	.		0.393	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1			A	55641327	G	A	55641327	3	1	102	1	0	0	0	0	1	0	0	0	11207	1000	35	3	258	3	OR6C74	12	55641327	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	3900922	55641327	78210568	89	14571										
MARS	4141	hgsc.bcm.edu	37	chr12	57910075	57910076	+	Frame_Shift_Ins	INS	-	-	A													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tagagactgttacaacagccINSaagccacagcagatacaagc							TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:57910075_57910076insA	ENST00000262027.5	+	20	2645_2646	c.2511_2512insA	c.(2512-2514)aagfs	p.K838fs	MIR616_ENST00000385293.1_RNA|RN7SL312P_ENST00000582079.1_RNA	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	838					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	TTACAACAGCCAAGCCACAGCA	0.455																																					p.A837fs		Atlas-INDEL	.											.	MARS	84	.	0			c.2511_2512insA						.																																			SO:0001589	frameshift_variant	4141	exon20			.	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.2513dupA	chr12.hg19:g.57910077_57910077dupA	ENSP00000262027:p.Lys838fs	57.0	0.0		275.0	20.0	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Frame_Shift_Ins	INS	ENST00000262027.5	hg19	CCDS8942.1																																																																																			.	.		0.455	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		A	57910076	-	A	57910075	7	5	102	1	0	1	1	0	0	0	0	0	9325	581	21	0	2589	0	MARS	12	57910075	Frame_Shift_Ins	INS	-	TCGA-DD-A1EF-01A-11D-A12Z-10	2268748	57910075	75941820	90	14572										
ANO4	121601	hgsc.bcm.edu	37	chr12	101365128	101365128	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	atctttgtgaagttgcatgcCccatgggaagtccttggaag	12	8	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:101365128C>T	ENST00000392977.3	+	6	711	c.501C>T	c.(499-501)gcC>gcT	p.A167A	ANO4_ENST00000538618.1_Silent_p.A333A|ANO4_ENST00000392979.3_Silent_p.A132A|ANO4_ENST00000299222.9_5'UTR			Q32M45	ANO4_HUMAN	anoctamin 4	167					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						AGTTGCATGCCCCATGGGAAG	0.368										HNSCC(74;0.22)																											p.A132A		Atlas-SNP	.											.	ANO4	183	.	0			c.C396T						.						145	140	142					12																	101365128		2203	4300	6503	SO:0001819	synonymous_variant	121601	exon5			GCATGCCCCATGG	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.501C>T	chr12.hg19:g.101365128C>T		80.0	0.0		152.0	30.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Silent	SNP	ENST00000392977.3	hg19																																																																																				.	.		0.368	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		T	101365128	C	T	101365128	2	4	102	1	0	0	0	0	0	0	0	1	699	610	22	3		3	ANO4	12	101365128	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	43455053	101365128	32486767	91	14573										
C12orf42	374470	hgsc.bcm.edu	37	chr12	103696092	103696092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cgcctgaggcctcctgtcccGcggggtatgaggatgcttgg	16	12	0	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:103696092G>A	ENST00000378113.2	-	6	1102	c.877C>T	c.(877-879)Cgg>Tgg	p.R293W	C12orf42_ENST00000548048.1_Missense_Mutation_p.R226W|C12orf42_ENST00000548883.1_Missense_Mutation_p.R293W|C12orf42_ENST00000315192.8_Intron	NM_001099336.1	NP_001092806.1	Q96LP6	CL042_HUMAN	chromosome 12 open reading frame 42	293										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)	22						CTCCTGTCCCGCGGGGTATGA	0.652																																					p.R293W		Atlas-SNP	.											.	C12orf42	50	.	0			c.C877T						.						33	38	37					12																	103696092		1946	4154	6100	SO:0001583	missense	374470	exon6			TGTCCCGCGGGGT	AK058052	CCDS44963.1	12q23.2	2012-05-30			ENSG00000179088	ENSG00000179088			24729	protein-coding gene	gene with protein product							Standard	NM_001099336		Approved	FLJ25323	uc001tjt.2	Q96LP6	OTTHUMG00000169988	ENST00000378113.2:c.877C>T	chr12.hg19:g.103696092G>A	ENSP00000367353:p.Arg293Trp	45.0	0.0		75.0	10.0	NM_001099336	Q49A64|Q4G0S2	Missense_Mutation	SNP	ENST00000378113.2	hg19	CCDS44963.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.920532	0.52653	.	.	ENSG00000179088	ENST00000548883;ENST00000548048;ENST00000378113	T;T;T	0.49432	0.78;0.78;0.78	4.75	-4.14	0.03892	.	1.597520	0.04173	N	0.325091	T	0.26955	0.0660	N	0.24115	0.695	0.09310	N	1	B	0.27166	0.17	B	0.20184	0.028	T	0.23332	-1.0191	10	0.66056	D	0.02	-0.607	0.4303	0.00470	0.2949:0.1302:0.2716:0.3033	.	293	Q96LP6	CL042_HUMAN	W	293;226;293	ENSP00000447908:R293W;ENSP00000449362:R226W;ENSP00000367353:R293W	ENSP00000367353:R293W	R	-	1	2	C12orf42	102220222	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.312000	0.08113	-0.207000	0.10187	-0.211000	0.12701	CGG	.	.		0.652	C12orf42-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406754.1	NM_198521		A	103696092	G	A	103696092	3	1	102	1	0	0	0	0	1	0	0	0	1690	1086	38	1	209	1	C12orf42	12	103696092	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	2330964	103696092	30155803	92	14574										
NOS1	4842	hgsc.bcm.edu	37	chr12	117710212	117710212	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ccaggatattgtagcgggagTtgtcacagtagtcgcggaca	14	8	1	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:117710212T>C	ENST00000338101.4	-	9	1821	c.1817A>G	c.(1816-1818)aAc>aGc	p.N606S	NOS1_ENST00000317775.6_Missense_Mutation_p.N606S|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GTAGCGGGAGTTGTCACAGTA	0.587																																					p.N606S	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.A1817G						.						78	87	84					12																	117710212		2193	4296	6489	SO:0001583	missense	4842	exon10			CGGGAGTTGTCAC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1817A>G	chr12.hg19:g.117710212T>C	ENSP00000337459:p.Asn606Ser	51.0	0.0		96.0	8.0	NM_000620		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	T	6.547	0.469221	0.12461	.	.	ENSG00000089250	ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.20598	2.06;2.06	4.7	2.36	0.29203	Nitric oxide synthase, oxygenase domain (2);	0.224065	0.52532	N	0.000067	T	0.04407	0.0121	N	0.00268	-1.735	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27673	-1.0067	10	0.18276	T	0.48	-19.7626	8.3814	0.32474	0.0:0.2441:0.0:0.7559	.	606	P29475	NOS1_HUMAN	S	606	ENSP00000320758:N606S;ENSP00000337459:N606S	ENSP00000320758:N606S	N	-	2	0	NOS1	116194595	0.990000	0.36364	0.988000	0.46212	0.990000	0.78478	0.231000	0.17872	0.324000	0.23333	0.533000	0.62120	AAC	.	.		0.587	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			C	117710212	T	C	117710212	3	2	102	1	0	0	0	0	1	0	0	0	10550	1725	60	2	2567	2	NOS1	12	117710212	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	14014120	117710212	16141683	93	14575										
MTMR6	9107	hgsc.bcm.edu	37	chr13	25823570	25823570	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aggtgattcaggatgaactgAatgtaacaattccttggtga	11	5	1	4			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr13:25823570A>C	ENST00000381801.5	-	14	2427	c.1666T>G	c.(1666-1668)Tca>Gca	p.S556A	MTMR6_ENST00000540661.1_Intron|AL590787.1_ENST00000408397.1_RNA	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	556					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		GGATGAACTGAATGTAACAAT	0.368																																					p.S556A		Atlas-SNP	.											.	MTMR6	75	.	0			c.T1666G						.						149	142	145					13																	25823570		2203	4300	6503	SO:0001583	missense	9107	exon14			GAACTGAATGTAA	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.1666T>G	chr13.hg19:g.25823570A>C	ENSP00000371221:p.Ser556Ala	141.0	0.0		237.0	58.0	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Missense_Mutation	SNP	ENST00000381801.5	hg19	CCDS9313.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.711226	0.00712	.	.	ENSG00000139505	ENST00000381801;ENST00000319298	D	0.94046	-3.34	5.87	0.686	0.18015	.	0.861348	0.10383	N	0.681302	D	0.86539	0.5957	L	0.39147	1.195	0.45490	D	0.998459	B	0.02656	0.0	B	0.04013	0.001	T	0.74751	-0.3559	10	0.23302	T	0.38	.	2.6648	0.05041	0.5311:0.2354:0.1255:0.108	.	556	Q9Y217	MTMR6_HUMAN	A	556;124	ENSP00000371221:S556A	ENSP00000317987:S124A	S	-	1	0	MTMR6	24721570	0.096000	0.21769	0.012000	0.15200	0.023000	0.10783	0.591000	0.23969	0.182000	0.20032	0.533000	0.62120	TCA	.	.		0.368	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		C	25823570	A	C	25823570	3	2	102	1	0	0	0	0	1	0	0	0	9956	246	9	5	203	5	MTMR6	13	25823570	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10		25823570	89346308	94	14576										
SLC15A1	6564	hgsc.bcm.edu	37	chr13	99371494	99371494	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aaccgatttccacttactcaGggctacagccatgagagcag	9	12	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr13:99371494G>A	ENST00000376503.5	-	8	692	c.637C>T	c.(637-639)Ctg>Ttg	p.L213L		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	213					digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CACTTACTCAGGGCTACAGCC	0.443																																					p.L213L		Atlas-SNP	.											.	SLC15A1	92	.	0			c.C637T						.						128	131	130					13																	99371494		2203	4300	6503	SO:0001819	synonymous_variant	6564	exon8			TACTCAGGGCTAC	U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"Solute carriers"	10920	protein-coding gene	gene with protein product	"peptide transporter HPEPT1", "bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)", "solute carrier family 15 oligopeptide transporter member 1"	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.637C>T	chr13.hg19:g.99371494G>A		25.0	0.0		53.0	18.0	NM_005073	Q5VW82	Silent	SNP	ENST00000376503.5	hg19	CCDS9489.1																																																																																			.	.		0.443	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073		A	99371494	G	A	99371494	2	1	102	1	0	0	0	0	0	0	0	1	14413	991	35	3		3	SLC15A1	13	99371494	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	73547924	99371494	15798384	95	14577										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72054832	72054832	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ggggtaagggcaaggattgcAgattggcccccaagaaagga	16	7	0	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr14:72054832A>T	ENST00000555818.1	+	2	591	c.243A>T	c.(241-243)gcA>gcT	p.A81A	SIPA1L1_ENST00000358550.2_Silent_p.A81A|SIPA1L1_ENST00000381232.3_Silent_p.A81A	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	81					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CAAGGATTGCAGATTGGCCCC	0.493																																					p.A81A		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.A243T						.						87	95	92					14																	72054832		2203	4300	6503	SO:0001819	synonymous_variant	26037	exon2			GATTGCAGATTGG	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.243A>T	chr14.hg19:g.72054832A>T		63.0	0.0		103.0	46.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	hg19	CCDS9807.1																																																																																			.	.		0.493	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		T	72054832	A	T	72054832	2	4	102	1	0	0	0	0	0	0	0	1	14344	175	7	4		4	SIPA1L1	14	72054832	Silent	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10		72054832	35294708	96	14578										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96809512	96809512	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tgatgcagaaaactcatcccAgaagagagacactccagaga	9	10	1	6			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr14:96809512A>T	ENST00000359933.4	-	5	1581	c.688T>A	c.(688-690)Tgg>Agg	p.W230R		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	230					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AACTCATCCCAGAAGAGAGAC	0.413																																					p.W230R		Atlas-SNP	.											.	ATG2B	169	.	0			c.T688A						.						99	94	95					14																	96809512		1886	4117	6003	SO:0001583	missense	55102	exon5			CATCCCAGAAGAG	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.688T>A	chr14.hg19:g.96809512A>T	ENSP00000353010:p.Trp230Arg	106.0	0.0		192.0	14.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	20.7	4.032808	0.75504	.	.	ENSG00000066739	ENST00000359933	T	0.09817	2.94	5.31	5.31	0.75309	.	0.265541	0.33515	U	0.004839	T	0.19846	0.0477	N	0.22421	0.69	0.58432	D	0.999997	D	0.76494	0.999	D	0.85130	0.997	T	0.06607	-1.0817	10	0.30078	T	0.28	.	15.2648	0.73651	1.0:0.0:0.0:0.0	.	230	Q96BY7	ATG2B_HUMAN	R	230	ENSP00000353010:W230R	ENSP00000353010:W230R	W	-	1	0	ATG2B	95879265	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.730000	0.91510	2.007000	0.58848	0.482000	0.46254	TGG	.	.		0.413	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		T	96809512	A	T	96809512	3	4	102	1	0	0	0	0	1	0	0	0	1094	188	7	4	5700	4	ATG2B	14	96809512	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	24754680	96809512	10540028	97	14579										
PLDN	26258	hgsc.bcm.edu	37	chr15	45884374	45884374	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	atgaagggttaatagaggacTtgactatagaagacaaagca	11	4	0	5			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:45884374T>A	ENST00000220531.3	+	2	445	c.124T>A	c.(124-126)Ttg>Atg	p.L42M	BLOC1S6_ENST00000568816.1_5'UTR|BLOC1S6_ENST00000565323.1_Missense_Mutation_p.L47M|BLOC1S6_ENST00000565409.1_5'UTR|Y_RNA_ENST00000363549.1_RNA|BLOC1S6_ENST00000566753.1_Missense_Mutation_p.L42M|BLOC1S6_ENST00000565216.1_Intron|RP11-96O20.4_ENST00000564080.1_Intron|BLOC1S6_ENST00000562384.1_Intron|BLOC1S6_ENST00000567740.1_Intron|BLOC1S6_ENST00000564765.1_5'UTR|BLOC1S6_ENST00000567461.1_Intron	NM_012388.2	NP_036520.1	Q9UL45	BL1S6_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	42					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|endosome to melanosome transport (GO:0035646)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of pigment cell differentiation (GO:0050942)|post-Golgi vesicle-mediated transport (GO:0006892)|secretion of lysosomal enzymes (GO:0033299)|synaptic vesicle docking involved in exocytosis (GO:0016081)	BLOC-1 complex (GO:0031083)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|transport vesicle (GO:0030133)	actin filament binding (GO:0051015)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)										AATAGAGGACTTGACTATAGA	0.398																																					p.L42M		Atlas-SNP	.											.	.	.	.	0			c.T124A						.						94	93	93					15																	45884374		2198	4298	6496	SO:0001583	missense	26258	exon2			GAGGACTTGACTA	AF080470	CCDS10126.1	15q21.1	2013-09-27	2012-08-07	2012-08-01	ENSG00000104164	ENSG00000104164		"Biogenesis of lysosomal organelles complex-1 subunits"	8549	protein-coding gene	gene with protein product		604310	"pallid (mouse) homolog, pallidin", "pallidin homolog (mouse)"	PA, PLDN		10610180	Standard	NM_012388		Approved	HPS9	uc001zvq.3	Q9UL45	OTTHUMG00000131477	ENST00000220531.3:c.124T>A	chr15.hg19:g.45884374T>A	ENSP00000220531:p.Leu42Met	53.0	0.0		73.0	25.0	NM_012388		Missense_Mutation	SNP	ENST00000220531.3	hg19	CCDS10126.1	.	.	.	.	.	.	.	.	.	.	T	17.76	3.467683	0.63625	.	.	ENSG00000104164	ENST00000220531	.	.	.	5.74	0.369	0.16151	.	0.559941	0.20041	N	0.100502	T	0.47563	0.1452	L	0.47716	1.5	0.58432	D	0.999999	P	0.40875	0.731	P	0.47528	0.549	T	0.39781	-0.9597	9	0.59425	D	0.04	1.1294	4.9159	0.13846	0.0:0.1755:0.295:0.5295	.	42	Q9UL45	PLDN_HUMAN	M	42	.	ENSP00000220531:L42M	L	+	1	2	PLDN	43671666	0.159000	0.22864	0.409000	0.26459	0.884000	0.51177	-0.555000	0.05999	0.085000	0.17107	0.460000	0.39030	TTG	.	.		0.398	BLOC1S6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254320.2	NM_012388		A	45884374	T	A	45884374	3	1	102	1	0	0	0	0	1	0	0	0	12060	1606	56	4	130	4	PLDN	15	45884374	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10		45884374	56647018	98	14580										
RFX7	64864	hgsc.bcm.edu	37	chr15	56387953	56387953	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gcaatgtagaagacagtcgtTttcttgggcttttagtgcat	11	6	1	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:56387953T>C	ENST00000559447.2	-	9	1953	c.1682A>G	c.(1681-1683)aAa>aGa	p.K561R	RFX7_ENST00000317318.6_Missense_Mutation_p.K658R|RFX7_ENST00000423270.1_Missense_Mutation_p.K658R|RFX7_ENST00000422057.1_Missense_Mutation_p.K561R			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	561					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						AGACAGTCGTTTTCTTGGGCT	0.448																																					p.K658R		Atlas-SNP	.											.	RFX7	170	.	0			c.A1973G						.						97	94	95					15																	56387953		1901	4113	6014	SO:0001583	missense	64864	exon9			AGTCGTTTTCTTG			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.1682A>G	chr15.hg19:g.56387953T>C	ENSP00000453281:p.Lys561Arg	87.0	0.0		151.0	55.0	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	hg19		.	.	.	.	.	.	.	.	.	.	T	21.2	4.119947	0.77323	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	T;T;T	0.54675	0.56;0.56;0.56	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	T	0.54415	0.1857	N	0.24115	0.695	0.58432	D	0.999991	D;D	0.67145	0.996;0.996	P;P	0.60609	0.877;0.877	T	0.51513	-0.8696	10	0.26408	T	0.33	-15.3416	14.6501	0.68792	0.0:0.0:0.0:1.0	.	561;561	Q2KHR2;C9JU50	RFX7_HUMAN;.	R	561;658;658	ENSP00000387504:K561R;ENSP00000313299:K658R;ENSP00000397644:K658R	ENSP00000313299:K658R	K	-	2	0	RFX7	54175245	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.193000	0.77780	2.030000	0.59900	0.533000	0.62120	AAA	.	.		0.448	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		C	56387953	T	C	56387953	3	2	102	1	0	0	0	0	1	0	0	0	13283	1841	64	2	2413	2	RFX7	15	56387953	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	10503579	56387953	46143439	99	14581										
ANP32A	8125	hgsc.bcm.edu	37	chr15	69076893	69076893	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tcgttcaggttggttacctcGcaattgaaaaggtctaagct	10	8	2	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:69076893G>A	ENST00000465139.2	-	4	512	c.369C>T	c.(367-369)tgC>tgT	p.C123C	ANP32A_ENST00000560303.1_Silent_p.C123C|ANP32A_ENST00000483551.2_5'UTR	NM_006305.3	NP_006296.1	P39687	AN32A_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	123	LRRCT.				gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA metabolic process (GO:0016071)|nucleocytoplasmic transport (GO:0006913)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						TGGTTACCTCGCAATTGAAAA	0.483																																					p.C123C		Atlas-SNP	.											.	ANP32A	15	.	0			c.C369T						.						93	98	96					15																	69076893		2200	4298	6498	SO:0001819	synonymous_variant	8125	exon4			TACCTCGCAATTG	AF025684	CCDS45292.1	15q23	2008-05-14			ENSG00000140350	ENSG00000140350		"ANP32 acidic nuclear phosphoproteins"	13233	protein-coding gene	gene with protein product		600832		C15orf1		8970164, 9144194	Standard	NM_006305		Approved	LANP, PP32, I1PP2A, PHAPI, MAPM, mapmodulin	uc002arl.3	P39687	OTTHUMG00000154502	ENST00000465139.2:c.369C>T	chr15.hg19:g.69076893G>A		120.0	0.0		255.0	60.0	NM_006305	B2R6T4|Q53FK4|Q5J8L8|Q7M4N6	Silent	SNP	ENST00000465139.2	hg19	CCDS45292.1																																																																																			.	.		0.483	ANP32A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335525.2			A	69076893	G	A	69076893	2	1	102	1	0	0	0	0	0	0	0	1	705	1079	38	1		1	ANP32A	15	69076893	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	12688940	69076893	33454499	100	14582										
PTPN9	5780	hgsc.bcm.edu	37	chr15	75762179	75762180	+	Frame_Shift_Del	DEL	AG	AG	-													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tggaccacaatgggtggctcAgggcactgccctttggagcg							TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:75762179_75762180delAG	ENST00000306726.2	-	12	2032_2033	c.1520_1521delCT	c.(1519-1521)cctfs	p.P507fs		NM_002833.2	NP_002824.1	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type 9	507	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGGGTGGCTCAGGGCACTGCCC	0.574																																					p.507_508del		Atlas-Indel,Pindel	.											.	PTPN9	53	.	0			c.1521_1522del						.																																			SO:0001589	frameshift_variant	5780	exon12			.		CCDS10280.1	15q23	2011-06-09			ENSG00000169410	ENSG00000169410		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9661	protein-coding gene	gene with protein product		600768				1557404	Standard	NM_002833		Approved	MEG2	uc002bal.3	P43378	OTTHUMG00000142838	ENST00000306726.2:c.1520_1521delCT	chr15.hg19:g.75762179_75762180delAG	ENSP00000303554:p.Pro507fs	62.0	0.0		123.0	37.0	NM_002833	Q53XR9	Frame_Shift_Del	DEL	ENST00000306726.2	hg19	CCDS10280.1																																																																																			.	.		0.574	PTPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286474.1			-	75762180	AG	-	75762179	7	5	102	1	0	1	0	1	0	0	0	0	12809	175	7	0	268	0	PTPN9	15	75762179	Frame_Shift_Del	DEL	AG	TCGA-DD-A1EF-01A-11D-A12Z-10	6685286	75762179	26769213	101	14583										
RCN2	5955	hgsc.bcm.edu	37	chr15	77227917	77227917	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttaagcattatgctatgcaaGaagcaaaacaacagtttgtt	7	6	0	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:77227917G>A	ENST00000394885.3	+	3	524	c.301G>A	c.(301-303)Gaa>Aaa	p.E101K	RCN2_ENST00000394883.3_Intron|RCN2_ENST00000320963.5_Missense_Mutation_p.E101K	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	101	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						TGCTATGCAAGAAGCAAAACA	0.348																																					p.E101K		Atlas-SNP	.											.	RCN2	16	.	0			c.G301A						.						165	146	153					15																	77227917		2196	4294	6490	SO:0001583	missense	5955	exon3			ATGCAAGAAGCAA	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"EF-hand domain containing"	9935	protein-coding gene	gene with protein product	"Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.301G>A	chr15.hg19:g.77227917G>A	ENSP00000378349:p.Glu101Lys	53.0	0.0		74.0	20.0	NM_002902	A8MTG6|F8WCY5|Q53XN8	Missense_Mutation	SNP	ENST00000394885.3	hg19	CCDS10291.1	.	.	.	.	.	.	.	.	.	.	G	34	5.408127	0.96051	.	.	ENSG00000117906	ENST00000394885;ENST00000320963	T;T	0.74315	-0.83;-0.83	5.47	5.47	0.80525	EF-hand-like domain (1);	0.048133	0.85682	D	0.000000	T	0.81475	0.4830	M	0.80183	2.485	0.80722	D	1	D;P	0.53462	0.96;0.92	P;P	0.47603	0.497;0.551	D	0.84779	0.0772	10	0.72032	D	0.01	-22.0183	19.328	0.94270	0.0:0.0:1.0:0.0	.	101;101	F8WCY5;Q14257	.;RCN2_HUMAN	K	101	ENSP00000378349:E101K;ENSP00000319739:E101K	ENSP00000319739:E101K	E	+	1	0	RCN2	75014972	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.789000	0.91839	2.559000	0.86315	0.591000	0.81541	GAA	.	.		0.348	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902		A	77227917	G	A	77227917	3	1	102	1	0	0	0	0	1	0	0	0	13195	943	33	3	311	3	RCN2	15	77227917	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	1465738	77227917	25303475	102	14584										
FAM169B	283777	hgsc.bcm.edu	37	chr15	99023985	99023985	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gtttagaatgaaaagcacaaCcctttccccaaacgactgaa	6	11	0	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:99023985C>G	ENST00000558256.1	-	4	277	c.28G>C	c.(28-30)Gtt>Ctt	p.V10L	FAM169B_ENST00000332908.4_Missense_Mutation_p.V10L	NM_182562.2	NP_872368.2	Q8N8A8	F169B_HUMAN	family with sequence similarity 169, member B	10										large_intestine(3)|lung(3)|urinary_tract(1)	7						AAAAGCACAACCCTTTCCCCA	0.373																																					p.V10L		Atlas-SNP	.											.	FAM169B	23	.	0			c.G28C						.						72	69	70					15																	99023985		1864	4095	5959	SO:0001583	missense	283777	exon4			GCACAACCCTTTC		CCDS45360.1	15q26.3	2008-08-08			ENSG00000185087	ENSG00000185087			26835	protein-coding gene	gene with protein product							Standard	NM_182562		Approved	FLJ39743, KIAA0888L	uc002buk.1	Q8N8A8		ENST00000558256.1:c.28G>C	chr15.hg19:g.99023985C>G	ENSP00000453554:p.Val10Leu	63.0	0.0		105.0	29.0	NM_182562	B5MDL8	Missense_Mutation	SNP	ENST00000558256.1	hg19	CCDS45360.1	.	.	.	.	.	.	.	.	.	.	C	11.33	1.608089	0.28623	.	.	ENSG00000185087	ENST00000332908	T	0.72282	-0.64	5.27	2.89	0.33648	.	0.290655	0.33110	N	0.005280	T	0.50411	0.1614	N	0.17082	0.46	0.26442	N	0.975758	B	0.02656	0.0	B	0.01281	0.0	T	0.39231	-0.9624	10	0.44086	T	0.13	-9.8168	7.3417	0.26640	0.0:0.0771:0.1438:0.7791	.	10	Q8N8A8	F169B_HUMAN	L	10	ENSP00000332615:V10L	ENSP00000332615:V10L	V	-	1	0	FAM169B	96841508	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.945000	0.40273	0.283000	0.22279	-0.294000	0.09567	GTT	.	.		0.373	FAM169B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415488.1	NM_182562		G	99023985	C	G	99023985	3	3	102	1	0	0	0	0	1	0	0	0	5493	507	18	4	566	4	FAM169B	15	99023985	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	21796068	99023985	3507407	103	14585										
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27761333	27761333	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	taaaagcagaccctcccgatAtcaatattttaccagcctat	4	12	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr16:27761333A>G	ENST00000261588.4	+	16	3071	c.3052A>G	c.(3052-3054)Atc>Gtc	p.I1018V		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1018						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						CCCTCCCGATATCAATATTTT	0.527																																					p.I1018V		Atlas-SNP	.											.	KIAA0556	348	.	0			c.A3052G						.						41	40	40					16																	27761333		2197	4300	6497	SO:0001583	missense	23247	exon16			CCCGATATCAATA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.3052A>G	chr16.hg19:g.27761333A>G	ENSP00000261588:p.Ile1018Val	54.0	0.0		83.0	14.0	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.844112	0.51164	.	.	ENSG00000047578	ENST00000261588	T	0.15834	2.39	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.22975	0.0555	L	0.39147	1.195	0.42620	D	0.993346	P	0.40302	0.712	P	0.47573	0.55	T	0.01617	-1.1311	10	0.34782	T	0.22	-11.2124	15.0765	0.72080	1.0:0.0:0.0:0.0	.	1018	O60303	K0556_HUMAN	V	1018	ENSP00000261588:I1018V	ENSP00000261588:I1018V	I	+	1	0	KIAA0556	27668834	1.000000	0.71417	1.000000	0.80357	0.324000	0.28378	7.377000	0.79668	2.085000	0.62840	0.533000	0.62120	ATC	.	.		0.527	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		G	27761333	A	G	27761333	3	3	102	1	0	0	0	0	1	0	0	0	8192	449	16	2	3114	2	KIAA0556	16	27761333	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10		27761333	62593420	104	14586										
FUS	2521	hgsc.bcm.edu	37	chr16	31201608	31201608	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tgcattaggacccatgggccGtggaggctatggaggtggtg	18	7	0	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr16:31201608G>T	ENST00000254108.7	+	12	1286	c.1181G>T	c.(1180-1182)cGt>cTt	p.R394L	FUS_ENST00000474990.1_3'UTR|FUS_ENST00000380244.3_Missense_Mutation_p.R393L|FUS_ENST00000568685.1_Missense_Mutation_p.R395L	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	394	Arg/Gly-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		CCCATGGGCCgtggaggctat	0.567			T	"DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"	"liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"																																p.R394L		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"fusion, derived from t(12;16) malignant liposarcoma"		"M, L"	.	FUS	52	.	0			c.G1181T						.						144	110	121					16																	31201608		2197	4300	6497	SO:0001583	missense	2521	exon12			TGGGCCGTGGAGG	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"RNA binding motif (RRM) containing"	4010	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein P2", "translocated in liposarcoma"	137070	"fusion, derived from t(12;16) malignant liposarcoma", "amyotrophic lateral sclerosis 6", "fusion (involved in t(12;16) in malignant liposarcoma)", "fused in sarcoma"	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.1181G>T	chr16.hg19:g.31201608G>T	ENSP00000254108:p.Arg394Leu	84.0	0.0		168.0	29.0	NM_004960	Q9H4A8	Missense_Mutation	SNP	ENST00000254108.7	hg19	CCDS10707.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.726726	0.48833	.	.	ENSG00000089280	ENST00000254108;ENST00000380244;ENST00000394533	D	0.97114	-4.25	5.31	3.35	0.38373	.	0.360924	0.28796	N	0.014116	D	0.93976	0.8071	L	0.50333	1.59	0.58432	D	0.999991	B;P;P;P;P;P	0.44429	0.145;0.835;0.704;0.804;0.835;0.704	B;B;B;B;B;B	0.38985	0.073;0.264;0.149;0.287;0.264;0.149	D	0.90342	0.4360	10	0.24483	T	0.36	-1.1004	11.0266	0.47748	0.155:0.0:0.845:0.0	.	393;394;394;393;168;394	A8K4H1;Q8TBR3;Q6IBQ5;P35637-2;Q59H57;P35637	.;.;.;.;.;FUS_HUMAN	L	394;121;323	ENSP00000254108:R394L	ENSP00000254108:R394L	R	+	2	0	FUS	31109109	1.000000	0.71417	0.993000	0.49108	0.542000	0.35054	8.422000	0.90262	0.622000	0.30249	-0.150000	0.13652	CGT	.	.		0.567	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960		T	31201608	G	T	31201608	3	4	102	1	0	0	0	0	1	0	0	0	6108	1145	40	1	1227	1	FUS	16	31201608	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	3440275	31201608	59153145	105	14587										
FTO	79068	hgsc.bcm.edu	37	chr16	53878098	53878098	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gaaagtgaggatgactctcaTctcgaaggcagggatcctga	13	8	2	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr16:53878098T>A	ENST00000471389.1	+	4	1005	c.783T>A	c.(781-783)caT>caA	p.H261Q	FTO_ENST00000394647.3_5'UTR	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	261	Fe2OG dioxygenase domain.				adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)			endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						ATGACTCTCATCTCGAAGGCA	0.418																																					p.H261Q		Atlas-SNP	.											.	FTO	51	.	0			c.T783A						.						149	137	141					16																	53878098		2198	4300	6498	SO:0001583	missense	79068	exon4			CTCTCATCTCGAA	BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718		"Alkylation repair homologs"	24678	protein-coding gene	gene with protein product	"AlkB homolog 9", "alpha-ketoglutarate-dependent dioxygenase"	610966				17434869, 17991826, 22002720	Standard	NM_001080432		Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.783T>A	chr16.hg19:g.53878098T>A	ENSP00000418823:p.His261Gln	107.0	0.0		203.0	34.0	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	hg19	CCDS32448.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.814678	0.32053	.	.	ENSG00000140718	ENST00000471389	T	0.62105	0.05	5.81	-8.48	0.00935	Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain (1);	1.011690	0.07895	N	0.971788	T	0.22282	0.0537	N	0.02011	-0.69	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.17561	-1.0365	10	0.11182	T	0.66	-1.814	2.9424	0.05835	0.3523:0.1889:0.3573:0.1014	.	261	Q9C0B1	FTO_HUMAN	Q	261	ENSP00000418823:H261Q	ENSP00000418823:H261Q	H	+	3	2	FTO	52435599	0.000000	0.05858	0.000000	0.03702	0.535000	0.34838	-1.869000	0.01643	-1.627000	0.01550	0.533000	0.62120	CAT	.	.		0.418	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432		A	53878098	T	A	53878098	3	1	102	1	0	0	0	0	1	0	0	0	6094	1432	50	4	797	4	FTO	16	53878098	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	22676490	53878098	36476655	106	14588										
CES3	23491	hgsc.bcm.edu	37	chr16	67006590	67006590	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gcctttccagaggccacagaGgaggagaagcagctaagcct	13	11	0	3	rs377447761		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr16:67006590G>A	ENST00000303334.4	+	12	1532	c.1461G>A	c.(1459-1461)gaG>gaA	p.E487E	CES3_ENST00000394037.1_Silent_p.E484E|CES3_ENST00000543856.1_Silent_p.E126E	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	487						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		AGGCCACAGAGGAGGAGAAGC	0.587																																					p.E487E		Atlas-SNP	.											.	CES3	56	.	0			c.G1461A						.	G	,,	1,4399	2.1+/-5.4	0,1,2199	83	76	78		378,1452,1461	2	1	16		78	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CES3	NM_001185176.1,NM_001185177.1,NM_024922.5	,,	0,1,6499	AA,AG,GG		0.0,0.0227,0.0077	,,	126/211,484/569,487/572	67006590	1,12999	2200	4300	6500	SO:0001819	synonymous_variant	23491	exon12			CACAGAGGAGGAG	AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"Carboxylesterases"	1865	protein-coding gene	gene with protein product	"esterase 31", "brain carboxylesterase BR3"	605279	"carboxylesterase 3 (brain)"			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.1461G>A	chr16.hg19:g.67006590G>A		43.0	0.0		66.0	17.0	NM_024922	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Silent	SNP	ENST00000303334.4	hg19	CCDS10826.1																																																																																			.	.		0.587	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922		A	67006590	G	A	67006590	2	1	102	1	0	0	0	0	0	0	0	1	3273	991	35	3		3	CES3	16	67006590	Silent	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	13128492	67006590	23348163	107	14589										
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2604781	2604781	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ccccgggggcgggttccatcCgctcatggtgagtactttca	13	13	2	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:2604781C>T	ENST00000570628.2	-	6	769	c.664G>A	c.(664-666)Gga>Aga	p.G222R	CLUH_ENST00000538975.1_Missense_Mutation_p.G222R|CLUH_ENST00000435359.1_Missense_Mutation_p.G222R			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	222					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											GGGTTCCATCCGCTCATGGTG	0.657																																					p.G222R		Atlas-SNP	.											.	.	.	.	0			c.G664A						.						30	36	34					17																	2604781		1981	4154	6135	SO:0001583	missense	23277	exon6			TCCATCCGCTCAT	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"KIAA0664"	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.664G>A	chr17.hg19:g.2604781C>T	ENSP00000458986:p.Gly222Arg	23.0	0.0		53.0	18.0	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	hg19	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.509303	0.85282	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	T;T	0.80738	-1.41;-1.41	4.75	4.75	0.60458	GSKIP/TIF31 domain (1);	0.048785	0.85682	D	0.000000	D	0.86802	0.6020	M	0.77820	2.39	0.80722	D	1	D;D	0.65815	0.988;0.995	P;P	0.54346	0.749;0.749	D	0.88515	0.3092	10	0.59425	D	0.04	.	16.898	0.86106	0.0:1.0:0.0:0.0	.	222;222	O75153;C9J6D7	K0664_HUMAN;.	R	222	ENSP00000388872:G222R;ENSP00000439628:G222R	ENSP00000320468:G222R	G	-	1	0	KIAA0664	2551531	1.000000	0.71417	0.994000	0.49952	0.833000	0.47200	5.862000	0.69560	2.476000	0.83614	0.591000	0.81541	GGA	.	.		0.657	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		T	2604781	C	T	2604781	3	4	102	1	0	0	0	0	1	0	0	0	8198	661	23	1	3349	1	KIAA0664	17	2604781	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10		2604781	78590429	108	14590										
TMEM102	284114	hgsc.bcm.edu	37	chr17	7339378	7339378	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gggagccgatctcctccgggCcaaggactttgtcttctctt	11	13	3	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:7339378C>T	ENST00000323206.1	+	2	461	c.188C>T	c.(187-189)gCc>gTc	p.A63V	TMEM102_ENST00000396568.1_Missense_Mutation_p.A63V|FGF11_ENST00000293829.4_5'Flank|RP11-104H15.9_ENST00000570444.1_RNA|FGF11_ENST00000575235.1_5'Flank|RP11-104H15.7_ENST00000575310.1_RNA	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	63					apoptotic process (GO:0006915)|positive regulation of cell adhesion (GO:0045785)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				kidney(1)|lung(3)|skin(1)	5		Prostate(122;0.173)				CTCCTCCGGGCCAAGGACTTT	0.632																																					p.A63V		Atlas-SNP	.											.	TMEM102	11	.	0			c.C188T						.						88	114	105					17																	7339378		2203	4299	6502	SO:0001583	missense	284114	exon2			TCCGGGCCAAGGA	AK094197	CCDS11104.1	17p13.1	2008-04-21			ENSG00000181284	ENSG00000181284			26722	protein-coding gene	gene with protein product		613936				12477932	Standard	NM_178518		Approved	FLJ36878	uc002ggx.1	Q8N9M5	OTTHUMG00000132901	ENST00000323206.1:c.188C>T	chr17.hg19:g.7339378C>T	ENSP00000315387:p.Ala63Val	46.0	0.0		132.0	46.0	NM_178518	D3DTP8	Missense_Mutation	SNP	ENST00000323206.1	hg19	CCDS11104.1	.	.	.	.	.	.	.	.	.	.	C	33	5.232363	0.95207	.	.	ENSG00000181284	ENST00000323206;ENST00000396568	T;T	0.54479	0.57;0.57	5.66	5.66	0.87406	.	0.000000	0.56097	D	0.000039	T	0.72087	0.3417	M	0.72894	2.215	0.51012	D	0.999909	D	0.89917	1.0	D	0.74674	0.984	T	0.74237	-0.3730	10	0.72032	D	0.01	-8.6371	17.2341	0.86994	0.0:1.0:0.0:0.0	.	63	Q8N9M5	TM102_HUMAN	V	63	ENSP00000315387:A63V;ENSP00000379815:A63V	ENSP00000315387:A63V	A	+	2	0	TMEM102	7280102	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.801000	0.62532	2.652000	0.90054	0.655000	0.94253	GCC	.	.		0.632	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518		T	7339378	C	T	7339378	3	4	102	1	0	0	0	0	1	0	0	0	16032	739	26	3	190	3	TMEM102	17	7339378	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	4734597	7339378	73855832	109	14591										
MYH1	4619	hgsc.bcm.edu	37	chr17	10404577	10404577	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ctatctgcatgcttcttcctCagggtggccgccgtggcttc	11	14	3	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:10404577C>T	ENST00000226207.5	-	27	3682	c.3588G>A	c.(3586-3588)ctG>ctA	p.L1196L	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1196					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						GCTTCTTCCTCAGGGTGGCCG	0.562																																					p.L1196L		Atlas-SNP	.											.	MYH1	403	.	0			c.G3588A						.						88	86	87					17																	10404577		2203	4300	6503	SO:0001819	synonymous_variant	4619	exon27			CTTCCTCAGGGTG		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3588G>A	chr17.hg19:g.10404577C>T		103.0	0.0		183.0	51.0	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	hg19	CCDS11155.1																																																																																			.	.		0.562	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10404577	C	T	10404577	2	4	102	1	0	0	0	0	0	0	0	1	10038	813	29	3		3	MYH1	17	10404577	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	3065199	10404577	70790633	110	14592										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11786904	11786904	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tcttgcttgatatttgcagtCcgatctcacaaagcagcaga	8	10	2	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:11786904C>A	ENST00000262442.4	+	56	10876	c.10808C>A	c.(10807-10809)tCc>tAc	p.S3603Y	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000454412.2_Splice_Site_p.S3603Y|DNAH9_ENST00000608377.1_5'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3603	AAA 5. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TATTTGCAGTCCGATCTCACA	0.498																																					p.S3603Y		Atlas-SNP	.											.	DNAH9	695	.	0			c.C10808A						.						112	99	103					17																	11786904		2203	4300	6503	SO:0001630	splice_region_variant	1770	exon56			TGCAGTCCGATCT	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10807-1C>A	chr17.hg19:g.11786904C>A		52.0	0.0		73.0	15.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197228	0.79015	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.27557	1.66;1.66	4.91	4.91	0.64330	.	0.200493	0.45361	D	0.000376	T	0.58708	0.2141	M	0.84948	2.725	0.80722	D	1	P	0.40211	0.707	P	0.55667	0.781	T	0.63323	-0.6663	10	0.72032	D	0.01	.	18.6493	0.91425	0.0:1.0:0.0:0.0	.	3603	Q9NYC9	DYH9_HUMAN	Y	3603;3603;2185	ENSP00000262442:S3603Y;ENSP00000414874:S3603Y	ENSP00000262442:S3603Y	S	+	2	0	DNAH9	11727629	0.998000	0.40836	0.984000	0.44739	0.961000	0.63080	3.923000	0.56469	2.709000	0.92574	0.655000	0.94253	TCC	.	.		0.498	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	Missense_Mutation	A	11786904	C	A	11786904	5	1	102	1	0	0	0	0	0	0	1	0	4610	869	30	3	11030	3	DNAH9	17	11786904	Splice_Site	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	1382327	11786904	69408306	111	14593										
RICH2	9912	hgsc.bcm.edu	37	chr17	12819314	12819314	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gagacgtgattgagcccctgTttttgctggcggaggtaagc	15	8	0	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:12819314T>A	ENST00000379672.5	+	5	673	c.373T>A	c.(373-375)Ttt>Att	p.F125I	ARHGAP44_ENST00000340825.3_Missense_Mutation_p.F125I|ARHGAP44_ENST00000262444.9_Missense_Mutation_p.F125I|MIR1269B_ENST00000580405.1_RNA	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	125	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						TGAGCCCCTGTTTTTGCTGGC	0.522																																					p.F125I		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.T373A						.						80	81	80					17																	12819314		2080	4207	6287	SO:0001583	missense	9912	exon5			CCCCTGTTTTTGC		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"Rho GTPase activating proteins"	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.373T>A	chr17.hg19:g.12819314T>A	ENSP00000368994:p.Phe125Ile	61.0	0.0		99.0	29.0	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Missense_Mutation	SNP	ENST00000379672.5	hg19	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.667102	0.47677	.	.	ENSG00000006740	ENST00000379672;ENST00000340825	T;T	0.63096	-0.02;-0.02	5.92	5.92	0.95590	BAR (3);	0.182798	0.49916	D	0.000131	T	0.51398	0.1672	N	0.22421	0.69	0.41260	D	0.986773	P;B	0.38677	0.642;0.409	B;B	0.41135	0.316;0.348	T	0.50668	-0.8801	10	0.25106	T	0.35	.	14.3183	0.66468	0.0:0.0:0.0:1.0	.	125;125	A6NCP5;Q17R89	.;RHG44_HUMAN	I	125	ENSP00000368994:F125I;ENSP00000342566:F125I	ENSP00000342566:F125I	F	+	1	0	ARHGAP44	12760039	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	5.166000	0.64965	2.274000	0.75844	0.533000	0.62120	TTT	.	.		0.522	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859		A	12819314	T	A	12819314	3	1	102	1	0	0	0	0	1	0	0	0	13372	1725	60	4	391	4	RICH2	17	12819314	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	1032410	12819314	68375896	112	14594										
PTRF	284119	hgsc.bcm.edu	37	chr17	40574856	40574856	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tcagctcgccctggatgctcTgcactgcgccctccatctcc	8	19	3	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:40574856T>A	ENST00000357037.5	-	1	679	c.260A>T	c.(259-261)cAg>cTg	p.Q87L		NM_012232.5	NP_036364.2			polymerase I and transcript release factor											breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		CTGGATGCTCTGCACTGCGCC	0.627																																					p.Q87L		Atlas-SNP	.											.	PTRF	48	.	0			c.A260T						.						54	37	43					17																	40574856		2203	4300	6503	SO:0001583	missense	284119	exon1			ATGCTCTGCACTG	AF000421	CCDS11425.1	17q21.31	2011-04-20				ENSG00000177469			9688	protein-coding gene	gene with protein product		603198				9582279	Standard	NM_012232		Approved	cavin-1, CAVIN1	uc002hzo.3	Q6NZI2		ENST00000357037.5:c.260A>T	chr17.hg19:g.40574856T>A	ENSP00000349541:p.Gln87Leu	44.0	0.0		98.0	24.0	NM_012232		Missense_Mutation	SNP	ENST00000357037.5	hg19	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.667526	0.47677	.	.	ENSG00000177469	ENST00000357037;ENST00000357684	T	0.58940	0.3	5.12	5.12	0.69794	.	0.749618	0.13072	N	0.416048	T	0.39200	0.1069	N	0.22421	0.69	0.27481	N	0.952569	B;B	0.12013	0.005;0.003	B;B	0.14023	0.01;0.01	T	0.21930	-1.0231	10	0.49607	T	0.09	-42.1904	2.4995	0.04630	0.1369:0.082:0.2341:0.547	.	87;87	B4DNU9;Q6NZI2	.;PTRF_HUMAN	L	87;42	ENSP00000349541:Q87L	ENSP00000349541:Q87L	Q	-	2	0	PTRF	37828382	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.907000	0.39897	1.917000	0.55516	0.454000	0.30748	CAG	.	.		0.627	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232		A	40574856	T	A	40574856	3	1	102	1	0	0	0	0	1	0	0	0	12830	1580	55	4	920	4	PTRF	17	40574856	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	27755542	40574856	40620354	113	14595										
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42475346	42475346	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tgtgatggaggtggcagaggCtgtagctggctgctgaatgt	18	5	0	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:42475346C>T	ENST00000591680.1	-	8	4129	c.4099G>A	c.(4099-4101)Gcc>Acc	p.A1367T	GPATCH8_ENST00000434000.1_Missense_Mutation_p.A1289T	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1367							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GTGGCAGAGGCTGTAGCTGGC	0.607																																					p.A1367T		Atlas-SNP	.											.	GPATCH8	114	.	0			c.G4099A						.						88	64	72					17																	42475346		2203	4300	6503	SO:0001583	missense	23131	exon8			CAGAGGCTGTAGC	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"G patch domain containing"	29066	protein-coding gene	gene with protein product		614396	"KIAA0553"	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.4099G>A	chr17.hg19:g.42475346C>T	ENSP00000467556:p.Ala1367Thr	80.0	0.0		206.0	12.0	NM_001002909	B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	hg19	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	C	18.94	3.730358	0.69074	.	.	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.14391	2.51	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.31231	0.0790	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.01198	-1.1421	10	0.46703	T	0.11	-12.7618	18.199	0.89832	0.0:1.0:0.0:0.0	.	1367	Q9UKJ3	GPTC8_HUMAN	T	1367;1289	ENSP00000395016:A1289T	ENSP00000335486:A1367T	A	-	1	0	GPATCH8	39830872	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.327000	0.79147	2.391000	0.81399	0.305000	0.20034	GCC	.	.		0.607	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		T	42475346	C	T	42475346	3	4	102	1	0	0	0	0	1	0	0	0	6602	797	28	3	413	3	GPATCH8	17	42475346	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	1900490	42475346	38719864	114	14596										
PLEKHM1	9842	hgsc.bcm.edu	37	chr17	43552916	43552916	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ggaggaactcgccctcctcaGcatcccggagcagggcggtg	15	14	1	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:43552916G>T	ENST00000430334.3	-	4	606	c.473C>A	c.(472-474)gCt>gAt	p.A158D	PLEKHM1_ENST00000421073.2_Missense_Mutation_p.A69D	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	158	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					GCCCTCCTCAGCATCCCGGAG	0.597																																					p.A158D		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.C473A						.						45	43	44					17																	43552916		2202	4300	6502	SO:0001583	missense	9842	exon4			TCCTCAGCATCCC	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"Pleckstrin homology (PH) domain containing"	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.473C>A	chr17.hg19:g.43552916G>T	ENSP00000389913:p.Ala158Asp	71.0	0.0		114.0	8.0	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Missense_Mutation	SNP	ENST00000430334.3	hg19	CCDS32671.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.782605	0.31502	.	.	ENSG00000225190	ENST00000430334;ENST00000446609;ENST00000421073	T;T	0.10477	2.87;2.87	5.03	5.03	0.67393	RUN (3);	0.123631	0.53938	D	0.000054	T	0.19565	0.0470	L	0.28504	0.86	0.50813	D	0.999891	D;D	0.69078	0.993;0.997	P;D	0.69824	0.854;0.966	T	0.05818	-1.0862	10	0.11794	T	0.64	.	17.1001	0.86647	0.0:0.0:1.0:0.0	.	69;158	F8W648;Q9Y4G2	.;PKHM1_HUMAN	D	158;107;69	ENSP00000389913:A158D;ENSP00000414352:A69D	ENSP00000414352:A69D	A	-	2	0	PLEKHM1	40908699	0.983000	0.35010	0.671000	0.29857	0.293000	0.27360	6.217000	0.72218	2.608000	0.88229	0.655000	0.94253	GCT	.	.		0.597	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798		T	43552916	G	T	43552916	3	4	102	1	0	0	0	0	1	0	0	0	12089	971	34	3	2733	3	PLEKHM1	17	43552916	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	1077570	43552916	37642294	115	14597										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2795979	2795979	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	agtatcgttctgctgtgtgcAaactagacagtgtgaataag	11	6	1	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:2795979A>T	ENST00000320876.6	+	46	6090	c.5752A>T	c.(5752-5754)Aaa>Taa	p.K1918*	RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1918					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TGCTGTGTGCAAACTAGACAG	0.358																																					p.K1918X		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A5752T						.						49	44	46					18																	2795979		1881	4109	5990	SO:0001587	stop_gained	23347	exon46			GTGTGCAAACTAG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.5752A>T	chr18.hg19:g.2795979A>T	ENSP00000326603:p.Lys1918*	130.0	0.0		281.0	80.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Nonsense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	A	47	13.308776	0.99733	.	.	ENSG00000101596	ENST00000320876	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.6976	14.5973	0.68415	1.0:0.0:0.0:0.0	.	.	.	.	X	1918	.	ENSP00000326603:K1918X	K	+	1	0	SMCHD1	2785979	0.996000	0.38824	0.185000	0.23176	0.281000	0.26958	6.053000	0.71089	2.174000	0.68829	0.533000	0.62120	AAA	.	.		0.358	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2795979	A	T	2795979	4	4	102	1	0	0	0	0	0	1	0	0	14803	131	5	4	5934	4	SMCHD1	18	2795979	Nonsense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10		2795979	75281269	116	14598										
LPIN2	9663	hgsc.bcm.edu	37	chr18	2925247	2925247	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ggtctgaggagaggcggagaGacttcttatatgaagttgtg	16	4	2	4			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:2925247G>C	ENST00000261596.4	-	14	2151	c.1913C>G	c.(1912-1914)tCt>tGt	p.S638C		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	638	C-LIP.				cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		GAGGCGGAGAGACTTCTTATA	0.493																																					p.S638C		Atlas-SNP	.											.	LPIN2	75	.	0			c.C1913G						.						98	95	96					18																	2925247		2203	4300	6503	SO:0001583	missense	9663	exon14			CGGAGAGACTTCT	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.1913C>G	chr18.hg19:g.2925247G>C	ENSP00000261596:p.Ser638Cys	88.0	0.0		186.0	53.0	NM_014646	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	hg19	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.998856	0.54147	.	.	ENSG00000101577	ENST00000261596	D	0.82433	-1.61	4.41	4.41	0.53225	.	0.117372	0.64402	D	0.000012	D	0.91690	0.7373	M	0.88775	2.98	0.80722	D	1	D	0.67145	0.996	P	0.62813	0.907	D	0.93294	0.6671	10	0.62326	D	0.03	-17.4867	17.9017	0.88906	0.0:0.0:1.0:0.0	.	638	Q92539	LPIN2_HUMAN	C	638	ENSP00000261596:S638C	ENSP00000261596:S638C	S	-	2	0	LPIN2	2915247	1.000000	0.71417	0.997000	0.53966	0.084000	0.17831	9.214000	0.95140	2.366000	0.80165	0.563000	0.77884	TCT	.	.		0.493	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		C	2925247	G	C	2925247	3	2	102	1	0	0	0	0	1	0	0	0	8928	942	33	4	805	4	LPIN2	18	2925247	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	129268	2925247	75152001	117	14599										
ZNF519	162655	hgsc.bcm.edu	37	chr18	14105690	14105690	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttctctccagtatgaattttCtgatgtccaagatgtaagcc	7	9	2	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:14105690C>T	ENST00000590202.1	-	3	1001	c.849G>A	c.(847-849)caG>caA	p.Q283Q	ZNF519_ENST00000589498.1_Intron|ZNF519_ENST00000589203.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	283					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						TATGAATTTTCTGATGTCCAA	0.368																																					p.Q283Q		Atlas-SNP	.											.	ZNF519	53	.	0			c.G849A						.						49	54	52					18																	14105690		2203	4299	6502	SO:0001819	synonymous_variant	162655	exon3			AATTTTCTGATGT	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"Zinc fingers, C2H2-type", "-"	30574	protein-coding gene	gene with protein product	"similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.849G>A	chr18.hg19:g.14105690C>T		52.0	0.0		42.0	7.0	NM_145287		Silent	SNP	ENST00000590202.1	hg19	CCDS32797.1																																																																																			.	.		0.368	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		T	14105690	C	T	14105690	2	4	102	1	0	0	0	0	0	0	0	1	17979	912	32	3		3	ZNF519	18	14105690	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	11180443	14105690	63971558	118	14600										
DSG4	147409	hgsc.bcm.edu	37	chr18	28956907	28956907	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttcttcagaaacatttgcctTttgatcattctaatggtaag	6	7	4	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:28956907T>C	ENST00000308128.4	+	1	168	c.33T>C	c.(31-33)ctT>ctC	p.L11L	RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Silent_p.L11L|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	11					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACATTTGCCTTTTGATCATTC	0.428																																					p.L11L		Atlas-SNP	.											.	DSG4	343	.	0			c.T33C						.						108	93	98					18																	28956907		2203	4300	6503	SO:0001819	synonymous_variant	147409	exon1			TTGCCTTTTGATC	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.33T>C	chr18.hg19:g.28956907T>C		84.0	0.0		142.0	53.0	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Silent	SNP	ENST00000308128.4	hg19	CCDS11897.1																																																																																			.	.		0.428	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		C	28956907	T	C	28956907	2	2	102	1	0	0	0	0	0	0	0	1	4781	1828	64	2		2	DSG4	18	28956907	Silent	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	14851217	28956907	49120341	119	14601										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31314285	31314285	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tctttttaggagagtttaccCcagaaatgcagttgcggata	10	7	1	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:31314285C>T	ENST00000269197.5	+	10	988	c.988C>T	c.(988-990)Cca>Tca	p.P330S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	330					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AGAGTTTACCCCAGAAATGCA	0.308																																					p.P330S		Atlas-SNP	.											.	ASXL3	405	.	0			c.C988T						.						51	50	50					18																	31314285		1798	4059	5857	SO:0001583	missense	80816	exon10			TTTACCCCAGAAA	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.988C>T	chr18.hg19:g.31314285C>T	ENSP00000269197:p.Pro330Ser	126.0	0.0		211.0	56.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566279	0.86439	.	.	ENSG00000141431	ENST00000269197	T	0.25250	1.81	5.71	5.71	0.89125	.	0.227351	0.38492	N	0.001663	T	0.50735	0.1633	M	0.61703	1.905	0.54753	D	0.999986	D	0.89917	1.0	D	0.81914	0.995	T	0.34428	-0.9829	10	0.41790	T	0.15	.	19.8549	0.96755	0.0:1.0:0.0:0.0	.	330	Q9C0F0	ASXL3_HUMAN	S	330	ENSP00000269197:P330S	ENSP00000269197:P330S	P	+	1	0	ASXL3	29568283	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.365000	0.79537	2.699000	0.92147	0.460000	0.39030	CCA	.	.		0.308	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			T	31314285	C	T	31314285	3	4	102	1	0	0	0	0	1	0	0	0	1068	623	22	3	1026	3	ASXL3	18	31314285	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	2357378	31314285	46762963	120	14602										
DSEL	92126	hgsc.bcm.edu	37	chr18	65180960	65180960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gttgttgatattaaaatggcGctgggccagaaaaacatact	10	6	0	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:65180960G>A	ENST00000310045.7	-	2	2389	c.916C>T	c.(916-918)Cgc>Tgc	p.R306C	CTD-2541J13.2_ENST00000581951.1_RNA|RP11-638L3.1_ENST00000583687.1_lincRNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	296					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				TTAAAATGGCGCTGGGCCAGA	0.398																																					p.R306C		Atlas-SNP	.											DSEL,NS,carcinoma,+1,1	DSEL	196	.	0			c.C916T						.						72	77	75					18																	65180960		2203	4300	6503	SO:0001583	missense	92126	exon2			AATGGCGCTGGGC	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.916C>T	chr18.hg19:g.65180960G>A	ENSP00000310565:p.Arg306Cys	71.0	0.0		103.0	36.0	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	hg19	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.474135	0.63737	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.27720	1.65	4.62	3.75	0.43078	.	0.000000	0.85682	U	0.000000	T	0.36248	0.0960	M	0.78049	2.395	0.80722	D	1	B	0.13594	0.008	B	0.04013	0.001	T	0.34625	-0.9821	10	0.87932	D	0	.	12.9458	0.58371	0.0796:0.0:0.9204:0.0	.	296	Q8IZU8	DSEL_HUMAN	C	306;296	ENSP00000310565:R306C	ENSP00000310565:R306C	R	-	1	0	DSEL	63331940	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.761000	0.85260	1.093000	0.41377	0.462000	0.41574	CGC	.	.		0.398	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		A	65180960	G	A	65180960	3	1	102	1	0	0	0	0	1	0	0	0	4777	1087	38	1	2756	1	DSEL	18	65180960	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	33866675	65180960	12896288	121	14603										
CHAF1A	10036	hgsc.bcm.edu	37	chr19	4408946	4408946	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cttgtcccaaaggggaaagcCgatgacatgtcagacgatca	11	10	2	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:4408946C>T	ENST00000301280.5	+	3	251	c.150C>T	c.(148-150)gcC>gcT	p.A50A		NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	50	Binds to CBX1 chromo shadow domain.				cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGGGAAAGCCGATGACATGT	0.473								Chromatin Structure																													p.A50A		Atlas-SNP	.											.	CHAF1A	69	.	0			c.C150T						.						126	127	126					19																	4408946		2203	4300	6503	SO:0001819	synonymous_variant	10036	exon3			GAAAGCCGATGAC	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"chromatin assembly factor I (150 kDa)"	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.150C>T	chr19.hg19:g.4408946C>T		58.0	0.0		129.0	16.0	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Silent	SNP	ENST00000301280.5	hg19	CCDS32875.1																																																																																			.	.		0.473	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483		T	4408946	C	T	4408946	2	4	102	1	0	0	0	0	0	0	0	1	3313	639	23	1		1	CHAF1A	19	4408946	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10		4408946	54720037	122	14604										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11141502	11141502	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gctcagcacccgggctggggGgctcggcctgaacctccagt	15	15	1	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:11141502G>A	ENST00000429416.3	+	26	3760	c.3479G>A	c.(3478-3480)gGg>gAg	p.G1160E	SMARCA4_ENST00000589677.1_Missense_Mutation_p.G1160E|SMARCA4_ENST00000450717.3_Missense_Mutation_p.G1160E|SMARCA4_ENST00000413806.3_Missense_Mutation_p.G1160E|SMARCA4_ENST00000358026.2_Missense_Mutation_p.G1160E|SMARCA4_ENST00000344626.4_Missense_Mutation_p.G1160E|SMARCA4_ENST00000444061.3_Missense_Mutation_p.G1160E|SMARCA4_ENST00000590574.1_Missense_Mutation_p.G1160E|SMARCA4_ENST00000541122.2_Missense_Mutation_p.G1160E	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1160	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CGGGCTGGGGGGCTCGGCCTG	0.607			"F, N, Mis"		NSCLC																																p.G1160E		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.G3479A						.						25	26	26					19																	11141502		2197	4298	6495	SO:0001583	missense	6597	exon25			CTGGGGGGCTCGG	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3479G>A	chr19.hg19:g.11141502G>A	ENSP00000395654:p.Gly1160Glu	28.0	0.0		54.0	31.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785160	0.90282	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18;-1.18;-1.18	4.59	4.59	0.56863	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.93458	0.7913	H	0.99425	4.56	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.96329	0.9242	10	0.87932	D	0	-48.5831	16.3247	0.82975	0.0:0.0:1.0:0.0	.	1160;1160;1160;1160;1160;380;1160;1160	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	E	1160;1160;1224;1160;1160;1160;1160;1160	ENSP00000395654:G1160E;ENSP00000350720:G1160E;ENSP00000343896:G1160E;ENSP00000445036:G1160E;ENSP00000392837:G1160E;ENSP00000397783:G1160E;ENSP00000414727:G1160E	ENSP00000343896:G1160E	G	+	2	0	SMARCA4	11002502	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.356000	0.97091	2.389000	0.81357	0.563000	0.77884	GGG	.	.		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		A	11141502	G	A	11141502	3	1	102	1	0	0	0	0	1	0	0	0	14785	1232	43	3	3573	3	SMARCA4	19	11141502	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	6732556	11141502	47987481	123	14605										
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15063807	15063807	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gccgaccgacgtaagcacaaTgaccatggtgaccagacccg	11	14	0	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:15063807T>C	ENST00000221742.3	-	8	1439	c.1432A>G	c.(1432-1434)Att>Gtt	p.I478V	SLC1A6_ENST00000600144.1_Missense_Mutation_p.I400V|SLC1A6_ENST00000430939.2_Missense_Mutation_p.I414V	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	478					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						GTAAGCACAATGACCATGGTG	0.617																																					p.I478V		Atlas-SNP	.											.	SLC1A6	111	.	0			c.A1432G						.						161	133	143					19																	15063807		2203	4300	6503	SO:0001583	missense	6511	exon8			GCACAATGACCAT		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1432A>G	chr19.hg19:g.15063807T>C	ENSP00000221742:p.Ile478Val	55.0	0.0		217.0	42.0	NM_005071	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	hg19	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	-	23.9	4.469352	0.84533	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.57907	0.37;0.37	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.50480	0.1618	L	0.50333	1.59	0.80722	D	1	P;P	0.47350	0.865;0.894	B;P	0.44647	0.196;0.456	T	0.57306	-0.7834	10	0.87932	D	0	-20.4835	11.9112	0.52739	0.0:0.0:0.0:1.0	.	414;478	E7EV13;P48664	.;EAA4_HUMAN	V	414;478	ENSP00000409386:I414V;ENSP00000221742:I478V	ENSP00000221742:I478V	I	-	1	0	SLC1A6	14924807	1.000000	0.71417	0.990000	0.47175	0.943000	0.58893	5.943000	0.70211	1.983000	0.57843	0.366000	0.22137	ATT	.	.		0.617	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		C	15063807	T	C	15063807	3	2	102	1	0	0	0	0	1	0	0	0	14451	1464	51	2	270	2	SLC1A6	19	15063807	Missense_Mutation	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	3922305	15063807	44065176	124	14606										
ZNF100	163227	hgsc.bcm.edu	37	chr19	21910792	21910792	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gggaaaatgagaacatataaCtgaaagaaataaaaataaca	7	3	0	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:21910792C>G	ENST00000358296.6	-	5	521		c.e5-1		ZNF100_ENST00000305570.6_Splice_Site	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						GAACATATAACTGAAAGAAAT	0.303																																					.		Atlas-SNP	.											.	ZNF100	62	.	0			c.323-1G>C						.						20	19	19					19																	21910792		1852	4082	5934	SO:0001630	splice_region_variant	163227	exon6			ATATAACTGAAAG	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"Zinc fingers, C2H2-type", "-"	12880	protein-coding gene	gene with protein product		603982	"zinc finger protein 100 (Y1)"			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.323-1G>C	chr19.hg19:g.21910792C>G		55.0	0.0		77.0	8.0	NM_173531	Q7M4M0	Splice_Site	SNP	ENST00000358296.6	hg19	CCDS42538.1	.	.	.	.	.	.	.	.	.	.	C	4.678	0.126049	0.08931	.	.	ENSG00000197020	ENST00000358296	.	.	.	0.131	0.131	0.14755	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.741	0.28841	0.0:0.9999:0.0:1.0E-4	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF100	21702632	0.000000	0.05858	0.220000	0.23810	0.218000	0.24690	-0.194000	0.09559	0.171000	0.19730	0.174000	0.16983	.	.	.		0.303	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	Intron	G	21910792	C	G	21910792	5	3	102	1	0	0	0	0	0	0	1	0	17728	579	20	4	1310	4	ZNF100	19	21910792	Splice_Site	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	6846985	21910792	37218191	125	14607										
ZNF681	148213	hgsc.bcm.edu	37	chr19	23926971	23926971	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tgtagtaaggtttgagaactGgttaaaggctttcccacatt	10	6	0	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:23926971G>C	ENST00000402377.3	-	4	1522	c.1381C>G	c.(1381-1383)Cag>Gag	p.Q461E	ZNF681_ENST00000395385.3_Missense_Mutation_p.Q392E	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	461					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTTGAGAACTGGTTAAAGGCT	0.368																																					p.Q461E		Atlas-SNP	.											.	ZNF681	76	.	0			c.C1381G						.						51	54	53					19																	23926971		2203	4299	6502	SO:0001583	missense	148213	exon4			AGAACTGGTTAAA	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1381C>G	chr19.hg19:g.23926971G>C	ENSP00000384000:p.Gln461Glu	35.0	0.0		69.0	10.0	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	hg19	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	2.531	-0.308544	0.05458	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.07327	3.2;3.2	1.51	-2.25	0.06888	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04907	0.0132	L	0.42744	1.35	0.09310	N	1	B	0.32753	0.383	B	0.18561	0.022	T	0.37572	-0.9700	9	0.33141	T	0.24	.	2.0035	0.03472	0.4171:0.0:0.3248:0.2581	.	461	Q96N22	ZN681_HUMAN	E	461;392	ENSP00000384000:Q461E;ENSP00000378783:Q392E	ENSP00000378783:Q392E	Q	-	1	0	ZNF681	23718811	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.382000	0.02546	-0.077000	0.12752	0.313000	0.20887	CAG	.	.		0.368	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		C	23926971	G	C	23926971	3	2	102	1	0	0	0	0	1	0	0	0	18103	1357	47	4	560	4	ZNF681	19	23926971	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	2016179	23926971	35202012	126	14608										
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927977	23927977	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tggttaagtccattataaccTcctttttgcactttgcactc	5	11	0	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:23927977T>A	ENST00000402377.3	-	4	516	c.375A>T	c.(373-375)ggA>ggT	p.G125G	ZNF681_ENST00000395385.3_Silent_p.G56G	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				CATTATAACCTCCTTTTTGCA	0.299																																					p.G125G		Atlas-SNP	.											.	ZNF681	76	.	0			c.A375T						.						59	57	58					19																	23927977		2202	4300	6502	SO:0001819	synonymous_variant	148213	exon4			ATAACCTCCTTTT	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.375A>T	chr19.hg19:g.23927977T>A		74.0	0.0		118.0	48.0	NM_138286	B3KVF7	Silent	SNP	ENST00000402377.3	hg19	CCDS12414.2																																																																																			.	.		0.299	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		A	23927977	T	A	23927977	2	1	102	1	0	0	0	0	0	0	0	1	18103	1538	54	4		4	ZNF681	19	23927977	Silent	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	1006	23927977	35201006	127	14609										
PSG1	5669	hgsc.bcm.edu	37	chr19	43382236	43382236	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aggcccatatataattatttCaccgtctactacatatgatg	5	9	2	1	rs1058661	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:43382236C>G	ENST00000436291.2	-	2	375	c.259G>C	c.(259-261)Gaa>Caa	p.E87Q	PSG1_ENST00000595356.1_Missense_Mutation_p.E87Q|PSG1_ENST00000403380.3_Missense_Mutation_p.E87Q|PSG1_ENST00000595124.1_Missense_Mutation_p.E87Q|PSG1_ENST00000312439.6_Missense_Mutation_p.E87Q|PSG1_ENST00000244296.2_Missense_Mutation_p.E87Q|PSG1_ENST00000601073.1_5'UTR	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	87	Ig-like V-type.		E -> Q (in dbSNP:rs1058661).		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				ATAATTATTTCACCGTCTACT	0.453																																					p.E87Q		Atlas-SNP	.											.	PSG1	196	.	0			c.G259C						.						262	255	258					19																	43382236		2202	4299	6501	SO:0001583	missense	5669	exon2			TTATTTCACCGTC		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.259G>C	chr19.hg19:g.43382236C>G	ENSP00000413041:p.Glu87Gln	99.0	0.0		189.0	36.0	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	hg19	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	0.001	-3.014542	0.00042	.	.	ENSG00000231924	ENST00000270059;ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.01538	4.79;4.79;4.79;4.79	1.64	-3.28	0.05033	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01029	0.0034	N	0.17082	0.46	0.09310	N	1	B;B;B;B;B;B;B;B;B	0.12013	0.005;0.0;0.0;0.0;0.0;0.0;0.001;0.003;0.0	B;B;B;B;B;B;B;B;B	0.16722	0.016;0.001;0.001;0.001;0.002;0.001;0.002;0.012;0.002	T	0.46541	-0.9184	9	0.02654	T	1	.	6.1783	0.20457	0.0:0.1996:0.5902:0.2102	rs1058661;rs3199315;rs17173161	87;87;87;87;87;87;87;87;87	O75238;P11464-4;G5E9F7;P11464;Q8NBY8;P11464-3;Q9UPK8;O75237;P11464-2	.;.;.;PSG1_HUMAN;.;.;.;.;.	Q	87	ENSP00000413041:E87Q;ENSP00000385386:E87Q;ENSP00000308970:E87Q;ENSP00000244296:E87Q	ENSP00000244296:E87Q	E	-	1	0	PSG1	48074076	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.278000	0.02809	-3.999000	0.00083	-3.418000	0.00038	GAA	.	C|1.000;|0.000		0.453	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1			G	43382236	C	G	43382236	3	3	102	1	0	0	0	0	1	0	0	0	12665	835	29	4	1073	4	PSG1	19	43382236	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	19454259	43382236	15746747	128	14610										
ZNF284	342909	hgsc.bcm.edu	37	chr19	44590091	44590091	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ctgagcatgggaagtgtaaaAaattcttcagtgatgtctcc	10	7	3	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:44590091A>C	ENST00000421176.3	+	5	676	c.460A>C	c.(460-462)Aaa>Caa	p.K154Q	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	154					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				GAAGTGTAAAAAATTCTTCAG	0.418																																					p.K154Q		Atlas-SNP	.											.	ZNF284	38	.	0			c.A460C						.						60	59	59					19																	44590091		2122	4271	6393	SO:0001583	missense	342909	exon5			TGTAAAAAATTCT	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"Zinc fingers, C2H2-type", "-"	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.460A>C	chr19.hg19:g.44590091A>C	ENSP00000411032:p.Lys154Gln	63.0	0.0		95.0	9.0	NM_001037813	Q86WM1	Missense_Mutation	SNP	ENST00000421176.3	hg19	CCDS46099.1	.	.	.	.	.	.	.	.	.	.	A	2.020	-0.424865	0.04734	.	.	ENSG00000186026	ENST00000421176	T	0.35973	1.28	2.29	-4.58	0.03410	.	.	.	.	.	T	0.31513	0.0799	M	0.72576	2.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34576	-0.9823	9	0.56958	D	0.05	.	5.812	0.18471	0.4256:0.1435:0.4309:0.0	.	154	Q2VY69	ZN284_HUMAN	Q	154	ENSP00000411032:K154Q	ENSP00000411032:K154Q	K	+	1	0	ZNF284	49281931	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.270000	0.18607	-1.315000	0.02297	-0.648000	0.03929	AAA	.	.		0.418	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813		C	44590091	A	C	44590091	3	2	102	1	0	0	0	0	1	0	0	0	17836	15	1	5	474	5	ZNF284	19	44590091	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	1207855	44590091	14538892	129	14611										
ZNF285	26974	hgsc.bcm.edu	37	chr19	44890916	44890916	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ctttgatgtaagtgaaaataTgaactgtaactgaagcactt	8	5	0	4	rs548413151		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:44890916T>C	ENST00000330997.4	-	4	1555	c.1491A>G	c.(1489-1491)tcA>tcG	p.S497S	ZNF285_ENST00000544719.2_Silent_p.S497S|ZNF285_ENST00000591679.1_Silent_p.S504S|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	497					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						AGTGAAAATATGAACTGTAAC	0.378													T|||	1	0.000199681	8e-04	0	5008	,	,		24359	0		0	False		,,,				2504	0				p.S497S		Atlas-SNP	.											.	ZNF285	86	.	0			c.A1491G						.						84	86	86					19																	44890916		2203	4300	6503	SO:0001819	synonymous_variant	26974	exon4			AAAATATGAACTG	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1491A>G	chr19.hg19:g.44890916T>C		105.0	0.0		215.0	116.0	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Silent	SNP	ENST00000330997.4	hg19	CCDS12638.1																																																																																			.	.		0.378	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		C	44890916	T	C	44890916	2	2	102	1	0	0	0	0	0	0	0	1	17837	1451	51	2		2	ZNF285	19	44890916	Silent	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	300825	44890916	14238067	130	14612										
PGLYRP1	8993	hgsc.bcm.edu	37	chr19	46525997	46525997	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cccctgccacactcacttgtAgcccacgtcgcaccagccca	6	21	1	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:46525997A>T	ENST00000008938.4	-	1	326	c.283T>A	c.(283-285)Tac>Aac	p.Y95N		NM_005091.2	NP_005082.1	O75594	PGRP1_HUMAN	peptidoglycan recognition protein 1	95					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|lung(3)|ovary(2)	10		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.0036)|GBM - Glioblastoma multiforme(486;0.022)|Epithelial(262;0.208)		ACTCACTTGTAGCCCACGTCG	0.657																																					p.Y95N		Atlas-SNP	.											.	PGLYRP1	21	.	0			c.T283A						.						48	50	50					19																	46525997		2203	4298	6501	SO:0001583	missense	8993	exon1			ACTTGTAGCCCAC	AF076483	CCDS12680.1	19q13.2-q13.3	2008-02-05	2004-03-17	2004-03-19		ENSG00000008438			8904	protein-coding gene	gene with protein product		604963	"peptidoglycan recognition protein"	TNFSF3L, PGLYRP		9707603, 12669421	Standard	NM_005091		Approved	TAG7, PGRP, PGRP-S, PGRPS	uc002pdx.2	O75594		ENST00000008938.4:c.283T>A	chr19.hg19:g.46525997A>T	ENSP00000008938:p.Tyr95Asn	85.0	0.0		278.0	20.0	NM_005091	Q4VB36	Missense_Mutation	SNP	ENST00000008938.4	hg19	CCDS12680.1	.	.	.	.	.	.	.	.	.	.	A	19.84	3.902747	0.72754	.	.	ENSG00000008438	ENST00000008938	T	0.58060	0.36	4.38	4.38	0.52667	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.113326	0.38492	N	0.001671	T	0.76898	0.4052	M	0.93720	3.45	0.40078	D	0.976098	D	0.89917	1.0	D	0.97110	1.0	T	0.82309	-0.0521	10	0.87932	D	0	.	9.9415	0.41583	1.0:0.0:0.0:0.0	.	95	O75594	PGRP1_HUMAN	N	95	ENSP00000008938:Y95N	ENSP00000008938:Y95N	Y	-	1	0	PGLYRP1	51217837	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.748000	0.62148	1.849000	0.53698	0.472000	0.43445	TAC	.	.		0.657	PGLYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461695.1	NM_005091		T	46525997	A	T	46525997	3	4	102	1	0	0	0	0	1	0	0	0	11802	420	15	4	319	4	PGLYRP1	19	46525997	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	1635081	46525997	12602986	131	14613										
HRC	3270	hgsc.bcm.edu	37	chr19	49657916	49657916	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tcctcctcctcctcctcctcTtctccttcatcatcttcccc	0	23	5	0	rs7409255		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:49657916T>C	ENST00000252825.4	-	1	765	c.579A>G	c.(577-579)gaA>gaG	p.E193E	HRC_ENST00000595625.1_Silent_p.E193E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	193	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cctcctcctcttcTCCTTCAT	0.557																																					p.E193E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A579G						.						119	95	103					19																	49657916		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCTCCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.579A>G	chr19.hg19:g.49657916T>C		96.0	0.0		201.0	18.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.557	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657916	T	C	49657916	2	2	102	1	0	0	0	0	0	0	0	1	7361	1606	56	2		2	HRC	19	49657916	Silent	SNP	T	TCGA-DD-A1EF-01A-11D-A12Z-10	3131919	49657916	9471067	132	14614										
LILRA1	11024	hgsc.bcm.edu	37	chr19	55106781	55106781	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ccccgtgagcccgagtcgcaGgtggtcgtacaggtgctatg	15	12	0	1			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:55106781G>A	ENST00000251372.3	+	5	757	c.575G>A	c.(574-576)aGg>aAg	p.R192K	LILRA1_ENST00000453777.1_Missense_Mutation_p.R192K|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	192	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CCGAGTCGCAGGTGGTCGTAC	0.572																																					p.R192K		Atlas-SNP	.											LILRA1,NS,carcinoma,0,2	LILRA1	105	.	0			c.G575A						.						157	162	160					19																	55106781		2203	4300	6503	SO:0001583	missense	11024	exon5			GTCGCAGGTGGTC	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.575G>A	chr19.hg19:g.55106781G>A	ENSP00000251372:p.Arg192Lys	120.0	0.0		376.0	65.0	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	hg19	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.045528	0.36085	.	.	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.03181	4.02;4.02	2.24	-4.48	0.03515	Immunoglobulin-like fold (1);	0.777662	0.11613	N	0.546521	T	0.07503	0.0189	M	0.84082	2.675	0.09310	N	1	P;P	0.45715	0.865;0.512	P;P	0.48270	0.572;0.569	T	0.05257	-1.0896	10	0.54805	T	0.06	.	3.8719	0.09041	0.2278:0.4018:0.3704:0.0	.	192;192	O75019-2;O75019	.;LIRA1_HUMAN	K	192	ENSP00000251372:R192K;ENSP00000413715:R192K	ENSP00000251372:R192K	R	+	2	0	LILRA1	59798593	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-0.310000	0.08135	-0.489000	0.06716	0.194000	0.17425	AGG	.	.		0.572	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863		A	55106781	G	A	55106781	3	1	102	1	0	0	0	0	1	0	0	0	8793	1000	35	3	589	3	LILRA1	19	55106781	Missense_Mutation	SNP	G	TCGA-DD-A1EF-01A-11D-A12Z-10	5448865	55106781	4022202	133	14615										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31016044	31016044	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	gccagcactgtgagtggtgaAaacgatggtaaggacccttt	13	8	0	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr20:31016044A>G	ENST00000375687.4	+	5	790	c.366A>G	c.(364-366)gaA>gaG	p.E122E	ASXL1_ENST00000542461.1_3'UTR|ASXL1_ENST00000306058.5_Silent_p.E117E|ASXL1_ENST00000470145.1_3'UTR	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	122					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						TGAGTGGTGAAAACGATGGTA	0.517			"F, N, Mis"		"MDS, CMML"																																p.E122E		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.A366G						.						186	170	175					20																	31016044		2203	4300	6503	SO:0001819	synonymous_variant	171023	exon4			TGGTGAAAACGAT	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.366A>G	chr20.hg19:g.31016044A>G		73.0	0.0		142.0	17.0	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	hg19	CCDS13201.1																																																																																			.	.		0.517	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		G	31016044	A	G	31016044	2	3	102	1	0	0	0	0	0	0	0	1	1066	11	1	2		2	ASXL1	20	31016044	Silent	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10		31016044	32009476	134	14616										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50287725	50287725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tgctggagcgaaccacggtcCcggggattttcgagtccctt	13	12	0	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr20:50287725C>T	ENST00000338821.5	-	12	1373	c.1109G>A	c.(1108-1110)gGg>gAg	p.G370E	ATP9A_ENST00000311637.5_Missense_Mutation_p.G234E|ATP9A_ENST00000402822.1_Missense_Mutation_p.G249E	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	370					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						AACCACGGTCCCGGGGATTTT	0.547																																					p.G370E		Atlas-SNP	.											.,1	ATP9A	135	.	0			c.G1109A						.						94	80	85					20																	50287725		2203	4300	6503	SO:0001583	missense	10079	exon12			ACGGTCCCGGGGA	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1109G>A	chr20.hg19:g.50287725C>T	ENSP00000342481:p.Gly370Glu	47.0	0.0		107.0	30.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	hg19	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.301899	0.40694	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	D;D;D	0.89485	-2.52;-2.52;-2.52	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.95108	0.8415	M	0.86028	2.79	0.80722	D	1	D;P	0.89917	1.0;0.691	D;B	0.87578	0.998;0.259	D	0.95410	0.8497	10	0.59425	D	0.04	-38.0659	18.6624	0.91475	0.0:1.0:0.0:0.0	.	249;370	O75110-2;O75110	.;ATP9A_HUMAN	E	234;370;249	ENSP00000309086:G234E;ENSP00000342481:G370E;ENSP00000385875:G249E	ENSP00000309086:G234E	G	-	2	0	ATP9A	49721132	1.000000	0.71417	0.988000	0.46212	0.105000	0.19272	5.704000	0.68347	2.397000	0.81536	0.313000	0.20887	GGG	.	.		0.547	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		T	50287725	C	T	50287725	3	4	102	1	0	0	0	0	1	0	0	0	1198	623	22	3	2102	3	ATP9A	20	50287725	Missense_Mutation	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	19271681	50287725	12737795	135	14617										
TPTE	7179	hgsc.bcm.edu	37	chr21	10921977	10921977	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	aggcaataaggaaggcacaaAccatagttcctgttctatct	8	9	2	0			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr21:10921977A>G	ENST00000361285.4	-	18	1375	c.1046T>C	c.(1045-1047)gTt>gCt	p.V349A	TPTE_ENST00000298232.7_Missense_Mutation_p.V331A|TPTE_ENST00000342420.5_Missense_Mutation_p.V311A|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	349	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GAAGGCACAAACCATAGTTCC	0.333																																					p.V349A		Atlas-SNP	.											.	TPTE	513	.	0			c.T1046C						.						137	117	124					21																	10921977		2203	4299	6502	SO:0001583	missense	7179	exon18			GCACAAACCATAG	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1046T>C	chr21.hg19:g.10921977A>G	ENSP00000355208:p.Val349Ala	149.0	0.0		321.0	14.0	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	8.949	0.967657	0.18659	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.98947	-5.26;-5.26;-5.26	2.26	2.26	0.28386	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.203904	0.40554	N	0.001072	D	0.96941	0.9001	L	0.53617	1.68	0.31777	N	0.631393	B;P;B	0.37101	0.378;0.582;0.31	B;B;B	0.42163	0.169;0.251;0.378	D	0.96828	0.9609	10	0.87932	D	0	-17.2387	6.5011	0.22170	1.0:0.0:0.0:0.0	.	311;331;349	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	A	331;349;311	ENSP00000298232:V331A;ENSP00000355208:V349A;ENSP00000344441:V311A	ENSP00000298232:V331A	V	-	2	0	TPTE	9943848	0.582000	0.26749	0.967000	0.41034	0.031000	0.12232	1.270000	0.33086	1.075000	0.40932	0.102000	0.15555	GTT	.	.		0.333	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			G	10921977	A	G	10921977	3	3	102	1	0	0	0	0	1	0	0	0	16445	43	2	2	637	2	TPTE	21	10921977	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10		10921977	37207918	136	14618										
LIPI	149998	hgsc.bcm.edu	37	chr21	15579205	15579206	+	Intron	INS	-	-	T													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	tgaaaagcatgagcactataINStttttggcacaagttattat							TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr21:15579205_15579206insT	ENST00000536861.1	-	1	46				LIPI_ENST00000344577.2_Frame_Shift_Ins_p.Y14fs			Q6XZB0	LIPI_HUMAN	lipase, member I						lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		TGAGCACTATATTTTTGGCACA	0.347																																					p.Y14fs		Atlas-INDEL	.											.	LIPI	95	.	0			c.40_41insA						.																																			SO:0001627	intron_variant	149998	exon1			.	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.46+3914->A	chr21.hg19:g.15579210_15579210dupT		60.0	0.0		72.0	10.0	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Frame_Shift_Ins	INS	ENST00000536861.1	hg19																																																																																				.	.		0.347	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		T	15579206	-	T	15579205	6	5	102	0	1	1	1	0	0	0	0	0	8834	449	16	0		0	LIPI	21	15579205	Intron	INS	-	TCGA-DD-A1EF-01A-11D-A12Z-10	4657228	15579205	32550690	137	14619										
COL6A2	1292	hgsc.bcm.edu	37	chr21	47531490	47531492	+	In_Frame_Del	DEL	AAC	AAC	-													0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cgccggacactaccgagagaAacaacaactgcccaggtgcc							TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr21:47531490_47531492delAAC	ENST00000300527.4	+	2	204_206	c.100_102delAAC	c.(100-102)aacdel	p.N36del	COL6A2_ENST00000310645.5_In_Frame_Del_p.N36del|COL6A2_ENST00000357838.4_In_Frame_Del_p.N36del|COL6A2_ENST00000397763.1_In_Frame_Del_p.N36del|COL6A2_ENST00000409416.1_In_Frame_Del_p.N36del	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	36	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TACCGAGAGAAACAACAACTGCC	0.695																																					p.33_34del		Atlas-Indel,Pindel	.											.	COL6A2	351	.	0			c.99_101del						.																																			SO:0001651	inframe_deletion	1292	exon2			.	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"Collagens"	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.100_102delAAC	chr21.hg19:g.47531496_47531498delAAC	ENSP00000300527:p.Asn36del	52.0	0.0		112.0	22.0	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	In_Frame_Del	DEL	ENST00000300527.4	hg19	CCDS13728.1																																																																																			.	.		0.695	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			-	47531492	AAC	-	47531490	7	5	102	1	0	1	0	1	0	0	0	0	3702	14	1	0	102	0	COL6A2	21	47531490	In_Frame_Del	DEL	AAC	TCGA-DD-A1EF-01A-11D-A12Z-10	31952285	47531490	598405	138	14620										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123517526	123517526	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	ttgaattttgccaactgggtAgttattttcaaaggagtaga	10	4	1	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chrX:123517526A>T	ENST00000371130.3	-	29	7297	c.7234T>A	c.(7234-7236)Tac>Aac	p.Y2412N	TENM1_ENST00000422452.2_Missense_Mutation_p.Y2419N|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2412					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CCAACTGGGTAGTTATTTTCA	0.358																																					p.Y2419N		Atlas-SNP	.											.	.	.	.	0			c.T7255A						.						116	113	114					X																	123517526		2203	4300	6503	SO:0001583	missense	10178	exon30			CTGGGTAGTTATT	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7234T>A	chrX.hg19:g.123517526A>T	ENSP00000360171:p.Tyr2412Asn	97.0	0.0		133.0	28.0	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	hg19	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	A	3.347	-0.133446	0.06711	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.83992	-1.79;-1.76	5.97	5.97	0.96955	.	0.058909	0.64402	D	0.000001	T	0.61862	0.2381	N	0.00329	-1.635	0.53688	D	0.999979	D;D;B	0.62365	0.991;0.991;0.012	P;P;B	0.52109	0.69;0.69;0.003	T	0.71307	-0.4632	10	0.06236	T	0.91	.	15.388	0.74718	1.0:0.0:0.0:0.0	.	2418;2419;2412	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	N	2412;2419	ENSP00000360171:Y2412N;ENSP00000403954:Y2419N	ENSP00000360171:Y2412N	Y	-	1	0	ODZ1	123345207	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.750000	0.62162	2.018000	0.59344	0.486000	0.48141	TAC	.	.		0.358	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123517526	A	T	123517526	3	4	102	1	0	0	0	0	1	0	0	0	10843	420	15	4	955	4	ODZ1	23	123517526	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10		123517526	31753034	139	14621										
GPR112	139378	hgsc.bcm.edu	37	chrX	135453612	135453612	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	cacaatgtgatgagataagtAtgaacctaactcatgttatg	8	6	1	3			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chrX:135453612A>G	ENST00000394143.1	+	14	7813	c.7522A>G	c.(7522-7524)Atg>Gtg	p.M2508V	GPR112_ENST00000394141.1_Missense_Mutation_p.M2303V|GPR112_ENST00000287534.4_Missense_Mutation_p.M2306V|GPR112_ENST00000412101.1_Missense_Mutation_p.M2303V|GPR112_ENST00000370652.1_Missense_Mutation_p.M2508V	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2508					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TGAGATAAGTATGAACCTAAC	0.313																																					p.M2508V		Atlas-SNP	.											.	GPR112	459	.	0			c.A7522G						.						65	59	61					X																	135453612		2203	4296	6499	SO:0001583	missense	139378	exon14			ATAAGTATGAACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.7522A>G	chrX.hg19:g.135453612A>G	ENSP00000377699:p.Met2508Val	138.0	0.0		191.0	86.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	a	8.194	0.796709	0.16327	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.27557	1.7;1.7;1.66;1.92;1.66	5.14	2.52	0.30459	.	.	.	.	.	T	0.14787	0.0357	N	0.14661	0.345	0.09310	N	0.999996	B;B	0.17667	0.023;0.002	B;B	0.14023	0.01;0.008	T	0.32375	-0.9909	9	0.14252	T	0.57	.	5.4056	0.16320	0.7028:0.1896:0.1076:0.0	.	2303;2508	Q8IZF6-3;Q8IZF6	.;GP112_HUMAN	V	2508;2508;2303;2306;2303	ENSP00000377699:M2508V;ENSP00000359686:M2508V;ENSP00000416526:M2303V;ENSP00000287534:M2306V;ENSP00000377697:M2303V	ENSP00000287534:M2306V	M	+	1	0	GPR112	135281278	0.986000	0.35501	1.000000	0.80357	0.981000	0.71138	0.168000	0.16622	0.612000	0.30071	0.483000	0.47432	ATG	.	.		0.313	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			G	135453612	A	G	135453612	3	3	102	1	0	0	0	0	1	0	0	0	6637	449	16	2	7564	2	GPR112	23	135453612	Missense_Mutation	SNP	A	TCGA-DD-A1EF-01A-11D-A12Z-10	11936086	135453612	19816948	140	14622										
HCFC1	3054	hgsc.bcm.edu	37	chrX	153222832	153222832	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	10	1	1.01500649887747	1.91836228287841	0.844562011330118	0.226194642616772	0.852228299960161	0	atgatggtggtcgtgccgggCttggtggtactgggggagac	20	6	0	2			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chrX:153222832C>T	ENST00000310441.7	-	13	3252	c.2286G>A	c.(2284-2286)aaG>aaA	p.K762K	HCFC1_ENST00000369984.4_Silent_p.K762K|HCFC1_ENST00000461098.1_5'Flank|HCFC1_ENST00000354233.3_Silent_p.K693K	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	762	Interaction with ZBTB17.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCGTGCCGGGCTTGGTGGTAC	0.642																																					p.K762K		Atlas-SNP	.											.	HCFC1	284	.	0			c.G2286A						.						116	127	123					X																	153222832		2147	4204	6351	SO:0001819	synonymous_variant	3054	exon13			GCCGGGCTTGGTG		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"VP16-accessory protein", "protein phosphatase 1, regulatory subunit 89"	300019	"mental retardation, X-linked 3", "host cell factor C1 (VP16-accessory protein)"	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.2286G>A	chrX.hg19:g.153222832C>T		111.0	0.0		212.0	89.0	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	hg19	CCDS44020.1																																																																																			.	.		0.642	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		T	153222832	C	T	153222832	2	4	102	1	0	0	0	0	0	0	0	1	7000	796	28	3		3	HCFC1	23	153222832	Silent	SNP	C	TCGA-DD-A1EF-01A-11D-A12Z-10	17769220	153222832	2047728	141	14623										
SAMD11	148398	hgsc.bcm.edu	37	chr1	874450	874450	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggcaagaggctgggccgctCcccccgtatcagcagcgact							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:874450delC	ENST00000342066.3	+	6	544	c.461delC	c.(460-462)tccfs	p.S154fs		NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	154					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		CTGGGCCGCTCCCCCCGTATC	0.622																																					p.S154fs		Atlas-INDEL	.											.	SAMD11	34	.	0			c.460delT						.						38	35	36					1																	874450		2201	4300	6501	SO:0001589	frameshift_variant	148398	exon6			.	BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"Sterile alpha motif (SAM) domain containing"	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.461delC	chr1.hg19:g.874450delC	ENSP00000342313:p.Ser154fs	157.0	0.0		176.0	12.0	NM_152486	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	Frame_Shift_Del	DEL	ENST00000342066.3	hg19	CCDS2.2																																																																																			.	.		0.622	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276866.2	NM_152486		-	874450	C	-	874450	7	5	103	1	0	1	0	1	0	0	0	0	13831	855	30	0	479	0	SAMD11	1	874450	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10		874450	248376171	1	14624										
CPSF3L	54973	hgsc.bcm.edu	37	chr1	1256455	1256455	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaccaggatgcagcttcggCccacgtcctggccggcccct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:1256455delC	ENST00000435064.1	-	2	129	c.47delG	c.(46-48)ggcfs	p.G16fs	CPSF3L_ENST00000450926.2_Frame_Shift_Del_p.G16fs|CPSF3L_ENST00000411962.1_Intron|CPSF3L_ENST00000545578.1_5'UTR|CPSF3L_ENST00000421495.2_Intron|RP5-890O3.9_ENST00000444968.1_RNA|CPSF3L_ENST00000419704.1_Frame_Shift_Del_p.G16fs|CPSF3L_ENST00000540437.1_Frame_Shift_Del_p.G22fs	NM_001256460.1|NM_017871.5	NP_001243389.1|NP_060341.2	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor 3-like	16					snRNA processing (GO:0016180)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|integrator complex (GO:0032039)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(3)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		GCAGCTTCGGCCCACGTCCTG	0.647																																					p.G22fs		Atlas-INDEL	.											.	CPSF3L	33	.	0			c.66delC						.						101	91	95					1																	1256455		2203	4300	6503	SO:0001589	frameshift_variant	54973	exon4			.	AL136813	CCDS21.1, CCDS57959.1, CCDS57960.1, CCDS57961.1, CCDS72678.1	1p36.33	2008-02-05			ENSG00000127054	ENSG00000127054			26052	protein-coding gene	gene with protein product	"integrator complex subunit 11"	611354				15684398, 16239144	Standard	NM_001256456		Approved	FLJ20542, RC-68, CPSF73L, INT11, INTS11	uc001aee.2	Q5TA45	OTTHUMG00000003330	ENST00000435064.1:c.47delG	chr1.hg19:g.1256455delC	ENSP00000413493:p.Gly16fs	194.0	0.0		199.0	12.0	NM_001256456	A8K5S2|B3KPR3|B4DM87|G3V1S5|Q5TA46|Q5TA48|Q5TA52|Q5TA53|Q5TA54|Q7L3D7|Q96HY1|Q9BW36|Q9H0F9|Q9H8R5|Q9HAA6|Q9NWX9	Frame_Shift_Del	DEL	ENST00000435064.1	hg19	CCDS21.1																																																																																			.	.		0.647	CPSF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009360.2	NM_017871		-	1256455	C	-	1256455	7	5	103	1	0	1	0	1	0	0	0	0	3829	739	26	0	1819	0	CPSF3L	1	1256455	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	382005	1256455	247994166	2	14625										
MORN1	79906	hgsc.bcm.edu	37	chr1	2268183	2268183	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggctgtccaggaacaggaaGgggtggtacccaggcggggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:2268183delG	ENST00000378531.3	-	11	1316	c.1143delC	c.(1141-1143)cccfs	p.P381fs	MORN1_ENST00000606372.1_5'UTR	NM_024848.1	NP_079124.1	Q5T089	MORN1_HUMAN	MORN repeat containing 1	381										breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(1)|ovary(2)	9	all_cancers(77;0.000194)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.3e-15)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;2.21e-37)|OV - Ovarian serous cystadenocarcinoma(86;5.01e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00137)|BRCA - Breast invasive adenocarcinoma(365;0.00488)|STAD - Stomach adenocarcinoma(132;0.00665)|KIRC - Kidney renal clear cell carcinoma(229;0.0203)|Lung(427;0.212)		GGAACAGGAAGGGGTGGTACC	0.677																																					p.F382fs		Atlas-INDEL	.											.	MORN1	38	.	0			c.1144delT						.						23	25	24					1																	2268183		2201	4296	6497	SO:0001589	frameshift_variant	79906	exon11			.	AK024003	CCDS40.1, CCDS72688.1	1p36.33-p36.32	2008-02-05			ENSG00000116151	ENSG00000116151			25852	protein-coding gene	gene with protein product						12477932	Standard	XM_005244798		Approved	FLJ13941	uc001ajb.1	Q5T089	OTTHUMG00000001402	ENST00000378531.3:c.1143delC	chr1.hg19:g.2268183delG	ENSP00000367792:p.Pro381fs	142.0	0.0		151.0	11.0	NM_024848	A6NKZ6|Q8WW30|Q9H852	Frame_Shift_Del	DEL	ENST00000378531.3	hg19	CCDS40.1																																																																																			.	.		0.677	MORN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004055.1	NM_024848		-	2268183	G	-	2268183	7	5	103	1	0	1	0	1	0	0	0	0	9717	987	35	0	366	0	MORN1	1	2268183	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1011728	2268183	246982438	3	14626										
NPHP4	261734	hgsc.bcm.edu	37	chr1	6046337	6046337	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttttgggtgaagatcctgtGccagtcgttcatcctgcccg	12	11	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:6046337G>A	ENST00000378156.4	-	2	278	c.13C>T	c.(13-15)Cac>Tac	p.H5Y	NPHP4_ENST00000478423.2_Intron	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	5					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		AAGATCCTGTGCCAGTCGTTC	0.577																																					p.H5Y		Atlas-SNP	.											.	NPHP4	119	.	0			c.C13T						.						53	57	56					1																	6046337		2015	4169	6184	SO:0001583	missense	261734	exon2			TCCTGTGCCAGTC	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.13C>T	chr1.hg19:g.6046337G>A	ENSP00000367398:p.His5Tyr	115.0	0.0		110.0	5.0	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	hg19	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.409964	0.25465	.	.	ENSG00000131697	ENST00000378156	D	0.86627	-2.15	5.41	4.47	0.54385	.	0.608208	0.16633	N	0.205999	T	0.77850	0.4192	L	0.44542	1.39	0.28107	N	0.931154	P	0.37864	0.61	B	0.35353	0.201	T	0.67879	-0.5556	10	0.02654	T	1	.	9.2336	0.37453	0.0:0.1593:0.6756:0.165	.	5	O75161	NPHP4_HUMAN	Y	5	ENSP00000367398:H5Y	ENSP00000367398:H5Y	H	-	1	0	NPHP4	5968924	1.000000	0.71417	0.936000	0.37596	0.119000	0.20118	2.207000	0.42788	1.367000	0.46095	0.655000	0.94253	CAC	.	.		0.577	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			A	6046337	G	A	6046337	3	1	103	1	0	0	0	0	1	0	0	0	10590	1319	46	3	4383	3	NPHP4	1	6046337	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	3778154	6046337	243204284	4	14627										
CHD5	26038	hgsc.bcm.edu	37	chr1	6202277	6202277	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caccgagcggctctccttgtCccccgtgtaggtgaccacgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:6202277delC	ENST00000262450.3	-	15	2446	c.2347delG	c.(2347-2349)gacfs	p.D783fs	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		CTCTCCTTGTCCCCCGTGTAG	0.582																																					p.D783fs		Atlas-INDEL	.											.	CHD5	267	.	0			c.2348delA						.						126	119	121					1																	6202277		2203	4300	6503	SO:0001589	frameshift_variant	26038	exon15			.	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2347delG	chr1.hg19:g.6202277delC	ENSP00000262450:p.Asp783fs	148.0	0.0		158.0	10.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Frame_Shift_Del	DEL	ENST00000262450.3	hg19	CCDS57.1																																																																																			.	.		0.582	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		-	6202277	C	-	6202277	7	5	103	1	0	1	0	1	0	0	0	0	3330	855	30	0	3625	0	CHD5	1	6202277	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	155940	6202277	243048344	5	14628										
PER3	8863	hgsc.bcm.edu	37	chr1	7895908	7895908	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcaatctcaggacgtacagAaaaaagaaacatttcctaat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:7895908delA	ENST00000361923.2	+	19	3449	c.3274delA	c.(3274-3276)aaafs	p.K1093fs	PER3_ENST00000377532.3_Frame_Shift_Del_p.K1102fs	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1093					circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GGACGTACAGAAAAAAGAAAC	0.433																																					p.Q1091fs		Atlas-INDEL	.											.	PER3	95	.	0			c.3273delG						.						94	89	91					1																	7895908		2203	4300	6503	SO:0001589	frameshift_variant	8863	exon19			.	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3274delA	chr1.hg19:g.7895908delA	ENSP00000355031:p.Lys1093fs	167.0	0.0		222.0	15.0	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Frame_Shift_Del	DEL	ENST00000361923.2	hg19	CCDS89.1																																																																																			.	.		0.433	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		-	7895908	A	-	7895908	7	5	103	1	0	1	0	1	0	0	0	0	11740	247	9	0	3348	0	PER3	1	7895908	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1693631	7895908	241354713	6	14629										
RERE	473	hgsc.bcm.edu	37	chr1	8418658	8418658	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagctcccgctctcggatctCccgctctcggatctcccgct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:8418658delC	ENST00000337907.3	-	21	4571	c.3937delG	c.(3937-3939)gagfs	p.E1313fs	RERE_ENST00000476556.1_Frame_Shift_Del_p.E759fs|RERE_ENST00000400908.2_Frame_Shift_Del_p.E1313fs|RERE_ENST00000377464.1_Frame_Shift_Del_p.E1045fs|RERE_ENST00000400907.2_Intron	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1313	Arg/Glu-rich (mixed charge).				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		TCTCGGATCTCCCGCTCTCGG	0.697																																					p.E1313fs		Atlas-INDEL	.											.	RERE	129	.	0			c.3938delA						.						20	25	24					1																	8418658		2189	4292	6481	SO:0001589	frameshift_variant	473	exon21			.	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.3937delG	chr1.hg19:g.8418658delC	ENSP00000338629:p.Glu1313fs	105.0	0.0		131.0	11.0	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Frame_Shift_Del	DEL	ENST00000337907.3	hg19	CCDS95.1																																																																																			.	.		0.697	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			-	8418658	C	-	8418658	7	5	103	1	0	1	0	1	0	0	0	0	13246	864	30	0	779	0	RERE	1	8418658	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	522750	8418658	240831963	7	14630										
RERE	473	hgsc.bcm.edu	37	chr1	8421412	8421412	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgagtcactctcattgtcctGggggctggggatgctcgggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:8421412delG	ENST00000337907.3	-	19	2789	c.2155delC	c.(2155-2157)cagfs	p.Q719fs	RERE_ENST00000476556.1_Frame_Shift_Del_p.Q165fs|RERE_ENST00000400908.2_Frame_Shift_Del_p.Q719fs|RERE_ENST00000377464.1_Frame_Shift_Del_p.Q451fs|RERE_ENST00000400907.2_Intron	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	719					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		TCATTGTCCTGGGGGCTGGGG	0.632																																					p.Q719fs		Atlas-INDEL	.											.	RERE	129	.	0			c.2156delA						.						92	88	90					1																	8421412		2203	4300	6503	SO:0001589	frameshift_variant	473	exon19			.	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2155delC	chr1.hg19:g.8421412delG	ENSP00000338629:p.Gln719fs	124.0	0.0		136.0	10.0	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Frame_Shift_Del	DEL	ENST00000337907.3	hg19	CCDS95.1																																																																																			.	.		0.632	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			-	8421412	G	-	8421412	7	5	103	1	0	1	0	1	0	0	0	0	13246	1357	47	0	2569	0	RERE	1	8421412	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2754	8421412	240829209	8	14631										
KIF1B	23095	hgsc.bcm.edu	37	chr1	10327488	10327488	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtacgagatttgctgaatccAaaaaacaagggtaatttgcg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:10327488delA	ENST00000377086.1	+	6	682	c.480delA	c.(478-480)ccafs	p.P160fs	KIF1B_ENST00000263934.6_Frame_Shift_Del_p.P160fs|KIF1B_ENST00000377083.1_Frame_Shift_Del_p.P160fs|KIF1B_ENST00000377081.1_Frame_Shift_Del_p.P160fs|KIF1B_ENST00000377093.4_Frame_Shift_Del_p.P160fs			O60333	KIF1B_HUMAN	kinesin family member 1B	160	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		TGCTGAATCCAAAAAACAAGG	0.398																																					p.P160fs		Atlas-INDEL	.											.	KIF1B	242	.	0			c.479delC						.						103	90	94					1																	10327488		2203	4300	6503	SO:0001589	frameshift_variant	23095	exon6			.	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.480delA	chr1.hg19:g.10327488delA	ENSP00000366290:p.Pro160fs	144.0	0.0		160.0	10.0	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Frame_Shift_Del	DEL	ENST00000377086.1	hg19																																																																																				.	.		0.398	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			-	10327488	A	-	10327488	7	5	103	1	0	1	0	1	0	0	0	0	8293	117	5	0	498	0	KIF1B	1	10327488	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1906076	10327488	238923133	9	14632										
MTOR	2475	hgsc.bcm.edu	37	chr1	11292498	11292498	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcagtaatactcacctgccTtttggccaacaaagaggaat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:11292498delT	ENST00000361445.4	-	16	2585	c.2509delA	c.(2509-2511)aggfs	p.R837fs		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	837					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CTCACCTGCCTTTTGGCCAAC	0.448																																					p.R837fs		Atlas-INDEL	.											.	MTOR	327	.	0			c.2510delG						.						135	127	129					1																	11292498		2203	4300	6503	SO:0001589	frameshift_variant	2475	exon16			.	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.2509delA	chr1.hg19:g.11292498delT	ENSP00000354558:p.Arg837fs	138.0	0.0		138.0	11.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Frame_Shift_Del	DEL	ENST00000361445.4	hg19	CCDS127.1																																																																																			.	.		0.448	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		-	11292498	T	-	11292498	7	5	103	1	0	1	0	1	0	0	0	0	9963	1608	56	0	5312	0	MTOR	1	11292498	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	965010	11292498	237958123	10	14633										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12339690	12339690	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcatgaagattgaaggaaaaTttgtcaatccagttcaggta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:12339690delT	ENST00000358136.3	+	20	4715	c.4585delT	c.(4585-4587)tttfs	p.F1529fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.F1529fs	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TGAAGGAAAATTTGTCAATCC	0.328																																					p.K1528fs		Atlas-INDEL	.											.	VPS13D	316	.	0			c.4584delA						.						65	65	65					1																	12339690		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon20			.	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.4585delT	chr1.hg19:g.12339690delT	ENSP00000350854:p.Phe1529fs	163.0	0.0		166.0	12.0	NM_015378		Frame_Shift_Del	DEL	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.328	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		-	12339690	T	-	12339690	7	5	103	1	0	1	0	1	0	0	0	0	17207	1493	52	0	4659	0	VPS13D	1	12339690	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1047192	12339690	236910931	11	14634										
AADACL4	343066	hgsc.bcm.edu	37	chr1	12704616	12704616	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcattgcccatctttttcctGggggtctttgtctgggctgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:12704616delG	ENST00000376221.1	+	1	51	c.51delG	c.(49-51)ctgfs	p.L17fs		NM_001013630.1	NP_001013652.1	Q5VUY2	ADCL4_HUMAN	arylacetamide deacetylase-like 4	17						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)	17	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000937)|all_lung(284;0.00122)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.81e-07)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0384)		TCTTTTTCCTGGGGGTCTTTG	0.542																																					p.L17fs		Atlas-INDEL	.											.	AADACL4	48	.	0			c.50delT						.						183	160	168					1																	12704616		2203	4300	6503	SO:0001589	frameshift_variant	343066	exon1			.		CCDS30590.1	1p36.21	2010-12-14			ENSG00000204518	ENSG00000204518			32038	protein-coding gene	gene with protein product							Standard	XM_006710608		Approved	OTTHUMG00000001889	uc001auf.3	Q5VUY2	OTTHUMG00000001889	ENST00000376221.1:c.51delG	chr1.hg19:g.12704616delG	ENSP00000365395:p.Leu17fs	153.0	0.0		189.0	12.0	NM_001013630		Frame_Shift_Del	DEL	ENST00000376221.1	hg19	CCDS30590.1																																																																																			.	.		0.542	AADACL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005328.1	NM_001013630		-	12704616	G	-	12704616	7	5	103	1	0	1	0	1	0	0	0	0	13	1335	47	0	53	0	AADACL4	1	12704616	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	364926	12704616	236546005	12	14635										
CELA2A	63036	hgsc.bcm.edu	37	chr1	15783592	15783592	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttttcacagccctcagttgtGgggaccccacttacccacct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:15783592delG	ENST00000359621.4	+	2	77	c.52delG	c.(52-54)gggfs	p.G18fs	CELA2A_ENST00000497590.1_3'UTR	NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	18						extracellular region (GO:0005576)|keratohyalin granule (GO:0036457)	serine hydrolase activity (GO:0017171)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						CCTCAGTTGTGGGGACCCCAC	0.542																																					p.C17fs		Atlas-INDEL	.											.	CELA2A	32	.	0			c.51delT						.						90	85	87					1																	15783592		2203	4300	6503	SO:0001589	frameshift_variant	63036	exon2			.		CCDS157.1	1p36.21	2009-07-09			ENSG00000142615	ENSG00000142615	3.4.21.71		24609	protein-coding gene	gene with protein product	"elastase 2A"	609443				3646943, 2834346	Standard	NM_033440		Approved	ELA2A	uc001awk.3	P08217	OTTHUMG00000002258	ENST00000359621.4:c.52delG	chr1.hg19:g.15783592delG	ENSP00000352639:p.Gly18fs	207.0	0.0		238.0	15.0	NM_033440	B2R5I4|Q14243	Frame_Shift_Del	DEL	ENST00000359621.4	hg19	CCDS157.1																																																																																			.	.		0.542	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440		-	15783592	G	-	15783592	7	5	103	1	0	1	0	1	0	0	0	0	3213	1348	47	0	58	0	CELA2A	1	15783592	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	3078976	15783592	233467029	13	14636										
SPEN	23013	hgsc.bcm.edu	37	chr1	16260282	16260282	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggctcagtctactccatctcCagctcttcccccagacacaa	5	18	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:16260282C>T	ENST00000375759.3	+	11	7751	c.7547C>T	c.(7546-7548)cCa>cTa	p.P2516L		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2516	Pro-rich.|RID.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.P2516L(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		ACTCCATCTCCAGCTCTTCCC	0.582																																					p.P2516L		Atlas-SNP	.											SPEN,NS,carcinoma,0,1	SPEN	374	.	1	Substitution - Missense(1)	lung(1)	c.C7547T						.						137	142	140					1																	16260282		2203	4300	6503	SO:0001583	missense	23013	exon11			CATCTCCAGCTCT		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.7547C>T	chr1.hg19:g.16260282C>T	ENSP00000364912:p.Pro2516Leu	34.0	0.0		35.0	2.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.937496	0.52972	.	.	ENSG00000065526	ENST00000375759	T	0.37915	1.17	5.16	5.16	0.70880	.	.	.	.	.	T	0.55561	0.1928	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.64144	0.922	T	0.53542	-0.8424	9	0.42905	T	0.14	-11.4672	18.6444	0.91406	0.0:1.0:0.0:0.0	.	2516	Q96T58	MINT_HUMAN	L	2516	ENSP00000364912:P2516L	ENSP00000364912:P2516L	P	+	2	0	SPEN	16132869	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	6.357000	0.73051	2.418000	0.82041	0.561000	0.74099	CCA	.	.		0.582	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16260282	C	T	16260282	3	4	103	1	0	0	0	0	1	0	0	0	15053	594	21	3	7589	3	SPEN	1	16260282	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	476690	16260282	232990339	14	14637										
CLCNKA	1187	hgsc.bcm.edu	37	chr1	16353907	16353907	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggccttcatattccggctccTggcagtcttcaacagcgagc	10	14	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:16353907T>C	ENST00000331433.4	+	8	777	c.758T>C	c.(757-759)cTg>cCg	p.L253P	CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000420078.1_Missense_Mutation_p.L253P|CLCNKA_ENST00000375692.1_Missense_Mutation_p.L253P|CLCNKA_ENST00000439316.2_Missense_Mutation_p.L210P			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	253					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	TTCCGGCTCCTGGCAGTCTTC	0.642																																					p.L253P		Atlas-SNP	.											.	CLCNKA	56	.	0			c.T758C						.						63	69	67					1																	16353907		2203	4300	6503	SO:0001583	missense	1187	exon8			GGCTCCTGGCAGT		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"Ion channels / Chloride channels : Voltage-sensitive"	2026	protein-coding gene	gene with protein product		602024	"chloride channel Ka"			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.758T>C	chr1.hg19:g.16353907T>C	ENSP00000332771:p.Leu253Pro	101.0	0.0		106.0	5.0	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	hg19	CCDS167.1	.	.	.	.	.	.	.	.	.	.	T	17.74	3.463288	0.63513	.	.	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.95412	-3.7;-3.7;-3.7;-3.7	3.02	3.02	0.34903	Chloride channel, core (2);	0.078357	0.49305	D	0.000145	D	0.97838	0.9290	M	0.92923	3.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97998	1.0358	10	0.87932	D	0	.	10.7799	0.46371	0.0:0.0:0.0:1.0	.	210;253;253	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	P	253;253;210;253	ENSP00000364844:L253P;ENSP00000410353:L253P;ENSP00000414445:L210P;ENSP00000332771:L253P	ENSP00000332771:L253P	L	+	2	0	CLCNKA	16226494	1.000000	0.71417	0.997000	0.53966	0.516000	0.34256	7.614000	0.82996	1.368000	0.46115	0.260000	0.18958	CTG	.	.		0.642	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1			C	16353907	T	C	16353907	3	2	103	1	0	0	0	0	1	0	0	0	3471	1580	55	2	784	2	CLCNKA	1	16353907	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	93625	16353907	232896714	15	14638										
PADI3	51702	hgsc.bcm.edu	37	chr1	17593227	17593227	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttggcagcggcagtgggtctGggggcccagtgggtatggcg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:17593227delG	ENST00000375460.3	+	5	462	c.422delG	c.(421-423)tggfs	p.W141fs		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	141					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CAGTGGGTCTGGGGGCCCAGT	0.587																																					p.W141fs		Atlas-INDEL	.											.	PADI3	81	.	0			c.421delT						.						118	104	109					1																	17593227		2203	4300	6503	SO:0001589	frameshift_variant	51702	exon5			.	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"Peptidyl arginine deiminases"	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.422delG	chr1.hg19:g.17593227delG	ENSP00000364609:p.Trp141fs	151.0	0.0		184.0	12.0	NM_016233	Q58EY7|Q70SX5	Frame_Shift_Del	DEL	ENST00000375460.3	hg19	CCDS179.1																																																																																			.	.		0.587	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1			-	17593227	G	-	17593227	7	5	103	1	0	1	0	1	0	0	0	0	11388	1357	47	0	440	0	PADI3	1	17593227	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1239320	17593227	231657394	16	14639										
KLHDC7A	127707	hgsc.bcm.edu	37	chr1	18808294	18808294	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgcgtccgaatggaggagcaTttcatacagaaggcggaggg	16	8	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:18808294T>A	ENST00000400664.1	+	1	871	c.819T>A	c.(817-819)caT>caA	p.H273Q		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	273			H -> N (in dbSNP:rs2992753). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGGAGGAGCATTTCATACAGA	0.592																																					p.H273Q		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.T819A						.						79	83	82					1																	18808294		2203	4300	6503	SO:0001583	missense	127707	exon1			GGAGCATTTCATA	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.819T>A	chr1.hg19:g.18808294T>A	ENSP00000383505:p.His273Gln	69.0	0.0		97.0	5.0	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	hg19	CCDS185.2	.	.	.	.	.	.	.	.	.	.	T	10.46	1.355191	0.24512	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.71461	-0.57	4.92	-3.68	0.04463	.	0.547006	0.17223	U	0.182256	T	0.46658	0.1404	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.01281	0.0	T	0.32798	-0.9893	10	0.66056	D	0.02	.	13.1005	0.59218	0.0:0.6158:0.0:0.3842	.	273	Q5VTJ3	KLD7A_HUMAN	Q	273;210	ENSP00000383505:H273Q	ENSP00000383505:H273Q	H	+	3	2	KLHDC7A	18680881	0.000000	0.05858	0.019000	0.16419	0.298000	0.27526	-0.923000	0.04000	-0.682000	0.05197	0.260000	0.18958	CAT	.	.		0.592	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375		A	18808294	T	A	18808294	3	1	103	1	0	0	0	0	1	0	0	0	8369	1490	52	4	821	4	KLHDC7A	1	18808294	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1215067	18808294	230442327	17	14640										
ALDH4A1	8659	hgsc.bcm.edu	37	chr1	19213000	19213000	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccaccttatgtccatggttAaaaggctgaaaggagagaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:19213000delA	ENST00000375341.3	-	4	512	c.255delT	c.(253-255)tttfs	p.F85fs	ALDH4A1_ENST00000538839.1_Frame_Shift_Del_p.F85fs|ALDH4A1_ENST00000290597.5_Frame_Shift_Del_p.F85fs|ALDH4A1_ENST00000538309.1_Frame_Shift_Del_p.F25fs|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000454547.1_5'Flank	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	85					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GTCCATGGTTAAAAGGCTGAA	0.562																																					p.N86fs		Atlas-INDEL	.											.	ALDH4A1	72	.	0			c.256delA						.						152	112	126					1																	19213000		2203	4300	6503	SO:0001589	frameshift_variant	8659	exon4			.	U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"Aldehyde dehydrogenases"	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.255delT	chr1.hg19:g.19213000delA	ENSP00000364490:p.Phe85fs	135.0	0.0		142.0	13.0	NM_003748	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Frame_Shift_Del	DEL	ENST00000375341.3	hg19	CCDS188.1																																																																																			.	.		0.562	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1			-	19213000	A	-	19213000	7	5	103	1	0	1	0	1	0	0	0	0	501	359	13	0	1484	0	ALDH4A1	1	19213000	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	404706	19213000	230037621	18	14641										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22207984	22207984	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccgggctgcgcaggcattgTcacattcacacctgtgggtg	14	12	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:22207984T>C	ENST00000374695.3	-	14	1745	c.1666A>G	c.(1666-1668)Aca>Gca	p.T556A		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	556	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCAGGCATTGTCACATTCACA	0.637																																					p.T556A		Atlas-SNP	.											.	HSPG2	311	.	0			c.A1666G						.						91	91	91					1																	22207984		2203	4300	6503	SO:0001583	missense	3339	exon14			GCATTGTCACATT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.1666A>G	chr1.hg19:g.22207984T>C	ENSP00000363827:p.Thr556Ala	93.0	0.0		82.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	T	5.321	0.244635	0.10077	.	.	ENSG00000142798	ENST00000374695	T	0.75154	-0.91	5.52	3.19	0.36642	Laminin B type IV (1);	0.785217	0.10745	N	0.639015	D	0.83862	0.5346	M	0.69823	2.125	0.25115	N	0.990681	D	0.58268	0.982	D	0.67548	0.952	T	0.70773	-0.4781	10	0.56958	D	0.05	.	10.783	0.46388	0.0:0.1472:0.0:0.8528	.	556	P98160	PGBM_HUMAN	A	556	ENSP00000363827:T556A	ENSP00000363827:T556A	T	-	1	0	HSPG2	22080571	1.000000	0.71417	0.058000	0.19502	0.000000	0.00434	2.119000	0.41958	0.123000	0.18342	-1.139000	0.01908	ACA	.	.		0.637	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		C	22207984	T	C	22207984	3	2	103	1	0	0	0	0	1	0	0	0	7439	1667	58	2	11845	2	HSPG2	1	22207984	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2994984	22207984	227042637	19	14642										
MYOM3	127294	hgsc.bcm.edu	37	chr1	24390564	24390564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccatcgccagctcctaccgTcacccgtgaggtccaatatg	8	17	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:24390564T>C	ENST00000374434.3	-	30	3782	c.3620A>G	c.(3619-3621)gAc>gGc	p.D1207G	RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000338909.5_Missense_Mutation_p.D100G|MYOM3_ENST00000330966.7_Missense_Mutation_p.D1210G|RP11-293P20.2_ENST00000439239.2_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1207						M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		GCTCCTACCGTCACCCGTGAG	0.527																																					p.D1207G		Atlas-SNP	.											.	MYOM3	131	.	0			c.A3620G						.						99	108	105					1																	24390564		2122	4238	6360	SO:0001583	missense	127294	exon30			CTACCGTCACCCG	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	26679	protein-coding gene	gene with protein product			"myomesin family, member 3"			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.3620A>G	chr1.hg19:g.24390564T>C	ENSP00000363557:p.Asp1207Gly	88.0	0.0		87.0	4.0	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	hg19	CCDS41281.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.435411	0.43224	.	.	ENSG00000142661	ENST00000338909;ENST00000374434;ENST00000330966;ENST00000374442	T;T;T	0.56103	0.48;0.58;0.56	5.77	4.58	0.56647	Immunoglobulin subtype (1);	0.233454	0.43260	D	0.000593	T	0.27313	0.0670	N	0.08118	0	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.10450	0.0;0.005	T	0.12863	-1.0531	10	0.20519	T	0.43	.	6.2415	0.20793	0.0:0.0864:0.1632:0.7504	.	1207;100	Q5VTT5;Q5VTT5-3	MYOM3_HUMAN;.	G	100;1207;1210;102	ENSP00000342689:D100G;ENSP00000363557:D1207G;ENSP00000332670:D1210G	ENSP00000332670:D1210G	D	-	2	0	MYOM3	24263151	0.989000	0.36119	0.997000	0.53966	0.621000	0.37620	1.356000	0.34079	2.192000	0.70111	0.533000	0.62120	GAC	.	.		0.527	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372		C	24390564	T	C	24390564	3	2	103	1	0	0	0	0	1	0	0	0	10102	1667	58	2	725	2	MYOM3	1	24390564	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2182580	24390564	224860057	20	14643										
C1orf201	90529	hgsc.bcm.edu	37	chr1	24696176	24696176	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggactcacgggaaaagagtcTtttttggaacttttgtgcaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:24696176delT	ENST00000374409.1	-	7	979	c.725delA	c.(724-726)aagfs	p.K242fs	STPG1_ENST00000468303.1_5'UTR|STPG1_ENST00000003583.8_Frame_Shift_Del_p.K195fs|STPG1_ENST00000440416.1_Frame_Shift_Del_p.K195fs|STPG1_ENST00000337248.4_Frame_Shift_Del_p.K242fs	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	242					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GAAAAGAGTCTTTTTTGGAAC	0.438																																					p.K242fs		Atlas-INDEL	.											.	.	.	.	0			c.726delG						.						117	117	117					1																	24696176		2203	4300	6503	SO:0001589	frameshift_variant	90529	exon7			.	BC047705	CCDS253.1, CCDS55581.1	1p36.11	2012-10-31	2012-07-30	2012-07-30	ENSG00000001460	ENSG00000001460			28070	protein-coding gene	gene with protein product	"O6-methylguanine-induced apoptosis 2"	615826	"chromosome 1 open reading frame 201"	C1orf201		23028632	Standard	NM_001199012		Approved	FLJ33340, MAPO2	uc001bjc.3	Q5TH74	OTTHUMG00000003297	ENST00000374409.1:c.725delA	chr1.hg19:g.24696176delT	ENSP00000363530:p.Lys242fs	107.0	0.0		157.0	10.0	NM_001199012	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Frame_Shift_Del	DEL	ENST00000374409.1	hg19	CCDS55581.1																																																																																			.	.		0.438	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122		-	24696176	T	-	24696176	7	5	103	1	0	1	0	1	0	0	0	0	2029	1609	56	0	291	0	C1orf201	1	24696176	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	305612	24696176	224554445	21	14644										
AHDC1	27245	hgsc.bcm.edu	37	chr1	27876868	27876868	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttctgcttccgccgccgtcGtttttttacctctggcatgg	9	14	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:27876868G>T	ENST00000247087.5	-	5	2355	c.1759C>A	c.(1759-1761)Cga>Aga	p.R587R	AHDC1_ENST00000374011.2_Silent_p.R587R			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	587							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CGCCGCCGTCGTTTTTTTACC	0.652																																					p.R587R		Atlas-SNP	.											AHDC1,NS,carcinoma,0,1	AHDC1	98	.	0			c.C1759A						.						65	62	63					1																	27876868		2203	4300	6503	SO:0001819	synonymous_variant	27245	exon6			GCCGTCGTTTTTT	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.1759C>A	chr1.hg19:g.27876868G>T		236.0	0.0		257.0	33.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Silent	SNP	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.		0.652	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			T	27876868	G	T	27876868	2	4	103	1	0	0	0	0	0	0	0	1	412	1153	40	1		1	AHDC1	1	27876868	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	3180692	27876868	221373753	22	14645										
PHACTR4	65979	hgsc.bcm.edu	37	chr1	28793167	28793167	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccaggactctgcctgctgcTcctgccagcactaacactac	7	18	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:28793167T>C	ENST00000373839.3	+	6	972	c.711T>C	c.(709-711)gcT>gcC	p.A237A	PHACTR4_ENST00000373836.3_Silent_p.A247A|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	237	Pro-rich.				actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCTGCTGCTCCTGCCAGCA	0.577																																					p.A247A		Atlas-SNP	.											.	PHACTR4	64	.	0			c.T741C						.						52	60	57					1																	28793167		2080	4223	6303	SO:0001819	synonymous_variant	65979	exon5			TGCTGCTCCTGCC	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.711T>C	chr1.hg19:g.28793167T>C		116.0	0.0		114.0	5.0	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Silent	SNP	ENST00000373839.3	hg19	CCDS41293.1																																																																																			.	.		0.577	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		C	28793167	T	C	28793167	2	2	103	1	0	0	0	0	0	0	0	1	11821	1538	54	2		2	PHACTR4	1	28793167	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	916299	28793167	220457454	23	14646										
SDC3	9672	hgsc.bcm.edu	37	chr1	31351530	31351530	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atcgggaaaggagtcatcatCcccagagccctccaggtcca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:31351530delC	ENST00000339394.6	-	2	370	c.196delG	c.(196-198)gatfs	p.D68fs	SDC3_ENST00000471567.1_5'UTR|SDC3_ENST00000336798.7_5'UTR	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	68					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		GAGTCATCATCCCCAGAGCCC	0.632																																					p.D66fs		Atlas-INDEL	.											.	SDC3	45	.	0			c.197delA						.						134	119	124					1																	31351530		2203	4300	6503	SO:0001589	frameshift_variant	9672	exon2			.	AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"Proteoglycans / Cell Surface : Syndecans"	10660	protein-coding gene	gene with protein product	"syndecan proteoglycan 3"	186357	"syndecan 3 (N-syndecan)"			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.196delG	chr1.hg19:g.31351530delC	ENSP00000344468:p.Asp68fs	141.0	0.0		161.0	10.0	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Frame_Shift_Del	DEL	ENST00000339394.6	hg19	CCDS30661.1																																																																																			.	.		0.632	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654		-	31351530	C	-	31351530	7	5	103	1	0	1	0	1	0	0	0	0	13968	855	30	0	1148	0	SDC3	1	31351530	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2558363	31351530	217899091	24	14647										
BAI2	576	hgsc.bcm.edu	37	chr1	32196841	32196841	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcctgtgggggcggaggctCccccagccctggtgaggctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:32196841delC	ENST00000373658.3	-	29	4281	c.3940delG	c.(3940-3942)gagfs	p.E1314fs	BAI2_ENST00000257070.4_Frame_Shift_Del_p.E1281fs|BAI2_ENST00000440175.2_Frame_Shift_Del_p.E923fs|BAI2_ENST00000398538.1_Frame_Shift_Del_p.E1302fs|BAI2_ENST00000373655.2_Frame_Shift_Del_p.E1314fs|BAI2_ENST00000398556.3_Frame_Shift_Del_p.E1229fs|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000527361.1_Frame_Shift_Del_p.E1281fs|BAI2_ENST00000398542.1_Frame_Shift_Del_p.E1214fs|BAI2_ENST00000398547.1_Frame_Shift_Del_p.E1247fs	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1314					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GGCGGAGGCTCCCCCAGCCCT	0.677																																					p.E1314fs		Atlas-INDEL	.											.	BAI2	128	.	0			c.3941delA						.						23	21	22					1																	32196841		2199	4298	6497	SO:0001589	frameshift_variant	576	exon29			.	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.3940delG	chr1.hg19:g.32196841delC	ENSP00000362762:p.Glu1314fs	182.0	0.0		178.0	12.0	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Frame_Shift_Del	DEL	ENST00000373658.3	hg19	CCDS346.2																																																																																			.	.		0.677	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		-	32196841	C	-	32196841	7	5	103	1	0	1	0	1	0	0	0	0	1299	864	30	0	837	0	BAI2	1	32196841	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	845311	32196841	217053780	25	14648										
TXLNA	200081	hgsc.bcm.edu	37	chr1	32660695	32660695	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcctggggctcaagcacccAgctcccccagggtcacagaa	12	16	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:32660695A>G	ENST00000373609.1	+	10	1821	c.1540A>G	c.(1540-1542)Agc>Ggc	p.S514G	TXLNA_ENST00000373610.3_Missense_Mutation_p.S514G			P40222	TXLNA_HUMAN	taxilin alpha	514					B cell activation (GO:0042113)|cell proliferation (GO:0008283)|exocytosis (GO:0006887)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	cytokine activity (GO:0005125)|high molecular weight B cell growth factor receptor binding (GO:0030372)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TCAAGCACCCAGCTCCCCCAG	0.657																																					p.S514G		Atlas-SNP	.											.	TXLNA	34	.	0			c.A1540G						.						37	38	37					1																	32660695		2203	4300	6503	SO:0001583	missense	200081	exon11			GCACCCAGCTCCC	AF516206	CCDS353.1	1p35	2012-02-21			ENSG00000084652	ENSG00000084652			30685	protein-coding gene	gene with protein product		608676				15184072, 14623251	Standard	NM_175852		Approved	DKFZp451J0118	uc001bui.3	P40222	OTTHUMG00000004423	ENST00000373609.1:c.1540A>G	chr1.hg19:g.32660695A>G	ENSP00000362711:p.Ser514Gly	192.0	0.0		185.0	9.0	NM_175852	D3DPP6|Q5TFJ6|Q66K62|Q86T54|Q86T85|Q86T86|Q86Y86|Q86YW3|Q8N2Y3	Missense_Mutation	SNP	ENST00000373609.1	hg19	CCDS353.1	.	.	.	.	.	.	.	.	.	.	A	11.39	1.624997	0.28889	.	.	ENSG00000084652	ENST00000373610;ENST00000373609	T;T	0.34275	1.37;1.37	4.61	3.47	0.39725	.	1.237840	0.05167	N	0.498896	T	0.26376	0.0644	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20075	-1.0286	10	0.42905	T	0.14	-1.5236	7.202	0.25887	0.7733:0.0:0.2267:0.0	.	514	P40222	TXLNA_HUMAN	G	514	ENSP00000362712:S514G;ENSP00000362711:S514G	ENSP00000362711:S514G	S	+	1	0	TXLNA	32433282	0.006000	0.16342	0.151000	0.22473	0.965000	0.64279	1.793000	0.38764	0.913000	0.36797	0.460000	0.39030	AGC	.	.		0.657	TXLNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012844.1	NM_175852		G	32660695	A	G	32660695	3	3	103	1	0	0	0	0	1	0	0	0	16802	188	7	2	1578	2	TXLNA	1	32660695	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	463854	32660695	216589926	26	14649										
C1orf113	79729	hgsc.bcm.edu	37	chr1	36785322	36785322	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggccccctctgtgaagagaaCccccatgccggacaagactg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:36785322delC	ENST00000426732.2	+	13	995	c.710delC	c.(709-711)accfs	p.T237fs	SH3D21_ENST00000453908.2_Frame_Shift_Del_p.T353fs|SH3D21_ENST00000505871.1_Frame_Shift_Del_p.T242fs|EVA1B_ENST00000490466.1_5'Flank|SH3D21_ENST00000312808.4_5'UTR			A4FU49	SH321_HUMAN	SH3 domain containing 21	237						extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(6)|lung(4)|pancreas(1)	12						GTGAAGAGAACCCCCATGCCG	0.627																																					p.T353fs		Atlas-INDEL	.											.	SH3D21	73	.	0			c.1057delA						.						29	42	38					1																	36785322		2194	4296	6490	SO:0001589	frameshift_variant	79729	exon14			.	AK056459	CCDS30674.1, CCDS30674.2	1p34.3	2011-02-21	2011-02-21	2011-02-21	ENSG00000214193	ENSG00000214193			26236	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 113"	C1orf113		12477932	Standard	NM_024676		Approved	FLJ22938	uc010oia.1	A4FU49	OTTHUMG00000007868	ENST00000426732.2:c.710delC	chr1.hg19:g.36785322delC	ENSP00000408613:p.Thr237fs	228.0	0.0		247.0	16.0	NM_001162530	B4DLI6|D3DPS6|J3KQM5|Q5VTK7|Q86XZ6|Q8N445|Q96DN4|Q9H5W5	Frame_Shift_Del	DEL	ENST00000426732.2	hg19																																																																																				.	.		0.627	SH3D21-202	KNOWN	basic	protein_coding	protein_coding		NM_024676		-	36785322	C	-	36785322	7	5	103	1	0	1	0	1	0	0	0	0	1988	507	18	0	1112	0	C1orf113	1	36785322	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	4124627	36785322	212465299	27	14650										
RRAGC	64121	hgsc.bcm.edu	37	chr1	39318159	39318159	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atagatactagtcagataaaAgctgaaaaacacaacatagc	6	7	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:39318159A>G	ENST00000373001.3	-	4	819	c.643T>C	c.(643-645)Ttt>Ctt	p.F215L		NM_022157.2	NP_071440.1			Ras-related GTP binding C											endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)	10	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)				GTCAGATAAAAGCTGAAAAAC	0.294																																					p.F215L		Atlas-SNP	.											.	RRAGC	28	.	0			c.T643C						.						91	97	95					1																	39318159		2203	4299	6502	SO:0001630	splice_region_variant	64121	exon4			GATAAAAGCTGAA	AF323609	CCDS430.1	1p34	2008-02-05			ENSG00000116954	ENSG00000116954			19902	protein-coding gene	gene with protein product		608267				11073942	Standard	NM_022157		Approved	GTR2, FLJ13311	uc001ccq.3	Q9HB90	OTTHUMG00000000490	ENST00000373001.3:c.642-1T>C	chr1.hg19:g.39318159A>G		92.0	0.0		109.0	5.0	NM_022157		Missense_Mutation	SNP	ENST00000373001.3	hg19	CCDS430.1	.	.	.	.	.	.	.	.	.	.	A	34	5.386225	0.95967	.	.	ENSG00000116954	ENST00000373001	D	0.82711	-1.64	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.92593	0.7647	M	0.91717	3.235	0.80722	D	1	D;D;P	0.76494	0.975;0.999;0.912	P;D;P	0.66716	0.792;0.946;0.551	D	0.93720	0.7032	10	0.59425	D	0.04	-48.8638	16.4277	0.83824	1.0:0.0:0.0:0.0	.	181;149;215	E7ENI3;D3DPT8;Q9HB90	.;.;RRAGC_HUMAN	L	215	ENSP00000362092:F215L	ENSP00000362092:F215L	F	-	1	0	RRAGC	39090746	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.279000	0.76181	0.533000	0.62120	TTT	.	.		0.294	RRAGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001222.2	NM_022157	Missense_Mutation	G	39318159	A	G	39318159	5	3	103	1	0	0	0	0	0	0	1	0	13689	86	3	2	572	2	RRAGC	1	39318159	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2532837	39318159	209932462	28	14651										
COL9A2	1298	hgsc.bcm.edu	37	chr1	40773421	40773421	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catccttgccgttgatgcctGgggggccctacccaggagga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:40773421delG	ENST00000372748.3	-	18	1004	c.908delC	c.(907-909)ccafs	p.P303fs	COL9A2_ENST00000466267.1_5'Flank	NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	303	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			GTTGATGCCTGGGGGGCCCTA	0.627																																					p.P303fs		Atlas-INDEL	.											.	COL9A2	63	.	0			c.909delA						.						43	40	41					1																	40773421		2203	4300	6503	SO:0001589	frameshift_variant	1298	exon18			.	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.908delC	chr1.hg19:g.40773421delG	ENSP00000361834:p.Pro303fs	180.0	0.0		176.0	11.0	NM_001852	B2RMP9	Frame_Shift_Del	DEL	ENST00000372748.3	hg19	CCDS450.1																																																																																			.	.		0.627	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852		-	40773421	G	-	40773421	7	5	103	1	0	1	0	1	0	0	0	0	3710	1348	47	0	1221	0	COL9A2	1	40773421	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1455262	40773421	208477200	29	14652										
MAST2	23139	hgsc.bcm.edu	37	chr1	46487680	46487680	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agctgagggccacgccaaagAgggacaagggattaaatgtg	15	7	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:46487680A>G	ENST00000361297.2	+	12	1632	c.1349A>G	c.(1348-1350)gAg>gGg	p.E450G	MAST2_ENST00000372009.2_Missense_Mutation_p.E380G	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CACGCCAAAGAGGGACAAGGG	0.527																																					p.E450G		Atlas-SNP	.											.	MAST2	136	.	0			c.A1349G						.						198	203	201					1																	46487680		2049	4218	6267	SO:0001583	missense	23139	exon12			CCAAAGAGGGACA	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.1349A>G	chr1.hg19:g.46487680A>G	ENSP00000354671:p.Glu450Gly	113.0	0.0		103.0	5.0	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	hg19	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	A	34	5.400533	0.96030	.	.	ENSG00000086015	ENST00000361297;ENST00000372009;ENST00000432341;ENST00000372008	T;T;T	0.30714	1.52;1.52;1.52	5.74	5.74	0.90152	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.104885	0.64402	D	0.000007	T	0.62270	0.2414	M	0.87180	2.865	0.80722	D	1	B;D;B;D;D	0.89917	0.087;0.989;0.087;1.0;1.0	B;D;B;D;D	0.87578	0.168;0.979;0.168;0.998;0.994	T	0.68938	-0.5277	10	0.72032	D	0.01	-24.9249	16.3545	0.83230	1.0:0.0:0.0:0.0	.	124;380;124;380;450	B3KU51;Q6P0Q8-2;E7EWL1;E7ERL6;Q6P0Q8	.;.;.;.;MAST2_HUMAN	G	450;380;124;335	ENSP00000354671:E450G;ENSP00000361079:E380G;ENSP00000361078:E335G	ENSP00000354671:E450G	E	+	2	0	MAST2	46260267	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.274000	0.72587	2.326000	0.78906	0.533000	0.62120	GAG	.	.		0.527	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		G	46487680	A	G	46487680	3	3	103	1	0	0	0	0	1	0	0	0	9334	304	11	2	1395	2	MAST2	1	46487680	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	5714259	46487680	202762941	30	14653										
CYP4B1	1580	hgsc.bcm.edu	37	chr1	47284387	47284387	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgctttgagttctctctggaCccctcacggctgcccatcaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:47284387delC	ENST00000271153.4	+	12	1473	c.1437delC	c.(1435-1437)gacfs	p.D479fs	CYP4B1_ENST00000371919.4_Frame_Shift_Del_p.D465fs|CYP4B1_ENST00000371923.4_Frame_Shift_Del_p.D480fs|CYP4B1_ENST00000452782.2_Frame_Shift_Del_p.D317fs			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	479					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	TCTCTCTGGACCCCTCACGGC	0.577																																					p.D480fs		Atlas-INDEL	.											.	CYP4B1	81	.	0			c.1439delA						.						163	140	148					1																	47284387		2203	4300	6503	SO:0001589	frameshift_variant	1580	exon12			.	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"Cytochrome P450s"	2644	protein-coding gene	gene with protein product		124075	"cytochrome P450, subfamily IVB, polypeptide 1"				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.1437delC	chr1.hg19:g.47284387delC	ENSP00000271153:p.Asp479fs	163.0	0.0		156.0	10.0	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Frame_Shift_Del	DEL	ENST00000271153.4	hg19	CCDS542.1																																																																																			.	.		0.577	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779		-	47284387	C	-	47284387	7	5	103	1	0	1	0	1	0	0	0	0	4187	506	18	0	1486	0	CYP4B1	1	47284387	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	796707	47284387	201966234	31	14654										
GPX7	2882	hgsc.bcm.edu	37	chr1	53074002	53074002	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccccagatggaaaggtggtaGgggcttgggacccaactgtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:53074002delG	ENST00000361314.4	+	3	507	c.469delG	c.(469-471)gggfs	p.G157fs		NM_015696.4	NP_056511.2	Q96SL4	GPX7_HUMAN	glutathione peroxidase 7	157					response to oxidative stress (GO:0006979)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	glutathione peroxidase activity (GO:0004602)|peroxidase activity (GO:0004601)			breast(1)|kidney(1)|lung(4)|upper_aerodigestive_tract(1)	7					Glutathione(DB00143)	AAAGGTGGTAGGGGCTTGGGA	0.537																																					p.V156fs		Atlas-INDEL	.											.	GPX7	16	.	0			c.468delA						.						122	116	118					1																	53074002		2203	4300	6503	SO:0001589	frameshift_variant	2882	exon3			.	AF091092	CCDS569.1	1p32	2008-02-05			ENSG00000116157	ENSG00000116157			4559	protein-coding gene	gene with protein product		615784				15294905	Standard	NM_015696		Approved	FLJ14777, GPX6, NPGPx	uc001cue.3	Q96SL4	OTTHUMG00000008322	ENST00000361314.4:c.469delG	chr1.hg19:g.53074002delG	ENSP00000354677:p.Gly157fs	77.0	0.0		103.0	10.0	NM_015696	O95337|Q5T501	Frame_Shift_Del	DEL	ENST00000361314.4	hg19	CCDS569.1																																																																																			.	.		0.537	GPX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022913.1	NM_015696		-	53074002	G	-	53074002	7	5	103	1	0	1	0	1	0	0	0	0	6754	1000	35	0	479	0	GPX7	1	53074002	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	5789615	53074002	196176619	32	14655										
DMRTB1	63948	hgsc.bcm.edu	37	chr1	53925136	53925136	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgaccctgccaatggccgacAaaatggtgcgcacccccaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:53925136delA	ENST00000371445.3	+	1	65	c.10delA	c.(10-12)aaafs	p.K4fs		NM_033067.1	NP_149056.1	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal, 1	4					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(5)|ovary(1)|skin(1)	10						AATGGCCGACAAAATGGTGCG	0.627																																					p.D3fs		Atlas-INDEL	.											.	DMRTB1	38	.	0			c.9delC						.						50	44	46					1																	53925136		2202	4300	6502	SO:0001589	frameshift_variant	63948	exon1			.	AJ291671	CCDS581.1	1p32	2008-08-29			ENSG00000143006	ENSG00000143006			13913	protein-coding gene	gene with protein product		614805					Standard	NM_033067		Approved		uc001cvq.1	Q96MA1	OTTHUMG00000008080	ENST00000371445.3:c.10delA	chr1.hg19:g.53925136delA	ENSP00000360500:p.Lys4fs	185.0	0.0		174.0	11.0	NM_033067	Q96SD2	Frame_Shift_Del	DEL	ENST00000371445.3	hg19	CCDS581.1																																																																																			.	.		0.627	DMRTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022110.1			-	53925136	A	-	53925136	7	5	103	1	0	1	0	1	0	0	0	0	4592	131	5	0	12	0	DMRTB1	1	53925136	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	851134	53925136	195325485	33	14656										
SSBP3	23648	hgsc.bcm.edu	37	chr1	54870545	54870545	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	actcacctccgataagaaggTctgtgcagatttctgtgctc	9	11	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:54870545T>C	ENST00000371320.3	-	2	525	c.115A>G	c.(115-117)Acc>Gcc	p.T39A	SSBP3_ENST00000357475.4_Missense_Mutation_p.T39A|SSBP3_ENST00000417664.2_5'UTR|SSBP3_ENST00000371319.3_Missense_Mutation_p.T39A	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	39	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.				head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						GATAAGAAGGTCTGTGCAGAT	0.512																																					p.T39A		Atlas-SNP	.											.	SSBP3	65	.	0			c.A115G						.						55	53	54					1																	54870545		2203	4300	6503	SO:0001583	missense	23648	exon2			AGAAGGTCTGTGC		CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"single-stranded DNA-binding protein 3"			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.115A>G	chr1.hg19:g.54870545T>C	ENSP00000360371:p.Thr39Ala	89.0	0.0		120.0	5.0	NM_145716	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Missense_Mutation	SNP	ENST00000371320.3	hg19	CCDS591.1	.	.	.	.	.	.	.	.	.	.	T	19.18	3.777305	0.70107	.	.	ENSG00000157216	ENST00000371320;ENST00000371319;ENST00000357475	.	.	.	4.84	4.84	0.62591	LisH dimerisation motif (2);	0.074636	0.50627	U	0.000101	T	0.64962	0.2646	L	0.50333	1.59	0.58432	D	0.999997	B;P;P	0.50528	0.433;0.936;0.826	B;P;B	0.55577	0.107;0.779;0.424	T	0.67530	-0.5647	9	0.56958	D	0.05	-6.1723	13.7158	0.62695	0.0:0.0:0.0:1.0	.	39;39;39	Q9BWW4-2;Q9BWW4-3;Q9BWW4	.;.;SSBP3_HUMAN	A	39	.	ENSP00000350067:T39A	T	-	1	0	SSBP3	54643133	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.403000	0.79983	1.949000	0.56562	0.459000	0.35465	ACC	.	.		0.512	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070		C	54870545	T	C	54870545	3	2	103	1	0	0	0	0	1	0	0	0	15196	1667	58	2	1119	2	SSBP3	1	54870545	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	945409	54870545	194380076	34	14657										
C1orf168	199920	hgsc.bcm.edu	37	chr1	57216837	57216837	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctacctgtgtggacgttggTcatctgaattttttcaggtg	11	7	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:57216837T>C	ENST00000343433.6	-	9	1347	c.1267A>G	c.(1267-1269)Acc>Gcc	p.T423A	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	423										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						TGGACGTTGGTCATCTGAATT	0.473																																					p.T423A		Atlas-SNP	.											.	C1orf168	102	.	0			c.A1267G						.						127	108	115					1																	57216837		2203	4300	6503	SO:0001583	missense	199920	exon9			CGTTGGTCATCTG	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.1267A>G	chr1.hg19:g.57216837T>C	ENSP00000345972:p.Thr423Ala	112.0	0.0		85.0	4.0	NM_001004303	Q63HM3|Q6ZUY6	Missense_Mutation	SNP	ENST00000343433.6	hg19	CCDS30729.1	.	.	.	.	.	.	.	.	.	.	T	2.033	-0.421864	0.04734	.	.	ENSG00000187889	ENST00000343433	T	0.27256	1.68	4.11	-5.64	0.02466	.	1.382770	0.04566	N	0.392460	T	0.07908	0.0198	N	0.04508	-0.205	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.23119	-1.0197	10	0.07175	T	0.84	4.4247	2.2065	0.03937	0.1362:0.3874:0.2344:0.242	.	423	Q5VWT5	CA168_HUMAN	A	423	ENSP00000345972:T423A	ENSP00000345972:T423A	T	-	1	0	C1orf168	56989425	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.639000	0.05446	-1.142000	0.02869	-0.274000	0.10170	ACC	.	.		0.473	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303		C	57216837	T	C	57216837	3	2	103	1	0	0	0	0	1	0	0	0	2014	1667	58	2	967	2	C1orf168	1	57216837	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2346292	57216837	192033784	35	14658										
INADL	10207	hgsc.bcm.edu	37	chr1	62483532	62483532	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtttttcccaaacagataaAcaatcagattctgtatggaa	7	7	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:62483532A>G	ENST00000371158.2	+	29	3986	c.3872A>G	c.(3871-3873)aAc>aGc	p.N1291S	INADL_ENST00000543708.1_Missense_Mutation_p.N75S|INADL_ENST00000545929.1_Intron|INADL_ENST00000316485.6_Missense_Mutation_p.N1291S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1291	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AAACAGATAAACAATCAGATT	0.328																																					p.N1291S		Atlas-SNP	.											.	INADL	179	.	0			c.A3872G						.						107	99	102					1																	62483532		2203	4300	6503	SO:0001583	missense	10207	exon29			AGATAAACAATCA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.3872A>G	chr1.hg19:g.62483532A>G	ENSP00000360200:p.Asn1291Ser	82.0	0.0		74.0	4.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	19.83	3.899556	0.72754	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000307297;ENST00000543708	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.35	5.35	0.76521	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.79423	0.4443	M	0.89534	3.04	0.80722	D	1	P;P;P;D;D	0.61697	0.502;0.691;0.691;0.986;0.99	P;P;B;D;P	0.65684	0.505;0.488;0.36;0.937;0.86	D	0.84384	0.0551	10	0.87932	D	0	.	15.3286	0.74186	1.0:0.0:0.0:0.0	.	75;750;1291;1291;1291	B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;INADL_HUMAN;.	S	1291;1291;1291;1291;75;75	ENSP00000360200:N1291S;ENSP00000326199:N1291S;ENSP00000307496:N75S;ENSP00000445790:N75S	ENSP00000307496:N75S	N	+	2	0	INADL	62256120	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.042000	0.89430	2.029000	0.59856	0.482000	0.46254	AAC	.	.		0.328	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62483532	A	G	62483532	3	3	103	1	0	0	0	0	1	0	0	0	7740	43	2	2	3982	2	INADL	1	62483532	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	5266695	62483532	186767089	36	14659										
KANK4	163782	hgsc.bcm.edu	37	chr1	62739460	62739460	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccagctttcagactccatgCtgcctagaaggttgacttca	8	13	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:62739460C>G	ENST00000371153.4	-	3	1694	c.1316G>C	c.(1315-1317)aGc>aCc	p.S439T	KANK4_ENST00000371150.1_5'Flank|KANK4_ENST00000354381.3_Intron	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	439						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						AGACTCCATGCTGCCTAGAAG	0.557																																					p.S439T		Atlas-SNP	.											.	KANK4	135	.	0			c.G1316C						.						191	183	186					1																	62739460		2203	4300	6503	SO:0001583	missense	163782	exon3			TCCATGCTGCCTA	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	27263	protein-coding gene	gene with protein product		614612	"ankyrin repeat domain 38"	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.1316G>C	chr1.hg19:g.62739460C>G	ENSP00000360195:p.Ser439Thr	121.0	0.0		199.0	47.0	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	hg19	CCDS620.1	.	.	.	.	.	.	.	.	.	.	C	4.425	0.078600	0.08533	.	.	ENSG00000132854	ENST00000371153	T	0.46063	0.88	5.81	-2.06	0.07298	.	0.996520	0.08124	N	0.994228	T	0.21881	0.0527	N	0.15975	0.35	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.29181	-1.0020	10	0.10902	T	0.67	-0.3381	9.8642	0.41134	0.1688:0.5557:0.2754:0.0	.	439	Q5T7N3	KANK4_HUMAN	T	439	ENSP00000360195:S439T	ENSP00000360195:S439T	S	-	2	0	KANK4	62512048	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.114000	0.15520	-0.006000	0.14370	-0.262000	0.10625	AGC	.	.		0.557	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		G	62739460	C	G	62739460	3	3	103	1	0	0	0	0	1	0	0	0	7988	797	28	4	1703	4	KANK4	1	62739460	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	255928	62739460	186511161	37	14660										
SLC35D1	23169	hgsc.bcm.edu	37	chr1	67512956	67512956	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attgctacttacttttgaatCtaatttttgttttacgtatg	5	5	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:67512956C>T	ENST00000235345.5	-	7	713	c.628G>A	c.(628-630)Gat>Aat	p.D210N	SLC35D1_ENST00000506472.2_Missense_Mutation_p.D131N	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	210					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						ACTTTTGAATCTAATTTTTGT	0.353																																					p.D210N		Atlas-SNP	.											.	SLC35D1	22	.	0			c.G628A						.						161	148	153					1																	67512956		2203	4300	6503	SO:0001583	missense	23169	exon7			TTGAATCTAATTT	AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"Solute carriers"	20800	protein-coding gene	gene with protein product		610804	"solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.628G>A	chr1.hg19:g.67512956C>T	ENSP00000235345:p.Asp210Asn	54.0	0.0		54.0	4.0	NM_015139	A8K185|B7Z3X2|Q52LU5|Q92548	Missense_Mutation	SNP	ENST00000235345.5	hg19	CCDS636.1	.	.	.	.	.	.	.	.	.	.	C	18.72	3.683636	0.68157	.	.	ENSG00000116704	ENST00000235345;ENST00000506472	T;T	0.63255	-0.03;-0.03	5.15	5.15	0.70609	Domain of unknown function DUF250 (1);	0.090486	0.85682	D	0.000000	T	0.40670	0.1126	L	0.35793	1.09	0.80722	D	1	B;B	0.20368	0.035;0.044	B;B	0.24269	0.05;0.052	T	0.27872	-1.0061	10	0.23302	T	0.38	-14.2744	17.7823	0.88527	0.0:1.0:0.0:0.0	.	131;210	B7Z3X2;Q9NTN3	.;S35D1_HUMAN	N	210;131	ENSP00000235345:D210N;ENSP00000445189:D131N	ENSP00000235345:D210N	D	-	1	0	SLC35D1	67285544	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.435000	0.80391	2.567000	0.86603	0.655000	0.94253	GAT	.	.		0.353	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139		T	67512956	C	T	67512956	3	4	103	1	0	0	0	0	1	0	0	0	14596	913	32	3	463	3	SLC35D1	1	67512956	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	4773496	67512956	181737665	38	14661										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70397188	70397188	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatttttctccatctgttgtAggtcaatgcacaaactggcc	7	10	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:70397188A>G	ENST00000035383.5	+	6	563		c.e6-1		LRRC7_ENST00000415775.2_Splice_Site|LRRC7_ENST00000310961.5_Splice_Site	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7							cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CATCTGTTGTAGGTCAATGCA	0.403																																					.		Atlas-SNP	.											.	LRRC7	400	.	0			c.534-2A>G						.						90	83	86					1																	70397188		2203	4300	6503	SO:0001630	splice_region_variant	57554	exon6			TGTTGTAGGTCAA		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.534-1A>G	chr1.hg19:g.70397188A>G		85.0	0.0		119.0	5.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Splice_Site	SNP	ENST00000035383.5	hg19	CCDS645.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.64|14.64	2.594771|2.594771	0.46318|0.46318	.|.	.|.	ENSG00000033122|ENSG00000033122	ENST00000310961;ENST00000035383|ENST00000370957	.|.	.|.	.|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|.	.|.	.|.	.|.	.|T	.|0.55033	.|0.1895	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.56896	.|-0.7903	.|4	.|.	.|.	.|.	.|.	12.7596|12.7596	0.57356|0.57356	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	.|G	-1|1	.|.	.|.	.|R	+|+	.|1	.|2	LRRC7|LRRC7	70169776|70169776	1.000000|1.000000	0.71417|0.71417	0.938000|0.938000	0.37757|0.37757	0.406000|0.406000	0.30931|0.30931	5.974000|5.974000	0.70465|0.70465	2.254000|2.254000	0.74563|0.74563	0.528000|0.528000	0.53228|0.53228	.|AGG	.	.		0.403	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794	Intron	G	70397188	A	G	70397188	5	3	103	1	0	0	0	0	0	0	1	0	9029	434	15	2	554	2	LRRC7	1	70397188	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2884232	70397188	178853433	39	14662										
C1orf173	127254	hgsc.bcm.edu	37	chr1	75112405	75112405	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctaagcattcccggatataTttttgatgatcccgcttcat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:75112405delT	ENST00000326665.5	-	3	407	c.189delA	c.(187-189)aaafs	p.K63fs		NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		63										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CCCGGATATATTTTTGATGAT	0.259																																					p.Y64fs		Atlas-INDEL	.											.	C1orf173	380	.	0			c.190delT						.						28	26	26					1																	75112405		2084	4072	6156	SO:0001589	frameshift_variant	127254	exon3			.																												ENST00000326665.5:c.189delA	chr1.hg19:g.75112405delT	ENSP00000322609:p.Lys63fs	166.0	0.0		208.0	14.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Frame_Shift_Del	DEL	ENST00000326665.5	hg19	CCDS30755.1																																																																																			.	.		0.259	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			-	75112405	T	-	75112405	7	5	103	1	0	1	0	1	0	0	0	0	2016	1490	52	0	4451	0	C1orf173	1	75112405	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	4715217	75112405	174138216	40	14663										
SLC44A5	204962	hgsc.bcm.edu	37	chr1	75684228	75684228	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatcgtgggatgtcatcaggTtttttcatggcccagtaata							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:75684228delT	ENST00000370855.5	-	17	1589	c.1476delA	c.(1474-1476)aaafs	p.K492fs	SLC44A5_ENST00000370859.3_Frame_Shift_Del_p.K492fs|SLC44A5_ENST00000535611.1_Frame_Shift_Del_p.K362fs	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	492					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						TGTCATCAGGTTTTTTCATGG	0.418																																					p.P493fs		Atlas-INDEL	.											.	SLC44A5	231	.	0			c.1477delC						.						174	162	166					1																	75684228		2203	4300	6503	SO:0001589	frameshift_variant	204962	exon17			.	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.1476delA	chr1.hg19:g.75684228delT	ENSP00000359892:p.Lys492fs	113.0	0.0		136.0	10.0	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Frame_Shift_Del	DEL	ENST00000370855.5	hg19	CCDS667.1																																																																																			.	.		0.418	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		-	75684228	T	-	75684228	7	5	103	1	0	1	0	1	0	0	0	0	14654	1722	60	0	826	0	SLC44A5	1	75684228	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	571823	75684228	173566393	41	14664										
FUBP1	8880	hgsc.bcm.edu	37	chr1	78432435	78432435	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttctggaaggccaccactgTctacaatttaaaacaaacag	6	10	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:78432435T>C	ENST00000370768.2	-	7	497	c.416A>G	c.(415-417)gAc>gGc	p.D139G	FUBP1_ENST00000370767.1_Splice_Site_p.D139G|FUBP1_ENST00000436586.2_Splice_Site_p.D160G	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	139	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						GCCACCACTGTCTACAATTTA	0.323			"F, N"		oligodendroglioma																																p.D139G		Atlas-SNP	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1	112	.	0			c.A416G						.						54	57	56					1																	78432435		2203	4300	6503	SO:0001630	splice_region_variant	8880	exon7			CCACTGTCTACAA	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.416-1A>G	chr1.hg19:g.78432435T>C		69.0	0.0		87.0	4.0	NM_003902	Q12828	Missense_Mutation	SNP	ENST00000370768.2	hg19	CCDS683.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845678	0.91197	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586;ENST00000421641	T;T;T;T	0.46063	1.4;1.4;1.4;0.88	5.67	5.67	0.87782	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.042455	0.85682	N	0.000000	T	0.49304	0.1549	M	0.71036	2.16	0.80722	D	1	B;P	0.46952	0.337;0.887	B;P	0.53722	0.346;0.733	T	0.54695	-0.8255	10	0.72032	D	0.01	.	16.1994	0.82060	0.0:0.0:0.0:1.0	.	160;139	B4DT31;Q96AE4	.;FUBP1_HUMAN	G	138;139;139;138;160;159	ENSP00000359803:D139G;ENSP00000359804:D139G;ENSP00000389536:D160G;ENSP00000402630:D159G	ENSP00000294623:D138G	D	-	2	0	FUBP1	78205023	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	5.919000	0.70005	2.281000	0.76405	0.528000	0.53228	GAC	.	.		0.323	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902	Missense_Mutation	C	78432435	T	C	78432435	5	2	103	1	0	0	0	0	0	0	1	0	6100	1681	58	2	1574	2	FUBP1	1	78432435	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2748207	78432435	170818186	42	14665										
BCL10	8915	hgsc.bcm.edu	37	chr1	85733444	85733444	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccaggtctgggaagtgtagTtgaagagaagatggtatttt	14	4	1	3	rs556621354	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:85733444T>C	ENST00000370580.1	-	3	1305	c.568A>G	c.(568-570)Act>Gct	p.T190A		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	190					adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		GGAAGTGTAGTTGAAGAGAAG	0.448			T	IGH@	MALT								T|||	2	0.000399361	0	0	5008	,	,		14905	0		0	False		,,,				2504	0.002				p.T190A	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.A568G						.						96	102	100					1																	85733444		2203	4300	6503	SO:0001583	missense	8915	exon3			GTGTAGTTGAAGA	AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"CARD-like apoptotic protein", "CARD-containing apoptotic signaling protein", "CARD containing molecule enhancing NF-kB", "caspase-recruiting domain-containing protein", "CARD-containing proapoptotic protein"	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.568A>G	chr1.hg19:g.85733444T>C	ENSP00000359612:p.Thr190Ala	74.0	0.0		77.0	15.0	NM_003921	Q5VUF1	Missense_Mutation	SNP	ENST00000370580.1	hg19	CCDS704.1	.	.	.	.	.	.	.	.	.	.	T	8.104	0.777202	0.16120	.	.	ENSG00000142867	ENST00000370580;ENST00000271015	.	.	.	5.82	-1.91	0.07641	.	0.499537	0.23742	N	0.045015	T	0.04363	0.0120	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38735	-0.9647	9	0.30854	T	0.27	-0.3714	6.7252	0.23353	0.1519:0.5344:0.0:0.3137	.	190	O95999	BCL10_HUMAN	A	190	.	ENSP00000271015:T190A	T	-	1	0	BCL10	85506032	0.056000	0.20664	0.026000	0.17262	0.985000	0.73830	0.587000	0.23909	-0.344000	0.08338	0.383000	0.25322	ACT	.	.		0.448	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921		C	85733444	T	C	85733444	3	2	103	1	0	0	0	0	1	0	0	0	1362	1725	60	2	137	2	BCL10	1	85733444	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	7301009	85733444	163517177	43	14666										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86916286	86916286	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatggaatttactcgaggtaTtttttctcctttgctgcaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:86916286delT	ENST00000370565.4	+	12	2187	c.2025delT	c.(2023-2025)tatfs	p.Y675fs	CLCA2_ENST00000498802.1_3'UTR	NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	675					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		ACTCGAGGTATTTTTTCTCCT	0.358																																					p.Y675fs	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-INDEL	.											.	CLCA2	102	.	0			c.2024delA						.						102	104	103					1																	86916286		2203	4300	6503	SO:0001589	frameshift_variant	9635	exon12			.		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2025delT	chr1.hg19:g.86916286delT	ENSP00000359596:p.Tyr675fs	78.0	0.0		128.0	11.0	NM_006536	A8K2T3|Q9Y6N2	Frame_Shift_Del	DEL	ENST00000370565.4	hg19	CCDS708.1																																																																																			.	.		0.358	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		-	86916286	T	-	86916286	7	5	103	1	0	1	0	1	0	0	0	0	3460	1500	52	0	2071	0	CLCA2	1	86916286	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1182842	86916286	162334335	44	14667										
CLCA1	1179	hgsc.bcm.edu	37	chr1	86957056	86957056	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctctcagcgctccatccaggTtggagttcttaatctttggt	9	11	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:86957056T>C	ENST00000234701.3	+	10	1815		c.e10+2		CLCA1_ENST00000394711.1_Splice_Site			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1						calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		TCCATCCAGGTTGGAGTTCTT	0.398																																					.		Atlas-SNP	.											.	CLCA1	109	.	0			c.1464+2T>C						.						87	86	86					1																	86957056		2203	4300	6503	SO:0001630	splice_region_variant	1179	exon9			TCCAGGTTGGAGT		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.1464+2T>C	chr1.hg19:g.86957056T>C		82.0	0.0		108.0	5.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Splice_Site	SNP	ENST00000234701.3	hg19	CCDS709.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336922	0.60963	.	.	ENSG00000016490	ENST00000234701;ENST00000394711;ENST00000539889	.	.	.	5.92	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9498	0.47323	0.0:0.074:0.0:0.926	.	.	.	.	.	-1	.	.	.	+	.	.	CLCA1	86729644	1.000000	0.71417	0.939000	0.37840	0.794000	0.44872	4.835000	0.62781	1.073000	0.40885	0.533000	0.62120	.	.	.		0.398	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285	Intron	C	86957056	T	C	86957056	5	2	103	1	0	0	0	0	0	0	1	0	3459	1739	60	2	1500	2	CLCA1	1	86957056	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	40770	86957056	162293565	45	14668										
PKN2	5586	hgsc.bcm.edu	37	chr1	89236054	89236054	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggatcggaaactccatggtaCagctcagcaactgctccagg	11	12	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:89236054C>A	ENST00000370521.3	+	4	883	c.524C>A	c.(523-525)aCa>aAa	p.T175K	PKN2_ENST00000316005.7_Missense_Mutation_p.T175K|PKN2_ENST00000370513.5_Missense_Mutation_p.T175K|PKN2_ENST00000370505.3_Missense_Mutation_p.T18K	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	175					apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		CTCCATGGTACAGCTCAGCAA	0.353																																					p.T175K		Atlas-SNP	.											.	PKN2	109	.	0			c.C524A						.						98	92	94					1																	89236054		1890	4110	6000	SO:0001583	missense	5586	exon4			ATGGTACAGCTCA	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"cardiolipin-activated protein kinase Pak2"	602549	"protein kinase C-like 2"	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.524C>A	chr1.hg19:g.89236054C>A	ENSP00000359552:p.Thr175Lys	132.0	0.0		141.0	34.0	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	hg19	CCDS714.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.980601	0.74474	.	.	ENSG00000065243	ENST00000370521;ENST00000316005;ENST00000370505;ENST00000370513	T;T;T;T	0.28895	2.42;2.42;1.59;2.42	5.45	5.45	0.79879	.	0.000000	0.46442	U	0.000300	T	0.39358	0.1075	M	0.80616	2.505	0.80722	D	1	P;P;P;P	0.45126	0.851;0.586;0.82;0.608	P;B;B;B	0.47603	0.551;0.236;0.397;0.402	T	0.32903	-0.9889	10	0.48119	T	0.1	.	19.6523	0.95822	0.0:1.0:0.0:0.0	.	175;175;175;175	B4DTP5;E7ESL7;Q16513;B1AL79	.;.;PKN2_HUMAN;.	K	175;175;18;175	ENSP00000359552:T175K;ENSP00000317851:T175K;ENSP00000359536:T18K;ENSP00000359544:T175K	ENSP00000317851:T175K	T	+	2	0	PKN2	89008642	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.445000	0.80570	2.706000	0.92434	0.655000	0.94253	ACA	.	.		0.353	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		A	89236054	C	A	89236054	3	1	103	1	0	0	0	0	1	0	0	0	11989	478	17	3	538	3	PKN2	1	89236054	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	2278998	89236054	160014567	46	14669										
GBP7	388646	hgsc.bcm.edu	37	chr1	89613446	89613446	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcagcacaaagtcttccttcTttttctccatggtgtcctgc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:89613446delT	ENST00000294671.2	-	8	1307	c.1169delA	c.(1168-1170)aagfs	p.K391fs		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	391						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		GTCTTCCTTCTTTTTCTCCAT	0.438																																					p.K390fs		Atlas-INDEL	.											GBP7,NS,carcinoma,-1,1	GBP7	57	.	0			c.1170delG						.						115	113	113					1																	89613446		2203	4300	6503	SO:0001589	frameshift_variant	388646	exon8			.	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1169delA	chr1.hg19:g.89613446delT	ENSP00000294671:p.Lys391fs	122.0	0.0		183.0	11.0	NM_207398		Frame_Shift_Del	DEL	ENST00000294671.2	hg19	CCDS720.1																																																																																			.	.		0.438	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		-	89613446	T	-	89613446	7	5	103	1	0	1	0	1	0	0	0	0	6287	1609	56	0	763	0	GBP7	1	89613446	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	377392	89613446	159637175	47	14670										
HFM1	164045	hgsc.bcm.edu	37	chr1	91846518	91846518	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgaaatatggaaattctttgAaaatacttctaaattttgcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:91846518delA	ENST00000370425.3	-	7	922	c.824delT	c.(823-825)ttcfs	p.F275fs	HFM1_ENST00000370424.3_Intron|HFM1_ENST00000294696.5_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	275					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AAATTCTTTGAAAATACTTCT	0.234																																					p.F275fs		Atlas-INDEL	.											.	HFM1	188	.	0			c.825delC						.						56	67	63					1																	91846518		2198	4293	6491	SO:0001589	frameshift_variant	164045	exon7			.	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.824delT	chr1.hg19:g.91846518delA	ENSP00000359454:p.Phe275fs	150.0	0.0		170.0	11.0	NM_001017975	B1B0B6|Q8N9Q0	Frame_Shift_Del	DEL	ENST00000370425.3	hg19	CCDS30769.2																																																																																			.	.		0.234	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		-	91846518	A	-	91846518	7	5	103	1	0	1	0	1	0	0	0	0	7092	246	9	0	3615	0	HFM1	1	91846518	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2233072	91846518	157404103	48	14671										
DNTTIP2	30836	hgsc.bcm.edu	37	chr1	94341253	94341253	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggttctcttgttagactgtAgtttatctgcattaaaatta	8	5	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:94341253A>G	ENST00000436063.2	-	3	1811	c.1754T>C	c.(1753-1755)cTa>cCa	p.L585P	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	585	TdBR region; mediates interaction with DNTT.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		GTTAGACTGTAGTTTATCTGC	0.363																																					p.L585P		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.T1754C						.						236	203	213					1																	94341253		1839	4085	5924	SO:0001583	missense	30836	exon3			GACTGTAGTTTAT	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"acidic 82 kDa protein mRNA"	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.1754T>C	chr1.hg19:g.94341253A>G	ENSP00000411010:p.Leu585Pro	41.0	0.0		81.0	4.0	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	hg19	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.363373	0.24684	.	.	ENSG00000067334	ENST00000436063	T	0.15487	2.42	5.93	2.28	0.28536	.	0.567223	0.16965	N	0.192349	T	0.03651	0.0104	L	0.39898	1.24	0.23704	N	0.997067	B	0.06786	0.001	B	0.08055	0.003	T	0.41910	-0.9482	10	0.25751	T	0.34	.	4.3301	0.11059	0.3615:0.0:0.1381:0.5004	.	585	Q5QJE6	TDIF2_HUMAN	P	585	ENSP00000411010:L585P	ENSP00000411010:L585P	L	-	2	0	DNTTIP2	94113841	1.000000	0.71417	0.421000	0.26609	0.963000	0.63663	2.802000	0.47916	0.443000	0.26582	0.533000	0.62120	CTA	.	.		0.363	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		G	94341253	A	G	94341253	3	3	103	1	0	0	0	0	1	0	0	0	4684	420	15	2	536	2	DNTTIP2	1	94341253	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2494735	94341253	154909368	49	14672										
SLC35A3	23443	hgsc.bcm.edu	37	chr1	100483342	100483342	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttatcaacattgatctcctaTttttggcttcaagattttgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:100483342delT	ENST00000370155.3	+	7	1250	c.858delT	c.(856-858)tatfs	p.Y286fs	SLC35A3_ENST00000427993.2_Frame_Shift_Del_p.Y286fs|SLC35A3_ENST00000370156.3_3'UTR|SLC35A3_ENST00000465289.1_Intron|SLC35A3_ENST00000370153.1_Frame_Shift_Del_p.Y328fs	NM_012243.1	NP_036375.1	Q9Y2D2	S35A3_HUMAN	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3	286					transmembrane transport (GO:0055085)|UDP-N-acetylglucosamine metabolic process (GO:0006047)|UDP-N-acetylglucosamine transport (GO:0015788)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)|UDP-N-acetylglucosamine transmembrane transporter activity (GO:0005462)			biliary_tract(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	11		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.124)|all cancers(265;0.198)|Lung(183;0.199)		TGATCTCCTATTTTTGGCTTC	0.299																																					p.Y328fs	Ovarian(7;298 356 944 2149 6911)	Atlas-INDEL	.											.	SLC35A3	25	.	0			c.983delA						.						65	67	66					1																	100483342		2202	4288	6490	SO:0001589	frameshift_variant	23443	exon7			.	AB021981	CCDS762.1, CCDS60204.1, CCDS60205.1	1p21	2013-05-22			ENSG00000117620	ENSG00000117620		"Solute carriers"	11023	protein-coding gene	gene with protein product		605632	"solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3"			10393322	Standard	NM_001271685		Approved		uc001dsr.2	Q9Y2D2	OTTHUMG00000010805	ENST00000370155.3:c.858delT	chr1.hg19:g.100483342delT	ENSP00000359174:p.Tyr286fs	194.0	0.0		186.0	12.0	NM_001271685	A8K3F8|D3DT54|Q68CR2|Q9BSB7	Frame_Shift_Del	DEL	ENST00000370155.3	hg19	CCDS762.1																																																																																			.	.		0.299	SLC35A3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000029783.1	NM_012243		-	100483342	T	-	100483342	7	5	103	1	0	1	0	1	0	0	0	0	14587	1500	52	0	880	0	SLC35A3	1	100483342	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	6142089	100483342	148767279	50	14673										
HIAT1	64645	hgsc.bcm.edu	37	chr1	100525518	100525518	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccttcttgctgctaacggtgTttttcacatgtgccccaatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:100525518delT	ENST00000370152.3	+	4	464	c.328delT	c.(328-330)tttfs	p.F111fs	RP4-714D9.2_ENST00000432294.1_RNA	NM_033055.2	NP_149044.2	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	111					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|skin(1)	16		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		GCTAACGGTGTTTTTCACATG	0.383																																					p.V109fs		Atlas-INDEL	.											.	HIAT1	46	.	0			c.327delG						.						235	222	226					1																	100525518		2203	4300	6503	SO:0001589	frameshift_variant	64645	exon4			.	AK096669	CCDS763.1	1p21.3	2008-02-05			ENSG00000156875	ENSG00000156875			23363	protein-coding gene	gene with protein product						9299464	Standard	NM_033055		Approved	DKFZP564L0864	uc001dst.3	Q96MC6	OTTHUMG00000010755	ENST00000370152.3:c.328delT	chr1.hg19:g.100525518delT	ENSP00000359171:p.Phe111fs	177.0	0.0		194.0	12.0	NM_033055	Q6P2N7|Q8N8K2|Q8NBV3|Q96NY0|Q9NT25	Frame_Shift_Del	DEL	ENST00000370152.3	hg19	CCDS763.1																																																																																			.	.		0.383	HIAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029657.1	NM_033055		-	100525518	T	-	100525518	7	5	103	1	0	1	0	1	0	0	0	0	7106	1725	60	0	342	0	HIAT1	1	100525518	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	42176	100525518	148725103	51	14674										
SASS6	163786	hgsc.bcm.edu	37	chr1	100587007	100587007	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggtaaaagttttagtgagAggtgtgtaagatgcttaaaa	12	2	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:100587007A>G	ENST00000287482.5	-	5	550	c.410T>C	c.(409-411)cTc>cCc	p.L137P	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_5'UTR	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	137					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		TTTTAGTGAGAGGTGTGTAAG	0.338																																					p.L137P		Atlas-SNP	.											.	SASS6	61	.	0			c.T410C						.						73	75	75					1																	100587007		2203	4299	6502	SO:0001583	missense	163786	exon5			AGTGAGAGGTGTG	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.410T>C	chr1.hg19:g.100587007A>G	ENSP00000287482:p.Leu137Pro	87.0	0.0		124.0	5.0	NM_194292	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	hg19	CCDS764.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.225033	0.79576	.	.	ENSG00000156876	ENST00000287482;ENST00000539329	T	0.39056	1.1	5.61	5.61	0.85477	.	0.128399	0.52532	D	0.000061	T	0.65238	0.2672	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73553	-0.3946	10	0.87932	D	0	-7.8256	16.1025	0.81194	1.0:0.0:0.0:0.0	.	137	Q6UVJ0	SAS6_HUMAN	P	137;110	ENSP00000287482:L137P	ENSP00000287482:L137P	L	-	2	0	SASS6	100359595	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.937000	0.87672	2.254000	0.74563	0.533000	0.62120	CTC	.	.		0.338	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292		G	100587007	A	G	100587007	3	3	103	1	0	0	0	0	1	0	0	0	13865	304	11	2	1615	2	SASS6	1	100587007	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	61489	100587007	148663614	52	14675										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103453237	103453237	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggtctccagttgggcctgcTcgacctttgggtccttcagg	14	12	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:103453237T>C	ENST00000370096.3	-	30	2766	c.2454A>G	c.(2452-2454)cgA>cgG	p.R818R	COL11A1_ENST00000358392.2_Silent_p.R830R|COL11A1_ENST00000512756.1_Silent_p.R702R|COL11A1_ENST00000353414.4_Silent_p.R779R	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	818	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTGGGCCTGCTCGACCTTTGG	0.478																																					p.R830R		Atlas-SNP	.											COL11A1_ENST00000370096,NS,carcinoma,0,2	COL11A1	972	.	0			c.A2490G						.						92	87	88					1																	103453237		2203	4300	6503	SO:0001819	synonymous_variant	1301	exon30			GCCTGCTCGACCT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2454A>G	chr1.hg19:g.103453237T>C		52.0	0.0		71.0	4.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	8.092	0.774792	0.16051	.	.	ENSG00000060718	ENST00000370090	.	.	.	4.39	0.723	0.18231	.	.	.	.	.	T	0.22666	0.0547	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09773	-1.0659	7	0.49607	T	0.09	.	3.6269	0.08116	0.3362:0.1692:0.0:0.4946	.	33	F5H5Z5	.	G	33	.	ENSP00000359108:E33G	E	-	2	0	COL11A1	103225825	1.000000	0.71417	0.999000	0.59377	0.733000	0.41908	0.666000	0.25097	0.012000	0.14892	0.377000	0.23210	GAG	.	.		0.478	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		C	103453237	T	C	103453237	2	2	103	1	0	0	0	0	0	0	0	1	3669	1538	54	2		2	COL11A1	1	103453237	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2866230	103453237	145797384	53	14676										
VAV3	10451	hgsc.bcm.edu	37	chr1	108226149	108226149	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agttcttcgcagtccattggTccgtttctgtgcagtaaagt	10	9	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:108226149T>C	ENST00000370056.4	-	19	2012	c.1738A>G	c.(1738-1740)Acc>Gcc	p.T580A	VAV3_ENST00000371846.4_Missense_Mutation_p.T515A|VAV3_ENST00000527011.1_Missense_Mutation_p.T580A|VAV3_ENST00000544443.1_Intron|VAV3_ENST00000415432.2_Missense_Mutation_p.T20A|VAV3_ENST00000343258.4_5'UTR	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	580	Sufficient for interaction with ROS1.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		AGTCCATTGGTCCGTTTCTGT	0.363																																					p.T580A		Atlas-SNP	.											.	VAV3	176	.	0			c.A1738G						.						131	108	116					1																	108226149		2203	4300	6503	SO:0001583	missense	10451	exon19			CATTGGTCCGTTT	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1738A>G	chr1.hg19:g.108226149T>C	ENSP00000359073:p.Thr580Ala	108.0	0.0		130.0	7.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.	.	.	.	.	.	.	.	.	.	T	8.594	0.885170	0.17540	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000415432;ENST00000371846	T;T;T;T	0.77750	0.22;0.23;1.96;-1.12	5.5	1.84	0.25277	Src homology-3 domain (1);	0.536026	0.21020	N	0.081522	T	0.40956	0.1138	L	0.43152	1.355	0.29564	N	0.850424	B;B;B;B;B	0.14012	0.009;0.003;0.001;0.0;0.002	B;B;B;B;B	0.11329	0.004;0.006;0.002;0.001;0.002	T	0.14062	-1.0486	10	0.08599	T	0.76	.	5.2311	0.15422	0.0:0.1788:0.168:0.6532	.	580;580;515;580;20	B7ZLR1;E9PQ97;B4DHL6;Q9UKW4;Q9UKW4-3	.;.;.;VAV3_HUMAN;.	A	580;580;20;515	ENSP00000359073:T580A;ENSP00000432540:T580A;ENSP00000394897:T20A;ENSP00000360912:T515A	ENSP00000359073:T580A	T	-	1	0	VAV3	108027672	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.567000	0.23608	0.928000	0.37168	0.477000	0.44152	ACC	.	.		0.363	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		C	108226149	T	C	108226149	3	2	103	1	0	0	0	0	1	0	0	0	17148	1667	58	2	841	2	VAV3	1	108226149	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4772912	108226149	141024472	54	14677										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109810210	109810210	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatgagcacagggggtggctCcccccaaacctcttcaactg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:109810210delC	ENST00000271332.3	+	16	6115	c.6054delC	c.(6052-6054)ctcfs	p.L2018fs		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2018					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GGGGGTGGCTCCCCCCAAACC	0.587																																					p.L2018fs	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-INDEL	.											.	CELSR2	228	.	0			c.6053delT						.						105	103	104					1																	109810210		2203	4300	6503	SO:0001589	frameshift_variant	1952	exon16			.	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.6054delC	chr1.hg19:g.109810210delC	ENSP00000271332:p.Leu2018fs	157.0	0.0		145.0	11.0	NM_001408	Q5T2Y7|Q92566	Frame_Shift_Del	DEL	ENST00000271332.3	hg19	CCDS796.1																																																																																			.	.		0.587	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		-	109810210	C	-	109810210	7	5	103	1	0	1	0	1	0	0	0	0	3224	842	30	0	6116	0	CELSR2	1	109810210	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1584061	109810210	139440411	55	14678										
PSRC1	84722	hgsc.bcm.edu	37	chr1	109823600	109823600	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcagctgctccctgcggccGgggcaggcgttgagagttgc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:109823600delG	ENST00000438534.2	-	5	931	c.793delC	c.(793-795)cggfs	p.R265fs	PSRC1_ENST00000369903.2_Frame_Shift_Del_p.R235fs|PSRC1_ENST00000409267.1_Frame_Shift_Del_p.R235fs|PSRC1_ENST00000369904.3_Intron|PSRC1_ENST00000369907.3_Frame_Shift_Del_p.R235fs|PSRC1_ENST00000369909.2_Frame_Shift_Del_p.R235fs|PSRC1_ENST00000409138.2_Frame_Shift_Del_p.R265fs	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	265	Pro/Ser-rich.				microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		CCCTGCGGCCGGGGCAGGCGT	0.642																																					p.R235fs		Atlas-INDEL	.											.	PSRC1	12	.	0			c.704delG						.						39	43	42					1																	109823600		2203	4300	6503	SO:0001589	frameshift_variant	84722	exon6			.		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"differential display and activated by p53"	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.793delC	chr1.hg19:g.109823600delG	ENSP00000413591:p.Arg265fs	132.0	0.0		163.0	10.0	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Frame_Shift_Del	DEL	ENST00000438534.2	hg19																																																																																				.	.		0.642	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636		-	109823600	G	-	109823600	7	5	103	1	0	1	0	1	0	0	0	0	12731	1115	39	0	342	0	PSRC1	1	109823600	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	13390	109823600	139427021	56	14679										
PSMA5	5686	hgsc.bcm.edu	37	chr1	109954503	109954503	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acaaaatggtacttacagctGgggtcctttctcatcaactc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:109954503delG	ENST00000271308.4	-	6	474	c.454delC	c.(454-456)cagfs	p.Q152fs	PSMA5_ENST00000490870.1_5'UTR|PSMA5_ENST00000538610.1_Frame_Shift_Del_p.Q94fs	NM_002790.3	NP_002781.2	P28066	PSA5_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 5	152					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)	5		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.045)|Colorectal(144;0.116)|Epithelial(280;0.187)|all cancers(265;0.196)|LUSC - Lung squamous cell carcinoma(189;0.235)		ACTTACAGCTGGGGTCCTTTC	0.373																																					p.Q152fs		Atlas-INDEL	.											.	PSMA5	14	.	0			c.455delA						.						61	64	63					1																	109954503		2203	4300	6503	SO:0001589	frameshift_variant	5686	exon6			.	X61970	CCDS799.1, CCDS55619.1	1p13	2008-02-05			ENSG00000143106	ENSG00000143106		"Proteasome (prosome, macropain) subunits"	9534	protein-coding gene	gene with protein product		176844				1888762	Standard	NM_002790		Approved	ZETA	uc001dxn.3	P28066	OTTHUMG00000012001	ENST00000271308.4:c.454delC	chr1.hg19:g.109954503delG	ENSP00000271308:p.Gln152fs	184.0	0.0		265.0	16.0	NM_002790	B2R8F6|B4E2V4|Q3T1C1|Q6IBF7	Frame_Shift_Del	DEL	ENST00000271308.4	hg19	CCDS799.1																																																																																			.	.		0.373	PSMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033192.2	NM_002790		-	109954503	G	-	109954503	7	5	103	1	0	1	0	1	0	0	0	0	12682	1357	47	0	287	0	PSMA5	1	109954503	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	130903	109954503	139296118	57	14680										
ATXN7L2	127002	hgsc.bcm.edu	37	chr1	110033680	110033680	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgcctgcccagcctccatgCcccccaccaaggacaacctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:110033680delC	ENST00000369870.3	+	10	1510	c.1495delC	c.(1495-1497)cccfs	p.P500fs	ATXN7L2_ENST00000459635.1_3'UTR|CYB561D1_ENST00000393709.3_5'Flank	NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	500								p.T501fs*21(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		AGCCTCCATGCCCCCCACCAA	0.662											OREG0013635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M498fs		Atlas-INDEL	.											.,1	ATXN7L2	60	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1494delG						.						37	42	41					1																	110033680		2203	4300	6503	SO:0001589	frameshift_variant	127002	exon10			.	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.1495delC	chr1.hg19:g.110033680delC	ENSP00000358886:p.Pro500fs	164.0	0.0	1424	162.0	11.0	NM_153340		Frame_Shift_Del	DEL	ENST00000369870.3	hg19	CCDS30794.1																																																																																			.	.		0.662	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		-	110033680	C	-	110033680	7	5	103	1	0	1	0	1	0	0	0	0	1217	739	26	0	1533	0	ATXN7L2	1	110033680	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	79177	110033680	139216941	58	14681										
CSF1	1435	hgsc.bcm.edu	37	chr1	110466713	110466713	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagtccgagggatccttcagCccgcagctccaggagtctgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:110466713delC	ENST00000329608.6	+	6	1861	c.1470delC	c.(1468-1470)agcfs	p.S490fs	CSF1_ENST00000369802.3_Frame_Shift_Del_p.S490fs|CSF1_ENST00000344188.5_Frame_Shift_Del_p.S374fs|CSF1_ENST00000369801.1_Frame_Shift_Del_p.S374fs|CSF1_ENST00000420111.2_Frame_Shift_Del_p.S192fs	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	490					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|developmental process involved in reproduction (GO:0003006)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary duct terminal end bud growth (GO:0060763)|mammary gland fat development (GO:0060611)|monocyte activation (GO:0042117)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of macrophage derived foam cell differentiation (GO:0010743)|regulation of ossification (GO:0030278)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|macrophage colony-stimulating factor receptor binding (GO:0005157)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		GATCCTTCAGCCCGCAGCTCC	0.627																																					p.S490fs		Atlas-INDEL	.											.	CSF1	40	.	0			c.1469delG						.						53	56	55					1																	110466713		2203	4300	6503	SO:0001589	frameshift_variant	1435	exon6			.	BC021117	CCDS816.1, CCDS817.1, CCDS30797.1	1p13.3	2012-09-20			ENSG00000184371	ENSG00000184371			2432	protein-coding gene	gene with protein product		120420				1540160	Standard	NM_172210		Approved	M-CSF, MCSF, MGC31930	uc001dyw.4	P09603	OTTHUMG00000011646	ENST00000329608.6:c.1470delC	chr1.hg19:g.110466713delC	ENSP00000327513:p.Ser490fs	135.0	0.0		177.0	11.0	NM_000757	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Frame_Shift_Del	DEL	ENST00000329608.6	hg19	CCDS816.1																																																																																			.	.		0.627	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757		-	110466713	C	-	110466713	7	5	103	1	0	1	0	1	0	0	0	0	3933	738	26	0	1492	0	CSF1	1	110466713	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	433033	110466713	138783908	59	14682										
OVGP1	5016	hgsc.bcm.edu	37	chr1	111957947	111957947	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatgacagccaaaattgtggTaaagaagttgaactgaactc	10	6	0	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:111957947T>C	ENST00000369732.3	-	11	1231	c.1176A>G	c.(1174-1176)ttA>ttG	p.L392L	OVGP1_ENST00000540696.1_3'UTR	NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	392					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		AAAATTGTGGTAAAGAAGTTG	0.418																																					p.L392L		Atlas-SNP	.											.	OVGP1	177	.	0			c.A1176G						.						46	44	45					1																	111957947		2203	4300	6503	SO:0001819	synonymous_variant	5016	exon11			TTGTGGTAAAGAA	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"Mucins"	8524	protein-coding gene	gene with protein product	"oviductin"	603578	"mucin 9"	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1176A>G	chr1.hg19:g.111957947T>C		84.0	0.0		95.0	29.0	NM_002557	A0AV19|B9EGE1|Q15841	Silent	SNP	ENST00000369732.3	hg19	CCDS834.1																																																																																			.	.		0.418	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		C	111957947	T	C	111957947	2	2	103	1	0	0	0	0	0	0	0	1	11334	1635	57	2		2	OVGP1	1	111957947	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1491234	111957947	137292674	60	14683										
MOV10	4343	hgsc.bcm.edu	37	chr1	113243060	113243060	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccccacagccatgactacctCccccaggagcgggagggtga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:113243060delC	ENST00000413052.2	+	21	3333	c.2943delC	c.(2941-2943)ctcfs	p.L981fs	RP11-426L16.10_ENST00000471038.2_5'Flank|MOV10_ENST00000369644.1_Frame_Shift_Del_p.L925fs|MOV10_ENST00000357443.2_Frame_Shift_Del_p.L981fs|MOV10_ENST00000369645.1_Frame_Shift_Del_p.L981fs|MOV10_ENST00000468624.1_3'UTR	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	981					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		ATGACTACCTCCCCCAGGAGC	0.612																																					p.L981fs		Atlas-INDEL	.											.	MOV10	74	.	0			c.2942delT						.						74	77	76					1																	113243060		2203	4300	6503	SO:0001589	frameshift_variant	4343	exon21			.	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 113"	610742	"Mov10 (Moloney leukemia virus 10, mouse) homolog", "Mov10, Moloney leukemia virus 10, homolog (mouse)"			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.2943delC	chr1.hg19:g.113243060delC	ENSP00000399797:p.Leu981fs	169.0	0.0		173.0	12.0	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Frame_Shift_Del	DEL	ENST00000413052.2	hg19	CCDS853.1																																																																																			.	.		0.612	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		-	113243060	C	-	113243060	7	5	103	1	0	1	0	1	0	0	0	0	9727	842	30	0	3021	0	MOV10	1	113243060	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1285113	113243060	136007561	61	14684										
PHTF1	10745	hgsc.bcm.edu	37	chr1	114252943	114252943	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggtattcacatgggcccccTcactgtcactggtgacagat	11	12	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:114252943T>C	ENST00000369604.1	-	11	1685	c.1202A>G	c.(1201-1203)gAg>gGg	p.E401G	PHTF1_ENST00000474926.1_5'UTR|PHTF1_ENST00000393357.2_Missense_Mutation_p.E401G|PHTF1_ENST00000447664.2_3'UTR|PHTF1_ENST00000357783.2_Missense_Mutation_p.E401G|PHTF1_ENST00000369596.2_Missense_Mutation_p.E348G|PHTF1_ENST00000369600.1_Missense_Mutation_p.E348G|PHTF1_ENST00000369598.1_Missense_Mutation_p.E356G			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	401					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATGGGCCCCCTCACTGTCACT	0.522																																					p.E401G		Atlas-SNP	.											.	PHTF1	69	.	0			c.A1202G						.						85	77	80					1																	114252943		2203	4300	6503	SO:0001583	missense	10745	exon10			GCCCCCTCACTGT	AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.1202A>G	chr1.hg19:g.114252943T>C	ENSP00000358617:p.Glu401Gly	144.0	0.0		136.0	6.0	NM_006608	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Missense_Mutation	SNP	ENST00000369604.1	hg19	CCDS861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	29.8|29.8	5.039560|5.039560	0.93630|0.93630	.|.	.|.	ENSG00000116793|ENSG00000116793	ENST00000369597;ENST00000393357;ENST00000369596;ENST00000369598;ENST00000369600;ENST00000369604;ENST00000357783|ENST00000412670	.|.	.|.	.|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	0.217764|.	0.46442|.	D|.	0.000282|.	T|T	0.47691|0.47691	0.1459|0.1459	L|L	0.38531|0.38531	1.155|1.155	0.80722|0.80722	D|D	1|1	D;P;D|.	0.58268|.	0.969;0.952;0.982|.	P;P;P|.	0.58970|.	0.585;0.724;0.849|.	T|T	0.45425|0.45425	-0.9262|-0.9262	9|5	0.87932|.	D|.	0|.	-24.3535|-24.3535	16.0225|16.0225	0.80509|0.80509	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	401;156;401|.	Q9UMS5;Q5TCR1;Q9UMS5-2|.	PHTF1_HUMAN;.;.|.	G|G	356;401;348;356;348;401;401|157	.|.	ENSP00000350428:E401G|.	E|R	-|-	2|1	0|2	PHTF1|PHTF1	114054466|114054466	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.944000|0.944000	0.59088|0.59088	5.033000|5.033000	0.64146|0.64146	2.198000|2.198000	0.70561|0.70561	0.533000|0.533000	0.62120|0.62120	GAG|AGG	.	.		0.522	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608		C	114252943	T	C	114252943	3	2	103	1	0	0	0	0	1	0	0	0	11871	1551	54	2	1122	2	PHTF1	1	114252943	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1009883	114252943	134997678	62	14685										
TRIM33	51592	hgsc.bcm.edu	37	chr1	114942160	114942160	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atttggtagtgttgggaatgTtttttctgaagcttcttttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:114942160delT	ENST00000358465.2	-	18	3122	c.3039delA	c.(3037-3039)aaafs	p.K1013fs	TRIM33_ENST00000369543.2_Frame_Shift_Del_p.K1013fs|TRIM33_ENST00000450349.2_Frame_Shift_Del_p.K645fs	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	1013	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.H1014fs*10(1)		breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTGGGAATGTTTTTTCTGAA	0.348			T	RET	papillary thyroid																																p.H1014fs		Atlas-INDEL	.		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	.,1	TRIM33	115	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.3040delC						.						144	155	152					1																	114942160		2203	4300	6503	SO:0001589	frameshift_variant	51592	exon18			.	AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.3039delA	chr1.hg19:g.114942160delT	ENSP00000351250:p.Lys1013fs	207.0	0.0		188.0	13.0	NM_033020	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Frame_Shift_Del	DEL	ENST00000358465.2	hg19	CCDS872.1																																																																																			.	.		0.348	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		-	114942160	T	-	114942160	7	5	103	1	0	1	0	1	0	0	0	0	16522	1722	60	0	356	0	TRIM33	1	114942160	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	689217	114942160	134308461	63	14686										
SYCP1	6847	hgsc.bcm.edu	37	chr1	115487538	115487538	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgaagcagtaaaattacagAaagaaattgataagcgatgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:115487538delA	ENST00000369522.3	+	25	2329	c.2089delA	c.(2089-2091)aaafs	p.K697fs	SYCP1_ENST00000369518.1_Frame_Shift_Del_p.K697fs	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	697					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAAATTACAGAAAGAAATTGA	0.249																																					p.Q696fs		Atlas-INDEL	.											.	SYCP1	149	.	0			c.2088delG						.						37	39	38					1																	115487538		2198	4278	6476	SO:0001589	frameshift_variant	6847	exon25			.	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2089delA	chr1.hg19:g.115487538delA	ENSP00000358535:p.Lys697fs	122.0	0.0		153.0	10.0	NM_003176	O14963|Q5VXJ6	Frame_Shift_Del	DEL	ENST00000369522.3	hg19	CCDS879.1																																																																																			.	.		0.249	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		-	115487538	A	-	115487538	7	5	103	1	0	1	0	1	0	0	0	0	15446	247	9	0	2183	0	SYCP1	1	115487538	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	545378	115487538	133763083	64	14687										
BCL9	607	hgsc.bcm.edu	37	chr1	147084890	147084890	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggagcatggggctgaagaatGgggctggaaatggtgccaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:147084890delG	ENST00000234739.3	+	5	1002	c.262delG	c.(262-264)gggfs	p.G88fs	BCL9_ENST00000473292.1_Intron	NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	88					canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					GCTGAAGAATGGGGCTGGAAA	0.582			T	"IGH@, IGL@"	B-ALL																																p.N87fs		Atlas-INDEL	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.261delT						.						39	43	42					1																	147084890		2203	4300	6503	SO:0001589	frameshift_variant	607	exon5			.	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.262delG	chr1.hg19:g.147084890delG	ENSP00000234739:p.Gly88fs	108.0	0.0		244.0	16.0	NM_004326	Q5T489	Frame_Shift_Del	DEL	ENST00000234739.3	hg19	CCDS30833.1																																																																																			.	.		0.582	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		-	147084890	G	-	147084890	7	5	103	1	0	1	0	1	0	0	0	0	1381	1348	47	0	268	0	BCL9	1	147084890	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	31597352	147084890	102165731	65	14688										
SF3B4	10262	hgsc.bcm.edu	37	chr1	149895562	149895562	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggagggccagtgtatccatGggggggcatcagtggaggag					rs387907187		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:149895562delG	ENST00000271628.8	-	6	1731	c.1147delC	c.(1147-1149)catfs	p.H383fs		NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	383					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.H383fs*>43(1)|p.H383fs*>42(1)		endometrium(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)	17	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			GTGTATCCATGGGGGGGCATC	0.622																																					p.H383fs		Atlas-INDEL	.											.,1	SF3B4	37	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(2)	c.1148delA						.						19	23	21					1																	149895562		2203	4297	6500	SO:0001589	frameshift_variant	10262	exon6			.	L35013	CCDS72900.1	1q21.2	2013-02-12	2002-08-29		ENSG00000143368	ENSG00000143368		"RNA binding motif (RRM) containing"	10771	protein-coding gene	gene with protein product		605593	"splicing factor 3b, subunit 4, 49kD"			7958871	Standard	NM_005850		Approved	SAP49, SF3b49, Hsh49	uc001etk.2	Q15427	OTTHUMG00000012208	ENST00000271628.8:c.1147delC	chr1.hg19:g.149895562delG	ENSP00000271628:p.His383fs	86.0	0.0		180.0	11.0	NM_005850	Q5SZ63	Frame_Shift_Del	DEL	ENST00000271628.8	hg19	CCDS941.1																																																																																			.	.		0.622	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033753.1	NM_005850		-	149895562	G	-	149895562	7	5	103	1	0	1	0	1	0	0	0	0	14168	1348	47	0	131	0	SF3B4	1	149895562	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2810672	149895562	99355059	66	14689										
OTUD7B	56957	hgsc.bcm.edu	37	chr1	149922079	149922079	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgagcaaggacaaagacgtgAaactcttcaaggctctcata							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:149922079delA	ENST00000369135.4	-	8	1185	c.891delT	c.(889-891)tttfs	p.F297fs		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	297	Catalytic.|OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.				mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CAAAGACGTGAAACTCTTCAA	0.532																																					p.H298fs		Atlas-INDEL	.											.	OTUD7B	76	.	0			c.892delC						.						74	75	75					1																	149922079		2030	4195	6225	SO:0001589	frameshift_variant	56957	exon8			.	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"OTU domain containing"	16683	protein-coding gene	gene with protein product		611748	"zinc finger, A20 domain containing 1", "OTU domain containing 7B"	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.891delT	chr1.hg19:g.149922079delA	ENSP00000358131:p.Phe297fs	85.0	0.0		179.0	12.0	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Frame_Shift_Del	DEL	ENST00000369135.4	hg19	CCDS41389.1																																																																																			.	.		0.532	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205		-	149922079	A	-	149922079	7	5	103	1	0	1	0	1	0	0	0	0	11328	243	9	0	1660	0	OTUD7B	1	149922079	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	26517	149922079	99328542	67	14690										
ECM1	1893	hgsc.bcm.edu	37	chr1	150484838	150484838	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggtccacagtgggaggataCccttgacaaatactgtgacc					rs202156901		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:150484838delC	ENST00000369047.4	+	8	1219	c.1094delC	c.(1093-1095)accfs	p.T365fs	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000346569.6_Frame_Shift_Del_p.T240fs|ECM1_ENST00000369049.4_Frame_Shift_Del_p.T392fs	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	365	2 X approximate repeats.				angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			TGGGAGGATACCCTTGACAAA	0.567																																					p.T392fs	Melanoma(156;1696 2560 11093 19685)	Atlas-INDEL	.											.	ECM1	96	.	0			c.1174delA						.						88	77	81					1																	150484838		2203	4300	6503	SO:0001589	frameshift_variant	1893	exon8			.	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.1094delC	chr1.hg19:g.150484838delC	ENSP00000358043:p.Thr365fs	99.0	0.0		226.0	14.0	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Frame_Shift_Del	DEL	ENST00000369047.4	hg19	CCDS953.1																																																																																			.	.		0.567	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425		-	150484838	C	-	150484838	7	5	103	1	0	1	0	1	0	0	0	0	4899	507	18	0	1124	0	ECM1	1	150484838	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	562759	150484838	98765783	68	14691										
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150532255	150532255	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtgttctcgctcctgccaaGggggaacgcagacacgggag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:150532255delG	ENST00000369038.2	+	16	3163	c.2962delG	c.(2962-2964)gggfs	p.G989fs	RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000369039.5_Frame_Shift_Del_p.G1012fs|ADAMTSL4_ENST00000271643.4_Frame_Shift_Del_p.G989fs			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	989	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CTCCTGCCAAGGGGGAACGCA	0.637											OREG0013787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q987fs		Atlas-INDEL	.											.	ADAMTSL4	101	.	0			c.2961delA						.						89	98	95					1																	150532255		2203	4300	6503	SO:0001589	frameshift_variant	54507	exon18			.	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.2962delG	chr1.hg19:g.150532255delG	ENSP00000358034:p.Gly989fs	72.0	0.0	1733	165.0	10.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Frame_Shift_Del	DEL	ENST00000369038.2	hg19	CCDS955.1																																																																																			.	.		0.637	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		-	150532255	G	-	150532255	7	5	103	1	0	1	0	1	0	0	0	0	277	1000	35	0	3099	0	ADAMTSL4	1	150532255	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	47417	150532255	98718366	69	14692										
ARNT	405	hgsc.bcm.edu	37	chr1	150808762	150808762	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacataactctcacctgtcaGggcattttctgaagtggaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:150808762delG	ENST00000358595.5	-	7	894	c.694delC	c.(694-696)ctgfs	p.L232fs	ARNT_ENST00000468970.1_5'UTR|ARNT_ENST00000354396.2_Frame_Shift_Del_p.L232fs|ARNT_ENST00000505755.1_Frame_Shift_Del_p.L217fs|ARNT_ENST00000515192.1_Frame_Shift_Del_p.L223fs	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	232	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCACCTGTCAGGGCATTTTCT	0.423			T	ETV6	AML																																p.L232fs		Atlas-INDEL	.		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	.	ARNT	68	.	0			c.695delT						.						92	73	79					1																	150808762		2203	4300	6503	SO:0001589	frameshift_variant	405	exon7			.	AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"Basic helix-loop-helix proteins"	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.694delC	chr1.hg19:g.150808762delG	ENSP00000351407:p.Leu232fs	75.0	0.0		194.0	12.0	NM_001668	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Frame_Shift_Del	DEL	ENST00000358595.5	hg19	CCDS970.1																																																																																			.	.		0.423	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2			-	150808762	G	-	150808762	7	5	103	1	0	1	0	1	0	0	0	0	965	991	35	0	1739	0	ARNT	1	150808762	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	276507	150808762	98441859	70	14693										
SETDB1	9869	hgsc.bcm.edu	37	chr1	150933041	150933041	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aattctcttcattctcaggcAaaatcctgacagatgacttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:150933041delA	ENST00000271640.5	+	16	2693	c.2503delA	c.(2503-2505)aaafs	p.K835fs	SETDB1_ENST00000368969.4_Frame_Shift_Del_p.K835fs|SETDB1_ENST00000459773.1_3'UTR	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	835	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			ATTCTCAGGCAAAATCCTGAC	0.388																																					p.G834fs		Atlas-INDEL	.											.	SETDB1	204	.	0			c.2502delC						.						66	66	66					1																	150933041		2203	4300	6503	SO:0001589	frameshift_variant	9869	exon16			.	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.2503delA	chr1.hg19:g.150933041delA	ENSP00000271640:p.Lys835fs	79.0	0.0		154.0	10.0	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Frame_Shift_Del	DEL	ENST00000271640.5	hg19	CCDS44217.1																																																																																			.	.		0.388	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			-	150933041	A	-	150933041	7	5	103	1	0	1	0	1	0	0	0	0	14153	131	5	0	2561	0	SETDB1	1	150933041	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	124279	150933041	98317580	71	14694										
LINGO4	339398	hgsc.bcm.edu	37	chr1	151773948	151773948	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gactttcggatcagggctggTttgcaggtgaagtgccctgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:151773948delT	ENST00000368820.3	-	2	2170	c.1233delA	c.(1231-1233)aaafs	p.K411fs	RP11-98D18.17_ENST00000601909.1_lincRNA	NM_001004432.2	NP_001004432.1	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	411	LRRCT.					integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			TCAGGGCTGGTTTGCAGGTGA	0.617																																					p.P412fs		Atlas-INDEL	.											.	LINGO4	51	.	0			c.1234delC						.						43	43	43					1																	151773948		2203	4299	6502	SO:0001589	frameshift_variant	339398	exon2			.		CCDS30855.1	1q21.3	2013-01-11	2007-02-01	2007-02-01	ENSG00000213171	ENSG00000213171		"Immunoglobulin superfamily / I-set domain containing"	31814	protein-coding gene	gene with protein product		609794	"leucine rich repeat neuronal 6D"	LRRN6D			Standard	NM_001004432		Approved		uc001ezf.1	Q6UY18	OTTHUMG00000013059	ENST00000368820.3:c.1233delA	chr1.hg19:g.151773948delT	ENSP00000357810:p.Lys411fs	91.0	0.0		162.0	10.0	NM_001004432		Frame_Shift_Del	DEL	ENST00000368820.3	hg19	CCDS30855.1																																																																																			.	.		0.617	LINGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036639.1	XM_291387		-	151773948	T	-	151773948	7	5	103	1	0	1	0	1	0	0	0	0	8826	1722	60	0	552	0	LINGO4	1	151773948	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	840907	151773948	97476673	72	14695										
TPM3	7170	hgsc.bcm.edu	37	chr1	154148611	154148611	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctctcactctcatcagcagcTttttcagcttcttccagctt					rs35013279		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:154148611delT	ENST00000368530.2	-	3	549	c.357delA	c.(355-357)aaafs	p.K119fs	TPM3_ENST00000302206.5_5'UTR|TPM3_ENST00000368531.2_Frame_Shift_Del_p.K82fs|TPM3_ENST00000469717.1_Intron|TPM3_ENST00000271850.7_Frame_Shift_Del_p.K119fs|TPM3_ENST00000341372.3_Frame_Shift_Del_p.K57fs|TPM3_ENST00000328159.4_Frame_Shift_Del_p.K82fs|TPM3_ENST00000368533.3_Frame_Shift_Del_p.K82fs|TPM3_ENST00000341485.5_Frame_Shift_Del_p.K82fs|TPM3_ENST00000323144.7_Frame_Shift_Del_p.K82fs|TPM3_ENST00000330188.9_Frame_Shift_Del_p.K82fs	NM_152263.2	NP_689476.2	P06753	TPM3_HUMAN	tropomyosin 3	119					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle thin filament tropomyosin (GO:0005862)|stress fiber (GO:0001725)			TPM3/NTRK1_ENST00000392302(70)|TPM3/ALK(33)	breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					CATCAGCAGCTTTTTCAGCTT	0.483			T	"NTRK1, ALK, ROS1"	"papillary thyroid, ALCL, NSCLC"																																p.A120fs		Atlas-INDEL	.		Dom	yes		1	1q22-q23	7170	tropomyosin 3		"E, L"	.	TPM3	46	.	0			c.358delG						.						133	125	127					1																	154148611		2203	4300	6503	SO:0001589	frameshift_variant	7170	exon3			.	BC008425	CCDS1060.1, CCDS41400.1, CCDS41401.1, CCDS41402.1, CCDS41403.1, CCDS60274.1, CCDS60275.1, CCDS72922.1	1q21.2	2014-09-17			ENSG00000143549	ENSG00000143549		"Tropomyosins"	12012	protein-coding gene	gene with protein product		191030		NEM1		1829807	Standard	NM_153649		Approved	TRK	uc001fec.2	P06753	OTTHUMG00000035853	ENST00000368530.2:c.357delA	chr1.hg19:g.154148611delT	ENSP00000357516:p.Lys119fs	148.0	0.0		247.0	16.0	NM_152263	D3DV71|P12324|Q2QD06|Q5VU58|Q5VU63|Q5VU66|Q5VU71|Q5VU72|Q8TCG3|Q969Q2|Q9NQH8	Frame_Shift_Del	DEL	ENST00000368530.2	hg19	CCDS41403.1																																																																																			.	.		0.483	TPM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087271.2	NM_152263		-	154148611	T	-	154148611	7	5	103	1	0	1	0	1	0	0	0	0	16422	1606	56	0	783	0	TPM3	1	154148611	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2374663	154148611	95102010	73	14696										
PYGO2	90780	hgsc.bcm.edu	37	chr1	154931663	154931663	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctgagtggggctcctggggAaaagcagtagaagcaggtgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:154931663delA	ENST00000368457.2	-	3	984	c.813delT	c.(811-813)tttfs	p.F271fs	RP11-307C12.12_ENST00000605085.1_RNA|PYGO2_ENST00000483463.1_5'Flank|PYGO2_ENST00000368456.1_Frame_Shift_Del_p.F234fs	NM_138300.3	NP_612157.1	Q9BRQ0	PYGO2_HUMAN	pygopus family PHD finger 2	271	Pro-rich.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|developmental growth (GO:0048589)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mammary gland development (GO:0030879)|palate development (GO:0060021)|positive regulation of chromatin binding (GO:0035563)|post-embryonic development (GO:0009791)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|spermatid nucleus differentiation (GO:0007289)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase regulator activity (GO:0035034)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)|skin(2)|urinary_tract(1)	10	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCTCCTGGGGAAAAGCAGTAG	0.632																																					p.P272fs	NSCLC(87;357 1460 1955 21029 23522)	Atlas-INDEL	.											.	PYGO2	32	.	0			c.814delC						.						10	10	10					1																	154931663		2200	4295	6495	SO:0001589	frameshift_variant	90780	exon3			.	BC006132	CCDS1075.1	1q22	2013-10-09	2013-10-09		ENSG00000163348	ENSG00000163348		"Zinc fingers, PHD-type"	30257	protein-coding gene	gene with protein product		606903	"pygopus homolog 2 (Drosophila)"			11988739	Standard	NM_138300		Approved		uc001fft.3	Q9BRQ0	OTTHUMG00000037370	ENST00000368457.2:c.813delT	chr1.hg19:g.154931663delA	ENSP00000357442:p.Phe271fs	95.0	0.0		205.0	14.0	NM_138300	Q8WYZ4|Q96CY2	Frame_Shift_Del	DEL	ENST00000368457.2	hg19	CCDS1075.1																																																																																			.	.		0.632	PYGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090949.1	NM_138300		-	154931663	A	-	154931663	7	5	103	1	0	1	0	1	0	0	0	0	12879	243	9	0	411	0	PYGO2	1	154931663	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	783052	154931663	94318958	74	14697										
CLK2	1196	hgsc.bcm.edu	37	chr1	155240721	155240721	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgatagtgttcacggtaactCccccggctgcctcgctctga					rs371622938		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:155240721delC	ENST00000368361.4	-	2	363	c.48delG	c.(46-48)gggfs	p.G16fs	CLK2_ENST00000355560.4_Frame_Shift_Del_p.G16fs|CLK2_ENST00000497188.1_5'Flank|CLK2_ENST00000361168.5_Frame_Shift_Del_p.G16fs|CLK2_ENST00000536801.1_Frame_Shift_Del_p.G16fs			P49760	CLK2_HUMAN	CDC-like kinase 2	16					negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CACGGTAACTCCCCCGGCTGC	0.552								Other conserved DNA damage response genes																													p.S17fs		Atlas-INDEL	.											.	CLK2	55	.	0			c.49delA						.						127	122	123					1																	155240721		2203	4300	6503	SO:0001589	frameshift_variant	1196	exon2			.	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"CDC-like kinases"	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.48delG	chr1.hg19:g.155240721delC	ENSP00000357345:p.Gly16fs	93.0	0.0		174.0	12.0	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Frame_Shift_Del	DEL	ENST00000368361.4	hg19																																																																																				.	.		0.552	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993		-	155240721	C	-	155240721	7	5	103	1	0	1	0	1	0	0	0	0	3539	842	30	0	1496	0	CLK2	1	155240721	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	309058	155240721	94009900	75	14698										
ISG20L2	81875	hgsc.bcm.edu	37	chr1	156697122	156697122	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tagcagcaacagaatcagccTtttttgaaggggcaggggtc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:156697122delT	ENST00000313146.6	-	1	1105	c.323delA	c.(322-324)aagfs	p.K108fs	RRNAD1_ENST00000368218.4_5'Flank|RRNAD1_ENST00000524343.1_5'Flank|ISG20L2_ENST00000368219.1_Frame_Shift_Del_p.K108fs|RRNAD1_ENST00000368216.4_5'Flank|ISG20L2_ENST00000472824.2_5'Flank	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene 20kDa-like 2	108					ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGAATCAGCCTTTTTTGAAGG	0.517											OREG0013885	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K108fs		Atlas-INDEL	.											.	ISG20L2	43	.	0			c.324delG						.						71	73	72					1																	156697122		2203	4300	6503	SO:0001589	frameshift_variant	81875	exon1			.	AK095697	CCDS1153.1	1q23.1	2013-10-11			ENSG00000143319	ENSG00000143319			25745	protein-coding gene	gene with protein product		611930				18065403	Standard	NM_030980		Approved	FLJ12671	uc001fps.1	Q9H9L3	OTTHUMG00000041301	ENST00000313146.6:c.323delA	chr1.hg19:g.156697122delT	ENSP00000323424:p.Lys108fs	89.0	0.0	1780	180.0	13.0	NM_030980	D3DVC6|Q64KA2	Frame_Shift_Del	DEL	ENST00000313146.6	hg19	CCDS1153.1																																																																																			.	.		0.517	ISG20L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098969.1	NM_030980		-	156697122	T	-	156697122	7	5	103	1	0	1	0	1	0	0	0	0	7864	1609	56	0	750	0	ISG20L2	1	156697122	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1456401	156697122	92553499	76	14699										
ATP1A4	480	hgsc.bcm.edu	37	chr1	160136351	160136351	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcacagccaagcgcatggcgCggaagaactgcctggtgaag	14	11	1	2	rs143083729	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:160136351C>A	ENST00000368081.4	+	8	1552	c.1081C>A	c.(1081-1083)Cgg>Agg	p.R361R		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	361					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCGCATGGCGCGGAAGAACTG	0.567																																					p.R361R		Atlas-SNP	.											ATP1A4,NS,carcinoma,0,1	ATP1A4	167	.	0			c.C1081A						.						89	80	83					1																	160136351		2203	4300	6503	SO:0001819	synonymous_variant	480	exon8			ATGGCGCGGAAGA	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1081C>A	chr1.hg19:g.160136351C>A		152.0	0.0		393.0	0.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	hg19	CCDS1197.1																																																																																			.	C|0.999;T|0.001		0.567	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		A	160136351	C	A	160136351	2	1	103	1	0	0	0	0	0	0	0	1	1131	759	27	1		1	ATP1A4	1	160136351	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	3439229	160136351	89114270	77	14700										
KLHDC9	126823	hgsc.bcm.edu	37	chr1	161068653	161068653	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcttggccacagtgaccgcaCtggacacagagcgcggtgtg	15	12	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:161068653C>T	ENST00000368011.4	+	1	470	c.328C>T	c.(328-330)Ctg>Ttg	p.L110L	PFDN2_ENST00000468311.1_5'Flank|KLHDC9_ENST00000490724.2_3'UTR|KLHDC9_ENST00000392192.2_Silent_p.L110L	NM_152366.4	NP_689579.3	Q8NEP7	KLDC9_HUMAN	kelch domain containing 9	110										lung(5)|upper_aerodigestive_tract(1)	6	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			AGTGACCGCACTGGACACAGA	0.716																																					p.L110L		Atlas-SNP	.											.	KLHDC9	16	.	0			c.C328T						.						9	11	10					1																	161068653		2181	4270	6451	SO:0001819	synonymous_variant	126823	exon1			ACCGCACTGGACA	BC022077	CCDS30919.1, CCDS41425.1	1q23.3	2008-02-05			ENSG00000162755	ENSG00000162755			28489	protein-coding gene	gene with protein product	"kelch/ankyrin repeat containing cyclin A1 interacting protein"					15159402	Standard	NM_152366		Approved	KARCA1	uc001fxr.3	Q8NEP7	OTTHUMG00000031479	ENST00000368011.4:c.328C>T	chr1.hg19:g.161068653C>T		43.0	0.0		97.0	5.0	NM_001007255	Q5SY56|Q6NXT9|Q6PKN4|Q8N5E1|Q8NA16	Silent	SNP	ENST00000368011.4	hg19	CCDS30919.1																																																																																			.	.		0.716	KLHDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077092.1	NM_152366		T	161068653	C	T	161068653	2	4	103	1	0	0	0	0	0	0	0	1	8373	564	20	3		3	KLHDC9	1	161068653	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	932302	161068653	88181968	78	14701										
APOA2	336	hgsc.bcm.edu	37	chr1	161192790	161192790	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacggtctggaagtactgagAaaccaggctctccacacatg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:161192790delA	ENST00000367990.3	-	3	160	c.103delT	c.(103-105)tctfs	p.S35fs	APOA2_ENST00000470459.2_Frame_Shift_Del_p.S35fs|APOA2_ENST00000464492.1_Frame_Shift_Del_p.S68fs|APOA2_ENST00000491350.1_Intron|APOA2_ENST00000468465.1_Intron|APOA2_ENST00000463812.1_5'UTR	NM_001643.1	NP_001634.1	P02652	APOA2_HUMAN	apolipoprotein A-II	35	O-glycosylated at one site.				acute inflammatory response (GO:0002526)|cellular lipid metabolic process (GO:0044255)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of cholesterol import (GO:0060621)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cholesterol transporter activity (GO:0060695)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of lipase activity (GO:0060192)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of very-low-density lipoprotein particle remodeling (GO:0010903)|organ regeneration (GO:0031100)|peptidyl-methionine modification (GO:0018206)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid catabolic process (GO:0009395)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of lipid catabolic process (GO:0050996)|protein folding (GO:0006457)|protein oxidation (GO:0018158)|regulation of intestinal cholesterol absorption (GO:0030300)|regulation of protein stability (GO:0031647)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|viral process (GO:0016032)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein receptor binding (GO:0034190)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor binding (GO:0070653)|lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|phospholipid binding (GO:0005543)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(2)|skin(2)	6	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			AAGTACTGAGAAACCAGGCTC	0.542																																					p.S35fs		Atlas-INDEL	.											.	APOA2	12	.	0			c.104delC						.						124	116	119					1																	161192790		2203	4300	6503	SO:0001589	frameshift_variant	336	exon3			.		CCDS1226.1	1q23.3	2013-01-24			ENSG00000158874	ENSG00000158874		"Apolipoproteins"	601	protein-coding gene	gene with protein product		107670				2415515	Standard	NM_001643		Approved		uc001fzc.1	P02652	OTTHUMG00000034346	ENST00000367990.3:c.103delT	chr1.hg19:g.161192790delA	ENSP00000356969:p.Ser35fs	89.0	0.0		161.0	10.0	NM_001643	B2R524	Frame_Shift_Del	DEL	ENST00000367990.3	hg19	CCDS1226.1																																																																																			.	.		0.542	APOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083037.1	NM_001643		-	161192790	A	-	161192790	7	5	103	1	0	1	0	1	0	0	0	0	782	246	9	0	207	0	APOA2	1	161192790	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	124137	161192790	88057831	79	14702										
C1orf226	400793	hgsc.bcm.edu	37	chr1	162351912	162351912	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagaaaggagccctccagccTgggcagtgtgggtgtgacag	17	9	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:162351912T>C	ENST00000458626.2	+	1	393	c.221T>C	c.(220-222)cTg>cCg	p.L74P	C1orf226_ENST00000426197.2_Missense_Mutation_p.L117P	NM_001085375.1	NP_001078844.1	A1L170	CA226_HUMAN	chromosome 1 open reading frame 226	74										central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12						CCCTCCAGCCTGGGCAGTGTG	0.597																																					p.L117P		Atlas-SNP	.											.	C1orf226	49	.	0			c.T350C						.						13	16	15					1																	162351912		2050	4197	6247	SO:0001583	missense	400793	exon2			CCAGCCTGGGCAG	AI480219, AK023199, AK125122, AL512785, BC127743	CCDS44268.1, CCDS53422.1	1q23.3	2013-10-11			ENSG00000239887	ENSG00000239887			34351	protein-coding gene	gene with protein product						14702039	Standard	NM_001085375		Approved	FLJ13137	uc010pkt.1	A1L170	OTTHUMG00000031376	ENST00000458626.2:c.221T>C	chr1.hg19:g.162351912T>C	ENSP00000437071:p.Leu74Pro	61.0	0.0		121.0	5.0	NM_001135240	B4DF31	Missense_Mutation	SNP	ENST00000458626.2	hg19	CCDS53422.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.346658	0.41599	.	.	ENSG00000239887	ENST00000420220;ENST00000426197;ENST00000458626	.	.	.	5.54	3.21	0.36854	.	0.300651	0.21136	N	0.079569	T	0.09335	0.0230	N	0.20986	0.625	.	.	.	B;B	0.27700	0.186;0.046	B;B	0.27170	0.077;0.03	T	0.15896	-1.0421	8	0.40728	T	0.16	-1.4367	1.2255	0.01932	0.149:0.1604:0.1553:0.5354	.	117;74	A1L170-2;A1L170	.;CA226_HUMAN	P	74;117;74	.	ENSP00000398035:L74P	L	+	2	0	C1orf226	160618536	0.409000	0.25368	0.004000	0.12327	0.592000	0.36648	2.274000	0.43390	0.382000	0.24878	0.533000	0.62120	CTG	.	.		0.597	C1orf226-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076793.2	NM_001085375		C	162351912	T	C	162351912	3	2	103	1	0	0	0	0	1	0	0	0	2034	1580	55	2	356	2	C1orf226	1	162351912	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1159122	162351912	86898709	80	14703										
ADCY10	55811	hgsc.bcm.edu	37	chr1	167874253	167874253	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaaatatcaacaaacatcagGactccgtcaaaataatccat	4	10	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:167874253G>C	ENST00000367851.4	-	2	310	c.126C>G	c.(124-126)gtC>gtG	p.V42V	ADCY10_ENST00000367848.1_5'UTR|ADCY10_ENST00000545172.1_Intron|ADCY10_ENST00000476818.2_Silent_p.V42V	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	42	Guanylate cyclase 1. {ECO:0000255|PROSITE-ProRule:PRU00099}.				cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						CAAACATCAGGACTCCGTCAA	0.453																																					p.V42V		Atlas-SNP	.											.	ADCY10	175	.	0			c.C126G						.						111	106	107					1																	167874253		2203	4300	6503	SO:0001819	synonymous_variant	55811	exon2			CATCAGGACTCCG	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.126C>G	chr1.hg19:g.167874253G>C		167.0	0.0		372.0	84.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Silent	SNP	ENST00000367851.4	hg19	CCDS1265.1																																																																																			.	.		0.453	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		C	167874253	G	C	167874253	2	2	103	1	0	0	0	0	0	0	0	1	293	1161	41	4		4	ADCY10	1	167874253	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	5522341	167874253	81376368	81	14704										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171483721	171483721	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caaaacctggggttgcagctCccccagaagtagcacctgct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:171483721delC	ENST00000338920.4	+	4	568	c.331delC	c.(331-333)cccfs	p.P112fs	PRRC2C_ENST00000367742.3_Frame_Shift_Del_p.P114fs|PRRC2C_ENST00000476522.1_3'UTR|PRRC2C_ENST00000392078.3_Frame_Shift_Del_p.P114fs|PRRC2C_ENST00000426496.2_Frame_Shift_Del_p.P112fs	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	112					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										GGTTGCAGCTCCCCCAGAAGT	0.453																																					p.A110fs		Atlas-INDEL	.											.	.	.	.	0			c.330delT						.						56	44	48					1																	171483721		2193	4277	6470	SO:0001589	frameshift_variant	23215	exon4			.	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.331delC	chr1.hg19:g.171483721delC	ENSP00000343629:p.Pro112fs	157.0	0.0		312.0	21.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Frame_Shift_Del	DEL	ENST00000338920.4	hg19	CCDS1296.2																																																																																			.	.		0.453	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		-	171483721	C	-	171483721	7	5	103	1	0	1	0	1	0	0	0	0	1321	855	30	0	341	0	BAT2L2	1	171483721	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	3609468	171483721	77766900	82	14705										
DNM3	26052	hgsc.bcm.edu	37	chr1	172356459	172356459	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaccgtgtccactccggcaCcccctccagtggatgactcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:172356459delC	ENST00000355305.5	+	19	2420	c.2263delC	c.(2263-2265)cccfs	p.P757fs	DNM3_ENST00000367731.1_Frame_Shift_Del_p.P747fs|DNM3_ENST00000358155.4_Frame_Shift_Del_p.P751fs			Q9UQ16	DYN3_HUMAN	dynamin 3	757					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CACTCCGGCACCCCCTCCAGT	0.587																																					p.A748fs		Atlas-INDEL	.											.	DNM3	85	.	0			c.2244delA						.						28	31	30					1																	172356459		2053	4188	6241	SO:0001589	frameshift_variant	26052	exon19			.	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.2263delC	chr1.hg19:g.172356459delC	ENSP00000347457:p.Pro757fs	81.0	0.0		158.0	11.0	NM_015569	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Frame_Shift_Del	DEL	ENST00000355305.5	hg19																																																																																				.	.		0.587	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		-	172356459	C	-	172356459	7	5	103	1	0	1	0	1	0	0	0	0	4675	507	18	0	2319	0	DNM3	1	172356459	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	872738	172356459	76894162	83	14706										
TNN	63923	hgsc.bcm.edu	37	chr1	175113579	175113579	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caacttttgacagagacaatGatatcgcactcagcaactgt	7	10	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:175113579G>C	ENST00000239462.4	+	18	3765	c.3652G>C	c.(3652-3654)Gat>Cat	p.D1218H		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	1218	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		CAGAGACAATGATATCGCACT	0.512																																					p.D1218H		Atlas-SNP	.											TNN,NS,carcinoma,0,1	TNN	297	.	0			c.G3652C						.						152	134	140					1																	175113579		2203	4300	6503	SO:0001583	missense	63923	exon18			GACAATGATATCG	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.3652G>C	chr1.hg19:g.175113579G>C	ENSP00000239462:p.Asp1218His	155.0	0.0		217.0	0.0	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	19.07	3.756837	0.69648	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	D	0.83075	-1.68	5.01	5.01	0.66863	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.95503	0.8539	H	0.99600	4.65	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97983	1.0350	10	0.87932	D	0	.	17.9026	0.88909	0.0:0.0:1.0:0.0	.	1218	Q9UQP3	TENN_HUMAN	H	1218;1041	ENSP00000239462:D1218H	ENSP00000239462:D1218H	D	+	1	0	TNN	173380202	1.000000	0.71417	0.558000	0.28319	0.489000	0.33432	9.636000	0.98440	2.312000	0.78011	0.478000	0.44815	GAT	.	.		0.512	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		C	175113579	G	C	175113579	3	2	103	1	0	0	0	0	1	0	0	0	16338	1290	45	4	3718	4	TNN	1	175113579	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	2757120	175113579	74137042	84	14707										
TNR	7143	hgsc.bcm.edu	37	chr1	175372615	175372615	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcactggccatccacacacaCcccccggctggagcaaccca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:175372615delC	ENST00000367674.2	-	4	1345	c.637delG	c.(637-639)gtgfs	p.V213fs	TNR_ENST00000263525.2_Frame_Shift_Del_p.V213fs			Q92752	TENR_HUMAN	tenascin R	213	Cys-rich.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TCCACACACACCCCCCGGCTG	0.607																																					p.V213fs		Atlas-INDEL	.											.	TNR	399	.	0			c.638delT						.						104	109	107					1																	175372615		2203	4300	6503	SO:0001589	frameshift_variant	7143	exon4			.	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.637delG	chr1.hg19:g.175372615delC	ENSP00000356646:p.Val213fs	88.0	0.0		165.0	10.0	NM_003285	C9J563|Q15568|Q5R3G0	Frame_Shift_Del	DEL	ENST00000367674.2	hg19	CCDS1318.1																																																																																			.	.		0.607	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		-	175372615	C	-	175372615	7	5	103	1	0	1	0	1	0	0	0	0	16353	507	18	0	3519	0	TNR	1	175372615	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	259036	175372615	73878006	85	14708										
TNR	7143	hgsc.bcm.edu	37	chr1	175375844	175375844	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaccactgtttccccatctgCccccatcctctcagccagag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:175375844delC	ENST00000367674.2	-	3	715	c.7delG	c.(7-9)gcafs	p.A3fs	TNR_ENST00000263525.2_Frame_Shift_Del_p.A3fs			Q92752	TENR_HUMAN	tenascin R	3					associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TCCCCATCTGCCCCCATCCTC	0.532																																					p.A3fs		Atlas-INDEL	.											.	TNR	399	.	0			c.8delC						.						103	98	100					1																	175375844		2203	4300	6503	SO:0001589	frameshift_variant	7143	exon3			.	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.7delG	chr1.hg19:g.175375844delC	ENSP00000356646:p.Ala3fs	97.0	0.0		166.0	10.0	NM_003285	C9J563|Q15568|Q5R3G0	Frame_Shift_Del	DEL	ENST00000367674.2	hg19	CCDS1318.1																																																																																			.	.		0.532	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		-	175375844	C	-	175375844	7	5	103	1	0	1	0	1	0	0	0	0	16353	739	26	0	4153	0	TNR	1	175375844	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	3229	175375844	73874777	86	14709										
ABL2	27	hgsc.bcm.edu	37	chr1	179078242	179078242	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggttcctctgtgcaaagctCcccccatagcacttgggtgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:179078242delC	ENST00000502732.1	-	12	2363	c.2160delG	c.(2158-2160)gggfs	p.G720fs	ABL2_ENST00000507173.1_Intron|ABL2_ENST00000512653.1_Frame_Shift_Del_p.G705fs|ABL2_ENST00000511413.1_Intron|ABL2_ENST00000504405.1_Intron|ABL2_ENST00000344730.3_Intron|ABL2_ENST00000408940.3_Frame_Shift_Del_p.G684fs|ABL2_ENST00000367623.4_Frame_Shift_Del_p.G699fs	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	720	F-actin-binding. {ECO:0000250}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	GTGCAAAGCTCCCCCCATAGC	0.567			T	ETV6	AML																																p.S721fs		Atlas-INDEL	.		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	ABL2	307	.	0			c.2161delA						.						53	55	54					1																	179078242		2203	4300	6503	SO:0001589	frameshift_variant	27	exon12			.	M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.2160delG	chr1.hg19:g.179078242delC	ENSP00000427562:p.Gly720fs	80.0	0.0		148.0	10.0	NM_007314	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Frame_Shift_Del	DEL	ENST00000502732.1	hg19	CCDS30947.1																																																																																			.	.		0.567	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		-	179078242	C	-	179078242	7	5	103	1	0	1	0	1	0	0	0	0	93	842	30	0	1392	0	ABL2	1	179078242	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	3702398	179078242	70172379	87	14710										
RNASEL	6041	hgsc.bcm.edu	37	chr1	182555572	182555572	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catgaaggctgtgaagccatAaaaatcacactcattgacat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:182555572delA	ENST00000367559.3	-	2	623	c.370delT	c.(370-372)tatfs	p.Y124fs	RNASEL_ENST00000539397.1_Frame_Shift_Del_p.Y124fs|RNASEL_ENST00000444138.1_Frame_Shift_Del_p.Y124fs	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	124					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						GTGAAGCCATAAAAATCACAC	0.463																																					p.Y124fs		Atlas-INDEL	.											.	RNASEL	83	.	0			c.371delA						.						46	47	47					1																	182555572		2203	4300	6503	SO:0001589	frameshift_variant	6041	exon2			.	L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"Ankyrin repeat domain containing"	10050	protein-coding gene	gene with protein product		180435	"prostate cancer 1"	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.370delT	chr1.hg19:g.182555572delA	ENSP00000356530:p.Tyr124fs	74.0	0.0		150.0	10.0	NM_021133	Q5W0L2|Q6AI46	Frame_Shift_Del	DEL	ENST00000367559.3	hg19	CCDS1347.1																																																																																			.	.		0.463	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085189.1	NM_021133		-	182555572	A	-	182555572	7	5	103	1	0	1	0	1	0	0	0	0	13431	362	13	0	1879	0	RNASEL	1	182555572	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3477330	182555572	66695049	88	14711										
C1orf26	54823	hgsc.bcm.edu	37	chr1	185135718	185135718	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcttaggacaagaaagagagAaaaaccccagcaagttctac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:185135718delA	ENST00000367500.4	+	3	264	c.99delA	c.(97-99)agafs	p.R33fs	SWT1_ENST00000367501.3_Frame_Shift_Del_p.R33fs	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	33										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						AGAAAGAGAGAAAAACCCCAG	0.289																																					p.R33fs		Atlas-INDEL	.											.	SWT1	88	.	0			c.98delG						.						59	65	63					1																	185135718		2201	4292	6493	SO:0001589	frameshift_variant	54823	exon3			.	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.99delA	chr1.hg19:g.185135718delA	ENSP00000356470:p.Arg33fs	123.0	0.0		180.0	11.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Frame_Shift_Del	DEL	ENST00000367500.4	hg19	CCDS1367.1																																																																																			.	.		0.289	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		-	185135718	A	-	185135718	7	5	103	1	0	1	0	1	0	0	0	0	2037	243	9	0	105	0	C1orf26	1	185135718	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2580146	185135718	64114903	89	14712										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186086675	186086675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tacctgcactgcttcgggagTtccatttccctcaattcact	6	14	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:186086675T>C	ENST00000271588.4	+	77	11997	c.11768T>C	c.(11767-11769)gTt>gCt	p.V3923A	HMCN1_ENST00000367492.2_Missense_Mutation_p.V3923A	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3923	Ig-like C2-type 38.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GCTTCGGGAGTTCCATTTCCC	0.453																																					p.V3923A		Atlas-SNP	.											.	HMCN1	797	.	0			c.T11768C						.						108	103	104					1																	186086675		2203	4300	6503	SO:0001583	missense	83872	exon77			CGGGAGTTCCATT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11768T>C	chr1.hg19:g.186086675T>C	ENSP00000271588:p.Val3923Ala	73.0	0.0		145.0	6.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.827410	0.90955	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.66815	-0.23;-0.23	5.65	5.65	0.86999	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.71247	0.3317	L	0.38733	1.17	0.80722	D	1	D	0.65815	0.995	D	0.78314	0.991	T	0.65463	-0.6162	10	0.06625	T	0.88	.	15.8909	0.79296	0.0:0.0:0.0:1.0	.	3923	Q96RW7	HMCN1_HUMAN	A	3923	ENSP00000271588:V3923A;ENSP00000356462:V3923A	ENSP00000271588:V3923A	V	+	2	0	HMCN1	184353298	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.223000	0.72257	2.146000	0.66826	0.533000	0.62120	GTT	.	.		0.453	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186086675	T	C	186086675	3	2	103	1	0	0	0	0	1	0	0	0	7229	1725	60	2	12074	2	HMCN1	1	186086675	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	950957	186086675	63163946	90	14713										
C1orf27	54953	hgsc.bcm.edu	37	chr1	186367553	186367553	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atatccacagcagtaaacccAaagttaaagatgctgtgcag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:186367553delA	ENST00000287859.6	+	10	1014	c.889delA	c.(889-891)aaafs	p.K297fs	C1orf27_ENST00000432021.3_Frame_Shift_Del_p.K274fs|OCLM_ENST00000574641.1_5'Flank|AL596220.1_ENST00000598663.1_5'Flank|C1orf27_ENST00000419367.3_Frame_Shift_Del_p.K265fs|C1orf27_ENST00000367470.3_Frame_Shift_Del_p.K274fs	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	297						integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						CAGTAAACCCAAAGTTAAAGA	0.373																																					p.P296fs		Atlas-INDEL	.											.	C1orf27	41	.	0			c.888delC						.						88	82	84					1																	186367553		1861	4111	5972	SO:0001589	frameshift_variant	54953	exon10			.	BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"transactivated by recombinant transforming growth factor beta"	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.889delA	chr1.hg19:g.186367553delA	ENSP00000287859:p.Lys297fs	99.0	0.0		160.0	14.0	NM_017847	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Frame_Shift_Del	DEL	ENST00000287859.6	hg19	CCDS53448.1																																																																																			.	.		0.373	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847		-	186367553	A	-	186367553	7	5	103	1	0	1	0	1	0	0	0	0	2038	131	5	0	923	0	C1orf27	1	186367553	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	280878	186367553	62883068	91	14714										
CDC73	79577	hgsc.bcm.edu	37	chr1	193111006	193111006	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtctgaagctatgtcagtggAaaaaattgctgcaatcaaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:193111006delA	ENST00000367435.3	+	7	723	c.539delA	c.(538-540)gaafs	p.E180fs		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	180					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						ATGTCAGTGGAAAAAATTGCT	0.328																																					p.E180fs		Atlas-INDEL	.											.	CDC73	163	.	0			c.538delG						.						45	42	43					1																	193111006		2203	4300	6503	SO:0001589	frameshift_variant	79577	exon7			.	AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"Paf1/RNA polymerase II complex component"	607393	"chromosome 1 open reading frame 28", "hyperparathyroidism 2 (with jaw tumor)", "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)", "hyperparathyroidism 1"	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.539delA	chr1.hg19:g.193111006delA	ENSP00000356405:p.Glu180fs	103.0	0.0		153.0	10.0	NM_024529	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Frame_Shift_Del	DEL	ENST00000367435.3	hg19	CCDS1382.1																																																																																			.	.		0.328	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529		-	193111006	A	-	193111006	7	5	103	1	0	1	0	1	0	0	0	0	3087	246	9	0	565	0	CDC73	1	193111006	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	6743453	193111006	56139615	92	14715										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196227429	196227429	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttcagtcgctgctgggttaTtttttcagctgttttaccag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:196227429delT	ENST00000294725.9	-	26	4021	c.3106delA	c.(3106-3108)atafs	p.I1036fs	KCNT2_ENST00000367431.4_Frame_Shift_Del_p.I970fs|KCNT2_ENST00000367433.5_Frame_Shift_Del_p.I1012fs|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000451324.2_3'UTR|KCNT2_ENST00000609185.1_Frame_Shift_Del_p.I969fs			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	1036					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						TGCTGGGTTATTTTTTCAGCT	0.473																																					p.I1036fs		Atlas-Indel,Pindel	.											.	KCNT2	243	.	0			c.3107delT						.						113	108	110					1																	196227429		2203	4300	6503	SO:0001589	frameshift_variant	343450	exon26			.	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.3106delA	chr1.hg19:g.196227429delT	ENSP00000294725:p.Ile1036fs	229.0	0.0		346.0	22.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Frame_Shift_Del	DEL	ENST00000294725.9	hg19	CCDS1384.1																																																																																			.	.		0.473	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		-	196227429	T	-	196227429	7	5	103	1	0	1	0	1	0	0	0	0	8101	1493	52	0	313	0	KCNT2	1	196227429	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3116423	196227429	53023192	93	14716										
ASPM	259266	hgsc.bcm.edu	37	chr1	197115430	197115430	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgaagcaaaggaaaggagaCctgcagaagtggctgagaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:197115430delC	ENST00000367409.4	-	1	394	c.138delG	c.(136-138)aggfs	p.R46fs	ASPM_ENST00000294732.7_Frame_Shift_Del_p.R46fs	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	46					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						GGAAAGGAGACCTGCAGAAGT	0.672																																					p.S47fs		Atlas-INDEL	.											.	ASPM	444	.	0			c.139delT						.						89	97	94					1																	197115430		2203	4300	6503	SO:0001589	frameshift_variant	259266	exon1			.	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.138delG	chr1.hg19:g.197115430delC	ENSP00000356379:p.Arg46fs	57.0	0.0		104.0	10.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Frame_Shift_Del	DEL	ENST00000367409.4	hg19	CCDS1389.1																																																																																			.	.		0.672	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		-	197115430	C	-	197115430	7	5	103	1	0	1	0	1	0	0	0	0	1056	506	18	0	10407	0	ASPM	1	197115430	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	888001	197115430	52135191	94	14717										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200944033	200944033	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acccagtccttgtgcgcattGgggatttgctgtgagaggat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:200944033delG	ENST00000422435.2	-	34	4939	c.4623delC	c.(4621-4623)cccfs	p.P1541fs	KIF21B_ENST00000461742.2_Frame_Shift_Del_p.P1541fs|KIF21B_ENST00000360529.5_Frame_Shift_Del_p.P1528fs|KIF21B_ENST00000332129.2_Frame_Shift_Del_p.P1528fs	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1541					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TGTGCGCATTGGGGATTTGCT	0.642																																					p.N1542fs		Atlas-INDEL	.											.	KIF21B	208	.	0			c.4624delA						.						68	71	70					1																	200944033		2203	4300	6503	SO:0001589	frameshift_variant	23046	exon34			.	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.4623delC	chr1.hg19:g.200944033delG	ENSP00000411831:p.Pro1541fs	110.0	0.0		164.0	10.0	NM_001252102	B2RP62|B7ZMI0|Q5T4J3	Frame_Shift_Del	DEL	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	.		0.642	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		-	200944033	G	-	200944033	7	5	103	1	0	1	0	1	0	0	0	0	8298	1335	47	0	298	0	KIF21B	1	200944033	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	3828603	200944033	48306588	95	14718										
NAV1	89796	hgsc.bcm.edu	37	chr1	201750396	201750396	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccacctgtggctgtaacttCccccatcactcacacagccc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:201750396delC	ENST00000367296.4	+	5	2042	c.1622delC	c.(1621-1623)tccfs	p.S541fs	NAV1_ENST00000367302.1_Frame_Shift_Del_p.S554fs|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000367300.3_Frame_Shift_Del_p.S541fs|NAV1_ENST00000295624.6_Frame_Shift_Del_p.S541fs|NAV1_ENST00000367295.1_Frame_Shift_Del_p.S150fs|NAV1_ENST00000367297.4_Frame_Shift_Del_p.S541fs	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	541					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						GCTGTAACTTCCCCCATCACT	0.537																																					p.S541fs		Atlas-INDEL	.											.	NAV1	143	.	0			c.1621delT						.						47	47	47					1																	201750396		2203	4300	6503	SO:0001589	frameshift_variant	89796	exon5			.	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"neuron navigator-1", "pore membrane and/or filament interacting like protein 3"	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.1622delC	chr1.hg19:g.201750396delC	ENSP00000356265:p.Ser541fs	99.0	0.0		159.0	11.0	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Frame_Shift_Del	DEL	ENST00000367296.4	hg19	CCDS1414.2																																																																																			.	.		0.537	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		-	201750396	C	-	201750396	7	5	103	1	0	1	0	1	0	0	0	0	10192	855	30	0	1697	0	NAV1	1	201750396	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	806363	201750396	47500225	96	14719										
PPP1R12B	4660	hgsc.bcm.edu	37	chr1	202394814	202394814	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcgctcaggggctacagcccTtcatgtggctgctgccaagg	13	13	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:202394814T>C	ENST00000608999.1	+	4	815	c.662T>C	c.(661-663)cTt>cCt	p.L221P	PPP1R12B_ENST00000356764.2_Missense_Mutation_p.L221P|PPP1R12B_ENST00000336894.4_Missense_Mutation_p.L221P|PPP1R12B_ENST00000480184.1_Missense_Mutation_p.L221P	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	221					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			GCTACAGCCCTTCATGTGGCT	0.512																																					p.L221P		Atlas-SNP	.											.	PPP1R12B	100	.	0			c.T662C						.						136	146	143					1																	202394814		2203	4300	6503	SO:0001583	missense	4660	exon4			CAGCCCTTCATGT	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7619	protein-coding gene	gene with protein product	"myosin phosphatase regulatory subunit", "myosin phosphatase, target subunit 2"	603768	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.662T>C	chr1.hg19:g.202394814T>C	ENSP00000476755:p.Leu221Pro	65.0	0.0		174.0	7.0	NM_002481	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Missense_Mutation	SNP	ENST00000608999.1	hg19	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.378634	0.82682	.	.	ENSG00000077157	ENST00000406302;ENST00000336894;ENST00000480184;ENST00000356764	T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26	5.51	5.51	0.81932	Ankyrin repeat-containing domain (3);	0.000000	0.56097	D	0.000039	D	0.92603	0.7650	H	0.98199	4.17	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.95263	0.8370	10	0.87932	D	0	.	15.625	0.76848	0.0:0.0:0.0:1.0	.	221;221;221;221	O60237-2;O60237;F8W8M3;Q2TAI8	.;MYPT2_HUMAN;.;.	P	221	ENSP00000384496:L221P;ENSP00000337897:L221P;ENSP00000417159:L221P;ENSP00000349206:L221P	ENSP00000337897:L221P	L	+	2	0	PPP1R12B	200661437	1.000000	0.71417	0.717000	0.30585	0.908000	0.53690	8.027000	0.88791	2.094000	0.63399	0.383000	0.25322	CTT	.	.		0.512	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105		C	202394814	T	C	202394814	3	2	103	1	0	0	0	0	1	0	0	0	12367	1609	56	2	676	2	PPP1R12B	1	202394814	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	644418	202394814	46855807	97	14720										
ADIPOR1	51094	hgsc.bcm.edu	37	chr1	202917518	202917518	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacctcctcctcttcttcctGgggcactgggcatgtttgct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:202917518delG	ENST00000340990.5	-	3	470	c.172delC	c.(172-174)cagfs	p.Q58fs	ADIPOR1_ENST00000436244.1_Frame_Shift_Del_p.Q58fs|ADIPOR1_ENST00000367254.3_Frame_Shift_Del_p.Q58fs	NM_015999.4	NP_057083.2	Q96A54	ADR1_HUMAN	adiponectin receptor 1	58					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|hormone-mediated signaling pathway (GO:0009755)|leptin-mediated signaling pathway (GO:0033210)|negative regulation of cell growth (GO:0030308)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of JAK-STAT cascade (GO:0046427)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	16			BRCA - Breast invasive adenocarcinoma(75;0.141)			TCTTCTTCCTGGGGCACTGGG	0.507																																					p.Q58fs		Atlas-INDEL	.											.	ADIPOR1	32	.	0			c.173delA						.						95	86	89					1																	202917518		2203	4300	6503	SO:0001589	frameshift_variant	51094	exon3			.		CCDS1430.1	1q32.1	2012-08-22			ENSG00000159346	ENSG00000159346		"GPCR / Unclassified : Adiponectin receptors"	24040	protein-coding gene	gene with protein product		607945				12802337	Standard	XM_006711360		Approved	PAQR1, ACDCR1	uc001gyq.5	Q96A54	OTTHUMG00000041391	ENST00000340990.5:c.172delC	chr1.hg19:g.202917518delG	ENSP00000341785:p.Gln58fs	80.0	0.0		130.0	10.0	NM_015999	B3KMB0|Q53HS7|Q53YY6|Q9Y360	Frame_Shift_Del	DEL	ENST00000340990.5	hg19	CCDS1430.1																																																																																			.	.		0.507	ADIPOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099160.2	NM_015999		-	202917518	G	-	202917518	7	5	103	1	0	1	0	1	0	0	0	0	318	1357	47	0	979	0	ADIPOR1	1	202917518	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	522704	202917518	46333103	98	14721										
NUAK2	81788	hgsc.bcm.edu	37	chr1	205275421	205275421	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgatggtagaggttggagagAccgaagtcagcaatctgcag					rs4951197	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:205275421delA	ENST00000367157.3	-	5	711	c.585delT	c.(583-585)ggtfs	p.G195fs		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GGTTGGAGAGACCGAAGTCAG	0.562																																					p.L196fs		Atlas-INDEL	.											.	NUAK2	107	.	0			c.586delC						.						113	108	110					1																	205275421		2203	4300	6503	SO:0001589	frameshift_variant	81788	exon5			.	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"SNF1/AMP activated protein kinase"	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.585delT	chr1.hg19:g.205275421delA	ENSP00000356125:p.Gly195fs	94.0	0.0		167.0	11.0	NM_030952		Frame_Shift_Del	DEL	ENST00000367157.3	hg19	CCDS1453.1																																																																																			.	.		0.562	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		-	205275421	A	-	205275421	7	5	103	1	0	1	0	1	0	0	0	0	10722	262	10	0	1313	0	NUAK2	1	205275421	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2357903	205275421	43975200	99	14722										
KLHDC8A	55220	hgsc.bcm.edu	37	chr1	205308534	205308534	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgcgtacttggactgtcgtCcccctgggggccagagcagg					rs369573058		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:205308534delC	ENST00000367156.3	-	7	1361	c.545delG	c.(544-546)ggafs	p.G182fs	KLHDC8A_ENST00000460687.1_Frame_Shift_Del_p.G48fs|KLHDC8A_ENST00000539253.1_Frame_Shift_Del_p.G182fs|KLHDC8A_ENST00000367155.3_Frame_Shift_Del_p.G182fs|KLHDC8A_ENST00000537168.1_Frame_Shift_Del_p.G69fs	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	182										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GGACTGTCGTCCCCCTGGGGG	0.542																																					p.G182fs		Atlas-INDEL	.											.	KLHDC8A	31	.	0			c.546delA						.						30	29	29					1																	205308534		2203	4300	6503	SO:0001589	frameshift_variant	55220	exon5			.		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.545delG	chr1.hg19:g.205308534delC	ENSP00000356124:p.Gly182fs	67.0	0.0		161.0	10.0	NM_001271864	B3KU70|Q9NVG5	Frame_Shift_Del	DEL	ENST00000367156.3	hg19	CCDS30985.1																																																																																			.	.		0.542	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203		-	205308534	C	-	205308534	7	5	103	1	0	1	0	1	0	0	0	0	8371	855	30	0	519	0	KLHDC8A	1	205308534	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	33113	205308534	43942087	100	14723										
C1orf107	27042	hgsc.bcm.edu	37	chr1	210010321	210010321	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaaatcaagcagcccattcaCccccctccagaaagaactct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:210010321delC	ENST00000491415.2	+	6	884	c.827delC	c.(826-828)accfs	p.T276fs		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	276					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						AGCCCATTCACCCCCCTCCAG	0.493																																					p.T276fs		Atlas-INDEL	.											.	DIEXF	97	.	0			c.826delA						.			5,4261		2,1,2130	119	128	125			4.7	0.8	1		126	6,8248		3,0,4124	no	frameshift	DIEXF	NM_014388.6		5,1,6254	A1A1,A1R,RR		0.0727,0.1172,0.0879			210010321	11,12509	2203	4300	6503	SO:0001589	frameshift_variant	27042	exon6			.	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.827delC	chr1.hg19:g.210010321delC	ENSP00000419005:p.Thr276fs	110.0	0.0		162.0	11.0	NM_014388	O75992|Q4VY00|Q63HL9	Frame_Shift_Del	DEL	ENST00000491415.2	hg19	CCDS1493.1																																																																																			.	.		0.493	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		-	210010321	C	-	210010321	7	5	103	1	0	1	0	1	0	0	0	0	1983	507	18	0	849	0	C1orf107	1	210010321	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	4701787	210010321	39240300	101	14724										
TAF1A	9015	hgsc.bcm.edu	37	chr1	222753126	222753126	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aataattcatgacgccaataTttttcatccggttagcaaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:222753126delT	ENST00000352967.4	-	4	568	c.380delA	c.(379-381)aatfs	p.N127fs	TAF1A_ENST00000350027.4_Frame_Shift_Del_p.N127fs|TAF1A_ENST00000465263.1_5'UTR|TAF1A_ENST00000543857.1_Frame_Shift_Del_p.N127fs|TAF1A_ENST00000366890.1_Frame_Shift_Del_p.N13fs|TAF1A_ENST00000391882.1_Frame_Shift_Del_p.N13fs	NM_005681.3	NP_005672.1	Q15573	TAF1A_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa	127					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA binding (GO:0003677)			kidney(3)|large_intestine(3)|lung(11)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(131;0.0186)		GACGCCAATATTTTTCATCCG	0.338																																					p.N127fs		Atlas-INDEL	.											.	TAF1A	35	.	0			c.381delT						.						106	116	113					1																	222753126		2203	4299	6502	SO:0001589	frameshift_variant	9015	exon4			.	L39060	CCDS1531.1, CCDS1532.1	1q42	2008-02-05	2002-08-29		ENSG00000143498	ENSG00000143498			11532	protein-coding gene	gene with protein product		604903	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kD"			7801123	Standard	NM_005681		Approved	TAFI48, SL1	uc009xdz.2	Q15573	OTTHUMG00000037544	ENST00000352967.4:c.380delA	chr1.hg19:g.222753126delT	ENSP00000327072:p.Asn127fs	139.0	0.0		202.0	13.0	NM_005681	B2RDZ8|D3DTB7|Q9NWA1	Frame_Shift_Del	DEL	ENST00000352967.4	hg19	CCDS1531.1																																																																																			.	.		0.338	TAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091493.2	NM_005681		-	222753126	T	-	222753126	7	5	103	1	0	1	0	1	0	0	0	0	15534	1493	52	0	1004	0	TAF1A	1	222753126	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	12742805	222753126	26497495	102	14725										
CAPN2	824	hgsc.bcm.edu	37	chr1	223934727	223934727	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatgctatgaagcgctatcaGggggtgccaccactgagggc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:223934727delG	ENST00000295006.5	+	5	898	c.589delG	c.(589-591)gggfs	p.G198fs	CAPN2_ENST00000433674.2_Frame_Shift_Del_p.G120fs	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	198	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)			breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		AGCGCTATCAGGGGGTGCCAC	0.527																																					p.S196fs		Atlas-INDEL	.											.	CAPN2	69	.	0			c.588delA						.						112	107	109					1																	223934727		2203	4300	6503	SO:0001589	frameshift_variant	824	exon5			.	J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"EF-hand domain containing"	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.589delG	chr1.hg19:g.223934727delG	ENSP00000295006:p.Gly198fs	133.0	0.0		193.0	14.0	NM_001748	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Frame_Shift_Del	DEL	ENST00000295006.5	hg19	CCDS31035.1																																																																																			.	.		0.527	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748		-	223934727	G	-	223934727	7	5	103	1	0	1	0	1	0	0	0	0	2629	1000	35	0	614	0	CAPN2	1	223934727	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1181601	223934727	25315894	103	14726										
TMEM63A	9725	hgsc.bcm.edu	37	chr1	226055702	226055702	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggtagtggatggcgtcctCcccacaccattccaggatct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:226055702delC	ENST00000366835.3	-	7	670	c.400delG	c.(400-402)gagfs	p.E134fs	TMEM63A_ENST00000537914.1_5'Flank|TMEM63A_ENST00000474478.1_5'Flank	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	134					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					ATGGCGTCCTCCCCACACCAT	0.532																																					p.E134fs		Atlas-INDEL	.											.	TMEM63A	75	.	0			c.401delA						.						166	122	137					1																	226055702		2203	4300	6503	SO:0001589	frameshift_variant	9725	exon7			.		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"KIAA0792"	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.400delG	chr1.hg19:g.226055702delC	ENSP00000355800:p.Glu134fs	73.0	0.0		178.0	11.0	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Frame_Shift_Del	DEL	ENST00000366835.3	hg19	CCDS31042.1																																																																																			.	.		0.532	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698		-	226055702	C	-	226055702	7	5	103	1	0	1	0	1	0	0	0	0	16205	864	30	0	2095	0	TMEM63A	1	226055702	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2120975	226055702	23194919	104	14727										
PARP1	142	hgsc.bcm.edu	37	chr1	226570841	226570841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggggaatatacggtcctgtTttttaaccttcaatttcttg	9	7	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:226570841T>C	ENST00000366794.5	-	8	1198	c.1055A>G	c.(1054-1056)aAa>aGa	p.K352R		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	352					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		ACGGTCCTGTTTTTTAACCTT	0.502								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.K352R		Atlas-SNP	.											PARP1,NS,carcinoma,0,1	PARP1	100	.	0			c.A1055G						.						115	143	134					1																	226570841		2203	4300	6503	SO:0001583	missense	142	exon8			TCCTGTTTTTTAA	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"Poly (ADP-ribose) polymerases"	270	protein-coding gene	gene with protein product		173870	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)", "poly (ADP-ribose) polymerase family, member 1"	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.1055A>G	chr1.hg19:g.226570841T>C	ENSP00000355759:p.Lys352Arg	78.0	0.0		148.0	0.0	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	hg19	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	T	8.952	0.968513	0.18659	.	.	ENSG00000143799	ENST00000366794	T	0.10192	2.9	5.27	2.95	0.34219	.	0.147960	0.64402	N	0.000015	T	0.04724	0.0128	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42258	-0.9462	10	0.15952	T	0.53	-10.5467	7.8417	0.29402	0.0:0.2327:0.0:0.7673	.	352	P09874	PARP1_HUMAN	R	352	ENSP00000355759:K352R	ENSP00000355759:K352R	K	-	2	0	PARP1	224637464	0.897000	0.30589	0.987000	0.45799	0.573000	0.36030	0.922000	0.28734	0.323000	0.23307	0.459000	0.35465	AAA	.	.		0.502	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		C	226570841	T	C	226570841	3	2	103	1	0	0	0	0	1	0	0	0	11463	1841	64	2	2053	2	PARP1	1	226570841	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	515139	226570841	22679780	105	14728										
WNT3A	89780	hgsc.bcm.edu	37	chr1	228238561	228238561	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcgggagttcgccgacgcccGggagaaccggccagatgccc	15	15	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:228238561G>A	ENST00000284523.1	+	3	596	c.518G>A	c.(517-519)cGg>cAg	p.R173Q	WNT3A_ENST00000366753.2_Missense_Mutation_p.R173Q	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	173					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				GCCGACGCCCGGGAGAACCGG	0.657																																					p.R173Q		Atlas-SNP	.											.	WNT3A	40	.	0			c.G518A						.						56	56	56					1																	228238561		2203	4300	6503	SO:0001583	missense	89780	exon3			ACGCCCGGGAGAA	AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"Wingless-type MMTV integration sites", "Endogenous ligands"	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.518G>A	chr1.hg19:g.228238561G>A	ENSP00000284523:p.Arg173Gln	123.0	0.0		237.0	47.0	NM_033131	Q3SY79|Q3SY80|Q969P2	Missense_Mutation	SNP	ENST00000284523.1	hg19	CCDS1564.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.127804	0.77549	.	.	ENSG00000154342	ENST00000284523;ENST00000366753	T;T	0.76578	-1.03;-1.03	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.76169	0.3950	L	0.57130	1.785	0.80722	D	1	B;B	0.27416	0.059;0.178	B;B	0.28139	0.025;0.086	T	0.75181	-0.3408	10	0.45353	T	0.12	.	17.8158	0.88634	0.0:0.0:1.0:0.0	.	173;173	P56704;Q3SY79	WNT3A_HUMAN;.	Q	173	ENSP00000284523:R173Q;ENSP00000355715:R173Q	ENSP00000284523:R173Q	R	+	2	0	WNT3A	226305184	1.000000	0.71417	0.876000	0.34364	0.740000	0.42216	9.787000	0.99055	2.221000	0.72209	0.591000	0.81541	CGG	.	.		0.657	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131		A	228238561	G	A	228238561	3	1	103	1	0	0	0	0	1	0	0	0	17404	1116	39	1	528	1	WNT3A	1	228238561	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	1667720	228238561	21012060	106	14729										
ARF1	375	hgsc.bcm.edu	37	chr1	228284858	228284858	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcttcaagggcctttttggcAaaaaagaaatgcgcatcctc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:228284858delA	ENST00000541182.1	+	2	305	c.43delA	c.(43-45)aaafs	p.K16fs	ARF1_ENST00000540651.1_Frame_Shift_Del_p.K16fs|MIR3620_ENST00000584469.1_RNA|ARF1_ENST00000478424.1_3'UTR|ARF1_ENST00000272102.5_Frame_Shift_Del_p.K16fs	NM_001024227.1|NM_001024228.1	NP_001019398.1|NP_001019399.1	P84077	ARF1_HUMAN	ADP-ribosylation factor 1	16					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular copper ion homeostasis (GO:0006878)|COPI coating of Golgi vesicle (GO:0048205)|dendritic spine organization (GO:0097061)|GTP catabolic process (GO:0006184)|long term synaptic depression (GO:0060292)|membrane organization (GO:0061024)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of Arp2/3 complex-mediated actin nucleation (GO:0034315)|regulation of defense response to virus by virus (GO:0050690)|regulation of receptor internalization (GO:0002090)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)	10		Prostate(94;0.0405)				CCTTTTTGGCAAAAAAGAAAT	0.547																																					p.G14fs		Atlas-INDEL	.											.,1	ARF1	24	.	0			c.42delC						.						121	101	108					1																	228284858		2203	4300	6503	SO:0001589	frameshift_variant	375	exon2			.	M84326	CCDS1565.1	1q42.13	2014-01-30			ENSG00000143761	ENSG00000143761		"ADP-ribosylation factors", "Endogenous ligands"	652	protein-coding gene	gene with protein product		103180				1577740	Standard	NM_001658		Approved		uc001hrr.3	P84077	OTTHUMG00000037595	ENST00000541182.1:c.43delA	chr1.hg19:g.228284858delA	ENSP00000440005:p.Lys16fs	105.0	0.0		162.0	10.0	NM_001024228	P10947|P32889	Frame_Shift_Del	DEL	ENST00000541182.1	hg19	CCDS1565.1																																																																																			.	.		0.547	ARF1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091650.1	NM_001024227		-	228284858	A	-	228284858	7	5	103	1	0	1	0	1	0	0	0	0	844	131	5	0	45	0	ARF1	1	228284858	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	46297	228284858	20965763	107	14730										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228564975	228564975	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgctctgggcccgagctgctCccctgcctggccgagaggtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:228564975delC	ENST00000422127.1	+	101	23306	c.23262delC	c.(23260-23262)ctcfs	p.L7754fs	OBSCN_ENST00000570156.2_Frame_Shift_Del_p.L8711fs|OBSCN_ENST00000366707.4_Frame_Shift_Del_p.L5388fs	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7754	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCGAGCTGCTCCCCTGCCTGG	0.692																																					p.L8711fs		Atlas-INDEL	.											.	OBSCN	2142	.	0			c.26132delT						.						11	15	13					1																	228564975		1939	3919	5858	SO:0001589	frameshift_variant	84033	exon112			.	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.23262delC	chr1.hg19:g.228564975delC	ENSP00000409493:p.Leu7754fs	55.0	0.0		115.0	10.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Del	DEL	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		-	228564975	C	-	228564975	7	5	103	1	0	1	0	1	0	0	0	0	10821	842	30	0	24870	0	OBSCN	1	228564975	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	280117	228564975	20685646	108	14731										
COG2	22796	hgsc.bcm.edu	37	chr1	230800279	230800279	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcggtcagttgagaaaattgAaaaaatcttaaactctcaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:230800279delA	ENST00000366669.4	+	5	546	c.431delA	c.(430-432)gaafs	p.E144fs	COG2_ENST00000535166.1_Frame_Shift_Del_p.E28fs|COG2_ENST00000534989.1_Frame_Shift_Del_p.E85fs|COG2_ENST00000366668.3_Frame_Shift_Del_p.E144fs	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	144					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GAGAAAATTGAAAAAATCTTA	0.269																																					p.E144fs		Atlas-INDEL	.											.	COG2	61	.	0			c.430delG						.						28	30	29					1																	230800279		2196	4274	6470	SO:0001589	frameshift_variant	22796	exon5			.	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"Components of oligomeric golgi complex"	6546	protein-coding gene	gene with protein product		606974	"low density lipoprotein receptor defect C complementing"	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.431delA	chr1.hg19:g.230800279delA	ENSP00000355629:p.Glu144fs	86.0	0.0		178.0	11.0	NM_007357	Q86U99	Frame_Shift_Del	DEL	ENST00000366669.4	hg19	CCDS1584.1																																																																																			.	.		0.269	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357		-	230800279	A	-	230800279	7	5	103	1	0	1	0	1	0	0	0	0	3660	246	9	0	449	0	COG2	1	230800279	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2235304	230800279	18450342	109	14732										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232568017	232568017	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gacattcagtcacttcaggcTcctcgggcggtgggctgccc	13	14	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:232568017T>C	ENST00000366630.1	-	15	4590	c.4232A>G	c.(4231-4233)gAg>gGg	p.E1411G	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.E1411G|SIPA1L2_ENST00000308942.4_Missense_Mutation_p.E485G			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1411					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CACTTCAGGCTCCTCGGGCGG	0.537																																					p.E1411G		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.A4232G						.						51	49	50					1																	232568017		1888	4116	6004	SO:0001583	missense	57568	exon14			TCAGGCTCCTCGG	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.4232A>G	chr1.hg19:g.232568017T>C	ENSP00000355589:p.Glu1411Gly	105.0	0.0		180.0	8.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	T	14.42	2.530028	0.45073	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.79033	-1.23;-1.23;2.71	5.92	5.92	0.95590	.	0.207654	0.43579	D	0.000549	T	0.71584	0.3357	L	0.43152	1.355	0.54753	D	0.999984	B;B	0.14012	0.001;0.009	B;B	0.15484	0.003;0.013	T	0.65747	-0.6093	10	0.23302	T	0.38	-29.9839	16.3648	0.83312	0.0:0.0:0.0:1.0	.	1411;485	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	G	1411;1411;485	ENSP00000355589:E1411G;ENSP00000262861:E1411G;ENSP00000309102:E485G	ENSP00000262861:E1411G	E	-	2	0	SIPA1L2	230634640	1.000000	0.71417	0.996000	0.52242	0.895000	0.52256	4.830000	0.62745	2.263000	0.75096	0.533000	0.62120	GAG	.	.		0.537	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		C	232568017	T	C	232568017	3	2	103	1	0	0	0	0	1	0	0	0	14345	1551	54	2	968	2	SIPA1L2	1	232568017	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1767738	232568017	16682604	110	14733										
LYST	1130	hgsc.bcm.edu	37	chr1	235880039	235880039	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgtccacataacgatcttcTttttctttatactgaacagc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:235880039delT	ENST00000389794.3	-	41	9774	c.9600delA	c.(9598-9600)aaafs	p.K3200fs	LYST_ENST00000389793.2_Frame_Shift_Del_p.K3200fs|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3200	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AACGATCTTCTTTTTCTTTAT	0.289																																					p.E3201fs		Atlas-INDEL	.											.	LYST	370	.	0			c.9601delG						.						69	71	70					1																	235880039		2200	4297	6497	SO:0001589	frameshift_variant	1130	exon41			.	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.9600delA	chr1.hg19:g.235880039delT	ENSP00000374444:p.Lys3200fs	103.0	0.0		220.0	15.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Frame_Shift_Del	DEL	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.289	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			-	235880039	T	-	235880039	7	5	103	1	0	1	0	1	0	0	0	0	9137	1606	56	0	1857	0	LYST	1	235880039	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3312022	235880039	13370582	111	14734										
RYR2	6262	hgsc.bcm.edu	37	chr1	237693788	237693788	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacatgctgaagacaaggtgAaaaaaatgaagctacccaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:237693788delA	ENST00000366574.2	+	25	3201	c.2884delA	c.(2884-2886)aaafs	p.K963fs	RYR2_ENST00000360064.6_Frame_Shift_Del_p.K961fs|RYR2_ENST00000542537.1_Frame_Shift_Del_p.K947fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	963	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGACAAGGTGAAAAAAATGAA	0.358																																					p.V961fs		Atlas-INDEL	.											.	RYR2	1273	.	0			c.2883delG						.						103	95	98					1																	237693788		1861	4097	5958	SO:0001589	frameshift_variant	6262	exon25			.	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2884delA	chr1.hg19:g.237693788delA	ENSP00000355533:p.Lys963fs	70.0	0.0		131.0	10.0	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Del	DEL	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.358	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		-	237693788	A	-	237693788	7	5	103	1	0	1	0	1	0	0	0	0	13784	247	9	0	2982	0	RYR2	1	237693788	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1813749	237693788	11556833	112	14735										
RGS7	6000	hgsc.bcm.edu	37	chr1	241262025	241262025	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgtacgaataggaattccaTttttttcatcttgcatccgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:241262025delT	ENST00000407727.1	-	2	115	c.116delA	c.(115-117)aatfs	p.N39fs	RGS7_ENST00000401882.1_Frame_Shift_Del_p.N39fs|RGS7_ENST00000366563.1_Frame_Shift_Del_p.N39fs|RGS7_ENST00000348120.2_Frame_Shift_Del_p.N39fs|RGS7_ENST00000366562.4_Frame_Shift_Del_p.N39fs|RGS7_ENST00000366564.1_Frame_Shift_Del_p.N39fs|RGS7_ENST00000366565.1_Frame_Shift_Del_p.N39fs|RGS7_ENST00000331110.7_Frame_Shift_Del_p.N13fs|RGS7_ENST00000446183.2_De_novo_Start_OutOfFrame			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	39	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			AGGAATTCCATTTTTTTCATC	0.353																																					p.N39fs		Atlas-INDEL	.											.	RGS7	308	.	0			c.117delT						.						184	162	170					1																	241262025		2203	4300	6503	SO:0001589	frameshift_variant	6000	exon3			.	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"Regulators of G-protein signaling"	10003	protein-coding gene	gene with protein product		602517	"regulator of G-protein signalling 7"			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.116delA	chr1.hg19:g.241262025delT	ENSP00000384428:p.Asn39fs	52.0	0.0		107.0	11.0	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Frame_Shift_Del	DEL	ENST00000407727.1	hg19																																																																																				.	.		0.353	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		-	241262025	T	-	241262025	7	5	103	1	0	1	0	1	0	0	0	0	13325	1493	52	0	1411	0	RGS7	1	241262025	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3568237	241262025	7988596	113	14736										
OR2C3	81472	hgsc.bcm.edu	37	chr1	247695757	247695757	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtttctagtgagggtcgtgtGgagaagcccaggaggacaaa	16	6	1	2	rs61746303|rs386641879	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:247695757G>C	ENST00000366487.3	-	2	418	c.57C>G	c.(55-57)tcC>tcG	p.S19S	GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000531662.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S19S(1)|p.S18S(1)		breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			AGGGTCGTGTGGAGAAGCCCA	0.488																																					p.S19S		Atlas-SNP	.											OR2C3,NS,carcinoma,0,2	OR2C3	92	.	2	Substitution - coding silent(2)	prostate(2)	c.C57G						.						78	73	74					1																	247695757		2203	4300	6503	SO:0001819	synonymous_variant	81472	exon2			TCGTGTGGAGAAG	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"GPCR / Class A : Olfactory receptors"	15005	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily C, member 4"	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.57C>G	chr1.hg19:g.247695757G>C		108.0	0.0		195.0	0.0	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Silent	SNP	ENST00000366487.3	hg19	CCDS1634.2																																																																																			.	G|0.996;A|0.004		0.488	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074		C	247695757	G	C	247695757	2	2	103	1	0	0	0	0	0	0	0	1	11002	1335	47	4		4	OR2C3	1	247695757	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	6433732	247695757	1554864	114	14737										
TAF1B	9014	hgsc.bcm.edu	37	chr2	10045015	10045015	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgactacgaggacatctacAaaaaaacagtagaagttgga	9	7	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:10045015A>T	ENST00000263663.5	+	9	1023	c.835A>T	c.(835-837)Aaa>Taa	p.K279*	TAF1B_ENST00000396242.3_Nonsense_Mutation_p.K24*	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	279	C-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGACATCTACAAAAAAACAGT	0.328																																					p.K279X		Atlas-SNP	.											TAF1B,NS,carcinoma,0,1	TAF1B	62	.	0			c.A835T						.						75	65	68					2																	10045015		2203	4300	6503	SO:0001587	stop_gained	9014	exon9			ATCTACAAAAAAA	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.835A>T	chr2.hg19:g.10045015A>T	ENSP00000263663:p.Lys279*	29.0	0.0		72.0	0.0	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Nonsense_Mutation	SNP	ENST00000263663.5	hg19	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648783	0.87958	.	.	ENSG00000115750	ENST00000263663;ENST00000396242	.	.	.	5.46	0.00658	0.14068	.	0.641420	0.17120	N	0.186264	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.238	2.8251	0.05483	0.6069:0.1237:0.1497:0.1198	.	.	.	.	X	279;24	.	.	K	+	1	0	TAF1B	9962466	0.964000	0.33143	0.630000	0.29268	0.414000	0.31173	0.565000	0.23578	0.355000	0.24131	0.383000	0.25322	AAA	.	.		0.328	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		T	10045015	A	T	10045015	4	4	103	1	0	0	0	0	0	1	0	0	15535	131	5	4	869	4	TAF1B	2	10045015	Nonsense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10		10045015	233154358	115	14738										
NOL10	79954	hgsc.bcm.edu	37	chr2	10742949	10742949	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttcttctattttctgtcgtaTtttatctttcctatattctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:10742949delT	ENST00000381685.5	-	16	1390	c.1285delA	c.(1285-1287)atafs	p.I429fs	NOL10_ENST00000538384.1_Frame_Shift_Del_p.I403fs|NOL10_ENST00000345985.3_Frame_Shift_Del_p.I379fs|AC092687.5_ENST00000414538.1_RNA|NOL10_ENST00000542668.1_Frame_Shift_Del_p.I379fs	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	429						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		TTCTGTCGTATTTTATCTTTC	0.279																																					p.I429fs		Atlas-INDEL	.											.	NOL10	22	.	0			c.1286delT						.						116	120	119					2																	10742949		2202	4298	6500	SO:0001589	frameshift_variant	79954	exon16			.	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"polyglutamine binding protein 5"	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1285delA	chr2.hg19:g.10742949delT	ENSP00000371101:p.Ile429fs	94.0	0.0		156.0	10.0	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Frame_Shift_Del	DEL	ENST00000381685.5	hg19	CCDS1673.2																																																																																			.	.		0.279	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894		-	10742949	T	-	10742949	7	5	103	1	0	1	0	1	0	0	0	0	10529	1493	52	0	805	0	NOL10	2	10742949	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	697934	10742949	232456424	116	14739										
WDR35	57539	hgsc.bcm.edu	37	chr2	20162082	20162082	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accaaatgtctccatctcgtTctcctcctttgaagcaatat	4	13	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:20162082T>C	ENST00000345530.3	-	11	1316	c.1201A>G	c.(1201-1203)Aac>Gac	p.N401D	WDR35_ENST00000281405.4_Intron|WDR35_ENST00000416055.2_Intron	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	401					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCATCTCGTTCTCCTCCTTT	0.333																																					p.N401D		Atlas-SNP	.											.	WDR35	92	.	0			c.A1201G						.						125	120	122					2																	20162082		2203	4300	6503	SO:0001583	missense	57539	exon11			TCTCGTTCTCCTC	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"WD repeat domain containing", "Intraflagellar transport homologs"	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.1201A>G	chr2.hg19:g.20162082T>C	ENSP00000314444:p.Asn401Asp	26.0	0.0		67.0	4.0	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	hg19	CCDS33152.1	.	.	.	.	.	.	.	.	.	.	T	9.584	1.124435	0.20959	.	.	ENSG00000118965	ENST00000345530	T	0.64438	-0.1	4.95	2.51	0.30379	.	0.627364	0.17343	N	0.177670	T	0.29190	0.0726	N	0.02539	-0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04495	-1.0947	10	0.33141	T	0.24	-7.5428	2.2218	0.03974	0.1562:0.0885:0.1619:0.5934	.	401	Q9P2L0	WDR35_HUMAN	D	401	ENSP00000314444:N401D	ENSP00000314444:N401D	N	-	1	0	WDR35	20025563	0.899000	0.30636	0.981000	0.43875	0.993000	0.82548	0.641000	0.24720	0.415000	0.25817	0.482000	0.46254	AAC	.	.		0.333	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779		C	20162082	T	C	20162082	3	2	103	1	0	0	0	0	1	0	0	0	17304	1783	62	2	2416	2	WDR35	2	20162082	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	9419133	20162082	223037291	117	14740										
ITSN2	50618	hgsc.bcm.edu	37	chr2	24469141	24469141	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtcccttggagaaactgagcTcatcttcattatttgctgca	8	10	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:24469141T>C	ENST00000355123.4	-	29	3877	c.3434A>G	c.(3433-3435)gAg>gGg	p.E1145G	ITSN2_ENST00000361999.3_Missense_Mutation_p.E1118G|ITSN2_ENST00000406921.3_Missense_Mutation_p.E1145G	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1145	SH3 5. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAACTGAGCTCATCTTCATT	0.368																																					p.E1145G		Atlas-SNP	.											.	ITSN2	224	.	0			c.A3434G						.						150	137	141					2																	24469141		2203	4300	6503	SO:0001583	missense	50618	exon29			CTGAGCTCATCTT	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.3434A>G	chr2.hg19:g.24469141T>C	ENSP00000347244:p.Glu1145Gly	82.0	0.0		120.0	5.0	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	hg19	CCDS1710.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.1|28.1	4.893867|4.893867	0.91889|0.91889	.|.	.|.	ENSG00000198399|ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000406921|ENST00000416160	T;T;T;T|.	0.65732|.	-0.17;-0.17;-0.17;-0.17|.	5.53|5.53	5.53|5.53	0.82687|0.82687	Src homology-3 domain (5);|.	0.000000|.	0.34245|.	U|.	0.004122|.	T|T	0.77519|0.77519	0.4142|0.4142	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.999|.	T|T	0.79112|0.79112	-0.1937|-0.1937	10|5	0.87932|.	D|.	0|.	.|.	15.9649|15.9649	0.79961|0.79961	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1145;1118;1145|.	Q9NZM3-3;Q9NZM3-2;Q9NZM3|.	.;.;ITSN2_HUMAN|.	G|G	1118;1145;1118;1145|73	ENSP00000354561:E1118G;ENSP00000347244:E1145G;ENSP00000370250:E1118G;ENSP00000384499:E1145G|.	ENSP00000347244:E1145G|.	E|S	-|-	2|1	0|0	ITSN2|ITSN2	24322645|24322645	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	7.649000|7.649000	0.83500|0.83500	2.239000|2.239000	0.73571|0.73571	0.383000|0.383000	0.25322|0.25322	GAG|AGC	.	.		0.368	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		C	24469141	T	C	24469141	3	2	103	1	0	0	0	0	1	0	0	0	7936	1551	54	2	1758	2	ITSN2	2	24469141	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4307059	24469141	218730232	118	14741										
NCOA1	8648	hgsc.bcm.edu	37	chr2	24920612	24920612	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgaggaagtgcatttatgcTtttttccaacctcagggcag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:24920612delT	ENST00000406961.1	+	11	1546	c.894delT	c.(892-894)gctfs	p.A298fs	NCOA1_ENST00000538539.1_Frame_Shift_Del_p.A298fs|NCOA1_ENST00000348332.3_Frame_Shift_Del_p.A298fs|NCOA1_ENST00000405141.1_Frame_Shift_Del_p.A298fs|NCOA1_ENST00000288599.5_Frame_Shift_Del_p.A298fs|NCOA1_ENST00000395856.3_Frame_Shift_Del_p.A298fs|NCOA1_ENST00000407230.1_Frame_Shift_Del_p.A147fs			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	298					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCATTTATGCTTTTTTCCAAC	0.388			T	PAX3	alveolar rhadomyosarcoma																																p.A298fs		Atlas-INDEL	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.893delC						.						129	124	126					2																	24920612		2203	4300	6503	SO:0001589	frameshift_variant	8648	exon9			.	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.894delT	chr2.hg19:g.24920612delT	ENSP00000385216:p.Ala298fs	101.0	0.0		182.0	11.0	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Frame_Shift_Del	DEL	ENST00000406961.1	hg19	CCDS1712.1																																																																																			.	.		0.388	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		-	24920612	T	-	24920612	7	5	103	1	0	1	0	1	0	0	0	0	10237	1596	56	0	920	0	NCOA1	2	24920612	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	451471	24920612	218278761	119	14742										
RAB10	10890	hgsc.bcm.edu	37	chr2	26257589	26257589	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgatgccttcaatactaccTttatttccaccataggtaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:26257589delT	ENST00000264710.4	+	1	611	c.112delT	c.(112-114)tttfs	p.F38fs		NM_016131.4	NP_057215.3	P61026	RAB10_HUMAN	RAB10, member RAS oncogene family	38					antigen processing and presentation (GO:0019882)|axonogenesis (GO:0007409)|basolateral protein localization (GO:0061467)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum tubular network organization (GO:0071786)|endosomal transport (GO:0016197)|establishment of neuroblast polarity (GO:0045200)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|establishment of protein localization to membrane (GO:0090150)|Golgi to plasma membrane protein transport (GO:0043001)|Golgi to plasma membrane transport (GO:0006893)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|polarized epithelial cell differentiation (GO:0030859)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum tubular network (GO:0071782)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|insulin-responsive compartment (GO:0032593)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			lung(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAATACTACCTTTATTTCCAC	0.488																																					p.T37fs		Atlas-INDEL	.											.	RAB10	14	.	0			c.111delC						.						156	146	149					2																	26257589		2203	4300	6503	SO:0001589	frameshift_variant	10890	exon1			.	AF106681	CCDS1720.1	2p23.3	2008-05-21			ENSG00000084733	ENSG00000084733		"RAB, member RAS oncogene"	9759	protein-coding gene	gene with protein product	"ras-related GTP-binding protein"	612672				7688123	Standard	NM_016131		Approved		uc002rgv.3	P61026	OTTHUMG00000094796	ENST00000264710.4:c.112delT	chr2.hg19:g.26257589delT	ENSP00000264710:p.Phe38fs	173.0	0.0		204.0	13.0	NM_016131	D6W538|O88386|Q6IA52|Q9D7X6|Q9H0T3	Frame_Shift_Del	DEL	ENST00000264710.4	hg19	CCDS1720.1																																																																																			.	.		0.488	RAB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211610.1	NM_016131		-	26257589	T	-	26257589	7	5	103	1	0	1	0	1	0	0	0	0	12905	1609	56	0	114	0	RAB10	2	26257589	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1336977	26257589	216941784	120	14743										
HADHB	3032	hgsc.bcm.edu	37	chr2	26505888	26505888	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctagggattttatgtatgtgTctcaggatccaaaagatcaa	9	6	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:26505888T>C	ENST00000317799.5	+	12	1134	c.1030T>C	c.(1030-1032)Tct>Cct	p.S344P	HADHB_ENST00000405867.3_Missense_Mutation_p.S221P|HADHB_ENST00000545822.1_Missense_Mutation_p.S322P|HADHB_ENST00000537713.1_Missense_Mutation_p.S329P|HADHB_ENST00000494615.1_3'UTR	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	344					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATGTATGTGTCTCAGGATCC	0.318																																					p.S344P		Atlas-SNP	.											.	HADHB	50	.	0			c.T1030C						.						158	160	159					2																	26505888		2203	4300	6503	SO:0001583	missense	3032	exon12			TATGTGTCTCAGG		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"mitochondrial trifunctional protein, beta subunit"	143450	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.1030T>C	chr2.hg19:g.26505888T>C	ENSP00000325136:p.Ser344Pro	87.0	0.0		129.0	6.0	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Missense_Mutation	SNP	ENST00000317799.5	hg19	CCDS1722.1	.	.	.	.	.	.	.	.	.	.	T	19.86	3.905481	0.72868	.	.	ENSG00000138029	ENST00000317799;ENST00000405867;ENST00000537713;ENST00000545822	D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15	5.95	5.95	0.96441	Thiolase-like, subgroup (1);Thiolase-like (1);Thiolase, C-terminal (1);	0.048692	0.85682	D	0.000000	D	0.97012	0.9024	M	0.86573	2.825	0.80722	D	1	P;P;D;D	0.76494	0.952;0.933;0.999;0.961	P;P;D;P	0.83275	0.713;0.811;0.996;0.811	D	0.97637	1.0146	10	0.87932	D	0	-14.1637	15.2563	0.73588	0.0:0.0:0.0:1.0	.	329;322;221;344	F5GZQ3;B4E2W0;B5MD38;P55084	.;.;.;ECHB_HUMAN	P	344;221;329;322	ENSP00000325136:S344P;ENSP00000385411:S221P;ENSP00000444295:S329P;ENSP00000442665:S322P	ENSP00000325136:S344P	S	+	1	0	HADHB	26359392	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.599000	0.82757	2.281000	0.76405	0.528000	0.53228	TCT	.	.		0.318	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183		C	26505888	T	C	26505888	3	2	103	1	0	0	0	0	1	0	0	0	6953	1667	58	2	1072	2	HADHB	2	26505888	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	248299	26505888	216693485	121	14744										
GPR113	165082	hgsc.bcm.edu	37	chr2	26540962	26540962	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcggccaaagctagaagataGggggatggggcaggcaggga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:26540962delG	ENST00000311519.1	-	2	207	c.208delC	c.(208-210)ctafs	p.L70fs	GPR113_ENST00000421160.2_Intron|GPR113_ENST00000459892.1_Intron|GPR113_ENST00000333478.6_Intron|GPR113_ENST00000541401.1_Intron	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	70					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTAGAAGATAGGGGGATGGGG	0.577																																					p.L70fs		Atlas-INDEL	.											.	GPR113	134	.	0			c.209delT						.						57	63	61					2																	26540962		692	1591	2283	SO:0001589	frameshift_variant	165082	exon2			.	AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"-", "GPCR / Class B : Orphans"	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.208delC	chr2.hg19:g.26540962delG	ENSP00000307831:p.Leu70fs	107.0	0.0		161.0	13.0	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Frame_Shift_Del	DEL	ENST00000311519.1	hg19	CCDS46239.1																																																																																			.	.		0.577	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		-	26540962	G	-	26540962	7	5	103	1	0	1	0	1	0	0	0	0	6638	991	35	0	3168	0	GPR113	2	26540962	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	35074	26540962	216658411	122	14745										
FOSL2	2355	hgsc.bcm.edu	37	chr2	28635091	28635091	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcaagcccatcagcattgctGggggcttctacggtgaggag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:28635091delG	ENST00000264716.4	+	4	1620	c.757delG	c.(757-759)gggfs	p.G254fs	FOSL2_ENST00000545753.1_Frame_Shift_Del_p.G215fs|FOSL2_ENST00000379619.1_Frame_Shift_Del_p.G246fs	NM_005253.3	NP_005244.1	P15408	FOSL2_HUMAN	FOS-like antigen 2	254					cell death (GO:0008219)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)					CAGCATTGCTGGGGGCTTCTA	0.632																																					p.A252fs		Atlas-INDEL	.											.	FOSL2	39	.	0			c.756delT						.						44	40	41					2																	28635091		2203	4300	6503	SO:0001589	frameshift_variant	2355	exon4			.		CCDS1766.1	2p23.3	2013-01-10			ENSG00000075426	ENSG00000075426		"basic leucine zipper proteins"	3798	protein-coding gene	gene with protein product		601575					Standard	NM_005253		Approved	FRA2, FLJ23306	uc002rma.3	P15408	OTTHUMG00000097832	ENST00000264716.4:c.757delG	chr2.hg19:g.28635091delG	ENSP00000264716:p.Gly254fs	93.0	0.0		137.0	11.0	NM_005253	B2RD58|B3KP27|B4DYV4|Q6FG46	Frame_Shift_Del	DEL	ENST00000264716.4	hg19	CCDS1766.1																																																																																			.	.		0.632	FOSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215116.2	NM_005253		-	28635091	G	-	28635091	7	5	103	1	0	1	0	1	0	0	0	0	5996	1348	47	0	771	0	FOSL2	2	28635091	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2094129	28635091	214564282	123	14746										
PLB1	151056	hgsc.bcm.edu	37	chr2	28788183	28788183	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtccacacctgggaacgtcTtggacgtcttgactcagtac	11	12	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:28788183T>C	ENST00000327757.5	+	19	1287	c.1243T>C	c.(1243-1245)Ttg>Ctg	p.L415L	PLB1_ENST00000422425.2_Silent_p.L426L|PLB1_ENST00000329020.6_Silent_p.L103L	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	415	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TGGGAACGTCTTGGACGTCTT	0.612																																					p.L426L		Atlas-SNP	.											.	PLB1	255	.	0			c.T1276C						.						69	61	64					2																	28788183		2203	4300	6503	SO:0001819	synonymous_variant	151056	exon19			AACGTCTTGGACG		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.1243T>C	chr2.hg19:g.28788183T>C		86.0	0.0		99.0	4.0	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	hg19	CCDS33168.1																																																																																			.	.		0.612	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			C	28788183	T	C	28788183	2	2	103	1	0	0	0	0	0	0	0	1	12033	1606	56	2		2	PLB1	2	28788183	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	153092	28788183	214411190	124	14747										
SPDYA	245711	hgsc.bcm.edu	37	chr2	29041943	29041943	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taattcaagatttcttgtggAtggactgctgctgtaaaatt	9	5	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:29041943A>G	ENST00000334056.5	+	4	454	c.265A>G	c.(265-267)Atg>Gtg	p.M89V	SPDYA_ENST00000379579.4_Missense_Mutation_p.M89V|SPDYA_ENST00000462832.1_3'UTR	NM_182756.3	NP_877433.2			speedy/RINGO cell cycle regulator family member A											cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(172;0.155)					TTTCTTGTGGATGGACTGCTG	0.303																																					p.M89V		Atlas-SNP	.											.	SPDYA	41	.	0			c.A265G						.						129	131	130					2																	29041943		2203	4300	6503	SO:0001583	missense	245711	exon3			TTGTGGATGGACT	AA424209	CCDS1767.2	2p23	2013-05-08	2013-05-08	2006-03-31	ENSG00000163806	ENSG00000163806		"Speedy homologs"	30613	protein-coding gene	gene with protein product		614029	"speedy homolog 1 (Drosophila)", "speedy homolog A (Xenopus laevis)"	SPDY1		11980914, 12839962, 15611625	Standard	NM_182756		Approved	SPY1, Ringo3	uc002rmk.3	Q5MJ70	OTTHUMG00000074041	ENST00000334056.5:c.265A>G	chr2.hg19:g.29041943A>G	ENSP00000335628:p.Met89Val	62.0	0.0		95.0	4.0	NM_001142634		Missense_Mutation	SNP	ENST00000334056.5	hg19	CCDS1767.2	.	.	.	.	.	.	.	.	.	.	A	18.87	3.716049	0.68844	.	.	ENSG00000163806	ENST00000379579;ENST00000334056;ENST00000449210	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	U	0.000000	T	0.67468	0.2896	M	0.67953	2.075	0.58432	D	0.999996	D;P	0.54047	0.964;0.915	P;P	0.53102	0.718;0.596	T	0.71619	-0.4538	9	0.59425	D	0.04	-17.5259	15.054	0.71897	1.0:0.0:0.0:0.0	.	89;89	Q5MJ70;Q5MJ70-1	SPDYA_HUMAN;.	V	89	.	ENSP00000335628:M89V	M	+	1	0	SPDYA	28895447	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.343000	0.65976	2.016000	0.59253	0.533000	0.62120	ATG	.	.		0.303	SPDYA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157171.1	NM_182756		G	29041943	A	G	29041943	3	3	103	1	0	0	0	0	1	0	0	0	15042	333	12	2	271	2	SPDYA	2	29041943	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	253760	29041943	214157430	125	14748										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29294038	29294038	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggggctcacaggtgggctGgggggcgtctgcacagcaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:29294038delG	ENST00000331664.5	-	1	3089	c.3090delC	c.(3088-3090)cccfs	p.P1030fs		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1030	Pro-rich.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CAGGTGGGCTGGGGGGCGTCT	0.667																																					p.S1031fs		Atlas-INDEL	.											.	C2orf71	146	.	0			c.3091delA						.						29	35	33					2																	29294038		1942	4118	6060	SO:0001589	frameshift_variant	388939	exon1			.		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3090delC	chr2.hg19:g.29294038delG	ENSP00000332809:p.Pro1030fs	128.0	0.0		190.0	12.0	NM_001029883		Frame_Shift_Del	DEL	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.		0.667	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		-	29294038	G	-	29294038	7	5	103	1	0	1	0	1	0	0	0	0	2193	1335	47	0	784	0	C2orf71	2	29294038	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	252095	29294038	213905335	126	14749										
XDH	7498	hgsc.bcm.edu	37	chr2	31571774	31571774	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaagcaattacctgattcagAaaaggaactgtaaagcttat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:31571774delA	ENST00000379416.3	-	27	3090	c.3042delT	c.(3040-3042)tttfs	p.F1014fs		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	1014					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	CCTGATTCAGAAAAGGAACTG	0.383																																					p.L1015X	Colon(66;682 1445 30109 40147)	Atlas-INDEL	.											.	XDH	191	.	0			c.3043delC						.						95	94	94					2																	31571774		2203	4300	6503	SO:0001589	frameshift_variant	7498	exon27			.	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.3042delT	chr2.hg19:g.31571774delA	ENSP00000368727:p.Phe1014fs	90.0	0.0		173.0	11.0	NM_000379	Q16681|Q16712|Q4PJ16	Frame_Shift_Del	DEL	ENST00000379416.3	hg19	CCDS1775.1																																																																																			.	.		0.383	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		-	31571774	A	-	31571774	7	5	103	1	0	1	0	1	0	0	0	0	17441	243	9	0	999	0	XDH	2	31571774	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2277736	31571774	211627599	127	14750										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32733177	32733177	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaagccgaagtagcttctgcTgtctgccttagactacatcg	9	11	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:32733177T>C	ENST00000421745.2	+	51	9965	c.9831T>C	c.(9829-9831)gcT>gcC	p.A3277A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3277					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TAGCTTCTGCTGTCTGCCTTA	0.458																																					p.A3277A	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T9831C						.						96	88	91					2																	32733177		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon51			TTCTGCTGTCTGC	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.9831T>C	chr2.hg19:g.32733177T>C		167.0	0.0		216.0	92.0	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.		0.458	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32733177	T	C	32733177	2	2	103	1	0	0	0	0	0	0	0	1	1438	1567	55	2		2	BIRC6	2	32733177	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1161403	32733177	210466196	128	14751										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33413701	33413701	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acatcctcctgaagcttccgTccagatacatcaggtttcaa	6	13	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:33413701T>C	ENST00000404816.2	+	7	1837	c.1484T>C	c.(1483-1485)gTc>gCc	p.V495A	LTBP1_ENST00000390003.4_Missense_Mutation_p.V169A|LTBP1_ENST00000418533.2_Missense_Mutation_p.V169A|LTBP1_ENST00000407925.1_Missense_Mutation_p.V169A|LTBP1_ENST00000404525.1_Missense_Mutation_p.V169A|LTBP1_ENST00000402934.1_Missense_Mutation_p.V169A|LTBP1_ENST00000354476.3_Missense_Mutation_p.V495A			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	495					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GAAGCTTCCGTCCAGATACAT	0.443																																					p.V495A		Atlas-SNP	.											.	LTBP1	317	.	0			c.T1484C						.						93	90	91					2																	33413701		2203	4300	6503	SO:0001583	missense	4052	exon7			CTTCCGTCCAGAT		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.1484T>C	chr2.hg19:g.33413701T>C	ENSP00000386043:p.Val495Ala	37.0	0.0		59.0	4.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	T	22.2	4.258067	0.80246	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000432635;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925	D;D;D;D;D;D;D	0.87650	-2.28;-2.19;-2.01;-2.02;-2.06;-2.05;-1.98	5.38	5.38	0.77491	.	.	.	.	.	D	0.92799	0.7710	M	0.69523	2.12	0.80722	D	1	D;D;D;D;D;D	0.89917	0.968;0.962;1.0;0.99;0.99;0.981	P;B;D;P;P;P	0.97110	0.708;0.339;1.0;0.624;0.624;0.694	D	0.93616	0.6943	9	0.87932	D	0	.	15.7502	0.77980	0.0:0.0:0.0:1.0	.	495;169;169;169;169;495	Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	LTBP1_HUMAN;.;.;.;.;.	A	495;495;184;169;169;169;169;169	ENSP00000386043:V495A;ENSP00000346467:V495A;ENSP00000374653:V169A;ENSP00000393057:V169A;ENSP00000384373:V169A;ENSP00000385359:V169A;ENSP00000384091:V169A	ENSP00000346467:V495A	V	+	2	0	LTBP1	33267205	1.000000	0.71417	0.954000	0.39281	0.612000	0.37316	7.350000	0.79385	2.192000	0.70111	0.449000	0.29647	GTC	.	.		0.443	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		C	33413701	T	C	33413701	3	2	103	1	0	0	0	0	1	0	0	0	9082	1667	58	2	1565	2	LTBP1	2	33413701	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	680524	33413701	209785672	129	14752										
STRN	6801	hgsc.bcm.edu	37	chr2	37129784	37129784	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catttacaactgagtcctgaTttttgtcatcttccctgtcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:37129784delT	ENST00000263918.4	-	5	610	c.602delA	c.(601-603)aatfs	p.N201fs	STRN_ENST00000379213.2_Frame_Shift_Del_p.N189fs	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	201					dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				TGAGTCCTGATTTTTGTCATC	0.393																																					p.N201fs		Atlas-INDEL	.											.	STRN	71	.	0			c.603delT						.						203	186	192					2																	37129784		2203	4300	6503	SO:0001589	frameshift_variant	6801	exon5			.	AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"WD repeat domain containing"	11424	protein-coding gene	gene with protein product		614765	"striatin, calmodulin-binding protein"			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.602delA	chr2.hg19:g.37129784delT	ENSP00000263918:p.Asn201fs	145.0	0.0		202.0	15.0	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Frame_Shift_Del	DEL	ENST00000263918.4	hg19	CCDS1784.1																																																																																			.	.		0.393	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1			-	37129784	T	-	37129784	7	5	103	1	0	1	0	1	0	0	0	0	15344	1493	52	0	1796	0	STRN	2	37129784	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3716083	37129784	206069589	130	14753										
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37449611	37449611	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	actgtttcctctgtctcaagTtttttcactatctctgtttc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:37449611delT	ENST00000234170.5	-	4	2122	c.1977delA	c.(1975-1977)aaafs	p.K659fs		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	659					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				CTGTCTCAAGTTTTTTCACTA	0.353																																					p.L660fs		Atlas-INDEL	.											.	CEBPZ	68	.	0			c.1978delC						.						142	134	137					2																	37449611		2203	4300	6503	SO:0001589	frameshift_variant	10153	exon4			.	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1977delA	chr2.hg19:g.37449611delT	ENSP00000234170:p.Lys659fs	150.0	0.0		188.0	12.0	NM_005760	Q8NE75	Frame_Shift_Del	DEL	ENST00000234170.5	hg19	CCDS1787.1																																																																																			.	.		0.353	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		-	37449611	T	-	37449611	7	5	103	1	0	1	0	1	0	0	0	0	3206	1722	60	0	1239	0	CEBPZ	2	37449611	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	319827	37449611	205749762	131	14754										
C2orf56	55471	hgsc.bcm.edu	37	chr2	37475305	37475305	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tagataaatcaaatgagccaTcagtgaggcagcagttactt	9	7	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:37475305T>C	ENST00000002125.4	+	10	1178	c.1138T>C	c.(1138-1140)Tca>Cca	p.S380P	NDUFAF7_ENST00000336237.6_Missense_Mutation_p.S282P	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	380					methylation (GO:0032259)|mitochondrial respiratory chain complex I assembly (GO:0032981)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|methyltransferase activity (GO:0008168)										AAATGAGCCATCAGTGAGGCA	0.348																																					p.S380P		Atlas-SNP	.											.	.	.	.	0			c.T1138C						.						85	80	82					2																	37475305		2203	4300	6503	SO:0001583	missense	55471	exon10			GAGCCATCAGTGA		CCDS1788.1, CCDS42673.1	2p22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000003509	ENSG00000003509		"Mitochondrial respiratory chain complex assembly factors"	28816	protein-coding gene	gene with protein product	"mitochondrial dysfunction protein A homolog"	615898	"chromosome 2 open reading frame 56"	C2orf56			Standard	NM_144736		Approved	PRO1853, MidA	uc002rqa.4	Q7L592	OTTHUMG00000128468	ENST00000002125.4:c.1138T>C	chr2.hg19:g.37475305T>C	ENSP00000002125:p.Ser380Pro	80.0	0.0		125.0	5.0	NM_144736	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	hg19	CCDS1788.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.247530	0.39697	.	.	ENSG00000003509	ENST00000002125;ENST00000336237	T;T	0.77750	-1.12;-1.12	5.94	-3.35	0.04928	.	0.417340	0.28688	N	0.014471	T	0.65144	0.2663	L	0.60455	1.87	0.09310	N	0.999995	B;B;B;B	0.19331	0.007;0.016;0.035;0.007	B;B;B;B	0.22152	0.006;0.011;0.038;0.006	T	0.55088	-0.8195	10	0.51188	T	0.08	-9.3551	3.5821	0.07957	0.2383:0.0651:0.4088:0.2878	.	353;309;282;380	E7EUC2;B4DQY3;Q7L592-2;Q7L592	.;.;.;MIDA_HUMAN	P	380;282	ENSP00000002125:S380P;ENSP00000337431:S282P	ENSP00000002125:S380P	S	+	1	0	C2orf56	37328809	0.002000	0.14202	0.525000	0.27900	0.912000	0.54170	0.187000	0.16998	-0.131000	0.11578	0.482000	0.46254	TCA	.	.		0.348	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736		C	37475305	T	C	37475305	3	2	103	1	0	0	0	0	1	0	0	0	2179	1435	50	2	1176	2	C2orf56	2	37475305	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	25694	37475305	205724068	132	14755										
DHX57	90957	hgsc.bcm.edu	37	chr2	39033812	39033812	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctccagtactggtcttctgAaattttccttctgggctttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:39033812delA	ENST00000295373.6	-	22	3831	c.3705delT	c.(3703-3705)tttfs	p.F1235fs		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1235							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TGGTCTTCTGAAATTTTCCTT	0.363																																					p.Q1236fs	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-INDEL	.											.	DHX57	127	.	0			c.3706delC						.						124	114	117					2																	39033812		2203	4300	6503	SO:0001589	frameshift_variant	90957	exon22			.	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3705delT	chr2.hg19:g.39033812delA	ENSP00000295373:p.Phe1235fs	124.0	0.0		183.0	12.0	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Frame_Shift_Del	DEL	ENST00000295373.6	hg19	CCDS1800.1																																																																																			.	.		0.363	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		-	39033812	A	-	39033812	7	5	103	1	0	1	0	1	0	0	0	0	4515	243	9	0	467	0	DHX57	2	39033812	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1558507	39033812	204165561	133	14756										
MSH2	4436	hgsc.bcm.edu	37	chr2	47639551	47639551	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taaactatttctttcaaaatAgataattcaaagaggaggaa	6	4	3	2	rs587779169|rs267607929		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:47639551A>T	ENST00000233146.2	+	4	868		c.e4-1		MSH2_ENST00000543555.1_Splice_Site|MSH2_ENST00000406134.1_Splice_Site	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2						ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTTTCAAAATAGATAATTCAA	0.299			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												.		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.646-2A>T						.						32	34	34					2																	47639551		2200	4300	6500	SO:0001630	splice_region_variant	4436	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CAAAATAGATAAT	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.646-1A>T	chr2.hg19:g.47639551A>T		211.0	0.0		293.0	83.0	NM_000251	B4E2Z2|O75488	Splice_Site	SNP	ENST00000233146.2	hg19	CCDS1834.1	.	.	.	.	.	.	.	.	.	.	A	10.91	1.483210	0.26598	.	.	ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000448533;ENST00000394792;ENST00000413880	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0583	0.71933	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MSH2	47493055	1.000000	0.71417	0.932000	0.37286	0.041000	0.13682	8.975000	0.93437	2.037000	0.60232	0.456000	0.33151	.	.	.		0.299	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		Intron	T	47639551	A	T	47639551	5	4	103	1	0	0	0	0	0	0	1	0	9879	434	15	4	658	4	MSH2	2	47639551	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	8605739	47639551	195559822	134	14757										
MSH6	2956	hgsc.bcm.edu	37	chr2	48025968	48025968	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatgaaataagcagtggagtGggggatagtgagagtgaagg					rs573638836		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:48025968delG	ENST00000234420.5	+	4	998	c.846delG	c.(844-846)gtgfs	p.V282fs	MSH6_ENST00000540021.1_Frame_Shift_Del_p.V152fs|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_5'UTR	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	282					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GCAGTGGAGTGGGGGATAGTG	0.468			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.V282fs		Atlas-INDEL	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.845delT						.						166	174	171					2																	48025968		2203	4300	6503	SO:0001589	frameshift_variant	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	.	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.846delG	chr2.hg19:g.48025968delG	ENSP00000234420:p.Val282fs	80.0	0.0		130.0	10.0	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Frame_Shift_Del	DEL	ENST00000234420.5	hg19	CCDS1836.1																																																																																			.	.		0.468	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		-	48025968	G	-	48025968	7	5	103	1	0	1	0	1	0	0	0	0	9883	1335	47	0	860	0	MSH6	2	48025968	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	386417	48025968	195173405	135	14758										
BCL11A	53335	hgsc.bcm.edu	37	chr2	60688969	60688969	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcggattgcagaggagggaGggggggcgtcgccaggaagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:60688969delG	ENST00000335712.6	-	4	1305	c.1078delC	c.(1078-1080)ctcfs	p.L360fs	BCL11A_ENST00000358510.4_Frame_Shift_Del_p.L326fs|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000538214.1_Frame_Shift_Del_p.L326fs|BCL11A_ENST00000356842.4_Frame_Shift_Del_p.L360fs|BCL11A_ENST00000537768.1_Intron|BCL11A_ENST00000359629.5_Intron	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	360	Pro-rich.				B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			AGAGGAGGGAGGGGGGGCGTC	0.632			T	IGH@	B-CLL																																p.L360fs		Atlas-INDEL	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.1079delT						.						39	48	44					2																	60688969		2198	4297	6495	SO:0001589	frameshift_variant	53335	exon4			.	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"Zinc fingers, C2H2-type"	13221	protein-coding gene	gene with protein product		606557	"ecotropic viral integration site 9"	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.1078delC	chr2.hg19:g.60688969delG	ENSP00000338774:p.Leu360fs	147.0	0.0		147.0	10.0	NM_022893	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Frame_Shift_Del	DEL	ENST00000335712.6	hg19	CCDS1862.1																																																																																			.	.		0.632	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		-	60688969	G	-	60688969	7	5	103	1	0	1	0	1	0	0	0	0	1363	1000	35	0	1539	0	BCL11A	2	60688969	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	12663001	60688969	182510404	136	14759										
REL	5966	hgsc.bcm.edu	37	chr2	61149213	61149213	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catttacaacaatgccgatgAcatagtcggaatggaagcgt	10	8	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:61149213A>G	ENST00000295025.8	+	11	1723	c.1403A>G	c.(1402-1404)gAc>gGc	p.D468G	REL_ENST00000394479.3_Missense_Mutation_p.D436G	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	468					cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			AATGCCGATGACATAGTCGGA	0.403			A		Hodgkin Lymphoma																																p.D468G		Atlas-SNP	.		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	REL	48	.	0			c.A1403G						.						111	97	102					2																	61149213		2203	4300	6503	SO:0001583	missense	5966	exon11			CCGATGACATAGT	M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.1403A>G	chr2.hg19:g.61149213A>G	ENSP00000295025:p.Asp468Gly	90.0	0.0		100.0	4.0	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Missense_Mutation	SNP	ENST00000295025.8	hg19	CCDS1864.1	.	.	.	.	.	.	.	.	.	.	A	6.162	0.398046	0.11696	.	.	ENSG00000162924	ENST00000295025;ENST00000394479	T;T	0.51071	0.72;0.82	5.4	4.27	0.50696	.	1.005800	0.07990	N	0.986987	T	0.27765	0.0683	N	0.12746	0.255	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.11767	-1.0574	10	0.30078	T	0.28	-14.0714	4.1185	0.10094	0.7971:0.0:0.2029:0.0	.	436;468	Q17RU2;Q04864	.;REL_HUMAN	G	468;436	ENSP00000295025:D468G;ENSP00000377989:D436G	ENSP00000295025:D468G	D	+	2	0	REL	61002717	0.981000	0.34729	0.184000	0.23157	0.115000	0.19883	1.999000	0.40806	2.044000	0.60594	0.528000	0.53228	GAC	.	.		0.403	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908		G	61149213	A	G	61149213	3	3	103	1	0	0	0	0	1	0	0	0	13230	275	10	2	1445	2	REL	2	61149213	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	460244	61149213	182050160	137	14760										
USP34	9736	hgsc.bcm.edu	37	chr2	61571112	61571112	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctgattttgcactaacctGggagctactacaactgacat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:61571112delG	ENST00000398571.2	-	16	2414	c.2338delC	c.(2338-2340)cagfs	p.Q780fs		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	780					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			GCACTAACCTGGGAGCTACTA	0.378																																					p.Q780fs		Atlas-INDEL	.											.	USP34	334	.	0			c.2339delA						.						110	98	102					2																	61571112		1899	4130	6029	SO:0001589	frameshift_variant	9736	exon16			.	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.2338delC	chr2.hg19:g.61571112delG	ENSP00000381577:p.Gln780fs	152.0	0.0		149.0	10.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Frame_Shift_Del	DEL	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.		0.378	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			-	61571112	G	-	61571112	7	5	103	1	0	1	0	1	0	0	0	0	17080	1357	47	0	8562	0	USP34	2	61571112	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	421899	61571112	181628261	138	14761										
COMMD1	150684	hgsc.bcm.edu	37	chr2	62132979	62132979	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcccctttctggcaaagatgAgggggattcttaaggtactg	13	8	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:62132979A>G	ENST00000311832.5	+	1	198	c.166A>G	c.(166-168)Agg>Ggg	p.R56G	COMMD1_ENST00000538736.1_Missense_Mutation_p.R56G|COMMD1_ENST00000472729.1_Intron	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	56					copper ion homeostasis (GO:0055070)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of protein ubiquitination (GO:0031398)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			GGCAAAGATGAGGGGGATTCT	0.592																																					p.R56G		Atlas-SNP	.											.	COMMD1	17	.	0			c.A166G						.						51	49	50					2																	62132979		2203	4300	6503	SO:0001583	missense	150684	exon1			AAGATGAGGGGGA	BC022046	CCDS1869.1	2p15	2004-03-02	2004-02-13	2004-02-18	ENSG00000173163	ENSG00000173163			23024	protein-coding gene	gene with protein product	"copper metabolism gene MURR1"	607238	"chromosome 2 open reading frame 5 (MURR1)"	C2orf5		9001233, 11809725	Standard	NM_152516		Approved	MURR1, MGC27155	uc002sbp.3	Q8N668	OTTHUMG00000129445	ENST00000311832.5:c.166A>G	chr2.hg19:g.62132979A>G	ENSP00000308236:p.Arg56Gly	81.0	0.0		85.0	5.0	NM_152516	B4DFQ4|Q96GS0	Missense_Mutation	SNP	ENST00000311832.5	hg19	CCDS1869.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.937999	0.73557	.	.	ENSG00000173163	ENST00000311832;ENST00000538736	T;T	0.09817	2.94;2.94	5.78	3.22	0.36961	.	0.248111	0.44688	D	0.000433	T	0.09247	0.0228	L	0.39397	1.21	0.46849	D	0.999227	B	0.13145	0.007	B	0.17979	0.02	T	0.12293	-1.0553	10	0.32370	T	0.25	.	9.9166	0.41439	0.7418:0.2581:0.0:0.0	.	56	Q8N668	COMD1_HUMAN	G	56	ENSP00000308236:R56G;ENSP00000438961:R56G	ENSP00000308236:R56G	R	+	1	2	COMMD1	61986483	0.997000	0.39634	0.996000	0.52242	0.973000	0.67179	0.240000	0.18042	2.220000	0.72140	0.533000	0.62120	AGG	.	.		0.592	COMMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251607.2	NM_152516		G	62132979	A	G	62132979	3	3	103	1	0	0	0	0	1	0	0	0	3716	295	11	2	168	2	COMMD1	2	62132979	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	561867	62132979	181066394	139	14762										
EHBP1	23301	hgsc.bcm.edu	37	chr2	62934345	62934345	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcatggcttcagtttggaagAgactgcagcgtgtgggaaaa	14	6	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:62934345A>G	ENST00000263991.5	+	2	501	c.19A>G	c.(19-21)Aga>Gga	p.R7G	EHBP1_ENST00000405015.3_Missense_Mutation_p.R7G|EHBP1_ENST00000354487.3_Missense_Mutation_p.R7G|EHBP1_ENST00000405289.1_Missense_Mutation_p.R7G|EHBP1_ENST00000431489.1_Missense_Mutation_p.R7G	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	7						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			AGTTTGGAAGAGACTGCAGCG	0.473																																					p.R7G		Atlas-SNP	.											.	EHBP1	127	.	0			c.A19G						.						158	149	152					2																	62934345		2203	4300	6503	SO:0001583	missense	23301	exon2			TGGAAGAGACTGC	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.19A>G	chr2.hg19:g.62934345A>G	ENSP00000263991:p.Arg7Gly	159.0	0.0		156.0	9.0	NM_001142616	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	hg19	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.092655	0.56075	.	.	ENSG00000115504	ENST00000405015;ENST00000405482;ENST00000427809;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	D;T;D;D;D;D	0.81908	-1.55;0.28;-1.55;-1.54;-1.54;-1.54	4.85	3.67	0.42095	.	0.000000	0.64402	D	0.000001	D	0.89894	0.6847	M	0.78637	2.42	0.52501	D	0.999956	D;D;D;D	0.89917	0.996;0.967;1.0;0.995	D;P;D;D	0.83275	0.99;0.879;0.996;0.989	D	0.89685	0.3893	10	0.87932	D	0	.	11.3547	0.49609	0.8418:0.1582:0.0:0.0	.	7;7;7;7	Q8NDI1-2;A8K930;Q8NDI1-3;Q8NDI1	.;.;.;EHBP1_HUMAN	G	7	ENSP00000384143:R7G;ENSP00000384829:R7G;ENSP00000403783:R7G;ENSP00000263991:R7G;ENSP00000346482:R7G;ENSP00000385524:R7G	ENSP00000263991:R7G	R	+	1	2	EHBP1	62787849	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.971000	0.63749	0.673000	0.31224	0.460000	0.39030	AGA	.	.		0.473	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		G	62934345	A	G	62934345	3	3	103	1	0	0	0	0	1	0	0	0	4977	296	11	2	21	2	EHBP1	2	62934345	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	801366	62934345	180265028	140	14763										
C1D	10438	hgsc.bcm.edu	37	chr2	68270088	68270088	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attttggttcccagagggcaTtttttacaaatcttgaagct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:68270088delT	ENST00000355848.3	-	5	406	c.359delA	c.(358-360)aatfs	p.N120fs	C1D_ENST00000409302.1_Frame_Shift_Del_p.N120fs|C1D_ENST00000407324.1_Frame_Shift_Del_p.N159fs|C1D_ENST00000410067.3_Frame_Shift_Del_p.N120fs			Q13901	C1D_HUMAN	C1D nuclear receptor corepressor	120	Interaction with NCOR1 and NCOR2. {ECO:0000250}.				apoptotic process (GO:0006915)|maturation of 5.8S rRNA (GO:0000460)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)			lung(2)|urinary_tract(1)	3						CCAGAGGGCATTTTTTACAAA	0.348																																					p.N120fs		Atlas-INDEL	.											.	C1D	11	.	0			c.360delT						.						24	28	27					2																	68270088		2199	4296	6495	SO:0001589	frameshift_variant	10438	exon6			.		CCDS1883.1	2p13-p12	2010-06-10	2010-06-10		ENSG00000197223	ENSG00000197223			29911	protein-coding gene	gene with protein product	"small unique nuclear receptor co-repressor"	606997	"C1D nuclear receptor co-repressor"			9469821, 17599775, 17412707, 11801738, 9405624	Standard	NM_006333		Approved	SUNCOR, SUN-CoR, LRP1	uc002seb.3	Q13901	OTTHUMG00000129564	ENST00000355848.3:c.359delA	chr2.hg19:g.68270088delT	ENSP00000348107:p.Asn120fs	122.0	0.0		164.0	10.0	NM_001190265	A8K336|D6W5F8|Q05D64	Frame_Shift_Del	DEL	ENST00000355848.3	hg19	CCDS1883.1																																																																																			.	.		0.348	C1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251757.3	NM_006333		-	68270088	T	-	68270088	7	5	103	1	0	1	0	1	0	0	0	0	1953	1493	52	0	70	0	C1D	2	68270088	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5335743	68270088	174929285	141	14764										
GMCL1	64395	hgsc.bcm.edu	37	chr2	70076825	70076825	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccttcttggaatggatctttAaaacagcttttgacagaaac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:70076825delA	ENST00000282570.3	+	8	1136	c.885delA	c.(883-885)ttafs	p.L295fs		NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	295					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)				endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						ATGGATCTTTAAAACAGCTTT	0.289																																					p.L295X		Atlas-INDEL	.											.	GMCL1	50	.	0			c.884delT						.						86	88	87					2																	70076825		2203	4298	6501	SO:0001589	frameshift_variant	64395	exon8			.	AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"BTB/POZ domain containing"	23843	protein-coding gene	gene with protein product	"spermatogenesis associated 29"		"germ cell-less homolog 1 (Drosophila)"				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.885delA	chr2.hg19:g.70076825delA	ENSP00000282570:p.Leu295fs	175.0	0.0		221.0	14.0	NM_178439	Q9H826|Q9H8V7|Q9H927	Frame_Shift_Del	DEL	ENST00000282570.3	hg19	CCDS1895.1																																																																																			.	.		0.289	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439		-	70076825	A	-	70076825	7	5	103	1	0	1	0	1	0	0	0	0	6493	359	13	0	915	0	GMCL1	2	70076825	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1806737	70076825	173122548	142	14765										
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71043906	71043906	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctggtgttttctaaactgcTttttaagaaattcagcgtct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:71043906delT	ENST00000272367.2	-	4	683	c.607delA	c.(607-609)agcfs	p.S204fs	CLEC4F_ENST00000426626.1_Frame_Shift_Del_p.S204fs	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	204					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						TCTAAACTGCTTTTTAAGAAA	0.443																																					p.S203fs	Colon(107;10 2157 6841 26035)	Atlas-INDEL	.											.	CLEC4F	95	.	0			c.608delG						.						98	94	96					2																	71043906		2203	4300	6503	SO:0001589	frameshift_variant	165530	exon4			.	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.607delA	chr2.hg19:g.71043906delT	ENSP00000272367:p.Ser204fs	149.0	0.0		172.0	11.0	NM_001258027	A4QPA5	Frame_Shift_Del	DEL	ENST00000272367.2	hg19	CCDS1910.1																																																																																			.	.		0.443	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		-	71043906	T	-	71043906	7	5	103	1	0	1	0	1	0	0	0	0	3518	1609	56	0	1178	0	CLEC4F	2	71043906	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	967081	71043906	172155467	143	14766										
DCTN1	1639	hgsc.bcm.edu	37	chr2	74597423	74597423	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttcttcttttccatgagctTctggagcttcacatgctcct	7	12	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:74597423T>C	ENST00000361874.3	-	12	1494	c.1177A>G	c.(1177-1179)Aag>Gag	p.K393E	DCTN1_ENST00000407639.2_Missense_Mutation_p.K259E|DCTN1_ENST00000409567.3_Missense_Mutation_p.K373E|DCTN1_ENST00000409438.1_Missense_Mutation_p.K259E|DCTN1_ENST00000409240.1_Missense_Mutation_p.K356E|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409868.1_Missense_Mutation_p.K376E|DCTN1_ENST00000394003.3_Missense_Mutation_p.K386E	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	393					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						TCCATGAGCTTCTGGAGCTTC	0.537																																					p.K393E		Atlas-SNP	.											.	DCTN1	110	.	0			c.A1177G						.						71	66	68					2																	74597423		2203	4300	6503	SO:0001583	missense	1639	exon12			TGAGCTTCTGGAG		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"p150 glued homolog (Drosophila)"	601143	"dynactin 1 (p150, Glued (Drosophila) homolog)"			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.1177A>G	chr2.hg19:g.74597423T>C	ENSP00000354791:p.Lys393Glu	83.0	0.0		96.0	4.0	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	hg19	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.624418	0.87560	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.76839	-1.0;-1.0;-1.0;-1.0;-1.0;-1.05;-1.0	4.97	4.97	0.65823	.	0.000000	0.45126	D	0.000383	D	0.86948	0.6056	M	0.78456	2.415	0.80722	D	1	D;P;D;B;P;D	0.76494	0.999;0.863;0.993;0.427;0.754;0.975	D;B;D;B;P;P	0.70935	0.971;0.445;0.956;0.436;0.71;0.833	D	0.87983	0.2744	10	0.54805	T	0.06	-8.0299	13.7753	0.63050	0.0:0.0:0.0:1.0	.	373;356;393;386;259;259	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	E	393;386;376;259;259;356;376;373	ENSP00000354791:K393E;ENSP00000377571:K386E;ENSP00000384844:K259E;ENSP00000387270:K259E;ENSP00000386406:K356E;ENSP00000387327:K376E;ENSP00000386843:K373E	ENSP00000354791:K393E	K	-	1	0	DCTN1	74450931	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.845000	0.86875	2.076000	0.62316	0.528000	0.53228	AAG	.	.		0.537	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		C	74597423	T	C	74597423	3	2	103	1	0	0	0	0	1	0	0	0	4308	1792	62	2	2743	2	DCTN1	2	74597423	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3553517	74597423	168601950	144	14767										
REG1B	5968	hgsc.bcm.edu	37	chr2	79313509	79313509	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgaccttttttgggtcatggAggccaatccagacattgctg	11	9	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:79313509A>G	ENST00000305089.3	-	4	385	c.305T>C	c.(304-306)cTc>cCc	p.L102P		NM_006507.3	NP_006498.1	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta	102	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell proliferation (GO:0008283)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)	p.I100fs*39(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(40)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	51						TGGGTCATGGAGGCCAATCCA	0.512																																					p.L102P		Atlas-SNP	.											.,1	REG1B	83	.	1	Deletion - Frameshift(1)	prostate(1)	c.T305C						.						114	101	106					2																	79313509		2203	4300	6503	SO:0001583	missense	5968	exon4			TCATGGAGGCCAA		CCDS1963.1	2p12	2008-06-04	2008-06-04		ENSG00000172023	ENSG00000172023			9952	protein-coding gene	gene with protein product	"lithostathine 1 beta", "secretory pancreatic stone protein 2"	167771	"regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic thread protein)"			8110835	Standard	NM_006507		Approved	REGL, PSPS2, REGH, REGI-BETA	uc002sny.2	P48304	OTTHUMG00000130019	ENST00000305089.3:c.305T>C	chr2.hg19:g.79313509A>G	ENSP00000303206:p.Leu102Pro	117.0	0.0		142.0	7.0	NM_006507		Missense_Mutation	SNP	ENST00000305089.3	hg19	CCDS1963.1	.	.	.	.	.	.	.	.	.	.	a	12.18	1.859750	0.32884	.	.	ENSG00000172023	ENST00000454188;ENST00000305089	T;T	0.15372	2.43;2.43	3.51	2.29	0.28610	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.33792	N	0.004541	T	0.53981	0.1830	H	0.99042	4.41	0.32787	N	0.501657	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.66760	-0.5842	10	0.87932	D	0	.	6.7304	0.23381	0.7573:0.2427:0.0:0.0	.	102;102	Q6ICS1;P48304	.;REG1B_HUMAN	P	53;102	ENSP00000387410:L53P;ENSP00000303206:L102P	ENSP00000303206:L102P	L	-	2	0	REG1B	79167017	0.116000	0.22171	0.024000	0.17045	0.013000	0.08279	2.145000	0.42207	0.501000	0.28013	-0.619000	0.04042	CTC	.	.		0.512	REG1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252292.2	NM_006507		G	79313509	A	G	79313509	3	3	103	1	0	0	0	0	1	0	0	0	13226	304	11	2	207	2	REG1B	2	79313509	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	4716086	79313509	163885864	145	14768										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84861633	84861633	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttattttgatttcagatgatGgggcgcttcttcagtggctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:84861633delG	ENST00000237449.6	+	29	4529	c.4521delG	c.(4519-4521)atgfs	p.M1507fs	DNAH6_ENST00000389394.3_Frame_Shift_Del_p.M1507fs|DNAH6_ENST00000398278.2_Frame_Shift_Del_p.M1507fs			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1507	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTCAGATGATGGGGCGCTTCT	0.408																																					p.M1507fs		Atlas-INDEL	.											.	DNAH6	194	.	0			c.4520delT						.						44	42	43					2																	84861633		692	1591	2283	SO:0001589	frameshift_variant	1768	exon30			.	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.4521delG	chr2.hg19:g.84861633delG	ENSP00000237449:p.Met1507fs	101.0	0.0		144.0	10.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Frame_Shift_Del	DEL	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.408	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		-	84861633	G	-	84861633	7	5	103	1	0	1	0	1	0	0	0	0	4607	1348	47	0	4635	0	DNAH6	2	84861633	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	5548124	84861633	158337740	146	14769										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84913642	84913642	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attgcaattgacctggaataTtttttgaataagcccatcat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:84913642delT	ENST00000237449.6	+	43	7106	c.7098delT	c.(7096-7098)tatfs	p.Y2366fs	DNAH6_ENST00000602588.1_Frame_Shift_Del_p.Y338fs|DNAH6_ENST00000389394.3_Frame_Shift_Del_p.Y2366fs|DNAH6_ENST00000398278.2_Frame_Shift_Del_p.Y2317fs			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2366					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						ACCTGGAATATTTTTTGAATA	0.259																																					p.Y2366fs		Atlas-INDEL	.											.	DNAH6	194	.	0			c.7097delA						.						101	85	90					2																	84913642		692	1587	2279	SO:0001589	frameshift_variant	1768	exon44			.	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7098delT	chr2.hg19:g.84913642delT	ENSP00000237449:p.Tyr2366fs	251.0	0.0		254.0	16.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Frame_Shift_Del	DEL	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.259	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		-	84913642	T	-	84913642	7	5	103	1	0	1	0	1	0	0	0	0	4607	1500	52	0	7268	0	DNAH6	2	84913642	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	52009	84913642	158285731	147	14770										
POLR1A	25885	hgsc.bcm.edu	37	chr2	86265933	86265933	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tacacctggaatttgttctgTttttcttccatacagaagga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:86265933delT	ENST00000263857.6	-	27	4302	c.3924delA	c.(3922-3924)aaafs	p.K1308fs	POLR1A_ENST00000409681.1_Frame_Shift_Del_p.K1308fs			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1308					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						ATTTGTTCTGTTTTTCTTCCA	0.502																																					p.Q1309fs		Atlas-INDEL	.											.	POLR1A	137	.	0			c.3925delC						.						106	99	101					2																	86265933		1952	4164	6116	SO:0001589	frameshift_variant	25885	exon27			.	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.3924delA	chr2.hg19:g.86265933delT	ENSP00000263857:p.Lys1308fs	157.0	0.0		220.0	14.0	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Frame_Shift_Del	DEL	ENST00000263857.6	hg19	CCDS42706.1																																																																																			.	.		0.502	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		-	86265933	T	-	86265933	7	5	103	1	0	1	0	1	0	0	0	0	12218	1722	60	0	1270	0	POLR1A	2	86265933	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1352291	86265933	156933440	148	14771										
IMMT	10989	hgsc.bcm.edu	37	chr2	86393732	86393732	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgcagagtgacacttgcagTttgcctcagagcatcttcta	9	11	3	3	rs556796647		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:86393732T>C	ENST00000410111.3	-	7	1078	c.691A>G	c.(691-693)Act>Gct	p.T231A	IMMT_ENST00000449247.2_Missense_Mutation_p.T220A|IMMT_ENST00000442664.2_Missense_Mutation_p.T230A|IMMT_ENST00000409051.2_Missense_Mutation_p.T184A|IMMT_ENST00000254636.5_Missense_Mutation_p.T132A|IMMT_ENST00000490238.1_5'UTR	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	231					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						ACACTTGCAGTTTGCCTCAGA	0.423													T|||	1	0.000199681	0	0	5008	,	,		15210	0.001		0	False		,,,				2504	0				p.T231A		Atlas-SNP	.											.	IMMT	65	.	0			c.A691G						.						55	52	53					2																	86393732		1887	4104	5991	SO:0001583	missense	10989	exon7			TTGCAGTTTGCCT	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.691A>G	chr2.hg19:g.86393732T>C	ENSP00000387262:p.Thr231Ala	62.0	0.0		88.0	4.0	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	hg19	CCDS46355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.94|11.94	1.787670|1.787670	0.31593|0.31593	.|.	.|.	ENSG00000132305|ENSG00000132305	ENST00000419070|ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715	.|T;T;T;T;T	.|0.30448	.|1.53;1.53;1.53;1.53;1.53	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	.|0.051776	.|0.85682	.|D	.|0.000000	T|T	0.39036|0.39036	0.1063|0.1063	L|L	0.39898|0.39898	1.24|1.24	0.47245|0.47245	D|D	0.999366|0.999366	.|B;P;B;P;D;P;B;P;P	.|0.55385	.|0.324;0.47;0.375;0.73;0.971;0.55;0.324;0.55;0.604	.|B;P;B;P;P;B;B;B;B	.|0.62298	.|0.273;0.512;0.394;0.644;0.9;0.273;0.273;0.273;0.394	T|T	0.11155|0.11155	-1.0599|-1.0599	5|10	.|0.06365	.|T	.|0.9	-19.9405|-19.9405	14.6434|14.6434	0.68742|0.68742	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|220;184;219;228;219;199;220;199;231	.|F5GZ32;B9A067;B4DKR1;Q05DN3;B4E2B5;F8W9I1;Q16891-2;Q16891-3;Q16891	.|.;.;.;.;.;.;.;.;IMMT_HUMAN	S|A	85|132;220;231;230;184;220;199;219;153	.|ENSP00000254636:T132A;ENSP00000396899:T220A;ENSP00000387262:T231A;ENSP00000407788:T230A;ENSP00000387227:T184A	.|ENSP00000254636:T132A	N|T	-|-	2|1	0|0	IMMT|IMMT	86247243|86247243	0.999000|0.999000	0.42202|0.42202	0.871000|0.871000	0.34182|0.34182	0.785000|0.785000	0.44390|0.44390	3.200000|3.200000	0.51051|0.51051	2.160000|2.160000	0.67779|0.67779	0.523000|0.523000	0.50628|0.50628	AAC|ACT	.	.		0.423	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		C	86393732	T	C	86393732	3	2	103	1	0	0	0	0	1	0	0	0	7727	1725	60	2	1621	2	IMMT	2	86393732	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	127799	86393732	156805641	149	14772										
COX5B	1329	hgsc.bcm.edu	37	chr2	98264520	98264520	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaaggcgaggcccagcgatgCccccgctgtggagcccatta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:98264520delC	ENST00000258424.2	+	4	386	c.339delC	c.(337-339)tgcfs	p.C113fs	COX5B_ENST00000464949.1_3'UTR	NM_001862.2	NP_001853.2	P10606	COX5B_HUMAN	cytochrome c oxidase subunit Vb	113					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|metal ion binding (GO:0046872)			endometrium(1)|lung(1)|urinary_tract(1)	3						CCCAGCGATGCCCCCGCTGTG	0.507																																					p.C113fs		Atlas-INDEL	.											.	COX5B	9	.	0			c.338delG						.						49	48	49					2																	98264520		2203	4300	6503	SO:0001589	frameshift_variant	1329	exon4			.	BC006229	CCDS2032.1	2q11.2	2011-07-04			ENSG00000135940	ENSG00000135940	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2269	protein-coding gene	gene with protein product		123866					Standard	NM_001862		Approved		uc002sya.3	P10606	OTTHUMG00000130548	ENST00000258424.2:c.339delC	chr2.hg19:g.98264520delC	ENSP00000258424:p.Cys113fs	183.0	0.0		215.0	13.0	NM_001862	Q53YB7|Q96J18|Q99610	Frame_Shift_Del	DEL	ENST00000258424.2	hg19	CCDS2032.1																																																																																			.	.		0.507	COX5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252972.2	NM_001862		-	98264520	C	-	98264520	7	5	103	1	0	1	0	1	0	0	0	0	3775	747	26	0	353	0	COX5B	2	98264520	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	11870788	98264520	144934853	150	14773										
TMEM131	23505	hgsc.bcm.edu	37	chr2	98460710	98460710	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acatcaaatgatgtatttccTcctggaagaattttctgaaa	6	7	2	3	rs202141365		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:98460710T>C	ENST00000186436.5	-	6	726	c.498A>G	c.(496-498)ggA>ggG	p.G166G	TMEM131_ENST00000425805.2_Silent_p.G117G	NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	166						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						ATGTATTTCCTCCTGGAAGAA	0.274																																					p.G166G		Atlas-SNP	.											.	TMEM131	258	.	0			c.A498G						.						11	11	11					2																	98460710		1702	3855	5557	SO:0001819	synonymous_variant	23505	exon6			ATTTCCTCCTGGA	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.498A>G	chr2.hg19:g.98460710T>C		92.0	0.0		146.0	6.0	NM_015348		Silent	SNP	ENST00000186436.5	hg19	CCDS46368.1																																																																																			.	T|1.000;G|0.000		0.274	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		C	98460710	T	C	98460710	2	2	103	1	0	0	0	0	0	0	0	1	16059	1538	54	2		2	TMEM131	2	98460710	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	196190	98460710	144738663	151	14774										
TSGA10	80705	hgsc.bcm.edu	37	chr2	99721887	99721887	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agccttctcattaaatgctgTctcttgagcaatctgattaa	6	9	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:99721887T>C	ENST00000393483.3	-	9	1238	c.394A>G	c.(394-396)Aca>Gca	p.T132A	TSGA10_ENST00000410001.1_Missense_Mutation_p.T132A|TSGA10_ENST00000355053.4_Missense_Mutation_p.T132A|TSGA10_ENST00000539964.1_Missense_Mutation_p.T132A|TSGA10_ENST00000542655.1_Missense_Mutation_p.T132A|TSGA10_ENST00000478090.1_5'UTR	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	132					cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						TTAAATGCTGTCTCTTGAGCA	0.318																																					p.T132A		Atlas-SNP	.											.	TSGA10	81	.	0			c.A394G						.						68	72	71					2																	99721887		2202	4300	6502	SO:0001583	missense	80705	exon8			ATGCTGTCTCTTG	AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.394A>G	chr2.hg19:g.99721887T>C	ENSP00000377123:p.Thr132Ala	83.0	0.0		95.0	4.0	NM_182911	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	hg19	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.246682	0.59103	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482;ENST00000542655	T;T;T;T;T;T;T	0.77620	0.95;0.95;0.95;0.95;-1.11;-1.11;-1.11	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000012	T	0.76004	0.3927	L	0.31065	0.9	0.35300	D	0.782925	D;D	0.64830	0.994;0.994	P;P	0.58520	0.791;0.84	T	0.75221	-0.3394	10	0.11182	T	0.66	-15.3955	13.6914	0.62549	0.0:0.0:0.0:1.0	.	132;132	B7Z925;Q9BZW7	.;TSG10_HUMAN	A	132	ENSP00000377123:T132A;ENSP00000386956:T132A;ENSP00000347161:T132A;ENSP00000444419:T132A;ENSP00000386508:T132A;ENSP00000377122:T132A;ENSP00000445623:T132A	ENSP00000347161:T132A	T	-	1	0	TSGA10	99088319	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	3.236000	0.51336	2.096000	0.63516	0.529000	0.55759	ACA	.	.		0.318	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		C	99721887	T	C	99721887	3	2	103	1	0	0	0	0	1	0	0	0	16632	1667	58	2	1754	2	TSGA10	2	99721887	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1261177	99721887	143477486	152	14775										
C2orf29	55571	hgsc.bcm.edu	37	chr2	101885729	101885729	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tccaatccttgatccgtaacAaaattattaatgtacaggat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:101885729delA	ENST00000289382.3	+	7	1550	c.1387delA	c.(1387-1389)aaafs	p.K463fs	RNF149_ENST00000485752.1_5'Flank	NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	463					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											GATCCGTAACAAAATTATTAA	0.393																																					p.N462fs		Atlas-INDEL	.											.	.	.	.	0			c.1386delC						.						79	83	81					2																	101885729		2203	4300	6503	SO:0001589	frameshift_variant	55571	exon7			.	AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 29"	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.1387delA	chr2.hg19:g.101885729delA	ENSP00000289382:p.Lys463fs	130.0	0.0		161.0	10.0	NM_017546	Q6P2M9|Q8N681	Frame_Shift_Del	DEL	ENST00000289382.3	hg19	CCDS2050.1																																																																																			.	.		0.393	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546		-	101885729	A	-	101885729	7	5	103	1	0	1	0	1	0	0	0	0	2163	131	5	0	1413	0	C2orf29	2	101885729	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2163842	101885729	141313644	153	14776										
GCC2	9648	hgsc.bcm.edu	37	chr2	109088158	109088158	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcagtcggtgaatccttggcAaaaataaatgaggaaaaatg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:109088158delA	ENST00000309863.6	+	6	3087	c.2373delA	c.(2371-2373)gcafs	p.A791fs		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	791					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						AATCCTTGGCAAAAATAAATG	0.368																																					p.A791fs		Atlas-Indel,Pindel	.											.	GCC2	129	.	0			c.2372delC						.						61	64	63					2																	109088158		2203	4297	6500	SO:0001589	frameshift_variant	9648	exon6			.	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.2373delA	chr2.hg19:g.109088158delA	ENSP00000307939:p.Ala791fs	274.0	0.0		347.0	21.0	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Frame_Shift_Del	DEL	ENST00000309863.6	hg19	CCDS33268.1																																																																																			.	.		0.368	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		-	109088158	A	-	109088158	7	5	103	1	0	1	0	1	0	0	0	0	6294	117	5	0	2395	0	GCC2	2	109088158	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	7202429	109088158	134111215	154	14777										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109379816	109379816	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctctcaggagatgtatggtCctcctgcattgcgttttgag	11	9	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:109379816C>A	ENST00000283195.6	+	20	2947	c.2821C>A	c.(2821-2823)Cct>Act	p.P941T		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	941					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GATGTATGGTCCTCCTGCATT	0.473																																					p.P941T		Atlas-SNP	.											.	RANBP2	488	.	0			c.C2821A						.						130	120	124					2																	109379816		2203	4300	6503	SO:0001583	missense	5903	exon20			TATGGTCCTCCTG	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2821C>A	chr2.hg19:g.109379816C>A	ENSP00000283195:p.Pro941Thr	174.0	0.0		247.0	11.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392009	0.42410	.	.	ENSG00000153201	ENST00000283195	T	0.23147	1.92	5.19	5.19	0.71726	.	.	.	.	.	T	0.20292	0.0488	L	0.29908	0.895	0.32255	N	0.570945	B	0.22276	0.067	B	0.15052	0.012	T	0.08764	-1.0706	9	0.28530	T	0.3	-17.2047	14.6488	0.68780	0.2118:0.7882:0.0:0.0	.	941	P49792	RBP2_HUMAN	T	941	ENSP00000283195:P941T	ENSP00000283195:P941T	P	+	1	0	RANBP2	108746248	0.996000	0.38824	1.000000	0.80357	0.893000	0.52053	1.412000	0.34714	2.570000	0.86706	0.563000	0.77884	CCT	.	.		0.473	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		A	109379816	C	A	109379816	3	1	103	1	0	0	0	0	1	0	0	0	13043	855	30	3	2899	3	RANBP2	2	109379816	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	291658	109379816	133819557	155	14778										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109379840	109379840	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgcattgcgttttgagtctCctgcaacgggaattctatcg	10	10	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:109379840C>G	ENST00000283195.6	+	20	2971	c.2845C>G	c.(2845-2847)Cct>Gct	p.P949A		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	949					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TTTTGAGTCTCCTGCAACGGG	0.468																																					p.P949A		Atlas-SNP	.											.	RANBP2	488	.	0			c.C2845G						.						121	115	117					2																	109379840		2203	4300	6503	SO:0001583	missense	5903	exon20			GAGTCTCCTGCAA	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2845C>G	chr2.hg19:g.109379840C>G	ENSP00000283195:p.Pro949Ala	140.0	0.0		223.0	10.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.826229	0.71143	.	.	ENSG00000153201	ENST00000283195	T	0.26660	1.72	5.08	5.08	0.68730	.	.	.	.	.	T	0.40979	0.1139	L	0.34521	1.04	0.49299	D	0.999771	D	0.89917	1.0	D	0.67548	0.952	T	0.18999	-1.0319	9	0.49607	T	0.09	-19.2482	18.8287	0.92128	0.0:1.0:0.0:0.0	.	949	P49792	RBP2_HUMAN	A	949	ENSP00000283195:P949A	ENSP00000283195:P949A	P	+	1	0	RANBP2	108746272	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.339000	0.52135	2.511000	0.84671	0.563000	0.77884	CCT	.	.		0.468	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109379840	C	G	109379840	3	3	103	1	0	0	0	0	1	0	0	0	13043	855	30	4	2923	4	RANBP2	2	109379840	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	24	109379840	133819533	156	14779										
CCDC138	165055	hgsc.bcm.edu	37	chr2	109429147	109429147	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggctaaaagagttcaagctCgtttagataatttacaggta	9	5	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:109429147C>A	ENST00000295124.4	+	8	976	c.916C>A	c.(916-918)Cgt>Agt	p.R306S	CCDC138_ENST00000412964.2_Missense_Mutation_p.R306S	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	306										endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						AGTTCAAGCTCGTTTAGATAA	0.318																																					p.R306S		Atlas-SNP	.											CCDC138,caecum,carcinoma,0,1	CCDC138	49	.	0			c.C916A						.						114	124	121					2																	109429147		2203	4298	6501	SO:0001583	missense	165055	exon8			CAAGCTCGTTTAG	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.916C>A	chr2.hg19:g.109429147C>A	ENSP00000295124:p.Arg306Ser	110.0	0.0		162.0	0.0	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	hg19	CCDS2080.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.131642	0.77662	.	.	ENSG00000163006	ENST00000412964;ENST00000295124	D;D	0.88741	-2.42;-2.42	5.72	4.8	0.61643	.	0.000000	0.85682	D	0.000000	D	0.93729	0.7996	M	0.74258	2.255	0.40555	D	0.981157	D;D	0.89917	1.0;0.988	D;P	0.87578	0.998;0.795	D	0.94349	0.7577	10	0.87932	D	0	2.2356	14.457	0.67423	0.148:0.852:0.0:0.0	.	306;306	Q96M89-2;Q96M89	.;CC138_HUMAN	S	306	ENSP00000411800:R306S;ENSP00000295124:R306S	ENSP00000295124:R306S	R	+	1	0	CCDC138	108795579	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.452000	0.52971	2.694000	0.91930	0.655000	0.94253	CGT	.	.		0.318	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978		A	109429147	C	A	109429147	3	1	103	1	0	0	0	0	1	0	0	0	2774	884	31	1	946	1	CCDC138	2	109429147	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	49307	109429147	133770226	157	14780										
EDAR	10913	hgsc.bcm.edu	37	chr2	109546604	109546604	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctcctctcccggcccacacGgggggcactcctggcacagc					rs375891208		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:109546604delG	ENST00000258443.2	-	3	576	c.146delC	c.(145-147)ccgfs	p.P49fs	EDAR_ENST00000376651.1_Frame_Shift_Del_p.P49fs|EDAR_ENST00000409271.1_Frame_Shift_Del_p.P49fs	NM_022336.3	NP_071731.1	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor	49					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|epidermis development (GO:0008544)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|salivary gland cavitation (GO:0060662)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16						CGGCCCACACGGGGGGCACTC	0.632																																					p.P49fs		Atlas-INDEL	.											.,1	EDAR	49	.	0			c.147delG						.						54	49	51					2																	109546604		2203	4300	6503	SO:0001589	frameshift_variant	10913	exon3			.	AF130988	CCDS2081.1	2q13	2013-05-22	2004-08-09		ENSG00000135960	ENSG00000135960		"Tumor necrosis factor receptor superfamily"	2895	protein-coding gene	gene with protein product		604095	"ectodysplasin 1, anhidrotic receptor"	ED3, DL		10431241, 9375732	Standard	NM_022336		Approved	ED5, EDA3, Edar, ED1R, EDA1R	uc002teq.4	Q9UNE0	OTTHUMG00000130982	ENST00000258443.2:c.146delC	chr2.hg19:g.109546604delG	ENSP00000258443:p.Pro49fs	196.0	0.0		258.0	17.0	NM_022336	B2R9H2|B4DLC5|D3DX74|E9PC98|Q52LL5|Q9UND9	Frame_Shift_Del	DEL	ENST00000258443.2	hg19	CCDS2081.1																																																																																			.	.		0.632	EDAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253595.1			-	109546604	G	-	109546604	7	5	103	1	0	1	0	1	0	0	0	0	4907	1116	39	0	1240	0	EDAR	2	109546604	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	117457	109546604	133652769	158	14781										
RGPD5	84220	hgsc.bcm.edu	37	chr2	110588995	110588995	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcggtgcctgatggatatcaGgggtcacagacatttcatgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:110588995delG	ENST00000016946.3	+	18	2726	c.2568delG	c.(2566-2568)cagfs	p.Q856fs	RGPD5_ENST00000393283.1_Frame_Shift_Del_p.Q856fs|RGPD5_ENST00000272454.6_Frame_Shift_Del_p.Q856fs	NM_005054.2	NP_005045.2	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 5	856					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)				central_nervous_system(1)	1						ATGGATATCAGGGGTCACAGA	0.438																																					p.Q856fs		Atlas-INDEL	.											.	RGPD5	1	.	0			c.2567delA						.																																			SO:0001589	frameshift_variant	84220	exon18			.	U64675	CCDS2082.1, CCDS2083.1	2q13	2013-01-10			ENSG00000015568	ENSG00000015568		"Tetratricopeptide (TTC) repeat domain containing"	32418	protein-coding gene	gene with protein product		612708				15710750, 15815621	Standard	NM_032260		Approved	RGP5, BS-63, DKFZp686I1842		Q99666	OTTHUMG00000130985	ENST00000016946.3:c.2568delG	chr2.hg19:g.110588995delG	ENSP00000016946:p.Gln856fs	80.0	0.0		145.0	10.0	NM_005054	Q53QN2|Q53T03|Q59GM7|Q9H0B2	Frame_Shift_Del	DEL	ENST00000016946.3	hg19	CCDS2082.1																																																																																			.	.		0.438	RGPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253599.3	NM_005054		-	110588995	G	-	110588995	7	5	103	1	0	1	0	1	0	0	0	0	13304	991	35	0	2638	0	RGPD5	2	110588995	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1042391	110588995	132610378	159	14782										
BUB1	699	hgsc.bcm.edu	37	chr2	111406915	111406915	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaagcccagataaaagtttgAaaatcagcttatcatcccat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:111406915delA	ENST00000302759.6	-	19	2361	c.2243delT	c.(2242-2244)ttcfs	p.F748fs	BUB1_ENST00000535254.1_Frame_Shift_Del_p.F728fs|BUB1_ENST00000409311.1_Frame_Shift_Del_p.F748fs	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	748					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		TAAAAGTTTGAAAATCAGCTT	0.353																																					p.F748fs		Atlas-INDEL	.											.	BUB1	91	.	0			c.2244delC						.						93	97	95					2																	111406915		2203	4300	6503	SO:0001589	frameshift_variant	699	exon19			.	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"budding uninhibited by benzimidazoles 1 (yeast homolog)", "budding uninhibited by benzimidazoles 1 homolog (yeast)"	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.2243delT	chr2.hg19:g.111406915delA	ENSP00000302530:p.Phe748fs	163.0	0.0		238.0	16.0	NM_004336	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Frame_Shift_Del	DEL	ENST00000302759.6	hg19	CCDS33273.1																																																																																			.	.		0.353	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		-	111406915	A	-	111406915	7	5	103	1	0	1	0	1	0	0	0	0	1572	246	9	0	1042	0	BUB1	2	111406915	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	817920	111406915	131792458	160	14783										
MERTK	10461	hgsc.bcm.edu	37	chr2	112754915	112754915	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accaggttgggtagattatgCcccctcttcaactccggcgc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:112754915delC	ENST00000295408.4	+	10	1723	c.1466delC	c.(1465-1467)gccfs	p.A489fs	MERTK_ENST00000409780.1_Frame_Shift_Del_p.A313fs|MERTK_ENST00000421804.2_Frame_Shift_Del_p.A489fs			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	489					apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						GTAGATTATGCCCCCTCTTCA	0.438																																					p.A489fs		Atlas-INDEL	.											.	MERTK	112	.	0			c.1465delG						.						201	200	200					2																	112754915		2203	4300	6503	SO:0001589	frameshift_variant	10461	exon10			.	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7027	protein-coding gene	gene with protein product		604705	"c-mer proto-oncogene tyrosine kinase"			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1466delC	chr2.hg19:g.112754915delC	ENSP00000295408:p.Ala489fs	117.0	0.0		172.0	11.0	NM_006343	Q9HBB4	Frame_Shift_Del	DEL	ENST00000295408.4	hg19	CCDS2094.1																																																																																			.	.		0.438	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			-	112754915	C	-	112754915	7	5	103	1	0	1	0	1	0	0	0	0	9488	739	26	0	1504	0	MERTK	2	112754915	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1348000	112754915	130444458	161	14784										
FOXD4L1	200350	hgsc.bcm.edu	37	chr2	114257385	114257385	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcacctactggagcctggaCcccgcctcccaggacatgtt					rs369834731		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:114257385delC	ENST00000306507.5	+	1	725	c.552delC	c.(550-552)gacfs	p.D184fs		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	184					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						GGAGCCTGGACCCCGCCTCCC	0.652																																					p.D184fs		Atlas-INDEL	.											.	FOXD4L1	48	.	0			c.551delA						.						49	65	59					2																	114257385		2114	4099	6213	SO:0001589	frameshift_variant	200350	exon1			.	AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.552delC	chr2.hg19:g.114257385delC	ENSP00000302756:p.Asp184fs	125.0	0.0		181.0	11.0	NM_012184	B3KWN1|B9EGF3	Frame_Shift_Del	DEL	ENST00000306507.5	hg19	CCDS2117.1																																																																																			.	.		0.652	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184		-	114257385	C	-	114257385	7	5	103	1	0	1	0	1	0	0	0	0	6008	506	18	0	554	0	FOXD4L1	2	114257385	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1502470	114257385	128941988	162	14785										
DPP10	57628	hgsc.bcm.edu	37	chr2	116447448	116447448	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttaaatcctccagaagtagAggactccgtcttgcagtacg	10	10	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:116447448A>G	ENST00000410059.1	+	7	1007	c.527A>G	c.(526-528)gAg>gGg	p.E176G	DPP10_ENST00000409163.1_Missense_Mutation_p.E126G|DPP10_ENST00000393147.2_Missense_Mutation_p.E180G|DPP10_ENST00000310323.8_Missense_Mutation_p.E169G|DPP10_ENST00000488208.1_3'UTR	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	176						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						CCAGAAGTAGAGGACTCCGTC	0.438																																					p.E180G		Atlas-SNP	.											.	DPP10	415	.	0			c.A539G						.						88	95	93					2																	116447448		2203	4300	6503	SO:0001583	missense	57628	exon7			AAGTAGAGGACTC	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.527A>G	chr2.hg19:g.116447448A>G	ENSP00000386565:p.Glu176Gly	57.0	0.0		71.0	5.0	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	A	14.47	2.544759	0.45280	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393146;ENST00000393147;ENST00000310323;ENST00000476155	T;T;D;T;T	0.95377	1.61;1.61;-3.69;1.61;1.61	5.44	4.26	0.50523	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.353745	0.29286	N	0.012582	D	0.92084	0.7491	N	0.19112	0.55	0.35228	D	0.776657	P;D;P;P	0.53312	0.73;0.959;0.772;0.772	B;P;P;B	0.50049	0.284;0.629;0.526;0.407	D	0.92101	0.5688	10	0.34782	T	0.22	-17.821	10.5101	0.44857	0.8372:0.1628:0.0:0.0	.	169;180;172;176	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	G	176;126;172;180;169;126	ENSP00000386565:E176G;ENSP00000387038:E126G;ENSP00000376854:E172G;ENSP00000376855:E180G;ENSP00000309066:E169G	ENSP00000309066:E169G	E	+	2	0	DPP10	116163918	0.812000	0.29077	0.999000	0.59377	0.988000	0.76386	1.342000	0.33919	0.865000	0.35603	0.477000	0.44152	GAG	.	.		0.438	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		G	116447448	A	G	116447448	3	3	103	1	0	0	0	0	1	0	0	0	4729	304	11	2	724	2	DPP10	2	116447448	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2190063	116447448	126751925	163	14786										
CLASP1	23332	hgsc.bcm.edu	37	chr2	122182819	122182819	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggtgggcctcgtgaggagCccccagtaagtccaccataa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:122182819delC	ENST00000263710.4	-	22	2497	c.2108delG	c.(2107-2109)ggcfs	p.G703fs	CLASP1_ENST00000455322.2_Frame_Shift_Del_p.G703fs|CLASP1_ENST00000409078.3_Frame_Shift_Del_p.G703fs|CLASP1_ENST00000545861.1_Frame_Shift_Del_p.G479fs|CLASP1_ENST00000397587.3_Frame_Shift_Del_p.G711fs|CLASP1_ENST00000541859.1_Frame_Shift_Del_p.G472fs|CLASP1_ENST00000541377.1_Frame_Shift_Del_p.G710fs	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	703	Interaction with microtubules, MAPRE1 and MAPRE3.|Ser-rich.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					TCGTGAGGAGCCCCCAGTAAG	0.498																																					p.G711fs		Atlas-INDEL	.											.	CLASP1	135	.	0			c.2133delC						.						88	86	87					2																	122182819		1837	4085	5922	SO:0001589	frameshift_variant	23332	exon23			.	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"multiple asters 1"	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.2108delG	chr2.hg19:g.122182819delC	ENSP00000263710:p.Gly703fs	104.0	0.0		144.0	10.0	NM_001142273	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Frame_Shift_Del	DEL	ENST00000263710.4	hg19																																																																																				.	.		0.498	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		-	122182819	C	-	122182819	7	5	103	1	0	1	0	1	0	0	0	0	3456	739	26	0	2608	0	CLASP1	2	122182819	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	5735371	122182819	121016554	164	14787										
MYO7B	4648	hgsc.bcm.edu	37	chr2	128384760	128384760	+	Splice_Site	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgccgtctctcctggccaggCccccgcctgcccaagacgca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:128384760delC	ENST00000409816.2	+	31	4289	c.4257delC	c.(4255-4257)ggc>gg	p.G1419fs	MYO7B_ENST00000409090.1_Splice_Site_p.G272fs|RP11-286H15.1_ENST00000609697.1_RNA|MYO7B_ENST00000389524.4_Splice_Site_p.G1419fs|MYO7B_ENST00000428314.1_Splice_Site_p.G1419fs			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1419	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CCTGGCCAGGCCCCCGCCTGC	0.612																																					p.G1419fs		Atlas-INDEL	.											.	MYO7B	359	.	0			c.4256delG						.						22	24	23					2																	128384760		1968	4142	6110	SO:0001630	splice_region_variant	4648	exon32			.		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.4256-1C>-	chr2.hg19:g.128384760delC		131.0	0.0		156.0	10.0	NM_001080527	Q14786|Q8TEE1	Frame_Shift_Del	DEL	ENST00000409816.2	hg19	CCDS46405.1																																																																																			.	.		0.612	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	Frame_Shift_Del	-	128384760	C	-	128384760	8	5	103	1	0	1	0	1	0	0	1	0	10092	753	26	0	4379	0	MYO7B	2	128384760	Splice_Site	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	6201941	128384760	114814613	165	14788										
WDR33	55339	hgsc.bcm.edu	37	chr2	128477145	128477145	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgagggccgtgtcccagtagTccacctggagggtgaggtcc	16	11	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:128477145T>C	ENST00000322313.4	-	16	2612	c.2454A>G	c.(2452-2454)ggA>ggG	p.G818G		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	818					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		GTCCCAGTAGTCCACCTGGAG	0.632																																					p.G818G		Atlas-SNP	.											.	WDR33	136	.	0			c.A2454G						.						31	34	33					2																	128477145		2203	4300	6503	SO:0001819	synonymous_variant	55339	exon16			CAGTAGTCCACCT		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.2454A>G	chr2.hg19:g.128477145T>C		69.0	0.0		110.0	5.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Silent	SNP	ENST00000322313.4	hg19	CCDS2150.1																																																																																			.	.		0.632	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		C	128477145	T	C	128477145	2	2	103	1	0	0	0	0	0	0	0	1	17302	1654	58	2		2	WDR33	2	128477145	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	92385	128477145	114722228	166	14789										
UGGT1	56886	hgsc.bcm.edu	37	chr2	128900693	128900693	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taacaaggtgaggactggagAaaaagtgaaagttgaacatg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:128900693delA	ENST00000259253.6	+	17	1792	c.1745delA	c.(1744-1746)gaafs	p.E582fs	UGGT1_ENST00000375990.3_Frame_Shift_Del_p.E558fs	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	582					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						AGGACTGGAGAAAAAGTGAAA	0.348																																					p.E582fs		Atlas-INDEL	.											.	UGGT1	126	.	0			c.1744delG						.						131	127	128					2																	128900693		2203	4300	6503	SO:0001589	frameshift_variant	56886	exon17			.	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.1745delA	chr2.hg19:g.128900693delA	ENSP00000259253:p.Glu582fs	80.0	0.0		129.0	10.0	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Frame_Shift_Del	DEL	ENST00000259253.6	hg19	CCDS2154.1																																																																																			.	.		0.348	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		-	128900693	A	-	128900693	7	5	103	1	0	1	0	1	0	0	0	0	16956	246	9	0	1811	0	UGGT1	2	128900693	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	423548	128900693	114298680	167	14790										
TUBA3E	112714	hgsc.bcm.edu	37	chr2	130951451	130951451	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gacgtctttggggaccacgtCccccctgtacaacatgcagc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:130951451delC	ENST00000312988.7	-	4	1064	c.964delG	c.(964-966)gacfs	p.D322fs		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	322					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					GGGACCACGTCCCCCCTGTAC	0.557																																					p.D322fs		Atlas-INDEL	.											.	TUBA3E	73	.	0			c.965delA						.						154	134	141					2																	130951451		2203	4300	6503	SO:0001589	frameshift_variant	112714	exon4			.	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"Tubulins"	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.964delG	chr2.hg19:g.130951451delC	ENSP00000318197:p.Asp322fs	169.0	0.0		231.0	14.0	NM_207312		Frame_Shift_Del	DEL	ENST00000312988.7	hg19	CCDS2158.1																																																																																			.	.		0.557	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312		-	130951451	C	-	130951451	7	5	103	1	0	1	0	1	0	0	0	0	16763	855	30	0	396	0	TUBA3E	2	130951451	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2050758	130951451	112247922	168	14791										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141272298	141272298	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atccaatgcttagaaatacaTttttgtgcggaacaagcaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:141272298delT	ENST00000389484.3	-	51	9164	c.8193delA	c.(8191-8193)aaafs	p.K2731fs		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2731	LDL-receptor class A 16. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TAGAAATACATTTTTGTGCGG	0.378										TSP Lung(27;0.18)																											p.C2732fs	Colon(99;50 2074 2507 20106)	Atlas-INDEL	.											.	LRP1B	1315	.	0			c.8194delT						.						112	105	107					2																	141272298		2203	4300	6503	SO:0001589	frameshift_variant	53353	exon51			.	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8193delA	chr2.hg19:g.141272298delT	ENSP00000374135:p.Lys2731fs	145.0	0.0		194.0	12.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Frame_Shift_Del	DEL	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.		0.378	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		-	141272298	T	-	141272298	7	5	103	1	0	1	0	1	0	0	0	0	8964	1490	52	0	5770	0	LRP1B	2	141272298	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	10320847	141272298	101927075	169	14792										
NEB	4703	hgsc.bcm.edu	37	chr2	152424933	152424933	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtctttccggtatttaatcTaaaaaaaaaaaaatgagagg	7	4	2	1	rs3214503|rs397772995|rs539518038|rs75873810	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:152424933T>A	ENST00000172853.10	-	84	12679		c.e84-2		NEB_ENST00000603639.1_Splice_Site|NEB_ENST00000604864.1_Splice_Site|NEB_ENST00000397345.3_Splice_Site|NEB_ENST00000409198.1_Splice_Site|NEB_ENST00000427231.2_Splice_Site			P20929	NEBU_HUMAN	nebulin						muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GTATTTAATCTAAAAAAAAAA	0.423																																					.		Atlas-SNP	.											.,3	NEB	1697	.	0			c.17635-2A>T						.						47	51	49					2																	152424933		1813	4075	5888	SO:0001630	splice_region_variant	4703	exon113			TTAATCTAAAAAA	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.12532-2A>T	chr2.hg19:g.152424933T>A		59.0	2.0		70.0	5.0	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Splice_Site	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	T	19.92	3.916138	0.73098	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NEB	152133179	1.000000	0.71417	0.996000	0.52242	0.705000	0.40729	6.287000	0.72671	2.371000	0.80710	0.533000	0.62120	.	.	.		0.423	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	Intron	A	152424933	T	A	152424933	5	1	103	1	0	0	0	0	0	0	1	0	10311	1536	53	4	8337	4	NEB	2	152424933	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	11152635	152424933	90774440	170	14793										
GRB14	2888	hgsc.bcm.edu	37	chr2	165378510	165378510	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctttgatgttcctttagtagAaaaatataaaccagatcttc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:165378510delA	ENST00000263915.3	-	6	1334	c.796delT	c.(796-798)tctfs	p.S266fs	GRB14_ENST00000543549.1_Frame_Shift_Del_p.S179fs	NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	266	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						CCTTTAGTAGAAAAATATAAA	0.299																																					p.S266fs		Atlas-INDEL	.											.	GRB14	73	.	0			c.797delC						.						51	56	54					2																	165378510		2195	4285	6480	SO:0001589	frameshift_variant	2888	exon6			.		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.796delT	chr2.hg19:g.165378510delA	ENSP00000263915:p.Ser266fs	136.0	0.0		213.0	13.0	NM_004490	B7Z7F9|Q7Z6I1	Frame_Shift_Del	DEL	ENST00000263915.3	hg19	CCDS2222.1																																																																																			.	.		0.299	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			-	165378510	A	-	165378510	7	5	103	1	0	1	0	1	0	0	0	0	6766	246	9	0	862	0	GRB14	2	165378510	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	12953577	165378510	77820863	171	14794										
SLC38A11	151258	hgsc.bcm.edu	37	chr2	165755103	165755103	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtaatagccatgacgaatccAaaaaccatcaccacagcacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:165755103delA	ENST00000409149.3	-	11	1356	c.1065delT	c.(1063-1065)tttfs	p.F355fs	RNA5SP111_ENST00000411386.1_RNA|SLC38A11_ENST00000409662.1_Frame_Shift_Del_p.F355fs|SLC38A11_ENST00000409058.1_Frame_Shift_Del_p.F386fs|SLC38A11_ENST00000303735.4_Frame_Shift_Del_p.F333fs	NM_001199148.1	NP_001186077.1	Q08AI6	S38AB_HUMAN	solute carrier family 38, member 11	355					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15						TGACGAATCCAAAAACCATCA	0.433																																					p.G356fs		Atlas-INDEL	.											.	SLC38A11	41	.	0			c.1066delG						.						130	114	119					2																	165755103		2203	4300	6503	SO:0001589	frameshift_variant	151258	exon11			.		CCDS2224.1, CCDS56142.1	2q24.3	2013-05-22			ENSG00000169507	ENSG00000169507		"Solute carriers"	26836	protein-coding gene	gene with protein product							Standard	NM_173512		Approved	FLJ39822, AVT2	uc002ucw.2	Q08AI6	OTTHUMG00000132144	ENST00000409149.3:c.1065delT	chr2.hg19:g.165755103delA	ENSP00000386272:p.Phe355fs	135.0	0.0		179.0	11.0	NM_001199148	B4DF99|Q8N887	Frame_Shift_Del	DEL	ENST00000409149.3	hg19	CCDS56142.1																																																																																			.	.		0.433	SLC38A11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333390.1	NM_173512		-	165755103	A	-	165755103	7	5	103	1	0	1	0	1	0	0	0	0	14618	127	5	0	159	0	SLC38A11	2	165755103	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	376593	165755103	77444270	172	14795										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167094772	167094772	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctttcaatataaatatcttcAaaagcctgtggaaataatat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:167094772delA	ENST00000409435.1	-	19	3632	c.3633delT	c.(3631-3633)tttfs	p.F1211fs	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.F1212fs|SCN9A_ENST00000409672.1_Frame_Shift_Del_p.F1200fs|SCN9A_ENST00000375387.4_Frame_Shift_Del_p.F1212fs			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1211					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAATATCTTCAAAAGCCTGTG	0.294																																					p.E1201fs		Atlas-INDEL	.											.	SCN9A	296	.	0			c.3601delG	GRCh37	CD072484	SCN9A	D		.						19	18	18					2																	167094772		1862	4135	5997	SO:0001589	frameshift_variant	6335	exon20			.	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.3633delT	chr2.hg19:g.167094772delA	ENSP00000386330:p.Phe1211fs	213.0	0.0		234.0	17.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	hg19	CCDS46441.1																																																																																			.	.		0.294	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		-	167094772	A	-	167094772	7	5	103	1	0	1	0	1	0	0	0	0	13940	127	5	0	2365	0	SCN9A	2	167094772	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1339669	167094772	76104601	173	14796										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167288989	167288989	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtttttctctgtgccactgcTtttttccttatctttgagaa					rs146072866	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:167288989delT	ENST00000409855.1	-	15	2557	c.2431delA	c.(2431-2433)agcfs	p.S812fs		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	812					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	GTGCCACTGCTTTTTTCCTTA	0.388																																					p.S811fs		Atlas-INDEL	.											.	SCN7A	410	.	0			c.2432delG						.						242	228	233					2																	167288989		1834	4091	5925	SO:0001589	frameshift_variant	6332	exon15			.	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.2431delA	chr2.hg19:g.167288989delT	ENSP00000386796:p.Ser812fs	151.0	0.0		192.0	14.0	NM_002976		Frame_Shift_Del	DEL	ENST00000409855.1	hg19	CCDS46442.1																																																																																			.	.		0.388	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			-	167288989	T	-	167288989	7	5	103	1	0	1	0	1	0	0	0	0	13938	1609	56	0	2661	0	SCN7A	2	167288989	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	194217	167288989	75910384	174	14797										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168101503	168101503	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggagatgtttccagcatgAggtataaatttgaaaatcag	10	5	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:168101503A>G	ENST00000409195.1	+	9	3690	c.3601A>G	c.(3601-3603)Agg>Ggg	p.R1201G	XIRP2_ENST00000409273.1_Missense_Mutation_p.R979G|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R1201G	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1026					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTCCAGCATGAGGTATAAATT	0.338																																					p.R1201G		Atlas-SNP	.											.	XIRP2	914	.	0			c.A3601G						.						63	59	61					2																	168101503		1826	4078	5904	SO:0001583	missense	129446	exon9			AGCATGAGGTATA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.3601A>G	chr2.hg19:g.168101503A>G	ENSP00000386840:p.Arg1201Gly	62.0	0.0		74.0	5.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	9.332	1.060875	0.19987	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.03035	4.07;4.07;4.07	5.91	-2.05	0.07321	.	0.216956	0.44688	D	0.000426	T	0.04543	0.0124	L	0.59436	1.845	0.28443	N	0.916692	B;B;B	0.26258	0.09;0.145;0.145	B;B;B	0.27380	0.036;0.079;0.079	T	0.21724	-1.0237	10	0.72032	D	0.01	-0.1624	9.4277	0.38590	0.6968:0.1362:0.0:0.167	.	1026;1026;979	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	G	1201;1201;979	ENSP00000386840:R1201G;ENSP00000295237:R1201G;ENSP00000387255:R979G	ENSP00000295237:R1201G	R	+	1	2	XIRP2	167809749	1.000000	0.71417	0.251000	0.24312	0.712000	0.41017	1.734000	0.38166	-0.255000	0.09486	0.533000	0.62120	AGG	.	.		0.338	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168101503	A	G	168101503	3	3	103	1	0	0	0	0	1	0	0	0	17445	295	11	2	3631	2	XIRP2	2	168101503	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	812514	168101503	75097870	175	14798										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168105629	168105629	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cattgttaaaactcaaagccAaaatcaacacataacagagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:168105629delA	ENST00000409195.1	+	9	7816	c.7727delA	c.(7726-7728)caafs	p.Q2576fs	XIRP2_ENST00000409273.1_Frame_Shift_Del_p.Q2354fs|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Frame_Shift_Del_p.Q2576fs	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2401					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ACTCAAAGCCAAAATCAACAC	0.338																																					p.Q2576fs		Atlas-INDEL	.											XIRP2,NS,carcinoma,0,1	XIRP2	914	.	0			c.7726delC						.						96	90	92					2																	168105629		1831	4081	5912	SO:0001589	frameshift_variant	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.7727delA	chr2.hg19:g.168105629delA	ENSP00000386840:p.Gln2576fs	134.0	0.0		182.0	11.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Del	DEL	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.338	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		-	168105629	A	-	168105629	7	5	103	1	0	1	0	1	0	0	0	0	17445	130	5	0	7757	0	XIRP2	2	168105629	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	4126	168105629	75093744	176	14799										
RAPGEF4	11069	hgsc.bcm.edu	37	chr2	173882175	173882175	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acaaggttcttttgcaacagTtcaatacgggcgatgagaga	11	7	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:173882175T>C	ENST00000397081.3	+	21	2094	c.1951T>C	c.(1951-1953)Ttc>Ctc	p.F651L	RAPGEF4_ENST00000397087.3_Missense_Mutation_p.F507L|RAPGEF4_ENST00000538974.1_Missense_Mutation_p.F480L|RAPGEF4_ENST00000535187.1_Missense_Mutation_p.F431L|RAPGEF4_ENST00000539331.1_Missense_Mutation_p.F498L|RAPGEF4_ENST00000540783.1_Missense_Mutation_p.F498L|RAPGEF4_ENST00000409036.1_Missense_Mutation_p.F651L|RAPGEF4_ENST00000264111.6_Missense_Mutation_p.F650L	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	651					blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			TTTGCAACAGTTCAATACGGG	0.473																																					p.F651L		Atlas-SNP	.											.	RAPGEF4	103	.	0			c.T1951C						.						85	80	82					2																	173882175		1912	4125	6037	SO:0001583	missense	11069	exon21			CAACAGTTCAATA	U78516	CCDS42775.1, CCDS42776.1, CCDS63060.1, CCDS63061.1, CCDS74604.1	2q31-q32	2008-02-05	2004-03-26		ENSG00000091428	ENSG00000091428			16626	protein-coding gene	gene with protein product	"cAMP-regulated guanine nucleotide exchange factor II", " exchange protein directly activated by cAMP 2"	606058	"RAP guanine-nucleotide-exchange factor (GEF) 4"			10777494, 9856955	Standard	NM_007023		Approved	cAMP-GEFII, CGEF2	uc002uhv.4	Q8WZA2	OTTHUMG00000133677	ENST00000397081.3:c.1951T>C	chr2.hg19:g.173882175T>C	ENSP00000380271:p.Phe651Leu	79.0	0.0		90.0	4.0	NM_007023	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Missense_Mutation	SNP	ENST00000397081.3	hg19	CCDS42775.1	.	.	.	.	.	.	.	.	.	.	T	12.54	1.967815	0.34754	.	.	ENSG00000091428	ENST00000264111;ENST00000397081;ENST00000409036;ENST00000397087;ENST00000538974;ENST00000540783;ENST00000539331;ENST00000535187	T;T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58	5.46	5.46	0.80206	Ras guanine nucleotide exchange factor, domain (1);	0.090261	0.85682	D	0.000000	T	0.25158	0.0611	L	0.45228	1.405	0.80722	D	1	B;B	0.24651	0.108;0.066	B;B	0.25506	0.061;0.046	T	0.06661	-1.0814	10	0.02654	T	1	.	15.8863	0.79251	0.0:0.0:0.0:1.0	.	507;651	Q8WZA2-3;Q8WZA2	.;RPGF4_HUMAN	L	650;651;651;507;480;498;498;431	ENSP00000264111:F650L;ENSP00000380271:F651L;ENSP00000387104:F651L;ENSP00000380276:F507L;ENSP00000440135:F480L;ENSP00000440250:F498L;ENSP00000437384:F498L;ENSP00000438011:F431L	ENSP00000264111:F650L	F	+	1	0	RAPGEF4	173590421	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.655000	0.83696	2.223000	0.72356	0.454000	0.30748	TTC	.	.		0.473	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023		C	173882175	T	C	173882175	3	2	103	1	0	0	0	0	1	0	0	0	13061	1725	60	2	2049	2	RAPGEF4	2	173882175	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	5776546	173882175	69317198	177	14800										
ZAK	51776	hgsc.bcm.edu	37	chr2	174130888	174130888	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtcaccgttcttctcacacTttgatggccaggattcctac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:174130888delT	ENST00000375213.3	+	20	1891	c.1813delT	c.(1813-1815)tttfs	p.F605fs	MLK7-AS1_ENST00000422703.1_RNA|MLK7-AS1_ENST00000423106.2_RNA|MLTK_ENST00000409176.2_Frame_Shift_Del_p.F605fs	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		605					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										CTTCTCACACTTTGATGGCCA	0.517																																					p.H604fs		Atlas-INDEL	.											.	ZAK	62	.	0			c.1812delC						.						63	59	60					2																	174130888		2005	4193	6198	SO:0001589	frameshift_variant	0	exon20			.																												ENST00000375213.3:c.1813delT	chr2.hg19:g.174130888delT	ENSP00000364361:p.Phe605fs	202.0	0.0		233.0	14.0	NM_016653	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Frame_Shift_Del	DEL	ENST00000375213.3	hg19	CCDS42777.1																																																																																			.	.		0.517	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1			-	174130888	T	-	174130888	7	5	103	1	0	1	0	1	0	0	0	0	17527	1609	56	0	2272	0	ZAK	2	174130888	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	248713	174130888	69068485	178	14801										
GPR155	151556	hgsc.bcm.edu	37	chr2	175326315	175326315	+	Splice_Site	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacagagaactaccaacttaCccccagccagatattatgat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:175326315delC	ENST00000392552.2	-	8	1708		c.e8+1		GPR155_ENST00000392551.2_Splice_Site|GPR155_ENST00000295500.4_Splice_Site	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155						cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						TACCAACTTACCCCCAGCCAG	0.363																																					.		Atlas-INDEL	.											.	GPR155	76	.	0			c.1385+2G>-						.						121	131	128					2																	175326315		2203	4300	6503	SO:0001630	splice_region_variant	151556	exon8			.	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.1469+1G>-	chr2.hg19:g.175326315delC		135.0	0.0		178.0	13.0	NM_001267051	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Splice_Site	DEL	ENST00000392552.2	hg19	CCDS2259.1																																																																																			.	.		0.363	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529	Intron	-	175326315	C	-	175326315	8	5	103	1	0	1	0	1	0	0	1	0	6668	521	18	0	1178	0	GPR155	2	175326315	Splice_Site	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1195427	175326315	67873058	179	14802										
PLEKHA3	65977	hgsc.bcm.edu	37	chr2	179355529	179355529	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtttgactgatacaaggactAaaaaagaaaaaggtaactat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179355529delA	ENST00000234453.5	+	3	703	c.301delA	c.(301-303)aaafs	p.K102fs	PLEKHA3_ENST00000461474.1_3'UTR	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	102						Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			TACAAGGACTAAAAAAGAAAA	0.383																																					p.T100fs		Atlas-INDEL	.											.	PLEKHA3	25	.	0			c.300delT						.						47	47	47					2																	179355529		2203	4300	6503	SO:0001589	frameshift_variant	65977	exon3			.	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"Pleckstrin homology (PH) domain containing"	14338	protein-coding gene	gene with protein product	"four-phosphate-adaptor protein 1"	607774	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.301delA	chr2.hg19:g.179355529delA	ENSP00000234453:p.Lys102fs	131.0	0.0		192.0	14.0	NM_019091	Q4ZG69|Q86TQ1|Q9NXT3	Frame_Shift_Del	DEL	ENST00000234453.5	hg19	CCDS33336.1																																																																																			.	.		0.383	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091		-	179355529	A	-	179355529	7	5	103	1	0	1	0	1	0	0	0	0	12066	363	13	0	311	0	PLEKHA3	2	179355529	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	4029214	179355529	63843844	180	14803										
TTN	7273	hgsc.bcm.edu	37	chr2	179391906	179391906	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccctgttcttgactgtggaTttttcttccaccacaggacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179391906delT	ENST00000591111.1	-	313	103110	c.102886delA	c.(102886-102888)atcfs	p.I34296fs	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000587576.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.I27064fs|TTN_ENST00000589042.1_Frame_Shift_Del_p.I35937fs|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.I33369fs|TTN_ENST00000460472.2_Frame_Shift_Del_p.I26872fs|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.I26997fs|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	34296	Ig-like 152.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGACTGTGGATTTTTCTTCCA	0.453																																					p.I35937fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.107810delT						.						180	158	165					2																	179391906		1929	4132	6061	SO:0001589	frameshift_variant	7273	exon363			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.102886delA	chr2.hg19:g.179391906delT	ENSP00000465570:p.Ile34296fs	221.0	0.0		281.0	17.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179391906	T	-	179391906	7	5	103	1	0	1	0	1	0	0	0	0	16750	1493	52	0	170	0	TTN	2	179391906	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	36377	179391906	63807467	181	14804										
TTN	7273	hgsc.bcm.edu	37	chr2	179397453	179397453	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcgggctggtctcactatcTcaagatcatcttgggacagt	12	10	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179397453T>C	ENST00000591111.1	-	308	99190	c.98966A>G	c.(98965-98967)gAg>gGg	p.E32989G	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E25757G|TTN_ENST00000589042.1_Missense_Mutation_p.E34630G|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E32062G|TTN_ENST00000460472.2_Missense_Mutation_p.E25565G|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E25690G|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32989					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTCACTATCTCAAGATCATC	0.448																																					p.E34630G		Atlas-SNP	.											.	TTN	18412	.	0			c.A103889G						.						76	71	73					2																	179397453		1937	4124	6061	SO:0001583	missense	7273	exon358			ACTATCTCAAGAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.98966A>G	chr2.hg19:g.179397453T>C	ENSP00000465570:p.Glu32989Gly	61.0	0.0		104.0	5.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.76	3.212556	0.58452	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.64991	-0.13;0.11;0.09;0.08	5.95	5.95	0.96441	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.68016	0.2955	N	0.19112	0.55	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.994;0.994;0.994;0.994	T	0.73000	-0.4120	9	0.87932	D	0	.	16.0715	0.80940	0.0:0.0:0.0:1.0	.	25565;25690;25757;32989	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	32062;25565;25757;25690;25562	ENSP00000343764:E32062G;ENSP00000434586:E25565G;ENSP00000340554:E25757G;ENSP00000352154:E25690G	ENSP00000340554:E25757G	E	-	2	0	TTN	179105699	1.000000	0.71417	0.994000	0.49952	0.942000	0.58702	8.015000	0.88690	2.280000	0.76307	0.460000	0.39030	GAG	.	.		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179397453	T	C	179397453	3	2	103	1	0	0	0	0	1	0	0	0	16750	1551	54	2	4110	2	TTN	2	179397453	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	5547	179397453	63801920	182	14805										
TTN	7273	hgsc.bcm.edu	37	chr2	179438689	179438689	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tccattccattgttggaggtGggcggcctgaaacatcagct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179438689delG	ENST00000591111.1	-	276	67471	c.67247delC	c.(67246-67248)ccafs	p.P22418fs	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.P15186fs|TTN_ENST00000589042.1_Frame_Shift_Del_p.P24059fs|TTN_ENST00000342992.6_Frame_Shift_Del_p.P21491fs|TTN_ENST00000460472.2_Frame_Shift_Del_p.P14994fs|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.P15119fs|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	22418	Ig-like 116.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTTGGAGGTGGGCGGCCTGA	0.403																																					p.P24057fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.72171delA						.						62	59	60					2																	179438689		1867	4106	5973	SO:0001589	frameshift_variant	7273	exon326			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.67247delC	chr2.hg19:g.179438689delG	ENSP00000465570:p.Pro22418fs	147.0	0.0		192.0	12.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179438689	G	-	179438689	7	5	103	1	0	1	0	1	0	0	0	0	16750	1348	47	0	35957	0	TTN	2	179438689	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	41236	179438689	63760684	183	14806										
TTN	7273	hgsc.bcm.edu	37	chr2	179490077	179490077	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagcatcttctaactttacaTccctcagagtaagtgtatga	6	10	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179490077T>C	ENST00000591111.1	-	191	39772	c.39548A>G	c.(39547-39549)gAt>gGt	p.D13183G	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D5951G|TTN_ENST00000589042.1_Missense_Mutation_p.D14824G|TTN_ENST00000342992.6_Missense_Mutation_p.D12256G|TTN_ENST00000460472.2_Missense_Mutation_p.D5759G|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D5884G|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13183	Ig-like 87.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAACTTTACATCCCTCAGAGT	0.368																																					p.D14824G		Atlas-SNP	.											.	TTN	18412	.	0			c.A44471G						.						234	223	226					2																	179490077		1842	4072	5914	SO:0001583	missense	7273	exon241			TTTACATCCCTCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.39548A>G	chr2.hg19:g.179490077T>C	ENSP00000465570:p.Asp13183Gly	83.0	0.0		99.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.10	3.302537	0.60195	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.95	5.95	0.96441	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.39784	0.1091	N	0.26162	0.8	0.58432	D	0.999994	P;P;P;P	0.45715	0.865;0.865;0.865;0.865	P;P;P;P	0.45610	0.487;0.487;0.487;0.487	T	0.35251	-0.9796	9	0.87932	D	0	.	16.4116	0.83717	0.0:0.0:0.0:1.0	.	5759;5884;5951;13183	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	12256;5759;5951;5884;5759	ENSP00000343764:D12256G;ENSP00000434586:D5759G;ENSP00000340554:D5951G;ENSP00000352154:D5884G	ENSP00000340554:D5951G	D	-	2	0	TTN	179198322	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.612000	0.82975	2.276000	0.75962	0.528000	0.53228	GAT	.	.		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179490077	T	C	179490077	3	2	103	1	0	0	0	0	1	0	0	0	16750	1435	50	2	63710	2	TTN	2	179490077	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	51388	179490077	63709296	184	14807										
TTN	7273	hgsc.bcm.edu	37	chr2	179501512	179501512	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcttctattggtgaaggagTctttttgggtacacctaatt	11	6	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179501512T>C	ENST00000591111.1	-	175	36243	c.36019A>G	c.(36019-36021)Act>Gct	p.T12007A	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T4775A|TTN_ENST00000589042.1_Missense_Mutation_p.T13648A|TTN_ENST00000342992.6_Missense_Mutation_p.T11080A|TTN_ENST00000460472.2_Missense_Mutation_p.T4583A|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T4708A|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12007	Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTGAAGGAGTCTTTTTGGGT	0.443																																					p.T13648A		Atlas-SNP	.											.	TTN	18412	.	0			c.A40942G						.						45	45	45					2																	179501512		1863	4099	5962	SO:0001583	missense	7273	exon225			AAGGAGTCTTTTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.36019A>G	chr2.hg19:g.179501512T>C	ENSP00000465570:p.Thr12007Ala	72.0	0.0		125.0	5.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.82	2.947088	0.53186	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000414766	T;T;T;T	0.74315	-0.83;-0.23;-0.24;-0.25	5.77	5.77	0.91146	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	D	0.84853	0.5564	M	0.65498	2.005	0.58432	D	0.999995	D;D;D;D	0.69078	0.997;0.997;0.997;0.997	D;D;D;D	0.75020	0.985;0.985;0.985;0.985	D	0.86468	0.1783	9	0.87932	D	0	.	16.0836	0.81023	0.0:0.0:0.0:1.0	.	4583;4708;4775;12007	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	11080;4583;4775;4708;4583;952	ENSP00000343764:T11080A;ENSP00000434586:T4583A;ENSP00000340554:T4775A;ENSP00000352154:T4708A	ENSP00000340554:T4775A	T	-	1	0	TTN	179209757	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.959000	0.87885	2.196000	0.70406	0.528000	0.53228	ACT	.	.		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179501512	T	C	179501512	3	2	103	1	0	0	0	0	1	0	0	0	16750	1667	58	2	67303	2	TTN	2	179501512	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	11435	179501512	63697861	185	14808										
CWC22	57703	hgsc.bcm.edu	37	chr2	180835748	180835748	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tagctacttcaacgctatcaTctgttggtctttccaggagc	8	11	4	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:180835748T>C	ENST00000410053.3	-	9	1159	c.860A>G	c.(859-861)gAt>gGt	p.D287G	CWC22_ENST00000295749.6_Missense_Mutation_p.D287G	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	287	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.				mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						AACGCTATCATCTGTTGGTCT	0.358																																					p.D287G		Atlas-SNP	.											.	CWC22	62	.	0			c.A860G						.						113	107	109					2																	180835748		1871	4113	5984	SO:0001583	missense	57703	exon9			CTATCATCTGTTG		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"functional spliceosome-associated protein b"	615186	"CWC22 spliceosome-associated protein homolog (S. cerevisiae)"			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.860A>G	chr2.hg19:g.180835748T>C	ENSP00000387006:p.Asp287Gly	75.0	0.0		107.0	5.0	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	hg19	CCDS46465.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.700738	0.88924	.	.	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.23348	1.91;1.91;1.91	5.91	5.91	0.95273	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.49983	0.1589	H	0.94582	3.555	0.80722	D	1	P	0.44816	0.844	P	0.45610	0.487	T	0.65249	-0.6214	10	0.87932	D	0	-39.4203	15.5295	0.75942	0.0:0.0:0.0:1.0	.	287	Q9HCG8	CWC22_HUMAN	G	287	ENSP00000387006:D287G;ENSP00000295749:D287G;ENSP00000384159:D287G	ENSP00000295749:D287G	D	-	2	0	CWC22	180543993	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.825000	0.86693	2.254000	0.74563	0.533000	0.62120	GAT	.	.		0.358	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943		C	180835748	T	C	180835748	3	2	103	1	0	0	0	0	1	0	0	0	4070	1435	50	2	1914	2	CWC22	2	180835748	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1334236	180835748	62363625	186	14809										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185800708	185800708	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtgcaaataattatacagcAaaaaataaccaagttgggga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:185800708delA	ENST00000302277.6	+	4	1179	c.585delA	c.(583-585)gcafs	p.A195fs		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	195							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						ATTATACAGCAAAAAATAACC	0.388																																					p.A195fs		Atlas-INDEL	.											.	ZNF804A	322	.	0			c.584delC						.						62	65	64					2																	185800708		2203	4300	6503	SO:0001589	frameshift_variant	91752	exon4			.	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.585delA	chr2.hg19:g.185800708delA	ENSP00000303252:p.Ala195fs	115.0	0.0		134.0	10.0	NM_194250	A7E253|Q6ZN26	Frame_Shift_Del	DEL	ENST00000302277.6	hg19	CCDS2291.1																																																																																			.	.		0.388	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		-	185800708	A	-	185800708	7	5	103	1	0	1	0	1	0	0	0	0	18185	117	5	0	599	0	ZNF804A	2	185800708	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	4964960	185800708	57398665	187	14810										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187605011	187605011	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcatcagtcgtcagtacctgAgccaagcagttgtagaagtg	11	9	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:187605011A>G	ENST00000304698.5	+	2	498	c.295A>G	c.(295-297)Agc>Ggc	p.S99G		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	99						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						TCAGTACCTGAGCCAAGCAGT	0.398																																					p.S99G		Atlas-SNP	.											.	FAM171B	146	.	0			c.A295G						.						112	96	102					2																	187605011		2203	4300	6503	SO:0001583	missense	165215	exon2			TACCTGAGCCAAG	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.295A>G	chr2.hg19:g.187605011A>G	ENSP00000304108:p.Ser99Gly	121.0	0.0		201.0	11.0	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.609599	0.46527	.	.	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.35236	1.32	6.16	5.06	0.68205	.	0.292241	0.38663	N	0.001605	T	0.28333	0.0700	L	0.38175	1.15	0.28359	N	0.920569	B;B	0.20164	0.042;0.042	B;B	0.28385	0.089;0.089	T	0.14309	-1.0477	10	0.48119	T	0.1	-15.5391	6.7577	0.23523	0.6417:0.272:0.0863:0.0	.	99;100	Q6P995;A8K122	F171B_HUMAN;.	G	99	ENSP00000304108:S99G	ENSP00000272804:S99G	S	+	1	0	FAM171B	187313256	0.933000	0.31639	1.000000	0.80357	0.960000	0.62799	2.113000	0.41902	2.367000	0.80283	0.528000	0.53228	AGC	.	.		0.398	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		G	187605011	A	G	187605011	3	3	103	1	0	0	0	0	1	0	0	0	5496	304	11	2	301	2	FAM171B	2	187605011	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1804303	187605011	55594362	188	14811										
ZSWIM2	151112	hgsc.bcm.edu	37	chr2	187713741	187713741	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tccctcagcaggaagccagtGgggcccatctctcgtaggag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:187713741delG	ENST00000295131.2	-	1	156	c.117delC	c.(115-117)cccfs	p.P39fs		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	39					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			GGAAGCCAGTGGGGCCCATCT	0.602																																					p.T40fs		Atlas-INDEL	.											.	ZSWIM2	119	.	0			c.118delA						.						60	57	58					2																	187713741		2203	4300	6503	SO:0001589	frameshift_variant	151112	exon1			.	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.117delC	chr2.hg19:g.187713741delG	ENSP00000295131:p.Pro39fs	193.0	0.0		244.0	16.0	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Frame_Shift_Del	DEL	ENST00000295131.2	hg19	CCDS33348.1																																																																																			.	.		0.602	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		-	187713741	G	-	187713741	7	5	103	1	0	1	0	1	0	0	0	0	18256	1335	47	0	1820	0	ZSWIM2	2	187713741	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	108730	187713741	55485632	189	14812										
COL5A2	1290	hgsc.bcm.edu	37	chr2	189951464	189951464	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agacttacttgctgtccttgTaaaccctgtggtccccttgg	9	12	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:189951464T>C	ENST00000374866.3	-	9	952	c.678A>G	c.(676-678)ttA>ttG	p.L226L		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	226					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			GCTGTCCTTGTAAACCCTGTG	0.363																																					p.L226L		Atlas-SNP	.											.	COL5A2	230	.	0			c.A678G						.						46	44	45					2																	189951464		2203	4297	6500	SO:0001819	synonymous_variant	1290	exon9			TCCTTGTAAACCC	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.678A>G	chr2.hg19:g.189951464T>C		30.0	0.0		60.0	4.0	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Silent	SNP	ENST00000374866.3	hg19	CCDS33350.1																																																																																			.	.		0.363	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		C	189951464	T	C	189951464	2	2	103	1	0	0	0	0	0	0	0	1	3699	1635	57	2		2	COL5A2	2	189951464	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2237723	189951464	53247909	190	14813										
ANKAR	150709	hgsc.bcm.edu	37	chr2	190611122	190611122	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttagggaaggagcaccgaagAaaattaaaacctaaaattca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:190611122delA	ENST00000520309.1	+	23	4162	c.4074delA	c.(4072-4074)agafs	p.R1358fs	ANKAR_ENST00000281412.6_3'UTR|ANKAR_ENST00000438402.2_3'UTR|ANKAR_ENST00000313581.4_Frame_Shift_Del_p.R1358fs|ANKAR_ENST00000431575.2_Frame_Shift_Del_p.R1287fs	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	1358						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			AGCACCGAAGAAAATTAAAAC	0.348																																					p.R1358fs		Atlas-INDEL	.											.	ANKAR	184	.	0			c.4073delG						.						95	107	103					2																	190611122		2202	4298	6500	SO:0001589	frameshift_variant	150709	exon23			.	AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"Ankyrin repeat domain containing", "Armadillo repeat containing"	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.4074delA	chr2.hg19:g.190611122delA	ENSP00000427882:p.Arg1358fs	147.0	0.0		158.0	10.0	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Frame_Shift_Del	DEL	ENST00000520309.1	hg19	CCDS33351.2																																																																																			.	.		0.348	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		-	190611122	A	-	190611122	7	5	103	1	0	1	0	1	0	0	0	0	623	243	9	0	4160	0	ANKAR	2	190611122	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	659658	190611122	52588251	191	14814										
HIBCH	26275	hgsc.bcm.edu	37	chr2	191159295	191159295	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgatatcacccccggcacagAaagcctttcctcctgctccc	6	18	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:191159295A>G	ENST00000359678.5	-	4	575	c.281T>C	c.(280-282)tTc>tCc	p.F94S	HIBCH_ENST00000392332.3_Missense_Mutation_p.F94S	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	94					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			CCCGGCACAGAAAGCCTTTCC	0.388																																					p.F94S		Atlas-SNP	.											.	HIBCH	28	.	0			c.T281C						.						85	82	83					2																	191159295		2203	4300	6503	SO:0001583	missense	26275	exon4			GCACAGAAAGCCT	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"3-hydroxyisobutyryl-Coenzyme A hydrolase"			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.281T>C	chr2.hg19:g.191159295A>G	ENSP00000352706:p.Phe94Ser	72.0	0.0		96.0	4.0	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Missense_Mutation	SNP	ENST00000359678.5	hg19	CCDS2304.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.453349	0.84209	.	.	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000409934	D;D;T	0.90563	-2.69;-2.69;-1.32	5.43	5.43	0.79202	Crotonase, core (1);	0.044752	0.85682	D	0.000000	D	0.97504	0.9183	H	0.99545	4.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98652	1.0680	10	0.87932	D	0	-10.5228	13.4412	0.61114	1.0:0.0:0.0:0.0	.	94;94	Q6NVY1-2;Q6NVY1	.;HIBCH_HUMAN	S	94;94;148	ENSP00000376144:F94S;ENSP00000352706:F94S;ENSP00000387247:F148S	ENSP00000352706:F94S	F	-	2	0	HIBCH	190867540	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.743000	0.85020	2.053000	0.61076	0.460000	0.39030	TTC	.	.		0.388	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1			G	191159295	A	G	191159295	3	3	103	1	0	0	0	0	1	0	0	0	7109	246	9	2	923	2	HIBCH	2	191159295	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	548173	191159295	52040078	192	14815										
TMEFF2	23671	hgsc.bcm.edu	37	chr2	192818525	192818525	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgtatagaacactgtagtccTttttttcacagtgttgtcca					rs200174014		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:192818525delT	ENST00000272771.5	-	9	2092	c.908delA	c.(907-909)aagfs	p.K303fs	AC098617.1_ENST00000424116.2_RNA|AC098617.1_ENST00000428980.2_RNA|TMEFF2_ENST00000392314.1_Frame_Shift_Del_p.K303fs	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2	303	Required for shedding.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(12)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			ACTGTAGTCCTTTTTTTCACA	0.398																																					p.K303fs	Pancreas(50;1277 1381 28487 47072)	Atlas-INDEL	.											.	TMEFF2	54	.	0			c.909delG						.			2,4264		1,0,2132	111	97	102			4.1	1	2		103	0,8254		0,0,4127	no	frameshift	TMEFF2	NM_016192.2		1,0,6259	A1A1,A1R,RR		0.0,0.0469,0.016			192818525	2,12518	2203	4300	6503	SO:0001589	frameshift_variant	23671	exon9			.	AB017269	CCDS2314.1	2q32.3	2010-05-04			ENSG00000144339	ENSG00000144339			11867	protein-coding gene	gene with protein product	"transmembrane protein TENB2", "tomoregulin", "cancer/testis antigen family 120, member 2"	605734				10903839	Standard	NM_016192		Approved	TENB2, HPP1, TR, TPEF, CT120.2	uc002utc.3	Q9UIK5	OTTHUMG00000132723	ENST00000272771.5:c.908delA	chr2.hg19:g.192818525delT	ENSP00000272771:p.Lys303fs	113.0	0.0		138.0	11.0	NM_016192	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Frame_Shift_Del	DEL	ENST00000272771.5	hg19	CCDS2314.1																																																																																			.	.		0.398	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192		-	192818525	T	-	192818525	7	5	103	1	0	1	0	1	0	0	0	0	16029	1609	56	0	224	0	TMEFF2	2	192818525	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1659230	192818525	50380848	193	14816										
ICA1L	130026	hgsc.bcm.edu	37	chr2	203650685	203650685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgaaggcactggctggttaTcagtgtgtgaaagacaaagt	14	5	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:203650685T>C	ENST00000392237.2	-	13	1446	c.1289A>G	c.(1288-1290)gAt>gGt	p.D430G	ICA1L_ENST00000358299.2_Missense_Mutation_p.D430G	NM_138468.4	NP_612477.3	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like	430										breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGGCTGGTTATCAGTGTGTGA	0.343																																					p.D430G		Atlas-SNP	.											.	ICA1L	33	.	0			c.A1289G						.						101	107	105					2																	203650685		2203	4300	6503	SO:0001583	missense	130026	exon13			TGGTTATCAGTGT	AB053317	CCDS2354.1, CCDS74632.1	2q33	2008-02-05	2006-05-26	2006-05-26	ENSG00000163596	ENSG00000163596			14442	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14"	ALS2CR15, ALS2CR14		11586298	Standard	NM_138468		Approved		uc002uzh.1	Q8NDH6	OTTHUMG00000132856	ENST00000392237.2:c.1289A>G	chr2.hg19:g.203650685T>C	ENSP00000376070:p.Asp430Gly	39.0	0.0		55.0	5.0	NM_138468	B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2	Missense_Mutation	SNP	ENST00000392237.2	hg19	CCDS2354.1	.	.	.	.	.	.	.	.	.	.	T	7.626	0.677752	0.14841	.	.	ENSG00000163596	ENST00000392237;ENST00000358299	.	.	.	4.99	2.54	0.30619	Islet cell autoantigen Ica1, C-terminal (1);	0.797344	0.11643	N	0.543540	T	0.34250	0.0891	N	0.25647	0.755	0.80722	D	1	B	0.23185	0.081	B	0.21917	0.037	T	0.07790	-1.0754	9	0.20519	T	0.43	.	4.8407	0.13489	0.0:0.0972:0.1899:0.7129	.	430	Q8NDH6	ICA1L_HUMAN	G	430	.	ENSP00000351047:D430G	D	-	2	0	ICA1L	203358930	0.786000	0.28738	0.562000	0.28370	0.688000	0.40055	0.933000	0.28897	0.357000	0.24183	0.456000	0.33151	GAT	.	.		0.343	ICA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256330.1	NM_138468		C	203650685	T	C	203650685	3	2	103	1	0	0	0	0	1	0	0	0	7487	1435	50	2	167	2	ICA1L	2	203650685	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	10832160	203650685	39548688	194	14817										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	203974873	203974873	+	Splice_Site	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ataatacgtattttttttagTttttttacaggaagtggcat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:203974873delT	ENST00000449802.1	+	14	2196	c.1863delT	c.(1861-1863)agt>ag	p.S621fs		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	621										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TTTTTTTTAGTTTTTTTACAG	0.348																																					.		Atlas-INDEL	.											.	NBEAL1	266	.	0			c.1863-1T>-						.						201	159	172					2																	203974873		692	1591	2283	SO:0001630	splice_region_variant	65065	exon14			.	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.1863-1T>-	chr2.hg19:g.203974873delT		98.0	0.0		166.0	11.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Splice_Site	DEL	ENST00000449802.1	hg19	CCDS46495.1																																																																																			.	.		0.348	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		Frame_Shift_Del	-	203974873	T	-	203974873	8	5	103	1	0	1	0	1	0	0	1	0	10197	1739	60	0	1913	0	NBEAL1	2	203974873	Splice_Site	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	324188	203974873	39224500	195	14818										
CREB1	1385	hgsc.bcm.edu	37	chr2	208442310	208442310	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggagttgttatggcatcctCcccagcacttcctacacagc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:208442310delC	ENST00000432329.2	+	8	1063	c.812delC	c.(811-813)tccfs	p.S271fs	CREB1_ENST00000353267.3_Frame_Shift_Del_p.S257fs|CREB1_ENST00000430624.1_Frame_Shift_Del_p.S257fs|CREB1_ENST00000374397.4_Intron	NM_134442.3	NP_604391.1	P16220	CREB1_HUMAN	cAMP responsive element binding protein 1	271					activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|cellular response to zinc ion (GO:0071294)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|lactation (GO:0007595)|lung saccule development (GO:0060430)|memory (GO:0007613)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription by competitive promoter binding (GO:0010944)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|pituitary gland development (GO:0021983)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of hormone secretion (GO:0046887)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of cell size (GO:0008361)|response to drug (GO:0042493)|response to glucagon (GO:0033762)|response to organic substance (GO:0010033)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|Type I pneumocyte differentiation (GO:0060509)|viral process (GO:0016032)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	cAMP response element binding (GO:0035497)|enzyme binding (GO:0019899)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)		EWSR1/CREB1(44)	NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|upper_aerodigestive_tract(1)	5				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Naloxone(DB01183)	ATGGCATCCTCCCCAGCACTT	0.468			T	EWSR1	"clear cell sarcoma, angiomatoid fibrous histiocytoma"																																p.S271fs		Atlas-INDEL	.		Dom	yes		2	2q34	1385	cAMP responsive element binding protein 1		M	.	CREB1	21	.	0			c.811delT						.						142	117	125					2																	208442310		2203	4300	6503	SO:0001589	frameshift_variant	1385	exon8			.	M27691	CCDS2374.1, CCDS2375.1	2q34	2013-01-10			ENSG00000118260	ENSG00000118260		"basic leucine zipper proteins"	2345	protein-coding gene	gene with protein product		123810					Standard	NM_134442		Approved		uc002vcc.3	P16220	OTTHUMG00000132936	ENST00000432329.2:c.812delC	chr2.hg19:g.208442310delC	ENSP00000387699:p.Ser271fs	139.0	0.0		181.0	12.0	NM_134442	P21934|Q6V963|Q9UMA7	Frame_Shift_Del	DEL	ENST00000432329.2	hg19	CCDS2375.1																																																																																			.	.		0.468	CREB1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256467.3	NM_134442		-	208442310	C	-	208442310	7	5	103	1	0	1	0	1	0	0	0	0	3856	855	30	0	838	0	CREB1	2	208442310	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	4467437	208442310	34757063	196	14819										
IDH1	3417	hgsc.bcm.edu	37	chr2	209110110	209110110	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtgtgtaggttatctctacTtttccaggcccaggaacaac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:209110110delT	ENST00000415913.1	-	5	834	c.453delA	c.(451-453)aaafs	p.K151fs	IDH1_ENST00000345146.2_Frame_Shift_Del_p.K151fs|IDH1_ENST00000446179.1_Frame_Shift_Del_p.K151fs	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	151					2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TTATCTCTACTTTTCCAGGCC	0.388			Mis		gliobastoma																																p.V152X	Pancreas(158;264 1958 3300 35450 36047)	Atlas-INDEL	.		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	.	IDH1	6310	.	0			c.454delG						.						152	137	142					2																	209110110		2203	4300	6503	SO:0001589	frameshift_variant	3417	exon5			.		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.453delA	chr2.hg19:g.209110110delT	ENSP00000390265:p.Lys151fs	147.0	0.0		208.0	13.0	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Frame_Shift_Del	DEL	ENST00000415913.1	hg19	CCDS2381.1																																																																																			.	.		0.388	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			-	209110110	T	-	209110110	7	5	103	1	0	1	0	1	0	0	0	0	7503	1606	56	0	815	0	IDH1	2	209110110	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	667800	209110110	34089263	197	14820										
FN1	2335	hgsc.bcm.edu	37	chr2	216230250	216230250	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggtcacacttgaattctccTtttccgttcccaagacatgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:216230250delT	ENST00000359671.1	-	42	7114	c.6849delA	c.(6847-6849)aaafs	p.K2283fs	FN1_ENST00000346544.3_Frame_Shift_Del_p.K2108fs|FN1_ENST00000443816.1_Frame_Shift_Del_p.K2162fs|FN1_ENST00000421182.1_Frame_Shift_Del_p.K2137fs|FN1_ENST00000446046.1_Frame_Shift_Del_p.K2227fs|FN1_ENST00000323926.6_Frame_Shift_Del_p.K2343fs|FN1_ENST00000345488.5_Frame_Shift_Del_p.K2081fs|FN1_ENST00000357867.4_Frame_Shift_Del_p.K2073fs|FN1_ENST00000357009.2_3'UTR|FN1_ENST00000356005.4_Frame_Shift_Del_p.K2193fs|FN1_ENST00000354785.4_Frame_Shift_Del_p.K2374fs|FN1_ENST00000432072.2_Frame_Shift_Del_p.K2164fs|FN1_ENST00000336916.4_Frame_Shift_Del_p.K2252fs			P02751	FINC_HUMAN	fibronectin 1	2283	Fibrin-binding 2.|Fibronectin type-I 11. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TGAATTCTCCTTTTCCGTTCC	0.443																																					p.G2375fs		Atlas-INDEL	.											.	FN1	521	.	0			c.7123delG						.						324	278	293					2																	216230250		2203	4300	6503	SO:0001589	frameshift_variant	2335	exon43			.		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.6849delA	chr2.hg19:g.216230250delT	ENSP00000352696:p.Lys2283fs	163.0	0.0		151.0	11.0	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Frame_Shift_Del	DEL	ENST00000359671.1	hg19																																																																																				.	.		0.443	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		-	216230250	T	-	216230250	7	5	103	1	0	1	0	1	0	0	0	0	5970	1606	56	0	327	0	FN1	2	216230250	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	7120140	216230250	26969123	198	14821										
TTLL4	9654	hgsc.bcm.edu	37	chr2	219602445	219602445	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atagtattggcctccgccagAaaaacagcttcaagcagagt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:219602445delA	ENST00000392102.1	+	3	386	c.46delA	c.(46-48)aaafs	p.K16fs	TTLL4_ENST00000258398.4_Frame_Shift_Del_p.K16fs|TTLL4_ENST00000457313.1_Intron|TTLL4_ENST00000442769.1_Frame_Shift_Del_p.K16fs	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	16					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		CCTCCGCCAGAAAAACAGCTT	0.587																																					p.Q15fs	GBM(172;1818 2053 15407 20943 49753)	Atlas-INDEL	.											.	TTLL4	96	.	0			c.45delG						.						58	58	58					2																	219602445		2203	4300	6503	SO:0001589	frameshift_variant	9654	exon3			.		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"Tubulin tyrosine ligase-like family"	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.46delA	chr2.hg19:g.219602445delA	ENSP00000375951:p.Lys16fs	123.0	0.0		170.0	11.0	NM_014640	A8K6V5|Q8WW29	Frame_Shift_Del	DEL	ENST00000392102.1	hg19	CCDS2422.1																																																																																			.	.		0.587	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		-	219602445	A	-	219602445	7	5	103	1	0	1	0	1	0	0	0	0	16744	247	9	0	48	0	TTLL4	2	219602445	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3372195	219602445	23596928	199	14822										
TTLL4	9654	hgsc.bcm.edu	37	chr2	219604821	219604821	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagatcaggctgagactgaaGatacagaagaagaactagta	11	6	1	7	rs371385094	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:219604821G>T	ENST00000392102.1	+	4	1868	c.1528G>T	c.(1528-1530)Gat>Tat	p.D510Y	TTLL4_ENST00000258398.4_Missense_Mutation_p.D510Y|TTLL4_ENST00000457313.1_Missense_Mutation_p.D345Y|TTLL4_ENST00000442769.1_Missense_Mutation_p.D510Y	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	510					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		TGAGACTGAAGATACAGAAGA	0.458																																					p.D510Y	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.G1528T						.						122	117	118					2																	219604821		2203	4300	6503	SO:0001583	missense	9654	exon4			ACTGAAGATACAG		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"Tubulin tyrosine ligase-like family"	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.1528G>T	chr2.hg19:g.219604821G>T	ENSP00000375951:p.Asp510Tyr	185.0	0.0		231.0	25.0	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	hg19	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.796399	0.70567	.	.	ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398	T;T;T;T	0.06294	3.49;3.71;3.32;3.71	4.69	4.69	0.59074	.	0.793840	0.11423	N	0.565537	T	0.16938	0.0407	L	0.34521	1.04	0.44531	D	0.997485	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.74023	0.936;0.927;0.982	T	0.01879	-1.1255	10	0.62326	D	0.03	.	14.4975	0.67700	0.0:0.0:1.0:0.0	.	345;510;510	E9PH58;E7EX20;Q14679	.;.;TTLL4_HUMAN	Y	345;510;510;510	ENSP00000393332:D345Y;ENSP00000375951:D510Y;ENSP00000396555:D510Y;ENSP00000258398:D510Y	ENSP00000258398:D510Y	D	+	1	0	TTLL4	219313065	1.000000	0.71417	0.996000	0.52242	0.908000	0.53690	5.584000	0.67490	2.433000	0.82419	0.561000	0.74099	GAT	.	.		0.458	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		T	219604821	G	T	219604821	3	4	103	1	0	0	0	0	1	0	0	0	16744	942	33	3	1534	3	TTLL4	2	219604821	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	2376	219604821	23594552	200	14823										
ATG9A	79065	hgsc.bcm.edu	37	chr2	220088847	220088847	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctgcacacggtcacggtgaCccccaggagtgtgacggtgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:220088847delC	ENST00000409618.1	-	8	1685	c.1246delG	c.(1246-1248)gtcfs	p.V416fs	ATG9A_ENST00000409422.1_Frame_Shift_Del_p.V355fs|ATG9A_ENST00000396761.2_Frame_Shift_Del_p.V416fs|ATG9A_ENST00000488833.1_5'Flank|ATG9A_ENST00000361242.4_Frame_Shift_Del_p.V416fs|AC068946.1_ENST00000408417.1_RNA			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	416					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTCACGGTGACCCCCAGGAGT	0.582																																					p.V416fs		Atlas-INDEL	.											.	ATG9A	50	.	0			c.1247delT						.						107	116	113					2																	220088847		2124	4227	6351	SO:0001589	frameshift_variant	79065	exon8			.	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"APG9 autophagy 9-like 1 (S. cerevisiae)", "ATG9 autophagy related 9 homolog A (S. cerevisiae)"	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.1246delG	chr2.hg19:g.220088847delC	ENSP00000386710:p.Val416fs	138.0	0.0		171.0	11.0	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Frame_Shift_Del	DEL	ENST00000409618.1	hg19	CCDS42820.1																																																																																			.	.		0.582	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		-	220088847	C	-	220088847	7	5	103	1	0	1	0	1	0	0	0	0	1102	507	18	0	1309	0	ATG9A	2	220088847	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	484026	220088847	23110526	201	14824										
DNPEP	23549	hgsc.bcm.edu	37	chr2	220246820	220246820	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atccgccgcagcaccagctcTgtcagcagtgactgtgctcc	10	16	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:220246820T>C	ENST00000273075.4	-	11	1198	c.978A>G	c.(976-978)acA>acG	p.T326T	DNPEP_ENST00000373972.1_Silent_p.T251T|DNPEP_ENST00000523282.1_Silent_p.T334T|DNPEP_ENST00000490371.1_5'Flank	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	316					peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCACCAGCTCTGTCAGCAGTG	0.602																																					p.T326T		Atlas-SNP	.											.	DNPEP	40	.	0			c.A978G						.						50	57	55					2																	220246820		2134	4248	6382	SO:0001819	synonymous_variant	23549	exon11			CAGCTCTGTCAGC		CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.978A>G	chr2.hg19:g.220246820T>C		38.0	0.0		85.0	4.0	NM_012100	Q9BW44|Q9NUV5	Silent	SNP	ENST00000273075.4	hg19	CCDS42823.1																																																																																			.	.		0.602	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100		C	220246820	T	C	220246820	2	2	103	1	0	0	0	0	0	0	0	1	4681	1567	55	2		2	DNPEP	2	220246820	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	157973	220246820	22952553	202	14825										
DES	1674	hgsc.bcm.edu	37	chr2	220286238	220286238	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgaagatggccctggatgtGgagattgccacctaccggaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:220286238delG	ENST00000373960.3	+	6	1286	c.1200delG	c.(1198-1200)gtgfs	p.V400fs		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	400	Coil 2B.|Rod.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		CCCTGGATGTGGAGATTGCCA	0.642																																					p.V400fs		Atlas-INDEL	.											.	DES	53	.	0			c.1199delT						.						55	52	53					2																	220286238		2203	4300	6503	SO:0001589	frameshift_variant	1674	exon6			.	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"Intermediate filaments type III"	2770	protein-coding gene	gene with protein product	"intermediate filament protein"	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.1200delG	chr2.hg19:g.220286238delG	ENSP00000363071:p.Val400fs	91.0	0.0		106.0	10.0	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Frame_Shift_Del	DEL	ENST00000373960.3	hg19	CCDS33383.1																																																																																			.	.		0.642	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927		-	220286238	G	-	220286238	7	5	103	1	0	1	0	1	0	0	0	0	4451	1335	47	0	1222	0	DES	2	220286238	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	39418	220286238	22913135	203	14826										
ACCN4	55515	hgsc.bcm.edu	37	chr2	220402417	220402417	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccccctgcggacctccactGggggcatctccactttgggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:220402417delG	ENST00000347842.3	+	8	1803	c.1789delG	c.(1789-1791)gggfs	p.G598fs	ASIC4_ENST00000358078.4_Frame_Shift_Del_p.G617fs	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	598					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										GACCTCCACTGGGGGCATCTC	0.612																																					p.T596fs		Atlas-INDEL	.											.	.	.	.	0			c.1788delT						.						32	31	31					2																	220402417		2202	4300	6502	SO:0001589	frameshift_variant	55515	exon8			.	AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"Ion channels / Acid-sensing (proton-gated) ion channels"	21263	protein-coding gene	gene with protein product		606715	"amiloride-sensitive cation channel 4, pituitary", "amiloride-sensitive cation channel family member 4, pituitary"	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1789delG	chr2.hg19:g.220402417delG	ENSP00000326627:p.Gly598fs	125.0	0.0		159.0	10.0	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Frame_Shift_Del	DEL	ENST00000347842.3	hg19	CCDS2442.1																																																																																			.	.		0.612	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674		-	220402417	G	-	220402417	7	5	103	1	0	1	0	1	0	0	0	0	131	1348	47	0	1880	0	ACCN4	2	220402417	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	116179	220402417	22796956	204	14827										
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226491650	226491650	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagaatcaacagaggaactgAaagtccgaagccacagcacg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:226491650delA	ENST00000272907.6	+	5	2049	c.1636delA	c.(1636-1638)aaafs	p.K546fs	NYAP2_ENST00000409269.2_Frame_Shift_Del_p.E80fs	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	546					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												AGAGGAACTGAAAGTCCGAAG	0.423																																					p.L545fs		Atlas-INDEL	.											.	.	.	.	0			c.1635delG						.						23	24	24					2																	226491650		1874	4099	5973	SO:0001589	frameshift_variant	57624	exon5			.	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1636delA	chr2.hg19:g.226491650delA	ENSP00000272907:p.Lys546fs	104.0	0.0		148.0	10.0	NM_020864	A2RRN4|Q96NL2	Frame_Shift_Del	DEL	ENST00000272907.6	hg19	CCDS46529.1																																																																																			.	.		0.423	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		-	226491650	A	-	226491650	7	5	103	1	0	1	0	1	0	0	0	0	8246	247	9	0	1650	0	KIAA1486	2	226491650	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	6089233	226491650	16707723	205	14828										
COL4A3	1285	hgsc.bcm.edu	37	chr2	228111436	228111436	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaggactcccagggacactGggctacccagggatcccggt	13	15	0	0	rs559126084	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:228111436G>C	ENST00000396578.3	+	7	585	c.423G>C	c.(421-423)ctG>ctC	p.L141L	AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000606119.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	141	Triple-helical region.		L -> P (in dbSNP:rs10178458). {ECO:0000269|PubMed:11134255, ECO:0000269|PubMed:8083201}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		CAGGGACACTGGGCTACCCAG	0.413																																					p.L141L		Atlas-SNP	.											COL4A3_ENST00000328380,NS,carcinoma,0,2	COL4A3	293	.	0			c.G423C						.						65	64	64					2																	228111436		1839	4084	5923	SO:0001819	synonymous_variant	1285	exon7			GACACTGGGCTAC		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.423G>C	chr2.hg19:g.228111436G>C		135.0	0.0		180.0	0.0	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	hg19	CCDS42829.1																																																																																			.	.		0.413	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		C	228111436	G	C	228111436	2	2	103	1	0	0	0	0	0	0	0	1	3693	1335	47	4		4	COL4A3	2	228111436	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	1619786	228111436	15087937	206	14829										
AGFG1	3267	hgsc.bcm.edu	37	chr2	228418462	228418462	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acaaacaaagccagtagtaaCcccttttggtcaagttgcag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:228418462delC	ENST00000310078.8	+	12	1840	c.1580delC	c.(1579-1581)accfs	p.T527fs	AGFG1_ENST00000373671.3_Frame_Shift_Del_p.T487fs|AGFG1_ENST00000409171.1_Frame_Shift_Del_p.T525fs|AGFG1_ENST00000409315.1_Frame_Shift_Del_p.T506fs|AGFG1_ENST00000409979.2_Frame_Shift_Del_p.T549fs	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	527					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						CCAGTAGTAACCCCTTTTGGT	0.333																																					p.T549fs		Atlas-INDEL	.											.	AGFG1	80	.	0			c.1645delA						.						104	110	108					2																	228418462		2203	4300	6503	SO:0001589	frameshift_variant	3267	exon13			.		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"ADP-ribosylation factor GTPase activating proteins"	5175	protein-coding gene	gene with protein product		600862	"HIV-1 Rev binding protein"	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.1580delC	chr2.hg19:g.228418462delC	ENSP00000312059:p.Thr527fs	108.0	0.0		182.0	12.0	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Frame_Shift_Del	DEL	ENST00000310078.8	hg19	CCDS2467.1																																																																																			.	.		0.333	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		-	228418462	C	-	228418462	7	5	103	1	0	1	0	1	0	0	0	0	380	507	18	0	1702	0	AGFG1	2	228418462	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	307026	228418462	14780911	207	14830										
ITM2C	81618	hgsc.bcm.edu	37	chr2	231741644	231741644	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcaacaccaccattgtgctgCcccctcgcaacttctgggag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:231741644delC	ENST00000326427.6	+	4	649	c.523delC	c.(523-525)cccfs	p.P176fs	ITM2C_ENST00000492029.1_3'UTR|ITM2C_ENST00000326407.6_Intron|ITM2C_ENST00000335005.6_Frame_Shift_Del_p.P129fs|ITM2C_ENST00000409704.2_Frame_Shift_Del_p.P114fs	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	176	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)	p.P176fs*9(1)		cervix(2)|lung(1)|ovary(1)|skin(1)	5		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		CATTGTGCTGCCCCCTCGCAA	0.582																																					p.L174fs		Atlas-INDEL	.											.	ITM2C	17	.	1	Deletion - Frameshift(1)	lung(1)	c.522delG						.						152	141	144					2																	231741644		2203	4300	6503	SO:0001589	frameshift_variant	81618	exon4			.	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"BRICHOS domain containing"	6175	protein-coding gene	gene with protein product	"BRICHOS domain containing 2C"	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.523delC	chr2.hg19:g.231741644delC	ENSP00000322730:p.Pro176fs	124.0	0.0		178.0	11.0	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Frame_Shift_Del	DEL	ENST00000326427.6	hg19	CCDS2479.1																																																																																			.	.		0.582	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926		-	231741644	C	-	231741644	7	5	103	1	0	1	0	1	0	0	0	0	7923	739	26	0	537	0	ITM2C	2	231741644	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	3323182	231741644	11457729	208	14831										
ASB18	401036	hgsc.bcm.edu	37	chr2	237103580	237103580	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggctttggcaagggtaacaGggggatgaggtcaaagcacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:237103580delG	ENST00000409749.3	-	6	1335	c.1336delC	c.(1336-1338)ctgfs	p.L447fs	AC079135.1_ENST00000483218.1_RNA|AC079135.1_ENST00000415226.1_RNA|ASB18_ENST00000330842.6_Frame_Shift_Del_p.L418fs	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	447	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					large_intestine(1)|lung(3)|ovary(1)|prostate(1)	6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		AAGGGTAACAGGGGGATGAGG	0.542																																					p.L446fs		Atlas-INDEL	.											.	ASB18	34	.	0			c.1337delT						.						63	73	70					2																	237103580		2063	4217	6280	SO:0001589	frameshift_variant	401036	exon6			.	AK123854	CCDS46548.1	2q37.2	2013-01-10	2011-01-25		ENSG00000182177	ENSG00000182177		"Ankyrin repeat domain containing"	19770	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 18"			12076535	Standard	NM_212556		Approved		uc010znh.2	Q6ZVZ8	OTTHUMG00000153086	ENST00000409749.3:c.1336delC	chr2.hg19:g.237103580delG	ENSP00000386532:p.Leu447fs	130.0	0.0		138.0	10.0	NM_212556	B6ZDL7	Frame_Shift_Del	DEL	ENST00000409749.3	hg19	CCDS46548.1																																																																																			.	.		0.542	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556		-	237103580	G	-	237103580	7	5	103	1	0	1	0	1	0	0	0	0	1022	991	35	0	67	0	ASB18	2	237103580	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	5361936	237103580	6095793	209	14832										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238277223	238277223	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tacctggccgtgaaggaggaGgggtgtccacccctggaggt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:238277223delG	ENST00000295550.4	-	10	5335	c.4883delC	c.(4882-4884)cctfs	p.P1630fs	COL6A3_ENST00000353578.4_Frame_Shift_Del_p.P1424fs|COL6A3_ENST00000346358.4_Frame_Shift_Del_p.P1430fs|COL6A3_ENST00000347401.3_Frame_Shift_Del_p.P1429fs|COL6A3_ENST00000472056.1_Frame_Shift_Del_p.P1023fs|COL6A3_ENST00000409809.1_Frame_Shift_Del_p.P1424fs	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1630	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TGAAGGAGGAGGGGTGTCCAC	0.468																																					p.P1628fs		Atlas-INDEL	.											.	COL6A3	608	.	0			c.4884delT						.						61	63	63					2																	238277223		2203	4300	6503	SO:0001589	frameshift_variant	1293	exon10			.	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4883delC	chr2.hg19:g.238277223delG	ENSP00000295550:p.Pro1630fs	117.0	0.0		129.0	10.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Frame_Shift_Del	DEL	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.		0.468	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		-	238277223	G	-	238277223	7	5	103	1	0	1	0	1	0	0	0	0	3703	1000	35	0	4790	0	COL6A3	2	238277223	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1173643	238277223	4922150	210	14833										
LRRFIP1	9208	hgsc.bcm.edu	37	chr2	238681566	238681566	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acttgcaaaatctgagcaagAgataactgcattagaacaaa	7	7	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:238681566A>G	ENST00000308482.9	+	22	1754	c.1685A>G	c.(1684-1686)gAg>gGg	p.E562G	LRRFIP1_ENST00000468950.1_3'UTR	NM_001137550.1	NP_001131022.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	0	DNA-binding.			L -> F (in Ref. 4; AAI08915). {ECO:0000305}.	innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		TCTGAGCAAGAGATAACTGCA	0.418																																					p.E562G		Atlas-SNP	.											LRRFIP1_ENST00000308482,NS,carcinoma,0,1	LRRFIP1	171	.	0			c.A1685G						.						91	81	84					2																	238681566		1568	3582	5150	SO:0001583	missense	9208	exon22			AGCAAGAGATAAC	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"GC-binding factor 2"	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000308482.9:c.1685A>G	chr2.hg19:g.238681566A>G	ENSP00000310109:p.Glu562Gly	86.0	0.0		113.0	5.0	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000308482.9	hg19	CCDS46551.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.640973	0.87859	.	.	ENSG00000124831	ENST00000308482;ENST00000391999	T	0.60040	0.22	5.44	5.44	0.79542	.	.	.	.	.	T	0.74076	0.3669	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.77273	-0.2649	9	0.87932	D	0	.	14.6865	0.69052	1.0:0.0:0.0:0.0	.	316;562	B4DPC0;E9PGZ2	.;.	G	562;552	ENSP00000310109:E562G	ENSP00000310109:E562G	E	+	2	0	LRRFIP1	238346305	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.628000	0.90979	2.065000	0.61736	0.460000	0.39030	GAG	.	.		0.418	LRRFIP1-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000257169.3	NM_004735		G	238681566	A	G	238681566	3	3	103	1	0	0	0	0	1	0	0	0	9036	304	11	2	3383	2	LRRFIP1	2	238681566	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	404343	238681566	4517807	211	14834										
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241465814	241465814	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtgcaaagccactgcgcttCccctccaggatggcgcccat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:241465814delC	ENST00000272972.3	-	5	949	c.735delG	c.(733-735)gggfs	p.G245fs	ANKMY1_ENST00000403283.1_Intron|ANKMY1_ENST00000405002.1_Intron|ANKMY1_ENST00000401804.1_Frame_Shift_Del_p.G334fs|ANKMY1_ENST00000373320.4_Intron|ANKMY1_ENST00000361678.4_Intron|ANKMY1_ENST00000391987.1_Frame_Shift_Del_p.G245fs|ANKMY1_ENST00000462004.1_5'UTR|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000536462.1_Intron|ANKMY1_ENST00000373318.2_Intron|ANKMY1_ENST00000405523.3_Intron	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	245							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		CACTGCGCTTCCCCTCCAGGA	0.552																																					p.K246fs		Atlas-INDEL	.											.	ANKMY1	112	.	0			c.736delA						.						115	97	103					2																	241465814		2203	4300	6503	SO:0001589	frameshift_variant	51281	exon5			.	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.735delG	chr2.hg19:g.241465814delC	ENSP00000272972:p.Gly245fs	169.0	0.0		183.0	11.0	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Frame_Shift_Del	DEL	ENST00000272972.3	hg19	CCDS2536.1																																																																																			.	.		0.552	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		-	241465814	C	-	241465814	7	5	103	1	0	1	0	1	0	0	0	0	634	842	30	0	2142	0	ANKMY1	2	241465814	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2784248	241465814	1733559	212	14835										
FARP2	9855	hgsc.bcm.edu	37	chr2	242373660	242373660	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttgtgtggagtatcacaccTtttttagacttttggaccaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:242373660delT	ENST00000264042.3	+	10	1125	c.955delT	c.(955-957)tttfs	p.F320fs	FARP2_ENST00000373287.4_Frame_Shift_Del_p.F320fs|FARP2_ENST00000545004.1_Frame_Shift_Del_p.F320fs	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	320	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GTATCACACCTTTTTTAGACT	0.453																																					p.T318fs		Atlas-INDEL	.											.	FARP2	92	.	0			c.954delC						.						140	144	142					2																	242373660		2203	4300	6503	SO:0001589	frameshift_variant	9855	exon10			.	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.955delT	chr2.hg19:g.242373660delT	ENSP00000264042:p.Phe320fs	126.0	0.0		159.0	12.0	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Frame_Shift_Del	DEL	ENST00000264042.3	hg19	CCDS33424.1																																																																																			.	.		0.453	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			-	242373660	T	-	242373660	7	5	103	1	0	1	0	1	0	0	0	0	5685	1609	56	0	989	0	FARP2	2	242373660	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	907846	242373660	825713	213	14836										
RAD18	56852	hgsc.bcm.edu	37	chr3	8977726	8977726	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agttttgggcagcggcttccTtttgtgaacagaactgaaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:8977726delT	ENST00000264926.2	-	7	834	c.718delA	c.(718-720)aggfs	p.R240fs		NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase	240					DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		AGCGGCTTCCTTTTGTGAACA	0.338								Rad6 pathway																													p.R240fs		Atlas-INDEL	.											.	RAD18	52	.	0			c.719delG						.						79	79	79					3																	8977726		2203	4300	6503	SO:0001589	frameshift_variant	56852	exon7			.		CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950		"RING-type (C3HC4) zinc fingers"	18278	protein-coding gene	gene with protein product		605256	"RAD18 homolog (S. cerevisiae)"			10884424, 10908344	Standard	NM_020165		Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.718delA	chr3.hg19:g.8977726delT	ENSP00000264926:p.Arg240fs	131.0	0.0		175.0	11.0	NM_020165	Q58F55|Q9NRT6	Frame_Shift_Del	DEL	ENST00000264926.2	hg19	CCDS2571.1																																																																																			.	.		0.338	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207071.2	NM_020165		-	8977726	T	-	8977726	7	5	103	1	0	1	0	1	0	0	0	0	12995	1608	56	0	797	0	RAD18	3	8977726	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10		8977726	189044704	214	14837										
CIDEC	63924	hgsc.bcm.edu	37	chr3	9911858	9911858	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggacctcacctgttctgatGggggctgccatttctgcccc					rs145091411		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:9911858delG	ENST00000336832.2	-	4	495	c.356delC	c.(355-357)ccafs	p.P119fs	CIDEC_ENST00000423850.1_Frame_Shift_Del_p.P45fs|CIDEC_ENST00000455015.1_Frame_Shift_Del_p.P45fs|CIDEC_ENST00000443115.1_Intron|CIDEC_ENST00000383817.1_Intron|CIDEC_ENST00000430427.1_Frame_Shift_Del_p.P129fs	NM_001199552.1|NM_001199623.1|NM_022094.3	NP_001186481.1|NP_001186552.1|NP_071377.2	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	119					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|lipid particle organization (GO:0034389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)|nucleus (GO:0005634)		p.P119Q(1)		breast(2)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	8	Medulloblastoma(99;0.227)					CTGTTCTGATGGGGGCTGCCA	0.532																																					p.P132fs		Atlas-INDEL	.											.	CIDEC	22	.	1	Substitution - Missense(1)	lung(1)	c.396delA						.						64	67	66					3																	9911858		2203	4300	6503	SO:0001589	frameshift_variant	63924	exon4			.		CCDS2587.1, CCDS56239.1, CCDS74897.1	3p25	2004-07-26			ENSG00000187288	ENSG00000187288			24229	protein-coding gene	gene with protein product		612120				12429024	Standard	NM_001199623		Approved	CIDE-3, FLJ20871, Fsp27	uc021wsw.1	Q96AQ7	OTTHUMG00000128522	ENST00000336832.2:c.356delC	chr3.hg19:g.9911858delG	ENSP00000338642:p.Pro119fs	92.0	0.0		131.0	13.0	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Frame_Shift_Del	DEL	ENST00000336832.2	hg19	CCDS2587.1																																																																																			.	.		0.532	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094		-	9911858	G	-	9911858	7	5	103	1	0	1	0	1	0	0	0	0	3429	1348	47	0	372	0	CIDEC	3	9911858	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	934132	9911858	188110572	215	14838										
IL17RE	132014	hgsc.bcm.edu	37	chr3	9952818	9952818	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctcctcccacagtggtatgTtttggagaaggtggacctgc					rs370860056		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:9952818delT	ENST00000383814.3	+	10	1091	c.986delT	c.(985-987)gttfs	p.V329fs	IL17RE_ENST00000295980.3_Frame_Shift_Del_p.V329fs|IL17RE_ENST00000454190.2_Frame_Shift_Del_p.V329fs|IL17RE_ENST00000421412.1_Frame_Shift_Del_p.V362fs	NM_153480.1	NP_705613.1	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E	329					inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(11)|skin(1)	21				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		CAGTGGTATGTTTTGGAGAAG	0.552																																					p.V369fs		Atlas-INDEL	.											.	IL17RE	62	.	0			c.1105delG						.						153	150	151					3																	9952818		2203	4300	6503	SO:0001589	frameshift_variant	132014	exon11			.	AF458069	CCDS2589.1, CCDS54552.1	3p25.3	2008-02-05			ENSG00000163701	ENSG00000163701		"Interleukins and interleukin receptors"	18439	protein-coding gene	gene with protein product		614995					Standard	NM_153480		Approved	FLJ23658	uc003btu.3	Q8NFR9	OTTHUMG00000128649	ENST00000383814.3:c.986delT	chr3.hg19:g.9952818delT	ENSP00000373325:p.Val329fs	158.0	0.0		210.0	13.0	NM_153483	B2RB34|B2RNR1|B9EH65|Q6P532|Q8N8H7|Q8N8H8|Q8TEC2	Frame_Shift_Del	DEL	ENST00000383814.3	hg19	CCDS2589.1																																																																																			.	.		0.552	IL17RE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250529.1	NM_153480		-	9952818	T	-	9952818	7	5	103	1	0	1	0	1	0	0	0	0	7652	1725	60	0	1024	0	IL17RE	3	9952818	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	40960	9952818	188069612	216	14839										
UBE2E1	7324	hgsc.bcm.edu	37	chr3	23929187	23929187	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaatatcccttcaagcctccAaaggtaagaaatctccctgt					rs564357209	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:23929187delA	ENST00000306627.3	+	4	552	c.333delA	c.(331-333)ccafs	p.P111fs	UBE2E1_ENST00000475680.1_3'UTR|UBE2E1_ENST00000424381.1_Frame_Shift_Del_p.P78fs|UBE2E1_ENST00000346855.3_Frame_Shift_Del_p.P94fs|UBE2E1_ENST00000467766.1_Frame_Shift_Del_p.P78fs	NM_003341.4	NP_003332.1	P51965	UB2E1_HUMAN	ubiquitin-conjugating enzyme E2E 1	111					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cytokine-mediated signaling pathway (GO:0019221)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ISG15-protein conjugation (GO:0032020)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|large_intestine(4)	7						TCAAGCCTCCAAAGGTAAGAA	0.383																																					p.P111fs		Atlas-INDEL	.											.	UBE2E1	15	.	0			c.332delC						.						106	102	103					3																	23929187		2203	4300	6503	SO:0001589	frameshift_variant	7324	exon4			.	X92963	CCDS2638.1, CCDS2639.1, CCDS56244.1	3p24.2	2011-05-19	2011-05-19		ENSG00000170142	ENSG00000170142		"Ubiquitin-conjugating enzymes E2"	12477	protein-coding gene	gene with protein product		602916	"ubiquitin-conjugating enzyme E2E 1 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2E 1 (UBC4/5 homolog, yeast)"			8576257	Standard	NM_003341		Approved	UbcH6	uc003cch.3	P51965	OTTHUMG00000130483	ENST00000306627.3:c.333delA	chr3.hg19:g.23929187delA	ENSP00000303709:p.Pro111fs	139.0	0.0		179.0	11.0	NM_003341	B2RBX4|C9J8K2|K4DI90	Frame_Shift_Del	DEL	ENST00000306627.3	hg19	CCDS2638.1																																																																																			.	.		0.383	UBE2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252882.2	NM_003341		-	23929187	A	-	23929187	7	5	103	1	0	1	0	1	0	0	0	0	16867	117	5	0	343	0	UBE2E1	3	23929187	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	13976369	23929187	174093243	217	14840										
AZI2	64343	hgsc.bcm.edu	37	chr3	28373874	28373874	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcataccttgaaatgcttagTttttggagatctctgctctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:28373874delT	ENST00000479665.1	-	6	1164	c.633delA	c.(631-633)aaafs	p.K211fs	AZI2_ENST00000334100.6_Frame_Shift_Del_p.K211fs|AZI2_ENST00000457172.1_Frame_Shift_Del_p.K211fs|AZI2_ENST00000295748.3_5'UTR|AZI2_ENST00000420543.2_Frame_Shift_Del_p.K211fs	NM_022461.3	NP_071906.1	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2	211					dendritic cell differentiation (GO:0097028)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-alpha production (GO:0032607)|interferon-gamma production (GO:0032609)|interleukin-6 production (GO:0032635)|mitotic cell cycle (GO:0000278)|T cell activation (GO:0042110)|tumor necrosis factor production (GO:0032640)	cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15						AAATGCTTAGTTTTTGGAGAT	0.313																																					p.L212X		Atlas-INDEL	.											AZI2,NS,carcinoma,0,1	AZI2	33	.	0			c.634delC						.						199	185	190					3																	28373874		2203	4300	6503	SO:0001589	frameshift_variant	64343	exon6			.	AC093142	CCDS2647.1, CCDS46782.1, CCDS46783.1	3p23	2006-03-01			ENSG00000163512	ENSG00000163512			24002	protein-coding gene	gene with protein product		609916				10580148	Standard	NM_001134432		Approved	NAP1, FLJ21939, AZ2	uc003ceb.4	Q9H6S1	OTTHUMG00000130573	ENST00000479665.1:c.633delA	chr3.hg19:g.28373874delT	ENSP00000419371:p.Lys211fs	141.0	0.0		199.0	16.0	NM_001134432	A8K3M2|C9JB40|H7BXU6|Q86W99|Q9BQF1	Frame_Shift_Del	DEL	ENST00000479665.1	hg19	CCDS2647.1																																																																																			.	.		0.313	AZI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252998.2	NM_203326		-	28373874	T	-	28373874	7	5	103	1	0	1	0	1	0	0	0	0	1241	1722	60	0	646	0	AZI2	3	28373874	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	4444687	28373874	169648556	218	14841										
C3orf35	339883	hgsc.bcm.edu	37	chr3	37476531	37476531	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgtggggatgcctggaaaacAaaattaggagagccctgggt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:37476531delA	ENST00000328376.5	+	6	1402	c.423delA	c.(421-423)acafs	p.T141fs	C3orf35_ENST00000481400.1_3'UTR	NM_178339.2	NP_848029.2	Q8IVJ8	APRG1_HUMAN	chromosome 3 open reading frame 35	141						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	11						CCTGGAAAACAAAATTAGGAG	0.537																																					p.T141fs		Atlas-INDEL	.											.	C3orf35	21	.	0			c.422delC						.						47	51	50					3																	37476531		1915	4122	6037	SO:0001589	frameshift_variant	339883	exon6			.	AJ493599	CCDS43065.1, CCDS46792.1	3p22.3	2014-05-22			ENSG00000198590	ENSG00000198590			24082	protein-coding gene	gene with protein product	"AP20 region protein", "APRG1 tumor suppressor candidate"	611429				12543795	Standard	NM_178342		Approved	APRG1	uc003cha.4	Q8IVJ8	OTTHUMG00000155923	ENST00000328376.5:c.423delA	chr3.hg19:g.37476531delA	ENSP00000331625:p.Thr141fs	95.0	0.0		138.0	10.0	NM_178339	B7ZMA0|Q8IVJ5|Q8IVJ9	Frame_Shift_Del	DEL	ENST00000328376.5	hg19	CCDS43065.1																																																																																			.	.		0.537	C3orf35-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342344.2	NM_178338		-	37476531	A	-	37476531	7	5	103	1	0	1	0	1	0	0	0	0	2227	117	5	0	563	0	C3orf35	3	37476531	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	9102657	37476531	160545899	219	14842										
ACVR2B	93	hgsc.bcm.edu	37	chr3	38519754	38519754	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggatgtaccggcatcgcaagCccccctacggtcatgtggac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:38519754delC	ENST00000352511.4	+	4	965	c.493delC	c.(493-495)cccfs	p.P166fs		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	166					activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		GCATCGCAAGCCCCCCTACGG	0.617																																					p.K164fs		Atlas-INDEL	.											.	ACVR2B	88	.	0			c.492delG						.						68	67	67					3																	38519754		2203	4300	6503	SO:0001589	frameshift_variant	93	exon4			.	X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	ENST00000352511.4:c.493delC	chr3.hg19:g.38519754delC	ENSP00000340361:p.Pro166fs	100.0	0.0		146.0	12.0	NM_001106	Q4VAV0	Frame_Shift_Del	DEL	ENST00000352511.4	hg19	CCDS2679.1																																																																																			.	.		0.617	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106		-	38519754	C	-	38519754	7	5	103	1	0	1	0	1	0	0	0	0	224	739	26	0	507	0	ACVR2B	3	38519754	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1043223	38519754	159502676	220	14843										
TRAK1	22906	hgsc.bcm.edu	37	chr3	42166974	42166974	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcctgctggaggagcagctgCcccattataagttaagagcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:42166974delC	ENST00000327628.5	+	2	554	c.154delC	c.(154-156)cccfs	p.P52fs	TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	52	HAP1 N-terminal.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						GGAGCAGCTGCCCCATTATAA	0.488																																					p.L51fs	GBM(44;195 884 22595 31865 41850)	Atlas-INDEL	.											.	TRAK1	188	.	0			c.153delG						.						92	89	90					3																	42166974		1952	4161	6113	SO:0001589	frameshift_variant	22906	exon2			.		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.154delC	chr3.hg19:g.42166974delC	ENSP00000328998:p.Pro52fs	111.0	0.0		159.0	10.0	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Frame_Shift_Del	DEL	ENST00000327628.5	hg19	CCDS43072.1																																																																																			.	.		0.488	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		-	42166974	C	-	42166974	7	5	103	1	0	1	0	1	0	0	0	0	16464	739	26	0	160	0	TRAK1	3	42166974	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	3647220	42166974	155855456	221	14844										
SEC22C	9117	hgsc.bcm.edu	37	chr3	42599114	42599114	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aactcctcgaatgagattcaGggcagcacacatgatgttga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:42599114delG	ENST00000264454.3	-	5	744	c.601delC	c.(601-603)ctgfs	p.L201fs	SEC22C_ENST00000536332.1_Frame_Shift_Del_p.L131fs|SEC22C_ENST00000273156.7_Frame_Shift_Del_p.L201fs|SEC22C_ENST00000417572.1_Frame_Shift_Del_p.L201fs|SEC22C_ENST00000423701.2_Frame_Shift_Del_p.L201fs			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	201					ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		ATGAGATTCAGGGCAGCACAC	0.383																																					p.L201fs		Atlas-INDEL	.											.	SEC22C	27	.	0			c.602delT						.						106	109	108					3																	42599114		2203	4300	6503	SO:0001589	frameshift_variant	9117	exon5			.	AF039568	CCDS2699.1, CCDS2700.1, CCDS56246.1	3p24.3-p22.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000093183	ENSG00000093183			16828	protein-coding gene	gene with protein product		604028	"SEC22 vesicle trafficking protein-like 3 (S. cerevisiae)"	SEC22L3		9501016, 11001058	Standard	NM_004206		Approved	MGC13261, MGC5373	uc003clj.3	Q9BRL7	OTTHUMG00000131797	ENST00000264454.3:c.601delC	chr3.hg19:g.42599114delG	ENSP00000264454:p.Leu201fs	180.0	0.0		164.0	11.0	NM_004206	O95152|Q68CX3|Q6UW18	Frame_Shift_Del	DEL	ENST00000264454.3	hg19	CCDS2700.1																																																																																			.	.		0.383	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206		-	42599114	G	-	42599114	7	5	103	1	0	1	0	1	0	0	0	0	14005	991	35	0	368	0	SEC22C	3	42599114	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	432140	42599114	155423316	222	14845										
NKTR	4820	hgsc.bcm.edu	37	chr3	42679487	42679487	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagacttagatccagtgggaAaaaaaatagcgtttcacata	9	6	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:42679487A>G	ENST00000232978.8	+	13	2479	c.2291A>G	c.(2290-2292)aAa>aGa	p.K764R	RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	764	Arg/Ser-rich.				protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		TCCAGTGGGAAAAAAAATAGC	0.383																																					p.K764R		Atlas-SNP	.											NKTR,NS,carcinoma,0,1	NKTR	116	.	0			c.A2291G						.						86	86	86					3																	42679487		2203	4300	6503	SO:0001583	missense	4820	exon13			GTGGGAAAAAAAA		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"NK-tumor recognition protein", "natural-killer cells cyclophilin-related protein", "NK-TR protein"	161565	"natural killer-tumor recognition sequence"			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.2291A>G	chr3.hg19:g.42679487A>G	ENSP00000232978:p.Lys764Arg	88.0	0.0		133.0	0.0	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	hg19	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	A	4.945	0.175619	0.09391	.	.	ENSG00000114857	ENST00000232978	T	0.12147	2.71	5.64	1.93	0.25924	.	0.627824	0.17249	N	0.181233	T	0.11750	0.0286	L	0.49350	1.555	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.11329	0.006;0.002	T	0.22626	-1.0211	10	0.39692	T	0.17	-4.6749	5.8403	0.18629	0.5922:0.2633:0.1445:0.0	.	464;764	Q6M1B8;P30414	.;NKTR_HUMAN	R	764	ENSP00000232978:K764R	ENSP00000232978:K764R	K	+	2	0	NKTR	42654491	0.034000	0.19679	0.001000	0.08648	0.159000	0.22180	0.458000	0.21892	0.386000	0.24997	0.482000	0.46254	AAA	.	.		0.383	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385		G	42679487	A	G	42679487	3	3	103	1	0	0	0	0	1	0	0	0	10457	14	1	2	2337	2	NKTR	3	42679487	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	80373	42679487	155342943	223	14846										
SNRK	54861	hgsc.bcm.edu	37	chr3	43389468	43389468	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gacgggatagcagcgaggggCcccctggcagtgagggggat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:43389468delC	ENST00000296088.7	+	7	2021	c.1717delC	c.(1717-1719)cccfs	p.P574fs	SNRK_ENST00000437827.1_Frame_Shift_Del_p.P368fs|RP11-188P20.3_ENST00000607513.1_RNA|SNRK_ENST00000454177.1_Frame_Shift_Del_p.P574fs|SNRK_ENST00000429705.2_Frame_Shift_Del_p.P574fs|SNRK-AS1_ENST00000422681.1_RNA	NM_017719.4	NP_060189.3			SNF related kinase											breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(5)|prostate(1)|skin(2)|stomach(1)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)		CAGCGAGGGGCCCCCTGGCAG	0.627																																					p.G572fs		Atlas-INDEL	.											.	SNRK	118	.	0			c.1716delG						.						28	34	32					3																	43389468		1911	4105	6016	SO:0001589	frameshift_variant	54861	exon6			.	D43636	CCDS43075.1	3p22.1	2005-08-09			ENSG00000163788	ENSG00000163788			30598	protein-coding gene	gene with protein product		612760				8654423, 7788527	Standard	NM_017719		Approved	FLJ20224, HSNFRK, KIAA0096	uc003cmt.4	Q9NRH2	OTTHUMG00000156491	ENST00000296088.7:c.1717delC	chr3.hg19:g.43389468delC	ENSP00000296088:p.Pro574fs	129.0	0.0		153.0	10.0	NM_001100594		Frame_Shift_Del	DEL	ENST00000296088.7	hg19	CCDS43075.1																																																																																			.	.		0.627	SNRK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344325.1	NM_017719		-	43389468	C	-	43389468	7	5	103	1	0	1	0	1	0	0	0	0	14866	739	26	0	1735	0	SNRK	3	43389468	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	709981	43389468	154632962	224	14847										
ZNF197	10168	hgsc.bcm.edu	37	chr3	44683956	44683956	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgcttaccttctaaaccatcAgaggatccacactggggaga	9	11	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:44683956A>G	ENST00000396058.1	+	5	1501	c.1334A>G	c.(1333-1335)cAg>cGg	p.Q445R	ZNF197_ENST00000383745.2_Intron|ZNF197_ENST00000344387.4_Missense_Mutation_p.Q445R|ZNF197_ENST00000383744.4_Intron|RP11-944L7.4_ENST00000457331.1_RNA			O14709	ZN197_HUMAN	zinc finger protein 197	445					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		CTAAACCATCAGAGGATCCAC	0.428																																					p.Q445R		Atlas-SNP	.											.	ZNF197	81	.	0			c.A1334G						.						63	67	66					3																	44683956		2203	4300	6503	SO:0001583	missense	10168	exon6			ACCATCAGAGGAT	AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"Zinc fingers, C2H2-type", "-", "-", "-"	12988	protein-coding gene	gene with protein product			"zinc finger protein 166"	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.1334A>G	chr3.hg19:g.44683956A>G	ENSP00000379370:p.Gln445Arg	54.0	0.0		85.0	4.0	NM_006991	B2RAH8|Q86VG0	Missense_Mutation	SNP	ENST00000396058.1	hg19	CCDS2717.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.274445	0.40194	.	.	ENSG00000186448	ENST00000344387;ENST00000396058	T;T	0.17691	2.26;2.26	4.32	3.11	0.35812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33553	N	0.004789	T	0.12860	0.0312	N	0.02775	-0.495	0.09310	N	0.999994	D	0.62365	0.991	P	0.61592	0.891	T	0.05784	-1.0864	10	0.45353	T	0.12	.	5.899	0.18955	0.6627:0.1719:0.0:0.1654	.	445	O14709	ZN197_HUMAN	R	445	ENSP00000345809:Q445R;ENSP00000379370:Q445R	ENSP00000345809:Q445R	Q	+	2	0	ZNF197	44658960	0.001000	0.12720	1.000000	0.80357	0.988000	0.76386	1.083000	0.30815	0.757000	0.33036	0.374000	0.22700	CAG	.	.		0.428	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991		G	44683956	A	G	44683956	3	3	103	1	0	0	0	0	1	0	0	0	17774	188	7	2	1352	2	ZNF197	3	44683956	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1294488	44683956	153338474	225	14848										
LZTFL1	54585	hgsc.bcm.edu	37	chr3	45874602	45874602	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcaagttttggctttgtgacAtctaagatgggctgaaacaa	11	6	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:45874602A>G	ENST00000296135.6	-	5	570	c.396T>C	c.(394-396)gaT>gaC	p.D132D	LZTFL1_ENST00000536047.1_Silent_p.D115D|LZTFL1_ENST00000490463.1_5'UTR|LZTFL1_ENST00000539217.1_Silent_p.D128D	NM_001276378.1|NM_020347.2	NP_001263307.1|NP_065080.1	Q9NQ48	LZTL1_HUMAN	leucine zipper transcription factor-like 1	132					establishment of protein localization to organelle (GO:0072594)	BBSome (GO:0034464)|cytoplasm (GO:0005737)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	8				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		GCTTTGTGACATCTAAGATGG	0.353																																					p.D132D		Atlas-SNP	.											.	LZTFL1	37	.	0			c.T396C						.						119	117	118					3																	45874602		2203	4300	6503	SO:0001819	synonymous_variant	54585	exon5			TGTGACATCTAAG	AJ297351	CCDS2731.1, CCDS63608.1, CCDS63609.1	3p21.3	2014-01-28			ENSG00000163818	ENSG00000163818			6741	protein-coding gene	gene with protein product		606568				11352561, 22510444	Standard	NM_020347		Approved	BBS17	uc003cox.2	Q9NQ48	OTTHUMG00000133452	ENST00000296135.6:c.396T>C	chr3.hg19:g.45874602A>G		79.0	0.0		68.0	4.0	NM_020347	B3KSI9|B4E0K7|Q8TC61|Q9NQ56	Silent	SNP	ENST00000296135.6	hg19	CCDS2731.1	.	.	.	.	.	.	.	.	.	.	A	5.468	0.271472	0.10349	.	.	ENSG00000163818	ENST00000440576	.	.	.	5.77	-11.5	0.00074	.	.	.	.	.	T	0.54983	0.1892	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67273	-0.5712	4	.	.	.	-14.0683	12.74	0.57246	0.2111:0.4242:0.3646:0.0	.	.	.	.	R	90	.	.	C	-	1	0	LZTFL1	45849606	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-2.259000	0.01178	-2.136000	0.00810	-0.340000	0.08031	TGT	.	.		0.353	LZTFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257326.3	NM_020347		G	45874602	A	G	45874602	2	3	103	1	0	0	0	0	0	0	0	1	9145	214	8	2		2	LZTFL1	3	45874602	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1190646	45874602	152147828	226	14849										
LTF	4057	hgsc.bcm.edu	37	chr3	46479553	46479553	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgttgtcattgaacagaaggTttttggtttcagactggaat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:46479553delT	ENST00000231751.4	-	16	2271	c.1976delA	c.(1975-1977)aacfs	p.N659fs	LTF_ENST00000426532.2_Frame_Shift_Del_p.N615fs|LTF_ENST00000493056.1_5'UTR|LTF_ENST00000417439.1_Frame_Shift_Del_p.N657fs	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	659	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		GAACAGAAGGTTTTTGGTTTC	0.433																																					p.N659fs		Atlas-INDEL	.											.	LTF	98	.	0			c.1977delC						.						162	163	163					3																	46479553		2203	4300	6503	SO:0001589	frameshift_variant	4057	exon16			.		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.1976delA	chr3.hg19:g.46479553delT	ENSP00000231751:p.Asn659fs	136.0	0.0		193.0	12.0	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Frame_Shift_Del	DEL	ENST00000231751.4	hg19	CCDS33747.1																																																																																			.	.		0.433	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		-	46479553	T	-	46479553	7	5	103	1	0	1	0	1	0	0	0	0	9088	1725	60	0	164	0	LTF	3	46479553	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	604951	46479553	151542877	227	14850										
LRRC2	79442	hgsc.bcm.edu	37	chr3	46580564	46580564	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggaagatgtgagatttggTtttttggcagatccagaatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:46580564delT	ENST00000395905.3	-	4	853	c.461delA	c.(460-462)aacfs	p.N154fs	LRRC2_ENST00000296144.3_Frame_Shift_Del_p.N154fs	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	154										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		TGAGATTTGGTTTTTTGGCAG	0.438																																					p.N154fs		Atlas-INDEL	.											.	LRRC2	37	.	0			c.462delC						.						148	133	138					3																	46580564		2203	4300	6503	SO:0001589	frameshift_variant	79442	exon4			.	AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"leucine-rich repeat-containing 2"			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.461delA	chr3.hg19:g.46580564delT	ENSP00000379241:p.Asn154fs	118.0	0.0		162.0	10.0	NM_024512	B2RDQ7|Q96LT5	Frame_Shift_Del	DEL	ENST00000395905.3	hg19	CCDS2741.1																																																																																			.	.		0.438	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2			-	46580564	T	-	46580564	7	5	103	1	0	1	0	1	0	0	0	0	8985	1725	60	0	678	0	LRRC2	3	46580564	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	101011	46580564	151441866	228	14851										
ALS2CL	259173	hgsc.bcm.edu	37	chr3	46724741	46724741	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgggagggctccaggccagCccccagcacggggaagtcct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:46724741delC	ENST00000318962.4	-	10	1071	c.988delG	c.(988-990)gctfs	p.A330fs	ALS2CL_ENST00000415953.1_Frame_Shift_Del_p.A330fs	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	330					endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		TCCAGGCCAGCCCCCAGCACG	0.667																																					p.A330fs		Atlas-INDEL	.											.	ALS2CL	78	.	0			c.989delC						.						17	21	20					3																	46724741		2203	4300	6503	SO:0001589	frameshift_variant	259173	exon10			.	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.988delG	chr3.hg19:g.46724741delC	ENSP00000313670:p.Ala330fs	114.0	0.0		144.0	10.0	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Frame_Shift_Del	DEL	ENST00000318962.4	hg19	CCDS2743.1																																																																																			.	.		0.667	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129		-	46724741	C	-	46724741	7	5	103	1	0	1	0	1	0	0	0	0	551	739	26	0	1941	0	ALS2CL	3	46724741	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	144177	46724741	151297689	229	14852										
SETD2	29072	hgsc.bcm.edu	37	chr3	47143007	47143007	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctgaaggaaccagtttggtGgtaaaaaacccaaccctcag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:47143007delG	ENST00000409792.3	-	8	4998	c.4956delC	c.(4954-4956)accfs	p.T1653fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1653	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CCAGTTTGGTGGTAAAAAACC	0.398			"N, F, S, Mis"		clear cell renal carcinoma																																p.T1653fs		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.4957delA						.						159	159	159					3																	47143007		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon8			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4956delC	chr3.hg19:g.47143007delG	ENSP00000386759:p.Thr1653fs	126.0	0.0		160.0	10.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.		0.398	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47143007	G	-	47143007	7	5	103	1	0	1	0	1	0	0	0	0	14146	1335	47	0	2794	0	SETD2	3	47143007	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	418266	47143007	150879423	230	14853	65	2								
SETD2	29072	hgsc.bcm.edu	37	chr3	47143010	47143010	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaaggaaccagtttggtggtAaaaaacccaaccctcagttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:47143010delA	ENST00000409792.3	-	8	4995	c.4953delT	c.(4951-4953)tttfs	p.F1651fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1651	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GTTTGGTGGTAAAAAACCCAA	0.398			"N, F, S, Mis"		clear cell renal carcinoma																																p.T1652fs		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.4954delA						.						157	156	156					3																	47143010		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon8			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4953delT	chr3.hg19:g.47143010delA	ENSP00000386759:p.Phe1651fs	128.0	0.0		160.0	12.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.		0.398	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47143010	A	-	47143010	7	5	103	1	0	1	0	1	0	0	0	0	14146	359	13	0	2797	0	SETD2	3	47143010	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3	47143010	150879420	231	14854	65	2								
SETD2	29072	hgsc.bcm.edu	37	chr3	47164899	47164899	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttagttctagagcctctctcAgacctagagtgagatctgct	9	10	4	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:47164899A>G	ENST00000409792.3	-	3	1269	c.1227T>C	c.(1225-1227)tcT>tcC	p.S409S		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	409	Arg-rich.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AGCCTCTCTCAGACCTAGAGT	0.428			"N, F, S, Mis"		clear cell renal carcinoma																																p.S409S		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.T1227C						.						80	64	69					3																	47164899		692	1591	2283	SO:0001819	synonymous_variant	29072	exon3			TCTCTCAGACCTA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.1227T>C	chr3.hg19:g.47164899A>G		113.0	0.0		142.0	7.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.		0.428	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		G	47164899	A	G	47164899	2	3	103	1	0	0	0	0	0	0	0	1	14146	175	7	2		2	SETD2	3	47164899	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	21889	47164899	150857531	232	14855										
KIF9	64147	hgsc.bcm.edu	37	chr3	47282419	47282419	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttcattcaagatggatttgTtttctttgaaaattcggttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:47282419delT	ENST00000265529.3	-	18	2476	c.1796delA	c.(1795-1797)aacfs	p.N599fs	KIF9_ENST00000487440.1_5'UTR|KIF9_ENST00000352910.4_Frame_Shift_Del_p.N441fs|KIF9_ENST00000335044.2_Frame_Shift_Del_p.N599fs|KIF9_ENST00000452770.2_Frame_Shift_Del_p.N599fs|KIF9-AS1_ENST00000429315.3_RNA|KIF9_ENST00000444589.2_Frame_Shift_Del_p.N534fs			Q9HAQ2	KIF9_HUMAN	kinesin family member 9	599					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle disassembly (GO:1903008)|regulation of podosome assembly (GO:0071801)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|podosome (GO:0002102)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein dimerization activity (GO:0046983)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(15)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)	34		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		GATGGATTTGTTTTCTTTGAA	0.483																																					p.N599fs	Colon(44;962 1147 15977 24541)	Atlas-INDEL	.											.	KIF9	59	.	0			c.1797delC						.						146	135	138					3																	47282419		2203	4300	6503	SO:0001589	frameshift_variant	64147	exon17			.	AF311212	CCDS2751.1, CCDS2752.1	3p21.31	2008-03-03			ENSG00000088727	ENSG00000088727		"Kinesins"	16666	protein-coding gene	gene with protein product		607910				11483511	Standard	NM_022342		Approved	MGC104186	uc003cqx.3	Q9HAQ2	OTTHUMG00000133512	ENST00000265529.3:c.1796delA	chr3.hg19:g.47282419delT	ENSP00000265529:p.Asn599fs	122.0	0.0		146.0	10.0	NM_182902	Q86Z28|Q9H8A4	Frame_Shift_Del	DEL	ENST00000265529.3	hg19	CCDS2752.1																																																																																			.	.		0.483	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257475.2			-	47282419	T	-	47282419	7	5	103	1	0	1	0	1	0	0	0	0	8319	1725	60	0	596	0	KIF9	3	47282419	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	117520	47282419	150740011	233	14856										
DHX30	22907	hgsc.bcm.edu	37	chr3	47884619	47884619	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcatgcagttccatactgtGggcaccaagaccaagctgtc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:47884619delG	ENST00000445061.1	+	9	1220	c.813delG	c.(811-813)gtgfs	p.V271fs	DHX30_ENST00000457607.1_Frame_Shift_Del_p.V299fs|DHX30_ENST00000446256.2_Frame_Shift_Del_p.V232fs|DHX30_ENST00000348968.4_Frame_Shift_Del_p.V243fs	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	271						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		TCCATACTGTGGGCACCAAGA	0.532																																					p.V271fs		Atlas-INDEL	.											.	DHX30	101	.	0			c.812delT						.						167	153	158					3																	47884619		2203	4300	6503	SO:0001589	frameshift_variant	22907	exon9			.	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.813delG	chr3.hg19:g.47884619delG	ENSP00000405620:p.Val271fs	148.0	0.0		177.0	12.0	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Frame_Shift_Del	DEL	ENST00000445061.1	hg19	CCDS2759.1																																																																																			.	.		0.532	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		-	47884619	G	-	47884619	7	5	103	1	0	1	0	1	0	0	0	0	4506	1335	47	0	850	0	DHX30	3	47884619	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	602200	47884619	150137811	234	14857										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48610137	48610137	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccgtggggccaggttctccTttaggtccgacagggccagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:48610137delT	ENST00000328333.8	-	87	6974	c.6867delA	c.(6865-6867)aaafs	p.K2289fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.K2257fs	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2289	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CAGGTTCTCCTTTAGGTCCGA	0.632																																					p.G2290fs		Atlas-INDEL	.											.	COL7A1	320	.	0			c.6868delG						.						24	30	28					3																	48610137		2201	4297	6498	SO:0001589	frameshift_variant	1294	exon87			.	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6867delA	chr3.hg19:g.48610137delT	ENSP00000332371:p.Lys2289fs	136.0	0.0		192.0	12.0	NM_000094	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.632	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		-	48610137	T	-	48610137	7	5	103	1	0	1	0	1	0	0	0	0	3706	1606	56	0	2095	0	COL7A1	3	48610137	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	725518	48610137	149412293	235	14858										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48631052	48631052	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagcccctgtgcgagtgttgCcccccttgtagctaagctca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:48631052delC	ENST00000328333.8	-	3	451	c.344delG	c.(343-345)ggcfs	p.G115fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.G115fs	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	115	Nonhelical region (NC1).|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCGAGTGTTGCCCCCCTTGTA	0.617																																					p.G115fs		Atlas-INDEL	.											.	COL7A1	320	.	0			c.345delC						.						138	119	126					3																	48631052		2203	4300	6503	SO:0001589	frameshift_variant	1294	exon3			.	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.344delG	chr3.hg19:g.48631052delC	ENSP00000332371:p.Gly115fs	149.0	0.0		167.0	12.0	NM_000094	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.617	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		-	48631052	C	-	48631052	7	5	103	1	0	1	0	1	0	0	0	0	3706	739	26	0	8954	0	COL7A1	3	48631052	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	20915	48631052	149391378	236	14859										
USP19	10869	hgsc.bcm.edu	37	chr3	49153294	49153294	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcctcctcctggcctgtcaGggggtggggagcacctcctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:49153294delG	ENST00000398888.2	-	10	1564	c.1246delC	c.(1246-1248)ctgfs	p.L416fs	USP19_ENST00000488993.1_5'Flank|USP19_ENST00000434032.2_Frame_Shift_Del_p.L517fs|USP19_ENST00000398898.2_Frame_Shift_Del_p.L456fs|USP19_ENST00000417901.1_Frame_Shift_Del_p.L519fs|USP19_ENST00000398896.1_Frame_Shift_Del_p.L224fs|USP19_ENST00000398892.3_Frame_Shift_Del_p.L456fs|USP19_ENST00000453664.1_Frame_Shift_Del_p.L507fs	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	416					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGGCCTGTCAGGGGGTGGGGA	0.607																																					p.L519fs		Atlas-INDEL	.											.	USP19	158	.	0			c.1556delT						.						57	60	59					3																	49153294		1964	4142	6106	SO:0001589	frameshift_variant	10869	exon11			.	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"Zinc fingers, MYND-type", "Ubiquitin-specific peptidases"	12617	protein-coding gene	gene with protein product		614471	"ubiquitin specific protease 19"			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.1246delC	chr3.hg19:g.49153294delG	ENSP00000381863:p.Leu416fs	171.0	0.0		205.0	13.0	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Frame_Shift_Del	DEL	ENST00000398888.2	hg19	CCDS43090.1																																																																																			.	.		0.607	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		-	49153294	G	-	49153294	7	5	103	1	0	1	0	1	0	0	0	0	17065	991	35	0	2778	0	USP19	3	49153294	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	522242	49153294	148869136	237	14860										
BSN	8927	hgsc.bcm.edu	37	chr3	49692373	49692373	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgggccccggggaagacccaGggaggccaagtttgccagat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:49692373delG	ENST00000296452.4	+	5	5498	c.5384delG	c.(5383-5385)aggfs	p.R1795fs		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1795					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GGAAGACCCAGGGAGGCCAAG	0.602																																					p.R1795fs		Atlas-INDEL	.											.	BSN	272	.	0			c.5383delA						.						71	76	74					3																	49692373		2203	4300	6503	SO:0001589	frameshift_variant	8927	exon5			.	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.5384delG	chr3.hg19:g.49692373delG	ENSP00000296452:p.Arg1795fs	143.0	0.0		164.0	10.0	NM_003458	O43161|Q7LGH3	Frame_Shift_Del	DEL	ENST00000296452.4	hg19	CCDS2800.1																																																																																			.	.		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		-	49692373	G	-	49692373	7	5	103	1	0	1	0	1	0	0	0	0	1532	1000	35	0	5402	0	BSN	3	49692373	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	539079	49692373	148330057	238	14861										
RNF123	63891	hgsc.bcm.edu	37	chr3	49740924	49740924	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tactttgacctgcagcgcctGgggggcctcctctcgcacct					rs138522949	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:49740924delG	ENST00000327697.6	+	21	1959	c.1815delG	c.(1813-1815)ctgfs	p.L605fs	RNF123_ENST00000432042.1_Frame_Shift_Del_p.L459fs	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	605					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		TGCAGCGCCTGGGGGGCCTCC	0.632											OREG0015571	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L605fs		Atlas-INDEL	.											.	RNF123	100	.	0			c.1814delT						.						38	38	38					3																	49740924		2203	4300	6503	SO:0001589	frameshift_variant	63891	exon21			.	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1815delG	chr3.hg19:g.49740924delG	ENSP00000328287:p.Leu605fs	208.0	0.0	964	241.0	20.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Frame_Shift_Del	DEL	ENST00000327697.6	hg19	CCDS33758.1																																																																																			.	.		0.632	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		-	49740924	G	-	49740924	7	5	103	1	0	1	0	1	0	0	0	0	13448	1335	47	0	1893	0	RNF123	3	49740924	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	48551	49740924	148281506	239	14862										
GMPPB	29925	hgsc.bcm.edu	37	chr3	49759218	49759218	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgaggctctggcactgactcGccaatagacttgtggggcag	14	11	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:49759218G>A	ENST00000480687.1	-	10	1166	c.1050C>T	c.(1048-1050)ggC>ggT	p.G350G	AMIGO3_ENST00000535833.1_5'UTR|AMIGO3_ENST00000320431.7_5'Flank|GMPPB_ENST00000308375.6_Silent_p.G377G|GMPPB_ENST00000308388.6_Silent_p.G350G			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B	350					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCACTGACTCGCCAATAGACT	0.577																																					p.G377G		Atlas-SNP	.											.	GMPPB	14	.	0			c.C1131T						.						50	48	49					3																	49759218		2203	4300	6503	SO:0001819	synonymous_variant	29925	exon8			TGACTCGCCAATA	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.1050C>T	chr3.hg19:g.49759218G>A		32.0	0.0		36.0	4.0	NM_013334	A8K6N5|Q9H7U3	Silent	SNP	ENST00000480687.1	hg19	CCDS2803.1																																																																																			.	.		0.577	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334		A	49759218	G	A	49759218	2	1	103	1	0	0	0	0	0	0	0	1	6503	1074	38	1		1	GMPPB	3	49759218	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	18294	49759218	148263212	240	14863										
CACNA2D2	9254	hgsc.bcm.edu	37	chr3	50417242	50417242	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagcttcagggtcaggccgcTcacactgccactcctggaga	11	15	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:50417242T>C	ENST00000479441.1	-	10	906	c.907A>G	c.(907-909)Agc>Ggc	p.S303G	CACNA2D2_ENST00000424201.2_Missense_Mutation_p.S303G|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.S303G|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.S303G|CACNA2D2_ENST00000360963.3_Missense_Mutation_p.S234G|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.S303G|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.S303G|CACNA2D2_ENST00000423994.2_Missense_Mutation_p.S303G			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	303	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GTCAGGCCGCTCACACTGCCA	0.587																																					p.S303G		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.A907G						.						98	83	88					3																	50417242		2203	4300	6503	SO:0001583	missense	9254	exon10			GGCCGCTCACACT	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"Calcium channel subunits"	1400	protein-coding gene	gene with protein product	"gene 26"	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.907A>G	chr3.hg19:g.50417242T>C	ENSP00000418081:p.Ser303Gly	130.0	0.0		158.0	7.0	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	hg19	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.140503	0.77775	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	D;D;D;D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54	5.0	5.0	0.66597	von Willebrand factor, type A (3);	0.085016	0.85682	D	0.000000	D	0.87966	0.6311	M	0.65975	2.015	0.50171	D	0.999852	D;D	0.71674	0.998;0.997	D;D	0.72338	0.977;0.977	D	0.88920	0.3365	10	0.59425	D	0.04	-14.2627	14.7124	0.69244	0.0:0.0:0.0:1.0	.	303;303	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	G	303;303;303;234;303;303;303;303	ENSP00000407393:S303G;ENSP00000404631:S303G;ENSP00000266039:S303G;ENSP00000354228:S234G;ENSP00000390526:S303G;ENSP00000378519:S303G;ENSP00000390329:S303G;ENSP00000418081:S303G	ENSP00000266039:S303G	S	-	1	0	CACNA2D2	50392246	1.000000	0.71417	0.785000	0.31869	0.899000	0.52679	7.969000	0.87988	1.878000	0.54408	0.459000	0.35465	AGC	.	.		0.587	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		C	50417242	T	C	50417242	3	2	103	1	0	0	0	0	1	0	0	0	2551	1551	54	2	2671	2	CACNA2D2	3	50417242	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	658024	50417242	147605188	241	14864										
GNL3	26354	hgsc.bcm.edu	37	chr3	52727059	52727059	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctttcccaggctgatgctcgAcaggtaaaaggaccccttct	9	13	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:52727059A>G	ENST00000418458.1	+	10	1214	c.1041A>G	c.(1039-1041)cgA>cgG	p.R347R	SNORD19B_ENST00000459623.1_RNA|SNORD69_ENST00000391150.1_RNA|SNORD19_ENST00000410413.1_RNA|GLT8D1_ENST00000463827.1_5'Flank|GNL3_ENST00000394799.2_Silent_p.R335R	NM_014366.4|NM_206826.1	NP_055181.3|NP_996562.1	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)	347	Intermediate. {ECO:0000250}.				cell proliferation (GO:0008283)|GTP catabolic process (GO:0006184)|regulation of cell proliferation (GO:0042127)|ribosome biogenesis (GO:0042254)	extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|large_intestine(3)|lung(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		CTGATGCTCGACAGGTAAAAG	0.458																																					p.R347R		Atlas-SNP	.											.	GNL3	37	.	0			c.A1041G						.						63	61	62					3																	52727059		2203	4300	6503	SO:0001819	synonymous_variant	26354	exon10			TGCTCGACAGGTA	AK027514	CCDS2861.1, CCDS43100.1	3p21.1	2005-01-10			ENSG00000163938	ENSG00000163938			29931	protein-coding gene	gene with protein product		608011				11085516, 12464630	Standard	NM_014366		Approved	C77032, E2IG3, MGC800, NS, nucleostemin	uc003dfd.3	Q9BVP2	OTTHUMG00000158752	ENST00000418458.1:c.1041A>G	chr3.hg19:g.52727059A>G		64.0	0.0		98.0	4.0	NM_014366	B2RDC1|Q5PU80|Q96SV6|Q96SV7|Q9UJY0	Silent	SNP	ENST00000418458.1	hg19	CCDS2861.1																																																																																			.	.		0.458	GNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352032.1	NM_014366		G	52727059	A	G	52727059	2	3	103	1	0	0	0	0	0	0	0	1	6545	262	10	2		2	GNL3	3	52727059	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2309817	52727059	145295371	242	14865										
PDE12	201626	hgsc.bcm.edu	37	chr3	57545384	57545384	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcataccagttatattttgtGgggactttaatagtacacca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:57545384delG	ENST00000311180.8	+	3	1586	c.1483delG	c.(1483-1485)gggfs	p.G495fs	PDE12_ENST00000487257.1_3'UTR	NM_177966.5	NP_808881.3	Q6L8Q7	PDE12_HUMAN	phosphodiesterase 12	495					mRNA processing (GO:0006397)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(4)|lung(3)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.011)|Kidney(284;0.0127)		TATATTTTGTGGGGACTTTAA	0.433																																					p.C494fs	Colon(125;308 1634 19198 50622 50717)	Atlas-INDEL	.											.	PDE12	32	.	0			c.1482delT						.						101	100	101					3																	57545384		2203	4300	6503	SO:0001589	frameshift_variant	201626	exon3			.	AK074423	CCDS33772.1	3p14.3	2013-10-11			ENSG00000174840	ENSG00000174840			25386	protein-coding gene	gene with protein product	"2'-phosphodiesterase"					15231837	Standard	NM_177966		Approved	DKFZp667B1218, 2'-PDE	uc003diw.4	Q6L8Q7	OTTHUMG00000158599	ENST00000311180.8:c.1483delG	chr3.hg19:g.57545384delG	ENSP00000309142:p.Gly495fs	166.0	0.0		211.0	13.0	NM_177966	B4DTU8|Q8IYU3|Q8NDU2|Q8TE78	Frame_Shift_Del	DEL	ENST00000311180.8	hg19	CCDS33772.1																																																																																			.	.		0.433	PDE12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351440.2	NM_177966		-	57545384	G	-	57545384	7	5	103	1	0	1	0	1	0	0	0	0	11641	1348	47	0	1493	0	PDE12	3	57545384	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	4818325	57545384	140477046	243	14866										
FLNB	2317	hgsc.bcm.edu	37	chr3	58087998	58087998	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaggcgtccgtatccgggagAccacagatttcaaggttgac	12	10	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:58087998A>G	ENST00000295956.4	+	9	1579	c.1414A>G	c.(1414-1416)Acc>Gcc	p.T472A	FLNB_ENST00000493452.1_Missense_Mutation_p.T303A|FLNB_ENST00000358537.3_Missense_Mutation_p.T472A|FLNB_ENST00000357272.4_Missense_Mutation_p.T472A|FLNB_ENST00000348383.5_Missense_Mutation_p.T472A|FLNB_ENST00000490882.1_Missense_Mutation_p.T472A|FLNB_ENST00000429972.2_Missense_Mutation_p.T472A|FLNB_ENST00000419752.2_Missense_Mutation_p.T303A	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	472					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		TATCCGGGAGACCACAGATTT	0.517																																					p.T472A		Atlas-SNP	.											.	FLNB	430	.	0			c.A1414G						.						119	123	122					3																	58087998		2203	4300	6503	SO:0001583	missense	2317	exon9			CGGGAGACCACAG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.1414A>G	chr3.hg19:g.58087998A>G	ENSP00000295956:p.Thr472Ala	121.0	0.0		123.0	5.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.338940	0.24253	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84;-1.84;-1.84;-1.84;-1.84	5.43	5.43	0.79202	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.158239	0.56097	D	0.000025	T	0.79569	0.4468	N	0.20986	0.625	0.41804	D	0.989936	B;B;B;B;B;B	0.22604	0.059;0.025;0.072;0.001;0.04;0.04	B;B;B;B;B;B	0.32980	0.097;0.034;0.156;0.013;0.156;0.156	T	0.75059	-0.3451	10	0.30078	T	0.28	.	15.7645	0.78114	1.0:0.0:0.0:0.0	.	472;472;303;303;472;472	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	A	472;472;472;472;472;472;303;303	ENSP00000295956:T472A;ENSP00000420213:T472A;ENSP00000351339:T472A;ENSP00000415599:T472A;ENSP00000232447:T472A;ENSP00000349819:T472A;ENSP00000418510:T303A;ENSP00000414532:T303A	ENSP00000295956:T472A	T	+	1	0	FLNB	58063038	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	4.553000	0.60753	2.196000	0.70406	0.482000	0.46254	ACC	.	.		0.517	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		G	58087998	A	G	58087998	3	3	103	1	0	0	0	0	1	0	0	0	5942	275	10	2	1448	2	FLNB	3	58087998	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	542614	58087998	139934432	244	14867										
SUCLG2	8801	hgsc.bcm.edu	37	chr3	67660015	67660015	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catcttctggaggttaattgAactgcctacagaaattgaag	9	7	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:67660015A>G	ENST00000307227.5	-	2	117	c.90T>C	c.(88-90)gtT>gtC	p.V30V	SUCLG2_ENST00000492795.1_Silent_p.V30V|SUCLG2_ENST00000493112.1_Silent_p.V30V	NM_003848.3	NP_003839.2	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming, beta subunit	30					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP binding (GO:0005524)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	10		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	AGGTTAATTGAACTGCCTACA	0.408																																					p.V30V		Atlas-SNP	.											.	SUCLG2	95	.	0			c.T90C						.						84	73	77					3																	67660015		1852	4092	5944	SO:0001819	synonymous_variant	8801	exon2			TAATTGAACTGCC	AF058954	CCDS43104.1, CCDS54605.1	3p14.3	2004-05-17			ENSG00000172340	ENSG00000172340	6.2.1.4		11450	protein-coding gene	gene with protein product		603922				9765291	Standard	NM_001177599		Approved		uc003dna.4	Q96I99	OTTHUMG00000158740	ENST00000307227.5:c.90T>C	chr3.hg19:g.67660015A>G		66.0	0.0		76.0	4.0	NM_001177599	C9JVT2|O95195|Q6NUH7|Q86VX8|Q8WUQ1	Silent	SNP	ENST00000307227.5	hg19	CCDS43104.1																																																																																			.	.		0.408	SUCLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351993.1	NM_003848		G	67660015	A	G	67660015	2	3	103	1	0	0	0	0	0	0	0	1	15380	233	9	2		2	SUCLG2	3	67660015	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	9572017	67660015	130362415	245	14868										
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69239069	69239069	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcatcataggtggtggtgtcAgacaaagagctactctctga	11	8	4	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:69239069A>G	ENST00000398540.3	-	18	1832	c.1749T>C	c.(1747-1749)tcT>tcC	p.S583S	FRMD4B_ENST00000478263.1_Silent_p.S235S|FRMD4B_ENST00000542259.1_Silent_p.S529S	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	583					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TGGTGGTGTCAGACAAAGAGC	0.323																																					p.S583S		Atlas-SNP	.											.	FRMD4B	90	.	0			c.T1749C						.						90	90	90					3																	69239069		1813	4082	5895	SO:0001819	synonymous_variant	23150	exon18			GGTGTCAGACAAA	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.1749T>C	chr3.hg19:g.69239069A>G		65.0	0.0		99.0	4.0	NM_015123	Q8TAI3	Silent	SNP	ENST00000398540.3	hg19	CCDS46863.1																																																																																			.	.		0.323	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			G	69239069	A	G	69239069	2	3	103	1	0	0	0	0	0	0	0	1	6060	175	7	2		2	FRMD4B	3	69239069	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1579054	69239069	128783361	246	14869										
POU1F1	5449	hgsc.bcm.edu	37	chr3	87309133	87309133	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctctctgcctccggttgcAaaaccaaactcttactactt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:87309133delA	ENST00000350375.2	-	6	911	c.787delT	c.(787-789)tgcfs	p.C263fs	POU1F1_ENST00000560656.1_3'UTR|POU1F1_ENST00000344265.3_Frame_Shift_Del_p.C289fs	NM_000306.2	NP_000297.1	P28069	PIT1_HUMAN	POU class 1 homeobox 1	263					B cell differentiation (GO:0030183)|cell fate specification (GO:0001708)|determination of adult lifespan (GO:0008340)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear transport (GO:0051169)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin-like growth factor receptor signaling pathway (GO:0043567)|somatotropin secreting cell development (GO:0060133)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(2)	18	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)		CTCCGGTTGCAAAACCAAACT	0.383																																					p.C289fs		Atlas-INDEL	.											.	POU1F1	70	.	0			c.866delG						.						94	96	95					3																	87309133		2202	4300	6502	SO:0001589	frameshift_variant	5449	exon6			.	D10216	CCDS2919.1, CCDS46873.1	3p11.2	2011-06-20	2007-07-13		ENSG00000064835	ENSG00000064835		"Homeoboxes / POU class"	9210	protein-coding gene	gene with protein product	"growth hormone factor 1"	173110	"POU domain class 1, transcription factor 1"	PIT1		1956794	Standard	NM_001122757		Approved	GHF-1, POU1F1a	uc010hoj.1	P28069	OTTHUMG00000158992	ENST00000350375.2:c.787delT	chr3.hg19:g.87309133delA	ENSP00000263781:p.Cys263fs	194.0	0.0		231.0	14.0	NM_001122757	O75757|Q15132|Q15133|Q9UD34|Q9UEL3	Frame_Shift_Del	DEL	ENST00000350375.2	hg19	CCDS2919.1																																																																																			.	.		0.383	POU1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352827.1	NM_000306		-	87309133	A	-	87309133	7	5	103	1	0	1	0	1	0	0	0	0	12278	130	5	0	92	0	POU1F1	3	87309133	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	18070064	87309133	110713297	247	14870										
DCBLD2	131566	hgsc.bcm.edu	37	chr3	98544174	98544174	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catacctgaactcaggttccAaaaaattggatgcagtgtcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:98544174delA	ENST00000326840.6	-	4	970	c.608delT	c.(607-609)ttgfs	p.L203fs	DCBLD2_ENST00000469648.1_5'UTR|DCBLD2_ENST00000326857.9_Frame_Shift_Del_p.L203fs	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	203	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						CTCAGGTTCCAAAAAATTGGA	0.279																																					p.L203fs		Atlas-INDEL	.											.	DCBLD2	62	.	0			c.609delG						.						33	30	31					3																	98544174		1792	4061	5853	SO:0001589	frameshift_variant	131566	exon4			.		CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.608delT	chr3.hg19:g.98544174delA	ENSP00000321573:p.Leu203fs	100.0	0.0		134.0	10.0	NM_080927	B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Frame_Shift_Del	DEL	ENST00000326840.6	hg19	CCDS46878.1																																																																																			.	.		0.279	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324675.2	NM_080927		-	98544174	A	-	98544174	7	5	103	1	0	1	0	1	0	0	0	0	4283	131	5	0	1771	0	DCBLD2	3	98544174	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	11235041	98544174	99478256	248	14871										
TOMM70A	9868	hgsc.bcm.edu	37	chr3	100093979	100093979	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tacatgctgcctcttttgatGagagcatttgctcgaagcta	9	9	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:100093979G>A	ENST00000284320.5	-	7	1558	c.1110C>T	c.(1108-1110)ctC>ctT	p.L370L		NM_014820.4	NP_055635.3	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70 homolog A (S. cerevisiae)	370					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			endometrium(11)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	32						CTCTTTTGATGAGAGCATTTG	0.398																																					p.L370L		Atlas-SNP	.											.	TOMM70A	65	.	0			c.C1110T						.						129	126	127					3																	100093979		2203	4300	6503	SO:0001819	synonymous_variant	9868	exon7			TTTGATGAGAGCA	AB018262	CCDS33807.1	3q12.2	2013-01-10	2006-04-04		ENSG00000154174	ENSG00000154174		"Tetratricopeptide (TTC) repeat domain containing"	11985	protein-coding gene	gene with protein product		606081	"translocase of outer mitochondrial membrane 70 (yeast) homolog A", "translocase of outer mitochondrial membrane 70 homolog A (yeast)"			10582581	Standard	NM_014820		Approved	KIAA0719	uc003dtw.3	O94826	OTTHUMG00000159065	ENST00000284320.5:c.1110C>T	chr3.hg19:g.100093979G>A		58.0	0.0		54.0	19.0	NM_014820	D3DN48	Silent	SNP	ENST00000284320.5	hg19	CCDS33807.1																																																																																			.	.		0.398	TOMM70A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353141.2			A	100093979	G	A	100093979	2	1	103	1	0	0	0	0	0	0	0	1	16377	1277	45	3		3	TOMM70A	3	100093979	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	1549805	100093979	97928451	249	14872										
CBLB	868	hgsc.bcm.edu	37	chr3	105452913	105452913	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caaggctcaatcttgacatcTttgtcattctctgcacaaat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:105452913delT	ENST00000264122.4	-	9	1464	c.1143delA	c.(1141-1143)aaafs	p.K381fs	CBLB_ENST00000394027.3_Frame_Shift_Del_p.K403fs|CBLB_ENST00000403724.1_Frame_Shift_Del_p.K381fs|CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000405772.1_Frame_Shift_Del_p.K381fs	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	381					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						TCTTGACATCTTTGTCATTCT	0.413			Mis S		AML																																p.D382fs	GBM(93;588 1337 9788 29341 43499)	Atlas-INDEL	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.1144delG						.						108	101	103					3																	105452913		2203	4300	6503	SO:0001589	frameshift_variant	868	exon9			.	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"RING-type (C3HC4) zinc fingers"	1542	protein-coding gene	gene with protein product		604491	"Cas-Br-M (murine) ectropic retroviral transforming sequence b", "Cas-Br-M (murine) ecotropic retroviral transforming sequence b"			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.1143delA	chr3.hg19:g.105452913delT	ENSP00000264122:p.Lys381fs	216.0	0.0		250.0	15.0	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Frame_Shift_Del	DEL	ENST00000264122.4	hg19	CCDS2948.1																																																																																			.	.		0.413	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662		-	105452913	T	-	105452913	7	5	103	1	0	1	0	1	0	0	0	0	2703	1606	56	0	1849	0	CBLB	3	105452913	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5358934	105452913	92569517	250	14873										
TMPRSS7	344805	hgsc.bcm.edu	37	chr3	111780666	111780666	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctacatggatcatcagacaaTttttcgagtgcccagccctc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:111780666delT	ENST00000452346.2	+	11	1346	c.1343delT	c.(1342-1344)attfs	p.I448fs	TMPRSS7_ENST00000419127.1_Frame_Shift_Del_p.I322fs			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	448	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CATCAGACAATTTTTCGAGTG	0.488																																					p.I322fs		Atlas-INDEL	.											.	TMPRSS7	126	.	0			c.964delA						.						128	128	128					3																	111780666		1929	4133	6062	SO:0001589	frameshift_variant	344805	exon9			.	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.1343delT	chr3.hg19:g.111780666delT	ENSP00000398236:p.Ile448fs	139.0	0.0		172.0	12.0	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Frame_Shift_Del	DEL	ENST00000452346.2	hg19																																																																																				.	.		0.488	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		-	111780666	T	-	111780666	7	5	103	1	0	1	0	1	0	0	0	0	16267	1493	52	0	995	0	TMPRSS7	3	111780666	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	6327753	111780666	86241764	251	14874										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112335650	112335650	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatctttgattcgggactggAaagtatcgatcagatcaaac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:112335650delA	ENST00000206423.3	-	5	3181	c.2228delT	c.(2227-2229)ttcfs	p.F743fs	CCDC80_ENST00000439685.2_Frame_Shift_Del_p.F743fs	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	743					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						TCGGGACTGGAAAGTATCGAT	0.393																																					p.F743fs		Atlas-INDEL	.											.	CCDC80	100	.	0			c.2229delC						.						181	162	168					3																	112335650		2203	4300	6503	SO:0001589	frameshift_variant	151887	exon5			.	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.2228delT	chr3.hg19:g.112335650delA	ENSP00000206423:p.Phe743fs	119.0	0.0		158.0	11.0	NM_199512	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Frame_Shift_Del	DEL	ENST00000206423.3	hg19	CCDS2968.1																																																																																			.	.		0.393	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		-	112335650	A	-	112335650	7	5	103	1	0	1	0	1	0	0	0	0	2856	246	9	0	640	0	CCDC80	3	112335650	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	554984	112335650	85686780	252	14875										
GPR156	165829	hgsc.bcm.edu	37	chr3	119887020	119887020	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccgggcagccatgccaggaTcattctgaaagtcagagagg	13	11	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:119887020T>C	ENST00000464295.1	-	10	1749	c.1304A>G	c.(1303-1305)gAt>gGt	p.D435G	GPR156_ENST00000315843.3_Missense_Mutation_p.D435G|GPR156_ENST00000461057.1_Missense_Mutation_p.D431G			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	435						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		CATGCCAGGATCATTCTGAAA	0.627																																					p.D435G		Atlas-SNP	.											.	GPR156	85	.	0			c.A1304G						.						28	31	30					3																	119887020		2203	4300	6503	SO:0001583	missense	165829	exon9			CCAGGATCATTCT	AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"GPCR / Class C : Orphans"	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.1304A>G	chr3.hg19:g.119887020T>C	ENSP00000417261:p.Asp435Gly	119.0	0.0		146.0	6.0	NM_153002	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Missense_Mutation	SNP	ENST00000464295.1	hg19	CCDS2997.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.284076	0.40394	.	.	ENSG00000175697	ENST00000464295;ENST00000315843;ENST00000461057	T;T;T	0.26518	1.73;1.73;1.73	5.53	5.53	0.82687	.	0.510934	0.20398	N	0.093101	T	0.21674	0.0522	L	0.36672	1.1	0.29812	N	0.831588	P;P	0.47106	0.89;0.89	B;B	0.40066	0.318;0.318	T	0.08911	-1.0699	9	.	.	.	-3.0169	13.6518	0.62314	0.0:0.0:0.0:1.0	.	431;435	E9PFZ4;Q8NFN8	.;GP156_HUMAN	G	435;435;431	ENSP00000417261:D435G;ENSP00000324553:D435G;ENSP00000418758:D431G	.	D	-	2	0	GPR156	121369710	0.000000	0.05858	0.684000	0.30055	0.069000	0.16628	0.805000	0.27112	2.319000	0.78375	0.533000	0.62120	GAT	.	.		0.627	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		C	119887020	T	C	119887020	3	2	103	1	0	0	0	0	1	0	0	0	6669	1435	50	2	1144	2	GPR156	3	119887020	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	7551370	119887020	78135410	253	14876										
HGD	3081	hgsc.bcm.edu	37	chr3	120352071	120352071	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcagtcagcatcaggtccatGgggggtcattgtgctgtgta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:120352071delG	ENST00000283871.5	-	13	1570	c.1111delC	c.(1111-1113)catfs	p.H371fs		NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	371			H -> R (in AKU). {ECO:0000269|PubMed:10594001}.		cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	homogentisate 1,2-dioxygenase activity (GO:0004411)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25				GBM - Glioblastoma multiforme(114;0.158)		TCAGGTCCATGGGGGGTCATT	0.542																																					p.H371fs		Atlas-INDEL	.											.	HGD	65	.	0			c.1112delA						.						132	105	114					3																	120352071		2203	4296	6499	SO:0001589	frameshift_variant	3081	exon13			.		CCDS3000.1	3q	2010-04-27	2010-04-27		ENSG00000113924	ENSG00000113924	1.13.11.5		4892	protein-coding gene	gene with protein product	"homogentisate oxidase"	607474	"homogentisate 1,2-dioxygenase (homogentisate oxidase)"	AKU		8188241	Standard	NM_000187		Approved	HGO	uc003edw.3	Q93099	OTTHUMG00000159441	ENST00000283871.5:c.1111delC	chr3.hg19:g.120352071delG	ENSP00000283871:p.His371fs	119.0	0.0		182.0	15.0	NM_000187	A8K417|B2R8Z0	Frame_Shift_Del	DEL	ENST00000283871.5	hg19	CCDS3000.1																																																																																			.	.		0.542	HGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355410.1			-	120352071	G	-	120352071	7	5	103	1	0	1	0	1	0	0	0	0	7093	1348	47	0	234	0	HGD	3	120352071	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	465051	120352071	77670359	254	14877										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	121001118	121001118	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggcatgttccaaagacaacTtttgcatgcgtggcctgtct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:121001118delT	ENST00000273666.6	+	20	2387	c.2116delT	c.(2116-2118)tttfs	p.F706fs	STXBP5L_ENST00000492541.1_Frame_Shift_Del_p.F706fs|STXBP5L_ENST00000497029.1_Frame_Shift_Del_p.F706fs|STXBP5L_ENST00000472879.1_Intron|STXBP5L_ENST00000471454.1_Intron	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	706					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		CAAAGACAACTTTTGCATGCG	0.393																																					p.N705fs		Atlas-INDEL	.											.	STXBP5L	159	.	0			c.2115delC						.						101	90	93					3																	121001118		1956	4168	6124	SO:0001589	frameshift_variant	9515	exon20			.	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.2116delT	chr3.hg19:g.121001118delT	ENSP00000273666:p.Phe706fs	103.0	0.0		138.0	11.0	NM_014980	Q4G1B4|Q6PIC3	Frame_Shift_Del	DEL	ENST00000273666.6	hg19	CCDS43137.1																																																																																			.	.		0.393	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			-	121001118	T	-	121001118	7	5	103	1	0	1	0	1	0	0	0	0	15372	1609	56	0	2190	0	STXBP5L	3	121001118	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	649047	121001118	77021312	255	14878										
POLQ	10721	hgsc.bcm.edu	37	chr3	121192306	121192306	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtttttcatctctctatttGggggcaacttcaattccaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:121192306delG	ENST00000264233.5	-	21	6562	c.6434delC	c.(6433-6435)ccafs	p.P2145fs		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2145					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTCTCTATTTGGGGGCAACTT	0.383								DNA polymerases (catalytic subunits)																													p.P2145fs	Pancreas(152;907 1925 26081 31236 36904)	Atlas-INDEL	.											.	POLQ	273	.	0			c.6435delA						.						181	188	186					3																	121192306		2203	4300	6503	SO:0001589	frameshift_variant	10721	exon21			.	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.6434delC	chr3.hg19:g.121192306delG	ENSP00000264233:p.Pro2145fs	102.0	0.0		111.0	11.0	NM_199420	O95160|Q6VMB5	Frame_Shift_Del	DEL	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.383	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		-	121192306	G	-	121192306	7	5	103	1	0	1	0	1	0	0	0	0	12217	1348	47	0	1378	0	POLQ	3	121192306	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	191188	121192306	76830124	256	14879										
SLC15A2	6565	hgsc.bcm.edu	37	chr3	121613346	121613346	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaatcctttccagaaaaatgAgtccaaggaaactctttttt	6	8	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:121613346A>G	ENST00000489711.1	+	1	411	c.23A>G	c.(22-24)gAg>gGg	p.E8G	SLC15A2_ENST00000295605.2_Missense_Mutation_p.E8G	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	8					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CAGAAAAATGAGTCCAAGGAA	0.483																																					p.E8G		Atlas-SNP	.											.	SLC15A2	92	.	0			c.A23G						.						161	174	169					3																	121613346		2203	4300	6503	SO:0001583	missense	6565	exon1			AAAATGAGTCCAA	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.23A>G	chr3.hg19:g.121613346A>G	ENSP00000417085:p.Glu8Gly	64.0	0.0		85.0	4.0	NM_001145998	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	hg19	CCDS3007.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.38|15.38	2.815373|2.815373	0.50527|0.50527	.|.	.|.	ENSG00000163406|ENSG00000163406	ENST00000489711;ENST00000295605|ENST00000542599	T;T|.	0.03358|.	4.33;3.96|.	5.1|5.1	3.94|3.94	0.45596|0.45596	Major facilitator superfamily domain, general substrate transporter (1);|.	0.196743|.	0.35235|.	N|.	0.003355|.	T|T	0.44993|0.44993	0.1320|0.1320	L|L	0.31926|0.31926	0.97|0.97	0.36739|0.36739	D|D	0.882148|0.882148	P;P|.	0.39665|.	0.682;0.682|.	B;B|.	0.33890|.	0.172;0.172|.	T|T	0.46303|0.46303	-0.9201|-0.9201	10|5	0.87932|.	D|.	0|.	-5.1703|-5.1703	8.1849|8.1849	0.31333|0.31333	0.8228:0.0:0.0:0.1772|0.8228:0.0:0.0:0.1772	.|.	8;8|.	B4E2A7;Q16348|.	.;S15A2_HUMAN|.	G|G	8|2	ENSP00000417085:E8G;ENSP00000295605:E8G|.	ENSP00000295605:E8G|.	E|S	+|+	2|1	0|0	SLC15A2|SLC15A2	123096036|123096036	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.349000|2.349000	0.44054|0.44054	0.946000|0.946000	0.37632|0.37632	0.455000|0.455000	0.32223|0.32223	GAG|AGT	.	.		0.483	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		G	121613346	A	G	121613346	3	3	103	1	0	0	0	0	1	0	0	0	14414	304	11	2	25	2	SLC15A2	3	121613346	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	421040	121613346	76409084	257	14880										
PARP14	54625	hgsc.bcm.edu	37	chr3	122437236	122437236	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttttcaaagcaatctccccAaaaaaagaatcatttggttt					rs61732768	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:122437236delA	ENST00000474629.2	+	14	4504	c.4238delA	c.(4237-4239)caafs	p.Q1413fs	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CAATCTCCCCAAAAAAAGAAT	0.358																																					p.Q1413fs		Atlas-INDEL	.											.,2	PARP14	242	.	0			c.4237delC						.						86	84	84					3																	122437236		1897	4109	6006	SO:0001589	frameshift_variant	54625	exon14			.	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4238delA	chr3.hg19:g.122437236delA	ENSP00000418194:p.Gln1413fs	88.0	0.0		158.0	13.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Frame_Shift_Del	DEL	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.		0.358	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		-	122437236	A	-	122437236	7	5	103	1	0	1	0	1	0	0	0	0	11467	130	5	0	4292	0	PARP14	3	122437236	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	823890	122437236	75585194	258	14881										
CCDC14	64770	hgsc.bcm.edu	37	chr3	123675247	123675247	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaatagccagaatctgcattAaaacgtggtatttttcttaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:123675247delA	ENST00000488653.2	-	3	348	c.258delT	c.(256-258)tttfs	p.F86fs	CCDC14_ENST00000483247.1_Intron|CCDC14_ENST00000433542.2_Frame_Shift_Del_p.F86fs|CCDC14_ENST00000489746.1_5'UTR|CCDC14_ENST00000485727.1_5'UTR			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	86					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		AATCTGCATTAAAACGTGGTA	0.279																																					p.N87fs		Atlas-INDEL	.											.	CCDC14	97	.	0			c.259delA						.						64	61	62					3																	123675247		692	1585	2277	SO:0001589	frameshift_variant	64770	exon3			.	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.258delT	chr3.hg19:g.123675247delA	ENSP00000420180:p.Phe86fs	96.0	0.0		189.0	12.0	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Frame_Shift_Del	DEL	ENST00000488653.2	hg19																																																																																				.	.		0.279	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757		-	123675247	A	-	123675247	7	5	103	1	0	1	0	1	0	0	0	0	2775	359	13	0	2520	0	CCDC14	3	123675247	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1238011	123675247	74347183	259	14882										
KALRN	8997	hgsc.bcm.edu	37	chr3	124210257	124210257	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcaccccatcctcagacaatAaaacagtgctgaaagtaagt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:124210257delA	ENST00000240874.3	+	31	4826	c.4669delA	c.(4669-4671)aaafs	p.K1557fs	KALRN_ENST00000460856.1_Frame_Shift_Del_p.K1548fs|KALRN_ENST00000360013.3_Frame_Shift_Del_p.K1557fs	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1557	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						CTCAGACAATAAAACAGTGCT	0.542																																					p.N1556fs		Atlas-INDEL	.											.	KALRN	556	.	0			c.4668delT						.						77	69	72					3																	124210257		2203	4300	6503	SO:0001589	frameshift_variant	8997	exon31			.	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4669delA	chr3.hg19:g.124210257delA	ENSP00000240874:p.Lys1557fs	74.0	0.0		103.0	10.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Frame_Shift_Del	DEL	ENST00000240874.3	hg19	CCDS3027.1																																																																																			.	.		0.542	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		-	124210257	A	-	124210257	7	5	103	1	0	1	0	1	0	0	0	0	7984	363	13	0	4791	0	KALRN	3	124210257	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	535010	124210257	73812173	260	14883										
C3orf22	152065	hgsc.bcm.edu	37	chr3	126270923	126270923	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagtcgtttgtgacctcccaGggctgcaggggctcagggtc	16	11	1	1	rs34760151	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:126270923G>A	ENST00000318225.2	-	3	510	c.132C>T	c.(130-132)ccC>ccT	p.P44P		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	44										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		TGACCTCCCAGGGCTGCAGGG	0.602																																					p.P44P		Atlas-SNP	.											.	C3orf22	17	.	0			c.C132T						.						83	77	79					3																	126270923		2203	4300	6503	SO:0001819	synonymous_variant	152065	exon3			CTCCCAGGGCTGC		CCDS3040.1	3q21.3	2011-09-30			ENSG00000180697	ENSG00000180697			28534	protein-coding gene	gene with protein product						12477932	Standard	NM_152533		Approved	MGC34728	uc003ejb.3	Q8N5N4	OTTHUMG00000162731	ENST00000318225.2:c.132C>T	chr3.hg19:g.126270923G>A		93.0	0.0		113.0	31.0	NM_152533	B3KUS9	Silent	SNP	ENST00000318225.2	hg19	CCDS3040.1																																																																																			.	G|0.912;C|0.088		0.602	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533		A	126270923	G	A	126270923	2	1	103	1	0	0	0	0	0	0	0	1	2217	987	35	3		3	C3orf22	3	126270923	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	2060666	126270923	71751507	261	14884										
TXNRD3IT1	645840	hgsc.bcm.edu	37	chr3	126291337	126291337	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctccagtggcatctgctgcTcagctttcagctccggctgc	11	15	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:126291337T>C	ENST00000404489.2	-	1	142	c.50A>G	c.(49-51)gAg>gGg	p.E17G	TXNRD3NB_ENST00000383572.2_Missense_Mutation_p.E17G			Q6F5E7	TR3N_HUMAN	thioredoxin reductase 3 neighbor	17										endometrium(1)|large_intestine(2)|skin(2)	5						CATCTGCTGCTCAGCTTTCAG	0.602																																					p.E17G		Atlas-SNP	.											.	TXNRD3NB	13	.	0			c.A50G						.						42	39	40					3																	126291337		2203	4300	6503	SO:0001583	missense	645840	exon3			TGCTGCTCAGCTT	BC130546	CCDS33846.1	3q21.3	2011-04-13	2011-04-13	2011-04-13	ENSG00000206483	ENSG00000206483			33870	protein-coding gene	gene with protein product	"thioredoxin reductase 3 new transcript 1"		"thioredoxin reductase 3 intronic transcript 1"	TXNRD3IT1		15674732	Standard	NM_001039783		Approved	TR2IT1, TXNRD3NT1	uc003ejc.3	Q6F5E7	OTTHUMG00000162732	ENST00000404489.2:c.50A>G	chr3.hg19:g.126291337T>C	ENSP00000384071:p.Glu17Gly	80.0	0.0		121.0	5.0	NM_001039783		Missense_Mutation	SNP	ENST00000404489.2	hg19	CCDS33846.1	.	.	.	.	.	.	.	.	.	.	T	3.066	-0.192235	0.06259	.	.	ENSG00000206483	ENST00000383572;ENST00000404489	.	.	.	0.661	0.661	0.17874	.	.	.	.	.	T	0.32912	0.0845	N	0.08118	0	0.09310	N	1	D	0.69078	0.997	D	0.65140	0.932	T	0.19647	-1.0299	7	0.87932	D	0	.	.	.	.	.	17	Q6F5E7	TR3N_HUMAN	G	17	.	ENSP00000373066:E17G	E	-	2	0	TXNRD3NB	127774027	0.004000	0.15560	0.091000	0.20842	0.012000	0.07955	-0.033000	0.12246	0.536000	0.28733	0.383000	0.25322	GAG	.	.		0.602	TXNRD3NB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370233.2	NM_001039783		C	126291337	T	C	126291337	3	2	103	1	0	0	0	0	1	0	0	0	16824	1551	54	2	359	2	TXNRD3IT1	3	126291337	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	20414	126291337	71731093	262	14885										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126710277	126710277	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggacttcaaccagcccctGgggggcacagtcaccattga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:126710277delG	ENST00000393409.2	+	2	1245	c.1245delG	c.(1243-1245)ctgfs	p.L415fs	PLXNA1_ENST00000251772.4_Frame_Shift_Del_p.L392fs	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	415	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		ACCAGCCCCTGGGGGGCACAG	0.647																																					p.L415fs		Atlas-INDEL	.											.	PLXNA1	185	.	0			c.1244delT						.						47	42	44					3																	126710277		2203	4299	6502	SO:0001589	frameshift_variant	5361	exon2			.	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.1245delG	chr3.hg19:g.126710277delG	ENSP00000377061:p.Leu415fs	196.0	0.0		215.0	14.0	NM_032242		Frame_Shift_Del	DEL	ENST00000393409.2	hg19	CCDS33847.2																																																																																			.	.		0.647	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		-	126710277	G	-	126710277	7	5	103	1	0	1	0	1	0	0	0	0	12128	1335	47	0	1251	0	PLXNA1	3	126710277	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	418940	126710277	71312153	263	14886										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130284285	130284285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caccctgggcatagagggcgCcagcgacacccagttggaaa	13	13	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:130284285C>A	ENST00000358511.6	+	3	1140	c.1109C>A	c.(1108-1110)gCc>gAc	p.A370D	COL6A6_ENST00000453409.2_Missense_Mutation_p.A370D	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	370	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.		A -> T (in dbSNP:rs9830253).		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						ATAGAGGGCGCCAGCGACACC	0.547																																					p.A370D		Atlas-SNP	.											COL6A6_ENST00000358511,right_upper_lobe,carcinoma,0,2	COL6A6	497	.	0			c.C1109A						.						117	131	126					3																	130284285		2049	4205	6254	SO:0001583	missense	131873	exon3			AGGGCGCCAGCGA	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1109C>A	chr3.hg19:g.130284285C>A	ENSP00000351310:p.Ala370Asp	96.0	0.0		88.0	0.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.000937	0.54254	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.80738	-1.41;-1.41	5.01	5.01	0.66863	von Willebrand factor, type A (3);	0.103399	0.42821	D	0.000652	D	0.87517	0.6197	M	0.77406	2.37	0.45194	D	0.998205	D	0.63880	0.993	D	0.65874	0.939	D	0.87045	0.2143	10	0.44086	T	0.13	.	11.035	0.47795	0.0:0.9126:0.0:0.0874	.	370	A6NMZ7	CO6A6_HUMAN	D	370	ENSP00000351310:A370D;ENSP00000399236:A370D	ENSP00000351310:A370D	A	+	2	0	COL6A6	131766975	0.998000	0.40836	0.551000	0.28230	0.043000	0.13939	4.381000	0.59587	2.492000	0.84095	0.561000	0.74099	GCC	.	.		0.547	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130284285	C	A	130284285	3	1	103	1	0	0	0	0	1	0	0	0	3705	739	26	3	1119	3	COL6A6	3	130284285	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	3574008	130284285	67738145	264	14887										
PIK3R4	30849	hgsc.bcm.edu	37	chr3	130454770	130454770	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acttgttcagggaaaaaatgTccatttctataagccaaaag	7	7	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:130454770T>C	ENST00000356763.3	-	3	1367	c.810A>G	c.(808-810)ggA>ggG	p.G270G		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	270	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						GGAAAAAATGTCCATTTCTAT	0.323																																					p.G270G		Atlas-SNP	.											.	PIK3R4	145	.	0			c.A810G						.						120	129	126					3																	130454770		2203	4300	6503	SO:0001819	synonymous_variant	30849	exon3			AAAATGTCCATTT	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.810A>G	chr3.hg19:g.130454770T>C		58.0	0.0		64.0	4.0	NM_014602	Q2TBF4	Silent	SNP	ENST00000356763.3	hg19	CCDS3067.1																																																																																			.	.		0.323	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		C	130454770	T	C	130454770	2	2	103	1	0	0	0	0	0	0	0	1	11930	1654	58	2		2	PIK3R4	3	130454770	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	170485	130454770	67567660	265	14888										
NEK11	79858	hgsc.bcm.edu	37	chr3	130887702	130887702	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acatttaaaaggaatggaagAaaaggaggagcaacctgagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:130887702delA	ENST00000510769.1	+	9	1143	c.890delA	c.(889-891)gaafs	p.E297fs	NEK11_ENST00000510688.1_Frame_Shift_Del_p.E402fs|NEK11_ENST00000356918.4_Frame_Shift_Del_p.E402fs|NEK11_ENST00000511262.1_Frame_Shift_Del_p.E402fs|NEK11_ENST00000508196.1_Frame_Shift_Del_p.E402fs|NEK11_ENST00000383366.4_Frame_Shift_Del_p.E402fs|NEK11_ENST00000507910.1_Frame_Shift_Del_p.E402fs|NEK11_ENST00000412440.2_Intron|NEK11_ENST00000429253.2_Frame_Shift_Del_p.E402fs					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						GGAATGGAAGAAAAGGAGGAG	0.428																																					p.E402fs		Atlas-INDEL	.											.	NEK11	76	.	0			c.1204delG						.						68	65	66					3																	130887702		2203	4300	6503	SO:0001589	frameshift_variant	79858	exon13			.	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"NIMA (never in mitosis gene a)- related kinase 11"				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.890delA	chr3.hg19:g.130887702delA	ENSP00000421549:p.Glu297fs	101.0	0.0		160.0	10.0	NM_024800		Frame_Shift_Del	DEL	ENST00000510769.1	hg19																																																																																				.	.		0.428	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800		-	130887702	A	-	130887702	7	5	103	1	0	1	0	1	0	0	0	0	10332	246	9	0	1247	0	NEK11	3	130887702	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	432932	130887702	67134728	266	14889										
NPHP3	27031	hgsc.bcm.edu	37	chr3	132438560	132438560	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggaatttaccttgaattgccTtttaactttatctctgtcat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:132438560delT	ENST00000337331.5	-	2	594	c.508delA	c.(508-510)aggfs	p.R170fs	NPHP3-AS1_ENST00000504440.1_RNA|NPHP3_ENST00000343113.4_Frame_Shift_Del_p.R170fs|NPHP3_ENST00000326682.8_Frame_Shift_Del_p.R170fs|NPHP3_ENST00000476742.1_5'Flank|NPHP3-AS1_ENST00000489343.1_RNA	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	170					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TTGAATTGCCTTTTAACTTTA	0.303																																					p.R170fs		Atlas-INDEL	.											.	NPHP3	110	.	0			c.509delG						.						156	152	154					3																	132438560		2202	4300	6502	SO:0001589	frameshift_variant	27031	exon2			.	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"Tetratricopeptide (TTC) repeat domain containing"	7907	protein-coding gene	gene with protein product	"nephrocystin-3", "Meckel syndrome, type 7", "cilia and flagella associated protein 31"	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.508delA	chr3.hg19:g.132438560delT	ENSP00000338766:p.Arg170fs	122.0	0.0		152.0	11.0	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Frame_Shift_Del	DEL	ENST00000337331.5	hg19	CCDS3078.1																																																																																			.	.		0.303	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		-	132438560	T	-	132438560	7	5	103	1	0	1	0	1	0	0	0	0	10589	1608	56	0	3588	0	NPHP3	3	132438560	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1550858	132438560	65583870	267	14890										
NPHP3	27031	hgsc.bcm.edu	37	chr3	132440946	132440946	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgtactcggccgccgcgtacTccagctctggcaccgacgag	12	17	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:132440946T>C	ENST00000337331.5	-	1	340	c.254A>G	c.(253-255)gAg>gGg	p.E85G	NPHP3_ENST00000383282.2_Missense_Mutation_p.E85G|NPHP3-AS1_ENST00000504440.1_RNA|NPHP3_ENST00000343113.4_Missense_Mutation_p.E85G|NPHP3_ENST00000326682.8_Missense_Mutation_p.E85G|NPHP3-AS1_ENST00000489343.1_RNA	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	85					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CGCCGCGTACTCCAGCTCTGG	0.706																																					p.E85G		Atlas-SNP	.											.	NPHP3	110	.	0			c.A254G						.						16	19	18					3																	132440946		2110	4112	6222	SO:0001583	missense	27031	exon1			GCGTACTCCAGCT	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"Tetratricopeptide (TTC) repeat domain containing"	7907	protein-coding gene	gene with protein product	"nephrocystin-3", "Meckel syndrome, type 7", "cilia and flagella associated protein 31"	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.254A>G	chr3.hg19:g.132440946T>C	ENSP00000338766:p.Glu85Gly	55.0	0.0		61.0	6.0	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	hg19	CCDS3078.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.494485	0.64186	.	.	ENSG00000113971	ENST00000326682;ENST00000337331;ENST00000343113;ENST00000383282	D;D;D;D	0.93426	-3.22;-3.13;-1.97;-1.99	3.6	3.6	0.41247	.	0.000000	0.64402	D	0.000001	D	0.93106	0.7805	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.93537	0.6874	10	0.62326	D	0.03	-18.1579	12.6567	0.56791	0.0:0.0:0.0:1.0	.	85	Q7Z494	NPHP3_HUMAN	G	85	ENSP00000319909:E85G;ENSP00000338766:E85G;ENSP00000344802:E85G;ENSP00000372769:E85G	ENSP00000319909:E85G	E	-	2	0	NPHP3	133923636	1.000000	0.71417	1.000000	0.80357	0.003000	0.03518	7.508000	0.81686	1.615000	0.50252	0.454000	0.30748	GAG	.	.		0.706	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		C	132440946	T	C	132440946	3	2	103	1	0	0	0	0	1	0	0	0	10589	1551	54	2	3846	2	NPHP3	3	132440946	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2386	132440946	65581484	268	14891										
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135745883	135745883	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctaagcagaattgaaactgcTttcatggatattgaagaaca	8	6	1	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:135745883T>C	ENST00000264977.3	+	3	2822	c.2205T>C	c.(2203-2205)gcT>gcC	p.A735A	PPP2R3A_ENST00000490467.1_5'UTR|PPP2R3A_ENST00000334546.2_Silent_p.A114A|PPP2R3A_ENST00000492624.2_5'UTR	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	735					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TTGAAACTGCTTTCATGGATA	0.368																																					p.A735A		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T2205C						.						48	46	46					3																	135745883		2203	4300	6503	SO:0001819	synonymous_variant	5523	exon3			AACTGCTTTCATG	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.2205T>C	chr3.hg19:g.135745883T>C		58.0	0.0		79.0	4.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	hg19	CCDS3087.1																																																																																			.	.		0.368	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		C	135745883	T	C	135745883	2	2	103	1	0	0	0	0	0	0	0	1	12400	1596	56	2		2	PPP2R3A	3	135745883	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3304937	135745883	62276547	269	14892										
PCCB	5096	hgsc.bcm.edu	37	chr3	135979364	135979364	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctgtcaggagcacatgcccAaaagatctgcaaagtaagtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:135979364delA	ENST00000251654.4	+	4	486	c.416delA	c.(415-417)caafs	p.Q139fs	PCCB_ENST00000474833.1_Intron|PCCB_ENST00000490504.1_Intron|PCCB_ENST00000478469.1_Frame_Shift_Del_p.Q139fs|PCCB_ENST00000469217.1_Frame_Shift_Del_p.Q159fs|PCCB_ENST00000468777.1_Frame_Shift_Del_p.Q170fs|PCCB_ENST00000471595.1_Frame_Shift_Del_p.Q139fs|PCCB_ENST00000466072.1_Frame_Shift_Del_p.Q139fs|PCCB_ENST00000483687.1_Intron|PCCB_ENST00000462637.1_Frame_Shift_Del_p.Q116fs|PCCB_ENST00000482086.1_Intron	NM_000532.4	NP_000523.2	P05166	PCCB_HUMAN	propionyl CoA carboxylase, beta polypeptide	139	Carboxyltransferase.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	25					Biotin(DB00121)|L-Valine(DB00161)	GCACATGCCCAAAAGATCTGC	0.373																																					p.Q159fs		Atlas-INDEL	.											.	PCCB	52	.	0			c.475delC						.						130	118	122					3																	135979364		2203	4300	6503	SO:0001589	frameshift_variant	5096	exon5			.		CCDS3089.1, CCDS54643.1	3q21-q22	2010-07-01	2010-04-30		ENSG00000114054	ENSG00000114054	6.4.1.3		8654	protein-coding gene	gene with protein product		232050	"propionyl Coenzyme A carboxylase, beta polypeptide"			2895916	Standard	NM_000532		Approved		uc003eqy.2	P05166	OTTHUMG00000159792	ENST00000251654.4:c.416delA	chr3.hg19:g.135979364delA	ENSP00000251654:p.Gln139fs	122.0	0.0		152.0	10.0	NM_001178014	B7Z2Z4|Q16813|Q96CX0	Frame_Shift_Del	DEL	ENST00000251654.4	hg19	CCDS3089.1																																																																																			.	.		0.373	PCCB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357335.1			-	135979364	A	-	135979364	7	5	103	1	0	1	0	1	0	0	0	0	11514	130	5	0	494	0	PCCB	3	135979364	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	233481	135979364	62043066	270	14893										
PIK3CB	5291	hgsc.bcm.edu	37	chr3	138461437	138461437	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaacagctacgatgagctttCccccataaagtttatcttct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:138461437delC	ENST00000477593.1	-	4	657	c.584delG	c.(583-585)ggafs	p.G195fs	PIK3CB_ENST00000289153.2_Frame_Shift_Del_p.G195fs			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	195	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	GATGAGCTTTCCCCCATAAAG	0.353																																					p.G195fs		Atlas-INDEL	.											.	PIK3CB	103	.	0			c.585delA						.						99	94	96					3																	138461437		2203	4300	6503	SO:0001589	frameshift_variant	5291	exon3			.		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.584delG	chr3.hg19:g.138461437delC	ENSP00000418143:p.Gly195fs	134.0	0.0		146.0	10.0	NM_006219	D3DNF0|Q24JU2	Frame_Shift_Del	DEL	ENST00000477593.1	hg19	CCDS3104.1																																																																																			.	.		0.353	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			-	138461437	C	-	138461437	7	5	103	1	0	1	0	1	0	0	0	0	11923	855	30	0	2706	0	PIK3CB	3	138461437	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2482073	138461437	59560993	271	14894										
COPB2	9276	hgsc.bcm.edu	37	chr3	139096994	139096994	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacacttgtgagcaagaccaTtttttatcccagtcccagag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:139096994delT	ENST00000333188.5	-	5	574	c.393delA	c.(391-393)aaafs	p.K131fs	COPB2_ENST00000510491.1_5'Flank|COPB2_ENST00000507777.1_Frame_Shift_Del_p.K102fs	NM_004766.2	NP_004757.1	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta prime)	131					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	24						AGCAAGACCATTTTTTATCCC	0.383																																					p.W132fs		Atlas-INDEL	.											.	COPB2	80	.	0			c.394delT						.						239	224	229					3																	139096994		2203	4300	6503	SO:0001589	frameshift_variant	9276	exon5			.	BC000326	CCDS3108.1	3q23	2013-01-10			ENSG00000184432	ENSG00000184432		"WD repeat domain containing"	2232	protein-coding gene	gene with protein product		606990				9858824	Standard	NM_004766		Approved	beta'-COP, betaprime-COP	uc003etf.4	P35606	OTTHUMG00000159959	ENST00000333188.5:c.393delA	chr3.hg19:g.139096994delT	ENSP00000329419:p.Lys131fs	111.0	0.0		128.0	10.0	NM_004766	B4DZI8	Frame_Shift_Del	DEL	ENST00000333188.5	hg19	CCDS3108.1																																																																																			.	.		0.383	COPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358495.2	NM_004766		-	139096994	T	-	139096994	7	5	103	1	0	1	0	1	0	0	0	0	3731	1490	52	0	2399	0	COPB2	3	139096994	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	635557	139096994	58925436	272	14895										
GRK7	131890	hgsc.bcm.edu	37	chr3	141497152	141497152	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggacatgggggccctggacaAcctgatcgccaacaccgcct	12	15	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:141497152A>G	ENST00000264952.2	+	1	163	c.26A>G	c.(25-27)aAc>aGc	p.N9S		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	9					protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						GCCCTGGACAACCTGATCGCC	0.692																																					p.N9S		Atlas-SNP	.											.	GRK7	65	.	0			c.A26G						.						47	57	54					3																	141497152		2199	4300	6499	SO:0001583	missense	131890	exon1			TGGACAACCTGAT		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.26A>G	chr3.hg19:g.141497152A>G	ENSP00000264952:p.Asn9Ser	87.0	0.0		121.0	5.0	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	hg19	CCDS3120.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582379	0.46006	.	.	ENSG00000114124	ENST00000264952	T	0.61742	0.08	4.5	3.3	0.37823	.	0.099517	0.64402	D	0.000002	T	0.55940	0.1952	M	0.79123	2.44	0.40643	D	0.981967	P	0.43750	0.816	B	0.39185	0.293	T	0.59511	-0.7441	10	0.56958	D	0.05	-8.2697	10.1305	0.42676	0.85:0.0:0.0:0.15	.	9	Q8WTQ7	GRK7_HUMAN	S	9	ENSP00000264952:N9S	ENSP00000264952:N9S	N	+	2	0	GRK7	142979842	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.949000	0.56668	0.542000	0.28846	0.533000	0.62120	AAC	.	.		0.692	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209		G	141497152	A	G	141497152	3	3	103	1	0	0	0	0	1	0	0	0	6803	43	2	2	28	2	GRK7	3	141497152	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2400158	141497152	56525278	273	14896										
GK5	256356	hgsc.bcm.edu	37	chr3	141917719	141917719	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaagtgaacaaactggctgtAaaaagtcgtttacttctagt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:141917719delA	ENST00000392993.2	-	5	619	c.468delT	c.(466-468)tttfs	p.F156fs	GK5_ENST00000544571.1_Frame_Shift_Del_p.F156fs	NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	156					glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						AACTGGCTGTAAAAAGTCGTT	0.348																																					p.T157fs		Atlas-INDEL	.											.	GK5	45	.	0			c.469delA						.						81	80	81					3																	141917719		2203	4300	6503	SO:0001589	frameshift_variant	256356	exon5			.	BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066		"Glycerol kinases"	28635	protein-coding gene	gene with protein product						12477932	Standard	NM_001039547		Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.468delT	chr3.hg19:g.141917719delA	ENSP00000418001:p.Phe156fs	158.0	0.0		192.0	12.0	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Frame_Shift_Del	DEL	ENST00000392993.2	hg19	CCDS33871.1																																																																																			.	.		0.348	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547		-	141917719	A	-	141917719	7	5	103	1	0	1	0	1	0	0	0	0	6430	359	13	0	1169	0	GK5	3	141917719	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	420567	141917719	56104711	274	14897										
ATR	545	hgsc.bcm.edu	37	chr3	142178110	142178110	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttctcagaaaccactcatgAaaaataggaggatgcctggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:142178110delA	ENST00000350721.4	-	43	7429	c.7308delT	c.(7306-7308)tttfs	p.F2436fs	ATR_ENST00000383101.3_Frame_Shift_Del_p.F2372fs	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2436	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						ACCACTCATGAAAAATAGGAG	0.363								Other conserved DNA damage response genes																													p.H2437fs		Atlas-INDEL	.											.	ATR	285	.	0			c.7309delC						.						68	69	69					3																	142178110		2203	4300	6503	SO:0001589	frameshift_variant	545	exon43			.	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7308delT	chr3.hg19:g.142178110delA	ENSP00000343741:p.Phe2436fs	112.0	0.0		139.0	10.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Frame_Shift_Del	DEL	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.363	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		-	142178110	A	-	142178110	7	5	103	1	0	1	0	1	0	0	0	0	1204	243	9	0	646	0	ATR	3	142178110	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	260391	142178110	55844320	275	14898										
ATR	545	hgsc.bcm.edu	37	chr3	142281476	142281476	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctggtagtcctccaagctgAaaaagttctgttaaaaagct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:142281476delA	ENST00000350721.4	-	4	889	c.768delT	c.(766-768)tttfs	p.F256fs	ATR_ENST00000383101.3_Frame_Shift_Del_p.F256fs	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	256					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CTCCAAGCTGAAAAAGTTCTG	0.373								Other conserved DNA damage response genes																													p.Q257fs		Atlas-INDEL	.											.	ATR	285	.	0			c.769delC						.						61	63	62					3																	142281476		2203	4300	6503	SO:0001589	frameshift_variant	545	exon4			.	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.768delT	chr3.hg19:g.142281476delA	ENSP00000343741:p.Phe256fs	128.0	0.0		170.0	11.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Frame_Shift_Del	DEL	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.373	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		-	142281476	A	-	142281476	7	5	103	1	0	1	0	1	0	0	0	0	1204	243	9	0	7342	0	ATR	3	142281476	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	103366	142281476	55740954	276	14899										
PLOD2	5352	hgsc.bcm.edu	37	chr3	145794581	145794581	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atacataccacaggattttcAaaaatctgccagaggtcatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:145794581delA	ENST00000360060.3	-	14	1779	c.1602delT	c.(1600-1602)tttfs	p.F534fs	PLOD2_ENST00000494950.1_Frame_Shift_Del_p.F500fs|PLOD2_ENST00000282903.5_Frame_Shift_Del_p.F555fs|PLOD2_ENST00000461497.1_Frame_Shift_Del_p.F215fs|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	534					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	CAGGATTTTCAAAAATCTGCC	0.294																																					p.E556fs		Atlas-INDEL	.											.	PLOD2	81	.	0			c.1666delG						.						78	86	83					3																	145794581		2202	4285	6487	SO:0001589	frameshift_variant	5352	exon15			.	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"lysyl hydroxlase 2"	601865	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.1602delT	chr3.hg19:g.145794581delA	ENSP00000353170:p.Phe534fs	126.0	0.0		161.0	12.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Frame_Shift_Del	DEL	ENST00000360060.3	hg19	CCDS3131.1																																																																																			.	.		0.294	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		-	145794581	A	-	145794581	7	5	103	1	0	1	0	1	0	0	0	0	12111	127	5	0	635	0	PLOD2	3	145794581	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3513105	145794581	52227849	277	14900										
HLTF	6596	hgsc.bcm.edu	37	chr3	148778638	148778638	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctatgtactggacagcagTttttcttctaaaattaagta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:148778638delT	ENST00000310053.5	-	11	1361	c.1168delA	c.(1168-1170)actfs	p.T390fs	HLTF_ENST00000392912.2_Frame_Shift_Del_p.T390fs|HLTF_ENST00000465259.1_Frame_Shift_Del_p.T390fs|HLTF_ENST00000494055.1_Frame_Shift_Del_p.T390fs	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	390					chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TGGACAGCAGTTTTTCTTCTA	0.289																																					p.T390fs		Atlas-INDEL	.											.	HLTF	87	.	0			c.1169delC						.						54	52	53					3																	148778638		2202	4292	6494	SO:0001589	frameshift_variant	6596	exon11			.	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"RING-type (C3HC4) zinc fingers"	11099	protein-coding gene	gene with protein product		603257	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.1168delA	chr3.hg19:g.148778638delT	ENSP00000308944:p.Thr390fs	120.0	0.0		143.0	10.0	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Frame_Shift_Del	DEL	ENST00000310053.5	hg19	CCDS33875.1																																																																																			.	.		0.289	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1			-	148778638	T	-	148778638	7	5	103	1	0	1	0	1	0	0	0	0	7224	1725	60	0	1921	0	HLTF	3	148778638	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2984057	148778638	49243792	278	14901										
CP	1356	hgsc.bcm.edu	37	chr3	148927955	148927955	+	Splice_Site	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caataaggagaagatgtaccTtttttacagattattaaagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:148927955delT	ENST00000264613.6	-	3	868	c.606delA	c.(604-606)aaa>aa	p.K202fs		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	202	F5/8 type A 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	AAGATGTACCTTTTTTACAGA	0.398																																					p.D203fs		Atlas-INDEL	.											.	CP	112	.	0			c.607delG						.						132	119	124					3																	148927955		2203	4300	6503	SO:0001630	splice_region_variant	1356	exon3			.	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.607+1A>-	chr3.hg19:g.148927955delT		112.0	0.0		139.0	10.0	NM_000096	Q14063|Q2PP18|Q9UKS4	Frame_Shift_Del	DEL	ENST00000264613.6	hg19	CCDS3141.1																																																																																			.	.		0.398	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096	Frame_Shift_Del	-	148927955	T	-	148927955	8	5	103	1	0	1	0	1	0	0	1	0	3789	1623	56	0	2659	0	CP	3	148927955	Splice_Site	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	149317	148927955	49094475	279	14902										
TM4SF18	116441	hgsc.bcm.edu	37	chr3	149051109	149051109	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taatatgttcacgattatacTccaaagtgcaagcggaatca	7	8	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:149051109T>C	ENST00000296059.2	-	2	326	c.61A>G	c.(61-63)Agt>Ggt	p.S21G	TM4SF18_ENST00000470080.1_Missense_Mutation_p.S21G|RP11-206M11.7_ENST00000489011.1_RNA	NM_138786.3	NP_620141.1	Q96CE8	T4S18_HUMAN	transmembrane 4 L six family member 18	21						integral component of membrane (GO:0016021)				lung(1)|ovary(1)|prostate(1)	3			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			ACGATTATACTCCAAAGTGCA	0.438																																					p.S21G		Atlas-SNP	.											.	TM4SF18	12	.	0			c.A61G						.						74	70	72					3																	149051109		2203	4300	6503	SO:0001583	missense	116441	exon1			TTATACTCCAAAG	BC014339	CCDS3142.1	3q25.1	2005-08-09			ENSG00000163762	ENSG00000163762			25181	protein-coding gene	gene with protein product						10975581	Standard	NM_001184723		Approved	L6D	uc021xfl.1	Q96CE8	OTTHUMG00000159582	ENST00000296059.2:c.61A>G	chr3.hg19:g.149051109T>C	ENSP00000296059:p.Ser21Gly	104.0	0.0		137.0	6.0	NM_001184723	B2R8K0|D3DNH5	Missense_Mutation	SNP	ENST00000296059.2	hg19	CCDS3142.1	.	.	.	.	.	.	.	.	.	.	T	11.19	1.566440	0.27915	.	.	ENSG00000163762	ENST00000296059;ENST00000470080;ENST00000474754	T;T;T	0.27557	1.66;1.66;1.66	4.81	4.81	0.61882	.	0.112361	0.64402	D	0.000009	T	0.25232	0.0613	L	0.34521	1.04	0.35286	D	0.781733	B	0.30542	0.284	B	0.34093	0.175	T	0.28586	-1.0039	10	0.19147	T	0.46	-13.1318	14.023	0.64568	0.0:0.0:0.0:1.0	.	21	Q96CE8	T4S18_HUMAN	G	21	ENSP00000296059:S21G;ENSP00000419278:S21G;ENSP00000418372:S21G	ENSP00000296059:S21G	S	-	1	0	TM4SF18	150533799	1.000000	0.71417	0.999000	0.59377	0.922000	0.55478	2.511000	0.45476	1.781000	0.52344	0.533000	0.62120	AGT	.	.		0.438	TM4SF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356326.1	NM_138786		C	149051109	T	C	149051109	3	2	103	1	0	0	0	0	1	0	0	0	15982	1551	54	2	564	2	TM4SF18	3	149051109	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	123154	149051109	48971321	280	14903										
MED12L	116931	hgsc.bcm.edu	37	chr3	150874054	150874054	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggccctgtccctgtgccaccAgaggtggagcaagccatgaa	13	13	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:150874054A>G	ENST00000474524.1	+	5	701	c.663A>G	c.(661-663)ccA>ccG	p.P221P	MED12L_ENST00000273432.4_Silent_p.P221P|MED12L_ENST00000422248.2_Silent_p.P221P|MED12L_ENST00000309237.4_Silent_p.P221P	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	221						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CTGTGCCACCAGAGGTGGAGC	0.493																																					p.P221P		Atlas-SNP	.											.	MED12L	271	.	0			c.A663G						.						118	109	112					3																	150874054		2203	4300	6503	SO:0001819	synonymous_variant	116931	exon5			GCCACCAGAGGTG	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.663A>G	chr3.hg19:g.150874054A>G		82.0	0.0		97.0	5.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	hg19	CCDS33876.1																																																																																			.	.		0.493	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		G	150874054	A	G	150874054	2	3	103	1	0	0	0	0	0	0	0	1	9438	175	7	2		2	MED12L	3	150874054	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1822945	150874054	47148376	281	14904										
MME	4311	hgsc.bcm.edu	37	chr3	154834710	154834710	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aactgaattctaaatatgggAaaaaagtccttattaatttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:154834710delA	ENST00000460393.1	+	7	709	c.589delA	c.(589-591)aaafs	p.K198fs	MME_ENST00000462745.1_Frame_Shift_Del_p.K198fs|MME_ENST00000493237.1_Frame_Shift_Del_p.K198fs|MME_ENST00000360490.2_Frame_Shift_Del_p.K198fs|MME_ENST00000492661.1_Frame_Shift_Del_p.K198fs	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	198					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)	p.K197E(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	TAAATATGGGAAAAAAGTCCT	0.299																																					p.G196fs		Atlas-INDEL	.											.	MME	133	.	1	Substitution - Missense(1)	endometrium(1)	c.588delG						.						58	62	60					3																	154834710		2203	4296	6499	SO:0001589	frameshift_variant	4311	exon7			.		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.589delA	chr3.hg19:g.154834710delA	ENSP00000418525:p.Lys198fs	133.0	0.0		221.0	14.0	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Frame_Shift_Del	DEL	ENST00000460393.1	hg19	CCDS3172.1																																																																																			.	.		0.299	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		-	154834710	A	-	154834710	7	5	103	1	0	1	0	1	0	0	0	0	9654	247	9	0	611	0	MME	3	154834710	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3960656	154834710	43187720	282	14905										
KCNAB1	7881	hgsc.bcm.edu	37	chr3	155838473	155838473	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaagttaaggagacagtctGggttttctgtagcagggaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:155838473delG	ENST00000490337.1	+	1	137	c.73delG	c.(73-75)gggfs	p.G25fs	KCNAB1_ENST00000389636.5_Frame_Shift_Del_p.G25fs	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	25					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GAGACAGTCTGGGTTTTCTGT	0.542																																					p.S24fs		Atlas-Indel,Pindel	.											.	KCNAB1	176	.	0			c.72delT						.						98	108	105					3																	155838473		2203	4300	6503	SO:0001589	frameshift_variant	7881	exon1			.	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.73delG	chr3.hg19:g.155838473delG	ENSP00000419952:p.Gly25fs	109.0	0.0		128.0	26.0	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Frame_Shift_Del	DEL	ENST00000490337.1	hg19	CCDS3174.1																																																																																			.	.		0.542	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		-	155838473	G	-	155838473	7	5	103	1	0	1	0	1	0	0	0	0	8018	1348	47	0	75	0	KCNAB1	3	155838473	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1003763	155838473	42183957	283	14906										
WDR49	151790	hgsc.bcm.edu	37	chr3	167254660	167254660	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtgaaagttcaatttacccGtaacaagagtttgtggaggt	11	5	1	2	rs200695837		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:167254660G>A	ENST00000308378.3	-	7	1201	c.896C>T	c.(895-897)aCg>aTg	p.T299M	WDR49_ENST00000479765.1_Intron|WDR49_ENST00000453925.2_Missense_Mutation_p.T363M|WDR49_ENST00000476376.1_Missense_Mutation_p.T124M	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	299										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						CAATTTACCCGTAACAAGAGT	0.373																																					p.T299M		Atlas-SNP	.											WDR49,bladder,carcinoma,0,2	WDR49	188	.	0			c.C896T						.						64	60	62					3																	167254660		2203	4300	6503	SO:0001583	missense	151790	exon7			TTACCCGTAACAA	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.896C>T	chr3.hg19:g.167254660G>A	ENSP00000311343:p.Thr299Met	81.0	0.0		75.0	19.0	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	hg19	CCDS3201.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.00|15.00	2.702932|2.702932	0.48412|0.48412	.|.	.|.	ENSG00000174776|ENSG00000174776	ENST00000472600|ENST00000308378;ENST00000476376;ENST00000453925	.|T;T;T	.|0.68181	.|-0.31;-0.31;-0.31	5.69|5.69	5.69|5.69	0.88448|0.88448	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88559|0.88559	0.6469|0.6469	H|H	0.96633|0.96633	3.855|3.855	0.39988|0.39988	D|D	0.975001|0.975001	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.997	D|D	0.92253|0.92253	0.5810|0.5810	5|10	.|0.87932	.|D	.|0	.|.	18.5851|18.5851	0.91187|0.91187	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|363;299	.|E7EQK3;Q8IV35	.|.;WDR49_HUMAN	W|M	375|299;124;363	.|ENSP00000311343:T299M;ENSP00000420508:T124M;ENSP00000410863:T363M	.|ENSP00000311343:T299M	R|T	-|-	1|2	2|0	WDR49|WDR49	168737354|168737354	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.003000|0.003000	0.03518|0.03518	6.671000|6.671000	0.74472|0.74472	2.700000|2.700000	0.92200|0.92200	0.655000|0.655000	0.94253|0.94253	CGG|ACG	.	G|0.999;A|0.001		0.373	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		A	167254660	G	A	167254660	3	1	103	1	0	0	0	0	1	0	0	0	17317	1145	40	1	1233	1	WDR49	3	167254660	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	11416187	167254660	30767770	284	14907										
MYNN	55892	hgsc.bcm.edu	37	chr3	169504444	169504444	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtattcagaaccacagttgaTttttttacaacaattatact							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:169504444delT	ENST00000349841.5	+	8	2474	c.1811delT	c.(1810-1812)attfs	p.I604fs	MYNN_ENST00000356716.4_Frame_Shift_Del_p.I604fs|MYNN_ENST00000544106.1_Frame_Shift_Del_p.I575fs	NM_018657.4	NP_061127.1	Q9NPC7	MYNN_HUMAN	myoneurin	604					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			CCACAGTTGATTTTTTTACAA	0.368																																					p.I604fs		Atlas-INDEL	.											.	MYNN	36	.	0			c.1810delA						.						50	51	51					3																	169504444		2203	4300	6503	SO:0001589	frameshift_variant	55892	exon8			.	AF148848	CCDS3207.1, CCDS54671.1	3q26.31	2013-01-09			ENSG00000085274	ENSG00000085274		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	14955	protein-coding gene	gene with protein product		606042				10873615	Standard	NM_001185118		Approved	SBBIZ1, ZBTB31, ZNF902	uc010hwo.3	Q9NPC7		ENST00000349841.5:c.1811delT	chr3.hg19:g.169504444delT	ENSP00000326240:p.Ile604fs	137.0	0.0		154.0	11.0	NM_018657	B2R6C9|Q6QHA6|Q6QHA7|Q6R3G1|Q6R3G2|Q6R4A0|Q7Z716|Q7Z717|Q86Z11|Q86Z12|Q9NS01|Q9UIW8	Frame_Shift_Del	DEL	ENST00000349841.5	hg19	CCDS3207.1																																																																																			.	.		0.368	MYNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467801.1	NM_018657		-	169504444	T	-	169504444	7	5	103	1	0	1	0	1	0	0	0	0	10070	1493	52	0	1837	0	MYNN	3	169504444	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2249784	169504444	28517986	285	14908										
LRRC34	151827	hgsc.bcm.edu	37	chr3	169514647	169514647	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtagtgcaacaagacagtgaTtttctttcaacatgcggcct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:169514647delT	ENST00000316515.7	-	7	935	c.659delA	c.(658-660)aatfs	p.N220fs	RP11-362K14.6_ENST00000602835.1_RNA|RP11-362K14.7_ENST00000602913.1_RNA|LRRC34_ENST00000522526.2_Frame_Shift_Del_p.N233fs|LRRC34_ENST00000524327.1_5'UTR|LRRC34_ENST00000522830.1_Frame_Shift_Del_p.N204fs|LRRC34_ENST00000446859.1_Frame_Shift_Del_p.N265fs	NM_153353.4	NP_699184.2	Q8IZ02	LRC34_HUMAN	leucine rich repeat containing 34	220										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(2)	10	all_cancers(22;4.12e-22)|all_epithelial(15;7.54e-27)|all_lung(20;1.63e-16)|Lung NSC(18;6.92e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			AAGACAGTGATTTTCTTTCAA	0.348																																					p.N265fs		Atlas-INDEL	.											.	LRRC34	30	.	0			c.795delT						.						137	122	127					3																	169514647		2203	4300	6503	SO:0001589	frameshift_variant	151827	exon8			.	AK095125	CCDS3208.1, CCDS3208.2, CCDS54672.1	3q26.2	2014-03-18			ENSG00000171757	ENSG00000171757			28408	protein-coding gene	gene with protein product						12477932	Standard	NM_153353		Approved	MGC27085	uc003ffy.3	Q8IZ02	OTTHUMG00000164419	ENST00000316515.7:c.659delA	chr3.hg19:g.169514647delT	ENSP00000326150:p.Asn220fs	152.0	0.0		212.0	13.0	NM_001172779	B4DEJ7|E9PBH2|G5E9T7	Frame_Shift_Del	DEL	ENST00000316515.7	hg19																																																																																				.	.		0.348	LRRC34-201	KNOWN	basic	protein_coding	protein_coding		NM_153353		-	169514647	T	-	169514647	7	5	103	1	0	1	0	1	0	0	0	0	8998	1493	52	0	638	0	LRRC34	3	169514647	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	10203	169514647	28507783	286	14909										
SAMD7	344658	hgsc.bcm.edu	37	chr3	169644580	169644580	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accacactttgaggagagctGggggcagagatgtcgtcgac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:169644580delG	ENST00000428432.2	+	6	919	c.530delG	c.(529-531)tggfs	p.W177fs	SAMD7_ENST00000335556.3_Frame_Shift_Del_p.W177fs	NM_182610.2	NP_872416.1	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	177										NS(1)|biliary_tract(1)|breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			GAGGAGAGCTGGGGGCAGAGA	0.493																																					p.W177fs		Atlas-INDEL	.											.	SAMD7	69	.	0			c.529delT						.						62	65	64					3																	169644580		2203	4300	6503	SO:0001589	frameshift_variant	344658	exon6			.	BX537903	CCDS3209.1	3q26.31	2013-01-10			ENSG00000187033	ENSG00000187033		"Sterile alpha motif (SAM) domain containing"	25394	protein-coding gene	gene with protein product							Standard	NM_182610		Approved	DKFZp686E1583	uc003fgd.3	Q7Z3H4	OTTHUMG00000158730	ENST00000428432.2:c.530delG	chr3.hg19:g.169644580delG	ENSP00000391299:p.Trp177fs	140.0	0.0		169.0	12.0	NM_182610		Frame_Shift_Del	DEL	ENST00000428432.2	hg19	CCDS3209.1																																																																																			.	.		0.493	SAMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351959.1	NM_182610		-	169644580	G	-	169644580	7	5	103	1	0	1	0	1	0	0	0	0	13839	1357	47	0	544	0	SAMD7	3	169644580	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	129933	169644580	28377850	287	14910										
SLC2A2	6514	hgsc.bcm.edu	37	chr3	170716076	170716076	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggacgtggtccttgactgAaaaactcagccaccatgaac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:170716076delA	ENST00000314251.3	-	10	1359	c.1280delT	c.(1279-1281)ttcfs	p.F427fs	SLC2A2_ENST00000382808.4_Frame_Shift_Del_p.F308fs	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	427					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)	p.F427S(1)		central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TCCTTGACTGAAAAACTCAGC	0.473																																					p.F427fs		Atlas-INDEL	.											.	SLC2A2	71	.	1	Substitution - Missense(1)	lung(1)	c.1281delC						.						80	80	80					3																	170716076		2203	4300	6503	SO:0001589	frameshift_variant	6514	exon10			.	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.1280delT	chr3.hg19:g.170716076delA	ENSP00000323568:p.Phe427fs	156.0	0.0		174.0	11.0	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Frame_Shift_Del	DEL	ENST00000314251.3	hg19	CCDS3215.1																																																																																			.	.		0.473	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		-	170716076	A	-	170716076	7	5	103	1	0	1	0	1	0	0	0	0	14559	246	9	0	302	0	SLC2A2	3	170716076	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1071496	170716076	27306354	288	14911										
TNIK	23043	hgsc.bcm.edu	37	chr3	170805183	170805183	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttgagacgcgccccagtcccTcagtcggggttccagctgga	13	14	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:170805183T>C	ENST00000436636.2	-	24	3178	c.2834A>G	c.(2833-2835)gAg>gGg	p.E945G	TNIK_ENST00000475336.1_Missense_Mutation_p.E853G|TNIK_ENST00000357327.5_Missense_Mutation_p.E916G|TNIK_ENST00000488470.1_Missense_Mutation_p.E890G|TNIK_ENST00000460047.1_Missense_Mutation_p.E882G|TNIK_ENST00000284483.8_Missense_Mutation_p.E937G|TNIK_ENST00000341852.6_Missense_Mutation_p.E861G|TNIK_ENST00000470834.1_Missense_Mutation_p.E908G|TNIK_ENST00000538048.1_Missense_Mutation_p.E897G|TNIK_ENST00000369326.5_Missense_Mutation_p.E923G	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	945	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			CCCCAGTCCCTCAGTCGGGGT	0.582																																					p.E945G		Atlas-SNP	.											.	TNIK	313	.	0			c.A2834G						.						82	84	84					3																	170805183		2006	4175	6181	SO:0001583	missense	23043	exon24			AGTCCCTCAGTCG	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.2834A>G	chr3.hg19:g.170805183T>C	ENSP00000399511:p.Glu945Gly	71.0	0.0		92.0	4.0	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	hg19	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.959234	0.53400	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	T;T;T;T;T;T;T;T;T;T	0.73681	-0.76;-0.76;-0.75;-0.76;-0.76;-0.77;-0.77;-0.77;-0.76;-0.77	5.93	5.93	0.95920	.	0.129005	0.51477	D	0.000083	T	0.52306	0.1726	N	0.02539	-0.55	0.58432	D	0.999997	B;B;B;B;B;B;B;B	0.30281	0.275;0.002;0.275;0.275;0.002;0.003;0.275;0.001	B;B;B;B;B;B;B;B	0.25291	0.059;0.01;0.059;0.059;0.01;0.01;0.059;0.005	T	0.59359	-0.7469	10	0.59425	D	0.04	.	16.3943	0.83563	0.0:0.0:0.0:1.0	.	853;908;882;861;937;916;890;945	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	G	945;923;897;861;937;853;916;882;890;908	ENSP00000399511:E945G;ENSP00000358332:E923G;ENSP00000443278:E897G;ENSP00000345352:E861G;ENSP00000284483:E937G;ENSP00000418156:E853G;ENSP00000349880:E916G;ENSP00000418916:E882G;ENSP00000418378:E890G;ENSP00000419990:E908G	ENSP00000284483:E937G	E	-	2	0	TNIK	172287877	1.000000	0.71417	0.997000	0.53966	0.610000	0.37248	6.155000	0.71833	2.281000	0.76405	0.533000	0.62120	GAG	.	.		0.582	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		C	170805183	T	C	170805183	3	2	103	1	0	0	0	0	1	0	0	0	16328	1551	54	2	1288	2	TNIK	3	170805183	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	89107	170805183	27217247	289	14912										
MFN1	55669	hgsc.bcm.edu	37	chr3	179082955	179082955	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcggctttccaagcctaataTtttcattctcaataatcgtt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:179082955delT	ENST00000471841.1	+	7	821	c.695delT	c.(694-696)attfs	p.I232fs	MFN1_ENST00000263969.5_Frame_Shift_Del_p.I232fs|MFN1_ENST00000280653.7_Frame_Shift_Del_p.I232fs	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	232	Dynamin-type G.				mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			AAGCCTAATATTTTCATTCTC	0.328																																					p.I232fs		Atlas-INDEL	.											.	MFN1	72	.	0			c.694delA						.						57	62	60					3																	179082955		2203	4299	6502	SO:0001589	frameshift_variant	55669	exon7			.	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.695delT	chr3.hg19:g.179082955delT	ENSP00000420617:p.Ile232fs	153.0	0.0		155.0	11.0	NM_033540	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Frame_Shift_Del	DEL	ENST00000471841.1	hg19	CCDS3228.1																																																																																			.	.		0.328	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		-	179082955	T	-	179082955	7	5	103	1	0	1	0	1	0	0	0	0	9532	1493	52	0	717	0	MFN1	3	179082955	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	8277772	179082955	18939475	290	14913										
MCCC1	56922	hgsc.bcm.edu	37	chr3	182788998	182788998	+	Splice_Site	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acaagcatgcacaatcttacTtttcctcctccaccccggac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:182788998delT	ENST00000265594.4	-	6	785	c.639delA	c.(637-639)aaa>aa	p.K213fs	MCCC1_ENST00000492597.1_Splice_Site_p.K104fs|MCCC1_ENST00000539926.1_Splice_Site_p.K78fs	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	213	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	ACAATCTTACTTTTCCTCCTC	0.433																																					.		Atlas-INDEL	.											.	MCCC1	87	.	0			c.639+1A>-						.						107	112	110					3																	182788998		2203	4300	6503	SO:0001630	splice_region_variant	56922	exon7			.	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.639+1A>-	chr3.hg19:g.182788998delT		144.0	0.0		250.0	17.0	NM_020166	Q59ES4|Q9H959|Q9NS97	Splice_Site	DEL	ENST00000265594.4	hg19	CCDS3241.1																																																																																			.	.		0.433	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	Frame_Shift_Del	-	182788998	T	-	182788998	8	5	103	1	0	1	0	1	0	0	1	0	9383	1623	56	0	1594	0	MCCC1	3	182788998	Splice_Site	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3706043	182788998	15233432	291	14914										
MCF2L2	23101	hgsc.bcm.edu	37	chr3	182946091	182946091	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagtacagacttactctcttGagaaagcaatgtgccagaag	10	8	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:182946091G>A	ENST00000328913.3	-	18	2406	c.2109C>T	c.(2107-2109)ctC>ctT	p.L703L	MCF2L2_ENST00000447025.2_Silent_p.L703L|MCF2L2_ENST00000473233.1_Silent_p.L703L	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	703	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TTACTCTCTTGAGAAAGCAAT	0.358																																					p.L703L		Atlas-SNP	.											.	MCF2L2	164	.	0			c.C2109T						.						86	84	84					3																	182946091		2203	4300	6503	SO:0001819	synonymous_variant	23101	exon18			TCTCTTGAGAAAG	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.2109C>T	chr3.hg19:g.182946091G>A		59.0	0.0		81.0	4.0	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Silent	SNP	ENST00000328913.3	hg19	CCDS3243.1																																																																																			.	.		0.358	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		A	182946091	G	A	182946091	2	1	103	1	0	0	0	0	0	0	0	1	9389	1277	45	3		3	MCF2L2	3	182946091	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	157093	182946091	15076339	292	14915										
ABCC5	10057	hgsc.bcm.edu	37	chr3	183699624	183699624	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcatccgtggcggccacgcaTtttctcctgaaatatgctgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:183699624delT	ENST00000334444.6	-	8	1278	c.1038delA	c.(1036-1038)aaafs	p.K346fs	ABCC5_ENST00000492216.1_5'UTR|ABCC5_ENST00000265586.6_Frame_Shift_Del_p.K346fs	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	346	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	CGGCCACGCATTTTCTCCTGA	0.408																																					p.C347fs		Atlas-INDEL	.											.	ABCC5	142	.	0			c.1039delT						.						52	51	51					3																	183699624		1882	4111	5993	SO:0001589	frameshift_variant	10057	exon8			.	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.1038delA	chr3.hg19:g.183699624delT	ENSP00000333926:p.Lys346fs	106.0	0.0		165.0	12.0	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Frame_Shift_Del	DEL	ENST00000334444.6	hg19	CCDS43176.1																																																																																			.	.		0.408	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		-	183699624	T	-	183699624	7	5	103	1	0	1	0	1	0	0	0	0	56	1490	52	0	3367	0	ABCC5	3	183699624	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	753533	183699624	14322806	293	14916										
PSMD2	5708	hgsc.bcm.edu	37	chr3	184025287	184025287	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaagtttcctataactccaTttttgccatgggcatggtgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:184025287delT	ENST00000310118.4	+	17	2735	c.2177delT	c.(2176-2178)attfs	p.I726fs	PSMD2_ENST00000435761.1_Frame_Shift_Del_p.I567fs|EIF2B5_ENST00000444495.1_Intron|PSMD2_ENST00000439383.1_Frame_Shift_Del_p.I596fs	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	726					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|liver(1)|lung(12)|prostate(3)|upper_aerodigestive_tract(2)	27	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	TATAACTCCATTTTTGCCATG	0.458																																					p.I726fs	Colon(24;313 636 6917 9932 15554)	Atlas-INDEL	.											.	PSMD2	56	.	0			c.2176delA						.						90	89	89					3																	184025287		2203	4300	6503	SO:0001589	frameshift_variant	5708	exon17			.	AK095245	CCDS3258.1, CCDS63853.1, CCDS63854.1	3q27.3	2008-05-22			ENSG00000175166	ENSG00000175166		"Proteasome (prosome, macropain) subunits"	9559	protein-coding gene	gene with protein product		606223				8774743	Standard	NM_002808		Approved	S2, P97, TRAP2, MGC14274, Rpn1	uc003fnn.1	Q13200	OTTHUMG00000156796	ENST00000310118.4:c.2177delT	chr3.hg19:g.184025287delT	ENSP00000310129:p.Ile726fs	120.0	0.0		159.0	11.0	NM_002808	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Frame_Shift_Del	DEL	ENST00000310118.4	hg19	CCDS3258.1																																																																																			.	.		0.458	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808		-	184025287	T	-	184025287	7	5	103	1	0	1	0	1	0	0	0	0	12710	1493	52	0	2243	0	PSMD2	3	184025287	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	325663	184025287	13997143	294	14917										
MAP3K13	9175	hgsc.bcm.edu	37	chr3	185165720	185165720	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acggaatgaacctgtctctgAaaaagttgatatatggtgag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:185165720delA	ENST00000265026.3	+	5	1329	c.995delA	c.(994-996)gaafs	p.E332fs	MAP3K13_ENST00000446828.1_Frame_Shift_Del_p.E125fs|MAP3K13_ENST00000535426.1_Frame_Shift_Del_p.E188fs|MAP3K13_ENST00000424227.1_Frame_Shift_Del_p.E332fs|MAP3K13_ENST00000443863.1_Frame_Shift_Del_p.E188fs	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			CCTGTCTCTGAAAAAGTTGAT	0.468																																					p.E332fs		Atlas-INDEL	.											.	MAP3K13	209	.	0			c.994delG						.						58	55	56					3																	185165720		2203	4300	6503	SO:0001589	frameshift_variant	9175	exon6			.	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.995delA	chr3.hg19:g.185165720delA	ENSP00000265026:p.Glu332fs	150.0	0.0		163.0	12.0	NM_001242314		Frame_Shift_Del	DEL	ENST00000265026.3	hg19	CCDS3270.1																																																																																			.	.		0.468	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		-	185165720	A	-	185165720	7	5	103	1	0	1	0	1	0	0	0	0	9256	246	9	0	1009	0	MAP3K13	3	185165720	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1140433	185165720	12856710	295	14918										
TBCCD1	55171	hgsc.bcm.edu	37	chr3	186272330	186272330	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcattgggtaatgtgtatgAaaaggggcaaaagttactgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:186272330delA	ENST00000424280.1	-	6	1736	c.1257delT	c.(1255-1257)tttfs	p.F419fs	TBCCD1_ENST00000338733.5_Frame_Shift_Del_p.F419fs|TBCCD1_ENST00000446782.1_Frame_Shift_Del_p.F323fs|TBCCD1_ENST00000479590.1_5'Flank	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	419	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		AATGTGTATGAAAAGGGGCAA	0.463																																					p.H420fs		Atlas-INDEL	.											.	TBCCD1	42	.	0			c.1258delC						.						98	93	95					3																	186272330		2203	4300	6503	SO:0001589	frameshift_variant	55171	exon6			.	BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.1257delT	chr3.hg19:g.186272330delA	ENSP00000411253:p.Phe419fs	85.0	0.0		113.0	10.0	NM_001134415	B3KW69|D3DNU6|G5E9J4	Frame_Shift_Del	DEL	ENST00000424280.1	hg19	CCDS3276.1																																																																																			.	.		0.463	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138		-	186272330	A	-	186272330	7	5	103	1	0	1	0	1	0	0	0	0	15647	243	9	0	424	0	TBCCD1	3	186272330	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1106610	186272330	11750100	296	14919										
APOD	347	hgsc.bcm.edu	37	chr3	195295847	195295847	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgttattagaagtcaggataTtttttagagagtccactgtt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:195295847delT	ENST00000343267.3	-	5	855	c.494delA	c.(493-495)aatfs	p.N165fs		NM_001647.3	NP_001638.1	P05090	APOD_HUMAN	apolipoprotein D	165					aging (GO:0007568)|angiogenesis (GO:0001525)|brain development (GO:0007420)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of lipoprotein lipid oxidation (GO:0060588)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of T cell migration (GO:2000405)|peripheral nervous system axon regeneration (GO:0014012)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to reactive oxygen species (GO:0000302)|tissue regeneration (GO:0042246)	cytosolic ribosome (GO:0022626)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		AGTCAGGATATTTTTTAGAGA	0.448																																					p.N165fs		Atlas-INDEL	.											.	APOD	28	.	0			c.495delT						.						157	160	159					3																	195295847		2203	4300	6503	SO:0001589	frameshift_variant	347	exon5			.		CCDS33925.1	3q29	2013-09-19			ENSG00000189058	ENSG00000189058		"Lipocalins", "Apolipoproteins"	612	protein-coding gene	gene with protein product		107740				2439269, 3453108	Standard	NM_001647		Approved		uc003fur.2	P05090	OTTHUMG00000155854	ENST00000343267.3:c.494delA	chr3.hg19:g.195295847delT	ENSP00000345179:p.Asn165fs	198.0	0.0		180.0	11.0	NM_001647	B2R579|D3DNW6|Q6IBG6	Frame_Shift_Del	DEL	ENST00000343267.3	hg19	CCDS33925.1																																																																																			.	.		0.448	APOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342004.1	NM_001647		-	195295847	T	-	195295847	7	5	103	1	0	1	0	1	0	0	0	0	801	1493	52	0	79	0	APOD	3	195295847	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	9023517	195295847	2726583	297	14920										
UBXN7	26043	hgsc.bcm.edu	37	chr3	196089423	196089423	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatgaactcctcactgccagAaaaaagttcagattcagatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:196089423delA	ENST00000296328.4	-	9	1044	c.970delT	c.(970-972)tctfs	p.S324fs	UBXN7_ENST00000428095.1_Frame_Shift_Del_p.S162fs|UBXN7_ENST00000535858.1_Frame_Shift_Del_p.S176fs	NM_015562.1	NP_056377.1	O94888	UBXN7_HUMAN	UBX domain protein 7	324						Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|nucleus (GO:0005634)	transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						TCACTGCCAGAAAAAAGTTCA	0.438																																					p.S324fs		Atlas-INDEL	.											.	UBXN7	43	.	0			c.971delC						.						105	100	102					3																	196089423		1845	4099	5944	SO:0001589	frameshift_variant	26043	exon9			.	AB018337	CCDS43191.1	3q29	2012-07-06	2008-07-25	2008-07-25	ENSG00000163960	ENSG00000163960		"UBX domain containing"	29119	protein-coding gene	gene with protein product			"UBX domain containing 7"	UBXD7		9872452, 22537386	Standard	NM_015562		Approved	KIAA0794	uc003fwm.4	O94888	OTTHUMG00000155639	ENST00000296328.4:c.970delT	chr3.hg19:g.196089423delA	ENSP00000296328:p.Ser324fs	152.0	0.0		163.0	10.0	NM_015562	D3DXB3|Q6ZP77|Q86X20|Q8N327	Frame_Shift_Del	DEL	ENST00000296328.4	hg19	CCDS43191.1																																																																																			.	.		0.438	UBXN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340938.2	XM_087353		-	196089423	A	-	196089423	7	5	103	1	0	1	0	1	0	0	0	0	16933	246	9	0	511	0	UBXN7	3	196089423	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	793576	196089423	1933007	298	14921										
PAK2	5062	hgsc.bcm.edu	37	chr3	196541368	196541368	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggtcatggaataccttgctGgggggtcactcactgatgtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:196541368delG	ENST00000327134.3	+	11	1304	c.982delG	c.(982-984)gggfs	p.G329fs		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	329	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			G -> R (in Ref. 3; AAA75468). {ECO:0000305}.	apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		ATACCTTGCTGGGGGGTCACT	0.408																																					p.A327fs		Atlas-INDEL	.											.	PAK2	113	.	0			c.981delT						.						164	159	161					3																	196541368		2203	4300	6503	SO:0001589	frameshift_variant	5062	exon11			.	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"S6/H4 kinase"	605022	"p21 (CDKN1A)-activated kinase 2"			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.982delG	chr3.hg19:g.196541368delG	ENSP00000314067:p.Gly329fs	152.0	0.0		222.0	14.0	NM_002577	Q13154|Q6ISC3	Frame_Shift_Del	DEL	ENST00000327134.3	hg19	CCDS3321.1																																																																																			.	.		0.408	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577		-	196541368	G	-	196541368	7	5	103	1	0	1	0	1	0	0	0	0	11410	1348	47	0	1020	0	PAK2	3	196541368	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	451945	196541368	1481062	299	14922										
IQCG	84223	hgsc.bcm.edu	37	chr3	197659165	197659165	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatctgcaatcacatcgctgAaaaactgcctgtaaggagaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:197659165delA	ENST00000265239.6	-	6	948	c.524delT	c.(523-525)ttcfs	p.F175fs	IQCG_ENST00000455191.1_Frame_Shift_Del_p.F175fs|IQCG_ENST00000453254.1_Frame_Shift_Del_p.F175fs	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	175						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		CACATCGCTGAAAAACTGCCT	0.433																																					p.F175fs		Atlas-INDEL	.											.	IQCG	44	.	0			c.525delC						.						96	90	93					3																	197659165		2203	4300	6503	SO:0001589	frameshift_variant	84223	exon6			.	AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 9"	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.524delT	chr3.hg19:g.197659165delA	ENSP00000265239:p.Phe175fs	113.0	0.0		160.0	11.0	NM_032263	Q9BST2|Q9HAG8	Frame_Shift_Del	DEL	ENST00000265239.6	hg19	CCDS3331.1																																																																																			.	.		0.433	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263		-	197659165	A	-	197659165	7	5	103	1	0	1	0	1	0	0	0	0	7819	246	9	0	835	0	IQCG	3	197659165	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1117797	197659165	363265	300	14923										
GAK	2580	hgsc.bcm.edu	37	chr4	877197	877197	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtccaggaacaaccgcacaTcttcgatgttgtttttgagc	9	10	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:877197T>C	ENST00000314167.4	-	13	1420	c.1310A>G	c.(1309-1311)gAt>gGt	p.D437G	GAK_ENST00000511163.1_Missense_Mutation_p.D358G	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	437	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		CAACCGCACATCTTCGATGTT	0.577																																					p.D437G		Atlas-SNP	.											.	GAK	104	.	0			c.A1310G						.						202	169	180					4																	877197		2203	4300	6503	SO:0001583	missense	2580	exon13			CGCACATCTTCGA	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"Heat shock proteins / DNAJ (HSP40)"	4113	protein-coding gene	gene with protein product	"auxilin-2"	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.1310A>G	chr4.hg19:g.877197T>C	ENSP00000314499:p.Asp437Gly	74.0	0.0		99.0	4.0	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	hg19	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	T	16.32	3.091156	0.55968	.	.	ENSG00000178950	ENST00000314167;ENST00000511163	D;D	0.98617	-5.03;-5.03	5.34	5.34	0.76211	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99214	0.9727	M	0.90870	3.155	0.80722	D	1	D;D;D;D	0.76494	0.999;0.983;0.999;0.997	D;P;D;D	0.74023	0.982;0.898;0.959;0.914	D	0.99239	1.0884	10	0.87932	D	0	-31.1922	13.2844	0.60235	0.0:0.0:0.0:1.0	.	358;358;437;333	Q5U4P5;E9PGR2;O14976;Q59HA5	.;.;GAK_HUMAN;.	G	437;358	ENSP00000314499:D437G;ENSP00000421361:D358G	ENSP00000314499:D437G	D	-	2	0	GAK	867197	1.000000	0.71417	0.103000	0.21229	0.023000	0.10783	7.874000	0.87199	2.022000	0.59522	0.482000	0.46254	GAT	.	.		0.577	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255		C	877197	T	C	877197	3	2	103	1	0	0	0	0	1	0	0	0	6203	1435	50	2	2689	2	GAK	4	877197	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10		877197	190277079	301	14924										
NOP14	8602	hgsc.bcm.edu	37	chr4	2950011	2950011	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcaatccacgtacttctaaTtttgctttgtttccttctgc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:2950011delT	ENST00000314262.6	-	9	1455	c.1407delA	c.(1405-1407)aaafs	p.K469fs	NOP14_ENST00000502735.1_Frame_Shift_Del_p.K469fs|NOP14-AS1_ENST00000507702.1_RNA|NOP14_ENST00000416614.2_Frame_Shift_Del_p.K469fs|NOP14-AS1_ENST00000515194.1_RNA|NOP14-AS1_ENST00000505731.1_RNA|NOP14-AS1_ENST00000503709.1_RNA|NOP14_ENST00000398071.4_Frame_Shift_Del_p.K469fs	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	469					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						GTACTTCTAATTTTGCTTTGT	0.483																																					p.L470X		Atlas-INDEL	.											.	NOP14	69	.	0			c.1408delT						.						312	248	269					4																	2950011		2203	4300	6503	SO:0001589	frameshift_variant	8602	exon9			.	AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"NOP14 homolog (S. cerevisiae)"	611526	"chromosome 4 open reading frame 9", "nucleolar protein 14", "nucleolar protein 14 homolog (yeast)", "NOP14 nucleolar protein homolog (yeast)"	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.1407delA	chr4.hg19:g.2950011delT	ENSP00000315674:p.Lys469fs	134.0	0.0		158.0	10.0	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Frame_Shift_Del	DEL	ENST00000314262.6	hg19	CCDS33945.1																																																																																			.	.		0.483	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703		-	2950011	T	-	2950011	7	5	103	1	0	1	0	1	0	0	0	0	10545	1490	52	0	1206	0	NOP14	4	2950011	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2072814	2950011	188204265	302	14925										
HTT	3064	hgsc.bcm.edu	37	chr4	3129309	3129309	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agggcctgattcagctgttaCcccttcagacagttctgaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:3129309delC	ENST00000355072.5	+	12	1866	c.1721delC	c.(1720-1722)accfs	p.T574fs		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	574					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TCAGCTGTTACCCCTTCAGAC	0.517																																					p.T574fs		Atlas-INDEL	.											.	HTT	221	.	0			c.1720delA						.						49	51	50					4																	3129309		1960	4139	6099	SO:0001589	frameshift_variant	3064	exon12			.	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1721delC	chr4.hg19:g.3129309delC	ENSP00000347184:p.Thr574fs	225.0	0.0		253.0	17.0	NM_002111	Q9UQB7	Frame_Shift_Del	DEL	ENST00000355072.5	hg19	CCDS43206.1																																																																																			.	.		0.517	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		-	3129309	C	-	3129309	7	5	103	1	0	1	0	1	0	0	0	0	7466	507	18	0	1767	0	HTT	4	3129309	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	179298	3129309	188024967	303	14926										
HTT	3064	hgsc.bcm.edu	37	chr4	3241656	3241656	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtcgccacagacttctacaGacaccagatagaggaggagc	12	11	1	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:3241656G>A	ENST00000355072.5	+	67	9444	c.9299G>A	c.(9298-9300)aGa>aAa	p.R3100K		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	3100					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GACTTCTACAGACACCAGATA	0.572																																					p.R3100K		Atlas-SNP	.											.	HTT	221	.	0			c.G9299A						.						39	43	41					4																	3241656		2170	4250	6420	SO:0001583	missense	3064	exon67			TCTACAGACACCA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.9299G>A	chr4.hg19:g.3241656G>A	ENSP00000347184:p.Arg3100Lys	139.0	0.0		176.0	28.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.260136	0.59321	.	.	ENSG00000197386	ENST00000355072	T	0.04758	3.56	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.03695	0.0105	N	0.17723	0.515	0.45183	D	0.998196	B	0.13145	0.007	B	0.12837	0.008	T	0.50499	-0.8821	10	0.22109	T	0.4	.	10.8622	0.46833	0.0869:0.0:0.9131:0.0	.	3100	P42858	HD_HUMAN	K	3100	ENSP00000347184:R3100K	ENSP00000347184:R3100K	R	+	2	0	HTT	3211454	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.819000	0.75262	2.284000	0.76573	0.655000	0.94253	AGA	.	.		0.572	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3241656	G	A	3241656	3	1	103	1	0	0	0	0	1	0	0	0	7466	942	33	3	9565	3	HTT	4	3241656	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	112347	3241656	187912620	304	14927										
HGFAC	3083	hgsc.bcm.edu	37	chr4	3443797	3443797	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggccccttcctcctcctcctCctgctgctgctgctgctgcc	8	21	0	0	rs538844201	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:3443797C>G	ENST00000382774.3	+	1	184	c.69C>G	c.(67-69)ctC>ctG	p.L23L	HGFAC_ENST00000511533.1_Silent_p.L23L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	23					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCCTCCTCCTCCTGCTGCTGC	0.716													C|||	2	0.000399361	8e-04	0	5008	,	,		13350	0		0	False		,,,				2504	0.001				p.L23L		Atlas-SNP	.											HGFAC,NS,carcinoma,0,2	HGFAC	69	.	0			c.C69G						.						13	16	15					4																	3443797		1723	3604	5327	SO:0001819	synonymous_variant	3083	exon1			CCTCCTCCTGCTG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.69C>G	chr4.hg19:g.3443797C>G		16.0	0.0		26.0	2.0	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	hg19	CCDS3369.1																																																																																			.	.		0.716	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			G	3443797	C	G	3443797	2	3	103	1	0	0	0	0	0	0	0	1	7095	842	30	4		4	HGFAC	4	3443797	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	202141	3443797	187710479	305	14928										
OTOP1	133060	hgsc.bcm.edu	37	chr4	4204211	4204211	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaaacccagagtgatgagccGttccttgtgctcattgagtt	10	9	1	4	rs200612216		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:4204211G>A	ENST00000296358.4	-	4	718	c.694C>T	c.(694-696)Cgg>Tgg	p.R232W		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	232					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.R232W(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GTGATGAGCCGTTCCTTGTGC	0.507																																					p.R232W		Atlas-SNP	.											OTOP1,NS,carcinoma,0,3	OTOP1	118	.	2	Substitution - Missense(2)	prostate(1)|liver(1)	c.C694T						.						144	123	130					4																	4204211		2203	4300	6503	SO:0001583	missense	133060	exon4			TGAGCCGTTCCTT	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.694C>T	chr4.hg19:g.4204211G>A	ENSP00000296358:p.Arg232Trp	119.0	0.0		141.0	6.0	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	hg19	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.781817	0.31502	.	.	ENSG00000163982	ENST00000296358	T	0.09817	2.94	5.28	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.06690	0.0171	N	0.14661	0.345	0.80722	D	1	P	0.35328	0.495	B	0.32583	0.148	T	0.26224	-1.0109	10	0.72032	D	0.01	.	10.6877	0.45852	0.0:0.0:0.5681:0.4319	.	232	Q7RTM1	OTOP1_HUMAN	W	232	ENSP00000296358:R232W	ENSP00000296358:R232W	R	-	1	2	OTOP1	4255112	1.000000	0.71417	0.547000	0.28179	0.267000	0.26476	2.487000	0.45268	2.462000	0.83206	0.603000	0.83216	CGG	.	.		0.507	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		A	4204211	G	A	4204211	3	1	103	1	0	0	0	0	1	0	0	0	11314	1144	40	1	1156	1	OTOP1	4	4204211	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	760414	4204211	186950065	306	14929										
OTOP1	133060	hgsc.bcm.edu	37	chr4	4204302	4204302	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacaccgagtggatcactccAaacctgaaaaacacaaggac	7	12	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:4204302A>C	ENST00000296358.4	-	4	627	c.603T>G	c.(601-603)ttT>ttG	p.F201L		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	201					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GGATCACTCCAAACCTGAAAA	0.527																																					p.F201L		Atlas-SNP	.											.	OTOP1	118	.	0			c.T603G						.						75	72	73					4																	4204302		2203	4299	6502	SO:0001583	missense	133060	exon4			CACTCCAAACCTG	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.603T>G	chr4.hg19:g.4204302A>C	ENSP00000296358:p.Phe201Leu	66.0	0.0		91.0	5.0	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	hg19	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.836374	0.71373	.	.	ENSG00000163982	ENST00000296358	T	0.32988	1.43	5.46	1.68	0.24146	.	0.000000	0.85682	D	0.000000	T	0.51601	0.1684	M	0.79926	2.475	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.47522	-0.9111	10	0.40728	T	0.16	.	9.2419	0.37502	0.789:0.0:0.211:0.0	.	201	Q7RTM1	OTOP1_HUMAN	L	201	ENSP00000296358:F201L	ENSP00000296358:F201L	F	-	3	2	OTOP1	4255203	0.998000	0.40836	0.997000	0.53966	0.852000	0.48524	0.634000	0.24614	0.394000	0.25230	0.491000	0.48974	TTT	.	.		0.527	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		C	4204302	A	C	4204302	3	2	103	1	0	0	0	0	1	0	0	0	11314	127	5	5	1247	5	OTOP1	4	4204302	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	91	4204302	186949974	307	14930										
FBXL5	26234	hgsc.bcm.edu	37	chr4	15627530	15627530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggaaatcttctctagggccaCatctgtgattttctcacaac	7	11	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:15627530C>T	ENST00000341285.3	-	9	1319	c.1195G>A	c.(1195-1197)Gtg>Atg	p.V399M	FBXL5_ENST00000412094.2_Missense_Mutation_p.V382M|FBXL5_ENST00000382358.4_Missense_Mutation_p.V273M	NM_001193534.1|NM_001193535.1|NM_012161.3	NP_001180463.1|NP_001180464.1|NP_036293.1	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5	399					iron ion homeostasis (GO:0055072)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	iron ion binding (GO:0005506)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13						TCTAGGGCCACATCTGTGATT	0.398																																					p.V399M		Atlas-SNP	.											.	FBXL5	52	.	0			c.G1195A						.						37	37	37					4																	15627530		2202	4298	6500	SO:0001583	missense	26234	exon9			GGGCCACATCTGT	AF174591	CCDS3415.1, CCDS54745.1	4p15.33	2011-06-09			ENSG00000118564	ENSG00000118564		"F-boxes / Leucine-rich repeats"	13602	protein-coding gene	gene with protein product		605655				10531035	Standard	NM_012161		Approved	FBL4, FBL5, FLR1	uc003goc.2	Q9UKA1	OTTHUMG00000097097	ENST00000341285.3:c.1195G>A	chr4.hg19:g.15627530C>T	ENSP00000344866:p.Val399Met	75.0	0.0		85.0	4.0	NM_012161	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Missense_Mutation	SNP	ENST00000341285.3	hg19	CCDS3415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.00|11.00	1.509797|1.509797	0.27036|0.27036	.|.	.|.	ENSG00000118564|ENSG00000118564	ENST00000513163|ENST00000341285;ENST00000412094;ENST00000382358	.|T;T;T	.|0.17370	.|2.28;2.28;2.28	5.92|5.92	4.18|4.18	0.49190|0.49190	.|.	.|0.785384	.|0.12899	.|N	.|0.429994	T|T	0.15176|0.15176	0.0366|0.0366	L|L	0.43152|0.43152	1.355|1.355	0.24901|0.24901	N|N	0.992104|0.992104	.|B;B	.|0.09022	.|0.001;0.002	.|B;B	.|0.11329	.|0.003;0.006	T|T	0.20605|0.20605	-1.0270|-1.0270	5|10	.|0.45353	.|T	.|0.12	-2.0215|-2.0215	7.0631|7.0631	0.25137|0.25137	0.139:0.7173:0.0:0.1437|0.139:0.7173:0.0:0.1437	.|.	.|382;399	.|Q9UKA1-2;Q9UKA1	.|.;FBXL5_HUMAN	Y|M	319|399;382;273	.|ENSP00000344866:V399M;ENSP00000408679:V382M;ENSP00000371795:V273M	.|ENSP00000344866:V399M	C|V	-|-	2|1	0|0	FBXL5|FBXL5	15236628|15236628	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.904000|0.904000	0.53231|0.53231	2.974000|2.974000	0.49272|0.49272	0.815000|0.815000	0.34398|0.34398	-0.157000|-0.157000	0.13467|0.13467	TGT|GTG	.	.		0.398	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2			T	15627530	C	T	15627530	3	4	103	1	0	0	0	0	1	0	0	0	5730	478	17	3	892	3	FBXL5	4	15627530	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	11423228	15627530	175526746	308	14931										
NCAPG	64151	hgsc.bcm.edu	37	chr4	17816898	17816898	+	Splice_Site	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttataaattatttttaaggTtttagctgaaaaggttcata							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:17816898delT	ENST00000251496.2	+	5	868	c.692delT	c.(691-693)gtt>gt	p.V231fs		NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	231					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		ATTTTTAAGGTTTTAGCTGAA	0.318																																					p.V231fs		Atlas-INDEL	.											.	NCAPG	76	.	0			c.691delG						.						46	48	47					4																	17816898		2202	4296	6498	SO:0001630	splice_region_variant	64151	exon5			.	AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"chromosome condensation protein G"	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.691-1T>-	chr4.hg19:g.17816898delT		103.0	0.0		111.0	10.0	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Frame_Shift_Del	DEL	ENST00000251496.2	hg19	CCDS3424.1																																																																																			.	.		0.318	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346	Frame_Shift_Del	-	17816898	T	-	17816898	8	5	103	1	0	1	0	1	0	0	1	0	10216	1739	60	0	710	0	NCAPG	4	17816898	Splice_Site	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2189368	17816898	173337378	309	14932										
KLHL5	51088	hgsc.bcm.edu	37	chr4	39064232	39064232	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacaaatctgtgtgcagtgcTttttgcccgttgcctagacg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:39064232delT	ENST00000504108.1	+	1	381	c.98delT	c.(97-99)cttfs	p.L33fs	KLHL5_ENST00000508137.2_Intron|KLHL5_ENST00000359687.2_Frame_Shift_Del_p.L33fs|KLHL5_ENST00000381930.3_Frame_Shift_Del_p.L33fs|KLHL5_ENST00000261425.3_5'UTR|KLHL5_ENST00000261426.5_Frame_Shift_Del_p.L33fs	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	33						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						TGTGCAGTGCTTTTTGCCCGT	0.393																																					p.L33fs		Atlas-INDEL	.											.	KLHL5	75	.	0			c.97delC						.						233	219	224					4																	39064232		2203	4300	6503	SO:0001589	frameshift_variant	51088	exon1			.	AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"Kelch-like", "BTB/POZ domain containing"	6356	protein-coding gene	gene with protein product		608064	"kelch (Drosophila)-like 5", "kelch-like 5 (Drosophila)"			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.98delT	chr4.hg19:g.39064232delT	ENSP00000423897:p.Leu33fs	203.0	0.0		260.0	16.0	NM_015990	A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Frame_Shift_Del	DEL	ENST00000504108.1	hg19	CCDS33974.1																																																																																			.	.		0.393	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1			-	39064232	T	-	39064232	7	5	103	1	0	1	0	1	0	0	0	0	8401	1609	56	0	100	0	KLHL5	4	39064232	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	21247334	39064232	152090044	310	14933										
KLB	152831	hgsc.bcm.edu	37	chr4	39436265	39436265	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttgctgagaatggctggttcAcagacagtcgtgtgaaaaca	12	7	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:39436265A>G	ENST00000257408.4	+	2	1358	c.1261A>G	c.(1261-1263)Aca>Gca	p.T421A		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	421	Glycosyl hydrolase-1 1.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						TGGCTGGTTCACAGACAGTCG	0.413																																					p.T421A		Atlas-SNP	.											.	KLB	95	.	0			c.A1261G						.						77	77	77					4																	39436265		2203	4300	6503	SO:0001583	missense	152831	exon2			TGGTTCACAGACA	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.1261A>G	chr4.hg19:g.39436265A>G	ENSP00000257408:p.Thr421Ala	77.0	0.0		91.0	4.0	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	hg19	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.259851	0.59321	.	.	ENSG00000134962	ENST00000257408	T	0.28454	1.61	6.06	6.06	0.98353	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.109144	0.64402	D	0.000006	T	0.26666	0.0652	N	0.16098	0.37	0.37100	D	0.899867	P;P	0.51791	0.948;0.948	P;P	0.54499	0.754;0.754	T	0.13229	-1.0517	10	0.09338	T	0.73	-20.9716	11.6645	0.51366	0.8678:0.0:0.0:0.1322	.	421;421	B7ZL50;Q86Z14	.;KLOTB_HUMAN	A	421	ENSP00000257408:T421A	ENSP00000257408:T421A	T	+	1	0	KLB	39112660	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	3.182000	0.50910	2.315000	0.78130	0.533000	0.62120	ACA	.	.		0.413	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		G	39436265	A	G	39436265	3	3	103	1	0	0	0	0	1	0	0	0	8341	159	6	2	1267	2	KLB	4	39436265	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	372033	39436265	151718011	311	14934										
LIMCH1	22998	hgsc.bcm.edu	37	chr4	41668635	41668635	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgacatttccatttctggacAaaatgcctgaagccaaccaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:41668635delA	ENST00000313860.7	+	16	2248	c.2194delA	c.(2194-2196)aaafs	p.K732fs	LIMCH1_ENST00000513024.1_Frame_Shift_Del_p.K561fs|LIMCH1_ENST00000512632.1_Intron|LIMCH1_ENST00000503057.1_Frame_Shift_Del_p.K1117fs|LIMCH1_ENST00000509277.1_Frame_Shift_Del_p.K566fs|LIMCH1_ENST00000512946.1_Frame_Shift_Del_p.K732fs|LIMCH1_ENST00000396595.3_Frame_Shift_Del_p.K578fs|LIMCH1_ENST00000511496.1_Frame_Shift_Del_p.K573fs|LIMCH1_ENST00000514096.1_Frame_Shift_Del_p.K573fs|LIMCH1_ENST00000512820.1_Frame_Shift_Del_p.K720fs|LIMCH1_ENST00000508501.1_Frame_Shift_Del_p.K732fs|LIMCH1_ENST00000381753.4_Frame_Shift_Del_p.K566fs	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	732					actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						ATTTCTGGACAAAATGCCTGA	0.418																																					p.D731fs		Atlas-INDEL	.											.	LIMCH1	233	.	0			c.2193delC						.						116	99	104					4																	41668635		2203	4300	6503	SO:0001589	frameshift_variant	22998	exon16			.	AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.2194delA	chr4.hg19:g.41668635delA	ENSP00000316891:p.Lys732fs	104.0	0.0		148.0	11.0	NM_014988	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Frame_Shift_Del	DEL	ENST00000313860.7	hg19	CCDS33977.1																																																																																			.	.		0.418	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988		-	41668635	A	-	41668635	7	5	103	1	0	1	0	1	0	0	0	0	8806	131	5	0	2284	0	LIMCH1	4	41668635	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2232370	41668635	149485641	312	14935										
PHOX2B	8929	hgsc.bcm.edu	37	chr4	41750584	41750584	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccatcccagccatacaggacTcgtaggcagaggaattgagg	12	11	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:41750584T>C	ENST00000226382.2	-	1	403	c.44A>G	c.(43-45)gAg>gGg	p.E15G	RP11-227F19.1_ENST00000508038.1_RNA|RP11-227F19.2_ENST00000510602.1_lincRNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	15					autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						CATACAGGACTCGTAGGCAGA	0.468			"Mis, F"		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.E15G		Atlas-SNP	.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B	53	.	0			c.A44G						.						33	34	34					4																	41750584		2203	4300	6503	SO:0001583	missense	8929	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CAGGACTCGTAGG	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"Homeoboxes / PRD class"	9143	protein-coding gene	gene with protein product		603851	"paired mesoderm homeobox 2b"	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.44A>G	chr4.hg19:g.41750584T>C	ENSP00000226382:p.Glu15Gly	86.0	0.0		99.0	4.0	NM_003924	Q6PJD9	Missense_Mutation	SNP	ENST00000226382.2	hg19	CCDS3463.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.596671	0.46318	.	.	ENSG00000109132	ENST00000226382	D	0.92149	-2.98	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.88941	0.6574	N	0.14661	0.345	0.80722	D	1	D	0.57257	0.979	P	0.49999	0.628	D	0.91078	0.4897	10	0.72032	D	0.01	.	15.8882	0.79269	0.0:0.0:0.0:1.0	.	15	Q99453	PHX2B_HUMAN	G	15	ENSP00000226382:E15G	ENSP00000226382:E15G	E	-	2	0	PHOX2B	41445341	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.845000	0.86875	2.166000	0.68216	0.454000	0.30748	GAG	.	.		0.468	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2			C	41750584	T	C	41750584	3	2	103	1	0	0	0	0	1	0	0	0	11868	1551	54	2	912	2	PHOX2B	4	41750584	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	81949	41750584	149403692	313	14936										
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42588395	42588395	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcaagccttatgtttccaacAaaatcgtagagatgtctgtt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:42588395delA	ENST00000381668.5	-	9	924	c.693delT	c.(691-693)tttfs	p.F231fs	ATP8A1_ENST00000264449.10_Frame_Shift_Del_p.F231fs	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	231					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	TGTTTCCAACAAAATCGTAGA	0.393																																					p.V232fs		Atlas-INDEL	.											.	ATP8A1	206	.	0			c.694delG						.						125	118	120					4																	42588395		2203	4300	6503	SO:0001589	frameshift_variant	10396	exon9			.	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.693delT	chr4.hg19:g.42588395delA	ENSP00000371084:p.Phe231fs	182.0	0.0		179.0	11.0	NM_006095	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Frame_Shift_Del	DEL	ENST00000381668.5	hg19	CCDS3466.1																																																																																			.	.		0.393	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		-	42588395	A	-	42588395	7	5	103	1	0	1	0	1	0	0	0	0	1192	127	5	0	2917	0	ATP8A1	4	42588395	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	837811	42588395	148565881	314	14937										
GABRA4	2557	hgsc.bcm.edu	37	chr4	46979532	46979532	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cattcctgaagaaagtatcaGgggtccacactttcgttacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:46979532delG	ENST00000264318.3	-	4	1371	c.389delC	c.(388-390)cctfs	p.P130fs		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	130					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	GAAAGTATCAGGGGTCCACAC	0.348																																					p.P130fs	Ovarian(6;283 369 8234 12290 33402)	Atlas-INDEL	.											.	GABRA4	129	.	0			c.390delT						.						99	98	98					4																	46979532		2202	4300	6502	SO:0001589	frameshift_variant	2557	exon4			.		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4078	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 4"	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.389delC	chr4.hg19:g.46979532delG	ENSP00000264318:p.Pro130fs	182.0	0.0		192.0	12.0	NM_000809	Q8IYR7	Frame_Shift_Del	DEL	ENST00000264318.3	hg19	CCDS3473.1																																																																																			.	.		0.348	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			-	46979532	G	-	46979532	7	5	103	1	0	1	0	1	0	0	0	0	6171	1000	35	0	1299	0	GABRA4	4	46979532	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	4391137	46979532	144174744	315	14938										
ATP10D	57205	hgsc.bcm.edu	37	chr4	47574996	47574996	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctttccaacatgattctctaTtttttctataagaatgtggt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:47574996delT	ENST00000273859.3	+	18	3617	c.3348delT	c.(3346-3348)tatfs	p.Y1116fs		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1116					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						TGATTCTCTATTTTTTCTATA	0.438																																					p.Y1116fs		Atlas-INDEL	.											.	ATP10D	168	.	0			c.3347delA						.						209	202	204					4																	47574996		2203	4300	6503	SO:0001589	frameshift_variant	57205	exon18			.	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.3348delT	chr4.hg19:g.47574996delT	ENSP00000273859:p.Tyr1116fs	159.0	0.0		206.0	14.0	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Frame_Shift_Del	DEL	ENST00000273859.3	hg19	CCDS3476.1																																																																																			.	.		0.438	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		-	47574996	T	-	47574996	7	5	103	1	0	1	0	1	0	0	0	0	1118	1500	52	0	3414	0	ATP10D	4	47574996	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	595464	47574996	143579280	316	14939										
SCFD2	152579	hgsc.bcm.edu	37	chr4	54231690	54231690	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgttgcccatccattcacacAgcttctcctccagctgctcg	6	17	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:54231690A>G	ENST00000401642.3	-	1	552	c.419T>C	c.(418-420)cTg>cCg	p.L140P	SCFD2_ENST00000388940.4_Missense_Mutation_p.L140P	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	140					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)					breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CCATTCACACAGCTTCTCCTC	0.592																																					p.L140P		Atlas-SNP	.											.	SCFD2	78	.	0			c.T419C						.						93	76	82					4																	54231690		2203	4300	6503	SO:0001583	missense	152579	exon1			TCACACAGCTTCT	AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.419T>C	chr4.hg19:g.54231690A>G	ENSP00000384182:p.Leu140Pro	95.0	0.0		121.0	5.0	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	hg19	CCDS33984.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.460545	0.84317	.	.	ENSG00000184178	ENST00000401642;ENST00000388940	T;T	0.54071	0.61;0.59	5.51	5.51	0.81932	.	0.070367	0.64402	D	0.000018	T	0.66684	0.2814	L	0.59436	1.845	0.80722	D	1	D;D	0.76494	0.999;0.992	D;P	0.65233	0.933;0.816	T	0.69752	-0.5060	10	0.87932	D	0	.	13.6279	0.62178	1.0:0.0:0.0:0.0	.	140;140	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	P	140	ENSP00000384182:L140P;ENSP00000373592:L140P	ENSP00000373592:L140P	L	-	2	0	SCFD2	53926447	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.172000	0.89677	2.317000	0.78254	0.459000	0.35465	CTG	.	.		0.592	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540		G	54231690	A	G	54231690	3	3	103	1	0	0	0	0	1	0	0	0	13905	188	7	2	1671	2	SCFD2	4	54231690	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	6656694	54231690	136922586	317	14940										
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54265950	54265950	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaaactgcccttccatctacAaaagctgagtttacttctcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:54265950delA	ENST00000337488.6	+	10	953	c.759delA	c.(757-759)acafs	p.T253fs	FIP1L1_ENST00000507922.1_Frame_Shift_Del_p.T238fs|FIP1L1_ENST00000358575.5_Frame_Shift_Del_p.T238fs|FIP1L1_ENST00000306932.6_Frame_Shift_Del_p.T215fs|FIP1L1_ENST00000507166.1_Frame_Shift_Del_p.T253fs	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	253	Necessary for stimulating PAPOLA activity.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TTCCATCTACAAAAGCTGAGT	0.383			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.T253fs		Atlas-INDEL	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.758delC						.						167	164	165					4																	54265950		2203	4300	6503	SO:0001589	frameshift_variant	81608	exon10			.	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.759delA	chr4.hg19:g.54265950delA	ENSP00000336752:p.Thr253fs	116.0	0.0		138.0	11.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Frame_Shift_Del	DEL	ENST00000337488.6	hg19	CCDS3491.1																																																																																			.	.		0.383	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		-	54265950	A	-	54265950	7	5	103	1	0	1	0	1	0	0	0	0	5904	117	5	0	797	0	FIP1L1	4	54265950	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	34260	54265950	136888326	318	14941										
PPAT	5471	hgsc.bcm.edu	37	chr4	57267544	57267544	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ataaacatattcaaagatacAaaaagccactgggtttcctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:57267544delA	ENST00000264220.2	-	7	975	c.838delT	c.(838-840)tgtfs	p.C280fs	PPAT_ENST00000507648.1_5'Flank	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	280					'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	TCAAAGATACAAAAAGCCACT	0.348																																					p.C280fs		Atlas-INDEL	.											.	PPAT	41	.	0			c.839delG						.						184	188	187					4																	57267544		2203	4299	6502	SO:0001589	frameshift_variant	5471	exon7			.		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.838delT	chr4.hg19:g.57267544delA	ENSP00000264220:p.Cys280fs	190.0	0.0		179.0	11.0	NM_002703		Frame_Shift_Del	DEL	ENST00000264220.2	hg19	CCDS3505.1																																																																																			.	.		0.348	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		-	57267544	A	-	57267544	7	5	103	1	0	1	0	1	0	0	0	0	12311	130	5	0	735	0	PPAT	4	57267544	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3001594	57267544	133886732	319	14942										
SRP72	6731	hgsc.bcm.edu	37	chr4	57333820	57333820	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agatggcgagcggcggcagcGggggggtgtcagtacctgcg					rs17524437	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:57333820delG	ENST00000342756.5	+	1	740	c.19delG	c.(19-21)gggfs	p.G8fs	SRP72_ENST00000504757.1_Frame_Shift_Del_p.G8fs|SRP72_ENST00000510663.1_Frame_Shift_Del_p.G8fs	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	8					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					CGGCGGCAGCGGGGGGGTGTC	0.642																																					p.S6fs		Atlas-INDEL	.											.,1	SRP72	59	.	0			c.18delC						.						14	16	15					4																	57333820		2193	4293	6486	SO:0001589	frameshift_variant	6731	exon1			.	AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"Tetratricopeptide (TTC) repeat domain containing"	11303	protein-coding gene	gene with protein product		602122	"signal recognition particle 72kD"			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.19delG	chr4.hg19:g.57333820delG	ENSP00000342181:p.Gly8fs	135.0	0.0		134.0	10.0	NM_001267722	G5E9Z8|Q7Z3C0	Frame_Shift_Del	DEL	ENST00000342756.5	hg19	CCDS3506.1																																																																																			.	.		0.642	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7			-	57333820	G	-	57333820	7	5	103	1	0	1	0	1	0	0	0	0	15172	1116	39	0	21	0	SRP72	4	57333820	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	66276	57333820	133820456	320	14943										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66467955	66467955	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agttattctgattctgttccAtcactttgcatacttggtat	6	8	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:66467955A>G	ENST00000273854.3	-	3	914	c.314T>C	c.(313-315)aTg>aCg	p.M105T	EPHA5_ENST00000354839.4_Missense_Mutation_p.M105T|EPHA5_ENST00000511294.1_Missense_Mutation_p.M105T|EPHA5_ENST00000432638.2_Missense_Mutation_p.M105T	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	105	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						ATTCTGTTCCATCACTTTGCA	0.383										TSP Lung(17;0.13)																											p.M105T		Atlas-SNP	.											.	EPHA5	315	.	0			c.T314C						.						124	132	130					4																	66467955		2203	4300	6503	SO:0001583	missense	2044	exon3			TGTTCCATCACTT	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.314T>C	chr4.hg19:g.66467955A>G	ENSP00000273854:p.Met105Thr	41.0	0.0		32.0	4.0	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	hg19	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.554799	0.65425	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	5.68	5.68	0.88126	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.30262	0.0759	L	0.58101	1.795	0.80722	D	1	D;P;D;P	0.63880	0.993;0.766;0.991;0.87	D;P;D;P	0.81914	0.995;0.565;0.991;0.613	T	0.00763	-1.1576	10	0.52906	T	0.07	.	15.9206	0.79562	1.0:0.0:0.0:0.0	.	105;105;105;105	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	T	105	ENSP00000273854:M105T;ENSP00000389208:M105T;ENSP00000346899:M105T;ENSP00000427638:M105T	ENSP00000273854:M105T	M	-	2	0	EPHA5	66150550	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.339000	0.96797	2.166000	0.68216	0.533000	0.62120	ATG	.	.		0.383	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		G	66467955	A	G	66467955	3	3	103	1	0	0	0	0	1	0	0	0	5172	217	8	2	2863	2	EPHA5	4	66467955	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	9134135	66467955	124686321	321	14944										
STAP1	26228	hgsc.bcm.edu	37	chr4	68472044	68472044	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagtatggaagggagaagtgAaaagttgaagaaaaatccac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:68472044delA	ENST00000265404.2	+	9	939	c.857delA	c.(856-858)gaafs	p.E286fs	STAP1_ENST00000396225.1_Frame_Shift_Del_p.E286fs	NM_012108.2	NP_036240.1	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	286					intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	12						GGGAGAAGTGAAAAGTTGAAG	0.318																																					p.E286fs		Atlas-INDEL	.											.	STAP1	46	.	0			c.856delG						.						102	109	106					4																	68472044		2203	4300	6503	SO:0001589	frameshift_variant	26228	exon9			.	AB023483	CCDS3515.1	4q13.2	2013-02-14	2007-08-09		ENSG00000035720	ENSG00000035720		"SH2 domain containing"	24133	protein-coding gene	gene with protein product	"BCR downstream signaling 1"	604298				10518561, 10679268	Standard	NM_012108		Approved	STAP-1, BRDG1	uc003hde.4	Q9ULZ2	OTTHUMG00000129304	ENST00000265404.2:c.857delA	chr4.hg19:g.68472044delA	ENSP00000265404:p.Glu286fs	176.0	0.0		165.0	11.0	NM_012108	B2R980	Frame_Shift_Del	DEL	ENST00000265404.2	hg19	CCDS3515.1																																																																																			.	.		0.318	STAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251434.1	NM_012108		-	68472044	A	-	68472044	7	5	103	1	0	1	0	1	0	0	0	0	15267	246	9	0	891	0	STAP1	4	68472044	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2004089	68472044	122682232	322	14945										
CSN2	1447	hgsc.bcm.edu	37	chr4	70824773	70824773	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgtgaaaatttaccttgtaTtctgtaatagattcctacag	6	6	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:70824773T>C	ENST00000353151.3	-	3	104	c.93A>G	c.(91-93)gaA>gaG	p.E31E		NM_001891.2	NP_001882.1	P61201	CSN2_HUMAN	casein beta	0					cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|skin(2)	12						TTACCTTGTATTCTGTAATAG	0.219																																					p.E31E		Atlas-SNP	.											.	CSN2	30	.	0			c.A93G						.						10	10	10					4																	70824773		2115	4158	6273	SO:0001819	synonymous_variant	1447	exon3			CTTGTATTCTGTA	X17070	CCDS3532.1	4q21.1	2008-02-05			ENSG00000135222	ENSG00000135222			2447	protein-coding gene	gene with protein product		115460		CASB		1577486	Standard	NM_001891		Approved		uc003hes.4	P05814	OTTHUMG00000129409	ENST00000353151.3:c.93A>G	chr4.hg19:g.70824773T>C		32.0	0.0		41.0	4.0	NM_001891	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Silent	SNP	ENST00000353151.3	hg19	CCDS3532.1																																																																																			.	.		0.219	CSN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251565.1			C	70824773	T	C	70824773	2	2	103	1	0	0	0	0	0	0	0	1	3950	1490	52	2		2	CSN2	4	70824773	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2352729	70824773	120329503	323	14946										
PF4	5196	hgsc.bcm.edu	37	chr4	74847216	74847216	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggacggacctgggaggtggTcttcacacacaggcactgca	15	11	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:74847216T>C	ENST00000296029.3	-	2	306	c.136A>G	c.(136-138)Acc>Gcc	p.T46A		NM_002619.3	NP_002610.1	P02776	PLF4_HUMAN	platelet factor 4	46					blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|leukocyte chemotaxis (GO:0030595)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cytolysis (GO:0045918)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of MHC class II biosynthetic process (GO:0045347)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|platelet alpha granule lumen (GO:0031093)	chemokine activity (GO:0008009)|CXCR3 chemokine receptor binding (GO:0048248)|heparin binding (GO:0008201)			kidney(1)|lung(1)	2	Breast(15;0.00136)		all cancers(17;0.0034)|Lung(101;0.196)		Drotrecogin alfa(DB00055)	TGGGAGGTGGTCTTCACACAC	0.602																																					p.T46A		Atlas-SNP	.											.	PF4	13	.	0			c.A136G						.						68	61	63					4																	74847216		2203	4296	6499	SO:0001583	missense	5196	exon2			AGGTGGTCTTCAC	M25897	CCDS3562.1	4q12-q21	2012-10-02	2008-08-29		ENSG00000163737	ENSG00000163737			8861	protein-coding gene	gene with protein product	"chemokine (C-X-C motif) ligand 4"	173460	"platelet factor 4"			3622011	Standard	NM_002619		Approved	SCYB4, CXCL4	uc003hhi.3	P02776	OTTHUMG00000130009	ENST00000296029.3:c.136A>G	chr4.hg19:g.74847216T>C	ENSP00000296029:p.Thr46Ala	180.0	0.0		147.0	6.0	NM_002619	Q53X61|Q9UC64|Q9UC65	Missense_Mutation	SNP	ENST00000296029.3	hg19	CCDS3562.1	.	.	.	.	.	.	.	.	.	.	T	19.53	3.845795	0.71603	.	.	ENSG00000163737	ENST00000296029	T	0.05319	3.46	2.63	2.63	0.31362	CXC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.210963	0.43260	D	0.000587	T	0.22742	0.0549	M	0.89287	3.02	0.09310	N	1	D	0.69078	0.997	D	0.66196	0.942	T	0.02560	-1.1141	10	0.52906	T	0.07	.	7.0001	0.24805	0.0:0.0:0.0:1.0	.	46	P02776	PLF4_HUMAN	A	46	ENSP00000296029:T46A	ENSP00000296029:T46A	T	-	1	0	PF4	75066080	0.847000	0.29606	0.037000	0.18230	0.973000	0.67179	1.962000	0.40442	1.207000	0.43291	0.254000	0.18369	ACC	.	.		0.602	PF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252282.1			C	74847216	T	C	74847216	3	2	103	1	0	0	0	0	1	0	0	0	11761	1667	58	2	177	2	PF4	4	74847216	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4022443	74847216	116307060	324	14947										
CDKL2	8999	hgsc.bcm.edu	37	chr4	76551036	76551036	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgatttctcgcattgcaatcTttttaaccattttgtcatcg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:76551036delT	ENST00000429927.2	-	2	840	c.137delA	c.(136-138)aagfs	p.K46fs	CDKL2_ENST00000307465.4_Frame_Shift_Del_p.K46fs	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	46	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CATTGCAATCTTTTTAACCAT	0.313																																					p.K46fs		Atlas-INDEL	.											.	CDKL2	58	.	0			c.138delG						.						176	166	169					4																	76551036		2202	4299	6501	SO:0001589	frameshift_variant	8999	exon2			.	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"Cyclin-dependent kinases"	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.137delA	chr4.hg19:g.76551036delT	ENSP00000412365:p.Lys46fs	103.0	0.0		127.0	11.0	NM_003948	B2R695	Frame_Shift_Del	DEL	ENST00000429927.2	hg19	CCDS3570.1																																																																																			.	.		0.313	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		-	76551036	T	-	76551036	7	5	103	1	0	1	0	1	0	0	0	0	3156	1609	56	0	1384	0	CDKL2	4	76551036	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1703820	76551036	114603240	325	14948										
CCNI	10983	hgsc.bcm.edu	37	chr4	77977228	77977228	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acatccacagaaactgtctcTtgccaatacctttagtactg	5	12	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:77977228T>C	ENST00000237654.4	-	5	922	c.346A>G	c.(346-348)Aga>Gga	p.R116G	CCNI_ENST00000504697.1_5'UTR|CCNI_ENST00000537948.1_Missense_Mutation_p.R102G	NM_006835.2	NP_006826.1	Q14094	CCNI_HUMAN	cyclin I	116					regulation of cell cycle (GO:0051726)|spermatogenesis (GO:0007283)					NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9						AAACTGTCTCTTGCCAATACC	0.383																																					p.R116G		Atlas-SNP	.											.	CCNI	22	.	0			c.A346G						.						92	94	93					4																	77977228		2203	4300	6503	SO:0001583	missense	10983	exon5			TGTCTCTTGCCAA	D50310	CCDS3580.1	4q21.1	2014-07-03			ENSG00000118816	ENSG00000118816			1595	protein-coding gene	gene with protein product						7493655	Standard	NM_006835		Approved	CCNI1	uc003hkm.3	Q14094	OTTHUMG00000130106	ENST00000237654.4:c.346A>G	chr4.hg19:g.77977228T>C	ENSP00000237654:p.Arg116Gly	59.0	0.0		73.0	4.0	NM_006835	B2R6M0|B7Z6X4	Missense_Mutation	SNP	ENST00000237654.4	hg19	CCDS3580.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.583842	0.28268	.	.	ENSG00000118816	ENST00000237654;ENST00000537948;ENST00000505609	T;T;T	0.17691	2.75;2.75;2.26	6.16	6.16	0.99307	Cyclin, N-terminal (1);Cyclin-like (3);	0.241545	0.50627	D	0.000117	T	0.14743	0.0356	L	0.33792	1.035	0.36034	D	0.839633	B;B	0.23806	0.091;0.034	B;B	0.25987	0.065;0.038	T	0.19418	-1.0306	10	0.26408	T	0.33	-14.152	12.5783	0.56375	0.0:0.0:0.2408:0.7591	.	102;116	B7Z6X4;Q14094	.;CCNI_HUMAN	G	116;102;116	ENSP00000237654:R116G;ENSP00000441001:R102G;ENSP00000426467:R116G	ENSP00000237654:R116G	R	-	1	2	CCNI	78196252	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	1.651000	0.37302	2.367000	0.80283	0.528000	0.53228	AGA	.	.		0.383	CCNI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252412.2	NM_006835		C	77977228	T	C	77977228	3	2	103	1	0	0	0	0	1	0	0	0	2928	1617	56	2	799	2	CCNI	4	77977228	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1426192	77977228	113177048	326	14949										
CNOT6L	246175	hgsc.bcm.edu	37	chr4	78697453	78697453	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctaattctgcccagtgagaTtttttcccattggctacctc					rs200743940		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:78697453delT	ENST00000504123.1	-	2	229	c.99delA	c.(97-99)aaafs	p.K33fs	CNOT6L_ENST00000264903.4_Frame_Shift_Del_p.K33fs|CNOT6L_ENST00000506166.1_5'UTR			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	33	Required for interaction with CNOT1, CNOT3 and CNOT7.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						CCCAGTGAGATTTTTTCCCAT	0.373																																					p.S34fs		Atlas-INDEL	.											.	CNOT6L	57	.	0			c.100delT						.						125	120	121					4																	78697453		1812	4081	5893	SO:0001589	frameshift_variant	246175	exon2			.	AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.99delA	chr4.hg19:g.78697453delT	ENSP00000424896:p.Lys33fs	123.0	0.0		128.0	11.0	NM_144571	Q9UF92	Frame_Shift_Del	DEL	ENST00000504123.1	hg19																																																																																				.	.		0.373	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1			-	78697453	T	-	78697453	7	5	103	1	0	1	0	1	0	0	0	0	3625	1490	52	0	1612	0	CNOT6L	4	78697453	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	720225	78697453	112456823	327	14950										
HNRPDL	9987	hgsc.bcm.edu	37	chr4	83348625	83348625	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggtatctgctttctaacaaTttttttactggctcttcatc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:83348625delT	ENST00000295470.5	-	4	1042	c.867delA	c.(865-867)aaafs	p.K289fs	HNRNPDL_ENST00000602300.1_Frame_Shift_Del_p.K170fs|HNRNPDL_ENST00000502762.1_Frame_Shift_Del_p.K289fs|HNRNPDL_ENST00000514511.1_5'UTR|HNRNPDL_ENST00000349655.4_Frame_Shift_Del_p.K170fs	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	289	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										TTTCTAACAATTTTTTTACTG	0.289																																					p.L290fs		Atlas-INDEL	.											.	HNRPDL	35	.	0			c.868delT						.						74	75	75					4																	83348625		2202	4299	6501	SO:0001589	frameshift_variant	9987	exon4			.	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"RNA binding motif (RRM) containing"	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.867delA	chr4.hg19:g.83348625delT	ENSP00000295470:p.Lys289fs	135.0	0.0		125.0	11.0	NM_031372	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Frame_Shift_Del	DEL	ENST00000295470.5	hg19	CCDS3593.1																																																																																			.	.		0.289	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463		-	83348625	T	-	83348625	7	5	103	1	0	1	0	1	0	0	0	0	7285	1490	52	0	411	0	HNRPDL	4	83348625	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	4651172	83348625	107805651	328	14951										
CDS1	1040	hgsc.bcm.edu	37	chr4	85555086	85555086	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaaaatctgtttgaaggcaTgatatggtaaggcaacagaa	10	6	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:85555086T>C	ENST00000295887.5	+	7	1139	c.716T>C	c.(715-717)aTg>aCg	p.M239T		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> K (in prostate cancer; germline mutation). {ECO:0000269|PubMed:12533788}.		cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		TTTGAAGGCATGATATGGTAA	0.353																																					p.M239T		Atlas-SNP	.											.	CDS1	58	.	0			c.T716C						.						169	139	149					4																	85555086		2203	4300	6503	SO:0001583	missense	1040	exon7			AAGGCATGATATG	U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.716T>C	chr4.hg19:g.85555086T>C	ENSP00000295887:p.Met239Thr	70.0	0.0		89.0	4.0	NM_001263	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000295887.5	hg19	CCDS3608.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.226338	0.58668	.	.	ENSG00000163624	ENST00000295887	T	0.42131	0.98	5.96	5.96	0.96718	.	0.035649	0.85682	D	0.000000	T	0.42494	0.1205	L	0.50919	1.6	0.80722	D	1	B	0.32968	0.392	B	0.33960	0.173	T	0.39418	-0.9615	10	0.72032	D	0.01	-25.9657	16.4221	0.83766	0.0:0.0:0.0:1.0	.	239	Q92903	CDS1_HUMAN	T	239	ENSP00000295887:M239T	ENSP00000295887:M239T	M	+	2	0	CDS1	85774110	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.283000	0.76528	0.477000	0.44152	ATG	.	.		0.353	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2			C	85555086	T	C	85555086	3	2	103	1	0	0	0	0	1	0	0	0	3179	1464	51	2	742	2	CDS1	4	85555086	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2206461	85555086	105599190	329	14952										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90816715	90816715	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagccaaagaactgactaccAaaaatcaaatttcgaaacaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:90816715delA	ENST00000394980.1	+	2	912	c.593delA	c.(592-594)caafs	p.Q198fs	MMRN1_ENST00000264790.2_Frame_Shift_Del_p.Q198fs|MMRN1_ENST00000394981.1_Frame_Shift_Del_p.Q164fs			Q13201	MMRN1_HUMAN	multimerin 1	198					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		ACTGACTACCAAAAATCAAAT	0.443																																					p.Q198fs		Atlas-INDEL	.											.	MMRN1	174	.	0			c.592delC						.						32	33	33					4																	90816715		2203	4300	6503	SO:0001589	frameshift_variant	22915	exon1			.	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.593delA	chr4.hg19:g.90816715delA	ENSP00000378431:p.Gln198fs	73.0	0.0		76.0	11.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Frame_Shift_Del	DEL	ENST00000394980.1	hg19	CCDS3635.1																																																																																			.	.		0.443	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		-	90816715	A	-	90816715	7	5	103	1	0	1	0	1	0	0	0	0	9679	130	5	0	595	0	MMRN1	4	90816715	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	5261629	90816715	100337561	330	14953										
SMARCAD1	56916	hgsc.bcm.edu	37	chr4	95129594	95129594	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctttgagaaaaggaataagAttgaggaagcgcccgaagca	13	6	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:95129594A>G	ENST00000354268.4	+	2	122	c.49A>G	c.(49-51)Att>Gtt	p.I17V	SMARCAD1_ENST00000457823.2_Missense_Mutation_p.I17V|RP11-363G15.2_ENST00000501965.2_lincRNA			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	17					ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		AAGGAATAAGATTGAGGAAGC	0.473																																					p.I17V		Atlas-SNP	.											.	SMARCAD1	97	.	0			c.A49G						.						93	102	98					4																	95129594		2203	4300	6503	SO:0001583	missense	56916	exon2			AATAAGATTGAGG	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.49A>G	chr4.hg19:g.95129594A>G	ENSP00000346217:p.Ile17Val	107.0	0.0		90.0	4.0	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	hg19	CCDS3639.1	.	.	.	.	.	.	.	.	.	.	A	10.03	1.240084	0.22711	.	.	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000536267;ENST00000354268	T;T;T	0.44482	0.92;0.92;0.92	4.83	-0.286	0.12862	.	0.249386	0.20883	N	0.083966	T	0.21468	0.0517	N	0.14661	0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.03534	-1.1027	10	0.39692	T	0.17	-4.0883	7.4486	0.27225	0.6081:0.0:0.3919:0.0	.	17;17	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	V	17	ENSP00000351947:I17V;ENSP00000415576:I17V;ENSP00000346217:I17V	ENSP00000346217:I17V	I	+	1	0	SMARCAD1	95348617	0.054000	0.20591	0.988000	0.46212	0.620000	0.37586	0.179000	0.16840	0.059000	0.16252	0.459000	0.35465	ATT	.	.		0.473	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		G	95129594	A	G	95129594	3	3	103	1	0	0	0	0	1	0	0	0	14787	333	12	2	51	2	SMARCAD1	4	95129594	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	4312879	95129594	96024682	331	14954										
ADH1B	125	hgsc.bcm.edu	37	chr4	100231959	100231959	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggtcaaatccttcatttaTtttttcaaaaggtaaaacat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:100231959delT	ENST00000305046.8	-	8	1133	c.1066delA	c.(1066-1068)atafs	p.I356fs	ADH1B_ENST00000394887.3_Frame_Shift_Del_p.I316fs			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	356					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	CCTTCATTTATTTTTTCAAAA	0.348																																					p.I356fs		Atlas-INDEL	.											.	ADH1B	68	.	0			c.1067delT						.						96	96	96					4																	100231959		2203	4300	6503	SO:0001589	frameshift_variant	125	exon8			.	AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"Alcohol dehydrogenases"	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.1066delA	chr4.hg19:g.100231959delT	ENSP00000306606:p.Ile356fs	166.0	0.0		202.0	14.0	NM_000668	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Frame_Shift_Del	DEL	ENST00000305046.8	hg19	CCDS34033.1																																																																																			.	.		0.348	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668		-	100231959	T	-	100231959	7	5	103	1	0	1	0	1	0	0	0	0	308	1493	52	0	69	0	ADH1B	4	100231959	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5102365	100231959	90922317	332	14955										
DDIT4L	115265	hgsc.bcm.edu	37	chr4	101108955	101108955	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaagcgacctctactaaagAaaaagtccctgaagctagtc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:101108955delA	ENST00000273990.2	-	3	675	c.461delT	c.(460-462)ttcfs	p.F155fs	RP11-588P8.1_ENST00000515782.1_RNA|RP11-15B17.1_ENST00000515026.1_RNA	NM_145244.3	NP_660287.1	Q96D03	DDT4L_HUMAN	DNA-damage-inducible transcript 4-like	155					negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(2)	12				OV - Ovarian serous cystadenocarcinoma(123;5.75e-09)		TCTACTAAAGAAAAAGTCCCT	0.428																																					p.F154fs		Atlas-INDEL	.											.	DDIT4L	33	.	0			c.462delC						.						90	92	91					4																	101108955		2203	4300	6503	SO:0001589	frameshift_variant	115265	exon3			.	BC013592	CCDS34036.1	4q23	2008-02-05				ENSG00000145358			30555	protein-coding gene	gene with protein product	"regulated in development and DNA damage response 2", " similar to Smhs1 protein"	607730				12477932	Standard	NM_145244		Approved	REDD2, Rtp801L	uc003hvq.3	Q96D03		ENST00000273990.2:c.461delT	chr4.hg19:g.101108955delA	ENSP00000354830:p.Phe155fs	178.0	0.0		181.0	13.0	NM_145244	B2R7C3	Frame_Shift_Del	DEL	ENST00000273990.2	hg19	CCDS34036.1																																																																																			.	.		0.428	DDIT4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363423.1	NM_145244		-	101108955	A	-	101108955	7	5	103	1	0	1	0	1	0	0	0	0	4334	246	9	0	124	0	DDIT4L	4	101108955	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	876996	101108955	90045321	333	14956										
BANK1	55024	hgsc.bcm.edu	37	chr4	102946503	102946503	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcccactagaggttggcagTgagagttctgaagaccagta	13	8	1	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:102946503T>C	ENST00000322953.4	+	9	1705	c.1431T>C	c.(1429-1431)agT>agC	p.S477S	BANK1_ENST00000510950.1_3'UTR|BANK1_ENST00000508653.1_Silent_p.S344S|BANK1_ENST00000428908.1_Silent_p.S344S|BANK1_ENST00000504592.1_Silent_p.S462S|BANK1_ENST00000444316.2_Silent_p.S447S|RP11-498M5.2_ENST00000505091.1_RNA	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	477					B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		AGGTTGGCAGTGAGAGTTCTG	0.483																																					p.S477S		Atlas-SNP	.											.	BANK1	95	.	0			c.T1431C						.						215	177	190					4																	102946503		2203	4300	6503	SO:0001819	synonymous_variant	55024	exon9			TGGCAGTGAGAGT	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.1431T>C	chr4.hg19:g.102946503T>C		107.0	0.0		91.0	4.0	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Silent	SNP	ENST00000322953.4	hg19	CCDS34038.1																																																																																			.	.		0.483	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		C	102946503	T	C	102946503	2	2	103	1	0	0	0	0	0	0	0	1	1309	1693	59	2		2	BANK1	4	102946503	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1837548	102946503	88207773	334	14957										
PAPSS1	9061	hgsc.bcm.edu	37	chr4	108615045	108615045	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttcaggactaaagccaagaTttttattgagaccttgacga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:108615045delT	ENST00000265174.4	-	3	565	c.293delA	c.(292-294)aatfs	p.N98fs	PAPSS1_ENST00000511304.1_Intron	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	98					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		AAAGCCAAGATTTTTATTGAG	0.443																																					p.N98fs		Atlas-INDEL	.											.	PAPSS1	57	.	0			c.294delT						.						140	125	130					4																	108615045		2203	4300	6503	SO:0001589	frameshift_variant	9061	exon3			.	Y10387	CCDS3676.1	4q24	2012-07-13			ENSG00000138801	ENSG00000138801	2.7.7.4, 2.7.1.25		8603	protein-coding gene	gene with protein product		603262				9576487, 9771708	Standard	NM_005443		Approved	ATPSK1, PAPSS	uc003hyk.3	O43252	OTTHUMG00000131210	ENST00000265174.4:c.293delA	chr4.hg19:g.108615045delT	ENSP00000265174:p.Asn98fs	102.0	0.0		107.0	11.0	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Frame_Shift_Del	DEL	ENST00000265174.4	hg19	CCDS3676.1																																																																																			.	.		0.443	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2			-	108615045	T	-	108615045	7	5	103	1	0	1	0	1	0	0	0	0	11443	1493	52	0	1621	0	PAPSS1	4	108615045	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5668542	108615045	82539231	335	14958										
RRH	10692	hgsc.bcm.edu	37	chr4	110758642	110758642	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttgcgataaattttattgtgCccttgacagtgatgttttac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:110758642delC	ENST00000317735.4	+	5	635	c.601delC	c.(601-603)cccfs	p.P201fs		NM_006583.2	NP_006574.1	O14718	OPSX_HUMAN	retinal pigment epithelium-derived rhodopsin homolog	201					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	12		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)		TTTTATTGTGCCCTTGACAGT	0.393																																					p.V200fs		Atlas-INDEL	.											.	RRH	24	.	0			c.600delG						.						182	154	163					4																	110758642		2203	4300	6503	SO:0001589	frameshift_variant	10692	exon5			.	AF012270	CCDS3687.1	4q25	2012-08-08			ENSG00000180245	ENSG00000180245		"GPCR / Class A : Opsin receptors"	10450	protein-coding gene	gene with protein product	"peropsin"	605224				9275222	Standard	NM_006583		Approved	peropsin	uc003hzv.3	O14718	OTTHUMG00000132045	ENST00000317735.4:c.601delC	chr4.hg19:g.110758642delC	ENSP00000314992:p.Pro201fs	198.0	0.0		173.0	11.0	NM_006583	A1A4V2|Q7RTS4	Frame_Shift_Del	DEL	ENST00000317735.4	hg19	CCDS3687.1																																																																																			.	.		0.393	RRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255066.1	NM_006583		-	110758642	C	-	110758642	7	5	103	1	0	1	0	1	0	0	0	0	13695	739	26	0	619	0	RRH	4	110758642	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2143597	110758642	80395634	336	14959										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113333009	113333009	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgagggcctccatcctcgcTcgggactgtgcggctgcggc	15	15	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:113333009T>C	ENST00000458497.1	+	5	582	c.303T>C	c.(301-303)gcT>gcC	p.A101A	ALPK1_ENST00000177648.9_Silent_p.A101A|ALPK1_ENST00000505912.1_3'UTR|ALPK1_ENST00000504176.2_Silent_p.A23A	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	101							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CCATCCTCGCTCGGGACTGTG	0.632																																					p.A101A		Atlas-SNP	.											.	ALPK1	125	.	0			c.T303C						.						38	37	37					4																	113333009		2203	4300	6503	SO:0001819	synonymous_variant	80216	exon5			CCTCGCTCGGGAC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.303T>C	chr4.hg19:g.113333009T>C		155.0	0.0		138.0	6.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Silent	SNP	ENST00000458497.1	hg19	CCDS3697.1																																																																																			.	.		0.632	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		C	113333009	T	C	113333009	2	2	103	1	0	0	0	0	0	0	0	1	544	1538	54	2		2	ALPK1	4	113333009	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2574367	113333009	77821267	337	14960										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113356354	113356354	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgaactgtggacggcccagGaaactattgtctatttgggg	13	8	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:113356354G>A	ENST00000458497.1	+	12	3364	c.3085G>A	c.(3085-3087)Gaa>Aaa	p.E1029K	ALPK1_ENST00000177648.9_Missense_Mutation_p.E1029K|ALPK1_ENST00000504176.2_Missense_Mutation_p.E951K	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	1029	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		GACGGCCCAGGAAACTATTGT	0.353																																					p.E1029K		Atlas-SNP	.											.	ALPK1	125	.	0			c.G3085A						.						130	155	147					4																	113356354		2203	4300	6503	SO:0001583	missense	80216	exon12			GCCCAGGAAACTA	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.3085G>A	chr4.hg19:g.113356354G>A	ENSP00000398048:p.Glu1029Lys	130.0	0.0		120.0	20.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	hg19	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.653679	0.88056	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.07114	3.22;3.22;3.22	5.84	5.84	0.93424	MHCK/EF2 kinase (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.33614	0.0869	M	0.78801	2.425	0.52099	D	0.999943	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.995;0.994	T	0.01301	-1.1391	10	0.62326	D	0.03	-29.2293	20.1393	0.98055	0.0:0.0:1.0:0.0	.	951;951;1029	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	K	1029;1029;951	ENSP00000398048:E1029K;ENSP00000177648:E1029K;ENSP00000426044:E951K	ENSP00000177648:E1029K	E	+	1	0	ALPK1	113575803	1.000000	0.71417	1.000000	0.80357	0.513000	0.34164	8.521000	0.90569	2.759000	0.94783	0.563000	0.77884	GAA	.	.		0.353	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		A	113356354	G	A	113356354	3	1	103	1	0	0	0	0	1	0	0	0	544	1175	41	3	3123	3	ALPK1	4	113356354	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	23345	113356354	77797922	338	14961										
LARP7	51574	hgsc.bcm.edu	37	chr4	113565838	113565838	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcacaggaatggaaactgaaAgtggaaatcaggaaaaggta	12	4	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:113565838A>G	ENST00000344442.5	+	2	291	c.13A>G	c.(13-15)Agt>Ggt	p.S5G	LARP7_ENST00000509061.1_Missense_Mutation_p.S12G|MIR302B_ENST00000505215.1_RNA|MIR302B_ENST00000510655.1_RNA|LARP7_ENST00000324052.6_Missense_Mutation_p.S5G|MIR302B_ENST00000509938.1_RNA	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	5					RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		GGAAACTGAAAGTGGAAATCA	0.308																																					p.S12G		Atlas-SNP	.											.	LARP7	54	.	0			c.A34G						.						47	44	45					4																	113565838		1802	4067	5869	SO:0001583	missense	51574	exon4			ACTGAAAGTGGAA	AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	24912	protein-coding gene	gene with protein product	"P-TEFb-interaction protein for 7SK stability"	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.13A>G	chr4.hg19:g.113565838A>G	ENSP00000344950:p.Ser5Gly	47.0	0.0		45.0	4.0	NM_001267039	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Missense_Mutation	SNP	ENST00000344442.5	hg19	CCDS3701.2	.	.	.	.	.	.	.	.	.	.	A	9.573	1.121416	0.20877	.	.	ENSG00000174720	ENST00000344442;ENST00000509061;ENST00000508577;ENST00000513553;ENST00000505034;ENST00000324052;ENST00000507443	T;T;T;T;T;T;T	0.49139	2.24;2.21;0.93;0.79;2.25;2.24;0.93	5.17	-4.86	0.03132	.	1.490870	0.03334	N	0.193878	T	0.33118	0.0852	L	0.40543	1.245	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16335	-1.0406	10	0.41790	T	0.15	-1.3374	2.402	0.04404	0.3838:0.2079:0.3069:0.1014	.	5;5	D6RFF0;Q4G0J3	.;LARP7_HUMAN	G	5;12;5;5;5;5;5	ENSP00000344950:S5G;ENSP00000422626:S12G;ENSP00000426646:S5G;ENSP00000422013:S5G;ENSP00000421541:S5G;ENSP00000314311:S5G;ENSP00000421963:S5G	ENSP00000314311:S5G	S	+	1	0	LARP7	113785287	0.009000	0.17119	0.026000	0.17262	0.973000	0.67179	0.199000	0.17237	-0.617000	0.05664	-0.328000	0.08392	AGT	.	.		0.308	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648		G	113565838	A	G	113565838	3	3	103	1	0	0	0	0	1	0	0	0	8642	72	3	2	15	2	LARP7	4	113565838	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	209484	113565838	77588438	339	14962										
ANK2	287	hgsc.bcm.edu	37	chr4	114278579	114278579	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaaaatgtcccttcccaatcTtttttctctagtgaagaaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:114278579delT	ENST00000357077.4	+	38	8858	c.8805delT	c.(8803-8805)tctfs	p.S2935fs	ANK2_ENST00000264366.6_Frame_Shift_Del_p.S2902fs|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2935					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CTTCCCAATCTTTTTTCTCTA	0.398																																					p.S2935fs		Atlas-INDEL	.											.	ANK2	576	.	0			c.8804delC						.						170	178	175					4																	114278579		2203	4300	6503	SO:0001589	frameshift_variant	287	exon38			.	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.8805delT	chr4.hg19:g.114278579delT	ENSP00000349588:p.Ser2935fs	130.0	0.0		166.0	10.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Frame_Shift_Del	DEL	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.		0.398	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		-	114278579	T	-	114278579	7	5	103	1	0	1	0	1	0	0	0	0	621	1596	56	0	9020	0	ANK2	4	114278579	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	712741	114278579	76875697	340	14963										
NDST3	9348	hgsc.bcm.edu	37	chr4	119035960	119035960	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ataatatttccccccctaaaGgaactgaagaggaagatgaa	8	8	0	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:119035960G>A	ENST00000296499.5	+	4	1472		c.e4-1		NDST3_ENST00000433996.2_Intron	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3						heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						CCCCCCTAAAGGAACTGAAGA	0.398																																					.		Atlas-SNP	.											.	NDST3	107	.	0			c.1070-1G>A						.						129	120	123					4																	119035960		2203	4300	6503	SO:0001630	splice_region_variant	9348	exon4			CCTAAAGGAACTG	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.1070-1G>A	chr4.hg19:g.119035960G>A		176.0	0.0		162.0	7.0	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Splice_Site	SNP	ENST00000296499.5	hg19	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.920286	0.73098	.	.	ENSG00000164100	ENST00000296499	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9278	0.97110	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NDST3	119255408	1.000000	0.71417	0.997000	0.53966	0.662000	0.39071	9.695000	0.98691	2.770000	0.95276	0.650000	0.86243	.	.	.		0.398	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784	Intron	A	119035960	G	A	119035960	5	1	103	1	0	0	0	0	0	0	1	0	10266	1014	35	3	1079	3	NDST3	4	119035960	Splice_Site	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	4757381	119035960	72118316	341	14964										
SEC24D	9871	hgsc.bcm.edu	37	chr4	119736614	119736614	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtccgccttaccctgctgcGgaggatatccagcacccaag	10	15	0	0	rs138326987		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:119736614G>T	ENST00000280551.6	-	5	903	c.665C>A	c.(664-666)cCg>cAg	p.P222Q	SEC24D_ENST00000419654.2_5'UTR|SEC24D_ENST00000379735.5_Missense_Mutation_p.P222Q			O94855	SC24D_HUMAN	SEC24 family member D	222	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						ACCCTGCTGCGGAGGATATCC	0.557																																					p.P222Q		Atlas-SNP	.											SEC24D,NS,carcinoma,0,1	SEC24D	96	.	0			c.C665A						.						73	71	71					4																	119736614		2203	4300	6503	SO:0001583	missense	9871	exon5			TGCTGCGGAGGAT	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"SEC24 (S. cerevisiae) related gene family, member D", "SEC24 family, member D (S. cerevisiae)"			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.665C>A	chr4.hg19:g.119736614G>T	ENSP00000280551:p.Pro222Gln	71.0	0.0		86.0	0.0	NM_014822	Q8IYI7	Missense_Mutation	SNP	ENST00000280551.6	hg19	CCDS3710.1	.	.	.	.	.	.	.	.	.	.	G	9.325	1.059060	0.19987	.	.	ENSG00000150961	ENST00000280551;ENST00000379735	T;T	0.19669	2.13;2.13	5.71	3.99	0.46301	.	0.285018	0.40385	N	0.001109	T	0.17152	0.0412	L	0.37750	1.13	0.80722	D	1	B;B	0.16166	0.016;0.008	B;B	0.17722	0.019;0.007	T	0.03268	-1.1054	10	0.46703	T	0.11	-4.68	10.2628	0.43436	0.1565:0.0:0.8435:0.0	.	222;222	O94855-2;O94855	.;SC24D_HUMAN	Q	222	ENSP00000280551:P222Q;ENSP00000369059:P222Q	ENSP00000280551:P222Q	P	-	2	0	SEC24D	119956062	0.998000	0.40836	0.266000	0.24541	0.145000	0.21501	3.054000	0.49908	0.778000	0.33520	-0.150000	0.13652	CCG	.	G|1.000;A|0.000		0.557	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4			T	119736614	G	T	119736614	3	4	103	1	0	0	0	0	1	0	0	0	14012	1116	39	1	2509	1	SEC24D	4	119736614	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	700654	119736614	71417662	342	14965										
CCNA2	890	hgsc.bcm.edu	37	chr4	122742218	122742218	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcttttcatcttctaatatAattgacatgtccatagtatg	6	7	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:122742218A>C	ENST00000274026.5	-	3	789	c.486T>G	c.(484-486)atT>atG	p.I162M		NM_001237.3	NP_001228	P20248	CCNA2_HUMAN	cyclin A2	162					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|organ regeneration (GO:0031100)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|response to estradiol (GO:0032355)|response to glucagon (GO:0033762)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	12						CTTCTAATATAATTGACATGT	0.343																																					p.I162M		Atlas-SNP	.											CCNA2,colon,carcinoma,0,1	CCNA2	30	.	0			c.T486G						.						196	187	190					4																	122742218		2203	4299	6502	SO:0001583	missense	890	exon3			TAATATAATTGAC		CCDS3723.1	4q27	2012-07-12			ENSG00000145386	ENSG00000145386			1578	protein-coding gene	gene with protein product		123835		CCNA, CCN1		1675006	Standard	NM_001237		Approved		uc003iec.4	P20248	OTTHUMG00000133072	ENST00000274026.5:c.486T>G	chr4.hg19:g.122742218A>C	ENSP00000274026:p.Ile162Met	149.0	0.0		156.0	0.0	NM_001237	A8K7B6|Q2M3U6|Q4W5P4|Q6LER8	Missense_Mutation	SNP	ENST00000274026.5	hg19	CCDS3723.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.121146	0.37436	.	.	ENSG00000145386	ENST00000274026	T	0.15256	2.44	5.86	3.55	0.40652	.	0.665471	0.12795	U	0.438573	T	0.14787	0.0357	L	0.58101	1.795	0.32550	N	0.532438	B	0.12630	0.006	B	0.12156	0.007	T	0.18429	-1.0337	10	0.33940	T	0.23	.	1.6245	0.02720	0.5393:0.1859:0.0894:0.1854	.	162	P20248	CCNA2_HUMAN	M	162	ENSP00000274026:I162M	ENSP00000274026:I162M	I	-	3	3	CCNA2	122961668	0.997000	0.39634	0.569000	0.28460	0.977000	0.68977	1.504000	0.35726	1.038000	0.40049	0.482000	0.46254	ATT	.	.		0.343	CCNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256712.2	NM_001237		C	122742218	A	C	122742218	3	2	103	1	0	0	0	0	1	0	0	0	2912	358	13	5	836	5	CCNA2	4	122742218	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	3005604	122742218	68412058	343	14966										
NUDT6	11162	hgsc.bcm.edu	37	chr4	123833749	123833749	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcgatcttgtacaaccagtaTttttctagtactttcatcaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:123833749delT	ENST00000304430.5	-	3	505	c.472delA	c.(472-474)atafs	p.I158fs	NUDT6_ENST00000339154.2_5'UTR|NUDT6_ENST00000502270.1_5'UTR	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	158	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)			endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						ACAACCAGTATTTTTCTAGTA	0.289																																					p.I158fs		Atlas-INDEL	.											.	NUDT6	50	.	0			c.473delT						.						58	59	59					4																	123833749		1800	4056	5856	SO:0001589	frameshift_variant	11162	exon3			.	AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"Nudix motif containing"	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.472delA	chr4.hg19:g.123833749delT	ENSP00000306070:p.Ile158fs	123.0	0.0		182.0	11.0	NM_007083	A8K756|O95097|Q9UQD9	Frame_Shift_Del	DEL	ENST00000304430.5	hg19	CCDS43268.1																																																																																			.	.		0.289	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083		-	123833749	T	-	123833749	7	5	103	1	0	1	0	1	0	0	0	0	10752	1493	52	0	490	0	NUDT6	4	123833749	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1091531	123833749	67320527	344	14967										
PCDH18	54510	hgsc.bcm.edu	37	chr4	138452456	138452456	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attcagatctaagagcaaagTgccaaccggggagttttcta	10	8	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:138452456T>C	ENST00000344876.4	-	1	1173	c.787A>G	c.(787-789)Act>Gct	p.T263A	PCDH18_ENST00000507846.1_Missense_Mutation_p.T43A|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000412923.2_Missense_Mutation_p.T263A	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	263	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					AAGAGCAAAGTGCCAACCGGG	0.413																																					p.T263A		Atlas-SNP	.											PCDH18,NS,carcinoma,0,1	PCDH18	229	.	0			c.A787G						.						61	64	63					4																	138452456		2203	4300	6503	SO:0001583	missense	54510	exon1			GCAAAGTGCCAAC	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.787A>G	chr4.hg19:g.138452456T>C	ENSP00000355082:p.Thr263Ala	47.0	0.0		40.0	3.0	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	hg19	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.850980	0.51270	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846	T;T;T	0.57107	0.42;0.42;0.42	5.7	5.7	0.88788	Cadherin (4);Cadherin-like (1);	0.000000	0.42420	U	0.000710	T	0.63792	0.2541	L	0.58969	1.84	0.80722	D	1	P;P;P	0.47762	0.835;0.57;0.9	P;B;P	0.53518	0.728;0.253;0.484	T	0.66889	-0.5809	10	0.72032	D	0.01	.	15.9803	0.80105	0.0:0.0:0.0:1.0	.	43;263;263	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	A	263;263;43	ENSP00000355082:T263A;ENSP00000390688:T263A;ENSP00000425903:T43A	ENSP00000355082:T263A	T	-	1	0	PCDH18	138671906	1.000000	0.71417	0.994000	0.49952	0.714000	0.41099	6.143000	0.71756	2.170000	0.68504	0.455000	0.32223	ACT	.	.		0.413	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		C	138452456	T	C	138452456	3	2	103	1	0	0	0	0	1	0	0	0	11522	1696	59	2	2636	2	PCDH18	4	138452456	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	14618707	138452456	52701820	345	14968										
SCOC	60592	hgsc.bcm.edu	37	chr4	141302170	141302170	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaatctgaagctaaaatcagAaaaccaagttcttggacaat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:141302170delA	ENST00000608372.1	+	4	419	c.392delA	c.(391-393)gaafs	p.E131fs	SCOC_ENST00000394205.3_Frame_Shift_Del_p.E94fs|SCOC_ENST00000394201.4_Frame_Shift_Del_p.E54fs|SCOC_ENST00000512749.1_Frame_Shift_Del_p.E54fs|SCOC_ENST00000502535.1_Frame_Shift_Del_p.E54fs|SCOC_ENST00000510586.1_Frame_Shift_Del_p.E54fs|SCOC_ENST00000338517.4_Frame_Shift_Del_p.E94fs|SCOC_ENST00000506597.1_Frame_Shift_Del_p.E103fs|SCOC_ENST00000394203.3_Frame_Shift_Del_p.E94fs|SCOC_ENST00000506322.1_Frame_Shift_Del_p.E54fs			Q9UIL1	SCOC_HUMAN	short coiled-coil protein	131					positive regulation of macroautophagy (GO:0016239)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5	all_hematologic(180;0.162)					CTAAAATCAGAAAACCAAGTT	0.313																																					p.E131fs		Atlas-INDEL	.											.	SCOC	11	.	0			c.391delG						.						51	56	55					4																	141302170		2203	4298	6501	SO:0001589	frameshift_variant	60592	exon4			.	AK027797	CCDS3750.1, CCDS54806.1, CCDS54807.1	4q28.3	2014-05-22	2003-03-19		ENSG00000153130	ENSG00000153130			20335	protein-coding gene	gene with protein product			"short coiled coil protein"			11303027	Standard	NM_032547		Approved	HRIHFB2072, SCOCO	uc011che.1	Q9UIL1	OTTHUMG00000133416	ENST00000608372.1:c.392delA	chr4.hg19:g.141302170delA	ENSP00000477352:p.Glu131fs	161.0	0.0		165.0	11.0	NM_001153484	B7WPH7|D3DNY7|E9PB65|Q6P5T9|Q7L2Y0|Q7Z4P2|Q96JY9|Q9BZB2	Frame_Shift_Del	DEL	ENST00000608372.1	hg19	CCDS54806.1																																																																																			.	.		0.313	SCOC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257274.2			-	141302170	A	-	141302170	7	5	103	1	0	1	0	1	0	0	0	0	13948	246	9	0	480	0	SCOC	4	141302170	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2849714	141302170	49852106	346	14969										
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141560268	141560268	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagcataaagttcttccagcTcatcaatggtaaaggaagtt	9	7	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:141560268T>C	ENST00000442267.2	-	15	2551	c.2477A>G	c.(2476-2478)gAg>gGg	p.E826G		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	826							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				TTCTTCCAGCTCATCAATGGT	0.348																																					p.E826G		Atlas-SNP	.											.	TBC1D9	198	.	0			c.A2477G						.						48	43	45					4																	141560268		1849	4086	5935	SO:0001583	missense	23158	exon15			TCCAGCTCATCAA	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.2477A>G	chr4.hg19:g.141560268T>C	ENSP00000411197:p.Glu826Gly	90.0	0.0		91.0	5.0	NM_015130	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	hg19	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845946	0.91277	.	.	ENSG00000109436	ENST00000442267	T	0.37235	1.21	5.69	5.69	0.88448	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.71921	0.3397	H	0.96547	3.84	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	T	0.82137	-0.0606	10	0.87932	D	0	-11.2177	15.9538	0.79865	0.0:0.0:0.0:1.0	.	826	Q6ZT07	TBCD9_HUMAN	G	826	ENSP00000411197:E826G	ENSP00000411197:E826G	E	-	2	0	TBC1D9	141779718	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.967000	0.87967	2.163000	0.67991	0.533000	0.62120	GAG	.	.		0.348	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		C	141560268	T	C	141560268	3	2	103	1	0	0	0	0	1	0	0	0	15642	1551	54	2	1351	2	TBC1D9	4	141560268	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	258098	141560268	49594008	347	14970										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148744064	148744064	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagatgcttccttacgtgaaTtttcaaattttttgaagaat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:148744064delT	ENST00000336498.3	+	3	507	c.268delT	c.(268-270)tttfs	p.F90fs		NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		CTTACGTGAATTTTCAAATTT	0.358																																					p.E89fs		Atlas-INDEL	.											.	ARHGAP10	92	.	0			c.267delA						.						90	87	88					4																	148744064		2203	4300	6503	SO:0001589	frameshift_variant	79658	exon3			.	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.268delT	chr4.hg19:g.148744064delT	ENSP00000336923:p.Phe90fs	124.0	0.0		157.0	10.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Frame_Shift_Del	DEL	ENST00000336498.3	hg19	CCDS34075.1																																																																																			.	.		0.358	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		-	148744064	T	-	148744064	7	5	103	1	0	1	0	1	0	0	0	0	862	1493	52	0	278	0	ARHGAP10	4	148744064	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	7183796	148744064	42410212	348	14971										
RBM46	166863	hgsc.bcm.edu	37	chr4	155720193	155720193	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccatgtctgttatgaatggAaaatgcattgatggagcaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:155720193delA	ENST00000281722.3	+	4	1114	c.879delA	c.(877-879)ggafs	p.G293fs	RBM46_ENST00000510397.1_Frame_Shift_Del_p.G293fs|RBM46_ENST00000514866.1_Frame_Shift_Del_p.G293fs	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	293	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				TTATGAATGGAAAATGCATTG	0.388																																					p.G293fs		Atlas-INDEL	.											.	RBM46	76	.	0			c.878delG						.						91	83	86					4																	155720193		2203	4300	6503	SO:0001589	frameshift_variant	166863	exon4			.	BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"RNA binding motif (RRM) containing"	28401	protein-coding gene	gene with protein product	"cancer/testis antigen 68"					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.879delA	chr4.hg19:g.155720193delA	ENSP00000281722:p.Gly293fs	149.0	0.0		148.0	10.0	NM_144979	B3KWU8|B4DZ27	Frame_Shift_Del	DEL	ENST00000281722.3	hg19	CCDS3790.1																																																																																			.	.		0.388	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979		-	155720193	A	-	155720193	7	5	103	1	0	1	0	1	0	0	0	0	13155	233	9	0	889	0	RBM46	4	155720193	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	6976129	155720193	35434083	349	14972										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186570678	186570678	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggactggaggtggaacatgtGggggaggcactggggaggac					rs113864748		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:186570678delG	ENST00000284776.7	-	9	1021	c.512delC	c.(511-513)ccafs	p.P171fs	SORBS2_ENST00000448662.2_Frame_Shift_Del_p.P240fs|SORBS2_ENST00000431808.1_Frame_Shift_Del_p.P171fs|SORBS2_ENST00000319471.9_Frame_Shift_Del_p.P257fs|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000437304.2_Frame_Shift_Del_p.P350fs|SORBS2_ENST00000355634.5_Frame_Shift_Del_p.P271fs|SORBS2_ENST00000418609.1_Frame_Shift_Del_p.P75fs|SORBS2_ENST00000393528.3_Frame_Shift_Del_p.P217fs|SORBS2_ENST00000449407.2_Frame_Shift_Del_p.P242fs	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	171	Pro-rich.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TGGAACATGTGGGGGAGGCAC	0.552																																					p.P350fs	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-INDEL	.											.	SORBS2	300	.	0			c.1050delA						.						106	106	106					4																	186570678		2203	4300	6503	SO:0001589	frameshift_variant	8470	exon10			.		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.512delC	chr4.hg19:g.186570678delG	ENSP00000284776:p.Pro171fs	230.0	0.0		192.0	12.0	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Frame_Shift_Del	DEL	ENST00000284776.7	hg19	CCDS3845.1																																																																																			.	.		0.552	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		-	186570678	G	-	186570678	7	5	103	1	0	1	0	1	0	0	0	0	14943	1348	47	0	3154	0	SORBS2	4	186570678	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	30850485	186570678	4583598	350	14973										
KLKB1	3818	hgsc.bcm.edu	37	chr4	187172371	187172371	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgcttttttttaaaaaaaatAgaaatgtttgtcttcttaaa	4	3	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:187172371A>T	ENST00000264690.6	+	8	945		c.e8-1		KLKB1_ENST00000513864.1_Splice_Site	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1						blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		TAAAAAAAATAGAAATGTTTG	0.348																																					.		Atlas-SNP	.											.	KLKB1	155	.	0			c.759-2A>T						.						40	45	43					4																	187172371		2199	4296	6495	SO:0001630	splice_region_variant	3818	exon8			AAAAATAGAAATG	M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"Kallikreins"	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.759-1A>T	chr4.hg19:g.187172371A>T		44.0	0.0		62.0	4.0	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Splice_Site	SNP	ENST00000264690.6	hg19	CCDS34120.1	.	.	.	.	.	.	.	.	.	.	a	11.20	1.569288	0.28003	.	.	ENSG00000164344	ENST00000511608;ENST00000264690;ENST00000513864;ENST00000418715	.	.	.	4.24	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.459	0.67435	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KLKB1	187409365	1.000000	0.71417	1.000000	0.80357	0.342000	0.28953	6.055000	0.71103	2.157000	0.67596	0.468000	0.43344	.	.	.		0.348	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892	Intron	T	187172371	A	T	187172371	5	4	103	1	0	0	0	0	0	0	1	0	8421	434	15	4	783	4	KLKB1	4	187172371	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	601693	187172371	3981905	351	14974										
FAT1	2195	hgsc.bcm.edu	37	chr4	187539266	187539266	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgatctgaattactctacttCcccctggcaggttttcaaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:187539266delC	ENST00000441802.2	-	10	8683	c.8474delG	c.(8473-8475)ggafs	p.G2825fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2825	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TACTCTACTTCCCCCTGGCAG	0.438										HNSCC(5;0.00058)																											p.G2825fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.8475delA						.						109	103	105					4																	187539266		1880	4131	6011	SO:0001589	frameshift_variant	2195	exon10			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8474delG	chr4.hg19:g.187539266delC	ENSP00000406229:p.Gly2825fs	153.0	0.0		129.0	11.0	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.438	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187539266	C	-	187539266	7	5	103	1	0	1	0	1	0	0	0	0	5697	855	30	0	5364	0	FAT1	4	187539266	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	366895	187539266	3615010	352	14975										
FAT1	2195	hgsc.bcm.edu	37	chr4	187628769	187628769	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caaggtcagtggagttcatgAaaattacactggaacccaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:187628769delA	ENST00000441802.2	-	2	2422	c.2213delT	c.(2212-2214)ttcfs	p.F738fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	738	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GGAGTTCATGAAAATTACACT	0.433										HNSCC(5;0.00058)																											p.F738fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.2214delC						.						70	67	68					4																	187628769		1887	4106	5993	SO:0001589	frameshift_variant	2195	exon2			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.2213delT	chr4.hg19:g.187628769delA	ENSP00000406229:p.Phe738fs	123.0	0.0		124.0	10.0	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.433	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187628769	A	-	187628769	7	5	103	1	0	1	0	1	0	0	0	0	5697	246	9	0	11657	0	FAT1	4	187628769	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	89503	187628769	3525507	353	14976										
CMBL	134147	hgsc.bcm.edu	37	chr5	10282342	10282342	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atcacaacatcattttcagcAaaaatgaacaaagtggggtt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:10282342delA	ENST00000296658.3	-	5	945	c.525delT	c.(523-525)tttfs	p.F175fs	CMBL_ENST00000510532.1_Intron	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	175						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						CATTTTCAGCAAAAATGAACA	0.408																																					p.A176fs		Atlas-INDEL	.											.	CMBL	24	.	0			c.526delG						.						98	101	100					5																	10282342		2203	4300	6503	SO:0001589	frameshift_variant	134147	exon5			.		CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	"carboxymethylenebutenolidase-like (Pseudomonas)"			3804974, 20177059	Standard	NM_138809		Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.525delT	chr5.hg19:g.10282342delA	ENSP00000296658:p.Phe175fs	109.0	0.0		178.0	13.0	NM_138809	D3DTC7|Q8TED6	Frame_Shift_Del	DEL	ENST00000296658.3	hg19	CCDS3878.1																																																																																			.	.		0.408	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253689.1	NM_138809		-	10282342	A	-	10282342	7	5	103	1	0	1	0	1	0	0	0	0	3578	127	5	0	220	0	CMBL	5	10282342	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10		10282342	170632918	354	14977										
CDH9	1007	hgsc.bcm.edu	37	chr5	26988315	26988315	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgtagcattttaccgtcatcTtttgtcagacccgctatctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:26988315delT	ENST00000231021.4	-	2	298	c.126delA	c.(124-126)aaafs	p.K42fs		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	42					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TACCGTCATCTTTTGTCAGAC	0.403																																					p.D43fs	Melanoma(8;187 585 15745 40864 52829)	Atlas-INDEL	.											.	CDH9	305	.	0			c.127delG						.						138	132	134					5																	26988315		2203	4300	6503	SO:0001589	frameshift_variant	1007	exon2			.	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.126delA	chr5.hg19:g.26988315delT	ENSP00000231021:p.Lys42fs	207.0	0.0		205.0	14.0	NM_016279	Q3B7I5	Frame_Shift_Del	DEL	ENST00000231021.4	hg19	CCDS3893.1																																																																																			.	.		0.403	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		-	26988315	T	-	26988315	7	5	103	1	0	1	0	1	0	0	0	0	3119	1606	56	0	2287	0	CDH9	5	26988315	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	16705973	26988315	153926945	355	14978										
C5orf22	55322	hgsc.bcm.edu	37	chr5	31541441	31541441	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catcaattagaggatttagaAgccactttcgctgatttgtg	9	7	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:31541441A>G	ENST00000325366.9	+	6	1051	c.924A>G	c.(922-924)gaA>gaG	p.E308E	C5orf22_ENST00000355907.3_5'UTR	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	308										kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						AGGATTTAGAAGCCACTTTCG	0.353																																					p.E308E		Atlas-SNP	.											.	C5orf22	48	.	0			c.A924G						.						118	120	119					5																	31541441		2203	4300	6503	SO:0001819	synonymous_variant	55322	exon6			TTTAGAAGCCACT	AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.924A>G	chr5.hg19:g.31541441A>G		62.0	0.0		86.0	4.0	NM_018356	Q8ND28|Q8WU61|Q9NUR1	Silent	SNP	ENST00000325366.9	hg19	CCDS3895.1																																																																																			.	.		0.353	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356		G	31541441	A	G	31541441	2	3	103	1	0	0	0	0	0	0	0	1	2287	69	3	2		2	C5orf22	5	31541441	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	4553126	31541441	149373819	356	14979										
LMBRD2	92255	hgsc.bcm.edu	37	chr5	36108707	36108707	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatttctgttcctagtggaaTcttctctattgtgtccataa	6	8	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:36108707T>C	ENST00000296603.4	-	16	2288	c.1826A>G	c.(1825-1827)gAt>gGt	p.D609G		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	609						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CCTAGTGGAATCTTCTCTATT	0.328																																					p.D609G		Atlas-SNP	.											.	LMBRD2	89	.	0			c.A1826G						.						142	134	136					5																	36108707		2203	4300	6503	SO:0001583	missense	92255	exon16			GTGGAATCTTCTC		CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.1826A>G	chr5.hg19:g.36108707T>C	ENSP00000296603:p.Asp609Gly	125.0	0.0		188.0	8.0	NM_001007527	B3KRB6|Q9NTC7	Missense_Mutation	SNP	ENST00000296603.4	hg19	CCDS34145.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.811551	0.50527	.	.	ENSG00000164187	ENST00000296603;ENST00000546130	.	.	.	5.7	5.7	0.88788	.	0.177935	0.64402	D	0.000015	T	0.46718	0.1407	L	0.35723	1.085	0.46678	D	0.999159	B	0.31383	0.321	B	0.25759	0.063	T	0.39078	-0.9631	9	0.22109	T	0.4	-15.3148	16.2617	0.82550	0.0:0.0:0.0:1.0	.	609	Q68DH5	LMBD2_HUMAN	G	609;503	.	ENSP00000296603:D609G	D	-	2	0	LMBRD2	36144464	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.894000	0.63206	2.302000	0.77476	0.528000	0.53228	GAT	.	.		0.328	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527		C	36108707	T	C	36108707	3	2	103	1	0	0	0	0	1	0	0	0	8852	1435	50	2	273	2	LMBRD2	5	36108707	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4567266	36108707	144806553	357	14980										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37115123	37115123	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctgctttggctccaccagcTtttttctgtatggtgaaagt	10	9	1	1	rs368603190		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:37115123T>C	ENST00000508244.1	-	49	9270	c.9177A>G	c.(9175-9177)aaA>aaG	p.K3059K	C5orf42_ENST00000425232.2_Silent_p.K3059K|C5orf42_ENST00000274258.7_Silent_p.K1957K			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	3059						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CTCCACCAGCTTTTTTCTGTA	0.363																																					p.K3059K		Atlas-SNP	.											.	C5orf42	422	.	0			c.A9177G						.	T		2,4404	4.2+/-10.8	0,2,2201	94	84	88		9177	3.6	0.1	5		88	0,8600		0,0,4300	no	coding-synonymous	C5orf42	NM_023073.3		0,2,6501	CC,CT,TT		0.0,0.0454,0.0154		3059/3198	37115123	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	65250	exon50			ACCAGCTTTTTTC		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.9177A>G	chr5.hg19:g.37115123T>C		55.0	0.0		65.0	4.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	hg19	CCDS34146.2																																																																																			.	.		0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37115123	T	C	37115123	2	2	103	1	0	0	0	0	0	0	0	1	2303	1606	56	2		2	C5orf42	5	37115123	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1006416	37115123	143800137	358	14981										
WDR70	55100	hgsc.bcm.edu	37	chr5	37703139	37703139	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcagcggcaaacttgttttcTttgagcgtaggactttccaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:37703139delT	ENST00000265107.4	+	13	1522	c.1366delT	c.(1366-1368)tttfs	p.F456fs	RNU6-484P_ENST00000384016.1_RNA	NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	456							enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACTTGTTTTCTTTGAGCGTAG	0.413																																					p.F455fs		Atlas-INDEL	.											.	WDR70	76	.	0			c.1365delC						.						122	111	115					5																	37703139		2203	4300	6503	SO:0001589	frameshift_variant	55100	exon13			.	BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068		"WD repeat domain containing"	25495	protein-coding gene	gene with protein product						12477932	Standard	NM_018034		Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000265107.4:c.1366delT	chr5.hg19:g.37703139delT	ENSP00000265107:p.Phe456fs	163.0	0.0		194.0	14.0	NM_018034	Q9H053	Frame_Shift_Del	DEL	ENST00000265107.4	hg19	CCDS34147.1																																																																																			.	.		0.413	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034		-	37703139	T	-	37703139	7	5	103	1	0	1	0	1	0	0	0	0	17336	1609	56	0	1416	0	WDR70	5	37703139	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	588016	37703139	143212121	359	14982										
LIFR	3977	hgsc.bcm.edu	37	chr5	38510584	38510584	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acatccagcaaaaataacggTtccaaatatgttatcttcgg	6	9	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:38510584T>C	ENST00000263409.4	-	7	1135	c.973A>G	c.(973-975)Acc>Gcc	p.T325A	LIFR_ENST00000453190.2_Missense_Mutation_p.T325A|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	325					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					AAAATAACGGTTCCAAATATG	0.348			T	PLAG1	salivary adenoma																																p.T325A	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.A973G						.						68	67	67					5																	38510584		2203	4300	6503	SO:0001583	missense	3977	exon7			TAACGGTTCCAAA	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.973A>G	chr5.hg19:g.38510584T>C	ENSP00000263409:p.Thr325Ala	62.0	0.0		114.0	5.0	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	T	5.638	0.302460	0.10678	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.61040	0.14;0.14	5.61	3.22	0.36961	Fibronectin, type III (1);	0.518280	0.22053	N	0.065296	T	0.33702	0.0872	L	0.35414	1.06	0.29968	N	0.818779	P	0.39520	0.676	B	0.26517	0.07	T	0.27262	-1.0079	10	0.12430	T	0.62	-8.1867	7.3052	0.26443	0.0:0.1742:0.0:0.8258	.	325	P42702	LIFR_HUMAN	A	325	ENSP00000263409:T325A;ENSP00000398368:T325A	ENSP00000263409:T325A	T	-	1	0	LIFR	38546341	1.000000	0.71417	0.976000	0.42696	0.049000	0.14656	3.009000	0.49552	0.425000	0.26087	-0.256000	0.11100	ACC	.	.		0.348	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		C	38510584	T	C	38510584	3	2	103	1	0	0	0	0	1	0	0	0	8789	1725	60	2	2376	2	LIFR	5	38510584	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	807445	38510584	142404676	360	14983										
OXCT1	5019	hgsc.bcm.edu	37	chr5	41862804	41862804	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcttctactggatctgtatAaaacttggtatggcgatgag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:41862804delA	ENST00000196371.5	-	2	287	c.127delT	c.(127-129)tatfs	p.Y43fs		NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	43					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	GGATCTGTATAAAACTTGGTA	0.373																																					p.Y43fs		Atlas-INDEL	.											.	OXCT1	54	.	0			c.128delA						.						128	114	119					5																	41862804		2203	4300	6503	SO:0001589	frameshift_variant	5019	exon2			.	U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"3-oxoacid CoA transferase"	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.127delT	chr5.hg19:g.41862804delA	ENSP00000196371:p.Tyr43fs	172.0	0.0		185.0	13.0	NM_000436	B2R5V2|B7Z528	Frame_Shift_Del	DEL	ENST00000196371.5	hg19	CCDS3937.1																																																																																			.	.		0.373	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436		-	41862804	A	-	41862804	7	5	103	1	0	1	0	1	0	0	0	0	11338	362	13	0	1499	0	OXCT1	5	41862804	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3352220	41862804	139052456	361	14984										
C5orf51	285636	hgsc.bcm.edu	37	chr5	41909898	41909898	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacaagctagtagatgaagaTtttcctgaagactcttcttc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:41909898delT	ENST00000381647.2	+	3	277	c.258delT	c.(256-258)gatfs	p.D86fs	C5orf51_ENST00000505931.2_3'UTR	NM_175921.4	NP_787117.3	A6NDU8	CE051_HUMAN	chromosome 5 open reading frame 51	86										endometrium(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						TAGATGAAGATTTTCCTGAAG	0.279																																					p.D86fs		Atlas-INDEL	.											.	C5orf51	28	.	0			c.257delA						.						45	49	48					5																	41909898		2198	4286	6484	SO:0001589	frameshift_variant	285636	exon3			.	AL833916, AK094002	CCDS34151.1	5p13.1	2008-07-18			ENSG00000205765	ENSG00000205765			27750	protein-coding gene	gene with protein product						14702039	Standard	NM_175921		Approved	LOC285636	uc003jmo.3	A6NDU8	OTTHUMG00000162084	ENST00000381647.2:c.258delT	chr5.hg19:g.41909898delT	ENSP00000371061:p.Asp86fs	129.0	0.0		172.0	13.0	NM_175921	A2RRM9	Frame_Shift_Del	DEL	ENST00000381647.2	hg19	CCDS34151.1																																																																																			.	.		0.279	C5orf51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367144.1	NM_175921		-	41909898	T	-	41909898	7	5	103	1	0	1	0	1	0	0	0	0	2310	1490	52	0	268	0	C5orf51	5	41909898	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	47094	41909898	139005362	362	14985										
FST	10468	hgsc.bcm.edu	37	chr5	52779494	52779494	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgcaatgaatgtgcactcctAaaggcaagatgtaaagagca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:52779494delA	ENST00000256759.3	+	3	821	c.438delA	c.(436-438)ctafs	p.L146fs	FST_ENST00000396947.3_Frame_Shift_Del_p.L146fs	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	146	Kazal-like 1. {ECO:0000255|PROSITE- ProRule:PRU00798}.				BMP signaling pathway (GO:0030509)|female gonad development (GO:0008585)|gamete generation (GO:0007276)|hair follicle morphogenesis (GO:0031069)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinocyte proliferation (GO:0043616)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|pattern specification process (GO:0007389)|positive regulation of hair follicle development (GO:0051798)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	activin binding (GO:0048185)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|urinary_tract(1)	15		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				GTGCACTCCTAAAGGCAAGAT	0.542																																					p.L146fs		Atlas-INDEL	.											.	FST	42	.	0			c.437delT						.						70	65	67					5																	52779494		2203	4300	6503	SO:0001589	frameshift_variant	10468	exon3			.	M19481	CCDS3959.1, CCDS43315.1	5q11.2	2008-02-05			ENSG00000134363	ENSG00000134363			3971	protein-coding gene	gene with protein product		136470				10411917, 3380788	Standard	NM_006350		Approved	FS	uc003jpd.3	P19883	OTTHUMG00000131183	ENST00000256759.3:c.438delA	chr5.hg19:g.52779494delA	ENSP00000256759:p.Leu146fs	136.0	0.0		213.0	15.0	NM_006350	B5BU94|Q9BTH0	Frame_Shift_Del	DEL	ENST00000256759.3	hg19	CCDS3959.1																																																																																			.	.		0.542	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409		-	52779494	A	-	52779494	7	5	103	1	0	1	0	1	0	0	0	0	6084	349	13	0	448	0	FST	5	52779494	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	10869596	52779494	128135766	363	14986										
NDUFS4	4724	hgsc.bcm.edu	37	chr5	52899338	52899338	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccagactcaagacacacaacTcataacagttgatgaaaaat	5	10	2	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:52899338T>C	ENST00000296684.5	+	2	183	c.155T>C	c.(154-156)cTc>cCc	p.L52P		NM_002495.2	NP_002486.1	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase)	52					brain development (GO:0007420)|cAMP-mediated signaling (GO:0019933)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|positive regulation of fibroblast proliferation (GO:0048146)|reactive oxygen species metabolic process (GO:0072593)|regulation of protein phosphorylation (GO:0001932)|respiratory electron transport chain (GO:0022904)|response to cAMP (GO:0051591)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.L52P(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(3)	10		Lung NSC(810;8.27e-05)|Breast(144;0.0848)				GACACACAACTCATAACAGTT	0.403																																					p.L52P		Atlas-SNP	.											NDUFS4,NS,carcinoma,0,1	NDUFS4	17	.	1	Substitution - Missense(1)	kidney(1)	c.T155C						.						126	116	120					5																	52899338		2203	4300	6503	SO:0001583	missense	4724	exon2			CACAACTCATAAC	AF020351	CCDS3960.1	5q11.1	2011-07-04	2002-08-29		ENSG00000164258	ENSG00000164258		"Mitochondrial respiratory chain complex / Complex I"	7711	protein-coding gene	gene with protein product	"complex I 18kDa subunit"	602694	"NADH dehydrogenase (ubiquinone) Fe-S protein 4 (18kD) (NADH-coenzyme Q reductase)"			9463323, 9763677	Standard	NM_002495		Approved	AQDQ, CI-18	uc003jpe.2	O43181	OTTHUMG00000096987	ENST00000296684.5:c.155T>C	chr5.hg19:g.52899338T>C	ENSP00000296684:p.Leu52Pro	49.0	0.0		51.0	3.0	NM_002495	Q9BS69	Missense_Mutation	SNP	ENST00000296684.5	hg19	CCDS3960.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.793957	0.70452	.	.	ENSG00000164258	ENST00000296684;ENST00000506765	T	0.66099	-0.19	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.77465	0.4134	M	0.74258	2.255	0.80722	D	1	D	0.76494	0.999	D	0.65233	0.933	T	0.78006	-0.2373	10	0.44086	T	0.13	.	16.1138	0.81283	0.0:0.0:0.0:1.0	.	52	O43181	NDUS4_HUMAN	P	52;48	ENSP00000296684:L52P	ENSP00000296684:L52P	L	+	2	0	NDUFS4	52935095	1.000000	0.71417	0.998000	0.56505	0.841000	0.47740	6.863000	0.75489	2.220000	0.72140	0.533000	0.62120	CTC	.	.		0.403	NDUFS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214062.2	NM_002495		C	52899338	T	C	52899338	3	2	103	1	0	0	0	0	1	0	0	0	10303	1551	54	2	161	2	NDUFS4	5	52899338	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	119844	52899338	128015922	364	14987										
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56170970	56170970	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggccctgctgttggcaaatGgggagagcactggaaattct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:56170970delG	ENST00000399503.3	+	10	1798	c.1798delG	c.(1798-1800)gggfs	p.G600fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	600					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GTTGGCAAATGGGGAGAGCAC	0.562																																					p.N599fs		Atlas-INDEL	.											.	MAP3K1	355	.	0			c.1797delT						.						81	82	81					5																	56170970		1923	4124	6047	SO:0001589	frameshift_variant	4214	exon10			.	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.1798delG	chr5.hg19:g.56170970delG	ENSP00000382423:p.Gly600fs	197.0	0.0		193.0	14.0	NM_005921		Frame_Shift_Del	DEL	ENST00000399503.3	hg19	CCDS43318.1																																																																																			.	.		0.562	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		-	56170970	G	-	56170970	7	5	103	1	0	1	0	1	0	0	0	0	9252	1348	47	0	1836	0	MAP3K1	5	56170970	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	3271632	56170970	124744290	365	14988										
PDE4D	5144	hgsc.bcm.edu	37	chr5	58271490	58271490	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acttcatgcattacctgtgaTttttccacggaagcattgtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:58271490delT	ENST00000340635.6	-	14	2182	c.2007delA	c.(2005-2007)aaafs	p.K669fs	PDE4D_ENST00000503258.1_Frame_Shift_Del_p.K539fs|PDE4D_ENST00000360047.5_Frame_Shift_Del_p.K533fs|PDE4D_ENST00000546160.1_Frame_Shift_Del_p.K608fs|PDE4D_ENST00000317118.8_Frame_Shift_Del_p.K378fs|PDE4D_ENST00000507116.1_Frame_Shift_Del_p.K605fs|PDE4D_ENST00000405755.2_Frame_Shift_Del_p.K547fs|PDE4D_ENST00000358923.6_Frame_Shift_Del_p.K367fs|PDE4D_ENST00000502484.2_Frame_Shift_Del_p.K608fs	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	669					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	TTACCTGTGATTTTTCCACGG	0.438																																					p.S670fs		Atlas-INDEL	.											.	PDE4D	345	.	0			c.2008delT						.						81	85	84					5																	58271490		2147	4290	6437	SO:0001589	frameshift_variant	5144	exon14			.		CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"Phosphodiesterases"	8783	protein-coding gene	gene with protein product	"phosphodiesterase E3 dunce homolog (Drosophila)"	600129	"phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.2007delA	chr5.hg19:g.58271490delT	ENSP00000345502:p.Lys669fs	142.0	0.0		180.0	11.0	NM_001104631	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Frame_Shift_Del	DEL	ENST00000340635.6	hg19	CCDS47213.1																																																																																			.	.		0.438	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3			-	58271490	T	-	58271490	7	5	103	1	0	1	0	1	0	0	0	0	11651	1490	52	0	430	0	PDE4D	5	58271490	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2100520	58271490	122643770	366	14989										
DEPDC1B	55789	hgsc.bcm.edu	37	chr5	59893603	59893603	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cattcgaaaacttctagttcTttgaaatggttggaaaggct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:59893603delT	ENST00000265036.5	-	11	1634	c.1567delA	c.(1567-1569)agafs	p.R523fs	DEPDC1B_ENST00000453022.2_Frame_Shift_Del_p.R461fs|DEPDC1B_ENST00000545085.1_Frame_Shift_Del_p.R434fs	NM_018369.2	NP_060839.2	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B	523					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(2)|skin(2)	17		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				CTTCTAGTTCTTTGAAATGGT	0.423																																					p.R523fs		Atlas-INDEL	.											.	DEPDC1B	56	.	0			c.1568delG						.						192	184	187					5																	59893603		2203	4300	6503	SO:0001589	frameshift_variant	55789	exon11			.	AF303178	CCDS3977.1, CCDS47214.1	5q12	2008-02-05			ENSG00000035499	ENSG00000035499			24902	protein-coding gene	gene with protein product	"breast cancer cell 3"					12477932	Standard	NM_001145208		Approved	XTP1, BRCC3	uc003jsh.3	Q8WUY9	OTTHUMG00000097083	ENST00000265036.5:c.1567delA	chr5.hg19:g.59893603delT	ENSP00000265036:p.Arg523fs	108.0	0.0		164.0	11.0	NM_018369	A8K3R9|B4DUT4|Q86WJ3|Q8IZY6|Q9NUN3|Q9NW57	Frame_Shift_Del	DEL	ENST00000265036.5	hg19	CCDS3977.1																																																																																			.	.		0.423	DEPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214207.1	NM_018369		-	59893603	T	-	59893603	7	5	103	1	0	1	0	1	0	0	0	0	4442	1617	56	0	26	0	DEPDC1B	5	59893603	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1622113	59893603	121021657	367	14990										
ELOVL7	79993	hgsc.bcm.edu	37	chr5	60050627	60050627	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atcctccatgaaaaagaactGgcttatgtggatggcgacaa	10	8	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:60050627G>A	ENST00000508821.1	-	9	984	c.670C>T	c.(670-672)Cag>Tag	p.Q224*	ELOVL7_ENST00000438340.1_Nonsense_Mutation_p.Q224*|ELOVL7_ENST00000425382.1_Nonsense_Mutation_p.Q224*|ELOVL7_ENST00000505959.1_Nonsense_Mutation_p.Q211*	NM_024930.2	NP_079206.2	A1L3X0	ELOV7_HUMAN	ELOVL fatty acid elongase 7	224					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	9		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)				AAAAAGAACTGGCTTATGTGG	0.353																																					p.Q224X		Atlas-SNP	.											.	ELOVL7	24	.	0			c.C670T						.						97	89	92					5																	60050627		2203	4300	6503	SO:0001587	stop_gained	79993	exon8			AGAACTGGCTTAT	AK027216	CCDS34164.1	5q12	2011-05-25	2011-05-25			ENSG00000164181			26292	protein-coding gene	gene with protein product		614451	"ELOVL family member 7, elongation of long chain fatty acids (yeast)"			19826053	Standard	NM_024930		Approved	FLJ23563	uc010iwk.3	A1L3X0		ENST00000508821.1:c.670C>T	chr5.hg19:g.60050627G>A	ENSP00000424123:p.Gln224*	82.0	0.0		111.0	33.0	NM_001104558	Q589T3|Q9H5D0|Q9NT66	Nonsense_Mutation	SNP	ENST00000508821.1	hg19	CCDS34164.1	.	.	.	.	.	.	.	.	.	.	G	40	8.445576	0.98815	.	.	ENSG00000164181	ENST00000508821;ENST00000438340;ENST00000425382;ENST00000505959	.	.	.	5.89	5.89	0.94794	.	0.166857	0.53938	D	0.000041	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-2.6046	20.2469	0.98398	0.0:0.0:1.0:0.0	.	.	.	.	X	224;224;224;211	.	ENSP00000402634:Q224X	Q	-	1	0	ELOVL7	60086384	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.428000	0.97476	2.781000	0.95711	0.555000	0.69702	CAG	.	.		0.353	ELOVL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368195.1			A	60050627	G	A	60050627	4	1	103	1	0	0	0	0	0	1	0	0	5081	1357	47	3	179	3	ELOVL7	5	60050627	Nonsense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	157024	60050627	120864633	368	14991										
PPWD1	23398	hgsc.bcm.edu	37	chr5	64859205	64859205	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgggacccggaggaaccggAaaaaacagaactcagcgaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:64859205delA	ENST00000261308.5	+	1	140	c.68delA	c.(67-69)gaafs	p.E23fs	CENPK_ENST00000510354.1_5'Flank|CENPK_ENST00000510693.1_5'Flank|CENPK_ENST00000508421.1_5'Flank|CENPK_ENST00000506282.2_5'Flank|CENPK_ENST00000514814.1_5'Flank|CENPK_ENST00000396679.1_5'Flank|PPWD1_ENST00000538977.1_5'UTR|PPWD1_ENST00000535264.1_5'UTR	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	23					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		GAGGAACCGGAAAAAACAGAA	0.562																																					p.E23fs		Atlas-INDEL	.											.,1	PPWD1	47	.	0			c.67delG						.						72	75	74					5																	64859205		2203	4300	6503	SO:0001589	frameshift_variant	23398	exon1			.	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"WD repeat domain containing"	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.68delA	chr5.hg19:g.64859205delA	ENSP00000261308:p.Glu23fs	108.0	0.0		154.0	10.0	NM_015342	B4DWR9|Q15002|Q7KZ89	Frame_Shift_Del	DEL	ENST00000261308.5	hg19	CCDS3985.1																																																																																			.	.		0.562	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342		-	64859205	A	-	64859205	7	5	103	1	0	1	0	1	0	0	0	0	12426	246	9	0	70	0	PPWD1	5	64859205	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	4808578	64859205	116056055	369	14992										
PPWD1	23398	hgsc.bcm.edu	37	chr5	64865782	64865782	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgataaagcaatgaaggtgTttgatgtagtgaactttgac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:64865782delT	ENST00000261308.5	+	4	550	c.478delT	c.(478-480)tttfs	p.F160fs	PPWD1_ENST00000538977.1_Frame_Shift_Del_p.F4fs|PPWD1_ENST00000535264.1_Frame_Shift_Del_p.F130fs	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	160					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		AATGAAGGTGTTTGATGTAGT	0.313																																					p.V159fs		Atlas-INDEL	.											.	PPWD1	47	.	0			c.477delG						.						134	132	133					5																	64865782		2203	4300	6503	SO:0001589	frameshift_variant	23398	exon4			.	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"WD repeat domain containing"	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.478delT	chr5.hg19:g.64865782delT	ENSP00000261308:p.Phe160fs	110.0	0.0		164.0	10.0	NM_015342	B4DWR9|Q15002|Q7KZ89	Frame_Shift_Del	DEL	ENST00000261308.5	hg19	CCDS3985.1																																																																																			.	.		0.313	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342		-	64865782	T	-	64865782	7	5	103	1	0	1	0	1	0	0	0	0	12426	1725	60	0	492	0	PPWD1	5	64865782	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	6577	64865782	116049478	370	14993										
PPWD1	23398	hgsc.bcm.edu	37	chr5	64878960	64878960	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaagaagtcatggcagctacTcaagctgaaggacctaaacg	11	9	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:64878960T>C	ENST00000261308.5	+	8	1518	c.1446T>C	c.(1444-1446)acT>acC	p.T482T	PPWD1_ENST00000538977.1_Silent_p.T326T|PPWD1_ENST00000535264.1_Silent_p.T452T	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	482					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		TGGCAGCTACTCAAGCTGAAG	0.408																																					p.T482T		Atlas-SNP	.											.	PPWD1	47	.	0			c.T1446C						.						153	147	149					5																	64878960		2203	4300	6503	SO:0001819	synonymous_variant	23398	exon8			AGCTACTCAAGCT	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"WD repeat domain containing"	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.1446T>C	chr5.hg19:g.64878960T>C		75.0	0.0		122.0	5.0	NM_015342	B4DWR9|Q15002|Q7KZ89	Silent	SNP	ENST00000261308.5	hg19	CCDS3985.1																																																																																			.	.		0.408	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342		C	64878960	T	C	64878960	2	2	103	1	0	0	0	0	0	0	0	1	12426	1538	54	2		2	PPWD1	5	64878960	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	13178	64878960	116036300	371	14994										
C5orf44	80006	hgsc.bcm.edu	37	chr5	64931772	64931772	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtttttctcttcattcaggAgatctctttaaccagctgat	6	9	4	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:64931772A>G	ENST00000399438.3	+	3	462	c.117A>G	c.(115-117)ggA>ggG	p.G39G	TRAPPC13_ENST00000231526.4_Splice_Site_p.G39G|TRAPPC13_ENST00000545191.1_Splice_Site_p.G39G|TRAPPC13_ENST00000438419.2_Splice_Site_p.G39G|TRAPPC13_ENST00000505553.1_Splice_Site_p.G39G	NM_001093755.1|NM_024941.3	NP_001087224.1|NP_079217.2	A5PLN9	TPC13_HUMAN	trafficking protein particle complex 13	39																	TTCATTCAGGAGATCTCTTTA	0.328																																					p.G39G		Atlas-SNP	.											.	TRAPPC13	1	.	0			c.A117G						.						72	60	64					5																	64931772		1813	4086	5899	SO:0001630	splice_region_variant	80006	exon3			TTCAGGAGATCTC		CCDS47221.1, CCDS47222.1, CCDS47223.1, CCDS58950.1	5q12.3	2013-01-31	2013-01-24	2013-01-24	ENSG00000113597	ENSG00000113597			25828	protein-coding gene	gene with protein product	"Trs65-related"		"chromosome 5 open reading frame 44"	C5orf44		12477932	Standard	NM_024941		Approved	FLJ13611, FLJ26957, MGC48585	uc010iwu.1	A5PLN9	OTTHUMG00000163649	ENST00000399438.3:c.116-1A>G	chr5.hg19:g.64931772A>G		76.0	0.0		115.0	5.0	NM_001243737	Q17RZ9|Q49A23|Q4JHG0|Q6MZG4|Q8TCM2|Q9H8I3	Silent	SNP	ENST00000399438.3	hg19	CCDS47222.1																																																																																			.	.		0.328	TRAPPC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370113.1	NM_024941	Silent	G	64931772	A	G	64931772	5	3	103	1	0	0	0	0	0	0	1	0	2305	318	11	2	127	2	C5orf44	5	64931772	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	52812	64931772	115983488	372	14995										
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65321734	65321734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagttgaagctttgccttcaTctattgggcagcttactaac	8	9	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:65321734T>C	ENST00000284037.5	+	12	1338	c.949T>C	c.(949-951)Tct>Cct	p.S317P	ERBB2IP_ENST00000380936.1_Missense_Mutation_p.S317P|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.S317P|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.S317P|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.S317P|ERBB2IP_ENST00000416865.2_Missense_Mutation_p.S317P|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.S317P|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.S317P|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.S317P|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.S317P	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	317					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		TTTGCCTTCATCTATTGGGCA	0.294																																					p.S317P		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.T949C						.						55	54	54					5																	65321734		2202	4298	6500	SO:0001583	missense	55914	exon12			CCTTCATCTATTG		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"densin-180-like protein", "ERBB2-interacting protein"	606944	"erbb2-interacting protein"			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.949T>C	chr5.hg19:g.65321734T>C	ENSP00000284037:p.Ser317Pro	155.0	0.0		170.0	7.0	NM_001253701	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	hg19	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736203	0.89482	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000416865;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T;T	0.48201	1.04;1.03;2.31;1.03;1.22;0.82;1.1;1.03;1.06;0.82	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.63224	0.2493	L	0.48877	1.53	0.80722	D	1	D;D;D;D;D;D;D;D	0.76494	0.997;0.997;0.997;0.999;0.999;0.999;0.998;0.999	D;D;D;D;D;D;D;D	0.80764	0.922;0.928;0.929;0.926;0.939;0.994;0.975;0.962	T	0.65755	-0.6091	10	0.87932	D	0	.	16.188	0.81967	0.0:0.0:0.0:1.0	.	317;317;317;317;317;317;317;317	B4DIP2;Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;.;LAP2_HUMAN;.;.	P	317	ENSP00000284037:S317P;ENSP00000370330:S317P;ENSP00000397833:S317P;ENSP00000370326:S317P;ENSP00000370323:S317P;ENSP00000370322:S317P;ENSP00000370325:S317P;ENSP00000422766:S317P;ENSP00000426632:S317P;ENSP00000422015:S317P	ENSP00000284037:S317P	S	+	1	0	ERBB2IP	65357490	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	2.230000	0.42999	2.270000	0.75569	0.533000	0.62120	TCT	.	.		0.294	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		C	65321734	T	C	65321734	3	2	103	1	0	0	0	0	1	0	0	0	5209	1435	50	2	987	2	ERBB2IP	5	65321734	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	389962	65321734	115593526	373	14996										
NAIP	4671	hgsc.bcm.edu	37	chr5	70307197	70307197	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaacactgtaccgtgtcctgTttacctatatatgaaggaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:70307197delT	ENST00000517649.1	-	5	863	c.573delA	c.(571-573)aaafs	p.K191fs	NAIP_ENST00000194097.4_Frame_Shift_Del_p.K191fs|NAIP_ENST00000523981.1_Intron|NAIP_ENST00000508426.2_Frame_Shift_Del_p.K191fs|NAIP_ENST00000503719.2_Intron	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	191					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		CCGTGTCCTGTTTACCTATAT	0.438																																					p.Q192fs		Atlas-INDEL	.											.	NAIP	38	.	0			c.574delC						.						122	106	111					5																	70307197		2202	4296	6498	SO:0001589	frameshift_variant	4671	exon5			.	U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"Baculoviral IAP repeat containing", "Nucleotide-binding domain and leucine rich repeat containing"	7634	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1", "NLR family, BIR domain containing 1"	600355	"baculoviral IAP repeat-containing 1"	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.573delA	chr5.hg19:g.70307197delT	ENSP00000428657:p.Lys191fs	145.0	0.0		163.0	10.0	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Del	DEL	ENST00000517649.1	hg19	CCDS4009.1																																																																																			.	.		0.438	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536		-	70307197	T	-	70307197	7	5	103	1	0	1	0	1	0	0	0	0	10156	1722	60	0	3690	0	NAIP	5	70307197	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	4985463	70307197	110608063	374	14997										
MCCC2	64087	hgsc.bcm.edu	37	chr5	70936850	70936850	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtcattgctagaatcgtggaTggaagcagattcactgagtt	12	6	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:70936850T>C	ENST00000340941.6	+	11	1149	c.1020T>C	c.(1018-1020)gaT>gaC	p.D340D	MCCC2_ENST00000323375.8_Silent_p.D302D|MCCC2_ENST00000509358.2_Silent_p.D340D	NM_022132.4	NP_071415.1	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-CoA carboxylase 2 (beta)	340	Carboxyltransferase.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|coenzyme A metabolic process (GO:0015936)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			endometrium(2)|kidney(15)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	30		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	GAATCGTGGATGGAAGCAGAT	0.328																																					p.D340D		Atlas-SNP	.											.	MCCC2	47	.	0			c.T1020C						.						129	122	125					5																	70936850		2203	4300	6503	SO:0001819	synonymous_variant	64087	exon11			CGTGGATGGAAGC	AF310971	CCDS34184.1	5q12-q13	2010-04-30	2010-04-30		ENSG00000131844	ENSG00000131844	6.4.1.4		6937	protein-coding gene	gene with protein product		609014	"methylcrotonoyl-Coenzyme A carboxylase 2 (beta)"				Standard	NM_022132		Approved	MCCB	uc003kbs.4	Q9HCC0	OTTHUMG00000162505	ENST00000340941.6:c.1020T>C	chr5.hg19:g.70936850T>C		69.0	0.0		93.0	4.0	NM_022132	A6NIY9|Q96C27|Q9Y4L7	Silent	SNP	ENST00000340941.6	hg19	CCDS34184.1																																																																																			.	.		0.328	MCCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369243.4			C	70936850	T	C	70936850	2	2	103	1	0	0	0	0	0	0	0	1	9384	1461	51	2		2	MCCC2	5	70936850	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	629653	70936850	109978410	375	14998										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71492183	71492183	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccagtggggatgaccgagccGaagaagacatggatgaggcc	16	9	0	4	rs144088322		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:71492183G>A	ENST00000296755.7	+	5	3299	c.3001G>A	c.(3001-3003)Gaa>Aaa	p.E1001K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1001					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TGACCGAGCCGAAGAAGACAT	0.542																																					p.E1001K	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											MAP1B,colon,carcinoma,0,1	MAP1B	243	.	0			c.G3001A						.	G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	92	91	91		3001	6.1	1	5	dbSNP_134	91	0,8600		0,0,4300	no	missense	MAP1B	NM_005909.3	56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1001/2469	71492183	1,13005	2203	4300	6503	SO:0001583	missense	4131	exon5			CGAGCCGAAGAAG	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3001G>A	chr5.hg19:g.71492183G>A	ENSP00000296755:p.Glu1001Lys	128.0	0.0		127.0	43.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.872172	0.72180	2.27E-4	0.0	ENSG00000131711	ENST00000296755	T	0.03801	3.8	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000004	T	0.08935	0.0221	N	0.08118	0	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	T	0.54556	-0.8276	10	0.10111	T	0.7	-23.6485	20.2738	0.98482	0.0:0.0:1.0:0.0	.	875;1001	A2BDK6;P46821	.;MAP1B_HUMAN	K	1001	ENSP00000296755:E1001K	ENSP00000296755:E1001K	E	+	1	0	MAP1B	71527939	1.000000	0.71417	0.957000	0.39632	0.861000	0.49209	5.156000	0.64905	2.894000	0.99253	0.655000	0.94253	GAA	.	G|1.000;A|0.000		0.542	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71492183	G	A	71492183	3	1	103	1	0	0	0	0	1	0	0	0	9237	1059	37	1	3019	1	MAP1B	5	71492183	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	555333	71492183	109423077	376	14999										
MRPS27	23107	hgsc.bcm.edu	37	chr5	71519665	71519665	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagagccttcagcactgcacCcagcacatcgagctgtggag	11	14	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:71519665C>T	ENST00000261413.5	-	10	889	c.850G>A	c.(850-852)Ggt>Agt	p.G284S	MRPS27_ENST00000513900.1_Missense_Mutation_p.G298S|MRPS27_ENST00000457646.4_Missense_Mutation_p.G228S|MRPS27_ENST00000522562.1_5'UTR	NM_015084.2	NP_055899.2	Q92552	RT27_HUMAN	mitochondrial ribosomal protein S27	284			G -> D (polymorphism confirmed at protein level; dbSNP:rs3209157). {ECO:0000269|PubMed:17488105, ECO:0000269|PubMed:9039502}.			mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)		AGCACTGCACCCAGCACATCG	0.502																																					p.G284S		Atlas-SNP	.											MRPS27,NS,neuroblastoma,0,1	MRPS27	23	.	0			c.G850A						.						63	62	62					5																	71519665		2203	4300	6503	SO:0001583	missense	23107	exon10			CTGCACCCAGCAC	D87453	CCDS4013.1, CCDS68890.1, CCDS75257.1	5q13.2	2012-09-13			ENSG00000113048	ENSG00000113048		"Mitochondrial ribosomal proteins / small subunits"	14512	protein-coding gene	gene with protein product		611989					Standard	NM_015084		Approved	KIAA0264	uc003kbz.4	Q92552	OTTHUMG00000100951	ENST00000261413.5:c.850G>A	chr5.hg19:g.71519665C>T	ENSP00000261413:p.Gly284Ser	93.0	0.0		103.0	0.0	NM_015084	B4DRT2|Q6P1S1	Missense_Mutation	SNP	ENST00000261413.5	hg19	CCDS4013.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.708945	0.30322	.	.	ENSG00000113048	ENST00000261413;ENST00000457646;ENST00000513900;ENST00000508863	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	6.16	5.3	0.74995	.	0.384491	0.32785	N	0.005656	T	0.27559	0.0677	N	0.14661	0.345	0.80722	D	1	B;B;B	0.20671	0.047;0.0;0.047	B;B;B	0.19148	0.024;0.0;0.024	T	0.05321	-1.0892	10	0.30078	T	0.28	-7.2913	13.9186	0.63916	0.0:0.9303:0.0:0.0697	.	298;65;284	B4DRT2;E7ETN4;Q92552	.;.;RT27_HUMAN	S	284;228;298;228	ENSP00000261413:G284S;ENSP00000428120:G228S;ENSP00000426941:G298S;ENSP00000426176:G228S	ENSP00000261413:G284S	G	-	1	0	MRPS27	71555421	0.999000	0.42202	0.931000	0.37212	0.004000	0.04260	3.247000	0.51422	1.628000	0.50416	-0.145000	0.13849	GGT	.	.		0.502	MRPS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218560.2	NM_015084		T	71519665	C	T	71519665	3	4	103	1	0	0	0	0	1	0	0	0	9847	623	22	3	402	3	MRPS27	5	71519665	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	27482	71519665	109395595	377	15000										
WDR41	55255	hgsc.bcm.edu	37	chr5	76729042	76729042	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atccagattctcgctctccaTttttccacaaaataatgaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:76729042delT	ENST00000296679.4	-	13	1673	c.1298delA	c.(1297-1299)aatfs	p.N433fs	WDR41_ENST00000512033.1_5'UTR|WDR41_ENST00000507029.1_Frame_Shift_Del_p.N378fs|WDR41_ENST00000414719.2_Frame_Shift_Del_p.N179fs	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	433						lysosomal membrane (GO:0005765)				NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		TCGCTCTCCATTTTTCCACAA	0.338																																					p.N433fs		Atlas-INDEL	.											.	WDR41	29	.	0			c.1299delT						.						96	98	97					5																	76729042		2203	4300	6503	SO:0001589	frameshift_variant	55255	exon13			.	AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"WD repeat domain containing"	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.1298delA	chr5.hg19:g.76729042delT	ENSP00000296679:p.Asn433fs	153.0	0.0		162.0	10.0	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Frame_Shift_Del	DEL	ENST00000296679.4	hg19	CCDS4038.1																																																																																			.	.		0.338	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268		-	76729042	T	-	76729042	7	5	103	1	0	1	0	1	0	0	0	0	17309	1493	52	0	85	0	WDR41	5	76729042	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5209377	76729042	104186218	378	15001										
BHMT2	23743	hgsc.bcm.edu	37	chr5	78375194	78375194	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacccaactactttgtagttCgtcaacttcacatggaattc	5	11	2	0	rs141648685		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:78375194C>T	ENST00000255192.3	+	3	235	c.169C>T	c.(169-171)Cgt>Tgt	p.R57C	BHMT2_ENST00000521567.1_Missense_Mutation_p.R57C|DMGDH_ENST00000520388.1_Intron	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	57	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)	p.R57C(1)		endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)	CTTTGTAGTTCGTCAACTTCA	0.368													C|||	1	0.000199681	8e-04	0	5008	,	,		18926	0		0	False		,,,				2504	0				p.R57C		Atlas-SNP	.											BHMT2,NS,carcinoma,0,2	BHMT2	44	.	1	Substitution - Missense(1)	large_intestine(1)	c.C169T						.	C	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	82	77	79		169,169	2.9	1	5	dbSNP_134	79	0,8600		0,0,4300	no	missense,missense	BHMT2	NM_001178005.1,NM_017614.4	180,180	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	57/300,57/364	78375194	2,13004	2203	4300	6503	SO:0001583	missense	23743	exon3			GTAGTTCGTCAAC		CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.169C>T	chr5.hg19:g.78375194C>T	ENSP00000255192:p.Arg57Cys	51.0	0.0		49.0	2.0	NM_017614	B7Z516|Q9NXX7	Missense_Mutation	SNP	ENST00000255192.3	hg19	CCDS4045.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.818425	0.71028	4.54E-4	0.0	ENSG00000132840	ENST00000255192;ENST00000521567	T;T	0.14022	2.54;2.54	5.72	2.9	0.33743	Homocysteine S-methyltransferase (4);	0.181464	0.47852	D	0.000204	T	0.37517	0.1006	M	0.85710	2.77	0.34390	D	0.694072	B;D	0.89917	0.047;1.0	B;D	0.71184	0.012;0.972	T	0.56141	-0.8028	10	0.52906	T	0.07	-0.4777	11.419	0.49969	0.0:0.7013:0.2339:0.0648	.	57;57	B7Z516;Q9H2M3	.;BHMT2_HUMAN	C	57	ENSP00000255192:R57C;ENSP00000430278:R57C	ENSP00000255192:R57C	R	+	1	0	BHMT2	78410950	0.998000	0.40836	0.954000	0.39281	0.992000	0.81027	1.973000	0.40550	0.737000	0.32582	0.655000	0.94253	CGT	.	C|1.000;T|0.000		0.368	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614		T	78375194	C	T	78375194	3	4	103	1	0	0	0	0	1	0	0	0	1426	884	31	1	179	1	BHMT2	5	78375194	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	1646152	78375194	102540066	379	15002										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79031144	79031144	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aatcgtggatgtccagcttgTtttttggatcgagcactcca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:79031144delT	ENST00000446378.2	+	2	6587	c.6556delT	c.(6556-6558)tttfs	p.F2187fs		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2187					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GTCCAGCTTGTTTTTTGGATC	0.433																																					p.L2185fs		Atlas-INDEL	.											.	CMYA5	643	.	0			c.6555delG						.						72	71	71					5																	79031144		1876	4124	6000	SO:0001589	frameshift_variant	202333	exon2			.	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6556delT	chr5.hg19:g.79031144delT	ENSP00000394770:p.Phe2187fs	98.0	0.0		150.0	13.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Frame_Shift_Del	DEL	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.		0.433	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		-	79031144	T	-	79031144	7	5	103	1	0	1	0	1	0	0	0	0	3592	1725	60	0	6562	0	CMYA5	5	79031144	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	655950	79031144	101884116	380	15003										
ZCCHC9	84240	hgsc.bcm.edu	37	chr5	80608454	80608454	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaaccgcaaaaacccaaaacAaaaatacctaaagttgttaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:80608454delA	ENST00000254037.2	+	5	3944	c.789delA	c.(787-789)acafs	p.T263fs	ZCCHC9_ENST00000380199.5_Frame_Shift_Del_p.T263fs|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000407610.3_Frame_Shift_Del_p.T263fs|ZCCHC9_ENST00000438268.2_Frame_Shift_Del_p.T263fs			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	263					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		AACCCAAAACAAAAATACCTA	0.403																																					p.T263fs		Atlas-INDEL	.											.	ZCCHC9	26	.	0			c.788delC						.						88	83	85					5																	80608454		2203	4300	6503	SO:0001589	frameshift_variant	84240	exon6			.	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"Zinc fingers, CCHC domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25424	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 41"					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.789delA	chr5.hg19:g.80608454delA	ENSP00000254037:p.Thr263fs	122.0	0.0		165.0	10.0	NM_001131036	B2RAE7|Q9H027	Frame_Shift_Del	DEL	ENST00000254037.2	hg19	CCDS4054.1																																																																																			.	.		0.403	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280		-	80608454	A	-	80608454	7	5	103	1	0	1	0	1	0	0	0	0	17610	117	5	0	807	0	ZCCHC9	5	80608454	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1577310	80608454	100306806	381	15004										
VCAN	1462	hgsc.bcm.edu	37	chr5	82833962	82833962	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgaaacagacacttctgagTggatttccagtaccactgtt	9	9	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:82833962T>C	ENST00000265077.3	+	8	5705	c.5140T>C	c.(5140-5142)Tgg>Cgg	p.W1714R	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Missense_Mutation_p.W727R|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1714	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CACTTCTGAGTGGATTTCCAG	0.428																																					p.W1714R		Atlas-SNP	.											.	VCAN	498	.	0			c.T5140C						.						85	86	86					5																	82833962		2203	4299	6502	SO:0001583	missense	1462	exon8			TCTGAGTGGATTT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.5140T>C	chr5.hg19:g.82833962T>C	ENSP00000265077:p.Trp1714Arg	77.0	0.0		89.0	30.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	T	11.53	1.665094	0.29604	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.84660	-1.86;-1.88;3.26	5.96	2.37	0.29283	.	0.511459	0.18635	N	0.135473	T	0.77631	0.4159	M	0.62723	1.935	0.09310	N	1	P;P	0.46457	0.878;0.806	B;B	0.40285	0.325;0.269	T	0.64943	-0.6288	10	0.12766	T	0.61	.	5.2198	0.15362	0.0:0.1645:0.3648:0.4707	.	727;1714	P13611-2;P13611	.;CSPG2_HUMAN	R	1714;727;727	ENSP00000265077:W1714R;ENSP00000340062:W727R;ENSP00000426251:W727R	ENSP00000265077:W1714R	W	+	1	0	VCAN	82869718	0.023000	0.18921	0.503000	0.27626	0.054000	0.15201	0.285000	0.18883	0.512000	0.28257	0.533000	0.62120	TGG	.	.		0.428	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		C	82833962	T	C	82833962	3	2	103	1	0	0	0	0	1	0	0	0	17153	1696	59	2	5166	2	VCAN	5	82833962	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2225508	82833962	98081298	382	15005										
VCAN	1462	hgsc.bcm.edu	37	chr5	82836233	82836233	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccctggaaaaacatcctgagGtgccaagcgctaaagctgtt	10	11	0	1	rs370712172		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:82836233G>T	ENST00000265077.3	+	8	7976	c.7411G>T	c.(7411-7413)Gtg>Ttg	p.V2471L	VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Missense_Mutation_p.V1484L|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2471	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	ACATCCTGAGGTGCCAAGCGC	0.458																																					p.V2471L		Atlas-SNP	.											.	VCAN	498	.	0			c.G7411T						.						94	91	92					5																	82836233		2203	4300	6503	SO:0001583	missense	1462	exon8			CCTGAGGTGCCAA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7411G>T	chr5.hg19:g.82836233G>T	ENSP00000265077:p.Val2471Leu	116.0	0.0		187.0	54.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	8.393	0.840202	0.16891	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.40476	1.03;1.03	5.97	1.77	0.24775	.	0.697942	0.12964	N	0.424758	T	0.35770	0.0943	M	0.64997	1.995	0.09310	N	1	B;B	0.17667	0.023;0.013	B;B	0.16722	0.016;0.007	T	0.24657	-1.0154	10	0.25106	T	0.35	.	6.7271	0.23363	0.1472:0.0:0.5844:0.2684	.	1484;2471	P13611-2;P13611	.;CSPG2_HUMAN	L	2471;1484	ENSP00000265077:V2471L;ENSP00000340062:V1484L	ENSP00000265077:V2471L	V	+	1	0	VCAN	82871989	0.000000	0.05858	0.001000	0.08648	0.128000	0.20619	0.194000	0.17135	0.819000	0.34492	0.655000	0.94253	GTG	.	.		0.458	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82836233	G	T	82836233	3	4	103	1	0	0	0	0	1	0	0	0	17153	1261	44	3	7437	3	VCAN	5	82836233	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	2271	82836233	98079027	383	15006										
GPR98	84059	hgsc.bcm.edu	37	chr5	90149916	90149916	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaaaggtcagagttcacaacTcctgactaatgacaatgagg	10	8	2	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:90149916T>C	ENST00000405460.2	+	81	17588	c.17492T>C	c.(17491-17493)cTc>cCc	p.L5831P	GPR98_ENST00000425867.2_Missense_Mutation_p.L1492P	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5831					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGTTCACAACTCCTGACTAAT	0.383																																					p.L5831P		Atlas-SNP	.											.	GPR98	605	.	0			c.T17492C						.						131	105	113					5																	90149916		1853	4090	5943	SO:0001583	missense	84059	exon81			CACAACTCCTGAC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.17492T>C	chr5.hg19:g.90149916T>C	ENSP00000384582:p.Leu5831Pro	68.0	0.0		70.0	4.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	1.975	-0.435647	0.04669	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.28069	1.69;1.63	5.3	-0.133	0.13485	.	0.279181	0.41097	N	0.000950	T	0.04407	0.0121	N	0.00104	-2.125	0.19300	N	0.99998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38394	-0.9663	9	.	.	.	.	3.7169	0.08441	0.1162:0.5088:0.1151:0.2599	.	1492;5831;1492	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	P	5831;5831;1492	ENSP00000384582:L5831P;ENSP00000392618:L1492P	.	L	+	2	0	GPR98	90185672	0.006000	0.16342	0.255000	0.24374	0.258000	0.26162	1.228000	0.32588	-0.262000	0.09392	-0.624000	0.04008	CTC	.	.		0.383	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	90149916	T	C	90149916	3	2	103	1	0	0	0	0	1	0	0	0	6730	1551	54	2	17814	2	GPR98	5	90149916	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	7313683	90149916	90765344	384	15007										
POU5F2	134187	hgsc.bcm.edu	37	chr5	93076558	93076558	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcaatgtggctgatttgctGgggtgtgggcttagggcacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:93076558delG	ENST00000510627.4	-	1	785	c.712delC	c.(712-714)cagfs	p.Q239fs	FAM172A_ENST00000509163.1_Intron|RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000505869.1_Intron|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000395965.3_Intron|POU5F2_ENST00000606183.1_5'UTR	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	239					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		CTGATTTGCTGGGGTGTGGGC	0.552																																					p.Q238fs		Atlas-INDEL	.											.	POU5F2	10	.	0			c.713delA						.						52	52	52					5																	93076558		1995	4178	6173	SO:0001589	frameshift_variant	134187	exon1			.		CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.712delC	chr5.hg19:g.93076558delG	ENSP00000464890:p.Gln239fs	201.0	0.0		221.0	14.0	NM_153216	Q15169|Q6MZL7|Q8N748	Frame_Shift_Del	DEL	ENST00000510627.4	hg19	CCDS59489.1																																																																																			.	.		0.552	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		-	93076558	G	-	93076558	7	5	103	1	0	1	0	1	0	0	0	0	12292	1357	47	0	278	0	POU5F2	5	93076558	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2926642	93076558	87838702	385	15008										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101774421	101774421	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ataactaaatattctgtagcTtttgacagagctaggcatat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:101774421delT	ENST00000506729.1	-	7	1347	c.1176delA	c.(1174-1176)aaafs	p.K392fs	SLCO6A1_ENST00000389019.3_Frame_Shift_Del_p.K330fs|SLCO6A1_ENST00000514551.1_5'UTR|SLCO6A1_ENST00000379807.3_Frame_Shift_Del_p.K392fs|SLCO6A1_ENST00000513675.1_Intron|SLCO6A1_ENST00000379810.1_Intron			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	392						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		ATTCTGTAGCTTTTGACAGAG	0.294																																					p.A393fs		Atlas-INDEL	.											.	SLCO6A1	153	.	0			c.1177delG						.						36	41	39					5																	101774421		2200	4291	6491	SO:0001589	frameshift_variant	133482	exon7			.	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1176delA	chr5.hg19:g.101774421delT	ENSP00000421339:p.Lys392fs	123.0	0.0		143.0	11.0	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Frame_Shift_Del	DEL	ENST00000506729.1	hg19	CCDS34206.1																																																																																			.	.		0.294	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		-	101774421	T	-	101774421	7	5	103	1	0	1	0	1	0	0	0	0	14747	1606	56	0	1011	0	SLCO6A1	5	101774421	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	8697863	101774421	79140839	386	15009										
PPIP5K2	23262	hgsc.bcm.edu	37	chr5	102472511	102472511	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caatgacttgaatatgcagtAtctcatacaagataggtgag	9	6	1	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:102472511A>G	ENST00000358359.3	+	4	895	c.386A>G	c.(385-387)tAt>tGt	p.Y129C	PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000321521.9_Missense_Mutation_p.Y129C|PPIP5K2_ENST00000414217.1_Missense_Mutation_p.Y129C	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	129					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)	p.Y129C(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						AATATGCAGTATCTCATACAA	0.363																																					p.Y129C		Atlas-SNP	.											PPIP5K2,NS,carcinoma,0,1	PPIP5K2	98	.	1	Substitution - Missense(1)	lung(1)	c.A386G						.						166	178	174					5																	102472511		2203	4299	6502	SO:0001583	missense	23262	exon3			TGCAGTATCTCAT	AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"histidine acid phosphatase domain containing 1"	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.386A>G	chr5.hg19:g.102472511A>G	ENSP00000351126:p.Tyr129Cys	57.0	0.0		69.0	3.0	NM_015216	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	hg19		.	.	.	.	.	.	.	.	.	.	A	19.77	3.889958	0.72524	.	.	ENSG00000145725	ENST00000321521;ENST00000507921;ENST00000358359;ENST00000451606;ENST00000414217;ENST00000507310	T;T;T;T	0.14893	2.47;3.11;2.47;2.47	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000008	T	0.46600	0.1401	M	0.88570	2.965	0.80722	D	1	D;D;D	0.76494	0.994;0.999;0.999	P;P;P	0.62885	0.792;0.902;0.908	T	0.57341	-0.7828	10	0.87932	D	0	-17.488	15.4885	0.75587	1.0:0.0:0.0:0.0	.	51;129;129	D6RBU4;O43314-2;O43314	.;.;VIP2_HUMAN	C	129;51;129;129;129;59	ENSP00000313070:Y129C;ENSP00000422525:Y51C;ENSP00000351126:Y129C;ENSP00000416016:Y129C	ENSP00000313070:Y129C	Y	+	2	0	PPIP5K2	102500410	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.910000	0.92685	2.117000	0.64856	0.383000	0.25322	TAT	.	.		0.363	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		G	102472511	A	G	102472511	3	3	103	1	0	0	0	0	1	0	0	0	12345	449	16	2	396	2	PPIP5K2	5	102472511	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	698090	102472511	78442749	387	15010										
SHROOM1	134549	hgsc.bcm.edu	37	chr5	132159877	132159877	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggtcactctctgcagctgtGgggggattggtggtcagtcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:132159877delG	ENST00000378679.3	-	7	2280	c.1476delC	c.(1474-1476)cccfs	p.P492fs	SHROOM1_ENST00000378676.1_Frame_Shift_Del_p.P423fs|SHROOM1_ENST00000488072.1_5'Flank|SHROOM1_ENST00000319854.3_Frame_Shift_Del_p.P492fs	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	492					actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTGCAGCTGTGGGGGGATTGG	0.542																																					p.T493fs		Atlas-INDEL	.											.	SHROOM1	35	.	0			c.1477delA						.						102	94	97					5																	132159877		2203	4300	6503	SO:0001589	frameshift_variant	134549	exon4			.	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.1476delC	chr5.hg19:g.132159877delG	ENSP00000367950:p.Pro492fs	269.0	0.0		294.0	18.0	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Frame_Shift_Del	DEL	ENST00000378679.3	hg19	CCDS54902.1																																																																																			.	.		0.542	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		-	132159877	G	-	132159877	7	5	103	1	0	1	0	1	0	0	0	0	14308	1335	47	0	1098	0	SHROOM1	5	132159877	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	29687366	132159877	48755383	388	15011										
FSTL4	23105	hgsc.bcm.edu	37	chr5	132553042	132553042	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	actggcagggctgggttgcaTttttttctctttgaggacag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:132553042delT	ENST00000265342.7	-	13	1736	c.1487delA	c.(1486-1488)aatfs	p.N496fs	CTB-49A3.2_ENST00000509051.1_RNA|CTB-49A3.2_ENST00000502776.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	496						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTGGGTTGCATTTTTTTCTCT	0.493																																					p.N496fs		Atlas-INDEL	.											.	FSTL4	74	.	0			c.1488delT						.						87	85	86					5																	132553042		2203	4300	6503	SO:0001589	frameshift_variant	23105	exon13			.	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.1487delA	chr5.hg19:g.132553042delT	ENSP00000265342:p.Asn496fs	137.0	0.0		180.0	12.0	NM_015082	Q8TBU0|Q9UPU1	Frame_Shift_Del	DEL	ENST00000265342.7	hg19	CCDS34238.1																																																																																			.	.		0.493	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786		-	132553042	T	-	132553042	7	5	103	1	0	1	0	1	0	0	0	0	6087	1493	52	0	1057	0	FSTL4	5	132553042	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	393165	132553042	48362218	389	15012										
PCBD2	84105	hgsc.bcm.edu	37	chr5	134296318	134296318	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgactgtggtgaactgaccAaaaaagatgtgaagctggcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:134296318delA	ENST00000512783.1	+	4	360	c.340delA	c.(340-342)aaafs	p.K115fs	PCBD2_ENST00000254908.6_Frame_Shift_Del_p.K115fs			Q9H0N5	PHS2_HUMAN	pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2	115					positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein homotetramerization (GO:0051289)|tetrahydrobiopterin biosynthetic process (GO:0006729)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	4-alpha-hydroxytetrahydrobiopterin dehydratase activity (GO:0008124)|phenylalanine 4-monooxygenase activity (GO:0004505)			kidney(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGAACTGACCAAAAAAGATGT	0.368																																					p.T113fs		Atlas-INDEL	.											.	PCBD2	3	.	0			c.339delC						.						86	77	80					5																	134296318		1830	4098	5928	SO:0001589	frameshift_variant	84105	exon4			.	AF499009	CCDS43364.1	5q31.1	2008-02-05	2006-01-10			ENSG00000132570			24474	protein-coding gene	gene with protein product		609836	"6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2"			15182178, 11980910	Standard	NM_032151		Approved	DCOHM, DCOH2	uc010jdz.3	Q9H0N5		ENST00000512783.1:c.340delA	chr5.hg19:g.134296318delA	ENSP00000421544:p.Lys115fs	166.0	0.0		198.0	15.0	NM_032151	Q8TD40	Frame_Shift_Del	DEL	ENST00000512783.1	hg19	CCDS43364.1																																																																																			.	.		0.368	PCBD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371578.1	NM_032151		-	134296318	A	-	134296318	7	5	103	1	0	1	0	1	0	0	0	0	11508	131	5	0	354	0	PCBD2	5	134296318	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1743276	134296318	46618942	390	15013										
SLC35A4	113829	hgsc.bcm.edu	37	chr5	139946770	139946770	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgggtatgagtgtagaggatGggggtatgccaggcctgggc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:139946770delG	ENST00000514199.1	+	2	1702	c.16delG	c.(16-18)gggfs	p.G7fs	APBB3_ENST00000412920.3_5'Flank|APBB3_ENST00000507279.1_Intron|APBB3_ENST00000356738.2_5'Flank|SLC35A4_ENST00000508770.1_3'UTR|APBB3_ENST00000358580.5_5'Flank|APBB3_ENST00000354402.5_5'Flank|SLC35A4_ENST00000323146.3_Frame_Shift_Del_p.G7fs|APBB3_ENST00000511201.2_5'Flank|APBB3_ENST00000357560.4_5'Flank|APBB3_ENST00000508496.2_5'Flank			Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	7						Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTAGAGGATGGGGGTATGCC	0.602																																					p.D5fs		Atlas-INDEL	.											.	SLC35A4	25	.	0			c.15delT						.						74	78	77					5																	139946770		2203	4300	6503	SO:0001589	frameshift_variant	113829	exon3			.	AJ420598	CCDS4231.1	5q31.3	2013-05-22			ENSG00000176087	ENSG00000176087		"Solute carriers"	20753	protein-coding gene	gene with protein product							Standard	NM_080670		Approved		uc003lgg.1	Q96G79	OTTHUMG00000129495	ENST00000514199.1:c.16delG	chr5.hg19:g.139946770delG	ENSP00000424566:p.Gly7fs	120.0	0.0		159.0	12.0	NM_080670	A8K013	Frame_Shift_Del	DEL	ENST00000514199.1	hg19	CCDS4231.1																																																																																			.	.		0.602	SLC35A4-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372815.1	NM_080670		-	139946770	G	-	139946770	7	5	103	1	0	1	0	1	0	0	0	0	14588	1348	47	0	18	0	SLC35A4	5	139946770	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	5650452	139946770	40968490	391	15014										
PCDHAC1	56135	hgsc.bcm.edu	37	chr5	140306876	140306876	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcgacgtgcagctgcacatCcccgagttcctgacgcccgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:140306876delC	ENST00000253807.2	+	1	399	c.399delC	c.(397-399)atcfs	p.I133fs	PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHAC1_ENST00000409700.3_Frame_Shift_Del_p.I133fs|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	133	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTGCACATCCCCGAGTTCC	0.587																																					p.I133fs		Atlas-INDEL	.											.	PCDHAC1	141	.	0			c.398delT						.						65	62	63					5																	140306876		2203	4300	6503	SO:0001589	frameshift_variant	56135	exon1			.	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"Cadherins / Protocadherins : Clustered"	8676	other	complex locus constituent	"PCDH-ALPHA-C1"	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.399delC	chr5.hg19:g.140306876delC	ENSP00000253807:p.Ile133fs	145.0	0.0		180.0	11.0	NM_031882	Q9Y5F5|Q9Y5I5	Frame_Shift_Del	DEL	ENST00000253807.2	hg19	CCDS4241.1																																																																																			.	.		0.587	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		-	140306876	C	-	140306876	7	5	103	1	0	1	0	1	0	0	0	0	11541	845	30	0	401	0	PCDHAC1	5	140306876	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	360106	140306876	40608384	392	15015										
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140590838	140590838	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtagtgaagtcgaagaaaatCccccatttcagaataatttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:140590838delC	ENST00000239450.2	+	1	2548	c.2359delC	c.(2359-2361)cccfs	p.P788fs	PCDHB13_ENST00000341948.4_5'Flank|PCDHB12_ENST00000541609.1_Frame_Shift_Del_p.P451fs	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	788					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGAAGAAAATCCCCCATTTCA	0.378																																					p.N786fs		Atlas-INDEL	.											.	PCDHB12	179	.	0			c.2358delT						.						55	57	56					5																	140590838		2202	4300	6502	SO:0001589	frameshift_variant	56124	exon1			.	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.2359delC	chr5.hg19:g.140590838delC	ENSP00000239450:p.Pro788fs	138.0	0.0		194.0	12.0	NM_018932	B4DDU1	Frame_Shift_Del	DEL	ENST00000239450.2	hg19	CCDS4254.1																																																																																			.	.		0.378	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		-	140590838	C	-	140590838	7	5	103	1	0	1	0	1	0	0	0	0	11546	855	30	0	2361	0	PCDHB12	5	140590838	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	283962	140590838	40324422	393	15016										
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140711785	140711785	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctccatcaactccgacactGgggtcctgtatgcgctgcga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:140711785delG	ENST00000517417.1	+	1	1534	c.1534delG	c.(1534-1536)gggfs	p.G512fs	PCDHGA1_ENST00000378105.3_Frame_Shift_Del_p.G512fs|AC005618.6_ENST00000606901.1_lincRNA	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	512	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCGACACTGGGGTCCTGTA	0.552																																					p.T511fs		Atlas-INDEL	.											.	PCDHGA1	397	.	0			c.1533delT						.						136	148	144					5																	140711785		2203	4300	6503	SO:0001589	frameshift_variant	56114	exon1			.	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1534delG	chr5.hg19:g.140711785delG	ENSP00000431083:p.Gly512fs	111.0	0.0		149.0	11.0	NM_018912	Q2M273|Q9Y5D6	Frame_Shift_Del	DEL	ENST00000517417.1	hg19	CCDS54922.1																																																																																			.	.		0.552	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		-	140711785	G	-	140711785	7	5	103	1	0	1	0	1	0	0	0	0	11559	1348	47	0	1536	0	PCDHGA1	5	140711785	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	120947	140711785	40203475	394	15017										
NR3C1	2908	hgsc.bcm.edu	37	chr5	142680214	142680214	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgacaccagggtaggggtgAgttgtggtaacgttgcagga	18	5	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:142680214A>C	ENST00000343796.2	-	5	2576	c.1583T>G	c.(1582-1584)cTc>cGc	p.L528R	NR3C1_ENST00000394464.2_Missense_Mutation_p.L528R|NR3C1_ENST00000394466.2_Missense_Mutation_p.L529R|NR3C1_ENST00000424646.2_Missense_Mutation_p.L502R|NR3C1_ENST00000416954.2_Missense_Mutation_p.L131R|NR3C1_ENST00000415690.2_Missense_Mutation_p.L528R|NR3C1_ENST00000504336.1_5'UTR|NR3C1_ENST00000503201.1_Missense_Mutation_p.L528R|NR3C1_ENST00000504572.1_Missense_Mutation_p.L529R|NR3C1_ENST00000231509.3_Missense_Mutation_p.L529R	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	528	Interaction with CLOCK.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	GGTAGGGGTGAGTTGTGGTAA	0.423																																					p.L529R		Atlas-SNP	.											.	NR3C1	124	.	0			c.T1586G						.						217	197	204					5																	142680214		2203	4300	6503	SO:0001583	missense	2908	exon5			GGGGTGAGTTGTG	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.1583T>G	chr5.hg19:g.142680214A>C	ENSP00000343205:p.Leu528Arg	234.0	0.0		251.0	76.0	NM_001024094	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	hg19	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.751525	0.89753	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000416954;ENST00000503201	D;D;D;D;D;D;D;D;D	0.87491	-1.91;-1.91;-1.87;-1.88;-1.91;-1.91;-1.91;-2.26;-1.91	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.94830	0.8330	M	0.91561	3.22	0.80722	D	1	D;D;D	0.89917	1.0;0.987;0.997	D;P;D	0.85130	0.997;0.836;0.995	D	0.95753	0.8793	10	0.72032	D	0.01	.	15.94	0.79747	1.0:0.0:0.0:0.0	.	528;528;529	E5KQF5;P04150;E5KQF6	.;GCR_HUMAN;.	R	528;528;528;502;529;529;529;131;528	ENSP00000377977:L528R;ENSP00000343205:L528R;ENSP00000387672:L528R;ENSP00000405282:L502R;ENSP00000422518:L529R;ENSP00000377979:L529R;ENSP00000231509:L529R;ENSP00000404218:L131R;ENSP00000427672:L528R	ENSP00000231509:L529R	L	-	2	0	NR3C1	142660407	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.979000	0.76154	2.156000	0.67533	0.533000	0.62120	CTC	.	.		0.423	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			C	142680214	A	C	142680214	3	2	103	1	0	0	0	0	1	0	0	0	10639	304	11	5	822	5	NR3C1	5	142680214	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1968429	142680214	38235046	395	15018										
RBM27	54439	hgsc.bcm.edu	37	chr5	145608566	145608566	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaaaaaagaaatatcctagtCcccagaagactcgttcagaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:145608566delC	ENST00000265271.5	+	4	527	c.361delC	c.(361-363)cccfs	p.P121fs	RBM27_ENST00000506502.1_Frame_Shift_Del_p.P121fs	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	121					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATATCCTAGTCCCCAGAAGAC	0.398																																					p.S120fs		Atlas-INDEL	.											.	RBM27	119	.	0			c.360delT						.						151	146	147					5																	145608566		1568	3582	5150	SO:0001589	frameshift_variant	54439	exon4			.	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.361delC	chr5.hg19:g.145608566delC	ENSP00000265271:p.Pro121fs	171.0	0.0		164.0	14.0	NM_018989	Q8IYW9	Frame_Shift_Del	DEL	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.		0.398	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		-	145608566	C	-	145608566	7	5	103	1	0	1	0	1	0	0	0	0	13142	855	30	0	375	0	RBM27	5	145608566	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2928352	145608566	35306694	396	15019										
PPARGC1B	133522	hgsc.bcm.edu	37	chr5	149219630	149219630	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagcagagggccgtgttcagAcagaacgccaagcatccggc	14	12	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:149219630A>G	ENST00000309241.5	+	9	2677	c.2645A>G	c.(2644-2646)gAc>gGc	p.D882G	PPARGC1B_ENST00000403750.1_Missense_Mutation_p.D818G|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.D882G|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.D843G	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	882					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCGTGTTCAGACAGAACGCCA	0.597																																					p.D882G		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.A2645G						.						74	66	69					5																	149219630		2203	4300	6503	SO:0001583	missense	133522	exon9			GTTCAGACAGAAC	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"RNA binding motif (RRM) containing"	30022	protein-coding gene	gene with protein product		608886	"peroxisome proliferative activated receptor, gamma, coactivator 1, beta"			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.2645A>G	chr5.hg19:g.149219630A>G	ENSP00000312649:p.Asp882Gly	101.0	0.0		120.0	5.0	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	hg19	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	A	9.700	1.154333	0.21371	.	.	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.05	3.88	0.44766	.	0.508876	0.21102	N	0.080145	T	0.37758	0.1015	N	0.21448	0.665	0.19300	N	0.999977	B;P;B;B;B	0.50943	0.007;0.94;0.003;0.004;0.027	B;P;B;B;B	0.54629	0.009;0.757;0.023;0.006;0.019	T	0.10314	-1.0635	10	0.30078	T	0.28	-9.2187	7.2627	0.26212	0.7389:0.0:0.2611:0.0	.	861;861;843;882;882	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	G	843;882;882;818	ENSP00000353638:D843G;ENSP00000377855:D882G;ENSP00000312649:D882G;ENSP00000384403:D818G	ENSP00000312649:D882G	D	+	2	0	PPARGC1B	149199823	0.966000	0.33281	0.989000	0.46669	0.989000	0.77384	2.090000	0.41682	0.774000	0.33427	0.379000	0.24179	GAC	.	.		0.597	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		G	149219630	A	G	149219630	3	3	103	1	0	0	0	0	1	0	0	0	12310	275	10	2	2686	2	PPARGC1B	5	149219630	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	3611064	149219630	31695630	397	15020										
PDE6A	5145	hgsc.bcm.edu	37	chr5	149276290	149276290	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcaccaggatctcagccagcTcctcttcctcacactcccat	4	19	4	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:149276290T>C	ENST00000255266.5	-	11	1576	c.1457A>G	c.(1456-1458)gAg>gGg	p.E486G		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	486					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CTCAGCCAGCTCCTCTTCCTC	0.532																																					p.E486G		Atlas-SNP	.											.	PDE6A	98	.	0			c.A1457G						.						165	158	160					5																	149276290		2203	4300	6503	SO:0001583	missense	5145	exon11			GCCAGCTCCTCTT		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.1457A>G	chr5.hg19:g.149276290T>C	ENSP00000255266:p.Glu486Gly	125.0	0.0		101.0	7.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.078394	0.76528	.	.	ENSG00000132915	ENST00000255266	T	0.65178	-0.14	5.9	5.9	0.94986	.	0.162346	0.52532	D	0.000067	T	0.71213	0.3313	M	0.85373	2.75	0.53688	D	0.999975	P	0.35226	0.491	B	0.40825	0.341	T	0.75288	-0.3370	10	0.72032	D	0.01	.	14.2745	0.66170	0.0:0.0:0.0:1.0	.	486	P16499	PDE6A_HUMAN	G	486	ENSP00000255266:E486G	ENSP00000255266:E486G	E	-	2	0	PDE6A	149256483	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.556000	0.67307	2.263000	0.75096	0.533000	0.62120	GAG	.	.		0.532	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			C	149276290	T	C	149276290	3	2	103	1	0	0	0	0	1	0	0	0	11654	1551	54	2	1173	2	PDE6A	5	149276290	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	56660	149276290	31638970	398	15021										
CAMK2A	815	hgsc.bcm.edu	37	chr5	149636381	149636381	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacgatatcttcaaacagttCcccaccagtgaccctgggga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:149636381delC	ENST00000348628.6	-	5	951	c.286delG	c.(286-288)gaafs	p.E96fs	CAMK2A_ENST00000398376.3_Frame_Shift_Del_p.E96fs	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCAAACAGTTCCCCACCAGTG	0.587																																					p.E96fs		Atlas-INDEL	.											.	CAMK2A	42	.	0			c.287delA						.						67	70	69					5																	149636381		2059	4203	6262	SO:0001589	frameshift_variant	815	exon5			.	AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"CaM-kinase II alpha chain", "calcium/calmodulin-dependent protein kinase II alpha-B subunit", "CaM kinase II alpha subunit", "CaMK-II alpha subunit", "calcium/calmodulin-dependent protein kinase type II alpha chain"	114078	"calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.286delG	chr5.hg19:g.149636381delC	ENSP00000261793:p.Glu96fs	155.0	0.0		177.0	12.0	NM_171825	Q9UL21|Q9Y2H4|Q9Y352	Frame_Shift_Del	DEL	ENST00000348628.6	hg19	CCDS43386.1																																																																																			.	.		0.587	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981		-	149636381	C	-	149636381	7	5	103	1	0	1	0	1	0	0	0	0	2601	864	30	0	1243	0	CAMK2A	5	149636381	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	360091	149636381	31278879	399	15022										
SLC36A3	285641	hgsc.bcm.edu	37	chr5	150666921	150666921	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacaccaacaggatcaggaaGggcaggattatcagcatgta	11	8	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:150666921G>T	ENST00000335230.3	-	6	1005	c.594C>A	c.(592-594)ccC>ccA	p.P198P	SLC36A3_ENST00000377713.3_Silent_p.P239P	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	198						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGATCAGGAAGGGCAGGATTA	0.527																																					p.P239P		Atlas-SNP	.											.	SLC36A3	54	.	0			c.C717A						.						168	156	160					5																	150666921		2203	4300	6503	SO:0001819	synonymous_variant	285641	exon7			CAGGAAGGGCAGG	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"Solute carriers"	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.594C>A	chr5.hg19:g.150666921G>T		165.0	0.0		224.0	61.0	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Silent	SNP	ENST00000335230.3	hg19	CCDS4314.1																																																																																			.	.		0.527	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774		T	150666921	G	T	150666921	2	4	103	1	0	0	0	0	0	0	0	1	14610	987	35	3		3	SLC36A3	5	150666921	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	1030540	150666921	30248339	400	15023										
LARP1	23367	hgsc.bcm.edu	37	chr5	154181822	154181822	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attacatgcgccggcacccaGggggggaccgcacaggcaac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:154181822delG	ENST00000336314.4	+	11	1765	c.1741delG	c.(1741-1743)gggfs	p.G582fs		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	659					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CCGGCACCCAGGGGGGGACCG	0.547																																					p.P580fs		Atlas-INDEL	.											.	LARP1	187	.	0			c.1740delA						.						79	76	77					5																	154181822		2203	4300	6503	SO:0001589	frameshift_variant	23367	exon11			.	AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"La ribonucleoprotein domain containing"	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.1741delG	chr5.hg19:g.154181822delG	ENSP00000336721:p.Gly582fs	119.0	0.0		157.0	16.0	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Frame_Shift_Del	DEL	ENST00000336314.4	hg19	CCDS4328.1																																																																																			.	.		0.547	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		-	154181822	G	-	154181822	7	5	103	1	0	1	0	1	0	0	0	0	8637	1000	35	0	1783	0	LARP1	5	154181822	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	3514901	154181822	26733438	401	15024										
FAM71B	153745	hgsc.bcm.edu	37	chr5	156592606	156592606	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttgtcttcgggtggtgcgtCcccagatagaagtgttgggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:156592606delC	ENST00000302938.4	-	1	669	c.574delG	c.(574-576)gacfs	p.D192fs		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	192						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGTGGTGCGTCCCCAGATAGA	0.507																																					p.D192fs		Atlas-INDEL	.											.	FAM71B	145	.	0			c.575delA						.						200	201	200					5																	156592606		2203	4300	6503	SO:0001589	frameshift_variant	153745	exon1			.		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.574delG	chr5.hg19:g.156592606delC	ENSP00000305596:p.Asp192fs	208.0	0.0		265.0	17.0	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Frame_Shift_Del	DEL	ENST00000302938.4	hg19	CCDS4335.1																																																																																			.	.		0.507	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		-	156592606	C	-	156592606	7	5	103	1	0	1	0	1	0	0	0	0	5616	855	30	0	1251	0	FAM71B	5	156592606	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2410784	156592606	24322654	402	15025										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167553853	167553853	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcgcagcgtgtgaccagcgCgtgtgccacccccgctgcat	14	16	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:167553853C>T	ENST00000518659.1	+	12	2343	c.2304C>T	c.(2302-2304)cgC>cgT	p.R768R	CTB-178M22.1_ENST00000517408.1_RNA|TENM2_ENST00000403607.2_Silent_p.R601R|TENM2_ENST00000545108.1_Silent_p.R768R|TENM2_ENST00000519204.1_Silent_p.R647R|TENM2_ENST00000520394.1_Silent_p.R536R	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	768					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										GTGACCAGCGCGTGTGCCACC	0.597																																					p.R768R		Atlas-SNP	.											.	.	.	.	0			c.C2304T						.						45	51	49					5																	167553853		2036	4168	6204	SO:0001819	synonymous_variant	57451	exon12			CCAGCGCGTGTGC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.2304C>T	chr5.hg19:g.167553853C>T		199.0	0.0		231.0	66.0	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	hg19																																																																																				.	.		0.597	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	167553853	C	T	167553853	2	4	103	1	0	0	0	0	0	0	0	1	10844	755	27	1		1	ODZ2	5	167553853	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	10961247	167553853	13361407	403	15026										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168100194	168100194	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcattacctccaaggtagaGggggctgttgatgcccactg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:168100194delG	ENST00000519560.1	-	33	4248	c.3829delC	c.(3829-3831)ctcfs	p.L1277fs	SLIT3_ENST00000404867.3_Frame_Shift_Del_p.L1277fs|SLIT3_ENST00000332966.8_Frame_Shift_Del_p.L1284fs	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1277	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCAAGGTAGAGGGGGCTGTTG	0.567																																					p.L1284fs	Ovarian(29;311 847 10864 17279 24903)	Atlas-INDEL	.											.	SLIT3	224	.	0			c.3851delT						.						158	156	156					5																	168100194		2203	4300	6503	SO:0001589	frameshift_variant	6586	exon33			.	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.3829delC	chr5.hg19:g.168100194delG	ENSP00000430333:p.Leu1277fs	162.0	0.0		151.0	11.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Frame_Shift_Del	DEL	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.567	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		-	168100194	G	-	168100194	7	5	103	1	0	1	0	1	0	0	0	0	14756	1000	35	0	758	0	SLIT3	5	168100194	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	546341	168100194	12815066	404	15027										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168678426	168678426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttgagcccagcgaagtccaTcttggtgatcctggtgatat	11	10	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:168678426T>C	ENST00000519560.1	-	2	654	c.235A>G	c.(235-237)Atg>Gtg	p.M79V	SLIT3_ENST00000404867.3_Missense_Mutation_p.M79V|SLIT3_ENST00000332966.8_Missense_Mutation_p.M79V|SLIT3_ENST00000521130.1_5'UTR	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	79					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCGAAGTCCATCTTGGTGATC	0.413																																					p.M79V	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.A235G						.						172	159	163					5																	168678426		2203	4300	6503	SO:0001583	missense	6586	exon2			AGTCCATCTTGGT	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.235A>G	chr5.hg19:g.168678426T>C	ENSP00000430333:p.Met79Val	57.0	0.0		85.0	4.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	hg19	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	T	10.49	1.364632	0.24684	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.75154	-0.91;-0.91;-0.9	4.95	3.79	0.43588	.	0.365925	0.25122	N	0.032962	T	0.55545	0.1927	N	0.17474	0.49	0.25971	N	0.982505	B;B	0.10296	0.003;0.0	B;B	0.09377	0.004;0.002	T	0.47195	-0.9136	10	0.45353	T	0.12	.	7.2019	0.25885	0.0:0.1015:0.0:0.8985	.	79;79	O75094-2;O75094	.;SLIT3_HUMAN	V	79	ENSP00000430333:M79V;ENSP00000332164:M79V;ENSP00000384890:M79V	ENSP00000332164:M79V	M	-	1	0	SLIT3	168611004	0.960000	0.32886	1.000000	0.80357	0.998000	0.95712	1.722000	0.38042	0.751000	0.32900	0.533000	0.62120	ATG	.	.		0.413	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		C	168678426	T	C	168678426	3	2	103	1	0	0	0	0	1	0	0	0	14756	1435	50	2	4476	2	SLIT3	5	168678426	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	578232	168678426	12236834	405	15028										
TLX3	30012	hgsc.bcm.edu	37	chr5	170736706	170736706	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcgcgctacccgccatgcccTccgtgcccacggtctccagc	10	21	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:170736706T>C	ENST00000296921.5	+	1	419	c.337T>C	c.(337-339)Tcc>Ccc	p.S113P		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	113					central nervous system development (GO:0007417)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|respiratory gaseous exchange (GO:0007585)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CGCCATGCCCTCCGTGCCCAC	0.706			T	BCL11B	T-ALL																																p.S113P	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"T-cell leukemia, homeobox 3 (HOX11L2)"		L	.	TLX3	23	.	0			c.T337C						.						13	15	14					5																	170736706		2165	4256	6421	SO:0001583	missense	30012	exon1			ATGCCCTCCGTGC	AJ223798	CCDS34288.1	5q35.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000164438	ENSG00000164438		"Homeoboxes / ANTP class : NKL subclass"	13532	protein-coding gene	gene with protein product		604640	"homeo box 11-like 2", "T-cell leukemia, homeobox 3"	HOX11L2		11435718, 11435716	Standard	NM_021025		Approved	RNX	uc003mbf.3	O43711	OTTHUMG00000163207	ENST00000296921.5:c.337T>C	chr5.hg19:g.170736706T>C	ENSP00000296921:p.Ser113Pro	55.0	0.0		75.0	5.0	NM_021025	Q96AD3	Missense_Mutation	SNP	ENST00000296921.5	hg19	CCDS34288.1	.	.	.	.	.	.	.	.	.	.	T	12.60	1.987211	0.35036	.	.	ENSG00000164438	ENST00000296921	D	0.91686	-2.89	4.4	3.23	0.37069	.	0.157179	0.40144	N	0.001163	D	0.82793	0.5114	N	0.17082	0.46	0.25980	N	0.982389	P	0.45634	0.863	B	0.41988	0.372	T	0.74293	-0.3712	10	0.19590	T	0.45	.	8.8572	0.35236	0.0:0.0:0.3788:0.6212	.	113	O43711	TLX3_HUMAN	P	113	ENSP00000296921:S113P	ENSP00000296921:S113P	S	+	1	0	TLX3	170669311	0.846000	0.29590	1.000000	0.80357	0.994000	0.84299	0.797000	0.26999	1.861000	0.53984	0.454000	0.30748	TCC	.	.		0.706	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3			C	170736706	T	C	170736706	3	2	103	1	0	0	0	0	1	0	0	0	15977	1551	54	2	339	2	TLX3	5	170736706	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2058280	170736706	10178554	406	15029										
TLX3	30012	hgsc.bcm.edu	37	chr5	170736779	170736779	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagccgccgcttcgtgaaagAccgcttcacaggtgagcaga	12	13	1	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:170736779A>G	ENST00000296921.5	+	1	492	c.410A>G	c.(409-411)gAc>gGc	p.D137G		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	137					central nervous system development (GO:0007417)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|respiratory gaseous exchange (GO:0007585)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTCGTGAAAGACCGCTTCACA	0.682			T	BCL11B	T-ALL																																p.D137G	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"T-cell leukemia, homeobox 3 (HOX11L2)"		L	.	TLX3	23	.	0			c.A410G						.						15	18	17					5																	170736779		2184	4277	6461	SO:0001583	missense	30012	exon1			TGAAAGACCGCTT	AJ223798	CCDS34288.1	5q35.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000164438	ENSG00000164438		"Homeoboxes / ANTP class : NKL subclass"	13532	protein-coding gene	gene with protein product		604640	"homeo box 11-like 2", "T-cell leukemia, homeobox 3"	HOX11L2		11435718, 11435716	Standard	NM_021025		Approved	RNX	uc003mbf.3	O43711	OTTHUMG00000163207	ENST00000296921.5:c.410A>G	chr5.hg19:g.170736779A>G	ENSP00000296921:p.Asp137Gly	51.0	0.0		54.0	4.0	NM_021025	Q96AD3	Missense_Mutation	SNP	ENST00000296921.5	hg19	CCDS34288.1	.	.	.	.	.	.	.	.	.	.	A	18.55	3.649208	0.67358	.	.	ENSG00000164438	ENST00000296921	D	0.91843	-2.92	4.31	4.31	0.51392	.	0.051376	0.85682	D	0.000000	D	0.93383	0.7890	M	0.70595	2.14	0.44098	D	0.99686	P	0.42248	0.774	P	0.50896	0.653	D	0.93590	0.6920	10	0.56958	D	0.05	.	12.6052	0.56519	1.0:0.0:0.0:0.0	.	137	O43711	TLX3_HUMAN	G	137	ENSP00000296921:D137G	ENSP00000296921:D137G	D	+	2	0	TLX3	170669384	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.019000	0.76412	1.823000	0.53134	0.454000	0.30748	GAC	.	.		0.682	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3			G	170736779	A	G	170736779	3	3	103	1	0	0	0	0	1	0	0	0	15977	275	10	2	412	2	TLX3	5	170736779	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	73	170736779	10178481	407	15030										
CPLX2	10814	hgsc.bcm.edu	37	chr5	175305939	175305939	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaggacatggggaagatgctGgggggagaggaggagaagga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:175305939delG	ENST00000359546.4	+	4	703	c.60delG	c.(58-60)ctgfs	p.L20fs	CPLX2_ENST00000515094.1_Frame_Shift_Del_p.L20fs|CPLX2_ENST00000393745.3_Frame_Shift_Del_p.L20fs|CPLX2_ENST00000512824.1_Frame_Shift_Del_p.L20fs	NM_001008220.1|NM_006650.3	NP_001008221.1|NP_006641.1	Q6PUV4	CPLX2_HUMAN	complexin 2	20					cell differentiation (GO:0030154)|mast cell degranulation (GO:0043303)|nervous system development (GO:0007399)|positive regulation of synaptic plasticity (GO:0031915)|regulation of exocytosis (GO:0017157)|synaptic vesicle exocytosis (GO:0016079)|vesicle docking involved in exocytosis (GO:0006904)	dendrite (GO:0030425)|mast cell granule (GO:0042629)|neuronal cell body (GO:0043025)|synapse (GO:0045202)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)|synaptobrevin 2-SNAP-25-syntaxin-3-complexin complex (GO:0070554)				endometrium(3)|kidney(2)|lung(3)|ovary(2)	10	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGAAGATGCTggggggagagg	0.682																																					p.L20fs		Atlas-INDEL	.											.	CPLX2	42	.	0			c.59delT						.						18	18	18					5																	175305939		2203	4300	6503	SO:0001589	frameshift_variant	10814	exon4			.	U35100	CCDS4396.1	5q35.2	2008-05-23			ENSG00000145920	ENSG00000145920			2310	protein-coding gene	gene with protein product		605033				7553862, 16162394	Standard	XM_005265798		Approved	CPX-2, DKFZp547D155	uc003mdf.1	Q6PUV4	OTTHUMG00000130665	ENST00000359546.4:c.60delG	chr5.hg19:g.175305939delG	ENSP00000352544:p.Leu20fs	162.0	0.0		194.0	13.0	NM_006650	B2RAG2|O09056|Q13329|Q28184|Q52M15|Q64386	Frame_Shift_Del	DEL	ENST00000359546.4	hg19	CCDS4396.1																																																																																			.	.		0.682	CPLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253157.2			-	175305939	G	-	175305939	7	5	103	1	0	1	0	1	0	0	0	0	3807	1335	47	0	66	0	CPLX2	5	175305939	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	4569160	175305939	5609321	408	15031										
UIMC1	51720	hgsc.bcm.edu	37	chr5	176396191	176396191	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agagaccggctcctcttcagTtttttcagtgtggtcccaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:176396191delT	ENST00000377227.4	-	6	697	c.565delA	c.(565-567)actfs	p.T189fs	UIMC1_ENST00000503273.1_5'Flank|UIMC1_ENST00000506128.1_Frame_Shift_Del_p.T189fs|UIMC1_ENST00000511320.1_Frame_Shift_Del_p.T189fs|UIMC1_ENST00000377219.2_Frame_Shift_Del_p.T189fs			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	189	Necessary for interaction with NR6A1 N- terminus.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCCTCTTCAGTTTTTTCAGTG	0.498																																					p.T189fs		Atlas-INDEL	.											.	UIMC1	55	.	0			c.566delC						.						66	66	66					5																	176396191		2203	4300	6503	SO:0001589	frameshift_variant	51720	exon6			.	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"receptor associated protein 80"	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.565delA	chr5.hg19:g.176396191delT	ENSP00000366434:p.Thr189fs	171.0	0.0		238.0	16.0	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Frame_Shift_Del	DEL	ENST00000377227.4	hg19	CCDS4408.1																																																																																			.	.		0.498	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290		-	176396191	T	-	176396191	7	5	103	1	0	1	0	1	0	0	0	0	16986	1725	60	0	1634	0	UIMC1	5	176396191	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1090252	176396191	4519069	409	15032										
UIMC1	51720	hgsc.bcm.edu	37	chr5	176409596	176409596	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gattcggagacttctttaacTtttttctttctccgtggcat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:176409596delT	ENST00000377227.4	-	2	153	c.21delA	c.(19-21)aaafs	p.K7fs	UIMC1_ENST00000506128.1_Frame_Shift_Del_p.K7fs|UIMC1_ENST00000511320.1_Frame_Shift_Del_p.K7fs|UIMC1_ENST00000377219.2_Frame_Shift_Del_p.K7fs			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	7	Necessary for transcriptional repression.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTTCTTTAACTTTTTTCTTTC	0.358																																					p.V8fs		Atlas-INDEL	.											.	UIMC1	55	.	0			c.22delG						.						103	99	100					5																	176409596		2203	4300	6503	SO:0001589	frameshift_variant	51720	exon2			.	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"receptor associated protein 80"	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.21delA	chr5.hg19:g.176409596delT	ENSP00000366434:p.Lys7fs	168.0	0.0		236.0	15.0	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Frame_Shift_Del	DEL	ENST00000377227.4	hg19	CCDS4408.1																																																																																			.	.		0.358	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290		-	176409596	T	-	176409596	7	5	103	1	0	1	0	1	0	0	0	0	16986	1606	56	0	2194	0	UIMC1	5	176409596	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	13405	176409596	4505664	410	15033										
NSD1	64324	hgsc.bcm.edu	37	chr5	176638499	176638499	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcatccaaattgcgagatgcTttttcagcccaaatggtaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:176638499delT	ENST00000439151.2	+	5	3144	c.3099delT	c.(3097-3099)gctfs	p.A1033fs	NSD1_ENST00000354179.4_Frame_Shift_Del_p.A764fs|NSD1_ENST00000361032.4_Frame_Shift_Del_p.A930fs|NSD1_ENST00000347982.4_Frame_Shift_Del_p.A764fs	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1033					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TGCGAGATGCTTTTTCAGCCC	0.463			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.A1033fs		Atlas-INDEL	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.3098delC						.						126	124	125					5																	176638499		2203	4300	6503	SO:0001589	frameshift_variant	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	.	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.3099delT	chr5.hg19:g.176638499delT	ENSP00000395929:p.Ala1033fs	120.0	0.0		166.0	12.0	NM_022455	Q96PD8|Q96RN7	Frame_Shift_Del	DEL	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.		0.463	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		-	176638499	T	-	176638499	7	5	103	1	0	1	0	1	0	0	0	0	10678	1596	56	0	3113	0	NSD1	5	176638499	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	228903	176638499	4276761	411	15034										
EXOC2	55770	hgsc.bcm.edu	37	chr6	556513	556513	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcccggcttgcactccagaaCccccttcagtgactgcagag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:556513delC	ENST00000230449.4	-	18	2038	c.1903delG	c.(1903-1905)gttfs	p.V635fs	EXOC2_ENST00000448181.3_Frame_Shift_Del_p.V230fs	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	635					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		CACTCCAGAACCCCCTTCAGT	0.478																																					p.V635fs		Atlas-INDEL	.											.	EXOC2	81	.	0			c.1904delT						.						75	68	70					6																	556513		2203	4300	6503	SO:0001589	frameshift_variant	55770	exon18			.	AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"SEC5-like 1 (S. cerevisiae)"	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.1903delG	chr6.hg19:g.556513delC	ENSP00000230449:p.Val635fs	180.0	0.0		243.0	15.0	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Frame_Shift_Del	DEL	ENST00000230449.4	hg19	CCDS34327.1																																																																																			.	.		0.478	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303		-	556513	C	-	556513	7	5	103	1	0	1	0	1	0	0	0	0	5304	507	18	0	915	0	EXOC2	6	556513	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10		556513	170558554	412	15035										
LY86	9450	hgsc.bcm.edu	37	chr6	6588976	6588976	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggcccccaccatgaagggTttcacagccactctcttcct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:6588976delT	ENST00000379953.2	+	2	361	c.9delT	c.(7-9)ggtfs	p.G3fs	LY86-AS1_ENST00000429345.1_RNA|LY86-AS1_ENST00000435641.1_RNA|LY86-AS1_ENST00000447858.1_RNA|LY86_ENST00000230568.4_Frame_Shift_Del_p.G3fs			O95711	LY86_HUMAN	lymphocyte antigen 86	3					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				large_intestine(2)|lung(6)	8	Ovarian(93;0.0377)					CCATGAAGGGTTTCACAGCCA	0.542																																					p.G3fs		Atlas-INDEL	.											.	LY86	18	.	0			c.8delG						.						82	80	80					6																	6588976		2203	4300	6503	SO:0001589	frameshift_variant	9450	exon1			.	AF057178	CCDS4498.1	6p24.3	2010-07-08			ENSG00000112799	ENSG00000112799			16837	protein-coding gene	gene with protein product		605241				9763566	Standard	NM_004271		Approved	MD-1, dJ80N2.1	uc003mwy.1	O95711	OTTHUMG00000014190	ENST00000379953.2:c.9delT	chr6.hg19:g.6588976delT	ENSP00000369286:p.Gly3fs	55.0	0.0		135.0	10.0	NM_004271	Q9UQC4	Frame_Shift_Del	DEL	ENST00000379953.2	hg19	CCDS4498.1																																																																																			.	.		0.542	LY86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039762.2			-	6588976	T	-	6588976	7	5	103	1	0	1	0	1	0	0	0	0	9109	1712	60	0	11	0	LY86	6	6588976	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	6032463	6588976	164526091	413	15036										
GCM2	9247	hgsc.bcm.edu	37	chr6	10876681	10876681	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttctcacctgacctacctgAaaaaagatcgcgttgccatc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:10876681delA	ENST00000379491.4	-	3	600	c.453delT	c.(451-453)tttfs	p.F151fs	RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	151					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				GACCTACCTGAAAAAAGATCG	0.502																																					p.Q152fs		Atlas-INDEL	.											.	GCM2	81	.	0			c.454delC						.						88	76	80					6																	10876681		2203	4300	6503	SO:0001589	frameshift_variant	9247	exon3			.	AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"glial cells missing (Drosophila) homolog b"	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.453delT	chr6.hg19:g.10876681delA	ENSP00000368805:p.Phe151fs	98.0	0.0		177.0	14.0	NM_004752	D3GDV6|Q5THN5	Frame_Shift_Del	DEL	ENST00000379491.4	hg19	CCDS4517.1																																																																																			.	.		0.502	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1			-	10876681	A	-	10876681	7	5	103	1	0	1	0	1	0	0	0	0	6306	243	9	0	1079	0	GCM2	6	10876681	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	4287705	10876681	160238386	414	15037										
NEDD9	4739	hgsc.bcm.edu	37	chr6	11190264	11190264	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catcactgctgctacagtcaGgggcctgctccttgctcagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:11190264delG	ENST00000379446.5	-	5	2004	c.1838delC	c.(1837-1839)cctfs	p.P613fs	NEDD9_ENST00000504387.1_Frame_Shift_Del_p.P613fs|RP3-510L9.1_ENST00000500636.2_RNA	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	613					actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)				endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			GCTACAGTCAGGGGCCTGCTC	0.577																																					p.P613fs		Atlas-INDEL	.											.	NEDD9	191	.	0			c.1839delT						.						99	88	92					6																	11190264		2203	4300	6503	SO:0001589	frameshift_variant	4739	exon6			.	L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"Cas scaffolding proteins"	7733	protein-coding gene	gene with protein product	"Cas scaffolding protein family member 2", "Cas-like"	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.1838delC	chr6.hg19:g.11190264delG	ENSP00000368759:p.Pro613fs	112.0	0.0		164.0	13.0	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Frame_Shift_Del	DEL	ENST00000379446.5	hg19	CCDS4520.1																																																																																			.	.		0.577	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403		-	11190264	G	-	11190264	7	5	103	1	0	1	0	1	0	0	0	0	10322	1000	35	0	678	0	NEDD9	6	11190264	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	313583	11190264	159924803	415	15038										
DTNBP1	84062	hgsc.bcm.edu	37	chr6	15615504	15615504	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttttcaaactcacctcttaTttttcttgtaattctccagt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:15615504delT	ENST00000344537.5	-	6	654	c.482delA	c.(481-483)aatfs	p.N161fs	DTNBP1_ENST00000355917.3_Frame_Shift_Del_p.N161fs|DTNBP1_ENST00000338950.5_Frame_Shift_Del_p.N161fs	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	161					actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			TCACCTCTTATTTTTCTTGTA	0.393									Hermansky-Pudlak syndrome																												p.N161fs		Atlas-INDEL	.											.	DTNBP1	56	.	0			c.483delT						.						168	160	163					6																	15615504		2203	4300	6503	SO:0001589	frameshift_variant	84062	exon6	Familial Cancer Database	HPS, HPS1-8	.	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"Biogenesis of lysosomal organelles complex-1 subunits"	17328	protein-coding gene	gene with protein product	"dysbindin-1", "biogenesis of lysosomal organelles complex-1, subunit 8"	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.482delA	chr6.hg19:g.15615504delT	ENSP00000341680:p.Asn161fs	161.0	0.0		251.0	18.0	NM_183040	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Frame_Shift_Del	DEL	ENST00000344537.5	hg19	CCDS4534.1																																																																																			.	.		0.393	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122		-	15615504	T	-	15615504	7	5	103	1	0	1	0	1	0	0	0	0	4792	1493	52	0	694	0	DTNBP1	6	15615504	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	4425240	15615504	155499563	416	15039										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327684	16327684	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tattgcatgacgacctgggaGgggggccccagggtgagcgt					rs202200269	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:16327684delG	ENST00000244769.4	-	8	1794	c.858delC	c.(856-858)cccfs	p.P286fs	ATXN1_ENST00000436367.1_Frame_Shift_Del_p.P286fs	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	286					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CGACCTGGGAGGGGGGCCCCA	0.682																																					p.S287fs		Atlas-INDEL	.											.	ATXN1	117	.	0			c.859delT						.						31	34	33					6																	16327684		2203	4300	6503	SO:0001589	frameshift_variant	6310	exon7			.	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.858delC	chr6.hg19:g.16327684delG	ENSP00000244769:p.Pro286fs	181.0	0.0		334.0	21.0	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Frame_Shift_Del	DEL	ENST00000244769.4	hg19	CCDS34342.1																																																																																			.	.		0.682	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		-	16327684	G	-	16327684	7	5	103	1	0	1	0	1	0	0	0	0	1209	987	35	0	1597	0	ATXN1	6	16327684	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	712180	16327684	154787383	417	15040										
RBM24	221662	hgsc.bcm.edu	37	chr6	17281858	17281858	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgtacaccaagatcttcgtcGgggggctgccctaccacacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:17281858delG	ENST00000379052.5	+	1	282	c.46delG	c.(46-48)gggfs	p.G17fs	RBM24_ENST00000318204.5_5'Flank|RBM24_ENST00000425446.2_5'Flank	NM_001143942.1	NP_001137414.1	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24	17	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|regulation of mRNA stability (GO:0043488)|regulation of myotube differentiation (GO:0010830)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)	13	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)			GATCTTCGTCGGGGGGCTGCC	0.692																																					p.V15fs		Atlas-INDEL	.											.	RBM24	40	.	0			c.45delC						.						26	35	32					6																	17281858		692	1591	2283	SO:0001589	frameshift_variant	221662	exon1			.	BC040928	CCDS4538.1, CCDS47378.1, CCDS47379.1	6p22.3	2013-02-12	2004-04-23	2004-04-23	ENSG00000112183	ENSG00000112183		"RNA binding motif (RRM) containing"	21539	protein-coding gene	gene with protein product			"RNA-binding region (RNP1, RRM) containing 6"	RNPC6			Standard	NM_153020		Approved	FLJ30829, dJ259A10.1	uc003nbz.4	Q9BX46	OTTHUMG00000014306	ENST00000379052.5:c.46delG	chr6.hg19:g.17281858delG	ENSP00000368341:p.Gly17fs	167.0	0.0		282.0	19.0	NM_001143942	E9PAY4|Q6QDA4|Q8N9D3|Q96NI3	Frame_Shift_Del	DEL	ENST00000379052.5	hg19	CCDS47378.1																																																																																			.	.		0.692	RBM24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039946.2	NM_153020		-	17281858	G	-	17281858	7	5	103	1	0	1	0	1	0	0	0	0	13139	1116	39	0	48	0	RBM24	6	17281858	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	954174	17281858	153833209	418	15041										
NUP153	9972	hgsc.bcm.edu	37	chr6	17665533	17665533	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccagaaggagtcagagatggTttaaaataaacacttcgatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:17665533delT	ENST00000262077.2	-	9	1151	c.1152delA	c.(1150-1152)aaafs	p.K384fs	NUP153_ENST00000537253.1_Frame_Shift_Del_p.K384fs	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	384					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			TCAGAGATGGTTTAAAATAAA	0.363																																					p.P385fs		Atlas-INDEL	.											.	NUP153	116	.	0			c.1153delC						.						113	109	111					6																	17665533		2203	4300	6503	SO:0001589	frameshift_variant	9972	exon9			.	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"nucleoporin 153kD"			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.1152delA	chr6.hg19:g.17665533delT	ENSP00000262077:p.Lys384fs	108.0	0.0		163.0	10.0	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Frame_Shift_Del	DEL	ENST00000262077.2	hg19	CCDS4541.1																																																																																			.	.		0.363	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			-	17665533	T	-	17665533	7	5	103	1	0	1	0	1	0	0	0	0	10764	1722	60	0	3331	0	NUP153	6	17665533	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	383675	17665533	153449534	419	15042										
FAM65B	9750	hgsc.bcm.edu	37	chr6	24843580	24843580	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgagctggtgtcatccataCcctcattctgggaggccaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:24843580delC	ENST00000259698.4	-	14	1605	c.1430delG	c.(1429-1431)ggtfs	p.G477fs	FAM65B_ENST00000540914.1_Frame_Shift_Del_p.G427fs|FAM65B_ENST00000473070.1_5'Flank|FAM65B_ENST00000538035.1_Frame_Shift_Del_p.G456fs|FAM65B_ENST00000378023.4_Frame_Shift_Del_p.G427fs|FAM65B_ENST00000510784.2_Frame_Shift_Del_p.G461fs	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	477					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						GTCATCCATACCCTCATTCTG	0.537																																					p.G477fs		Atlas-INDEL	.											.	FAM65B	134	.	0			c.1431delT						.						111	103	105					6																	24843580		1944	4145	6089	SO:0001589	frameshift_variant	9750	exon14			.	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.1430delG	chr6.hg19:g.24843580delC	ENSP00000259698:p.Gly477fs	102.0	0.0		177.0	11.0	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Frame_Shift_Del	DEL	ENST00000259698.4	hg19	CCDS47383.1																																																																																			.	.		0.537	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			-	24843580	C	-	24843580	7	5	103	1	0	1	0	1	0	0	0	0	5608	507	18	0	1826	0	FAM65B	6	24843580	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	7178047	24843580	146271487	420	15043										
SLC17A1	6568	hgsc.bcm.edu	37	chr6	25813132	25813132	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcatgatgttatgtgaccagAaaaacgtaaaactaccagtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:25813132delA	ENST00000244527.4	-	8	939	c.824delT	c.(823-825)ttcfs	p.F275fs	SLC17A1_ENST00000476801.1_Frame_Shift_Del_p.F275fs|SLC17A1_ENST00000468082.1_Intron|SLC17A1_ENST00000427328.1_Intron	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	275					ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						ATGTGACCAGAAAAACGTAAA	0.358																																					p.F275fs		Atlas-INDEL	.											.	SLC17A1	71	.	0			c.825delC						.						70	70	70					6																	25813132		2203	4300	6503	SO:0001589	frameshift_variant	6568	exon8			.		CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"Solute carriers"	10929	protein-coding gene	gene with protein product		182308	"solute carrier family 17 (sodium phosphate), member 1"	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.824delT	chr6.hg19:g.25813132delA	ENSP00000244527:p.Phe275fs	104.0	0.0		160.0	10.0	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Frame_Shift_Del	DEL	ENST00000244527.4	hg19	CCDS4565.1																																																																																			.	.		0.358	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2			-	25813132	A	-	25813132	7	5	103	1	0	1	0	1	0	0	0	0	14431	246	9	0	599	0	SLC17A1	6	25813132	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	969552	25813132	145301935	421	15044										
PRSS16	10279	hgsc.bcm.edu	37	chr6	27218543	27218543	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcccctggatctgcttcggAggctcctatgccggctcctt	11	15	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:27218543A>G	ENST00000230582.3	+	5	564	c.549A>G	c.(547-549)ggA>ggG	p.G183G	PRSS16_ENST00000421826.2_Intron	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	183					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						TCTGCTTCGGAGGCTCCTATG	0.672																																					p.G183G	NSCLC(178;1118 2105 17078 23587 44429)	Atlas-SNP	.											.	PRSS16	66	.	0			c.A549G						.						47	45	46					6																	27218543		2203	4300	6503	SO:0001819	synonymous_variant	10279	exon5			CTTCGGAGGCTCC	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"Serine peptidases / Serine peptidases"	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.549A>G	chr6.hg19:g.27218543A>G		90.0	0.0		119.0	5.0	NM_005865	O75416	Silent	SNP	ENST00000230582.3	hg19	CCDS4623.1	.	.	.	.	.	.	.	.	.	.	A	12.11	1.840679	0.32513	.	.	ENSG00000112812	ENST00000485993;ENST00000475106	.	.	.	4.4	3.18	0.36537	.	.	.	.	.	T	0.45577	0.1349	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39901	-0.9591	4	.	.	.	-20.829	9.2991	0.37833	0.8183:0.1817:0.0:0.0	.	.	.	.	G	75	.	.	R	+	1	2	PRSS16	27326522	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.952000	0.29149	0.790000	0.33803	0.460000	0.39030	AGG	.	.		0.672	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2			G	27218543	A	G	27218543	2	3	103	1	0	0	0	0	0	0	0	1	12628	291	11	2		2	PRSS16	6	27218543	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1405411	27218543	143896524	422	15045										
HIST1H2AM	8336	hgsc.bcm.edu	37	chr6	27860701	27860701	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcgcgggatgatgcgggtcTttttgttgtcgcgggctgcg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:27860701delT	ENST00000359611.2	-	1	262	c.227delA	c.(226-228)aagfs	p.K76fs	HIST1H3J_ENST00000479986.1_5'UTR|HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000359303.2_5'Flank	NM_003514.2	NP_003505.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	76						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)	14						GATGCGGGTCTTTTTGTTGTC	0.642																																					p.K76fs		Atlas-INDEL	.											HIST1H2AM,NS,carcinoma,0,1	HIST1H2AM	27	.	0			c.228delG						.						102	107	105					6																	27860701		2203	4300	6503	SO:0001589	frameshift_variant	8336	exon1			.	X57138	CCDS4639.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000233224	ENSG00000278677		"Histones / Replication-dependent"	4735	protein-coding gene	gene with protein product		602796	"H2A histone family, member N", "histone 1, H2am"	H2AFN		1768865, 9439656, 12408966	Standard	NM_003514		Approved	H2A/n, H2A.1	uc003nkb.1	P0C0S8	OTTHUMG00000014494	ENST00000359611.2:c.227delA	chr6.hg19:g.27860701delT	ENSP00000352627:p.Lys76fs	200.0	0.0		414.0	26.0	NM_003514	P02261|Q2M1R2|Q76PA6	Frame_Shift_Del	DEL	ENST00000359611.2	hg19	CCDS4639.1																																																																																			.	.		0.642	HIST1H2AM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040162.1	NM_003514		-	27860701	T	-	27860701	7	5	103	1	0	1	0	1	0	0	0	0	7148	1609	56	0	169	0	HIST1H2AM	6	27860701	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	642158	27860701	143254366	423	15046										
ZKSCAN3	80317	hgsc.bcm.edu	37	chr6	28333941	28333941	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tacaggcctcattgaacatcAaaaaatccacactggtgaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:28333941delA	ENST00000377255.3	+	7	1793	c.1496delA	c.(1495-1497)caafs	p.Q499fs	ZKSCAN3_ENST00000341464.5_Frame_Shift_Del_p.Q351fs|ZKSCAN3_ENST00000252211.2_Frame_Shift_Del_p.Q499fs	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	499					autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						ATTGAACATCAAAAAATCCAC	0.408																																					p.Q499fs		Atlas-INDEL	.											.	ZKSCAN3	50	.	0			c.1495delC						.						79	82	81					6																	28333941		2203	4300	6503	SO:0001589	frameshift_variant	80317	exon6			.	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"Zinc fingers, C2H2-type", "-", "-", "-"	13853	protein-coding gene	gene with protein product		612791	"zinc finger protein 306", "zinc finger protein 309"	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.1496delA	chr6.hg19:g.28333941delA	ENSP00000366465:p.Gln499fs	84.0	0.0		140.0	11.0	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Frame_Shift_Del	DEL	ENST00000377255.3	hg19	CCDS4650.1																																																																																			.	.		0.408	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493		-	28333941	A	-	28333941	7	5	103	1	0	1	0	1	0	0	0	0	17703	130	5	0	1514	0	ZKSCAN3	6	28333941	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	473240	28333941	142781126	424	15047										
OR14J1	442191	hgsc.bcm.edu	37	chr6	29274914	29274914	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgatagctgtgtggattgctGggggcctctctgggctcatg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:29274914delG	ENST00000377160.2	+	1	512	c.448delG	c.(448-450)gggfs	p.G151fs		NM_030946.1	NP_112208.1	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 14, subfamily J, member 1	151						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(2)	17						GTGGATTGCTGGGGGCCTCTC	0.488																																					p.A149fs		Atlas-INDEL	.											.	OR14J1	43	.	0			c.447delT						.						154	156	155					6																	29274914		1511	2709	4220	SO:0001589	frameshift_variant	442191	exon1			.		CCDS34362.1	6p21.3	2012-08-09	2008-04-02	2008-04-02	ENSG00000204695	ENSG00000204695		"GPCR / Class A : Olfactory receptors"	13971	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily U, member 1"	OR5U1			Standard	NM_030946		Approved	hs6M1-28	uc011dln.2	Q9UGF5	OTTHUMG00000031184	ENST00000377160.2:c.448delG	chr6.hg19:g.29274914delG	ENSP00000366365:p.Gly151fs	116.0	0.0		252.0	16.0	NM_030946	A2BEC2|B0V078|Q5ST27	Frame_Shift_Del	DEL	ENST00000377160.2	hg19	CCDS34362.1																																																																																			.	.		0.488	OR14J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076362.2			-	29274914	G	-	29274914	7	5	103	1	0	1	0	1	0	0	0	0	10957	1348	47	0	450	0	OR14J1	6	29274914	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	940973	29274914	141840153	425	15048										
TRIM31	11074	hgsc.bcm.edu	37	chr6	30075888	30075888	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttgattttgcttcactgagTtttttctccagttccagagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30075888delT	ENST00000376734.3	-	6	950	c.825delA	c.(823-825)aaafs	p.K275fs	TRIM31_ENST00000540829.1_Frame_Shift_Del_p.K275fs|TRIM31_ENST00000485864.1_5'UTR|TRIM31-AS1_ENST00000440874.1_RNA	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	275					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						CTTCACTGAGTTTTTTCTCCA	0.438																																					p.L276fs		Atlas-INDEL	.											.	TRIM31	40	.	0			c.826delC						.						82	82	82					6																	30075888		1511	2709	4220	SO:0001589	frameshift_variant	11074	exon6			.	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16289	protein-coding gene	gene with protein product		609316	"tripartite motif-containing 31"			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.825delA	chr6.hg19:g.30075888delT	ENSP00000365924:p.Lys275fs	139.0	0.0		264.0	16.0	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Frame_Shift_Del	DEL	ENST00000376734.3	hg19	CCDS34374.1																																																																																			.	.		0.438	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2			-	30075888	T	-	30075888	7	5	103	1	0	1	0	1	0	0	0	0	16520	1722	60	0	468	0	TRIM31	6	30075888	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	800974	30075888	141039179	426	15049										
RPP21	79897	hgsc.bcm.edu	37	chr6	30313126	30313126	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaaccaggcgctggcgaggTtttactgctacactgagagg	14	9	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30313126T>C	ENST00000442966.2	+	2	122	c.109T>C	c.(109-111)Ttt>Ctt	p.F37L	TRIM39-RPP21_ENST00000513556.1_Missense_Mutation_p.F298L|RPP21_ENST00000428040.2_Missense_Mutation_p.F60L|RPP21_ENST00000433076.2_Missense_Mutation_p.F37L|RPP21_ENST00000436442.2_Missense_Mutation_p.F37L|RPP21_ENST00000466327.1_3'UTR			Q9H633	RPP21_HUMAN	ribonuclease P/MRP 21kDa subunit	37					response to drug (GO:0042493)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonuclease P activity (GO:0004526)			endometrium(2)|ovary(1)|prostate(1)	4						GCTGGCGAGGTTTTACTGCTA	0.697																																					p.F386L		Atlas-SNP	.											.	.	.	.	0			c.T1156C						.						43	50	48					6																	30313126		1511	2709	4220	SO:0001583	missense	202658	exon7			GCGAGGTTTTACT	AK026291	CCDS4679.1, CCDS56409.1, CCDS56410.1	6p21.32	2012-05-21	2007-06-26	2004-03-19	ENSG00000241370	ENSG00000241370			21300	protein-coding gene	gene with protein product		612524	"chromosome 6 open reading frame 135", "ribonuclease P 21kDa subunit"	C6orf135			Standard	NM_001199120		Approved	FLJ22638, Em:AB014085.3		Q9H633	OTTHUMG00000031220	ENST00000442966.2:c.109T>C	chr6.hg19:g.30313126T>C	ENSP00000403833:p.Phe37Leu	97.0	0.0		220.0	9.0	NM_001199119	A2AAZ8|B0S834|B0S835|Q5JPL9|Q5JPM1|Q5STF8|Q5STF9|Q5STG2|Q5SU41|Q5SU42|Q86Y49|Q86Y50|Q86Y51|Q96F16	Missense_Mutation	SNP	ENST00000442966.2	hg19	CCDS4679.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.974023	0.92919	.	.	ENSG00000204599;ENSG00000248167;ENSG00000241370;ENSG00000241370;ENSG00000241370;ENSG00000241370	ENST00000412529;ENST00000513556;ENST00000433076;ENST00000442966;ENST00000428040;ENST00000436442	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.48040	0.1478	L	0.58101	1.795	0.46131	D	0.998889	D;D;D;D	0.69078	0.994;0.99;0.997;0.992	P;P;D;P	0.66196	0.877;0.853;0.942;0.902	T	0.53885	-0.8375	10	0.87932	D	0	-4.499	11.2433	0.48982	0.0:0.0:0.0:1.0	.	300;37;37;60	F5H2V3;Q9H633-3;Q9H633;Q9H633-2	.;.;RPP21_HUMAN;.	L	300;298;37;37;60;37	ENSP00000424048:F298L;ENSP00000409799:F37L;ENSP00000403833:F37L;ENSP00000394320:F60L;ENSP00000397778:F37L	ENSP00000394320:F60L	F	+	1	0	RPP21;TRIM39-RPP21;TRIM39	30421105	1.000000	0.71417	0.997000	0.53966	0.855000	0.48748	5.398000	0.66308	2.146000	0.66826	0.460000	0.39030	TTT	.	.		0.697	RPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076451.2	NM_024839		C	30313126	T	C	30313126	3	2	103	1	0	0	0	0	1	0	0	0	13625	1725	60	2	115	2	RPP21	6	30313126	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	237238	30313126	140801941	427	15050										
PRR3	80742	hgsc.bcm.edu	37	chr6	30525950	30525950	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacccagccttctgggccctCcccccatggccaatggaaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30525950delC	ENST00000376560.3	+	2	589	c.130delC	c.(130-132)cccfs	p.P45fs	PRR3_ENST00000376557.3_Intron|PRR3_ENST00000498336.1_3'UTR|GNL1_ENST00000376621.3_5'Flank	NM_025263.3	NP_079539.2	P79522	PRR3_HUMAN	proline rich 3	45	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						TCTGGGCCCTCCCCCCATGGC	0.502																																					p.P43fs		Atlas-Indel,Pindel	.											.	PRR3	5	.	0			c.129delT						.						95	97	96					6																	30525950		1161	2503	3664	SO:0001589	frameshift_variant	80742	exon2			.	AK074531	CCDS43440.1, CCDS43441.1	6p21.32	2013-01-18	2004-05-27		ENSG00000204576	ENSG00000204576		"Zinc fingers, CCCH-type domain containing"	21149	protein-coding gene	gene with protein product			"proline-rich polpeptide 3"				Standard	NM_025263		Approved	CAT56, Em:AB014077.1, Em:AB023052.2	uc003nqi.2	P79522	OTTHUMG00000031037	ENST00000376560.3:c.130delC	chr6.hg19:g.30525950delC	ENSP00000365744:p.Pro45fs	91.0	0.0		135.0	12.0	NM_025263	A1A4H4|Q5RJB5|Q5STN6	Frame_Shift_Del	DEL	ENST00000376560.3	hg19	CCDS43440.1																																																																																			.	.		0.502	PRR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076033.2	NM_025263		-	30525950	C	-	30525950	7	5	103	1	0	1	0	1	0	0	0	0	12610	855	30	0	136	0	PRR3	6	30525950	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	212824	30525950	140589117	428	15051										
ABCF1	23	hgsc.bcm.edu	37	chr6	30553664	30553664	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttctgccccagtgaccttcAaaaagatgtaccagcagaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30553664delA	ENST00000326195.8	+	17	1721	c.1609delA	c.(1609-1611)aaafs	p.K538fs	ABCF1_ENST00000376545.3_Frame_Shift_Del_p.K500fs|ABCF1_ENST00000396515.4_Intron|MIR877_ENST00000401282.1_RNA	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	538	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						AGTGACCTTCAAAAAGATGTA	0.527																																					p.F536fs		Atlas-INDEL	.											.	ABCF1	61	.	0			c.1608delC						.						21	17	18					6																	30553664		1510	2708	4218	SO:0001589	frameshift_variant	23	exon17			.	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"ATP binding cassette transporters / subfamily F"	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.1609delA	chr6.hg19:g.30553664delA	ENSP00000313603:p.Lys538fs	57.0	0.0		123.0	10.0	NM_001025091	A2BF75|O14897|Q69YP6	Frame_Shift_Del	DEL	ENST00000326195.8	hg19	CCDS34380.1																																																																																			.	.		0.527	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			-	30553664	A	-	30553664	7	5	103	1	0	1	0	1	0	0	0	0	65	131	5	0	1675	0	ABCF1	6	30553664	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	27714	30553664	140561403	429	15052										
FLOT1	10211	hgsc.bcm.edu	37	chr6	30698207	30698207	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccacatgacctccagacctGgggcagcttctctagcagca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30698207delG	ENST00000376389.3	-	11	1307	c.1087delC	c.(1087-1089)cagfs	p.Q363fs	FLOT1_ENST00000456573.2_Frame_Shift_Del_p.Q315fs	NM_005803.2	NP_005794.1	P41440	S19A1_HUMAN	flotillin 1	0					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)	p.Q363K(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	13					Methotrexate(DB00563)|Pralatrexate(DB06813)	CTCCAGACCTGGGGCAGCTTC	0.592																																					p.Q363fs		Atlas-INDEL	.											.	FLOT1	28	.	1	Substitution - Missense(1)	lung(1)	c.1088delA						.						140	152	148					6																	30698207		2203	4299	6502	SO:0001589	frameshift_variant	10211	exon11			.	AF089750	CCDS4688.1	6p21.3	2010-02-17			ENSG00000137312	ENSG00000137312			3757	protein-coding gene	gene with protein product		606998					Standard	XM_005248780		Approved		uc003nrm.3	O75955	OTTHUMG00000031151	ENST00000376389.3:c.1087delC	chr6.hg19:g.30698207delG	ENSP00000365569:p.Gln363fs	122.0	0.0		210.0	14.0	NM_005803	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Frame_Shift_Del	DEL	ENST00000376389.3	hg19	CCDS4688.1																																																																																			.	.		0.592	FLOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076276.2			-	30698207	G	-	30698207	7	5	103	1	0	1	0	1	0	0	0	0	5944	1357	47	0	208	0	FLOT1	6	30698207	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	144543	30698207	140416860	430	15053										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30918020	30918020	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accccatttgccaatgagaaGaccacatcatcctcagcaga	6	14	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30918020G>A	ENST00000462446.1	+	2	1807	c.1779G>A	c.(1777-1779)aaG>aaA	p.K593K	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	145						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CCAATGAGAAGACCACATCAT	0.502																																					p.K593K		Atlas-SNP	.											.	DPCR1	99	.	0			c.G1779A						.						48	51	50					6																	30918020		692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			TGAGAAGACCACA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.1779G>A	chr6.hg19:g.30918020G>A		98.0	0.0		222.0	9.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	hg19	CCDS4692.2																																																																																			.	.		0.502	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		A	30918020	G	A	30918020	2	1	103	1	0	0	0	0	0	0	0	1	4714	933	33	3		3	DPCR1	6	30918020	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	219813	30918020	140197047	431	15054										
POU5F1	5460	hgsc.bcm.edu	37	chr6	31138149	31138149	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagccgccttggggcactagCcccactccaacctggggccc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:31138149delC	ENST00000259915.8	-	1	321	c.249delG	c.(247-249)gggfs	p.G83fs	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	83					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)		EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	GGGGCACTAGCCCCACTCCAA	0.687			T	EWSR1	sarcoma																																p.L84X		Atlas-INDEL	.		Dom	yes		6	6p21.31	5460	"POU domain, class 5, transcription factor 1"		M	.	POU5F1	25	.	0			c.250delC						.						31	31	31					6																	31138149		1510	2708	4218	SO:0001589	frameshift_variant	5460	exon1			.	Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"Homeoboxes / POU class"	9221	protein-coding gene	gene with protein product		164177	"POU domain class 5, transcription factor 1"	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.249delG	chr6.hg19:g.31138149delC	ENSP00000259915:p.Gly83fs	78.0	0.0		200.0	13.0	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Frame_Shift_Del	DEL	ENST00000259915.8	hg19	CCDS34391.1																																																																																			.	.		0.687	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701		-	31138149	C	-	31138149	7	5	103	1	0	1	0	1	0	0	0	0	12290	726	26	0	853	0	POU5F1	6	31138149	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	220129	31138149	139976918	432	15055										
MICA	100507436	hgsc.bcm.edu	37	chr6	31380100	31380101	+	Splice_Site	DNP	AG	AG	CA													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ataacaagtccctttttttcAgggaaagtgctggtgcttca					rs41558418		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:31380100_31380101AG>CA	ENST00000449934.2	+	5	946		c.e5-1		HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CCTTTTTTTCAGGGAAAGTGCT	0.5																																					.		Atlas-SNP	.											.	MICA	21	.	0			c.893-2A>C|c.893-1G>A						.																																			SO:0001630	splice_region_variant	100507436	exon5			TTTTTCAGGGAAA|TTTTCAGGGAAAG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"Immunoglobulin superfamily / C1-set domain containing"	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	Exception_encountered	chr6.hg19:g.31380100_31380101delinsCA		138.0	0.0		219.0|218.0	13.0|10.0	NM_001177519		Splice_Site	SNP	ENST00000449934.2	hg19	CCDS56412.1																																																																																			.	.		0.5	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	Intron	CA	31380101	AG	CA	31380100	5	2	103	1	0	0	0	0	0	0	1	0	9577	202	7	5	909	5	MICA	6	31380100	Splice_Site	DNP	AG	TCGA-DD-A1EG-01A-11D-A20W-10	241951	31380100	139734967	433	15056										
BAT2	7916	hgsc.bcm.edu	37	chr6	31603384	31603384	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcctgtatcacgagactgggAgctgcttcccagtgctgctg	12	12	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:31603384A>G	ENST00000376033.2	+	24	5633	c.5399A>G	c.(5398-5400)gAg>gGg	p.E1800G	PRRC2A_ENST00000376007.4_Missense_Mutation_p.E1800G	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1800	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CGAGACTGGGAGCTGCTTCCC	0.612																																					p.E1800G		Atlas-SNP	.											.	PRRC2A	152	.	0			c.A5399G						.						56	65	62					6																	31603384		1511	2708	4219	SO:0001583	missense	7916	exon24			ACTGGGAGCTGCT	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5399A>G	chr6.hg19:g.31603384A>G	ENSP00000365201:p.Glu1800Gly	85.0	0.0		132.0	7.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	hg19	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	A	13.69	2.313751	0.40996	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.02085	4.46;4.46	5.4	5.4	0.78164	.	0.106321	0.42172	D	0.000745	T	0.01627	0.0052	L	0.43152	1.355	0.41508	D	0.988325	P	0.40970	0.734	B	0.40329	0.326	T	0.57021	-0.7882	10	0.87932	D	0	-17.3397	13.0364	0.58875	1.0:0.0:0.0:0.0	.	1800	P48634	PRC2A_HUMAN	G	1794;1783;1800;1800;1025	ENSP00000365175:E1800G;ENSP00000365201:E1800G	ENSP00000365175:E1800G	E	+	2	0	PRRC2A	31711363	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	4.337000	0.59310	2.270000	0.75569	0.459000	0.35465	GAG	.	.		0.612	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		G	31603384	A	G	31603384	3	3	103	1	0	0	0	0	1	0	0	0	1319	304	11	2	5489	2	BAT2	6	31603384	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	223284	31603384	139511683	434	15057										
C4A	720	hgsc.bcm.edu	37	chr6	31964732	31964732	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gattgaaaccacagcctacgCcctgctgcacctcctgcttc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:31964732delC	ENST00000428956.2	+	29	3887	c.3803delC	c.(3802-3804)gccfs	p.A1268fs	C4A_ENST00000498271.1_Frame_Shift_Del_p.A1268fs	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1268					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	ACAGCCTACGCCCTGCTGCAC	0.652																																					p.A1268fs		Atlas-INDEL	.											.	C4A	15	.	0			c.3802delG						.						4	8	7					6																	31964732		329	1219	1548	SO:0001589	frameshift_variant	720	exon29			.	L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731		"Blood group antigens", "Complement system"	1323	protein-coding gene	gene with protein product		120810	"complement component 4A"				Standard	NM_001252204		Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.3803delC	chr6.hg19:g.31964732delC	ENSP00000396688:p.Ala1268fs	88.0	0.0		150.0	10.0	NM_007293	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	Frame_Shift_Del	DEL	ENST00000428956.2	hg19	CCDS47404.1																																																																																			.	.		0.652	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293		-	31964732	C	-	31964732	7	5	103	1	0	1	0	1	0	0	0	0	2249	739	26	0	3580	0	C4A	6	31964732	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	361348	31964732	139150335	435	15058										
HLA-DRB5	3127	hgsc.bcm.edu	37	chr6	32487268	32487268	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaggtccagtctccattctgAatcaggcctgtggacaccac					rs75732937	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:32487268delA	ENST00000374975.3	-	3	593	c.531delT	c.(529-531)attfs	p.I177fs		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CTCCATTCTGAATCAGGCCTG	0.547																																					p.Q178fs		Atlas-INDEL	.											.	HLA-DRB5	31	.	0			c.532delC						.						61	67	65					6																	32487268		1928	3907	5835	SO:0001589	frameshift_variant	3127	exon3			.		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.531delT	chr6.hg19:g.32487268delA	ENSP00000364114:p.Ile177fs	117.0	0.0		158.0	10.0	NM_002125		Frame_Shift_Del	DEL	ENST00000374975.3	hg19	CCDS4751.1																																																																																			.	.		0.547	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125		-	32487268	A	-	32487268	7	5	103	1	0	1	0	1	0	0	0	0	7218	242	9	0	285	0	HLA-DRB5	6	32487268	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	522536	32487268	138627799	436	15059										
HLA-DRB1	3123	hgsc.bcm.edu	37	chr6	32549502	32549502	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttctcttcctggccgttcaGgaaccacctgacttcaatgc	7	15	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:32549502G>C	ENST00000360004.5	-	3	589	c.484C>G	c.(484-486)Ctg>Gtg	p.L162V		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	162	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)		p.L162L(1)		large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TGGCCGTTCAGGAACCACCTG	0.552										Multiple Myeloma(14;0.17)																											p.L162V		Atlas-SNP	.											HLA-DRB1,NS,carcinoma,0,1	HLA-DRB1	41	.	1	Substitution - coding silent(1)	prostate(1)	c.C484G						.						79	94	89					6																	32549502		1509	2709	4218	SO:0001583	missense	3123	exon3			CGTTCAGGAACCA	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.484C>G	chr6.hg19:g.32549502G>C	ENSP00000353099:p.Leu162Val	279.0	2.0		438.0	0.0	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	hg19	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	8.248	0.808286	0.16467	.	.	ENSG00000196126	ENST00000360004	T	0.08546	3.08	3.87	1.89	0.25635	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.305223	0.33180	N	0.005193	T	0.05364	0.0142	M	0.86502	2.82	0.18873	N	0.999984	B	0.20052	0.041	B	0.25759	0.063	T	0.21621	-1.0240	10	0.87932	D	0	.	5.3486	0.16024	0.1119:0.0:0.5869:0.3012	.	162	P01911	2B1F_HUMAN	V	162	ENSP00000353099:L162V	ENSP00000353099:L162V	L	-	1	2	HLA-DRB1	32657480	0.170000	0.23016	0.526000	0.27913	0.421000	0.31385	0.849000	0.27723	0.751000	0.32900	0.453000	0.30009	CTG	.	.		0.552	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124		C	32549502	G	C	32549502	3	2	103	1	0	0	0	0	1	0	0	0	7217	991	35	4	332	4	HLA-DRB1	6	32549502	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	62234	32549502	138565565	437	15060										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33132109	33132109	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctcagctcatcctcattggCcccacggagtctcaggggac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:33132109delC	ENST00000374708.4	-	63	5005	c.4747delG	c.(4747-4749)gccfs	p.A1583fs	COL11A2_ENST00000374713.1_Frame_Shift_Del_p.A1622fs|COL11A2_ENST00000361917.1_Frame_Shift_Del_p.A1562fs|COL11A2_ENST00000374714.1_Frame_Shift_Del_p.A1643fs|COL11A2_ENST00000357486.1_Frame_Shift_Del_p.A1648fs|COL11A2_ENST00000341947.2_Frame_Shift_Del_p.A1669fs|COL11A2_ENST00000395197.1_Frame_Shift_Del_p.A1609fs|COL11A2_ENST00000477772.1_5'UTR|COL11A2_ENST00000374712.1_Frame_Shift_Del_p.A1588fs	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1669	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TCCTCATTGGCCCCACGGAGT	0.622																																					p.A1669fs	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.5006delC						.						35	33	34					6																	33132109		1511	2708	4219	SO:0001589	frameshift_variant	1302	exon65			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.4747delG	chr6.hg19:g.33132109delC	ENSP00000363840:p.Ala1583fs	127.0	0.0		177.0	13.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Del	DEL	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.622	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			-	33132109	C	-	33132109	7	5	103	1	0	1	0	1	0	0	0	0	3670	739	26	0	213	0	COL11A2	6	33132109	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	582607	33132109	137982958	438	15061										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33139837	33139837	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccagactcactgcagggccaGgggggccagacggaccttca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:33139837delG	ENST00000374708.4	-	39	3032	c.2774delC	c.(2773-2775)cctfs	p.P925fs	COL11A2_ENST00000374713.1_Frame_Shift_Del_p.P964fs|COL11A2_ENST00000361917.1_Frame_Shift_Del_p.P904fs|COL11A2_ENST00000374714.1_Frame_Shift_Del_p.P985fs|COL11A2_ENST00000357486.1_Frame_Shift_Del_p.P990fs|COL11A2_ENST00000341947.2_Frame_Shift_Del_p.P1011fs|COL11A2_ENST00000395197.1_Frame_Shift_Del_p.P951fs|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374712.1_Frame_Shift_Del_p.P930fs	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1011	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TGCAGGGCCAGGGGGGCCAGA	0.582																																					p.P1011fs	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.3033delT						.						128	161	149					6																	33139837		1508	2706	4214	SO:0001589	frameshift_variant	1302	exon41			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.2774delC	chr6.hg19:g.33139837delG	ENSP00000363840:p.Pro925fs	96.0	0.0		199.0	12.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Del	DEL	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.582	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			-	33139837	G	-	33139837	7	5	103	1	0	1	0	1	0	0	0	0	3670	1000	35	0	2282	0	COL11A2	6	33139837	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	7728	33139837	137975230	439	15062										
RXRB	6257	hgsc.bcm.edu	37	chr6	33164342	33164342	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcccccagccccctccccatCcccatccttgtcctttcccc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:33164342delC	ENST00000374680.3	-	5	1073	c.862delG	c.(862-864)gatfs	p.D288fs	RXRB_ENST00000544186.1_Frame_Shift_Del_p.D98fs|RXRB_ENST00000413614.2_Frame_Shift_Del_p.D192fs|RXRB_ENST00000374685.4_Frame_Shift_Del_p.D288fs	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	288	Hinge.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	CCCTCCCCATCCCCATCCTTG	0.622																																					p.D288fs		Atlas-INDEL	.											.	RXRB	34	.	0			c.863delA						.						51	66	61					6																	33164342		1508	2705	4213	SO:0001589	frameshift_variant	6257	exon5			.	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"Nuclear hormone receptors"	10478	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 2"	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.862delG	chr6.hg19:g.33164342delC	ENSP00000363812:p.Asp288fs	86.0	0.0		152.0	10.0	NM_021976	P28703|Q59G65|Q5JP92|Q5STQ1	Frame_Shift_Del	DEL	ENST00000374680.3	hg19	CCDS4768.1																																																																																			.	.		0.622	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		-	33164342	C	-	33164342	7	5	103	1	0	1	0	1	0	0	0	0	13779	855	30	0	763	0	RXRB	6	33164342	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	24505	33164342	137950725	440	15063										
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33400496	33400496	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgacggctaaaaagctccaTcaaacgaacgaagtcacaac	7	13	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:33400496T>C	ENST00000418600.2	+	5	523	c.422T>C	c.(421-423)aTc>aCc	p.I141T	SYNGAP1_ENST00000293748.5_Missense_Mutation_p.I141T|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.I82T	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	141					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						AAAAGCTCCATCAAACGAACG	0.587																																					p.I141T		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.T422C						.						68	58	62					6																	33400496		2203	4300	6503	SO:0001583	missense	8831	exon5			GCTCCATCAAACG	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.422T>C	chr6.hg19:g.33400496T>C	ENSP00000403636:p.Ile141Thr	76.0	0.0		99.0	4.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	hg19	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	T	15.56	2.869711	0.51588	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.26518	1.73;1.82;1.81	4.36	4.36	0.52297	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.23451	0.0567	M	0.69358	2.11	0.58432	D	0.999999	B;B;P	0.37688	0.272;0.392;0.605	B;B;P	0.44696	0.167;0.315;0.458	T	0.06320	-1.0833	10	0.87932	D	0	.	11.5483	0.50706	0.0:0.0:0.0:1.0	.	141;141;141	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	T	141;141;141;82	ENSP00000293748:I141T;ENSP00000403636:I141T;ENSP00000412475:I82T	ENSP00000293748:I141T	I	+	2	0	SYNGAP1	33508474	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.107000	0.77047	1.840000	0.53500	0.383000	0.25322	ATC	.	.		0.587	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		C	33400496	T	C	33400496	3	2	103	1	0	0	0	0	1	0	0	0	15462	1435	50	2	440	2	SYNGAP1	6	33400496	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	236154	33400496	137714571	441	15064										
ZBTB9	221504	hgsc.bcm.edu	37	chr6	33423129	33423129	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttctgggggatgcgcctcgTctcactctaccgagtgtcat	11	13	4	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:33423129T>C	ENST00000395064.2	+	2	520	c.252T>C	c.(250-252)cgT>cgC	p.R84R		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	84	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						ATGCGCCTCGTCTCACTCTAC	0.582																																					p.R84R		Atlas-SNP	.											.	ZBTB9	23	.	0			c.T252C						.						172	177	176					6																	33423129		2203	4300	6503	SO:0001819	synonymous_variant	221504	exon2			GCCTCGTCTCACT	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.252T>C	chr6.hg19:g.33423129T>C		66.0	0.0		140.0	6.0	NM_152735	A2AB19	Silent	SNP	ENST00000395064.2	hg19	CCDS4780.1																																																																																			.	.		0.582	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735		C	33423129	T	C	33423129	2	2	103	1	0	0	0	0	0	0	0	1	17573	1654	58	2		2	ZBTB9	6	33423129	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	22633	33423129	137691938	442	15065										
ETV7	51513	hgsc.bcm.edu	37	chr6	36339181	36339181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctgggtcctgcagccgagcTctgcacagtgacataagttg	12	12	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:36339181T>C	ENST00000340181.4	-	5	831	c.590A>G	c.(589-591)gAg>gGg	p.E197G	ETV7_ENST00000373737.4_Intron|ETV7_ENST00000339796.5_Missense_Mutation_p.E197G|ETV7_ENST00000538992.1_Missense_Mutation_p.E46G|ETV7_ENST00000373738.1_Missense_Mutation_p.E142G	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	197					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(4)	10						GCAGCCGAGCTCTGCACAGTG	0.647																																					p.E197G		Atlas-SNP	.											.	ETV7	31	.	0			c.A590G						.						52	45	47					6																	36339181		2203	4300	6503	SO:0001583	missense	51513	exon5			CCGAGCTCTGCAC	AF116508	CCDS4819.1, CCDS56422.1, CCDS56423.1, CCDS56424.1, CCDS56425.1, CCDS75440.1, CCDS75441.1	6p21	2008-09-12	2008-09-12		ENSG00000010030	ENSG00000010030			18160	protein-coding gene	gene with protein product	"TEL2 oncogene"	605255	"ets variant gene 7 (TEL2 oncogene)"			10828014, 11108721	Standard	NM_016135		Approved	TEL2, TEL-2	uc003omb.3	Q9Y603	OTTHUMG00000014594	ENST00000340181.4:c.590A>G	chr6.hg19:g.36339181T>C	ENSP00000341843:p.Glu197Gly	56.0	0.0		95.0	5.0	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Missense_Mutation	SNP	ENST00000340181.4	hg19	CCDS4819.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.496980	0.26861	.	.	ENSG00000010030	ENST00000339796;ENST00000340181;ENST00000373738;ENST00000538992	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	3.26	3.26	0.37387	.	0.297121	0.31427	N	0.007661	T	0.08626	0.0214	L	0.34521	1.04	0.09310	N	1	B;P;P;D;B	0.71674	0.022;0.939;0.82;0.998;0.011	B;P;P;D;B	0.66351	0.037;0.565;0.496;0.943;0.03	T	0.13548	-1.0505	10	0.27082	T	0.32	.	5.4496	0.16556	0.0:0.1353:0.0:0.8647	.	138;142;197;142;197	Q9Y603-2;Q9Y603-4;Q9Y603;Q9Y603-6;Q9Y603-5	.;.;ETV7_HUMAN;.;.	G	197;197;142;46	ENSP00000342260:E197G;ENSP00000341843:E197G;ENSP00000362843:E142G;ENSP00000440592:E46G	ENSP00000342260:E197G	E	-	2	0	ETV7	36447159	0.030000	0.19436	0.101000	0.21167	0.098000	0.18820	1.827000	0.39102	1.264000	0.44198	0.460000	0.39030	GAG	.	.		0.647	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135		C	36339181	T	C	36339181	3	2	103	1	0	0	0	0	1	0	0	0	5286	1551	54	2	451	2	ETV7	6	36339181	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2916052	36339181	134775886	443	15066										
MDGA1	266727	hgsc.bcm.edu	37	chr6	37616904	37616904	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgggaacaacaggcggcggcGgcagcagctgccctttgaaa	15	12	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:37616904G>T	ENST00000434837.3	-	9	2926	c.1748C>A	c.(1747-1749)cCg>cAg	p.P583Q	MDGA1_ENST00000505425.1_Missense_Mutation_p.P583Q|MDGA1_ENST00000510077.1_5'Flank|MDGA1_ENST00000297153.7_Missense_Mutation_p.P586Q	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	583	Ig-like 6.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						AGGCGGCGGCGGCAGCAGCTG	0.736																																					p.P583Q		Atlas-SNP	.											.	MDGA1	104	.	0			c.C1748A						.						2	2	2					6																	37616904		1356	2933	4289	SO:0001583	missense	266727	exon9			GGCGGCGGCAGCA	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.1748C>A	chr6.hg19:g.37616904G>T	ENSP00000402584:p.Pro583Gln	0.0	0.0		9.0	8.0	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	hg19	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.302747	0.23736	.	.	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425	T;T;T	0.65549	-0.16;-0.16;-0.16	3.73	3.73	0.42828	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.159905	0.29293	N	0.012576	T	0.28400	0.0702	L	0.27053	0.805	0.27978	N	0.936153	B	0.15719	0.014	B	0.24701	0.055	T	0.09975	-1.0650	10	0.13853	T	0.58	.	13.2016	0.59772	0.0:0.0:1.0:0.0	.	583	Q8NFP4	MDGA1_HUMAN	Q	583;586;583	ENSP00000402584:P583Q;ENSP00000297153:P586Q;ENSP00000422042:P583Q	ENSP00000297153:P586Q	P	-	2	0	MDGA1	37724882	0.071000	0.21146	0.991000	0.47740	0.898000	0.52572	1.972000	0.40540	2.089000	0.63090	0.561000	0.74099	CCG	.	.		0.736	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			T	37616904	G	T	37616904	3	4	103	1	0	0	0	0	1	0	0	0	9415	1116	39	1	1155	1	MDGA1	6	37616904	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	1277723	37616904	133498163	444	15067										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38834389	38834389	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccctggatatgctgggcgccAggaactaccagaaaacctaa	10	12	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:38834389A>G	ENST00000359357.3	+	44	6124	c.5870A>G	c.(5869-5871)cAg>cGg	p.Q1957R	DNAH8_ENST00000449981.2_Missense_Mutation_p.Q2174R|DNAH8_ENST00000441566.1_Missense_Mutation_p.Q1957R			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1957	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GCTGGGCGCCAGGAACTACCA	0.323																																					p.Q2174R		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A6521G						.						67	68	67					6																	38834389		2203	4300	6503	SO:0001583	missense	1769	exon46			GGCGCCAGGAACT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.5870A>G	chr6.hg19:g.38834389A>G	ENSP00000352312:p.Gln1957Arg	53.0	0.0		92.0	4.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.478637|4.478637	0.84747|0.84747	.|.	.|.	ENSG00000124721|ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566|ENST00000394393	T;T;T|.	0.09255|.	3.0;3.0;3.0|.	5.87|5.87	4.68|4.68	0.58851|0.58851	ATPase, AAA+ type, core (1);|.	0.054564|.	0.85682|.	D|.	0.000000|.	T|T	0.52224|0.52224	0.1721|0.1721	L|L	0.56396|0.56396	1.775|1.775	0.58432|0.58432	D|D	0.999998|0.999998	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.52668|0.52668	-0.8545|-0.8545	10|5	0.54805|.	T|.	0.06|.	.|.	13.2981|13.2981	0.60309|0.60309	0.8679:0.1321:0.0:0.0|0.8679:0.1321:0.0:0.0	.|.	1957|.	Q96JB1|.	DYH8_HUMAN|.	R|G	2162;2162;1957;1957|39	ENSP00000333363:Q2162R;ENSP00000352312:Q1957R;ENSP00000402294:Q1957R|.	ENSP00000333363:Q2162R|.	Q|R	+|+	2|1	0|2	DNAH8|DNAH8	38942367|38942367	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.277000|9.277000	0.95755|0.95755	1.104000|1.104000	0.41587|0.41587	0.533000|0.533000	0.62120|0.62120	CAG|AGG	.	.		0.323	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38834389	A	G	38834389	3	3	103	1	0	0	0	0	1	0	0	0	4609	188	7	2	6036	2	DNAH8	6	38834389	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1217485	38834389	132280678	445	15068										
CUL9	23113	hgsc.bcm.edu	37	chr6	43172517	43172517	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcaagggtcgggaccggagCccggcgccttcgccagtgct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:43172517delC	ENST00000252050.4	+	22	4455	c.4371delC	c.(4369-4371)agcfs	p.S1457fs	CUL9_ENST00000354495.3_Frame_Shift_Del_p.S1347fs|CUL9_ENST00000372647.2_Frame_Shift_Del_p.S1457fs	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1457					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GGGACCGGAGCCCGGCGCCTT	0.597																																					p.S1457fs		Atlas-INDEL	.											.	CUL9	248	.	0			c.4370delG						.						78	85	83					6																	43172517		2203	4300	6503	SO:0001589	frameshift_variant	23113	exon22			.	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.4371delC	chr6.hg19:g.43172517delC	ENSP00000252050:p.Ser1457fs	99.0	0.0		172.0	11.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Frame_Shift_Del	DEL	ENST00000252050.4	hg19	CCDS4890.1																																																																																			.	.		0.597	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		-	43172517	C	-	43172517	7	5	103	1	0	1	0	1	0	0	0	0	4063	738	26	0	4453	0	CUL9	6	43172517	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	4338128	43172517	127942550	446	15069										
HSP90AB1	3326	hgsc.bcm.edu	37	chr6	44218079	44218079	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgatgaggcagaggaagagAaaggtgagaaagaagaggaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:44218079delA	ENST00000371554.1	+	6	914	c.700delA	c.(700-702)aaafs	p.K234fs	HSP90AB1_ENST00000371646.5_Frame_Shift_Del_p.K234fs|HSP90AB1_ENST00000353801.3_Frame_Shift_Del_p.K234fs			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	234					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			agaggaagagaaaggtgagaa	0.413																																					p.E233fs		Atlas-INDEL	.											.	HSP90AB1	83	.	0			c.699delG						.						56	58	57					6																	44218079		2203	4299	6502	SO:0001589	frameshift_variant	3326	exon6			.	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"Heat shock proteins / HSPC"	5258	protein-coding gene	gene with protein product		140572	"heat shock 90kD protein 1, beta", "heat shock 90kDa protein 1, beta"	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.700delA	chr6.hg19:g.44218079delA	ENSP00000360609:p.Lys234fs	102.0	0.0		165.0	10.0	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Frame_Shift_Del	DEL	ENST00000371554.1	hg19	CCDS4909.1																																																																																			.	.		0.413	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355		-	44218079	A	-	44218079	7	5	103	1	0	1	0	1	0	0	0	0	7411	247	9	0	718	0	HSP90AB1	6	44218079	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1045562	44218079	126896988	447	15070										
TDRD6	221400	hgsc.bcm.edu	37	chr6	46660975	46660975	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aatattctaagactggtattAaaagtgctcttccctatgaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:46660975delA	ENST00000316081.6	+	1	5110	c.5110delA	c.(5110-5112)aaafs	p.K1704fs	TDRD6_ENST00000544460.1_Frame_Shift_Del_p.K1704fs	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1704					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			GACTGGTATTAAAAGTGCTCT	0.333																																					p.I1703fs		Atlas-INDEL	.											.	TDRD6	205	.	0			c.5109delT						.						30	35	33					6																	46660975		2172	4283	6455	SO:0001589	frameshift_variant	221400	exon1			.	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.5110delA	chr6.hg19:g.46660975delA	ENSP00000346065:p.Lys1704fs	84.0	0.0		164.0	10.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Frame_Shift_Del	DEL	ENST00000316081.6	hg19	CCDS34470.1																																																																																			.	.		0.333	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		-	46660975	A	-	46660975	7	5	103	1	0	1	0	1	0	0	0	0	15749	363	13	0	5112	0	TDRD6	6	46660975	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2442896	46660975	124454092	448	15071										
EFHC1	114327	hgsc.bcm.edu	37	chr6	52303144	52303144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tccaagaagatgttcctatgTcaactgaggaacagtatagg	10	7	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:52303144T>C	ENST00000371068.5	+	3	431	c.328T>C	c.(328-330)Tca>Cca	p.S110P	EFHC1_ENST00000538167.1_Missense_Mutation_p.S91P|EFHC1_ENST00000491749.1_3'UTR|EFHC1_ENST00000433625.2_Missense_Mutation_p.S19P	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	110	DM10 1. {ECO:0000255|PROSITE- ProRule:PRU00665}.					axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					TGTTCCTATGTCAACTGAGGA	0.368																																					p.S110P		Atlas-SNP	.											.	EFHC1	68	.	0			c.T328C						.						50	45	46					6																	52303144		2202	4300	6502	SO:0001583	missense	114327	exon3			CCTATGTCAACTG	AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"EF-hand domain containing"	16406	protein-coding gene	gene with protein product	"myoclonin-1"	608815	"epilepsy, juvenile myoclonic 1"	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.328T>C	chr6.hg19:g.52303144T>C	ENSP00000360107:p.Ser110Pro	58.0	0.0		104.0	5.0	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Missense_Mutation	SNP	ENST00000371068.5	hg19	CCDS4942.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.791581	0.90367	.	.	ENSG00000096093	ENST00000371068;ENST00000433625;ENST00000538167	T;T;T	0.71341	-0.32;-0.56;-0.53	5.78	5.78	0.91487	Uncharacterised domain DM10 (2);	0.056069	0.64402	D	0.000001	D	0.86406	0.5925	M	0.94101	3.495	0.54753	D	0.999989	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.993	D	0.89968	0.4091	10	0.72032	D	0.01	-1.4504	16.1205	0.81351	0.0:0.0:0.0:1.0	.	91;19;110	F5GZD8;B7Z2S4;Q5JVL4	.;.;EFHC1_HUMAN	P	110;19;91	ENSP00000360107:S110P;ENSP00000416492:S19P;ENSP00000444521:S91P	ENSP00000360107:S110P	S	+	1	0	EFHC1	52411103	1.000000	0.71417	0.694000	0.30210	0.934000	0.57294	8.040000	0.89188	2.205000	0.71048	0.533000	0.62120	TCA	.	.		0.368	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		C	52303144	T	C	52303144	3	2	103	1	0	0	0	0	1	0	0	0	4948	1667	58	2	348	2	EFHC1	6	52303144	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	5642169	52303144	118811923	449	15072										
LRRC1	55227	hgsc.bcm.edu	37	chr6	53787490	53787490	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agttaaagcacatgaaaaagAcagtggagaatttacggaat	10	4	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:53787490A>G	ENST00000370888.1	+	14	1751	c.1474A>G	c.(1474-1476)Aca>Gca	p.T492A	RP3-523E19.2_ENST00000474641.2_RNA	NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	492						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		CATGAAAAAGACAGTGGAGAA	0.433																																					p.T492A		Atlas-SNP	.											.	LRRC1	59	.	0			c.A1474G						.						213	211	212					6																	53787490		1932	4145	6077	SO:0001583	missense	55227	exon14			AAAAAGACAGTGG	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"leucine-rich repeat-containing 1"				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.1474A>G	chr6.hg19:g.53787490A>G	ENSP00000359925:p.Thr492Ala	68.0	0.0		115.0	6.0	NM_018214	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	hg19	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	A	6.065	0.380386	0.11466	.	.	ENSG00000137269	ENST00000370888	T	0.78003	-1.14	5.91	4.76	0.60689	.	0.058928	0.64402	D	0.000002	T	0.43700	0.1259	N	0.20685	0.6	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37220	-0.9715	10	0.15952	T	0.53	.	11.0763	0.48034	0.9281:0.0:0.0719:0.0	.	492	Q9BTT6	LRRC1_HUMAN	A	492	ENSP00000359925:T492A	ENSP00000359925:T492A	T	+	1	0	LRRC1	53895449	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.922000	0.56462	1.072000	0.40860	0.533000	0.62120	ACA	.	.		0.433	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168		G	53787490	A	G	53787490	3	3	103	1	0	0	0	0	1	0	0	0	8975	275	10	2	1528	2	LRRC1	6	53787490	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1484346	53787490	117327577	450	15073										
GFRAL	389400	hgsc.bcm.edu	37	chr6	55198671	55198671	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagcaatttccaatttaaagAgtgtctttgcactgatgact	7	7	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:55198671A>G	ENST00000340465.2	+	3	331	c.245A>G	c.(244-246)gAg>gGg	p.E82G		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	82					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			CAATTTAAAGAGTGTCTTTGC	0.338																																					p.E82G		Atlas-SNP	.											.	GFRAL	91	.	0			c.A245G						.						135	135	135					6																	55198671		2203	4300	6503	SO:0001583	missense	389400	exon3			TTAAAGAGTGTCT	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.245A>G	chr6.hg19:g.55198671A>G	ENSP00000343636:p.Glu82Gly	73.0	0.0		94.0	4.0	NM_207410	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	hg19	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	A	7.176	0.588646	0.13812	.	.	ENSG00000187871	ENST00000340465	T	0.31769	1.48	5.12	3.92	0.45320	GDNF/GAS1 (1);	0.565954	0.17857	N	0.159657	T	0.04861	0.0131	N	0.08118	0	0.25933	N	0.982967	B	0.02656	0.0	B	0.04013	0.001	T	0.38714	-0.9648	10	0.25106	T	0.35	-19.2804	7.9232	0.29859	0.9045:0.0:0.0955:0.0	.	82	Q6UXV0	GFRAL_HUMAN	G	82	ENSP00000343636:E82G	ENSP00000343636:E82G	E	+	2	0	GFRAL	55306630	0.989000	0.36119	0.825000	0.32803	0.394000	0.30568	1.867000	0.39499	0.739000	0.32628	0.528000	0.53228	GAG	.	.		0.338	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		G	55198671	A	G	55198671	3	3	103	1	0	0	0	0	1	0	0	0	6359	304	11	2	255	2	GFRAL	6	55198671	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1411181	55198671	115916396	451	15074										
ZNF451	26036	hgsc.bcm.edu	37	chr6	57012815	57012815	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtgctcactgcagaaagccTtttcataagatagaaacatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:57012815delT	ENST00000370706.4	+	10	2176	c.1932delT	c.(1930-1932)cctfs	p.P644fs	RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|ZNF451_ENST00000357489.3_Frame_Shift_Del_p.P644fs|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|ZNF451_ENST00000491832.2_Frame_Shift_Del_p.P644fs|RP11-203B9.4_ENST00000586466.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000589263.1_RNA|RP11-203B9.4_ENST00000589549.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	644					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GCAGAAAGCCTTTTCATAAGA	0.378																																					p.P644fs		Atlas-INDEL	.											.	ZNF451	181	.	0			c.1931delC						.						87	88	87					6																	57012815		2202	4299	6501	SO:0001589	frameshift_variant	26036	exon10			.	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"Zinc fingers, C2H2-type"	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.1932delT	chr6.hg19:g.57012815delT	ENSP00000359740:p.Pro644fs	78.0	0.0		157.0	10.0	NM_001031623	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Frame_Shift_Del	DEL	ENST00000370706.4	hg19	CCDS43477.1																																																																																			.	.		0.378	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555		-	57012815	T	-	57012815	7	5	103	1	0	1	0	1	0	0	0	0	17937	1596	56	0	1970	0	ZNF451	6	57012815	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1814144	57012815	114102252	452	15075										
COL19A1	1310	hgsc.bcm.edu	37	chr6	70610184	70610184	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgcattttgtgaaagtgatAaaacctgtttcaaattggga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:70610184delA	ENST00000322773.4	+	4	322	c.220delA	c.(220-222)aaafs	p.K74fs		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	74	Laminin G-like.				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						TGAAAGTGATAAAACCTGTTT	0.264																																					p.D73fs		Atlas-INDEL	.											.	COL19A1	232	.	0			c.219delT						.						75	76	76					6																	70610184		2203	4298	6501	SO:0001589	frameshift_variant	1310	exon4			.		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.220delA	chr6.hg19:g.70610184delA	ENSP00000316030:p.Lys74fs	163.0	0.0		164.0	11.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Frame_Shift_Del	DEL	ENST00000322773.4	hg19	CCDS4970.1																																																																																			.	.		0.264	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			-	70610184	A	-	70610184	7	5	103	1	0	1	0	1	0	0	0	0	3678	363	13	0	230	0	COL19A1	6	70610184	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	13597369	70610184	100504883	453	15076										
COL9A1	1297	hgsc.bcm.edu	37	chr6	71010083	71010083	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cattagaattggaattgacaGggaatcctgcaaaagagata							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:71010083delG	ENST00000357250.6	-	3	253	c.95delC	c.(94-96)cctfs	p.P32fs	COL9A1_ENST00000370496.3_Frame_Shift_Del_p.P32fs	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	32	Nonhelical region (NC4).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						GGAATTGACAGGGAATCCTGC	0.308																																					p.P32fs		Atlas-INDEL	.											.	COL9A1	228	.	0			c.96delT						.						105	96	99					6																	71010083		2203	4300	6503	SO:0001589	frameshift_variant	1297	exon3			.		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.95delC	chr6.hg19:g.71010083delG	ENSP00000349790:p.Pro32fs	134.0	0.0		165.0	12.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Frame_Shift_Del	DEL	ENST00000357250.6	hg19	CCDS4971.1																																																																																			.	.		0.308	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			-	71010083	G	-	71010083	7	5	103	1	0	1	0	1	0	0	0	0	3709	1000	35	0	2890	0	COL9A1	6	71010083	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	399899	71010083	100104984	454	15077										
FAM135A	57579	hgsc.bcm.edu	37	chr6	71191751	71191751	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttcctacatcatgcgtatcgTtttcattatacactttgtgc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:71191751delT	ENST00000418814.2	+	10	1331	c.717delT	c.(715-717)cgtfs	p.R239fs	FAM135A_ENST00000361499.3_Frame_Shift_Del_p.R239fs|FAM135A_ENST00000505769.1_Frame_Shift_Del_p.R239fs|FAM135A_ENST00000505868.1_Frame_Shift_Del_p.R239fs|FAM135A_ENST00000457062.2_Frame_Shift_Del_p.R196fs|FAM135A_ENST00000370479.3_Frame_Shift_Del_p.R196fs	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	239										breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						ATGCGTATCGTTTTCATTATA	0.388																																					p.R239fs		Atlas-INDEL	.											.	FAM135A	181	.	0			c.716delG						.						210	180	190					6																	71191751		2203	4300	6503	SO:0001589	frameshift_variant	57579	exon8			.	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"KIAA1411"	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.717delT	chr6.hg19:g.71191751delT	ENSP00000410768:p.Arg239fs	142.0	0.0		154.0	10.0	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Frame_Shift_Del	DEL	ENST00000418814.2	hg19	CCDS55028.1																																																																																			.	.		0.388	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		-	71191751	T	-	71191751	7	5	103	1	0	1	0	1	0	0	0	0	5453	1712	60	0	743	0	FAM135A	6	71191751	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	181668	71191751	99923316	455	15078										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75818818	75818818	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttccagcttccttgatgtcTttttctataatttcatagca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:75818818delT	ENST00000322507.8	-	52	8325	c.8016delA	c.(8014-8016)aaafs	p.K2672fs	COL12A1_ENST00000483888.2_Frame_Shift_Del_p.K2672fs|COL12A1_ENST00000345356.6_Frame_Shift_Del_p.K1508fs|COL12A1_ENST00000416123.2_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2672	Laminin G-like.|Nonhelical region (NC3).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CCTTGATGTCTTTTTCTATAA	0.308																																					p.D2673fs		Atlas-INDEL	.											.	COL12A1	385	.	0			c.8017delG						.						83	81	81					6																	75818818		1799	4070	5869	SO:0001589	frameshift_variant	1303	exon52			.	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.8016delA	chr6.hg19:g.75818818delT	ENSP00000325146:p.Lys2672fs	175.0	0.0		173.0	11.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Frame_Shift_Del	DEL	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.308	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		-	75818818	T	-	75818818	7	5	103	1	0	1	0	1	0	0	0	0	3671	1606	56	0	1235	0	COL12A1	6	75818818	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	4627067	75818818	95296249	456	15079										
TPBG	7162	hgsc.bcm.edu	37	chr6	83075723	83075723	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggactgtgacccgattcttCccccatccctgcaaacctct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:83075723delC	ENST00000369750.3	+	2	1662	c.1045delC	c.(1045-1047)cccfs	p.P350fs	TPBG_ENST00000535040.1_Frame_Shift_Del_p.P350fs|TPBG_ENST00000543496.1_Frame_Shift_Del_p.P350fs			Q13641	TPBG_HUMAN	trophoblast glycoprotein	350					cell adhesion (GO:0007155)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15		all_cancers(76;0.000805)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0897)		BRCA - Breast invasive adenocarcinoma(397;0.107)		CCCGATTCTTCCCCCATCCCT	0.498																																					p.L348fs		Atlas-INDEL	.											.	TPBG	37	.	0			c.1044delT						.						107	100	102					6																	83075723		2203	4300	6503	SO:0001589	frameshift_variant	7162	exon2			.	AJ012159	CCDS4995.1	6q14-q15	2008-07-29			ENSG00000146242	ENSG00000146242			12004	protein-coding gene	gene with protein product		190920				8132670	Standard	NM_006670		Approved	5T4-AG, 5T4	uc003pjo.3	Q13641	OTTHUMG00000015103	ENST00000369750.3:c.1045delC	chr6.hg19:g.83075723delC	ENSP00000358765:p.Pro350fs	138.0	0.0		156.0	10.0	NM_001166392	A8K555	Frame_Shift_Del	DEL	ENST00000369750.3	hg19	CCDS4995.1																																																																																			.	.		0.498	TPBG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041340.1			-	83075723	C	-	83075723	7	5	103	1	0	1	0	1	0	0	0	0	16409	855	30	0	1047	0	TPBG	6	83075723	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	7256905	83075723	88039344	457	15080										
UBE2CBP	90025	hgsc.bcm.edu	37	chr6	83667146	83667146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttagcgggtggacgctgatgTcactttcccacaagctgaca	11	11	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:83667146T>C	ENST00000369747.3	-	9	1156	c.1034A>G	c.(1033-1035)gAc>gGc	p.D345G		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	345					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										GACGCTGATGTCACTTTCCCA	0.418																																					p.D345G		Atlas-SNP	.											.	.	.	.	0			c.A1034G						.						115	97	103					6																	83667146		2203	4300	6503	SO:0001583	missense	90025	exon9			CTGATGTCACTTT	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"UBCH10 binding protein with a hect-like domain"	612495	"chromosome 6 open reading frame 157", "ubiquitin-conjugating enzyme E2C binding protein"	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.1034A>G	chr6.hg19:g.83667146T>C	ENSP00000358762:p.Asp345Gly	99.0	0.0		88.0	4.0	NM_198920	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	hg19	CCDS34491.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.716883	0.68844	.	.	ENSG00000118420	ENST00000369747	T	0.34275	1.37	5.57	5.57	0.84162	.	0.143601	0.64402	D	0.000007	T	0.51415	0.1673	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.57751	-0.7757	10	0.66056	D	0.02	-14.4416	13.2543	0.60070	0.0:0.0:0.0:1.0	.	345	Q7Z6J8	UB2CB_HUMAN	G	345	ENSP00000358762:D345G	ENSP00000358762:D345G	D	-	2	0	UBE2CBP	83723865	1.000000	0.71417	1.000000	0.80357	0.746000	0.42486	4.374000	0.59543	2.123000	0.65237	0.379000	0.24179	GAC	.	.		0.418	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920		C	83667146	T	C	83667146	3	2	103	1	0	0	0	0	1	0	0	0	16862	1667	58	2	143	2	UBE2CBP	6	83667146	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	591423	83667146	87447921	458	15081										
HTR1E	3354	hgsc.bcm.edu	37	chr6	87725971	87725971	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcattttatcctggctgccaTttttcatcaaagagttgatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:87725971delT	ENST00000305344.5	+	2	1622	c.919delT	c.(919-921)tttfs	p.F308fs		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	308	Agonist binding. {ECO:0000250}.				adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	CTGGCTGCCATTTTTCATCAA	0.512																																					p.P306fs		Atlas-INDEL	.											.	HTR1E	89	.	0			c.918delA						.						159	160	160					6																	87725971		2203	4300	6503	SO:0001589	frameshift_variant	3354	exon2			.		CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5291	protein-coding gene	gene with protein product		182132	"5-hydroxytryptamine (serotonin) receptor 1E"			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.919delT	chr6.hg19:g.87725971delT	ENSP00000307766:p.Phe308fs	195.0	0.0		200.0	12.0	NM_000865	E1P503|Q9P1Y1	Frame_Shift_Del	DEL	ENST00000305344.5	hg19	CCDS5006.1																																																																																			.	.		0.512	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2	NM_000865		-	87725971	T	-	87725971	7	5	103	1	0	1	0	1	0	0	0	0	7448	1493	52	0	921	0	HTR1E	6	87725971	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	4058825	87725971	83389096	459	15082										
KIAA0776	23376	hgsc.bcm.edu	37	chr6	96990799	96990799	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaagcatgagaggaggaggtGggggcaatgccagagagtac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:96990799delG	ENST00000369278.4	+	12	1375	c.1309delG	c.(1309-1311)gggfs	p.G438fs		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	438					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										AGGAGGAGGTGGGGGCAATGC	0.373																																					p.G436fs		Atlas-INDEL	.											.	.	.	.	0			c.1308delT						.						54	56	55					6																	96990799		2203	4300	6503	SO:0001589	frameshift_variant	23376	exon12			.	BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"novel LZAP-binding protein", "Regulator of CDK5RAP3 and DDRGK1"	613372	"KIAA0776"	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1309delG	chr6.hg19:g.96990799delG	ENSP00000358283:p.Gly438fs	223.0	0.0		232.0	14.0	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Frame_Shift_Del	DEL	ENST00000369278.4	hg19	CCDS5034.1																																																																																			.	.		0.373	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323		-	96990799	G	-	96990799	7	5	103	1	0	1	0	1	0	0	0	0	8202	1348	47	0	1355	0	KIAA0776	6	96990799	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	9264828	96990799	74124268	460	15083										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101163393	101163393	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cataacatacttcatccatgTtattcaactgctgcatcttg	4	11	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:101163393T>C	ENST00000369162.2	-	13	2440	c.2096A>G	c.(2095-2097)aAc>aGc	p.N699S	ASCC3_ENST00000522650.1_Missense_Mutation_p.N699S	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	699					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TTCATCCATGTTATTCAACTG	0.279																																					p.N699S		Atlas-SNP	.											.	ASCC3	205	.	0			c.A2096G						.						81	78	79					6																	101163393		2200	4291	6491	SO:0001583	missense	10973	exon13			TCCATGTTATTCA	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.2096A>G	chr6.hg19:g.101163393T>C	ENSP00000358159:p.Asn699Ser	71.0	0.0		75.0	4.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	T	10.38	1.335422	0.24253	.	.	ENSG00000112249	ENST00000369162;ENST00000522650	T;T	0.57273	0.44;0.41	4.84	4.84	0.62591	Helicase, C-terminal (1);	0.221701	0.45867	D	0.000324	T	0.22551	0.0544	L	0.33137	0.985	0.80722	D	1	B;B	0.20052	0.041;0.041	B;B	0.20184	0.026;0.028	T	0.10451	-1.0629	10	0.08599	T	0.76	.	14.7165	0.69272	0.0:0.0:0.0:1.0	.	699;699	E7EW23;Q8N3C0	.;HELC1_HUMAN	S	699	ENSP00000358159:N699S;ENSP00000430769:N699S	ENSP00000358159:N699S	N	-	2	0	ASCC3	101270114	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.736000	0.68597	1.943000	0.56356	0.477000	0.44152	AAC	.	.		0.279	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		C	101163393	T	C	101163393	3	2	103	1	0	0	0	0	1	0	0	0	1033	1725	60	2	4632	2	ASCC3	6	101163393	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4172594	101163393	69951674	461	15084										
ATG5	9474	hgsc.bcm.edu	37	chr6	106727570	106727570	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atccagagttgcttgtgatcTtttttctgcatttcattgat					rs34601838	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:106727570delT	ENST00000369076.3	-	5	767	c.444delA	c.(442-444)aaafs	p.K148fs	ATG5_ENST00000360666.4_Intron|ATG5_ENST00000369070.1_Frame_Shift_Del_p.K70fs|ATG5_ENST00000343245.3_Frame_Shift_Del_p.K148fs	NM_004849.2	NP_004840.1	Q9H1Y0	ATG5_HUMAN	autophagy related 5	148					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|blood vessel remodeling (GO:0001974)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of type I interferon production (GO:0032480)|negative stranded viral RNA replication (GO:0039689)|otolith development (GO:0048840)|post-translational protein modification (GO:0043687)|regulation of cilium assembly (GO:1902017)|regulation of cytokine secretion involved in immune response (GO:0002739)|response to drug (GO:0042493)|response to fungus (GO:0009620)|vasodilation (GO:0042311)|ventricular cardiac muscle cell development (GO:0055015)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|membrane (GO:0016020)|pre-autophagosomal structure membrane (GO:0034045)				endometrium(1)|large_intestine(5)|lung(1)|prostate(1)	8	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		GCTTGTGATCTTTTTTCTGCA	0.318																																					p.D149fs		Atlas-INDEL	.											.	ATG5	23	.	0			c.445delG						.						116	107	110					6																	106727570		2203	4300	6503	SO:0001589	frameshift_variant	9474	exon5			.	Y11588	CCDS5055.1, CCDS69159.1, CCDS75498.1	6q21	2014-02-12	2012-06-06	2005-09-11	ENSG00000057663	ENSG00000057663			589	protein-coding gene	gene with protein product		604261	"APG5 (autophagy 5, S. cerevisiae)-like", "APG5 autophagy 5-like (S. cerevisiae)", "ATG5 autophagy related 5 homolog (S. cerevisiae)"	APG5L		9563500, 11349150, 15778222	Standard	NM_001286111		Approved	ASP, APG5, hAPG5	uc003prf.3	Q9H1Y0	OTTHUMG00000016193	ENST00000369076.3:c.444delA	chr6.hg19:g.106727570delT	ENSP00000358072:p.Lys148fs	178.0	0.0		161.0	10.0	NM_004849	O60875|Q5JVR2|Q68DI4|Q9H2B8|Q9HCZ7	Frame_Shift_Del	DEL	ENST00000369076.3	hg19	CCDS5055.1																																																																																			.	.		0.318	ATG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043476.1	NM_004849		-	106727570	T	-	106727570	7	5	103	1	0	1	0	1	0	0	0	0	1100	1606	56	0	399	0	ATG5	6	106727570	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5564177	106727570	64387497	462	15085										
AIM1	202	hgsc.bcm.edu	37	chr6	106973032	106973032	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttagaggaagtgtccaaaatAaactcaatccccgacctgga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:106973032delA	ENST00000369066.3	+	3	3533	c.3046delA	c.(3046-3048)aaafs	p.K1016fs		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TGTCCAAAATAAACTCAATCC	0.378																																					p.N1015fs		Atlas-INDEL	.											.	AIM1	161	.	0			c.3045delT						.						177	172	174					6																	106973032		2203	4300	6503	SO:0001589	frameshift_variant	202	exon3			.	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.3046delA	chr6.hg19:g.106973032delA	ENSP00000358062:p.Lys1016fs	168.0	0.0		199.0	12.0	NM_001624	Q6P2P0|Q9BTM3	Frame_Shift_Del	DEL	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.		0.378	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			-	106973032	A	-	106973032	7	5	103	1	0	1	0	1	0	0	0	0	430	363	13	0	3056	0	AIM1	6	106973032	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	245462	106973032	64142035	463	15086										
NR2E1	7101	hgsc.bcm.edu	37	chr6	108499301	108499301	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctttcttccctacccagtaCccccatgaagtgaatgggac					rs143132592	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:108499301delC	ENST00000368986.4	+	5	1206	c.498delC	c.(496-498)tacfs	p.Y166fs	NR2E1_ENST00000484978.1_3'UTR|NR2E1_ENST00000368983.3_Frame_Shift_Del_p.Y203fs	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	166					aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		CTACCCAGTACCCCCATGAAG	0.463																																					p.Y166fs		Atlas-INDEL	.											.	NR2E1	57	.	0			c.497delA						.						95	91	93					6																	108499301		2203	4300	6503	SO:0001589	frameshift_variant	7101	exon5			.	Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"Nuclear hormone receptors"	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.498delC	chr6.hg19:g.108499301delC	ENSP00000357982:p.Tyr166fs	122.0	0.0		157.0	10.0	NM_003269	Q6ZMP8	Frame_Shift_Del	DEL	ENST00000368986.4	hg19	CCDS5063.1																																																																																			.	.		0.463	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2			-	108499301	C	-	108499301	7	5	103	1	0	1	0	1	0	0	0	0	10634	518	18	0	516	0	NR2E1	6	108499301	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1526269	108499301	62615766	464	15087										
REV3L	5980	hgsc.bcm.edu	37	chr6	111686477	111686477	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtatagttacctttgcttgTgttaacagtactcttctaag	7	7	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:111686477T>C	ENST00000358835.3	-	16	7198	c.6744A>G	c.(6742-6744)acA>acG	p.T2248T	REV3L_ENST00000368802.3_Silent_p.T2248T|REV3L_ENST00000368805.1_Silent_p.T2248T|REV3L_ENST00000435970.1_Silent_p.T2170T			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2248					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CCTTTGCTTGTGTTAACAGTA	0.294								DNA polymerases (catalytic subunits)																													p.T2248T		Atlas-SNP	.											.	REV3L	386	.	0			c.A6744G						.						129	120	123					6																	111686477		2198	4297	6495	SO:0001819	synonymous_variant	5980	exon15			TGCTTGTGTTAAC	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.6744A>G	chr6.hg19:g.111686477T>C		33.0	0.0		51.0	4.0	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	hg19	CCDS5091.2																																																																																			.	.		0.294	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		C	111686477	T	C	111686477	2	2	103	1	0	0	0	0	0	0	0	1	13255	1683	59	2		2	REV3L	6	111686477	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3187176	111686477	59428590	465	15088										
GOPC	57120	hgsc.bcm.edu	37	chr6	117923306	117923306	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgatctctcccaggagcagaTccacatccacaaaagctttg	7	14	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:117923306T>C	ENST00000368498.2	-	1	221	c.146A>G	c.(145-147)gAt>gGt	p.D49G	GOPC_ENST00000052569.6_Missense_Mutation_p.D49G|GOPC_ENST00000535237.1_Missense_Mutation_p.D49G	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	49					apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)		GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		CAGGAGCAGATCCACATCCAC	0.602			O	ROS1	glioblastoma						OREG0017633	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D49G		Atlas-SNP	.		Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	.	GOPC	29	.	0			c.A146G						.						89	81	84					6																	117923306		2203	4300	6503	SO:0001583	missense	57120	exon1			AGCAGATCCACAT	AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.146A>G	chr6.hg19:g.117923306T>C	ENSP00000357484:p.Asp49Gly	74.0	0.0	1484	63.0	4.0	NM_001017408	A6NM30|Q59FS4|Q969U8	Missense_Mutation	SNP	ENST00000368498.2	hg19	CCDS5117.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.392147	0.83011	.	.	ENSG00000047932	ENST00000052569;ENST00000368498;ENST00000535237	T;T;T	0.32515	1.46;1.45;1.46	5.71	4.55	0.56014	.	0.096929	0.64402	D	0.000002	T	0.43919	0.1269	M	0.73962	2.25	0.53688	D	0.999976	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.50355	-0.8838	10	0.87932	D	0	.	11.5711	0.50834	0.0:0.0697:0.0:0.9303	.	49;49	Q9HD26-2;Q9HD26	.;GOPC_HUMAN	G	49	ENSP00000052569:D49G;ENSP00000357484:D49G;ENSP00000445690:D49G	ENSP00000052569:D49G	D	-	2	0	GOPC	118029999	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	7.355000	0.79434	0.996000	0.38943	-0.250000	0.11733	GAT	.	.		0.602	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399		C	117923306	T	C	117923306	3	2	103	1	0	0	0	0	1	0	0	0	6581	1435	50	2	1278	2	GOPC	6	117923306	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	6236829	117923306	53191761	466	15089										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129826417	129826417	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaacagaaccatcagtcccAaaaaagccgacatcctggat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:129826417delA	ENST00000421865.2	+	61	8669	c.8620delA	c.(8620-8622)aaafs	p.K2875fs		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2875	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CATCAGTCCCAAAAAAGCCGA	0.403																																					p.P2873fs		Atlas-INDEL	.											.,1	LAMA2	481	.	0			c.8619delC						.						91	93	93					6																	129826417		2203	4300	6503	SO:0001589	frameshift_variant	3908	exon61			.	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.8620delA	chr6.hg19:g.129826417delA	ENSP00000400365:p.Lys2875fs	187.0	0.0		173.0	13.0	NM_000426	Q14736|Q5VUM2|Q93022	Frame_Shift_Del	DEL	ENST00000421865.2	hg19	CCDS5138.1																																																																																			.	.		0.403	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			-	129826417	A	-	129826417	7	5	103	1	0	1	0	1	0	0	0	0	8615	131	5	0	8862	0	LAMA2	6	129826417	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	11903111	129826417	41288650	467	15090										
C6orf191	253582	hgsc.bcm.edu	37	chr6	130166960	130166960	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acacatagtacacagtgtagAaaagaatgacacatagaaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:130166960delA	ENST00000368143.1	-	2	153	c.71delT	c.(70-72)ttcfs	p.F24fs	TMEM244_ENST00000438392.1_Frame_Shift_Del_p.F24fs	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	24						integral component of membrane (GO:0016021)											CACAGTGTAGAAAAGAATGAC	0.398																																					p.F24fs		Atlas-INDEL	.											.	.	.	.	0			c.72delC						.						113	103	106					6																	130166960		2203	4300	6503	SO:0001589	frameshift_variant	253582	exon2			.		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 191"	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.71delT	chr6.hg19:g.130166960delA	ENSP00000357125:p.Phe24fs	122.0	0.0		151.0	10.0	NM_001010876		Frame_Shift_Del	DEL	ENST00000368143.1	hg19	CCDS34536.1																																																																																			.	.		0.398	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876		-	130166960	A	-	130166960	7	5	103	1	0	1	0	1	0	0	0	0	2350	246	9	0	331	0	C6orf191	6	130166960	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	340543	130166960	40948107	468	15091										
C6orf191	253582	hgsc.bcm.edu	37	chr6	130182310	130182310	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttctctttaccttgcttggAgcaactctgacctggagagc	9	11	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:130182310A>G	ENST00000368143.1	-	1	106	c.24T>C	c.(22-24)gcT>gcC	p.A8A	TMEM244_ENST00000438392.1_Silent_p.A8A	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	8						integral component of membrane (GO:0016021)											CCTTGCTTGGAGCAACTCTGA	0.443																																					p.A8A		Atlas-SNP	.											.	.	.	.	0			c.T24C						.						164	147	153					6																	130182310		2203	4300	6503	SO:0001819	synonymous_variant	253582	exon1			GCTTGGAGCAACT		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 191"	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.24T>C	chr6.hg19:g.130182310A>G		91.0	0.0		102.0	5.0	NM_001010876		Silent	SNP	ENST00000368143.1	hg19	CCDS34536.1																																																																																			.	.		0.443	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876		G	130182310	A	G	130182310	2	3	103	1	0	0	0	0	0	0	0	1	2350	291	11	2		2	C6orf191	6	130182310	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	15350	130182310	40932757	469	15092										
SAMD3	154075	hgsc.bcm.edu	37	chr6	130467230	130467230	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gattggattgtccaccactgAaaaagaagtcagtatatttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:130467230delA	ENST00000368134.2	-	12	1728	c.1120delT	c.(1120-1122)tcafs	p.S374fs	RP11-73O6.3_ENST00000609978.1_RNA|SAMD3_ENST00000437477.2_Frame_Shift_Del_p.S374fs|SAMD3_ENST00000457563.2_Frame_Shift_Del_p.S398fs|SAMD3_ENST00000439090.2_Frame_Shift_Del_p.S374fs	NM_001258275.1	NP_001245204.1	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3	374										breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(15)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	29				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		TCCACCACTGAAAAAGAAGTC	0.318																																					p.S374X		Atlas-INDEL	.											.	SAMD3	98	.	0			c.1121delC						.						98	101	100					6																	130467230		2202	4293	6495	SO:0001589	frameshift_variant	154075	exon10			.	AK091351	CCDS34539.1, CCDS64525.1	6q23.1	2013-01-10			ENSG00000164483	ENSG00000164483		"Sterile alpha motif (SAM) domain containing"	21574	protein-coding gene	gene with protein product							Standard	NM_001017373		Approved	bA73O6.2, FLJ34032	uc031spp.1	Q8N6K7	OTTHUMG00000015556	ENST00000368134.2:c.1120delT	chr6.hg19:g.130467230delA	ENSP00000357116:p.Ser374fs	80.0	0.0		97.0	10.0	NM_001017373	B4DY20|E1P576|J3KQK4|Q4VXD8|Q8NAY1|Q8NB96	Frame_Shift_Del	DEL	ENST00000368134.2	hg19	CCDS34539.1																																																																																			.	.		0.318	SAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042197.3	NM_152552		-	130467230	A	-	130467230	7	5	103	1	0	1	0	1	0	0	0	0	13835	246	9	0	454	0	SAMD3	6	130467230	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	284920	130467230	40647837	470	15093										
AKAP7	9465	hgsc.bcm.edu	37	chr6	131481221	131481221	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	actgatgaacctcaaataaaTttgaagagaagtcaagaaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:131481221delT	ENST00000431975.2	+	3	272	c.174delT	c.(172-174)aatfs	p.N58fs	AKAP7_ENST00000368123.4_Frame_Shift_Del_p.N36fs|AKAP7_ENST00000366358.2_3'UTR|AKAP7_ENST00000541650.1_Frame_Shift_Del_p.N57fs	NM_016377.3	NP_057461.2	Q9P0M2	AKA7G_HUMAN	A kinase (PRKA) anchor protein 7	58						cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|nucleotide binding (GO:0000166)|protein kinase A binding (GO:0051018)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|stomach(1)	13	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		CTCAAATAAATTTGAAGAGAA	0.303																																					p.N58fs		Atlas-INDEL	.											.	AKAP7	61	.	0			c.173delA						.						51	50	50					6																	131481221		2203	4295	6498	SO:0001589	frameshift_variant	9465	exon3			.	AF047715	CCDS5142.1, CCDS5143.1, CCDS5144.1, CCDS5142.2	6q23.2	2012-10-24			ENSG00000118507	ENSG00000118507		"A-kinase anchor proteins"	377	protein-coding gene	gene with protein product		604693				9545239	Standard	NM_016377		Approved	AKAP18, AKAP15	uc003qck.4	O43687	OTTHUMG00000015563	ENST00000431975.2:c.174delT	chr6.hg19:g.131481221delT	ENSP00000405252:p.Asn58fs	145.0	0.0		163.0	10.0	NM_016377	B4DUC3|Q9HCZ8	Frame_Shift_Del	DEL	ENST00000431975.2	hg19	CCDS5142.2																																																																																			.	.		0.303	AKAP7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042209.2	NM_004842		-	131481221	T	-	131481221	7	5	103	1	0	1	0	1	0	0	0	0	456	1490	52	0	114	0	AKAP7	6	131481221	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1013991	131481221	39633846	471	15094										
AKAP7	9465	hgsc.bcm.edu	37	chr6	131540900	131540900	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atctttgctccatgctgaagAaaaaacaaagtaatggttat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:131540900delA	ENST00000431975.2	+	7	900	c.802delA	c.(802-804)aaafs	p.K269fs	AKAP7_ENST00000368123.4_Frame_Shift_Del_p.K247fs|AKAP7_ENST00000537868.1_Frame_Shift_Del_p.K5fs|AKAP7_ENST00000263050.3_Frame_Shift_Del_p.K5fs|AKAP7_ENST00000541650.1_Frame_Shift_Del_p.K268fs	NM_016377.3	NP_057461.2	Q9P0M2	AKA7G_HUMAN	A kinase (PRKA) anchor protein 7	269						cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|nucleotide binding (GO:0000166)|protein kinase A binding (GO:0051018)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|stomach(1)	13	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		CATGCTGAAGAAAAAACAAAG	0.279																																					p.K267fs		Atlas-INDEL	.											.	AKAP7	61	.	0			c.801delG						.						78	84	82					6																	131540900		2202	4299	6501	SO:0001589	frameshift_variant	9465	exon7			.	AF047715	CCDS5142.1, CCDS5143.1, CCDS5144.1, CCDS5142.2	6q23.2	2012-10-24			ENSG00000118507	ENSG00000118507		"A-kinase anchor proteins"	377	protein-coding gene	gene with protein product		604693				9545239	Standard	NM_016377		Approved	AKAP18, AKAP15	uc003qck.4	O43687	OTTHUMG00000015563	ENST00000431975.2:c.802delA	chr6.hg19:g.131540900delA	ENSP00000405252:p.Lys269fs	242.0	0.0		208.0	15.0	NM_016377	B4DUC3|Q9HCZ8	Frame_Shift_Del	DEL	ENST00000431975.2	hg19	CCDS5142.2																																																																																			.	.		0.279	AKAP7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042209.2	NM_004842		-	131540900	A	-	131540900	7	5	103	1	0	1	0	1	0	0	0	0	456	247	9	0	758	0	AKAP7	6	131540900	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	59679	131540900	39574167	472	15095										
HBS1L	10767	hgsc.bcm.edu	37	chr6	135323883	135323883	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagtcttacccaggcacttcAaatcccatagtttgcttctt	5	12	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:135323883A>G	ENST00000367837.5	-	5	734	c.528T>C	c.(526-528)ttT>ttC	p.F176F	HBS1L_ENST00000415177.2_Silent_p.F111F|HBS1L_ENST00000314674.3_3'UTR|HBS1L_ENST00000367826.2_Silent_p.F134F|HBS1L_ENST00000367824.4_Silent_p.F12F|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000527578.1_Silent_p.F12F	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	176					signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		CAGGCACTTCAAATCCCATAG	0.428																																					p.F176F		Atlas-SNP	.											.	HBS1L	75	.	0			c.T528C						.						112	100	104					6																	135323883		2203	4300	6503	SO:0001819	synonymous_variant	10767	exon5			CACTTCAAATCCC	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"eRF3 family member"	612450	"HBS1 (S. cerevisiae)-like", "HBS1-like (S. cerevisiae)"			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.528T>C	chr6.hg19:g.135323883A>G		118.0	0.0		124.0	5.0	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	hg19	CCDS5173.1																																																																																			.	.		0.428	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			G	135323883	A	G	135323883	2	3	103	1	0	0	0	0	0	0	0	1	6996	127	5	2		2	HBS1L	6	135323883	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	3782983	135323883	35791184	473	15096										
FAM54A	113115	hgsc.bcm.edu	37	chr6	136562707	136562707	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttcatttacaggcaggtcaTttttcacagtttctttctgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:136562707delT	ENST00000420702.1	-	5	778	c.389delA	c.(388-390)aatfs	p.N130fs	MTFR2_ENST00000451457.2_Frame_Shift_Del_p.N130fs	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	130					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											AGGCAGGTCATTTTTCACAGT	0.398																																					p.N130fs		Atlas-INDEL	.											.	.	.	.	0			c.390delT						.						107	98	101					6																	136562707		2203	4300	6503	SO:0001589	frameshift_variant	113115	exon5			.	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"DUF729 domain containing 1", "family with sequence similarity 54, member A"	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.389delA	chr6.hg19:g.136562707delT	ENSP00000395232:p.Asn130fs	116.0	0.0		138.0	10.0	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Frame_Shift_Del	DEL	ENST00000420702.1	hg19	CCDS5176.1																																																																																			.	.		0.398	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419		-	136562707	T	-	136562707	7	5	103	1	0	1	0	1	0	0	0	0	5590	1493	52	0	784	0	FAM54A	6	136562707	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1238824	136562707	34552360	474	15097										
VTA1	51534	hgsc.bcm.edu	37	chr6	142525139	142525139	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggtgtagcaagtaatactAtccaacctactccacagact	6	12	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:142525139A>G	ENST00000367630.4	+	7	773	c.715A>G	c.(715-717)Atc>Gtc	p.I239V	VTA1_ENST00000452973.2_Intron|VTA1_ENST00000367621.1_Missense_Mutation_p.I181V	NM_016485.3	NP_057569.2	Q9NP79	VTA1_HUMAN	vesicle (multivesicular body) trafficking 1	239	Interaction with VPS4B. {ECO:0000250}.		I -> M (in dbSNP:rs2232307).		endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;1.34e-05)|GBM - Glioblastoma multiforme(68;0.00182)		AAGTAATACTATCCAACCTAC	0.383																																					p.I239V		Atlas-SNP	.											.	VTA1	29	.	0			c.A715G						.						143	127	132					6																	142525139		2203	4300	6503	SO:0001583	missense	51534	exon7			AATACTATCCAAC	AF060225	CCDS5197.1, CCDS69214.1, CCDS75531.1	6q24.1	2013-08-05	2013-08-05	2007-04-03	ENSG00000009844	ENSG00000009844			20954	protein-coding gene	gene with protein product		610902	"chromosome 6 open reading frame 55", "Vps20-associated 1 homolog (S. cerevisiae)"	C6orf55		11489251, 15644320	Standard	NM_001286372		Approved	HSPC228, My012	uc003qiw.3	Q9NP79	OTTHUMG00000015707	ENST00000367630.4:c.715A>G	chr6.hg19:g.142525139A>G	ENSP00000356602:p.Ile239Val	102.0	0.0		80.0	4.0	NM_016485	B4DW55|E1P594|E7ETQ7|Q5TGM1|Q6IAE8|Q9H0R2|Q9H3K9|Q9P0Q0	Missense_Mutation	SNP	ENST00000367630.4	hg19	CCDS5197.1	.	.	.	.	.	.	.	.	.	.	A	4.862	0.160165	0.09287	.	.	ENSG00000009844	ENST00000367630;ENST00000367621	T;T	0.40756	1.02;1.02	5.79	1.63	0.23807	.	0.268964	0.42172	N	0.000745	T	0.07503	0.0189	N	0.11560	0.145	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.16158	-1.0412	10	0.26408	T	0.33	-3.3433	5.0273	0.14391	0.631:0.1599:0.2091:0.0	.	239	Q9NP79	VTA1_HUMAN	V	239;181	ENSP00000356602:I239V;ENSP00000356593:I181V	ENSP00000356593:I181V	I	+	1	0	VTA1	142566832	1.000000	0.71417	0.997000	0.53966	0.934000	0.57294	1.452000	0.35156	0.028000	0.15324	0.533000	0.62120	ATC	.	.		0.383	VTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042483.2	NM_016485		G	142525139	A	G	142525139	3	3	103	1	0	0	0	0	1	0	0	0	17248	449	16	2	741	2	VTA1	6	142525139	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	5962432	142525139	28589928	475	15098										
GPR126	57211	hgsc.bcm.edu	37	chr6	142741019	142741019	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgggtattttggagtcatgTtttttctgaacattgccatg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:142741019delT	ENST00000230173.6	+	22	3573	c.3097delT	c.(3097-3099)tttfs	p.F1034fs	GPR126_ENST00000296932.8_Frame_Shift_Del_p.F1006fs|GPR126_ENST00000367608.2_Frame_Shift_Del_p.F1006fs|GPR126_ENST00000367609.3_Frame_Shift_Del_p.F1034fs	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	1034					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		TGGAGTCATGTTTTTTCTGAA	0.383																																					p.M1032fs		Atlas-INDEL	.											.	GPR126	192	.	0			c.3096delG						.						219	195	202					6																	142741019		1898	4125	6023	SO:0001589	frameshift_variant	57211	exon22			.	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.3097delT	chr6.hg19:g.142741019delT	ENSP00000230173:p.Phe1034fs	215.0	0.0		221.0	15.0	NM_198569	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Frame_Shift_Del	DEL	ENST00000230173.6	hg19	CCDS47490.1																																																																																			.	.		0.383	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			-	142741019	T	-	142741019	7	5	103	1	0	1	0	1	0	0	0	0	6648	1725	60	0	3183	0	GPR126	6	142741019	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	215880	142741019	28374048	476	15099										
LATS1	9113	hgsc.bcm.edu	37	chr6	150001577	150001577	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctcatttgatcctgggcaTcttgagataatccaacctag	7	10	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:150001577T>C	ENST00000543571.1	-	5	2574	c.2027A>G	c.(2026-2028)gAt>gGt	p.D676G	LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_Missense_Mutation_p.D676G	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		ATCCTGGGCATCTTGAGATAA	0.318																																					p.D676G		Atlas-SNP	.											.	LATS1	241	.	0			c.A2027G						.						70	76	74					6																	150001577		2190	4288	6478	SO:0001583	missense	9113	exon5			TGGGCATCTTGAG	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2027A>G	chr6.hg19:g.150001577T>C	ENSP00000437550:p.Asp676Gly	60.0	0.0		77.0	4.0	NM_004690		Missense_Mutation	SNP	ENST00000543571.1	hg19	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	T	13.33	2.204434	0.38905	.	.	ENSG00000131023	ENST00000543571;ENST00000253339	T;T	0.42900	0.96;0.96	5.49	5.49	0.81192	.	0.202990	0.34046	N	0.004319	T	0.11665	0.0284	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.11131	-1.0600	9	.	.	.	.	15.8809	0.79205	0.0:0.0:0.0:1.0	.	676	O95835	LATS1_HUMAN	G	676	ENSP00000437550:D676G;ENSP00000253339:D676G	.	D	-	2	0	LATS1	150043270	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.929000	0.70096	2.205000	0.71048	0.455000	0.32223	GAT	.	.		0.318	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		C	150001577	T	C	150001577	3	2	103	1	0	0	0	0	1	0	0	0	8655	1435	50	2	1381	2	LATS1	6	150001577	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	7260558	150001577	21113490	477	15100										
PCMT1	5110	hgsc.bcm.edu	37	chr6	150123486	150123486	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatacgtgcctttaacagatAaagaaaagcagtggtccagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:150123486delA	ENST00000367380.5	+	7	862	c.655delA	c.(655-657)aaafs	p.K219fs	PCMT1_ENST00000544496.1_Frame_Shift_Del_p.K184fs|PCMT1_ENST00000367384.2_Frame_Shift_Del_p.K277fs|PCMT1_ENST00000464889.1_Frame_Shift_Del_p.K277fs|PCMT1_ENST00000367378.1_Frame_Shift_Del_p.K277fs	NM_001252049.1|NM_001252050.1|NM_001252051.1|NM_001252052.1|NM_005389.2	NP_001238978.1|NP_001238979.1|NP_001238980.1|NP_001238981.1|NP_005380.2	P22061	PIMT_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase	219					protein methylation (GO:0006479)|protein repair (GO:0030091)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		TTTAACAGATAAAGAAAAGCA	0.433																																					p.D276fs		Atlas-INDEL	.											.	PCMT1	27	.	0			c.828delT						.						111	108	109					6																	150123486		2203	4300	6503	SO:0001589	frameshift_variant	5110	exon7			.		CCDS5219.1, CCDS5219.2, CCDS59041.1, CCDS75533.1, CCDS75534.1	6q22.3-q24	2008-02-05			ENSG00000120265	ENSG00000120265	2.1.1.77		8728	protein-coding gene	gene with protein product		176851				1478665, 10343128	Standard	NM_005389		Approved		uc003qne.3	P22061	OTTHUMG00000015794	ENST00000367380.5:c.655delA	chr6.hg19:g.150123486delA	ENSP00000356350:p.Lys219fs	164.0	0.0		182.0	11.0	NM_005389	A8K109|J3KP72|Q14661|Q16556|Q5VYC1|Q5VYC2|Q93061|Q96II9|Q99625|Q9BQV7|Q9BQV8|Q9NP03	Frame_Shift_Del	DEL	ENST00000367380.5	hg19																																																																																				.	.		0.433	PCMT1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				-	150123486	A	-	150123486	7	5	103	1	0	1	0	1	0	0	0	0	11594	363	13	0	855	0	PCMT1	6	150123486	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	121909	150123486	20991581	478	15101										
RAET1L	154064	hgsc.bcm.edu	37	chr6	150343212	150343212	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttctgtgctttccaggccaTtgtgacatttagtttcttcc	8	10	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:150343212T>G	ENST00000367341.1	-	2	252	c.253A>C	c.(253-255)Atg>Ctg	p.M85L	RAET1L_ENST00000286380.2_Missense_Mutation_p.M85L			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	85	MHC class I alpha-1 like. {ECO:0000250}.		M -> T (in dbSNP:rs912565). {ECO:0000269|PubMed:11827464, ECO:0000269|PubMed:15489334}.		antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		TTCCAGGCCATTGTGACATTT	0.483																																					p.M85L		Atlas-SNP	.											RAET1L,NS,carcinoma,0,2	RAET1L	21	.	0			c.A253C						.																																			SO:0001583	missense	154064	exon2			AGGCCATTGTGAC	AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918			16798	protein-coding gene	gene with protein product		611047				11827464	Standard	NM_130900		Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.253A>C	chr6.hg19:g.150343212T>G	ENSP00000356310:p.Met85Leu	263.0	0.0		247.0	0.0	NM_130900	A3KME4|Q8TE74	Missense_Mutation	SNP	ENST00000367341.1	hg19	CCDS5224.1	.	.	.	.	.	.	.	.	.	.	t	6.430	0.447513	0.12223	.	.	ENSG00000155918	ENST00000367341;ENST00000286380	T;T	0.06218	3.33;3.33	1.91	-2.05	0.07321	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00967	0.0032	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.47548	-0.9109	9	0.87932	D	0	.	5.9233	0.19094	0.0:0.5665:0.0:0.4335	.	85	Q5VY80	RET1L_HUMAN	L	85	ENSP00000356310:M85L;ENSP00000286380:M85L	ENSP00000286380:M85L	M	-	1	0	RAET1L	150384905	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.287000	0.01151	-0.549000	0.06191	0.402000	0.26972	ATG	.	.		0.483	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042676.1	NM_130900		G	150343212	T	G	150343212	3	3	103	1	0	0	0	0	1	0	0	0	13016	1493	52	5	498	5	RAET1L	6	150343212	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	219726	150343212	20771855	479	15102										
MTHFD1L	25902	hgsc.bcm.edu	37	chr6	151209073	151209073	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgttccagagaaaagggtccAtgacaatgagcatccagtgg	12	8	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:151209073A>G	ENST00000367321.3	+	7	1010	c.736A>G	c.(736-738)Atg>Gtg	p.M246V	MTHFD1L_ENST00000367307.4_Missense_Mutation_p.M246V	NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	246	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		AAAAGGGTCCATGACAATGAG	0.438																																					p.M247V		Atlas-SNP	.											.	MTHFD1L	75	.	0			c.A739G						.						101	101	101					6																	151209073		2203	4300	6503	SO:0001583	missense	25902	exon7			GGGTCCATGACAA	BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"10-formyl-THF synthetase", "mitochondrial C1-tetrahydrofolate synthase", "monofunctional C1-tetrahydrofolate synthase, mitochondrial"	611427	"formyltetrahydrofolate synthetase domain containing 1"	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.736A>G	chr6.hg19:g.151209073A>G	ENSP00000356290:p.Met246Val	105.0	0.0		84.0	4.0	NM_001242767	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Missense_Mutation	SNP	ENST00000367321.3	hg19	CCDS5228.1	.	.	.	.	.	.	.	.	.	.	A	5.497	0.276697	0.10403	.	.	ENSG00000120254	ENST00000367321;ENST00000367307;ENST00000443074;ENST00000425276	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.37	1.49	0.22878	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (1);NAD(P)-binding domain (1);	0.624222	0.18361	N	0.143566	T	0.14227	0.0344	N	0.12182	0.205	0.27183	N	0.960617	B;B;B;B	0.21309	0.002;0.0;0.002;0.054	B;B;B;B	0.20577	0.003;0.002;0.003;0.03	T	0.19976	-1.0289	10	0.72032	D	0.01	.	7.9037	0.29750	0.4834:0.4421:0.0745:0.0	.	247;1;246;246	B7ZM99;B2RD24;Q6UB35;Q6UB35-2	.;.;C1TM_HUMAN;.	V	246;246;91;91	ENSP00000356290:M246V;ENSP00000356276:M246V;ENSP00000415039:M91V;ENSP00000414412:M91V	ENSP00000356276:M246V	M	+	1	0	MTHFD1L	151250766	0.997000	0.39634	0.952000	0.39060	0.768000	0.43524	0.781000	0.26774	0.100000	0.17581	-0.340000	0.08031	ATG	.	.		0.438	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440		G	151209073	A	G	151209073	3	3	103	1	0	0	0	0	1	0	0	0	9937	217	8	2	762	2	MTHFD1L	6	151209073	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	865861	151209073	19905994	480	15103										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152472763	152472763	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgagctgcagatccatctcTgtgagccagaccagaatgct	11	11	1	5			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:152472763T>C	ENST00000367255.5	-	135	24976	c.24375A>G	c.(24373-24375)acA>acG	p.T8125T	SYNE1_ENST00000539504.1_Silent_p.T280T|SYNE1_ENST00000356820.4_Silent_p.T2649T|SYNE1_ENST00000354674.4_Silent_p.T280T|SYNE1_ENST00000265368.4_Silent_p.T8125T|SYNE1_ENST00000448038.1_Silent_p.T8054T|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000341594.5_Silent_p.T7737T|SYNE1_ENST00000423061.1_Silent_p.T8054T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8125					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GATCCATCTCTGTGAGCCAGA	0.393										HNSCC(10;0.0054)																											p.T8125T		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A24375G						.						47	47	47					6																	152472763		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon135			CATCTCTGTGAGC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.24375A>G	chr6.hg19:g.152472763T>C		86.0	0.0		71.0	4.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152472763	T	C	152472763	2	2	103	1	0	0	0	0	0	0	0	1	15460	1567	55	2		2	SYNE1	6	152472763	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1263690	152472763	18642304	481	15104										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152553297	152553297	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttgccttgtaacctatggaaTttttaatattatcttcatcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:152553297delT	ENST00000367255.5	-	113	21417	c.20816delA	c.(20815-20817)aatfs	p.N6939fs	SYNE1_ENST00000356820.4_Frame_Shift_Del_p.N1463fs|SYNE1_ENST00000265368.4_Frame_Shift_Del_p.N6939fs|SYNE1_ENST00000448038.1_Frame_Shift_Del_p.N6868fs|SYNE1_ENST00000341594.5_Frame_Shift_Del_p.N6551fs|SYNE1_ENST00000423061.1_Frame_Shift_Del_p.N6868fs	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6939					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ACCTATGGAATTTTTAATATT	0.299										HNSCC(10;0.0054)																											p.N6939fs		Atlas-INDEL	.											.	SYNE1	3227	.	0			c.20817delT						.						55	62	60					6																	152553297		2203	4299	6502	SO:0001589	frameshift_variant	23345	exon113			.	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.20816delA	chr6.hg19:g.152553297delT	ENSP00000356224:p.Asn6939fs	183.0	0.0		180.0	13.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Frame_Shift_Del	DEL	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.299	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		-	152553297	T	-	152553297	7	5	103	1	0	1	0	1	0	0	0	0	15460	1493	52	0	5786	0	SYNE1	6	152553297	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	80534	152553297	18561770	482	15105										
CNKSR3	154043	hgsc.bcm.edu	37	chr6	154731499	154731499	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttcctgccatgacctcgaggTctggcaaaagggtccacaat	10	12	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:154731499T>C	ENST00000607772.1	-	12	1891	c.1347A>G	c.(1345-1347)agA>agG	p.R449R	CNKSR3_ENST00000479339.1_Silent_p.R369R|CNKSR3_ENST00000433165.2_Silent_p.R274R	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	449	DUF1170.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		GACCTCGAGGTCTGGCAAAAG	0.532																																					p.R449R		Atlas-SNP	.											.	CNKSR3	56	.	0			c.A1347G						.						107	97	101					6																	154731499		2203	4300	6503	SO:0001819	synonymous_variant	154043	exon12			TCGAGGTCTGGCA	AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"Sterile alpha motif (SAM) domain containing"	23034	protein-coding gene	gene with protein product			"membrane associated guanylate kinase interacting protein-like 1"	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.1347A>G	chr6.hg19:g.154731499T>C		67.0	0.0		88.0	5.0	NM_173515	Q5SGD5|Q96N65	Silent	SNP	ENST00000607772.1	hg19	CCDS5246.1																																																																																			.	.		0.532	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2	NM_173515		C	154731499	T	C	154731499	2	2	103	1	0	0	0	0	0	0	0	1	3610	1664	58	2		2	CNKSR3	6	154731499	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2178202	154731499	16383568	483	15106										
TCP1	6950	hgsc.bcm.edu	37	chr6	160202000	160202000	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcaatgcgtttaaggtcccTttttaaaactcttctaactg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:160202000delT	ENST00000321394.7	-	8	1220	c.940delA	c.(940-942)aggfs	p.R314fs	TCP1_ENST00000392168.2_Frame_Shift_Del_p.R159fs|SNORA20_ENST00000384662.1_RNA|TCP1_ENST00000420894.2_Frame_Shift_Del_p.R314fs|TCP1_ENST00000544255.1_Frame_Shift_Del_p.R90fs	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1	314					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|tubulin complex assembly (GO:0007021)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|nuclear heterochromatin (GO:0005720)|pericentriolar material (GO:0000242)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(2)	10		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		TTAAGGTCCCTTTTTAAAACT	0.393																																					p.R314fs		Atlas-INDEL	.											.	TCP1	37	.	0			c.941delG						.						127	127	127					6																	160202000		2203	4300	6503	SO:0001589	frameshift_variant	6950	exon8			.	X52882	CCDS5269.1, CCDS43522.1	6q25-q27	2012-10-02			ENSG00000120438	ENSG00000120438		"Heat Shock Proteins / Chaperonins"	11655	protein-coding gene	gene with protein product		186980				3476253, 3653076	Standard	NM_030752		Approved	D6S230E, CCT1, Ccta	uc003qsr.3	P17987	OTTHUMG00000015937	ENST00000321394.7:c.940delA	chr6.hg19:g.160202000delT	ENSP00000317334:p.Arg314fs	213.0	0.0		179.0	12.0	NM_030752	E1P5B2|Q15556|Q5TCM3	Frame_Shift_Del	DEL	ENST00000321394.7	hg19	CCDS5269.1																																																																																			.	.		0.393	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042917.2	NM_030752		-	160202000	T	-	160202000	7	5	103	1	0	1	0	1	0	0	0	0	15724	1608	56	0	750	0	TCP1	6	160202000	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5470501	160202000	10913067	484	15107										
PACRG	135138	hgsc.bcm.edu	37	chr6	163483224	163483224	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accatcattatctgcctctgTtttttgatgggctttgtgaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:163483224delT	ENST00000337019.3	+	4	558	c.334delT	c.(334-336)tttfs	p.F113fs	PACRG_ENST00000366889.2_Frame_Shift_Del_p.F113fs|PACRG_ENST00000366888.2_Frame_Shift_Del_p.F113fs	NM_152410.2	NP_689623.2	Q96M98	PACRG_HUMAN	PARK2 co-regulated	113					spermatid development (GO:0007286)	cell body (GO:0044297)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm midpiece (GO:0097225)				endometrium(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		TCTGCCTCTGTTTTTTGATGG	0.448																																					p.L111fs		Atlas-INDEL	.											.	PACRG	48	.	0			c.333delG						.						109	110	109					6																	163483224		2203	4300	6503	SO:0001589	frameshift_variant	135138	exon3			.	AK057286	CCDS5284.1, CCDS43524.1	6q26	2004-07-01			ENSG00000112530	ENSG00000112530			19152	protein-coding gene	gene with protein product		608427				12547187	Standard	NM_001080378		Approved	PARK2CRG, FLJ32724, Glup, HAK005771	uc003qua.3	Q96M98	OTTHUMG00000016116	ENST00000337019.3:c.334delT	chr6.hg19:g.163483224delT	ENSP00000337946:p.Phe113fs	165.0	0.0		210.0	13.0	NM_001080379	E1P5B5|Q6IMB8|Q8IZM1|Q8NHP5|Q9H1V9	Frame_Shift_Del	DEL	ENST00000337019.3	hg19	CCDS5284.1																																																																																			.	.		0.448	PACRG-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400424.1	NM_152410		-	163483224	T	-	163483224	7	5	103	1	0	1	0	1	0	0	0	0	11379	1725	60	0	344	0	PACRG	6	163483224	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3281224	163483224	7631843	485	15108										
T	6862	hgsc.bcm.edu	37	chr6	166578153	166578153	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catcatctctttgtgatcacTtctatcaaaatgaaaaaaaa	3	8	5	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:166578153T>C	ENST00000296946.2	-	6	1138	c.670A>G	c.(670-672)Agt>Ggt	p.S224G	T_ENST00000366871.3_Splice_Site_p.S224G	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	224					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		TTGTGATCACTTCTATCAAAA	0.378									Chordoma, Familial Clustering of																												p.S224G		Atlas-SNP	.											.	T	77	.	0			c.A670G						.						81	84	83					6																	166578153		2203	4300	6503	SO:0001630	splice_region_variant	6862	exon6	Familial Cancer Database		GATCACTTCTATC	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"T-boxes"	11515	protein-coding gene	gene with protein product		601397	"T brachyury (mouse) homolog"			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.669-1A>G	chr6.hg19:g.166578153T>C		59.0	0.0		71.0	4.0	NM_003181	E7ERD6|Q4KMP4	Missense_Mutation	SNP	ENST00000296946.2	hg19	CCDS5290.1	.	.	.	.	.	.	.	.	.	.	T	11.68	1.711687	0.30322	.	.	ENSG00000164458	ENST00000366876;ENST00000296946;ENST00000366871	D;D;D	0.83755	-1.74;-1.76;-1.76	5.44	5.44	0.79542	p53-like transcription factor, DNA-binding (1);	0.377574	0.30126	N	0.010358	T	0.78426	0.4281	M	0.85299	2.745	0.40635	D	0.98189	B;B;B	0.18968	0.032;0.001;0.032	B;B;B	0.19946	0.027;0.003;0.027	T	0.77205	-0.2673	10	0.32370	T	0.25	.	14.707	0.69198	0.0:0.0:0.0:1.0	.	224;224;224	E7ERD6;O15178;Q4KMP4	.;BRAC_HUMAN;.	G	224	ENSP00000355841:S224G;ENSP00000296946:S224G;ENSP00000355836:S224G	ENSP00000296946:S224G	S	-	1	0	T	166498143	1.000000	0.71417	0.969000	0.41365	0.069000	0.16628	7.008000	0.76341	2.061000	0.61500	0.528000	0.53228	AGT	.	.		0.378	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	Missense_Mutation	C	166578153	T	C	166578153	5	2	103	1	0	0	0	0	0	0	1	0	15503	1623	56	2	653	2	T	6	166578153	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3094929	166578153	4536914	486	15109										
PDGFA	5154	hgsc.bcm.edu	37	chr7	540104	540104	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtgggttttaacctttttcTtttccgttttttacctgact							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:540104delT	ENST00000354513.5	-	6	1005	c.613delA	c.(613-615)agafs	p.R205fs	PDGFA_ENST00000402802.3_Intron	NM_002607.5	NP_002598.4	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha polypeptide	205					actin cytoskeleton organization (GO:0030036)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell activation (GO:0001775)|cell projection assembly (GO:0030031)|cell-cell signaling (GO:0007267)|embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|negative chemotaxis (GO:0050919)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling (GO:0060683)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of smooth muscle cell migration (GO:0014910)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|microvillus (GO:0005902)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|growth factor activity (GO:0008083)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		AACCTTTTTCTTTTCCGTTTT	0.557																																					p.R205fs		Atlas-INDEL	.											.	PDGFA	34	.	0			c.614delG						.						226	176	193					7																	540104		2203	4296	6499	SO:0001589	frameshift_variant	5154	exon6			.		CCDS34578.1, CCDS47524.1	7p22	2008-07-18			ENSG00000197461	ENSG00000197461			8799	protein-coding gene	gene with protein product	"PDGF A-chain", "platelet-derived growth factor alpha chain"	173430				1505216, 2536956	Standard	NM_002607		Approved	PDGF1, PDGF-A	uc003sir.3	P04085	OTTHUMG00000151412	ENST00000354513.5:c.613delA	chr7.hg19:g.540104delT	ENSP00000346508:p.Arg205fs	133.0	0.0		165.0	11.0	NM_002607	B5BU73	Frame_Shift_Del	DEL	ENST00000354513.5	hg19	CCDS34578.1																																																																																			.	.		0.557	PDGFA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322534.1			-	540104	T	-	540104	7	5	103	1	0	1	0	1	0	0	0	0	11666	1617	56	0	41	0	PDGFA	7	540104	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10		540104	158598559	487	15110										
INTS1	26173	hgsc.bcm.edu	37	chr7	1542815	1542815	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccagagcaatgaagtctcctGggggagggtgccctgcagag	16	10	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:1542815G>C	ENST00000404767.3	-	3	156	c.71C>G	c.(70-72)cCa>cGa	p.P24R	INTS1_ENST00000389470.4_Missense_Mutation_p.P152R|INTS1_ENST00000493531.1_5'Flank	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	24					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)		p.P152Q(1)		autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GAAGTCTCCTGGGGGAGGGTG	0.562																																					p.P24R		Atlas-SNP	.											INTS1,colon,carcinoma,0,1	INTS1	145	.	1	Substitution - Missense(1)	lung(1)	c.C71G						.						43	49	47					7																	1542815		1905	4123	6028	SO:0001583	missense	26173	exon3			TCTCCTGGGGGAG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.71C>G	chr7.hg19:g.1542815G>C	ENSP00000385722:p.Pro24Arg	115.0	0.0		156.0	0.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.679394	0.47886	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.52526	0.66;0.67	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.46833	0.1413	L	0.55481	1.735	0.58432	D	0.999999	P;P	0.51240	0.725;0.943	B;B	0.41813	0.135;0.367	T	0.56275	-0.8006	10	0.72032	D	0.01	.	16.6607	0.85240	0.0:0.0:1.0:0.0	.	152;24	A4D212;Q8N201	.;INT1_HUMAN	R	24;152	ENSP00000385722:P24R;ENSP00000374121:P152R	ENSP00000374121:P152R	P	-	2	0	INTS1	1509341	1.000000	0.71417	0.145000	0.22337	0.617000	0.37484	8.978000	0.93450	2.455000	0.83008	0.563000	0.77884	CCA	.	.		0.562	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			C	1542815	G	C	1542815	3	2	103	1	0	0	0	0	1	0	0	0	7784	1348	47	4	6685	4	INTS1	7	1542815	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	1002711	1542815	157595848	488	15111										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5353050	5353050	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggctcttgggctcctgccagCcccccgcccccggatcctcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:5353050delC	ENST00000430969.1	-	27	7820	c.7472delG	c.(7471-7473)ggcfs	p.G2491fs	TNRC18_ENST00000399537.4_Frame_Shift_Del_p.G2491fs	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2491							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CTCCTGCCAGCCCCCCGCCCC	0.692																																					p.G2491fs		Atlas-INDEL	.											.	TNRC18	311	.	0			c.7473delC						.						10	11	11					7																	5353050		1563	3573	5136	SO:0001589	frameshift_variant	84629	exon27			.	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7472delG	chr7.hg19:g.5353050delC	ENSP00000395538:p.Gly2491fs	91.0	0.0		168.0	11.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Frame_Shift_Del	DEL	ENST00000430969.1	hg19	CCDS47534.1																																																																																			.	.		0.692	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				-	5353050	C	-	5353050	7	5	103	1	0	1	0	1	0	0	0	0	16354	739	26	0	1450	0	TNRC18	7	5353050	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	3810235	5353050	153785613	489	15112										
CYTH3	9265	hgsc.bcm.edu	37	chr7	6210573	6210573	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggttgtggaggctggtgttgAgcatgatgatggcgaatgac	18	4	0	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:6210573A>G	ENST00000350796.3	-	8	735	c.599T>C	c.(598-600)cTc>cCc	p.L200P	CYTH3_ENST00000488964.1_5'UTR|CYTH3_ENST00000396741.2_Missense_Mutation_p.L115P	NM_004227.3	NP_004218.1	O43739	CYH3_HUMAN	cytohesin 3	200	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				establishment of epithelial cell polarity (GO:0090162)|Golgi vesicle transport (GO:0048193)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|urinary_tract(1)	19						GCTGGTGTTGAGCATGATGAT	0.627																																					p.L200P		Atlas-SNP	.											.	CYTH3	44	.	0			c.T599C						.						176	126	143					7																	6210573		2203	4300	6503	SO:0001583	missense	9265	exon8			GTGTTGAGCATGA	AJ223957	CCDS5346.1	7p22.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000008256	ENSG00000008256		"Pleckstrin homology (PH) domain containing"	9504	protein-coding gene	gene with protein product		605081	"pleckstrin homology, Sec7 and coiled-coil domains 3"	PSCD3		9072969	Standard	NM_004227		Approved	GRP1, ARNO3, cytohesin-3	uc003spt.3	O43739	OTTHUMG00000023440	ENST00000350796.3:c.599T>C	chr7.hg19:g.6210573A>G	ENSP00000297044:p.Leu200Pro	94.0	0.0		150.0	7.0	NM_004227	A4D2N8	Missense_Mutation	SNP	ENST00000350796.3	hg19	CCDS5346.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.786967	0.90367	.	.	ENSG00000008256	ENST00000350796;ENST00000396741	D;D	0.81821	-1.54;-1.54	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.93779	0.8011	H	0.98351	4.21	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96116	0.9081	10	0.87932	D	0	.	15.1785	0.72934	1.0:0.0:0.0:0.0	.	115;200	B7Z2V9;O43739-2	.;.	P	200;115	ENSP00000297044:L200P;ENSP00000379967:L115P	ENSP00000297044:L200P	L	-	2	0	CYTH3	6177098	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.092000	0.94157	1.996000	0.58369	0.533000	0.62120	CTC	.	.		0.627	CYTH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207396.2	NM_004227		G	6210573	A	G	6210573	3	3	103	1	0	0	0	0	1	0	0	0	4207	304	11	2	624	2	CYTH3	7	6210573	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	857523	6210573	152928090	490	15113										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11632925	11632925	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccttgagacaaacagggttcTttttcttcaaattctggaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:11632925delT	ENST00000423059.4	-	3	1478	c.1227delA	c.(1225-1227)aaafs	p.K409fs		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	409	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		AACAGGGTTCTTTTTCTTCAA	0.478										HNSCC(18;0.044)																											p.E410fs		Atlas-INDEL	.											THSD7A,colon,carcinoma,0,1	THSD7A	219	.	0			c.1228delG						.						88	85	86					7																	11632925		1910	4133	6043	SO:0001589	frameshift_variant	221981	exon3			.		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.1227delA	chr7.hg19:g.11632925delT	ENSP00000406482:p.Lys409fs	96.0	0.0		124.0	10.0	NM_015204		Frame_Shift_Del	DEL	ENST00000423059.4	hg19	CCDS47543.1																																																																																			.	.		0.478	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		-	11632925	T	-	11632925	7	5	103	1	0	1	0	1	0	0	0	0	15894	1606	56	0	3846	0	THSD7A	7	11632925	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5422352	11632925	147505738	491	15114										
ETV1	2115	hgsc.bcm.edu	37	chr7	14027750	14027750	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atctctgttaatgaattttcTtttcctgacatttgttggtt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:14027750delT	ENST00000430479.1	-	4	761	c.94delA	c.(94-96)agafs	p.R32fs	ETV1_ENST00000403527.1_5'Flank|ETV1_ENST00000242066.5_Frame_Shift_Del_p.R32fs|ETV1_ENST00000403685.1_Frame_Shift_Del_p.R32fs|ETV1_ENST00000476720.2_5'Flank|ETV1_ENST00000399357.3_5'Flank|ETV1_ENST00000405218.2_Frame_Shift_Del_p.R32fs|ETV1_ENST00000405358.4_Frame_Shift_Del_p.R46fs|ETV1_ENST00000343495.5_Frame_Shift_Del_p.R32fs|ETV1_ENST00000420159.2_5'Flank|ETV1_ENST00000405192.2_Frame_Shift_Del_p.R32fs	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	32					axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						ATGAATTTTCTTTTCCTGACA	0.383			T	"EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"	"Ewing sarcoma, prostate"																																p.R32fs		Atlas-INDEL	.		Dom	yes		7	7p22	2115	ets variant gene 1		"M, E"	.	ETV1	138	.	0			c.95delG						.						148	153	151					7																	14027750		2184	4288	6472	SO:0001589	frameshift_variant	2115	exon3			.		CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"ets variant gene 1"			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.94delA	chr7.hg19:g.14027750delT	ENSP00000405327:p.Arg32fs	189.0	0.0		185.0	12.0	NM_001163149	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Frame_Shift_Del	DEL	ENST00000430479.1	hg19	CCDS55088.1																																																																																			.	.		0.383	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956		-	14027750	T	-	14027750	7	5	103	1	0	1	0	1	0	0	0	0	5279	1617	56	0	1448	0	ETV1	7	14027750	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2394825	14027750	145110913	492	15115										
ITGB8	3696	hgsc.bcm.edu	37	chr7	20438514	20438514	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaagtgaaagttcaggtggAaaaccaggtacaaggcatct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:20438514delA	ENST00000222573.4	+	9	1862	c.1178delA	c.(1177-1179)gaafs	p.E393fs	ITGB8_ENST00000537992.1_Frame_Shift_Del_p.E258fs	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	393					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						GTTCAGGTGGAAAACCAGGTA	0.418																																					p.E393fs		Atlas-INDEL	.											.	ITGB8	159	.	0			c.1177delG						.						100	97	98					7																	20438514		2203	4300	6503	SO:0001589	frameshift_variant	3696	exon9			.		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.1178delA	chr7.hg19:g.20438514delA	ENSP00000222573:p.Glu393fs	135.0	0.0		181.0	12.0	NM_002214	A4D133|B4DHD4	Frame_Shift_Del	DEL	ENST00000222573.4	hg19	CCDS5370.1																																																																																			.	.		0.418	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		-	20438514	A	-	20438514	7	5	103	1	0	1	0	1	0	0	0	0	7910	246	9	0	1212	0	ITGB8	7	20438514	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	6410764	20438514	138700149	493	15116										
IGF2BP3	10643	hgsc.bcm.edu	37	chr7	23387322	23387322	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtaatcgacttctcagcagCccccgcattttctttacggt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:23387322delC	ENST00000258729.3	-	7	1071	c.715delG	c.(715-717)gctfs	p.A240fs		NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	240	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						TTCTCAGCAGCCCCCGCATTT	0.458																																					p.A239fs		Atlas-INDEL	.											.	IGF2BP3	71	.	0			c.716delC						.						103	93	96					7																	23387322		2203	4300	6503	SO:0001589	frameshift_variant	10643	exon7			.	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"RNA binding motif (RRM) containing"	28868	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 3", "cancer/testis antigen 98"	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.715delG	chr7.hg19:g.23387322delC	ENSP00000258729:p.Ala240fs	166.0	0.0		206.0	14.0	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Frame_Shift_Del	DEL	ENST00000258729.3	hg19	CCDS5382.1																																																																																			.	.		0.458	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547		-	23387322	C	-	23387322	7	5	103	1	0	1	0	1	0	0	0	0	7584	739	26	0	1060	0	IGF2BP3	7	23387322	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2948808	23387322	135751341	494	15117										
DFNA5	1687	hgsc.bcm.edu	37	chr7	24738821	24738821	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaacctttctgtatctttcaGgggagtcaaggttgggtctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:24738821delG	ENST00000342947.3	-	10	1740	c.1315delC	c.(1315-1317)ctgfs	p.L439fs	DFNA5_ENST00000419307.1_Frame_Shift_Del_p.L275fs|DFNA5_ENST00000409970.1_Frame_Shift_Del_p.L275fs|DFNA5_ENST00000545231.1_Frame_Shift_Del_p.L275fs|DFNA5_ENST00000409775.3_Frame_Shift_Del_p.L439fs	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	439					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						GTATCTTTCAGGGGAGTCAAG	0.418																																					p.L439fs	GBM(78;184 1250 20134 20900 23600)	Atlas-INDEL	.											.	DFNA5	51	.	0			c.1316delT						.						69	64	66					7																	24738821		2203	4300	6503	SO:0001589	frameshift_variant	1687	exon10			.	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.1315delC	chr7.hg19:g.24738821delG	ENSP00000339587:p.Leu439fs	227.0	0.0		306.0	22.0	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Frame_Shift_Del	DEL	ENST00000342947.3	hg19	CCDS5389.1																																																																																			.	.		0.418	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		-	24738821	G	-	24738821	7	5	103	1	0	1	0	1	0	0	0	0	4456	991	35	0	179	0	DFNA5	7	24738821	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1351499	24738821	134399842	495	15118										
GGCT	79017	hgsc.bcm.edu	37	chr7	30540183	30540183	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atttaaattgcttttgttcaTtttccatactactccccaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:30540183delT	ENST00000275428.4	-	2	390	c.256delA	c.(256-258)atgfs	p.M86fs	GGCT_ENST00000409390.1_Frame_Shift_Del_p.M86fs|GGCT_ENST00000409144.1_Intron|GGCT_ENST00000598361.1_Start_Codon_Del|GGCT_ENST00000005374.6_Frame_Shift_Del_p.M86fs|GGCT_ENST00000409436.1_Frame_Shift_Del_p.M86fs	NM_024051.3	NP_076956.1	O75223	GGCT_HUMAN	gamma-glutamylcyclotransferase	86					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|release of cytochrome c from mitochondria (GO:0001836)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	gamma-glutamylcyclotransferase activity (GO:0003839)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8						CTTTTGTTCATTTTCCATACT	0.388																																					p.M86fs		Atlas-INDEL	.											.	GGCT	17	.	0			c.257delT						.						158	148	151					7																	30540183		2202	4300	6502	SO:0001589	frameshift_variant	79017	exon2			.	BC019243	CCDS5428.1, CCDS56474.1, CCDS56475.1, CCDS56476.1	7p15-p14	2010-04-23	2010-04-23	2008-08-04	ENSG00000006625	ENSG00000006625	2.3.2.4		21705	protein-coding gene	gene with protein product		137170	"chromosome 7 open reading frame 24"	C7orf24, GCTG		17932939, 18515354	Standard	NM_024051		Approved	MGC3077, CRF21, Ggc	uc003tba.3	O75223	OTTHUMG00000128593	ENST00000275428.4:c.256delA	chr7.hg19:g.30540183delT	ENSP00000275428:p.Met86fs	98.0	0.0		133.0	10.0	NM_024051	B2RDN0|B8ZZN4|B8ZZR8|Q9BS37	Frame_Shift_Del	DEL	ENST00000275428.4	hg19	CCDS5428.1																																																																																			.	.		0.388	GGCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250447.2	NM_024051		-	30540183	T	-	30540183	7	5	103	1	0	1	0	1	0	0	0	0	6363	1493	52	0	322	0	GGCT	7	30540183	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5801362	30540183	128598480	496	15119										
GHRHR	2692	hgsc.bcm.edu	37	chr7	31015405	31015405	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttccaggtgaactttgggcTttttctcaatattatccgca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:31015405delT	ENST00000326139.2	+	10	942	c.896delT	c.(895-897)cttfs	p.L299fs	GHRHR_ENST00000461424.1_3'UTR|GHRHR_ENST00000409904.3_Frame_Shift_Del_p.L235fs|GHRHR_ENST00000409316.1_Frame_Shift_Del_p.A65fs	NM_000823.3	NP_000814.2	Q02643	GHRHR_HUMAN	growth hormone releasing hormone receptor	299					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP-mediated signaling (GO:0019933)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|determination of adult lifespan (GO:0008340)|growth hormone secretion (GO:0030252)|hormone metabolic process (GO:0042445)|lactation (GO:0007595)|multicellular organismal reproductive process (GO:0048609)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of intracellular steroid hormone receptor signaling pathway (GO:0033143)|regulation of protein metabolic process (GO:0051246)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|somatotropin secreting cell development (GO:0060133)|water homeostasis (GO:0030104)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nuclear matrix (GO:0016363)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	G-protein coupled receptor activity (GO:0004930)|growth factor binding (GO:0019838)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35					Sermorelin(DB00010)|Tesamorelin(DB08869)	AACTTTGGGCTTTTTCTCAAT	0.542																																					p.L299fs		Atlas-INDEL	.											.	GHRHR	55	.	0			c.895delC						.						112	96	101					7																	31015405		2203	4300	6503	SO:0001589	frameshift_variant	2692	exon10			.		CCDS5432.1	7p14	2012-08-10			ENSG00000106128	ENSG00000106128		"GPCR / Class B : Glucagon receptors"	4266	protein-coding gene	gene with protein product		139191				7680413, 7514564	Standard	NM_000823		Approved		uc003tbx.3	Q02643	OTTHUMG00000152801	ENST00000326139.2:c.896delT	chr7.hg19:g.31015405delT	ENSP00000320180:p.Leu299fs	129.0	0.0		183.0	12.0	NM_000823	Q99863	Frame_Shift_Del	DEL	ENST00000326139.2	hg19	CCDS5432.1																																																																																			.	.		0.542	GHRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327967.2			-	31015405	T	-	31015405	7	5	103	1	0	1	0	1	0	0	0	0	6381	1609	56	0	934	0	GHRHR	7	31015405	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	475222	31015405	128123258	497	15120										
AVL9	23080	hgsc.bcm.edu	37	chr7	32535339	32535339	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccatggagaaggccaggagAggcggggatggcgtcccccg	18	12	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:32535339A>G	ENST00000318709.4	+	1	239	c.18A>G	c.(16-18)agA>agG	p.R6R	LSM5_ENST00000409952.3_5'Flank|AVL9_ENST00000409301.1_Silent_p.R6R|LSM5_ENST00000409909.3_5'Flank|AVL9_ENST00000404479.1_Silent_p.R6R|AVL9_ENST00000459629.1_3'UTR	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	6					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						AGGCCAGGAGAGGCGGGGATG	0.721																																					p.R6R		Atlas-SNP	.											.	AVL9	66	.	0			c.A18G						.						8	12	11					7																	32535339		1821	3622	5443	SO:0001819	synonymous_variant	23080	exon1			CAGGAGAGGCGGG	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"KIAA0241"	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.18A>G	chr7.hg19:g.32535339A>G		41.0	0.0		125.0	8.0	NM_015060	Q92573	Silent	SNP	ENST00000318709.4	hg19	CCDS34613.1																																																																																			.	.		0.721	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		G	32535339	A	G	32535339	2	3	103	1	0	0	0	0	0	0	0	1	1228	301	11	2		2	AVL9	7	32535339	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1519934	32535339	126603324	498	15121										
BMPER	168667	hgsc.bcm.edu	37	chr7	33976905	33976905	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtctctttttgtctagaacaAggaagtgacatgtaagagag	11	5	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:33976905A>G	ENST00000297161.2	+	4	598	c.224A>G	c.(223-225)aAg>aGg	p.K75R	BMPER_ENST00000426693.1_Missense_Mutation_p.K75R	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	75	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GTCTAGAACAAGGAAGTGACA	0.488																																					p.K75R		Atlas-SNP	.											.	BMPER	131	.	0			c.A224G						.						92	88	89					7																	33976905		2203	4300	6503	SO:0001583	missense	168667	exon4			AGAACAAGGAAGT		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"crossveinless-2"	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.224A>G	chr7.hg19:g.33976905A>G	ENSP00000297161:p.Lys75Arg	73.0	0.0		98.0	4.0	NM_133468	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	hg19	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.153705	0.78114	.	.	ENSG00000164619	ENST00000297161;ENST00000426693	T;T	0.64618	-0.11;-0.11	5.09	5.09	0.68999	von Willebrand factor, type C (2);	0.204689	0.41938	D	0.000788	T	0.52789	0.1756	L	0.44542	1.39	0.48236	D	0.999613	P	0.39282	0.666	B	0.33339	0.162	T	0.58434	-0.7637	10	0.52906	T	0.07	.	14.84	0.70217	1.0:0.0:0.0:0.0	.	75	Q8N8U9	BMPER_HUMAN	R	75	ENSP00000297161:K75R;ENSP00000393950:K75R	ENSP00000297161:K75R	K	+	2	0	BMPER	33943430	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.522000	0.67092	1.898000	0.54952	0.460000	0.39030	AAG	.	.		0.488	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		G	33976905	A	G	33976905	3	3	103	1	0	0	0	0	1	0	0	0	1468	72	3	2	234	2	BMPER	7	33976905	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1441566	33976905	125161758	499	15122										
BMPER	168667	hgsc.bcm.edu	37	chr7	33976996	33976996	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggagcctgttgtgaacagtgCaaaggtgattgatgtcttgg	15	5	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:33976996C>A	ENST00000297161.2	+	4	689	c.315C>A	c.(313-315)tgC>tgA	p.C105*	BMPER_ENST00000426693.1_Nonsense_Mutation_p.C105*	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	105	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GTGAACAGTGCAAAGGTGATT	0.502																																					p.C105X		Atlas-SNP	.											.	BMPER	131	.	0			c.C315A						.						118	106	110					7																	33976996		2203	4300	6503	SO:0001587	stop_gained	168667	exon4			ACAGTGCAAAGGT		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"crossveinless-2"	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.315C>A	chr7.hg19:g.33976996C>A	ENSP00000297161:p.Cys105*	109.0	0.0		97.0	24.0	NM_133468	A8K1P8|Q8TF36	Nonsense_Mutation	SNP	ENST00000297161.2	hg19	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098639	0.56183	.	.	ENSG00000164619	ENST00000297161;ENST00000426693	.	.	.	5.18	3.37	0.38596	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.5775	0.33607	0.0:0.6989:0.0:0.3011	.	.	.	.	X	105	.	ENSP00000297161:C105X	C	+	3	2	BMPER	33943521	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	0.978000	0.29488	1.165000	0.42670	0.563000	0.77884	TGC	.	.		0.502	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		A	33976996	C	A	33976996	4	1	103	1	0	0	0	0	0	1	0	0	1468	718	25	3	325	3	BMPER	7	33976996	Nonsense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	91	33976996	125161667	500	15123										
CDK13	8621	hgsc.bcm.edu	37	chr7	40027428	40027428	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaagcaactaaggctgctgAggctgctgccaaggctgcaa	13	10	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:40027428A>G	ENST00000181839.4	+	2	2047	c.1442A>G	c.(1441-1443)gAg>gGg	p.E481G	CDK13_ENST00000340829.5_Missense_Mutation_p.E481G	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	481					alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						AAGGCTGCTGAGGCTGCTGCC	0.502																																					p.E481G		Atlas-SNP	.											.	CDK13	114	.	0			c.A1442G						.						43	42	42					7																	40027428		2203	4300	6503	SO:0001583	missense	8621	exon2			CTGCTGAGGCTGC	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.1442A>G	chr7.hg19:g.40027428A>G	ENSP00000181839:p.Glu481Gly	70.0	0.0		89.0	4.0	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Missense_Mutation	SNP	ENST00000181839.4	hg19	CCDS5461.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.419165	0.42918	.	.	ENSG00000065883	ENST00000181839;ENST00000340829	T;T	0.70631	-0.5;-0.5	4.56	4.56	0.56223	.	.	.	.	.	T	0.55097	0.1899	L	0.29908	0.895	0.34445	D	0.700002	P;P	0.40731	0.728;0.608	B;B	0.36186	0.219;0.109	T	0.64558	-0.6379	8	.	.	.	-9.874	10.6057	0.45392	1.0:0.0:0.0:0.0	.	481;481	Q14004-2;Q14004	.;CDK13_HUMAN	G	481	ENSP00000181839:E481G;ENSP00000340557:E481G	.	E	+	2	0	CDK13	39993953	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	2.298000	0.43602	2.280000	0.76307	0.460000	0.39030	GAG	.	.		0.502	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		G	40027428	A	G	40027428	3	3	103	1	0	0	0	0	1	0	0	0	3131	304	11	2	1448	2	CDK13	7	40027428	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	6050432	40027428	119111235	501	15124										
MYO1G	64005	hgsc.bcm.edu	37	chr7	45006272	45006272	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggtgtcaggtgccagtaccTgagcaggaatcgagagtagg	17	7	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:45006272T>C	ENST00000258787.7	-	15	2084	c.1948A>G	c.(1948-1950)Agg>Ggg	p.R650G		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	650	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						TGCCAGTACCTGAGCAGGAAT	0.617																																					p.R650G		Atlas-SNP	.											.	MYO1G	86	.	0			c.A1948G						.						55	54	55					7																	45006272		2203	4300	6503	SO:0001630	splice_region_variant	64005	exon15			AGTACCTGAGCAG	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"Myosins / Myosin superfamily : Class I"	13880	protein-coding gene	gene with protein product	"minor histocompatibility antigen HA-2"	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.1949+1A>G	chr7.hg19:g.45006272T>C		83.0	0.0		82.0	4.0	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	hg19	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.530275	0.64860	.	.	ENSG00000136286	ENST00000258787	D	0.91295	-2.82	4.61	4.61	0.57282	Myosin head, motor domain (2);	0.000000	0.42682	D	0.000676	D	0.96519	0.8864	H	0.96662	3.86	0.58432	D	0.99999	D;D	0.89917	0.999;1.0	D;D	0.97110	0.999;1.0	D	0.96806	0.9593	10	0.87932	D	0	.	10.0732	0.42345	0.0:0.0:0.1685:0.8315	.	650;650	B0I1T2-4;B0I1T2	.;MYO1G_HUMAN	G	650	ENSP00000258787:R650G	ENSP00000258787:R650G	R	-	1	2	MYO1G	44972797	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.812000	0.38952	1.829000	0.53265	0.482000	0.46254	AGG	.	.		0.617	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		Missense_Mutation	C	45006272	T	C	45006272	5	2	103	1	0	0	0	0	0	0	1	0	10083	1594	55	2	1140	2	MYO1G	7	45006272	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4978844	45006272	114132391	502	15125										
ADCY1	107	hgsc.bcm.edu	37	chr7	45743294	45743294	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagctggacggcaacaacatGggggtggagtgtctgcggct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:45743294delG	ENST00000297323.7	+	16	2689	c.2667delG	c.(2665-2667)atgfs	p.M889fs		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	889					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GCAACAACATGGGGGTGGAGT	0.577																																					p.M889fs		Atlas-INDEL	.											.	ADCY1	187	.	0			c.2666delT						.						146	133	137					7																	45743294		2203	4300	6503	SO:0001589	frameshift_variant	107	exon16			.	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.2667delG	chr7.hg19:g.45743294delG	ENSP00000297323:p.Met889fs	215.0	0.0		249.0	15.0	NM_021116	A4D2L8|Q75MI1	Frame_Shift_Del	DEL	ENST00000297323.7	hg19	CCDS34631.1																																																																																			.	.		0.577	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		-	45743294	G	-	45743294	7	5	103	1	0	1	0	1	0	0	0	0	292	1348	47	0	2729	0	ADCY1	7	45743294	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	737022	45743294	113395369	503	15126										
SUN3	256979	hgsc.bcm.edu	37	chr7	48026998	48026998	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atacttcgggtgtccccagtTgctaaagatattaagtttca	8	8	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:48026998T>C	ENST00000297325.4	-	10	1162	c.1003A>G	c.(1003-1005)Aac>Gac	p.N335D	SUN3_ENST00000412142.1_Missense_Mutation_p.N247D|SUN3_ENST00000473723.1_5'UTR|SUN3_ENST00000395572.2_Missense_Mutation_p.N335D|SUN3_ENST00000453192.2_Missense_Mutation_p.N323D	NM_001030019.1	NP_001025190.1	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 3	335	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.					integral component of membrane (GO:0016021)|SUN-KASH complex (GO:0034993)				central_nervous_system(1)|endometrium(3)|large_intestine(8)|liver(1)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TGTCCCCAGTTGCTAAAGATA	0.378																																					p.N335D		Atlas-SNP	.											.	SUN3	52	.	0			c.A1003G						.						134	137	136					7																	48026998		2203	4300	6503	SO:0001583	missense	256979	exon11			CCCAGTTGCTAAA	AF429967	CCDS34636.1, CCDS64647.1	7p12.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164744	ENSG00000164744			22429	protein-coding gene	gene with protein product			"Sad1 and UNC84 domain containing 1"	SUNC1			Standard	NM_001284350		Approved	MGC33329	uc003tof.3	Q8TAQ9	OTTHUMG00000155646	ENST00000297325.4:c.1003A>G	chr7.hg19:g.48026998T>C	ENSP00000297325:p.Asn335Asp	89.0	0.0		108.0	5.0	NM_152782	A4D2F3|B4DXK1|D3DVM3|E7EWC8|Q4F965|Q7Z4U8	Missense_Mutation	SNP	ENST00000297325.4	hg19	CCDS34636.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.844774	0.91197	.	.	ENSG00000164744	ENST00000297325;ENST00000412142;ENST00000395572;ENST00000453192;ENST00000438771	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	5.64	5.64	0.86602	Sad1/UNC-like, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.79707	0.4492	H	0.94847	3.59	0.54753	D	0.999982	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	D	0.85379	0.1118	10	0.87932	D	0	.	13.8147	0.63283	0.0:0.0:0.0:1.0	.	323;247;335	E7EWC8;Q8TAQ9-2;Q8TAQ9	.;.;SUN3_HUMAN	D	335;247;335;323;247	ENSP00000297325:N335D;ENSP00000410204:N247D;ENSP00000378939:N335D;ENSP00000387525:N323D;ENSP00000409077:N247D	ENSP00000297325:N335D	N	-	1	0	SUN3	47993523	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.443000	0.80521	2.151000	0.67156	0.477000	0.44152	AAC	.	.		0.378	SUN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340962.1	NM_152782		C	48026998	T	C	48026998	3	2	103	1	0	0	0	0	1	0	0	0	15408	1812	63	2	74	2	SUN3	7	48026998	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2283704	48026998	111111665	504	15127										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48313397	48313397	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttacgtattctagacacgttAaattccacattttcctctga	4	10	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:48313397A>G	ENST00000435803.1	+	17	4158	c.4134A>G	c.(4132-4134)ttA>ttG	p.L1378L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1378					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TAGACACGTTAAATTCCACAT	0.343																																					p.L1378L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A4134G						.						52	49	50					7																	48313397		1867	4093	5960	SO:0001819	synonymous_variant	154664	exon17			CACGTTAAATTCC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4134A>G	chr7.hg19:g.48313397A>G		66.0	0.0		82.0	21.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.343	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48313397	A	G	48313397	2	3	103	1	0	0	0	0	0	0	0	1	31	359	13	2		2	ABCA13	7	48313397	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	286399	48313397	110825266	505	15128										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48391899	48391899	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcgtgcgaacagatgtggtAaaaaacccttcttggaagtt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:48391899delA	ENST00000435803.1	+	31	10527	c.10503delA	c.(10501-10503)gtafs	p.V3501fs		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3501					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CAGATGTGGTAAAAAACCCTT	0.453																																					p.V3501fs		Atlas-INDEL	.											.	ABCA13	1192	.	0			c.10502delT						.						87	87	87					7																	48391899		1951	4154	6105	SO:0001589	frameshift_variant	154664	exon31			.	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.10503delA	chr7.hg19:g.48391899delA	ENSP00000411096:p.Val3501fs	120.0	0.0		162.0	10.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Frame_Shift_Del	DEL	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.453	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		-	48391899	A	-	48391899	7	5	103	1	0	1	0	1	0	0	0	0	31	349	13	0	10454	0	ABCA13	7	48391899	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	78502	48391899	110746764	506	15129										
IKZF1	10320	hgsc.bcm.edu	37	chr7	50467992	50467992	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacaacgaggagcagcgcagCggtctcatctacctgaccaa	10	13	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:50467992C>T	ENST00000331340.3	+	8	1382	c.1227C>T	c.(1225-1227)agC>agT	p.S409S	IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000357364.4_Silent_p.S322S|IKZF1_ENST00000349824.4_Silent_p.S266S|IKZF1_ENST00000346667.4_Silent_p.S179S|IKZF1_ENST00000359197.5_Silent_p.S367S|IKZF1_ENST00000439701.1_Silent_p.S367S|IKZF1_ENST00000438033.1_Silent_p.S322S|IKZF1_ENST00000343574.5_Silent_p.S322S	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	409					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(28)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				AGCAGCGCAGCGGTCTCATCT	0.677			"D,T"	BCL6	"ALL, DLBCL"																																p.S409S		Atlas-SNP	.		"Rec,Dom"	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	28	Unknown(28)	haematopoietic_and_lymphoid_tissue(28)	c.C1227T						.						31	39	36					7																	50467992		2178	4258	6436	SO:0001819	synonymous_variant	10320	exon8			GCGCAGCGGTCTC	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13176	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 92"	603023	"zinc finger protein, subfamily 1A, 1 (Ikaros)"	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.1227C>T	chr7.hg19:g.50467992C>T		71.0	0.0		117.0	20.0	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Silent	SNP	ENST00000331340.3	hg19																																																																																				.	.		0.677	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060		T	50467992	C	T	50467992	2	4	103	1	0	0	0	0	0	0	0	1	7623	767	27	1		1	IKZF1	7	50467992	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	2076093	50467992	108670671	507	15130										
EGFR	1956	hgsc.bcm.edu	37	chr7	55220290	55220290	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgggcgctgccgtggcaagtCccccagtgactgctgccaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:55220290delC	ENST00000275493.2	+	6	857	c.680delC	c.(679-681)tccfs	p.S227fs	EGFR_ENST00000420316.2_Frame_Shift_Del_p.S227fs|EGFR_ENST00000442591.1_Frame_Shift_Del_p.S227fs|EGFR_ENST00000455089.1_Frame_Shift_Del_p.S182fs|EGFR_ENST00000344576.2_Frame_Shift_Del_p.S227fs|EGFR_ENST00000342916.3_Frame_Shift_Del_p.S227fs|EGFR_ENST00000454757.2_Frame_Shift_Del_p.S174fs	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	227			Missing (variant EGFR vIII; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed). {ECO:0000269|PubMed:16672372}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CGTGGCAAGTCCCCCAGTGAC	0.612		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.S227fs		Atlas-INDEL	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	.	EGFR	20426	.	0			c.679delT						.						72	82	78					7																	55220290		2203	4299	6502	SO:0001589	frameshift_variant	1956	exon6	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	.		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.680delC	chr7.hg19:g.55220290delC	ENSP00000275493:p.Ser227fs	157.0	0.0		180.0	11.0	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Frame_Shift_Del	DEL	ENST00000275493.2	hg19	CCDS5514.1																																																																																			.	.		0.612	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		-	55220290	C	-	55220290	7	5	103	1	0	1	0	1	0	0	0	0	4969	855	30	0	702	0	EGFR	7	55220290	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	4752298	55220290	103918373	508	15131										
GUSB	2990	hgsc.bcm.edu	37	chr7	65444761	65444761	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtccctggtggcagggtggtGggggtgagtgtgttgttgat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:65444761delG	ENST00000304895.4	-	3	664	c.534delC	c.(532-534)cccfs	p.P178fs	GUSB_ENST00000345660.6_Frame_Shift_Del_p.P178fs|GUSB_ENST00000476486.1_Intron|GUSB_ENST00000421103.1_Intron	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	178					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)	p.T179fs*13(1)		breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						GCAGGGTGGTGGGGGTGAGTG	0.627																																					p.T179fs		Atlas-INDEL	.											.,1	GUSB	52	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.535delA						.						180	181	181					7																	65444761		2203	4300	6503	SO:0001589	frameshift_variant	2990	exon3			.	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.534delC	chr7.hg19:g.65444761delG	ENSP00000302728:p.Pro178fs	80.0	0.0		121.0	10.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Frame_Shift_Del	DEL	ENST00000304895.4	hg19	CCDS5530.1																																																																																			.	.		0.627	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		-	65444761	G	-	65444761	7	5	103	1	0	1	0	1	0	0	0	0	6911	1335	47	0	1461	0	GUSB	7	65444761	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	10224471	65444761	93693902	509	15132										
RABGEF1	27342	hgsc.bcm.edu	37	chr7	66270287	66270287	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tacattgttttgaagggcaaCcccccacgccttcagtctaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:66270287delC	ENST00000284957.5	+	8	1058	c.981delC	c.(979-981)aacfs	p.N327fs	KCTD7_ENST00000451741.2_Frame_Shift_Del_p.N327fs|KCTD7_ENST00000380828.2_Frame_Shift_Del_p.N367fs|RABGEF1_ENST00000437078.2_Frame_Shift_Del_p.N341fs|RABGEF1_ENST00000484547.2_3'UTR|KCTD7_ENST00000510829.2_Frame_Shift_Del_p.N327fs|RABGEF1_ENST00000439720.2_Frame_Shift_Del_p.N340fs|RABGEF1_ENST00000450873.2_Frame_Shift_Del_p.N327fs			Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	544					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein targeting to membrane (GO:0006612)	early endosome (GO:0005769)	DNA binding (GO:0003677)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|stomach(1)	27						TGAAGGGCAACCCCCCACGCC	0.507																																					p.N327fs		Atlas-INDEL	.											.	RABGEF1	56	.	0			c.980delA						.						129	106	114					7																	66270287		2203	4300	6503	SO:0001589	frameshift_variant	27342	exon8			.	AJ250042	CCDS5535.1, CCDS69308.1, CCDS75610.1	7q11.21	2010-07-09			ENSG00000154710	ENSG00000154710			17676	protein-coding gene	gene with protein product		609700				12505986, 11098082	Standard	NM_014504		Approved	rabex-5, RABEX5	uc003tvh.3	Q9UJ41	OTTHUMG00000129547	ENST00000284957.5:c.981delC	chr7.hg19:g.66270287delC	ENSP00000284957:p.Asn327fs	115.0	0.0		162.0	10.0	NM_014504	B4DZM7|Q3HKR2|Q3HKR3|Q53FG0	Frame_Shift_Del	DEL	ENST00000284957.5	hg19	CCDS5535.1																																																																																			.	.		0.507	RABGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251737.3	NM_014504		-	66270287	C	-	66270287	7	5	103	1	0	1	0	1	0	0	0	0	12981	506	18	0	1007	0	RABGEF1	7	66270287	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	825526	66270287	92868376	510	15133										
GTF2I	2969	hgsc.bcm.edu	37	chr7	74163404	74163404	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggacctaaaacagaaagttgAaaatctcttcaatgagaaat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:74163404delA	ENST00000324896.4	+	25	2602	c.2213delA	c.(2212-2214)gaafs	p.E738fs	GTF2I_ENST00000416070.1_Frame_Shift_Del_p.E697fs|GTF2I_ENST00000353920.4_Frame_Shift_Del_p.E718fs|GTF2I_ENST00000438130.2_3'UTR|GTF2I_ENST00000346152.4_Frame_Shift_Del_p.E717fs	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	738					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						CAGAAAGTTGAAAATCTCTTC	0.403																																					p.E738fs		Atlas-INDEL	.											.	GTF2I	40	.	0			c.2212delG						.						1	1	1					7																	74163404		25	63	88	SO:0001589	frameshift_variant	2969	exon25			.	U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"General transcription factors"	4659	protein-coding gene	gene with protein product		601679	"general transcription factor II, i"	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.2213delA	chr7.hg19:g.74163404delA	ENSP00000322542:p.Glu738fs	106.0	0.0		177.0	11.0	NM_032999	O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Frame_Shift_Del	DEL	ENST00000324896.4	hg19	CCDS5573.1																																																																																			.	.		0.403	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252708.1	NM_032999		-	74163404	A	-	74163404	7	5	103	1	0	1	0	1	0	0	0	0	6876	246	9	0	2307	0	GTF2I	7	74163404	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	7893117	74163404	84975259	511	15134										
GTF2IRD2	84163	hgsc.bcm.edu	37	chr7	74212037	74212037	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcgaccagtcgatacagaacTttttcaggctcttctcaaca	6	12	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:74212037T>G	ENST00000405086.2	-	16	2003	c.1814A>C	c.(1813-1815)aAg>aCg	p.K605T	GTF2IRD2_ENST00000451013.2_Missense_Mutation_p.K152T	NM_173537.2	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2	605					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	11						gatacagaactttttcaggct	0.502																																					p.K605T	NSCLC(40;560 1096 7501 40315 49546)	Atlas-SNP	.											GTF2IRD2,colon,carcinoma,+1,1	GTF2IRD2	38	.	0			c.A1814C						.						39	39	39					7																	74212037		2203	4299	6502	SO:0001583	missense	84163	exon16			CAGAACTTTTTCA	BC047706	CCDS5576.1, CCDS64682.1	7q11.23	2014-05-06			ENSG00000196275	ENSG00000196275			30775	protein-coding gene	gene with protein product	"transcription factor GTF2IRD2"	608899				15243160	Standard	NM_173537		Approved	FLJ37938, GTF2IRD2A	uc003ubd.1	Q86UP8	OTTHUMG00000181527	ENST00000405086.2:c.1814A>C	chr7.hg19:g.74212037T>G	ENSP00000385491:p.Lys605Thr	601.0	1.0		736.0	0.0	NM_173537	A8K5W6|B3KUZ2|Q69G40|Q6EKI8|Q6EKI9|Q6NVW2|Q6P7N8|Q86WX4|Q8ND85|Q8NDE5	Missense_Mutation	SNP	ENST00000405086.2	hg19	CCDS5576.1	.	.	.	.	.	.	.	.	.	.	t	7.862	0.726215	0.15439	.	.	ENSG00000196275	ENST00000405086;ENST00000451013	D;D	0.85955	-2.05;-2.05	1.74	0.525	0.17072	Ribonuclease H-like (1);	.	.	.	.	T	0.71500	0.3347	L	0.37630	1.12	0.58432	D	0.999999	P	0.36065	0.535	B	0.32805	0.153	T	0.60026	-0.7343	9	0.30078	T	0.28	-13.8646	3.6893	0.08340	0.0:0.2067:0.0:0.7933	.	605	Q86UP8	GTD2A_HUMAN	T	605;152	ENSP00000385491:K605T;ENSP00000406723:K152T	ENSP00000385491:K605T	K	-	2	0	GTF2IRD2	73849973	0.912000	0.30974	0.826000	0.32828	0.704000	0.40688	0.249000	0.18216	0.158000	0.19367	0.363000	0.22086	AAG	.	.		0.502	GTF2IRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252712.3	NM_173537		G	74212037	T	G	74212037	3	3	103	1	0	0	0	0	1	0	0	0	6878	1609	56	5	1039	5	GTF2IRD2	7	74212037	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	48633	74212037	84926626	512	15135										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77579071	77579071	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggtgcatctcgttaacacTttttctcctaagatttgtta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:77579071delT	ENST00000248550.7	+	16	2112	c.2036delT	c.(2035-2037)cttfs	p.L679fs	PHTF2_ENST00000416283.2_Frame_Shift_Del_p.L645fs|PHTF2_ENST00000422959.2_Frame_Shift_Del_p.L645fs|PHTF2_ENST00000275575.7_Intron|PHTF2_ENST00000307305.8_Frame_Shift_Del_p.L641fs			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	679					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						TCGTTAACACTTTTTCTCCTA	0.338																																					p.L645fs		Atlas-INDEL	.											.	PHTF2	104	.	0			c.1933delC						.						129	116	120					7																	77579071		1850	4085	5935	SO:0001589	frameshift_variant	57157	exon15			.	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.2036delT	chr7.hg19:g.77579071delT	ENSP00000248550:p.Leu679fs	143.0	0.0		201.0	13.0	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Frame_Shift_Del	DEL	ENST00000248550.7	hg19																																																																																				.	.		0.338	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		-	77579071	T	-	77579071	7	5	103	1	0	1	0	1	0	0	0	0	11872	1609	56	0	2046	0	PHTF2	7	77579071	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3367034	77579071	81559592	513	15136										
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80447658	80447658	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtaagtacagacaggactgAaagcgccactcccacagaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:80447658delA	ENST00000265361.3	-	5	965	c.404delT	c.(403-405)ttcfs	p.F135fs	SEMA3C_ENST00000536800.1_Intron|SEMA3C_ENST00000419255.2_Frame_Shift_Del_p.F135fs|SEMA3C_ENST00000544525.1_Frame_Shift_Del_p.F153fs	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	135	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GACAGGACTGAAAGCGCCACT	0.388																																					p.F135fs		Atlas-INDEL	.											.	SEMA3C	106	.	0			c.405delC						.						88	79	82					7																	80447658		2203	4300	6503	SO:0001589	frameshift_variant	10512	exon5			.	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"Semaphorins", "Immunoglobulin superfamily / I-set domain containing"	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.404delT	chr7.hg19:g.80447658delA	ENSP00000265361:p.Phe135fs	162.0	0.0		167.0	11.0	NM_006379	B4DRL8	Frame_Shift_Del	DEL	ENST00000265361.3	hg19	CCDS5596.1																																																																																			.	.		0.388	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		-	80447658	A	-	80447658	7	5	103	1	0	1	0	1	0	0	0	0	14041	246	9	0	1907	0	SEMA3C	7	80447658	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2868587	80447658	78691005	514	15137										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81624216	81624216	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttaaccagagttctgaatgTtttttctccactttccccat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:81624216delT	ENST00000356253.5	-	21	2014	c.1759delA	c.(1759-1761)acafs	p.T587fs	CACNA2D1_ENST00000356860.3_Frame_Shift_Del_p.T568fs			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	587					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GTTCTGAATGTTTTTTCTCCA	0.299																																					p.T568fs		Atlas-INDEL	.											.	CACNA2D1	191	.	0			c.1703delC						.						79	77	78					7																	81624216		2200	4292	6492	SO:0001589	frameshift_variant	781	exon20			.	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.1759delA	chr7.hg19:g.81624216delT	ENSP00000348589:p.Thr587fs	216.0	0.0		240.0	16.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Frame_Shift_Del	DEL	ENST00000356253.5	hg19																																																																																				.	.		0.299	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				-	81624216	T	-	81624216	7	5	103	1	0	1	0	1	0	0	0	0	2550	1725	60	0	1653	0	CACNA2D1	7	81624216	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1176558	81624216	77514447	515	15138										
ABCB4	5244	hgsc.bcm.edu	37	chr7	87081038	87081038	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aatcccactatgaatcctgcAaaaaacgtggctactgcttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:87081038delA	ENST00000265723.4	-	7	720	c.609delT	c.(607-609)tttfs	p.F203fs	ABCB4_ENST00000358400.3_Frame_Shift_Del_p.F203fs|ABCB4_ENST00000359206.3_Frame_Shift_Del_p.F203fs|ABCB4_ENST00000453593.1_Frame_Shift_Del_p.F203fs|ABCB4_ENST00000545634.1_Frame_Shift_Del_p.F203fs	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	203	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	TGAATCCTGCAAAAAACGTGG	0.448																																					p.A204fs		Atlas-INDEL	.											.	ABCB4	177	.	0			c.610delG						.						192	158	169					7																	87081038		2203	4300	6503	SO:0001589	frameshift_variant	5244	exon7			.	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.609delT	chr7.hg19:g.87081038delA	ENSP00000265723:p.Phe203fs	137.0	0.0		182.0	13.0	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Frame_Shift_Del	DEL	ENST00000265723.4	hg19	CCDS5606.1																																																																																			.	.		0.448	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		-	87081038	A	-	87081038	7	5	103	1	0	1	0	1	0	0	0	0	43	127	5	0	3339	0	ABCB4	7	87081038	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	5456822	87081038	72057625	516	15139										
ADAM22	53616	hgsc.bcm.edu	37	chr7	87808298	87808298	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagcctggagatggtgactcTttttatagcgacattcctcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:87808298delT	ENST00000265727.7	+	27	2428	c.2349delT	c.(2347-2349)tctfs	p.S783fs	ADAM22_ENST00000315984.7_Intron|ADAM22_ENST00000398204.4_Intron|ADAM22_ENST00000398209.3_Intron|ADAM22_ENST00000398201.4_Frame_Shift_Del_p.S783fs			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	783					adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			ATGGTGACTCTTTTTATAGCG	0.413																																					p.S783fs		Atlas-INDEL	.											.	ADAM22	280	.	0			c.2348delC						.						115	123	121					7																	87808298		2186	4292	6478	SO:0001589	frameshift_variant	53616	exon27			.	AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277		"ADAM metallopeptidase domain containing"	201	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2"	603709	"a disintegrin and metalloproteinase domain 22"			9693107, 10524237	Standard	NM_021723		Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.2349delT	chr7.hg19:g.87808298delT	ENSP00000265727:p.Ser783fs	188.0	0.0		240.0	16.0	NM_021723	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Frame_Shift_Del	DEL	ENST00000265727.7	hg19	CCDS47637.1																																																																																			.	.		0.413	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723		-	87808298	T	-	87808298	7	5	103	1	0	1	0	1	0	0	0	0	244	1596	56	0	2455	0	ADAM22	7	87808298	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	727260	87808298	71330365	517	15140										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88389389	88389389	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccctgtgcaagaacggatcTccctctccggtaatgtgcgc	10	15	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:88389389T>C	ENST00000333190.4	+	1	708	c.99T>C	c.(97-99)tcT>tcC	p.S33S		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	33							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AGAACGGATCTCCCTCTCCGG	0.478										HNSCC(36;0.09)																											p.S33S		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T99C						.						108	98	101					7																	88389389		2203	4300	6503	SO:0001819	synonymous_variant	219578	exon1			CGGATCTCCCTCT	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.99T>C	chr7.hg19:g.88389389T>C		128.0	0.0		144.0	6.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	hg19	CCDS5613.1																																																																																			.	.		0.478	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		C	88389389	T	C	88389389	2	2	103	1	0	0	0	0	0	0	0	1	18186	1538	54	2		2	ZNF804B	7	88389389	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	581091	88389389	70749274	518	15141										
ANKIB1	54467	hgsc.bcm.edu	37	chr7	91980374	91980374	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaaagtgtagtttcaaaggAgatggacaaacgatacctac	10	6	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:91980374A>G	ENST00000265742.3	+	8	1572	c.1196A>G	c.(1195-1197)gAg>gGg	p.E399G		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	399							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GTTTCAAAGGAGATGGACAAA	0.333																																					p.E399G		Atlas-SNP	.											.	ANKIB1	92	.	0			c.A1196G						.						88	83	85					7																	91980374		1855	4098	5953	SO:0001583	missense	54467	exon8			CAAAGGAGATGGA	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"Ankyrin repeat domain containing"	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.1196A>G	chr7.hg19:g.91980374A>G	ENSP00000265742:p.Glu399Gly	81.0	0.0		98.0	5.0	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	hg19	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.710258	0.89018	.	.	ENSG00000001629	ENST00000265742	T	0.13657	2.57	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.27629	0.0679	M	0.73962	2.25	0.58432	D	0.999998	P	0.41214	0.742	P	0.46237	0.508	T	0.01951	-1.1241	10	0.72032	D	0.01	.	16.0698	0.80914	1.0:0.0:0.0:0.0	.	399	Q9P2G1	AKIB1_HUMAN	G	399	ENSP00000265742:E399G	ENSP00000265742:E399G	E	+	2	0	ANKIB1	91818310	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.650000	0.91073	2.245000	0.73994	0.455000	0.32223	GAG	.	.		0.333	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			G	91980374	A	G	91980374	3	3	103	1	0	0	0	0	1	0	0	0	630	304	11	2	1222	2	ANKIB1	7	91980374	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	3590985	91980374	67158289	519	15142										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94043219	94043219	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctttcagggtgttcaaggtgGaaaaggtgaacagggtcccc	14	8	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:94043219G>T	ENST00000297268.6	+	28	2096	c.1625G>T	c.(1624-1626)gGa>gTa	p.G542V		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	542					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GTTCAAGGTGGAAAAGGTGAA	0.443										HNSCC(75;0.22)																											p.G542V		Atlas-SNP	.											.	COL1A2	240	.	0			c.G1625T						.						137	123	128					7																	94043219		2203	4300	6503	SO:0001583	missense	1278	exon28			AAGGTGGAAAAGG	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1625G>T	chr7.hg19:g.94043219G>T	ENSP00000297268:p.Gly542Val	157.0	0.0		183.0	20.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.853704	0.51270	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93366	-3.21	5.66	5.66	0.87406	.	0.112949	0.64402	D	0.000011	D	0.84083	0.5394	N	0.03209	-0.39	0.53005	D	0.999965	B	0.22800	0.075	B	0.26864	0.074	T	0.80725	-0.1254	10	0.87932	D	0	.	10.3124	0.43716	0.0718:0.2067:0.7215:0.0	.	542	P08123	CO1A2_HUMAN	V	542;543	ENSP00000297268:G542V	ENSP00000297268:G542V	G	+	2	0	COL1A2	93881155	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	2.969000	0.49232	2.840000	0.97914	0.655000	0.94253	GGA	.	.		0.443	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		T	94043219	G	T	94043219	3	4	103	1	0	0	0	0	1	0	0	0	3680	1174	41	3	1735	3	COL1A2	7	94043219	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	2062845	94043219	65095444	520	15143										
BAIAP2L1	55971	hgsc.bcm.edu	37	chr7	97939854	97939854	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatgctctgcctgaaggagcGgggggcatctttggtgagca					rs200900587		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:97939854delG	ENST00000005260.8	-	9	1073	c.858delC	c.(856-858)cccfs	p.P286fs	BAIAP2L1_ENST00000462558.1_5'UTR|RP4-607J23.2_ENST00000608882.1_RNA|RP4-607J23.2_ENST00000609873.1_RNA	NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	286					filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			CTGAAGGAGCGGGGGGCATCT	0.428																																					p.A287fs		Atlas-INDEL	.											BAIAP2L1,NS,carcinoma,0,1	BAIAP2L1	61	.	0			c.859delG						.						95	101	99					7																	97939854		2203	4300	6503	SO:0001589	frameshift_variant	55971	exon9			.	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.858delC	chr7.hg19:g.97939854delG	ENSP00000005260:p.Pro286fs	111.0	0.0		169.0	13.0	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Frame_Shift_Del	DEL	ENST00000005260.8	hg19	CCDS34687.1																																																																																			.	.		0.428	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842		-	97939854	G	-	97939854	7	5	103	1	0	1	0	1	0	0	0	0	1302	1103	39	0	701	0	BAIAP2L1	7	97939854	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	3896635	97939854	61198809	521	15144										
COPS6	10980	hgsc.bcm.edu	37	chr7	99687281	99687281	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggagggccgaaatatcgaGgtgatgaactcctttgagct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:99687281delG	ENST00000303904.3	+	3	283	c.246delG	c.(244-246)gagfs	p.E82fs	COPS6_ENST00000418625.1_Frame_Shift_Del_p.E81fs	NM_006833.4	NP_006824.2	Q7L5N1	CSN6_HUMAN	COP9 signalosome subunit 6	82	MPN.				cullin deneddylation (GO:0010388)|viral process (GO:0016032)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|stomach(1)	12	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			GAAATATCGAGGTGATGAACT	0.468																																					p.E82fs		Atlas-INDEL	.											.	COPS6	31	.	0			c.245delA						.						147	133	138					7																	99687281		2203	4300	6503	SO:0001589	frameshift_variant	10980	exon3			.	BC002520	CCDS5682.1	7q22.1	2013-03-14	2013-03-14		ENSG00000168090	ENSG00000168090			21749	protein-coding gene	gene with protein product	"COP9 subunit 6 (MOV34 homolog, 34 kD)"	614729	"COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)"			12477932	Standard	NM_006833		Approved	MOV34-34KD, CSN6	uc003usu.3	Q7L5N1	OTTHUMG00000154632	ENST00000303904.3:c.246delG	chr7.hg19:g.99687281delG	ENSP00000304102:p.Glu82fs	199.0	0.0		199.0	12.0	NM_006833	A4D2A3|O15387	Frame_Shift_Del	DEL	ENST00000303904.3	hg19	CCDS5682.1																																																																																			.	.		0.468	COPS6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336412.3	NM_006833		-	99687281	G	-	99687281	7	5	103	1	0	1	0	1	0	0	0	0	3739	991	35	0	256	0	COPS6	7	99687281	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1747427	99687281	59451382	522	15145										
ZCWPW1	55063	hgsc.bcm.edu	37	chr7	100013617	100013617	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaaaaccacttatctctccTttttgctggtccctgatctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:100013617delT	ENST00000398027.2	-	8	979	c.732delA	c.(730-732)aaafs	p.K244fs	ZCWPW1_ENST00000360951.4_Frame_Shift_Del_p.K245fs|ZCWPW1_ENST00000490721.1_Frame_Shift_Del_p.K124fs|ZCWPW1_ENST00000324725.6_Frame_Shift_Del_p.K124fs	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	244							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TTATCTCTCCTTTTTGCTGGT	0.443																																					p.G246fs		Atlas-INDEL	.											.	ZCWPW1	41	.	0			c.736delG						.						258	238	244					7																	100013617		1901	4118	6019	SO:0001589	frameshift_variant	55063	exon8			.	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"zinc finger, CW-type with PWWP domain 1"			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.732delA	chr7.hg19:g.100013617delT	ENSP00000381109:p.Lys244fs	153.0	0.0		207.0	14.0	NM_001258008	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Frame_Shift_Del	DEL	ENST00000398027.2	hg19	CCDS43623.1																																																																																			.	.		0.443	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984		-	100013617	T	-	100013617	7	5	103	1	0	1	0	1	0	0	0	0	17612	1606	56	0	1258	0	ZCWPW1	7	100013617	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	326336	100013617	59125046	523	15146										
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100459490	100459490	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttggccaaccagcttaagaaGggggggctgtatgtgctggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:100459490delG	ENST00000354161.3	+	12	1793	c.1668delG	c.(1666-1668)aagfs	p.K556fs	SLC12A9_ENST00000415287.1_Frame_Shift_Del_p.K467fs|SLC12A9_ENST00000275729.3_Frame_Shift_Del_p.K467fs|SLC12A9_ENST00000428758.1_Frame_Shift_Del_p.K556fs|SLC12A9_ENST00000540482.1_Frame_Shift_Del_p.K556fs	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	556					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					AGCTTAAGAAGGGGGGGCTGT	0.642																																					p.K556fs		Atlas-INDEL	.											.,1	SLC12A9	81	.	0			c.1667delA						.						28	32	31					7																	100459490		2203	4300	6503	SO:0001589	frameshift_variant	56996	exon12			.	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"Solute carriers"	17435	protein-coding gene	gene with protein product	"cation-chloride cotransporter-interacting protein"					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.1668delG	chr7.hg19:g.100459490delG	ENSP00000275730:p.Lys556fs	135.0	0.0		165.0	12.0	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Frame_Shift_Del	DEL	ENST00000354161.3	hg19	CCDS5707.1																																																																																			.	.		0.642	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		-	100459490	G	-	100459490	7	5	103	1	0	1	0	1	0	0	0	0	14405	991	35	0	1710	0	SLC12A9	7	100459490	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	445873	100459490	58679173	524	15147										
RELN	5649	hgsc.bcm.edu	37	chr7	103202088	103202088	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatgtaaattcccattgaaaTcgtctttaagaatcgagggc	9	7	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:103202088T>C	ENST00000428762.1	-	36	5579	c.5420A>G	c.(5419-5421)gAt>gGt	p.D1807G	RELN_ENST00000343529.5_Missense_Mutation_p.D1807G|RELN_ENST00000424685.2_Missense_Mutation_p.D1807G	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1807					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CCCATTGAAATCGTCTTTAAG	0.453																																					p.D1807G	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A5420G						.						99	95	97					7																	103202088		2203	4300	6503	SO:0001583	missense	5649	exon36			TTGAAATCGTCTT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.5420A>G	chr7.hg19:g.103202088T>C	ENSP00000392423:p.Asp1807Gly	97.0	0.0		96.0	5.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.311650	0.81358	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.26957	1.7;1.7;1.7	5.86	5.86	0.93980	Neuraminidase (1);	0.000000	0.85682	D	0.000000	T	0.49270	0.1547	L	0.61387	1.9	0.58432	D	0.999999	D;P	0.76494	0.999;0.512	D;B	0.72625	0.978;0.263	T	0.47983	-0.9074	10	0.62326	D	0.03	.	16.2555	0.82515	0.0:0.0:0.0:1.0	.	1807;1807	P78509-2;P78509	.;RELN_HUMAN	G	1807	ENSP00000392423:D1807G;ENSP00000345694:D1807G;ENSP00000388446:D1807G	ENSP00000345694:D1807G	D	-	2	0	RELN	102989324	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	7.499000	0.81566	2.242000	0.73789	0.460000	0.39030	GAT	.	.		0.453	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103202088	T	C	103202088	3	2	103	1	0	0	0	0	1	0	0	0	13235	1435	50	2	5082	2	RELN	7	103202088	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2742598	103202088	55936575	525	15148										
RINT1	60561	hgsc.bcm.edu	37	chr7	105190572	105190572	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atttctggatgagaagattcAgccaatattagacaaagtag	9	5	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:105190572A>G	ENST00000257700.2	+	8	1298	c.1067A>G	c.(1066-1068)cAg>cGg	p.Q356R		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	356	RINT1/TIP20. {ECO:0000255|PROSITE- ProRule:PRU00717}.				G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GAGAAGATTCAGCCAATATTA	0.378																																					p.Q356R		Atlas-SNP	.											.	RINT1	65	.	0			c.A1067G						.						126	127	126					7																	105190572		2203	4300	6503	SO:0001583	missense	60561	exon8			AGATTCAGCCAAT	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.1067A>G	chr7.hg19:g.105190572A>G	ENSP00000257700:p.Gln356Arg	115.0	0.0		148.0	6.0	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	hg19	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.476680	0.84640	.	.	ENSG00000135249	ENST00000257700	T	0.41758	0.99	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.63236	0.2494	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64214	-0.6460	10	0.49607	T	0.09	-14.3338	15.8976	0.79346	1.0:0.0:0.0:0.0	.	356	Q6NUQ1	RINT1_HUMAN	R	356	ENSP00000257700:Q356R	ENSP00000257700:Q356R	Q	+	2	0	RINT1	104977808	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.843000	0.75384	2.212000	0.71576	0.528000	0.53228	CAG	.	.		0.378	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		G	105190572	A	G	105190572	3	3	103	1	0	0	0	0	1	0	0	0	13391	188	7	2	1097	2	RINT1	7	105190572	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1988484	105190572	53948091	526	15149										
GPR22	2845	hgsc.bcm.edu	37	chr7	107115730	107115730	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acaactcttggatagatcctAaaagaaacaaaaaaattacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:107115730delA	ENST00000304402.4	+	3	2568	c.1225delA	c.(1225-1227)aaafs	p.K409fs	COG5_ENST00000393603.2_Intron|COG5_ENST00000475638.2_Intron|COG5_ENST00000297135.3_Intron|COG5_ENST00000347053.3_Intron	NM_005295.2	NP_005286.2	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	409					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(3)|lung(6)|ovary(2)|stomach(1)	12						GATAGATCCTAAAAGAAACAA	0.338																																					p.P408fs		Atlas-INDEL	.											.	GPR22	43	.	0			c.1224delT						.						35	40	38					7																	107115730		2195	4281	6476	SO:0001589	frameshift_variant	2845	exon3			.	U66581	CCDS5744.1	7q22-q31.1	2012-08-21			ENSG00000172209	ENSG00000172209		"GPCR / Class A : Orphans"	4477	protein-coding gene	gene with protein product		601910				9073069	Standard	NM_005295		Approved		uc003vef.3	Q99680	OTTHUMG00000154902	ENST00000304402.4:c.1225delA	chr7.hg19:g.107115730delA	ENSP00000302676:p.Lys409fs	118.0	0.0		163.0	10.0	NM_005295	O14554	Frame_Shift_Del	DEL	ENST00000304402.4	hg19	CCDS5744.1																																																																																			.	.		0.338	GPR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337598.1			-	107115730	A	-	107115730	7	5	103	1	0	1	0	1	0	0	0	0	6690	363	13	0	1227	0	GPR22	7	107115730	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1925158	107115730	52022933	527	15150										
C7orf60	154743	hgsc.bcm.edu	37	chr7	112461887	112461887	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aatctgagtcatatggcgcaTcagggagttctgtgaaacca	11	8	4	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:112461887T>C	ENST00000297145.4	-	5	1295	c.1130A>G	c.(1129-1131)gAt>gGt	p.D377G	C7orf60_ENST00000485446.1_5'Flank	NM_152556.2	NP_689769.2	Q1RMZ1	BMT2_HUMAN	chromosome 7 open reading frame 60	377							rRNA (adenine) methyltransferase activity (GO:0016433)			breast(1)|endometrium(2)|lung(7)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	17						ATATGGCGCATCAGGGAgttc	0.378																																					p.D377G		Atlas-SNP	.											.	C7orf60	55	.	0			c.A1130G						.						68	66	67					7																	112461887		1851	4100	5951	SO:0001583	missense	154743	exon5			GGCGCATCAGGGA		CCDS43634.1	7q31.1	2011-01-11	2008-06-19		ENSG00000164603	ENSG00000164603			26475	protein-coding gene	gene with protein product	"hypothetical protein FLJ31818"						Standard	NM_152556		Approved	DKFZp762M126, FLJ31818	uc003vgo.1	Q1RMZ1	OTTHUMG00000155233	ENST00000297145.4:c.1130A>G	chr7.hg19:g.112461887T>C	ENSP00000297145:p.Asp377Gly	84.0	0.0		104.0	5.0	NM_152556	Q8N3D0|Q96MV7	Missense_Mutation	SNP	ENST00000297145.4	hg19	CCDS43634.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.510788	0.64522	.	.	ENSG00000164603	ENST00000297145;ENST00000432572;ENST00000358032	.	.	.	5.83	5.83	0.93111	.	0.044615	0.85682	D	0.000000	T	0.51941	0.1704	N	0.19112	0.55	0.80722	D	1	P;D	0.56968	0.7;0.978	B;P	0.53224	0.221;0.721	T	0.57940	-0.7724	9	0.72032	D	0.01	-14.2384	16.1967	0.82036	0.0:0.0:0.0:1.0	.	324;377	B4DST1;Q1RMZ1	.;CG060_HUMAN	G	377;359;324	.	ENSP00000297145:D377G	D	-	2	0	C7orf60	112249123	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.275000	0.72594	2.217000	0.71921	0.477000	0.44152	GAT	.	.		0.378	C7orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338923.1	NM_152556		C	112461887	T	C	112461887	3	2	103	1	0	0	0	0	1	0	0	0	2409	1435	50	2	91	2	C7orf60	7	112461887	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	5346157	112461887	46676776	528	15151										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117398002	117398002	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggggactgcgcgaagctctgAcccactgaccacggcacatt	12	14	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:117398002A>G	ENST00000160373.3	-	11	3286	c.3195T>C	c.(3193-3195)ggT>ggC	p.G1065G		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1065					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		CGAAGCTCTGACCCACTGACC	0.448																																					p.G1065G		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.T3195C						.						71	57	62					7																	117398002		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon11			GCTCTGACCCACT		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.3195T>C	chr7.hg19:g.117398002A>G		59.0	0.0		33.0	4.0	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	hg19	CCDS5774.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.803|3.803	-0.041242|-0.041242	0.07452|0.07452	.|.	.|.	ENSG00000077063|ENSG00000077063	ENST00000446636|ENST00000435233;ENST00000416239	.|.	.|.	.|.	5.73|5.73	0.331|0.331	0.15933|0.15933	.|.	.|.	.|.	.|.	.|.	T|T	0.50274|0.50274	0.1606|0.1606	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.35699|0.35699	-0.9778|-0.9778	4|4	.|.	.|.	.|.	-0.5958|-0.5958	4.7776|4.7776	0.13187|0.13187	0.6041:0.2254:0.062:0.1085|0.6041:0.2254:0.062:0.1085	.|.	.|.	.|.	.|.	P|A	553|79;61	.|.	.|.	S|V	-|-	1|2	0|0	CTTNBP2|CTTNBP2	117185238|117185238	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.232000|0.232000	0.25224|0.25224	1.637000|1.637000	0.37155|0.37155	0.117000|0.117000	0.18138|0.18138	0.533000|0.533000	0.62120|0.62120	TCA|GTC	.	.		0.448	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		G	117398002	A	G	117398002	2	3	103	1	0	0	0	0	0	0	0	1	4047	262	10	2		2	CTTNBP2	7	117398002	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	4936115	117398002	41740661	529	15152										
AASS	10157	hgsc.bcm.edu	37	chr7	121758669	121758669	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccttaaacccattccatgtAaaatgttgatcattcctgtt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:121758669delA	ENST00000393376.1	-	4	583	c.488delT	c.(487-489)ttafs	p.L163fs	AASS_ENST00000417368.2_Frame_Shift_Del_p.L163fs|AASS_ENST00000473553.1_Intron			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	163	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						CATTCCATGTAAAATGTTGAT	0.373																																					p.L163fs		Atlas-INDEL	.											.	AASS	123	.	0			c.489delA						.						78	71	74					7																	121758669		2203	4300	6503	SO:0001589	frameshift_variant	10157	exon5			.	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.488delT	chr7.hg19:g.121758669delA	ENSP00000377040:p.Leu163fs	167.0	0.0		203.0	14.0	NM_005763	O95462	Frame_Shift_Del	DEL	ENST00000393376.1	hg19	CCDS5783.1																																																																																			.	.		0.373	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		-	121758669	A	-	121758669	7	5	103	1	0	1	0	1	0	0	0	0	24	372	13	0	2372	0	AASS	7	121758669	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	4360667	121758669	37379994	530	15153										
NRF1	4899	hgsc.bcm.edu	37	chr7	129297391	129297391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctccacagcagctgatgaggTgacagctcatctggcagctg	12	12	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:129297391T>C	ENST00000393232.1	+	2	317	c.200T>C	c.(199-201)gTg>gCg	p.V67A	NRF1_ENST00000393231.3_Missense_Mutation_p.V67A|NRF1_ENST00000539636.1_5'UTR|NRF1_ENST00000311967.2_Missense_Mutation_p.V67A|NRF1_ENST00000353868.4_Missense_Mutation_p.V67A|NRF1_ENST00000393230.2_Missense_Mutation_p.V67A|NRF1_ENST00000223190.4_Missense_Mutation_p.V67A	NM_005011.3	NP_005002.3	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	67	Dimerization.				cellular lipid metabolic process (GO:0044255)|generation of precursor metabolites and energy (GO:0006091)|mitochondrion organization (GO:0007005)|organ regeneration (GO:0031100)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	24						GCTGATGAGGTGACAGCTCAT	0.443																																					p.V67A		Atlas-SNP	.											.	NRF1	40	.	0			c.T200C						.						80	72	75					7																	129297391		2203	4300	6503	SO:0001583	missense	4899	exon2			ATGAGGTGACAGC	L22454	CCDS5813.2	7q32	2008-07-18			ENSG00000106459	ENSG00000106459			7996	protein-coding gene	gene with protein product	"alpha palindromic-binding protein"	600879				2584221	Standard	NM_005011		Approved	EWG, ALPHA-PAL	uc003voz.3	Q16656	OTTHUMG00000143736	ENST00000393232.1:c.200T>C	chr7.hg19:g.129297391T>C	ENSP00000376924:p.Val67Ala	62.0	0.0		81.0	4.0	NM_005011	A8K4C6|B4DDV6|Q15305|Q96AN2	Missense_Mutation	SNP	ENST00000393232.1	hg19	CCDS5813.2	.	.	.	.	.	.	.	.	.	.	T	17.50	3.404457	0.62288	.	.	ENSG00000106459	ENST00000393232;ENST00000353868;ENST00000454688;ENST00000223190;ENST00000311967;ENST00000393230;ENST00000393231	.	.	.	5.23	5.23	0.72850	.	0.112091	0.64402	D	0.000013	T	0.36635	0.0974	N	0.14661	0.345	0.80722	D	1	P;B	0.34562	0.457;0.392	B;B	0.31390	0.129;0.125	T	0.42258	-0.9462	9	0.87932	D	0	-15.8507	14.5973	0.68415	0.0:0.0:0.0:1.0	.	67;67	Q96AN2;Q16656	.;NRF1_HUMAN	A	67	.	ENSP00000223190:V67A	V	+	2	0	NRF1	129084627	1.000000	0.71417	0.999000	0.59377	0.835000	0.47333	7.563000	0.82314	2.115000	0.64714	0.477000	0.44152	GTG	.	.		0.443	NRF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289813.1	NM_001040110		C	129297391	T	C	129297391	3	2	103	1	0	0	0	0	1	0	0	0	10655	1696	59	2	202	2	NRF1	7	129297391	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	7538722	129297391	29841272	531	15154										
TSGA14	95681	hgsc.bcm.edu	37	chr7	130039927	130039927	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttccagataatattctatcTtttttaagtcttctggggta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:130039927delT	ENST00000223208.5	-	10	1196	c.926delA	c.(925-927)aagfs	p.K309fs	CEP41_ENST00000343969.5_Intron|CEP41_ENST00000541543.1_Intron	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	309					cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein polyglutamylation (GO:0018095)|protein transport (GO:0015031)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|primary cilium (GO:0072372)											ATATTCTATCTTTTTTAAGTC	0.453																																					p.K309fs		Atlas-INDEL	.											TSGA14,bladder,carcinoma,0,1	.	.	.	0			c.927delG						.						70	76	74					7																	130039927		2203	4300	6503	SO:0001589	frameshift_variant	95681	exon10			.	AJ278890	CCDS5821.1, CCDS59078.1, CCDS59079.1, CCDS59080.1	7q32	2014-02-20	2011-10-04	2011-10-04	ENSG00000106477	ENSG00000106477			12370	protein-coding gene	gene with protein product		610523	"testis specific, 14"	TSGA14		14654843, 22246503	Standard	NM_018718		Approved	DKFZp762H1311, FLJ22445, JBTS15	uc003vpz.4	Q9BYV8	OTTHUMG00000157823	ENST00000223208.5:c.926delA	chr7.hg19:g.130039927delT	ENSP00000223208:p.Lys309fs	62.0	0.0		115.0	11.0	NM_018718	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Frame_Shift_Del	DEL	ENST00000223208.5	hg19	CCDS5821.1																																																																																			.	.		0.453	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718		-	130039927	T	-	130039927	7	5	103	1	0	1	0	1	0	0	0	0	16635	1609	56	0	203	0	TSGA14	7	130039927	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	742536	130039927	29098736	532	15155										
DENND2A	27147	hgsc.bcm.edu	37	chr7	140244510	140244510	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acgctgagggaggagaagagAgactcaaagtccacgtgctc	14	9	1	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:140244510A>G	ENST00000275884.6	-	13	2652	c.2235T>C	c.(2233-2235)tcT>tcC	p.S745S	DENND2A_ENST00000537639.1_Silent_p.S745S|DENND2A_ENST00000496613.1_Silent_p.S745S|DENND2A_ENST00000492720.1_Silent_p.S745S			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	745	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					AGGAGAAGAGAGACTCAAAGT	0.617																																					p.S745S		Atlas-SNP	.											.	DENND2A	132	.	0			c.T2235C						.						42	51	48					7																	140244510		2184	4284	6468	SO:0001819	synonymous_variant	27147	exon12			GAAGAGAGACTCA	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.2235T>C	chr7.hg19:g.140244510A>G		89.0	0.0		128.0	8.0	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	hg19	CCDS43659.1																																																																																			.	.		0.617	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		G	140244510	A	G	140244510	2	3	103	1	0	0	0	0	0	0	0	1	4431	291	11	2		2	DENND2A	7	140244510	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	10204583	140244510	18894153	533	15156										
AGK	55750	hgsc.bcm.edu	37	chr7	141333731	141333731	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacagcctgtatttgcaatgAccggccttcgatggggatct	11	10	1	1	rs561898521	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:141333731A>T	ENST00000355413.4	+	10	879	c.619A>T	c.(619-621)Acc>Tcc	p.T207S	AGK_ENST00000473247.1_Missense_Mutation_p.T179S|AGK_ENST00000535825.1_Missense_Mutation_p.T204S	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	207					ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					ATTTGCAATGACCGGCCTTCG	0.348																																					p.T207S		Atlas-SNP	.											.	AGK	43	.	0			c.A619T						.						122	122	122					7																	141333731		2203	4300	6503	SO:0001583	missense	55750	exon10			GCAATGACCGGCC	BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"multiple substrate lipid kinase"	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.619A>T	chr7.hg19:g.141333731A>T	ENSP00000347581:p.Thr207Ser	34.0	0.0		58.0	20.0	NM_018238	Q75KN1|Q96GC3|Q9NP48	Missense_Mutation	SNP	ENST00000355413.4	hg19	CCDS5865.1	.	.	.	.	.	.	.	.	.	.	A	7.523	0.657045	0.14580	.	.	ENSG00000006530	ENST00000355413;ENST00000473247;ENST00000535825	T;T;T	0.40756	2.61;2.61;1.02	5.85	4.59	0.56863	.	0.356129	0.35436	N	0.003216	T	0.18045	0.0433	N	0.04090	-0.28	0.27369	N	0.955738	B	0.02656	0.0	B	0.06405	0.002	T	0.13072	-1.0523	10	0.06625	T	0.88	.	11.1992	0.48730	0.8531:0.0:0.0:0.1469	.	207	Q53H12	AGK_HUMAN	S	207;179;204	ENSP00000347581:T207S;ENSP00000420776:T179S;ENSP00000444349:T204S	ENSP00000347581:T207S	T	+	1	0	AGK	140980200	1.000000	0.71417	0.980000	0.43619	0.982000	0.71751	3.263000	0.51546	2.246000	0.74042	0.533000	0.62120	ACC	.	.		0.348	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1	NM_018238		T	141333731	A	T	141333731	3	4	103	1	0	0	0	0	1	0	0	0	383	275	10	4	653	4	AGK	7	141333731	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1089221	141333731	17804932	534	15157										
MGAM	8972	hgsc.bcm.edu	37	chr7	141727459	141727459	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgggcgcttggatttcaccTcagtcgttacgaatatggaa	11	9	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:141727459T>C	ENST00000549489.2	+	10	1240	c.1145T>C	c.(1144-1146)cTc>cCc	p.L382P	MGAM_ENST00000475668.2_Missense_Mutation_p.L382P	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	382	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GGATTTCACCTCAGTCGTTAC	0.443																																					p.L382P		Atlas-SNP	.											.	MGAM	767	.	0			c.T1145C						.						64	62	63					7																	141727459		1858	4102	5960	SO:0001583	missense	8972	exon10			TTCACCTCAGTCG	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.1145T>C	chr7.hg19:g.141727459T>C	ENSP00000447378:p.Leu382Pro	57.0	0.0		79.0	4.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.323594	0.81580	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.91996	-2.95	5.55	5.55	0.83447	Glycoside hydrolase, superfamily (1);	0.000000	0.49916	D	0.000140	D	0.97365	0.9138	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98389	1.0562	10	0.87932	D	0	.	13.6922	0.62553	0.0:0.0:0.0:1.0	.	382	O43451	MGA_HUMAN	P	382;382;259	ENSP00000447378:L382P	ENSP00000316431:L259P	L	+	2	0	MGAM	141373928	0.987000	0.35691	0.989000	0.46669	0.765000	0.43378	7.457000	0.80775	2.326000	0.78906	0.533000	0.62120	CTC	.	.		0.443	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			C	141727459	T	C	141727459	3	2	103	1	0	0	0	0	1	0	0	0	9550	1551	54	2	1179	2	MGAM	7	141727459	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	393728	141727459	17411204	535	15158										
NOBOX	135935	hgsc.bcm.edu	37	chr7	144096122	144096122	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catcagcagtggcatcagttGgggggtgtggacagggccaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:144096122delG	ENST00000467773.1	-	8	1389	c.1390delC	c.(1390-1392)caafs	p.Q464fs	NOBOX_ENST00000223140.5_Frame_Shift_Del_p.Q347fs|NOBOX_ENST00000483238.1_Frame_Shift_Del_p.Q432fs	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	464	Pro-rich.				oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					GGCATCAGTTGGGGGGTGTGG	0.637																																					p.Q464fs		Atlas-INDEL	.											.	NOBOX	130	.	0			c.1391delA						.						10	11	10					7																	144096122		1905	4132	6037	SO:0001589	frameshift_variant	135935	exon8			.			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"Homeoboxes / PRD class"	22448	protein-coding gene	gene with protein product	"newborn ovary homeobox-encoding gene"	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1390delC	chr7.hg19:g.144096122delG	ENSP00000419457:p.Gln464fs	223.0	0.0		193.0	13.0	NM_001080413	A6NCD3|A8MZN5	Frame_Shift_Del	DEL	ENST00000467773.1	hg19																																																																																				.	.		0.637	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420		-	144096122	G	-	144096122	7	5	103	1	0	1	0	1	0	0	0	0	10521	1357	47	0	697	0	NOBOX	7	144096122	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2368663	144096122	15042541	536	15159										
NOBOX	135935	hgsc.bcm.edu	37	chr7	144096920	144096920	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttcccattcagtttctccaTttttcgccacttggcccggc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:144096920delT	ENST00000467773.1	-	6	1083	c.1084delA	c.(1084-1086)atgfs	p.M362fs	NOBOX_ENST00000223140.5_Frame_Shift_Del_p.M245fs|NOBOX_ENST00000483238.1_Frame_Shift_Del_p.M330fs	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	362					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					AGTTTCTCCATTTTTCGCCAC	0.532																																					p.M362fs		Atlas-INDEL	.											.	NOBOX	130	.	0			c.1085delT						.						97	100	99					7																	144096920		1954	4153	6107	SO:0001589	frameshift_variant	135935	exon6			.			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"Homeoboxes / PRD class"	22448	protein-coding gene	gene with protein product	"newborn ovary homeobox-encoding gene"	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1084delA	chr7.hg19:g.144096920delT	ENSP00000419457:p.Met362fs	168.0	0.0		161.0	12.0	NM_001080413	A6NCD3|A8MZN5	Frame_Shift_Del	DEL	ENST00000467773.1	hg19																																																																																				.	.		0.532	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420		-	144096920	T	-	144096920	7	5	103	1	0	1	0	1	0	0	0	0	10521	1493	52	0	1011	0	NOBOX	7	144096920	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	798	144096920	15041743	537	15160										
KRBA1	84626	hgsc.bcm.edu	37	chr7	149420823	149420823	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaacatgttcctttttccttAgtgaagaccgaggcggtttc	9	9	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:149420823A>T	ENST00000485033.2	+	7	772		c.e7-1		KRBA1_ENST00000255992.10_Splice_Site|KRBA1_ENST00000479560.1_Splice_Site|KRBA1_ENST00000319551.8_Splice_Site			A5PL33	KRBA1_HUMAN	KRAB-A domain containing 1											breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(17)|ovary(1)|prostate(1)	27	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTTTTTCCTTAGTGAAGACCG	0.557																																					.		Atlas-SNP	.											.	KRBA1	68	.	0			c.773-2A>T						.						48	52	51					7																	149420823		1978	4140	6118	SO:0001630	splice_region_variant	84626	exon8			TTCCTTAGTGAAG	AB058765	CCDS75674.1	7q36	2014-02-12	2006-08-15		ENSG00000133619	ENSG00000133619		"-"	22228	protein-coding gene	gene with protein product			"KRAB A domain containing 1"				Standard	NM_001290187		Approved	KIAA1862	uc003wfz.3	A5PL33	OTTHUMG00000157886	ENST00000485033.2:c.773-1A>T	chr7.hg19:g.149420823A>T		95.0	0.0		103.0	5.0	NM_032534	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Splice_Site	SNP	ENST00000485033.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.55	3.155080	0.57259	.	.	ENSG00000133619	ENST00000255992;ENST00000319551;ENST00000485033	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5898	0.50939	1.0:0.0:0.0:0.0	rs11462346	.	.	.	.	-1	.	.	.	+	.	.	KRBA1	149051756	0.978000	0.34361	0.920000	0.36463	0.793000	0.44817	2.679000	0.46909	1.996000	0.58369	0.533000	0.62120	.	.	.		0.557	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534	Intron	T	149420823	A	T	149420823	5	4	103	1	0	0	0	0	0	0	1	0	8448	434	15	4	797	4	KRBA1	7	149420823	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	5323903	149420823	9717840	538	15161										
ZNF862	643641	hgsc.bcm.edu	37	chr7	149558251	149558251	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctctctacagtgagacagcaGatgggtacttcgagaccatc	10	11	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:149558251G>A	ENST00000223210.4	+	7	2247	c.2002G>A	c.(2002-2004)Gat>Aat	p.D668N	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	668					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						TGAGACAGCAGATGGGTACTT	0.587																																					p.D668N		Atlas-SNP	.											.	ZNF862	97	.	0			c.G2002A						.						28	30	29					7																	149558251		2070	4216	6286	SO:0001583	missense	643641	exon7			ACAGCAGATGGGT	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"Zinc fingers, C2H2-type", "-"	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.2002G>A	chr7.hg19:g.149558251G>A	ENSP00000223210:p.Asp668Asn	177.0	0.0		187.0	64.0	NM_001099220	A0AUL8	Missense_Mutation	SNP	ENST00000223210.4	hg19	CCDS47741.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.848402	0.32699	.	.	ENSG00000106479	ENST00000223210	T	0.22539	1.95	5.17	5.17	0.71159	Ribonuclease H-like (1);	0.000000	0.52532	D	0.000075	T	0.39489	0.1080	L	0.50333	1.59	0.34382	D	0.693181	D	0.89917	1.0	D	0.80764	0.994	T	0.48559	-0.9025	10	0.41790	T	0.15	-21.8278	14.1976	0.65682	0.0:0.0:1.0:0.0	.	668	O60290	ZN862_HUMAN	N	668	ENSP00000223210:D668N	ENSP00000223210:D668N	D	+	1	0	ZNF862	149189184	0.985000	0.35326	0.163000	0.22734	0.026000	0.11368	4.329000	0.59260	2.407000	0.81776	0.655000	0.94253	GAT	.	.		0.587	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220		A	149558251	G	A	149558251	3	1	103	1	0	0	0	0	1	0	0	0	18210	942	33	3	2028	3	ZNF862	7	149558251	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	137428	149558251	9580412	539	15162										
CHPF2	54480	hgsc.bcm.edu	37	chr7	150932436	150932436	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggatgacacatatgtgcaggCcccccgcctggcagcccttg					rs146139489	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:150932436delC	ENST00000035307.2	+	2	2079	c.566delC	c.(565-567)gccfs	p.A189fs	CHPF2_ENST00000495645.1_Frame_Shift_Del_p.A181fs	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	189					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						TATGTGCAGGCCCCCCGCCTG	0.617																																					p.A189fs		Atlas-INDEL	.											.	CHPF2	52	.	0			c.565delG						.						90	93	92					7																	150932436		2203	4300	6503	SO:0001589	frameshift_variant	54480	exon2			.	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.566delC	chr7.hg19:g.150932436delC	ENSP00000035307:p.Ala189fs	94.0	0.0		107.0	10.0	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Frame_Shift_Del	DEL	ENST00000035307.2	hg19	CCDS34779.1																																																																																			.	.		0.617	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015		-	150932436	C	-	150932436	7	5	103	1	0	1	0	1	0	0	0	0	3371	739	26	0	572	0	CHPF2	7	150932436	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1374185	150932436	8206227	540	15163										
PRKAG2	51422	hgsc.bcm.edu	37	chr7	151372597	151372597	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaacctctgccctgtgtccGggggggaagacgaggcatag					rs41317142		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:151372597delG	ENST00000287878.4	-	4	1097	c.593delC	c.(592-594)ccgfs	p.P198fs	PRKAG2_ENST00000492843.1_Frame_Shift_Del_p.P74fs|PRKAG2_ENST00000461529.1_5'Flank|PRKAG2_ENST00000433631.2_Frame_Shift_Del_p.P74fs|PRKAG2_ENST00000392801.2_Frame_Shift_Del_p.P154fs	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	198					ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	CCCTGTGTCCGGGGGGGAAGA	0.582																																					p.P198fs		Atlas-INDEL	.											.,4	PRKAG2	86	.	0			c.594delG						.						93	85	88					7																	151372597		2203	4300	6503	SO:0001589	frameshift_variant	51422	exon4			.	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"AMPK gamma2"	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.593delC	chr7.hg19:g.151372597delG	ENSP00000287878:p.Pro198fs	111.0	0.0		174.0	14.0	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Frame_Shift_Del	DEL	ENST00000287878.4	hg19	CCDS5928.1																																																																																			.	.		0.582	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		-	151372597	G	-	151372597	7	5	103	1	0	1	0	1	0	0	0	0	12513	1116	39	0	1168	0	PRKAG2	7	151372597	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	440161	151372597	7766066	541	15164										
MLL3	58508	hgsc.bcm.edu	37	chr7	151874093	151874093	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acctcattggtaacagtggaTtttttctgtggtgaatgttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:151874093delT	ENST00000262189.6	-	38	8663	c.8445delA	c.(8443-8445)aaafs	p.K2815fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.K2815fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2815					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TAACAGTGGATTTTTTCTGTG	0.323																																					p.S2816fs		Atlas-INDEL	.											.	MLL3	1564	.	0			c.8446delT						.						151	145	147					7																	151874093		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon38			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8445delA	chr7.hg19:g.151874093delT	ENSP00000262189:p.Lys2815fs	158.0	0.0		221.0	16.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.		0.323	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151874093	T	-	151874093	7	5	103	1	0	1	0	1	0	0	0	0	9631	1490	52	0	6378	0	MLL3	7	151874093	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	501496	151874093	7264570	542	15165										
NOM1	64434	hgsc.bcm.edu	37	chr7	156754952	156754952	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgaggaaactgcagagagcTttggtgagtcaaggaacttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:156754952delT	ENST00000275820.3	+	5	1755	c.1740delT	c.(1738-1740)gctfs	p.A580fs		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	580						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		TGCAGAGAGCTTTGGTGAGTC	0.488																																					p.A580fs		Atlas-INDEL	.											.	NOM1	73	.	0			c.1739delC						.						130	121	124					7																	156754952		2203	4300	6503	SO:0001589	frameshift_variant	64434	exon5			.	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 113"	611269	"chromosome 7 open reading frame 3"	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1740delT	chr7.hg19:g.156754952delT	ENSP00000275820:p.Ala580fs	174.0	0.0		228.0	14.0	NM_138400	Q96I08	Frame_Shift_Del	DEL	ENST00000275820.3	hg19	CCDS34787.1																																																																																			.	.		0.488	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		-	156754952	T	-	156754952	7	5	103	1	0	1	0	1	0	0	0	0	10539	1596	56	0	1758	0	NOM1	7	156754952	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	4880859	156754952	2383711	543	15166										
MYOM2	9172	hgsc.bcm.edu	37	chr8	2092705	2092705	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgaaggtggagcaggccaagTacgtcagcatgaccatcaaa	12	9	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:2092705T>C	ENST00000262113.4	+	37	4339	c.4198T>C	c.(4198-4200)Tac>Cac	p.Y1400H	MYOM2_ENST00000523438.1_Missense_Mutation_p.Y825H|MYOM2_ENST00000520298.1_3'UTR	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1400	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GCAGGCCAAGTACGTCAGCAT	0.537																																					p.Y1400H		Atlas-SNP	.											.	MYOM2	251	.	0			c.T4198C						.						128	105	113					8																	2092705		2203	4300	6503	SO:0001583	missense	9172	exon37			GCCAAGTACGTCA		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.4198T>C	chr8.hg19:g.2092705T>C	ENSP00000262113:p.Tyr1400His	112.0	0.0		96.0	5.0	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	hg19	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	T	17.30	3.354298	0.61293	.	.	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.66280	-0.2;-0.2	5.24	4.05	0.47172	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.183408	0.49916	D	0.000129	T	0.67392	0.2888	L	0.47016	1.485	0.40680	D	0.982295	D	0.58970	0.984	P	0.62491	0.903	T	0.63143	-0.6703	10	0.21540	T	0.41	.	11.4574	0.50189	0.1351:0.0:0.0:0.8649	.	1400	P54296	MYOM2_HUMAN	H	1400;825	ENSP00000262113:Y1400H;ENSP00000428396:Y825H	ENSP00000262113:Y1400H	Y	+	1	0	MYOM2	2080112	1.000000	0.71417	0.985000	0.45067	0.988000	0.76386	3.261000	0.51530	0.875000	0.35847	0.533000	0.62120	TAC	.	.		0.537	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		C	2092705	T	C	2092705	3	2	103	1	0	0	0	0	1	0	0	0	10101	1638	57	2	4340	2	MYOM2	8	2092705	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10		2092705	144271317	544	15167										
DLC1	10395	hgsc.bcm.edu	37	chr8	13356655	13356655	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgccatcttctgccttgaccTttggtggacttttgttttga					rs34242235	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:13356655delT	ENST00000276297.4	-	2	1335	c.926delA	c.(925-927)aagfs	p.K309fs	DLC1_ENST00000316609.5_Frame_Shift_Del_p.K309fs|DLC1_ENST00000511869.1_Frame_Shift_Del_p.K309fs	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	309					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						TGCCTTGACCTTTGGTGGACT	0.478																																					p.K309fs		Atlas-INDEL	.											.	DLC1	411	.	0			c.927delG						.						202	180	187					8																	13356655		2203	4300	6503	SO:0001589	frameshift_variant	10395	exon2			.	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.926delA	chr8.hg19:g.13356655delT	ENSP00000276297:p.Lys309fs	188.0	0.0		162.0	10.0	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Frame_Shift_Del	DEL	ENST00000276297.4	hg19	CCDS5989.1																																																																																			.	.		0.478	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		-	13356655	T	-	13356655	7	5	103	1	0	1	0	1	0	0	0	0	4552	1609	56	0	3813	0	DLC1	8	13356655	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	11263950	13356655	133007367	545	15168										
TUSC3	7991	hgsc.bcm.edu	37	chr8	15398006	15398006	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggctgcggtacctgcccaccGggagctttcccttccttctc	10	17	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:15398006G>A	ENST00000503731.1	+	1	215	c.67G>A	c.(67-69)Ggg>Agg	p.G23R	TUSC3_ENST00000382020.4_Missense_Mutation_p.G23R|TUSC3_ENST00000509380.1_Missense_Mutation_p.G23R|TUSC3_ENST00000503191.1_Intron|TUSC3_ENST00000506802.1_Missense_Mutation_p.G23R	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	23					cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		CCTGCCCACCGGGAGCTTTCC	0.672																																					p.G23R		Atlas-SNP	.											.	TUSC3	98	.	0			c.G67A						.						26	26	26					8																	15398006		2200	4298	6498	SO:0001583	missense	7991	exon1			CCCACCGGGAGCT	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.67G>A	chr8.hg19:g.15398006G>A	ENSP00000424544:p.Gly23Arg	152.0	0.0		198.0	81.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.788938	0.49997	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.46819	0.87;0.86;0.86;0.86	4.2	3.31	0.37934	.	0.301186	0.27645	N	0.018454	T	0.23766	0.0575	N	0.08118	0	0.29524	N	0.853302	B;B;B;B;B;B	0.26195	0.031;0.012;0.021;0.012;0.012;0.144	B;B;B;B;B;B	0.13407	0.001;0.001;0.003;0.001;0.001;0.009	T	0.12502	-1.0545	10	0.25106	T	0.35	-5.3103	10.034	0.42118	0.0:0.2049:0.7951:0.0	.	23;23;23;23;23;23	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	R	23	ENSP00000371450:G23R;ENSP00000425777:G23R;ENSP00000423426:G23R;ENSP00000424544:G23R	ENSP00000221167:G23R	G	+	1	0	TUSC3	15442377	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	3.994000	0.56994	1.335000	0.45486	0.563000	0.77884	GGG	.	.		0.672	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		A	15398006	G	A	15398006	3	1	103	1	0	0	0	0	1	0	0	0	16793	1116	39	1	69	1	TUSC3	8	15398006	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	2041351	15398006	130966016	546	15169										
DOCK5	80005	hgsc.bcm.edu	37	chr8	25240190	25240190	+	Splice_Site	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtcttgttttgttttccagAaaaaaagggcctcattttat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:25240190delA	ENST00000276440.7	+	40	4071	c.4027delA	c.(4027-4029)aaa>aa	p.K1344fs		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1344	DHR-2.				positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TGTTTTCCAGAAAAAAAGGGC	0.408																																					.	Pancreas(145;34 1887 3271 10937 30165)	Atlas-INDEL	.											.	DOCK5	167	.	0			c.4027-1A>-						.						85	80	82					8																	25240190		2203	4300	6503	SO:0001630	splice_region_variant	80005	exon40			.		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.4027-1A>-	chr8.hg19:g.25240190delA		74.0	0.0		78.0	10.0	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Splice_Site	DEL	ENST00000276440.7	hg19	CCDS6047.1																																																																																			.	.		0.408	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	Frame_Shift_Del	-	25240190	A	-	25240190	8	5	103	1	0	1	0	1	0	0	1	0	4692	260	9	0	4185	0	DOCK5	8	25240190	Splice_Site	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	9842184	25240190	121123832	547	15170										
GOT1L1	137362	hgsc.bcm.edu	37	chr8	37791908	37791908	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cattgatgccctcagtgatgTaatttatgttgttggcattg	10	6	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:37791908T>C	ENST00000307599.4	-	9	1268	c.1169A>G	c.(1168-1170)tAc>tGc	p.Y390C		NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	glutamic-oxaloacetic transaminase 1-like 1	390					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)	cytoplasm (GO:0005737)	pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)			CTCAGTGATGTAATTTATGTT	0.423																																					p.Y390C		Atlas-SNP	.											.	GOT1L1	87	.	0			c.A1169G						.						251	241	244					8																	37791908		1910	4139	6049	SO:0001583	missense	137362	exon9			GTGATGTAATTTA	BC029504	CCDS47839.1	8p12	2005-09-22			ENSG00000169154	ENSG00000169154			28487	protein-coding gene	gene with protein product						12477932	Standard	NM_152413		Approved	MGC33309	uc011lbj.1	Q8NHS2	OTTHUMG00000164027	ENST00000307599.4:c.1169A>G	chr8.hg19:g.37791908T>C	ENSP00000303077:p.Tyr390Cys	331.0	0.0		301.0	67.0	NM_152413	A8MWL4	Missense_Mutation	SNP	ENST00000307599.4	hg19	CCDS47839.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.480254	0.44044	.	.	ENSG00000169154	ENST00000307599	T	0.26660	1.72	5.37	5.37	0.77165	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.098157	0.42053	D	0.000761	T	0.59032	0.2164	M	0.92169	3.28	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.69224	-0.5201	10	0.87932	D	0	-21.863	13.0005	0.58672	0.0:0.0:0.0:1.0	.	390	Q8NHS2	AATC2_HUMAN	C	390	ENSP00000303077:Y390C	ENSP00000303077:Y390C	Y	-	2	0	GOT1L1	37911066	1.000000	0.71417	1.000000	0.80357	0.101000	0.19017	5.628000	0.67791	2.266000	0.75297	0.528000	0.53228	TAC	.	.		0.423	GOT1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376823.1	NM_152413		C	37791908	T	C	37791908	3	2	103	1	0	0	0	0	1	0	0	0	6588	1638	57	2	100	2	GOT1L1	8	37791908	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	12551718	37791908	108572114	548	15171										
WHSC1L1	54904	hgsc.bcm.edu	37	chr8	38146052	38146052	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccccagcctctccgctccgTtttgatgatctctgcatcag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:38146052delT	ENST00000317025.8	-	19	3971	c.3454delA	c.(3454-3456)acgfs	p.T1152fs	WHSC1L1_ENST00000433384.2_Frame_Shift_Del_p.T1103fs|WHSC1L1_ENST00000527502.1_Frame_Shift_Del_p.T1152fs	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	1152	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			CTCCGCTCCGTTTTGATGATC	0.537			T	NUP98	AML																																p.T1152fs		Atlas-INDEL	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.3455delC						.						118	116	117					8																	38146052		1932	4141	6073	SO:0001589	frameshift_variant	54904	exon19			.	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.3454delA	chr8.hg19:g.38146052delT	ENSP00000313983:p.Thr1152fs	133.0	0.0		130.0	10.0	NM_023034	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Frame_Shift_Del	DEL	ENST00000317025.8	hg19	CCDS43729.1																																																																																			.	.		0.537	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		-	38146052	T	-	38146052	7	5	103	1	0	1	0	1	0	0	0	0	17378	1725	60	0	883	0	WHSC1L1	8	38146052	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	354144	38146052	108217970	549	15172										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52396242	52396242	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gattagaaaagctcccagctGgaattttagataatttgttg	9	5	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:52396242G>C	ENST00000356297.4	-	6	585	c.485C>G	c.(484-486)cCa>cGa	p.P162R	PXDNL_ENST00000543296.1_Missense_Mutation_p.P162R	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	162					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.P162L(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GCTCCCAGCTGGAATTTTAGA	0.284																																					p.P162R		Atlas-SNP	.											PXDNL_ENST00000356297,rectum,carcinoma,0,1	PXDNL	414	.	1	Substitution - Missense(1)	large_intestine(1)	c.C485G						.						29	26	27					8																	52396242		1578	3669	5247	SO:0001583	missense	137902	exon6			CCAGCTGGAATTT		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.485C>G	chr8.hg19:g.52396242G>C	ENSP00000348645:p.Pro162Arg	167.0	0.0		300.0	0.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	8.607	0.888212	0.17540	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.60299	0.2;0.2	4.6	-0.399	0.12415	.	.	.	.	.	T	0.51160	0.1658	L	0.56769	1.78	0.20074	N	0.999937	P	0.42010	0.768	B	0.43445	0.42	T	0.41251	-0.9519	9	0.20046	T	0.44	.	8.0724	0.30697	0.4475:0.0:0.5525:0.0	.	162	A1KZ92	PXDNL_HUMAN	R	162	ENSP00000348645:P162R;ENSP00000444865:P162R	ENSP00000348645:P162R	P	-	2	0	PXDNL	52558795	0.061000	0.20836	0.007000	0.13788	0.098000	0.18820	0.545000	0.23268	-0.355000	0.08199	-0.742000	0.03525	CCA	.	.		0.284	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		C	52396242	G	C	52396242	3	2	103	1	0	0	0	0	1	0	0	0	12863	1348	47	4	3978	4	PXDNL	8	52396242	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	14250190	52396242	93967780	550	15173										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53569774	53569774	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caagtttaccttcatattcaTtttttaaagacagtagttct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:53569774delT	ENST00000025008.5	-	15	3138	c.2615delA	c.(2614-2616)aatfs	p.N872fs	RB1CC1_ENST00000435644.2_Frame_Shift_Del_p.N872fs|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Frame_Shift_Del_p.N872fs	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	872					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TTCATATTCATTTTTTAAAGA	0.289																																					p.N872fs	GBM(180;1701 2102 13475 42023 52570)	Atlas-INDEL	.											.,1	RB1CC1	163	.	0			c.2616delT						.						31	34	33					8																	53569774		2176	4252	6428	SO:0001589	frameshift_variant	9821	exon15			.	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.2615delA	chr8.hg19:g.53569774delT	ENSP00000025008:p.Asn872fs	54.0	0.0		159.0	10.0	NM_001083617	Q86YR4|Q8WVU9|Q92601	Frame_Shift_Del	DEL	ENST00000025008.5	hg19	CCDS34892.1																																																																																			.	.		0.289	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		-	53569774	T	-	53569774	7	5	103	1	0	1	0	1	0	0	0	0	13114	1493	52	0	2209	0	RB1CC1	8	53569774	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1173532	53569774	92794248	551	15174										
RP1	6101	hgsc.bcm.edu	37	chr8	55539238	55539238	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatccaactttaaagcctatAaaatcagctccagtatgtag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:55539238delA	ENST00000220676.1	+	4	2944	c.2796delA	c.(2794-2796)atafs	p.I932fs		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	932					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TAAAGCCTATAAAATCAGCTC	0.323																																					p.I932fs	Colon(91;1014 1389 7634 14542 40420)	Atlas-INDEL	.											.	RP1	429	.	0			c.2795delT						.						35	38	37					8																	55539238		2202	4300	6502	SO:0001589	frameshift_variant	6101	exon4			.	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2796delA	chr8.hg19:g.55539238delA	ENSP00000220676:p.Ile932fs	68.0	0.0		170.0	11.0	NM_006269		Frame_Shift_Del	DEL	ENST00000220676.1	hg19	CCDS6160.1																																																																																			.	.		0.323	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		-	55539238	A	-	55539238	7	5	103	1	0	1	0	1	0	0	0	0	13547	352	13	0	2806	0	RP1	8	55539238	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1969464	55539238	90824784	552	15175										
PDE7A	5150	hgsc.bcm.edu	37	chr8	66753692	66753692	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcggcggctgaggacgtgctGggggaccggcctgtccaggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:66753692delG	ENST00000401827.3	-	1	495	c.52delC	c.(52-54)cagfs	p.Q18fs	CTD-2532N20.1_ENST00000607622.1_lincRNA|PDE7A_ENST00000396642.3_Frame_Shift_Del_p.Q18fs	NM_001242318.2	NP_001229247.1	Q13946	PDE7A_HUMAN	phosphodiesterase 7A	18					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			large_intestine(5)|lung(3)|stomach(1)|urinary_tract(1)	10			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	AGGACGTGCTGGGGGACCGGC	0.706																																					p.Q18fs		Atlas-INDEL	.											.	PDE7A	78	.	0			c.53delA						.						13	19	17					8																	66753692		1957	4152	6109	SO:0001589	frameshift_variant	5150	exon1			.	L12052	CCDS34901.1, CCDS56538.1	8q13	2008-03-18				ENSG00000205268	3.1.4.17	"Phosphodiesterases"	8791	protein-coding gene	gene with protein product		171885				8389765, 9521885	Standard	NM_001242318		Approved	HCP1	uc003xvq.3	Q13946		ENST00000401827.3:c.52delC	chr8.hg19:g.66753692delG	ENSP00000385632:p.Gln18fs	111.0	0.0		232.0	14.0	NM_001242318	A0AVH6|A8K436|A8K9G5|O15380|Q96T72	Frame_Shift_Del	DEL	ENST00000401827.3	hg19	CCDS56538.1																																																																																			.	.		0.706	PDE7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378905.1			-	66753692	G	-	66753692	7	5	103	1	0	1	0	1	0	0	0	0	11660	1357	47	0	1544	0	PDE7A	8	66753692	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	11214454	66753692	79610330	553	15176										
RBM12B	389677	hgsc.bcm.edu	37	chr8	94746698	94746698	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggttgcctgaagtcctcctcGgggagctgcctgaagtcctc					rs3133974	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:94746698delG	ENST00000399300.2	-	3	2154	c.1941delC	c.(1939-1941)cccfs	p.P647fs	RBM12B_ENST00000520961.1_Intron|RBM12B_ENST00000517700.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	647							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			AGTCCTCCTCGGGGAGCTGCC	0.647																																					p.E648fs		Atlas-INDEL	.											.	RBM12B	78	.	0			c.1942delG						.						86	89	88					8																	94746698		1874	4107	5981	SO:0001589	frameshift_variant	389677	exon3			.		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.1941delC	chr8.hg19:g.94746698delG	ENSP00000382239:p.Pro647fs	75.0	0.0		159.0	10.0	NM_203390	A8MYB5	Frame_Shift_Del	DEL	ENST00000399300.2	hg19	CCDS43755.1																																																																																			.	.		0.647	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		-	94746698	G	-	94746698	7	5	103	1	0	1	0	1	0	0	0	0	13129	1103	39	0	1068	0	RBM12B	8	94746698	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	27993006	94746698	51617324	554	15177										
C8orf38	137682	hgsc.bcm.edu	37	chr8	96060727	96060727	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctacggaggaaccaagatAaaaatgtgagagatgtaata							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:96060727delA	ENST00000396124.4	+	7	780	c.757delA	c.(757-759)aaafs	p.K253fs	NDUFAF6_ENST00000396111.2_Frame_Shift_Del_p.K161fs|NDUFAF6_ENST00000286687.4_Frame_Shift_Del_p.K101fs|NDUFAF6_ENST00000396113.1_Frame_Shift_Del_p.K161fs|NDUFAF6_ENST00000542894.1_Frame_Shift_Del_p.K201fs	NM_152416.3	NP_689629.2	Q330K2	NDUF6_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 6	253					biosynthetic process (GO:0009058)|mitochondrial respiratory chain complex I assembly (GO:0032981)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	transferase activity (GO:0016740)										GAACCAAGATAAAAATGTGAG	0.383																																					p.D252fs		Atlas-INDEL	.											.	.	.	.	0			c.756delT						.						120	110	113					8																	96060727		1850	4111	5961	SO:0001589	frameshift_variant	137682	exon7			.	BC028166	CCDS6266.2	8q22.1	2013-10-21	2012-05-08	2012-05-08	ENSG00000156170	ENSG00000156170		"Mitochondrial respiratory chain complex assembly factors"	28625	protein-coding gene	gene with protein product		612392	"chromosome 8 open reading frame 38"	C8orf38		22019594, 23509070	Standard	NM_152416		Approved	MGC40214	uc003yhj.3	Q330K2	OTTHUMG00000150173	ENST00000396124.4:c.757delA	chr8.hg19:g.96060727delA	ENSP00000379430:p.Lys253fs	69.0	0.0		178.0	11.0	NM_152416	A8MT28|A8MWF0|B4DQ45|Q8N6U6	Frame_Shift_Del	DEL	ENST00000396124.4	hg19	CCDS6266.2																																																																																			.	.		0.383	NDUFAF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316700.2	NM_152416		-	96060727	A	-	96060727	7	5	103	1	0	1	0	1	0	0	0	0	2426	363	13	0	783	0	C8orf38	8	96060727	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1314029	96060727	50303295	555	15178										
MTERFD1	51001	hgsc.bcm.edu	37	chr8	97258633	97258633	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaatggtgcttttctgaccaTctgtgcaacatctgctttac	7	10	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:97258633T>C	ENST00000287025.3	-	5	825	c.727A>G	c.(727-729)Atg>Gtg	p.M243V	MTERFD1_ENST00000522822.1_Missense_Mutation_p.M122V|MTERFD1_ENST00000524341.1_Missense_Mutation_p.M53V|MTERFD1_ENST00000523821.1_Missense_Mutation_p.M243V	NM_015942.3	NP_057026.3	Q96E29	MTEF3_HUMAN		243					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)	transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	24	Breast(36;5.16e-05)					TTTCTGACCATCTGTGCAACA	0.348																																					p.M243V		Atlas-SNP	.											.	MTERFD1	50	.	0			c.A727G						.						88	84	85					8																	97258633		2203	4300	6503	SO:0001583	missense	51001	exon5			TGACCATCTGTGC																												ENST00000287025.3:c.727A>G	chr8.hg19:g.97258633T>C	ENSP00000287025:p.Met243Val	53.0	0.0		174.0	7.0	NM_015942	B3KMG6|G3V130|Q9Y301	Missense_Mutation	SNP	ENST00000287025.3	hg19	CCDS6270.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.193889	0.78902	.	.	ENSG00000156469	ENST00000523821;ENST00000522822;ENST00000524341;ENST00000287025	T;T;T;T	0.20738	2.05;2.05;2.05;2.05	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.36276	0.0961	M	0.78637	2.42	0.80722	D	1	D;D	0.55385	0.971;0.971	P;P	0.53185	0.72;0.72	T	0.28396	-1.0045	10	0.09084	T	0.74	-8.8963	15.1204	0.72438	0.0:0.0:0.0:1.0	.	243;243	E5RIK9;Q96E29	.;MTER1_HUMAN	V	243;122;53;243	ENSP00000429400:M243V;ENSP00000430138:M122V;ENSP00000429267:M53V;ENSP00000287025:M243V	ENSP00000287025:M243V	M	-	1	0	MTERFD1	97327809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.641000	0.83368	2.299000	0.77371	0.528000	0.53228	ATG	.	.		0.348	MTERFD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379876.1			C	97258633	T	C	97258633	3	2	103	1	0	0	0	0	1	0	0	0	9928	1435	50	2	542	2	MTERFD1	8	97258633	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1197906	97258633	49105389	556	15179										
SPAG1	6674	hgsc.bcm.edu	37	chr8	101199429	101199429	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttacagaactggaatagtgcTtttcaggattgtgaaaaggt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:101199429delT	ENST00000388798.2	+	8	974	c.783delT	c.(781-783)gctfs	p.A261fs	SPAG1_ENST00000520643.1_Frame_Shift_Del_p.A261fs|SPAG1_ENST00000251809.3_Frame_Shift_Del_p.A261fs|SPAG1_ENST00000520508.1_Frame_Shift_Del_p.A261fs|Y_RNA_ENST00000362797.1_RNA	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	261					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GGAATAGTGCTTTTCAGGATT	0.358																																					p.A261fs		Atlas-INDEL	.											.	SPAG1	80	.	0			c.782delC						.						85	85	85					8																	101199429		2203	4300	6503	SO:0001589	frameshift_variant	6674	exon8			.	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.783delT	chr8.hg19:g.101199429delT	ENSP00000373450:p.Ala261fs	87.0	0.0		156.0	10.0	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Frame_Shift_Del	DEL	ENST00000388798.2	hg19	CCDS34930.1																																																																																			.	.		0.358	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		-	101199429	T	-	101199429	7	5	103	1	0	1	0	1	0	0	0	0	14990	1596	56	0	809	0	SPAG1	8	101199429	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3940796	101199429	45164593	557	15180										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106573666	106573666	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acttccagtgggaacaacctGggggccgtttcctgggaaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:106573666delG	ENST00000407775.2	+	4	627	c.377delG	c.(376-378)tggfs	p.W126fs	ZFPM2_ENST00000520492.1_5'UTR|ZFPM2_ENST00000517361.1_5'UTR	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	126					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.W126L(1)		NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GGAACAACCTGGGGGCCGTTT	0.433																																					p.W126fs		Atlas-INDEL	.											.	ZFPM2	219	.	1	Substitution - Missense(1)	lung(1)	c.376delT						.						56	57	57					8																	106573666		1844	4080	5924	SO:0001589	frameshift_variant	23414	exon4			.	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.377delG	chr8.hg19:g.106573666delG	ENSP00000384179:p.Trp126fs	49.0	0.0		155.0	11.0	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Frame_Shift_Del	DEL	ENST00000407775.2	hg19	CCDS47908.1																																																																																			.	.		0.433	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			-	106573666	G	-	106573666	7	5	103	1	0	1	0	1	0	0	0	0	17673	1357	47	0	391	0	ZFPM2	8	106573666	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	5374237	106573666	39790356	558	15181										
TTC35	9694	hgsc.bcm.edu	37	chr8	109468100	109468100	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtttctttttctttttaaatAgatatgatgatgctatacag	6	4	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:109468100A>G	ENST00000220853.3	+	5	340		c.e5-1			NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2							cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											CTTTTTAAATAGATATGATGA	0.229																																					.		Atlas-SNP	.											.	.	.	.	0			c.306-2A>G						.						15	17	17					8																	109468100		2109	4128	6237	SO:0001630	splice_region_variant	9694	exon5			TTAAATAGATATG	BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"tetratricopeptide repeat domain 35"	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.306-1A>G	chr8.hg19:g.109468100A>G		54.0	0.0		117.0	6.0	NM_014673	Q8WUE1	Splice_Site	SNP	ENST00000220853.3	hg19	CCDS6309.1	.	.	.	.	.	.	.	.	.	.	A	19.65	3.867002	0.72065	.	.	ENSG00000104412	ENST00000524143;ENST00000220853;ENST00000519642	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.716	0.77670	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TTC35	109537276	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.688000	0.84153	2.167000	0.68274	0.528000	0.53228	.	.	.		0.229	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673	Intron	G	109468100	A	G	109468100	5	3	103	1	0	0	0	0	0	0	1	0	16718	434	15	2	322	2	TTC35	8	109468100	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2894434	109468100	36895922	559	15182										
TAF2	6873	hgsc.bcm.edu	37	chr8	120759116	120759116	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggaaggtctactgaggccAaaaagtgtgaagtacaagtc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:120759116delA	ENST00000378164.2	-	23	3235	c.2937delT	c.(2935-2937)tttfs	p.F979fs	TAF2_ENST00000519355.1_5'UTR	NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	979					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TACTGAGGCCAAAAAGTGTGA	0.408																																					p.G980fs		Atlas-INDEL	.											.	TAF2	204	.	0			c.2938delG						.						114	100	105					8																	120759116		2203	4300	6503	SO:0001589	frameshift_variant	6873	exon23			.	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2937delT	chr8.hg19:g.120759116delA	ENSP00000367406:p.Phe979fs	74.0	0.0		173.0	13.0	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Frame_Shift_Del	DEL	ENST00000378164.2	hg19	CCDS34937.1																																																																																			.	.		0.408	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		-	120759116	A	-	120759116	7	5	103	1	0	1	0	1	0	0	0	0	15539	127	5	0	678	0	TAF2	8	120759116	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	11291016	120759116	25604906	560	15183										
TAF2	6873	hgsc.bcm.edu	37	chr8	120774703	120774703	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaagaagtttttccatattcAaaaatctggtgatttcttca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:120774703delA	ENST00000378164.2	-	19	2808	c.2510delT	c.(2509-2511)ttgfs	p.L837fs	TAF2_ENST00000519355.1_5'UTR	NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	837					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TTCCATATTCAAAAATCTGGT	0.333																																					p.L837fs		Atlas-INDEL	.											.	TAF2	204	.	0			c.2511delG						.						69	69	69					8																	120774703		2203	4300	6503	SO:0001589	frameshift_variant	6873	exon19			.	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2510delT	chr8.hg19:g.120774703delA	ENSP00000367406:p.Leu837fs	96.0	0.0		184.0	12.0	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Frame_Shift_Del	DEL	ENST00000378164.2	hg19	CCDS34937.1																																																																																			.	.		0.333	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		-	120774703	A	-	120774703	7	5	103	1	0	1	0	1	0	0	0	0	15539	131	5	0	1121	0	TAF2	8	120774703	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	15587	120774703	25589319	561	15184										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125103757	125103757	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggatggaccctactttcaCcctgggaaaatacagatagg	10	10	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:125103757C>T	ENST00000522917.1	+	34	4691	c.4485C>T	c.(4483-4485)caC>caT	p.H1495H	FER1L6_ENST00000399018.1_Silent_p.H1495H|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1495						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CCTACTTTCACCCTGGGAAAA	0.453																																					p.H1495H		Atlas-SNP	.											.	FER1L6	268	.	0			c.C4485T						.						122	113	116					8																	125103757		1879	4104	5983	SO:0001819	synonymous_variant	654463	exon34			CTTTCACCCTGGG	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.4485C>T	chr8.hg19:g.125103757C>T		99.0	0.0		206.0	123.0	NM_001039112		Silent	SNP	ENST00000522917.1	hg19	CCDS43767.1																																																																																			.	.		0.453	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		T	125103757	C	T	125103757	2	4	103	1	0	0	0	0	0	0	0	1	5823	506	18	3		3	FER1L6	8	125103757	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	4329054	125103757	21260265	562	15185										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125115501	125115501	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caagatctctatattccagcAaaaacgtgtgcgtggctggt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:125115501delA	ENST00000522917.1	+	39	5446	c.5240delA	c.(5239-5241)caafs	p.Q1747fs	FER1L6_ENST00000399018.1_Frame_Shift_Del_p.Q1747fs|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1747						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			ATATTCCAGCAAAAACGTGTG	0.483																																					p.Q1747fs		Atlas-INDEL	.											.	FER1L6	268	.	0			c.5239delC						.						151	147	148					8																	125115501		1910	4133	6043	SO:0001589	frameshift_variant	654463	exon39			.	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.5240delA	chr8.hg19:g.125115501delA	ENSP00000428280:p.Gln1747fs	94.0	0.0		188.0	12.0	NM_001039112		Frame_Shift_Del	DEL	ENST00000522917.1	hg19	CCDS43767.1																																																																																			.	.		0.483	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		-	125115501	A	-	125115501	7	5	103	1	0	1	0	1	0	0	0	0	5823	130	5	0	5390	0	FER1L6	8	125115501	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	11744	125115501	21248521	563	15186										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133192520	133192520	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcgcagggaggtggccagaaCattgccttggtttcccacag	13	11	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:133192520C>T	ENST00000388996.4	-	4	1081	c.661G>A	c.(661-663)Gtt>Att	p.V221I	KCNQ3_ENST00000519445.1_Missense_Mutation_p.V221I|KCNQ3_ENST00000521134.1_Missense_Mutation_p.V101I	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	221					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GTGGCCAGAACATTGCCTTGG	0.587																																					p.V221I		Atlas-SNP	.											.	KCNQ3	164	.	0			c.G661A						.						108	93	98					8																	133192520		2203	4300	6503	SO:0001583	missense	3786	exon4			CCAGAACATTGCC	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.661G>A	chr8.hg19:g.133192520C>T	ENSP00000373648:p.Val221Ile	38.0	0.0		99.0	4.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	hg19	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.535878	0.45176	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.97404	-4.37;-4.37;-4.37	5.52	5.52	0.82312	Ion transport (1);	0.182209	0.46758	D	0.000267	D	0.92331	0.7567	N	0.11845	0.185	0.51767	D	0.999933	P;P	0.48089	0.905;0.905	B;B	0.43331	0.416;0.416	D	0.91376	0.5123	10	0.05833	T	0.94	-20.0986	18.4101	0.90549	0.0:1.0:0.0:0.0	.	221;221	E7ET42;O43525	.;KCNQ3_HUMAN	I	221;101;221;210;100	ENSP00000373648:V221I;ENSP00000429799:V101I;ENSP00000428790:V221I	ENSP00000373648:V221I	V	-	1	0	KCNQ3	133261702	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.822000	0.62686	2.610000	0.88304	0.561000	0.74099	GTT	.	.		0.587	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		T	133192520	C	T	133192520	3	4	103	1	0	0	0	0	1	0	0	0	8093	478	17	3	2005	3	KCNQ3	8	133192520	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	8077019	133192520	13171502	564	15187										
EIF2C2	27161	hgsc.bcm.edu	37	chr8	141595382	141595382	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttgaaggcatatccttggatGgggggcggcggcgcaggagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:141595382delG	ENST00000220592.5	-	2	163	c.51delC	c.(49-51)cccfs	p.P17fs	AGO2_ENST00000519980.1_Frame_Shift_Del_p.P17fs|AGO2_ENST00000517293.1_5'UTR	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	17					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										ATCCTTGGATGGGGGGCGGCG	0.592																																					p.I18fs		Atlas-INDEL	.											.	.	.	.	0			c.52delA						.						54	59	57					8																	141595382		2203	4300	6503	SO:0001589	frameshift_variant	27161	exon2			.	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"Argonaute/PIWI family"	3263	protein-coding gene	gene with protein product	"argonaute 2"	606229	"eukaryotic translation initiation factor 2C, 2"	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.51delC	chr8.hg19:g.141595382delG	ENSP00000220592:p.Pro17fs	98.0	0.0		181.0	12.0	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Frame_Shift_Del	DEL	ENST00000220592.5	hg19	CCDS6380.1																																																																																			.	.		0.592	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4			-	141595382	G	-	141595382	7	5	103	1	0	1	0	1	0	0	0	0	5008	1335	47	0	2600	0	EIF2C2	8	141595382	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	8402862	141595382	4768640	565	15188										
SLC45A4	57210	hgsc.bcm.edu	37	chr8	142231725	142231725	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acgccaaagaggacgccaacGcagagggcgaggatgaaggg	17	9	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:142231725G>A	ENST00000024061.3	-	2	535	c.228C>T	c.(226-228)tgC>tgT	p.C76C	SLC45A4_ENST00000519067.1_Silent_p.C76C|SLC45A4_ENST00000433583.2_Silent_p.C69C|SLC45A4_ENST00000517878.1_Silent_p.C127C	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			GGACGCCAACGCAGAGGGCGA	0.622																																					p.C76C		Atlas-SNP	.											.	SLC45A4	71	.	0			c.C228T						.						74	81	79					8																	142231725		2203	4300	6503	SO:0001819	synonymous_variant	57210	exon2			GCCAACGCAGAGG	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"Solute carriers"	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.228C>T	chr8.hg19:g.142231725G>A		101.0	0.0		216.0	32.0	NM_001080431	Q6ZRI2|Q9ULU3	Silent	SNP	ENST00000024061.3	hg19	CCDS34948.1																																																																																			.	.		0.622	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325		A	142231725	G	A	142231725	2	1	103	1	0	0	0	0	0	0	0	1	14658	1079	38	1		1	SLC45A4	8	142231725	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	636343	142231725	4132297	566	15189										
MAPK15	225689	hgsc.bcm.edu	37	chr8	144802914	144802914	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctcctaccgccagacacctCcccagaggccttggacctcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:144802914delC	ENST00000338033.4	+	9	940	c.821delC	c.(820-822)tccfs	p.S274fs	RP11-429J17.5_ENST00000527908.1_RNA	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	274	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				MAPK cascade (GO:0000165)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|SH3 domain binding (GO:0017124)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CCAGACACCTCCCCAGAGGCC	0.667																																					p.S274fs		Atlas-INDEL	.											.	MAPK15	32	.	0			c.820delT						.						33	46	41					8																	144802914		2145	4246	6391	SO:0001589	frameshift_variant	225689	exon9			.	AY065978	CCDS6409.2	8q24.3	2011-06-09			ENSG00000181085	ENSG00000181085		"Mitogen-activated protein kinase cascade / Kinases"	24667	protein-coding gene	gene with protein product	"extracellular signal regulated kinase 8"					11875070	Standard	XM_006716528		Approved	ERK8, ERK7	uc003yzj.3	Q8TD08	OTTHUMG00000146450	ENST00000338033.4:c.821delC	chr8.hg19:g.144802914delC	ENSP00000337691:p.Ser274fs	60.0	0.0		198.0	13.0	NM_139021	Q2TCF9|Q8N362	Frame_Shift_Del	DEL	ENST00000338033.4	hg19	CCDS6409.2																																																																																			.	.		0.667	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021		-	144802914	C	-	144802914	7	5	103	1	0	1	0	1	0	0	0	0	9286	855	30	0	855	0	MAPK15	8	144802914	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2571189	144802914	1561108	567	15190										
NRBP2	340371	hgsc.bcm.edu	37	chr8	144919257	144919257	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggcgtcggggtcttggccTtttggacctcctccgggggt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:144919257delT	ENST00000442628.2	-	14	1356	c.1217delA	c.(1216-1218)aagfs	p.K406fs	NRBP2_ENST00000327830.5_Frame_Shift_Del_p.K163fs	NM_178564.3	NP_848659.2			nuclear receptor binding protein 2											central_nervous_system(2)|kidney(1)|large_intestine(2)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GGTCTTGGCCTTTTGGACCTC	0.612																																					p.K406fs		Atlas-INDEL	.											.	NRBP2	20	.	0			c.1218delG						.						46	52	50					8																	144919257		2203	4300	6503	SO:0001589	frameshift_variant	340371	exon14			.	BC037396	CCDS34959.1, CCDS34959.2	8q24.3	2005-01-24							19339	protein-coding gene	gene with protein product		615563				14702039	Standard	NM_178564		Approved	DKFZp434P086	uc011lkt.2	Q9NSY0		ENST00000442628.2:c.1217delA	chr8.hg19:g.144919257delT	ENSP00000414055:p.Lys406fs	146.0	0.0		231.0	14.0	NM_178564		Frame_Shift_Del	DEL	ENST00000442628.2	hg19	CCDS34959.2																																																																																			.	.		0.612	NRBP2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382247.1	NM_178564		-	144919257	T	-	144919257	7	5	103	1	0	1	0	1	0	0	0	0	10652	1609	56	0	308	0	NRBP2	8	144919257	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	116343	144919257	1444765	568	15191										
PLEC	5339	hgsc.bcm.edu	37	chr8	144991218	144991218	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggagacggcggggctgatGgggtaggaggaggaggatcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:144991218delG	ENST00000322810.4	-	32	13351	c.13182delC	c.(13180-13182)cccfs	p.P4394fs	PLEC_ENST00000354589.3_Frame_Shift_Del_p.P4257fs|PLEC_ENST00000436759.2_Frame_Shift_Del_p.P4284fs|PLEC_ENST00000345136.3_Frame_Shift_Del_p.P4257fs|PLEC_ENST00000527096.1_Frame_Shift_Del_p.P4280fs|PLEC_ENST00000398774.2_Frame_Shift_Del_p.P4225fs|PLEC_ENST00000356346.3_Frame_Shift_Del_p.P4243fs|PLEC_ENST00000357649.2_Frame_Shift_Del_p.P4261fs|PLEC_ENST00000354958.2_Frame_Shift_Del_p.P4235fs	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4394	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CGGGGCTGATGGGGTAGGAGG	0.682																																					p.I4395fs		Atlas-INDEL	.											.	PLEC	1144	.	0			c.13183delA						.						38	48	45					8																	144991218		2042	4190	6232	SO:0001589	frameshift_variant	5339	exon32			.	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.13182delC	chr8.hg19:g.144991218delG	ENSP00000323856:p.Pro4394fs	99.0	0.0		248.0	15.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Frame_Shift_Del	DEL	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.		0.682	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		-	144991218	G	-	144991218	7	5	103	1	0	1	0	1	0	0	0	0	12061	1335	47	0	876	0	PLEC	8	144991218	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	71961	144991218	1372804	569	15192										
KIFC2	90990	hgsc.bcm.edu	37	chr8	145693776	145693776	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcccaagacaccacagaagCcctccgagcccaggtgggca					rs144988968		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:145693776delC	ENST00000301332.2	+	8	1252	c.875delC	c.(874-876)gccfs	p.A292fs	CYHR1_ENST00000306145.5_5'Flank|CYHR1_ENST00000403000.2_5'Flank|KIFC2_ENST00000301331.5_Frame_Shift_Del_p.A40fs|CYHR1_ENST00000424149.2_5'Flank	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	292	Gln-rich.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			ACCACAGAAGCCCTCCGAGCC	0.672																																					p.A292fs		Atlas-INDEL	.											.	KIFC2	53	.	0			c.874delG						.						20	25	23					8																	145693776		2200	4299	6499	SO:0001589	frameshift_variant	90990	exon8			.	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"Kinesins"	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.875delC	chr8.hg19:g.145693776delC	ENSP00000301332:p.Ala292fs	99.0	0.0		163.0	10.0	NM_145754	E9PHB2|Q96NN6	Frame_Shift_Del	DEL	ENST00000301332.2	hg19	CCDS6427.1																																																																																			.	.		0.672	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754		-	145693776	C	-	145693776	7	5	103	1	0	1	0	1	0	0	0	0	8322	739	26	0	905	0	KIFC2	8	145693776	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	702558	145693776	670246	570	15193										
SLC1A1	6505	hgsc.bcm.edu	37	chr9	4561480	4561480	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggattccaacgtatccggAaaaattggtctgcgcgctgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:4561480delA	ENST00000262352.3	+	3	500	c.264delA	c.(262-264)ggafs	p.G88fs	SLC1A1_ENST00000490167.1_3'UTR	NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	88					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	ACGTATCCGGAAAAATTGGTC	0.388																																					p.G88fs		Atlas-INDEL	.											.	SLC1A1	43	.	0			c.263delG						.						328	310	316					9																	4561480		2203	4300	6503	SO:0001589	frameshift_variant	6505	exon3			.		CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"Solute carriers"	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.264delA	chr9.hg19:g.4561480delA	ENSP00000262352:p.Gly88fs	115.0	0.0		140.0	11.0	NM_004170	O75587|Q5VZ24|Q8N199|Q9UEW2	Frame_Shift_Del	DEL	ENST00000262352.3	hg19	CCDS6452.1																																																																																			.	.		0.388	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1			-	4561480	A	-	4561480	7	5	103	1	0	1	0	1	0	0	0	0	14446	233	9	0	274	0	SLC1A1	9	4561480	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10		4561480	136651951	571	15194										
KDM4C	23081	hgsc.bcm.edu	37	chr9	7169999	7169999	+	Intron	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgggcttttggattaattctAaaaaaagccaatgcaacatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:7169999delA	ENST00000381309.3	+	21	3559				KDM4C_ENST00000381306.3_Frame_Shift_Del_p.K1036fs|KDM4C_ENST00000428870.2_Intron|KDM4C_ENST00000442236.2_Intron	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C						histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						GATTAATTCTAAAAAAAGCCA	0.408																																					p.S1034fs		Atlas-INDEL	.											.	KDM4C	186	.	0			c.3102delT						.						45	40	42					9																	7169999		692	1591	2283	SO:0001627	intron_variant	23081	exon21			.	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	17071	protein-coding gene	gene with protein product	"tudor domain containing 14C"	605469	"jumonji domain containing 2C"	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.2994+109A>-	chr9.hg19:g.7169999delA		100.0	0.0		134.0	11.0	NM_001146694	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Frame_Shift_Del	DEL	ENST00000381309.3	hg19	CCDS6471.1																																																																																			.	.		0.408	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		-	7169999	A	-	7169999	6	5	103	0	1	1	0	1	0	0	0	0	8139	363	13	0		0	KDM4C	9	7169999	Intron	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2608519	7169999	134043432	572	15195										
C9orf93	203238	hgsc.bcm.edu	37	chr9	15623298	15623298	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgtgcaaaatatgcataagAaagtagaaaaattagaaaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:15623298delA	ENST00000380701.3	+	7	1037	c.709delA	c.(709-711)aaafs	p.K237fs	CCDC171_ENST00000297641.3_Frame_Shift_Del_p.K237fs|CCDC171_ENST00000535968.1_Frame_Shift_Del_p.K237fs	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	237	Glu-rich.																TATGCATAAGAAAGTAGAAAA	0.363																																					p.K236fs		Atlas-INDEL	.											.	.	.	.	0			c.708delG						.						131	133	132					9																	15623298		2203	4300	6503	SO:0001589	frameshift_variant	203238	exon7			.	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.709delA	chr9.hg19:g.15623298delA	ENSP00000370077:p.Lys237fs	147.0	0.0		180.0	11.0	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Frame_Shift_Del	DEL	ENST00000380701.3	hg19	CCDS6481.1																																																																																			.	.		0.363	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		-	15623298	A	-	15623298	7	5	103	1	0	1	0	1	0	0	0	0	2508	247	9	0	731	0	C9orf93	9	15623298	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	8453299	15623298	125590133	573	15196										
DENND4C	55667	hgsc.bcm.edu	37	chr9	19361944	19361944	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accaagagaacctctgtatgTctcatggaggaattttagta	9	7	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:19361944T>C	ENST00000380432.2	+	25	4685	c.4652T>C	c.(4651-4653)gTc>gCc	p.V1551A	DENND4C_ENST00000602925.1_Missense_Mutation_p.V1787A|DENND4C_ENST00000434457.2_Missense_Mutation_p.V1836A			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1551					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CCTCTGTATGTCTCATGGAGG	0.438																																					p.V1787A		Atlas-SNP	.											.	DENND4C	120	.	0			c.T5360C						.						86	82	83					9																	19361944		2203	4300	6503	SO:0001583	missense	55667	exon29			TGTATGTCTCATG	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.4652T>C	chr9.hg19:g.19361944T>C	ENSP00000369797:p.Val1551Ala	61.0	0.0		97.0	4.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	T	6.248	0.413951	0.11870	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T	0.24151	1.88;1.87	5.02	2.71	0.32032	.	0.813120	0.11399	N	0.568016	T	0.19446	0.0467	L	0.42686	1.345	0.09310	N	1	B;B;B	0.11235	0.002;0.004;0.0	B;B;B	0.12837	0.008;0.008;0.002	T	0.29912	-0.9996	9	.	.	.	-1.8163	5.178	0.15145	0.0:0.1578:0.1516:0.6905	.	881;733;1551	B7Z660;Q5VZ89-3;Q5VZ89	.;.;DEN4C_HUMAN	A	1551;1024;733;881;1024;733;548	ENSP00000305795:V1024A;ENSP00000443804:V881A	.	V	+	2	0	DENND4C	19351944	0.998000	0.40836	0.949000	0.38748	0.152000	0.21847	2.811000	0.47986	0.410000	0.25675	-0.334000	0.08254	GTC	.	.		0.438	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		C	19361944	T	C	19361944	3	2	103	1	0	0	0	0	1	0	0	0	4437	1667	58	2	4750	2	DENND4C	9	19361944	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3738646	19361944	121851487	574	15197										
DDX58	23586	hgsc.bcm.edu	37	chr9	32488833	32488833	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccttttgtccttgtgggaaTtttttaagatgatgttcaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:32488833delT	ENST00000379883.2	-	7	1009	c.852delA	c.(850-852)aaafs	p.K284fs	DDX58_ENST00000542096.1_Frame_Shift_Del_p.K213fs|DDX58_ENST00000379868.1_Frame_Shift_Del_p.K81fs|DDX58_ENST00000545044.1_Frame_Shift_Del_p.K81fs|DDX58_ENST00000379882.1_Frame_Shift_Del_p.K239fs	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	284	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Interaction with ZC3HAV1.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		CTTGTGGGAATTTTTTAAGAT	0.323																																					p.F285fs		Atlas-INDEL	.											.	DDX58	82	.	0			c.853delT						.						72	65	68					9																	32488833		2203	4300	6503	SO:0001589	frameshift_variant	23586	exon7			.	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.852delA	chr9.hg19:g.32488833delT	ENSP00000369213:p.Lys284fs	140.0	0.0		187.0	12.0	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Frame_Shift_Del	DEL	ENST00000379883.2	hg19	CCDS6526.1																																																																																			.	.		0.323	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		-	32488833	T	-	32488833	7	5	103	1	0	1	0	1	0	0	0	0	4377	1490	52	0	1973	0	DDX58	9	32488833	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	13126889	32488833	108724598	575	15198										
NOL6	65083	hgsc.bcm.edu	37	chr9	33464082	33464082	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacagagtttttgcggtcttGgggggtaacaatgaccatga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:33464082delG	ENST00000379471.2	-	22	2944	c.2857delC	c.(2857-2859)caafs	p.Q953fs	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Frame_Shift_Del_p.Q901fs			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	953					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		TTGCGGTCTTGGGGGGTAACA	0.567																																					p.Q953fs		Atlas-INDEL	.											.	NOL6	85	.	0			c.2858delA						.						140	125	130					9																	33464082		2203	4300	6503	SO:0001589	frameshift_variant	65083	exon22			.	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"nucleolar protein family 6 (RNA-associated)"			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.2857delC	chr9.hg19:g.33464082delG	ENSP00000368784:p.Gln953fs	137.0	0.0		167.0	11.0	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Frame_Shift_Del	DEL	ENST00000379471.2	hg19																																																																																				.	.		0.567	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		-	33464082	G	-	33464082	7	5	103	1	0	1	0	1	0	0	0	0	10534	1357	47	0	603	0	NOL6	9	33464082	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	975249	33464082	107749349	576	15199										
UBAP2	55833	hgsc.bcm.edu	37	chr9	34017099	34017099	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtgctgctgaaatctgtggTttttcccgagcacctcgaca					rs566017101		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:34017099delT	ENST00000379238.1	-	2	165	c.48delA	c.(46-48)aaafs	p.K16fs	UBAP2_ENST00000539807.1_5'UTR|UBAP2_ENST00000360802.1_Frame_Shift_Del_p.K16fs|RNU7-36P_ENST00000516597.1_RNA|UBAP2_ENST00000480885.1_5'UTR|UBAP2_ENST00000418786.2_Frame_Shift_Del_p.K16fs|UBAP2_ENST00000449054.1_Frame_Shift_Del_p.K16fs|UBAP2_ENST00000379239.4_Intron					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		AAATCTGTGGTTTTTCCCGAG	0.343																																					p.P17fs		Pindel	.											.	UBAP2	82	.	0			c.49delC						.						140	120	127					9																	34017099		2203	4300	6503	SO:0001589	frameshift_variant	55833	exon2			.	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.48delA	chr9.hg19:g.34017099delT	ENSP00000368540:p.Lys16fs	107.0	0.0		135.0	11.0	NM_018449		Frame_Shift_Del	DEL	ENST00000379238.1	hg19	CCDS6547.1																																																																																			.	.		0.343	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		-	34017099	T	-	34017099	7	5	103	1	0	1	0	1	0	0	0	0	16852	1722	60	0	3423	0	UBAP2	9	34017099	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	553017	34017099	107196332	577	15200										
KIF24	347240	hgsc.bcm.edu	37	chr9	34306393	34306393	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttttcgaacacaaactctgaTtttctccatctcagtccaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:34306393delT	ENST00000402558.2	-	2	694	c.670delA	c.(670-672)atcfs	p.I224fs	KIF24_ENST00000379166.2_Frame_Shift_Del_p.I224fs|KIF24_ENST00000379174.3_Frame_Shift_Del_p.I224fs|KIF24_ENST00000345050.2_Frame_Shift_Del_p.I224fs			Q5T7B8	KIF24_HUMAN	kinesin family member 24	224	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			CAAACTCTGATTTTCTCCATC	0.363																																					p.I224fs		Atlas-INDEL	.											.	KIF24	64	.	0			c.671delT						.						182	172	175					9																	34306393		1818	4082	5900	SO:0001589	frameshift_variant	347240	exon3			.	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"Kinesins", "Sterile alpha motif (SAM) domain containing"	19916	protein-coding gene	gene with protein product		613747	"chromosome 9 open reading frame 48"	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.670delA	chr9.hg19:g.34306393delT	ENSP00000384433:p.Ile224fs	192.0	0.0		207.0	13.0	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Frame_Shift_Del	DEL	ENST00000402558.2	hg19	CCDS6551.2																																																																																			.	.		0.363	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5			-	34306393	T	-	34306393	7	5	103	1	0	1	0	1	0	0	0	0	8301	1493	52	0	3480	0	KIF24	9	34306393	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	289294	34306393	106907038	578	15201										
DNAI1	27019	hgsc.bcm.edu	37	chr9	34500786	34500787	+	Missense_Mutation	DNP	GG	GG	AT													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggtaccctgctgccgctctGgaagttccaaaatgacaaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:34500786_34500787GG>AT	ENST00000242317.4	+	11	1139_1140	c.968_969GG>AT	c.(967-969)tGG>tAT	p.W323Y		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	323					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)			autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		CTGCCGCTCTGGAAGTTCCAAA	0.53									Kartagener syndrome		OREG0019152	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W323X|p.W323C		Atlas-SNP	.											.	DNAI1	72	.	0			c.G968A|c.G969T						.																																			SO:0001583	missense	27019	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CGCTCTGGAAGTT|GCTCTGGAAGTTC	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"Axonemal dyneins", "WD repeat domain containing"	2954	protein-coding gene	gene with protein product		604366	"dynein, axonemal, intermediate polypeptide 1"			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	Exception_encountered	chr9.hg19:g.34500786_34500787delinsAT	ENSP00000242317:p.Trp323Tyr	83.0|82.0	0.0	848	98.0	4.0	NM_012144	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000242317.4	hg19	CCDS6557.1																																																																																			.	.		0.53	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1			AT	34500787	GG	AT	34500786	3	1	103	1	0	0	0	0	1	0	0	0	4611	1357	47	3	1010	3	DNAI1	9	34500786	Missense_Mutation	DNP	GG	TCGA-DD-A1EG-01A-11D-A20W-10	194393	34500786	106712645	579	15202										
CNTFR	1271	hgsc.bcm.edu	37	chr9	34556395	34556395	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcactggccgggctaccacaTtttctggaggatcaggcttc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:34556395delT	ENST00000378980.3	-	7	919	c.626delA	c.(625-627)aatfs	p.N209fs	CNTFR_ENST00000351266.4_Frame_Shift_Del_p.N209fs	NM_001207011.1|NM_147164.2	NP_001193940.1|NP_671693.1	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor	209	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brainstem development (GO:0003360)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|skeletal muscle organ development (GO:0060538)|suckling behavior (GO:0001967)	anchored component of membrane (GO:0031225)|CNTFR-CLCF1 complex (GO:0097059)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|cytokine binding (GO:0019955)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(4)|skin(1)	15	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)		GGCTACCACATTTTCTGGAGG	0.552																																					p.N209fs		Atlas-INDEL	.											.	CNTFR	46	.	0			c.627delT						.						67	65	66					9																	34556395		2203	4300	6503	SO:0001589	frameshift_variant	1271	exon7			.	M73238	CCDS6558.1	9p13	2013-02-11			ENSG00000122756	ENSG00000122756		"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2170	protein-coding gene	gene with protein product		118946				1648265	Standard	NM_001842		Approved		uc003zuq.2	P26992	OTTHUMG00000019821	ENST00000378980.3:c.626delA	chr9.hg19:g.34556395delT	ENSP00000368265:p.Asn209fs	90.0	0.0		140.0	10.0	NM_147164	Q5U050	Frame_Shift_Del	DEL	ENST00000378980.3	hg19	CCDS6558.1																																																																																			.	.		0.552	CNTFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052176.1			-	34556395	T	-	34556395	7	5	103	1	0	1	0	1	0	0	0	0	3640	1493	52	0	508	0	CNTFR	9	34556395	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	55609	34556395	106657036	580	15203										
TPM2	7169	hgsc.bcm.edu	37	chr9	35683240	35683240	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctgggcatagacttcatcTggggggggtccagggagggg	19	7	3	1	rs368128547|rs149115565	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:35683240T>G	ENST00000360958.2	-	9	877		c.e9-2		TPM2_ENST00000378300.5_Intron|TPM2_ENST00000378292.3_Intron|TPM2_ENST00000329305.2_Intron	NM_003289.3	NP_003280.2	P07951	TPM2_HUMAN	tropomyosin 2 (beta)						muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)	cytosol (GO:0005829)|muscle thin filament tropomyosin (GO:0005862)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_epithelial(49;0.121)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			AGACTTCATCTGGGGGGGGTC	0.547																																					.		Atlas-SNP	.											.,1	TPM2	64	.	0			c.773-2A>C						.						95	66	76					9																	35683240		2186	4268	6454	SO:0001630	splice_region_variant	7169	exon10			TTCATCTGGGGGG		CCDS6586.1, CCDS6587.1	9p13	2014-09-17	2003-12-02		ENSG00000198467	ENSG00000198467		"Tropomyosins"	12011	protein-coding gene	gene with protein product	"nemaline myopathy type 4"	190990	"arthrogryposis multiplex congenital, distal, type 1"	AMCD1		7606936	Standard	NM_003289		Approved	DA1, NEM4	uc003zxq.3	P07951	OTTHUMG00000019878	ENST00000360958.2:c.773-2A>C	chr9.hg19:g.35683240T>G		216.0	2.0		237.0	14.0	NM_003289	A6NM85|P06468|Q13894|Q53FM4|Q5TCU4|Q5TCU7|Q9UH67	Splice_Site	SNP	ENST00000360958.2	hg19	CCDS6587.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.285674	0.80803	.	.	ENSG00000198467	ENST00000360958	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.286	0.66247	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TPM2	35673240	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	7.793000	0.85851	2.224000	0.72417	0.533000	0.62120	.	.	.		0.547	TPM2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052376.1	NM_003289	Intron	G	35683240	T	G	35683240	5	3	103	1	0	0	0	0	0	0	1	0	16421	1594	55	5	174	5	TPM2	9	35683240	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1126845	35683240	105530191	581	15204										
ZCCHC7	84186	hgsc.bcm.edu	37	chr9	37349430	37349430	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atattgctatcactgcgcgcAaaaaggccattatggacacg					rs555354129		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:37349430delA	ENST00000336755.5	+	7	1170	c.1064delA	c.(1063-1065)caafs	p.Q355fs	ZCCHC7_ENST00000534928.1_Frame_Shift_Del_p.Q65fs|ZCCHC7_ENST00000461038.1_3'UTR	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	355						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	30				GBM - Glioblastoma multiforme(29;0.0137)		CACTGCGCGCAAAAAGGCCAT	0.438																																					p.Q355fs		Atlas-INDEL	.											.	ZCCHC7	56	.	0			c.1063delC						.						154	124	134					9																	37349430		2203	4300	6503	SO:0001589	frameshift_variant	84186	exon7			.	AK026264	CCDS6608.2	9p13.1	2008-05-02			ENSG00000147905	ENSG00000147905		"Zinc fingers, CCHC domain containing"	26209	protein-coding gene	gene with protein product							Standard	NM_032226		Approved	FLJ22611, AIR1	uc003zzq.3	Q8N3Z6	OTTHUMG00000019915	ENST00000336755.5:c.1064delA	chr9.hg19:g.37349430delA	ENSP00000337839:p.Gln355fs	113.0	0.0		147.0	11.0	NM_032226	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Frame_Shift_Del	DEL	ENST00000336755.5	hg19	CCDS6608.2																																																																																			.	.		0.438	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226		-	37349430	A	-	37349430	7	5	103	1	0	1	0	1	0	0	0	0	17608	130	5	0	1086	0	ZCCHC7	9	37349430	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1666190	37349430	103864001	582	15205										
FAM75A1	647060	hgsc.bcm.edu	37	chr9	39358166	39358166	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagagcacctgatggagcctCccagtcctctcatgagccta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:39358166delC	ENST00000377647.3	+	4	433	c.404delC	c.(403-405)tccfs	p.S135fs	SPATA31A1_ENST00000473440.1_3'UTR	NM_001085452.1	NP_001078921.1	Q5TZJ5	S31A1_HUMAN	SPATA31 subfamily A, member 1	135	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GATGGAGCCTCCCAGTCCTCT	0.597																																					p.S135fs		Atlas-INDEL	.											.	.	.	.	0			c.403delT						.						1	1	1					9																	39358166		51	27	78	SO:0001589	frameshift_variant	647060	exon4			.		CCDS43808.1	9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000204849	ENSG00000204849			23394	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 36", "family with sequence similarity 75, member A1"	C9orf36, FAM75A1		20850414	Standard	XM_006716851		Approved	DKFZP434B204, C9orf36A, OTTHUMG00000013156		Q5TZJ5	OTTHUMG00000013156	ENST00000377647.3:c.404delC	chr9.hg19:g.39358166delC	ENSP00000366875:p.Ser135fs	135.0	0.0		157.0	10.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000377647.3	hg19	CCDS43808.1																																																																																			.	.		0.597	SPATA31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036910.1	NM_001085452		-	39358166	C	-	39358166	7	5	103	1	0	1	0	1	0	0	0	0	5627	855	30	0	418	0	FAM75A1	9	39358166	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2008736	39358166	101855265	583	15206										
FAM75A6	389730	hgsc.bcm.edu	37	chr9	43625186	43625186	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctttgaaaaaatccactgAaaaaattgcttgatgttttc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:43625186delA	ENST00000332857.6	-	4	3529	c.3501delT	c.(3499-3501)tttfs	p.F1167fs	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	1167					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AAATCCACTGAAAAAATTGCT	0.428																																					p.Q1168fs		Atlas-INDEL	.											FAM75A6,bladder,carcinoma,0,1	.	.	.	0			c.3502delC						.						128	134	132					9																	43625186		632	1548	2180	SO:0001589	frameshift_variant	389730	exon4			.		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"family with sequence similarity 75, member A6"	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.3501delT	chr9.hg19:g.43625186delA	ENSP00000329825:p.Phe1167fs	362.0	0.0		284.0	19.0	NM_001145196		Frame_Shift_Del	DEL	ENST00000332857.6	hg19	CCDS47973.1																																																																																			.	.		0.428	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196		-	43625186	A	-	43625186	7	5	103	1	0	1	0	1	0	0	0	0	5630	243	9	0	534	0	FAM75A6	9	43625186	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	4267020	43625186	97588245	584	15207										
ANKRD20A1	84210	hgsc.bcm.edu	37	chr9	67934789	67934789	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaatggtggaatttttattgAaaaagaaagcaagttcacat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:67934789delA	ENST00000377477.2	+	4	671	c.559delA	c.(559-561)aaafs	p.K189fs	RNU6-368P_ENST00000391117.1_RNA	NM_032250.3	NP_115626.2	Q5TYW2	A20A1_HUMAN	ankyrin repeat domain 20 family, member A1	189						plasma membrane (GO:0005886)				kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	11						ATTTTTATTGAAAAAGAAAGC	0.313																																					p.L186fs		Atlas-INDEL	.											.	ANKRD20A1	16	.	0			c.558delG						.						1	1	1					9																	67934789		284	618	902	SO:0001589	frameshift_variant	84210	exon4			.	AL136793	CCDS6620.1	9p12	2014-04-16	2005-08-23	2005-08-23	ENSG00000196774	ENSG00000260691		"Ankyrin repeat domain containing"	23665	protein-coding gene	gene with protein product			"ankyrin repeat domain 20A"	ANKRD20A			Standard	NM_032250		Approved	DKFZp434A171		Q5TYW2	OTTHUMG00000188594	ENST00000377477.2:c.559delA	chr9.hg19:g.67934789delA	ENSP00000366697:p.Lys189fs	198.0	0.0		193.0	12.0	NM_032250	Q9H0H6	Frame_Shift_Del	DEL	ENST00000377477.2	hg19	CCDS6620.1																																																																																			.	.		0.313	ANKRD20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083800.1			-	67934789	A	-	67934789	7	5	103	1	0	1	0	1	0	0	0	0	648	247	9	0	573	0	ANKRD20A1	9	67934789	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	24309603	67934789	73278642	585	15208										
ANKRD20A4	728747	hgsc.bcm.edu	37	chr9	69386012	69386012	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgagagcacctcactggcagAaaaactgctttcccatggtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:69386012delA	ENST00000357336.3	+	3	730	c.449delA	c.(448-450)gaafs	p.E150fs		NM_001098805.1	NP_001092275.1	Q4UJ75	A20A4_HUMAN	ankyrin repeat domain 20 family, member A4	150										breast(1)|large_intestine(1)|liver(1)|lung(9)|pancreas(2)|skin(2)	16						TCACTGGCAGAAAAACTGCTT	0.418																																					p.E150fs		Atlas-INDEL	.											.	ANKRD20A4	38	.	0			c.448delG						.						1	1	1					9																	69386012		77	175	252	SO:0001589	frameshift_variant	728747	exon3			.		CCDS43828.1	9q21.11	2013-01-10			ENSG00000172014	ENSG00000172014		"Ankyrin repeat domain containing"	31982	protein-coding gene	gene with protein product							Standard	NM_001098805		Approved	OTTHUMG00000066855	uc004afn.3	Q4UJ75	OTTHUMG00000066855	ENST00000357336.3:c.449delA	chr9.hg19:g.69386012delA	ENSP00000349891:p.Glu150fs	99.0	0.0		91.0	11.0	NM_001098805		Frame_Shift_Del	DEL	ENST00000357336.3	hg19	CCDS43828.1																																																																																			.	.		0.418	ANKRD20A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143287.3	NM_001098805		-	69386012	A	-	69386012	7	5	103	1	0	1	0	1	0	0	0	0	650	246	9	0	459	0	ANKRD20A4	9	69386012	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1451223	69386012	71827419	586	15209										
DAPK1	1612	hgsc.bcm.edu	37	chr9	90296403	90296403	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agctcaagctgtttggccacTcgggatccgggaaaaccacc	11	13	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:90296403T>C	ENST00000408954.3	+	20	2421	c.2086T>C	c.(2086-2088)Tcg>Ccg	p.S696P	DAPK1_ENST00000472284.1_Missense_Mutation_p.S696P|DAPK1_ENST00000469640.2_Missense_Mutation_p.S696P|DAPK1_ENST00000491893.1_Missense_Mutation_p.S696P|DAPK1_ENST00000358077.5_Missense_Mutation_p.S696P	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	696					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						GTTTGGCCACTCGGGATCCGG	0.547									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.S696P		Atlas-SNP	.											.	DAPK1	329	.	0			c.T2086C						.						108	111	110					9																	90296403		1949	4154	6103	SO:0001583	missense	1612	exon20	Familial Cancer Database	Familial CLL	GGCCACTCGGGAT	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.2086T>C	chr9.hg19:g.90296403T>C	ENSP00000386135:p.Ser696Pro	109.0	0.0		112.0	6.0	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	hg19	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.742742	0.30865	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.68181	-0.31;-0.31;-0.3;-0.31;-0.25	5.17	5.17	0.71159	.	0.336419	0.21420	N	0.074823	T	0.51381	0.1671	N	0.21448	0.665	0.48901	D	0.999726	B;B;B	0.18310	0.001;0.027;0.001	B;B;B	0.15484	0.001;0.013;0.001	T	0.50717	-0.8795	10	0.51188	T	0.08	.	10.1557	0.42820	0.1488:0.0:0.0:0.8511	.	696;250;696	B7ZLE7;P53355-2;P53355	.;.;DAPK1_HUMAN	P	696	ENSP00000350785:S696P;ENSP00000417076:S696P;ENSP00000418885:S696P;ENSP00000386135:S696P;ENSP00000419026:S696P	ENSP00000350785:S696P	S	+	1	0	DAPK1	89486223	1.000000	0.71417	0.997000	0.53966	0.437000	0.31866	1.944000	0.40263	2.189000	0.69895	0.459000	0.35465	TCG	.	.		0.547	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		C	90296403	T	C	90296403	3	2	103	1	0	0	0	0	1	0	0	0	4237	1551	54	2	2160	2	DAPK1	9	90296403	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	20910391	90296403	50917028	587	15210										
C9orf79	286234	hgsc.bcm.edu	37	chr9	90502871	90502871	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtccacctcccagagtgtgTctggtaagaacatgacagct	10	11	1	3	rs201052734		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:90502871T>C	ENST00000325643.5	+	4	3535	c.3469T>C	c.(3469-3471)Tct>Cct	p.S1157P		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1157					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCAGAGTGTGTCTGGTAAGAA	0.637																																					p.S1157P		Atlas-SNP	.											.	.	.	.	0			c.T3469C						.						36	40	39					9																	90502871		2203	4300	6503	SO:0001583	missense	286234	exon4			AGTGTGTCTGGTA	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.3469T>C	chr9.hg19:g.90502871T>C	ENSP00000322640:p.Ser1157Pro	82.0	0.0		87.0	5.0	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	hg19	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	t	11.91	1.780467	0.31502	.	.	ENSG00000177992	ENST00000325643	T	0.05258	3.47	3.03	-4.74	0.03249	.	1.526110	0.04322	N	0.350822	T	0.08223	0.0205	N	0.12182	0.205	0.09310	N	1	D	0.76494	0.999	D	0.71656	0.974	T	0.21484	-1.0244	10	0.31617	T	0.26	.	4.5911	0.12307	0.6368:0.1188:0.0:0.2444	.	1157	Q6ZUB1	CI079_HUMAN	P	1157	ENSP00000322640:S1157P	ENSP00000322640:S1157P	S	+	1	0	C9orf79	89692691	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.864000	0.04254	-0.879000	0.04002	0.533000	0.62120	TCT	.	T|0.999;A|0.001		0.637	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		C	90502871	T	C	90502871	3	2	103	1	0	0	0	0	1	0	0	0	2499	1667	58	2	3483	2	C9orf79	9	90502871	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	206468	90502871	50710560	588	15211										
SECISBP2	79048	hgsc.bcm.edu	37	chr9	91943618	91943618	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggaaatccagaatcattgcAaaaaatgtatctacctccaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:91943618delA	ENST00000375807.3	+	5	689	c.618delA	c.(616-618)gcafs	p.A206fs	SECISBP2_ENST00000470305.1_3'UTR|SECISBP2_ENST00000339901.4_Frame_Shift_Del_p.A133fs|SECISBP2_ENST00000534113.2_Frame_Shift_Del_p.A138fs	NM_001282688.1|NM_001282690.1|NM_024077.3	NP_001269617.1|NP_001269619.1|NP_076982.3	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	206					translation (GO:0006412)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)	p.N208fs*8(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2)	32						GAATCATTGCAAAAAATGTAT	0.358																																					p.A206fs		Atlas-INDEL	.											.,1	SECISBP2	64	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.617delC						.						82	75	78					9																	91943618		2203	4300	6503	SO:0001589	frameshift_variant	79048	exon5			.	AF380995	CCDS6683.1, CCDS65076.1, CCDS65077.1	9q22	2008-02-05			ENSG00000187742	ENSG00000187742			30972	protein-coding gene	gene with protein product		607693				11230166	Standard	XM_005252193		Approved		uc004aqj.1	Q96T21	OTTHUMG00000020182	ENST00000375807.3:c.618delA	chr9.hg19:g.91943618delA	ENSP00000364965:p.Ala206fs	165.0	0.0		186.0	12.0	NM_024077	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Frame_Shift_Del	DEL	ENST00000375807.3	hg19	CCDS6683.1																																																																																			.	.		0.358	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077		-	91943618	A	-	91943618	7	5	103	1	0	1	0	1	0	0	0	0	14021	117	5	0	636	0	SECISBP2	9	91943618	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1440747	91943618	49269813	589	15212										
ZNF484	83744	hgsc.bcm.edu	37	chr9	95609839	95609839	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cattcagtacatacataaggTttttctcctgtatggatttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:95609839delT	ENST00000375495.3	-	5	1378	c.1230delA	c.(1228-1230)aaafs	p.K410fs	ZNF484_ENST00000395506.3_Frame_Shift_Del_p.K412fs|ZNF484_ENST00000332591.6_Frame_Shift_Del_p.K374fs|ANKRD19P_ENST00000473204.1_RNA|ZNF484_ENST00000395505.2_Frame_Shift_Del_p.K374fs	NM_031486.2	NP_113674.1	Q5JVG2	ZN484_HUMAN	zinc finger protein 484	410					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|kidney(8)|large_intestine(10)|lung(10)|prostate(2)	33						ATACATAAGGTTTTTCTCCTG	0.373																																					p.P413fs		Atlas-INDEL	.											.	ZNF484	81	.	0			c.1237delC						.						69	74	72					9																	95609839		2203	4300	6503	SO:0001589	frameshift_variant	83744	exon4			.	AK091203	CCDS35066.1, CCDS35067.1, CCDS59136.1	9q22.32	2013-01-08			ENSG00000127081	ENSG00000127081		"Zinc fingers, C2H2-type", "-"	23385	protein-coding gene	gene with protein product							Standard	NM_001007101		Approved	BA526D8.4, FLJ33884	uc004asu.2	Q5JVG2	OTTHUMG00000020236	ENST00000375495.3:c.1230delA	chr9.hg19:g.95609839delT	ENSP00000364645:p.Lys410fs	98.0	0.0		146.0	11.0	NM_001261458	B1AL89|B4DRI2	Frame_Shift_Del	DEL	ENST00000375495.3	hg19	CCDS35066.1																																																																																			.	.		0.373	ZNF484-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053111.2	XM_046861		-	95609839	T	-	95609839	7	5	103	1	0	1	0	1	0	0	0	0	17952	1722	60	0	1332	0	ZNF484	9	95609839	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3666221	95609839	45603592	590	15213										
FAM120AOS	158293	hgsc.bcm.edu	37	chr9	96209929	96209929	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aatgatcttagtgttggtggTtttgtggttttctttgagac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:96209929delT	ENST00000375412.5	-	3	1617	c.735delA	c.(733-735)aaafs	p.K245fs	FAM120AOS_ENST00000423591.1_Frame_Shift_Del_p.K63fs|FAM120AOS_ENST00000479094.1_5'UTR	NM_198841.2	NP_942138.2	Q5T036	F120S_HUMAN	family with sequence similarity 120A opposite strand	245										kidney(1)|large_intestine(1)|lung(3)|skin(1)	6						GTGTTGGTGGTTTTGTGGTTT	0.353																																					p.P246fs		Atlas-INDEL	.											FAM120AOS,NS,carcinoma,0,1	FAM120AOS	13	.	0			c.736delC						.						225	210	215					9																	96209929		2203	4300	6503	SO:0001589	frameshift_variant	158293	exon3			.	AK056096	CCDS6705.1	9q22.32	2008-02-05	2006-07-04	2006-07-04	ENSG00000188938	ENSG00000188938			23389	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 10 opposite strand"	C9orf10OS		14585507	Standard	NM_198841		Approved		uc004atu.4	Q5T036	OTTHUMG00000020251	ENST00000375412.5:c.735delA	chr9.hg19:g.96209929delT	ENSP00000364561:p.Lys245fs	149.0	0.0		156.0	12.0	NM_198841	A6NN20	Frame_Shift_Del	DEL	ENST00000375412.5	hg19	CCDS6705.1																																																																																			.	.		0.353	FAM120AOS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053154.1			-	96209929	T	-	96209929	7	5	103	1	0	1	0	1	0	0	0	0	5421	1722	60	0	39	0	FAM120AOS	9	96209929	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	600090	96209929	45003502	591	15214										
ZNF782	158431	hgsc.bcm.edu	37	chr9	99581649	99581649	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caagaaaagcttttctacttTcattatattcaaaatcttgc	3	8	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:99581649T>C	ENST00000481138.1	-	6	1317	c.656A>G	c.(655-657)gAa>gGa	p.E219G	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Missense_Mutation_p.E87G	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	219					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				TTTTCTACTTTCATTATATTC	0.343																																					p.E219G		Atlas-SNP	.											.	ZNF782	64	.	0			c.A656G						.						51	54	53					9																	99581649		2201	4297	6498	SO:0001583	missense	158431	exon6			CTACTTTCATTAT	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"Zinc fingers, C2H2-type", "-"	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.656A>G	chr9.hg19:g.99581649T>C	ENSP00000419397:p.Glu219Gly	61.0	0.0		75.0	4.0	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	hg19	CCDS35075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.43|11.43	1.636755|1.636755	0.29068|0.29068	.|.	.|.	ENSG00000196597|ENSG00000196597	ENST00000481138;ENST00000535338|ENST00000289032	T;T|.	0.07327|.	3.37;3.2|.	3.38|3.38	2.25|2.25	0.28309|0.28309	.|.	.|.	.|.	.|.	.|.	T|.	0.41604|.	0.1166|.	L|L	0.56199|0.56199	1.76|1.76	0.09310|0.09310	N|N	1|1	B|.	0.09022|.	0.002|.	B|.	0.06405|.	0.002|.	T|.	0.27365|.	-1.0076|.	9|.	0.66056|.	D|.	0.02|.	.|.	6.9339|6.9339	0.24457|0.24457	0.0:0.1156:0.0:0.8843|0.0:0.1156:0.0:0.8843	.|.	219|.	Q6ZMW2|.	ZN782_HUMAN|.	G|W	219;87|207	ENSP00000419397:E219G;ENSP00000440624:E87G|.	ENSP00000419397:E219G|.	E|X	-|-	2|3	0|0	ZNF782|ZNF782	98621470|98621470	0.000000|0.000000	0.05858|0.05858	0.059000|0.059000	0.19551|0.19551	0.307000|0.307000	0.27823|0.27823	0.451000|0.451000	0.21779|0.21779	0.691000|0.691000	0.31592|0.31592	0.529000|0.529000	0.55759|0.55759	GAA|TGA	.	.		0.343	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		C	99581649	T	C	99581649	3	2	103	1	0	0	0	0	1	0	0	0	18170	1783	62	2	1447	2	ZNF782	9	99581649	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3371720	99581649	41631782	592	15215										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113132231	113132231	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttatgtcccgtccaagaagAaagacagtgacatcggtttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:113132231delA	ENST00000401783.2	-	47	11002	c.10666delT	c.(10666-10668)tctfs	p.S3557fs	SVEP1_ENST00000374469.1_Frame_Shift_Del_p.S3534fs|SVEP1_ENST00000297826.5_Frame_Shift_Del_p.S1483fs|RNU6-1039P_ENST00000383931.1_RNA	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3557	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GTCCAAGAAGAAAGACAGTGA	0.368																																					p.S3556fs		Atlas-INDEL	.											.	SVEP1	326	.	0			c.10667delC						.						90	83	85					9																	113132231		1858	4098	5956	SO:0001589	frameshift_variant	79987	exon47			.	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.10666delT	chr9.hg19:g.113132231delA	ENSP00000384917:p.Ser3557fs	125.0	0.0		121.0	10.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Frame_Shift_Del	DEL	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.		0.368	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				-	113132231	A	-	113132231	7	5	103	1	0	1	0	1	0	0	0	0	15435	246	9	0	57	0	SVEP1	9	113132231	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	13550582	113132231	28081200	593	15216										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113191515	113191515	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttatattttccggactagaAcacttcactggttcacacac	5	11	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:113191515A>G	ENST00000401783.2	-	35	6051	c.5715T>C	c.(5713-5715)tgT>tgC	p.C1905C	SVEP1_ENST00000374469.1_Silent_p.C1882C|SVEP1_ENST00000297826.5_5'Flank	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1905	Sushi 9. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CCGGACTAGAACACTTCACTG	0.393																																					p.C1905C		Atlas-SNP	.											.	SVEP1	326	.	0			c.T5715C						.						38	36	37					9																	113191515		1840	4089	5929	SO:0001819	synonymous_variant	79987	exon35			ACTAGAACACTTC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.5715T>C	chr9.hg19:g.113191515A>G		57.0	0.0		43.0	4.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.		0.393	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	113191515	A	G	113191515	2	3	103	1	0	0	0	0	0	0	0	1	15435	41	2	2		2	SVEP1	9	113191515	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	59284	113191515	28021916	594	15217										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114213753	114213753	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagagtttgagcaaaacaggAggaaggaatttagatataat	12	2	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:114213753A>G	ENST00000338205.5	-	2	324	c.105T>C	c.(103-105)ccT>ccC	p.P35P	KIAA0368_ENST00000259335.4_Silent_p.P213P			Q5VYK3	ECM29_HUMAN	KIAA0368	41					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						GCAAAACAGGAGGAAGGAATT	0.358																																					p.P213P		Atlas-SNP	.											.	KIAA0368	144	.	0			c.T639C						.						59	55	56					9																	114213753		1831	4091	5922	SO:0001819	synonymous_variant	23392	exon4			AACAGGAGGAAGG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.105T>C	chr9.hg19:g.114213753A>G		60.0	0.0		75.0	5.0	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	hg19																																																																																				.	.		0.358	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		G	114213753	A	G	114213753	2	3	103	1	0	0	0	0	0	0	0	1	8180	291	11	2		2	KIAA0368	9	114213753	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1022238	114213753	26999678	595	15218										
TNFSF8	944	hgsc.bcm.edu	37	chr9	117666406	117666406	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacactgtcaccagggcctgTtttttgatatgcttgttgat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:117666406delT	ENST00000223795.2	-	4	623	c.510delA	c.(508-510)aaafs	p.K170fs	TNFSF8_ENST00000474301.1_Intron	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	170					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						CCAGGGCCTGTTTTTTGATAT	0.428																																					p.Q171fs		Atlas-INDEL	.											.	TNFSF8	34	.	0			c.511delC						.						205	180	189					9																	117666406		2203	4300	6503	SO:0001589	frameshift_variant	944	exon4			.	L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.510delA	chr9.hg19:g.117666406delT	ENSP00000223795:p.Lys170fs	255.0	0.0		255.0	16.0	NM_001244	O43404	Frame_Shift_Del	DEL	ENST00000223795.2	hg19	CCDS6810.1																																																																																			.	.		0.428	TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1			-	117666406	T	-	117666406	7	5	103	1	0	1	0	1	0	0	0	0	16326	1722	60	0	198	0	TNFSF8	9	117666406	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3452653	117666406	23547025	596	15219										
TLR4	7099	hgsc.bcm.edu	37	chr9	120476060	120476060	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccctccaggttcttgattacAgtctcaatcacataatgact	5	12	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:120476060A>G	ENST00000355622.6	+	3	1755	c.1654A>G	c.(1654-1656)Agt>Ggt	p.S552G	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.S512G	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	552					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	TCTTGATTACAGTCTCAATCA	0.373																																					p.S552G		Atlas-SNP	.											.	TLR4	220	.	0			c.A1654G						.						91	82	85					9																	120476060		2203	4300	6503	SO:0001583	missense	7099	exon3			GATTACAGTCTCA	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"CD molecules"	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.1654A>G	chr9.hg19:g.120476060A>G	ENSP00000363089:p.Ser552Gly	61.0	0.0		91.0	4.0	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	hg19	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	A	11.37	1.619216	0.28801	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.01126	5.3;5.3	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.02012	0.0063	L	0.58510	1.815	0.34300	D	0.684272	P	0.38535	0.635	B	0.36092	0.217	T	0.44937	-0.9295	10	0.62326	D	0.03	.	12.9843	0.58583	0.8654:0.1346:0.0:0.0	.	552	O00206	TLR4_HUMAN	G	512;552	ENSP00000377997:S512G;ENSP00000363089:S552G	ENSP00000363089:S552G	S	+	1	0	TLR4	119515881	0.997000	0.39634	0.929000	0.37066	0.035000	0.12851	3.156000	0.50708	2.304000	0.77564	0.528000	0.53228	AGT	.	.		0.373	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		G	120476060	A	G	120476060	3	3	103	1	0	0	0	0	1	0	0	0	15968	188	7	2	1664	2	TLR4	9	120476060	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2809654	120476060	20737371	597	15220										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123152026	123152026	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcaaagggcatacctccaggTttcctctggccttccgaagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:123152026delT	ENST00000349780.4	-	37	5797	c.5618delA	c.(5617-5619)aacfs	p.N1873fs	CDK5RAP2_ENST00000480467.1_5'UTR|CDK5RAP2_ENST00000360190.4_Frame_Shift_Del_p.N1794fs|CDK5RAP2_ENST00000360822.3_Frame_Shift_Del_p.N1841fs|CDK5RAP2_ENST00000359309.3_Frame_Shift_Del_p.N1832fs	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1873	Interaction with PCNT and AKAP9.				brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TACCTCCAGGTTTCCTCTGGC	0.512																																					p.N1873fs		Atlas-INDEL	.											.	CDK5RAP2	157	.	0			c.5619delC						.						161	136	144					9																	123152026		2203	4300	6503	SO:0001589	frameshift_variant	55755	exon37			.	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.5618delA	chr9.hg19:g.123152026delT	ENSP00000343818:p.Asn1873fs	156.0	0.0		157.0	11.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Frame_Shift_Del	DEL	ENST00000349780.4	hg19	CCDS6823.1																																																																																			.	.		0.512	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		-	123152026	T	-	123152026	7	5	103	1	0	1	0	1	0	0	0	0	3148	1725	60	0	71	0	CDK5RAP2	9	123152026	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2675966	123152026	18061405	598	15221										
SCAI	286205	hgsc.bcm.edu	37	chr9	127904935	127904935	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttctccgttttcgaggcggTttctccactgtgccagtcag	10	13	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:127904935T>C	ENST00000336505.6	-	2	133	c.75A>G	c.(73-75)aaA>aaG	p.K25K	SCAI_ENST00000373549.4_Silent_p.K25K	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	25	Necessary to inhibit MKL1-induced SRF transcriptional activity. {ECO:0000250}.				negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						TTCGAGGCGGTTTCTCCACTG	0.463																																					p.K25K		Atlas-SNP	.											.	SCAI	84	.	0			c.A75G						.						84	89	88					9																	127904935		1929	4124	6053	SO:0001819	synonymous_variant	286205	exon2			AGGCGGTTTCTCC	AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 126"	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.75A>G	chr9.hg19:g.127904935T>C		96.0	0.0		72.0	4.0	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Silent	SNP	ENST00000336505.6	hg19	CCDS48017.1																																																																																			.	.		0.463	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690		C	127904935	T	C	127904935	2	2	103	1	0	0	0	0	0	0	0	1	13884	1722	60	2		2	SCAI	9	127904935	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4752909	127904935	13308496	599	15222										
TTC16	158248	hgsc.bcm.edu	37	chr9	130491908	130491908	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggtggcgtccctgtctgacAgctaccttgaccagacctct	10	14	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:130491908A>G	ENST00000373289.3	+	13	1893	c.1813A>G	c.(1813-1815)Agc>Ggc	p.S605G	TOR2A_ENST00000472723.1_5'Flank|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	605										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						CCTGTCTGACAGCTACCTTGA	0.542																																					p.S605G		Atlas-SNP	.											.	TTC16	55	.	0			c.A1813G						.						107	92	98					9																	130491908		2203	4300	6503	SO:0001583	missense	158248	exon13			TCTGACAGCTACC	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"Tetratricopeptide (TTC) repeat domain containing"	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.1813A>G	chr9.hg19:g.130491908A>G	ENSP00000362386:p.Ser605Gly	68.0	0.0		78.0	5.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.164593	0.38217	.	.	ENSG00000167094	ENST00000373289	T	0.25912	1.77	3.8	0.0857	0.14443	.	0.247869	0.29198	N	0.012841	T	0.21509	0.0518	L	0.36672	1.1	0.09310	N	1	D;D	0.58268	0.982;0.982	P;P	0.48598	0.583;0.583	T	0.11446	-1.0587	10	0.72032	D	0.01	-17.2498	6.1433	0.20271	0.6681:0.0:0.3319:0.0	.	592;605	B4DZ42;Q8NEE8	.;TTC16_HUMAN	G	605	ENSP00000362386:S605G	ENSP00000362386:S605G	S	+	1	0	TTC16	129531729	0.270000	0.24152	0.025000	0.17156	0.001000	0.01503	0.395000	0.20850	0.012000	0.14892	-0.388000	0.06559	AGC	.	.		0.542	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965		G	130491908	A	G	130491908	3	3	103	1	0	0	0	0	1	0	0	0	16698	188	7	2	1863	2	TTC16	9	130491908	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2586973	130491908	10721523	600	15223										
TTC16	158248	hgsc.bcm.edu	37	chr9	130492952	130492952	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcagagactgagatgtcggcTatctgccaggaatacaggag	13	8	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:130492952T>C	ENST00000373289.3	+	14	1970	c.1890T>C	c.(1888-1890)gcT>gcC	p.A630A	TOR2A_ENST00000472723.1_5'Flank|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	630										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						AGATGTCGGCTATCTGCCAGG	0.592																																					p.A630A		Atlas-SNP	.											.	TTC16	55	.	0			c.T1890C						.						61	51	54					9																	130492952		2203	4300	6503	SO:0001819	synonymous_variant	158248	exon14			GTCGGCTATCTGC	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"Tetratricopeptide (TTC) repeat domain containing"	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.1890T>C	chr9.hg19:g.130492952T>C		94.0	0.0		97.0	4.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Silent	SNP	ENST00000373289.3	hg19	CCDS6875.1																																																																																			.	.		0.592	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965		C	130492952	T	C	130492952	2	2	103	1	0	0	0	0	0	0	0	1	16698	1509	53	2		2	TTC16	9	130492952	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1044	130492952	10720479	601	15224										
GOLGA2	2801	hgsc.bcm.edu	37	chr9	131036199	131036199	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cattttttattttcttcttcTttttcgctcctgtaggaaca					rs142168936		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:131036199delT	ENST00000421699.2	-	2	149	c.137delA	c.(136-138)aagfs	p.K49fs	GOLGA2_ENST00000609374.1_Frame_Shift_Del_p.K37fs|GOLGA2_ENST00000490628.1_Frame_Shift_Del_p.K49fs|SWI5_ENST00000418976.1_5'Flank|SWI5_ENST00000608796.1_5'Flank|SWI5_ENST00000419867.2_5'Flank|SWI5_ENST00000320188.5_5'Flank|SWI5_ENST00000495313.1_5'Flank	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	49	Poly-Lys.				mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						TTTCTTCTTCTTTTTCGCTCC	0.468																																					p.K46fs		Atlas-INDEL	.											.	GOLGA2	69	.	0			c.138delG						.						157	172	167					9																	131036199		2203	4300	6503	SO:0001589	frameshift_variant	2801	exon2			.	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"Golgi matrix protein GM130", "SY11 protein"	602580	"golgi autoantigen, golgin subfamily a, 2"			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.137delA	chr9.hg19:g.131036199delT	ENSP00000416097:p.Lys49fs	182.0	0.0		187.0	14.0	NM_004486	Q6GRM9|Q9BRB0|Q9NYF9	Frame_Shift_Del	DEL	ENST00000421699.2	hg19	CCDS6896.2																																																																																			.	.		0.468	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486		-	131036199	T	-	131036199	7	5	103	1	0	1	0	1	0	0	0	0	6560	1609	56	0	2971	0	GOLGA2	9	131036199	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	543247	131036199	10177232	602	15225										
TRUB2	26995	hgsc.bcm.edu	37	chr9	131076096	131076096	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccggttctcaccataggttgTcttctctaccagcctcccgt	7	16	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:131076096T>C	ENST00000372890.4	-	5	784	c.451A>G	c.(451-453)Aca>Gca	p.T151A	TRUB2_ENST00000546104.1_Missense_Mutation_p.T95A|RP11-339B21.13_ENST00000609315.1_RNA|TRUB2_ENST00000460320.1_5'UTR	NM_015679.1	NP_056494.1	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase family member 2	151					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			kidney(2)|large_intestine(2)|lung(3)|ovary(1)	8						CCATAGGTTGTCTTCTCTACC	0.592																																					p.T151A		Atlas-SNP	.											.	TRUB2	26	.	0			c.A451G						.						192	156	168					9																	131076096		2203	4300	6503	SO:0001583	missense	26995	exon5			AGGTTGTCTTCTC	AK001956	CCDS6897.1	9q34.11	2014-01-28	2013-09-02		ENSG00000167112	ENSG00000167112			17170	protein-coding gene	gene with protein product		610727	"TruB pseudouridine (psi) synthase homolog 2 (E. coli)"			12736709	Standard	NM_015679		Approved	CLONE24922	uc004buq.1	O95900	OTTHUMG00000020741	ENST00000372890.4:c.451A>G	chr9.hg19:g.131076096T>C	ENSP00000361982:p.Thr151Ala	107.0	0.0		119.0	5.0	NM_015679	B7Z7G5	Missense_Mutation	SNP	ENST00000372890.4	hg19	CCDS6897.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.434736	0.43224	.	.	ENSG00000167112	ENST00000372890;ENST00000546104	T;T	0.49720	0.77;0.77	5.53	4.37	0.52481	Pseudouridine synthase, catalytic domain (1);	0.188576	0.47455	D	0.000228	T	0.45094	0.1325	L	0.29908	0.895	0.49798	D	0.999823	P	0.51653	0.947	P	0.57502	0.822	T	0.36187	-0.9758	10	0.05833	T	0.94	-9.4758	11.827	0.52273	0.1315:0.0:0.0:0.8685	.	151	O95900	TRUB2_HUMAN	A	151;95	ENSP00000361982:T151A;ENSP00000438084:T95A	ENSP00000361982:T151A	T	-	1	0	TRUB2	130115917	1.000000	0.71417	0.952000	0.39060	0.593000	0.36681	2.194000	0.42668	0.896000	0.36366	0.459000	0.35465	ACA	.	.		0.592	TRUB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054419.1	NM_015679		C	131076096	T	C	131076096	3	2	103	1	0	0	0	0	1	0	0	0	16618	1667	58	2	560	2	TRUB2	9	131076096	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	39897	131076096	10137335	603	15226										
FNBP1	23048	hgsc.bcm.edu	37	chr9	132662819	132662819	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccggccttcaacctcagccAgccaggcctggagacaaaag	11	15	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:132662819A>G	ENST00000446176.2	-	14	1622	c.1436T>C	c.(1435-1437)cTg>cCg	p.L479P	FNBP1_ENST00000355681.3_Missense_Mutation_p.L450P|FNBP1_ENST00000443566.2_Missense_Mutation_p.L107P|FNBP1_ENST00000478129.1_5'UTR|FNBP1_ENST00000420781.1_Missense_Mutation_p.L470P	NM_015033.2	NP_055848.1	Q96RU3	FNBP1_HUMAN	formin binding protein 1	479	Interaction with RND2. {ECO:0000250}.|Required for self-association and induction of membrane tubulation.				endocytosis (GO:0006897)	coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)						Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		AACCTCAGCCAGCCAGGCCTG	0.627			T	MLL	AML																																p.L479P		Atlas-SNP	.		Dom	yes		9	9q23	23048	formin binding protein 1 (FBP17)		L	.	FNBP1	51	.	0			c.T1436C						.						23	24	24					9																	132662819		1967	4154	6121	SO:0001583	missense	23048	exon14			TCAGCCAGCCAGG	AB011126	CCDS48040.1	9q34	2008-02-05			ENSG00000187239	ENSG00000187239			17069	protein-coding gene	gene with protein product		606191				9628581, 11438682	Standard	XM_005251815		Approved	FBP17, KIAA0554	uc004byw.1	Q96RU3	OTTHUMG00000020800	ENST00000446176.2:c.1436T>C	chr9.hg19:g.132662819A>G	ENSP00000413625:p.Leu479Pro	70.0	0.0		59.0	4.0	NM_015033	O60301|Q3MIN8|Q5TC87|Q5TC88|Q6P658|Q7LGG2|Q9H8H8|Q9NWD1	Missense_Mutation	SNP	ENST00000446176.2	hg19	CCDS48040.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.92|19.92	3.916158|3.916158	0.73098|0.73098	.|.	.|.	ENSG00000187239|ENSG00000187239	ENST00000372416;ENST00000446176;ENST00000420781;ENST00000372415;ENST00000443566;ENST00000355681|ENST00000449089	T;T;T;T|.	0.78364|.	-1.17;-1.17;-1.17;-1.17|.	4.24|4.24	4.24|4.24	0.50183|0.50183	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.77857|0.77857	0.4193|0.4193	M|M	0.87269|0.87269	2.87|2.87	0.80722|0.80722	D|D	1|1	B;D;D;D;D;D;D;D|.	0.89917|.	0.435;0.999;0.999;1.0;1.0;0.999;1.0;1.0|.	B;D;D;D;D;D;D;D|.	0.79108|.	0.155;0.982;0.987;0.992;0.99;0.968;0.992;0.982|.	T|T	0.81413|0.81413	-0.0944|-0.0944	10|5	0.87932|.	D|.	0|.	-24.3011|-24.3011	12.942|12.942	0.58350|0.58350	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	474;469;107;413;450;430;474;479|.	B7ZL12;B7ZL13;E7EPB7;B7ZL14;Q96RU3-3;Q5QP69;Q96RU3-2;Q96RU3|.	.;.;.;.;.;.;.;FNBP1_HUMAN|.	P|R	479;479;470;479;107;450|431	ENSP00000413625:L479P;ENSP00000407548:L470P;ENSP00000389117:L107P;ENSP00000347907:L450P|.	ENSP00000347907:L450P|.	L|W	-|-	2|1	0|0	FNBP1|FNBP1	131702640|131702640	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.950000|0.950000	0.60333|0.60333	8.203000|8.203000	0.89739|0.89739	1.895000|1.895000	0.54865|0.54865	0.260000|0.260000	0.18958|0.18958	CTG|TGG	.	.		0.627	FNBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054630.2			G	132662819	A	G	132662819	3	3	103	1	0	0	0	0	1	0	0	0	5973	188	7	2	433	2	FNBP1	9	132662819	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1586723	132662819	8550612	604	15227										
ABL1	25	hgsc.bcm.edu	37	chr9	133759994	133759995	+	Frame_Shift_Del	DEL	GA	GA	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggcaggggagaacaggtctGaccaggtgacccgaggcaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:133759994_133759995delGA	ENST00000318560.5	+	11	2698_2699	c.2317_2318delGA	c.(2317-2319)gacfs	p.D773fs		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	773					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GAACAGGTCTGACCAGGTGACC	0.569			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.791_792del		Atlas-Indel,Pindel	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.2373_2374del						.																																			SO:0001589	frameshift_variant	25	exon11			.	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2317_2318delGA	chr9.hg19:g.133759994_133759995delGA	ENSP00000323315:p.Asp773fs	36.0	0.0		32.0	13.0	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Frame_Shift_Del	DEL	ENST00000318560.5	hg19	CCDS35166.1																																																																																			.	.		0.569	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		-	133759995	GA	-	133759994	7	5	103	1	0	1	0	1	0	0	0	0	92	1290	45	0	2499	0	ABL1	9	133759994	Frame_Shift_Del	DEL	GA	TCGA-DD-A1EG-01A-11D-A20W-10	1097175	133759994	7453437	605	15228										
NTNG2	84628	hgsc.bcm.edu	37	chr9	135042407	135042407	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcaggcatcacatgtggagaCccccctgagaggttctgctc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:135042407delC	ENST00000393229.3	+	2	965	c.189delC	c.(187-189)gacfs	p.D63fs	NTNG2_ENST00000393228.4_Frame_Shift_Del_p.D63fs|NTNG2_ENST00000372179.3_Frame_Shift_Del_p.D63fs|NTNG2_ENST00000360670.3_Frame_Shift_Del_p.D63fs	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	63	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)				central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		CATGTGGAGACCCCCCTGAGA	0.592																																					p.D63fs		Atlas-INDEL	.											.	NTNG2	66	.	0			c.188delA						.						104	109	108					9																	135042407		2203	4300	6503	SO:0001589	frameshift_variant	84628	exon2			.	AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"Netrins"	14288	protein-coding gene	gene with protein product	"Netrin-G2"		"netrin G1"	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.189delC	chr9.hg19:g.135042407delC	ENSP00000376921:p.Asp63fs	164.0	0.0		200.0	12.0	NM_032536	Q5JUJ2|Q6UXY0|Q96JH0	Frame_Shift_Del	DEL	ENST00000393229.3	hg19	CCDS6946.1																																																																																			.	.		0.592	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536		-	135042407	C	-	135042407	7	5	103	1	0	1	0	1	0	0	0	0	10714	506	18	0	191	0	NTNG2	9	135042407	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1282413	135042407	6171024	606	15229										
SURF1	6834	hgsc.bcm.edu	37	chr9	136218808	136218808	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtaggaatttcttaaaccacAggtaggatgtagctgcagag	12	6	1	1	rs200841752		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:136218808A>G	ENST00000371974.3	-	9	894	c.863T>C	c.(862-864)cTg>cCg	p.L288P	SURF1_ENST00000495952.1_5'UTR|SNORD36A_ENST00000362874.1_RNA|SNORD24_ENST00000383884.1_RNA|SNORD36C_ENST00000516733.1_RNA|SNORD36B_ENST00000363961.1_RNA	NM_001280787.1|NM_003172.2	NP_001267716.1|NP_003163.1	Q15526	SURF1_HUMAN	surfeit 1	288					aerobic respiration (GO:0009060)|ATP biosynthetic process (GO:0006754)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|respiratory chain complex IV assembly (GO:0008535)	integral component of membrane (GO:0016021)|mitochondrial respiratory chain (GO:0005746)	cytochrome-c oxidase activity (GO:0004129)			breast(2)|endometrium(1)|ovary(2)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(145;5.06e-07)|Epithelial(140;4.25e-06)|all cancers(34;3.93e-05)		CTTAAACCACAGGTAGGATGT	0.532											OREG0019585	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L288P		Atlas-SNP	.											.	SURF1	15	.	0			c.T863C						.						72	68	70					9																	136218808		2203	4300	6503	SO:0001583	missense	6834	exon9			AACCACAGGTAGG		CCDS6966.1, CCDS75928.1	9q33-q34	2012-10-12			ENSG00000148290	ENSG00000148290		"Mitochondrial respiratory chain complex assembly factors"	11474	protein-coding gene	gene with protein product	"surfeit locus protein 1"	185620				8499913, 9843204	Standard	NM_003172		Approved		uc004cdh.1	Q15526	OTTHUMG00000020866	ENST00000371974.3:c.863T>C	chr9.hg19:g.136218808A>G	ENSP00000361042:p.Leu288Pro	83.0	0.0	1624	83.0	4.0	NM_003172	Q5T8T3|Q5T8T4	Missense_Mutation	SNP	ENST00000371974.3	hg19	CCDS6966.1	.	.	.	.	.	.	.	.	.	.	A	19.02	3.745721	0.69418	.	.	ENSG00000148290	ENST00000371974;ENST00000437995	D	0.95001	-3.58	5.27	5.27	0.74061	.	0.120040	0.56097	D	0.000032	D	0.96300	0.8793	M	0.83774	2.66	0.80722	D	1	D	0.55605	0.972	P	0.55667	0.781	D	0.96637	0.9471	10	0.72032	D	0.01	-17.5262	13.2078	0.59807	1.0:0.0:0.0:0.0	.	288	Q15526	SURF1_HUMAN	P	288;258	ENSP00000361042:L288P	ENSP00000361042:L288P	L	-	2	0	SURF1	135208629	1.000000	0.71417	0.939000	0.37840	0.429000	0.31625	6.581000	0.74045	2.118000	0.64928	0.379000	0.24179	CTG	.	A|1.000;C|0.000		0.532	SURF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054879.1	NM_003172		G	136218808	A	G	136218808	3	3	103	1	0	0	0	0	1	0	0	0	15418	188	7	2	43	2	SURF1	9	136218808	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1176401	136218808	4994623	607	15230										
GLT6D1	360203	hgsc.bcm.edu	37	chr9	138516016	138516016	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tattgagtccatttttgatgTcatgaataactccgttcaga	7	7	2	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:138516016T>C	ENST00000371763.1	-	5	1011	c.758A>G	c.(757-759)gAc>gGc	p.D253G		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	253					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		ATTTTTGATGTCATGAATAAC	0.373																																					p.D253G		Atlas-SNP	.											.	GLT6D1	56	.	0			c.A758G						.						165	162	163					9																	138516016		1849	4099	5948	SO:0001583	missense	360203	exon5			TTGATGTCATGAA	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"Glycosyltransferase family 6 domain containing"	23671	protein-coding gene	gene with protein product		613699	"galactosyltransferase family 6 domain containing 1"	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.758A>G	chr9.hg19:g.138516016T>C	ENSP00000360829:p.Asp253Gly	102.0	0.0		126.0	6.0	NM_182974		Missense_Mutation	SNP	ENST00000371763.1	hg19	CCDS43900.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.064491	0.55432	.	.	ENSG00000204007	ENST00000371763	T	0.02472	4.28	2.8	2.8	0.32819	.	0.000000	0.56097	D	0.000023	T	0.14874	0.0359	M	0.86420	2.815	0.39432	D	0.967096	D	0.89917	1.0	D	0.97110	1.0	T	0.00948	-1.1504	10	0.87932	D	0	-62.4897	9.3621	0.38201	0.0:0.0:0.0:1.0	.	253	Q7Z4J2	GL6D1_HUMAN	G	253	ENSP00000360829:D253G	ENSP00000360829:D253G	D	-	2	0	GLT6D1	137655837	1.000000	0.71417	0.012000	0.15200	0.010000	0.07245	5.826000	0.69293	1.526000	0.49068	0.482000	0.46254	GAC	.	.		0.373	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974		C	138516016	T	C	138516016	3	2	103	1	0	0	0	0	1	0	0	0	6476	1667	58	2	76	2	GLT6D1	9	138516016	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2297208	138516016	2697415	608	15231										
QSOX2	169714	hgsc.bcm.edu	37	chr9	139100989	139100989	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaggttgtcgcggccatagTgctgcttcaagaatgtgagc	14	8	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:139100989T>C	ENST00000358701.5	-	12	1719	c.1682A>G	c.(1681-1683)cAc>cGc	p.H561R		NM_181701.3	NP_859052.3	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2	561					cell redox homeostasis (GO:0045454)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	thiol oxidase activity (GO:0016972)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)		GCGGCCATAGTGCTGCTTCAA	0.582																																					p.H561R		Atlas-SNP	.											.	QSOX2	63	.	0			c.A1682G						.						101	103	102					9																	139100989		2203	4300	6503	SO:0001583	missense	169714	exon12			CCATAGTGCTGCT	AJ318051	CCDS35178.1	9q34.3	2008-02-05	2007-04-23	2007-04-23	ENSG00000165661	ENSG00000165661			30249	protein-coding gene	gene with protein product		612860	"quiescin Q6-like 1"	QSCN6L1		12176051	Standard	NM_181701		Approved	SOXN, DKFZp762A2013	uc010nbi.2	Q6ZRP7	OTTHUMG00000020923	ENST00000358701.5:c.1682A>G	chr9.hg19:g.139100989T>C	ENSP00000351536:p.His561Arg	91.0	0.0		87.0	4.0	NM_181701	A2CEE0|A6NLB0|Q5TB37|Q7Z7B6|Q86VV7|Q8N3G2	Missense_Mutation	SNP	ENST00000358701.5	hg19	CCDS35178.1	.	.	.	.	.	.	.	.	.	.	T	12.21	1.870040	0.33069	.	.	ENSG00000165661	ENST00000358701	T	0.15256	2.44	4.91	3.69	0.42338	.	0.376195	0.28908	N	0.013745	T	0.35770	0.0943	M	0.75615	2.305	0.43494	D	0.99573	D	0.76494	0.999	D	0.66196	0.942	T	0.07578	-1.0765	10	0.40728	T	0.16	-28.9019	9.8401	0.40993	0.1533:0.0:0.0:0.8467	.	561	Q6ZRP7	QSOX2_HUMAN	R	561	ENSP00000351536:H561R	ENSP00000351536:H561R	H	-	2	0	QSOX2	138240810	1.000000	0.71417	0.984000	0.44739	0.072000	0.16883	5.469000	0.66749	1.831000	0.53308	0.456000	0.33151	CAC	.	.		0.582	QSOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055046.2	NM_181701		C	139100989	T	C	139100989	3	2	103	1	0	0	0	0	1	0	0	0	12899	1696	59	2	418	2	QSOX2	9	139100989	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	584973	139100989	2112442	609	15232										
PMPCA	23203	hgsc.bcm.edu	37	chr9	139313097	139313097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcccggcaagggcatgttcTccaggctctacctcaacgtg	12	14	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:139313097T>C	ENST00000371717.3	+	9	1090	c.1081T>C	c.(1081-1083)Tcc>Ccc	p.S361P	PMPCA_ENST00000462616.1_3'UTR|PMPCA_ENST00000399219.3_Missense_Mutation_p.S230P	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	361					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	14		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		GGGCATGTTCTCCAGGCTCTA	0.587																																					p.S361P		Atlas-SNP	.											.	PMPCA	29	.	0			c.T1081C						.						94	86	89					9																	139313097		2203	4300	6503	SO:0001583	missense	23203	exon9			ATGTTCTCCAGGC	D21064	CCDS35180.1, CCDS65192.1	9q34.3	2008-02-05	2003-06-13	2003-06-20	ENSG00000165688	ENSG00000165688			18667	protein-coding gene	gene with protein product		613036	"inositol polyphosphate-5-phosphatase, 72 kD"	INPP5E		8590280, 7788527	Standard	NM_015160		Approved	KIAA0123, Alpha-MPP	uc004chl.3	Q10713	OTTHUMG00000020926	ENST00000371717.3:c.1081T>C	chr9.hg19:g.139313097T>C	ENSP00000360782:p.Ser361Pro	117.0	0.0		154.0	7.0	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371717.3	hg19	CCDS35180.1	.	.	.	.	.	.	.	.	.	.	t	22.6	4.304958	0.81247	.	.	ENSG00000165688	ENST00000371717;ENST00000399219;ENST00000444897	T;T;T	0.15718	2.4;2.4;2.4	5.23	4.08	0.47627	Peptidase M16, C-terminal (1);Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.044808	0.85682	D	0.000000	T	0.42921	0.1224	M	0.86651	2.83	0.40934	D	0.984415	D;P;D;P	0.67145	0.996;0.845;0.992;0.845	D;P;D;P	0.71184	0.972;0.742;0.917;0.742	T	0.44421	-0.9329	10	0.87932	D	0	.	8.9403	0.35725	0.7686:0.0:0.0:0.2314	.	230;361;69;361	B4DKL3;Q5SXM9;Q5SXN9;Q10713	.;.;.;MPPA_HUMAN	P	361;230;69	ENSP00000360782:S361P;ENSP00000416702:S230P;ENSP00000408393:S69P	ENSP00000360782:S361P	S	+	1	0	PMPCA	138432918	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.082000	0.76851	0.829000	0.34733	0.454000	0.30748	TCC	.	.		0.587	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160		C	139313097	T	C	139313097	3	2	103	1	0	0	0	0	1	0	0	0	12149	1551	54	2	1115	2	PMPCA	9	139313097	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	212108	139313097	1900334	610	15233										
IDI2	91734	hgsc.bcm.edu	37	chr10	1065633	1065633	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgggacaggtagaggatgcTtttcgtttcactgggatccg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:1065633delT	ENST00000277517.1	-	5	572	c.508delA	c.(508-510)agcfs	p.S170fs	GTPBP4_ENST00000360803.4_3'UTR|IDI2-AS1_ENST00000536039.1_RNA|IDI2-AS1_ENST00000434470.1_RNA|IDI2-AS1_ENST00000428780.2_RNA|IDI2-AS1_ENST00000437374.1_RNA|IDI2-AS1_ENST00000420381.1_RNA	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	170	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isopentenyl diphosphate metabolic process (GO:0046490)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.143)	Epithelial(11;0.067)|OV - Ovarian serous cystadenocarcinoma(14;0.169)|all cancers(11;0.192)		TAGAGGATGCTTTTCGTTTCA	0.522																																					p.S170fs		Atlas-INDEL	.											.	IDI2	20	.	0			c.509delG						.						99	89	92					10																	1065633		2203	4300	6503	SO:0001589	frameshift_variant	91734	exon5			.	AF271725	CCDS7055.1	10p15.3	2003-11-19			ENSG00000148377	ENSG00000148377			23487	protein-coding gene	gene with protein product		615389				12477932	Standard	NM_033261		Approved	IPPI2	uc001ifv.1	Q9BXS1	OTTHUMG00000017537	ENST00000277517.1:c.508delA	chr10.hg19:g.1065633delT	ENSP00000277517:p.Ser170fs	180.0	0.0		183.0	11.0	NM_033261		Frame_Shift_Del	DEL	ENST00000277517.1	hg19	CCDS7055.1																																																																																			.	.		0.522	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261		-	1065633	T	-	1065633	7	5	103	1	0	1	0	1	0	0	0	0	7509	1609	56	0	179	0	IDI2	10	1065633	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10		1065633	134469114	611	15234										
PITRM1	10531	hgsc.bcm.edu	37	chr10	3207693	3207693	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtccttgggattttgtgtggAaaatggatacagagtataat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:3207693delA	ENST00000224949.4	-	5	479	c.445delT	c.(445-447)tccfs	p.S149fs	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Frame_Shift_Del_p.S149fs|PITRM1_ENST00000451104.2_Frame_Shift_Del_p.S117fs|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	149					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TTTTGTGTGGAAAATGGATAC	0.363																																					p.S149fs		Atlas-INDEL	.											.	PITRM1	109	.	0			c.446delC						.						89	91	91					10																	3207693		1830	4086	5916	SO:0001589	frameshift_variant	10531	exon5			.	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.445delT	chr10.hg19:g.3207693delA	ENSP00000224949:p.Ser149fs	106.0	0.0		147.0	10.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Frame_Shift_Del	DEL	ENST00000224949.4	hg19	CCDS59208.1																																																																																			.	.		0.363	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			-	3207693	A	-	3207693	7	5	103	1	0	1	0	1	0	0	0	0	11962	246	9	0	2760	0	PITRM1	10	3207693	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2142060	3207693	132327054	612	15235										
CAMK1D	57118	hgsc.bcm.edu	37	chr10	12856212	12856212	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggctctgcggctaccctccTttttatgatgaaaatgactc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:12856212delT	ENST00000378847.3	+	7	997	c.660delT	c.(658-660)cctfs	p.P220fs	CAMK1D_ENST00000378845.1_Frame_Shift_Del_p.P220fs	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		GCTACCCTCCTTTTTATGATG	0.473																																					p.P220fs		Atlas-INDEL	.											.	CAMK1D	99	.	0			c.659delC						.						91	81	84					10																	12856212		2203	4300	6503	SO:0001589	frameshift_variant	57118	exon7			.	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.660delT	chr10.hg19:g.12856212delT	ENSP00000368124:p.Pro220fs	159.0	0.0		191.0	13.0	NM_153498	B0YIY0|Q9HD31	Frame_Shift_Del	DEL	ENST00000378847.3	hg19	CCDS7091.1																																																																																			.	.		0.473	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		-	12856212	T	-	12856212	7	5	103	1	0	1	0	1	0	0	0	0	2599	1596	56	0	686	0	CAMK1D	10	12856212	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	9648519	12856212	122678535	613	15236										
MCM10	55388	hgsc.bcm.edu	37	chr10	13239739	13239739	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggaggtgaaggaacgtgtAgaaaaaaacaccatgttttc	11	6	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:13239739A>G	ENST00000484800.2	+	15	2197	c.2094A>G	c.(2092-2094)gtA>gtG	p.V698V	MCM10_ENST00000378694.1_Silent_p.V697V|MCM10_ENST00000378714.3_Silent_p.V697V			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	698					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						AGGAACGTGTAGAAAAAAACA	0.398																																					p.V698V		Atlas-SNP	.											.	MCM10	76	.	0			c.A2094G						.						88	78	82					10																	13239739		2203	4300	6503	SO:0001819	synonymous_variant	55388	exon15			ACGTGTAGAAAAA	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.2094A>G	chr10.hg19:g.13239739A>G		59.0	0.0		93.0	4.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Silent	SNP	ENST00000484800.2	hg19	CCDS7096.1																																																																																			.	.		0.398	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		G	13239739	A	G	13239739	2	3	103	1	0	0	0	0	0	0	0	1	9394	407	15	2		2	MCM10	10	13239739	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	383527	13239739	122295008	614	15237										
DCLRE1C	64421	hgsc.bcm.edu	37	chr10	14950883	14950883	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgttgactgggaagaattctGggaggagatgtgagttgatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:14950883delG	ENST00000378278.2	-	14	1640	c.1603delC	c.(1603-1605)cagfs	p.Q535fs	DCLRE1C_ENST00000357717.2_Frame_Shift_Del_p.Q420fs|DCLRE1C_ENST00000378289.4_Intron|DCLRE1C_ENST00000378255.1_Frame_Shift_Del_p.Q415fs|DCLRE1C_ENST00000453695.2_Frame_Shift_Del_p.Q415fs|DCLRE1C_ENST00000492201.1_5'UTR|DCLRE1C_ENST00000378242.1_Frame_Shift_Del_p.Q188fs|DCLRE1C_ENST00000378246.2_Frame_Shift_Del_p.Q420fs|DCLRE1C_ENST00000378258.1_Frame_Shift_Del_p.Q415fs|DCLRE1C_ENST00000378249.1_Frame_Shift_Del_p.Q420fs|DCLRE1C_ENST00000396817.2_Frame_Shift_Del_p.Q415fs|DCLRE1C_ENST00000378254.1_Frame_Shift_Del_p.Q415fs			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	535					B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						GAAGAATTCTGGGAGGAGATG	0.463								Non-homologous end-joining																													p.Q535fs		Atlas-INDEL	.											.	DCLRE1C	136	.	0			c.1604delA						.						75	73	74					10																	14950883		2203	4300	6503	SO:0001589	frameshift_variant	64421	exon14			.	BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	605988	"severe combined immunodeficiency, type a (Athabascan)", "DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.1603delC	chr10.hg19:g.14950883delG	ENSP00000367527:p.Gln535fs	101.0	0.0		132.0	12.0	NM_001033855	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Frame_Shift_Del	DEL	ENST00000378278.2	hg19	CCDS31149.1																																																																																			.	.		0.463	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487		-	14950883	G	-	14950883	7	5	103	1	0	1	0	1	0	0	0	0	4298	1357	47	0	479	0	DCLRE1C	10	14950883	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1711144	14950883	120583864	615	15238										
THNSL1	79896	hgsc.bcm.edu	37	chr10	25314273	25314273	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttacctccactgcatgaggcTttattagagagaacaaaaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:25314273delT	ENST00000524413.1	+	3	2468	c.2121delT	c.(2119-2121)gctfs	p.A707fs	THNSL1_ENST00000376356.4_Frame_Shift_Del_p.A707fs			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	707						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	TGCATGAGGCTTTATTAGAGA	0.398																																					p.A707fs		Atlas-INDEL	.											.	THNSL1	70	.	0			c.2120delC						.						84	82	83					10																	25314273		2203	4300	6503	SO:0001589	frameshift_variant	79896	exon3			.	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"threonine synthase-like 1 (bacterial)"			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.2121delT	chr10.hg19:g.25314273delT	ENSP00000434887:p.Ala707fs	118.0	0.0		241.0	15.0	NM_024838	B3KWL1|D3DRV3|Q5VV21	Frame_Shift_Del	DEL	ENST00000524413.1	hg19	CCDS7147.1																																																																																			.	.		0.398	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838		-	25314273	T	-	25314273	7	5	103	1	0	1	0	1	0	0	0	0	15877	1596	56	0	2123	0	THNSL1	10	25314273	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	10363390	25314273	110220474	616	15239										
GPR158	57512	hgsc.bcm.edu	37	chr10	25887118	25887118	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cactggaatccctgtcgggtAaaaaactaacacaaaaacta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:25887118delA	ENST00000376351.3	+	11	2922	c.2563delA	c.(2563-2565)aaafs	p.K856fs	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	856					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CCTGTCGGGTAAAAAACTAAC	0.507																																					p.G854fs		Atlas-INDEL	.											.	GPR158	255	.	0			c.2562delT						.						82	92	88					10																	25887118		2203	4300	6503	SO:0001589	frameshift_variant	57512	exon11			.	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.2563delA	chr10.hg19:g.25887118delA	ENSP00000365529:p.Lys856fs	93.0	0.0		148.0	11.0	NM_020752	Q6QR81|Q9ULT3	Frame_Shift_Del	DEL	ENST00000376351.3	hg19	CCDS31166.1																																																																																			.	.		0.507	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		-	25887118	A	-	25887118	7	5	103	1	0	1	0	1	0	0	0	0	6671	363	13	0	2605	0	GPR158	10	25887118	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	572845	25887118	109647629	617	15240										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27324168	27324168	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctaggctattgagtttacTttcagttttaaatagttgtt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:27324168delT	ENST00000376087.4	-	24	3376	c.3211delA	c.(3211-3213)agtfs	p.S1071fs	ANKRD26_ENST00000376070.3_Frame_Shift_Del_p.S628fs|ANKRD26_ENST00000436985.2_Frame_Shift_Del_p.S1087fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1070					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TTGAGTTTACTTTCAGTTTTA	0.358																																					p.S1071fs		Atlas-INDEL	.											.	ANKRD26	179	.	0			c.3212delG						.						84	82	82					10																	27324168		1838	4092	5930	SO:0001589	frameshift_variant	22852	exon24			.	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3211delA	chr10.hg19:g.27324168delT	ENSP00000365255:p.Ser1071fs	138.0	0.0		135.0	10.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Del	DEL	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.358	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			-	27324168	T	-	27324168	7	5	103	1	0	1	0	1	0	0	0	0	654	1609	56	0	1965	0	ANKRD26	10	27324168	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1437050	27324168	108210579	618	15241										
MASTL	84930	hgsc.bcm.edu	37	chr10	27448581	27448581	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttattgggggagatgtcaagTctctcctacatatatatggt	10	6	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:27448581T>C	ENST00000375940.4	+	3	415	c.358T>C	c.(358-360)Tct>Cct	p.S120P	MASTL_ENST00000342386.6_Missense_Mutation_p.S120P|MASTL_ENST00000375946.4_Missense_Mutation_p.S120P			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	120	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGATGTCAAGTCTCTCCTACA	0.308																																					p.S120P		Atlas-SNP	.											.	MASTL	81	.	0			c.T358C						.						68	74	72					10																	27448581		2203	4298	6501	SO:0001583	missense	84930	exon3			GTCAAGTCTCTCC	BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.358T>C	chr10.hg19:g.27448581T>C	ENSP00000365107:p.Ser120Pro	54.0	0.0		62.0	4.0	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	hg19	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.293671	0.80914	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.41758	0.99;0.99;0.99	5.7	4.55	0.56014	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047398	0.85682	D	0.000000	T	0.66356	0.2781	M	0.83483	2.645	0.80722	D	1	D;D;D	0.89917	0.998;0.999;1.0	D;D;D	0.91635	0.994;0.997;0.999	T	0.71052	-0.4704	10	0.87932	D	0	-17.7169	13.0503	0.58950	0.0:0.0:0.1343:0.8657	.	120;120;120	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	P	120	ENSP00000365113:S120P;ENSP00000343446:S120P;ENSP00000365107:S120P	ENSP00000343446:S120P	S	+	1	0	MASTL	27488587	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.493000	0.81493	0.979000	0.38497	0.459000	0.35465	TCT	.	.		0.308	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		C	27448581	T	C	27448581	3	2	103	1	0	0	0	0	1	0	0	0	9337	1667	58	2	368	2	MASTL	10	27448581	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	124413	27448581	108086166	619	15242										
MAP3K8	1326	hgsc.bcm.edu	37	chr10	30740592	30740592	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacattgttttcatgtccacAaaagctgttttggtggattt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:30740592delA	ENST00000263056.1	+	6	1488	c.792delA	c.(790-792)acafs	p.T264fs	MAP3K8_ENST00000542547.1_Frame_Shift_Del_p.T264fs|MAP3K8_ENST00000375321.1_Frame_Shift_Del_p.T264fs	NM_001244134.1|NM_005204.3	NP_001231063.1|NP_005195.2	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase 8	264	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|protein phosphorylation (GO:0006468)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Prostate(175;0.151)				TCATGTCCACAAAAGCTGTTT	0.323																																					p.T264fs		Atlas-INDEL	.											.	MAP3K8	46	.	0			c.791delC						.						86	86	86					10																	30740592		2203	4300	6503	SO:0001589	frameshift_variant	1326	exon5			.	D14497	CCDS7166.1	10p11.2	2011-06-09			ENSG00000107968	ENSG00000107968		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6860	protein-coding gene	gene with protein product		191195		COT, ESTF		2072910, 8479752	Standard	NM_005204		Approved	Tpl-2, EST, c-COT, MEKK8	uc009xlf.2	P41279	OTTHUMG00000017889	ENST00000263056.1:c.792delA	chr10.hg19:g.30740592delA	ENSP00000263056:p.Thr264fs	94.0	0.0		120.0	11.0	NM_001244134	A8K2Q5|D3DRX1|Q14275|Q5T855|Q9HC81	Frame_Shift_Del	DEL	ENST00000263056.1	hg19	CCDS7166.1																																																																																			.	.		0.323	MAP3K8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047416.2	NM_005204		-	30740592	A	-	30740592	7	5	103	1	0	1	0	1	0	0	0	0	9265	117	5	0	806	0	MAP3K8	10	30740592	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3292011	30740592	104794155	620	15243										
PTPN20A	653129	hgsc.bcm.edu	37	chr10	46568210	46568210	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcattgatgtagtccttgcTttttccaagaggaacgcgtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:46568210delT	ENST00000374339.3	-	7	689	c.613delA	c.(613-615)agcfs	p.S205fs	PTPN20A_ENST00000506080.1_Frame_Shift_Del_p.S177fs|PTPN20A_ENST00000502705.1_Intron|PTPN20A_ENST00000437863.1_Frame_Shift_Del_p.S177fs|PTPN20A_ENST00000395721.2_Frame_Shift_Del_p.S124fs|PTPN20A_ENST00000508602.1_Intron|PTPN20A_ENST00000503851.1_Intron|PTPN20A_ENST00000509599.1_Intron|PTPN20A_ENST00000509774.1_Intron|PTPN20A_ENST00000511769.1_Frame_Shift_Del_p.S196fs|PTPN20A_ENST00000374218.2_Frame_Shift_Del_p.S124fs|PTPN20A_ENST00000505814.1_Frame_Shift_Del_p.S124fs|PTPN20A_ENST00000513156.1_Intron|PTPN20A_ENST00000395722.3_Intron|PTPN20A_ENST00000395725.3_Intron|PTPN20A_ENST00000374346.3_Intron|PTPN20A_ENST00000509900.1_Intron|PTPN20A_ENST00000513266.1_Intron|PTPN20A_ENST00000502254.1_Intron|PTPN20A_ENST00000374340.3_5'UTR|PTPN20A_ENST00000395727.2_Frame_Shift_Del_p.S13fs|PTPN20A_ENST00000374342.2_Intron			Q4JDL3	PTN20_HUMAN	protein tyrosine phosphatase, non-receptor type 20A	205	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.					cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)								Kidney(211;0.201)		TAGTCCTTGCTTTTTCCAAGA	0.393																																					p.S205fs		Atlas-INDEL	.											.	.	.	.	0			c.614delG						.																																			SO:0001589	frameshift_variant	653129	exon7			.			10q11.22	2011-06-09			ENSG00000204179	ENSG00000204179		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	23422	protein-coding gene	gene with protein product	"cancer/testis antigen 126"						Standard			Approved	bA142I17.1, CT126		Q4JDL3	OTTHUMG00000018094	ENST00000374339.3:c.613delA	chr10.hg19:g.46568210delT	ENSP00000363459:p.Ser205fs	194.0	0.0		181.0	12.0	NM_001042389	A6NNH8|B7ZKV3|Q4JDG6|Q4JDK1|Q4JDK5|Q4JDK6|Q4JDK8|Q4JDK9|Q4JDL0|Q4JDL1|Q4JDL4|Q4JDL5|Q4JDL6|Q4JDL7|Q4JDL8|Q5RJ33|Q5T1G3	Frame_Shift_Del	DEL	ENST00000374339.3	hg19	CCDS31190.1																																																																																			.	.		0.393	PTPN20A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358639.1			-	46568210	T	-	46568210	7	5	103	1	0	1	0	1	0	0	0	0	12799	1609	56	0	665	0	PTPN20A	10	46568210	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	15827618	46568210	88966537	621	15244										
PPYR1	5540	hgsc.bcm.edu	37	chr10	47087668	47087668	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gactggcaccatgaggccatCcccatctgccacgggaacct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:47087668delC	ENST00000395716.1	+	2	970	c.885delC	c.(883-885)atcfs	p.I295fs	NPY4R_ENST00000374312.1_Frame_Shift_Del_p.I295fs			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	295					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										ATGAGGCCATCCCCATCTGCC	0.552																																					p.I295fs		Atlas-INDEL	.											.	PPYR1	54	.	0			c.884delT						.						176	145	156					10																	47087668		2203	4300	6503	SO:0001589	frameshift_variant	5540	exon3			.		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"GPCR / Class A : Neuropeptide receptors : Y"	9329	protein-coding gene	gene with protein product		601790	"pancreatic polypeptide receptor 1"	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.885delC	chr10.hg19:g.47087668delC	ENSP00000379066:p.Ile295fs	155.0	0.0		152.0	11.0	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Frame_Shift_Del	DEL	ENST00000395716.1	hg19	CCDS31193.1																																																																																			.	.		0.552	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1			-	47087668	C	-	47087668	7	5	103	1	0	1	0	1	0	0	0	0	12428	845	30	0	887	0	PPYR1	10	47087668	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	519458	47087668	88447079	622	15245										
FAM21B	387680	hgsc.bcm.edu	37	chr10	47915896	47915896	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggttaccttatcttccagcAaaaatctcaagccctcatca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:47915896delA	ENST00000358474.5	+	15	1303	c.1303delA	c.(1303-1305)aaafs	p.K435fs		NM_018232.1	NP_060702.1	Q5SNT6	FA21B_HUMAN		435					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10						ATCTTCCAGCAAAAATCTCAA	0.403																																					p.S434fs		Atlas-INDEL	.											.	FAM21B	31	.	0			c.1302delC						.						20	29	27					10																	47915896		1763	4023	5786	SO:0001589	frameshift_variant	55747	exon15			.																												ENST00000358474.5:c.1303delA	chr10.hg19:g.47915896delA	ENSP00000351259:p.Lys435fs	203.0	0.0		190.0	16.0	NM_018232		Frame_Shift_Del	DEL	ENST00000358474.5	hg19	CCDS44379.1																																																																																			.	.		0.403	FAM21B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047871.2			-	47915896	A	-	47915896	7	5	103	1	0	1	0	1	0	0	0	0	5546	131	5	0	1361	0	FAM21B	10	47915896	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	828228	47915896	87618851	623	15246										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49661399	49661399	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggccgcagaatgttaggtccAaaaacggttgccagattctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:49661399delA	ENST00000249601.4	-	8	1232	c.936delT	c.(934-936)tttfs	p.F312fs	ARHGAP22_ENST00000374170.1_Frame_Shift_Del_p.F153fs|ARHGAP22_ENST00000417247.2_Frame_Shift_Del_p.F222fs|ARHGAP22_ENST00000435790.2_Frame_Shift_Del_p.F318fs|ARHGAP22_ENST00000477708.2_5'Flank|ARHGAP22_ENST00000374172.1_Frame_Shift_Del_p.F203fs|ARHGAP22_ENST00000417912.2_Frame_Shift_Del_p.F328fs	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	312	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TGTTAGGTCCAAAAACGGTTG	0.517																																					p.G329fs		Atlas-INDEL	.											.	ARHGAP22	94	.	0			c.985delG						.						158	135	143					10																	49661399		2202	4300	6502	SO:0001589	frameshift_variant	58504	exon8			.	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.936delT	chr10.hg19:g.49661399delA	ENSP00000249601:p.Phe312fs	169.0	0.0		193.0	12.0	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Frame_Shift_Del	DEL	ENST00000249601.4	hg19	CCDS7227.1																																																																																			.	.		0.517	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		-	49661399	A	-	49661399	7	5	103	1	0	1	0	1	0	0	0	0	872	127	5	0	1172	0	ARHGAP22	10	49661399	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1745503	49661399	85873348	624	15247										
PARG	8505	hgsc.bcm.edu	37	chr10	51077558	51077558	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctaaagtagcagaagagcgTtttaagtttctccggtttcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:51077558delT	ENST00000402038.3	-	6	576	c.577delA	c.(577-579)acgfs	p.T193fs		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	678	A-domain.				carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		CAGAAGAGCGTTTTAAGTTTC	0.338																																					p.T678fs		Atlas-INDEL	.											.	PARG	46	.	0			c.2033delC						.						41	36	38					10																	51077558		692	1588	2280	SO:0001589	frameshift_variant	8505	exon10			.	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.577delA	chr10.hg19:g.51077558delT	ENSP00000384408:p.Thr193fs	179.0	0.0		212.0	13.0	NM_003631	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Frame_Shift_Del	DEL	ENST00000402038.3	hg19																																																																																				.	.		0.338	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		-	51077558	T	-	51077558	7	5	103	1	0	1	0	1	0	0	0	0	11457	1725	60	0	934	0	PARG	10	51077558	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1416159	51077558	84457189	625	15248										
A1CF	29974	hgsc.bcm.edu	37	chr10	52603752	52603752	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttaaatttggactcacttttTcacataatggtataagctca	5	7	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:52603752T>C	ENST00000373993.1	-	2	274	c.230A>G	c.(229-231)gAa>gGa	p.E77G	A1CF_ENST00000374001.2_Missense_Mutation_p.E77G|A1CF_ENST00000373995.3_Missense_Mutation_p.E85G|A1CF_ENST00000395489.2_Missense_Mutation_p.E70G|A1CF_ENST00000395495.1_Missense_Mutation_p.E77G|A1CF_ENST00000373997.3_Missense_Mutation_p.E77G|A1CF_ENST00000282641.2_Missense_Mutation_p.E77G			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	77	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						ACTCACTTTTTCACATAATGG	0.403																																					p.E85G		Atlas-SNP	.											.	A1CF	190	.	0			c.A254G						.						104	122	116					10																	52603752		2202	4300	6502	SO:0001583	missense	29974	exon5			ACTTTTTCACATA	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"RNA binding motif (RRM) containing"	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.230A>G	chr10.hg19:g.52603752T>C	ENSP00000363105:p.Glu77Gly	82.0	0.0		90.0	4.0	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	hg19	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.571540	0.86542	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489;ENST00000414883	T;T;T;T;T;T;T;T	0.16196	2.36;2.36;2.36;2.36;2.36;2.36;2.36;2.36	5.55	5.55	0.83447	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.32224	0.0822	L	0.37561	1.115	0.80722	D	1	D;D;D;D	0.89917	0.964;0.971;1.0;0.983	P;D;D;P	0.85130	0.839;0.93;0.997;0.889	T	0.03981	-1.0987	10	0.87932	D	0	.	13.6488	0.62299	0.0:0.0:0.0:1.0	.	70;77;77;85	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	G	77;77;77;85;77;77;60;70;77	ENSP00000363113:E77G;ENSP00000363105:E77G;ENSP00000363109:E77G;ENSP00000363107:E85G;ENSP00000282641:E77G;ENSP00000378873:E77G;ENSP00000378868:E70G;ENSP00000397953:E77G	ENSP00000282641:E77G	E	-	2	0	A1CF	52273758	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.112000	0.64535	0.528000	0.53228	GAA	.	.		0.403	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576		C	52603752	T	C	52603752	3	2	103	1	0	0	0	0	1	0	0	0	2	1783	62	2	1594	2	A1CF	10	52603752	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1526194	52603752	82930995	626	15249										
IPMK	253430	hgsc.bcm.edu	37	chr10	59986874	59986874	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttcgtagctctagaagaacAccatcaaaacagtcagcagc	7	11	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:59986874A>G	ENST00000373935.3	-	3	625	c.303T>C	c.(301-303)ggT>ggC	p.G101G		NM_152230.4	NP_689416.1	Q8NFU5	IPMK_HUMAN	inositol polyphosphate multikinase	101					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|neural tube formation (GO:0001841)|small molecule metabolic process (GO:0044281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol tetrakisphosphate 3-kinase activity (GO:0000824)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)|inositol-1,4,5-trisphosphate 6-kinase activity (GO:0000823)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)	22						CTAGAAGAACACCATCAAAAC	0.358																																					p.G101G		Atlas-SNP	.											.	IPMK	45	.	0			c.T303C						.						95	94	95					10																	59986874		2203	4300	6503	SO:0001819	synonymous_variant	253430	exon3			AAGAACACCATCA	AF432853	CCDS7250.1	10q21.1	2010-11-29		2004-07-22	ENSG00000151151	ENSG00000151151			20739	protein-coding gene	gene with protein product		609851				12223481, 12027805	Standard	NM_152230		Approved		uc001jkb.3	Q8NFU5	OTTHUMG00000018268	ENST00000373935.3:c.303T>C	chr10.hg19:g.59986874A>G		57.0	0.0		58.0	4.0	NM_152230		Silent	SNP	ENST00000373935.3	hg19	CCDS7250.1																																																																																			.	.		0.358	IPMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048142.1	NM_152230		G	59986874	A	G	59986874	2	3	103	1	0	0	0	0	0	0	0	1	7801	146	6	2		2	IPMK	10	59986874	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	7383122	59986874	75547873	627	15250										
BICC1	80114	hgsc.bcm.edu	37	chr10	60549664	60549664	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acctccagggcaccattgagTctgtctgtcttgcaaggcaa	10	12	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:60549664T>C	ENST00000373886.3	+	8	1022	c.1018T>C	c.(1018-1020)Tct>Cct	p.S340P		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	340	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						CACCATTGAGTCTGTCTGTCT	0.408																																					p.S340P		Atlas-SNP	.											.	BICC1	121	.	0			c.T1018C						.						156	145	149					10																	60549664		2203	4300	6503	SO:0001583	missense	80114	exon8			ATTGAGTCTGTCT	AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"Sterile alpha motif (SAM) domain containing"	19351	protein-coding gene	gene with protein product		614295	"bicaudal C homolog 1 (Drosophila)"				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.1018T>C	chr10.hg19:g.60549664T>C	ENSP00000362993:p.Ser340Pro	80.0	0.0		96.0	5.0	NM_001080512		Missense_Mutation	SNP	ENST00000373886.3	hg19	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.247095	0.80024	.	.	ENSG00000122870	ENST00000373886	T	0.34667	1.35	5.67	5.67	0.87782	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.60025	0.2237	M	0.74647	2.275	0.80722	D	1	D	0.76494	0.999	D	0.69824	0.966	T	0.61212	-0.7108	10	0.45353	T	0.12	-13.0028	15.9271	0.79628	0.0:0.0:0.0:1.0	.	340	Q9H694	BICC1_HUMAN	P	340	ENSP00000362993:S340P	ENSP00000362993:S340P	S	+	1	0	BICC1	60219670	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.081000	0.71309	2.159000	0.67721	0.533000	0.62120	TCT	.	.		0.408	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		C	60549664	T	C	60549664	3	2	103	1	0	0	0	0	1	0	0	0	1427	1667	58	2	1048	2	BICC1	10	60549664	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	562790	60549664	74985083	628	15251										
SLC16A9	220963	hgsc.bcm.edu	37	chr10	61413574	61413574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accagtaagaaaccctaggaTcccagaaagcaacgccaatg	8	12	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:61413574T>C	ENST00000395348.3	-	5	1846	c.1210A>G	c.(1210-1212)Atc>Gtc	p.I404V	SLC16A9_ENST00000395347.1_Missense_Mutation_p.I404V	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	404					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						AACCCTAGGATCCCAGAAAGC	0.413																																					p.I404V		Atlas-SNP	.											.	SLC16A9	58	.	0			c.A1210G						.						138	129	132					10																	61413574		2203	4300	6503	SO:0001583	missense	220963	exon5			CTAGGATCCCAGA	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.1210A>G	chr10.hg19:g.61413574T>C	ENSP00000378757:p.Ile404Val	70.0	0.0		97.0	4.0	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	hg19	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-2.009250	0.00426	.	.	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.60299	0.2;0.2	5.2	1.38	0.22167	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.463258	0.26019	N	0.026834	T	0.25644	0.0624	N	0.04355	-0.22	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.17715	-1.0360	10	0.09590	T	0.72	.	5.4943	0.16793	0.128:0.1438:0.0:0.7282	.	404	Q7RTY1	MOT9_HUMAN	V	404	ENSP00000378757:I404V;ENSP00000378756:I404V	ENSP00000378756:I404V	I	-	1	0	SLC16A9	61083580	0.008000	0.16893	0.001000	0.08648	0.002000	0.02628	0.103000	0.15292	0.310000	0.22990	-0.326000	0.08463	ATC	.	.		0.413	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		C	61413574	T	C	61413574	3	2	103	1	0	0	0	0	1	0	0	0	14430	1435	50	2	327	2	SLC16A9	10	61413574	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	863910	61413574	74121173	629	15252										
ANK3	288	hgsc.bcm.edu	37	chr10	61819139	61819139	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacccaccagttactcttcgAgcttgagcgcaggactctag	9	13	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:61819139A>G	ENST00000280772.2	-	41	12836	c.12645T>C	c.(12643-12645)gcT>gcC	p.A4215A	ANK3_ENST00000355288.2_Silent_p.A839A|ANK3_ENST00000373827.2_Silent_p.A1699A|RP11-388P9.2_ENST00000414383.1_RNA|ANK3_ENST00000503366.1_Silent_p.A1706A	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	4215					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTACTCTTCGAGCTTGAGCGC	0.413																																					p.A4215A		Atlas-SNP	.											.	ANK3	703	.	0			c.T12645C						.						201	175	184					10																	61819139		2203	4300	6503	SO:0001819	synonymous_variant	288	exon41			TCTTCGAGCTTGA	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.12645T>C	chr10.hg19:g.61819139A>G		165.0	0.0		173.0	7.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.		0.413	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		G	61819139	A	G	61819139	2	3	103	1	0	0	0	0	0	0	0	1	622	291	11	2		2	ANK3	10	61819139	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	405565	61819139	73715608	630	15253										
TET1	80312	hgsc.bcm.edu	37	chr10	70333306	70333306	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gattcctggtgctattccagTccaaggagaggtctttggta	12	8	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:70333306T>C	ENST00000373644.4	+	2	1420	c.1211T>C	c.(1210-1212)gTc>gCc	p.V404A		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	404					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GCTATTCCAGTCCAAGGAGAG	0.507																																					p.V404A		Atlas-SNP	.											.	TET1	255	.	0			c.T1211C						.						150	157	154					10																	70333306		2203	4300	6503	SO:0001583	missense	80312	exon2			TTCCAGTCCAAGG	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.1211T>C	chr10.hg19:g.70333306T>C	ENSP00000362748:p.Val404Ala	99.0	0.0		111.0	5.0	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	T	7.745	0.702023	0.15172	.	.	ENSG00000138336	ENST00000373644	T	0.07688	3.17	4.48	1.92	0.25849	.	0.363501	0.20071	N	0.099866	T	0.03915	0.0110	N	0.24115	0.695	0.22017	N	0.999413	B	0.06786	0.001	B	0.04013	0.001	T	0.43750	-0.9372	10	0.07644	T	0.81	.	3.424	0.07403	0.1975:0.1082:0.0:0.6943	.	404	Q8NFU7	TET1_HUMAN	A	404	ENSP00000362748:V404A	ENSP00000362748:V404A	V	+	2	0	TET1	70003312	0.995000	0.38212	0.998000	0.56505	0.649000	0.38597	0.204000	0.17335	0.813000	0.34350	-0.400000	0.06385	GTC	.	.		0.507	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		C	70333306	T	C	70333306	3	2	103	1	0	0	0	0	1	0	0	0	15784	1667	58	2	1213	2	TET1	10	70333306	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	8514167	70333306	65201441	631	15254										
HKDC1	80201	hgsc.bcm.edu	37	chr10	71017124	71017124	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcagtcgtgaatgatacagtGgggaccatgatgacctgtgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:71017124delG	ENST00000354624.5	+	14	2107	c.1974delG	c.(1972-1974)gtgfs	p.V658fs	HKDC1_ENST00000395086.2_Frame_Shift_Del_p.V658fs	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	658	Hexokinase type-1 2.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						ATGATACAGTGGGGACCATGA	0.438																																					p.V658fs		Atlas-INDEL	.											.	HKDC1	98	.	0			c.1973delT						.						249	210	223					10																	71017124		2203	4300	6503	SO:0001589	frameshift_variant	80201	exon14			.		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.1974delG	chr10.hg19:g.71017124delG	ENSP00000346643:p.Val658fs	149.0	0.0		183.0	12.0	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Frame_Shift_Del	DEL	ENST00000354624.5	hg19	CCDS7288.1																																																																																			.	.		0.438	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		-	71017124	G	-	71017124	7	5	103	1	0	1	0	1	0	0	0	0	7202	1335	47	0	2028	0	HKDC1	10	71017124	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	683818	71017124	64517623	632	15255										
TACR2	6865	hgsc.bcm.edu	37	chr10	71164684	71164684	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tccccactggtagcctcggaGggggctgtgtccccagccat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:71164684delG	ENST00000373306.4	-	5	1638	c.1095delC	c.(1093-1095)cccfs	p.P365fs	TACR2_ENST00000373307.1_Frame_Shift_Del_p.P153fs	NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	365					excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						TAGCCTCGGAGGGGGCTGTGT	0.562																																					p.S366fs		Atlas-INDEL	.											.	TACR2	37	.	0			c.1096delT						.						83	81	82					10																	71164684		2203	4300	6503	SO:0001589	frameshift_variant	6865	exon5			.		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"GPCR / Class A : Tachykinin receptors"	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.1095delC	chr10.hg19:g.71164684delG	ENSP00000362403:p.Pro365fs	132.0	0.0		165.0	10.0	NM_001057	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Frame_Shift_Del	DEL	ENST00000373306.4	hg19	CCDS7293.1																																																																																			.	.		0.562	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1			-	71164684	G	-	71164684	7	5	103	1	0	1	0	1	0	0	0	0	15521	987	35	0	105	0	TACR2	10	71164684	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	147560	71164684	64370063	633	15256										
NEUROG3	50674	hgsc.bcm.edu	37	chr10	71332756	71332756	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggaaggaccgctccgtctcaCgggtcacttggacagtgggc	15	12	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:71332756C>T	ENST00000242462.4	-	2	73	c.44G>A	c.(43-45)cGt>cAt	p.R15H	RP11-343J3.2_ENST00000428753.1_RNA	NM_020999.3	NP_066279.2	Q9Y4Z2	NGN3_HUMAN	neurogenin 3	15					central nervous system development (GO:0007417)|endocrine pancreas development (GO:0031018)|epithelial cell differentiation (GO:0030855)|forebrain development (GO:0030900)|hindbrain development (GO:0030902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|peripheral nervous system development (GO:0007422)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of dendrite morphogenesis (GO:0048814)|spinal cord development (GO:0021510)|transdifferentiation (GO:0060290)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription coactivator activity (GO:0003713)			endometrium(4)|large_intestine(2)|lung(6)|prostate(1)	13						CTCCGTCTCACGGGTCACTTG	0.677																																					p.R15H		Atlas-SNP	.											NEUROG3,NS,carcinoma,0,1	NEUROG3	33	.	0			c.G44A						.						43	48	47					10																	71332756		2203	4300	6503	SO:0001583	missense	50674	exon2			GTCTCACGGGTCA	AJ133776	CCDS31212.1	10q21.3	2013-05-21			ENSG00000122859	ENSG00000122859		"Basic helix-loop-helix proteins"	13806	protein-coding gene	gene with protein product		604882				9000438, 10677506	Standard	NM_020999		Approved	Atoh5, Math4B, ngn3, bHLHa7	uc001jpp.3	Q9Y4Z2	OTTHUMG00000018391	ENST00000242462.4:c.44G>A	chr10.hg19:g.71332756C>T	ENSP00000242462:p.Arg15His	97.0	0.0		74.0	3.0	NM_020999	Q5VVI0|Q6DJX6|Q9BY24	Missense_Mutation	SNP	ENST00000242462.4	hg19	CCDS31212.1	.	.	.	.	.	.	.	.	.	.	C	1.655	-0.513026	0.04200	.	.	ENSG00000122859	ENST00000242462	D	0.94280	-3.39	4.69	-8.44	0.00950	.	17.827300	0.00166	U	0.000006	T	0.79452	0.4448	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.75224	-0.3393	10	0.14656	T	0.56	2.4082	0.7377	0.00968	0.3346:0.3365:0.111:0.218	.	15	Q9Y4Z2	NGN3_HUMAN	H	15	ENSP00000242462:R15H	ENSP00000242462:R15H	R	-	2	0	NEUROG3	71002762	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.014000	0.01449	-2.087000	0.00862	-0.150000	0.13652	CGT	.	.		0.677	NEUROG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048464.1	NM_020999		T	71332756	C	T	71332756	3	4	103	1	0	0	0	0	1	0	0	0	10363	536	19	1	604	1	NEUROG3	10	71332756	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	168072	71332756	64201991	634	15257										
OIT3	170392	hgsc.bcm.edu	37	chr10	74673122	74673122	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acatccccagggagctggttGgtggcctggagctcttcctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:74673122delG	ENST00000334011.5	+	6	1065	c.847delG	c.(847-849)ggtfs	p.G284fs		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	284	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					GGAGCTGGTTGGTGGCCTGGA	0.527																																					p.V282fs	Colon(7;19 345 13446 17537)	Atlas-INDEL	.											.	OIT3	62	.	0			c.846delT						.						167	156	160					10																	74673122		2203	4300	6503	SO:0001589	frameshift_variant	170392	exon6			.		CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.847delG	chr10.hg19:g.74673122delG	ENSP00000333900:p.Gly284fs	114.0	0.0		157.0	11.0	NM_152635	A0AVP3|Q8N1M8	Frame_Shift_Del	DEL	ENST00000334011.5	hg19	CCDS7318.1																																																																																			.	.		0.527	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1	NM_152635		-	74673122	G	-	74673122	7	5	103	1	0	1	0	1	0	0	0	0	10858	1348	47	0	869	0	OIT3	10	74673122	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	3340366	74673122	60861625	635	15258										
SYNPO2L	79933	hgsc.bcm.edu	37	chr10	75407601	75407601	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgagcgctggggggctcaggAgcccctgggcctggggcagg	21	12	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:75407601A>G	ENST00000394810.2	-	4	1958	c.1809T>C	c.(1807-1809)gcT>gcC	p.A603A	SYNPO2L_ENST00000372873.4_Silent_p.A379A	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	603	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					GGGGCTCAGGAGCCCCTGGGC	0.701																																					p.A603A		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.T1809C						.						18	22	21					10																	75407601		2006	4174	6180	SO:0001819	synonymous_variant	79933	exon4			CTCAGGAGCCCCT	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.1809T>C	chr10.hg19:g.75407601A>G		42.0	0.0		62.0	4.0	NM_001114133	A5PKV9|Q68A20	Silent	SNP	ENST00000394810.2	hg19	CCDS44438.1																																																																																			.	.		0.701	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875		G	75407601	A	G	75407601	2	3	103	1	0	0	0	0	0	0	0	1	15473	291	11	2		2	SYNPO2L	10	75407601	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	734479	75407601	60127146	636	15259										
PLAU	414236	hgsc.bcm.edu	37	chr10	75673438	75673438	+	Intron	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggccatctacaggaggcaccGggggggctctgtcacctacg					rs549461157	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:75673438delG	ENST00000409178.1	-	3	268				PLAU_ENST00000372764.3_Frame_Shift_Del_p.R201fs|PLAU_ENST00000372762.4_Frame_Shift_Del_p.R165fs|C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000446342.1_Frame_Shift_Del_p.R184fs|PLAU_ENST00000494287.1_3'UTR	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55											endometrium(1)	1	Prostate(51;0.0112)					AGGAGGCACCGGGGGGGCTCT	0.587																																					p.R201fs		Atlas-INDEL	.											.,1	PLAU	47	.	0			c.601delC						.		,,	17,4245		5,7,2119					,,	2	0.9			66	27,8227		11,5,4111	no	frameshift,frameshift,intron	PLAU,C10orf55	NM_002658.3,NM_001145031.1,NM_001001791.2	,,	16,12,6230	A1A1,A1R,RR		0.3271,0.3989,0.3516	,,	,,		44,12472				SO:0001627	intron_variant	5328	exon7			.		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.73-605C>-	chr10.hg19:g.75673438delG		156.0	0.0		186.0	12.0	NM_002658	Q3KRG4|Q8NAK4	Frame_Shift_Del	DEL	ENST00000409178.1	hg19	CCDS53541.1																																																																																			.	.		0.587	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791		-	75673438	G	-	75673438	6	5	103	0	1	1	0	1	0	0	0	0	12031	1116	39	0		0	PLAU	10	75673438	Intron	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	265837	75673438	59861309	637	15260										
C10orf58	84293	hgsc.bcm.edu	37	chr10	82182254	82182254	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcggaggccaggctgtttccTctgtcgagaggtgagtgcag	17	9	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:82182254T>C	ENST00000372181.1	+	2	730	c.260T>C	c.(259-261)cTc>cCc	p.L87P	FAM213A_ENST00000372188.1_Missense_Mutation_p.L87P|FAM213A_ENST00000372185.1_Missense_Mutation_p.L76P|FAM213A_ENST00000372187.5_Missense_Mutation_p.L87P	NM_001243778.1|NM_001243782.1	NP_001230707.1|NP_001230711.1	Q9BRX8	F213A_HUMAN	family with sequence similarity 213, member A	87	Thioredoxin fold. {ECO:0000250}.				oxidation-reduction process (GO:0055114)|regulation of osteoclast differentiation (GO:0045670)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)										GGCTGTTTCCTCTGTCGAGAG	0.498																																					p.L87P		Atlas-SNP	.											.	.	.	.	0			c.T260C						.						80	88	85					10																	82182254		2203	4300	6503	SO:0001583	missense	84293	exon3			GTTTCCTCTGTCG	AF086462	CCDS7368.1, CCDS58089.1	10q23.1	2011-12-08	2011-12-08	2011-12-08	ENSG00000122378	ENSG00000122378			28651	protein-coding gene	gene with protein product	"peroxiredoxin-like 2 activated in M-CSF stimulated monocytes"		"chromosome 10 open reading frame 58"	C10orf58		11483580, 19951071	Standard	NM_032333		Approved	MGC4248, PAMM	uc001kce.4	Q9BRX8	OTTHUMG00000018614	ENST00000372181.1:c.260T>C	chr10.hg19:g.82182254T>C	ENSP00000361254:p.Leu87Pro	62.0	0.0		69.0	4.0	NM_032333	B2RD81|Q6UW08|Q8N2K3|Q8NBK9|Q96JR0	Missense_Mutation	SNP	ENST00000372181.1	hg19	CCDS7368.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.481600	0.84747	.	.	ENSG00000122378	ENST00000372188;ENST00000372187;ENST00000372185;ENST00000372181	.	.	.	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000001	T	0.78629	0.4313	M	0.81497	2.545	0.80722	D	1	D	0.76494	0.999	D	0.69654	0.965	T	0.81055	-0.1106	9	0.56958	D	0.05	0.1713	13.6543	0.62328	0.0:0.0:0.0:1.0	.	87	Q9BRX8	PAMM_HUMAN	P	87;87;76;87	.	ENSP00000361254:L87P	L	+	2	0	C10orf58	82172234	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.507000	0.81676	2.113000	0.64589	0.533000	0.62120	CTC	.	.		0.498	FAM213A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049077.2			C	82182254	T	C	82182254	3	2	103	1	0	0	0	0	1	0	0	0	1612	1551	54	2	266	2	C10orf58	10	82182254	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	6508816	82182254	53352493	638	15261										
GHITM	27069	hgsc.bcm.edu	37	chr10	85904722	85904722	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagctttgtctgccatagcaAtcagcagaacgcctgttctc	8	13	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:85904722A>C	ENST00000372134.3	+	5	626	c.433A>C	c.(433-435)Atc>Ctc	p.I145L		NM_014394.2	NP_055209.2	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein	145					apoptotic process (GO:0006915)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(2)	10						TGCCATAGCAATCAGCAGAAC	0.388																																					p.I145L		Atlas-SNP	.											.	GHITM	30	.	0			c.A433C						.						181	167	172					10																	85904722		1897	4115	6012	SO:0001583	missense	27069	exon5			ATAGCAATCAGCA	AB009685	CCDS41542.1	10q23.1	2008-02-01			ENSG00000165678	ENSG00000165678			17281	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 5"					8619474, 9110174	Standard	NM_014394		Approved	HSPC282, PTD010, DERP2, My021, TMBIM5	uc001kcs.1	Q9H3K2	OTTHUMG00000018637	ENST00000372134.3:c.433A>C	chr10.hg19:g.85904722A>C	ENSP00000361207:p.Ile145Leu	175.0	0.0		182.0	67.0	NM_014394	A8K9Z9|D3DWE0|O95894|Q5VT95|Q9H0P2	Missense_Mutation	SNP	ENST00000372134.3	hg19	CCDS41542.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.601023	0.28534	.	.	ENSG00000165678	ENST00000372134;ENST00000538477;ENST00000436406;ENST00000339736	T	0.40476	1.03	6.17	-4.32	0.03688	.	0.565075	0.19863	N	0.104385	T	0.14570	0.0352	N	0.10945	0.07	0.18873	N	0.999982	B;B	0.12013	0.005;0.0	B;B	0.15484	0.013;0.001	T	0.31024	-0.9958	10	0.07325	T	0.83	-31.854	5.9594	0.19291	0.3654:0.0:0.4463:0.1883	.	76;145	B4DNL0;Q9H3K2	.;GHITM_HUMAN	L	145;132;145;125	ENSP00000361207:I145L	ENSP00000342214:I125L	I	+	1	0	GHITM	85894702	0.998000	0.40836	0.017000	0.16124	0.390000	0.30446	1.230000	0.32612	-0.828000	0.04273	-0.290000	0.09829	ATC	.	.		0.388	GHITM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049125.1	NM_014394		C	85904722	A	C	85904722	3	2	103	1	0	0	0	0	1	0	0	0	6378	101	4	5	447	5	GHITM	10	85904722	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	3722468	85904722	49630025	639	15262										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88230752	88230752	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaaacttaaaaaatacctgAtggtgctgggaatcatccaa	8	7	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:88230752A>G	ENST00000298767.5	-	8	2611	c.2139T>C	c.(2137-2139)caT>caC	p.H713H	WAPAL_ENST00000263070.7_5'UTR	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	713	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						AAAATACCTGATGGTGCTGGG	0.373																																					p.H713H		Atlas-SNP	.											.	WAPAL	81	.	0			c.T2139C						.						66	61	62					10																	88230752		2203	4300	6503	SO:0001819	synonymous_variant	23063	exon8			TACCTGATGGTGC	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.2139T>C	chr10.hg19:g.88230752A>G		92.0	0.0		92.0	4.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Silent	SNP	ENST00000298767.5	hg19	CCDS7375.1																																																																																			.	.		0.373	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		G	88230752	A	G	88230752	2	3	103	1	0	0	0	0	0	0	0	1	17263	330	12	2		2	WAPAL	10	88230752	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2326030	88230752	47303995	640	15263										
MYOF	26509	hgsc.bcm.edu	37	chr10	95111559	95111559	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagggttgaatggatgatctCagtggttttgctccgatgga	14	6	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:95111559C>T	ENST00000359263.4	-	33	3525	c.3526G>A	c.(3526-3528)Gag>Aag	p.E1176K	MYOF_ENST00000371502.4_Missense_Mutation_p.E1176K|MYOF_ENST00000358334.5_Missense_Mutation_p.E1163K|MYOF_ENST00000371501.4_Missense_Mutation_p.E1176K	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1176	C2 4. {ECO:0000255|PROSITE- ProRule:PRU00041}.				blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TGGATGATCTCAGTGGTTTTG	0.433																																					p.E1176K		Atlas-SNP	.											.	MYOF	177	.	0			c.G3526A						.						118	110	113					10																	95111559		1858	4099	5957	SO:0001583	missense	26509	exon33			TGATCTCAGTGGT	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.3526G>A	chr10.hg19:g.95111559C>T	ENSP00000352208:p.Glu1176Lys	58.0	0.0		79.0	5.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	C	8.823	0.938041	0.18206	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.77	5.77	0.91146	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.53722	0.1814	N	0.20357	0.565	0.80722	D	1	B;B	0.24368	0.008;0.102	B;B	0.31337	0.026;0.128	T	0.51204	-0.8735	10	0.02654	T	1	-27.5578	19.9826	0.97334	0.0:1.0:0.0:0.0	.	1163;1176	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	K	1163;1176;1176;1176	ENSP00000351094:E1163K;ENSP00000352208:E1176K;ENSP00000360556:E1176K;ENSP00000360557:E1176K	ENSP00000351094:E1163K	E	-	1	0	MYOF	95101549	1.000000	0.71417	0.999000	0.59377	0.777000	0.43975	6.050000	0.71063	2.734000	0.93682	0.650000	0.86243	GAG	.	.		0.433	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		T	95111559	C	T	95111559	3	4	103	1	0	0	0	0	1	0	0	0	10098	835	29	3	2747	3	MYOF	10	95111559	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	6880807	95111559	40423188	641	15264										
GPR120	338557	hgsc.bcm.edu	37	chr10	95338962	95338962	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agctgtcgtgactcacagtgAggtaaaagggcactctgagt	13	8	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:95338962A>G	ENST00000371483.4	+	3	799	c.743A>G	c.(742-744)gAg>gGg	p.E248G	FFAR4_ENST00000371481.4_Intron|FFAR4_ENST00000604414.1_Intron	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	248					hormone secretion (GO:0046879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of inflammatory response (GO:0050728)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of glucose transport (GO:0010827)	endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fatty acid binding (GO:0005504)|taste receptor activity (GO:0008527)										ACTCACAGTGAGGTAAAAGGG	0.517																																					p.E248G		Atlas-SNP	.											.	.	.	.	0			c.A743G						.						116	98	104					10																	95338962		2203	4300	6503	SO:0001630	splice_region_variant	338557	exon3			ACAGTGAGGTAAA		CCDS31248.1, CCDS55720.1	10q23.33	2012-11-16	2012-11-16	2012-11-16	ENSG00000186188	ENSG00000186188		"GPCR / Class A : Fatty acid receptors"	19061	protein-coding gene	gene with protein product		609044	"G protein-coupled receptor 129", "G protein-coupled receptor 120", "omega-3 fatty acid receptor 1"	GPR129, GPR120, O3FAR1		20471368, 19723586, 15619630, 20813258	Standard	NM_181745		Approved	PGR4	uc010qnt.2	Q5NUL3	OTTHUMG00000034409	ENST00000371483.4:c.744+1A>G	chr10.hg19:g.95338962A>G		53.0	0.0		80.0	5.0	NM_181745	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Missense_Mutation	SNP	ENST00000371483.4	hg19	CCDS31248.1	.	.	.	.	.	.	.	.	.	.	A	0.109	-1.141138	0.01728	.	.	ENSG00000186188	ENST00000371483	T	0.65732	-0.17	0.893	-1.79	0.07932	GPCR, rhodopsin-like superfamily (1);	9.965130	0.00166	N	0.000001	T	0.42314	0.1197	N	0.17082	0.46	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.04607	-1.0939	10	0.31617	T	0.26	27.4512	2.0073	0.03480	0.2646:0.3067:0.0:0.4286	.	248	Q5NUL3	O3FA1_HUMAN	G	248	ENSP00000360538:E248G	ENSP00000360538:E248G	E	+	2	0	O3FAR1	95328952	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.953000	0.03877	-1.247000	0.02507	-0.783000	0.03347	GAG	.	.		0.517	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745	Missense_Mutation	G	95338962	A	G	95338962	5	3	103	1	0	0	0	0	0	0	1	0	6644	318	11	2	753	2	GPR120	10	95338962	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	227403	95338962	40195785	642	15265										
GPR120	338557	hgsc.bcm.edu	37	chr10	95347278	95347278	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggaatgagtggaagaaaaTtttttgctgcttctggttcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:95347278delT	ENST00000371483.4	+	4	1102	c.1046delT	c.(1045-1047)attfs	p.I349fs	FFAR4_ENST00000371481.4_Frame_Shift_Del_p.I333fs|FFAR4_ENST00000604414.1_Intron	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	349					hormone secretion (GO:0046879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of inflammatory response (GO:0050728)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of glucose transport (GO:0010827)	endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fatty acid binding (GO:0005504)|taste receptor activity (GO:0008527)										TGGAAGAAAATTTTTTGCTGC	0.418																																					p.I349fs		Atlas-INDEL	.											O3FAR1,colon,carcinoma,0,1	.	.	.	0			c.1045delA						.						119	127	124					10																	95347278		2203	4300	6503	SO:0001589	frameshift_variant	338557	exon4			.		CCDS31248.1, CCDS55720.1	10q23.33	2012-11-16	2012-11-16	2012-11-16	ENSG00000186188	ENSG00000186188		"GPCR / Class A : Fatty acid receptors"	19061	protein-coding gene	gene with protein product		609044	"G protein-coupled receptor 129", "G protein-coupled receptor 120", "omega-3 fatty acid receptor 1"	GPR129, GPR120, O3FAR1		20471368, 19723586, 15619630, 20813258	Standard	NM_181745		Approved	PGR4	uc010qnt.2	Q5NUL3	OTTHUMG00000034409	ENST00000371483.4:c.1046delT	chr10.hg19:g.95347278delT	ENSP00000360538:p.Ile349fs	170.0	0.0		195.0	12.0	NM_181745	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Frame_Shift_Del	DEL	ENST00000371483.4	hg19	CCDS31248.1																																																																																			.	.		0.418	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745		-	95347278	T	-	95347278	7	5	103	1	0	1	0	1	0	0	0	0	6644	1493	52	0	1060	0	GPR120	10	95347278	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	8316	95347278	40187469	643	15266										
HELLS	3070	hgsc.bcm.edu	37	chr10	96348094	96348094	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttcaaagaagcaggagatcTtttatacagccattgtgaac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:96348094delT	ENST00000348459.5	+	13	1540	c.1435delT	c.(1435-1437)tttfs	p.F479fs	HELLS_ENST00000394036.1_3'UTR|HELLS_ENST00000394045.1_Frame_Shift_Del_p.F381fs|RP11-119K6.6_ENST00000432120.1_RNA|HELLS_ENST00000239026.6_3'UTR|HELLS_ENST00000371332.4_Frame_Shift_Del_p.F525fs	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		GCAGGAGATCTTTTATACAGC	0.368																																					p.I478fs		Atlas-INDEL	.											.	HELLS	63	.	0			c.1434delC						.						109	106	107					10																	96348094		2203	4300	6503	SO:0001589	frameshift_variant	3070	exon13			.	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6", "proliferation-associated SNF2-like protein"	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.1435delT	chr10.hg19:g.96348094delT	ENSP00000239027:p.Phe479fs	135.0	0.0		130.0	10.0	NM_018063		Frame_Shift_Del	DEL	ENST00000348459.5	hg19	CCDS7434.1																																																																																			.	.		0.368	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		-	96348094	T	-	96348094	7	5	103	1	0	1	0	1	0	0	0	0	7055	1609	56	0	1485	0	HELLS	10	96348094	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1000816	96348094	39186653	644	15267										
ZFYVE27	118813	hgsc.bcm.edu	37	chr10	99517436	99517436	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggaaacagcttctgctctcGatgctgctccttcaaggtgc	10	12	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:99517436G>T	ENST00000393677.4	+	12	1331	c.1127G>T	c.(1126-1128)cGa>cTa	p.R376L	ZFYVE27_ENST00000357540.4_Missense_Mutation_p.R283L|ZFYVE27_ENST00000477521.1_3'UTR|ZFYVE27_ENST00000359980.3_Missense_Mutation_p.R369L|ZFYVE27_ENST00000356257.4_Missense_Mutation_p.R381L|ZFYVE27_ENST00000370613.3_Missense_Mutation_p.R251L|ZFYVE27_ENST00000337540.7_Missense_Mutation_p.R337L|ZFYVE27_ENST00000370610.3_Missense_Mutation_p.R276L|ZFYVE27_ENST00000453958.2_3'UTR	NM_144588.6	NP_653189.3	Q5T4F4	ZFY27_HUMAN	zinc finger, FYVE domain containing 27	376					cell death (GO:0008219)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein localization to plasma membrane (GO:0072659)	axon (GO:0030424)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)	metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	8		Colorectal(252;0.0846)		Epithelial(162;7.08e-10)|all cancers(201;5.18e-08)		TTCTGCTCTCGATGCTGCTCC	0.592																																					p.R381L		Atlas-SNP	.											.	ZFYVE27	31	.	0			c.G1142T						.						123	118	120					10																	99517436		2203	4300	6503	SO:0001583	missense	118813	exon11			GCTCTCGATGCTG	BC030621	CCDS31263.1, CCDS31264.1, CCDS53562.1, CCDS53563.1, CCDS53564.1, CCDS53565.1	10q24.2	2013-09-11			ENSG00000155256	ENSG00000155256		"Zinc fingers, FYVE domain containing"	26559	protein-coding gene	gene with protein product	"protrudin"	610243				14702039	Standard	NM_144588		Approved	FLJ32919, SPG33	uc001kol.2	Q5T4F4	OTTHUMG00000018867	ENST00000393677.4:c.1127G>T	chr10.hg19:g.99517436G>T	ENSP00000377282:p.Arg376Leu	158.0	0.0		172.0	57.0	NM_001002261	B7Z3S0|B7Z404|B7Z626|G8JLC3|G8JLF0|J3KP98|Q5T4F1|Q5T4F2|Q5T4F3|Q8N1K0|Q8N6D6|Q8NCA0|Q8NDE4|Q96M08	Missense_Mutation	SNP	ENST00000393677.4	hg19	CCDS31263.1	.	.	.	.	.	.	.	.	.	.	G	33	5.208201	0.95033	.	.	ENSG00000155256	ENST00000337540;ENST00000357540;ENST00000370613;ENST00000370610;ENST00000393677;ENST00000359980;ENST00000356257;ENST00000423811	T;T;T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	5.52	5.52	0.82312	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.87261	0.6133	M	0.67953	2.075	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.997;0.996;1.0;0.999;1.0	D;D;D;D;D;D;D	0.91635	0.998;0.999;0.994;0.995;0.998;0.996;0.999	D	0.87894	0.2686	10	0.66056	D	0.02	-20.3208	17.6242	0.88090	0.0:0.0:1.0:0.0	.	337;276;251;283;381;369;376	B7Z404;B7Z3S0;B7Z626;Q5T4F4-5;Q5T4F4-3;Q5T4F4-2;Q5T4F4	.;.;.;.;.;.;ZFY27_HUMAN	L	337;283;251;276;376;369;381;359	ENSP00000337993:R337L;ENSP00000350148:R283L;ENSP00000359646:R251L;ENSP00000359642:R276L;ENSP00000377282:R376L;ENSP00000353069:R369L;ENSP00000348593:R381L;ENSP00000409594:R359L	ENSP00000337993:R337L	R	+	2	0	ZFYVE27	99507426	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.507000	0.90522	2.600000	0.87896	0.561000	0.74099	CGA	.	.		0.592	ZFYVE27-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049745.2	NM_144588		T	99517436	G	T	99517436	3	4	103	1	0	0	0	0	1	0	0	0	17684	1058	37	1	1184	1	ZFYVE27	10	99517436	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	3169342	99517436	36017311	645	15268										
C10orf28	27291	hgsc.bcm.edu	37	chr10	99991437	99991437	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accttctacgggttttctgcAgttatcagtgagtatgcaaa	9	8	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:99991437A>G	ENST00000298999.3	+	6	2257	c.1954A>G	c.(1954-1956)Agt>Ggt	p.S652G	R3HCC1L_ENST00000370584.3_Missense_Mutation_p.S652G|R3HCC1L_ENST00000314594.5_Missense_Mutation_p.S68G|R3HCC1L_ENST00000370586.2_Missense_Mutation_p.S58G	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	666							nucleotide binding (GO:0000166)										GGTTTTCTGCAGTTATCAGTG	0.363																																					p.S666G		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.A1996G						.						93	92	93					10																	99991437		2203	4300	6503	SO:0001583	missense	27291	exon7			TTCTGCAGTTATC	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 28"	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1954A>G	chr10.hg19:g.99991437A>G	ENSP00000298999:p.Ser652Gly	79.0	0.0		109.0	5.0	NM_001256619	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	hg19	CCDS31267.1	.	.	.	.	.	.	.	.	.	.	A	14.84	2.655847	0.47467	.	.	ENSG00000166024	ENST00000370584;ENST00000298999;ENST00000370586;ENST00000314594;ENST00000544834	T;T;T;T	0.27402	1.67;1.67;1.67;1.67	5.73	5.73	0.89815	Nucleotide-binding, alpha-beta plait (1);	0.130755	0.64402	D	0.000002	T	0.35770	0.0943	L	0.42245	1.32	0.49130	D	0.999758	B;P;B	0.50943	0.042;0.94;0.332	B;P;B	0.49012	0.033;0.598;0.156	T	0.04005	-1.0985	9	.	.	.	-7.0369	14.9743	0.71257	1.0:0.0:0.0:0.0	.	58;666;652	Q7Z5L2-3;Q7Z5L2;Q7Z5L2-2	.;GIDRP_HUMAN;.	G	652;652;58;68;59	ENSP00000359616:S652G;ENSP00000298999:S652G;ENSP00000359618:S58G;ENSP00000314018:S68G	.	S	+	1	0	C10orf28	99981427	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	1.865000	0.39479	2.169000	0.68431	0.533000	0.62120	AGT	.	.		0.363	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472		G	99991437	A	G	99991437	3	3	103	1	0	0	0	0	1	0	0	0	1603	188	7	2	1960	2	C10orf28	10	99991437	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	474001	99991437	35543310	646	15269										
PSD	5662	hgsc.bcm.edu	37	chr10	104163074	104163074	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggagtgagaaggagggagTccatcctctgtgctcccggc	15	11	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:104163074T>C	ENST00000020673.5	-	17	3484	c.2958A>G	c.(2956-2958)ggA>ggG	p.G986G	PSD_ENST00000406432.1_Silent_p.G986G	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	986					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		AAGGAGGGAGTCCATCCTCTG	0.667																																					p.G986G		Atlas-SNP	.											.	PSD	164	.	0			c.A2958G						.						82	59	67					10																	104163074		2203	4300	6503	SO:0001819	synonymous_variant	5662	exon18			AGGGAGTCCATCC	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.2958A>G	chr10.hg19:g.104163074T>C		132.0	0.0		133.0	6.0	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Silent	SNP	ENST00000020673.5	hg19	CCDS31272.1																																																																																			.	.		0.667	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			C	104163074	T	C	104163074	2	2	103	1	0	0	0	0	0	0	0	1	12658	1654	58	2		2	PSD	10	104163074	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4171637	104163074	31371673	647	15270										
CALHM1	255022	hgsc.bcm.edu	37	chr10	105215220	105215220	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctttcctcctccgcaccatcGggggtcgtgggggcagctgc					rs184539423		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:105215220delG	ENST00000329905.5	-	2	976	c.840delC	c.(838-840)cccfs	p.P280fs	RP11-225H22.4_ENST00000411906.1_RNA|CALHM2_ENST00000393235.1_5'Flank	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	280					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						CCGCACCATCGGGGGTCGTGG	0.632																																					p.D281fs		Atlas-INDEL	.											.	CALHM1	33	.	0			c.841delG						.						47	37	40					10																	105215220		2203	4300	6503	SO:0001589	frameshift_variant	255022	exon2			.	BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"family with sequence similarity 26, member C"	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.840delC	chr10.hg19:g.105215220delG	ENSP00000329926:p.Pro280fs	185.0	0.0		172.0	11.0	NM_001001412	Q5W091	Frame_Shift_Del	DEL	ENST00000329905.5	hg19	CCDS7550.1																																																																																			.	.		0.632	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412		-	105215220	G	-	105215220	7	5	103	1	0	1	0	1	0	0	0	0	2584	1103	39	0	204	0	CALHM1	10	105215220	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1052146	105215220	30319527	648	15271										
TDRD1	56165	hgsc.bcm.edu	37	chr10	115987018	115987018	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctagtgacatttggtctggcAaaaaacatcacacctcaaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:115987018delA	ENST00000251864.2	+	23	3516	c.3363delA	c.(3361-3363)gcafs	p.A1121fs	TDRD1_ENST00000369282.1_Intron|TDRD1_ENST00000369281.2_Frame_Shift_Del_p.A1007fs|TDRD1_ENST00000369280.1_Intron|TDRD1_ENST00000422662.1_Intron	NM_198795.1	NP_942090.1	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	1121					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TTGGTCTGGCAAAAAACATCA	0.358																																					p.A1121fs		Atlas-INDEL	.											.	TDRD1	126	.	0			c.3362delC						.						172	165	167					10																	115987018		2203	4300	6503	SO:0001589	frameshift_variant	56165	exon23			.	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000251864.2:c.3363delA	chr10.hg19:g.115987018delA	ENSP00000251864:p.Ala1121fs	194.0	0.0		209.0	13.0	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Frame_Shift_Del	DEL	ENST00000251864.2	hg19	CCDS7588.1																																																																																			.	.		0.358	TDRD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				-	115987018	A	-	115987018	7	5	103	1	0	1	0	1	0	0	0	0	15745	117	5	0	3449	0	TDRD1	10	115987018	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	10771798	115987018	19547729	649	15272										
PRDX3	10935	hgsc.bcm.edu	37	chr10	120933332	120933332	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttcacagttcacgtcgtgaaAttcgttagctttgtcactaa	7	9	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:120933332A>G	ENST00000298510.2	-	4	406	c.364T>C	c.(364-366)Ttt>Ctt	p.F122L	PRDX3_ENST00000494433.1_5'Flank|PRDX3_ENST00000356951.3_Missense_Mutation_p.F104L	NM_006793.2	NP_006784.1	P30048	PRDX3_HUMAN	peroxiredoxin 3	122	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular response to oxidative stress (GO:0034599)|cellular response to reactive oxygen species (GO:0034614)|hydrogen peroxide catabolic process (GO:0042744)|maternal placenta development (GO:0001893)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of kinase activity (GO:0033673)|peptidyl-cysteine oxidation (GO:0018171)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of mitochondrial membrane potential (GO:0051881)|response to hydrogen peroxide (GO:0042542)|response to lipopolysaccharide (GO:0032496)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	alkyl hydroperoxide reductase activity (GO:0008785)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|kinase binding (GO:0019900)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|thioredoxin peroxidase activity (GO:0008379)			endometrium(1)|lung(2)	3		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0245)		ACGTCGTGAAATTCGTTAGCT	0.403																																					p.F122L	Pancreas(36;562 1096 2447 42526)	Atlas-SNP	.											.	PRDX3	15	.	0			c.T364C						.						102	95	98					10																	120933332		2203	4300	6503	SO:0001583	missense	10935	exon4			CGTGAAATTCGTT	D49396	CCDS7611.1	10q25-q26	2010-11-24			ENSG00000165672	ENSG00000165672			9354	protein-coding gene	gene with protein product		604769	"antioxidant protein 1"	AOP1		7733872, 9363753	Standard	NM_006793		Approved	MER5, AOP-1, SP-22	uc001lec.3	P30048	OTTHUMG00000019146	ENST00000298510.2:c.364T>C	chr10.hg19:g.120933332A>G	ENSP00000298510:p.Phe122Leu	53.0	0.0		77.0	4.0	NM_006793	B2R7Z0|D3DRC9|E9PH29|P35690|Q0D2H1|Q13776|Q5T5V2|Q96HK4	Missense_Mutation	SNP	ENST00000298510.2	hg19	CCDS7611.1	.	.	.	.	.	.	.	.	.	.	A	33	5.202622	0.94997	.	.	ENSG00000165672	ENST00000356951;ENST00000298510	T;T	0.19532	2.14;2.14	4.81	4.81	0.61882	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant (1);Thioredoxin-like fold (3);	0.044938	0.85682	D	0.000000	T	0.46014	0.1371	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.49312	-0.8953	10	0.87932	D	0	-20.3557	14.676	0.68981	1.0:0.0:0.0:0.0	.	122	P30048	PRDX3_HUMAN	L	104;122	ENSP00000349432:F104L;ENSP00000298510:F122L	ENSP00000298510:F122L	F	-	1	0	PRDX3	120923322	1.000000	0.71417	0.996000	0.52242	0.909000	0.53808	9.107000	0.94261	1.926000	0.55796	0.533000	0.62120	TTT	.	.		0.403	PRDX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050639.1	NM_006793		G	120933332	A	G	120933332	3	3	103	1	0	0	0	0	1	0	0	0	12478	101	4	2	422	2	PRDX3	10	120933332	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	4946314	120933332	14601415	650	15273										
C10orf119	79892	hgsc.bcm.edu	37	chr10	121607167	121607167	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcagcacaggatccacagacAgtatgccatatagctcaaga	8	11	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:121607167A>G	ENST00000360003.3	-	8	954	c.785T>C	c.(784-786)cTg>cCg	p.L262P	MCMBP_ENST00000369077.3_Missense_Mutation_p.L262P|MCMBP_ENST00000466047.1_5'UTR	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	262					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						ATCCACAGACAGTATGCCATA	0.348																																					p.L262P		Atlas-SNP	.											.	MCMBP	49	.	0			c.T785C						.						152	135	141					10																	121607167		2203	4300	6503	SO:0001583	missense	79892	exon8			ACAGACAGTATGC	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"chromosome 10 open reading frame 119"	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.785T>C	chr10.hg19:g.121607167A>G	ENSP00000353098:p.Leu262Pro	72.0	0.0		78.0	4.0	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Missense_Mutation	SNP	ENST00000360003.3	hg19	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.974558	0.74246	.	.	ENSG00000197771	ENST00000360003;ENST00000369077	T;T	0.67171	-0.25;-0.25	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.80803	0.4693	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.82938	-0.0209	10	0.87932	D	0	-23.0419	14.7194	0.69294	1.0:0.0:0.0:0.0	.	262;262	Q9BTE3-2;Q9BTE3	.;MCMBP_HUMAN	P	262	ENSP00000353098:L262P;ENSP00000358073:L262P	ENSP00000353098:L262P	L	-	2	0	MCMBP	121597157	0.998000	0.40836	0.027000	0.17364	0.983000	0.72400	7.675000	0.84002	2.272000	0.75746	0.459000	0.35465	CTG	.	.		0.348	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		G	121607167	A	G	121607167	3	3	103	1	0	0	0	0	1	0	0	0	1590	188	7	2	1179	2	C10orf119	10	121607167	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	673835	121607167	13927580	651	15274										
WDR11	55717	hgsc.bcm.edu	37	chr10	122625230	122625230	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcgaagatcttataataacaTttttaccacttcaaatgagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:122625230delT	ENST00000263461.6	+	7	1214	c.968delT	c.(967-969)attfs	p.I323fs		NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	1332					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						TATAATAACATTTTTACCACT	0.303																																					p.I323fs		Atlas-INDEL	.											.	WDR11	95	.	0			c.967delA						.						78	76	77					10																	122625230		2201	4295	6496	SO:0001589	frameshift_variant	55717	exon7			.	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.968delT	chr10.hg19:g.122625230delT	ENSP00000263461:p.Ile323fs	108.0	0.0		148.0	13.0	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Frame_Shift_Del	DEL	ENST00000263461.6	hg19	CCDS7619.1																																																																																			.	.		0.303	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			-	122625230	T	-	122625230	7	5	103	1	0	1	0	1	0	0	0	0	17288	1493	52	0	994	0	WDR11	10	122625230	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1018063	122625230	12909517	652	15275										
WDR11	55717	hgsc.bcm.edu	37	chr10	122643322	122643322	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcagtcgtattcagagataaAcccctggagctatgggatgt	12	8	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:122643322A>G	ENST00000263461.6	+	14	2016	c.1770A>G	c.(1768-1770)aaA>aaG	p.K590K	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	247					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						TCAGAGATAAACCCCTGGAGC	0.338																																					p.K590K		Atlas-SNP	.											WDR11,colon,carcinoma,0,1	WDR11	95	.	0			c.A1770G						.						108	104	106					10																	122643322		2203	4300	6503	SO:0001819	synonymous_variant	55717	exon14			AGATAAACCCCTG	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.1770A>G	chr10.hg19:g.122643322A>G		63.0	0.0		71.0	3.0	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	hg19	CCDS7619.1																																																																																			.	.		0.338	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			G	122643322	A	G	122643322	2	3	103	1	0	0	0	0	0	0	0	1	17288	40	2	2		2	WDR11	10	122643322	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	18092	122643322	12891425	653	15276										
IKZF5	64376	hgsc.bcm.edu	37	chr10	124753859	124753859	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaggccaccagttggtgtggTttttgccatactttcatagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:124753859delT	ENST00000368886.5	-	5	1017	c.697delA	c.(697-699)accfs	p.T234fs	PSTK_ENST00000497219.1_Intron	NM_001271840.1	NP_001258769.1	Q9H5V7	IKZF5_HUMAN	IKAROS family zinc finger 5 (Pegasus)	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|lung(3)|prostate(1)	6		all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222)		Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754)		GTTGGTGTGGTTTTTGCCATA	0.483																																					p.T233fs		Atlas-INDEL	.											.	IKZF5	26	.	0			c.698delC						.						160	158	159					10																	124753859		1966	4147	6113	SO:0001589	frameshift_variant	64376	exon5			.	AF230808	CCDS41574.1	10q26	2011-05-31	2006-08-25	2006-08-25	ENSG00000095574	ENSG00000095574		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	14283	protein-coding gene	gene with protein product		606238	"zinc finger protein, subfamily 1A, 5", "zinc finger protein, subfamily 1A, 5 (Pegasus)"	ZNFN1A5		10978333	Standard	NM_001271840		Approved	Pegasus, FLJ22973	uc021qaj.2	Q9H5V7	OTTHUMG00000019192	ENST00000368886.5:c.697delA	chr10.hg19:g.124753859delT	ENSP00000357881:p.Thr234fs	208.0	0.0		246.0	17.0	NM_001271840	B3KVH7|D3DRE7|Q9H2T0	Frame_Shift_Del	DEL	ENST00000368886.5	hg19	CCDS41574.1																																																																																			.	.		0.483	IKZF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050820.2	NM_022466		-	124753859	T	-	124753859	7	5	103	1	0	1	0	1	0	0	0	0	7627	1725	60	0	566	0	IKZF5	10	124753859	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2110537	124753859	10780888	654	15277										
DHX32	55760	hgsc.bcm.edu	37	chr10	127542640	127542640	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctttgataaacttggcatcTtttttctgtttcatcgagtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:127542640delT	ENST00000284690.3	-	4	1472	c.982delA	c.(982-984)agafs	p.R328fs	DHX32_ENST00000284688.6_Intron|DHX32_ENST00000368721.1_5'UTR	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	328						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				ACTTGGCATCTTTTTTCTGTT	0.403																																					p.R328fs		Atlas-INDEL	.											.	DHX32	67	.	0			c.983delG						.						154	153	153					10																	127542640		2203	4300	6503	SO:0001589	frameshift_variant	55760	exon4			.		CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"DEAH-boxes"	16717	protein-coding gene	gene with protein product		607960	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.982delA	chr10.hg19:g.127542640delT	ENSP00000284690:p.Arg328fs	148.0	0.0		156.0	10.0	NM_018180	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Frame_Shift_Del	DEL	ENST00000284690.3	hg19	CCDS7652.1																																																																																			.	.		0.403	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180		-	127542640	T	-	127542640	7	5	103	1	0	1	0	1	0	0	0	0	4507	1617	56	0	1281	0	DHX32	10	127542640	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2788781	127542640	7992107	655	15278										
PRAP1	118471	hgsc.bcm.edu	37	chr10	135165935	135165935	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaccaagaccacatctaccaCccccagtagggctccagggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:135165935delC	ENST00000433452.2	+	5	719	c.447delC	c.(445-447)cacfs	p.H149fs	PRAP1_ENST00000463201.1_3'UTR|RP11-122K13.7_ENST00000452591.1_RNA|FUOM_ENST00000465384.1_5'Flank|PRAP1_ENST00000423766.1_Frame_Shift_Del_p.H150fs|PRAP1_ENST00000458230.1_Frame_Shift_Del_p.H140fs|ZNF511_ENST00000368554.4_Frame_Shift_Del_p.H308fs			Q96NZ9	PRAP1_HUMAN	proline-rich acidic protein 1	149						extracellular region (GO:0005576)				large_intestine(1)|lung(2)	3		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		all cancers(32;7.08e-06)|OV - Ovarian serous cystadenocarcinoma(35;7.88e-06)|Epithelial(32;9.48e-06)		ACATCTACCACCCCCAGTAGG	0.652																																					p.H149fs		Atlas-INDEL	.											.	PRAP1	20	.	0			c.446delA						.						71	67	69					10																	135165935		2203	4300	6503	SO:0001589	frameshift_variant	118471	exon5			.	AF421885	CCDS7679.1	10q26.3	2012-10-01			ENSG00000165828	ENSG00000165828			23304	protein-coding gene	gene with protein product		609776				14583459, 20674898	Standard	NM_001145201		Approved	UPA		Q96NZ9	OTTHUMG00000019312	ENST00000433452.2:c.447delC	chr10.hg19:g.135165935delC	ENSP00000416126:p.His149fs	114.0	0.0		163.0	10.0	NM_145202	B7ZL57|B7ZL58|E9KL31|Q5VWY4|Q7Z4X5|Q8IWR3|Q8NCS2	Frame_Shift_Del	DEL	ENST00000433452.2	hg19	CCDS7679.1																																																																																			.	.		0.652	PRAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051132.1	NM_145202		-	135165935	C	-	135165935	7	5	103	1	0	1	0	1	0	0	0	0	12453	506	18	0	465	0	PRAP1	10	135165935	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	7623295	135165935	368812	656	15279										
RIC8A	60626	hgsc.bcm.edu	37	chr11	211289	211289	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggagactccacggagttcatGggagtgaatatggatgtgat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:211289delG	ENST00000526104.1	+	5	2253	c.909delG	c.(907-909)atgfs	p.M303fs	RIC8A_ENST00000325207.5_Frame_Shift_Del_p.M303fs|RIC8A_ENST00000527696.1_Frame_Shift_Del_p.M297fs			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	303					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CGGAGTTCATGGGAGTGAATA	0.577																																					p.M303fs		Atlas-INDEL	.											.	RIC8A	45	.	0			c.908delT						.						129	111	117					11																	211289		2203	4300	6503	SO:0001589	frameshift_variant	60626	exon5			.	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069	ENST00000526104.1:c.909delG	chr11.hg19:g.211289delG	ENSP00000432008:p.Met303fs	150.0	0.0		158.0	10.0	NM_021932	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Frame_Shift_Del	DEL	ENST00000526104.1	hg19																																																																																				.	.		0.577	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		-	211289	G	-	211289	7	5	103	1	0	1	0	1	0	0	0	0	13370	1348	47	0	927	0	RIC8A	11	211289	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10		211289	134795227	657	15280										
NLRP6	171389	hgsc.bcm.edu	37	chr11	281492	281492	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagggacagggacagggctgCcccggagtggcaccagaggt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:281492delC	ENST00000312165.5	+	4	1758	c.1758delC	c.(1756-1758)tgcfs	p.C586fs	NLRP6_ENST00000534750.1_Frame_Shift_Del_p.C586fs	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	586					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		GACAGGGCTGCCCCGGAGTGG	0.672																																					p.C586fs		Atlas-INDEL	.											.	NLRP6	4	.	0			c.1757delG						.						29	34	32					11																	281492		2202	4300	6502	SO:0001589	frameshift_variant	171389	exon4			.	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"Nucleotide-binding domain and leucine rich repeat containing"	22944	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"	609650	"NACHT, leucine rich repeat and PYD containing 6"	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.1758delC	chr11.hg19:g.281492delC	ENSP00000309767:p.Cys586fs	124.0	0.0		153.0	10.0	NM_138329	A8K9F3|E9PJZ8	Frame_Shift_Del	DEL	ENST00000312165.5	hg19	CCDS7693.1																																																																																			.	.		0.672	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		-	281492	C	-	281492	7	5	103	1	0	1	0	1	0	0	0	0	10490	747	26	0	1772	0	NLRP6	11	281492	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	70203	281492	134725024	658	15281										
MUC2	4583	hgsc.bcm.edu	37	chr11	1094691	1094691	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccactcgcggtaccacgaccGggtcatcttcagcccccacc	8	20	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:1094691G>T	ENST00000441003.2	+	31	5806	c.5779G>T	c.(5779-5781)Ggg>Tgg	p.G1927W	MUC2_ENST00000361558.6_Missense_Mutation_p.G65W|MUC2_ENST00000333592.6_Missense_Mutation_p.G215W	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4289					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TACCACGACCGGGTCATCTTC	0.632																																					p.G1923W		Atlas-SNP	.											.	MUC2	614	.	0			c.G5767T						.						78	97	90					11																	1094691		2117	4220	6337	SO:0001583	missense	4583	exon32			ACGACCGGGTCAT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5779G>T	chr11.hg19:g.1094691G>T	ENSP00000415183:p.Gly1927Trp	108.0	0.0		146.0	7.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	G	10.79	1.449554	0.26074	.	.	ENSG00000198788	ENST00000441003;ENST00000361558;ENST00000333592	T;T;T	0.41758	2.56;0.99;2.9	1.97	-1.24	0.09435	.	.	.	.	.	T	0.40171	0.1106	L	0.51422	1.61	0.09310	N	1	D	0.63880	0.993	P	0.49665	0.618	T	0.31613	-0.9937	9	0.66056	D	0.02	.	5.8132	0.18477	0.5036:0.0:0.4964:0.0	.	1927	E7EUV1	.	W	1927;65;215	ENSP00000415183:G1927W;ENSP00000354885:G65W;ENSP00000331373:G215W	ENSP00000331373:G215W	G	+	1	0	MUC2	1084691	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.996000	0.00655	-0.225000	0.09913	0.479000	0.44913	GGG	.	.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1094691	G	T	1094691	3	4	103	1	0	0	0	0	1	0	0	0	9984	1116	39	1	5893	1	MUC2	11	1094691	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	813199	1094691	133911825	659	15282										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1278487	1278487	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagcctgcgtgggacccgatGggtttcctaaatttgtgagt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:1278487delG	ENST00000529681.1	+	40	16313	c.16255delG	c.(16255-16257)gggfs	p.G5419fs	MUC5B_ENST00000447027.1_Frame_Shift_Del_p.G5422fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5419	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GGGACCCGATGGGTTTCCTAA	0.632																																					p.D5418fs		Atlas-INDEL	.											.	MUC5B	473	.	0			c.16254delT						.						96	104	102					11																	1278487		2025	4175	6200	SO:0001589	frameshift_variant	727897	exon40			.	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16255delG	chr11.hg19:g.1278487delG	ENSP00000436812:p.Gly5419fs	191.0	0.0		208.0	13.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.632	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		-	1278487	G	-	1278487	7	5	103	1	0	1	0	1	0	0	0	0	9988	1348	47	0	16422	0	MUC5B	11	1278487	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	183796	1278487	133728029	660	15283										
KCNQ1	3784	hgsc.bcm.edu	37	chr11	2609986	2609986	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggacaaagacaatggggtgaCtcctggagagaagatgctca	14	7	1	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:2609986C>T	ENST00000155840.5	+	10	1403	c.1295C>T	c.(1294-1296)aCt>aTt	p.T432I	KCNQ1_ENST00000335475.5_Missense_Mutation_p.T305I	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	432					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	AATGGGGTGACTCCTGGAGAG	0.512																																					p.T432I		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1295T						.						67	66	66					11																	2609986		2202	4299	6501	SO:0001583	missense	3784	exon10			GGGTGACTCCTGG	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6294	protein-coding gene	gene with protein product	"Jervell and Lange-Nielsen syndrome 1"	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.1295C>T	chr11.hg19:g.2609986C>T	ENSP00000155840:p.Thr432Ile	51.0	0.0		100.0	5.0	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Missense_Mutation	SNP	ENST00000155840.5	hg19	CCDS7736.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.472772	0.26423	.	.	ENSG00000053918	ENST00000155840;ENST00000335475	D;D	0.99264	-5.65;-5.58	5.02	3.16	0.36331	.	1.079220	0.07093	N	0.839072	D	0.97099	0.9052	N	0.22421	0.69	0.09310	N	1	B;B;B	0.12630	0.006;0.004;0.002	B;B;B	0.17722	0.019;0.008;0.004	D	0.94232	0.7477	10	0.87932	D	0	-9.5083	7.2776	0.26294	0.0929:0.1723:0.7348:0.0	.	305;305;432	P51787-2;Q14D14;P51787	.;.;KCNQ1_HUMAN	I	432;305	ENSP00000155840:T432I;ENSP00000334497:T305I	ENSP00000155840:T432I	T	+	2	0	KCNQ1	2566562	0.003000	0.15002	0.113000	0.21522	0.893000	0.52053	0.558000	0.23469	0.658000	0.30925	-0.359000	0.07587	ACT	.	.		0.512	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218		T	2609986	C	T	2609986	3	4	103	1	0	0	0	0	1	0	0	0	8091	565	20	3	1342	3	KCNQ1	11	2609986	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	1331499	2609986	132396530	661	15284										
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411960	6411960	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcgctggcgctggcgctggcGctggcgctggctctgtctga	18	13	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:6411960G>T	ENST00000342245.4	+	1	300	c.132G>T	c.(130-132)gcG>gcT	p.A44A	SMPD1_ENST00000356761.2_Silent_p.A44A|SMPD1_ENST00000527275.1_Silent_p.A44A|SMPD1_ENST00000299397.3_Silent_p.A44A|SMPD1_ENST00000533196.1_3'UTR	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	44					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	tggcgctggcgctggcgctgg	0.692																																					p.A44A		Atlas-SNP	.											.	SMPD1	108	.	0			c.G132T						.						19	22	21					11																	6411960		2199	4295	6494	SO:0001819	synonymous_variant	6609	exon1			GCTGGCGCTGGCG	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.132G>T	chr11.hg19:g.6411960G>T		18.0	0.0		46.0	6.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	hg19	CCDS44531.1																																																																																			.	.		0.692	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		T	6411960	G	T	6411960	2	4	103	1	0	0	0	0	0	0	0	1	14819	1074	38	1		1	SMPD1	11	6411960	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	3801974	6411960	128594556	662	15285										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6592498	6592498	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcgtcttccacctgtcagccTttcgccacccgcgccgcctg	9	20	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:6592498T>C	ENST00000527990.2	+	40	13756	c.13756T>C	c.(13756-13758)Ttt>Ctt	p.F4586L	DNHD1_ENST00000254579.6_Missense_Mutation_p.F4586L			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4586					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CCTGTCAGCCTTTCGCCACCC	0.647																																					p.F4586L		Atlas-SNP	.											.	DNHD1	198	.	0			c.T13756C						.						31	37	35					11																	6592498		2149	4255	6404	SO:0001583	missense	144132	exon42			TCAGCCTTTCGCC	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.13756T>C	chr11.hg19:g.6592498T>C	ENSP00000436180:p.Phe4586Leu	62.0	0.0		88.0	4.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.742265	0.89573	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000530197	T;T	0.07908	3.15;3.15	4.27	4.27	0.50696	Dynein heavy chain (1);	0.000000	0.64402	D	0.000001	T	0.23727	0.0574	M	0.67953	2.075	0.30964	N	0.723378	D;D;D	0.76494	0.997;0.999;0.997	D;D;D	0.87578	0.983;0.998;0.983	T	0.04128	-1.0975	10	0.51188	T	0.08	-10.0864	9.9508	0.41638	0.0:0.0:0.0:1.0	.	3674;639;4586	B0I1S4;Q9NSW8;Q96M86	.;.;DNHD1_HUMAN	L	4586;4586;854	ENSP00000254579:F4586L;ENSP00000436180:F4586L	ENSP00000254579:F4586L	F	+	1	0	DNHD1	6549074	1.000000	0.71417	0.995000	0.50966	0.927000	0.56198	3.992000	0.56980	1.915000	0.55452	0.455000	0.32223	TTT	.	.		0.647	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		C	6592498	T	C	6592498	3	2	103	1	0	0	0	0	1	0	0	0	4670	1609	56	2	13923	2	DNHD1	11	6592498	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	180538	6592498	128414018	663	15286										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6647877	6647877	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctcctgcatggacggccctGggggagacaataggagtccc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:6647877delG	ENST00000299441.3	-	15	6681	c.6270delC	c.(6268-6270)cccfs	p.P2090fs		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2090	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGACGGCCCTGGGGGAGACAA	0.532																																					p.R2091fs		Atlas-INDEL	.											.	DCHS1	277	.	0			c.6271delA						.						131	130	130					11																	6647877		2201	4296	6497	SO:0001589	frameshift_variant	8642	exon15			.	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.6270delC	chr11.hg19:g.6647877delG	ENSP00000299441:p.Pro2090fs	116.0	0.0		160.0	10.0	NM_003737	O15098	Frame_Shift_Del	DEL	ENST00000299441.3	hg19	CCDS7771.1																																																																																			.	.		0.532	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		-	6647877	G	-	6647877	7	5	103	1	0	1	0	1	0	0	0	0	4289	1335	47	0	3654	0	DCHS1	11	6647877	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	55379	6647877	128358639	664	15287										
ZNF214	7761	hgsc.bcm.edu	37	chr11	7022374	7022374	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgaactatgagcttctgttcTttttccatggagaggttttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:7022374delT	ENST00000278314.4	-	3	855	c.540delA	c.(538-540)aaafs	p.K180fs	ZNF214_ENST00000536068.1_Frame_Shift_Del_p.K180fs|ZNF214_ENST00000531083.1_5'Flank	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		GCTTCTGTTCTTTTTCCATGG	0.438																																					p.E181fs	Ovarian(22;251 657 736 21522 46864)	Atlas-INDEL	.											.	ZNF214	65	.	0			c.541delG						.						110	111	111					11																	7022374		2200	4294	6494	SO:0001589	frameshift_variant	7761	exon3			.	AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"Zinc fingers, C2H2-type", "-"	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.540delA	chr11.hg19:g.7022374delT	ENSP00000278314:p.Lys180fs	83.0	0.0		134.0	10.0	NM_013249	B2R8Q1	Frame_Shift_Del	DEL	ENST00000278314.4	hg19	CCDS31418.1																																																																																			.	.		0.438	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1			-	7022374	T	-	7022374	7	5	103	1	0	1	0	1	0	0	0	0	17785	1606	56	0	1284	0	ZNF214	11	7022374	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	374497	7022374	127984142	665	15288										
SBF2	81846	hgsc.bcm.edu	37	chr11	9864304	9864304	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttggcacctttcacaattgTttttgagaaggtactacaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:9864304delT	ENST00000256190.8	-	25	3261	c.3124delA	c.(3124-3126)acafs	p.T1042fs	RNU7-28P_ENST00000516759.1_RNA|RP11-1H15.2_ENST00000533659.1_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	1042					cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		TTCACAATTGTTTTTGAGAAG	0.363																																					p.T1042fs		Atlas-INDEL	.											.	SBF2	146	.	0			c.3125delC						.						117	100	106					11																	9864304		2201	4294	6495	SO:0001589	frameshift_variant	81846	exon25			.	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.3124delA	chr11.hg19:g.9864304delT	ENSP00000256190:p.Thr1042fs	143.0	0.0		197.0	12.0	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Frame_Shift_Del	DEL	ENST00000256190.8	hg19	CCDS31427.1																																																																																			.	.		0.363	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		-	9864304	T	-	9864304	7	5	103	1	0	1	0	1	0	0	0	0	13874	1725	60	0	2489	0	SBF2	11	9864304	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2841930	9864304	125142212	666	15289										
MICALCL	84953	hgsc.bcm.edu	37	chr11	12345559	12345559	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tagaagaagaaagaagctagAaaaagcaatgaagcagttgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:12345559delA	ENST00000256186.2	+	5	1868	c.1577delA	c.(1576-1578)gaafs	p.E526fs		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	526					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		AAGAAGCTAGAAAAAGCAATG	0.368																																					p.E526fs		Atlas-INDEL	.											.	MICALCL	59	.	0			c.1576delG						.						81	82	81					11																	12345559		1821	4077	5898	SO:0001589	frameshift_variant	84953	exon5			.	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.1577delA	chr11.hg19:g.12345559delA	ENSP00000256186:p.Glu526fs	136.0	0.0		178.0	11.0	NM_032867	Q7RTP7|Q96JU6	Frame_Shift_Del	DEL	ENST00000256186.2	hg19	CCDS41620.1																																																																																			.	.		0.368	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867		-	12345559	A	-	12345559	7	5	103	1	0	1	0	1	0	0	0	0	9581	246	9	0	1591	0	MICALCL	11	12345559	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2481255	12345559	122660957	667	15290										
FAR1	84188	hgsc.bcm.edu	37	chr11	13732397	13732397	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggccatcgattgttggtgccAgttggaaagaaccttttcca	11	9	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:13732397A>G	ENST00000354817.3	+	5	847	c.703A>G	c.(703-705)Agt>Ggt	p.S235G	FAR1_ENST00000527202.1_3'UTR	NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	235					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)|wax biosynthetic process (GO:0010025)	integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13						TGTTGGTGCCAGTTGGAAAGA	0.348																																					p.S235G		Atlas-SNP	.											.	FAR1	40	.	0			c.A703G						.						84	80	82					11																	13732397		2200	4294	6494	SO:0001583	missense	84188	exon5			GGTGCCAGTTGGA	AK026381	CCDS7813.1	11p15.2	2011-09-14	2008-06-06	2008-06-06	ENSG00000197601	ENSG00000197601	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	26222	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 1"		"male sterility domain containing 2"	MLSTD2		15220348, 15220349, 19027726	Standard	NM_032228		Approved	FLJ22728, SDR10E1	uc001mld.3	Q8WVX9	OTTHUMG00000165743	ENST00000354817.3:c.703A>G	chr11.hg19:g.13732397A>G	ENSP00000346874:p.Ser235Gly	104.0	0.0		119.0	5.0	NM_032228	D3DQW8|Q5CZA3	Missense_Mutation	SNP	ENST00000354817.3	hg19	CCDS7813.1	.	.	.	.	.	.	.	.	.	.	A	32	5.142686	0.94560	.	.	ENSG00000197601	ENST00000354817;ENST00000532701;ENST00000355107	T;T	0.30182	1.54;1.54	5.79	5.79	0.91817	NAD(P)-binding domain (1);Male sterility, NAD-binding (1);	0.000000	0.85682	D	0.000000	T	0.57607	0.2065	M	0.87038	2.855	0.80722	D	1	P;D	0.56287	0.949;0.975	P;P	0.58660	0.796;0.843	T	0.65627	-0.6122	10	0.72032	D	0.01	-17.5084	15.7869	0.78310	1.0:0.0:0.0:0.0	.	235;235	E7ETC1;Q8WVX9	.;FACR1_HUMAN	G	235	ENSP00000346874:S235G;ENSP00000437111:S235G	ENSP00000346874:S235G	S	+	1	0	FAR1	13688973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.205000	0.71048	0.477000	0.44152	AGT	.	.		0.348	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228		G	13732397	A	G	13732397	3	3	103	1	0	0	0	0	1	0	0	0	5682	188	7	2	717	2	FAR1	11	13732397	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1386838	13732397	121274119	668	15291										
COPB1	1315	hgsc.bcm.edu	37	chr11	14487826	14487826	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctgaatggtaagtttcctcAcctagtgtagctagttctaa	8	9	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:14487826A>G	ENST00000249923.3	-	17	2591		c.e17+1		COPB1_ENST00000439561.2_Splice_Site	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1						COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						AAGTTTCCTCACCTAGTGTAG	0.378																																					.		Atlas-SNP	.											.	COPB1	81	.	0			c.2290+2T>C						.						209	196	201					11																	14487826		2200	4294	6494	SO:0001630	splice_region_variant	1315	exon18			TTCCTCACCTAGT	BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"coatomer protein complex, subunit beta"	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.2290+1T>C	chr11.hg19:g.14487826A>G		66.0	0.0		97.0	4.0	NM_001144062	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Splice_Site	SNP	ENST00000249923.3	hg19	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.762212	0.89932	.	.	ENSG00000129083	ENST00000249923;ENST00000439561	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7062	0.77583	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COPB1	14444402	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.339000	0.96797	2.117000	0.64856	0.533000	0.62120	.	.	.		0.378	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451	Intron	G	14487826	A	G	14487826	5	3	103	1	0	0	0	0	0	0	1	0	3730	173	6	2	593	2	COPB1	11	14487826	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	755429	14487826	120518690	669	15292										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17150951	17150951	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgctctgatttaaaattccAaaaagagtaaggtgaagaac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:17150951delA	ENST00000265970.7	-	12	2294	c.2295delT	c.(2293-2295)tttfs	p.F765fs	PIK3C2A_ENST00000540361.1_Frame_Shift_Del_p.F385fs|PIK3C2A_ENST00000531428.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	765	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00041, ECO:0000255|PROSITE- ProRule:PRU00880}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TTAAAATTCCAAAAAGAGTAA	0.348																																					p.G766fs		Atlas-INDEL	.											.	PIK3C2A	148	.	0			c.2296delG						.						80	87	84					11																	17150951		2200	4292	6492	SO:0001589	frameshift_variant	5286	exon12			.	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.2295delT	chr11.hg19:g.17150951delA	ENSP00000265970:p.Phe765fs	126.0	0.0		167.0	13.0	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Frame_Shift_Del	DEL	ENST00000265970.7	hg19	CCDS7824.1																																																																																			.	.		0.348	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		-	17150951	A	-	17150951	7	5	103	1	0	1	0	1	0	0	0	0	11918	127	5	0	2849	0	PIK3C2A	11	17150951	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2663125	17150951	117855565	670	15293										
SAAL1	113174	hgsc.bcm.edu	37	chr11	18111818	18111818	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	actggccacttctgcctgggAaaggcaagtaagcaacaacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:18111818delA	ENST00000524803.1	-	6	542	c.493delT	c.(493-495)tccfs	p.S165fs	SAAL1_ENST00000300013.4_Frame_Shift_Del_p.S165fs|SAAL1_ENST00000529318.1_Frame_Shift_Del_p.S165fs|SAAL1_ENST00000533851.1_5'UTR			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	165										breast(2)|large_intestine(5)|lung(8)	15						TCTGCCTGGGAAAGGCAAGTA	0.343																																					p.S165fs		Atlas-INDEL	.											.	SAAL1	34	.	0			c.494delC						.						52	48	49					11																	18111818		2200	4293	6493	SO:0001589	frameshift_variant	113174	exon6			.	AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.493delT	chr11.hg19:g.18111818delA	ENSP00000432487:p.Ser165fs	101.0	0.0		133.0	10.0	NM_138421	A6NH05	Frame_Shift_Del	DEL	ENST00000524803.1	hg19	CCDS31439.1																																																																																			.	.		0.343	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421		-	18111818	A	-	18111818	7	5	103	1	0	1	0	1	0	0	0	0	13816	246	9	0	959	0	SAAL1	11	18111818	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	960867	18111818	116894698	671	15294										
EIF3M	10480	hgsc.bcm.edu	37	chr11	32610663	32610663	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtggggccatccagtacatCccaactgagctggatcaagt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:32610663delC	ENST00000531120.1	+	4	483	c.420delC	c.(418-420)atcfs	p.I140fs	EIF3M_ENST00000524896.1_Intron	NM_006360.4	NP_006351.2			eukaryotic translation initiation factor 3, subunit M											breast(3)|endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16	Breast(20;0.109)					TCCAGTACATCCCAACTGAGC	0.413																																					p.I140fs		Atlas-INDEL	.											.	EIF3M	37	.	0			c.419delT						.						117	100	106					11																	32610663		2202	4299	6501	SO:0001589	frameshift_variant	10480	exon4			.	AK131064	CCDS7880.1	11p13	2012-12-13	2007-07-27	2007-07-27	ENSG00000149100	ENSG00000149100			24460	protein-coding gene	gene with protein product	"transport and golgi organization 7 homolog (Drosophila)"	609641	"PCI domain containing 1 (herpesvirus entry mediator)"	PCID1		15919898, 15919899	Standard	NM_006360		Approved	hfl-B5, FLJ29030, GA17, eIF3m, TANGO7	uc001mtu.4	Q7L2H7	OTTHUMG00000166258	ENST00000531120.1:c.420delC	chr11.hg19:g.32610663delC	ENSP00000436049:p.Ile140fs	95.0	0.0		108.0	10.0	NM_006360		Frame_Shift_Del	DEL	ENST00000531120.1	hg19	CCDS7880.1																																																																																			.	.		0.413	EIF3M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388762.2	NM_006360		-	32610663	C	-	32610663	7	5	103	1	0	1	0	1	0	0	0	0	5025	845	30	0	434	0	EIF3M	11	32610663	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	14498845	32610663	102395853	672	15295										
SLC1A2	6506	hgsc.bcm.edu	37	chr11	35333900	35333900	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatagccaagaccagaatgaCccccagtactgcagcaatga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:35333900delC	ENST00000278379.3	-	4	688	c.406delG	c.(406-408)gtcfs	p.V136fs	SLC1A2_ENST00000395753.1_Frame_Shift_Del_p.V127fs|SLC1A2_ENST00000606205.1_Frame_Shift_Del_p.V136fs|SLC1A2_ENST00000395750.1_Frame_Shift_Del_p.V127fs	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	136					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			ACCAGAATGACCCCCAGTACT	0.552																																					p.V136fs	NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)	Atlas-INDEL	.											.	SLC1A2	54	.	0			c.407delT						.						179	165	170					11																	35333900		2202	4298	6500	SO:0001589	frameshift_variant	6506	exon4			.	AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"Solute carriers"	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.406delG	chr11.hg19:g.35333900delC	ENSP00000278379:p.Val136fs	140.0	0.0		157.0	11.0	NM_004171	B4DQE9|Q14417|Q541G6|U3KQQ4	Frame_Shift_Del	DEL	ENST00000278379.3	hg19	CCDS31459.1																																																																																			.	.		0.552	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171		-	35333900	C	-	35333900	7	5	103	1	0	1	0	1	0	0	0	0	14447	507	18	0	1350	0	SLC1A2	11	35333900	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2723237	35333900	99672616	673	15296										
RAG2	5897	hgsc.bcm.edu	37	chr11	36614735	36614735	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttgtctcctggtatgccaagAaaaacagttccatttcccat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:36614735delA	ENST00000311485.3	-	2	1145	c.984delT	c.(982-984)tttfs	p.F328fs	C11orf74_ENST00000446510.2_5'Flank|RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000334307.5_5'Flank|C11orf74_ENST00000347206.4_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	328					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				GTATGCCAAGAAAAACAGTTC	0.388									Familial Hemophagocytic Lymphohistiocytosis																												p.L329fs		Atlas-INDEL	.											.	RAG2	92	.	0			c.985delC						.						223	215	218					11																	36614735		2202	4298	6500	SO:0001589	frameshift_variant	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	.	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.984delT	chr11.hg19:g.36614735delA	ENSP00000308620:p.Phe328fs	187.0	0.0		310.0	20.0	NM_001243785	A8K9E9|Q8TBL4	Frame_Shift_Del	DEL	ENST00000311485.3	hg19	CCDS7903.1																																																																																			.	.		0.388	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536		-	36614735	A	-	36614735	7	5	103	1	0	1	0	1	0	0	0	0	13020	243	9	0	603	0	RAG2	11	36614735	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1280835	36614735	98391781	674	15297										
DGKZ	8525	hgsc.bcm.edu	37	chr11	46396358	46396358	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaagatccaggacctgaaaCcccagtgtgttgttttcctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:46396358delC	ENST00000454345.1	+	19	2256	c.2131delC	c.(2131-2133)cccfs	p.P711fs	MIR4688_ENST00000577966.1_RNA|DGKZ_ENST00000318201.8_Frame_Shift_Del_p.P500fs|DGKZ_ENST00000527911.1_Frame_Shift_Del_p.P523fs|DGKZ_ENST00000395574.3_Frame_Shift_Del_p.P489fs|DGKZ_ENST00000532868.2_Frame_Shift_Del_p.P527fs|DGKZ_ENST00000343674.6_Frame_Shift_Del_p.P539fs|DGKZ_ENST00000528615.1_Frame_Shift_Del_p.P301fs|DGKZ_ENST00000456247.2_Frame_Shift_Del_p.P522fs|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000421244.2_Frame_Shift_Del_p.P523fs	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	711					blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		GGACCTGAAACCCCAGTGTGT	0.612																																					p.K710fs		Atlas-INDEL	.											.	DGKZ	199	.	0			c.2130delA						.						86	84	85					11																	46396358		2202	4299	6501	SO:0001589	frameshift_variant	8525	exon19			.	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"diacylglycerol kinase, zeta 104kDa"			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.2131delC	chr11.hg19:g.46396358delC	ENSP00000412178:p.Pro711fs	96.0	0.0		161.0	10.0	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Frame_Shift_Del	DEL	ENST00000454345.1	hg19	CCDS41640.1																																																																																			.	.		0.612	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540		-	46396358	C	-	46396358	7	5	103	1	0	1	0	1	0	0	0	0	4476	507	18	0	2648	0	DGKZ	11	46396358	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	9781623	46396358	88610158	675	15298										
MADD	8567	hgsc.bcm.edu	37	chr11	47315481	47315481	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accttggtgagacagaggagAaaaagtcccagatcagcgca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:47315481delA	ENST00000311027.5	+	22	3628	c.3463delA	c.(3463-3465)aaafs	p.K1156fs	MADD_ENST00000395336.3_Frame_Shift_Del_p.K1156fs|MADD_ENST00000405573.2_5'UTR|MADD_ENST00000395344.3_Frame_Shift_Del_p.K1075fs|MADD_ENST00000349238.3_Frame_Shift_Del_p.K1138fs|MADD_ENST00000342922.4_Frame_Shift_Del_p.K1118fs|MADD_ENST00000406482.1_Frame_Shift_Del_p.K1075fs|MADD_ENST00000402799.1_Frame_Shift_Del_p.K1075fs|MADD_ENST00000402192.2_Frame_Shift_Del_p.K1118fs|MADD_ENST00000407859.3_Frame_Shift_Del_p.K1095fs	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GACAGAGGAGAAAAAGTCCCA	0.483																																					p.E1154fs		Atlas-INDEL	.											.	MADD	172	.	0			c.3462delG						.						158	143	148					11																	47315481		2201	4298	6499	SO:0001589	frameshift_variant	8567	exon22			.	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.3463delA	chr11.hg19:g.47315481delA	ENSP00000310933:p.Lys1156fs	110.0	0.0		150.0	12.0	NM_130475		Frame_Shift_Del	DEL	ENST00000311027.5	hg19	CCDS7930.1																																																																																			.	.		0.483	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			-	47315481	A	-	47315481	7	5	103	1	0	1	0	1	0	0	0	0	9161	247	9	0	3545	0	MADD	11	47315481	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	919123	47315481	87691035	676	15299										
NDUFS3	4722	hgsc.bcm.edu	37	chr11	47603658	47603658	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agattgtctacaacctgttgTctctgcgcttcaactcacgg	8	12	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:47603658T>C	ENST00000263774.4	+	5	482	c.400T>C	c.(400-402)Tct>Cct	p.S134P	NDUFS3_ENST00000533507.1_3'UTR	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	134					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	CAACCTGTTGTCTCTGCGCTT	0.522																																					p.S134P	Pancreas(15;551 601 22438 23457 52512)	Atlas-SNP	.											.	NDUFS3	19	.	0			c.T400C						.						169	158	162					11																	47603658		2201	4298	6499	SO:0001583	missense	4722	exon5			CTGTTGTCTCTGC	AF067139	CCDS7941.1	11p11.11	2011-08-03	2002-08-29		ENSG00000213619	ENSG00000213619	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7710	protein-coding gene	gene with protein product	"complex I 30kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial"	603846	"NADH dehydrogenase (ubiquinone) Fe-S protein 3 (30kD) (NADH-coenzyme Q reductase)"			9763677	Standard	NM_004551		Approved	CI-30	uc001nga.2	O75489	OTTHUMG00000166893	ENST00000263774.4:c.400T>C	chr11.hg19:g.47603658T>C	ENSP00000263774:p.Ser134Pro	207.0	0.0		219.0	9.0	NM_004551	B2R9J1|B4DFM8|Q9UNQ8	Missense_Mutation	SNP	ENST00000263774.4	hg19	CCDS7941.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.547972	0.86022	.	.	ENSG00000213619	ENST00000263774	D	0.88586	-2.4	6.08	6.08	0.98989	NADH:ubiquinone oxidoreductase, 30kDa subunit (1);	0.000000	0.85682	D	0.000000	D	0.97495	0.9180	H	0.99874	4.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99490	1.0950	10	0.87932	D	0	-38.2705	16.6438	0.85155	0.0:0.0:0.0:1.0	.	134;60	O75489;Q9UF24	NDUS3_HUMAN;.	P	134	ENSP00000263774:S134P	ENSP00000263774:S134P	S	+	1	0	NDUFS3	47560234	1.000000	0.71417	0.932000	0.37286	0.680000	0.39746	7.468000	0.80943	2.333000	0.79357	0.533000	0.62120	TCT	.	.		0.522	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391749.1	NM_004551		C	47603658	T	C	47603658	3	2	103	1	0	0	0	0	1	0	0	0	10302	1667	58	2	418	2	NDUFS3	11	47603658	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	288177	47603658	87402858	677	15300										
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48149344	48149344	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctcacagatgctattcaggTttttgacgtcaccgctgtga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:48149344delT	ENST00000418331.2	+	7	1458	c.1106delT	c.(1105-1107)gttfs	p.V369fs	PTPRJ_ENST00000440289.2_Frame_Shift_Del_p.V369fs	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	369	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GCTATTCAGGTTTTTGACGTC	0.493																																					p.V369fs		Atlas-INDEL	.											.	PTPRJ	225	.	0			c.1105delG						.						94	85	88					11																	48149344		2201	4298	6499	SO:0001589	frameshift_variant	5795	exon7			.	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.1106delT	chr11.hg19:g.48149344delT	ENSP00000400010:p.Val369fs	71.0	0.0		104.0	10.0	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Frame_Shift_Del	DEL	ENST00000418331.2	hg19	CCDS7945.1																																																																																			.	.		0.493	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			-	48149344	T	-	48149344	7	5	103	1	0	1	0	1	0	0	0	0	12819	1725	60	0	1132	0	PTPRJ	11	48149344	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	545686	48149344	86857172	678	15301										
OR4C16	219428	hgsc.bcm.edu	37	chr11	55339830	55339830	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttgcctctctacttccataaCccctagaatgattgtggatg	7	11	1	2	rs372108090		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:55339830C>G	ENST00000314634.3	+	1	227	c.227C>G	c.(226-228)aCc>aGc	p.T76S		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	76			T -> A (in dbSNP:rs557590). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T76S(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				ACTTCCATAACCCCTAGAATG	0.428																																					p.T76S		Atlas-SNP	.											OR4C16,mouth,carcinoma,0,3	OR4C16	104	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C227G						.						262	243	249					11																	55339830		2201	4296	6497	SO:0001583	missense	219428	exon1			CCATAACCCCTAG	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"GPCR / Class A : Olfactory receptors"	15172	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily C, member 16"				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.227C>G	chr11.hg19:g.55339830C>G	ENSP00000324913:p.Thr76Ser	145.0	0.0		217.0	11.0	NM_001004701	Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	hg19	CCDS31502.1	.	.	.	.	.	.	.	.	.	.	C	10.01	1.234160	0.22626	.	.	ENSG00000181935	ENST00000314634	T	0.03035	4.07	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.092864	0.47852	D	0.000208	T	0.04998	0.0134	L	0.43701	1.375	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.30592	-0.9973	10	0.29301	T	0.29	.	15.7881	0.78326	0.0:1.0:0.0:0.0	.	76	Q8NGL9	OR4CG_HUMAN	S	76	ENSP00000324913:T76S	ENSP00000324913:T76S	T	+	2	0	OR4C16	55096406	0.000000	0.05858	0.278000	0.24718	0.584000	0.36387	-0.144000	0.10280	2.595000	0.87683	0.549000	0.68633	ACC	.	.		0.428	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701		G	55339830	C	G	55339830	3	3	103	1	0	0	0	0	1	0	0	0	11058	507	18	4	229	4	OR4C16	11	55339830	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	7190486	55339830	79666686	679	15302										
OR5T3	390154	hgsc.bcm.edu	37	chr11	56020026	56020026	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgttggtcaatttcctggcAaaaaataaatccatttcatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:56020026delA	ENST00000303059.3	+	1	351	c.351delA	c.(349-351)gcafs	p.A117fs		NM_001004747.1	NP_001004747.1	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T, member 3	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(23)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	39	Esophageal squamous(21;0.00448)					ATTTCCTGGCAAAAAATAAAT	0.363																																					p.A117fs		Atlas-INDEL	.											.	OR5T3	98	.	0			c.350delC						.						136	138	137					11																	56020026		2201	4295	6496	SO:0001589	frameshift_variant	390154	exon1			.	AB065837	CCDS31524.1	11q11	2012-08-09			ENSG00000172489	ENSG00000172489		"GPCR / Class A : Olfactory receptors"	15297	protein-coding gene	gene with protein product							Standard	NM_001004747		Approved	OR5T3Q	uc010rjd.2	Q8NGG3	OTTHUMG00000166852	ENST00000303059.3:c.351delA	chr11.hg19:g.56020026delA	ENSP00000305403:p.Ala117fs	100.0	0.0		157.0	10.0	NM_001004747	Q6IFC7	Frame_Shift_Del	DEL	ENST00000303059.3	hg19	CCDS31524.1																																																																																			.	.		0.363	OR5T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391599.1	NM_001004747		-	56020026	A	-	56020026	7	5	103	1	0	1	0	1	0	0	0	0	11192	117	5	0	353	0	OR5T3	11	56020026	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	680196	56020026	78986490	680	15303										
OR5M3	219482	hgsc.bcm.edu	37	chr11	56237709	56237709	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acaaccagcataagtaattgTttttttatctgataacaggt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:56237709delT	ENST00000312240.2	-	1	305	c.265delA	c.(265-267)acafs	p.T89fs		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					TAAGTAATTGTTTTTTTATCT	0.363																																					p.T89fs		Atlas-INDEL	.											.	OR5M3	103	.	0			c.266delC						.						87	80	83					11																	56237709		2201	4295	6496	SO:0001589	frameshift_variant	219482	exon1			.	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"GPCR / Class A : Olfactory receptors"	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.265delA	chr11.hg19:g.56237709delT	ENSP00000312208:p.Thr89fs	113.0	0.0		148.0	10.0	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Frame_Shift_Del	DEL	ENST00000312240.2	hg19	CCDS31532.1																																																																																			.	.		0.363	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		-	56237709	T	-	56237709	7	5	103	1	0	1	0	1	0	0	0	0	11184	1725	60	0	660	0	OR5M3	11	56237709	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	217683	56237709	78768807	681	15304										
SMTNL1	219537	hgsc.bcm.edu	37	chr11	57310817	57310817	+	Intron	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcaaaagaggaggctgatgcAaaagaggaggcggaggatgc					rs373299953		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:57310817delA	ENST00000399154.2	+	2	621				SMTNL1_ENST00000527972.1_Frame_Shift_Del_p.A234fs|SMTNL1_ENST00000457912.1_Frame_Shift_Del_p.A252fs			A8MU46	SMTL1_HUMAN	smoothelin-like 1						negative regulation of vasodilation (GO:0045908)|positive regulation of vasoconstriction (GO:0045907)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	8						AGGCTGATGCAAAAGAGGAGG	0.567																																					p.A234fs		Atlas-INDEL	.											.	SMTNL1	68	.	0			c.701delC						.						39	41	40					11																	57310817		2116	4229	6345	SO:0001627	intron_variant	219537	exon1			.	BX116227		11q12.1	2006-02-02				ENSG00000214872			32394	protein-coding gene	gene with protein product	"calponin homology-associated smooth muscle protein"	613664				15327999	Standard	NM_001105565		Approved	CHASM	uc021qjh.1	A8MU46		ENST00000399154.2:c.621+3A>-	chr11.hg19:g.57310817delA		129.0	0.0		151.0	10.0	NM_001105565		Frame_Shift_Del	DEL	ENST00000399154.2	hg19																																																																																				.	.		0.567	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203		-	57310817	A	-	57310817	6	5	103	0	1	1	0	1	0	0	0	0	14830	117	5	0		0	SMTNL1	11	57310817	Intron	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1073108	57310817	77695699	682	15305										
OSBP	5007	hgsc.bcm.edu	37	chr11	59345771	59345771	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccagaagagcaaagtggacTtttcctgatggatctgtcac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:59345771delT	ENST00000263847.1	-	12	2390	c.1911delA	c.(1909-1911)aaafs	p.K637fs		NM_002556.2	NP_002547.1	P22059	OSBP1_HUMAN	oxysterol binding protein	637					lipid transport (GO:0006869)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	oxysterol binding (GO:0008142)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CAAAGTGGACTTTTCCTGATG	0.488																																					p.V638fs		Atlas-INDEL	.											.	OSBP	57	.	0			c.1912delG						.						158	142	148					11																	59345771		2201	4295	6496	SO:0001589	frameshift_variant	5007	exon12			.	AF185696	CCDS7974.1	11q12-q13	2013-01-10			ENSG00000110048	ENSG00000110048		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	8503	protein-coding gene	gene with protein product		167040					Standard	NM_002556		Approved	OSBP1	uc001noc.1	P22059	OTTHUMG00000167422	ENST00000263847.1:c.1911delA	chr11.hg19:g.59345771delT	ENSP00000263847:p.Lys637fs	212.0	0.0		235.0	15.0	NM_002556	Q6P524	Frame_Shift_Del	DEL	ENST00000263847.1	hg19	CCDS7974.1																																																																																			.	.		0.488	OSBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394555.1			-	59345771	T	-	59345771	7	5	103	1	0	1	0	1	0	0	0	0	11282	1606	56	0	524	0	OSBP	11	59345771	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2034954	59345771	75660745	683	15306										
TCN1	6947	hgsc.bcm.edu	37	chr11	59626598	59626598	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttccaatgagaccattttcTtttttctcagacagaatctt					rs4987226		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:59626598delT	ENST00000257264.3	-	5	803	c.699delA	c.(697-699)aaafs	p.K233fs	TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	233	Globular N-terminal alpha domain.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GACCATTTTCTTTTTTCTCAG	0.403																																					p.E234fs		Atlas-INDEL	.											.	TCN1	64	.	0			c.700delG						.						169	160	163					11																	59626598		2201	4295	6496	SO:0001589	frameshift_variant	6947	exon5			.	J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"haptocorin", "haptocorrin"	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.699delA	chr11.hg19:g.59626598delT	ENSP00000257264:p.Lys233fs	98.0	0.0		124.0	10.0	NM_001062	A8KAC5|Q8WV77	Frame_Shift_Del	DEL	ENST00000257264.3	hg19	CCDS7978.1																																																																																			.	.		0.403	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062		-	59626598	T	-	59626598	7	5	103	1	0	1	0	1	0	0	0	0	15721	1606	56	0	622	0	TCN1	11	59626598	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	280827	59626598	75379918	684	15307										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62300880	62300880	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccgcccttgtgccccacagAgacttcaggtgcagaaaccc	10	16	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:62300880A>G	ENST00000378024.4	-	5	1283	c.1009T>C	c.(1009-1011)Tct>Cct	p.S337P	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	337					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGCCCCACAGAGACTTCAGGT	0.552																																					p.S337P		Atlas-SNP	.											.	AHNAK	532	.	0			c.T1009C						.						53	57	56					11																	62300880		2202	4299	6501	SO:0001583	missense	79026	exon5			CCACAGAGACTTC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.1009T>C	chr11.hg19:g.62300880A>G	ENSP00000367263:p.Ser337Pro	85.0	0.0		143.0	7.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	A	14.11	2.437034	0.43224	.	.	ENSG00000124942	ENST00000378024	T	0.00912	5.55	5.05	5.05	0.67936	.	0.239940	0.21619	U	0.071678	T	0.02342	0.0072	L	0.59436	1.845	0.09310	N	1	D	0.58620	0.983	P	0.53861	0.736	T	0.49652	-0.8917	10	0.34782	T	0.22	-6.36	9.1238	0.36803	0.8158:0.1841:0.0:0.0	.	337	Q09666	AHNK_HUMAN	P	337	ENSP00000367263:S337P	ENSP00000367263:S337P	S	-	1	0	AHNAK	62057456	0.003000	0.15002	0.967000	0.41034	0.810000	0.45777	-0.347000	0.07750	1.904000	0.55121	0.528000	0.53228	TCT	.	.		0.552	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		G	62300880	A	G	62300880	3	3	103	1	0	0	0	0	1	0	0	0	414	304	11	2	16783	2	AHNAK	11	62300880	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2674282	62300880	72705636	685	15308										
SLC3A2	6520	hgsc.bcm.edu	37	chr11	62649372	62649372	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcccccatttcaggtctgaaGgggcgtctcgattacctgag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:62649372delG	ENST00000377890.2	+	5	903	c.735delG	c.(733-735)aagfs	p.K245fs	SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000338663.7_Frame_Shift_Del_p.K144fs|SLC3A2_ENST00000535296.1_Frame_Shift_Del_p.K214fs|SLC3A2_ENST00000377892.1_Frame_Shift_Del_p.K276fs|SLC3A2_ENST00000377891.2_Frame_Shift_Del_p.K246fs|SLC3A2_ENST00000377889.2_Frame_Shift_Del_p.K183fs|SLC3A2_ENST00000538682.1_3'UTR	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	245					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						CAGGTCTGAAGGGGCGTCTCG	0.592																																					p.K246fs		Atlas-INDEL	.											.	SLC3A2	55	.	0			c.737delA						.						84	84	84					11																	62649372		2201	4298	6499	SO:0001589	frameshift_variant	6520	exon5			.		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"Solute carriers"	11026	protein-coding gene	gene with protein product	"antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43", "antigen defined by monoclonal antibody 4F2", "heavy chain", "4F2 heavy chain", "CD98 heavy chain", "monoclonal antibody 44D7", "4F2 cell-surface antigen heavy chain", "lymphocyte activation antigen 4F2 large subunit"	158070	"solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.735delG	chr11.hg19:g.62649372delG	ENSP00000367122:p.Lys245fs	99.0	0.0		122.0	10.0	NM_001012662	Q13543	Frame_Shift_Del	DEL	ENST00000377890.2	hg19	CCDS8039.2																																																																																			.	.		0.592	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661		-	62649372	G	-	62649372	7	5	103	1	0	1	0	1	0	0	0	0	14642	991	35	0	853	0	SLC3A2	11	62649372	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	348492	62649372	72357144	686	15309										
C11orf84	144097	hgsc.bcm.edu	37	chr11	63586276	63586276	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcccgtcctcccttccagagCccccatcgccagactcgccc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:63586276delC	ENST00000294244.4	+	5	1035	c.736delC	c.(736-738)cccfs	p.P247fs		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	247	Pro-rich.									endometrium(3)|kidney(1)|lung(3)|skin(1)	8						CCTTCCAGAGCCCCCATCGCC	0.632																																					p.E245fs		Atlas-INDEL	.											.	C11orf84	33	.	0			c.735delG						.						64	65	65					11																	63586276		2201	4298	6499	SO:0001589	frameshift_variant	144097	exon5			.	BC007540	CCDS31594.1	11q13.1	2014-02-10			ENSG00000168005	ENSG00000168005			25115	protein-coding gene	gene with protein product						12477932	Standard	NM_138471		Approved		uc001nxt.3	Q9BUA3	OTTHUMG00000167746	ENST00000294244.4:c.736delC	chr11.hg19:g.63586276delC	ENSP00000294244:p.Pro247fs	97.0	0.0		117.0	10.0	NM_138471	Q68CV7|Q6PHS2|Q96IH0	Frame_Shift_Del	DEL	ENST00000294244.4	hg19	CCDS31594.1																																																																																			.	.		0.632	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471		-	63586276	C	-	63586276	7	5	103	1	0	1	0	1	0	0	0	0	1669	739	26	0	754	0	C11orf84	11	63586276	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	936904	63586276	71420240	687	15310										
MARK2	283248	hgsc.bcm.edu	37	chr11	63675749	63675749	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaggaacctgaatgaacctgAaagcaaagaccgagtggaga	13	7	0	5			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:63675749A>G	ENST00000301459.4	-	0	2604				MARK2_ENST00000361128.5_Intron|MARK2_ENST00000377810.3_Missense_Mutation_p.E563G|MARK2_ENST00000402010.2_Missense_Mutation_p.E660G|MARK2_ENST00000508192.1_Missense_Mutation_p.E596G|MARK2_ENST00000413835.2_Missense_Mutation_p.E606G|MARK2_ENST00000502399.3_Missense_Mutation_p.E650G|MARK2_ENST00000315032.8_Missense_Mutation_p.E651G|MARK2_ENST00000425897.2_Missense_Mutation_p.E571G|MARK2_ENST00000350490.7_Intron|MARK2_ENST00000513765.2_Missense_Mutation_p.E627G|MARK2_ENST00000377809.4_Intron|MARK2_ENST00000509502.2_Missense_Mutation_p.E617G|MARK2_ENST00000408948.3_Missense_Mutation_p.E563G	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2						negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						AATGAACCTGAAAGCAAAGAC	0.607																																					p.E660G		Atlas-SNP	.											.	MARK2	91	.	0			c.A1979G						.						46	42	43					11																	63675749		2192	4291	6483	SO:0001628	intergenic_variant	2011	exon18			AACCTGAAAGCAA	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472		chr11.hg19:g.63675749A>G		85.0	0.0		82.0	4.0	NM_001039469	Q96FP3	Missense_Mutation	SNP	ENST00000301459.4	hg19	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.398225	0.62177	.	.	ENSG00000072518	ENST00000402010;ENST00000315032;ENST00000413835;ENST00000377810;ENST00000508192;ENST00000502399;ENST00000509502;ENST00000513765;ENST00000408948;ENST00000425897	T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	4.43	4.43	0.53597	.	0.293370	0.30293	N	0.009945	T	0.40815	0.1132	L	0.48362	1.52	0.80722	D	1	B;B;B;B	0.26902	0.001;0.163;0.037;0.004	B;B;B;B	0.20384	0.005;0.029;0.028;0.018	T	0.38520	-0.9657	10	0.51188	T	0.08	.	13.1231	0.59338	1.0:0.0:0.0:0.0	.	571;617;660;596	E7ETY4;Q7KZI7-14;Q7KZI7;Q7KZI7-16	.;.;MARK2_HUMAN;.	G	660;651;606;563;596;652;617;627;563;571	ENSP00000385751:E660G;ENSP00000326632:E651G;ENSP00000389184:E606G;ENSP00000367041:E563G;ENSP00000425765:E596G;ENSP00000423974:E617G;ENSP00000421075:E627G;ENSP00000386128:E563G;ENSP00000415494:E571G	ENSP00000326632:E651G	E	+	2	0	MARK2	63432325	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.589000	0.67523	2.003000	0.58678	0.454000	0.30748	GAA	.	.		0.607	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		G	63675749	A	G	63675749	1	3	103	0	1	0	0	0	0	0	0	0	9322	246	9	2		2	MARK2	11	63675749	IGR	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	89473	63675749	71330767	688	15311										
ATG2A	23130	hgsc.bcm.edu	37	chr11	64664282	64664282	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggccgggcagctggttcttgCggatgtcctgcagccactcg	15	13	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:64664282C>A	ENST00000377264.3	-	38	5322	c.5210G>T	c.(5209-5211)cGc>cTc	p.R1737L	ATG2A_ENST00000421419.2_Missense_Mutation_p.R1739L	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1737					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						CTGGTTCTTGCGGATGTCCTG	0.622											OREG0004026	type=REGULATORY REGION|Gene=BC027481|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R1737L		Atlas-SNP	.											.	ATG2A	133	.	0			c.G5210T						.						54	54	54					11																	64664282		2201	4297	6498	SO:0001583	missense	23130	exon38			TTCTTGCGGATGT		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"ATG2 autophagy related 2 homolog A (S. cerevisiae)"			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.5210G>T	chr11.hg19:g.64664282C>A	ENSP00000366475:p.Arg1737Leu	109.0	0.0	1078	143.0	27.0	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	hg19	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165441	0.78339	.	.	ENSG00000110046	ENST00000421419;ENST00000377262;ENST00000377264	T;T	0.07327	3.2;3.2	4.05	3.11	0.35812	.	0.000000	0.64402	D	0.000001	T	0.18964	0.0455	L	0.44542	1.39	0.51482	D	0.99992	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	T	0.00557	-1.1672	10	0.52906	T	0.07	.	11.0151	0.47685	0.1878:0.8122:0.0:0.0	.	1737;1739	Q2TAZ0;Q2TAZ0-3	ATG2A_HUMAN;.	L	1739;130;1737	ENSP00000410522:R1739L;ENSP00000366475:R1737L	ENSP00000366473:R130L	R	-	2	0	ATG2A	64420858	0.920000	0.31207	1.000000	0.80357	0.877000	0.50540	1.424000	0.34848	1.042000	0.40150	-0.314000	0.08810	CGC	.	.		0.622	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		A	64664282	C	A	64664282	3	1	103	1	0	0	0	0	1	0	0	0	1093	768	27	1	622	1	ATG2A	11	64664282	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	988533	64664282	70342234	689	15312										
ATG2A	23130	hgsc.bcm.edu	37	chr11	64665805	64665805	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcccacccaggttggtagtGggggccacatgcagcgcttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:64665805delG	ENST00000377264.3	-	33	4813	c.4701delC	c.(4699-4701)cccfs	p.P1567fs	ATG2A_ENST00000421419.2_Frame_Shift_Del_p.P1569fs	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1567					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GGTTGGTAGTGGGGGCCACAT	0.637											OREG0004029	type=REGULATORY REGION|Gene=BC033850|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T1568fs		Atlas-INDEL	.											.	ATG2A	133	.	0			c.4702delA						.						50	52	51					11																	64665805		2201	4297	6498	SO:0001589	frameshift_variant	23130	exon33			.		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"ATG2 autophagy related 2 homolog A (S. cerevisiae)"			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.4701delC	chr11.hg19:g.64665805delG	ENSP00000366475:p.Pro1567fs	101.0	0.0	1078	141.0	11.0	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Frame_Shift_Del	DEL	ENST00000377264.3	hg19	CCDS31602.1																																																																																			.	.		0.637	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		-	64665805	G	-	64665805	7	5	103	1	0	1	0	1	0	0	0	0	1093	1335	47	0	1151	0	ATG2A	11	64665805	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1523	64665805	70340711	690	15313										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65350589	65350589	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tagcgactgggacagcagaaActgagatattggggacccaa	13	8	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:65350589A>G	ENST00000309295.4	+	9	2711	c.2446A>G	c.(2446-2448)Act>Gct	p.T816A		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	816	Glu-rich.					membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GACAGCAGAAACTGAGATATT	0.557																																					p.T816A		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.A2446G						.						45	47	46					11																	65350589		1872	4093	5965	SO:0001583	missense	254102	exon9			GCAGAAACTGAGA	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.2446A>G	chr11.hg19:g.65350589A>G	ENSP00000312671:p.Thr816Ala	92.0	0.0		135.0	6.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	A	5.751	0.323072	0.10900	.	.	ENSG00000173442	ENST00000309295	T	0.61627	0.09	4.81	-5.02	0.02982	.	1.470350	0.04895	N	0.450284	T	0.19446	0.0467	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28618	-1.0038	10	0.02654	T	1	.	0.9903	0.01455	0.3781:0.112:0.2832:0.2268	.	816	Q8N3D4	EH1L1_HUMAN	A	816	ENSP00000312671:T816A	ENSP00000312671:T816A	T	+	1	0	EHBP1L1	65107165	0.000000	0.05858	0.000000	0.03702	0.248000	0.25809	-2.366000	0.01078	-0.482000	0.06782	-0.177000	0.13119	ACT	.	.		0.557	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		G	65350589	A	G	65350589	3	3	103	1	0	0	0	0	1	0	0	0	4978	43	2	2	2480	2	EHBP1L1	11	65350589	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	684784	65350589	69655927	691	15314										
PCNXL3	399909	hgsc.bcm.edu	37	chr11	65391400	65391400	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgtagccctgtctcttccagAgcgtgcagcctgatgcggcg	13	14	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:65391400A>G	ENST00000355703.3	+	13	3051	c.2512A>G	c.(2512-2514)Agc>Ggc	p.S838G		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	838						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						TCTCTTCCAGAGCGTGCAGCC	0.642																																					p.S838G		Atlas-SNP	.											.	PCNXL3	140	.	0			c.A2512G						.						55	63	60					11																	65391400		2056	4191	6247	SO:0001630	splice_region_variant	399909	exon13			TTCCAGAGCGTGC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.2512-1A>G	chr11.hg19:g.65391400A>G		98.0	0.0		124.0	5.0	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	hg19	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494570	0.64186	.	.	ENSG00000197136	ENST00000355703	T	0.76839	-1.05	4.82	4.82	0.62117	.	.	.	.	.	D	0.85062	0.5611	M	0.82132	2.575	0.43430	D	0.995598	P	0.49447	0.924	P	0.57776	0.827	D	0.85850	0.1403	8	.	.	.	.	10.7496	0.46200	1.0:0.0:0.0:0.0	.	838	Q9H6A9	PCX3_HUMAN	G	838	ENSP00000347931:S838G	.	S	+	1	0	PCNXL3	65147976	1.000000	0.71417	0.997000	0.53966	0.188000	0.23474	8.106000	0.89555	1.813000	0.52934	0.379000	0.24179	AGC	.	.		0.642	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	Missense_Mutation	G	65391400	A	G	65391400	5	3	103	1	0	0	0	0	0	0	1	0	11602	318	11	2	2562	2	PCNXL3	11	65391400	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	40811	65391400	69615116	692	15315										
RELA	5970	hgsc.bcm.edu	37	chr11	65422151	65422151	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtgctgttgccaagcaaggCccccaggtcttcatcatcaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:65422151delC	ENST00000406246.3	-	11	1615	c.1354delG	c.(1354-1356)gccfs	p.A452fs	RELA_ENST00000525693.1_3'UTR|RELA_ENST00000308639.9_Frame_Shift_Del_p.A449fs	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	452	Activation domain.				acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						ccaagcaaggcccccaggtct	0.617																																					p.A452fs		Atlas-INDEL	.											.	RELA	44	.	0			c.1355delC						.						37	37	37					11																	65422151		2201	4297	6498	SO:0001589	frameshift_variant	5970	exon11			.	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1354delG	chr11.hg19:g.65422151delC	ENSP00000384273:p.Ala452fs	84.0	0.0		119.0	10.0	NM_021975	Q6GTV1|Q6SLK1	Frame_Shift_Del	DEL	ENST00000406246.3	hg19	CCDS31609.1																																																																																			.	.		0.617	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		-	65422151	C	-	65422151	7	5	103	1	0	1	0	1	0	0	0	0	13231	739	26	0	305	0	RELA	11	65422151	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	30751	65422151	69584365	693	15316										
NPAS4	266743	hgsc.bcm.edu	37	chr11	66193455	66193455	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaagtggaggggaaccaacgTtttgaataagtctgtgactt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:66193455delT	ENST00000311034.2	+	8	2580	c.2404delT	c.(2404-2406)tttfs	p.F802fs		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	802					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						GGAACCAACGTTTTGAATAAG	0.498																																					p.T801fs		Atlas-INDEL	.											.	NPAS4	133	.	0			c.2403delG						.						197	169	179					11																	66193455		2200	4295	6495	SO:0001589	frameshift_variant	266743	exon8			.	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"Basic helix-loop-helix proteins"	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.2404delT	chr11.hg19:g.66193455delT	ENSP00000311196:p.Phe802fs	129.0	0.0		181.0	12.0	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Frame_Shift_Del	DEL	ENST00000311034.2	hg19	CCDS8138.1																																																																																			.	.		0.498	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		-	66193455	T	-	66193455	7	5	103	1	0	1	0	1	0	0	0	0	10574	1725	60	0	2434	0	NPAS4	11	66193455	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	771304	66193455	68813061	694	15317										
DPP3	10072	hgsc.bcm.edu	37	chr11	66252728	66252728	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaagtttgttcccaacttgCccaaggtgagccaagggagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:66252728delC	ENST00000360510.2	+	3	420	c.355delC	c.(355-357)cccfs	p.P119fs	DPP3_ENST00000532677.1_Frame_Shift_Del_p.P138fs|DPP3_ENST00000531863.1_Frame_Shift_Del_p.P139fs|DPP3_ENST00000541961.1_Frame_Shift_Del_p.P119fs|DPP3_ENST00000453114.1_Frame_Shift_Del_p.P119fs|DPP3_ENST00000530165.1_Intron			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	119					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						TCCCAACTTGCCCAAGGTGAG	0.572																																					p.L118fs		Atlas-INDEL	.											.	DPP3	61	.	0			c.354delG						.						68	58	61					11																	66252728		2200	4295	6495	SO:0001589	frameshift_variant	10072	exon3			.	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"dipeptidylpeptidase III", "dipeptidylpeptidase 3"			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.355delC	chr11.hg19:g.66252728delC	ENSP00000353701:p.Pro119fs	105.0	0.0		109.0	10.0	NM_130443	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Frame_Shift_Del	DEL	ENST00000360510.2	hg19	CCDS8141.1																																																																																			.	.		0.572	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2			-	66252728	C	-	66252728	7	5	103	1	0	1	0	1	0	0	0	0	4730	739	26	0	361	0	DPP3	11	66252728	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	59273	66252728	68753788	695	15318										
LRFN4	78999	hgsc.bcm.edu	37	chr11	66627324	66627324	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggaccctgaccgtggccgtGgggggtgtgctggtggctgc					rs142190580		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:66627324delG	ENST00000309602.4	+	2	1809	c.1566delG	c.(1564-1566)gtgfs	p.V522fs	LRFN4_ENST00000393952.3_Intron|PC_ENST00000393955.2_Intron|PC_ENST00000393958.2_Intron|PC_ENST00000393960.1_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	522						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						CCGTGGCCGTGGGGGGTGTGC	0.716																																					p.V522fs		Atlas-INDEL	.											.	LRFN4	25	.	0			c.1565delT						.						28	22	24					11																	66627324		2187	4280	6467	SO:0001589	frameshift_variant	78999	exon2			.	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28456	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 6"	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.1566delG	chr11.hg19:g.66627324delG	ENSP00000312535:p.Val522fs	67.0	0.0		124.0	11.0	NM_024036	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Frame_Shift_Del	DEL	ENST00000309602.4	hg19	CCDS8153.1																																																																																			.	.		0.716	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		-	66627324	G	-	66627324	7	5	103	1	0	1	0	1	0	0	0	0	8949	1335	47	0	1572	0	LRFN4	11	66627324	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	374596	66627324	68379192	696	15319										
PC	5091	hgsc.bcm.edu	37	chr11	66638785	66638785	+	Splice_Site	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttgcttgcccgttatattcaCccgcagcaatggcgatggcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:66638785delC	ENST00000393958.2	-	5	581		c.e5+1		PC_ENST00000524491.1_Splice_Site|PC_ENST00000393955.2_Splice_Site|PC_ENST00000355677.3_Splice_Site|PC_ENST00000393960.1_Splice_Site	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase						biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	GTTATATTCACCCGCAGCAAT	0.647																																					.		Atlas-INDEL	.											.	PC	116	.	0			c.487+2G>-						.						63	72	69					11																	66638785		2200	4295	6495	SO:0001630	splice_region_variant	5091	exon7			.	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.487+1G>-	chr11.hg19:g.66638785delC		107.0	0.0		154.0	10.0	NM_001040716	B4DN00|Q16705	Splice_Site	DEL	ENST00000393958.2	hg19	CCDS8152.1																																																																																			.	.		0.647	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716	Intron	-	66638785	C	-	66638785	8	5	103	1	0	1	0	1	0	0	1	0	11506	521	18	0	3120	0	PC	11	66638785	Splice_Site	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	11461	66638785	68367731	697	15320										
SYT12	91683	hgsc.bcm.edu	37	chr11	66811279	66811279	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctttctgtgcttgacctcccGctgcagcccttcagtggctg	10	15	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:66811279G>A	ENST00000393946.2	+	8	1954	c.792G>A	c.(790-792)ccG>ccA	p.P264P	SYT12_ENST00000525457.1_Silent_p.P264P|SYT12_ENST00000527043.1_Silent_p.P264P			Q8IV01	SYT12_HUMAN	synaptotagmin XII	264	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|synapse (GO:0045202)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	20						TTGACCTCCCGCTGCAGCCCT	0.552																																					p.P264P	Ovarian(65;2862 3307)	Atlas-SNP	.											.	SYT12	60	.	0			c.G792A						.						97	74	82					11																	66811279		2200	4295	6495	SO:0001819	synonymous_variant	91683	exon5			CCTCCCGCTGCAG	AK024280	CCDS8154.1	11q13.2	2014-07-02			ENSG00000173227	ENSG00000173227		"Synaptotagmins"	18381	protein-coding gene	gene with protein product		606436				8987811	Standard	NM_177963		Approved	SRG1	uc001oju.3	Q8IV01	OTTHUMG00000167101	ENST00000393946.2:c.792G>A	chr11.hg19:g.66811279G>A		84.0	0.0		109.0	17.0	NM_001177880		Silent	SNP	ENST00000393946.2	hg19	CCDS8154.1																																																																																			.	.		0.552	SYT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393129.1	NM_177963		A	66811279	G	A	66811279	2	1	103	1	0	0	0	0	0	0	0	1	15483	1074	38	1		1	SYT12	11	66811279	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	172494	66811279	68195237	698	15321										
ADRBK1	156	hgsc.bcm.edu	37	chr11	67048975	67048975	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagcgcatcaagatgaagcaGggggagaccctggccctgaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:67048975delG	ENST00000308595.5	+	9	983	c.693delG	c.(691-693)cagfs	p.Q231fs	ADRBK1_ENST00000526285.1_Frame_Shift_Del_p.Q231fs	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	AGATGAAGCAGGGGGAGACCC	0.657																																					p.Q231fs		Atlas-INDEL	.											.	ADRBK1	51	.	0			c.692delA						.						79	71	74					11																	67048975		2200	4295	6495	SO:0001589	frameshift_variant	156	exon9			.	X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"Pleckstrin homology (PH) domain containing"	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.693delG	chr11.hg19:g.67048975delG	ENSP00000312262:p.Gln231fs	91.0	0.0		154.0	10.0	NM_001619	B0ZBE1|Q13837|Q6GTT3	Frame_Shift_Del	DEL	ENST00000308595.5	hg19	CCDS8156.1																																																																																			.	.		0.657	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619		-	67048975	G	-	67048975	7	5	103	1	0	1	0	1	0	0	0	0	343	991	35	0	727	0	ADRBK1	11	67048975	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	237696	67048975	67957541	699	15322										
AIP	9049	hgsc.bcm.edu	37	chr11	67258394	67258394	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtgagccgagagctgcaggCcctggaggcacggatccggc	18	12	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:67258394C>G	ENST00000279146.3	+	6	1041	c.923C>G	c.(922-924)gCc>gGc	p.A308G	PITPNM1_ENST00000526450.1_5'Flank	NM_003977.2	NP_003968.2	O00170	AIP_HUMAN	aryl hydrocarbon receptor interacting protein	308					negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|protein maturation by protein folding (GO:0022417)|protein targeting to mitochondrion (GO:0006626)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GAF domain binding (GO:0036004)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(2)	7						GAGCTGCAGGCCCTGGAGGCA	0.652									Familial Isolated Pituitary Adenoma																												p.A308G		Atlas-SNP	.											.	AIP	26	.	0			c.C923G						.						22	22	22					11																	67258394		2195	4289	6484	SO:0001583	missense	9049	exon6	Familial Cancer Database	FIPA, incl. Familial Isolated Somatotropinomas, FIS, IFS, Familial Acromegaly	TGCAGGCCCTGGA	U31913	CCDS8168.1	11q13.3	2014-09-17	2001-11-29		ENSG00000110711	ENSG00000110711			358	protein-coding gene	gene with protein product		605555	"aryl hydrocarbon receptor-interacting protein"			8972861, 9111057	Standard	NM_003977		Approved	XAP2, ARA9, FKBP16	uc001olv.3	O00170	OTTHUMG00000167674	ENST00000279146.3:c.923C>G	chr11.hg19:g.67258394C>G	ENSP00000279146:p.Ala308Gly	125.0	0.0		192.0	8.0	NM_003977	A0SZW3|A0SZW4|A0SZW5|A0SZW6|Q2M3Q2|Q99606	Missense_Mutation	SNP	ENST00000279146.3	hg19	CCDS8168.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.332847	0.24167	.	.	ENSG00000110711	ENST00000279146	T	0.74209	-0.82	5.39	3.42	0.39159	.	0.737123	0.13434	N	0.388207	T	0.58047	0.2095	L	0.39898	1.24	0.30196	N	0.799055	B	0.27264	0.173	B	0.23275	0.045	T	0.49204	-0.8964	10	0.23302	T	0.38	-18.9647	3.1863	0.06602	0.274:0.4925:0.1448:0.0887	.	308	O00170	AIP_HUMAN	G	308	ENSP00000279146:A308G	ENSP00000279146:A308G	A	+	2	0	AIP	67014970	0.760000	0.28428	1.000000	0.80357	0.718000	0.41266	0.510000	0.22723	2.703000	0.92315	0.561000	0.74099	GCC	.	.		0.652	AIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395516.1			G	67258394	C	G	67258394	3	3	103	1	0	0	0	0	1	0	0	0	435	739	26	4	945	4	AIP	11	67258394	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	209419	67258394	67748122	700	15323										
CABP2	51475	hgsc.bcm.edu	37	chr11	67290137	67290137	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgctccttggggctggagctGgggctggggcaggagcccct					rs559061168	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:67290137delG	ENST00000294288.4	-	2	162	c.93delC	c.(91-93)cccfs	p.P31fs	CABP2_ENST00000353903.5_Intron	NM_016366.2	NP_057450.2	Q9NPB3	CABP2_HUMAN	calcium binding protein 2	31					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	9						ggctggagctggggctggggc	0.726																																					p.S32fs		Atlas-INDEL	.											.	CABP2	25	.	0			c.94delA						.						5	6	5					11																	67290137		1933	3696	5629	SO:0001589	frameshift_variant	51475	exon2			.	AF169154	CCDS8170.1	11q13.1	2013-01-10			ENSG00000167791	ENSG00000167791		"EF-hand domain containing"	1385	protein-coding gene	gene with protein product		607314				10625670	Standard	NM_016366		Approved		uc001omc.1	Q9NPB3	OTTHUMG00000168014	ENST00000294288.4:c.93delC	chr11.hg19:g.67290137delG	ENSP00000294288:p.Pro31fs	39.0	0.0		139.0	10.0	NM_016366		Frame_Shift_Del	DEL	ENST00000294288.4	hg19	CCDS8170.1																																																																																			.	.		0.726	CABP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397516.1			-	67290137	G	-	67290137	7	5	103	1	0	1	0	1	0	0	0	0	2534	1335	47	0	593	0	CABP2	11	67290137	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	31743	67290137	67716379	701	15324										
TBX10	347853	hgsc.bcm.edu	37	chr11	67402373	67402373	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccaggatcttcacctggaaGggggggaacatcctcctgcg					rs144542807		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:67402373delG	ENST00000335385.3	-	3	378	c.291delC	c.(289-291)cccfs	p.P97fs		NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	97					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						TCACCTGGAAGGGGGGGAACA	0.677																																					p.F98fs		Atlas-INDEL	.											.	TBX10	25	.	0			c.292delT						.						50	49	49					11																	67402373		2200	4294	6494	SO:0001589	frameshift_variant	347853	exon3			.	AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"T-boxes"	11593	protein-coding gene	gene with protein product		604648	"T-box 7"	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.291delC	chr11.hg19:g.67402373delG	ENSP00000335191:p.Pro97fs	107.0	0.0		178.0	11.0	NM_005995	Q14D64|Q86XS3	Frame_Shift_Del	DEL	ENST00000335385.3	hg19	CCDS31621.1																																																																																			.	.		0.677	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995		-	67402373	G	-	67402373	7	5	103	1	0	1	0	1	0	0	0	0	15666	987	35	0	890	0	TBX10	11	67402373	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	112236	67402373	67604143	702	15325										
SHANK2	22941	hgsc.bcm.edu	37	chr11	70332097	70332097	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctgcttcactaagtctgagAgagccgggacagaagctgcc	12	11	3	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:70332097A>G	ENST00000423696.2	-	15	3200	c.3164T>C	c.(3163-3165)cTc>cCc	p.L1055P	SHANK2_ENST00000338508.4_Missense_Mutation_p.L1435P|SHANK2_ENST00000449833.2_Missense_Mutation_p.L839P|SHANK2_ENST00000409161.1_Missense_Mutation_p.L838P			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	1055					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			TAAGTCTGAGAGAGCCGGGAC	0.502																																					p.L846P		Atlas-SNP	.											.	SHANK2	340	.	0			c.T2537C						.						80	91	88					11																	70332097		2200	4294	6494	SO:0001583	missense	22941	exon10			TCTGAGAGAGCCG	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14295	protein-coding gene	gene with protein product		603290	"cortactin binding protein 1"	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.3164T>C	chr11.hg19:g.70332097A>G	ENSP00000394536:p.Leu1055Pro	63.0	0.0		107.0	5.0	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	hg19		.	.	.	.	.	.	.	.	.	.	A	11.78	1.741649	0.30865	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.44083	2.17;2.2;2.86;0.93;2.31;2.31	5.42	1.97	0.26223	.	1.267120	0.04920	N	0.454912	T	0.58991	0.2161	L	0.58810	1.83	0.20074	N	0.999937	P;D;D	0.69078	0.954;0.997;0.959	P;D;P	0.67382	0.736;0.951;0.812	T	0.41502	-0.9505	10	0.41790	T	0.15	.	9.1686	0.37067	0.7972:0.0:0.2028:0.0	.	1055;1434;839	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	P	839;838;713;1435;1055;1073;1058	ENSP00000399423:L839P;ENSP00000386491:L838P;ENSP00000402944:L713P;ENSP00000345193:L1435P;ENSP00000394536:L1055P;ENSP00000294018:L1058P	ENSP00000294018:L1058P	L	-	2	0	SHANK2	70009745	0.576000	0.26700	0.134000	0.22075	0.923000	0.55619	2.706000	0.47135	0.922000	0.37019	0.533000	0.62120	CTC	.	.		0.502	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		G	70332097	A	G	70332097	3	3	103	1	0	0	0	0	1	0	0	0	14280	304	11	2	1256	2	SHANK2	11	70332097	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2929724	70332097	64674419	703	15326										
KRTAP5-10	387273	hgsc.bcm.edu	37	chr11	71276925	71276925	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggggggctgtggctcctgtGggggctccaaggggggctgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:71276925delG	ENST00000398531.1	+	1	317	c.292delG	c.(292-294)gggfs	p.G99fs	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	99	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						TGGCTCCTGTGGGGGCTCCAA	0.682																																					p.C97fs		Atlas-INDEL	.											.	KRTAP5-10	37	.	0			c.291delT						.						33	53	46					11																	71276925		2100	4221	6321	SO:0001589	frameshift_variant	387273	exon1			.	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"Keratin associated proteins"	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.292delG	chr11.hg19:g.71276925delG	ENSP00000381542:p.Gly99fs	78.0	0.0		166.0	11.0	NM_001012710	B9EHA4	Frame_Shift_Del	DEL	ENST00000398531.1	hg19	CCDS41684.1																																																																																			.	.		0.682	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2			-	71276925	G	-	71276925	7	5	103	1	0	1	0	1	0	0	0	0	8568	1348	47	0	294	0	KRTAP5-10	11	71276925	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	944828	71276925	63729591	704	15327										
ARAP1	116985	hgsc.bcm.edu	37	chr11	72437746	72437746	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aatgccgcttagcaggcagcGggggcagcacagggtctggg					rs372690916	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:72437746delG	ENST00000393609.3	-	3	630	c.428delC	c.(427-429)ccgfs	p.P143fs	ARAP1_ENST00000455638.2_Frame_Shift_Del_p.P143fs|ARAP1_ENST00000359373.5_Frame_Shift_Del_p.P143fs	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	143					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						AGCAGGCAGCGGGGGCAGCAC	0.721																																					p.P143fs	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-INDEL	.											.	ARAP1	168	.	0			c.429delG						.						4	6	5					11																	72437746		1930	4038	5968	SO:0001589	frameshift_variant	116985	exon3			.	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16925	protein-coding gene	gene with protein product		606646	"centaurin, delta 2"	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.428delC	chr11.hg19:g.72437746delG	ENSP00000377233:p.Pro143fs	86.0	0.0		135.0	11.0	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Frame_Shift_Del	DEL	ENST00000393609.3	hg19	CCDS41687.1																																																																																			.	.		0.721	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		-	72437746	G	-	72437746	7	5	103	1	0	1	0	1	0	0	0	0	838	1116	39	0	4056	0	ARAP1	11	72437746	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1160821	72437746	62568770	705	15328										
CAPN5	726	hgsc.bcm.edu	37	chr11	76834767	76834767	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagtgctgaaggatgaatttCtgggccaggtgcacctaaag	14	7	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:76834767C>T	ENST00000278559.3	+	13	1963	c.1774C>T	c.(1774-1776)Ctg>Ttg	p.L592L	CAPN5_ENST00000529629.1_Silent_p.L592L|CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000456580.2_Silent_p.L632L	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	592	C2.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						GGATGAATTTCTGGGCCAGGT	0.602																																					p.L592L		Atlas-SNP	.											.	CAPN5	67	.	0			c.C1774T						.						113	114	114					11																	76834767		2200	4292	6492	SO:0001819	synonymous_variant	726	exon13			GAATTTCTGGGCC		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"vitreoretinopathy, neovascular inflammatory"	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.1774C>T	chr11.hg19:g.76834767C>T		98.0	0.0		96.0	4.0	NM_004055	O00263	Silent	SNP	ENST00000278559.3	hg19	CCDS8248.1																																																																																			.	.		0.602	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055		T	76834767	C	T	76834767	2	4	103	1	0	0	0	0	0	0	0	1	2631	912	32	3		3	CAPN5	11	76834767	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	4397021	76834767	58171749	706	15329										
SYTL2	54843	hgsc.bcm.edu	37	chr11	85435856	85435856	+	Intron	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttccctgtatcactttcataTtttgaggggaaggtttcagt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:85435856delT	ENST00000528231.1	-	7	1737				SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000525423.1_Frame_Shift_Del_p.K548fs|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000354566.3_Frame_Shift_Del_p.K548fs|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000359152.5_Frame_Shift_Del_p.K1072fs	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CACTTTCATATTTTGAGGGGA	0.418																																					p.Y549fs		Atlas-INDEL	.											.	SYTL2	231	.	0			c.1645delT						.						104	102	102					11																	85435856		2203	4299	6502	SO:0001627	intron_variant	54843	exon1			.	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+3082A>-	chr11.hg19:g.85435856delT		103.0	0.0		153.0	10.0	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Frame_Shift_Del	DEL	ENST00000528231.1	hg19	CCDS53688.1																																																																																			.	.		0.418	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		-	85435856	T	-	85435856	6	5	103	0	1	1	0	1	0	0	0	0	15498	1490	52	0		0	SYTL2	11	85435856	Intron	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	8601089	85435856	49570660	707	15330										
NAALAD2	10003	hgsc.bcm.edu	37	chr11	89914834	89914834	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctcagaggctgcttcagaTtttcataaacgacttataca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:89914834delT	ENST00000534061.1	+	17	2135	c.1905delT	c.(1903-1905)gatfs	p.D635fs	NAALAD2_ENST00000321955.4_Frame_Shift_Del_p.D602fs|NAALAD2_ENST00000375944.3_Intron	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	635					neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CTGCTTCAGATTTTCATAAAC	0.289																																					p.D635fs		Atlas-INDEL	.											.	NAALAD2	113	.	0			c.1904delA						.						37	41	40					11																	89914834		2199	4291	6490	SO:0001589	frameshift_variant	10003	exon17			.	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1905delT	chr11.hg19:g.89914834delT	ENSP00000432481:p.Asp635fs	148.0	0.0		163.0	11.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Frame_Shift_Del	DEL	ENST00000534061.1	hg19	CCDS8288.1																																																																																			.	.		0.289	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		-	89914834	T	-	89914834	7	5	103	1	0	1	0	1	0	0	0	0	10137	1490	52	0	1971	0	NAALAD2	11	89914834	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	4478978	89914834	45091682	708	15331										
FAT3	120114	hgsc.bcm.edu	37	chr11	92533028	92533028	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttaatgatgtaaatgacaaCccccctattttcgatcagcc					rs370953208		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:92533028delC	ENST00000298047.6	+	9	6866	c.6849delC	c.(6847-6849)aacfs	p.N2283fs	FAT3_ENST00000525166.1_Frame_Shift_Del_p.N2133fs|FAT3_ENST00000409404.2_Frame_Shift_Del_p.N2283fs			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2283	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TAAATGACAACCCCCCTATTT	0.428										TCGA Ovarian(4;0.039)																											p.N2283fs		Atlas-INDEL	.											.	FAT3	1822	.	0			c.6848delA						.						99	89	92					11																	92533028		1917	4130	6047	SO:0001589	frameshift_variant	120114	exon9			.	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.6849delC	chr11.hg19:g.92533028delC	ENSP00000298047:p.Asn2283fs	86.0	0.0		120.0	10.0	NM_001008781	B5MDB0|Q96AU6	Frame_Shift_Del	DEL	ENST00000298047.6	hg19																																																																																				.	.		0.428	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		-	92533028	C	-	92533028	7	5	103	1	0	1	0	1	0	0	0	0	5699	506	18	0	6883	0	FAT3	11	92533028	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2618194	92533028	42473488	709	15332										
SLC36A4	120103	hgsc.bcm.edu	37	chr11	92901154	92901154	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacaagactgacagccatggAaacgttggcaaggaatgaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:92901154delA	ENST00000326402.4	-	7	854	c.724delT	c.(724-726)tccfs	p.S242fs	SLC36A4_ENST00000529184.1_Frame_Shift_Del_p.S107fs	NM_152313.2	NP_689526.2	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 4	242					L-alanine transport (GO:0015808)|proline transport (GO:0015824)|tryptophan transport (GO:0015827)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	25		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ACAGCCATGGAAACGTTGGCA	0.303																																					p.S242fs		Atlas-INDEL	.											.	SLC36A4	61	.	0			c.725delC						.						101	100	101					11																	92901154		2201	4295	6496	SO:0001589	frameshift_variant	120103	exon7			.	AY162216	CCDS8291.1, CCDS66202.1	11q21	2013-05-22			ENSG00000180773	ENSG00000180773		"Solute carriers"	19660	protein-coding gene	gene with protein product		613760					Standard	XM_005273758		Approved	PAT4, FLJ38932	uc001pdn.3	Q6YBV0	OTTHUMG00000167368	ENST00000326402.4:c.724delT	chr11.hg19:g.92901154delA	ENSP00000317382:p.Ser242fs	114.0	0.0		185.0	12.0	NM_152313	Q86X30|Q8IVM5|Q8N8S6	Frame_Shift_Del	DEL	ENST00000326402.4	hg19	CCDS8291.1																																																																																			.	.		0.303	SLC36A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394329.2			-	92901154	A	-	92901154	7	5	103	1	0	1	0	1	0	0	0	0	14611	246	9	0	810	0	SLC36A4	11	92901154	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	368126	92901154	42105362	710	15333										
C11orf54	28970	hgsc.bcm.edu	37	chr11	93488394	93488394	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtttatgccagttattcagAcagaaagtgaacacaagcct	8	8	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:93488394A>G	ENST00000331239.4	+	6	528	c.349A>G	c.(349-351)Aca>Gca	p.T117A	C11orf54_ENST00000528288.1_Missense_Mutation_p.T117A|C11orf54_ENST00000528099.1_Missense_Mutation_p.T117A|C11orf54_ENST00000540113.1_Missense_Mutation_p.T98A|C11orf54_ENST00000354421.3_Missense_Mutation_p.T117A			Q9H0W9	CK054_HUMAN	chromosome 11 open reading frame 54	117					metabolic process (GO:0008152)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(5)	8		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				AGTTATTCAGACAGAAAGTGA	0.378																																					p.T117A		Atlas-SNP	.											.	C11orf54	23	.	0			c.A349G						.						90	85	86					11																	93488394		2201	4298	6499	SO:0001583	missense	28970	exon6			ATTCAGACAGAAA	AF092133	CCDS8294.1, CCDS66204.1, CCDS73365.1, CCDS73366.1	11q21	2012-08-09			ENSG00000182919	ENSG00000182919			30204	protein-coding gene	gene with protein product		615810				16522806	Standard	NM_014039		Approved	PTD012	uc001pef.3	Q9H0W9	OTTHUMG00000167452	ENST00000331239.4:c.349A>G	chr11.hg19:g.93488394A>G	ENSP00000331209:p.Thr117Ala	55.0	0.0		95.0	4.0	NM_014039	A8K850|Q6FI88|Q6XYB0|Q96EI3|Q96IX1|Q9Y6B4	Missense_Mutation	SNP	ENST00000331239.4	hg19		.	.	.	.	.	.	.	.	.	.	A	13.39	2.223398	0.39300	.	.	ENSG00000182919	ENST00000528288;ENST00000331239;ENST00000528099;ENST00000354421;ENST00000540113;ENST00000530620;ENST00000524485;ENST00000527363;ENST00000526335;ENST00000533154	.	.	.	5.94	3.65	0.41850	Domain of unknown function DUF1907 (1);	0.183784	0.64402	N	0.000016	T	0.43897	0.1268	L	0.42581	1.335	0.53005	D	0.999966	B;B	0.06786	0.001;0.001	B;B	0.10450	0.004;0.005	T	0.22208	-1.0223	9	0.16896	T	0.51	-6.3971	7.8365	0.29374	0.7181:0.0:0.2819:0.0	.	117;117	Q9H0W9;Q9H0W9-3	CK054_HUMAN;.	A	117;117;117;117;98;98;98;117;117;6	.	ENSP00000331209:T117A	T	+	1	0	C11orf54	93128042	0.998000	0.40836	0.999000	0.59377	0.989000	0.77384	2.450000	0.44943	1.063000	0.40649	0.482000	0.46254	ACA	.	.		0.378	C11orf54-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394671.1	NM_014039		G	93488394	A	G	93488394	3	3	103	1	0	0	0	0	1	0	0	0	1651	275	10	2	367	2	C11orf54	11	93488394	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	587240	93488394	41518122	711	15334										
YAP1	10413	hgsc.bcm.edu	37	chr11	101984981	101984981	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtttctcctgggacactgaCccccactggagtagtctctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:101984981delC	ENST00000282441.5	+	2	816	c.428delC	c.(427-429)accfs	p.T143fs	YAP1_ENST00000531439.1_Frame_Shift_Del_p.T143fs|YAP1_ENST00000524575.1_5'UTR|YAP1_ENST00000537274.1_Frame_Shift_Del_p.T143fs|YAP1_ENST00000345877.2_Frame_Shift_Del_p.T143fs|YAP1_ENST00000526343.1_Frame_Shift_Del_p.T143fs	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	143					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		GGGACACTGACCCCCACTGGA	0.552																																					p.T143fs	Colon(50;247 1103 7861 28956)	Atlas-INDEL	.											.	YAP1	45	.	0			c.427delA						.						82	81	81					11																	101984981		2203	4299	6502	SO:0001589	frameshift_variant	10413	exon2			.		CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"Yes-associated protein 1, 65kDa"			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.428delC	chr11.hg19:g.101984981delC	ENSP00000282441:p.Thr143fs	162.0	0.0		164.0	10.0	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Frame_Shift_Del	DEL	ENST00000282441.5	hg19	CCDS44716.1																																																																																			.	.		0.552	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		-	101984981	C	-	101984981	7	5	103	1	0	1	0	1	0	0	0	0	17481	507	18	0	434	0	YAP1	11	101984981	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	8496587	101984981	33021535	712	15335										
MMP27	64066	hgsc.bcm.edu	37	chr11	102564704	102564704	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atcacagacggctgcatctaTtttcttcacacgtcctggaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:102564704delT	ENST00000260229.4	-	8	1217	c.1126delA	c.(1126-1128)atafs	p.I376fs		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	376					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	GCTGCATCTATTTTCTTCACA	0.403																																					p.I376fs		Atlas-INDEL	.											.	MMP27	84	.	0			c.1127delT						.						151	143	145					11																	102564704		2203	4299	6502	SO:0001589	frameshift_variant	64066	exon8			.	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"matrix metalloprotease 27"		"matrix metalloproteinase 27"			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.1126delA	chr11.hg19:g.102564704delT	ENSP00000260229:p.Ile376fs	152.0	0.0		164.0	10.0	NM_022122	Q6UWK6	Frame_Shift_Del	DEL	ENST00000260229.4	hg19	CCDS8319.1																																																																																			.	.		0.403	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		-	102564704	T	-	102564704	7	5	103	1	0	1	0	1	0	0	0	0	9673	1493	52	0	427	0	MMP27	11	102564704	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	579723	102564704	32441812	713	15336										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103173919	103173919	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ataattatttctccgggtgcTgatccttctcaggaacttca	7	10	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:103173919T>C	ENST00000375735.2	+	76	11337	c.11193T>C	c.(11191-11193)gcT>gcC	p.A3731A	DYNC2H1_ENST00000398093.3_Silent_p.A3738A|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3731	AAA 6. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CTCCGGGTGCTGATCCTTCTC	0.413																																					p.A3738A		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T11214C						.						100	97	98					11																	103173919		1826	4086	5912	SO:0001819	synonymous_variant	79659	exon77			GGGTGCTGATCCT	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.11193T>C	chr11.hg19:g.103173919T>C		74.0	0.0		95.0	4.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.413	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103173919	T	C	103173919	2	2	103	1	0	0	0	0	0	0	0	1	4848	1567	55	2		2	DYNC2H1	11	103173919	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	609215	103173919	31832597	714	15337										
CASP5	838	hgsc.bcm.edu	37	chr11	104871171	104871171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taccaagaacgtgctgtcagAggacttgtgctctggtctgg	13	9	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:104871171A>G	ENST00000260315.3	-	6	768	c.769T>C	c.(769-771)Tct>Cct	p.S257P	CASP5_ENST00000444749.2_Missense_Mutation_p.S199P|CASP5_ENST00000526056.1_Missense_Mutation_p.S270P|CASP5_ENST00000393141.2_Missense_Mutation_p.S270P|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000418434.1_Missense_Mutation_p.S115P|CASP5_ENST00000531367.1_Missense_Mutation_p.S115P			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	257					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		GTGCTGTCAGAGGACTTGTGC	0.453																																					p.S270P		Atlas-SNP	.											.	CASP5	213	.	0			c.T808C						.						116	105	109					11																	104871171		2202	4299	6501	SO:0001583	missense	838	exon6			TGTCAGAGGACTT		CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"Caspases"	1506	protein-coding gene	gene with protein product		602665	"caspase 5, apoptosis-related cysteine protease"			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.769T>C	chr11.hg19:g.104871171A>G	ENSP00000260315:p.Ser257Pro	134.0	0.0		171.0	7.0	NM_001136112	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Missense_Mutation	SNP	ENST00000260315.3	hg19	CCDS8328.2	.	.	.	.	.	.	.	.	.	.	.	11.35	1.613899	0.28712	.	.	ENSG00000137757	ENST00000393141;ENST00000418434;ENST00000260315;ENST00000444749;ENST00000526056;ENST00000531367	T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94	4.21	3.04	0.35103	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.067331	0.64402	D	0.000009	T	0.51432	0.1674	M	0.92077	3.27	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;0.999	T	0.55829	-0.8079	10	0.72032	D	0.01	.	9.0406	0.36316	0.8133:0.1867:0.0:0.0	.	115;199;257;270	P51878-3;P51878-2;P51878;P51878-5	.;.;CASP5_HUMAN;.	P	270;115;257;199;270;115	ENSP00000376849:S270P;ENSP00000398130:S115P;ENSP00000260315:S257P;ENSP00000388365:S199P;ENSP00000436877:S270P;ENSP00000434471:S115P	ENSP00000260315:S257P	S	-	1	0	CASP5	104376381	0.996000	0.38824	0.144000	0.22314	0.035000	0.12851	3.443000	0.52907	0.569000	0.29329	0.172000	0.16884	TCT	.	.		0.453	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347		G	104871171	A	G	104871171	3	3	103	1	0	0	0	0	1	0	0	0	2676	304	11	2	551	2	CASP5	11	104871171	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1697252	104871171	30135345	715	15338										
CWF19L2	143884	hgsc.bcm.edu	37	chr11	107197734	107197734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaagctttctcggatgccttTcctccaaagtcttggttcta	7	11	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:107197734T>C	ENST00000282251.5	-	18	2614	c.2587A>G	c.(2587-2589)Aaa>Gaa	p.K863E		NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	863							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		CGGATGCCTTTCCTCCAAAGT	0.383																																					p.K863E		Atlas-SNP	.											.	CWF19L2	135	.	0			c.A2587G						.						143	147	146					11																	107197734		2201	4298	6499	SO:0001583	missense	143884	exon18			TGCCTTTCCTCCA	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.2587A>G	chr11.hg19:g.107197734T>C	ENSP00000282251:p.Lys863Glu	65.0	0.0		74.0	4.0	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	hg19	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	T	28.9	4.962710	0.92791	.	.	ENSG00000152404	ENST00000282251	T	0.32272	1.46	5.57	5.57	0.84162	Cwf19-like protein, C-terminal domain-2 (1);	0.044248	0.85682	D	0.000000	T	0.54367	0.1854	M	0.76328	2.33	0.80722	D	1	D	0.60575	0.988	D	0.64877	0.93	T	0.58951	-0.7545	10	0.72032	D	0.01	-18.2671	14.921	0.70838	0.0:0.0:0.0:1.0	.	863	Q2TBE0	C19L2_HUMAN	E	863	ENSP00000282251:K863E	ENSP00000282251:K863E	K	-	1	0	CWF19L2	106702944	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.940000	0.87693	2.127000	0.65507	0.528000	0.53228	AAA	.	.		0.383	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		C	107197734	T	C	107197734	3	2	103	1	0	0	0	0	1	0	0	0	4074	1792	62	2	101	2	CWF19L2	11	107197734	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2326563	107197734	27808782	716	15339										
NPAT	4863	hgsc.bcm.edu	37	chr11	108043363	108043363	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcatttaactagttctgcaTttttagtaggtgatttagta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:108043363delT	ENST00000278612.8	-	13	2453	c.2348delA	c.(2347-2349)aatfs	p.N783fs	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	783					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		TAGTTCTGCATTTTTAGTAGG	0.383																																					p.N783fs		Atlas-INDEL	.											.	NPAT	124	.	0			c.2349delT						.						71	67	68					11																	108043363		1836	4096	5932	SO:0001589	frameshift_variant	4863	exon13			.	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.2348delA	chr11.hg19:g.108043363delT	ENSP00000278612:p.Asn783fs	131.0	0.0		191.0	13.0	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Frame_Shift_Del	DEL	ENST00000278612.8	hg19	CCDS41710.1																																																																																			.	.		0.383	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		-	108043363	T	-	108043363	7	5	103	1	0	1	0	1	0	0	0	0	10575	1493	52	0	1959	0	NPAT	11	108043363	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	845629	108043363	26963153	717	15340										
ZC3H12C	85463	hgsc.bcm.edu	37	chr11	110035965	110035965	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	actccgctgtgggcgcccggTccagctgtcctggcgactac	13	16	0	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:110035965T>C	ENST00000278590.3	+	6	2206	c.2155T>C	c.(2155-2157)Tcc>Ccc	p.S719P	ZC3H12C_ENST00000528673.1_Missense_Mutation_p.S720P|ZC3H12C_ENST00000453089.2_Missense_Mutation_p.S688P	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	719							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GGGCGCCCGGTCCAGCTGTCC	0.592																																					p.S719P		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.T2155C						.						142	161	155					11																	110035965		2149	4237	6386	SO:0001583	missense	85463	exon6			GCCCGGTCCAGCT		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.2155T>C	chr11.hg19:g.110035965T>C	ENSP00000278590:p.Ser719Pro	113.0	0.0		137.0	6.0	NM_033390	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	hg19	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	T	19.49	3.836541	0.71373	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.43294	0.95;0.95;0.98	5.94	5.94	0.96194	.	0.055406	0.85682	D	0.000000	T	0.63988	0.2558	M	0.66939	2.045	0.40146	D	0.976894	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.75484	0.986;0.986;0.986	T	0.67669	-0.5611	10	0.72032	D	0.01	-20.3697	16.3947	0.83586	0.0:0.0:0.0:1.0	.	720;719;719	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	P	719;720;688	ENSP00000278590:S719P;ENSP00000431821:S720P;ENSP00000413094:S688P	ENSP00000278590:S719P	S	+	1	0	ZC3H12C	109541175	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.827000	0.55745	2.272000	0.75746	0.459000	0.35465	TCC	.	.		0.592	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		C	110035965	T	C	110035965	3	2	103	1	0	0	0	0	1	0	0	0	17578	1667	58	2	2177	2	ZC3H12C	11	110035965	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1992602	110035965	24970551	718	15341										
PPP2R1B	5519	hgsc.bcm.edu	37	chr11	111618722	111618722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ataaagaattcagcttttcaTcaaagaattccacaccctac	3	11	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:111618722T>C	ENST00000527614.1	-	11	1420	c.1355A>G	c.(1354-1356)gAt>gGt	p.D452G	PPP2R1B_ENST00000311129.5_Missense_Mutation_p.D452G|PPP2R1B_ENST00000426998.2_Missense_Mutation_p.D388G|PPP2R1B_ENST00000341980.6_Missense_Mutation_p.D407G|PPP2R1B_ENST00000427203.2_Missense_Mutation_p.D291G|PPP2R1B_ENST00000393055.2_Missense_Mutation_p.D325G	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	452					apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		CAGCTTTTCATCAAAGAATTC	0.343																																					p.D452G		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A1355G						.						110	99	103					11																	111618722		2201	4296	6497	SO:0001583	missense	5519	exon11			TTTTCATCAAAGA	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9303	protein-coding gene	gene with protein product	"PP2A-A-beta", "protein phosphatase 2A, regulatory subunit A, beta isoform"	603113	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741	ENST00000527614.1:c.1355A>G	chr11.hg19:g.111618722T>C	ENSP00000437193:p.Asp452Gly	56.0	0.0		66.0	4.0	NM_002716	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	hg19	CCDS8349.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.551621	0.65311	.	.	ENSG00000137713	ENST00000311129;ENST00000412902;ENST00000426998;ENST00000527614;ENST00000427203;ENST00000341980;ENST00000393055	T;T;T;T;T;T	0.31510	2.23;2.23;2.23;2.23;1.49;2.23	5.73	5.73	0.89815	Armadillo-like helical (1);Armadillo-type fold (1);	0.044662	0.85682	D	0.000000	T	0.45498	0.1345	M	0.75884	2.315	0.80722	D	1	B;B;B;B;B;B	0.27013	0.166;0.01;0.026;0.09;0.016;0.041	B;B;B;B;B;B	0.40602	0.209;0.049;0.053;0.334;0.053;0.08	T	0.48031	-0.9070	10	0.87932	D	0	-22.5378	14.2586	0.66070	0.0:0.0:0.0:1.0	.	325;407;291;388;452;452	A8MY67;F8W8G1;B7Z1G3;B4DWW5;P30154;P30154-2	.;.;.;.;2AAB_HUMAN;.	G	452;325;388;452;291;407;325	ENSP00000311344:D452G;ENSP00000410671:D388G;ENSP00000437193:D452G;ENSP00000415759:D291G;ENSP00000343317:D407G;ENSP00000376775:D325G	ENSP00000311344:D452G	D	-	2	0	PPP2R1B	111123932	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.387000	0.79785	2.308000	0.77769	0.533000	0.62120	GAT	.	.		0.343	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716		C	111618722	T	C	111618722	3	2	103	1	0	0	0	0	1	0	0	0	12395	1435	50	2	693	2	PPP2R1B	11	111618722	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1582757	111618722	23387794	719	15342										
FDXACB1	91893	hgsc.bcm.edu	37	chr11	111747356	111747356	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctacatgaaaggacttatCttgactcctggcaaaataga	7	8	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:111747356C>T	ENST00000260257.4	-	4	588	c.541G>A	c.(541-543)Gat>Aat	p.D181N	C11orf1_ENST00000530214.1_5'Flank|FDXACB1_ENST00000542429.1_Missense_Mutation_p.D32N|C11orf1_ENST00000260276.3_5'Flank|ALG9_ENST00000524880.1_Missense_Mutation_p.D181N|ALG9_ENST00000527377.1_5'UTR|C11orf1_ENST00000528125.1_5'Flank	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	181					phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						AAGGACTTATCTTGACTCCTG	0.383																																					p.D181N		Atlas-SNP	.											.	FDXACB1	74	.	0			c.G541A						.						77	74	75					11																	111747356		1882	4110	5992	SO:0001583	missense	91893	exon4			ACTTATCTTGACT		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"hypothetical protein BC006136"						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.541G>A	chr11.hg19:g.111747356C>T	ENSP00000260257:p.Asp181Asn	56.0	0.0		86.0	4.0	NM_138378	A0PJW7|B4DUU2	Missense_Mutation	SNP	ENST00000260257.4	hg19	CCDS44729.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.409998	0.42715	.	.	ENSG00000086848;ENSG00000255561;ENSG00000255561;ENSG00000255561	ENST00000428306;ENST00000260257;ENST00000542429;ENST00000528274	T;T;T	0.77229	0.27;-1.08;0.63	5.91	2.22	0.28083	.	0.144081	0.64402	N	0.000009	T	0.72187	0.3429	L	0.58810	1.83	0.54753	D	0.999984	B	0.18968	0.032	B	0.17722	0.019	T	0.69716	-0.5070	10	0.59425	D	0.04	.	11.3577	0.49625	0.0:0.7457:0.0:0.2543	.	181	Q9BRP7	FDXA1_HUMAN	N	181;181;32;92	ENSP00000260257:D181N;ENSP00000441304:D32N;ENSP00000435572:D92N	ENSP00000387627:D181N	D	-	1	0	FDXACB1;ALG9	111252566	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	1.784000	0.38674	0.655000	0.30866	0.655000	0.94253	GAT	.	.		0.383	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378		T	111747356	C	T	111747356	3	4	103	1	0	0	0	0	1	0	0	0	5814	913	32	3	1341	3	FDXACB1	11	111747356	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	128634	111747356	23259160	720	15343										
USP28	57646	hgsc.bcm.edu	37	chr11	113704215	113704215	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acgggtctacaaattttctaTttgatcccatcattagagca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:113704215delT	ENST00000003302.4	-	7	754	c.686delA	c.(685-687)aatfs	p.N229fs	USP28_ENST00000542033.1_5'UTR|USP28_ENST00000545540.1_Frame_Shift_Del_p.N104fs|USP28_ENST00000537706.1_Frame_Shift_Del_p.N229fs|USP28_ENST00000260188.5_Frame_Shift_Del_p.N229fs	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	229	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		AAATTTTCTATTTGATCCCAT	0.383																																					p.N229fs	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	Atlas-INDEL	.											.	USP28	135	.	0			c.687delT						.						109	110	110					11																	113704215		2201	4296	6497	SO:0001589	frameshift_variant	57646	exon7			.	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.686delA	chr11.hg19:g.113704215delT	ENSP00000003302:p.Asn229fs	133.0	0.0		148.0	10.0	NM_020886	B0YJC0|B0YJC1|Q9P213	Frame_Shift_Del	DEL	ENST00000003302.4	hg19	CCDS31680.1																																																																																			.	.		0.383	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			-	113704215	T	-	113704215	7	5	103	1	0	1	0	1	0	0	0	0	17073	1493	52	0	2623	0	USP28	11	113704215	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1956859	113704215	21302301	721	15344										
REXO2	25996	hgsc.bcm.edu	37	chr11	114316717	114316717	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctaggaaattcagttcatgaAgataagaagtttcttgacaa	8	5	3	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:114316717A>G	ENST00000265881.5	+	5	581	c.438A>G	c.(436-438)gaA>gaG	p.E146E	REXO2_ENST00000539275.1_Intron|REXO2_ENST00000538791.1_Silent_p.E56E|REXO2_ENST00000539754.1_Silent_p.E131E	NM_015523.3	NP_056338.2	Q9Y3B8	ORN_HUMAN	RNA exonuclease 2	146	Exonuclease.				nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide metabolic process (GO:0009117)	focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|kidney(1)|lung(1)	4		all_cancers(61;5.06e-12)|all_epithelial(67;5.3e-06)|all_hematologic(158;7.68e-05)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.65e-06)|Epithelial(105;6.09e-05)|all cancers(92;0.000494)		CAGTTCATGAAGATAAGAAGT	0.328																																					p.E146E		Atlas-SNP	.											.	REXO2	12	.	0			c.A438G						.						133	138	136					11																	114316717		2201	4296	6497	SO:0001819	synonymous_variant	25996	exon5			TCATGAAGATAAG	AF151872	CCDS8371.1	11q23.2	2013-06-10	2013-06-10		ENSG00000076043	ENSG00000076043			17851	protein-coding gene	gene with protein product		607149	"REX2, RNA exonuclease 2 homolog (S. cerevisiae)"			10851236, 10810093, 23741365	Standard	NM_015523		Approved	DKFZP566E144, SFN, CGI-114	uc001poy.3	Q9Y3B8	OTTHUMG00000168271	ENST00000265881.5:c.438A>G	chr11.hg19:g.114316717A>G		49.0	0.0		98.0	5.0	NM_015523	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	Silent	SNP	ENST00000265881.5	hg19	CCDS8371.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.690|2.690	-0.273420|-0.273420	0.05679|0.05679	.|.	.|.	ENSG00000076043|ENSG00000076043	ENST00000544827|ENST00000539119;ENST00000538403	.|.	.|.	.|.	5.59|5.59	4.4|4.4	0.53042|0.53042	.|.	.|.	.|.	.|.	.|.	T|T	0.62974|0.62974	0.2472|0.2472	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.61662|0.61662	-0.7017|-0.7017	5|4	0.02654|.	T|.	1|.	-1.8711|-1.8711	11.6412|11.6412	0.51233|0.51233	0.8517:0.1483:0.0:0.0|0.8517:0.1483:0.0:0.0	.|.	.|.	.|.	.|.	R|G	106|101;63	.|.	ENSP00000442703:K109R|.	K|R	+|+	2|1	0|2	REXO2|REXO2	113821927|113821927	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.346000|1.346000	0.33964|0.33964	2.133000|2.133000	0.65898|0.65898	0.455000|0.455000	0.32223|0.32223	AAG|AGA	.	.		0.328	REXO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399087.1	NM_015523		G	114316717	A	G	114316717	2	3	103	1	0	0	0	0	0	0	0	1	13257	69	3	2		2	REXO2	11	114316717	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	612502	114316717	20689799	722	15345										
CADM1	23705	hgsc.bcm.edu	37	chr11	115099840	115099840	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccagggtactcacactgtacTtctagataccgctgggtctg	10	12	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:115099840T>C	ENST00000452722.3	-	5	734	c.714A>G	c.(712-714)gaA>gaG	p.E238E	CADM1_ENST00000542447.2_Silent_p.E238E|CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000536727.1_Silent_p.E238E|CADM1_ENST00000331581.6_Silent_p.E238E|CADM1_ENST00000537058.1_Silent_p.E238E	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		CACACTGTACTTCTAGATACC	0.478																																					p.E238E		Atlas-SNP	.											.	CADM1	74	.	0			c.A714G						.						65	54	58					11																	115099840		2201	4296	6497	SO:0001819	synonymous_variant	23705	exon5			CTGTACTTCTAGA	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5951	protein-coding gene	gene with protein product	"nectin-like 2"	605686	"tumor suppressor in lung cancer 1", "immunoglobulin superfamily, member 4"	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.714A>G	chr11.hg19:g.115099840T>C		54.0	0.0		72.0	6.0	NM_014333		Silent	SNP	ENST00000452722.3	hg19	CCDS8373.1	.	.	.	.	.	.	.	.	.	.	T	9.852	1.193982	0.22037	.	.	ENSG00000182985	ENST00000545380	.	.	.	6.17	5.05	0.67936	.	.	.	.	.	T	0.56093	0.1962	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54282	-0.8317	4	.	.	.	.	6.1386	0.20247	0.0:0.1356:0.1368:0.7276	.	.	.	.	G	237	.	.	S	-	1	0	CADM1	114605050	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	0.850000	0.27737	1.159000	0.42565	0.533000	0.62120	AGT	.	.		0.478	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		C	115099840	T	C	115099840	2	2	103	1	0	0	0	0	0	0	0	1	2568	1606	56	2		2	CADM1	11	115099840	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	783123	115099840	19906676	723	15346										
BACE1	23621	hgsc.bcm.edu	37	chr11	117186306	117186306	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtagccctgccccgacttgCccctcaggttgtccaccatc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:117186306delC	ENST00000313005.6	-	1	666	c.206delG	c.(205-207)ggcfs	p.G69fs	BACE1_ENST00000514464.1_5'UTR|BACE1_ENST00000528053.1_Frame_Shift_Del_p.G69fs|BACE1_ENST00000445823.2_Frame_Shift_Del_p.G69fs|AP000892.4_ENST00000504906.1_RNA|BACE1_ENST00000428381.2_Frame_Shift_Del_p.G69fs|BACE1_ENST00000513780.1_Frame_Shift_Del_p.G69fs	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	69					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		CCCCGACTTGCCCCTCAGGTT	0.706																																					p.G69fs		Atlas-INDEL	.											.	BACE1	33	.	0			c.207delC						.						49	47	48					11																	117186306		2201	4296	6497	SO:0001589	frameshift_variant	23621	exon1			.	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"beta-site APP-cleaving enzyme"	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.206delG	chr11.hg19:g.117186306delC	ENSP00000318585:p.Gly69fs	140.0	0.0		166.0	12.0	NM_138972	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Frame_Shift_Del	DEL	ENST00000313005.6	hg19	CCDS8383.1																																																																																			.	.		0.706	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1			-	117186306	C	-	117186306	7	5	103	1	0	1	0	1	0	0	0	0	1281	739	26	0	1335	0	BACE1	11	117186306	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2086466	117186306	17820210	724	15347										
IL10RA	3587	hgsc.bcm.edu	37	chr11	117860327	117860327	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caccaacacccgcttctctgTggatgaaggtgcttttcctc	8	14	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:117860327T>C	ENST00000227752.3	+	3	479	c.359T>C	c.(358-360)gTg>gCg	p.V120A	IL10RA_ENST00000541785.1_Missense_Mutation_p.V100A|IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000545409.1_Intron	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	120					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		CGCTTCTCTGTGGATGAAGGT	0.552																																					p.V120A		Atlas-SNP	.											.	IL10RA	46	.	0			c.T359C						.						49	46	47					11																	117860327		2200	4296	6496	SO:0001583	missense	3587	exon3			TCTCTGTGGATGA	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"Interleukins and interleukin receptors", "CD molecules"	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.359T>C	chr11.hg19:g.117860327T>C	ENSP00000227752:p.Val120Ala	80.0	0.0		73.0	4.0	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	hg19	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	T	14.57	2.575457	0.45902	.	.	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000536858	T;T	0.57907	0.37;0.37	4.95	-0.957	0.10350	Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.775030	0.03457	N	0.211530	T	0.43523	0.1251	L	0.56769	1.78	0.09310	N	1	B;B	0.34290	0.447;0.319	B;B	0.30029	0.11;0.083	T	0.14364	-1.0475	10	0.17832	T	0.49	0.3079	5.4281	0.16438	0.5307:0.0823:0.0:0.3869	.	100;120	F5GYV8;Q13651	.;I10R1_HUMAN	A	120;100;100	ENSP00000227752:V120A;ENSP00000441397:V100A	ENSP00000227752:V120A	V	+	2	0	IL10RA	117365537	0.000000	0.05858	0.021000	0.16686	0.791000	0.44710	-0.527000	0.06200	-0.019000	0.14055	0.460000	0.39030	GTG	.	.		0.552	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			C	117860327	T	C	117860327	3	2	103	1	0	0	0	0	1	0	0	0	7629	1696	59	2	369	2	IL10RA	11	117860327	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	674021	117860327	17146189	725	15348										
BCL9L	283149	hgsc.bcm.edu	37	chr11	118771996	118771996	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgctgttctgggcccgaaccCgggccatctcctcaggactg	12	15	3	0	rs374181286		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:118771996C>T	ENST00000334801.3	-	6	3420	c.2456G>A	c.(2455-2457)cGg>cAg	p.R819Q	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	819	Met-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GGCCCGAACCCGGGCCATCTC	0.647																																					p.R819Q		Atlas-SNP	.											.	BCL9L	254	.	0			c.G2456A						.	C	GLN/ARG	1,4399		0,1,2199	43	43	43		2456	4.3	1	11		43	0,8590		0,0,4295	no	missense	BCL9L	NM_182557.2	43	0,1,6494	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	819/1500	118771996	1,12989	2200	4295	6495	SO:0001583	missense	283149	exon6			CGAACCCGGGCCA	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.2456G>A	chr11.hg19:g.118771996C>T	ENSP00000335320:p.Arg819Gln	74.0	0.0		80.0	5.0	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	hg19	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.821447	0.71028	2.27E-4	0.0	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000392849;ENST00000431085	T	0.41065	1.01	5.21	4.29	0.51040	.	0.000000	0.45867	D	0.000327	T	0.30008	0.0751	L	0.38531	1.155	0.43061	D	0.994683	P;P	0.48016	0.904;0.846	B;B	0.36666	0.23;0.115	T	0.14952	-1.0454	10	0.42905	T	0.14	-21.2794	12.8474	0.57837	0.0:0.9208:0.0:0.0792	.	814;819	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	Q	819;782;112;819;819	ENSP00000335320:R819Q	ENSP00000335320:R819Q	R	-	2	0	BCL9L	118277206	0.994000	0.37717	0.981000	0.43875	0.955000	0.61496	3.106000	0.50322	2.415000	0.81967	0.655000	0.94253	CGG	.	.		0.647	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		T	118771996	C	T	118771996	3	4	103	1	0	0	0	0	1	0	0	0	1382	652	23	1	2055	1	BCL9L	11	118771996	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	911669	118771996	16234520	726	15349										
HYOU1	10525	hgsc.bcm.edu	37	chr11	118926262	118926262	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctttcagggtcacgatcacCggtgttttcctccgagattc	9	12	4	1	rs376675681		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:118926262C>T	ENST00000404233.3	-	4	331	c.207G>A	c.(205-207)ccG>ccA	p.P69P	HYOU1_ENST00000525859.1_Silent_p.P69P|HYOU1_ENST00000529972.1_Silent_p.P69P|HYOU1_ENST00000543287.1_5'UTR	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	69					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		TCACGATCACCGGTGTTTTCC	0.517																																					p.P69P		Atlas-SNP	.											.	HYOU1	88	.	0			c.G207A						.	C	,	1,4399	2.1+/-5.4	0,1,2199	99	99	99		207,207	-7.8	0.9	11		99	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous	HYOU1	NM_001130991.1,NM_006389.3	,	0,1,6494	TT,TC,CC		0.0,0.0227,0.0077	,	69/1000,69/1000	118926262	1,12989	2200	4295	6495	SO:0001819	synonymous_variant	10525	exon4			GATCACCGGTGTT	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"Heat shock proteins / HSP70"	16931	protein-coding gene	gene with protein product	"glucose-regulated protein 170"	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.207G>A	chr11.hg19:g.118926262C>T		107.0	0.0		152.0	20.0	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Silent	SNP	ENST00000404233.3	hg19	CCDS8408.1																																																																																			.	.		0.517	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389		T	118926262	C	T	118926262	2	4	103	1	0	0	0	0	0	0	0	1	7479	639	23	1		1	HYOU1	11	118926262	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	154266	118926262	16080254	727	15350										
TECTA	7007	hgsc.bcm.edu	37	chr11	120989419	120989419	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tccccaaaggaagctatggaAgagtcaaggtgagccccttt	11	10	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:120989419A>G	ENST00000392793.1	+	7	1466	c.1195A>G	c.(1195-1197)Aga>Gga	p.R399G	TECTA_ENST00000264037.2_Missense_Mutation_p.R399G			O75443	TECTA_HUMAN	tectorin alpha	399	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AAGCTATGGAAGAGTCAAGGT	0.512																																					p.R399G		Atlas-SNP	.											.	TECTA	329	.	0			c.A1195G						.						55	59	58					11																	120989419		2203	4298	6501	SO:0001583	missense	7007	exon6			TATGGAAGAGTCA	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1195A>G	chr11.hg19:g.120989419A>G	ENSP00000376543:p.Arg399Gly	40.0	0.0		76.0	4.0	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	A	10.30	1.313395	0.23908	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.59224	0.28;0.28	5.72	4.54	0.55810	von Willebrand factor, type D domain (3);	0.372961	0.27912	N	0.017350	T	0.41003	0.1140	N	0.16862	0.45	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19679	-1.0298	10	0.28530	T	0.3	.	14.1639	0.65464	0.8672:0.1328:0.0:0.0	.	399	O75443	TECTA_HUMAN	G	399	ENSP00000376543:R399G;ENSP00000264037:R399G	ENSP00000264037:R399G	R	+	1	2	TECTA	120494629	1.000000	0.71417	0.956000	0.39512	0.947000	0.59692	3.980000	0.56895	2.180000	0.69256	0.460000	0.39030	AGA	.	.		0.512	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		G	120989419	A	G	120989419	3	3	103	1	0	0	0	0	1	0	0	0	15762	64	3	2	1217	2	TECTA	11	120989419	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2063157	120989419	14017097	728	15351										
CRTAM	56253	hgsc.bcm.edu	37	chr11	122722405	122722405	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttccctcttgtacagctttAaaaaattccaaataccagct					rs367891560		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:122722405delA	ENST00000227348.4	+	3	245	c.198delA	c.(196-198)ttafs	p.L66fs		NM_019604.2	NP_062550.2			cytotoxic and regulatory T cell molecule											breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|prostate(1)	19		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		GTACAGCTTTAAAAAATTCCA	0.463																																					p.L66X		Atlas-INDEL	.											.	CRTAM	50	.	0			c.197delT						.						125	124	125					11																	122722405		2202	4299	6501	SO:0001589	frameshift_variant	56253	exon3			.	AF001622	CCDS8437.1	11q24.1	2013-01-11			ENSG00000109943	ENSG00000109943		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	24313	protein-coding gene	gene with protein product	"class I MHC restricted T cell associated molecule"	612597				10811014, 16300832	Standard	NM_019604		Approved	CD355	uc001pyj.3	O95727	OTTHUMG00000166026	ENST00000227348.4:c.198delA	chr11.hg19:g.122722405delA	ENSP00000227348:p.Leu66fs	137.0	0.0		186.0	15.0	NM_019604		Frame_Shift_Del	DEL	ENST00000227348.4	hg19	CCDS8437.1																																																																																			.	.		0.463	CRTAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387507.1	NM_019604		-	122722405	A	-	122722405	7	5	103	1	0	1	0	1	0	0	0	0	3899	359	13	0	208	0	CRTAM	11	122722405	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1732986	122722405	12284111	729	15352										
OR8D1	283159	hgsc.bcm.edu	37	chr11	124180206	124180206	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgagtcaaggcagagagaaAgcccaagaagaaggcagcca	13	8	1	5			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:124180206A>G	ENST00000357821.2	-	1	527	c.457T>C	c.(457-459)Ttt>Ctt	p.F153L		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		GCAGAGAGAAAGCCCAAGAAG	0.458																																					p.F153L		Atlas-SNP	.											.	OR8D1	53	.	0			c.T457C						.						73	64	67					11																	124180206		2201	4299	6500	SO:0001583	missense	283159	exon1			AGAGAAAGCCCAA	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"GPCR / Class A : Olfactory receptors"	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.457T>C	chr11.hg19:g.124180206A>G	ENSP00000350474:p.Phe153Leu	61.0	0.0		81.0	4.0	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Missense_Mutation	SNP	ENST00000357821.2	hg19	CCDS31706.1	.	.	.	.	.	.	.	.	.	.	c	6.379	0.438002	0.12104	.	.	ENSG00000196341	ENST00000357821	T	0.00039	8.85	4.29	-8.35	0.00984	GPCR, rhodopsin-like superfamily (1);	0.670897	0.12166	N	0.493560	T	0.00073	0.0002	L	0.28344	0.845	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.30149	-0.9988	10	0.25751	T	0.34	.	1.8553	0.03177	0.1601:0.3845:0.1856:0.2698	.	153	Q8WZ84	OR8D1_HUMAN	L	153	ENSP00000350474:F153L	ENSP00000350474:F153L	F	-	1	0	OR8D1	123685416	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.077000	0.01371	-2.024000	0.00936	-0.456000	0.05471	TTT	.	.		0.458	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917		G	124180206	A	G	124180206	3	3	103	1	0	0	0	0	1	0	0	0	11240	72	3	2	472	2	OR8D1	11	124180206	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1457801	124180206	10826310	730	15353										
HEPN1	641654	hgsc.bcm.edu	37	chr11	124789756	124789756	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcattaaggaggagggaatGgaatacacagagggcctcct	15	7	0	1	rs201178398		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:124789756G>C	ENST00000408930.5	+	1	611	c.110G>C	c.(109-111)tGg>tCg	p.W37S	HEPACAM_ENST00000298251.4_3'UTR	NM_001037558.2	NP_001032647.2	Q6WQI6	HEPN1_HUMAN	hepatocellular carcinoma, down-regulated 1	37			W -> R (in dbSNP:rs3802904). {ECO:0000269|PubMed:12971969}.			cytoplasm (GO:0005737)				large_intestine(1)|lung(1)|stomach(1)	3	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0287)		AGGAGGGAATGGAATACACAG	0.502																																					p.W37S		Atlas-SNP	.											HEPN1,NS,carcinoma,0,1	HEPN1	11	.	0			c.G110C						.						121	124	123					11																	124789756		1967	4153	6120	SO:0001583	missense	641654	exon1			GGGAATGGAATAC	BC148521	CCDS41729.1	11q24	2013-07-02	2011-02-11		ENSG00000221932	ENSG00000221932			34400	protein-coding gene	gene with protein product	"cancer susceptibility gene HEPN1"	611641	"HEPACAM opposite strand 1"			12971969, 23548416	Standard	NM_001037558		Approved		uc001qbj.1	Q6WQI6	OTTHUMG00000165939	ENST00000408930.5:c.110G>C	chr11.hg19:g.124789756G>C	ENSP00000386143:p.Trp37Ser	170.0	0.0		167.0	0.0	NM_001037558		Missense_Mutation	SNP	ENST00000408930.5	hg19	CCDS41729.1	.	.	.	.	.	.	.	.	.	.	G	2.538	-0.306935	0.05458	.	.	ENSG00000221932	ENST00000408930	T	0.56941	0.43	4.85	-0.241	0.13043	.	.	.	.	.	T	0.40222	0.1108	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.33979	-0.9847	8	0.87932	D	0	.	8.4933	0.33112	0.749:0.0:0.251:0.0	.	37	Q6WQI6	HEPN1_HUMAN	S	37	ENSP00000386143:W37S	ENSP00000386143:W37S	W	+	2	0	HEPN1	124294966	0.000000	0.05858	0.011000	0.14972	0.002000	0.02628	-0.123000	0.10611	-0.328000	0.08539	-1.232000	0.01568	TGG	.	.		0.502	HEPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387129.1	NM_001037558		C	124789756	G	C	124789756	3	2	103	1	0	0	0	0	1	0	0	0	7065	1357	47	4	112	4	HEPN1	11	124789756	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	609550	124789756	10216760	731	15354										
SRPR	6734	hgsc.bcm.edu	37	chr11	126136482	126136482	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agttcccacacccggggtgcTtttttgcccttctcctttgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:126136482delT	ENST00000332118.6	-	6	883	c.729delA	c.(727-729)aaafs	p.K243fs	SRPR_ENST00000532259.1_Frame_Shift_Del_p.K215fs|FOXRED1_ENST00000532125.1_5'Flank|SRPR_ENST00000530680.1_5'Flank|FOXRED1_ENST00000263578.5_5'Flank|FOXRED1_ENST00000442061.2_5'Flank	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	243					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		CCCGGGGTGCTTTTTTGCCCT	0.502																																					p.A244fs		Atlas-INDEL	.											.	SRPR	60	.	0			c.730delG						.						109	109	109					11																	126136482		2201	4299	6500	SO:0001589	frameshift_variant	6734	exon6			.	BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"signal recognition particle receptor ('docking protein')"			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.729delA	chr11.hg19:g.126136482delT	ENSP00000328023:p.Lys243fs	193.0	0.0		230.0	14.0	NM_003139	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Frame_Shift_Del	DEL	ENST00000332118.6	hg19	CCDS31717.1																																																																																			.	.		0.502	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139		-	126136482	T	-	126136482	7	5	103	1	0	1	0	1	0	0	0	0	15177	1606	56	0	1223	0	SRPR	11	126136482	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1346726	126136482	8870034	732	15355										
SPATA19	219938	hgsc.bcm.edu	37	chr11	133711936	133711936	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctctctcacctgttgctctcAgcagtctgaggaggagggtc	12	12	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:133711936A>G	ENST00000299140.3	-	6	556	c.502T>C	c.(502-504)Tga>Cga	p.*168R	SPATA19_ENST00000532889.1_Nonstop_Mutation_p.*168R	NM_174927.1	NP_777587.1	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	0					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	mitochondrial outer membrane (GO:0005741)				cervix(1)|endometrium(2)|large_intestine(2)|lung(5)|prostate(1)	11	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		TGTTGCTCTCAGCAGTCTGAG	0.562																																					p.X168R		Atlas-SNP	.											.	SPATA19	36	.	0			c.T502C						.						136	126	129					11																	133711936		2201	4297	6498	SO:0001578	stop_lost	219938	exon6			GCTCTCAGCAGTC	AK098717	CCDS8493.1	11q25	2010-04-23				ENSG00000166118			30614	protein-coding gene	gene with protein product	"spergen 1", "cancer/testis antigen 132"	609805				12477932	Standard	XM_005271448		Approved	FLJ25851, spergen1, SPAS1, CT132	uc001qgv.1	Q7Z5L4		ENST00000299140.3:c.502T>C	chr11.hg19:g.133711936A>G	ENSP00000299140:p.*168Glyext*61	66.0	0.0		117.0	41.0	NM_174927	Q8N7A9	Missense_Mutation	SNP	ENST00000299140.3	hg19	CCDS8493.1	.	.	.	.	.	.	.	.	.	.	A	10.17	1.277183	0.23307	.	.	ENSG00000166118	ENST00000299140;ENST00000532889	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9127	0.52747	1.0:0.0:0.0:0.0	.	.	.	.	R	168	.	.	X	-	1	0	SPATA19	133217146	0.998000	0.40836	1.000000	0.80357	0.530000	0.34684	4.100000	0.57762	2.062000	0.61559	0.459000	0.35465	TGA	.	.		0.562	SPATA19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393281.1	NM_174927		G	133711936	A	G	133711936	4	3	103	1	0	0	0	0	0	0	0	0	15019	201	7	2	5	2	SPATA19	11	133711936	Nonstop_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	7575454	133711936	1294580	733	15356										
EFCAB4B	84766	hgsc.bcm.edu	37	chr12	3789421	3789421	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tactaaatccagtagtgaacTcctgtggggtcagatagcca	10	9	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:3789421T>C	ENST00000252322.1	-	5	791	c.323A>G	c.(322-324)gAg>gGg	p.E108G	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.E108G|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.E108G	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		108	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			AGTAGTGAACTCCTGTGGGGT	0.512																																					p.E108G		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.A323G						.						114	90	98					12																	3789421		2203	4300	6503	SO:0001583	missense	84766	exon5			GTGAACTCCTGTG																												ENST00000252322.1:c.323A>G	chr12.hg19:g.3789421T>C	ENSP00000252322:p.Glu108Gly	134.0	0.0		158.0	7.0	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	hg19	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	T	15.49	2.847989	0.51164	.	.	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	D;D;D	0.90261	-2.64;-2.17;-2.64	4.69	4.69	0.59074	EF-hand-like domain (1);	0.187168	0.45606	D	0.000351	D	0.96685	0.8918	H	0.96916	3.905	0.46564	D	0.999103	D;D;D	0.89917	0.993;1.0;0.989	P;D;P	0.85130	0.905;0.997;0.9	D	0.97464	1.0036	10	0.87932	D	0	-26.3189	12.1539	0.54066	0.0:0.0:0.0:1.0	.	108;108;108	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	G	108	ENSP00000409382:E108G;ENSP00000412496:E108G;ENSP00000252322:E108G	ENSP00000252322:E108G	E	-	2	0	EFCAB4B	3659682	1.000000	0.71417	0.998000	0.56505	0.492000	0.33523	3.631000	0.54280	1.991000	0.58162	0.459000	0.35465	GAG	.	.		0.512	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1			C	3789421	T	C	3789421	3	2	103	1	0	0	0	0	1	0	0	0	4939	1551	54	2	2128	2	EFCAB4B	12	3789421	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10		3789421	130062474	734	15357										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7521548	7521548	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctgaggaggcattcagtgaTttcagcgactgtcctgagag	13	9	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:7521548T>C	ENST00000313599.3	-	16	4110	c.4053A>G	c.(4051-4053)aaA>aaG	p.K1351K	CD163L1_ENST00000416109.2_Silent_p.K1361K|CD163L1_ENST00000396630.1_Silent_p.K1351K			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1351						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CATTCAGTGATTTCAGCGACT	0.453																																					p.K1351K		Atlas-SNP	.											.	CD163L1	238	.	0			c.A4053G						.						132	119	124					12																	7521548		2203	4300	6503	SO:0001819	synonymous_variant	283316	exon16			CAGTGATTTCAGC	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.4053A>G	chr12.hg19:g.7521548T>C		43.0	0.0		61.0	5.0	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	hg19	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	T	1.607	-0.525079	0.04141	.	.	ENSG00000177675	ENST00000539726	.	.	.	0.802	-0.499	0.12015	.	.	.	.	.	T	0.21227	0.0511	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24512	-1.0158	4	.	.	.	.	2.9066	0.05722	0.0:0.3328:0.0:0.6672	.	.	.	.	V	7	.	.	I	-	1	0	CD163L1	7412815	0.002000	0.14202	0.001000	0.08648	0.044000	0.14063	-0.049000	0.11924	-0.204000	0.10235	-0.475000	0.04921	ATC	.	.		0.453	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		C	7521548	T	C	7521548	2	2	103	1	0	0	0	0	0	0	0	1	2970	1490	52	2		2	CD163L1	12	7521548	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3732127	7521548	126330347	735	15358										
SLC2A3	6515	hgsc.bcm.edu	37	chr12	8085609	8085609	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagcggttgacgaagagtccGacggaaaaggagccgatcat	14	8	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:8085609G>A	ENST00000075120.7	-	3	483	c.243C>T	c.(241-243)gtC>gtT	p.V81V		NM_006931.2	NP_008862.1	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 3	81					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(14)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				Kidney(36;0.0866)		CGAAGAGTCCGACGGAAAAGG	0.547											OREG0021656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V81V	Colon(96;424 1461 14416 20933 23688)	Atlas-SNP	.											.	SLC2A3	83	.	0			c.C243T						.						94	87	89					12																	8085609		2203	4300	6503	SO:0001819	synonymous_variant	6515	exon3			GAGTCCGACGGAA	M20681	CCDS8586.1	12p13.3	2013-05-22			ENSG00000059804	ENSG00000059804		"Solute carriers"	11007	protein-coding gene	gene with protein product		138170		GLUT3			Standard	NM_006931		Approved		uc001qtr.3	P11169	OTTHUMG00000133685	ENST00000075120.7:c.243C>T	chr12.hg19:g.8085609G>A		109.0	0.0	646	89.0	4.0	NM_006931	B2R606|D3DUU6|Q6I9U2|Q9UG15	Silent	SNP	ENST00000075120.7	hg19	CCDS8586.1																																																																																			.	.		0.547	SLC2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257914.1	NM_006931		A	8085609	G	A	8085609	2	1	103	1	0	0	0	0	0	0	0	1	14560	1045	37	1		1	SLC2A3	12	8085609	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	564061	8085609	125766286	736	15359										
PRH1	5554	hgsc.bcm.edu	37	chr12	11035175	11035175	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttgctgctggcctccttgttGgggtggtccctgctgagggc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:11035175delG	ENST00000428168.2	-	3	260	c.223delC	c.(223-225)caafs	p.Q76fs	PRR4_ENST00000536668.1_5'UTR	NM_006250.3	NP_006241.2	P02810	PRPC_HUMAN	proline-rich protein HaeIII subfamily 1	76						extracellular space (GO:0005615)				endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(232;0.245)		CCTCCTTGTTGGGGTGGTCCC	0.602																																					p.Q75fs		Atlas-INDEL	.											.	PRH1	17	.	0			c.224delA						.						153	131	138					12																	11035175		2203	4300	6503	SO:0001589	frameshift_variant	5554	exon3			.			12p13.2	2013-05-10			ENSG00000231887	ENSG00000231887			9366	protein-coding gene	gene with protein product		168730				3009472	Standard	NM_001291314		Approved	Pa	uc021qvf.1	P02810		ENST00000428168.2:c.223delC	chr12.hg19:g.11035175delG	ENSP00000412436:p.Gln76fs	220.0	0.0		214.0	14.0	NM_006250	A2VCM0|A3KN66|A5D902|B2RMW2|Q4VBP2|Q53XA2|Q6P2F6	Frame_Shift_Del	DEL	ENST00000428168.2	hg19																																																																																				.	.		0.602	PRH1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006250		-	11035175	G	-	11035175	7	5	103	1	0	1	0	1	0	0	0	0	12494	1357	47	0	285	0	PRH1	12	11035175	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2949566	11035175	122816720	737	15360										
TAS2R42	353164	hgsc.bcm.edu	37	chr12	11338615	11338615	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgtctacaaaggtaaagcaTttggtgtttttgtatagttc	9	5	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:11338615T>G	ENST00000334266.1	-	1	928	c.929A>C	c.(928-930)aAt>aCt	p.N310T		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	310					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			AGGTAAAGCATTTGGTGTTTT	0.413																																					p.N310T	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.A929C						.						58	54	55					12																	11338615		2203	4300	6503	SO:0001583	missense	353164	exon1			AAAGCATTTGGTG	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.929A>C	chr12.hg19:g.11338615T>G	ENSP00000334050:p.Asn310Thr	103.0	0.0		99.0	6.0	NM_181429	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	hg19	CCDS31747.1	.	.	.	.	.	.	.	.	.	.	T	7.528	0.658085	0.14645	.	.	ENSG00000186136	ENST00000334266	T	0.00784	5.7	2.9	0.223	0.15292	.	1.148940	0.06597	U	0.753108	T	0.00496	0.0016	N	0.08118	0	0.09310	N	1	P	0.39480	0.675	B	0.27887	0.084	T	0.50118	-0.8865	10	0.54805	T	0.06	.	6.8753	0.24143	0.0:0.0:0.4872:0.5128	.	310	Q7RTR8	T2R42_HUMAN	T	310	ENSP00000334050:N310T	ENSP00000334050:N310T	N	-	2	0	TAS2R42	11229882	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.039000	0.13884	0.048000	0.15891	0.528000	0.53228	AAT	.	.		0.413	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429		G	11338615	T	G	11338615	3	3	103	1	0	0	0	0	1	0	0	0	15595	1493	52	5	19	5	TAS2R42	12	11338615	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	303440	11338615	122513280	738	15361										
PRB4	5545	hgsc.bcm.edu	37	chr12	11461606	11461606	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggactggtttcctccttgtGggggtggtctttctggcttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:11461606delG	ENST00000535904.1	-	3	344	c.311delC	c.(310-312)ccafs	p.P104fs	PRB4_ENST00000279575.1_Frame_Shift_Del_p.P104fs|PRB4_ENST00000445719.2_Frame_Shift_Del_p.P104fs			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	125	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.					extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						TCCTCCTTGTGGGGGTGGTCT	0.622										HNSCC(22;0.051)																											p.P104fs		Atlas-INDEL	.											.	PRB4	59	.	0			c.312delA						.						226	237	233					12																	11461606		2202	4299	6501	SO:0001589	frameshift_variant	5545	exon3			.		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.311delC	chr12.hg19:g.11461606delG	ENSP00000442834:p.Pro104fs	83.0	0.0		131.0	11.0	NM_001261399	A1L439|O00600|P02813|P10161|P10162|P81489	Frame_Shift_Del	DEL	ENST00000535904.1	hg19	CCDS8641.1																																																																																			.	.		0.622	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723		-	11461606	G	-	11461606	7	5	103	1	0	1	0	1	0	0	0	0	12457	1348	47	0	436	0	PRB4	12	11461606	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	122991	11461606	122390289	739	15362										
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14829894	14829894	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggctgtgacattgtcctcaAagtactggtcactgtaataa	10	8	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:14829894A>C	ENST00000261170.3	-	7	978	c.842T>G	c.(841-843)tTt>tGt	p.F281C	RP11-174G6.1_ENST00000501178.2_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	281			F -> L (in dbSNP:rs1420635). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1680854, ECO:0000269|PubMed:1718270, ECO:0000269|PubMed:8381596, ECO:0000269|Ref.4}.		intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	ATTGTCCTCAAAGTACTGGTC	0.388																																					p.F281C		Atlas-SNP	.											GUCY2C,NS,carcinoma,0,1	GUCY2C	126	.	0			c.T842G						.						76	76	76					12																	14829894		2203	4300	6503	SO:0001583	missense	2984	exon7			TCCTCAAAGTACT		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.842T>G	chr12.hg19:g.14829894A>C	ENSP00000261170:p.Phe281Cys	151.0	0.0		206.0	0.0	NM_004963	B2RMY6	Missense_Mutation	SNP	ENST00000261170.3	hg19	CCDS8664.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.115603	0.37339	.	.	ENSG00000070019	ENST00000261170	T	0.74842	-0.88	5.77	5.77	0.91146	Extracellular ligand-binding receptor (1);	0.053419	0.85682	D	0.000000	T	0.81148	0.4762	L	0.54323	1.7	0.42978	D	0.994453	D	0.67145	0.996	P	0.62813	0.907	T	0.82493	-0.0430	10	0.56958	D	0.05	.	12.5394	0.56161	1.0:0.0:0.0:0.0	.	281	P25092	GUC2C_HUMAN	C	281	ENSP00000261170:F281C	ENSP00000261170:F281C	F	-	2	0	GUCY2C	14721161	0.997000	0.39634	0.922000	0.36590	0.026000	0.11368	4.745000	0.62125	2.213000	0.71641	0.529000	0.55759	TTT	.	.		0.388	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			C	14829894	A	C	14829894	3	2	103	1	0	0	0	0	1	0	0	0	6905	14	1	5	2463	5	GUCY2C	12	14829894	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	3368288	14829894	119022001	740	15363										
SLCO1C1	53919	hgsc.bcm.edu	37	chr12	20885932	20885932	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcagtgtgtgtggagctgcaAaactctacttgggatcatct	11	8	4	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:20885932A>G	ENST00000266509.2	+	10	1644	c.1276A>G	c.(1276-1278)Aaa>Gaa	p.K426E	SLCO1C1_ENST00000545604.1_Missense_Mutation_p.K426E|SLCO1C1_ENST00000545102.1_Missense_Mutation_p.K308E|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.K426E|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.K377E	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	426					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	TGGAGCTGCAAAACTCTACTT	0.443																																					p.K426E		Atlas-SNP	.											SLCO1C1_ENST00000381552,NS,carcinoma,0,2	SLCO1C1	216	.	0			c.A1276G						.						204	180	189					12																	20885932		2203	4300	6503	SO:0001583	missense	53919	exon10			GCTGCAAAACTCT	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"Solute carriers"	13819	protein-coding gene	gene with protein product		613389	"solute carrier family 21 (organic anion transporter), member 14"	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1276A>G	chr12.hg19:g.20885932A>G	ENSP00000266509:p.Lys426Glu	154.0	0.0		159.0	0.0	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	hg19	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.801568	0.90538	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552;ENST00000545102	T;T;T;T;D	0.82167	0.1;0.1;0.1;0.1;-1.58	5.11	5.11	0.69529	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.047896	0.85682	D	0.000000	D	0.92315	0.7562	M	0.91300	3.195	0.54753	D	0.999982	D;D;P;P	0.58620	0.982;0.983;0.815;0.607	P;D;P;P	0.67900	0.805;0.954;0.793;0.686	D	0.93834	0.7130	10	0.66056	D	0.02	.	15.0568	0.71921	1.0:0.0:0.0:0.0	.	308;377;426;426	F5GZD6;B7Z3Q3;Q5JPA4;Q9NYB5	.;.;.;SO1C1_HUMAN	E	426;377;426;426;308	ENSP00000444149:K426E;ENSP00000438665:K377E;ENSP00000266509:K426E;ENSP00000370964:K426E;ENSP00000444527:K308E	ENSP00000266509:K426E	K	+	1	0	SLCO1C1	20777199	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.774000	0.75012	2.134000	0.65973	0.482000	0.46254	AAA	.	.		0.443	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		G	20885932	A	G	20885932	3	3	103	1	0	0	0	0	1	0	0	0	14740	15	1	2	1310	2	SLCO1C1	12	20885932	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	6056038	20885932	112965963	741	15364										
SLCO1B3	28234	hgsc.bcm.edu	37	chr12	21032426	21032426	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttttaggaggatttatcattAaaaaattcaaattgtcttta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:21032426delA	ENST00000381545.3	+	11	1411	c.1192delA	c.(1192-1194)aaafs	p.K399fs	LST3_ENST00000540229.1_Frame_Shift_Del_p.K399fs|SLCO1B3_ENST00000553473.1_Frame_Shift_Del_p.K399fs|SLCO1B3_ENST00000261196.2_Frame_Shift_Del_p.K399fs|LST3_ENST00000381541.3_Intron|SLCO1B7_ENST00000554957.1_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	399					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	ATTTATCATTAAAAAATTCAA	0.294																																					p.I397fs		Atlas-INDEL	.											.	SLCO1B3	151	.	0			c.1191delT						.						65	66	66					12																	21032426		2203	4300	6503	SO:0001589	frameshift_variant	28234	exon11			.		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1192delA	chr12.hg19:g.21032426delA	ENSP00000370956:p.Lys399fs	139.0	0.0		134.0	17.0	NM_019844	E7EMT8|Q5JAR4	Frame_Shift_Del	DEL	ENST00000381545.3	hg19	CCDS8684.1																																																																																			.	.		0.294	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		-	21032426	A	-	21032426	7	5	103	1	0	1	0	1	0	0	0	0	14739	363	13	0	1226	0	SLCO1B3	12	21032426	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	146494	21032426	112819469	742	15365										
OVCH1	341350	hgsc.bcm.edu	37	chr12	29626034	29626034	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggttcaaatttgtttaaagActctgtagaagaaaaaaaaa	7	3	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:29626034A>G	ENST00000318184.5	-	15	1602	c.1603T>C	c.(1603-1605)Tct>Cct	p.S535P	OVCH1-AS1_ENST00000549411.1_Intron|OVCH1-AS1_ENST00000551108.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	535						extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TTGTTTAAAGACTCTGTAGAA	0.343																																					p.S535P		Atlas-SNP	.											.	OVCH1	195	.	0			c.T1603C						.						83	79	80					12																	29626034		1818	4078	5896	SO:0001583	missense	341350	exon15			TTAAAGACTCTGT	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1603T>C	chr12.hg19:g.29626034A>G	ENSP00000326708:p.Ser535Pro	35.0	0.0		48.0	4.0	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	hg19		.	.	.	.	.	.	.	.	.	.	A	6.862	0.528315	0.13127	.	.	ENSG00000187950	ENST00000318184	D	0.86865	-2.18	2.46	1.25	0.21368	.	.	.	.	.	T	0.72890	0.3517	N	0.08118	0	0.09310	N	1	P	0.50617	0.937	P	0.45506	0.483	T	0.63739	-0.6569	9	0.29301	T	0.29	.	4.628	0.12488	0.6723:0.0:0.0:0.3277	.	535	Q7RTY7	OVCH1_HUMAN	P	535	ENSP00000326708:S535P	ENSP00000326708:S535P	S	-	1	0	OVCH1	29517301	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	1.049000	0.30392	0.344000	0.23847	-0.438000	0.05819	TCT	.	.		0.343	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		G	29626034	A	G	29626034	3	3	103	1	0	0	0	0	1	0	0	0	11332	275	10	2	1857	2	OVCH1	12	29626034	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	8593608	29626034	104225861	743	15366										
BICD1	636	hgsc.bcm.edu	37	chr12	32369392	32369392	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtcgtgcaggatctgaaggAggtaaataaacaaattccct	10	7	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:32369392A>G	ENST00000281474.5	+	2	528	c.425A>G	c.(424-426)gAg>gGg	p.E142G	BICD1_ENST00000548411.1_Splice_Site_p.E142G	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	142					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GATCTGAAGGAGGTAAATAAA	0.443																																					p.E142G		Atlas-SNP	.											.	BICD1	89	.	0			c.A425G						.						48	45	46					12																	32369392		2203	4300	6503	SO:0001630	splice_region_variant	636	exon2			TGAAGGAGGTAAA	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.426+1A>G	chr12.hg19:g.32369392A>G		53.0	0.0		76.0	4.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.546311	0.86022	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	T;T	0.30182	1.54;1.54	5.58	5.58	0.84498	.	0.059936	0.64402	D	0.000003	T	0.58495	0.2126	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	T	0.61845	-0.6979	10	0.49607	T	0.09	.	15.7616	0.78087	1.0:0.0:0.0:0.0	.	142;142	F8W113;Q96G01	.;BICD1_HUMAN	G	142	ENSP00000446793:E142G;ENSP00000281474:E142G	ENSP00000281474:E142G	E	+	2	0	BICD1	32260659	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	8.987000	0.93497	2.121000	0.65114	0.533000	0.62120	GAG	.	.		0.443	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	Missense_Mutation	G	32369392	A	G	32369392	5	3	103	1	0	0	0	0	0	0	1	0	1428	318	11	2	431	2	BICD1	12	32369392	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2743358	32369392	101482503	744	15367										
PLEKHA9	51054	hgsc.bcm.edu	37	chr12	45567655	45567655	+	RNA	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagacaagttattgtcatgaTttttcaggttttccattcta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:45567655delT	ENST00000256692.5	-	0	1030					NR_037144.1		O95397	PKHA9_HUMAN	pleckstrin homology domain containing, family A member 8 pseudogene 1							cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						ATTGTCATGATTTTTCAGGTT	0.398																																					.		Atlas-INDEL	.											PLEKHA8P1,NS,carcinoma,0,1	PLEKHA8P1	38	.	0			.						.						151	146	148					12																	45567655		2203	4300	6503			51054	.			.	AF103731		12q12	2010-11-24	2010-11-24	2010-11-24	ENSG00000134297	ENSG00000134297			30222	pseudogene	pseudogene	"putative glycolipid transfer protein"		"pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 9"	PLEKHA9		12477932	Standard	NR_037144		Approved	FLJ14156	uc001rom.2	O95397			chr12.hg19:g.45567655delT		205.0	0.0		246.0	15.0	.		RNA	DEL	ENST00000256692.5	hg19																																																																																				.	.		0.398	PLEKHA8P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000404814.1	NR_037144		-	45567655	T	-	45567655	6	5	103	0	1	1	0	1	0	0	0	0	12072	1493	52	0		0	PLEKHA9	12	45567655	RNA	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	13198263	45567655	88284240	745	15368										
SENP1	29843	hgsc.bcm.edu	37	chr12	48482714	48482714	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaaggttcttaaatcgcctgAgccaagaaaactgtctgagg	10	8	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:48482714A>G	ENST00000004980.5	-	5	728	c.250T>C	c.(250-252)Tca>Cca	p.S84P	SENP1_ENST00000339976.6_Silent_p.A159A|SENP1_ENST00000549518.1_Missense_Mutation_p.S84P|SENP1_ENST00000551330.1_Missense_Mutation_p.S84P|SENP1_ENST00000547886.1_5'UTR|SENP1_ENST00000549595.1_Missense_Mutation_p.S84P|SENP1_ENST00000448372.1_Missense_Mutation_p.S84P			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	84	Ser-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				AAATCGCCTGAGCCAAGAAAA	0.383																																					p.S84P		Atlas-SNP	.											.	SENP1	44	.	0			c.T250C						.						92	76	81					12																	48482714		1811	4071	5882	SO:0001583	missense	29843	exon5			CGCCTGAGCCAAG	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"SUMO1/sentrin specific protease 1"			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.250T>C	chr12.hg19:g.48482714A>G	ENSP00000004980:p.Ser84Pro	67.0	0.0		100.0	38.0	NM_001267594	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	hg19	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	A	16.13	3.035373	0.54896	.	.	ENSG00000079387	ENST00000004980;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518;ENST00000551798	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	4.91	3.73	0.42828	.	0.394176	0.21727	N	0.070034	T	0.17408	0.0418	N	0.19112	0.55	0.80722	D	1	D;D	0.58268	0.969;0.982	P;P	0.53549	0.54;0.729	T	0.02358	-1.1171	10	0.36615	T	0.2	-9.3972	10.0544	0.42237	0.8303:0.1697:0.0:0.0	.	84;84	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	P	84;84;84;84;84;77	ENSP00000004980:S84P;ENSP00000394791:S84P;ENSP00000446681:S84P;ENSP00000450076:S84P;ENSP00000447328:S84P	ENSP00000004980:S84P	S	-	1	0	SENP1	46768981	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.298000	0.43602	0.934000	0.37316	0.454000	0.30748	TCA	.	.		0.383	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554		G	48482714	A	G	48482714	3	3	103	1	0	0	0	0	1	0	0	0	14061	304	11	2	1737	2	SENP1	12	48482714	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2915059	48482714	85369181	746	15369										
ADCY6	112	hgsc.bcm.edu	37	chr12	49170245	49170245	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgcctccatgtggttggccaGggtcacatcattggaccaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:49170245delG	ENST00000307885.4	-	6	2195	c.1501delC	c.(1501-1503)ctgfs	p.L501fs	ADCY6_ENST00000550422.1_Frame_Shift_Del_p.L501fs|ADCY6_ENST00000357869.3_Frame_Shift_Del_p.L501fs|ADCY6_ENST00000552090.1_5'UTR	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	501					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						TGGTTGGCCAGGGTCACATCA	0.647																																					p.L501fs		Atlas-INDEL	.											.	ADCY6	81	.	0			c.1502delT						.						61	56	58					12																	49170245		2203	4299	6502	SO:0001589	frameshift_variant	112	exon7			.		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"Adenylate cyclases"	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.1501delC	chr12.hg19:g.49170245delG	ENSP00000311405:p.Leu501fs	128.0	0.0		104.0	10.0	NM_020983	Q9NR75|Q9UDB0	Frame_Shift_Del	DEL	ENST00000307885.4	hg19	CCDS8767.1																																																																																			.	.		0.647	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		-	49170245	G	-	49170245	7	5	103	1	0	1	0	1	0	0	0	0	298	991	35	0	2069	0	ADCY6	12	49170245	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	687531	49170245	84681650	747	15370										
DNAJC22	79962	hgsc.bcm.edu	37	chr12	49743118	49743118	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccccatagccatactgcccAttagcgtggccgccagcatt	9	16	0	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:49743118A>G	ENST00000549441.2	+	3	1667	c.463A>G	c.(463-465)Att>Gtt	p.I155V	DNAJC22_ENST00000395069.3_Missense_Mutation_p.I155V			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	155						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						CATACTGCCCATTAGCGTGGC	0.562																																					p.I155V		Atlas-SNP	.											.	DNAJC22	29	.	0			c.A463G						.						76	74	75					12																	49743118		2203	4300	6503	SO:0001583	missense	79962	exon2			CTGCCCATTAGCG	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"Heat shock proteins / DNAJ (HSP40)"	25802	protein-coding gene	gene with protein product	"wurst homolog (Drosophila)"					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.463A>G	chr12.hg19:g.49743118A>G	ENSP00000446830:p.Ile155Val	54.0	0.0		86.0	18.0	NM_024902	B3KP54	Missense_Mutation	SNP	ENST00000549441.2	hg19	CCDS8785.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.243418	0.39697	.	.	ENSG00000178401	ENST00000549441;ENST00000395069	T;T	0.46063	0.88;0.88	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.40670	0.1126	M	0.64997	1.995	0.50813	D	0.999898	P	0.39748	0.686	B	0.35607	0.206	T	0.46247	-0.9205	10	0.59425	D	0.04	-11.3242	13.7297	0.62781	1.0:0.0:0.0:0.0	.	155	Q8N4W6	DJC22_HUMAN	V	155	ENSP00000446830:I155V;ENSP00000378508:I155V	ENSP00000378508:I155V	I	+	1	0	DNAJC22	48029385	1.000000	0.71417	1.000000	0.80357	0.190000	0.23558	4.345000	0.59360	1.939000	0.56221	0.454000	0.30748	ATT	.	.		0.562	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902		G	49743118	A	G	49743118	3	3	103	1	0	0	0	0	1	0	0	0	4643	217	8	2	465	2	DNAJC22	12	49743118	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	572873	49743118	84108777	748	15371										
LARP4	113251	hgsc.bcm.edu	37	chr12	50822817	50822817	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tacaggcattgaagaatcaaCtgatgggatgattttaggac	11	5	1	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:50822817C>T	ENST00000398473.2	+	3	378	c.266C>T	c.(265-267)aCt>aTt	p.T89I	LARP4_ENST00000522085.1_Missense_Mutation_p.T89I|LARP4_ENST00000518444.1_Missense_Mutation_p.T88I|LARP4_ENST00000293618.8_Missense_Mutation_p.T89I|LARP4_ENST00000518561.1_Missense_Mutation_p.T19I|LARP4_ENST00000429001.3_Missense_Mutation_p.T95I|LARP4_ENST00000347328.5_Missense_Mutation_p.T89I	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	89					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						GAAGAATCAACTGATGGGATG	0.333																																					p.T89I		Atlas-SNP	.											.	LARP4	58	.	0			c.C266T						.						119	112	114					12																	50822817		1827	4086	5913	SO:0001583	missense	113251	exon3			AATCAACTGATGG	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.266C>T	chr12.hg19:g.50822817C>T	ENSP00000381490:p.Thr89Ile	55.0	0.0		75.0	4.0	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Missense_Mutation	SNP	ENST00000398473.2	hg19	CCDS41782.1	.	.	.	.	.	.	.	.	.	.	C	16.17	3.046455	0.55110	.	.	ENSG00000161813	ENST00000550522;ENST00000293618;ENST00000429001;ENST00000548174;ENST00000548697;ENST00000548993;ENST00000398473;ENST00000441650;ENST00000522085;ENST00000398464;ENST00000518444;ENST00000551886;ENST00000523389;ENST00000518561;ENST00000520064;ENST00000347328;ENST00000550260;ENST00000517559;ENST00000552445	T;T;T;T;T;T;T	0.45668	1.5;1.49;1.48;0.89;1.47;0.9;1.51	5.37	5.37	0.77165	.	0.265880	0.35903	N	0.002903	T	0.37732	0.1014	L	0.29908	0.895	0.25653	N	0.986074	B;B;B;B;B	0.30281	0.016;0.275;0.12;0.008;0.026	B;B;B;B;B	0.33196	0.015;0.159;0.099;0.012;0.019	T	0.37619	-0.9698	10	0.52906	T	0.07	.	18.7183	0.91684	0.0:1.0:0.0:0.0	.	88;89;89;89;95	Q71RC2-3;G3XAA8;G5E976;Q71RC2;Q71RC2-4	.;.;.;LARP4_HUMAN;.	I	19;89;95;97;19;19;89;19;89;89;88;89;19;19;88;89;88;19;19	ENSP00000293618:T89I;ENSP00000415464:T95I;ENSP00000381490:T89I;ENSP00000429781:T89I;ENSP00000429077:T88I;ENSP00000430851:T19I;ENSP00000340901:T89I	ENSP00000293618:T89I	T	+	2	0	LARP4	49109084	0.958000	0.32768	0.998000	0.56505	0.989000	0.77384	5.186000	0.65082	2.513000	0.84729	0.585000	0.79938	ACT	.	.		0.333	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879		T	50822817	C	T	50822817	3	4	103	1	0	0	0	0	1	0	0	0	8639	565	20	3	276	3	LARP4	12	50822817	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	1079699	50822817	83029078	749	15372										
KRT79	338785	hgsc.bcm.edu	37	chr12	53227932	53227932	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cactgccactgctccgagacAccgtcactgagctgaagctg	10	15	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:53227932A>G	ENST00000330553.5	-	1	147	c.113T>C	c.(112-114)gTg>gCg	p.V38A		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	38	Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCTCCGAGACACCGTCACTGA	0.632																																					p.V38A		Atlas-SNP	.											.	KRT79	78	.	0			c.T113C						.						35	38	37					12																	53227932		2202	4298	6500	SO:0001583	missense	338785	exon1			CGAGACACCGTCA	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"-", "Intermediate filaments type II, keratins (basic)"	28930	protein-coding gene	gene with protein product	"keratin 6-like"	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.113T>C	chr12.hg19:g.53227932A>G	ENSP00000328358:p.Val38Ala	80.0	0.0		93.0	4.0	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	hg19	CCDS8839.1	.	.	.	.	.	.	.	.	.	.	A	7.981	0.751258	0.15778	.	.	ENSG00000185640	ENST00000330553	T	0.75589	-0.95	3.98	3.98	0.46160	.	0.531595	0.16412	N	0.215553	T	0.62454	0.2429	L	0.28649	0.875	0.25847	N	0.983985	B	0.09022	0.002	B	0.06405	0.002	T	0.55630	-0.8111	10	0.45353	T	0.12	.	11.4762	0.50300	1.0:0.0:0.0:0.0	.	38	Q5XKE5	K2C79_HUMAN	A	38	ENSP00000328358:V38A	ENSP00000328358:V38A	V	-	2	0	KRT79	51514199	0.031000	0.19500	0.914000	0.36105	0.417000	0.31264	1.133000	0.31430	2.045000	0.60652	0.533000	0.62120	GTG	.	.		0.632	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		G	53227932	A	G	53227932	3	3	103	1	0	0	0	0	1	0	0	0	8501	159	6	2	1530	2	KRT79	12	53227932	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2405115	53227932	80623963	750	15373										
TENC1	23371	hgsc.bcm.edu	37	chr12	53453176	53453176	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctcggagtgtatccaggccAtaggcctggcctcagccgcc	12	16	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:53453176A>G	ENST00000314250.6	+	18	2041	c.1751A>G	c.(1750-1752)cAt>cGt	p.H584R	TENC1_ENST00000546602.1_Missense_Mutation_p.H584R|TENC1_ENST00000314276.3_Missense_Mutation_p.H594R|TENC1_ENST00000552570.1_Missense_Mutation_p.H584R|TENC1_ENST00000549700.1_Missense_Mutation_p.H584R|TENC1_ENST00000451358.1_Missense_Mutation_p.H584R|TENC1_ENST00000379902.3_Missense_Mutation_p.H460R	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	584					cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						TATCCAGGCCATAGGCCTGGC	0.706																																					p.H594R		Atlas-SNP	.											.	TENC1	148	.	0			c.A1781G						.						3	4	4					12																	53453176		1798	3800	5598	SO:0001583	missense	23371	exon18			CAGGCCATAGGCC	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	19737	protein-coding gene	gene with protein product	"tensin 2"	607717	"tensin like C1 domain-containing phosphatase"				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.1751A>G	chr12.hg19:g.53453176A>G	ENSP00000319684:p.His584Arg	36.0	0.0		52.0	5.0	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Missense_Mutation	SNP	ENST00000314250.6	hg19	CCDS8843.1	.	.	.	.	.	.	.	.	.	.	A	2.881	-0.231906	0.05983	.	.	ENSG00000111077	ENST00000379902;ENST00000314276;ENST00000314250;ENST00000451358;ENST00000443113;ENST00000546602;ENST00000552570;ENST00000549700	D;D;D;D;D;D;D	0.93859	-3.29;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3	4.08	0.219	0.15274	.	0.614111	0.15823	N	0.242888	T	0.78394	0.4276	N	0.02539	-0.55	0.23653	N	0.997196	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.67971	-0.5532	10	0.33141	T	0.24	.	4.4517	0.11624	0.4175:0.3844:0.198:0.0	.	584;584;584;594	Q63HR2-6;Q63HR2-2;Q63HR2;Q63HR2-4	.;.;TENC1_HUMAN;.	R	460;594;584;584;584;584;584;584	ENSP00000369232:H460R;ENSP00000319756:H594R;ENSP00000319684:H584R;ENSP00000393362:H584R;ENSP00000449363:H584R;ENSP00000447021:H584R;ENSP00000449361:H584R	ENSP00000319684:H584R	H	+	2	0	TENC1	51739443	0.002000	0.14202	0.465000	0.27155	0.852000	0.48524	-0.041000	0.12084	-0.047000	0.13423	-0.689000	0.03729	CAT	.	.		0.706	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754		G	53453176	A	G	53453176	3	3	103	1	0	0	0	0	1	0	0	0	15773	217	8	2	1930	2	TENC1	12	53453176	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	225244	53453176	80398719	751	15374										
HOXC10	3226	hgsc.bcm.edu	37	chr12	54383171	54383171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaaatcgcagaatgaaactcAagaaaatgaaccgagagaat	8	6	1	5			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:54383171A>G	ENST00000303460.4	+	2	1044	c.970A>G	c.(970-972)Aag>Gag	p.K324E	RP11-834C11.12_ENST00000513209.1_Intron|MIR196A2_ENST00000385189.1_RNA|HOXC10_ENST00000511575.1_3'UTR	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	324					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|neuromuscular process (GO:0050905)|positive regulation of cell proliferation (GO:0008284)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(3)|lung(14)|pancreas(1)	20						AATGAAACTCAAGAAAATGAA	0.483											OREG0021882	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K324E		Atlas-SNP	.											.	HOXC10	42	.	0			c.A970G						.						61	57	59					12																	54383171		2203	4300	6503	SO:0001583	missense	3226	exon2			AAACTCAAGAAAA		CCDS8868.1	12q13.13	2011-06-20	2005-12-22		ENSG00000180818	ENSG00000180818		"Homeoboxes / ANTP class : HOXL subclass"	5122	protein-coding gene	gene with protein product		605560	"homeo box C10"	HOX3I		1358459	Standard	NM_017409		Approved		uc001sen.3	Q9NYD6	OTTHUMG00000160031	ENST00000303460.4:c.970A>G	chr12.hg19:g.54383171A>G	ENSP00000307321:p.Lys324Glu	95.0	0.0	999	86.0	4.0	NM_017409	O15219|O15220|Q9BVD5	Missense_Mutation	SNP	ENST00000303460.4	hg19	CCDS8868.1	.	.	.	.	.	.	.	.	.	.	A	18.50	3.638476	0.67130	.	.	ENSG00000180818	ENST00000303460	D	0.98296	-4.85	3.81	3.81	0.43845	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99381	0.9782	H	0.99182	4.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98098	1.0413	10	0.87932	D	0	.	12.2389	0.54532	1.0:0.0:0.0:0.0	.	324	Q9NYD6	HXC10_HUMAN	E	324	ENSP00000307321:K324E	ENSP00000307321:K324E	K	+	1	0	HOXC10	52669438	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.225000	0.95219	1.680000	0.50976	0.379000	0.24179	AAG	.	.		0.483	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2			G	54383171	A	G	54383171	3	3	103	1	0	0	0	0	1	0	0	0	7318	131	5	2	976	2	HOXC10	12	54383171	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	929995	54383171	79468724	752	15375										
NFE2	4778	hgsc.bcm.edu	37	chr12	54686722	54686722	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttggagtgggccaaggagttGggcatgagtgagtaggggta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:54686722delG	ENST00000540264.2	-	2	1067	c.558delC	c.(556-558)cccfs	p.P186fs	NFE2_ENST00000312156.4_Frame_Shift_Del_p.P186fs|RP11-968A15.8_ENST00000553061.1_RNA|NFE2_ENST00000553070.1_Frame_Shift_Del_p.P186fs|NFE2_ENST00000435572.2_Frame_Shift_Del_p.P186fs			Q16621	NFE2_HUMAN	nuclear factor, erythroid 2	186	Transactivation domain.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|hemostasis (GO:0007599)|labyrinthine layer blood vessel development (GO:0060716)|multicellular organismal development (GO:0007275)|negative regulation of bone mineralization (GO:0030502)|negative regulation of syncytium formation by plasma membrane fusion (GO:0034242)|nucleosome disassembly (GO:0006337)|positive regulation of peptidyl-lysine acetylation (GO:2000758)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(7)|upper_aerodigestive_tract(2)	16						CCAAGGAGTTGGGCATGAGTG	0.607																																					p.N187fs		Atlas-INDEL	.											.	NFE2	28	.	0			c.559delA						.						89	84	86					12																	54686722		2203	4300	6503	SO:0001589	frameshift_variant	4778	exon4			.	BC005044	CCDS8876.1	12q13	2013-08-23	2013-08-23			ENSG00000123405		"basic leucine zipper proteins"	7780	protein-coding gene	gene with protein product		601490	"nuclear factor (erythroid-derived 2), 45kD", "nuclear factor (erythroid-derived 2), 45kDa"			8355703	Standard	NM_001136023		Approved	NF-E2	uc001sfr.5	Q16621		ENST00000540264.2:c.558delC	chr12.hg19:g.54686722delG	ENSP00000439120:p.Pro186fs	141.0	0.0		155.0	11.0	NM_001261461	Q07720|Q6ICV9	Frame_Shift_Del	DEL	ENST00000540264.2	hg19	CCDS8876.1																																																																																			.	.		0.607	NFE2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405747.1	NM_006163		-	54686722	G	-	54686722	7	5	103	1	0	1	0	1	0	0	0	0	10375	1335	47	0	567	0	NFE2	12	54686722	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	303551	54686722	79165173	753	15376										
OR6C6	283365	hgsc.bcm.edu	37	chr12	55688668	55688668	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcaacgtagcggtcataggAcatggcagccaggaggtaaa	15	8	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:55688668A>G	ENST00000358433.2	-	1	348	c.349T>C	c.(349-351)Tcc>Ccc	p.S117P		NM_001005493.1	NP_001005493.1	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C, member 6	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CGGTCATAGGACATGGCAGCC	0.408																																					p.S117P		Atlas-SNP	.											.	OR6C6	56	.	0			c.T349C						.						61	59	59					12																	55688668		2203	4300	6503	SO:0001583	missense	283365	exon1			CATAGGACATGGC		CCDS31817.1	12q13.13	2012-08-09			ENSG00000188324	ENSG00000188324		"GPCR / Class A : Olfactory receptors"	31293	protein-coding gene	gene with protein product							Standard	NM_001005493		Approved		uc010sph.2	A6NF89	OTTHUMG00000168101	ENST00000358433.2:c.349T>C	chr12.hg19:g.55688668A>G	ENSP00000351211:p.Ser117Pro	62.0	0.0		78.0	4.0	NM_001005493		Missense_Mutation	SNP	ENST00000358433.2	hg19	CCDS31817.1	.	.	.	.	.	.	.	.	.	.	-	16.53	3.149275	0.57151	.	.	ENSG00000188324	ENST00000358433	T	0.01369	4.97	4.24	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000139	T	0.09686	0.0238	M	0.92923	3.36	0.36330	D	0.858817	D	0.67145	0.996	D	0.65874	0.939	T	0.01829	-1.1265	10	0.87932	D	0	.	9.7725	0.40598	0.8264:0.1736:0.0:0.0	.	117	A6NF89	OR6C6_HUMAN	P	117	ENSP00000351211:S117P	ENSP00000351211:S117P	S	-	1	0	OR6C6	53974935	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	0.927000	0.28818	1.908000	0.55244	0.473000	0.43528	TCC	.	.		0.408	OR6C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398151.1			G	55688668	A	G	55688668	3	3	103	1	0	0	0	0	1	0	0	0	11203	275	10	2	597	2	OR6C6	12	55688668	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1001946	55688668	78163227	754	15377										
OR6C1	390321	hgsc.bcm.edu	37	chr12	55714705	55714705	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcttcattctcttgggagtcAcagagttttaccttctggct	8	10	5	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:55714705A>G	ENST00000379668.2	+	1	360	c.322A>G	c.(322-324)Aca>Gca	p.T108A		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	108						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						CTTGGGAGTCACAGAGTTTTA	0.408																																					p.T108A		Atlas-SNP	.											.	OR6C1	58	.	0			c.A322G						.						54	55	55					12																	55714705		2202	4300	6502	SO:0001583	missense	390321	exon1			GGAGTCACAGAGT	AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"GPCR / Class A : Olfactory receptors"	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.322A>G	chr12.hg19:g.55714705A>G	ENSP00000368990:p.Thr108Ala	57.0	0.0		58.0	4.0	NM_001005182	B2RNM0	Missense_Mutation	SNP	ENST00000379668.2	hg19	CCDS31818.1	.	.	.	.	.	.	.	.	.	.	a	9.634	1.137090	0.21123	.	.	ENSG00000205330	ENST00000379668	T	0.00873	5.59	4.84	1.09	0.20402	GPCR, rhodopsin-like superfamily (1);	0.094648	0.46758	N	0.000279	T	0.00784	0.0026	L	0.28115	0.83	0.09310	N	1	B	0.15141	0.012	B	0.21151	0.033	T	0.48151	-0.9060	10	0.54805	T	0.06	.	4.1894	0.10414	0.6671:0.0:0.1792:0.1537	.	108	Q96RD1	OR6C1_HUMAN	A	108	ENSP00000368990:T108A	ENSP00000368990:T108A	T	+	1	0	OR6C1	54000972	0.000000	0.05858	0.658000	0.29665	0.647000	0.38526	0.360000	0.20250	0.869000	0.35703	0.374000	0.22700	ACA	.	.		0.408	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182		G	55714705	A	G	55714705	3	3	103	1	0	0	0	0	1	0	0	0	11199	159	6	2	324	2	OR6C1	12	55714705	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	26037	55714705	78137190	755	15378										
OR10P1	121130	hgsc.bcm.edu	37	chr12	56031281	56031281	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcgagatctccgtgatgacAgccaccatagtcttcattat	8	11	3	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:56031281A>G	ENST00000309675.2	+	1	638	c.606A>G	c.(604-606)acA>acG	p.T202T	RP11-644F5.16_ENST00000556606.1_RNA	NM_206899.1	NP_996782.1	Q8NGE3	O10P1_HUMAN	olfactory receptor, family 10, subfamily P, member 1	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26						CCGTGATGACAGCCACCATAG	0.562																																					p.T202T		Atlas-SNP	.											.	OR10P1	48	.	0			c.A606G						.						123	100	107					12																	56031281		2203	4300	6503	SO:0001819	synonymous_variant	121130	exon1			GATGACAGCCACC	BK004259	CCDS31828.1	12q13.13	2012-08-09		2004-03-10		ENSG00000175398		"GPCR / Class A : Olfactory receptors"	15378	protein-coding gene	gene with protein product				OR10P1P, OR10P2P, OR10P3P			Standard	NM_206899		Approved	OST701	uc010spq.2	Q8NGE3	OTTHUMG00000169961	ENST00000309675.2:c.606A>G	chr12.hg19:g.56031281A>G		77.0	0.0		87.0	4.0	NM_206899	B9EGY4	Silent	SNP	ENST00000309675.2	hg19	CCDS31828.1																																																																																			.	.		0.562	OR10P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406680.1			G	56031281	A	G	56031281	2	3	103	1	0	0	0	0	0	0	0	1	10924	175	7	2		2	OR10P1	12	56031281	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	316576	56031281	77820614	756	15379										
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56565643	56565643	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aatgggaagacgaagaaaatGcaagatgcactcgtcctgtg	12	7	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:56565643G>C	ENST00000267064.4	-	20	1998	c.1912C>G	c.(1912-1914)Cat>Gat	p.H638D	RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000394023.3_Missense_Mutation_p.H669D|SMARCC2_ENST00000347471.4_Missense_Mutation_p.H669D|SMARCC2_ENST00000550164.1_Missense_Mutation_p.H669D	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	638	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			CGAAGAAAATGCAAGATGCAC	0.547																																					p.H669D		Atlas-SNP	.											.	SMARCC2	212	.	0			c.C2005G						.						98	85	89					12																	56565643		2203	4300	6503	SO:0001583	missense	6601	exon21			GAAAATGCAAGAT	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.1912C>G	chr12.hg19:g.56565643G>C	ENSP00000267064:p.His638Asp	93.0	0.0		106.0	21.0	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419195	0.83559	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.55052	0.54;0.54;0.54;0.54	3.73	3.73	0.42828	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	T	0.77974	0.4211	M	0.92880	3.355	0.58432	D	0.999999	D;D;D;D;D	0.62365	0.991;0.96;0.968;0.968;0.96	D;D;D;D;D	0.76071	0.987;0.923;0.954;0.954;0.923	D	0.84481	0.0605	10	0.87932	D	0	-8.9217	15.4916	0.75611	0.0:0.0:1.0:0.0	.	558;669;673;638;669	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	D	669;669;669;638	ENSP00000377591:H669D;ENSP00000449396:H669D;ENSP00000302919:H669D;ENSP00000267064:H638D	ENSP00000267064:H638D	H	-	1	0	SMARCC2	54851910	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.601000	0.98297	2.385000	0.81259	0.655000	0.94253	CAT	.	.		0.547	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			C	56565643	G	C	56565643	3	2	103	1	0	0	0	0	1	0	0	0	14791	1319	46	4	1768	4	SMARCC2	12	56565643	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	534362	56565643	77286252	757	15380										
CS	1431	hgsc.bcm.edu	37	chr12	56676682	56676682	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgtccagttaccagcagccAaaataagccctcaggcaggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:56676682delA	ENST00000351328.3	-	5	551	c.361delT	c.(361-363)tggfs	p.W121fs	CS_ENST00000548567.1_Frame_Shift_Del_p.W55fs|CS_ENST00000542324.2_Frame_Shift_Del_p.W108fs	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	121					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		ACCAGCAGCCAAAATAAGCCC	0.478																																					p.W121fs		Atlas-INDEL	.											.	CS	44	.	0			c.362delG						.						109	111	110					12																	56676682		2203	4300	6503	SO:0001589	frameshift_variant	1431	exon5			.		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.361delT	chr12.hg19:g.56676682delA	ENSP00000342056:p.Trp121fs	103.0	0.0		134.0	10.0	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Frame_Shift_Del	DEL	ENST00000351328.3	hg19	CCDS8913.1																																																																																			.	.		0.478	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077		-	56676682	A	-	56676682	7	5	103	1	0	1	0	1	0	0	0	0	3926	130	5	0	1067	0	CS	12	56676682	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	111039	56676682	77175213	758	15381										
SHMT2	6472	hgsc.bcm.edu	37	chr12	57627373	57627373	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccccatgttccgggagtacTccctgcaggttctgaagaat	10	13	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:57627373T>C	ENST00000328923.3	+	9	1503	c.1051T>C	c.(1051-1053)Tcc>Ccc	p.S351P	SHMT2_ENST00000553474.1_Missense_Mutation_p.S330P|SHMT2_ENST00000557487.1_Missense_Mutation_p.S341P|SHMT2_ENST00000449049.3_Missense_Mutation_p.S330P|SHMT2_ENST00000393827.4_Missense_Mutation_p.S255P|SHMT2_ENST00000414700.3_Missense_Mutation_p.S330P	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	351					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	CCGGGAGTACTCCCTGCAGGT	0.617																																					p.S351P	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.T1051C						.						77	65	69					12																	57627373		2203	4300	6503	SO:0001583	missense	6472	exon9			GAGTACTCCCTGC	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.1051T>C	chr12.hg19:g.57627373T>C	ENSP00000333667:p.Ser351Pro	94.0	0.0		76.0	5.0	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	hg19	CCDS8934.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.30|14.30	2.494793|2.494793	0.44352|0.44352	.|.	.|.	ENSG00000182199|ENSG00000182199	ENST00000557529|ENST00000328923;ENST00000557487;ENST00000555634;ENST00000414700;ENST00000553474;ENST00000449049;ENST00000393827	.|T;T;T;T;T;T;T	.|0.44881	.|1.54;0.91;0.91;1.54;1.54;1.54;0.91	4.32|4.32	3.17|3.17	0.36434|0.36434	.|Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.252384	.|0.40064	.|N	.|0.001187	T|T	0.42314|0.42314	0.1197|0.1197	L|L	0.49126|0.49126	1.545|1.545	0.30033|0.30033	N|N	0.813261|0.813261	.|P;B;P;P;B	.|0.44478	.|0.62;0.052;0.836;0.62;0.051	.|P;B;B;P;B	.|0.46885	.|0.53;0.167;0.439;0.53;0.131	T|T	0.45948|0.45948	-0.9226|-0.9226	5|10	.|0.66056	.|D	.|0.02	-23.9224|-23.9224	9.6897|9.6897	0.40120|0.40120	0.0:0.0:0.3633:0.6366|0.0:0.0:0.3633:0.6366	.|.	.|360;341;255;282;351	.|B4DWA7;Q8N1A5;B4DLV4;B4DP88;P34897	.|.;.;.;.;GLYM_HUMAN	P|P	150|351;341;190;330;330;330;255	.|ENSP00000333667:S351P;ENSP00000452315:S341P;ENSP00000450930:S190P;ENSP00000406881:S330P;ENSP00000452419:S330P;ENSP00000413770:S330P;ENSP00000377413:S255P	.|ENSP00000333667:S351P	L|S	+|+	2|1	0|0	SHMT2|SHMT2	55913640|55913640	0.000000|0.000000	0.05858|0.05858	0.999000|0.999000	0.59377|0.59377	0.989000|0.989000	0.77384|0.77384	0.093000|0.093000	0.15086|0.15086	0.810000|0.810000	0.34279|0.34279	0.459000|0.459000	0.35465|0.35465	CTC|TCC	.	.		0.617	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412		C	57627373	T	C	57627373	3	2	103	1	0	0	0	0	1	0	0	0	14301	1551	54	2	1085	2	SHMT2	12	57627373	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	950691	57627373	76224522	759	15382										
DCTN2	10540	hgsc.bcm.edu	37	chr12	57926541	57926541	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccgagcctccacttgatccAaaactgcaaggtctagggcg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:57926541delA	ENST00000548249.1	-	10	1094	c.827delT	c.(826-828)ttgfs	p.L276fs	DCTN2_ENST00000543672.1_Frame_Shift_Del_p.L281fs|DCTN2_ENST00000537439.1_Frame_Shift_Del_p.L253fs|DCTN2_ENST00000434715.3_Frame_Shift_Del_p.L281fs|DCTN2_ENST00000551400.1_5'Flank	NM_001261412.1|NM_001261413.1	NP_001248341.1|NP_001248342.1	Q13561	DCTN2_HUMAN	dynactin 2 (p50)	276					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|vesicle (GO:0031982)	motor activity (GO:0003774)|spectrin binding (GO:0030507)			endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|upper_aerodigestive_tract(2)	11						CACTTGATCCAAAACTGCAAG	0.478																																					p.L278fs		Atlas-INDEL	.											.	DCTN2	51	.	0			c.834delG						.						83	80	81					12																	57926541		1909	4131	6040	SO:0001589	frameshift_variant	10540	exon10			.	U50733	CCDS44930.1, CCDS58245.1, CCDS73489.1	12q13.3	2008-05-14				ENSG00000175203			2712	protein-coding gene	gene with protein product		607376				8647893	Standard	NM_001261412		Approved	RBP50, DCTN-50	uc001som.2	Q13561	OTTHUMG00000170124	ENST00000548249.1:c.827delT	chr12.hg19:g.57926541delA	ENSP00000447824:p.Leu276fs	141.0	0.0		155.0	16.0	NM_001261412	B2RBK5|Q86YN2|Q9BW17	Frame_Shift_Del	DEL	ENST00000548249.1	hg19	CCDS58245.1																																																																																			.	.		0.478	DCTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407393.2	NM_006400		-	57926541	A	-	57926541	7	5	103	1	0	1	0	1	0	0	0	0	4309	131	5	0	398	0	DCTN2	12	57926541	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	299168	57926541	75925354	760	15383										
SRGAP1	57522	hgsc.bcm.edu	37	chr12	64536183	64536183	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggataccctggagcaagtgAaaaactctcccacccctgcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:64536183delA	ENST00000355086.3	+	22	3513	c.2989delA	c.(2989-2991)aaafs	p.K997fs	SRGAP1_ENST00000357825.3_Frame_Shift_Del_p.K974fs|SRGAP1_ENST00000543397.1_Frame_Shift_Del_p.K934fs	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	997					axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		GGAGCAAGTGAAAAACTCTCC	0.542																																					p.V996fs		Atlas-INDEL	.											.	SRGAP1	146	.	0			c.2988delG						.						114	87	96					12																	64536183		2203	4300	6503	SO:0001589	frameshift_variant	57522	exon22			.	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.2989delA	chr12.hg19:g.64536183delA	ENSP00000347198:p.Lys997fs	112.0	0.0		136.0	10.0	NM_020762	Q9H8A3|Q9P2P2	Frame_Shift_Del	DEL	ENST00000355086.3	hg19	CCDS8967.1																																																																																			.	.		0.542	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			-	64536183	A	-	64536183	7	5	103	1	0	1	0	1	0	0	0	0	15160	247	9	0	3075	0	SRGAP1	12	64536183	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	6609642	64536183	69315712	761	15384										
CAND1	55832	hgsc.bcm.edu	37	chr12	67698891	67698891	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttggctttttaggaatcatTttctcactgaatgataaatc	7	6	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:67698891T>C	ENST00000545606.1	+	10	1880	c.1443T>C	c.(1441-1443)atT>atC	p.I481I		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	481					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TAGGAATCATTTTCTCACTGA	0.348																																					p.I481I		Atlas-SNP	.											.	CAND1	100	.	0			c.T1443C						.						94	91	92					12																	67698891		2203	4300	6503	SO:0001819	synonymous_variant	55832	exon10			AATCATTTTCTCA		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.1443T>C	chr12.hg19:g.67698891T>C		48.0	0.0		59.0	4.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Silent	SNP	ENST00000545606.1	hg19	CCDS8977.1																																																																																			.	.		0.348	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		C	67698891	T	C	67698891	2	2	103	1	0	0	0	0	0	0	0	1	2617	1829	64	2		2	CAND1	12	67698891	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3162708	67698891	66153004	762	15385										
NAV3	89795	hgsc.bcm.edu	37	chr12	78531131	78531131	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcattcgggctcattcagagAcagcatggaagaaggtaagc	12	8	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:78531131A>G	ENST00000397909.2	+	19	4789	c.4616A>G	c.(4615-4617)gAc>gGc	p.D1539G	NAV3_ENST00000266692.7_Missense_Mutation_p.D1362G|NAV3_ENST00000228327.6_Missense_Mutation_p.D1539G|NAV3_ENST00000536525.2_Missense_Mutation_p.D1539G			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1539	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.D1539G(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TCATTCAGAGACAGCATGGAA	0.468										HNSCC(70;0.22)																											p.D1539G		Atlas-SNP	.											NAV3,larynx,carcinoma,0,1	NAV3	506	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.A4616G						.						82	80	81					12																	78531131		1904	4130	6034	SO:0001583	missense	89795	exon19			TCAGAGACAGCAT	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.4616A>G	chr12.hg19:g.78531131A>G	ENSP00000381007:p.Asp1539Gly	31.0	0.0		39.0	2.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	A	25.2	4.612702	0.87258	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788	T;T;T;T;T	0.38077	1.16;1.18;1.21;1.3;2.18	5.87	5.87	0.94306	.	0.000000	0.41938	U	0.000792	T	0.56630	0.1998	L	0.54323	1.7	0.80722	D	1	P;D;D;D	0.89917	0.942;0.996;1.0;1.0	P;D;D;D	0.87578	0.636;0.993;0.998;0.998	T	0.56469	-0.7974	10	0.54805	T	0.06	-21.8703	16.2736	0.82632	1.0:0.0:0.0:0.0	.	1539;1362;1539;1539	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2	.;.;NAV3_HUMAN;.	G	1539;1539;1539;1362;160;168	ENSP00000446132:D1539G;ENSP00000381007:D1539G;ENSP00000228327:D1539G;ENSP00000266692:D1362G;ENSP00000448303:D168G	ENSP00000228327:D1539G	D	+	2	0	NAV3	77055262	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.963000	0.93385	2.247000	0.74100	0.477000	0.44152	GAC	.	.		0.468	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		G	78531131	A	G	78531131	3	3	103	1	0	0	0	0	1	0	0	0	10194	275	10	2	4690	2	NAV3	12	78531131	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	10832240	78531131	55320764	763	15386										
ACSS3	79611	hgsc.bcm.edu	37	chr12	81647384	81647384	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtttgtcaaacagctacccAaaaccagatctggcaagatc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:81647384delA	ENST00000548058.1	+	15	2840	c.1930delA	c.(1930-1932)aaafs	p.K644fs	ACSS3_ENST00000261206.3_Frame_Shift_Del_p.K643fs|ACSS3_ENST00000548324.1_Frame_Shift_Del_p.K326fs			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	644						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						ACAGCTACCCAAAACCAGATC	0.418																																					p.P643fs		Atlas-INDEL	.											.	ACSS3	118	.	0			c.1929delC						.						96	97	96					12																	81647384		2203	4300	6503	SO:0001589	frameshift_variant	79611	exon15			.		CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"Acyl-CoA synthetase family"	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.1930delA	chr12.hg19:g.81647384delA	ENSP00000449535:p.Lys644fs	93.0	0.0		108.0	10.0	NM_024560	Q8NC66	Frame_Shift_Del	DEL	ENST00000548058.1	hg19	CCDS9022.1																																																																																			.	.		0.418	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560		-	81647384	A	-	81647384	7	5	103	1	0	1	0	1	0	0	0	0	190	131	5	0	1988	0	ACSS3	12	81647384	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3116253	81647384	52204511	764	15387										
GALNT4	8693	hgsc.bcm.edu	37	chr12	89918093	89918093	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agctggagtttgctggctttCccccactccccaagtgcacg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:89918093delC	ENST00000529983.2	-	1	490	c.234delG	c.(232-234)gggfs	p.G78fs	GALNT4_ENST00000413530.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000541909.1_Intron|POC1B-GALNT4_ENST00000547474.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000313546.3_Intron|POC1B-GALNT4_ENST00000548729.1_Frame_Shift_Del_p.G75fs|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000549035.1_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	78					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						TGCTGGCTTTCCCCCACTCCC	0.498											OREG0022018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K79fs		Atlas-INDEL	.											.	GALNT4	38	.	0			c.235delA						.						123	126	125					12																	89918093		1911	4116	6027	SO:0001589	frameshift_variant	8693	exon1			.	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4126	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 4"	603565	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.234delG	chr12.hg19:g.89918093delC	ENSP00000436604:p.Gly78fs	144.0	0.0	1271	161.0	10.0	NM_003774	B2R775|B4DMX6|O00208	Frame_Shift_Del	DEL	ENST00000529983.2	hg19	CCDS53817.1																																																																																			.	.		0.498	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774		-	89918093	C	-	89918093	7	5	103	1	0	1	0	1	0	0	0	0	6223	842	30	0	1506	0	GALNT4	12	89918093	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	8270709	89918093	43933802	765	15388										
FGD6	55785	hgsc.bcm.edu	37	chr12	95604472	95604472	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgggcctgtgcttctgtgcAgaaataaaaggtggcatttg	14	6	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:95604472A>G	ENST00000343958.4	-	2	811	c.588T>C	c.(586-588)tcT>tcC	p.S196S	FGD6_ENST00000549499.1_Silent_p.S196S|FGD6_ENST00000546711.1_Silent_p.S196S|FGD6_ENST00000550368.1_5'Flank	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	196					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						GCTTCTGTGCAGAAATAAAAG	0.438																																					p.S196S		Atlas-SNP	.											.	FGD6	127	.	0			c.T588C						.						90	84	86					12																	95604472		2203	4300	6503	SO:0001819	synonymous_variant	55785	exon2			CTGTGCAGAAATA	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.588T>C	chr12.hg19:g.95604472A>G		131.0	0.0		146.0	6.0	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Silent	SNP	ENST00000343958.4	hg19	CCDS31878.1																																																																																			.	.		0.438	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		G	95604472	A	G	95604472	2	3	103	1	0	0	0	0	0	0	0	1	5845	175	7	2		2	FGD6	12	95604472	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	5686379	95604472	38247423	766	15389										
APAF1	317	hgsc.bcm.edu	37	chr12	99042548	99042548	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgatggcattcctgttgtcTcttcttccagtggtaaagat	9	8	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:99042548T>C	ENST00000551964.1	+	3	1019	c.283T>C	c.(283-285)Tct>Cct	p.S95P	APAF1_ENST00000552268.1_Missense_Mutation_p.S95P|APAF1_ENST00000333991.1_Missense_Mutation_p.S95P|APAF1_ENST00000547743.1_Missense_Mutation_p.S95P|APAF1_ENST00000547045.1_Missense_Mutation_p.S95P|APAF1_ENST00000359972.2_Missense_Mutation_p.S95P|APAF1_ENST00000339433.3_Missense_Mutation_p.S95P|APAF1_ENST00000550527.1_Missense_Mutation_p.S95P|APAF1_ENST00000549007.1_Missense_Mutation_p.S95P|APAF1_ENST00000357310.1_Missense_Mutation_p.S95P	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	95	Poly-Ser.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	TCCTGTTGTCTCTTCTTCCAG	0.358																																					p.S95P		Atlas-SNP	.											.	APAF1	111	.	0			c.T283C						.						204	201	202					12																	99042548		2203	4300	6503	SO:0001583	missense	317	exon3			GTTGTCTCTTCTT	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.283T>C	chr12.hg19:g.99042548T>C	ENSP00000448165:p.Ser95Pro	111.0	0.0		151.0	7.0	NM_001160	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.294126	0.60086	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000333991;ENST00000547743;ENST00000552268;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.61040	0.17;0.26;0.26;0.37;0.14;0.26;0.37	5.23	1.15	0.20763	DEATH-like (1);	0.679445	0.15917	N	0.238328	T	0.61974	0.2390	L	0.54323	1.7	0.09310	N	0.999999	P;P;P;P;D	0.63880	0.948;0.922;0.908;0.928;0.993	P;P;P;P;D	0.73708	0.62;0.804;0.641;0.641;0.981	T	0.49041	-0.8980	10	0.37606	T	0.19	-2.8146	1.7186	0.02907	0.1368:0.1485:0.1425:0.5723	.	95;95;95;95;95	O14727-6;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	P	95	ENSP00000448165:S95P;ENSP00000353059:S95P;ENSP00000349862:S95P;ENSP00000341830:S95P;ENSP00000448449:S95P;ENSP00000449791:S95P;ENSP00000448161:S95P	ENSP00000334558:S95P	S	+	1	0	APAF1	97566679	0.856000	0.29760	0.216000	0.23742	0.950000	0.60333	1.201000	0.32259	0.341000	0.23771	0.533000	0.62120	TCT	.	.		0.358	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		C	99042548	T	C	99042548	3	2	103	1	0	0	0	0	1	0	0	0	755	1551	54	2	289	2	APAF1	12	99042548	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3438076	99042548	34809347	767	15390										
APAF1	317	hgsc.bcm.edu	37	chr12	99119233	99119233	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttgccacttcatgaattgaGgggccacaacggctgtgtgc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:99119233delG	ENST00000551964.1	+	25	4107	c.3371delG	c.(3370-3372)aggfs	p.R1124fs	APAF1_ENST00000547045.1_Frame_Shift_Del_p.R1081fs|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000552268.1_Intron|APAF1_ENST00000339433.3_Intron|APAF1_ENST00000549007.1_Intron|APAF1_ENST00000550527.1_Frame_Shift_Del_p.R1113fs|APAF1_ENST00000359972.2_Frame_Shift_Del_p.R1070fs|APAF1_ENST00000357310.1_Frame_Shift_Del_p.R1081fs	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	1124					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	CATGAATTGAGGGGCCACAAC	0.478																																					p.R1124fs		Atlas-INDEL	.											.	APAF1	111	.	0			c.3370delA						.						131	114	120					12																	99119233		2203	4300	6503	SO:0001589	frameshift_variant	317	exon25			.	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.3371delG	chr12.hg19:g.99119233delG	ENSP00000448165:p.Arg1124fs	129.0	0.0		167.0	11.0	NM_181861	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Frame_Shift_Del	DEL	ENST00000551964.1	hg19	CCDS9069.1																																																																																			.	.		0.478	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		-	99119233	G	-	99119233	7	5	103	1	0	1	0	1	0	0	0	0	755	1000	35	0	3465	0	APAF1	12	99119233	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	76685	99119233	34732662	768	15391										
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99446958	99446958	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aataagttcaacctcccagaTttttttcaacaggtccatcg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:99446958delT	ENST00000547776.2	-	17	2754	c.2755delA	c.(2755-2757)atcfs	p.I919fs	ANKS1B_ENST00000546568.1_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000546960.1_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000549493.2_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000332712.7_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000549558.2_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000549025.2_Frame_Shift_Del_p.I88fs|ANKS1B_ENST00000550693.2_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000547010.1_Frame_Shift_Del_p.I495fs|ANKS1B_ENST00000329257.7_Frame_Shift_Del_p.I919fs|ANKS1B_ENST00000547446.1_Frame_Shift_Del_p.I114fs	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	919	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		ACCTCCCAGATTTTTTTCAAC	0.373																																					p.I919fs		Atlas-INDEL	.											.	ANKS1B	180	.	0			c.2756delT						.						41	39	40					12																	99446958		1835	4089	5924	SO:0001589	frameshift_variant	56899	exon17			.	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.2755delA	chr12.hg19:g.99446958delT	ENSP00000449629:p.Ile919fs	187.0	0.0		200.0	12.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Frame_Shift_Del	DEL	ENST00000547776.2	hg19	CCDS55872.1																																																																																			.	.		0.373	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		-	99446958	T	-	99446958	7	5	103	1	0	1	0	1	0	0	0	0	689	1493	52	0	1222	0	ANKS1B	12	99446958	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	327725	99446958	34404937	769	15392										
SCYL2	55681	hgsc.bcm.edu	37	chr12	100729661	100729661	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtccgaaaataaagaggacGggttacagaataaacataaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:100729661delG	ENST00000360820.2	+	16	2439	c.2002delG	c.(2002-2004)gggfs	p.G668fs		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	668					endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						TAAAGAGGACGGGTTACAGAA	0.358																																					p.D667fs		Atlas-INDEL	.											.	SCYL2	99	.	0			c.2001delC						.						81	89	86					12																	100729661		2203	4300	6503	SO:0001589	frameshift_variant	55681	exon16			.	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.2002delG	chr12.hg19:g.100729661delG	ENSP00000354061:p.Gly668fs	98.0	0.0		148.0	10.0	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Frame_Shift_Del	DEL	ENST00000360820.2	hg19	CCDS9076.1																																																																																			.	.		0.358	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		-	100729661	G	-	100729661	7	5	103	1	0	1	0	1	0	0	0	0	13963	1116	39	0	2060	0	SCYL2	12	100729661	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1282703	100729661	33122234	770	15393										
HSP90B1	7184	hgsc.bcm.edu	37	chr12	104331534	104331534	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atacaattaaaaatctcgtcAaaaaatattcacagttcata							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:104331534delA	ENST00000299767.5	+	6	987	c.805delA	c.(805-807)aaafs	p.K270fs		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	270					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	AAATCTCGTCAAAAAATATTC	0.299																																					p.V268fs		Atlas-INDEL	.											.	HSP90B1	72	.	0			c.804delC						.						48	51	50					12																	104331534		2201	4298	6499	SO:0001589	frameshift_variant	7184	exon6			.	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.805delA	chr12.hg19:g.104331534delA	ENSP00000299767:p.Lys270fs	162.0	0.0		179.0	11.0	NM_003299	Q96A97	Frame_Shift_Del	DEL	ENST00000299767.5	hg19	CCDS9094.1																																																																																			.	.		0.299	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		-	104331534	A	-	104331534	7	5	103	1	0	1	0	1	0	0	0	0	7412	131	5	0	827	0	HSP90B1	12	104331534	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3601873	104331534	29520361	771	15394										
WSCD2	9671	hgsc.bcm.edu	37	chr12	108589990	108589990	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgggagaaggaggaagagcgAggtaagagcgaggaacatct	18	5	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:108589990A>G	ENST00000332082.4	+	3	1199	c.381A>G	c.(379-381)cgA>cgG	p.R127R	WSCD2_ENST00000549903.1_Splice_Site_p.R127R|WSCD2_ENST00000547525.1_Splice_Site_p.R127R|WSCD2_ENST00000261400.3_Splice_Site_p.R127R			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	127	WSC 1. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						AGGAAGAGCGAGGTAAGAGCG	0.542																																					p.R127R		Atlas-SNP	.											.	WSCD2	125	.	0			c.A381G						.						26	28	27					12																	108589990		1988	4153	6141	SO:0001630	splice_region_variant	9671	exon2			AGAGCGAGGTAAG		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.382+1A>G	chr12.hg19:g.108589990A>G		56.0	0.0		71.0	5.0	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Silent	SNP	ENST00000332082.4	hg19	CCDS41828.1																																																																																			.	.		0.542	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653	Silent	G	108589990	A	G	108589990	5	3	103	1	0	0	0	0	0	0	1	0	17422	318	11	2	383	2	WSCD2	12	108589990	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	4258456	108589990	25261905	772	15395										
MYO1H	283446	hgsc.bcm.edu	37	chr12	109879445	109879445	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcaaaaggtagttacaagtgAaatcttcaggggaaggaaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:109879445delA	ENST00000431443.2	+	25	2546	c.2546delA	c.(2545-2547)gaafs	p.E849fs	MYO1H_ENST00000310903.5_Frame_Shift_Del_p.E839fs	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	849	Myosin tail. {ECO:0000255}.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						GTTACAAGTGAAATCTTCAGG	0.408																																					p.E839fs		Atlas-INDEL	.											.	MYO1H	98	.	0			c.2515delG						.						93	82	85					12																	109879445		1861	4101	5962	SO:0001589	frameshift_variant	283446	exon25			.		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.2546delA	chr12.hg19:g.109879445delA	ENSP00000444076:p.Glu849fs	171.0	0.0		204.0	14.0	NM_001101421	F5H3C6	Frame_Shift_Del	DEL	ENST00000431443.2	hg19																																																																																				.	.		0.408	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		-	109879445	A	-	109879445	7	5	103	1	0	1	0	1	0	0	0	0	10084	246	9	0	2614	0	MYO1H	12	109879445	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1289455	109879445	23972450	773	15396										
ANAPC7	51434	hgsc.bcm.edu	37	chr12	110826388	110826388	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggtgactgaagggcgctccTgaccagccttcttgtacagg	13	11	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:110826388T>C	ENST00000455511.3	-	4	551	c.551A>G	c.(550-552)cAg>cGg	p.Q184R	RP11-478C19.2_ENST00000550231.1_RNA|ANAPC7_ENST00000450008.2_Missense_Mutation_p.Q184R	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	184				Q -> R (in Ref. 1; AAF05754). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						AGGGCGCTCCTGACCAGCCTT	0.443																																					p.Q184R		Atlas-SNP	.											.	ANAPC7	68	.	0			c.A551G						.						130	112	118					12																	110826388		2203	4300	6503	SO:0001583	missense	51434	exon4			CGCTCCTGACCAG	AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	17380	protein-coding gene	gene with protein product		606949					Standard	NM_016238		Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.551A>G	chr12.hg19:g.110826388T>C	ENSP00000394394:p.Gln184Arg	87.0	0.0		98.0	4.0	NM_016238	Q96AC4|Q96GF4|Q9BU24|Q9NT16	Missense_Mutation	SNP	ENST00000455511.3	hg19	CCDS9145.2	.	.	.	.	.	.	.	.	.	.	T	22.6	4.310656	0.81358	.	.	ENSG00000196510;ENSG00000196510;ENSG00000258210	ENST00000455511;ENST00000450008;ENST00000550231	T;T	0.73258	1.27;-0.73	5.74	5.74	0.90152	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.73697	0.3620	L	0.34521	1.04	0.80722	D	1	P;P	0.48294	0.908;0.753	P;B	0.61397	0.888;0.316	T	0.68108	-0.5496	10	0.13108	T	0.6	-19.9339	16.0294	0.80567	0.0:0.0:0.0:1.0	.	184;184	Q9UJX3-2;Q9UJX3	.;APC7_HUMAN	R	184;184;83	ENSP00000394394:Q184R;ENSP00000402314:Q184R	ENSP00000402314:Q184R	Q	-	2	0	RP11-478C19.2;ANAPC7	109310771	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.185000	0.69588	0.455000	0.32223	CAG	.	.		0.443	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347075.3	NM_016238		C	110826388	T	C	110826388	3	2	103	1	0	0	0	0	1	0	0	0	606	1580	55	2	1284	2	ANAPC7	12	110826388	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	946943	110826388	23025507	774	15397										
TMEM116	89894	hgsc.bcm.edu	37	chr12	112374971	112374971	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agttcttacttacttgtggcTctgactgaagttttggaaac	9	7	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:112374971T>C	ENST00000550831.3	-	6	534	c.166A>G	c.(166-168)Agc>Ggc	p.S56G	TMEM116_ENST00000355445.3_Missense_Mutation_p.S113G|TMEM116_ENST00000437003.2_Missense_Mutation_p.S56G|TMEM116_ENST00000549537.2_Missense_Mutation_p.E8G|TMEM116_ENST00000354825.3_Missense_Mutation_p.S56G|TMEM116_ENST00000552374.2_Missense_Mutation_p.S148G	NM_138341.2	NP_612350.1	Q8NCL8	TM116_HUMAN	transmembrane protein 116	56						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)	8						TACTTGTGGCTCTGACTGAAG	0.368																																					p.S148G		Atlas-SNP	.											.	TMEM116	17	.	0			c.A442G						.						139	148	145					12																	112374971		2203	4300	6503	SO:0001583	missense	89894	exon7			TGTGGCTCTGACT	AK074648	CCDS9157.1, CCDS55886.1, CCDS55887.1	12q24.13	2012-03-02			ENSG00000198270	ENSG00000198270			25084	protein-coding gene	gene with protein product						12477932	Standard	NM_001193453		Approved	FLJ90167	uc001ttd.2	Q8NCL8	OTTHUMG00000169606	ENST00000550831.3:c.166A>G	chr12.hg19:g.112374971T>C	ENSP00000450377:p.Ser56Gly	108.0	0.0		120.0	5.0	NM_001193531	G3V1W7|G5E985|Q6NSH5|Q8IZ66	Missense_Mutation	SNP	ENST00000550831.3	hg19	CCDS9157.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	5.843|5.843	0.339846|0.339846	0.11069|0.11069	.|.	.|.	ENSG00000198270|ENSG00000198270	ENST00000549537|ENST00000355445;ENST00000354825;ENST00000550831;ENST00000437003;ENST00000552374;ENST00000550037	.|T;T;T;T;T;T	.|0.47528	.|1.24;1.24;1.24;1.24;1.24;0.84	4.9|4.9	4.9|4.9	0.64082|0.64082	.|.	.|0.568027	.|0.19459	.|N	.|0.113751	T|T	0.43299|0.43299	0.1241|0.1241	L|L	0.48642|0.48642	1.525|1.525	0.27114|0.27114	N|N	0.962309|0.962309	D|B;B;P;B	0.76494|0.35272	0.999|0.105;0.313;0.493;0.177	D|B;B;B;B	0.68943|0.40702	0.961|0.131;0.165;0.338;0.09	T|T	0.32719|0.32719	-0.9896|-0.9896	7|10	.|0.22706	.|T	.|0.39	-0.762|-0.762	9.823|9.823	0.40894|0.40894	0.0:0.0:0.1726:0.8274|0.0:0.0:0.1726:0.8274	.|.	8|148;113;148;56	G3V1Z3|F8VNZ8;G5E985;G3V1W7;Q8NCL8	.|.;.;.;TM116_HUMAN	G|G	8|113;56;56;56;148;148	.|ENSP00000347620:S113G;ENSP00000346883:S56G;ENSP00000450377:S56G;ENSP00000395861:S56G;ENSP00000447731:S148G;ENSP00000446516:S148G	.|ENSP00000346883:S56G	E|S	-|-	2|1	0|0	TMEM116|TMEM116	110859354|110859354	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.076000|0.076000	0.17211|0.17211	4.105000|4.105000	0.57797|0.57797	1.848000|1.848000	0.53677|0.53677	0.383000|0.383000	0.25322|0.25322	GAG|AGC	.	.		0.368	TMEM116-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405026.3	NM_138341		C	112374971	T	C	112374971	3	2	103	1	0	0	0	0	1	0	0	0	16045	1551	54	2	591	2	TMEM116	12	112374971	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1548583	112374971	21476924	775	15398										
SDS	10993	hgsc.bcm.edu	37	chr12	113835064	113835064	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catggcgatgacaggcacgtCcccccagcccacctcctgca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:113835064delC	ENST00000257549.4	-	6	681	c.559delG	c.(559-561)gacfs	p.D187fs		NM_006843.2	NP_006834.2	P20132	SDHL_HUMAN	serine dehydratase	187					gluconeogenesis (GO:0006094)|L-serine catabolic process (GO:0006565)|pyruvate biosynthetic process (GO:0042866)|response to amino acid (GO:0043200)|response to cobalamin (GO:0033590)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	L-serine ammonia-lyase activity (GO:0003941)|L-threonine ammonia-lyase activity (GO:0004794)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(1)	11					L-Serine(DB00133)	ACAGGCACGTCCCCCCAGCCC	0.662																																					p.D187fs		Atlas-INDEL	.											.	SDS	35	.	0			c.560delA						.						74	63	67					12																	113835064		2203	4300	6503	SO:0001589	frameshift_variant	10993	exon6			.	J05037	CCDS9169.1	12q24.13	2014-06-24			ENSG00000135094	ENSG00000135094	4.3.1.17		10691	protein-coding gene	gene with protein product	"L-serine ammonia-lyase"	182128				2674117	Standard	NM_006843		Approved	SDH	uc001tvg.3	P20132	OTTHUMG00000169554	ENST00000257549.4:c.559delG	chr12.hg19:g.113835064delC	ENSP00000257549:p.Asp187fs	231.0	0.0		223.0	14.0	NM_006843	A8K9P5	Frame_Shift_Del	DEL	ENST00000257549.4	hg19	CCDS9169.1																																																																																			.	.		0.662	SDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404790.1	NM_006843		-	113835064	C	-	113835064	7	5	103	1	0	1	0	1	0	0	0	0	13990	855	30	0	439	0	SDS	12	113835064	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1460093	113835064	20016831	776	15399										
SUDS3	64426	hgsc.bcm.edu	37	chr12	118838515	118838515	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaagttgcggaggcgaccaaAtgatcccgtccccatcccag	10	14	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:118838515A>G	ENST00000543473.1	+	7	881	c.569A>G	c.(568-570)aAt>aGt	p.N190S	SUDS3_ENST00000397564.2_Missense_Mutation_p.N191S	NM_022491.2	NP_071936.2	Q9H7L9	SDS3_HUMAN	suppressor of defective silencing 3 homolog (S. cerevisiae)	190	Sin3 interaction domain (SID). {ECO:0000250|UniProtKB:Q8BR65}.				apoptotic process (GO:0006915)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)			breast(1)|lung(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGCGACCAAATGATCCCGTC	0.458																																					p.N190S		Atlas-SNP	.											.	SUDS3	26	.	0			c.A569G						.						128	126	126					12																	118838515		1889	4110	5999	SO:0001583	missense	64426	exon7			GACCAAATGATCC	AK023801	CCDS44993.1	12q24.23	2006-02-13	2006-02-13		ENSG00000111707	ENSG00000111707			29545	protein-coding gene	gene with protein product	"sin3A-associated protein, 45kDa"	608250	"suppressor of defective silencing 3 homolog (SDS3, S. cerevisiae)"			11909966	Standard	NM_022491		Approved	SDS3, FLJ00052, SAP45	uc001twz.3	Q9H7L9	OTTHUMG00000168884	ENST00000543473.1:c.569A>G	chr12.hg19:g.118838515A>G	ENSP00000443988:p.Asn190Ser	85.0	0.0		97.0	4.0	NM_022491	Q4KMQ5|Q8N6H0|Q9H8D2	Missense_Mutation	SNP	ENST00000543473.1	hg19	CCDS44993.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.195064	0.58017	.	.	ENSG00000111707	ENST00000543473;ENST00000397564	.	.	.	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.78298	0.4261	M	0.80183	2.485	0.80722	D	1	D	0.57257	0.979	D	0.71414	0.973	T	0.78578	-0.2150	9	0.35671	T	0.21	.	14.3469	0.66672	1.0:0.0:0.0:0.0	.	190	Q9H7L9	SDS3_HUMAN	S	190;191	.	ENSP00000380695:N191S	N	+	2	0	SUDS3	117322898	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	8.887000	0.92456	1.928000	0.55862	0.402000	0.26972	AAT	.	.		0.458	SUDS3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401504.1	NM_022491		G	118838515	A	G	118838515	3	3	103	1	0	0	0	0	1	0	0	0	15382	101	4	2	595	2	SUDS3	12	118838515	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	5003451	118838515	15013380	777	15400										
CCDC60	160777	hgsc.bcm.edu	37	chr12	119968734	119968734	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taaagaacttccgccccgccAaaaagatcctggtgaaactg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:119968734delA	ENST00000327554.2	+	13	1882	c.1417delA	c.(1417-1419)aaafs	p.K474fs	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	474										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CCGCCCCGCCAAAAAGATCCT	0.488																																					p.A472fs		Atlas-INDEL	.											.	CCDC60	84	.	0			c.1416delC						.						88	85	86					12																	119968734		2203	4300	6503	SO:0001589	frameshift_variant	160777	exon13			.	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.1417delA	chr12.hg19:g.119968734delA	ENSP00000333374:p.Lys474fs	148.0	0.0		162.0	10.0	NM_178499		Frame_Shift_Del	DEL	ENST00000327554.2	hg19	CCDS9190.1																																																																																			.	.		0.488	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		-	119968734	A	-	119968734	7	5	103	1	0	1	0	1	0	0	0	0	2833	131	5	0	1467	0	CCDC60	12	119968734	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1130219	119968734	13883161	778	15401										
PXN	5829	hgsc.bcm.edu	37	chr12	120652962	120652962	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcctttggcgactgtggcgaCccccagcttgttcaggtcag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:120652962delC	ENST00000228307.7	-	8	1189	c.1048delG	c.(1048-1050)gtcfs	p.V350fs	PXN_ENST00000538144.1_5'UTR|PXN-AS1_ENST00000542265.1_RNA|PXN-AS1_ENST00000535200.1_RNA|PXN_ENST00000458477.2_Frame_Shift_Del_p.V183fs|PXN_ENST00000536957.1_Frame_Shift_Del_p.V348fs|PXN_ENST00000424649.2_Frame_Shift_Del_p.V316fs|PXN_ENST00000267257.7_Frame_Shift_Del_p.V364fs|PXN_ENST00000397506.3_Frame_Shift_Del_p.V162fs	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin	350					activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACTGTGGCGACCCCCAGCTTG	0.687																																					p.V364fs		Atlas-INDEL	.											.	PXN	69	.	0			c.1091delT						.						18	21	20					12																	120652962		2166	4268	6434	SO:0001589	frameshift_variant	5829	exon7			.	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.1048delG	chr12.hg19:g.120652962delC	ENSP00000228307:p.Val350fs	249.0	0.0		210.0	13.0	NM_001243756	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	Frame_Shift_Del	DEL	ENST00000228307.7	hg19	CCDS44997.1																																																																																			.	.		0.687	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859		-	120652962	C	-	120652962	7	5	103	1	0	1	0	1	0	0	0	0	12867	507	18	0	747	0	PXN	12	120652962	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	684228	120652962	13198933	779	15402										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124289391	124289391	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctctccaggcgtgaaggaaTtttttgaacacattgagcga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:124289391delT	ENST00000409039.3	+	17	2462	c.2437delT	c.(2437-2439)tttfs	p.F814fs		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	814	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CGTGAAGGAATTTTTTGAACA	0.507																																					p.E812fs		Atlas-INDEL	.											.	DNAH10	888	.	0			c.2436delA						.						118	121	120					12																	124289391		2203	4300	6503	SO:0001589	frameshift_variant	196385	exon17			.	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.2437delT	chr12.hg19:g.124289391delT	ENSP00000386770:p.Phe814fs	148.0	0.0		159.0	10.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Frame_Shift_Del	DEL	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.507	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			-	124289391	T	-	124289391	7	5	103	1	0	1	0	1	0	0	0	0	4600	1493	52	0	2503	0	DNAH10	12	124289391	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3636429	124289391	9562504	780	15403										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124413861	124413861	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgggctgaaactcaacatgAgggcaacttacttcaagatc	9	9	2	3	rs537787991		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:124413861A>G	ENST00000409039.3	+	70	12017	c.11992A>G	c.(11992-11994)Agg>Ggg	p.R3998G	CCDC92_ENST00000544798.1_Intron|DNAH10OS_ENST00000514254.2_3'UTR	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3998	AAA 6. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		ACTCAACATGAGGGCAACTTA	0.537													A|||	1	0.000199681	0	0.0014	5008	,	,		20013	0		0	False		,,,				2504	0				p.R3998G		Atlas-SNP	.											.	DNAH10	888	.	0			c.A11992G						.						38	39	38					12																	124413861		2046	4198	6244	SO:0001583	missense	196385	exon70			AACATGAGGGCAA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.11992A>G	chr12.hg19:g.124413861A>G	ENSP00000386770:p.Arg3998Gly	83.0	0.0		98.0	6.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	19.51	3.841923	0.71488	.	.	ENSG00000197653	ENST00000409039	T	0.08984	3.03	5.16	1.02	0.19986	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.30198	0.0757	M	0.87900	2.915	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	T	0.20306	-1.0279	10	0.35671	T	0.21	.	14.6974	0.69132	0.6009:0.3991:0.0:0.0	.	3998	Q8IVF4	DYH10_HUMAN	G	3998	ENSP00000386770:R3998G	ENSP00000386770:R3998G	R	+	1	2	DNAH10	122979814	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	1.788000	0.38714	0.324000	0.23333	0.482000	0.46254	AGG	.	.		0.537	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			G	124413861	A	G	124413861	3	3	103	1	0	0	0	0	1	0	0	0	4600	295	11	2	12270	2	DNAH10	12	124413861	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	124470	124413861	9438034	781	15404										
EP400	57634	hgsc.bcm.edu	37	chr12	132502833	132502833	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggcagagttgctgtctaagAaaaagataccgcggaaactc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:132502833delA	ENST00000333577.4	+	22	4406	c.4297delA	c.(4297-4299)aaafs	p.K1434fs	EP400_ENST00000332482.4_Frame_Shift_Del_p.K1361fs|EP400_ENST00000330386.6_Frame_Shift_Del_p.K1398fs|EP400_ENST00000389561.2_Frame_Shift_Del_p.K1398fs|EP400_ENST00000389562.2_Frame_Shift_Del_p.K1397fs			Q96L91	EP400_HUMAN	E1A binding protein p400	1434					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		GCTGTCTAAGAAAAAGATACC	0.483																																					p.K1396fs		Atlas-INDEL	.											.	EP400	370	.	0			c.4188delG						.						55	58	57					12																	132502833		2203	4300	6503	SO:0001589	frameshift_variant	57634	exon21			.	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.4297delA	chr12.hg19:g.132502833delA	ENSP00000333602:p.Lys1434fs	148.0	0.0		159.0	11.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Frame_Shift_Del	DEL	ENST00000333577.4	hg19																																																																																				.	.		0.483	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		-	132502833	A	-	132502833	7	5	103	1	0	1	0	1	0	0	0	0	5151	247	9	0	4264	0	EP400	12	132502833	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	8088972	132502833	1349062	782	15405										
POLE	5426	hgsc.bcm.edu	37	chr12	133249252	133249252	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atatcgctgcggaaaaccccAgactcgagggcctccacgtg	11	14	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:133249252A>G	ENST00000320574.5	-	15	1690	c.1647T>C	c.(1645-1647)tcT>tcC	p.S549S	POLE_ENST00000535270.1_Silent_p.S522S	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	549					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GGAAAACCCCAGACTCGAGGG	0.572								DNA polymerases (catalytic subunits)																													p.S549S		Atlas-SNP	.											.	POLE	416	.	0			c.T1647C						.						97	98	98					12																	133249252		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon15			AACCCCAGACTCG		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.1647T>C	chr12.hg19:g.133249252A>G		73.0	0.0		54.0	4.0	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	hg19	CCDS9278.1																																																																																			.	.		0.572	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		G	133249252	A	G	133249252	2	3	103	1	0	0	0	0	0	0	0	1	12205	175	7	2		2	POLE	12	133249252	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	746419	133249252	602643	783	15406										
ANKLE2	23141	hgsc.bcm.edu	37	chr12	133310972	133310972	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacgcctgcacatgcttaccAgacgtggtggctttatctcg	10	13	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:133310972A>G	ENST00000357997.5	-	10	1979	c.1890T>C	c.(1888-1890)tcT>tcC	p.S630S	ANKLE2_ENST00000542657.1_5'Flank|ANKLE2_ENST00000337516.5_Splice_Site_p.S630S|ANKLE2_ENST00000542282.1_5'Flank|ANKLE2_ENST00000542374.1_5'UTR|ANKLE2_ENST00000539605.1_Splice_Site_p.S568S	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	630					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		CATGCTTACCAGACGTGGTGG	0.542																																					p.S630S		Atlas-SNP	.											.	ANKLE2	76	.	0			c.T1890C						.						93	100	98					12																	133310972		1987	4159	6146	SO:0001630	splice_region_variant	23141	exon10			CTTACCAGACGTG	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"Ankyrin repeat domain containing"	29101	protein-coding gene	gene with protein product	"LEM domain containing 7"		"KIAA0692"	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.1891+1T>C	chr12.hg19:g.133310972A>G		70.0	0.0		93.0	4.0	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Silent	SNP	ENST00000357997.5	hg19	CCDS41869.1																																																																																			.	.		0.542	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		Silent	G	133310972	A	G	133310972	5	3	103	1	0	0	0	0	0	0	1	0	633	202	7	2	942	2	ANKLE2	12	133310972	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	61720	133310972	540923	784	15407										
IFT88	8100	hgsc.bcm.edu	37	chr13	21148532	21148532	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttcctaggtacaaatgatgcAaaatgtgcacctggctccag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:21148532delA	ENST00000319980.6	+	4	362	c.35delA	c.(34-36)caafs	p.Q12fs	IFT88_ENST00000351808.5_Frame_Shift_Del_p.Q3fs|IFT88_ENST00000537103.1_Frame_Shift_Del_p.Q3fs|IFT88_ENST00000382778.4_Frame_Shift_Del_p.Q12fs	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	12					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		CAAATGATGCAAAATGTGCAC	0.353																																					p.Q12fs		Atlas-INDEL	.											.	IFT88	83	.	0			c.34delC						.						92	86	88					13																	21148532		2203	4300	6503	SO:0001589	frameshift_variant	8100	exon4			.	AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	20606	protein-coding gene	gene with protein product	"polaris homolog"	600595	"tetratricopeptide repeat domain 10", "intraflagellar transport 88 homolog (Chlamydomonas)"	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.35delA	chr13.hg19:g.21148532delA	ENSP00000323580:p.Gln12fs	211.0	0.0		322.0	21.0	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Frame_Shift_Del	DEL	ENST00000319980.6	hg19	CCDS31944.1																																																																																			.	.		0.353	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		-	21148532	A	-	21148532	7	5	103	1	0	1	0	1	0	0	0	0	7575	130	5	0	41	0	IFT88	13	21148532	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10		21148532	94021346	785	15408										
RNF17	56163	hgsc.bcm.edu	37	chr13	25363884	25363884	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtatgttcaacaatatgggAaagattgaatttagggactc	10	4	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:25363884A>G	ENST00000255324.5	+	9	961	c.909A>G	c.(907-909)ggA>ggG	p.G303G	RNF17_ENST00000381921.1_Silent_p.G303G|RNF17_ENST00000255325.6_Silent_p.G303G|RNF17_ENST00000255326.4_3'UTR	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	303					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		ACAATATGGGAAAGATTGAAT	0.303																																					p.G303G		Atlas-SNP	.											.	RNF17	259	.	0			c.A909G						.						160	162	161					13																	25363884		2203	4296	6499	SO:0001819	synonymous_variant	56163	exon9			TATGGGAAAGATT	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.909A>G	chr13.hg19:g.25363884A>G		59.0	0.0		86.0	4.0	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	hg19	CCDS9308.2																																																																																			.	.		0.303	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		G	25363884	A	G	25363884	2	3	103	1	0	0	0	0	0	0	0	1	13476	233	9	2		2	RNF17	13	25363884	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	4215352	25363884	89805994	786	15409										
KATNAL1	84056	hgsc.bcm.edu	37	chr13	30815176	30815176	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcataaccagcaccatcaaaTtttggcatttcaccatcact							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:30815176delT	ENST00000380615.3	-	5	707	c.540delA	c.(538-540)aaafs	p.K180fs	KATNAL1_ENST00000380617.3_Frame_Shift_Del_p.K180fs	NM_032116.4	NP_115492.1			katanin p60 subunit A-like 1											autonomic_ganglia(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)|urinary_tract(3)	19		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		CACCATCAAATTTTGGCATTT	0.368																																					p.F181fs		Atlas-INDEL	.											.	KATNAL1	53	.	0			c.541delT						.						205	186	192					13																	30815176		2203	4300	6503	SO:0001589	frameshift_variant	84056	exon5			.	AK097423	CCDS31956.1	13q12.3	2010-04-21			ENSG00000102781	ENSG00000102781		"ATPases / AAA-type"	28361	protein-coding gene	gene with protein product		614764				12477932	Standard	NM_001014380		Approved	MGC2599	uc001uss.4	Q9BW62	OTTHUMG00000016665	ENST00000380615.3:c.540delA	chr13.hg19:g.30815176delT	ENSP00000369989:p.Lys180fs	70.0	0.0		146.0	10.0	NM_001014380		Frame_Shift_Del	DEL	ENST00000380615.3	hg19	CCDS31956.1																																																																																			.	.		0.368	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116		-	30815176	T	-	30815176	7	5	103	1	0	1	0	1	0	0	0	0	7994	1490	52	0	960	0	KATNAL1	13	30815176	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5451292	30815176	84354702	787	15410										
KL	9365	hgsc.bcm.edu	37	chr13	33628034	33628034	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccacagcatcaaagaatgtcAaaaatctctggactttgtac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:33628034delA	ENST00000380099.3	+	2	958	c.950delA	c.(949-951)caafs	p.Q317fs	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_Frame_Shift_Del_p.Q10fs	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	317	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		AAAGAATGTCAAAAATCTCTG	0.453																																					p.Q317fs		Atlas-INDEL	.											.	KL	106	.	0			c.949delC						.						171	163	165					13																	33628034		2203	4300	6503	SO:0001589	frameshift_variant	9365	exon2			.	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.950delA	chr13.hg19:g.33628034delA	ENSP00000369442:p.Gln317fs	122.0	0.0		144.0	10.0	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Frame_Shift_Del	DEL	ENST00000380099.3	hg19	CCDS9347.1																																																																																			.	.		0.453	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			-	33628034	A	-	33628034	7	5	103	1	0	1	0	1	0	0	0	0	8340	130	5	0	956	0	KL	13	33628034	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2812858	33628034	81541844	788	15411										
SPG20	23111	hgsc.bcm.edu	37	chr13	36878657	36878657	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgtcctgtttgtgttgcagTtttcttcaccattgctttga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:36878657delT	ENST00000451493.1	-	9	2063	c.1846delA	c.(1846-1848)actfs	p.T616fs	SPG20_ENST00000355182.4_Frame_Shift_Del_p.T616fs|SPG20_ENST00000438666.2_Frame_Shift_Del_p.T616fs|SPG20_ENST00000494062.2_Frame_Shift_Del_p.T616fs	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)	616					abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)		TGTGTTGCAGTTTTCTTCACC	0.443																																					p.T616fs		Atlas-INDEL	.											.	SPG20	87	.	0			c.1847delC						.						285	245	258					13																	36878657		2203	4300	6503	SO:0001589	frameshift_variant	23111	exon9			.	AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"spartin"	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.1846delA	chr13.hg19:g.36878657delT	ENSP00000414147:p.Thr616fs	143.0	0.0		162.0	10.0	NM_015087	O60349|Q86Y67|Q9H1T2|Q9H1T3	Frame_Shift_Del	DEL	ENST00000451493.1	hg19	CCDS9356.1																																																																																			.	.		0.443	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2			-	36878657	T	-	36878657	7	5	103	1	0	1	0	1	0	0	0	0	15057	1725	60	0	158	0	SPG20	13	36878657	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	3250623	36878657	78291221	789	15412										
FREM2	341640	hgsc.bcm.edu	37	chr13	39265691	39265691	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgtgactgatggaataaatCccctcatagatcgttacttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:39265691delC	ENST00000280481.7	+	1	4426	c.4210delC	c.(4210-4212)cccfs	p.P1404fs		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1404					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TGGAATAAATCCCCTCATAGA	0.418																																					p.N1403fs		Atlas-INDEL	.											.	FREM2	385	.	0			c.4209delT						.						151	134	140					13																	39265691		2203	4300	6503	SO:0001589	frameshift_variant	341640	exon1			.	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.4210delC	chr13.hg19:g.39265691delC	ENSP00000280481:p.Pro1404fs	89.0	0.0		157.0	10.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Frame_Shift_Del	DEL	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.418	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		-	39265691	C	-	39265691	7	5	103	1	0	1	0	1	0	0	0	0	6053	855	30	0	4212	0	FREM2	13	39265691	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2387034	39265691	75904187	790	15413										
ELF1	1997	hgsc.bcm.edu	37	chr13	41523943	41523943	+	Splice_Site	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacaaagtaacccacctaccTtttttcctcttaggctgttc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:41523943delT	ENST00000239882.3	-	5	842	c.528delA	c.(526-528)aaa>aa	p.K176fs	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Splice_Site_p.K152fs	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	176					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		CCCACCTACCTTTTTTCCTCT	0.423																																					p.G177fs		Atlas-INDEL	.											.	ELF1	65	.	0			c.529delG						.						197	194	195					13																	41523943		2203	4300	6503	SO:0001630	splice_region_variant	1997	exon5			.	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.529+1A>-	chr13.hg19:g.41523943delT		214.0	0.0		270.0	17.0	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Frame_Shift_Del	DEL	ENST00000239882.3	hg19	CCDS9374.1																																																																																			.	.		0.423	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	Frame_Shift_Del	-	41523943	T	-	41523943	8	5	103	1	0	1	0	1	0	0	1	0	5055	1623	56	0	1351	0	ELF1	13	41523943	Splice_Site	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2258252	41523943	73645935	791	15414										
MTRF1	9617	hgsc.bcm.edu	37	chr13	41800662	41800662	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacgaaaggctatttctttaTtttttatctgtgatctttct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:41800662delT	ENST00000379480.4	-	8	1131	c.1031delA	c.(1030-1032)aatfs	p.N344fs	MTRF1_ENST00000430347.2_Frame_Shift_Del_p.N357fs|MTRF1_ENST00000379477.1_Frame_Shift_Del_p.N344fs	NM_004294.2	NP_004285.2	O75570	RF1M_HUMAN	mitochondrial translational release factor 1	344					regulation of translational termination (GO:0006449)	mitochondrion (GO:0005739)	translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)			breast(1)|endometrium(4)|large_intestine(3)|lung(6)	14		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)		TATTTCTTTATTTTTTATCTG	0.383																																					p.N344fs		Atlas-INDEL	.											.	MTRF1	24	.	0			c.1032delT						.						164	158	160					13																	41800662		2203	4300	6503	SO:0001589	frameshift_variant	9617	exon8			.	AF072934	CCDS9378.1	13q14.1-q14.3	2008-07-18			ENSG00000120662	ENSG00000120662			7469	protein-coding gene	gene with protein product	"mitochontrial peptide chain release factor 1"	604601				9838146, 10773675	Standard	NM_004294		Approved	RF1, MTTRF1, MGC47721	uc001uxy.3	O75570	OTTHUMG00000016790	ENST00000379480.4:c.1031delA	chr13.hg19:g.41800662delT	ENSP00000368793:p.Asn344fs	151.0	0.0		219.0	14.0	NM_004294	B4DG01|Q5T6Y5|Q8IUQ6	Frame_Shift_Del	DEL	ENST00000379480.4	hg19	CCDS9378.1																																																																																			.	.		0.383	MTRF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044666.3	NM_004294		-	41800662	T	-	41800662	7	5	103	1	0	1	0	1	0	0	0	0	9968	1493	52	0	318	0	MTRF1	13	41800662	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	276719	41800662	73369216	792	15415										
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42263625	42263625	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgatcactggaaattttatgAggtatgctgaactctgtttc	9	6	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:42263625A>G	ENST00000379310.3	-	34	4064	c.3996T>C	c.(3994-3996)ccT>ccC	p.P1332P	VWA8_ENST00000478987.1_5'UTR	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1332						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										AAATTTTATGAGGTATGCTGA	0.348																																					p.P1332P		Atlas-SNP	.											.	.	.	.	0			c.T3996C						.						89	80	83					13																	42263625		1823	4086	5909	SO:0001819	synonymous_variant	23078	exon34			TTTATGAGGTATG	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.3996T>C	chr13.hg19:g.42263625A>G		62.0	0.0		82.0	4.0	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Silent	SNP	ENST00000379310.3	hg19	CCDS41881.1																																																																																			.	.		0.348	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		G	42263625	A	G	42263625	2	3	103	1	0	0	0	0	0	0	0	1	8194	291	11	2		2	KIAA0564	13	42263625	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	462963	42263625	72906253	793	15416										
SUCLA2	8803	hgsc.bcm.edu	37	chr13	48562793	48562793	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccgtttgcttggtaaacaaTtttttcccaatcatttgtga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:48562793delT	ENST00000378654.3	-	4	473	c.417delA	c.(415-417)aaafs	p.K139fs	SUCLA2_ENST00000544100.1_Frame_Shift_Del_p.K5fs|SUCLA2_ENST00000534875.1_Frame_Shift_Del_p.K81fs|SUCLA2_ENST00000497202.1_5'UTR|SUCLA2_ENST00000543413.1_Frame_Shift_Del_p.K81fs	NM_003850.2	NP_003841.1	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	139	ATP-grasp.				cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|succinyl-CoA pathway (GO:0006781)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(4)	15		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)	TGGTAAACAATTTTTTCCCAA	0.348																																					p.L140fs		Atlas-INDEL	.											.	SUCLA2	40	.	0			c.418delT						.						95	87	90					13																	48562793		2202	4299	6501	SO:0001589	frameshift_variant	8803	exon4			.	AF058953	CCDS9406.1	13q12.2-q13.3	2010-04-16			ENSG00000136143	ENSG00000136143	6.2.1.5		11448	protein-coding gene	gene with protein product		603921				9765291	Standard	NM_003850		Approved		uc001vbs.3	Q9P2R7	OTTHUMG00000016889	ENST00000378654.3:c.417delA	chr13.hg19:g.48562793delT	ENSP00000367923:p.Lys139fs	118.0	0.0		160.0	10.0	NM_003850	B2RDE7|O95194|Q5T9Q4|Q5T9Q6|Q9NV21|Q9NVP7	Frame_Shift_Del	DEL	ENST00000378654.3	hg19	CCDS9406.1																																																																																			.	.		0.348	SUCLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044852.1			-	48562793	T	-	48562793	7	5	103	1	0	1	0	1	0	0	0	0	15378	1490	52	0	1006	0	SUCLA2	13	48562793	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	6299168	48562793	66607085	794	15417										
RCBTB1	55213	hgsc.bcm.edu	37	chr13	50118925	50118925	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atattttccatcaattcgaaActtcagatcagcagtttctg	5	9	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:50118925A>G	ENST00000378302.2	-	10	1380	c.1120T>C	c.(1120-1122)Ttt>Ctt	p.F374L	RCBTB1_ENST00000258646.3_Missense_Mutation_p.F374L	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	374	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		TCAATTCGAAACTTCAGATCA	0.328																																					p.F374L		Atlas-SNP	.											.	RCBTB1	34	.	0			c.T1120C						.						106	97	100					13																	50118925		2202	4300	6502	SO:0001583	missense	55213	exon10			TTCGAAACTTCAG	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"BTB/POZ domain containing"	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.1120T>C	chr13.hg19:g.50118925A>G	ENSP00000367552:p.Phe374Leu	72.0	0.0		88.0	4.0	NM_018191	Q8IY29|Q969U9	Missense_Mutation	SNP	ENST00000378302.2	hg19	CCDS9418.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.001329	0.93227	.	.	ENSG00000136144	ENST00000258646;ENST00000378302	T;T	0.62498	0.02;0.02	5.44	5.44	0.79542	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.70456	0.3226	L	0.53671	1.685	0.80722	D	1	P	0.51933	0.949	P	0.56648	0.803	T	0.69624	-0.5095	10	0.37606	T	0.19	-18.7715	15.5123	0.75793	1.0:0.0:0.0:0.0	.	374	Q8NDN9	RCBT1_HUMAN	L	374	ENSP00000258646:F374L;ENSP00000367552:F374L	ENSP00000258646:F374L	F	-	1	0	RCBTB1	49016926	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.962000	0.93254	2.056000	0.61249	0.528000	0.53228	TTT	.	.		0.328	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191		G	50118925	A	G	50118925	3	3	103	1	0	0	0	0	1	0	0	0	13186	43	2	2	491	2	RCBTB1	13	50118925	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1556132	50118925	65050953	795	15418										
NEK5	341676	hgsc.bcm.edu	37	chr13	52650224	52650224	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctttatatttctgttctggaTttttactttcctttgtgttc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:52650224delT	ENST00000355568.4	-	19	1842	c.1703delA	c.(1702-1704)aatfs	p.N568fs		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	568					positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		CTGTTCTGGATTTTTACTTTC	0.358																																					p.N568fs		Atlas-INDEL	.											.	NEK5	189	.	0			c.1704delT						.						141	137	139					13																	52650224		2203	4299	6502	SO:0001589	frameshift_variant	341676	exon19			.	BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)-related kinase 5"			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.1703delA	chr13.hg19:g.52650224delT	ENSP00000347767:p.Asn568fs	96.0	0.0		131.0	10.0	NM_199289	Q5TAP5	Frame_Shift_Del	DEL	ENST00000355568.4	hg19	CCDS31979.1																																																																																			.	.		0.358	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289		-	52650224	T	-	52650224	7	5	103	1	0	1	0	1	0	0	0	0	10336	1493	52	0	439	0	NEK5	13	52650224	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2531299	52650224	62519654	796	15419										
DACH1	1602	hgsc.bcm.edu	37	chr13	72440861	72440861	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acgtggagattgggggttgaGgggggaccagctgggtcgga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:72440861delG	ENST00000359684.2	-	1	46	c.47delC	c.(46-48)cctfs	p.P16fs	DACH1_ENST00000305425.4_Frame_Shift_Del_p.P16fs|DACH1_ENST00000313174.7_Frame_Shift_Del_p.P16fs|DACH1_ENST00000354591.4_Frame_Shift_Del_p.P16fs			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	16					cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)	p.P16fs*180(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		TGGGGGTTGAGGGGGGACCAG	0.622																																					p.P16fs		Atlas-INDEL	.											.	DACH1	123	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.48delT						.						22	29	27					13																	72440861		2017	4176	6193	SO:0001589	frameshift_variant	1602	exon1			.	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.47delC	chr13.hg19:g.72440861delG	ENSP00000352712:p.Pro16fs	182.0	0.0		179.0	11.0	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Frame_Shift_Del	DEL	ENST00000359684.2	hg19																																																																																				.	.		0.622	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		-	72440861	G	-	72440861	7	5	103	1	0	1	0	1	0	0	0	0	4222	1000	35	0	2123	0	DACH1	13	72440861	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	19790637	72440861	42729017	797	15420										
PIBF1	10464	hgsc.bcm.edu	37	chr13	73482702	73482702	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aattttatagtctccaagccTcttctgaaaaacgcattact	4	10	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:73482702T>C	ENST00000326291.6	+	12	1860	c.1522T>C	c.(1522-1524)Tct>Cct	p.S508P		NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	508						centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		TCTCCAAGCCTCTTCTGAAAA	0.348																																					p.S508P		Atlas-SNP	.											.	PIBF1	65	.	0			c.T1522C						.						61	61	61					13																	73482702		2203	4300	6503	SO:0001583	missense	10464	exon12			CAAGCCTCTTCTG	AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"progesterone-induced blocking factor 1"	607532	"chromosome 13 open reading frame 24"	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.1522T>C	chr13.hg19:g.73482702T>C	ENSP00000317144:p.Ser508Pro	55.0	0.0		95.0	7.0	NM_006346	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Missense_Mutation	SNP	ENST00000326291.6	hg19	CCDS31991.1	.	.	.	.	.	.	.	.	.	.	T	15.34	2.805039	0.50315	.	.	ENSG00000083535	ENST00000326291	T	0.55930	0.49	5.73	5.73	0.89815	.	0.176258	0.52532	D	0.000070	T	0.57066	0.2028	M	0.68593	2.085	0.49687	D	0.999811	P;P	0.51537	0.946;0.946	P;P	0.49012	0.598;0.598	T	0.59968	-0.7354	10	0.45353	T	0.12	-3.9568	9.9198	0.41457	0.2621:0.0:0.0:0.7379	.	508;508	Q8WXW3;Q4G0R1	PIBF1_HUMAN;.	P	508	ENSP00000317144:S508P	ENSP00000317144:S508P	S	+	1	0	PIBF1	72380703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.944000	0.49034	2.179000	0.69175	0.528000	0.53228	TCT	.	.		0.348	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346		C	73482702	T	C	73482702	3	2	103	1	0	0	0	0	1	0	0	0	11888	1551	54	2	1564	2	PIBF1	13	73482702	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1041841	73482702	41687176	798	15421										
KLF5	688	hgsc.bcm.edu	37	chr13	73636093	73636093	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tagacgagacagtgcctcagTcgtagaccagttcttcactg	10	11	3	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:73636093T>C	ENST00000377687.4	+	2	892	c.356T>C	c.(355-357)gTc>gCc	p.V119A	KLF5_ENST00000539231.1_Missense_Mutation_p.V28A|KLF5_ENST00000477333.1_3'UTR	NM_001730.3	NP_001721.2	Q13887	KLF5_HUMAN	Kruppel-like factor 5 (intestinal)	119					angiogenesis (GO:0001525)|cellular response to organic cyclic compound (GO:0071407)|cellular response to peptide (GO:1901653)|intestinal epithelial cell development (GO:0060576)|microvillus assembly (GO:0030033)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microvillus assembly (GO:0032534)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		AGTGCCTCAGTCGTAGACCAG	0.438																																					p.V119A		Atlas-SNP	.											.	KLF5	59	.	0			c.T356C						.						186	172	177					13																	73636093		2203	4300	6503	SO:0001583	missense	688	exon2			CCTCAGTCGTAGA	D14520	CCDS9448.1, CCDS66562.1	13q21.3	2013-01-08			ENSG00000102554	ENSG00000102554		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6349	protein-coding gene	gene with protein product		602903		BTEB2		8479902, 9973612	Standard	NM_001730		Approved	IKLF, CKLF	uc001vje.3	Q13887	OTTHUMG00000017074	ENST00000377687.4:c.356T>C	chr13.hg19:g.73636093T>C	ENSP00000366915:p.Val119Ala	83.0	0.0		100.0	4.0	NM_001730	L0R3U5|L0R4T9|Q9UHP8	Missense_Mutation	SNP	ENST00000377687.4	hg19	CCDS9448.1	.	.	.	.	.	.	.	.	.	.	T	12.65	2.002916	0.35320	.	.	ENSG00000102554	ENST00000539231;ENST00000377687;ENST00000545883	T;T	0.09350	3.24;2.99	6.04	6.04	0.98038	.	0.437392	0.26432	N	0.024416	T	0.13072	0.0317	L	0.55990	1.75	0.31999	N	0.603602	B	0.30406	0.278	B	0.30179	0.112	T	0.06058	-1.0848	10	0.42905	T	0.14	.	12.4367	0.55602	0.0:0.0:0.1397:0.8603	.	119	Q13887	KLF5_HUMAN	A	28;119;99	ENSP00000440407:V28A;ENSP00000366915:V119A	ENSP00000366915:V119A	V	+	2	0	KLF5	72534094	0.998000	0.40836	0.999000	0.59377	0.995000	0.86356	2.434000	0.44802	2.317000	0.78254	0.460000	0.39030	GTC	.	.		0.438	KLF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045263.1			C	73636093	T	C	73636093	3	2	103	1	0	0	0	0	1	0	0	0	8358	1667	58	2	362	2	KLF5	13	73636093	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	153391	73636093	41533785	799	15422										
KLF5	688	hgsc.bcm.edu	37	chr13	73650024	73650024	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgaagaggcaccagaactgAgcactgcccgtgtgacccgt	12	12	0	5			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:73650024A>G	ENST00000377687.4	+	4	1910	c.1374A>G	c.(1372-1374)tgA>tgG	p.*458W	KLF5_ENST00000539231.1_Nonstop_Mutation_p.*367W	NM_001730.3	NP_001721.2	Q13887	KLF5_HUMAN	Kruppel-like factor 5 (intestinal)	0					angiogenesis (GO:0001525)|cellular response to organic cyclic compound (GO:0071407)|cellular response to peptide (GO:1901653)|intestinal epithelial cell development (GO:0060576)|microvillus assembly (GO:0030033)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microvillus assembly (GO:0032534)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		ACCAGAACTGAGCACTGCCCG	0.547																																					p.X458W		Atlas-SNP	.											.	KLF5	59	.	0			c.A1374G						.						38	34	36					13																	73650024		2203	4299	6502	SO:0001578	stop_lost	688	exon4			GAACTGAGCACTG	D14520	CCDS9448.1, CCDS66562.1	13q21.3	2013-01-08			ENSG00000102554	ENSG00000102554		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6349	protein-coding gene	gene with protein product		602903		BTEB2		8479902, 9973612	Standard	NM_001730		Approved	IKLF, CKLF	uc001vje.3	Q13887	OTTHUMG00000017074	ENST00000377687.4:c.1374A>G	chr13.hg19:g.73650024A>G	ENSP00000366915:p.*458Trpext*5	70.0	0.0		91.0	4.0	NM_001730	L0R3U5|L0R4T9|Q9UHP8	Missense_Mutation	SNP	ENST00000377687.4	hg19	CCDS9448.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.533803	0.45073	.	.	ENSG00000102554	ENST00000539231;ENST00000377687;ENST00000545883	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7963	0.40737	0.8767:0.0:0.1233:0.0	.	.	.	.	W	367;458;438	.	.	X	+	3	0	KLF5	72548025	1.000000	0.71417	0.997000	0.53966	0.855000	0.48748	2.990000	0.49401	2.057000	0.61298	0.533000	0.62120	TGA	.	.		0.547	KLF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045263.1			G	73650024	A	G	73650024	4	3	103	1	0	0	0	0	0	0	0	0	8358	317	11	2	1388	2	KLF5	13	73650024	Nonstop_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	13931	73650024	41519854	800	15423										
LMO7	4008	hgsc.bcm.edu	37	chr13	76381924	76381924	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcgagatataattttacagtGtagagaaggtgaacttgtac	11	4	0	3	rs369620389		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:76381924G>A	ENST00000321797.8	+	8	1527	c.806G>A	c.(805-807)tGt>tAt	p.C269Y	LMO7_ENST00000357063.3_Missense_Mutation_p.C554Y|LMO7_ENST00000377534.3_Missense_Mutation_p.C554Y|LMO7_ENST00000341547.4_Intron|LMO7_ENST00000526202.1_Intron|LMO7_ENST00000465261.2_Missense_Mutation_p.C269Y|RP11-29G8.3_ENST00000563635.1_RNA			Q8WWI1	LMO7_HUMAN	LIM domain 7	554					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		ATTTTACAGTGTAGAGAAGGT	0.433																																					p.C269Y		Atlas-SNP	.											.	LMO7	334	.	0			c.G806A						.						91	90	90					13																	76381924		1568	3582	5150	SO:0001583	missense	4008	exon7			TACAGTGTAGAGA	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"F-box only protein 20"	604362	"LIM domain only 7"	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.806G>A	chr13.hg19:g.76381924G>A	ENSP00000317802:p.Cys269Tyr	54.0	0.0		91.0	5.0	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.	.	.	.	.	.	.	.	.	.	G	5.512	0.279477	0.10458	.	.	ENSG00000136153	ENST00000357063;ENST00000377534;ENST00000321797;ENST00000465261	T;T;T;T	0.53640	0.61;0.61;0.61;0.61	5.53	4.45	0.53987	.	0.403718	0.26692	N	0.022982	T	0.31167	0.0788	L	0.47716	1.5	0.09310	N	0.99999	P;P	0.41265	0.744;0.744	B;B	0.30943	0.122;0.122	T	0.27226	-1.0080	10	0.30854	T	0.27	-15.7611	6.5405	0.22377	0.1286:0.3545:0.5169:0.0	.	554;269	Q8WWI1;E9PLH4	LMO7_HUMAN;.	Y	554;554;269;269	ENSP00000349571:C554Y;ENSP00000366757:C554Y;ENSP00000317802:C269Y;ENSP00000433352:C269Y	ENSP00000317802:C269Y	C	+	2	0	LMO7	75279925	0.070000	0.21116	0.992000	0.48379	0.984000	0.73092	0.622000	0.24433	2.756000	0.94617	0.655000	0.94253	TGT	.	.		0.433	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		A	76381924	G	A	76381924	3	1	103	1	0	0	0	0	1	0	0	0	8864	1377	48	3	1703	3	LMO7	13	76381924	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	2731900	76381924	38787954	801	15424										
SLITRK6	84189	hgsc.bcm.edu	37	chr13	86369434	86369434	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taggttcataaacgatccttCttcaagaacttcaatacgat	5	9	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:86369434C>T	ENST00000400286.2	-	2	1808	c.1210G>A	c.(1210-1212)Gaa>Aaa	p.E404K		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	404					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		AACGATCCTTCTTCAAGAACT	0.353																																					p.E404K		Atlas-SNP	.											.	SLITRK6	150	.	0			c.G1210A						.						74	69	71					13																	86369434		1846	4091	5937	SO:0001583	missense	84189	exon2			ATCCTTCTTCAAG	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.1210G>A	chr13.hg19:g.86369434C>T	ENSP00000383143:p.Glu404Lys	40.0	0.0		107.0	15.0	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	hg19	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.820070	0.50633	.	.	ENSG00000184564	ENST00000400286	T	0.02421	4.3	5.76	5.76	0.90799	.	0.151890	0.43747	U	0.000536	T	0.07234	0.0183	L	0.31371	0.925	0.52501	D	0.999956	D	0.53312	0.959	P	0.57846	0.828	T	0.54925	-0.8220	10	0.23302	T	0.38	-12.071	18.5388	0.91020	0.0:1.0:0.0:0.0	.	404	Q9H5Y7	SLIK6_HUMAN	K	404	ENSP00000383143:E404K	ENSP00000383143:E404K	E	-	1	0	SLITRK6	85267435	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	5.956000	0.70315	2.724000	0.93272	0.585000	0.79938	GAA	.	.		0.353	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		T	86369434	C	T	86369434	3	4	103	1	0	0	0	0	1	0	0	0	14762	922	32	3	1319	3	SLITRK6	13	86369434	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	9987510	86369434	28800444	802	15425										
GPR180	160897	hgsc.bcm.edu	37	chr13	95278272	95278272	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcttgcatgcatttctgtcaTttttagcgactaccaaagag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:95278272delT	ENST00000376958.4	+	8	1164	c.1139delT	c.(1138-1140)attfs	p.I380fs		NM_180989.5	NP_851320.1	Q86V85	GP180_HUMAN	G protein-coupled receptor 180	380					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	10	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					ATTTCTGTCATTTTTAGCGAC	0.318																																					p.I380fs		Atlas-INDEL	.											.	GPR180	24	.	0			c.1138delA						.						145	126	133					13																	95278272		2203	4300	6503	SO:0001589	frameshift_variant	160897	exon8			.	AF339823	CCDS9472.1	13q32.1	2006-04-05			ENSG00000152749	ENSG00000152749			28899	protein-coding gene	gene with protein product	"intimal thickness related receptor"	607787				12538434	Standard	NM_180989		Approved	ITR	uc001vly.3	Q86V85	OTTHUMG00000017207	ENST00000376958.4:c.1139delT	chr13.hg19:g.95278272delT	ENSP00000366157:p.Ile380fs	78.0	0.0		160.0	12.0	NM_180989	A8K1D5	Frame_Shift_Del	DEL	ENST00000376958.4	hg19	CCDS9472.1																																																																																			.	.		0.318	GPR180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045465.3	NM_180989		-	95278272	T	-	95278272	7	5	103	1	0	1	0	1	0	0	0	0	6684	1493	52	0	1169	0	GPR180	13	95278272	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	8908838	95278272	19891606	803	15426										
TMTC4	84899	hgsc.bcm.edu	37	chr13	101278382	101278382	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggttgcctttatcagccaggTttttgccaatgttgtagtga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:101278382delT	ENST00000376234.3	-	12	1661	c.1472delA	c.(1471-1473)aacfs	p.N491fs	TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000328767.5_Frame_Shift_Del_p.N380fs|TMTC4_ENST00000342624.5_Frame_Shift_Del_p.N510fs	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	491						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ATCAGCCAGGTTTTTGCCAAT	0.463																																					p.N510fs		Atlas-INDEL	.											.	TMTC4	103	.	0			c.1530delC						.						123	116	118					13																	101278382		2203	4300	6503	SO:0001589	frameshift_variant	84899	exon13			.		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"Tetratricopeptide (TTC) repeat domain containing"	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1472delA	chr13.hg19:g.101278382delT	ENSP00000365408:p.Asn491fs	264.0	0.0		320.0	23.0	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Frame_Shift_Del	DEL	ENST00000376234.3	hg19	CCDS41904.1																																																																																			.	.		0.463	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		-	101278382	T	-	101278382	7	5	103	1	0	1	0	1	0	0	0	0	16278	1725	60	0	781	0	TMTC4	13	101278382	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	6000110	101278382	13891496	804	15427										
KDELC1	79070	hgsc.bcm.edu	37	chr13	103449216	103449216	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atttaatttccaccttcagaTttttgtagcttgcatacatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:103449216delT	ENST00000376004.4	-	2	662	c.326delA	c.(325-327)aatfs	p.N109fs	BIVM_ENST00000419638.1_5'Flank|KDELC1_ENST00000460338.1_5'UTR|BIVM_ENST00000257336.1_5'Flank|BIVM_ENST00000448849.2_5'Flank	NM_024089.2	NP_076994.2	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1	109				N -> S (in Ref. 2; BAD96287). {ECO:0000305}.		endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CACCTTCAGATTTTTGTAGCT	0.363																																					p.N109fs		Atlas-INDEL	.											.	KDELC1	66	.	0			c.327delT						.						131	127	128					13																	103449216		2203	4300	6503	SO:0001589	frameshift_variant	79070	exon2			.	BC001297	CCDS9504.1	13q33	2010-11-18			ENSG00000134901	ENSG00000134901			19350	protein-coding gene	gene with protein product		611613					Standard	NM_024089		Approved	MGC5302, EP58	uc001vpq.4	Q6UW63	OTTHUMG00000017307	ENST00000376004.4:c.326delA	chr13.hg19:g.103449216delT	ENSP00000365172:p.Asn109fs	117.0	0.0		147.0	11.0	NM_024089	Q53HL3|Q9BVD2	Frame_Shift_Del	DEL	ENST00000376004.4	hg19	CCDS9504.1																																																																																			.	.		0.363	KDELC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045699.1			-	103449216	T	-	103449216	7	5	103	1	0	1	0	1	0	0	0	0	8126	1493	52	0	1218	0	KDELC1	13	103449216	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2170834	103449216	11720662	805	15428										
BIVM	54841	hgsc.bcm.edu	37	chr13	103486900	103486900	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catcctgccattcactgtaaAaagtatgttaacttcccttt	4	11	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:103486900A>G	ENST00000257336.1	+	9	1798	c.1119A>G	c.(1117-1119)aaA>aaG	p.K373K	BIVM_ENST00000419638.1_3'UTR|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.K345E|BIVM_ENST00000448849.2_Silent_p.K144K	NM_017693.3	NP_060163.2	Q86UB2	BIVM_HUMAN	basic, immunoglobulin-like variable motif containing	373						cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|skin(2)|urinary_tract(1)	25	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TTCACTGTAAAAAGTATGTTA	0.308																																					p.K373K		Atlas-SNP	.											.	.	.	.	0			c.A1119G						.						120	117	118					13																	103486900		2203	4299	6502	SO:0001819	synonymous_variant	0	exon7			CTGTAAAAAGTAT	AF411385	CCDS9505.1, CCDS53879.1	13q33.1	2008-05-14			ENSG00000134897	ENSG00000134897			16034	protein-coding gene	gene with protein product						12036287	Standard	NM_017693		Approved	FLJ20159		Q86UB2	OTTHUMG00000017309	ENST00000257336.1:c.1119A>G	chr13.hg19:g.103486900A>G		59.0	0.0		99.0	4.0	NM_001204425	Q2M1J2|Q9NXM4	Silent	SNP	ENST00000257336.1	hg19	CCDS9505.1																																																																																			.	.		0.308	BIVM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045704.2			G	103486900	A	G	103486900	2	3	103	1	0	0	0	0	0	0	0	1	1441	11	1	2		2	BIVM	13	103486900	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	37684	103486900	11682978	806	15429										
LAMP1	3916	hgsc.bcm.edu	37	chr13	113960838	113960838	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagcagcaatgtttatggtgAaaaatggcaacgggaccgcg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:113960838delA	ENST00000332556.4	+	2	294	c.100delA	c.(100-102)aaafs	p.K34fs	LAMP1_ENST00000397181.3_Frame_Shift_Del_p.K34fs	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	34	First lumenal domain.			VKNGNGTA -> MARGGRVR (in Ref. 7; AAA59524). {ECO:0000305}.	autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			GTTTATGGTGAAAAATGGCAA	0.498																																					p.V33fs		Atlas-INDEL	.											.	LAMP1	41	.	0			c.99delG						.						167	163	165					13																	113960838		2025	4189	6214	SO:0001589	frameshift_variant	3916	exon2			.	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.100delA	chr13.hg19:g.113960838delA	ENSP00000333298:p.Lys34fs	152.0	0.0		162.0	10.0	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Frame_Shift_Del	DEL	ENST00000332556.4	hg19	CCDS41909.1																																																																																			.	.		0.498	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			-	113960838	A	-	113960838	7	5	103	1	0	1	0	1	0	0	0	0	8626	247	9	0	106	0	LAMP1	13	113960838	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	10473938	113960838	1209040	807	15430										
OR11G2	390439	hgsc.bcm.edu	37	chr14	20665742	20665742	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctcatgggcaatggttccaTcatctgtgctgtgcactggg	12	11	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:20665742T>C	ENST00000357366.3	+	1	248	c.248T>C	c.(247-249)aTc>aCc	p.I83T		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	83						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		AATGGTTCCATCATCTGTGCT	0.542																																					p.I83T		Atlas-SNP	.											.	OR11G2	73	.	0			c.T248C						.						122	99	107					14																	20665742		2203	4300	6503	SO:0001583	missense	390439	exon1			GTTCCATCATCTG		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"GPCR / Class A : Olfactory receptors"	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.248T>C	chr14.hg19:g.20665742T>C	ENSP00000349930:p.Ile83Thr	110.0	0.0		105.0	5.0	NM_001005503	Q6IF09|Q96R33	Missense_Mutation	SNP	ENST00000357366.3	hg19	CCDS32032.1	.	.	.	.	.	.	.	.	.	.	t	17.07	3.294964	0.60086	.	.	ENSG00000196832	ENST00000357366	T	0.00531	6.76	4.53	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	U	0.000461	T	0.02267	0.0070	M	0.90145	3.09	0.27370	N	0.955714	D	0.89917	1.0	D	0.80764	0.994	T	0.05099	-1.0906	10	0.87932	D	0	.	12.9846	0.58583	0.0:0.0:0.0:1.0	.	83	Q8NGC1	O11G2_HUMAN	T	83	ENSP00000349930:I83T	ENSP00000349930:I83T	I	+	2	0	OR11G2	19735582	0.819000	0.29175	0.999000	0.59377	0.977000	0.68977	3.110000	0.50352	1.900000	0.55004	0.454000	0.30748	ATC	.	.		0.542	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1			C	20665742	T	C	20665742	3	2	103	1	0	0	0	0	1	0	0	0	10934	1435	50	2	250	2	OR11G2	14	20665742	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10		20665742	86683798	808	15431										
OR6S1	341799	hgsc.bcm.edu	37	chr14	21109487	21109487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatggccaggtagcgatccgCagacatgacagccaacagta	12	11	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:21109487C>T	ENST00000320704.3	-	1	363	c.364G>A	c.(364-366)Gcg>Acg	p.A122T		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		TAGCGATCCGCAGACATGACA	0.542																																					p.A122T		Atlas-SNP	.											.	OR6S1	49	.	0			c.G364A						.						93	81	85					14																	21109487		2203	4300	6503	SO:0001583	missense	341799	exon1			GATCCGCAGACAT	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"GPCR / Class A : Olfactory receptors"	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.364G>A	chr14.hg19:g.21109487C>T	ENSP00000313110:p.Ala122Thr	114.0	0.0		117.0	23.0	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	hg19	CCDS32038.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.539756	0.45176	.	.	ENSG00000181803	ENST00000320704	T	0.01335	5.0	5.46	3.52	0.40303	GPCR, rhodopsin-like superfamily (1);	0.313169	0.22962	N	0.053534	T	0.01092	0.0036	N	0.14661	0.345	0.22305	N	0.999211	B	0.06786	0.001	B	0.04013	0.001	T	0.46898	-0.9158	10	0.87932	D	0	-5.6108	6.3811	0.21536	0.2803:0.6321:0.0:0.0876	.	122	Q8NH40	OR6S1_HUMAN	T	122	ENSP00000313110:A122T	ENSP00000313110:A122T	A	-	1	0	OR6S1	20179327	0.000000	0.05858	1.000000	0.80357	0.972000	0.66771	0.882000	0.28186	1.439000	0.47511	-0.140000	0.14226	GCG	.	.		0.542	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1			T	21109487	C	T	21109487	3	4	103	1	0	0	0	0	1	0	0	0	11218	710	25	3	635	3	OR6S1	14	21109487	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	443745	21109487	86240053	809	15432										
TPPP2	122664	hgsc.bcm.edu	37	chr14	21498757	21498757	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaccatggcatcagaggcagAaaaaacattccatcggtttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:21498757delA	ENST00000321760.6	+	2	165	c.17delA	c.(16-18)gaafs	p.E6fs	AL161668.5_ENST00000533984.1_lincRNA|RP11-998D10.1_ENST00000531638.1_5'Flank|NDRG2_ENST00000403829.3_Intron|TPPP2_ENST00000460647.2_Frame_Shift_Del_p.E6fs|TPPP2_ENST00000530140.2_Frame_Shift_Del_p.E6fs	NM_173846.4	NP_776245.2	P59282	TPPP2_HUMAN	tubulin polymerization-promoting protein family member 2	6						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		TCAGAGGCAGAAAAAACATTC	0.522																																					p.E6fs		Atlas-INDEL	.											.,1	TPPP2	22	.	0			c.16delG						.						78	55	63					14																	21498757		2203	4300	6503	SO:0001589	frameshift_variant	122664	exon2			.	AY072034	CCDS9566.1	14q11.2	2014-01-21	2007-05-02	2007-05-02	ENSG00000179636	ENSG00000179636			19293	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 8"	C14orf8		15590652, 17105200	Standard	NM_173846		Approved	p25beta, p18, CT152	uc001vzh.3	P59282	OTTHUMG00000029642	ENST00000321760.6:c.17delA	chr14.hg19:g.21498757delA	ENSP00000317595:p.Glu6fs	172.0	0.0		181.0	11.0	NM_173846	Q2VYF3	Frame_Shift_Del	DEL	ENST00000321760.6	hg19	CCDS9566.1																																																																																			.	.		0.522	TPPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073914.3	NM_173846		-	21498757	A	-	21498757	7	5	103	1	0	1	0	1	0	0	0	0	16429	246	9	0	19	0	TPPP2	14	21498757	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	389270	21498757	85850783	810	15433										
CHD8	57680	hgsc.bcm.edu	37	chr14	21876929	21876929	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attcccgtagctggtttctgTttttatattcatgtgatagc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:21876929delT	ENST00000557364.1	-	12	2683	c.2420delA	c.(2419-2421)aacfs	p.N807fs	CHD8_ENST00000430710.3_Frame_Shift_Del_p.N528fs|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000399982.2_Frame_Shift_Del_p.N807fs			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	807					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CTGGTTTCTGTTTTTATATTC	0.388																																					p.N807fs		Atlas-INDEL	.											.	CHD8	339	.	0			c.2421delC						.						87	75	79					14																	21876929		1807	4075	5882	SO:0001589	frameshift_variant	57680	exon11			.	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.2420delA	chr14.hg19:g.21876929delT	ENSP00000451601:p.Asn807fs	117.0	0.0		164.0	11.0	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	hg19	CCDS53885.1																																																																																			.	.		0.388	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		-	21876929	T	-	21876929	7	5	103	1	0	1	0	1	0	0	0	0	3333	1725	60	0	5433	0	CHD8	14	21876929	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	378172	21876929	85472611	811	15434										
OR10G2	26534	hgsc.bcm.edu	37	chr14	22102864	22102864	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgagcagaatgagcaggttCcccagctgagtgaggatgta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:22102864delC	ENST00000542433.1	-	1	232	c.135delG	c.(133-135)gggfs	p.G45fs		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	45						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		TGAGCAGGTTCCCCAGCTGAG	0.512																																					p.N46fs		Atlas-INDEL	.											.	OR10G2	35	.	0			c.136delA						.						75	73	74					14																	22102864		2203	4300	6503	SO:0001589	frameshift_variant	26534	exon1			.		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"GPCR / Class A : Olfactory receptors"	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.135delG	chr14.hg19:g.22102864delC	ENSP00000445383:p.Gly45fs	243.0	0.0		231.0	14.0	NM_001005466	B2RPD0	Frame_Shift_Del	DEL	ENST00000542433.1	hg19	CCDS32047.1																																																																																			.	.		0.512	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1			-	22102864	C	-	22102864	7	5	103	1	0	1	0	1	0	0	0	0	10908	842	30	0	800	0	OR10G2	14	22102864	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	225935	22102864	85246676	812	15435										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31575935	31575935	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aattttgtgttcttctcatcTtcagaaagacctttgttgct	6	8	4	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:31575935T>C	ENST00000399332.1	-	38	7631	c.7143A>G	c.(7141-7143)gaA>gaG	p.E2381E	HECTD1_ENST00000553700.1_Silent_p.E2381E	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2381	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TCTTCTCATCTTCAGAAAGAC	0.378																																					p.E2381E		Atlas-SNP	.											.	HECTD1	159	.	0			c.A7143G						.						104	95	98					14																	31575935		1842	4097	5939	SO:0001819	synonymous_variant	25831	exon38			CTCATCTTCAGAA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.7143A>G	chr14.hg19:g.31575935T>C		82.0	0.0		95.0	4.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	T	6.222	0.409153	0.11812	.	.	ENSG00000092148	ENST00000554882;ENST00000399323	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	T	0.39064	0.1064	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24261	-1.0165	5	0.07990	T	0.79	-13.609	10.4936	0.44764	0.0:0.0722:0.0:0.9278	.	.	.	.	R	747;5	.	ENSP00000382263:K5R	K	-	2	0	HECTD1	30645686	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.137000	0.50562	2.210000	0.71456	0.533000	0.62120	AAG	.	.		0.378	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			C	31575935	T	C	31575935	2	2	103	1	0	0	0	0	0	0	0	1	7048	1606	56	2		2	HECTD1	14	31575935	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	9473071	31575935	75773605	813	15436										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31617938	31617938	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagatataccttttgctttgTtttttctaacttagatttca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:31617938delT	ENST00000399332.1	-	15	2973	c.2485delA	c.(2485-2487)acafs	p.T829fs	HECTD1_ENST00000553700.1_Frame_Shift_Del_p.T829fs	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	829					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTTTGCTTTGTTTTTTCTAAC	0.333																																					p.T829fs		Atlas-INDEL	.											.	HECTD1	159	.	0			c.2486delC						.						107	94	98					14																	31617938		1803	4068	5871	SO:0001589	frameshift_variant	25831	exon15			.	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.2485delA	chr14.hg19:g.31617938delT	ENSP00000382269:p.Thr829fs	131.0	0.0		142.0	10.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Frame_Shift_Del	DEL	ENST00000399332.1	hg19	CCDS41939.1																																																																																			.	.		0.333	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			-	31617938	T	-	31617938	7	5	103	1	0	1	0	1	0	0	0	0	7048	1725	60	0	5463	0	HECTD1	14	31617938	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	42003	31617938	75731602	814	15437										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31626433	31626433	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggcaaattgtgaccaacatCagaatcacaaacttctttta	5	9	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:31626433C>T	ENST00000399332.1	-	11	2187	c.1699G>A	c.(1699-1701)Gat>Aat	p.D567N	HECTD1_ENST00000553700.1_Missense_Mutation_p.D567N	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	567					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TGACCAACATCAGAATCACAA	0.338																																					p.D567N		Atlas-SNP	.											.	HECTD1	159	.	0			c.G1699A						.						167	159	162					14																	31626433		1852	4095	5947	SO:0001583	missense	25831	exon11			CAACATCAGAATC	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.1699G>A	chr14.hg19:g.31626433C>T	ENSP00000382269:p.Asp567Asn	194.0	0.0		186.0	70.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.580644	0.65992	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957;ENST00000556224	T;T;T;T	0.64991	-0.13;-0.13;1.44;-0.13	6.17	6.17	0.99709	Armadillo-like helical (1);Armadillo-type fold (1);	0.089401	0.85682	N	0.000000	T	0.54271	0.1848	N	0.22421	0.69	0.80722	D	1	B;B	0.27498	0.008;0.18	B;B	0.27796	0.004;0.083	T	0.50320	-0.8842	10	0.54805	T	0.06	-19.9409	20.8794	0.99867	0.0:1.0:0.0:0.0	.	567;567	D3DS86;Q9ULT8	.;HECD1_HUMAN	N	567;567;567;41;567	ENSP00000450697:D567N;ENSP00000382269:D567N;ENSP00000451860:D41N;ENSP00000452015:D567N	ENSP00000261312:D567N	D	-	1	0	HECTD1	30696184	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.070000	0.71220	2.941000	0.99782	0.655000	0.94253	GAT	.	.		0.338	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			T	31626433	C	T	31626433	3	4	103	1	0	0	0	0	1	0	0	0	7048	826	29	3	6265	3	HECTD1	14	31626433	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	8495	31626433	75723107	815	15438										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33290855	33290855	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtatgcctcaaatattactgCcccctctagtccacacattt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:33290855delC	ENST00000280979.4	+	13	4006	c.3836delC	c.(3835-3837)gccfs	p.A1279fs	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1279					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		AATATTACTGCCCCCTCTAGT	0.463																																					p.A1279fs	Melanoma(49;821 1200 7288 13647 42351)	Atlas-INDEL	.											.	AKAP6	308	.	0			c.3835delG						.						83	69	74					14																	33290855		2203	4300	6503	SO:0001589	frameshift_variant	9472	exon13			.	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.3836delC	chr14.hg19:g.33290855delC	ENSP00000280979:p.Ala1279fs	121.0	0.0		156.0	11.0	NM_004274	A7E242|A7E2D4|O15028	Frame_Shift_Del	DEL	ENST00000280979.4	hg19	CCDS9644.1																																																																																			.	.		0.463	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		-	33290855	C	-	33290855	7	5	103	1	0	1	0	1	0	0	0	0	455	739	26	0	3882	0	AKAP6	14	33290855	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1664422	33290855	74058685	816	15439										
NPAS3	64067	hgsc.bcm.edu	37	chr14	33684760	33684760	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagggatacaaatgtggaaaTctgaactctgcatgagaaag	11	5	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:33684760T>C	ENST00000356141.4	+	3	385				NPAS3_ENST00000551492.1_Intron|NPAS3_ENST00000346562.2_Intron|NPAS3_ENST00000548645.1_Intron|NPAS3_ENST00000357798.5_Missense_Mutation_p.S105P|NPAS3_ENST00000551008.1_Intron|NPAS3_ENST00000547068.1_Intron|NPAS3_ENST00000341321.4_Intron			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3						locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		AATGTGGAAATCTGAACTCTG	0.333																																					p.S105P		Atlas-SNP	.											.	NPAS3	266	.	0			c.T313C						.						92	100	97					14																	33684760		2165	4280	6445	SO:0001627	intron_variant	64067	exon3			TGGAAATCTGAAC	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.385+128T>C	chr14.hg19:g.33684760T>C		83.0	0.0		97.0	4.0	NM_173159	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	T	16.22	3.062697	0.55432	.	.	ENSG00000151322	ENST00000357798	T	0.07021	3.23	5.95	5.95	0.96441	.	.	.	.	.	T	0.23532	0.0569	.	.	.	0.80722	D	1	D	0.64830	0.994	P	0.59889	0.865	T	0.00286	-1.1847	8	0.41790	T	0.15	.	14.978	0.71289	0.0:0.0:0.0:1.0	.	105	Q8IXF0-3	.	P	105	ENSP00000350446:S105P	ENSP00000350446:S105P	S	+	1	0	NPAS3	32754511	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.771000	0.68881	2.272000	0.75746	0.460000	0.39030	TCT	.	.		0.333	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			C	33684760	T	C	33684760	1	2	103	0	1	0	0	0	0	0	0	0	10573	1435	50	2		2	NPAS3	14	33684760	Intron	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	393905	33684760	73664780	817	15440										
PPP2R3C	55012	hgsc.bcm.edu	37	chr14	35554856	35554856	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcaacaagagcctctctgttCtcgtaagtccagaagccatt	8	12	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:35554856C>T	ENST00000261475.5	-	13	1655	c.1302G>A	c.(1300-1302)gaG>gaA	p.E434E		NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	434					activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		CCTCTCTGTTCTCGTAAGTCC	0.383																																					p.E434E		Atlas-SNP	.											.	PPP2R3C	44	.	0			c.G1302A						.						137	128	131					14																	35554856		2203	4300	6503	SO:0001819	synonymous_variant	55012	exon13			TCTGTTCTCGTAA	AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	17485	protein-coding gene	gene with protein product		615902	"chromosome 14 open reading frame 10", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.1302G>A	chr14.hg19:g.35554856C>T		110.0	0.0		86.0	4.0	NM_017917	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Silent	SNP	ENST00000261475.5	hg19	CCDS9654.1																																																																																			.	.		0.383	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917		T	35554856	C	T	35554856	2	4	103	1	0	0	0	0	0	0	0	1	12402	912	32	3		3	PPP2R3C	14	35554856	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	1870096	35554856	71794684	818	15441										
FBXO33	254170	hgsc.bcm.edu	37	chr14	39868748	39868748	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttcactgaagctttgcatcTctctgtaaaaatgacgattt	6	9	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:39868748T>C	ENST00000298097.7	-	4	1977	c.1640A>G	c.(1639-1641)gAg>gGg	p.E547G		NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	547					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		GCTTTGCATCTCTCTGTAAAA	0.403																																					p.E547G		Atlas-SNP	.											.	FBXO33	21	.	0			c.A1640G						.						80	70	73					14																	39868748		2203	4300	6503	SO:0001583	missense	254170	exon4			TGCATCTCTCTGT	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"F-boxes /  "other""	19833	protein-coding gene	gene with protein product		609103	"F-box only protein 33"				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.1640A>G	chr14.hg19:g.39868748T>C	ENSP00000298097:p.Glu547Gly	179.0	0.0		125.0	5.0	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Missense_Mutation	SNP	ENST00000298097.7	hg19	CCDS9677.1	.	.	.	.	.	.	.	.	.	.	T	16.84	3.234378	0.58886	.	.	ENSG00000165355	ENST00000298097	T	0.51071	0.72	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.54967	0.1891	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.53229	-0.8468	9	.	.	.	-16.3324	16.2271	0.82306	0.0:0.0:0.0:1.0	.	547	Q7Z6M2	FBX33_HUMAN	G	547	ENSP00000298097:E547G	.	E	-	2	0	FBXO33	38938499	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.422000	0.80217	2.234000	0.73211	0.460000	0.39030	GAG	.	.		0.403	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2			C	39868748	T	C	39868748	3	2	103	1	0	0	0	0	1	0	0	0	5751	1551	54	2	31	2	FBXO33	14	39868748	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4313892	39868748	67480792	819	15442										
SDCCAG1	9147	hgsc.bcm.edu	37	chr14	50295460	50295460	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttttggtggttcagtttcaTttttctcaacattgacgtca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:50295460delT	ENST00000298310.5	-	14	1747	c.1298delA	c.(1297-1299)aatfs	p.N433fs	NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000546046.1_Frame_Shift_Del_p.N433fs|NEMF_ENST00000545773.1_Frame_Shift_Del_p.N391fs			O60524	NEMF_HUMAN	nuclear export mediator factor	433					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						TTCAGTTTCATTTTTCTCAAC	0.343																																					p.N433fs		Atlas-INDEL	.											.	NEMF	79	.	0			c.1299delT						.						79	76	77					14																	50295460		2203	4300	6503	SO:0001589	frameshift_variant	9147	exon14			.	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.1298delA	chr14.hg19:g.50295460delT	ENSP00000298310:p.Asn433fs	135.0	0.0		148.0	10.0	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Frame_Shift_Del	DEL	ENST00000298310.5	hg19	CCDS9694.1																																																																																			.	.		0.343	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		-	50295460	T	-	50295460	7	5	103	1	0	1	0	1	0	0	0	0	13972	1493	52	0	2012	0	SDCCAG1	14	50295460	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	10426712	50295460	57054080	820	15443										
CDKL1	8814	hgsc.bcm.edu	37	chr14	50805678	50805678	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aactcaccatatcttcagggTctggaattttcactccactg	6	12	5	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:50805678T>C	ENST00000216378.2	-	7	1372	c.728A>G	c.(727-729)gAc>gGc	p.D243G	CDKL1_ENST00000356146.1_5'UTR|CDKL1_ENST00000395834.1_Missense_Mutation_p.D243G	NM_001282236.1	NP_001269165.1	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1 (CDC2-related kinase)	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				heart development (GO:0007507)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|stomach(1)	12	all_epithelial(31;0.000746)|Breast(41;0.0102)					ATCTTCAGGGTCTGGAATTTT	0.473																																					p.D243G		Atlas-SNP	.											.	CDKL1	50	.	0			c.A728G						.						207	204	205					14																	50805678		2203	4300	6503	SO:0001583	missense	8814	exon6			TCAGGGTCTGGAA	AF390028	CCDS9699.1, CCDS73637.1	14q21.3	2011-11-04			ENSG00000100490	ENSG00000100490		"Cyclin-dependent kinases"	1781	protein-coding gene	gene with protein product		603441				1639063, 7595554	Standard	XM_005268157		Approved	KKIALRE	uc010anu.2	Q00532	OTTHUMG00000140290	ENST00000216378.2:c.728A>G	chr14.hg19:g.50805678T>C	ENSP00000216378:p.Asp243Gly	96.0	0.0		117.0	7.0	NM_004196	Q2M3A4|Q6QUA0|Q8WXQ5	Missense_Mutation	SNP	ENST00000216378.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.37|18.37	3.608466|3.608466	0.66558|0.66558	.|.	.|.	ENSG00000100490|ENSG00000100490	ENST00000395834;ENST00000216378|ENST00000525911	T;T|.	0.42131|.	0.98;0.98|.	5.23|5.23	5.23|5.23	0.72850|0.72850	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	.|.	.|.	.|.	.|.	T|T	0.52821|0.52821	0.1758|0.1758	N|N	0.25031|0.25031	0.7|0.7	0.80722|0.80722	D|D	1|1	D;B|.	0.63880|.	0.993;0.009|.	P;B|.	0.60789|.	0.879;0.102|.	T|T	0.49615|0.49615	-0.8921|-0.8921	9|5	0.52906|.	T|.	0.07|.	.|.	15.8314|15.8314	0.78757|0.78757	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	914;242|.	Q00532-2;Q00532|.	.;CDKL1_HUMAN|.	G|A	243|24	ENSP00000379176:D243G;ENSP00000216378:D243G|.	ENSP00000216378:D243G|.	D|T	-|-	2|1	0|0	CDKL1|CDKL1	49875428|49875428	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	7.858000|7.858000	0.86971|0.86971	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	GAC|ACC	.	.		0.473	CDKL1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382103.1			C	50805678	T	C	50805678	3	2	103	1	0	0	0	0	1	0	0	0	3155	1667	58	2	364	2	CDKL1	14	50805678	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	510218	50805678	56543862	821	15444										
MAP4K5	11183	hgsc.bcm.edu	37	chr14	50889884	50889884	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcttgtttcatctgaaatcTcctgggtaacctaggaaaga	8	9	4	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:50889884T>C	ENST00000013125.4	-	31	2726	c.2408A>G	c.(2407-2409)gAg>gGg	p.E803G		NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	803	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					ATCTGAAATCTCCTGGGTAAC	0.308																																					p.E803G		Atlas-SNP	.											.	MAP4K5	48	.	0			c.A2408G						.						50	49	49					14																	50889884		1807	4065	5872	SO:0001583	missense	11183	exon31			GAAATCTCCTGGG	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6867	protein-coding gene	gene with protein product	"germinal center kinase-related"	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.2408A>G	chr14.hg19:g.50889884T>C	ENSP00000013125:p.Glu803Gly	74.0	0.0		113.0	5.0	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	hg19		.	.	.	.	.	.	.	.	.	.	T	26.2	4.718108	0.89205	.	.	ENSG00000012983	ENST00000013125	T	0.05855	3.38	5.64	5.64	0.86602	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.30854	0.0778	M	0.86740	2.835	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.12400	-1.0549	10	0.87932	D	0	.	15.8718	0.79127	0.0:0.0:0.0:1.0	.	803;803	B2R928;Q9Y4K4	.;M4K5_HUMAN	G	803	ENSP00000013125:E803G	ENSP00000013125:E803G	E	-	2	0	MAP4K5	49959634	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.624000	0.83124	2.160000	0.67779	0.528000	0.53228	GAG	.	.		0.308	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575		C	50889884	T	C	50889884	3	2	103	1	0	0	0	0	1	0	0	0	9272	1551	54	2	140	2	MAP4K5	14	50889884	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	84206	50889884	56459656	822	15445										
MAP4K5	11183	hgsc.bcm.edu	37	chr14	50933308	50933308	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctttaactcaccattttgTtttgtcctttagttttggag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:50933308delT	ENST00000013125.4	-	11	1048	c.730delA	c.(730-732)acafs	p.T244fs	Y_RNA_ENST00000364703.1_RNA|MAP4K5_ENST00000557578.1_5'Flank	NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	244	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					CACCATTTTGTTTTGTCCTTT	0.279																																					p.T244fs		Atlas-INDEL	.											.	MAP4K5	48	.	0			c.731delC						.						45	39	41					14																	50933308		1604	3619	5223	SO:0001589	frameshift_variant	11183	exon11			.	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6867	protein-coding gene	gene with protein product	"germinal center kinase-related"	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.730delA	chr14.hg19:g.50933308delT	ENSP00000013125:p.Thr244fs	112.0	0.0		159.0	10.0	NM_006575	Q8IYF6	Frame_Shift_Del	DEL	ENST00000013125.4	hg19																																																																																				.	.		0.279	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575		-	50933308	T	-	50933308	7	5	103	1	0	1	0	1	0	0	0	0	9272	1725	60	0	1898	0	MAP4K5	14	50933308	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	43424	50933308	56416232	823	15446										
NID2	22795	hgsc.bcm.edu	37	chr14	52505655	52505655	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catgtttggttgattgcaccAaaagtcagagagtagtctct					rs150250347		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:52505655delA	ENST00000216286.5	-	9	2066	c.2067delT	c.(2065-2067)tttfs	p.F689fs	NID2_ENST00000541773.1_Frame_Shift_Del_p.F636fs	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	689	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					TGATTGCACCAAAAGTCAGAG	0.473																																					p.G690fs		Atlas-INDEL	.											.	NID2	201	.	0			c.2068delG						.						113	107	109					14																	52505655		2203	4300	6503	SO:0001589	frameshift_variant	22795	exon9			.	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.2067delT	chr14.hg19:g.52505655delA	ENSP00000216286:p.Phe689fs	123.0	0.0		155.0	11.0	NM_007361	A8K6I7|B4DU19|O43710	Frame_Shift_Del	DEL	ENST00000216286.5	hg19	CCDS9706.1																																																																																			.	.		0.473	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			-	52505655	A	-	52505655	7	5	103	1	0	1	0	1	0	0	0	0	10424	127	5	0	2116	0	NID2	14	52505655	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1572347	52505655	54843885	824	15447										
ERO1L	30001	hgsc.bcm.edu	37	chr14	53119839	53119839	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttgttttcctcatcctgaaTtttatttccagtaaagagtt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:53119839delT	ENST00000395686.3	-	12	1226	c.1003delA	c.(1003-1005)attfs	p.I335fs		NM_014584.1	NP_055399.1	Q96HE7	ERO1A_HUMAN	ERO1-like (S. cerevisiae)	335					4-hydroxyproline metabolic process (GO:0019471)|brown fat cell differentiation (GO:0050873)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum unfolded protein response (GO:0030968)|extracellular matrix organization (GO:0030198)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to temperature stimulus (GO:0009266)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)		ERO1L/FERMT2(2)	breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12	Breast(41;0.226)					TCATCCTGAATTTTATTTCCA	0.289																																					p.I335fs		Atlas-INDEL	.											.	ERO1L	35	.	0			c.1004delT						.						46	50	49					14																	53119839		2202	4298	6500	SO:0001589	frameshift_variant	30001	exon12			.	AF081886	CCDS9709.1	14q22.1	2010-10-06	2001-11-28		ENSG00000197930	ENSG00000197930			13280	protein-coding gene	gene with protein product		615435	"ERO1 (S. cerevisiae)-like"			10671517	Standard	NM_014584		Approved	ERO1A, ERO1-alpha	uc001wzv.3	Q96HE7	OTTHUMG00000140301	ENST00000395686.3:c.1003delA	chr14.hg19:g.53119839delT	ENSP00000379042:p.Ile335fs	140.0	0.0		142.0	10.0	NM_014584	A8K9X4|A8MYW1|Q7LD45|Q9P1Q9|Q9UKV6	Frame_Shift_Del	DEL	ENST00000395686.3	hg19	CCDS9709.1																																																																																			.	.		0.289	ERO1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276892.1	NM_014584		-	53119839	T	-	53119839	7	5	103	1	0	1	0	1	0	0	0	0	5241	1493	52	0	423	0	ERO1L	14	53119839	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	614184	53119839	54229701	825	15448										
KTN1	3895	hgsc.bcm.edu	37	chr14	56114751	56114751	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttataatttcagcattcaagAaaaagatgagaagttaaaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:56114751delA	ENST00000395314.3	+	20	2284	c.2216delA	c.(2215-2217)gaafs	p.E739fs	KTN1_ENST00000554507.1_Frame_Shift_Del_p.E34fs|KTN1_ENST00000438792.2_Frame_Shift_Del_p.E739fs|KTN1_ENST00000395311.1_Frame_Shift_Del_p.E739fs|KTN1_ENST00000416613.1_Frame_Shift_Del_p.E739fs|KTN1_ENST00000413890.2_Frame_Shift_Del_p.E739fs|KTN1_ENST00000395308.1_Frame_Shift_Del_p.E739fs|KTN1_ENST00000395309.3_Frame_Shift_Del_p.E739fs	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	739					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AGCATTCAAGAAAAAGATGAG	0.269			T	RET	papillary thryoid																																p.E739fs		Atlas-INDEL	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.2215delG						.						59	62	61					14																	56114751		2203	4298	6501	SO:0001589	frameshift_variant	3895	exon20			.		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.2216delA	chr14.hg19:g.56114751delA	ENSP00000378725:p.Glu739fs	176.0	0.0		160.0	10.0	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Frame_Shift_Del	DEL	ENST00000395314.3	hg19	CCDS41957.1																																																																																			.	.		0.269	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			-	56114751	A	-	56114751	7	5	103	1	0	1	0	1	0	0	0	0	8594	246	9	0	2290	0	KTN1	14	56114751	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2994912	56114751	51234789	826	15449										
ARID4A	5926	hgsc.bcm.edu	37	chr14	58796774	58796774	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagttgttcctgataattggAaaatggatataagtgaaatc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:58796774delA	ENST00000355431.3	+	11	1166	c.793delA	c.(793-795)aaafs	p.K265fs	ARID4A_ENST00000395168.3_Frame_Shift_Del_p.K265fs|ARID4A_ENST00000431317.2_Frame_Shift_Del_p.K265fs|ARID4A_ENST00000348476.3_Frame_Shift_Del_p.K265fs	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	265					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						TGATAATTGGAAAATGGATAT	0.393																																					p.W264X		Atlas-INDEL	.											.	ARID4A	222	.	0			c.792delG						.						98	101	100					14																	58796774		2203	4300	6503	SO:0001589	frameshift_variant	5926	exon11			.	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.793delA	chr14.hg19:g.58796774delA	ENSP00000347602:p.Lys265fs	166.0	0.0		148.0	10.0	NM_002892	Q15991|Q15992|Q15993	Frame_Shift_Del	DEL	ENST00000355431.3	hg19	CCDS9732.1																																																																																			.	.		0.393	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		-	58796774	A	-	58796774	7	5	103	1	0	1	0	1	0	0	0	0	919	247	9	0	831	0	ARID4A	14	58796774	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2682023	58796774	48552766	827	15450										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63174303	63174303	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aatatcctgacatggtatctGggggggtacttggagtggca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:63174303delG	ENST00000322893.7	-	11	3158	c.2890delC	c.(2890-2892)cagfs	p.Q964fs	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	964					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CATGGTATCTGGGGGGGTACT	0.393																																					p.Q964fs		Atlas-INDEL	.											KCNH5,NS,carcinoma,-1,1	KCNH5	320	.	0			c.2891delA						.						110	126	120					14																	63174303		2203	4300	6503	SO:0001589	frameshift_variant	27133	exon11			.	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2890delC	chr14.hg19:g.63174303delG	ENSP00000321427:p.Gln964fs	147.0	0.0		159.0	11.0	NM_139318	C9JP98	Frame_Shift_Del	DEL	ENST00000322893.7	hg19	CCDS9756.1																																																																																			.	.		0.393	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		-	63174303	G	-	63174303	7	5	103	1	0	1	0	1	0	0	0	0	8044	1357	47	0	80	0	KCNH5	14	63174303	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	4377529	63174303	44175237	828	15451										
WDR89	112840	hgsc.bcm.edu	37	chr14	64066253	64066253	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacaatgcatcatcatcaacTttttctgtaccagcacaaat					rs376382796|rs148702795		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:64066253delT	ENST00000394942.2	-	2	496	c.408delA	c.(406-408)aaafs	p.K136fs	WDR89_ENST00000267522.3_Frame_Shift_Del_p.K136fs|CTD-2302E22.2_ENST00000553983.1_lincRNA	NM_001008726.2|NM_001258272.1|NM_080666.3	NP_001008726.1|NP_001245201.1|NP_542397.1	Q96FK6	WDR89_HUMAN	WD repeat domain 89	136										endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.00543)|all cancers(60;0.0181)|BRCA - Breast invasive adenocarcinoma(234;0.101)		CATCATCAACTTTTTCTGTAC	0.338																																					p.V137fs		Atlas-INDEL	.											.	WDR89	22	.	0			c.409delG						.						70	67	68					14																	64066253		2203	4300	6503	SO:0001589	frameshift_variant	112840	exon3			.	AF115513	CCDS9759.1	14q23.2	2013-01-09		2006-07-07	ENSG00000140006	ENSG00000140006		"WD repeat domain containing"	20489	protein-coding gene	gene with protein product				C14orf150			Standard	NM_080666		Approved	MGC9907	uc001xgi.4	Q96FK6	OTTHUMG00000140340	ENST00000394942.2:c.408delA	chr14.hg19:g.64066253delT	ENSP00000378399:p.Lys136fs	153.0	0.0		150.0	10.0	NM_080666		Frame_Shift_Del	DEL	ENST00000394942.2	hg19	CCDS9759.1																																																																																			.	.		0.338	WDR89-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411879.2	NM_080666		-	64066253	T	-	64066253	7	5	103	1	0	1	0	1	0	0	0	0	17351	1606	56	0	759	0	WDR89	14	64066253	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	891950	64066253	43283287	829	15452										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64460661	64460661	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agatgtctttagaagaaaagAgtagagatgtctgtgccaaa	11	4	2	5			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:64460661A>G	ENST00000344113.4	+	22	2967	c.2755A>G	c.(2755-2757)Agt>Ggt	p.S919G	SYNE2_ENST00000554584.1_Missense_Mutation_p.S919G|SYNE2_ENST00000358025.3_Missense_Mutation_p.S919G|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	919					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGAAGAAAAGAGTAGAGATGT	0.348																																					p.S919G		Atlas-SNP	.											.	SYNE2	577	.	0			c.A2755G						.						115	111	113					14																	64460661		1865	4100	5965	SO:0001583	missense	23224	exon22			GAAAAGAGTAGAG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.2755A>G	chr14.hg19:g.64460661A>G	ENSP00000341781:p.Ser919Gly	83.0	0.0		124.0	5.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.477194	0.26511	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.59083	0.66;0.66;0.29	5.1	5.1	0.69264	.	0.108697	0.39985	N	0.001216	T	0.67144	0.2862	L	0.53249	1.67	0.80722	D	1	D;D	0.60160	0.978;0.987	P;P	0.59171	0.717;0.853	T	0.70368	-0.4891	10	0.66056	D	0.02	.	13.1187	0.59314	1.0:0.0:0.0:0.0	.	919;919	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	G	919	ENSP00000350719:S919G;ENSP00000341781:S919G;ENSP00000452570:S919G	ENSP00000261678:S919G	S	+	1	0	SYNE2	63530414	1.000000	0.71417	0.981000	0.43875	0.083000	0.17756	2.730000	0.47335	1.921000	0.55644	0.460000	0.39030	AGT	.	.		0.348	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64460661	A	G	64460661	3	3	103	1	0	0	0	0	1	0	0	0	15461	304	11	2	2837	2	SYNE2	14	64460661	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	394408	64460661	42888879	830	15453										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72196875	72196875	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagcatttacaatagccagaGggagcactttttcacctcca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:72196875delG	ENST00000555818.1	+	18	5129	c.4781delG	c.(4780-4782)aggfs	p.R1594fs	SIPA1L1_ENST00000381232.3_Frame_Shift_Del_p.R1573fs|SIPA1L1_ENST00000537413.1_Frame_Shift_Del_p.R1048fs|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000358550.2_Frame_Shift_Del_p.R1573fs	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1594					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AATAGCCAGAGGGAGCACTTT	0.597																																					p.R1594fs		Atlas-INDEL	.											.	SIPA1L1	219	.	0			c.4780delA						.						106	90	95					14																	72196875		2203	4300	6503	SO:0001589	frameshift_variant	26037	exon18			.	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.4781delG	chr14.hg19:g.72196875delG	ENSP00000450832:p.Arg1594fs	167.0	0.0		185.0	13.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Frame_Shift_Del	DEL	ENST00000555818.1	hg19	CCDS9807.1																																																																																			.	.		0.597	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		-	72196875	G	-	72196875	7	5	103	1	0	1	0	1	0	0	0	0	14344	1000	35	0	4847	0	SIPA1L1	14	72196875	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	7736214	72196875	35152665	831	15454										
HEATR4	399671	hgsc.bcm.edu	37	chr14	73945358	73945358	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggagaagacatgatgggagAaaaaaatgttctctctgaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:73945358delA	ENST00000553558.1	-	18	3355	c.3034delT	c.(3034-3036)tctfs	p.S1012fs	HEATR4_ENST00000560393.1_Frame_Shift_Del_p.S965fs|HEATR4_ENST00000334988.2_Frame_Shift_Del_p.S1012fs|HEATR4_ENST00000566478.1_5'UTR|RP1-240K6.3_ENST00000515412.2_RNA	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	1012										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		ATGATGGGAGAAAAAAATGTT	0.458																																					p.S1012fs		Atlas-INDEL	.											.	HEATR4	126	.	0			c.3035delC						.						91	90	90					14																	73945358		2203	4300	6503	SO:0001589	frameshift_variant	399671	exon17			.	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.3034delT	chr14.hg19:g.73945358delA	ENSP00000450444:p.Ser1012fs	121.0	0.0		129.0	10.0	NM_203309	B7Z7V9|E9KL41	Frame_Shift_Del	DEL	ENST00000553558.1	hg19	CCDS9815.2																																																																																			.	.		0.458	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		-	73945358	A	-	73945358	7	5	103	1	0	1	0	1	0	0	0	0	7039	246	9	0	50	0	HEATR4	14	73945358	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1748483	73945358	33404182	832	15455										
LTBP2	4053	hgsc.bcm.edu	37	chr14	74976066	74976066	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggaaggcacactcatctaggTctgcagacagacagcgctcg	12	12	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:74976066T>C	ENST00000261978.4	-	22	3664	c.3278A>G	c.(3277-3279)gAc>gGc	p.D1093G	LTBP2_ENST00000556690.1_Splice_Site_p.D1093G	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1093	Cys-rich.|EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CTCATCTAGGTCTGCAGACAG	0.667																																					p.D1093G		Atlas-SNP	.											.	LTBP2	158	.	0			c.A3278G						.						57	65	62					14																	74976066		2203	4300	6503	SO:0001630	splice_region_variant	4053	exon22			TCTAGGTCTGCAG		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.3278-1A>G	chr14.hg19:g.74976066T>C		112.0	0.0		109.0	5.0	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	hg19	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.636580	0.87760	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	D;D	0.99060	-5.38;-5.38	5.31	5.31	0.75309	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);	0.000000	0.42294	D	0.000738	D	0.99149	0.9706	H	0.95982	3.75	0.53005	D	0.999968	B	0.29341	0.242	B	0.40410	0.328	D	0.99856	1.1077	10	0.87932	D	0	.	12.8848	0.58038	0.0:0.0:0.0:1.0	.	1093	Q14767	LTBP2_HUMAN	G	1093	ENSP00000261978:D1093G;ENSP00000451477:D1093G	ENSP00000261978:D1093G	D	-	2	0	LTBP2	74045819	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.485000	0.60279	2.234000	0.73211	0.402000	0.26972	GAC	.	.		0.667	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	Missense_Mutation	C	74976066	T	C	74976066	5	2	103	1	0	0	0	0	0	0	1	0	9083	1681	58	2	2247	2	LTBP2	14	74976066	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1030708	74976066	32373474	833	15456										
MLH3	27030	hgsc.bcm.edu	37	chr14	75515828	75515828	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaagggtgcatgagtgagagAgcttctattctctgcctaac	12	8	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:75515828A>G	ENST00000556740.1	-	1	566	c.531T>C	c.(529-531)gcT>gcC	p.A177A	MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000355774.2_Silent_p.A177A|MLH3_ENST00000238662.7_Silent_p.A177A|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000556257.1_Silent_p.A177A			Q9UHC1	MLH3_HUMAN	mutL homolog 3	177					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TGAGTGAGAGAGCTTCTATTC	0.428								Mismatch excision repair (MMR)																													p.A177A		Atlas-SNP	.											.	MLH3	200	.	0			c.T531C						.						75	70	72					14																	75515828		2203	4300	6503	SO:0001819	synonymous_variant	27030	exon2			TGAGAGAGCTTCT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.531T>C	chr14.hg19:g.75515828A>G		74.0	0.0		62.0	5.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Silent	SNP	ENST00000556740.1	hg19	CCDS32123.1																																																																																			.	.		0.428	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		G	75515828	A	G	75515828	2	3	103	1	0	0	0	0	0	0	0	1	9627	291	11	2		2	MLH3	14	75515828	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	539762	75515828	31833712	834	15457										
ACYP1	97	hgsc.bcm.edu	37	chr14	75520310	75520310	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcaattgtccttgcactgtgCcccggtcagtgttctggacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:75520310delC	ENST00000238618.3	-	3	240	c.137delG	c.(136-138)ggcfs	p.G46fs	ACYP1_ENST00000555463.1_Frame_Shift_Del_p.G76fs|ACYP1_ENST00000357971.3_3'UTR|ACYP1_ENST00000555694.1_Frame_Shift_Del_p.G46fs|MLH3_ENST00000380968.2_5'Flank|MLH3_ENST00000355774.2_5'Flank|MLH3_ENST00000238662.7_5'Flank|MLH3_ENST00000556257.1_5'Flank	NM_001107.3	NP_001098.1	P07311	ACYP1_HUMAN	acylphosphatase 1, erythrocyte (common) type	46	Acylphosphatase-like. {ECO:0000255|PROSITE-ProRule:PRU00520}.				phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)	acylphosphatase activity (GO:0003998)			large_intestine(2)	2				BRCA - Breast invasive adenocarcinoma(234;0.00646)		TTGCACTGTGCCCCGGTCAGT	0.488																																					p.G46fs		Atlas-INDEL	.											.	ACYP1	6	.	0			c.138delC						.						202	177	186					14																	75520310		2203	4300	6503	SO:0001589	frameshift_variant	97	exon3			.	X84194	CCDS9838.1, CCDS45137.1	14q24.3	2014-08-08			ENSG00000119640	ENSG00000119640	3.6.1.7		179	protein-coding gene	gene with protein product		600875				7796909, 9730610	Standard	NM_001107		Approved		uc001xrg.3	P07311	OTTHUMG00000171767	ENST00000238618.3:c.137delG	chr14.hg19:g.75520310delC	ENSP00000238618:p.Gly46fs	140.0	0.0		147.0	10.0	NM_001107	A6NDV8|B2R590	Frame_Shift_Del	DEL	ENST00000238618.3	hg19	CCDS9838.1																																																																																			.	.		0.488	ACYP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415013.1			-	75520310	C	-	75520310	7	5	103	1	0	1	0	1	0	0	0	0	228	739	26	0	166	0	ACYP1	14	75520310	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	4482	75520310	31829230	835	15458										
C14orf179	112752	hgsc.bcm.edu	37	chr14	76549846	76549846	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atctgttcactgaggtgtccTcagaggtcctcactgagtgg	12	10	4	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:76549846T>C	ENST00000314067.6	+	9	587	c.553T>C	c.(553-555)Tca>Cca	p.S185P	IFT43_ENST00000238628.6_Missense_Mutation_p.S190P	NM_001102564.1	NP_001096034.1	Q96FT9	IFT43_HUMAN	intraflagellar transport 43	185					cilium morphogenesis (GO:0060271)|intraciliary retrograde transport (GO:0035721)	cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)				endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						TGAGGTGTCCTCAGAGGTCCT	0.582																																					p.S190P		Atlas-SNP	.											.	IFT43	63	.	0			c.T568C						.						81	75	77					14																	76549846		2203	4300	6503	SO:0001583	missense	112752	exon8			GTGTCCTCAGAGG	BC010436	CCDS9847.1, CCDS41973.1, CCDS58330.1	14q24.3	2014-07-03	2014-07-03	2011-06-09				"Intraflagellar transport homologs"	29669	protein-coding gene	gene with protein product		614068	"chromosome 14 open reading frame 179", "intraflagellar transport 43 homolog (Chlamydomonas)"	C14orf179		21378380	Standard	NM_052873		Approved	FLJ32173, MGC16028	uc010asm.1	Q96FT9		ENST00000314067.6:c.553T>C	chr14.hg19:g.76549846T>C	ENSP00000324177:p.Ser185Pro	65.0	0.0		58.0	4.0	NM_052873	B3KPT6|B4DZI9|G3V385|O95418|Q9ULA9	Missense_Mutation	SNP	ENST00000314067.6	hg19	CCDS41973.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.640458	0.87859	.	.	ENSG00000119650	ENST00000314067;ENST00000238628	T;T	0.52295	0.67;0.67	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.73024	0.3534	M	0.86420	2.815	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.78745	-0.2084	10	0.87932	D	0	-9.9166	15.87	0.79108	0.0:0.0:0.0:1.0	.	185;190	Q96FT9;Q96FT9-2	IFT43_HUMAN;.	P	185;190	ENSP00000324177:S185P;ENSP00000238628:S190P	ENSP00000238628:S190P	S	+	1	0	IFT43	75619599	1.000000	0.71417	0.997000	0.53966	0.764000	0.43329	7.247000	0.78257	2.145000	0.66743	0.533000	0.62120	TCA	.	.		0.582	IFT43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052873		C	76549846	T	C	76549846	3	2	103	1	0	0	0	0	1	0	0	0	1764	1551	54	2	686	2	C14orf179	14	76549846	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1029536	76549846	30799694	836	15459										
C14orf148	122945	hgsc.bcm.edu	37	chr14	77872475	77872475	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acttgatattgaggattattCcccctacacatcaatgagaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:77872475delC	ENST00000380835.2	-	5	852	c.686delG	c.(685-687)ggafs	p.G229fs		NM_001113475.2	NP_001106946.1	Q6NXP6	NXRD1_HUMAN	NADP-dependent oxidoreductase domain containing 1	229					proline biosynthetic process (GO:0006561)		pyrroline-5-carboxylate reductase activity (GO:0004735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9						GAGGATTATTCCCCCTACACA	0.453																																					p.G229fs		Atlas-INDEL	.											.	NOXRED1	23	.	0			c.687delA						.						65	55	58					14																	77872475		1568	3582	5150	SO:0001589	frameshift_variant	122945	exon5			.	AK057371	CCDS45142.1	14q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000165555	ENSG00000165555			20487	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 148"	C14orf148			Standard	NM_001113475		Approved	FLJ32809	uc001xtr.3	Q6NXP6	OTTHUMG00000171554	ENST00000380835.2:c.686delG	chr14.hg19:g.77872475delC	ENSP00000370215:p.Gly229fs	169.0	0.0		150.0	10.0	NM_001113475	B3KQ47|O95435	Frame_Shift_Del	DEL	ENST00000380835.2	hg19	CCDS45142.1																																																																																			.	.		0.453	NOXRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414103.1	NM_138791		-	77872475	C	-	77872475	7	5	103	1	0	1	0	1	0	0	0	0	1753	855	30	0	401	0	C14orf148	14	77872475	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1322629	77872475	29477065	837	15460										
SEL1L	6400	hgsc.bcm.edu	37	chr14	81952089	81952089	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcacctacaatgcttgcttcTcctacaggaaaagaaatgaa	6	10	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:81952089T>C	ENST00000336735.4	-	18	1916	c.1800A>G	c.(1798-1800)agA>agG	p.R600R		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	600	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		TGCTTGCTTCTCCTACAGGAA	0.373																																					p.R600R		Atlas-SNP	.											.	SEL1L	67	.	0			c.A1800G						.						106	106	106					14																	81952089		2203	4300	6503	SO:0001630	splice_region_variant	6400	exon18			TGCTTCTCCTACA		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.1799-1A>G	chr14.hg19:g.81952089T>C		121.0	0.0		125.0	5.0	NM_005065	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	hg19	CCDS9876.1																																																																																			.	.		0.373	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065	Silent	C	81952089	T	C	81952089	5	2	103	1	0	0	0	0	0	0	1	0	14025	1565	54	2	600	2	SEL1L	14	81952089	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4079614	81952089	25397451	838	15461										
SEL1L	6400	hgsc.bcm.edu	37	chr14	81961452	81961452	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctgttctactccacgcccTccgtgcaggtgcagttgtcc	9	15	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:81961452T>C	ENST00000336735.4	-	11	1274	c.1158A>G	c.(1156-1158)ggA>ggG	p.G386G		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	386	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		CTCCACGCCCTCCGTGCAGGT	0.438																																					p.G386G		Atlas-SNP	.											.	SEL1L	67	.	0			c.A1158G						.						134	100	111					14																	81961452		2203	4300	6503	SO:0001819	synonymous_variant	6400	exon11			ACGCCCTCCGTGC		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.1158A>G	chr14.hg19:g.81961452T>C		81.0	0.0		90.0	5.0	NM_005065	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	hg19	CCDS9876.1																																																																																			.	.		0.438	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		C	81961452	T	C	81961452	2	2	103	1	0	0	0	0	0	0	0	1	14025	1538	54	2		2	SEL1L	14	81961452	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	9363	81961452	25388088	839	15462										
MOAP1	64112	hgsc.bcm.edu	37	chr14	93650222	93650222	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccattttcatgtccaagagcTctgctcaactcacccactgt	5	15	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:93650222T>C	ENST00000556883.1	-	2	850	c.366A>G	c.(364-366)agA>agG	p.R122R	RP11-371E8.4_ENST00000557574.1_5'Flank|TMEM251_ENST00000283534.4_5'Flank|MOAP1_ENST00000298894.4_Silent_p.R122R|TMEM251_ENST00000415050.2_5'Flank			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	122	BH3-like.				apoptotic signaling pathway (GO:0097190)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	13		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		gtccaagagctctgctcaact	0.493																																					p.R122R		Atlas-SNP	.											.	MOAP1	32	.	0			c.A366G						.						92	93	93					14																	93650222		2203	4300	6503	SO:0001819	synonymous_variant	64112	exon3			AAGAGCTCTGCTC	BC015044	CCDS9908.1	14q32.12	2012-02-09			ENSG00000165943	ENSG00000165943		"Paraneoplastic Ma antigens"	16658	protein-coding gene	gene with protein product	"paraneoplastic Ma antigen family member 4"	609485				11060313	Standard	NM_022151		Approved	MAP-1, PNMA4	uc001ybj.3	Q96BY2	OTTHUMG00000169184	ENST00000556883.1:c.366A>G	chr14.hg19:g.93650222T>C		98.0	0.0		97.0	6.0	NM_022151	B2RDF6|Q9H833|Q9HAS1	Silent	SNP	ENST00000556883.1	hg19	CCDS9908.1																																																																																			.	.		0.493	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1			C	93650222	T	C	93650222	2	2	103	1	0	0	0	0	0	0	0	1	9689	1548	54	2		2	MOAP1	14	93650222	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	11688770	93650222	13699318	840	15463										
IFI27	3429	hgsc.bcm.edu	37	chr14	94582130	94582130	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctcctcttccctgcagttgTggctgtgcccatggtgctca	11	14	2	0	rs3833507	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:94582130T>C	ENST00000555744.1	+	4	313	c.125T>C	c.(124-126)gTg>gCg	p.V42A	IFI27_ENST00000444961.1_Splice_Site_p.V45A|IFI27_ENST00000298902.5_Missense_Mutation_p.V42A|IFI27_ENST00000557098.1_5'UTR|IFI27_ENST00000557634.1_Missense_Mutation_p.V32A|IFI27_ENST00000448882.1_Missense_Mutation_p.V45A			P40305	IFI27_HUMAN	interferon, alpha-inducible protein 27	42				V -> VAMA (in Ref. 1; CAA47739). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)		p.A43_V44insMAA(1)		breast(1)|lung(3)	4				Epithelial(152;0.112)|all cancers(159;0.187)|COAD - Colon adenocarcinoma(157;0.206)		CCTGCAGTTGTGGCTGTGCCC	0.627																																					p.V42A	GBM(128;797 1667 20895 29868 47129)	Atlas-SNP	.											IFI27,colon,carcinoma,0,16	IFI27	39	.	1	Insertion - In frame(1)	breast(1)	c.T125C						.						14	13	13					14																	94582130		2184	4278	6462	SO:0001583	missense	3429	exon4			CAGTTGTGGCTGT	X67325	CCDS32148.1	14q32.12	2012-10-02			ENSG00000165949	ENSG00000165949			5397	protein-coding gene	gene with protein product		600009				8358738	Standard	NM_005532		Approved	P27, FAM14D	uc021sba.1	P40305	OTTHUMG00000171303	ENST00000555744.1:c.125T>C	chr14.hg19:g.94582130T>C	ENSP00000451956:p.Val42Ala	31.0	1.0		55.0	4.0	NM_005532	Q53YA6|Q6IEC1|Q96BK3	Missense_Mutation	SNP	ENST00000555744.1	hg19	CCDS32148.1	.	.	.	.	.	.	.	.	.	.	T	0.082	-1.181118	0.01633	.	.	ENSG00000165949	ENST00000554448;ENST00000444961;ENST00000448882;ENST00000554800;ENST00000556544;ENST00000298902;ENST00000557634;ENST00000555744	T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;1.62	3.52	-1.47	0.08772	.	0.951477	0.08752	N	0.898966	T	0.09642	0.0237	N	0.02674	-0.535	0.09310	N	1	B	0.18166	0.026	B	0.19391	0.025	T	0.34925	-0.9809	10	0.02654	T	1	.	7.2043	0.25899	0.0:0.4761:0.0:0.5239	.	42	P40305	IFI27_HUMAN	A	42;45;45;42;42;42;32;42	ENSP00000451370:V42A;ENSP00000413536:V45A;ENSP00000410901:V45A;ENSP00000451875:V42A;ENSP00000298902:V42A;ENSP00000452560:V32A;ENSP00000451956:V42A	ENSP00000298902:V42A	V	+	2	0	IFI27	93651883	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.001000	0.13038	-0.296000	0.08947	-0.400000	0.06385	GTG	.	.		0.627	IFI27-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412889.1	NM_005532		C	94582130	T	C	94582130	3	2	103	1	0	0	0	0	1	0	0	0	7521	1710	59	2	135	2	IFI27	14	94582130	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	931908	94582130	12767410	841	15464										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96807965	96807965	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaggtgctatctctggtaaaTttctagttagctgtgggtgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:96807965delT	ENST00000359933.4	-	6	1711	c.818delA	c.(817-819)aatfs	p.N273fs		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	273					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		CTCTGGTAAATTTCTAGTTAG	0.418																																					p.N273fs		Atlas-INDEL	.											.	ATG2B	169	.	0			c.819delT						.						135	129	131					14																	96807965		1883	4109	5992	SO:0001589	frameshift_variant	55102	exon6			.	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.818delA	chr14.hg19:g.96807965delT	ENSP00000353010:p.Asn273fs	95.0	0.0		103.0	10.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Frame_Shift_Del	DEL	ENST00000359933.4	hg19	CCDS9944.2																																																																																			.	.		0.418	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		-	96807965	T	-	96807965	7	5	103	1	0	1	0	1	0	0	0	0	1094	1493	52	0	5566	0	ATG2B	14	96807965	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2225835	96807965	10541575	842	15465										
PAPOLA	10914	hgsc.bcm.edu	37	chr14	96991682	96991682	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtaattgaaaatgttggaggAaaaatttttacatttggatc					rs35783174		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:96991682delA	ENST00000216277.8	+	4	505	c.285delA	c.(283-285)ggafs	p.G95fs	PAPOLA_ENST00000557471.1_Frame_Shift_Del_p.G95fs|PAPOLA_ENST00000554130.1_Intron|PAPOLA_ENST00000557320.1_Frame_Shift_Del_p.G95fs|PAPOLA_ENST00000392990.2_Frame_Shift_Del_p.G95fs	NM_032632.4	NP_116021.2	P51003	PAPOA_HUMAN	poly(A) polymerase alpha	95					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|RNA polyadenylation (GO:0043631)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		ATGTTGGAGGAAAAATTTTTA	0.299																																					p.G95fs	NSCLC(19;254 734 11908 35501 39234)	Atlas-INDEL	.											.	PAPOLA	58	.	0			c.284delG						.						56	62	60					14																	96991682		2203	4298	6501	SO:0001589	frameshift_variant	10914	exon4			.	X76770	CCDS9946.1, CCDS58334.1, CCDS58335.1	14q32.1-q32.2	2008-02-08				ENSG00000090060	2.7.7.19		14981	protein-coding gene	gene with protein product		605553				8302877, 10429366	Standard	NM_032632		Approved	PAP	uc001yfq.3	P51003		ENST00000216277.8:c.285delA	chr14.hg19:g.96991682delA	ENSP00000216277:p.Gly95fs	112.0	0.0		135.0	10.0	NM_001252006	Q86SX4|Q86TV0|Q8IYF5|Q9BVU2	Frame_Shift_Del	DEL	ENST00000216277.8	hg19	CCDS9946.1																																																																																			.	.		0.299	PAPOLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413411.2			-	96991682	A	-	96991682	7	5	103	1	0	1	0	1	0	0	0	0	11438	233	9	0	299	0	PAPOLA	14	96991682	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	183717	96991682	10357858	843	15466										
PPP2R5C	5527	hgsc.bcm.edu	37	chr14	102349777	102349777	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttcttctcaaagcttttagaGctctttgacagtgaagatcc	7	9	3	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:102349777G>A	ENST00000334743.5	+	5	555	c.507G>A	c.(505-507)gaG>gaA	p.E169E	PPP2R5C_ENST00000445439.3_Silent_p.E169E|PPP2R5C_ENST00000328724.5_Silent_p.E224E|PPP2R5C_ENST00000350249.3_Silent_p.E169E|PPP2R5C_ENST00000422945.2_Silent_p.E200E|PPP2R5C_ENST00000557095.1_Silent_p.E169E	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	169					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						AGCTTTTAGAGCTCTTTGACA	0.418																																					p.E224E		Atlas-SNP	.											.	PPP2R5C	74	.	0			c.G672A						.						90	95	93					14																	102349777		2202	4299	6501	SO:0001819	synonymous_variant	5527	exon7			TTTAGAGCTCTTT	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.507G>A	chr14.hg19:g.102349777G>A		94.0	0.0		91.0	15.0	NM_001161726	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Silent	SNP	ENST00000334743.5	hg19	CCDS9964.1																																																																																			.	.		0.418	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719		A	102349777	G	A	102349777	2	1	103	1	0	0	0	0	0	0	0	1	12406	962	34	3		3	PPP2R5C	14	102349777	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	5358095	102349777	4999763	844	15467										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102489191	102489191	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaaggcaatgagccgacccAtcttgtacagcaactggctg	11	11	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:102489191A>G	ENST00000360184.4	+	43	8775	c.8611A>G	c.(8611-8613)Atc>Gtc	p.I2871V		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2871					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GAGCCGACCCATCTTGTACAG	0.468																																					p.I2871V		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A8611G						.						227	182	197					14																	102489191		2203	4300	6503	SO:0001583	missense	1778	exon43			CGACCCATCTTGT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.8611A>G	chr14.hg19:g.102489191A>G	ENSP00000348965:p.Ile2871Val	128.0	0.0		125.0	22.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.559353	0.65538	.	.	ENSG00000197102	ENST00000360184	T	0.29917	1.55	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.41511	0.1162	M	0.78344	2.41	0.80722	D	1	P	0.45902	0.868	P	0.45167	0.472	T	0.38972	-0.9636	10	0.34782	T	0.22	.	15.0033	0.71492	1.0:0.0:0.0:0.0	.	2871	Q14204	DYHC1_HUMAN	V	2871	ENSP00000348965:I2871V	ENSP00000348965:I2871V	I	+	1	0	DYNC1H1	101558944	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	9.209000	0.95087	1.949000	0.56562	0.383000	0.25322	ATC	.	.		0.468	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		G	102489191	A	G	102489191	3	3	103	1	0	0	0	0	1	0	0	0	4843	217	8	2	8781	2	DYNC1H1	14	102489191	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	139414	102489191	4860349	845	15468										
C14orf153	84334	hgsc.bcm.edu	37	chr14	104056544	104056544	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtacaagcgcaattttgccaTcaccttcttcatgggaaaag	8	10	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:104056544T>C	ENST00000409074.2	+	5	543	c.542T>C	c.(541-543)aTc>aCc	p.I181T	RP11-73M18.2_ENST00000472726.2_Intron|APOPT1_ENST00000477116.1_3'UTR|APOPT1_ENST00000247618.4_Missense_Mutation_p.I168T|APOPT1_ENST00000556253.2_3'UTR	NM_032374.3	NP_115750.2	Q96IL0	APOP1_HUMAN	apoptogenic 1, mitochondrial	181					intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)	mitochondrion (GO:0005739)											AATTTTGCCATCACCTTCTTC	0.512																																					p.I181T		Atlas-SNP	.											.	.	.	.	0			c.T542C						.						196	194	195					14																	104056544		2203	4300	6503	SO:0001583	missense	84334	exon5			TTGCCATCACCTT	BC007412	CCDS9983.2	14q32.33	2012-06-28	2012-06-28	2011-09-07	ENSG00000256053	ENSG00000256053			20492	protein-coding gene	gene with protein product	"apoptogenic protein 1"		"chromosome 14 open reading frame 153", "apoptogenic 1"	C14orf153		16782708, 18977203	Standard	NM_032374		Approved	MGC2562, APOP-1		Q96IL0	OTTHUMG00000153929	ENST00000409074.2:c.542T>C	chr14.hg19:g.104056544T>C	ENSP00000386485:p.Ile181Thr	78.0	0.0		83.0	4.0	NM_032374	Q53G28	Missense_Mutation	SNP	ENST00000409074.2	hg19	CCDS9983.2	.	.	.	.	.	.	.	.	.	.	T	18.01	3.528619	0.64860	.	.	ENSG00000256053;ENSG00000256053;ENSG00000256500	ENST00000409074;ENST00000440963;ENST00000247618	T;T;T	0.52983	0.64;0.64;0.64	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.48223	0.1488	M	0.71206	2.165	0.40554	D	0.981143	B	0.11235	0.004	B	0.14578	0.011	T	0.49173	-0.8967	10	0.51188	T	0.08	.	12.1161	0.53866	0.0:0.0:0.0:1.0	.	181	Q96IL0	APOP1_HUMAN	T	181;93;168	ENSP00000386485:I181T;ENSP00000388067:I93T;ENSP00000247618:I168T	ENSP00000247618:I168T	I	+	2	0	C14orf153;RP11-73M18.2	103126297	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.509000	0.53386	2.109000	0.64355	0.533000	0.62120	ATC	.	.		0.512	APOPT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333060.2	NM_032374		C	104056544	T	C	104056544	3	2	103	1	0	0	0	0	1	0	0	0	1755	1435	50	2	560	2	C14orf153	14	104056544	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1567353	104056544	3292996	846	15469										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105418454	105418454	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtgacttccgccttggggcTtttcaggtccagcttggggc					rs200174203	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:105418454delT	ENST00000333244.5	-	7	3453	c.3334delA	c.(3334-3336)agcfs	p.S1112fs	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1112						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCCTTGGGGCTTTTCAGGTCC	0.647																																					p.S1112fs		Atlas-INDEL	.											.	AHNAK2	719	.	0			c.3335delG						.						116	145	136					14																	105418454		1882	4115	5997	SO:0001589	frameshift_variant	113146	exon7			.	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3334delA	chr14.hg19:g.105418454delT	ENSP00000353114:p.Ser1112fs	153.0	0.0		177.0	11.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Del	DEL	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		-	105418454	T	-	105418454	7	5	103	1	0	1	0	1	0	0	0	0	415	1609	56	0	14057	0	AHNAK2	14	105418454	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1361910	105418454	1931086	847	15470										
MTA1	9112	hgsc.bcm.edu	37	chr14	105916421	105916421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tagaagaggaaatggagaacCcggaaatggtggacctgccc	14	8	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:105916421C>T	ENST00000331320.7	+	5	482	c.268C>T	c.(268-270)Ccg>Tcg	p.P90S	MTA1_ENST00000405646.1_Missense_Mutation_p.P73S|MTA1_ENST00000406191.1_Missense_Mutation_p.P90S	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	90	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		AATGGAGAACCCGGAAATGGT	0.627																																					p.P90S		Atlas-SNP	.											MTA1,NS,carcinoma,0,1	MTA1	61	.	0			c.C268T						.						61	66	64					14																	105916421		2203	4300	6503	SO:0001583	missense	9112	exon5			GAGAACCCGGAAA	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"GATA zinc finger domain containing"	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.268C>T	chr14.hg19:g.105916421C>T	ENSP00000333633:p.Pro90Ser	132.0	0.0		169.0	0.0	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	19.02	3.746070	0.69418	.	.	ENSG00000182979	ENST00000331320;ENST00000406191;ENST00000405646;ENST00000498644	D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02	4.14	4.14	0.48551	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	U	0.000000	D	0.83367	0.5239	L	0.56396	1.775	0.80722	D	1	P	0.38250	0.624	B	0.39465	0.3	D	0.83910	0.0295	10	0.41790	T	0.15	-11.5496	14.9627	0.71169	0.0:1.0:0.0:0.0	.	90	Q13330	MTA1_HUMAN	S	90;90;73;4	ENSP00000333633:P90S;ENSP00000385702:P90S;ENSP00000384180:P73S;ENSP00000448146:P4S	ENSP00000333633:P90S	P	+	1	0	MTA1	104987466	1.000000	0.71417	0.914000	0.36105	0.674000	0.39518	3.448000	0.52943	1.839000	0.53478	0.306000	0.20318	CCG	.	.		0.627	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			T	105916421	C	T	105916421	3	4	103	1	0	0	0	0	1	0	0	0	9917	623	22	3	286	3	MTA1	14	105916421	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	497967	105916421	1433119	848	15471										
SNURF	8926	hgsc.bcm.edu	37	chr15	25213117	25213117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcgttctcagcagcagcaagTacctgtggtggatttccagg	13	10	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:25213117T>C	ENST00000577949.1	+	3	212	c.149T>C	c.(148-150)gTa>gCa	p.V50A	SNRPN_ENST00000577565.1_5'UTR|SNURF_ENST00000338327.4_Missense_Mutation_p.V50A|SNRPN_ENST00000400098.1_5'UTR|SNRPN_ENST00000553597.1_3'UTR|SNRPN_ENST00000400097.1_5'UTR|SNURF_ENST00000338094.6_Missense_Mutation_p.V50A|SNRPN_ENST00000390687.4_5'UTR|SNRPN_ENST00000346403.6_5'UTR|SNRPN_ENST00000554227.2_5'UTR|SNURF_ENST00000551312.2_Missense_Mutation_p.V50A|SNRPN_ENST00000400100.1_5'UTR			Q9Y675	SNURF_HUMAN	SNRPN upstream reading frame	50						nucleus (GO:0005634)				breast(2)|large_intestine(2)|lung(1)	5		all_cancers(20;1.4e-21)|Breast(32;0.000625)		all cancers(64;3.48e-07)|Epithelial(43;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0142)		CAGCAGCAAGTACCTGTGGTG	0.428																																					p.V50A		Atlas-SNP	.											.	SNURF	17	.	0			c.T149C						.						142	133	136					15																	25213117		2203	4300	6503	SO:0001583	missense	8926	exon3			AGCAAGTACCTGT		CCDS10016.1	15q11.2	2013-08-27			ENSG00000214265	ENSG00000214265			11171	protein-coding gene	gene with protein product						10318933	Standard	NM_022804		Approved		uc001ywu.3	Q9Y675	OTTHUMG00000129181	ENST00000577949.1:c.149T>C	chr15.hg19:g.25213117T>C	ENSP00000463201:p.Val50Ala	85.0	0.0		86.0	4.0	NM_005678	A6NCW2	Missense_Mutation	SNP	ENST00000577949.1	hg19	CCDS10016.1	.	.	.	.	.	.	.	.	.	.	T	5.100	0.204138	0.09704	.	.	ENSG00000214265	ENST00000338094;ENST00000338327	.	.	.	3.25	0.914	0.19360	.	.	.	.	.	T	0.25827	0.0629	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.18524	-1.0334	7	0.37606	T	0.19	-1.1304	5.0222	0.14367	0.0:0.2608:0.0:0.7392	.	50	Q9Y675	SNURF_HUMAN	A	50	.	ENSP00000336543:V50A	V	+	2	0	SNURF	22764210	0.011000	0.17503	0.135000	0.22099	0.820000	0.46376	-0.238000	0.08977	0.161000	0.19458	-0.376000	0.06991	GTA	.	.		0.428	SNURF-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446300.1	NM_005678		C	25213117	T	C	25213117	3	2	103	1	0	0	0	0	1	0	0	0	14893	1638	57	2	159	2	SNURF	15	25213117	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10		25213117	77318275	849	15472										
HERC2	8924	hgsc.bcm.edu	37	chr15	28366565	28366565	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttgcttgtactactttccggAaagccgcctcctaaaacaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:28366565delA	ENST00000261609.7	-	86	13307	c.13199delT	c.(13198-13200)ttcfs	p.F4400fs		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TACTTTCCGGAAAGCCGCCTC	0.438																																					p.F4400fs		Atlas-INDEL	.											.	HERC2	501	.	0			c.13200delC						.						110	105	106					15																	28366565		2203	4300	6503	SO:0001589	frameshift_variant	8924	exon86			.	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.13199delT	chr15.hg19:g.28366565delA	ENSP00000261609:p.Phe4400fs	132.0	0.0		162.0	10.0	NM_004667		Frame_Shift_Del	DEL	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.438	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		-	28366565	A	-	28366565	7	5	103	1	0	1	0	1	0	0	0	0	7067	246	9	0	1337	0	HERC2	15	28366565	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3153448	28366565	74164827	850	15473										
HERC2	8924	hgsc.bcm.edu	37	chr15	28436339	28436339	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtcagcaggatctacgatcaTttttaatctatgaacaagaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:28436339delT	ENST00000261609.7	-	54	8611	c.8503delA	c.(8503-8505)atgfs	p.M2835fs		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TCTACGATCATTTTTAATCTA	0.358																																					p.M2835fs		Atlas-INDEL	.											.	HERC2	501	.	0			c.8504delT						.						97	100	99					15																	28436339		2203	4300	6503	SO:0001589	frameshift_variant	8924	exon54			.	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.8503delA	chr15.hg19:g.28436339delT	ENSP00000261609:p.Met2835fs	86.0	0.0		116.0	11.0	NM_004667		Frame_Shift_Del	DEL	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.358	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		-	28436339	T	-	28436339	7	5	103	1	0	1	0	1	0	0	0	0	7067	1493	52	0	6161	0	HERC2	15	28436339	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	69774	28436339	74095053	851	15474										
APBA2	321	hgsc.bcm.edu	37	chr15	29346583	29346583	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	actacccagacggccaactgCccattccggaggatgagccc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:29346583delC	ENST00000558402.1	+	5	1095	c.496delC	c.(496-498)cccfs	p.P166fs	APBA2_ENST00000558259.1_Frame_Shift_Del_p.P166fs|APBA2_ENST00000411764.1_Frame_Shift_Del_p.P166fs|APBA2_ENST00000561069.1_Frame_Shift_Del_p.P166fs|APBA2_ENST00000558330.1_Frame_Shift_Del_p.P166fs			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	166					in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CGGCCAACTGCCCATTCCGGA	0.647																																					p.L165fs		Atlas-INDEL	.											.	APBA2	132	.	0			c.495delG						.						41	41	41					15																	29346583		2203	4300	6503	SO:0001589	frameshift_variant	321	exon3			.	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.496delC	chr15.hg19:g.29346583delC	ENSP00000453293:p.Pro166fs	159.0	0.0		159.0	10.0	NM_005503	E9PGI4|O60571|Q5XKC0	Frame_Shift_Del	DEL	ENST00000558402.1	hg19	CCDS10022.1																																																																																			.	.		0.647	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		-	29346583	C	-	29346583	7	5	103	1	0	1	0	1	0	0	0	0	757	739	26	0	498	0	APBA2	15	29346583	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	910244	29346583	73184809	852	15475										
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32928096	32928096	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctttttagcccagatgttgAtgaaaagttaccaaagaaag	9	6	0	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:32928096A>G	ENST00000361627.3	+	11	2185	c.1463A>G	c.(1462-1464)gAt>gGt	p.D488G	ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.D299G|ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.D460G|ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.D299G|ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.D488G	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	488					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		CCAGATGTTGATGAAAAGTTA	0.299																																					p.D488G	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.A1463G						.						75	73	73					15																	32928096		2201	4298	6499	SO:0001583	missense	9824	exon11			ATGTTGATGAAAA	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1463A>G	chr15.hg19:g.32928096A>G	ENSP00000355090:p.Asp488Gly	82.0	0.0		119.0	5.0	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	hg19	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	11.02	1.516057	0.27123	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.09723	2.95	5.8	-0.261	0.12963	.	0.423937	0.22398	N	0.060596	T	0.08044	0.0201	L	0.41027	1.25	0.26149	N	0.980169	B;B	0.24043	0.001;0.096	B;B	0.22386	0.003;0.039	T	0.35847	-0.9772	10	0.21014	T	0.42	.	10.0965	0.42478	0.5669:0.0:0.4331:0.0	.	488;299	Q6P4F7;B4DZN9	RHGBA_HUMAN;.	G	488;299	ENSP00000355090:D488G	ENSP00000355090:D488G	D	+	2	0	ARHGAP11A	30715388	0.945000	0.32115	0.995000	0.50966	0.993000	0.82548	0.001000	0.13038	-0.064000	0.13043	0.528000	0.53228	GAT	.	.		0.299	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		G	32928096	A	G	32928096	3	3	103	1	0	0	0	0	1	0	0	0	863	333	12	2	1505	2	ARHGAP11A	15	32928096	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	3581513	32928096	69603296	853	15476										
FSIP1	161835	hgsc.bcm.edu	37	chr15	39910069	39910069	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgccaagagtcttcgacatAaaatagtcttttgtgtcact							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:39910069delA	ENST00000350221.3	-	11	1775	c.1566delT	c.(1564-1566)tttfs	p.F522fs		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	522										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCTTCGACATAAAATAGTCTT	0.408																																					p.M523fs		Atlas-INDEL	.											.	FSIP1	53	.	0			c.1567delA						.						106	100	102					15																	39910069		2200	4297	6497	SO:0001589	frameshift_variant	161835	exon11			.	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1566delT	chr15.hg19:g.39910069delA	ENSP00000280236:p.Phe522fs	122.0	0.0		198.0	13.0	NM_152597	Q6X2C8|Q86Y89	Frame_Shift_Del	DEL	ENST00000350221.3	hg19	CCDS10050.1																																																																																			.	.		0.408	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		-	39910069	A	-	39910069	7	5	103	1	0	1	0	1	0	0	0	0	6082	359	13	0	187	0	FSIP1	15	39910069	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	6981973	39910069	62621323	854	15477										
RTF1	23168	hgsc.bcm.edu	37	chr15	41768645	41768645	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatctcctctctggtacagaTtgtaaaagagaaagaaaggt	9	6	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:41768645T>C	ENST00000389629.4	+	12	1496	c.1484T>C	c.(1483-1485)aTt>aCt	p.I495T		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	495					DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		CTGGTACAGATTGTAAAAGAG	0.428																																					p.I495T		Atlas-SNP	.											RTF1,NS,carcinoma,0,1	RTF1	76	.	0			c.T1484C						.						117	111	113					15																	41768645		2203	4300	6503	SO:0001630	splice_region_variant	23168	exon12			TACAGATTGTAAA	D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"KIAA0252"	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.1483-1T>C	chr15.hg19:g.41768645T>C		45.0	0.0		64.0	3.0	NM_015138	Q96BX6	Missense_Mutation	SNP	ENST00000389629.4	hg19	CCDS32200.2	.	.	.	.	.	.	.	.	.	.	T	22.3	4.265249	0.80358	.	.	ENSG00000137815	ENST00000389629	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.76004	0.3927	M	0.72894	2.215	0.80722	D	1	P	0.50156	0.932	P	0.61397	0.888	T	0.75314	-0.3361	9	0.37606	T	0.19	-10.4476	15.8085	0.78534	0.0:0.0:0.0:1.0	.	495	Q92541	RTF1_HUMAN	T	495	.	ENSP00000374280:I495T	I	+	2	0	RTF1	39555937	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.825000	0.86693	2.134000	0.65973	0.533000	0.62120	ATT	.	.		0.428	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138	Missense_Mutation	C	41768645	T	C	41768645	5	2	103	1	0	0	0	0	0	0	1	0	13736	1507	52	2	1530	2	RTF1	15	41768645	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1858576	41768645	60762747	855	15478										
LTK	4058	hgsc.bcm.edu	37	chr15	41796336	41796336	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gactcagttcctggggctgtGggggtcttaggcactccaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:41796336delG	ENST00000263800.6	-	20	2549	c.2453delC	c.(2452-2454)ccafs	p.P818fs	LTK_ENST00000561619.1_Frame_Shift_Del_p.P516fs|LTK_ENST00000453182.2_Frame_Shift_Del_p.P688fs|LTK_ENST00000355166.5_Frame_Shift_Del_p.P757fs	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	818					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CTGGGGCTGTGGGGGTCTTAG	0.602										TSP Lung(18;0.14)																											p.P818fs		Atlas-INDEL	.											.	LTK	117	.	0			c.2454delA						.						44	51	48					15																	41796336		2203	4300	6503	SO:0001589	frameshift_variant	4058	exon20			.	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.2453delC	chr15.hg19:g.41796336delG	ENSP00000263800:p.Pro818fs	170.0	0.0		157.0	11.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Frame_Shift_Del	DEL	ENST00000263800.6	hg19	CCDS10077.1																																																																																			.	.		0.602	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			-	41796336	G	-	41796336	7	5	103	1	0	1	0	1	0	0	0	0	9089	1348	47	0	145	0	LTK	15	41796336	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	27691	41796336	60735056	856	15479										
LTK	4058	hgsc.bcm.edu	37	chr15	41797198	41797198	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atctcgtgccatcccaaagtCcccaatcttggccactcggc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:41797198delC	ENST00000263800.6	-	16	2086	c.1990delG	c.(1990-1992)gacfs	p.D664fs	LTK_ENST00000561619.1_Frame_Shift_Del_p.D362fs|LTK_ENST00000453182.2_Frame_Shift_Del_p.D534fs|LTK_ENST00000355166.5_Frame_Shift_Del_p.D603fs	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	664	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		ATCCCAAAGTCCCCAATCTTG	0.572										TSP Lung(18;0.14)																											p.D664fs		Atlas-INDEL	.											.	LTK	117	.	0			c.1991delA						.						45	45	45					15																	41797198		2203	4300	6503	SO:0001589	frameshift_variant	4058	exon16			.	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.1990delG	chr15.hg19:g.41797198delC	ENSP00000263800:p.Asp664fs	127.0	0.0		140.0	10.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Frame_Shift_Del	DEL	ENST00000263800.6	hg19	CCDS10077.1																																																																																			.	.		0.572	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			-	41797198	C	-	41797198	7	5	103	1	0	1	0	1	0	0	0	0	9089	855	30	0	624	0	LTK	15	41797198	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	862	41797198	60734194	857	15480										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42166056	42166056	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atcctacctgctggaaagtgAcagcctgctgcagacactgg	11	12	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:42166056A>G	ENST00000320955.6	-	25	5104	c.4877T>C	c.(4876-4878)gTc>gCc	p.V1626A		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1626					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTGGAAAGTGACAGCCTGCTG	0.632																																					p.V1591A		Atlas-SNP	.											.	SPTBN5	171	.	0			c.T4772C						.						53	57	56					15																	42166056		2010	4186	6196	SO:0001583	missense	51332	exon25			AAAGTGACAGCCT	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.4877T>C	chr15.hg19:g.42166056A>G	ENSP00000317790:p.Val1626Ala	109.0	0.0		113.0	6.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	11.47	1.648218	0.29336	.	.	ENSG00000137877	ENST00000320955	T	0.35048	1.33	5.19	-3.13	0.05266	.	0.647525	0.14016	N	0.347115	T	0.17408	0.0418	L	0.35487	1.065	0.09310	N	1	B	0.25048	0.117	B	0.25884	0.064	T	0.31138	-0.9954	10	0.11182	T	0.66	.	1.9549	0.03374	0.4678:0.1253:0.2858:0.1211	.	1626	Q9NRC6	SPTN5_HUMAN	A	1626	ENSP00000317790:V1626A	ENSP00000317790:V1626A	V	-	2	0	SPTBN5	39953348	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.924000	0.28777	-0.979000	0.03529	0.529000	0.55759	GTC	.	.		0.632	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		G	42166056	A	G	42166056	3	3	103	1	0	0	0	0	1	0	0	0	15137	275	10	2	6323	2	SPTBN5	15	42166056	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	368858	42166056	60365336	858	15481										
TMEM62	80021	hgsc.bcm.edu	37	chr15	43446967	43446967	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgtgtctggtcccattttcGtactgaagtggaatcctaga	10	8	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:43446967G>C	ENST00000260403.2	+	9	1399	c.1120G>C	c.(1120-1122)Gta>Cta	p.V374L		NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	374						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		TCCCATTTTCGTACTGAAGTG	0.373																																					p.V374L		Atlas-SNP	.											.	TMEM62	47	.	0			c.G1120C						.						127	110	116					15																	43446967		2203	4299	6502	SO:0001583	missense	80021	exon9			ATTTTCGTACTGA	BC009981	CCDS32210.1	15q15.2	2014-09-11			ENSG00000137842	ENSG00000137842			26269	protein-coding gene	gene with protein product							Standard	NM_024956		Approved	FLJ23375	uc001zqr.3	Q0P6H9	OTTHUMG00000176485	ENST00000260403.2:c.1120G>C	chr15.hg19:g.43446967G>C	ENSP00000260403:p.Val374Leu	101.0	0.0		152.0	15.0	NM_024956	Q6I9Y5|Q9H5J6	Missense_Mutation	SNP	ENST00000260403.2	hg19	CCDS32210.1	.	.	.	.	.	.	.	.	.	.	G	14.80	2.642270	0.47153	.	.	ENSG00000137842	ENST00000260403	.	.	.	5.67	1.92	0.25849	.	0.486384	0.25130	N	0.032911	T	0.49983	0.1589	M	0.64997	1.995	0.34404	D	0.695626	B	0.26744	0.158	B	0.28465	0.09	T	0.54139	-0.8338	9	0.33940	T	0.23	-0.6828	7.7929	0.29131	0.6476:0.0:0.3524:0.0	.	374	Q0P6H9	TMM62_HUMAN	L	374	.	ENSP00000260403:V374L	V	+	1	0	TMEM62	41234259	1.000000	0.71417	0.996000	0.52242	0.857000	0.48899	3.399000	0.52586	0.499000	0.27970	-0.438000	0.05819	GTA	.	.		0.373	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956		C	43446967	G	C	43446967	3	2	103	1	0	0	0	0	1	0	0	0	16204	1145	40	4	1154	4	TMEM62	15	43446967	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	1280911	43446967	59084425	859	15482										
STRC	161497	hgsc.bcm.edu	37	chr15	43909880	43909880	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcctgaaaggcagcatagaGgggggcccccactgtgcgta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:43909880delG	ENST00000450892.2	-	2	816	c.739delC	c.(739-741)ctcfs	p.L247fs	STRC_ENST00000541030.1_5'UTR	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	247					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		GCAGCATAGAGGGGGGCCCCC	0.592																																					p.L247fs		Atlas-INDEL	.											.	STRC	58	.	0			c.740delT						.						1	2	2					15																	43909880		536	1524	2060	SO:0001589	frameshift_variant	161497	exon2			.	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.739delC	chr15.hg19:g.43909880delG	ENSP00000401513:p.Leu247fs	75.0	0.0		110.0	10.0	NM_153700		Frame_Shift_Del	DEL	ENST00000450892.2	hg19	CCDS10098.1																																																																																			.	.		0.592	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700		-	43909880	G	-	43909880	7	5	103	1	0	1	0	1	0	0	0	0	15343	1000	35	0	4700	0	STRC	15	43909880	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	462913	43909880	58621512	860	15483										
DUOX2	50506	hgsc.bcm.edu	37	chr15	45386375	45386375	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctcatagtggtgcatgaaGtgggctcggtcctgcctgtt	13	9	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:45386375G>A	ENST00000603300.1	-	34	4822	c.4620C>T	c.(4618-4620)caC>caT	p.H1540H	DUOX2_ENST00000389039.6_Silent_p.H1540H	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1540					adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		GGTGCATGAAGTGGGCTCGGT	0.577																																					p.H1540H		Atlas-SNP	.											.	DUOX2	137	.	0			c.C4620T						.						149	127	134					15																	45386375		2198	4298	6496	SO:0001819	synonymous_variant	50506	exon34			CATGAAGTGGGCT	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"EF-hand domain containing"	13273	protein-coding gene	gene with protein product	"dual oxidase-like domains 2", "nicotinamide adenine dinucleotide phosphate oxidase", "flavoprotein NADPH oxidase", "NADPH thyroid oxidase 2", "NADH/NADPH thyroid oxidase p138-tox", "NADPH oxidase/peroxidase DUOX2"	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.4620C>T	chr15.hg19:g.45386375G>A		126.0	0.0		171.0	51.0	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Silent	SNP	ENST00000603300.1	hg19	CCDS10117.1																																																																																			.	.		0.577	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		A	45386375	G	A	45386375	2	1	103	1	0	0	0	0	0	0	0	1	4803	1020	36	3		3	DUOX2	15	45386375	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	1476495	45386375	57145017	861	15484										
AP4E1	23431	hgsc.bcm.edu	37	chr15	51289642	51289642	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcttcctttagttctttgtcAaatgtggcatatgaagatga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:51289642delA	ENST00000261842.5	+	18	2572	c.2466delA	c.(2464-2466)tcafs	p.S822fs	AP4E1_ENST00000560508.1_Frame_Shift_Del_p.S747fs	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	822					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		GTTCTTTGTCAAATGTGGCAT	0.348																																					p.S822X		Atlas-INDEL	.											.	AP4E1	78	.	0			c.2465delC						.						127	123	124					15																	51289642		2196	4294	6490	SO:0001589	frameshift_variant	23431	exon18			.	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2466delA	chr15.hg19:g.51289642delA	ENSP00000261842:p.Ser822fs	107.0	0.0		163.0	11.0	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Frame_Shift_Del	DEL	ENST00000261842.5	hg19	CCDS32240.1																																																																																			.	.		0.348	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			-	51289642	A	-	51289642	7	5	103	1	0	1	0	1	0	0	0	0	752	117	5	0	2536	0	AP4E1	15	51289642	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	5903267	51289642	51241750	862	15485										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51914662	51914662	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cggccgccgctcaccgtgaaGgggacatccccgacgctgcc					rs2278990	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:51914662delG	ENST00000251076.5	-	1	368	c.81delC	c.(79-81)cccfs	p.P27fs	DMXL2_ENST00000449909.3_Frame_Shift_Del_p.P27fs|DMXL2_ENST00000543779.2_Frame_Shift_Del_p.P27fs	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	27						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TCACCGTGAAGGGGACATCCC	0.687																																					p.F28fs		Atlas-INDEL	.											.	DMXL2	262	.	0			c.82delT						.						22	19	20					15																	51914662		2177	4261	6438	SO:0001589	frameshift_variant	23312	exon1			.	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.81delC	chr15.hg19:g.51914662delG	ENSP00000251076:p.Pro27fs	128.0	0.0		156.0	10.0	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Frame_Shift_Del	DEL	ENST00000251076.5	hg19	CCDS10141.1																																																																																			.	.		0.687	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		-	51914662	G	-	51914662	7	5	103	1	0	1	0	1	0	0	0	0	4597	987	35	0	9204	0	DMXL2	15	51914662	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	625020	51914662	50616730	863	15486										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54626040	54626040	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acctgttaacaagtatcaccTtttttaggatgaaggtatct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:54626040delT	ENST00000260323.11	+	15	4570	c.4570delT	c.(4570-4572)tttfs	p.F1525fs	UNC13C_ENST00000537900.1_Frame_Shift_Del_p.F1523fs|UNC13C_ENST00000545554.1_Frame_Shift_Del_p.F1525fs	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1525					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AAGTATCACCTTTTTTAGGAT	0.368																																					p.T1523fs		Atlas-INDEL	.											.	UNC13C	674	.	0			c.4569delC						.						137	125	129					15																	54626040		1853	4078	5931	SO:0001589	frameshift_variant	440279	exon14			.	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.4570delT	chr15.hg19:g.54626040delT	ENSP00000260323:p.Phe1525fs	113.0	0.0		165.0	11.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Frame_Shift_Del	DEL	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.368	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		-	54626040	T	-	54626040	7	5	103	1	0	1	0	1	0	0	0	0	17001	1609	56	0	4624	0	UNC13C	15	54626040	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2711378	54626040	47905352	864	15487										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54860046	54860046	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgaaaaagaatttcttggagAaaagcccagatcttcagtct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:54860046delA	ENST00000260323.11	+	29	6007	c.6007delA	c.(6007-6009)aaafs	p.K2003fs	UNC13C_ENST00000537900.1_Frame_Shift_Del_p.K2001fs|UNC13C_ENST00000545554.1_Frame_Shift_Del_p.K2003fs	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	2003	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TTTCTTGGAGAAAAGCCCAGA	0.378																																					p.E2002fs		Atlas-INDEL	.											.	UNC13C	674	.	0			c.6006delG						.						68	64	65					15																	54860046		1797	4068	5865	SO:0001589	frameshift_variant	440279	exon28			.	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.6007delA	chr15.hg19:g.54860046delA	ENSP00000260323:p.Lys2003fs	137.0	0.0		160.0	10.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Frame_Shift_Del	DEL	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.378	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		-	54860046	A	-	54860046	7	5	103	1	0	1	0	1	0	0	0	0	17001	247	9	0	6117	0	UNC13C	15	54860046	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	234006	54860046	47671346	865	15488										
MNS1	55329	hgsc.bcm.edu	37	chr15	56721375	56721375	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caagcagatcaatatcatccTcttttttaaatactccctac	2	12	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:56721375T>C	ENST00000260453.3	-	10	1576	c.1412A>G	c.(1411-1413)gAg>gGg	p.E471G	TEX9_ENST00000537232.1_Intron|MNS1_ENST00000566386.1_5'UTR|TEX9_ENST00000352903.2_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	471					cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		AATATCATCCTCTTTTTTAAA	0.318																																					p.E471G		Atlas-SNP	.											.	MNS1	39	.	0			c.A1412G						.						84	81	82					15																	56721375		2191	4285	6476	SO:0001583	missense	55329	exon10			TCATCCTCTTTTT	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"spermatogenesis associated 40"	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.1412A>G	chr15.hg19:g.56721375T>C	ENSP00000260453:p.Glu471Gly	88.0	0.0		113.0	7.0	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	hg19	CCDS10158.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.716836	0.68844	.	.	ENSG00000138587	ENST00000260453	T	0.18016	2.24	6.08	4.97	0.65823	.	0.162086	0.56097	D	0.000031	T	0.20861	0.0502	M	0.65498	2.005	0.52501	D	0.999955	D	0.56746	0.977	B	0.42827	0.399	T	0.01899	-1.1251	10	0.54805	T	0.06	-10.6378	10.9711	0.47441	0.0:0.072:0.0:0.928	.	471	Q8NEH6	MNS1_HUMAN	G	471	ENSP00000260453:E471G	ENSP00000260453:E471G	E	-	2	0	MNS1	54508667	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.727000	0.47311	2.333000	0.79357	0.482000	0.46254	GAG	.	.		0.318	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365		C	56721375	T	C	56721375	3	2	103	1	0	0	0	0	1	0	0	0	9686	1551	54	2	79	2	MNS1	15	56721375	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1861329	56721375	45810017	866	15489										
LDHAL6B	92483	hgsc.bcm.edu	37	chr15	59499975	59499975	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcctgagcaatggaaaaatgTccacaaagaagtgactgcaa	9	8	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:59499975T>C	ENST00000307144.4	+	1	934	c.836T>C	c.(835-837)gTc>gCc	p.V279A	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	279					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						TGGAAAAATGTCCACAAAGAA	0.408																																					p.V279A		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.T836C						.						67	66	66					15																	59499975		2191	4290	6481	SO:0001583	missense	92483	exon1			AAAATGTCCACAA	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"lactate dehydrogenase A-like 6"	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.836T>C	chr15.hg19:g.59499975T>C	ENSP00000302393:p.Val279Ala	54.0	0.0		68.0	5.0	NM_033195	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	hg19	CCDS10171.1	.	.	.	.	.	.	.	.	.	.	T	16.41	3.115298	0.56505	.	.	ENSG00000171989	ENST00000307144	T	0.67698	-0.28	1.47	1.47	0.22746	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.206606	0.30575	U	0.009333	T	0.67239	0.2872	M	0.85542	2.76	0.43000	D	0.99451	P	0.39831	0.69	B	0.41619	0.361	T	0.67837	-0.5567	10	0.62326	D	0.03	.	6.659	0.23004	0.0:0.0:0.0:1.0	.	279	Q9BYZ2	LDH6B_HUMAN	A	279	ENSP00000302393:V279A	ENSP00000302393:V279A	V	+	2	0	LDHAL6B	57287267	0.587000	0.26791	0.044000	0.18714	0.689000	0.40095	2.261000	0.43276	0.654000	0.30846	0.254000	0.18369	GTC	.	.		0.408	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195		C	59499975	T	C	59499975	3	2	103	1	0	0	0	0	1	0	0	0	8709	1667	58	2	838	2	LDHAL6B	15	59499975	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2778600	59499975	43031417	867	15490										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62243167	62243167	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtcagtaacattttcagaaGgggttcgtcagtcacattag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:62243167delG	ENST00000261517.5	-	40	4586	c.4513delC	c.(4513-4515)cttfs	p.L1506fs	VPS13C_ENST00000395898.3_Frame_Shift_Del_p.L1463fs|VPS13C_ENST00000395896.4_Frame_Shift_Del_p.L1506fs|VPS13C_ENST00000249837.3_Frame_Shift_Del_p.L1463fs	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ATTTTCAGAAGGGGTTCGTCA	0.289																																					p.L1505fs		Atlas-INDEL	.											.	VPS13C	506	.	0			c.4514delT						.						46	46	46					15																	62243167		2202	4295	6497	SO:0001589	frameshift_variant	54832	exon40			.	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.4513delC	chr15.hg19:g.62243167delG	ENSP00000261517:p.Leu1506fs	146.0	0.0		250.0	16.0	NM_020821		Frame_Shift_Del	DEL	ENST00000261517.5	hg19	CCDS32257.1																																																																																			.	.		0.289	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		-	62243167	G	-	62243167	7	5	103	1	0	1	0	1	0	0	0	0	17206	1000	35	0	6960	0	VPS13C	15	62243167	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2743192	62243167	40288225	868	15491										
CSNK1G1	53944	hgsc.bcm.edu	37	chr15	64508813	64508813	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagtaaatgttcggtcacagAggtcaaacaagtcctccaag	9	9	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:64508813A>G	ENST00000303052.7	-	5	815	c.392T>C	c.(391-393)cTc>cCc	p.L131P	CSNK1G1_ENST00000607537.1_Missense_Mutation_p.L131P|CSNK1G1_ENST00000303032.6_Missense_Mutation_p.L131P|CTD-2116N17.1_ENST00000606793.1_Missense_Mutation_p.L104P	NM_022048.3	NP_071331.2	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	131	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	13						TCGGTCACAGAGGTCAAACAA	0.473																																					p.L131P		Atlas-SNP	.											.	CSNK1G1	56	.	0			c.T392C						.						100	82	88					15																	64508813		2203	4300	6503	SO:0001583	missense	53944	exon5			TCACAGAGGTCAA	AB042562	CCDS10192.2	15q22.1-q22.31	2013-01-17			ENSG00000169118	ENSG00000169118			2454	protein-coding gene	gene with protein product		606274				11124537	Standard	NM_022048		Approved	CK1gamma1	uc002anf.3	Q9HCP0	OTTHUMG00000133019	ENST00000303052.7:c.392T>C	chr15.hg19:g.64508813A>G	ENSP00000305777:p.Leu131Pro	112.0	0.0		85.0	4.0	NM_022048	Q5JPH1|Q96AE9|Q9HCP1	Missense_Mutation	SNP	ENST00000303052.7	hg19	CCDS10192.2	.	.	.	.	.	.	.	.	.	.	A	25.6	4.655024	0.88056	.	.	ENSG00000169118	ENST00000303052;ENST00000447727;ENST00000303032	T;T	0.68624	-0.34;-0.34	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.171885	0.52532	D	0.000063	D	0.86037	0.5837	M	0.93808	3.46	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.80764	0.972;0.994;0.989	D	0.89895	0.4040	10	0.87932	D	0	.	15.4792	0.75511	1.0:0.0:0.0:0.0	.	131;131;131	Q9HCP0-2;Q8IXA3;Q9HCP0	.;.;KC1G1_HUMAN	P	131;87;131	ENSP00000305777:L131P;ENSP00000307753:L131P	ENSP00000307753:L131P	L	-	2	0	CSNK1G1	62295866	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.287000	0.95975	2.120000	0.65058	0.459000	0.35465	CTC	.	.		0.473	CSNK1G1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256605.1	NM_022048		G	64508813	A	G	64508813	3	3	103	1	0	0	0	0	1	0	0	0	3956	304	11	2	908	2	CSNK1G1	15	64508813	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2265646	64508813	38022579	869	15492										
PIF1	80119	hgsc.bcm.edu	37	chr15	65108937	65108937	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcaaacacacggcccagagAaatctccacacaatccaggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:65108937delA	ENST00000268043.4	-	12	1796	c.1702delT	c.(1702-1704)tctfs	p.S568fs	PIF1_ENST00000333425.6_Frame_Shift_Del_p.S568fs|PIF1_ENST00000559239.1_Frame_Shift_Del_p.S568fs					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						CGGCCCAGAGAAATCTCCACA	0.612																																					p.S568fs		Atlas-INDEL	.											PIF1_ENST00000268043,NS,carcinoma,0,1	PIF1	43	.	0			c.1703delC						.						42	38	40					15																	65108937		2200	4295	6495	SO:0001589	frameshift_variant	80119	exon12			.	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"chromosome 15 open reading frame 20", "PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.1702delT	chr15.hg19:g.65108937delA	ENSP00000268043:p.Ser568fs	180.0	0.0		209.0	13.0	NM_025049		Frame_Shift_Del	DEL	ENST00000268043.4	hg19	CCDS10195.2																																																																																			.	.		0.612	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049		-	65108937	A	-	65108937	7	5	103	1	0	1	0	1	0	0	0	0	11892	246	9	0	231	0	PIF1	15	65108937	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	600124	65108937	37422455	870	15493										
DENND4A	10260	hgsc.bcm.edu	37	chr15	65983623	65983623	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atttttgcatcagctcccaaTttttcaactatatctccagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:65983623delT	ENST00000431932.2	-	22	3385	c.3177delA	c.(3175-3177)aaafs	p.K1059fs	DENND4A_ENST00000567323.1_5'Flank|DENND4A_ENST00000443035.3_Frame_Shift_Del_p.K1102fs	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1059					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						CAGCTCCCAATTTTTCAACTA	0.383																																					p.L1103fs		Atlas-INDEL	.											.	DENND4A	217	.	0			c.3307delT						.						49	45	47					15																	65983623		1811	4062	5873	SO:0001589	frameshift_variant	10260	exon23			.	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.3177delA	chr15.hg19:g.65983623delT	ENSP00000396830:p.Lys1059fs	119.0	0.0		118.0	10.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Frame_Shift_Del	DEL	ENST00000431932.2	hg19	CCDS45285.1																																																																																			.	.		0.383	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		-	65983623	T	-	65983623	7	5	103	1	0	1	0	1	0	0	0	0	4435	1490	52	0	2458	0	DENND4A	15	65983623	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	874686	65983623	36547769	871	15494										
NOX5	79400	hgsc.bcm.edu	37	chr15	69339868	69339868	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgcttccattctgcagagtaTcatgtacaggtgggtgaaca	11	8	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:69339868T>C	ENST00000388866.3	+	12	1849	c.1808T>C	c.(1807-1809)aTc>aCc	p.I603T	NOX5_ENST00000525163.1_3'UTR|NOX5_ENST00000260364.5_Missense_Mutation_p.I585T|NOX5_ENST00000448182.3_Missense_Mutation_p.I557T|NOX5_ENST00000530406.2_Missense_Mutation_p.I575T|NOX5_ENST00000455873.3_Missense_Mutation_p.I568T	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	603					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						CTGCAGAGTATCATGTACAGG	0.597																																					p.I603T		Atlas-SNP	.											.	NOX5	60	.	0			c.T1808C						.						98	93	95					15																	69339868		2200	4298	6498	SO:0001583	missense	79400	exon12			AGAGTATCATGTA	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"EF-hand domain containing"	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.1808T>C	chr15.hg19:g.69339868T>C	ENSP00000373518:p.Ile603Thr	74.0	0.0		79.0	5.0	NM_024505	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Missense_Mutation	SNP	ENST00000388866.3	hg19	CCDS32276.2	.	.	.	.	.	.	.	.	.	.	T	11.52	1.663214	0.29515	.	.	ENSG00000255346	ENST00000455873;ENST00000448182;ENST00000388866;ENST00000530406	D;D;D	0.95137	-3.62;-3.62;-3.62	3.02	3.02	0.34903	Ferric reductase, NAD binding (1);	0.000000	0.85682	D	0.000000	D	0.97551	0.9198	H	0.94222	3.51	0.49483	D	0.999797	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.81914	0.973;0.995;0.992	D	0.97344	0.9959	10	0.87932	D	0	.	9.9894	0.41860	0.0:0.0:0.0:1.0	.	568;603;575	Q96PH1-6;Q96PH1;Q96PH1-3	.;NOX5_HUMAN;.	T	568;585;603;575	ENSP00000416828:I568T;ENSP00000373518:I603T;ENSP00000432440:I575T	ENSP00000373518:I603T	I	+	2	0	NOX5	67126922	1.000000	0.71417	0.993000	0.49108	0.148000	0.21650	4.693000	0.61753	1.028000	0.39785	0.172000	0.16884	ATC	.	.		0.597	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505		C	69339868	T	C	69339868	3	2	103	1	0	0	0	0	1	0	0	0	10568	1435	50	2	1887	2	NOX5	15	69339868	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3356245	69339868	33191524	872	15495										
NEO1	4756	hgsc.bcm.edu	37	chr15	73470686	73470686	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttttgggtctggtgaaatcAgatgaagggttctatcagtg	14	4	4	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:73470686A>G	ENST00000339362.5	+	8	1656	c.1209A>G	c.(1207-1209)tcA>tcG	p.S403S	NEO1_ENST00000560262.1_Silent_p.S403S|NEO1_ENST00000261908.6_Silent_p.S403S|NEO1_ENST00000558964.1_Silent_p.S403S			Q92859	NEO1_HUMAN	neogenin 1	403	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						TGGTGAAATCAGATGAAGGGT	0.343																																					p.S403S		Atlas-SNP	.											.	NEO1	102	.	0			c.A1209G						.						96	94	95					15																	73470686		2198	4297	6495	SO:0001819	synonymous_variant	4756	exon7			GAAATCAGATGAA	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.1209A>G	chr15.hg19:g.73470686A>G		105.0	0.0		98.0	4.0	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Silent	SNP	ENST00000339362.5	hg19	CCDS10247.1																																																																																			.	.		0.343	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		G	73470686	A	G	73470686	2	3	103	1	0	0	0	0	0	0	0	1	10345	175	7	2		2	NEO1	15	73470686	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	4130818	73470686	29060706	873	15496										
GOLGA6A	342096	hgsc.bcm.edu	37	chr15	74364639	74364639	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcctcactgtccagatgttGtcctccatctcctgtaggga	8	14	2	1	rs200350318		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:74364639G>C	ENST00000290438.3	-	14	1553	c.1513C>G	c.(1513-1515)Caa>Gaa	p.Q505E	RN7SL429P_ENST00000479090.2_RNA	NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	505						Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						TCCAGATGTTGTCCTCCATCT	0.632																																					p.Q505E		Atlas-SNP	.											GOLGA6A,NS,carcinoma,0,1	GOLGA6A	28	.	0			c.C1513G						.	C	GLU/GLN	13,2839		0,13,1413	43	76	64		1513	-1.8	0	15		64	41,5189		0,41,2574	no	missense	GOLGA6A	NM_001038640.2	29	0,54,3987	CC,CG,GG		0.7839,0.4558,0.6682	benign	505/694	74364639	54,8028	1426	2615	4041	SO:0001583	missense	342096	exon14			GATGTTGTCCTCC	AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289			13567	protein-coding gene	gene with protein product		610288	"golgi autoantigen, golgin subfamily a, member 6", "golgi autoantigen, golgin subfamily a, 6", "golgi autoantigen, golgin subfamily a, 6A"	GOLGA6		11161787	Standard	NM_001038640		Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1513C>G	chr15.hg19:g.74364639G>C	ENSP00000290438:p.Gln505Glu	13.0	1.0		58.0	5.0	NM_001038640	A8K959|Q9NYA7	Missense_Mutation	SNP	ENST00000290438.3	hg19	CCDS32290.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.871708	0.00062	0.004558	0.007839	ENSG00000159289	ENST00000290438	T	0.17213	2.29	0.887	-1.77	0.07982	.	.	.	.	.	T	0.02193	0.0068	N	0.00677	-1.265	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22068	-1.0227	9	0.02654	T	1	.	5.0871	0.14689	0.1703:0.3999:0.4298:0.0	.	505	Q9NYA3	GOG6A_HUMAN	E	505	ENSP00000290438:Q505E	ENSP00000290438:Q505E	Q	-	1	0	GOLGA6A	72151692	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.799000	0.00762	-2.200000	0.00747	-2.001000	0.00444	CAA	.	G|0.999;C|0.001		0.632	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421835.1	XM_292357		C	74364639	G	C	74364639	3	2	103	1	0	0	0	0	1	0	0	0	6565	1386	48	4	588	4	GOLGA6A	15	74364639	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	893953	74364639	28166753	874	15497										
CCDC33	80125	hgsc.bcm.edu	37	chr15	74560701	74560701	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcccactgagtctgggaaaGccgatgaagccactgccaag	12	12	1	2	rs538969678		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:74560701G>A	ENST00000398814.3	+	5	879	c.448G>A	c.(448-450)Gcc>Acc	p.A150T	CCDC33_ENST00000321288.5_Missense_Mutation_p.A353T	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	353										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GTCTGGGAAAGCCGATGAAGC	0.572													G|||	1	0.000199681	0	0	5008	,	,		15392	0		0	False		,,,				2504	0.001				p.A150T		Atlas-SNP	.											.	CCDC33	160	.	0			c.G448A						.						49	54	53					15																	74560701		1961	4161	6122	SO:0001583	missense	80125	exon5			GGGAAAGCCGATG	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"cancer/testis antigen 61"					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.448G>A	chr15.hg19:g.74560701G>A	ENSP00000381795:p.Ala150Thr	131.0	0.0		160.0	42.0	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	hg19	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	G	6.961	0.547158	0.13312	.	.	ENSG00000140481	ENST00000321288;ENST00000398814	T;T	0.23552	1.9;2.23	4.17	-3.93	0.04143	.	3.081050	0.01073	N	0.004855	T	0.18676	0.0448	L	0.47716	1.5	0.09310	N	1	B	0.24426	0.103	B	0.19391	0.025	T	0.09552	-1.0669	10	0.27785	T	0.31	.	1.3327	0.02138	0.195:0.3649:0.2146:0.2255	.	150	Q8N5R6-6	.	T	353;150	ENSP00000325012:A353T;ENSP00000381795:A150T	ENSP00000325012:A353T	A	+	1	0	CCDC33	72347754	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.913000	0.04042	-0.555000	0.06142	0.514000	0.50259	GCC	.	.		0.572	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791		A	74560701	G	A	74560701	3	1	103	1	0	0	0	0	1	0	0	0	2808	971	34	3	466	3	CCDC33	15	74560701	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	196062	74560701	27970691	875	15498										
CLK3	1198	hgsc.bcm.edu	37	chr15	74921281	74921281	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	actccacccccttaattttcAggaagcagaaatatttctac	4	12	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:74921281A>G	ENST00000395066.3	+	12	2110		c.e12-1		CLK3_ENST00000345005.4_Splice_Site|CLK3_ENST00000352989.5_Splice_Site|CLK3_ENST00000348245.3_Splice_Site	NM_001130028.1	NP_001123500.1	P49761	CLK3_HUMAN	CDC-like kinase 3						protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	cytoplasmic vesicle (GO:0031410)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)|stomach(2)|urinary_tract(1)	15						CTTAATTTTCAGGAAGCAGAA	0.522																																					.	Ovarian(133;694 1754 28950 29027 31859)	Atlas-SNP	.											.	CLK3	78	.	0			c.1206-2A>G						.						50	54	53					15																	74921281		2197	4296	6493	SO:0001630	splice_region_variant	1198	exon12			ATTTTCAGGAAGC	L29220	CCDS10265.1, CCDS45304.1	15q24	2008-05-02			ENSG00000179335	ENSG00000179335		"CDC-like kinases"	2071	protein-coding gene	gene with protein product		602990				7990150, 9856501	Standard	NM_003992		Approved	clk3	uc010uln.2	P49761	OTTHUMG00000141320	ENST00000395066.3:c.1650-1A>G	chr15.hg19:g.74921281A>G		68.0	0.0		89.0	5.0	NM_003992	D3DW59|Q53Y48|Q9BRS3|Q9BUJ7	Splice_Site	SNP	ENST00000395066.3	hg19	CCDS45304.1	.	.	.	.	.	.	.	.	.	.	A	18.21	3.572663	0.65765	.	.	ENSG00000179335	ENST00000345005;ENST00000395066;ENST00000454830;ENST00000352989	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3135	0.66432	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CLK3	72708334	1.000000	0.71417	0.982000	0.44146	0.930000	0.56654	9.224000	0.95209	2.057000	0.61298	0.459000	0.35465	.	.	.		0.522	CLK3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390442.3		Intron	G	74921281	A	G	74921281	5	3	103	1	0	0	0	0	0	0	1	0	3540	202	7	2	1694	2	CLK3	15	74921281	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	360580	74921281	27610111	876	15499										
SIN3A	25942	hgsc.bcm.edu	37	chr15	75693144	75693144	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtaaggctcgatagctggagCccaatcgtttacaagaagca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:75693144delC	ENST00000394947.3	-	11	1978	c.1664delG	c.(1663-1665)ggcfs	p.G555fs	SIN3A_ENST00000394949.4_Frame_Shift_Del_p.G555fs|SIN3A_ENST00000360439.4_Frame_Shift_Del_p.G555fs	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A									p.G555V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						ATAGCTGGAGCCCAATCGTTT	0.488																																					p.G555fs		Atlas-INDEL	.											.	SIN3A	152	.	1	Substitution - Missense(1)	endometrium(1)	c.1665delC						.						115	99	105					15																	75693144		2197	4294	6491	SO:0001589	frameshift_variant	25942	exon11			.	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.1664delG	chr15.hg19:g.75693144delC	ENSP00000378402:p.Gly555fs	116.0	0.0		142.0	10.0	NM_001145358		Frame_Shift_Del	DEL	ENST00000394947.3	hg19	CCDS10279.1																																																																																			.	.		0.488	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		-	75693144	C	-	75693144	7	5	103	1	0	1	0	1	0	0	0	0	14340	739	26	0	2201	0	SIN3A	15	75693144	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	771863	75693144	26838248	877	15500										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75980311	75980311	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tagtcagcagccgccgcccaCcccgggccacatggaagatc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:75980311delC	ENST00000308508.5	-	3	3187	c.3095delG	c.(3094-3096)ggtfs	p.G1033fs		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1033	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.|Interaction with COL6A2. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCGCCGCCCACCCCGGGCCAC	0.647																																					p.G1032fs		Atlas-INDEL	.											.	CSPG4	175	.	0			c.3096delT						.						34	39	38					15																	75980311		2197	4293	6490	SO:0001589	frameshift_variant	1464	exon3			.	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.3095delG	chr15.hg19:g.75980311delC	ENSP00000312506:p.Gly1033fs	114.0	0.0		130.0	10.0	NM_001897	D3DW77|Q92675	Frame_Shift_Del	DEL	ENST00000308508.5	hg19	CCDS10284.1																																																																																			.	.		0.647	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		-	75980311	C	-	75980311	7	5	103	1	0	1	0	1	0	0	0	0	3962	507	18	0	3905	0	CSPG4	15	75980311	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	287167	75980311	26551081	878	15501										
SGK269	79834	hgsc.bcm.edu	37	chr15	77472174	77472174	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttctgagccactgagccccTtttatgctctgtgctgtttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:77472174delT	ENST00000560626.2	-	4	2570	c.2095delA	c.(2095-2097)aggfs	p.R699fs	PEAK1_ENST00000312493.4_Frame_Shift_Del_p.R699fs|PEAK1_ENST00000558305.1_Frame_Shift_Del_p.R699fs			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	699					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ACTGAGCCCCTTTTATGCTCT	0.448																																					p.R699fs		Atlas-INDEL	.											.	.	.	.	0			c.2096delG						.						161	152	154					15																	77472174		1900	4133	6033	SO:0001589	frameshift_variant	0	exon5			.		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.2095delA	chr15.hg19:g.77472174delT	ENSP00000452796:p.Arg699fs	126.0	0.0		144.0	10.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Frame_Shift_Del	DEL	ENST00000560626.2	hg19	CCDS42062.1																																																																																			.	.		0.448	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			-	77472174	T	-	77472174	7	5	103	1	0	1	0	1	0	0	0	0	14226	1608	56	0	3161	0	SGK269	15	77472174	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1491863	77472174	25059218	879	15502										
ARNT2	9915	hgsc.bcm.edu	37	chr15	80867380	80867380	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgaggccgggaagtccgtggAaaaggcggatgcaatcttct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:80867380delA	ENST00000303329.4	+	14	1607	c.1442delA	c.(1441-1443)gaafs	p.E481fs	ARNT2_ENST00000527771.1_Frame_Shift_Del_p.E470fs|ARNT2_ENST00000533983.1_Frame_Shift_Del_p.E470fs	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	481					central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			AAGTCCGTGGAAAAGGCGGAT	0.478																																					p.E481fs		Atlas-INDEL	.											.	ARNT2	88	.	0			c.1441delG						.						177	171	173					15																	80867380		2203	4300	6503	SO:0001589	frameshift_variant	9915	exon14			.	AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"Basic helix-loop-helix proteins"	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.1442delA	chr15.hg19:g.80867380delA	ENSP00000307479:p.Glu481fs	124.0	0.0		165.0	10.0	NM_014862	B4DIS7|O15024|Q8IYC2	Frame_Shift_Del	DEL	ENST00000303329.4	hg19	CCDS32307.1																																																																																			.	.		0.478	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2			-	80867380	A	-	80867380	7	5	103	1	0	1	0	1	0	0	0	0	966	246	9	0	1496	0	ARNT2	15	80867380	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3395206	80867380	21664012	880	15503										
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81221438	81221438	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttggcgagagtggcaacgtGgggacggaaatgatggacaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:81221438delG	ENST00000394685.3	+	21	2954	c.2535delG	c.(2533-2535)gtgfs	p.V845fs	KIAA1199_ENST00000356249.5_Frame_Shift_Del_p.V845fs|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Frame_Shift_Del_p.V845fs			Q8WUJ3	CEMIP_HUMAN		845					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GTGGCAACGTGGGGACGGAAA	0.527																																					p.V845fs		Atlas-INDEL	.											.	KIAA1199	118	.	0			c.2534delT						.						140	132	135					15																	81221438		2203	4300	6503	SO:0001589	frameshift_variant	57214	exon20			.																												ENST00000394685.3:c.2535delG	chr15.hg19:g.81221438delG	ENSP00000378177:p.Val845fs	229.0	0.0		313.0	19.0	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Frame_Shift_Del	DEL	ENST00000394685.3	hg19	CCDS10315.1																																																																																			.	.		0.527	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			-	81221438	G	-	81221438	7	5	103	1	0	1	0	1	0	0	0	0	8222	1335	47	0	2609	0	KIAA1199	15	81221438	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	354058	81221438	21309954	881	15504										
TM6SF1	53346	hgsc.bcm.edu	37	chr15	83790732	83790732	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tattattatgagtgttgttgTttttgtgccaggaaacattg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:83790732delT	ENST00000322019.9	+	5	732	c.458delT	c.(457-459)gttfs	p.V153fs	TM6SF1_ENST00000565774.1_Frame_Shift_Del_p.V153fs|TM6SF1_ENST00000379386.4_Frame_Shift_Del_p.V156fs|TM6SF1_ENST00000379390.6_Frame_Shift_Del_p.V153fs			Q9BZW5	TM6S1_HUMAN	transmembrane 6 superfamily member 1	153						integral component of membrane (GO:0016021)				endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						AGTGTTGTTGTTTTTGTGCCA	0.318																																					p.V153fs		Atlas-INDEL	.											.	TM6SF1	38	.	0			c.457delG						.						254	242	246					15																	83790732		2203	4299	6502	SO:0001589	frameshift_variant	53346	exon5			.	AF255922	CCDS10323.1, CCDS45338.1	15q24-q26	2003-04-04			ENSG00000136404	ENSG00000136404			11860	protein-coding gene	gene with protein product		606562				11124529	Standard	NM_001144903		Approved		uc002bjp.3	Q9BZW5	OTTHUMG00000147365	ENST00000322019.9:c.458delT	chr15.hg19:g.83790732delT	ENSP00000317000:p.Val153fs	148.0	0.0		220.0	15.0	NM_001144903	A8K7T5|H3BU56|Q4U0U5	Frame_Shift_Del	DEL	ENST00000322019.9	hg19	CCDS10323.1																																																																																			.	.		0.318	TM6SF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000304009.1	NM_023003		-	83790732	T	-	83790732	7	5	103	1	0	1	0	1	0	0	0	0	15987	1725	60	0	476	0	TM6SF1	15	83790732	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2569294	83790732	18740660	882	15505										
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84592778	84592778	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctgtaacacagagccctgtCcccccaggtatgtgctgtct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:84592778delC	ENST00000286744.5	+	17	2334	c.2110delC	c.(2110-2112)cccfs	p.P705fs	ADAMTSL3_ENST00000567476.1_Frame_Shift_Del_p.P705fs	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	705	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AGAGCCCTGTCCCCCCAGGTA	0.547																																					p.C703fs		Atlas-INDEL	.											ADAMTSL3,mouth,carcinoma,0,1	ADAMTSL3	290	.	0			c.2109delT						.						101	70	81					15																	84592778		2203	4300	6503	SO:0001589	frameshift_variant	57188	exon17			.	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2110delC	chr15.hg19:g.84592778delC	ENSP00000286744:p.Pro705fs	156.0	0.0		172.0	11.0	NM_207517	A1A566|A1A567|Q9ULI7	Frame_Shift_Del	DEL	ENST00000286744.5	hg19	CCDS10326.1																																																																																			.	.		0.547	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		-	84592778	C	-	84592778	7	5	103	1	0	1	0	1	0	0	0	0	276	855	30	0	2172	0	ADAMTSL3	15	84592778	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	802046	84592778	17938614	883	15506										
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85438313	85438313	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaaagctgaggaggtttctCaagcctcagggccatccccg	11	14	2	1	rs371921369|rs2277576		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:85438313C>T	ENST00000286749.3	+	5	510	c.420C>T	c.(418-420)ctC>ctT	p.L140L	SLC28A1_ENST00000537624.1_Silent_p.L140L|SLC28A1_ENST00000394573.1_Silent_p.L140L|SLC28A1_ENST00000537703.1_Silent_p.L62L|SLC28A1_ENST00000538177.1_Silent_p.L140L|SLC28A1_ENST00000537216.1_Silent_p.L140L|SLC28A1_ENST00000338602.2_Silent_p.L140L			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	140			L -> LV (in A). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.L140L(2)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GGAGGTTTCTCAAGCCTCAGG	0.637																																					p.L140L		Atlas-SNP	.											SLC28A1_ENST00000338602,NS,carcinoma,0,1	SLC28A1	118	.	2	Substitution - coding silent(2)	lung(2)	c.C420T						.						45	47	47					15																	85438313		2203	4298	6501	SO:0001819	synonymous_variant	9154	exon6			GTTTCTCAAGCCT	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"Solute carriers"	11001	protein-coding gene	gene with protein product		606207	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.420C>T	chr15.hg19:g.85438313C>T		87.0	1.0		90.0	4.0	NM_201651	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	hg19	CCDS10334.1																																																																																			.	.		0.637	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			T	85438313	C	T	85438313	2	4	103	1	0	0	0	0	0	0	0	1	14546	813	29	3		3	SLC28A1	15	85438313	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	845535	85438313	17093079	884	15507										
AGBL1	123624	hgsc.bcm.edu	37	chr15	87089360	87089360	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatcctagaggaggtcaactAcagggtaagccgctgtgggg	15	8	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:87089360A>G	ENST00000441037.2	+	19	2770	c.2675A>G	c.(2674-2676)tAc>tGc	p.Y892C	AGBL1_ENST00000421325.2_Missense_Mutation_p.Y892C|AGBL1_ENST00000389298.3_Missense_Mutation_p.Y623C	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	892					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GAGGTCAACTACAGGGTAAGC	0.428																																					p.Y892C		Atlas-SNP	.											.	AGBL1	151	.	0			c.A2675G						.						72	67	68					15																	87089360		1972	4181	6153	SO:0001583	missense	123624	exon19			TCAACTACAGGGT	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2675A>G	chr15.hg19:g.87089360A>G	ENSP00000413001:p.Tyr892Cys	86.0	0.0		98.0	4.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	hg19	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.715038	0.48622	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.10763	2.84;2.84	5.38	5.38	0.77491	Peptidase M14, carboxypeptidase A (1);	0.000000	0.36167	U	0.002753	T	0.27765	0.0683	L	0.50333	1.59	0.45403	D	0.99838	D	0.89917	1.0	D	0.97110	1.0	T	0.00533	-1.1685	10	0.56958	D	0.05	-12.4782	14.7196	0.69297	1.0:0.0:0.0:0.0	.	892	Q96MI9	CBPC4_HUMAN	C	927;892;623	ENSP00000397173:Y892C;ENSP00000373949:Y623C	ENSP00000373949:Y623C	Y	+	2	0	AGBL1	84890364	1.000000	0.71417	1.000000	0.80357	0.136000	0.21042	8.322000	0.90000	2.264000	0.75181	0.533000	0.62120	TAC	.	.		0.428	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		G	87089360	A	G	87089360	3	3	103	1	0	0	0	0	1	0	0	0	375	391	14	2	2745	2	AGBL1	15	87089360	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1651047	87089360	15442032	885	15508										
FANCI	55215	hgsc.bcm.edu	37	chr15	89803947	89803947	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgtttaaaacaataaggttCcccctgctctgaggaagctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:89803947delC	ENST00000310775.7	+	4	247	c.161delC	c.(160-162)tccfs	p.S54fs	FANCI_ENST00000451393.2_5'UTR|FANCI_ENST00000300027.8_Frame_Shift_Del_p.S54fs|FANCI_ENST00000567996.1_Frame_Shift_Del_p.S54fs	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	54					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CAATAAGGTTCCCCCTGCTCT	0.398								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S54fs		Atlas-INDEL	.											.	FANCI	129	.	0			c.160delT						.		,	14,4250		6,2,2124	93	89	91		,	5.6	1	15		90	46,8208		23,0,4104	no	frameshift,frameshift	FANCI	NM_018193.2,NM_001113378.1	,	29,2,6228	A1A1,A1R,RR		0.5573,0.3283,0.4793	,	,	89803947	60,12458	2200	4299	6499	SO:0001589	frameshift_variant	55215	exon4	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.161delC	chr15.hg19:g.89803947delC	ENSP00000310842:p.Ser54fs	93.0	0.0		149.0	10.0	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Frame_Shift_Del	DEL	ENST00000310775.7	hg19	CCDS45346.1																																																																																			.	.		0.398	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		-	89803947	C	-	89803947	7	5	103	1	0	1	0	1	0	0	0	0	5677	855	30	0	171	0	FANCI	15	89803947	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2714587	89803947	12727445	886	15509										
FANCI	55215	hgsc.bcm.edu	37	chr15	89837107	89837107	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgagcttatttatgtgttacAaaaaactctctgacattctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:89837107delA	ENST00000310775.7	+	23	2421	c.2335delA	c.(2335-2337)aaafs	p.K780fs	FANCI_ENST00000300027.8_Frame_Shift_Del_p.K780fs	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	780					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					TATGTGTTACAAAAAACTCTC	0.343								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.Y778X		Atlas-INDEL	.											.	FANCI	129	.	0			c.2334delC						.						100	100	100					15																	89837107		2199	4299	6498	SO:0001589	frameshift_variant	55215	exon23	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.2335delA	chr15.hg19:g.89837107delA	ENSP00000310842:p.Lys780fs	102.0	0.0		180.0	11.0	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Frame_Shift_Del	DEL	ENST00000310775.7	hg19	CCDS45346.1																																																																																			.	.		0.343	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		-	89837107	A	-	89837107	7	5	103	1	0	1	0	1	0	0	0	0	5677	131	5	0	2421	0	FANCI	15	89837107	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	33160	89837107	12694285	887	15510										
PLIN1	5346	hgsc.bcm.edu	37	chr15	90210976	90210976	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgcacttcgctcctccgccGggacaccgcctgcatggcca					rs8179070	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:90210976delG	ENST00000300055.5	-	7	985	c.820delC	c.(820-822)cggfs	p.R276fs	PLIN1_ENST00000430628.2_Frame_Shift_Del_p.R276fs	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	276					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						CTCCTCCGCCGGGACACCGCC	0.667																																					p.R274fs		Atlas-INDEL	.											.	PLIN1	36	.	0			c.821delG						.						65	45	52					15																	90210976		2186	4280	6466	SO:0001589	frameshift_variant	5346	exon7			.	AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"Perilipins"	9076	protein-coding gene	gene with protein product		170290	"perilipin"	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.820delC	chr15.hg19:g.90210976delG	ENSP00000300055:p.Arg276fs	97.0	0.0		150.0	11.0	NM_001145311	Q8N5Y6	Frame_Shift_Del	DEL	ENST00000300055.5	hg19	CCDS10353.1																																																																																			.	.		0.667	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313424.2	NM_002666		-	90210976	G	-	90210976	7	5	103	1	0	1	0	1	0	0	0	0	12098	1115	39	0	760	0	PLIN1	15	90210976	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	373869	90210976	12320416	888	15511										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91009653	91009653	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atcttgctgaagccaagaagAaaaaactggcagtaggtgag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:91009653delA	ENST00000268182.5	+	17	2144	c.2020delA	c.(2020-2022)aaafs	p.K675fs	IQGAP1_ENST00000560738.1_Frame_Shift_Del_p.K103fs	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	675					cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AGCCAAGAAGAAAAAACTGGC	0.463																																					p.K673fs		Atlas-INDEL	.											.	IQGAP1	140	.	0			c.2019delG						.						75	64	68					15																	91009653		2198	4298	6496	SO:0001589	frameshift_variant	8826	exon17			.	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.2020delA	chr15.hg19:g.91009653delA	ENSP00000268182:p.Lys675fs	95.0	0.0		144.0	11.0	NM_003870	A7MBM3	Frame_Shift_Del	DEL	ENST00000268182.5	hg19	CCDS10362.1																																																																																			.	.		0.463	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		-	91009653	A	-	91009653	7	5	103	1	0	1	0	1	0	0	0	0	7823	247	9	0	2086	0	IQGAP1	15	91009653	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	798677	91009653	11521739	889	15512										
RCCD1	91433	hgsc.bcm.edu	37	chr15	91500927	91500927	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtcatggctgaggtggccgcGgggggctggcattctgtgtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:91500927delG	ENST00000394258.2	+	4	853	c.651delG	c.(649-651)gcgfs	p.A217fs	RCCD1_ENST00000556618.1_Frame_Shift_Del_p.A217fs|AC068831.6_ENST00000553321.1_RNA|RCCD1_ENST00000555155.1_Frame_Shift_Del_p.A217fs|RCCD1_ENST00000556774.1_Intron	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	217						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			AGGTGGCCGCGGGGGGCTGGC	0.597																																					p.A217fs		Atlas-INDEL	.											.	RCCD1	9	.	0			c.650delC						.						109	107	108					15																	91500927		2198	4298	6496	SO:0001589	frameshift_variant	91433	exon4			.		CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.651delG	chr15.hg19:g.91500927delG	ENSP00000377801:p.Ala217fs	136.0	0.0		174.0	16.0	NM_001017919	B2RTP9|Q29RX6	Frame_Shift_Del	DEL	ENST00000394258.2	hg19	CCDS32333.1																																																																																			.	.		0.597	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544		-	91500927	G	-	91500927	7	5	103	1	0	1	0	1	0	0	0	0	13190	1103	39	0	661	0	RCCD1	15	91500927	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	491274	91500927	11030465	890	15513										
CHD2	1106	hgsc.bcm.edu	37	chr15	93540530	93540530	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgcacattttgatgtagagtGgggggtggaagatgattctc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:93540530delG	ENST00000394196.4	+	30	4850	c.3782delG	c.(3781-3783)tggfs	p.W1261fs	CHD2_ENST00000557381.1_Frame_Shift_Del_p.W1261fs	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1261					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GATGTAGAGTGGGGGGTGGAA	0.413																																					p.W1261fs		Atlas-INDEL	.											.	CHD2	280	.	0			c.3781delT						.						139	138	138					15																	93540530		2197	4298	6495	SO:0001589	frameshift_variant	1106	exon30			.	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.3782delG	chr15.hg19:g.93540530delG	ENSP00000377747:p.Trp1261fs	142.0	0.0		170.0	12.0	NM_001271	C6G482|Q96IP5	Frame_Shift_Del	DEL	ENST00000394196.4	hg19	CCDS10374.2																																																																																			.	.		0.413	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		-	93540530	G	-	93540530	7	5	103	1	0	1	0	1	0	0	0	0	3327	1357	47	0	3900	0	CHD2	15	93540530	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2039603	93540530	8990862	891	15514										
MEF2A	4205	hgsc.bcm.edu	37	chr15	100252908	100252908	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctccaattgtgcttggccgaCccccaaacactgaggacaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:100252908delC	ENST00000557785.1	+	11	1775	c.1426delC	c.(1426-1428)cccfs	p.P477fs	MEF2A_ENST00000453228.2_Frame_Shift_Del_p.P477fs|MEF2A_ENST00000338042.6_Frame_Shift_Del_p.P486fs|MEF2A_ENST00000557942.1_Frame_Shift_Del_p.P485fs|MEF2A_ENST00000354410.5_Frame_Shift_Del_p.P479fs|LYSMD4_ENST00000604213.1_5'Flank|MEF2A_ENST00000449277.2_Frame_Shift_Del_p.P409fs|MEF2A_ENST00000558812.1_Frame_Shift_Del_p.P417fs	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	487					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			GCTTGGCCGACCCCCAAACAC	0.532																																					p.R477fs		Atlas-INDEL	.											.	MEF2A	138	.	0			c.1431delA						.						37	40	39					15																	100252908		2046	4187	6233	SO:0001589	frameshift_variant	4205	exon11			.		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"Myocyte enhancer factors"	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.1426delC	chr15.hg19:g.100252908delC	ENSP00000453441:p.Pro477fs	193.0	0.0		195.0	12.0	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Frame_Shift_Del	DEL	ENST00000557785.1	hg19	CCDS53978.1																																																																																			.	.		0.532	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1			-	100252908	C	-	100252908	7	5	103	1	0	1	0	1	0	0	0	0	9464	507	18	0	1630	0	MEF2A	15	100252908	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	6712378	100252908	2278484	892	15515										
TM2D3	80213	hgsc.bcm.edu	37	chr15	102190269	102190269	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggcttcccataggtacaggAgaaatttgttgtgcagtcta	11	7	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:102190269A>G	ENST00000333202.3	-	3	270	c.265T>C	c.(265-267)Tcc>Ccc	p.S89P	RNU6-807P_ENST00000516805.1_RNA|TM2D3_ENST00000561373.1_Missense_Mutation_p.S24P|TM2D3_ENST00000559107.1_Missense_Mutation_p.S89P|TM2D3_ENST00000347970.3_Missense_Mutation_p.S63P|TM2D3_ENST00000428002.2_Missense_Mutation_p.S63P	NM_078474.2	NP_510883.2	Q9BRN9	TM2D3_HUMAN	TM2 domain containing 3	89						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(6)|ovary(1)	10	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TAGGTACAGGAGAAATTTGTT	0.413																																					p.S89P		Atlas-SNP	.											.	TM2D3	18	.	0			c.T265C						.						117	104	108					15																	102190269		2203	4300	6503	SO:0001583	missense	80213	exon3			TACAGGAGAAATT	AK094955	CCDS10392.1, CCDS10393.1	15q26.3	2014-02-12			ENSG00000184277	ENSG00000184277			24128	protein-coding gene	gene with protein product		610014				11278849	Standard	XM_005254980		Approved	BLP2, FLJ22604	uc002bxi.3	Q9BRN9	OTTHUMG00000149872	ENST00000333202.3:c.265T>C	chr15.hg19:g.102190269A>G	ENSP00000330433:p.Ser89Pro	91.0	0.0		123.0	5.0	NM_078474	B2RDK9|Q9H046|Q9H651	Missense_Mutation	SNP	ENST00000333202.3	hg19	CCDS10393.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308257	0.81247	.	.	ENSG00000184277	ENST00000428002;ENST00000347970;ENST00000333202	T;T;T	0.74526	-0.85;-0.85;-0.85	5.53	5.53	0.82687	.	0.115201	0.64402	D	0.000010	D	0.84942	0.5584	M	0.76574	2.34	0.38091	D	0.936973	D;D;D;D	0.89917	0.999;1.0;0.979;0.997	D;D;P;P	0.74023	0.952;0.982;0.865;0.818	D	0.87949	0.2722	10	0.66056	D	0.02	-34.125	13.6005	0.62015	1.0:0.0:0.0:0.0	.	89;63;63;89	B4DKG4;E7EPS7;Q9BRN9-2;Q9BRN9	.;.;.;TM2D3_HUMAN	P	63;63;89	ENSP00000402179:S63P;ENSP00000327584:S63P;ENSP00000330433:S89P	ENSP00000330433:S89P	S	-	1	0	TM2D3	100007792	1.000000	0.71417	0.992000	0.48379	0.958000	0.62258	6.229000	0.72294	2.091000	0.63221	0.533000	0.62120	TCC	.	.		0.413	TM2D3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313623.1	NM_078474		G	102190269	A	G	102190269	3	3	103	1	0	0	0	0	1	0	0	0	15980	304	11	2	494	2	TM2D3	15	102190269	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1937361	102190269	341123	893	15516										
RHBDF1	64285	hgsc.bcm.edu	37	chr16	109097	109097	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgcaggacagtcatctggaAgcagatggacaccaggcagt	13	11	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:109097A>G	ENST00000262316.6	-	17	2165	c.2023T>C	c.(2023-2025)Ttc>Ctc	p.F675L		NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	675					cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				GTCATCTGGAAGCAGATGGAC	0.612																																					p.F675L		Atlas-SNP	.											.	RHBDF1	54	.	0			c.T2023C						.						37	36	36					16																	109097		2203	4300	6503	SO:0001583	missense	64285	exon17			TCTGGAAGCAGAT	BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"chromosome 16 open reading frame 8", "rhomboid family 1 (Drosophila)"	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.2023T>C	chr16.hg19:g.109097A>G	ENSP00000262316:p.Phe675Leu	77.0	0.0		82.0	4.0	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Missense_Mutation	SNP	ENST00000262316.6	hg19	CCDS32344.1	.	.	.	.	.	.	.	.	.	.	.	27.5	4.837917	0.91117	.	.	ENSG00000007384	ENST00000262316	T	0.13778	2.56	5.65	5.65	0.86999	Peptidase S54, rhomboid domain (1);	0.000000	0.85682	D	0.000000	T	0.25901	0.0631	L	0.42632	1.34	0.80722	D	1	P	0.42123	0.771	P	0.54460	0.753	T	0.00489	-1.1709	10	0.56958	D	0.05	-32.5993	15.069	0.72021	1.0:0.0:0.0:0.0	.	675	Q96CC6	RHDF1_HUMAN	L	675	ENSP00000262316:F675L	ENSP00000262316:F675L	F	-	1	0	RHBDF1	49097	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.502000	0.81614	2.163000	0.67991	0.533000	0.62120	TTC	.	.		0.612	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450		G	109097	A	G	109097	3	3	103	1	0	0	0	0	1	0	0	0	13334	72	3	2	552	2	RHBDF1	16	109097	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10		109097	90245656	894	15517										
MPG	4350	hgsc.bcm.edu	37	chr16	129299	129299	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacaacccacaggatggtcaCccccgctttgcagatgaaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:129299delC	ENST00000219431.4	+	2	239	c.8delC	c.(7-9)accfs	p.T3fs	MPG_ENST00000475280.1_Intron|MPG_ENST00000397817.1_Intron|RHBDF1_ENST00000454039.2_5'Flank	NM_002434.3	NP_002425.2	P29372	3MG_HUMAN	N-methylpurine-DNA glycosylase	3					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)	alkylbase DNA N-glycosylase activity (GO:0003905)|damaged DNA binding (GO:0003684)|DNA-3-methyladenine glycosylase activity (GO:0008725)|DNA-3-methylguanine glycosylase activity (GO:0052822)|DNA-7-methyladenine glycosylase activity (GO:0052821)|DNA-7-methylguanine glycosylase activity (GO:0043916)			endometrium(4)|kidney(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)				aggatggtcacccccgctttg	0.552								Base excision repair (BER), DNA glycosylases																													p.T3fs		Atlas-INDEL	.											.,1	MPG	26	.	0			c.7delA						.						112	95	101					16																	129299		2193	4294	6487	SO:0001589	frameshift_variant	4350	exon2			.		CCDS32345.1, CCDS32346.1, CCDS42087.1	16p13.3	2008-07-29			ENSG00000103152	ENSG00000103152	3.2.2.21		7211	protein-coding gene	gene with protein product	"alkyladenine DNA glycosylase"	156565				1874728	Standard	NM_002434		Approved	MDG	uc002cfo.4	P29372	OTTHUMG00000047887	ENST00000219431.4:c.8delC	chr16.hg19:g.129299delC	ENSP00000219431:p.Thr3fs	159.0	0.0		177.0	11.0	NM_002434	G5E9E2|Q13770|Q15275|Q15961|Q5J9I4|Q96BZ6|Q96S33|Q9NNX5	Frame_Shift_Del	DEL	ENST00000219431.4	hg19	CCDS32346.1																																																																																			.	.		0.552	MPG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109121.4			-	129299	C	-	129299	7	5	103	1	0	1	0	1	0	0	0	0	9733	507	18	0	38	0	MPG	16	129299	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	20202	129299	90225454	895	15518										
WDR90	197335	hgsc.bcm.edu	37	chr16	705305	705305	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctcagtcctcattccttgcAggatggcgtcgtgcgggcag	14	12	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:705305A>G	ENST00000293879.4	+	15	1556		c.e15-1		LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Splice_Site			Q96KV7	WDR90_HUMAN	WD repeat domain 90											endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CATTCCTTGCAGGATGGCGTC	0.706																																					.		Atlas-SNP	.											.	WDR90	107	.	0			c.1557-2A>G						.						23	32	29					16																	705305		2191	4285	6476	SO:0001630	splice_region_variant	197335	exon15			CCTTGCAGGATGG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.1557-1A>G	chr16.hg19:g.705305A>G		16.0	0.0		87.0	4.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Splice_Site	SNP	ENST00000293879.4	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.600321	0.28534	.	.	ENSG00000161996	ENST00000549091;ENST00000293879	.	.	.	4.67	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3099	0.60374	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WDR90	645306	1.000000	0.71417	0.878000	0.34440	0.069000	0.16628	5.788000	0.69020	1.753000	0.51906	0.459000	0.35465	.	.	.		0.706	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	Intron	G	705305	A	G	705305	5	3	103	1	0	0	0	0	0	0	1	0	17352	202	7	2	1613	2	WDR90	16	705305	Splice_Site	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	576006	705305	89649448	896	15519										
MEFV	4210	hgsc.bcm.edu	37	chr16	3306370	3306370	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctggttgatggcccgcaggAcctgcagggtgagctgcacg	17	11	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:3306370A>G	ENST00000219596.1	-	1	257	c.218T>C	c.(217-219)gTc>gCc	p.V73A	MEFV_ENST00000541159.1_Missense_Mutation_p.V73A|MEFV_ENST00000536379.1_Missense_Mutation_p.V73A|MEFV_ENST00000339854.4_Missense_Mutation_p.V73A	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	73	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GGCCCGCAGGACCTGCAGGGT	0.652																																					p.V73A		Atlas-SNP	.											.	MEFV	170	.	0			c.T218C						.						47	48	48					16																	3306370		2197	4300	6497	SO:0001583	missense	4210	exon1			CGCAGGACCTGCA	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.218T>C	chr16.hg19:g.3306370A>G	ENSP00000219596:p.Val73Ala	90.0	0.0		145.0	6.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	hg19	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.919875	0.73098	.	.	ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000541159;ENST00000536379;ENST00000534868	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	5.98	5.98	0.97165	Pyrin (2);DEATH-like (2);	0.573434	0.15698	N	0.249041	T	0.67202	0.2868	M	0.64404	1.975	0.23440	N	0.997672	D	0.63046	0.992	P	0.61328	0.887	T	0.62599	-0.6820	10	0.87932	D	0	-17.3031	12.8496	0.57850	1.0:0.0:0.0:0.0	.	73	O15553	MEFV_HUMAN	A	73	ENSP00000219596:V73A;ENSP00000339639:V73A;ENSP00000438711:V73A;ENSP00000445079:V73A	ENSP00000219596:V73A	V	-	2	0	MEFV	3246371	0.985000	0.35326	1.000000	0.80357	0.607000	0.37147	3.228000	0.51270	2.288000	0.76882	0.482000	0.46254	GTC	.	.		0.652	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		G	3306370	A	G	3306370	3	3	103	1	0	0	0	0	1	0	0	0	9468	275	10	2	2167	2	MEFV	16	3306370	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2601065	3306370	87048383	897	15520										
TRAP1	10131	hgsc.bcm.edu	37	chr16	3708188	3708188	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcggcccaccatggccctaGggtcgtcaacaagtccagca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:3708188delG	ENST00000246957.5	-	18	2145	c.2057delC	c.(2056-2058)cctfs	p.P686fs	DNASE1_ENST00000414110.2_Intron|TRAP1_ENST00000538171.1_Frame_Shift_Del_p.P633fs|TRAP1_ENST00000575671.1_Frame_Shift_Del_p.P477fs	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	686					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				CATGGCCCTAGGGTCGTCAAC	0.547																																					p.P686fs		Atlas-INDEL	.											.	TRAP1	53	.	0			c.2058delT						.						60	57	58					16																	3708188		2197	4300	6497	SO:0001589	frameshift_variant	10131	exon18			.	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"Heat shock proteins / HSPC"	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.2057delC	chr16.hg19:g.3708188delG	ENSP00000246957:p.Pro686fs	112.0	0.0		141.0	10.0	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Frame_Shift_Del	DEL	ENST00000246957.5	hg19	CCDS10508.1																																																																																			.	.		0.547	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292		-	3708188	G	-	3708188	7	5	103	1	0	1	0	1	0	0	0	0	16470	1000	35	0	61	0	TRAP1	16	3708188	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	401818	3708188	86646565	898	15521										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3777763	3777763	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tagcgtgtcccccgtggtgtCcccgaccagggacagttcgc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:3777763delC	ENST00000262367.5	-	31	8094	c.7285delG	c.(7285-7287)gacfs	p.D2429fs	CREBBP_ENST00000382070.3_Frame_Shift_Del_p.D2391fs	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2429					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CCCGTGGTGTCCCCGACCAGG	0.552			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.D2429fs		Atlas-INDEL	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.7286delA						.						102	104	103					16																	3777763		2197	4300	6497	SO:0001589	frameshift_variant	1387	exon31			.	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.7285delG	chr16.hg19:g.3777763delC	ENSP00000262367:p.Asp2429fs	83.0	0.0		121.0	11.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Frame_Shift_Del	DEL	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.		0.552	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		-	3777763	C	-	3777763	7	5	103	1	0	1	0	1	0	0	0	0	3863	855	30	0	47	0	CREBBP	16	3777763	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	69575	3777763	86576990	899	15522										
TIMM16	51025	hgsc.bcm.edu	37	chr16	4391385	4391385	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcaccttctggacctcctcaGggctcagcttggacacgttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:4391385delG	ENST00000318059.3	-	3	346	c.209delC	c.(208-210)cctfs	p.P70fs	PAM16_ENST00000576217.1_Frame_Shift_Del_p.P70fs|PAM16_ENST00000573553.1_Frame_Shift_Del_p.P90fs|CORO7-PAM16_ENST00000572274.1_5'UTR|PAM16_ENST00000577031.1_Frame_Shift_Del_p.P70fs|CORO7-PAM16_ENST00000572467.1_Frame_Shift_Del_p.P993fs|PAM16_ENST00000571941.1_Frame_Shift_Del_p.P90fs|PAM16_ENST00000575848.1_Frame_Shift_Del_p.P82fs	NM_016069.9	NP_057153.8	Q9Y3D7	TIM16_HUMAN	presequence translocase-associated motor 16 homolog (S. cerevisiae)	70	J-like.				cellular protein metabolic process (GO:0044267)|protein import into mitochondrial matrix (GO:0030150)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane presequence translocase complex (GO:0005744)				lung(3)	3						GACCTCCTCAGGGCTCAGCTT	0.652																																					p.P993fs		Atlas-INDEL	.											.	.	.	.	0			c.2979delT						.						34	29	30					16																	4391385		2179	4294	6473	SO:0001589	frameshift_variant	100529144	exon29			.	AK026514	CCDS10512.1	16p13.3	2010-10-12	2010-10-12		ENSG00000217930	ENSG00000217930			29679	protein-coding gene	gene with protein product	"mitochondria associated protein involved in granulocyte macrophage colony stimulating factor signal transduction"	614336				10810093, 11750097	Standard	NM_016069		Approved	Magmas, Tim16, TIMM16		Q9Y3D7	OTTHUMG00000129466	ENST00000318059.3:c.209delC	chr16.hg19:g.4391385delG	ENSP00000315693:p.Pro70fs	194.0	0.0		202.0	15.0	NM_001201479	Q6I9Z3|Q9H5X3	Frame_Shift_Del	DEL	ENST00000318059.3	hg19	CCDS10512.1																																																																																			.	.		0.652	PAM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251629.2	NM_016069		-	4391385	G	-	4391385	7	5	103	1	0	1	0	1	0	0	0	0	15922	1000	35	0	180	0	TIMM16	16	4391385	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	613622	4391385	85963368	900	15523										
ZC3H7A	29066	hgsc.bcm.edu	37	chr16	11868316	11868316	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcacttccaacttcatgagAaaaactgggtgccggtaaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:11868316delA	ENST00000396516.2	-	8	876	c.679delT	c.(679-681)tctfs	p.S227fs	ZC3H7A_ENST00000355758.4_Frame_Shift_Del_p.S227fs|ZC3H7A_ENST00000575170.1_5'Flank			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	227						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						ACTTCATGAGAAAAACTGGGT	0.448																																					p.S227fs		Atlas-INDEL	.											.	ZC3H7A	72	.	0			c.680delC						.						87	86	86					16																	11868316		2197	4300	6497	SO:0001589	frameshift_variant	29066	exon9			.	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30959	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 7", "zinc finger CCCH-type containing 7"	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.679delT	chr16.hg19:g.11868316delA	ENSP00000379773:p.Ser227fs	84.0	0.0		112.0	11.0	NM_014153	D3DUG5|Q9NPE9	Frame_Shift_Del	DEL	ENST00000396516.2	hg19	CCDS10550.1																																																																																			.	.		0.448	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153		-	11868316	A	-	11868316	7	5	103	1	0	1	0	1	0	0	0	0	17587	246	9	0	2296	0	ZC3H7A	16	11868316	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	7476931	11868316	78486437	901	15524										
KIAA0430	9665	hgsc.bcm.edu	37	chr16	15705583	15705583	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcagacgtttggagcccatTccaagaatctgcaaagcaaa	9	10	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:15705583T>C	ENST00000396368.3	-	18	3689	c.3483A>G	c.(3481-3483)ggA>ggG	p.G1161G	KIAA0430_ENST00000602337.1_Silent_p.G1158G|KIAA0430_ENST00000551742.1_Silent_p.G1161G|KIAA0430_ENST00000344181.3_Silent_p.G763G|CTB-193M12.1_ENST00000549756.1_RNA|KIAA0430_ENST00000548025.1_Silent_p.G1158G|KIAA0430_ENST00000540441.2_Silent_p.G996G	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	1161	HTH OST-type 3. {ECO:0000255|PROSITE- ProRule:PRU00975}.				double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						TGGAGCCCATTCCAAGAATCT	0.488																																					p.G1161G		Atlas-SNP	.											.	KIAA0430	154	.	0			c.A3483G						.						71	70	70					16																	15705583		1914	4125	6039	SO:0001819	synonymous_variant	9665	exon18			GCCCATTCCAAGA	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29562	protein-coding gene	gene with protein product	"limkain b1", "protein phosphatase 1, regulatory subunit 34", "meiosis arrest female 1"	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.3483A>G	chr16.hg19:g.15705583T>C		78.0	0.0		112.0	5.0	NM_001184998	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Silent	SNP	ENST00000396368.3	hg19	CCDS10562.2																																																																																			.	.		0.488	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647		C	15705583	T	C	15705583	2	2	103	1	0	0	0	0	0	0	0	1	8186	1770	62	2		2	KIAA0430	16	15705583	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3837267	15705583	74649170	902	15525										
OTOA	146183	hgsc.bcm.edu	37	chr16	21742178	21742178	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	actccctcagcactggacagCcgagaccacgaaggacttgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:21742178delC	ENST00000286149.4	+	20	2271	c.2270delC	c.(2269-2271)gccfs	p.A757fs	OTOA_ENST00000388956.4_Frame_Shift_Del_p.A664fs|OTOA_ENST00000388958.3_Frame_Shift_Del_p.A743fs|OTOA_ENST00000388957.3_Frame_Shift_Del_p.A419fs			Q7RTW8	OTOAN_HUMAN	otoancorin	757					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CACTGGACAGCCGAGACCACG	0.448																																					p.A743fs		Atlas-INDEL	.											.	OTOA	144	.	0			c.2227delG						.						102	81	88					16																	21742178		2195	4271	6466	SO:0001589	frameshift_variant	146183	exon20			.	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.2270delC	chr16.hg19:g.21742178delC	ENSP00000286149:p.Ala757fs	154.0	0.0		153.0	10.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Frame_Shift_Del	DEL	ENST00000286149.4	hg19																																																																																				.	.		0.448	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			-	21742178	C	-	21742178	7	5	103	1	0	1	0	1	0	0	0	0	11311	739	26	0	2352	0	OTOA	16	21742178	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	6036595	21742178	68612575	903	15526										
PLK1	5347	hgsc.bcm.edu	37	chr16	23695373	23695373	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attgctcccagcagcctggaCcccagcaaccggaagcccct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:23695373delC	ENST00000300093.4	+	5	1110	c.999delC	c.(997-999)gacfs	p.D333fs	CTD-2196E14.5_ENST00000566143.1_RNA	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	333					activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		GCAGCCTGGACCCCAGCAACC	0.547																																					p.D333fs	Colon(12;240 564 27038 33155)	Atlas-INDEL	.											.	PLK1	67	.	0			c.998delA						.						103	108	107					16																	23695373		2197	4300	6497	SO:0001589	frameshift_variant	5347	exon5			.		CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"polo-like kinase (Drosophila)"	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.999delC	chr16.hg19:g.23695373delC	ENSP00000300093:p.Asp333fs	115.0	0.0		153.0	10.0	NM_005030	Q15153|Q99746	Frame_Shift_Del	DEL	ENST00000300093.4	hg19	CCDS10616.1																																																																																			.	.		0.547	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		-	23695373	C	-	23695373	7	5	103	1	0	1	0	1	0	0	0	0	12103	506	18	0	1017	0	PLK1	16	23695373	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1953195	23695373	66659380	904	15527										
RBBP6	5930	hgsc.bcm.edu	37	chr16	24560285	24560285	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaagtcgaactgaaccagcgAtggcaactacaaaagcagta	10	9	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:24560285A>G	ENST00000319715.4	+	3	718	c.286A>G	c.(286-288)Atg>Gtg	p.M96V	RBBP6_ENST00000348022.2_Missense_Mutation_p.M96V|RBBP6_ENST00000452655.2_Missense_Mutation_p.M96V|RBBP6_ENST00000381039.3_Missense_Mutation_p.M96V	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	96					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TGAACCAGCGATGGCAACTAC	0.279																																					p.M96V		Atlas-SNP	.											.	RBBP6	158	.	0			c.A286G						.						101	87	92					16																	24560285		2197	4298	6495	SO:0001583	missense	5930	exon3			CCAGCGATGGCAA		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.286A>G	chr16.hg19:g.24560285A>G	ENSP00000317872:p.Met96Val	44.0	0.0		59.0	4.0	NM_018703	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	hg19	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.507309	0.27036	.	.	ENSG00000122257	ENST00000381039;ENST00000452655;ENST00000319715;ENST00000348022	T;T;T;T	0.40476	2.41;1.03;2.67;2.67	5.25	5.25	0.73442	.	0.303560	0.40144	N	0.001171	T	0.30727	0.0774	N	0.19112	0.55	0.37471	D	0.915612	B;B;B;B	0.18610	0.004;0.029;0.017;0.002	B;B;B;B	0.21546	0.002;0.035;0.016;0.003	T	0.16660	-1.0395	10	0.28530	T	0.3	-16.8275	15.4517	0.75279	1.0:0.0:0.0:0.0	.	96;96;96;96	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9;Q7Z6E9-3	.;.;RBBP6_HUMAN;.	V	96	ENSP00000370427:M96V;ENSP00000390537:M96V;ENSP00000317872:M96V;ENSP00000316291:M96V	ENSP00000317872:M96V	M	+	1	0	RBBP6	24467786	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.099000	0.76981	2.115000	0.64714	0.477000	0.44152	ATG	.	.		0.279	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		G	24560285	A	G	24560285	3	3	103	1	0	0	0	0	1	0	0	0	13118	333	12	2	296	2	RBBP6	16	24560285	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	864912	24560285	65794468	905	15528										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24826473	24826473	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttcttcccttgttaggtgctAtttcaagtggtttcaggctg	10	8	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:24826473A>C	ENST00000395799.3	+	19	4807	c.4678A>C	c.(4678-4680)Att>Ctt	p.I1560L	CTD-2515A14.1_ENST00000568895.1_RNA|TNRC6A_ENST00000432286.2_Missense_Mutation_p.I38L|TNRC6A_ENST00000315183.7_Missense_Mutation_p.I1511L	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1560					cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		GTTAGGTGCTATTTCAAGTGG	0.383																																					p.I1560L		Atlas-SNP	.											.	TNRC6A	171	.	0			c.A4678C						.						141	133	136					16																	24826473		2197	4300	6497	SO:0001583	missense	27327	exon19			GGTGCTATTTCAA	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.4678A>C	chr16.hg19:g.24826473A>C	ENSP00000379144:p.Ile1560Leu	178.0	0.0		212.0	60.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.6|20.6	4.010138|4.010138	0.75046|0.75046	.|.	.|.	ENSG00000090905|ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286|ENST00000450465	T;T|.	0.13089|.	2.66;2.62|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.125092|.	0.64402|.	D|.	0.000005|.	T|T	0.72358|0.72358	0.3450|0.3450	M|M	0.64997|0.64997	1.995|1.995	0.54753|0.54753	D|D	0.999982|0.999982	B;B;B;P|.	0.39480|.	0.194;0.003;0.028;0.675|.	B;B;B;B|.	0.35413|.	0.107;0.01;0.047;0.202|.	T|T	0.71144|0.71144	-0.4678|-0.4678	10|5	0.51188|.	T|.	0.08|.	-12.8497|-12.8497	16.3631|16.3631	0.83280|0.83280	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	227;699;1511;1560|.	B3KSX2;C9JA83;Q8NDV7-6;Q8NDV7|.	.;.;.;TNR6A_HUMAN|.	L|S	1511;1560;38|450	ENSP00000326900:I1511L;ENSP00000379144:I1560L|.	ENSP00000326900:I1511L|.	I|Y	+|+	1|2	0|0	TNRC6A|TNRC6A	24733974|24733974	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.975000|7.975000	0.88055|0.88055	2.266000|2.266000	0.75297|0.75297	0.533000|0.533000	0.62120|0.62120	ATT|TAT	.	.		0.383	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		C	24826473	A	C	24826473	3	2	103	1	0	0	0	0	1	0	0	0	16355	449	16	5	4752	5	TNRC6A	16	24826473	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	266188	24826473	65528280	906	15529										
HS3ST4	9951	hgsc.bcm.edu	37	chr16	25704315	25704315	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgtcagcacccccgactatGgggagaagaagctgccacag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:25704315delG	ENST00000331351.5	+	1	969	c.577delG	c.(577-579)gggfs	p.G193fs		NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	193					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		CCCCGACTATGGGGAGAAGAA	0.701																																					p.Y192X		Atlas-INDEL	.											.	HS3ST4	120	.	0			c.576delT						.						11	17	15					16																	25704315		1966	4115	6081	SO:0001589	frameshift_variant	9951	exon1			.	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"Sulfotransferases, membrane-bound"	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.577delG	chr16.hg19:g.25704315delG	ENSP00000330606:p.Gly193fs	94.0	0.0		146.0	10.0	NM_006040	Q5QI42|Q8NDC2	Frame_Shift_Del	DEL	ENST00000331351.5	hg19	CCDS53995.1																																																																																			.	.		0.701	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		-	25704315	G	-	25704315	7	5	103	1	0	1	0	1	0	0	0	0	7376	1348	47	0	579	0	HS3ST4	16	25704315	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	877842	25704315	64650438	907	15530										
MAZ	4150	hgsc.bcm.edu	37	chr16	29821464	29821464	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcggcagcagcggcagcagTagcagcccctcccacagctg	13	16	0	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:29821464T>C	ENST00000322945.6	+	5	1511	c.1346T>C	c.(1345-1347)gTa>gCa	p.V449A	AC009133.14_ENST00000563806.1_RNA|AC009133.14_ENST00000569981.1_RNA|PRRT2_ENST00000358758.7_5'Flank|MAZ_ENST00000568282.1_3'UTR|MAZ_ENST00000563402.1_Silent_p.S105S|PRRT2_ENST00000300797.6_5'Flank|AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000568544.1_Missense_Mutation_p.V50A|MAZ_ENST00000566906.2_Silent_p.S103S|PRRT2_ENST00000567659.1_5'Flank|MAZ_ENST00000545521.1_Missense_Mutation_p.V426A|MAZ_ENST00000562337.1_Missense_Mutation_p.V144A|MAZ_ENST00000219782.6_3'UTR|AC009133.20_ENST00000569039.1_RNA	NM_002383.2	NP_002374.2	P56270	MAZ_HUMAN	MYC-associated zinc finger protein (purine-binding transcription factor)	449	Poly-Ala.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|termination of RNA polymerase II transcription (GO:0006369)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						gcggcagcagtagcagcCCCT	0.672																																					p.V449A	Colon(72;875 1167 15364 30899 37091)	Atlas-SNP	.											.,1	MAZ	48	.	0			c.T1346C						.						10	15	13					16																	29821464		1943	4046	5989	SO:0001583	missense	4150	exon5			CAGCAGTAGCAGC	M93339	CCDS42143.1, CCDS42144.1, CCDS61902.1, CCDS61903.1	16p11.2	2013-01-08			ENSG00000103495	ENSG00000103495		"Zinc fingers, C2H2-type"	6914	protein-coding gene	gene with protein product		600999				1567856, 1502157	Standard	NM_001276275		Approved	ZF87, Pur-1, Zif87, ZNF801	uc002dtx.4	P56270	OTTHUMG00000132119	ENST00000322945.6:c.1346T>C	chr16.hg19:g.29821464T>C	ENSP00000313362:p.Val449Ala	25.0	0.0		65.0	5.0	NM_002383	A8QJL9|C6G496|G5E927|H3BQD6|Q15703|Q8NFN7|Q99443	Missense_Mutation	SNP	ENST00000322945.6	hg19	CCDS42143.1	.	.	.	.	.	.	.	.	.	.	T	9.414	1.081337	0.20309	.	.	ENSG00000103495	ENST00000545521;ENST00000322945;ENST00000544343	T;T	0.08807	3.11;3.05	3.91	3.91	0.45181	.	.	.	.	.	T	0.12561	0.0305	N	0.14661	0.345	0.80722	D	1	P;D;P	0.61697	0.924;0.99;0.924	P;D;P	0.70935	0.857;0.971;0.857	T	0.08229	-1.0732	9	0.72032	D	0.01	.	9.4274	0.38588	0.0:0.0:0.0:1.0	.	426;224;449	C6G496;F5H7A6;P56270	.;.;MAZ_HUMAN	A	426;449;224	ENSP00000443956:V426A;ENSP00000313362:V449A	ENSP00000313362:V449A	V	+	2	0	MAZ	29728965	0.628000	0.27138	1.000000	0.80357	0.417000	0.31264	1.133000	0.31430	2.008000	0.58898	0.454000	0.30748	GTA	.	.		0.672	MAZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435536.1	NM_002383		C	29821464	T	C	29821464	3	2	103	1	0	0	0	0	1	0	0	0	9349	1638	57	2	1571	2	MAZ	16	29821464	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4117149	29821464	60533289	908	15531										
KCTD13	253980	hgsc.bcm.edu	37	chr16	29922397	29922397	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaccagcagcagatctcgtCccccaggacatccttgagga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:29922397delC	ENST00000568000.1	-	5	1656	c.655delG	c.(655-657)gacfs	p.D219fs		NM_178863.3	NP_849194.1	Q8WZ19	BACD1_HUMAN	potassium channel tetramerization domain containing 13	219					cell migration (GO:0016477)|DNA replication (GO:0006260)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of DNA replication (GO:0045740)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)	GTP-Rho binding (GO:0017049)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	7						CAGATCTCGTCCCCCAGGACA	0.562																																					p.D219fs		Atlas-INDEL	.											.	KCTD13	19	.	0			c.656delA						.						85	71	76					16																	29922397		2197	4300	6497	SO:0001589	frameshift_variant	253980	exon5			.	AF289573	CCDS10661.1	16p11.2	2013-06-20	2013-06-20		ENSG00000174943	ENSG00000174943			22234	protein-coding gene	gene with protein product	"polymerase delta-interacting protein 1", "TNFAIP1-like"	608947	"potassium channel tetramerisation domain containing 13"			11593007	Standard	NM_178863		Approved	PDIP1, FKSG86, POLDIP1	uc002duv.4	Q8WZ19	OTTHUMG00000132120	ENST00000568000.1:c.655delG	chr16.hg19:g.29922397delC	ENSP00000455785:p.Asp219fs	144.0	0.0		170.0	12.0	NM_178863	A8K0R5|Q96P93|Q96SA1	Frame_Shift_Del	DEL	ENST00000568000.1	hg19	CCDS10661.1																																																																																			.	.		0.562	KCTD13-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255162.2	NM_178863		-	29922397	C	-	29922397	7	5	103	1	0	1	0	1	0	0	0	0	8109	855	30	0	342	0	KCTD13	16	29922397	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	100933	29922397	60432356	909	15532										
TAOK2	9344	hgsc.bcm.edu	37	chr16	29998911	29998911	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgcagggctgtggggctgtGggggaccggggtctgtttgc					rs200539809		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:29998911delG	ENST00000308893.4	+	16	4361	c.3318delG	c.(3316-3318)gtgfs	p.V1106fs	TAOK2_ENST00000543033.1_Frame_Shift_Del_p.V993fs|TAOK2_ENST00000416441.2_Frame_Shift_Del_p.V933fs|TAOK2_ENST00000279394.3_Intron	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	1106					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						GTGGGGCTGTGGGGGACCGGG	0.697																																					p.V1106fs		Atlas-INDEL	.											.	TAOK2	142	.	0			c.3317delT						.						52	61	58					16																	29998911		2197	4299	6496	SO:0001589	frameshift_variant	9344	exon16			.	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.3318delG	chr16.hg19:g.29998911delG	ENSP00000310094:p.Val1106fs	104.0	0.0		179.0	13.0	NM_016151	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Frame_Shift_Del	DEL	ENST00000308893.4	hg19	CCDS10663.1																																																																																			.	.		0.697	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151		-	29998911	G	-	29998911	7	5	103	1	0	1	0	1	0	0	0	0	15563	1335	47	0	3376	0	TAOK2	16	29998911	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	76514	29998911	60355842	910	15533										
ZNF689	115509	hgsc.bcm.edu	37	chr16	30615727	30615727	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgaggcaggggaaaggcttcTcccccgtgtgcagcagctgg	16	12	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:30615727T>C	ENST00000287461.3	-	3	1698	c.1361A>G	c.(1360-1362)gAg>gGg	p.E454G	RP11-146F11.5_ENST00000563540.1_RNA|ZNF689_ENST00000566673.1_5'Flank	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	454					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			GAAAGGCTTCTCCCCCGTGTG	0.647																																					p.E454G		Atlas-SNP	.											.	ZNF689	48	.	0			c.A1361G						.						33	27	29					16																	30615727		2197	4300	6497	SO:0001583	missense	115509	exon3			GGCTTCTCCCCCG	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"Zinc fingers, C2H2-type", "-"	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.1361A>G	chr16.hg19:g.30615727T>C	ENSP00000287461:p.Glu454Gly	71.0	0.0		168.0	7.0	NM_138447	Q658J5	Missense_Mutation	SNP	ENST00000287461.3	hg19	CCDS10686.1	.	.	.	.	.	.	.	.	.	.	t	15.02	2.708418	0.48517	.	.	ENSG00000156853	ENST00000287461;ENST00000443190	T	0.27557	1.66	4.52	4.52	0.55395	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000135	T	0.39860	0.1094	M	0.67625	2.065	0.41007	D	0.984979	P	0.36909	0.573	B	0.43680	0.427	T	0.45011	-0.9290	10	0.87932	D	0	-21.9359	12.5088	0.55995	0.0:0.0:0.0:1.0	.	454	Q96CS4	ZN689_HUMAN	G	454	ENSP00000287461:E454G	ENSP00000287461:E454G	E	-	2	0	ZNF689	30523228	0.586000	0.26782	1.000000	0.80357	0.165000	0.22458	1.714000	0.37961	2.272000	0.75746	0.524000	0.50904	GAG	.	.		0.647	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		C	30615727	T	C	30615727	3	2	103	1	0	0	0	0	1	0	0	0	18109	1551	54	2	145	2	ZNF689	16	30615727	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	616816	30615727	59739026	911	15534										
ZNF629	23361	hgsc.bcm.edu	37	chr16	30795213	30795213	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcagatgtagggcttctccgCccccgccgggcggccctgca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:30795213delC	ENST00000262525.4	-	3	643	c.436delG	c.(436-438)gcgfs	p.A146fs		NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			GGCTTCTCCGCCCCCGCCGGG	0.697																																					p.A146fs		Atlas-INDEL	.											.	ZNF629	44	.	0			c.437delC						.						17	19	18					16																	30795213		2187	4293	6480	SO:0001589	frameshift_variant	23361	exon3			.	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"Zinc fingers, C2H2-type"	29008	protein-coding gene	gene with protein product			"zinc finger protein 65"	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.436delG	chr16.hg19:g.30795213delC	ENSP00000262525:p.Ala146fs	28.0	0.0		139.0	10.0	NM_001080417	Q15938	Frame_Shift_Del	DEL	ENST00000262525.4	hg19	CCDS45463.1																																																																																			.	.		0.697	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		-	30795213	C	-	30795213	7	5	103	1	0	1	0	1	0	0	0	0	18068	739	26	0	2177	0	ZNF629	16	30795213	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	179486	30795213	59559540	912	15535										
STX1B	112755	hgsc.bcm.edu	37	chr16	31012910	31012910	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggaccacctcctcttcatcAtcactgtctttcgcctgggg	8	15	5	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:31012910A>G	ENST00000215095.5	-	2	276	c.45T>C	c.(43-45)gaT>gaC	p.D15D	STX1B_ENST00000565419.1_Silent_p.D15D	NM_052874.3	NP_443106.1	P61266	STX1B_HUMAN	syntaxin 1B	15					intracellular protein transport (GO:0006886)|neurotransmitter transport (GO:0006836)|regulation of exocytosis (GO:0017157)|regulation of gene expression (GO:0010468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|large_intestine(5)|lung(5)	13						CCTCTTCATCATCACTGTCTT	0.617																																					p.D15D		Atlas-SNP	.											.	STX1B	26	.	0			c.T45C						.						73	63	67					16																	31012910		2197	4300	6497	SO:0001819	synonymous_variant	112755	exon2			TTCATCATCACTG	AY028792	CCDS10699.1	16p12-p11	2008-02-05	2007-06-20	2007-06-20	ENSG00000099365	ENSG00000099365			18539	protein-coding gene	gene with protein product		601485	"syntaxin 1B1", "syntaxin 1B2"	STX1B1, STX1B2			Standard	NM_052874		Approved		uc010cad.2	P61266	OTTHUMG00000132391	ENST00000215095.5:c.45T>C	chr16.hg19:g.31012910A>G		72.0	0.0		84.0	4.0	NM_052874	Q15531|Q2VPS2	Silent	SNP	ENST00000215095.5	hg19	CCDS10699.1																																																																																			.	.		0.617	STX1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255521.2			G	31012910	A	G	31012910	2	3	103	1	0	0	0	0	0	0	0	1	15359	214	8	2		2	STX1B	16	31012910	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	217697	31012910	59341843	913	15536										
PRSS53	339105	hgsc.bcm.edu	37	chr16	31098992	31098992	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgttgccctcctgaggcttGggggggccggggccacgctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:31098992delG	ENST00000280606.6	-	3	261	c.108delC	c.(106-108)cccfs	p.P36fs	RP11-196G11.1_ENST00000529564.1_Frame_Shift_Del_p.P111fs	NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	36	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						CCTGAGGCTTGGGGGGGCCGG	0.647																																					p.K37fs		Atlas-INDEL	.											.,1	PRSS53	29	.	0			c.109delA						.						21	26	25					16																	31098992		2009	4177	6186	SO:0001589	frameshift_variant	339105	exon3			.		CCDS42153.1	16p11.2	2010-05-07			ENSG00000151006	ENSG00000151006		"Serine peptidases / Serine peptidases"	34407	protein-coding gene	gene with protein product	"polyserase 3"	610561				16566820	Standard	NM_001039503		Approved	POL3S	uc002eaq.3	Q2L4Q9	OTTHUMG00000047358	ENST00000280606.6:c.108delC	chr16.hg19:g.31098992delG	ENSP00000280606:p.Pro36fs	114.0	0.0		128.0	11.0	NM_001039503		Frame_Shift_Del	DEL	ENST00000280606.6	hg19	CCDS42153.1																																																																																			.	.		0.647	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268		-	31098992	G	-	31098992	7	5	103	1	0	1	0	1	0	0	0	0	12644	1335	47	0	1589	0	PRSS53	16	31098992	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	86082	31098992	59255761	914	15537										
FUS	2521	hgsc.bcm.edu	37	chr16	31202283	31202283	+	Splice_Site	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atcttgtttcttttgtcctaGggggtaactacggggatgat					rs35711706		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:31202283delG	ENST00000254108.7	+	14	1498		c.e14-1		FUS_ENST00000380244.3_Splice_Site|FUS_ENST00000474990.1_Splice_Site|FUS_ENST00000568685.1_Splice_Site	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein						cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		TTTTGTCCTAGGGGGTAACTA	0.587			T	"DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"	"liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"																																.		Atlas-INDEL	.		Dom	yes		16	16p11.2	2521	"fusion, derived from t(12;16) malignant liposarcoma"		"M, L"	.	FUS	52	.	0			c.1382-2G>-						.						64	76	72					16																	31202283		2197	4300	6497	SO:0001630	splice_region_variant	2521	exon14			.	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"RNA binding motif (RRM) containing"	4010	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein P2", "translocated in liposarcoma"	137070	"fusion, derived from t(12;16) malignant liposarcoma", "amyotrophic lateral sclerosis 6", "fusion (involved in t(12;16) in malignant liposarcoma)", "fused in sarcoma"	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.1394-1G>-	chr16.hg19:g.31202283delG		110.0	0.0		134.0	10.0	NM_001170937	Q9H4A8	Splice_Site	DEL	ENST00000254108.7	hg19	CCDS10707.1																																																																																			.	.		0.587	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	Intron	-	31202283	G	-	31202283	8	5	103	1	0	1	0	1	0	0	1	0	6108	1014	35	0	1447	0	FUS	16	31202283	Splice_Site	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	103291	31202283	59152470	915	15538										
LONP2	83752	hgsc.bcm.edu	37	chr16	48295434	48295434	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgacattgtcatgctagagAaaaaaatacgaacatctagt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:48295434delA	ENST00000285737.4	+	5	916	c.823delA	c.(823-825)aaafs	p.K276fs	LONP2_ENST00000535754.1_Frame_Shift_Del_p.K232fs	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						CATGCTAGAGAAAAAAATACG	0.343																																					p.E274fs		Atlas-INDEL	.											.	LONP2	63	.	0			c.822delG						.						132	131	131					16																	48295434		2200	4300	6500	SO:0001589	frameshift_variant	83752	exon5			.	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.823delA	chr16.hg19:g.48295434delA	ENSP00000285737:p.Lys276fs	127.0	0.0		171.0	11.0	NM_031490		Frame_Shift_Del	DEL	ENST00000285737.4	hg19	CCDS10734.1																																																																																			.	.		0.343	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		-	48295434	A	-	48295434	7	5	103	1	0	1	0	1	0	0	0	0	8902	247	9	0	841	0	LONP2	16	48295434	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	17093151	48295434	42059319	916	15539										
BBS2	583	hgsc.bcm.edu	37	chr16	56534909	56534909	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctgtaaaaattccttctgcAaaaatcaatactgctcggat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:56534909delA	ENST00000245157.5	-	11	1674	c.1254delT	c.(1252-1254)tttfs	p.F418fs	BBS2_ENST00000568104.1_Frame_Shift_Del_p.F418fs|BBS2_ENST00000561951.1_5'Flank	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	418					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						TTCCTTCTGCAAAAATCAATA	0.468									Bardet-Biedl syndrome																												p.A419fs		Atlas-INDEL	.											.	BBS2	67	.	0			c.1255delG						.						140	137	138					16																	56534909		2198	4300	6498	SO:0001589	frameshift_variant	583	exon11	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	.	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.1254delT	chr16.hg19:g.56534909delA	ENSP00000245157:p.Phe418fs	191.0	0.0		212.0	14.0	NM_031885	Q96CM0|Q96SN9	Frame_Shift_Del	DEL	ENST00000245157.5	hg19	CCDS32451.1																																																																																			.	.		0.468	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		-	56534909	A	-	56534909	7	5	103	1	0	1	0	1	0	0	0	0	1338	127	5	0	939	0	BBS2	16	56534909	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	8239475	56534909	33819844	917	15540										
CNGB1	1258	hgsc.bcm.edu	37	chr16	57949179	57949179	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acagcggggcaggcggaggaGggggttcacaccgactttca					rs572146377		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:57949179delG	ENST00000251102.8	-	23	2338	c.2278delC	c.(2278-2280)ctcfs	p.L761fs	CNGB1_ENST00000564448.1_Frame_Shift_Del_p.L755fs	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	761					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						AGGCGGAGGAGGGGGTTCACA	0.577																																					p.L760fs	Colon(156;1293 1853 16336 28962 38659)	Atlas-INDEL	.											.	CNGB1	105	.	0			c.2279delT						.						45	48	47					16																	57949179		1936	4128	6064	SO:0001589	frameshift_variant	1258	exon23			.	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2151	protein-coding gene	gene with protein product	"glutamic acid-rich protein"	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2278delC	chr16.hg19:g.57949179delG	ENSP00000251102:p.Leu761fs	134.0	0.0		133.0	10.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Frame_Shift_Del	DEL	ENST00000251102.8	hg19	CCDS42169.1																																																																																			.	.		0.577	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		-	57949179	G	-	57949179	7	5	103	1	0	1	0	1	0	0	0	0	3602	1000	35	0	1521	0	CNGB1	16	57949179	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1414270	57949179	32405574	918	15541										
CNGB1	1258	hgsc.bcm.edu	37	chr16	57953155	57953155	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctctggggctttcttggctGgggctgtgggatgacattgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:57953155delG	ENST00000251102.8	-	20	1865	c.1805delC	c.(1804-1806)ccafs	p.P602fs	CNGB1_ENST00000564448.1_Frame_Shift_Del_p.P596fs	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	602					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						TTTCTTGGCTGGGGCTGTGGG	0.567																																					p.P602fs	Colon(156;1293 1853 16336 28962 38659)	Atlas-INDEL	.											.	CNGB1	105	.	0			c.1806delA						.						70	73	72					16																	57953155		1953	4166	6119	SO:0001589	frameshift_variant	1258	exon20			.	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2151	protein-coding gene	gene with protein product	"glutamic acid-rich protein"	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.1805delC	chr16.hg19:g.57953155delG	ENSP00000251102:p.Pro602fs	200.0	0.0		228.0	14.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Frame_Shift_Del	DEL	ENST00000251102.8	hg19	CCDS42169.1																																																																																			.	.		0.567	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		-	57953155	G	-	57953155	7	5	103	1	0	1	0	1	0	0	0	0	3602	1348	47	0	2006	0	CNGB1	16	57953155	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	3976	57953155	32401598	919	15542										
CDH16	1014	hgsc.bcm.edu	37	chr16	66947073	66947073	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatgctgactgtggggtcacGgggagggcagataggcacgt					rs532055028		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:66947073delG	ENST00000299752.4	-	9	1208	c.1015delC	c.(1015-1017)cgtfs	p.R339fs	CDH16_ENST00000570262.1_Frame_Shift_Del_p.R259fs|CDH16_ENST00000565796.1_Frame_Shift_Del_p.R339fs|CDH16_ENST00000568632.1_Frame_Shift_Del_p.R242fs|CDH16_ENST00000394055.3_Frame_Shift_Del_p.R339fs	NM_001204744.1|NM_001204745.1|NM_004062.3	NP_001191673.1|NP_001191674.1|NP_004053.1	O75309	CAD16_HUMAN	cadherin 16, KSP-cadherin	339					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(3)|large_intestine(10)|lung(15)|ovary(2)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		GTGGGGTCACGGGGAGGGCAG	0.582																																					p.R339fs		Atlas-INDEL	.											.	CDH16	91	.	0			c.1016delG						.						157	148	151					16																	66947073		2200	4300	6500	SO:0001589	frameshift_variant	1014	exon9			.	AF016272	CCDS10823.1, CCDS56002.1, CCDS58471.1, CCDS58472.1	16q22.1	2010-01-26			ENSG00000166589	ENSG00000166589		"Cadherins / Major cadherins"	1755	protein-coding gene	gene with protein product		603118				9721215, 7615566	Standard	NM_004062		Approved		uc002eql.3	O75309	OTTHUMG00000137518	ENST00000299752.4:c.1015delC	chr16.hg19:g.66947073delG	ENSP00000299752:p.Arg339fs	120.0	0.0		127.0	10.0	NM_004062	B4DPA8|H3BPD3|Q6UW93	Frame_Shift_Del	DEL	ENST00000299752.4	hg19	CCDS10823.1																																																																																			.	.		0.582	CDH16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268839.2	NM_004062		-	66947073	G	-	66947073	7	5	103	1	0	1	0	1	0	0	0	0	3103	1116	39	0	1514	0	CDH16	16	66947073	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	8993918	66947073	23407680	920	15543										
LRRC36	55282	hgsc.bcm.edu	37	chr16	67381385	67381385	+	Intron	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaaacatgctcagaccacggTttttgcctccagatgaccga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:67381385delT	ENST00000329956.6	+	4	410				LRRC36_ENST00000563189.1_Frame_Shift_Del_p.F6fs|LRRC36_ENST00000435835.3_Frame_Shift_Del_p.F6fs|LRRC36_ENST00000541146.1_5'UTR|LRRC36_ENST00000563303.1_Intron|LRRC36_ENST00000290940.7_5'UTR	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36											endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	24		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		CAGACCACGGTTTTTGCCTCC	0.408																																					p.R5fs		Atlas-INDEL	.											.	LRRC36	68	.	0			c.15delG						.						98	95	96					16																	67381385		2198	4300	6498	SO:0001627	intron_variant	55282	exon1			.	BC026156	CCDS32467.1, CCDS58474.1	16q22.1	2008-02-05				ENSG00000159708			25615	protein-coding gene	gene with protein product						12477932	Standard	NM_001161575		Approved	FLJ11004	uc002esv.3	Q1X8D7		ENST00000329956.6:c.392-13T>-	chr16.hg19:g.67381385delT		125.0	0.0		152.0	10.0	NM_001161575	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Frame_Shift_Del	DEL	ENST00000329956.6	hg19	CCDS32467.1																																																																																			.	.		0.408	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296		-	67381385	T	-	67381385	6	5	103	0	1	1	0	1	0	0	0	0	8999	1725	60	0		0	LRRC36	16	67381385	Intron	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	434312	67381385	22973368	921	15544										
NOB1	28987	hgsc.bcm.edu	37	chr16	69782138	69782138	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggcaccagctacatacttgAaacagccatggcagcgcaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:69782138delA	ENST00000268802.5	-	7	850	c.821delT	c.(820-822)ttcfs	p.F274fs		NM_014062.1	NP_054781.1	Q9ULX3	NOB1_HUMAN	NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)	274					visual perception (GO:0007601)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TACATACTTGAAACAGCCATG	0.537																																					p.F274fs		Atlas-INDEL	.											.	NOB1	24	.	0			c.822delC						.						62	56	58					16																	69782138		2198	4300	6498	SO:0001589	frameshift_variant	28987	exon7			.	AB026125	CCDS10884.1	16q22.1	2008-02-05	2006-04-20	2006-04-20	ENSG00000141101	ENSG00000141101			29540	protein-coding gene	gene with protein product	"nin one binding protein"	613586	"PSMD8 binding protein 1"	PSMD8BP1		16172919	Standard	NM_014062		Approved	NOB1P, ART-4, MST158	uc002exs.4	Q9ULX3	OTTHUMG00000137576	ENST00000268802.5:c.821delT	chr16.hg19:g.69782138delA	ENSP00000268802:p.Phe274fs	136.0	0.0		164.0	10.0	NM_014062	Q7L6B7|Q7M4M4|Q7Z4B5|Q9NWB0	Frame_Shift_Del	DEL	ENST00000268802.5	hg19	CCDS10884.1																																																																																			.	.		0.537	NOB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268958.2	NM_014062		-	69782138	A	-	69782138	7	5	103	1	0	1	0	1	0	0	0	0	10520	246	9	0	429	0	NOB1	16	69782138	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2400753	69782138	20572615	922	15545										
COG4	197258	hgsc.bcm.edu	37	chr16	70514950	70514950	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgatatcttcactgcggaagTctatccgcagggccagcacc	10	13	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:70514950T>C	ENST00000288078.6	+	0	4081				COG4_ENST00000323786.5_Missense_Mutation_p.D778G	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase							cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				ACTGCGGAAGTCTATCCGCAG	0.617																																					p.D778G		Atlas-SNP	.											.	COG4	64	.	0			c.A2333G						.						48	49	48					16																	70514950		2198	4300	6498	SO:0001628	intergenic_variant	25839	exon19			CGGAAGTCTATCC		CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"L-fucose kinase"	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085		chr16.hg19:g.70514950T>C		67.0	0.0		89.0	5.0	NM_015386	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	hg19	CCDS10891.2	.	.	.	.	.	.	.	.	.	.	T	33	5.274405	0.95459	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000526700;ENST00000539961	T	0.69561	-0.41	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.85771	0.5774	M	0.91717	3.235	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.998	D	0.88873	0.3334	10	0.87932	D	0	-22.4546	16.4504	0.83984	0.0:0.0:0.0:1.0	.	684;752;774;234	Q8N8L9;Q6PIW8;Q9H9E3;E9PQK0	.;.;COG4_HUMAN;.	G	778;753;234;436	ENSP00000315775:D778G	ENSP00000315775:D778G	D	-	2	0	COG4	69072451	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.755000	0.85180	2.288000	0.76882	0.533000	0.62120	GAC	.	.		0.617	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059		C	70514950	T	C	70514950	1	2	103	0	1	0	0	0	0	0	0	0	3662	1667	58	2		2	COG4	16	70514950	IGR	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	732812	70514950	19839803	923	15546										
VAC14	55697	hgsc.bcm.edu	37	chr16	70820186	70820186	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccggctgtgggggtgctgagAcagggcaaactcctgggaca	17	10	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:70820186A>G	ENST00000261776.5	-	2	447	c.187T>C	c.(187-189)Tct>Cct	p.S63P		NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)	63					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				GGGTGCTGAGACAGGGCAAAC	0.612																																					p.S63P		Atlas-SNP	.											.	VAC14	65	.	0			c.T187C						.						93	95	94					16																	70820186		2198	4300	6498	SO:0001583	missense	55697	exon2			GCTGAGACAGGGC	AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"Tax1 (human T-cell leukemia virus type I) binding protein 2"	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583	ENST00000261776.5:c.187T>C	chr16.hg19:g.70820186A>G	ENSP00000261776:p.Ser63Pro	99.0	0.0		94.0	4.0	NM_018052	B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Missense_Mutation	SNP	ENST00000261776.5	hg19	CCDS10896.1	.	.	.	.	.	.	.	.	.	.	A	31	5.068020	0.93950	.	.	ENSG00000103043	ENST00000261776	.	.	.	5.49	5.49	0.81192	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.84492	0.5484	M	0.89840	3.065	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.87902	0.2691	9	0.72032	D	0.01	-15.7429	15.5895	0.76517	1.0:0.0:0.0:0.0	.	63	Q08AM6	VAC14_HUMAN	P	63	.	ENSP00000261776:S63P	S	-	1	0	VAC14	69377687	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.274000	0.95731	2.085000	0.62840	0.528000	0.53228	TCT	.	.		0.612	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3	NM_018052		G	70820186	A	G	70820186	3	3	103	1	0	0	0	0	1	0	0	0	17126	275	10	2	2233	2	VAC14	16	70820186	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	305236	70820186	19534567	924	15547										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72828411	72828411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatatgagcctcaagagcagTcttggctttgaagagcgctc	12	9	2	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:72828411T>C	ENST00000268489.5	-	9	8842	c.8170A>G	c.(8170-8172)Act>Gct	p.T2724A	RP5-991G20.4_ENST00000569195.1_RNA|ZFHX3_ENST00000397992.5_Missense_Mutation_p.T1810A	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2724					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TCAAGAGCAGTCTTGGCTTTG	0.572																																					p.T2724A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.A8170G						.						73	63	66					16																	72828411		2198	4300	6498	SO:0001583	missense	463	exon9			GAGCAGTCTTGGC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.8170A>G	chr16.hg19:g.72828411T>C	ENSP00000268489:p.Thr2724Ala	98.0	0.0		98.0	4.0	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	hg19	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.685672	0.29962	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.27402	1.67;1.67	5.77	5.77	0.91146	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.51477	D	0.000089	T	0.49440	0.1557	L	0.47716	1.5	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.46569	-0.9182	10	0.56958	D	0.05	.	16.0858	0.81049	0.0:0.0:0.0:1.0	.	2724	Q15911	ZFHX3_HUMAN	A	2724;1810	ENSP00000268489:T2724A;ENSP00000438926:T1810A	ENSP00000268489:T2724A	T	-	1	0	ZFHX3	71385912	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.221000	0.72243	2.198000	0.70561	0.533000	0.62120	ACT	.	.		0.572	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		C	72828411	T	C	72828411	3	2	103	1	0	0	0	0	1	0	0	0	17649	1667	58	2	2949	2	ZFHX3	16	72828411	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	2008225	72828411	17526342	925	15548										
GLG1	2734	hgsc.bcm.edu	37	chr16	74525009	74525009	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggaacaatggtgttcaatctCcccccgacagcttaggatga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:74525009delC	ENST00000422840.2	-	8	1338	c.1339delG	c.(1339-1341)gagfs	p.E447fs	GLG1_ENST00000447066.2_Frame_Shift_Del_p.E436fs|GLG1_ENST00000205061.5_Frame_Shift_Del_p.E447fs	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	447					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						TGTTCAATCTCCCCCCGACAG	0.512																																					p.E447fs		Atlas-INDEL	.											.	GLG1	106	.	0			c.1340delA						.						176	147	157					16																	74525009		2198	4300	6498	SO:0001589	frameshift_variant	2734	exon8			.		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.1339delG	chr16.hg19:g.74525009delC	ENSP00000405984:p.Glu447fs	185.0	0.0		182.0	12.0	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Frame_Shift_Del	DEL	ENST00000422840.2	hg19	CCDS45527.1																																																																																			.	.		0.512	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		-	74525009	C	-	74525009	7	5	103	1	0	1	0	1	0	0	0	0	6444	864	30	0	2356	0	GLG1	16	74525009	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1696598	74525009	15829744	926	15549										
RFWD3	55159	hgsc.bcm.edu	37	chr16	74678605	74678605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catccatagaagcagaaggtAgcagaggctcagacttctgg	12	9	2	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:74678605A>G	ENST00000361070.4	-	5	918	c.821T>C	c.(820-822)cTa>cCa	p.L274P	RFWD3_ENST00000571750.1_Missense_Mutation_p.L274P	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	274					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						AGCAGAAGGTAGCAGAGGCTC	0.443																																					p.L274P		Atlas-SNP	.											.	RFWD3	49	.	0			c.T821C						.						77	74	75					16																	74678605		2198	4300	6498	SO:0001583	missense	55159	exon5			GAAGGTAGCAGAG	AK001382	CCDS32486.1	16q22.3	2013-01-09						"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.821T>C	chr16.hg19:g.74678605A>G	ENSP00000354361:p.Leu274Pro	156.0	0.0		194.0	8.0	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Missense_Mutation	SNP	ENST00000361070.4	hg19	CCDS32486.1	.	.	.	.	.	.	.	.	.	.	A	8.649	0.897741	0.17686	.	.	ENSG00000168411	ENST00000361070	T	0.21191	2.02	5.14	-7.62	0.01294	.	2.609730	0.00953	N	0.002993	T	0.10723	0.0262	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15435	-1.0437	10	0.27785	T	0.31	-8.4184	5.2825	0.15682	0.3366:0.1038:0.4577:0.102	.	274	Q6PCD5	RFWD3_HUMAN	P	274	ENSP00000354361:L274P	ENSP00000354361:L274P	L	-	2	0	RFWD3	73236106	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.057000	0.11768	-1.576000	0.01652	-1.527000	0.00925	CTA	.	.		0.443	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124		G	74678605	A	G	74678605	3	3	103	1	0	0	0	0	1	0	0	0	13276	420	15	2	1539	2	RFWD3	16	74678605	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	153596	74678605	15676148	927	15550										
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84456800	84456800	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctcaccctttcagacacctAaaactcctttgcagaaaagc					rs200531713	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:84456800delA	ENST00000262429.4	+	10	939	c.850delA	c.(850-852)aaafs	p.K284fs	ATP2C2_ENST00000420010.2_3'UTR|ATP2C2_ENST00000416219.2_Frame_Shift_Del_p.K284fs	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	284					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						TCAGACACCTAAAACTCCTTT	0.458																																					p.P283fs		Atlas-INDEL	.											.	ATP2C2	75	.	0			c.849delT						.						112	106	108					16																	84456800		1975	4162	6137	SO:0001589	frameshift_variant	9914	exon10			.	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"ATPases / P-type"	29103	protein-coding gene	gene with protein product	"secretory pathway calcium ATPase 2"	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.850delA	chr16.hg19:g.84456800delA	ENSP00000262429:p.Lys284fs	172.0	0.0		162.0	10.0	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Frame_Shift_Del	DEL	ENST00000262429.4	hg19	CCDS42207.1																																																																																			.	.		0.458	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		-	84456800	A	-	84456800	7	5	103	1	0	1	0	1	0	0	0	0	1144	363	13	0	888	0	ATP2C2	16	84456800	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	9778195	84456800	5897953	928	15551										
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84486788	84486788	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggaagctgcaagccatgtccGgggaggaggtggacagcgtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:84486788delG	ENST00000262429.4	+	19	1965	c.1876delG	c.(1876-1878)gggfs	p.G626fs	ATP2C2_ENST00000420010.2_3'UTR|ATP2C2_ENST00000416219.2_Frame_Shift_Del_p.G626fs	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	626					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						AGCCATGTCCGGGGAGGAGGT	0.657																																					p.S625fs		Atlas-INDEL	.											.	ATP2C2	75	.	0			c.1875delC						.						45	52	50					16																	84486788		2041	4182	6223	SO:0001589	frameshift_variant	9914	exon19			.	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"ATPases / P-type"	29103	protein-coding gene	gene with protein product	"secretory pathway calcium ATPase 2"	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.1876delG	chr16.hg19:g.84486788delG	ENSP00000262429:p.Gly626fs	103.0	0.0		150.0	10.0	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Frame_Shift_Del	DEL	ENST00000262429.4	hg19	CCDS42207.1																																																																																			.	.		0.657	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		-	84486788	G	-	84486788	7	5	103	1	0	1	0	1	0	0	0	0	1144	1116	39	0	1950	0	ATP2C2	16	84486788	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	29988	84486788	5867965	929	15552										
MTHFSD	64779	hgsc.bcm.edu	37	chr16	86565823	86565823	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggtcactcacacgggcgtCcccggggaggttcccaacgt					rs142996375	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:86565823delC	ENST00000360900.6	-	8	971	c.946delG	c.(946-948)gacfs	p.D316fs	MTHFSD_ENST00000381214.5_Frame_Shift_Del_p.D316fs|MTHFSD_ENST00000543303.2_Frame_Shift_Del_p.D315fs|MTHFSD_ENST00000322911.6_Frame_Shift_Del_p.D315fs|MTHFSD_ENST00000546093.1_Frame_Shift_Del_p.D153fs	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	316	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						ACACGGGCGTCCCCGGGGAGG	0.677																																					p.D316fs		Atlas-INDEL	.											.	MTHFSD	52	.	0			c.947delA						.						11	14	13					16																	86565823		1873	4094	5967	SO:0001589	frameshift_variant	64779	exon8			.	AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"RNA binding motif (RRM) containing"	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.946delG	chr16.hg19:g.86565823delC	ENSP00000354152:p.Asp316fs	106.0	0.0		159.0	11.0	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Frame_Shift_Del	DEL	ENST00000360900.6	hg19	CCDS54047.1																																																																																			.	.		0.677	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764		-	86565823	C	-	86565823	7	5	103	1	0	1	0	1	0	0	0	0	9942	855	30	0	209	0	MTHFSD	16	86565823	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2079035	86565823	3788930	930	15553										
KLHDC4	54758	hgsc.bcm.edu	37	chr16	87788891	87788891	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agacatagagctcgttatacAaaaaagtctacaggaaggaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:87788891delA	ENST00000270583.5	-	4	336	c.278delT	c.(277-279)ttgfs	p.L93fs	KLHDC4_ENST00000353170.5_Frame_Shift_Del_p.L36fs|KLHDC4_ENST00000347925.5_Frame_Shift_Del_p.L93fs	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	93										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		CTCGTTATACAAAAAAGTCTA	0.453																																					p.L93fs		Atlas-INDEL	.											.	KLHDC4	45	.	0			c.279delG						.						134	128	130					16																	87788891		2198	4300	6498	SO:0001589	frameshift_variant	54758	exon4			.	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.278delT	chr16.hg19:g.87788891delA	ENSP00000270583:p.Leu93fs	152.0	0.0		166.0	11.0	NM_001184856	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Frame_Shift_Del	DEL	ENST00000270583.5	hg19	CCDS10963.1																																																																																			.	.		0.453	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		-	87788891	A	-	87788891	7	5	103	1	0	1	0	1	0	0	0	0	8367	131	5	0	1316	0	KLHDC4	16	87788891	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1223068	87788891	2565862	931	15554										
ZNF778	197320	hgsc.bcm.edu	37	chr16	89293177	89293177	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcagtgaacactcaggcctcAgcacacacgtgagaactcaa	8	13	4	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:89293177A>G	ENST00000433976.2	+	6	729	c.397A>G	c.(397-399)Agc>Ggc	p.S133G	ZNF778_ENST00000306502.6_Missense_Mutation_p.S91G|RP11-46C24.6_ENST00000563182.1_RNA	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	133					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		CTCAGGCCTCAGCACACACGT	0.463																																					p.S161G		Atlas-SNP	.											.	ZNF778	67	.	0			c.A481G						.						74	77	76					16																	89293177		2072	4241	6313	SO:0001583	missense	197320	exon7			GGCCTCAGCACAC	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"Zinc fingers, C2H2-type", "-"	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.397A>G	chr16.hg19:g.89293177A>G	ENSP00000405289:p.Ser133Gly	106.0	0.0		147.0	6.0	NM_001201407	Q08AG0	Missense_Mutation	SNP	ENST00000433976.2	hg19	CCDS45550.1	.	.	.	.	.	.	.	.	.	.	A	9.372	1.070822	0.20147	.	.	ENSG00000170100	ENST00000433976;ENST00000306502	T;T	0.29655	1.56;1.56	1.21	-0.189	0.13260	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.	.	.	.	T	0.19525	0.0469	L	0.38175	1.15	0.09310	N	1	P;B	0.35493	0.505;0.208	B;B	0.33960	0.173;0.057	T	0.16305	-1.0407	9	0.30854	T	0.27	.	5.5952	0.17323	0.4044:0.5956:0.0:0.0	.	91;133	Q96MU6-2;Q96MU6	.;ZN778_HUMAN	G	133;91	ENSP00000405289:S133G;ENSP00000305203:S91G	ENSP00000305203:S91G	S	+	1	0	ZNF778	87820678	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.008000	0.13197	-0.061000	0.13110	0.378000	0.23410	AGC	.	.		0.463	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		G	89293177	A	G	89293177	3	3	103	1	0	0	0	0	1	0	0	0	18166	188	7	2	415	2	ZNF778	16	89293177	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1504286	89293177	1061576	932	15555										
CPNE7	27132	hgsc.bcm.edu	37	chr16	89649911	89649911	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgtgaggtggtggacgtgcaGgggtggccacacgcagggat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:89649911delG	ENST00000268720.5	+	4	687	c.557delG	c.(556-558)aggfs	p.R186fs	CPNE7_ENST00000319518.8_Intron	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	186					lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		TGGACGTGCAGGGGTGGCCAC	0.647																																					p.R186fs		Atlas-INDEL	.											.	CPNE7	56	.	0			c.556delA						.						24	17	20					16																	89649911		2127	4229	6356	SO:0001589	frameshift_variant	27132	exon4			.	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.557delG	chr16.hg19:g.89649911delG	ENSP00000268720:p.Arg186fs	136.0	0.0		146.0	10.0	NM_014427		Frame_Shift_Del	DEL	ENST00000268720.5	hg19	CCDS10980.1																																																																																			.	.		0.647	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2			-	89649911	G	-	89649911	7	5	103	1	0	1	0	1	0	0	0	0	3819	1000	35	0	571	0	CPNE7	16	89649911	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	356734	89649911	704842	933	15556										
FANCA	2175	hgsc.bcm.edu	37	chr16	89857909	89857909	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catgctgtccagctggcagcTctcgaatgcctgggccatca	11	14	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:89857909T>C	ENST00000389301.3	-	14	1291	c.1261A>G	c.(1261-1263)Agc>Ggc	p.S421G	FANCA_ENST00000568369.1_Missense_Mutation_p.S421G	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	421					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		AGCTGGCAGCTCTCGAATGCC	0.572			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S421G		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.A1261G						.						68	54	58					16																	89857909		2198	4300	6498	SO:0001583	missense	2175	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGCAGCTCTCGAA	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"Fanconi anemia, complementation groups"	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1261A>G	chr16.hg19:g.89857909T>C	ENSP00000373952:p.Ser421Gly	82.0	0.0		99.0	4.0	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	hg19	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	T	15.44	2.835030	0.50951	.	.	ENSG00000187741	ENST00000389301	D	0.98747	-5.11	5.13	5.13	0.70059	.	0.284959	0.30365	N	0.009785	D	0.98343	0.9450	M	0.73598	2.24	0.80722	D	1	D;D	0.62365	0.991;0.991	P;P	0.51266	0.664;0.664	D	0.98607	1.0661	10	0.62326	D	0.03	-4.3847	14.1777	0.65552	0.0:0.0:0.0:1.0	.	421;421	B4DRI7;O15360	.;FANCA_HUMAN	G	421	ENSP00000373952:S421G	ENSP00000373952:S421G	S	-	1	0	FANCA	88385410	1.000000	0.71417	0.651000	0.29564	0.054000	0.15201	2.685000	0.46959	1.957000	0.56846	0.529000	0.55759	AGC	.	.		0.572	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			C	89857909	T	C	89857909	3	2	103	1	0	0	0	0	1	0	0	0	5670	1551	54	2	3226	2	FANCA	16	89857909	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	207998	89857909	496844	934	15557										
TUBB3	10381	hgsc.bcm.edu	37	chr16	90001894	90001894	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agctacttcgtggagtggatCcccaacaacgtgaaggtggc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:90001894delC	ENST00000315491.7	+	4	1158	c.1035delC	c.(1033-1035)atcfs	p.I345fs	TUBB3_ENST00000556922.1_Frame_Shift_Del_p.I692fs|TUBB3_ENST00000555576.1_Intron|TUBB3_ENST00000554444.1_Frame_Shift_Del_p.I273fs|TUBB3_ENST00000304984.5_Frame_Shift_Del_p.I273fs	NM_006086.3	NP_006077.2	Q13509	TBB3_HUMAN	tubulin, beta 3 class III	345					'de novo' posttranslational protein folding (GO:0051084)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)	Ixabepilone(DB04845)	TGGAGTGGATCCCCAACAACG	0.617																																					p.I345fs		Atlas-INDEL	.											.	TUBB3	49	.	0			c.1034delT						.						189	159	169					16																	90001894		2198	4300	6498	SO:0001589	frameshift_variant	10381	exon4			.	BC000748	CCDS10988.1, CCDS56012.1	16q24.3	2014-02-04	2011-10-10		ENSG00000198211	ENSG00000198211		"Tubulins"	20772	protein-coding gene	gene with protein product	"class III beta-tubulin"	602661	"tubulin, beta 3", "fibrosis of extraocular muscles, congenital, 3"	FEOM3		9473684, 8098743, 20074521	Standard	NM_006086		Approved	beta-4, CFEOM3, CFEOM3A	uc002fph.2	Q13509	OTTHUMG00000138985	ENST00000315491.7:c.1035delC	chr16.hg19:g.90001894delC	ENSP00000320295:p.Ile345fs	125.0	0.0		168.0	12.0	NM_006086	A8K854|Q9BTZ0|Q9BW10	Frame_Shift_Del	DEL	ENST00000315491.7	hg19	CCDS10988.1																																																																																			.	.		0.617	TUBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272874.1	NM_006086		-	90001894	C	-	90001894	7	5	103	1	0	1	0	1	0	0	0	0	16772	845	30	0	1049	0	TUBB3	16	90001894	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	143985	90001894	352859	935	15558										
GLOD4	51031	hgsc.bcm.edu	37	chr17	673366	673366	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagtcagaatcttctggttcTcccttttcatcaagtcttct	6	11	8	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:673366T>C	ENST00000301328.5	-	8	730	c.707A>G	c.(706-708)gAg>gGg	p.E236G	GLOD4_ENST00000536578.1_Missense_Mutation_p.E212G|GLOD4_ENST00000301329.6_Missense_Mutation_p.E221G			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4	236						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CTTCTGGTTCTCCCTTTTCAT	0.532																																					p.E221G		Atlas-SNP	.											.	GLOD4	12	.	0			c.A662G						.						68	61	63					17																	673366		2203	4300	6503	SO:0001583	missense	51031	exon7			TGGTTCTCCCTTT	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 25"	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38		ENST00000301328.5:c.707A>G	chr17.hg19:g.673366T>C	ENSP00000301328:p.Glu236Gly	124.0	0.0		112.0	5.0	NM_016080	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	hg19		.	.	.	.	.	.	.	.	.	.	T	16.36	3.102000	0.56183	.	.	ENSG00000167699	ENST00000301329;ENST00000397393;ENST00000301328;ENST00000536578	T;T;T	0.53206	0.63;0.63;0.63	5.79	5.79	0.91817	.	0.092459	0.64402	D	0.000001	T	0.47619	0.1455	L	0.56769	1.78	0.80722	D	1	B;B;B	0.18863	0.031;0.009;0.016	B;B;B	0.24848	0.056;0.012;0.022	T	0.37934	-0.9684	10	0.33940	T	0.23	-16.881	15.3033	0.73972	0.0:0.0:0.0:1.0	.	212;236;221	B7Z403;Q9HC38;Q9HC38-2	.;GLOD4_HUMAN;.	G	221;424;236;212	ENSP00000301329:E221G;ENSP00000301328:E236G;ENSP00000444315:E212G	ENSP00000301328:E236G	E	-	2	0	GLOD4	620116	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.721000	0.84768	2.198000	0.70561	0.533000	0.62120	GAG	.	.		0.532	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080		C	673366	T	C	673366	3	2	103	1	0	0	0	0	1	0	0	0	6458	1551	54	2	246	2	GLOD4	17	673366	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10		673366	80521844	936	15559										
TRPV3	162514	hgsc.bcm.edu	37	chr17	3424284	3424284	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tacctactccaaatccaagcAaaaacacgatatatacaaac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:3424284delA	ENST00000576742.1	-	14	2114	c.1793delT	c.(1792-1794)ttgfs	p.L599fs	TRPV3_ENST00000301365.4_Frame_Shift_Del_p.L599fs|TRPV3_ENST00000572519.1_Frame_Shift_Del_p.L599fs	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	599					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	AAATCCAAGCAAAAACACGAT	0.333																																					p.L598fs		Atlas-INDEL	.											.	TRPV3	85	.	0			c.1794delG						.						85	78	81					17																	3424284		2201	4300	6501	SO:0001589	frameshift_variant	162514	exon14			.	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.1793delT	chr17.hg19:g.3424284delA	ENSP00000461518:p.Leu599fs	160.0	0.0		178.0	12.0	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Frame_Shift_Del	DEL	ENST00000576742.1	hg19	CCDS11029.1																																																																																			.	.		0.333	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		-	3424284	A	-	3424284	7	5	103	1	0	1	0	1	0	0	0	0	16612	131	5	0	599	0	TRPV3	17	3424284	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2750918	3424284	77770926	937	15560										
MINK1	50488	hgsc.bcm.edu	37	chr17	4794826	4794826	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccagtccctgcaggaccagCccacccgaaacctggctgcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:4794826delC	ENST00000355280.6	+	16	2012	c.1816delC	c.(1816-1818)cccfs	p.P606fs	MINK1_ENST00000453408.3_Frame_Shift_Del_p.P586fs|MINK1_ENST00000347992.7_Frame_Shift_Del_p.P606fs	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						GCAGGACCAGCCCACCCGAAA	0.677																																					p.Q605fs		Atlas-INDEL	.											.	MINK1	110	.	0			c.1815delG						.						39	52	48					17																	4794826		2083	4211	6294	SO:0001589	frameshift_variant	50488	exon16			.	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"misshapen/NIK-related kinase"	609426	"misshapen-like kinase 1 (zebrafish)"			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.1816delC	chr17.hg19:g.4794826delC	ENSP00000347427:p.Pro606fs	176.0	0.0		153.0	10.0	NM_170663		Frame_Shift_Del	DEL	ENST00000355280.6	hg19	CCDS45588.1																																																																																			.	.		0.677	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		-	4794826	C	-	4794826	7	5	103	1	0	1	0	1	0	0	0	0	9596	739	26	0	1617	0	MINK1	17	4794826	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1370542	4794826	76400384	938	15561										
CAMTA2	23125	hgsc.bcm.edu	37	chr17	4883160	4883160	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggtcctccaaacaaggccTctcctcttcctaccctgctt	5	18	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:4883160T>C	ENST00000348066.3	-	9	1580	c.1457A>G	c.(1456-1458)gAg>gGg	p.E486G	CAMTA2_ENST00000358183.4_Missense_Mutation_p.E486G|CAMTA2_ENST00000571831.1_5'Flank|CAMTA2_ENST00000572543.1_Missense_Mutation_p.E491G|CAMTA2_ENST00000361571.5_Missense_Mutation_p.E485G|CAMTA2_ENST00000414043.3_Missense_Mutation_p.E509G|CAMTA2_ENST00000381311.5_Missense_Mutation_p.E488G	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	486					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						AAACAAGGCCTCTCCTCTTCC	0.597																																					p.E509G		Atlas-SNP	.											.	CAMTA2	93	.	0			c.A1526G						.						96	96	96					17																	4883160		2203	4300	6503	SO:0001583	missense	23125	exon9			AAGGCCTCTCCTC	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.1457A>G	chr17.hg19:g.4883160T>C	ENSP00000321813:p.Glu486Gly	58.0	0.0		62.0	5.0	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	hg19	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.022487	0.54683	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.35048	2.55;1.57;1.33;1.58;1.35	5.09	5.09	0.68999	.	0.286088	0.29730	N	0.011354	T	0.44286	0.1286	N	0.24115	0.695	0.28150	N	0.929429	D;D;D;D;B	0.67145	0.993;0.993;0.996;0.993;0.002	D;D;D;D;B	0.75484	0.968;0.968;0.986;0.968;0.005	T	0.33599	-0.9862	10	0.42905	T	0.14	-7.3284	12.8738	0.57980	0.0:0.0:0.0:1.0	.	462;509;488;486;485	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	G	509;488;485;486;486	ENSP00000412886:E509G;ENSP00000370712:E488G;ENSP00000354828:E485G;ENSP00000350910:E486G;ENSP00000321813:E486G	ENSP00000321813:E486G	E	-	2	0	CAMTA2	4823884	0.376000	0.25098	0.938000	0.37757	0.748000	0.42578	1.624000	0.37018	2.144000	0.66660	0.533000	0.62120	GAG	.	.		0.597	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099		C	4883160	T	C	4883160	3	2	103	1	0	0	0	0	1	0	0	0	2616	1551	54	2	2261	2	CAMTA2	17	4883160	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	88334	4883160	76312050	939	15562										
ZNF594	84622	hgsc.bcm.edu	37	chr17	5085336	5085336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catccttgctgaaggttttcTcacattcttcaagtttctct	5	11	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:5085336T>C	ENST00000399604.4	-	1	2356	c.2216A>G	c.(2215-2217)gAg>gGg	p.E739G	ZNF594_ENST00000575779.1_Missense_Mutation_p.E739G			Q96JF6	ZN594_HUMAN	zinc finger protein 594	739					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GAAGGTTTTCTCACATTCTTC	0.438																																					p.E739G		Atlas-SNP	.											.	ZNF594	89	.	0			c.A2216G						.						198	205	203					17																	5085336		2088	4237	6325	SO:0001583	missense	84622	exon2			GTTTTCTCACATT	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"Zinc fingers, C2H2-type"	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.2216A>G	chr17.hg19:g.5085336T>C	ENSP00000382513:p.Glu739Gly	98.0	0.0		95.0	5.0	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	hg19	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	T	0.035	-1.311791	0.01342	.	.	ENSG00000180626	ENST00000399604	T	0.08984	3.03	1.04	-0.84	0.10755	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01489	0.0048	N	0.00380	-1.58	0.22096	N	0.999369	B	0.02656	0.0	B	0.01281	0.0	T	0.43637	-0.9379	9	0.02654	T	1	.	4.4455	0.11595	0.0:0.5034:0.0:0.4966	.	739	Q96JF6	ZN594_HUMAN	G	739	ENSP00000382513:E739G	ENSP00000382513:E739G	E	-	2	0	ZNF594	5026060	0.001000	0.12720	0.025000	0.17156	0.271000	0.26615	0.332000	0.19751	-0.398000	0.07679	0.248000	0.18094	GAG	.	.		0.438	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		C	5085336	T	C	5085336	3	2	103	1	0	0	0	0	1	0	0	0	18039	1551	54	2	211	2	ZNF594	17	5085336	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	202176	5085336	76109874	940	15563										
NLGN2	57555	hgsc.bcm.edu	37	chr17	7319293	7319293	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtgggcagatgcggcgcacGgggatgaactgccctatgtc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:7319293delG	ENST00000302926.2	+	6	1574	c.1501delG	c.(1501-1503)gggfs	p.G501fs	NLGN2_ENST00000575301.1_Frame_Shift_Del_p.G501fs	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	501					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				TGCGGCGCACGGGGATGAACT	0.607																																					p.H500fs		Atlas-INDEL	.											.	NLGN2	61	.	0			c.1500delC						.						77	61	66					17																	7319293		2203	4300	6503	SO:0001589	frameshift_variant	57555	exon6			.	AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.1501delG	chr17.hg19:g.7319293delG	ENSP00000305288:p.Gly501fs	172.0	0.0		154.0	10.0	NM_020795	Q9P2I1	Frame_Shift_Del	DEL	ENST00000302926.2	hg19	CCDS11103.1																																																																																			.	.		0.607	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795		-	7319293	G	-	7319293	7	5	103	1	0	1	0	1	0	0	0	0	10471	1116	39	0	1523	0	NLGN2	17	7319293	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2233957	7319293	73875917	941	15564										
SOX15	6665	hgsc.bcm.edu	37	chr17	7492683	7492683	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgcaggtgtcgggcgcggagCcgcttggcctcctccacgaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:7492683delC	ENST00000250055.2	-	1	805	c.312delG	c.(310-312)cggfs	p.R104fs	SOX15_ENST00000538513.2_Frame_Shift_Del_p.R104fs|MPDU1_ENST00000423172.2_Intron|FXR2_ENST00000573057.1_5'Flank|SOX15_ENST00000570788.1_Frame_Shift_Del_p.R104fs	NM_006942.1	NP_008873.1	O60248	SOX15_HUMAN	SRY (sex determining region Y)-box 15	104					cell differentiation (GO:0030154)|chromatin organization (GO:0006325)|male gonad development (GO:0008584)|myoblast development (GO:0048627)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G0 to G1 transition (GO:0070318)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue regeneration (GO:0043403)	cytoplasm (GO:0005737)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|prostate(1)	2						GGGCGCGGAGCCGCTTGGCCT	0.682											OREG0024139	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L105fs		Atlas-INDEL	.											.	SOX15	10	.	0			c.313delC						.						23	26	25					17																	7492683		2202	4298	6500	SO:0001589	frameshift_variant	6665	exon1			.	AJ006222	CCDS32549.1	17p13.1	2014-08-12	2002-07-22	2002-07-26	ENSG00000129194	ENSG00000129194		"SRY (sex determining region Y)-boxes"	11196	protein-coding gene	gene with protein product		601297	"SRY (sex determining region Y)-box 20"	SOX20		8978787, 9730625	Standard	NM_006942		Approved	SOX27, SOX26	uc002ghz.1	O60248	OTTHUMG00000178146	ENST00000250055.2:c.312delG	chr17.hg19:g.7492683delC	ENSP00000355354:p.Arg104fs	126.0	0.0	642	158.0	11.0	NM_006942	B4DWU7|D3DTQ0|P35717|Q9Y6W7	Frame_Shift_Del	DEL	ENST00000250055.2	hg19	CCDS32549.1																																																																																			.	.		0.682	SOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440757.1	NM_006942		-	7492683	C	-	7492683	7	5	103	1	0	1	0	1	0	0	0	0	14961	726	26	0	397	0	SOX15	17	7492683	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	173390	7492683	73702527	942	15565										
TP53	7157	hgsc.bcm.edu	37	chr17	7578460	7578460	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtagatggccatggcgcggAcgcgggtgccgggcgggggt	22	9	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:7578460A>C	ENST00000269305.4	-	5	659	c.470T>G	c.(469-471)gTc>gGc	p.V157G	TP53_ENST00000359597.4_Missense_Mutation_p.V157G|TP53_ENST00000413465.2_Missense_Mutation_p.V157G|TP53_ENST00000455263.2_Missense_Mutation_p.V157G|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.V157G|TP53_ENST00000445888.2_Missense_Mutation_p.V157G	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	157	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> A (in sporadic cancers; somatic mutation).|V -> D (in sporadic cancers; somatic mutation).|V -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|V -> G (in sporadic cancers; somatic mutation).|V -> I (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9419979}.|V -> L (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V157D(8)|p.0?(8)|p.V157G(7)|p.R156_I162delRVRAMAI(2)|p.T155fs*23(2)|p.V157del(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.V157fs*22(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156_V157del(1)|p.V157A(1)|p.R156_R158delRVR(1)|p.R156fs*12(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.V157_M160delVRAM(1)|p.D148fs*23(1)|p.V157_R158delVR(1)|p.S149fs*72(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*20(1)|p.V157_I162delVRAMAI(1)|p.V157fs*21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CATGGCGCGGACGCGGGTGCC	0.617		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.V157G	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	53	Substitution - Missense(16)|Deletion - In frame(14)|Deletion - Frameshift(14)|Whole gene deletion(8)|Complex - frameshift(1)	lung(8)|stomach(6)|oesophagus(6)|breast(5)|ovary(5)|upper_aerodigestive_tract(4)|central_nervous_system(4)|bone(4)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|pancreas(2)|biliary_tract(1)|prostate(1)|liver(1)	c.T470G						.						51	52	51					17																	7578460		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GCGCGGACGCGGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.470T>G	chr17.hg19:g.7578460A>C	ENSP00000269305:p.Val157Gly	145.0	0.0		93.0	37.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	17.25	3.342925	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99825	-6.97;-6.97;-6.97;-6.97;-6.97;-6.97;-6.97;-6.97;-6.97	5.47	5.47	0.80525	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.216722	0.39210	N	0.001429	D	0.99816	0.9919	M	0.86420	2.815	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.996;0.99;0.988;0.998;0.999;1.0	D	0.96765	0.9564	10	0.87932	D	0	-16.7152	13.8032	0.63214	1.0:0.0:0.0:0.0	.	118;157;157;64;157;157;157	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	G	157;157;157;157;157;157;146;64;25;64;25;157	ENSP00000410739:V157G;ENSP00000352610:V157G;ENSP00000269305:V157G;ENSP00000398846:V157G;ENSP00000391127:V157G;ENSP00000391478:V157G;ENSP00000425104:V25G;ENSP00000423862:V64G;ENSP00000424104:V157G	ENSP00000269305:V157G	V	-	2	0	TP53	7519185	1.000000	0.71417	0.032000	0.17829	0.165000	0.22458	9.287000	0.95975	2.208000	0.71279	0.460000	0.39030	GTC	.	.		0.617	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578460	A	C	7578460	3	2	103	1	0	0	0	0	1	0	0	0	16396	275	10	5	828	5	TP53	17	7578460	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	85777	7578460	73616750	943	15566										
CHD3	1107	hgsc.bcm.edu	37	chr17	7806316	7806316	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctgggggcctgggcatcaaTctggccactgctgacactgt	14	12	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:7806316T>C	ENST00000330494.7	+	22	3582	c.3432T>C	c.(3430-3432)aaT>aaC	p.N1144N	CHD3_ENST00000358181.4_Silent_p.N1144N|CHD3_ENST00000380358.4_Silent_p.N1203N	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1144	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				TGGGCATCAATCTGGCCACTG	0.542																																					p.N1203N		Atlas-SNP	.											.	CHD3	169	.	0			c.T3609C						.						97	97	97					17																	7806316		2203	4300	6503	SO:0001819	synonymous_variant	1107	exon22			CATCAATCTGGCC	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.3432T>C	chr17.hg19:g.7806316T>C		111.0	0.0		105.0	10.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Silent	SNP	ENST00000330494.7	hg19	CCDS32554.1																																																																																			.	.		0.542	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		C	7806316	T	C	7806316	2	2	103	1	0	0	0	0	0	0	0	1	3328	1432	50	2		2	CHD3	17	7806316	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	227856	7806316	73388894	944	15567										
MYH10	4628	hgsc.bcm.edu	37	chr17	8455401	8455401	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctccagataacaactggtaAaagatatgaaaagtacgttc	8	7	0	3	rs200432425		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:8455401A>G	ENST00000269243.4	-	8	990	c.852T>C	c.(850-852)ttT>ttC	p.F284F	MYH10_ENST00000360416.3_Silent_p.F294F|MYH10_ENST00000396239.1_Silent_p.F284F|MYH10_ENST00000379980.4_Silent_p.F300F	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	284	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						ACAACTGGTAAAAGATATGAA	0.303																																					p.F294F		Atlas-SNP	.											.	MYH10	148	.	0			c.T882C						.						47	48	48					17																	8455401		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon9			CTGGTAAAAGATA	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.852T>C	chr17.hg19:g.8455401A>G		124.0	0.0		90.0	7.0	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	hg19	CCDS11144.1																																																																																			.	A|0.999;G|0.001		0.303	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			G	8455401	A	G	8455401	2	3	103	1	0	0	0	0	0	0	0	1	10039	11	1	2		2	MYH10	17	8455401	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	649085	8455401	72739809	945	15568										
WDR16	146845	hgsc.bcm.edu	37	chr17	9545098	9545098	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagaattggaaggttccctgTctgggtcgataaatggcatg	14	6	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:9545098T>C	ENST00000352665.5	+	13	1702	c.1633T>C	c.(1633-1635)Tct>Cct	p.S545P	WDR16_ENST00000299764.5_Missense_Mutation_p.S555P|RP11-55L4.2_ENST00000584676.1_RNA|WDR16_ENST00000396219.3_Missense_Mutation_p.S477P	NM_145054.4	NP_659491.4			WD repeat domain 16											NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						AGGTTCCCTGTCTGGGTCGAT	0.458																																					p.S545P		Atlas-SNP	.											.	WDR16	67	.	0			c.T1633C						.						119	117	118					17																	9545098		2203	4300	6503	SO:0001583	missense	146845	exon13			TCCCTGTCTGGGT	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"WD repeat domain containing"	16053	protein-coding gene	gene with protein product	"WD40-repeat protein upregulated in HCC"	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000352665.5:c.1633T>C	chr17.hg19:g.9545098T>C	ENSP00000339449:p.Ser545Pro	112.0	0.0		98.0	5.0	NM_145054		Missense_Mutation	SNP	ENST00000352665.5	hg19	CCDS11149.2	.	.	.	.	.	.	.	.	.	.	T	19.49	3.836856	0.71373	.	.	ENSG00000166596	ENST00000352665;ENST00000396219;ENST00000299764	T;T;T	0.39997	1.05;2.76;2.16	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.144192	0.64402	D	0.000004	T	0.66771	0.2823	M	0.85299	2.745	0.58432	D	0.999993	D;D;D	0.69078	0.997;0.997;0.983	D;D;P	0.65874	0.939;0.939;0.894	T	0.72711	-0.4211	10	0.66056	D	0.02	-17.9464	14.7694	0.69665	0.0:0.0:0.0:1.0	.	555;477;545	Q8N1V2-2;Q8N1V2-3;Q8N1V2	.;.;WDR16_HUMAN	P	545;477;555	ENSP00000339449:S545P;ENSP00000379521:S477P;ENSP00000299764:S555P	ENSP00000299764:S555P	S	+	1	0	WDR16	9485823	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	2.764000	0.47613	2.140000	0.66376	0.460000	0.39030	TCT	.	.		0.458	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054		C	9545098	T	C	9545098	3	2	103	1	0	0	0	0	1	0	0	0	17291	1667	58	2	1683	2	WDR16	17	9545098	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1089697	9545098	71650112	946	15569										
MYH2	4620	hgsc.bcm.edu	37	chr17	10427784	10427784	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctttgtgctgaatcccaccTgggtgtgcagtagctgaaca	11	10	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:10427784T>C	ENST00000245503.5	-	35	5558	c.5174A>G	c.(5173-5175)cAg>cGg	p.Q1725R	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Splice_Site_p.Q1725R|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000399342.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1725					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						GAATCCCACCTGGGTGTGCAG	0.473																																					p.Q1725R		Atlas-SNP	.											.	MYH2	390	.	0			c.A5174G						.						75	78	77					17																	10427784		2203	4300	6503	SO:0001630	splice_region_variant	4620	exon35			CCCACCTGGGTGT		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.5175+1A>G	chr17.hg19:g.10427784T>C		120.0	0.0		120.0	8.0	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	hg19	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.521326	0.64747	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	T;T	0.79845	-1.31;-1.31	5.42	5.42	0.78866	Myosin tail (1);	0.000000	0.37483	U	0.002063	D	0.87892	0.6292	H	0.95850	3.73	0.58432	D	0.999992	B	0.18013	0.025	B	0.27887	0.084	D	0.87505	0.2436	10	0.72032	D	0.01	.	15.6229	0.76820	0.0:0.0:0.0:1.0	.	1725	Q9UKX2	MYH2_HUMAN	R	1725	ENSP00000245503:Q1725R;ENSP00000380367:Q1725R	ENSP00000245503:Q1725R	Q	-	2	0	MYH2	10368509	1.000000	0.71417	1.000000	0.80357	0.549000	0.35272	7.781000	0.85668	2.279000	0.76181	0.402000	0.26972	CAG	.	.		0.473	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	Missense_Mutation	C	10427784	T	C	10427784	5	2	103	1	0	0	0	0	0	0	1	0	10044	1594	55	2	675	2	MYH2	17	10427784	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	882686	10427784	70767426	947	15570										
MYH3	4621	hgsc.bcm.edu	37	chr17	10535885	10535885	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatctcgatttcattcaggtCcccctccatcttcttcttga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:10535885delC	ENST00000583535.1	-	34	4951	c.4864delG	c.(4864-4866)gacfs	p.D1622fs	MYH3_ENST00000226209.7_Frame_Shift_Del_p.D1622fs	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1622			D -> A (in DA2B). {ECO:0000269|PubMed:16642020}.		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)	p.D1622N(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TCATTCAGGTCCCCCTCCATC	0.587																																					p.D1622fs		Atlas-INDEL	.											.	MYH3	227	.	1	Substitution - Missense(1)	lung(1)	c.4865delA						.						210	206	207					17																	10535885		2203	4300	6503	SO:0001589	frameshift_variant	4621	exon34			.		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4864delG	chr17.hg19:g.10535885delC	ENSP00000464317:p.Asp1622fs	123.0	0.0		135.0	10.0	NM_002470	Q15492	Frame_Shift_Del	DEL	ENST00000583535.1	hg19	CCDS11157.1																																																																																			.	.		0.587	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		-	10535885	C	-	10535885	7	5	103	1	0	1	0	1	0	0	0	0	10045	855	30	0	990	0	MYH3	17	10535885	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	108101	10535885	70659325	948	15571										
MYH3	4621	hgsc.bcm.edu	37	chr17	10546255	10546255	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcacgaacatgtggtggttgAaaaactgttgcagtttctca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:10546255delA	ENST00000583535.1	-	15	1556	c.1469delT	c.(1468-1470)ttcfs	p.F490fs	MYH3_ENST00000226209.7_Frame_Shift_Del_p.F490fs	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	490	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						GTGGTGGTTGAAAAACTGTTG	0.453																																					p.F490fs		Atlas-INDEL	.											.	MYH3	227	.	0			c.1470delC						.						131	120	124					17																	10546255		2203	4297	6500	SO:0001589	frameshift_variant	4621	exon15			.		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.1469delT	chr17.hg19:g.10546255delA	ENSP00000464317:p.Phe490fs	108.0	0.0		110.0	10.0	NM_002470	Q15492	Frame_Shift_Del	DEL	ENST00000583535.1	hg19	CCDS11157.1																																																																																			.	.		0.453	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		-	10546255	A	-	10546255	7	5	103	1	0	1	0	1	0	0	0	0	10045	246	9	0	4461	0	MYH3	17	10546255	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	10370	10546255	70648955	949	15572										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12666622	12666622	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgagtgatgtcacccttctAaaaattgggagcgaagagcc					rs369384824	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:12666622delA	ENST00000343344.4	+	13	2478	c.2478delA	c.(2476-2478)ctafs	p.L826fs	RP11-1090M7.1_ENST00000584772.1_RNA|MYOCD_ENST00000425538.1_Frame_Shift_Del_p.L874fs			Q8IZQ8	MYCD_HUMAN	myocardin	826					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		TCACCCTTCTAAAAATTGGGA	0.478																																					p.L874fs		Atlas-INDEL	.											.	MYOCD	291	.	0			c.2621delT						.						73	71	71					17																	12666622		2203	4300	6503	SO:0001589	frameshift_variant	93649	exon14			.	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.2478delA	chr17.hg19:g.12666622delA	ENSP00000341835:p.Leu826fs	170.0	0.0		179.0	11.0	NM_001146312	Q5UBU5|Q8N7Q1	Frame_Shift_Del	DEL	ENST00000343344.4	hg19	CCDS11163.1																																																																																			.	.		0.478	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		-	12666622	A	-	12666622	7	5	103	1	0	1	0	1	0	0	0	0	10096	349	13	0	2688	0	MYOCD	17	12666622	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2120367	12666622	68528588	950	15573										
SLC47A2	146802	hgsc.bcm.edu	37	chr17	19617255	19617255	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgccccgctgcaggatcacgCccacgtgcttcttgttgggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:19617255delC	ENST00000325411.5	-	4	376	c.326delG	c.(325-327)ggcfs	p.G109fs	SLC47A2_ENST00000463318.1_5'UTR|SLC47A2_ENST00000350657.5_Frame_Shift_Del_p.G109fs	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	109					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	CAGGATCACGCCCACGTGCTT	0.662																																					p.G109fs		Atlas-INDEL	.											.	SLC47A2	61	.	0			c.327delC						.						74	69	71					17																	19617255		2203	4300	6503	SO:0001589	frameshift_variant	146802	exon4			.	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"Solute carriers"	26439	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 2"	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.326delG	chr17.hg19:g.19617255delC	ENSP00000326671:p.Gly109fs	133.0	0.0		131.0	11.0	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Frame_Shift_Del	DEL	ENST00000325411.5	hg19	CCDS11211.1																																																																																			.	.		0.662	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908		-	19617255	C	-	19617255	7	5	103	1	0	1	0	1	0	0	0	0	14663	739	26	0	1538	0	SLC47A2	17	19617255	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	6950633	19617255	61577955	951	15574										
CYTSB	92521	hgsc.bcm.edu	37	chr17	19999991	19999991	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtgcagccaagccctggaaCccagccatcagagcaggggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:19999991delC	ENST00000261503.5	+	2	78	c.27delC	c.(25-27)aacfs	p.N9fs	SPECC1_ENST00000395529.3_Frame_Shift_Del_p.N9fs|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395527.4_Frame_Shift_Del_p.N9fs	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	9					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		AGCCCTGGAACCCAGCCATCA	0.562																																					p.N9fs		Atlas-INDEL	.											.	SPECC1	100	.	0			c.26delA						.						74	84	81					17																	19999991		2203	4300	6503	SO:0001589	frameshift_variant	92521	exon2			.	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"sperm antigen HCMOGT 1", "cytokinesis and spindle organization B", "cytospin B"	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.27delC	chr17.hg19:g.19999991delC	ENSP00000261503:p.Asn9fs	168.0	0.0		158.0	11.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Frame_Shift_Del	DEL	ENST00000261503.5	hg19	CCDS32590.1																																																																																			.	.		0.562	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904		-	19999991	C	-	19999991	7	5	103	1	0	1	0	1	0	0	0	0	4212	506	18	0	29	0	CYTSB	17	19999991	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	382736	19999991	61195219	952	15575										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27438464	27438464	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgggagtcctgcaggagccGgggggcattctgggtggctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:27438464delG	ENST00000527372.1	-	17	3058	c.2878delC	c.(2878-2880)cggfs	p.R960fs	MYO18A_ENST00000533112.1_Frame_Shift_Del_p.R960fs|MYO18A_ENST00000531253.1_Frame_Shift_Del_p.R960fs|MYO18A_ENST00000354329.4_Frame_Shift_Del_p.R960fs	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	960	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			TGCAGGAGCCGGGGGGCATTC	0.592											OREG0024287	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R960fs	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-INDEL	.											MYO18A_ENST00000527372,colon,carcinoma,0,2	MYO18A	217	.	0			c.2879delG						.						69	71	70					17																	27438464		1919	4134	6053	SO:0001589	frameshift_variant	399687	exon17			.	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.2878delC	chr17.hg19:g.27438464delG	ENSP00000437073:p.Arg960fs	135.0	0.0	794	148.0	10.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Frame_Shift_Del	DEL	ENST00000527372.1	hg19	CCDS45642.1																																																																																			.	.		0.592	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		-	27438464	G	-	27438464	7	5	103	1	0	1	0	1	0	0	0	0	10074	1115	39	0	3390	0	MYO18A	17	27438464	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	7438473	27438464	53756746	953	15576										
RHOT1	55288	hgsc.bcm.edu	37	chr17	30535190	30535190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaagtcagacctgcatgaagTtaaacaagaatacagtattt	7	6	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:30535190T>C	ENST00000333942.6	+	18	1840	c.1601T>C	c.(1600-1602)gTt>gCt	p.V534A	RHOT1_ENST00000358365.3_Missense_Mutation_p.V534A|RHOT1_ENST00000354266.3_Missense_Mutation_p.V513A|RHOT1_ENST00000545287.2_Missense_Mutation_p.V534A|RHOT1_ENST00000394692.2_Missense_Mutation_p.V534A|RHOT1_ENST00000583994.1_Missense_Mutation_p.V407A|RHOT1_ENST00000581094.1_Missense_Mutation_p.V534A	NM_018307.3	NP_060777.3	Q8IXI2	MIRO1_HUMAN	ras homolog family member T1	534	Miro 2.				cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				CTGCATGAAGTTAAACAAGAA	0.393																																					p.V534A		Atlas-SNP	.											.	RHOT1	69	.	0			c.T1601C						.						117	109	112					17																	30535190		2203	4300	6503	SO:0001583	missense	55288	exon18			ATGAAGTTAAACA	AJ517412	CCDS32610.1, CCDS32611.1, CCDS32612.1, CCDS74030.1, CCDS74031.1	17q11.2-q12	2013-01-10	2012-02-27	2004-03-24		ENSG00000126858		"EF-hand domain containing"	21168	protein-coding gene	gene with protein product	"mitochondrial Rho (MIRO) GTPase 1"	613888	"ras homolog gene family, member T1"	ARHT1		12482879	Standard	NM_001033567		Approved	MIRO-1, FLJ11040	uc002hgw.3	Q8IXI2		ENST00000333942.6:c.1601T>C	chr17.hg19:g.30535190T>C	ENSP00000334724:p.Val534Ala	104.0	0.0		97.0	4.0	NM_001033568	A4FVB6|A6NFV0|B4DG48|J9JIH9|Q6NUR3|Q6P9F8|Q6PJG1|Q6YMW8|Q86UB0|Q8IW28|Q8IXJ7|Q9H067|Q9H9N8|Q9NUZ2	Missense_Mutation	SNP	ENST00000333942.6	hg19	CCDS32612.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.193786	0.38707	.	.	ENSG00000126858	ENST00000358365;ENST00000354266;ENST00000394692;ENST00000333942	T;T;T	0.19806	2.12;2.12;2.12	5.93	5.93	0.95920	MIRO (1);	0.108387	0.64402	D	0.000007	T	0.18215	0.0437	L	0.28649	0.875	0.80722	D	1	B;B;B;B	0.16603	0.001;0.002;0.018;0.002	B;B;B;B	0.19148	0.004;0.007;0.024;0.011	T	0.04153	-1.0973	10	0.27082	T	0.32	-13.8372	16.3766	0.83401	0.0:0.0:0.0:1.0	.	534;534;534;534	Q8IXI2-2;Q8IXI2;Q8IXI2-5;Q8IXI2-3	.;MIRO1_HUMAN;.;.	A	534	ENSP00000351132:V534A;ENSP00000378184:V534A;ENSP00000334724:V534A	ENSP00000334724:V534A	V	+	2	0	RHOT1	27559303	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.231000	0.72307	2.263000	0.75096	0.533000	0.62120	GTT	.	.		0.393	RHOT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000447097.1	NM_018307		C	30535190	T	C	30535190	3	2	103	1	0	0	0	0	1	0	0	0	13358	1725	60	2	1671	2	RHOT1	17	30535190	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	3096726	30535190	50660020	954	15577										
MYO1D	4642	hgsc.bcm.edu	37	chr17	30980960	30980960	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctgaggtctgaggtgtatcTggcttctgaaagagaaagga	14	6	3	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:30980960T>C	ENST00000318217.5	-	19	2800	c.2496A>G	c.(2494-2496)ccA>ccG	p.P832P	MYO1D_ENST00000579584.1_Silent_p.P832P|RP11-220C2.1_ENST00000582272.1_RNA|MYO1D_ENST00000394649.4_Silent_p.P744P	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	832	Myosin tail. {ECO:0000255}.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.P832P(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			GAGGTGTATCTGGCTTCTGAA	0.393																																					p.P832P		Atlas-SNP	.											MYO1D,colon,carcinoma,0,1	MYO1D	93	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2496G						.						87	72	77					17																	30980960		2203	4300	6503	SO:0001819	synonymous_variant	4642	exon19			TGTATCTGGCTTC	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"Myosins / Myosin superfamily : Class I"	7598	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 108"	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.2496A>G	chr17.hg19:g.30980960T>C		37.0	0.0		43.0	2.0	NM_015194	A6H8V3|Q8NHP9	Silent	SNP	ENST00000318217.5	hg19	CCDS32615.1																																																																																			.	.		0.393	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			C	30980960	T	C	30980960	2	2	103	1	0	0	0	0	0	0	0	1	10080	1567	55	2		2	MYO1D	17	30980960	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	445770	30980960	50214250	955	15578										
MYO1D	4642	hgsc.bcm.edu	37	chr17	31094666	31094666	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctactcaccaagtgcagaatAgcagccaaaatcttatacac	5	12	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:31094666A>G	ENST00000318217.5	-	7	1123	c.819T>C	c.(817-819)gcT>gcC	p.A273A	MYO1D_ENST00000579584.1_Silent_p.A273A|MYO1D_ENST00000583621.1_Silent_p.A273A|MYO1D_ENST00000394649.4_Silent_p.A185A	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	273	Myosin motor.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			AGTGCAGAATAGCAGCCAAAA	0.413																																					p.A273A		Atlas-SNP	.											.	MYO1D	93	.	0			c.T819C						.						121	101	108					17																	31094666		2203	4300	6503	SO:0001819	synonymous_variant	4642	exon7			CAGAATAGCAGCC	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"Myosins / Myosin superfamily : Class I"	7598	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 108"	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.819T>C	chr17.hg19:g.31094666A>G		56.0	0.0		86.0	5.0	NM_015194	A6H8V3|Q8NHP9	Silent	SNP	ENST00000318217.5	hg19	CCDS32615.1																																																																																			.	.		0.413	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			G	31094666	A	G	31094666	2	3	103	1	0	0	0	0	0	0	0	1	10080	407	15	2		2	MYO1D	17	31094666	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	113706	31094666	50100544	956	15579										
SLFN11	91607	hgsc.bcm.edu	37	chr17	33680769	33680769	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacacaccttcccggtgtagCcccccatgttcactagcttc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:33680769delC	ENST00000394566.1	-	6	1780	c.1508delG	c.(1507-1509)ggcfs	p.G503fs	SLFN11_ENST00000308377.4_Frame_Shift_Del_p.G503fs	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	503					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCCGGTGTAGCCCCCCATGTT	0.577																																					p.G503fs		Atlas-INDEL	.											.	SLFN11	112	.	0			c.1509delC						.						8	7	7					17																	33680769		2087	4116	6203	SO:0001589	frameshift_variant	91607	exon4			.	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.1508delG	chr17.hg19:g.33680769delC	ENSP00000378067:p.Gly503fs	366.0	0.0		338.0	21.0	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Frame_Shift_Del	DEL	ENST00000394566.1	hg19	CCDS11294.1																																																																																			.	.		0.577	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		-	33680769	C	-	33680769	7	5	103	1	0	1	0	1	0	0	0	0	14748	739	26	0	1205	0	SLFN11	17	33680769	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2586103	33680769	47514441	957	15580										
GAS2L2	246176	hgsc.bcm.edu	37	chr17	34073357	34073357	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcggcctttttgggtagatgAggactgggggctgggtgggc	20	6	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:34073357A>G	ENST00000254466.6	-	6	1186	c.1159T>C	c.(1159-1161)Tca>Cca	p.S387P	GAS2L2_ENST00000587565.1_Missense_Mutation_p.S371P	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	387					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TGGGTAGATGAGGACTGGGGG	0.587																																					p.S387P		Atlas-SNP	.											.	GAS2L2	94	.	0			c.T1159C						.						84	97	93					17																	34073357		2203	4300	6503	SO:0001583	missense	246176	exon6			TAGATGAGGACTG	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1159T>C	chr17.hg19:g.34073357A>G	ENSP00000254466:p.Ser387Pro	73.0	0.0		77.0	4.0	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	hg19	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	A	18.55	3.649306	0.67358	.	.	ENSG00000132139	ENST00000254466	T	0.20332	2.08	5.03	5.03	0.67393	.	0.528731	0.15747	N	0.246619	T	0.35038	0.0918	L	0.53249	1.67	0.09310	N	1	D	0.64830	0.994	P	0.58721	0.844	T	0.11767	-1.0574	10	0.33141	T	0.24	-3.1015	12.2752	0.54730	1.0:0.0:0.0:0.0	.	387	Q8NHY3	GA2L2_HUMAN	P	387	ENSP00000254466:S387P	ENSP00000254466:S387P	S	-	1	0	GAS2L2	31097470	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	1.143000	0.31553	2.118000	0.64928	0.533000	0.62120	TCA	.	.		0.587	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		G	34073357	A	G	34073357	3	3	103	1	0	0	0	0	1	0	0	0	6255	304	11	2	1487	2	GAS2L2	17	34073357	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	392588	34073357	47121853	958	15581										
ACACA	31	hgsc.bcm.edu	37	chr17	35487101	35487101	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgttgtgcataatctggatgCcccccagctggttattggag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:35487101delC	ENST00000394406.2	-	46	5802	c.5612delG	c.(5611-5613)ggcfs	p.G1871fs	ACACA_ENST00000335166.5_Frame_Shift_Del_p.G1793fs|ACACA_ENST00000361253.5_5'UTR|ACACA_ENST00000353139.5_Frame_Shift_Del_p.G1908fs|ACACA_ENST00000360679.3_Frame_Shift_Del_p.G1813fs	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1871	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AATCTGGATGCCCCCCAGCTG	0.493																																					p.G1908fs	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-INDEL	.											.	ACACA	395	.	0			c.5724delC						.						182	162	169					17																	35487101		2203	4300	6503	SO:0001589	frameshift_variant	31	exon46			.	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.5612delG	chr17.hg19:g.35487101delC	ENSP00000377928:p.Gly1871fs	200.0	0.0		192.0	13.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Frame_Shift_Del	DEL	ENST00000394406.2	hg19	CCDS11317.1																																																																																			.	.		0.493	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		-	35487101	C	-	35487101	7	5	103	1	0	1	0	1	0	0	0	0	106	739	26	0	1472	0	ACACA	17	35487101	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1413744	35487101	45708109	959	15582										
DDX52	11056	hgsc.bcm.edu	37	chr17	35988606	35988606	+	Splice_Site	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccatgtatgaattccttaccAaactttttagatgatttagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:35988606delA	ENST00000349699.2	-	6	901	c.858delT	c.(856-858)ttt>tt	p.F286fs	DDX52_ENST00000394367.3_Splice_Site_p.F178fs	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	286	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				ATTCCTTACCAAACTTTTTAG	0.343																																					p.D287fs		Atlas-INDEL	.											.	DDX52	40	.	0			c.859delG						.						116	110	112					17																	35988606		2203	4300	6503	SO:0001630	splice_region_variant	11056	exon6			.	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"DEAD-boxes"	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.859+1T>-	chr17.hg19:g.35988606delA		102.0	0.0		142.0	11.0	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Frame_Shift_Del	DEL	ENST00000349699.2	hg19	CCDS11323.1																																																																																			.	.		0.343	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300	Frame_Shift_Del	-	35988606	A	-	35988606	8	5	103	1	0	1	0	1	0	0	1	0	4372	144	5	0	981	0	DDX52	17	35988606	Splice_Site	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	501505	35988606	45206604	960	15583										
DDX52	11056	hgsc.bcm.edu	37	chr17	36002258	36002258	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgatgctccacacacacctGggacagacttcttgtttcca					rs139568647		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:36002258delG	ENST00000349699.2	-	2	210	c.167delC	c.(166-168)ccafs	p.P56fs	RP11-697E22.2_ENST00000586950.1_RNA|RP11-697E22.2_ENST00000586163.1_RNA|DDX52_ENST00000394367.3_5'UTR	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	56						membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				ACACACACCTGGGACAGACTT	0.408																																					p.P56fs		Atlas-INDEL	.											.	DDX52	40	.	0			c.168delA						.						116	116	116					17																	36002258		2203	4300	6503	SO:0001589	frameshift_variant	11056	exon2			.	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"DEAD-boxes"	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.167delC	chr17.hg19:g.36002258delG	ENSP00000268854:p.Pro56fs	185.0	0.0		181.0	11.0	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Frame_Shift_Del	DEL	ENST00000349699.2	hg19	CCDS11323.1																																																																																			.	.		0.408	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		-	36002258	G	-	36002258	7	5	103	1	0	1	0	1	0	0	0	0	4372	1348	47	0	1688	0	DDX52	17	36002258	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	13652	36002258	45192952	961	15584										
FBXO47	494188	hgsc.bcm.edu	37	chr17	37101381	37101381	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gattcttaactccagtttttGggcacttcctatgaagacaa	7	9	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:37101381G>C	ENST00000378079.2	-	7	824	c.625C>G	c.(625-627)Caa>Gaa	p.Q209E		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	209			Q -> R (in dbSNP:rs9906595). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15723337}.							NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						TCCAGTTTTTGGGCACTTCCT	0.363																																					p.Q209E		Atlas-SNP	.											.	FBXO47	34	.	0			c.C625G						.						93	83	86					17																	37101381		2203	4300	6503	SO:0001583	missense	494188	exon7			GTTTTTGGGCACT		CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"F-boxes /  "other""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.625C>G	chr17.hg19:g.37101381G>C	ENSP00000367319:p.Gln209Glu	81.0	0.0		100.0	5.0	NM_001008777	B2RTZ4	Missense_Mutation	SNP	ENST00000378079.2	hg19	CCDS32639.1	.	.	.	.	.	.	.	.	.	.	G	8.497	0.863270	0.17250	.	.	ENSG00000204952	ENST00000378079	T	0.69435	-0.4	5.53	0.682	0.17992	.	0.314310	0.34156	N	0.004213	T	0.35364	0.0929	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.28902	-1.0029	10	0.02654	T	1	-0.0407	8.2704	0.31840	0.0778:0.0:0.3612:0.5611	.	209	Q5MNV8	FBX47_HUMAN	E	209	ENSP00000367319:Q209E	ENSP00000367319:Q209E	Q	-	1	0	FBXO47	34354907	0.998000	0.40836	0.801000	0.32222	0.799000	0.45148	0.964000	0.29306	0.662000	0.31006	0.585000	0.79938	CAA	.	.		0.363	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777		C	37101381	G	C	37101381	3	2	103	1	0	0	0	0	1	0	0	0	5764	1357	47	4	753	4	FBXO47	17	37101381	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	1099123	37101381	44093829	962	15585										
PSMD3	5709	hgsc.bcm.edu	37	chr17	38137367	38137367	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcgacgggtggcgggtcgacGggggaggcagacggcaagac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:38137367delG	ENST00000264639.4	+	1	318	c.144delG	c.(142-144)acgfs	p.T48fs	PSMD3_ENST00000541736.1_Intron	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	48					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Colorectal(19;0.000442)					GCGGGTCGACGGGGGAGGCAG	0.711											OREG0024385	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T48fs	Ovarian(186;531 2051 6385 19668 48409)	Atlas-INDEL	.											.	PSMD3	56	.	0			c.143delC						.						10	18	15					17																	38137367		1961	3796	5757	SO:0001589	frameshift_variant	5709	exon1			.	D67025	CCDS11356.1	17q21.2	2010-07-23			ENSG00000108344	ENSG00000108344		"Proteasome (prosome, macropain) subunits"	9560	protein-coding gene	gene with protein product			"tissue specific transplantation antigen 2"	TSTA2		9017604	Standard	NM_002809		Approved	S3, P58, Rpn3	uc002htn.2	O43242	OTTHUMG00000133251	ENST00000264639.4:c.144delG	chr17.hg19:g.38137367delG	ENSP00000264639:p.Thr48fs	119.0	0.0	875	175.0	12.0	NM_002809	B3KMW9|B4DT72|Q96EI2|Q9BQA4	Frame_Shift_Del	DEL	ENST00000264639.4	hg19	CCDS11356.1																																																																																			.	.		0.711	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1	NM_002809		-	38137367	G	-	38137367	7	5	103	1	0	1	0	1	0	0	0	0	12711	1103	39	0	146	0	PSMD3	17	38137367	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1035986	38137367	43057843	963	15586										
KRT28	162605	hgsc.bcm.edu	37	chr17	38948685	38948685	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctctaaaatgacagctagaaAggaaccctttgttctgtctt	7	9	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:38948685A>G	ENST00000306658.7	-	8	1454	c.1389T>C	c.(1387-1389)ccT>ccC	p.P463P		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				ACAGCTAGAAAGGAACCCTTT	0.338																																					p.P463P	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.T1389C						.						107	99	101					17																	38948685		2202	4300	6502	SO:0001819	synonymous_variant	162605	exon8			CTAGAAAGGAACC	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"-", "Intermediate filaments type I, keratins (acidic)"	30842	protein-coding gene	gene with protein product			"keratin 25D"	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.1389T>C	chr17.hg19:g.38948685A>G		90.0	0.0		93.0	4.0	NM_181535		Silent	SNP	ENST00000306658.7	hg19	CCDS11376.1																																																																																			.	.		0.338	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535		G	38948685	A	G	38948685	2	3	103	1	0	0	0	0	0	0	0	1	8474	59	3	2		2	KRT28	17	38948685	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	811318	38948685	42246525	964	15587										
KRT38	8687	hgsc.bcm.edu	37	chr17	39595478	39595478	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcgtggttgctcttgagggAgagctgctcctccttcaggg	14	11	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:39595478A>G	ENST00000246646.3	-	3	708	c.709T>C	c.(709-711)Tcc>Ccc	p.S237P		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	237	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				CTCTTGAGGGAGAGCTGCTCC	0.662																																					p.S237P		Atlas-SNP	.											.	KRT38	63	.	0			c.T709C						.						55	50	52					17																	39595478		2203	4300	6503	SO:0001583	missense	8687	exon3			TGAGGGAGAGCTG	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"-", "Intermediate filaments type I, keratins (acidic)"	6456	protein-coding gene	gene with protein product		604542	"keratin, hair, acidic, 8"	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.709T>C	chr17.hg19:g.39595478A>G	ENSP00000246646:p.Ser237Pro	97.0	0.0		97.0	4.0	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	hg19	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	A	12.07	1.826498	0.32329	.	.	ENSG00000171360	ENST00000246646	D	0.88741	-2.42	4.31	0.455	0.16649	Filament (1);	0.877622	0.09568	N	0.784620	D	0.88983	0.6586	L	0.47190	1.495	0.09310	N	1	D	0.57571	0.98	P	0.57468	0.821	T	0.77778	-0.2460	10	0.72032	D	0.01	.	5.4669	0.16648	0.3567:0.2612:0.0:0.3821	.	237	O76015	KRT38_HUMAN	P	237	ENSP00000246646:S237P	ENSP00000246646:S237P	S	-	1	0	KRT38	36849004	0.000000	0.05858	0.660000	0.29694	0.330000	0.28571	0.233000	0.17911	-0.127000	0.11661	-0.636000	0.03981	TCC	.	.		0.662	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		G	39595478	A	G	39595478	3	3	103	1	0	0	0	0	1	0	0	0	8484	304	11	2	681	2	KRT38	17	39595478	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	646793	39595478	41599732	965	15588										
SC65	10609	hgsc.bcm.edu	37	chr17	39959614	39959614	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccctcctcgtagtcaccctCcccctcaaactcggcgtcag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:39959614delC	ENST00000355468.3	-	8	1682	c.1216delG	c.(1216-1218)gagfs	p.E406fs	LEPREL4_ENST00000393928.1_Frame_Shift_Del_p.E406fs			Q92791	SC65_HUMAN	leprecan-like 4	406	Asp/Glu-rich (acidic).				synaptonemal complex assembly (GO:0007130)	condensed nuclear chromosome (GO:0000794)|nucleolus (GO:0005730)|synaptonemal complex (GO:0000795)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	8						TAGTCACCCTCCCCCTCAAAC	0.627																																					p.E406fs		Atlas-INDEL	.											.	LEPREL4	20	.	0			c.1217delA						.						188	147	161					17																	39959614		2203	4300	6503	SO:0001589	frameshift_variant	10609	exon7			.	BC001047	CCDS11408.1	17q12	2013-05-03	2002-08-29		ENSG00000141696	ENSG00000141696			16946	protein-coding gene	gene with protein product			"nucleolar autoantigen (55kD)", "rat synaptonemal complex protein"			8862517	Standard	NM_006455		Approved	SC65, NO55	uc002hxt.3	Q92791	OTTHUMG00000133501	ENST00000355468.3:c.1216delG	chr17.hg19:g.39959614delC	ENSP00000347649:p.Glu406fs	252.0	0.0		219.0	14.0	NM_006455	Q53GI6|Q9H4F6	Frame_Shift_Del	DEL	ENST00000355468.3	hg19	CCDS11408.1																																																																																			.	.		0.627	LEPREL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257439.2			-	39959614	C	-	39959614	7	5	103	1	0	1	0	1	0	0	0	0	13882	864	30	0	105	0	SC65	17	39959614	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	364136	39959614	41235596	966	15589										
STAT5A	6776	hgsc.bcm.edu	37	chr17	40456369	40456369	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcctttgcagcgagtgcagTggtgagatcctgaacaactg	12	10	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:40456369T>C	ENST00000345506.4	+	11	1821	c.1179T>C	c.(1177-1179)agT>agC	p.S393S	STAT5A_ENST00000590949.1_Silent_p.S393S|STAT5A_ENST00000588868.1_Silent_p.S393S|STAT5A_ENST00000452307.2_Silent_p.S393S|STAT5A_ENST00000587646.1_5'Flank|STAT5A_ENST00000546010.2_Silent_p.S363S	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	393					2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		GCGAGTGCAGTGGTGAGATCC	0.642																																					p.S393S		Atlas-SNP	.											.	STAT5A	49	.	0			c.T1179C						.						65	56	59					17																	40456369		2203	4300	6503	SO:0001819	synonymous_variant	6776	exon11			GTGCAGTGGTGAG	U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"SH2 domain containing"	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.1179T>C	chr17.hg19:g.40456369T>C		86.0	0.0		85.0	4.0	NM_003152	Q1KLZ6	Silent	SNP	ENST00000345506.4	hg19	CCDS11424.1																																																																																			.	.		0.642	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152		C	40456369	T	C	40456369	2	2	103	1	0	0	0	0	0	0	0	1	15283	1693	59	2		2	STAT5A	17	40456369	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	496755	40456369	40738841	967	15590										
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42478249	42478249	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttttactttgcagtgtgctGgggggatgtagtggtaatac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:42478249delG	ENST00000591680.1	-	8	1226	c.1196delC	c.(1195-1197)ccafs	p.P399fs	GPATCH8_ENST00000434000.1_Frame_Shift_Del_p.P321fs	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	399							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GCAGTGTGCTGGGGGGATGTA	0.438											OREG0024461	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P399fs		Atlas-INDEL	.											.	GPATCH8	114	.	0			c.1197delA						.						110	110	110					17																	42478249		2203	4300	6503	SO:0001589	frameshift_variant	23131	exon8			.	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"G patch domain containing"	29066	protein-coding gene	gene with protein product		614396	"KIAA0553"	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.1196delC	chr17.hg19:g.42478249delG	ENSP00000467556:p.Pro399fs	110.0	0.0	909	122.0	10.0	NM_001002909	B9EGP9|O60300|Q8TB99	Frame_Shift_Del	DEL	ENST00000591680.1	hg19	CCDS32666.1																																																																																			.	.		0.438	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		-	42478249	G	-	42478249	7	5	103	1	0	1	0	1	0	0	0	0	6602	1348	47	0	3316	0	GPATCH8	17	42478249	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2021880	42478249	38716961	968	15591										
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42929803	42929803	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtggtggaagacagacagagAaaaggcttgtccctgggtgt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:42929803delA	ENST00000426333.2	-	26	2986	c.2689delT	c.(2689-2691)tctfs	p.S897fs	EFTUD2_ENST00000591382.1_Frame_Shift_Del_p.S897fs|EFTUD2_ENST00000592576.1_Frame_Shift_Del_p.S887fs|EFTUD2_ENST00000402521.3_Frame_Shift_Del_p.S862fs	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	897					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				ACAGACAGAGAAAAGGCTTGT	0.557																																					p.S897fs	Ovarian(10;65 485 10258 29980 30707)	Atlas-INDEL	.											.	EFTUD2	85	.	0			c.2690delC						.						76	66	69					17																	42929803		2203	4300	6503	SO:0001589	frameshift_variant	9343	exon26			.	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.2689delT	chr17.hg19:g.42929803delA	ENSP00000392094:p.Ser897fs	157.0	0.0		156.0	13.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Frame_Shift_Del	DEL	ENST00000426333.2	hg19	CCDS11489.1																																																																																			.	.		0.557	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		-	42929803	A	-	42929803	7	5	103	1	0	1	0	1	0	0	0	0	4963	246	9	0	241	0	EFTUD2	17	42929803	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	451554	42929803	38265407	969	15592										
MAPT	4137	hgsc.bcm.edu	37	chr17	44060593	44060593	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggcttcctccgagagccaggCcccccaggtctgagccacca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:44060593delC	ENST00000571987.1	+	5	423	c.423delC	c.(421-423)ggcfs	p.G141fs	MAPT_ENST00000347967.5_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000415613.2_Frame_Shift_Del_p.G141fs|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Frame_Shift_Del_p.G141fs|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000262410.5_Frame_Shift_Del_p.G141fs			P10636	TAU_HUMAN	microtubule-associated protein tau	141					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GAGAGCCAGGCCCCCCAGGTC	0.657																																					p.G141fs		Atlas-INDEL	.											.	MAPT	135	.	0			c.422delG						.						20	18	19					17																	44060593		2203	4298	6501	SO:0001589	frameshift_variant	4137	exon6			.	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.423delC	chr17.hg19:g.44060593delC	ENSP00000458742:p.Gly141fs	169.0	0.0		163.0	10.0	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Frame_Shift_Del	DEL	ENST00000571987.1	hg19	CCDS11501.1																																																																																			.	.		0.657	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		-	44060593	C	-	44060593	7	5	103	1	0	1	0	1	0	0	0	0	9306	726	26	0	441	0	MAPT	17	44060593	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1130790	44060593	37134617	970	15593										
C17orf57	124989	hgsc.bcm.edu	37	chr17	45451902	45451902	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagttatcaagtgtagcaggAtgctatctaaaatataagaa	8	4	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:45451902A>G	ENST00000331493.2	+	12	1353	c.942A>G	c.(940-942)ggA>ggG	p.G314G	EFCAB13_ENST00000517484.1_Silent_p.G218G	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	314						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										GTGTAGCAGGATGCTATCTAA	0.284																																					p.G314G		Atlas-SNP	.											.	.	.	.	0			c.A942G						.						31	35	34					17																	45451902		2189	4260	6449	SO:0001819	synonymous_variant	124989	exon12			AGCAGGATGCTAT	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.942A>G	chr17.hg19:g.45451902A>G		76.0	0.0		92.0	4.0	NM_152347	G3V128|Q49AG9	Silent	SNP	ENST00000331493.2	hg19	CCDS11512.1																																																																																			.	.		0.284	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		G	45451902	A	G	45451902	2	3	103	1	0	0	0	0	0	0	0	1	1867	320	12	2		2	C17orf57	17	45451902	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1391309	45451902	35743308	971	15594										
C17orf57	124989	hgsc.bcm.edu	37	chr17	45468832	45468832	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgtcattaaagccattgatAaaattaaagataaaaatgtg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:45468832delA	ENST00000331493.2	+	15	2023	c.1612delA	c.(1612-1614)aaafs	p.K538fs	EFCAB13_ENST00000517484.1_Frame_Shift_Del_p.K442fs	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	538	EF-hand 2.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										AGCCATTGATAAAATTAAAGA	0.279																																					p.D537fs		Atlas-INDEL	.											.	.	.	.	0			c.1611delT						.						47	51	49					17																	45468832		2203	4299	6502	SO:0001589	frameshift_variant	124989	exon15			.	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.1612delA	chr17.hg19:g.45468832delA	ENSP00000332111:p.Lys538fs	134.0	0.0		161.0	10.0	NM_152347	G3V128|Q49AG9	Frame_Shift_Del	DEL	ENST00000331493.2	hg19	CCDS11512.1																																																																																			.	.		0.279	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		-	45468832	A	-	45468832	7	5	103	1	0	1	0	1	0	0	0	0	1867	363	13	0	1658	0	C17orf57	17	45468832	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	16930	45468832	35726378	972	15595										
HOXB2	3212	hgsc.bcm.edu	37	chr17	46620942	46620942	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttctgaaaccagactttgaCctgcctttcggtgaggtcca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:46620942delC	ENST00000330070.4	-	2	1726	c.559delG	c.(559-561)gtcfs	p.V187fs	HOXB-AS1_ENST00000435312.1_RNA|HOXB-AS1_ENST00000504972.3_RNA|HOXB-AS1_ENST00000508688.1_RNA|HOXB2_ENST00000504772.3_5'Flank	NM_002145.3	NP_002136.1	P14652	HXB2_HUMAN	homeobox B2	187					anterior/posterior pattern specification (GO:0009952)|blood circulation (GO:0008015)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|neural nucleus development (GO:0048857)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	11						CAGACTTTGACCTGCCTTTCG	0.627																																					p.V187fs		Atlas-INDEL	.											.	HOXB2	23	.	0			c.560delT						.						54	59	57					17																	46620942		2193	4294	6487	SO:0001589	frameshift_variant	3212	exon2			.		CCDS11527.1	17q21.32	2012-02-22	2005-12-22		ENSG00000173917	ENSG00000173917		"Homeoboxes / ANTP class : HOXL subclass"	5113	protein-coding gene	gene with protein product		142967	"homeo box B2"	HOX2, HOX2H		1973146, 1358459	Standard	XM_005257276		Approved		uc002inm.3	P14652	OTTHUMG00000159930	ENST00000330070.4:c.559delG	chr17.hg19:g.46620942delC	ENSP00000331741:p.Val187fs	218.0	0.0		181.0	11.0	NM_002145	P10913|P17485	Frame_Shift_Del	DEL	ENST00000330070.4	hg19	CCDS11527.1																																																																																			.	.		0.627	HOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358384.2			-	46620942	C	-	46620942	7	5	103	1	0	1	0	1	0	0	0	0	7310	507	18	0	515	0	HOXB2	17	46620942	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1152110	46620942	34574268	973	15596										
OR4D1	26689	hgsc.bcm.edu	37	chr17	56232912	56232912	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcccagcccctccggtatgTcaccatcatgaacactcaat	5	17	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:56232912T>C	ENST00000268912.5	+	1	419	c.398T>C	c.(397-399)gTc>gCc	p.V133A		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	133					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13						CTCCGGTATGTCACCATCATG	0.532																																					p.V133A		Atlas-SNP	.											.	OR4D1	48	.	0			c.T398C						.						74	77	76					17																	56232912		2196	4295	6491	SO:0001583	missense	26689	exon1			GGTATGTCACCAT	X89670	CCDS42365.1	17q22	2012-08-09			ENSG00000141194	ENSG00000141194		"GPCR / Class A : Olfactory receptors"	8293	protein-coding gene	gene with protein product				OR4D3		9119360	Standard	NM_012374		Approved	TPCR16	uc010wno.2	Q15615		ENST00000268912.5:c.398T>C	chr17.hg19:g.56232912T>C	ENSP00000365451:p.Val133Ala	89.0	0.0		110.0	7.0	NM_012374	B2RN14|Q8NGB1|Q96R76	Missense_Mutation	SNP	ENST00000268912.5	hg19	CCDS42365.1	.	.	.	.	.	.	.	.	.	.	t	10.31	1.313907	0.23908	.	.	ENSG00000141194	ENST00000268912	T	0.18960	2.18	5.63	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	0.229124	0.30667	N	0.009135	T	0.11067	0.0270	N	0.13371	0.34	0.21697	N	0.999589	B	0.09022	0.002	B	0.14578	0.011	T	0.28681	-1.0036	10	0.22706	T	0.39	-20.0359	7.2199	0.25981	0.0:0.1716:0.0:0.8284	.	133	Q15615	OR4D1_HUMAN	A	133	ENSP00000365451:V133A	ENSP00000365451:V133A	V	+	2	0	OR4D1	53587911	0.000000	0.05858	0.905000	0.35620	0.888000	0.51559	-0.368000	0.07543	0.966000	0.38159	0.443000	0.29094	GTC	.	.		0.532	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1			C	56232912	T	C	56232912	3	2	103	1	0	0	0	0	1	0	0	0	11062	1667	58	2	400	2	OR4D1	17	56232912	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	9611970	56232912	24962298	974	15597										
RAD51C	5889	hgsc.bcm.edu	37	chr17	56798130	56798130	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attttaaccaatcagatgacAacaaagattgatagaaatca	5	6	2	5			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:56798130A>G	ENST00000337432.4	+	6	932	c.861A>G	c.(859-861)acA>acG	p.T287T	RAD51C_ENST00000583539.1_Silent_p.T287T	NM_058216.1	NP_478123.1	O43502	RA51C_HUMAN	RAD51 paralog C	287			T -> A (in BROVCA3; dbSNP:rs28363317). {ECO:0000269|PubMed:20400964, ECO:0000269|PubMed:21990120, ECO:0000269|Ref.2}.		blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|female meiosis sister chromatid cohesion (GO:0007066)|male meiosis I (GO:0007141)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)|sister chromatid cohesion (GO:0007062)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|Rad51C-XRCC3 complex (GO:0033065)|replication fork (GO:0005657)	ATP binding (GO:0005524)|crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)			upper_aerodigestive_tract(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ATCAGATGACAACAAAGATTG	0.323								Homologous recombination	Hereditary Breast-Ovarian Cancer, non-BRCA1/2																												p.T287T		Atlas-SNP	.											.	RAD51C	39	.	0			c.A861G						.						102	105	104					17																	56798130		2203	4300	6503	SO:0001819	synonymous_variant	5889	exon6	Familial Cancer Database	BRCAX	GATGACAACAAAG	AF029670	CCDS11611.1, CCDS45745.1	17q25.1	2014-09-17	2013-07-02		ENSG00000108384	ENSG00000108384		"Fanconi anemia, complementation groups"	9820	protein-coding gene	gene with protein product		602774	"RAD51 (S. cerevisiae) homolog C", "RAD51 homolog C (S. cerevisiae)"			9469824, 22167183	Standard	NM_058216		Approved	RAD51L2, FANCO	uc002iwu.3	O43502	OTTHUMG00000141292	ENST00000337432.4:c.861A>G	chr17.hg19:g.56798130A>G		60.0	0.0		65.0	4.0	NM_058216	O43503|Q3B783	Silent	SNP	ENST00000337432.4	hg19	CCDS11611.1	.	.	.	.	.	.	.	.	.	.	A	8.905	0.957398	0.18507	.	.	ENSG00000108384	ENST00000413590	.	.	.	5.07	3.91	0.45181	.	.	.	.	.	T	0.59418	0.2192	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57341	-0.7828	4	.	.	.	-17.848	9.3048	0.37867	0.8192:0.1808:0.0:0.0	.	.	.	.	D	167	.	.	N	+	1	0	RAD51C	54153129	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.373000	0.34272	1.907000	0.55213	0.383000	0.25322	AAC	.	.		0.323	RAD51C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280540.2	NM_058216		G	56798130	A	G	56798130	2	3	103	1	0	0	0	0	0	0	0	1	13003	117	5	2		2	RAD51C	17	56798130	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	565218	56798130	24397080	975	15598										
DHX40	79665	hgsc.bcm.edu	37	chr17	57656854	57656854	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatgtggtagatggtggcttCgtgaagcagttaaatcacaa					rs375795771		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:57656854delC	ENST00000251241.4	+	9	1242	c.1095delC	c.(1093-1095)ttcfs	p.F365fs	DHX40_ENST00000451169.2_Frame_Shift_Del_p.F317fs|DHX40_ENST00000425628.3_Frame_Shift_Del_p.F288fs	NM_024612.4	NP_078888.4	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	365	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(7)|large_intestine(6)|lung(6)|prostate(1)	20	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					ATGGTGGCTTCGTGAAGCAGT	0.358																																					p.F365fs		Atlas-INDEL	.											.	DHX40	40	.	0			c.1094delT						.						38	57	53					17																	57656854		984	4080	5064	SO:0001589	frameshift_variant	79665	exon9			.	AF260270	CCDS11617.1, CCDS54150.1	17q22	2014-01-28	2003-06-13	2003-06-20		ENSG00000108406		"DEAH-boxes"	18018	protein-coding gene	gene with protein product		607570	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 40 (RNA helicase)"	DDX40			Standard	NM_024612		Approved	ARG147, PAD, FLJ22060	uc002ixn.2	Q8IX18		ENST00000251241.4:c.1095delC	chr17.hg19:g.57656854delC	ENSP00000251241:p.Phe365fs	3.0	0.0		10.0	10.0	NM_024612	B3KTJ5|C9JR60|Q5JPH4|Q8TC86|Q8WY53|Q9BXM1|Q9H6M9	Frame_Shift_Del	DEL	ENST00000251241.4	hg19	CCDS11617.1																																																																																			.	.		0.358	DHX40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446095.1	NM_024612		-	57656854	C	-	57656854	7	5	103	1	0	1	0	1	0	0	0	0	4514	883	31	0	1129	0	DHX40	17	57656854	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	858724	57656854	23538356	976	15599										
CLTC	1213	hgsc.bcm.edu	37	chr17	57756782	57756782	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcaatgagaattccctcttcAaaagtctttctcgctacctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:57756782delA	ENST00000269122.3	+	18	3095	c.2821delA	c.(2821-2823)aaafs	p.K941fs	CLTC_ENST00000579456.1_Intron|CLTC_ENST00000393043.1_Frame_Shift_Del_p.K941fs	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	941	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TTCCCTCTTCAAAAGTCTTTC	0.403			T	"ALK, TFE3"	"ALCL, renal "																																p.F940fs		Atlas-INDEL	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.2820delC						.						75	72	73					17																	57756782		2203	4300	6503	SO:0001589	frameshift_variant	1213	exon18			.	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2821delA	chr17.hg19:g.57756782delA	ENSP00000269122:p.Lys941fs	169.0	0.0		189.0	13.0	NM_004859	D3DU00|Q6N0A0|Q86TF2	Frame_Shift_Del	DEL	ENST00000269122.3	hg19	CCDS32696.1																																																																																			.	.		0.403	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		-	57756782	A	-	57756782	7	5	103	1	0	1	0	1	0	0	0	0	3568	131	5	0	2891	0	CLTC	17	57756782	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	99928	57756782	23438428	977	15600										
PTRH2	51651	hgsc.bcm.edu	37	chr17	57774925	57774925	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atcttgaattaaacttacagTcagtcccagcatttttgcat	5	9	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:57774925T>C	ENST00000470557.2	-	1	3861	c.415A>G	c.(415-417)Act>Gct	p.T139A	PTRH2_ENST00000537860.1_Missense_Mutation_p.T139A|PTRH2_ENST00000579915.1_5'Flank|PTRH2_ENST00000409433.2_Missense_Mutation_p.T140A|PTRH2_ENST00000393038.2_Missense_Mutation_p.T139A			Q9Y3E5	PTH2_HUMAN	peptidyl-tRNA hydrolase 2	139					apoptotic process (GO:0006915)|negative regulation of anoikis (GO:2000811)|negative regulation of gene expression (GO:0010629)|positive regulation of anoikis (GO:2000210)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	aminoacyl-tRNA hydrolase activity (GO:0004045)			large_intestine(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					AAACTTACAGTCAGTCCCAGC	0.478																																					p.T139A		Atlas-SNP	.											.	PTRH2	8	.	0			c.A415G						.						147	138	141					17																	57774925		2203	4300	6503	SO:0001583	missense	51651	exon2			TTACAGTCAGTCC	AF151905	CCDS11618.1	17q23.2	2014-07-18			ENSG00000141378	ENSG00000141378			24265	protein-coding gene	gene with protein product	"Bcl-2 inhibitor of transcription", "cilia and flagella associated protein 37"	608625				10810093, 15006356, 14660562	Standard	XM_005257447		Approved	BIT1, CGI-147, PTH2, CFAP37	uc002ixt.3	Q9Y3E5	OTTHUMG00000154532	ENST00000470557.2:c.415A>G	chr17.hg19:g.57774925T>C	ENSP00000464327:p.Thr139Ala	162.0	0.0		210.0	9.0	NM_016077	B3KUY4|Q9NTE5	Missense_Mutation	SNP	ENST00000470557.2	hg19	CCDS11618.1	.	.	.	.	.	.	.	.	.	.	T	11.21	1.572956	0.28092	.	.	ENSG00000141378	ENST00000393038;ENST00000409433;ENST00000537860	.	.	.	5.82	5.82	0.92795	Peptidyl-tRNA hydrolase II domain (2);	0.123586	0.53938	U	0.000042	T	0.45776	0.1359	L	0.31578	0.945	0.47547	D	0.99945	B	0.33288	0.406	B	0.34180	0.177	T	0.38200	-0.9672	9	0.10902	T	0.67	-14.1597	16.1814	0.81903	0.0:0.0:0.0:1.0	.	139	Q9Y3E5	PTH2_HUMAN	A	139;140;139	.	ENSP00000376758:T139A	T	-	1	0	PTRH2	55129707	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	5.044000	0.64214	2.234000	0.73211	0.533000	0.62120	ACT	.	.		0.478	PTRH2-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000448482.1	NM_016077		C	57774925	T	C	57774925	3	2	103	1	0	0	0	0	1	0	0	0	12832	1667	58	2	128	2	PTRH2	17	57774925	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	18143	57774925	23420285	978	15601										
MRC2	9902	hgsc.bcm.edu	37	chr17	60743521	60743521	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccccttcaaatatgacaaccAgtggttccacggctgcacca	7	15	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:60743521A>G	ENST00000303375.5	+	3	989	c.587A>G	c.(586-588)cAg>cGg	p.Q196R		NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	196	Fibronectin type-II. {ECO:0000255|PROSITE-ProRule:PRU00479}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						TATGACAACCAGTGGTTCCAC	0.637																																					p.Q196R		Atlas-SNP	.											.	MRC2	126	.	0			c.A587G						.						68	49	56					17																	60743521		2203	4300	6503	SO:0001583	missense	9902	exon3			ACAACCAGTGGTT	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.587A>G	chr17.hg19:g.60743521A>G	ENSP00000307513:p.Gln196Arg	94.0	0.0		88.0	4.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.425345	0.83667	.	.	ENSG00000011028	ENST00000303375	T	0.48836	0.8	4.67	4.67	0.58626	Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.000000	0.85682	D	0.000000	T	0.57651	0.2068	L	0.35723	1.085	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.55879	-0.8071	10	0.36615	T	0.2	-20.6129	14.2837	0.66232	1.0:0.0:0.0:0.0	.	196	Q9UBG0	MRC2_HUMAN	R	196	ENSP00000307513:Q196R	ENSP00000307513:Q196R	Q	+	2	0	MRC2	58097253	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.118000	0.71583	1.967000	0.57214	0.459000	0.35465	CAG	.	.		0.637	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			G	60743521	A	G	60743521	3	3	103	1	0	0	0	0	1	0	0	0	9767	188	7	2	597	2	MRC2	17	60743521	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	2968596	60743521	20451689	979	15602										
DDX42	11325	hgsc.bcm.edu	37	chr17	61877936	61877936	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaaatccaattgcacctaccAaaaaaatcattgatcctctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:61877936delA	ENST00000578681.1	+	7	1181	c.580delA	c.(580-582)aaafs	p.K195fs	DDX42_ENST00000583590.1_Frame_Shift_Del_p.K195fs|DDX42_ENST00000457800.2_Frame_Shift_Del_p.K195fs|DDX42_ENST00000389924.2_Frame_Shift_Del_p.K195fs|DDX42_ENST00000359353.5_Frame_Shift_Del_p.K76fs	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	195					protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						TGCACCTACCAAAAAAATCAT	0.403																																					p.T193fs		Atlas-INDEL	.											.	DDX42	86	.	0			c.579delC						.						239	198	212					17																	61877936		2203	4300	6503	SO:0001589	frameshift_variant	11325	exon6			.	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"DEAD-boxes"	18676	protein-coding gene	gene with protein product	"splicing factor 3b, subunit 8"	613369	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.580delA	chr17.hg19:g.61877936delA	ENSP00000464050:p.Lys195fs	135.0	0.0		191.0	15.0	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Frame_Shift_Del	DEL	ENST00000578681.1	hg19	CCDS32704.1																																																																																			.	.		0.403	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372		-	61877936	A	-	61877936	7	5	103	1	0	1	0	1	0	0	0	0	4364	131	5	0	598	0	DDX42	17	61877936	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1134415	61877936	19317274	980	15603										
GH2	2689	hgsc.bcm.edu	37	chr17	61958073	61958073	+	Intron	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagggcagcagtgtttctctCcccagtccctggaagccagt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:61958073delC	ENST00000423893.2	-	4	518				GH2_ENST00000449787.2_Intron|GH2_ENST00000332800.7_Frame_Shift_Del_p.G172fs|GH2_ENST00000456543.2_Intron			P01242	SOM2_HUMAN	growth hormone 2						JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	24						GTGTTTCTCTCCCCAGTCCCT	0.567																																					p.G172fs		Atlas-INDEL	.											.	GH2	73	.	0			c.516delA						.						77	81	79					17																	61958073		2203	4300	6503	SO:0001627	intron_variant	2689	exon4			.	J03756	CCDS11647.1, CCDS11648.1, CCDS45757.1, CCDS45758.1	17q22-q24	2014-01-30						"Endogenous ligands"	4262	protein-coding gene	gene with protein product	"placental-specific growth hormone", "placenta-specific growth hormone"	139240				6306568	Standard	NM_002059		Approved	GH-V, GHV, GHL, hGH-V	uc002jcl.2	P01242		ENST00000423893.2:c.456+58G>-	chr17.hg19:g.61958073delC		124.0	0.0		168.0	11.0	NM_022557	B1A4H5|B1A4H7|O14643|O14644|P09587	Frame_Shift_Del	DEL	ENST00000423893.2	hg19	CCDS11647.1																																																																																			.	.		0.567	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1	NM_002059		-	61958073	C	-	61958073	6	5	103	0	1	1	0	1	0	0	0	0	6376	855	30	0		0	GH2	17	61958073	Intron	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	80137	61958073	19237137	981	15604										
BPTF	2186	hgsc.bcm.edu	37	chr17	65871699	65871699	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agaagttggggataaaggtaActctgtgtcagcaaatcttg	12	5	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:65871699A>G	ENST00000321892.4	+	5	1953	c.1892A>G	c.(1891-1893)aAc>aGc	p.N631S	BPTF_ENST00000335221.5_Missense_Mutation_p.N631S|BPTF_ENST00000306378.6_Intron|BPTF_ENST00000424123.3_Missense_Mutation_p.N492S			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	631					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GATAAAGGTAACTCTGTGTCA	0.443																																					p.N631S		Atlas-SNP	.											.	BPTF	415	.	0			c.A1892G						.						100	96	97					17																	65871699		2203	4300	6503	SO:0001583	missense	2186	exon5			AAGGTAACTCTGT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.1892A>G	chr17.hg19:g.65871699A>G	ENSP00000315454:p.Asn631Ser	39.0	0.0		52.0	4.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	A	12.07	1.829063	0.32329	.	.	ENSG00000171634	ENST00000544491;ENST00000335221;ENST00000321892;ENST00000544778	T;T	0.61510	0.11;0.1	5.04	5.04	0.67666	.	.	.	.	.	T	0.65133	0.2662	L	0.36672	1.1	0.28525	N	0.91287	D;D	0.69078	0.997;0.994	D;D	0.70716	0.97;0.913	T	0.57516	-0.7798	9	0.23302	T	0.38	.	14.0636	0.64815	1.0:0.0:0.0:0.0	.	631;631	Q12830;Q12830-4	BPTF_HUMAN;.	S	536;631;631;492	ENSP00000334351:N631S;ENSP00000315454:N631S	ENSP00000315454:N631S	N	+	2	0	BPTF	63302161	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.372000	0.52387	2.204000	0.70986	0.383000	0.25322	AAC	.	.		0.443	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65871699	A	G	65871699	3	3	103	1	0	0	0	0	1	0	0	0	1497	43	2	2	1910	2	BPTF	17	65871699	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	3913626	65871699	15323511	982	15605										
AMZ2	51321	hgsc.bcm.edu	37	chr17	66251989	66251989	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcacaagttgcagtgtgctgTtggcttcagcattgtagaaa	12	7	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:66251989T>C	ENST00000359904.3	+	6	2031	c.899T>C	c.(898-900)gTt>gCt	p.V300A	AMZ2_ENST00000577985.1_Missense_Mutation_p.V300A|AMZ2_ENST00000585050.1_Intron|AMZ2_ENST00000392720.2_Missense_Mutation_p.V300A|AMZ2_ENST00000580753.1_Missense_Mutation_p.V300A|AMZ2_ENST00000577273.1_Intron|AMZ2_ENST00000577866.1_Missense_Mutation_p.V300A|AMZ2_ENST00000359783.4_Missense_Mutation_p.V242A	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	300							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			CAGTGTGCTGTTGGCTTCAGC	0.478																																					p.V300A		Atlas-SNP	.											.	AMZ2	15	.	0			c.T899C						.						55	54	55					17																	66251989		2203	4300	6503	SO:0001583	missense	51321	exon7			GTGCTGTTGGCTT	CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"archaemetzincin-2"	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.899T>C	chr17.hg19:g.66251989T>C	ENSP00000352976:p.Val300Ala	80.0	0.0		86.0	4.0	NM_001033572	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Missense_Mutation	SNP	ENST00000359904.3	hg19	CCDS11674.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.117584	0.37339	.	.	ENSG00000196704	ENST00000359904;ENST00000359783;ENST00000392720	T;T;T	0.44482	0.92;0.92;0.92	3.64	3.64	0.41730	.	0.680538	0.12900	N	0.429867	T	0.32164	0.0820	L	0.29908	0.895	0.80722	D	1	B;B	0.23377	0.084;0.012	B;B	0.21708	0.036;0.022	T	0.18023	-1.0350	10	0.54805	T	0.06	-25.5489	10.8589	0.46815	0.0:0.0:0.0:1.0	.	242;300	A6NLD9;Q86W34	.;AMZ2_HUMAN	A	300;242;300	ENSP00000352976:V300A;ENSP00000352831:V242A;ENSP00000376481:V300A	ENSP00000352831:V242A	V	+	2	0	AMZ2	63763584	0.830000	0.29337	0.553000	0.28255	0.603000	0.37013	6.532000	0.73825	1.873000	0.54277	0.383000	0.25322	GTT	.	.		0.478	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627		C	66251989	T	C	66251989	3	2	103	1	0	0	0	0	1	0	0	0	597	1725	60	2	917	2	AMZ2	17	66251989	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	380290	66251989	14943221	983	15606										
MAP2K6	5608	hgsc.bcm.edu	37	chr17	67537867	67537867	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaaggaacagatgtggcatcTtttgtaaaactgattcttgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:67537867delT	ENST00000590474.1	+	12	1265	c.978delT	c.(976-978)tctfs	p.S326fs	MAP2K6_ENST00000589647.1_Frame_Shift_Del_p.S270fs	NM_002758.3	NP_002749.2	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6	326	DVD domain.				activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|cardiac muscle contraction (GO:0060048)|cell cycle arrest (GO:0007050)|cellular response to sorbitol (GO:0072709)|DNA damage induced protein phosphorylation (GO:0006975)|innate immune response (GO:0045087)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to ischemia (GO:0002931)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	20	Breast(10;6.05e-10)					ATGTGGCATCTTTTGTAAAAC	0.393																																					p.S326fs		Atlas-INDEL	.											.	MAP2K6	41	.	0			c.977delC						.						122	114	117					17																	67537867		2203	4300	6503	SO:0001589	frameshift_variant	5608	exon12			.	U39064	CCDS11686.1	17q	2011-06-09						"Mitogen-activated protein kinase cascade / Kinase kinases"	6846	protein-coding gene	gene with protein product	"protein kinase, mitogen-activated, kinase 6 (MAP kinase kinase 6)"	601254		PRKMK6		8621675	Standard	XM_005257515		Approved	MEK6, MKK6, SAPKK3, MAPKK6	uc002jij.3	P52564		ENST00000590474.1:c.978delT	chr17.hg19:g.67537867delT	ENSP00000468348:p.Ser326fs	163.0	0.0		171.0	11.0	NM_002758		Frame_Shift_Del	DEL	ENST00000590474.1	hg19	CCDS11686.1																																																																																			.	.		0.393	MAP2K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450689.1	NM_002758		-	67537867	T	-	67537867	7	5	103	1	0	1	0	1	0	0	0	0	9250	1596	56	0	1024	0	MAP2K6	17	67537867	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1285878	67537867	13657343	984	15607										
TMEM104	54868	hgsc.bcm.edu	37	chr17	72791152	72791152	+	Splice_Site	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atggctgtgttcctttcagtGggggtcaacttgttctattt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:72791152delG	ENST00000335464.5	+	7	591	c.429delG	c.(427-429)gtg>gt	p.V143fs	TMEM104_ENST00000582330.1_Splice_Site_p.V143fs|TMEM104_ENST00000582773.1_Splice_Site_p.V143fs|TMEM104_ENST00000417024.2_Splice_Site_p.V156fs	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	143						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					TCCTTTCAGTGGGGGTCAACT	0.463																																					p.V143fs		Atlas-INDEL	.											.	TMEM104	49	.	0			c.428delT						.						178	149	159					17																	72791152		2203	4300	6503	SO:0001630	splice_region_variant	54868	exon7			.	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.428-1G>-	chr17.hg19:g.72791152delG		147.0	0.0		131.0	10.0	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Frame_Shift_Del	DEL	ENST00000335464.5	hg19	CCDS32723.1																																																																																			.	.		0.463	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728	Frame_Shift_Del	-	72791152	G	-	72791152	8	5	103	1	0	1	0	1	0	0	1	0	16033	1362	47	0	451	0	TMEM104	17	72791152	Splice_Site	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	5253285	72791152	8404058	985	15608										
UNK	85451	hgsc.bcm.edu	37	chr17	73818612	73818612	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttttgcctctggaagcttctCcccgggcacttcccccgctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:73818612delC	ENST00000589666.1	+	14	2002	c.1892delC	c.(1891-1893)tccfs	p.S631fs	RP11-552F3.4_ENST00000586808.1_RNA|UNK_ENST00000293218.3_Frame_Shift_Del_p.S707fs	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	631							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S631C(1)|p.S707C(1)		cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGAAGCTTCTCCCCGGGCACT	0.617																																					p.S631fs		Atlas-INDEL	.											.	UNK	87	.	2	Substitution - Missense(2)	lung(2)	c.1891delT						.						93	101	99					17																	73818612		1944	4137	6081	SO:0001589	frameshift_variant	85451	exon14			.	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"Zinc fingers, CCCH-type domain containing"	29369	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 5", "zinc finger CCCH-type containing 5", "unkempt homolog (Drosophila)"	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.1892delC	chr17.hg19:g.73818612delC	ENSP00000464893:p.Ser631fs	127.0	0.0		152.0	10.0	NM_001080419		Frame_Shift_Del	DEL	ENST00000589666.1	hg19	CCDS45778.2																																																																																			.	.		0.617	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		-	73818612	C	-	73818612	7	5	103	1	0	1	0	1	0	0	0	0	17015	855	30	0	2178	0	UNK	17	73818612	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1027460	73818612	7376598	986	15609										
SRP68	6730	hgsc.bcm.edu	37	chr17	74044023	74044023	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gattagacaccttccctggcTctccttcaaggatataatct	6	12	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:74044023T>C	ENST00000307877.2	-	10	1267	c.1106A>G	c.(1105-1107)gAg>gGg	p.E369G	SRP68_ENST00000539137.1_Missense_Mutation_p.E331G|SRP68_ENST00000542536.2_5'UTR|SRP68_ENST00000355113.5_Missense_Mutation_p.E268G|SRP68_ENST00000602720.1_Missense_Mutation_p.E30G	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	369					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						CTTCCCTGGCTCTCCTTCAAG	0.333																																					p.E369G		Atlas-SNP	.											.	SRP68	61	.	0			c.A1106G						.						110	108	108					17																	74044023		2203	4300	6503	SO:0001583	missense	6730	exon10			CCTGGCTCTCCTT	AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"signal recognition particle 68kD"			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.1106A>G	chr17.hg19:g.74044023T>C	ENSP00000312066:p.Glu369Gly	198.0	0.0		189.0	8.0	NM_014230	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Missense_Mutation	SNP	ENST00000307877.2	hg19	CCDS11738.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.359200	0.41801	.	.	ENSG00000167881	ENST00000411758;ENST00000539137;ENST00000542536;ENST00000307877;ENST00000304220;ENST00000355113	.	.	.	6.17	6.17	0.99709	.	0.094899	0.85682	D	0.000000	T	0.39145	0.1067	N	0.12961	0.28	0.80722	D	1	B;B	0.34290	0.447;0.447	B;B	0.33690	0.168;0.109	T	0.37934	-0.9684	9	0.52906	T	0.07	-30.2755	16.0034	0.80327	0.0:0.0:0.0:1.0	.	331;369	G3V1U4;Q9UHB9	.;SRP68_HUMAN	G	109;331;30;369;338;268	.	ENSP00000307756:E338G	E	-	2	0	SRP68	71555618	1.000000	0.71417	0.855000	0.33649	0.158000	0.22134	6.963000	0.76055	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.333	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230		C	74044023	T	C	74044023	3	2	103	1	0	0	0	0	1	0	0	0	15171	1551	54	2	805	2	SRP68	17	74044023	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	225411	74044023	7151187	987	15610										
MXRA7	439921	hgsc.bcm.edu	37	chr17	74681205	74681205	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcatcttcttgtactggtttCccctcagcttcccggggctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:74681205delC	ENST00000355797.3	-	3	457	c.449delG	c.(448-450)ggafs	p.G150fs	MXRA7_ENST00000588114.1_5'UTR|MXRA7_ENST00000592148.1_Frame_Shift_Del_p.G193fs|MXRA7_ENST00000449428.2_Frame_Shift_Del_p.G150fs|MXRA7_ENST00000585519.1_5'UTR|MXRA7_ENST00000375036.2_Frame_Shift_Del_p.G150fs|MXRA7_ENST00000589082.1_5'UTR	NM_001008528.1	NP_001008528.1	P84157	MXRA7_HUMAN	matrix-remodelling associated 7	150						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						GTACTGGTTTCCCCTCAGCTT	0.617																																					p.G150fs		Atlas-INDEL	.											.	MXRA7	11	.	0			c.450delA						.						157	148	151					17																	74681205		2203	4300	6503	SO:0001589	frameshift_variant	439921	exon3			.	BC053983	CCDS32745.1, CCDS32746.1, CCDS45786.1	17q25.1	2007-08-01				ENSG00000182534			7541	protein-coding gene	gene with protein product							Standard	XM_005257382		Approved	FLJ46603, TMAP1, PS1TP1	uc002jsk.1	P84157		ENST00000355797.3:c.449delG	chr17.hg19:g.74681205delC	ENSP00000348050:p.Gly150fs	158.0	0.0		152.0	10.0	NM_001008529	Q0P5W3	Frame_Shift_Del	DEL	ENST00000355797.3	hg19	CCDS32745.1																																																																																			.	.		0.617	MXRA7-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450983.1	NM_001008529		-	74681205	C	-	74681205	7	5	103	1	0	1	0	1	0	0	0	0	10013	855	30	0	228	0	MXRA7	17	74681205	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	637182	74681205	6514005	988	15611										
CHMP6	79643	hgsc.bcm.edu	37	chr17	78969500	78969500	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tattgagttcacccagatcgAaatgaaagtgatggaggggc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:78969500delA	ENST00000325167.5	+	4	368	c.290delA	c.(289-291)gaafs	p.E97fs		NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	97					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein N-terminus binding (GO:0047485)			lung(2)|ovary(1)	3	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0175)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			ACCCAGATCGAAATGAAAGTG	0.582																																					p.E97fs		Atlas-INDEL	.											.	CHMP6	16	.	0			c.289delG						.						103	94	97					17																	78969500		2203	4300	6503	SO:0001589	frameshift_variant	79643	exon4			.	BC010108	CCDS11774.1	17q25.3	2014-08-13	2011-09-21		ENSG00000176108	ENSG00000176108		"Charged multivesicular body proteins"	25675	protein-coding gene	gene with protein product		610901	"chromatin modifying protein 6"			11559748, 15511219	Standard	NM_024591		Approved	FLJ11749, VPS20	uc002jyw.4	Q96FZ7	OTTHUMG00000177645	ENST00000325167.5:c.290delA	chr17.hg19:g.78969500delA	ENSP00000317468:p.Glu97fs	162.0	0.0		198.0	14.0	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Frame_Shift_Del	DEL	ENST00000325167.5	hg19	CCDS11774.1																																																																																			.	.		0.582	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591		-	78969500	A	-	78969500	7	5	103	1	0	1	0	1	0	0	0	0	3362	246	9	0	304	0	CHMP6	17	78969500	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	4288295	78969500	2225710	989	15612										
DYSFIP1	116729	hgsc.bcm.edu	37	chr17	79792500	79792500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacgcattccaggtttccagAgagcacggcttcatgcaagg	11	12	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:79792500A>G	ENST00000330261.4	-	2	299	c.220T>C	c.(220-222)Tct>Cct	p.S74P	FAM195B_ENST00000572645.1_5'Flank|PPP1R27_ENST00000573182.1_5'Flank|FAM195B_ENST00000538396.1_5'Flank|FAM195B_ENST00000455127.2_5'Flank|FAM195B_ENST00000575061.1_5'Flank|FAM195B_ENST00000573478.1_5'Flank|FAM195B_ENST00000576431.1_5'Flank|PPP1R27_ENST00000570394.1_Missense_Mutation_p.S74P	NM_001007533.3	NP_001007534.1	Q86WC6	PPR27_HUMAN	protein phosphatase 1, regulatory subunit 27	74					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										AGGTTTCCAGAGAGCACGGCT	0.632																																					p.S74P		Atlas-SNP	.											.	.	.	.	0			c.T220C						.						138	110	119					17																	79792500		2203	4300	6503	SO:0001583	missense	116729	exon2			TTCCAGAGAGCAC	AF434846	CCDS32767.1	17q25.3	2013-01-10	2011-10-11	2011-10-11	ENSG00000182676	ENSG00000182676		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	16813	protein-coding gene	gene with protein product			"dysferlin-interacting protein 1 (toonin)", "dysferlin interacting protein 1 (toonin)", "dysferlin interacting protein 1"	DYSFIP1			Standard	NM_001007533		Approved	toonin	uc002kbj.1	Q86WC6		ENST00000330261.4:c.220T>C	chr17.hg19:g.79792500A>G	ENSP00000331065:p.Ser74Pro	122.0	0.0		96.0	4.0	NM_001007533		Missense_Mutation	SNP	ENST00000330261.4	hg19	CCDS32767.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.968670	0.74131	.	.	ENSG00000182676	ENST00000330261	T	0.67345	-0.26	4.86	3.7	0.42460	.	0.059038	0.64402	D	0.000001	T	0.72153	0.3425	L	0.59967	1.855	0.42293	D	0.992145	D	0.59767	0.986	P	0.60473	0.875	T	0.74272	-0.3719	10	0.72032	D	0.01	.	7.279	0.26300	0.712:0.1465:0.0:0.1415	.	74	Q86WC6	PPR27_HUMAN	P	74	ENSP00000331065:S74P	ENSP00000331065:S74P	S	-	1	0	DYSFIP1	77385789	0.967000	0.33354	0.954000	0.39281	0.809000	0.45718	2.280000	0.43443	1.826000	0.53198	0.459000	0.35465	TCT	.	.		0.632	PPP1R27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439692.1	NM_001007533		G	79792500	A	G	79792500	3	3	103	1	0	0	0	0	1	0	0	0	4862	304	11	2	252	2	DYSFIP1	17	79792500	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	823000	79792500	1402710	990	15613										
WDR45L	56270	hgsc.bcm.edu	37	chr17	80575188	80575188	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctacctggactgtttattccTttttggatcttcagctgcaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:80575188delT	ENST00000392325.4	-	8	984	c.790delA	c.(790-792)aggfs	p.R264fs	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	264																	TGTTTATTCCTTTTTGGATCT	0.532																																					p.R264fs		Atlas-INDEL	.											.	.	.	.	0			c.791delG						.						134	107	116					17																	80575188		2203	4300	6503	SO:0001589	frameshift_variant	56270	exon8			.	AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"WD repeat domain containing"	25072	protein-coding gene	gene with protein product		609226	"WDR45-like"	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.790delA	chr17.hg19:g.80575188delT	ENSP00000376139:p.Arg264fs	150.0	0.0		148.0	11.0	NM_019613	O95328|Q2MCP6|Q6IBN2	Frame_Shift_Del	DEL	ENST00000392325.4	hg19	CCDS11815.2																																																																																			.	.		0.532	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613		-	80575188	T	-	80575188	7	5	103	1	0	1	0	1	0	0	0	0	17313	1608	56	0	256	0	WDR45L	17	80575188	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	782688	80575188	620022	991	15614										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5428316	5428316	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgtgggtatacttacctctCccggccggatcttaatgtaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:5428316delC	ENST00000341928.2	-	9	1401	c.1061delG	c.(1060-1062)ggafs	p.G354fs	EPB41L3_ENST00000540638.2_Frame_Shift_Del_p.G354fs|EPB41L3_ENST00000544123.1_Frame_Shift_Del_p.G354fs|EPB41L3_ENST00000342933.3_Frame_Shift_Del_p.G354fs|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000400111.3_Frame_Shift_Del_p.G354fs	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	354	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						ACTTACCTCTCCCGGCCGGAT	0.438																																					p.G354fs		Atlas-INDEL	.											.	EPB41L3	222	.	0			c.1062delA						.						117	111	113					18																	5428316		2203	4300	6503	SO:0001589	frameshift_variant	23136	exon9			.	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.1061delG	chr18.hg19:g.5428316delC	ENSP00000343158:p.Gly354fs	123.0	0.0		160.0	10.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Frame_Shift_Del	DEL	ENST00000341928.2	hg19	CCDS11838.1																																																																																			.	.		0.438	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		-	5428316	C	-	5428316	7	5	103	1	0	1	0	1	0	0	0	0	5156	855	30	0	2258	0	EPB41L3	18	5428316	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10		5428316	72648932	992	15615										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7034631	7034631	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtctaaccacgtttaggtacTcttcataaggctgcaatgac	8	10	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:7034631T>C	ENST00000389658.3	-	14	1991	c.1898A>G	c.(1897-1899)gAg>gGg	p.E633G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	633	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GTTTAGGTACTCTTCATAAGG	0.408																																					p.E633G		Atlas-SNP	.											.	LAMA1	458	.	0			c.A1898G						.						138	124	129					18																	7034631		2203	4300	6503	SO:0001583	missense	284217	exon14			AGGTACTCTTCAT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.1898A>G	chr18.hg19:g.7034631T>C	ENSP00000374309:p.Glu633Gly	114.0	0.0		144.0	6.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.567018	0.45694	.	.	ENSG00000101680	ENST00000389658	T	0.37058	1.22	5.9	5.9	0.94986	Laminin B type IV (2);Laminin B, subgroup (1);	0.059369	0.64402	D	0.000004	T	0.60314	0.2259	M	0.78456	2.415	0.42300	D	0.992178	D	0.76494	0.999	D	0.72625	0.978	T	0.58713	-0.7588	10	0.25106	T	0.35	.	16.3283	0.82996	0.0:0.0:0.0:1.0	.	633	P25391	LAMA1_HUMAN	G	633	ENSP00000374309:E633G	ENSP00000374309:E633G	E	-	2	0	LAMA1	7024631	1.000000	0.71417	0.997000	0.53966	0.102000	0.19082	5.146000	0.64845	2.257000	0.74773	0.533000	0.62120	GAG	.	.		0.408	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		C	7034631	T	C	7034631	3	2	103	1	0	0	0	0	1	0	0	0	8614	1551	54	2	7529	2	LAMA1	18	7034631	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1606315	7034631	71042617	993	15616										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7044819	7044819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctccccgcaagtattatgcTcacattgacactgcagtttc	6	13	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:7044819T>C	ENST00000389658.3	-	7	971	c.878A>G	c.(877-879)gAg>gGg	p.E293G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	293	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AGTATTATGCTCACATTGACA	0.448																																					p.E293G		Atlas-SNP	.											.	LAMA1	458	.	0			c.A878G						.						115	111	112					18																	7044819		2203	4300	6503	SO:0001583	missense	284217	exon7			TTATGCTCACATT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.878A>G	chr18.hg19:g.7044819T>C	ENSP00000374309:p.Glu293Gly	120.0	0.0		106.0	5.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.552286	0.65311	.	.	ENSG00000101680	ENST00000389658	T	0.64085	-0.08	4.97	4.97	0.65823	EGF-like, laminin (4);	0.063251	0.64402	D	0.000011	T	0.80082	0.4558	M	0.82923	2.615	0.53005	D	0.999963	D	0.89917	1.0	D	0.77557	0.99	T	0.83052	-0.0152	10	0.59425	D	0.04	.	14.9339	0.70938	0.0:0.0:0.0:1.0	.	293	P25391	LAMA1_HUMAN	G	293	ENSP00000374309:E293G	ENSP00000374309:E293G	E	-	2	0	LAMA1	7034819	1.000000	0.71417	0.954000	0.39281	0.312000	0.27988	6.223000	0.72257	1.987000	0.57996	0.533000	0.62120	GAG	.	.		0.448	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		C	7044819	T	C	7044819	3	2	103	1	0	0	0	0	1	0	0	0	8614	1551	54	2	8577	2	LAMA1	18	7044819	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	10188	7044819	71032429	994	15617										
PTPRM	5797	hgsc.bcm.edu	37	chr18	8248169	8248169	+	Intron	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccatttgtgccaactgcaaTtttaggtgagaacatttccc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:8248169delT	ENST00000332175.8	+	16	3564				PTPRM_ENST00000400060.4_Frame_Shift_Del_p.I850fs|PTPRM_ENST00000444013.1_Intron|PTPRM_ENST00000580170.1_Frame_Shift_Del_p.I850fs|PTPRM_ENST00000400053.4_Intron	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CCAACTGCAATTTTAGGTGAG	0.388																																					p.I850fs		Atlas-INDEL	.											.	PTPRM	185	.	0			c.2548delA						.						277	275	275					18																	8248169		2114	4235	6349	SO:0001627	intron_variant	5797	exon17			.	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2527+252T>-	chr18.hg19:g.8248169delT		189.0	0.0		202.0	14.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Frame_Shift_Del	DEL	ENST00000332175.8	hg19	CCDS11840.1																																																																																			.	.		0.388	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			-	8248169	T	-	8248169	6	5	103	0	1	1	0	1	0	0	0	0	12821	1493	52	0		0	PTPRM	18	8248169	Intron	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1203350	8248169	69829079	995	15618										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8825894	8825894	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgcaggaccccttccagaaGgggctgcgggccggcagtcg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:8825894delG	ENST00000306329.11	+	13	5343	c.5343delG	c.(5341-5343)aagfs	p.K1781fs	SOGA2_ENST00000400050.3_Frame_Shift_Del_p.K1421fs|SOGA2_ENST00000517570.1_Frame_Shift_Del_p.K1421fs|SOGA2_ENST00000359865.3_Frame_Shift_Del_p.K1462fs|SOGA2_ENST00000518815.1_Frame_Shift_Del_p.K787fs|SOGA2_ENST00000306285.7_Frame_Shift_Del_p.K787fs																							CCTTCCAGAAGGGGCTGCGGG	0.642																																					p.K1462fs		Atlas-INDEL	.											.	.	.	.	0			c.4385delA						.						35	41	39					18																	8825894		2201	4296	6497	SO:0001589	frameshift_variant	23255	exon15			.																												ENST00000306329.11:c.5343delG	chr18.hg19:g.8825894delG	ENSP00000305027:p.Lys1781fs	125.0	0.0		155.0	10.0	NM_015210		Frame_Shift_Del	DEL	ENST00000306329.11	hg19																																																																																				.	.		0.642	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			-	8825894	G	-	8825894	7	5	103	1	0	1	0	1	0	0	0	0	8203	991	35	0	4436	0	KIAA0802	18	8825894	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	577725	8825894	69251354	996	15619										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9279637	9279637	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggatgataaatttgacaaaTtaaaggtatgtatgtttgga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:9279637delT	ENST00000262126.4	+	12	6238	c.5998delT	c.(5998-6000)ttafs	p.L2000fs	ANKRD12_ENST00000383440.2_Frame_Shift_Del_p.L1977fs|ANKRD12_ENST00000400020.3_Frame_Shift_Del_p.L1977fs|snoU13_ENST00000459594.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	2000						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						ATTTGACAAATTAAAGGTATG	0.333																																					p.K1999fs		Atlas-INDEL	.											.	ANKRD12	167	.	0			c.5997delA						.						94	101	99					18																	9279637		2203	4299	6502	SO:0001589	frameshift_variant	23253	exon12			.	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5998delT	chr18.hg19:g.9279637delT	ENSP00000262126:p.Leu2000fs	145.0	0.0		180.0	12.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Frame_Shift_Del	DEL	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.333	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		-	9279637	T	-	9279637	7	5	103	1	0	1	0	1	0	0	0	0	640	1490	52	0	6040	0	ANKRD12	18	9279637	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	453743	9279637	68797611	997	15620										
TTC39C	125488	hgsc.bcm.edu	37	chr18	21698147	21698147	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttgattcctttgagaggctAaaaaatgagtccaggtggtc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:21698147delA	ENST00000317571.3	+	8	1373	c.1137delA	c.(1135-1137)ctafs	p.L379fs	RP11-799B12.2_ENST00000583782.1_RNA|TTC39C_ENST00000304621.6_Frame_Shift_Del_p.L318fs|TTC39C_ENST00000540918.2_Frame_Shift_Del_p.L72fs	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	379										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						TTGAGAGGCTAAAAAATGAGT	0.448																																					p.L379fs		Atlas-INDEL	.											.	TTC39C	83	.	0			c.1136delT						.						131	119	123					18																	21698147		2203	4300	6503	SO:0001589	frameshift_variant	125488	exon8			.	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"Tetratricopeptide (TTC) repeat domain containing"	26595	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 17"	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.1137delA	chr18.hg19:g.21698147delA	ENSP00000323645:p.Leu379fs	115.0	0.0		129.0	11.0	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Frame_Shift_Del	DEL	ENST00000317571.3	hg19	CCDS45839.1																																																																																			.	.		0.448	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211		-	21698147	A	-	21698147	7	5	103	1	0	1	0	1	0	0	0	0	16724	349	13	0	1167	0	TTC39C	18	21698147	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	12418510	21698147	56379101	998	15621										
DSC3	1825	hgsc.bcm.edu	37	chr18	28611062	28611062	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccctggctgtgtacactgaCccatcatttagaactctgaa	8	12	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:28611062C>T	ENST00000360428.4	-	3	311	c.231G>A	c.(229-231)ggG>ggA	p.G77G	DSC3_ENST00000434452.1_Silent_p.G77G	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	77					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			TGTACACTGACCCATCATTTA	0.418																																					p.G77G		Atlas-SNP	.											DSC3_ENST00000434452,right_lower_lobe,carcinoma,0,2	DSC3	225	.	0			c.G231A						.						72	64	67					18																	28611062		2203	4300	6503	SO:0001819	synonymous_variant	1825	exon3			CACTGACCCATCA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"Cadherins / Major cadherins"	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.231G>A	chr18.hg19:g.28611062C>T		59.0	0.0		78.0	0.0	NM_024423	A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	hg19	CCDS32810.1																																																																																			.	.		0.418	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		T	28611062	C	T	28611062	2	4	103	1	0	0	0	0	0	0	0	1	4769	494	18	3		3	DSC3	18	28611062	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	6912915	28611062	49466186	999	15622										
DSC2	1824	hgsc.bcm.edu	37	chr18	28649035	28649035	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgatggtctcctgacctccgTttttgattcctgatcccacg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:28649035delT	ENST00000280904.6	-	15	2776	c.2333delA	c.(2332-2334)aacfs	p.N778fs	DSC2_ENST00000251081.6_Frame_Shift_Del_p.N778fs	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	778					bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			CTGACCTCCGTTTTTGATTCC	0.542																																					p.N778fs		Atlas-INDEL	.											.	DSC2	168	.	0			c.2334delC						.						72	66	68					18																	28649035		2203	4300	6503	SO:0001589	frameshift_variant	1824	exon15			.	X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"Cadherins / Major cadherins"	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.2333delA	chr18.hg19:g.28649035delT	ENSP00000280904:p.Asn778fs	119.0	0.0		156.0	11.0	NM_024422		Frame_Shift_Del	DEL	ENST00000280904.6	hg19	CCDS11892.1																																																																																			.	.		0.542	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		-	28649035	T	-	28649035	7	5	103	1	0	1	0	1	0	0	0	0	4768	1725	60	0	420	0	DSC2	18	28649035	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	37973	28649035	49428213	1000	15623										
DSG4	147409	hgsc.bcm.edu	37	chr18	28986275	28986275	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaagaccaagctggagtttcAaatgttggtcttggaccagc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:28986275delA	ENST00000308128.4	+	12	2007	c.1872delA	c.(1870-1872)tcafs	p.S624fs	DSG4_ENST00000359747.4_Frame_Shift_Del_p.S624fs|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	624					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CTGGAGTTTCAAATGTTGGTC	0.478																																					p.S624X		Atlas-INDEL	.											.	DSG4	343	.	0			c.1871delC						.						99	99	99					18																	28986275		2203	4300	6503	SO:0001589	frameshift_variant	147409	exon12			.	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.1872delA	chr18.hg19:g.28986275delA	ENSP00000311859:p.Ser624fs	157.0	0.0		180.0	12.0	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Frame_Shift_Del	DEL	ENST00000308128.4	hg19	CCDS11897.1																																																																																			.	.		0.478	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		-	28986275	A	-	28986275	7	5	103	1	0	1	0	1	0	0	0	0	4781	117	5	0	1918	0	DSG4	18	28986275	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	337240	28986275	49090973	1001	15624										
DSG3	1830	hgsc.bcm.edu	37	chr18	29037066	29037066	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agagaaggagaagataactcAaaaagaaacccaattgccaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:29037066delA	ENST00000257189.4	+	3	278	c.195delA	c.(193-195)tcafs	p.S65fs		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	65	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			AAGATAACTCAAAAAGAAACC	0.343																																					p.S65X		Atlas-INDEL	.											.	DSG3	172	.	0			c.194delC						.						108	102	104					18																	29037066		2203	4300	6503	SO:0001589	frameshift_variant	1830	exon3			.	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.195delA	chr18.hg19:g.29037066delA	ENSP00000257189:p.Ser65fs	86.0	0.0		139.0	10.0	NM_001944	A8K2V2	Frame_Shift_Del	DEL	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.343	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		-	29037066	A	-	29037066	7	5	103	1	0	1	0	1	0	0	0	0	4780	117	5	0	205	0	DSG3	18	29037066	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	50791	29037066	49040182	1002	15625										
KLHL14	57565	hgsc.bcm.edu	37	chr18	30349862	30349862	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agcgccagctccgactccacGgggggcggcagcgagtccag					rs147661052		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:30349862delG	ENST00000359358.4	-	2	1131	c.693delC	c.(691-693)cccfs	p.P231fs	AC012123.1_ENST00000426194.1_Frame_Shift_Del_p.T30fs|KLHL14_ENST00000358095.4_Frame_Shift_Del_p.P231fs	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	231	BACK.					endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						CCGACTCCACGGGGGGCGGCA	0.642																																					p.V232fs		Atlas-INDEL	.											.	KLHL14	92	.	0			c.694delG						.						45	38	40					18																	30349862		2203	4300	6503	SO:0001589	frameshift_variant	57565	exon2			.	AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"Kelch-like", "BTB/POZ domain containing"	29266	protein-coding gene	gene with protein product	"printor"	613772	"kelch-like 14 (Drosophila)"			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.693delC	chr18.hg19:g.30349862delG	ENSP00000352314:p.Pro231fs	159.0	0.0		191.0	12.0	NM_020805	A6NNW1|B4DHA0|Q8WU41	Frame_Shift_Del	DEL	ENST00000359358.4	hg19	CCDS32813.1																																																																																			.	.		0.642	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1			-	30349862	G	-	30349862	7	5	103	1	0	1	0	1	0	0	0	0	8379	1103	39	0	1225	0	KLHL14	18	30349862	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1312796	30349862	47727386	1003	15626										
PIK3C3	5289	hgsc.bcm.edu	37	chr18	39542519	39542519	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggaatgcccaagtggcccTcaccatatgggatgtgtatg	12	10	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:39542519T>C	ENST00000262039.4	+	3	409	c.323T>C	c.(322-324)cTc>cCc	p.L108P	PIK3C3_ENST00000398870.3_Missense_Mutation_p.L45P|PIK3C3_ENST00000586545.1_Missense_Mutation_p.L108P	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	108	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						CAAGTGGCCCTCACCATATGG	0.453										TSP Lung(28;0.18)																											p.L108P	NSCLC(37;552 1060 2683 16430 37914)	Atlas-SNP	.											.	PIK3C3	138	.	0			c.T323C						.						105	94	98					18																	39542519		2203	4300	6503	SO:0001583	missense	5289	exon3			TGGCCCTCACCAT	Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"phosphoinositide-3-kinase, class 3"			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.323T>C	chr18.hg19:g.39542519T>C	ENSP00000262039:p.Leu108Pro	95.0	0.0		124.0	5.0	NM_002647	Q15134	Missense_Mutation	SNP	ENST00000262039.4	hg19	CCDS11920.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.613515	0.87359	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	T;T	0.81415	-1.49;-1.49	5.88	5.88	0.94601	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.000000	0.85682	D	0.000000	D	0.89015	0.6595	M	0.79258	2.445	0.80722	D	1	D;D	0.58970	0.972;0.984	P;D	0.65323	0.781;0.934	D	0.89265	0.3600	9	.	.	.	.	16.2898	0.82742	0.0:0.0:0.0:1.0	.	45;108	A8MYT4;Q8NEB9	.;PK3C3_HUMAN	P	108;45	ENSP00000262039:L108P;ENSP00000381845:L45P	.	L	+	2	0	PIK3C3	37796517	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.832000	0.86757	2.250000	0.74265	0.482000	0.46254	CTC	.	.		0.453	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647		C	39542519	T	C	39542519	3	2	103	1	0	0	0	0	1	0	0	0	11921	1551	54	2	333	2	PIK3C3	18	39542519	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	9192657	39542519	38534729	1004	15627										
SETBP1	26040	hgsc.bcm.edu	37	chr18	42456590	42456590	+	Intron	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaggccaaggcatcccattcAaaaagcaattcctgtcccag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:42456590delA	ENST00000282030.5	+	3	836				SETBP1_ENST00000426838.4_Frame_Shift_Del_p.K202fs	NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1							nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		CATCCCATTCAAAAAGCAATT	0.493									Schinzel-Giedion syndrome																												p.F200fs		Atlas-INDEL	.											.	SETBP1	577	.	0			c.600delC						.						103	100	101					18																	42456590		692	1591	2283	SO:0001627	intron_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	.	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.540+7342A>-	chr18.hg19:g.42456590delA		164.0	0.0		173.0	11.0	NM_001130110	A6H8W5|Q6P6C3|Q9UEF3	Frame_Shift_Del	DEL	ENST00000282030.5	hg19	CCDS11923.2																																																																																			.	.		0.493	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		-	42456590	A	-	42456590	6	5	103	0	1	1	0	1	0	0	0	0	14144	131	5	0		0	SETBP1	18	42456590	Intron	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2914071	42456590	35620658	1005	15628										
PIAS2	9063	hgsc.bcm.edu	37	chr18	44444168	44444168	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acttgttgaggtgtcaaagcAaaaataaaaaacttctcttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:44444168delA	ENST00000585916.1	-	3	542	c.543delT	c.(541-543)tttfs	p.F181fs	PIAS2_ENST00000545673.1_5'UTR|PIAS2_ENST00000324794.7_Frame_Shift_Del_p.F181fs	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	181	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						GTGTCAAAGCAAAAATAAAAA	0.313																																					p.A182fs		Atlas-INDEL	.											.	PIAS2	85	.	0			c.544delG						.						53	58	56					18																	44444168		2202	4300	6502	SO:0001589	frameshift_variant	9063	exon3			.	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"Zinc fingers, MIZ-type"	17311	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 4"	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.543delT	chr18.hg19:g.44444168delA	ENSP00000465676:p.Phe181fs	118.0	0.0		167.0	13.0	NM_173206	O75927|Q96BT5|Q96KE3	Frame_Shift_Del	DEL	ENST00000585916.1	hg19	CCDS32824.1																																																																																			.	.		0.313	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671		-	44444168	A	-	44444168	7	5	103	1	0	1	0	1	0	0	0	0	11885	127	5	0	1445	0	PIAS2	18	44444168	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1987578	44444168	33633080	1006	15629										
KIAA0427	9811	hgsc.bcm.edu	37	chr18	46288021	46288021	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atggcgctctttatggtggaGgggaccaagttccggagcct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:46288021delG	ENST00000256413.3	+	9	1627	c.1332delG	c.(1330-1332)gagfs	p.E444fs	CTIF_ENST00000382998.4_Frame_Shift_Del_p.E446fs	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	444	MIF4G.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						TTATGGTGGAGGGGACCAAGT	0.632																																					p.E446fs		Atlas-INDEL	.											.	CTIF	102	.	0			c.1337delA						.						76	74	75					18																	46288021		2203	4300	6503	SO:0001589	frameshift_variant	9811	exon10			.	AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"KIAA0427"	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.1332delG	chr18.hg19:g.46288021delG	ENSP00000256413:p.Glu444fs	109.0	0.0		141.0	11.0	NM_001142397	B3KTR8|Q8IVD5	Frame_Shift_Del	DEL	ENST00000256413.3	hg19	CCDS11935.1																																																																																			.	.		0.632	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772		-	46288021	G	-	46288021	7	5	103	1	0	1	0	1	0	0	0	0	8185	991	35	0	1368	0	KIAA0427	18	46288021	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1843853	46288021	31789227	1007	15630										
LIPG	9388	hgsc.bcm.edu	37	chr18	47095818	47095818	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttctataggagaaggacgaTttttctctcgggaatgtcca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:47095818delT	ENST00000261292.4	+	4	749	c.471delT	c.(469-471)gatfs	p.D157fs	LIPG_ENST00000580036.1_Frame_Shift_Del_p.D157fs|LIPG_ENST00000427224.2_Frame_Shift_Del_p.D157fs|LIPG_ENST00000577628.1_Frame_Shift_Del_p.D193fs	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial	157					cell proliferation (GO:0008283)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle remodeling (GO:0034375)|lipid metabolic process (GO:0006629)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|regulation of lipoprotein metabolic process (GO:0050746)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)	extracellular space (GO:0005615)	heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phospholipase activity (GO:0004620)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(2)	18						AGAAGGACGATTTTTCTCTCG	0.542																																					p.D157fs	Pancreas(126;280 1778 12814 26243 34948)	Atlas-INDEL	.											LIPG,NS,carcinoma,0,1	LIPG	47	.	0			c.470delA						.						62	58	59					18																	47095818		2203	4300	6503	SO:0001589	frameshift_variant	9388	exon4			.	AF118767	CCDS11938.1	18q21.1	2006-04-22				ENSG00000101670			6623	protein-coding gene	gene with protein product		603684				10318835, 10192396	Standard	XM_005258390		Approved	EDL	uc002ldv.3	Q9Y5X9		ENST00000261292.4:c.471delT	chr18.hg19:g.47095818delT	ENSP00000261292:p.Asp157fs	154.0	0.0		163.0	10.0	NM_006033	B0LPG6|Q6P9C8|Q6UW82	Frame_Shift_Del	DEL	ENST00000261292.4	hg19	CCDS11938.1																																																																																			.	.		0.542	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	NM_006033		-	47095818	T	-	47095818	7	5	103	1	0	1	0	1	0	0	0	0	8832	1490	52	0	485	0	LIPG	18	47095818	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	807797	47095818	30981430	1008	15631										
CCDC11	220136	hgsc.bcm.edu	37	chr18	47787507	47787507	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttctcttttagtaatttagTtttctctctcatcctatctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:47787507delT	ENST00000398545.4	-	3	517	c.400delA	c.(400-402)actfs	p.T134fs		NM_145020.3	NP_659457.2														endometrium(1)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|pancreas(1)|skin(1)	20				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		AGTAATTTAGTTTTCTCTCTC	0.338																																					p.T134fs		Atlas-INDEL	.											.	CCDC11	59	.	0			c.401delC						.						170	159	162					18																	47787507		1802	4076	5878	SO:0001589	frameshift_variant	220136	exon3			.																												ENST00000398545.4:c.400delA	chr18.hg19:g.47787507delT	ENSP00000381553:p.Thr134fs	88.0	0.0		155.0	11.0	NM_145020		Frame_Shift_Del	DEL	ENST00000398545.4	hg19	CCDS11940.2																																																																																			.	.		0.338	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3			-	47787507	T	-	47787507	7	5	103	1	0	1	0	1	0	0	0	0	2748	1725	60	0	1168	0	CCDC11	18	47787507	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	691689	47787507	30289741	1009	15632										
MAPK4	5596	hgsc.bcm.edu	37	chr18	48190827	48190827	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggacctcgtgctcaagattGgggatttcgggttggcaagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:48190827delG	ENST00000400384.2	+	2	1535	c.499delG	c.(499-501)gggfs	p.G167fs	MAPK4_ENST00000588540.1_Frame_Shift_Del_p.G167fs|MAPK4_ENST00000592595.1_Frame_Shift_Del_p.G167fs|MAPK4_ENST00000587823.1_3'UTR|MAPK4_ENST00000540640.1_Intron	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	167	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			lung(4)|skin(3)|upper_aerodigestive_tract(1)	8		Colorectal(6;0.0297)		Colorectal(21;0.156)		GCTCAAGATTGGGGATTTCGG	0.552																																					p.I166fs		Atlas-INDEL	.											.	MAPK4	75	.	0			c.498delT						.						67	68	68					18																	48190827		2173	4281	6454	SO:0001589	frameshift_variant	5596	exon2			.	X59727	CCDS42437.1	18q21.1	2012-10-02			ENSG00000141639	ENSG00000141639		"Mitogen-activated protein kinase cascade / Kinases"	6878	protein-coding gene	gene with protein product		176949		PRKM4		8290275	Standard	XM_005258299		Approved	Erk3-related, Erk4	uc002lev.3	P31152	OTTHUMG00000179853	ENST00000400384.2:c.499delG	chr18.hg19:g.48190827delG	ENSP00000383234:p.Gly167fs	106.0	0.0		157.0	10.0	NM_002747	A1A4C4|Q0VG04	Frame_Shift_Del	DEL	ENST00000400384.2	hg19	CCDS42437.1																																																																																			.	.		0.552	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448631.2	NM_002747		-	48190827	G	-	48190827	7	5	103	1	0	1	0	1	0	0	0	0	9289	1348	47	0	501	0	MAPK4	18	48190827	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	403320	48190827	29886421	1010	15633										
ZNF532	55205	hgsc.bcm.edu	37	chr18	56585671	56585671	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgctcacggagaggatgactCccacgcaccatcatcttctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:56585671delC	ENST00000336078.4	+	4	928	c.152delC	c.(151-153)tccfs	p.S51fs	ZNF532_ENST00000589288.1_Frame_Shift_Del_p.S51fs|ZNF532_ENST00000591083.1_Frame_Shift_Del_p.S51fs|ZNF532_ENST00000591808.1_Frame_Shift_Del_p.S51fs|ZNF532_ENST00000591230.1_Frame_Shift_Del_p.S51fs	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	51					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						GAGGATGACTCCCACGCACCA	0.512																																					p.S51fs		Atlas-INDEL	.											.	ZNF532	108	.	0			c.151delT						.						98	78	85					18																	56585671		2203	4300	6503	SO:0001589	frameshift_variant	55205	exon4			.	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.152delC	chr18.hg19:g.56585671delC	ENSP00000338217:p.Ser51fs	83.0	0.0		107.0	10.0	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Frame_Shift_Del	DEL	ENST00000336078.4	hg19	CCDS11969.1																																																																																			.	.		0.512	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		-	56585671	C	-	56585671	7	5	103	1	0	1	0	1	0	0	0	0	17987	855	30	0	154	0	ZNF532	18	56585671	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	8394844	56585671	21491577	1011	15634										
CDH20	28316	hgsc.bcm.edu	37	chr18	59167713	59167713	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attcttcagggccagccataTttttctgtggactctaaaac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:59167713delT	ENST00000262717.4	+	4	1037	c.639delT	c.(637-639)tatfs	p.Y213fs	CDH20_ENST00000536675.2_Frame_Shift_Del_p.Y213fs|CDH20_ENST00000538374.1_Frame_Shift_Del_p.Y213fs			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	213	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				GCCAGCCATATTTTTCTGTGG	0.488																																					p.Y213fs		Atlas-INDEL	.											.	CDH20	117	.	0			c.638delA						.						144	140	141					18																	59167713		2203	4300	6503	SO:0001589	frameshift_variant	28316	exon3			.	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.639delT	chr18.hg19:g.59167713delT	ENSP00000262717:p.Tyr213fs	106.0	0.0		163.0	11.0	NM_031891	Q495S3	Frame_Shift_Del	DEL	ENST00000262717.4	hg19	CCDS11977.1																																																																																			.	.		0.488	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		-	59167713	T	-	59167713	7	5	103	1	0	1	0	1	0	0	0	0	3108	1500	52	0	649	0	CDH20	18	59167713	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2582042	59167713	18909535	1012	15635										
KIAA1468	57614	hgsc.bcm.edu	37	chr18	59936142	59936142	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtcctcactaaagctacagtCcccatttatgcaacaggagt					rs17645999	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:59936142delC	ENST00000398130.2	+	20	2953	c.2721delC	c.(2719-2721)gtcfs	p.V907fs	KIAA1468_ENST00000256858.6_Frame_Shift_Del_p.V907fs	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	907										autonomic_ganglia(1)|breast(4)|endometrium(4)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47		Colorectal(73;0.186)				AAGCTACAGTCCCCATTTATG	0.303																																					p.V907fs		Atlas-INDEL	.											.	KIAA1468	93	.	0			c.2720delT						.						49	49	49					18																	59936142		2203	4299	6502	SO:0001589	frameshift_variant	57614	exon20			.	BC011992	CCDS11979.2	18q21.33	2005-11-03			ENSG00000134444	ENSG00000134444			29289	protein-coding gene	gene with protein product						11973628	Standard	NM_020854		Approved	HsT885, HsT3308, FLJ33841	uc002lil.3	Q9P260	OTTHUMG00000132780	ENST00000398130.2:c.2721delC	chr18.hg19:g.59936142delC	ENSP00000381198:p.Val907fs	170.0	0.0		211.0	18.0	NM_020854		Frame_Shift_Del	DEL	ENST00000398130.2	hg19	CCDS11979.2																																																																																			.	.		0.303	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854		-	59936142	C	-	59936142	7	5	103	1	0	1	0	1	0	0	0	0	8245	842	30	0	2799	0	KIAA1468	18	59936142	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	768429	59936142	18141106	1013	15636										
SERPINB2	5055	hgsc.bcm.edu	37	chr18	61569003	61569003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caaacttgttacctgaaggtTctgtagatggggataccagg	12	7	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:61569003T>C	ENST00000299502.4	+	6	645	c.565T>C	c.(565-567)Tct>Cct	p.S189P	SERPINB2_ENST00000482254.1_3'UTR|SERPINB2_ENST00000457692.1_Missense_Mutation_p.S189P	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	189					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	ACCTGAAGGTTCTGTAGATGG	0.368																																					p.S189P		Atlas-SNP	.											.	SERPINB2	63	.	0			c.T565C						.						113	114	114					18																	61569003		2203	4300	6503	SO:0001583	missense	5055	exon6			GAAGGTTCTGTAG	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"Serine (or cysteine) peptidase inhibitors"	8584	protein-coding gene	gene with protein product		173390	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.565T>C	chr18.hg19:g.61569003T>C	ENSP00000299502:p.Ser189Pro	75.0	0.0		80.0	4.0	NM_002575	Q96E96	Missense_Mutation	SNP	ENST00000299502.4	hg19	CCDS11989.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.39|15.39	2.818519|2.818519	0.50633|0.50633	.|.	.|.	ENSG00000242550|ENSG00000197632	ENST00000397996;ENST00000418725|ENST00000299502;ENST00000457692	.|T;T	.|0.13538	.|2.58;2.58	5.9|5.9	3.34|3.34	0.38264|0.38264	.|Serpin domain (3);	.|0.406771	.|0.30210	.|N	.|0.010142	T|T	0.15782|0.15782	0.0380|0.0380	M|M	0.77103|0.77103	2.36|2.36	0.29012|0.29012	N|N	0.886802|0.886802	.|B	.|0.29531	.|0.247	.|B	.|0.29077	.|0.098	T|T	0.18398|0.18398	-1.0338|-1.0338	5|10	.|0.66056	.|D	.|0.02	.|.	4.1622|4.1622	0.10289|0.10289	0.126:0.0702:0.1313:0.6725|0.126:0.0702:0.1313:0.6725	.|.	.|189	.|P05120	.|PAI2_HUMAN	S|P	65|189	.|ENSP00000299502:S189P;ENSP00000401645:S189P	.|ENSP00000299502:S189P	F|S	+|+	2|1	0|0	SERPINB10|SERPINB2	59719983|59719983	0.000000|0.000000	0.05858|0.05858	0.999000|0.999000	0.59377|0.59377	0.578000|0.578000	0.36192|0.36192	-0.303000|-0.303000	0.08210|0.08210	1.036000|1.036000	0.39998|0.39998	0.528000|0.528000	0.53228|0.53228	TTC|TCT	.	.		0.368	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575		C	61569003	T	C	61569003	3	2	103	1	0	0	0	0	1	0	0	0	14116	1783	62	2	583	2	SERPINB2	18	61569003	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1632861	61569003	16508245	1014	15637										
TMX3	54495	hgsc.bcm.edu	37	chr18	66367677	66367677	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcaaactcaataatatcatcTtttgttcgtggtcctctata							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:66367677delT	ENST00000299608.2	-	6	673	c.357delA	c.(355-357)aaafs	p.K119fs	TMX3_ENST00000443099.2_Intron|TMX3_ENST00000562706.1_Frame_Shift_Del_p.K119fs	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	119	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						TAATATCATCTTTTGTTCGTG	0.249																																					p.D120fs		Atlas-INDEL	.											.	TMX3	44	.	0			c.358delG						.						90	96	94					18																	66367677		2203	4287	6490	SO:0001589	frameshift_variant	54495	exon6			.	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"Protein disulfide isomerases"	24718	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 13"		"thioredoxin domain containing 10"	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.357delA	chr18.hg19:g.66367677delT	ENSP00000299608:p.Lys119fs	130.0	0.0		187.0	12.0	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Frame_Shift_Del	DEL	ENST00000299608.2	hg19	CCDS32840.1																																																																																			.	.		0.249	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022		-	66367677	T	-	66367677	7	5	103	1	0	1	0	1	0	0	0	0	16283	1606	56	0	1051	0	TMX3	18	66367677	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	4798674	66367677	11709571	1015	15638										
GALR1	2587	hgsc.bcm.edu	37	chr18	74962810	74962810	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tacgcgctgcccacctgggtGctgggcgccttcatctgcaa	12	15	2	0	rs5375	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:74962810G>A	ENST00000299727.3	+	1	306	c.306G>A	c.(304-306)gtG>gtA	p.V102V		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	102					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|digestion (GO:0007586)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		CCACCTGGGTGCTGGGCGCCT	0.612																																					p.V102V		Atlas-SNP	.											GALR1,NS,carcinoma,0,1	GALR1	53	.	0			c.G306A						.						129	114	119					18																	74962810		2203	4300	6503	SO:0001819	synonymous_variant	2587	exon1			CTGGGTGCTGGGC	U90658	CCDS12012.1	18q23	2012-08-08			ENSG00000166573	ENSG00000166573		"GPCR / Class A : Galanin receptors"	4132	protein-coding gene	gene with protein product		600377		GALNR1, GALNR		7524088	Standard	NM_001480		Approved		uc002lms.4	P47211	OTTHUMG00000132875	ENST00000299727.3:c.306G>A	chr18.hg19:g.74962810G>A		127.0	0.0		181.0	59.0	NM_001480	Q4VBL7	Silent	SNP	ENST00000299727.3	hg19	CCDS12012.1																																																																																			.	G|0.936;T|0.064		0.612	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1			A	74962810	G	A	74962810	2	1	103	1	0	0	0	0	0	0	0	1	6235	1306	46	3		3	GALR1	18	74962810	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	8595133	74962810	3114438	1016	15639										
NFATC1	4772	hgsc.bcm.edu	37	chr18	77193695	77193695	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctacgagacggagggcagccGgggggccgtgaaggcgtcgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:77193695delG	ENST00000427363.2	+	3	1343	c.1343delG	c.(1342-1344)cggfs	p.R448fs	NFATC1_ENST00000591814.1_Frame_Shift_Del_p.R448fs|NFATC1_ENST00000587635.1_Frame_Shift_Del_p.R448fs|NFATC1_ENST00000318065.5_Frame_Shift_Del_p.R435fs|NFATC1_ENST00000253506.5_Frame_Shift_Del_p.R448fs|NFATC1_ENST00000542384.1_Frame_Shift_Del_p.R448fs|NFATC1_ENST00000397790.2_5'UTR|NFATC1_ENST00000545796.1_5'UTR|NFATC1_ENST00000586434.1_Frame_Shift_Del_p.R435fs|NFATC1_ENST00000592223.1_Frame_Shift_Del_p.R435fs|NFATC1_ENST00000329101.4_Frame_Shift_Del_p.R435fs			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	448	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	GAGGGCAGCCGGGGGGCCGTG	0.642																																					p.R448fs	GBM(151;1210 2593 28719 45011)	Atlas-INDEL	.											.	NFATC1	105	.	0			c.1342delC						.						52	57	56					18																	77193695		2202	4297	6499	SO:0001589	frameshift_variant	4772	exon3			.	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"Nuclear factor of activated T-cells"	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.1343delG	chr18.hg19:g.77193695delG	ENSP00000389377:p.Arg448fs	99.0	0.0		155.0	10.0	NM_006162	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Frame_Shift_Del	DEL	ENST00000427363.2	hg19																																																																																				.	.		0.642	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390		-	77193695	G	-	77193695	7	5	103	1	0	1	0	1	0	0	0	0	10370	1116	39	0	1445	0	NFATC1	18	77193695	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2230885	77193695	883553	1017	15640										
C18orf22	79863	hgsc.bcm.edu	37	chr18	77796689	77796689	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaaaaggtttggtatgaaagTccttccttgggttctcactc	9	8	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:77796689T>C	ENST00000306735.5	+	2	318	c.180T>C	c.(178-180)agT>agC	p.S60S	TXNL4A_ENST00000585474.1_5'Flank|TXNL4A_ENST00000592957.1_5'Flank|RP11-795F19.5_ENST00000569722.1_Intron|RBFA_ENST00000586847.1_3'UTR|RBFA_ENST00000262197.7_Silent_p.S60S|TXNL4A_ENST00000589926.1_5'Flank	NM_024805.2	NP_079081.2	Q8N0V3	RBFA_HUMAN	ribosome binding factor A (putative)	60					rRNA processing (GO:0006364)	mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						GGTATGAAAGTCCTTCCTTGG	0.378																																					p.S60S		Atlas-SNP	.											.	RBFA	27	.	0			c.T180C						.						122	118	119					18																	77796689		2203	4300	6503	SO:0001819	synonymous_variant	79863	exon2			TGAAAGTCCTTCC	BC014195	CCDS12021.1, CCDS54194.1	18q23	2010-10-21	2010-10-21	2010-10-21	ENSG00000101546	ENSG00000101546			26120	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 22"	C18orf22		12477932	Standard	NM_024805		Approved	FLJ21172, HsT169	uc002lns.3	Q8N0V3	OTTHUMG00000132923	ENST00000306735.5:c.180T>C	chr18.hg19:g.77796689T>C		45.0	0.0		68.0	4.0	NM_024805	Q6PF07|Q8WZ65|Q9H776	Silent	SNP	ENST00000306735.5	hg19	CCDS12021.1																																																																																			.	.		0.378	RBFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256436.2	NM_024805		C	77796689	T	C	77796689	2	2	103	1	0	0	0	0	0	0	0	1	1900	1664	58	2		2	C18orf22	18	77796689	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	602994	77796689	280559	1018	15641										
DOT1L	84444	hgsc.bcm.edu	37	chr19	2191141	2191141	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caacaactacgagcccttctCccccgaggtgtacggggaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:2191141delC	ENST00000398665.3	+	5	431	c.395delC	c.(394-396)tccfs	p.S132fs		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	132	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGCCCTTCTCCCCCGAGGTG	0.597																																					p.S132fs		Atlas-INDEL	.											.	DOT1L	205	.	0			c.394delT						.						95	105	102					19																	2191141		2088	4218	6306	SO:0001589	frameshift_variant	84444	exon5			.	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.395delC	chr19.hg19:g.2191141delC	ENSP00000381657:p.Ser132fs	157.0	0.0		159.0	10.0	NM_032482	O60379|Q96JL1	Frame_Shift_Del	DEL	ENST00000398665.3	hg19	CCDS42460.1																																																																																			.	.		0.597	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		-	2191141	C	-	2191141	7	5	103	1	0	1	0	1	0	0	0	0	4711	855	30	0	413	0	DOT1L	19	2191141	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10		2191141	56937842	1019	15642										
TLE2	7089	hgsc.bcm.edu	37	chr19	3013796	3013796	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagggggtggtagccgggctGgggggctctgagggttggtc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:3013796delG	ENST00000262953.6	-	11	1006	c.744delC	c.(742-744)cccfs	p.P248fs	TLE2_ENST00000426948.2_Frame_Shift_Del_p.P262fs|TLE2_ENST00000447365.2_5'UTR|TLE2_ENST00000455444.2_Frame_Shift_Del_p.P126fs|TLE2_ENST00000586422.1_Intron|TLE2_ENST00000590536.1_Frame_Shift_Del_p.P249fs|TLE2_ENST00000587217.1_5'UTR|TLE2_ENST00000591529.1_Frame_Shift_Del_p.P262fs|TLE2_ENST00000443826.3_Frame_Shift_Del_p.P126fs	NM_003260.4	NP_003251.2	Q04725	TLE2_HUMAN	transducin-like enhancer of split 2	248	CCN domain.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TAGCCGGGCTGGGGGGCTCTG	0.607																																					p.S263fs		Atlas-INDEL	.											.	TLE2	35	.	0			c.787delA						.						48	53	51					19																	3013796		1896	4104	6000	SO:0001589	frameshift_variant	7089	exon12			.	M99436	CCDS45911.1, CCDS45912.1, CCDS45913.1, CCDS74255.1	19p13.3	2014-03-07	2014-03-07					"WD repeat domain containing"	11838	protein-coding gene	gene with protein product	"enhancer of split groucho 2"	601041	"transducin-like enhancer of split 2, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 2 (E(sp1) homolog, Drosophila)"			8808280	Standard	NM_003260		Approved	ESG2, GRG2, ESG, FLJ41188	uc002lww.3	Q04725		ENST00000262953.6:c.744delC	chr19.hg19:g.3013796delG	ENSP00000262953:p.Pro248fs	133.0	0.0		160.0	10.0	NM_001144761	B4DE03|E9PEV7|F8WCH2|Q8WVY0|Q9Y6S0	Frame_Shift_Del	DEL	ENST00000262953.6	hg19	CCDS45911.1																																																																																			.	.		0.607	TLE2-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452194.2	NM_003260		-	3013796	G	-	3013796	7	5	103	1	0	1	0	1	0	0	0	0	15954	1335	47	0	1527	0	TLE2	19	3013796	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	822655	3013796	56115187	1020	15643										
UBXN6	80700	hgsc.bcm.edu	37	chr19	4453507	4453507	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgacggtggcttcggcttgaAgttcctttctcactggaagg	13	9	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:4453507A>G	ENST00000301281.6	-	3	384	c.260T>C	c.(259-261)cTt>cCt	p.L87P	CTB-50L17.9_ENST00000592034.1_RNA|UBXN6_ENST00000394765.3_Missense_Mutation_p.L34P	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	87						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						TTCGGCTTGAAGTTCCTTTCT	0.642																																					p.L87P		Atlas-SNP	.											.	UBXN6	27	.	0			c.T260C						.						52	47	49					19																	4453507		2203	4300	6503	SO:0001583	missense	80700	exon3			GCTTGAAGTTCCT	AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"UBX domain containing"	14928	protein-coding gene	gene with protein product		611946	"UBX domain-containing 1", "UBX domain containing 1"	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.260T>C	chr19.hg19:g.4453507A>G	ENSP00000301281:p.Leu87Pro	73.0	0.0		53.0	4.0	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	hg19	CCDS12129.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.629811	0.46944	.	.	ENSG00000167671	ENST00000301281;ENST00000394765	T;T	0.53423	0.62;0.62	3.75	2.69	0.31865	.	0.086838	0.47852	D	0.000206	T	0.65133	0.2662	M	0.83012	2.62	0.58432	D	0.999996	D;P	0.89917	1.0;0.884	D;P	0.75020	0.985;0.721	T	0.67894	-0.5552	10	0.87932	D	0	-16.2294	7.2616	0.26207	0.8923:0.0:0.1077:0.0	.	34;87	Q9BZV1-2;Q9BZV1	.;UBXN6_HUMAN	P	87;34	ENSP00000301281:L87P;ENSP00000378246:L34P	ENSP00000301281:L87P	L	-	2	0	UBXN6	4404507	0.999000	0.42202	0.647000	0.29507	0.855000	0.48748	5.517000	0.67061	1.578000	0.49821	0.402000	0.26972	CTT	.	.		0.642	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241		G	4453507	A	G	4453507	3	3	103	1	0	0	0	0	1	0	0	0	16932	72	3	2	1101	2	UBXN6	19	4453507	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1439711	4453507	54675476	1021	15644										
ACER1	125981	hgsc.bcm.edu	37	chr19	6307247	6307247	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atccagctggtcagagcaacAgcccataaaaccacggagac	9	13	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:6307247A>G	ENST00000301452.4	-	5	620	c.543T>C	c.(541-543)gcT>gcC	p.A181A		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	181					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						TCAGAGCAACAGCCCATAAAA	0.552																																					p.A181A		Atlas-SNP	.											.	ACER1	38	.	0			c.T543C						.						95	91	93					19																	6307247		2203	4300	6503	SO:0001819	synonymous_variant	125981	exon5			AGCAACAGCCCAT	AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"Alkaline ceramidase"	18356	protein-coding gene	gene with protein product		613491	"N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.543T>C	chr19.hg19:g.6307247A>G		64.0	0.0		72.0	4.0	NM_133492		Silent	SNP	ENST00000301452.4	hg19	CCDS12161.1																																																																																			.	.		0.552	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492		G	6307247	A	G	6307247	2	3	103	1	0	0	0	0	0	0	0	1	138	175	7	2		2	ACER1	19	6307247	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	1853740	6307247	52821736	1022	15645										
C3	718	hgsc.bcm.edu	37	chr19	6718129	6718129	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgttgaccatgaccgtccgGcccacgggtagcagcttgtg	13	12	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:6718129G>A	ENST00000245907.6	-	4	572	c.480C>T	c.(478-480)ggC>ggT	p.G160G		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	160					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGACCGTCCGGCCCACGGGTA	0.622																																					p.G160G		Atlas-SNP	.											.	C3	192	.	0			c.C480T						.						100	95	96					19																	6718129		2203	4300	6503	SO:0001819	synonymous_variant	718	exon4			CGTCCGGCCCACG	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.480C>T	chr19.hg19:g.6718129G>A		91.0	0.0		96.0	31.0	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	hg19	CCDS32883.1																																																																																			.	.		0.622	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		A	6718129	G	A	6718129	2	1	103	1	0	0	0	0	0	0	0	1	2206	1190	42	3		3	C3	19	6718129	Silent	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	410882	6718129	52410854	1023	15646										
XAB2	56949	hgsc.bcm.edu	37	chr19	7684695	7684695	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccagctggatctcctcggggTtgacctgctgtgccagctct	12	14	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:7684695T>C	ENST00000358368.4	-	18	2481	c.2444A>G	c.(2443-2445)aAc>aGc	p.N815S	XAB2_ENST00000534844.1_Missense_Mutation_p.N812S	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	815					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CTCCTCGGGGTTGACCTGCTG	0.697								Direct reversal of damage;Nucleotide excision repair (NER)																													p.N815S		Atlas-SNP	.											.	XAB2	69	.	0			c.A2444G						.						118	120	119					19																	7684695		2203	4300	6503	SO:0001583	missense	56949	exon18			TCGGGGTTGACCT	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"SYF1 homolog, RNA splicing factor (S. cerevisiae)", "SYF1 pre-mRNA-splicing factor"	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.2444A>G	chr19.hg19:g.7684695T>C	ENSP00000351137:p.Asn815Ser	87.0	0.0		100.0	4.0	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	hg19	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	T	15.26	2.781387	0.49891	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.31510	1.49;1.49	4.57	3.51	0.40186	.	0.058234	0.64402	D	0.000004	T	0.56659	0.2000	M	0.92367	3.3	0.58432	D	0.999994	D	0.55605	0.972	P	0.58013	0.831	T	0.63305	-0.6667	10	0.87932	D	0	-46.047	10.0458	0.42186	0.0:0.0:0.1702:0.8298	.	815	Q9HCS7	SYF1_HUMAN	S	815;812	ENSP00000351137:N815S;ENSP00000438225:N812S	ENSP00000351137:N815S	N	-	2	0	XAB2	7590695	1.000000	0.71417	0.997000	0.53966	0.629000	0.37895	5.366000	0.66122	0.566000	0.29273	0.254000	0.18369	AAC	.	.		0.697	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		C	7684695	T	C	7684695	3	2	103	1	0	0	0	0	1	0	0	0	17433	1725	60	2	131	2	XAB2	19	7684695	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	966566	7684695	51444288	1024	15647										
MUC16	94025	hgsc.bcm.edu	37	chr19	9085053	9085053	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtcacttcagtatcaggggaGggggaaaaggagacagtggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:9085053delG	ENST00000397910.4	-	1	6965	c.6762delC	c.(6760-6762)cccfs	p.P2254fs		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2254	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TATCAGGGGAGGGGGAAAAGG	0.453																																					p.S2255fs		Atlas-INDEL	.											.	MUC16	4315	.	0			c.6763delT						.						79	76	77					19																	9085053		1945	4141	6086	SO:0001589	frameshift_variant	94025	exon1			.	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.6762delC	chr19.hg19:g.9085053delG	ENSP00000381008:p.Pro2254fs	89.0	0.0		110.0	10.0	NM_024690	Q6ZQW5|Q96RK2	Frame_Shift_Del	DEL	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		-	9085053	G	-	9085053	7	5	103	1	0	1	0	1	0	0	0	0	9982	987	35	0	37097	0	MUC16	19	9085053	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1400358	9085053	50043930	1025	15648										
ZNF562	54811	hgsc.bcm.edu	37	chr19	9767254	9767254	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagtgaatatttgattcttcAaaaaaccctgctgaagtgat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:9767254delA	ENST00000448622.1	-	5	479	c.317delT	c.(316-318)ttgfs	p.L106fs	ZNF562_ENST00000590155.1_Frame_Shift_Del_p.L106fs|ZNF562_ENST00000537617.1_5'UTR|ZNF562_ENST00000453372.2_Frame_Shift_Del_p.L106fs|ZNF562_ENST00000541032.1_Frame_Shift_Del_p.L69fs|ZNF562_ENST00000453792.2_Frame_Shift_Del_p.L37fs|ZNF562_ENST00000293648.4_Frame_Shift_Del_p.L34fs|ZNF562_ENST00000587392.1_Intron	NM_001130031.1|NM_001130032.1	NP_001123503.1|NP_001123504.1	Q6V9R5	ZN562_HUMAN	zinc finger protein 562	106	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	17						TTGATTCTTCAAAAAACCCTG	0.373																																					p.L106fs		Atlas-INDEL	.											.	ZNF562	72	.	0			c.318delG						.						145	142	143					19																	9767254		2203	4300	6503	SO:0001589	frameshift_variant	54811	exon5			.	AK000086	CCDS12217.1, CCDS45956.1, CCDS74280.1	19p13.2	2013-09-20			ENSG00000171466	ENSG00000171466		"Zinc fingers, C2H2-type", "-"	25950	protein-coding gene	gene with protein product							Standard	NM_001130031		Approved	FLJ20079	uc010xks.2	Q6V9R5	OTTHUMG00000180205	ENST00000448622.1:c.317delT	chr19.hg19:g.9767254delA	ENSP00000411784:p.Leu106fs	169.0	0.0		165.0	11.0	NM_001130032	Q32MN2|Q9NXS5	Frame_Shift_Del	DEL	ENST00000448622.1	hg19	CCDS45956.1																																																																																			.	.		0.373	ZNF562-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450239.1	NM_017656		-	9767254	A	-	9767254	7	5	103	1	0	1	0	1	0	0	0	0	18008	131	5	0	971	0	ZNF562	19	9767254	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	682201	9767254	49361729	1026	15649										
RGL3	57139	hgsc.bcm.edu	37	chr19	11517507	11517507	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgcgcaggcctctgaagagTctgggtcagaagtttgggca	15	10	3	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:11517507T>C	ENST00000380456.3	-	6	734	c.671A>G	c.(670-672)gAc>gGc	p.D224G	Y_RNA_ENST00000365487.1_RNA|RGL3_ENST00000393423.3_Missense_Mutation_p.D224G	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	224					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						CTCTGAAGAGTCTGGGTCAGA	0.562																																					p.D224G	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.A671G						.						52	51	51					19																	11517507		2203	4299	6502	SO:0001583	missense	57139	exon6			GAAGAGTCTGGGT	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.671A>G	chr19.hg19:g.11517507T>C	ENSP00000369823:p.Asp224Gly	64.0	0.0		70.0	4.0	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	hg19	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	T	7.823	0.718103	0.15372	.	.	ENSG00000205517	ENST00000342684;ENST00000393423;ENST00000380456	T;T	0.29142	1.58;1.58	4.25	-6.52	0.01872	Ras guanine nucleotide exchange factor, domain (1);	1.713730	0.03182	N	0.172253	T	0.16300	0.0392	N	0.19112	0.55	0.09310	N	1	B;B	0.13145	0.001;0.007	B;B	0.10450	0.005;0.003	T	0.15263	-1.0443	10	0.49607	T	0.09	.	2.6115	0.04892	0.1318:0.2904:0.4004:0.1774	.	224;224	Q3MIN7;B5ME84	RGL3_HUMAN;.	G	21;224;224	ENSP00000377075:D224G;ENSP00000369823:D224G	ENSP00000344665:D21G	D	-	2	0	RGL3	11378507	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.581000	0.05820	-1.433000	0.01977	-0.435000	0.05868	GAC	.	.		0.562	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867		C	11517507	T	C	11517507	3	2	103	1	0	0	0	0	1	0	0	0	13293	1667	58	2	1535	2	RGL3	19	11517507	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1750253	11517507	47611476	1027	15650										
RGL3	57139	hgsc.bcm.edu	37	chr19	11526669	11526669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctcagcctcctccaaaaaaTcttccagaagcttctctgct	5	15	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:11526669T>C	ENST00000380456.3	-	5	644	c.581A>G	c.(580-582)gAt>gGt	p.D194G	RGL3_ENST00000393423.3_Missense_Mutation_p.D194G	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	194	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						CTCCAAAAAATCTTCCAGAAG	0.592																																					p.D194G	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.A581G						.						126	140	135					19																	11526669		2203	4300	6503	SO:0001583	missense	57139	exon5			AAAAAATCTTCCA	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.581A>G	chr19.hg19:g.11526669T>C	ENSP00000369823:p.Asp194Gly	84.0	0.0		113.0	5.0	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	hg19	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.672144	0.29693	.	.	ENSG00000205517	ENST00000393423;ENST00000380456	T;T	0.28666	1.6;1.6	4.88	1.66	0.24008	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (2);	0.981440	0.08360	N	0.957927	T	0.21674	0.0522	L	0.44542	1.39	0.09310	N	1	B;P	0.35328	0.082;0.495	B;B	0.26517	0.07;0.041	T	0.20405	-1.0276	10	0.54805	T	0.06	.	4.6926	0.12788	0.0:0.2647:0.1571:0.5782	.	194;194	Q3MIN7;B5ME84	RGL3_HUMAN;.	G	194	ENSP00000377075:D194G;ENSP00000369823:D194G	ENSP00000369823:D194G	D	-	2	0	RGL3	11387669	0.000000	0.05858	0.279000	0.24732	0.927000	0.56198	0.349000	0.20055	0.241000	0.21283	0.418000	0.28097	GAT	.	.		0.592	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867		C	11526669	T	C	11526669	3	2	103	1	0	0	0	0	1	0	0	0	13293	1435	50	2	1629	2	RGL3	19	11526669	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	9162	11526669	47602314	1028	15651										
ZNF44	51710	hgsc.bcm.edu	37	chr19	12384103	12384103	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatcatgtgtctttgaaagcTtccaagatgacaaaacgctt	7	8	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:12384103T>C	ENST00000356109.5	-	5	1229	c.1111A>G	c.(1111-1113)Agc>Ggc	p.S371G	ZNF44_ENST00000355684.5_Missense_Mutation_p.S323G	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	371					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		CTTTGAAAGCTTCCAAGATGA	0.413																																					p.S371G		Atlas-SNP	.											.	ZNF44	55	.	0			c.A1111G						.						140	142	142					19																	12384103		2203	4300	6503	SO:0001583	missense	51710	exon5			GAAAGCTTCCAAG	X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"Zinc fingers, C2H2-type", "-"	13110	protein-coding gene	gene with protein product		194542	"zinc finger protein 58", "zinc finger protein 44 (KOX 7)", "zinc finger protein 55"	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.1111A>G	chr19.hg19:g.12384103T>C	ENSP00000348419:p.Ser371Gly	62.0	0.0		95.0	4.0	NM_001164276	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Missense_Mutation	SNP	ENST00000356109.5	hg19	CCDS54223.1	.	.	.	.	.	.	.	.	.	.	T	13.31	2.198311	0.38806	.	.	ENSG00000197857	ENST00000393337;ENST00000356109;ENST00000457673;ENST00000355684	T;T;T	0.16073	2.37;2.37;2.37	0.997	-0.072	0.13741	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21145	0.0509	L	0.28776	0.89	.	.	.	P;D	0.76494	0.891;0.999	P;D	0.80764	0.783;0.994	T	0.25363	-1.0134	8	0.42905	T	0.14	.	2.1582	0.03818	0.0:0.2424:0.3278:0.4299	.	371;323	P15621;F8W7T7	ZNF44_HUMAN;.	G	371;371;323;323	ENSP00000377008:S371G;ENSP00000348419:S371G;ENSP00000347910:S323G	ENSP00000347910:S323G	S	-	1	0	ZNF44	12245103	0.000000	0.05858	0.001000	0.08648	0.794000	0.44872	-4.679000	0.00199	-0.064000	0.13043	0.254000	0.18369	AGC	.	.		0.413	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264		C	12384103	T	C	12384103	3	2	103	1	0	0	0	0	1	0	0	0	17927	1609	56	2	884	2	ZNF44	19	12384103	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	857434	12384103	46744880	1029	15652										
ZNF799	90576	hgsc.bcm.edu	37	chr19	12502459	12502459	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cactgtttacattcatacagTttctccccagtatgtgttct	5	11	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:12502459T>G	ENST00000430385.3	-	4	953	c.753A>C	c.(751-753)aaA>aaC	p.K251N	ZNF799_ENST00000419318.1_Missense_Mutation_p.K219N|CTD-3105H18.14_ENST00000435033.1_Intron	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	251					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						ATTCATACAGTTTCTCCCCAG	0.378																																					p.K251N		Atlas-SNP	.											.	ZNF799	111	.	0			c.A753C						.						78	90	86					19																	12502459		2203	4296	6499	SO:0001583	missense	90576	exon4			ATACAGTTTCTCC	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"Zinc fingers, C2H2-type", "-"	28071	protein-coding gene	gene with protein product			"zinc finger protein 842"	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.753A>C	chr19.hg19:g.12502459T>G	ENSP00000411084:p.Lys251Asn	62.0	0.0		79.0	4.0	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	hg19	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.208657	0.39003	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.26067	1.76;1.76	1.31	-0.963	0.10330	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41534	0.1163	M	0.73319	2.225	0.26579	N	0.973419	D	0.89917	1.0	D	0.91635	0.999	T	0.27123	-1.0083	9	0.66056	D	0.02	.	3.0181	0.06066	0.0:0.3938:0.265:0.3412	.	251	Q96GE5	ZN799_HUMAN	N	219;251	ENSP00000415278:K219N;ENSP00000411084:K251N	ENSP00000415278:K219N	K	-	3	2	ZNF799	12363459	0.000000	0.05858	0.001000	0.08648	0.117000	0.20001	-1.622000	0.02042	-0.408000	0.07565	0.352000	0.21897	AAA	.	.		0.378	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		G	12502459	T	G	12502459	3	3	103	1	0	0	0	0	1	0	0	0	18181	1722	60	5	1182	5	ZNF799	19	12502459	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	118356	12502459	46626524	1030	15653										
NFIX	4784	hgsc.bcm.edu	37	chr19	13184726	13184726	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcgttcttcccagctcctgTtgcaacagcatcagggccca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:13184726delT	ENST00000592199.1	+	5	704	c.704delT	c.(703-705)gttfs	p.V235fs	AC007787.2_ENST00000588095.1_RNA|NFIX_ENST00000358552.3_Frame_Shift_Del_p.V234fs|NFIX_ENST00000585575.1_Frame_Shift_Del_p.V227fs|NFIX_ENST00000587760.1_Frame_Shift_Del_p.V227fs|NFIX_ENST00000397661.2_Frame_Shift_Del_p.V235fs|NFIX_ENST00000588680.1_3'UTR|NFIX_ENST00000360105.4_Frame_Shift_Del_p.V238fs|NFIX_ENST00000588228.1_Frame_Shift_Del_p.V188fs|NFIX_ENST00000587260.1_Frame_Shift_Del_p.V234fs			Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription factor)	235					astrocyte differentiation (GO:0048708)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell layer development (GO:0021680)|DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			CCAGCTCCTGTTGCAACAGCA	0.597																																					p.V243fs		Atlas-INDEL	.											.	NFIX	61	.	0			c.727delG						.						74	81	79					19																	13184726		1955	4138	6093	SO:0001589	frameshift_variant	4784	exon5			.	U18761	CCDS45996.1, CCDS59359.1	19p13.3	2008-02-05				ENSG00000008441			7788	protein-coding gene	gene with protein product		164005				8340106, 7590749	Standard	NM_001271043		Approved	NF1A	uc010xmx.2	Q14938		ENST00000592199.1:c.704delT	chr19.hg19:g.13184726delT	ENSP00000467512:p.Val235fs	131.0	0.0		152.0	10.0	NM_001271043	B4DM25|O60413|Q0VG09|Q12859|Q13050|Q13052|Q5U094|Q9UPH1|Q9Y6R8	Frame_Shift_Del	DEL	ENST00000592199.1	hg19																																																																																				.	.		0.597	NFIX-013	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000452763.1	NM_002501		-	13184726	T	-	13184726	7	5	103	1	0	1	0	1	0	0	0	0	10383	1725	60	0	722	0	NFIX	19	13184726	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	682267	13184726	45944257	1031	15654										
PODNL1	79883	hgsc.bcm.edu	37	chr19	14044198	14044198	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgcaggatagccagggtccGgggcaggccggcgggcactg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:14044198delG	ENST00000339560.5	-	8	1132	c.859delC	c.(859-861)cggfs	p.R287fs	PODNL1_ENST00000254320.3_Frame_Shift_Del_p.R205fs|PODNL1_ENST00000538371.2_Frame_Shift_Del_p.R285fs|PODNL1_ENST00000538517.2_Frame_Shift_Del_p.R196fs	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	287	Leu-rich.					proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			GCCAGGGTCCGGGGCAGGCCG	0.652																																					p.R287fs		Atlas-INDEL	.											.	PODNL1	27	.	0			c.860delG						.						16	21	20					19																	14044198		2194	4288	6482	SO:0001589	frameshift_variant	79883	exon8			.	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.859delC	chr19.hg19:g.14044198delG	ENSP00000345175:p.Arg287fs	158.0	0.0		168.0	12.0	NM_024825	B7Z564|Q9H5G9	Frame_Shift_Del	DEL	ENST00000339560.5	hg19	CCDS12300.1																																																																																			.	.		0.652	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825		-	14044198	G	-	14044198	7	5	103	1	0	1	0	1	0	0	0	0	12188	1115	39	0	683	0	PODNL1	19	14044198	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	859472	14044198	45084785	1032	15655										
OR7A10	390892	hgsc.bcm.edu	37	chr19	14952035	14952035	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatggaggaaactatcttagAgtaagagtacaggatcccag	11	6	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:14952035A>C	ENST00000248058.1	-	1	654	c.655T>G	c.(655-657)Tct>Gct	p.S219A		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					ACTATCTTAGAGTAAGAGTAC	0.468																																					p.S219A		Atlas-SNP	.											.	OR7A10	33	.	0			c.T655G						.						66	61	63					19																	14952035		2203	4300	6503	SO:0001583	missense	390892	exon1			TCTTAGAGTAAGA		CCDS32936.1	19p13.1	2012-08-09						"GPCR / Class A : Olfactory receptors"	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.655T>G	chr19.hg19:g.14952035A>C	ENSP00000248058:p.Ser219Ala	43.0	0.0		65.0	15.0	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	hg19	CCDS32936.1	.	.	.	.	.	.	.	.	.	.	a	10.12	1.263886	0.23136	.	.	ENSG00000127515	ENST00000248058	T	0.00048	8.82	2.75	0.126	0.14722	GPCR, rhodopsin-like superfamily (1);	0.830271	0.09655	N	0.773210	T	0.00144	0.0004	N	0.25201	0.72	0.09310	N	1	B	0.25486	0.127	B	0.35931	0.214	T	0.09143	-1.0688	10	0.59425	D	0.04	.	5.9723	0.19359	0.3999:0.0:0.0:0.6001	.	219	O76100	OR7AA_HUMAN	A	219	ENSP00000248058:S219A	ENSP00000248058:S219A	S	-	1	0	OR7A10	14813035	0.000000	0.05858	0.010000	0.14722	0.413000	0.31143	-0.733000	0.04898	0.274000	0.22072	0.113000	0.15668	TCT	.	.		0.468	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190		C	14952035	A	C	14952035	3	2	103	1	0	0	0	0	1	0	0	0	11223	304	11	5	278	5	OR7A10	19	14952035	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	907837	14952035	44176948	1033	15656										
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15065025	15065025	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggcagccagggcctcgtagAgggcagtgccatccatgttg	15	11	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:15065025A>G	ENST00000221742.3	-	7	1293	c.1286T>C	c.(1285-1287)cTc>cCc	p.L429P	SLC1A6_ENST00000600144.1_Missense_Mutation_p.L351P|SLC1A6_ENST00000430939.2_Missense_Mutation_p.L365P	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	429					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						GGCCTCGTAGAGGGCAGTGCC	0.612																																					p.L429P		Atlas-SNP	.											.	SLC1A6	111	.	0			c.T1286C						.						90	80	84					19																	15065025		2203	4300	6503	SO:0001583	missense	6511	exon7			TCGTAGAGGGCAG		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1286T>C	chr19.hg19:g.15065025A>G	ENSP00000221742:p.Leu429Pro	105.0	0.0		115.0	5.0	NM_005071	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	hg19	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	a	21.6	4.180501	0.78677	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.64085	-0.01;-0.08	4.52	4.52	0.55395	Sodium:dicarboxylate symporter, conserved site (1);	0.068216	0.56097	D	0.000023	D	0.84306	0.5443	H	0.96333	3.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.88577	0.3134	10	0.87932	D	0	-27.6715	12.1227	0.53900	1.0:0.0:0.0:0.0	.	365;429	E7EV13;P48664	.;EAA4_HUMAN	P	365;429	ENSP00000409386:L365P;ENSP00000221742:L429P	ENSP00000221742:L429P	L	-	2	0	SLC1A6	14926025	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.919000	0.92770	2.037000	0.60232	0.446000	0.29264	CTC	.	.		0.612	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		G	15065025	A	G	15065025	3	3	103	1	0	0	0	0	1	0	0	0	14451	304	11	2	420	2	SLC1A6	19	15065025	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	112990	15065025	44063958	1034	15657										
CYP4F2	8529	hgsc.bcm.edu	37	chr19	16008363	16008363	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccccgaccagcaggaggagcAgccaaggggatgctgccact	14	14	0	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:16008363A>G	ENST00000221700.6	-	2	154	c.59T>C	c.(58-60)cTg>cCg	p.L20P	CYP4F2_ENST00000011989.7_5'UTR	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CAGGAGGAGCAGCCAAGGGGA	0.657																																					p.L20P		Atlas-SNP	.											.	CYP4F2	97	.	0			c.T59C						.						38	41	40					19																	16008363		2203	4300	6503	SO:0001583	missense	8529	exon2			AGGAGCAGCCAAG	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"Cytochrome P450s"	2645	protein-coding gene	gene with protein product		604426	"cytochrome P450, subfamily IVF, polypeptide 2"			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.59T>C	chr19.hg19:g.16008363A>G	ENSP00000221700:p.Leu20Pro	74.0	0.0		94.0	5.0	NM_001082		Missense_Mutation	SNP	ENST00000221700.6	hg19	CCDS12336.1	.	.	.	.	.	.	.	.	.	.	a	8.377	0.836582	0.16891	.	.	ENSG00000186115	ENST00000221700	D	0.91945	-2.94	2.99	0.675	0.17952	.	2.133910	0.04135	N	0.318526	D	0.89371	0.6696	M	0.63428	1.95	0.45183	D	0.998197	B	0.10296	0.003	B	0.08055	0.003	T	0.75728	-0.3216	10	0.48119	T	0.1	.	3.2861	0.06932	0.6202:0.2404:0.1394:0.0	.	20	P78329	CP4F2_HUMAN	P	20	ENSP00000221700:L20P	ENSP00000221700:L20P	L	-	2	0	CYP4F2	15869363	0.000000	0.05858	0.135000	0.22099	0.048000	0.14542	-0.025000	0.12413	-0.047000	0.13423	-0.533000	0.04299	CTG	.	.		0.657	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082		G	16008363	A	G	16008363	3	3	103	1	0	0	0	0	1	0	0	0	4190	188	7	2	1551	2	CYP4F2	19	16008363	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	943338	16008363	43120620	1035	15658										
CIB3	117286	hgsc.bcm.edu	37	chr19	16275654	16275654	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcacctcctcggcactcagCcccccccgcgtcagtttggt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:16275654delC	ENST00000269878.4	-	5	466	c.417delG	c.(415-417)gggfs	p.G139fs	CIB3_ENST00000379859.3_Frame_Shift_Del_p.G90fs|CIB3_ENST00000541493.1_5'UTR	NM_054113.2	NP_473454.1	Q96Q77	CIB3_HUMAN	calcium and integrin binding family member 3	139			G -> E (in dbSNP:rs6512087). {ECO:0000269|PubMed:15489334}.				calcium ion binding (GO:0005509)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16						CGGCACTCAGCCCCCCCCGCG	0.567																																					p.L140X		Atlas-INDEL	.											CIB3,NS,carcinoma,0,3	CIB3	35	.	0			c.418delC						.						131	118	122					19																	16275654		2203	4300	6503	SO:0001589	frameshift_variant	117286	exon5			.	AB050868	CCDS12340.1, CCDS74305.1	19p13.12	2013-01-10						"EF-hand domain containing"	24580	protein-coding gene	gene with protein product		610645					Standard	XM_005259728		Approved	KIP3	uc002nds.3	Q96Q77		ENST00000269878.4:c.417delG	chr19.hg19:g.16275654delC	ENSP00000269878:p.Gly139fs	157.0	0.0		167.0	15.0	NM_054113	E7EUX1|Q2M1W0|Q6ISP1	Frame_Shift_Del	DEL	ENST00000269878.4	hg19	CCDS12340.1																																																																																			.	.		0.567	CIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460351.1	NM_054113		-	16275654	C	-	16275654	7	5	103	1	0	1	0	1	0	0	0	0	3424	726	26	0	154	0	CIB3	19	16275654	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	267291	16275654	42853329	1036	15659										
NWD1	284434	hgsc.bcm.edu	37	chr19	16908642	16908642	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agacatggtggagacggctgTttttggtactgagaacaacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:16908642delT	ENST00000552788.1	+	14	3404	c.3404delT	c.(3403-3405)gttfs	p.V1135fs	NWD1_ENST00000549814.1_Frame_Shift_Del_p.V1135fs|NWD1_ENST00000523826.1_Frame_Shift_Del_p.V929fs|NWD1_ENST00000339803.6_Frame_Shift_Del_p.V1000fs|NWD1_ENST00000379808.3_Frame_Shift_Del_p.V1135fs|NWD1_ENST00000524140.2_Frame_Shift_Del_p.V1135fs			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1135							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GAGACGGCTGTTTTTGGTACT	0.552																																					p.V1135fs		Atlas-INDEL	.											.	NWD1	303	.	0			c.3403delG						.						301	275	284					19																	16908642		2203	4300	6503	SO:0001589	frameshift_variant	284434	exon16			.	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"WD repeat domain containing"	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.3404delT	chr19.hg19:g.16908642delT	ENSP00000447224:p.Val1135fs	153.0	0.0		162.0	15.0	NM_001007525	C9J021|Q68CT3	Frame_Shift_Del	DEL	ENST00000552788.1	hg19																																																																																				.	.		0.552	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		-	16908642	T	-	16908642	7	5	103	1	0	1	0	1	0	0	0	0	10790	1725	60	0	3045	0	NWD1	19	16908642	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	632988	16908642	42220341	1037	15660										
OCEL1	79629	hgsc.bcm.edu	37	chr19	17337947	17337947	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccctcctgggcgccaagaagCctattggagccatccctaag	10	15	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:17337947C>T	ENST00000215061.4	+	3	435	c.391C>T	c.(391-393)Cct>Tct	p.P131S	OCEL1_ENST00000597836.1_Missense_Mutation_p.P75S|OCEL1_ENST00000601576.1_3'UTR|OCEL1_ENST00000601529.1_Missense_Mutation_p.P131S	NM_024578.1	NP_078854.1	Q9H607	OCEL1_HUMAN	occludin/ELL domain containing 1	131										central_nervous_system(2)|endometrium(2)|kidney(1)|lung(2)	7						CGCCAAGAAGCCTATTGGAGC	0.597																																					p.P131S		Atlas-SNP	.											.	OCEL1	20	.	0			c.C391T						.						66	76	72					19																	17337947		2203	4300	6503	SO:0001583	missense	79629	exon3			AAGAAGCCTATTG	BC029361	CCDS12351.1	19p13.11	2008-02-05				ENSG00000099330			26221	protein-coding gene	gene with protein product						12477932	Standard	NM_024578		Approved	FLJ22709	uc002nfp.3	Q9H607		ENST00000215061.4:c.391C>T	chr19.hg19:g.17337947C>T	ENSP00000215061:p.Pro131Ser	105.0	0.0		92.0	4.0	NM_024578		Missense_Mutation	SNP	ENST00000215061.4	hg19	CCDS12351.1	.	.	.	.	.	.	.	.	.	.	C	7.427	0.637979	0.14386	.	.	ENSG00000099330	ENST00000215061	T	0.29655	1.56	3.94	-2.51	0.06365	.	1.270950	0.05366	N	0.534623	T	0.13286	0.0322	N	0.08118	0	0.09310	N	1	B	0.17038	0.02	B	0.12837	0.008	T	0.24764	-1.0151	10	0.22706	T	0.39	-0.0364	4.1263	0.10129	0.0:0.3416:0.183:0.4755	.	131	Q9H607	OCEL1_HUMAN	S	131	ENSP00000215061:P131S	ENSP00000215061:P131S	P	+	1	0	OCEL1	17198947	0.000000	0.05858	0.003000	0.11579	0.061000	0.15899	0.014000	0.13333	0.015000	0.14971	-0.339000	0.08088	CCT	.	.		0.597	OCEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463307.1	NM_024578		T	17337947	C	T	17337947	3	4	103	1	0	0	0	0	1	0	0	0	10825	739	26	3	401	3	OCEL1	19	17337947	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	429305	17337947	41791036	1038	15661										
C19orf62	29086	hgsc.bcm.edu	37	chr19	17389796	17389796	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcagcggccttgccagagccAtgcttcctacagcctgctgg	12	15	0	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:17389796A>G	ENST00000359435.4	+	9	1122	c.929A>G	c.(928-930)cAt>cGt	p.H310R	ANKLE1_ENST00000394458.3_5'Flank|ANKLE1_ENST00000433424.2_5'Flank|ANKLE1_ENST00000598347.1_5'Flank|BABAM1_ENST00000447614.2_Missense_Mutation_p.H310R|BABAM1_ENST00000601043.1_Missense_Mutation_p.H310R|ANKLE1_ENST00000594072.1_5'Flank|BABAM1_ENST00000598188.1_Missense_Mutation_p.H310R|CTD-2278I10.6_ENST00000596542.1_Intron|ANKLE1_ENST00000404085.1_5'Flank|BABAM1_ENST00000595632.1_Missense_Mutation_p.H235R	NM_001033549.1	NP_001028721.1	Q9NWV8	BABA1_HUMAN	BRISC and BRCA1 A complex member 1	310					chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5						TGCCAGAGCCATGCTTCCTAC	0.577																																					p.H310R		Atlas-SNP	.											.	BABAM1	14	.	0			c.A929G						.						32	37	36					19																	17389796		2048	4199	6247	SO:0001583	missense	29086	exon9			AGAGCCATGCTTC	AK000578	CCDS46012.1, CCDS74310.1	19p13.11	2011-02-21	2011-02-21	2011-01-31	ENSG00000105393	ENSG00000105393			25008	protein-coding gene	gene with protein product	"Mediator of Rap80 Interactions and Targeting 40 kD", "new component of the BRCA1 A complex"	612766	"chromosome 19 open reading frame 62"	C19orf62		11042152	Standard	NM_001288756		Approved	FLJ20571, HSPC142, NBA1, MERIT40	uc002nfv.3	Q9NWV8		ENST00000359435.4:c.929A>G	chr19.hg19:g.17389796A>G	ENSP00000352408:p.His310Arg	95.0	0.0		94.0	4.0	NM_014173	A8MQT0|B4DRY9|B4DVR1|Q6FIA0|Q9P018	Missense_Mutation	SNP	ENST00000359435.4	hg19	CCDS46012.1	.	.	.	.	.	.	.	.	.	.	A	17.16	3.317593	0.60524	.	.	ENSG00000105393	ENST00000359435;ENST00000447614	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	T	0.69160	0.3080	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.66854	-0.5818	8	0.32370	T	0.25	-7.3688	12.8452	0.57825	1.0:0.0:0.0:0.0	.	310	Q9NWV8	BABA1_HUMAN	R	310	.	ENSP00000352408:H310R	H	+	2	0	BABAM1	17250796	1.000000	0.71417	0.983000	0.44433	0.427000	0.31564	8.515000	0.90548	2.137000	0.66172	0.533000	0.62120	CAT	.	.		0.577	BABAM1-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463471.1	NM_014173		G	17389796	A	G	17389796	3	3	103	1	0	0	0	0	1	0	0	0	1946	217	8	2	959	2	C19orf62	19	17389796	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	51849	17389796	41739187	1039	15662										
DDX49	54555	hgsc.bcm.edu	37	chr19	19030629	19030629	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgggtttgaagcagcccacgCccgtgcagctcggctgcatc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:19030629delC	ENST00000247003.4	+	1	146	c.79delC	c.(79-81)cccfs	p.P27fs	COPE_ENST00000600932.1_5'Flank|COPE_ENST00000262812.4_5'Flank|COPE_ENST00000349893.4_5'Flank|DDX49_ENST00000438170.2_5'UTR|COPE_ENST00000351079.4_5'Flank|AC002985.3_ENST00000596918.1_Intron	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	27							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	18			Epithelial(12;0.0289)			GCAGCCCACGCCCGTGCAGCT	0.652																																					p.T26fs		Atlas-INDEL	.											.	DDX49	37	.	0			c.78delG						.						28	29	29					19																	19030629		2201	4300	6501	SO:0001589	frameshift_variant	54555	exon1			.		CCDS12390.1	19p12	2008-02-05				ENSG00000105671		"DEAD-boxes"	18684	protein-coding gene	gene with protein product							Standard	NM_019070		Approved	FLJ10432	uc002nkq.2	Q9Y6V7		ENST00000247003.4:c.79delC	chr19.hg19:g.19030629delC	ENSP00000247003:p.Pro27fs	143.0	0.0		164.0	10.0	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Frame_Shift_Del	DEL	ENST00000247003.4	hg19	CCDS12390.1																																																																																			.	.		0.652	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070		-	19030629	C	-	19030629	7	5	103	1	0	1	0	1	0	0	0	0	4368	739	26	0	81	0	DDX49	19	19030629	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1640833	19030629	40098354	1040	15663										
PBX4	80714	hgsc.bcm.edu	37	chr19	19681606	19681606	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcctcaggagctgggcgtcaGggggatcttcgtcttgaatg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:19681606delG	ENST00000251203.9	-	3	516	c.230delC	c.(229-231)cctfs	p.P77fs		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	77					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|XY body (GO:0001741)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(4)|ovary(1)|prostate(3)	9						CTGGGCGTCAGGGGGATCTTC	0.552																																					p.P77fs		Atlas-INDEL	.											.	PBX4	34	.	0			c.231delT						.						67	69	69					19																	19681606		2203	4300	6503	SO:0001589	frameshift_variant	80714	exon3			.	AJ300182	CCDS12406.1	19p13.11	2014-09-11	2007-01-30		ENSG00000105717			"Homeoboxes / TALE class"	13403	protein-coding gene	gene with protein product		608127	"pre-B-cell leukemia transcription factor 4"				Standard	NM_025245		Approved		uc002nmy.3	Q9BYU1	OTTHUMG00000172310	ENST00000251203.9:c.230delC	chr19.hg19:g.19681606delG	ENSP00000251203:p.Pro77fs	96.0	0.0		133.0	10.0	NM_025245	A5D8Y0|B3KUK9	Frame_Shift_Del	DEL	ENST00000251203.9	hg19	CCDS12406.1																																																																																			.	.		0.552	PBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417784.6			-	19681606	G	-	19681606	7	5	103	1	0	1	0	1	0	0	0	0	11504	1000	35	0	918	0	PBX4	19	19681606	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	650977	19681606	39447377	1041	15664										
GMIP	51291	hgsc.bcm.edu	37	chr19	19751152	19751152	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttcagcgatcttcatggtgcTcttagcaaactccagctctg	8	12	5	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:19751152T>C	ENST00000203556.4	-	6	519	c.382A>G	c.(382-384)Agc>Ggc	p.S128G	GMIP_ENST00000587238.1_Missense_Mutation_p.S128G|GMIP_ENST00000445806.2_Missense_Mutation_p.S128G	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	128					intracellular signal transduction (GO:0035556)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						TTCATGGTGCTCTTAGCAAAC	0.612																																					p.S128G		Atlas-SNP	.											.	GMIP	55	.	0			c.A382G						.						69	76	73					19																	19751152		2203	4300	6503	SO:0001583	missense	51291	exon6			TGGTGCTCTTAGC	AF132541	CCDS12408.1, CCDS74318.1	19p13.11	2011-09-07				ENSG00000089639		"Rho GTPase activating proteins"	24852	protein-coding gene	gene with protein product		609694				12093360, 16086184	Standard	XM_005259927		Approved	ARHGAP46	uc002nnd.3	Q9P107		ENST00000203556.4:c.382A>G	chr19.hg19:g.19751152T>C	ENSP00000203556:p.Ser128Gly	90.0	0.0		92.0	4.0	NM_016573	A0AVN9|B7ZLZ0	Missense_Mutation	SNP	ENST00000203556.4	hg19	CCDS12408.1	.	.	.	.	.	.	.	.	.	.	T	14.13	2.443194	0.43429	.	.	ENSG00000089639	ENST00000203556;ENST00000445806	T;T	0.43294	0.95;0.95	4.98	4.98	0.66077	.	0.382465	0.22419	N	0.060305	T	0.24198	0.0586	N	0.13327	0.33	0.26813	N	0.968955	B;B;B	0.11235	0.004;0.004;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.11494	-1.0585	10	0.09590	T	0.72	-4.2856	12.6474	0.56742	0.0:0.0:0.0:1.0	.	128;128;128	E7ERB7;B7ZLZ0;Q9P107	.;.;GMIP_HUMAN	G	128	ENSP00000203556:S128G;ENSP00000397075:S128G	ENSP00000203556:S128G	S	-	1	0	GMIP	19612152	0.956000	0.32656	0.065000	0.19835	0.742000	0.42306	2.654000	0.46699	1.871000	0.54225	0.459000	0.35465	AGC	.	.		0.612	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573		C	19751152	T	C	19751152	3	2	103	1	0	0	0	0	1	0	0	0	6499	1551	54	2	2594	2	GMIP	19	19751152	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	69546	19751152	39377831	1042	15665										
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19774122	19774122	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgcgcgtgcacagaccaatgCcccgagaggacagtgagcgc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:19774122delC	ENST00000357324.6	-	1	380	c.354delG	c.(352-354)gggfs	p.G118fs	ATP13A1_ENST00000291503.5_5'Flank	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	118						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CAGACCAATGCCCCGAGAGGA	0.687																																					p.H119fs	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-INDEL	.											.	ATP13A1	82	.	0			c.355delC						.						10	14	13					19																	19774122		1545	3561	5106	SO:0001589	frameshift_variant	57130	exon1			.	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"ATPases / P-type"	24215	protein-coding gene	gene with protein product	"cation transporting ATPase"		"ATPase type 13A"	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.354delG	chr19.hg19:g.19774122delC	ENSP00000349877:p.Gly118fs	187.0	0.0		191.0	12.0	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Frame_Shift_Del	DEL	ENST00000357324.6	hg19	CCDS32970.2																																																																																			.	.		0.687	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		-	19774122	C	-	19774122	7	5	103	1	0	1	0	1	0	0	0	0	1123	726	26	0	3364	0	ATP13A1	19	19774122	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	22970	19774122	39354861	1043	15666										
ZNF14	7561	hgsc.bcm.edu	37	chr19	19823792	19823792	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctgcattcatgtggttttgCtccagtaaaagtttccttgt	9	8	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:19823792C>T	ENST00000344099.3	-	4	436	c.298G>A	c.(298-300)Gca>Aca	p.A100T		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	100					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				TGTGGTTTTGCTCCAGTAAAA	0.403																																					p.A100T		Atlas-SNP	.											.	ZNF14	89	.	0			c.G298A						.						155	141	146					19																	19823792		2203	4300	6503	SO:0001583	missense	7561	exon4			GTTTTGCTCCAGT	AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"Zinc fingers, C2H2-type", "-"	12924	protein-coding gene	gene with protein product		194556	"zinc finger protein 14 (KOX 6)"				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.298G>A	chr19.hg19:g.19823792C>T	ENSP00000340514:p.Ala100Thr	78.0	0.0		116.0	6.0	NM_021030	B9EGA4|Q9ULZ5	Missense_Mutation	SNP	ENST00000344099.3	hg19	CCDS12409.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382501	0.24944	.	.	ENSG00000105708	ENST00000344099	T	0.15017	2.46	1.4	-1.49	0.08718	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11580	0.0282	L	0.35542	1.07	0.23076	N	0.998338	B	0.06786	0.001	B	0.08055	0.003	T	0.30357	-0.9981	9	0.66056	D	0.02	.	6.0221	0.19634	0.0:0.6719:0.0:0.3281	.	100	P17017	ZNF14_HUMAN	T	100	ENSP00000340514:A100T	ENSP00000340514:A100T	A	-	1	0	ZNF14	19684792	0.001000	0.12720	0.002000	0.10522	0.048000	0.14542	0.621000	0.24418	-0.253000	0.09514	-0.384000	0.06662	GCA	.	.		0.403	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030		T	19823792	C	T	19823792	3	4	103	1	0	0	0	0	1	0	0	0	17743	797	28	3	1634	3	ZNF14	19	19823792	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	49670	19823792	39305191	1044	15667										
SLC7A9	11136	hgsc.bcm.edu	37	chr19	33353026	33353026	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catctcaggacacctcaccaTccatcataggcccagagtcc	6	17	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:33353026T>C	ENST00000023064.4	-	6	893	c.702A>G	c.(700-702)ggA>ggG	p.G234G	SLC7A9_ENST00000590341.1_Silent_p.G234G|RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000587772.1_Silent_p.G234G	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	234					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	CACCTCACCATCCATCATAGG	0.512																																					p.G234G	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											.	SLC7A9	78	.	0			c.A702G						.						109	105	107					19																	33353026		2203	4300	6503	SO:0001819	synonymous_variant	11136	exon6			TCACCATCCATCA	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"Solute carriers"	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.702A>G	chr19.hg19:g.33353026T>C		70.0	0.0		105.0	6.0	NM_001243036	B2R9A6	Silent	SNP	ENST00000023064.4	hg19	CCDS12425.1																																																																																			.	.		0.512	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			C	33353026	T	C	33353026	2	2	103	1	0	0	0	0	0	0	0	1	14720	1422	50	2		2	SLC7A9	19	33353026	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	13529234	33353026	25775957	1045	15668										
GPATCH1	55094	hgsc.bcm.edu	37	chr19	33605287	33605287	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtccagccccttagtaaacAaagaggaagagcatgcacca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:33605287delA	ENST00000170564.2	+	15	2472	c.2158delA	c.(2158-2160)aaafs	p.K720fs		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	720					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					CTTAGTAAACAAAGAGGAAGA	0.433																																					p.N719fs	Pancreas(67;88 1713 4567 18227)	Atlas-INDEL	.											.	GPATCH1	79	.	0			c.2157delC						.						72	78	76					19																	33605287		2203	4300	6503	SO:0001589	frameshift_variant	55094	exon15			.	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"G patch domain containing"	24658	protein-coding gene	gene with protein product	"evolutionarily conserved G patch domain containing"			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.2158delA	chr19.hg19:g.33605287delA	ENSP00000170564:p.Lys720fs	126.0	0.0		157.0	10.0	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Frame_Shift_Del	DEL	ENST00000170564.2	hg19	CCDS12428.1																																																																																			.	.		0.433	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		-	33605287	A	-	33605287	7	5	103	1	0	1	0	1	0	0	0	0	6598	131	5	0	2216	0	GPATCH1	19	33605287	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	252261	33605287	25523696	1046	15669										
ZNF181	339318	hgsc.bcm.edu	37	chr19	35230499	35230499	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aagagccctggatgatggagAaaaaactgtcaaaaggtatg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:35230499delA	ENST00000492450.1	+	3	291	c.202delA	c.(202-204)aaafs	p.K69fs	ZNF181_ENST00000392232.3_Frame_Shift_Del_p.K113fs|ZNF181_ENST00000459757.2_Frame_Shift_Del_p.K68fs			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			GATGATGGAGAAAAAACTGTC	0.383																																					p.E67fs		Atlas-INDEL	.											.	ZNF181	65	.	0			c.201delG						.						146	142	143					19																	35230499		2203	4300	6503	SO:0001589	frameshift_variant	339318	exon3			.	BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"Zinc fingers, C2H2-type", "-"	12971	protein-coding gene	gene with protein product		606741	"zinc finger protein 181 (HHZ181)"				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.202delA	chr19.hg19:g.35230499delA	ENSP00000420727:p.Lys69fs	131.0	0.0		169.0	12.0	NM_001029997	B7ZKX3|Q49A75	Frame_Shift_Del	DEL	ENST00000492450.1	hg19	CCDS32990.2																																																																																			.	.		0.383	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997		-	35230499	A	-	35230499	7	5	103	1	0	1	0	1	0	0	0	0	17764	247	9	0	212	0	ZNF181	19	35230499	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1625212	35230499	23898484	1047	15670										
ZNF599	148103	hgsc.bcm.edu	37	chr19	35250292	35250292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggtttttgtccactgtgggTcctattatgtcgaataaaaa	10	6	0	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:35250292T>C	ENST00000329285.8	-	4	1787	c.1414A>G	c.(1414-1416)Acc>Gcc	p.T472A		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	472					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			CCACTGTGGGTCCTATTATGT	0.418																																					p.T472A		Atlas-SNP	.											.	ZNF599	72	.	0			c.A1414G						.						95	100	98					19																	35250292		2203	4300	6503	SO:0001583	missense	148103	exon4			TGTGGGTCCTATT	AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1414A>G	chr19.hg19:g.35250292T>C	ENSP00000333802:p.Thr472Ala	94.0	0.0		128.0	6.0	NM_001007248	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	hg19	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	T	6.943	0.543839	0.13312	.	.	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	T	0.20332	2.08	2.67	1.65	0.23941	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15955	0.0384	L	0.39633	1.23	0.48236	D	0.999618	B	0.12630	0.006	B	0.18561	0.022	T	0.06607	-1.0817	9	0.87932	D	0	.	6.1035	0.20061	0.0:0.1358:0.0:0.8642	.	472	Q96NL3	ZN599_HUMAN	A	471;472;246	ENSP00000333802:T472A	ENSP00000333802:T472A	T	-	1	0	ZNF599	39942132	0.000000	0.05858	0.768000	0.31515	0.481000	0.33189	0.297000	0.19101	0.448000	0.26722	-0.353000	0.07706	ACC	.	.		0.418	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		C	35250292	T	C	35250292	3	2	103	1	0	0	0	0	1	0	0	0	18044	1667	58	2	356	2	ZNF599	19	35250292	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	19793	35250292	23878691	1048	15671										
LGI4	163175	hgsc.bcm.edu	37	chr19	35617456	35617456	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacagcagcgtggtgctgccCgccttggaggcatcggccac	14	15	0	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:35617456C>T	ENST00000310123.3	-	8	1536	c.1017G>A	c.(1015-1017)gcG>gcA	p.A339A	LGI4_ENST00000392225.3_Missense_Mutation_p.R365Q|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	339					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			TGGTGCTGCCCGCCTTGGAGG	0.726																																					p.A339A		Atlas-SNP	.											.	LGI4	32	.	0			c.G1017A						.						6	7	7					19																	35617456		2048	4028	6076	SO:0001819	synonymous_variant	163175	exon8			GCTGCCCGCCTTG	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.1017G>A	chr19.hg19:g.35617456C>T		2.0	0.0		7.0	6.0	NM_139284	B2RN53|B9EGS7|Q5M8T1	Silent	SNP	ENST00000310123.3	hg19	CCDS12444.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.047239	0.36085	.	.	ENSG00000153902	ENST00000392225	T	0.64085	-0.08	4.48	-8.96	0.00761	.	.	.	.	.	T	0.51449	0.1675	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60409	-0.7269	6	0.87932	D	0	.	0.0813	0.00032	0.2884:0.226:0.175:0.3106	.	.	.	.	Q	365	ENSP00000376059:R365Q	ENSP00000376059:R365Q	R	-	2	0	LGI4	40309296	0.000000	0.05858	0.823000	0.32752	0.930000	0.56654	-4.706000	0.00196	-1.885000	0.01118	-1.676000	0.00740	CGG	.	.		0.726	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1			T	35617456	C	T	35617456	2	4	103	1	0	0	0	0	0	0	0	1	8763	639	23	1		1	LGI4	19	35617456	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	367164	35617456	23511527	1049	15672										
FAM187B	148109	hgsc.bcm.edu	37	chr19	35715793	35715793	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtggatgcacttgagcagcgCccccagcagggccaggacgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:35715793delC	ENST00000324675.3	-	2	1093	c.1045delG	c.(1045-1047)gcgfs	p.A349fs		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	349						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						TTGAGCAGCGCCCCCAGCAGG	0.687																																					p.A349fs		Atlas-INDEL	.											FAM187B,NS,carcinoma,0,1	FAM187B	28	.	0			c.1046delC						.						29	31	30					19																	35715793		2203	4300	6503	SO:0001589	frameshift_variant	148109	exon2			.	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558			26366	protein-coding gene	gene with protein product			"transmembrane protein 162"	TMEM162			Standard	NM_152481		Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.1045delG	chr19.hg19:g.35715793delC	ENSP00000323355:p.Ala349fs	145.0	0.0		189.0	12.0	NM_152481	Q8N7G6	Frame_Shift_Del	DEL	ENST00000324675.3	hg19	CCDS12448.1																																																																																			.	.		0.687	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481		-	35715793	C	-	35715793	7	5	103	1	0	1	0	1	0	0	0	0	5518	739	26	0	68	0	FAM187B	19	35715793	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	98337	35715793	23413190	1050	15673										
ZBTB32	27033	hgsc.bcm.edu	37	chr19	36205963	36205963	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagagagaactgggggacccTggagagaagcagaaaccaga	16	7	0	5			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36205963T>C	ENST00000392197.2	+	3	753	c.435T>C	c.(433-435)ccT>ccC	p.P145P	KMT2B_ENST00000341701.1_5'Flank|KMT2B_ENST00000222270.7_5'Flank|KMT2B_ENST00000420124.1_5'Flank|KMT2B_ENST00000607650.1_RNA|ZBTB32_ENST00000262630.3_Silent_p.P145P			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	145					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGGGGGACCCTGGAGAGAAGC	0.547																																					p.P145P		Atlas-SNP	.											.	ZBTB32	33	.	0			c.T435C						.						41	44	43					19																	36205963		2203	4300	6503	SO:0001819	synonymous_variant	27033	exon2			GGACCCTGGAGAG	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16763	protein-coding gene	gene with protein product	"repressor of GATA"	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.435T>C	chr19.hg19:g.36205963T>C		47.0	0.0		67.0	4.0	NM_014383	Q8WVP2	Silent	SNP	ENST00000392197.2	hg19	CCDS12471.1																																																																																			.	.		0.547	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383		C	36205963	T	C	36205963	2	2	103	1	0	0	0	0	0	0	0	1	17550	1567	55	2		2	ZBTB32	19	36205963	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	490170	36205963	22923020	1051	15674										
MLL4	9757	hgsc.bcm.edu	37	chr19	36214631	36214631	+	Splice_Site	SNP	C	C	A													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tactaagtcccctgttcccgCagccggacgatagtgaagac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36214631C>A	ENST00000222270.7	+	8	3058		c.e8-1		KMT2B_ENST00000420124.1_Intron|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B						chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CCTGTTCCCGCAGCCGGACGA	0.627																																					.		Atlas-SNP	.											.	MLL4	229	.	0			c.3059-2C>A						.						11	12	11					19																	36214631		1824	3882	5706	SO:0001630	splice_region_variant	8085	exon8			TTCCCGCAGCCGG	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.3059-1C>A	chr19.hg19:g.36214631C>A		35.0	0.0		65.0	4.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Splice_Site	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220574	0.58560	.	.	ENSG00000105663	ENST00000222270	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6648	0.77221	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AD000671.1	40906471	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.194000	0.58393	2.757000	0.94681	0.655000	0.94253	.	.	.		0.627	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	Intron	A	36214631	C	A	36214631	5	1	103	1	0	0	0	0	0	0	1	0	9632	724	25	3	3087	3	MLL4	19	36214631	Splice_Site	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	8668	36214631	22914352	1052	15675	66	2								
MLL4	9757	hgsc.bcm.edu	37	chr19	36214634	36214634	+	Splice_Site	SNP	C	C	G													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taagtcccctgttcccgcagCcggacgatagtgaagacgct					rs373624638		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36214634C>G	ENST00000222270.7	+	8	3060	c.3060C>G	c.(3058-3060)ggC>ggG	p.G1020G	KMT2B_ENST00000420124.1_Splice_Site_p.G1020G|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1020					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GTTCCCGCAGCCGGACGATAG	0.637																																					p.G1020G		Atlas-SNP	.											.	MLL4	229	.	0			c.C3060G						.						11	12	11					19																	36214634		1825	3889	5714	SO:0001630	splice_region_variant	8085	exon8			CCGCAGCCGGACG	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.3059-1C>G	chr19.hg19:g.36214634C>G		34.0	0.0		67.0	6.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.637	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	Silent	G	36214634	C	G	36214634	5	3	103	1	0	0	0	0	0	0	1	0	9632	753	26	4	3090	4	MLL4	19	36214634	Splice_Site	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	3	36214634	22914349	1053	15676	66	2								
U2AF1L4	199746	hgsc.bcm.edu	37	chr19	36236292	36236292	+	Start_Codon_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgaagctaaatattcagccaTttttacccaagccctccagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36236292delT	ENST00000412391.2	-	0	14				IGFLR1_ENST00000246532.1_5'Flank|U2AF1L4_ENST00000292879.5_Start_Codon_Del|AC002398.11_ENST00000585365.1_RNA|IGFLR1_ENST00000588992.1_5'Flank|IGFLR1_ENST00000344990.3_5'Flank|IGFLR1_ENST00000592537.1_5'Flank|AC002398.11_ENST00000591091.1_RNA|LIN37_ENST00000301159.9_5'Flank|PSENEN_ENST00000591949.1_5'Flank|PSENEN_ENST00000222266.2_5'Flank|AC002398.9_ENST00000591613.2_5'Flank|PSENEN_ENST00000587708.2_5'UTR|AD000671.6_ENST00000589807.1_Start_Codon_Del|U2AF1L4_ENST00000588100.1_5'UTR|U2AF1L4_ENST00000378975.3_Start_Codon_Del			Q8WU68	U2AF4_HUMAN	U2 small nuclear RNA auxiliary factor 1-like 4						mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TATTCAGCCATTTTTACCCAA	0.572																																					p.M1fs		Atlas-INDEL	.											.	U2AF1L4	34	.	0			c.2delT						.						123	136	132					19																	36236292		2203	4300	6503	SO:0001582	initiator_codon_variant	199746	exon1			.	BC021186, AY569437	CCDS12473.1, CCDS42551.1	19q13.13	2013-02-12	2006-04-12	2006-04-12		ENSG00000161265		"RNA binding motif (RRM) containing"	23020	protein-coding gene	gene with protein product		601080	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 3", "U2 small nuclear RNA auxiliary factor 1-like 3"	U2AF1L3		8586425, 11739736	Standard	NM_001040425		Approved	MGC33901, U2af26	uc002obf.3	Q8WU68			chr19.hg19:g.36236292delT		124.0	0.0		146.0	12.0	NM_144987	A6NKI8|Q56UU3	Frame_Shift_Del	DEL	ENST00000412391.2	hg19																																																																																				.	.		0.572	U2AF1L4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144987		-	36236292	T	-	36236292	7	5	103	1	0	1	0	1	0	0	0	0	16837	1493	52	0	689	0	U2AF1L4	19	36236292	Start_Codon_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	21658	36236292	22892691	1054	15677										
ARHGAP33	115703	hgsc.bcm.edu	37	chr19	36273373	36273373	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgcaagctctacttccgagAgcttccgaaccctctgctca	7	16	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36273373A>G	ENST00000007510.4	+	13	1328	c.1184A>G	c.(1183-1185)gAg>gGg	p.E395G	ARHGAP33_ENST00000314737.5_Missense_Mutation_p.E395G|ARHGAP33_ENST00000378944.5_Missense_Mutation_p.E259G			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	395	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						TACTTCCGAGAGCTTCCGAAC	0.617																																					p.E395G		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.A1184G						.						82	71	75					19																	36273373		2203	4300	6503	SO:0001583	missense	115703	exon13			TCCGAGAGCTTCC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.1184A>G	chr19.hg19:g.36273373A>G	ENSP00000007510:p.Glu395Gly	70.0	0.0		93.0	4.0	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Missense_Mutation	SNP	ENST00000007510.4	hg19		.	.	.	.	.	.	.	.	.	.	a	19.62	3.862145	0.71949	.	.	ENSG00000004777	ENST00000007510;ENST00000314737;ENST00000378944	T;T;T	0.15017	2.46;2.46;2.46	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.53254	0.1785	H	0.94345	3.525	0.51767	D	0.999939	D;D	0.89917	0.998;1.0	D;D	0.91635	0.99;0.999	T	0.67432	-0.5672	10	0.87932	D	0	.	14.0423	0.64684	1.0:0.0:0.0:0.0	.	259;395	O14559-10;O14559-11	.;.	G	395;395;259	ENSP00000007510:E395G;ENSP00000320038:E395G;ENSP00000368227:E259G	ENSP00000007510:E395G	E	+	2	0	ARHGAP33	40965213	1.000000	0.71417	1.000000	0.80357	0.388000	0.30384	9.142000	0.94618	1.969000	0.57287	0.375000	0.23000	GAG	.	.		0.617	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		G	36273373	A	G	36273373	3	3	103	1	0	0	0	0	1	0	0	0	882	304	11	2	1234	2	ARHGAP33	19	36273373	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	37081	36273373	22855610	1055	15678										
ZFP82	284406	hgsc.bcm.edu	37	chr19	36883842	36883842	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagtatgaatgctctgatgtAgagtaagtttttggcgcaat	11	5	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36883842A>G	ENST00000392161.3	-	5	1642	c.1400T>C	c.(1399-1401)cTa>cCa	p.L467P	ZFP82_ENST00000392171.1_Missense_Mutation_p.L467P	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	467					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GCTCTGATGTAGAGTAAGTTT	0.383																																					p.L467P		Atlas-SNP	.											.	ZFP82	71	.	0			c.T1400C						.						105	101	102					19																	36883842		2203	4300	6503	SO:0001583	missense	284406	exon5			TGATGTAGAGTAA	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"Zinc fingers, C2H2-type", "-"	28682	protein-coding gene	gene with protein product			"zinc finger protein 545", "zinc finger protein 82 homolog (mouse)", "zinc finger protein 82"	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.1400T>C	chr19.hg19:g.36883842A>G	ENSP00000431265:p.Leu467Pro	96.0	0.0		92.0	4.0	NM_133466	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	hg19	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	A	12.39	1.923466	0.33908	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.07444	3.19;3.19	4.2	3.1	0.35709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.32430	N	0.006102	T	0.11665	0.0284	L	0.33137	0.985	0.24293	N	0.995154	D	0.53619	0.961	P	0.60068	0.868	T	0.08066	-1.0740	10	0.44086	T	0.13	.	4.0395	0.09745	0.6759:0.2134:0.1107:0.0	.	467	Q8N141	ZFP82_HUMAN	P	467	ENSP00000431265:L467P;ENSP00000446080:L467P	ENSP00000431265:L467P	L	-	2	0	ZFP82	41575682	0.000000	0.05858	0.993000	0.49108	0.972000	0.66771	-1.441000	0.02409	1.905000	0.55150	0.482000	0.46254	CTA	.	.		0.383	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		G	36883842	A	G	36883842	3	3	103	1	0	0	0	0	1	0	0	0	17668	420	15	2	202	2	ZFP82	19	36883842	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	610469	36883842	22245141	1056	15679										
ZNF527	84503	hgsc.bcm.edu	37	chr19	37879579	37879579	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attcagtcataattgaatatAaaagactccatgctgagaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:37879579delA	ENST00000436120.2	+	5	735	c.628delA	c.(628-630)aaafs	p.K210fs	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	210					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AATTGAATATAAAAGACTCCA	0.333																																					p.Y209X		Atlas-INDEL	.											.	ZNF527	78	.	0			c.627delT						.						50	50	50					19																	37879579		1807	4062	5869	SO:0001589	frameshift_variant	84503	exon5			.	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"Zinc fingers, C2H2-type", "-"	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.628delA	chr19.hg19:g.37879579delA	ENSP00000390179:p.Lys210fs	87.0	0.0		151.0	10.0	NM_032453	B4DVL5	Frame_Shift_Del	DEL	ENST00000436120.2	hg19	CCDS42559.1																																																																																			.	.		0.333	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453		-	37879579	A	-	37879579	7	5	103	1	0	1	0	1	0	0	0	0	17983	363	13	0	642	0	ZNF527	19	37879579	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	995737	37879579	21249404	1057	15680										
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38655235	38655235	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccctggagccagagcaagaCcccctctccaagggtggctc					rs142602797	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:38655235delC	ENST00000222345.6	+	15	4406	c.3897delC	c.(3895-3897)gacfs	p.D1299fs		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1299					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CAGAGCAAGACCCCCTCTCCA	0.647																																					p.D1299fs		Atlas-INDEL	.											.	SIPA1L3	150	.	0			c.3896delA						.						73	65	67					19																	38655235		2203	4300	6503	SO:0001589	frameshift_variant	23094	exon15			.	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3897delC	chr19.hg19:g.38655235delC	ENSP00000222345:p.Asp1299fs	176.0	0.0		191.0	12.0	NM_015073	Q2TV87	Frame_Shift_Del	DEL	ENST00000222345.6	hg19	CCDS33007.1																																																																																			.	.		0.647	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		-	38655235	C	-	38655235	7	5	103	1	0	1	0	1	0	0	0	0	14346	506	18	0	3947	0	SIPA1L3	19	38655235	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	775656	38655235	20473748	1058	15681										
CATSPERG	57828	hgsc.bcm.edu	37	chr19	38828049	38828049	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtttaagagggtaggcgagAgtggtgtgagcgacagcttc	17	5	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:38828049A>G	ENST00000409235.3	+	2	290	c.175A>G	c.(175-177)Agt>Ggt	p.S59G	CATSPERG_ENST00000215069.4_Missense_Mutation_p.S75G|CATSPERG_ENST00000410018.1_Missense_Mutation_p.S59G	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	59					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						GGTAGGCGAGAGTGGTGTGAG	0.582																																					p.S59G		Atlas-SNP	.											.	CATSPERG	121	.	0			c.A175G						.						221	191	200					19																	38828049		692	1591	2283	SO:0001583	missense	57828	exon2			GGCGAGAGTGGTG	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"chromosome 19 open reading frame 15", "cation channel, sperm-associated, gamma"	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.175A>G	chr19.hg19:g.38828049A>G	ENSP00000386962:p.Ser59Gly	83.0	0.0		98.0	5.0	NM_021185	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	hg19	CCDS12514.2	.	.	.	.	.	.	.	.	.	.	a	3.734	-0.054957	0.07362	.	.	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410;ENST00000215069	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	3.09	-1.47	0.08772	.	1.630730	0.03644	N	0.239973	T	0.16214	0.0390	N	0.03608	-0.345	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.11329	0.003;0.006	T	0.18713	-1.0328	10	0.13853	T	0.58	-0.6351	7.3282	0.26567	0.5014:0.0:0.4986:0.0	.	59;59	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	G	59;59;59;75	ENSP00000387057:S59G;ENSP00000386962:S59G;ENSP00000386950:S59G;ENSP00000215069:S75G	ENSP00000215069:S75G	S	+	1	0	CATSPERG	43519889	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.622000	0.05553	-0.439000	0.07222	-0.638000	0.03974	AGT	.	.		0.582	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185		G	38828049	A	G	38828049	3	3	103	1	0	0	0	0	1	0	0	0	2694	304	11	2	177	2	CATSPERG	19	38828049	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	172814	38828049	20300934	1059	15682										
RYR1	6261	hgsc.bcm.edu	37	chr19	39008261	39008261	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaccacctcaactccctgctGgggaatatcctgagaatcat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:39008261delG	ENST00000359596.3	+	66	9948	c.9948delG	c.(9946-9948)ctgfs	p.L3316fs	RYR1_ENST00000360985.3_Frame_Shift_Del_p.L3316fs|RYR1_ENST00000355481.4_Frame_Shift_Del_p.L3316fs			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3316					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACTCCCTGCTGGGGAATATCC	0.682																																					p.L3316fs		Atlas-INDEL	.											.	RYR1	708	.	0			c.9947delT						.						48	47	47					19																	39008261		2203	4300	6503	SO:0001589	frameshift_variant	6261	exon66			.	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.9948delG	chr19.hg19:g.39008261delG	ENSP00000352608:p.Leu3316fs	155.0	0.0		234.0	16.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Frame_Shift_Del	DEL	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			-	39008261	G	-	39008261	7	5	103	1	0	1	0	1	0	0	0	0	13783	1335	47	0	10210	0	RYR1	19	39008261	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	180212	39008261	20120722	1060	15683										
ACTN4	81	hgsc.bcm.edu	37	chr19	39191331	39191331	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgagacgggctcaagctcaTgctgctcctggaggtcatat	12	12	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:39191331T>C	ENST00000252699.2	+	2	330	c.254T>C	c.(253-255)aTg>aCg	p.M85T	ACTN4_ENST00000424234.2_Missense_Mutation_p.M85T|ACTN4_ENST00000390009.3_Intron	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	85	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CTCAAGCTCATGCTGCTCCTG	0.627																																					p.M85T	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.T254C						.						115	92	100					19																	39191331		2203	4300	6503	SO:0001583	missense	81	exon2			AGCTCATGCTGCT	D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"EF-hand domain containing"	166	protein-coding gene	gene with protein product		604638	"focal segmental glomerulosclerosis 1"	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.254T>C	chr19.hg19:g.39191331T>C	ENSP00000252699:p.Met85Thr	91.0	0.0		122.0	5.0	NM_004924	A4K467|D6PXK4|O76048	Missense_Mutation	SNP	ENST00000252699.2	hg19	CCDS12518.1	.	.	.	.	.	.	.	.	.	.	T	14.37	2.515842	0.44763	.	.	ENSG00000130402	ENST00000252699;ENST00000445727;ENST00000424234	D;D	0.94793	-3.52;-3.52	4.35	4.35	0.52113	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.93635	0.7967	N	0.12663	0.25	0.40631	D	0.98185	P;P	0.48407	0.91;0.78	D;D	0.76071	0.987;0.986	D	0.94932	0.8083	10	0.87932	D	0	.	12.9372	0.58322	0.0:0.0:0.0:1.0	.	85;85	E7EV83;O43707	.;ACTN4_HUMAN	T	85	ENSP00000252699:M85T;ENSP00000411187:M85T	ENSP00000252699:M85T	M	+	2	0	ACTN4	43883171	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	7.781000	0.85668	1.964000	0.57103	0.459000	0.35465	ATG	.	.		0.627	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1			C	39191331	T	C	39191331	3	2	103	1	0	0	0	0	1	0	0	0	207	1464	51	2	260	2	ACTN4	19	39191331	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	183070	39191331	19937652	1061	15684										
SHKBP1	92799	hgsc.bcm.edu	37	chr19	41095066	41095066	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cagccagctcttcgtgcgtcTctcatctactgggcagcggt	11	14	4	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:41095066T>C	ENST00000291842.5	+	15	1620	c.1571T>C	c.(1570-1572)cTc>cCc	p.L524P	SHKBP1_ENST00000600733.1_Missense_Mutation_p.L499P|SHKBP1_ENST00000597649.1_3'UTR	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	524					protein homooligomerization (GO:0051260)					breast(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(3)|urinary_tract(1)	29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TTCGTGCGTCTCTCATCTACT	0.637																																					p.L524P		Atlas-SNP	.											.	SHKBP1	68	.	0			c.T1571C						.						72	52	59					19																	41095066		2203	4300	6503	SO:0001583	missense	92799	exon15			TGCGTCTCTCATC	AF258553	CCDS12560.1	19q13.2	2013-01-10				ENSG00000160410		"WD repeat domain containing"	19214	protein-coding gene	gene with protein product						11152963	Standard	NM_138392		Approved	PP203, Sb1	uc002oob.3	Q8TBC3		ENST00000291842.5:c.1571T>C	chr19.hg19:g.41095066T>C	ENSP00000291842:p.Leu524Pro	89.0	0.0		128.0	6.0	NM_138392	Q8N2I6|Q8WY93|Q96IB8	Missense_Mutation	SNP	ENST00000291842.5	hg19	CCDS12560.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.078549	0.76528	.	.	ENSG00000160410	ENST00000291842;ENST00000446701	T	0.54675	0.56	5.05	5.05	0.67936	WD40 repeat-like-containing domain (1);	0.069879	0.56097	D	0.000028	T	0.72342	0.3448	M	0.77103	2.36	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;0.999	D;D;D;D;D;D	0.91635	0.991;0.988;0.998;0.999;0.998;0.997	T	0.76621	-0.2892	10	0.87932	D	0	-8.6062	13.9039	0.63821	0.0:0.0:0.0:1.0	.	402;304;447;361;524;524	B4DLI0;B4DUW2;B4DUV2;B3KVX8;B2R6W9;Q8TBC3	.;.;.;.;.;SHKB1_HUMAN	P	524;304	ENSP00000291842:L524P	ENSP00000291842:L524P	L	+	2	0	SHKBP1	45786906	0.993000	0.37304	0.180000	0.23079	0.985000	0.73830	7.250000	0.78287	2.129000	0.65627	0.459000	0.35465	CTC	.	.		0.637	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462613.2	NM_138392		C	41095066	T	C	41095066	3	2	103	1	0	0	0	0	1	0	0	0	14299	1551	54	2	1629	2	SHKBP1	19	41095066	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1903735	41095066	18033917	1062	15685										
ADCK4	79934	hgsc.bcm.edu	37	chr19	41220002	41220002	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggccaagcggctgatgcgggAggcaggcaccttgcgttctc	16	12	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:41220002A>G	ENST00000324464.3	-	4	560	c.259T>C	c.(259-261)Tcc>Ccc	p.S87P	ADCK4_ENST00000450541.1_Missense_Mutation_p.S87P|ADCK4_ENST00000243583.6_Missense_Mutation_p.S87P	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	87						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CTGATGCGGGAGGCAGGCACC	0.562																																					p.S87P		Atlas-SNP	.											.	ADCK4	92	.	0			c.T259C						.						89	83	85					19																	41220002		2203	4300	6503	SO:0001583	missense	79934	exon4			TGCGGGAGGCAGG	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.259T>C	chr19.hg19:g.41220002A>G	ENSP00000315118:p.Ser87Pro	81.0	0.0		137.0	6.0	NM_001142555	Q8TAJ1|Q9HA52	Missense_Mutation	SNP	ENST00000324464.3	hg19	CCDS12562.1	.	.	.	.	.	.	.	.	.	.	a	23.3	4.398852	0.83120	.	.	ENSG00000123815	ENST00000324464;ENST00000450541;ENST00000243583	T;T;T	0.76968	-1.06;-0.72;-0.72	5.46	5.46	0.80206	.	0.055160	0.64402	D	0.000001	D	0.88020	0.6325	M	0.88310	2.945	0.44388	D	0.997298	D;D	0.69078	0.996;0.997	D;D	0.71870	0.944;0.975	D	0.89413	0.3704	10	0.87932	D	0	-4.8201	8.9137	0.35568	0.834:0.0:0.0:0.166	.	87;87	Q96D53;Q96D53-2	ADCK4_HUMAN;.	P	87	ENSP00000315118:S87P;ENSP00000412839:S87P;ENSP00000243583:S87P	ENSP00000243583:S87P	S	-	1	0	ADCK4	45911842	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	3.562000	0.53777	2.075000	0.62263	0.454000	0.30748	TCC	.	.		0.562	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876		G	41220002	A	G	41220002	3	3	103	1	0	0	0	0	1	0	0	0	290	304	11	2	1423	2	ADCK4	19	41220002	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	124936	41220002	17908981	1063	15686										
HNRNPUL1	11100	hgsc.bcm.edu	37	chr19	41811722	41811722	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccccctataccccaccgccaCcccccactgcacagacctac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:41811722delC	ENST00000392006.3	+	14	2577	c.2404delC	c.(2404-2406)cccfs	p.P803fs	HNRNPUL1_ENST00000595018.1_Frame_Shift_Del_p.P703fs|HNRNPUL1_ENST00000593587.1_Frame_Shift_Del_p.P703fs|HNRNPUL1_ENST00000352456.3_Frame_Shift_Del_p.P713fs|HNRNPUL1_ENST00000378215.4_Frame_Shift_Del_p.P699fs|HNRNPUL1_ENST00000602130.1_Intron|HNRNPUL1_ENST00000263367.3_Frame_Shift_Del_p.P714fs	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	803	Necessary for interaction with TP53.|Pro-rich.|Tyr-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						CCCACCGCCACCCCCCACTGC	0.637																																					p.P801fs		Atlas-INDEL	.											.	HNRNPUL1	73	.	0			c.2403delA						.						36	38	37					19																	41811722		2202	4299	6501	SO:0001589	frameshift_variant	11100	exon14			.	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"E1B 55kDa associated protein 5"	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.2404delC	chr19.hg19:g.41811722delC	ENSP00000375863:p.Pro803fs	98.0	0.0		112.0	10.0	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Frame_Shift_Del	DEL	ENST00000392006.3	hg19	CCDS12576.1																																																																																			.	.		0.637	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040		-	41811722	C	-	41811722	7	5	103	1	0	1	0	1	0	0	0	0	7283	507	18	0	2458	0	HNRNPUL1	19	41811722	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	591720	41811722	17317261	1064	15687										
CEACAM3	1084	hgsc.bcm.edu	37	chr19	42314895	42314895	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccctctctccactgcccaggCccccctacccaaccccagga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:42314895delC	ENST00000357396.3	+	6	894	c.653delC	c.(652-654)gccfs	p.A218fs	CEACAM3_ENST00000344550.4_Frame_Shift_Del_p.G200fs|CEACAM3_ENST00000221999.4_Frame_Shift_Del_p.G200fs	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	218						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						ACTGCCCAGGCCCCCCTACCC	0.612																																					p.A218fs		Atlas-INDEL	.											.	CEACAM3	37	.	0			c.652delG						.						85	76	79					19																	42314895		2203	4300	6503	SO:0001589	frameshift_variant	1084	exon6			.	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.653delC	chr19.hg19:g.42314895delC	ENSP00000349971:p.Ala218fs	131.0	0.0		166.0	13.0	NM_001815	G5E978|Q3KPH9	Frame_Shift_Del	DEL	ENST00000357396.3	hg19	CCDS12586.2																																																																																			.	.		0.612	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815		-	42314895	C	-	42314895	7	5	103	1	0	1	0	1	0	0	0	0	3195	739	26	0	675	0	CEACAM3	19	42314895	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	503173	42314895	16814088	1065	15688										
ARHGEF1	9138	hgsc.bcm.edu	37	chr19	42407036	42407036	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccctgctcctgcagagcatcGggcagaacacaggtaccgcg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:42407036delG	ENST00000354532.3	+	18	1874	c.1726delG	c.(1726-1728)gggfs	p.G576fs	ARHGEF1_ENST00000337665.4_Frame_Shift_Del_p.G591fs|ARHGEF1_ENST00000347545.4_Frame_Shift_Del_p.G543fs|ARHGEF1_ENST00000378152.4_Frame_Shift_Del_p.G558fs|ARHGEF1_ENST00000599846.1_Frame_Shift_Del_p.G632fs	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1	576	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		GCAGAGCATCGGGCAGAACAC	0.567																																					p.I590fs		Atlas-INDEL	.											.	ARHGEF1	95	.	0			c.1770delC						.						30	32	31					19																	42407036		2203	4300	6503	SO:0001589	frameshift_variant	9138	exon18			.	U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"Rho guanine nucleotide exchange factors"	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.1726delG	chr19.hg19:g.42407036delG	ENSP00000346532:p.Gly576fs	99.0	0.0		108.0	10.0	NM_199002	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Frame_Shift_Del	DEL	ENST00000354532.3	hg19	CCDS12591.1																																																																																			.	.		0.567	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002		-	42407036	G	-	42407036	7	5	103	1	0	1	0	1	0	0	0	0	893	1116	39	0	1841	0	ARHGEF1	19	42407036	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	92141	42407036	16721947	1066	15689										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42840481	42840481	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgctggtccatggtggacaCcggccctccactgcccggta	12	16	0	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:42840481C>T	ENST00000251268.6	+	6	1227	c.1227C>T	c.(1225-1227)caC>caT	p.H409H	MEGF8_ENST00000334370.4_Silent_p.H409H	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	409					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				ATGGTGGACACCGGCCCTCCA	0.637																																					p.H409H		Atlas-SNP	.											.	MEGF8	358	.	0			c.C1227T						.						23	25	24					19																	42840481		2072	4184	6256	SO:0001819	synonymous_variant	1954	exon6			TGGACACCGGCCC	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.1227C>T	chr19.hg19:g.42840481C>T		43.0	0.0		53.0	4.0	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	hg19																																																																																				.	.		0.637	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		T	42840481	C	T	42840481	2	4	103	1	0	0	0	0	0	0	0	1	9472	506	18	3		3	MEGF8	19	42840481	Silent	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	433445	42840481	16288502	1067	15690										
ZNF221	7638	hgsc.bcm.edu	37	chr19	44471324	44471324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catgcaccagagggtccacgGgggagagcgaccctataatt	13	11	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:44471324G>A	ENST00000251269.5	+	6	1998	c.1670G>A	c.(1669-1671)gGg>gAg	p.G557E	ZNF221_ENST00000592350.1_Missense_Mutation_p.G557E|ZNF221_ENST00000587682.1_Missense_Mutation_p.G557E	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	557			G -> R (in dbSNP:rs366111). {ECO:0000269|PubMed:12743021, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G557V(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				AGGGTCCACGGGGGAGAGCGA	0.453																																					p.G557E		Atlas-SNP	.											.,1	ZNF221	59	.	1	Substitution - Missense(1)	lung(1)	c.G1670A						.						86	84	85					19																	44471324		2203	4300	6503	SO:0001583	missense	7638	exon6			TCCACGGGGGAGA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1670G>A	chr19.hg19:g.44471324G>A	ENSP00000251269:p.Gly557Glu	64.0	0.0		86.0	0.0	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	hg19	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	g	15.07	2.725374	0.48833	.	.	ENSG00000159905	ENST00000251269	T	0.17054	2.3	2.77	0.498	0.16908	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07593	0.0191	N	0.04508	-0.205	0.09310	N	0.999994	B	0.02656	0.0	B	0.04013	0.001	T	0.31916	-0.9926	9	0.87932	D	0	.	6.751	0.23487	0.0:0.6588:0.2182:0.123	.	557	Q9UK13	ZN221_HUMAN	E	557	ENSP00000251269:G557E	ENSP00000251269:G557E	G	+	2	0	ZNF221	49163164	0.011000	0.17503	0.260000	0.24451	0.883000	0.51084	0.266000	0.18534	0.463000	0.27118	0.456000	0.33151	GGG	.	.		0.453	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			A	44471324	G	A	44471324	3	1	103	1	0	0	0	0	1	0	0	0	17790	1232	43	3	1684	3	ZNF221	19	44471324	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	1630843	44471324	14657659	1068	15691										
ZNF222	7673	hgsc.bcm.edu	37	chr19	44537092	44537092	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acaaagagaccacagtggagAaaacccatccaaatgtgagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:44537092delA	ENST00000187879.8	+	4	1427	c.1265delA	c.(1264-1266)gaafs	p.E422fs	ZNF223_ENST00000591793.1_Intron|ZNF222_ENST00000391960.3_Frame_Shift_Del_p.E462fs	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				CACAGTGGAGAAAACCCATCC	0.393																																					p.E462fs		Atlas-INDEL	.											.	ZNF222	90	.	0			c.1384delG						.						71	74	73					19																	44537092		2203	4300	6503	SO:0001589	frameshift_variant	7673	exon4			.	AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.1265delA	chr19.hg19:g.44537092delA	ENSP00000187879:p.Glu422fs	77.0	0.0		157.0	10.0	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Frame_Shift_Del	DEL	ENST00000187879.8	hg19	CCDS33045.1																																																																																			.	.		0.393	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			-	44537092	A	-	44537092	7	5	103	1	0	1	0	1	0	0	0	0	17791	246	9	0	1418	0	ZNF222	19	44537092	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	65768	44537092	14591891	1069	15692										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44739699	44739699	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aattttcagtgccatcagagAgtccacactgaagaaaaacc	7	10	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:44739699A>G	ENST00000313040.7	+	6	1321	c.1116A>G	c.(1114-1116)agA>agG	p.R372R	ZNF227_ENST00000589005.1_Silent_p.R321R|ZNF227_ENST00000391961.2_Silent_p.R321R	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	372					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				GCCATCAGAGAGTCCACACTG	0.428																																					p.R372R		Atlas-SNP	.											.	ZNF227	62	.	0			c.A1116G						.						75	84	81					19																	44739699		2203	4300	6503	SO:0001819	synonymous_variant	7770	exon6			TCAGAGAGTCCAC	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.1116A>G	chr19.hg19:g.44739699A>G		41.0	0.0		32.0	4.0	NM_182490	B3KRU7|B7Z5P9	Silent	SNP	ENST00000313040.7	hg19	CCDS12636.1																																																																																			.	.		0.428	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		G	44739699	A	G	44739699	2	3	103	1	0	0	0	0	0	0	0	1	17796	301	11	2		2	ZNF227	19	44739699	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	202607	44739699	14389284	1070	15693										
FBXO46	23403	hgsc.bcm.edu	37	chr19	46216117	46216117	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggaccgccgttcagatcccaCccccttggccggtccacctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:46216117delC	ENST00000317683.3	-	2	770	c.637delG	c.(637-639)gtgfs	p.V213fs		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	213										breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		TCAGATCCCACCCCCTTGGCC	0.687																																					p.V213fs		Atlas-INDEL	.											.	FBXO46	34	.	0			c.638delT						.						20	23	22					19																	46216117		2006	4141	6147	SO:0001589	frameshift_variant	23403	exon2			.	BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"F-boxes /  "other""	25069	protein-coding gene	gene with protein product		609117	"F-box only protein 34-like"	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.637delG	chr19.hg19:g.46216117delC	ENSP00000410007:p.Val213fs	130.0	0.0		130.0	10.0	NM_001080469		Frame_Shift_Del	DEL	ENST00000317683.3	hg19	CCDS46116.1																																																																																			.	.		0.687	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179		-	46216117	C	-	46216117	7	5	103	1	0	1	0	1	0	0	0	0	5763	507	18	0	1178	0	FBXO46	19	46216117	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1476418	46216117	12912866	1071	15694										
NPAS1	4861	hgsc.bcm.edu	37	chr19	47546077	47546077	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttctccccagccaagccgaGggtggccaaactcctttgga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:47546077delG	ENST00000602212.1	+	11	1447	c.1227delG	c.(1225-1227)gagfs	p.E409fs	NPAS1_ENST00000602189.1_Frame_Shift_Del_p.E234fs|NPAS1_ENST00000449844.2_Frame_Shift_Del_p.E409fs|NPAS1_ENST00000439365.2_Frame_Shift_Del_p.G218fs			Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	409					central nervous system development (GO:0007417)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		GCCAAGCCGAGGGTGGCCAAA	0.632																																					p.E409fs		Atlas-INDEL	.											.	NPAS1	32	.	0			c.1226delA						.						58	43	48					19																	47546077		2203	4300	6503	SO:0001589	frameshift_variant	4861	exon10			.	U77968	CCDS12694.1	19q13.2-q13.3	2013-05-21				ENSG00000130751		"Basic helix-loop-helix proteins"	7894	protein-coding gene	gene with protein product	"neuronal PAS1", "member of PAS superfamily 5"	603346				9012850, 9079689	Standard	NM_002517		Approved	MOP5, PASD5, bHLHe11	uc002pfy.3	Q99742		ENST00000602212.1:c.1227delG	chr19.hg19:g.47546077delG	ENSP00000469142:p.Glu409fs	180.0	0.0		201.0	13.0	NM_002517	B4DR69|Q99632|Q9BY83	Frame_Shift_Del	DEL	ENST00000602212.1	hg19	CCDS12694.1																																																																																			.	.		0.632	NPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466658.1	NM_002517		-	47546077	G	-	47546077	7	5	103	1	0	1	0	1	0	0	0	0	10571	991	35	0	1265	0	NPAS1	19	47546077	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1329960	47546077	11582906	1072	15695										
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47570722	47570722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caggggaatgttcacggcctTctcccgcagggcccgctccc	12	17	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:47570722T>C	ENST00000253048.5	-	15	2840	c.2803A>G	c.(2803-2805)Aag>Gag	p.K935E	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	935							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		TTCACGGCCTTCTCCCGCAGG	0.672																																					p.K935E		Atlas-SNP	.											.	ZC3H4	96	.	0			c.A2803G						.						67	79	75					19																	47570722		1986	4139	6125	SO:0001583	missense	23211	exon15			CGGCCTTCTCCCG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"Zinc fingers, CCCH-type domain containing"	17808	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 7"	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2803A>G	chr19.hg19:g.47570722T>C	ENSP00000253048:p.Lys935Glu	79.0	0.0		95.0	4.0	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	hg19	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.112675	0.56398	.	.	ENSG00000130749	ENST00000253048	T	0.34859	1.34	5.17	5.17	0.71159	.	0.129536	0.50627	D	0.000105	T	0.56906	0.2017	M	0.64404	1.975	0.49483	D	0.999791	D	0.71674	0.998	D	0.77004	0.989	T	0.60429	-0.7265	10	0.72032	D	0.01	.	14.2891	0.66265	0.0:0.0:0.0:1.0	.	935	Q9UPT8	ZC3H4_HUMAN	E	935	ENSP00000253048:K935E	ENSP00000253048:K935E	K	-	1	0	ZC3H4	52262562	1.000000	0.71417	1.000000	0.80357	0.345000	0.29048	3.675000	0.54605	2.078000	0.62432	0.460000	0.39030	AAG	.	.		0.672	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			C	47570722	T	C	47570722	3	2	103	1	0	0	0	0	1	0	0	0	17585	1792	62	2	1112	2	ZC3H4	19	47570722	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	24645	47570722	11558261	1073	15696										
DHX34	9704	hgsc.bcm.edu	37	chr19	47884149	47884149	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accccagaccatcccagccaCcccccatcttcctggcctct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:47884149delC	ENST00000328771.4	+	15	3408	c.3059delC	c.(3058-3060)accfs	p.T1020fs		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	1020					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		ATCCCAGCCACCCCCCATCTT	0.592																																					p.T1020fs		Atlas-INDEL	.											.	DHX34	98	.	0			c.3058delA						.						97	93	94					19																	47884149		2203	4300	6503	SO:0001589	frameshift_variant	9704	exon15			.	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"DEAH-boxes"	16719	protein-coding gene	gene with protein product		615475	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.3059delC	chr19.hg19:g.47884149delC	ENSP00000331907:p.Thr1020fs	103.0	0.0		158.0	11.0	NM_014681	B4DMY8	Frame_Shift_Del	DEL	ENST00000328771.4	hg19	CCDS12700.1																																																																																			.	.		0.592	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		-	47884149	C	-	47884149	7	5	103	1	0	1	0	1	0	0	0	0	4509	507	18	0	3113	0	DHX34	19	47884149	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	313427	47884149	11244834	1074	15697										
PNKP	11284	hgsc.bcm.edu	37	chr19	50368611	50368611	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attgaccaaatacagtgtgtCccccacccccagagagccct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:50368611delC	ENST00000322344.3	-	4	380	c.271delG	c.(271-273)gacfs	p.D91fs	PNKP_ENST00000596014.1_Frame_Shift_Del_p.D91fs|PNKP_ENST00000600573.1_Frame_Shift_Del_p.D91fs|PNKP_ENST00000600910.1_Frame_Shift_Del_p.D91fs|PNKP_ENST00000595792.1_5'Flank	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	91	FHA.				dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		TACAGTGTGTCCCCCACCCCC	0.622								Other BER factors																													p.D91fs		Atlas-INDEL	.											.	PNKP	71	.	0			c.272delA						.						64	61	62					19																	50368611		2203	4300	6503	SO:0001589	frameshift_variant	11284	exon4			.	AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.271delG	chr19.hg19:g.50368611delC	ENSP00000323511:p.Asp91fs	114.0	0.0		157.0	10.0	NM_007254	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Frame_Shift_Del	DEL	ENST00000322344.3	hg19	CCDS12783.1																																																																																			.	.		0.622	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254		-	50368611	C	-	50368611	7	5	103	1	0	1	0	1	0	0	0	0	12156	855	30	0	1350	0	PNKP	19	50368611	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	2484462	50368611	8760372	1075	15698										
NR1H2	7376	hgsc.bcm.edu	37	chr19	50881820	50881820	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tccggaagaagaagattcggAaacagcagcaggagtcacag	13	8	1	3	rs397738863|rs78398331|rs55652650	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:50881820A>C	ENST00000253727.5	+	6	749	c.514A>C	c.(514-516)Aaa>Caa	p.K172Q	NR1H2_ENST00000598168.1_Missense_Mutation_p.K172Q|NR1H2_ENST00000542413.1_5'UTR|NR1H2_ENST00000593926.1_Missense_Mutation_p.K172Q|NR1H2_ENST00000599105.1_Missense_Mutation_p.K172Q|NR1H2_ENST00000411902.2_Missense_Mutation_p.K75Q	NM_007121.5	NP_009052	P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2	172					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pinocytosis (GO:0048550)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	apolipoprotein A-I receptor binding (GO:0034191)|ATPase binding (GO:0051117)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	8		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		GAAGATTCGGAAACAGCAGCA	0.637																																					p.K172Q		Atlas-SNP	.											.,1	NR1H2	47	.	0			c.A514C						.						36	45	42					19																	50881820		2126	4246	6372	SO:0001583	missense	7376	exon6			ATTCGGAAACAGC	U14534	CCDS42593.1, CCDS58673.1	19q13.3	2013-01-16				ENSG00000131408		"Nuclear hormone receptors"	7965	protein-coding gene	gene with protein product	"liver X receptor-beta"	600380	"ubiquitously-expressed nuclear receptor"	UNR		7782080, 7971966	Standard	NM_007121		Approved	NER, NER-I, RIP15, LXR-b	uc010enw.4	P55055		ENST00000253727.5:c.514A>C	chr19.hg19:g.50881820A>C	ENSP00000253727:p.Lys172Gln	85.0	2.0		92.0	4.0	NM_007121	A8K490|B4DNM6|E7EWA6|Q12970|Q5I0Y1	Missense_Mutation	SNP	ENST00000253727.5	hg19	CCDS42593.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.090515	0.55968	.	.	ENSG00000131408	ENST00000253727;ENST00000411902;ENST00000376942	D;D	0.92545	-3.05;-3.06	4.44	3.39	0.38822	Nuclear hormone receptor, ligand-binding (2);	0.390877	0.22454	N	0.059841	D	0.93103	0.7804	L	0.42245	1.32	0.80722	D	1	D;B;D	0.76494	0.999;0.416;0.984	D;B;P	0.72982	0.979;0.063;0.889	D	0.91856	0.5495	10	0.54805	T	0.06	.	10.3348	0.43844	0.8342:0.1658:0.0:0.0	.	172;75;172	P55055;E7EWA6;F1D8P7	NR1H2_HUMAN;.;.	Q	172;75;172	ENSP00000253727:K172Q;ENSP00000396151:K75Q	ENSP00000253727:K172Q	K	+	1	0	NR1H2	55573632	1.000000	0.71417	0.848000	0.33437	0.651000	0.38670	3.746000	0.55127	0.814000	0.34374	0.459000	0.35465	AAA	.	.		0.637	NR1H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464724.2			C	50881820	A	C	50881820	3	2	103	1	0	0	0	0	1	0	0	0	10626	247	9	5	528	5	NR1H2	19	50881820	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	513209	50881820	8247163	1076	15699										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52004796	52004797	+	Missense_Mutation	DNP	GA	GA	TG													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttacatggtcccctgcccgGaaccagtagccatgaactgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:52004796_52004797GA>TG	ENST00000291707.3	-	1	246_247	c.191_192TC>CA	c.(190-192)tTC>tCA	p.F64S	SIGLEC12_ENST00000598614.1_5'Flank	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	64	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CCCCTGCCCGGAACCAGTAGCC	0.599																																					p.F64L|p.F64S		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.C192A|c.T191C						.																																			SO:0001583	missense	89858	exon1			TGCCCGGAACCAG|GCCCGGAACCAGT	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.191_192delinsTG	chr19.hg19:g.52004796_52004797delinsTG	ENSP00000291707:p.Phe64Ser	112.0|114.0	0.0		155.0	14.0|9.0	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	hg19	CCDS12833.1																																																																																			.	.		0.599	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		TG	52004797	GA	TG	52004796	3	4	103	1	0	0	0	0	1	0	0	0	14323	1165	41	3	1700	3	SIGLEC12	19	52004796	Missense_Mutation	DNP	GA	TCGA-DD-A1EG-01A-11D-A20W-10	1122976	52004796	7124187	1077	15700										
SIGLEC6	946	hgsc.bcm.edu	37	chr19	52034030	52034030	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgctgtggtcctggggccgtGgggtgattgtgagcaccgag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:52034030delG	ENST00000425629.3	-	3	765	c.611delC	c.(610-612)ccafs	p.P204fs	SIGLEC6_ENST00000343300.4_Frame_Shift_Del_p.P204fs|SIGLEC6_ENST00000436458.1_Frame_Shift_Del_p.P168fs|SIGLEC6_ENST00000346477.3_Frame_Shift_Del_p.P204fs|SIGLEC6_ENST00000391797.3_Frame_Shift_Del_p.P193fs|SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000359982.4_Frame_Shift_Del_p.P204fs	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	204	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		CTGGGGCCGTGGGGTGATTGT	0.637																																					p.P204fs		Atlas-INDEL	.											.	SIGLEC6	142	.	0			c.612delA						.						63	69	67					19																	52034030		2203	4300	6503	SO:0001589	frameshift_variant	946	exon3			.	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.611delC	chr19.hg19:g.52034030delG	ENSP00000401502:p.Pro204fs	126.0	0.0		159.0	14.0	NM_198845	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Frame_Shift_Del	DEL	ENST00000425629.3	hg19	CCDS12834.3																																																																																			.	.		0.637	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245		-	52034030	G	-	52034030	7	5	103	1	0	1	0	1	0	0	0	0	14327	1348	47	0	807	0	SIGLEC6	19	52034030	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	29234	52034030	7094953	1078	15701										
ZNF350	59348	hgsc.bcm.edu	37	chr19	52468815	52468815	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttcctttctggatgaagccTtttccacattcactgcatat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:52468815delT	ENST00000243644.4	-	5	1118	c.891delA	c.(889-891)aaafs	p.K297fs	ZNF350_ENST00000600703.1_5'Flank|HCCAT3_ENST00000600253.1_RNA|HCCAT3_ENST00000595010.1_RNA	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	297					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		GGATGAAGCCTTTTCCACATT	0.408																																					p.G298fs		Atlas-INDEL	.											.	ZNF350	48	.	0			c.892delG						.						119	113	115					19																	52468815		2203	4300	6503	SO:0001589	frameshift_variant	59348	exon5			.	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"Zinc fingers, C2H2-type", "-"	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.891delA	chr19.hg19:g.52468815delT	ENSP00000243644:p.Lys297fs	87.0	0.0		152.0	10.0	NM_021632	Q96G73|Q9HAQ4	Frame_Shift_Del	DEL	ENST00000243644.4	hg19	CCDS12845.1																																																																																			.	.		0.408	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632		-	52468815	T	-	52468815	7	5	103	1	0	1	0	1	0	0	0	0	17878	1606	56	0	711	0	ZNF350	19	52468815	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	434785	52468815	6660168	1079	15702										
ZNF665	79788	hgsc.bcm.edu	37	chr19	53686151	53686151	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctcacctgaggaagagccaTccctgactcctttgccttcc	7	16	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:53686151T>C	ENST00000600412.1	-	1	63				ZNF665_ENST00000598440.1_5'UTR|ZNF665_ENST00000396424.3_Start_Codon_SNP_p.M1V			Q9H7R5	ZN665_HUMAN	zinc finger protein 665						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		GGAAGAGCCATCCCTGACTCC	0.448																																					p.M1V		Atlas-SNP	.											.	ZNF665	136	.	0			c.A1G						.						166	130	142					19																	53686151		2203	4300	6503	SO:0001627	intron_variant	79788	exon2			GAGCCATCCCTGA		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.52+10413A>G	chr19.hg19:g.53686151T>C		16.0	0.0		50.0	4.0	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.08	1.532935	0.27387	.	.	ENSG00000197497	ENST00000396424	T	0.00792	5.69	2.37	1.33	0.21861	.	.	.	.	.	T	0.00666	0.0022	.	.	.	0.80722	D	1	P	0.36171	0.541	B	0.31337	0.128	T	0.69098	-0.5235	8	0.62326	D	0.03	.	3.5461	0.07829	0.0:0.2023:0.0:0.7977	.	1	Q9H7R5-2	.	V	1	ENSP00000379702:M1V	ENSP00000379702:M1V	M	-	1	0	ZNF665	58377963	0.352000	0.24895	0.303000	0.25071	0.072000	0.16883	1.070000	0.30653	1.078000	0.41014	0.459000	0.35465	ATG	.	.		0.448	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		C	53686151	T	C	53686151	1	2	103	0	1	0	0	0	0	0	0	0	18088	1435	50	2		2	ZNF665	19	53686151	Intron	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1217336	53686151	5442832	1080	15703										
ZNF677	342926	hgsc.bcm.edu	37	chr19	53740870	53740870	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catttgtaaggtttctctccAgtatgaattctttcatgacc	6	9	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:53740870A>G	ENST00000598513.1	-	5	1260	c.1110T>C	c.(1108-1110)acT>acC	p.T370T	ZNF677_ENST00000333952.4_Silent_p.T370T	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	370					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		GTTTCTCTCCAGTATGAATTC	0.403																																					p.T370T		Atlas-SNP	.											.	ZNF677	94	.	0			c.T1110C						.						79	74	76					19																	53740870		2203	4300	6503	SO:0001819	synonymous_variant	342926	exon5			CTCTCCAGTATGA	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1110T>C	chr19.hg19:g.53740870A>G		72.0	0.0		112.0	5.0	NM_182609		Silent	SNP	ENST00000598513.1	hg19	CCDS12861.1																																																																																			.	.		0.403	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		G	53740870	A	G	53740870	2	3	103	1	0	0	0	0	0	0	0	1	18099	175	7	2		2	ZNF677	19	53740870	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	54719	53740870	5388113	1081	15704										
TMC4	147798	hgsc.bcm.edu	37	chr19	54672280	54672280	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtcggggccgggagggcctGggggagcgcctcccaaccag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:54672280delG	ENST00000376591.4	-	4	718	c.587delC	c.(586-588)ccafs	p.P196fs	TMC4_ENST00000476013.2_5'UTR|TMC4_ENST00000301187.4_Frame_Shift_Del_p.P190fs	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	196					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GGGAGGGCCTGGGGGAGCGCC	0.647											OREG0025670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P196fs		Atlas-INDEL	.											.	TMC4	89	.	0			c.588delA						.						25	21	23					19																	54672280		2181	4282	6463	SO:0001589	frameshift_variant	147798	exon4			.	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.587delC	chr19.hg19:g.54672280delG	ENSP00000365776:p.Pro196fs	127.0	0.0	1002	195.0	13.0	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Frame_Shift_Del	DEL	ENST00000376591.4	hg19	CCDS46174.1																																																																																			.	.		0.647	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2			-	54672280	G	-	54672280	7	5	103	1	0	1	0	1	0	0	0	0	16002	1348	47	0	1599	0	TMC4	19	54672280	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	931410	54672280	4456703	1082	15705										
LILRB2	10288	hgsc.bcm.edu	37	chr19	54781769	54781769	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggagatgggaccggtgggtGgggggctggaacccatggag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:54781769delG	ENST00000391749.4	-	8	1554	c.1283delC	c.(1282-1284)ccafs	p.P429fs	LILRB2_ENST00000314446.5_Frame_Shift_Del_p.P429fs|LILRB2_ENST00000434421.1_Frame_Shift_Del_p.P313fs|LILRB2_ENST00000391748.1_Frame_Shift_Del_p.P429fs|LILRB2_ENST00000391746.1_Frame_Shift_Del_p.P429fs|LILRB2_ENST00000471216.1_5'Flank	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	429					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACCGGTGGGTGGGGGGCTGGA	0.607																																					p.P428fs		Atlas-INDEL	.											.	LILRB2	94	.	0			c.1284delA						.						19	25	23					19																	54781769		2081	4048	6129	SO:0001589	frameshift_variant	10288	exon8			.	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.1283delC	chr19.hg19:g.54781769delG	ENSP00000375629:p.Pro429fs	147.0	0.0		242.0	16.0	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Frame_Shift_Del	DEL	ENST00000391749.4	hg19	CCDS12886.1																																																																																			.	.		0.607	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1			-	54781769	G	-	54781769	7	5	103	1	0	1	0	1	0	0	0	0	8800	1348	47	0	541	0	LILRB2	19	54781769	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	109489	54781769	4347214	1083	15706										
LENG8	114823	hgsc.bcm.edu	37	chr19	54967951	54967951	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccgccgcctgcgcctcgagCccctggtgctgcagatgagc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:54967951delC	ENST00000326764.5	+	11	2061	c.1582delC	c.(1582-1584)cccfs	p.P528fs	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	491										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GCGCCTCGAGCCCCTGGTGCT	0.667																																					p.E527fs		Atlas-INDEL	.											.	LENG8	73	.	0			c.1581delG						.						28	27	27					19																	54967951		2202	4298	6500	SO:0001589	frameshift_variant	114823	exon11			.	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1582delC	chr19.hg19:g.54967951delC	ENSP00000318374:p.Pro528fs	73.0	0.0		127.0	10.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Frame_Shift_Del	DEL	ENST00000326764.5	hg19	CCDS12894.1																																																																																			.	.		0.667	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		-	54967951	C	-	54967951	7	5	103	1	0	1	0	1	0	0	0	0	8733	739	26	0	1620	0	LENG8	19	54967951	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	186182	54967951	4161032	1084	15707										
LILRA2	11027	hgsc.bcm.edu	37	chr19	55098671	55098671	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgacctctttgtccagcatCcctaggccaacacccccagg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:55098671delC	ENST00000251377.3	+	9	1443	c.1310delC	c.(1309-1311)tccfs	p.S437fs	LILRA2_ENST00000251376.3_Frame_Shift_Del_p.S420fs|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000396321.2_Intron|CTB-83J4.2_ENST00000596330.1_lincRNA|LILRA2_ENST00000391738.3_Frame_Shift_Del_p.S437fs|LILRA2_ENST00000391737.1_Frame_Shift_Del_p.S408fs			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	437					defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		TGTCCAGCATCCCTAGGCCAA	0.582																																					p.S437fs		Atlas-INDEL	.											.	LILRA2	99	.	0			c.1309delT						.						134	113	120					19																	55098671		2203	4300	6503	SO:0001589	frameshift_variant	11027	exon8			.	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.1310delC	chr19.hg19:g.55098671delC	ENSP00000251377:p.Ser437fs	198.0	0.0		205.0	13.0	NM_001130917	O75020	Frame_Shift_Del	DEL	ENST00000251377.3	hg19	CCDS46179.1																																																																																			.	.		0.582	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			-	55098671	C	-	55098671	7	5	103	1	0	1	0	1	0	0	0	0	8794	855	30	0	1340	0	LILRA2	19	55098671	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	130720	55098671	4030312	1085	15708										
EPN1	29924	hgsc.bcm.edu	37	chr19	56206189	56206189	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggctgaggctgtgggcagCcccccacctgcagccacacc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:56206189delC	ENST00000270460.6	+	10	1673	c.1362delC	c.(1360-1362)agcfs	p.S454fs	AC010525.7_ENST00000589698.1_lincRNA|EPN1_ENST00000085079.7_Frame_Shift_Del_p.S428fs|AC010525.4_ENST00000585559.1_RNA|EPN1_ENST00000411543.2_Frame_Shift_Del_p.S540fs|AC010525.6_ENST00000587937.1_lincRNA	NM_001130072.1	NP_001123544.1	Q9Y6I3	EPN1_HUMAN	epsin 1	454	Ala/Gly/Pro-rich.				embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|female pregnancy (GO:0007565)|in utero embryonic development (GO:0001701)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|Notch signaling pathway (GO:0007219)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	17		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)		CTGTGGGCAGCCCCCCACCTG	0.687																																					p.S540fs		Atlas-INDEL	.											.	EPN1	98	.	0			c.1619delG						.						19	31	27					19																	56206189		2055	4179	6234	SO:0001589	frameshift_variant	29924	exon10			.	AF073727	CCDS46198.1, CCDS46199.1, CCDS46200.1	19q13.42	2014-08-12			ENSG00000063245	ENSG00000063245			21604	protein-coding gene	gene with protein product		607262				9723620, 10557078	Standard	NM_001130072		Approved		uc002qlx.3	Q9Y6I3	OTTHUMG00000180911	ENST00000270460.6:c.1362delC	chr19.hg19:g.56206189delC	ENSP00000270460:p.Ser454fs	155.0	0.0		188.0	13.0	NM_001130071	Q86ST3|Q9HA18	Frame_Shift_Del	DEL	ENST00000270460.6	hg19	CCDS46199.1																																																																																			.	.		0.687	EPN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453610.1	NM_013333		-	56206189	C	-	56206189	7	5	103	1	0	1	0	1	0	0	0	0	5187	738	26	0	1737	0	EPN1	19	56206189	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1107518	56206189	2922794	1086	15709										
ZNF667	63934	hgsc.bcm.edu	37	chr19	56953129	56953129	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccttacactcaaatagtttcTttttctttgtatgaactttc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:56953129delT	ENST00000504904.3	-	7	1954	c.1235delA	c.(1234-1236)aagfs	p.K413fs	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Frame_Shift_Del_p.K541fs|ZNF667_ENST00000292069.6_Frame_Shift_Del_p.K413fs			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		AAATAGTTTCTTTTTCTTTGT	0.333																																					p.K412fs		Atlas-INDEL	.											.	ZNF667	95	.	0			c.1236delG						.						54	53	53					19																	56953129		2203	4300	6503	SO:0001589	frameshift_variant	63934	exon5			.		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"Zinc fingers, C2H2-type", "-"	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1235delA	chr19.hg19:g.56953129delT	ENSP00000439402:p.Lys413fs	129.0	0.0		145.0	10.0	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Frame_Shift_Del	DEL	ENST00000504904.3	hg19	CCDS12944.1																																																																																			.	.		0.333	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		-	56953129	T	-	56953129	7	5	103	1	0	1	0	1	0	0	0	0	18089	1609	56	0	601	0	ZNF667	19	56953129	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	746940	56953129	2175854	1087	15710										
ZNF667	63934	hgsc.bcm.edu	37	chr19	56953864	56953864	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attcaaaaggcttctctcctGtatgaatgttctgatgaagt	8	7	3	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:56953864G>C	ENST00000504904.3	-	7	1219	c.500C>G	c.(499-501)aCa>aGa	p.T167R	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Missense_Mutation_p.T295R|ZNF667_ENST00000292069.6_Missense_Mutation_p.T167R			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	167					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		CTTCTCTCCTGTATGAATGTT	0.378																																					p.T167R		Atlas-SNP	.											ZNF667,caecum,carcinoma,0,1	ZNF667	95	.	0			c.C500G						.						83	87	85					19																	56953864		2203	4300	6503	SO:0001583	missense	63934	exon5			TCTCCTGTATGAA		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"Zinc fingers, C2H2-type", "-"	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.500C>G	chr19.hg19:g.56953864G>C	ENSP00000439402:p.Thr167Arg	112.0	0.0		164.0	0.0	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	hg19	CCDS12944.1	.	.	.	.	.	.	.	.	.	.	G	8.465	0.856145	0.17106	.	.	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000360227	T;T;T	0.25749	1.78;1.78;1.78	4.86	2.68	0.31781	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.308196	0.23591	N	0.046547	T	0.37237	0.0996	L	0.60067	1.865	0.09310	N	1	D;P	0.58620	0.983;0.942	P;P	0.57101	0.813;0.725	T	0.08973	-1.0696	10	0.87932	D	0	-0.7584	9.5492	0.39299	0.1798:0.0:0.8202:0.0	.	295;167	E7EPS0;Q5HYK9	.;ZN667_HUMAN	R	295;167;167;41	ENSP00000344699:T295R;ENSP00000439402:T167R;ENSP00000292069:T167R	ENSP00000292069:T167R	T	-	2	0	ZNF667	61645676	0.003000	0.15002	0.006000	0.13384	0.004000	0.04260	1.077000	0.30741	1.275000	0.44379	-0.237000	0.12165	ACA	.	.		0.378	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		C	56953864	G	C	56953864	3	2	103	1	0	0	0	0	1	0	0	0	18089	1377	48	4	1336	4	ZNF667	19	56953864	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	735	56953864	2175119	1088	15711										
ZFP28	140612	hgsc.bcm.edu	37	chr19	57066048	57066048	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccttcagcatcagttctcagCttgccactcatcagagaatc	6	14	5	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:57066048C>T	ENST00000301318.3	+	8	1965	c.1894C>T	c.(1894-1896)Ctt>Ttt	p.L632F	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	632					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		CAGTTCTCAGCTTGCCACTCA	0.453																																					p.L632F	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.C1894T						.						89	96	93					19																	57066048		2203	4300	6503	SO:0001583	missense	140612	exon8			TCTCAGCTTGCCA		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.1894C>T	chr19.hg19:g.57066048C>T	ENSP00000301318:p.Leu632Phe	80.0	0.0		96.0	4.0	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	hg19	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.188855	0.57909	.	.	ENSG00000196867	ENST00000301318	T	0.52057	0.68	4.23	4.23	0.50019	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40302	N	0.001133	T	0.70745	0.3259	M	0.82193	2.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76610	-0.2896	10	0.72032	D	0.01	.	15.8942	0.79323	0.0:1.0:0.0:0.0	.	632	Q8NHY6	ZFP28_HUMAN	F	632	ENSP00000301318:L632F	ENSP00000301318:L632F	L	+	1	0	ZFP28	61757860	0.245000	0.23899	1.000000	0.80357	0.995000	0.86356	1.319000	0.33655	2.357000	0.79964	0.555000	0.69702	CTT	.	.		0.453	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		T	57066048	C	T	57066048	3	4	103	1	0	0	0	0	1	0	0	0	17657	797	28	3	1924	3	ZFP28	19	57066048	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	112184	57066048	2062935	1089	15712										
ZNF134	7693	hgsc.bcm.edu	37	chr19	58132374	58132374	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgcagtgattgtgggaaagTcttcagacacaaatctacac	10	8	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:58132374T>C	ENST00000396161.5	+	3	1197	c.887T>C	c.(886-888)gTc>gCc	p.V296A		NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	296					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		TGTGGGAAAGTCTTCAGACAC	0.398																																					p.V296A		Atlas-SNP	.											.	ZNF134	34	.	0			c.T887C						.						111	114	113					19																	58132374		2200	4299	6499	SO:0001583	missense	7693	exon3			GGAAAGTCTTCAG	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"Zinc fingers, C2H2-type"	12918	protein-coding gene	gene with protein product		604076	"zinc finger protein 134 (clone pHZ-15)"			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.887T>C	chr19.hg19:g.58132374T>C	ENSP00000379464:p.Val296Ala	72.0	0.0		85.0	4.0	NM_003435	Q9Y4B2	Missense_Mutation	SNP	ENST00000396161.5	hg19	CCDS42638.1	.	.	.	.	.	.	.	.	.	.	T	3.925	-0.017305	0.07681	.	.	ENSG00000213762	ENST00000418193;ENST00000541849;ENST00000396161	T	0.00949	5.51	4.45	-0.858	0.10689	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00384	0.0012	N	0.01152	-0.98	0.19775	N	0.999959	B	0.18013	0.025	B	0.15052	0.012	T	0.43410	-0.9393	9	0.02654	T	1	.	6.4658	0.21981	0.0:0.4523:0.2503:0.2974	.	296	P52741	ZN134_HUMAN	A	363;216;296	ENSP00000379464:V296A	ENSP00000379464:V296A	V	+	2	0	ZNF134	62824186	0.000000	0.05858	0.660000	0.29694	0.888000	0.51559	-0.618000	0.05578	-0.080000	0.12685	0.459000	0.35465	GTC	.	.		0.398	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435		C	58132374	T	C	58132374	3	2	103	1	0	0	0	0	1	0	0	0	17739	1667	58	2	893	2	ZNF134	19	58132374	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1066326	58132374	996609	1090	15713										
ZNF8	7554	hgsc.bcm.edu	37	chr19	58797546	58797546	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagctatgggtggctgagagAggaaccacccagggctgcca	16	10	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:58797546A>G	ENST00000196548.5	+	3	395	c.264A>G	c.(262-264)agA>agG	p.R88R	CTD-3138B18.4_ENST00000600029.1_3'UTR|AC010642.1_ENST00000591325.1_3'UTR|ZNF8_ENST00000608843.1_Silent_p.R88R			P17098	ZNF8_HUMAN	zinc finger protein 8	88	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				BMP signaling pathway (GO:0030509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	19		all_cancers(17;6.46e-05)|Lung NSC(17;0.0233)|all_neural(62;0.0381)|all_epithelial(17;0.0427)|all_lung(17;0.057)|Ovarian(87;0.17)|Colorectal(82;0.227)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.00619)		TGGCTGAGAGAGGAACCACCC	0.572																																					p.R88R		Atlas-SNP	.											.	ZNF8	60	.	0			c.A264G						.						54	47	50					19																	58797546		2203	4300	6503	SO:0001819	synonymous_variant	7554	exon3			TGAGAGAGGAACC	M29581	CCDS12974.1	19q13.43	2013-01-08	2006-05-09					"Zinc fingers, C2H2-type", "-"	13154	protein-coding gene	gene with protein product		194532	"zinc finger protein 8 (clone HF.18)"			2106481	Standard	NM_021089		Approved	HF.18, Zfp128	uc002qry.1	P17098		ENST00000196548.5:c.264A>G	chr19.hg19:g.58797546A>G		85.0	0.0		87.0	4.0	NM_021089	Q6PI99	Silent	SNP	ENST00000196548.5	hg19	CCDS12974.1																																																																																			.	.		0.572	ZNF8-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000459135.1	NM_021089		G	58797546	A	G	58797546	2	3	103	1	0	0	0	0	0	0	0	1	18182	301	11	2		2	ZNF8	19	58797546	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	665172	58797546	331437	1091	15714										
ZNF132	7691	hgsc.bcm.edu	37	chr19	58945615	58945615	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgcactcataaggtcttaccTgtgtgtgaactttctgatgc	9	9	3	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:58945615T>C	ENST00000254166.3	-	3	1596	c.1196A>G	c.(1195-1197)cAg>cGg	p.Q399R		NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	399					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		AGGTCTTACCTGTGTGTGAAC	0.468																																					p.Q399R		Atlas-SNP	.											.	ZNF132	56	.	0			c.A1196G						.						100	94	96					19																	58945615		2203	4300	6503	SO:0001583	missense	7691	exon3			CTTACCTGTGTGT	U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"Zinc fingers, C2H2-type", "-"	12916	protein-coding gene	gene with protein product		604074	"zinc finger protein 132 (clone pHZ-12)"			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.1196A>G	chr19.hg19:g.58945615T>C	ENSP00000254166:p.Gln399Arg	43.0	0.0		70.0	4.0	NM_003433	Q32MI9	Missense_Mutation	SNP	ENST00000254166.3	hg19	CCDS12980.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.63|10.63	1.404504|1.404504	0.25378|0.25378	.|.	.|.	ENSG00000131849|ENSG00000131849	ENST00000391695|ENST00000254166	.|T	.|0.18338	.|2.22	3.78|3.78	-1.83|-1.83	0.07833|0.07833	.|Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	.|T	.|0.06781	.|0.0173	N|N	0.03917|0.03917	-0.325|-0.325	0.09310|0.09310	N|N	1|1	.|B	.|0.16166	.|0.016	.|B	.|0.13407	.|0.009	.|T	.|0.34104	.|-0.9842	.|9	.|0.87932	.|D	.|0	.|.	5.9234|5.9234	0.19094|0.19094	0.0:0.5743:0.199:0.2266|0.0:0.5743:0.199:0.2266	.|.	.|399	.|P52740	.|ZN132_HUMAN	.|R	-1|399	.|ENSP00000254166:Q399R	.|ENSP00000254166:Q399R	.|Q	-|-	.|2	.|0	ZNF132|ZNF132	63637427|63637427	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.912000|0.912000	0.54170|0.54170	-0.469000|-0.469000	0.06648|0.06648	-0.269000|-0.269000	0.09298|0.09298	0.533000|0.533000	0.62120|0.62120	.|CAG	.	.		0.468	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433		C	58945615	T	C	58945615	3	2	103	1	0	0	0	0	1	0	0	0	17737	1580	55	2	928	2	ZNF132	19	58945615	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	148069	58945615	183368	1092	15715										
TBC1D20	128637	hgsc.bcm.edu	37	chr20	428697	428697	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtgtatctctgccactttcTttttccttttggcgttaaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:428697delT	ENST00000354200.4	-	2	239	c.92delA	c.(91-93)aagfs	p.K32fs	Y_RNA_ENST00000384070.1_RNA	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	32					acrosome assembly (GO:0001675)|cargo loading into COPII-coated vesicle (GO:0090110)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|lens fiber cell morphogenesis (GO:0070309)|lipid particle organization (GO:0034389)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|seminiferous tubule development (GO:0072520)|virion assembly (GO:0019068)	endoplasmic reticulum membrane (GO:0005789)|integral component of Golgi membrane (GO:0030173)|nuclear membrane (GO:0031965)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(17;0.228)|Breast(17;0.231)				TGCCACTTTCTTTTTCCTTTT	0.478																																					p.K31fs		Atlas-INDEL	.											.	TBC1D20	34	.	0			c.93delG						.						169	130	143					20																	428697		2203	4300	6503	SO:0001589	frameshift_variant	128637	exon2			.	AK055573	CCDS13002.1	20p13	2013-07-10	2005-01-05	2005-01-05	ENSG00000125875	ENSG00000125875			16133	protein-coding gene	gene with protein product		611663	"chromosome 20 open reading frame 140"	C20orf140		17901050	Standard	XM_005260661		Approved	dJ852M4.2	uc002wds.3	Q96BZ9	OTTHUMG00000031637	ENST00000354200.4:c.92delA	chr20.hg19:g.428697delT	ENSP00000346139:p.Lys32fs	125.0	0.0		166.0	11.0	NM_144628	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Frame_Shift_Del	DEL	ENST00000354200.4	hg19	CCDS13002.1																																																																																			.	.		0.478	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628		-	428697	T	-	428697	7	5	103	1	0	1	0	1	0	0	0	0	15624	1609	56	0	1147	0	TBC1D20	20	428697	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10		428697	62596823	1093	15716										
SIRPB1	10326	hgsc.bcm.edu	37	chr20	1551499	1551499	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggtgcgctgagatctccaGggcatagcttttgctgactg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:1551499delG	ENST00000381605.4	-	4	1100	c.1036delC	c.(1036-1038)ctgfs	p.L346fs	RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000262929.5_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	346	Ig-like C1-type 2.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						GAGATCTCCAGGGCATAGCTT	0.507																																					p.L346fs		Atlas-INDEL	.											.	SIRPB1	83	.	0			c.1037delT						.						186	174	178					20																	1551499		2203	4300	6503	SO:0001589	frameshift_variant	10326	exon4			.	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.1036delC	chr20.hg19:g.1551499delG	ENSP00000371018:p.Leu346fs	115.0	0.0		161.0	10.0	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Frame_Shift_Del	DEL	ENST00000381605.4	hg19	CCDS13019.1																																																																																			.	.		0.507	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		-	1551499	G	-	1551499	7	5	103	1	0	1	0	1	0	0	0	0	14348	991	35	0	168	0	SIRPB1	20	1551499	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1122802	1551499	61474021	1094	15717										
TGM6	343641	hgsc.bcm.edu	37	chr20	2384126	2384126	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggcaggttctggatgccaCcccccaggaggagagtgaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:2384126delC	ENST00000202625.2	+	8	1134	c.1073delC	c.(1072-1074)accfs	p.T358fs	TGM6_ENST00000381423.1_Frame_Shift_Del_p.T358fs	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	358					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	CTGGATGCCACCCCCCAGGAG	0.582																																					p.T358fs		Atlas-INDEL	.											.	TGM6	126	.	0			c.1072delA						.						58	56	57					20																	2384126		2203	4300	6503	SO:0001589	frameshift_variant	343641	exon8			.	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"Transglutaminases"	16255	protein-coding gene	gene with protein product	"spinocerebellar ataxia 35"	613900	"transglutaminase 3-like"	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1073delC	chr20.hg19:g.2384126delC	ENSP00000202625:p.Thr358fs	120.0	0.0		154.0	10.0	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Frame_Shift_Del	DEL	ENST00000202625.2	hg19	CCDS13025.1																																																																																			.	.		0.582	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		-	2384126	C	-	2384126	7	5	103	1	0	1	0	1	0	0	0	0	15849	507	18	0	1103	0	TGM6	20	2384126	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	832627	2384126	60641394	1095	15718										
SLC4A11	83959	hgsc.bcm.edu	37	chr20	3218620	3218620	+	5'Flank	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccgggcccgagcgggcctctCcccctctctcctcggatgcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:3218620delC	ENST00000380056.3	-	0	0				SLC4A11_ENST00000539553.2_Intron|SLC4A11_ENST00000380059.3_Frame_Shift_Del_p.E31fs	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11						bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						GCGGGCCTCTCCCCCTCTCTC	0.617																																					p.E31fs	NSCLC(190;922 2139 10266 10292 38692)	Atlas-INDEL	.											.	SLC4A11	188	.	0			c.92delA						.																																			SO:0001631	upstream_gene_variant	83959	exon1			.	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"Solute carriers"	16438	protein-coding gene	gene with protein product		610206	"corneal endothelial dystrophy 2 (autosomal recessive)", "solute carrier family 4, sodium bicarbonate transporter-like, member 11", "corneal dystrophy and perceptive deafness 1"	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740		chr20.hg19:g.3218620delC	Exception_encountered	111.0	0.0		147.0	10.0	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Frame_Shift_Del	DEL	ENST00000380056.3	hg19	CCDS13052.1																																																																																			.	.		0.617	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1			-	3218620	C	-	3218620	6	5	103	0	1	1	0	1	0	0	0	0	14667	864	30	0		0	SLC4A11	20	3218620	5'Flank	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	834494	3218620	59806900	1096	15719										
HSPA12B	116835	hgsc.bcm.edu	37	chr20	3723057	3723057	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggccatccacatgatgaggTgaggtcggctgggctgagag	17	8	0	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:3723057T>C	ENST00000254963.2	+	4	411		c.e4+2		HSPA12B_ENST00000542646.1_Intron	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B								ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						CATGATGAGGTGAGGTCGGCT	0.577																																					.		Atlas-SNP	.											.	HSPA12B	43	.	0			c.266+2T>C						.						51	48	49					20																	3723057		2203	4300	6503	SO:0001630	splice_region_variant	116835	exon4			ATGAGGTGAGGTC	AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"Heat shock proteins / HSP70"	16193	protein-coding gene	gene with protein product		610702	"chromosome 20 open reading frame 60"	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.266+2T>C	chr20.hg19:g.3723057T>C		62.0	0.0		84.0	4.0	NM_001197327	D3DVX7|Q2TAK3|Q9BR52	Splice_Site	SNP	ENST00000254963.2	hg19	CCDS13061.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.840376	0.51057	.	.	ENSG00000132622	ENST00000254963;ENST00000399701	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5017	0.55960	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HSPA12B	3671057	1.000000	0.71417	0.993000	0.49108	0.617000	0.37484	5.934000	0.70138	2.122000	0.65172	0.533000	0.62120	.	.	.		0.577	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970	Intron	C	3723057	T	C	3723057	5	2	103	1	0	0	0	0	0	0	1	0	7414	1710	59	2	278	2	HSPA12B	20	3723057	Splice_Site	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	504437	3723057	59302463	1097	15720										
PROKR2	128674	hgsc.bcm.edu	37	chr20	5283258	5283258	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttgacaataaagaggaccgTttctgttgcaaagtaagccg	10	8	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:5283258T>G	ENST00000217270.3	-	2	582	c.583A>C	c.(583-585)Acg>Ccg	p.T195P	PROKR2_ENST00000546004.1_Missense_Mutation_p.T195P	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	195					circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						AAGAGGACCGTTTCTGTTGCA	0.488										HNSCC(71;0.22)																											p.T195P		Atlas-SNP	.											.	PROKR2	90	.	0			c.A583C						.						145	145	145					20																	5283258		2203	4300	6503	SO:0001583	missense	128674	exon2			GGACCGTTTCTGT	AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292		"GPCR / Class A : Prokineticin receptors"	15836	protein-coding gene	gene with protein product		607123	"G protein-coupled receptor 73-like 1", "Kallmann syndrome 3 (autosomal dominant)"	GPR73L1, KAL3		11886876, 17054399	Standard	NM_144773		Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.583A>C	chr20.hg19:g.5283258T>G	ENSP00000217270:p.Thr195Pro	145.0	0.0		173.0	7.0	NM_144773	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Missense_Mutation	SNP	ENST00000217270.3	hg19	CCDS13089.1	.	.	.	.	.	.	.	.	.	.	T	16.00	2.999718	0.54147	.	.	ENSG00000101292	ENST00000546004;ENST00000217270	T;T	0.72835	-0.69;-0.69	5.31	4.21	0.49690	GPCR, rhodopsin-like superfamily (1);	0.144071	0.64402	D	0.000006	T	0.66954	0.2842	L	0.55481	1.735	0.45502	D	0.99846	P	0.48016	0.904	P	0.48738	0.588	T	0.63363	-0.6654	10	0.33141	T	0.24	.	4.8238	0.13405	0.1643:0.0886:0.0:0.7471	.	195	Q8NFJ6	PKR2_HUMAN	P	195	ENSP00000440790:T195P;ENSP00000217270:T195P	ENSP00000217270:T195P	T	-	1	0	PROKR2	5231258	1.000000	0.71417	0.368000	0.25939	0.913000	0.54294	5.692000	0.68256	0.869000	0.35703	0.533000	0.62120	ACG	.	.		0.488	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773		G	5283258	T	G	5283258	3	3	103	1	0	0	0	0	1	0	0	0	12565	1725	60	5	574	5	PROKR2	20	5283258	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1560201	5283258	57742262	1098	15721										
CHGB	1114	hgsc.bcm.edu	37	chr20	5904345	5904345	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgaaaagaggaagagattaGgggaactgttcaacccatac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:5904345delG	ENST00000378961.4	+	4	1759	c.1555delG	c.(1555-1557)gggfs	p.G519fs		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	519						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GAAGAGATTAGGGGAACTGTT	0.458																																					p.L518fs		Atlas-INDEL	.											.	CHGB	112	.	0			c.1554delA						.						69	71	71					20																	5904345		2203	4300	6503	SO:0001589	frameshift_variant	1114	exon4			.		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1555delG	chr20.hg19:g.5904345delG	ENSP00000368244:p.Gly519fs	95.0	0.0		163.0	10.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Frame_Shift_Del	DEL	ENST00000378961.4	hg19	CCDS13092.1																																																																																			.	.		0.458	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		-	5904345	G	-	5904345	7	5	103	1	0	1	0	1	0	0	0	0	3341	1000	35	0	1569	0	CHGB	20	5904345	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	621087	5904345	57121175	1099	15722										
KIF16B	55614	hgsc.bcm.edu	37	chr20	16351274	16351274	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggtgccattgtgaagtttcTcattatcctgaaaagaaaag	9	6	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:16351274T>C	ENST00000354981.2	-	22	3612	c.3455A>G	c.(3454-3456)gAg>gGg	p.E1152G	KIF16B_ENST00000378003.2_Missense_Mutation_p.E378G|KIF16B_ENST00000355755.3_Missense_Mutation_p.E1152G|KIF16B_ENST00000408042.1_Missense_Mutation_p.E1152G	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	1152					ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GTGAAGTTTCTCATTATCCTG	0.368																																					p.E1152G		Atlas-SNP	.											.	KIF16B	305	.	0			c.A3455G						.						104	99	101					20																	16351274		2202	4300	6502	SO:0001583	missense	55614	exon22			AGTTTCTCATTAT	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.3455A>G	chr20.hg19:g.16351274T>C	ENSP00000347076:p.Glu1152Gly	42.0	0.0		72.0	4.0	NM_001199866	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	hg19	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.766397	0.90020	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000378003;ENST00000408042	T;T;T;T	0.77098	-0.72;-1.07;2.17;-0.79	5.76	5.76	0.90799	.	0.051713	0.85682	D	0.000000	D	0.83487	0.5265	L	0.55481	1.735	0.40287	D	0.978464	D;D;D	0.69078	0.978;0.997;0.995	P;P;P	0.59825	0.773;0.864;0.735	D	0.84314	0.0512	10	0.46703	T	0.11	.	16.0643	0.80861	0.0:0.0:0.0:1.0	.	1152;1152;1152	Q96L93-2;Q96L93-6;Q96L93	.;.;KI16B_HUMAN	G	1152;1152;996;378;1152	ENSP00000347076:E1152G;ENSP00000347995:E1152G;ENSP00000367242:E378G;ENSP00000384164:E1152G	ENSP00000347076:E1152G	E	-	2	0	KIF16B	16299274	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.825000	0.69286	2.202000	0.70862	0.450000	0.29827	GAG	.	.		0.368	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		C	16351274	T	C	16351274	3	2	103	1	0	0	0	0	1	0	0	0	8287	1551	54	2	518	2	KIF16B	20	16351274	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	10446929	16351274	46674246	1100	15723										
MYLK2	85366	hgsc.bcm.edu	37	chr20	30419520	30419520	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctctaggctgagcggcctctCccccttcctgggagatgatg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:30419520delC	ENST00000375994.2	+	10	1712	c.1439delC	c.(1438-1440)tccfs	p.S480fs	MYLK2_ENST00000468730.1_3'UTR|MYLK2_ENST00000375985.4_Frame_Shift_Del_p.S480fs			Q9H1R3	MYLK2_HUMAN	myosin light chain kinase 2	480	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|neuromuscular synaptic transmission (GO:0007274)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of gene expression (GO:0010628)|protein autophosphorylation (GO:0046777)|regulation of muscle filament sliding (GO:0032971)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle satellite cell differentiation (GO:0014816)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			AGCGGCCTCTCCCCCTTCCTG	0.572																																					p.S480fs		Atlas-INDEL	.											.	MYLK2	76	.	0			c.1438delT						.						109	93	99					20																	30419520		2203	4300	6503	SO:0001589	frameshift_variant	85366	exon11			.	AF325549	CCDS13191.1	20q13.31	2014-09-17	2008-01-23		ENSG00000101306	ENSG00000101306	2.7.11.18		16243	protein-coding gene	gene with protein product	"skeletal muscle myosin light chain kinase"	606566	"myosin light chain kinase 2, skeletal muscle"				Standard	NM_033118		Approved	skMLCK, KMLC, MLCK2	uc002wwq.2	Q9H1R3	OTTHUMG00000032194	ENST00000375994.2:c.1439delC	chr20.hg19:g.30419520delC	ENSP00000365162:p.Ser480fs	89.0	0.0		145.0	11.0	NM_033118	Q569L1|Q96I84	Frame_Shift_Del	DEL	ENST00000375994.2	hg19	CCDS13191.1																																																																																			.	.		0.572	MYLK2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078583.2	NM_033118		-	30419520	C	-	30419520	7	5	103	1	0	1	0	1	0	0	0	0	10066	855	30	0	1477	0	MYLK2	20	30419520	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	14068246	30419520	32606000	1101	15724										
ZNF341	84905	hgsc.bcm.edu	37	chr20	32346565	32346565	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaactcaagtgctcatactgTgacaagtcattcaccaaaaa	5	10	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:32346565T>C	ENST00000375200.1	+	7	1346	c.981T>C	c.(979-981)tgT>tgC	p.C327C	ZNF341_ENST00000342427.2_Silent_p.C320C	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						GCTCATACTGTGACAAGTCAT	0.557																																					p.C320C		Atlas-SNP	.											.	ZNF341	73	.	0			c.T960C						.						96	73	81					20																	32346565		2203	4300	6503	SO:0001819	synonymous_variant	84905	exon7			ATACTGTGACAAG	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"Zinc fingers, C2H2-type"	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.981T>C	chr20.hg19:g.32346565T>C		68.0	0.0		89.0	4.0	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	hg19																																																																																				.	.		0.557	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				C	32346565	T	C	32346565	2	2	103	1	0	0	0	0	0	0	0	1	17872	1702	59	2		2	ZNF341	20	32346565	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1927045	32346565	30678955	1102	15725										
RALY	22913	hgsc.bcm.edu	37	chr20	32664985	32664985	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctgaggcaggcctgccccaGggggaagcacggacccgaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:32664985delG	ENST00000246194.3	+	8	1312	c.810delG	c.(808-810)cagfs	p.Q270fs	RALY_ENST00000375114.3_Frame_Shift_Del_p.Q254fs	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	270					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						GCCTGCCCCAGGGGGAAGCAC	0.697																																					p.Q270fs		Atlas-INDEL	.											.	RALY	44	.	0			c.809delA						.						26	28	27					20																	32664985		2199	4298	6497	SO:0001589	frameshift_variant	22913	exon8			.	AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"RNA binding motif (RRM) containing"	15921	protein-coding gene	gene with protein product		614663	"RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)", "RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	ENST00000246194.3:c.810delG	chr20.hg19:g.32664985delG	ENSP00000246194:p.Gln270fs	157.0	0.0		197.0	12.0	NM_016732	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	Frame_Shift_Del	DEL	ENST00000246194.3	hg19	CCDS13230.1																																																																																			.	.		0.697	RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1			-	32664985	G	-	32664985	7	5	103	1	0	1	0	1	0	0	0	0	13034	991	35	0	832	0	RALY	20	32664985	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	318420	32664985	30360535	1103	15726										
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36842112	36842112	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtccagcctgagctgggccaTcaggtcctgacagtccatgt	12	13	1	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:36842112T>C	ENST00000279024.4	-	14	3206	c.2935A>G	c.(2935-2937)Atg>Gtg	p.M979V		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	979										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AGCTGGGCCATCAGGTCCTGA	0.607																																					p.M979V		Atlas-SNP	.											.	KIAA1755	145	.	0			c.A2935G						.						18	16	17					20																	36842112		2202	4300	6502	SO:0001583	missense	85449	exon14			GGGCCATCAGGTC	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2935A>G	chr20.hg19:g.36842112T>C	ENSP00000279024:p.Met979Val	65.0	0.0		100.0	4.0	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	T	5.990	0.366597	0.11352	.	.	ENSG00000149633	ENST00000279024	T	0.04603	3.59	5.14	-2.67	0.06059	.	0.360778	0.23926	N	0.043189	T	0.04318	0.0119	L	0.50919	1.6	0.09310	N	0.999994	B	0.02656	0.0	B	0.04013	0.001	T	0.30446	-0.9978	10	0.48119	T	0.1	.	6.4846	0.22081	0.0:0.4782:0.1678:0.354	.	979	Q5JYT7	K1755_HUMAN	V	979	ENSP00000279024:M979V	ENSP00000279024:M979V	M	-	1	0	KIAA1755	36275526	0.769000	0.28531	0.126000	0.21872	0.993000	0.82548	-0.119000	0.10676	-0.368000	0.08040	0.459000	0.35465	ATG	.	.		0.607	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		C	36842112	T	C	36842112	3	2	103	1	0	0	0	0	1	0	0	0	8266	1435	50	2	671	2	KIAA1755	20	36842112	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	4177127	36842112	26183408	1104	15727										
LBP	3929	hgsc.bcm.edu	37	chr20	36989407	36989407	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctccgatctacagccttatcTccaaactctgccaggtagga	7	14	3	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:36989407T>C	ENST00000217407.2	+	6	799	c.638T>C	c.(637-639)cTc>cCc	p.L213P		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	213					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				CAGCCTTATCTCCAAACTCTG	0.418																																					p.L213P		Atlas-SNP	.											.	LBP	60	.	0			c.T638C						.						170	167	168					20																	36989407		2203	4300	6503	SO:0001583	missense	3929	exon6			CTTATCTCCAAAC		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"BPI fold containing"	6517	protein-coding gene	gene with protein product	"BPI fold containing family D, member 2"	151990	"lipopolysaccharide-binding protein"			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.638T>C	chr20.hg19:g.36989407T>C	ENSP00000217407:p.Leu213Pro	95.0	0.0		131.0	6.0	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	hg19	CCDS13304.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.815307	0.70912	.	.	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.14766	2.48	5.28	5.28	0.74379	Lipid-binding serum glycoprotein, N-terminal (1);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.000000	0.64402	D	0.000011	T	0.43433	0.1247	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.50980	-0.8763	10	0.87932	D	0	-35.8502	13.2224	0.59896	0.0:0.0:0.0:1.0	.	213	P18428	LBP_HUMAN	P	213	ENSP00000217407:L213P	ENSP00000217407:L213P	L	+	2	0	LBP	36422821	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.379000	0.59575	2.225000	0.72522	0.533000	0.62120	CTC	.	.		0.418	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139		C	36989407	T	C	36989407	3	2	103	1	0	0	0	0	1	0	0	0	8660	1551	54	2	660	2	LBP	20	36989407	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	147295	36989407	26036113	1105	15728										
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42143323	42143323	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acatggcgggagtggagcagCccccgagccccgagctgcgg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:42143323delC	ENST00000427442.2	+	4	502	c.343delC	c.(343-345)cccfs	p.P116fs	L3MBTL1_ENST00000373135.3_Frame_Shift_Del_p.P48fs|L3MBTL1_ENST00000444063.1_Frame_Shift_Del_p.P48fs|L3MBTL1_ENST00000418998.1_Frame_Shift_Del_p.P116fs|L3MBTL1_ENST00000373134.1_Frame_Shift_Del_p.P48fs|L3MBTL1_ENST00000457824.1_3'UTR			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	48					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						AGTGGAGCAGCCCCCGAGCCC	0.682																																					p.Q114fs		Atlas-INDEL	.											.	L3MBTL1	105	.	0			c.342delG						.						19	20	20					20																	42143323		2180	4274	6454	SO:0001589	frameshift_variant	26013	exon4			.	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.343delC	chr20.hg19:g.42143323delC	ENSP00000402107:p.Pro116fs	104.0	0.0		160.0	10.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Frame_Shift_Del	DEL	ENST00000427442.2	hg19	CCDS46602.2																																																																																			.	.		0.682	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		-	42143323	C	-	42143323	7	5	103	1	0	1	0	1	0	0	0	0	8600	739	26	0	141	0	L3MBTL	20	42143323	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	5153916	42143323	20882197	1106	15729										
IFT52	51098	hgsc.bcm.edu	37	chr20	42249541	42249541	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acaggagacatccacctaaaCcagattgatgctgaggaccc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:42249541delC	ENST00000373030.3	+	9	874	c.744delC	c.(742-744)aacfs	p.N248fs	IFT52_ENST00000373039.4_Frame_Shift_Del_p.N248fs	NM_016004.2	NP_057088.2	Q9Y366	IFT52_HUMAN	intraflagellar transport 52	248					cilium morphogenesis (GO:0060271)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube formation (GO:0001841)|regulation of protein processing (GO:0070613)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)	protein C-terminus binding (GO:0008022)			endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TCCACCTAAACCAGATTGATG	0.368																																					p.N248fs		Atlas-INDEL	.											.	IFT52	40	.	0			c.743delA						.						96	101	99					20																	42249541		2203	4300	6503	SO:0001589	frameshift_variant	51098	exon9			.	AF151811	CCDS33470.1	20q12-q13.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000101052	ENSG00000101052		"Intraflagellar transport homologs"	15901	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 9", "intraflagellar transport 52 homolog (Chlamydomonas)"	C20orf9		10810093	Standard	NM_016004		Approved	CGI-53, NGD5, dJ1028D15.1, NGD2	uc002xkw.3	Q9Y366	OTTHUMG00000032513	ENST00000373030.3:c.744delC	chr20.hg19:g.42249541delC	ENSP00000362121:p.Asn248fs	160.0	0.0		169.0	11.0	NM_016004	B3KMA1|E1P5W9|Q5H8Z0|Q9H1G3|Q9H1G4|Q9H1H2	Frame_Shift_Del	DEL	ENST00000373030.3	hg19	CCDS33470.1																																																																																			.	.		0.368	IFT52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079317.1	NM_016004		-	42249541	C	-	42249541	7	5	103	1	0	1	0	1	0	0	0	0	7570	506	18	0	774	0	IFT52	20	42249541	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	106218	42249541	20775979	1107	15730										
TOX2	84969	hgsc.bcm.edu	37	chr20	42694616	42694616	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgcaccagcagctgtcactgCcccctcacgcccagggcgcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:42694616delC	ENST00000358131.5	+	6	1379	c.1171delC	c.(1171-1173)cccfs	p.P392fs	TOX2_ENST00000372999.1_Frame_Shift_Del_p.P368fs|TOX2_ENST00000423191.2_Frame_Shift_Del_p.P368fs|TOX2_ENST00000341197.4_Frame_Shift_Del_p.P410fs|TOX2_ENST00000435864.2_3'UTR	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	392	Pro-rich.				female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			GCTGTCACTGCCCCCTCACGC	0.706																																					p.L408fs		Atlas-INDEL	.											.	TOX2	158	.	0			c.1224delG						.						27	30	29					20																	42694616		2202	4299	6501	SO:0001589	frameshift_variant	84969	exon7			.	BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"granulosa cell HMG box 1"	611163	"chromosome 20 open reading frame 100"	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.1171delC	chr20.hg19:g.42694616delC	ENSP00000350849:p.Pro392fs	115.0	0.0		206.0	16.0	NM_001098797	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Frame_Shift_Del	DEL	ENST00000358131.5	hg19	CCDS42875.1																																																																																			.	.		0.706	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2			-	42694616	C	-	42694616	7	5	103	1	0	1	0	1	0	0	0	0	16393	739	26	0	1381	0	TOX2	20	42694616	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	445075	42694616	20330904	1108	15731										
SEMG1	6406	hgsc.bcm.edu	37	chr20	43836178	43836178	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aatgatcatgaccagtcccgAaaaagtcagcaatatgattt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:43836178delA	ENST00000372781.3	+	2	297	c.240delA	c.(238-240)cgafs	p.R80fs	SEMG1_ENST00000244069.6_Frame_Shift_Del_p.R80fs	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	80	Repeat-rich region. {ECO:0000250}.				insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				ACCAGTCCCGAAAAAGTCAGC	0.383																																					p.R80fs		Atlas-INDEL	.											.	SEMG1	71	.	0			c.239delG						.						148	133	138					20																	43836178		2203	4300	6503	SO:0001589	frameshift_variant	6406	exon2			.		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"semen coagulating protein", "cancer/testis antigen 103"	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.240delA	chr20.hg19:g.43836178delA	ENSP00000361867:p.Arg80fs	156.0	0.0		280.0	17.0	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Frame_Shift_Del	DEL	ENST00000372781.3	hg19	CCDS13345.1																																																																																			.	.		0.383	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007		-	43836178	A	-	43836178	7	5	103	1	0	1	0	1	0	0	0	0	14059	233	9	0	246	0	SEMG1	20	43836178	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1141562	43836178	19189342	1109	15732										
UBE2C	11065	hgsc.bcm.edu	37	chr20	44444540	44444540	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacatgctgccgagctctggAaaaaccccacaggtgagtcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:44444540delA	ENST00000356455.4	+	5	589	c.469delA	c.(469-471)aaafs	p.K157fs	UBE2C_ENST00000405520.1_Frame_Shift_Del_p.K118fs|UBE2C_ENST00000243893.6_3'UTR|UBE2C_ENST00000372568.4_Frame_Shift_Del_p.K118fs|UBE2C_ENST00000335046.3_Frame_Shift_Del_p.K139fs|UBE2C_ENST00000352551.5_Frame_Shift_Del_p.K128fs|UBE2C_ENST00000496085.1_3'UTR	NM_007019.2	NP_008950.1	O00762	UBE2C_HUMAN	ubiquitin-conjugating enzyme E2C	157					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cyclin catabolic process (GO:0008054)|exit from mitosis (GO:0010458)|free ubiquitin chain polymerization (GO:0010994)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			large_intestine(2)|lung(2)|skin(1)	5		Myeloproliferative disorder(115;0.0122)				CGAGCTCTGGAAAAACCCCAC	0.557																																					p.W156X		Atlas-INDEL	.											.	UBE2C	31	.	0			c.468delG						.						127	122	124					20																	44444540		2203	4300	6503	SO:0001589	frameshift_variant	11065	exon5			.	U73379	CCDS13370.1, CCDS13371.1, CCDS13372.1, CCDS13374.1, CCDS74733.1, CCDS74734.1	20q13.12	2007-02-05			ENSG00000175063	ENSG00000175063		"Ubiquitin-conjugating enzymes E2"	15937	protein-coding gene	gene with protein product		605574				9122200	Standard	NM_007019		Approved	UBCH10	uc002xpm.3	O00762	OTTHUMG00000033038	ENST00000356455.4:c.469delA	chr20.hg19:g.44444540delA	ENSP00000348838:p.Lys157fs	82.0	0.0		105.0	10.0	NM_007019	A6NP33|E1P5N7|G3XAB7	Frame_Shift_Del	DEL	ENST00000356455.4	hg19	CCDS13370.1																																																																																			.	.		0.557	UBE2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080309.2	NM_007019		-	44444540	A	-	44444540	7	5	103	1	0	1	0	1	0	0	0	0	16861	247	9	0	638	0	UBE2C	20	44444540	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	608362	44444540	18580980	1110	15733										
C20orf165	128497	hgsc.bcm.edu	37	chr20	44515612	44515612	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgtagtgtctcccagctagtCcccccagggcagcccctggc					rs529491989		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:44515612delC	ENST00000372519.3	-	2	272	c.228delG	c.(226-228)gggfs	p.G76fs		NM_080608.3	NP_542175.1	Q9BR10	SPT25_HUMAN	spermatogenesis associated 25	76					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCCAGCTAGTCCCCCCAGGGC	0.627																																					p.T77fs		Atlas-INDEL	.											.	.	.	.	0			c.229delA						.						98	104	102					20																	44515612		2203	4300	6503	SO:0001589	frameshift_variant	128497	exon2			.	AL008726	CCDS13383.1	20q13.12	2011-11-24	2011-11-24	2011-11-24	ENSG00000149634	ENSG00000149634			16158	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 165"	C20orf165		19240080	Standard	NM_080608		Approved	dJ337O18.8, TSG23	uc002xqf.3	Q9BR10	OTTHUMG00000032628	ENST00000372519.3:c.228delG	chr20.hg19:g.44515612delC	ENSP00000361597:p.Gly76fs	127.0	0.0		187.0	15.0	NM_080608		Frame_Shift_Del	DEL	ENST00000372519.3	hg19	CCDS13383.1																																																																																			.	.		0.627	SPATA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079541.1			-	44515612	C	-	44515612	7	5	103	1	0	1	0	1	0	0	0	0	2096	842	30	0	459	0	C20orf165	20	44515612	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	71072	44515612	18509908	1111	15734										
SLC35C2	51006	hgsc.bcm.edu	37	chr20	44979150	44979150	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cccagccccttcaaggccttGgggccaccatcaccttggga					rs199919922		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:44979150delG	ENST00000372227.1	-	10	1521	c.981delC	c.(979-981)cccfs	p.P327fs	SLC35C2_ENST00000243896.2_Frame_Shift_Del_p.P327fs|SLC35C2_ENST00000372229.1_Frame_Shift_Del_p.P194fs|SLC35C2_ENST00000493599.1_5'UTR|SLC35C2_ENST00000543605.1_Frame_Shift_Del_p.P356fs|SLC35C2_ENST00000372230.5_Frame_Shift_Del_p.P327fs|SLC35C2_ENST00000317734.8_Frame_Shift_Del_p.P306fs	NM_001281458.1|NM_001281460.1	NP_001268387.1|NP_001268389.1	Q9NQQ7	S35C2_HUMAN	solute carrier family 35 (GDP-fucose transporter), member C2	327					negative regulation of gene expression (GO:0010629)|positive regulation of Notch signaling pathway (GO:0045747)|protein O-linked fucosylation (GO:0036066)|transport (GO:0006810)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	16		Myeloproliferative disorder(115;0.0122)				TCAAGGCCTTGGGGCCACCAT	0.592																																					p.K328fs		Atlas-INDEL	.											.	SLC35C2	35	.	0			c.982delA						.						38	41	40					20																	44979150		2203	4300	6503	SO:0001589	frameshift_variant	51006	exon10			.		CCDS13396.1, CCDS13397.1, CCDS63292.1	20q13.12	2013-07-17	2013-07-17	2003-10-10	ENSG00000080189	ENSG00000080189		"Solute carriers"	17117	protein-coding gene	gene with protein product			"ovarian cancer overexpressed 1", "solute carrier family 35, member C2"	C20orf5, OVCOV1		10810093, 11549316	Standard	NM_173179		Approved	CGI-15, bA394O2.1	uc002xrq.3	Q9NQQ7	OTTHUMG00000033050	ENST00000372227.1:c.981delC	chr20.hg19:g.44979150delG	ENSP00000361301:p.Pro327fs	125.0	0.0		180.0	11.0	NM_173179	B7Z6V6|E1P5T0|Q53GK3|Q5JW05|Q96CJ8|Q9Y304	Frame_Shift_Del	DEL	ENST00000372227.1	hg19	CCDS13396.1																																																																																			.	.		0.592	SLC35C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080363.1	NM_015945		-	44979150	G	-	44979150	7	5	103	1	0	1	0	1	0	0	0	0	14595	1335	47	0	120	0	SLC35C2	20	44979150	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	463538	44979150	18046370	1112	15735										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52193620	52193620	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtaacatctttggcaccatcAaaaaatcttttcaaattttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:52193620delA	ENST00000371471.2	-	4	2108	c.1683delT	c.(1681-1683)tttfs	p.F561fs	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Frame_Shift_Del_p.F561fs			O75362	ZN217_HUMAN	zinc finger protein 217	561					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			TGGCACCATCAAAAAATCTTT	0.443																																					p.D562fs		Atlas-INDEL	.											.	ZNF217	227	.	0			c.1684delG						.						129	125	126					20																	52193620		2203	4300	6503	SO:0001589	frameshift_variant	7764	exon3			.	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1683delT	chr20.hg19:g.52193620delA	ENSP00000360526:p.Phe561fs	81.0	0.0		126.0	12.0	NM_006526	E1P5Y6|Q14DB8	Frame_Shift_Del	DEL	ENST00000371471.2	hg19	CCDS13443.1																																																																																			.	.		0.443	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		-	52193620	A	-	52193620	7	5	103	1	0	1	0	1	0	0	0	0	17787	127	5	0	1471	0	ZNF217	20	52193620	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	7214470	52193620	10831900	1113	15736										
SLCO4A1	28231	hgsc.bcm.edu	37	chr20	61303147	61303147	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tagcctgcttcttatacaagCccctgtcggagtcttcagat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:61303147delC	ENST00000370507.1	+	11	2167	c.2071delC	c.(2071-2073)cccfs	p.P691fs	SLCO4A1_ENST00000217159.1_Frame_Shift_Del_p.P691fs			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	691					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	CTTATACAAGCCCCTGTCGGA	0.612																																					p.K690fs	Pancreas(168;741 2006 10379 40139 45334)	Atlas-INDEL	.											.	SLCO4A1	65	.	0			c.2070delG						.						88	87	87					20																	61303147		2203	4300	6503	SO:0001589	frameshift_variant	28231	exon12			.	AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"Solute carriers"	10953	protein-coding gene	gene with protein product		612436	"solute carrier family 21 (organic anion transporter), member 12"	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.2071delC	chr20.hg19:g.61303147delC	ENSP00000359538:p.Pro691fs	134.0	0.0		182.0	11.0	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Frame_Shift_Del	DEL	ENST00000370507.1	hg19	CCDS13501.1																																																																																			.	.		0.612	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354		-	61303147	C	-	61303147	7	5	103	1	0	1	0	1	0	0	0	0	14744	739	26	0	2113	0	SLCO4A1	20	61303147	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	9109527	61303147	1722373	1114	15737										
OGFR	11054	hgsc.bcm.edu	37	chr20	61444462	61444462	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggctggacacagtgagaacGgggttgaggaggacacagaa					rs369405396		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:61444462delG	ENST00000290291.6	+	7	1520	c.1495delG	c.(1495-1497)gggfs	p.G499fs	OGFR_ENST00000370461.1_Frame_Shift_Del_p.G447fs	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	499					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CAGTGAGAACGGGGTTGAGGA	0.682																																					p.N498fs		Atlas-INDEL	.											OGFR,NS,carcinoma,0,1	OGFR	63	.	0			c.1494delC						.						21	24	23					20																	61444462		2164	4259	6423	SO:0001589	frameshift_variant	11054	exon7			.	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1495delG	chr20.hg19:g.61444462delG	ENSP00000290291:p.Gly499fs	63.0	0.0		152.0	10.0	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Frame_Shift_Del	DEL	ENST00000290291.6	hg19	CCDS13504.1																																																																																			.	.		0.682	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			-	61444462	G	-	61444462	7	5	103	1	0	1	0	1	0	0	0	0	10852	1116	39	0	1521	0	OGFR	20	61444462	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	141315	61444462	1581058	1115	15738										
SLC17A9	63910	hgsc.bcm.edu	37	chr20	61588797	61588797	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tctgtcttccctccaggattGggggtgagaaggtcatcctg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:61588797delG	ENST00000370351.4	+	3	393	c.262delG	c.(262-264)gggfs	p.G89fs	SLC17A9_ENST00000370349.3_Frame_Shift_Del_p.G83fs|SLC17A9_ENST00000488738.1_3'UTR	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	89					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						CTCCAGGATTGGGGGTGAGAA	0.642																																					p.I87fs		Atlas-INDEL	.											.	SLC17A9	54	.	0			c.261delT						.						74	81	78					20																	61588797		2175	4259	6434	SO:0001589	frameshift_variant	63910	exon3			.	AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"Solute carriers"	16192	protein-coding gene	gene with protein product		612107	"chromosome 20 open reading frame 59", "solute carrier family 17, member 9"	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.262delG	chr20.hg19:g.61588797delG	ENSP00000359376:p.Gly89fs	113.0	0.0		153.0	10.0	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Frame_Shift_Del	DEL	ENST00000370351.4	hg19	CCDS42901.1																																																																																			.	.		0.642	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082		-	61588797	G	-	61588797	7	5	103	1	0	1	0	1	0	0	0	0	14439	1348	47	0	272	0	SLC17A9	20	61588797	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	144335	61588797	1436723	1116	15739										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61981195	61981195	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgcacggagagggctggtctGggggtgggagctcagccgag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:61981195delG	ENST00000370263.4	-	5	1789	c.1568delC	c.(1567-1569)ccafs	p.P523fs	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	523					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GGGCTGGTCTGGGGGTGGGAG	0.687																																					p.P523fs		Atlas-INDEL	.											.	CHRNA4	98	.	0			c.1569delA						.						28	28	28					20																	61981195		2195	4297	6492	SO:0001589	frameshift_variant	1137	exon5			.		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1568delC	chr20.hg19:g.61981195delG	ENSP00000359285:p.Pro523fs	68.0	0.0		147.0	10.0	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Frame_Shift_Del	DEL	ENST00000370263.4	hg19	CCDS13517.1																																																																																			.	.		0.687	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			-	61981195	G	-	61981195	7	5	103	1	0	1	0	1	0	0	0	0	3387	1348	47	0	323	0	CHRNA4	20	61981195	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	392398	61981195	1044325	1117	15740										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19770597	19770597	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggattatatgtaactccggaTgttattttaaatgtcgctct	8	6	1	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:19770597T>C	ENST00000284885.3	-	2	228	c.195A>G	c.(193-195)acA>acG	p.T65T		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	65	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.		T -> I (in dbSNP:rs35987974).			brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TAACTCCGGATGTTATTTTAA	0.378																																					p.T65T		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A195G						.						79	81	80					21																	19770597		2203	4300	6503	SO:0001819	synonymous_variant	5651	exon2			TCCGGATGTTATT		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.195A>G	chr21.hg19:g.19770597T>C		44.0	0.0		71.0	23.0	NM_002772	Q2NKL7	Silent	SNP	ENST00000284885.3	hg19	CCDS13571.1																																																																																			.	.		0.378	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		C	19770597	T	C	19770597	2	2	103	1	0	0	0	0	0	0	0	1	16261	1451	51	2		2	TMPRSS15	21	19770597	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10		19770597	28359298	1118	15741										
HUNK	30811	hgsc.bcm.edu	37	chr21	33312481	33312481	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttttgtttatttcagagacTtgaagatagagaatttgcta	9	3	1	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:33312481T>C	ENST00000270112.2	+	3	919	c.559T>C	c.(559-561)Ttg>Ctg	p.L187L		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	187	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						TTTCAGAGACTTGAAGATAGA	0.303																																					p.L187L		Atlas-SNP	.											.	HUNK	74	.	0			c.T559C						.						122	119	120					21																	33312481		2201	4298	6499	SO:0001819	synonymous_variant	30811	exon3			AGAGACTTGAAGA	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"hormonally upregulated Neu-associated kinase"			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.559T>C	chr21.hg19:g.33312481T>C		57.0	0.0		50.0	4.0	NM_014586		Silent	SNP	ENST00000270112.2	hg19	CCDS13610.1																																																																																			.	.		0.303	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		C	33312481	T	C	33312481	2	2	103	1	0	0	0	0	0	0	0	1	7467	1606	56	2		2	HUNK	21	33312481	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	13541884	33312481	14817414	1119	15742										
IFNAR1	3454	hgsc.bcm.edu	37	chr21	34707933	34707933	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagtctgtcgggaatgtgacTttttcattcgattatcaaaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:34707933delT	ENST00000270139.3	+	2	332	c.180delT	c.(178-180)actfs	p.T60fs	IFNAR1_ENST00000416947.2_5'UTR|IFNAR1_ENST00000442357.2_Frame_Shift_Del_p.T60fs	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	60	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""Interferon Alfa-2a(DB00034)|""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"	GGAATGTGACTTTTTCATTCG	0.338																																					p.T60fs	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-INDEL	.											.	IFNAR1	44	.	0			c.179delC						.						132	119	124					21																	34707933		2203	4300	6503	SO:0001589	frameshift_variant	3454	exon2			.		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"Interferons"	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.180delT	chr21.hg19:g.34707933delT	ENSP00000270139:p.Thr60fs	99.0	0.0		116.0	11.0	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Frame_Shift_Del	DEL	ENST00000270139.3	hg19	CCDS13624.1																																																																																			.	.		0.338	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4			-	34707933	T	-	34707933	7	5	103	1	0	1	0	1	0	0	0	0	7553	1596	56	0	186	0	IFNAR1	21	34707933	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1395452	34707933	13421962	1120	15743										
GART	2618	hgsc.bcm.edu	37	chr21	34882122	34882122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttaagacagccactctggccTtttttttttcaaaagagaaa	6	8	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:34882122T>C	ENST00000381831.3	-	18	2683	c.2420A>G	c.(2419-2421)aAg>aGg	p.K807R	GART_ENST00000543717.1_Missense_Mutation_p.K359R|GART_ENST00000381839.3_Missense_Mutation_p.K807R|GART_ENST00000381815.4_Missense_Mutation_p.K807R	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	807	AIRS.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)	p.K807fs*7(2)		NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	CACTCTGGCCTTTTTTTTTTC	0.448																																					p.K807R		Atlas-SNP	.											.,5	GART	81	.	2	Deletion - Frameshift(2)	ovary(2)	c.A2420G						.						66	70	68					21																	34882122		2203	4300	6503	SO:0001583	missense	2618	exon18			CTGGCCTTTTTTT	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2420A>G	chr21.hg19:g.34882122T>C	ENSP00000371253:p.Lys807Arg	62.0	1.0		69.0	3.0	NM_001136005	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	hg19	CCDS13627.1	.	.	.	.	.	.	.	.	.	.	T	8.259	0.810646	0.16537	.	.	ENSG00000159131	ENST00000414353;ENST00000381815;ENST00000381831;ENST00000381839;ENST00000543717	T;T;T;T	0.46063	1.46;1.46;1.46;0.88	5.52	1.39	0.22231	.	0.269064	0.42420	N	0.000720	T	0.19927	0.0479	N	0.08118	0	0.42171	D	0.991646	B	0.09022	0.002	B	0.12156	0.007	T	0.05699	-1.0869	10	0.20046	T	0.44	-12.4071	9.947	0.41616	0.0:0.2362:0.0:0.7638	.	807	P22102	PUR2_HUMAN	R	71;807;807;807;359	ENSP00000371236:K807R;ENSP00000371253:K807R;ENSP00000371261:K807R;ENSP00000443579:K359R	ENSP00000371236:K807R	K	-	2	0	GART	33803992	1.000000	0.71417	0.803000	0.32268	0.561000	0.35649	1.563000	0.36364	0.393000	0.25203	0.482000	0.46254	AAG	.	.		0.448	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819		C	34882122	T	C	34882122	3	2	103	1	0	0	0	0	1	0	0	0	6251	1609	56	2	632	2	GART	21	34882122	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	174189	34882122	13247773	1121	15744										
DONSON	29980	hgsc.bcm.edu	37	chr21	34954281	34954281	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgatagaaagtatgtctggcTttttaattttatcttgcaca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:34954281delT	ENST00000303071.5	-	7	1193	c.1127delA	c.(1126-1128)aagfs	p.K376fs	DONSON_ENST00000432378.1_Frame_Shift_Del_p.K376fs|DONSON_ENST00000453626.1_Frame_Shift_Del_p.K376fs|DONSON_ENST00000303113.6_Frame_Shift_Del_p.K362fs	NM_017613.3	NP_060083.1	Q9NYP3	DONS_HUMAN	downstream neighbor of SON	376					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|ovary(1)	11						TATGTCTGGCTTTTTAATTTT	0.368																																					p.K376fs		Atlas-INDEL	.											.	DONSON	34	.	0			c.1128delG						.						98	98	98					21																	34954281		2203	4300	6503	SO:0001589	frameshift_variant	29980	exon7			.	AF000002	CCDS13632.1	21q22.1	2008-07-31			ENSG00000159147	ENSG00000159147			2993	protein-coding gene	gene with protein product		611428		C21orf60		10773462, 10950926	Standard	NM_017613		Approved	B17, C2TA, DKFZP434M035	uc002ysk.4	Q9NYP3	OTTHUMG00000065904	ENST00000303071.5:c.1127delA	chr21.hg19:g.34954281delT	ENSP00000307143:p.Lys376fs	195.0	0.0		164.0	11.0	NM_017613	Q8NC53|Q9NSR9|Q9NVZ5|Q9NYP1|Q9NYP2	Frame_Shift_Del	DEL	ENST00000303071.5	hg19	CCDS13632.1																																																																																			.	.		0.368	DONSON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141184.1	NM_017613		-	34954281	T	-	34954281	7	5	103	1	0	1	0	1	0	0	0	0	4708	1609	56	0	589	0	DONSON	21	34954281	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	72159	34954281	13175614	1122	15745										
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38852951	38852951	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcatttcaggtttactatgcAaaaaagaagcgaagacacca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:38852951delA	ENST00000398960.2	+	4	414	c.339delA	c.(337-339)gcafs	p.A113fs	DYRK1A_ENST00000321219.8_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000451934.1_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000398956.2_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000339659.4_Frame_Shift_Del_p.A104fs|DYRK1A_ENST00000462274.1_3'UTR|DYRK1A_ENST00000338785.3_Frame_Shift_Del_p.A113fs	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	113					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TTTACTATGCAAAAAAGAAGC	0.363																																					p.A113fs	Melanoma(114;464 1602 31203 43785 45765)	Atlas-INDEL	.											.	DYRK1A	85	.	0			c.338delC						.						98	97	98					21																	38852951		2203	4300	6503	SO:0001589	frameshift_variant	1859	exon4			.	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.339delA	chr21.hg19:g.38852951delA	ENSP00000381932:p.Ala113fs	101.0	0.0		108.0	10.0	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Frame_Shift_Del	DEL	ENST00000398960.2	hg19	CCDS42925.1																																																																																			.	.		0.363	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		-	38852951	A	-	38852951	7	5	103	1	0	1	0	1	0	0	0	0	4856	117	5	0	353	0	DYRK1A	21	38852951	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3898670	38852951	9276944	1123	15746										
ERG	2078	hgsc.bcm.edu	37	chr21	39755389	39755389	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcctagtgttggggtatataCccccagttggtgaattccag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:39755389delC	ENST00000417133.2	-	12	1582	c.1397delG	c.(1396-1398)ggtfs	p.G466fs	ERG_ENST00000398905.1_Frame_Shift_Del_p.G435fs|ERG_ENST00000398919.2_Frame_Shift_Del_p.G466fs|ERG_ENST00000398910.1_Frame_Shift_Del_p.G443fs|ERG_ENST00000453032.2_Frame_Shift_Del_p.G367fs|ERG_ENST00000288319.7_Frame_Shift_Del_p.G459fs|ERG_ENST00000398907.1_Frame_Shift_Del_p.G436fs|ERG_ENST00000398911.1_Frame_Shift_Del_p.G442fs|ERG_ENST00000442448.1_Frame_Shift_Del_p.G442fs|ERG_ENST00000398897.1_Frame_Shift_Del_p.G343fs	NM_001136154.1|NM_001243432.1	NP_001129626.1|NP_001230361.1	Q12809	KCNH2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog	0					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)		EWSR1/ERG(178)|NDRG1/ERG(5)|TMPRSS2/ERG(3582)|FUS/ERG(167)|SLC45A3/ERG(50)	lung(2)|ovary(1)|skin(1)	4		Prostate(19;3.6e-06)			Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GGGGTATATACCCCCAGTTGG	0.537			T	"EWSR1, TMPRSS2, ELF4, FUS, HERPUD1, NDRG1"	"Ewing sarcoma, prostate, AML"																																p.G466fs	Esophageal Squamous(130;336 1700 3010 3083 40589)	Atlas-INDEL	.		Dom	yes		21	21q22.3	2078	v-ets erythroblastosis virus E26 oncogene like (avian)		"M, E, L"	.	ERG	78	.	0			c.1398delT						.						34	35	35					21																	39755389		2203	4300	6503	SO:0001589	frameshift_variant	2078	exon12			.		CCDS13657.1, CCDS13658.1, CCDS46648.1, CCDS46649.1, CCDS58789.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157554	ENSG00000157554			3446	protein-coding gene	gene with protein product	"v-ets avian erythroblastosis virus E26 oncogene related", "transcriptional regulator ERG (transforming protein ERG)", "v-ets erythroblastosis virus E26 oncogene like", "TMPRSS2-ERG prostate cancer specific"	165080	"v-ets avian erythroblastosis virus E26 oncogene related"			3274086	Standard	NM_001136154		Approved	erg-3, p55	uc002yxa.3	P11308	OTTHUMG00000090767	ENST00000417133.2:c.1397delG	chr21.hg19:g.39755389delC	ENSP00000414150:p.Gly466fs	131.0	0.0		150.0	10.0	NM_001136154	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Frame_Shift_Del	DEL	ENST00000417133.2	hg19	CCDS46648.1																																																																																			.	.		0.537	ERG-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207532.2	NM_182918		-	39755389	C	-	39755389	7	5	103	1	0	1	0	1	0	0	0	0	5224	507	18	0	67	0	ERG	21	39755389	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	902438	39755389	8374506	1124	15747										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41452224	41452224	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggggctgattggaaaactCccccactgctcactattgtc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:41452224delC	ENST00000400454.1	-	25	4752	c.4275delG	c.(4273-4275)gggfs	p.G1425fs		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1425	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TTGGAAAACTCCCCCACTGCT	0.478																																					p.S1426fs	Melanoma(134;970 1778 1785 21664 32388)	Atlas-INDEL	.											.	DSCAM	347	.	0			c.4276delA						.						106	99	101					21																	41452224		1904	4126	6030	SO:0001589	frameshift_variant	1826	exon25			.	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4275delG	chr21.hg19:g.41452224delC	ENSP00000383303:p.Gly1425fs	180.0	0.0		179.0	11.0	NM_001271534	O60468	Frame_Shift_Del	DEL	ENST00000400454.1	hg19	CCDS42929.1																																																																																			.	.		0.478	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		-	41452224	C	-	41452224	7	5	103	1	0	1	0	1	0	0	0	0	4770	842	30	0	1799	0	DSCAM	21	41452224	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1696835	41452224	6677671	1125	15748										
MX2	4600	hgsc.bcm.edu	37	chr21	42767625	42767625	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctacatgattgtgaagtgccGgggccagcaggagatcacaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:42767625delG	ENST00000330714.3	+	7	1167	c.983delG	c.(982-984)cggfs	p.R328fs	MX2_ENST00000543692.1_3'UTR|MX2_ENST00000496774.1_3'UTR	NM_002463.1	NP_002454.1	P20592	MX2_HUMAN	MX dynamin-like GTPase 2	328	Dynamin-type G.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|GTP catabolic process (GO:0006184)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of nucleocytoplasmic transport (GO:0046822)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R328Q(1)		breast(2)|endometrium(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	34		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				GTGAAGTGCCGGGGCCAGCAG	0.483																																					p.R328fs		Atlas-INDEL	.											.	MX2	84	.	1	Substitution - Missense(1)	large_intestine(1)	c.982delC						.						109	99	102					21																	42767625		2203	4300	6503	SO:0001589	frameshift_variant	4600	exon7			.		CCDS13672.1	21q22.3	2014-07-15	2014-07-15		ENSG00000183486	ENSG00000183486			7533	protein-coding gene	gene with protein product	"interferon-regulated resistance GTP-binding protein MXB", "second interferon-induced protein p78"	147890	"myxovirus (influenza) resistance 2, homolog of murine", "myxovirus (influenza virus) resistance 2 (mouse)"			2481229, 8798556	Standard	NM_002463		Approved	MXB	uc002yzf.1	P20592	OTTHUMG00000086753	ENST00000330714.3:c.983delG	chr21.hg19:g.42767625delG	ENSP00000333657:p.Arg328fs	138.0	0.0		151.0	10.0	NM_002463	B7Z5D3|D3DSI7	Frame_Shift_Del	DEL	ENST00000330714.3	hg19	CCDS13672.1																																																																																			.	.		0.483	MX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195147.1	NM_002463		-	42767625	G	-	42767625	7	5	103	1	0	1	0	1	0	0	0	0	10007	1116	39	0	1005	0	MX2	21	42767625	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1315401	42767625	5362270	1126	15749										
PRDM15	63977	hgsc.bcm.edu	37	chr21	43256618	43256618	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcaggttgctgctgttctggAagatcttgctgcagatattg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:43256618delA	ENST00000269844.3	-	16	2350	c.2240delT	c.(2239-2241)ttcfs	p.F747fs	PRDM15_ENST00000398548.1_Frame_Shift_Del_p.F418fs|PRDM15_ENST00000447207.2_Frame_Shift_Del_p.F381fs|PRDM15_ENST00000538201.1_Frame_Shift_Del_p.F381fs|PRDM15_ENST00000422911.1_Frame_Shift_Del_p.F418fs	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	747					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						GCTGTTCTGGAAGATCTTGCT	0.627																																					p.F747fs		Atlas-INDEL	.											.	PRDM15	110	.	0			c.2241delC						.						172	158	163					21																	43256618		2203	4300	6503	SO:0001589	frameshift_variant	63977	exon16			.	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.2240delT	chr21.hg19:g.43256618delA	ENSP00000269844:p.Phe747fs	179.0	0.0		204.0	14.0	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Frame_Shift_Del	DEL	ENST00000269844.3	hg19	CCDS13676.1																																																																																			.	.		0.627	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		-	43256618	A	-	43256618	7	5	103	1	0	1	0	1	0	0	0	0	12468	246	9	0	2347	0	PRDM15	21	43256618	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	488993	43256618	4873277	1127	15750										
RRP1	8568	hgsc.bcm.edu	37	chr21	45222190	45222190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atgagatcccagagaaggccTgcaggcgcctgcttgaaggg	15	10	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:45222190T>C	ENST00000497547.1	+	12	1162	c.1045T>C	c.(1045-1047)Tgc>Cgc	p.C349R	RRP1_ENST00000471909.1_3'UTR	NM_003683.5	NP_003674.1	P05386	RLA1_HUMAN	ribosomal RNA processing 1	0					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|lung(4)|stomach(2)	8				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)		AGAGAAGGCCTGCAGGCGCCT	0.587																																					p.C349R		Atlas-SNP	.											.	RRP1	23	.	0			c.T1045C						.						77	87	84					21																	45222190		1900	4120	6020	SO:0001583	missense	8568	exon12			AAGGCCTGCAGGC	U79775	CCDS42951.1	21q22.3	2013-07-02	2013-07-02		ENSG00000160214	ENSG00000160214			18785	protein-coding gene	gene with protein product	"DNA segment on chromosome 21 (unique) 2056 expressed sequence", "Nnp1 homolog, nucleolar protein (Drosophila)"	610653	"ribosomal RNA processing 1 homolog (S. cerevisiae)"			10830953, 10341208	Standard	NM_003683		Approved	NNP-1, Nop52, NOP52, RRP1A, D21S2056E	uc002zds.2	P56182	OTTHUMG00000086884	ENST00000497547.1:c.1045T>C	chr21.hg19:g.45222190T>C	ENSP00000417464:p.Cys349Arg	90.0	0.0		77.0	4.0	NM_003683	A6NIB2	Missense_Mutation	SNP	ENST00000497547.1	hg19	CCDS42951.1	.	.	.	.	.	.	.	.	.	.	T	8.391	0.839676	0.16891	.	.	ENSG00000160214	ENST00000497547;ENST00000400387	T	0.00940	5.52	3.23	3.23	0.37069	.	0.652897	0.15680	N	0.249974	T	0.01156	0.0038	N	0.22421	0.69	0.09310	N	0.999997	P;D;B	0.56521	0.697;0.976;0.396	B;P;B	0.47528	0.201;0.549;0.059	T	0.56631	-0.7947	10	0.87932	D	0	.	8.2511	0.31717	0.0:0.0:0.0:1.0	.	349;216;349	B4DZM3;Q96J73;P56182	.;.;RRP1_HUMAN	R	349	ENSP00000417464:C349R	ENSP00000383237:C349R	C	+	1	0	RRP1	44046618	0.178000	0.23122	0.005000	0.12908	0.070000	0.16714	2.964000	0.49192	1.735000	0.51646	0.459000	0.35465	TGC	.	.		0.587	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683		C	45222190	T	C	45222190	3	2	103	1	0	0	0	0	1	0	0	0	13700	1580	55	2	1091	2	RRP1	21	45222190	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1965572	45222190	2907705	1128	15751										
KRTAP10-4	386672	hgsc.bcm.edu	37	chr21	45993943	45993943	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctggcttgctgtgcctcctCcccctgccagcaggcctgct					rs587672472		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:45993943delC	ENST00000400374.3	+	1	338	c.308delC	c.(307-309)tccfs	p.S103fs	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_5'Flank	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	103	36 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						TGTGCCTCCTCCCCCTGCCAG	0.657																																					p.S103fs		Atlas-INDEL	.											.	KRTAP10-4	44	.	0			c.307delT						.						15	15	15					21																	45993943		2086	4131	6217	SO:0001589	frameshift_variant	386672	exon1			.	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"Keratin associated proteins"	20521	protein-coding gene	gene with protein product			"keratin associated protein 18-4"	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.308delC	chr21.hg19:g.45993943delC	ENSP00000383225:p.Ser103fs	230.0	0.0		262.0	17.0	NM_198687	Q08AS0	Frame_Shift_Del	DEL	ENST00000400374.3	hg19	CCDS42957.1																																																																																			.	.		0.657	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687		-	45993943	C	-	45993943	7	5	103	1	0	1	0	1	0	0	0	0	8520	855	30	0	310	0	KRTAP10-4	21	45993943	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	771753	45993943	2135952	1129	15752										
ITGB2	3689	hgsc.bcm.edu	37	chr21	46309403	46309403	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cacttcccgcagaagcagagCcccctccctggaagacgggg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:46309403delC	ENST00000397850.2	-	14	2117	c.1665delG	c.(1663-1665)gggfs	p.G555fs	ITGB2_ENST00000355153.4_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000397854.3_Frame_Shift_Del_p.G498fs|ITGB2_ENST00000302347.5_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000397857.1_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000397852.1_Frame_Shift_Del_p.G555fs			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	555	Cysteine-rich tandem repeats.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	AGAAGCAGAGCCCCCTCCCTG	0.697																																					p.L556fs		Atlas-INDEL	.											.	ITGB2	107	.	0			c.1666delC						.						24	20	22					21																	46309403		2160	4257	6417	SO:0001589	frameshift_variant	3689	exon13			.	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.1665delG	chr21.hg19:g.46309403delC	ENSP00000380948:p.Gly555fs	159.0	0.0		174.0	11.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Frame_Shift_Del	DEL	ENST00000397850.2	hg19	CCDS13716.1																																																																																			.	.		0.697	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		-	46309403	C	-	46309403	7	5	103	1	0	1	0	1	0	0	0	0	7903	726	26	0	660	0	ITGB2	21	46309403	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	315460	46309403	1820492	1130	15753										
PCBP3	54039	hgsc.bcm.edu	37	chr21	47320946	47320946	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacatctcagagggaaactgCccagagaggattgtgaccat	11	9	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:47320946C>A	ENST00000400314.1	+	7	596	c.258C>A	c.(256-258)tgC>tgA	p.C86*	PCBP3_ENST00000400310.1_Nonsense_Mutation_p.C86*|PCBP3_ENST00000400309.1_Nonsense_Mutation_p.C86*|PCBP3_ENST00000400304.1_Nonsense_Mutation_p.C54*|PCBP3_ENST00000400308.1_Nonsense_Mutation_p.C86*|PCBP3_ENST00000449640.1_Nonsense_Mutation_p.C86*			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	86	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		AGGGAAACTGCCCAGAGAGGA	0.557																																					p.C86X		Atlas-SNP	.											.	PCBP3	82	.	0			c.C258A						.						99	111	107					21																	47320946		2007	4160	6167	SO:0001587	stop_gained	54039	exon5			AAACTGCCCAGAG	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"poly(rC)-binding protein 3"			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.258C>A	chr21.hg19:g.47320946C>A	ENSP00000383168:p.Cys86*	93.0	0.0		89.0	12.0	NM_001130141	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Nonsense_Mutation	SNP	ENST00000400314.1	hg19	CCDS42974.2	.	.	.	.	.	.	.	.	.	.	C	39	7.893716	0.98548	.	.	ENSG00000183570	ENST00000400314;ENST00000400310;ENST00000400309;ENST00000400308;ENST00000449640;ENST00000346743;ENST00000400305;ENST00000400304	.	.	.	4.86	2.07	0.26955	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6788	9.6505	0.39895	0.0:0.6423:0.0:0.3577	.	.	.	.	X	86;86;86;86;86;86;62;54	.	ENSP00000330225:C86X	C	+	3	2	PCBP3	46145374	0.884000	0.30299	1.000000	0.80357	0.992000	0.81027	-0.039000	0.12124	0.230000	0.21059	-0.136000	0.14681	TGC	.	.		0.557	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2			A	47320946	C	A	47320946	4	1	103	1	0	0	0	0	0	1	0	0	11511	747	26	3	276	3	PCBP3	21	47320946	Nonsense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	1011543	47320946	808949	1131	15754										
COL6A1	1291	hgsc.bcm.edu	37	chr21	47418082	47418082	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accgagggcttccccggcttCcccgtaagtgtccggaggct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:47418082delC	ENST00000361866.3	+	23	1686	c.1572delC	c.(1570-1572)ttcfs	p.F524fs		NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	524	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		TCCCCGGCTTCCCCGTAAGTG	0.682																																					p.F524fs		Atlas-INDEL	.											.	COL6A1	101	.	0			c.1571delT						.						23	29	27					21																	47418082		2197	4296	6493	SO:0001589	frameshift_variant	1291	exon23			.	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"Collagens"	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.1572delC	chr21.hg19:g.47418082delC	ENSP00000355180:p.Phe524fs	89.0	0.0		140.0	10.0	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Frame_Shift_Del	DEL	ENST00000361866.3	hg19	CCDS13727.1																																																																																			.	.		0.682	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		-	47418082	C	-	47418082	7	5	103	1	0	1	0	1	0	0	0	0	3701	854	30	0	1662	0	COL6A1	21	47418082	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	97136	47418082	711813	1132	15755										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47700452	47700452	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agatagccatgtctttatgcAaacttttccccttctttcta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:47700452delA	ENST00000397708.1	-	4	1735	c.1481delT	c.(1480-1482)ttgfs	p.L494fs	MCM3AP_ENST00000291688.1_Frame_Shift_Del_p.L494fs			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	494	DNA primase.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					GTCTTTATGCAAACTTTTCCC	0.348																																					p.L494fs		Atlas-INDEL	.											.	MCM3AP	146	.	0			c.1482delG						.						74	79	77					21																	47700452		2203	4300	6503	SO:0001589	frameshift_variant	8888	exon3			.	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.1481delT	chr21.hg19:g.47700452delA	ENSP00000380820:p.Leu494fs	228.0	0.0		261.0	16.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Frame_Shift_Del	DEL	ENST00000397708.1	hg19	CCDS13734.1																																																																																			.	.		0.348	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		-	47700452	A	-	47700452	7	5	103	1	0	1	0	1	0	0	0	0	9397	131	5	0	4565	0	MCM3AP	21	47700452	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	282370	47700452	429443	1133	15756										
DIP2A	23181	hgsc.bcm.edu	37	chr21	47977529	47977529	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gacaccaatcagtgctggtgCccccgctggagctggagagc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:47977529delC	ENST00000417564.2	+	31	3682	c.3661delC	c.(3661-3663)cccfs	p.P1222fs	DIP2A_ENST00000318711.7_Frame_Shift_Del_p.P1223fs|DIP2A_ENST00000400274.1_Frame_Shift_Del_p.P1218fs			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1222					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		AGTGCTGGTGCCCCCGCTGGA	0.642																																					p.V1220fs		Atlas-INDEL	.											.	DIP2A	332	.	0			c.3660delG						.						34	42	40					21																	47977529		2116	4213	6329	SO:0001589	frameshift_variant	23181	exon31			.	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.3661delC	chr21.hg19:g.47977529delC	ENSP00000392066:p.Pro1222fs	124.0	0.0		125.0	11.0	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Frame_Shift_Del	DEL	ENST00000417564.2	hg19	CCDS46655.1																																																																																			.	.		0.642	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		-	47977529	C	-	47977529	7	5	103	1	0	1	0	1	0	0	0	0	4529	739	26	0	3896	0	DIP2A	21	47977529	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	277077	47977529	152366	1134	15757										
CECR1	51816	hgsc.bcm.edu	37	chr22	17690247	17690247	+	Splice_Site	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	acccctttccaaaccttaccTtttggcatcatccttagaat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:17690247delT	ENST00000399839.1	-	2	591	c.321delA	c.(319-321)aaa>aa	p.K107fs	CECR1_ENST00000262607.3_Splice_Site_p.K107fs|CECR1_ENST00000399837.2_Splice_Site_p.K107fs|CECR1_ENST00000449907.2_Splice_Site_p.K65fs	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	107					adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				AAACCTTACCTTTTGGCATCA	0.483																																					p.G108fs		Atlas-INDEL	.											.	CECR1	77	.	0			c.322delG						.						56	53	54					22																	17690247		2203	4300	6503	SO:0001630	splice_region_variant	51816	exon1			.	AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.322+1A>-	chr22.hg19:g.17690247delT		163.0	0.0		161.0	10.0	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Frame_Shift_Del	DEL	ENST00000399839.1	hg19	CCDS13742.1																																																																																			.	.		0.483	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1		Frame_Shift_Del	-	17690247	T	-	17690247	8	5	103	1	0	1	0	1	0	0	1	0	3207	1623	56	0	1284	0	CECR1	22	17690247	Splice_Site	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10		17690247	33614319	1135	15758										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18310443	18310443	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggactcagaggccggcgccaTcctctcttcctcctctctct	8	18	4	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:18310443T>C	ENST00000441493.2	-	22	3512	c.3160A>G	c.(3160-3162)Atg>Gtg	p.M1054V		NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1054	Glu-rich.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		GCCGGCGCCATCCTCTCTTCC	0.647																																					p.M1054V		Atlas-SNP	.											.	MICAL3	53	.	0			c.A3160G						.						20	24	22					22																	18310443		1995	4152	6147	SO:0001583	missense	57553	exon22			GCGCCATCCTCTC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.3160A>G	chr22.hg19:g.18310443T>C	ENSP00000416015:p.Met1054Val	86.0	0.0		60.0	5.0	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	T	3.985	-0.005707	0.07773	.	.	ENSG00000093100	ENST00000441493	T	0.61980	0.06	4.95	1.63	0.23807	.	.	.	.	.	T	0.50154	0.1599	L	0.42245	1.32	0.09310	N	0.999992	B	0.02656	0.0	B	0.01281	0.0	T	0.34601	-0.9822	9	0.29301	T	0.29	.	8.5145	0.33237	0.0:0.3186:0.0:0.6814	.	1054	Q7RTP6	MICA3_HUMAN	V	1054	ENSP00000416015:M1054V	ENSP00000416015:M1054V	M	-	1	0	XXbac-B461K10.4	16690443	0.004000	0.15560	0.006000	0.13384	0.554000	0.35429	0.207000	0.17395	0.039000	0.15632	0.448000	0.29417	ATG	.	.		0.647	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			C	18310443	T	C	18310443	3	2	103	1	0	0	0	0	1	0	0	0	9580	1435	50	2	2892	2	MICAL3	22	18310443	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	620196	18310443	32994123	1136	15759										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18387542	18387542	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcaataacaaccaccttggCccccagtaaggataagtcga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:18387542delC	ENST00000441493.2	-	3	680	c.328delG	c.(328-330)gccfs	p.A110fs	MICAL3_ENST00000383094.3_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000207726.7_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000400561.2_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000444520.1_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000429452.1_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000414725.2_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000585038.1_Frame_Shift_Del_p.A110fs	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	110	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		ACCACCTTGGCCCCCAGTAAG	0.532																																					p.A110fs		Atlas-INDEL	.											.	MICAL3	53	.	0			c.329delC						.						106	96	99					22																	18387542		1568	3582	5150	SO:0001589	frameshift_variant	57553	exon3			.	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.328delG	chr22.hg19:g.18387542delC	ENSP00000416015:p.Ala110fs	156.0	0.0		164.0	12.0	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Frame_Shift_Del	DEL	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.		0.532	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			-	18387542	C	-	18387542	7	5	103	1	0	1	0	1	0	0	0	0	9580	739	26	0	6537	0	MICAL3	22	18387542	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	77099	18387542	32917024	1137	15760										
PRODH	5625	hgsc.bcm.edu	37	chr22	18905911	18905911	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgccgcacgggctcgctcctGggccaggtatgcgccccgca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:18905911delG	ENST00000357068.6	-	11	1610	c.1345delC	c.(1345-1347)cagfs	p.Q449fs	PRODH_ENST00000334029.2_Frame_Shift_Del_p.Q341fs|PRODH_ENST00000420436.1_Frame_Shift_Del_p.Q341fs	NM_016335.4	NP_057419	O43272	PROD_HUMAN	proline dehydrogenase (oxidase) 1	449					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)	FAD binding (GO:0071949)|proline dehydrogenase activity (GO:0004657)			breast(1)|endometrium(3)|lung(4)|upper_aerodigestive_tract(1)	9					L-Proline(DB00172)	GCTCGCTCCTGGGCCAGGTAT	0.652																																					p.Q449fs		Atlas-INDEL	.											.	PRODH	42	.	0			c.1346delA						.						98	91	93					22																	18905911		2203	4300	6503	SO:0001589	frameshift_variant	5625	exon12			.	AF010310	CCDS13754.1, CCDS56223.1	22q11.2	2014-07-10	2001-12-05		ENSG00000100033	ENSG00000100033	1.5.5.2		9453	protein-coding gene	gene with protein product		606810	"proline dehydrogenase (proline oxidase )"			9385373, 10192398	Standard	NM_001195226		Approved	HSPOX2, PRODH1, PIG6, PRODH2, TP53I6	uc002zok.4	O43272	OTTHUMG00000150163	ENST00000357068.6:c.1345delC	chr22.hg19:g.18905911delG	ENSP00000349577:p.Gln449fs	169.0	0.0		224.0	14.0	NM_016335	A6NF53|O14680|Q0P507|Q147W8|Q504W1|Q59FI8|Q6NV86|Q9UF13	Frame_Shift_Del	DEL	ENST00000357068.6	hg19	CCDS13754.1																																																																																			.	.		0.652	PRODH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316637.2	NM_016335		-	18905911	G	-	18905911	7	5	103	1	0	1	0	1	0	0	0	0	12560	1357	47	0	473	0	PRODH	22	18905911	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	518369	18905911	32398655	1138	15761										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19189001	19189001	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcctcgtaacagcggtctcCaactacggataatagggtag	10	11	1	0	rs374660081		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:19189001C>A	ENST00000263200.10	-	23	3676	c.3604G>T	c.(3604-3606)Gga>Tga	p.G1202*	CLTCL1_ENST00000353891.5_Nonsense_Mutation_p.G1202*|CLTCL1_ENST00000442042.2_5'UTR|CLTCL1_ENST00000427926.1_Intron	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1202	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					CAGCGGTCTCCAACTACGGAT	0.483			T	?	ALCL																																p.G1202X		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.G3604T						.						73	77	76					22																	19189001		1951	4165	6116	SO:0001587	stop_gained	8218	exon23			GGTCTCCAACTAC		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.3604G>T	chr22.hg19:g.19189001C>A	ENSP00000445677:p.Gly1202*	85.0	0.0		102.0	7.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Nonsense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	C	39	7.894032	0.98548	.	.	ENSG00000070371	ENST00000353891;ENST00000263200	.	.	.	3.33	3.33	0.38152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.834	0.70169	0.0:1.0:0.0:0.0	.	.	.	.	X	1202	.	ENSP00000445677:G1202X	G	-	1	0	CLTCL1	17569001	1.000000	0.71417	0.981000	0.43875	0.267000	0.26476	6.846000	0.75399	1.668000	0.50843	0.491000	0.48974	GGA	.	.		0.483	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		A	19189001	C	A	19189001	4	1	103	1	0	0	0	0	0	1	0	0	3569	603	21	3	1358	3	CLTCL1	22	19189001	Nonsense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	283090	19189001	32115565	1139	15762										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19209481	19209481	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aaggacaccttacctatttcTtttttctacttcagccacca							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:19209481delT	ENST00000263200.10	-	16	2626	c.2554delA	c.(2554-2556)agafs	p.R852fs	CLTCL1_ENST00000353891.5_Frame_Shift_Del_p.R852fs|CLTCL1_ENST00000427926.1_Frame_Shift_Del_p.R852fs	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	852	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					TACCTATTTCTTTTTTCTACT	0.418			T	?	ALCL																																p.R852fs		Atlas-INDEL	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	CLTCL1,NS,carcinoma,0,1	CLTCL1	115	.	0			c.2555delG						.						111	115	114					22																	19209481		1941	4119	6060	SO:0001589	frameshift_variant	8218	exon16			.		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.2554delA	chr22.hg19:g.19209481delT	ENSP00000445677:p.Arg852fs	112.0	0.0		165.0	12.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Frame_Shift_Del	DEL	ENST00000263200.10	hg19	CCDS46662.1																																																																																			.	.		0.418	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		-	19209481	T	-	19209481	7	5	103	1	0	1	0	1	0	0	0	0	3569	1617	56	0	2436	0	CLTCL1	22	19209481	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	20480	19209481	32095085	1140	15763										
DGCR8	54487	hgsc.bcm.edu	37	chr22	20094164	20094164	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtttgaagtggttcctgggAaaaaccagaagagtgaatac							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:20094164delA	ENST00000351989.3	+	11	2368	c.1939delA	c.(1939-1941)aaafs	p.K647fs	DGCR8_ENST00000407755.1_Frame_Shift_Del_p.K614fs|DGCR8_ENST00000383024.2_Frame_Shift_Del_p.K614fs	NM_022720.6	NP_073557.3	Q8WYQ5	DGCR8_HUMAN	DGCR8 microprocessor complex subunit	647	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.|Necessary for heme-binding and pri-miRNA processing.|Necessary for interaction with DROSHA.				gene expression (GO:0010467)|primary miRNA processing (GO:0031053)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			NS(2)|breast(1)|endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	Colorectal(54;0.0993)					GGTTCCTGGGAAAAACCAGAA	0.557																																					p.G646fs		Atlas-INDEL	.											.	DGCR8	53	.	0			c.1938delG						.						137	129	132					22																	20094164		2203	4300	6503	SO:0001589	frameshift_variant	54487	exon11			.	AF165527, AB050770	CCDS13773.1, CCDS54501.1	22q11.2	2013-05-02	2013-05-02		ENSG00000128191	ENSG00000128191			2847	protein-coding gene	gene with protein product		609030	"chromosome 22 open reading frame 12", "DiGeorge syndrome critical region gene 8"	C22orf12		21454614	Standard	NM_001190326		Approved	DGCRK6, Gy1, pasha	uc002zri.3	Q8WYQ5	OTTHUMG00000150503	ENST00000351989.3:c.1939delA	chr22.hg19:g.20094164delA	ENSP00000263209:p.Lys647fs	195.0	0.0		230.0	14.0	NM_022720	B2R8G1|Q6DCB2|Q6MZE9|Q6Y2L0|Q96G39|Q96GP8|Q9H6L8|Q9H6T7|Q9NRW2	Frame_Shift_Del	DEL	ENST00000351989.3	hg19	CCDS13773.1																																																																																			.	.		0.557	DGCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318654.1			-	20094164	A	-	20094164	7	5	103	1	0	1	0	1	0	0	0	0	4466	247	9	0	1977	0	DGCR8	22	20094164	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	884683	20094164	31210402	1141	15764										
ZDHHC8	29801	hgsc.bcm.edu	37	chr22	20131139	20131139	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccggggccccggcccagcagTggctcacacaggtcacctgc	13	18	2	0			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:20131139T>C	ENST00000334554.7	+	10	2127	c.1986T>C	c.(1984-1986)agT>agC	p.S662S	ZDHHC8_ENST00000405930.3_Silent_p.S662S|ZDHHC8_ENST00000320602.7_Silent_p.S570S	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	662					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					GGCCCAGCAGTGGCTCACACA	0.711																																					p.S662S		Atlas-SNP	.											.	ZDHHC8	77	.	0			c.T1986C						.						15	17	17					22																	20131139		2187	4292	6479	SO:0001819	synonymous_variant	29801	exon10			CAGCAGTGGCTCA	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"Zinc fingers, DHHC-type"	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.1986T>C	chr22.hg19:g.20131139T>C		13.0	0.0		88.0	4.0	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	hg19	CCDS13776.1																																																																																			.	.		0.711	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373		C	20131139	T	C	20131139	2	2	103	1	0	0	0	0	0	0	0	1	17636	1693	59	2		2	ZDHHC8	22	20131139	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	36975	20131139	31173427	1142	15765										
PPIL2	23759	hgsc.bcm.edu	37	chr22	22043036	22043036	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tccaggtggggagtcatactGggggaagcccttcaaagacg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:22043036delG	ENST00000335025.8	+	15	1128	c.1037delG	c.(1036-1038)tggfs	p.W346fs	PPIL2_ENST00000446951.1_3'UTR|PPIL2_ENST00000492445.2_Frame_Shift_Del_p.W346fs|PPIL2_ENST00000456792.2_Frame_Shift_Del_p.W325fs|PPIL2_ENST00000412327.1_Frame_Shift_Del_p.W346fs|PPIL2_ENST00000398831.3_Frame_Shift_Del_p.W346fs|PPIL2_ENST00000406385.1_Frame_Shift_Del_p.W346fs					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					GAGTCATACTGGGGGAAGCCC	0.622																																					p.W346fs		Atlas-INDEL	.											.	PPIL2	38	.	0			c.1036delT						.						67	66	66					22																	22043036		2203	4300	6503	SO:0001589	frameshift_variant	23759	exon15			.		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"U-box domain containing"	9261	protein-coding gene	gene with protein product	"U-box domain containing 7"	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.1037delG	chr22.hg19:g.22043036delG	ENSP00000334553:p.Trp346fs	125.0	0.0		183.0	11.0	NM_014337		Frame_Shift_Del	DEL	ENST00000335025.8	hg19	CCDS13793.1																																																																																			.	.		0.622	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4			-	22043036	G	-	22043036	7	5	103	1	0	1	0	1	0	0	0	0	12339	1357	47	0	1095	0	PPIL2	22	22043036	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	1911897	22043036	29261530	1143	15766										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26164213	26164213	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	attctgggcaaggagagcgaGgggtcccgcagccccgaccc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:26164213delG	ENST00000407587.2	+	4	499	c.330delG	c.(328-330)gagfs	p.E110fs	MYO18B_ENST00000335473.7_Frame_Shift_Del_p.E110fs|MYO18B_ENST00000536101.1_Frame_Shift_Del_p.E110fs			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	110	Ser-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AGGAGAGCGAGGGGTCCCGCA	0.597																																					p.E110fs		Atlas-INDEL	.											.	MYO18B	322	.	0			c.329delA						.						59	66	64					22																	26164213		1980	4145	6125	SO:0001589	frameshift_variant	84700	exon4			.	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.330delG	chr22.hg19:g.26164213delG	ENSP00000386096:p.Glu110fs	120.0	0.0		158.0	10.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Frame_Shift_Del	DEL	ENST00000407587.2	hg19																																																																																				.	.		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		-	26164213	G	-	26164213	7	5	103	1	0	1	0	1	0	0	0	0	10075	991	35	0	340	0	MYO18B	22	26164213	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	4121177	26164213	25140353	1144	15767										
AP1B1	162	hgsc.bcm.edu	37	chr22	29736724	29736724	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaggggtgggccgctcactGgggggccgaggtccaggttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:29736724delG	ENST00000405198.1	-	13	1950	c.1919delC	c.(1918-1920)ccafs	p.P640fs	AP1B1_ENST00000317368.7_Frame_Shift_Del_p.P640fs|AP1B1_ENST00000432560.2_Frame_Shift_Del_p.P640fs|AP1B1_ENST00000402502.1_Frame_Shift_Del_p.P640fs|AP1B1_ENST00000415447.1_Frame_Shift_Del_p.P640fs|AP1B1_ENST00000472057.1_5'UTR|AP1B1_ENST00000356015.2_Frame_Shift_Del_p.P640fs|AP1B1_ENST00000357586.2_Frame_Shift_Del_p.P640fs			Q10567	AP1B1_HUMAN	adaptor-related protein complex 1, beta 1 subunit	640	Pro-rich (stalk region).				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GCCGCTCACTGGGGGGCCGAG	0.677																																					p.P640fs		Atlas-INDEL	.											.	AP1B1	72	.	0			c.1920delA						.						18	19	18					22																	29736724		2198	4294	6492	SO:0001589	frameshift_variant	162	exon14			.	L13939	CCDS13855.1, CCDS13856.1, CCDS13856.2, CCDS54515.1	22q12.2	2010-06-18			ENSG00000100280	ENSG00000100280			554	protein-coding gene	gene with protein product		600157		ADTB1, CLAPB2		7987321, 8812422	Standard	NM_145730		Approved	BAM22, AP105A	uc003afj.3	Q10567	OTTHUMG00000151109	ENST00000405198.1:c.1919delC	chr22.hg19:g.29736724delG	ENSP00000384194:p.Pro640fs	114.0	0.0		137.0	11.0	NM_001127	C9JRD1|F8WDL0|P78436|Q20WL3|Q86X54	Frame_Shift_Del	DEL	ENST00000405198.1	hg19	CCDS13855.1																																																																																			.	.		0.677	AP1B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321374.1	NM_001127		-	29736724	G	-	29736724	7	5	103	1	0	1	0	1	0	0	0	0	731	1348	47	0	970	0	AP1B1	22	29736724	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	3572511	29736724	21567842	1145	15768										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885884	29885884	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtccccagagaaggccaagtCcccagagaaggccaagactc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:29885884delC	ENST00000310624.6	+	4	2288	c.2255delC	c.(2254-2256)tccfs	p.S752fs		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	758	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAGGCCAAGTCCCCAGAGAAG	0.552																																					p.S752fs		Atlas-INDEL	.											.	NEFH	178	.	0			c.2254delT						.						96	95	95					22																	29885884		2203	4300	6503	SO:0001589	frameshift_variant	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2255delC	chr22.hg19:g.29885884delC	ENSP00000311997:p.Ser752fs	135.0	0.0		164.0	11.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Frame_Shift_Del	DEL	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.552	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		-	29885884	C	-	29885884	7	5	103	1	0	1	0	1	0	0	0	0	10323	855	30	0	2269	0	NEFH	22	29885884	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	149160	29885884	21418682	1146	15769										
NIPSNAP1	8508	hgsc.bcm.edu	37	chr22	29957568	29957568	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctcattccagaagctgaacTcgaggagcagctggtttctc	11	11	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:29957568T>C	ENST00000216121.7	-	6	760	c.506A>G	c.(505-507)gAg>gGg	p.E169G		NM_001202502.1|NM_003634.3	NP_001189431.1|NP_003625.2	Q9BPW8	NIPS1_HUMAN	nipsnap homolog 1 (C. elegans)	169					sensory perception of pain (GO:0019233)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|synaptic membrane (GO:0097060)	neurotransmitter binding (GO:0042165)	p.?(1)		large_intestine(2)|lung(2)|skin(1)	5						GAAGCTGAACTCGAGGAGCAG	0.577																																					p.E169G		Atlas-SNP	.											.	NIPSNAP1	17	.	1	Unknown(1)	lung(1)	c.A506G						.						98	94	96					22																	29957568		2203	4300	6503	SO:0001583	missense	8508	exon6			CTGAACTCGAGGA	AJ001258	CCDS13860.1	22q12	2013-09-12	2001-11-28		ENSG00000184117	ENSG00000184117			7827	protein-coding gene	gene with protein product	"4-nitrophenylphosphatase domain and non-neuronal SNAP25-like 1"	603249	"NIPSNAP, C. elegans, homolog 1"			9661659	Standard	NM_003634		Approved		uc003afx.4	Q9BPW8	OTTHUMG00000151294	ENST00000216121.7:c.506A>G	chr22.hg19:g.29957568T>C	ENSP00000216121:p.Glu169Gly	72.0	0.0		75.0	5.0	NM_003634	B2RAY3|O43800	Missense_Mutation	SNP	ENST00000216121.7	hg19	CCDS13860.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.430142	0.83776	.	.	ENSG00000184117	ENST00000216121;ENST00000437094	T;T	0.70516	0.92;-0.49	4.83	4.83	0.62350	Dimeric alpha-beta barrel (1);	0.000000	0.85682	D	0.000000	T	0.80358	0.4608	M	0.85542	2.76	0.80722	D	1	P;P	0.47409	0.82;0.895	P;P	0.50860	0.652;0.468	D	0.83783	0.0226	10	0.56958	D	0.05	-23.3612	14.8543	0.70323	0.0:0.0:0.0:1.0	.	149;169	B4DQI7;Q9BPW8	.;NIPS1_HUMAN	G	169;34	ENSP00000216121:E169G;ENSP00000403448:E34G	ENSP00000216121:E169G	E	-	2	0	NIPSNAP1	28287568	1.000000	0.71417	0.992000	0.48379	0.885000	0.51271	7.596000	0.82721	2.165000	0.68154	0.379000	0.24179	GAG	.	.		0.577	NIPSNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322117.1			C	29957568	T	C	29957568	3	2	103	1	0	0	0	0	1	0	0	0	10438	1551	54	2	368	2	NIPSNAP1	22	29957568	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	71684	29957568	21346998	1147	15770										
SF3A1	10291	hgsc.bcm.edu	37	chr22	30733103	30733103	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctcatcttccatgggaggtGggggatgcacagggggcatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:30733103delG	ENST00000215793.8	-	13	2172	c.2018delC	c.(2017-2019)ccafs	p.P675fs	SF3A1_ENST00000439242.1_Frame_Shift_Del_p.P610fs	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	675	Poly-Pro.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						CATGGGAGGTGGGGGATGCAC	0.567																																					p.P673fs		Atlas-INDEL	.											.	SF3A1	61	.	0			c.2019delA						.						61	60	61					22																	30733103		2203	4300	6503	SO:0001589	frameshift_variant	10291	exon13			.	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"splicing factor 3a, subunit 1, 120kD"			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.2018delC	chr22.hg19:g.30733103delG	ENSP00000215793:p.Pro675fs	113.0	0.0		166.0	10.0	NM_005877	E9PAW1	Frame_Shift_Del	DEL	ENST00000215793.8	hg19	CCDS13875.1																																																																																			.	.		0.567	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877		-	30733103	G	-	30733103	7	5	103	1	0	1	0	1	0	0	0	0	14161	1348	47	0	379	0	SF3A1	22	30733103	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	775535	30733103	20571463	1148	15771										
SEC14L4	284904	hgsc.bcm.edu	37	chr22	30890192	30890192	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taatttgcttccaggatgctAaaaaactgtggagtcaagat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:30890192delA	ENST00000255858.7	-	7	608	c.525delT	c.(523-525)tttfs	p.F175fs	SEC14L4_ENST00000392772.2_Frame_Shift_Del_p.F121fs|SEC14L4_ENST00000381982.3_Frame_Shift_Del_p.F175fs|SEC14L4_ENST00000540456.1_Frame_Shift_Del_p.F160fs|RP4-539M6.14_ENST00000442126.1_RNA|RP4-539M6.14_ENST00000610156.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	175	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	CCAGGATGCTAAAAAACTGTG	0.517																																					p.S176fs		Atlas-INDEL	.											.	SEC14L4	43	.	0			c.526delA						.						112	116	114					22																	30890192		2203	4300	6503	SO:0001589	frameshift_variant	284904	exon7			.	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.525delT	chr22.hg19:g.30890192delA	ENSP00000255858:p.Phe175fs	145.0	0.0		199.0	12.0	NM_001161368	A5D6W7|A6NCV4	Frame_Shift_Del	DEL	ENST00000255858.7	hg19	CCDS13878.1																																																																																			.	.		0.517	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977		-	30890192	A	-	30890192	7	5	103	1	0	1	0	1	0	0	0	0	13999	359	13	0	725	0	SEC14L4	22	30890192	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	157089	30890192	20414374	1149	15772										
C22orf28	51493	hgsc.bcm.edu	37	chr22	32784009	32784009	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	atcacagcaattggtctcagTttaatggctttcttgctgat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:32784009delT	ENST00000216038.5	-	12	1586	c.1488delA	c.(1486-1488)aaafs	p.K496fs	RTCB_ENST00000451746.2_3'UTR|RP1-149A16.17_ENST00000444848.1_lincRNA	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		TTGGTCTCAGTTTAATGGCTT	0.468																																					p.L497X		Atlas-INDEL	.											.	C22orf28	43	.	0			c.1489delC						.						210	173	186					22																	32784009		2203	4300	6503	SO:0001589	frameshift_variant	51493	exon12			.	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"focal adhesion-associated protein"	613901	"chromosome 22 open reading frame 28"	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.1488delA	chr22.hg19:g.32784009delT	ENSP00000216038:p.Lys496fs	191.0	0.0		198.0	12.0	NM_014306		Frame_Shift_Del	DEL	ENST00000216038.5	hg19	CCDS13905.1																																																																																			.	.		0.468	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306		-	32784009	T	-	32784009	7	5	103	1	0	1	0	1	0	0	0	0	2142	1722	60	0	33	0	C22orf28	22	32784009	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1893817	32784009	18520557	1150	15773										
SYN3	8224	hgsc.bcm.edu	37	chr22	32914045	32914045	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cttacttgagatgcggatggGgtggtgctggcttcttggac	16	7	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:32914045G>A	ENST00000358763.2	-	13	1837	c.1595C>T	c.(1594-1596)cCc>cTc	p.P532L	SYN3_ENST00000332840.5_Missense_Mutation_p.P532L|SYN3_ENST00000467095.1_5'UTR	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	532	E.				neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						ATGCGGATGGGGTGGTGCTGG	0.592																																					p.P532L		Atlas-SNP	.											.	SYN3	77	.	0			c.C1595T						.						71	80	77					22																	32914045		2203	4300	6503	SO:0001583	missense	8224	exon12			GGATGGGGTGGTG	AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666			11496	protein-coding gene	gene with protein product		602705				9539796	Standard	NM_003490		Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.1595C>T	chr22.hg19:g.32914045G>A	ENSP00000351614:p.Pro532Leu	87.0	0.0		90.0	4.0	NM_003490	B1B1F9	Missense_Mutation	SNP	ENST00000358763.2	hg19	CCDS13908.1	.	.	.	.	.	.	.	.	.	.	G	19.53	3.844091	0.71488	.	.	ENSG00000185666	ENST00000358763;ENST00000332840;ENST00000445154	T;T	0.35421	1.31;1.31	5.97	5.97	0.96955	.	0.207650	0.42172	N	0.000756	T	0.57533	0.2060	L	0.55990	1.75	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66084	0.941;0.941	T	0.55379	-0.8150	10	0.72032	D	0.01	-8.266	20.428	0.99075	0.0:0.0:1.0:0.0	.	531;532	Q17R54;O14994	.;SYN3_HUMAN	L	532;532;138	ENSP00000351614:P532L;ENSP00000330219:P532L	ENSP00000330219:P532L	P	-	2	0	SYN3	31244045	1.000000	0.71417	0.924000	0.36721	0.276000	0.26787	5.335000	0.65929	2.837000	0.97791	0.655000	0.94253	CCC	.	.		0.592	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075892.4			A	32914045	G	A	32914045	3	1	103	1	0	0	0	0	1	0	0	0	15457	1232	43	3	155	3	SYN3	22	32914045	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	130036	32914045	18390521	1151	15774										
ST13	6767	hgsc.bcm.edu	37	chr22	41244327	41244327	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttcctcacttgatggttcgTctgcctttaagtcttcctcc	6	13	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:41244327T>C	ENST00000216218.3	-	3	696	c.215A>G	c.(214-216)gAc>gGc	p.D72G		NM_003932.3	NP_003923.2	P50502	F10A1_HUMAN	suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein)	72					chaperone cofactor-dependent protein refolding (GO:0070389)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	dATP binding (GO:0032564)|protein binding, bridging (GO:0030674)			cervix(1)|large_intestine(1)|lung(3)|skin(1)	6						TGATGGTTCGTCTGCCTTTAA	0.353																																					p.D72G		Atlas-SNP	.											.	ST13	16	.	0			c.A215G						.						102	85	91					22																	41244327		2203	4300	6503	SO:0001583	missense	6767	exon3			GGTTCGTCTGCCT		CCDS14006.1	22q13.2	2013-01-10	2001-11-29		ENSG00000100380	ENSG00000100380		"Tetratricopeptide (TTC) repeat domain containing"	11343	protein-coding gene	gene with protein product	"progesterone receptor-associated p48 protein"	606796	"suppression of tumorigenicity 13 (colon carcinoma) (Hsp70-interacting protein)"			9925927, 8721986	Standard	NM_003932		Approved	SNC6, HSPABP1, HIP, P48, FAM10A1	uc003aze.3	P50502	OTTHUMG00000151201	ENST00000216218.3:c.215A>G	chr22.hg19:g.41244327T>C	ENSP00000216218:p.Asp72Gly	74.0	0.0		76.0	4.0	NM_003932	O14999|Q2TU77	Missense_Mutation	SNP	ENST00000216218.3	hg19	CCDS14006.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.688006	0.48097	.	.	ENSG00000100380	ENST00000216218;ENST00000542699;ENST00000401032;ENST00000411695	T;T	0.49720	2.07;0.77	5.74	5.74	0.90152	.	0.864536	0.10555	N	0.660944	T	0.53222	0.1783	M	0.76838	2.35	0.28390	N	0.919121	B;B	0.14805	0.011;0.011	B;B	0.17979	0.02;0.011	T	0.50939	-0.8768	10	0.56958	D	0.05	.	12.4232	0.55532	0.0:0.0:0.0:1.0	.	62;72	B4E0U6;P50502	.;F10A1_HUMAN	G	72;72;72;35	ENSP00000216218:D72G;ENSP00000392067:D35G	ENSP00000216218:D72G	D	-	2	0	ST13	39574273	0.987000	0.35691	0.921000	0.36526	0.784000	0.44337	2.496000	0.45346	2.193000	0.70182	0.402000	0.26972	GAC	.	.		0.353	ST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321759.1	NM_003932		C	41244327	T	C	41244327	3	2	103	1	0	0	0	0	1	0	0	0	15225	1667	58	2	934	2	ST13	22	41244327	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	8330282	41244327	10060239	1152	15775										
EP300	2033	hgsc.bcm.edu	37	chr22	41574679	41574679	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctccacggccacagtcccagCccccccactccagtccttcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:41574679delC	ENST00000263253.7	+	31	8183	c.6964delC	c.(6964-6966)cccfs	p.P2323fs	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2323					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						ACAGTCCCAGCCCCCCCACTC	0.612			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.Q2321fs		Atlas-INDEL	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.6963delG						.						87	91	90					22																	41574679		2203	4300	6503	SO:0001589	frameshift_variant	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	.	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.6964delC	chr22.hg19:g.41574679delC	ENSP00000263253:p.Pro2323fs	116.0	0.0		154.0	11.0	NM_001429	B1AKC2	Frame_Shift_Del	DEL	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.		0.612	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		-	41574679	C	-	41574679	7	5	103	1	0	1	0	1	0	0	0	0	5150	739	26	0	7086	0	EP300	22	41574679	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	330352	41574679	9729887	1153	15776										
TSPO	706	hgsc.bcm.edu	37	chr22	43557161	43557161	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tggccctgaactgggcatggCcccccatcttctttggtgcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:43557161delC	ENST00000396265.3	+	2	180	c.5delC	c.(4-6)gccfs	p.A2fs	TSPO_ENST00000583777.1_5'UTR|TSPO_ENST00000329563.4_Frame_Shift_Del_p.P97fs|TSPO_ENST00000337554.3_Frame_Shift_Del_p.P97fs			B1AH88	TSPOB_HUMAN	translocator protein (18kDa)	2					adrenal gland development (GO:0030325)|aging (GO:0007568)|behavioral response to pain (GO:0048266)|cellular hypotonic response (GO:0071476)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to zinc ion (GO:0071294)|chloride transport (GO:0006821)|contact inhibition (GO:0060242)|glial cell migration (GO:0008347)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of tumor necrosis factor production (GO:0032720)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of necrotic cell death (GO:0010940)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of steroid biosynthetic process (GO:0050810)|response to drug (GO:0042493)|response to manganese ion (GO:0010042)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to vitamin B1 (GO:0010266)|steroid biosynthetic process (GO:0006694)	mitochondrial outer membrane (GO:0005741)	androgen binding (GO:0005497)|benzodiazepine receptor activity (GO:0008503)			endometrium(1)|prostate(1)	2		Ovarian(80;0.0694)				CTGGGCATGGCCCCCCATCTT	0.617																																					p.W95fs		Atlas-INDEL	.											.	TSPO	6	.	0			c.285delG						.						76	66	70					22																	43557161		2203	4300	6503	SO:0001589	frameshift_variant	706	exon3			.	AF075589	CCDS33661.1	22q13.3	2006-07-12	2006-07-12	2006-07-12	ENSG00000100300	ENSG00000100300			1158	protein-coding gene	gene with protein product	"peripheral-type benzodiazepine receptor/recognition site"	109610	"benzodiazapine receptor (peripheral)"	BZRP		1326278, 1847678, 16822554	Standard	NM_000714		Approved	PBR, MBR, PKBS, mDRC, DBI, IBP, pk18	uc003bdo.4	B1AH88	OTTHUMG00000150573	ENST00000396265.3:c.5delC	chr22.hg19:g.43557161delC	ENSP00000379563:p.Ala2fs	173.0	0.0		195.0	15.0	NM_001256531	Q13849|Q6IAZ7	Frame_Shift_Del	DEL	ENST00000396265.3	hg19																																																																																				.	.		0.617	TSPO-201	KNOWN	basic	protein_coding	protein_coding		NM_007311		-	43557161	C	-	43557161	7	5	103	1	0	1	0	1	0	0	0	0	16670	739	26	0	292	0	TSPO	22	43557161	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	1982482	43557161	7747405	1154	15777										
SAMM50	25813	hgsc.bcm.edu	37	chr22	44368791	44368791	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taatcttcttggtcgtgcagAaaaggtgacctttcagtttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:44368791delA	ENST00000350028.4	+	6	627	c.470delA	c.(469-471)gaafs	p.E157fs	SAMM50_ENST00000396202.3_Intron|SAMM50_ENST00000493161.1_3'UTR	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	157					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)				endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				GGTCGTGCAGAAAAGGTGACC	0.433																																					p.E157fs		Atlas-INDEL	.											.	SAMM50	30	.	0			c.469delG						.						126	131	129					22																	44368791		2203	4300	6503	SO:0001589	frameshift_variant	25813	exon6			.	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"sorting and assembly machinery component 50 homolog (S. cerevisiae)"			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.470delA	chr22.hg19:g.44368791delA	ENSP00000345445:p.Glu157fs	122.0	0.0		138.0	10.0	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Frame_Shift_Del	DEL	ENST00000350028.4	hg19	CCDS14055.1																																																																																			.	.		0.433	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380		-	44368791	A	-	44368791	7	5	103	1	0	1	0	1	0	0	0	0	13844	246	9	0	492	0	SAMM50	22	44368791	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	811630	44368791	6935775	1155	15778										
TTC38	55020	hgsc.bcm.edu	37	chr22	46671215	46671215	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cgacagacatgttggccctgAaattttcccatgatgcttat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:46671215delA	ENST00000381031.3	+	5	512	c.436delA	c.(436-438)aaafs	p.K146fs	TTC38_ENST00000445282.2_Intron	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	146						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						GTTGGCCCTGAAATTTTCCCA	0.473																																					p.L145fs		Atlas-INDEL	.											TTC38,NS,carcinoma,0,1	TTC38	40	.	0			c.435delG						.						111	107	108					22																	46671215		1857	4105	5962	SO:0001589	frameshift_variant	55020	exon5			.		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"Tetratricopeptide (TTC) repeat domain containing"	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.436delA	chr22.hg19:g.46671215delA	ENSP00000370419:p.Lys146fs	116.0	0.0		162.0	10.0	NM_017931	Q8WV27|Q9NWP8	Frame_Shift_Del	DEL	ENST00000381031.3	hg19	CCDS43030.1																																																																																			.	.		0.473	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931		-	46671215	A	-	46671215	7	5	103	1	0	1	0	1	0	0	0	0	16721	247	9	0	454	0	TTC38	22	46671215	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2302424	46671215	4633351	1156	15779										
GTSE1	51512	hgsc.bcm.edu	37	chr22	46704068	46704068	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cattcttcttttggccgatgAaaaatttgacttcgatcttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:46704068delA	ENST00000454366.1	+	3	313	c.101delA	c.(100-102)gaafs	p.E34fs		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	15					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		TTGGCCGATGAAAAATTTGAC	0.373																																					p.E34fs	GBM(153;542 1915 12487 29016 50495)	Atlas-INDEL	.											.	GTSE1	100	.	0			c.100delG						.						130	131	131					22																	46704068		2203	4300	6503	SO:0001589	frameshift_variant	51512	exon3			.	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.101delA	chr22.hg19:g.46704068delA	ENSP00000415430:p.Glu34fs	127.0	0.0		174.0	11.0	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Frame_Shift_Del	DEL	ENST00000454366.1	hg19	CCDS14074.2																																																																																			.	.		0.373	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		-	46704068	A	-	46704068	7	5	103	1	0	1	0	1	0	0	0	0	6894	246	9	0	107	0	GTSE1	22	46704068	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	32853	46704068	4600498	1157	15780										
GTSE1	51512	hgsc.bcm.edu	37	chr22	46725998	46725998	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gccctgaggctgacaaggagAacgtggattccccactcctc	11	14	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:46725998A>G	ENST00000454366.1	+	12	2403	c.2191A>G	c.(2191-2193)Aac>Gac	p.N731D		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	712					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		TGACAAGGAGAACGTGGATTC	0.532																																					p.N731D	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.A2191G						.						106	83	91					22																	46725998		2203	4300	6503	SO:0001583	missense	51512	exon12			AAGGAGAACGTGG	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.2191A>G	chr22.hg19:g.46725998A>G	ENSP00000415430:p.Asn731Asp	77.0	0.0		90.0	4.0	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	hg19	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	A	16.79	3.220206	0.58560	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.20069	2.1	5.39	5.39	0.77823	.	0.048570	0.85682	D	0.000000	T	0.47303	0.1438	M	0.79475	2.455	0.51482	D	0.999925	D	0.89917	1.0	D	0.70935	0.971	T	0.51756	-0.8665	10	0.87932	D	0	-39.8752	14.3849	0.66938	1.0:0.0:0.0:0.0	.	712	Q9NYZ3	GTSE1_HUMAN	D	731;691	ENSP00000415430:N731D	ENSP00000354634:N691D	N	+	1	0	GTSE1	45104662	1.000000	0.71417	0.863000	0.33907	0.151000	0.21798	5.620000	0.67736	2.027000	0.59764	0.374000	0.22700	AAC	.	.		0.532	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		G	46725998	A	G	46725998	3	3	103	1	0	0	0	0	1	0	0	0	6894	246	9	2	2233	2	GTSE1	22	46725998	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	21930	46725998	4578568	1158	15781										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46776815	46776815	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctcgctgtacaccagcgtgcTcaccatcggggtattaatga	10	12	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:46776815T>C	ENST00000262738.3	-	22	7125	c.7126A>G	c.(7126-7128)Agc>Ggc	p.S2376G		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2376					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)	p.S2376C(1)		breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		ACCAGCGTGCTCACCATCGGG	0.617																																					p.S2376G		Atlas-SNP	.											CELSR1,NS,carcinoma,0,1	CELSR1	242	.	1	Substitution - Missense(1)	breast(1)	c.A7126G						.						39	40	40					22																	46776815		2203	4300	6503	SO:0001583	missense	9620	exon22			GCGTGCTCACCAT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.7126A>G	chr22.hg19:g.46776815T>C	ENSP00000262738:p.Ser2376Gly	70.0	1.0		72.0	3.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	T	19.42	3.824348	0.71143	.	.	ENSG00000075275	ENST00000262738	T	0.11712	2.75	4.28	4.28	0.50868	Domain of unknown function DUF3497 (1);	0.122517	0.52532	U	0.000077	T	0.31857	0.0810	M	0.81497	2.545	0.80722	D	1	D;D	0.65815	0.995;0.971	D;P	0.63957	0.92;0.868	T	0.14448	-1.0472	10	0.87932	D	0	.	13.091	0.59167	0.0:0.0:0.0:1.0	.	697;2376	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	G	2376	ENSP00000262738:S2376G	ENSP00000262738:S2376G	S	-	1	0	CELSR1	45155479	1.000000	0.71417	0.950000	0.38849	0.335000	0.28730	7.363000	0.79516	1.592000	0.50018	0.260000	0.18958	AGC	.	.		0.617	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		C	46776815	T	C	46776815	3	2	103	1	0	0	0	0	1	0	0	0	3223	1551	54	2	1974	2	CELSR1	22	46776815	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	50817	46776815	4527751	1159	15782										
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50659190	50659190	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agccatgtctgacacagactCccccaagctgatgctggcat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:50659190delC	ENST00000248846.5	-	16	3702	c.3598delG	c.(3598-3600)gagfs	p.E1200fs	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_Frame_Shift_Del_p.E1200fs			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1200	9 X 27 AA tandem repeats.				G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GACACAGACTCCCCCAAGCTG	0.622																																					p.E1200fs		Atlas-INDEL	.											.	TUBGCP6	132	.	0			c.3599delA						.						75	68	70					22																	50659190		2203	4300	6503	SO:0001589	frameshift_variant	85378	exon16			.	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.3598delG	chr22.hg19:g.50659190delC	ENSP00000248846:p.Glu1200fs	126.0	0.0		157.0	11.0	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Frame_Shift_Del	DEL	ENST00000248846.5	hg19	CCDS14087.1																																																																																			.	.		0.622	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		-	50659190	C	-	50659190	7	5	103	1	0	1	0	1	0	0	0	0	16785	864	30	0	1901	0	TUBGCP6	22	50659190	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	3882375	50659190	645376	1160	15783										
KLHDC7B	113730	hgsc.bcm.edu	37	chr22	50988068	50988068	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tccagcgacatcgtggcactGgggggcttcctgtaccgctt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:50988068delG	ENST00000395676.2	+	1	1607	c.1473delG	c.(1471-1473)ctgfs	p.L491fs	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	491										central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	14		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TCGTGGCACTGGGGGGCTTCC	0.667																																					p.L491fs		Atlas-INDEL	.											.	KLHDC7B	39	.	0			c.1472delT						.						47	53	51					22																	50988068		2202	4296	6498	SO:0001589	frameshift_variant	113730	exon1			.	BC009980	CCDS14097.2	22q13.33	2006-11-29		2005-12-13	ENSG00000130487	ENSG00000130487			25145	protein-coding gene	gene with protein product							Standard	NM_138433		Approved	MGC16635	uc003bmi.3	Q96G42	OTTHUMG00000150250	ENST00000395676.2:c.1473delG	chr22.hg19:g.50988068delG	ENSP00000379034:p.Leu491fs	78.0	0.0		105.0	10.0	NM_138433		Frame_Shift_Del	DEL	ENST00000395676.2	hg19	CCDS14097.2																																																																																			.	.		0.667	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433		-	50988068	G	-	50988068	7	5	103	1	0	1	0	1	0	0	0	0	8370	1335	47	0	1475	0	KLHDC7B	22	50988068	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	328878	50988068	316498	1161	15784										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51160703	51160703	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gggggaccccgtggagagccGggggctccctgggcctgaag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:51160703delG	ENST00000414786.2	+	21	4627	c.4400delG	c.(4399-4401)cggfs	p.R1467fs	SHANK3_ENST00000262795.3_Frame_Shift_Del_p.R1497fs|SHANK3_ENST00000445220.2_Frame_Shift_Del_p.R1483fs			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1481					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		GTGGAGAGCCGGGGGCTCCCT	0.677																																					p.R1467fs		Atlas-INDEL	.											.	SHANK3	96	.	0			c.4399delC						.						24	28	27					22																	51160703		1843	3976	5819	SO:0001589	frameshift_variant	85358	exon21			.	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.4400delG	chr22.hg19:g.51160703delG	ENSP00000464552:p.Arg1467fs	177.0	0.0		214.0	13.0	NM_033517	D7UT47|Q8TET3	Frame_Shift_Del	DEL	ENST00000414786.2	hg19																																																																																				.	.		0.677	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		-	51160703	G	-	51160703	7	5	103	1	0	1	0	1	0	0	0	0	14281	1116	39	0	4576	0	SHANK3	22	51160703	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	172635	51160703	143863	1162	15785										
ZBED1	9189	hgsc.bcm.edu	37	chrX	2408092	2408092	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gagcccatggacaggcagttGggggcgcccaggcccaggaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:2408092delG	ENST00000381223.4	-	2	872	c.669delC	c.(667-669)cccfs	p.P223fs	ZBED1_ENST00000515319.1_5'Flank|ZBED1_ENST00000381218.3_Frame_Shift_Del_p.P223fs|DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381222.2_Frame_Shift_Del_p.P223fs	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	223					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)			endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACAGGCAGTTGGGGGCGCCCA	0.637																																					p.N224fs		Atlas-INDEL	.											.	ZBED1	64	.	0			c.670delA						.						93	101	98					X																	2408092		2203	4296	6499	SO:0001589	frameshift_variant	9189	exon2			.	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"Pseudoautosomal regions / PAR1", "Zinc fingers, BED-type"	447	protein-coding gene	gene with protein product		300178	"Ac-like transposable element"	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.669delC	chrX.hg19:g.2408092delG	ENSP00000370621:p.Pro223fs	119.0	0.0		161.0	10.0	NM_001171135	Q96BY4	Frame_Shift_Del	DEL	ENST00000381223.4	hg19	CCDS14118.1																																																																																			.	.		0.637	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729		-	2408092	G	-	2408092	7	5	103	1	0	1	0	1	0	0	0	0	17532	1335	47	0	1419	0	ZBED1	23	2408092	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10		2408092	152862468	1163	15786										
PNPLA4	8228	hgsc.bcm.edu	37	chrX	7894068	7894068	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctttgacatccttcacaagTtttttgccatgtctgcaaag					rs375654820		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:7894068delT	ENST00000381042.4	-	2	263	c.93delA	c.(91-93)aaafs	p.K31fs	PNPLA4_ENST00000444736.1_Frame_Shift_Del_p.K31fs|PNPLA4_ENST00000537427.1_Intron	NM_004650.2	NP_004641.1	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	31	Patatin.				lipid catabolic process (GO:0016042)		triglyceride lipase activity (GO:0004806)			kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				CCTTCACAAGTTTTTTGCCAT	0.468											OREG0019651	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L32fs		Atlas-INDEL	.											.	PNPLA4	24	.	0			c.94delC						.						94	77	83					X																	7894068		2203	4299	6502	SO:0001589	frameshift_variant	8228	exon2			.	U03886	CCDS14129.1, CCDS55368.1	Xp22.3	2014-03-14			ENSG00000006757	ENSG00000006757	3.1.1.3	"Patatin-like phospholipase domain containing"	24887	protein-coding gene	gene with protein product		300102				7806223, 16799181, 19029121	Standard	NM_004650		Approved	DXS1283E, GS2, iPLA2eta	uc011mhr.1	P41247	OTTHUMG00000021103	ENST00000381042.4:c.93delA	chrX.hg19:g.7894068delT	ENSP00000370430:p.Lys31fs	159.0	0.0	645	154.0	10.0	NM_004650	A8K1H3|B4E362|Q8WW83	Frame_Shift_Del	DEL	ENST00000381042.4	hg19	CCDS14129.1																																																																																			.	.		0.468	PNPLA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055687.1	NM_004650		-	7894068	T	-	7894068	7	5	103	1	0	1	0	1	0	0	0	0	12176	1722	60	0	692	0	PNPLA4	23	7894068	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	5485976	7894068	147376492	1164	15787										
VCX3B	425054	hgsc.bcm.edu	37	chrX	8433809	8433809	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	accaaggtggccaagaagggAaaagcagttcgtagagggag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:8433809delA	ENST00000381032.1	+	3	433	c.126delA	c.(124-126)ggafs	p.G42fs	VCX3B_ENST00000381029.4_Frame_Shift_Del_p.G42fs|VCX3B_ENST00000440654.2_Frame_Shift_Del_p.G42fs|VCX3B_ENST00000444481.1_Frame_Shift_Del_p.G42fs|VCX3B_ENST00000453306.1_Frame_Shift_Del_p.G42fs	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	42						nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						CCAAGAAGGGAAAAGCAGTTC	0.632																																					p.G42fs		Atlas-INDEL	.											.	VCX3B	34	.	0			c.125delG						.						1	1	1					X																	8433809		146	519	665	SO:0001589	frameshift_variant	425054	exon3			.		CCDS48077.1, CCDS48077.2	Xp22.31	2009-01-14			ENSG00000205642	ENSG00000205642			31838	protein-coding gene	gene with protein product							Standard	NM_001001888		Approved	VCX-C	uc011mht.2	Q9H321	OTTHUMG00000021106	ENST00000381032.1:c.126delA	chrX.hg19:g.8433809delA	ENSP00000370420:p.Gly42fs	135.0	0.0		229.0	15.0	NM_001001888	C9JS46|Q4KN12	Frame_Shift_Del	DEL	ENST00000381032.1	hg19	CCDS48077.2																																																																																			.	.		0.632	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055691.1			-	8433809	A	-	8433809	7	5	103	1	0	1	0	1	0	0	0	0	17160	233	9	0	132	0	VCX3B	23	8433809	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	539741	8433809	146836751	1165	15788										
MSL3	10943	hgsc.bcm.edu	37	chrX	11776451	11776451	+	Frame_Shift_Del	DEL	C	C	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtgctgtgcttcgagcctgaCcccaccaaggcgcgagtgct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:11776451delC	ENST00000312196.4	+	1	174	c.69delC	c.(67-69)gacfs	p.D23fs	MSL3_ENST00000380693.3_5'Flank|MSL3_ENST00000337339.2_Frame_Shift_Del_p.D23fs|MSL3_ENST00000361672.2_5'UTR|MSL3_ENST00000398527.2_5'Flank	NM_078629.3	NP_523353.2	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3 homolog (Drosophila)	23					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|multicellular organismal development (GO:0007275)|transcription from RNA polymerase II promoter (GO:0006366)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	19						TCGAGCCTGACCCCACCAAGG	0.687																																					p.D23fs		Atlas-INDEL	.											.	MSL3	88	.	0			c.68delA						.						28	21	24					X																	11776451		2193	4297	6490	SO:0001589	frameshift_variant	10943	exon1			.	AF117065	CCDS14147.1, CCDS14148.1, CCDS14149.1, CCDS55369.1, CCDS65213.1	Xp22.3	2008-10-29	2008-10-29	2008-10-29	ENSG00000005302	ENSG00000005302			7370	protein-coding gene	gene with protein product		300609	"male-specific lethal-3 (Drosophila)-like 1", "male-specific lethal 3-like 1 (Drosophila)"	MSL3L1		10395802, 10908644	Standard	NM_078628		Approved		uc004cuw.3	Q8N5Y2	OTTHUMG00000021132	ENST00000312196.4:c.69delC	chrX.hg19:g.11776451delC	ENSP00000312244:p.Asp23fs	111.0	0.0		127.0	11.0	NM_078628	A6NCU2|A6NHW8|A8K165|B4DUV8|B7Z227|Q9UG70|Q9Y5Z8	Frame_Shift_Del	DEL	ENST00000312196.4	hg19	CCDS14147.1																																																																																			.	.		0.687	MSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055757.1	NM_006800		-	11776451	C	-	11776451	7	5	103	1	0	1	0	1	0	0	0	0	9888	506	18	0	71	0	MSL3	23	11776451	Frame_Shift_Del	DEL	C	TCGA-DD-A1EG-01A-11D-A20W-10	3342642	11776451	143494109	1166	15789										
TLR8	51311	hgsc.bcm.edu	37	chrX	12938331	12938331	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agatgatttccagcccctgaTgcagcttccaaacttatcga	7	12	0	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:12938331T>C	ENST00000218032.6	+	2	1259	c.1172T>C	c.(1171-1173)aTg>aCg	p.M391T	TLR8_ENST00000311912.5_Missense_Mutation_p.M409T	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	391					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CAGCCCCTGATGCAGCTTCCA	0.348																																					p.M391T		Atlas-SNP	.											.	TLR8	134	.	0			c.T1172C						.						77	80	79					X																	12938331		2200	4299	6499	SO:0001583	missense	51311	exon2			CCCTGATGCAGCT	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1172T>C	chrX.hg19:g.12938331T>C	ENSP00000218032:p.Met391Thr	42.0	0.0		79.0	4.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.752097	0.00663	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.00892	5.57;5.57	5.57	-1.24	0.09435	.	0.820841	0.10242	N	0.698262	T	0.00608	0.0020	N	0.16166	0.38	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.06405	0.002;0.002	T	0.45411	-0.9263	10	0.22706	T	0.39	.	3.8548	0.08971	0.1213:0.0747:0.3998:0.4042	.	391;409	Q9NR97;D1CS70	TLR8_HUMAN;.	T	391;409	ENSP00000218032:M391T;ENSP00000312082:M409T	ENSP00000218032:M391T	M	+	2	0	TLR8	12848252	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.193000	0.09573	-0.242000	0.09667	0.486000	0.48141	ATG	.	.		0.348	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		C	12938331	T	C	12938331	3	2	103	1	0	0	0	0	1	0	0	0	15972	1464	51	2	1178	2	TLR8	23	12938331	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1161880	12938331	142332229	1167	15790										
FANCB	2187	hgsc.bcm.edu	37	chrX	14863048	14863048	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tcttctagacttaaaaaaacTctgccacacacaacataacg	3	12	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:14863048T>C	ENST00000324138.3	-	7	2010	c.1857A>G	c.(1855-1857)agA>agG	p.R619R	FANCB_ENST00000398334.1_Silent_p.R619R	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	619					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					TTAAAAAAACTCTGCCACACA	0.338								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R619R		Atlas-SNP	.											.	FANCB	78	.	0			c.A1857G						.						138	142	141					X																	14863048		2203	4300	6503	SO:0001819	synonymous_variant	2187	exon7	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAAAACTCTGCCA	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"Fanconi anemia, complementation groups"	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.1857A>G	chrX.hg19:g.14863048T>C		60.0	0.0		88.0	4.0	NM_152633	B2RMZ4|Q7Z2U2|Q86XG1	Silent	SNP	ENST00000324138.3	hg19	CCDS14161.1																																																																																			.	.		0.338	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633		C	14863048	T	C	14863048	2	2	103	1	0	0	0	0	0	0	0	1	5671	1548	54	2		2	FANCB	23	14863048	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1924717	14863048	140407512	1168	15791										
SCML1	6322	hgsc.bcm.edu	37	chrX	17763578	17763578	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttggtaaattttcctcagatAaaaacaagaatacctactta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:17763578delA	ENST00000380041.3	+	3	364	c.36delA	c.(34-36)atafs	p.I12fs	SCML1_ENST00000380043.3_Intron|SCML1_ENST00000398080.1_Intron|SCML1_ENST00000380045.3_Intron	NM_001037540.1	NP_001032629.1	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 (Drosophila)	12					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)	10	Hepatocellular(33;0.183)					TTCCTCAGATAAAAACAAGAA	0.303																																					p.I12fs		Atlas-INDEL	.											.	SCML1	55	.	0			c.35delT						.						65	58	60					X																	17763578		2198	4295	6493	SO:0001589	frameshift_variant	6322	exon3			.		CCDS14182.2, CCDS35210.1, CCDS35211.1	Xp22	2013-01-10	2001-11-28		ENSG00000047634	ENSG00000047634		"Sterile alpha motif (SAM) domain containing"	10580	protein-coding gene	gene with protein product		300227	"sex comb on midleg (Drosophila)-like 1"			9570953	Standard	XM_005274578		Approved		uc004cyc.3	Q9UN30	OTTHUMG00000021206	ENST00000380041.3:c.36delA	chrX.hg19:g.17763578delA	ENSP00000369380:p.Ile12fs	138.0	0.0		152.0	12.0	NM_001037540	B0FZN6|B2RA08|Q5H968|Q5H969	Frame_Shift_Del	DEL	ENST00000380041.3	hg19	CCDS35210.1																																																																																			.	.		0.303	SCML1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060495.5	NM_006746		-	17763578	A	-	17763578	7	5	103	1	0	1	0	1	0	0	0	0	13924	352	13	0	42	0	SCML1	23	17763578	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2900530	17763578	137506982	1169	15792										
PHKA2	5256	hgsc.bcm.edu	37	chrX	18949832	18949832	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccttccccataggaactcggTctactgtgtgaggattcttg	10	11	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:18949832T>C	ENST00000379942.4	-	12	1837	c.1172A>G	c.(1171-1173)gAc>gGc	p.D391G		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	391					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					AGGAACTCGGTCTACTGTGTG	0.498											OREG0019698	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D391G		Atlas-SNP	.											.	PHKA2	122	.	0			c.A1172G						.						239	191	207					X																	18949832		2203	4300	6503	SO:0001583	missense	5256	exon12			ACTCGGTCTACTG		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.1172A>G	chrX.hg19:g.18949832T>C	ENSP00000369274:p.Asp391Gly	89.0	0.0	729	88.0	4.0	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	hg19	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	t	23.4	4.413831	0.83449	.	.	ENSG00000044446	ENST00000379942	D	0.91237	-2.81	5.28	5.28	0.74379	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.088152	0.85682	D	0.000000	D	0.89567	0.6752	L	0.61036	1.89	0.80722	D	1	B	0.24721	0.11	B	0.29077	0.098	D	0.87324	0.2320	10	0.48119	T	0.1	-24.7587	14.4937	0.67670	0.0:0.0:0.0:1.0	.	391	P46019	KPB2_HUMAN	G	391	ENSP00000369274:D391G	ENSP00000369274:D391G	D	-	2	0	PHKA2	18859753	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	7.991000	0.88244	1.870000	0.54199	0.478000	0.44815	GAC	.	.		0.498	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		C	18949832	T	C	18949832	3	2	103	1	0	0	0	0	1	0	0	0	11853	1667	58	2	2623	2	PHKA2	23	18949832	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1186254	18949832	136320728	1170	15793										
SH3KBP1	30011	hgsc.bcm.edu	37	chrX	19663542	19663542	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtcctgctgtccatttctgTttttgatgagtctggagttg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:19663542delT	ENST00000397821.3	-	7	1068	c.778delA	c.(778-780)acafs	p.T260fs	SH3KBP1_ENST00000379698.4_Frame_Shift_Del_p.T223fs|SH3KBP1_ENST00000379716.1_Frame_Shift_Del_p.T22fs|SH3KBP1_ENST00000379697.3_Frame_Shift_Del_p.T304fs|SH3KBP1_ENST00000541422.1_5'UTR|SH3KBP1_ENST00000477102.1_5'UTR	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	260					apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						TCCATTTCTGTTTTTGATGAG	0.348																																					p.T260fs		Atlas-INDEL	.											.	SH3KBP1	96	.	0			c.779delC						.						246	217	227					X																	19663542		2203	4300	6503	SO:0001589	frameshift_variant	30011	exon7			.	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.778delA	chrX.hg19:g.19663542delT	ENSP00000380921:p.Thr260fs	89.0	0.0		160.0	10.0	NM_031892	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Frame_Shift_Del	DEL	ENST00000397821.3	hg19	CCDS14193.1																																																																																			.	.		0.348	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892		-	19663542	T	-	19663542	7	5	103	1	0	1	0	1	0	0	0	0	14270	1725	60	0	1267	0	SH3KBP1	23	19663542	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	713710	19663542	135607018	1171	15794										
DDX53	168400	hgsc.bcm.edu	37	chrX	23018954	23018954	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaattattctacaaggaatAgatcttatagtagttgcaca	6	7	2	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:23018954A>G	ENST00000327968.5	+	1	868	c.780A>G	c.(778-780)atA>atG	p.I260M	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	260	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						TACAAGGAATAGATCTTATAG	0.393																																					p.I260M		Atlas-SNP	.											.	DDX53	76	.	0			c.A780G						.						72	69	70					X																	23018954		2203	4300	6503	SO:0001583	missense	168400	exon1			AGGAATAGATCTT	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"DEAD-boxes"	20083	protein-coding gene	gene with protein product	"cancer associated gene", "cancer/testis antigen 26"						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.780A>G	chrX.hg19:g.23018954A>G	ENSP00000368667:p.Ile260Met	58.0	0.0		100.0	4.0	NM_182699	Q0D2N2|Q6NVV4	Missense_Mutation	SNP	ENST00000327968.5	hg19	CCDS35214.1	.	.	.	.	.	.	.	.	.	.	A	7.824	0.718360	0.15372	.	.	ENSG00000184735	ENST00000327968	T	0.14640	2.49	4.07	-1.57	0.08506	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.552762	0.18269	N	0.146369	T	0.05593	0.0147	N	0.05124	-0.11	0.30013	N	0.815048	B	0.31769	0.339	B	0.37267	0.245	T	0.23619	-1.0183	10	0.42905	T	0.14	1.9321	2.9999	0.06010	0.3189:0.0:0.2216:0.4595	.	260	Q86TM3	DDX53_HUMAN	M	260	ENSP00000368667:I260M	ENSP00000368667:I260M	I	+	3	3	DDX53	22928875	0.997000	0.39634	0.915000	0.36163	0.417000	0.31264	0.348000	0.20031	-0.148000	0.11234	0.486000	0.48141	ATA	.	.		0.393	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699		G	23018954	A	G	23018954	3	3	103	1	0	0	0	0	1	0	0	0	4373	410	15	2	782	2	DDX53	23	23018954	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	3355412	23018954	132251606	1172	15795										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23411607	23411607	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaagaccatggaaacaaacAgagaagaactctatgatctc	7	10	2	4			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:23411607A>G	ENST00000379361.4	+	3	2832	c.1972A>G	c.(1972-1974)Aga>Gga	p.R658G		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	658					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						GGAAACAAACAGAGAAGAACT	0.423																																					p.R658G		Atlas-SNP	.											.	PTCHD1	213	.	0			c.A1972G						.						70	66	67					X																	23411607		2203	4300	6503	SO:0001583	missense	139411	exon3			ACAAACAGAGAAG	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.1972A>G	chrX.hg19:g.23411607A>G	ENSP00000368666:p.Arg658Gly	54.0	0.0		86.0	4.0	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	hg19	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	A	14.76	2.632079	0.46944	.	.	ENSG00000165186	ENST00000379361	D	0.85339	-1.97	5.48	4.24	0.50183	.	0.051778	0.85682	D	0.000000	T	0.79155	0.4398	L	0.46157	1.445	0.38785	D	0.954854	B	0.22346	0.068	B	0.24006	0.05	T	0.75007	-0.3469	10	0.23302	T	0.38	-9.8247	10.9957	0.47573	0.6293:0.3707:0.0:0.0	.	658	Q96NR3	PTHD1_HUMAN	G	658	ENSP00000368666:R658G	ENSP00000368666:R658G	R	+	1	2	PTCHD1	23321528	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.306000	0.59117	1.816000	0.52996	0.486000	0.48141	AGA	.	.		0.423	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		G	23411607	A	G	23411607	3	3	103	1	0	0	0	0	1	0	0	0	12744	180	7	2	1982	2	PTCHD1	23	23411607	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	392653	23411607	131858953	1173	15796										
FAM48B2	170067	hgsc.bcm.edu	37	chrX	24330071	24330071	+	IGR	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggatgtttctctcccttcccGgatactgaagactggaccca					rs147318848		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:24330071delG								AC096509.1 (25277 upstream) : AC004552.1 (36854 downstream)																							CTCCCTTCCCGGATACTGAAG	0.547																																					p.G455fs		Atlas-INDEL	.											.	.	.	.	0			c.1363delG						.						83	78	79					X																	24330071		1529	3560	5089	SO:0001628	intergenic_variant	170067	exon1			.																													chrX.hg19:g.24330071delG		91.0	0.0		112.0	12.0	NM_001136233		Frame_Shift_Del	DEL		hg19																																																																																				.	.	0	0.547									-	24330071	G	-	24330071	6	5	103	0	1	1	0	1	0	0	0	0	5582	1103	39	0		0	FAM48B2	23	24330071	IGR	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	918464	24330071	130940489	1174	15797										
DCAF8L1	139425	hgsc.bcm.edu	37	chrX	27997984	27997984	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	caacacaggtaggtaagggtGgggttcaagacagtttacta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:27997984delG	ENST00000441525.1	-	1	1582	c.1468delC	c.(1468-1470)cacfs	p.H490fs		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	490										NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						AGGTAAGGGTGGGGTTCAAGA	0.498																																					p.H490fs		Atlas-INDEL	.											.	DCAF8L1	121	.	0			c.1469delA						.						76	69	72					X																	27997984		2202	4300	6502	SO:0001589	frameshift_variant	139425	exon1			.		CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"WD repeat domain containing"	31810	protein-coding gene	gene with protein product			"WD repeat domain 42B"	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.1468delC	chrX.hg19:g.27997984delG	ENSP00000405222:p.His490fs	141.0	0.0		166.0	10.0	NM_001017930	B3KXX1	Frame_Shift_Del	DEL	ENST00000441525.1	hg19	CCDS35222.1																																																																																			.	.		0.498	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690		-	27997984	G	-	27997984	7	5	103	1	0	1	0	1	0	0	0	0	4279	1348	47	0	338	0	DCAF8L1	23	27997984	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	3667913	27997984	127272576	1175	15798										
GK	2710	hgsc.bcm.edu	37	chrX	30719015	30719015	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gcttccagattggacaagccAaaaatacgtgagtttaagaa							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:30719015delA	ENST00000378943.3	+	10	1005	c.826delA	c.(826-828)aaafs	p.K276fs	GK-AS1_ENST00000464659.1_RNA|GK_ENST00000378946.3_Frame_Shift_Del_p.K282fs|GK_ENST00000427190.1_Frame_Shift_Del_p.K77fs|RP11-242C19.2_ENST00000497961.1_RNA|GK_ENST00000378945.3_Frame_Shift_Del_p.K276fs	NM_001128127.2	NP_001121599.1	P32189	GLPK_HUMAN	glycerol kinase	282					cellular lipid metabolic process (GO:0044255)|glucose homeostasis (GO:0042593)|glycerol catabolic process (GO:0019563)|glycerol metabolic process (GO:0006071)|glycerol-3-phosphate biosynthetic process (GO:0046167)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			central_nervous_system(1)|large_intestine(3)	4						TGGACAAGCCAAAAATACGTG	0.368																																					p.A281fs		Atlas-INDEL	.											.	GK	95	.	0			c.843delC						.						82	76	78					X																	30719015		2202	4300	6502	SO:0001589	frameshift_variant	2710	exon11			.	X78711	CCDS14225.1, CCDS35224.1, CCDS48090.1, CCDS75963.1	Xp21.3	2014-09-17			ENSG00000198814	ENSG00000198814	2.7.1.30	"Glycerol kinases"	4289	protein-coding gene	gene with protein product		300474				7987308	Standard	NM_203391		Approved	GK1, GKD	uc022buj.1	P32189	OTTHUMG00000021328	ENST00000378943.3:c.826delA	chrX.hg19:g.30719015delA	ENSP00000368226:p.Lys276fs	98.0	0.0		142.0	10.0	NM_203391	A6NJP5|B2R833|Q6IQ27|Q8IVR5|Q9UMP0|Q9UMP1	Frame_Shift_Del	DEL	ENST00000378943.3	hg19	CCDS48090.1																																																																																			.	.		0.368	GK-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056170.1	NM_000167		-	30719015	A	-	30719015	7	5	103	1	0	1	0	1	0	0	0	0	6428	131	5	0	886	0	GK	23	30719015	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	2721031	30719015	124551545	1176	15799										
SYTL5	94122	hgsc.bcm.edu	37	chrX	37981401	37981401	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctggaggaatactagaagtgTtcatcaaagaggcaaagaat	11	5	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:37981401T>C	ENST00000357972.5	+	15	2320	c.1774T>C	c.(1774-1776)Ttc>Ctc	p.F592L	SYTL5_ENST00000297875.2_Missense_Mutation_p.F592L|TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000456733.2_Missense_Mutation_p.F614L			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	592	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						ACTAGAAGTGTTCATCAAAGA	0.408																																					p.F614L		Atlas-SNP	.											.	SYTL5	72	.	0			c.T1840C						.						111	96	101					X																	37981401		2202	4300	6502	SO:0001583	missense	94122	exon15			GAAGTGTTCATCA		CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"exophilin 9"						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.1774T>C	chrX.hg19:g.37981401T>C	ENSP00000350657:p.Phe592Leu	80.0	0.0		97.0	4.0	NM_001163334	A2RRF2	Missense_Mutation	SNP	ENST00000357972.5	hg19	CCDS14244.1	.	.	.	.	.	.	.	.	.	.	T	3.540	-0.093825	0.07053	.	.	ENSG00000147041	ENST00000297875;ENST00000357972;ENST00000456733	T;T;T	0.68624	-0.34;-0.34;-0.34	5.44	0.0938	0.14478	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.307265	0.36703	N	0.002455	T	0.28200	0.0696	N	0.01761	-0.735	0.20489	N	0.999893	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.001	T	0.22034	-1.0228	10	0.07990	T	0.79	-13.4634	4.011	0.09623	0.1189:0.4331:0.1206:0.3274	.	614;592	A2RRF2;Q8TDW5	.;SYTL5_HUMAN	L	592;592;614	ENSP00000297875:F592L;ENSP00000350657:F592L;ENSP00000395220:F614L	ENSP00000297875:F592L	F	+	1	0	SYTL5	37866345	0.117000	0.22190	0.773000	0.31616	0.992000	0.81027	0.239000	0.18023	-0.353000	0.08224	0.486000	0.48141	TTC	.	.		0.408	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780		C	37981401	T	C	37981401	3	2	103	1	0	0	0	0	1	0	0	0	15501	1725	60	2	1898	2	SYTL5	23	37981401	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	7262386	37981401	117289159	1177	15800										
MED14	9282	hgsc.bcm.edu	37	chrX	40562784	40562784	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttaccacagggctccaagatGggaacaacaagagctgggag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:40562784delG	ENST00000324817.1	-	11	1441	c.1323delC	c.(1321-1323)cccfs	p.P441fs		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	441	Interaction with STAT2.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GCTCCAAGATGGGAACAACAA	0.343																																					p.I442fs		Atlas-INDEL	.											.	MED14	108	.	0			c.1324delA						.						52	46	48					X																	40562784		2203	4300	6503	SO:0001589	frameshift_variant	9282	exon11			.	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.1323delC	chrX.hg19:g.40562784delG	ENSP00000323720:p.Pro441fs	132.0	0.0		199.0	14.0	NM_004229	Q4KMR7|Q9UNB3	Frame_Shift_Del	DEL	ENST00000324817.1	hg19	CCDS14254.1																																																																																			.	.		0.343	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		-	40562784	G	-	40562784	7	5	103	1	0	1	0	1	0	0	0	0	9441	1335	47	0	3125	0	MED14	23	40562784	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	2581383	40562784	114707776	1178	15801										
USP9X	8239	hgsc.bcm.edu	37	chrX	41069811	41069811	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aacaacacgatgctttagaaTtttttaattcattggtggat							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:41069811delT	ENST00000324545.8	+	33	5698	c.5065delT	c.(5065-5067)tttfs	p.F1690fs	USP9X_ENST00000378308.2_Frame_Shift_Del_p.F1690fs	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1690	USP.				axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TGCTTTAGAATTTTTTAATTC	0.353																																					p.E1688fs	Ovarian(172;1807 2695 35459 49286)	Atlas-INDEL	.											.	USP9X	385	.	0			c.5064delA						.						114	109	111					X																	41069811		2172	4290	6462	SO:0001589	frameshift_variant	8239	exon33			.	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.5065delT	chrX.hg19:g.41069811delT	ENSP00000316357:p.Phe1690fs	113.0	0.0		160.0	12.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Frame_Shift_Del	DEL	ENST00000324545.8	hg19	CCDS43930.1																																																																																			.	.		0.353	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		-	41069811	T	-	41069811	7	5	103	1	0	1	0	1	0	0	0	0	17105	1493	52	0	5191	0	USP9X	23	41069811	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	507027	41069811	114200749	1179	15802										
ZNF630	57232	hgsc.bcm.edu	37	chrX	47919479	47919479	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctgattatcaatatgccagaTttttaaaacagagtacaatg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:47919479delT	ENST00000409324.3	-	5	578	c.352delA	c.(352-354)atcfs	p.I118fs	ZNF630-AS1_ENST00000436124.1_RNA|ZNF630_ENST00000276054.4_5'UTR|ZNF630_ENST00000442455.3_Frame_Shift_Del_p.I104fs	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	118					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						ATATGCCAGATTTTTAAAACA	0.373																																					p.I118fs		Atlas-INDEL	.											.	ZNF630	71	.	0			c.353delT						.						49	41	44					X																	47919479		2193	4284	6477	SO:0001589	frameshift_variant	57232	exon5			.	AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"Zinc fingers, C2H2-type", "-"	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.352delA	chrX.hg19:g.47919479delT	ENSP00000386393:p.Ile118fs	126.0	0.0		176.0	11.0	NM_001037735	F8WAG4|Q5H8Z5	Frame_Shift_Del	DEL	ENST00000409324.3	hg19	CCDS35237.2																																																																																			.	.		0.373	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735		-	47919479	T	-	47919479	7	5	103	1	0	1	0	1	0	0	0	0	18069	1493	52	0	1625	0	ZNF630	23	47919479	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	6849668	47919479	107351081	1180	15803										
RBM3	5935	hgsc.bcm.edu	37	chrX	48434040	48434040	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	catgcttcagttgccatgagAgccatgaacggagaggtggg	15	8	1	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:48434040A>G	ENST00000376759.3	+	3	258	c.195A>G	c.(193-195)agA>agG	p.R65R	RBM3_ENST00000466764.1_3'UTR|RBM3_ENST00000376755.1_Silent_p.R65R|RBM3_ENST00000430348.2_5'UTR|AC115618.1_ENST00000376775.2_5'Flank|RBM3_ENST00000354480.2_5'Flank	NM_006743.4	NP_006734.1	P98179	RBM3_HUMAN	RNA binding motif (RNP1, RRM) protein 3	65	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				positive regulation of translation (GO:0045727)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of translation (GO:0006417)|response to cold (GO:0009409)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						TTGCCATGAGAGCCATGAACG	0.552																																					p.R65R		Atlas-SNP	.											.	RBM3	20	.	0			c.A195G						.						65	55	59					X																	48434040		2203	4300	6503	SO:0001819	synonymous_variant	5935	exon3			CATGAGAGCCATG	BC006825	CCDS14301.1	Xp11.2	2014-05-19	2004-04-23		ENSG00000102317	ENSG00000102317		"RNA binding motif (RRM) containing"	9900	protein-coding gene	gene with protein product		300027	"RNA binding motif protein 3"			8634703	Standard	NM_006743		Approved	IS1-RNPL	uc004dkf.2	P98179	OTTHUMG00000024121	ENST00000376759.3:c.195A>G	chrX.hg19:g.48434040A>G		92.0	0.0		99.0	4.0	NM_006743		Silent	SNP	ENST00000376759.3	hg19	CCDS14301.1																																																																																			.	.		0.552	RBM3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060755.1	NM_006743		G	48434040	A	G	48434040	2	3	103	1	0	0	0	0	0	0	0	1	13144	301	11	2		2	RBM3	23	48434040	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	514561	48434040	106836520	1181	15804										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50351077	50351077	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtttgaagtctccaaggaggTcaagagaagaaattgctcgg	13	6	2	3			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:50351077T>C	ENST00000289292.7	-	6	3348	c.3065A>G	c.(3064-3066)gAc>gGc	p.D1022G	SHROOM4_ENST00000376020.2_Missense_Mutation_p.D1022G|SHROOM4_ENST00000460112.3_Missense_Mutation_p.D906G			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1022					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					TCCAAGGAGGTCAAGAGAAGA	0.502																																					p.D1022G		Atlas-SNP	.											.	SHROOM4	171	.	0			c.A3065G						.						55	50	51					X																	50351077		2203	4300	6503	SO:0001583	missense	57477	exon6			AGGAGGTCAAGAG	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3065A>G	chrX.hg19:g.50351077T>C	ENSP00000289292:p.Asp1022Gly	119.0	0.0		186.0	9.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812003	0.50527	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.18810	2.61;2.61;2.19	5.78	5.78	0.91487	.	0.213352	0.40640	N	0.001058	T	0.35068	0.0919	L	0.34521	1.04	0.45580	D	0.998525	D	0.89917	1.0	D	0.80764	0.994	T	0.11767	-1.0574	10	0.87932	D	0	.	12.8679	0.57949	0.0:0.0:0.0:1.0	.	1022	Q9ULL8	SHRM4_HUMAN	G	1022;1022;906	ENSP00000289292:D1022G;ENSP00000365188:D1022G;ENSP00000421450:D906G	ENSP00000289292:D1022G	D	-	2	0	SHROOM4	50367817	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.453000	0.52978	1.946000	0.56461	0.486000	0.48141	GAC	.	.		0.502	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		C	50351077	T	C	50351077	3	2	103	1	0	0	0	0	1	0	0	0	14311	1667	58	2	1432	2	SHROOM4	23	50351077	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	1917037	50351077	104919483	1182	15805										
APEX2	27301	hgsc.bcm.edu	37	chrX	55033694	55033694	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctggaagtctgtgctggcGgggcccttgcgcacacccct							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:55033694delG	ENST00000374987.3	+	6	1449	c.1383delG	c.(1381-1383)gcgfs	p.A461fs	ALAS2_ENST00000498636.1_5'Flank	NM_014481.2	NP_055296.2	Q9UBZ4	APEX2_HUMAN	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	461					base-excision repair (GO:0006284)|cell cycle (GO:0007049)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1)	21						CTGTGCTGGCGGGGCCCTTGC	0.582								Other BER factors																													p.A461fs		Atlas-INDEL	.											.	APEX2	50	.	0			c.1382delC						.						41	32	35					X																	55033694		2203	4300	6503	SO:0001589	frameshift_variant	27301	exon6			.	AB021260	CCDS14365.1	Xp11.23	2014-02-18			ENSG00000169188	ENSG00000169188	4.2.99.18		17889	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 2"	300773				11376153	Standard	NM_014481		Approved	APEXL2, APE2, XTH2, ZGRF2	uc004dtz.4	Q9UBZ4	OTTHUMG00000021642	ENST00000374987.3:c.1383delG	chrX.hg19:g.55033694delG	ENSP00000364126:p.Ala461fs	122.0	0.0		147.0	10.0	NM_014481	Q9Y5X7	Frame_Shift_Del	DEL	ENST00000374987.3	hg19	CCDS14365.1																																																																																			.	.		0.582	APEX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056845.1			-	55033694	G	-	55033694	7	5	103	1	0	1	0	1	0	0	0	0	770	1103	39	0	1405	0	APEX2	23	55033694	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	4682617	55033694	100236866	1183	15806										
TAF1	6872	hgsc.bcm.edu	37	chrX	70597472	70597472	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ggtgttacgttttctacgtcTttttggaccagggaagaatg							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:70597472delT	ENST00000373790.4	+	6	782	c.731delT	c.(730-732)cttfs	p.L244fs	TAF1_ENST00000276072.3_Frame_Shift_Del_p.L265fs|TAF1_ENST00000423759.1_Frame_Shift_Del_p.L265fs|TAF1_ENST00000449580.1_Frame_Shift_Del_p.L244fs	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	244	Protein kinase 1.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				TTTCTACGTCTTTTTGGACCA	0.473																																					p.L265fs		Atlas-INDEL	.											.	TAF1	439	.	0			c.793delC						.						128	98	108					X																	70597472		2203	4300	6503	SO:0001589	frameshift_variant	6872	exon6			.		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.731delT	chrX.hg19:g.70597472delT	ENSP00000362895:p.Leu244fs	113.0	0.0		159.0	10.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Frame_Shift_Del	DEL	ENST00000373790.4	hg19	CCDS35325.1																																																																																			.	.		0.473	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		-	70597472	T	-	70597472	7	5	103	1	0	1	0	1	0	0	0	0	15528	1609	56	0	816	0	TAF1	23	70597472	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	15563778	70597472	84673088	1184	15807										
OGT	8473	hgsc.bcm.edu	37	chrX	70783055	70783055	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttctgaatggcatcgacctcAaagcatttcttgatagtcta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:70783055delA	ENST00000373719.3	+	17	2441	c.2224delA	c.(2224-2226)aaafs	p.K742fs	OGT_ENST00000373701.3_Frame_Shift_Del_p.K732fs	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	742					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					CATCGACCTCAAAGCATTTCT	0.358																																					p.L741fs		Atlas-INDEL	.											.	OGT	207	.	0			c.2223delC						.						132	116	121					X																	70783055		2203	4300	6503	SO:0001589	frameshift_variant	8473	exon17			.	U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"Tetratricopeptide (TTC) repeat domain containing"	8127	protein-coding gene	gene with protein product	"UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"	300255	"O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.2224delA	chrX.hg19:g.70783055delA	ENSP00000362824:p.Lys742fs	115.0	0.0		174.0	11.0	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Frame_Shift_Del	DEL	ENST00000373719.3	hg19	CCDS14414.1																																																																																			.	.		0.358	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		-	70783055	A	-	70783055	7	5	103	1	0	1	0	1	0	0	0	0	10856	131	5	0	2290	0	OGT	23	70783055	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	185583	70783055	84487505	1185	15808										
ATRX	546	hgsc.bcm.edu	37	chrX	76938413	76938413	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tgtagaactttttcgtttccTttttcctttatcatctttcc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:76938413delT	ENST00000373344.5	-	9	2549	c.2335delA	c.(2335-2337)aggfs	p.R779fs	ATRX_ENST00000395603.3_Frame_Shift_Del_p.R741fs|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	779					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TTTCGTTTCCTTTTTCCTTTA	0.338			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.R779fs		Atlas-INDEL	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.2336delG						.						133	139	137					X																	76938413		2203	4295	6498	SO:0001589	frameshift_variant	546	exon9			.	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.2335delA	chrX.hg19:g.76938413delT	ENSP00000362441:p.Arg779fs	134.0	0.0		197.0	12.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	hg19	CCDS14434.1																																																																																			.	.		0.338	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		-	76938413	T	-	76938413	7	5	103	1	0	1	0	1	0	0	0	0	1208	1608	56	0	5251	0	ATRX	23	76938413	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	6155358	76938413	78332147	1186	15809										
HDX	139324	hgsc.bcm.edu	37	chrX	83730320	83730320	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtaatatgagctgaaagcaaTttttactttgatttgtcatt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:83730320delT	ENST00000297977.5	-	2	197	c.86delA	c.(85-87)aatfs	p.N29fs	HDX_ENST00000373177.2_Frame_Shift_Del_p.N29fs|HDX_ENST00000506585.2_Intron	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	29						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						CTGAAAGCAATTTTTACTTTG	0.328																																					p.N29fs	Pancreas(53;231 1169 36156 43751 51139)	Atlas-INDEL	.											.	HDX	124	.	0			c.87delT						.						99	82	87					X																	83730320		2203	4300	6503	SO:0001589	frameshift_variant	139324	exon2			.	BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"Homeoboxes / POU class"	26411	protein-coding gene	gene with protein product			"chromosome X open reading frame 43"	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.86delA	chrX.hg19:g.83730320delT	ENSP00000297977:p.Asn29fs	146.0	0.0		148.0	10.0	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Frame_Shift_Del	DEL	ENST00000297977.5	hg19	CCDS35342.1																																																																																			.	.		0.328	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		-	83730320	T	-	83730320	7	5	103	1	0	1	0	1	0	0	0	0	7035	1493	52	0	2022	0	HDX	23	83730320	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	6791907	83730320	71540240	1187	15810										
CENPI	2491	hgsc.bcm.edu	37	chrX	100357276	100357276	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ttttcaggtcccattaaagcTtcacagaataaagataaaac	5	8	2	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:100357276T>C	ENST00000372927.1	+	3	517	c.240T>C	c.(238-240)gcT>gcC	p.A80A	CENPI_ENST00000372926.1_Silent_p.A80A|CENPI_ENST00000218507.5_Silent_p.A80A|CENPI_ENST00000423383.1_Silent_p.A80A	NM_006733.2	NP_006724.2	Q92674	CENPI_HUMAN	centromere protein I	80					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|sex differentiation (GO:0007548)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(19)|prostate(1)|skin(2)	30						CCATTAAAGCTTCACAGAATA	0.303																																					p.A80A		Atlas-SNP	.											.	CENPI	70	.	0			c.T240C						.						86	90	89					X																	100357276		2203	4299	6502	SO:0001819	synonymous_variant	2491	exon3			TAAAGCTTCACAG	X97249	CCDS14479.1	Xq22.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000102384	ENSG00000102384			3968	protein-coding gene	gene with protein product		300065	"FSH primary response (LRPR1, rat) homolog 1", "FSH primary response (LRPR1 homolog, rat) 1"	FSHPRH1		16622420	Standard	NM_006733		Approved	LRPR1, CENP-I, Mis6	uc004egx.3	Q92674	OTTHUMG00000022018	ENST00000372927.1:c.240T>C	chrX.hg19:g.100357276T>C		73.0	0.0		84.0	4.0	NM_006733	Q5JWZ9|Q96ED0	Silent	SNP	ENST00000372927.1	hg19	CCDS14479.1																																																																																			.	.		0.303	CENPI-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057519.1	NM_006733		C	100357276	T	C	100357276	2	2	103	1	0	0	0	0	0	0	0	1	3235	1596	56	2		2	CENPI	23	100357276	Silent	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	16626956	100357276	54913284	1188	15811										
ZMAT1	84460	hgsc.bcm.edu	37	chrX	101138606	101138606	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gtacatcatggctttttttcTtttttcgatgcttaagcttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:101138606delT	ENST00000372782.3	-	7	1840	c.1793delA	c.(1792-1794)aagfs	p.K600fs	ZMAT1_ENST00000494068.1_5'UTR|ZMAT1_ENST00000458570.1_Frame_Shift_Del_p.K429fs|ZMAT1_ENST00000540921.1_Frame_Shift_Del_p.K600fs	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	600						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						GCTTTTTTTCTTTTTTCGATG	0.388																																					p.K598fs		Atlas-INDEL	.											.	ZMAT1	143	.	0			c.1794delG						.						178	153	161					X																	101138606		2203	4300	6503	SO:0001589	frameshift_variant	84460	exon7			.	Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"Zinc fingers, matrin-type"	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.1793delA	chrX.hg19:g.101138606delT	ENSP00000361868:p.Lys600fs	119.0	0.0		141.0	10.0	NM_001011657	Q8NDS3|Q96JN6	Frame_Shift_Del	DEL	ENST00000372782.3	hg19	CCDS35348.1																																																																																			.	.		0.388	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1			-	101138606	T	-	101138606	7	5	103	1	0	1	0	1	0	0	0	0	17706	1609	56	0	127	0	ZMAT1	23	101138606	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	781330	101138606	54131954	1189	15812										
TCEAL6	158931	hgsc.bcm.edu	37	chrX	101395773	101395773	+	Missense_Mutation	SNP	G	G	T													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cactcccctgacaccccgttGtccccttgggcgaatggatc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:101395773G>T	ENST00000372774.3	-	3	780	c.531C>A	c.(529-531)gaC>gaA	p.D177E	TCEAL6_ENST00000372773.1_Missense_Mutation_p.D177E	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						ACACCCCGTTGTCCCCTTGGG	0.502																																					p.D177E		Atlas-SNP	.											.	TCEAL6	27	.	0			c.C531A						.						22	21	21					X																	101395773		2197	4275	6472	SO:0001583	missense	158931	exon3			CCCGTTGTCCCCT	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.531C>A	chrX.hg19:g.101395773G>T	ENSP00000361860:p.Asp177Glu	68.0	0.0		141.0	10.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.032|0.032	-1.327438|-1.327438	0.01309|0.01309	.|.	.|.	ENSG00000204071|ENSG00000204071	ENST00000372774;ENST00000372773|ENST00000536102	T;T|.	0.21191|.	2.02;2.02|.	2.82|2.82	2.82|2.82	0.32997|0.32997	.|.	0.272209|.	0.20313|.	N|.	0.094788|.	T|T	0.20455|0.20455	0.0492|0.0492	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B|.	0.16396|.	0.017|.	B|.	0.13407|.	0.009|.	T|T	0.20638|0.20638	-1.0269|-1.0269	10|6	0.22706|0.06236	T|T	0.39|0.91	.|.	8.3639|8.3639	0.32374|0.32374	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	177|.	Q6IPX3-2|.	.|.	E|K	177|177	ENSP00000361860:D177E;ENSP00000361859:D177E|.	ENSP00000361859:D177E|ENSP00000437364:Q177K	D|Q	-|-	3|1	2|0	TCEAL6|TCEAL6	101282429|101282429	0.014000|0.014000	0.17966|0.17966	0.012000|0.012000	0.15200|0.15200	0.864000|0.864000	0.49448|0.49448	2.835000|2.835000	0.48175|0.48175	1.692000|1.692000	0.51112|0.51112	0.468000|0.468000	0.43344|0.43344	GAC|CAA	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938		T	101395773	G	T	101395773	3	4	103	1	0	0	0	0	1	0	0	0	15690	1368	48	3	24	3	TCEAL6	23	101395773	Missense_Mutation	SNP	G	TCGA-DD-A1EG-01A-11D-A20W-10	257167	101395773	53874787	1190	15813	67	2								
TCEAL6	158931	hgsc.bcm.edu	37	chrX	101395778	101395778	+	Missense_Mutation	SNP	C	C	T													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccctgacaccccgttgtcccCttgggcgaatggatcctgta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:101395778C>T	ENST00000372774.3	-	3	775	c.526G>A	c.(526-528)Ggg>Agg	p.G176R	TCEAL6_ENST00000372773.1_Missense_Mutation_p.G176R	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						CCGTTGTCCCCTTGGGCGAAT	0.502																																					p.G176R		Atlas-SNP	.											.	TCEAL6	27	.	0			c.G526A						.						13	13	13					X																	101395778		2197	4251	6448	SO:0001583	missense	158931	exon3			TGTCCCCTTGGGC	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.526G>A	chrX.hg19:g.101395778C>T	ENSP00000361860:p.Gly176Arg	65.0	0.0		138.0	18.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.605|9.605	1.129729|1.129729	0.21041|0.21041	.|.	.|.	ENSG00000204071|ENSG00000204071	ENST00000372774;ENST00000372773|ENST00000536102	T;T|.	0.40225|.	1.04;1.04|.	2.82|2.82	2.82|2.82	0.32997|0.32997	.|.	0.000000|.	0.39341|.	N|.	0.001392|.	T|T	0.27832|0.27832	0.0685|0.0685	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	D|.	0.57257|.	0.979|.	P|.	0.56563|.	0.801|.	T|T	0.22243|0.22243	-1.0222|-1.0222	10|6	0.54805|0.06365	T|T	0.06|0.9	.|.	8.3639|8.3639	0.32374|0.32374	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	176|.	Q6IPX3-2|.	.|.	R|K	176|175	ENSP00000361860:G176R;ENSP00000361859:G176R|.	ENSP00000361859:G176R|ENSP00000437364:R175K	G|R	-|-	1|2	0|0	TCEAL6|TCEAL6	101282434|101282434	0.007000|0.007000	0.16637|0.16637	0.089000|0.089000	0.20774|0.20774	0.743000|0.743000	0.42351|0.42351	1.059000|1.059000	0.30517|0.30517	1.692000|1.692000	0.51112|0.51112	0.468000|0.468000	0.43344|0.43344	GGG|AGG	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938		T	101395778	C	T	101395778	3	4	103	1	0	0	0	0	1	0	0	0	15690	681	24	3	29	3	TCEAL6	23	101395778	Missense_Mutation	SNP	C	TCGA-DD-A1EG-01A-11D-A20W-10	5	101395778	53874782	1191	15814	67	2								
TBC1D8B	54885	hgsc.bcm.edu	37	chrX	106096825	106096825	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	aggttcaaatgtgagtgatgAaaaaaccagtcatactagag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:106096825delA	ENST00000357242.5	+	13	2372	c.2198delA	c.(2197-2199)gaafs	p.E733fs	TBC1D8B_ENST00000276175.3_Frame_Shift_Del_p.E727fs	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	733							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GTGAGTGATGAAAAAACCAGT	0.308																																					p.E733fs		Atlas-INDEL	.											.	TBC1D8B	181	.	0			c.2197delG						.						116	112	114					X																	106096825		2203	4300	6503	SO:0001589	frameshift_variant	54885	exon13			.	AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"EF-hand domain containing"	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.2198delA	chrX.hg19:g.106096825delA	ENSP00000349781:p.Glu733fs	141.0	0.0		201.0	13.0	NM_017752	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Frame_Shift_Del	DEL	ENST00000357242.5	hg19	CCDS14522.1																																																																																			.	.		0.308	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752		-	106096825	A	-	106096825	7	5	103	1	0	1	0	1	0	0	0	0	15641	246	9	0	2314	0	TBC1D8B	23	106096825	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	4701047	106096825	49173735	1192	15815										
HTR2C	3358	hgsc.bcm.edu	37	chrX	114141772	114141772	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gttgcaattataaggtagagAaaaagcctcctgtcaggcag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:114141772delA	ENST00000276198.1	+	6	1899	c.1171delA	c.(1171-1173)aaafs	p.K392fs	HTR2C_ENST00000371951.1_Frame_Shift_Del_p.K392fs|HTR2C_ENST00000371950.3_3'UTR	NM_000868.2	NP_000859.1	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C, G protein-coupled	392					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|cGMP biosynthetic process (GO:0006182)|feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|regulation of appetite (GO:0032098)|regulation of corticotropin-releasing hormone secretion (GO:0043397)|regulation of neurological system process (GO:0031644)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|Gq/11-coupled serotonin receptor activity (GO:0001587)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50					Agomelatine(DB06594)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Lorcaserin(DB04871)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TAAGGTAGAGAAAAAGCCTCC	0.428																																					p.E390fs		Atlas-INDEL	.											.	HTR2C	117	.	0			c.1170delG						.						84	84	84					X																	114141772		2203	4300	6503	SO:0001589	frameshift_variant	3358	exon6			.		CCDS14564.1, CCDS59174.1	Xq23	2013-12-19	2012-02-03		ENSG00000147246	ENSG00000147246		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5295	protein-coding gene	gene with protein product		312861	"5-hydroxytryptamine (serotonin) receptor 2C"	HTR1C		7895773	Standard	NM_000868		Approved	5-HT2C, 5HTR2C	uc004epu.1	P28335	OTTHUMG00000022226	ENST00000276198.1:c.1171delA	chrX.hg19:g.114141772delA	ENSP00000276198:p.Lys392fs	131.0	0.0		166.0	11.0	NM_000868	B1AMW4|Q5VUF8|Q9NP28	Frame_Shift_Del	DEL	ENST00000276198.1	hg19	CCDS14564.1																																																																																			.	.		0.428	HTR2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057962.1	NM_000868		-	114141772	A	-	114141772	7	5	103	1	0	1	0	1	0	0	0	0	7452	247	9	0	1185	0	HTR2C	23	114141772	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	8044947	114141772	41128788	1193	15816										
GRIA3	2892	hgsc.bcm.edu	37	chrX	122528895	122528895	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tttccagattgtcaacaatgAaaaccctatggttcagcagt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:122528895delA	ENST00000371251.1	+	6	879	c.827delA	c.(826-828)gaafs	p.E276fs	GRIA3_ENST00000541091.1_Frame_Shift_Del_p.E260fs|GRIA3_ENST00000371256.5_Frame_Shift_Del_p.E276fs|GRIA3_ENST00000542149.1_Frame_Shift_Del_p.E276fs|GRIA3_ENST00000264357.5_Frame_Shift_Del_p.E276fs			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	276					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	GTCAACAATGAAAACCCTATG	0.443																																					p.E276fs		Atlas-INDEL	.											.	GRIA3	386	.	0			c.826delG						.						132	122	126					X																	122528895		2203	4300	6503	SO:0001589	frameshift_variant	2892	exon6			.	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.827delA	chrX.hg19:g.122528895delA	ENSP00000360297:p.Glu276fs	144.0	0.0		185.0	12.0	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Frame_Shift_Del	DEL	ENST00000371251.1	hg19	CCDS14604.1																																																																																			.	.		0.443	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		-	122528895	A	-	122528895	7	5	103	1	0	1	0	1	0	0	0	0	6778	246	9	0	849	0	GRIA3	23	122528895	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	8387123	122528895	32741665	1194	15817										
STAG2	10735	hgsc.bcm.edu	37	chrX	123217394	123217394	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ctacttcgacaagacaaaagAacagtgtatgtatttgctgg	9	7	0	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:123217394A>G	ENST00000371160.1	+	29	3338	c.3048A>G	c.(3046-3048)agA>agG	p.R1016R	STAG2_ENST00000218089.9_Silent_p.R1016R|STAG2_ENST00000371157.3_Silent_p.R1016R|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371144.3_Silent_p.R1016R|STAG2_ENST00000371145.3_Silent_p.R1016R|STAG2_ENST00000354548.5_Silent_p.R947R	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	1016					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AAGACAAAAGAACAGTGTATG	0.358																																					p.R1016R		Atlas-SNP	.											.	STAG2	309	.	0			c.A3048G						.						78	75	76					X																	123217394		2203	4299	6502	SO:0001819	synonymous_variant	10735	exon29			CAAAAGAACAGTG	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.3048A>G	chrX.hg19:g.123217394A>G		51.0	0.0		73.0	4.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.		0.358	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		G	123217394	A	G	123217394	2	3	103	1	0	0	0	0	0	0	0	1	15258	243	9	2		2	STAG2	23	123217394	Silent	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	688499	123217394	32053166	1195	15818										
AIFM1	9131	hgsc.bcm.edu	37	chrX	129290533	129290533	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agagctagccatttgtcttgTcatctggagttctagaggaa	11	7	4	2			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:129290533T>C	ENST00000287295.3	-	2	381	c.151A>G	c.(151-153)Aca>Gca	p.T51A	AIFM1_ENST00000346424.2_Intron|AIFM1_ENST00000319908.3_Intron|AIFM1_ENST00000535724.1_Intron	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	51					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	ATTTGTCTTGTCATCTGGAGT	0.393																																					p.T51A		Atlas-SNP	.											.	AIFM1	75	.	0			c.A151G						.						217	187	197					X																	129290533		2203	4300	6503	SO:0001583	missense	9131	exon2			GTCTTGTCATCTG	AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"programmed cell death 8 (apoptosis-inducing factor)", "neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.151A>G	chrX.hg19:g.129290533T>C	ENSP00000287295:p.Thr51Ala	87.0	0.0		72.0	4.0	NM_001130847	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Missense_Mutation	SNP	ENST00000287295.3	hg19	CCDS14618.1	.	.	.	.	.	.	.	.	.	.	T	9.404	1.078720	0.20227	.	.	ENSG00000156709	ENST00000287295	T	0.20200	2.09	5.49	1.86	0.25419	.	0.395064	0.30771	N	0.008908	T	0.09247	0.0228	N	0.10874	0.06	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23440	-1.0188	10	0.21540	T	0.41	-4.1489	7.3059	0.26447	0.0:0.2604:0.0:0.7396	.	51;51	Q1L6K6;O95831	.;AIFM1_HUMAN	A	51	ENSP00000287295:T51A	ENSP00000287295:T51A	T	-	1	0	AIFM1	129118214	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.179000	0.31993	0.242000	0.21303	0.437000	0.28790	ACA	.	.		0.393	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2			C	129290533	T	C	129290533	3	2	103	1	0	0	0	0	1	0	0	0	426	1667	58	2	1897	2	AIFM1	23	129290533	Missense_Mutation	SNP	T	TCGA-DD-A1EG-01A-11D-A20W-10	6073139	129290533	25980027	1196	15819										
GPR119	139760	hgsc.bcm.edu	37	chrX	129518461	129518461	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agtgacgatgtgacaggaacTttccctgggcctctctgggc							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:129518461delT	ENST00000276218.2	-	1	1050	c.961delA	c.(961-963)agtfs	p.S322fs		NM_178471.2	NP_848566.1	Q8TDV5	GP119_HUMAN	G protein-coupled receptor 119	322					insulin secretion (GO:0030073)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(1)	11						TGACAGGAACTTTCCCTGGGC	0.537																																					p.S321fs		Atlas-INDEL	.											.	GPR119	34	.	0			c.962delG						.						99	90	93					X																	129518461		2203	4300	6503	SO:0001589	frameshift_variant	139760	exon1			.	AY288416	CCDS14625.1	Xq26.1	2014-01-30			ENSG00000147262	ENSG00000147262		"GPCR / Class A : Orphans"	19060	protein-coding gene	gene with protein product		300513				12044878, 14623098	Standard	NM_178471		Approved	hGPCR2, GPCR2	uc011muv.2	Q8TDV5	OTTHUMG00000022397	ENST00000276218.2:c.961delA	chrX.hg19:g.129518461delT	ENSP00000276218:p.Ser322fs	78.0	0.0		127.0	10.0	NM_178471	Q495H7|Q4VBN3	Frame_Shift_Del	DEL	ENST00000276218.2	hg19	CCDS14625.1																																																																																			.	.		0.537	GPR119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058270.1	NM_178471		-	129518461	T	-	129518461	7	5	103	1	0	1	0	1	0	0	0	0	6642	1609	56	0	50	0	GPR119	23	129518461	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	227928	129518461	25752099	1197	15820										
FRMD7	90167	hgsc.bcm.edu	37	chrX	131211907	131211907	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	taggttcacacttttaagctAaaaagtaattacatggtttt							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:131211907delA	ENST00000298542.4	-	12	2313	c.2138delT	c.(2137-2139)ttafs	p.L713fs	FRMD7_ENST00000370879.1_Frame_Shift_Del_p.L593fs|FRMD7_ENST00000464296.1_Frame_Shift_Del_p.L698fs	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	713					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					CTTTTAAGCTAAAAAGTAATT	0.363																																					p.L713fs		Atlas-INDEL	.											.	FRMD7	69	.	0			c.2139delA						.			0,3721		0,0,0,1592,537	95	84	88			5.7	1	X		89	2,6482		0,1,1,2356,1769	no	frameshift	FRMD7	NM_194277.2		0,1,1,3948,2306	A1A1,A1R,A1,RR,R		0.0308,0.0,0.0196			131211907	2,10203	2203	4300	6503	SO:0001589	frameshift_variant	90167	exon12			.	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"nystagmus 1, congenital"	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.2138delT	chrX.hg19:g.131211907delA	ENSP00000298542:p.Leu713fs	181.0	0.0		233.0	14.0	NM_194277	C0LLJ3|Q5JX99	Frame_Shift_Del	DEL	ENST00000298542.4	hg19	CCDS35397.1																																																																																			.	.		0.363	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		-	131211907	A	-	131211907	7	5	103	1	0	1	0	1	0	0	0	0	6063	372	13	0	10	0	FRMD7	23	131211907	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	1693446	131211907	24058653	1198	15821										
TFDP3	51270	hgsc.bcm.edu	37	chrX	132351743	132351743	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gaccaatccacttgatcttcTttttctccctggagatgata							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:132351743delT	ENST00000310125.4	-	1	633	c.545delA	c.(544-546)aagfs	p.K183fs		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	183	Involved in negatively regulating E2F activity.				cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					CTTGATCTTCTTTTTCTCCCT	0.448																																					p.K182fs		Atlas-INDEL	.											.	TFDP3	92	.	0			c.546delG						.						101	90	94					X																	132351743		2203	4300	6503	SO:0001589	frameshift_variant	51270	exon1			.	AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"E2F-like protein", "cancer/testis antigen 30"	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.545delA	chrX.hg19:g.132351743delT	ENSP00000385461:p.Lys183fs	64.0	0.0		95.0	10.0	NM_016521	Q6DK49|Q9NZ54	Frame_Shift_Del	DEL	ENST00000310125.4	hg19	CCDS14636.2																																																																																			.	.		0.448	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521		-	132351743	T	-	132351743	7	5	103	1	0	1	0	1	0	0	0	0	15814	1609	56	0	676	0	TFDP3	23	132351743	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	1139836	132351743	22918817	1199	15822										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135323367	135323367	+	Frame_Shift_Del	DEL	T	T	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	agagcctccccatgaccatcTtttttgctgataatcatcag							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:135323367delT	ENST00000316077.9	-	5	707	c.487delA	c.(487-489)agafs	p.R163fs	MAP7D3_ENST00000370661.1_Frame_Shift_Del_p.R163fs|MAP7D3_ENST00000370663.5_Frame_Shift_Del_p.R145fs	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	163					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					CATGACCATCTTTTTTGCTGA	0.328																																					p.R163fs		Atlas-INDEL	.											.	MAP7D3	102	.	0			c.488delG						.						63	57	59					X																	135323367		1846	4102	5948	SO:0001589	frameshift_variant	79649	exon5			.	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.487delA	chrX.hg19:g.135323367delT	ENSP00000318086:p.Arg163fs	146.0	0.0		157.0	10.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Frame_Shift_Del	DEL	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.328	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			-	135323367	T	-	135323367	7	5	103	1	0	1	0	1	0	0	0	0	9278	1617	56	0	2199	0	MAP7D3	23	135323367	Frame_Shift_Del	DEL	T	TCGA-DD-A1EG-01A-11D-A20W-10	2971624	135323367	19947193	1200	15823										
ATP11C	286410	hgsc.bcm.edu	37	chrX	138869386	138869386	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	tatatccatttcgatttcctAaaaatgtgaacccgtaccta							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:138869386delA	ENST00000327569.3	-	15	1645	c.1547delT	c.(1546-1548)ttafs	p.L516fs	ATP11C_ENST00000361648.2_Frame_Shift_Del_p.L516fs|ATP11C_ENST00000359686.2_Frame_Shift_Del_p.L516fs|ATP11C_ENST00000370557.1_Frame_Shift_Del_p.L513fs|ATP11C_ENST00000370543.1_Frame_Shift_Del_p.L516fs|ATP11C_ENST00000460773.1_5'UTR	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	516					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					TCGATTTCCTAAAAATGTGAA	0.294																																					p.L516fs		Atlas-INDEL	.											.	ATP11C	319	.	0			c.1548delA						.						101	83	89					X																	138869386		2201	4298	6499	SO:0001589	frameshift_variant	286410	exon15			.	AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.1547delT	chrX.hg19:g.138869386delA	ENSP00000332756:p.Leu516fs	149.0	0.0		147.0	10.0	NM_001010986	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Frame_Shift_Del	DEL	ENST00000327569.3	hg19	CCDS14668.1																																																																																			.	.		0.294	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		-	138869386	A	-	138869386	7	5	103	1	0	1	0	1	0	0	0	0	1121	372	13	0	1978	0	ATP11C	23	138869386	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	3546019	138869386	16401174	1201	15824										
CDR1	1038	hgsc.bcm.edu	37	chrX	139866088	139866088	+	Frame_Shift_Del	DEL	A	A	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	cctgaaaatctacgtcttccAaaaaagccatgtcttccaga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:139866088delA	ENST00000370532.2	-	1	635	c.444delT	c.(442-444)tttfs	p.F148fs		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	148	6 X 6 AA approximate repeats.									breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				TACGTCTTCCAAAAAAGCCAT	0.433																																					p.G149fs		Atlas-INDEL	.											.	CDR1	58	.	0			c.445delG						.						126	133	131					X																	139866088		2202	4300	6502	SO:0001589	frameshift_variant	1038	exon1			.		CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"Cerebellar degeneration-related protein-1 (34kD)"	302650	"cerebellar degeneration-related protein (34kD)"	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.444delT	chrX.hg19:g.139866088delA	ENSP00000359563:p.Phe148fs	131.0	0.0		213.0	14.0	NM_004065	Q5JXH6	Frame_Shift_Del	DEL	ENST00000370532.2	hg19	CCDS14670.1																																																																																			.	.		0.433	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065		-	139866088	A	-	139866088	7	5	103	1	0	1	0	1	0	0	0	0	3173	127	5	0	348	0	CDR1	23	139866088	Frame_Shift_Del	DEL	A	TCGA-DD-A1EG-01A-11D-A20W-10	996702	139866088	15404472	1202	15825										
ABCD1	215	hgsc.bcm.edu	37	chrX	153009116	153009116	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gctctgccagatcctgggcgAggccgtggccccagcgcatg	15	15	1	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:153009116A>G	ENST00000218104.3	+	10	2564	c.2165A>G	c.(2164-2166)gAg>gGg	p.E722G	U52111.14_ENST00000434284.1_RNA	NM_000033.3	NP_000024.2	P33897	ABCD1_HUMAN	ATP-binding cassette, sub-family D (ALD), member 1	722					alpha-linolenic acid metabolic process (GO:0036109)|ATP catabolic process (GO:0006200)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|linoleic acid metabolic process (GO:0043651)|long-chain fatty acid catabolic process (GO:0042758)|peroxisomal long-chain fatty acid import (GO:0015910)|peroxisomal membrane transport (GO:0015919)|peroxisome organization (GO:0007031)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid catabolic process (GO:0042760)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|peroxisomal fatty-acyl-CoA transporter activity (GO:0005325)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(2)	18	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ATCCTGGGCGAGGCCGTGGCC	0.721																																					p.E722G		Atlas-SNP	.											.	ABCD1	59	.	0			c.A2165G						.						6	6	6					X																	153009116		2130	4176	6306	SO:0001583	missense	215	exon10			TGGGCGAGGCCGT	Z21876	CCDS14728.1	Xq28	2012-03-14			ENSG00000101986	ENSG00000101986		"ATP binding cassette transporters / subfamily D"	61	protein-coding gene	gene with protein product		300371		ALD		8441467, 6795626	Standard	NM_000033		Approved	AMN, ALDP, adrenoleukodystrophy	uc004fif.2	P33897	OTTHUMG00000024215	ENST00000218104.3:c.2165A>G	chrX.hg19:g.153009116A>G	ENSP00000218104:p.Glu722Gly	24.0	0.0		63.0	4.0	NM_000033	Q6GTZ2	Missense_Mutation	SNP	ENST00000218104.3	hg19	CCDS14728.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.088547	0.76756	.	.	ENSG00000101986	ENST00000218104	D	0.94793	-3.52	4.65	4.65	0.58169	.	0.443226	0.17631	N	0.167383	D	0.95765	0.8622	M	0.85710	2.77	0.80722	D	1	P	0.44044	0.825	P	0.48524	0.58	D	0.95633	0.8691	10	0.66056	D	0.02	-16.8889	12.2981	0.54859	1.0:0.0:0.0:0.0	.	722	P33897	ABCD1_HUMAN	G	722	ENSP00000218104:E722G	ENSP00000218104:E722G	E	+	2	0	ABCD1	152662310	0.999000	0.42202	0.814000	0.32528	0.456000	0.32438	4.668000	0.61568	1.537000	0.49254	0.425000	0.28330	GAG	.	.		0.721	ABCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061041.1	NM_000033		G	153009116	A	G	153009116	3	3	103	1	0	0	0	0	1	0	0	0	60	304	11	2	2203	2	ABCD1	23	153009116	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	13143028	153009116	2261444	1203	15826										
PDZD4	57595	hgsc.bcm.edu	37	chrX	153070036	153070036	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	ccaggtggcacttgatctccAggagctcacggtagcgctca	12	13	3	1			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:153070036A>G	ENST00000164640.4	-	8	1273	c.1082T>C	c.(1081-1083)cTg>cCg	p.L361P	PDZD4_ENST00000544474.1_Missense_Mutation_p.L252P|PDZD4_ENST00000475140.1_5'Flank|PDZD4_ENST00000393758.2_Missense_Mutation_p.L286P	NM_032512.2	NP_115901.2	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	361						cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(5)|lung(13)|skin(1)	23	all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTTGATCTCCAGGAGCTCACG	0.667																																					p.L361P		Atlas-SNP	.											.	PDZD4	67	.	0			c.T1082C						.						47	41	43					X																	153070036		2203	4300	6503	SO:0001583	missense	57595	exon8			ATCTCCAGGAGCT	AK091444	CCDS14732.1	Xq28	2008-02-05		2006-01-24	ENSG00000067840	ENSG00000067840			21167	protein-coding gene	gene with protein product		300634		PDZK4		10819331, 15077175	Standard	NM_032512		Approved	KIAA1444, LU1, FLJ34125, PDZRN4L	uc004fiz.1	Q76G19	OTTHUMG00000024209	ENST00000164640.4:c.1082T>C	chrX.hg19:g.153070036A>G	ENSP00000164640:p.Leu361Pro	84.0	0.0		106.0	5.0	NM_032512	B3KXB1|B7ZKY3|Q8NB75|Q9BUH9|Q9P284	Missense_Mutation	SNP	ENST00000164640.4	hg19	CCDS14732.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.944624	0.53079	.	.	ENSG00000067840	ENST00000164640;ENST00000393758;ENST00000537633;ENST00000544474	T;T;T	0.19394	2.15;2.17;2.4	5.15	5.15	0.70609	.	0.000000	0.64402	D	0.000001	T	0.44350	0.1289	M	0.67397	2.05	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.998;0.999;1.0	T	0.42599	-0.9442	10	0.87932	D	0	-18.6317	13.0044	0.58696	1.0:0.0:0.0:0.0	.	252;367;361;286;265	B7ZKY3;Q17RL8;Q76G19;D3DWW0;B3KVR9	.;.;PDZD4_HUMAN;.;.	P	361;286;265;252	ENSP00000164640:L361P;ENSP00000377355:L286P;ENSP00000442033:L252P	ENSP00000164640:L361P	L	-	2	0	PDZD4	152723230	1.000000	0.71417	0.998000	0.56505	0.463000	0.32649	9.332000	0.96446	1.711000	0.51337	0.430000	0.28490	CTG	.	.		0.667	PDZD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061013.3	NM_032512		G	153070036	A	G	153070036	3	3	103	1	0	0	0	0	1	0	0	0	11712	188	7	2	1231	2	PDZD4	23	153070036	Missense_Mutation	SNP	A	TCGA-DD-A1EG-01A-11D-A20W-10	60920	153070036	2200524	1204	15827										
FLNA	2316	hgsc.bcm.edu	37	chrX	153596402	153596402	+	Frame_Shift_Del	DEL	G	G	-													0.0116472545757072	14	1	1.12693534844668	0.335397425132942	1.37689469265102	2.18672913285359e-05	0.00276632013778537	0	gatggagtagtgcaggatcaGggtccagatgaggcccagga							TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:153596402delG	ENST00000369850.3	-	3	666	c.430delC	c.(430-432)ctgfs	p.L144fs	FLNA_ENST00000422373.1_Frame_Shift_Del_p.L144fs|FLNA_ENST00000344736.4_Frame_Shift_Del_p.L144fs|FLNA_ENST00000360319.4_Frame_Shift_Del_p.L144fs	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	144	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGCAGGATCAGGGTCCAGATG	0.617																																					p.L144fs		Atlas-INDEL	.											.	FLNA	373	.	0			c.431delT						.						133	142	139					X																	153596402		2189	4286	6475	SO:0001589	frameshift_variant	2316	exon3			.	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.430delC	chrX.hg19:g.153596402delG	ENSP00000358866:p.Leu144fs	122.0	0.0		182.0	11.0	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Frame_Shift_Del	DEL	ENST00000369850.3	hg19	CCDS48194.1																																																																																			.	.		0.617	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			-	153596402	G	-	153596402	7	5	103	1	0	1	0	1	0	0	0	0	5941	991	35	0	7697	0	FLNA	23	153596402	Frame_Shift_Del	DEL	G	TCGA-DD-A1EG-01A-11D-A20W-10	526366	153596402	1674158	1205	15828										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27105550	27105550	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agctccttgtagaatatttcCgacgatgcctgattgagatc	9	9	0	3			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr1:27105550C>T	ENST00000324856.7	+	20	5532	c.5161C>T	c.(5161-5163)Cga>Tga	p.R1721*	ARID1A_ENST00000457599.2_Nonsense_Mutation_p.R1504*|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.R1338*|ARID1A_ENST00000540690.1_Nonsense_Mutation_p.R49*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1721					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.R1721*(3)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGAATATTTCCGACGATGCCT	0.443			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.R1721X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	ARID1A,NS,carcinoma,0,8	ARID1A	842	.	3	Substitution - Nonsense(3)	ovary(1)|large_intestine(1)|endometrium(1)	c.C5161T						.						184	203	196					1																	27105550		2203	4300	6503	SO:0001587	stop_gained	8289	exon20			TATTTCCGACGAT	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5161C>T	chr1.hg19:g.27105550C>T	ENSP00000320485:p.Arg1721*	122.0	0.0		234.0	117.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	41|41	9.126146|9.126146	0.99073|0.99073	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000430799|ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	.|.	.|.	.|.	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	.|0.060827	.|0.64402	.|D	.|0.000007	T|.	0.34745|.	0.0908|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.15954|.	-1.0419|.	4|.	.|0.02654	.|T	.|1	-6.2012|-6.2012	13.2131|13.2131	0.59836|0.59836	0.159:0.841:0.0:0.0|0.159:0.841:0.0:0.0	.|.	.|.	.|.	.|.	L|X	617|1721;1504;1338;49	.|.	.|ENSP00000320485:R1721X	P|R	+|+	2|1	0|2	ARID1A|ARID1A	26978137|26978137	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.413000|2.413000	0.44618|0.44618	2.622000|2.622000	0.88805|0.88805	0.591000|0.591000	0.81541|0.81541	CCG|CGA	.	.		0.443	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27105550	C	T	27105550	4	4	104	1	0	0	0	0	0	1	0	0	913	644	23	1	5239	1	ARID1A	1	27105550	Nonsense_Mutation	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10		27105550	222145071	1	15829										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27106893	27106894	+	Frame_Shift_Ins	INS	-	-	T													0	0	1	0	0	0	1	1	0	tgtgccgggagatggctgtgINSgtactgctggccaacctggc							TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr1:27106893_27106894insT	ENST00000324856.7	+	20	6875_6876	c.6504_6505insT	c.(6505-6507)gtafs	p.V2169fs	ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.V1952fs|ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.V1786fs|ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.V497fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2169					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGATGGCTGTGGTACTGCTGGC	0.609			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.V2168fs		Atlas-Indel,Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.6504_6505insT						.																																			SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	Exception_encountered	chr1.hg19:g.27106893_27106894insT	ENSP00000320485:p.Val2169fs	49.0	0.0		73.0	16.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.609	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27106894	-	T	27106893	7	5	104	1	0	1	1	0	0	0	0	0	913	1335	47	0	6582	0	ARID1A	1	27106893	Frame_Shift_Ins	INS	-	TCGA-DD-A1EH-01A-11D-A12Z-10	1343	27106893	222143728	2	15830										
MCL1	4170	hgsc.bcm.edu	37	chr1	150551926	150551927	+	Frame_Shift_Ins	INS	-	-	C													0	0	1	0	0	0	1	1	0	gccctcccgggcgggtggcgINSccgccgctgccggcccccaa							TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr1:150551926_150551927insC	ENST00000369026.2	-	1	139_140	c.80_81insG	c.(79-81)ggcfs	p.G27fs	MCL1_ENST00000307940.3_Frame_Shift_Ins_p.G27fs|MCL1_ENST00000464132.1_5'Flank	NM_001197320.1|NM_021960.4	NP_001184249.1|NP_068779.1	Q07820	MCL1_HUMAN	myeloid cell leukemia 1	27					apoptotic mitochondrial changes (GO:0008637)|cell fate determination (GO:0001709)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|protein transmembrane transport (GO:0071806)|regulation of response to DNA damage stimulus (GO:2001020)|response to cytokine (GO:0034097)	Bcl-2 family protein complex (GO:0097136)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	BH3 domain binding (GO:0051434)|protein channel activity (GO:0015266)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)	8	all_cancers(9;1.69e-53)|all_epithelial(9;1.95e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GGCGGGTGGCGCCGCCGCTGCC	0.703																																					p.G27fs		Atlas-INDEL	.											.	MCL1	27	.	0			c.81_82insG						.																																			SO:0001589	frameshift_variant	4170	exon1			.	BC017197	CCDS956.1, CCDS957.1, CCDS72909.1	1q21	2014-03-07	2014-03-07		ENSG00000143384	ENSG00000143384			6943	protein-coding gene	gene with protein product		159552	"myeloid cell leukemia sequence 1 (BCL2-related)"			7682708, 7835896	Standard	NM_021960		Approved	BCL2L3, Mcl-1	uc001euz.3	Q07820	OTTHUMG00000034867	ENST00000369026.2:c.81dupG	chr1.hg19:g.150551928_150551928dupC	ENSP00000358022:p.Gly27fs	13.0	0.0		209.0	13.0	NM_021960	B2R6B2|D3DV03|D3DV04|Q9HD91|Q9NRQ3|Q9NRQ4|Q9UHR7|Q9UHR8|Q9UHR9|Q9UNJ1	Frame_Shift_Ins	INS	ENST00000369026.2	hg19	CCDS957.1																																																																																			.	.		0.703	MCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084402.1	NM_021960		C	150551927	-	C	150551926	7	5	104	1	0	1	1	0	0	0	0	0	9393	1074	38	0	994	0	MCL1	1	150551926	Frame_Shift_Ins	INS	-	TCGA-DD-A1EH-01A-11D-A12Z-10	123445033	150551926	98698695	3	15831										
LCE1B	353132	hgsc.bcm.edu	37	chr1	152785040	152785040	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtccccctaagtgtcctccaGtctcttcctgctgcagtgtc	8	16	1	0			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr1:152785040G>T	ENST00000360090.3	+	1	594	c.118G>T	c.(118-120)Gtc>Ttc	p.V40F		NM_178349.1	NP_848126.1	Q5T7P3	LCE1B_HUMAN	late cornified envelope 1B	40					keratinization (GO:0031424)					breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|skin(2)	18	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GTGTCCTCCAGTCTCTTCCTG	0.647																																					p.V40F		Atlas-SNP	.											.	LCE1B	45	.	0			c.G118T						.						92	95	94					1																	152785040		2203	4300	6503	SO:0001583	missense	353132	exon1			CCTCCAGTCTCTT	BI670515	CCDS1027.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000196734	ENSG00000196734		"Late cornified envelopes"	16611	protein-coding gene	gene with protein product		612604	"small proline rich-like (epidermal differentiation complex) 2A"	SPRL2A		11698679	Standard	NM_178349		Approved	LEP2	uc001faq.3	Q5T7P3	OTTHUMG00000014402	ENST00000360090.3:c.118G>T	chr1.hg19:g.152785040G>T	ENSP00000353203:p.Val40Phe	100.0	0.0		839.0	180.0	NM_178349	A4IF40	Missense_Mutation	SNP	ENST00000360090.3	hg19	CCDS1027.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696611	0.30142	.	.	ENSG00000196734	ENST00000360090;ENST00000439693	T	0.04862	3.54	4.34	4.34	0.51931	.	0.856987	0.09501	N	0.793570	T	0.06735	0.0172	L	0.51422	1.61	0.27140	N	0.961677	D	0.54207	0.965	P	0.50708	0.648	T	0.16158	-1.0412	10	0.87932	D	0	.	12.5252	0.56083	0.0:0.0:1.0:0.0	.	40	Q5T7P3	LCE1B_HUMAN	F	40	ENSP00000353203:V40F	ENSP00000353203:V40F	V	+	1	0	LCE1B	151051664	0.397000	0.25270	0.932000	0.37286	0.872000	0.50106	2.780000	0.47742	2.398000	0.81561	0.650000	0.86243	GTC	.	.		0.647	LCE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040060.1	NM_178349		T	152785040	G	T	152785040	3	4	104	1	0	0	0	0	1	0	0	0	8669	1029	36	3	120	3	LCE1B	1	152785040	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	2233114	152785040	96465581	4	15832										
OR2M3	127062	hgsc.bcm.edu	37	chr1	248366773	248366773	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccctctaagatacaccaatcTcatgagccctaaaatttgtg	5	12	2	2			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr1:248366773T>C	ENST00000456743.1	+	1	442	c.404T>C	c.(403-405)cTc>cCc	p.L135P		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TACACCAATCTCATGAGCCCT	0.438																																					p.L135P		Atlas-SNP	.											.	OR2M3	116	.	0			c.T404C						.						218	219	218					1																	248366773		2203	4300	6503	SO:0001583	missense	127062	exon1			CCAATCTCATGAG		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"GPCR / Class A : Olfactory receptors"	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.404T>C	chr1.hg19:g.248366773T>C	ENSP00000389625:p.Leu135Pro	147.0	0.0		911.0	202.0	NM_001004689	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	hg19	CCDS31107.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.249464	0.39797	.	.	ENSG00000228198	ENST00000456743	T	0.33654	1.4	2.55	2.55	0.30701	GPCR, rhodopsin-like superfamily (1);	0.321128	0.17282	U	0.179973	T	0.65091	0.2658	M	0.93241	3.395	0.29984	N	0.817421	D	0.65815	0.995	D	0.66716	0.946	T	0.66280	-0.5963	10	0.87932	D	0	.	10.4551	0.44546	0.0:0.0:0.0:1.0	.	135	Q8NG83	OR2M3_HUMAN	P	135	ENSP00000389625:L135P	ENSP00000389625:L135P	L	+	2	0	OR2M3	246433396	0.007000	0.16637	0.077000	0.20336	0.007000	0.05969	1.217000	0.32455	1.168000	0.42723	0.333000	0.21579	CTC	.	.		0.438	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		C	248366773	T	C	248366773	3	2	104	1	0	0	0	0	1	0	0	0	11020	1551	54	2	406	2	OR2M3	1	248366773	Missense_Mutation	SNP	T	TCGA-DD-A1EH-01A-11D-A12Z-10	95581733	248366773	883848	5	15833										
IL18RAP	8807	hgsc.bcm.edu	37	chr2	103068506	103068506	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctaggttctgggccaaaatGcgctaccacatgcctgtgaa	10	11	2	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr2:103068506G>T	ENST00000264260.2	+	12	2254	c.1665G>T	c.(1663-1665)atG>atT	p.M555I	IL18RAP_ENST00000409369.1_Missense_Mutation_p.M413I	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	555	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						GGGCCAAAATGCGCTACCACA	0.453																																					p.M555I		Atlas-SNP	.											.	IL18RAP	102	.	0			c.G1665T						.						138	149	145					2																	103068506		2203	4300	6503	SO:0001583	missense	8807	exon12			CAAAATGCGCTAC	AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.1665G>T	chr2.hg19:g.103068506G>T	ENSP00000264260:p.Met555Ile	67.0	0.0		152.0	61.0	NM_003853	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Missense_Mutation	SNP	ENST00000264260.2	hg19	CCDS2061.1	.	.	.	.	.	.	.	.	.	.	G	0.037	-1.300447	0.01364	.	.	ENSG00000115607	ENST00000264260;ENST00000409369	T;T	0.02103	4.45;4.45	6.02	-6.57	0.01842	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.758254	0.13065	N	0.416553	T	0.00936	0.0031	N	0.11313	0.125	0.09310	N	0.999997	B	0.02656	0.0	B	0.06405	0.002	T	0.45086	-0.9285	10	0.35671	T	0.21	.	0.2591	0.00216	0.2796:0.1562:0.2495:0.3148	.	555	O95256	I18RA_HUMAN	I	555;413	ENSP00000264260:M555I;ENSP00000387201:M413I	ENSP00000264260:M555I	M	+	3	0	IL18RAP	102434938	0.000000	0.05858	0.044000	0.18714	0.081000	0.17604	-0.750000	0.04808	-0.699000	0.05077	-0.158000	0.13435	ATG	.	.		0.453	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853		T	103068506	G	T	103068506	3	4	104	1	0	0	0	0	1	0	0	0	7657	1319	46	3	1703	3	IL18RAP	2	103068506	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10		103068506	140130867	6	15834										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160833216	160833216	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cgtactggtaccagaacggaAtcttgggtttcacatctgca	10	10	3	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr2:160833216A>G	ENST00000283243.7	-	16	2623	c.2417T>C	c.(2416-2418)aTt>aCt	p.I806T	PLA2R1_ENST00000392771.1_Missense_Mutation_p.I806T	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	806					cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CCAGAACGGAATCTTGGGTTT	0.353																																					p.I806T		Atlas-SNP	.											.	PLA2R1	153	.	0			c.T2417C						.						88	81	84					2																	160833216		2203	4300	6503	SO:0001583	missense	22925	exon16			AACGGAATCTTGG	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.2417T>C	chr2.hg19:g.160833216A>G	ENSP00000283243:p.Ile806Thr	121.0	0.0		250.0	115.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	hg19	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	A	1.441	-0.567640	0.03910	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.06218	3.37;3.33	4.77	3.62	0.41486	.	0.335919	0.30528	N	0.009440	T	0.06554	0.0168	L	0.60455	1.87	0.28249	N	0.925339	B;P;B	0.36959	0.004;0.575;0.265	B;B;B	0.33620	0.011;0.167;0.116	T	0.21245	-1.0251	10	0.14252	T	0.57	.	9.3311	0.38023	0.913:0.0:0.087:0.0	.	806;806;806	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	T	806	ENSP00000283243:I806T;ENSP00000376524:I806T	ENSP00000283243:I806T	I	-	2	0	PLA2R1	160541462	0.985000	0.35326	0.894000	0.35097	0.968000	0.65278	1.144000	0.31565	0.798000	0.33994	0.459000	0.35465	ATT	.	.		0.353	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			G	160833216	A	G	160833216	3	3	104	1	0	0	0	0	1	0	0	0	12019	101	4	2	2042	2	PLA2R1	2	160833216	Missense_Mutation	SNP	A	TCGA-DD-A1EH-01A-11D-A12Z-10	57764710	160833216	82366157	7	15835										
TNS1	7145	hgsc.bcm.edu	37	chr2	218696257	218696257	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggggtgtcttggccagaccCgggggggaccgcactgtgcc	18	12	1	1	rs545831386		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr2:218696257C>T	ENST00000171887.4	-	20	3371	c.2919G>A	c.(2917-2919)ccG>ccA	p.P973P	TNS1_ENST00000419504.1_Silent_p.P973P|TNS1_ENST00000430930.1_Silent_p.P973P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	973					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TGGCCAGACCCGGGGGGGACC	0.632													C|||	1	0.000199681	0	0	5008	,	,		15732	0.001		0	False		,,,				2504	0				p.P973P		Atlas-SNP	.											.	TNS1	251	.	0			c.G2919A						.																																			SO:0001819	synonymous_variant	7145	exon20			CAGACCCGGGGGG	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.2919G>A	chr2.hg19:g.218696257C>T		16.0	0.0		35.0	18.0	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	hg19	CCDS2407.1																																																																																			.	.		0.632	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		T	218696257	C	T	218696257	2	4	104	1	0	0	0	0	0	0	0	1	16358	639	23	1		1	TNS1	2	218696257	Silent	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10	57863041	218696257	24503116	8	15836										
IQCA1	79781	hgsc.bcm.edu	37	chr2	237300683	237300683	+	Frame_Shift_Del	DEL	T	T	-													0	0	1	0	0	0	1	1	0	tgtccacagctagctttaagTttttaagttcctgtctcatc							TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr2:237300683delT	ENST00000409907.3	-	11	1623	c.1349delA	c.(1348-1350)aacfs	p.N450fs	IQCA1_ENST00000309507.5_Frame_Shift_Del_p.N446fs|AC019068.2_ENST00000413353.1_RNA|IQCA1_ENST00000431676.2_Frame_Shift_Del_p.N409fs|IQCA1_ENST00000465621.1_5'Flank	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	450	Lys-rich.						ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						TAGCTTTAAGTTTTTAAGTTC	0.438																																					p.N457fs		Atlas-Indel,Pindel	.											.	IQCA1	170	.	0			c.1371delC						.						169	171	170					2																	237300683		1868	4103	5971	SO:0001589	frameshift_variant	79781	exon11			.	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"ATPases / AAA-type"	26195	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 11"		"IQ motif containing with AAA domain"	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.1349delA	chr2.hg19:g.237300683delT	ENSP00000387347:p.Asn450fs	114.0	0.0		340.0	149.0	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Frame_Shift_Del	DEL	ENST00000409907.3	hg19	CCDS46549.1																																																																																			.	.		0.438	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		-	237300683	T	-	237300683	7	5	104	1	0	1	0	1	0	0	0	0	7811	1725	60	0	1155	0	IQCA1	2	237300683	Frame_Shift_Del	DEL	T	TCGA-DD-A1EH-01A-11D-A12Z-10	18604426	237300683	5898690	9	15837										
HEG1	57493	hgsc.bcm.edu	37	chr3	124732433	124732434	+	In_Frame_Ins	INS	-	-	AGAGGAGGAGGAGGAGGA													0	0	1	0	0	0	1	1	0	gaagaagaggaggaggaggaINSagaggaggaggaggagtcac					rs374949821		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr3:124732433_124732434insAGAGGAGGAGGAGGAGGA	ENST00000311127.4	-	6	2056_2057	c.1989_1990insTCCTCCTCCTCCTCCTCT	c.(1987-1992)tcttcc>tctTCCTCCTCCTCCTCCTCTtcc	p.663_664SS>SSSSSSSS	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	663	Ser-rich.				cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						gaggaggaggaagaggaggagg	0.49																																					p.S664delinsSSSSSSS		Atlas-INDEL	.											.	HEG1	109	.	0			c.1990_1991insTCCTCCTCCTCCTCCTCT						.																																			SO:0001652	inframe_insertion	57493	exon6			.	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.1989_1990insTCCTCCTCCTCCTCCTCT	chr3.hg19:g.124732433_124732434insAGAGGAGGAGGAGGAGGA	ENSP00000311502:p.Ser669_Ser670dup	36.0	0.0		102.0	14.0	NM_020733	Q6NX66|Q8NC40|Q9BSV0	In_Frame_Ins	INS	ENST00000311127.4	hg19	CCDS46898.1																																																																																			.	.		0.49	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		AGAGGAGGAGGAGGAGGA	124732434	-	AGAGGAGGAGGAGGAGGA	124732433	7	5	104	1	0	1	1	0	0	0	0	0	7053	246	9	0	2203	0	HEG1	3	124732433	In_Frame_Ins	INS	-	TCGA-DD-A1EH-01A-11D-A12Z-10		124732433	73289997	10	15838										
SI	6476	hgsc.bcm.edu	37	chr3	164750329	164750329	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctggttagaagcatcataaGtgaaattggaatgagcgttc	11	6	1	3			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr3:164750329G>A	ENST00000264382.3	-	24	2779	c.2717C>T	c.(2716-2718)aCt>aTt	p.T906I		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	906	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	AGCATCATAAGTGAAATTGGA	0.313										HNSCC(35;0.089)																											p.T906I		Atlas-SNP	.											.	SI	500	.	0			c.C2717T						.						136	132	133					3																	164750329		2202	4300	6502	SO:0001583	missense	6476	exon24			TCATAAGTGAAAT	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.2717C>T	chr3.hg19:g.164750329G>A	ENSP00000264382:p.Thr906Ile	49.0	0.0		96.0	35.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	hg19	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	G	9.509	1.105222	0.20632	.	.	ENSG00000090402	ENST00000264382	T	0.13901	2.55	4.88	1.8	0.24995	.	0.881571	0.10133	N	0.711840	T	0.21347	0.0514	M	0.85197	2.74	0.23930	N	0.996436	B	0.18863	0.031	B	0.16289	0.015	T	0.22591	-1.0212	10	0.72032	D	0.01	.	9.0727	0.36502	0.0:0.4573:0.3861:0.1566	.	906	P14410	SUIS_HUMAN	I	906	ENSP00000264382:T906I	ENSP00000264382:T906I	T	-	2	0	SI	166233023	0.996000	0.38824	0.364000	0.25888	0.701000	0.40568	0.488000	0.22371	0.720000	0.32209	0.655000	0.94253	ACT	.	.		0.313	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		A	164750329	G	A	164750329	3	1	104	1	0	0	0	0	1	0	0	0	14312	1029	36	3	2866	3	SI	3	164750329	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	40017896	164750329	33272101	11	15839										
DSPP	1834	hgsc.bcm.edu	37	chr4	88536324	88536324	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgacagcagcgatagcagcaAcagcagtgatagcagcgaca	12	10	0	2			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr4:88536324A>G	ENST00000282478.7	+	4	2543	c.2510A>G	c.(2509-2511)aAc>aGc	p.N837S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.N837S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	837	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gatagcagcaacagcagtgat	0.498																																					p.N837S		Atlas-SNP	.											.	DSPP	174	.	0			c.A2510G						.						89	111	103					4																	88536324		1649	2948	4597	SO:0001583	missense	1834	exon5			GCAGCAACAGCAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2510A>G	chr4.hg19:g.88536324A>G	ENSP00000282478:p.Asn837Ser	112.0	0.0		313.0	19.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	a	0.880	-0.728918	0.03135	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88201	-2.35;-2.35	0.918	-1.71	0.08133	.	.	.	.	.	T	0.70587	0.3241	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.58912	-0.7552	9	0.02654	T	1	.	3.1451	0.06469	0.7043:0.0:0.2957:0.0	.	837	Q9NZW4	DSPP_HUMAN	S	837	ENSP00000382213:N837S;ENSP00000282478:N837S	ENSP00000282478:N837S	N	+	2	0	DSPP	88755348	0.287000	0.24315	0.010000	0.14722	0.001000	0.01503	0.825000	0.27393	-0.158000	0.11040	-1.782000	0.00648	AAC	.	.		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		G	88536324	A	G	88536324	3	3	104	1	0	0	0	0	1	0	0	0	4784	43	2	2	2524	2	DSPP	4	88536324	Missense_Mutation	SNP	A	TCGA-DD-A1EH-01A-11D-A12Z-10		88536324	102617952	12	15840										
IRF2	3660	hgsc.bcm.edu	37	chr4	185320192	185320192	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tggcggattggtgacaatctCttgattctcaatgttgctgt	11	7	2	2			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr4:185320192C>A	ENST00000393593.3	-	7	778	c.571G>T	c.(571-573)Gag>Tag	p.E191*		NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	191					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		GTGACAATCTCTTGATTCTCA	0.493																																					p.E191X		Atlas-SNP	.											.	IRF2	53	.	0			c.G571T						.						135	112	120					4																	185320192		2203	4300	6503	SO:0001587	stop_gained	3660	exon7			CAATCTCTTGATT		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.571G>T	chr4.hg19:g.185320192C>A	ENSP00000377218:p.Glu191*	73.0	0.0		104.0	88.0	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Nonsense_Mutation	SNP	ENST00000393593.3	hg19	CCDS3835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.1|24.1	4.494998|4.494998	0.85069|0.85069	.|.	.|.	ENSG00000168310|ENSG00000168310	ENST00000393593;ENST00000502750|ENST00000505067	.|.	.|.	.|.	5.9|5.9	5.06|5.06	0.68205|0.68205	.|.	0.652135|.	0.15902|.	N|.	0.239008|.	.|T	.|0.53465	.|0.1798	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.61486	.|-0.7053	.|3	0.06891|.	T|.	0.86|.	-10.9067|-10.9067	10.0205|10.0205	0.42039|0.42039	0.0:0.8011:0.0:0.1989|0.0:0.8011:0.0:0.1989	.|.	.|.	.|.	.|.	X|I	191;48|124	.|.	ENSP00000377218:E191X|.	E|R	-|-	1|2	0|0	IRF2|IRF2	185557186|185557186	0.993000|0.993000	0.37304|0.37304	1.000000|1.000000	0.80357|0.80357	0.855000|0.855000	0.48748|0.48748	0.884000|0.884000	0.28214|0.28214	2.806000|2.806000	0.96561|0.96561	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.		0.493	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1			A	185320192	C	A	185320192	4	1	104	1	0	0	0	0	0	1	0	0	7837	922	32	3	490	3	IRF2	4	185320192	Nonsense_Mutation	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10	96783868	185320192	5834084	13	15841										
VCAN	1462	hgsc.bcm.edu	37	chr5	82833574	82833574	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acttctgtcacatacactccCactatagttccaagttctgc	4	14	3	0			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr5:82833574C>T	ENST00000265077.3	+	8	5317	c.4752C>T	c.(4750-4752)ccC>ccT	p.P1584P	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Silent_p.P597P|VCAN_ENST00000342785.4_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1584	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CATACACTCCCACTATAGTTC	0.408																																					p.P1584P		Atlas-SNP	.											.	VCAN	498	.	0			c.C4752T						.						89	91	90					5																	82833574		2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			CACTCCCACTATA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.4752C>T	chr5.hg19:g.82833574C>T		77.0	0.0		119.0	30.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	hg19	CCDS4060.1																																																																																			.	.		0.408	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82833574	C	T	82833574	2	4	104	1	0	0	0	0	0	0	0	1	17153	581	21	3		3	VCAN	5	82833574	Silent	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10		82833574	98081686	14	15842										
FBN2	2201	hgsc.bcm.edu	37	chr5	127681089	127681089	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtaagaacatcccctcggttAgcaaagccagccccgcgggg	12	14	0	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr5:127681089A>T	ENST00000508053.1	-	30	4151	c.3177T>A	c.(3175-3177)gcT>gcA	p.A1059A	FBN2_ENST00000508989.1_Silent_p.A1026A|FBN2_ENST00000262464.4_Silent_p.A1059A			P35556	FBN2_HUMAN	fibrillin 2	1059					anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CCCCTCGGTTAGCAAAGCCAG	0.607																																					p.A1059A		Atlas-SNP	.											.	FBN2	858	.	0			c.T3177A						.						79	85	83					5																	127681089		2203	4300	6503	SO:0001819	synonymous_variant	2201	exon24			TCGGTTAGCAAAG	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.3177T>A	chr5.hg19:g.127681089A>T		45.0	0.0		93.0	26.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	.		0.607	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127681089	A	T	127681089	2	4	104	1	0	0	0	0	0	0	0	1	5711	407	15	4		4	FBN2	5	127681089	Silent	SNP	A	TCGA-DD-A1EH-01A-11D-A12Z-10	44847515	127681089	53234171	15	15843										
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12125147	12125148	+	Frame_Shift_Ins	INS	-	-	A													0	0	1	0	0	0	1	1	0	agagaaggaatttctatgtgINSaaaatgttttttcagagatg							TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr6:12125147_12125148insA	ENST00000379388.2	+	4	5451_5452	c.5119_5120insA	c.(5119-5121)gaafs	p.E1707fs	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1707					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				ATTTCTATGTGAAAATGTTTTT	0.376																																					p.E1707fs		Atlas-Indel,Pindel	.											.	HIVEP1	242	.	0			c.5119_5120insA						.																																			SO:0001589	frameshift_variant	3096	exon4			.	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.5123dupA	chr6.hg19:g.12125151_12125151dupA	ENSP00000368698:p.Glu1707fs	63.0	0.0		246.0	43.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Frame_Shift_Ins	INS	ENST00000379388.2	hg19	CCDS43426.1																																																																																			.	.		0.376	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		A	12125148	-	A	12125147	7	5	104	1	0	1	1	0	0	0	0	0	7195	1291	45	0	5129	0	HIVEP1	6	12125147	Frame_Shift_Ins	INS	-	TCGA-DD-A1EH-01A-11D-A12Z-10		12125147	158989920	16	15844										
MUC21	394263	hgsc.bcm.edu	37	chr6	30954774	30954774	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggcacagccaccaactctgaGtccagcacagtgtccagtgg	11	14	1	1	rs41288649		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr6:30954774G>C	ENST00000376296.3	+	2	1063	c.822G>C	c.(820-822)gaG>gaC	p.E274D	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	274	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAACTCTGAGTCCAGCACAG	0.612																																					p.E274D		Atlas-SNP	.											.	MUC21	98	.	0			c.G822C						.						185	181	182					6																	30954774		2203	4300	6503	SO:0001583	missense	394263	exon2			CTCTGAGTCCAGC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.822G>C	chr6.hg19:g.30954774G>C	ENSP00000365473:p.Glu274Asp	63.0	0.0		472.0	46.0	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	hg19	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	7.723	0.697571	0.15106	.	.	ENSG00000204544	ENST00000376296	T	0.01963	4.53	3.7	-3.24	0.05094	.	.	.	.	.	T	0.00552	0.0018	L	0.29908	0.895	0.09310	N	1	P	0.40834	0.73	B	0.37451	0.25	T	0.48080	-0.9066	8	.	.	.	0.085	4.9779	0.14149	0.291:0.3326:0.3764:0.0	.	274	Q5SSG8	MUC21_HUMAN	D	274	ENSP00000365473:E274D	.	E	+	3	2	MUC21	31062753	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	-2.404000	0.01045	-0.243000	0.09653	0.472000	0.43445	GAG	.	G|0.500;C|0.500		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		C	30954774	G	C	30954774	3	2	104	1	0	0	0	0	1	0	0	0	9986	1020	36	4	828	4	MUC21	6	30954774	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	18829627	30954774	140160293	17	15845										
TPD52L1	7164	hgsc.bcm.edu	37	chr6	125584076	125584076	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agagcttggcaggaggctccCggcggaccaaggaggaggag	19	9	0	1	rs559154046		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr6:125584076C>T	ENST00000534000.1	+	7	879	c.583C>T	c.(583-585)Cgg>Tgg	p.R195W	TPD52L1_ENST00000524679.1_3'UTR|TPD52L1_ENST00000392482.2_3'UTR|TPD52L1_ENST00000532429.1_Missense_Mutation_p.R166W|TPD52L1_ENST00000304877.13_Missense_Mutation_p.R200W|TPD52L1_ENST00000527711.1_Missense_Mutation_p.R182W|TPD52L1_ENST00000534199.1_3'UTR|HDDC2_ENST00000608456.1_Intron|TPD52L1_ENST00000530868.1_3'UTR|TPD52L1_ENST00000528193.1_3'UTR|TPD52L1_ENST00000368402.5_3'UTR|TPD52L1_ENST00000368388.2_3'UTR	NM_003287.2	NP_003278.1	Q16890	TPD53_HUMAN	tumor protein D52-like 1	195					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|prostate(1)	5			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)		AGGAGGCTCCCGGCGGACCAA	0.612													C|||	1	0.000199681	8e-04	0	5008	,	,		14409	0		0	False		,,,				2504	0				p.R195W		Atlas-SNP	.											.	TPD52L1	14	.	0			c.C583T						.						37	35	36					6																	125584076		2203	4300	6503	SO:0001583	missense	7164	exon7			GGCTCCCGGCGGA	U44427	CCDS5130.1, CCDS34527.1, CCDS34528.1, CCDS43502.1, CCDS75513.1, CCDS75514.1	6q22-q23	2008-07-29			ENSG00000111907	ENSG00000111907			12006	protein-coding gene	gene with protein product		604069				8812487, 16112108	Standard	NM_003287		Approved	D53, hD53	uc003pzu.1	Q16890	OTTHUMG00000015505	ENST00000534000.1:c.583C>T	chr6.hg19:g.125584076C>T	ENSP00000434142:p.Arg195Trp	16.0	0.0		18.0	10.0	NM_003287	A8K757|A8K772|A8MUD2|A8MUJ7|A8MW70|F6V707|O43397|Q5TC99|Q5TDQ0|Q9BUQ6|Q9C054	Missense_Mutation	SNP	ENST00000534000.1	hg19	CCDS5130.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.896287	0.33442	.	.	ENSG00000111907	ENST00000304877;ENST00000534000;ENST00000527711;ENST00000532429;ENST00000392484	T;T;T;T	0.48201	1.4;1.39;1.77;0.82	5.53	2.67	0.31697	.	1.108680	0.06628	N	0.758775	T	0.10981	0.0268	N	0.08118	0	0.22666	N	0.998871	B	0.02656	0.0	B	0.01281	0.0	T	0.31806	-0.9930	10	0.66056	D	0.02	-3.2296	5.1614	0.15064	0.1497:0.627:0.1444:0.0789	.	195	Q16890	TPD53_HUMAN	W	200;195;182;166;195	ENSP00000306285:R200W;ENSP00000434142:R195W;ENSP00000436953:R182W;ENSP00000435447:R166W	ENSP00000306285:R200W	R	+	1	2	TPD52L1	125625775	0.004000	0.15560	0.012000	0.15200	0.850000	0.48378	1.103000	0.31062	0.253000	0.21552	-0.133000	0.14855	CGG	.	.		0.612	TPD52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042065.2			T	125584076	C	T	125584076	3	4	104	1	0	0	0	0	1	0	0	0	16413	643	23	1	609	1	TPD52L1	6	125584076	Missense_Mutation	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10	94629302	125584076	45530991	18	15846										
ARHGAP18	93663	hgsc.bcm.edu	37	chr6	129927037	129927037	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgaccttcagtgtgtccctGtttgcatcaggtaggaggat	12	9	2	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr6:129927037G>A	ENST00000368149.2	-	10	1438	c.1350C>T	c.(1348-1350)aaC>aaT	p.N450N		NM_033515.2	NP_277050.2			Rho GTPase activating protein 18											NS(2)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(3)	18				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		GTGTGTCCCTGTTTGCATCAG	0.363																																					p.N450N		Atlas-SNP	.											.	ARHGAP18	52	.	0			c.C1350T						.						156	161	160					6																	129927037		2203	4300	6503	SO:0001819	synonymous_variant	93663	exon10			GTCCCTGTTTGCA	AB053293	CCDS34535.1	6q23.1	2011-06-29			ENSG00000146376	ENSG00000146376		"Rho GTPase activating proteins"	21035	protein-coding gene	gene with protein product		613351					Standard	NM_033515		Approved	MacGAP, bA307O14.2	uc003qbr.3	Q8N392	OTTHUMG00000015547	ENST00000368149.2:c.1350C>T	chr6.hg19:g.129927037G>A		68.0	0.0		89.0	65.0	NM_033515		Silent	SNP	ENST00000368149.2	hg19	CCDS34535.1																																																																																			.	.		0.363	ARHGAP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042185.2	NM_033515		A	129927037	G	A	129927037	2	1	104	1	0	0	0	0	0	0	0	1	868	1368	48	3		3	ARHGAP18	6	129927037	Silent	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	4342961	129927037	41188030	19	15847										
INHBA	3624	hgsc.bcm.edu	37	chr7	41729607	41729607	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acactccaagccccgccgacGccggcgatgagggtggtctt	13	15	1	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr7:41729607G>A	ENST00000242208.4	-	3	1168	c.922C>T	c.(922-924)Cgt>Tgt	p.R308C	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Missense_Mutation_p.R308C	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	308					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						CCCCGCCGACGCCGGCGATGA	0.557										TSP Lung(11;0.080)																											p.R308C		Atlas-SNP	.											INHBA,colon,carcinoma,0,1	INHBA	118	.	0			c.C922T						.						102	107	106					7																	41729607		2203	4300	6503	SO:0001583	missense	3624	exon3			GCCGACGCCGGCG		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.922C>T	chr7.hg19:g.41729607G>A	ENSP00000242208:p.Arg308Cys	32.0	1.0		65.0	38.0	NM_002192	Q14599	Missense_Mutation	SNP	ENST00000242208.4	hg19	CCDS5464.1	.	.	.	.	.	.	.	.	.	.	.	14.88	2.667375	0.47677	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.81078	-1.45;-1.45	5.82	3.97	0.46021	Transforming growth factor-beta, C-terminal (1);	0.169098	0.53938	D	0.000059	D	0.89252	0.6662	M	0.87269	2.87	0.80722	D	1	D	0.76494	0.999	P	0.61275	0.886	D	0.90438	0.4429	10	0.87932	D	0	-20.4552	13.9132	0.63881	0.0:0.0:0.6004:0.3996	.	308	P08476	INHBA_HUMAN	C	308	ENSP00000242208:R308C;ENSP00000397197:R308C	ENSP00000242208:R308C	R	-	1	0	INHBA	41696132	0.898000	0.30612	0.799000	0.32177	0.986000	0.74619	2.807000	0.47955	0.762000	0.33152	0.484000	0.47621	CGT	.	.		0.557	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			A	41729607	G	A	41729607	3	1	104	1	0	0	0	0	1	0	0	0	7750	1087	38	1	362	1	INHBA	7	41729607	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10		41729607	117409056	20	15848										
ZNF107	51427	hgsc.bcm.edu	37	chr7	64167564	64167564	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aataaacaggagaaaattcaTactggagggaaactcaacaa	8	6	2	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr7:64167564T>C	ENST00000395391.1	+	4	2257	c.882T>C	c.(880-882)caT>caC	p.H294H	ZNF107_ENST00000344930.3_Silent_p.H294H|ZNF107_ENST00000423627.1_Silent_p.H294H			Q9UII5	ZN107_HUMAN	zinc finger protein 107	294					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				AGAAAATTCATACTGGAGGGA	0.358																																					p.H294H		Atlas-SNP	.											.	ZNF107	107	.	0			c.T882C						.						41	46	45					7																	64167564		2195	4298	6493	SO:0001819	synonymous_variant	51427	exon7			AATTCATACTGGA	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"Zinc fingers, C2H2-type"	12887	protein-coding gene	gene with protein product		603989	"zinc finger protein 588", "zinc finger protein 107 (Y8)"	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.882T>C	chr7.hg19:g.64167564T>C		43.0	0.0		81.0	40.0	NM_016220		Silent	SNP	ENST00000395391.1	hg19	CCDS5527.1																																																																																			.	.		0.358	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		C	64167564	T	C	64167564	2	2	104	1	0	0	0	0	0	0	0	1	17730	1403	49	2		2	ZNF107	7	64167564	Silent	SNP	T	TCGA-DD-A1EH-01A-11D-A12Z-10	22437957	64167564	94971099	21	15849										
ELN	2006	hgsc.bcm.edu	37	chr7	73474235	73474235	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggttagttcctggtgtcggCgtggctcctggagttggcgt	18	8	0	0			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr7:73474235C>T	ENST00000252034.7	+	23	1833	c.1434C>T	c.(1432-1434)ggC>ggT	p.G478G	ELN_ENST00000380584.4_Silent_p.G445G|ELN_ENST00000414324.1_Silent_p.G454G|ELN_ENST00000357036.5_Silent_p.G483G|ELN_ENST00000380553.4_Silent_p.G342G|ELN_ENST00000380575.4_Silent_p.G449G|ELN_ENST00000380562.4_Silent_p.G484G|ELN_ENST00000445912.1_Silent_p.G478G|ELN_ENST00000380576.5_Silent_p.G459G|ELN_ENST00000429192.1_Silent_p.G464G|CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000320492.7_Silent_p.G397G|ELN_ENST00000458204.1_Silent_p.G468G|ELN_ENST00000358929.4_Silent_p.G513G|ELN_ENST00000320399.6_Silent_p.G478G	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				CTGGTGTCGGCGTGGCTCCTG	0.572			T	PAX5	B-ALL		"Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"																														p.G483G		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN	81	.	0			c.C1449T						.						247	236	239					7																	73474235		2203	4300	6503	SO:0001819	synonymous_variant	2006	exon23			TGTCGGCGTGGCT		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"tropoelastin", "supravalvular aortic stenosis", "Williams-Beuren syndrome"	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1434C>T	chr7.hg19:g.73474235C>T		99.0	0.0		614.0	39.0	NM_001081754	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Silent	SNP	ENST00000252034.7	hg19	CCDS5562.2																																																																																			.	.		0.572	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501		T	73474235	C	T	73474235	2	4	104	1	0	0	0	0	0	0	0	1	5073	755	27	1		1	ELN	7	73474235	Silent	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10	9306671	73474235	85664428	22	15850										
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107315471	107315471	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtggcttcacaacagctgctGccttccaagtgctggtctca	10	13	2	0			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr7:107315471G>T	ENST00000265715.3	+	6	906	c.682G>T	c.(682-684)Gcc>Tcc	p.A228S		NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	228					chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						AACAGCTGCTGCCTTCCAAGT	0.418									Pendred syndrome																												p.A228S		Atlas-SNP	.											.	SLC26A4	117	.	0			c.G682T	GRCh37	CD073698	SLC26A4	D		.						251	232	238					7																	107315471		2203	4300	6503	SO:0001583	missense	5172	exon6	Familial Cancer Database	Goiter-Deafness syndrome	GCTGCTGCCTTCC	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.682G>T	chr7.hg19:g.107315471G>T	ENSP00000265715:p.Ala228Ser	108.0	0.0		310.0	23.0	NM_000441	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	hg19	CCDS5746.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.017519	0.93404	.	.	ENSG00000091137	ENST00000265715	D	0.96365	-3.99	5.41	5.41	0.78517	Sulphate transporter (1);	0.000000	0.64402	D	0.000001	D	0.97448	0.9165	L	0.53780	1.695	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96871	0.9639	10	0.35671	T	0.21	.	19.1848	0.93639	0.0:0.0:1.0:0.0	.	228	O43511	S26A4_HUMAN	S	228	ENSP00000265715:A228S	ENSP00000265715:A228S	A	+	1	0	SLC26A4	107102707	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.494000	0.81503	2.536000	0.85505	0.650000	0.86243	GCC	.	.		0.418	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		T	107315471	G	T	107315471	3	4	104	1	0	0	0	0	1	0	0	0	14534	1319	46	3	700	3	SLC26A4	7	107315471	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	33841236	107315471	51823192	23	15851										
PCMTD1	115294	hgsc.bcm.edu	37	chr8	52733023	52733023	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctctggcttcattgcttcaTtgtgatctttttcctcctct	5	13	5	1	rs114725410		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr8:52733023T>C	ENST00000360540.5	-	7	1368	c.962A>G	c.(961-963)aAt>aGt	p.N321S	PCMTD1_ENST00000544451.1_Missense_Mutation_p.N245S|PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000522514.1_Missense_Mutation_p.N321S	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	321						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				CATTGCTTCATTGTGAtcttt	0.388																																					p.N321S		Atlas-SNP	.											.	PCMTD1	73	.	0			c.A962G						.																																			SO:0001583	missense	115294	exon6			GCTTCATTGTGAT		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.962A>G	chr8.hg19:g.52733023T>C	ENSP00000353739:p.Asn321Ser	162.0	0.0		754.0	40.0	NM_052937	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	hg19	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.817162	0.00595	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.42131	1.6;0.98;1.6	5.97	2.0	0.26442	.	1.095890	0.06623	N	0.757821	T	0.14743	0.0356	N	0.02011	-0.69	0.22552	N	0.998991	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.29549	-1.0008	10	0.10377	T	0.69	-34.7335	2.3892	0.04374	0.1206:0.4542:0.2261:0.1992	.	191;245;321	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	S	321;245;321	ENSP00000353739:N321S;ENSP00000444026:N245S;ENSP00000428099:N321S	ENSP00000353739:N321S	N	-	2	0	PCMTD1	52895576	0.883000	0.30277	0.240000	0.24138	0.035000	0.12851	0.110000	0.15437	0.419000	0.25927	-0.132000	0.14878	AAT	.	.		0.388	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937		C	52733023	T	C	52733023	3	2	104	1	0	0	0	0	1	0	0	0	11595	1493	52	2	115	2	PCMTD1	8	52733023	Missense_Mutation	SNP	T	TCGA-DD-A1EH-01A-11D-A12Z-10		52733023	93630999	24	15852										
TM7SF4	81501	hgsc.bcm.edu	37	chr8	105361088	105361088	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgctttgattgcagctggcaCagggatcgtcatcttgggac	13	9	2	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr8:105361088C>A	ENST00000297581.2	+	2	357	c.308C>A	c.(307-309)aCa>aAa	p.T103K	DCSTAMP_ENST00000517991.1_Missense_Mutation_p.T103K|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	103					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											GCAGCTGGCACAGGGATCGTC	0.443																																					p.T103K		Atlas-SNP	.											.	.	.	.	0			c.C308A						.						65	63	64					8																	105361088		2203	4300	6503	SO:0001583	missense	81501	exon2			CTGGCACAGGGAT	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"Dendritic cells (DC)-specific transmembrane protein", "IL-Four INDuced"	605933	"transmembrane 7 superfamily member 4"	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.308C>A	chr8.hg19:g.105361088C>A	ENSP00000297581:p.Thr103Lys	90.0	0.0		222.0	89.0	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	hg19	CCDS6301.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.481689	0.84747	.	.	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.34859	1.34	5.84	5.84	0.93424	.	0.097167	0.64402	D	0.000001	T	0.59945	0.2231	M	0.66939	2.045	0.58432	D	0.999997	D	0.89917	1.0	D	0.77004	0.989	T	0.55679	-0.8103	9	.	.	.	-18.0528	18.3185	0.90229	0.0:1.0:0.0:0.0	.	103	Q9H295	TM7S4_HUMAN	K	103	ENSP00000297581:T103K	.	T	+	2	0	TM7SF4	105430264	0.991000	0.36638	0.993000	0.49108	0.993000	0.82548	2.937000	0.48979	2.779000	0.95612	0.655000	0.94253	ACA	.	.		0.443	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		A	105361088	C	A	105361088	3	1	104	1	0	0	0	0	1	0	0	0	15991	478	17	3	310	3	TM7SF4	8	105361088	Missense_Mutation	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10	52628065	105361088	41002934	25	15853										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79867172	79867172	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tgataattggagagaagcacGaaaactcagtgtatctaccc	9	8	2	2			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr9:79867172G>A	ENST00000360280.3	+	22	2452	c.2192G>A	c.(2191-2193)cGa>cAa	p.R731Q	VPS13A_ENST00000357409.5_Missense_Mutation_p.R731Q|VPS13A_ENST00000376634.4_Missense_Mutation_p.R731Q|VPS13A_ENST00000376636.3_Missense_Mutation_p.R731Q	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	731					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AGAGAAGCACGAAAACTCAGT	0.353																																					p.R731Q		Atlas-SNP	.											VPS13A_ENST00000376634,caecum,carcinoma,0,3	VPS13A	735	.	0			c.G2192A						.						193	183	186					9																	79867172		2203	4300	6503	SO:0001583	missense	23230	exon22			AAGCACGAAAACT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.2192G>A	chr9.hg19:g.79867172G>A	ENSP00000353422:p.Arg731Gln	61.0	0.0		139.0	64.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	G	31	5.085841	0.94100	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.55588	0.51;0.51;0.51;0.51	5.46	5.46	0.80206	.	0.148405	0.45606	D	0.000352	T	0.73305	0.3570	M	0.81802	2.56	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.95;0.997;1.0;1.0	T	0.69172	-0.5215	10	0.17369	T	0.5	.	18.9119	0.92489	0.0:0.0:1.0:0.0	.	731;731;731;731	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	Q	731	ENSP00000365821:R731Q;ENSP00000365823:R731Q;ENSP00000353422:R731Q;ENSP00000349985:R731Q	ENSP00000349985:R731Q	R	+	2	0	VPS13A	79056992	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.938000	0.87678	2.552000	0.86080	0.561000	0.74099	CGA	.	.		0.353	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		A	79867172	G	A	79867172	3	1	104	1	0	0	0	0	1	0	0	0	17204	1058	37	1	2278	1	VPS13A	9	79867172	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10		79867172	61346259	26	15854										
ASAH2	56624	hgsc.bcm.edu	37	chr10	52008360	52008360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctccaagttagagaaggtgCgtttggccatttcttctcag	10	9	3	1	rs376205298		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr10:52008360C>T	ENST00000395526.4	-	1	10	c.11G>A	c.(10-12)cGc>cAc	p.R4H	ASAH2_ENST00000447815.1_Missense_Mutation_p.R4H|ASAH2_ENST00000329428.6_5'Flank	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	4					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ceramidase activity (GO:0017040)			large_intestine(1)|lung(9)|urinary_tract(1)	11						AGAGAAGGTGCGTTTGGCCAT	0.438																																					p.R4H		Atlas-SNP	.											.	ASAH2	69	.	0			c.G11A						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	94	91	92		11,11	4.1	0.9	10		92	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ASAH2	NM_001143974.1,NM_019893.2	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	4/746,4/781	52008360	1,13005	2203	4300	6503	SO:0001583	missense	56624	exon1			AAGGTGCGTTTGG	AF250847	CCDS7239.2, CCDS44398.1	10q11.23	2008-08-11			ENSG00000188611	ENSG00000188611			18860	protein-coding gene	gene with protein product		611202				10781606	Standard	NM_019893		Approved		uc001jjd.3	Q9NR71	OTTHUMG00000018223	ENST00000395526.4:c.11G>A	chr10.hg19:g.52008360C>T	ENSP00000378897:p.Arg4His	65.0	0.0		104.0	37.0	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Missense_Mutation	SNP	ENST00000395526.4	hg19	CCDS7239.2	.	.	.	.	.	.	.	.	.	.	C	13.80	2.346638	0.41599	0.0	1.16E-4	ENSG00000188611	ENST00000395526;ENST00000447815	T;T	0.34859	1.38;1.34	5.94	4.1	0.47936	.	0.271361	0.30593	U	0.009284	T	0.26122	0.0637	L	0.31926	0.97	0.58432	D	0.999999	B;B	0.21821	0.061;0.036	B;B	0.13407	0.009;0.004	T	0.04307	-1.0961	10	0.40728	T	0.16	.	9.5095	0.39067	0.0:0.8371:0.0:0.1629	.	4;4	Q9NR71-2;Q9NR71	.;ASAH2_HUMAN	H	4	ENSP00000378897:R4H;ENSP00000388206:R4H	ENSP00000378897:R4H	R	-	2	0	ASAH2	51678366	0.002000	0.14202	0.876000	0.34364	0.987000	0.75469	0.461000	0.21940	0.852000	0.35287	0.563000	0.77884	CGC	.	.		0.438	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893		T	52008360	C	T	52008360	3	4	104	1	0	0	0	0	1	0	0	0	1007	768	27	1	2411	1	ASAH2	10	52008360	Missense_Mutation	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10		52008360	83526387	27	15855										
EIF4G2	1982	hgsc.bcm.edu	37	chr11	10821282	10821282	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cttccaaaatctccaacatgCggtccttattctgatcaatt	4	12	3	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr11:10821282C>T	ENST00000526148.1	-	19	2651	c.2141G>A	c.(2140-2142)cGc>cAc	p.R714H	EIF4G2_ENST00000396525.2_Missense_Mutation_p.R676H|SNORD97_ENST00000459187.1_RNA|EIF4G2_ENST00000525681.1_Missense_Mutation_p.R714H|EIF4G2_ENST00000339995.5_Missense_Mutation_p.R714H|RP11-685M7.5_ENST00000532365.1_RNA	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2									p.R714H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		CTCCAACATGCGGTCCTTATT	0.418																																					p.R714H		Atlas-SNP	.											EIF4G2,colon,carcinoma,0,2	EIF4G2	89	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2141A						.						103	99	100					11																	10821282		2201	4294	6495	SO:0001583	missense	1982	exon19			AACATGCGGTCCT	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.2141G>A	chr11.hg19:g.10821282C>T	ENSP00000433664:p.Arg714His	55.0	0.0		112.0	18.0	NM_001172705		Missense_Mutation	SNP	ENST00000526148.1	hg19	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.270710	0.80469	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000379653	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.71	5.71	0.89125	Armadillo-type fold (1);	0.107006	0.64402	D	0.000005	T	0.58293	0.2112	M	0.62266	1.93	0.47308	D	0.999387	D;D	0.89917	0.999;1.0	P;P	0.55508	0.665;0.777	T	0.57700	-0.7766	9	0.52906	T	0.07	-4.1326	19.8493	0.96733	0.0:1.0:0.0:0.0	.	714;787	P78344;B4DZF2	IF4G2_HUMAN;.	H	714;714;714;676;787;96	ENSP00000433664:R714H;ENSP00000433371:R714H;ENSP00000340281:R714H;ENSP00000379778:R676H	ENSP00000340281:R714H	R	-	2	0	EIF4G2	10777858	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.022000	0.70839	2.701000	0.92244	0.563000	0.77884	CGC	.	.		0.418	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418		T	10821282	C	T	10821282	3	4	104	1	0	0	0	0	1	0	0	0	5039	768	27	1	598	1	EIF4G2	11	10821282	Missense_Mutation	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10		10821282	124185234	28	15856										
NXF1	10482	hgsc.bcm.edu	37	chr11	62566040	62566040	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	taacttgggaaatcgttcgcGaatggcgctgtcaagaacgg	13	8	1	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr11:62566040G>C	ENST00000532297.1	-	12	1653	c.1024C>G	c.(1024-1026)Cgc>Ggc	p.R342G	NXF1_ENST00000533048.1_5'Flank|NXF1_ENST00000294172.2_Missense_Mutation_p.R342G|NXF1_ENST00000531709.2_3'UTR			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	342					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear inclusion body (GO:0042405)|nuclear pore (GO:0005643)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AATCGTTCGCGAATGGCGCTG	0.493																																					p.R342G		Atlas-SNP	.											.	NXF1	67	.	0			c.C1024G						.						143	133	136					11																	62566040		2201	4299	6500	SO:0001583	missense	10482	exon11			GTTCGCGAATGGC	AF112880	CCDS8037.1, CCDS44629.1	11q12-q13	2008-07-21			ENSG00000162231	ENSG00000162231			8071	protein-coding gene	gene with protein product	"tip associating protein"	602647				9175835, 9660949	Standard	NM_001081491		Approved	TAP, Mex67, DKFZp667O0311	uc001nvf.1	Q9UBU9	OTTHUMG00000167612	ENST00000532297.1:c.1024C>G	chr11.hg19:g.62566040G>C	ENSP00000436679:p.Arg342Gly	49.0	0.0		99.0	49.0	NM_006362	B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	hg19	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999048	0.74818	.	.	ENSG00000162231	ENST00000294172;ENST00000532297;ENST00000530875	T;T;T	0.55760	0.5;0.5;0.5	5.77	5.77	0.91146	U2A&apos (1);/phosphoprotein 32 family A, C-terminal (1);	0.127200	0.53938	D	0.000042	T	0.77025	0.4070	M	0.89904	3.07	0.80722	D	1	P;D	0.89917	0.954;1.0	P;D	0.78314	0.612;0.991	T	0.76038	-0.3105	10	0.26408	T	0.33	-7.8345	17.535	0.87827	0.0:0.0:1.0:0.0	.	385;342	E9PIN3;Q9UBU9	.;NXF1_HUMAN	G	342;342;385	ENSP00000294172:R342G;ENSP00000436679:R342G;ENSP00000435742:R385G	ENSP00000294172:R342G	R	-	1	0	NXF1	62322616	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	5.605000	0.67634	2.751000	0.94390	0.650000	0.86243	CGC	.	.		0.493	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362		C	62566040	G	C	62566040	3	2	104	1	0	0	0	0	1	0	0	0	10791	1058	37	4	879	4	NXF1	11	62566040	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	51744758	62566040	72440476	29	15857										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76917166	76917166	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggtcccggaagtaccctccGcacctggtggaggtggaggc	17	12	0	0	rs375627342		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr11:76917166G>A	ENST00000409709.3	+	41	5933	c.5661G>A	c.(5659-5661)ccG>ccA	p.P1887P	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Silent_p.P1838P|MYO7A_ENST00000458637.2_Silent_p.P1849P	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1887	MyTH4 2. {ECO:0000255|PROSITE- ProRule:PRU00359}.		P -> L (in USH1B). {ECO:0000269|PubMed:10930322}.		actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AGTACCCTCCGCACCTGGTGG	0.607																																					p.P1887P		Atlas-SNP	.											MYO7A,NS,carcinoma,0,1	MYO7A	164	.	0			c.G5661A						.		,	1,4047		0,1,2023	62	70	68		5661,5547	-9.1	0.5	11		68	0,8338		0,0,4169	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	0,1,6192	AA,AG,GG		0.0,0.0247,0.0081	,	1887/2216,1849/2176	76917166	1,12385	2024	4169	6193	SO:0001819	synonymous_variant	4647	exon41			CCCTCCGCACCTG	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.5661G>A	chr11.hg19:g.76917166G>A		37.0	0.0		84.0	32.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	hg19	CCDS53683.1																																																																																			.	.		0.607	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		A	76917166	G	A	76917166	2	1	104	1	0	0	0	0	0	0	0	1	10091	1074	38	1		1	MYO7A	11	76917166	Silent	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	14351126	76917166	58089350	30	15858										
NCAM1	4684	hgsc.bcm.edu	37	chr11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-													0	0	1	0	0	0	1	1	0	ccctcccagccagcagattaCaatgctgccaaactaaggat					rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000532002.1_RNA|RP11-629G13.1_ENST00000500537.2_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		0.0	0.0		26.0	26.0	NM_001242608	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		-	112832363	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	112832332	6	5	104	0	1	1	0	1	0	0	0	0	10211	493	17	0		0	NCAM1	11	112832332	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	TCGA-DD-A1EH-01A-11D-A12Z-10	35915166	112832332	22174184	31	15859										
ROBO4	54538	hgsc.bcm.edu	37	chr11	124763622	124763622	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcctcactggtatatctgtaCagacctgggagaaggcagga	12	9	2	2			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr11:124763622C>A	ENST00000306534.3	-	10	1994	c.1509G>T	c.(1507-1509)ctG>ctT	p.L503L	ROBO4_ENST00000526899.1_5'Flank|ROBO4_ENST00000533054.1_Silent_p.L358L	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	503					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		TATATCTGTACAGACCTGGGA	0.547																																					p.L503L		Atlas-SNP	.											.	ROBO4	130	.	0			c.G1509T						.						153	131	139					11																	124763622		2201	4299	6500	SO:0001819	synonymous_variant	54538	exon10			TCTGTACAGACCT	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.1509G>T	chr11.hg19:g.124763622C>A		93.0	0.0		283.0	106.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	hg19	CCDS8455.1																																																																																			.	.		0.547	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		A	124763622	C	A	124763622	2	1	104	1	0	0	0	0	0	0	0	1	13531	465	17	3		3	ROBO4	11	124763622	Silent	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10	11931290	124763622	10242894	32	15860										
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134029862	134029862	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tttgctagctcctgctcctgGaccagctgttcctggtactt	9	13	0	0			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr11:134029862G>A	ENST00000534548.2	-	29	3856	c.3792C>T	c.(3790-3792)gtC>gtT	p.V1264V		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	1264					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		CCTGCTCCTGGACCAGCTGTT	0.552																																					p.V1264V		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C3792T						.						143	115	124					11																	134029862		2201	4297	6498	SO:0001819	synonymous_variant	23310	exon29			CTCCTGGACCAGC	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.3792C>T	chr11.hg19:g.134029862G>A		43.0	0.0		117.0	60.0	NM_015261	A6NFS2|Q4KMQ9	Silent	SNP	ENST00000534548.2	hg19	CCDS31723.1																																																																																			.	.		0.552	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		A	134029862	G	A	134029862	2	1	104	1	0	0	0	0	0	0	0	1	10215	1161	41	3		3	NCAPD3	11	134029862	Silent	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	9266240	134029862	976654	33	15861										
CELA1	1990	hgsc.bcm.edu	37	chr12	51740405	51740433	+	Start_Codon_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-													0	0	1	0	0	0	1	1	0	cgactggaccatatccacttAccataaaggaccagcatgtt					rs150350903|rs573952082|rs201074609|rs141305161|rs117443541|rs377599213|rs143199509|rs61761206|rs148235680|rs370927847|rs148270827|rs116944010|rs386762976|rs149358345|rs55827519	byFrequency	TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr12:51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC	ENST00000293636.1	-	0	30_57					NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1						exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)|p.L4P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ATATCCACTTACCATAAAGGACCAGCATGTTGCCGATGGAGTAGACCAC	0.524																																					p.3_6del		Pindel	.											.	CELA1	39	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.8_16del						.																																			SO:0001582	initiator_codon_variant	1990	exon1			.		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"elastase 1, pancreatic"	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523		chr12.hg19:g.51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC		0.0	0.0		28.0	28.0	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	In_Frame_Del	DEL	ENST00000293636.1	hg19	CCDS8812.1																																																																																			.	-|0.574;CACCAGGAAGCG|0.426		0.524	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971		-	51740433	CTGGACCATATCCACTTACCATAAAGGAC	-	51740405	7	5	104	1	0	1	0	1	0	0	0	0	3212	405	14	0	790	0	CELA1	12	51740405	Start_Codon_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	TCGA-DD-A1EH-01A-11D-A12Z-10		51740405	82111490	34	15862										
ZBTB1	22890	hgsc.bcm.edu	37	chr14	64989700	64989700	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaaaatggacttggaagagaAtcctgatgagcagtccgaaa	12	6	0	3			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr14:64989700A>G	ENST00000554015.1	+	4	1909	c.1478A>G	c.(1477-1479)aAt>aGt	p.N493S	RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000358738.3_Missense_Mutation_p.N493S|ZBTB1_ENST00000394712.2_Missense_Mutation_p.N493S			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	493					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		TTGGAAGAGAATCCTGATGAG	0.418																																					p.N493S		Atlas-SNP	.											.	ZBTB1	93	.	0			c.A1478G						.						107	107	107					14																	64989700		2203	4300	6503	SO:0001583	missense	22890	exon2			AAGAGAATCCTGA	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.1478A>G	chr14.hg19:g.64989700A>G	ENSP00000451000:p.Asn493Ser	50.0	0.0		98.0	44.0	NM_014950	A8K6S8|Q86SW8	Missense_Mutation	SNP	ENST00000554015.1	hg19	CCDS45126.1	.	.	.	.	.	.	.	.	.	.	A	9.080	0.999089	0.19121	.	.	ENSG00000126804	ENST00000554015;ENST00000358738;ENST00000394712	T;T;T	0.10288	2.89;3.45;2.89	6.03	6.03	0.97812	.	0.754534	0.13075	N	0.415753	T	0.08492	0.0211	N	0.24115	0.695	0.31274	N	0.691353	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.04427	-1.0952	10	0.62326	D	0.03	-25.5236	7.5825	0.27974	0.7872:0.1426:0.0702:0.0	.	493;493	Q9Y2K1-2;Q9Y2K1	.;ZBTB1_HUMAN	S	493	ENSP00000451000:N493S;ENSP00000351587:N493S;ENSP00000378201:N493S	ENSP00000351587:N493S	N	+	2	0	ZBTB1	64059453	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.408000	0.59761	2.308000	0.77769	0.533000	0.62120	AAT	.	.		0.418	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1			G	64989700	A	G	64989700	3	3	104	1	0	0	0	0	1	0	0	0	17537	101	4	2	1480	2	ZBTB1	14	64989700	Missense_Mutation	SNP	A	TCGA-DD-A1EH-01A-11D-A12Z-10		64989700	42359840	35	15863										
ZDHHC22	283576	hgsc.bcm.edu	37	chr14	77606003	77606003	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctgggcaggaagaggaagaGctgcagcacgaaggtcacca	16	9	1	2			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr14:77606003G>A	ENST00000319374.4	-	2	281	c.79C>T	c.(79-81)Ctc>Ttc	p.L27F	AC007375.1_ENST00000600936.1_5'Flank|RP11-463C8.4_ENST00000557752.1_Intron	NM_174976.2	NP_777636.2	Q8N966	ZDH22_HUMAN	zinc finger, DHHC-type containing 22	27					protein localization to plasma membrane (GO:0072659)|protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)|urinary_tract(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0277)		AAGAGGAAGAGCTGCAGCACG	0.667											OREG0022834	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L27F		Atlas-SNP	.											.	ZDHHC22	30	.	0			c.C79T						.						10	13	12					14																	77606003		2096	4206	6302	SO:0001583	missense	283576	exon2			GGAAGAGCTGCAG	AK095612	CCDS45140.1	14q24.3	2008-08-06	2004-03-05	2004-03-10	ENSG00000177108	ENSG00000177108		"Zinc fingers, DHHC-type"	20106	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 59"	C14orf59			Standard	NM_174976		Approved		uc010asp.3	Q8N966		ENST00000319374.4:c.79C>T	chr14.hg19:g.77606003G>A	ENSP00000318222:p.Leu27Phe	26.0	0.0	1177	57.0	20.0	NM_174976	A6NH02|B7Z2L5|Q149P4	Missense_Mutation	SNP	ENST00000319374.4	hg19	CCDS45140.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.765692	0.49574	.	.	ENSG00000177108	ENST00000319374;ENST00000555389;ENST00000555327	T	0.58652	0.32	5.67	5.67	0.87782	.	0.128302	0.53938	D	0.000046	T	0.36717	0.0977	N	0.08118	0	0.40340	D	0.979024	B	0.17038	0.02	B	0.10450	0.005	T	0.25082	-1.0142	10	0.21540	T	0.41	.	13.8634	0.63574	0.0:0.0:0.8382:0.1617	.	27	Q8N966	ZDH22_HUMAN	F	27	ENSP00000318222:L27F	ENSP00000318222:L27F	L	-	1	0	ZDHHC22	76675756	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.584000	0.53936	2.677000	0.91161	0.561000	0.74099	CTC	.	.		0.667	ZDHHC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414289.1	NM_174976		A	77606003	G	A	77606003	3	1	104	1	0	0	0	0	1	0	0	0	17628	971	34	3	720	3	ZDHHC22	14	77606003	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	12616303	77606003	29743537	36	15864										
STON2	85439	hgsc.bcm.edu	37	chr14	81744756	81744756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aagcctcagttacagaaggcGtgcggtttaaagaggaaata	12	6	1	2	rs201611443		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr14:81744756G>A	ENST00000267540.2	-	4	1099	c.899C>T	c.(898-900)aCg>aTg	p.T300M	STON2_ENST00000555447.1_Missense_Mutation_p.T300M|STON2_ENST00000556280.1_5'Flank	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	300					hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		TACAGAAGGCGTGCGGTTTAA	0.468																																					p.T300M		Atlas-SNP	.											STON2,NS,carcinoma,0,2	STON2	94	.	0			c.C899T						.	G	MET/THR	0,4406		0,0,2203	112	115	114		899	4.3	0	14		114	2,8598	2.2+/-6.3	0,2,4298	yes	missense	STON2	NM_033104.2	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	300/906	81744756	2,13004	2203	4300	6503	SO:0001583	missense	85439	exon6			GAAGGCGTGCGGT	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"stoned B homolog 2 (Drosophila)"	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.899C>T	chr14.hg19:g.81744756G>A	ENSP00000267540:p.Thr300Met	61.0	0.0		118.0	15.0	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	hg19	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	G	1.425	-0.571785	0.03882	0.0	2.33E-4	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.48836	0.8;0.8	6.17	4.34	0.51931	Stonin-2, N-terminal (1);	0.666605	0.15615	N	0.253176	T	0.23572	0.0570	N	0.14661	0.345	0.09310	N	1	P;P	0.44344	0.711;0.833	B;B	0.34093	0.175;0.109	T	0.09122	-1.0689	10	0.46703	T	0.11	-10.8204	4.5608	0.12160	0.1776:0.0:0.5212:0.3011	.	300;300	Q8WXE9;G3V2T7	STON2_HUMAN;.	M	300;312;300	ENSP00000450857:T300M;ENSP00000267540:T300M	ENSP00000267540:T300M	T	-	2	0	STON2	80814509	0.011000	0.17503	0.032000	0.17829	0.013000	0.08279	0.914000	0.28624	0.918000	0.36919	-0.126000	0.14955	ACG	.	.		0.468	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104		A	81744756	G	A	81744756	3	1	104	1	0	0	0	0	1	0	0	0	15333	1145	40	1	1824	1	STON2	14	81744756	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	4138753	81744756	25604784	37	15865										
RTL1	388015	hgsc.bcm.edu	37	chr14	101348750	101348750	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctgttatgatggtcatgacGttcttgttcagtttcacccc	8	11	4	2			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr14:101348750G>A	ENST00000534062.1	-	1	2434	c.2376C>T	c.(2374-2376)aaC>aaT	p.N792N	MIR432_ENST00000606207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	792					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TGGTCATGACGTTCTTGTTCA	0.547																																					p.N792N		Atlas-SNP	.											.	RTL1	120	.	0			c.C2376T						.						195	182	186					14																	101348750		692	1591	2283	SO:0001819	synonymous_variant	388015	exon1			CATGACGTTCTTG		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.2376C>T	chr14.hg19:g.101348750G>A		56.0	0.0		159.0	69.0	NM_001134888	E9PKS8	Silent	SNP	ENST00000534062.1	hg19	CCDS53910.1																																																																																			.	.		0.547	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		A	101348750	G	A	101348750	2	1	104	1	0	0	0	0	0	0	0	1	13739	1136	40	1		1	RTL1	14	101348750	Silent	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	19603994	101348750	6000790	38	15866										
PACS2	23241	hgsc.bcm.edu	37	chr14	105858084	105858084	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctcctccccgtcggtgagcGgaggcctgtcctcccccagg	12	19	0	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr14:105858084G>A	ENST00000325438.8	+	21	2695	c.2191G>A	c.(2191-2193)Gga>Aga	p.G731R	PACS2_ENST00000551743.1_Missense_Mutation_p.G245R|PACS2_ENST00000547217.1_Missense_Mutation_p.G701R|PACS2_ENST00000551801.1_5'UTR|PACS2_ENST00000447393.1_Missense_Mutation_p.G735R|PACS2_ENST00000430725.2_Missense_Mutation_p.G656R|PACS2_ENST00000458164.2_Missense_Mutation_p.G746R			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	731					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to plasma membrane (GO:0072661)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)				endometrium(2)|kidney(2)|lung(7)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	21		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		GTCGGTGAGCGGAGGCCTGTC	0.682																																					p.G746R		Atlas-SNP	.											.	PACS2	75	.	0			c.G2236A						.						15	16	16					14																	105858084		2190	4289	6479	SO:0001583	missense	23241	exon22			GTGAGCGGAGGCC	AB011174	CCDS32168.1, CCDS45178.1, CCDS45178.2, CCDS58339.1	14q32	2005-02-15	2005-02-15	2005-02-15		ENSG00000179364			23794	protein-coding gene	gene with protein product		610423	"phosphofurin acidic cluster sorting protein 1-like"	PACS1L		15692567	Standard	NM_001100913		Approved	KIAA0602	uc001yqu.3	Q86VP3	OTTHUMG00000170450	ENST00000325438.8:c.2191G>A	chr14.hg19:g.105858084G>A	ENSP00000321834:p.Gly731Arg	19.0	0.0		80.0	28.0	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Missense_Mutation	SNP	ENST00000325438.8	hg19	CCDS32168.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.482761	0.63962	.	.	ENSG00000179364	ENST00000430725;ENST00000325438;ENST00000458164;ENST00000447393;ENST00000547217;ENST00000551743	T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99	4.71	2.84	0.33178	.	0.477834	0.22074	N	0.064997	T	0.38852	0.1056	N	0.14661	0.345	0.31163	N	0.70415	D;D;D;D	0.71674	0.985;0.982;0.998;0.985	P;P;D;P	0.64506	0.647;0.592;0.926;0.498	T	0.34254	-0.9836	10	0.17832	T	0.49	-12.5467	9.7367	0.40392	0.1761:0.0:0.8239:0.0	.	735;746;731;732	E9PB38;Q86VP3-2;Q86VP3;Q86VP3-3	.;.;PACS2_HUMAN;.	R	656;731;746;735;701;245	ENSP00000393524:G656R;ENSP00000321834:G731R;ENSP00000399732:G746R;ENSP00000393559:G735R;ENSP00000449525:G701R;ENSP00000449254:G245R	ENSP00000321834:G731R	G	+	1	0	PACS2	104929129	0.678000	0.27586	0.894000	0.35097	0.938000	0.57974	1.005000	0.29834	0.389000	0.25086	0.462000	0.41574	GGA	.	.		0.682	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355		A	105858084	G	A	105858084	3	1	104	1	0	0	0	0	1	0	0	0	11382	1117	39	1	2285	1	PACS2	14	105858084	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	4509334	105858084	1491456	39	15867										
TJP1	7082	hgsc.bcm.edu	37	chr15	30012108	30012108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggtggaaggagctggggtgGgctcctccagtctgacatta	16	8	1	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr15:30012108G>A	ENST00000346128.6	-	20	3350	c.2876C>T	c.(2875-2877)cCc>cTc	p.P959L	TJP1_ENST00000545208.2_Intron|TJP1_ENST00000400011.2_Intron|TJP1_ENST00000356107.6_Missense_Mutation_p.P959L	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	959					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		AGCTGGGGTGGGCTCCTCCAG	0.443																																					p.P959L	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.C2876T						.						139	135	136					15																	30012108		1923	4119	6042	SO:0001583	missense	7082	exon20			GGGGTGGGCTCCT		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.2876C>T	chr15.hg19:g.30012108G>A	ENSP00000281537:p.Pro959Leu	93.0	0.0		268.0	119.0	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	hg19	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	G	13.74	2.328456	0.41197	.	.	ENSG00000104067	ENST00000346128;ENST00000545208	T	0.07444	3.19	6.03	4.17	0.49024	.	0.111162	0.64402	N	0.000007	T	0.10465	0.0256	L	0.55103	1.725	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.04229	-1.0967	10	0.41790	T	0.15	.	13.0562	0.58982	0.13:0.0:0.87:0.0	.	952;959	A9CQZ8;Q07157	.;ZO1_HUMAN	L	959	ENSP00000281537:P959L	ENSP00000281537:P959L	P	-	2	0	TJP1	27799400	1.000000	0.71417	0.814000	0.32528	0.996000	0.88848	3.536000	0.53582	0.890000	0.36211	0.655000	0.94253	CCC	.	.		0.443	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		A	30012108	G	A	30012108	3	1	104	1	0	0	0	0	1	0	0	0	15944	1232	43	3	2406	3	TJP1	15	30012108	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10		30012108	72519284	40	15868										
AXIN1	8312	hgsc.bcm.edu	37	chr16	347071	347072	+	Frame_Shift_Ins	INS	-	-	G													0	0	1	0	0	0	1	1	0	tcacccgtggccggtcctgcINSggtgcctgctgatctccttt							TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr16:347071_347072insG	ENST00000262320.3	-	7	2310_2311	c.1939_1940insC	c.(1939-1941)cgcfs	p.R647fs	AXIN1_ENST00000354866.3_Frame_Shift_Ins_p.R647fs|AXIN1_ENST00000481769.1_5'Flank	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	647	Interaction with PPP2CA.|Interaction with RNF111.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)	p.R647C(1)		biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GCCGGTCCTGCGGTGCCTGCTG	0.639																																					p.R647fs		Atlas-Indel,Pindel	.											.	AXIN1	290	.	1	Substitution - Missense(1)	endometrium(1)	c.1940_1941insC						.																																			SO:0001589	frameshift_variant	8312	exon7			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1940dupC	chr16.hg19:g.347073_347073dupG	ENSP00000262320:p.Arg647fs	36.0	0.0		66.0	48.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Ins	INS	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.639	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			G	347072	-	G	347071	7	5	104	1	0	1	1	0	0	0	0	0	1236	768	27	0	668	0	AXIN1	16	347071	Frame_Shift_Ins	INS	-	TCGA-DD-A1EH-01A-11D-A12Z-10		347071	90007682	41	15869										
BRD7	29117	hgsc.bcm.edu	37	chr16	50357576	50357576	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctatctgccatgacatacggAtaatcttggcacgtggccaa	9	11	2	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr16:50357576A>C	ENST00000394688.3	-	12	1524	c.1365T>G	c.(1363-1365)taT>taG	p.Y455*	BRD7_ENST00000394689.2_Nonsense_Mutation_p.Y455*			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	455					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				TGACATACGGATAATCTTGGC	0.443																																					p.Y455X		Atlas-SNP	.											BRD7,NS,carcinoma,0,1	BRD7	61	.	0			c.T1365G						.						108	91	97					16																	50357576		2198	4300	6498	SO:0001587	stop_gained	29117	exon12			ATACGGATAATCT	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"bromodomain-containing 7"			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.1365T>G	chr16.hg19:g.50357576A>C	ENSP00000378180:p.Tyr455*	55.0	0.0		68.0	46.0	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Nonsense_Mutation	SNP	ENST00000394688.3	hg19	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	A	37	6.084326	0.97267	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	.	.	.	5.53	-0.728	0.11162	.	0.187371	0.48767	D	0.000165	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.8448	7.115	0.25411	0.3973:0.0:0.4736:0.129	.	.	.	.	X	455	.	ENSP00000378180:Y455X	Y	-	3	2	BRD7	48915077	0.990000	0.36364	0.914000	0.36105	0.920000	0.55202	0.345000	0.19979	-0.161000	0.10983	0.533000	0.62120	TAT	.	.		0.443	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		C	50357576	A	C	50357576	4	2	104	1	0	0	0	0	0	1	0	0	1507	340	12	5	617	5	BRD7	16	50357576	Nonsense_Mutation	SNP	A	TCGA-DD-A1EH-01A-11D-A12Z-10	50010505	50357576	39997177	42	15870										
ITGB3	3690	hgsc.bcm.edu	37	chr17	45387555	45387555	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctaccttcaccaatatcacGtaccggggcacttaatgata	6	12	3	1	rs565628822		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr17:45387555G>C	ENST00000559488.1	+	15	2368	c.2352G>C	c.(2350-2352)acG>acC	p.T784T	ITGB3_ENST00000435993.2_Intron|RP11-290H9.4_ENST00000575039.1_RNA|ITGB3_ENST00000560629.1_Intron	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	784					activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	CCAATATCACGTACCGGGGCA	0.468																																					p.T784T		Atlas-SNP	.											.	ITGB3	157	.	0			c.G2352C						.						177	137	151					17																	45387555		2203	4300	6503	SO:0001819	synonymous_variant	3690	exon15			TATCACGTACCGG		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.2352G>C	chr17.hg19:g.45387555G>C		76.0	0.0		237.0	100.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	hg19	CCDS11511.1																																																																																			.	.		0.468	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		C	45387555	G	C	45387555	2	2	104	1	0	0	0	0	0	0	0	1	7904	1132	40	4		4	ITGB3	17	45387555	Silent	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10		45387555	35807655	43	15871										
EPN3	55040	hgsc.bcm.edu	37	chr17	48614425	48614425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgggcagctgggcttcagcCgccgctacggcgaggactac	16	13	1	0	rs146173668	byFrequency	TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr17:48614425C>T	ENST00000268933.3	+	2	1087	c.508C>T	c.(508-510)Cgc>Tgc	p.R170C	RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000537145.1_Missense_Mutation_p.R225C|EPN3_ENST00000541226.1_Missense_Mutation_p.R114C	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	170						clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			GGGCTTCAGCCGCCGCTACGG	0.682													C|||	4	0.000798722	0.0015	0	5008	,	,		15206	0		0.002	False		,,,				2504	0				p.R170C		Atlas-SNP	.											.	EPN3	32	.	0			c.C508T						.	C	CYS/ARG	0,4292		0,0,2146	17	15	16		508	5.2	1	17	dbSNP_134	16	1,8445		0,1,4222	no	missense	EPN3	NM_017957.2	180	0,1,6368	TT,TC,CC		0.0118,0.0,0.0079	probably-damaging	170/633	48614425	1,12737	2146	4223	6369	SO:0001583	missense	55040	exon2			TTCAGCCGCCGCT	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.508C>T	chr17.hg19:g.48614425C>T	ENSP00000268933:p.Arg170Cys	14.0	0.0		44.0	19.0	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	hg19	CCDS11570.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171748	0.78452	0.0	1.18E-4	ENSG00000049283	ENST00000268933;ENST00000442715;ENST00000537145;ENST00000541226;ENST00000411703	T;T;T	0.50813	2.33;2.22;0.73	5.24	5.24	0.73138	.	0.659654	0.11791	N	0.529152	T	0.68210	0.2976	L	0.58810	1.83	0.48901	D	0.999725	D;D;D	0.89917	1.0;1.0;0.961	D;D;P	0.91635	0.972;0.999;0.586	T	0.64799	-0.6322	10	0.49607	T	0.09	-18.696	18.4459	0.90683	0.0:1.0:0.0:0.0	.	225;225;170	B4DK18;F6QWW5;Q9H201	.;.;EPN3_HUMAN	C	170;225;225;114;170	ENSP00000268933:R170C;ENSP00000439512:R225C;ENSP00000440540:R114C	ENSP00000268933:R170C	R	+	1	0	EPN3	45969424	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.620000	0.36976	2.457000	0.83068	0.561000	0.74099	CGC	.	C|1.000;T|0.000		0.682	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957		T	48614425	C	T	48614425	3	4	104	1	0	0	0	0	1	0	0	0	5189	652	23	1	510	1	EPN3	17	48614425	Missense_Mutation	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10	3226870	48614425	32580785	44	15872										
TOM1L1	10040	hgsc.bcm.edu	37	chr17	52991114	52991114	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atctcttgaattcagacttgGtcacagggcttcccaggagg	11	10	3	2			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr17:52991114G>C	ENST00000575882.1	+	5	731	c.378G>C	c.(376-378)tgG>tgC	p.W126C	TOM1L1_ENST00000572405.1_Missense_Mutation_p.W91C|TOM1L1_ENST00000570371.1_Missense_Mutation_p.W126C|TOM1L1_ENST00000445275.2_Missense_Mutation_p.W126C|TOM1L1_ENST00000536554.1_Missense_Mutation_p.W49C|TOM1L1_ENST00000348161.4_Missense_Mutation_p.W49C|TOM1L1_ENST00000575333.1_Missense_Mutation_p.W126C|TOM1L1_ENST00000572158.1_Missense_Mutation_p.W119C|TOM1L1_ENST00000540336.1_Missense_Mutation_p.W49C	NM_005486.2	NP_005477.2	O75674	TM1L1_HUMAN	target of myb1 (chicken)-like 1	126	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				activation of protein kinase activity (GO:0032147)|intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|positive regulation of protein autophosphorylation (GO:0031954)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	clathrin binding (GO:0030276)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|ubiquitin binding (GO:0043130)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	15						TTCAGACTTGGTCACAGGGCT	0.403																																					p.W126C		Atlas-SNP	.											.	TOM1L1	33	.	0			c.G378C						.						99	96	97					17																	52991114		2203	4300	6503	SO:0001583	missense	10040	exon5			GACTTGGTCACAG	AJ010071	CCDS11582.1	17q23.2	2008-01-03	2007-01-12			ENSG00000141198			11983	protein-coding gene	gene with protein product		604701	"target of myb1 (chicken) homolog-like 1"			10329004, 15611048, 17977829	Standard	NM_005486		Approved	SRCASM	uc002iud.2	O75674		ENST00000575882.1:c.378G>C	chr17.hg19:g.52991114G>C	ENSP00000460823:p.Trp126Cys	69.0	0.0		146.0	69.0	NM_005486	Q53G06|Q8N749	Missense_Mutation	SNP	ENST00000575882.1	hg19	CCDS11582.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.765230	0.49574	.	.	ENSG00000141198	ENST00000445275;ENST00000540336;ENST00000348161;ENST00000536554	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.44	4.48	0.54585	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.000000	0.64402	D	0.000006	T	0.71247	0.3317	M	0.92784	3.345	0.80722	D	1	B;P;P;P;D;P	0.89917	0.44;0.869;0.685;0.869;1.0;0.473	B;P;B;P;D;B	0.97110	0.209;0.621;0.347;0.545;1.0;0.347	T	0.78700	-0.2102	10	0.66056	D	0.02	-6.0111	13.5452	0.61699	0.0:0.0:0.8428:0.1572	.	49;119;49;126;126;49	B4DUW5;B4E1N0;B7Z9E2;O75674;Q8N749;B4E1M9	.;.;.;TM1L1_HUMAN;.;.	C	126;49;49;49	ENSP00000408958:W126C;ENSP00000441242:W49C;ENSP00000343901:W49C;ENSP00000443099:W49C	ENSP00000343901:W49C	W	+	3	0	TOM1L1	50346113	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	4.082000	0.57635	1.305000	0.44909	-0.224000	0.12420	TGG	.	.		0.403	TOM1L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439029.2	NM_005486		C	52991114	G	C	52991114	3	2	104	1	0	0	0	0	1	0	0	0	16367	1270	44	4	396	4	TOM1L1	17	52991114	Missense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10	4376689	52991114	28204096	45	15873										
PSMC5	5705	hgsc.bcm.edu	37	chr17	61908431	61908431	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggagctgtttgtcatggcaCgggaacatgctccatctatc	12	10	2	0			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr17:61908431C>T	ENST00000310144.6	+	8	1023	c.715C>T	c.(715-717)Cgg>Tgg	p.R239W	PSMC5_ENST00000581882.1_Missense_Mutation_p.R231W|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000580864.1_Missense_Mutation_p.R231W|PSMC5_ENST00000375812.4_Missense_Mutation_p.R231W	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	239	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						TGTCATGGCACGGGAACATGC	0.567																																					p.R239W		Atlas-SNP	.											.	PSMC5	41	.	0			c.C715T						.						84	81	82					17																	61908431		2203	4300	6503	SO:0001583	missense	5705	exon8			ATGGCACGGGAAC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.715C>T	chr17.hg19:g.61908431C>T	ENSP00000310572:p.Arg239Trp	51.0	0.0		118.0	34.0	NM_002805	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	hg19	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.525518	0.64860	.	.	ENSG00000087191	ENST00000310144;ENST00000375812	D;D	0.93859	-3.3;-3.3	5.64	5.64	0.86602	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.97704	0.9247	H	0.94925	3.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	D	0.98241	1.0488	10	0.87932	D	0	.	17.243	0.87019	0.0:1.0:0.0:0.0	.	231;239	A8K3Z3;P62195	.;PRS8_HUMAN	W	239;231	ENSP00000310572:R239W;ENSP00000364970:R231W	ENSP00000310572:R239W	R	+	1	2	PSMC5	59262163	0.089000	0.21612	0.993000	0.49108	0.817000	0.46193	0.559000	0.23485	2.937000	0.99478	0.650000	0.86243	CGG	.	.		0.567	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		T	61908431	C	T	61908431	3	4	104	1	0	0	0	0	1	0	0	0	12702	527	19	1	745	1	PSMC5	17	61908431	Missense_Mutation	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10	8917317	61908431	19286779	46	15874										
MAPK4	5596	hgsc.bcm.edu	37	chr18	48190630	48190630	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctgttcaagttcagcgtggCgtacatcgtccaggagtaca	12	10	2	0	rs556250636		TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr18:48190630C>T	ENST00000400384.2	+	2	1338	c.302C>T	c.(301-303)gCg>gTg	p.A101V	MAPK4_ENST00000592595.1_Missense_Mutation_p.A101V|MAPK4_ENST00000540640.1_Intron|MAPK4_ENST00000588540.1_Missense_Mutation_p.A101V	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	101	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			lung(4)|skin(3)|upper_aerodigestive_tract(1)	8		Colorectal(6;0.0297)		Colorectal(21;0.156)		TTCAGCGTGGCGTACATCGTC	0.592																																					p.A101V		Atlas-SNP	.											.	MAPK4	75	.	0			c.C302T						.						78	80	79					18																	48190630		2199	4293	6492	SO:0001583	missense	5596	exon2			GCGTGGCGTACAT	X59727	CCDS42437.1	18q21.1	2012-10-02			ENSG00000141639	ENSG00000141639		"Mitogen-activated protein kinase cascade / Kinases"	6878	protein-coding gene	gene with protein product		176949		PRKM4		8290275	Standard	XM_005258299		Approved	Erk3-related, Erk4	uc002lev.3	P31152	OTTHUMG00000179853	ENST00000400384.2:c.302C>T	chr18.hg19:g.48190630C>T	ENSP00000383234:p.Ala101Val	15.0	0.0		36.0	14.0	NM_002747	A1A4C4|Q0VG04	Missense_Mutation	SNP	ENST00000400384.2	hg19	CCDS42437.1	.	.	.	.	.	.	.	.	.	.	C	8.290	0.817600	0.16607	.	.	ENSG00000141639	ENST00000400384	T	0.63744	-0.06	5.87	4.08	0.47627	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.112351	0.45126	D	0.000386	T	0.19725	0.0474	N	0.00332	-1.63	0.38982	D	0.95897	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.35025	-0.9805	10	0.02654	T	1	-4.275	6.5478	0.22416	0.0:0.6886:0.0:0.3114	.	101;101	Q0VG04;P31152	.;MK04_HUMAN	V	101	ENSP00000383234:A101V	ENSP00000383234:A101V	A	+	2	0	MAPK4	46444628	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	4.845000	0.62853	1.491000	0.48482	0.561000	0.74099	GCG	.	.		0.592	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448631.2	NM_002747		T	48190630	C	T	48190630	3	4	104	1	0	0	0	0	1	0	0	0	9289	768	27	1	304	1	MAPK4	18	48190630	Missense_Mutation	SNP	C	TCGA-DD-A1EH-01A-11D-A12Z-10		48190630	29886618	47	15875										
DONSON	29980	hgsc.bcm.edu	37	chr21	34956952	34956953	+	Frame_Shift_Ins	INS	-	-	C													0	0	1	0	0	0	1	1	0	ttgaccaaggacttgtctttINSccagccatttttctatcagc							TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chr21:34956952_34956953insC	ENST00000303071.5	-	4	794_795	c.728_729insG	c.(727-729)ggafs	p.G243fs	DONSON_ENST00000303113.6_Frame_Shift_Ins_p.G229fs|DONSON_ENST00000453626.1_Frame_Shift_Ins_p.G243fs|DONSON_ENST00000432378.1_Frame_Shift_Ins_p.G243fs	NM_017613.3	NP_060083.1	Q9NYP3	DONS_HUMAN	downstream neighbor of SON	243					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|ovary(1)	11						GACTTGTCTTTCCAGCCATTTT	0.421																																					p.G243fs		Atlas-INDEL	.											.	DONSON	34	.	0			c.729_730insG						.																																			SO:0001589	frameshift_variant	29980	exon4			.	AF000002	CCDS13632.1	21q22.1	2008-07-31			ENSG00000159147	ENSG00000159147			2993	protein-coding gene	gene with protein product		611428		C21orf60		10773462, 10950926	Standard	NM_017613		Approved	B17, C2TA, DKFZP434M035	uc002ysk.4	Q9NYP3	OTTHUMG00000065904	ENST00000303071.5:c.729dupG	chr21.hg19:g.34956954_34956954dupC	ENSP00000307143:p.Gly243fs	66.0	0.0		172.0	11.0	NM_017613	Q8NC53|Q9NSR9|Q9NVZ5|Q9NYP1|Q9NYP2	Frame_Shift_Ins	INS	ENST00000303071.5	hg19	CCDS13632.1																																																																																			.	.		0.421	DONSON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141184.1	NM_017613		C	34956953	-	C	34956952	7	5	104	1	0	1	1	0	0	0	0	0	4708	1770	62	0	999	0	DONSON	21	34956952	Frame_Shift_Ins	INS	-	TCGA-DD-A1EH-01A-11D-A12Z-10		34956952	13172943	48	15876										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20252926	20252926	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggttcatccataatttgctGtccattctgtgaaaagcaca	7	9	2	1			TCGA-DD-A1EH-01A-11D-A12Z-10	TCGA-DD-A1EH-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9f03936-1de5-4330-8b0f-6d0ab533876e	47c44a9a-cfe6-4305-a9ea-b0fb5f2b5137	g.chrX:20252926G>A	ENST00000379565.3	-	2	283	c.76C>T	c.(76-78)Cag>Tag	p.Q26*	RPS6KA3_ENST00000544447.1_5'UTR|RPS6KA3_ENST00000540702.1_5'UTR	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	26					axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	ATAATTTGCTGTCCATTCTGT	0.338																																					p.Q26X		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.C76T						.						93	77	83					X																	20252926		2203	4300	6503	SO:0001587	stop_gained	6197	exon2			TTTGCTGTCCATT	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.76C>T	chrX.hg19:g.20252926G>A	ENSP00000368884:p.Gln26*	108.0	0.0		243.0	204.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Nonsense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	G	37	6.183972	0.97357	.	.	ENSG00000177189	ENST00000379565	.	.	.	5.31	5.31	0.75309	.	0.484849	0.20103	N	0.099190	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	.	13.3469	0.60578	0.0:0.0:1.0:0.0	.	.	.	.	X	26	.	ENSP00000368884:Q26X	Q	-	1	0	RPS6KA3	20162847	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.349000	0.66010	2.213000	0.71641	0.594000	0.82650	CAG	.	.		0.338	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		A	20252926	G	A	20252926	4	1	104	1	0	0	0	0	0	1	0	0	13667	1386	48	3	2230	3	RPS6KA3	23	20252926	Nonsense_Mutation	SNP	G	TCGA-DD-A1EH-01A-11D-A12Z-10		20252926	135017634	49	15877										
CYP4Z1	199974	hgsc.bcm.edu	37	chr1	47571829	47571829	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gagccagatgccttacaccaCgatgtgcatcaaggaatgcc	10	12	1	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr1:47571829C>G	ENST00000334194.3	+	9	1100	c.1097C>G	c.(1096-1098)aCg>aGg	p.T366R	CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_178134.2	NP_835235.1	Q86W10	CP4Z1_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 1	366						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			cervix(1)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	11						CCTTACACCACGATGTGCATC	0.517																																					p.T366R		.	.											.	CYP4Z1	.	.	0			c.C1097G						.						140	119	126					1																	47571829		2203	4300	6503	SO:0001583	missense	199974	exon9			ACACCACGATGTG	AY262056	CCDS545.1	1p33	2008-02-05			ENSG00000186160	ENSG00000186160		"Cytochrome P450s"	20583	protein-coding gene	gene with protein product						15059886	Standard	NM_178134		Approved	CYP4A20	uc001cqu.1	Q86W10	OTTHUMG00000008019	ENST00000334194.3:c.1097C>G	1.37:g.47571829C>G	ENSP00000334246:p.Thr366Arg	226.0	0.0		308.0	107.0	NM_178134	Q5VVE4	Missense_Mutation	SNP	ENST00000334194.3	37	CCDS545.1	.	.	.	.	.	.	.	.	.	.	C	18.60	3.658365	0.67586	.	.	ENSG00000186160	ENST00000334194	T	0.68331	-0.32	3.25	3.25	0.37280	.	0.000000	0.64402	U	0.000002	T	0.76870	0.4048	L	0.55834	1.745	0.42596	D	0.993266	D	0.89917	1.0	D	0.85130	0.997	T	0.80487	-0.1361	10	0.87932	D	0	.	13.8624	0.63569	0.0:1.0:0.0:0.0	.	366	Q86W10	CP4Z1_HUMAN	R	366	ENSP00000334246:T366R	ENSP00000334246:T366R	T	+	2	0	CYP4Z1	47344416	1.000000	0.71417	0.979000	0.43373	0.689000	0.40095	5.029000	0.64121	1.847000	0.53656	0.289000	0.19496	ACG	.	.		0.517	CYP4Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022020.1	NM_178134		G	47571829	C	G	47571829	3	3	105	1	0	0	0	0	1	0	0	0	4196	536	19	4	1131	4	CYP4Z1	1	47571829	Missense_Mutation	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10		47571829	201678792	1	15878										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67787396	67787396	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	acaaggctgctttcactattCcagacgtaacaagttaatcc	6	11	1	1	rs149868445	byFrequency	TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr1:67787396C>A	ENST00000262345.1	+	3	828	c.188C>A	c.(187-189)tCc>tAc	p.S63Y	IL12RB2_ENST00000371000.1_Missense_Mutation_p.S63Y|IL12RB2_ENST00000541374.1_Missense_Mutation_p.S63Y|IL12RB2_ENST00000544434.1_Missense_Mutation_p.S63Y	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	63					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						TTTCACTATTCCAGACGTAAC	0.433																																					p.S63Y		.	.											.	IL12RB2	.	.	0			c.C188A						.						146	138	141					1																	67787396		2203	4300	6503	SO:0001583	missense	3595	exon3			ACTATTCCAGACG	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.188C>A	1.37:g.67787396C>A	ENSP00000262345:p.Ser63Tyr	185.0	0.0		204.0	65.0	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.082057	0.55861	.	.	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21	5.11	5.11	0.69529	Immunoglobulin C2-set-like, ligand-binding (1);	0.644323	0.17020	N	0.190164	T	0.65821	0.2728	L	0.29908	0.895	0.09310	N	1	B;D;D;D	0.71674	0.171;0.998;0.975;0.995	B;D;P;D	0.65443	0.128;0.935;0.743;0.934	T	0.56565	-0.7958	10	0.02654	T	1	-0.6441	13.9166	0.63902	0.0:1.0:0.0:0.0	.	63;63;63;63	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	Y	63	ENSP00000262345:S63Y;ENSP00000360039:S63Y;ENSP00000445276:S63Y;ENSP00000442443:S63Y	ENSP00000262345:S63Y	S	+	2	0	IL12RB2	67559984	0.017000	0.18338	0.691000	0.30163	0.016000	0.09150	3.545000	0.53648	2.657000	0.90304	0.650000	0.86243	TCC	C|1.000;T|0.000	.		0.433	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		A	67787396	C	A	67787396	3	1	105	1	0	0	0	0	1	0	0	0	7636	855	30	3	194	3	IL12RB2	1	67787396	Missense_Mutation	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10	20215567	67787396	181463225	2	15879										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103491141	103491141	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	tttccattgttccatagttgTattcttgaaaatcatcaacg	5	8	3	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr1:103491141T>C	ENST00000370096.3	-	7	1238	c.926A>G	c.(925-927)tAc>tGc	p.Y309C	COL11A1_ENST00000512756.1_Intron|COL11A1_ENST00000353414.4_Missense_Mutation_p.Y270C|COL11A1_ENST00000358392.2_Missense_Mutation_p.Y321C	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	309	Nonhelical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TCCATAGTTGTATTCTTGAAA	0.353																																					p.Y321C		.	.											.	COL11A1	.	.	0			c.A962G						.						125	118	121					1																	103491141		2203	4299	6502	SO:0001583	missense	1301	exon7			TAGTTGTATTCTT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.926A>G	1.37:g.103491141T>C	ENSP00000359114:p.Tyr309Cys	329.0	0.0		443.0	67.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	12.59	1.983984	0.35036	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000427239	D;T;D;T	0.88586	-2.38;-0.6;-2.4;-0.55	5.53	5.53	0.82687	.	0.480685	0.22400	N	0.060545	D	0.89413	0.6708	M	0.83953	2.67	0.43564	D	0.99588	D;D;P	0.54964	0.969;0.969;0.947	P;P;B	0.50378	0.54;0.639;0.339	D	0.89488	0.3755	10	0.42905	T	0.14	.	12.215	0.54402	0.0:0.0:0.1422:0.8578	.	270;321;309	P12107-3;P12107-2;P12107	.;.;COBA1_HUMAN	C	309;321;270;321	ENSP00000359114:Y309C;ENSP00000351163:Y321C;ENSP00000302551:Y270C;ENSP00000408640:Y321C	ENSP00000302551:Y270C	Y	-	2	0	COL11A1	103263729	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.758000	0.68776	2.106000	0.64143	0.519000	0.50382	TAC	.	.		0.353	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		C	103491141	T	C	103491141	3	2	105	1	0	0	0	0	1	0	0	0	3669	1638	57	2	4738	2	COL11A1	1	103491141	Missense_Mutation	SNP	T	TCGA-DD-A1EI-01A-11D-A12Z-10	35703745	103491141	145759480	3	15880										
FAM63A	55793	hgsc.bcm.edu	37	chr1	150974678	150974679	+	In_Frame_Ins	INS	-	-	GAG													0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gatgttcatgatggcaaggaINSgagggcaagggccgttagtg							TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr1:150974678_150974679insGAG	ENST00000361936.5	-	3	1369_1370	c.415_416insCTC	c.(415-417)ctc>cCTCtc	p.138_139insP	FAM63A_ENST00000312210.5_5'UTR|FAM63A_ENST00000361738.6_In_Frame_Ins_p.186_187insP|FAM63A_ENST00000470877.1_Intron|FAM63A_ENST00000493834.2_In_Frame_Ins_p.43_44insP	NM_018379.4	NP_060849	Q8N5J2	FA63A_HUMAN	family with sequence similarity 63, member A	138						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(3)|large_intestine(4)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GATGGCAAGGAGAGGGCAAGGG	0.495																																					p.L187delinsPL		.	.											.	FAM63A	.	.	0			c.560_561insCTC						.																																			SO:0001652	inframe_insertion	55793	exon3			.	BC032321	CCDS976.1, CCDS30854.1, CCDS53361.1, CCDS55635.1	1q21.2	2008-02-05			ENSG00000143409	ENSG00000143409			25648	protein-coding gene	gene with protein product						10718198	Standard	NM_001040217		Approved	FLJ11280	uc010pcn.2	Q8N5J2	OTTHUMG00000035061	ENST00000361936.5:c.416_418dupCTC	1.37:g.150974679_150974681dupGAG	ENSP00000354814:p.Pro138_Pro138dup	197.0	0.0		270.0	62.0	NM_001163258	B3KWP4|B3KWV8|B4DXF2|B4E1S4|D3DV09|J3KP53|Q5SZF0|Q9NUL9|Q9P2F7	In_Frame_Ins	INS	ENST00000361936.5	37	CCDS976.1																																																																																			.	.		0.495	FAM63A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411753.1	NM_018379		GAG	150974679	-	GAG	150974678	7	5	105	1	0	1	1	0	0	0	0	0	5604	304	11	0	1029	0	FAM63A	1	150974678	In_Frame_Ins	INS	-	TCGA-DD-A1EI-01A-11D-A12Z-10	47483537	150974678	98275943	4	15881										
ZNF687	5298	hgsc.bcm.edu	37	chr1	151262327	151262328	+	IGR	INS	-	-	C													0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	aagtacccagctcccctgagINScccccccgtccagccaaacg							TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr1:151262327_151262328insC	ENST00000368873.1	-	0	3340				ZNF687_ENST00000368879.2_Frame_Shift_Ins_p.P937fs			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta						phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GCTCCCCTGAGCCCCCCCGTCC	0.649																																					p.E936fs	Colon(154;765 1838 9854 28443 37492)	.	.											.	ZNF687	.	.	0			c.2808_2809insC						.																																			SO:0001628	intergenic_variant	57592	exon6			.	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348		1.37:g.151262334_151262334dupC		94.0	0.0		105.0	17.0	NM_020832	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	Frame_Shift_Ins	INS	ENST00000368873.1	37																																																																																				.	.		0.649	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651		C	151262328	-	C	151262327	6	5	105	0	1	1	1	0	0	0	0	0	18107	962	34	0		0	ZNF687	1	151262327	IGR	INS	-	TCGA-DD-A1EI-01A-11D-A12Z-10	287649	151262327	97988294	5	15882										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155308071	155308071	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	cctccaggctgggtatctcaTtggctgcttgctcttgactg	11	12	2	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr1:155308071T>G	ENST00000368346.3	-	27	9266	c.8627A>C	c.(8626-8628)aAt>aCt	p.N2876T	ASH1L_ENST00000392403.3_Missense_Mutation_p.N2871T			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2876					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			GGGTATCTCATTGGCTGCTTG	0.517																																					p.N2871T		.	.											.	ASH1L	.	.	0			c.A8612C						.						150	139	143					1																	155308071		2203	4300	6503	SO:0001583	missense	55870	exon27			ATCTCATTGGCTG	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.8627A>C	1.37:g.155308071T>G	ENSP00000357330:p.Asn2876Thr	127.0	0.0		192.0	57.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	T	5.808	0.333387	0.11013	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.88124	-2.34;-2.34	5.65	0.582	0.17412	.	0.699661	0.15155	N	0.277477	T	0.44912	0.1316	N	0.02011	-0.69	0.80722	D	1	B;B	0.15473	0.008;0.013	B;B	0.16289	0.007;0.015	T	0.16600	-1.0397	10	0.12103	T	0.63	.	8.8976	0.35474	0.0:0.4142:0.0:0.5858	.	2876;2871	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	T	2876;2871	ENSP00000357330:N2876T;ENSP00000376204:N2871T	ENSP00000357330:N2876T	N	-	2	0	ASH1L	153574695	0.000000	0.05858	0.958000	0.39756	0.387000	0.30353	-0.141000	0.10327	-0.051000	0.13334	-1.139000	0.01908	AAT	.	.		0.517	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		G	155308071	T	G	155308071	3	3	105	1	0	0	0	0	1	0	0	0	1041	1493	52	5	290	5	ASH1L	1	155308071	Missense_Mutation	SNP	T	TCGA-DD-A1EI-01A-11D-A12Z-10	4045744	155308071	93942550	6	15883										
SLAMF6	114836	hgsc.bcm.edu	37	chr1	160461021	160461021	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	atcctggggtcccaggagacAgtgaggtttggctgacttga	15	8	0	4			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr1:160461021A>G	ENST00000368057.3	-	3	600	c.540T>C	c.(538-540)acT>acC	p.T180T	SLAMF6_ENST00000368059.3_Silent_p.T180T|SLAMF6_ENST00000368055.1_Silent_p.T69T			Q96DU3	SLAF6_HUMAN	SLAM family member 6	180	Ig-like C2-type.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(4)	22	all_cancers(52;1.05e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0923)			CCCAGGAGACAGTGAGGTTTG	0.493																																					p.T180T		.	.											.	SLAMF6	.	.	0			c.T540C						.						148	139	142					1																	160461021		2203	4300	6503	SO:0001819	synonymous_variant	114836	exon3			GGAGACAGTGAGG	AL832854	CCDS1205.1, CCDS53393.1, CCDS53394.1	1q23.1	2013-01-29			ENSG00000162739	ENSG00000162739		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21392	protein-coding gene	gene with protein product		606446				11489943	Standard	NM_052931		Approved	KALI, NTBA, KALIb, Ly108, SF2000, NTB-A, CD352	uc001fwe.2	Q96DU3	OTTHUMG00000022729	ENST00000368057.3:c.540T>C	1.37:g.160461021A>G		181.0	0.0		238.0	71.0	NM_052931	A6NMW2|B2R8X8|Q14CF0|Q5TAS4|Q5TAS6|Q5TAT3|Q96DV0	Silent	SNP	ENST00000368057.3	37	CCDS53394.1																																																																																			.	.		0.493	SLAMF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059010.1	NM_052931		G	160461021	A	G	160461021	2	3	105	1	0	0	0	0	0	0	0	1	14383	175	7	2		2	SLAMF6	1	160461021	Silent	SNP	A	TCGA-DD-A1EI-01A-11D-A12Z-10	5152950	160461021	88789600	7	15884										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196274453	196274458	+	In_Frame_Del	DEL	TAATAC	TAATAC	-													0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ggggtgagttagctctgtgaTaatactgagactggaaaaca							TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	TAATAC	TAATAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr1:196274453_196274458delTAATAC	ENST00000294725.9	-	22	3416_3421	c.2501_2506delGTATTA	c.(2500-2508)agtattatc>atc	p.SI834del	KCNT2_ENST00000367433.5_In_Frame_Del_p.SI810del|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000609185.1_In_Frame_Del_p.SI760del|KCNT2_ENST00000451324.2_Intron|KCNT2_ENST00000367431.4_In_Frame_Del_p.SI760del			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	834					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						AGCTCTGTGATAATACTGAGACTGGA	0.364																																					p.834_836del		.	.											.	KCNT2	.	.	0			c.2502_2507del						.																																			SO:0001651	inframe_deletion	343450	exon22			.	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.2501_2506delGTATTA	1.37:g.196274453_196274458delTAATAC	ENSP00000294725:p.Ser834_Ile835del	84.0	0.0		106.0	17.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	In_Frame_Del	DEL	ENST00000294725.9	37	CCDS1384.1																																																																																			.	.		0.364	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		-	196274458	TAATAC	-	196274453	7	5	105	1	0	1	0	1	0	0	0	0	8101	1406	49	0	929	0	KCNT2	1	196274453	In_Frame_Del	DEL	TAATAC	TCGA-DD-A1EI-01A-11D-A12Z-10	35813432	196274453	52976168	8	15885										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50758388	50758388	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gattgaccgtcagtttcacaCgtcctgcgtctagctccagg	10	13	3	1	rs369744946		TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr2:50758388C>T	ENST00000406316.2	-	11	3800	c.2324G>A	c.(2323-2325)cGt>cAt	p.R775H	NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000405472.3_Missense_Mutation_p.R767H|NRXN1_ENST00000404971.1_Missense_Mutation_p.R815H|NRXN1_ENST00000401669.2_Missense_Mutation_p.R775H|NRXN1_ENST00000402717.3_Missense_Mutation_p.R767H|NRXN1_ENST00000406859.3_Missense_Mutation_p.R775H	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	775	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CAGTTTCACACGTCCTGCGTC	0.473																																					p.R815H		.	.											.	NRXN1	.	.	0			c.G2444A						.	C	HIS/ARG,HIS/ARG	1,4079		0,1,2039	68	72	71		2444,2324	5.8	1	2		71	0,8422		0,0,4211	no	missense,missense	NRXN1	NM_001135659.1,NM_004801.4	29,29	0,1,6250	TT,TC,CC		0.0,0.0245,0.0080	probably-damaging,probably-damaging	815/1548,775/1478	50758388	1,12501	2040	4211	6251	SO:0001583	missense	9378	exon12			TTCACACGTCCTG	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.2324G>A	2.37:g.50758388C>T	ENSP00000384311:p.Arg775His	78.0	0.0		101.0	20.0	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	C	35	5.473955	0.96291	2.45E-4	0.0	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.88662	0.6497	M	0.80982	2.52	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;1.0	D;P;D	0.70935	0.966;0.867;0.971	D	0.86309	0.1685	10	0.35671	T	0.21	.	20.3316	0.98722	0.0:1.0:0.0:0.0	.	815;775;767	Q9ULB1-3;F8WB18;A7E294	.;.;.	H	815;775;767;775;816;767;775	ENSP00000385142:R815H;ENSP00000384311:R775H;ENSP00000434015:R767H;ENSP00000385017:R775H;ENSP00000385434:R767H;ENSP00000385681:R775H	ENSP00000385017:R775H	R	-	2	0	NRXN1	50611892	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	7.772000	0.85439	2.871000	0.98454	0.655000	0.94253	CGT	.	.		0.473	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50758388	C	T	50758388	3	4	105	1	0	0	0	0	1	0	0	0	10674	536	19	1	2514	1	NRXN1	2	50758388	Missense_Mutation	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10		50758388	192440985	9	15886										
BCL11A	53335	hgsc.bcm.edu	37	chr2	60688821	60688821	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gggtgcacgcgtggtcgcacAggttgcacttgtagggcttc	16	10	0	0			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr2:60688821A>C	ENST00000335712.6	-	4	1453	c.1226T>G	c.(1225-1227)cTg>cGg	p.L409R	BCL11A_ENST00000538214.1_Missense_Mutation_p.L375R|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000358510.4_Missense_Mutation_p.L375R|BCL11A_ENST00000356842.4_Missense_Mutation_p.L409R|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000537768.1_Missense_Mutation_p.L78R	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	409					B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			GTGGTCGCACAGGTTGCACTT	0.597			T	IGH@	B-CLL																																p.L409R		.	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	.	.	0			c.T1226G						.						97	92	94					2																	60688821		2203	4300	6503	SO:0001583	missense	53335	exon4			TCGCACAGGTTGC	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"Zinc fingers, C2H2-type"	13221	protein-coding gene	gene with protein product		606557	"ecotropic viral integration site 9"	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.1226T>G	2.37:g.60688821A>C	ENSP00000338774:p.Leu409Arg	118.0	0.0		132.0	29.0	NM_018014	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	37	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	A	13.02	2.113028	0.37242	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000537768;ENST00000335712;ENST00000358510	T;T;T;T;T	0.20881	3.01;3.01;2.04;2.04;2.04	5.54	5.54	0.83059	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.083845	0.49305	D	0.000150	T	0.31136	0.0787	N	0.25201	0.72	0.80722	D	1	D;D;D;D;D	0.89917	0.973;0.998;1.0;0.999;0.999	D;D;D;D;D	0.87578	0.941;0.951;0.998;0.996;0.993	T	0.06643	-1.0815	10	0.18710	T	0.47	-1.1401	15.6768	0.77332	1.0:0.0:0.0:0.0	.	375;78;375;409;409	F5H2Y4;B4DT16;Q9H165-6;Q9H165;D9YZV9	.;.;.;BC11A_HUMAN;.	R	409;445;375;78;409;375	ENSP00000349300:L409R;ENSP00000438303:L375R;ENSP00000443712:L78R;ENSP00000338774:L409R;ENSP00000351307:L375R	ENSP00000338774:L409R	L	-	2	0	BCL11A	60542325	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.306000	0.78905	2.110000	0.64415	0.533000	0.62120	CTG	.	.		0.597	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		C	60688821	A	C	60688821	3	2	105	1	0	0	0	0	1	0	0	0	1363	188	7	5	1391	5	BCL11A	2	60688821	Missense_Mutation	SNP	A	TCGA-DD-A1EI-01A-11D-A12Z-10	9930433	60688821	182510552	10	15887										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52393977	52393977	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gggggaagctgtcccgcatgCagcgggcagtgctgtcagcg	18	11	1	0	rs200763734		TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr3:52393977C>T	ENST00000420323.2	+	27	4714	c.4453C>T	c.(4453-4455)Cag>Tag	p.Q1485*		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1485	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GTCCCGCATGCAGCGGGCAGT	0.577																																					p.Q1485X		.	.											.	DNAH1	.	.	0			c.C4453T						.						162	170	167					3																	52393977		2156	4253	6409	SO:0001587	stop_gained	25981	exon27			CGCATGCAGCGGG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.4453C>T	3.37:g.52393977C>T	ENSP00000401514:p.Gln1485*	111.0	0.0		129.0	38.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Nonsense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	C	44	11.065208	0.99511	.	.	ENSG00000114841	ENST00000420323	.	.	.	5.13	5.13	0.70059	.	0.131609	0.34386	N	0.004003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	18.7672	0.91878	0.0:1.0:0.0:0.0	.	.	.	.	X	1485	.	ENSP00000401514:Q1485X	Q	+	1	0	DNAH1	52369017	1.000000	0.71417	1.000000	0.80357	0.514000	0.34195	2.306000	0.43673	2.677000	0.91161	0.561000	0.74099	CAG	C|0.998;G|0.002	.		0.577	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		T	52393977	C	T	52393977	4	4	105	1	0	0	0	0	0	1	0	0	4599	711	25	3	4555	3	DNAH1	3	52393977	Nonsense_Mutation	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10		52393977	145628453	11	15888										
MME	4311	hgsc.bcm.edu	37	chr3	154886382	154886382	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gcatggtgtatcagtatggaAacttttcctgggacctggca	12	8	1	0			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr3:154886382A>C	ENST00000460393.1	+	19	2002	c.1882A>C	c.(1882-1884)Aac>Cac	p.N628H	MME_ENST00000492661.1_Missense_Mutation_p.N628H|MME_ENST00000462745.1_Missense_Mutation_p.N628H|MME_ENST00000493237.1_Missense_Mutation_p.N628H|MME_ENST00000360490.2_Missense_Mutation_p.N628H|MME-AS1_ENST00000484721.1_RNA	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	628					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	TCAGTATGGAAACTTTTCCTG	0.418																																					p.N628H		.	.											.	MME	.	.	0			c.A1882C						.						139	131	134					3																	154886382		2203	4300	6503	SO:0001583	missense	4311	exon19			TATGGAAACTTTT		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.1882A>C	3.37:g.154886382A>C	ENSP00000418525:p.Asn628His	235.0	0.0		393.0	100.0	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.527222	0.85706	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	D;D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76;-1.76	5.25	5.25	0.73442	Peptidase M13, neprilysin, C-terminal (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91546	0.7330	M	0.85197	2.74	0.58432	D	0.999999	D	0.89917	1.0	D	0.80764	0.994	D	0.92612	0.6100	10	0.59425	D	0.04	-23.7422	15.1817	0.72965	1.0:0.0:0.0:0.0	.	628	P08473	NEP_HUMAN	H	628	ENSP00000420389:N628H;ENSP00000418525:N628H;ENSP00000419653:N628H;ENSP00000417079:N628H;ENSP00000353679:N628H	ENSP00000353679:N628H	N	+	1	0	MME	156369076	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.196000	0.94978	1.988000	0.58038	0.528000	0.53228	AAC	.	.		0.418	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		C	154886382	A	C	154886382	3	2	105	1	0	0	0	0	1	0	0	0	9654	14	1	5	1952	5	MME	3	154886382	Missense_Mutation	SNP	A	TCGA-DD-A1EI-01A-11D-A12Z-10	102492405	154886382	43136048	12	15889										
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77677614	77677618	+	Frame_Shift_Del	DEL	TTCTA	TTCTA	-													0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	cctggcagcttcaacaaactTtctaaagtgacaattgcaag					rs139635179	byFrequency	TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	TTCTA	TTCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr4:77677614_77677618delTTCTA	ENST00000296043.6	+	8	5675_5679	c.4722_4726delTTCTA	c.(4720-4728)ctttctaaafs	p.SK1575fs	RP11-359D14.3_ENST00000449007.1_RNA|RP11-359D14.2_ENST00000452412.1_RNA	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1575					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			TCAACAAACTTTCTAAAGTGACAAT	0.424																																					p.1574_1575del		.	.											.	SHROOM3	.	.	0			c.4721_4725del						.																																			SO:0001589	frameshift_variant	57619	exon8			.	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.4722_4726delTTCTA	4.37:g.77677614_77677618delTTCTA	ENSP00000296043:p.Ser1575fs	127.0	0.0		131.0	19.0	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Frame_Shift_Del	DEL	ENST00000296043.6	37	CCDS3579.2																																																																																			.	.		0.424	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		-	77677618	TTCTA	-	77677614	7	5	105	1	0	1	0	1	0	0	0	0	14310	1828	64	0	4752	0	SHROOM3	4	77677614	Frame_Shift_Del	DEL	TTCTA	TCGA-DD-A1EI-01A-11D-A12Z-10		77677614	113476662	13	15890										
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41065451	41065451	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	accatagctggttgccaattCagccagggcaagcacaacga	10	12	1	0			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr5:41065451C>T	ENST00000399564.4	-	4	793	c.343G>A	c.(343-345)Gaa>Aaa	p.E115K		NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	115																	GTTGCCAATTCAGCCAGGGCA	0.418																																					p.E115K		.	.											.	.	.	.	0			c.G343A						.						64	60	61					5																	41065451		1899	4119	6018	SO:0001583	missense	133558	exon4			CCAATTCAGCCAG		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.343G>A	5.37:g.41065451C>T	ENSP00000382476:p.Glu115Lys	47.0	0.0		80.0	10.0	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.466823	0.43839	.	.	ENSG00000171495	ENST00000399564	T	0.04194	3.68	6.16	6.16	0.99307	Armadillo-type fold (1);	0.000000	0.56097	D	0.000024	T	0.09992	0.0245	N	0.25286	0.73	0.37279	D	0.90774	D	0.69078	0.997	D	0.64042	0.921	T	0.47262	-0.9131	10	0.15952	T	0.53	.	16.3599	0.83257	0.0:1.0:0.0:0.0	.	115	Q7Z745	HTRB2_HUMAN	K	115	ENSP00000382476:E115K	ENSP00000382476:E115K	E	-	1	0	HEATR7B2	41101208	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.337000	0.43947	2.937000	0.99478	0.650000	0.86243	GAA	.	.		0.418	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		T	41065451	C	T	41065451	3	4	105	1	0	0	0	0	1	0	0	0	7044	835	29	3	4570	3	HEATR7B2	5	41065451	Missense_Mutation	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10		41065451	139849809	14	15891										
RGNEF	64283	hgsc.bcm.edu	37	chr5	73048919	73048919	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	agaccctgctgaccccatttGccttgacggcaggagcactg	11	14	0	3			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr5:73048919G>T	ENST00000426542.2	+	3	387	c.367G>T	c.(367-369)Gcc>Tcc	p.A123S	ARHGEF28_ENST00000296794.6_Missense_Mutation_p.A123S|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.A123S|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.A123S|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.A123S|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.A123S			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	123					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GACCCCATTTGCCTTGACGGC	0.597																																					p.A123S		.	.											.	.	.	.	0			c.G367T						.						38	41	40					5																	73048919		2144	4265	6409	SO:0001583	missense	64283	exon4			CCATTTGCCTTGA		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.367G>T	5.37:g.73048919G>T	ENSP00000412175:p.Ala123Ser	97.0	0.0		154.0	36.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.737841	0.30774	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542	T;T;T;T;T;T	0.09073	3.26;3.26;3.26;3.02;3.26;3.26	5.82	5.82	0.92795	.	.	.	.	.	T	0.07593	0.0191	N	0.25647	0.755	0.27325	N	0.956933	B;B;B;B	0.29988	0.068;0.068;0.264;0.112	B;B;B;B	0.27715	0.013;0.013;0.082;0.029	T	0.21965	-1.0230	9	0.39692	T	0.17	.	12.9148	0.58200	0.078:0.0:0.922:0.0	.	123;123;123;123	Q8N1W1;E9PC75;Q8N1W1-2;Q8N1W1-4	RGNEF_HUMAN;.;.;.	S	123	ENSP00000296794:A123S;ENSP00000441913:A123S;ENSP00000441436:A123S;ENSP00000287898:A123S;ENSP00000411459:A123S;ENSP00000412175:A123S	ENSP00000287898:A123S	A	+	1	0	RP11-428C6.1	73084675	1.000000	0.71417	1.000000	0.80357	0.255000	0.26057	4.806000	0.62569	2.757000	0.94681	0.561000	0.74099	GCC	.	.		0.597	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			T	73048919	G	T	73048919	3	4	105	1	0	0	0	0	1	0	0	0	13298	1319	46	3	377	3	RGNEF	5	73048919	Missense_Mutation	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10	31983468	73048919	107866341	15	15892										
LNPEP	4012	hgsc.bcm.edu	37	chr5	96358073	96358073	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ctgatgagggcactccatctAtgcgagagcttcggtcagcc	12	12	2	3			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr5:96358073A>G	ENST00000231368.5	+	14	3138	c.2446A>G	c.(2446-2448)Atg>Gtg	p.M816V	LNPEP_ENST00000395770.3_Missense_Mutation_p.M802V	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	816					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		CACTCCATCTATGCGAGAGCT	0.438																																					p.M816V		.	.											.	LNPEP	.	.	0			c.A2446G						.						102	96	98					5																	96358073		2203	4300	6503	SO:0001583	missense	4012	exon14			CCATCTATGCGAG	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"cystinyl aminopeptidase", "placental leucine aminopeptidase"	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.2446A>G	5.37:g.96358073A>G	ENSP00000231368:p.Met816Val	101.0	0.0		189.0	54.0	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	37	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	A	11.90	1.777424	0.31411	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.05025	3.51;3.51	5.9	-5.49	0.02584	.	0.693069	0.16311	N	0.220005	T	0.03564	0.0102	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25047	-1.0143	10	0.51188	T	0.08	.	17.7054	0.88308	0.2421:0.0:0.7579:0.0	.	816	Q9UIQ6	LCAP_HUMAN	V	816;802	ENSP00000231368:M816V;ENSP00000379117:M802V	ENSP00000231368:M816V	M	+	1	0	LNPEP	96383829	0.009000	0.17119	0.009000	0.14445	0.796000	0.44982	-0.148000	0.10219	-1.068000	0.03156	-0.256000	0.11100	ATG	.	.		0.438	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		G	96358073	A	G	96358073	3	3	105	1	0	0	0	0	1	0	0	0	8873	449	16	2	2500	2	LNPEP	5	96358073	Missense_Mutation	SNP	A	TCGA-DD-A1EI-01A-11D-A12Z-10	23309154	96358073	84557187	16	15893										
MICAL1	64780	hgsc.bcm.edu	37	chr6	109768571	109768571	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ggctctcacctcctggtgttGggatgggggtgtcaggggta	18	8	2	0			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr6:109768571G>A	ENST00000358807.3	-	16	2370	c.2059C>T	c.(2059-2061)Caa>Taa	p.Q687*	MICAL1_ENST00000368952.4_Nonsense_Mutation_p.Q706*|MICAL1_ENST00000358577.3_Nonsense_Mutation_p.Q601*	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	687					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		TCCTGGTGTTGGGATGGGGGT	0.627																																					p.Q687X		.	.											.	MICAL1	.	.	0			c.C2059T						.						65	65	65					6																	109768571		2203	4300	6503	SO:0001587	stop_gained	64780	exon16			GGTGTTGGGATGG	AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"NEDD9 interacting protein with calponin homology and LIM domains"	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.2059C>T	6.37:g.109768571G>A	ENSP00000351664:p.Gln687*	82.0	0.0		93.0	13.0	NM_022765	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Nonsense_Mutation	SNP	ENST00000358807.3	37	CCDS5076.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.683992|5.683992	0.96774|0.96774	.|.	.|.	ENSG00000135596|ENSG00000135596	ENST00000433205|ENST00000358807;ENST00000368952;ENST00000358577;ENST00000368957	.|.	.|.	.|.	4.93|4.93	1.88|1.88	0.25563|0.25563	.|.	.|1.121610	.|0.06568	.|N	.|0.747923	T|.	0.10551|.	0.0258|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.08106|.	-1.0738|.	3|.	.|0.06494	.|T	.|0.89	.|.	12.4069|12.4069	0.55445|0.55445	0.0:0.5319:0.4681:0.0|0.0:0.5319:0.4681:0.0	.|.	.|.	.|.	.|.	L|X	248|687;706;601;211	.|.	.|ENSP00000351385:Q601X	P|Q	-|-	2|1	0|0	MICAL1|MICAL1	109875264|109875264	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.619000|0.619000	0.37552|0.37552	-0.164000|-0.164000	0.09983|0.09983	0.733000|0.733000	0.32492|0.32492	0.655000|0.655000	0.94253|0.94253	CCA|CAA	.	.		0.627	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765		A	109768571	G	A	109768571	4	1	105	1	0	0	0	0	0	1	0	0	9578	1357	47	3	1184	3	MICAL1	6	109768571	Nonsense_Mutation	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10		109768571	61346496	17	15894										
C7orf64	84060	hgsc.bcm.edu	37	chr7	92158153	92158153	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gtcgagcggcggggagctagGgagtttatttgatcaccacg	16	8	1	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr7:92158153G>T	ENST00000265732.5	+	1	67	c.26G>T	c.(25-27)gGg>gTg	p.G9V	PEX1_ENST00000438045.1_5'Flank|RBM48_ENST00000481551.1_Missense_Mutation_p.G9V|PEX1_ENST00000248633.4_5'Flank|PEX1_ENST00000428214.1_5'Flank	NM_032120.2	NP_115496.2	Q5RL73	RBM48_HUMAN	RNA binding motif protein 48	9						nucleus (GO:0005634)	RNA binding (GO:0003723)										GGGGAGCTAGGGAGTTTATTT	0.557																																					p.G9V		.	.											.	.	.	.	0			c.G26T						.						69	74	72					7																	92158153		1983	4138	6121	SO:0001583	missense	84060	exon1			AGCTAGGGAGTTT	AL136619	CCDS43615.1	7q21.2	2013-02-12	2011-12-09	2011-12-09	ENSG00000127993	ENSG00000127993		"RNA binding motif (RRM) containing"	21785	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 64"	C7orf64			Standard	NM_032120		Approved	DKFZp564O0523, HSPC304	uc003ulz.3	Q5RL73	OTTHUMG00000159535	ENST00000265732.5:c.26G>T	7.37:g.92158153G>T	ENSP00000265732:p.Gly9Val	134.0	0.0		176.0	46.0	NM_032120	B7Z2K5|B7ZL51|Q5H9T2|Q8IYW7|Q96NS0|Q9H0V7	Missense_Mutation	SNP	ENST00000265732.5	37	CCDS43615.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.016717	0.54468	.	.	ENSG00000127993	ENST00000509224;ENST00000265732;ENST00000481551;ENST00000450580	.	.	.	4.77	4.77	0.60923	.	0.223472	0.47455	D	0.000224	T	0.53642	0.1809	L	0.48362	1.52	0.38410	D	0.945893	B;D;P	0.62365	0.261;0.991;0.894	B;P;B	0.50192	0.042;0.634;0.314	T	0.57579	-0.7787	9	0.45353	T	0.12	-1.3684	13.3215	0.60436	0.0:0.0:0.8421:0.1579	.	9;9;9	B4DGJ6;B7Z2K5;Q5RL73	.;.;CG064_HUMAN	V	11;9;9;9	.	ENSP00000265732:G9V	G	+	2	0	C7orf64	91996089	1.000000	0.71417	0.121000	0.21740	0.009000	0.06853	5.556000	0.67307	2.631000	0.89168	0.561000	0.74099	GGG	.	.		0.557	RBM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356076.1	NM_032120		T	92158153	G	T	92158153	3	4	105	1	0	0	0	0	1	0	0	0	2412	1232	43	3	28	3	C7orf64	7	92158153	Missense_Mutation	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10		92158153	66980510	18	15895										
PTCD1	26024	hgsc.bcm.edu	37	chr7	99032672	99032672	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ggctcgggtcagagcccaggCtgcccgtgttttcctgacgc	14	14	1	2			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr7:99032672C>T	ENST00000292478.4	-	2	444	c.194G>A	c.(193-195)aGc>aAc	p.S65N	PTCD1_ENST00000555673.1_Missense_Mutation_p.S114N|ATP5J2-PTCD1_ENST00000437572.1_5'UTR|PTCD1_ENST00000485746.1_5'Flank|ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.S114N	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	65					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			AGAGCCCAGGCTGCCCGTGTT	0.642																																					p.S114N		.	.											.	.	.	.	0			c.G341A						.						33	35	34					7																	99032672		2203	4300	6503	SO:0001583	missense	100526740	exon3			CCCAGGCTGCCCG	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.194G>A	7.37:g.99032672C>T	ENSP00000292478:p.Ser65Asn	46.0	0.0		47.0	15.0	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.448360	0.63178	.	.	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000555673;ENST00000430982;ENST00000430029;ENST00000419981;ENST00000437572;ENST00000413834	T;T;D;D;D;D;T	0.86030	-0.18;-0.16;-1.76;-1.76;-2.06;-1.84;-0.16	5.57	3.76	0.43208	.	0.389764	0.27682	N	0.018300	D	0.83764	0.5325	M	0.73962	2.25	0.09310	N	1	P;P	0.44816	0.844;0.608	P;B	0.44359	0.447;0.261	T	0.73313	-0.4022	10	0.18710	T	0.47	-14.0754	9.9101	0.41399	0.0:0.8368:0.0:0.1632	.	114;65	G3V325;O75127	.;PTCD1_HUMAN	N	65;114;65;65;65;65;114	ENSP00000292478:S65N;ENSP00000450995:S114N;ENSP00000390530:S65N;ENSP00000408059:S65N;ENSP00000401600:S65N;ENSP00000410697:S65N;ENSP00000400168:S114N	ENSP00000400168:S114N	S	-	2	0	ATP5J2-PTCD1;PTCD1	98870608	0.014000	0.17966	0.003000	0.11579	0.001000	0.01503	0.822000	0.27352	1.361000	0.45981	-0.251000	0.11542	AGC	.	.		0.642	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		T	99032672	C	T	99032672	3	4	105	1	0	0	0	0	1	0	0	0	12739	797	28	3	1936	3	PTCD1	7	99032672	Missense_Mutation	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10	6874519	99032672	60105991	19	15896										
SSPO	23145	hgsc.bcm.edu	37	chr7	149485526	149485526	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ggtggtggcctgtgtggaggGctgcttctgccccgagggga	20	9	1	0			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr7:149485526G>A	ENST00000378016.2	+	0	3932							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGTGTGGAGGGCTGCTTCTGC	0.652																																					p.G1311D		.	.											.	.	.	.	0			c.G3932A						.						38	47	44					7																	149485526		2119	4217	6336			23145	exon27			TGGAGGGCTGCTT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149485526G>A		109.0	0.0		100.0	26.0	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				.	.		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149485526	G	A	149485526	1	1	105	0	1	0	0	0	0	0	0	0	15204	1203	42	3		3	SSPO	7	149485526	RNA	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10	50452854	149485526	9653137	20	15897										
ZNF596	169270	hgsc.bcm.edu	37	chr8	195803	195803	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	tgggaaggctttcagtaaatGttcttaccttagacaacatg	9	7	2	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr8:195803G>A	ENST00000398612.1	+	6	1339	c.956G>A	c.(955-957)tGt>tAt	p.C319Y	ZNF596_ENST00000320552.2_Missense_Mutation_p.C249Y|ZNF596_ENST00000308811.4_Missense_Mutation_p.C319Y	NM_001042415.1|NM_001042416.1	NP_001035880.1|NP_001035881.1	Q8TC21	ZN596_HUMAN	zinc finger protein 596	319					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(5)	14		all_cancers(2;4.81e-29)|all_epithelial(2;5.03e-19)|Lung NSC(2;8.68e-08)|all_lung(2;1.52e-07)|Ovarian(12;0.00965)|Colorectal(14;0.0367)|all_neural(12;0.0837)|Myeloproliferative disorder(644;0.116)|all_hematologic(2;0.138)|Acute lymphoblastic leukemia(644;0.242)		Epithelial(5;3.77e-18)|all cancers(2;5.2e-17)|OV - Ovarian serous cystadenocarcinoma(5;5.37e-09)|BRCA - Breast invasive adenocarcinoma(11;1.7e-06)|Colorectal(2;6.51e-05)|READ - Rectum adenocarcinoma(2;0.0276)|COAD - Colon adenocarcinoma(149;0.0702)		TTCAGTAAATGTTCTTACCTT	0.388																																					p.C319Y		.	.											.	ZNF596	.	.	0			c.G956A						.						51	51	51					8																	195803		2203	4300	6503	SO:0001583	missense	169270	exon6			GTAAATGTTCTTA	BC026190	CCDS5951.2	8p23.3	2013-01-08			ENSG00000172748	ENSG00000172748		"Zinc fingers, C2H2-type", "-"	27268	protein-coding gene	gene with protein product						12477932	Standard	NM_001287256		Approved		uc003wot.3	Q8TC21	OTTHUMG00000086931	ENST00000398612.1:c.956G>A	8.37:g.195803G>A	ENSP00000381613:p.Cys319Tyr	116.0	0.0		149.0	54.0	NM_173539	B2R8P4|O95015|Q8N9X0	Missense_Mutation	SNP	ENST00000398612.1	37	CCDS5951.2	.	.	.	.	.	.	.	.	.	.	.	0.005	-2.165931	0.00318	.	.	ENSG00000172748	ENST00000308811;ENST00000320552;ENST00000398612	T;T;T	0.14516	2.5;3.21;2.5	2.62	-1.9	0.07665	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04907	0.0132	N	0.20685	0.6	0.09310	N	1	P	0.47302	0.893	B	0.39738	0.308	T	0.16867	-1.0388	9	0.02654	T	1	.	1.4284	0.02328	0.2628:0.3827:0.2178:0.1367	.	319	Q8TC21	ZN596_HUMAN	Y	319;249;319	ENSP00000310033:C319Y;ENSP00000318719:C249Y;ENSP00000381613:C319Y	ENSP00000310033:C319Y	C	+	2	0	ZNF596	185803	0.000000	0.05858	0.000000	0.03702	0.973000	0.67179	-2.420000	0.01032	-0.474000	0.06862	0.585000	0.79938	TGT	.	.		0.388	ZNF596-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195858.4	NM_173539		A	195803	G	A	195803	3	1	105	1	0	0	0	0	1	0	0	0	18041	1377	48	3	974	3	ZNF596	8	195803	Missense_Mutation	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10		195803	146168219	21	15898										
OSGIN2	734	hgsc.bcm.edu	37	chr8	90937753	90937753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	aagaggaggaggagatgggaTagcttaaagcaagtttacaa	14	3	0	2			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr8:90937753T>C	ENST00000297438.2	+	6	1866	c.1511T>C	c.(1510-1512)aTa>aCa	p.I504T	OSGIN2_ENST00000451899.2_Missense_Mutation_p.I548T	NM_004337.2	NP_004328.1	Q9Y236	OSGI2_HUMAN	oxidative stress induced growth inhibitor family member 2	504					meiotic nuclear division (GO:0007126)					breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(1)	17			BRCA - Breast invasive adenocarcinoma(11;0.0344)			GGAGATGGGATAGCTTAAAGC	0.383																																					p.I548T		.	.											.	OSGIN2	.	.	0			c.T1643C						.						46	44	44					8																	90937753		2203	4300	6503	SO:0001583	missense	734	exon6			ATGGGATAGCTTA	AF061326	CCDS6248.1, CCDS47888.1	8q21	2006-10-05	2006-10-05	2006-10-05	ENSG00000164823	ENSG00000164823			1355	protein-coding gene	gene with protein product		604598	"chromosome 8 open reading frame 1"	C8orf1		9933573	Standard	NM_004337		Approved	hT41	uc003yeh.3	Q9Y236	OTTHUMG00000163811	ENST00000297438.2:c.1511T>C	8.37:g.90937753T>C	ENSP00000297438:p.Ile504Thr	81.0	0.0		218.0	126.0	NM_001126111		Missense_Mutation	SNP	ENST00000297438.2	37	CCDS6248.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.083021	0.36758	.	.	ENSG00000164823	ENST00000297438;ENST00000451899	T;T	0.24908	1.86;1.83	5.79	5.79	0.91817	.	0.566107	0.20520	N	0.090702	T	0.16214	0.0390	N	0.08118	0	0.80722	D	1	B;B	0.26845	0.161;0.041	B;B	0.21151	0.033;0.01	T	0.07616	-1.0763	10	0.72032	D	0.01	-6.7707	16.1325	0.81454	0.0:0.0:0.0:1.0	.	548;504	Q9Y236-2;Q9Y236	.;OSGI2_HUMAN	T	504;548	ENSP00000297438:I504T;ENSP00000396445:I548T	ENSP00000297438:I504T	I	+	2	0	OSGIN2	91006928	0.997000	0.39634	0.986000	0.45419	0.953000	0.61014	6.574000	0.74014	2.219000	0.72066	0.460000	0.39030	ATA	.	.		0.383	OSGIN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375691.1	NM_004337		C	90937753	T	C	90937753	3	2	105	1	0	0	0	0	1	0	0	0	11299	1406	49	2	1665	2	OSGIN2	8	90937753	Missense_Mutation	SNP	T	TCGA-DD-A1EI-01A-11D-A12Z-10	90741950	90937753	55426269	22	15899										
TRHR	7201	hgsc.bcm.edu	37	chr8	110131669	110131669	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	tgcttggcttctgaggtatcCtttagccaaagttgattcat	9	8	2	2			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr8:110131669C>A	ENST00000518632.1	+	3	1533	c.1182C>A	c.(1180-1182)tcC>tcA	p.S394S	TRHR_ENST00000311762.2_Silent_p.S394S			P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	394					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thyrotropin-releasing hormone receptor activity (GO:0004997)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(12)|prostate(4)|skin(4)|urinary_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			CTGAGGTATCCTTTAGCCAAA	0.403																																					p.S394S		.	.											TRHR,nipple,malignant_melanoma,+1	TRHR	.	.	0			c.C1182A						.						63	63	63					8																	110131669		2203	4299	6502	SO:0001819	synonymous_variant	7201	exon2			GGTATCCTTTAGC		CCDS6311.1	8q23.1	2013-09-20			ENSG00000174417	ENSG00000174417			12299	protein-coding gene	gene with protein product		188545				8128317	Standard	NM_003301		Approved		uc003ymz.4	P34981	OTTHUMG00000164910	ENST00000518632.1:c.1182C>A	8.37:g.110131669C>A		117.0	0.0		297.0	67.0	NM_003301	Q2M339	Silent	SNP	ENST00000518632.1	37	CCDS6311.1																																																																																			.	.		0.403	TRHR-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380892.1			A	110131669	C	A	110131669	2	1	105	1	0	0	0	0	0	0	0	1	16495	668	24	3		3	TRHR	8	110131669	Silent	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10	19193916	110131669	36232353	23	15900										
ST3GAL1	6482	hgsc.bcm.edu	37	chr8	134477129	134477129	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ccagctcccggaagctctcaGggtacaccagatggtgggtg	14	12	1	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr8:134477129G>C	ENST00000319914.5	-	6	1602	c.575C>G	c.(574-576)cCt>cGt	p.P192R	ST3GAL1_ENST00000522652.1_Missense_Mutation_p.P192R|ST3GAL1_ENST00000521180.1_Missense_Mutation_p.P192R|ST3GAL1_ENST00000399640.2_Missense_Mutation_p.P192R			Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	192					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein phosphorylation (GO:0006468)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)			endometrium(3)|large_intestine(2)|lung(11)|prostate(1)	17	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			GAAGCTCTCAGGGTACACCAG	0.582																																					p.P192R		.	.											.	ST3GAL1	.	.	0			c.C575G						.						175	160	165					8																	134477129		2203	4300	6503	SO:0001583	missense	6482	exon7			CTCTCAGGGTACA	L29555	CCDS6373.1	8q24.22	2013-03-01	2003-01-14	2005-02-07	ENSG00000008513	ENSG00000008513	2.4.99.4	"Sialyltransferases"	10862	protein-coding gene	gene with protein product	"ST3Gal I"	607187	"sialyltransferase 4A (beta-galactosidase alpha-2,3-sialytransferase)"	SIAT4A		10504389, 7655169	Standard	NM_003033		Approved	ST3O, SIATFL, ST3GalA.1	uc003yuk.2	Q11201	OTTHUMG00000164534	ENST00000319914.5:c.575C>G	8.37:g.134477129G>C	ENSP00000318445:p.Pro192Arg	168.0	0.0		336.0	176.0	NM_173344	O60677|Q9UN51	Missense_Mutation	SNP	ENST00000319914.5	37	CCDS6373.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.913610	0.92178	.	.	ENSG00000008513	ENST00000319914;ENST00000399640;ENST00000521180;ENST00000522652;ENST00000523854	T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.67040	0.2851	M	0.88775	2.98	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75252	-0.3383	10	0.87932	D	0	-24.2124	17.094	0.86630	0.0:0.0:1.0:0.0	.	192	Q11201	SIA4A_HUMAN	R	192;192;192;192;62	ENSP00000318445:P192R;ENSP00000414073:P192R;ENSP00000428540:P192R;ENSP00000430515:P192R;ENSP00000429638:P62R	ENSP00000318445:P192R	P	-	2	0	ST3GAL1	134546311	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.648000	0.98483	2.271000	0.75665	0.561000	0.74099	CCT	.	.		0.582	ST3GAL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379132.1	NM_003033		C	134477129	G	C	134477129	3	2	105	1	0	0	0	0	1	0	0	0	15229	1000	35	4	463	4	ST3GAL1	8	134477129	Missense_Mutation	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10	24345460	134477129	11886893	24	15901										
DCLRE1C	64421	hgsc.bcm.edu	37	chr10	14976379	14976379	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	agaatgaacagtcaccatacCtggactcctaattcttcact	5	12	3	2			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr10:14976379C>T	ENST00000378278.2	-	8	715	c.678G>A	c.(676-678)caG>caA	p.Q226Q	DCLRE1C_ENST00000378254.1_Splice_Site_p.Q106Q|DCLRE1C_ENST00000396817.2_Splice_Site_p.Q106Q|DCLRE1C_ENST00000453695.2_Splice_Site_p.Q106Q|DCLRE1C_ENST00000378249.1_Splice_Site_p.Q111Q|DCLRE1C_ENST00000378255.1_Splice_Site_p.Q106Q|DCLRE1C_ENST00000357717.2_Splice_Site_p.Q111Q|DCLRE1C_ENST00000378258.1_Splice_Site_p.Q106Q|DCLRE1C_ENST00000378289.4_Splice_Site_p.Q226Q|DCLRE1C_ENST00000378246.2_Splice_Site_p.Q111Q			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	226					B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						GTCACCATACCTGGACTCCTA	0.438								Non-homologous end-joining																													p.Q226Q		.	.											.	DCLRE1C	.	.	0			c.G678A						.						86	100	95					10																	14976379		2203	4300	6503	SO:0001630	splice_region_variant	64421	exon8			CCATACCTGGACT	BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	605988	"severe combined immunodeficiency, type a (Athabascan)", "DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.678+1G>A	10.37:g.14976379C>T		166.0	0.0		242.0	75.0	NM_001033855	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Silent	SNP	ENST00000378278.2	37	CCDS31149.1																																																																																			.	.		0.438	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487	Silent	T	14976379	C	T	14976379	5	4	105	1	0	0	0	0	0	0	1	0	4298	695	24	3	1428	3	DCLRE1C	10	14976379	Splice_Site	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10		14976379	120558368	25	15902										
ZNF365	22891	hgsc.bcm.edu	37	chr10	64148204	64148204	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	aagcggcagctgagaaggagGttcaagggaaagcccggctc	16	9	1	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr10:64148204G>T	ENST00000395254.3	+	3	1073	c.793G>T	c.(793-795)Gtt>Ttt	p.V265F	ZNF365_ENST00000466727.1_3'UTR|ZNF365_ENST00000410046.3_Missense_Mutation_p.V265F|ZNF365_ENST00000395255.3_Missense_Mutation_p.V265F	NM_014951.2	NP_055766.2	Q70YC4	TALAN_HUMAN	zinc finger protein 365	0										breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					TGAGAAGGAGGTTCAAGGGAA	0.483																																					p.V265F		.	.											.	ZNF365	.	.	0			c.G793T						.						67	67	67					10																	64148204		2203	4300	6503	SO:0001583	missense	22891	exon3			AAGGAGGTTCAAG	AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395254.3:c.793G>T	10.37:g.64148204G>T	ENSP00000378674:p.Val265Phe	125.0	0.0		160.0	23.0	NM_014951		Missense_Mutation	SNP	ENST00000395254.3	37	CCDS31209.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.040020	0.35989	.	.	ENSG00000138311	ENST00000395254;ENST00000395255;ENST00000410046	T;T;T	0.37235	1.21;1.21;1.21	5.67	4.71	0.59529	.	0.404030	0.23418	N	0.048388	T	0.29817	0.0745	L	0.48362	1.52	0.80722	D	1	B;B;B;B	0.24721	0.11;0.01;0.001;0.003	B;B;B;B	0.17433	0.018;0.004;0.003;0.004	T	0.05273	-1.0895	10	0.38643	T	0.18	-11.2452	10.3383	0.43862	0.0:0.1254:0.6271:0.2475	.	265;265;265;280	Q70YC5-3;Q70YC5-2;Q70YC5;Q70YC5-4	.;.;ZN365_HUMAN;.	F	265	ENSP00000378674:V265F;ENSP00000378675:V265F;ENSP00000387091:V265F	ENSP00000378674:V265F	V	+	1	0	ZNF365	63818210	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.997000	0.40786	2.836000	0.97738	0.655000	0.94253	GTT	.	.		0.483	ZNF365-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048238.2	NM_014951		T	64148204	G	T	64148204	3	4	105	1	0	0	0	0	1	0	0	0	17884	1261	44	3	799	3	ZNF365	10	64148204	Missense_Mutation	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10	49171825	64148204	71386543	26	15903										
OR5B12	390191	hgsc.bcm.edu	37	chr11	58207461	58207461	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	tgaggaagaagtacatggggGtgtggagacaggagtccagt	18	4	0	3			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr11:58207461G>T	ENST00000302572.2	-	1	185	c.164C>A	c.(163-165)aCc>aAc	p.T55N		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	55						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GTACATGGGGGTGTGGAGACA	0.488																																					p.T55N		.	.											.	OR5B12	.	.	0			c.C164A						.						65	70	69					11																	58207461		2201	4295	6496	SO:0001583	missense	390191	exon1			ATGGGGGTGTGGA	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"GPCR / Class A : Olfactory receptors"	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.164C>A	11.37:g.58207461G>T	ENSP00000306657:p.Thr55Asn	102.0	0.0		178.0	47.0	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	.	.	.	.	.	.	.	.	.	.	G	3.547	-0.092466	0.07053	.	.	ENSG00000172362	ENST00000302572	T	0.00478	7.13	4.61	2.71	0.32032	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45126	D	0.000386	T	0.00608	0.0020	M	0.87456	2.885	0.09310	N	0.999996	B	0.21225	0.053	B	0.24394	0.053	T	0.41378	-0.9512	10	0.56958	D	0.05	-5.6865	5.8948	0.18933	0.078:0.1357:0.6461:0.1402	.	55	Q96R08	OR5BC_HUMAN	N	55	ENSP00000306657:T55N	ENSP00000306657:T55N	T	-	2	0	OR5B12	57964037	0.001000	0.12720	0.422000	0.26621	0.035000	0.12851	-0.061000	0.11693	0.660000	0.30964	0.462000	0.41574	ACC	.	.		0.488	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733		T	58207461	G	T	58207461	3	4	105	1	0	0	0	0	1	0	0	0	11157	1261	44	3	784	3	OR5B12	11	58207461	Missense_Mutation	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10		58207461	76799055	27	15904										
ZP1	22917	hgsc.bcm.edu	37	chr11	60641219	60641219	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ctaccttcgccctcctggacTcaggctcccagagagccctc	8	19	1	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr11:60641219T>G	ENST00000278853.5	+	9	1543	c.1543T>G	c.(1543-1545)Tca>Gca	p.S515A		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	515	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CCTCCTGGACTCAGGCTCCCA	0.602																																					p.S515A		.	.											.	ZP1	.	.	0			c.T1543G						.						88	91	90					11																	60641219		2203	4299	6502	SO:0001583	missense	22917	exon9			CTGGACTCAGGCT	BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"Zona pellucida glycoproteins"	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.1543T>G	11.37:g.60641219T>G	ENSP00000278853:p.Ser515Ala	36.0	0.0		50.0	12.0	NM_207341		Missense_Mutation	SNP	ENST00000278853.5	37	CCDS31572.1	.	.	.	.	.	.	.	.	.	.	T	11.82	1.751274	0.31046	.	.	ENSG00000149506	ENST00000278853;ENST00000544498	T	0.23950	1.88	5.29	-4.13	0.03904	Zona pellucida sperm-binding protein (3);	1.307360	0.04747	N	0.423896	T	0.28234	0.0697	M	0.79693	2.465	0.09310	N	1	B	0.25105	0.118	B	0.32149	0.141	T	0.37220	-0.9715	10	0.41790	T	0.15	-1.953	0.6784	0.00870	0.2335:0.3002:0.2071:0.2592	.	515	P60852	ZP1_HUMAN	A	515;222	ENSP00000278853:S515A	ENSP00000278853:S515A	S	+	1	0	ZP1	60397795	0.004000	0.15560	0.007000	0.13788	0.572000	0.35998	-0.289000	0.08365	-1.064000	0.03172	0.260000	0.18958	TCA	.	.		0.602	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341		G	60641219	T	G	60641219	3	3	105	1	0	0	0	0	1	0	0	0	18230	1551	54	5	1577	5	ZP1	11	60641219	Missense_Mutation	SNP	T	TCGA-DD-A1EI-01A-11D-A12Z-10	2433758	60641219	74365297	28	15905										
ASRGL1	80150	hgsc.bcm.edu	37	chr11	62159568	62159568	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	caggaaagacggtagaagagGctgcggacctatcgttgggt	16	7	0	3			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr11:62159568G>A	ENST00000415229.2	+	7	954	c.739G>A	c.(739-741)Gct>Act	p.A247T	CTD-2531D15.5_ENST00000526045.1_RNA|ASRGL1_ENST00000301776.5_Missense_Mutation_p.A247T	NM_001083926.1	NP_001077395.1	Q7L266	ASGL1_HUMAN	asparaginase like 1	247					asparagine catabolic process via L-aspartate (GO:0033345)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	asparaginase activity (GO:0004067)|beta-aspartyl-peptidase activity (GO:0008798)			endometrium(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	7					L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)	GGTAGAAGAGGCTGCGGACCT	0.453											OREG0021023	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A247T		.	.											.	ASRGL1	.	.	0			c.G739A						.						123	121	122					11																	62159568		2202	4299	6501	SO:0001583	missense	80150	exon7			GAAGAGGCTGCGG		CCDS8019.1	11q12.3	2008-07-18			ENSG00000162174	ENSG00000162174			16448	protein-coding gene	gene with protein product	"asparaginase-like 1 protein"	609212					Standard	NM_025080		Approved	FLJ22316, ALP1, ALP	uc001ntf.4	Q7L266	OTTHUMG00000167513	ENST00000415229.2:c.739G>A	11.37:g.62159568G>A	ENSP00000400057:p.Ala247Thr	88.0	0.0	1059	142.0	28.0	NM_001083926	B2R7Q0|Q567Q4|Q6P1P0|Q8NI34|Q9H6F7	Missense_Mutation	SNP	ENST00000415229.2	37	CCDS8019.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.994551	0.93167	.	.	ENSG00000162174	ENST00000415229;ENST00000301776	D;D	0.89050	-2.46;-2.46	5.24	5.24	0.73138	.	0.050242	0.85682	D	0.000000	D	0.96346	0.8808	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97615	1.0132	10	0.87932	D	0	-19.3664	16.3389	0.83075	0.0:0.0:1.0:0.0	.	247	Q7L266	ASGL1_HUMAN	T	247	ENSP00000400057:A247T;ENSP00000301776:A247T	ENSP00000301776:A247T	A	+	1	0	ASRGL1	61916144	1.000000	0.71417	0.977000	0.42913	0.949000	0.60115	8.389000	0.90172	2.424000	0.82194	0.655000	0.94253	GCT	.	.		0.453	ASRGL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394865.1	NM_001083926		A	62159568	G	A	62159568	3	1	105	1	0	0	0	0	1	0	0	0	1060	1203	42	3	761	3	ASRGL1	11	62159568	Missense_Mutation	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10	1518349	62159568	72846948	29	15906										
RBP5	9746	hgsc.bcm.edu	37	chr12	7281340	7281340	+	5'Flank	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ccatgttcttctgcgagacaAagcggtagtagccagtgagg	13	9	2	2			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr12:7281340A>T	ENST00000266546.6	+	0	0				RP11-273B20.1_ENST00000538062.1_RNA|RBP5_ENST00000266560.3_Missense_Mutation_p.F11Y|RP11-273B20.1_ENST00000544657.1_RNA|RBP5_ENST00000542370.1_Missense_Mutation_p.F11Y	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3						homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						CTGCGAGACAAAGCGGTAGTA	0.562																																					p.F11Y		.	.											.	RBP5	.	.	0			c.T32A						.						127	99	109					12																	7281340		2203	4300	6503	SO:0001631	upstream_gene_variant	83758	exon1			GAGACAAAGCGGT	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167		12.37:g.7281340A>T	Exception_encountered	223.0	0.0		296.0	73.0	NM_031491	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	37	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.161222	0.38119	.	.	ENSG00000139194	ENST00000266560;ENST00000542370	T;T	0.22134	1.97;1.97	2.86	2.86	0.33363	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.329652	0.35067	N	0.003464	T	0.25494	0.0620	M	0.71581	2.175	0.45439	D	0.998415	P	0.46457	0.878	B	0.41946	0.371	T	0.23440	-1.0188	10	0.87932	D	0	.	11.8957	0.52656	1.0:0.0:0.0:0.0	.	11	P82980	RET5_HUMAN	Y	11	ENSP00000266560:F11Y;ENSP00000438083:F11Y	ENSP00000266560:F11Y	F	-	2	0	RBP5	7172607	1.000000	0.71417	0.997000	0.53966	0.871000	0.50021	2.915000	0.48805	1.549000	0.49425	0.402000	0.26972	TTT	.	.		0.562	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		T	7281340	A	T	7281340	1	4	105	0	1	0	0	0	0	0	0	0	13174	14	1	4		4	RBP5	12	7281340	5'Flank	SNP	A	TCGA-DD-A1EI-01A-11D-A12Z-10		7281340	126570555	30	15907										
KCNJ8	3764	hgsc.bcm.edu	37	chr12	21926286	21926286	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ggccaccagccaccacatgaTagcgaagagcagccagctgc	11	15	0	2			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr12:21926286T>C	ENST00000240662.2	-	2	610	c.265A>G	c.(265-267)Atc>Gtc	p.I89V		NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	89					defense response to virus (GO:0051607)|heart development (GO:0007507)|kidney development (GO:0001822)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to pH (GO:0009268)|synaptic transmission (GO:0007268)|vasodilation (GO:0042311)	ATP-sensitive potassium channel complex (GO:0008282)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|inward rectifier potassium channel activity (GO:0005242)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Gliquidone(DB01251)|Glisoxepide(DB01289)|Glyburide(DB01016)|Levosimendan(DB00922)|Phenformin(DB00914)|Thiamylal(DB01154)|Yohimbine(DB01392)	CACCACATGATAGCGAAGAGC	0.517											OREG0021704	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I89V		.	.											.	KCNJ8	.	.	0			c.A265G						.						139	117	125					12																	21926286		2203	4300	6503	SO:0001583	missense	3764	exon2			ACATGATAGCGAA	BC000544	CCDS8692.1	12p12.1	2011-07-05			ENSG00000121361	ENSG00000121361		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6269	protein-coding gene	gene with protein product		600935				8595887, 16382105	Standard	NM_004982		Approved	Kir6.1	uc001rff.4	Q15842	OTTHUMG00000169093	ENST00000240662.2:c.265A>G	12.37:g.21926286T>C	ENSP00000240662:p.Ile89Val	75.0	0.0	752	126.0	15.0	NM_004982	O00657	Missense_Mutation	SNP	ENST00000240662.2	37	CCDS8692.1	.	.	.	.	.	.	.	.	.	.	T	12.14	1.849044	0.32699	.	.	ENSG00000121361	ENST00000240662;ENST00000539350;ENST00000537950	D;D	0.95622	-3.76;-3.76	4.44	4.44	0.53790	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.051415	0.85682	D	0.000000	D	0.87434	0.6176	N	0.04669	-0.19	0.40690	D	0.982383	B	0.02656	0.0	B	0.04013	0.001	D	0.83479	0.0063	10	0.20046	T	0.44	.	13.8791	0.63672	0.0:0.0:0.0:1.0	.	89	Q15842	IRK8_HUMAN	V	89	ENSP00000240662:I89V;ENSP00000440012:I89V	ENSP00000240662:I89V	I	-	1	0	KCNJ8	21817553	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.854000	0.86942	1.868000	0.54150	0.383000	0.25322	ATC	.	.		0.517	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982		C	21926286	T	C	21926286	3	2	105	1	0	0	0	0	1	0	0	0	8065	1406	49	2	1017	2	KCNJ8	12	21926286	Missense_Mutation	SNP	T	TCGA-DD-A1EI-01A-11D-A12Z-10	14644946	21926286	111925609	31	15908										
TMEM106C	79022	hgsc.bcm.edu	37	chr12	48359720	48359720	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gtccttgtggatgatgacggCatcaaagtggtgaaagtcac	13	7	2	3	rs370706223		TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr12:48359720C>T	ENST00000429772.2	+	4	464	c.351C>T	c.(349-351)ggC>ggT	p.G117G	TMEM106C_ENST00000550552.1_Silent_p.G117G|TMEM106C_ENST00000552561.1_Silent_p.G117G|TMEM106C_ENST00000552546.1_Silent_p.G46G|TMEM106C_ENST00000449758.2_Silent_p.G117G|TMEM106C_ENST00000256686.6_Silent_p.G117G|TMEM106C_ENST00000549288.1_Intron	NM_001143842.1	NP_001137314.1	Q9BVX2	T106C_HUMAN	transmembrane protein 106C	117						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	14		Acute lymphoblastic leukemia(13;0.11)		GBM - Glioblastoma multiforme(48;0.241)		ATGATGACGGCATCAAAGTGG	0.468																																					p.G117G		.	.											.	TMEM106C	.	.	0			c.C351T						.						316	284	295					12																	48359720		2203	4300	6503	SO:0001819	synonymous_variant	79022	exon4			TGACGGCATCAAA	BC000854	CCDS8758.1, CCDS44867.1	12q13.1	2005-12-19				ENSG00000134291			28775	protein-coding gene	gene with protein product							Standard	NM_024056		Approved	MGC5576	uc001rqr.3	Q9BVX2	OTTHUMG00000169892	ENST00000429772.2:c.351C>T	12.37:g.48359720C>T		453.0	0.0		740.0	47.0	NM_001143843	B2R998|B7Z5M4|Q3B761	Silent	SNP	ENST00000429772.2	37	CCDS8758.1	.	.	.	.	.	.	.	.	.	.	C	9.155	1.017150	0.19355	.	.	ENSG00000134291	ENST00000547682	.	.	.	4.48	1.63	0.23807	.	.	.	.	.	T	0.53498	0.1800	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42816	-0.9429	4	.	.	.	-5.8902	6.0324	0.19686	0.0:0.5351:0.2999:0.165	.	.	.	.	Y	4	.	.	H	+	1	0	TMEM106C	46645987	0.919000	0.31177	0.976000	0.42696	0.952000	0.60782	-0.035000	0.12205	0.381000	0.24851	-0.175000	0.13238	CAT	.	.		0.468	TMEM106C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406452.1	NM_024056		T	48359720	C	T	48359720	2	4	105	1	0	0	0	0	0	0	0	1	16037	697	25	3		3	TMEM106C	12	48359720	Silent	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10	26433434	48359720	85492175	32	15909										
NPFF	8620	hgsc.bcm.edu	37	chr12	53900573	53900573	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	tgacatgtcacttcttcccaAagcgttgaggggcagccagg	12	11	2	2			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr12:53900573A>G	ENST00000267017.3	-	3	492	c.329T>C	c.(328-330)tTt>tCt	p.F110S	NPFF_ENST00000609999.1_Missense_Mutation_p.F113S|RP11-793H13.10_ENST00000591834.1_3'UTR	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor	110					acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						CTTCTTCCCAAAGCGTTGAGG	0.527																																					p.F110S		.	.											.	NPFF	.	.	0			c.T329C						.						100	96	98					12																	53900573		2203	4300	6503	SO:0001583	missense	8620	exon3			TTCCCAAAGCGTT	AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"Endogenous ligands"	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856	ENST00000267017.3:c.329T>C	12.37:g.53900573A>G	ENSP00000267017:p.Phe110Ser	54.0	0.0		68.0	17.0	NM_003717	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	37	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.256940	0.80246	.	.	ENSG00000139574	ENST00000267017	T	0.66280	-0.2	4.59	4.59	0.56863	.	0.000000	0.64402	D	0.000001	T	0.75332	0.3835	M	0.72894	2.215	0.44409	D	0.997323	D	0.61080	0.989	D	0.63957	0.92	T	0.78964	-0.1996	10	0.87932	D	0	-1.7463	13.375	0.60732	1.0:0.0:0.0:0.0	.	110	O15130	NPFF_HUMAN	S	110	ENSP00000267017:F110S	ENSP00000267017:F110S	F	-	2	0	NPFF	52186840	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.617000	0.67716	2.057000	0.61298	0.402000	0.26972	TTT	.	.		0.527	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717		G	53900573	A	G	53900573	3	3	105	1	0	0	0	0	1	0	0	0	10585	14	1	2	16	2	NPFF	12	53900573	Missense_Mutation	SNP	A	TCGA-DD-A1EI-01A-11D-A12Z-10	5540853	53900573	79951322	33	15910										
SBNO1	55206	hgsc.bcm.edu	37	chr12	123825580	123825580	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ttcatgtcgtttatccacatTctagctccttctttattaga	4	10	3	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr12:123825580T>G	ENST00000602398.1	-	5	733	c.606A>C	c.(604-606)agA>agC	p.R202S	SBNO1_ENST00000602750.1_Missense_Mutation_p.R201S|SBNO1_ENST00000267176.4_Missense_Mutation_p.R201S|SBNO1_ENST00000420886.2_Missense_Mutation_p.R202S			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	202					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TTATCCACATTCTAGCTCCTT	0.353																																					p.R202S		.	.											.	SBNO1	.	.	0			c.A606C						.						146	138	141					12																	123825580		2203	4300	6503	SO:0001583	missense	55206	exon4			CCACATTCTAGCT	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.606A>C	12.37:g.123825580T>G	ENSP00000473665:p.Arg202Ser	145.0	0.0		237.0	66.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	T	19.42	3.823596	0.71143	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	T;T	0.33654	1.4;1.4	5.49	3.13	0.36017	.	0.000000	0.85682	D	0.000000	T	0.46288	0.1385	L	0.51422	1.61	0.47659	D	0.999484	D;D;D	0.61697	0.981;0.99;0.981	D;P;D	0.69824	0.966;0.852;0.943	T	0.26121	-1.0112	10	0.23302	T	0.38	-29.2449	7.7316	0.28789	0.0:0.2345:0.0:0.7655	.	202;201;200	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	S	202;201;201	ENSP00000387361:R202S;ENSP00000267176:R201S	ENSP00000267176:R201S	R	-	3	2	SBNO1	122391533	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	0.538000	0.23160	0.391000	0.25143	0.459000	0.35465	AGA	.	.		0.353	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		G	123825580	T	G	123825580	3	3	105	1	0	0	0	0	1	0	0	0	13877	1780	62	5	3687	5	SBNO1	12	123825580	Missense_Mutation	SNP	T	TCGA-DD-A1EI-01A-11D-A12Z-10	69925007	123825580	10026315	34	15911										
AK7	122481	hgsc.bcm.edu	37	chr14	96875279	96875279	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gctccaaagccctggaccccGtaagtagagcgttagctttc	10	13	0	1	rs377123131		TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr14:96875279G>A	ENST00000267584.4	+	4	542		c.e4+1		AK7_ENST00000554313.1_Splice_Site	NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7						axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		CCTGGACCCCGTAAGTAGAGC	0.473													G|||	1	0.000199681	0	0	5008	,	,		19210	0		0.001	False		,,,				2504	0				.		.	.											.	AK7	.	.	0			c.498+1G>A						.	G		0,4406		0,0,2203	66	65	66			4.9	0.7	14		66	1,8599	1.2+/-3.3	0,1,4299	no	splice-5	AK7	NM_152327.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077			96875279	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	122481	exon4			GACCCCGTAAGTA	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.498+1G>A	14.37:g.96875279G>A		77.0	0.0		61.0	8.0	NM_152327	Q8IYP6	Splice_Site	SNP	ENST00000267584.4	37	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.150997	0.57151	0.0	1.16E-4	ENSG00000140057	ENST00000267584	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3768	0.74610	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AK7	95945032	1.000000	0.71417	0.733000	0.30861	0.687000	0.40016	6.236000	0.72339	2.432000	0.82394	0.655000	0.94253	.	.	.		0.473	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1		Intron	A	96875279	G	A	96875279	5	1	105	1	0	0	0	0	0	0	1	0	444	1159	40	1	513	1	AK7	14	96875279	Splice_Site	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10		96875279	10474261	35	15912										
TP53	7157	hgsc.bcm.edu	37	chr17	7578419	7578419	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	ggggcagcgcctcacaacctCcgtcatgtgctgtgactgct	12	14	2	1	rs587781845		TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr17:7578419C>A	ENST00000269305.4	-	5	700	c.511G>T	c.(511-513)Gag>Tag	p.E171*	TP53_ENST00000413465.2_Nonsense_Mutation_p.E171*|TP53_ENST00000445888.2_Nonsense_Mutation_p.E171*|TP53_ENST00000455263.2_Nonsense_Mutation_p.E171*|TP53_ENST00000420246.2_Nonsense_Mutation_p.E171*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E171*|TP53_ENST00000574684.1_5'UTR	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	171	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		E -> A (in a sporadic cancer; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> Q (in a sporadic cancer; somatic mutation).|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E171K(11)|p.E171*(10)|p.0?(8)|p.E171Q(4)|p.E171fs*2(3)|p.E171fs*3(2)|p.E171fs*10(2)|p.V157_C176del20(1)|p.T170fs*8(1)|p.P151_V173del23(1)|p.E171fs*61(1)|p.E171fs*9(1)|p.T170fs*2(1)|p.E171fs*1(1)|p.E78fs*2(1)|p.H168fs*3(1)|p.H168fs*69(1)|p.T170_E171insXX(1)|p.E171_H179delEVVRRCPHH(1)|p.S149fs*72(1)|p.E39fs*2(1)|p.E171_V172delEV(1)|p.E39K(1)|p.E78K(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTCACAACCTCCGTCATGTGC	0.662		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E171X	Pancreas(47;798 1329 9957 10801)	.	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53,NS,carcinoma,0	TP53	.	.	57	Substitution - Missense(17)|Deletion - Frameshift(15)|Substitution - Nonsense(10)|Whole gene deletion(8)|Deletion - In frame(4)|Insertion - Frameshift(2)|Insertion - In frame(1)	urinary_tract(8)|lung(8)|breast(8)|oesophagus(6)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|large_intestine(3)|stomach(3)|central_nervous_system(3)|skin(3)|upper_aerodigestive_tract(2)|thyroid(1)|kidney(1)|endometrium(1)|liver(1)|ovary(1)	c.G511T						.						52	52	52					17																	7578419		2203	4300	6503	SO:0001587	stop_gained	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CAACCTCCGTCAT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.511G>T	17.37:g.7578419C>A	ENSP00000269305:p.Glu171*	88.0	0.0		64.0	23.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.186918	0.78789	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.47	5.47	0.80525	.	0.106949	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-29.8225	17.1938	0.86887	0.0:1.0:0.0:0.0	.	.	.	.	X	171;171;171;171;171;171;160;78;39;78;39	.	ENSP00000269305:E171X	E	-	1	0	TP53	7519144	1.000000	0.71417	0.689000	0.30133	0.389000	0.30415	7.775000	0.85489	2.735000	0.93741	0.563000	0.77884	GAG	.	.		0.662	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578419	C	A	7578419	4	1	105	1	0	0	0	0	0	1	0	0	16396	864	30	3	787	3	TP53	17	7578419	Nonsense_Mutation	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10		7578419	73616791	36	15913										
GSDMB	55876	hgsc.bcm.edu	37	chr17	38068752	38068752	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	tgaaactcagccttttgaccTggaaagagaatgataaaggt	10	6	1	4			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr17:38068752T>C	ENST00000394179.1	-	3	366		c.e3-2		GSDMB_ENST00000520542.1_Splice_Site|GSDMB_ENST00000418519.1_Splice_Site|GSDMB_ENST00000394175.2_Splice_Site|GSDMB_ENST00000360317.3_Splice_Site|GSDMB_ENST00000309481.7_Splice_Site			Q8TAX9	GSDMB_HUMAN	gasdermin B							cytoplasm (GO:0005737)				breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						CCTTTTGACCTGGAAAGAGAA	0.478																																					.		.	.											.	GSDMB	.	.	0			c.236-2A>G						.						98	96	97					17																	38068752		2203	4300	6503	SO:0001630	splice_region_variant	55876	exon4			TTGACCTGGAAAG	AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"gasdermin-like"	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.236-2A>G	17.37:g.38068752T>C		147.0	0.0		183.0	48.0	NM_001165958	B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	Splice_Site	SNP	ENST00000394179.1	37		.	.	.	.	.	.	.	.	.	.	T	13.12	2.142078	0.37825	.	.	ENSG00000073605	ENST00000420491;ENST00000360317;ENST00000394175;ENST00000309481;ENST00000520542;ENST00000418519;ENST00000394179	.	.	.	3.18	3.18	0.36537	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.1197	0.30963	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	GSDMB	35322278	0.141000	0.22595	0.454000	0.27019	0.457000	0.32468	2.645000	0.46621	1.686000	0.51046	0.421000	0.28195	.	.	.		0.478	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530	Intron	C	38068752	T	C	38068752	5	2	105	1	0	0	0	0	0	0	1	0	6826	1594	55	2	1052	2	GSDMB	17	38068752	Splice_Site	SNP	T	TCGA-DD-A1EI-01A-11D-A12Z-10	30490333	38068752	43126458	37	15914										
CD300LG	146894	hgsc.bcm.edu	37	chr17	41932594	41932594	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gggtgtccatcccgatggtcCgcatactggccccagtcctg	12	15	0	0			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr17:41932594C>T	ENST00000317310.4	+	5	780	c.739C>T	c.(739-741)Cgc>Tgc	p.R247C	CD300LG_ENST00000586233.1_Missense_Mutation_p.R162C|CD300LG_ENST00000539718.1_Missense_Mutation_p.R247C|CD300LG_ENST00000377203.4_Missense_Mutation_p.R213C|CD300LG_ENST00000293396.8_Missense_Mutation_p.R162C	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g	247					immune system process (GO:0002376)|immunoglobulin transcytosis in epithelial cells (GO:0002414)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|skin(4)	19		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		CCCGATGGTCCGCATACTGGC	0.607																																					p.R247C		.	.											.	CD300LG	.	.	0			c.C739T						.						49	36	41					17																	41932594		2203	4299	6502	SO:0001583	missense	146894	exon5			ATGGTCCGCATAC	BC025395	CCDS11470.1, CCDS54131.1, CCDS54132.1, CCDS54133.1	17q21.31	2013-01-11	2006-03-29					"Immunoglobulin superfamily / V-set domain containing"	30455	protein-coding gene	gene with protein product	"nepmucin"	610520	"CD300 antigen like family member G"			16876123, 16754720	Standard	NM_001168322		Approved	Trem4, CLM9	uc002iem.3	Q6UXG3		ENST00000317310.4:c.739C>T	17.37:g.41932594C>T	ENSP00000321005:p.Arg247Cys	60.0	0.0		116.0	25.0	NM_145273	B4DNY5|F5H7P9|F8W9M3|Q8IX38|Q8IX39|Q8TA95	Missense_Mutation	SNP	ENST00000317310.4	37	CCDS11470.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.722740	0.68959	.	.	ENSG00000161649	ENST00000317310;ENST00000539718;ENST00000377203;ENST00000293396	T;T;T;T	0.17213	2.36;2.29;2.99;3.51	3.91	3.91	0.45181	.	0.138905	0.34046	N	0.004305	T	0.32585	0.0834	L	0.47190	1.495	0.40040	D	0.975638	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.988;0.996;0.988;0.974;0.997	T	0.04593	-1.0940	10	0.87932	D	0	-0.6434	11.7259	0.51710	0.0:1.0:0.0:0.0	.	213;162;247;247;162	F8W9M3;Q6UXG3-3;F5H7P9;Q6UXG3;Q6UXG3-2	.;.;.;CLM9_HUMAN;.	C	247;247;213;162	ENSP00000321005:R247C;ENSP00000442368:R247C;ENSP00000366408:R213C;ENSP00000293396:R162C	ENSP00000293396:R162C	R	+	1	0	CD300LG	39288120	0.201000	0.23410	0.738000	0.30950	0.240000	0.25518	1.213000	0.32407	2.484000	0.83849	0.561000	0.74099	CGC	.	.		0.607	CD300LG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457646.1	NM_145273		T	41932594	C	T	41932594	3	4	105	1	0	0	0	0	1	0	0	0	3004	652	23	1	757	1	CD300LG	17	41932594	Missense_Mutation	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10	3863842	41932594	39262616	38	15915										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67110945	67110945	+	Frame_Shift_Del	DEL	A	A	-													0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	tgaatcccttttattttagcAaacaggctgaggttttcctt							TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr17:67110945delA	ENST00000284425.2	-	13	1914	c.1740delT	c.(1738-1740)tttfs	p.F580fs		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	580	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					TTATTTTAGCAAACAGGCTGA	0.403																																					p.A581fs		.	.											.	ABCA6	.	.	0			c.1741delG						.						184	163	170					17																	67110945		2203	4300	6503	SO:0001589	frameshift_variant	23460	exon13			.	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.1740delT	17.37:g.67110945delA	ENSP00000284425:p.Phe580fs	194.0	0.0		286.0	81.0	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Frame_Shift_Del	DEL	ENST00000284425.2	37	CCDS11683.1																																																																																			.	.		0.403	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		-	67110945	A	-	67110945	7	5	105	1	0	1	0	1	0	0	0	0	36	127	5	0	3221	0	ABCA6	17	67110945	Frame_Shift_Del	DEL	A	TCGA-DD-A1EI-01A-11D-A12Z-10	25178351	67110945	14084265	39	15916										
ZCCHC2	54877	hgsc.bcm.edu	37	chr18	60242702	60242702	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	cggggcccaagaagaatgggAatgtctcatgttacaattgt	12	7	1	2			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr18:60242702A>C	ENST00000269499.5	+	13	3806	c.3388A>C	c.(3388-3390)Aat>Cat	p.N1130H	ZCCHC2_ENST00000586834.1_Missense_Mutation_p.N809H	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	1130						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						GAAGAATGGGAATGTCTCATG	0.483																																					p.N1130H		.	.											.	ZCCHC2	.	.	0			c.A3388C						.						121	119	119					18																	60242702		2000	4184	6184	SO:0001583	missense	54877	exon13			AATGGGAATGTCT	AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"Zinc fingers, CCHC domain containing"	22916	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 49"	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.3388A>C	18.37:g.60242702A>C	ENSP00000269499:p.Asn1130His	125.0	0.0		197.0	55.0	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Missense_Mutation	SNP	ENST00000269499.5	37	CCDS45880.1	.	.	.	.	.	.	.	.	.	.	A	18.18	3.567109	0.65651	.	.	ENSG00000141664	ENST00000269499	T	0.77489	-1.1	5.57	5.57	0.84162	Zinc finger, CCHC retroviral-type (1);	0.335440	0.29459	N	0.012089	T	0.82245	0.4995	M	0.65498	2.005	0.52099	D	0.999944	P	0.47409	0.895	P	0.49708	0.62	D	0.84692	0.0723	10	0.87932	D	0	-3.8166	16.0262	0.80548	1.0:0.0:0.0:0.0	.	1130	Q9C0B9	ZCHC2_HUMAN	H	1130	ENSP00000269499:N1130H	ENSP00000269499:N1130H	N	+	1	0	ZCCHC2	58393682	1.000000	0.71417	0.125000	0.21846	0.982000	0.71751	8.372000	0.90127	2.243000	0.73865	0.533000	0.62120	AAT	.	.		0.483	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742		C	60242702	A	C	60242702	3	2	105	1	0	0	0	0	1	0	0	0	17602	246	9	5	3438	5	ZCCHC2	18	60242702	Missense_Mutation	SNP	A	TCGA-DD-A1EI-01A-11D-A12Z-10		60242702	17834546	40	15917										
SARS2	54938	hgsc.bcm.edu	37	chr19	39408640	39408640	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	cccggtagcaggtgctggagCaaaccatcctggcagagagc	14	12	0	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr19:39408640C>A	ENST00000221431.6	-	11	1130	c.971G>T	c.(970-972)tGc>tTc	p.C324F	CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.L393F|SARS2_ENST00000430193.3_Missense_Mutation_p.C324F|SARS2_ENST00000600042.1_Missense_Mutation_p.C326F|SARS2_ENST00000448145.2_Missense_Mutation_p.C324F|SARS2_ENST00000594171.1_Missense_Mutation_p.C134F|SARS2_ENST00000598831.1_5'Flank	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	324					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			GGTGCTGGAGCAAACCATCCT	0.572																																					p.C326F		.	.											.	SARS2	.	.	0			c.G977T						.						112	85	94					19																	39408640		2203	4300	6503	SO:0001583	missense	54938	exon12			CTGGAGCAAACCA	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"Aminoacyl tRNA synthetases / Class II"	17697	protein-coding gene	gene with protein product	"serine tRNA ligase 2, mitochondrial"	612804	"serine-tRNA ligase, mitochondrial", "seryl-tRNA synthetase 2"	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.971G>T	19.37:g.39408640C>A	ENSP00000221431:p.Cys324Phe	140.0	0.0		190.0	60.0	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Missense_Mutation	SNP	ENST00000221431.6	37	CCDS33017.1	.	.	.	.	.	.	.	.	.	.	c	21.0	4.088615	0.76756	.	.	ENSG00000104835	ENST00000430193;ENST00000221431;ENST00000448145	T;T	0.76316	-1.01;-1.01	4.88	4.88	0.63580	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.000000	0.85682	D	0.000000	D	0.85712	0.5760	M	0.67953	2.075	.	.	.	D;D;D;D	0.76494	0.999;0.996;0.999;0.979	D;P;D;P	0.65010	0.931;0.875;0.931;0.77	D	0.88857	0.3323	9	0.87932	D	0	.	15.5397	0.76031	0.0:1.0:0.0:0.0	.	324;326;324;324	E7EX87;B4DE10;B4DXB9;Q9NP81	.;.;.;SYSM_HUMAN	F	326;324;324	ENSP00000221431:C324F;ENSP00000399330:C324F	ENSP00000221431:C324F	C	-	2	0	FBXO17	44100480	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	7.079000	0.76829	2.263000	0.75096	0.424000	0.28305	TGC	.	.		0.572	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827		A	39408640	C	A	39408640	3	1	105	1	0	0	0	0	1	0	0	0	13860	710	25	3	609	3	SARS2	19	39408640	Missense_Mutation	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10		39408640	19720343	41	15918										
FLT3LG	2323	hgsc.bcm.edu	37	chr19	49979723	49979723	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gcggctggtcctggcacagcGctggatggagcggctcaaga	17	11	1	1			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr19:49979723G>A	ENST00000594009.1	+	4	321	c.242G>A	c.(241-243)cGc>cAc	p.R81H	FLT3LG_ENST00000344019.3_Missense_Mutation_p.R81H|FLT3LG_ENST00000597551.1_Missense_Mutation_p.R81H|CTD-3148I10.15_ENST00000595815.1_RNA|FLT3LG_ENST00000204637.2_De_novo_Start_OutOfFrame|FLT3LG_ENST00000600429.1_Missense_Mutation_p.R81H|CTD-3148I10.9_ENST00000599536.1_Intron|FLT3LG_ENST00000596435.1_Missense_Mutation_p.R81H|FLT3LG_ENST00000595510.1_De_novo_Start_OutOfFrame	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand	81					embryonic hemopoiesis (GO:0035162)|lymphocyte differentiation (GO:0030098)|positive regulation of cell proliferation (GO:0008284)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|membrane (GO:0016020)	receptor binding (GO:0005102)			large_intestine(2)|lung(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	10		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		CTGGCACAGCGCTGGATGGAG	0.632											OREG0025623	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R81H		.	.											.	FLT3LG	.	.	0			c.G242A						.						44	41	42					19																	49979723		2203	4300	6503	SO:0001583	missense	2323	exon4			CACAGCGCTGGAT	U04806	CCDS12767.1, CCDS62753.1	19q13.3	2014-01-30				ENSG00000090554		"Endogenous ligands"	3766	protein-coding gene	gene with protein product		600007				8145851, 7824267	Standard	NM_001204502		Approved		uc010yau.2	P49771		ENST00000594009.1:c.242G>A	19.37:g.49979723G>A	ENSP00000469613:p.Arg81His	48.0	0.0	966	68.0	16.0	NM_001204503	A0AVC2|B9EGH2|Q05C96	Missense_Mutation	SNP	ENST00000594009.1	37	CCDS12767.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.258204	0.80246	.	.	ENSG00000090554	ENST00000204637;ENST00000344019	.	.	.	4.52	3.41	0.39046	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.418278	0.21683	N	0.070696	T	0.53400	0.1794	L	0.29908	0.895	0.37468	D	0.915471	D	0.76494	0.999	P	0.58970	0.849	T	0.60999	-0.7151	9	0.72032	D	0.01	-16.2833	10.318	0.43749	0.0:0.0:0.8041:0.1959	.	81	P49771	FLT3L_HUMAN	H	81	.	ENSP00000204637:R81H	R	+	2	0	FLT3LG	54671535	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.280000	0.33202	2.215000	0.71742	0.549000	0.68633	CGC	.	.		0.632	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465305.1			A	49979723	G	A	49979723	3	1	105	1	0	0	0	0	1	0	0	0	5951	1087	38	1	256	1	FLT3LG	19	49979723	Missense_Mutation	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10	10571083	49979723	9149260	42	15919										
SEMG2	6407	hgsc.bcm.edu	37	chr20	43851219	43851219	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	tatccaaaggcagcatttctAtccaaactgaagagaaaata	6	8	1	2			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chr20:43851219A>T	ENST00000372769.3	+	2	1036	c.946A>T	c.(946-948)Atc>Ttc	p.I316F		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	316	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				CAGCATTTCTATCCAAACTGA	0.373																																					p.I316F		.	.											.	SEMG2	.	.	0			c.A946T						.						84	78	80					20																	43851219		2203	4300	6503	SO:0001583	missense	6407	exon2			ATTTCTATCCAAA		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"Semenogelin 2"	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.946A>T	20.37:g.43851219A>T	ENSP00000361855:p.Ile316Phe	172.0	0.0		257.0	64.0	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Missense_Mutation	SNP	ENST00000372769.3	37	CCDS13346.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.600133	0.28534	.	.	ENSG00000124157	ENST00000372769	T	0.06933	3.24	1.2	1.2	0.21068	.	.	.	.	.	T	0.09512	0.0234	L	0.39898	1.24	0.09310	N	1	P;P;P	0.37122	0.553;0.583;0.583	B;B;B	0.43916	0.436;0.36;0.36	T	0.29701	-1.0003	9	0.62326	D	0.03	.	4.5711	0.12210	1.0:0.0:0.0:0.0	.	316;316;316	A8K6Z6;Q6IRW3;Q02383	.;.;SEMG2_HUMAN	F	316	ENSP00000361855:I316F	ENSP00000361855:I316F	I	+	1	0	SEMG2	43284633	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	0.359000	0.20233	0.799000	0.34018	0.338000	0.21704	ATC	.	.		0.373	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		T	43851219	A	T	43851219	3	4	105	1	0	0	0	0	1	0	0	0	14060	449	16	4	952	4	SEMG2	20	43851219	Missense_Mutation	SNP	A	TCGA-DD-A1EI-01A-11D-A12Z-10		43851219	19174301	43	15920										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140993326	140993326	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	agagttctcctgagagcgacGacaccctgtatcctctccag	9	14	2	2			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chrX:140993326G>C	ENST00000285879.4	+	4	422	c.136G>C	c.(136-138)Gac>Cac	p.D46H	MAGEC1_ENST00000406005.2_5'UTR	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	46										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					TGAGAGCGACGACACCCTGTA	0.587										HNSCC(15;0.026)																											p.D46H		.	.											.	MAGEC1	.	.	0			c.G136C						.						86	88	87					X																	140993326		2203	4300	6503	SO:0001583	missense	9947	exon4			AGCGACGACACCC	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.136G>C	X.37:g.140993326G>C	ENSP00000285879:p.Asp46His	41.0	0.0		59.0	24.0	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	g	9.828	1.187711	0.21954	.	.	ENSG00000155495	ENST00000285879	T	0.03330	3.97	0.131	0.131	0.14755	.	.	.	.	.	T	0.02929	0.0087	N	0.08118	0	0.18873	N	0.999989	D	0.55605	0.972	P	0.48815	0.591	T	0.47674	-0.9099	9	0.87932	D	0	.	5.9545	0.19265	6.0E-4:0.0:0.9994:0.0	.	46	O60732	MAGC1_HUMAN	H	46	ENSP00000285879:D46H	ENSP00000285879:D46H	D	+	1	0	MAGEC1	140820992	0.002000	0.14202	0.008000	0.14137	0.008000	0.06430	0.141000	0.16076	0.157000	0.19338	0.158000	0.16466	GAC	.	.		0.587	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		C	140993326	G	C	140993326	3	2	105	1	0	0	0	0	1	0	0	0	9189	1058	37	4	142	4	MAGEC1	23	140993326	Missense_Mutation	SNP	G	TCGA-DD-A1EI-01A-11D-A12Z-10		140993326	14277234	44	15921										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144904543	144904543	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	aaagtaatgccttttgctggCgtccttgaacatattggagg	11	7	0	1	rs377679182		TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chrX:144904543C>A	ENST00000370490.1	+	1	4855	c.600C>A	c.(598-600)ggC>ggA	p.G200G	SLITRK2_ENST00000447897.2_Silent_p.G200G|SLITRK2_ENST00000428560.2_Silent_p.G200G|SLITRK2_ENST00000413937.2_Silent_p.G200G|SLITRK2_ENST00000434188.2_Silent_p.G200G			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	200					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CTTTTGCTGGCGTCCTTGAAC	0.488																																					p.G200G		.	.											.	SLITRK2	.	.	0			c.C600A						.	C	,,,,,,,	1,3834		0,1,1631,571	141	125	130		600,600,600,600,600,600,600,600	-10	0	X		130	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLITRK2	NM_001144003.2,NM_001144004.2,NM_001144005.2,NM_001144006.2,NM_001144008.2,NM_001144009.2,NM_001144010.2,NM_032539.4	,,,,,,,	0,1,4059,2443	AA,AC,CC,C		0.0,0.0261,0.0095	,,,,,,,	200/846,200/846,200/846,200/846,200/846,200/846,200/846,200/846	144904543	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	84631	exon5			TGCTGGCGTCCTT	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.600C>A	X.37:g.144904543C>A		78.0	0.0		93.0	37.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																			.	.		0.488	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144904543	C	A	144904543	2	1	105	1	0	0	0	0	0	0	0	1	14758	755	27	1		1	SLITRK2	23	144904543	Silent	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10	3911217	144904543	10366017	45	15922										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	4968285	4968285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	1	1	0.516477272727273	0	0.635664335664336	1	1	0	gaattctgaatgggctacccCaaacccagaaaacaggcaga	9	11	1	3			TCGA-DD-A1EI-01A-11D-A12Z-10	TCGA-DD-A1EI-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c016d025-3c92-41c5-b846-493b1fcce79e	f48e484a-7373-4ffb-bbd7-41c3d2f91d5f	g.chrY:4968285C>A	ENST00000333703.4	+	5	3146	c.2633C>A	c.(2632-2634)cCa>cAa	p.P878Q	PCDH11Y_ENST00000362095.5_Missense_Mutation_p.P889Q|PCDH11Y_ENST00000215473.6_Missense_Mutation_p.P889Q	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	889					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						TGGGCTACCCCAAACCCAGAA	0.413																																					p.P889Q		.	.											.	.	.	.	0			c.C2666A						.						39	36	36					Y																	4968285		616	1950	2566	SO:0001583	missense	83259	exon2			CTACCCCAAACCC	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000333703.4:c.2633C>A	Y.37:g.4968285C>A	ENSP00000330552:p.Pro878Gln	258.0	0.0		484.0	120.0	NM_032972	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000333703.4	37	CCDS14776.1																																																																																			.	.		0.413	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	NM_032973		A	4968285	C	A	4968285	3	1	105	1	0	0	0	0	1	0	0	0	11518	594	21	3	2708	3	PCDH11Y	24	4968285	Missense_Mutation	SNP	C	TCGA-DD-A1EI-01A-11D-A12Z-10		4968285	54405281	46	15923										
WASF2	10163	hgsc.bcm.edu	37	chr1	27739169	27739169	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	cggatagctacttgcatccaCgttttcaacacagccaatgc	7	13	1	0			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr1:27739169C>T	ENST00000430629.2	-	7	936	c.721G>A	c.(721-723)Gtg>Atg	p.V241M	WASF2_ENST00000536657.1_Missense_Mutation_p.V241M	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	241					actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		CTTGCATCCACGTTTTCAACA	0.493																																					p.V241M		Atlas-SNP	.											.	WASF2	41	.	0			c.G721A						.						179	158	165					1																	27739169		2203	4300	6503	SO:0001583	missense	10163	exon7			CATCCACGTTTTC	AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195			12733	protein-coding gene	gene with protein product		605875				10381382	Standard	NM_006990		Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.721G>A	chr1.hg19:g.27739169C>T	ENSP00000396211:p.Val241Met	49.0	0.0		228.0	88.0	NM_006990	B4DZN0|O60794|Q9UDY7	Missense_Mutation	SNP	ENST00000430629.2	hg19	CCDS304.1	.	.	.	.	.	.	.	.	.	.	C	9.400	1.077732	0.20227	.	.	ENSG00000158195	ENST00000430629;ENST00000536657	T	0.45276	0.9	5.51	-1.37	0.09056	.	0.630246	0.16535	N	0.210185	T	0.16811	0.0404	N	0.08118	0	0.09310	N	0.999997	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.26360	-1.0105	10	0.13108	T	0.6	0.4698	6.928	0.24426	0.1277:0.2917:0.0:0.5806	.	241;241	B4DZN0;Q9Y6W5	.;WASF2_HUMAN	M	241	ENSP00000396211:V241M	ENSP00000396211:V241M	V	-	1	0	WASF2	27611756	0.000000	0.05858	0.063000	0.19743	0.517000	0.34286	-1.404000	0.02494	-0.405000	0.07599	0.557000	0.71058	GTG	.	.		0.493	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009516.1	NM_006990		T	27739169	C	T	27739169	3	4	106	1	0	0	0	0	1	0	0	0	17268	536	19	1	787	1	WASF2	1	27739169	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10		27739169	221511452	1	15924										
PDE4B	5142	hgsc.bcm.edu	37	chr1	66723358	66723358	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	atgacttgattgtaactcctTttgcccaggtatgtattatg	8	7	0	2			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr1:66723358T>G	ENST00000329654.4	+	5	692	c.505T>G	c.(505-507)Ttt>Gtt	p.F169V	PDE4B_ENST00000423207.2_Missense_Mutation_p.F154V|PDE4B_ENST00000371049.3_Missense_Mutation_p.F169V|PDE4B_ENST00000371048.3_3'UTR	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	169					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	TGTAACTCCTTTTGCCCAGGT	0.383																																					p.F169V		Atlas-SNP	.											.	PDE4B	231	.	0			c.T505G						.						262	254	257					1																	66723358		2203	4300	6503	SO:0001583	missense	5142	exon5			ACTCCTTTTGCCC	L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"Phosphodiesterases"	8781	protein-coding gene	gene with protein product	"phosphodiesterase E4 dunce homolog (Drosophila)"	600127	"phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)", "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.505T>G	chr1.hg19:g.66723358T>G	ENSP00000332116:p.Phe169Val	50.0	0.0		252.0	164.0	NM_001037341	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	hg19	CCDS632.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.7|23.7	4.447079|4.447079	0.84101|0.84101	.|.	.|.	ENSG00000184588|ENSG00000184588	ENST00000491340|ENST00000329654;ENST00000341517;ENST00000371049;ENST00000423207;ENST00000412480	.|T;T;T;T;D	.|0.87491	.|-1.42;-1.42;-1.42;-1.43;-2.26	5.07|5.07	5.07|5.07	0.68467|0.68467	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.89876|0.89876	0.6842|0.6842	M|M	0.79123|0.79123	2.44|2.44	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.48230	.|0.907;0.85;0.85	.|P;P;P	.|0.55055	.|0.767;0.589;0.589	D|D	0.91466|0.91466	0.5193|0.5193	6|10	.|0.87932	.|D	.|0	.|.	14.4679|14.4679	0.67497|0.67497	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|154;159;169	.|Q07343-3;Q59GM8;Q07343	.|.;.;PDE4B_HUMAN	C|V	10|169;169;169;154;77	.|ENSP00000332116:F169V;ENSP00000342637:F169V;ENSP00000360088:F169V;ENSP00000392947:F154V;ENSP00000397548:F77V	.|ENSP00000332116:F169V	F|F	+|+	2|1	0|0	PDE4B|PDE4B	66495946|66495946	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.881000|0.881000	0.50899|0.50899	7.093000|7.093000	0.76937|0.76937	2.251000|2.251000	0.74343|0.74343	0.528000|0.528000	0.53228|0.53228	TTT|TTT	.	.		0.383	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		G	66723358	T	G	66723358	3	3	106	1	0	0	0	0	1	0	0	0	11649	1841	64	5	759	5	PDE4B	1	66723358	Missense_Mutation	SNP	T	TCGA-DD-A1EJ-01A-11D-A152-10	38984189	66723358	182527263	2	15925										
ZNF326	284695	hgsc.bcm.edu	37	chr1	90487903	90487903	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	gcgatatgaacgttttgttaAggtaagattttagggcaaaa	11	3	0	2			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr1:90487903A>C	ENST00000340281.4	+	11	1543	c.1400A>C	c.(1399-1401)aAg>aCg	p.K467T	ZNF326_ENST00000455342.2_Splice_Site_p.K261T|ZNF326_ENST00000370447.3_Splice_Site_p.K378T	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	467					mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		CGTTTTGTTAAGGTAAGATTT	0.303																																					p.K467T		Atlas-SNP	.											.	ZNF326	60	.	0			c.A1400C						.						158	176	170					1																	90487903		2203	4299	6502	SO:0001630	splice_region_variant	284695	exon11			TTGTTAAGGTAAG	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1401+1A>C	chr1.hg19:g.90487903A>C		72.0	0.0		395.0	76.0	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	hg19	CCDS727.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.549695	0.86127	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.56275	0.47;0.47;0.47	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.63815	0.2543	M	0.63843	1.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.69026	-0.5254	10	0.87932	D	0	-14.7564	15.4524	0.75282	1.0:0.0:0.0:0.0	.	467;467	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	T	467;467;378;261	ENSP00000340796:K467T;ENSP00000359476:K378T;ENSP00000403470:K261T	ENSP00000340796:K467T	K	+	2	0	ZNF326	90260491	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.335000	0.79234	2.104000	0.64026	0.482000	0.46254	AAG	.	.		0.303	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781	Missense_Mutation	C	90487903	A	C	90487903	5	2	106	1	0	0	0	0	0	0	1	0	17861	86	3	5	1446	5	ZNF326	1	90487903	Splice_Site	SNP	A	TCGA-DD-A1EJ-01A-11D-A152-10	23764545	90487903	158762718	3	15926										
KCNH1	3756	hgsc.bcm.edu	37	chr1	211093326	211093326	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ccagcacagcagctccatatTcaatgtagtggtccagctta	8	12	1	0			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr1:211093326T>C	ENST00000271751.4	-	7	1145	c.1118A>G	c.(1117-1119)gAa>gGa	p.E373G	KCNH1_ENST00000367007.4_Missense_Mutation_p.E346G			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	373					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		AGCTCCATATTCAATGTAGTG	0.552																																					p.E373G		Atlas-SNP	.											.	KCNH1	199	.	0			c.A1118G						.						120	120	120					1																	211093326		2203	4300	6503	SO:0001583	missense	3756	exon7			CCATATTCAATGT	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1118A>G	chr1.hg19:g.211093326T>C	ENSP00000271751:p.Glu373Gly	481.0	1.0		156.0	33.0	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	hg19	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.672251	0.88348	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.98150	-4.75;-4.75	5.69	5.69	0.88448	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98661	0.9551	M	0.84846	2.72	0.80722	D	1	P;P	0.50369	0.934;0.934	D;D	0.64687	0.928;0.928	D	0.99675	1.0997	10	0.87932	D	0	.	15.1339	0.72549	0.0:0.0:0.0:1.0	.	346;373	Q14CL3;O95259	.;KCNH1_HUMAN	G	373;346	ENSP00000271751:E373G;ENSP00000355974:E346G	ENSP00000271751:E373G	E	-	2	0	KCNH1	209159949	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.751000	0.85126	2.173000	0.68751	0.533000	0.62120	GAA	.	.		0.552	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		C	211093326	T	C	211093326	3	2	106	1	0	0	0	0	1	0	0	0	8040	1783	62	2	1871	2	KCNH1	1	211093326	Missense_Mutation	SNP	T	TCGA-DD-A1EJ-01A-11D-A152-10	120605423	211093326	38157295	4	15927										
DISC1	27185	hgsc.bcm.edu	37	chr1	231830097	231830097	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tggccctgaggtccccccaaCccctcctggctctcacagtg	9	19	1	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr1:231830097C>A	ENST00000602281.1	+	2	646	c.593C>A	c.(592-594)aCc>aAc	p.T198N	DISC1_ENST00000602873.1_Intron|DISC1_ENST00000539444.1_Missense_Mutation_p.T198N|DISC1_ENST00000317586.4_Missense_Mutation_p.T198N|DISC1_ENST00000535983.1_Missense_Mutation_p.T198N|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000366633.3_Missense_Mutation_p.T198N|DISC1_ENST00000537876.1_Missense_Mutation_p.T198N|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000366636.4_Missense_Mutation_p.T198N|DISC1_ENST00000439617.2_Missense_Mutation_p.T198N	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	198	Interaction with MAP1A.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				GTCCCCCCAACCCCTCCTGGC	0.612																																					p.T198N		Atlas-SNP	.											.	DISC1	207	.	0			c.C593A						.						62	60	60					1																	231830097		2203	4300	6503	SO:0001583	missense	27185	exon2			CCCCAACCCCTCC	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.593C>A	chr1.hg19:g.231830097C>A	ENSP00000473425:p.Thr198Asn	450.0	0.0		114.0	21.0	NM_001164541	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	hg19	CCDS59205.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.495903	0.26774	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000317586;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944;ENST00000366632	T;T;T;T;T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83	4.61	3.7	0.42460	.	1.182920	0.05667	N	0.587932	T	0.17577	0.0422	N	0.24115	0.695	0.09310	N	1	B;P;P;P;P;P;P;P;P;P;B;P;P;P;P;P;P;P;P;P;B	0.47302	0.062;0.804;0.804;0.804;0.589;0.893;0.804;0.804;0.589;0.804;0.062;0.744;0.61;0.804;0.589;0.589;0.744;0.589;0.589;0.589;0.118	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.40134	0.069;0.32;0.225;0.32;0.211;0.32;0.32;0.32;0.211;0.32;0.094;0.271;0.154;0.32;0.211;0.211;0.211;0.211;0.211;0.211;0.094	T	0.11446	-1.0587	10	0.28530	T	0.3	0.0954	5.7571	0.18178	0.1909:0.7102:0.0:0.0988	.	198;198;198;198;198;198;198;198;198;198;198;198;198;198;198;198;198;198;198;198;198	C4P094;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P091;C4P0D2;C4P0D3;C4P0B1;A7E2W8;Q5T409;C4P0D0;Q9NRI5-2;Q9NRI5;Q9NRI5-3;Q9NRI5-4	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.;.	N	198;198;198;198;198;198;198;198;198;198;198;198;49	ENSP00000403888:T198N;ENSP00000320784:T198N;ENSP00000355596:T198N;ENSP00000443996:T198N;ENSP00000440909:T198N;ENSP00000355593:T198N;ENSP00000440953:T198N;ENSP00000295051:T198N;ENSP00000441193:T198N	ENSP00000295051:T198N	T	+	2	0	DISC1	229896720	0.002000	0.14202	0.003000	0.11579	0.026000	0.11368	1.675000	0.37555	1.145000	0.42336	0.561000	0.74099	ACC	.	.		0.612	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		A	231830097	C	A	231830097	3	1	106	1	0	0	0	0	1	0	0	0	4540	507	18	3	599	3	DISC1	1	231830097	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	20736771	231830097	17420524	5	15928										
CGREF1	10669	hgsc.bcm.edu	37	chr2	27325451	27325451	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ggagctgatgctgcacttcaGagtctggcctggaggaggaa	16	8	2	2	rs376042252	byFrequency	TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr2:27325451G>T	ENST00000260595.5	-	3	381	c.89C>A	c.(88-90)tCt>tAt	p.S30Y	CGREF1_ENST00000404694.3_Missense_Mutation_p.S152Y|CGREF1_ENST00000402394.1_Missense_Mutation_p.S30Y|CGREF1_ENST00000452318.2_De_novo_Start_OutOfFrame|CGREF1_ENST00000312734.4_Missense_Mutation_p.S30Y|CGREF1_ENST00000405600.1_Missense_Mutation_p.S30Y|CGREF1_ENST00000402550.1_Missense_Mutation_p.S30Y			Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	30					cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGCACTTCAGAGTCTGGCCT	0.637																																					p.S30Y		Atlas-SNP	.											.	CGREF1	31	.	0			c.C89A						.						50	53	52					2																	27325451		2203	4300	6503	SO:0001583	missense	10669	exon3			ACTTCAGAGTCTG	BC034764	CCDS33162.1, CCDS33162.2, CCDS54339.1	2p23.3	2013-01-10			ENSG00000138028	ENSG00000138028		"EF-hand domain containing"	16962	protein-coding gene	gene with protein product		606137				8968090	Standard	NM_006569		Approved	CGR11	uc002riq.3	Q99674	OTTHUMG00000152009	ENST00000260595.5:c.89C>A	chr2.hg19:g.27325451G>T	ENSP00000260595:p.Ser30Tyr	140.0	0.0		48.0	10.0	NM_001166239	A6NHV7|B4DXY8|B5MCB7|B5MCC9|B5MCP5|E7EU99|Q8N4B7	Missense_Mutation	SNP	ENST00000260595.5	hg19		.	.	.	.	.	.	.	.	.	.	G	12.57	1.978392	0.34942	.	.	ENSG00000138028	ENST00000402550;ENST00000402394;ENST00000405600;ENST00000389521;ENST00000312734;ENST00000404694;ENST00000260595	T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41	4.74	3.86	0.44501	.	0.815240	0.11022	N	0.608288	T	0.15825	0.0381	N	0.14661	0.345	0.09310	N	1	P;P;P	0.52316	0.952;0.875;0.875	B;B;B	0.38327	0.271;0.271;0.271	T	0.03364	-1.1044	10	0.23302	T	0.38	-2.1333	8.5357	0.33362	0.1038:0.0:0.8962:0.0	.	152;30;30	B5MCC9;B5MCP5;Q99674	.;.;CGRE1_HUMAN	Y	30;30;30;30;30;152;30	ENSP00000385452:S30Y;ENSP00000386113:S30Y;ENSP00000324025:S30Y;ENSP00000385574:S152Y;ENSP00000260595:S30Y	ENSP00000260595:S30Y	S	-	2	0	CGREF1	27178955	0.034000	0.19679	0.002000	0.10522	0.079000	0.17450	0.393000	0.20817	1.223000	0.43536	0.551000	0.68910	TCT	.	.		0.637	CGREF1-201	KNOWN	basic	protein_coding	protein_coding		NM_006569		T	27325451	G	T	27325451	3	4	106	1	0	0	0	0	1	0	0	0	3307	942	33	3	1075	3	CGREF1	2	27325451	Missense_Mutation	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10		27325451	215873922	6	15929										
SIX2	10736	hgsc.bcm.edu	37	chr2	45233509	45233509	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	gagcagtgcggggctggatgAtgagtggtctggcgtccccg	19	9	1	2			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr2:45233509A>T	ENST00000303077.6	-	2	995	c.676T>A	c.(676-678)Tca>Aca	p.S226T		NM_016932.4	NP_058628.3	Q9NPC8	SIX2_HUMAN	SIX homeobox 2	226					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|kidney development (GO:0001822)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesenchymal stem cell proliferation (GO:0097168)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|middle ear morphogenesis (GO:0042474)|nephron development (GO:0072006)|nephron morphogenesis (GO:0072028)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus (GO:0006606)|regulation of branching involved in ureteric bud morphogenesis (GO:0090189)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|large_intestine(3)|lung(8)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	22		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GGGCTGGATGATGAGTGGTCT	0.672																																					p.S226T		Atlas-SNP	.											.	SIX2	39	.	0			c.T676A						.						91	94	93					2																	45233509		2203	4300	6503	SO:0001583	missense	10736	exon2			TGGATGATGAGTG	AF136939	CCDS1822.1	2p21	2011-06-20	2007-07-13		ENSG00000170577	ENSG00000170577		"Homeoboxes / SINE class"	10888	protein-coding gene	gene with protein product		604994	"sine oculis homeobox (Drosophila) homolog 2", "sine oculis homeobox homolog 2 (Drosophila)"				Standard	NM_016932		Approved		uc002ruo.3	Q9NPC8	OTTHUMG00000152421	ENST00000303077.6:c.676T>A	chr2.hg19:g.45233509A>T	ENSP00000304502:p.Ser226Thr	114.0	0.0		16.0	12.0	NM_016932	Q9BXH7	Missense_Mutation	SNP	ENST00000303077.6	hg19	CCDS1822.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.453485	0.63290	.	.	ENSG00000170577	ENST00000303077	D	0.89123	-2.47	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.88235	0.6382	L	0.29908	0.895	0.58432	D	0.999996	P;P	0.49447	0.924;0.924	P;P	0.57776	0.827;0.827	D	0.84878	0.0829	10	0.13853	T	0.58	-11.6023	14.4287	0.67233	1.0:0.0:0.0:0.0	.	226;226	Q8TBA2;Q9NPC8	.;SIX2_HUMAN	T	226	ENSP00000304502:S226T	ENSP00000304502:S226T	S	-	1	0	SIX2	45087013	1.000000	0.71417	0.993000	0.49108	0.853000	0.48598	6.657000	0.74402	1.804000	0.52760	0.379000	0.24179	TCA	.	.		0.672	SIX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326188.2			T	45233509	A	T	45233509	3	4	106	1	0	0	0	0	1	0	0	0	14362	333	12	4	203	4	SIX2	2	45233509	Missense_Mutation	SNP	A	TCGA-DD-A1EJ-01A-11D-A152-10	17908058	45233509	197965864	7	15930										
STON1	11037	hgsc.bcm.edu	37	chr2	48809395	48809395	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	gttgtccagggagcatacgtGgaacttcaggcttttgtcaa	12	8	2	0			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr2:48809395G>A	ENST00000406226.1	+	3	1818	c.1623G>A	c.(1621-1623)gtG>gtA	p.V541V	STON1_ENST00000309835.3_Silent_p.V541V|STON1_ENST00000404752.1_Silent_p.V541V|STON1-GTF2A1L_ENST00000394754.1_Silent_p.V541V|STON1-GTF2A1L_ENST00000309827.2_Silent_p.V541V|STON1-GTF2A1L_ENST00000402114.2_Silent_p.V541V|STON1-GTF2A1L_ENST00000394751.3_Silent_p.V541V|STON1-GTF2A1L_ENST00000405008.1_Silent_p.V541V	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	541	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GAGCATACGTGGAACTTCAGG	0.468																																					p.V541V		Atlas-SNP	.											.	STON1	100	.	0			c.G1623A						.						162	156	158					2																	48809395		2203	4300	6503	SO:0001819	synonymous_variant	11037	exon3			ATACGTGGAACTT	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1623G>A	chr2.hg19:g.48809395G>A		56.0	0.0		285.0	43.0	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	hg19	CCDS1841.1																																																																																			.	.		0.468	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		A	48809395	G	A	48809395	2	1	106	1	0	0	0	0	0	0	0	1	15331	1335	47	3		3	STON1	2	48809395	Silent	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10	3575886	48809395	194389978	8	15931										
TTN	7273	hgsc.bcm.edu	37	chr2	179559565	179559565	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ttaaataatacctttggtgaCttgaactttttcttcctcca	4	9	1	2			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr2:179559565C>G	ENST00000591111.1	-	114	30612	c.30388G>C	c.(30388-30390)Gtc>Ctc	p.V10130L	TTN_ENST00000589042.1_Missense_Mutation_p.V10447L|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.V9203L|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTTTGGTGACTTGAACTTTT	0.294																																					p.V10447L		Atlas-SNP	.											.	TTN	18412	.	0			c.G31339C						.						114	105	108					2																	179559565		1785	4043	5828	SO:0001583	missense	7273	exon116			TGGTGACTTGAAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30388G>C	chr2.hg19:g.179559565C>G	ENSP00000465570:p.Val10130Leu	53.0	0.0		339.0	126.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.04	3.288235	0.59976	.	.	ENSG00000155657	ENST00000342992;ENST00000414766	T	0.65178	-0.14	5.66	5.66	0.87406	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.61060	0.2317	N	0.24115	0.695	0.80722	D	1	B;D	0.55385	0.231;0.971	B;P	0.54815	0.081;0.761	T	0.64525	-0.6387	9	0.87932	D	0	.	13.2577	0.60089	0.0:0.8409:0.1591:0.0	.	10130;10130	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	L	9203;325	ENSP00000343764:V9203L	ENSP00000343764:V9203L	V	-	1	0	TTN	179267810	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.160000	0.42348	2.826000	0.97356	0.655000	0.94253	GTC	.	.		0.294	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179559565	C	G	179559565	3	3	106	1	0	0	0	0	1	0	0	0	16750	565	20	4	73178	4	TTN	2	179559565	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	130750170	179559565	63639808	9	15932										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41268766	41268766	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	gaggacctatacttacgaaaAactactgtggaccacaagca	8	10	0	0			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr3:41268766A>T	ENST00000349496.5	+	7	1284	c.1004A>T	c.(1003-1005)aAa>aTa	p.K335I	CTNNB1_ENST00000396185.3_Missense_Mutation_p.K335I|CTNNB1_ENST00000396183.3_Missense_Mutation_p.K335I|CTNNB1_ENST00000453024.1_Missense_Mutation_p.K328I|CTNNB1_ENST00000405570.1_Missense_Mutation_p.K335I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	335					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.K335I(8)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACTTACGAAAAACTACTGTGG	0.383		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.K335I	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,colon,carcinoma,-1,11	CTNNB1	4904	.	8	Substitution - Missense(8)	liver(7)|kidney(1)	c.A1004T						.						110	108	109					3																	41268766		2203	4300	6503	SO:0001583	missense	1499	exon7	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACGAAAAACTACT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1004A>T	chr3.hg19:g.41268766A>T	ENSP00000344456:p.Lys335Ile	15.0	0.0		175.0	89.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.040885	0.93685	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.82148	0.4974	M	0.89287	3.02	0.80722	D	1	D;D	0.71674	0.995;0.998	D;D	0.75484	0.97;0.986	D	0.85830	0.1391	10	0.72032	D	0.01	-3.7939	15.5934	0.76558	1.0:0.0:0.0:0.0	.	263;335	B4DSW9;P35222	.;CTNB1_HUMAN	I	335;335;335;328;335	ENSP00000385604:K335I;ENSP00000379486:K335I;ENSP00000344456:K335I;ENSP00000411226:K328I;ENSP00000379488:K335I	ENSP00000344456:K335I	K	+	2	0	CTNNB1	41243770	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	9.339000	0.96797	2.094000	0.63399	0.482000	0.46254	AAA	.	.		0.383	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41268766	A	T	41268766	3	4	106	1	0	0	0	0	1	0	0	0	4018	14	1	4	1026	4	CTNNB1	3	41268766	Missense_Mutation	SNP	A	TCGA-DD-A1EJ-01A-11D-A152-10		41268766	156753664	10	15933										
CACNA1D	776	hgsc.bcm.edu	37	chr3	53707151	53707151	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	cttgtacttggtgtattgagCgggtaagctacacctctttc	10	9	1	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr3:53707151C>T	ENST00000350061.5	+	8	1729	c.1218C>T	c.(1216-1218)agC>agT	p.S406S	CACNA1D_ENST00000498251.1_3'UTR|CACNA1D_ENST00000422281.2_Silent_p.S406S|CACNA1D_ENST00000288139.4_Intron	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	406					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GTGTATTGAGCGGGTAAGCTA	0.468																																					p.S406S		Atlas-SNP	.											.	CACNA1D	324	.	0			c.C1218T						.						260	209	224					3																	53707151		692	1591	2283	SO:0001819	synonymous_variant	776	exon8			ATTGAGCGGGTAA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.1218C>T	chr3.hg19:g.53707151C>T		135.0	0.0		978.0	485.0	NM_001128840	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Silent	SNP	ENST00000350061.5	hg19	CCDS46848.1																																																																																			.	.		0.468	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		T	53707151	C	T	53707151	2	4	106	1	0	0	0	0	0	0	0	1	2543	767	27	1		1	CACNA1D	3	53707151	Silent	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	12438385	53707151	144315279	11	15934										
FAM116A	201627	hgsc.bcm.edu	37	chr3	57646514	57646514	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	accacccccatgattggcagGtgtaatgttttccctggcac	9	13	0	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr3:57646514G>A	ENST00000311128.5	-	7	742	c.672C>T	c.(670-672)caC>caT	p.H224H		NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	224					positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										TGATTGGCAGGTGTAATGTTT	0.333																																					p.H224H		Atlas-SNP	.											.	.	.	.	0			c.C672T						.						41	43	42					3																	57646514		2203	4300	6503	SO:0001819	synonymous_variant	201627	exon7			TGGCAGGTGTAAT	AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839		"DENN/MADD domain containing"	26635	protein-coding gene	gene with protein product			"family with sequence similarity 116, member A"	FAM116A		21330364	Standard	NM_152678		Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.672C>T	chr3.hg19:g.57646514G>A		103.0	0.0		400.0	170.0	NM_152678	Q7Z5T4|Q8N235|Q8TEG8	Silent	SNP	ENST00000311128.5	hg19	CCDS33773.1	.	.	.	.	.	.	.	.	.	.	G	6.885	0.532775	0.13127	.	.	ENSG00000174839	ENST00000477344	.	.	.	5.02	0.0298	0.14164	.	.	.	.	.	T	0.45256	0.1333	.	.	.	0.33649	D	0.608268	.	.	.	.	.	.	T	0.50600	-0.8809	4	.	.	.	-13.231	6.5539	0.22450	0.5001:0.1257:0.3742:0.0	.	.	.	.	S	14	.	.	P	-	1	0	FAM116A	57621554	0.063000	0.20901	0.521000	0.27850	0.979000	0.70002	-0.471000	0.06631	-0.332000	0.08489	0.460000	0.39030	CCT	.	.		0.333	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351594.1	NM_152678		A	57646514	G	A	57646514	2	1	106	1	0	0	0	0	0	0	0	1	5412	1252	44	3		3	FAM116A	3	57646514	Silent	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10	3939363	57646514	140375916	12	15935										
CADM2	253559	hgsc.bcm.edu	37	chr3	86114753	86114753	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	aatattttcctgtcttttccAgatcctaatgctttggctgg	7	9	1	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr3:86114753A>G	ENST00000407528.2	+	9	1125		c.e9-1		CADM2_ENST00000405615.2_Splice_Site|CADM2_ENST00000383699.3_Splice_Site	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2						adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		TGTCTTTTCCAGATCCTAATG	0.368																																					.		Atlas-SNP	.											.	CADM2	195	.	0			c.1064-2A>G						.						134	122	126					3																	86114753		2203	4300	6503	SO:0001630	splice_region_variant	253559	exon9			TTTTCCAGATCCT	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.1064-1A>G	chr3.hg19:g.86114753A>G		46.0	0.0		249.0	110.0	NM_001167674	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Splice_Site	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.622329	0.87460	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0708	0.80928	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CADM2	86197443	1.000000	0.71417	0.960000	0.40013	0.941000	0.58515	9.339000	0.96797	2.197000	0.70478	0.528000	0.53228	.	.	.		0.368	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184	Intron	G	86114753	A	G	86114753	5	3	106	1	0	0	0	0	0	0	1	0	2569	202	7	2	1167	2	CADM2	3	86114753	Splice_Site	SNP	A	TCGA-DD-A1EJ-01A-11D-A152-10	28468239	86114753	111907677	13	15936										
KALRN	8997	hgsc.bcm.edu	37	chr3	124165646	124165646	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	aagaaacaggtgaattttacCtctcaacacatacctccact	4	12	1	2			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr3:124165646C>G	ENST00000240874.3	+	21	3617	c.3460C>G	c.(3460-3462)Ctc>Gtc	p.L1154V	KALRN_ENST00000460856.1_Missense_Mutation_p.L1145V|KALRN_ENST00000360013.3_Missense_Mutation_p.L1154V	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1154					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TGAATTTTACCTCTCAACACA	0.488																																					p.L1154V		Atlas-SNP	.											.	KALRN	556	.	0			c.C3460G						.						125	127	127					3																	124165646		2203	4300	6503	SO:0001583	missense	8997	exon21			TTTTACCTCTCAA	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.3460C>G	chr3.hg19:g.124165646C>G	ENSP00000240874:p.Leu1154Val	13.0	0.0		77.0	29.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	hg19	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.972333	0.92919	.	.	ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013	T;T;T	0.54071	0.59;0.59;0.59	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000001	T	0.72590	0.3479	M	0.73217	2.22	0.80722	D	1	P;P;D;P	0.69078	0.933;0.921;0.997;0.918	P;P;D;P	0.79108	0.718;0.901;0.992;0.596	T	0.70945	-0.4734	10	0.44086	T	0.13	.	19.3628	0.94448	0.0:1.0:0.0:0.0	.	1145;500;1154;1154	C9IZQ6;F2Z3Q6;O60229;O60229-2	.;.;KALRN_HUMAN;.	V	1145;1154;1154	ENSP00000418611:L1145V;ENSP00000240874:L1154V;ENSP00000353109:L1154V	ENSP00000240874:L1154V	L	+	1	0	KALRN	125648336	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.782000	0.62396	2.802000	0.96397	0.561000	0.74099	CTC	.	.		0.488	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		G	124165646	C	G	124165646	3	3	106	1	0	0	0	0	1	0	0	0	7984	681	24	4	3542	4	KALRN	3	124165646	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	38050893	124165646	73856784	14	15937										
OSBPL11	114885	hgsc.bcm.edu	37	chr3	125313601	125313605	+	Frame_Shift_Del	DEL	CTCTC	CTCTC	-													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ggccctccagctttccttcgCtctccgagactttcattgtg							TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	CTCTC	CTCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr3:125313601_125313605delCTCTC	ENST00000296220.5	-	1	329_333	c.40_44delGAGAG	c.(40-45)gagagcfs	p.ES14fs		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	14					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						CTTTCCTTCGCTCTCCGAGACTTTC	0.566																																					p.14_15del		Atlas-Indel,Pindel	.											.	OSBPL11	64	.	0			c.41_45del						.																																			SO:0001589	frameshift_variant	114885	exon1			.	AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.40_44delGAGAG	chr3.hg19:g.125313601_125313605delCTCTC	ENSP00000296220:p.Glu14fs	384.0	0.0		153.0	36.0	NM_022776	A8K9I7	Frame_Shift_Del	DEL	ENST00000296220.5	hg19	CCDS3033.1																																																																																			.	.		0.566	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		-	125313605	CTCTC	-	125313601	7	5	106	1	0	1	0	1	0	0	0	0	11285	797	28	0	2251	0	OSBPL11	3	125313601	Frame_Shift_Del	DEL	CTCTC	TCGA-DD-A1EJ-01A-11D-A152-10	1147955	125313601	72708829	15	15938										
RAB7A	7879	hgsc.bcm.edu	37	chr3	128516808	128516808	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tcgggaagacatcactcatgAaccagtatgtgaataagaaa	9	7	2	4			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr3:128516808A>G	ENST00000265062.3	+	3	322	c.76A>G	c.(76-78)Aac>Gac	p.N26D	RAB7A_ENST00000482525.1_Missense_Mutation_p.N26D|RAB7A_ENST00000485280.1_Missense_Mutation_p.N26D	NM_004637.5	NP_004628.4	P51149	RAB7A_HUMAN	RAB7A, member RAS oncogene family	26					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|bone resorption (GO:0045453)|cell death (GO:0008219)|early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|epidermal growth factor catabolic process (GO:0007174)|GTP catabolic process (GO:0006184)|phagosome acidification (GO:0090383)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein targeting to lysosome (GO:0006622)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	alveolar lamellar body (GO:0097208)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	8				GBM - Glioblastoma multiforme(114;0.231)		ATCACTCATGAACCAGTATGT	0.403																																					p.N26D		Atlas-SNP	.											.	RAB7A	17	.	0			c.A76G						.						133	118	123					3																	128516808		2203	4300	6503	SO:0001583	missense	7879	exon3			CTCATGAACCAGT	X93499	CCDS3052.1	3q21	2014-09-17	2007-01-15	2007-01-15	ENSG00000075785	ENSG00000075785		"RAB, member RAS oncogene"	9788	protein-coding gene	gene with protein product		602298	"RAB7, member RAS oncogene family"	RAB7		9126495, 9428630	Standard	NM_004637		Approved		uc003eks.1	P51149	OTTHUMG00000159812	ENST00000265062.3:c.76A>G	chr3.hg19:g.128516808A>G	ENSP00000265062:p.Asn26Asp	29.0	0.0		205.0	33.0	NM_004637	A8K3V6|Q9NWJ0|Q9UPB0	Missense_Mutation	SNP	ENST00000265062.3	hg19	CCDS3052.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.894562	0.91962	.	.	ENSG00000075785	ENST00000265062;ENST00000482525;ENST00000464496;ENST00000490093;ENST00000493186;ENST00000483906;ENST00000485280	D;D;D;D;T;D;T	0.81821	-1.54;-1.54;-1.54;-1.54;-0.93;-1.54;-1.07	5.69	4.52	0.55395	Small GTP-binding protein domain (1);	.	.	.	.	T	0.79868	0.4520	M	0.65320	2	0.80722	D	1	B;B	0.20368	0.027;0.044	B;B	0.30316	0.114;0.089	T	0.76610	-0.2896	9	0.66056	D	0.02	-1.6018	12.9669	0.58490	0.8647:0.1353:0.0:0.0	.	26;26	C9J8S3;P51149	.;RAB7A_HUMAN	D	26	ENSP00000265062:N26D;ENSP00000417668:N26D;ENSP00000417978:N26D;ENSP00000418955:N26D;ENSP00000417189:N26D;ENSP00000417155:N26D;ENSP00000418283:N26D	ENSP00000265062:N26D	N	+	1	0	RAB7A	129999498	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.523000	0.90576	0.978000	0.38470	0.533000	0.62120	AAC	.	.		0.403	RAB7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357479.1			G	128516808	A	G	128516808	3	3	106	1	0	0	0	0	1	0	0	0	12969	246	9	2	82	2	RAB7A	3	128516808	Missense_Mutation	SNP	A	TCGA-DD-A1EJ-01A-11D-A152-10	3203207	128516808	69505622	16	15939										
CPB1	1360	hgsc.bcm.edu	37	chr3	148559613	148559613	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ccttttgtttgcaataggttGgcaaagctggacaaaataag	10	6	0	0			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr3:148559613G>A	ENST00000491148.1	+	7	812	c.478G>A	c.(478-480)Ggc>Agc	p.G160S	CPB1_ENST00000282957.4_Missense_Mutation_p.G160S			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	160						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			GCAATAGGTTGGCAAAGCTGG	0.453																																					p.G160S		Atlas-SNP	.											.	CPB1	74	.	0			c.G478A						.						150	138	142					3																	148559613		2203	4300	6503	SO:0001583	missense	1360	exon6			TAGGTTGGCAAAG	AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase B", "tissue carboxypeptidase B", "protaminase"	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.478G>A	chr3.hg19:g.148559613G>A	ENSP00000417222:p.Gly160Ser	35.0	0.0		212.0	93.0	NM_001871	O60834|Q53XJ0|Q96BQ8	Missense_Mutation	SNP	ENST00000491148.1	hg19	CCDS33874.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.958321	0.92726	.	.	ENSG00000153002	ENST00000491148;ENST00000282957;ENST00000468341	T;T;T	0.30714	1.52;1.52;2.89	5.28	5.28	0.74379	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.43523	0.1251	L	0.33668	1.02	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.08848	-1.0702	10	0.09338	T	0.73	.	19.2751	0.94029	0.0:0.0:1.0:0.0	.	160	P15086	CBPB1_HUMAN	S	160;160;126	ENSP00000417222:G160S;ENSP00000282957:G160S;ENSP00000419427:G126S	ENSP00000282957:G160S	G	+	1	0	CPB1	150042303	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.583000	0.74053	2.644000	0.89710	0.655000	0.94253	GGC	.	.		0.453	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871		A	148559613	G	A	148559613	3	1	106	1	0	0	0	0	1	0	0	0	3798	1348	47	3	500	3	CPB1	3	148559613	Missense_Mutation	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10	20042805	148559613	49462817	17	15940										
TP63	8626	hgsc.bcm.edu	37	chr3	189349323	189349323	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	aaatgaattttgaaacttcaCggtgtgccaccctacagtac	7	10	1	2	rs376627647		TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr3:189349323C>T	ENST00000264731.3	+	1	108	c.19C>T	c.(19-21)Cgg>Tgg	p.R7W	TP63_ENST00000382063.4_Missense_Mutation_p.R7W|TP63_ENST00000418709.2_Missense_Mutation_p.R7W|TP63_ENST00000392460.3_Missense_Mutation_p.R7W|TP63_ENST00000320472.5_Missense_Mutation_p.R7W|TP63_ENST00000440651.2_Missense_Mutation_p.R7W	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	7	Transcription activation.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		TGAAACTTCACGGTGTGCCAC	0.358										HNSCC(45;0.13)																											p.R7W		Atlas-SNP	.											.	TP63	187	.	0			c.C19T						.	C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	165	155	159		19,19,19	2.8	1	3		159	0,8600		0,0,4300	no	missense,missense,missense	TP63	NM_001114978.1,NM_001114979.1,NM_003722.4	101,101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	7/556,7/488,7/681	189349323	1,13005	2203	4300	6503	SO:0001583	missense	8626	exon1			ACTTCACGGTGTG	AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"tumor protein p73-like", "tumor protein p53-like", "tumor protein p53-competing protein"	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.19C>T	chr3.hg19:g.189349323C>T	ENSP00000264731:p.Arg7Trp	17.0	0.0		112.0	9.0	NM_001114979	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Missense_Mutation	SNP	ENST00000264731.3	hg19	CCDS3293.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.830276	0.32329	2.27E-4	0.0	ENSG00000073282	ENST00000264731;ENST00000418709;ENST00000320472;ENST00000392460;ENST00000440651;ENST00000382063	D;D;D;D;D;D	0.99730	-6.11;-6.43;-6.37;-6.36;-6.11;-6.56	5.72	2.84	0.33178	.	0.178925	0.33712	N	0.004636	D	0.97739	0.9258	N	0.08118	0	0.80722	D	1	P;P;P;P	0.47350	0.894;0.74;0.83;0.74	B;B;B;B	0.42771	0.397;0.397;0.129;0.397	D	0.95859	0.8881	9	.	.	.	-15.8525	14.0794	0.64912	0.3941:0.6059:0.0:0.0	.	7;7;7;7	Q9H3D4-7;Q9H3D4-3;Q9H3D4;Q9H3D4-5	.;.;P63_HUMAN;.	W	7	ENSP00000264731:R7W;ENSP00000407144:R7W;ENSP00000317510:R7W;ENSP00000376253:R7W;ENSP00000394337:R7W;ENSP00000371495:R7W	.	R	+	1	2	TP63	190832017	1.000000	0.71417	0.983000	0.44433	0.996000	0.88848	2.153000	0.42282	0.282000	0.22254	0.655000	0.94253	CGG	.	.		0.358	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722		T	189349323	C	T	189349323	3	4	106	1	0	0	0	0	1	0	0	0	16407	527	19	1	21	1	TP63	3	189349323	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	40789710	189349323	8673107	18	15941										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	193061790	193061790	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	atggcaatgaaaattttcctGgaagaataagaatgtctccg	9	6	1	3			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr3:193061790G>A	ENST00000342358.4	-	9	986	c.869C>T	c.(868-870)cCa>cTa	p.P290L		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	290						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		AAATTTTCCTGGAAGAATAAG	0.453																																					p.P290L		Atlas-SNP	.											.	ATP13A5	171	.	0			c.C869T						.						75	70	72					3																	193061790		2203	4300	6503	SO:0001583	missense	344905	exon9			TTTCCTGGAAGAA	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.869C>T	chr3.hg19:g.193061790G>A	ENSP00000341942:p.Pro290Leu	41.0	0.0		209.0	96.0	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	hg19	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.580969	0.46006	.	.	ENSG00000187527	ENST00000342358	D	0.90504	-2.68	5.57	4.64	0.57946	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.354064	0.28312	N	0.015802	D	0.87557	0.6207	L	0.54965	1.715	0.53005	D	0.999965	B	0.10296	0.003	B	0.18561	0.022	D	0.84365	0.0540	10	0.66056	D	0.02	-6.5577	10.9351	0.47241	0.0:0.1383:0.7192:0.1424	.	290	Q4VNC0	AT135_HUMAN	L	290	ENSP00000341942:P290L	ENSP00000341942:P290L	P	-	2	0	ATP13A5	194544484	0.933000	0.31639	1.000000	0.80357	0.848000	0.48234	3.592000	0.53993	2.802000	0.96397	0.650000	0.86243	CCA	.	.		0.453	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		A	193061790	G	A	193061790	3	1	106	1	0	0	0	0	1	0	0	0	1127	1348	47	3	2873	3	ATP13A5	3	193061790	Missense_Mutation	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10	3712467	193061790	4960640	19	15942										
PPP2R2C	5522	hgsc.bcm.edu	37	chr4	6335429	6335429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	gatttccgagaagaatgagcGgttactggggtcctcaggct	14	8	1	3			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr4:6335429G>A	ENST00000382599.4	-	7	1036	c.820C>T	c.(820-822)Cgc>Tgc	p.R274C	PPP2R2C_ENST00000335585.5_Missense_Mutation_p.R274C|PPP2R2C_ENST00000506140.1_Missense_Mutation_p.R267C|PPP2R2C_ENST00000515571.1_Missense_Mutation_p.R257C|PPP2R2C_ENST00000507294.1_Missense_Mutation_p.R267C			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	274					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						AAGAATGAGCGGTTACTGGGG	0.582											OREG0016071	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R274C		Atlas-SNP	.											PPP2R2C,colon,carcinoma,+1,1	PPP2R2C	63	.	0			c.C820T						.						105	109	108					4																	6335429		2203	4300	6503	SO:0001583	missense	5522	exon7			ATGAGCGGTTACT	AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9306	protein-coding gene	gene with protein product	"PP2A subunit B isoform gamma"	605997	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform"			10574460, 10945473	Standard	NM_020416		Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.820C>T	chr4.hg19:g.6335429G>A	ENSP00000372042:p.Arg274Cys	434.0	1.0	633	103.0	26.0	NM_181876	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Missense_Mutation	SNP	ENST00000382599.4	hg19		.	.	.	.	.	.	.	.	.	.	G	15.86	2.956552	0.53293	.	.	ENSG00000074211	ENST00000335585;ENST00000506140;ENST00000515571;ENST00000382599;ENST00000507294	T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56	4.2	3.26	0.37387	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.054165	0.64402	D	0.000001	T	0.38188	0.1031	M	0.81802	2.56	0.80722	D	1	B;P;D;B;D	0.63046	0.03;0.76;0.979;0.03;0.992	B;B;P;B;P	0.46275	0.015;0.102;0.51;0.015;0.51	T	0.44190	-0.9344	10	0.66056	D	0.02	.	9.1642	0.37041	0.0:0.0:0.602:0.398	.	267;370;274;257;274	B7Z3Y1;Q59GC6;Q9Y2T4;Q9Y2T4-3;Q9Y2T4-2	.;.;2ABG_HUMAN;.;.	C	274;267;257;274;267	ENSP00000335083:R274C;ENSP00000423649:R267C;ENSP00000422374:R257C;ENSP00000372042:R274C;ENSP00000425247:R267C	ENSP00000335083:R274C	R	-	1	0	PPP2R2C	6386330	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.393000	0.52544	2.187000	0.69744	0.491000	0.48974	CGC	.	.		0.582	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876		A	6335429	G	A	6335429	3	1	106	1	0	0	0	0	1	0	0	0	12398	1116	39	1	535	1	PPP2R2C	4	6335429	Missense_Mutation	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10		6335429	184818847	20	15943										
FBXL7	23194	hgsc.bcm.edu	37	chr5	15937055	15937055	+	Frame_Shift_Del	DEL	C	C	-													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tccctggatatcggcaaatgCcctttggtatccgacacggg							TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr5:15937055delC	ENST00000504595.1	+	4	1717	c.1236delC	c.(1234-1236)tgcfs	p.C412fs	FBXL7_ENST00000329673.7_Frame_Shift_Del_p.C400fs|FBXL7_ENST00000510662.1_Frame_Shift_Del_p.C365fs|MIR887_ENST00000401258.1_RNA	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	412					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						TCGGCAAATGCCCTTTGGTAT	0.607																																					p.C412fs		Atlas-Indel,Pindel	.											FBXL7,colon,carcinoma,0,1	FBXL7	138	.	0			c.1235delG						.						91	96	94					5																	15937055		2093	4214	6307	SO:0001589	frameshift_variant	23194	exon4			.	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.1236delC	chr5.hg19:g.15937055delC	ENSP00000423630:p.Cys412fs	326.0	0.0		68.0	17.0	NM_012304	B9EGF1|D6RDY7|O94926	Frame_Shift_Del	DEL	ENST00000504595.1	hg19	CCDS54833.1																																																																																			.	.		0.607	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		-	15937055	C	-	15937055	7	5	106	1	0	1	0	1	0	0	0	0	5732	747	26	0	1250	0	FBXL7	5	15937055	Frame_Shift_Del	DEL	C	TCGA-DD-A1EJ-01A-11D-A152-10		15937055	164978205	21	15944										
HSPA9	3313	hgsc.bcm.edu	37	chr5	137902698	137902699	+	Missense_Mutation	DNP	TG	TG	GT													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ttggtaactcacctctctctTgaactccttcacaatgtgcc					rs202180095|rs199831172		TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr5:137902698_137902699TG>GT	ENST00000297185.3	-	8	995_996	c.870_871CA>AC	c.(868-873)ttCAag>ttACag	p.290_291FK>LQ	HSPA9_ENST00000501917.2_5'Flank	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	290					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACCTCTCTCTTGAACTCCTTCA	0.416																																					p.K291Q|p.F290L		Atlas-SNP	.											.	HSPA9	49	.	0			c.A871C|c.C870A						.																																			SO:0001583	missense	3313	exon8			CTCTCTTGAACTC|TCTCTTGAACTCC	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"Heat shock proteins / HSP70"	5244	protein-coding gene	gene with protein product		600548	"heat shock 70kDa protein 9B (mortalin-2)"	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.870_871delinsGT	chr5.hg19:g.137902698_137902699delinsGT	ENSP00000297185:p.F290_K291delinsLQ	40.0|41.0	0.0		305.0|308.0	22.0	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	hg19	CCDS4208.1																																																																																			.	T|0.999;G|0.001|G|0.999;T|0.001		0.416	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134		GT	137902699	TG	GT	137902698	3	3	106	1	0	0	0	0	1	0	0	0	7426	1821	63	5	1208	5	HSPA9	5	137902698	Missense_Mutation	DNP	TG	TCGA-DD-A1EJ-01A-11D-A152-10	121965643	137902698	43012562	22	15945										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327918	16327919	+	In_Frame_Ins	INS	-	-	TGC													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	gctgctgctgatgctgatgcINStgctgctgctgctgctgctg					rs28555263	byFrequency	TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr6:16327918_16327919insTGC	ENST00000244769.4	-	8	1559_1560	c.623_624insGCA	c.(622-624)cag>caGCAg	p.208_208Q>QQ	ATXN1_ENST00000436367.1_In_Frame_Ins_p.208_208Q>QQ	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	208	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gatgctgatgctgctgctgctg	0.663																																					p.Q208delinsQQ		Atlas-INDEL	.											ATXN1,rectum,carcinoma,0,1	ATXN1	117	.	0			c.624_625insGCA						.																																			SO:0001652	inframe_insertion	6310	exon7			.	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.621_623dupGCA	chr6.hg19:g.16327925_16327927dupTGC	ENSP00000244769:p.Gln208dup	244.0	0.0		77.0	17.0	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	In_Frame_Ins	INS	ENST00000244769.4	hg19	CCDS34342.1																																																																																			.	.		0.663	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		TGC	16327919	-	TGC	16327918	7	5	106	1	0	1	1	0	0	0	0	0	1209	796	28	0	1831	0	ATXN1	6	16327918	In_Frame_Ins	INS	-	TCGA-DD-A1EJ-01A-11D-A152-10		16327918	154787149	23	15946										
RXRB	6257	hgsc.bcm.edu	37	chr6	33166198	33166198	+	Frame_Shift_Del	DEL	G	G	-													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ctggtggcttcacatcttcaGgggggccagacccaccccca							TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr6:33166198delG	ENST00000374680.3	-	3	738	c.527delC	c.(526-528)cctfs	p.P176fs	RXRB_ENST00000413614.2_Frame_Shift_Del_p.P80fs|RXRB_ENST00000544186.1_Intron|SLC39A7_ENST00000374675.3_5'Flank|RNY4P10_ENST00000365571.1_RNA|RXRB_ENST00000374685.4_Frame_Shift_Del_p.P176fs|SLC39A7_ENST00000374677.3_5'Flank	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	176	Modulating. {ECO:0000250}.|Pro-rich.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	CACATCTTCAGGGGGGCCAGA	0.592																																					p.P176fs		Atlas-Indel,Pindel	.											.	RXRB	34	.	0			c.528delT						.						94	114	107					6																	33166198		1508	2707	4215	SO:0001589	frameshift_variant	6257	exon3			.	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"Nuclear hormone receptors"	10478	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 2"	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.527delC	chr6.hg19:g.33166198delG	ENSP00000363812:p.Pro176fs	177.0	0.0		57.0	32.0	NM_001270401	P28703|Q59G65|Q5JP92|Q5STQ1	Frame_Shift_Del	DEL	ENST00000374680.3	hg19	CCDS4768.1																																																																																			.	.		0.592	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		-	33166198	G	-	33166198	7	5	106	1	0	1	0	1	0	0	0	0	13779	1000	35	0	1106	0	RXRB	6	33166198	Frame_Shift_Del	DEL	G	TCGA-DD-A1EJ-01A-11D-A152-10	16838280	33166198	137948869	24	15947										
KCTD20	222658	hgsc.bcm.edu	37	chr6	36447368	36447368	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tcttcctaatctatttacagGattattacaaaaccggtatc	4	9	2	0			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr6:36447368G>T	ENST00000373731.2	+	5	929	c.538G>T	c.(538-540)Gat>Tat	p.D180Y	KCTD20_ENST00000474988.1_Intron|KCTD20_ENST00000544295.1_Intron|KCTD20_ENST00000536244.1_Splice_Site_p.D35Y|KCTD20_ENST00000449081.2_Intron	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	180	BTB.				protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						CTATTTACAGGATTATTACAA	0.353																																					p.D180Y		Atlas-SNP	.											.	KCTD20	37	.	0			c.G538T						.						109	106	107					6																	36447368		2203	4300	6503	SO:0001630	splice_region_variant	222658	exon5			TTACAGGATTATT	BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"chromosome 6 open reading frame 69", "potassium channel tetramerisation domain containing 20"	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.538-1G>T	chr6.hg19:g.36447368G>T		11.0	0.0		41.0	11.0	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	hg19	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170316	0.78452	.	.	ENSG00000112078	ENST00000373731;ENST00000536244	D;D	0.82433	-1.61;-1.61	5.01	5.01	0.66863	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.90338	0.6977	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89978	0.4098	9	.	.	.	-26.3868	18.5249	0.90968	0.0:0.0:1.0:0.0	.	180	Q7Z5Y7	KCD20_HUMAN	Y	180;35	ENSP00000362836:D180Y;ENSP00000439118:D35Y	.	D	+	1	0	KCTD20	36555346	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	9.657000	0.98554	2.602000	0.87976	0.591000	0.81541	GAT	.	.		0.353	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562	Missense_Mutation	T	36447368	G	T	36447368	5	4	106	1	0	0	0	0	0	0	1	0	8117	1188	41	3	552	3	KCTD20	6	36447368	Splice_Site	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10	3281170	36447368	134667699	25	15948										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129637033	129637033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ctactcatgctagaattatcGtcaggcatatggctgctcct	8	11	2	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr6:129637033G>A	ENST00000421865.2	+	26	3911	c.3862G>A	c.(3862-3864)Gtc>Atc	p.V1288I		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1288	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TAGAATTATCGTCAGGCATAT	0.418																																					p.V1288I		Atlas-SNP	.											.	LAMA2	481	.	0			c.G3862A						.						110	111	111					6																	129637033		2203	4300	6503	SO:0001583	missense	3908	exon26			ATTATCGTCAGGC	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.3862G>A	chr6.hg19:g.129637033G>A	ENSP00000400365:p.Val1288Ile	12.0	0.0		52.0	11.0	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	6.966	0.548237	0.13312	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.34667	1.35	5.55	-8.19	0.01049	Laminin B type IV (2);Laminin B, subgroup (1);	1.139610	0.06183	N	0.679911	T	0.11707	0.0285	N	0.25647	0.755	0.09310	N	0.999995	B;B	0.14805	0.011;0.011	B;B	0.09377	0.004;0.004	T	0.09509	-1.0671	10	0.48119	T	0.1	.	19.8259	0.96617	0.2743:0.0:0.7257:0.0	.	1288;1288	A6NF00;P24043	.;LAMA2_HUMAN	I	1288	ENSP00000400365:V1288I	ENSP00000346769:V1288I	V	+	1	0	LAMA2	129678726	0.002000	0.14202	0.311000	0.25182	0.940000	0.58332	-0.187000	0.09656	-1.575000	0.01655	-1.083000	0.02208	GTC	.	.		0.418	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129637033	G	A	129637033	3	1	106	1	0	0	0	0	1	0	0	0	8615	1145	40	1	3964	1	LAMA2	6	129637033	Missense_Mutation	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10	93189665	129637033	41478034	26	15949										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48318518	48318518	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tgtgaaagaaatagctacttTaaaaaaaatagatcatttca	5	4	2	3	rs544493291	byFrequency	TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr7:48318518T>A	ENST00000435803.1	+	18	7751	c.7727T>A	c.(7726-7728)tTa>tAa	p.L2576*		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2576					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATAGCTACTTTAAAAAAAATA	0.318													T|||	3	0.000599042	0	0.0014	5008	,	,		18836	0		0	False		,,,				2504	0.002				p.L2576X		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T7727A						.						55	59	58					7																	48318518		1794	4040	5834	SO:0001587	stop_gained	154664	exon18			CTACTTTAAAAAA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.7727T>A	chr7.hg19:g.48318518T>A	ENSP00000411096:p.Leu2576*	18.0	0.0		167.0	17.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Nonsense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	47	13.299669	0.99733	.	.	ENSG00000179869	ENST00000435803	.	.	.	4.93	-0.0604	0.13789	.	1.145970	0.06770	N	0.783306	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.0212	0.09667	0.0:0.3009:0.2063:0.4928	.	.	.	.	X	2576	.	ENSP00000411096:L2576X	L	+	2	0	ABCA13	48289064	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-1.274000	0.02820	-0.020000	0.14032	-0.331000	0.08364	TTA	.	.		0.318	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48318518	T	A	48318518	4	1	106	1	0	0	0	0	0	1	0	0	31	1764	61	4	7626	4	ABCA13	7	48318518	Nonsense_Mutation	SNP	T	TCGA-DD-A1EJ-01A-11D-A152-10		48318518	110820145	27	15950										
MLXIPL	51085	hgsc.bcm.edu	37	chr7	73020290	73020290	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ggccggactgagtcatggtgAagagagtgtctgagatgtcg	17	6	2	4			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr7:73020290A>G	ENST00000313375.3	-	6	817	c.770T>C	c.(769-771)tTc>tCc	p.F257S	MLXIPL_ENST00000434326.1_Intron|MLXIPL_ENST00000354613.1_Missense_Mutation_p.F257S|MLXIPL_ENST00000429400.2_Missense_Mutation_p.F257S|MLXIPL_ENST00000395189.1_Intron|MLXIPL_ENST00000414749.2_Missense_Mutation_p.F257S	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	257					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				AGTCATGGTGAAGAGAGTGTC	0.627																																					p.F257S		Atlas-SNP	.											.	MLXIPL	54	.	0			c.T770C						.						36	33	34					7																	73020290		2201	4300	6501	SO:0001583	missense	51085	exon6			ATGGTGAAGAGAG	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"carbohydrate response element binding protein"	605678	"Williams Beuren syndrome chromosome region 14"	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.770T>C	chr7.hg19:g.73020290A>G	ENSP00000320886:p.Phe257Ser	220.0	1.0		54.0	28.0	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Missense_Mutation	SNP	ENST00000313375.3	hg19	CCDS5553.1	.	.	.	.	.	.	.	.	.	.	A	14.15	2.450017	0.43531	.	.	ENSG00000009950	ENST00000414749;ENST00000429400;ENST00000313375;ENST00000354613;ENST00000456640	T;T;T;T;T	0.58940	1.13;1.18;1.13;1.17;0.3	3.62	3.62	0.41486	.	0.000000	0.85682	D	0.000000	T	0.72301	0.3443	M	0.79475	2.455	0.80722	D	1	D;D;D;D	0.69078	0.995;0.997;0.997;0.997	D;D;D;D	0.75484	0.969;0.986;0.986;0.986	T	0.74677	-0.3585	10	0.87932	D	0	-19.6467	8.5243	0.33296	1.0:0.0:0.0:0.0	.	257;257;257;257	Q9NP71;Q9NP71-2;Q9NP71-3;Q9NP71-4	MLXPL_HUMAN;.;.;.	S	257;257;257;257;219	ENSP00000412330:F257S;ENSP00000406296:F257S;ENSP00000320886:F257S;ENSP00000346629:F257S;ENSP00000402615:F219S	ENSP00000320886:F257S	F	-	2	0	MLXIPL	72658226	1.000000	0.71417	1.000000	0.80357	0.603000	0.37013	7.470000	0.80973	1.508000	0.48769	0.260000	0.18958	TTC	.	.		0.627	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951		G	73020290	A	G	73020290	3	3	106	1	0	0	0	0	1	0	0	0	9646	246	9	2	1836	2	MLXIPL	7	73020290	Missense_Mutation	SNP	A	TCGA-DD-A1EJ-01A-11D-A152-10	24701772	73020290	86118373	28	15951										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83021890	83021890	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	cctttttgcatgtgtgcctgTtgggtaataccgggagcagg	14	8	0	0			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr7:83021890T>C	ENST00000307792.3	-	14	2115	c.1648A>G	c.(1648-1650)Aca>Gca	p.T550A	SEMA3E_ENST00000427262.1_Missense_Mutation_p.T490A	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	550					axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TGTGTGCCTGTTGGGTAATAC	0.448																																					p.T550A		Atlas-SNP	.											.	SEMA3E	125	.	0			c.A1648G						.						105	92	97					7																	83021890		2203	4300	6503	SO:0001583	missense	9723	exon14			TGCCTGTTGGGTA	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1648A>G	chr7.hg19:g.83021890T>C	ENSP00000303212:p.Thr550Ala	44.0	0.0		153.0	76.0	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	T	8.152	0.787505	0.16258	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.21361	2.01;2.01	5.32	5.32	0.75619	.	0.097215	0.41294	U	0.000901	T	0.13072	0.0317	N	0.16478	0.41	0.36679	D	0.878952	B	0.11235	0.004	B	0.09377	0.004	T	0.16482	-1.0401	10	0.25751	T	0.34	.	11.557	0.50755	0.0:0.0:0.1493:0.8507	.	550	O15041	SEM3E_HUMAN	A	550;490;550	ENSP00000303212:T550A;ENSP00000405052:T490A	ENSP00000303212:T550A	T	-	1	0	SEMA3E	82859826	0.900000	0.30661	0.883000	0.34634	0.411000	0.31082	0.922000	0.28734	2.142000	0.66516	0.477000	0.44152	ACA	.	.		0.448	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		C	83021890	T	C	83021890	3	2	106	1	0	0	0	0	1	0	0	0	14043	1725	60	2	695	2	SEMA3E	7	83021890	Missense_Mutation	SNP	T	TCGA-DD-A1EJ-01A-11D-A152-10	10001600	83021890	76116773	29	15952										
SGCE	8910	hgsc.bcm.edu	37	chr7	94232701	94232701	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ctacatctcaattgattctgTggattttcaacttctcgtaa	5	9	4	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr7:94232701T>A	ENST00000265735.7	-	6	836	c.726A>T	c.(724-726)ccA>ccT	p.P242P	SGCE_ENST00000428696.2_Silent_p.P242P|SGCE_ENST00000447873.1_Silent_p.P242P|SGCE_ENST00000415788.2_Silent_p.P278P|SGCE_ENST00000437425.2_Silent_p.P201P|SGCE_ENST00000445866.2_Silent_p.P242P	NM_003919.2	NP_003910.1	O43556	SGCE_HUMAN	sarcoglycan, epsilon	242	Cys-rich.				cell-matrix adhesion (GO:0007160)|muscle organ development (GO:0007517)	cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|dystrophin-associated glycoprotein complex (GO:0016010)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	14	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			ATTGATTCTGTGGATTTTCAA	0.348																																					p.P242P		Atlas-SNP	.											.	SGCE	68	.	0			c.A726T						.						89	84	86					7																	94232701		2203	4300	6503	SO:0001819	synonymous_variant	8910	exon6			ATTCTGTGGATTT	AF036364	CCDS5637.1, CCDS47642.1, CCDS47643.1, CCDS75634.1	7q21.3	2014-09-17			ENSG00000127990	ENSG00000127990			10808	protein-coding gene	gene with protein product		604149		DYT11		9475163, 9405466	Standard	NM_001099401		Approved		uc003unn.2	O43556	OTTHUMG00000022828	ENST00000265735.7:c.726A>T	chr7.hg19:g.94232701T>A		47.0	0.0		292.0	107.0	NM_001099401	B2R8N2|D6W5Q8|E9PF60|G5E9K6|Q6L8P0|Q75MH8|Q8NFG8|Q8WW28	Silent	SNP	ENST00000265735.7	hg19	CCDS5637.1																																																																																			.	.		0.348	SGCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255251.2			A	94232701	T	A	94232701	2	1	106	1	0	0	0	0	0	0	0	1	14217	1683	59	4		4	SGCE	7	94232701	Silent	SNP	T	TCGA-DD-A1EJ-01A-11D-A152-10	11210811	94232701	64905962	30	15953										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121684588	121684588	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tgcactcctcattcctggacCagcaggcaaaacaaagctag	8	13	1	0			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr7:121684588C>T	ENST00000393386.2	+	23	6461	c.6050C>T	c.(6049-6051)cCa>cTa	p.P2017L	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.P1150L	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	2017					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						ATTCCTGGACCAGCAGGCAAA	0.438																																					p.P2017L		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.C6050T						.						114	104	108					7																	121684588		2203	4300	6503	SO:0001583	missense	5803	exon23			CTGGACCAGCAGG	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.6050C>T	chr7.hg19:g.121684588C>T	ENSP00000377047:p.Pro2017Leu	27.0	0.0		138.0	24.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152865	0.57259	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.10382	2.88;2.88	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000004	T	0.19725	0.0474	M	0.67953	2.075	0.42409	D	0.99259	P;B;P	0.41313	0.589;0.069;0.745	B;B;B	0.41988	0.173;0.053;0.372	T	0.00888	-1.1526	10	0.59425	D	0.04	.	19.3942	0.94598	0.0:1.0:0.0:0.0	.	1156;1150;2017	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	L	2017;1150	ENSP00000377047:P2017L;ENSP00000410000:P1150L	ENSP00000377047:P2017L	P	+	2	0	PTPRZ1	121471824	0.176000	0.23096	0.986000	0.45419	0.706000	0.40770	2.601000	0.46249	2.587000	0.87381	0.655000	0.94253	CCA	.	.		0.438	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121684588	C	T	121684588	3	4	106	1	0	0	0	0	1	0	0	0	12829	594	21	3	6140	3	PTPRZ1	7	121684588	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	27451887	121684588	37454075	31	15954										
CLCN1	1180	hgsc.bcm.edu	37	chr7	143039472	143039472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tctccctccatagcaaatatAccatctttgttgaggacatc	5	12	2	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr7:143039472A>G	ENST00000343257.2	+	16	1891	c.1804A>G	c.(1804-1806)Acc>Gcc	p.T602A		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	602					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					TAGCAAATATACCATCTTTGT	0.463																																					p.T602A		Atlas-SNP	.											.	CLCN1	141	.	0			c.A1804G						.						147	114	125					7																	143039472		2203	4300	6503	SO:0001583	missense	1180	exon16			AAATATACCATCT	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.1804A>G	chr7.hg19:g.143039472A>G	ENSP00000339867:p.Thr602Ala	20.0	0.0		158.0	57.0	NM_000083	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	hg19	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.714293	0.68730	.	.	ENSG00000188037	ENST00000343257	D	0.87966	-2.32	5.82	5.82	0.92795	.	0.147273	0.64402	D	0.000020	T	0.81688	0.4875	N	0.24115	0.695	0.50171	D	0.999857	P	0.42296	0.775	B	0.42851	0.4	T	0.80632	-0.1296	10	0.27082	T	0.32	.	16.1771	0.81858	1.0:0.0:0.0:0.0	.	602	P35523	CLCN1_HUMAN	A	602	ENSP00000339867:T602A	ENSP00000339867:T602A	T	+	1	0	CLCN1	142749594	1.000000	0.71417	0.994000	0.49952	0.883000	0.51084	9.331000	0.96430	2.225000	0.72522	0.523000	0.50628	ACC	.	.		0.463	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		G	143039472	A	G	143039472	3	3	106	1	0	0	0	0	1	0	0	0	3464	391	14	2	1866	2	CLCN1	7	143039472	Missense_Mutation	SNP	A	TCGA-DD-A1EJ-01A-11D-A152-10	21354884	143039472	16099191	32	15955										
TRIM55	84675	hgsc.bcm.edu	37	chr8	67067941	67067941	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	cagtgcttgatttttactttAatgggtaggaaatattttct	8	4	1	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr8:67067941A>C	ENST00000315962.4	+	9	1897				TRIM55_ENST00000353317.5_Intron|TRIM55_ENST00000276573.7_Missense_Mutation_p.L536F|TRIM55_ENST00000350034.4_Intron	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55						signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			TTTTTACTTTAATGGGTAGGA	0.363																																					p.L536F		Atlas-SNP	.											.	TRIM55	91	.	0			c.A1608C						.						146	130	135					8																	67067941		2203	4299	6502	SO:0001627	intron_variant	84675	exon10			TACTTTAATGGGT	AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	14215	protein-coding gene	gene with protein product		606469	"ring finger protein 29", "tripartite motif-containing 55"	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.1524+1372A>C	chr8.hg19:g.67067941A>C		59.0	0.0		253.0	120.0	NM_033058	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	hg19	CCDS6184.1	.	.	.	.	.	.	.	.	.	.	A	17.21	3.330611	0.60743	.	.	ENSG00000147573	ENST00000276573	T	0.35048	1.33	5.8	3.04	0.35103	.	.	.	.	.	T	0.17959	0.0431	N	0.08118	0	0.80722	D	1	B	0.20671	0.047	B	0.19946	0.027	T	0.04991	-1.0913	9	0.31617	T	0.26	.	8.5873	0.33666	0.5693:0.3543:0.0763:0.0	.	536	Q9BYV6-3	.	F	536	ENSP00000276573:L536F	ENSP00000276573:L536F	L	+	3	2	TRIM55	67230495	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.539000	0.23175	1.000000	0.39049	0.529000	0.55759	TTA	.	.		0.363	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		C	67067941	A	C	67067941	1	2	106	0	1	0	0	0	0	0	0	0	16544	359	13	5		5	TRIM55	8	67067941	Intron	SNP	A	TCGA-DD-A1EJ-01A-11D-A152-10		67067941	79296081	33	15956										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113347573	113347574	+	Frame_Shift_Ins	INS	-	-	A													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	caaccgtgataactgagcacINSaaaaaagccacttgttgtga							TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr8:113347573_113347574insA	ENST00000297405.5	-	45	7393_7394	c.7149_7150insT	c.(7147-7152)tttgtgfs	p.V2384fs	CSMD3_ENST00000343508.3_Frame_Shift_Ins_p.V2344fs|CSMD3_ENST00000455883.2_Frame_Shift_Ins_p.V2280fs|CSMD3_ENST00000352409.3_Frame_Shift_Ins_p.V2314fs	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2384	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TAACTGAGCACAAAAAAGCCAC	0.351										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.V2384fs		Atlas-Indel,Pindel	.											.	CSMD3	2325	.	0			c.7150_7151insT						.																																			SO:0001589	frameshift_variant	114788	exon45			.	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7150dupT	chr8.hg19:g.113347579_113347579dupA	ENSP00000297405:p.Val2384fs	30.0	0.0		120.0	44.0	NM_198123	Q96PZ3	Frame_Shift_Ins	INS	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.351	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113347574	-	A	113347573	7	5	106	1	0	1	1	0	0	0	0	0	3948	478	17	0	4081	0	CSMD3	8	113347573	Frame_Shift_Ins	INS	-	TCGA-DD-A1EJ-01A-11D-A152-10	46279632	113347573	33016449	34	15957										
KLF9	687	hgsc.bcm.edu	37	chr9	73027906	73027906	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ccactccaggatggaggaggGagagcgggctgggcgcgctg	20	10	0	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr9:73027906G>C	ENST00000377126.2	-	1	1634	c.374C>G	c.(373-375)tCc>tGc	p.S125C		NM_001206.2	NP_001197.1	Q13886	KLF9_HUMAN	Kruppel-like factor 9	125					cellular response to thyroid hormone stimulus (GO:0097067)|embryo implantation (GO:0007566)|progesterone receptor signaling pathway (GO:0050847)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1)	9						ATGGAGGAGGGAGAGCGGGCT	0.612																																					p.S125C		Atlas-SNP	.											.	KLF9	16	.	0			c.C374G						.						92	95	94					9																	73027906		2203	4300	6503	SO:0001583	missense	687	exon1			AGGAGGGAGAGCG	BC069431	CCDS6633.1	9q21.11	2013-01-08	2004-11-29	2004-12-01	ENSG00000119138	ENSG00000119138		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	1123	protein-coding gene	gene with protein product		602902	"basic transcription element binding protein 1"	BTEB1		1356762	Standard	NM_001206		Approved		uc004aht.3	Q13886	OTTHUMG00000019991	ENST00000377126.2:c.374C>G	chr9.hg19:g.73027906G>C	ENSP00000366330:p.Ser125Cys	558.0	0.0		149.0	42.0	NM_001206	B2R943|Q16196	Missense_Mutation	SNP	ENST00000377126.2	hg19	CCDS6633.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.405712	0.42715	.	.	ENSG00000119138	ENST00000377126	T	0.05996	3.36	4.55	4.55	0.56014	.	0.219783	0.31636	N	0.007316	T	0.04861	0.0131	N	0.22421	0.69	0.35635	D	0.810482	P	0.43352	0.804	B	0.34652	0.187	T	0.49943	-0.8885	10	0.34782	T	0.22	.	15.1803	0.72952	0.0:0.0:1.0:0.0	.	125	Q13886	KLF9_HUMAN	C	125	ENSP00000366330:S125C	ENSP00000366330:S125C	S	-	2	0	KLF9	72217726	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.905000	0.39878	2.250000	0.74265	0.557000	0.71058	TCC	.	.		0.612	KLF9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052602.1	NM_001206		C	73027906	G	C	73027906	3	2	106	1	0	0	0	0	1	0	0	0	8362	1174	41	4	368	4	KLF9	9	73027906	Missense_Mutation	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10		73027906	68185525	35	15958										
DAPK1	1612	hgsc.bcm.edu	37	chr9	90318036	90318036	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	cccaaccagctgatgtcgctGcagcagtttgtgtacgacgt	11	12	0	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr9:90318036G>A	ENST00000408954.3	+	25	3299	c.2964G>A	c.(2962-2964)ctG>ctA	p.L988L	DAPK1_ENST00000469640.2_Silent_p.L1013L|DAPK1_ENST00000472284.1_Silent_p.L988L|DAPK1_ENST00000491893.1_Silent_p.L922L|DAPK1_ENST00000358077.5_Silent_p.L988L	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	988					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						TGATGTCGCTGCAGCAGTTTG	0.592									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.L988L		Atlas-SNP	.											.	DAPK1	329	.	0			c.G2964A						.						63	64	64					9																	90318036		2131	4240	6371	SO:0001819	synonymous_variant	1612	exon25	Familial Cancer Database	Familial CLL	GTCGCTGCAGCAG	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.2964G>A	chr9.hg19:g.90318036G>A		302.0	0.0		55.0	17.0	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	hg19	CCDS43842.1																																																																																			.	.		0.592	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		A	90318036	G	A	90318036	2	1	106	1	0	0	0	0	0	0	0	1	4237	1306	46	3		3	DAPK1	9	90318036	Silent	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10	17290130	90318036	50895395	36	15959										
RXRA	6256	hgsc.bcm.edu	37	chr9	137328351	137328351	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ccgcctgccggctctgcgctCcatcgggctcaaatgcctgg	12	17	2	0			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr9:137328351C>T	ENST00000481739.1	+	10	1332	c.1280C>T	c.(1279-1281)tCc>tTc	p.S427F	RXRA_ENST00000356384.4_3'UTR|RXRA_ENST00000540193.1_Missense_Mutation_p.S330F	NM_002957.4	NP_002948.1	P19793	RXRA_HUMAN	retinoid X receptor, alpha	427	Ligand-binding.				camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	GCTCTGCGCTCCATCGGGCTC	0.607																																					p.S427F		Atlas-SNP	.											RXRA,bladder,carcinoma,0,5	RXRA	52	.	0			c.C1280T						.						132	117	122					9																	137328351		2203	4300	6503	SO:0001583	missense	6256	exon10			TGCGCTCCATCGG	X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350		"Nuclear hormone receptors"	10477	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 1"	180245				2159111	Standard	XM_005263409		Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000481739.1:c.1280C>T	chr9.hg19:g.137328351C>T	ENSP00000419692:p.Ser427Phe	283.0	0.0		78.0	23.0	NM_002957	B3KY83|Q2NL52|Q2V504	Missense_Mutation	SNP	ENST00000481739.1	hg19	CCDS35172.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.825420	0.90955	.	.	ENSG00000186350	ENST00000481739;ENST00000540193	D;D	0.96940	-4.18;-4.18	4.76	4.76	0.60689	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.98369	0.9458	M	0.88241	2.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99744	1.1016	10	0.87932	D	0	.	17.7817	0.88526	0.0:1.0:0.0:0.0	.	427	P19793	RXRA_HUMAN	F	427;330	ENSP00000419692:S427F;ENSP00000442123:S330F	ENSP00000419692:S427F	S	+	2	0	RXRA	136468172	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.532000	0.81985	2.193000	0.70182	0.591000	0.81541	TCC	.	.		0.607	RXRA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054949.1	NM_002957		T	137328351	C	T	137328351	3	4	106	1	0	0	0	0	1	0	0	0	13778	855	30	3	1318	3	RXRA	9	137328351	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	47010315	137328351	3885080	37	15960										
HTR7	3363	hgsc.bcm.edu	37	chr10	92508894	92508894	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	gcacacggtaaaggccccgaCgatgatccccagggtggtgg	15	12	0	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr10:92508894C>T	ENST00000336152.3	-	2	1023	c.997G>A	c.(997-999)Gtc>Atc	p.V333I	HTR7_ENST00000371721.3_Missense_Mutation_p.V333I|HTR7_ENST00000277874.6_Missense_Mutation_p.V333I|HTR7_ENST00000371719.2_Missense_Mutation_p.V333I	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	333					blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	AAGGCCCCGACGATGATCCCC	0.537																																					p.V333I		Atlas-SNP	.											.	HTR7	122	.	0			c.G997A						.						81	73	76					10																	92508894		2203	4300	6503	SO:0001583	missense	3363	exon2			CCCCGACGATGAT	BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5302	protein-coding gene	gene with protein product		182137	"5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)"			8226867	Standard	NM_000872		Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000336152.3:c.997G>A	chr10.hg19:g.92508894C>T	ENSP00000337949:p.Val333Ile	252.0	0.0		156.0	43.0	NM_019860	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Missense_Mutation	SNP	ENST00000336152.3	hg19	CCDS7408.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.301775	0.81136	.	.	ENSG00000148680	ENST00000336152;ENST00000277874;ENST00000371719;ENST00000371721	T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82	5.35	5.35	0.76521	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.82033	0.4949	L	0.50993	1.605	0.50467	D	0.999875	D;D	0.76494	0.999;0.996	P;P	0.60886	0.88;0.803	T	0.83054	-0.0151	10	0.59425	D	0.04	.	19.0553	0.93062	0.0:1.0:0.0:0.0	.	333;333	P34969;P34969-2	5HT7R_HUMAN;.	I	333	ENSP00000337949:V333I;ENSP00000277874:V333I;ENSP00000360784:V333I;ENSP00000360786:V333I	ENSP00000277874:V333I	V	-	1	0	HTR7	92498874	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.086000	0.71352	2.499000	0.84300	0.650000	0.86243	GTC	.	.		0.537	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1	NM_000872		T	92508894	C	T	92508894	3	4	106	1	0	0	0	0	1	0	0	0	7461	536	19	1	458	1	HTR7	10	92508894	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10		92508894	43025853	38	15961										
ANKRD1	27063	hgsc.bcm.edu	37	chr10	92679010	92679011	+	Frame_Shift_Ins	INS	-	-	T													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	agctttgatctttgttctagINSttttttctttttgagctaaa							TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr10:92679010_92679011insT	ENST00000371697.3	-	3	470_471	c.222_223insA	c.(220-225)aaactafs	p.L75fs		NM_014391.2	NP_055206.2	Q15327	ANKR1_HUMAN	ankyrin repeat domain 1 (cardiac muscle)	75					cardiac muscle tissue morphogenesis (GO:0055008)|cellular lipid metabolic process (GO:0044255)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|skeletal muscle cell differentiation (GO:0035914)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I band (GO:0031674)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|p53 binding (GO:0002039)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|titin binding (GO:0031432)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|prostate(3)|skin(1)	27		Colorectal(252;0.0475)				CTTTGTTCTAGTTTTTTCTTTT	0.302																																					p.L75fs		Pindel	.											ANKRD1,NS,carcinoma,0,1	ANKRD1	50	.	0			c.223_224insA						.			1,4253		0,1,2126						4.9	1			47	1,8245		0,1,4122	no	frameshift	ANKRD1	NM_014391.2		0,2,6248	A1A1,A1R,RR		0.0121,0.0235,0.016				2,12498				SO:0001589	frameshift_variant	27063	exon3			.	X83703	CCDS7412.1	10q23.33	2014-09-17			ENSG00000148677	ENSG00000148677		"Ankyrin repeat domain containing"	15819	protein-coding gene	gene with protein product		609599				7730328	Standard	NM_014391		Approved	C-193, ALRP, CARP, CVARP, MCARP	uc001khe.1	Q15327	OTTHUMG00000018734	ENST00000371697.3:c.223dupA	chr10.hg19:g.92679016_92679016dupT	ENSP00000360762:p.Leu75fs	17.0	0.0		89.0	35.0	NM_014391	Q96LE7	Frame_Shift_Ins	INS	ENST00000371697.3	hg19	CCDS7412.1																																																																																			.	.		0.302	ANKRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049357.1	NM_014391		T	92679011	-	T	92679010	7	5	106	1	0	1	1	0	0	0	0	0	637	1020	36	0	764	0	ANKRD1	10	92679010	Frame_Shift_Ins	INS	-	TCGA-DD-A1EJ-01A-11D-A152-10	170116	92679010	42855737	39	15962										
MUC2	4583	hgsc.bcm.edu	37	chr11	1077628	1077628	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ccgcactacagccccgggctGctcattgagaagagcgatgc	12	14	1	2			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr11:1077628G>A	ENST00000441003.2	+	3	405	c.378G>A	c.(376-378)ctG>ctA	p.L126L	MUC2_ENST00000359061.5_Silent_p.L126L	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	126	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCCCCGGGCTGCTCATTGAGA	0.672																																					p.L126L		Atlas-SNP	.											.	MUC2	614	.	0			c.G378A						.						32	38	36					11																	1077628		1960	4126	6086	SO:0001819	synonymous_variant	4583	exon3			CGGGCTGCTCATT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.378G>A	chr11.hg19:g.1077628G>A		382.0	1.0		82.0	22.0	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.		0.672	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1077628	G	A	1077628	2	1	106	1	0	0	0	0	0	0	0	1	9984	1306	46	3		3	MUC2	11	1077628	Silent	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10		1077628	133928888	40	15963										
OR51I2	390064	hgsc.bcm.edu	37	chr11	5474986	5474986	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	gaaccttctgcctcaatgccCgcaacatcacttttgatgcc	6	15	3	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr11:5474986C>T	ENST00000341449.2	+	1	349	c.268C>T	c.(268-270)Cgc>Tgc	p.R90C	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	90					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCTCAATGCCCGCAACATCAC	0.473																																					p.R90C		Atlas-SNP	.											.	OR51I2	76	.	0			c.C268T						.						133	128	130					11																	5474986		2201	4297	6498	SO:0001583	missense	390064	exon1			AATGCCCGCAACA	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"GPCR / Class A : Olfactory receptors"	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.268C>T	chr11.hg19:g.5474986C>T	ENSP00000341987:p.Arg90Cys	97.0	0.0		123.0	28.0	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	hg19	CCDS31383.1	.	.	.	.	.	.	.	.	.	.	C	10.72	1.430705	0.25726	.	.	ENSG00000187918	ENST00000341449	T	0.38401	1.14	5.57	4.66	0.58398	GPCR, rhodopsin-like superfamily (1);	0.186707	0.35320	N	0.003289	T	0.41166	0.1147	M	0.83223	2.63	0.09310	N	1	D	0.61697	0.99	B	0.43623	0.425	T	0.53201	-0.8472	10	0.87932	D	0	.	7.1608	0.25662	0.2483:0.671:0.0:0.0806	.	90	Q9H344	O51I2_HUMAN	C	90	ENSP00000341987:R90C	ENSP00000341987:R90C	R	+	1	0	OR51I2	5431562	0.000000	0.05858	0.119000	0.21687	0.207000	0.24258	-0.274000	0.08537	1.593000	0.50029	0.650000	0.86243	CGC	.	.		0.473	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754		T	5474986	C	T	5474986	3	4	106	1	0	0	0	0	1	0	0	0	11110	652	23	1	270	1	OR51I2	11	5474986	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	4397358	5474986	129531530	41	15964										
NAV2	89797	hgsc.bcm.edu	37	chr11	19955620	19955620	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	cagctggacggcagacactcCagttcctcttccagcctggc	10	16	1	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr11:19955620C>G	ENST00000396087.3	+	8	1998	c.1899C>G	c.(1897-1899)tcC>tcG	p.S633S	NAV2_ENST00000540292.1_Silent_p.S564S|NAV2_ENST00000396085.1_Silent_p.S610S|NAV2_ENST00000527559.2_Silent_p.S562S|NAV2_ENST00000349880.4_Silent_p.S610S|NAV2_ENST00000360655.4_Silent_p.S546S	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	633	Poly-Ser.				glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						GCAGACACTCCAGTTCCTCTT	0.637																																					p.S633S		Atlas-SNP	.											.	NAV2	255	.	0			c.C1899G						.						49	52	51					11																	19955620		2199	4293	6492	SO:0001819	synonymous_variant	89797	exon8			ACACTCCAGTTCC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.1899C>G	chr11.hg19:g.19955620C>G		316.0	0.0		50.0	30.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	hg19	CCDS58126.1																																																																																			.	.		0.637	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		G	19955620	C	G	19955620	2	3	106	1	0	0	0	0	0	0	0	1	10193	581	21	4		4	NAV2	11	19955620	Silent	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	14480634	19955620	115050896	42	15965										
GDPD4	220032	hgsc.bcm.edu	37	chr11	76969478	76969478	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	attcagagtcgataggaaatCccagttgaagaaggcagggt	13	6	1	3			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr11:76969478C>T	ENST00000376217.2	-	10	1067	c.817G>A	c.(817-819)Gat>Aat	p.D273N	GDPD4_ENST00000315938.4_Missense_Mutation_p.D273N			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	273	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						GATAGGAAATCCCAGTTGAAG	0.438																																					p.D273N		Atlas-SNP	.											.	GDPD4	49	.	0			c.G817A						.						149	144	146					11																	76969478		2200	4292	6492	SO:0001583	missense	220032	exon10			GGAAATCCCAGTT	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.817G>A	chr11.hg19:g.76969478C>T	ENSP00000365390:p.Asp273Asn	33.0	0.0		164.0	93.0	NM_182833	Q7Z5B0	Missense_Mutation	SNP	ENST00000376217.2	hg19		.	.	.	.	.	.	.	.	.	.	C	9.854	1.194494	0.22037	.	.	ENSG00000178795	ENST00000376217;ENST00000315938	T;T	0.30448	1.53;1.53	4.84	-9.68	0.00528	.	1.705610	0.02590	N	0.099851	T	0.20292	0.0488	L	0.45228	1.405	0.09310	N	0.999999	B	0.32467	0.372	B	0.30316	0.114	T	0.05037	-1.0910	10	0.21014	T	0.42	0.3622	8.3392	0.32232	0.0:0.1276:0.1973:0.6751	.	273	Q6W3E5-2	.	N	273	ENSP00000365390:D273N;ENSP00000320815:D273N	ENSP00000320815:D273N	D	-	1	0	GDPD4	76647126	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-1.641000	0.02007	-1.708000	0.01401	-0.367000	0.07326	GAT	.	.		0.438	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833		T	76969478	C	T	76969478	3	4	106	1	0	0	0	0	1	0	0	0	6334	855	30	3	773	3	GDPD4	11	76969478	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	57013858	76969478	58037038	43	15966										
INTS4	92105	hgsc.bcm.edu	37	chr11	77672039	77672039	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ttctgacacgtgggtcttggTcactgaagtaatcccctata	9	10	3	2			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr11:77672039T>A	ENST00000534064.1	-	5	651	c.617A>T	c.(616-618)gAc>gTc	p.D206V	INTS4_ENST00000529807.1_Missense_Mutation_p.D206V	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	206					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			TGGGTCTTGGTCACTGAAGTA	0.403																																					p.D206V		Atlas-SNP	.											.	INTS4	89	.	0			c.A617T						.						225	214	218					11																	77672039		2200	4292	6492	SO:0001583	missense	92105	exon5			TCTTGGTCACTGA	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.617A>T	chr11.hg19:g.77672039T>A	ENSP00000434466:p.Asp206Val	53.0	0.0		195.0	23.0	NM_033547	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	hg19	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.366516	0.82463	.	.	ENSG00000149262	ENST00000534064;ENST00000354849;ENST00000529807	T;T	0.29917	1.55;1.55	4.48	4.48	0.54585	Armadillo-like helical (1);Armadillo-type fold (1);	0.102503	0.64402	D	0.000005	T	0.52677	0.1749	M	0.70275	2.135	0.80722	D	1	D	0.67145	0.996	D	0.67382	0.951	T	0.58578	-0.7612	10	0.87932	D	0	-15.2985	14.2195	0.65818	0.0:0.0:0.0:1.0	.	206	Q96HW7	INT4_HUMAN	V	206;57;206	ENSP00000434466:D206V;ENSP00000433644:D206V	ENSP00000346913:D57V	D	-	2	0	INTS4	77349687	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.146000	0.77373	1.999000	0.58509	0.528000	0.53228	GAC	.	.		0.403	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		A	77672039	T	A	77672039	3	1	106	1	0	0	0	0	1	0	0	0	7789	1667	58	4	2350	4	INTS4	11	77672039	Missense_Mutation	SNP	T	TCGA-DD-A1EJ-01A-11D-A152-10	702561	77672039	57334477	44	15967										
C12orf69	440087	hgsc.bcm.edu	37	chr12	14959587	14959587	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ttcccgcctttttgggttctCtgggtaaaggaagtcacttt	10	9	2	0			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr12:14959587C>G	ENST00000316048.2	-	2	100	c.28G>C	c.(28-30)Gag>Cag	p.E10Q	C12orf60_ENST00000527783.1_Intron|C12orf60_ENST00000330828.2_Intron	NM_001013698.2	NP_001013720.2	A2RU48	SMCO3_HUMAN	single-pass membrane protein with coiled-coil domains 3	10						integral component of membrane (GO:0016021)											TTTGGGTTCTCTGGGTAAAGG	0.388																																					p.E10Q		Atlas-SNP	.											.	.	.	.	0			c.G28C						.						81	81	81					12																	14959587		1829	4091	5920	SO:0001583	missense	0	exon2			GGTTCTCTGGGTA		CCDS41759.1	12p12.3	2013-03-11	2013-03-11	2013-03-11	ENSG00000179256	ENSG00000179256			34401	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 69"	C12orf69			Standard	NM_001013698		Approved	LOC440087	uc001rck.1	A2RU48	OTTHUMG00000167474	ENST00000316048.2:c.28G>C	chr12.hg19:g.14959587C>G	ENSP00000381895:p.Glu10Gln	41.0	0.0		94.0	72.0	NM_001013698	Q8NAI5	Missense_Mutation	SNP	ENST00000316048.2	hg19	CCDS41759.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828948	0.32329	.	.	ENSG00000179256	ENST00000316048	T	0.33865	1.39	5.25	4.34	0.51931	.	0.641612	0.12334	N	0.478087	T	0.20901	0.0503	N	0.12182	0.205	0.21256	N	0.999747	B	0.09022	0.002	B	0.08055	0.003	T	0.17018	-1.0383	10	0.15952	T	0.53	-19.9399	11.3905	0.49811	0.0:0.8093:0.1907:0.0	.	10	A2RU48	CL069_HUMAN	Q	10	ENSP00000381895:E10Q	ENSP00000381895:E10Q	E	-	1	0	C12orf69	14850854	1.000000	0.71417	0.990000	0.47175	0.853000	0.48598	2.512000	0.45485	1.398000	0.46701	0.555000	0.69702	GAG	.	.		0.388	SMCO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394738.1	NM_001013698		G	14959587	C	G	14959587	3	3	106	1	0	0	0	0	1	0	0	0	1713	922	32	4	653	4	C12orf69	12	14959587	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10		14959587	118892308	45	15968										
UGGT2	55757	hgsc.bcm.edu	37	chr13	96599294	96599294	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ttagtgcataaactcacgtgTactatagaaataaatgcttc	6	7	1	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr13:96599294T>C	ENST00000376747.3	-	15	1744	c.1674A>G	c.(1672-1674)gtA>gtG	p.V558V		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	558					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						AACTCACGTGTACTATAGAAA	0.303																																					p.V558V		Atlas-SNP	.											.	UGGT2	127	.	0			c.A1674G						.						48	52	51					13																	96599294		2202	4299	6501	SO:0001819	synonymous_variant	55757	exon15			CACGTGTACTATA	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.1674A>G	chr13.hg19:g.96599294T>C		39.0	0.0		261.0	105.0	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Silent	SNP	ENST00000376747.3	hg19	CCDS9480.1																																																																																			.	.		0.303	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		C	96599294	T	C	96599294	2	2	106	1	0	0	0	0	0	0	0	1	16957	1625	57	2		2	UGGT2	13	96599294	Silent	SNP	T	TCGA-DD-A1EJ-01A-11D-A152-10		96599294	18570584	46	15969										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48063289	48063289	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tacaacacgtctttctcaaaCtccaatgctcacaaagctga	4	13	3	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr15:48063289C>A	ENST00000316364.5	+	19	2968	c.2529C>A	c.(2527-2529)aaC>aaA	p.N843K	SEMA6D_ENST00000537942.1_Missense_Mutation_p.N781K|SEMA6D_ENST00000536845.2_Missense_Mutation_p.N843K|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000389433.2_Missense_Mutation_p.N824K|SEMA6D_ENST00000389432.2_Missense_Mutation_p.N800K|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000358066.4_Missense_Mutation_p.N781K|SEMA6D_ENST00000354744.4_Missense_Mutation_p.N787K|SEMA6D_ENST00000389428.3_Missense_Mutation_p.N768K|SEMA6D_ENST00000558014.1_Missense_Mutation_p.N781K	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	843					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CTTTCTCAAACTCCAATGCTC	0.458																																					p.N843K		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C2529A						.						105	96	99					15																	48063289		2198	4297	6495	SO:0001583	missense	80031	exon19			CTCAAACTCCAAT	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.2529C>A	chr15.hg19:g.48063289C>A	ENSP00000324857:p.Asn843Lys	23.0	0.0		111.0	36.0	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	C	11.11	1.543237	0.27563	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428	T;T;T;T;T;T;T;T	0.16897	2.31;2.34;2.34;2.31;2.31;2.31;2.31;2.32	5.58	2.23	0.28157	.	0.601453	0.16987	N	0.191479	T	0.11281	0.0275	N	0.22421	0.69	0.80722	D	1	B;P;B;P	0.47762	0.43;0.9;0.227;0.622	B;B;B;B	0.42522	0.1;0.39;0.138;0.146	T	0.15723	-1.0427	10	0.29301	T	0.29	.	8.8988	0.35481	0.0:0.6408:0.0:0.3592	.	768;787;843;781	Q8NFY4-3;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;SEM6D_HUMAN;.	K	781;843;843;824;800;787;781;768	ENSP00000442040:N781K;ENSP00000446152:N843K;ENSP00000324857:N843K;ENSP00000374084:N824K;ENSP00000374083:N800K;ENSP00000346786:N787K;ENSP00000350770:N781K;ENSP00000374079:N768K	ENSP00000324857:N843K	N	+	3	2	SEMA6D	45850581	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	0.593000	0.23999	0.712000	0.32039	0.563000	0.77884	AAC	.	.		0.458	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48063289	C	A	48063289	3	1	106	1	0	0	0	0	1	0	0	0	14057	564	20	3	2642	3	SEMA6D	15	48063289	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10		48063289	54468103	47	15970										
GNB5	10681	hgsc.bcm.edu	37	chr15	52476791	52476791	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	agctgagttgttgagacttcTtgaaaactggtctcagagct	11	7	2	4			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr15:52476791T>A	ENST00000261837.7	-	2	148	c.83A>T	c.(82-84)aAg>aTg	p.K28M	RP11-430B1.2_ENST00000560518.1_lincRNA	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	28					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		TTGAGACTTCTTGAAAACTGG	0.378																																					p.K28M		Atlas-SNP	.											.	GNB5	28	.	0			c.A83T						.						129	123	125					15																	52476791		2195	4293	6488	SO:0001583	missense	10681	exon2			GACTTCTTGAAAA	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"WD repeat domain containing"	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.83A>T	chr15.hg19:g.52476791T>A	ENSP00000261837:p.Lys28Met	25.0	0.0		77.0	37.0	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Missense_Mutation	SNP	ENST00000261837.7	hg19	CCDS10149.1	.	.	.	.	.	.	.	.	.	.	T	14.42	2.528624	0.44969	.	.	ENSG00000069966	ENST00000261837	T	0.61627	0.09	5.78	4.63	0.57726	.	0.222920	0.29480	N	0.012030	T	0.46308	0.1386	L	0.36672	1.1	0.80722	D	1	B	0.19445	0.036	B	0.17979	0.02	T	0.47235	-0.9133	10	0.59425	D	0.04	-28.8729	10.0548	0.42239	0.2612:0.0:0.0:0.7388	.	28	O14775	GBB5_HUMAN	M	28	ENSP00000261837:K28M	ENSP00000261837:K28M	K	-	2	0	GNB5	50264083	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.474000	0.60203	2.195000	0.70347	0.528000	0.53228	AAG	.	.		0.378	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			A	52476791	T	A	52476791	3	1	106	1	0	0	0	0	1	0	0	0	6529	1609	56	4	1152	4	GNB5	15	52476791	Missense_Mutation	SNP	T	TCGA-DD-A1EJ-01A-11D-A152-10	4413502	52476791	50054601	48	15971										
DNAJA2	10294	hgsc.bcm.edu	37	chr16	46991020	46991020	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tatcattataggcttcacgcCtctgaccacctcctgagcct	6	15	3	2			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr16:46991020C>A	ENST00000317089.5	-	9	1375	c.1160G>T	c.(1159-1161)aGg>aTg	p.R387M		NM_005880.3	NP_005871.1	O60884	DNJA2_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 2	387					positive regulation of cell proliferation (GO:0008284)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	14		all_cancers(37;0.00125)|all_lung(18;0.00338)|all_epithelial(9;0.00358)|Lung NSC(13;0.0309)|Breast(268;0.116)				GGCTTCACGCCTCTGACCACC	0.478																																					p.R387M		Atlas-SNP	.											.	DNAJA2	28	.	0			c.G1160T						.						268	262	264					16																	46991020		2203	4300	6503	SO:0001583	missense	10294	exon9			TCACGCCTCTGAC	AF116720	CCDS10726.1	16q12.1	2011-09-02			ENSG00000069345	ENSG00000069345		"Heat shock proteins / DNAJ (HSP40)"	14884	protein-coding gene	gene with protein product		611322				9710638, 11147971	Standard	NM_005880		Approved	HIRIP4, DNAJ, CPR3, DNJ3	uc002eeo.2	O60884	OTTHUMG00000133104	ENST00000317089.5:c.1160G>T	chr16.hg19:g.46991020C>A	ENSP00000314030:p.Arg387Met	18.0	0.0		143.0	66.0	NM_005880	B2R7L7|O14711	Missense_Mutation	SNP	ENST00000317089.5	hg19	CCDS10726.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.739595	0.89573	.	.	ENSG00000069345	ENST00000317089	T	0.38722	1.12	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.60353	0.2262	M	0.78456	2.415	0.80722	D	1	D	0.57571	0.98	P	0.52672	0.706	T	0.64769	-0.6329	10	0.62326	D	0.03	-18.9488	19.5403	0.95271	0.0:1.0:0.0:0.0	.	387	O60884	DNJA2_HUMAN	M	387	ENSP00000314030:R387M	ENSP00000314030:R387M	R	-	2	0	DNAJA2	45548521	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.610000	0.82949	2.623000	0.88846	0.561000	0.74099	AGG	.	.		0.478	DNAJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256769.2			A	46991020	C	A	46991020	3	1	106	1	0	0	0	0	1	0	0	0	4614	681	24	3	82	3	DNAJA2	16	46991020	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10		46991020	43363733	49	15972										
TMEM132E	124842	hgsc.bcm.edu	37	chr17	32956067	32956067	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ttggagatcttgcagctggaCtttgaaatggagaacttcac	11	7	2	3			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr17:32956067C>A	ENST00000321639.5	+	5	1240	c.912C>A	c.(910-912)gaC>gaA	p.D304E		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	304						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TGCAGCTGGACTTTGAAATGG	0.627																																					p.D304E		Atlas-SNP	.											.	TMEM132E	122	.	0			c.C912A						.						84	84	84					17																	32956067		2203	4300	6503	SO:0001583	missense	124842	exon5			GCTGGACTTTGAA	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.912C>A	chr17.hg19:g.32956067C>A	ENSP00000316532:p.Asp304Glu	466.0	0.0		138.0	27.0	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	hg19	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	c	10.69	1.420108	0.25552	.	.	ENSG00000181291	ENST00000321639	T	0.21361	2.01	4.51	4.51	0.55191	.	0.097095	0.64402	D	0.000002	T	0.19167	0.0460	L	0.52364	1.645	0.44492	D	0.997435	P	0.41393	0.748	B	0.40101	0.319	T	0.01545	-1.1328	10	0.23302	T	0.38	-35.2459	10.179	0.42957	0.0:0.8974:0.0:0.1026	.	304	Q6IEE7	T132E_HUMAN	E	304	ENSP00000316532:D304E	ENSP00000316532:D304E	D	+	3	2	TMEM132E	29980180	1.000000	0.71417	1.000000	0.80357	0.024000	0.10985	2.339000	0.43965	2.502000	0.84385	0.447000	0.29281	GAC	.	.		0.627	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		A	32956067	C	A	32956067	3	1	106	1	0	0	0	0	1	0	0	0	16063	564	20	3	930	3	TMEM132E	17	32956067	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10		32956067	48239143	50	15973										
CDC27	996	hgsc.bcm.edu	37	chr17	45234594	45234729	+	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	cactagaatataagacacttAcaattgtgtcctggggtgtt					rs149474782|rs113608268|rs370849730|rs78395997|rs76624491|rs370261409|rs75353677|rs368304141|rs376818791|rs372212798|rs375653477|rs374472811|rs76359747|rs147617501|rs374614181|rs78108688|rs142987740|rs143453365|rs75990396|rs144985864|rs367644695|rs202182614|rs139751753|rs11570485|rs372926889|rs140171160|rs368750026|rs201098929|rs199899451|rs75175938|rs200340309|rs537990668	byFrequency	TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr17:45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	ENST00000066544.3	-	6	590_724	c.497_631delAGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG	c.(496-633)cagttcttacggaaacaccccaggacacaattgtaagtgtcttatattctagtgttcaaaatattatgaaaactacaaagaatgatctgaactaaataatatattgtgaatgacttggtagaaattttctgtttcaga>cga	p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	CDC27_ENST00000531206.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000527547.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000446365.2_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF105fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.T167T(7)|p.T171T(3)|p.V201I(2)|p.E199E(2)|p.T200T(2)|p.L173S(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACTGTCTCAGGCTGTCTGTGAGATAAACTATGATTAGGTACTTGTGTTGTGCAAGAGTTGGGCAGACAGTTGCTAAAGTTCTGTAAAGATGTGAATTTAAATGTTTGGTCAGGATC	0.342																																					p.201_211del		Pindel	.											.	CDC27	337	.	17	Substitution - coding silent(14)|Substitution - Missense(3)	large_intestine(6)|prostate(6)|kidney(4)|NS(1)	c.601_631del						.																																			SO:0001630	splice_region_variant	996	exon6			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.631-104AGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG>-	chr17.hg19:g.45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT		30.0	0.0		214.0	19.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.342	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Frame_Shift_Del	-	45234729	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	45234594	8	5	106	1	0	1	0	1	0	0	1	0	3068	405	14	0	1916	0	CDC27	17	45234594	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	TCGA-DD-A1EJ-01A-11D-A152-10	12278527	45234594	35960616	51	15974										
APOH	350	hgsc.bcm.edu	37	chr17	64222231	64222231	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ttctaagattccagcaaaagGacatactctggctgtgatac	8	9	2	2	rs55645281		TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr17:64222231G>A	ENST00000205948.6	-	3	290	c.253C>T	c.(253-255)Cct>Tct	p.P85S		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	85	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			CCAGCAAAAGGACATACTCTG	0.318																																					p.P85S	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											APOH,NS,malignant_melanoma,0,1	APOH	45	.	0			c.C253T						.						91	84	86					17																	64222231		2203	4300	6503	SO:0001583	missense	350	exon3			CAAAAGGACATAC		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"Apolipoproteins"	616	protein-coding gene	gene with protein product	"beta-2-glycoprotein I"	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.253C>T	chr17.hg19:g.64222231G>A	ENSP00000205948:p.Pro85Ser	33.0	0.0		111.0	76.0	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	hg19	CCDS11663.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.039753	0.35989	.	.	ENSG00000091583	ENST00000205948	T	0.66099	-0.19	5.55	5.55	0.83447	Complement control module (2);Sushi/SCR/CCP (3);	0.050624	0.85682	D	0.000000	T	0.67011	0.2848	L	0.56396	1.775	0.46260	D	0.998959	D	0.57899	0.981	P	0.53266	0.722	T	0.61806	-0.6987	10	0.15952	T	0.53	.	15.0313	0.71708	0.0:0.0:1.0:0.0	rs55645281	85	P02749	APOH_HUMAN	S	85	ENSP00000205948:P85S	ENSP00000205948:P85S	P	-	1	0	APOH	61652693	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.458000	0.53014	2.611000	0.88343	0.563000	0.77884	CCT	.	.		0.318	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042		A	64222231	G	A	64222231	3	1	106	1	0	0	0	0	1	0	0	0	804	1174	41	3	808	3	APOH	17	64222231	Missense_Mutation	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10	18987637	64222231	16972979	52	15975										
HELZ	9931	hgsc.bcm.edu	37	chr17	65214794	65214794	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tggacaaggccctgtgaagtCtgccatggagtactggccaa	13	10	1	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr17:65214794C>A	ENST00000358691.5	-	4	293	c.127G>T	c.(127-129)Gac>Tac	p.D43Y	HELZ_ENST00000580662.1_5'UTR|HELZ_ENST00000580168.1_Missense_Mutation_p.D43Y	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	43						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					CCTGTGAAGTCTGCCATGGAG	0.458																																					p.D43Y		Atlas-SNP	.											.	HELZ	160	.	0			c.G127T						.						139	133	135					17																	65214794		1910	4120	6030	SO:0001583	missense	9931	exon4			TGAAGTCTGCCAT	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.127G>T	chr17.hg19:g.65214794C>A	ENSP00000351524:p.Asp43Tyr	31.0	0.0		169.0	33.0	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	c	10.18	1.278784	0.23307	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	T;T	0.73363	-0.74;-0.74	5.14	4.08	0.47627	.	0.294619	0.37577	N	0.002035	T	0.48750	0.1517	N	0.08118	0	0.28778	N	0.9	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.0;0.003;0.0	T	0.29792	-1.0000	10	0.45353	T	0.12	-16.3031	3.4952	0.07653	0.158:0.5465:0.1778:0.1177	.	43;43;43	B7ZLW2;F8WBX6;P42694	.;.;HELZ_HUMAN	Y	43	ENSP00000351524:D43Y;ENSP00000411144:D43Y	ENSP00000351524:D43Y	D	-	1	0	HELZ	62645256	0.526000	0.26298	0.857000	0.33713	0.825000	0.46686	0.971000	0.29396	2.382000	0.81193	0.460000	0.39030	GAC	.	.		0.458	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65214794	C	A	65214794	3	1	106	1	0	0	0	0	1	0	0	0	7058	913	32	3	5821	3	HELZ	17	65214794	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	992563	65214794	15980416	53	15976										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43435550	43435550	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	atactgacctgctgagctttGggggtcagatgtaattcaga	12	7	2	4			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr18:43435550G>C	ENST00000282041.5	-	43	7579	c.7545C>G	c.(7543-7545)ccC>ccG	p.P2515P	EPG5_ENST00000585906.1_5'Flank	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	2515					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						GCTGAGCTTTGGGGGTCAGAT	0.527																																					p.P2515P		Atlas-SNP	.											.	EPG5	199	.	0			c.C7545G						.						55	57	57					18																	43435550		1933	4149	6082	SO:0001819	synonymous_variant	57724	exon43			AGCTTTGGGGGTC	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.7545C>G	chr18.hg19:g.43435550G>C		27.0	0.0		75.0	11.0	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	hg19	CCDS11926.2																																																																																			.	.		0.527	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43435550	G	C	43435550	2	2	106	1	0	0	0	0	0	0	0	1	8258	1335	47	4		4	KIAA1632	18	43435550	Silent	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10		43435550	34641698	54	15977										
LMAN1	3998	hgsc.bcm.edu	37	chr18	56998712	56998712	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	acaaatataatgaagtggacCgtagacaaacatgatggaaa	9	5	0	3			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr18:56998712C>A	ENST00000251047.5	-	12	2151	c.1434G>T	c.(1432-1434)acG>acT	p.T478T		NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	478					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	TGAAGTGGACCGTAGACAAAC	0.348																																					p.T478T		Atlas-SNP	.											.	LMAN1	57	.	0			c.G1434T						.						131	125	127					18																	56998712		2203	4300	6503	SO:0001819	synonymous_variant	3998	exon12			GTGGACCGTAGAC	X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"endoplasmic reticulum-golgi intermediate compartment protein 53"	601567	"coagulation factor V-factor VIII combined deficiency"	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.1434G>T	chr18.hg19:g.56998712C>A		40.0	0.0		185.0	21.0	NM_005570	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Silent	SNP	ENST00000251047.5	hg19	CCDS11974.1																																																																																			.	.		0.348	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570		A	56998712	C	A	56998712	2	1	106	1	0	0	0	0	0	0	0	1	8845	639	23	1		1	LMAN1	18	56998712	Silent	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	13563162	56998712	21078536	55	15978										
SOCS6	9306	hgsc.bcm.edu	37	chr18	67992584	67992585	+	Frame_Shift_Ins	INS	-	-	C													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	attcagtatactgtgcctttINSagatgaggggatgtatcctt							TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr18:67992584_67992585insC	ENST00000397942.3	+	2	996_997	c.680_681insC	c.(679-684)ttagatfs	p.LD227fs	SOCS6_ENST00000582322.1_Frame_Shift_Ins_p.LD227fs	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	227					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				ACTGTGCCTTTAGATGAGGGGA	0.505																																					p.L227fs	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-INDEL	.											.	SOCS6	54	.	0			c.680_681insC						.																																			SO:0001589	frameshift_variant	9306	exon2			.	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	Exception_encountered	chr18.hg19:g.67992584_67992585insC	ENSP00000381034:p.Leu227fs	185.0	0.0		110.0	33.0	NM_004232	Q8WUM3	Frame_Shift_Ins	INS	ENST00000397942.3	hg19	CCDS11998.1																																																																																			.	.		0.505	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			C	67992585	-	C	67992584	7	5	106	1	0	1	1	0	0	0	0	0	14933	1764	61	0	682	0	SOCS6	18	67992584	Frame_Shift_Ins	INS	-	TCGA-DD-A1EJ-01A-11D-A152-10	10993872	67992584	10084664	56	15979	68	3	1	16		4	2	22	N	GATGAGGGGATGTATCCTTTG_AGATGAGGGGATGTATCCTTTG_-	4.20578e-05
SOCS6	9306	hgsc.bcm.edu	37	chr18	67992585	67992606	+	Frame_Shift_Del	DEL	AGATGAGGGGATGTATCCTTTG	AGATGAGGGGATGTATCCTTTG	-													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	attcagtatactgtgcctttAgatgaggggatgtatccttt					rs368115526|rs201797599		TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	AGATGAGGGGATGTATCCTTTG	AGATGAGGGGATGTATCCTTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr18:67992585_67992606delAGATGAGGGGATGTATCCTTTG	ENST00000397942.3	+	2	997_1018	c.681_702delAGATGAGGGGATGTATCCTTTG	c.(679-702)ttagatgaggggatgtatcctttgfs	p.LDEGMYPL227fs	SOCS6_ENST00000582322.1_Frame_Shift_Del_p.LDEGMYPL227fs	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	227					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				CTGTGCCTTTAGATGAGGGGATGTATCCTTTGGAAGGATCAC	0.514																																					p.227_234del	Melanoma(84;1024 1361 24382 36583 42651)	Pindel	.											.	SOCS6	54	.	0			c.680_701del						.																																			SO:0001589	frameshift_variant	9306	exon2			.	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.681_702delAGATGAGGGGATGTATCCTTTG	chr18.hg19:g.67992585_67992606delAGATGAGGGGATGTATCCTTTG	ENSP00000381034:p.Leu227fs	213.0	0.0		119.0	54.0	NM_004232	Q8WUM3	Frame_Shift_Del	DEL	ENST00000397942.3	hg19	CCDS11998.1																																																																																			.	.		0.514	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			-	67992606	AGATGAGGGGATGTATCCTTTG	-	67992585	7	5	106	1	0	1	0	1	0	0	0	0	14933	417	15	0	683	0	SOCS6	18	67992585	Frame_Shift_Del	DEL	AGATGAGGGGATGTATCCTTTG	TCGA-DD-A1EJ-01A-11D-A152-10	1	67992585	10084663	57	15980	68	3	1	16		4	2	22	N	GATGAGGGGATGTATCCTTTG_AGATGAGGGGATGTATCCTTTG_-	4.20578e-05
SOCS6	9306	hgsc.bcm.edu	37	chr18	67992586	67992606	+	In_Frame_Del	DEL	GATGAGGGGATGTATCCTTTG	GATGAGGGGATGTATCCTTTG	-													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ttcagtatactgtgcctttaGatgaggggatgtatcctttg					rs368115526|rs201797599		TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	GATGAGGGGATGTATCCTTTG	GATGAGGGGATGTATCCTTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr18:67992586_67992606delGATGAGGGGATGTATCCTTTG	ENST00000397942.3	+	2	998_1018	c.682_702delGATGAGGGGATGTATCCTTTG	c.(682-702)gatgaggggatgtatcctttgdel	p.DEGMYPL228del	SOCS6_ENST00000582322.1_In_Frame_Del_p.DEGMYPL228del	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	228					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				TGTGCCTTTAGATGAGGGGATGTATCCTTTGGAAGGATCAC	0.511																																					p.227_234del	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-INDEL	.											.	SOCS6	54	.	0			c.681_701del						.																																			SO:0001651	inframe_deletion	9306	exon2			.	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.682_702delGATGAGGGGATGTATCCTTTG	chr18.hg19:g.67992586_67992606delGATGAGGGGATGTATCCTTTG	ENSP00000381034:p.Asp228_Leu234del	186.0	0.0		96.0	28.0	NM_004232	Q8WUM3	In_Frame_Del	DEL	ENST00000397942.3	hg19	CCDS11998.1																																																																																			.	.		0.511	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			-	67992606	GATGAGGGGATGTATCCTTTG	-	67992586	7	5	106	1	0	1	0	1	0	0	0	0	14933	942	33	0	684	0	SOCS6	18	67992586	In_Frame_Del	DEL	GATGAGGGGATGTATCCTTTG	TCGA-DD-A1EJ-01A-11D-A152-10	1	67992586	10084662	58	15981	68	3	1	16		4	2	22	N	GATGAGGGGATGTATCCTTTG_AGATGAGGGGATGTATCCTTTG_-	4.20578e-05
SOCS6	9306	hgsc.bcm.edu	37	chr18	67992605	67992606	+	Frame_Shift_Ins	INS	-	-	C													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	gatgaggggatgtatcctttINSggaaggatcacggagctatt							TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr18:67992605_67992606insC	ENST00000397942.3	+	2	1017_1018	c.701_702insC	c.(700-705)ttggaafs	p.LE234fs	SOCS6_ENST00000582322.1_Frame_Shift_Ins_p.LE234fs	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	234					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				ATGTATCCTTTGGAAGGATCAC	0.515																																					p.L234fs	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-INDEL	.											.	SOCS6	54	.	0			c.701_702insC						.																																			SO:0001589	frameshift_variant	9306	exon2			.	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	Exception_encountered	chr18.hg19:g.67992605_67992606insC	ENSP00000381034:p.Leu234fs	236.0	0.0		124.0	34.0	NM_004232	Q8WUM3	Frame_Shift_Ins	INS	ENST00000397942.3	hg19	CCDS11998.1																																																																																			.	.		0.515	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			C	67992606	-	C	67992605	7	5	106	1	0	1	1	0	0	0	0	0	14933	1821	63	0	703	0	SOCS6	18	67992605	Frame_Shift_Ins	INS	-	TCGA-DD-A1EJ-01A-11D-A152-10	19	67992605	10084643	59	15982			1	16		4	2	22	N	GATGAGGGGATGTATCCTTTG_AGATGAGGGGATGTATCCTTTG_-	4.20578e-05
GRIN3B	116444	hgsc.bcm.edu	37	chr19	1004576	1004576	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ccccgtgtgggtgacaggcaGctcccaggtacacatgtctc	12	14	1	1			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr19:1004576G>A	ENST00000234389.3	+	3	1095	c.1076G>A	c.(1075-1077)aGc>aAc	p.S359N	AC004528.4_ENST00000588380.1_RNA|GRIN3B_ENST00000588335.1_3'UTR	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	359					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GTGACAGGCAGCTCCCAGGTA	0.706																																					p.S359N		Atlas-SNP	.											.	GRIN3B	46	.	0			c.G1076A						.						17	17	17					19																	1004576		2184	4272	6456	SO:0001583	missense	116444	exon3			CAGGCAGCTCCCA		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.1076G>A	chr19.hg19:g.1004576G>A	ENSP00000234389:p.Ser359Asn	225.0	0.0		44.0	12.0	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	hg19	CCDS32861.1	.	.	.	.	.	.	.	.	.	.	G	1.505	-0.551022	0.03996	.	.	ENSG00000116032	ENST00000234389	D	0.83591	-1.74	4.6	2.25	0.28309	.	2.023840	0.02223	N	0.064182	T	0.73776	0.3630	L	0.36672	1.1	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.57528	-0.7796	10	0.02654	T	1	.	7.6082	0.28113	0.3028:0.5331:0.1641:0.0	.	359	O60391	NMD3B_HUMAN	N	359	ENSP00000234389:S359N	ENSP00000234389:S359N	S	+	2	0	GRIN3B	955576	0.000000	0.05858	0.312000	0.25196	0.116000	0.19942	0.244000	0.18124	0.915000	0.36847	-0.507000	0.04495	AGC	.	.		0.706	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2			A	1004576	G	A	1004576	3	1	106	1	0	0	0	0	1	0	0	0	6793	971	34	3	1086	3	GRIN3B	19	1004576	Missense_Mutation	SNP	G	TCGA-DD-A1EJ-01A-11D-A152-10		1004576	58124407	60	15983										
C19orf42	79086	hgsc.bcm.edu	37	chr19	16770916	16770917	+	Missense_Mutation	DNP	GA	GA	TT													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ccgaacagcaggatgtctccGatcatcgttacggccgaagc					rs11555682	byFrequency	TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr19:16770916_16770917GA>TT	ENST00000487416.2	-	1	51_52	c.5_6TC>AA	c.(4-6)aTC>aAA	p.I2K	SMIM7_ENST00000397349.2_5'Flank|CTC-429P9.4_ENST00000600705.1_Missense_Mutation_p.I2K|CTC-429P9.4_ENST00000593962.1_5'Flank|SMIM7_ENST00000358726.6_Missense_Mutation_p.I2K|SMIM7_ENST00000597711.1_Missense_Mutation_p.I2K|TMEM38A_ENST00000187762.2_5'Flank	NM_024104.3	NP_077009.2	Q9BQ49	SMIM7_HUMAN	small integral membrane protein 7	2						integral component of membrane (GO:0016021)											GGATGTCTCCGATCATCGTTAC	0.609																																					p.I2I|p.I2N		Atlas-SNP	.											.	.	.	.	0			c.C6A|c.T5A						.																																			SO:0001583	missense	79086	exon1			GTCTCCGATCATC|TCTCCGATCATCG	AK025602	CCDS12348.2, CCDS74307.1	19p13.11	2012-10-26	2012-10-26	2012-10-26	ENSG00000214046	ENSG00000214046			28419	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 42"	C19orf42		12477932	Standard	NM_024104		Approved	MGC2747	uc002ner.3	Q9BQ49	OTTHUMG00000149895	ENST00000487416.2:c.5_6delinsTT	chr19.hg19:g.16770916_16770917delinsTT	ENSP00000417147:p.Ile2Lys	304.0|302.0	0.0		51.0	13.0	NM_024104	A8MX44	Silent|Missense_Mutation	SNP	ENST00000487416.2	hg19	CCDS12348.2																																																																																			.	.		0.609	SMIM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313801.2	NM_024104		TT	16770917	GA	TT	16770916	3	4	106	1	0	0	0	0	1	0	0	0	1927	1048	37	1	241	1	C19orf42	19	16770916	Missense_Mutation	DNP	GA	TCGA-DD-A1EJ-01A-11D-A152-10	15766340	16770916	42358067	61	15984										
LARGE	9215	hgsc.bcm.edu	37	chr22	33960897	33960897	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ggcaaaggtgatatccgtgtCaaggacgatgactctctcca	11	10	2	2			TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr22:33960897C>T	ENST00000354992.2	-	7	1295	c.724G>A	c.(724-726)Gac>Aac	p.D242N	LARGE_ENST00000402320.1_Missense_Mutation_p.D242N|LARGE_ENST00000452586.2_Missense_Mutation_p.D41N|LARGE_ENST00000437602.2_Missense_Mutation_p.D242N|LARGE_ENST00000337431.2_Missense_Mutation_p.D242N|LARGE_ENST00000397394.2_Missense_Mutation_p.D242N	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	242					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				ATATCCGTGTCAAGGACGATG	0.473																																					p.D242N	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											.	LARGE	98	.	0			c.G724A						.						141	122	129					22																	33960897		2203	4300	6503	SO:0001583	missense	9215	exon7			CCGTGTCAAGGAC	AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"Glycosyltransferase family 8 domain containing"	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.724G>A	chr22.hg19:g.33960897C>T	ENSP00000347088:p.Asp242Asn	13.0	0.0		119.0	46.0	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	ENST00000354992.2	hg19	CCDS13912.1	.	.	.	.	.	.	.	.	.	.	C	36	5.793450	0.96952	.	.	ENSG00000133424	ENST00000354992;ENST00000337431;ENST00000397394;ENST00000402320;ENST00000452586;ENST00000437602;ENST00000421768	D;D;D;D;D;D;D	0.92545	-3.06;-3.06;-3.06;-3.06;-3.06;-3.06;-3.06	6.16	6.16	0.99307	.	0.082524	0.85682	D	0.000000	D	0.97532	0.9192	H	0.94886	3.595	0.80722	D	1	D;D;D;D	0.89917	1.0;0.982;1.0;1.0	D;D;D;D	0.85130	0.997;0.968;0.995;0.995	D	0.97567	1.0102	10	0.87932	D	0	-5.881	20.8598	0.99761	0.0:1.0:0.0:0.0	.	242;41;242;242	B7Z2I9;E9PH73;O95461-2;O95461	.;.;.;LARGE_HUMAN	N	242;242;242;242;41;242;41	ENSP00000347088:D242N;ENSP00000336636:D242N;ENSP00000380549:D242N;ENSP00000385223:D242N;ENSP00000407917:D41N;ENSP00000388544:D242N;ENSP00000403841:D41N	ENSP00000336636:D242N	D	-	1	0	LARGE	32290897	1.000000	0.71417	0.991000	0.47740	0.996000	0.88848	7.414000	0.80117	2.937000	0.99478	0.650000	0.86243	GAC	.	.		0.473	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		T	33960897	C	T	33960897	3	4	106	1	0	0	0	0	1	0	0	0	8636	826	29	3	1586	3	LARGE	22	33960897	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10		33960897	17343669	62	15985										
CYB5R3	1727	hgsc.bcm.edu	37	chr22	43024254	43024254	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	ctgagacatcttccctccagCgggaaacttgggatgggtgt	13	10	1	1	rs367914897		TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chr22:43024254C>T	ENST00000352397.5	-	5	619	c.367G>A	c.(367-369)Gct>Act	p.A123T	CYB5R3_ENST00000396303.3_Missense_Mutation_p.A100T|CYB5R3_ENST00000361740.4_Missense_Mutation_p.A156T|CYB5R3_ENST00000402438.1_Missense_Mutation_p.A100T|CYB5R3_ENST00000407332.1_Missense_Mutation_p.A100T|CYB5R3_ENST00000407623.3_Missense_Mutation_p.A100T	NM_000398.6	NP_000389.1	P00387	NB5R3_HUMAN	cytochrome b5 reductase 3	123	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				blood circulation (GO:0008015)|cholesterol biosynthetic process (GO:0006695)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|hemoglobin complex (GO:0005833)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|FAD binding (GO:0071949)|flavin adenine dinucleotide binding (GO:0050660)|NAD binding (GO:0051287)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6					Flavin adenine dinucleotide(DB03147)	TTCCCTCCAGCGGGAAACTTG	0.597																																					p.A156T		Atlas-SNP	.											.	CYB5R3	31	.	0			c.G466A						.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	147	146	146		367,298,466,298,298	2.9	0.1	22		146	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,missense,missense	CYB5R3	NM_000398.6,NM_001129819.2,NM_001171660.1,NM_001171661.1,NM_007326.4	58,58,58,58,58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign,benign,benign	123/302,100/279,156/335,100/279,100/279	43024254	2,13004	2203	4300	6503	SO:0001583	missense	1727	exon5			CTCCAGCGGGAAA	M16461	CCDS14040.1, CCDS33658.1, CCDS54535.1	22q13.2	2012-10-02		2005-07-13	ENSG00000100243	ENSG00000100243	1.6.2.2		2873	protein-coding gene	gene with protein product		613213	"diaphorase (NADH) (cytochrome b-5 reductase)"	DIA1		2479590, 3268037	Standard	NM_001129819		Approved		uc011aps.2	P00387	OTTHUMG00000150745	ENST00000352397.5:c.367G>A	chr22.hg19:g.43024254C>T	ENSP00000338461:p.Ala123Thr	207.0	0.0		78.0	8.0	NM_001171660	B1AHF2|B7Z7L3|O75675|Q8TDL8|Q8WTS8|Q9UEN4|Q9UEN5|Q9UL55|Q9UL56	Missense_Mutation	SNP	ENST00000352397.5	hg19	CCDS33658.1	.	.	.	.	.	.	.	.	.	.	C	16.24	3.067960	0.55539	0.0	2.33E-4	ENSG00000100243	ENST00000361740;ENST00000396303;ENST00000352397;ENST00000407623;ENST00000407332;ENST00000402438;ENST00000438270	D;D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	3.92	2.9	0.33743	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);Oxidoreductase, FAD-binding domain (1);	0.285135	0.38164	N	0.001782	T	0.76428	0.3986	L	0.60957	1.885	0.28537	N	0.912314	P;B	0.49447	0.924;0.023	B;B	0.29353	0.101;0.008	T	0.74315	-0.3705	10	0.59425	D	0.04	-4.9064	11.1764	0.48601	0.0:0.9071:0.0:0.0929	.	156;123	B7Z7L3;P00387	.;NB5R3_HUMAN	T	156;100;123;100;100;100;100	ENSP00000354468:A156T;ENSP00000379597:A100T;ENSP00000338461:A123T;ENSP00000384834:A100T;ENSP00000384457:A100T;ENSP00000385679:A100T;ENSP00000403439:A100T	ENSP00000338461:A123T	A	-	1	0	CYB5R3	41354198	0.992000	0.36948	0.072000	0.20136	0.827000	0.46813	3.627000	0.54252	1.234000	0.43709	0.555000	0.69702	GCT	.	.		0.597	CYB5R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320439.1			T	43024254	C	T	43024254	3	4	106	1	0	0	0	0	1	0	0	0	4130	768	27	1	558	1	CYB5R3	22	43024254	Missense_Mutation	SNP	C	TCGA-DD-A1EJ-01A-11D-A152-10	9063357	43024254	8280312	63	15986										
GJB1	2705	hgsc.bcm.edu	37	chrX	70443636	70443637	+	In_Frame_Ins	INS	-	-	TCATCT													0.032258064516129	2	1	0.529794149512459	1.14788732394366	0.344366197183099	1	1	0	tggccgagtatggctctcggINStcatcttcatcttcagaatc							TCGA-DD-A1EJ-01A-11D-A152-10	TCGA-DD-A1EJ-10A-01D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c681cd9-25fb-42ac-aa6b-bb962882fa22	ff037e6b-c763-416f-91ef-bf0ec01a4225	g.chrX:70443636_70443637insTCATCT	ENST00000374022.3	+	2	174_175	c.79_80insTCATCT	c.(79-81)gtc>gTCATCTtc	p.31_32insIF	GJB1_ENST00000374029.1_In_Frame_Ins_p.31_32insIF|GJB1_ENST00000361726.6_In_Frame_Ins_p.31_32insIF	NM_001097642.2	NP_001091111.1	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa	31					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)|purine ribonucleotide transport (GO:0015868)|transport (GO:0006810)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(1)	10	Renal(35;0.156)					ATGGCTCTCGGTCATCTTCATC	0.53																																					p.V27delinsVIF		Atlas-Indel,Pindel	.											.	GJB1	21	.	0			c.79_80insTCATCT						.																																			SO:0001652	inframe_insertion	2705	exon2			.	X04325	CCDS14408.1	Xq13.1	2014-09-17	2007-01-16		ENSG00000169562	ENSG00000169562		"Ion channels / Gap junction proteins (connexins)"	4283	protein-coding gene	gene with protein product	"Charcot-Marie-Tooth neuropathy, X-linked", "connexin 32"	304040	"gap junction protein, beta 1, 32kD (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)", "gap junction protein, beta 1, 32kDa (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)", "gap junction protein, beta 1, 32kDa (connexin 32)"	CMTX1, CMTX		1319395	Standard	NM_000166		Approved	CX32	uc004dzf.3	P08034	OTTHUMG00000021797	ENST00000374022.3:c.86_91dupTCATCT	chrX.hg19:g.70443637_70443642dupTCATCT	ENSP00000363134:p.Ile30_Phe31dup	322.0	0.0		97.0	40.0	NM_001097642	B2R8R2|D3DVV2|Q5U0S4	In_Frame_Ins	INS	ENST00000374022.3	hg19	CCDS14408.1																																																																																			.	.		0.53	GJB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057133.1	NM_000166		TCATCT	70443637	-	TCATCT	70443636	7	5	106	1	0	1	1	0	0	0	0	0	6415	1261	44	0	81	0	GJB1	23	70443636	In_Frame_Ins	INS	-	TCGA-DD-A1EJ-01A-11D-A152-10		70443636	84826924	64	15987										
SLC25A24	29957	hgsc.bcm.edu	37	chr1	108735196	108735196	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	aaaatgtccaaggtcccatcCttgttatagtccaggtacca	7	11	0	0	rs150343087	byFrequency	TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr1:108735196C>A	ENST00000565488.1	-	2	403				SLC25A24_ENST00000370041.4_Missense_Mutation_p.K16N	NM_013386.4	NP_037518.3	Q6NUK1	SCMC1_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24						ATP transport (GO:0015867)|cellular response to calcium ion (GO:0071277)|cellular response to oxidative stress (GO:0034599)|mitochondrial transport (GO:0006839)|regulation of cell death (GO:0010941)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP transmembrane transporter activity (GO:0005347)|calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)		AGGTCCCATCCTTGTTATAGT	0.562																																					p.K16N		Atlas-SNP	.											.	SLC25A24	65	.	0			c.G48T						.						233	217	223					1																	108735196		2182	4133	6315	SO:0001627	intron_variant	29957	exon1			CCCATCCTTGTTA	AJ619961	CCDS786.1, CCDS41361.1	1p13.2	2013-05-22			ENSG00000085491	ENSG00000085491		"Solute carriers", "EF-hand domain containing"	20662	protein-coding gene	gene with protein product		608744				15123600	Standard	NM_013386		Approved	DKFZp586G0123, APC1	uc001dvn.5	Q6NUK1	OTTHUMG00000011013	ENST00000565488.1:c.184-6620G>T	chr1.hg19:g.108735196C>A		107.0	0.0		108.0	54.0	NM_213651	B7ZAI9|Q5T331|Q5T485|Q6PJJ9|Q705K4|Q9P129	Missense_Mutation	SNP	ENST00000565488.1	hg19	CCDS41361.1	.	.	.	.	.	.	.	.	.	.	C	4.066	0.010017	0.07912	.	.	ENSG00000085491	ENST00000370041	T	0.70399	-0.48	3.48	-6.96	0.01622	.	.	.	.	.	T	0.19046	0.0457	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.08106	-1.0738	8	0.18276	T	0.48	.	2.8286	0.05492	0.1357:0.4097:0.2752:0.1793	.	16	Q6NUK1-2	.	N	16	ENSP00000359058:K16N	ENSP00000359058:K16N	K	-	3	2	SLC25A24	108536719	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.700000	0.01905	-1.779000	0.01280	-0.339000	0.08088	AAG	.	C|0.996;T|0.004		0.562	SLC25A24-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030280.2	NM_013386		A	108735196	C	A	108735196	1	1	107	0	1	0	0	0	0	0	0	0	14502	680	24	3		3	SLC25A24	1	108735196	Intron	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10		108735196	140515425	1	15988										
TCHH	7062	hgsc.bcm.edu	37	chr1	152083976	152083976	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	cagcagctgatcgcgcctctCctcctgctcgcgcttcagcc	9	19	2	1	rs572401737		TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr1:152083976C>A	ENST00000368804.1	-	2	1716	c.1717G>T	c.(1717-1719)Gag>Tag	p.E573*		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	573	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCGCGCCTCTCCTCCTGCTCG	0.677																																					p.E573X		Atlas-SNP	.											.	TCHH	275	.	0			c.G1717T						.						53	58	57					1																	152083976		2002	4164	6166	SO:0001587	stop_gained	7062	exon3			GCCTCTCCTCCTG	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1717G>T	chr1.hg19:g.152083976C>A	ENSP00000357794:p.Glu573*	242.0	0.0		347.0	72.0	NM_007113	Q5VUI3	Nonsense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	c	22.0	4.225370	0.79576	.	.	ENSG00000159450	ENST00000368804	.	.	.	2.61	-5.23	0.02798	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	8.3188	0.32117	0.0:0.6084:0.2232:0.1684	.	.	.	.	X	573	.	ENSP00000357794:E573X	E	-	1	0	TCHH	150350600	0.000000	0.05858	0.002000	0.10522	0.291000	0.27294	-1.700000	0.01905	-0.582000	0.05929	0.175000	0.17021	GAG	.	.		0.677	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		A	152083976	C	A	152083976	4	1	107	1	0	0	0	0	0	1	0	0	15715	864	30	3	4118	3	TCHH	1	152083976	Nonsense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10	43348780	152083976	97166645	2	15989										
SELE	6401	hgsc.bcm.edu	37	chr1	169696929	169696929	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tgtccctgagatgtgcactcAagttgagttgatccatgtaa	10	8	1	3			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr1:169696929A>G	ENST00000333360.7	-	9	1558	c.1419T>C	c.(1417-1419)ctT>ctC	p.L473L	SELE_ENST00000367780.4_Silent_p.L348L|SELE_ENST00000367779.4_Intron|SELE_ENST00000367777.1_Intron|SELE_ENST00000367774.1_Intron|SELE_ENST00000367782.4_Intron|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367776.1_Silent_p.L410L|SELE_ENST00000367775.1_Silent_p.L348L|SELE_ENST00000367781.4_Silent_p.L410L	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	473	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	ATGTGCACTCAAGTTGAGTTG	0.448																																					p.L473L		Atlas-SNP	.											.	SELE	84	.	0			c.T1419C						.						134	128	130					1																	169696929		2203	4300	6503	SO:0001819	synonymous_variant	6401	exon9			GCACTCAAGTTGA	M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"CD molecules"	10718	protein-coding gene	gene with protein product		131210	"endothelial adhesion molecule 1"	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.1419T>C	chr1.hg19:g.169696929A>G		261.0	0.0		312.0	96.0	NM_000450	A2RRD6|P16111	Silent	SNP	ENST00000333360.7	hg19	CCDS1283.1																																																																																			.	.		0.448	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450		G	169696929	A	G	169696929	2	3	107	1	0	0	0	0	0	0	0	1	14028	117	5	2		2	SELE	1	169696929	Silent	SNP	A	TCGA-DD-A1EK-01A-11D-A20W-10	17612953	169696929	79553692	3	15990										
E2F6	1876	hgsc.bcm.edu	37	chr2	11593707	11593707	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	aaaagtttgaaagcaactcaCatccatctaatatggttctt	5	8	3	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr2:11593707C>G	ENST00000381525.3	-	3	650		c.e3+1		E2F6_ENST00000307236.4_Splice_Site|E2F6_ENST00000546212.1_Splice_Site|E2F6_ENST00000362009.4_Splice_Site|E2F6_ENST00000542100.1_Splice_Site	NM_198256.2	NP_937987.2	O75461	E2F6_HUMAN	E2F transcription factor 6						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|kidney(1)|lung(3)|prostate(1)|skin(2)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.114)|OV - Ovarian serous cystadenocarcinoma(76;0.168)		AAGCAACTCACATCCATCTAA	0.393																																					.		Atlas-SNP	.											.	E2F6	17	.	0			c.380+1G>C						.						102	98	100					2																	11593707		1879	4095	5974	SO:0001630	splice_region_variant	1876	exon4			AACTCACATCCAT	AF041381	CCDS1680.2, CCDS62858.1, CCDS62859.1	2p25.1	2008-02-05			ENSG00000169016	ENSG00000169016			3120	protein-coding gene	gene with protein product		602944				9501179	Standard	NM_198256		Approved	E2F-6	uc002rbh.4	O75461	OTTHUMG00000090565	ENST00000381525.3:c.380+1G>C	chr2.hg19:g.11593707C>G		186.0	0.0		113.0	38.0	NM_198256	A8K2Z8|G5E936|O60544|Q53QY9|Q6Q9Z6|Q7Z2H6	Splice_Site	SNP	ENST00000381525.3	hg19	CCDS1680.2	.	.	.	.	.	.	.	.	.	.	C	23.9	4.474381	0.84640	.	.	ENSG00000169016	ENST00000381525;ENST00000362009;ENST00000307236;ENST00000542100;ENST00000546212	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5369	0.95256	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	E2F6	11511158	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	7.723000	0.84788	2.610000	0.88304	0.557000	0.71058	.	.	.		0.393	E2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207101.2	NM_001952	Intron	G	11593707	C	G	11593707	5	3	107	1	0	0	0	0	0	0	1	0	4873	492	17	4	484	4	E2F6	2	11593707	Splice_Site	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10		11593707	231605666	4	15991										
APOB	338	hgsc.bcm.edu	37	chr2	21231070	21231070	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ttggggatgttcaatttgtgGaagtatttagtgttgctatc	12	3	1	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr2:21231070G>T	ENST00000233242.1	-	26	8797	c.8670C>A	c.(8668-8670)ttC>ttA	p.F2890L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2890					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAATTTGTGGAAGTATTTAG	0.423																																					p.F2890L		Atlas-SNP	.											APOB,NS,carcinoma,0,1	APOB	761	.	0			c.C8670A						.						180	177	178					2																	21231070		2203	4299	6502	SO:0001583	missense	338	exon26			TTTGTGGAAGTAT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8670C>A	chr2.hg19:g.21231070G>T	ENSP00000233242:p.Phe2890Leu	157.0	0.0		141.0	53.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.614336	0.28712	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00686	5.85	5.51	1.68	0.24146	.	0.727572	0.12466	N	0.466471	T	0.01156	0.0038	M	0.72479	2.2	0.80722	D	1	B	0.26318	0.146	B	0.19148	0.024	T	0.52931	-0.8509	10	0.52906	T	0.07	.	5.2808	0.15674	0.4271:0.0:0.4419:0.131	.	2890	P04114	APOB_HUMAN	L	2890	ENSP00000233242:F2890L	ENSP00000233242:F2890L	F	-	3	2	APOB	21084575	0.184000	0.23200	0.953000	0.39169	0.951000	0.60555	-0.299000	0.08254	0.301000	0.22738	-0.266000	0.10368	TTC	.	.		0.423	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21231070	G	T	21231070	3	4	107	1	0	0	0	0	1	0	0	0	785	1165	41	3	5037	3	APOB	2	21231070	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	9637363	21231070	221968303	5	15992										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32602706	32602706	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	atatctctgctgtggataaaGttatatttgtggatgattat	9	3	1	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr2:32602706G>T	ENST00000421745.2	+	2	510	c.376G>T	c.(376-378)Gtt>Ttt	p.V126F	BIRC6-AS1_ENST00000455572.1_RNA	NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	126					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TGTGGATAAAGTTATATTTGT	0.388																																					p.V126F	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.G376T						.						165	155	158					2																	32602706		2203	4300	6503	SO:0001583	missense	57448	exon2			GATAAAGTTATAT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.376G>T	chr2.hg19:g.32602706G>T	ENSP00000393596:p.Val126Phe	167.0	0.0		157.0	37.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	34	5.357197	0.95854	.	.	ENSG00000115760	ENST00000421745	T	0.79141	-1.24	4.56	4.56	0.56223	.	0.000000	0.64402	D	0.000001	D	0.85682	0.5753	L	0.53249	1.67	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	D	0.87596	0.2494	10	0.87932	D	0	.	17.6933	0.88275	0.0:0.0:1.0:0.0	.	126	Q9NR09	BIRC6_HUMAN	F	126	ENSP00000393596:V126F	ENSP00000393596:V126F	V	+	1	0	BIRC6	32456210	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.731000	0.98807	2.226000	0.72624	0.655000	0.94253	GTT	.	.		0.388	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32602706	G	T	32602706	3	4	107	1	0	0	0	0	1	0	0	0	1438	1029	36	3	382	3	BIRC6	2	32602706	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	11371636	32602706	210596667	6	15993										
TGFA	7039	hgsc.bcm.edu	37	chr2	70742002	70742002	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tgcactcaccactcagcgggGacgtgctgttctccaaggcc	11	15	3	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr2:70742002G>C	ENST00000295400.6	-	2	330	c.83C>G	c.(82-84)tCc>tGc	p.S28C	TGFA_ENST00000445399.1_Missense_Mutation_p.S28C|TGFA_ENST00000444975.1_Missense_Mutation_p.S34C|TGFA_ENST00000450929.1_Missense_Mutation_p.S34C|TGFA_ENST00000460808.1_5'UTR|TGFA_ENST00000418333.2_Missense_Mutation_p.S28C	NM_001099691.2|NM_003236.3	NP_001093161.1|NP_003227.1	P01135	TGFA_HUMAN	transforming growth factor, alpha	28					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|mammary gland alveolus development (GO:0060749)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell division (GO:0051781)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mitosis (GO:0045840)|response to drug (GO:0042493)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|MAP kinase kinase activity (GO:0004708)			haematopoietic_and_lymphoid_tissue(1)|lung(2)|prostate(1)	4						ACTCAGCGGGGACGTGCTGTT	0.607																																					p.S28C		Atlas-SNP	.											.	TGFA	14	.	0			c.C83G						.						80	66	71					2																	70742002		2203	4300	6503	SO:0001583	missense	7039	exon2			AGCGGGGACGTGC		CCDS1905.1, CCDS46316.1	2p13	2012-10-02			ENSG00000163235	ENSG00000163235			11765	protein-coding gene	gene with protein product		190170				3459638, 10552925	Standard	NM_003236		Approved		uc002sgs.4	P01135	OTTHUMG00000129669	ENST00000295400.6:c.83C>G	chr2.hg19:g.70742002G>C	ENSP00000295400:p.Ser28Cys	96.0	0.0		84.0	24.0	NM_001099691	A8K286|Q15577|Q53SK7|Q9BS56|Q9UEI3|Q9UKM1|Q9UKM2|Q9UKM3	Missense_Mutation	SNP	ENST00000295400.6	hg19	CCDS1905.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.177599	0.57692	.	.	ENSG00000163235	ENST00000295400;ENST00000445399;ENST00000418333;ENST00000450929;ENST00000444975;ENST00000394241	T;T;T;T;T;T	0.19394	2.4;2.17;2.17;2.15;2.16;2.18	5.14	5.14	0.70334	.	0.184997	0.39146	N	0.001450	T	0.42063	0.1186	M	0.64997	1.995	0.09310	N	0.999992	D;D;D;D;D;D;D	0.76494	0.999;0.999;0.994;0.999;0.972;0.979;0.994	D;D;D;D;P;P;D	0.70935	0.971;0.971;0.947;0.958;0.634;0.723;0.923	T	0.16276	-1.0408	10	0.48119	T	0.1	.	14.2994	0.66336	0.0:0.0:1.0:0.0	.	34;34;28;28;28;28;28	E7EPT6;F8VNR3;P01135-5;Q9UKM3;P01135-3;P01135-2;P01135	.;.;.;.;.;.;TGFA_HUMAN	C	28;28;28;34;34;28	ENSP00000295400:S28C;ENSP00000387493:S28C;ENSP00000404099:S28C;ENSP00000414127:S34C;ENSP00000404131:S34C;ENSP00000377787:S28C	ENSP00000295400:S28C	S	-	2	0	TGFA	70595510	0.877000	0.30153	0.108000	0.21378	0.685000	0.39939	3.044000	0.49830	2.837000	0.97791	0.655000	0.94253	TCC	.	.		0.607	TGFA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251870.2			C	70742002	G	C	70742002	3	2	107	1	0	0	0	0	1	0	0	0	15830	1174	41	4	419	4	TGFA	2	70742002	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	38139296	70742002	172457371	7	15994										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84931193	84931193	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tcatgtttcaatggttaggtCcgtaacactgtgcaggagga	12	7	2	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr2:84931193C>T	ENST00000237449.6	+	50	8240	c.8232C>T	c.(8230-8232)gtC>gtT	p.V2744V	DNAH6_ENST00000389394.3_Silent_p.V2744V			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2744	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						ATGGTTAGGTCCGTAACACTG	0.393																																					p.V2744V		Atlas-SNP	.											.	DNAH6	194	.	0			c.C8232T						.						127	103	110					2																	84931193		692	1591	2283	SO:0001819	synonymous_variant	1768	exon51			TTAGGTCCGTAAC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.8232C>T	chr2.hg19:g.84931193C>T		73.0	0.0		62.0	29.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.393	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84931193	C	T	84931193	2	4	107	1	0	0	0	0	0	0	0	1	4607	842	30	3		3	DNAH6	2	84931193	Silent	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10	14189191	84931193	158268180	8	15995										
ACVR1C	130399	hgsc.bcm.edu	37	chr2	158390474	158390474	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	acaaagttgagatatagtctTcttaatacgaagagcagtta	8	5	2	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr2:158390474T>C	ENST00000243349.8	-	9	1798	c.1438A>G	c.(1438-1440)Aag>Gag	p.K480E	ACVR1C_ENST00000348328.5_Missense_Mutation_p.K323E|ACVR1C_ENST00000409680.3_Missense_Mutation_p.K430E|ACVR1C_ENST00000335450.7_Missense_Mutation_p.K400E	NM_001111032.1|NM_145259.2	NP_001104502.1|NP_660302.2			activin A receptor, type IC											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	42						GATATAGTCTTCTTAATACGA	0.398																																					p.K480E		Atlas-SNP	.											.	ACVR1C	85	.	0			c.A1438G						.						95	105	101					2																	158390474		2203	4300	6503	SO:0001583	missense	130399	exon9			TAGTCTTCTTAAT	BC022530	CCDS2205.1, CCDS46432.1, CCDS46433.1, CCDS46434.1	2q24.2	2008-02-05			ENSG00000123612	ENSG00000123612			18123	protein-coding gene	gene with protein product		608981					Standard	NM_145259		Approved	ALK7, ACVRLK7	uc002tzk.4	Q8NER5	OTTHUMG00000131964	ENST00000243349.8:c.1438A>G	chr2.hg19:g.158390474T>C	ENSP00000243349:p.Lys480Glu	54.0	0.0		64.0	25.0	NM_145259		Missense_Mutation	SNP	ENST00000243349.8	hg19	CCDS2205.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.915585	0.92178	.	.	ENSG00000123612	ENST00000243349;ENST00000409680;ENST00000348328;ENST00000335450	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.51	5.51	0.81932	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000042	T	0.80555	0.4645	M	0.82630	2.6	0.80722	D	1	D;D;D	0.89917	0.995;1.0;0.999	D;D;D	0.78314	0.962;0.991;0.985	D	0.83835	0.0254	10	0.87932	D	0	.	15.2629	0.73637	0.0:0.0:0.0:1.0	.	323;400;480	Q8NER5-2;Q8NER5-3;Q8NER5	.;.;ACV1C_HUMAN	E	480;430;323;400	ENSP00000243349:K480E;ENSP00000387168:K430E;ENSP00000335139:K323E;ENSP00000335178:K400E	ENSP00000243349:K480E	K	-	1	0	ACVR1C	158098720	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.955000	0.87856	2.080000	0.62538	0.482000	0.46254	AAG	.	.		0.398	ACVR1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254924.2	NM_145259		C	158390474	T	C	158390474	3	2	107	1	0	0	0	0	1	0	0	0	222	1792	62	2	47	2	ACVR1C	2	158390474	Missense_Mutation	SNP	T	TCGA-DD-A1EK-01A-11D-A20W-10	73459281	158390474	84808899	9	15996										
AOX1	316	hgsc.bcm.edu	37	chr2	201478589	201478589	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tctgaatgaagtctccctttTgggctcggcgccaggtggga	14	10	2	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr2:201478589T>G	ENST00000374700.2	+	15	1752	c.1511T>G	c.(1510-1512)tTg>tGg	p.L504W	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	504					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	GTCTCCCTTTTGGGCTCGGCG	0.488																																					p.L504W		Atlas-SNP	.											.	AOX1	152	.	0			c.T1511G						.						90	87	88					2																	201478589		2203	4300	6503	SO:0001583	missense	316	exon15			CCCTTTTGGGCTC	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.1511T>G	chr2.hg19:g.201478589T>G	ENSP00000363832:p.Leu504Trp	159.0	0.0		178.0	67.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	hg19	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.112968	0.37242	.	.	ENSG00000138356	ENST00000374700	T	0.24908	1.83	5.33	4.45	0.53987	CO dehydrogenase flavoprotein, C-terminal (3);	0.370054	0.30989	N	0.008478	T	0.34077	0.0885	L	0.29908	0.895	0.09310	N	0.999999	P	0.35433	0.501	P	0.51016	0.656	T	0.32771	-0.9894	10	0.87932	D	0	-10.3192	14.0636	0.64815	0.0:0.9278:0.0:0.0722	.	504	Q06278	ADO_HUMAN	W	504	ENSP00000363832:L504W	ENSP00000363832:L504W	L	+	2	0	AOX1	201186834	0.015000	0.18098	0.091000	0.20842	0.006000	0.05464	2.663000	0.46774	1.488000	0.48433	-0.132000	0.14878	TTG	.	.		0.488	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		G	201478589	T	G	201478589	3	3	107	1	0	0	0	0	1	0	0	0	729	1821	63	5	1569	5	AOX1	2	201478589	Missense_Mutation	SNP	T	TCGA-DD-A1EK-01A-11D-A20W-10	43088115	201478589	41720784	10	15997										
RAPH1	65059	hgsc.bcm.edu	37	chr2	204304792	204304792	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tgacacacacccttgttggaGaactccaggaaggttgactc	10	11	0	3			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr2:204304792G>A	ENST00000319170.5	-	14	3420	c.3121C>T	c.(3121-3123)Ctc>Ttc	p.L1041F	RAPH1_ENST00000374493.3_Missense_Mutation_p.L1093F|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000295851.5_3'UTR	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1041					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CCTTGTTGGAGAACTCCAGGA	0.537																																					p.L1041F		Atlas-SNP	.											.	RAPH1	118	.	0			c.C3121T						.						44	51	48					2																	204304792		2203	4300	6503	SO:0001583	missense	65059	exon14			GTTGGAGAACTCC	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.3121C>T	chr2.hg19:g.204304792G>A	ENSP00000316543:p.Leu1041Phe	114.0	0.0		64.0	22.0	NM_213589	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	hg19	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.982762	0.34942	.	.	ENSG00000173166	ENST00000319170;ENST00000374493	T;T	0.57436	0.4;0.43	4.38	4.38	0.52667	.	.	.	.	.	T	0.36386	0.0965	N	0.17082	0.46	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.27226	-1.0080	9	0.66056	D	0.02	.	10.9302	0.47213	0.088:0.0:0.912:0.0	.	1041	Q70E73	RAPH1_HUMAN	F	1041;1093	ENSP00000316543:L1041F;ENSP00000363617:L1093F	ENSP00000316543:L1041F	L	-	1	0	RAPH1	204013037	1.000000	0.71417	0.020000	0.16555	0.483000	0.33249	4.034000	0.57289	2.164000	0.68074	0.313000	0.20887	CTC	.	.		0.537	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		A	204304792	G	A	204304792	3	1	107	1	0	0	0	0	1	0	0	0	13065	942	33	3	635	3	RAPH1	2	204304792	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	2826203	204304792	38894581	11	15998										
KIF1A	547	hgsc.bcm.edu	37	chr2	241712532	241712532	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ggctggagcaggcactcactGtcagtgatgtcgccaagacc	13	12	2	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr2:241712532G>C	ENST00000320389.7	-	13	1337	c.1179C>G	c.(1177-1179)gaC>gaG	p.D393E	KIF1A_ENST00000498729.2_Splice_Site_p.D393E	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	393					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		GGCACTCACTGTCAGTGATGT	0.617																																					p.D393E		Atlas-SNP	.											.	KIF1A	152	.	0			c.C1179G						.						41	45	44					2																	241712532		2155	4266	6421	SO:0001630	splice_region_variant	547	exon13			CTCACTGTCAGTG	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"Kinesins", "Pleckstrin homology (PH) domain containing"	888	protein-coding gene	gene with protein product		601255	"axonal transport of synaptic vesicles", "chromosome 2 open reading frame 20", "spastic paraplegia 30 (autosomal recessive)"	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.1180+1C>G	chr2.hg19:g.241712532G>C		114.0	0.0		87.0	34.0	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	hg19	CCDS46561.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.61|10.61	1.398812|1.398812	0.25291|0.25291	.|.	.|.	ENSG00000130294|ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283|ENST00000428768	T;T;T|.	0.71698|.	-0.46;-0.51;-0.59|.	3.83|3.83	2.92|2.92	0.33932|0.33932	.|.	0.112561|.	0.64402|.	U|.	0.000015|.	T|T	0.48132|0.48132	0.1483|0.1483	N|N	0.21373|0.21373	0.66|0.66	0.45366|0.45366	D|D	0.998354|0.998354	B;B;B|.	0.09022|.	0.002;0.002;0.001|.	B;B;B|.	0.12837|.	0.008;0.003;0.004|.	T|T	0.27938|0.27938	-1.0059|-1.0059	10|5	0.06365|.	T|.	0.9|.	.|.	12.3594|12.3594	0.55194|0.55194	0.0:0.0:0.8296:0.1704|0.0:0.0:0.8296:0.1704	.|.	393;393;393|.	F5H045;Q12756-2;Q12756|.	.;.;KIF1A_HUMAN|.	E|D	393|201	ENSP00000322791:D393E;ENSP00000438388:D393E;ENSP00000384231:D393E|.	ENSP00000322791:D393E|.	D|H	-|-	3|1	2|0	KIF1A|KIF1A	241361205|241361205	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.531000|0.531000	0.34715|0.34715	1.234000|1.234000	0.32660|0.32660	0.568000|0.568000	0.29311|0.29311	-0.500000|-0.500000	0.04577|0.04577	GAC|CAC	.	.		0.617	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	Missense_Mutation	C	241712532	G	C	241712532	5	2	107	1	0	0	0	0	0	0	1	0	8292	1391	48	4	4033	4	KIF1A	2	241712532	Splice_Site	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	37407740	241712532	1486841	12	15999										
RNF123	63891	hgsc.bcm.edu	37	chr3	49739578	49739578	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	acaataaagatgacaatgggGtgagtgactcccaggagccc	12	9	0	4			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr3:49739578G>A	ENST00000327697.6	+	18	1701		c.e18+1		RNF123_ENST00000432042.1_Splice_Site	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123						protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		TGACAATGGGGTGAGTGACTC	0.592																																					.		Atlas-SNP	.											.	RNF123	100	.	0			c.1557+1G>A						.						63	63	63					3																	49739578		2203	4300	6503	SO:0001630	splice_region_variant	63891	exon18			AATGGGGTGAGTG	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1557+1G>A	chr3.hg19:g.49739578G>A		176.0	0.0		168.0	63.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Splice_Site	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.639577	0.67244	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8474	0.57837	0.0815:0.0:0.9185:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RNF123	49714582	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	4.959000	0.63666	2.371000	0.80710	0.561000	0.74099	.	.	.		0.592	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	Intron	A	49739578	G	A	49739578	5	1	107	1	0	0	0	0	0	0	1	0	13448	1275	44	3	1624	3	RNF123	3	49739578	Splice_Site	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10		49739578	148282852	13	16000										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64579956	64579956	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	agctccaagggccagtactcCatgcagcgtcgtgtggacaa	12	12	0	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr3:64579956C>T	ENST00000498707.1	-	28	4676	c.4334G>A	c.(4333-4335)tGg>tAg	p.W1445*	ADAMTS9_ENST00000295903.4_Nonsense_Mutation_p.W1417*	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1445	TSP type-1 11. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		GCCAGTACTCCATGCAGCGTC	0.483																																					p.W1445X		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G4334A						.						163	149	154					3																	64579956		2203	4300	6503	SO:0001587	stop_gained	56999	exon28			GTACTCCATGCAG	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.4334G>A	chr3.hg19:g.64579956C>T	ENSP00000418735:p.Trp1445*	148.0	0.0		144.0	55.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Nonsense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.352656|6.352656	0.97498|0.97498	.|.	.|.	ENSG00000163638|ENSG00000163638	ENST00000481060|ENST00000295903;ENST00000498707	.|.	.|.	.|.	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	.|0.134382	.|0.53938	.|D	.|0.000047	T|.	0.47340|.	0.1440|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34054|.	-0.9844|.	4|.	.|0.02654	.|T	.|1	.|.	19.2909|19.2909	0.94098|0.94098	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	R|X	501|1417;1445	.|.	.|ENSP00000295903:W1417X	G|W	-|-	1|2	0|0	ADAMTS9|ADAMTS9	64554996|64554996	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.652000|0.652000	0.38707|0.38707	7.288000|7.288000	0.78691|0.78691	2.797000|2.797000	0.96272|0.96272	0.563000|0.563000	0.77884|0.77884	GGA|TGG	.	.		0.483	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			T	64579956	C	T	64579956	4	4	107	1	0	0	0	0	0	1	0	0	273	595	21	3	1521	3	ADAMTS9	3	64579956	Nonsense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10	14840378	64579956	133442474	14	16001										
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910061	184910061	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	caagctttgccattctttcaGgggagggtttccctgagaag	12	9	2	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr3:184910061G>A	ENST00000231887.3	-	7	2200	c.2125C>T	c.(2125-2127)Ctg>Ttg	p.L709L	EHHADH_ENST00000456310.1_Silent_p.L613L|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	709					fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CATTCTTTCAGGGGAGGGTTT	0.448																																					p.L709L		Atlas-SNP	.											.	EHHADH	73	.	0			c.C2125T						.						71	78	75					3																	184910061		2203	4300	6503	SO:0001819	synonymous_variant	1962	exon7			CTTTCAGGGGAGG	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.2125C>T	chr3.hg19:g.184910061G>A		146.0	0.0		150.0	12.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Silent	SNP	ENST00000231887.3	hg19	CCDS33901.1																																																																																			.	.		0.448	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			A	184910061	G	A	184910061	2	1	107	1	0	0	0	0	0	0	0	1	4984	991	35	3		3	EHHADH	3	184910061	Silent	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	120330105	184910061	13112369	15	16002			1	17		8	7	1026	N	G	6.175332e-20
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910094	184910094	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ctgagaagccagtttttttaGatagtcacttggctccagtt	9	8	1	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr3:184910094G>C	ENST00000231887.3	-	7	2167	c.2092C>G	c.(2092-2094)Cta>Gta	p.L698V	EHHADH_ENST00000456310.1_Missense_Mutation_p.L602V|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	698					fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			AGTTTTTTTAGATAGTCACTT	0.458																																					p.L698V		Atlas-SNP	.											.	EHHADH	73	.	0			c.C2092G						.						71	78	76					3																	184910094		2202	4300	6502	SO:0001583	missense	1962	exon7			TTTTTAGATAGTC	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.2092C>G	chr3.hg19:g.184910094G>C	ENSP00000231887:p.Leu698Val	156.0	0.0		140.0	12.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.323529	0.81580	.	.	ENSG00000113790	ENST00000231887;ENST00000456310	D;D	0.85258	-1.96;-1.96	5.91	5.91	0.95273	3-hydroxyacyl-CoA dehydrogenase, C-terminal (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.147361	0.47093	D	0.000252	D	0.94470	0.8220	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94704	0.7886	10	0.72032	D	0.01	-12.2218	20.2985	0.98592	0.0:0.0:1.0:0.0	.	698	Q08426	ECHP_HUMAN	V	698;602	ENSP00000231887:L698V;ENSP00000387746:L602V	ENSP00000231887:L698V	L	-	1	2	EHHADH	186392788	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	7.533000	0.81994	2.793000	0.96121	0.655000	0.94253	CTA	.	.		0.458	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			C	184910094	G	C	184910094	3	2	107	1	0	0	0	0	1	0	0	0	4984	933	33	4	83	4	EHHADH	3	184910094	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	33	184910094	13112336	16	16003			1	17		8	7	1026	N	G	6.175332e-20
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910309	184910309	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ggaatgcttcattgataagtGaatataagcagcgttcaagg	11	5	2	2	rs574285941		TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr3:184910309G>T	ENST00000231887.3	-	7	1952	c.1877C>A	c.(1876-1878)tCa>tAa	p.S626*	EHHADH_ENST00000456310.1_Nonsense_Mutation_p.S530*|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	626					fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			ATTGATAAGTGAATATAAGCA	0.443													G|||	1	0.000199681	0	0	5008	,	,		21816	0		0	False		,,,				2504	0.001				p.S626X		Atlas-SNP	.											.	EHHADH	73	.	0			c.C1877A						.						138	130	132					3																	184910309		2203	4300	6503	SO:0001587	stop_gained	1962	exon7			ATAAGTGAATATA	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1877C>A	chr3.hg19:g.184910309G>T	ENSP00000231887:p.Ser626*	143.0	0.0		109.0	6.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Nonsense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	G	40	8.462250	0.98822	.	.	ENSG00000113790	ENST00000231887;ENST00000456310	.	.	.	5.91	5.91	0.95273	.	0.421588	0.23918	N	0.043263	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-2.574	20.2985	0.98592	0.0:0.0:1.0:0.0	.	.	.	.	X	626;530	.	ENSP00000231887:S626X	S	-	2	0	EHHADH	186393003	0.999000	0.42202	0.035000	0.18076	0.985000	0.73830	7.542000	0.82095	2.793000	0.96121	0.655000	0.94253	TCA	.	.		0.443	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			T	184910309	G	T	184910309	4	4	107	1	0	0	0	0	0	1	0	0	4984	1294	45	3	298	3	EHHADH	3	184910309	Nonsense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	215	184910309	13112121	17	16004			1	17		8	7	1026	N	G	6.175332e-20
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910328	184910328	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tgaatataagcagcgttcaaGgatctcatcctggctaatgg	10	8	2	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr3:184910328G>T	ENST00000231887.3	-	7	1933	c.1858C>A	c.(1858-1860)Ctt>Att	p.L620I	EHHADH_ENST00000456310.1_Missense_Mutation_p.L524I|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	620					fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CAGCGTTCAAGGATCTCATCC	0.438																																					p.L620I		Atlas-SNP	.											.	EHHADH	73	.	0			c.C1858A						.						133	125	128					3																	184910328		2203	4300	6503	SO:0001583	missense	1962	exon7			GTTCAAGGATCTC	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1858C>A	chr3.hg19:g.184910328G>T	ENSP00000231887:p.Leu620Ile	123.0	0.0		106.0	7.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.742839	0.49151	.	.	ENSG00000113790	ENST00000231887;ENST00000456310	D;D	0.82893	-1.66;-1.66	5.91	5.0	0.66597	3-hydroxyacyl-CoA dehydrogenase, C-terminal (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.222293	0.41823	D	0.000801	T	0.78509	0.4294	L	0.39326	1.205	0.80722	D	1	B	0.24043	0.096	B	0.34931	0.192	T	0.73445	-0.3980	10	0.36615	T	0.2	-20.1494	11.4227	0.49991	0.0677:0.1268:0.8056:0.0	.	620	Q08426	ECHP_HUMAN	I	620;524	ENSP00000231887:L620I;ENSP00000387746:L524I	ENSP00000231887:L620I	L	-	1	0	EHHADH	186393022	1.000000	0.71417	0.998000	0.56505	0.913000	0.54294	3.613000	0.54152	2.793000	0.96121	0.655000	0.94253	CTT	.	.		0.438	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			T	184910328	G	T	184910328	3	4	107	1	0	0	0	0	1	0	0	0	4984	1000	35	3	317	3	EHHADH	3	184910328	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	19	184910328	13112102	18	16005			1	17		8	7	1026	N	G	6.175332e-20
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910834	184910834	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tggcaatggtagtgggggaaGagtattggctgggaataacc	17	4	0	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr3:184910834G>A	ENST00000231887.3	-	7	1427	c.1352C>T	c.(1351-1353)tCt>tTt	p.S451F	EHHADH_ENST00000456310.1_Missense_Mutation_p.S355F|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	451	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			AGTGGGGGAAGAGTATTGGCT	0.428																																					p.S451F		Atlas-SNP	.											.	EHHADH	73	.	0			c.C1352T						.						95	98	97					3																	184910834		2203	4300	6503	SO:0001583	missense	1962	exon7			GGGGAAGAGTATT	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1352C>T	chr3.hg19:g.184910834G>A	ENSP00000231887:p.Ser451Phe	184.0	0.0		173.0	11.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.193003	0.78902	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.78246	-1.16;-1.16	5.91	5.91	0.95273	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.178330	0.50627	D	0.000105	D	0.88081	0.6341	M	0.72894	2.215	0.80722	D	1	D	0.69078	0.997	D	0.70487	0.969	D	0.88163	0.2859	10	0.87932	D	0	-12.4806	20.2985	0.98592	0.0:0.0:1.0:0.0	.	451	Q08426	ECHP_HUMAN	F	451;451;355	ENSP00000231887:S451F;ENSP00000387746:S355F	ENSP00000231887:S451F	S	-	2	0	EHHADH	186393528	1.000000	0.71417	0.965000	0.40720	0.893000	0.52053	9.280000	0.95786	2.793000	0.96121	0.655000	0.94253	TCT	.	.		0.428	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			A	184910834	G	A	184910834	3	1	107	1	0	0	0	0	1	0	0	0	4984	942	33	3	823	3	EHHADH	3	184910834	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	506	184910834	13111596	19	16006			1	17		8	7	1026	N	G	6.175332e-20
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910910	184910910	+	Missense_Mutation	SNP	G	G	A													0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	gtgggtgccaatgaccaagtGaggacgatcagtggaagaag							TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr3:184910910G>A	ENST00000231887.3	-	7	1351	c.1276C>T	c.(1276-1278)Cac>Tac	p.H426Y	EHHADH_ENST00000456310.1_Missense_Mutation_p.H330Y|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	426	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			ATGACCAAGTGAGGACGATCA	0.468																																					p.H426Y		Atlas-SNP	.											.	EHHADH	73	.	0			c.C1276T						.						133	127	129					3																	184910910		2203	4300	6503	SO:0001583	missense	1962	exon7			CCAAGTGAGGACG	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1276C>T	chr3.hg19:g.184910910G>A	ENSP00000231887:p.His426Tyr	194.0	0.0		169.0	15.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.107045	0.56291	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.76448	-1.02;-1.02	6.08	4.19	0.49359	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.501640	0.23067	N	0.052317	T	0.71592	0.3358	L	0.32530	0.975	0.80722	D	1	P	0.43750	0.816	B	0.41691	0.364	T	0.76759	-0.2841	10	0.87932	D	0	-1.1369	16.7901	0.85586	0.0:0.2424:0.7576:0.0	.	426	Q08426	ECHP_HUMAN	Y	426;426;330	ENSP00000231887:H426Y;ENSP00000387746:H330Y	ENSP00000231887:H426Y	H	-	1	0	EHHADH	186393604	1.000000	0.71417	0.988000	0.46212	0.983000	0.72400	2.582000	0.46085	1.545000	0.49373	0.591000	0.81541	CAC	.	.		0.468	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			A	184910910	G	A	184910910	3	1	107	1	0	0	0	0	1	0	0	0	4984	1290	45	3	899	3	EHHADH	3	184910910	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	76	184910910	13111520	20	16007	69	2	1	17		8	7	1026	N	G	6.175332e-20
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910913	184910913	+	Missense_Mutation	SNP	G	G	A													0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ggtgccaatgaccaagtgagGacgatcagtggaagaagcaa							TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr3:184910913G>A	ENST00000231887.3	-	7	1348	c.1273C>T	c.(1273-1275)Cct>Tct	p.P425S	EHHADH_ENST00000456310.1_Missense_Mutation_p.P329S|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	425	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)	p.P425S(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			ACCAAGTGAGGACGATCAGTG	0.473																																					p.P425S		Atlas-SNP	.											EHHADH,trunk,malignant_melanoma,0,1	EHHADH	73	.	1	Substitution - Missense(1)	skin(1)	c.C1273T						.						137	130	132					3																	184910913		2203	4300	6503	SO:0001583	missense	1962	exon7			AGTGAGGACGATC	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1273C>T	chr3.hg19:g.184910913G>A	ENSP00000231887:p.Pro425Ser	193.0	0.0		164.0	13.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.624022	0.87560	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.80123	-1.34;-1.34	6.08	6.08	0.98989	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.90123	0.6914	M	0.76002	2.32	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.89868	0.4021	10	0.87932	D	0	-16.8302	20.6721	0.99693	0.0:0.0:1.0:0.0	.	425	Q08426	ECHP_HUMAN	S	425;425;329	ENSP00000231887:P425S;ENSP00000387746:P329S	ENSP00000231887:P425S	P	-	1	0	EHHADH	186393607	1.000000	0.71417	0.953000	0.39169	0.965000	0.64279	9.224000	0.95209	2.894000	0.99253	0.591000	0.81541	CCT	.	.		0.473	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			A	184910913	G	A	184910913	3	1	107	1	0	0	0	0	1	0	0	0	4984	1174	41	3	902	3	EHHADH	3	184910913	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	3	184910913	13111517	21	16008	69	2	1	17		8	7	1026	N	G	6.175332e-20
EHHADH	1962	hgsc.bcm.edu	37	chr3	184911086	184911086	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	caccaagctccttcacagatGaagttaacctgggttttggt	9	10	1	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr3:184911086G>A	ENST00000231887.3	-	7	1175	c.1100C>T	c.(1099-1101)tCa>tTa	p.S367L	EHHADH_ENST00000456310.1_Missense_Mutation_p.S271L|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	367	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CTTCACAGATGAAGTTAACCT	0.463																																					p.S367L		Atlas-SNP	.											.	EHHADH	73	.	0			c.C1100T						.						168	165	166					3																	184911086		2203	4300	6503	SO:0001583	missense	1962	exon7			ACAGATGAAGTTA	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1100C>T	chr3.hg19:g.184911086G>A	ENSP00000231887:p.Ser367Leu	176.0	0.0		203.0	14.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	G	1.388	-0.581509	0.03854	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.77098	-1.07;-1.07	6.08	3.35	0.38373	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.917318	0.09420	N	0.804539	T	0.57227	0.2039	N	0.04355	-0.22	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48692	-0.9013	10	0.46703	T	0.11	-2.2989	8.1777	0.31292	0.3266:0.0:0.6734:0.0	.	367	Q08426	ECHP_HUMAN	L	367;367;271	ENSP00000231887:S367L;ENSP00000387746:S271L	ENSP00000231887:S367L	S	-	2	0	EHHADH	186393780	0.999000	0.42202	0.085000	0.20634	0.925000	0.55904	3.017000	0.49615	0.916000	0.36871	0.591000	0.81541	TCA	.	.		0.463	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			A	184911086	G	A	184911086	3	1	107	1	0	0	0	0	1	0	0	0	4984	1294	45	3	1075	3	EHHADH	3	184911086	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	173	184911086	13111344	22	16009			1	17		8	7	1026	N	G	6.175332e-20
IDUA	3425	hgsc.bcm.edu	37	chr4	994398	994398	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	gacgctgaccgtccttctgcAgggggtccactggacggggc	16	13	1	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr4:994398A>T	ENST00000247933.4	+	3	387		c.e3-1		IDUA_ENST00000514224.1_Splice_Site|IDUA_ENST00000453894.1_Splice_Site	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-						carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GTCCTTCTGCAGGGGGTCCAC	0.642																																					.		Atlas-SNP	.											.	IDUA	33	.	0			c.300-2A>T						.						61	58	59					4																	994398		2202	4300	6502	SO:0001630	splice_region_variant	3425	exon3			TTCTGCAGGGGGT	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.300-1A>T	chr4.hg19:g.994398A>T		223.0	0.0		212.0	87.0	NM_000203	B3KWK6	Splice_Site	SNP	ENST00000247933.4	hg19	CCDS3343.1	.	.	.	.	.	.	.	.	.	.	a	12.72	2.022489	0.35701	.	.	ENSG00000127415	ENST00000247933;ENST00000453894;ENST00000502910;ENST00000504568;ENST00000514192;ENST00000509948	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8626	0.46835	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IDUA	984398	0.998000	0.40836	0.035000	0.18076	0.005000	0.04900	4.905000	0.63286	1.811000	0.52892	0.456000	0.33151	.	.	.		0.642	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	Intron	T	994398	A	T	994398	5	4	107	1	0	0	0	0	0	0	1	0	7513	202	7	4	308	4	IDUA	4	994398	Splice_Site	SNP	A	TCGA-DD-A1EK-01A-11D-A20W-10		994398	190159878	23	16010										
FRYL	285527	hgsc.bcm.edu	37	chr4	48578067	48578067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tttagaatcaatgctatagcCgctatctggggtagacgcca	10	9	2	2	rs375943517		TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr4:48578067C>T	ENST00000503238.1	-	21	2700	c.2701G>A	c.(2701-2703)Ggc>Agc	p.G901S	RNU5E-3P_ENST00000515913.1_RNA|FRYL_ENST00000358350.4_Missense_Mutation_p.G901S|FRYL_ENST00000537810.1_Missense_Mutation_p.G901S|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000507711.1_Missense_Mutation_p.G901S			O94915	FRYL_HUMAN	FRY-like	901					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						ATGCTATAGCCGCTATCTGGG	0.413																																					p.G901S		Atlas-SNP	.											.	FRYL	242	.	0			c.G2701A						.	C	SER/GLY	0,3754		0,0,1877	130	132	131		2701	5.3	1	4		131	1,8235		0,1,4117	no	missense	FRYL	NM_015030.1	56	0,1,5994	TT,TC,CC		0.0121,0.0,0.0083	benign	901/3014	48578067	1,11989	1877	4118	5995	SO:0001583	missense	285527	exon24			TATAGCCGCTATC	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.2701G>A	chr4.hg19:g.48578067C>T	ENSP00000426064:p.Gly901Ser	89.0	0.0		71.0	5.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	C	6.082	0.383411	0.11524	0.0	1.21E-4	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.26	5.26	0.73747	.	0.000000	0.85682	U	0.000000	T	0.45597	0.1350	N	0.12182	0.205	0.80722	D	1	D;B	0.89917	1.0;0.158	D;B	0.85130	0.997;0.022	T	0.34079	-0.9843	10	0.10902	T	0.67	.	18.8613	0.92273	0.0:1.0:0.0:0.0	.	901;901	F2Z2S2;O94915	.;FRYL_HUMAN	S	901	ENSP00000426064:G901S;ENSP00000351113:G901S;ENSP00000441114:G901S;ENSP00000421584:G901S	ENSP00000351113:G901S	G	-	1	0	FRYL	48272824	1.000000	0.71417	0.984000	0.44739	0.082000	0.17680	5.743000	0.68655	2.430000	0.82344	0.467000	0.42956	GGC	.	.		0.413	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48578067	C	T	48578067	3	4	107	1	0	0	0	0	1	0	0	0	6072	652	23	1	6504	1	FRYL	4	48578067	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10	47583669	48578067	142576209	24	16011										
ACSL1	2180	hgsc.bcm.edu	37	chr4	185709825	185709825	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	taatgttgtgacatcatcatAgaaatacaccaagggctcgt	8	8	2	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr4:185709825A>T	ENST00000515030.1	-	3	581	c.256T>A	c.(256-258)Tat>Aat	p.Y86N	ACSL1_ENST00000504342.1_Missense_Mutation_p.Y86N|ACSL1_ENST00000507295.1_Missense_Mutation_p.Y86N|ACSL1_ENST00000281455.2_Missense_Mutation_p.Y86N|ACSL1_ENST00000513317.1_Missense_Mutation_p.Y86N|ACSL1_ENST00000504900.1_Missense_Mutation_p.Y86N|ACSL1_ENST00000437665.3_5'UTR|ACSL1_ENST00000454703.2_5'UTR			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	86					adiponectin-activated signaling pathway (GO:0033211)|alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|linoleic acid metabolic process (GO:0043651)|lipid biosynthetic process (GO:0008610)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid metabolic process (GO:0033559)|xenobiotic catabolic process (GO:0042178)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(17)|ovary(2)|prostate(1)|skin(2)	38		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	ACATCATCATAGAAATACACC	0.488																																					p.Y86N		Atlas-SNP	.											.	ACSL1	77	.	0			c.T256A						.						127	111	117					4																	185709825		2203	4300	6503	SO:0001583	missense	2180	exon3			CATCATAGAAATA	BC026290	CCDS3839.1, CCDS68825.1, CCDS68826.1, CCDS75213.1	4q35.1	2014-08-08	2004-02-19	2004-02-20	ENSG00000151726	ENSG00000151726	6.2.1.3	"Acyl-CoA synthetase family"	3569	protein-coding gene	gene with protein product	"lignoceroyl-CoA synthase", "long-chain fatty-acid-coenzyme A ligase 1"	152425	"fatty-acid-Coenzyme A ligase, long-chain 2"	FACL2		2341402, 1531127	Standard	XM_005262828		Approved	LACS2, LACS, ACS1, LACS1, FACL1	uc003iwu.1	P33121	OTTHUMG00000160547	ENST00000515030.1:c.256T>A	chr4.hg19:g.185709825A>T	ENSP00000422607:p.Tyr86Asn	49.0	0.0		40.0	16.0	NM_001995	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Missense_Mutation	SNP	ENST00000515030.1	hg19	CCDS3839.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.143348	0.77888	.	.	ENSG00000151726	ENST00000515030;ENST00000281455;ENST00000507295;ENST00000504342;ENST00000513317;ENST00000504900	T;T;T;T;T;T	0.10477	2.87;2.87;2.87;2.87;2.87;2.87	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.33498	0.0865	M	0.79011	2.435	0.80722	D	1	B;P;D;P	0.76494	0.209;0.59;0.999;0.59	B;B;D;B	0.74023	0.06;0.087;0.982;0.087	T	0.03202	-1.1061	10	0.33940	T	0.23	-20.0264	15.6928	0.77469	1.0:0.0:0.0:0.0	.	86;86;86;86	E7EPM6;B7Z452;D6RER0;P33121	.;.;.;ACSL1_HUMAN	N	86	ENSP00000422607:Y86N;ENSP00000281455:Y86N;ENSP00000426244:Y86N;ENSP00000425006:Y86N;ENSP00000426150:Y86N;ENSP00000424935:Y86N	ENSP00000281455:Y86N	Y	-	1	0	ACSL1	185946819	1.000000	0.71417	0.778000	0.31720	0.911000	0.54048	5.192000	0.65115	2.247000	0.74100	0.482000	0.46254	TAT	.	.		0.488	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995		T	185709825	A	T	185709825	3	4	107	1	0	0	0	0	1	0	0	0	177	420	15	4	1916	4	ACSL1	4	185709825	Missense_Mutation	SNP	A	TCGA-DD-A1EK-01A-11D-A20W-10	137131758	185709825	5444451	25	16012										
C7	730	hgsc.bcm.edu	37	chr5	40981550	40981550	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	agtgcgaggaagaagggtttAgcatttgtgtggaagtgaac	16	3	0	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr5:40981550A>T	ENST00000313164.9	+	18	2766	c.2407A>T	c.(2407-2409)Agc>Tgc	p.S803C		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	803	Factor I module (FIM) 2.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)							Ovarian(839;0.0112)				AGAAGGGTTTAGCATTTGTGT	0.517																																					p.S803C		Atlas-SNP	.											.	C7	136	.	0			c.A2407T						.						74	76	75					5																	40981550		2132	4236	6368	SO:0001583	missense	730	exon18			GGGTTTAGCATTT	J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"Complement system"	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.2407A>T	chr5.hg19:g.40981550A>T	ENSP00000322061:p.Ser803Cys	205.0	0.0		151.0	70.0	NM_000587	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	hg19	CCDS47201.1	.	.	.	.	.	.	.	.	.	.	A	17.51	3.407957	0.62399	.	.	ENSG00000112936	ENST00000313164	T	0.64803	-0.12	5.83	-1.58	0.08479	Factor I / membrane attack complex (1);	1.436230	0.03721	N	0.251895	T	0.55768	0.1941	L	0.46157	1.445	0.09310	N	1	P	0.45176	0.852	P	0.45138	0.471	T	0.47484	-0.9114	10	0.41790	T	0.15	0.8743	3.3023	0.06987	0.3986:0.3284:0.0615:0.2115	.	803	P10643	CO7_HUMAN	C	803	ENSP00000322061:S803C	ENSP00000322061:S803C	S	+	1	0	C7	41017307	0.000000	0.05858	0.000000	0.03702	0.579000	0.36224	0.202000	0.17295	-0.131000	0.11578	0.460000	0.39030	AGC	.	.		0.517	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1			T	40981550	A	T	40981550	3	4	107	1	0	0	0	0	1	0	0	0	2377	420	15	4	2477	4	C7	5	40981550	Missense_Mutation	SNP	A	TCGA-DD-A1EK-01A-11D-A20W-10		40981550	139933710	26	16013										
CEP120	153241	hgsc.bcm.edu	37	chr5	122725672	122725672	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	taaactttccacttcactttCtgttgcatcatcttttgttg	4	10	4	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr5:122725672C>T	ENST00000306467.5	-	8	1505	c.1201G>A	c.(1201-1203)Gaa>Aaa	p.E401K	CEP120_ENST00000306481.6_Missense_Mutation_p.E375K|CEP120_ENST00000328236.5_Missense_Mutation_p.E401K			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	401					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						ACTTCACTTTCTGTTGCATCA	0.398																																					p.E401K		Atlas-SNP	.											.	CEP120	72	.	0			c.G1201A						.						184	166	172					5																	122725672		1895	4122	6017	SO:0001583	missense	153241	exon9			CACTTTCTGTTGC	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"coiled-coil domain containing 100"	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.1201G>A	chr5.hg19:g.122725672C>T	ENSP00000303058:p.Glu401Lys	339.0	0.0		282.0	100.0	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Missense_Mutation	SNP	ENST00000306467.5	hg19	CCDS4134.2	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387204	0.61956	.	.	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481;ENST00000508442	T;T;T;T	0.51071	2.05;2.05;2.05;0.72	5.28	5.28	0.74379	.	0.063920	0.64402	D	0.000009	T	0.51618	0.1685	M	0.67953	2.075	0.80722	D	1	B	0.28971	0.229	B	0.35114	0.196	T	0.47598	-0.9105	10	0.17832	T	0.49	-7.7679	18.8976	0.92430	0.0:1.0:0.0:0.0	.	401	Q8N960	CE120_HUMAN	K	401;401;375;375	ENSP00000303058:E401K;ENSP00000327504:E401K;ENSP00000307419:E375K;ENSP00000421620:E375K	ENSP00000303058:E401K	E	-	1	0	CEP120	122753571	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	5.658000	0.68003	2.483000	0.83821	0.467000	0.42956	GAA	.	.		0.398	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223		T	122725672	C	T	122725672	3	4	107	1	0	0	0	0	1	0	0	0	3248	922	32	3	1811	3	CEP120	5	122725672	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10	81744122	122725672	58189588	27	16014										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222268	140222268	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	gtgaacgacaatgctccggcGttcgcgcagcccgagtacac	12	14	0	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr5:140222268G>A	ENST00000531613.1	+	1	1362	c.1362G>A	c.(1360-1362)gcG>gcA	p.A454A	PCDHA8_ENST00000378123.3_Silent_p.A454A|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	454	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGCTCCGGCGTTCGCGCAGC	0.662																																					p.A454A		Atlas-SNP	.											PCDHA8_ENST00000531613,caecum,carcinoma,0,2	PCDHA8	366	.	0			c.G1362A						.						61	62	62					5																	140222268		2194	4266	6460	SO:0001819	synonymous_variant	56140	exon1			TCCGGCGTTCGCG	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1362G>A	chr5.hg19:g.140222268G>A		428.0	0.0		354.0	142.0	NM_031856	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	hg19	CCDS54919.1																																																																																			.	.		0.662	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		A	140222268	G	A	140222268	2	1	107	1	0	0	0	0	0	0	0	1	11539	1132	40	1		1	PCDHA8	5	140222268	Silent	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	17496596	140222268	40692992	28	16015										
TLX3	30012	hgsc.bcm.edu	37	chr5	170736448	170736448	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tcgaccagatccttaacagcCcggaccaggacagcgcaccc	9	17	0	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr5:170736448C>A	ENST00000296921.5	+	1	161	c.79C>A	c.(79-81)Ccg>Acg	p.P27T		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	27					central nervous system development (GO:0007417)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|respiratory gaseous exchange (GO:0007585)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CCTTAACAGCCCGGACCAGGA	0.761			T	BCL11B	T-ALL																																p.P27T	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"T-cell leukemia, homeobox 3 (HOX11L2)"		L	.	TLX3	23	.	0			c.C79A						.						12	15	14					5																	170736448		2184	4269	6453	SO:0001583	missense	30012	exon1			AACAGCCCGGACC	AJ223798	CCDS34288.1	5q35.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000164438	ENSG00000164438		"Homeoboxes / ANTP class : NKL subclass"	13532	protein-coding gene	gene with protein product		604640	"homeo box 11-like 2", "T-cell leukemia, homeobox 3"	HOX11L2		11435718, 11435716	Standard	NM_021025		Approved	RNX	uc003mbf.3	O43711	OTTHUMG00000163207	ENST00000296921.5:c.79C>A	chr5.hg19:g.170736448C>A	ENSP00000296921:p.Pro27Thr	23.0	0.0		28.0	10.0	NM_021025	Q96AD3	Missense_Mutation	SNP	ENST00000296921.5	hg19	CCDS34288.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.472224	0.26423	.	.	ENSG00000164438	ENST00000296921	D	0.91521	-2.86	4.51	3.64	0.41730	.	0.252179	0.39909	N	0.001227	D	0.82921	0.5142	L	0.28400	0.85	0.28954	N	0.890225	B	0.15930	0.015	B	0.16289	0.015	T	0.75059	-0.3451	10	0.48119	T	0.1	.	7.4648	0.27316	0.0:0.7386:0.1709:0.0905	.	27	O43711	TLX3_HUMAN	T	27	ENSP00000296921:P27T	ENSP00000296921:P27T	P	+	1	0	TLX3	170669053	0.991000	0.36638	1.000000	0.80357	0.962000	0.63368	0.849000	0.27723	1.105000	0.41606	0.455000	0.32223	CCG	.	.		0.761	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3			A	170736448	C	A	170736448	3	1	107	1	0	0	0	0	1	0	0	0	15977	623	22	3	81	3	TLX3	5	170736448	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10	30514180	170736448	10178812	29	16016										
UNC5A	90249	hgsc.bcm.edu	37	chr5	176305056	176305056	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ctcaagctgcttctgtttgcGccggtggcctgcacctccct	10	16	2	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr5:176305056G>A	ENST00000329542.4	+	11	2071	c.1797G>A	c.(1795-1797)gcG>gcA	p.A599A	UNC5A_ENST00000261961.3_Silent_p.A559A	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	599					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTCTGTTTGCGCCGGTGGCCT	0.662																																					p.A599A		Atlas-SNP	.											.	UNC5A	76	.	0			c.G1797A						.						44	42	42					5																	176305056		2203	4296	6499	SO:0001819	synonymous_variant	90249	exon11			GTTTGCGCCGGTG	AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"Immunoglobulin superfamily / I-set domain containing"	12567	protein-coding gene	gene with protein product		607869	"unc5 (C.elegans homolog) a"				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.1797G>A	chr5.hg19:g.176305056G>A		94.0	0.0		87.0	47.0	NM_133369	B2RXE6|Q8TF26|Q96GP4	Silent	SNP	ENST00000329542.4	hg19	CCDS34299.1																																																																																			.	.		0.662	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300		A	176305056	G	A	176305056	2	1	107	1	0	0	0	0	0	0	0	1	17006	1074	38	1		1	UNC5A	5	176305056	Silent	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	5568608	176305056	4610204	30	16017										
FLOT1	8870	hgsc.bcm.edu	37	chr6	30709635	30709635	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ccaccatgactggggggcttCggcagaaccctgcaaggtgt	14	12	0	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr6:30709635C>T	ENST00000259874.5	-	0	1244				FLOT1_ENST00000376389.3_Missense_Mutation_p.R18Q|FLOT1_ENST00000470643.1_5'UTR|FLOT1_ENST00000456573.2_Missense_Mutation_p.R18Q|XXbac-BPG252P9.10_ENST00000607333.1_RNA	NM_003897.3	NP_003888.2	P46695	IEX1_HUMAN	immediate early response 3						anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glycolytic process (GO:0045820)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|negative regulation of systemic arterial blood pressure (GO:0003085)|positive regulation of protein catabolic process (GO:0045732)|regulation of DNA repair (GO:0006282)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of response to DNA damage stimulus (GO:2001020)|response to protozoan (GO:0001562)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)	1						TGGGGGGCTTCGGCAGAACCC	0.617																																					p.R18Q		Atlas-SNP	.											.	FLOT1	28	.	0			c.G53A						.						51	54	53					6																	30709635		1509	2708	4217	SO:0001628	intergenic_variant	10211	exon3			GGGCTTCGGCAGA	AF083421	CCDS4689.1	6p21.3	2010-02-17			ENSG00000137331	ENSG00000137331			5392	protein-coding gene	gene with protein product		602996				8603392, 9703517	Standard	NM_003897		Approved	IEX-1, DIF-2, PRG1, IEX-1L	uc003nrn.3	P46695	OTTHUMG00000031265		chr6.hg19:g.30709635C>T		91.0	0.0		80.0	37.0	NM_005803	Q5SU30|Q92691|Q93044	Missense_Mutation	SNP	ENST00000259874.5	hg19	CCDS4689.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951338	0.53186	.	.	ENSG00000137312	ENST00000376389;ENST00000456573;ENST00000438162;ENST00000445853;ENST00000416018;ENST00000454845	T;T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29;1.29	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.17152	0.0412	L	0.42632	1.34	0.58432	D	0.999992	B;B	0.26809	0.011;0.16	B;B	0.20184	0.007;0.028	T	0.03344	-1.1046	10	0.29301	T	0.29	-20.1662	14.5746	0.68238	0.0:1.0:0.0:0.0	.	18;18	B4DVY7;O75955	.;FLOT1_HUMAN	Q	18	ENSP00000365569:R18Q;ENSP00000394375:R18Q;ENSP00000400615:R18Q;ENSP00000398834:R18Q;ENSP00000412058:R18Q;ENSP00000391341:R18Q	ENSP00000365569:R18Q	R	-	2	0	FLOT1	30817614	1.000000	0.71417	0.997000	0.53966	0.896000	0.52359	4.946000	0.63576	2.356000	0.79943	0.462000	0.41574	CGA	.	.		0.617	IER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076578.2			T	30709635	C	T	30709635	1	4	107	0	1	0	0	0	0	0	0	0	5944	884	31	1		1	FLOT1	6	30709635	IGR	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10		30709635	140405432	31	16018										
UBR2	23304	hgsc.bcm.edu	37	chr6	42585071	42585071	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tccagttcttcaccgcacctActctggtgagtagtgcttgc	9	13	3	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr6:42585071A>G	ENST00000372899.1	+	11	1534	c.1276A>G	c.(1276-1278)Act>Gct	p.T426A	UBR2_ENST00000372901.1_Intron|UBR2_ENST00000372903.2_Intron|UBR2_ENST00000372883.3_Intron	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	426					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			CACCGCACCTACTCTGGTGAG	0.448																																					p.T426A		Atlas-SNP	.											.	UBR2	134	.	0			c.A1276G						.						124	109	114					6																	42585071		2203	4300	6503	SO:0001583	missense	23304	exon11			GCACCTACTCTGG	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.1276A>G	chr6.hg19:g.42585071A>G	ENSP00000361990:p.Thr426Ala	157.0	0.0		147.0	62.0	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	hg19	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	A	18.18	3.566220	0.65651	.	.	ENSG00000024048	ENST00000372899	T	0.56776	0.44	4.95	4.95	0.65309	.	.	.	.	.	T	0.44201	0.1282	M	0.70595	2.14	0.80722	D	1	B	0.28026	0.198	B	0.35039	0.194	T	0.50101	-0.8867	9	0.42905	T	0.14	.	14.9141	0.70781	1.0:0.0:0.0:0.0	.	426	Q8IWV8	UBR2_HUMAN	A	426	ENSP00000361990:T426A	ENSP00000361990:T426A	T	+	1	0	UBR2	42693049	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.910000	0.92685	1.995000	0.58328	0.533000	0.62120	ACT	.	.		0.448	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		G	42585071	A	G	42585071	3	3	107	1	0	0	0	0	1	0	0	0	16917	391	14	2	1318	2	UBR2	6	42585071	Missense_Mutation	SNP	A	TCGA-DD-A1EK-01A-11D-A20W-10	11875436	42585071	128529996	32	16019										
GFRAL	389400	hgsc.bcm.edu	37	chr6	55198738	55198738	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ggaaaaaaatgtatcaataaAtcaggtaatattttgtttta	6	2	2	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr6:55198738A>G	ENST00000340465.2	+	3	398	c.312A>G	c.(310-312)aaA>aaG	p.K104K		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	104					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			GTATCAATAAATCAGGTAATA	0.274																																					p.K104K		Atlas-SNP	.											.	GFRAL	91	.	0			c.A312G						.						73	78	76					6																	55198738		2203	4298	6501	SO:0001819	synonymous_variant	389400	exon3			CAATAAATCAGGT	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.312A>G	chr6.hg19:g.55198738A>G		32.0	0.0		20.0	11.0	NM_207410	Q5VTF6	Silent	SNP	ENST00000340465.2	hg19	CCDS4957.1																																																																																			.	.		0.274	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		G	55198738	A	G	55198738	2	3	107	1	0	0	0	0	0	0	0	1	6359	98	4	2		2	GFRAL	6	55198738	Silent	SNP	A	TCGA-DD-A1EK-01A-11D-A20W-10	12613667	55198738	115916329	33	16020										
NT5C3	51251	hgsc.bcm.edu	37	chr7	33054407	33054407	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	atcttgtactaaaacaatatCataagagtccatgtactttt	4	7	2	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr7:33054407C>A	ENST00000242210.7	-	9	1022	c.946G>T	c.(946-948)Gat>Tat	p.D316Y	NT5C3A_ENST00000396152.2_Missense_Mutation_p.D277Y|AVL9_ENST00000404479.1_Intron|NT5C3A_ENST00000381626.2_Missense_Mutation_p.D265Y|NT5C3A_ENST00000409467.1_Missense_Mutation_p.D265Y|NT5C3A_ENST00000405342.1_Missense_Mutation_p.D277Y|NT5C3A_ENST00000610140.1_Missense_Mutation_p.D311Y	NM_001002009.2|NM_001002010.2	NP_001002009.1|NP_001002010.1	Q9H0P0	5NT3A_HUMAN	5'-nucleotidase, cytosolic IIIA	316					dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside metabolic process (GO:0006213)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	2'-phosphotransferase activity (GO:0008665)|5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)										AAAACAATATCATAAGAGTCC	0.338																																					p.D316Y		Atlas-SNP	.											.	.	.	.	0			c.G946T						.						92	95	94					7																	33054407		2203	4298	6501	SO:0001583	missense	0	exon9			CAATATCATAAGA	AF312735	CCDS34616.1, CCDS34617.1, CCDS55101.1	7p14.3	2013-03-06	2013-03-06	2013-03-06	ENSG00000122643	ENSG00000122643	3.1.3.5		17820	protein-coding gene	gene with protein product	"lupin"	606224	"5'-nucleotidase, cytosolic III"	NT5C3		11042152, 10942414	Standard	NM_001002010		Approved	UMPH1, PSN1, PN-I, UMPH, P5'N-1, cN-III, p36, POMP, hUMP1	uc003tdk.4	Q9H0P0	OTTHUMG00000152983	ENST00000242210.7:c.946G>T	chr7.hg19:g.33054407C>A	ENSP00000242210:p.Asp316Tyr	46.0	0.0		46.0	8.0	NM_001002010	A8K253|B2RAA5|B8ZZC4|Q6IPZ1|Q6NXS6|Q7L3G6|Q9P0P5|Q9UC42|Q9UC43|Q9UC44|Q9UC45	Missense_Mutation	SNP	ENST00000242210.7	hg19	CCDS34616.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891382	0.91889	.	.	ENSG00000122643	ENST00000381626;ENST00000396152;ENST00000242210;ENST00000405342;ENST00000409467	D;D;D;D;D	0.89617	-2.54;-2.54;-2.54;-2.54;-2.54	5.94	5.94	0.96194	HAD-like domain (1);	0.000000	0.85682	D	0.000000	D	0.96291	0.8790	M	0.94063	3.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.991	D	0.96512	0.9379	10	0.87932	D	0	.	20.3736	0.98901	0.0:1.0:0.0:0.0	.	316;277	Q9H0P0;Q9H0P0-1	5NT3_HUMAN;.	Y	265;277;316;277;265	ENSP00000371039:D265Y;ENSP00000379456:D277Y;ENSP00000242210:D316Y;ENSP00000385261:D277Y;ENSP00000387166:D265Y	ENSP00000242210:D316Y	D	-	1	0	NT5C3	33020932	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	7.818000	0.86416	2.820000	0.97059	0.650000	0.86243	GAT	.	.		0.338	NT5C3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328880.1	NM_016489		A	33054407	C	A	33054407	3	1	107	1	0	0	0	0	1	0	0	0	10697	826	29	3	68	3	NT5C3	7	33054407	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10		33054407	126084256	34	16021										
PCLO	27445	hgsc.bcm.edu	37	chr7	82580517	82580517	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ctatggtgcatggcaggtaaTgaagtcactgcatcagccgt	12	9	2	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr7:82580517T>G	ENST00000333891.9	-	6	9724	c.9387A>C	c.(9385-9387)tcA>tcC	p.S3129S	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Silent_p.S3129S	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGGCAGGTAATGAAGTCACTG	0.448																																					p.S3129S		Atlas-SNP	.											.	PCLO	1506	.	0			c.A9387C						.						67	69	69					7																	82580517		2025	4193	6218	SO:0001819	synonymous_variant	27445	exon6			AGGTAATGAAGTC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.9387A>C	chr7.hg19:g.82580517T>G		184.0	0.0		153.0	57.0	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.448	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82580517	T	G	82580517	2	3	107	1	0	0	0	0	0	0	0	1	11592	1451	51	5		5	PCLO	7	82580517	Silent	SNP	T	TCGA-DD-A1EK-01A-11D-A20W-10	49526110	82580517	76558146	35	16022										
C7orf45	136263	hgsc.bcm.edu	37	chr7	129847775	129847775	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	gagaccttttttccttatttTgggaggtagatcctccccca	8	11	0	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr7:129847775T>G	ENST00000297819.3	+	1	76	c.25T>G	c.(25-27)Tgg>Ggg	p.W9G	TMEM209_ENST00000397622.2_5'Flank|TMEM209_ENST00000462753.1_5'Flank|TMEM209_ENST00000473456.1_5'Flank|TMEM209_ENST00000336804.8_5'Flank|RP11-775D22.3_ENST00000483283.1_RNA	NM_145268.3	NP_660311.1	Q8WWF3	SSMM1_HUMAN	serine-rich single-pass membrane protein 1	9						integral component of membrane (GO:0016021)											TTCCTTATTTTGGGAGGTAGA	0.428																																					p.W9G		Atlas-SNP	.											.	.	.	.	0			c.T25G						.						178	169	172					7																	129847775		2203	4300	6503	SO:0001583	missense	0	exon1			TTATTTTGGGAGG	AK097635	CCDS5816.1	7q32.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000165120	ENSG00000165120			29580	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 45"	C7orf45		12477932	Standard	NM_145268		Approved	FLJ40316	uc003vpp.3	Q8WWF3	OTTHUMG00000157844	ENST00000297819.3:c.25T>G	chr7.hg19:g.129847775T>G	ENSP00000297819:p.Trp9Gly	198.0	0.0		164.0	62.0	NM_145268		Missense_Mutation	SNP	ENST00000297819.3	hg19	CCDS5816.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.304963	0.60305	.	.	ENSG00000165120	ENST00000297819	T	0.51817	0.69	5.54	4.39	0.52855	.	0.000000	0.64402	D	0.000014	T	0.61362	0.2341	M	0.67953	2.075	0.38034	D	0.935266	D	0.76494	0.999	D	0.65443	0.935	T	0.66480	-0.5913	10	0.87932	D	0	-0.5736	8.2812	0.31902	0.0:0.0896:0.0:0.9104	.	9	Q8WWF3	CG045_HUMAN	G	9	ENSP00000297819:W9G	ENSP00000297819:W9G	W	+	1	0	C7orf45	129635011	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.753000	0.38359	1.061000	0.40601	0.533000	0.62120	TGG	.	.		0.428	SSMEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349768.1	NM_145268		G	129847775	T	G	129847775	3	3	107	1	0	0	0	0	1	0	0	0	2397	1812	63	5	27	5	C7orf45	7	129847775	Missense_Mutation	SNP	T	TCGA-DD-A1EK-01A-11D-A20W-10	47267258	129847775	29290888	36	16023										
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885313	88885313	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tagtggccctcaagtcccacAgcttgatagttccagtcatg	9	12	2	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr8:88885313A>G	ENST00000319675.3	-	1	983	c.887T>C	c.(886-888)cTg>cCg	p.L296P		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	296										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						CAAGTCCCACAGCTTGATAGT	0.488																																					p.L296P		Atlas-SNP	.											.	DCAF4L2	187	.	0			c.T887C						.						106	95	99					8																	88885313		2203	4300	6503	SO:0001583	missense	138009	exon1			TCCCACAGCTTGA	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.887T>C	chr8.hg19:g.88885313A>G	ENSP00000316496:p.Leu296Pro	214.0	0.0		189.0	48.0	NM_152418		Missense_Mutation	SNP	ENST00000319675.3	hg19	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	A	19.99	3.929400	0.73327	.	.	ENSG00000176566	ENST00000319675	T	0.67345	-0.26	1.92	1.92	0.25849	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83871	0.5348	H	0.95114	3.625	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83456	0.0051	10	0.87932	D	0	.	7.449	0.27227	1.0:0.0:0.0:0.0	.	296	Q8NA75	DC4L2_HUMAN	P	296	ENSP00000316496:L296P	ENSP00000316496:L296P	L	-	2	0	DCAF4L2	88954429	0.998000	0.40836	0.443000	0.26883	0.758000	0.43043	3.314000	0.51943	0.627000	0.30340	0.383000	0.25322	CTG	.	.		0.488	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		G	88885313	A	G	88885313	3	3	107	1	0	0	0	0	1	0	0	0	4274	188	7	2	304	2	DCAF4L2	8	88885313	Missense_Mutation	SNP	A	TCGA-DD-A1EK-01A-11D-A20W-10		88885313	57478709	37	16024										
TSC1	7248	hgsc.bcm.edu	37	chr9	135782757	135782757	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tgcagaatccattctctcttCctgaaaagataagtatcatt	5	9	3	3			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr9:135782757C>A	ENST00000298552.3	-	13	1485	c.1264G>T	c.(1264-1266)Gaa>Taa	p.E422*	TSC1_ENST00000545250.1_Splice_Site_p.E371*|TSC1_ENST00000440111.2_Splice_Site_p.E422*	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	422					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		ATTCTCTCTTCCTGAAAAGAT	0.393			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.E422X		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.G1264T						.						121	106	111					9																	135782757		2203	4300	6503	SO:0001630	splice_region_variant	7248	exon13	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TCTCTTCCTGAAA	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.1264-1G>T	chr9.hg19:g.135782757C>A		169.0	0.0		93.0	60.0	NM_000368	B7Z897|Q5VVN5	Nonsense_Mutation	SNP	ENST00000298552.3	hg19	CCDS6956.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.231403|5.231403	0.95207|0.95207	.|.	.|.	ENSG00000165699|ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250|ENST00000424271	.|.	.|.	.|.	5.54|5.54	4.64|4.64	0.57946|0.57946	.|.	0.315793|.	0.39985|.	N|.	0.001210|.	.|T	.|0.72003	.|0.3407	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74842	.|-0.3527	.|5	0.48119|0.72032	T|D	0.1|0.01	-17.673|-17.673	11.7194|11.7194	0.51672|0.51672	0.0:0.9175:0.0:0.0825|0.0:0.9175:0.0:0.0825	.|.	.|.	.|.	.|.	X|S	422;422;371|300	.|.	ENSP00000298552:E422X|ENSP00000393473:R300S	E|R	-|-	1|3	0|2	TSC1|TSC1	134772578|134772578	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.074000|0.074000	0.17049|0.17049	2.584000|2.584000	0.46102|0.46102	1.352000|1.352000	0.45808|0.45808	-0.203000|-0.203000	0.12734|0.12734	GAA|AGG	.	.		0.393	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		Nonsense_Mutation	A	135782757	C	A	135782757	5	1	107	1	0	0	0	0	0	0	1	0	16620	869	30	3	2274	3	TSC1	9	135782757	Splice_Site	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10		135782757	5430674	38	16025										
BTAF1	9044	hgsc.bcm.edu	37	chr10	93722349	93722349	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ctagaataattgaaggactcCaggatcttgatgatgatgtc	10	6	1	5			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr10:93722349C>G	ENST00000265990.6	+	12	1626	c.1318C>G	c.(1318-1320)Cag>Gag	p.Q440E	BTAF1_ENST00000471217.1_3'UTR	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	440					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				TGAAGGACTCCAGGATCTTGA	0.313																																					p.Q440E		Atlas-SNP	.											.	BTAF1	148	.	0			c.C1318G						.						53	53	53					10																	93722349		2203	4300	6503	SO:0001583	missense	9044	exon12			GGACTCCAGGATC	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.1318C>G	chr10.hg19:g.93722349C>G	ENSP00000265990:p.Gln440Glu	405.0	0.0		375.0	150.0	NM_003972	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	hg19	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	C	9.298	1.052426	0.19907	.	.	ENSG00000095564	ENST00000265990	T	0.64618	-0.11	6.05	6.05	0.98169	Armadillo-like helical (1);Armadillo-type fold (1);	0.056876	0.64402	D	0.000001	T	0.47173	0.1431	N	0.19112	0.55	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.48293	-0.9048	10	0.02654	T	1	4.064	20.6013	0.99457	0.0:1.0:0.0:0.0	.	440	O14981	BTAF1_HUMAN	E	440	ENSP00000265990:Q440E	ENSP00000265990:Q440E	Q	+	1	0	BTAF1	93712329	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.788000	0.75105	2.878000	0.98634	0.650000	0.86243	CAG	.	.		0.313	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		G	93722349	C	G	93722349	3	3	107	1	0	0	0	0	1	0	0	0	1538	595	21	4	1364	4	BTAF1	10	93722349	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10		93722349	41812398	39	16026										
ANO9	338440	hgsc.bcm.edu	37	chr11	432029	432029	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ggtcttgttgttcatgacaaCgaagttcacgattcggattc	10	8	3	1	rs139380371		TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr11:432029C>T	ENST00000332826.6	-	5	460	c.376G>A	c.(376-378)Gtt>Att	p.V126I		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	126					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)	p.V126I(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						TTCATGACAACGAAGTTCACG	0.622																																					p.V126I		Atlas-SNP	.											ANO9,NS,carcinoma,0,1	ANO9	61	.	1	Substitution - Missense(1)	prostate(1)	c.G376A						.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	83	70	75		376	-5.6	0	11	dbSNP_134	75	0,8598		0,0,4299	no	missense	ANO9	NM_001012302.2	29	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	benign	126/783	432029	1,13003	2203	4299	6502	SO:0001583	missense	338440	exon5			TGACAACGAAGTT	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	20679	protein-coding gene	gene with protein product			"tumor protein p53 inducible protein 5", "transmembrane protein 16J"	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.376G>A	chr11.hg19:g.432029C>T	ENSP00000332788:p.Val126Ile	86.0	0.0		89.0	30.0	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	hg19	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	C	0.148	-1.094503	0.01858	2.27E-4	0.0	ENSG00000185101	ENST00000332826	T	0.62105	0.05	3.39	-5.56	0.02529	.	.	.	.	.	T	0.33118	0.0852	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.40664	-0.9551	9	0.02654	T	1	.	8.7427	0.34567	0.0:0.2539:0.1123:0.6338	.	126	A1A5B4	ANO9_HUMAN	I	126	ENSP00000332788:V126I	ENSP00000332788:V126I	V	-	1	0	ANO9	422029	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.468000	0.02350	-1.392000	0.02082	0.484000	0.47621	GTT	.	C|1.000;T|0.000		0.622	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302		T	432029	C	T	432029	3	4	107	1	0	0	0	0	1	0	0	0	704	536	19	1	2048	1	ANO9	11	432029	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10		432029	134574487	40	16027										
CHD4	1108	hgsc.bcm.edu	37	chr12	6692504	6692504	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	agtagtcaggatccacacttTcttcctgtttaatgatttcc	6	10	2	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr12:6692504T>C	ENST00000357008.2	-	26	4083	c.3920A>G	c.(3919-3921)gAa>gGa	p.E1307G	CHD4_ENST00000540960.1_5'UTR|CHD4_ENST00000309577.6_Missense_Mutation_p.E1307G|RP5-940J5.6_ENST00000501075.2_RNA|CHD4_ENST00000544040.1_Missense_Mutation_p.E1300G|CHD4_ENST00000544484.1_Missense_Mutation_p.E1304G|SCARNA11_ENST00000516089.1_RNA	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1307					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						ATCCACACTTTCTTCCTGTTT	0.517																																					p.E1307G	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.A3920G						.						221	211	214					12																	6692504		2203	4300	6503	SO:0001583	missense	1108	exon26			ACACTTTCTTCCT	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.3920A>G	chr12.hg19:g.6692504T>C	ENSP00000349508:p.Glu1307Gly	180.0	0.0		159.0	55.0	NM_001273	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	hg19	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.762199	0.69763	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	D;D;D;D	0.91686	-2.83;-2.89;-2.84;-2.89	5.96	5.96	0.96718	Domain of unknown function DUF1087 (1);	0.000000	0.85682	D	0.000000	D	0.95510	0.8541	M	0.68317	2.08	0.80722	D	1	D;D;P	0.89917	1.0;0.998;0.925	D;D;P	0.85130	0.997;0.987;0.621	D	0.95713	0.8759	10	0.66056	D	0.02	-8.5998	16.4484	0.83959	0.0:0.0:0.0:1.0	.	1307;1307;1300	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	G	1304;1300;1307;1307;1281	ENSP00000440392:E1304G;ENSP00000440542:E1300G;ENSP00000312419:E1307G;ENSP00000349508:E1307G	ENSP00000312419:E1307G	E	-	2	0	CHD4	6562765	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.013000	0.88655	2.285000	0.76669	0.533000	0.62120	GAA	.	.		0.517	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		C	6692504	T	C	6692504	3	2	107	1	0	0	0	0	1	0	0	0	3329	1783	62	2	1878	2	CHD4	12	6692504	Missense_Mutation	SNP	T	TCGA-DD-A1EK-01A-11D-A20W-10		6692504	127159391	41	16028										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43792900	43792900	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tattggctttccatgaagggCatctgacagatctacaggct	10	9	2	3			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr12:43792900C>A	ENST00000389420.3	-	29	4420	c.4421G>T	c.(4420-4422)tGc>tTc	p.C1474F		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1474	TSP type-1 11. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		CCATGAAGGGCATCTGACAGA	0.313																																					p.C1474F		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.G4421T						.						129	107	115					12																	43792900		2172	4242	6414	SO:0001583	missense	80070	exon29			GAAGGGCATCTGA	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.4421G>T	chr12.hg19:g.43792900C>A	ENSP00000374071:p.Cys1474Phe	177.0	0.0		147.0	51.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	C	17.89	3.500584	0.64298	.	.	ENSG00000173157	ENST00000389420	D	0.98762	-5.12	4.86	4.86	0.63082	.	0.000000	0.64402	D	0.000019	D	0.99527	0.9831	H	0.98818	4.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97777	1.0230	10	0.87932	D	0	.	15.7555	0.78021	0.0:1.0:0.0:0.0	.	1474	P59510	ATS20_HUMAN	F	1474	ENSP00000374071:C1474F	ENSP00000374071:C1474F	C	-	2	0	ADAMTS20	42079167	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	4.809000	0.62591	2.621000	0.88768	0.650000	0.86243	TGC	.	.		0.313	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		A	43792900	C	A	43792900	3	1	107	1	0	0	0	0	1	0	0	0	266	710	25	3	1354	3	ADAMTS20	12	43792900	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10	37100396	43792900	90058995	42	16029										
ADCY6	112	hgsc.bcm.edu	37	chr12	49170256	49170256	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ggttggccagggtcacatcaTtggaccacacatcgaactgc	11	12	2	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr12:49170256T>C	ENST00000307885.4	-	6	2184	c.1490A>G	c.(1489-1491)aAt>aGt	p.N497S	ADCY6_ENST00000357869.3_Missense_Mutation_p.N497S|ADCY6_ENST00000552090.1_5'UTR|ADCY6_ENST00000550422.1_Missense_Mutation_p.N497S	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	497					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						GGTCACATCATTGGACCACAC	0.647																																					p.N497S		Atlas-SNP	.											.	ADCY6	81	.	0			c.A1490G						.						68	61	63					12																	49170256		2203	4299	6502	SO:0001583	missense	112	exon7			ACATCATTGGACC		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"Adenylate cyclases"	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.1490A>G	chr12.hg19:g.49170256T>C	ENSP00000311405:p.Asn497Ser	131.0	0.0		95.0	36.0	NM_020983	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	hg19	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.127400	0.77549	.	.	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	D;D;D	0.84516	-1.86;-1.86;-1.86	4.17	4.17	0.49024	Adenylyl cyclase class-3/4/guanylyl cyclase, conserved site (1);Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.91372	0.7278	M	0.79258	2.445	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.983	D	0.91964	0.5581	10	0.59425	D	0.04	.	12.6197	0.56595	0.0:0.0:0.0:1.0	.	497;497	O43306-2;O43306	.;ADCY6_HUMAN	S	497	ENSP00000350536:N497S;ENSP00000446730:N497S;ENSP00000311405:N497S	ENSP00000311405:N497S	N	-	2	0	ADCY6	47456523	1.000000	0.71417	0.991000	0.47740	0.922000	0.55478	7.868000	0.87116	1.881000	0.54492	0.260000	0.18958	AAT	.	.		0.647	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		C	49170256	T	C	49170256	3	2	107	1	0	0	0	0	1	0	0	0	298	1493	52	2	2080	2	ADCY6	12	49170256	Missense_Mutation	SNP	T	TCGA-DD-A1EK-01A-11D-A20W-10	5377356	49170256	84681639	43	16030										
RBM19	9904	hgsc.bcm.edu	37	chr12	114386746	114386746	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ctcctcctcttcgttctcccCgagtatccggccttgccagg	8	18	2	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr12:114386746C>T	ENST00000545145.2	-	10	1246	c.1168G>A	c.(1168-1170)Ggg>Agg	p.G390R	RBM19_ENST00000392561.3_Missense_Mutation_p.G390R|RBM19_ENST00000261741.5_Missense_Mutation_p.G390R	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	390					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G390W(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TCGTTCTCCCCGAGTATCCGG	0.577																																					p.G390R		Atlas-SNP	.											.	RBM19	117	.	2	Substitution - Missense(2)	lung(2)	c.G1168A						.						190	184	186					12																	114386746		2203	4300	6503	SO:0001583	missense	9904	exon10			TCTCCCCGAGTAT	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"RNA binding motif (RRM) containing"	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1168G>A	chr12.hg19:g.114386746C>T	ENSP00000442053:p.Gly390Arg	321.0	0.0		260.0	93.0	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	hg19	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	C	8.335	0.827432	0.16749	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.06371	3.31;3.31;3.31	4.33	2.12	0.27331	Nucleotide-binding, alpha-beta plait (1);	0.242933	0.40728	N	0.001039	T	0.04497	0.0123	L	0.38531	1.155	0.29189	N	0.875971	B	0.18461	0.028	B	0.13407	0.009	T	0.32771	-0.9894	10	0.19590	T	0.45	-28.3677	5.452	0.16570	0.0:0.5618:0.0:0.4382	.	390	Q9Y4C8	RBM19_HUMAN	R	390	ENSP00000442053:G390R;ENSP00000376344:G390R;ENSP00000261741:G390R	ENSP00000261741:G390R	G	-	1	0	RBM19	112871129	0.999000	0.42202	0.936000	0.37596	0.387000	0.30353	3.592000	0.53993	0.820000	0.34516	0.561000	0.74099	GGG	.	.		0.577	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		T	114386746	C	T	114386746	3	4	107	1	0	0	0	0	1	0	0	0	13136	652	23	1	1774	1	RBM19	12	114386746	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10	65216490	114386746	19465149	44	16031										
ATP7B	540	hgsc.bcm.edu	37	chr13	52548363	52548363	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tgatctgtcccactcccttcGgctccatcaggaagagaaac	8	14	2	2	rs377294197		TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr13:52548363G>A	ENST00000242839.4	-	2	1149	c.993C>T	c.(991-993)gcC>gcT	p.A331A	ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000400370.3_Silent_p.A331A|ATP7B_ENST00000418097.2_Silent_p.A331A|ATP7B_ENST00000448424.2_Silent_p.A331A|ATP7B_ENST00000344297.5_Silent_p.A331A|ATP7B_ENST00000400366.3_Intron|ATP7B_ENST00000542656.1_Silent_p.A299A	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	331					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CACTCCCTTCGGCTCCATCAG	0.532									Wilson disease				G|||	1	0.000199681	8e-04	0	5008	,	,		18698	0		0	False		,,,				2504	0				p.A331A		Atlas-SNP	.											.	ATP7B	123	.	0			c.C993T						.	G	,	0,3804		0,0,1902	79	79	79		993,993	-1.4	0	13		79	2,8226		0,2,4112	no	coding-synonymous,coding-synonymous	ATP7B	NM_000053.3,NM_001005918.2	,	0,2,6014	AA,AG,GG		0.0243,0.0,0.0166	,	331/1466,331/1259	52548363	2,12030	1902	4114	6016	SO:0001819	synonymous_variant	540	exon2	Familial Cancer Database		CCCTTCGGCTCCA	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.993C>T	chr13.hg19:g.52548363G>A		69.0	0.0		38.0	7.0	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Silent	SNP	ENST00000242839.4	hg19	CCDS41892.1																																																																																			.	.		0.532	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		A	52548363	G	A	52548363	2	1	107	1	0	0	0	0	0	0	0	1	1191	1103	39	1		1	ATP7B	13	52548363	Silent	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10		52548363	62621515	45	16032										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42357103	42357103	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	gataaaattgtggtggcagaAgctacatcatcaacggcact	10	8	2	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr14:42357103A>T	ENST00000298119.4	+	3	2464	c.1275A>T	c.(1273-1275)gaA>gaT	p.E425D	LRFN5_ENST00000554120.1_Missense_Mutation_p.E425D|LRFN5_ENST00000554171.1_Missense_Mutation_p.E425D	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	425	Fibronectin type-III.					integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TGGTGGCAGAAGCTACATCAT	0.358										HNSCC(30;0.082)																											p.E425D		Atlas-SNP	.											.	LRFN5	269	.	0			c.A1275T						.						71	69	69					14																	42357103		2203	4300	6503	SO:0001583	missense	145581	exon3			GGCAGAAGCTACA	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.1275A>T	chr14.hg19:g.42357103A>T	ENSP00000298119:p.Glu425Asp	166.0	0.0		141.0	59.0	NM_152447	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	hg19	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	A	9.907	1.208354	0.22205	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.68765	-0.35;0.62;0.62	5.4	1.74	0.24563	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000018	T	0.59390	0.2190	M	0.62723	1.935	0.45867	D	0.998723	B;B	0.18013	0.002;0.025	B;B	0.21917	0.015;0.037	T	0.51020	-0.8758	10	0.37606	T	0.19	.	8.3374	0.32224	0.7634:0.0:0.2366:0.0	.	425;425	G3V364;Q96NI6	.;LRFN5_HUMAN	D	425	ENSP00000298119:E425D;ENSP00000451897:E425D;ENSP00000451067:E425D	ENSP00000298119:E425D	E	+	3	2	LRFN5	41426853	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.915000	0.48805	0.108000	0.17862	-0.376000	0.06991	GAA	.	.		0.358	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		T	42357103	A	T	42357103	3	4	107	1	0	0	0	0	1	0	0	0	8950	69	3	4	1277	4	LRFN5	14	42357103	Missense_Mutation	SNP	A	TCGA-DD-A1EK-01A-11D-A20W-10		42357103	64992437	46	16033										
ADAM21	8747	hgsc.bcm.edu	37	chr14	70925176	70925176	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ggaatatgtcgtccacctatTgattgtggagttgataattt	10	5	0	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr14:70925176T>G	ENST00000603540.1	+	2	1218	c.960T>G	c.(958-960)atT>atG	p.I320M	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.I320M	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	320	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GTCCACCTATTGATTGTGGAG	0.408																																					p.I320M		Atlas-SNP	.											.	ADAM21	181	.	0			c.T960G						.						126	126	126					14																	70925176		2202	4299	6501	SO:0001583	missense	8747	exon2			ACCTATTGATTGT	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"ADAM metallopeptidase domain containing"	200	protein-coding gene	gene with protein product		603713	"a disintegrin and metalloproteinase domain 21"			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.960T>G	chr14.hg19:g.70925176T>G	ENSP00000474385:p.Ile320Met	223.0	0.0		178.0	82.0	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	hg19	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	T	10.89	1.478808	0.26511	.	.	ENSG00000139985	ENST00000267499	T	0.09630	2.96	3.8	1.35	0.21983	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	2.136600	0.02510	N	0.091443	T	0.06872	0.0175	N	0.14661	0.345	0.22842	N	0.998662	B	0.30211	0.273	B	0.28232	0.087	T	0.27971	-1.0058	10	0.36615	T	0.2	.	2.8367	0.05516	0.1871:0.2133:0.0:0.5996	.	320	Q9UKJ8	ADA21_HUMAN	M	320	ENSP00000267499:I320M	ENSP00000267499:I320M	I	+	3	3	ADAM21	69994929	0.000000	0.05858	0.992000	0.48379	0.954000	0.61252	-0.054000	0.11826	0.286000	0.22352	0.455000	0.32223	ATT	.	.		0.408	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3			G	70925176	T	G	70925176	3	3	107	1	0	0	0	0	1	0	0	0	243	1800	63	5	962	5	ADAM21	14	70925176	Missense_Mutation	SNP	T	TCGA-DD-A1EK-01A-11D-A20W-10	28568073	70925176	36424364	47	16034										
PTPN9	5780	hgsc.bcm.edu	37	chr15	75798215	75798215	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ctcatcgaagggatctgggtGgccgttcacctggggtagga	16	9	3	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr15:75798215G>C	ENST00000306726.2	-	7	1281	c.769C>G	c.(769-771)Cac>Gac	p.H257D	PTPN9_ENST00000564970.1_5'Flank	NM_002833.2	NP_002824.1	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type 9	257					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGATCTGGGTGGCCGTTCACC	0.537																																					p.H257D		Atlas-SNP	.											.	PTPN9	53	.	0			c.C769G						.						107	99	102					15																	75798215		2197	4294	6491	SO:0001583	missense	5780	exon7			CTGGGTGGCCGTT		CCDS10280.1	15q23	2011-06-09			ENSG00000169410	ENSG00000169410		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9661	protein-coding gene	gene with protein product		600768				1557404	Standard	NM_002833		Approved	MEG2	uc002bal.3	P43378	OTTHUMG00000142838	ENST00000306726.2:c.769C>G	chr15.hg19:g.75798215G>C	ENSP00000303554:p.His257Asp	203.0	0.0		207.0	83.0	NM_002833	Q53XR9	Missense_Mutation	SNP	ENST00000306726.2	hg19	CCDS10280.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.852465	0.51270	.	.	ENSG00000169410	ENST00000306726;ENST00000544966	D	0.84516	-1.86	5.92	5.92	0.95590	Cellular retinaldehyde-binding/triple function, C-terminal (1);	0.140551	0.64402	D	0.000007	T	0.77772	0.4180	L	0.44542	1.39	0.39792	D	0.972457	P	0.48764	0.915	B	0.36922	0.236	T	0.77253	-0.2656	10	0.23302	T	0.38	.	14.2346	0.65916	0.0:0.0:0.851:0.149	.	257	P43378	PTN9_HUMAN	D	257;247	ENSP00000303554:H257D	ENSP00000303554:H257D	H	-	1	0	PTPN9	73585270	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.006000	0.57083	2.822000	0.97130	0.650000	0.86243	CAC	.	.		0.537	PTPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286474.1			C	75798215	G	C	75798215	3	2	107	1	0	0	0	0	1	0	0	0	12809	1348	47	4	1040	4	PTPN9	15	75798215	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10		75798215	26733177	48	16035										
KRT27	342574	hgsc.bcm.edu	37	chr17	38933922	38933922	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	gccccgatctgagcctggatCtgtgccagctgtgcacagta	12	13	2	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr17:38933922C>A	ENST00000301656.3	-	6	1075	c.1035G>T	c.(1033-1035)caG>caT	p.Q345H	KRT27_ENST00000540723.1_5'UTR	NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				GAGCCTGGATCTGTGCCAGCT	0.537																																					p.Q345H		Atlas-SNP	.											.	KRT27	41	.	0			c.G1035T						.						159	160	159					17																	38933922		2203	4300	6503	SO:0001583	missense	342574	exon6			CTGGATCTGTGCC	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.1035G>T	chr17.hg19:g.38933922C>A	ENSP00000301656:p.Gln345His	145.0	0.0		133.0	69.0	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	hg19	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.366662	0.41902	.	.	ENSG00000171446	ENST00000301656	D	0.89196	-2.48	5.7	0.856	0.19019	Filament (1);	0.096934	0.46145	N	0.000316	D	0.87330	0.6150	M	0.78344	2.41	0.32477	N	0.542004	B	0.18863	0.031	B	0.30316	0.114	D	0.84862	0.0820	10	0.62326	D	0.03	.	7.2399	0.26090	0.0:0.5836:0.1231:0.2934	.	345	Q7Z3Y8	K1C27_HUMAN	H	345	ENSP00000301656:Q345H	ENSP00000301656:Q345H	Q	-	3	2	KRT27	36187448	0.989000	0.36119	1.000000	0.80357	0.824000	0.46624	0.527000	0.22987	0.425000	0.26087	0.650000	0.86243	CAG	.	.		0.537	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		A	38933922	C	A	38933922	3	1	107	1	0	0	0	0	1	0	0	0	8473	912	32	3	356	3	KRT27	17	38933922	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10		38933922	42261288	49	16036										
UTS2R	2837	hgsc.bcm.edu	37	chr17	80332626	80332626	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	gccagcatcttcacgctgacCgtcatgagcagcgagcgcta	11	14	3	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr17:80332626C>A	ENST00000313135.2	+	1	474	c.426C>A	c.(424-426)acC>acA	p.T142T		NM_018949.1	NP_061822.1	Q9UKP6	UR2R_HUMAN	urotensin 2 receptor	142					blood circulation (GO:0008015)|negative regulation of blood pressure (GO:0045776)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cell growth (GO:0030307)|positive regulation of circadian sleep/wake cycle, REM sleep (GO:0046005)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of vasoconstriction (GO:0045907)|regulation of vasodilation (GO:0042312)|response to drug (GO:0042493)|signal transduction (GO:0007165)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)|urotensin II receptor activity (GO:0001604)			breast(1)|endometrium(4)|kidney(1)|lung(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.00928)|BRCA - Breast invasive adenocarcinoma(99;0.0833)			TCACGCTGACCGTCATGAGCA	0.682																																					p.T142T		Atlas-SNP	.											.	UTS2R	25	.	0			c.C426A						.						40	32	35					17																	80332626		2203	4300	6503	SO:0001819	synonymous_variant	2837	exon1			GCTGACCGTCATG	AF140631	CCDS11810.1	17q25.3	2013-04-30	2004-07-13	2004-07-13		ENSG00000181408			4468	protein-coding gene	gene with protein product		600896	"G protein-coupled receptor 14"	GPR14		8666380, 10499587	Standard	NM_018949		Approved		uc010wvl.2	Q9UKP6		ENST00000313135.2:c.426C>A	chr17.hg19:g.80332626C>A		71.0	0.0		56.0	24.0	NM_018949	B2RMV8	Silent	SNP	ENST00000313135.2	hg19	CCDS11810.1																																																																																			.	.		0.682	UTS2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443506.1	NM_018949		A	80332626	C	A	80332626	2	1	107	1	0	0	0	0	0	0	0	1	17121	639	23	1		1	UTS2R	17	80332626	Silent	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10	41398704	80332626	862584	50	16037										
ZNF20	7568	hgsc.bcm.edu	37	chr19	12243520	12243520	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tgtgagtcctttcatgatatCgaatgtaattggaaataaag	9	4	1	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr19:12243520C>T	ENST00000334213.5	-	4	1705	c.1481G>A	c.(1480-1482)cGa>cAa	p.R494Q	ZNF625-ZNF20_ENST00000430024.1_3'UTR|ZNF20_ENST00000485451.1_5'Flank|ZNF20_ENST00000600335.1_Intron	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	494					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|lung(6)	8						TTCATGATATCGAATGTAATT	0.413																																					p.R494Q		Atlas-SNP	.											.	ZNF20	86	.	0			c.G1481A						.						171	181	177					19																	12243520		2202	4297	6499	SO:0001583	missense	7568	exon4			TGATATCGAATGT	X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"Zinc fingers, C2H2-type", "-"	12992	protein-coding gene	gene with protein product		194557	"zinc finger protein 20 (KOX 13)"				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.1481G>A	chr19.hg19:g.12243520C>T	ENSP00000335437:p.Arg494Gln	102.0	0.0		70.0	25.0	NM_021143	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	hg19	CCDS45986.1	.	.	.	.	.	.	.	.	.	.	C	2.914	-0.224731	0.06022	.	.	ENSG00000132010	ENST00000334213;ENST00000292241	T	0.20598	2.06	0.94	-1.88	0.07713	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06600	0.0169	N	0.12569	0.235	0.09310	N	1	B	0.30709	0.291	B	0.15870	0.014	T	0.34254	-0.9836	9	0.07644	T	0.81	.	2.7371	0.05243	0.0:0.2394:0.2619:0.4987	.	494	P17024	ZNF20_HUMAN	Q	494	ENSP00000335437:R494Q	ENSP00000292241:R494Q	R	-	2	0	ZNF20	12104520	0.000000	0.05858	0.000000	0.03702	0.958000	0.62258	-2.754000	0.00790	-0.861000	0.04094	0.313000	0.20887	CGA	.	.		0.413	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143		T	12243520	C	T	12243520	3	4	107	1	0	0	0	0	1	0	0	0	17776	884	31	1	121	1	ZNF20	19	12243520	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10		12243520	46885463	51	16038										
ERF	2077	hgsc.bcm.edu	37	chr19	42753847	42753847	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ggagggaagcggaagtggctAccacccgacggcactggcgg	18	11	0	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr19:42753847A>C	ENST00000222329.4	-	4	574	c.417T>G	c.(415-417)ggT>ggG	p.G139G	ERF_ENST00000440177.2_Silent_p.G64G|ERF_ENST00000595941.1_5'Flank|AC006486.9_ENST00000594664.1_Intron	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	139					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				GGAAGTGGCTACCACCCGACG	0.657																																					p.G139G		Atlas-SNP	.											.	ERF	47	.	0			c.T417G						.						39	41	40					19																	42753847		2202	4300	6502	SO:0001819	synonymous_variant	2077	exon4			GTGGCTACCACCC	U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"Ets2 repressor factor"	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.417T>G	chr19.hg19:g.42753847A>C		74.0	0.0		46.0	22.0	NM_006494	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	Silent	SNP	ENST00000222329.4	hg19	CCDS12600.1																																																																																			.	.		0.657	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494		C	42753847	A	C	42753847	2	2	107	1	0	0	0	0	0	0	0	1	5223	378	14	5		5	ERF	19	42753847	Silent	SNP	A	TCGA-DD-A1EK-01A-11D-A20W-10	30510327	42753847	16375136	52	16039										
TRPM4	54795	hgsc.bcm.edu	37	chr19	49703678	49703678	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	tggggcccaagatcgtcatcGtgagcaagatggtgaggcag	16	8	1	4			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr19:49703678G>A	ENST00000252826.5	+	18	2893	c.2767G>A	c.(2767-2769)Gtg>Atg	p.V923M	TRPM4_ENST00000427978.2_Missense_Mutation_p.V778M|TRPM4_ENST00000355712.5_Missense_Mutation_p.V569M	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	923					calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		GATCGTCATCGTGAGCAAGAT	0.622																																					p.V923M		Atlas-SNP	.											.	TRPM4	119	.	0			c.G2767A						.						36	34	34					19																	49703678		2203	4300	6503	SO:0001583	missense	54795	exon18			GTCATCGTGAGCA	AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.2767G>A	chr19.hg19:g.49703678G>A	ENSP00000252826:p.Val923Met	75.0	0.0		68.0	34.0	NM_017636	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Missense_Mutation	SNP	ENST00000252826.5	hg19	CCDS33073.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.478645	0.84747	.	.	ENSG00000130529	ENST00000252826;ENST00000427978;ENST00000355712	D;T;D	0.98649	-5.05;-0.69;-5.05	4.21	4.21	0.49690	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98416	0.9473	L	0.39147	1.195	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;0.995	D	0.99187	1.0869	10	0.51188	T	0.08	-25.266	15.7186	0.77688	0.0:0.0:1.0:0.0	.	569;749;778;923	B4DIX5;Q8TD43-2;Q8TD43-3;Q8TD43	.;.;.;TRPM4_HUMAN	M	923;778;569	ENSP00000252826:V923M;ENSP00000407492:V778M;ENSP00000347944:V569M	ENSP00000252826:V923M	V	+	1	0	TRPM4	54395490	1.000000	0.71417	0.998000	0.56505	0.940000	0.58332	9.056000	0.93881	2.084000	0.62774	0.491000	0.48974	GTG	.	.		0.622	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		A	49703678	G	A	49703678	3	1	107	1	0	0	0	0	1	0	0	0	16603	1145	40	1	2837	1	TRPM4	19	49703678	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10	6949831	49703678	9425305	53	16040										
SLC2A4RG	56731	hgsc.bcm.edu	37	chr20	62373481	62373481	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	accctggcccctgttgctgcAgagcccggcccaggtcatgt	12	16	1	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr20:62373481A>G	ENST00000266077.2	+	5	631		c.e5-1		SLC2A4RG_ENST00000493772.1_Splice_Site|RP4-583P15.10_ENST00000447343.2_RNA	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					CTGTTGCTGCAGAGCCCGGCC	0.672																																					.		Atlas-SNP	.											.	SLC2A4RG	20	.	0			c.580-2A>G						.						21	29	26					20																	62373481		2173	4288	6461	SO:0001630	splice_region_variant	56731	exon5			TGCTGCAGAGCCC	AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"GLUT4 enhancer factor", "Huntington's disease gene regulatory region-binding protein 1"	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.580-1A>G	chr20.hg19:g.62373481A>G		123.0	0.0		88.0	26.0	NM_020062	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Splice_Site	SNP	ENST00000266077.2	hg19	CCDS13537.1	.	.	.	.	.	.	.	.	.	.	A	10.93	1.490574	0.26686	.	.	ENSG00000125520	ENST00000266077	.	.	.	3.88	3.88	0.44766	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6808	0.45813	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC2A4RG	61843925	1.000000	0.71417	0.144000	0.22314	0.205000	0.24178	3.589000	0.53972	1.416000	0.47057	0.260000	0.18958	.	.	.		0.672	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1	NM_020062	Intron	G	62373481	A	G	62373481	5	3	107	1	0	0	0	0	0	0	1	0	14562	202	7	2	596	2	SLC2A4RG	20	62373481	Splice_Site	SNP	A	TCGA-DD-A1EK-01A-11D-A20W-10		62373481	652039	54	16041										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41719859	41719859	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	accttcctgggactgatggtGgctttcagtggctctggagg	15	9	2	1			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr21:41719859G>T	ENST00000400454.1	-	6	1425	c.948C>A	c.(946-948)gcC>gcA	p.A316A		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	316	Ig-like C2-type 4.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GACTGATGGTGGCTTTCAGTG	0.473																																					p.A316A	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C948A						.						50	47	48					21																	41719859		1923	4150	6073	SO:0001819	synonymous_variant	1826	exon6			GATGGTGGCTTTC	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.948C>A	chr21.hg19:g.41719859G>T		69.0	0.0		56.0	21.0	NM_001271534	O60468	Silent	SNP	ENST00000400454.1	hg19	CCDS42929.1																																																																																			.	.		0.473	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		T	41719859	G	T	41719859	2	4	107	1	0	0	0	0	0	0	0	1	4770	1335	47	3		3	DSCAM	21	41719859	Silent	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10		41719859	6410036	55	16042										
LRRC3	81543	hgsc.bcm.edu	37	chr21	45876637	45876638	+	Frame_Shift_Ins	INS	-	-	C													0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	gccgcctgcccacagccctgINSccggtgccctgaccacgcag							TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr21:45876637_45876638insC	ENST00000291592.4	+	2	427_428	c.110_111insC	c.(109-114)tgccggfs	p.R38fs	LRRC3-AS1_ENST00000426578.1_RNA	NM_030891.3	NP_112153.1	Q9BY71	LRRC3_HUMAN	leucine rich repeat containing 3	38	LRRNT.					integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5		Breast(209;0.00908)		COAD - Colon adenocarcinoma(84;0.148)|Lung(125;0.195)		CCACAGCCCTGCCGGTGCCCTG	0.693																																					p.C37fs		Atlas-INDEL	.											.	LRRC3	22	.	0			c.110_111insC						.																																			SO:0001589	frameshift_variant	81543	exon2			.	AB058646	CCDS13711.1	21q22.3	2011-12-07	2002-06-20		ENSG00000160233	ENSG00000160233			14965	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 102"	C21orf102		12036297	Standard	NM_030891		Approved		uc002zfa.3	Q9BY71	OTTHUMG00000040847	ENST00000291592.4:c.112dupC	chr21.hg19:g.45876639_45876639dupC	ENSP00000291592:p.Arg38fs	46.0	0.0		33.0	10.0	NM_030891	Q0VDJ2	Frame_Shift_Ins	INS	ENST00000291592.4	hg19	CCDS13711.1																																																																																			.	.		0.693	LRRC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098095.3			C	45876638	-	C	45876637	7	5	107	1	0	1	1	0	0	0	0	0	8993	1319	46	0	112	0	LRRC3	21	45876637	Frame_Shift_Ins	INS	-	TCGA-DD-A1EK-01A-11D-A20W-10	4156778	45876637	2253258	56	16043										
ASCC2	84164	hgsc.bcm.edu	37	chr22	30218403	30218403	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	atctttggaatgtcaaagagGaagttattgtagaggatttc	11	3	2	2			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chr22:30218403G>T	ENST00000397771.2	-	6	639	c.462C>A	c.(460-462)ttC>ttA	p.F154L	ASCC2_ENST00000307790.3_Missense_Mutation_p.F154L|ASCC2_ENST00000542393.1_Intron			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	154					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			TGTCAAAGAGGAAGTTATTGT	0.448																																					p.F154L		Atlas-SNP	.											.	ASCC2	53	.	0			c.C462A						.						118	113	115					22																	30218403		2203	4300	6503	SO:0001583	missense	84164	exon5			AAAGAGGAAGTTA	AY013289	CCDS13869.1, CCDS56226.1	22q12.1	2004-07-27			ENSG00000100325	ENSG00000100325			24103	protein-coding gene	gene with protein product	"ASC 1 complex subunit P100"	614216				12077347, 9847074	Standard	NM_032204		Approved	ASC1p100, FLJ21588, DKFZp586O0223	uc003agr.3	Q9H1I8	OTTHUMG00000067658	ENST00000397771.2:c.462C>A	chr22.hg19:g.30218403G>T	ENSP00000380877:p.Phe154Leu	89.0	0.0		78.0	31.0	NM_032204	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	Missense_Mutation	SNP	ENST00000397771.2	hg19	CCDS13869.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.718702	0.89205	.	.	ENSG00000100325	ENST00000307790;ENST00000397771;ENST00000431535;ENST00000412689	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.85	5.85	0.93711	.	0.101226	0.64402	D	0.000001	T	0.54711	0.1875	M	0.74258	2.255	0.80722	D	1	D	0.61080	0.989	P	0.51999	0.687	T	0.49934	-0.8886	10	0.12430	T	0.62	-24.2021	18.7369	0.91757	0.0:0.0:1.0:0.0	.	154	Q9H1I8	ASCC2_HUMAN	L	154	ENSP00000305502:F154L;ENSP00000380877:F154L;ENSP00000412382:F154L;ENSP00000417032:F154L	ENSP00000305502:F154L	F	-	3	2	ASCC2	28548403	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.170000	0.64990	2.768000	0.95171	0.655000	0.94253	TTC	.	.		0.448	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322127.1	NM_032204		T	30218403	G	T	30218403	3	4	107	1	0	0	0	0	1	0	0	0	1032	1165	41	3	1875	3	ASCC2	22	30218403	Missense_Mutation	SNP	G	TCGA-DD-A1EK-01A-11D-A20W-10		30218403	21086163	57	16044										
ARMCX1	51309	hgsc.bcm.edu	37	chrX	100808329	100808329	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.087719298245614	5	1	1.50951086956522	1.15729166666667	1.63382352941176	0.282051282051282	0.956410256410256	0	ctctgggaacaggacccttgCaccgagtttaccctgcccag	10	15	1	0			TCGA-DD-A1EK-01A-11D-A20W-10	TCGA-DD-A1EK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf72fbdc-f5e1-4545-976f-36570cea82ee	5c357792-6f7d-4e11-9e4c-7fbbedc56de1	g.chrX:100808329C>A	ENST00000372829.3	+	4	787	c.416C>A	c.(415-417)gCa>gAa	p.A139E		NM_016608.1	NP_057692.1	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1	139						integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(2)|ovary(3)|pancreas(1)|urinary_tract(1)	19						AGGACCCTTGCACCGAGTTTA	0.612																																					p.A139E		Atlas-SNP	.											.	ARMCX1	67	.	0			c.C416A						.						69	64	66					X																	100808329		2203	4300	6503	SO:0001583	missense	51309	exon4			CCCTTGCACCGAG	AB039670	CCDS14487.1	Xq21.33-q22.2	2014-03-21			ENSG00000126947	ENSG00000126947		"Armadillo repeat containing"	18073	protein-coding gene	gene with protein product		300362				11162520, 16221301, 22569362	Standard	NM_016608		Approved	ALEX1, GASP7	uc004ehv.3	Q9P291	OTTHUMG00000022033	ENST00000372829.3:c.416C>A	chrX.hg19:g.100808329C>A	ENSP00000361917:p.Ala139Glu	92.0	0.0		73.0	35.0	NM_016608	Q53HK2|Q9H2Q0	Missense_Mutation	SNP	ENST00000372829.3	hg19	CCDS14487.1	.	.	.	.	.	.	.	.	.	.	c	10.96	1.499463	0.26861	.	.	ENSG00000126947	ENST00000372829	T	0.26957	1.7	3.86	2.98	0.34508	.	0.855686	0.09693	N	0.768061	T	0.17109	0.0411	N	0.19112	0.55	0.23809	N	0.996783	B	0.27498	0.18	B	0.26094	0.066	T	0.22382	-1.0218	10	0.46703	T	0.11	-0.7593	8.3508	0.32301	0.0:0.7638:0.2362:0.0	.	139	Q9P291	ARMX1_HUMAN	E	139	ENSP00000361917:A139E	ENSP00000361917:A139E	A	+	2	0	ARMCX1	100694985	0.026000	0.19158	0.908000	0.35775	0.774000	0.43823	0.539000	0.23175	0.957000	0.37930	-0.291000	0.09656	GCA	.	.		0.612	ARMCX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057561.1	NM_016608		A	100808329	C	A	100808329	3	1	107	1	0	0	0	0	1	0	0	0	959	710	25	3	418	3	ARMCX1	23	100808329	Missense_Mutation	SNP	C	TCGA-DD-A1EK-01A-11D-A20W-10		100808329	54462231	58	16045										
C1orf93	127281	hgsc.bcm.edu	37	chr1	2520399	2520399	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tgcatttcgtccagaagtccCcaggcgactacgtccccaag	9	15	0	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:2520399C>G	ENST00000378425.5	+	6	575	c.499C>G	c.(499-501)Cca>Gca	p.P167A	FAM213B_ENST00000444521.2_Missense_Mutation_p.P185A|FAM213B_ENST00000378424.4_Missense_Mutation_p.P204R|FAM213B_ENST00000419916.2_Missense_Mutation_p.P197A|FAM213B_ENST00000537325.1_Missense_Mutation_p.P160A|FAM213B_ENST00000484099.1_3'UTR			Q8TBF2	PGFS_HUMAN	family with sequence similarity 213, member B	167					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|myelin sheath (GO:0043209)	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|prostaglandin-F synthase activity (GO:0047017)	p.P167T(1)									CCAGAAGTCCCCAGGCGACTA	0.652																																					p.P215A		Atlas-SNP	.											C1orf93,caecum,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C643G						.						62	62	62					1																	2520399		2203	4300	6503	SO:0001583	missense	127281	exon6			AAGTCCCCAGGCG	AK075273	CCDS44.1, CCDS44.2, CCDS55564.1, CCDS72690.1, CCDS72691.1	1p36.32	2011-12-08	2011-11-24	2011-11-24	ENSG00000157870	ENSG00000157870	1.11.1.20		28390	protein-coding gene	gene with protein product	"prostamide/prostaglandin F synthase"		"chromosome 1 open reading frame 93"	C1orf93		18006499	Standard	NM_152371		Approved	MGC26818	uc001ajv.2	Q8TBF2	OTTHUMG00000000847	ENST00000378425.5:c.499C>G	chr1.hg19:g.2520399C>G	ENSP00000367682:p.Pro167Ala	108.0	0.0		88.0	41.0	NM_001195736	A8K793|B3KPY3|B4DQR9|B4E0S5|B7ZAC8|B9DI90|B9DI92|J3KQD0|Q8N2H0	Missense_Mutation	SNP	ENST00000378425.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.352|6.352	0.433117|0.433117	0.12045|0.12045	.|.	.|.	ENSG00000157870|ENSG00000157870	ENST00000419916;ENST00000537325;ENST00000378425;ENST00000444521|ENST00000378424	T;T;T;T|T	0.50548|0.50548	0.99;0.74;1.01;0.89|0.74	4.44|4.44	4.44|4.44	0.53790|0.53790	.|.	1.149570|1.149570	0.06726|0.06726	N|N	0.775697|0.775697	T|T	0.42381|0.42381	0.1200|0.1200	.|.	.|.	.|.	0.50632|0.50632	D|D	0.99988|0.99988	D;D;D;D;P|P	0.89917|0.36837	1.0;0.982;0.98;0.98;0.929|0.571	D;P;P;P;B|B	0.91635|0.33254	0.999;0.831;0.79;0.838;0.408|0.16	T|T	0.33033|0.33033	-0.9884|-0.9884	9|9	0.15952|0.56958	T|D	0.53|0.05	-3.3791|-3.3791	12.413|12.413	0.55478|0.55478	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	160;131;193;185;167|156	Q8TBF2-5;Q8TBF2-4;Q8TBF2-6;Q8TBF2-3;Q8TBF2|Q8TBF2-2	.;.;.;.;PGFS_HUMAN|.	A|R	197;160;167;185|204	ENSP00000394405:P197A;ENSP00000443605:P160A;ENSP00000367682:P167A;ENSP00000413218:P185A|ENSP00000367681:P204R	ENSP00000367682:P167A|ENSP00000367681:P204R	P|P	+|+	1|2	0|0	C1orf93|C1orf93	2510259|2510259	0.975000|0.975000	0.34042|0.34042	0.701000|0.701000	0.30321|0.30321	0.011000|0.011000	0.07611|0.07611	5.228000|5.228000	0.65310|0.65310	2.301000|2.301000	0.77427|0.77427	0.313000|0.313000	0.20887|0.20887	CCA|CCC	.	.		0.652	FAM213B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152371		G	2520399	C	G	2520399	3	3	108	1	0	0	0	0	1	0	0	0	2072	623	22	4	521	4	C1orf93	1	2520399	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		2520399	246730222	1	16046										
MEGF6	1953	hgsc.bcm.edu	37	chr1	3428670	3428670	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ccatgggcacactgggccagCcctgcggcacattcgtccac	11	17	0	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:3428670C>A	ENST00000356575.4	-	8	1102	c.876G>T	c.(874-876)ggG>ggT	p.G292G	MEGF6_ENST00000294599.4_Silent_p.G187G	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	292	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		ACTGGGCCAGCCCTGCGGCAC	0.647																																					p.G292G	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.G876T						.						56	66	62					1																	3428670		2122	4218	6340	SO:0001819	synonymous_variant	1953	exon8			GGCCAGCCCTGCG	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"EGF-like-domain, multiple 3"	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.876G>T	chr1.hg19:g.3428670C>A		174.0	0.0		177.0	65.0	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	hg19	CCDS41237.1																																																																																			.	.		0.647	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		A	3428670	C	A	3428670	2	1	108	1	0	0	0	0	0	0	0	1	9471	726	26	3		3	MEGF6	1	3428670	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	908271	3428670	245821951	2	16047										
SYF2	25949	hgsc.bcm.edu	37	chr1	25558651	25558651	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ctgttcgcgcttctgagcggCcagctccgccgccgcagcga	13	17	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:25558651C>A	ENST00000236273.4	-	2	101	c.76G>T	c.(76-78)Gcc>Tcc	p.A26S	SYF2_ENST00000476231.1_5'UTR|SYF2_ENST00000354361.3_Missense_Mutation_p.A26S	NM_015484.4	NP_056299.1	O95926	SYF2_HUMAN	SYF2 pre-mRNA-splicing factor	26					embryonic organ development (GO:0048568)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|mitotic G2 DNA damage checkpoint (GO:0007095)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(4)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-26)|Colorectal(126;2.54e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000455)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00145)|GBM - Glioblastoma multiforme(114;0.00443)|READ - Rectum adenocarcinoma(331;0.0936)|Lung(427;0.201)		TTCTGAGCGGCCAGCTCCGCC	0.647																																					p.A26S		Atlas-SNP	.											.	SYF2	13	.	0			c.G76T						.						21	25	24					1																	25558651		2203	4300	6503	SO:0001583	missense	25949	exon2			GAGCGGCCAGCTC	AF273089	CCDS258.1, CCDS259.1	1p36.11	2013-08-21	2013-08-21	2005-09-14	ENSG00000117614	ENSG00000117614			19824	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 29"	607090	"CCNDBP1 interactor", "SYF2 homolog, RNA splicing factor (S. cerevisiae)"	CBPIN		11118353	Standard	NM_207170		Approved	p29, DKFZp564O2082, NTC31, fSAP29	uc001bjt.1	O95926	OTTHUMG00000043610	ENST00000236273.4:c.76G>T	chr1.hg19:g.25558651C>A	ENSP00000236273:p.Ala26Ser	80.0	0.0		90.0	41.0	NM_207170	Q5TH73	Missense_Mutation	SNP	ENST00000236273.4	hg19	CCDS259.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.204648	0.79127	.	.	ENSG00000117614	ENST00000236273;ENST00000354361	T;T	0.47869	0.88;0.83	5.42	3.54	0.40534	.	0.104346	0.64402	N	0.000002	T	0.33847	0.0877	L	0.41236	1.265	0.54753	D	0.99998	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.08330	-1.0727	10	0.13470	T	0.59	-11.5655	9.2119	0.37324	0.146:0.7773:0.0:0.0768	.	26;26;26	B4E0Y8;B2RBX8;O95926	.;.;SYF2_HUMAN	S	26	ENSP00000236273:A26S;ENSP00000346330:A26S	ENSP00000236273:A26S	A	-	1	0	SYF2	25431238	1.000000	0.71417	0.992000	0.48379	0.806000	0.45545	2.272000	0.43373	0.651000	0.30788	0.561000	0.74099	GCC	.	.		0.647	SYF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000101962.1	NM_015484		A	25558651	C	A	25558651	3	1	108	1	0	0	0	0	1	0	0	0	15452	739	26	3	679	3	SYF2	1	25558651	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	22129981	25558651	223691970	3	16048										
DNAJC8	22826	hgsc.bcm.edu	37	chr1	28536505	28536505	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tgtgttccacgtattcttttCctgcctgaattacatccagg	7	11	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:28536505C>A	ENST00000263697.4	-	5	403	c.377G>T	c.(376-378)gGa>gTa	p.G126V	DNAJC8_ENST00000489277.1_5'UTR	NM_014280.2	NP_055095.2	O75937	DNJC8_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 8	126					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)				kidney(1)|large_intestine(3)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;4.08e-05)|all_lung(284;4.29e-05)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.0105)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		OV - Ovarian serous cystadenocarcinoma(117;2.81e-22)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00275)|BRCA - Breast invasive adenocarcinoma(304;0.0059)|STAD - Stomach adenocarcinoma(196;0.00671)|READ - Rectum adenocarcinoma(331;0.0649)		GTATTCTTTTCCTGCCTGAAT	0.418																																					p.G126V		Atlas-SNP	.											.	DNAJC8	13	.	0			c.G377T						.						128	111	116					1																	28536505		1894	4110	6004	SO:0001583	missense	22826	exon5			TCTTTTCCTGCCT	AF083190	CCDS41292.1	1p35	2011-09-02			ENSG00000126698	ENSG00000126698		"Heat shock proteins / DNAJ (HSP40)"	15470	protein-coding gene	gene with protein product						11147971	Standard	NM_014280		Approved	SPF31	uc001bpn.3	O75937	OTTHUMG00000003538	ENST00000263697.4:c.377G>T	chr1.hg19:g.28536505C>A	ENSP00000263697:p.Gly126Val	145.0	0.0		104.0	52.0	NM_014280	B4DUU4|D3DPM0|Q6IBA4|Q8N4Z5|Q9P051|Q9P067	Missense_Mutation	SNP	ENST00000263697.4	hg19	CCDS41292.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.825055	0.90955	.	.	ENSG00000126698	ENST00000263697	T	0.66638	-0.22	6.05	6.05	0.98169	Heat shock protein DnaJ, N-terminal (1);	0.100125	0.64402	D	0.000002	T	0.71341	0.3328	L	0.60455	1.87	0.80722	D	1	P	0.47910	0.902	P	0.45856	0.495	T	0.73855	-0.3851	10	0.87932	D	0	-12.2956	20.5934	0.99428	0.0:1.0:0.0:0.0	.	126	O75937	DNJC8_HUMAN	V	126	ENSP00000263697:G126V	ENSP00000263697:G126V	G	-	2	0	DNAJC8	28409092	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.396000	0.79891	2.872000	0.98467	0.650000	0.86243	GGA	.	.		0.418	DNAJC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009860.1	NM_014280		A	28536505	C	A	28536505	3	1	108	1	0	0	0	0	1	0	0	0	4657	855	30	3	404	3	DNAJC8	1	28536505	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	2977854	28536505	220714116	4	16049										
PHACTR4	65979	hgsc.bcm.edu	37	chr1	28800595	28800595	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ctttttgaaaacagtgacagCttttctgaggacagcagtac	9	8	1	3			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:28800595C>G	ENST00000373839.3	+	7	1614	c.1353C>G	c.(1351-1353)agC>agG	p.S451R	PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Missense_Mutation_p.S461R	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	451					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		ACAGTGACAGCTTTTCTGAGG	0.468																																					p.S461R		Atlas-SNP	.											.	PHACTR4	64	.	0			c.C1383G						.						120	121	121					1																	28800595		1970	4162	6132	SO:0001583	missense	65979	exon6			TGACAGCTTTTCT	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1353C>G	chr1.hg19:g.28800595C>G	ENSP00000362945:p.Ser451Arg	149.0	0.0		134.0	59.0	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	hg19	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	C	1.196	-0.633920	0.03584	.	.	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.23348	1.91;1.91	5.75	4.83	0.62350	.	1.347100	0.04068	N	0.307570	T	0.20659	0.0497	N	0.25647	0.755	0.19575	N	0.999967	B;B	0.31383	0.321;0.112	B;B	0.32465	0.146;0.068	T	0.29243	-1.0018	10	0.16420	T	0.52	-0.0126	7.5436	0.27753	0.0:0.7135:0.1374:0.1491	.	461;451	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	R	451;461;450	ENSP00000362945:S451R;ENSP00000362942:S461R	ENSP00000362942:S461R	S	+	3	2	PHACTR4	28673182	0.332000	0.24722	0.921000	0.36526	0.059000	0.15707	0.877000	0.28106	1.424000	0.47217	0.655000	0.94253	AGC	.	.		0.468	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		G	28800595	C	G	28800595	3	3	108	1	0	0	0	0	1	0	0	0	11821	796	28	4	1425	4	PHACTR4	1	28800595	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	264090	28800595	220450026	5	16050										
CLDN19	149461	hgsc.bcm.edu	37	chr1	43201511	43201511	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ctgggcaagggggccactggGtggggggctggccagggcag	23	9	0	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:43201511G>T	ENST00000296387.1	-	4	817				CLDN19_ENST00000539749.1_Missense_Mutation_p.H193Q|CLDN19_ENST00000372539.3_3'UTR	NM_001123395.1|NM_148960.2	NP_001116867.1|NP_683763.2	Q8N6F1	CLD19_HUMAN	claudin 19						apical junction assembly (GO:0043297)|calcium-independent cell-cell adhesion (GO:0016338)|neuronal action potential propagation (GO:0019227)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	apical junction complex (GO:0043296)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			breast(2)|large_intestine(1)|lung(2)|skin(1)	6	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GGGCCACTGGGTGGGGGGCTG	0.682																																					p.H193Q		Atlas-SNP	.											.	CLDN19	21	.	0			c.C579A						.						13	14	14					1																	43201511		2165	4223	6388	SO:0001627	intron_variant	149461	exon3			CACTGGGTGGGGG	AK096063	CCDS471.1, CCDS44125.1, CCDS53306.1	1p34.2	2008-05-14			ENSG00000164007	ENSG00000164007		"Claudins"	2040	protein-coding gene	gene with protein product		610036					Standard	NM_148960		Approved		uc001cht.1	Q8N6F1	OTTHUMG00000007524	ENST00000296387.1:c.626+37C>A	chr1.hg19:g.43201511G>T		72.0	0.0		73.0	24.0	NM_001185117	B7Z5I2|F5H5P9|Q5QT57|Q8N8X0	Missense_Mutation	SNP	ENST00000296387.1	hg19	CCDS471.1	.	.	.	.	.	.	.	.	.	.	g	3.560	-0.089945	0.07053	.	.	ENSG00000164007	ENST00000539749	D	0.84660	-1.88	2.79	1.85	0.25348	.	.	.	.	.	T	0.67468	0.2896	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.53114	-0.8484	9	0.21014	T	0.42	.	7.6324	0.28247	0.0:0.3179:0.6821:0.0	.	193	F5H5P9	.	Q	193	ENSP00000443229:H193Q	ENSP00000443229:H193Q	H	-	3	2	CLDN19	42974098	0.130000	0.22417	0.005000	0.12908	0.016000	0.09150	0.458000	0.21892	0.713000	0.32060	0.306000	0.20318	CAC	.	.		0.682	CLDN19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019788.1	NM_148960		T	43201511	G	T	43201511	1	4	108	0	1	0	0	0	0	0	0	0	3482	1252	44	3		3	CLDN19	1	43201511	Intron	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	14400916	43201511	206049110	6	16051										
TNNI3K	100144878	hgsc.bcm.edu	37	chr1	74957805	74957805	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tgtctcctgcatcaagtaacAgcagtgggtctctctcacct	8	13	4	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:74957805A>T	ENST00000294635.4	-	2	89				TNNI3K_ENST00000370891.2_Missense_Mutation_p.S837C|TNNI3K_ENST00000326637.3_Missense_Mutation_p.S736C|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.S850C			A6NM62	LRC53_HUMAN	leucine rich repeat containing 53							integral component of membrane (GO:0016021)				NS(1)|breast(1)|lung(2)	4						ATCAAGTAACAGCAGTGGGTC	0.453																																					p.S837C		Atlas-SNP	.											.	.	.	.	0			c.A2509T						.						201	202	202					1																	74957805		2203	4300	6503	SO:0001627	intron_variant	100526835	exon25			AGTAACAGCAGTG			1p31.3	2010-08-31			ENSG00000162621	ENSG00000162621			25255	protein-coding gene	gene with protein product							Standard			Approved			A6NM62	OTTHUMG00000009621	ENST00000294635.4:c.26-8746T>A	chr1.hg19:g.74957805A>T		284.0	0.0		92.0	16.0	NM_001112808		Missense_Mutation	SNP	ENST00000294635.4	hg19		.	.	.	.	.	.	.	.	.	.	A	26.5	4.741355	0.89573	.	.	ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000557284;ENST00000370891;ENST00000326637	T;T;T	0.76060	-0.99;-0.99;-0.98	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.72637	0.3485	N	0.19112	0.55	0.58432	D	0.999997	D;D	0.89917	0.999;1.0	D;D	0.85130	0.993;0.997	T	0.79339	-0.1844	10	0.72032	D	0.01	.	15.9579	0.79902	1.0:0.0:0.0:0.0	.	736;837	Q59H18;Q59H18-1	TNI3K_HUMAN;.	C	837;837;736	ENSP00000450895:S837C;ENSP00000359928:S837C;ENSP00000322251:S736C	ENSP00000322251:S736C	S	+	1	0	RP11-653A5.2;AC093158.1	74730393	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.464000	0.90380	2.178000	0.69098	0.533000	0.62120	AGC	.	.		0.453	LRRC53-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000026515.2			T	74957805	A	T	74957805	1	4	108	0	1	0	0	0	0	0	0	0	16344	188	7	4		4	TNNI3K	1	74957805	Intron	SNP	A	TCGA-DD-A1EL-01A-11D-A152-10	31756294	74957805	174292816	7	16052										
SNX7	51375	hgsc.bcm.edu	37	chr1	99203828	99203828	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ggaaaacttgaagataaagtGgaatgtgctaataatgccct	10	5	0	2			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:99203828G>C	ENST00000306121.3	+	8	1170	c.1161G>C	c.(1159-1161)gtG>gtC	p.V387V	SNX7_ENST00000529992.1_Silent_p.V332V|SNX7_ENST00000370189.5_Intron	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	323					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		AAGATAAAGTGGAATGTGCTA	0.353																																					p.V387V		Atlas-SNP	.											.	SNX7	76	.	0			c.G1161C						.						124	125	125					1																	99203828		2203	4299	6502	SO:0001819	synonymous_variant	51375	exon8			TAAAGTGGAATGT	AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"Sorting nexins"	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.1161G>C	chr1.hg19:g.99203828G>C		114.0	0.0		84.0	32.0	NM_015976	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Silent	SNP	ENST00000306121.3	hg19	CCDS755.2																																																																																			.	.		0.353	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2			C	99203828	G	C	99203828	2	2	108	1	0	0	0	0	0	0	0	1	14922	1335	47	4		4	SNX7	1	99203828	Silent	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	24246023	99203828	150046793	8	16053										
LRIG2	9860	hgsc.bcm.edu	37	chr1	113658968	113658968	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	cttcccaaggaacgctgtctGagccacaggaaggctacagc	11	13	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:113658968G>T	ENST00000361127.5	+	16	2788	c.2590G>T	c.(2590-2592)Gag>Tag	p.E864*	LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	864					innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		AACGCTGTCTGAGCCACAGGA	0.483																																					p.E864X		Atlas-SNP	.											.	LRIG2	67	.	0			c.G2590T						.						85	78	80					1																	113658968		2203	4300	6503	SO:0001587	stop_gained	9860	exon16			CTGTCTGAGCCAC	AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"Immunoglobulin superfamily / I-set domain containing"	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.2590G>T	chr1.hg19:g.113658968G>T	ENSP00000355396:p.Glu864*	192.0	0.0		162.0	66.0	NM_014813	Q9NSN2	Nonsense_Mutation	SNP	ENST00000361127.5	hg19	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	G	42	9.602370	0.99216	.	.	ENSG00000198799	ENST00000361127	.	.	.	5.92	5.02	0.67125	.	0.048832	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	17.3631	0.87356	0.0:0.125:0.875:0.0	.	.	.	.	X	864	.	ENSP00000355396:E864X	E	+	1	0	LRIG2	113460491	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.033000	0.88852	1.533000	0.49186	-0.217000	0.12591	GAG	.	.		0.483	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		T	113658968	G	T	113658968	4	4	108	1	0	0	0	0	0	1	0	0	8954	1291	45	3	2652	3	LRIG2	1	113658968	Nonsense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	14455140	113658968	135591653	9	16054										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153913916	153913916	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tgaatgaagtgggagatgtgCctgggggacagagaaacagg	18	4	0	4			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:153913916C>G	ENST00000361217.4	-	7	1474	c.1056G>C	c.(1054-1056)gcG>gcC	p.A352A		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	352	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGGAGATGTGCCTGGGGGACA	0.557																																					p.A352A		Atlas-SNP	.											.	DENND4B	210	.	0			c.G1056C						.						85	94	91					1																	153913916		2035	4183	6218	SO:0001630	splice_region_variant	9909	exon7			GATGTGCCTGGGG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.1056-1G>C	chr1.hg19:g.153913916C>G		73.0	0.0		88.0	45.0	NM_014856	Q5T4K0	Silent	SNP	ENST00000361217.4	hg19	CCDS44228.1																																																																																			.	.		0.557	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	Silent	G	153913916	C	G	153913916	5	3	108	1	0	0	0	0	0	0	1	0	4436	753	26	4	3522	4	DENND4B	1	153913916	Splice_Site	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	40254948	153913916	95336705	10	16055										
COPA	1314	hgsc.bcm.edu	37	chr1	160305090	160305090	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	caagcaatgtgaaaagacagCgccgaagcttgtaattccaa	9	9	0	2			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:160305090C>A	ENST00000241704.7	-	4	480	c.251G>T	c.(250-252)cGc>cTc	p.R84L	COPA_ENST00000368069.3_Missense_Mutation_p.R84L	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	84					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GAAAAGACAGCGCCGAAGCTT	0.378																																					p.R84L		Atlas-SNP	.											.	COPA	181	.	0			c.G251T						.						63	57	59					1																	160305090		2203	4300	6503	SO:0001583	missense	1314	exon4			AGACAGCGCCGAA	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"WD repeat domain containing", "Endogenous ligands"	2230	protein-coding gene	gene with protein product	"proxenin", "xenin"	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.251G>T	chr1.hg19:g.160305090C>A	ENSP00000241704:p.Arg84Leu	349.0	0.0		439.0	131.0	NM_001098398	Q5T201|Q8IXZ9	Missense_Mutation	SNP	ENST00000241704.7	hg19	CCDS1202.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.663848	0.88251	.	.	ENSG00000122218	ENST00000368069;ENST00000241704	T;T	0.59638	0.25;0.25	4.98	4.07	0.47477	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.056807	0.64402	D	0.000001	T	0.58380	0.2118	L	0.42245	1.32	0.80722	D	1	D;D	0.71674	0.998;0.989	D;D	0.78314	0.991;0.951	T	0.64618	-0.6365	10	0.87932	D	0	-9.4559	12.1766	0.54188	0.0:0.9165:0.0:0.0835	.	84;84	P53621;P53621-2	COPA_HUMAN;.	L	84	ENSP00000357048:R84L;ENSP00000241704:R84L	ENSP00000241704:R84L	R	-	2	0	COPA	158571714	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.988000	0.76212	1.105000	0.41606	0.655000	0.94253	CGC	.	.		0.378	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371		A	160305090	C	A	160305090	3	1	108	1	0	0	0	0	1	0	0	0	3729	768	27	1	3570	1	COPA	1	160305090	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	6391174	160305090	88945531	11	16056										
GLT25D2	23127	hgsc.bcm.edu	37	chr1	183938536	183938536	+	Silent	SNP	G	G	T													0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	aggaaggtggagtggaccatGgggacggggaagcagcctgt							TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:183938536G>T	ENST00000361927.4	-	5	1070	c.699C>A	c.(697-699)ccC>ccA	p.P233P	COLGALT2_ENST00000546159.1_Silent_p.P233P	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	233					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										AGTGGACCATGGGGACGGGGA	0.527																																					p.P233P		Atlas-SNP	.											.	.	.	.	0			c.C699A						.						124	118	120					1																	183938536		2203	4300	6503	SO:0001819	synonymous_variant	23127	exon5			GACCATGGGGACG	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.699C>A	chr1.hg19:g.183938536G>T		156.0	0.0		145.0	85.0	NM_015101	O60327|Q9BZR0	Silent	SNP	ENST00000361927.4	hg19	CCDS1360.1																																																																																			.	.		0.527	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		T	183938536	G	T	183938536	2	4	108	1	0	0	0	0	0	0	0	1	6475	1335	47	3		3	GLT25D2	1	183938536	Silent	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	23633446	183938536	65312085	12	16057	70	2								
GLT25D2	23127	hgsc.bcm.edu	37	chr1	183938539	183938539	+	Silent	SNP	G	G	T													0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	aaggtggagtggaccatgggGacggggaagcagcctgtcct							TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:183938539G>T	ENST00000361927.4	-	5	1067	c.696C>A	c.(694-696)gtC>gtA	p.V232V	COLGALT2_ENST00000546159.1_Silent_p.V232V	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	232					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										GGACCATGGGGACGGGGAAGC	0.522																																					p.V232V		Atlas-SNP	.											.	.	.	.	0			c.C696A						.						123	117	119					1																	183938539		2203	4300	6503	SO:0001819	synonymous_variant	23127	exon5			CATGGGGACGGGG	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.696C>A	chr1.hg19:g.183938539G>T		157.0	0.0		148.0	86.0	NM_015101	O60327|Q9BZR0	Silent	SNP	ENST00000361927.4	hg19	CCDS1360.1																																																																																			.	.		0.522	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		T	183938539	G	T	183938539	2	4	108	1	0	0	0	0	0	0	0	1	6475	1161	41	3		3	GLT25D2	1	183938539	Silent	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	3	183938539	65312082	13	16058	70	2								
KIF21B	23046	hgsc.bcm.edu	37	chr1	200946358	200946358	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	acctgctaagctcccagatgCggacggcattgcccgaggcg	13	14	0	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:200946358C>A	ENST00000422435.2	-	31	4623	c.4307G>T	c.(4306-4308)cGc>cTc	p.R1436L	KIF21B_ENST00000360529.5_Missense_Mutation_p.R1423L|KIF21B_ENST00000461742.2_Missense_Mutation_p.R1436L|KIF21B_ENST00000332129.2_Missense_Mutation_p.R1423L	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1436					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CTCCCAGATGCGGACGGCATT	0.642																																					p.R1436L		Atlas-SNP	.											KIF21B,NS,carcinoma,0,1	KIF21B	208	.	0			c.G4307T						.						114	107	110					1																	200946358		2203	4300	6503	SO:0001583	missense	23046	exon31			CAGATGCGGACGG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.4307G>T	chr1.hg19:g.200946358C>A	ENSP00000411831:p.Arg1436Leu	53.0	0.0		63.0	23.0	NM_001252102	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	hg19	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630802	0.67015	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.07567	3.18;3.18;3.18;3.18	4.88	4.88	0.63580	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.35970	0.0950	M	0.86953	2.85	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;0.999;0.998	D;D;D;D	0.91635	0.997;0.999;0.997;0.994	T	0.41448	-0.9508	10	0.87932	D	0	.	18.0342	0.89294	0.0:1.0:0.0:0.0	.	1423;1436;1436;1423	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	L	1423;1423;1436;1436;1436	ENSP00000328494:R1423L;ENSP00000353724:R1423L;ENSP00000433808:R1436L;ENSP00000411831:R1436L	ENSP00000328494:R1423L	R	-	2	0	KIF21B	199212981	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	5.761000	0.68801	2.249000	0.74217	0.561000	0.74099	CGC	.	.		0.642	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200946358	C	A	200946358	3	1	108	1	0	0	0	0	1	0	0	0	8298	768	27	1	626	1	KIF21B	1	200946358	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	17007819	200946358	48304263	14	16059										
KDM5B	10765	hgsc.bcm.edu	37	chr1	202702803	202702803	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gacaaagccagattcgcaggCcctgtgaaatactgggtacc	11	11	0	2			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:202702803C>A	ENST00000367265.3	-	23	4799	c.3635G>T	c.(3634-3636)gGc>gTc	p.G1212V	KDM5B_ENST00000367264.2_Missense_Mutation_p.G1248V	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1212					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						GATTCGCAGGCCCTGTGAAAT	0.542																																					p.G1212V		Atlas-SNP	.											.	KDM5B	166	.	0			c.G3635T						.						52	53	52					1																	202702803		2203	4300	6503	SO:0001583	missense	10765	exon23			CGCAGGCCCTGTG	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	18039	protein-coding gene	gene with protein product	"cancer/testis antigen 31", "protein phosphatase 1, regulatory subunit 98"	605393	"Jumonji, AT rich interactive domain 1B (RBP2-like)", "jumonji, AT rich interactive domain 1B"	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3635G>T	chr1.hg19:g.202702803C>A	ENSP00000356234:p.Gly1212Val	79.0	0.0		72.0	28.0	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	hg19	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	C	9.110	1.006216	0.19199	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	D;D;D	0.87966	-2.32;-2.32;-2.32	6.09	4.01	0.46588	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.449783	0.28871	N	0.013866	D	0.84826	0.5558	M	0.77486	2.375	0.47778	D	0.999517	B;B	0.27853	0.191;0.075	B;B	0.23275	0.045;0.039	T	0.79245	-0.1883	10	0.33141	T	0.24	-5.713	9.5632	0.39383	0.0:0.7531:0.0:0.2469	.	1248;1212	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	V	1212;1054;1248;1054	ENSP00000356234:G1212V;ENSP00000356233:G1248V;ENSP00000235790:G1054V	ENSP00000235790:G1054V	G	-	2	0	KDM5B	200969426	0.422000	0.25473	0.008000	0.14137	0.792000	0.44763	0.865000	0.27940	0.717000	0.32145	0.643000	0.83706	GGC	.	.		0.542	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		A	202702803	C	A	202702803	3	1	108	1	0	0	0	0	1	0	0	0	8143	739	26	3	1019	3	KDM5B	1	202702803	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	1756445	202702803	46547818	15	16060										
ADIPOR1	51094	hgsc.bcm.edu	37	chr1	202917500	202917500	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gggaagtgtcagtacccgcaCctcctcctcttcttcctggg	10	15	3	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:202917500C>A	ENST00000340990.5	-	3	488	c.190G>T	c.(190-192)Gtg>Ttg	p.V64L	ADIPOR1_ENST00000436244.1_Missense_Mutation_p.V64L|ADIPOR1_ENST00000367254.3_Missense_Mutation_p.V64L	NM_015999.4	NP_057083.2	Q96A54	ADR1_HUMAN	adiponectin receptor 1	64					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|hormone-mediated signaling pathway (GO:0009755)|leptin-mediated signaling pathway (GO:0033210)|negative regulation of cell growth (GO:0030308)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of JAK-STAT cascade (GO:0046427)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	16			BRCA - Breast invasive adenocarcinoma(75;0.141)			AGTACCCGCACCTCCTCCTCT	0.522																																					p.V64L		Atlas-SNP	.											.	ADIPOR1	32	.	0			c.G190T						.						123	104	111					1																	202917500		2203	4300	6503	SO:0001583	missense	51094	exon3			CCCGCACCTCCTC		CCDS1430.1	1q32.1	2012-08-22			ENSG00000159346	ENSG00000159346		"GPCR / Unclassified : Adiponectin receptors"	24040	protein-coding gene	gene with protein product		607945				12802337	Standard	XM_006711360		Approved	PAQR1, ACDCR1	uc001gyq.5	Q96A54	OTTHUMG00000041391	ENST00000340990.5:c.190G>T	chr1.hg19:g.202917500C>A	ENSP00000341785:p.Val64Leu	112.0	0.0		143.0	79.0	NM_015999	B3KMB0|Q53HS7|Q53YY6|Q9Y360	Missense_Mutation	SNP	ENST00000340990.5	hg19	CCDS1430.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.258016	0.39896	.	.	ENSG00000159346	ENST00000340990;ENST00000436244;ENST00000417068;ENST00000367254;ENST00000426229	D;D;D;D;D	0.96774	-4.12;-4.12;-4.12;-4.12;-4.12	5.85	4.93	0.64822	.	0.322267	0.33496	N	0.004841	D	0.90995	0.7168	N	0.16368	0.405	0.37180	D	0.903461	B	0.02656	0.0	B	0.01281	0.0	D	0.87943	0.2718	10	0.12430	T	0.62	.	15.0724	0.72049	0.1431:0.8569:0.0:0.0	.	64	Q96A54	ADR1_HUMAN	L	64	ENSP00000341785:V64L;ENSP00000395469:V64L;ENSP00000402178:V64L;ENSP00000356223:V64L;ENSP00000392946:V64L	ENSP00000341785:V64L	V	-	1	0	ADIPOR1	201184123	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.364000	0.66110	1.461000	0.47929	-0.182000	0.12963	GTG	.	.		0.522	ADIPOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099160.2	NM_015999		A	202917500	C	A	202917500	3	1	108	1	0	0	0	0	1	0	0	0	318	507	18	3	961	3	ADIPOR1	1	202917500	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	214697	202917500	46333121	16	16061										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228474710	228474710	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	acaagtgtgaggctgggggcGcctgcagcagctccattgtc	15	11	0	1	rs558072959		TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:228474710G>T	ENST00000422127.1	+	35	9558	c.9514G>T	c.(9514-9516)Gcc>Tcc	p.A3172S	OBSCN_ENST00000570156.2_Missense_Mutation_p.A3601S|OBSCN_ENST00000366709.4_Missense_Mutation_p.A291S|OBSCN_ENST00000366707.4_Missense_Mutation_p.A291S|OBSCN_ENST00000284548.11_Missense_Mutation_p.A3172S|OBSCN_ENST00000359599.6_Missense_Mutation_p.A2019S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3172	Ig-like 31.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGCTGGGGGCGCCTGCAGCAG	0.662																																					p.A3601S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G10801T						.						10	12	12					1																	228474710		2006	4171	6177	SO:0001583	missense	84033	exon40			GGGGGCGCCTGCA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.9514G>T	chr1.hg19:g.228474710G>T	ENSP00000409493:p.Ala3172Ser	71.0	0.0		62.0	48.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.462369	0.43736	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.05382	3.45;3.45;3.45;3.45;3.45	5.09	1.06	0.20224	Immunoglobulin subtype 2 (1);	0.367653	0.26467	N	0.024211	T	0.08447	0.0210	L	0.39147	1.195	0.09310	N	1	B;D	0.64830	0.13;0.994	B;P	0.58172	0.173;0.834	T	0.21415	-1.0246	10	0.09590	T	0.72	.	5.6767	0.17753	0.1333:0.0:0.4468:0.4199	.	3172;3172	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	3172;3172;291;291;2019	ENSP00000284548:A3172S;ENSP00000409493:A3172S;ENSP00000355668:A291S;ENSP00000355670:A291S;ENSP00000352613:A2019S	ENSP00000284548:A3172S	A	+	1	0	OBSCN	226541333	0.000000	0.05858	0.224000	0.23877	0.043000	0.13939	-0.225000	0.09151	0.034000	0.15491	0.561000	0.74099	GCC	.	.		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228474710	G	T	228474710	3	4	108	1	0	0	0	0	1	0	0	0	10821	1087	38	1	9648	1	OBSCN	1	228474710	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	25557210	228474710	20775911	17	16062										
ZNF238	10472	hgsc.bcm.edu	37	chr1	244218434	244218434	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ctacacatgcacccagtgcgGcaagagcttccagtactcgc	9	15	0	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:244218434G>T	ENST00000358704.4	+	2	1507	c.1358G>T	c.(1357-1359)gGc>gTc	p.G453V		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	444					cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										ACCCAGTGCGGCAAGAGCTTC	0.622																																					p.G453V		Atlas-SNP	.											.	.	.	.	0			c.G1358T						.						56	58	58					1																	244218434		2203	4300	6503	SO:0001583	missense	10472	exon2			AGTGCGGCAAGAG	U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13030	protein-coding gene	gene with protein product		608433	"zinc finger protein 238"	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.1358G>T	chr1.hg19:g.244218434G>T	ENSP00000351539:p.Gly453Val	83.0	0.0		105.0	86.0	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	hg19	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201224	0.58234	.	.	ENSG00000179456	ENST00000366538;ENST00000358704	T	0.07444	3.19	5.68	5.68	0.88126	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.40645	0.1125	M	0.91406	3.205	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.999	T	0.48091	-0.9065	10	0.72032	D	0.01	.	19.7964	0.96487	0.0:0.0:1.0:0.0	.	444;453	Q99592;Q99592-2	ZN238_HUMAN;.	V	453	ENSP00000351539:G453V	ENSP00000351539:G453V	G	+	2	0	ZNF238	242285057	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	9.869000	0.99810	2.702000	0.92279	0.655000	0.94253	GGC	.	.		0.622	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768		T	244218434	G	T	244218434	3	4	108	1	0	0	0	0	1	0	0	0	17805	1203	42	3	1364	3	ZNF238	1	244218434	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	15743724	244218434	5032187	18	16063										
OR2G2	81470	hgsc.bcm.edu	37	chr1	247751752	247751752	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ctcagttacagaaggttctaTttgtgctcatattgattctg	8	7	4	2			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr1:247751752T>G	ENST00000320065.1	+	1	91	c.91T>G	c.(91-93)Ttt>Gtt	p.F31V	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			GAAGGTTCTATTTGTGCTCAT	0.393																																					p.F31V		Atlas-SNP	.											.	OR2G2	88	.	0			c.T91G						.						214	205	208					1																	247751752		2203	4300	6503	SO:0001583	missense	81470	exon1			GTTCTATTTGTGC	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"GPCR / Class A : Olfactory receptors"	15007	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily G, member 2", "olfactory receptor, family 2, subfamily G, member 2 pseudogene"				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.91T>G	chr1.hg19:g.247751752T>G	ENSP00000326349:p.Phe31Val	632.0	0.0		474.0	141.0	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	hg19	CCDS31092.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.306108	0.60305	.	.	ENSG00000177489	ENST00000320065	T	0.04551	3.6	3.73	3.73	0.42828	.	0.000000	0.34338	U	0.004054	T	0.26048	0.0635	M	0.92833	3.35	0.09310	N	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.10636	-1.0621	10	0.87932	D	0	.	10.4648	0.44600	0.0:0.0:0.0:1.0	.	31	Q8NGZ5	OR2G2_HUMAN	V	31	ENSP00000326349:F31V	ENSP00000326349:F31V	F	+	1	0	OR2G2	245818375	0.975000	0.34042	0.048000	0.18961	0.888000	0.51559	3.914000	0.56401	1.535000	0.49220	0.481000	0.45027	TTT	.	.		0.393	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1			G	247751752	T	G	247751752	3	3	108	1	0	0	0	0	1	0	0	0	11007	1493	52	5	93	5	OR2G2	1	247751752	Missense_Mutation	SNP	T	TCGA-DD-A1EL-01A-11D-A152-10	3533318	247751752	1498869	19	16064										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29294437	29294437	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tgaggcttggtcaggctggcGgtgctcttgctgggcagcaa	17	9	2	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr2:29294437G>A	ENST00000331664.5	-	1	2690	c.2691C>T	c.(2689-2691)acC>acT	p.T897T		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	897					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TCAGGCTGGCGGTGCTCTTGC	0.682																																					p.T897T		Atlas-SNP	.											.	C2orf71	146	.	0			c.C2691T						.						22	25	24					2																	29294437		1970	4147	6117	SO:0001819	synonymous_variant	388939	exon1			GCTGGCGGTGCTC		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.2691C>T	chr2.hg19:g.29294437G>A		40.0	0.0		47.0	12.0	NM_001029883		Silent	SNP	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.		0.682	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29294437	G	A	29294437	2	1	108	1	0	0	0	0	0	0	0	1	2193	1103	39	1		1	C2orf71	2	29294437	Silent	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10		29294437	213904936	20	16065										
AUP1	165545	hgsc.bcm.edu	37	chr2	74755115	74755115	+	5'Flank	DEL	A	A	-													0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ttcgcttcccctagttggcgAtgaacaggacgaagccacct							TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr2:74755115delA	ENST00000404568.3	-	0	0				AUP1_ENST00000377526.3_Frame_Shift_Del_p.H230fs|HTRA2_ENST00000258080.3_5'Flank|HTRA2_ENST00000352222.3_5'Flank|DQX1_ENST00000393951.2_5'Flank	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1							nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						CTAGTTGGCGATGAACAGGAC	0.567																																					p.R231fs		Atlas-Indel,Pindel	.											.	AUP1	29	.	0			c.691delC						.						123	128	126					2																	74755115		1986	4170	6156	SO:0001631	upstream_gene_variant	550	exon7			.	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965		chr2.hg19:g.74755115delA	Exception_encountered	154.0	0.0		127.0	27.0	NM_181575	Q6B017|Q8NAM8	Frame_Shift_Del	DEL	ENST00000404568.3	hg19	CCDS1949.2																																																																																			.	.		0.567	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		-	74755115	A	-	74755115	6	5	108	0	1	1	0	1	0	0	0	0	1220	330	12	0		0	AUP1	2	74755115	5'Flank	DEL	A	TCGA-DD-A1EL-01A-11D-A152-10	45460678	74755115	168444258	21	16066										
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105924415	105924415	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	acgtggctgcccccttgatgCgggcccccgaaggcactggc	14	16	0	1	rs369840873		TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr2:105924415C>A	ENST00000393359.2	-	2	770	c.344G>T	c.(343-345)cGc>cTc	p.R115L	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.R115L			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	115	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						CCCCTTGATGCGGGCCCCCGA	0.582																																					p.R115L	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.G344T						.						57	63	61					2																	105924415		2203	4300	6503	SO:0001583	missense	9392	exon2			TTGATGCGGGCCC	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.344G>T	chr2.hg19:g.105924415C>A	ENSP00000377027:p.Arg115Leu	48.0	0.0		45.0	23.0	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	hg19	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168629	0.78339	.	.	ENSG00000135966	ENST00000393359;ENST00000258449	T;T	0.04706	3.57;3.57	5.02	5.02	0.67125	Citron-like (2);	0.055423	0.64402	D	0.000001	T	0.05456	0.0144	L	0.44542	1.39	0.45930	D	0.998766	B	0.34214	0.442	B	0.31614	0.133	T	0.40813	-0.9543	10	0.36615	T	0.2	-30.6776	12.2513	0.54599	0.0:0.9224:0.0:0.0776	.	115	Q8WUH2	TGFA1_HUMAN	L	115	ENSP00000377027:R115L;ENSP00000258449:R115L	ENSP00000258449:R115L	R	-	2	0	TGFBRAP1	105290847	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	4.578000	0.60929	2.760000	0.94817	0.655000	0.94253	CGC	.	.		0.582	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		A	105924415	C	A	105924415	3	1	108	1	0	0	0	0	1	0	0	0	15839	768	27	1	2282	1	TGFBRAP1	2	105924415	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	31169300	105924415	137274958	22	16067										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109380318	109380318	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tggaagcaaaaatgtgtctgGaatttcatttacagaaaaca	8	5	2	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr2:109380318G>T	ENST00000283195.6	+	20	3449	c.3323G>T	c.(3322-3324)gGa>gTa	p.G1108V		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1108					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						AATGTGTCTGGAATTTCATTT	0.423																																					p.G1108V		Atlas-SNP	.											.	RANBP2	488	.	0			c.G3323T						.						53	57	56					2																	109380318		2202	4299	6501	SO:0001583	missense	5903	exon20			TGTCTGGAATTTC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.3323G>T	chr2.hg19:g.109380318G>T	ENSP00000283195:p.Gly1108Val	214.0	0.0		118.0	45.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	G	6.438	0.448940	0.12223	.	.	ENSG00000153201	ENST00000283195	T	0.28069	1.63	5.52	-0.104	0.13605	.	.	.	.	.	T	0.26048	0.0635	M	0.62723	1.935	0.09310	N	0.999999	B	0.15473	0.013	B	0.14023	0.01	T	0.36383	-0.9750	9	0.66056	D	0.02	-5.9935	2.5502	0.04747	0.2776:0.1974:0.4212:0.1038	.	1108	P49792	RBP2_HUMAN	V	1108	ENSP00000283195:G1108V	ENSP00000283195:G1108V	G	+	2	0	RANBP2	108746750	0.999000	0.42202	0.928000	0.36995	0.018000	0.09664	1.335000	0.33839	0.034000	0.15491	0.557000	0.71058	GGA	.	.		0.423	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		T	109380318	G	T	109380318	3	4	108	1	0	0	0	0	1	0	0	0	13043	1174	41	3	3401	3	RANBP2	2	109380318	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	3455903	109380318	133819055	23	16068										
PRPF40A	151188	hgsc.bcm.edu	37	chr2	153573934	153573934	+	5'Flank	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ggctcagactgctccgccggCggccactgccgctacacata	11	17	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr2:153573934C>A	ENST00000326446.5	+	0	0				PRPF40A_ENST00000410080.1_Missense_Mutation_p.R7L|PRPF40A_ENST00000486100.1_5'UTR	NM_152522.5	NP_689735.1	Q8N6S5	AR6P6_HUMAN	ADP-ribosylation factor-like 6 interacting protein 6							integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|pancreas(1)	5						GCTCCGCCGGCGGCCACTGCC	0.647																																					p.R7L		Atlas-SNP	.											.	PRPF40A	149	.	0			c.G20T						.						30	37	35					2																	153573934		1934	4137	6071	SO:0001631	upstream_gene_variant	55660	exon1			CGCCGGCGGCCAC	AK023109	CCDS2197.1	2q23	2014-05-12	2014-05-12		ENSG00000177917	ENSG00000177917			24048	protein-coding gene	gene with protein product							Standard	NM_152522		Approved	MGC33864	uc002tyn.3	Q8N6S5	OTTHUMG00000131901		chr2.hg19:g.153573934C>A	Exception_encountered	87.0	0.0		84.0	30.0	NM_017892	B2RDS6|Q7Z4G7	Missense_Mutation	SNP	ENST00000326446.5	hg19	CCDS2197.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344018	0.61073	.	.	ENSG00000196504	ENST00000410080;ENST00000359961;ENST00000448428	T	0.34859	1.34	4.87	4.87	0.63330	.	.	.	.	.	T	0.19846	0.0477	N	0.08118	0	0.25132	N	0.990568	B	0.11235	0.004	B	0.06405	0.002	T	0.07731	-1.0757	9	0.14656	T	0.56	.	13.3945	0.60843	0.0:1.0:0.0:0.0	.	7	E9PFS0	.	L	7;7;13	ENSP00000386458:R7L	ENSP00000353046:R7L	R	-	2	0	PRPF40A	153282180	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.309000	0.51903	2.518000	0.84900	0.655000	0.94253	CGC	.	.		0.647	ARL6IP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254852.3	NM_152522		A	153573934	C	A	153573934	1	1	108	0	1	0	0	0	0	0	0	0	12583	768	27	1		1	PRPF40A	2	153573934	5'Flank	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	44193616	153573934	89625439	24	16069										
TRAK2	66008	hgsc.bcm.edu	37	chr2	202251196	202251196	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	aagctgctgccagtgatacaGagtttgtgatcctgaatatg	11	7	0	4			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr2:202251196G>A	ENST00000332624.3	-	14	2136	c.1708C>T	c.(1708-1710)Ctg>Ttg	p.L570L		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	570					protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)	p.L570M(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						CAGTGATACAGAGTTTGTGAT	0.423																																					p.L570L		Atlas-SNP	.											.	TRAK2	62	.	1	Substitution - Missense(1)	lung(1)	c.C1708T						.						91	97	95					2																	202251196		2203	4300	6503	SO:0001819	synonymous_variant	66008	exon14			GATACAGAGTTTG	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"gamma-aminobutyric acid(A) receptor-interacting factor", "milton homolog 2 (Drosophila)", "O-linked N-acetylglucosamine transferase interacting protein 98"	607334	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.1708C>T	chr2.hg19:g.202251196G>A		121.0	0.0		54.0	19.0	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Silent	SNP	ENST00000332624.3	hg19	CCDS2347.1																																																																																			.	.		0.423	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049		A	202251196	G	A	202251196	2	1	108	1	0	0	0	0	0	0	0	1	16465	933	33	3		3	TRAK2	2	202251196	Silent	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	48677262	202251196	40948177	25	16070										
ABCB6	10058	hgsc.bcm.edu	37	chr2	220079777	220079777	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ccaatgatgatgtcggccagCgtggggatgacattgaacac	13	9	0	4	rs548516506		TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr2:220079777C>A	ENST00000265316.3	-	6	1498	c.1182G>T	c.(1180-1182)acG>acT	p.T394T	ABCB6_ENST00000439002.2_Silent_p.T348T	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	394	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGTCGGCCAGCGTGGGGATGA	0.507																																					p.T394T		Atlas-SNP	.											.	ABCB6	76	.	0			c.G1182T						.						195	151	166					2																	220079777		2203	4300	6503	SO:0001819	synonymous_variant	10058	exon6			GGCCAGCGTGGGG	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.1182G>T	chr2.hg19:g.220079777C>A		110.0	0.0		102.0	22.0	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Silent	SNP	ENST00000265316.3	hg19	CCDS2436.1	.	.	.	.	.	.	.	.	.	.	C	6.018	0.371776	0.11409	.	.	ENSG00000115657	ENST00000295750	.	.	.	5.44	-7.71	0.01254	.	.	.	.	.	T	0.44477	0.1295	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48703	-0.9012	4	.	.	.	-13.0275	6.026	0.19656	0.0733:0.1189:0.4318:0.376	.	.	.	.	L	242	.	.	R	-	2	0	ABCB6	219788021	0.028000	0.19301	0.630000	0.29268	0.544000	0.35116	-0.928000	0.03980	-1.414000	0.02025	-0.894000	0.02916	CGC	.	.		0.507	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		A	220079777	C	A	220079777	2	1	108	1	0	0	0	0	0	0	0	1	45	755	27	1		1	ABCB6	2	220079777	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	17828581	220079777	23119596	26	16071										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230667054	230667054	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gcagcatgagtggcagctgtGgctgtcccactgctgactga	14	11	0	3			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr2:230667054G>A	ENST00000283943.5	-	20	3073	c.2895C>T	c.(2893-2895)gcC>gcT	p.A965A	TRIP12_ENST00000389044.4_Silent_p.A1013A|TRIP12_ENST00000389045.3_Silent_p.A695A|TRIP12_ENST00000543084.1_Intron	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	965					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TGGCAGCTGTGGCTGTCCCAC	0.502																																					p.A965A		Atlas-SNP	.											.	TRIP12	207	.	0			c.C2895T						.						66	57	60					2																	230667054		2203	4300	6503	SO:0001819	synonymous_variant	9320	exon20			AGCTGTGGCTGTC	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.2895C>T	chr2.hg19:g.230667054G>A		111.0	0.0		73.0	18.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.		0.502	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		A	230667054	G	A	230667054	2	1	108	1	0	0	0	0	0	0	0	1	16571	1335	47	3		3	TRIP12	2	230667054	Silent	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	10587277	230667054	12532319	27	16072										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266110	41266110	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ttacctggactctggaatccAttctggtgccactaccacag	8	13	2	0	rs121913416		TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr3:41266110A>C	ENST00000349496.5	+	3	387	c.107A>C	c.(106-108)cAt>cCt	p.H36P	CTNNB1_ENST00000405570.1_Missense_Mutation_p.H36P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.H29P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.H36P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.H36P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	36					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.H36P(24)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.H36R(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.I35_S37>T(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.S29_H36del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTGGAATCCATTCTGGTGCC	0.498		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.H36P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	159	Deletion - In frame(104)|Substitution - Missense(27)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(119)|large_intestine(20)|stomach(7)|kidney(6)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.A107C						.						95	80	85					3																	41266110		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GAATCCATTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.107A>C	chr3.hg19:g.41266110A>C	ENSP00000344456:p.His36Pro	252.0	0.0		134.0	54.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824526	0.50739	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88	5.76	5.76	0.90799	.	0.093481	0.85682	D	0.000000	T	0.51210	0.1661	M	0.64170	1.965	0.80722	D	1	P	0.40398	0.716	P	0.45946	0.498	T	0.54807	-0.8238	10	0.72032	D	0.01	-2.3155	16.0676	0.80897	1.0:0.0:0.0:0.0	.	36	P35222	CTNB1_HUMAN	P	29;36;36;36;36;29;36;36;36	ENSP00000400508:H29P;ENSP00000385604:H36P;ENSP00000412219:H36P;ENSP00000379486:H36P;ENSP00000344456:H36P;ENSP00000411226:H29P;ENSP00000379488:H36P;ENSP00000409302:H36P;ENSP00000401599:H36P	ENSP00000344456:H36P	H	+	2	0	CTNNB1	41241114	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	CAT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266110	A	C	41266110	3	2	108	1	0	0	0	0	1	0	0	0	4018	217	8	5	113	5	CTNNB1	3	41266110	Missense_Mutation	SNP	A	TCGA-DD-A1EL-01A-11D-A152-10		41266110	156756320	28	16073										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77651546	77651546	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gcatacatgaattggctgtcGatctgcctgatccacaatgg	10	10	1	2			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr3:77651546G>A	ENST00000461745.1	+	20	3940	c.3040G>A	c.(3040-3042)Gat>Aat	p.D1014N	ROBO2_ENST00000487694.3_Missense_Mutation_p.D1030N|ROBO2_ENST00000332191.8_Missense_Mutation_p.D1014N	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1014					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		ATTGGCTGTCGATCTGCCTGA	0.423																																					p.D1014N		Atlas-SNP	.											ROBO2_ENST00000487694,NS,carcinoma,0,6	ROBO2	527	.	0			c.G3040A						.						116	108	110					3																	77651546		1964	4162	6126	SO:0001583	missense	6092	exon20			GCTGTCGATCTGC	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3040G>A	chr3.hg19:g.77651546G>A	ENSP00000417164:p.Asp1014Asn	238.0	0.0		282.0	115.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.8|29.8	5.040614|5.040614	0.93630|0.93630	.|.	.|.	ENSG00000185008|ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191|ENST00000471893	T;T;T|.	0.64991|.	-0.13;-0.09;-0.08|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	0.000000|.	0.47455|.	D|.	0.000232|.	T|T	0.69178|0.69178	0.3082|0.3082	L|L	0.42245|0.42245	1.32|1.32	0.29415|.	N|.	0.860951|.	D;D;D|.	0.76494|.	0.998;0.999;0.997|.	P;P;P|.	0.62184|.	0.825;0.899;0.649|.	T|T	0.62756|0.62756	-0.6787|-0.6787	9|4	0.48119|.	T|.	0.1|.	.|.	20.1432|20.1432	0.98067|0.98067	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1030;1014;1014|.	Q19AB5;F8W703;Q9HCK4|.	.;.;ROBO2_HUMAN|.	N|Q	1030;1030;1034;1014;1014|88	ENSP00000417335:D1030N;ENSP00000417164:D1014N;ENSP00000327536:D1014N|.	ENSP00000327536:D1014N|.	D|R	+|+	1|2	0|0	ROBO2|ROBO2	77734236|77734236	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.476000|9.476000	0.97823|0.97823	2.769000|2.769000	0.95229|0.95229	0.561000|0.561000	0.74099|0.74099	GAT|CGA	.	.		0.423	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		A	77651546	G	A	77651546	3	1	108	1	0	0	0	0	1	0	0	0	13529	1058	37	1	3120	1	ROBO2	3	77651546	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	36385436	77651546	120370884	29	16074										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129279234	129279234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ccttcttgcgatggctctgcCggtgagacttcttgggctcc	12	13	3	1	rs201100072		TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr3:129279234C>T	ENST00000324093.4	-	31	5250	c.5072G>A	c.(5071-5073)cGg>cAg	p.R1691Q	PLXND1_ENST00000393239.1_Missense_Mutation_p.R1691Q	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1691					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						ATGGCTCTGCCGGTGAGACTT	0.662																																					p.R1691Q	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.G5072A						.						80	66	71					3																	129279234		2203	4299	6502	SO:0001583	missense	23129	exon31			CTCTGCCGGTGAG	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.5072G>A	chr3.hg19:g.129279234C>T	ENSP00000317128:p.Arg1691Gln	158.0	0.0		152.0	62.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695342	0.68386	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.15139	2.45;2.45	5.0	3.99	0.46301	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.066671	0.56097	D	0.000029	T	0.21590	0.0520	L	0.52126	1.63	0.48236	D	0.999611	P;D	0.64830	0.826;0.994	B;P	0.47864	0.185;0.559	T	0.01382	-1.1369	10	0.72032	D	0.01	.	11.9499	0.52948	0.0:0.8809:0.0:0.1191	.	286;1691	B4DRU3;Q9Y4D7	.;PLXD1_HUMAN	Q	1691	ENSP00000317128:R1691Q;ENSP00000376931:R1691Q	ENSP00000317128:R1691Q	R	-	2	0	PLXND1	130761924	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	3.723000	0.54955	2.326000	0.78906	0.462000	0.41574	CGG	.	C|1.000;G|0.000		0.662	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		T	129279234	C	T	129279234	3	4	108	1	0	0	0	0	1	0	0	0	12136	652	23	1	729	1	PLXND1	3	129279234	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	51627688	129279234	68743196	30	16075										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140281020	140281020	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gaggaaatgcttcataacttAgatttctgtgacattttggt	9	5	2	2			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr3:140281020A>T	ENST00000458420.3	+	13	2272	c.2082A>T	c.(2080-2082)ttA>ttT	p.L694F		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	694					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						TTCATAACTTAGATTTCTGTG	0.498										HNSCC(16;0.037)																											p.L694F	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.A2082T						.						102	98	99					3																	140281020		2203	4300	6503	SO:0001583	missense	64084	exon13			TAACTTAGATTTC	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2082A>T	chr3.hg19:g.140281020A>T	ENSP00000402460:p.Leu694Phe	90.0	0.0		95.0	40.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.228156	0.79576	.	.	ENSG00000158258	ENST00000458420	T	0.34072	1.38	5.43	-1.16	0.09678	.	0.000000	0.85682	D	0.000000	T	0.54806	0.1881	M	0.85630	2.765	0.46774	D	0.999195	D	0.76494	0.999	D	0.85130	0.997	T	0.54516	-0.8282	9	.	.	.	-32.6169	6.295	0.21081	0.2692:0.0:0.5783:0.1525	.	694	Q9H4D0	CSTN2_HUMAN	F	694	ENSP00000402460:L694F	.	L	+	3	2	CLSTN2	141763710	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	2.414000	0.44627	0.125000	0.18397	0.533000	0.62120	TTA	.	.		0.498	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		T	140281020	A	T	140281020	3	4	108	1	0	0	0	0	1	0	0	0	3564	417	15	4	2132	4	CLSTN2	3	140281020	Missense_Mutation	SNP	A	TCGA-DD-A1EL-01A-11D-A152-10	11001786	140281020	57741410	31	16076										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13617012	13617012	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ccttcctctttgtgatttagCgtggccaaaaactcatgcac	7	12	2	1	rs56295497	byFrequency	TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr4:13617012C>A	ENST00000040738.5	-	3	618	c.483G>T	c.(481-483)acG>acT	p.T161T		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	161						nucleus (GO:0005634)	DNA binding (GO:0003677)										TGTGATTTAGCGTGGCCAAAA	0.448																																					p.T161T		Atlas-SNP	.											.	.	.	.	0			c.G483T						.						232	223	226					4																	13617012		2203	4300	6503	SO:0001819	synonymous_variant	259282	exon3			ATTTAGCGTGGCC	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.483G>T	chr4.hg19:g.13617012C>A		342.0	1.0		166.0	73.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Silent	SNP	ENST00000040738.5	hg19	CCDS3411.2																																																																																			.	C|0.988;T|0.012		0.448	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13617012	C	A	13617012	2	1	108	1	0	0	0	0	0	0	0	1	1483	755	27	1		1	BOD1L	4	13617012	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		13617012	177537264	32	16077										
KCTD8	386617	hgsc.bcm.edu	37	chr4	44177219	44177219	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tatcagtgactttgtcatgtTtcctatcttcatgttcttgt	6	8	5	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr4:44177219T>C	ENST00000360029.3	-	2	1293	c.1010A>G	c.(1009-1011)aAa>aGa	p.K337R		NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	337					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						TTTGTCATGTTTCCTATCTTC	0.408										HNSCC(17;0.042)																											p.K337R		Atlas-SNP	.											.	KCTD8	96	.	0			c.A1010G						.						119	112	114					4																	44177219		2203	4300	6503	SO:0001583	missense	386617	exon2			TCATGTTTCCTAT	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.1010A>G	chr4.hg19:g.44177219T>C	ENSP00000353129:p.Lys337Arg	149.0	0.0		106.0	40.0	NM_198353	A2RU39	Missense_Mutation	SNP	ENST00000360029.3	hg19	CCDS3467.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.13|18.13	3.556000|3.556000	0.65425|0.65425	.|.	.|.	ENSG00000183783|ENSG00000183783	ENST00000360029|ENST00000515268	T|.	0.39787|.	1.06|.	4.65|4.65	4.65|4.65	0.58169|0.58169	.|.	0.000000|.	0.51477|.	D|.	0.000081|.	T|T	0.44540|0.44540	0.1298|0.1298	N|N	0.19112|0.19112	0.55|0.55	0.37078|0.37078	D|D	0.898854|0.898854	B|.	0.33739|.	0.422|.	B|.	0.29598|.	0.104|.	T|T	0.48801|0.48801	-0.9003|-0.9003	10|5	0.72032|.	D|.	0.01|.	.|.	13.6861|13.6861	0.62517|0.62517	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	337|.	Q6ZWB6|.	KCTD8_HUMAN|.	R|D	337|73	ENSP00000353129:K337R|.	ENSP00000353129:K337R|.	K|N	-|-	2|1	0|0	KCTD8|KCTD8	43871976|43871976	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.945000|0.945000	0.59286|0.59286	6.590000|6.590000	0.74085|0.74085	2.078000|2.078000	0.62432|0.62432	0.477000|0.477000	0.44152|0.44152	AAA|AAC	.	.		0.408	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			C	44177219	T	C	44177219	3	2	108	1	0	0	0	0	1	0	0	0	8124	1841	64	2	415	2	KCTD8	4	44177219	Missense_Mutation	SNP	T	TCGA-DD-A1EL-01A-11D-A152-10	30560207	44177219	146977057	33	16078										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11082847	11082847	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gacgtccaaggccatgttccGcagcgcagtggccaccgcgc	13	16	0	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr5:11082847G>A	ENST00000304623.8	-	16	2938	c.2749C>T	c.(2749-2751)Cgg>Tgg	p.R917W	CTNND2_ENST00000458100.2_Missense_Mutation_p.R484W|CTNND2_ENST00000503622.1_Missense_Mutation_p.R580W|CTNND2_ENST00000359640.2_Missense_Mutation_p.R859W|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000511377.1_Missense_Mutation_p.R826W	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	917					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GCCATGTTCCGCAGCGCAGTG	0.522																																					p.R917W		Atlas-SNP	.											CTNND2,NS,carcinoma,0,1	CTNND2	289	.	0			c.C2749T						.						133	116	121					5																	11082847		2203	4300	6503	SO:0001583	missense	1501	exon16			TGTTCCGCAGCGC	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.2749C>T	chr5.hg19:g.11082847G>A	ENSP00000307134:p.Arg917Trp	172.0	0.0		115.0	44.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281706	0.80692	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377;ENST00000538638;ENST00000458100;ENST00000503622	T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49	5.04	5.04	0.67666	Armadillo-like helical (1);Armadillo-type fold (1);	0.209202	0.40554	N	0.001070	D	0.87485	0.6189	M	0.90542	3.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.997	D	0.90094	0.4179	10	0.87932	D	0	-22.3756	18.7557	0.91832	0.0:0.0:1.0:0.0	.	580;509;917	B4DRK2;B4DG58;Q9UQB3	.;.;CTND2_HUMAN	W	917;859;826;12;484;580	ENSP00000307134:R917W;ENSP00000352661:R859W;ENSP00000426510:R826W;ENSP00000391155:R484W;ENSP00000426887:R580W	ENSP00000307134:R917W	R	-	1	2	CTNND2	11135847	1.000000	0.71417	0.997000	0.53966	0.955000	0.61496	3.392000	0.52537	2.505000	0.84491	0.563000	0.77884	CGG	.	.		0.522	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11082847	G	A	11082847	3	1	108	1	0	0	0	0	1	0	0	0	4022	1086	38	1	956	1	CTNND2	5	11082847	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10		11082847	169832413	34	16079										
SEPP1	100129792	hgsc.bcm.edu	37	chr5	42804757	42804757	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	aaaaataattcagaaaaataCcgtgagagagcagtttccac	7	7	1	3			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr5:42804757C>A	ENST00000361970.5	+	0	3431				SEPP1_ENST00000506577.1_Splice_Site|SEPP1_ENST00000511224.1_Splice_Site|SEPP1_ENST00000509276.1_Splice_Site|SEPP1_ENST00000507920.1_Intron|CTD-2325A15.5_ENST00000606056.1_RNA|SEPP1_ENST00000514985.1_Splice_Site	NM_001134848.1	NP_001128320.1	Q4G0S7	CC152_HUMAN	coiled-coil domain containing 152											endometrium(1)	1						CAGAAAAATACCGTGAGAGAG	0.343																																					.		Atlas-SNP	.											.	SEPP1	33	.	0			c.534+1G>T						.						86	82	83					5																	42804757		1800	4072	5872	SO:0001628	intergenic_variant	6414	exon5			AAAATACCGTGAG		CCDS47203.1	5p12	2008-07-14			ENSG00000198865	ENSG00000198865			34438	protein-coding gene	gene with protein product							Standard	NM_001134848		Approved	LOC100129792	uc003jmx.3	Q4G0S7	OTTHUMG00000162141		chr5.hg19:g.42804757C>A		304.0	1.0		314.0	106.0	NM_005410	B3KXI4|B4E0P7|Q5BLP6	Splice_Site	SNP	ENST00000361970.5	hg19	CCDS47203.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.572417	0.65765	.	.	ENSG00000250722	ENST00000514985;ENST00000511224;ENST00000506577;ENST00000514218;ENST00000510965	.	.	.	5.53	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2261	0.82293	0.0:0.8668:0.1332:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEPP1	42840514	1.000000	0.71417	0.696000	0.30242	0.986000	0.74619	6.174000	0.71943	1.276000	0.44395	0.557000	0.71058	.	.	.		0.343	CCDC152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367497.1	XM_001717416		A	42804757	C	A	42804757	1	1	108	0	1	0	0	0	0	0	0	0	14072	521	18	3		3	SEPP1	5	42804757	IGR	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	31721910	42804757	138110503	35	16080										
REEP5	7905	hgsc.bcm.edu	37	chr5	112238112	112238112	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gaaggggaaccatgacaggaAgatatcagagaagaattcag	13	5	2	4			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr5:112238112A>G	ENST00000379638.4	-	3	664	c.316T>C	c.(316-318)Ttc>Ctc	p.F106L	REEP5_ENST00000545426.1_Missense_Mutation_p.F106L|REEP5_ENST00000504247.1_Intron|REEP5_ENST00000513339.1_Missense_Mutation_p.F106L|REEP5_ENST00000474542.2_5'UTR	NM_005669.4	NP_005660.4	Q00765	REEP5_HUMAN	receptor accessory protein 5	106						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		Epithelial(69;1.3e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.26e-08)|all cancers(49;3.56e-07)|Colorectal(14;0.00778)|COAD - Colon adenocarcinoma(37;0.013)		CATGACAGGAAGATATCAGAG	0.418																																					p.F106L		Atlas-SNP	.											.	REEP5	12	.	0			c.T316C						.						162	141	148					5																	112238112		2202	4300	6502	SO:0001583	missense	7905	exon3			ACAGGAAGATATC	BC000232	CCDS4109.2	5q22-q23	2008-02-05	2006-02-07	2006-02-07	ENSG00000129625	ENSG00000129625		"Receptor accessory proteins"	30077	protein-coding gene	gene with protein product	"deleted in polyposis 1", "polyposis locus protein 1", "polyposis coli region hypothetical protein DP1"	125265	"chromosome 5 open reading frame 18"	C5orf18		16271481, 15550249	Standard	NM_005669		Approved	DP1, TB2, D5S346	uc003kqe.1	Q00765	OTTHUMG00000128807	ENST00000379638.4:c.316T>C	chr5.hg19:g.112238112A>G	ENSP00000368959:p.Phe106Leu	142.0	0.0		128.0	60.0	NM_005669	B7Z681|D3DT04|Q04198|Q5QGT0|Q9BWH9	Missense_Mutation	SNP	ENST00000379638.4	hg19	CCDS4109.2	.	.	.	.	.	.	.	.	.	.	A	9.689	1.151291	0.21371	.	.	ENSG00000129625	ENST00000379638;ENST00000513339;ENST00000545426;ENST00000261482	D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89	5.73	5.73	0.89815	.	0.043741	0.85682	D	0.000000	T	0.80270	0.4592	N	0.03948	-0.315	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.13407	0.009;0.009;0.006	T	0.76206	-0.3044	10	0.02654	T	1	-14.5387	16.0233	0.80516	1.0:0.0:0.0:0.0	.	106;79;106	B7Z510;B7Z2A3;Q00765	.;.;REEP5_HUMAN	L	106;106;106;97	ENSP00000368959:F106L;ENSP00000425901:F106L;ENSP00000442940:F106L;ENSP00000261482:F97L	ENSP00000261482:F97L	F	-	1	0	REEP5	112266011	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.401000	0.79962	2.186000	0.69663	0.533000	0.62120	TTC	.	.		0.418	REEP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250739.2	NM_005669		G	112238112	A	G	112238112	3	3	108	1	0	0	0	0	1	0	0	0	13223	72	3	2	265	2	REEP5	5	112238112	Missense_Mutation	SNP	A	TCGA-DD-A1EL-01A-11D-A152-10	69433355	112238112	68677148	36	16081										
PCDHGB7	56099	hgsc.bcm.edu	37	chr5	140798829	140798829	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gccagaaaacaaccagccggGtgcctccatagcgcaagtca	10	14	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr5:140798829G>A	ENST00000398594.2	+	1	1403	c.1403G>A	c.(1402-1404)gGt>gAt	p.G468D	PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA8_ENST00000398604.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	468	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACCAGCCGGGTGCCTCCATA	0.572																																					p.G468D		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.G1403A						.						79	92	88					5																	140798829		2123	4244	6367	SO:0001583	missense	56099	exon1			AGCCGGGTGCCTC	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1403G>A	chr5.hg19:g.140798829G>A	ENSP00000381594:p.Gly468Asp	147.0	0.0		129.0	29.0	NM_018927	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	hg19	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	g	19.66	3.869744	0.72065	.	.	ENSG00000254122	ENST00000398594	T	0.68624	-0.34	5.19	5.19	0.71726	Cadherin (3);Cadherin-like (1);	0.000000	0.32836	U	0.005596	D	0.83681	0.5307	M	0.82323	2.585	0.44123	D	0.9969	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.86331	0.1698	10	0.87932	D	0	.	18.3236	0.90246	0.0:0.0:1.0:0.0	.	468;468	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	D	468	ENSP00000381594:G468D	ENSP00000381594:G468D	G	+	2	0	PCDHGB7	140779013	1.000000	0.71417	0.083000	0.20561	0.903000	0.53119	5.657000	0.67996	2.410000	0.81850	0.491000	0.48974	GGT	.	.		0.572	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		A	140798829	G	A	140798829	3	1	108	1	0	0	0	0	1	0	0	0	11577	1261	44	3	1405	3	PCDHGB7	5	140798829	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	28560717	140798829	40116431	37	16082										
KIF13A	63971	hgsc.bcm.edu	37	chr6	17764367	17764367	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	acagcacagaacccaaaaggCtgcctctggaattattacct	7	12	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr6:17764367C>A	ENST00000259711.6	-	39	5497	c.5392G>T	c.(5392-5394)Gcc>Tcc	p.A1798S	KIF13A_ENST00000378826.2_Missense_Mutation_p.A1763S|KIF13A_ENST00000378816.5_Missense_Mutation_p.A1763S|KIF13A_ENST00000378843.2_Missense_Mutation_p.A1750S|KIF13A_ENST00000378814.5_Intron	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1798					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			ACCCAAAAGGCTGCCTCTGGA	0.488																																					p.A1798S		Atlas-SNP	.											.	KIF13A	276	.	0			c.G5392T						.						46	48	47					6																	17764367		1958	4138	6096	SO:0001583	missense	63971	exon39			AAAAGGCTGCCTC	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.5392G>T	chr6.hg19:g.17764367C>A	ENSP00000259711:p.Ala1798Ser	149.0	0.0		134.0	55.0	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	hg19	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	C	13.53	2.265412	0.40095	.	.	ENSG00000137177	ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	T;T;T;T	0.72394	-0.57;-0.65;-0.65;-0.65	5.78	1.77	0.24775	.	1.640970	0.03369	N	0.198705	T	0.26011	0.0634	N	0.14661	0.345	0.09310	N	1	B;B;B	0.11235	0.004;0.004;0.002	B;B;B	0.17433	0.018;0.008;0.008	T	0.09751	-1.0660	10	0.15066	T	0.55	.	2.8817	0.05649	0.1414:0.5369:0.1208:0.201	.	1750;1763;1798	Q9H1H9-4;Q9H1H9-2;Q9H1H9	.;.;KI13A_HUMAN	S	1798;1763;1750;1763	ENSP00000259711:A1798S;ENSP00000368103:A1763S;ENSP00000368120:A1750S;ENSP00000368093:A1763S	ENSP00000259711:A1798S	A	-	1	0	KIF13A	17872346	0.012000	0.17670	0.035000	0.18076	0.245000	0.25701	0.020000	0.13466	0.373000	0.24621	0.591000	0.81541	GCC	.	.		0.488	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			A	17764367	C	A	17764367	3	1	108	1	0	0	0	0	1	0	0	0	8283	797	28	3	54	3	KIF13A	6	17764367	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		17764367	153350700	38	16083										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33144991	33144991	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gggccgatggcaccctggggCccgggaagaccctacataca	14	14	0	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr6:33144991C>A	ENST00000374708.4	-	22	1983	c.1725G>T	c.(1723-1725)ggG>ggT	p.G575G	COL11A2_ENST00000341947.2_Silent_p.G661G|COL11A2_ENST00000374714.1_Silent_p.G635G|COL11A2_ENST00000477772.1_5'UTR|COL11A2_ENST00000357486.1_Silent_p.G640G|COL11A2_ENST00000395197.1_Silent_p.G601G|COL11A2_ENST00000361917.1_Silent_p.G554G|COL11A2_ENST00000374713.1_Silent_p.G614G|COL11A2_ENST00000374712.1_Silent_p.G580G	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	661	Collagen-like 3.|Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CACCCTGGGGCCCGGGAAGAC	0.557																																					p.G661G	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.G1983T						.						48	56	53					6																	33144991		1508	2707	4215	SO:0001819	synonymous_variant	1302	exon24			CTGGGGCCCGGGA	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.1725G>T	chr6.hg19:g.33144991C>A		65.0	0.0		63.0	16.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	hg19	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	C	5.857	0.342341	0.11069	.	.	ENSG00000204248	ENST00000395196	.	.	.	4.16	1.0	0.19881	.	0.000000	0.85682	D	0.000000	T	0.26376	0.0644	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.17837	-1.0356	8	0.87932	D	0	.	4.8495	0.13530	0.0:0.5753:0.1849:0.2398	.	67	A2ABA7	.	V	41	.	ENSP00000378622:G41V	G	-	2	0	COL11A2	33252969	0.000000	0.05858	0.980000	0.43619	0.534000	0.34807	-2.266000	0.01171	0.381000	0.24851	0.643000	0.83706	GGC	.	.		0.557	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			A	33144991	C	A	33144991	2	1	108	1	0	0	0	0	0	0	0	1	3670	726	26	3		3	COL11A2	6	33144991	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	15380624	33144991	137970076	39	16084										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38747836	38747836	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tggctgaacttgatgctactAagaaggcaagtgtcatgttt	11	6	1	3			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr6:38747836A>T	ENST00000359357.3	+	13	1737	c.1483A>T	c.(1483-1485)Aag>Tag	p.K495*	DNAH8_ENST00000449981.2_Nonsense_Mutation_p.K712*|DNAH8_ENST00000441566.1_Nonsense_Mutation_p.K495*			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	495					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGATGCTACTAAGAAGGCAAG	0.343																																					p.K712X		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A2134T						.						103	97	99					6																	38747836		2203	4300	6503	SO:0001587	stop_gained	1769	exon15			GCTACTAAGAAGG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.1483A>T	chr6.hg19:g.38747836A>T	ENSP00000352312:p.Lys495*	115.0	0.0		97.0	29.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Nonsense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	A	41	8.606517	0.98881	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	.	.	.	5.54	5.54	0.83059	.	0.062950	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.548	0.68047	1.0:0.0:0.0:0.0	.	.	.	.	X	700;700;495;495	.	ENSP00000333363:K700X	K	+	1	0	DNAH8	38855814	1.000000	0.71417	0.994000	0.49952	0.620000	0.37586	5.498000	0.66931	2.243000	0.73865	0.482000	0.46254	AAG	.	.		0.343	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38747836	A	T	38747836	4	4	108	1	0	0	0	0	0	1	0	0	4609	363	13	4	1525	4	DNAH8	6	38747836	Nonsense_Mutation	SNP	A	TCGA-DD-A1EL-01A-11D-A152-10	5602845	38747836	132367231	40	16085										
NT5DC1	221294	hgsc.bcm.edu	37	chr6	116542390	116542390	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ttctctgcgaatatattcttGggtgagtgatgagtcattca	10	6	4	3			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr6:116542390G>A	ENST00000319550.4	+	7	785	c.703G>A	c.(703-705)Ggg>Agg	p.G235R		NM_152729.2	NP_689942.2	Q5TFE4	NT5D1_HUMAN	5'-nucleotidase domain containing 1	235							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|stomach(1)	8		all_cancers(87;0.00367)|all_epithelial(87;0.00449)|Colorectal(196;0.0469)		all cancers(137;0.0327)|OV - Ovarian serous cystadenocarcinoma(136;0.0445)|GBM - Glioblastoma multiforme(226;0.0719)|Epithelial(106;0.112)		ATATATTCTTGGGTGAGTGAT	0.358																																					p.G235R	Colon(128;1440 1664 38087 41475 42869)	Atlas-SNP	.											.	NT5DC1	32	.	0			c.G703A						.						81	82	81					6																	116542390		2203	4300	6503	SO:0001630	splice_region_variant	221294	exon7			ATTCTTGGGTGAG	BC015138	CCDS5104.1	6q22.31	2008-02-05	2006-01-27	2006-01-27	ENSG00000178425	ENSG00000178425			21556	protein-coding gene	gene with protein product			"5'-nucleotidase, cytosolic II-like 1"	NT5C2L1			Standard	NM_152729		Approved	dJ486I3.1, MGC24302	uc003pwj.3	Q5TFE4	OTTHUMG00000015428	ENST00000319550.4:c.704+1G>A	chr6.hg19:g.116542390G>A		370.0	0.0		188.0	63.0	NM_152729	B2RND9|B3KR35|Q6XYD5	Missense_Mutation	SNP	ENST00000319550.4	hg19	CCDS5104.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.827017	0.90955	.	.	ENSG00000178425	ENST00000319550	T	0.23552	1.9	5.62	5.62	0.85841	HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.53658	0.1810	M	0.88842	2.985	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.61257	-0.7099	10	0.66056	D	0.02	-13.0406	18.6578	0.91460	0.0:0.0:1.0:0.0	.	185;235;235	B3KR35;A8K2Z3;Q5TFE4	.;.;NT5D1_HUMAN	R	235	ENSP00000326858:G235R	ENSP00000326858:G235R	G	+	1	0	NT5DC1	116649083	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	9.145000	0.94634	2.665000	0.90641	0.585000	0.79938	GGG	.	.		0.358	NT5DC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041931.3	NM_152729	Missense_Mutation	A	116542390	G	A	116542390	5	1	108	1	0	0	0	0	0	0	1	0	10699	1362	47	3	729	3	NT5DC1	6	116542390	Splice_Site	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	77794554	116542390	54572677	41	16086										
UNC93A	54346	hgsc.bcm.edu	37	chr6	167708073	167708073	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ctctatggaggcatgctcctGtcctccatgttcctcccacc	7	17	1	0	rs558415122		TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr6:167708073G>A	ENST00000230256.3	+	2	331	c.156G>A	c.(154-156)ctG>ctA	p.L52L	UNC93A_ENST00000366830.2_3'UTR|UNC93A_ENST00000366829.2_Silent_p.L52L	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GCATGCTCCTGTCCTCCATGT	0.617																																					p.L52L		Atlas-SNP	.											.	UNC93A	66	.	0			c.G156A						.						253	210	224					6																	167708073		2203	4300	6503	SO:0001819	synonymous_variant	54346	exon2			GCTCCTGTCCTCC	AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"unc93 (C.elegans) homolog A"			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.156G>A	chr6.hg19:g.167708073G>A		101.0	0.0		115.0	43.0	NM_018974	B3KRP5|Q4QQJ4|Q5JZD6	Silent	SNP	ENST00000230256.3	hg19	CCDS5300.1																																																																																			.	.		0.617	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974		A	167708073	G	A	167708073	2	1	108	1	0	0	0	0	0	0	0	1	17011	1364	48	3		3	UNC93A	6	167708073	Silent	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	51165683	167708073	3406994	42	16087										
IQUB	154865	hgsc.bcm.edu	37	chr7	123143008	123143008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	aaaacattacctgcgtatccCtacaaaatatactgagtctt	4	10	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr7:123143008C>T	ENST00000466202.1	-	5	1433	c.857G>A	c.(856-858)aGg>aAg	p.R286K	IQUB_ENST00000488987.1_5'UTR|IQUB_ENST00000434450.1_Missense_Mutation_p.R286K|IQUB_ENST00000324698.6_Missense_Mutation_p.R286K	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	286					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)				breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						CTGCGTATCCCTACAAAATAT	0.343																																					p.R286K		Atlas-SNP	.											.	IQUB	117	.	0			c.G857A						.						111	109	109					7																	123143008		2203	4300	6503	SO:0001583	missense	154865	exon5			GTATCCCTACAAA	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.857G>A	chr7.hg19:g.123143008C>T	ENSP00000417769:p.Arg286Lys	176.0	1.0		77.0	48.0	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	hg19	CCDS5787.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.785395	0.90282	.	.	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	T;T;T	0.62788	1.07;1.07;0.0	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.82637	0.5080	M	0.87758	2.905	0.52099	D	0.99994	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.973	D	0.84288	0.0498	10	0.56958	D	0.05	.	19.6556	0.95837	0.0:1.0:0.0:0.0	.	286;286	Q8NA54-2;Q8NA54	.;IQUB_HUMAN	K	286	ENSP00000417769:R286K;ENSP00000324882:R286K;ENSP00000388498:R286K	ENSP00000324882:R286K	R	-	2	0	IQUB	122930244	0.995000	0.38212	1.000000	0.80357	0.783000	0.44284	2.517000	0.45529	2.725000	0.93324	0.655000	0.94253	AGG	.	.		0.343	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827		T	123143008	C	T	123143008	3	4	108	1	0	0	0	0	1	0	0	0	7829	681	24	3	1554	3	IQUB	7	123143008	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		123143008	35995655	43	16088										
ADAM28	10863	hgsc.bcm.edu	37	chr8	24193031	24193031	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ctgaaatgtgtaatggtaaaTctggtaattgtcctgatgat	10	4	1	3			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr8:24193031T>C	ENST00000265769.4	+	14	1554	c.1444T>C	c.(1444-1446)Tct>Cct	p.S482P	RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000540823.1_Missense_Mutation_p.S249P|ADAM28_ENST00000437154.2_Missense_Mutation_p.S482P|ADAM28_ENST00000397649.3_Missense_Mutation_p.S229P	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	482	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.		S -> F (in a cutaneous metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:21618342}.		spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TAATGGTAAATCTGGTAATTG	0.468																																					p.S482P	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.T1444C						.						138	129	132					8																	24193031		2203	4300	6503	SO:0001583	missense	10863	exon14			GGTAAATCTGGTA	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.1444T>C	chr8.hg19:g.24193031T>C	ENSP00000265769:p.Ser482Pro	230.0	0.0		122.0	8.0	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	hg19	CCDS34865.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.97|14.97	2.693711|2.693711	0.48202|0.48202	.|.	.|.	ENSG00000042980|ENSG00000042980	ENST00000521629|ENST00000265769;ENST00000397649;ENST00000540823;ENST00000437154	.|T;T;T;T	.|0.15017	.|2.46;2.46;2.46;2.46	5.8|5.8	3.36|3.36	0.38483|0.38483	.|Blood coagulation inhibitor, Disintegrin (6);	.|.	.|.	.|.	.|.	T|T	0.54711|0.54711	0.1875|0.1875	H|H	0.97918|0.97918	4.105|4.105	0.58432|0.58432	D|D	0.999996|0.999996	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|1.0;0.999;0.999;1.0	T|T	0.63492|0.63492	-0.6625|-0.6625	5|9	.|0.87932	.|D	.|0	.|.	9.6176|9.6176	0.39701|0.39701	0.2791:0.0:0.0:0.7209|0.2791:0.0:0.0:0.7209	.|.	.|249;482;482;482	.|B4DDY3;B2RMV5;Q9UKQ2;Q9UKQ2-2	.|.;.;ADA28_HUMAN;.	T|P	114|482;229;249;482	.|ENSP00000265769:S482P;ENSP00000380770:S229P;ENSP00000443743:S249P;ENSP00000393699:S482P	.|ENSP00000265769:S482P	I|S	+|+	2|1	0|0	ADAM28|ADAM28	24248976|24248976	1.000000|1.000000	0.71417|0.71417	0.777000|0.777000	0.31699|0.31699	0.169000|0.169000	0.22640|0.22640	4.082000|4.082000	0.57635|0.57635	0.421000|0.421000	0.25980|0.25980	0.528000|0.528000	0.53228|0.53228	ATC|TCT	.	.		0.468	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		C	24193031	T	C	24193031	3	2	108	1	0	0	0	0	1	0	0	0	246	1435	50	2	1498	2	ADAM28	8	24193031	Missense_Mutation	SNP	T	TCGA-DD-A1EL-01A-11D-A152-10		24193031	122170991	44	16089										
SMC2	10592	hgsc.bcm.edu	37	chr9	106894408	106894408	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	aaatattgcatggcaaaaggTactttttatgtttgttttat	7	3	0	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr9:106894408T>G	ENST00000286398.7	+	22	3396		c.e22+2		SMC2_ENST00000374793.3_Splice_Site|SMC2_ENST00000374787.3_Splice_Site|SMC2_ENST00000303219.8_Splice_Site	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2						kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						TGGCAAAAGGTACTTTTTATG	0.303																																					.		Atlas-SNP	.											.	SMC2	127	.	0			c.3108+2T>G						.						67	72	70					9																	106894408		2203	4294	6497	SO:0001630	splice_region_variant	10592	exon22			AAAAGGTACTTTT	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.3108+2T>G	chr9.hg19:g.106894408T>G		503.0	0.0		287.0	123.0	NM_001042551	Q6IEE0|Q9P1P2	Splice_Site	SNP	ENST00000286398.7	hg19	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.106937	0.77096	.	.	ENSG00000136824	ENST00000286398;ENST00000374793;ENST00000303219;ENST00000374787	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1896	0.65630	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMC2	105934229	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	7.971000	0.88012	2.222000	0.72286	0.533000	0.62120	.	.	.		0.303	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1		Intron	G	106894408	T	G	106894408	5	3	108	1	0	0	0	0	0	0	1	0	14798	1652	57	5	3192	5	SMC2	9	106894408	Splice_Site	SNP	T	TCGA-DD-A1EL-01A-11D-A152-10		106894408	34319023	45	16090										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140953173	140953173	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	atagccctcaacactgtggtGctgatgatgaaggtgtgtgg	14	7	1	3	rs199714779		TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr9:140953173G>C	ENST00000371372.1	+	29	4606	c.4461G>C	c.(4459-4461)gtG>gtC	p.V1487V	CACNA1B_ENST00000371355.4_Silent_p.V1488V|CACNA1B_ENST00000371357.1_Silent_p.V1488V|CACNA1B_ENST00000277549.5_Silent_p.V683V|CACNA1B_ENST00000277551.2_Silent_p.V1487V|CACNA1B_ENST00000371363.1_Silent_p.V1487V	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1487					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	ACACTGTGGTGCTGATGATGA	0.557																																					p.V1487V		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G4461C						.						53	49	50					9																	140953173		2050	4207	6257	SO:0001819	synonymous_variant	774	exon29			TGTGGTGCTGATG	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.4461G>C	chr9.hg19:g.140953173G>C		96.0	0.0		107.0	38.0	NM_001243812	B1AQK5	Silent	SNP	ENST00000371372.1	hg19	CCDS59522.1																																																																																			.	.		0.557	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		C	140953173	G	C	140953173	2	2	108	1	0	0	0	0	0	0	0	1	2541	1306	46	4		4	CACNA1B	9	140953173	Silent	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	34058765	140953173	260258	46	16091										
ASAH2	56624	hgsc.bcm.edu	37	chr10	52005051	52005051	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	atatggtagccactgaagttCtgaaatagaggagactctgg	12	6	2	4			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr10:52005051C>A	ENST00000395526.4	-	2	290	c.291G>T	c.(289-291)caG>caT	p.Q97H	ASAH2_ENST00000329428.6_Missense_Mutation_p.Q78H|ASAH2_ENST00000447815.1_Missense_Mutation_p.Q97H	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	97					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ceramidase activity (GO:0017040)			large_intestine(1)|lung(9)|urinary_tract(1)	11						CACTGAAGTTCTGAAATAGAG	0.512																																					p.Q97H		Atlas-SNP	.											.	ASAH2	69	.	0			c.G291T						.						180	185	183					10																	52005051		2203	4300	6503	SO:0001583	missense	56624	exon2			GAAGTTCTGAAAT	AF250847	CCDS7239.2, CCDS44398.1	10q11.23	2008-08-11			ENSG00000188611	ENSG00000188611			18860	protein-coding gene	gene with protein product		611202				10781606	Standard	NM_019893		Approved		uc001jjd.3	Q9NR71	OTTHUMG00000018223	ENST00000395526.4:c.291G>T	chr10.hg19:g.52005051C>A	ENSP00000378897:p.Gln97His	361.0	0.0		339.0	178.0	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Missense_Mutation	SNP	ENST00000395526.4	hg19	CCDS7239.2	.	.	.	.	.	.	.	.	.	.	C	17.52	3.409294	0.62399	.	.	ENSG00000188611	ENST00000395526;ENST00000447815;ENST00000329428	T;T;T	0.32753	1.45;1.44;1.44	5.67	4.75	0.60458	.	0.276251	0.32952	N	0.005460	T	0.27629	0.0679	N	0.22421	0.69	0.80722	D	1	P;P	0.48503	0.911;0.906	P;B	0.47941	0.562;0.428	T	0.01561	-1.1324	10	0.46703	T	0.11	.	12.8939	0.58087	0.0:0.919:0.0:0.081	.	97;97	Q9NR71-2;Q9NR71	.;ASAH2_HUMAN	H	97;97;78	ENSP00000378897:Q97H;ENSP00000388206:Q97H;ENSP00000329886:Q78H	ENSP00000329886:Q78H	Q	-	3	2	ASAH2	51675057	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	2.840000	0.48215	2.649000	0.89929	0.655000	0.94253	CAG	.	.		0.512	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893		A	52005051	C	A	52005051	3	1	108	1	0	0	0	0	1	0	0	0	1007	912	32	3	2127	3	ASAH2	10	52005051	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		52005051	83529696	47	16092										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6643329	6643329	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	cgatacggggagctgggggaCatggccgagcttcatccttg	16	10	1	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr11:6643329C>A	ENST00000299441.3	-	21	9989	c.9578G>T	c.(9577-9579)tGt>tTt	p.C3193F	TPP1_ENST00000528657.1_5'Flank|RP11-732A19.5_ENST00000526456.1_RNA|TPP1_ENST00000299427.6_5'Flank|TPP1_ENST00000534644.1_5'Flank|TPP1_ENST00000533371.1_5'Flank|RP11-732A19.9_ENST00000545572.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	3193					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGCTGGGGGACATGGCCGAGC	0.617																																					p.C3193F		Atlas-SNP	.											.	DCHS1	277	.	0			c.G9578T						.						43	49	47					11																	6643329		2201	4296	6497	SO:0001583	missense	8642	exon21			GGGGGACATGGCC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.9578G>T	chr11.hg19:g.6643329C>A	ENSP00000299441:p.Cys3193Phe	112.0	0.0		86.0	30.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	8.080	0.772134	0.16051	.	.	ENSG00000166341	ENST00000299441	T	0.53423	0.62	4.88	4.88	0.63580	.	0.000000	0.46145	D	0.000314	T	0.38268	0.1034	N	0.22421	0.69	0.34786	D	0.735252	D	0.56521	0.976	P	0.44518	0.452	T	0.48948	-0.8989	10	0.31617	T	0.26	.	16.7719	0.85539	0.0:1.0:0.0:0.0	.	3193	Q96JQ0	PCD16_HUMAN	F	3193	ENSP00000299441:C3193F	ENSP00000299441:C3193F	C	-	2	0	DCHS1	6599905	0.999000	0.42202	0.990000	0.47175	0.865000	0.49528	3.651000	0.54431	2.531000	0.85337	0.313000	0.20887	TGT	.	.		0.617	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6643329	C	A	6643329	3	1	108	1	0	0	0	0	1	0	0	0	4289	478	17	3	322	3	DCHS1	11	6643329	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		6643329	128363187	48	16093										
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563794	55563795	+	Missense_Mutation	DNP	GG	GG	TT													0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	cttctatcaccatcttccatGggaccatccttttcctttac							TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr11:55563794_55563795GG>TT	ENST00000335605.1	+	1	763_764	c.763_764GG>TT	c.(763-765)GGg>TTg	p.G255L		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				CATCTTCCATGGGACCATCCTT	0.465																																					p.G255W|p.G255V		Atlas-SNP	.											.	OR5D14	116	.	0			c.G763T|c.G764T						.																																			SO:0001583	missense	219436	exon1			TTCCATGGGACCA|TCCATGGGACCAT	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	Exception_encountered	chr11.hg19:g.55563794_55563795delinsTT	ENSP00000334456:p.Gly255Leu	289.0|284.0	0.0|1.0		123.0|124.0	53.0	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	hg19	CCDS31508.1																																																																																			.	.		0.465	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		TT	55563795	GG	TT	55563794	3	4	108	1	0	0	0	0	1	0	0	0	11164	1348	47	3	765	3	OR5D14	11	55563794	Missense_Mutation	DNP	GG	TCGA-DD-A1EL-01A-11D-A152-10	48920465	55563794	79442722	49	16094										
ESRRA	2101	hgsc.bcm.edu	37	chr11	64082291	64082291	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tgccatgcctgaccccgcagGccctgatgggcacctcccag	11	18	0	2			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr11:64082291G>T	ENST00000405666.1	+	5	884	c.650G>T	c.(649-651)gGc>gTc	p.G217V	ESRRA_ENST00000406310.1_Missense_Mutation_p.G216V|ESRRA_ENST00000000442.6_Missense_Mutation_p.G217V	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	217	Ligand binding domain.				cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						GACCCCGCAGGCCCTGATGGG	0.577																																					p.G217V		Atlas-SNP	.											.	ESRRA	56	.	0			c.G650T						.						62	63	62					11																	64082291		2060	4218	6278	SO:0001583	missense	2101	exon5			CCGCAGGCCCTGA	X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"Nuclear hormone receptors"	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.650G>T	chr11.hg19:g.64082291G>T	ENSP00000384851:p.Gly217Val	59.0	0.0		60.0	31.0	NM_004451	Q14514	Missense_Mutation	SNP	ENST00000405666.1	hg19	CCDS41667.1	.	.	.	.	.	.	.	.	.	.	G	1.675	-0.507963	0.04231	.	.	ENSG00000173153	ENST00000406310;ENST00000000442;ENST00000539594;ENST00000405666	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	3.99	3.99	0.46301	Nuclear hormone receptor, ligand-binding (2);	0.279419	0.37348	N	0.002138	T	0.14485	0.0350	N	0.02539	-0.55	0.48511	D	0.999663	B;B	0.16802	0.019;0.002	B;B	0.20955	0.032;0.0	T	0.09487	-1.0672	10	0.24483	T	0.36	.	9.2555	0.37581	0.0:0.0:0.7845:0.2155	.	216;217	P11474-2;P11474	.;ERR1_HUMAN	V	216;217;74;217	ENSP00000385971:G216V;ENSP00000000442:G217V;ENSP00000439896:G74V;ENSP00000384851:G217V	ENSP00000000442:G217V	G	+	2	0	ESRRA	63838867	1.000000	0.71417	0.994000	0.49952	0.716000	0.41182	2.988000	0.49386	2.232000	0.73038	0.462000	0.41574	GGC	.	.		0.577	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451		T	64082291	G	T	64082291	3	4	108	1	0	0	0	0	1	0	0	0	5262	1203	42	3	664	3	ESRRA	11	64082291	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	8518497	64082291	70924225	50	16095										
TENC1	23371	hgsc.bcm.edu	37	chr12	53446269	53446269	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ggcgacgcacagaaaatgtgAagcaaaggtgggtatctgat	14	6	1	3			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr12:53446269A>T	ENST00000314250.6	+	3	505	c.215A>T	c.(214-216)gAa>gTa	p.E72V	TENC1_ENST00000314276.3_Missense_Mutation_p.E82V|RP11-983P16.4_ENST00000551890.1_RNA|TENC1_ENST00000451358.1_Missense_Mutation_p.E72V|TENC1_ENST00000552570.1_Missense_Mutation_p.E72V|RP11-983P16.4_ENST00000550601.1_RNA|TENC1_ENST00000549700.1_Missense_Mutation_p.E72V|TENC1_ENST00000546602.1_Missense_Mutation_p.E72V|TENC1_ENST00000379902.3_De_novo_Start_OutOfFrame|RP11-983P16.4_ENST00000546793.1_RNA	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	72					cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						AGAAAATGTGAAGCAAAGGTG	0.567																																					p.E82V		Atlas-SNP	.											.	TENC1	148	.	0			c.A245T						.						227	213	218					12																	53446269		2203	4300	6503	SO:0001583	missense	23371	exon3			AATGTGAAGCAAA	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	19737	protein-coding gene	gene with protein product	"tensin 2"	607717	"tensin like C1 domain-containing phosphatase"				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.215A>T	chr12.hg19:g.53446269A>T	ENSP00000319684:p.Glu72Val	100.0	0.0		111.0	43.0	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Missense_Mutation	SNP	ENST00000314250.6	hg19	CCDS8843.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.503466	0.85176	.	.	ENSG00000111077	ENST00000314276;ENST00000314250;ENST00000451358;ENST00000443113;ENST00000546602;ENST00000552570;ENST00000549700	D;D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73;-1.73	5.55	4.41	0.53225	Protein kinase C-like, phorbol ester/diacylglycerol binding (3);	0.000000	0.64402	D	0.000003	D	0.87966	0.6311	L	0.61218	1.895	0.40401	D	0.979645	D;D;D;D	0.89917	1.0;0.975;1.0;0.997	D;P;D;D	0.80764	0.963;0.668;0.983;0.994	D	0.88702	0.3216	10	0.87932	D	0	-3.8027	9.2442	0.37515	0.9148:0.0:0.0852:0.0	.	72;72;82;49	Q63HR2;F8W661;Q63HR2-4;Q6ZMJ1	TENC1_HUMAN;.;.;.	V	82;72;72;72;72;72;72	ENSP00000319756:E82V;ENSP00000319684:E72V;ENSP00000393362:E72V;ENSP00000449363:E72V;ENSP00000447021:E72V;ENSP00000449361:E72V	ENSP00000319684:E72V	E	+	2	0	TENC1	51732536	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.667000	0.54547	2.251000	0.74343	0.482000	0.46254	GAA	.	.		0.567	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754		T	53446269	A	T	53446269	3	4	108	1	0	0	0	0	1	0	0	0	15773	246	9	4	334	4	TENC1	12	53446269	Missense_Mutation	SNP	A	TCGA-DD-A1EL-01A-11D-A152-10		53446269	80405626	51	16096										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81746949	81746949	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	cctgaagcatcatggctagcGtctgggcatcggaatgacca	12	11	2	2			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr12:81746949G>T	ENST00000549396.1	-	17	2103	c.1943C>A	c.(1942-1944)aCg>aAg	p.T648K	PPFIA2_ENST00000548586.1_Missense_Mutation_p.T648K|PPFIA2_ENST00000550584.2_Missense_Mutation_p.T648K|PPFIA2_ENST00000333447.7_Missense_Mutation_p.T630K|PPFIA2_ENST00000443686.3_Missense_Mutation_p.T549K|PPFIA2_ENST00000552948.1_Missense_Mutation_p.T648K|PPFIA2_ENST00000550359.2_Missense_Mutation_p.T495K|PPFIA2_ENST00000549325.1_Missense_Mutation_p.T630K|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000541017.1_5'UTR|PPFIA2_ENST00000407050.4_Missense_Mutation_p.T574K|PPFIA2_ENST00000541570.2_Missense_Mutation_p.T215K	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	648					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						CATGGCTAGCGTCTGGGCATC	0.383																																					p.T648K		Atlas-SNP	.											.	PPFIA2	207	.	0			c.C1943A						.						148	142	144					12																	81746949		1952	4174	6126	SO:0001583	missense	8499	exon16			GCTAGCGTCTGGG	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.1943C>A	chr12.hg19:g.81746949G>T	ENSP00000450337:p.Thr648Lys	198.0	0.0		116.0	52.0	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	hg19	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.043873	0.93685	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000541570;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948;ENST00000553058	T;T;T;T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.56863	0.2014	M	0.83312	2.635	0.80722	D	1	D	0.63880	0.993	D	0.74023	0.982	T	0.61811	-0.6986	10	0.66056	D	0.02	-17.3587	19.2605	0.93966	0.0:0.0:1.0:0.0	.	648	O75334	LIPA2_HUMAN	K	648;630;215;574;659;630;648;549;648;229	ENSP00000450337:T648K;ENSP00000450298:T630K;ENSP00000438337:T215K;ENSP00000385093:T574K;ENSP00000327416:T630K;ENSP00000449338:T648K;ENSP00000388373:T549K;ENSP00000447868:T648K;ENSP00000448941:T229K	ENSP00000327416:T630K	T	-	2	0	PPFIA2	80271080	1.000000	0.71417	0.958000	0.39756	0.960000	0.62799	9.799000	0.99117	2.534000	0.85438	0.585000	0.79938	ACG	.	.		0.383	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			T	81746949	G	T	81746949	3	4	108	1	0	0	0	0	1	0	0	0	12319	1145	40	1	1894	1	PPFIA2	12	81746949	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	28300680	81746949	52104946	52	16097										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124305198	124305198	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gccgtcaggaactggctaacGctgagaaacttttcgatctt	10	10	2	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr12:124305198G>T	ENST00000409039.3	+	23	3743	c.3718G>T	c.(3718-3720)Gct>Tct	p.A1240S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1240	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		ACTGGCTAACGCTGAGAAACT	0.428																																					p.A1240S		Atlas-SNP	.											.	DNAH10	888	.	0			c.G3718T						.						123	125	125					12																	124305198		1907	4132	6039	SO:0001583	missense	196385	exon23			GCTAACGCTGAGA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.3718G>T	chr12.hg19:g.124305198G>T	ENSP00000386770:p.Ala1240Ser	155.0	0.0		133.0	66.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	14.73	2.622632	0.46840	.	.	ENSG00000197653	ENST00000409039	T	0.22539	1.95	5.18	5.18	0.71444	.	.	.	.	.	T	0.39572	0.1083	M	0.72479	2.2	0.53688	D	0.999971	D	0.53745	0.962	P	0.58013	0.831	T	0.19976	-1.0289	9	0.09843	T	0.71	.	18.6962	0.91601	0.0:0.0:1.0:0.0	.	1240	Q8IVF4	DYH10_HUMAN	S	1240	ENSP00000386770:A1240S	ENSP00000386770:A1240S	A	+	1	0	DNAH10	122871151	1.000000	0.71417	0.819000	0.32651	0.092000	0.18411	5.607000	0.67648	2.409000	0.81822	0.555000	0.69702	GCT	.	.		0.428	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124305198	G	T	124305198	3	4	108	1	0	0	0	0	1	0	0	0	4600	1087	38	1	3808	1	DNAH10	12	124305198	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	42558249	124305198	9546697	53	16098										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51791589	51791589	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ttcagtgtctccaaatttgaCagcatgcttccactgtgcat	7	11	2	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr15:51791589C>G	ENST00000251076.5	-	18	4119	c.3832G>C	c.(3832-3834)Gtc>Ctc	p.V1278L	DMXL2_ENST00000449909.3_Intron|DMXL2_ENST00000543779.2_Missense_Mutation_p.V1278L|RP11-707P17.1_ENST00000561007.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1278						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		CCAAATTTGACAGCATGCTTC	0.413																																					p.V1278L		Atlas-SNP	.											.	DMXL2	262	.	0			c.G3832C						.						183	178	180					15																	51791589		2195	4293	6488	SO:0001583	missense	23312	exon18			ATTTGACAGCATG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.3832G>C	chr15.hg19:g.51791589C>G	ENSP00000251076:p.Val1278Leu	140.0	0.0		86.0	51.0	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	1.984	-0.433474	0.04669	.	.	ENSG00000104093	ENST00000251076;ENST00000543779	T;T	0.20738	2.05;2.05	5.66	4.73	0.59995	.	0.164769	0.53938	D	0.000051	T	0.13970	0.0338	N	0.25647	0.755	0.80722	D	1	B;B	0.18741	0.03;0.017	B;B	0.17433	0.018;0.011	T	0.07404	-1.0774	10	0.27785	T	0.31	.	9.6847	0.40091	0.0:0.7935:0.0:0.2065	.	1278;1278	F5GWF1;Q8TDJ6	.;DMXL2_HUMAN	L	1278	ENSP00000251076:V1278L;ENSP00000441858:V1278L	ENSP00000251076:V1278L	V	-	1	0	DMXL2	49578881	0.999000	0.42202	1.000000	0.80357	0.901000	0.52897	1.791000	0.38744	2.669000	0.90835	0.591000	0.81541	GTC	.	.		0.413	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		G	51791589	C	G	51791589	3	3	108	1	0	0	0	0	1	0	0	0	4597	478	17	4	5385	4	DMXL2	15	51791589	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		51791589	50739803	54	16099										
STOML1	9399	hgsc.bcm.edu	37	chr15	74277722	74277722	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tcctcccaggaagtgcagggCcagctgctggagggtgctgt	16	11	0	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr15:74277722C>A	ENST00000316900.5	-	5	851	c.727G>T	c.(727-729)Gcc>Tcc	p.A243S	STOML1_ENST00000564777.1_Missense_Mutation_p.A193S|STOML1_ENST00000541638.1_Missense_Mutation_p.A201S|STOML1_ENST00000316911.6_Missense_Mutation_p.A193S|STOML1_ENST00000561656.1_Missense_Mutation_p.A156S|STOML1_ENST00000359750.4_Missense_Mutation_p.A243S	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	243						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						AAGTGCAGGGCCAGCTGCTGG	0.692																																					p.A243S		Atlas-SNP	.											.	STOML1	22	.	0			c.G727T						.						21	19	20					15																	74277722		2198	4297	6495	SO:0001583	missense	9399	exon5			GCAGGGCCAGCTG	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"stomatin-like 1", "stomatin (EBP72)-like 1"	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.727G>T	chr15.hg19:g.74277722C>A	ENSP00000319323:p.Ala243Ser	94.0	0.0		38.0	10.0	NM_001256672	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Missense_Mutation	SNP	ENST00000316900.5	hg19	CCDS10254.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.455809	0.63401	.	.	ENSG00000067221	ENST00000316900;ENST00000316911;ENST00000541638;ENST00000359750	D;D;D;D	0.98221	-3.13;-2.71;-3.1;-4.8	5.22	4.31	0.51392	.	0.107947	0.64402	D	0.000006	D	0.96433	0.8836	L	0.29908	0.895	0.51482	D	0.999928	P;P;P;P;P;P	0.45827	0.791;0.666;0.867;0.666;0.578;0.791	P;B;P;B;B;B	0.50314	0.535;0.194;0.637;0.194;0.272;0.389	D	0.94849	0.8012	10	0.34782	T	0.22	-14.6048	10.6367	0.45569	0.0:0.9109:0.0:0.0891	.	201;243;193;243;243;243	B4DUU5;E7ESC0;Q9UBI4-2;Q4PNR4;Q53HB6;Q9UBI4	.;.;.;.;.;STML1_HUMAN	S	243;193;201;243	ENSP00000319323:A243S;ENSP00000319384:A193S;ENSP00000442478:A201S;ENSP00000352788:A243S	ENSP00000319323:A243S	A	-	1	0	STOML1	72064775	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.057000	0.49931	1.201000	0.43203	0.655000	0.94253	GCC	.	.		0.692	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809		A	74277722	C	A	74277722	3	1	108	1	0	0	0	0	1	0	0	0	15328	739	26	3	481	3	STOML1	15	74277722	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	22486133	74277722	28253670	55	16100										
TTC23	64927	hgsc.bcm.edu	37	chr15	99759189	99759189	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gtattctcactatagggaggCacaatggagttggcgaggat	14	6	1	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr15:99759189C>A	ENST00000394132.2	-	7	1186	c.369G>T	c.(367-369)gtG>gtT	p.V123V	TTC23_ENST00000394136.1_Silent_p.V123V|TTC23_ENST00000394135.3_Silent_p.V123V|TTC23_ENST00000394129.2_Silent_p.V123V|TTC23_ENST00000394130.1_Silent_p.V123V|TTC23_ENST00000262074.4_Silent_p.V123V|TTC23_ENST00000558663.1_Silent_p.V123V|TTC23_ENST00000558613.1_Silent_p.V123V			Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23	123										endometrium(2)|large_intestine(3)|lung(9)|urinary_tract(2)	16	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)			TATAGGGAGGCACAATGGAGT	0.423																																					p.V123V		Atlas-SNP	.											.	TTC23	33	.	0			c.G369T						.						220	212	215					15																	99759189		2197	4297	6494	SO:0001819	synonymous_variant	64927	exon5			GGGAGGCACAATG		CCDS10379.2	15q26.3	2013-01-11			ENSG00000103852	ENSG00000103852		"Tetratricopeptide (TTC) repeat domain containing"	25730	protein-coding gene	gene with protein product						12477932	Standard	NM_001288615		Approved	FLJ12572, HCC-8	uc002bux.3	Q5W5X9	OTTHUMG00000147344	ENST00000394132.2:c.369G>T	chr15.hg19:g.99759189C>A		382.0	0.0		166.0	98.0	NM_001040657	A8K6M5|Q53HK0|Q96BC9|Q9H8W9|Q9H9S7	Silent	SNP	ENST00000394132.2	hg19	CCDS10379.2																																																																																			.	.		0.423	TTC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303953.2	NM_022905		A	99759189	C	A	99759189	2	1	108	1	0	0	0	0	0	0	0	1	16705	697	25	3		3	TTC23	15	99759189	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	25481467	99759189	2772203	56	16101										
SNRPA1	6627	hgsc.bcm.edu	37	chr15	101827889	101827889	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	agtcagcgatttgagagatgCcagagggtccagatcaccct	12	10	2	4			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr15:101827889C>A	ENST00000254193.6	-	4	400	c.328G>T	c.(328-330)Gca>Tca	p.A110S	SNRPA1_ENST00000560856.1_5'UTR	NM_003090.2	NP_003081.2	P09661	RU2A_HUMAN	small nuclear ribonucleoprotein polypeptide A'	110					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U2 snRNP (GO:0005686)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	Lung NSC(78;0.00156)|all_lung(78;0.00195)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00113)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TTGAGAGATGCCAGAGGGTCC	0.408																																					p.A110S		Atlas-SNP	.											.	SNRPA1	11	.	0			c.G328T						.						113	102	106					15																	101827889		2203	4300	6503	SO:0001583	missense	6627	exon4			GAGATGCCAGAGG	AJ130971	CCDS10391.1	15q26.3	2011-10-11			ENSG00000131876	ENSG00000131876			11152	protein-coding gene	gene with protein product		603521				2928112	Standard	NM_003090		Approved	Lea1	uc002bww.3	P09661	OTTHUMG00000149871	ENST00000254193.6:c.328G>T	chr15.hg19:g.101827889C>A	ENSP00000254193:p.Ala110Ser	196.0	1.0		99.0	66.0	NM_003090	B2R5I6|Q8TBD2	Missense_Mutation	SNP	ENST00000254193.6	hg19	CCDS10391.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396426	0.42512	.	.	ENSG00000131876	ENST00000254193	T	0.61274	0.12	5.82	4.89	0.63831	.	0.236329	0.43919	D	0.000519	T	0.45196	0.1330	L	0.38175	1.15	0.51767	D	0.999939	B	0.02656	0.0	B	0.06405	0.002	T	0.31833	-0.9929	10	0.15066	T	0.55	-11.4739	12.6983	0.57016	0.4164:0.5836:0.0:0.0	.	110	P09661	RU2A_HUMAN	S	110	ENSP00000254193:A110S	ENSP00000254193:A110S	A	-	1	0	SNRPA1	99645412	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	1.724000	0.38064	1.433000	0.47394	-0.181000	0.13052	GCA	.	.		0.408	SNRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313621.2	NM_003090		A	101827889	C	A	101827889	3	1	108	1	0	0	0	0	1	0	0	0	14875	739	26	3	463	3	SNRPA1	15	101827889	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	2068700	101827889	703503	57	16102										
ZNF423	23090	hgsc.bcm.edu	37	chr16	49671299	49671299	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tgggccagtggaatgttcttGtggttctccttgatgtgctt	13	7	2	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr16:49671299G>T	ENST00000561648.1	-	4	1817	c.1764C>A	c.(1762-1764)caC>caA	p.H588Q	ZNF423_ENST00000562520.1_Missense_Mutation_p.H528Q|ZNF423_ENST00000563137.2_Missense_Mutation_p.H528Q|ZNF423_ENST00000262383.2_Missense_Mutation_p.H588Q|ZNF423_ENST00000535559.1_Missense_Mutation_p.H471Q|ZNF423_ENST00000567169.1_Missense_Mutation_p.H471Q|ZNF423_ENST00000562871.1_Missense_Mutation_p.H528Q	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	588					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GAATGTTCTTGTGGTTCTCCT	0.577																																					p.H588Q		Atlas-SNP	.											.	ZNF423	463	.	0			c.C1764A						.						136	111	119					16																	49671299		2198	4300	6498	SO:0001583	missense	23090	exon4			GTTCTTGTGGTTC	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1764C>A	chr16.hg19:g.49671299G>T	ENSP00000455426:p.His588Gln	517.0	0.0		447.0	160.0	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.102786	0.56183	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.13420	2.59;2.7	4.99	4.99	0.66335	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.27967	0.0689	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.01834	-1.1264	9	.	.	.	-29.4823	18.2967	0.90148	0.0:0.0:1.0:0.0	.	588	Q2M1K9	ZN423_HUMAN	Q	588;471	ENSP00000262383:H588Q;ENSP00000442321:H471Q	.	H	-	3	2	ZNF423	48228800	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.379000	0.73154	2.320000	0.78422	0.561000	0.74099	CAC	.	.		0.577	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49671299	G	T	49671299	3	4	108	1	0	0	0	0	1	0	0	0	17913	1368	48	3	2110	3	ZNF423	16	49671299	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10		49671299	40683454	58	16103										
TP53	7157	hgsc.bcm.edu	37	chr17	7578449	7578449	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ctgtgactgcttgtagatggCcatggcgcggacgcgggtgc	17	10	0	2	rs193920817		TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr17:7578449C>A	ENST00000269305.4	-	5	670	c.481G>T	c.(481-483)Gcc>Tcc	p.A161S	TP53_ENST00000445888.2_Missense_Mutation_p.A161S|TP53_ENST00000359597.4_Missense_Mutation_p.A161S|TP53_ENST00000455263.2_Missense_Mutation_p.A161S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.A161S|TP53_ENST00000420246.2_Missense_Mutation_p.A161S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	161	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		A -> D (in sporadic cancers; somatic mutation).|A -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|A -> G (in sporadic cancers; somatic mutation).|A -> P (in sporadic cancers; somatic mutation).|A -> S (in sporadic cancers; somatic mutation).|A -> T (in sporadic cancers; somatic mutation).|A -> V (in sporadic cancers; somatic mutation).|MA -> IP (in a sporadic cancer; somatic mutation).|MA -> IS (in sporadic cancers; somatic mutation).|MA -> IT (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.A161T(54)|p.0?(8)|p.A68T(3)|p.A29T(3)|p.A161fs*9(3)|p.R156_I162delRVRAMAI(2)|p.M160fs*10(2)|p.V157_C176del20(1)|p.A161fs*19(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156fs*18(1)|p.A161fs*10(1)|p.R156_A161del(1)|p.V157fs*9(1)|p.A161fs*20(1)|p.M160_A161>IS(1)|p.A161fs*8(1)|p.S149fs*72(1)|p.A161fs*7(1)|p.T155_A161delTRVRAMA(1)|p.R156fs*20(1)|p.A161S(1)|p.A161P(1)|p.V157_I162delVRAMAI(1)|p.A161F(1)|p.A159_Q167delAMAIYKQSQ(1)|p.R158fs*8(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTGTAGATGGCCATGGCGCGG	0.632		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.A161S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,lymphoid_neoplasm,0,1	TP53	33396	.	96	Substitution - Missense(63)|Deletion - Frameshift(10)|Deletion - In frame(9)|Whole gene deletion(8)|Complex - frameshift(3)|Insertion - Frameshift(2)|Complex - compound substitution(1)	lung(15)|large_intestine(13)|urinary_tract(8)|stomach(7)|central_nervous_system(7)|upper_aerodigestive_tract(6)|oesophagus(6)|pancreas(6)|haematopoietic_and_lymphoid_tissue(5)|endometrium(5)|bone(4)|liver(4)|breast(3)|ovary(3)|thyroid(1)|meninges(1)|peritoneum(1)|skin(1)	c.G481T						.						52	53	53					17																	7578449		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGATGGCCATGGC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.481G>T	chr17.hg19:g.7578449C>A	ENSP00000269305:p.Ala161Ser	98.0	0.0		56.0	36.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.832703	0.50845	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99811	-6.87;-6.87;-6.87;-6.87;-6.87;-6.87;-6.87;-6.87;-6.87	5.59	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99711	0.9889	M	0.79805	2.47	0.48696	D	0.999696	D;P;D;D;D;D;D	0.89917	0.998;0.951;0.976;0.998;0.961;0.999;1.0	D;D;D;D;D;D;D	0.97110	0.998;0.989;0.981;0.998;0.994;1.0;1.0	D	0.97397	0.9993	10	0.59425	D	0.04	-25.6622	14.7187	0.69289	0.0:0.8543:0.1457:0.0	.	122;161;161;68;161;161;161	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	S	161;161;161;161;161;161;150;68;29;68;29;161	ENSP00000410739:A161S;ENSP00000352610:A161S;ENSP00000269305:A161S;ENSP00000398846:A161S;ENSP00000391127:A161S;ENSP00000391478:A161S;ENSP00000425104:A29S;ENSP00000423862:A68S;ENSP00000424104:A161S	ENSP00000269305:A161S	A	-	1	0	TP53	7519174	1.000000	0.71417	1.000000	0.80357	0.121000	0.20230	1.014000	0.29950	1.498000	0.48600	0.655000	0.94253	GCC	.	.		0.632	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578449	C	A	7578449	3	1	108	1	0	0	0	0	1	0	0	0	16396	739	26	3	817	3	TP53	17	7578449	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		7578449	73616761	59	16104										
PCGF2	7703	hgsc.bcm.edu	37	chr17	36891702	36891702	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gcagggaggaggaggtggctGgcagggtggcagggctggga	25	5	0	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr17:36891702G>A	ENST00000580830.1	-	12	1510	c.809C>T	c.(808-810)cCa>cTa	p.P270L	PCGF2_ENST00000360797.2_Missense_Mutation_p.P270L|PCGF2_ENST00000579882.1_3'UTR|PCGF2_ENST00000581345.1_Missense_Mutation_p.P270L|PCGF2_ENST00000585100.1_3'UTR|PCGF2_ENST00000578109.1_3'UTR			P35227	PCGF2_HUMAN	polycomb group ring finger 2	270	Pro/Ser-rich.				anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					GGAGGTGGCTGGCAGGGTGGC	0.701											OREG0024367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P270L		Atlas-SNP	.											.	PCGF2	24	.	0			c.C809T						.						19	16	17					17																	36891702		2189	4288	6477	SO:0001583	missense	7703	exon11			GTGGCTGGCAGGG	D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	12929	protein-coding gene	gene with protein product		600346	"ring finger protein 110"	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.809C>T	chr17.hg19:g.36891702G>A	ENSP00000461961:p.Pro270Leu	148.0	0.0	866	111.0	52.0	NM_007144	A6NGD8	Missense_Mutation	SNP	ENST00000580830.1	hg19	CCDS32638.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.965701	0.74131	.	.	ENSG00000056661	ENST00000360797	T	0.37411	1.2	4.92	3.95	0.45737	.	0.214785	0.40554	N	0.001080	T	0.30916	0.0780	L	0.46157	1.445	0.54753	D	0.999989	B	0.06786	0.001	B	0.08055	0.003	T	0.09058	-1.0692	10	0.40728	T	0.16	-15.7345	11.2214	0.48857	0.0894:0.0:0.9106:0.0	.	270	P35227	PCGF2_HUMAN	L	270	ENSP00000354033:P270L	ENSP00000354033:P270L	P	-	2	0	PCGF2	34145228	1.000000	0.71417	0.996000	0.52242	0.943000	0.58893	7.211000	0.77933	1.304000	0.44892	0.561000	0.74099	CCA	.	.		0.701	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144		A	36891702	G	A	36891702	3	1	108	1	0	0	0	0	1	0	0	0	11584	1348	47	3	229	3	PCGF2	17	36891702	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	29313253	36891702	44303508	60	16105										
KRTAP3-3	85293	hgsc.bcm.edu	37	chr17	39150290	39150290	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	cggcaggatttgtcagaggaGcagatggtggtggcaggccc	18	8	1	2			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr17:39150290G>T	ENST00000391586.1	-	1	95	c.60C>A	c.(58-60)tgC>tgA	p.C20*		NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	20	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			lung(2)|prostate(2)	4		Breast(137;0.00043)				TGTCAGAGGAGCAGATGGTGG	0.567																																					p.C20X		Atlas-SNP	.											.	KRTAP3-3	11	.	0			c.C60A						.						93	92	92					17																	39150290		2203	4296	6499	SO:0001587	stop_gained	85293	exon1			AGAGGAGCAGATG	AJ406933	CCDS32643.1	17q21.2	2013-06-25			ENSG00000212899	ENSG00000212899		"Keratin associated proteins"	18890	protein-coding gene	gene with protein product						11279113	Standard	NM_033185		Approved	KAP3.3	uc002hvr.1	Q9BYR6	OTTHUMG00000133591	ENST00000391586.1:c.60C>A	chr17.hg19:g.39150290G>T	ENSP00000375428:p.Cys20*	350.0	0.0		248.0	90.0	NM_033185	Q52LP0|Q6NTD4	Nonsense_Mutation	SNP	ENST00000391586.1	hg19	CCDS32643.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.957773	0.53400	.	.	ENSG00000212899	ENST00000391586	.	.	.	5.62	4.65	0.58169	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.41	0.44287	0.0894:0.0:0.9106:0.0	.	.	.	.	X	20	.	ENSP00000375428:C20X	C	-	3	2	KRTAP3-3	36403816	1.000000	0.71417	0.998000	0.56505	0.210000	0.24377	2.963000	0.49184	1.380000	0.46344	0.650000	0.86243	TGC	.	.		0.567	KRTAP3-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257695.1			T	39150290	G	T	39150290	4	4	108	1	0	0	0	0	0	1	0	0	8556	963	34	3	240	3	KRTAP3-3	17	39150290	Nonsense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	2258588	39150290	42044920	61	16106										
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40652840	40652840	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	acaagtggacggcctatgatGctcatacctctgagaatgca	10	10	2	2			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr17:40652840G>T	ENST00000343619.4	+	16	1918	c.1795G>T	c.(1795-1797)Gct>Tct	p.A599S	ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.A556S|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.A599S|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.A556S|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.A606S|ATP6V0A1_ENST00000544137.1_Missense_Mutation_p.A245S|ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.A599S	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	599					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		GGCCTATGATGCTCATACCTC	0.378																																					p.A606S		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.G1816T						.						215	195	202					17																	40652840		2203	4300	6503	SO:0001583	missense	535	exon16			TATGATGCTCATA	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"ATPases / V-type"	865	protein-coding gene	gene with protein product		192130	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 1", "ATPase, H+ transporting, lysosomal V0 subunit A1"	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.1795G>T	chr17.hg19:g.40652840G>T	ENSP00000342951:p.Ala599Ser	772.0	0.0		717.0	273.0	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	hg19	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.083018	0.76642	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728;ENST00000544137	D;D;D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17;-2.17;-2.17	4.91	4.91	0.64330	.	0.147766	0.64402	D	0.000010	D	0.90031	0.6887	L	0.60455	1.87	0.80722	D	1	B;B;B;P;B	0.46512	0.086;0.004;0.078;0.879;0.052	B;B;B;P;B	0.52823	0.156;0.02;0.063;0.71;0.056	D	0.89406	0.3699	10	0.44086	T	0.13	-9.9702	18.6406	0.91394	0.0:0.0:1.0:0.0	.	556;556;606;599;599	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1	.;.;.;VPP1_HUMAN;.	S	599;599;599;606;556;245	ENSP00000342951:A599S;ENSP00000444676:A599S;ENSP00000377415:A599S;ENSP00000264649:A606S;ENSP00000443991:A556S;ENSP00000446377:A245S	ENSP00000264649:A606S	A	+	1	0	ATP6V0A1	37906366	1.000000	0.71417	0.874000	0.34290	0.993000	0.82548	9.601000	0.98297	2.716000	0.92895	0.561000	0.74099	GCT	.	.		0.378	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020		T	40652840	G	T	40652840	3	4	108	1	0	0	0	0	1	0	0	0	1168	1319	46	3	1874	3	ATP6V0A1	17	40652840	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	1502550	40652840	40542370	62	16107										
RUNDC1	146923	hgsc.bcm.edu	37	chr17	41143400	41143400	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tcccagtccttcgcccttccTgttacgggaggcactgttgt	10	14	0	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr17:41143400T>A	ENST00000361677.1	+	5	1521	c.1509T>A	c.(1507-1509)ccT>ccA	p.P503P		NM_173079.2	NP_775102	Q96C34	RUND1_HUMAN	RUN domain containing 1	503	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.									breast(1)|large_intestine(2)|lung(4)|prostate(1)	8		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		TCGCCCTTCCTGTTACGGGAG	0.557																																					p.P503P		Atlas-SNP	.											.	RUNDC1	25	.	0			c.T1509A						.						67	66	66					17																	41143400		2203	4300	6503	SO:0001819	synonymous_variant	146923	exon5			CCTTCCTGTTACG	AL831813	CCDS11448.1	17q21.31	2004-02-27				ENSG00000198863			25418	protein-coding gene	gene with protein product						12477932	Standard	NM_173079		Approved	DKFZp761H0421	uc002ici.1	Q96C34		ENST00000361677.1:c.1509T>A	chr17.hg19:g.41143400T>A		122.0	0.0		106.0	36.0	NM_173079	Q6Y2K8|Q8IXT9|Q8N3W1	Silent	SNP	ENST00000361677.1	hg19	CCDS11448.1																																																																																			.	.		0.557	RUNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452464.1	NM_173079		A	41143400	T	A	41143400	2	1	108	1	0	0	0	0	0	0	0	1	13757	1567	55	4		4	RUNDC1	17	41143400	Silent	SNP	T	TCGA-DD-A1EL-01A-11D-A152-10	490560	41143400	40051810	63	16108										
CCDC43	124808	hgsc.bcm.edu	37	chr17	42756228	42756228	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	atagagtaggccaaggttatCgctttcgctcccctctctgt	9	12	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr17:42756228C>G	ENST00000315286.8	-	5	679	c.671G>C	c.(670-672)cGa>cCa	p.R224P	CCDC43_ENST00000457422.2_3'UTR|C17orf104_ENST00000588805.1_Intron|RP11-1072C15.4_ENST00000591628.1_RNA|CCDC43_ENST00000588210.1_Missense_Mutation_p.R227P	NM_144609.2	NP_653210.2	Q96MW1	CCD43_HUMAN	coiled-coil domain containing 43	224										lung(2)	2		Prostate(33;0.0322)				CCAAGGTTATCGCTTTCGCTC	0.453																																					p.R224P		Atlas-SNP	.											.	CCDC43	34	.	0			c.G671C						.						78	81	80					17																	42756228		1914	4123	6037	SO:0001583	missense	124808	exon5			GGTTATCGCTTTC	AK056357	CCDS45704.1, CCDS45705.1	17q21.31	2005-12-16							26472	protein-coding gene	gene with protein product						12477932	Standard	NM_001099225		Approved	FLJ31795	uc002ihc.2	Q96MW1		ENST00000315286.8:c.671G>C	chr17.hg19:g.42756228C>G	ENSP00000323782:p.Arg224Pro	465.0	0.0		400.0	157.0	NM_144609	C9JVK9	Missense_Mutation	SNP	ENST00000315286.8	hg19	CCDS45704.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058141	0.76074	.	.	ENSG00000180329	ENST00000315286	.	.	.	6.16	6.16	0.99307	.	0.120163	0.56097	D	0.000024	T	0.79499	0.4456	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79215	-0.1895	9	0.87932	D	0	.	19.6313	0.95704	0.0:1.0:0.0:0.0	.	224	Q96MW1	CCD43_HUMAN	P	224	.	ENSP00000323782:R224P	R	-	2	0	CCDC43	40111754	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.802000	0.75175	2.937000	0.99478	0.650000	0.86243	CGA	.	.		0.453	CCDC43-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457812.1	NM_144609		G	42756228	C	G	42756228	3	3	108	1	0	0	0	0	1	0	0	0	2817	884	31	4	7	4	CCDC43	17	42756228	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	1612828	42756228	38438982	64	16109										
SP6	80320	hgsc.bcm.edu	37	chr17	45925714	45925714	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gccctggtaagtttggagagGctgcaggtcgaggcgcggcg	19	9	0	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr17:45925714G>T	ENST00000536300.1	-	2	413	c.82C>A	c.(82-84)Cct>Act	p.P28T	SP6_ENST00000342234.2_Missense_Mutation_p.P28T	NM_001258248.1	NP_001245177.1	Q3SY56	SP6_HUMAN	Sp6 transcription factor	28					positive regulation of cell proliferation (GO:0008284)|regulation of odontogenesis (GO:0042481)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(5)|prostate(1)|skin(1)	8						GTTTGGAGAGGCTGCAGGTCG	0.716																																					p.P28T		Atlas-SNP	.											.	SP6	26	.	0			c.C82A						.						8	10	9					17																	45925714		2174	4232	6406	SO:0001583	missense	80320	exon2			GGAGAGGCTGCAG		CCDS11520.1	17q21.32	2013-01-08			ENSG00000189120	ENSG00000189120		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	14530	protein-coding gene	gene with protein product	"epiprofin"	608613				11087666, 14551215	Standard	NM_001258248		Approved	KLF14, Epfn	uc002img.2	Q3SY56	OTTHUMG00000132067	ENST00000536300.1:c.82C>A	chr17.hg19:g.45925714G>T	ENSP00000438209:p.Pro28Thr	42.0	0.0		52.0	21.0	NM_001258248	B3KXS4	Missense_Mutation	SNP	ENST00000536300.1	hg19	CCDS11520.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.195352	0.58126	.	.	ENSG00000189120	ENST00000342234;ENST00000536300	T;T	0.12774	2.65;2.65	4.44	4.44	0.53790	.	0.000000	0.43260	D	0.000581	T	0.07007	0.0178	N	0.08118	0	0.33950	D	0.644355	P	0.37233	0.588	B	0.36244	0.22	T	0.23261	-1.0193	10	0.37606	T	0.19	.	9.725	0.40326	0.0971:0.0:0.9029:0.0	.	28	Q3SY56	SP6_HUMAN	T	28	ENSP00000340799:P28T;ENSP00000438209:P28T	ENSP00000340799:P28T	P	-	1	0	SP6	43280713	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.972000	0.49256	2.288000	0.76882	0.462000	0.41574	CCT	.	.		0.716	SP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441395.1	NM_199262		T	45925714	G	T	45925714	3	4	108	1	0	0	0	0	1	0	0	0	14983	1203	42	3	1052	3	SP6	17	45925714	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	3169486	45925714	35269496	65	16110										
CSH1	1442	hgsc.bcm.edu	37	chr17	61972411	61972411	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	acagctgccctccacagagcGgcactgcaccatgcgcagga	11	16	0	1	rs61764004		TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr17:61972411G>T	ENST00000316193.8	-	5	766	c.625C>A	c.(625-627)Cgc>Agc	p.R209S	CSH1_ENST00000453363.3_Missense_Mutation_p.R114S|CSH1_ENST00000329882.8_3'UTR	NM_001317.5	NP_001308.1	P0DML2	CSH1_HUMAN	chorionic somatomammotropin hormone 1 (placental lactogen)	209						extracellular region (GO:0005576)	metal ion binding (GO:0046872)	p.R209C(1)		central_nervous_system(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						TCCACAGAGCGGCACTGCACC	0.607									Russell-Silver syndrome																												p.R209S		Atlas-SNP	.											CSH1,brain,atypical_teratoid-rhabdoid_tumour,0,1	CSH1	18	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.C625A						.						105	94	98					17																	61972411		2198	4299	6497	SO:0001583	missense	1442	exon5	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	CAGAGCGGCACTG	J00118	CCDS11649.1	17q22-q24	2008-07-18				ENSG00000136488			2440	protein-coding gene	gene with protein product	"chorionic somatomammotropin A", "placental lactogen", "choriomammotropin"	150200				6208192	Standard	NM_001317		Approved	hCS-A, CSA, PL, CSMT, FLJ75407	uc002jcs.2	P0DML2		ENST00000316193.8:c.625C>A	chr17.hg19:g.61972411G>T	ENSP00000316416:p.Arg209Ser	270.0	0.0		185.0	85.0	NM_001317	P01243|Q0VDB1|Q14407	Missense_Mutation	SNP	ENST00000316193.8	hg19	CCDS11649.1	.	.	.	.	.	.	.	.	.	.	g	10.94	1.491692	0.26774	.	.	ENSG00000136488	ENST00000316193;ENST00000453363	D;D	0.92911	-3.13;-3.13	2.56	1.57	0.23409	.	.	.	.	.	D	0.95319	0.8481	M	0.86651	2.83	0.43114	D	0.994825	D;D	0.71674	0.989;0.998	D;D	0.71414	0.973;0.955	D	0.93904	0.7191	9	0.72032	D	0.01	.	8.4239	0.32718	0.1261:0.0:0.8739:0.0	rs61764004	114;209	B1A4H2;Q6PF11	.;.	S	209;114	ENSP00000316416:R209S;ENSP00000402517:R114S	ENSP00000316416:R209S	R	-	1	0	CSH1	59326143	1.000000	0.71417	0.996000	0.52242	0.012000	0.07955	6.449000	0.73473	0.405000	0.25532	-0.671000	0.03813	CGC	.	G|0.993;T|0.007		0.607	CSH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416040.1	NM_001317		T	61972411	G	T	61972411	3	4	108	1	0	0	0	0	1	0	0	0	3942	1116	39	1	32	1	CSH1	17	61972411	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	16046697	61972411	19222799	66	16111										
PCYT2	5833	hgsc.bcm.edu	37	chr17	79864760	79864760	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	gataccccggtccaggggttCcgcccaccagggcactgcaa	12	16	0	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr17:79864760C>A	ENST00000538936.2	-	7	660	c.552G>T	c.(550-552)cgG>cgT	p.R184R	PCYT2_ENST00000570388.1_Silent_p.R106R|PCYT2_ENST00000571105.1_Silent_p.R184R|PCYT2_ENST00000331285.3_Silent_p.R106R|PCYT2_ENST00000570391.1_Silent_p.R152R|PCYT2_ENST00000538721.2_Silent_p.R202R	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine	184					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)	ethanolamine-phosphate cytidylyltransferase activity (GO:0004306)			breast(2)|endometrium(1)|lung(4)|ovary(1)	8	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		Lamivudine(DB00709)	TCCAGGGGTTCCGCCCACCAG	0.617																																					p.R202R		Atlas-SNP	.											.	PCYT2	23	.	0			c.G606T						.						48	50	49					17																	79864760		2203	4298	6501	SO:0001819	synonymous_variant	5833	exon8			GGGGTTCCGCCCA	D84307	CCDS11791.1, CCDS54178.1, CCDS58610.1, CCDS62364.1	17q25.3	2008-07-18				ENSG00000185813			8756	protein-coding gene	gene with protein product		602679				9083101	Standard	XM_005256386		Approved	ET	uc002kch.2	Q99447		ENST00000538936.2:c.552G>T	chr17.hg19:g.79864760C>A		53.0	0.0		69.0	31.0	NM_001184917	B7Z7A5|B7ZAS0|F5H8B1|Q6IBM3|Q96G08	Silent	SNP	ENST00000538936.2	hg19	CCDS11791.1																																																																																			.	.		0.617	PCYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439939.1	NM_002861		A	79864760	C	A	79864760	2	1	108	1	0	0	0	0	0	0	0	1	11621	842	30	3		3	PCYT2	17	79864760	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	17892349	79864760	1330450	67	16112										
LRG1	116844	hgsc.bcm.edu	37	chr19	4538450	4538450	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	agggtgaagttggccagcagCccggggggcagtttccggag	19	9	0	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr19:4538450C>A	ENST00000306390.6	-	2	1006	c.546G>T	c.(544-546)ggG>ggT	p.G182G	LRG1_ENST00000586883.1_5'Flank|CTB-50L17.14_ENST00000586020.1_Intron	NM_052972.2	NP_443204.1	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1	182					brown fat cell differentiation (GO:0050873)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				NS(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGCCAGCAGCCCGGGGGGCA	0.622																																					p.G182G		Atlas-SNP	.											.	LRG1	25	.	0			c.G546T						.						93	106	102					19																	4538450		2203	4300	6503	SO:0001819	synonymous_variant	116844	exon2			CAGCAGCCCGGGG		CCDS12130.1	19p13.3	2013-09-20			ENSG00000171236	ENSG00000171236			29480	protein-coding gene	gene with protein product	"leucine rich alpha 2 glycoprotein"	611289				3856868, 12223515	Standard	NM_052972		Approved	LRG	uc002mau.3	P02750	OTTHUMG00000182010	ENST00000306390.6:c.546G>T	chr19.hg19:g.4538450C>A		40.0	0.0		24.0	16.0	NM_052972	Q8N4F5|Q96QZ4	Silent	SNP	ENST00000306390.6	hg19	CCDS12130.1																																																																																			.	.		0.622	LRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458654.2	NM_052972		A	4538450	C	A	4538450	2	1	108	1	0	0	0	0	0	0	0	1	8951	726	26	3		3	LRG1	19	4538450	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		4538450	54590533	68	16113										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10602767	10602767	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	cgtcaacgagtggcagcgcaCggcccgcagcagcgcctgga	15	15	1	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr19:10602767C>A	ENST00000171111.5	-	3	1358	c.811G>T	c.(811-813)Gtg>Ttg	p.V271L	KEAP1_ENST00000588024.1_5'UTR|CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000393623.2_Missense_Mutation_p.V271L	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	271	BACK.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	TGGCAGCGCACGGCCCGCAGC	0.617																																					p.V271L		Atlas-SNP	.											KEAP1,right_upper_lobe,carcinoma,0,1	KEAP1	182	.	0			c.G811T						.						57	57	57					19																	10602767		2203	4300	6503	SO:0001583	missense	9817	exon3			AGCGCACGGCCCG	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.811G>T	chr19.hg19:g.10602767C>A	ENSP00000171111:p.Val271Leu	68.0	0.0		45.0	35.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	C	33	5.208480	0.95069	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.76316	-1.01;-1.01	5.61	5.61	0.85477	BTB/Kelch-associated (2);	0.056422	0.64402	N	0.000001	D	0.84897	0.5574	M	0.82630	2.6	0.80722	D	1	P	0.52170	0.951	P	0.50270	0.636	D	0.87391	0.2363	10	0.87932	D	0	.	17.1459	0.86766	0.0:1.0:0.0:0.0	.	271	Q14145	KEAP1_HUMAN	L	271	ENSP00000171111:V271L;ENSP00000377245:V271L	ENSP00000171111:V271L	V	-	1	0	KEAP1	10463767	1.000000	0.71417	0.997000	0.53966	0.942000	0.58702	5.874000	0.69652	2.656000	0.90262	0.561000	0.74099	GTG	.	.		0.617	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		A	10602767	C	A	10602767	3	1	108	1	0	0	0	0	1	0	0	0	8150	536	19	1	1079	1	KEAP1	19	10602767	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	6064317	10602767	48526216	69	16114										
HPN	3249	hgsc.bcm.edu	37	chr19	35556780	35556780	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ctcccctcccagggcgacagCggtggtccctttgtgtgtga	13	14	0	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr19:35556780C>T	ENST00000262626.2	+	12	1884	c.1059C>T	c.(1057-1059)agC>agT	p.S353S	HPN_ENST00000597419.1_Silent_p.S195S|HPN-AS1_ENST00000392227.2_RNA|HPN_ENST00000392226.1_Silent_p.S353S	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin	353	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				basement membrane disassembly (GO:0034769)|cholesterol homeostasis (GO:0042632)|cochlea morphogenesis (GO:0090103)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|epithelium development (GO:0060429)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pilomotor reflex (GO:0097195)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|positive regulation of gene expression (GO:0010628)|positive regulation of hepatocyte proliferation (GO:2000347)|positive regulation of plasminogen activation (GO:0010756)|positive regulation of thyroid hormone generation (GO:2000611)|potassium ion transmembrane transport (GO:0071805)|proteolysis (GO:0006508)|regulation of cell shape (GO:0008360)|response to thyroid hormone (GO:0097066)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	AGGGCGACAGCGGTGGTCCCT	0.657																																					p.S353S		Atlas-SNP	.											.	HPN	45	.	0			c.C1059T						.						78	78	78					19																	35556780		2203	4300	6503	SO:0001819	synonymous_variant	3249	exon12			CGACAGCGGTGGT		CCDS32993.1	19q13.12	2013-04-25	2008-12-08		ENSG00000105707	ENSG00000105707		"Serine peptidases / Transmembrane"	5155	protein-coding gene	gene with protein product	"transmembrane protease, serine 1"	142440				2835076	Standard	NM_182983		Approved	TMPRSS1	uc002nxq.2	P05981	OTTHUMG00000182474	ENST00000262626.2:c.1059C>T	chr19.hg19:g.35556780C>T		105.0	0.0		111.0	53.0	NM_182983	B2RDS4	Silent	SNP	ENST00000262626.2	hg19	CCDS32993.1																																																																																			.	.		0.657	HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1	NM_002151		T	35556780	C	T	35556780	2	4	108	1	0	0	0	0	0	0	0	1	7345	767	27	1		1	HPN	19	35556780	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	24954013	35556780	23572203	70	16115										
GAPDHS	26330	hgsc.bcm.edu	37	chr19	36033250	36033250	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	caaacagatcccctggagggCtgtcgggagcccctacgtgg	14	13	0	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr19:36033250C>A	ENST00000222286.4	+	5	595	c.479C>A	c.(478-480)gCt>gAt	p.A160D	AD000090.2_ENST00000590125.1_RNA|AD000090.2_ENST00000590717.1_RNA|AD000090.2_ENST00000589137.1_RNA|AD000090.2_ENST00000444728.1_RNA|AD000090.2_ENST00000588286.1_RNA	NM_014364.4	NP_055179.1	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	160					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	cytosol (GO:0005829)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|NAD binding (GO:0051287)|NADP binding (GO:0050661)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)	11	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CCCTGGAGGGCTGTCGGGAGC	0.617																																					p.A160D		Atlas-SNP	.											.	GAPDHS	34	.	0			c.C479A						.						50	49	50					19																	36033250		2203	4300	6503	SO:0001583	missense	26330	exon5			GGAGGGCTGTCGG	AJ005371	CCDS12465.1	19q13.1	2008-02-05		2005-05-06		ENSG00000105679			24864	protein-coding gene	gene with protein product		609169		GAPDS		10714828	Standard	NM_014364		Approved	GAPDH-2, GAPD2	uc002oaf.1	O14556		ENST00000222286.4:c.479C>A	chr19.hg19:g.36033250C>A	ENSP00000222286:p.Ala160Asp	76.0	0.0		64.0	29.0	NM_014364	B2RC82|O60823|Q6JTT9|Q9HCU6	Missense_Mutation	SNP	ENST00000222286.4	hg19	CCDS12465.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.516631	0.00151	.	.	ENSG00000105679	ENST00000222286	T	0.38077	1.16	5.0	-1.92	0.07618	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain (2);NAD(P)-binding domain (1);	1.245240	0.05109	N	0.488559	T	0.13884	0.0336	N	0.02765	-0.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30621	-0.9972	10	0.02654	T	1	-0.1971	9.8314	0.40944	0.4736:0.4112:0.1152:0.0	.	160	O14556	G3PT_HUMAN	D	160	ENSP00000222286:A160D	ENSP00000222286:A160D	A	+	2	0	GAPDHS	40725090	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	1.012000	0.29924	-0.284000	0.09102	-2.780000	0.00118	GCT	.	.		0.617	GAPDHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460423.1	NM_014364		A	36033250	C	A	36033250	3	1	108	1	0	0	0	0	1	0	0	0	6245	797	28	3	497	3	GAPDHS	19	36033250	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	476470	36033250	23095733	71	16116										
NPHS1	4868	hgsc.bcm.edu	37	chr19	36340537	36340537	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	accagcaactgcctattatcTgagctccggggtgtcaccct	9	14	2	1	rs111277506		TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr19:36340537T>A	ENST00000378910.5	-	6	626	c.627A>T	c.(625-627)tcA>tcT	p.S209S	NPHS1_ENST00000591817.1_5'Flank|NPHS1_ENST00000353632.6_Silent_p.S209S	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	209	Ig-like C2-type 2.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCCTATTATCTGAGCTCCGGG	0.537																																					p.S209S		Atlas-SNP	.											.	NPHS1	165	.	0			c.A627T						.						68	67	68					19																	36340537		2203	4300	6503	SO:0001819	synonymous_variant	4868	exon6			ATTATCTGAGCTC		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.627A>T	chr19.hg19:g.36340537T>A		72.0	0.0		59.0	17.0	NM_004646	A6NDH2|C3RX61	Silent	SNP	ENST00000378910.5	hg19	CCDS32996.1																																																																																			.	T|0.500;C|0.500		0.537	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			A	36340537	T	A	36340537	2	1	108	1	0	0	0	0	0	0	0	1	10591	1567	55	4		4	NPHS1	19	36340537	Silent	SNP	T	TCGA-DD-A1EL-01A-11D-A152-10	307287	36340537	22788446	72	16117										
C19orf33	64073	hgsc.bcm.edu	37	chr19	38795575	38795576	+	In_Frame_Ins	INS	-	-	AGGGCAAGAAGGAGA													0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ggagaagggcaagaaggagaINSagggcaagaagaaggaggct							TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr19:38795575_38795576insAGGGCAAGAAGGAGA	ENST00000301246.5	+	4	393_394	c.292_293insAGGGCAAGAAGGAGA	c.(292-294)aag>aAGGGCAAGAAGGAGAag	p.98_98K>KGKKEK	C19orf33_ENST00000588605.1_3'UTR	NM_033520.1	NP_277055.1	Q9GZP8	IMUP_HUMAN	chromosome 19 open reading frame 33	98						nucleus (GO:0005634)						all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			caagaaggagaagggcaagaag	0.599																																					p.K98delinsKGKKEK		Pindel	.											.	C19orf33	9	.	0			c.292_293insAGGGCAAGAAGGAGA						.																																			SO:0001652	inframe_insertion	64073	exon4			.	AF213678	CCDS12511.1	19q13.2	2012-10-26			ENSG00000167644	ENSG00000167644			16668	protein-coding gene	gene with protein product	"immortalization-upregulated protein", "HAI-2 related small protein", "hepatocyte growth factor activator inhibitor type 2-related small protein"					11080599	Standard	NM_033520		Approved	IMUP-1, IMUP-2, H2RSP, IMUP	uc002ohu.1	Q9GZP8	OTTHUMG00000181894	ENST00000301246.5:c.278_292dupAGGGCAAGAAGGAGA	chr19.hg19:g.38795575_38795576insAGGGCAAGAAGGAGA	ENSP00000301246:p.GlyLysLysGluLys98dup	315.0	0.0		293.0	18.0	NM_033520	Q0P6G2|Q96H58|Q9HCR4	In_Frame_Ins	INS	ENST00000301246.5	hg19	CCDS12511.1																																																																																			.	.		0.599	C19orf33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458168.1	NM_033520		AGGGCAAGAAGGAGA	38795576	-	AGGGCAAGAAGGAGA	38795575	7	5	108	1	0	1	1	0	0	0	0	0	1921	247	9	0	306	0	C19orf33	19	38795575	In_Frame_Ins	INS	-	TCGA-DD-A1EL-01A-11D-A152-10	2455038	38795575	20333408	73	16118										
CGB2	114336	hgsc.bcm.edu	37	chr19	49536324	49536324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tcaatgtgcactctgccgccGcagcaccactgactgcgggg	12	15	2	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr19:49536324G>A	ENST00000359342.6	+	3	456	c.338G>A	c.(337-339)cGc>cAc	p.R113H	CTB-60B18.6_ENST00000591656.1_Intron	NM_033378.1	NP_203696.2	Q6NT52	CGB2_HUMAN	chorionic gonadotropin, beta polypeptide 2	145						extracellular region (GO:0005576)				large_intestine(1)|lung(1)|stomach(1)	3		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		CTCTGCCGCCGCAGCACCACT	0.677																																					p.R113H		Atlas-SNP	.											CGB2,NS,carcinoma,0,1	CGB2	6	.	0			c.G338A						.						3	4	3					19																	49536324		1144	2702	3846	SO:0001583	missense	114336	exon3			GCCGCCGCAGCAC	K03184	CCDS12750.2	19q13.32	2008-02-05			ENSG00000104818	ENSG00000104818			16722	protein-coding gene	gene with protein product		608824				6194155	Standard	NM_033378		Approved		uc002plw.3	Q6NT52	OTTHUMG00000150185	ENST00000359342.6:c.338G>A	chr19.hg19:g.49536324G>A	ENSP00000352295:p.Arg113His	200.0	0.0		142.0	46.0	NM_033378	B9ZVM5	Missense_Mutation	SNP	ENST00000359342.6	hg19	CCDS12750.2	.	.	.	.	.	.	.	.	.	.	g	11.31	1.601514	0.28534	.	.	ENSG00000104818	ENST00000538959;ENST00000359342	T	0.57752	0.38	1.79	0.703	0.18116	Cystine knot (2);Gonadotropin, beta subunit, conserved site (2);	0.297707	0.34178	N	0.004191	T	0.62085	0.2399	M	0.68317	2.08	0.09310	N	0.999995	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.72625	0.913;0.913;0.978	T	0.51332	-0.8719	10	0.72032	D	0.01	-14.5685	4.6264	0.12481	0.0:0.0:0.3529:0.6471	.	145;115;131	Q6NT52;P01233;P01233-2	CGB2_HUMAN;CGHB_HUMAN;.	H	113	ENSP00000352295:R113H	ENSP00000352295:R113H	R	+	2	0	CGB2	54228136	1.000000	0.71417	0.242000	0.24170	0.154000	0.21943	1.208000	0.32345	0.148000	0.19059	0.184000	0.17185	CGC	.	.		0.677	CGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316745.1	NM_033378		A	49536324	G	A	49536324	3	1	108	1	0	0	0	0	1	0	0	0	3300	1087	38	1	348	1	CGB2	19	49536324	Missense_Mutation	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	10740749	49536324	9592659	74	16119										
SIGLEC7	27036	hgsc.bcm.edu	37	chr19	51645632	51645632	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	cctccaaccccagatatgctGctgctgctgctgctgcccct	8	18	0	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr19:51645632G>A	ENST00000317643.6	+	1	75	c.6G>A	c.(4-6)ctG>ctA	p.L2L	SIGLEC7_ENST00000305628.7_Silent_p.L2L|SIGLEC7_ENST00000600577.1_Silent_p.L2L	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	2					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		CAGATAtgctgctgctgctgc	0.597																																					p.L2L		Atlas-SNP	.											.	SIGLEC7	74	.	0			c.G6A						.						34	28	30					19																	51645632		2203	4300	6503	SO:0001819	synonymous_variant	27036	exon1			TATGCTGCTGCTG	AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10876	protein-coding gene	gene with protein product		604410	"sialic acid binding Ig-like lectin 19, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 2"	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.6G>A	chr19.hg19:g.51645632G>A		43.0	0.0		31.0	14.0	NM_016543	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Silent	SNP	ENST00000317643.6	hg19	CCDS12826.1																																																																																			.	.		0.597	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543		A	51645632	G	A	51645632	2	1	108	1	0	0	0	0	0	0	0	1	14328	1306	46	3		3	SIGLEC7	19	51645632	Silent	SNP	G	TCGA-DD-A1EL-01A-11D-A152-10	2109308	51645632	7483351	75	16120										
C20orf186	149954	hgsc.bcm.edu	37	chr20	31672752	31672752	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tccgtgcggctcctgcccggCgtgggtgtctacctgagctt	14	14	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr20:31672752C>T	ENST00000375483.3	+	4	732	c.732C>T	c.(730-732)ggC>ggT	p.G244G		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	244						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCCTGCCCGGCGTGGGTGTCT	0.667																																					p.G244G		Atlas-SNP	.											.	.	.	.	0			c.C732T						.						54	43	46					20																	31672752		2203	4300	6503	SO:0001819	synonymous_variant	149954	exon4			GCCCGGCGTGGGT	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"BPI fold containing"	16179	protein-coding gene	gene with protein product		615718	"chromosome 20 open reading frame 186"	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.732C>T	chr20.hg19:g.31672752C>T		60.0	0.0		51.0	18.0	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	hg19	CCDS13213.2																																																																																			.	.		0.667	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		T	31672752	C	T	31672752	2	4	108	1	0	0	0	0	0	0	0	1	2100	755	27	1		1	C20orf186	20	31672752	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		31672752	31352768	76	16121										
C20orf111	51526	hgsc.bcm.edu	37	chr20	42826208	42826208	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tctttaggggatgaaattccCagcccactgctgccatcagg	10	12	2	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr20:42826208C>A	ENST00000372970.2	-	6	543	c.363G>T	c.(361-363)ctG>ctT	p.L121L	OSER1_ENST00000255174.2_Silent_p.L121L			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	121					cellular response to hydrogen peroxide (GO:0070301)												ATGAAATTCCCAGCCCACTGC	0.473																																					p.L121L		Atlas-SNP	.											.	C20orf111	28	.	0			c.G363T						.						99	101	100					20																	42826208		2203	4300	6503	SO:0001819	synonymous_variant	51526	exon4			AATTCCCAGCCCA	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"peroxide-inducible transcript 1", "oxidative stress-responsive 1"		"chromosome 20 open reading frame 111"	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.363G>T	chr20.hg19:g.42826208C>A		108.0	0.0		102.0	38.0	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Silent	SNP	ENST00000372970.2	hg19	CCDS13327.1																																																																																			.	.		0.473	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470		A	42826208	C	A	42826208	2	1	108	1	0	0	0	0	0	0	0	1	2082	581	21	3		3	C20orf111	20	42826208	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	11153456	42826208	20199312	77	16122										
TAF4	6874	hgsc.bcm.edu	37	chr20	60578221	60578221	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	aggcccattccttaccgaaaCgaacctcccccaggctcctt	6	18	0	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr20:60578221C>A	ENST00000252996.4	-	9	2480	c.2481G>T	c.(2479-2481)tcG>tcT	p.S827S		NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	827					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			CTTACCGAAACGAACCTCCCC	0.572																																					p.S827S		Atlas-SNP	.											.	TAF4	84	.	0			c.G2481T						.						103	89	94					20																	60578221		2203	4300	6503	SO:0001819	synonymous_variant	6874	exon9			CCGAAACGAACCT	Y11354	CCDS33500.1	20q13.33	2010-02-26	2002-08-29	2002-01-18	ENSG00000130699	ENSG00000130699			11537	protein-coding gene	gene with protein product		601796	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1, 130kD"	TAF4A, TAF2C1, TAF2C		8942982, 9192867	Standard	NM_003185		Approved	TAFII130, TAFII135	uc002ybs.3	O00268	OTTHUMG00000032893	ENST00000252996.4:c.2481G>T	chr20.hg19:g.60578221C>A		105.0	0.0		103.0	46.0	NM_003185	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Silent	SNP	ENST00000252996.4	hg19	CCDS33500.1																																																																																			.	.		0.572	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185		A	60578221	C	A	60578221	2	1	108	1	0	0	0	0	0	0	0	1	15541	523	19	1		1	TAF4	20	60578221	Silent	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	17752013	60578221	2447299	78	16123										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61981117	61981117	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	ggggcggcgctttggtgctgCgggtcttgaccgtggcgctc	19	11	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chr20:61981117C>G	ENST00000370263.4	-	5	1867	c.1646G>C	c.(1645-1647)cGc>cCc	p.R549P	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	549					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	TTTGGTGCTGCGGGTCTTGAC	0.682																																					p.R549P		Atlas-SNP	.											.	CHRNA4	98	.	0			c.G1646C						.						35	40	39					20																	61981117		2200	4298	6498	SO:0001583	missense	1137	exon5			GTGCTGCGGGTCT		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1646G>C	chr20.hg19:g.61981117C>G	ENSP00000359285:p.Arg549Pro	43.0	0.0		30.0	15.0	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	hg19	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	C	0.287	-0.982264	0.02180	.	.	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	D	0.85702	-2.02	3.7	-2.82	0.05787	Neurotransmitter-gated ion-channel transmembrane domain (2);	6.549360	0.00610	N	0.000406	T	0.79522	0.4460	L	0.39898	1.24	0.09310	N	1	P;B	0.46142	0.873;0.002	P;B	0.46172	0.506;0.005	T	0.66324	-0.5952	10	0.30078	T	0.28	.	1.2964	0.02070	0.2231:0.197:0.1213:0.4586	.	478;549	Q4VAQ5;P43681	.;ACHA4_HUMAN	P	455;549;478	ENSP00000359285:R549P	ENSP00000359280:R455P	R	-	2	0	CHRNA4	61451561	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.591000	0.02100	-1.087000	0.03081	-0.339000	0.08088	CGC	.	.		0.682	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			G	61981117	C	G	61981117	3	3	108	1	0	0	0	0	1	0	0	0	3387	768	27	4	245	4	CHRNA4	20	61981117	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	1402896	61981117	1044403	79	16124										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63410708	63410708	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	caggattctcttcacacttgCcttccccatcccgttccaca	4	18	2	0			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chrX:63410708C>A	ENST00000330258.3	-	2	2731	c.2459G>T	c.(2458-2460)gGc>gTc	p.G820V	AMER1_ENST00000374869.3_Intron|AMER1_ENST00000403336.1_Intron	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	820					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									TTCACACTTGCCTTCCCCATC	0.502																																					p.G820V		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.G2459T						.						45	43	43					X																	63410708		2200	4296	6496	SO:0001583	missense	139285	exon2			CACTTGCCTTCCC	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.2459G>T	chrX.hg19:g.63410708C>A	ENSP00000329117:p.Gly820Val	56.0	0.0		62.0	58.0	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	hg19	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	17.92	3.507616	0.64410	.	.	ENSG00000184675	ENST00000330258	T	0.75367	-0.93	5.0	5.0	0.66597	.	.	.	.	.	T	0.76786	0.4036	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75542	-0.3281	8	.	.	.	0.4471	16.219	0.82244	0.0:1.0:0.0:0.0	.	820	Q5JTC6	F123B_HUMAN	V	820	ENSP00000329117:G820V	.	G	-	2	0	FAM123B	63327433	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.660000	0.74417	2.484000	0.83849	0.529000	0.55759	GGC	.	.		0.502	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63410708	C	A	63410708	3	1	108	1	0	0	0	0	1	0	0	0	5428	739	26	3	952	3	FAM123B	23	63410708	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10		63410708	91859852	80	16125										
ARHGEF6	9459	hgsc.bcm.edu	37	chrX	135757211	135757211	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0125	1	1	0.389266304347826	0	0.622826086956522	1	1	0	tgcgctggtgcagtaggcttCgatcactttaaggatttgag	13	7	1	1			TCGA-DD-A1EL-01A-11D-A152-10	TCGA-DD-A1EL-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d252f328-4583-4e97-9a71-bb2885f06f73	b43d641d-f1b1-474e-9475-a1f2e81835b8	g.chrX:135757211C>G	ENST00000250617.6	-	19	3195	c.1990G>C	c.(1990-1992)Gaa>Caa	p.E664Q	ARHGEF6_ENST00000370620.1_Missense_Mutation_p.E510Q|ARHGEF6_ENST00000535227.1_Missense_Mutation_p.E537Q|ARHGEF6_ENST00000370622.1_Missense_Mutation_p.E510Q	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	664					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					CAGTAGGCTTCGATCACTTTA	0.413																																					p.E664Q		Atlas-SNP	.											.	ARHGEF6	111	.	0			c.G1990C						.						162	137	145					X																	135757211		2203	4300	6503	SO:0001583	missense	9459	exon19			AGGCTTCGATCAC	D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	685	protein-coding gene	gene with protein product	"Rac/Cdc42 guanine exchange factor (GEF) 6", "PAK-interacting exchange factor, alpha", "rho guanine nucleotide exchange factor 6"	300267	"mental retardation, X-linked 46"	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.1990G>C	chrX.hg19:g.135757211C>G	ENSP00000250617:p.Glu664Gln	126.0	1.0		118.0	100.0	NM_004840	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Missense_Mutation	SNP	ENST00000250617.6	hg19	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.515693	0.64634	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	T;T;T;T	0.69926	-0.35;-0.23;-0.23;-0.44	5.59	5.59	0.84812	.	0.045466	0.85682	D	0.000000	D	0.83945	0.5364	M	0.82323	2.585	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.86296	0.1677	10	0.87932	D	0	.	18.6464	0.91411	0.0:1.0:0.0:0.0	.	537;664	B7Z3C7;Q15052	.;ARHG6_HUMAN	Q	664;510;510;510;537	ENSP00000250617:E664Q;ENSP00000359654:E510Q;ENSP00000359656:E510Q;ENSP00000439483:E537Q	ENSP00000250617:E664Q	E	-	1	0	ARHGEF6	135584877	1.000000	0.71417	0.925000	0.36789	0.224000	0.24922	7.153000	0.77428	2.347000	0.79759	0.600000	0.82982	GAA	.	.		0.413	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840		G	135757211	C	G	135757211	3	3	108	1	0	0	0	0	1	0	0	0	910	893	31	4	356	4	ARHGEF6	23	135757211	Missense_Mutation	SNP	C	TCGA-DD-A1EL-01A-11D-A152-10	72346503	135757211	19513349	81	16126										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27105581	27105582	+	Frame_Shift_Ins	INS	-	-	A													0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	attgagatctttggcattttINSaaaggagtatgaggtgggtg							TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr1:27105581_27105582insA	ENST00000324856.7	+	20	5563_5564	c.5192_5193insA	c.(5191-5196)ttaaagfs	p.LK1731fs	ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.LK1348fs|ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.LK1514fs|ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.LK59fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1731					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TTTGGCATTTTAAAGGAGTATG	0.48			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.L1731fs		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.5192_5193insA						.																																			SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5195dupA	chr1.hg19:g.27105584_27105584dupA	ENSP00000320485:p.Leu1731fs	222.0	0.0		97.0	53.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.48	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27105582	-	A	27105581	7	5	109	1	0	1	1	0	0	0	0	0	913	1764	61	0	5270	0	ARID1A	1	27105581	Frame_Shift_Ins	INS	-	TCGA-DD-A39V-01A-11D-A20W-10		27105581	222145040	1	16127										
DHCR24	1718	hgsc.bcm.edu	37	chr1	55340777	55340777	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tgaactcaccggagtgcatcGcacaaagctgccatcagcca	9	14	2	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr1:55340777G>A	ENST00000371269.3	-	4	699	c.601C>T	c.(601-603)Cga>Tga	p.R201*	DHCR24_ENST00000537443.1_Nonsense_Mutation_p.R33*|DHCR24_ENST00000535035.1_Nonsense_Mutation_p.R160*	NM_014762.3	NP_055577.1	Q15392	DHC24_HUMAN	24-dehydrocholesterol reductase	201	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				amyloid precursor protein catabolic process (GO:0042987)|apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cholesterol biosynthetic process (GO:0006695)|male genitalia development (GO:0030539)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|oxidation-reduction process (GO:0055114)|plasminogen activation (GO:0031639)|protein localization (GO:0008104)|Ras protein signal transduction (GO:0007265)|regulation of neuron death (GO:1901214)|response to hormone (GO:0009725)|response to oxidative stress (GO:0006979)|skin development (GO:0043588)|small molecule metabolic process (GO:0044281)|tissue development (GO:0009888)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	delta24(24-1) sterol reductase activity (GO:0000246)|delta24-sterol reductase activity (GO:0050614)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|peptide antigen binding (GO:0042605)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			large_intestine(2)|liver(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7						GGAGTGCATCGCACAAAGCTG	0.562																																					p.R201X	Pancreas(39;516 1021 24601 30715 32780)	Atlas-SNP	.											.	DHCR24	31	.	0			c.C601T						.						153	107	123					1																	55340777		2203	4300	6503	SO:0001587	stop_gained	1718	exon4			TGCATCGCACAAA	AF261758	CCDS600.1	1p32.3	2008-02-05			ENSG00000116133	ENSG00000116133			2859	protein-coding gene	gene with protein product		606418				11519011	Standard	NM_014762		Approved	KIAA0018, seladin-1	uc001cyc.1	Q15392	OTTHUMG00000009989	ENST00000371269.3:c.601C>T	chr1.hg19:g.55340777G>A	ENSP00000360316:p.Arg201*	107.0	0.0		80.0	33.0	NM_014762	B7Z817|D3DQ51|Q9HBA8	Nonsense_Mutation	SNP	ENST00000371269.3	hg19	CCDS600.1	.	.	.	.	.	.	.	.	.	.	G	38	6.689792	0.97764	.	.	ENSG00000116133	ENST00000371269;ENST00000537443;ENST00000535035	.	.	.	5.56	4.63	0.57726	.	0.053029	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6649	13.9681	0.64221	0.0:0.0:0.6703:0.3297	.	.	.	.	X	201;33;160	.	ENSP00000360316:R201X	R	-	1	2	DHCR24	55113365	1.000000	0.71417	0.996000	0.52242	0.925000	0.55904	4.904000	0.63279	1.454000	0.47793	0.609000	0.83330	CGA	.	.		0.562	DHCR24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027680.1	NM_014762		A	55340777	G	A	55340777	4	1	109	1	0	0	0	0	0	1	0	0	4478	1095	38	1	973	1	DHCR24	1	55340777	Nonsense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	28235196	55340777	193909844	2	16128										
C1orf43	25912	hgsc.bcm.edu	37	chr1	154184832	154184832	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tcagggcctcctgatagcgtAggtactcattctggccaaag	11	11	3	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr1:154184832A>G	ENST00000368521.5	-	6	728	c.530T>C	c.(529-531)cTa>cCa	p.L177P	C1orf43_ENST00000368518.1_Missense_Mutation_p.L177P|C1orf43_ENST00000368519.1_Missense_Mutation_p.L159P|C1orf43_ENST00000362076.4_Missense_Mutation_p.L125P|C1orf43_ENST00000368516.1_Missense_Mutation_p.L143P|C1orf43_ENST00000350592.3_Missense_Mutation_p.L143P	NM_001098616.1	NP_001092086.1	Q9BWL3	CA043_HUMAN	chromosome 1 open reading frame 43	177						integral component of membrane (GO:0016021)	coenzyme binding (GO:0050662)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	10	all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877)					CTGATAGCGTAGGTACTCATT	0.517																																					p.L177P		Atlas-SNP	.											.	C1orf43	36	.	0			c.T530C						.						145	138	140					1																	154184832		2203	4300	6503	SO:0001583	missense	25912	exon6			TAGCGTAGGTACT	AF077036	CCDS1061.1, CCDS1062.1, CCDS41404.1, CCDS72924.1	1q21.2	2012-06-25			ENSG00000143612	ENSG00000143612			29876	protein-coding gene	gene with protein product						11042152, 11230159	Standard	XM_005245077		Approved	NICE-3, DKFZp586G1722	uc001fei.2	Q9BWL3	OTTHUMG00000035981	ENST00000368521.5:c.530T>C	chr1.hg19:g.154184832A>G	ENSP00000357507:p.Leu177Pro	106.0	0.0		110.0	69.0	NM_001098616	A8K3G8|D3DV72|D3DV74|Q5M801|Q5VU73|Q5VU83|Q96HP7|Q9UFU2|Q9UGL7|Q9UGL8|Q9Y2R6	Missense_Mutation	SNP	ENST00000368521.5	hg19	CCDS41404.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.981191	0.74474	.	.	ENSG00000143612	ENST00000350592;ENST00000368521;ENST00000362076;ENST00000368519;ENST00000368518;ENST00000368516	.	.	.	5.39	5.39	0.77823	Dehydrogenase, multihelical (1);	0.229195	0.38492	N	0.001664	T	0.61664	0.2365	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.64830	0.98;0.994;0.971;0.984	P;D;P;P	0.69824	0.804;0.966;0.775;0.876	T	0.63093	-0.6714	9	0.37606	T	0.19	-22.5561	10.0457	0.42186	0.85:0.0:0.0:0.15	.	143;177;125;143	Q9BWL3-2;Q9BWL3;Q9BWL3-4;Q09GN0	.;CA043_HUMAN;.;.	P	143;177;125;159;177;143	.	ENSP00000271925:L143P	L	-	2	0	C1orf43	152451456	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.189000	0.65098	2.270000	0.75569	0.477000	0.44152	CTA	.	.		0.517	C1orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087664.2	NM_015449		G	154184832	A	G	154184832	3	3	109	1	0	0	0	0	1	0	0	0	2042	420	15	2	239	2	C1orf43	1	154184832	Missense_Mutation	SNP	A	TCGA-DD-A39V-01A-11D-A20W-10	98844055	154184832	95065789	3	16129										
PMVK	10654	hgsc.bcm.edu	37	chr1	154904854	154904854	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	atactgttccttgagtggacCagagagccggaggacagcac	13	10	0	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr1:154904854C>T	ENST00000368467.3	-	2	438	c.133G>A	c.(133-135)Ggt>Agt	p.G45S		NM_006556.3	NP_006547.1	Q15126	PMVK_HUMAN	phosphomevalonate kinase	45					cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|response to cholesterol (GO:0070723)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|phosphomevalonate kinase activity (GO:0004631)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.142)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TTGAGTGGACCAGAGAGCCGG	0.572																																					p.G45S		Atlas-SNP	.											.	PMVK	17	.	0			c.G133A						.						106	95	99					1																	154904854		2203	4300	6503	SO:0001583	missense	10654	exon2			GTGGACCAGAGAG	L77213	CCDS1073.1	1q21.3	2012-09-20			ENSG00000163344	ENSG00000163344	2.7.4.2		9141	protein-coding gene	gene with protein product		607622				8663599, 10191291	Standard	NM_006556		Approved	PMK, PMKA, HUMPMKI	uc001ffq.3	Q15126	OTTHUMG00000037415	ENST00000368467.3:c.133G>A	chr1.hg19:g.154904854C>T	ENSP00000357452:p.Gly45Ser	180.0	0.0		235.0	59.0	NM_006556	Q5TZW9	Missense_Mutation	SNP	ENST00000368467.3	hg19	CCDS1073.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.943002	0.53079	.	.	ENSG00000163344	ENST00000368467	T	0.41400	1.0	4.59	3.68	0.42216	.	0.130764	0.50627	D	0.000106	T	0.24928	0.0605	L	0.56199	1.76	0.24788	N	0.992778	P	0.42584	0.784	P	0.45449	0.481	T	0.04065	-1.0980	10	0.39692	T	0.17	-9.5168	8.7356	0.34525	0.0:0.8966:0.0:0.1034	.	45	Q15126	PMVK_HUMAN	S	45	ENSP00000357452:G45S	ENSP00000357452:G45S	G	-	1	0	PMVK	153171478	0.260000	0.24053	0.228000	0.23943	0.802000	0.45316	2.336000	0.43938	1.284000	0.44531	0.561000	0.74099	GGT	.	.		0.572	PMVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091088.1	NM_006556		T	154904854	C	T	154904854	3	4	109	1	0	0	0	0	1	0	0	0	12153	594	21	3	461	3	PMVK	1	154904854	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	720022	154904854	94345767	4	16130										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158651436	158651436	+	Frame_Shift_Del	DEL	G	G	-													0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	taacagcaggtcccacaggtGgcgtagctcctctatatggg							TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr1:158651436delG	ENST00000368147.4	-	4	592	c.412delC	c.(412-414)cacfs	p.H138fs		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	138					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TCCCACAGGTGGCGTAGCTCC	0.542																																					p.H138fs		Atlas-Indel,Pindel	.											.	SPTA1	720	.	0			c.413delA						.						94	96	95					1																	158651436		1992	4162	6154	SO:0001589	frameshift_variant	6708	exon4			.	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.412delC	chr1.hg19:g.158651436delG	ENSP00000357129:p.His138fs	184.0	0.0		226.0	70.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Frame_Shift_Del	DEL	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.		0.542	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		-	158651436	G	-	158651436	7	5	109	1	0	1	0	1	0	0	0	0	15131	1348	47	0	7043	0	SPTA1	1	158651436	Frame_Shift_Del	DEL	G	TCGA-DD-A39V-01A-11D-A20W-10	3746582	158651436	90599185	5	16131										
FMO2	2327	hgsc.bcm.edu	37	chr1	171174626	171174626	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	aagattcactcgttaaagtaGagaataatatggtctcactg	8	6	2	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr1:171174626G>C	ENST00000209929.7	+	7	1194	c.1036G>C	c.(1036-1038)Gag>Cag	p.E346Q	FMO2_ENST00000529935.1_3'UTR|RP1-127D3.4_ENST00000445909.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA|FMO2_ENST00000441535.1_Missense_Mutation_p.E346Q			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	345					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CGTTAAAGTAGAGAATAATAT	0.423																																					p.E346Q		Atlas-SNP	.											.	FMO2	66	.	0			c.G1036C						.						88	85	86					1																	171174626		2203	4300	6503	SO:0001583	missense	2327	exon7			AAAGTAGAGAATA	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"flavin containing monooxygenase 2"			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.1036G>C	chr1.hg19:g.171174626G>C	ENSP00000209929:p.Glu346Gln	95.0	0.0		119.0	25.0	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	hg19	CCDS1293.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.900165	0.33535	.	.	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.58060	0.36;0.36	5.85	4.94	0.65067	.	0.270105	0.42548	D	0.000688	T	0.44953	0.1318	M	0.66939	2.045	0.09310	N	1	P	0.47191	0.891	P	0.54889	0.763	T	0.38993	-0.9635	10	0.16896	T	0.51	-21.6784	10.742	0.46158	0.1534:0.0:0.8466:0.0	.	346	Q99518	FMO2_HUMAN	Q	346	ENSP00000209929:E346Q;ENSP00000405905:E346Q	ENSP00000209929:E346Q	E	+	1	0	FMO2	169441250	0.003000	0.15002	0.283000	0.24790	0.855000	0.48748	1.420000	0.34804	1.472000	0.48140	0.655000	0.94253	GAG	.	.		0.423	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		C	171174626	G	C	171174626	3	2	109	1	0	0	0	0	1	0	0	0	5963	943	33	4	1058	4	FMO2	1	171174626	Missense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	12523190	171174626	78075995	6	16132										
PPFIA4	8497	hgsc.bcm.edu	37	chr1	203037705	203037705	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ctggccctggacgagaacttCgaccacaacacactggccct	9	16	0	1	rs200137584		TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr1:203037705C>T	ENST00000447715.2	+	32	3648	c.3207C>T	c.(3205-3207)ttC>ttT	p.F1069F	PPFIA4_ENST00000272198.6_Silent_p.F585F|PPFIA4_ENST00000295706.4_Silent_p.F576F|PPFIA4_ENST00000414050.2_Silent_p.F798F|PPFIA4_ENST00000599966.1_Silent_p.F576F|PPFIA4_ENST00000367240.2_Silent_p.F1070F			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	1069	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						ACGAGAACTTCGACCACAACA	0.557																																					p.F585F		Atlas-SNP	.											.	PPFIA4	139	.	0			c.C1755T						.	C		0,4166		0,0,2083	68	69	69		1755	-2.3	1	1		69	4,8404		0,4,4200	no	coding-synonymous	PPFIA4	NM_015053.1		0,4,6283	TT,TC,CC		0.0476,0.0,0.0318		585/702	203037705	4,12570	2083	4204	6287	SO:0001819	synonymous_variant	8497	exon14			GAACTTCGACCAC	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"Sterile alpha motif (SAM) domain containing"	9248	protein-coding gene	gene with protein product	"Liprin-alpha4"	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.3207C>T	chr1.hg19:g.203037705C>T		94.0	0.0		104.0	59.0	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Silent	SNP	ENST00000447715.2	hg19																																																																																				.	C|0.998;T|0.002		0.557	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		T	203037705	C	T	203037705	2	4	109	1	0	0	0	0	0	0	0	1	12321	883	31	1		1	PPFIA4	1	203037705	Silent	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	31863079	203037705	46212916	7	16133										
MAP4K3	8491	hgsc.bcm.edu	37	chr2	39535117	39535117	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	gcagtgtagtatatttcttcTgaactgtccaaaaaaccatc	6	9	2	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr2:39535117T>C	ENST00000263881.3	-	15	1410	c.1086A>G	c.(1084-1086)tcA>tcG	p.S362S	MAP4K3_ENST00000536018.1_5'UTR|MAP4K3_ENST00000437545.1_Intron|MAP4K3_ENST00000341681.5_Intron	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	362					intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				ATATTTCTTCTGAACTGTCCA	0.348																																					p.S362S		Atlas-SNP	.											.	MAP4K3	109	.	0			c.A1086G						.						121	116	118					2																	39535117		2203	4300	6503	SO:0001819	synonymous_variant	8491	exon15			TTCTTCTGAACTG	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.1086A>G	chr2.hg19:g.39535117T>C		73.0	0.0		52.0	11.0	NM_003618	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Silent	SNP	ENST00000263881.3	hg19	CCDS1803.1																																																																																			.	.		0.348	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618		C	39535117	T	C	39535117	2	2	109	1	0	0	0	0	0	0	0	1	9270	1567	55	2		2	MAP4K3	2	39535117	Silent	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10		39535117	203664256	8	16134										
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113067682	113067682	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	aacctcaaatattgctttagGgtcatcattttctaaagaat	5	7	4	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr2:113067682G>A	ENST00000409871.1	+	4	958	c.557G>A	c.(556-558)gGg>gAg	p.G186E	ZC3H6_ENST00000343936.4_Missense_Mutation_p.G186E	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	186							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						ATTGCTTTAGGGTCATCATTT	0.363																																					p.G186E		Atlas-SNP	.											.	ZC3H6	93	.	0			c.G557A						.						65	62	63					2																	113067682		1836	4083	5919	SO:0001583	missense	376940	exon4			CTTTAGGGTCATC	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.557G>A	chr2.hg19:g.113067682G>A	ENSP00000386764:p.Gly186Glu	112.0	0.0		71.0	31.0	NM_198581	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	hg19	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	G	18.79	3.699941	0.68501	.	.	ENSG00000188177	ENST00000409871;ENST00000343936;ENST00000542974	T;T	0.15952	2.38;2.38	5.93	5.93	0.95920	.	2.702860	0.01326	N	0.011113	T	0.27384	0.0672	M	0.71581	2.175	0.53688	D	0.999976	P	0.46142	0.873	B	0.39904	0.313	T	0.43327	-0.9398	10	0.49607	T	0.09	-16.3411	10.6499	0.45642	0.1415:0.0:0.8585:0.0	.	186	P61129	ZC3H6_HUMAN	E	186;186;163	ENSP00000386764:G186E;ENSP00000340298:G186E	ENSP00000340298:G186E	G	+	2	0	ZC3H6	112784153	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	3.732000	0.55021	2.802000	0.96397	0.561000	0.74099	GGG	.	.		0.363	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		A	113067682	G	A	113067682	3	1	109	1	0	0	0	0	1	0	0	0	17586	1232	43	3	571	3	ZC3H6	2	113067682	Missense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	73532565	113067682	130131691	9	16135										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098799	178098799	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	gctggctgaattgggagaaaTtcacctgtctcttcatctag	10	9	4	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr2:178098799T>G	ENST00000397062.3	-	2	800	c.246A>C	c.(244-246)gaA>gaC	p.E82D	NFE2L2_ENST00000423513.1_Missense_Mutation_p.E66D|NFE2L2_ENST00000446151.2_Missense_Mutation_p.E66D|NFE2L2_ENST00000464747.1_Missense_Mutation_p.E66D|NFE2L2_ENST00000397063.4_Missense_Mutation_p.E66D	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	82					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E82D(8)|p.G81_F83delGEF(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			TTGGGAGAAATTCACCTGTCT	0.433			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.E82D		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,0,9	NFE2L2	225	.	9	Substitution - Missense(8)|Deletion - In frame(1)	endometrium(3)|liver(2)|upper_aerodigestive_tract(1)|cervix(1)|oesophagus(1)|kidney(1)	c.A246C						.						138	137	137					2																	178098799		1903	4104	6007	SO:0001583	missense	4780	exon2			GAGAAATTCACCT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.246A>C	chr2.hg19:g.178098799T>G	ENSP00000380252:p.Glu82Asp	180.0	0.0		127.0	52.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.706902	0.89018	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.67;1.67;1.53	5.78	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	M	0.87180	2.865	0.54753	D	0.999981	D;D;D;D	0.89917	0.999;0.997;1.0;0.999	D;D;D;D	0.83275	0.991;0.978;0.996;0.991	T	0.64976	-0.6280	10	0.72032	D	0.01	.	11.2269	0.48888	0.0:0.0712:0.0:0.9288	.	66;66;66;82	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	D	66;82;66;66;66;66	ENSP00000380253:E66D;ENSP00000380252:E82D;ENSP00000411575:E66D;ENSP00000400073:E66D;ENSP00000412191:E66D;ENSP00000410015:E66D	ENSP00000380252:E82D	E	-	3	2	NFE2L2	177807045	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.909000	0.39917	2.210000	0.71456	0.460000	0.39030	GAA	.	.		0.433	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		G	178098799	T	G	178098799	3	3	109	1	0	0	0	0	1	0	0	0	10377	1490	52	5	1587	5	NFE2L2	2	178098799	Missense_Mutation	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10	65031117	178098799	65100574	10	16136										
ANKZF1	55139	hgsc.bcm.edu	37	chr2	220095010	220095010	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ctccagatgcagccccggctCctgcgtcgatctccctgttt	9	17	1	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr2:220095010C>G	ENST00000323348.5	+	2	205	c.31C>G	c.(31-33)Cct>Gct	p.P11A	ANKZF1_ENST00000410034.3_Missense_Mutation_p.P11A|ATG9A_ENST00000409618.1_5'Flank|ATG9A_ENST00000361242.4_5'Flank|ANKZF1_ENST00000409849.1_Intron|ATG9A_ENST00000396761.2_5'Flank|ATG9A_ENST00000409422.1_5'Flank|ATG9A_ENST00000488833.1_5'Flank	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	11						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCCCCGGCTCCTGCGTCGAT	0.622																																					p.P11A		Atlas-SNP	.											.	ANKZF1	45	.	0			c.C31G						.						37	39	38					2																	220095010		1895	4113	6008	SO:0001583	missense	55139	exon2			CCGGCTCCTGCGT	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"Zinc fingers, C2H2-type", "Ankyrin repeat domain containing"	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.31C>G	chr2.hg19:g.220095010C>G	ENSP00000321617:p.Pro11Ala	218.0	0.0		140.0	38.0	NM_001042410	Q9NVZ4	Missense_Mutation	SNP	ENST00000323348.5	hg19	CCDS42821.1	.	.	.	.	.	.	.	.	.	.	C	9.315	1.056527	0.19907	.	.	ENSG00000163516	ENST00000323348;ENST00000416565;ENST00000410034;ENST00000447157;ENST00000436226	T;T	0.25749	1.78;1.78	5.53	2.81	0.32909	.	0.253994	0.39759	N	0.001265	T	0.23289	0.0563	L	0.55481	1.735	0.09310	N	1	B;B	0.29378	0.229;0.243	B;B	0.30572	0.117;0.079	T	0.13953	-1.0490	10	0.39692	T	0.17	-2.2277	8.7866	0.34825	0.0:0.7987:0.0:0.2013	.	11;11	B4DZT1;Q9H8Y5	.;ANKZ1_HUMAN	A	11	ENSP00000321617:P11A;ENSP00000386337:P11A	ENSP00000321617:P11A	P	+	1	0	ANKZF1	219803254	0.004000	0.15560	0.003000	0.11579	0.076000	0.17211	0.924000	0.28777	0.466000	0.27193	0.655000	0.94253	CCT	.	.		0.622	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089		G	220095010	C	G	220095010	3	3	109	1	0	0	0	0	1	0	0	0	693	855	30	4	33	4	ANKZF1	2	220095010	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	41996211	220095010	23104363	11	16137										
PAX3	5077	hgsc.bcm.edu	37	chr2	223084872	223084872	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	gactgacctgaggtgagaggCcattgccaatggtggggttc	16	8	0	3			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr2:223084872C>T	ENST00000350526.4	-	7	1296	c.1160G>A	c.(1159-1161)gGc>gAc	p.G387D	PAX3_ENST00000336840.6_Missense_Mutation_p.G387D|PAX3_ENST00000409551.3_Missense_Mutation_p.G386D|PAX3_ENST00000392069.2_Missense_Mutation_p.G387D|PAX3_ENST00000464706.1_5'UTR|PAX3_ENST00000344493.4_Missense_Mutation_p.G387D|PAX3_ENST00000392070.2_Missense_Mutation_p.G387D	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	387					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGTGAGAGGCCATTGCCAAT	0.517			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.G387D		Atlas-SNP	.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	PAX3	106	.	0			c.G1160A						.						79	80	80					2																	223084872		2203	4300	6503	SO:0001583	missense	5077	exon7			GAGAGGCCATTGC		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.1160G>A	chr2.hg19:g.223084872C>T	ENSP00000343052:p.Gly387Asp	180.0	0.0		118.0	42.0	NM_181457	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Missense_Mutation	SNP	ENST00000350526.4	hg19	CCDS42826.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.633641	0.87660	.	.	ENSG00000135903	ENST00000392069;ENST00000344493;ENST00000350526;ENST00000392070;ENST00000336840;ENST00000409551;ENST00000464706;ENST00000555548	D;D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92;-1.92	5.68	5.68	0.88126	.	0.049348	0.85682	D	0.000000	D	0.91536	0.7327	L	0.61218	1.895	0.80722	D	1	B;D;D;D;D	0.76494	0.091;0.993;0.998;0.999;0.992	B;D;D;D;P	0.70487	0.168;0.912;0.916;0.969;0.856	D	0.91681	0.5358	10	0.72032	D	0.01	.	19.7917	0.96461	0.0:1.0:0.0:0.0	.	387;386;387;387;387	P23760;Q494Z4;P23760-4;P23760-5;G5E9C1	PAX3_HUMAN;.;.;.;.	D	387;387;387;387;387;386;104;104	ENSP00000375921:G387D;ENSP00000342092:G387D;ENSP00000343052:G387D;ENSP00000375922:G387D;ENSP00000338767:G387D;ENSP00000386750:G386D	ENSP00000338767:G387D	G	-	2	0	PAX3	222793116	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.666000	0.68059	2.685000	0.91497	0.650000	0.86243	GGC	.	.		0.517	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			T	223084872	C	T	223084872	3	4	109	1	0	0	0	0	1	0	0	0	11489	739	26	3	401	3	PAX3	2	223084872	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	2989862	223084872	20114501	12	16138										
HJURP	55355	hgsc.bcm.edu	37	chr2	234749510	234749510	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	accccaggggtgatgatggcAacttctggaaaccctggaag	13	10	1	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr2:234749510A>C	ENST00000411486.2	-	8	1981	c.1916T>G	c.(1915-1917)tTg>tGg	p.L639W	HJURP_ENST00000434039.1_5'Flank|HJURP_ENST00000432087.1_Missense_Mutation_p.L585W|HJURP_ENST00000441687.1_Missense_Mutation_p.L554W	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	639					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		TGATGATGGCAACTTCTGGAA	0.473																																					p.L639W		Atlas-SNP	.											.	HJURP	72	.	0			c.T1916G						.						91	95	94					2																	234749510		2203	4300	6503	SO:0001583	missense	55355	exon8			GATGGCAACTTCT		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.1916T>G	chr2.hg19:g.234749510A>C	ENSP00000414109:p.Leu639Trp	47.0	0.0		30.0	8.0	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	hg19	CCDS33406.1	.	.	.	.	.	.	.	.	.	.	A	12.49	1.954969	0.34471	.	.	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924	T;T;T;T	0.11063	3.08;3.09;3.09;2.81	3.93	0.304	0.15796	.	1.458390	0.05284	N	0.519905	T	0.10078	0.0247	L	0.42245	1.32	0.09310	N	1	B;B;B	0.11235	0.004;0.004;0.002	B;B;B	0.11329	0.006;0.006;0.003	T	0.40021	-0.9585	10	0.54805	T	0.06	0.1896	3.1067	0.06344	0.4629:0.2482:0.2889:0.0	.	554;585;639	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	W	639;585;554;554	ENSP00000414109:L639W;ENSP00000407208:L585W;ENSP00000401944:L554W;ENSP00000393253:L554W	ENSP00000414109:L639W	L	-	2	0	HJURP	234414249	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.244000	0.08903	0.048000	0.15891	0.460000	0.39030	TTG	.	.		0.473	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410		C	234749510	A	C	234749510	3	2	109	1	0	0	0	0	1	0	0	0	7198	131	5	5	338	5	HJURP	2	234749510	Missense_Mutation	SNP	A	TCGA-DD-A39V-01A-11D-A20W-10	11664638	234749510	8449863	13	16139										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266100	41266100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	agcaacagtcttacctggacTctggaatccattctggtgcc	9	12	3	0	rs121913416		TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr3:41266100T>C	ENST00000349496.5	+	3	377	c.97T>C	c.(97-99)Tct>Cct	p.S33P	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.S33P(47)|p.S33A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.W25_D32del(4)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.D32_S33insS(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.S33T(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TTACCTGGACTCTGGAATCCA	0.488		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	212	Deletion - In frame(115)|Substitution - Missense(70)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Insertion - In frame(1)	liver(130)|large_intestine(20)|endometrium(14)|stomach(10)|pituitary(9)|pancreas(9)|central_nervous_system(8)|adrenal_gland(2)|small_intestine(2)|biliary_tract(2)|skin(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|breast(1)	c.T97C						.						93	77	82					3																	41266100		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTGGACTCTGGAA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.97T>C	chr3.hg19:g.41266100T>C	ENSP00000344456:p.Ser33Pro	339.0	0.0		245.0	78.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.395782	0.83011	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70281	0.3206	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74509	-0.3642	10	0.87932	D	0	-10.7796	16.0677	0.80897	0.0:0.0:0.0:1.0	.	33	P35222	CTNB1_HUMAN	P	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26P;ENSP00000385604:S33P;ENSP00000412219:S33P;ENSP00000379486:S33P;ENSP00000344456:S33P;ENSP00000411226:S26P;ENSP00000379488:S33P;ENSP00000409302:S33P;ENSP00000401599:S33P	ENSP00000344456:S33P	S	+	1	0	CTNNB1	41241104	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266100	T	C	41266100	3	2	109	1	0	0	0	0	1	0	0	0	4018	1551	54	2	103	2	CTNNB1	3	41266100	Missense_Mutation	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10		41266100	156756330	14	16140										
KIAA1257	57501	hgsc.bcm.edu	37	chr3	128712024	128712024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	agagtcagactcctgggcccTggccttggccttcaggtgtt	13	12	2	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr3:128712024T>C	ENST00000265068.5	-	2	291	c.124A>G	c.(124-126)Agg>Ggg	p.R42G	KIAA1257_ENST00000515659.1_5'Flank|KIAA1257_ENST00000511438.1_Missense_Mutation_p.R42G|KIAA1257_ENST00000510149.1_Intron	NM_020741.2	NP_065792.1	Q9ULG3	K1257_HUMAN	KIAA1257	42										breast(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(2)	14						TCCTGGGCCCTGGCCTTGGCC	0.617																																					p.R42G		Atlas-SNP	.											.	KIAA1257	33	.	0			c.A124G						.						65	75	72					3																	128712024		2161	4262	6423	SO:0001583	missense	57501	exon2			GGGCCCTGGCCTT	AB033083	CCDS46905.1	3q21.3	2011-11-07			ENSG00000114656	ENSG00000114656			29231	protein-coding gene	gene with protein product						10574462	Standard	NM_020741		Approved		uc003elj.4	Q9ULG3	OTTHUMG00000159946	ENST00000265068.5:c.124A>G	chr3.hg19:g.128712024T>C	ENSP00000265068:p.Arg42Gly	203.0	0.0		131.0	45.0	NM_020741	Q8IXY7|Q8N5T4	Missense_Mutation	SNP	ENST00000265068.5	hg19	CCDS46905.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.412774	0.42817	.	.	ENSG00000114656	ENST00000511438;ENST00000265068	.	.	.	4.25	-6.08	0.02151	.	.	.	.	.	T	0.09774	0.0240	N	0.08118	0	0.09310	N	0.999999	B;B	0.34161	0.439;0.439	B;B	0.27380	0.079;0.079	T	0.18777	-1.0326	8	0.48119	T	0.1	0.0416	1.3647	0.02199	0.1842:0.1103:0.4926:0.213	.	42;42	Q9ULG3;D6RH05	K1257_HUMAN;.	G	42	.	ENSP00000265068:R42G	R	-	1	2	KIAA1257	130194714	0.000000	0.05858	0.000000	0.03702	0.241000	0.25554	-0.683000	0.05179	-0.807000	0.04393	0.397000	0.26171	AGG	.	.		0.617	KIAA1257-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000358430.1	NM_020741		C	128712024	T	C	128712024	3	2	109	1	0	0	0	0	1	0	0	0	8227	1579	55	2	1133	2	KIAA1257	3	128712024	Missense_Mutation	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10	87445924	128712024	69310406	15	16141										
BFSP2	8419	hgsc.bcm.edu	37	chr3	133185754	133185754	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ggtggagttacacaacacttCgtgccaagtccagagcctcc	10	13	0	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr3:133185754C>A	ENST00000302334.2	+	5	1063	c.974C>A	c.(973-975)tCg>tAg	p.S325*	BFSP2_ENST00000511434.1_3'UTR	NM_003571.2	NP_003562.1	Q13515	BFSP2_HUMAN	beaded filament structural protein 2, phakinin	325	Rod.				cell maturation (GO:0048469)|intermediate filament cytoskeleton organization (GO:0045104)|lens fiber cell development (GO:0070307)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)	p.S325L(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|urinary_tract(1)	13						CACAACACTTCGTGCCAAGTC	0.562																																					p.S325X		Atlas-SNP	.											BFSP2,bladder,carcinoma,0,1	BFSP2	48	.	1	Substitution - Missense(1)	urinary_tract(1)	c.C974A						.						85	80	82					3																	133185754		2203	4300	6503	SO:0001587	stop_gained	8419	exon5			ACACTTCGTGCCA	U48224	CCDS33859.1	3q22.1	2013-01-16			ENSG00000170819	ENSG00000170819		"Intermediate filaments type VI, eye lens intermediate filaments"	1041	protein-coding gene	gene with protein product		603212					Standard	NM_003571		Approved	CP47, CP49, LIFL-L, phakinin	uc003epn.1	Q13515	OTTHUMG00000159719	ENST00000302334.2:c.974C>A	chr3.hg19:g.133185754C>A	ENSP00000304987:p.Ser325*	241.0	0.0		196.0	20.0	NM_003571	Q14D32|Q9HBW5	Nonsense_Mutation	SNP	ENST00000302334.2	hg19	CCDS33859.1	.	.	.	.	.	.	.	.	.	.	C	37	6.502503	0.97620	.	.	ENSG00000170819	ENST00000302334	.	.	.	5.74	5.74	0.90152	.	0.532920	0.17019	N	0.190217	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-2.63	19.919	0.97077	0.0:1.0:0.0:0.0	.	.	.	.	X	325	.	ENSP00000304987:S325X	S	+	2	0	BFSP2	134668444	0.638000	0.27225	0.020000	0.16555	0.988000	0.76386	4.123000	0.57917	2.712000	0.92718	0.561000	0.74099	TCG	.	.		0.562	BFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357031.1			A	133185754	C	A	133185754	4	1	109	1	0	0	0	0	0	1	0	0	1416	893	31	1	992	1	BFSP2	3	133185754	Nonsense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	4473730	133185754	64836676	16	16142										
HTR3E	285242	hgsc.bcm.edu	37	chr3	183822009	183822009	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tcagctggaacccagaggaaTgtgagggcatcacgaagatg	14	8	2	3			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr3:183822009T>A	ENST00000415389.2	+	4	785	c.319T>A	c.(319-321)Tgt>Agt	p.C107S	HTR3E_ENST00000440596.2_Missense_Mutation_p.C107S|HTR3E_ENST00000425359.2_Missense_Mutation_p.C92S|HTR3E-AS1_ENST00000431427.1_RNA|HTR3E_ENST00000436361.2_Missense_Mutation_p.C107S|HTR3E_ENST00000335304.2_Missense_Mutation_p.C122S	NM_001256613.1|NM_198313.2	NP_001243542.1|NP_938055.1	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine (serotonin) receptor 3E, ionotropic	107					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	40	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	CCCAGAGGAATGTGAGGGCAT	0.468																																					p.C122S	Melanoma(7;227 727 6634 44770)	Atlas-SNP	.											.	HTR3E	65	.	0			c.T364A						.						63	54	57					3																	183822009		2203	4300	6503	SO:0001583	missense	285242	exon3			GAGGAATGTGAGG	AY159813	CCDS3251.1, CCDS58868.1, CCDS58869.1, CCDS58870.1, CCDS58871.1	3q27	2012-05-22	2012-02-03		ENSG00000186038	ENSG00000186038		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24005	protein-coding gene	gene with protein product		610123	"5-hydroxytryptamine (serotonin) receptor 3, family member E"			12801637, 15157181	Standard	NM_001256613		Approved		uc010hxr.3	A5X5Y0	OTTHUMG00000156857	ENST00000415389.2:c.319T>A	chr3.hg19:g.183822009T>A	ENSP00000401444:p.Cys107Ser	66.0	0.0		49.0	11.0	NM_182589	A8IKD7|E9PGF1|Q495G1|Q495G3|Q6V706|Q6V707|Q7Z6B2	Missense_Mutation	SNP	ENST00000415389.2	hg19	CCDS58868.1	.	.	.	.	.	.	.	.	.	.	t	13.37	2.217041	0.39201	.	.	ENSG00000186038	ENST00000415389;ENST00000425359;ENST00000335304;ENST00000431041;ENST00000436361;ENST00000440596	T;T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1;-1.1	3.46	3.46	0.39613	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.64402	U	0.000003	D	0.87160	0.6108	M	0.84846	2.72	0.26614	N	0.972772	D;D;D;D;D	0.89917	0.991;1.0;1.0;1.0;1.0	D;D;D;D;D	0.79784	0.954;0.993;0.988;0.988;0.988	T	0.79150	-0.1922	10	0.62326	D	0.03	.	10.2155	0.43166	0.0:0.0:0.0:1.0	.	107;107;107;122;92	E9PGF1;A5X5Y0;A5X5Y0-4;A5X5Y0-3;A5X5Y0-2	.;5HT3E_HUMAN;.;.;.	S	107;92;122;36;107;107	ENSP00000401444:C107S;ENSP00000401900:C92S;ENSP00000335511:C122S;ENSP00000391254:C36S;ENSP00000395833:C107S;ENSP00000406050:C107S	ENSP00000335511:C122S	C	+	1	0	HTR3E	185304703	1.000000	0.71417	0.039000	0.18376	0.273000	0.26683	6.209000	0.72171	1.565000	0.49641	0.528000	0.53228	TGT	.	.		0.468	HTR3E-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346284.1	NM_182589		A	183822009	T	A	183822009	3	1	109	1	0	0	0	0	1	0	0	0	7457	1464	51	4	374	4	HTR3E	3	183822009	Missense_Mutation	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10	50636255	183822009	14200421	17	16143										
CRYGS	1427	hgsc.bcm.edu	37	chr3	186256648	186256648	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ccttacaggagtggatctctCgcatgtgaaattgctccatg	10	10	1	1	rs570966753		TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr3:186256648C>A	ENST00000392499.2	-	4	713	c.374G>T	c.(373-375)cGa>cTa	p.R125L	CRYGS_ENST00000307944.5_Missense_Mutation_p.R125L	NM_017541.2	NP_060011.1	P22914	CRBS_HUMAN	crystallin, gamma S	125	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|morphogenesis of an epithelium (GO:0002009)		structural constituent of eye lens (GO:0005212)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	11	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.5e-22)	GBM - Glioblastoma multiforme(93;0.0906)		GTGGATCTCTCGCATGTGAAA	0.488																																					p.R125L		Atlas-SNP	.											.	CRYGS	23	.	0			c.G374T						.						89	82	84					3																	186256648		2203	4300	6503	SO:0001583	missense	1427	exon3			ATCTCTCGCATGT		CCDS3275.1	3q27.3	2013-02-14			ENSG00000213139	ENSG00000213139			2417	protein-coding gene	gene with protein product	"crystallin, gamma 8"	123730		CRYG8			Standard	NM_017541		Approved		uc003fqe.3	P22914	OTTHUMG00000156615	ENST00000392499.2:c.374G>T	chr3.hg19:g.186256648C>A	ENSP00000376287:p.Arg125Leu	165.0	0.0		127.0	53.0	NM_017541	B2RAF8	Missense_Mutation	SNP	ENST00000392499.2	hg19	CCDS3275.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.036824	0.54896	.	.	ENSG00000213139	ENST00000392499;ENST00000307944	T;T	0.76316	-1.01;-1.01	5.95	5.08	0.68730	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.64402	U	0.000014	D	0.85062	0.5611	M	0.87180	2.865	0.41397	D	0.987655	P	0.49358	0.923	P	0.55112	0.769	D	0.85022	0.0912	10	0.36615	T	0.2	.	9.4977	0.38997	0.0:0.8397:0.0:0.1603	.	125	P22914	CRBS_HUMAN	L	125	ENSP00000376287:R125L;ENSP00000312099:R125L	ENSP00000312099:R125L	R	-	2	0	CRYGS	187739342	1.000000	0.71417	0.912000	0.35992	0.991000	0.79684	4.916000	0.63362	1.518000	0.48934	0.655000	0.94253	CGA	.	.		0.488	CRYGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344784.1	NM_017541		A	186256648	C	A	186256648	3	1	109	1	0	0	0	0	1	0	0	0	3921	884	31	1	166	1	CRYGS	3	186256648	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	2434639	186256648	11765782	18	16144										
FGFR3	2261	hgsc.bcm.edu	37	chr4	1808893	1808893	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	cagtactccccgggtggccaGgacacccccagctccagctc	10	19	0	0			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr4:1808893G>A	ENST00000260795.2	+	17	2427	c.2325G>A	c.(2323-2325)caG>caA	p.Q775Q	FGFR3_ENST00000412135.2_Silent_p.Q663Q|FGFR3_ENST00000340107.4_Silent_p.Q777Q|FGFR3_ENST00000440486.2_Silent_p.Q775Q|FGFR3_ENST00000481110.2_Missense_Mutation_p.G753R|FGFR3_ENST00000352904.1_Silent_p.Q663Q			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	775					alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	CGGGTGGCCAGGACACCCCCA	0.711		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.Q777Q		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3	3320	.	0			c.G2331A						.						24	26	25					4																	1808893		2192	4296	6488	SO:0001819	synonymous_variant	2261	exon18	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	TGGCCAGGACACC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.2325G>A	chr4.hg19:g.1808893G>A		204.0	0.0		133.0	43.0	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	hg19	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	g	17.10	3.302697	0.60195	.	.	ENSG00000068078	ENST00000481110	D	0.83075	-1.68	4.53	1.77	0.24775	.	.	.	.	.	T	0.77315	0.4112	.	.	.	0.80722	D	1	B	0.22414	0.069	B	0.21708	0.036	T	0.70985	-0.4723	8	0.87932	D	0	.	11.6551	0.51313	0.1322:0.0:0.8678:0.0	.	753	F8W9L4	.	R	753	ENSP00000420533:G753R	ENSP00000420533:G753R	G	+	1	0	FGFR3	1778691	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	1.636000	0.37144	0.095000	0.17434	0.511000	0.50034	GGA	.	.		0.711	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		A	1808893	G	A	1808893	2	1	109	1	0	0	0	0	0	0	0	1	5875	991	35	3		3	FGFR3	4	1808893	Silent	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10		1808893	189345383	19	16145										
PROM1	8842	hgsc.bcm.edu	37	chr4	16014922	16014922	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tacgacagtcgtggtttggcGttgtactctgtcaggtatat	12	7	2	0	rs137853006		TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr4:16014922G>T	ENST00000510224.1	-	11	1365	c.1117C>A	c.(1117-1119)Cgc>Agc	p.R373S	PROM1_ENST00000505450.1_Missense_Mutation_p.R364S|PROM1_ENST00000447510.2_Missense_Mutation_p.R373S|PROM1_ENST00000543373.1_Missense_Mutation_p.R364S|PROM1_ENST00000540805.1_Missense_Mutation_p.R373S|PROM1_ENST00000539194.1_Missense_Mutation_p.R373S|PROM1_ENST00000508167.1_Missense_Mutation_p.R364S			O43490	PROM1_HUMAN	prominin 1	373			R -> C (in CORD12, STGD4 and MCDR2; affects the interaction with actin). {ECO:0000269|PubMed:18654668}.		camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						GTGGTTTGGCGTTGTACTCTG	0.388																																					p.R373S		Atlas-SNP	.											.	PROM1	91	.	0			c.C1117A	GRCh37	CM083044	PROM1	M	rs137853006	.						171	165	167					4																	16014922		1904	4133	6037	SO:0001583	missense	8842	exon10			TTTGGCGTTGTAC	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.1117C>A	chr4.hg19:g.16014922G>T	ENSP00000426809:p.Arg373Ser	90.0	0.0		66.0	20.0	NM_006017	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	hg19	CCDS47029.1	.	.	.	.	.	.	.	.	.	.	G	3.924	-0.017604	0.07681	.	.	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373	T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.03	-0.568	0.11760	.	0.584607	0.19507	N	0.112589	T	0.18759	0.0450	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B	0.09022	0.002;0.002;0.002;0.002;0.001;0.002	B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.0;0.001	T	0.14008	-1.0488	10	0.32370	T	0.25	-3.9024	7.5319	0.27687	0.0:0.0774:0.4186:0.504	.	364;373;364;373;364;373	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490	.;.;.;.;.;PROM1_HUMAN	S	373;373;373;364;364;373;364	ENSP00000415481:R373S;ENSP00000438045:R373S;ENSP00000443620:R373S;ENSP00000426090:R364S;ENSP00000427346:R364S;ENSP00000426809:R373S;ENSP00000445526:R364S	ENSP00000415481:R373S	R	-	1	0	PROM1	15624020	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.100000	0.15231	-0.315000	0.08703	-1.532000	0.00920	CGC	.	.		0.388	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		T	16014922	G	T	16014922	3	4	109	1	0	0	0	0	1	0	0	0	12567	1145	40	1	1548	1	PROM1	4	16014922	Missense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	14206029	16014922	175139354	20	16146										
PTTG2	23216	hgsc.bcm.edu	37	chr4	37962092	37962092	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	acgttgataaggaaattggaGaaccaggcacccgtgtggct	13	8	0	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr4:37962092G>T	ENST00000261439.4	+	3	772				TBC1D1_ENST00000508802.1_Intron|PTTG2_ENST00000504686.1_Nonsense_Mutation_p.E13*	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1						membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						GGAAATTGGAGAACCAGGCAC	0.448																																					p.E13X		Atlas-SNP	.											.	PTTG2	15	.	0			c.G37T						.						61	67	65					4																	37962092		2203	4300	6503	SO:0001627	intron_variant	10744	exon1			ATTGGAGAACCAG	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.418-54038G>T	chr4.hg19:g.37962092G>T		187.0	0.0		164.0	57.0	NM_006607	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Nonsense_Mutation	SNP	ENST00000261439.4	hg19	CCDS33972.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.144170	0.37825	.	.	ENSG00000250254	ENST00000504686	.	.	.	1.36	1.36	0.22044	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	6.1977	0.20559	0.0:0.0:1.0:0.0	.	.	.	.	X	13	.	ENSP00000424261:E13X	E	+	1	0	PTTG2	37638487	0.981000	0.34729	0.038000	0.18304	0.042000	0.13812	1.040000	0.30278	1.097000	0.41459	0.558000	0.71614	GAA	.	.		0.448	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173		T	37962092	G	T	37962092	1	4	109	0	1	0	0	0	0	0	0	0	12836	943	33	3		3	PTTG2	4	37962092	Intron	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	21947170	37962092	153192184	21	16147										
TTC29	83894	hgsc.bcm.edu	37	chr4	147824847	147824847	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ttattgaagtaacaggccagAgcatacaagttattatgtac	8	6	0	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr4:147824847A>T	ENST00000325106.4	-	6	661	c.435T>A	c.(433-435)gcT>gcA	p.A145A	TTC29_ENST00000398886.4_Silent_p.A171A|TTC29_ENST00000513335.1_Silent_p.A171A	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	145								p.N142_E154>K(1)		breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					AACAGGCCAGAGCATACAAGT	0.393																																					p.A145A		Atlas-SNP	.											.	TTC29	63	.	1	Complex - deletion inframe(1)	breast(1)	c.T435A						.						62	59	60					4																	147824847		1867	4101	5968	SO:0001819	synonymous_variant	83894	exon6			GGCCAGAGCATAC	AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"Tetratricopeptide (TTC) repeat domain containing"	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.435T>A	chr4.hg19:g.147824847A>T		130.0	0.0		95.0	45.0	NM_031956	A4GU95|Q9BXB6	Silent	SNP	ENST00000325106.4	hg19	CCDS47141.1																																																																																			.	.		0.393	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956		T	147824847	A	T	147824847	2	4	109	1	0	0	0	0	0	0	0	1	16711	291	11	4		4	TTC29	4	147824847	Silent	SNP	A	TCGA-DD-A39V-01A-11D-A20W-10	109862755	147824847	43329429	22	16148										
FNIP2	57600	hgsc.bcm.edu	37	chr4	159782775	159782775	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	caaggttttttgctgccttaCtgactgcggtgttaacctac	9	10	0	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr4:159782775C>G	ENST00000264433.6	+	12	1387	c.1312C>G	c.(1312-1314)Ctg>Gtg	p.L438V	FNIP2_ENST00000379346.3_Missense_Mutation_p.L461V	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	438					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		TGCTGCCTTACTGACTGCGGT	0.483																																					p.L438V		Atlas-SNP	.											.	FNIP2	90	.	0			c.C1312G						.						133	128	129					4																	159782775		1984	4162	6146	SO:0001583	missense	57600	exon12			GCCTTACTGACTG	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"O6-methylguanine-induced apoptosis 1"	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.1312C>G	chr4.hg19:g.159782775C>G	ENSP00000264433:p.Leu438Val	222.0	0.0		170.0	49.0	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	hg19	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.911778	0.52439	.	.	ENSG00000052795	ENST00000264433;ENST00000512986;ENST00000379346	T;T;T	0.34667	1.35;1.35;1.35	5.27	5.27	0.74061	.	.	.	.	.	T	0.42108	0.1188	L	0.51914	1.62	0.46149	D	0.998898	D	0.60575	0.988	P	0.56398	0.797	T	0.30387	-0.9980	8	.	.	.	.	5.6762	0.17749	0.1912:0.6902:0.0:0.1185	.	438	Q9P278	FNIP2_HUMAN	V	438;461;461	ENSP00000264433:L438V;ENSP00000421488:L461V;ENSP00000368651:L461V	.	L	+	1	2	FNIP2	160002225	0.882000	0.30256	1.000000	0.80357	0.982000	0.71751	0.729000	0.26028	2.636000	0.89361	0.467000	0.42956	CTG	.	.		0.483	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		G	159782775	C	G	159782775	3	3	109	1	0	0	0	0	1	0	0	0	5984	564	20	4	1358	4	FNIP2	4	159782775	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	11957928	159782775	31371501	23	16149										
CDH18	1016	hgsc.bcm.edu	37	chr5	19838935	19838944	+	Frame_Shift_Del	DEL	CCCCTTTTGG	CCCCTTTTGG	-													0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	agaactgattccatacccatCcccttttgggacgatgatgg					rs200906154		TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	CCCCTTTTGG	CCCCTTTTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr5:19838935_19838944delCCCCTTTTGG	ENST00000507958.1	-	5	1142_1151	c.152_161delCCAAAAGGGG	c.(151-162)cccaaaaggggafs	p.PKRG51fs	CDH18_ENST00000506372.1_Frame_Shift_Del_p.PKRG51fs|CDH18_ENST00000274170.4_Frame_Shift_Del_p.PKRG51fs|CDH18_ENST00000511273.1_Frame_Shift_Del_p.PKRG51fs|CDH18_ENST00000382275.1_Frame_Shift_Del_p.PKRG51fs|CDH18_ENST00000502796.1_Frame_Shift_Del_p.PKRG51fs			Q13634	CAD18_HUMAN	cadherin 18, type 2	51					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CCATACCCATCCCCTTTTGGGACGATGATG	0.405																																					p.51_54del		Atlas-Indel,Pindel	.											.	CDH18	561	.	0			c.153_162del						.																																			SO:0001589	frameshift_variant	1016	exon3			.	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.152_161delCCAAAAGGGG	chr5.hg19:g.19838935_19838944delCCCCTTTTGG	ENSP00000425093:p.Pro51fs	144.0	0.0		116.0	38.0	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Frame_Shift_Del	DEL	ENST00000507958.1	hg19	CCDS3889.1																																																																																			.	.		0.405	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		-	19838944	CCCCTTTTGG	-	19838935	7	5	109	1	0	1	0	1	0	0	0	0	3105	855	30	0	2255	0	CDH18	5	19838935	Frame_Shift_Del	DEL	CCCCTTTTGG	TCGA-DD-A39V-01A-11D-A20W-10		19838935	161076325	24	16150										
PCSK1	5122	hgsc.bcm.edu	37	chr5	95733104	95733104	+	Frame_Shift_Del	DEL	A	A	-													0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	cccatgtgtgaacagacatgAagtcccaattcttaaagcca							TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr5:95733104delA	ENST00000311106.3	-	12	1895	c.1658delT	c.(1657-1659)ttcfs	p.F553fs	PCSK1_ENST00000508626.1_Frame_Shift_Del_p.F506fs|CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000513085.1_5'UTR	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	553					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	AACAGACATGAAGTCCCAATT	0.403																																					p.F553fs		Atlas-Indel,Pindel	.											.	PCSK1	93	.	0			c.1659delC						.						117	102	107					5																	95733104		2203	4300	6503	SO:0001589	frameshift_variant	5122	exon12			.		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"prohormone convertase 3", "prohormone convertase 1", "neuroendocrine convertase 1", "proprotein convertase 1"	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.1658delT	chr5.hg19:g.95733104delA	ENSP00000308024:p.Phe553fs	158.0	0.0		149.0	39.0	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Frame_Shift_Del	DEL	ENST00000311106.3	hg19	CCDS4081.1																																																																																			.	.		0.403	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		-	95733104	A	-	95733104	7	5	109	1	0	1	0	1	0	0	0	0	11609	246	9	0	615	0	PCSK1	5	95733104	Frame_Shift_Del	DEL	A	TCGA-DD-A39V-01A-11D-A20W-10	75894169	95733104	85182156	25	16151										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128958013	128958013	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	atgccagatcctttttgggcCattggcttctttttgtcagg	10	9	2	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr5:128958013C>G	ENST00000274487.4	+	10	1869	c.1724C>G	c.(1723-1725)cCa>cGa	p.P575R	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	575	Disintegrin.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		CTTTTTGGGCCATTGGCTTCT	0.443																																					p.P575R		Atlas-SNP	.											ADAMTS19,right_upper_lobe,carcinoma,0,1	ADAMTS19	216	.	0			c.C1724G						.						142	121	128					5																	128958013		2203	4300	6503	SO:0001583	missense	171019	exon10			TTGGGCCATTGGC	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1724C>G	chr5.hg19:g.128958013C>G	ENSP00000274487:p.Pro575Arg	247.0	0.0		241.0	55.0	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.769230	0.31320	.	.	ENSG00000145808	ENST00000274487	T	0.65178	-0.14	4.42	3.55	0.40652	.	0.078553	0.51477	D	0.000090	T	0.68007	0.2954	L	0.52759	1.655	0.49299	D	0.999779	D	0.63046	0.992	P	0.56434	0.798	T	0.68700	-0.5339	9	.	.	.	.	14.8773	0.70504	0.1449:0.8551:0.0:0.0	.	575	Q8TE59	ATS19_HUMAN	R	575	ENSP00000274487:P575R	.	P	+	2	0	ADAMTS19	128985912	0.994000	0.37717	0.890000	0.34922	0.299000	0.27559	3.939000	0.56591	1.452000	0.47756	-0.238000	0.12139	CCA	.	.		0.443	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		G	128958013	C	G	128958013	3	3	109	1	0	0	0	0	1	0	0	0	264	594	21	4	1762	4	ADAMTS19	5	128958013	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	33224909	128958013	51957247	26	16152										
HAVCR1	26762	hgsc.bcm.edu	37	chr5	156479625	156479625	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ctcgttcgaacagtcgtgacGgttggaacagttgtgacaat	12	8	0	2	rs566987531		TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr5:156479625G>A	ENST00000339252.3	-	3	952	c.420C>T	c.(418-420)acC>acT	p.T140T	HAVCR1_ENST00000522693.1_Silent_p.T140T|HAVCR1_ENST00000544197.1_Silent_p.T140T|HAVCR1_ENST00000523175.1_Silent_p.T140T|HAVCR1_ENST00000425854.1_Silent_p.T140T	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)	p.T140T(1)		endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CAGTCGTGACGGTTGGAACAG	0.468													G|||	1	0.000199681	0	0	5008	,	,		22690	0		0	False		,,,				2504	0.001				p.T140T		Atlas-SNP	.											HAVCR1,NS,carcinoma,-1,1	HAVCR1	84	.	1	Substitution - coding silent(1)	lung(1)	c.C420T						.						406	402	403					5																	156479625		2140	4255	6395	SO:0001819	synonymous_variant	26762	exon4			CGTGACGGTTGGA	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"Immunoglobulin superfamily / V-set domain containing"	17866	protein-coding gene	gene with protein product	"T-cell immunoglobulin mucin family member 1"	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.420C>T	chr5.hg19:g.156479625G>A		308.0	0.0		296.0	21.0	NM_001099414	O43656	Silent	SNP	ENST00000339252.3	hg19	CCDS43392.1																																																																																			.	.		0.468	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1			A	156479625	G	A	156479625	2	1	109	1	0	0	0	0	0	0	0	1	6982	1103	39	1		1	HAVCR1	5	156479625	Silent	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	27521612	156479625	24435635	27	16153										
TULP1	7287	hgsc.bcm.edu	37	chr6	35471393	35471393	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ctcatgccaggaatgatgacGgtcatgcgccgggggccacg	15	12	2	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr6:35471393G>A	ENST00000229771.6	-	13	1345	c.1266C>T	c.(1264-1266)acC>acT	p.T422T	TULP1_ENST00000322263.4_Silent_p.T369T	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	422					dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						GAATGATGACGGTCATGCGCC	0.642																																					p.T422T	GBM(55;1027 1091 11115 23439)	Atlas-SNP	.											.	TULP1	51	.	0			c.C1266T						.						23	23	23					6																	35471393		2199	4299	6498	SO:0001819	synonymous_variant	7287	exon13			GATGACGGTCATG	U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.1266C>T	chr6.hg19:g.35471393G>A		81.0	0.0		56.0	13.0	NM_003322	O43536|Q5TGM5|Q8N571	Silent	SNP	ENST00000229771.6	hg19	CCDS4807.1																																																																																			.	.		0.642	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2			A	35471393	G	A	35471393	2	1	109	1	0	0	0	0	0	0	0	1	16788	1103	39	1		1	TULP1	6	35471393	Silent	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10		35471393	135643674	28	16154										
BAI3	577	hgsc.bcm.edu	37	chr6	69703824	69703824	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	acagacacatttaaaagggcAagttacatccctgcatctga	7	10	1	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr6:69703824A>G	ENST00000370598.1	+	11	2720	c.1899A>G	c.(1897-1899)gcA>gcG	p.A633A		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	633					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TTAAAAGGGCAAGTTACATCC	0.443																																					p.A633A		Atlas-SNP	.											BAI3,colon,carcinoma,+1,1	BAI3	451	.	0			c.A1899G						.						104	103	103					6																	69703824		2203	4300	6503	SO:0001819	synonymous_variant	577	exon11			AAGGGCAAGTTAC	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1899A>G	chr6.hg19:g.69703824A>G		92.0	0.0		94.0	28.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	hg19	CCDS4968.1																																																																																			.	.		0.443	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			G	69703824	A	G	69703824	2	3	109	1	0	0	0	0	0	0	0	1	1300	117	5	2		2	BAI3	6	69703824	Silent	SNP	A	TCGA-DD-A39V-01A-11D-A20W-10	34232431	69703824	101411243	29	16155										
LCA5	167691	hgsc.bcm.edu	37	chr6	80196750	80196750	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tgctacttcttcaatttcatCttctacagaatcagctgctt	4	11	6	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr6:80196750C>A	ENST00000392959.1	-	9	2676	c.2065G>T	c.(2065-2067)Gat>Tat	p.D689Y	LCA5_ENST00000369846.4_Missense_Mutation_p.D689Y	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	689					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		TCAATTTCATCTTCTACAGAA	0.308																																					p.D689Y		Atlas-SNP	.											.	LCA5	71	.	0			c.G2065T						.						46	51	49					6																	80196750		2203	4300	6503	SO:0001583	missense	167691	exon8			TTTCATCTTCTAC		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.2065G>T	chr6.hg19:g.80196750C>A	ENSP00000376686:p.Asp689Tyr	128.0	0.0		100.0	39.0	NM_001122769	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	hg19	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.396518	0.62177	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.51325	0.71;0.71	5.57	5.57	0.84162	.	0.371680	0.26463	N	0.024232	T	0.55449	0.1921	L	0.43923	1.385	0.48511	D	0.999661	D	0.76494	0.999	D	0.68483	0.958	T	0.58405	-0.7642	10	0.87932	D	0	-7.9575	18.5368	0.91013	0.0:1.0:0.0:0.0	.	689	Q86VQ0	LCA5_HUMAN	Y	689	ENSP00000358861:D689Y;ENSP00000376686:D689Y	ENSP00000358861:D689Y	D	-	1	0	LCA5	80253469	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	5.677000	0.68142	2.609000	0.88269	0.591000	0.81541	GAT	.	.		0.308	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		A	80196750	C	A	80196750	3	1	109	1	0	0	0	0	1	0	0	0	8665	913	32	3	32	3	LCA5	6	80196750	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	10492926	80196750	90918317	30	16156										
MOXD1	26002	hgsc.bcm.edu	37	chr6	132649562	132649562	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	cattagccccacctctccacCaatagcccaggcaaaaatca	4	17	2	0			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr6:132649562C>A	ENST00000367963.3	-	5	953	c.835G>T	c.(835-837)Ggt>Tgt	p.G279C	MOXD1_ENST00000336749.3_Missense_Mutation_p.G211C	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	279						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		ACCTCTCCACCAATAGCCCAG	0.438																																					p.G279C		Atlas-SNP	.											.	MOXD1	136	.	0			c.G835T						.						90	84	86					6																	132649562		2203	4300	6503	SO:0001583	missense	26002	exon5			CTCCACCAATAGC	AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.835G>T	chr6.hg19:g.132649562C>A	ENSP00000356940:p.Gly279Cys	119.0	0.0		102.0	5.0	NM_015529	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	hg19	CCDS5152.2	.	.	.	.	.	.	.	.	.	.	C	23.1	4.378714	0.82682	.	.	ENSG00000079931	ENST00000367963;ENST00000336749	T;T	0.66995	-0.24;-0.24	4.82	4.82	0.62117	Copper type II, ascorbate-dependent monooxygenase, N-terminal (2);PHM/PNGase F domain (1);	0.000000	0.85682	D	0.000000	D	0.85995	0.5827	H	0.95645	3.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.975	D	0.90421	0.4417	10	0.87932	D	0	-22.6453	18.2459	0.89985	0.0:1.0:0.0:0.0	.	279;211	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	C	279;211	ENSP00000356940:G279C;ENSP00000336998:G211C	ENSP00000336998:G211C	G	-	1	0	MOXD1	132691255	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.470000	0.73558	2.376000	0.81061	0.650000	0.86243	GGT	.	.		0.438	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529		A	132649562	C	A	132649562	3	1	109	1	0	0	0	0	1	0	0	0	9729	594	21	3	1038	3	MOXD1	6	132649562	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	52452812	132649562	38465505	31	16157										
TIAM2	26230	hgsc.bcm.edu	37	chr6	155498016	155498016	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	cccgagacaatgcatgggaaAtccagacttatgtccacttt	8	11	0	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr6:155498016A>T	ENST00000461783.3	+	12	3701	c.2428A>T	c.(2428-2430)Atc>Ttc	p.I810F	TIAM2_ENST00000367174.2_Missense_Mutation_p.I186F|TIAM2_ENST00000360366.4_Missense_Mutation_p.I834F|TIAM2_ENST00000456877.2_Missense_Mutation_p.I122F|TIAM2_ENST00000529824.2_Missense_Mutation_p.I810F|TIAM2_ENST00000456144.1_Missense_Mutation_p.I810F|TIAM2_ENST00000528391.2_Missense_Mutation_p.I146F|TIAM2_ENST00000318981.5_Missense_Mutation_p.I810F			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	810	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		TGCATGGGAAATCCAGACTTA	0.428																																					p.I810F		Atlas-SNP	.											.	TIAM2	161	.	0			c.A2428T						.						181	157	165					6																	155498016		2203	4300	6503	SO:0001583	missense	26230	exon9			TGGGAAATCCAGA		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.2428A>T	chr6.hg19:g.155498016A>T	ENSP00000437188:p.Ile810Phe	99.0	0.0		71.0	37.0	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	hg19	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	A	9.712	1.157235	0.21454	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391	T;T;T;T;T;T;T;T;T	0.05382	3.62;3.52;3.59;3.62;3.46;3.63;3.59;3.45;3.46	5.55	-2.7	0.06004	Raf-like Ras-binding (2);	1.088580	0.06944	N	0.813320	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B;B;B;B	0.29432	0.006;0.244;0.113;0.158	B;B;B;B	0.32022	0.139;0.127;0.127;0.06	T	0.49082	-0.8976	10	0.56958	D	0.05	.	6.4663	0.21983	0.4947:0.1313:0.3741:0.0	.	146;810;834;810	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	F	810;1056;810;810;810;186;834;810;122;146	ENSP00000437188:I810F;ENSP00000434901:I810F;ENSP00000407746:I810F;ENSP00000327315:I810F;ENSP00000356142:I186F;ENSP00000353528:I834F;ENSP00000433348:I810F;ENSP00000407183:I122F;ENSP00000435335:I146F	ENSP00000327315:I810F	I	+	1	0	TIAM2	155539708	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.365000	0.20348	-0.644000	0.05465	-0.291000	0.09656	ATC	.	.		0.428	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155498016	A	T	155498016	3	4	109	1	0	0	0	0	1	0	0	0	15906	101	4	4	2454	4	TIAM2	6	155498016	Missense_Mutation	SNP	A	TCGA-DD-A39V-01A-11D-A20W-10	22848454	155498016	15617051	32	16158										
HECW1	23072	hgsc.bcm.edu	37	chr7	43484273	43484273	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	gagccgggctggaagggaagAagaggagaaggagcaggagg	22	4	0	3			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr7:43484273A>G	ENST00000395891.2	+	11	2107	c.1502A>G	c.(1501-1503)gAa>gGa	p.E501G	HECW1_ENST00000453890.1_Missense_Mutation_p.E501G	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	501	Glu-rich.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						GGAAGggaagaagaggagaag	0.632																																					p.E501G		Atlas-SNP	.											.	HECW1	540	.	0			c.A1502G						.						21	25	24					7																	43484273		2075	4202	6277	SO:0001583	missense	23072	exon11			GGGAAGAAGAGGA	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.1502A>G	chr7.hg19:g.43484273A>G	ENSP00000379228:p.Glu501Gly	93.0	0.0		96.0	8.0	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	hg19	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	A	13.71	2.317151	0.40996	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.33654	1.43;1.4	5.12	-4.16	0.03869	.	2.657370	0.00797	N	0.001399	T	0.17023	0.0409	N	0.08118	0	0.09310	N	1	B;B	0.19817	0.039;0.02	B;B	0.19148	0.014;0.024	T	0.18871	-1.0323	10	0.56958	D	0.05	.	1.5496	0.02572	0.3463:0.0936:0.1435:0.4165	.	501;501	B4DH42;Q76N89	.;HECW1_HUMAN	G	501	ENSP00000379228:E501G;ENSP00000407774:E501G	ENSP00000265522:E501G	E	+	2	0	HECW1	43450798	.	.	0.001000	0.08648	0.130000	0.20726	.	.	-0.304000	0.08843	0.459000	0.35465	GAA	.	.		0.632	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		G	43484273	A	G	43484273	3	3	109	1	0	0	0	0	1	0	0	0	7051	246	9	2	1536	2	HECW1	7	43484273	Missense_Mutation	SNP	A	TCGA-DD-A39V-01A-11D-A20W-10		43484273	115654390	33	16159										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84628838	84628838	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tcttcatttcctgcatgtgcTtccactttgggccccccttg	7	15	2	0			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr7:84628838T>G	ENST00000284136.6	-	17	2295	c.2252A>C	c.(2251-2253)aAg>aCg	p.K751T	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	751	Arg/Lys-rich (basic).				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CTGCATGTGCTTCCACTTTGG	0.483																																					p.K751T	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.A2252C						.						176	145	155					7																	84628838		2203	4300	6503	SO:0001583	missense	223117	exon17			ATGTGCTTCCACT	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.2252A>C	chr7.hg19:g.84628838T>G	ENSP00000284136:p.Lys751Thr	319.0	0.0		313.0	84.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	hg19	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.252452	0.80135	.	.	ENSG00000153993	ENST00000284136	T	0.35605	1.3	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.57388	0.2050	M	0.69823	2.125	0.80722	D	1	D	0.69078	0.997	P	0.60789	0.879	T	0.61038	-0.7143	10	0.72032	D	0.01	.	16.3798	0.83452	0.0:0.0:0.0:1.0	.	751	O95025	SEM3D_HUMAN	T	751	ENSP00000284136:K751T	ENSP00000284136:K751T	K	-	2	0	SEMA3D	84466774	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.718000	0.68455	2.271000	0.75665	0.533000	0.62120	AAG	.	.		0.483	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		G	84628838	T	G	84628838	3	3	109	1	0	0	0	0	1	0	0	0	14042	1609	56	5	85	5	SEMA3D	7	84628838	Missense_Mutation	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10	41144565	84628838	74509825	34	16160										
ST18	9705	hgsc.bcm.edu	37	chr8	53085080	53085080	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	aagagtatctgtcttccttcCtactggagttttcttgtgca	8	9	3	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr8:53085080C>T	ENST00000276480.7	-	10	1024	c.341G>A	c.(340-342)aGg>aAg	p.R114K		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	114					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				GTCTTCCTTCCTACTGGAGTT	0.348																																					p.R114K		Atlas-SNP	.											.	ST18	212	.	0			c.G341A						.						40	42	41					8																	53085080		2201	4299	6500	SO:0001583	missense	9705	exon10			TCCTTCCTACTGG	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.341G>A	chr8.hg19:g.53085080C>T	ENSP00000276480:p.Arg114Lys	38.0	0.0		66.0	8.0	NM_014682	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	hg19	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.509475	0.00984	.	.	ENSG00000147488	ENST00000276480;ENST00000517580	T;T	0.41400	1.01;1.0	5.25	-2.92	0.05615	.	1.019870	0.07799	N	0.956216	T	0.21062	0.0507	L	0.36672	1.1	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.30416	-0.9979	10	0.05959	T	0.93	0.0851	0.058	0.00014	0.2876:0.18:0.209:0.3233	.	114	O60284	ST18_HUMAN	K	114	ENSP00000276480:R114K;ENSP00000428521:R114K	ENSP00000276480:R114K	R	-	2	0	ST18	53247633	0.005000	0.15991	0.005000	0.12908	0.275000	0.26752	-0.078000	0.11375	-0.558000	0.06118	-0.345000	0.07892	AGG	.	.		0.348	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53085080	C	T	53085080	3	4	109	1	0	0	0	0	1	0	0	0	15227	681	24	3	2870	3	ST18	8	53085080	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10		53085080	93278942	35	16161										
ARHGAP39	80728	hgsc.bcm.edu	37	chr8	145773562	145773562	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	gttcatagccatagcgcgggGaggagggctgcgagtccccg	17	11	1	0			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr8:145773562G>A	ENST00000276826.5	-	4	1109	c.908C>T	c.(907-909)tCc>tTc	p.S303F	ARHGAP39_ENST00000528810.1_5'Flank|ARHGAP39_ENST00000540274.1_Missense_Mutation_p.S303F|ARHGAP39_ENST00000377307.2_Missense_Mutation_p.S303F			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	303	Pro-rich.				axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						ATAGCGCGGGGAGGAGGGCTG	0.682																																					p.S303F		Atlas-SNP	.											ARHGAP39,NS,carcinoma,0,1	ARHGAP39	80	.	0			c.C908T						.						16	21	19					8																	145773562		2184	4270	6454	SO:0001583	missense	80728	exon6			CGCGGGGAGGAGG		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"Rho GTPase activating proteins"	29351	protein-coding gene	gene with protein product	"RhoGAP93B homolog (Drosophila)", "crossGAP homolog (Drosophila)"	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.908C>T	chr8.hg19:g.145773562G>A	ENSP00000276826:p.Ser303Phe	66.0	0.0		62.0	11.0	NM_025251	B4E1I1	Missense_Mutation	SNP	ENST00000276826.5	hg19		.	.	.	.	.	.	.	.	.	.	G	21.2	4.107293	0.77096	.	.	ENSG00000147799	ENST00000276826;ENST00000377307;ENST00000540274	T;T;T	0.80653	-1.4;-1.13;-1.4	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.88358	0.6415	L	0.61218	1.895	0.51767	D	0.999931	D;D	0.89917	0.999;1.0	D;D	0.91635	0.997;0.999	D	0.89311	0.3633	10	0.87932	D	0	-5.6595	16.5924	0.84770	0.0:0.0:1.0:0.0	.	303;303	Q9C0H5;Q9C0H5-2	RHG39_HUMAN;.	F	303	ENSP00000276826:S303F;ENSP00000366522:S303F;ENSP00000445075:S303F	ENSP00000276826:S303F	S	-	2	0	ARHGAP39	145744370	1.000000	0.71417	0.996000	0.52242	0.719000	0.41307	9.646000	0.98474	2.513000	0.84729	0.655000	0.94253	TCC	.	.		0.682	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			A	145773562	G	A	145773562	3	1	109	1	0	0	0	0	1	0	0	0	884	1174	41	3	2468	3	ARHGAP39	8	145773562	Missense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	92688482	145773562	590460	36	16162										
GLDC	2731	hgsc.bcm.edu	37	chr9	6592200	6592200	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tccagatctttttcattgacTgtttcatcaagagaaatacc	5	9	4	3			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr9:6592200T>C	ENST00000321612.6	-	11	1575	c.1425A>G	c.(1423-1425)acA>acG	p.T475T		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	475					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	TTTCATTGACTGTTTCATCAA	0.373																																					p.T475T		Atlas-SNP	.											.	GLDC	118	.	0			c.A1425G						.						86	79	82					9																	6592200		2203	4300	6503	SO:0001819	synonymous_variant	2731	exon11			ATTGACTGTTTCA	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"glycine cleavage system protein P", "glycine decarboxylase"	238300	"glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.1425A>G	chr9.hg19:g.6592200T>C		69.0	0.0		46.0	21.0	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	hg19	CCDS34987.1																																																																																			.	.		0.373	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170		C	6592200	T	C	6592200	2	2	109	1	0	0	0	0	0	0	0	1	6441	1567	55	2		2	GLDC	9	6592200	Silent	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10		6592200	134621231	37	16163										
ZFAND5	7763	hgsc.bcm.edu	37	chr9	74970914	74970914	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	acaacaactggattctctttTctgatttttgctgcagcttc	6	10	2	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr9:74970914T>C	ENST00000237937.3	-	6	1154	c.597A>G	c.(595-597)agA>agG	p.R199R	ZFAND5_ENST00000488164.1_5'UTR|ZFAND5_ENST00000343431.2_Silent_p.R199R|ZFAND5_ENST00000376960.4_Silent_p.R199R|ZFAND5_ENST00000376962.5_Silent_p.R199R	NM_001102421.1|NM_001278243.1|NM_001278244.1|NM_001278245.1|NM_006007.2	NP_001095891.1|NP_001265172.1|NP_001265173.1|NP_001265174.1|NP_005998.1	O76080	ZFAN5_HUMAN	zinc finger, AN1-type domain 5	199					face development (GO:0060324)|fibroblast migration (GO:0010761)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|respiratory system process (GO:0003016)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|kidney(2)|lung(2)|prostate(1)	6						GATTCTCTTTTCTGATTTTTG	0.353																																					p.R199R		Atlas-SNP	.											.	ZFAND5	14	.	0			c.A597G						.						66	64	65					9																	74970914		2202	4296	6498	SO:0001819	synonymous_variant	7763	exon6			CTCTTTTCTGATT	AF062072	CCDS6642.1	9q13-q21	2008-05-02	2006-07-07	2006-07-07	ENSG00000107372	ENSG00000107372		"Zinc fingers, AN1-type domain containing"	13008	protein-coding gene	gene with protein product		604761	"zinc finger protein 216", "zinc finger, A20 domain containing 2"	ZNF216, ZA20D2		9758550	Standard	NM_001278243		Approved	ZFAND5A	uc004aiy.2	O76080	OTTHUMG00000020008	ENST00000237937.3:c.597A>G	chr9.hg19:g.74970914T>C		281.0	0.0		161.0	40.0	NM_001102421	A8K484	Silent	SNP	ENST00000237937.3	hg19	CCDS6642.1																																																																																			.	.		0.353	ZFAND5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052644.1			C	74970914	T	C	74970914	2	2	109	1	0	0	0	0	0	0	0	1	17645	1780	62	2		2	ZFAND5	9	74970914	Silent	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10	68378714	74970914	66242517	38	16164										
C9orf119	375757	hgsc.bcm.edu	37	chr9	131038585	131038585	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ccgggtcagagttcctggccCggtgcacctgagaggtcgct	15	13	1	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr9:131038585C>T	ENST00000320188.5	+	1	161	c.161C>T	c.(160-162)cCg>cTg	p.P54L	SWI5_ENST00000418976.1_5'UTR|SWI5_ENST00000419867.2_5'UTR|GOLGA2_ENST00000609374.1_5'Flank|SWI5_ENST00000495313.1_Intron|GOLGA2_ENST00000490628.1_5'Flank|SWI5_ENST00000608796.1_5'UTR|GOLGA2_ENST00000421699.2_5'Flank	NM_001040011.1	NP_001035100.1	Q1ZZU3	SWI5_HUMAN	SWI5 recombination repair homolog (yeast)	54					cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)	nucleus (GO:0005634)|Swi5-Sfr1 complex (GO:0032798)											GTTCCTGGCCCGGTGCACCTG	0.701																																					p.P54L		Atlas-SNP	.											.	.	.	.	0			c.C161T						.						12	16	15					9																	131038585		1897	4094	5991	SO:0001583	missense	375757	exon1			CTGGCCCGGTGCA	BC029911	CCDS43883.1	9q34.13	2011-07-29	2011-07-29	2011-07-29	ENSG00000175854	ENSG00000175854			31412	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 119"	C9orf119		21252223, 20976249	Standard	NM_001040011		Approved	bA395P17.9	uc004bup.3	Q1ZZU3	OTTHUMG00000020729	ENST00000320188.5:c.161C>T	chr9.hg19:g.131038585C>T	ENSP00000316609:p.Pro54Leu	134.0	0.0		82.0	29.0	NM_001040011	Q5SYX7|Q5SYX8|Q8N2W6	Missense_Mutation	SNP	ENST00000320188.5	hg19	CCDS43883.1	.	.	.	.	.	.	.	.	.	.	C	8.905	0.957255	0.18507	.	.	ENSG00000175854	ENST00000320188	.	.	.	4.02	-6.8	0.01709	.	4.315320	0.00714	N	0.000843	T	0.17746	0.0426	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31110	-0.9955	9	0.72032	D	0.01	.	5.9106	0.19027	0.0:0.3824:0.2663:0.3513	.	54	Q1ZZU3	SWI5_HUMAN	L	54	.	ENSP00000316609:P54L	P	+	2	0	SWI5	130078406	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.550000	0.00929	-0.855000	0.04125	-1.155000	0.01812	CCG	.	.		0.701	SWI5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001040011		T	131038585	C	T	131038585	3	4	109	1	0	0	0	0	1	0	0	0	2454	652	23	1	163	1	C9orf119	9	131038585	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	56067671	131038585	10174846	39	16165										
COMMD3	23412	hgsc.bcm.edu	37	chr10	22606855	22606855	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	cgacccagtggttttaaaacAttgtcatgcagcagctgcaa	9	10	1	0			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr10:22606855A>G	ENST00000376836.3	+	2	626	c.182A>G	c.(181-183)cAt>cGt	p.H61R	COMMD3-BMI1_ENST00000602390.1_Missense_Mutation_p.H61R|COMMD3-BMI1_ENST00000463409.2_3'UTR|COMMD3_ENST00000483684.1_3'UTR	NM_012071.3	NP_036203.1	Q9UBI1	COMD3_HUMAN	COMM domain containing 3	61										kidney(2)|lung(2)|ovary(1)	5						GTTTTAAAACATTGTCATGCA	0.353																																					p.H61R		Atlas-SNP	.											.	.	.	.	0			c.A182G						.						88	96	94					10																	22606855		2203	4300	6503	SO:0001583	missense	0	exon2			TAAAACATTGTCA	AY542159	CCDS7137.1	10p12.2	2012-09-20	2004-02-13	2004-02-18	ENSG00000148444	ENSG00000148444			23332	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 8"	C10orf8		11042152, 15799966	Standard	NM_012071		Approved	BUP		Q9UBI1	OTTHUMG00000017806	ENST00000376836.3:c.182A>G	chr10.hg19:g.22606855A>G	ENSP00000366032:p.His61Arg	296.0	0.0		193.0	69.0	NM_001204062	D3DRU7|Q5T8Y9	Missense_Mutation	SNP	ENST00000376836.3	hg19	CCDS7137.1	.	.	.	.	.	.	.	.	.	.	A	18.92	3.725088	0.68959	.	.	ENSG00000148444	ENST00000376836;ENST00000376776;ENST00000376787	T	0.09817	2.94	5.9	5.9	0.94986	.	0.101640	0.64402	D	0.000001	T	0.15176	0.0366	L	0.46157	1.445	0.80722	D	1	P;B	0.43231	0.801;0.288	B;B	0.43360	0.417;0.159	T	0.00870	-1.1533	10	0.44086	T	0.13	-23.1962	15.993	0.80220	1.0:0.0:0.0:0.0	.	61;61	Q9UBI1;E9PC68	COMD3_HUMAN;.	R	61	ENSP00000366032:H61R	ENSP00000365968:H61R	H	+	2	0	COMMD3	22646861	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.756000	0.74919	2.248000	0.74166	0.459000	0.35465	CAT	.	.		0.353	COMMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047159.1	NM_012071		G	22606855	A	G	22606855	3	3	109	1	0	0	0	0	1	0	0	0	3719	217	8	2	188	2	COMMD3	10	22606855	Missense_Mutation	SNP	A	TCGA-DD-A39V-01A-11D-A20W-10		22606855	112927892	40	16166										
OR51S1	119692	hgsc.bcm.edu	37	chr11	4869815	4869815	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	cccatggctgaaagaaccacAaataggctgtaggctgcacc	10	12	0	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr11:4869815A>G	ENST00000322101.2	-	1	699	c.624T>C	c.(622-624)ttT>ttC	p.F208F	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAAGAACCACAAATAGGCTGT	0.532																																					p.F208F		Atlas-SNP	.											.	OR51S1	83	.	0			c.T624C						.						80	85	83					11																	4869815		2201	4298	6499	SO:0001819	synonymous_variant	119692	exon1			AACCACAAATAGG	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"GPCR / Class A : Olfactory receptors"	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.624T>C	chr11.hg19:g.4869815A>G		90.0	0.0		46.0	16.0	NM_001004758	B9EGZ1|Q6IFI2	Silent	SNP	ENST00000322101.2	hg19	CCDS31362.1																																																																																			.	.		0.532	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758		G	4869815	A	G	4869815	2	3	109	1	0	0	0	0	0	0	0	1	11114	127	5	2		2	OR51S1	11	4869815	Silent	SNP	A	TCGA-DD-A39V-01A-11D-A20W-10		4869815	130136701	41	16167										
HOXC9	3225	hgsc.bcm.edu	37	chr12	54394044	54394044	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	cacgacaatgaagacctcctAgcgtccaggtttccggccac	9	15	0	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr12:54394044A>G	ENST00000303450.4	+	1	142	c.72A>G	c.(70-72)ctA>ctG	p.L24L	HOXC-AS1_ENST00000505700.1_RNA|HOXC9_ENST00000504557.1_Intron|HOXC9_ENST00000508190.1_Silent_p.L24L|HOXC-AS1_ENST00000512427.1_RNA|RP11-834C11.12_ENST00000513209.1_Intron	NM_006897.1	NP_008828.1	P31274	HXC9_HUMAN	homeobox C9	24					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(3)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14						AAGACCTCCTAGCGTCCAGGT	0.577																																					p.L24L		Atlas-SNP	.											.	HOXC9	25	.	0			c.A72G						.						54	55	54					12																	54394044		2203	4300	6503	SO:0001819	synonymous_variant	3225	exon1			CCTCCTAGCGTCC		CCDS8869.1	12q13.13	2011-06-20	2005-12-22			ENSG00000180806		"Homeoboxes / ANTP class : HOXL subclass"	5130	protein-coding gene	gene with protein product		142971	"homeo box C9"	HOX3, HOX3B		1973146	Standard	NM_006897		Approved		uc001seq.3	P31274		ENST00000303450.4:c.72A>G	chr12.hg19:g.54394044A>G		133.0	0.0		110.0	27.0	NM_006897	B2RCN7|Q9H1I0	Silent	SNP	ENST00000303450.4	hg19	CCDS8869.1																																																																																			.	.		0.577	HOXC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358958.1			G	54394044	A	G	54394044	2	3	109	1	0	0	0	0	0	0	0	1	7326	407	15	2		2	HOXC9	12	54394044	Silent	SNP	A	TCGA-DD-A39V-01A-11D-A20W-10		54394044	79457851	42	16168										
IKBIP	121457	hgsc.bcm.edu	37	chr12	99020519	99020519	+	Intron	DEL	T	T	-													0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	acatggatgatgtagcttccTgcaggatgctttcagtagac					rs375489943		TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr12:99020519delT	ENST00000342502.2	-	2	709				IKBIP_ENST00000299157.4_Frame_Shift_Del_p.Q108fs|IKBIP_ENST00000420861.1_Intron|IKBIP_ENST00000393042.3_Intron	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein						response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						TGTAGCTTCCTGCAGGATGCT	0.373																																					p.Q108fs		Atlas-Indel,Pindel	.											.	IKBIP	46	.	0			c.324delG						.						79	77	77					12																	99020519		2203	4299	6502	SO:0001627	intron_variant	121457	exon3			.	AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"I kappa B kinase interacting protein"	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.297+7554A>-	chr12.hg19:g.99020519delT		96.0	0.0		91.0	22.0	NM_153687	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Frame_Shift_Del	DEL	ENST00000342502.2	hg19	CCDS9067.1																																																																																			.	.		0.373	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687		-	99020519	T	-	99020519	6	5	109	0	1	1	0	1	0	0	0	0	7618	1580	55	0		0	IKBIP	12	99020519	Intron	DEL	T	TCGA-DD-A39V-01A-11D-A20W-10	44626475	99020519	34831376	43	16169										
NOS1	4842	hgsc.bcm.edu	37	chr12	117658021	117658022	+	Missense_Mutation	DNP	GG	GG	TT													0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tggcccccttgctccttcagGgctcggtacacagactccgc							TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr12:117658021_117658022GG>TT	ENST00000338101.4	-	27	4134_4135	c.4130_4131CC>AA	c.(4129-4131)gCC>gAA	p.A1377E	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.A1343E			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GCTCCTTCAGGGCTCGGTACAC	0.604																																					p.A1377A|p.A1377D	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C4131A|c.C4130A						.																																			SO:0001583	missense	4842	exon28			CTTCAGGGCTCGG|TTCAGGGCTCGGT		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.4130_4131delinsTT	chr12.hg19:g.117658021_117658022delinsTT	ENSP00000337459:p.Ala1377Glu	60.0	0.0		41.0|40.0	11.0	NM_001204218		Silent|Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1																																																																																			.	.		0.604	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			TT	117658022	GG	TT	117658021	3	4	109	1	0	0	0	0	1	0	0	0	10550	1219	43	3	287	3	NOS1	12	117658021	Missense_Mutation	DNP	GG	TCGA-DD-A39V-01A-11D-A20W-10	18637502	117658021	16193874	44	16170										
WASF3	10810	hgsc.bcm.edu	37	chr13	27255234	27255234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	attactcttacccggctactCccaaccattctctgcacccc	3	19	2	0			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr13:27255234C>T	ENST00000335327.5	+	8	938	c.760C>T	c.(760-762)Ccc>Tcc	p.P254S	WASF3_ENST00000361042.4_Missense_Mutation_p.P251S	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	254					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		CCCGGCTACTCCCAACCATTC	0.522																																					p.P254S		Atlas-SNP	.											.	WASF3	68	.	0			c.C760T						.						89	98	95					13																	27255234		2203	4300	6503	SO:0001583	missense	10810	exon8			GCTACTCCCAACC	AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.760C>T	chr13.hg19:g.27255234C>T	ENSP00000335055:p.Pro254Ser	209.0	0.0		107.0	32.0	NM_006646	O94974|Q86VQ2	Missense_Mutation	SNP	ENST00000335327.5	hg19	CCDS9318.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.860878	0.71834	.	.	ENSG00000132970	ENST00000361042;ENST00000335327	T;T	0.46451	0.87;0.88	5.94	5.94	0.96194	.	0.138542	0.64402	D	0.000003	T	0.45756	0.1358	M	0.69358	2.11	0.58432	D	0.999998	B;P	0.37141	0.434;0.584	B;B	0.34242	0.178;0.113	T	0.38499	-0.9658	10	0.37606	T	0.19	-29.0501	20.345	0.98787	0.0:1.0:0.0:0.0	.	251;254	Q86VQ2;Q9UPY6	.;WASF3_HUMAN	S	251;254	ENSP00000354325:P251S;ENSP00000335055:P254S	ENSP00000335055:P254S	P	+	1	0	WASF3	26153234	1.000000	0.71417	0.972000	0.41901	0.909000	0.53808	5.919000	0.70005	2.817000	0.96982	0.555000	0.69702	CCC	.	.		0.522	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1			T	27255234	C	T	27255234	3	4	109	1	0	0	0	0	1	0	0	0	17269	855	30	3	782	3	WASF3	13	27255234	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10		27255234	87914644	45	16171										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64497758	64497758	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tagagaatagactcagtttaCaagatggcacattaaagaag	9	5	1	4			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr14:64497758C>T	ENST00000344113.4	+	45	7116	c.6904C>T	c.(6904-6906)Caa>Taa	p.Q2302*	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Nonsense_Mutation_p.Q2302*|SYNE2_ENST00000358025.3_Nonsense_Mutation_p.Q2302*	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2302					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ACTCAGTTTACAAGATGGCAC	0.328																																					p.Q2302X		Atlas-SNP	.											.	SYNE2	577	.	0			c.C6904T						.						80	78	78					14																	64497758		1819	4082	5901	SO:0001587	stop_gained	23224	exon45			AGTTTACAAGATG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.6904C>T	chr14.hg19:g.64497758C>T	ENSP00000341781:p.Gln2302*	393.0	1.0		258.0	85.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Nonsense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	C	47	12.964400	0.99709	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	.	.	.	5.1	4.09	0.47781	.	0.468222	0.18438	N	0.141239	.	.	.	.	.	.	0.18873	N	0.999983	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	7.5303	0.27679	0.209:0.7009:0.0:0.0901	.	.	.	.	X	2302	.	ENSP00000261678:Q2302X	Q	+	1	0	SYNE2	63567511	0.968000	0.33430	0.939000	0.37840	0.986000	0.74619	0.565000	0.23578	2.521000	0.84997	0.462000	0.41574	CAA	.	.		0.328	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64497758	C	T	64497758	4	4	109	1	0	0	0	0	0	1	0	0	15461	479	17	3	7078	3	SYNE2	14	64497758	Nonsense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10		64497758	42851782	46	16172										
ZNF770	54989	hgsc.bcm.edu	37	chr15	35274530	35274530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	gctcaccagaaataagatcaCaatttctcaagaaactcttt	4	10	4	3			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr15:35274530C>T	ENST00000356321.4	-	3	1450	c.1106G>A	c.(1105-1107)tGt>tAt	p.C369Y		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	369					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		AATAAGATCACAATTTCTCAA	0.338																																					p.C369Y		Atlas-SNP	.											.	ZNF770	64	.	0			c.G1106A						.						27	30	29					15																	35274530		2193	4290	6483	SO:0001583	missense	54989	exon3			AGATCACAATTTC	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"Zinc fingers, C2H2-type"	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.1106G>A	chr15.hg19:g.35274530C>T	ENSP00000348673:p.Cys369Tyr	128.0	0.0		77.0	19.0	NM_014106	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	hg19	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.771374	0.00081	.	.	ENSG00000198146	ENST00000356321	T	0.08984	3.03	5.31	0.274	0.15654	.	0.867998	0.09875	N	0.744450	T	0.05593	0.0147	N	0.19112	0.55	0.09310	N	0.999994	B	0.06786	0.001	B	0.04013	0.001	T	0.39800	-0.9596	10	0.48119	T	0.1	2.3486	6.8583	0.24052	0.0:0.4639:0.1212:0.4149	.	369	Q6IQ21	ZN770_HUMAN	Y	369	ENSP00000348673:C369Y	ENSP00000348673:C369Y	C	-	2	0	ZNF770	33061822	0.000000	0.05858	0.004000	0.12327	0.797000	0.45037	-0.938000	0.03938	-0.082000	0.12640	-0.126000	0.14955	TGT	.	.		0.338	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106		T	35274530	C	T	35274530	3	4	109	1	0	0	0	0	1	0	0	0	18158	478	17	3	973	3	ZNF770	15	35274530	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10		35274530	67256862	47	16173										
DUOXA1	90527	hgsc.bcm.edu	37	chr15	45413291	45413291	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	gagccctccctcacctgtgaGtgtgatgttgactccaccca	9	15	1	3			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr15:45413291G>C	ENST00000560572.1	-	3	339	c.334C>G	c.(334-336)Ctc>Gtc	p.L112V	DUOXA1_ENST00000267803.4_Missense_Mutation_p.L112V|DUOXA1_ENST00000430224.2_Intron|DUOXA1_ENST00000559014.1_Missense_Mutation_p.L112V|DUOXA1_ENST00000558422.1_Intron|DUOXA1_ENST00000558996.1_Intron	NM_001276266.1	NP_001263195.1	Q1HG43	DOXA1_HUMAN	dual oxidase maturation factor 1	112					hydrogen peroxide metabolic process (GO:0042743)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)		TCACCTGTGAGTGTGATGTTG	0.557																																					p.L112V		Atlas-SNP	.											.	DUOXA1	32	.	0			c.C334G						.						100	67	78					15																	45413291		2198	4298	6496	SO:0001583	missense	90527	exon6			CTGTGAGTGTGAT	BC029819	CCDS10119.1, CCDS61619.1, CCDS61620.1, CCDS61621.1	15q21.1	2006-11-29	2006-01-23	2006-07-25	ENSG00000140254	ENSG00000140254			26507	protein-coding gene	gene with protein product		612771				16651268	Standard	NM_144565		Approved	FLJ32334, NUMBIP, NIP, mol	uc010bec.4	Q1HG43	OTTHUMG00000131352	ENST00000560572.1:c.334C>G	chr15.hg19:g.45413291G>C	ENSP00000454084:p.Leu112Val	115.0	0.0		110.0	37.0	NM_144565	Q8N6K9|Q96MI4	Missense_Mutation	SNP	ENST00000560572.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.98	2.992171	0.54041	.	.	ENSG00000140254	ENST00000267803	T	0.69806	-0.43	5.11	4.18	0.49190	.	0.067850	0.64402	D	0.000010	D	0.83046	0.5169	M	0.87547	2.89	0.45995	D	0.998801	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.85935	0.1454	10	0.62326	D	0.03	-23.9957	13.8867	0.63712	0.0:0.0:0.8349:0.1651	.	112;112	Q1HG43;A8K9Q6	DOXA1_HUMAN;.	V	112	ENSP00000267803:L112V	ENSP00000267803:L112V	L	-	1	0	DUOXA1	43200583	1.000000	0.71417	0.874000	0.34290	0.438000	0.31896	5.000000	0.63940	1.349000	0.45751	-0.284000	0.09977	CTC	.	.		0.557	DUOXA1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000416242.1	NM_144565		C	45413291	G	C	45413291	3	2	109	1	0	0	0	0	1	0	0	0	4804	1029	36	4	1141	4	DUOXA1	15	45413291	Missense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	10138761	45413291	57118101	48	16174										
DIS3L	115752	hgsc.bcm.edu	37	chr15	66604085	66604085	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tacctggacaatttctggccTgatttaaaagctgcccacga	8	11	1	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr15:66604085T>A	ENST00000319212.4	+	5	632	c.582T>A	c.(580-582)ccT>ccA	p.P194P	DIS3L_ENST00000319194.5_Silent_p.P111P|DIS3L_ENST00000441424.2_Silent_p.P60P	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	194					RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						ATTTCTGGCCTGATTTAAAAG	0.453																																					p.P194P		Atlas-SNP	.											.	DIS3L	175	.	0			c.T582A						.						119	121	120					15																	66604085		2201	4299	6500	SO:0001819	synonymous_variant	115752	exon5			CTGGCCTGATTTA		CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938			28698	protein-coding gene	gene with protein product		614183	"DIS3 mitotic control homolog (S. cerevisiae)-like"			20531386	Standard	NM_001143688		Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.582T>A	chr15.hg19:g.66604085T>A		63.0	0.0		30.0	12.0	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Silent	SNP	ENST00000319212.4	hg19	CCDS45286.1																																																																																			.	.		0.453	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375		A	66604085	T	A	66604085	2	1	109	1	0	0	0	0	0	0	0	1	4538	1567	55	4		4	DIS3L	15	66604085	Silent	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10	21190794	66604085	35927307	49	16175										
FBXL16	146330	hgsc.bcm.edu	37	chr16	745857	745857	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	caggctggaccacagcccggCctcggtgaagtcgttgcagc	14	14	0	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr16:745857C>A	ENST00000397621.1	-	3	1031	c.700G>T	c.(700-702)Gcc>Tcc	p.A234S	FBXL16_ENST00000562563.1_Missense_Mutation_p.A22S|FBXL16_ENST00000324361.5_Missense_Mutation_p.A234S|FBXL16_ENST00000562585.1_5'Flank	NM_153350.3	NP_699181.2	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	234										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)	10		Hepatocellular(780;0.0218)				CACAGCCCGGCCTCGGTGAAG	0.667																																					p.A234S		Atlas-SNP	.											.	FBXL16	25	.	0			c.G700T						.						27	27	27					16																	745857		2199	4288	6487	SO:0001583	missense	146330	exon3			GCCCGGCCTCGGT	BC036680	CCDS10421.1	16p13.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000127585	ENSG00000127585		"F-boxes / Leucine-rich repeats"	14150	protein-coding gene	gene with protein product		609082	"chromosome 16 open reading frame 22"	C16orf22		11157797	Standard	NM_153350		Approved	MGC33974, Fbl16	uc021taa.1	Q8N461	OTTHUMG00000090420	ENST00000397621.1:c.700G>T	chr16.hg19:g.745857C>A	ENSP00000380746:p.Ala234Ser	195.0	0.0		111.0	47.0	NM_153350	B3KR59|D3DU60|Q2MHR2|Q96S14|Q9UJI0	Missense_Mutation	SNP	ENST00000397621.1	hg19	CCDS10421.1	.	.	.	.	.	.	.	.	.	.	c	16.81	3.225517	0.58668	.	.	ENSG00000127585	ENST00000397621;ENST00000324361	T;T	0.16457	2.34;2.34	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.35068	0.0919	L	0.56199	1.76	0.58432	D	0.999994	D	0.76494	0.999	D	0.70016	0.967	T	0.01810	-1.1269	10	0.22109	T	0.4	.	16.7252	0.85419	0.0:1.0:0.0:0.0	.	234	Q8N461	FXL16_HUMAN	S	234	ENSP00000380746:A234S;ENSP00000318674:A234S	ENSP00000318674:A234S	A	-	1	0	FBXL16	685858	1.000000	0.71417	0.943000	0.38184	0.962000	0.63368	5.811000	0.69187	2.529000	0.85273	0.561000	0.74099	GCC	.	.		0.667	FBXL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206851.2	NM_153350		A	745857	C	A	745857	3	1	109	1	0	0	0	0	1	0	0	0	5720	739	26	3	755	3	FBXL16	16	745857	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10		745857	89608896	50	16176										
PDF	64146	hgsc.bcm.edu	37	chr16	69363005	69363005	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	aaacaggcagccctgcaggtGgtccatctcgtgctggatga	13	11	1	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr16:69363005G>T	ENST00000288022.1	-	2	676	c.652C>A	c.(652-654)Cac>Aac	p.H218N	RP11-343C2.12_ENST00000562949.1_Silent_p.T143T|COG8_ENST00000306875.4_3'UTR|COG8_ENST00000564419.1_5'Flank	NM_022341.1	NP_071736.1	Q9HBH1	DEFM_HUMAN	peptide deformylase (mitochondrial)	218					N-terminal protein amino acid modification (GO:0031365)|peptidyl-methionine modification (GO:0018206)|positive regulation of cell proliferation (GO:0008284)|translation (GO:0006412)	mitochondrion (GO:0005739)	iron ion binding (GO:0005506)|peptide deformylase activity (GO:0042586)			NS(1)|prostate(1)	2						CCCTGCAGGTGGTCCATCTCG	0.552																																					p.H218N		Atlas-SNP	.											.	PDF	4	.	0			c.C652A						.						93	82	86					16																	69363005		2198	4300	6498	SO:0001583	missense	64146	exon2			GCAGGTGGTCCAT	AF239156	CCDS10875.1	16q22.1	2008-02-05				ENSG00000258429	3.5.1.88		30012	protein-coding gene	gene with protein product						11060042, 15489958	Standard	NM_022341		Approved		uc002ewx.1	Q9HBH1		ENST00000288022.1:c.652C>A	chr16.hg19:g.69363005G>T	ENSP00000288022:p.His218Asn	83.0	0.0		67.0	23.0	NM_022341	Q8WUN6	Missense_Mutation	SNP	ENST00000288022.1	hg19	CCDS10875.1	.	.	.	.	.	.	.	.	.	.	g	28.2	4.900835	0.92035	.	.	ENSG00000258429	ENST00000288022	T	0.75477	-0.94	4.95	3.96	0.45880	Peptide deformylase (3);	0.000000	0.85682	U	0.000000	D	0.91781	0.7400	H	0.99074	4.42	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.94588	0.7785	10	0.87932	D	0	.	14.1757	0.65539	0.0:0.0:0.8487:0.1513	.	218	Q9HBH1	DEFM_HUMAN	N	218	ENSP00000288022:H218N	ENSP00000288022:H218N	H	-	1	0	PDF	67920506	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.159000	0.71856	1.126000	0.42016	0.556000	0.70494	CAC	.	.		0.552	PDF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413022.1	NM_022341		T	69363005	G	T	69363005	3	4	109	1	0	0	0	0	1	0	0	0	11665	1348	47	3	83	3	PDF	16	69363005	Missense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	68617148	69363005	20991748	51	16177										
WDR81	124997	hgsc.bcm.edu	37	chr17	1634133	1634133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ctaccagaagaggccggtccTgggcgacatcgtgtcagggc	15	12	1	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr17:1634133T>C	ENST00000409644.1	+	3	3860	c.3860T>C	c.(3859-3861)cTg>cCg	p.L1287P	WDR81_ENST00000419248.1_Missense_Mutation_p.L60P|WDR81_ENST00000545662.1_5'UTR|WDR81_ENST00000437219.2_Missense_Mutation_p.L84P|WDR81_ENST00000309182.5_Missense_Mutation_p.L236P|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000446363.1_5'UTR	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1287					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGGCCGGTCCTGGGCGACATC	0.652																																					p.L1287P		Atlas-SNP	.											.	WDR81	180	.	0			c.T3860C						.						56	57	56					17																	1634133		2203	4298	6501	SO:0001583	missense	124997	exon3			CGGTCCTGGGCGA	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"WD repeat domain containing"	26600	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 166"	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.3860T>C	chr17.hg19:g.1634133T>C	ENSP00000386609:p.Leu1287Pro	119.0	0.0		80.0	29.0	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	hg19	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	T	14.13	2.443927	0.43429	.	.	ENSG00000167716	ENST00000455636;ENST00000437219;ENST00000309182;ENST00000419248;ENST00000409644	T;T;T;T	0.54866	2.34;2.31;2.34;0.55	5.52	5.52	0.82312	.	0.303270	0.30519	N	0.009457	T	0.49081	0.1536	L	0.40543	1.245	0.80722	D	1	P;D;P	0.53885	0.681;0.963;0.828	B;P;B	0.46585	0.255;0.521;0.255	T	0.53507	-0.8429	10	0.66056	D	0.02	.	11.6173	0.51096	0.0:0.0:0.1486:0.8514	.	84;414;236	B7Z579;Q8TEL1;Q562E7	.;.;WDR81_HUMAN	P	84;84;236;60;1287	ENSP00000391074:L84P;ENSP00000312074:L236P;ENSP00000407845:L60P;ENSP00000386609:L1287P	ENSP00000312074:L236P	L	+	2	0	WDR81	1580883	1.000000	0.71417	0.853000	0.33588	0.197000	0.23852	4.938000	0.63519	2.099000	0.63709	0.533000	0.62120	CTG	.	.		0.652	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		C	1634133	T	C	1634133	3	2	109	1	0	0	0	0	1	0	0	0	17345	1580	55	2	3932	2	WDR81	17	1634133	Missense_Mutation	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10		1634133	79561077	52	16178										
DHX33	56919	hgsc.bcm.edu	37	chr17	5365670	5365670	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	gtttcccgagttcctttctcCtcttctgtgcagctttcacc	6	15	4	0			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr17:5365670C>A	ENST00000225296.3	-	3	847	c.647G>T	c.(646-648)aGg>aTg	p.R216M	DHX33_ENST00000433302.3_Intron	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	216	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TTCCTTTCTCCTCTTCTGTGC	0.463																																					p.R216M		Atlas-SNP	.											.	DHX33	41	.	0			c.G647T						.						72	64	66					17																	5365670		2203	4300	6503	SO:0001583	missense	56919	exon3			TTTCTCCTCTTCT	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"DEAH-boxes"	16718	protein-coding gene	gene with protein product		614405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.647G>T	chr17.hg19:g.5365670C>A	ENSP00000225296:p.Arg216Met	202.0	0.0		185.0	57.0	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	hg19	CCDS11072.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.772278	0.69992	.	.	ENSG00000005100	ENST00000225296	T	0.14266	2.52	5.78	3.72	0.42706	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.240452	0.50627	D	0.000115	T	0.27629	0.0679	M	0.82433	2.59	0.80722	D	1	P	0.52463	0.953	P	0.53954	0.738	T	0.03077	-1.1075	10	0.66056	D	0.02	.	5.8526	0.18701	0.0:0.6422:0.0:0.3578	.	216	Q9H6R0	DHX33_HUMAN	M	216	ENSP00000225296:R216M	ENSP00000225296:R216M	R	-	2	0	DHX33	5306394	0.999000	0.42202	0.999000	0.59377	0.983000	0.72400	1.732000	0.38146	1.386000	0.46466	-0.384000	0.06662	AGG	.	.		0.463	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162		A	5365670	C	A	5365670	3	1	109	1	0	0	0	0	1	0	0	0	4508	681	24	3	1516	3	DHX33	17	5365670	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	3731537	5365670	75829540	53	16179										
BRCA1	672	hgsc.bcm.edu	37	chr17	41203109	41203109	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tgttggtgaagggcccatagCaacagatttctagccccctg	11	11	1	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr17:41203109C>T	ENST00000357654.3	-	20	5421	c.5303G>A	c.(5302-5304)tGc>tAc	p.C1768Y	BRCA1_ENST00000591534.1_Missense_Mutation_p.C259Y|BRCA1_ENST00000346315.3_Missense_Mutation_p.C1529Y|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Missense_Mutation_p.C78Y|BRCA1_ENST00000493795.1_Missense_Mutation_p.C1721Y|BRCA1_ENST00000309486.4_Missense_Mutation_p.C1472Y|BRCA1_ENST00000468300.1_Missense_Mutation_p.C664Y|BRCA1_ENST00000354071.3_Missense_Mutation_p.C1503Y|BRCA1_ENST00000352993.3_Missense_Mutation_p.C626Y|BRCA1_ENST00000471181.2_Missense_Mutation_p.C1789Y|BRCA1_ENST00000351666.3_Missense_Mutation_p.C585Y|BRCA1_ENST00000491747.2_Missense_Mutation_p.C664Y	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1768	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GGGCCCATAGCAACAGATTTC	0.468			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.C1789Y		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.G5366A						.						70	69	69					17																	41203109		2203	4300	6503	SO:0001583	missense	672	exon21	Familial Cancer Database		CCATAGCAACAGA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.5303G>A	chr17.hg19:g.41203109C>T	ENSP00000350283:p.Cys1768Tyr	101.0	0.0		59.0	20.0	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	hg19	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.651732	0.67472	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000352993;ENST00000346315;ENST00000351666;ENST00000309486;ENST00000468300;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747	T;T;T;T;T;T;D;T;T;T	0.88431	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-2.38;-1.3;-1.3;-1.02	5.06	5.06	0.68205	BRCT (4);	0.000000	0.56097	D	0.000025	D	0.93265	0.7854	M	0.66939	2.045	0.38133	D	0.938226	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.984;1.0	D;D;D;D;D;P;D	0.97110	1.0;0.984;1.0;0.999;1.0;0.552;1.0	D	0.94247	0.7490	10	0.87932	D	0	.	14.1279	0.65233	0.0:1.0:0.0:0.0	.	617;78;663;664;1790;1768;1768	B4DES0;C6YB45;E7ETR2;Q6IN79;E9PFC7;P38398;P38398-2	.;.;.;.;.;BRCA1_HUMAN;.	Y	1768;1789;1503;626;1529;585;1472;664;617;1790;1721;663	ENSP00000350283:C1768Y;ENSP00000326002:C1503Y;ENSP00000312236:C626Y;ENSP00000246907:C1529Y;ENSP00000338007:C585Y;ENSP00000310938:C1472Y;ENSP00000417148:C664Y;ENSP00000377294:C617Y;ENSP00000418775:C1721Y;ENSP00000420705:C663Y	ENSP00000310938:C1472Y	C	-	2	0	BRCA1	38456635	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	4.302000	0.59092	2.793000	0.96121	0.561000	0.74099	TGC	.	.		0.468	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		T	41203109	C	T	41203109	3	4	109	1	0	0	0	0	1	0	0	0	1500	710	25	3	304	3	BRCA1	17	41203109	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	35837439	41203109	39992101	54	16180										
ATXN7L3	56970	hgsc.bcm.edu	37	chr17	42273177	42273177	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	cccatactcaccttaaaaggAtccgaattgctaagttcccc	5	14	1	0			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr17:42273177A>T	ENST00000454077.2	-	7	563	c.564T>A	c.(562-564)gaT>gaA	p.D188E	ATXN7L3_ENST00000593073.1_Intron|ATXN7L3_ENST00000389384.4_Missense_Mutation_p.D181E	NM_020218.1	NP_064603.1			ataxin 7-like 3											kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	12		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		CCTTAAAAGGATCCGAATTGC	0.488																																					p.D188E		Atlas-SNP	.											.	ATXN7L3	31	.	0			c.T564A						.						69	70	70					17																	42273177		1943	4129	6072	SO:0001583	missense	56970	exon7			AAAAGGATCCGAA	AK056002	CCDS42345.1, CCDS45697.1	17q21	2010-03-10			ENSG00000087152	ENSG00000087152			25416	protein-coding gene	gene with protein product						15115762	Standard	NM_001098833		Approved	DKFZp761G2113	uc002ifz.3	Q14CW9		ENST00000454077.2:c.564T>A	chr17.hg19:g.42273177A>T	ENSP00000397259:p.Asp188Glu	68.0	0.0		39.0	13.0	NM_020218		Missense_Mutation	SNP	ENST00000454077.2	hg19	CCDS45697.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.581899	0.28180	.	.	ENSG00000087152	ENST00000454077;ENST00000389384	.	.	.	5.23	3.03	0.35002	.	0.278174	0.33610	N	0.004737	T	0.17789	0.0427	N	0.08118	0	0.30721	N	0.748235	B;B	0.11235	0.002;0.004	B;B	0.06405	0.001;0.002	T	0.21042	-1.0257	9	0.09084	T	0.74	.	7.0771	0.25211	0.749:0.0:0.2509:0.0	.	181;188	Q14CW9;Q14CW9-2	AT7L3_HUMAN;.	E	188;181	.	ENSP00000374035:D181E	D	-	3	2	ATXN7L3	39628703	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	1.507000	0.35758	0.838000	0.34948	0.454000	0.30748	GAT	.	.		0.488	ATXN7L3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457724.1			T	42273177	A	T	42273177	3	4	109	1	0	0	0	0	1	0	0	0	1218	330	12	4	524	4	ATXN7L3	17	42273177	Missense_Mutation	SNP	A	TCGA-DD-A39V-01A-11D-A20W-10	1070068	42273177	38922033	55	16181										
MRC2	9902	hgsc.bcm.edu	37	chr17	60767531	60767531	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ccacagggccccctcctcccCgaagaataagctaccatggc	8	18	0	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr17:60767531C>A	ENST00000303375.5	+	26	4159	c.3757C>A	c.(3757-3759)Cga>Aga	p.R1253R	MRC2_ENST00000446119.2_Silent_p.R119R	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1253					collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						CCCTCCTCCCCGAAGAATAAG	0.642																																					p.R1253R		Atlas-SNP	.											.	MRC2	126	.	0			c.C3757A						.						35	43	40					17																	60767531		2203	4300	6503	SO:0001819	synonymous_variant	9902	exon26			CCTCCCCGAAGAA	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3757C>A	chr17.hg19:g.60767531C>A		366.0	1.0		252.0	74.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	hg19	CCDS11634.1																																																																																			.	.		0.642	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			A	60767531	C	A	60767531	2	1	109	1	0	0	0	0	0	0	0	1	9767	644	23	1		1	MRC2	17	60767531	Silent	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	18494354	60767531	20427679	56	16182										
ABCA10	10349	hgsc.bcm.edu	37	chr17	67210857	67210857	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	taacttaccaggtaaaactcGctcaaaatataatgtgaata	5	7	1	1	rs200246933		TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr17:67210857G>A	ENST00000269081.4	-	10	1903	c.994C>T	c.(994-996)Cga>Tga	p.R332*	ABCA10_ENST00000432313.2_Nonsense_Mutation_p.R332*|ABCA10_ENST00000416101.2_Nonsense_Mutation_p.R332*	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	332					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					GGTAAAACTCGCTCAAAATAT	0.279																																					p.R332X		Atlas-SNP	.											.	ABCA10	209	.	0			c.C994T						.						51	58	56					17																	67210857		2202	4288	6490	SO:0001587	stop_gained	10349	exon10			AAACTCGCTCAAA	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.994C>T	chr17.hg19:g.67210857G>A	ENSP00000269081:p.Arg332*	127.0	0.0		95.0	24.0	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Nonsense_Mutation	SNP	ENST00000269081.4	hg19	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	G	42	9.592029	0.99214	.	.	ENSG00000154263	ENST00000269081;ENST00000416101;ENST00000432313	.	.	.	3.34	-4.56	0.03431	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	7.6125	0.28139	0.1097:0.0:0.1764:0.7139	.	.	.	.	X	332	.	ENSP00000269081:R332X	R	-	1	2	ABCA10	64722452	0.000000	0.05858	0.002000	0.10522	0.831000	0.47069	-0.215000	0.09279	-0.507000	0.06549	0.508000	0.49915	CGA	.	G|1.000;C|0.000		0.279	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		A	67210857	G	A	67210857	4	1	109	1	0	0	0	0	0	1	0	0	29	1095	38	1	3761	1	ABCA10	17	67210857	Nonsense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	6443326	67210857	13984353	57	16183										
SLC26A11	284129	hgsc.bcm.edu	37	chr17	78222437	78222437	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tgtccttccctgccatggagGctctgcgggaggagatccta	13	12	1	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr17:78222437G>A	ENST00000361193.3	+	15	1766	c.1486G>A	c.(1486-1488)Gct>Act	p.A496T	SLC26A11_ENST00000411502.3_Missense_Mutation_p.A496T|SLC26A11_ENST00000546047.2_Missense_Mutation_p.A496T|SLC26A11_ENST00000572725.1_Missense_Mutation_p.A496T	NM_001166347.1|NM_173626.3	NP_001159819.1|NP_775897.3			solute carrier family 26 (anion exchanger), member 11											central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	28	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TGCCATGGAGGCTCTGCGGGA	0.687																																					p.A496T		Atlas-SNP	.											.	SLC26A11	60	.	0			c.G1486A						.						21	24	23					17																	78222437		2194	4292	6486	SO:0001583	missense	284129	exon15			ATGGAGGCTCTGC		CCDS11771.2	17q25	2013-07-18	2013-07-18		ENSG00000181045	ENSG00000181045		"Solute carriers"	14471	protein-coding gene	gene with protein product		610117	"solute carrier family 26, member 11"				Standard	NM_001166347		Approved		uc010dhv.2	Q86WA9	OTTHUMG00000133419	ENST00000361193.3:c.1486G>A	chr17.hg19:g.78222437G>A	ENSP00000355384:p.Ala496Thr	249.0	0.0		186.0	56.0	NM_173626		Missense_Mutation	SNP	ENST00000361193.3	hg19	CCDS11771.2	.	.	.	.	.	.	.	.	.	.	G	6.373	0.436940	0.12104	.	.	ENSG00000181045	ENST00000411502;ENST00000546047;ENST00000361193	D;D;D	0.87887	-2.31;-2.31;-2.31	4.47	-1.4	0.08968	Sulphate transporter/antisigma-factor antagonist STAS (4);	0.521522	0.20560	N	0.089924	T	0.66577	0.2803	N	0.08118	0	0.22171	N	0.999318	B	0.06786	0.001	B	0.11329	0.006	T	0.54636	-0.8264	10	0.45353	T	0.12	-16.4291	1.5866	0.02645	0.3551:0.1344:0.3737:0.1367	.	496	Q86WA9	S2611_HUMAN	T	496	ENSP00000403998:A496T;ENSP00000440724:A496T;ENSP00000355384:A496T	ENSP00000355384:A496T	A	+	1	0	SLC26A11	75837032	0.011000	0.17503	0.040000	0.18447	0.027000	0.11550	-0.424000	0.07025	-0.138000	0.11434	0.467000	0.42956	GCT	.	.		0.687	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1			A	78222437	G	A	78222437	3	1	109	1	0	0	0	0	1	0	0	0	14531	1203	42	3	1536	3	SLC26A11	17	78222437	Missense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	11011580	78222437	2972773	58	16184										
NOL4	8715	hgsc.bcm.edu	37	chr18	31685081	31685081	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ctgagcagctcattagaaatCgtgtcaccgcttctcttggt	9	11	3	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr18:31685081C>T	ENST00000261592.5	-	3	755	c.458G>A	c.(457-459)cGa>cAa	p.R153Q	NOL4_ENST00000535475.1_5'UTR|NOL4_ENST00000589544.1_Missense_Mutation_p.R153Q|NOL4_ENST00000538587.1_Missense_Mutation_p.R79Q|NOL4_ENST00000269185.4_Missense_Mutation_p.R39Q	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	153						nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						CATTAGAAATCGTGTCACCGC	0.383																																					p.R153Q		Atlas-SNP	.											.	NOL4	139	.	0			c.G458A						.						178	167	171					18																	31685081		2203	4299	6502	SO:0001583	missense	8715	exon3			AGAAATCGTGTCA	AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.458G>A	chr18.hg19:g.31685081C>T	ENSP00000261592:p.Arg153Gln	180.0	0.0		147.0	56.0	NM_003787	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Missense_Mutation	SNP	ENST00000261592.5	hg19	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	C	32	5.139103	0.94560	.	.	ENSG00000101746	ENST00000261592;ENST00000269185;ENST00000538587	.	.	.	5.38	5.38	0.77491	.	0.114059	0.38663	N	0.001607	T	0.78071	0.4226	L	0.61218	1.895	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;0.997;0.998	D;D;D;D	0.85130	0.997;0.964;0.964;0.986	T	0.79555	-0.1755	9	0.87932	D	0	-9.9234	18.4847	0.90824	0.0:1.0:0.0:0.0	.	39;79;153;153	B4DLW2;B4DSQ0;O94818;O94818-2	.;.;NOL4_HUMAN;.	Q	153;39;79	.	ENSP00000261592:R153Q	R	-	2	0	NOL4	29939079	1.000000	0.71417	0.985000	0.45067	0.998000	0.95712	7.289000	0.78701	2.677000	0.91161	0.563000	0.77884	CGA	.	.		0.383	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		T	31685081	C	T	31685081	3	4	109	1	0	0	0	0	1	0	0	0	10533	884	31	1	1494	1	NOL4	18	31685081	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10		31685081	46392167	59	16185										
THEG	51298	hgsc.bcm.edu	37	chr19	375911	375911	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ccgtcctgctccctttccgaCctgcccgcagcctcagagct	8	20	1	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr19:375911C>A	ENST00000342640.4	-	1	102	c.60G>T	c.(58-60)agG>agT	p.R20S	THEG_ENST00000346878.2_Missense_Mutation_p.R20S	NM_016585.4	NP_057669.1	Q9P2T0	THEG_HUMAN	theg spermatid protein	20					cell differentiation (GO:0030154)|chaperone-mediated protein complex assembly (GO:0051131)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)				NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)|soft_tissue(1)	29		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCTTTCCGACCTGCCCGCAG	0.692																																					p.R20S		Atlas-SNP	.											.	THEG	58	.	0			c.G60T						.						37	37	37					19																	375911		2203	4299	6502	SO:0001583	missense	51298	exon1			TTCCGACCTGCCC	AF268610	CCDS12025.1, CCDS12026.1	19p13.3	2012-02-24	2012-02-24		ENSG00000105549	ENSG00000105549			13706	protein-coding gene	gene with protein product	"cancer/testis antigen 56"	609503	"Theg homolog (mouse)"			11173852	Standard	NM_016585		Approved	CT56, THEG1	uc002lol.3	Q9P2T0	OTTHUMG00000165491	ENST00000342640.4:c.60G>T	chr19.hg19:g.375911C>A	ENSP00000340088:p.Arg20Ser	40.0	0.0		46.0	10.0	NM_016585	A6NMJ8	Missense_Mutation	SNP	ENST00000342640.4	hg19	CCDS12025.1	.	.	.	.	.	.	.	.	.	.	C	8.562	0.877921	0.17395	.	.	ENSG00000105549	ENST00000342640;ENST00000346878	T;T	0.18502	2.21;2.21	3.4	-1.53	0.08611	.	2.627730	0.01505	N	0.017697	T	0.09862	0.0242	N	0.14661	0.345	0.09310	N	1	B;B	0.21452	0.056;0.056	B;B	0.16289	0.015;0.015	T	0.21965	-1.0230	10	0.27082	T	0.32	-24.1828	5.0668	0.14585	0.0:0.4646:0.3269:0.2085	.	20;20	Q9P2T0-2;Q9P2T0	.;THEG_HUMAN	S	20	ENSP00000340088:R20S;ENSP00000264820:R20S	ENSP00000340088:R20S	R	-	3	2	THEG	326911	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.928000	0.03980	-0.168000	0.10853	-0.314000	0.08810	AGG	.	.		0.692	THEG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384431.2			A	375911	C	A	375911	3	1	109	1	0	0	0	0	1	0	0	0	15872	506	18	3	1111	3	THEG	19	375911	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10		375911	58753072	60	16186										
ZNF77	58492	hgsc.bcm.edu	37	chr19	2934207	2934207	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tctctaaaggaggagtaacaGctgaatgattttccacaatg	9	7	1	2			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr19:2934207G>A	ENST00000314531.4	-	4	1010	c.918C>T	c.(916-918)agC>agT	p.S306S		NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	306					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGAGTAACAGCTGAATGATT	0.458																																					p.S306S		Atlas-SNP	.											.	ZNF77	47	.	0			c.C918T						.						192	173	179					19																	2934207		2203	4300	6503	SO:0001819	synonymous_variant	58492	exon4			GTAACAGCTGAAT	X65230	CCDS12099.1	19p13.3	2013-01-08	2006-05-12					"Zinc fingers, C2H2-type", "-"	13150	protein-coding gene	gene with protein product		194551	"zinc finger protein 77 (pT1)"			8478004	Standard	NM_021217		Approved	pT1	uc002lws.4	Q15935		ENST00000314531.4:c.918C>T	chr19.hg19:g.2934207G>A		198.0	0.0		157.0	78.0	NM_021217	Q86XJ3|Q9NPP0	Silent	SNP	ENST00000314531.4	hg19	CCDS12099.1																																																																																			.	.		0.458	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217		A	2934207	G	A	2934207	2	1	109	1	0	0	0	0	0	0	0	1	18157	962	34	3		3	ZNF77	19	2934207	Silent	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	2558296	2934207	56194776	61	16187										
QTRT1	81890	hgsc.bcm.edu	37	chr19	10823446	10823446	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tcccacagcgctttggctctGccctggtgcccactgggaac	11	16	1	0			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr19:10823446G>T	ENST00000250237.5	+	8	884	c.874G>T	c.(874-876)Gcc>Tcc	p.A292S		NM_031209.2	NP_112486.1	Q9BXR0	TGT_HUMAN	queuine tRNA-ribosyltransferase 1	292					queuosine biosynthetic process (GO:0008616)|tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|queuine tRNA-ribosyltransferase activity (GO:0008479)			large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12			Epithelial(33;1.55e-05)|all cancers(31;3.42e-05)			CTTTGGCTCTGCCCTGGTGCC	0.622																																					p.A292S		Atlas-SNP	.											QTRT1,middle_lobe,carcinoma,0,1	QTRT1	25	.	0			c.G874T						.						114	108	110					19																	10823446		2203	4300	6503	SO:0001583	missense	81890	exon8			GGCTCTGCCCTGG	AF302783	CCDS12248.1	19p13.3	2014-06-11	2008-07-31		ENSG00000213339	ENSG00000213339	2.4.2.29		23797	protein-coding gene	gene with protein product	"tRNA-guanine transglycosylase"	609615				20354154	Standard	NM_031209		Approved	TGT	uc002mpr.3	Q9BXR0		ENST00000250237.5:c.874G>T	chr19.hg19:g.10823446G>T	ENSP00000250237:p.Ala292Ser	82.0	0.0		103.0	54.0	NM_031209	B4DFM7|Q96BQ4|Q9BXQ9	Missense_Mutation	SNP	ENST00000250237.5	hg19	CCDS12248.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.765824	0.69878	.	.	ENSG00000213339	ENST00000250237	.	.	.	3.87	3.87	0.44632	.	0.074633	0.52532	U	0.000062	D	0.87120	0.6098	H	0.97732	4.065	0.54753	D	0.999989	D	0.89917	1.0	D	0.97110	1.0	D	0.90943	0.4799	9	0.72032	D	0.01	-5.5173	12.8457	0.57829	0.0:0.0:1.0:0.0	.	292	Q9BXR0	TGT_HUMAN	S	292	.	ENSP00000250237:A292S	A	+	1	0	QTRT1	10684446	1.000000	0.71417	0.994000	0.49952	0.812000	0.45895	6.497000	0.73674	2.005000	0.58758	0.462000	0.41574	GCC	.	.		0.622	QTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452086.1	NM_031209		T	10823446	G	T	10823446	3	4	109	1	0	0	0	0	1	0	0	0	12900	1319	46	3	904	3	QTRT1	19	10823446	Missense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	7889239	10823446	48305537	62	16188										
GMIP	51291	hgsc.bcm.edu	37	chr19	19745726	19745726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	acggacccgggacccgctgaCccggtaaatgccctgcaggg	14	15	0	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr19:19745726C>T	ENST00000203556.4	-	17	1899	c.1762G>A	c.(1762-1764)Gtc>Atc	p.V588I	GMIP_ENST00000587238.1_Missense_Mutation_p.V562I|GMIP_ENST00000445806.2_Missense_Mutation_p.V559I|GMIP_ENST00000586269.1_5'UTR	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	588	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				intracellular signal transduction (GO:0035556)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						GACCCGCTGACCCGGTAAATG	0.607																																					p.V588I		Atlas-SNP	.											.	GMIP	55	.	0			c.G1762A						.						49	55	53					19																	19745726		2203	4300	6503	SO:0001583	missense	51291	exon17			CGCTGACCCGGTA	AF132541	CCDS12408.1, CCDS74318.1	19p13.11	2011-09-07				ENSG00000089639		"Rho GTPase activating proteins"	24852	protein-coding gene	gene with protein product		609694				12093360, 16086184	Standard	XM_005259927		Approved	ARHGAP46	uc002nnd.3	Q9P107		ENST00000203556.4:c.1762G>A	chr19.hg19:g.19745726C>T	ENSP00000203556:p.Val588Ile	69.0	0.0		83.0	25.0	NM_016573	A0AVN9|B7ZLZ0	Missense_Mutation	SNP	ENST00000203556.4	hg19	CCDS12408.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165659	0.38217	.	.	ENSG00000089639	ENST00000203556;ENST00000445806	T;T	0.20881	2.04;2.04	5.26	1.49	0.22878	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.558531	0.14956	N	0.288632	T	0.15392	0.0371	L	0.43598	1.365	0.28324	N	0.922096	P;B;P	0.34724	0.465;0.096;0.465	B;B;B	0.33392	0.152;0.163;0.152	T	0.12734	-1.0536	10	0.29301	T	0.29	-19.9459	7.5898	0.28015	0.0:0.6185:0.0:0.3815	.	559;562;588	E7ERB7;B7ZLZ0;Q9P107	.;.;GMIP_HUMAN	I	588;559	ENSP00000203556:V588I;ENSP00000397075:V559I	ENSP00000203556:V588I	V	-	1	0	GMIP	19606726	0.511000	0.26179	1.000000	0.80357	0.950000	0.60333	1.086000	0.30853	0.615000	0.30124	0.561000	0.74099	GTC	.	.		0.607	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573		T	19745726	C	T	19745726	3	4	109	1	0	0	0	0	1	0	0	0	6499	507	18	3	1170	3	GMIP	19	19745726	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	8922280	19745726	39383257	63	16189										
ZNF577	84765	hgsc.bcm.edu	37	chr19	52375810	52375810	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ctgatacaatatctgtaagaTacaagatataatttattact	4	5	1	3			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr19:52375810T>G	ENST00000301399.5	-	7	1798	c.1433A>C	c.(1432-1434)tAt>tCt	p.Y478S	ZNF577_ENST00000420592.1_Missense_Mutation_p.Y419S|ZNF577_ENST00000451628.2_Missense_Mutation_p.Y419S|ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000485702.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	478					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		ATCTGTAAGATACAAGATATA	0.353																																					p.Y478S		Atlas-SNP	.											.	ZNF577	63	.	0			c.A1433C						.						40	40	40					19																	52375810		2202	4300	6502	SO:0001583	missense	84765	exon7			GTAAGATACAAGA	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"Zinc fingers, C2H2-type", "-"	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1433A>C	chr19.hg19:g.52375810T>G	ENSP00000301399:p.Tyr478Ser	57.0	0.0		69.0	24.0	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	hg19	CCDS12842.2	.	.	.	.	.	.	.	.	.	.	.	6.263	0.416682	0.11870	.	.	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.06849	3.25;3.3;3.3;3.26	3.04	0.864	0.19068	.	.	.	.	.	T	0.05273	0.0140	L	0.36672	1.1	0.09310	N	1	B;B	0.26744	0.158;0.102	B;B	0.19391	0.019;0.025	T	0.44159	-0.9346	9	0.19147	T	0.46	.	2.3926	0.04382	0.2122:0.256:0.0:0.5318	.	478;419	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	S	478;419;419;478	ENSP00000301399:Y478S;ENSP00000413476:Y419S;ENSP00000389652:Y419S;ENSP00000404509:Y478S	ENSP00000301399:Y478S	Y	-	2	0	ZNF577	57067622	0.000000	0.05858	0.022000	0.16811	0.011000	0.07611	-0.203000	0.09438	-0.007000	0.14345	-0.256000	0.11100	TAT	.	.		0.353	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		G	52375810	T	G	52375810	3	3	109	1	0	0	0	0	1	0	0	0	18024	1406	49	5	28	5	ZNF577	19	52375810	Missense_Mutation	SNP	T	TCGA-DD-A39V-01A-11D-A20W-10	32630084	52375810	6753173	64	16190										
RALY	22913	hgsc.bcm.edu	37	chr20	32664868	32664868	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ggtgatggaggtggcgccggCggcggcggcggtggtggtgg	26	7	0	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr20:32664868C>T	ENST00000246194.3	+	8	1195	c.693C>T	c.(691-693)ggC>ggT	p.G231G	RALY_ENST00000375114.3_Silent_p.G215G	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	231	Epitope (recognized by BKRF1 antibodies).|Poly-Gly.				mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						gtggcgccggcggcggcggcg	0.667																																					p.G231G		Atlas-SNP	.											.	RALY	44	.	0			c.C693T						.																																			SO:0001819	synonymous_variant	22913	exon8			CGCCGGCGGCGGC	AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"RNA binding motif (RRM) containing"	15921	protein-coding gene	gene with protein product		614663	"RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)", "RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	ENST00000246194.3:c.693C>T	chr20.hg19:g.32664868C>T		12.0	0.0		11.0	4.0	NM_016732	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	Silent	SNP	ENST00000246194.3	hg19	CCDS13230.1																																																																																			.	.		0.667	RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1			T	32664868	C	T	32664868	2	4	109	1	0	0	0	0	0	0	0	1	13034	755	27	1		1	RALY	20	32664868	Silent	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10		32664868	30360652	65	16191										
BIRC7	79444	hgsc.bcm.edu	37	chr20	61870579	61870579	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	tccagtctgaaagtgcccagGagccaggtgcaggcccggga	15	12	1	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr20:61870579G>A	ENST00000217169.3	+	5	857	c.643G>A	c.(643-645)Gag>Aag	p.E215K	BIRC7_ENST00000342412.6_Missense_Mutation_p.E215K|MIR3196_ENST00000579556.1_RNA|NKAIN4_ENST00000466885.1_5'Flank|BIRC7_ENST00000395306.1_Missense_Mutation_p.E128K	NM_139317.1	NP_647478.1	Q96CA5	BIRC7_HUMAN	baculoviral IAP repeat containing 7	215					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of natural killer cell apoptotic process (GO:0070247)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(9)|ovary(1)	12	all_cancers(38;2.72e-09)					AAGTGCCCAGGAGCCAGGTGC	0.662																																					p.E215K		Atlas-SNP	.											.	BIRC7	25	.	0			c.G643A						.						46	53	51					20																	61870579		2203	4300	6503	SO:0001583	missense	79444	exon5			GCCCAGGAGCCAG	AF301009	CCDS13512.1, CCDS13513.1	20q13.3	2011-01-25	2011-01-25		ENSG00000101197	ENSG00000101197		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	13702	protein-coding gene	gene with protein product	"melanoma inhibitor of apoptosis protein", "kidney inhibitor of apoptosis protein", "livin inhibitor-of-apoptosis", "livin"	605737	"baculoviral IAP repeat-containing 7"			11024045, 11162435	Standard	NM_139317		Approved	mliap, ML-IAP, KIAP, RNF50	uc002yej.3	Q96CA5	OTTHUMG00000032957	ENST00000217169.3:c.643G>A	chr20.hg19:g.61870579G>A	ENSP00000217169:p.Glu215Lys	47.0	0.0		48.0	22.0	NM_139317	Q9BQV0|Q9H2A8|Q9HAP7	Missense_Mutation	SNP	ENST00000217169.3	hg19	CCDS13513.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.680859	0.47886	.	.	ENSG00000101197	ENST00000342412;ENST00000217169;ENST00000395306	T;T;T	0.50548	0.94;0.74;1.9	4.39	3.41	0.39046	.	0.750751	0.11309	N	0.577366	T	0.48466	0.1501	L	0.32530	0.975	0.35561	D	0.804661	D;P;D	0.69078	0.997;0.9;0.992	P;B;P	0.59889	0.839;0.376;0.865	T	0.41680	-0.9495	10	0.10377	T	0.69	.	10.0443	0.42177	0.0:0.0:0.7977:0.2023	.	215;215;215	Q6R308;Q96CA5;Q96CA5-2	.;BIRC7_HUMAN;.	K	215;215;128	ENSP00000345213:E215K;ENSP00000217169:E215K;ENSP00000378717:E128K	ENSP00000217169:E215K	E	+	1	0	BIRC7	61341024	0.211000	0.23529	0.513000	0.27749	0.190000	0.23558	2.170000	0.42443	1.099000	0.41499	0.563000	0.77884	GAG	.	.		0.662	BIRC7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080114.2	NM_139317		A	61870579	G	A	61870579	3	1	109	1	0	0	0	0	1	0	0	0	1439	1175	41	3	661	3	BIRC7	20	61870579	Missense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10	29205711	61870579	1154941	66	16192										
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29438502	29438502	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	ggccaagcgagcagtacagcGgggagctactgcagtcatct	14	11	2	0			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr22:29438502G>C	ENST00000544604.2	+	3	621	c.446G>C	c.(445-447)cGg>cCg	p.R149P	ZNRF3_ENST00000406323.3_Missense_Mutation_p.R49P|ZNRF3_ENST00000402174.1_Missense_Mutation_p.R49P|ZNRF3_ENST00000332811.4_Missense_Mutation_p.R49P	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	149					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						GCAGTACAGCGGGGAGCTACT	0.512																																					p.R149P		Atlas-SNP	.											.	ZNRF3	75	.	0			c.G446C						.						78	78	78					22																	29438502		1945	4147	6092	SO:0001583	missense	84133	exon3			TACAGCGGGGAGC	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"RING-type (C3HC4) zinc fingers"	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.446G>C	chr22.hg19:g.29438502G>C	ENSP00000443824:p.Arg149Pro	72.0	0.0		61.0	12.0	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	hg19	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.482183	0.84747	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000402174;ENST00000406323	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.64170	0.2574	L	0.43923	1.385	0.43564	D	0.995884	D	0.89917	1.0	D	0.91635	0.999	T	0.63782	-0.6559	10	0.72032	D	0.01	.	19.3307	0.94285	0.0:0.0:1.0:0.0	.	149	Q9ULT6	ZNRF3_HUMAN	P	149;49;49;49	ENSP00000443824:R149P;ENSP00000328614:R49P;ENSP00000384456:R49P;ENSP00000384553:R49P	ENSP00000328614:R49P	R	+	2	0	ZNRF3	27768502	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.058000	0.76676	2.881000	0.98747	0.650000	0.86243	CGG	.	.		0.512	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		C	29438502	G	C	29438502	3	2	109	1	0	0	0	0	1	0	0	0	18228	1116	39	4	152	4	ZNRF3	22	29438502	Missense_Mutation	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10		29438502	21866064	67	16193										
SBF1	6305	hgsc.bcm.edu	37	chr22	50906873	50906873	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	gaagcgctgcagaatctggcCctggccttccccactccctg	10	17	1	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chr22:50906873C>A	ENST00000390679.3	-	2	257	c.73G>T	c.(73-75)Ggc>Tgc	p.G25C	SBF1_ENST00000348911.6_Missense_Mutation_p.G25C|SBF1_ENST00000380817.3_Missense_Mutation_p.G25C			O95248	MTMR5_HUMAN	SET binding factor 1	25	UDENN.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		AGAATCTGGCCCTGGCCTTCC	0.642																																					p.G25C		Atlas-SNP	.											.	SBF1	211	.	0			c.G73T						.						44	51	49					22																	50906873		2019	4174	6193	SO:0001583	missense	6305	exon2			TCTGGCCCTGGCC	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.73G>T	chr22.hg19:g.50906873C>A	ENSP00000375097:p.Gly25Cys	50.0	0.0		52.0	14.0	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	C	28.0	4.881652	0.91740	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000356279;ENST00000337034;ENST00000390679	T;T;T	0.46819	0.86;0.86;0.86	4.84	4.84	0.62591	.	0.292022	0.31370	N	0.007769	T	0.70815	0.3267	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.75717	-0.3220	10	0.87932	D	0	.	16.8551	0.86004	0.0:1.0:0.0:0.0	.	25;25	G5E933;O95248-4	.;.	C	25;25;35;35;25	ENSP00000370196:G25C;ENSP00000252027:G25C;ENSP00000375097:G25C	ENSP00000336522:G35C	G	-	1	0	SBF1	49253739	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.166000	0.77553	2.500000	0.84329	0.655000	0.94253	GGC	.	.		0.642	SBF1-201	KNOWN	basic	protein_coding	protein_coding				A	50906873	C	A	50906873	3	1	109	1	0	0	0	0	1	0	0	0	13873	623	22	3	5768	3	SBF1	22	50906873	Missense_Mutation	SNP	C	TCGA-DD-A39V-01A-11D-A20W-10	21468371	50906873	397693	68	16194										
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765411	27765411	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0144927536231884	1	1	0.27205292702486	1.31492248062015	0	1	1	0	gaggaggaagaggaggaggaGgaggaggaggaggaggagga	26	0	0	1			TCGA-DD-A39V-01A-11D-A20W-10	TCGA-DD-A39V-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b73462a7-17f2-4187-87f1-9eb91590d20d	63c0be5f-ca62-4a05-a22d-9ddb8480fb65	g.chrX:27765411G>A	ENST00000451261.2	+	5	798	c.399G>A	c.(397-399)gaG>gaA	p.E133E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	133	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aggaggaggaggaggaggagg	0.572																																					p.E133E		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G399A						.						17	16	16					X																	27765411		692	1587	2279	SO:0001819	synonymous_variant	347442	exon1			GGAGGAGGAGGAG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.399G>A	chrX.hg19:g.27765411G>A		17.0	0.0		20.0	6.0	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.572	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		A	27765411	G	A	27765411	2	1	109	1	0	0	0	0	0	0	0	1	4280	991	35	3		3	DCAF8L2	23	27765411	Silent	SNP	G	TCGA-DD-A39V-01A-11D-A20W-10		27765411	127505149	69	16195										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27099008	27099008	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	cagcgggatcaggatctatgCaggggccccagactccccag	13	14	2	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr1:27099008C>T	ENST00000324856.7	+	13	3795	c.3424C>T	c.(3424-3426)Cag>Tag	p.Q1142*	ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q1142*|ARID1A_ENST00000540690.1_5'Flank|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q759*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1142					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.Q1142*(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGGATCTATGCAGGGGCCCCA	0.527			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Q1142X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	ARID1A,NS,carcinoma,0,1	ARID1A	842	.	1	Substitution - Nonsense(1)	liver(1)	c.C3424T						.						77	75	76					1																	27099008		2203	4300	6503	SO:0001587	stop_gained	8289	exon13			TCTATGCAGGGGC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3424C>T	chr1.hg19:g.27099008C>T	ENSP00000320485:p.Gln1142*	211.0	0.0		189.0	79.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.328846|9.328846	0.99138|0.99138	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000430799|ENST00000324856;ENST00000457599;ENST00000374152	.|.	.|.	.|.	5.16|5.16	5.16|5.16	0.70880|0.70880	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.74786|.	0.3762|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.73180|.	-0.4064|.	4|.	.|0.40728	.|T	.|0.16	-6.7363|-6.7363	18.8418|18.8418	0.92188|0.92188	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	V|X	39|1142;1142;759	.|.	.|ENSP00000320485:Q1142X	A|Q	+|+	2|1	0|0	ARID1A|ARID1A	26971595|26971595	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.320000|7.320000	0.79064|0.79064	2.690000|2.690000	0.91761|0.91761	0.655000|0.655000	0.94253|0.94253	GCA|CAG	.	.		0.527	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27099008	C	T	27099008	4	4	110	1	0	0	0	0	0	1	0	0	913	711	25	3	3474	3	ARID1A	1	27099008	Nonsense_Mutation	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10		27099008	222151613	1	16196										
FLG2	388698	hgsc.bcm.edu	37	chr1	152327767	152327767	+	Frame_Shift_Del	DEL	C	C	-													0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	tagactcatgctgtccaaagCcagaggattgtcctgagcca							TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr1:152327767delC	ENST00000388718.5	-	3	2567	c.2495delG	c.(2494-2496)ggcfs	p.G832fs	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	832	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGTCCAAAGCCAGAGGATTG	0.512																																					p.G832fs		Atlas-INDEL	.											.	FLG2	431	.	0			c.2496delC						.						314	303	307					1																	152327767		2203	4300	6503	SO:0001589	frameshift_variant	388698	exon3			.	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.2495delG	chr1.hg19:g.152327767delC	ENSP00000373370:p.Gly832fs	166.0	0.0		207.0	18.0	NM_001014342	Q9H4U1	Frame_Shift_Del	DEL	ENST00000388718.5	hg19	CCDS30861.1																																																																																			.	.		0.512	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		-	152327767	C	-	152327767	7	5	110	1	0	1	0	1	0	0	0	0	5931	739	26	0	4684	0	FLG2	1	152327767	Frame_Shift_Del	DEL	C	TCGA-DD-A39W-01A-11D-A20W-10	125228759	152327767	96922854	2	16197										
CD1B	910	hgsc.bcm.edu	37	chr1	158299817	158299817	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	ggcacacatgaagcattcttGacactcaggaaatccaatcc	7	12	2	2			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr1:158299817G>T	ENST00000368168.3	-	3	539	c.432C>A	c.(430-432)gtC>gtA	p.V144V		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	144					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					AAGCATTCTTGACACTCAGGA	0.483																																					p.V144V		Atlas-SNP	.											.	CD1B	78	.	0			c.C432A						.						163	163	163					1																	158299817		2203	4300	6503	SO:0001819	synonymous_variant	910	exon3			ATTCTTGACACTC	M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1635	protein-coding gene	gene with protein product		188360	"CD1B antigen, b polypeptide", "CD1b antigen"	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.432C>A	chr1.hg19:g.158299817G>T		238.0	0.0		263.0	86.0	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Silent	SNP	ENST00000368168.3	hg19	CCDS1176.1	.	.	.	.	.	.	.	.	.	.	G	1.957	-0.439910	0.04636	.	.	ENSG00000158485	ENST00000451207	.	.	.	4.28	-2.56	0.06268	.	.	.	.	.	T	0.08268	0.0206	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.36335	-0.9752	4	.	.	.	0.1558	4.4297	0.11522	0.3817:0.3069:0.3114:0.0	.	.	.	.	K	112	.	.	Q	-	1	0	CD1B	156566441	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	-0.021000	0.12504	-0.349000	0.08274	-0.793000	0.03317	CAA	.	.		0.483	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764		T	158299817	G	T	158299817	2	4	110	1	0	0	0	0	0	0	0	1	2977	1277	45	3		3	CD1B	1	158299817	Silent	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	5972050	158299817	90950804	3	16198										
DHX9	1660	hgsc.bcm.edu	37	chr1	182848473	182848473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	ttctgcgtctaggaggaattGgccaatttctggccaaagca	11	9	3	0			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr1:182848473G>A	ENST00000367549.3	+	21	2550	c.2440G>A	c.(2440-2442)Ggc>Agc	p.G814S	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	814					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						AGGAGGAATTGGCCAATTTCT	0.423																																					p.G814S	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G2440A						.						135	122	126					1																	182848473		1873	4108	5981	SO:0001583	missense	1660	exon21			GGAATTGGCCAAT	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.2440G>A	chr1.hg19:g.182848473G>A	ENSP00000356520:p.Gly814Ser	147.0	0.0		148.0	29.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	G	34	5.319258	0.95682	.	.	ENSG00000135829	ENST00000367549	T	0.02472	4.28	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.05456	0.0144	N	0.25890	0.77	0.80722	D	1	P;D	0.61080	0.879;0.989	P;P	0.52031	0.688;0.677	T	0.60969	-0.7157	10	0.16420	T	0.52	.	19.691	0.96000	0.0:0.0:1.0:0.0	.	93;814	B3KU66;Q08211	.;DHX9_HUMAN	S	814	ENSP00000356520:G814S	ENSP00000356520:G814S	G	+	1	0	DHX9	181115096	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.364000	0.79526	2.671000	0.90904	0.585000	0.79938	GGC	.	.		0.423	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		A	182848473	G	A	182848473	3	1	110	1	0	0	0	0	1	0	0	0	4518	1348	47	3	2518	3	DHX9	1	182848473	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	24548656	182848473	66402148	4	16199										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214542934	214542934	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	ttgcatagcaaacagaatccGttcgaaacttcgtggtgacc	9	10	0	2	rs61749333	byFrequency	TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr1:214542934G>T	ENST00000366956.5	-	17	3331	c.3137C>A	c.(3136-3138)aCg>aAg	p.T1046K	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	1046	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		AACAGAATCCGTTCGAAACTT	0.502																																					p.T1046K	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											PTPN14,NS,carcinoma,0,1	PTPN14	168	.	0			c.C3137A						.						264	240	248					1																	214542934		2203	4300	6503	SO:0001583	missense	5784	exon17			GAATCCGTTCGAA	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.3137C>A	chr1.hg19:g.214542934G>T	ENSP00000355923:p.Thr1046Lys	299.0	0.0		323.0	18.0	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.888274	0.91814	.	.	ENSG00000152104	ENST00000366956	D	0.82893	-1.66	5.51	5.51	0.81932	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.84982	0.5593	N	0.25485	0.75	0.80722	D	1	D	0.76494	0.999	D	0.70227	0.968	T	0.80350	-0.1419	10	0.13470	T	0.59	.	19.4235	0.94732	0.0:0.0:1.0:0.0	.	1046	Q15678	PTN14_HUMAN	K	1046	ENSP00000355923:T1046K	ENSP00000355923:T1046K	T	-	2	0	PTPN14	212609557	1.000000	0.71417	0.997000	0.53966	0.970000	0.65996	9.751000	0.98889	2.564000	0.86499	0.650000	0.86243	ACG	.	G|0.999;C|0.001		0.502	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		T	214542934	G	T	214542934	3	4	110	1	0	0	0	0	1	0	0	0	12796	1145	40	1	438	1	PTPN14	1	214542934	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	31694461	214542934	34707687	5	16200										
MAL	4118	hgsc.bcm.edu	37	chr2	95713853	95713853	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	attggagcccacggtggagaGacttcctgggtcaccttggt	14	10	1	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr2:95713853G>A	ENST00000309988.4	+	2	352	c.243G>A	c.(241-243)gaG>gaA	p.E81E	MAL_ENST00000349807.3_Intron|MAL_ENST00000353004.3_Silent_p.E81E|MAL_ENST00000354078.3_Intron	NM_002371.3	NP_002362.1	P21145	MAL_HUMAN	mal, T-cell differentiation protein	81	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|central nervous system development (GO:0007417)|membrane raft polarization (GO:0001766)|myelination (GO:0042552)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	channel activity (GO:0015267)|lipid binding (GO:0008289)|peptidase activator activity involved in apoptotic process (GO:0016505)|structural constituent of myelin sheath (GO:0019911)	p.E81E(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(2)	10				STAD - Stomach adenocarcinoma(1183;0.18)		ACGGTGGAGAGACTTCCTGGG	0.602																																					p.E81E		Atlas-SNP	.											MAL,NS,carcinoma,0,1	MAL	21	.	1	Substitution - coding silent(1)	lung(1)	c.G243A						.						90	84	86					2																	95713853		2203	4300	6503	SO:0001819	synonymous_variant	4118	exon2			TGGAGAGACTTCC		CCDS2006.1, CCDS2007.1, CCDS2008.1, CCDS2009.1	2q11.1	2008-07-29			ENSG00000172005	ENSG00000172005			6817	protein-coding gene	gene with protein product		188860					Standard	NM_002371		Approved		uc002stx.2	P21145	OTTHUMG00000132011	ENST00000309988.4:c.243G>A	chr2.hg19:g.95713853G>A		267.0	0.0		179.0	64.0	NM_022438	Q6FH77	Silent	SNP	ENST00000309988.4	hg19	CCDS2006.1																																																																																			.	.		0.602	MAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254982.3	NM_002371		A	95713853	G	A	95713853	2	1	110	1	0	0	0	0	0	0	0	1	9208	933	33	3		3	MAL	2	95713853	Silent	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10		95713853	147485520	6	16201										
STEAP3	55240	hgsc.bcm.edu	37	chr2	120012401	120012401	+	Frame_Shift_Del	DEL	T	T	-													0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	ccattgcaaactcgctcaacTggagggagttcagcttcgtt							TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr2:120012401delT	ENST00000354888.5	+	5	1666	c.1162delT	c.(1162-1164)tggfs	p.W388fs	STEAP3_ENST00000393110.2_Frame_Shift_Del_p.W398fs|STEAP3_ENST00000393108.2_Frame_Shift_Del_p.W388fs|STEAP3_ENST00000425223.2_Frame_Shift_Del_p.W388fs|STEAP3_ENST00000409811.1_Frame_Shift_Del_p.W388fs|STEAP3_ENST00000393106.2_Frame_Shift_Del_p.W388fs|STEAP3_ENST00000393107.2_Frame_Shift_Del_p.W388fs|STEAP3_ENST00000450943.2_Frame_Shift_Del_p.W388fs	NM_182915.2	NP_878919.2	Q658P3	STEA3_HUMAN	STEAP family member 3, metalloreductase	388	Ferric oxidoreductase.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cellular iron ion homeostasis (GO:0006879)|copper ion import (GO:0015677)|exosomal secretion (GO:1990182)|ferric iron import into cell (GO:0097461)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|protein secretion (GO:0009306)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	17						CTCGCTCAACTGGAGGGAGTT	0.592																																					p.N397fs		Atlas-Indel,Pindel	.											.	STEAP3	44	.	0			c.1191delC						.						92	79	84					2																	120012401		2203	4300	6503	SO:0001589	frameshift_variant	55240	exon5			.	AY029585	CCDS2125.1, CCDS42738.1	2q14.2	2011-09-30	2011-09-30		ENSG00000115107	ENSG00000115107			24592	protein-coding gene	gene with protein product		609671				12606722	Standard	NM_182915		Approved	TSAP6, dudlin-2, STMP3	uc002tlr.3	Q658P3	OTTHUMG00000131402	ENST00000354888.5:c.1162delT	chr2.hg19:g.120012401delT	ENSP00000346961:p.Trp388fs	170.0	0.0		102.0	39.0	NM_182915	A8K6E3|Q4VBR2|Q4ZG36|Q53SQ8|Q7Z389|Q86SF6|Q8NEW6|Q8TDP3|Q8TF03|Q9NVB5	Frame_Shift_Del	DEL	ENST00000354888.5	hg19	CCDS2125.1																																																																																			.	.		0.592	STEAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254193.1	NM_018234		-	120012401	T	-	120012401	7	5	110	1	0	1	0	1	0	0	0	0	15294	1580	55	0	1206	0	STEAP3	2	120012401	Frame_Shift_Del	DEL	T	TCGA-DD-A39W-01A-11D-A20W-10	24298548	120012401	123186972	7	16202										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266620	41266620	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	aaacatgcagttgtaaacttGattaactatcaagatgatgc	7	6	1	3			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr3:41266620G>T	ENST00000349496.5	+	4	697	c.417G>T	c.(415-417)ttG>ttT	p.L139F	CTNNB1_ENST00000396183.3_Missense_Mutation_p.L139F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.L139F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.L132F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.L139F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	139					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_Q143del(7)|p.W25_I140del(3)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.M5_N141>D(2)|p.M1_V173del(1)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.I35_K170del(1)|p.E15_I140>V(1)|p.A20_N141del(1)|p.D11_Y142>H(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TTGTAAACTTGATTAACTATC	0.448		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.L139F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	23	Deletion - In frame(16)|Complex - deletion inframe(7)	liver(22)|skin(1)	c.G417T						.						143	126	132					3																	41266620		2203	4300	6503	SO:0001583	missense	1499	exon4	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	AAACTTGATTAAC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.417G>T	chr3.hg19:g.41266620G>T	ENSP00000344456:p.Leu139Phe	78.0	0.0		52.0	8.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.842089	0.51057	.	.	ENSG00000168036	ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T;T	0.69040	-0.37;0.85;-0.37;-0.37;-0.37;-0.37	5.4	2.66	0.31614	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80088	0.4559	M	0.79926	2.475	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76575	0.984;0.988	T	0.80011	-0.1561	10	0.72032	D	0.01	-13.726	10.9463	0.47301	0.2042:0.0:0.7958:0.0	.	67;139	B4DSW9;P35222	.;CTNB1_HUMAN	F	139;139;139;139;132;139	ENSP00000385604:L139F;ENSP00000412219:L139F;ENSP00000379486:L139F;ENSP00000344456:L139F;ENSP00000411226:L132F;ENSP00000379488:L139F	ENSP00000344456:L139F	L	+	3	2	CTNNB1	41241624	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.408000	0.59761	0.362000	0.24319	-0.150000	0.13652	TTG	.	.		0.448	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266620	G	T	41266620	3	4	110	1	0	0	0	0	1	0	0	0	4018	1281	45	3	427	3	CTNNB1	3	41266620	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10		41266620	156755810	8	16203										
HPS3	84343	hgsc.bcm.edu	37	chr3	148868468	148868468	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	acatggacaccaccctgaagGtaagaactggcttatgaaga	10	9	0	4			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr3:148868468G>A	ENST00000296051.2	+	6	1385		c.e6+1		HPS3_ENST00000460120.1_Splice_Site	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3						organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CACCCTGAAGGTAAGAACTGG	0.498									Hermansky-Pudlak syndrome																												.		Atlas-SNP	.											.	HPS3	104	.	0			c.1245+1G>A						.						115	105	108					3																	148868468		2203	4300	6503	SO:0001630	splice_region_variant	84343	exon6	Familial Cancer Database	HPS, HPS1-8	CTGAAGGTAAGAA	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.1245+1G>A	chr3.hg19:g.148868468G>A		131.0	0.0		110.0	18.0	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Splice_Site	SNP	ENST00000296051.2	hg19	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.542860	0.86022	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2421	0.93888	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HPS3	150351158	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	8.266000	0.89871	2.621000	0.88768	0.650000	0.86243	.	.	.		0.498	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	Intron	A	148868468	G	A	148868468	5	1	110	1	0	0	0	0	0	0	1	0	7349	1275	44	3	1268	3	HPS3	3	148868468	Splice_Site	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	107601848	148868468	49153962	9	16204										
NIPBL	25836	hgsc.bcm.edu	37	chr5	37007558	37007558	+	Silent	SNP	A	A	C													0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	ctagagatacaacttcttacAgacacaacaattcttcaggt							TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr5:37007558A>C	ENST00000282516.8	+	18	4720	c.4221A>C	c.(4219-4221)acA>acC	p.T1407T	NIPBL_ENST00000448238.2_Silent_p.T1407T	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1407					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			AACTTCTTACAGACACAACAA	0.303																																					p.T1407T		Atlas-SNP	.											.	NIPBL	513	.	0			c.A4221C						.						54	53	53					5																	37007558		2199	4295	6494	SO:0001819	synonymous_variant	25836	exon18			TCTTACAGACACA	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.4221A>C	chr5.hg19:g.37007558A>C		162.0	0.0		118.0	51.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.		0.303	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		C	37007558	A	C	37007558	2	2	110	1	0	0	0	0	0	0	0	1	10437	175	7	5		5	NIPBL	5	37007558	Silent	SNP	A	TCGA-DD-A39W-01A-11D-A20W-10		37007558	143907702	10	16205	71	2								
NIPBL	25836	hgsc.bcm.edu	37	chr5	37007562	37007562	+	Missense_Mutation	SNP	A	A	G													0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	agatacaacttcttacagacAcaacaattcttcaggtaaga							TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr5:37007562A>G	ENST00000282516.8	+	18	4724	c.4225A>G	c.(4225-4227)Aca>Gca	p.T1409A	NIPBL_ENST00000448238.2_Missense_Mutation_p.T1409A	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1409					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TCTTACAGACACAACAATTCT	0.313																																					p.T1409A		Atlas-SNP	.											.	NIPBL	513	.	0			c.A4225G						.						51	50	51					5																	37007562		2199	4295	6494	SO:0001583	missense	25836	exon18			ACAGACACAACAA	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.4225A>G	chr5.hg19:g.37007562A>G	ENSP00000282516:p.Thr1409Ala	158.0	0.0		117.0	51.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	hg19	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.304292	0.81136	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.94046	-3.33;-3.34	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.95414	0.8511	L	0.56396	1.775	0.80722	D	1	D;D	0.69078	0.994;0.997	D;D	0.69479	0.942;0.964	D	0.95076	0.8209	10	0.44086	T	0.13	.	15.2464	0.73509	1.0:0.0:0.0:0.0	.	1409;1409	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	A	1409	ENSP00000282516:T1409A;ENSP00000406266:T1409A	ENSP00000282516:T1409A	T	+	1	0	NIPBL	37043319	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.019000	0.59389	0.528000	0.53228	ACA	.	.		0.313	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		G	37007562	A	G	37007562	3	3	110	1	0	0	0	0	1	0	0	0	10437	159	6	2	4291	2	NIPBL	5	37007562	Missense_Mutation	SNP	A	TCGA-DD-A39W-01A-11D-A20W-10	4	37007562	143907698	11	16206	71	2								
ELL2	22936	hgsc.bcm.edu	37	chr5	95224587	95224587	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	gcagagttctaggaccatgaCtctgcttgctgttggtcaaa	11	9	3	2			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr5:95224587C>T	ENST00000237853.4	-	12	2260	c.1911G>A	c.(1909-1911)gaG>gaA	p.E637E	ELL2_ENST00000431061.2_Silent_p.E387E	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	637					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		AGGACCATGACTCTGCTTGCT	0.358																																					p.E637E		Atlas-SNP	.											.	ELL2	63	.	0			c.G1911A						.						64	59	61					5																	95224587		2203	4300	6503	SO:0001819	synonymous_variant	22936	exon12			CCATGACTCTGCT	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1911G>A	chr5.hg19:g.95224587C>T		125.0	0.0		81.0	14.0	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	hg19	CCDS4080.1																																																																																			.	.		0.358	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		T	95224587	C	T	95224587	2	4	110	1	0	0	0	0	0	0	0	1	5065	564	20	3		3	ELL2	5	95224587	Silent	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10	58217025	95224587	85690673	12	16207										
KIF20A	10112	hgsc.bcm.edu	37	chr5	137519196	137519196	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	gtgcaagatgctgaggaggcCtggaagctcctaaaagtggg	16	7	0	2			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr5:137519196C>T	ENST00000394894.3	+	9	1291	c.1065C>T	c.(1063-1065)gcC>gcT	p.A355A	KIF20A_ENST00000508792.1_Silent_p.A337A	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	355	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule bundle formation (GO:0001578)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|liver(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(1)	27			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTGAGGAGGCCTGGAAGCTCC	0.512																																					p.A355A		Atlas-SNP	.											.	KIF20A	53	.	0			c.C1065T						.						112	115	114					5																	137519196		2203	4300	6503	SO:0001819	synonymous_variant	10112	exon9			GGAGGCCTGGAAG	AF070672	CCDS4199.1	5q31	2008-02-05	2003-01-13	2003-01-17	ENSG00000112984	ENSG00000112984		"Kinesins"	9787	protein-coding gene	gene with protein product		605664	"RAB6 interacting, kinesin-like (rabkinesin6)"	RAB6KIFL		11416179, 10806357	Standard	NM_005733		Approved		uc003lcj.3	O95235	OTTHUMG00000129195	ENST00000394894.3:c.1065C>T	chr5.hg19:g.137519196C>T		39.0	0.0		77.0	4.0	NM_005733	B4DL79|D3DQB6	Silent	SNP	ENST00000394894.3	hg19	CCDS4199.1																																																																																			.	.		0.512	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733		T	137519196	C	T	137519196	2	4	110	1	0	0	0	0	0	0	0	1	8295	668	24	3		3	KIF20A	5	137519196	Silent	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10	42294609	137519196	43396064	13	16208										
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140589809	140589809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	taaccgtgctggtctccgacGtcaatgacaacgcccccgcc	9	17	2	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr5:140589809G>A	ENST00000239450.2	+	1	1519	c.1330G>A	c.(1330-1332)Gtc>Atc	p.V444I	PCDHB12_ENST00000541609.1_Missense_Mutation_p.V107I	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	444	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGTCTCCGACGTCAATGACAA	0.597																																					p.V444I		Atlas-SNP	.											.	PCDHB12	179	.	0			c.G1330A						.						107	101	103					5																	140589809		2203	4300	6503	SO:0001583	missense	56124	exon1			TCCGACGTCAATG	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1330G>A	chr5.hg19:g.140589809G>A	ENSP00000239450:p.Val444Ile	135.0	0.0		165.0	9.0	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	hg19	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	G	2.818	-0.245539	0.05906	.	.	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.01258	5.09;5.09	3.83	0.945	0.19543	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.00875	0.0029	N	0.17564	0.495	0.25830	N	0.984187	B	0.32101	0.356	B	0.26094	0.066	T	0.43245	-0.9403	9	0.06099	T	0.92	.	8.266	0.31815	0.2798:0.0:0.7202:0.0	.	444	Q9Y5F1	PCDBC_HUMAN	I	107;444;64	ENSP00000440199:V107I;ENSP00000239450:V444I	ENSP00000239450:V444I	V	+	1	0	PCDHB12	140569993	0.981000	0.34729	0.803000	0.32268	0.037000	0.13140	1.824000	0.39072	-0.048000	0.13401	-0.343000	0.07986	GTC	.	.		0.597	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		A	140589809	G	A	140589809	3	1	110	1	0	0	0	0	1	0	0	0	11546	1145	40	1	1332	1	PCDHB12	5	140589809	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	3070613	140589809	40325451	14	16209										
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140744161	140744161	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	ggcagcttggtcaccgcgggCaggatagaccgggaggagct	18	10	1	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr5:140744161C>T	ENST00000518069.1	+	1	264	c.264C>T	c.(262-264)ggC>ggT	p.G88G	PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	88	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCACCGCGGGCAGGATAGACC	0.567																																					p.G88G		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.C264T						.						53	62	59					5																	140744161		2193	4297	6490	SO:0001819	synonymous_variant	56110	exon1			CGCGGGCAGGATA	AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.264C>T	chr5.hg19:g.140744161C>T		111.0	0.0		161.0	57.0	NM_032054	Q2M3F5|Q9Y5D2	Silent	SNP	ENST00000518069.1	hg19	CCDS54925.1																																																																																			.	.		0.567	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		T	140744161	C	T	140744161	2	4	110	1	0	0	0	0	0	0	0	1	11566	697	25	3		3	PCDHGA5	5	140744161	Silent	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10	154352	140744161	40171099	15	16210										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141051870	141051870	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	cccagactcggctgtgaagcTgaggggtggacagccagtcc	15	12	0	3			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr5:141051870T>A	ENST00000239440.4	-	10	1451		c.e10-2		ARAP3_ENST00000508305.1_Splice_Site|ARAP3_ENST00000513878.1_Splice_Site	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3						cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GCTGTGAAGCTGAGGGGTGGA	0.647																																					.		Atlas-SNP	.											.	ARAP3	139	.	0			c.1386-2A>T						.						25	29	28					5																	141051870		2194	4269	6463	SO:0001630	splice_region_variant	64411	exon11			TGAAGCTGAGGGG	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.1386-2A>T	chr5.hg19:g.141051870T>A		144.0	0.0		152.0	8.0	NM_022481	B4DIT1|D3DQE3	Splice_Site	SNP	ENST00000239440.4	hg19	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.197553	0.58126	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878;ENST00000504448	.	.	.	3.9	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8395	0.52346	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ARAP3	141032054	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	7.788000	0.85771	1.619000	0.50296	0.383000	0.25322	.	.	.		0.647	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	Intron	A	141051870	T	A	141051870	5	1	110	1	0	0	0	0	0	0	1	0	840	1594	55	4	3346	4	ARAP3	5	141051870	Splice_Site	SNP	T	TCGA-DD-A39W-01A-11D-A20W-10	307709	141051870	39863390	16	16211										
OR2J3	442186	hgsc.bcm.edu	37	chr6	29080097	29080097	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	tcctcatgcaccctcgtttcTgccacctgctggctgtggct	9	16	2	0			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr6:29080097T>G	ENST00000377169.1	+	1	430	c.430T>G	c.(430-432)Tgc>Ggc	p.C144G		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	144						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						CCCTCGTTTCTGCCACCTGCT	0.522																																					p.C144G		Atlas-SNP	.											.	OR2J3	53	.	0			c.T430G						.						366	390	381					6																	29080097		1385	2633	4018	SO:0001583	missense	442186	exon1			CGTTTCTGCCACC		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"GPCR / Class A : Olfactory receptors"	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.430T>G	chr6.hg19:g.29080097T>G	ENSP00000366374:p.Cys144Gly	450.0	1.0		331.0	132.0	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	hg19	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	T	15.19	2.760854	0.49468	.	.	ENSG00000204701	ENST00000377169	T	0.00224	8.51	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00468	0.0015	H	0.96604	3.85	0.41765	D	0.989732	D	0.89917	1.0	D	0.97110	1.0	T	0.44590	-0.9318	9	0.87932	D	0	.	10.804	0.46507	0.0:0.0:0.0:1.0	.	144	O76001	OR2J3_HUMAN	G	144	ENSP00000366374:C144G	ENSP00000366374:C144G	C	+	1	0	OR2J3	29188076	0.986000	0.35501	0.831000	0.32960	0.837000	0.47467	2.864000	0.48404	1.268000	0.44264	0.358000	0.22013	TGC	.	.		0.522	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			G	29080097	T	G	29080097	3	3	110	1	0	0	0	0	1	0	0	0	11013	1580	55	5	432	5	OR2J3	6	29080097	Missense_Mutation	SNP	T	TCGA-DD-A39W-01A-11D-A20W-10		29080097	142034970	17	16212										
OR12D3	81797	hgsc.bcm.edu	37	chr6	29342651	29342651	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	gcagctgccaacagaatacaCacctgggggttcatgatgac	11	11	1	3			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr6:29342651C>T	ENST00000396806.3	-	1	417	c.414G>A	c.(412-414)gtG>gtA	p.V138V	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						ACAGAATACACACCTGGGGGT	0.498																																					p.V138V		Atlas-SNP	.											.	OR12D3	55	.	0			c.G414A						.						56	57	57					6																	29342651		1510	2708	4218	SO:0001819	synonymous_variant	81797	exon1			AATACACACCTGG		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"GPCR / Class A : Olfactory receptors"	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.414G>A	chr6.hg19:g.29342651C>T		90.0	0.0		81.0	34.0	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Silent	SNP	ENST00000396806.3	hg19	CCDS4658.1																																																																																			.	.		0.498	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3			T	29342651	C	T	29342651	2	4	110	1	0	0	0	0	0	0	0	1	10941	465	17	3		3	OR12D3	6	29342651	Silent	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10	262554	29342651	141772416	18	16213										
SAMD5	389432	hgsc.bcm.edu	37	chr6	147830139	147830139	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	gcggagtccttcgtggataaCggctacgatgacctggaggt	15	9	0	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr6:147830139C>A	ENST00000367474.1	+	1	77	c.75C>A	c.(73-75)aaC>aaA	p.N25K		NM_001030060.2	NP_001025231.1	Q5TGI4	SAMD5_HUMAN	sterile alpha motif domain containing 5	25	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.												Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.55e-10)|GBM - Glioblastoma multiforme(68;0.112)		TCGTGGATAACGGCTACGATG	0.657																																					p.N25K		Atlas-SNP	.											.	SAMD5	4	.	0			c.C75A						.						54	50	52					6																	147830139		2203	4300	6503	SO:0001583	missense	389432	exon1			GGATAACGGCTAC	AL354880	CCDS34548.1	6q24.3	2013-01-10			ENSG00000203727	ENSG00000203727		"Sterile alpha motif (SAM) domain containing"	21180	protein-coding gene	gene with protein product							Standard	NM_001030060		Approved	dJ875H10.1	uc003qmc.2	Q5TGI4	OTTHUMG00000015767	ENST00000367474.1:c.75C>A	chr6.hg19:g.147830139C>A	ENSP00000356444:p.Asn25Lys	223.0	0.0		211.0	63.0	NM_001030060		Missense_Mutation	SNP	ENST00000367474.1	hg19	CCDS34548.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731009	0.69074	.	.	ENSG00000203727	ENST00000367474	T	0.45276	0.9	4.1	1.78	0.24846	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.56934	0.2019	M	0.91612	3.225	0.37125	D	0.901002	D	0.89917	1.0	D	0.91635	0.999	T	0.62562	-0.6828	10	0.66056	D	0.02	-10.4178	7.6911	0.28569	0.0:0.6513:0.0:0.3487	.	25	Q5TGI4	SAMD5_HUMAN	K	25	ENSP00000356444:N25K	ENSP00000356444:N25K	N	+	3	2	SAMD5	147871832	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.518000	0.22847	0.663000	0.31027	0.460000	0.39030	AAC	.	.		0.657	SAMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042610.1	NM_001030060		A	147830139	C	A	147830139	3	1	110	1	0	0	0	0	1	0	0	0	13838	535	19	1	77	1	SAMD5	6	147830139	Missense_Mutation	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10	118487488	147830139	23284928	19	16214										
MUC17	140453	hgsc.bcm.edu	37	chr7	100686943	100686943	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	acaacctctgcctcctccacGactgtgaaccctgaggctgt	8	16	1	2	rs201108444	byFrequency	TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr7:100686943G>A	ENST00000306151.4	+	3	12310	c.12246G>A	c.(12244-12246)acG>acA	p.T4082T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4082					cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CCTCCTCCACGACTGTGAACC	0.572													G|||	3	0.000599042	0.0023	0	5008	,	,		18996	0		0	False		,,,				2504	0				p.T4082T		Atlas-SNP	.											.	MUC17	804	.	0			c.G12246A						.	G		5,4401	9.9+/-24.2	0,5,2198	223	189	201		12246	-1.1	0	7		201	0,8600		0,0,4300	yes	coding-synonymous	MUC17	NM_001040105.1		0,5,6498	AA,AG,GG		0.0,0.1135,0.0384		4082/4494	100686943	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CTCCACGACTGTG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.12246G>A	chr7.hg19:g.100686943G>A		245.0	0.0		191.0	40.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.572	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100686943	G	A	100686943	2	1	110	1	0	0	0	0	0	0	0	1	9983	1045	37	1		1	MUC17	7	100686943	Silent	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10		100686943	58451720	20	16215										
ADAM28	10863	hgsc.bcm.edu	37	chr8	24170902	24170903	+	Splice_Site	DNP	GG	GG	TT													0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	aactctcatgttttttcaggGgctacttcagtcagggggat							TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr8:24170902_24170903GG>TT	ENST00000265769.4	+	6	495_496	c.385_386GG>TT	c.(385-387)GGc>TTc	p.G129F	ADAM28_ENST00000437154.2_Splice_Site_p.G129F|RP11-624C23.1_ENST00000523700.1_RNA|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000540823.1_Intron	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	129					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TTTTTTCAGGGGCTACTTCAGT	0.391																																					p.G129C|p.G129V	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.G385T|c.G386T						.																																			SO:0001630	splice_region_variant	10863	exon6			TTCAGGGGCTACT|TCAGGGGCTACTT	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	Exception_encountered	chr8.hg19:g.24170902_24170903delinsTT		153.0|155.0	0.0		123.0	10.0	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	hg19	CCDS34865.1																																																																																			.	.		0.391	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	Missense_Mutation	TT	24170903	GG	TT	24170902	5	4	110	1	0	0	0	0	0	0	1	0	246	1246	43	3	407	3	ADAM28	8	24170902	Splice_Site	DNP	GG	TCGA-DD-A39W-01A-11D-A20W-10		24170902	122193120	21	16216										
PHPT1	29085	hgsc.bcm.edu	37	chr9	139744956	139744962	+	Intron	DEL	CAGCAGA	CAGCAGA	-													0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	tcttcacaaaaaccaccagcAgatgagacccacgtgcgtcc							TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	CAGCAGA	CAGCAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr9:139744956_139744962delCAGCAGA	ENST00000247665.10	+	3	622				MAMDC4_ENST00000317446.2_5'Flank|PHPT1_ENST00000371661.1_Splice_Site_p.SR96fs|MAMDC4_ENST00000445819.1_5'Flank|PHPT1_ENST00000492540.1_3'UTR|PHPT1_ENST00000545326.1_Splice_Site_p.SR96fs	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1						negative regulation of ATP citrate synthase activity (GO:2000984)|negative regulation of lyase activity (GO:0051350)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-histidine dephosphorylation (GO:0035971)|positive regulation of cell motility (GO:2000147)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|protein dephosphorylation (GO:0006470)|regulation of actin cytoskeleton reorganization (GO:2000249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium channel inhibitor activity (GO:0019855)|ion channel binding (GO:0044325)|phosphohistidine phosphatase activity (GO:0008969)|phosphoprotein phosphatase activity (GO:0004721)	p.M96I(1)		NS(1)|large_intestine(1)|lung(1)	3	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		AACCACCAGCAGATGAGACCCACGTGC	0.643																																					.		Atlas-Indel,Pindel	.											.	PHPT1	14	.	1	Substitution - Missense(1)	cervix(1)	.						.																																			SO:0001627	intron_variant	29085	.			.	AF131857	CCDS7009.1, CCDS48060.1	9q34.3	2008-02-05			ENSG00000054148	ENSG00000054148	3.1.3.-		30033	protein-coding gene	gene with protein product	"phosphohistidine phosphatase 14kDa", " sex-regulated protein janus-a"	610167				11042152, 8619474	Standard	NM_014172		Approved	PHP14, HSPC141, CGI-202, DKFZp564M173, bA216L13.10	uc004cjq.4	Q9NRX4	OTTHUMG00000020950	ENST00000247665.10:c.286-245CAGCAGA>-	chr9.hg19:g.139744956_139744962delCAGCAGA		97.0	0.0		47.0	10.0	.	B1AMX0|B1AMX1|Q9H0Y3	Splice_Site	DEL	ENST00000247665.10	hg19	CCDS7009.1																																																																																			.	.		0.643	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172		-	139744962	CAGCAGA	-	139744956	6	5	110	0	1	1	0	1	0	0	0	0	11869	202	7	0		0	PHPT1	9	139744956	Intron	DEL	CAGCAGA	TCGA-DD-A39W-01A-11D-A20W-10		139744956	1468475	22	16217										
HKDC1	80201	hgsc.bcm.edu	37	chr10	71008284	71008284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	caagggggccgccatggtgaCcgcggtggcctcccgcgtgc	17	15	0	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr10:71008284C>T	ENST00000354624.5	+	10	1503	c.1370C>T	c.(1369-1371)aCc>aTc	p.T457I	HKDC1_ENST00000395086.2_Missense_Mutation_p.T457I|HKDC1_ENST00000488706.1_3'UTR	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	457	Hexokinase type-2 1.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						GCCATGGTGACCGCGGTGGCC	0.642																																					p.T457I		Atlas-SNP	.											.	HKDC1	98	.	0			c.C1370T						.						39	40	40					10																	71008284		2203	4300	6503	SO:0001583	missense	80201	exon10			TGGTGACCGCGGT		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.1370C>T	chr10.hg19:g.71008284C>T	ENSP00000346643:p.Thr457Ile	110.0	0.0		115.0	52.0	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	hg19	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.958283	0.92726	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	T;T	0.12255	2.7;2.7	4.97	4.97	0.65823	Hexokinase, C-terminal (1);	0.052599	0.64402	D	0.000001	T	0.48223	0.1488	M	0.91818	3.245	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.60414	-0.7268	10	0.87932	D	0	-15.1498	18.3972	0.90502	0.0:1.0:0.0:0.0	.	457	Q2TB90	HKDC1_HUMAN	I	457	ENSP00000346643:T457I;ENSP00000378521:T457I	ENSP00000346643:T457I	T	+	2	0	HKDC1	70678290	1.000000	0.71417	0.954000	0.39281	0.946000	0.59487	7.615000	0.83006	2.583000	0.87209	0.462000	0.41574	ACC	.	.		0.642	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		T	71008284	C	T	71008284	3	4	110	1	0	0	0	0	1	0	0	0	7202	507	18	3	1408	3	HKDC1	10	71008284	Missense_Mutation	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10		71008284	64526463	23	16218										
KRTAP5-3	387266	hgsc.bcm.edu	37	chr11	1629410	1629410	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	cccccttgcagcccccacaaGagccacagacccccttggag	8	20	0	2			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr11:1629410G>T	ENST00000399685.1	-	1	283	c.206C>A	c.(205-207)tCt>tAt	p.S69Y		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	69	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		GCCCCCACAAGAGCCACAGAC	0.667																																					p.S69Y		Atlas-SNP	.											.	KRTAP5-3	33	.	0			c.C206A						.						53	72	66					11																	1629410		2193	4294	6487	SO:0001583	missense	387266	exon1			CCACAAGAGCCAC	AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"Keratin associated proteins"	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.206C>A	chr11.hg19:g.1629410G>T	ENSP00000382592:p.Ser69Tyr	236.0	0.0		239.0	34.0	NM_001012708	Q6PL44|Q701N3	Missense_Mutation	SNP	ENST00000399685.1	hg19	CCDS41591.1	.	.	.	.	.	.	.	.	.	.	G	3.802	-0.041479	0.07452	.	.	ENSG00000196224	ENST00000399685	T	0.01647	4.71	3.39	3.39	0.38822	.	.	.	.	.	T	0.07458	0.0188	H	0.94542	3.55	0.20074	N	0.999933	B	0.28713	0.22	B	0.33121	0.158	T	0.02821	-1.1106	9	0.59425	D	0.04	.	12.6532	0.56774	0.0:0.0:1.0:0.0	.	69	Q6L8H2	KRA53_HUMAN	Y	69	ENSP00000382592:S69Y	ENSP00000382592:S69Y	S	-	2	0	KRTAP5-3	1585986	0.000000	0.05858	0.978000	0.43139	0.001000	0.01503	-0.220000	0.09215	1.616000	0.50265	0.289000	0.19496	TCT	.	.		0.667	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1			T	1629410	G	T	1629410	3	4	110	1	0	0	0	0	1	0	0	0	8571	942	33	3	514	3	KRTAP5-3	11	1629410	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10		1629410	133377106	24	16219										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6648374	6648374	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	tgggcggggcagacgtaggcGcagaggactggtggggaagg	23	6	0	2			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr11:6648374G>A	ENST00000299441.3	-	14	6307	c.5896C>T	c.(5896-5898)Cgc>Tgc	p.R1966C		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1966	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGACGTAGGCGCAGAGGACTG	0.617																																					p.R1966C		Atlas-SNP	.											.	DCHS1	277	.	0			c.C5896T						.						78	72	74					11																	6648374		2200	4295	6495	SO:0001583	missense	8642	exon14			GTAGGCGCAGAGG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.5896C>T	chr11.hg19:g.6648374G>A	ENSP00000299441:p.Arg1966Cys	149.0	0.0		123.0	30.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.890705	0.52014	.	.	ENSG00000166341	ENST00000299441	T	0.61158	0.13	5.18	3.09	0.35607	Cadherin (1);Cadherin-like (1);	0.000000	0.45361	D	0.000380	T	0.32255	0.0823	N	0.08118	0	0.40003	D	0.975191	B	0.31054	0.306	B	0.18871	0.023	T	0.32107	-0.9919	10	0.56958	D	0.05	.	10.4541	0.44539	0.0:0.0:0.4392:0.5608	.	1966	Q96JQ0	PCD16_HUMAN	C	1966	ENSP00000299441:R1966C	ENSP00000299441:R1966C	R	-	1	0	DCHS1	6604950	0.037000	0.19845	1.000000	0.80357	0.897000	0.52465	0.460000	0.21924	1.324000	0.45282	0.462000	0.41574	CGC	.	.		0.617	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6648374	G	A	6648374	3	1	110	1	0	0	0	0	1	0	0	0	4289	1087	38	1	4032	1	DCHS1	11	6648374	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	5018964	6648374	128358142	25	16220										
MRVI1	10335	hgsc.bcm.edu	37	chr11	10602112	10602112	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	ttcaggtcttgaagttctttGgtcttctttagaccttcttg	8	8	6	2			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr11:10602112G>A	ENST00000436272.1	-	19	2382	c.2304C>T	c.(2302-2304)acC>acT	p.T768T	MRVI1_ENST00000421747.1_Silent_p.T786T|MRVI1_ENST00000558540.1_Silent_p.T480T|MRVI1_ENST00000547195.1_Silent_p.T704T|MRVI1_ENST00000552103.1_Silent_p.T704T|MRVI1_ENST00000534266.2_Silent_p.T480T|MRVI1_ENST00000541483.1_Silent_p.T589T|MRVI1_ENST00000531107.1_Silent_p.T787T|LYVE1_ENST00000531706.1_Intron|MRVI1_ENST00000424001.1_Silent_p.T480T|MRVI1_ENST00000423302.2_Silent_p.T795T|MRVI1_ENST00000527509.2_Silent_p.T704T|MRVI1_ENST00000545852.1_Silent_p.T480T|MRVI1-AS1_ENST00000529829.1_RNA|MRVI1-AS1_ENST00000529979.1_RNA			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	768	Glu-rich.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		GAAGTTCTTTGGTCTTCTTTA	0.498																																					p.T795T		Atlas-SNP	.											.	MRVI1	113	.	0			c.C2385T						.						116	116	116					11																	10602112		1872	4118	5990	SO:0001819	synonymous_variant	10335	exon20			TTCTTTGGTCTTC	AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"inositol 1,4,5-triphosphate-associated cGMP kinase substrate", "IP3R-associated cGMP kinase substrate"	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.2304C>T	chr11.hg19:g.10602112G>A		87.0	0.0		59.0	5.0	NM_130385	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Silent	SNP	ENST00000436272.1	hg19																																																																																				.	.		0.498	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		A	10602112	G	A	10602112	2	1	110	1	0	0	0	0	0	0	0	1	9862	1335	47	3		3	MRVI1	11	10602112	Silent	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	3953738	10602112	124404404	26	16221										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17428453	17428453	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	acctggctgagggagcagttCctggctgcaggggtcagggt	18	9	1	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr11:17428453C>A	ENST00000389817.3	-	25	3212	c.3144G>T	c.(3142-3144)agG>agT	p.R1048S	ABCC8_ENST00000302539.4_Missense_Mutation_p.R1049S			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1048	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	GGGAGCAGTTCCTGGCTGCAG	0.637																																					p.R1048S		Atlas-SNP	.											.	ABCC8	170	.	0			c.G3144T						.						52	57	55					11																	17428453		2200	4293	6493	SO:0001583	missense	6833	exon25			GCAGTTCCTGGCT	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.3144G>T	chr11.hg19:g.17428453C>A	ENSP00000374467:p.Arg1048Ser	123.0	0.0		87.0	17.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Missense_Mutation	SNP	ENST00000389817.3	hg19	CCDS31437.1	.	.	.	.	.	.	.	.	.	.	C	7.954	0.745426	0.15710	.	.	ENSG00000006071	ENST00000389817;ENST00000302539	D;D	0.94457	-3.43;-3.43	5.73	2.75	0.32379	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.559684	0.20470	N	0.091704	D	0.84875	0.5569	N	0.16567	0.415	0.49483	D	0.999796	B	0.02656	0.0	B	0.09377	0.004	T	0.72107	-0.4390	10	0.07644	T	0.81	.	5.9956	0.19491	0.0:0.6241:0.1367:0.2392	.	1048	Q09428	ABCC8_HUMAN	S	1048;1049	ENSP00000374467:R1048S;ENSP00000303960:R1049S	ENSP00000303960:R1049S	R	-	3	2	ABCC8	17385029	0.990000	0.36364	0.999000	0.59377	0.780000	0.44128	0.711000	0.25764	0.390000	0.25115	-0.176000	0.13171	AGG	.	.		0.637	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		A	17428453	C	A	17428453	3	1	110	1	0	0	0	0	1	0	0	0	58	854	30	3	1661	3	ABCC8	11	17428453	Missense_Mutation	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10	6826341	17428453	117578063	27	16222										
FOLH1	2346	hgsc.bcm.edu	37	chr11	49229931	49229931	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	gcggcgcgcggtggccacagCcgagtcggtttcgtgaagga	18	11	0	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr11:49229931C>G	ENST00000256999.2	-	1	291	c.31G>C	c.(31-33)Gct>Cct	p.A11P	FOLH1_ENST00000533034.1_5'Flank|FOLH1_ENST00000340334.7_5'UTR|FOLH1_ENST00000356696.3_Missense_Mutation_p.A11P|FOLH1_ENST00000343844.4_5'UTR	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	11					folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	GTGGCCACAGCCGAGTCGGTT	0.716																																					p.A11P		Atlas-SNP	.											.	FOLH1	141	.	0			c.G31C						.						8	11	10					11																	49229931		2162	4235	6397	SO:0001583	missense	2346	exon1			CCACAGCCGAGTC	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"glutamate carboxylase II", "glutamate carboxypeptidase II"	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.31G>C	chr11.hg19:g.49229931C>G	ENSP00000256999:p.Ala11Pro	45.0	0.0		42.0	21.0	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	hg19	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	C	13.38	2.220849	0.39201	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000389724	T;T	0.38887	1.11;1.14	4.19	-1.61	0.08399	.	1.118390	0.07122	U	0.844044	T	0.19565	0.0470	N	0.08118	0	0.09310	N	0.999999	B;B	0.31153	0.232;0.31	B;B	0.28139	0.086;0.057	T	0.18335	-1.0340	10	0.35671	T	0.21	.	5.1131	0.14819	0.3404:0.5124:0.0:0.1472	.	11;11	Q04609-8;Q04609	.;FOLH1_HUMAN	P	11	ENSP00000256999:A11P;ENSP00000349129:A11P	ENSP00000256999:A11P	A	-	1	0	FOLH1	49186507	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.292000	0.19011	-0.199000	0.10317	0.591000	0.81541	GCT	.	.		0.716	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476		G	49229931	C	G	49229931	3	3	110	1	0	0	0	0	1	0	0	0	5987	739	26	4	2297	4	FOLH1	11	49229931	Missense_Mutation	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10	31801478	49229931	85776585	28	16223										
RNF214	257160	hgsc.bcm.edu	37	chr11	117150670	117150670	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	gactcaagaatcaggatggcGaaataaataggaacattatg	10	5	2	1	rs377377564		TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr11:117150670G>A	ENST00000531452.1	+	7	1052	c.1006G>A	c.(1006-1008)Gaa>Aaa	p.E336K	RNF214_ENST00000530849.1_Missense_Mutation_p.E181K|RNF214_ENST00000300650.4_Missense_Mutation_p.E336K|RNF214_ENST00000531287.1_Missense_Mutation_p.E181K	NM_001077239.1|NM_001278249.1	NP_001070707.1|NP_001265178.1	Q8ND24	RN214_HUMAN	ring finger protein 214	336							zinc ion binding (GO:0008270)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		TCAGGATGGCGAAATAAATAG	0.423													G|||	1	0.000199681	0	0	5008	,	,		17895	0		0	False		,,,				2504	0.001				p.E336K		Atlas-SNP	.											.	RNF214	54	.	0			c.G1006A						.	G	LYS/GLU,LYS/GLU	0,3784		0,0,1892	106	104	105		1006,1006	5	1	11		105	2,8220		0,2,4109	no	missense,missense	RNF214	NM_001077239.1,NM_207343.2	56,56	0,2,6001	AA,AG,GG		0.0243,0.0,0.0167	probably-damaging,probably-damaging	336/704,336/704	117150670	2,12004	1892	4111	6003	SO:0001583	missense	257160	exon7			GATGGCGAAATAA	AL834448	CCDS41720.1, CCDS60976.1	11q23.3	2014-02-12	2007-02-16		ENSG00000167257	ENSG00000167257		"RING-type (C3HC4) zinc fingers"	25335	protein-coding gene	gene with protein product							Standard	NM_001077239		Approved	DKFZp547C195	uc001pqt.4	Q8ND24	OTTHUMG00000167069	ENST00000531452.1:c.1006G>A	chr11.hg19:g.117150670G>A	ENSP00000431643:p.Glu336Lys	81.0	0.0		61.0	21.0	NM_207343	B2RUW0|B4DTD1	Missense_Mutation	SNP	ENST00000531452.1	hg19	CCDS41720.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.476885	0.63849	0.0	2.43E-4	ENSG00000167257	ENST00000531287;ENST00000531452;ENST00000530849;ENST00000300650	T;T;D;T	0.94758	2.57;1.17;-3.51;1.17	5.0	5.0	0.66597	.	0.172631	0.49916	D	0.000128	D	0.95993	0.8695	L	0.60455	1.87	0.47737	D	0.999509	D;D	0.89917	0.995;1.0	D;D	0.79108	0.97;0.992	D	0.93911	0.7197	10	0.13108	T	0.6	-5.6583	17.648	0.88154	0.0:0.0:1.0:0.0	.	181;336	B4DTD1;Q8ND24	.;RN214_HUMAN	K	181;336;181;336	ENSP00000435361:E181K;ENSP00000431643:E336K;ENSP00000432903:E181K;ENSP00000300650:E336K	ENSP00000300650:E336K	E	+	1	0	RNF214	116655880	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.740000	0.62087	2.476000	0.83614	0.462000	0.41574	GAA	.	.		0.423	RNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392884.1	NM_001077239		A	117150670	G	A	117150670	3	1	110	1	0	0	0	0	1	0	0	0	13493	1059	37	1	1028	1	RNF214	11	117150670	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	67920739	117150670	17855846	29	16224										
KRT2	3849	hgsc.bcm.edu	37	chr12	53045634	53045635	+	In_Frame_Ins	INS	-	-	CTCCAAAGCCGCTGCCGC													0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	acctccaaagctgctgccgcINSctccaaaaccacctcctctg							TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr12:53045634_53045635insCTCCAAAGCCGCTGCCGC	ENST00000309680.3	-	1	313_314	c.292_293insGCGGCAGCGGCTTTGGAG	c.(292-294)ggc>gGCGGCAGCGGCTTTGGAGgc	p.98_98G>GGSGFGG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	98	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		gctgctgccgcctccaaaacca	0.624																																					p.G98delinsGGSGFGG		Atlas-INDEL	.											.	KRT2	94	.	0			c.293_294insGCGGCAGCGGCTTTGGAG						.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.292_293insGCGGCAGCGGCTTTGGAG	chr12.hg19:g.53045634_53045635insCTCCAAAGCCGCTGCCGC	Exception_encountered	92.0	0.0		89.0	23.0	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.624	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		CTCCAAAGCCGCTGCCGC	53045635	-	CTCCAAAGCCGCTGCCGC	53045634	7	5	110	1	0	1	1	0	0	0	0	0	8466	739	26	0	1662	0	KRT2	12	53045634	In_Frame_Ins	INS	-	TCGA-DD-A39W-01A-11D-A20W-10		53045634	80806261	30	16225										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121431424	121431424	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	gtttcaagtggggcccagcaTcccagcagatcctgttccag	11	13	1	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr12:121431424T>A	ENST00000257555.6	+	3	854	c.628T>A	c.(628-630)Tcc>Acc	p.S210T	HNF1A_ENST00000541395.1_Missense_Mutation_p.S210T|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_Missense_Mutation_p.S210T|HNF1A_ENST00000402929.1_Missense_Mutation_p.S210T|HNF1A_ENST00000400024.2_Missense_Mutation_p.S210T|HNF1A_ENST00000543427.1_Missense_Mutation_p.S93T			P20823	HNF1A_HUMAN	HNF1 homeobox A	210					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.W206fs*10(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GGGCCCAGCATCCCAGCAGAT	0.592									Hepatic Adenoma, Familial Clustering of																												p.S210T		Atlas-SNP	.											.	HNF1A	302	.	1	Deletion - Frameshift(1)	liver(1)	c.T628A						.						99	92	94					12																	121431424		2203	4300	6503	SO:0001583	missense	6927	exon3	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCAGCATCCCAGC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.628T>A	chr12.hg19:g.121431424T>A	ENSP00000257555:p.Ser210Thr	131.0	0.0		109.0	21.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.497127	0.85069	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543027;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D;D	0.96168	-3.93;-3.93;-3.93;-3.93	4.55	4.55	0.56014	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000007	D	0.97021	0.9027	M	0.72118	2.19	0.58432	D	0.999993	D;D;D;D	0.71674	0.994;0.981;0.998;0.995	D;P;D;D	0.72338	0.942;0.88;0.977;0.966	D	0.97421	1.0009	10	0.72032	D	0.01	-27.0714	13.1155	0.59297	0.0:0.0:0.0:1.0	.	210;210;210;210	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	T	210;210;210;210;210;210;93;210;210;210;210;210	ENSP00000257555:S210T;ENSP00000439721:S93T;ENSP00000443112:S210T;ENSP00000438804:S210T	ENSP00000257555:S210T	S	+	1	0	HNF1A	119915807	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	7.564000	0.82326	1.701000	0.51217	0.423000	0.28283	TCC	.	.		0.592	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		A	121431424	T	A	121431424	3	1	110	1	0	0	0	0	1	0	0	0	7260	1435	50	4	638	4	HNF1A	12	121431424	Missense_Mutation	SNP	T	TCGA-DD-A39W-01A-11D-A20W-10	68385790	121431424	12420471	31	16226										
LHFP	10186	hgsc.bcm.edu	37	chr13	40175212	40175212	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	cacaggatatgagcacctccGgaaggtaccgaaggacacag	12	11	0	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr13:40175212G>A	ENST00000379589.3	-	2	604	c.142C>T	c.(142-144)Cgg>Tgg	p.R48W	LHFP_ENST00000495922.1_5'Flank	NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	48						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)		HMGA2/LHFP(2)	breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		GAGCACCTCCGGAAGGTACCG	0.572			T	HMGA2	lipoma																																p.R48W		Atlas-SNP	.		Dom	yes		13	13q12	10186	lipoma HMGIC fusion partner		M	.	LHFP	31	.	0			c.C142T						.						184	170	175					13																	40175212		2203	4300	6503	SO:0001583	missense	10186	exon2			ACCTCCGGAAGGT	AF098807	CCDS9369.1	13q12	2008-07-18			ENSG00000183722	ENSG00000183722			6586	protein-coding gene	gene with protein product		606710				10329012	Standard	NM_005780		Approved	MGC22429	uc001uxf.3	Q9Y693	OTTHUMG00000016767	ENST00000379589.3:c.142C>T	chr13.hg19:g.40175212G>A	ENSP00000368908:p.Arg48Trp	181.0	0.0		134.0	23.0	NM_005780	B2R7M2|Q53FC0|Q96SH5	Missense_Mutation	SNP	ENST00000379589.3	hg19	CCDS9369.1	.	.	.	.	.	.	.	.	.	.	G	32	5.128127	0.94473	.	.	ENSG00000183722	ENST00000379589	T	0.72942	-0.7	5.38	5.38	0.77491	.	0.000000	0.64402	D	0.000004	D	0.85999	0.5828	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87111	0.2185	9	.	.	.	.	18.101	0.89505	0.0:0.0:1.0:0.0	.	48	Q9Y693	LHFP_HUMAN	W	48	ENSP00000368908:R48W	.	R	-	1	2	LHFP	39073212	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.373000	0.97168	2.522000	0.85027	0.655000	0.94253	CGG	.	.		0.572	LHFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044619.1	NM_005780		A	40175212	G	A	40175212	3	1	110	1	0	0	0	0	1	0	0	0	8772	1115	39	1	472	1	LHFP	13	40175212	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10		40175212	74994666	32	16227										
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3085397	3085397	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	cccctcccaggaatgagtccCgccgctccagcacaaagggg	11	17	0	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr16:3085397C>T	ENST00000572449.1	-	2	163	c.101G>A	c.(100-102)cGg>cAg	p.R34Q	CCDC64B_ENST00000389347.4_Missense_Mutation_p.R34Q|CCDC64B_ENST00000573514.1_5'Flank|RP11-473M20.5_ENST00000382225.3_RNA			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	34										breast(1)|endometrium(2)|large_intestine(1)	4						GAATGAGTCCCGCCGCTCCAG	0.682																																					p.R34Q		Atlas-SNP	.											.	CCDC64B	19	.	0			c.G101A						.						11	14	13					16																	3085397		1864	4084	5948	SO:0001583	missense	146439	exon1			GAGTCCCGCCGCT	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.101G>A	chr16.hg19:g.3085397C>T	ENSP00000459043:p.Arg34Gln	97.0	0.0		87.0	37.0	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	c	22.3	4.265203	0.80358	.	.	ENSG00000162069	ENST00000389347	T	0.30981	1.51	5.08	4.12	0.48240	.	0.241759	0.26991	N	0.021474	T	0.29620	0.0739	N	0.19112	0.55	0.27577	N	0.949695	D	0.69078	0.997	P	0.55391	0.775	T	0.04946	-1.0916	10	0.34782	T	0.22	-34.7454	10.5633	0.45159	0.0:0.9061:0.0:0.0939	.	34	A1A5D9	BICR2_HUMAN	Q	34	ENSP00000373998:R34Q	ENSP00000373998:R34Q	R	-	2	0	CCDC64B	3025398	0.031000	0.19500	0.746000	0.31095	0.962000	0.63368	1.921000	0.40035	2.361000	0.80049	0.457000	0.33378	CGG	.	.		0.682	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1			T	3085397	C	T	3085397	3	4	110	1	0	0	0	0	1	0	0	0	2838	652	23	1	1461	1	CCDC64B	16	3085397	Missense_Mutation	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10		3085397	87269356	33	16228										
CTCF	10664	hgsc.bcm.edu	37	chr16	67660509	67660509	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	tgagcaaggcaagaaatgccGttactgtgatgctgtgtttc	12	7	0	3			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr16:67660509G>A	ENST00000264010.4	+	8	1853	c.1409G>A	c.(1408-1410)cGt>cAt	p.R470H	CTCF_ENST00000401394.1_Missense_Mutation_p.R142H	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	470					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		AAGAAATGCCGTTACTGTGAT	0.453																																					p.R470H	Colon(175;1200 1966 6945 23069 27405)	Atlas-SNP	.											.	CTCF	193	.	0			c.G1409A						.						115	92	100					16																	67660509		2198	4300	6498	SO:0001583	missense	10664	exon8			AATGCCGTTACTG	U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"Zinc fingers, C2H2-type"	13723	protein-coding gene	gene with protein product	"11 zinc finger transcriptional repressor"	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.1409G>A	chr16.hg19:g.67660509G>A	ENSP00000264010:p.Arg470His	130.0	0.0		98.0	32.0	NM_006565	B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	ENST00000264010.4	hg19	CCDS10841.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.653330	0.88056	.	.	ENSG00000102974	ENST00000264010;ENST00000401394	T;T	0.42131	0.98;0.98	5.2	4.23	0.50019	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000008	T	0.28366	0.0701	N	0.16790	0.44	0.80722	D	1	D	0.52996	0.957	B	0.39258	0.295	T	0.19321	-1.0309	10	0.66056	D	0.02	-2.7963	16.0322	0.80585	0.0:0.1347:0.8653:0.0	.	470	P49711	CTCF_HUMAN	H	470;142	ENSP00000264010:R470H;ENSP00000384707:R142H	ENSP00000264010:R470H	R	+	2	0	CTCF	66218010	1.000000	0.71417	0.979000	0.43373	0.994000	0.84299	9.813000	0.99286	1.303000	0.44873	0.561000	0.74099	CGT	.	.		0.453	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2	NM_006565		A	67660509	G	A	67660509	3	1	110	1	0	0	0	0	1	0	0	0	4002	1145	40	1	1431	1	CTCF	16	67660509	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	64575112	67660509	22694244	34	16229										
LIG3	3980	hgsc.bcm.edu	37	chr17	33310396	33310396	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	cgaattggcaaagtggtgccCaatcccttctcagagtctgg	11	11	2	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr17:33310396C>T	ENST00000378526.4	+	2	505	c.372C>T	c.(370-372)ccC>ccT	p.P124P	LIG3_ENST00000262327.5_Silent_p.P124P|LIG3_ENST00000586407.1_Intron	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	124					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	AAGTGGTGCCCAATCCCTTCT	0.493								Other BER factors																													p.P124P		Atlas-SNP	.											.	LIG3	164	.	0			c.C372T						.						73	68	70					17																	33310396		2203	4300	6503	SO:0001819	synonymous_variant	3980	exon2			GGTGCCCAATCCC		CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"ligase II, DNA, ATP-dependent"	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.372C>T	chr17.hg19:g.33310396C>T		131.0	0.0		81.0	14.0	NM_013975	Q16714|Q6NVK3	Silent	SNP	ENST00000378526.4	hg19	CCDS11284.2																																																																																			.	.		0.493	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975		T	33310396	C	T	33310396	2	4	110	1	0	0	0	0	0	0	0	1	8791	581	21	3		3	LIG3	17	33310396	Silent	SNP	C	TCGA-DD-A39W-01A-11D-A20W-10		33310396	47884814	35	16230										
FTSJ3	11325	hgsc.bcm.edu	37	chr17	61898837	61898837	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	ttcccttaggggcttcatctTggtacaggggagacattatc	11	9	2	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr17:61898837T>C	ENST00000578681.1	+	0	4337				FTSJ3_ENST00000427159.2_Missense_Mutation_p.Q588R	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42						protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						GGCTTCATCTTGGTACAGGGG	0.547																																					p.Q588R		Atlas-SNP	.											.	FTSJ3	63	.	0			c.A1763G						.						79	81	80					17																	61898837		2203	4300	6503	SO:0001628	intergenic_variant	117246	exon16			TCATCTTGGTACA	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"DEAD-boxes"	18676	protein-coding gene	gene with protein product	"splicing factor 3b, subunit 8"	613369	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3			chr17.hg19:g.61898837T>C		72.0	0.0		78.0	13.0	NM_017647	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	hg19	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	T	4.695	0.129276	0.08981	.	.	ENSG00000108592	ENST00000427159	T	0.30182	1.54	5.17	-8.58	0.00897	.	1.210430	0.05840	N	0.619246	T	0.10035	0.0246	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19647	-1.0299	10	0.18276	T	0.48	3.4868	0.8566	0.01184	0.1861:0.2774:0.2277:0.3088	.	588	Q8IY81	RRMJ3_HUMAN	R	588	ENSP00000396673:Q588R	ENSP00000396673:Q588R	Q	-	2	0	FTSJ3	59252569	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.612000	0.05616	-2.768000	0.00366	-2.866000	0.00100	CAA	.	.		0.547	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372		C	61898837	T	C	61898837	1	2	110	0	1	0	0	0	0	0	0	0	6097	1812	63	2		2	FTSJ3	17	61898837	IGR	SNP	T	TCGA-DD-A39W-01A-11D-A20W-10	28588441	61898837	19296373	36	16231										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73723530	73723530	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	cccaggcggagctgctggccGcgggctgccagcgggagagc	19	14	0	1	rs569235037		TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr17:73723530G>A	ENST00000200181.3	+	4	395	c.208G>A	c.(208-210)Gcg>Acg	p.A70T	ITGB4_ENST00000449880.2_Missense_Mutation_p.A70T|ITGB4_ENST00000339591.3_Missense_Mutation_p.A70T|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000450894.3_Missense_Mutation_p.A70T|ITGB4_ENST00000579662.1_Missense_Mutation_p.A70T	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	70	PSI.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCTGCTGGCCGCGGGCTGCCA	0.682													G|||	1	0.000199681	0	0.0014	5008	,	,		14709	0		0	False		,,,				2504	0				p.A70T		Atlas-SNP	.											.	ITGB4	165	.	0			c.G208A						.						22	26	25					17																	73723530		2201	4298	6499	SO:0001583	missense	3691	exon4			CTGGCCGCGGGCT		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.208G>A	chr17.hg19:g.73723530G>A	ENSP00000200181:p.Ala70Thr	155.0	0.0		132.0	36.0	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	5.370	0.253508	0.10185	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.92595	-3.07;-3.07;-3.07	5.46	0.956	0.19608	Integrin beta subunit, N-terminal (2);	0.865281	0.10275	N	0.694280	D	0.85062	0.5611	L	0.49640	1.575	0.09310	N	1	P;B;P;P	0.47409	0.455;0.172;0.895;0.484	B;B;B;B	0.35114	0.145;0.049;0.196;0.081	T	0.73285	-0.4031	10	0.14252	T	0.57	.	8.3329	0.32197	0.0765:0.0:0.421:0.5024	.	70;70;70;70	P16144-5;P16144-3;A0AVL6;P16144	.;.;.;ITB4_HUMAN	T	70	ENSP00000200181:A70T;ENSP00000344079:A70T;ENSP00000400217:A70T	ENSP00000200181:A70T	A	+	1	0	ITGB4	71235125	0.000000	0.05858	0.011000	0.14972	0.136000	0.21042	0.510000	0.22723	0.662000	0.31006	-0.152000	0.13540	GCG	.	.		0.682	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			A	73723530	G	A	73723530	3	1	110	1	0	0	0	0	1	0	0	0	7906	1087	38	1	218	1	ITGB4	17	73723530	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	11824693	73723530	7471680	37	16232										
WDR45L	56270	hgsc.bcm.edu	37	chr17	80576976	80576976	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	cctggattaaatgccctgatGaagtatcaaatattcttata	6	7	2	2			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr17:80576976G>C	ENST00000392325.4	-	7	841	c.647C>G	c.(646-648)tCa>tGa	p.S216*	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	216																	ATGCCCTGATGAAGTATCAAA	0.393																																					p.S216X		Atlas-SNP	.											.	.	.	.	0			c.C647G						.						87	82	83					17																	80576976		2203	4300	6503	SO:0001587	stop_gained	56270	exon7			CCTGATGAAGTAT	AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"WD repeat domain containing"	25072	protein-coding gene	gene with protein product		609226	"WDR45-like"	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.647C>G	chr17.hg19:g.80576976G>C	ENSP00000376139:p.Ser216*	113.0	0.0		76.0	17.0	NM_019613	O95328|Q2MCP6|Q6IBN2	Nonsense_Mutation	SNP	ENST00000392325.4	hg19	CCDS11815.2	.	.	.	.	.	.	.	.	.	.	G	39	7.360346	0.98235	.	.	ENSG00000141580	ENST00000392325;ENST00000539012	.	.	.	5.38	5.38	0.77491	.	0.121344	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-12.7597	19.4833	0.95018	0.0:0.0:1.0:0.0	.	.	.	.	X	216;188	.	ENSP00000376139:S216X	S	-	2	0	WDR45L	78170265	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.392000	0.79840	2.684000	0.91462	0.591000	0.81541	TCA	.	.		0.393	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613		C	80576976	G	C	80576976	4	2	110	1	0	0	0	0	0	1	0	0	17313	1294	45	4	403	4	WDR45L	17	80576976	Nonsense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	6853446	80576976	618234	38	16233										
CAPNS1	826	hgsc.bcm.edu	37	chr19	36637097	36637097	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	gaaggactacatccatcttaGggttccacctgaatgagcat	9	10	1	2			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr19:36637097G>C	ENST00000246533.3	+	9	1202		c.e9-1		AD001527.7_ENST00000604228.1_RNA|CAPNS1_ENST00000588780.1_Splice_Site|CAPNS1_ENST00000588815.1_Splice_Site|CAPNS1_ENST00000589146.1_Splice_Site|CAPNS1_ENST00000590874.1_Splice_Site|CAPNS1_ENST00000587718.1_Splice_Site	NM_001003962.1|NM_001749.2	NP_001003962.1|NP_001740.1	P04632	CPNS1_HUMAN	calpain, small subunit 1						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			cervix(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			ATCCATCTTAGGGTTCCACCT	0.522																																					.	Esophageal Squamous(129;1541 1691 5780 18353 34150)	Atlas-SNP	.											.	CAPNS1	19	.	0			c.605-1G>C						.						209	201	204					19																	36637097		2203	4300	6503	SO:0001630	splice_region_variant	826	exon9			ATCTTAGGGTTCC	X04106	CCDS12489.1	19q13.1	2013-01-10		2001-08-10	ENSG00000126247	ENSG00000126247	3.4.22.52	"EF-hand domain containing"	1481	protein-coding gene	gene with protein product		114170		CAPN4		3024120, 3016651	Standard	NM_001003962		Approved	CANP, CANPS, 30K, CDPS	uc002odj.3	P04632		ENST00000246533.3:c.605-1G>C	chr19.hg19:g.36637097G>C		88.0	0.0		57.0	7.0	NM_001749	A8K0P1|Q8WTX3|Q96EW0	Splice_Site	SNP	ENST00000246533.3	hg19	CCDS12489.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278835	0.59758	.	.	ENSG00000126247	ENST00000246533	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8777	0.86056	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CAPNS1	41328937	1.000000	0.71417	0.976000	0.42696	0.092000	0.18411	8.985000	0.93487	2.646000	0.89796	0.561000	0.74099	.	.	.		0.522	CAPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457411.2		Intron	C	36637097	G	C	36637097	5	2	110	1	0	0	0	0	0	0	1	0	2635	1014	35	4	634	4	CAPNS1	19	36637097	Splice_Site	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10		36637097	22491886	39	16234										
ZNF583	147949	hgsc.bcm.edu	37	chr19	56934521	56934521	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	taacaaatcttggcaaacatTccaccaggatacaatctttg	5	10	2	0			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr19:56934521T>G	ENST00000333201.9	+	5	704	c.494T>G	c.(493-495)tTc>tGc	p.F165C	ZNF583_ENST00000585612.1_3'UTR|ZNF583_ENST00000291598.7_Missense_Mutation_p.F165C	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	165					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		TGGCAAACATTCCACCAGGAT	0.333																																					p.F165C		Atlas-SNP	.											.	ZNF583	83	.	0			c.T494G						.						74	81	78					19																	56934521		2202	4300	6502	SO:0001583	missense	147949	exon5			AAACATTCCACCA	AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"Zinc fingers, C2H2-type", "-"	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.494T>G	chr19.hg19:g.56934521T>G	ENSP00000388502:p.Phe165Cys	39.0	0.0		42.0	17.0	NM_001159861	O14850|Q2NKK3	Missense_Mutation	SNP	ENST00000333201.9	hg19	CCDS12943.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.083349	0.36758	.	.	ENSG00000198440	ENST00000291598;ENST00000333201	T;T	0.13778	2.56;2.56	4.43	2.26	0.28386	.	0.680740	0.12861	N	0.433120	T	0.31888	0.0811	M	0.82716	2.605	0.09310	N	1	D	0.69078	0.997	P	0.60345	0.873	T	0.07309	-1.0779	9	.	.	.	.	6.6063	0.22727	0.0:0.0895:0.1588:0.7517	.	165	Q96ND8	ZN583_HUMAN	C	165	ENSP00000291598:F165C;ENSP00000388502:F165C	.	F	+	2	0	ZNF583	61626333	0.032000	0.19561	0.002000	0.10522	0.024000	0.10985	1.826000	0.39092	0.804000	0.34136	0.379000	0.24179	TTC	.	.		0.333	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478		G	56934521	T	G	56934521	3	3	110	1	0	0	0	0	1	0	0	0	18030	1783	62	5	508	5	ZNF583	19	56934521	Missense_Mutation	SNP	T	TCGA-DD-A39W-01A-11D-A20W-10	20297424	56934521	2194462	40	16235										
WFDC5	149708	hgsc.bcm.edu	37	chr20	43743715	43743715	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	ccccaggaggagaaggctctGggtcctcatatttctgctgc	12	12	3	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr20:43743715G>A	ENST00000307971.4	-	1	88	c.10C>T	c.(10-12)Cag>Tag	p.Q4*	WFDC5_ENST00000372789.4_Nonsense_Mutation_p.Q4*			Q8TCV5	WFDC5_HUMAN	WAP four-disulfide core domain 5	4						extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)				AGAAGGCTCTGGGTCCTCATA	0.607																																					p.Q4X	NSCLC(199;98 2227 9943 13455 41914)	Atlas-SNP	.											.	WFDC5	19	.	0			c.C10T						.						39	46	43					20																	43743715		2203	4300	6503	SO:0001587	stop_gained	149708	exon1			GGCTCTGGGTCCT	AY038181	CCDS33475.1	20q13.11	2013-01-21			ENSG00000175121	ENSG00000175121		"WAP four-disulfide core domain containing"	20477	protein-coding gene	gene with protein product		605161				12206714, 10680116	Standard	NM_145652		Approved	WAP1, dJ211D12.5	uc002xne.2	Q8TCV5	OTTHUMG00000046411	ENST00000307971.4:c.10C>T	chr20.hg19:g.43743715G>A	ENSP00000312381:p.Gln4*	42.0	0.0		36.0	7.0	NM_145652	Q5H981|Q6UWE4	Nonsense_Mutation	SNP	ENST00000307971.4	hg19		.	.	.	.	.	.	.	.	.	.	G	13.37	2.217248	0.39201	.	.	ENSG00000175121	ENST00000372789;ENST00000307971	.	.	.	5.61	-3.78	0.04333	.	2.576260	0.01580	N	0.021050	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-0.2248	2.0509	0.03571	0.412:0.1162:0.3427:0.1291	.	.	.	.	X	4	.	ENSP00000312381:Q4X	Q	-	1	0	WFDC5	43177129	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.339000	0.07832	-1.088000	0.03077	-0.282000	0.10007	CAG	.	.		0.607	WFDC5-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000107192.1			A	43743715	G	A	43743715	4	1	110	1	0	0	0	0	0	1	0	0	17369	1357	47	3	377	3	WFDC5	20	43743715	Nonsense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10		43743715	19281805	41	16236										
GABPA	2551	hgsc.bcm.edu	37	chr21	27141414	27141414	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	cttattggatacagtgcagcGgagttgaaccgtttggtcac	12	8	1	1	rs563533466		TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr21:27141414G>A	ENST00000354828.3	+	10	1763	c.1236G>A	c.(1234-1236)gcG>gcA	p.A412A	GABPA_ENST00000400075.3_Silent_p.A412A	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa	412					cell differentiation (GO:0030154)|in utero embryonic development (GO:0001701)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	24						ACAGTGCAGCGGAGTTGAACC	0.438													G|||	1	0.000199681	0	0	5008	,	,		16103	0		0.001	False		,,,				2504	0				p.A412A		Atlas-SNP	.											.	GABPA	59	.	0			c.G1236A						.						87	90	89					21																	27141414		2203	4300	6503	SO:0001819	synonymous_variant	2551	exon10			TGCAGCGGAGTTG		CCDS13575.1	21q21-q22.1	2008-07-31	2002-08-29		ENSG00000154727	ENSG00000154727			4071	protein-coding gene	gene with protein product	"human nuclear respiratory factor-2 subunit alpha", "nuclear respiratory factor 2 alpha subunit"	600609	"GA-binding protein transcription factor, alpha subunit (60kD)"			8441384	Standard	NM_002040		Approved	E4TF1A, NFT2, NRF2, E4TF1-60, NRF2A	uc002yly.4	Q06546	OTTHUMG00000078443	ENST00000354828.3:c.1236G>A	chr21.hg19:g.27141414G>A		334.0	0.0		225.0	89.0	NM_001197297	Q12939	Silent	SNP	ENST00000354828.3	hg19	CCDS13575.1																																																																																			.	.		0.438	GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171365.1	NM_002040		A	27141414	G	A	27141414	2	1	110	1	0	0	0	0	0	0	0	1	6165	1103	39	1		1	GABPA	21	27141414	Silent	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10		27141414	20988481	42	16237										
PPARA	5465	hgsc.bcm.edu	37	chr22	46611213	46611213	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	gctatcattacggagtccacGcgtgtgaaggctgcaaggta	13	9	1	1			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chr22:46611213G>T	ENST00000396000.2	+	4	617	c.352G>T	c.(352-354)Gcg>Tcg	p.A118S	PPARA_ENST00000407236.1_Missense_Mutation_p.A118S|PPARA_ENST00000434345.2_Missense_Mutation_p.A118S|PPARA_ENST00000402126.1_Missense_Mutation_p.A118S|PPARA_ENST00000262735.5_Missense_Mutation_p.A118S			Q07869	PPARA_HUMAN	peroxisome proliferator-activated receptor alpha	118					behavioral response to nicotine (GO:0035095)|cellular lipid metabolic process (GO:0044255)|circadian regulation of gene expression (GO:0032922)|enamel mineralization (GO:0070166)|epidermis development (GO:0008544)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|negative regulation of appetite (GO:0032099)|negative regulation of blood pressure (GO:0045776)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of glycolytic process (GO:0045820)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter (GO:0072366)|regulation of circadian rhythm (GO:0042752)|regulation of glycolytic by positive regulation of transcription from RNA polymerase II promoter (GO:0072363)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|lipid binding (GO:0008289)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	15		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Indomethacin(DB00328)	CGGAGTCCACGCGTGTGAAGG	0.547																																					p.A118S		Atlas-SNP	.											.	PPARA	36	.	0			c.G352T						.						76	64	68					22																	46611213		2203	4300	6503	SO:0001583	missense	5465	exon4			GTCCACGCGTGTG	L02932	CCDS33669.1	22q12-q13.1	2013-01-16	2006-10-17		ENSG00000186951	ENSG00000186951		"Nuclear hormone receptors"	9232	protein-coding gene	gene with protein product		170998	"peroxisome proliferative activated receptor, alpha"	PPAR		7684926, 10591208	Standard	XM_005261655		Approved	hPPAR, NR1C1	uc003bgx.1	Q07869	OTTHUMG00000150443	ENST00000396000.2:c.352G>T	chr22.hg19:g.46611213G>T	ENSP00000379322:p.Ala118Ser	119.0	0.0		80.0	27.0	NM_001001928	B0G0X3|Q16241|Q6I9S0|Q92486|Q92689|Q9Y3N1	Missense_Mutation	SNP	ENST00000396000.2	hg19	CCDS33669.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.305739	0.81247	.	.	ENSG00000186951	ENST00000396000;ENST00000262735;ENST00000420804;ENST00000407236;ENST00000402126;ENST00000434345	D;D;D;D;D;D	0.97089	-4.24;-4.24;-4.24;-4.24;-4.24;-4.24	5.15	5.15	0.70609	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (6);	0.000000	0.85682	D	0.000000	D	0.95589	0.8566	N	0.04820	-0.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93943	0.7225	10	0.15952	T	0.53	.	17.9572	0.89073	0.0:0.0:1.0:0.0	.	118;118	F1D8S4;Q07869	.;PPARA_HUMAN	S	118	ENSP00000379322:A118S;ENSP00000262735:A118S;ENSP00000414752:A118S;ENSP00000385523:A118S;ENSP00000385246:A118S;ENSP00000408149:A118S	ENSP00000262735:A118S	A	+	1	0	PPARA	44989877	1.000000	0.71417	0.141000	0.22245	0.909000	0.53808	9.522000	0.98032	2.546000	0.85860	0.591000	0.81541	GCG	.	.		0.547	PPARA-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318129.3	NM_001001928		T	46611213	G	T	46611213	3	4	110	1	0	0	0	0	1	0	0	0	12306	1087	38	1	358	1	PPARA	22	46611213	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10		46611213	4693353	43	16238										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20227476	20227476	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	gatctgccttttcatgtcctTcctttacatgatgtgtgatt	7	9	2	2			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chrX:20227476T>A	ENST00000379565.3	-	3	380	c.173A>T	c.(172-174)gAa>gTa	p.E58V	RPS6KA3_ENST00000544447.1_Missense_Mutation_p.E30V|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.E29V|RPS6KA3_ENST00000540702.1_Missense_Mutation_p.E30V	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	58					axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TTCATGTCCTTCCTTTACATG	0.393																																					p.E58V		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.A173T						.						217	165	183					X																	20227476		2203	4300	6503	SO:0001583	missense	6197	exon3			TGTCCTTCCTTTA	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.173A>T	chrX.hg19:g.20227476T>A	ENSP00000368884:p.Glu58Val	177.0	0.0		102.0	33.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	T	17.15	3.316031	0.60524	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702;ENST00000457145;ENST00000438357	T;T;T;T;T;T	0.73152	-0.61;-0.58;-0.59;-0.58;-0.72;3.2	4.83	4.83	0.62350	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.81297	0.4793	M	0.67397	2.05	0.80722	D	1	B;B;D;B	0.62365	0.03;0.029;0.991;0.0	B;B;D;B	0.72982	0.016;0.036;0.979;0.002	T	0.82426	-0.0463	10	0.54805	T	0.06	.	12.7122	0.57096	0.0:0.0:0.0:1.0	.	30;29;30;58	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	V	58;30;29;30;29;30	ENSP00000368884:E58V;ENSP00000440220:E30V;ENSP00000368865:E29V;ENSP00000444837:E30V;ENSP00000407655:E29V;ENSP00000388512:E30V	ENSP00000368865:E29V	E	-	2	0	RPS6KA3	20137397	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.775000	0.85489	1.708000	0.51301	0.417000	0.27973	GAA	.	.		0.393	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		A	20227476	T	A	20227476	3	1	110	1	0	0	0	0	1	0	0	0	13667	1783	62	4	2129	4	RPS6KA3	23	20227476	Missense_Mutation	SNP	T	TCGA-DD-A39W-01A-11D-A20W-10		20227476	135043084	44	16239										
MSN	4478	hgsc.bcm.edu	37	chrX	64955217	64955217	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	2	1	0.657692307692308	2.74038461538462	0.373688811188811	1	1	0	tgaactatacatgcgccgtcGcaagcctgataccattgagg	10	11	0	3			TCGA-DD-A39W-01A-11D-A20W-10	TCGA-DD-A39W-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	394130eb-5ab8-4437-8d73-d17f4db7ac24	a7177a22-2989-4bc0-a618-67ca2b279962	g.chrX:64955217G>A	ENST00000360270.5	+	8	1056	c.884G>A	c.(883-885)cGc>cAc	p.R295H		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	295	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|establishment of endothelial barrier (GO:0061028)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|regulation of lymphocyte migration (GO:2000401)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|uropod (GO:0001931)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|structural constituent of cytoskeleton (GO:0005200)		MSN/ALK(6)	breast(4)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	43						ATGCGCCGTCGCAAGCCTGAT	0.567			T	ALK	ALCL																																p.R295H		Atlas-SNP	.		Dom	yes		X	Xq11.2-q12	4478	moesin		L	.	MSN	89	.	0			c.G884A						.						63	43	50					X																	64955217		2203	4300	6503	SO:0001583	missense	4478	exon8			GCCGTCGCAAGCC	M69066	CCDS14382.1	Xq11.1	2010-10-20			ENSG00000147065	ENSG00000147065			7373	protein-coding gene	gene with protein product		309845				1924289, 7628534	Standard	XM_005262269		Approved		uc004dwf.3	P26038	OTTHUMG00000021723	ENST00000360270.5:c.884G>A	chrX.hg19:g.64955217G>A	ENSP00000353408:p.Arg295His	287.0	0.0		223.0	9.0	NM_002444		Missense_Mutation	SNP	ENST00000360270.5	hg19	CCDS14382.1	.	.	.	.	.	.	.	.	.	.	G	35	5.426694	0.96131	.	.	ENSG00000147065	ENST00000360270	D	0.83755	-1.76	5.45	5.45	0.79879	FERM, C-terminal PH-like domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.93439	0.7907	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95055	0.8190	10	0.87932	D	0	.	16.7763	0.85551	0.0:0.0:1.0:0.0	.	295	P26038	MOES_HUMAN	H	295	ENSP00000353408:R295H	ENSP00000353408:R295H	R	+	2	0	MSN	64871942	1.000000	0.71417	0.978000	0.43139	0.972000	0.66771	9.727000	0.98787	2.278000	0.76064	0.594000	0.82650	CGC	.	.		0.567	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444		A	64955217	G	A	64955217	3	1	110	1	0	0	0	0	1	0	0	0	9894	1087	38	1	914	1	MSN	23	64955217	Missense_Mutation	SNP	G	TCGA-DD-A39W-01A-11D-A20W-10	44727741	64955217	90315343	45	16240										
GNB1	2782	hgsc.bcm.edu	37	chr1	1720616	1720617	+	Frame_Shift_Ins	INS	-	-	T													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agatgatgttgtcatgggagINStaagtcatgagctcctggtc					rs201256388		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:1720616_1720617insT	ENST00000378609.4	-	10	1122_1123	c.791_792insA	c.(790-792)tacfs	p.Y264fs		NM_001282539.1|NM_002074.3	NP_001269468.1|NP_002065.1	P62873	GBB1_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1	264					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|blood coagulation (GO:0007596)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	12	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		TGTCATGGGAGTAAGTCATGAG	0.55											OREG0012998	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y264_S265delinsX		Atlas-Indel,Pindel	.											.	GNB1	39	.	0			c.792_793insA						.																																			SO:0001589	frameshift_variant	2782	exon10			.	BC004186	CCDS34.1, CCDS72685.1	1p36.33	2013-01-10			ENSG00000078369	ENSG00000078369		"WD repeat domain containing"	4396	protein-coding gene	gene with protein product		139380					Standard	NM_002074		Approved		uc001aif.3	P62873	OTTHUMG00000000940	ENST00000378609.4:c.792dupA	chr1.hg19:g.1720617_1720617dupT	ENSP00000367872:p.Tyr264fs	196.0	0.0	598	151.0	61.0	NM_002074	B1AJZ7|P04697|P04901|Q1RMY8	Frame_Shift_Ins	INS	ENST00000378609.4	hg19	CCDS34.1																																																																																			.	.		0.55	GNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002762.3	NM_002074		T	1720617	-	T	1720616	7	5	111	1	0	1	1	0	0	0	0	0	6523	1024	36	0	238	0	GNB1	1	1720616	Frame_Shift_Ins	INS	-	TCGA-DD-A39X-01A-11D-A20W-10		1720616	247530005	1	16241										
PLEKHG5	57449	hgsc.bcm.edu	37	chr1	6529206	6529206	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcctcctcctcctcctcctcCtcttcctcctcctgctcatc	1	24	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:6529206C>T	ENST00000400915.3	-	20	2379	c.2313G>A	c.(2311-2313)gaG>gaA	p.E771E	PLEKHG5_ENST00000377740.3_Silent_p.E792E|PLEKHG5_ENST00000377732.1_Silent_p.E752E|PLEKHG5_ENST00000377725.1_Silent_p.E715E|PLEKHG5_ENST00000377748.1_Silent_p.E792E|PLEKHG5_ENST00000377728.3_Silent_p.E715E|PLEKHG5_ENST00000377737.2_Silent_p.E715E|PLEKHG5_ENST00000544978.1_Silent_p.E715E|TNFRSF25_ENST00000356876.3_5'Flank|PLEKHG5_ENST00000535355.1_Silent_p.E784E|TNFRSF25_ENST00000377782.3_5'Flank|TNFRSF25_ENST00000351959.5_5'Flank|PLEKHG5_ENST00000400913.1_Silent_p.E715E|PLEKHG5_ENST00000537245.1_Silent_p.E794E|PLEKHG5_ENST00000340850.5_Silent_p.E715E	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	771	Glu-rich.				apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		cctcctcctcctcttcctcct	0.637																																					p.E794E		Atlas-SNP	.											PLEKHG5_ENST00000377748,colon,carcinoma,0,1	PLEKHG5	66	.	0			c.G2382A						.						75	76	76					1																	6529206		2203	4300	6503	SO:0001819	synonymous_variant	57449	exon20			CTCCTCCTCTTCC	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"Pleckstrin homology (PH) domain containing"	29105	protein-coding gene	gene with protein product	"synectin-binding guanine exchange factor"	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.2313G>A	chr1.hg19:g.6529206C>T		78.0	0.0		52.0	10.0	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Silent	SNP	ENST00000400915.3	hg19	CCDS41241.1																																																																																			.	.		0.637	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631		T	6529206	C	T	6529206	2	4	111	1	0	0	0	0	0	0	0	1	12082	680	24	3		3	PLEKHG5	1	6529206	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	4808590	6529206	242721415	2	16242										
UTS2	10911	hgsc.bcm.edu	37	chr1	7912998	7912998	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atttccctggagtcaaggagAggaagagataagagaggatt	14	4	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:7912998A>G	ENST00000361696.5	-	1	97	c.66T>C	c.(64-66)ccT>ccC	p.P22P	UTS2_ENST00000054668.5_Intron|UTS2_ENST00000377516.2_Silent_p.P22P	NM_006786.3	NP_006777.1	O95399	UTS2_HUMAN	urotensin 2	22					muscle contraction (GO:0006936)|negative regulation of blood pressure (GO:0045776)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cell differentiation (GO:0045597)|positive regulation of circadian sleep/wake cycle, REM sleep (GO:0046005)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of heart rate (GO:0010460)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to testosterone (GO:0033574)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			kidney(1)|lung(4)|urinary_tract(1)	6	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)		AGTCAAGGAGAGGAAGAGATA	0.393																																					p.P22P		Atlas-SNP	.											UTS2_ENST00000361696,right_lower_lobe,carcinoma,0,1	UTS2	18	.	0			c.T66C						.						84	91	89					1																	7912998		2203	4300	6503	SO:0001819	synonymous_variant	10911	exon1			AAGGAGAGGAAGA	AF104118	CCDS90.1, CCDS91.1	1p36	2013-02-28			ENSG00000049247	ENSG00000049247		"Endogenous ligands"	12636	protein-coding gene	gene with protein product	"prepro U-II"	604097				9861051, 10499587	Standard	NM_021995		Approved	UII, U-II, UCN2, PRO1068	uc001aos.3	O95399	OTTHUMG00000001218	ENST00000361696.5:c.66T>C	chr1.hg19:g.7912998A>G		192.0	0.0		120.0	5.0	NM_006786	Q5H8X7|Q6UXF6|Q9UKP7	Silent	SNP	ENST00000361696.5	hg19	CCDS91.1																																																																																			.	.		0.393	UTS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003612.1	NM_006786		G	7912998	A	G	7912998	2	3	111	1	0	0	0	0	0	0	0	1	17119	291	11	2		2	UTS2	1	7912998	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1383792	7912998	241337623	3	16243										
NPPB	4879	hgsc.bcm.edu	37	chr1	11917725	11917725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cttcctcttaatgccgcctcAgcactgtcagggaaagagag	10	12	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:11917725A>G	ENST00000376468.3	-	3	489	c.392T>C	c.(391-393)cTg>cCg	p.L131P		NM_002521.2	NP_002512.1	P16860	ANFB_HUMAN	natriuretic peptide B	131					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|protein complex (GO:0043234)	diuretic hormone activity (GO:0008613)|hormone activity (GO:0005179)|receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	Carvedilol(DB01136)	ATGCCGCCTCAGCACTGTCAG	0.552																																					p.L131P		Atlas-SNP	.											.	NPPB	24	.	0			c.T392C						.						126	116	120					1																	11917725		2203	4300	6503	SO:0001583	missense	4879	exon3			CGCCTCAGCACTG	BC025785	CCDS140.1	1p36.2	2014-01-30	2010-11-09		ENSG00000120937	ENSG00000120937		"Endogenous ligands"	7940	protein-coding gene	gene with protein product		600295	"natriuretic peptide precursor B"			2597152	Standard	NM_002521		Approved		uc001atj.3	P16860	OTTHUMG00000002389	ENST00000376468.3:c.392T>C	chr1.hg19:g.11917725A>G	ENSP00000365651:p.Leu131Pro	129.0	0.0		95.0	4.0	NM_002521	B0ZBE9|Q6FGY0|Q9P2Q7	Missense_Mutation	SNP	ENST00000376468.3	hg19	CCDS140.1	.	.	.	.	.	.	.	.	.	.	A	10.97	1.500439	0.26861	.	.	ENSG00000120937	ENST00000376468	T	0.27402	1.67	4.65	3.5	0.40072	.	.	.	.	.	T	0.36082	0.0954	L	0.28740	0.885	0.19775	N	0.999953	D	0.89917	1.0	D	0.65987	0.94	T	0.09207	-1.0685	9	0.30078	T	0.28	.	7.2828	0.26320	0.8935:0.0:0.1065:0.0	.	131	P16860	ANFB_HUMAN	P	131	ENSP00000365651:L131P	ENSP00000365651:L131P	L	-	2	0	NPPB	11840312	0.002000	0.14202	0.047000	0.18901	0.011000	0.07611	1.577000	0.36515	1.873000	0.54277	0.459000	0.35465	CTG	.	.		0.552	NPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006854.1	NM_002521		G	11917725	A	G	11917725	3	3	111	1	0	0	0	0	1	0	0	0	10601	188	7	2	16	2	NPPB	1	11917725	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	4004727	11917725	237332896	4	16244										
PLEKHM2	23207	hgsc.bcm.edu	37	chr1	16054156	16054156	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggctcaggagctggaggcccAgctgtccctggtcagggagg	18	11	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:16054156A>G	ENST00000375799.3	+	9	1816	c.1589A>G	c.(1588-1590)cAg>cGg	p.Q530R	PLEKHM2_ENST00000375793.2_Missense_Mutation_p.Q510R|RP11-288I21.1_ENST00000453804.1_RNA	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	530					Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		CTGGAGGCCCAGCTGTCCCTG	0.657																																					p.Q530R		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.A1589G						.						18	22	21					1																	16054156		1981	4152	6133	SO:0001583	missense	23207	exon9			AGGCCCAGCTGTC	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"Pleckstrin homology (PH) domain containing"	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.1589A>G	chr1.hg19:g.16054156A>G	ENSP00000364956:p.Gln530Arg	175.0	0.0		99.0	4.0	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Missense_Mutation	SNP	ENST00000375799.3	hg19	CCDS44063.1	.	.	.	.	.	.	.	.	.	.	A	6.388	0.439684	0.12104	.	.	ENSG00000116786	ENST00000375799;ENST00000375793	T;T	0.46063	0.89;0.88	5.43	-1.83	0.07833	.	1.563280	0.03544	N	0.224390	T	0.20618	0.0496	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13150	-1.0520	10	0.13470	T	0.59	-1.2905	5.9664	0.19328	0.575:0.2299:0.1951:0.0	.	530	Q8IWE5	PKHM2_HUMAN	R	530;510	ENSP00000364956:Q530R;ENSP00000364950:Q510R	ENSP00000364950:Q510R	Q	+	2	0	PLEKHM2	15926743	0.000000	0.05858	0.000000	0.03702	0.110000	0.19582	-0.153000	0.10144	-0.268000	0.09312	0.459000	0.35465	CAG	.	.		0.657	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164		G	16054156	A	G	16054156	3	3	111	1	0	0	0	0	1	0	0	0	12090	188	7	2	1623	2	PLEKHM2	1	16054156	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	4136431	16054156	233196465	5	16245										
USP48	84196	hgsc.bcm.edu	37	chr1	22083078	22083078	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gtctcccagcatgtagtcacTacaagtgcttggacataagt	9	10	2	0	rs4253886		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:22083078T>C	ENST00000308271.9	-	3	1021	c.373A>G	c.(373-375)Agt>Ggt	p.S125G	USP48_ENST00000421625.2_Missense_Mutation_p.S125G|USP48_ENST00000529637.1_Missense_Mutation_p.S125G|USP48_ENST00000400301.1_Missense_Mutation_p.S125G	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	125	USP.		S -> C (in dbSNP:rs4253886).		ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		ATGTAGTCACTACAAGTGCTT	0.443																																					p.S125G		Atlas-SNP	.											.	USP48	91	.	0			c.A373G						.						144	146	145					1																	22083078		2203	4300	6503	SO:0001583	missense	84196	exon3			AGTCACTACAAGT	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.373A>G	chr1.hg19:g.22083078T>C	ENSP00000309262:p.Ser125Gly	172.0	0.0		92.0	4.0	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	hg19	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	T	6.055	0.378418	0.11466	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000529637;ENST00000421625	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.56	2.91	0.33838	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.289149	0.43747	N	0.000538	T	0.20495	0.0493	L	0.38953	1.18	0.29154	N	0.87817	B;B;B;B;B;B	0.27068	0.0;0.0;0.089;0.167;0.0;0.0	B;B;B;B;B;B	0.26969	0.0;0.0;0.075;0.053;0.0;0.0	T	0.10428	-1.0630	10	0.33141	T	0.24	.	6.2343	0.20754	0.0:0.1648:0.1409:0.6943	.	125;125;125;125;125;125	B7ZKS7;B7ZKS3;Q86UV5-7;Q86UV5-3;Q86UV5-2;Q86UV5	.;.;.;.;.;UBP48_HUMAN	G	125	ENSP00000383157:S125G;ENSP00000309262:S125G;ENSP00000431949:S125G;ENSP00000406256:S125G	ENSP00000309262:S125G	S	-	1	0	USP48	21955665	0.729000	0.28090	0.913000	0.36048	0.026000	0.11368	1.070000	0.30653	0.944000	0.37579	0.459000	0.35465	AGT	.	T|1.000;|0.000		0.443	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		C	22083078	T	C	22083078	3	2	111	1	0	0	0	0	1	0	0	0	17094	1522	53	2	2842	2	USP48	1	22083078	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	6028922	22083078	227167543	6	16246										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22202397	22202397	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggtgctgggctggccggggcTgggctcctgggccacatggt	20	11	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:22202397T>C	ENST00000374695.3	-	24	3221	c.3142A>G	c.(3142-3144)Agc>Ggc	p.S1048G		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1048	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGGCCGGGGCTGGGCTCCTGG	0.662																																					p.S1048G		Atlas-SNP	.											.	HSPG2	311	.	0			c.A3142G						.						51	54	53					1																	22202397		2203	4299	6502	SO:0001583	missense	3339	exon24			CGGGGCTGGGCTC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.3142A>G	chr1.hg19:g.22202397T>C	ENSP00000363827:p.Ser1048Gly	116.0	0.0		97.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	T	6.614	0.481652	0.12581	.	.	ENSG00000142798	ENST00000374695	T	0.36157	1.27	5.51	-3.5	0.04710	Laminin B type IV (2);Laminin B, subgroup (1);	1.067630	0.07365	N	0.884655	T	0.24509	0.0594	L	0.36672	1.1	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.31668	-0.9935	10	0.21014	T	0.42	.	8.2737	0.31860	0.0:0.5058:0.1272:0.367	.	1048	P98160	PGBM_HUMAN	G	1048	ENSP00000363827:S1048G	ENSP00000363827:S1048G	S	-	1	0	HSPG2	22074984	0.000000	0.05858	0.000000	0.03702	0.573000	0.36030	-1.470000	0.02346	-0.521000	0.06426	-1.145000	0.01858	AGC	.	.		0.662	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		C	22202397	T	C	22202397	3	2	111	1	0	0	0	0	1	0	0	0	7439	1580	55	2	10329	2	HSPG2	1	22202397	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	119319	22202397	227048224	7	16247										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27057832	27057832	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaccaccacagctccagtccTctcagcctccatactcccag	4	20	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:27057832T>C	ENST00000324856.7	+	3	1911	c.1540T>C	c.(1540-1542)Tct>Cct	p.S514P	ARID1A_ENST00000457599.2_Missense_Mutation_p.S514P|ARID1A_ENST00000374152.2_Missense_Mutation_p.S131P	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	514					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCTCCAGTCCTCTCAGCCTCC	0.632			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.S514P		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.T1540C						.						311	285	294					1																	27057832		2203	4300	6503	SO:0001583	missense	8289	exon3			CAGTCCTCTCAGC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1540T>C	chr1.hg19:g.27057832T>C	ENSP00000320485:p.Ser514Pro	314.0	0.0		194.0	9.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	T	8.405	0.842792	0.16963	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.02631	4.42;4.22;4.24	5.33	2.85	0.33270	.	0.488806	0.22500	N	0.059256	T	0.02533	0.0077	N	0.19112	0.55	0.80722	D	1	P;P;P	0.40875	0.612;0.731;0.612	B;B;B	0.41894	0.203;0.369;0.203	T	0.63825	-0.6549	10	0.36615	T	0.2	-6.0452	8.4261	0.32729	0.1301:0.0:0.1362:0.7337	.	514;514;168	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	P	514;514;131	ENSP00000320485:S514P;ENSP00000387636:S514P;ENSP00000363267:S131P	ENSP00000320485:S514P	S	+	1	0	ARID1A	26930419	0.072000	0.21174	0.993000	0.49108	0.392000	0.30506	0.547000	0.23299	1.007000	0.39238	0.533000	0.62120	TCT	.	.		0.632	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		C	27057832	T	C	27057832	3	2	111	1	0	0	0	0	1	0	0	0	913	1551	54	2	1550	2	ARID1A	1	27057832	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	4855435	27057832	222192789	8	16248										
SERINC2	347735	hgsc.bcm.edu	37	chr1	31905905	31905905	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccacacagcagcagcagcagGtggcagcctgtgagggccgg	16	13	0	1	rs375057852		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:31905905G>C	ENST00000373709.3	+	9	1255	c.1105G>C	c.(1105-1107)Gtg>Ctg	p.V369L	SERINC2_ENST00000491976.1_3'UTR|SERINC2_ENST00000536384.1_Missense_Mutation_p.V373L|SERINC2_ENST00000373710.1_Missense_Mutation_p.V378L|SERINC2_ENST00000536859.1_Missense_Mutation_p.V373L	NM_178865.4	NP_849196.2	Q96SA4	SERC2_HUMAN	serine incorporator 2	369					phosphatidylserine metabolic process (GO:0006658)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	L-serine transmembrane transporter activity (GO:0015194)			cervix(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	12		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151)		GCAGCAGCAGGTGGCAGCCTG	0.632																																					p.V378L		Atlas-SNP	.											.	SERINC2	44	.	0			c.G1132C						.						67	56	60					1																	31905905		2202	4300	6502	SO:0001583	missense	347735	exon10			CAGCAGGTGGCAG	AY094595	CCDS30662.1, CCDS55583.1, CCDS55584.1, CCDS55585.1	1p35.1	2008-02-05	2005-11-01	2005-11-01	ENSG00000168528	ENSG00000168528			23231	protein-coding gene	gene with protein product		614549	"tumor differentially expressed 2-like"	TDE2L		12949800	Standard	NM_178865		Approved	FKSG84, PRO0899, TDE2	uc010ogh.2	Q96SA4	OTTHUMG00000003796	ENST00000373709.3:c.1105G>C	chr1.hg19:g.31905905G>C	ENSP00000362813:p.Val369Leu	138.0	0.0		117.0	8.0	NM_001199038	A0AVB4|B4DJK5|B7Z567|B7ZAP2|E7EUZ9|Q86Y23	Missense_Mutation	SNP	ENST00000373709.3	hg19	CCDS30662.1	.	.	.	.	.	.	.	.	.	.	g	1.843	-0.467044	0.04476	.	.	ENSG00000168528	ENST00000373710;ENST00000536859;ENST00000373709;ENST00000536384	T;T;T;T	0.14766	2.48;2.48;2.48;2.48	4.09	-7.44	0.01379	.	1.213580	0.05952	N	0.638996	T	0.09024	0.0223	N	0.25647	0.755	0.09310	N	1	B;B;B	0.22414	0.002;0.002;0.069	B;B;B	0.27500	0.026;0.044;0.08	T	0.38693	-0.9649	10	0.33940	T	0.23	-0.0225	8.8861	0.35404	0.2784:0.4843:0.2372:0.0	.	373;378;370	B4DJK5;E7EUZ9;Q96SA4	.;.;SERC2_HUMAN	L	378;373;369;373	ENSP00000362814:V378L;ENSP00000444307:V373L;ENSP00000362813:V369L;ENSP00000439048:V373L	ENSP00000362813:V369L	V	+	1	0	SERINC2	31678492	0.207000	0.23482	0.003000	0.11579	0.114000	0.19823	0.165000	0.16564	-1.522000	0.01769	-1.844000	0.00574	GTG	.	.		0.632	SERINC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010680.1	NM_018565		C	31905905	G	C	31905905	3	2	111	1	0	0	0	0	1	0	0	0	14095	1261	44	4	1139	4	SERINC2	1	31905905	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	4848073	31905905	217344716	9	16249										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34191012	34191012	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cggtagagaagaggaggtagAggtagttgctggtgctgatg	19	3	0	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:34191012A>G	ENST00000373381.4	-	17	2809	c.2633T>C	c.(2632-2634)cTc>cCc	p.L878P		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	838	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GAGGAGGTAGAGGTAGTTGCT	0.567																																					p.L838P		Atlas-SNP	.											.	CSMD2	946	.	0			c.T2513C						.						118	112	114					1																	34191012		2203	4300	6503	SO:0001583	missense	114784	exon17			AGGTAGAGGTAGT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.2633T>C	chr1.hg19:g.34191012A>G	ENSP00000362479:p.Leu878Pro	182.0	0.0		133.0	6.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	A	16.91	3.253989	0.59212	.	.	ENSG00000121904	ENST00000373381	T	0.23754	1.89	5.89	5.89	0.94794	CUB (5);	0.000000	0.64402	D	0.000001	T	0.64472	0.2601	H	0.96398	3.815	0.80722	D	1	D;D	0.76494	0.999;0.986	D;D	0.75020	0.985;0.985	T	0.76110	-0.3079	10	0.59425	D	0.04	.	15.497	0.75662	1.0:0.0:0.0:0.0	.	838;878	Q7Z408;E7EUA6	CSMD2_HUMAN;.	P	878	ENSP00000362479:L878P	ENSP00000241312:L838P	L	-	2	0	CSMD2	33963599	1.000000	0.71417	1.000000	0.80357	0.058000	0.15608	9.313000	0.96297	2.254000	0.74563	0.533000	0.62120	CTC	.	.		0.567	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		G	34191012	A	G	34191012	3	3	111	1	0	0	0	0	1	0	0	0	3947	304	11	2	8162	2	CSMD2	1	34191012	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	2285107	34191012	215059609	10	16250										
RIMKLA	284716	hgsc.bcm.edu	37	chr1	42865162	42865162	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctcagtgcagtcagacagtgAcatcactgtcctgcgacacc	9	14	3	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:42865162A>G	ENST00000431473.3	+	2	380	c.251A>G	c.(250-252)gAc>gGc	p.D84G		NM_173642.3	NP_775913.2	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family member A	84					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)			NS(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						TCAGACAGTGACATCACTGTC	0.537																																					p.D84G		Atlas-SNP	.											.	RIMKLA	32	.	0			c.A251G						.						59	50	53					1																	42865162		2203	4300	6503	SO:0001583	missense	284716	exon2			ACAGTGACATCAC	BC039737	CCDS466.2	1p34.2	2011-09-21	2008-10-13	2008-10-13	ENSG00000177181	ENSG00000177181	6.3.2.N6		28725	protein-coding gene	gene with protein product	"N-acetylaspartylglutamate synthetase II"		"family with sequence similarity 80, member A"	FAM80A		20657015, 21454531	Standard	NM_173642		Approved	MGC47816, RP11-157D18.1, NAAGS-II	uc001chi.2	Q8IXN7	OTTHUMG00000007335	ENST00000431473.3:c.251A>G	chr1.hg19:g.42865162A>G	ENSP00000414330:p.Asp84Gly	113.0	0.0		123.0	5.0	NM_173642	Q5VUS5	Missense_Mutation	SNP	ENST00000431473.3	hg19	CCDS466.2	.	.	.	.	.	.	.	.	.	.	A	16.58	3.163609	0.57476	.	.	ENSG00000177181	ENST00000431473	.	.	.	4.82	4.82	0.62117	.	0.100872	0.64402	D	0.000004	T	0.34106	0.0886	L	0.29908	0.895	0.53688	D	0.999971	P	0.34800	0.469	B	0.31751	0.135	T	0.22836	-1.0205	9	0.02654	T	1	-31.8	12.3756	0.55279	1.0:0.0:0.0:0.0	.	84	Q8IXN7	RIMKA_HUMAN	G	84	.	ENSP00000414330:D84G	D	+	2	0	RIMKLA	42637749	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	9.105000	0.94246	2.027000	0.59764	0.528000	0.53228	GAC	.	.		0.537	RIMKLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019174.3	NM_173642		G	42865162	A	G	42865162	3	3	111	1	0	0	0	0	1	0	0	0	13380	275	10	2	257	2	RIMKLA	1	42865162	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	8674150	42865162	206385459	11	16251										
LEPRE1	64175	hgsc.bcm.edu	37	chr1	43218242	43218242	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcagctcctgacactcgtggTcagagattacgccgtccatc	10	14	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:43218242T>C	ENST00000296388.5	-	9	1490	c.1439A>G	c.(1438-1440)gAc>gGc	p.D480G	LEPRE1_ENST00000236040.4_Missense_Mutation_p.D480G|LEPRE1_ENST00000397054.3_Missense_Mutation_p.D480G			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	480					bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	ACACTCGTGGTCAGAGATTAC	0.577																																					p.D480G		Atlas-SNP	.											.	LEPRE1	130	.	0			c.A1439G						.						107	93	97					1																	43218242		2203	4300	6503	SO:0001583	missense	64175	exon9			TCGTGGTCAGAGA	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 1", "growth suppressor 1"	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.1439A>G	chr1.hg19:g.43218242T>C	ENSP00000296388:p.Asp480Gly	101.0	0.0		88.0	4.0	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	hg19	CCDS472.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	7.280|7.280	0.608993|0.608993	0.14066|0.14066	.|.	.|.	ENSG00000117385|ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027|ENST00000447502	T;T;T|.	0.62941|.	-0.01;-0.01;-0.01|.	4.96|4.96	0.978|0.978	0.19740|0.19740	Prolyl 4-hydroxylase, alpha subunit (1);|.	0.794069|.	0.12097|.	N|.	0.499890|.	T|.	0.38532|.	0.1044|.	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	1|1	B;B;B|.	0.34399|.	0.452;0.025;0.126|.	B;B;B|.	0.36567|.	0.228;0.022;0.05|.	T|.	0.31336|.	-0.9947|.	10|.	0.62326|.	D|.	0.03|.	-5.3158|-5.3158	11.3813|11.3813	0.49759|0.49759	0.0:0.0:0.4386:0.5614|0.0:0.0:0.4386:0.5614	.|.	480;345;480|.	Q32P28-3;B4DNM8;Q32P28|.	.;.;P3H1_HUMAN|.	G|W	480;480;480;345|71	ENSP00000380245:D480G;ENSP00000236040:D480G;ENSP00000296388:D480G|.	ENSP00000236040:D480G|.	D|X	-|-	2|3	0|0	LEPRE1|LEPRE1	42990829|42990829	0.109000|0.109000	0.22037|0.22037	0.200000|0.200000	0.23457|0.23457	0.032000|0.032000	0.12392|0.12392	1.207000|1.207000	0.32333|0.32333	0.350000|0.350000	0.24002|0.24002	0.375000|0.375000	0.23000|0.23000	GAC|TGA	.	.		0.577	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356		C	43218242	T	C	43218242	3	2	111	1	0	0	0	0	1	0	0	0	8738	1667	58	2	818	2	LEPRE1	1	43218242	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	353080	43218242	206032379	12	16252										
NRD1	4898	hgsc.bcm.edu	37	chr1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	catcatcttcttcttcttccTccacctcctcttcttcttca	0	18	9	0	rs62648104		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:52306079T>A	ENST00000354831.7	-	2	638	c.449A>T	c.(448-450)gAg>gTg	p.E150V	NRD1_ENST00000544028.1_Missense_Mutation_p.E18V|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000352171.7_Missense_Mutation_p.E150V|NRD1_ENST00000539524.1_Missense_Mutation_p.E18V	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).|Poly-Glu.				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcttcttcctccacctcctc	0.378																																					p.E150V		Atlas-SNP	.											.	NRD1	89	.	0			c.A449T						.						163	138	146					1																	52306079		2203	4300	6503	SO:0001583	missense	4898	exon2			TCTTCCTCCACCT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.449A>T	chr1.hg19:g.52306079T>A	ENSP00000346890:p.Glu150Val	254.0	0.0		201.0	23.0	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	3.056	-0.194350	0.06259	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.38240	1.31;3.15;1.15;1.22	5.25	2.92	0.33932	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.525899	0.19688	N	0.108344	T	0.18341	0.0440	N	0.14661	0.345	0.09310	N	1	B;B;B	0.23650	0.062;0.089;0.01	B;B;B	0.17098	0.017;0.007;0.007	T	0.14755	-1.0461	10	0.38643	T	0.18	-0.0317	5.1939	0.15225	0.0:0.1704:0.2022:0.6274	rs62648104	150;150;150	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	V	150;150;18;150;18	ENSP00000262679:E150V;ENSP00000346890:E150V;ENSP00000444416:E18V;ENSP00000442262:E18V	ENSP00000262679:E150V	E	-	2	0	NRD1	52078667	0.129000	0.22400	0.012000	0.15200	0.145000	0.21501	0.870000	0.28010	0.317000	0.23160	0.454000	0.30748	GAG	.	T|0.024;A|0.976		0.378	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		A	52306079	T	A	52306079	3	1	111	1	0	0	0	0	1	0	0	0	10654	1551	54	4	3338	4	NRD1	1	52306079	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	9087837	52306079	196944542	13	16253										
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52703754	52703754	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	attgaatagaccgaaaacagAggggagatctgttaaccatc	10	7	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:52703754A>G	ENST00000371591.1	+	3	796	c.665A>G	c.(664-666)gAg>gGg	p.E222G	ZFYVE9_ENST00000287727.3_Missense_Mutation_p.E222G|ZFYVE9_ENST00000357206.2_Missense_Mutation_p.E222G	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	222					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						CCGAAAACAGAGGGGAGATCT	0.378																																					p.E222G		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.A665G						.						93	96	95					1																	52703754		2203	4300	6503	SO:0001583	missense	9372	exon4			AAACAGAGGGGAG	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.665A>G	chr1.hg19:g.52703754A>G	ENSP00000360647:p.Glu222Gly	80.0	0.0		98.0	4.0	NM_007323	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	hg19	CCDS563.1	.	.	.	.	.	.	.	.	.	.	A	2.181	-0.387466	0.04932	.	.	ENSG00000157077	ENST00000357206;ENST00000361625;ENST00000287727;ENST00000371591	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	5.12	1.43	0.22495	.	0.225560	0.30244	N	0.010070	T	0.29749	0.0743	N	0.19112	0.55	0.09310	N	1	B;B;P	0.43477	0.277;0.181;0.808	B;B;P	0.44359	0.203;0.062;0.447	T	0.08889	-1.0700	10	0.27785	T	0.31	.	4.8304	0.13437	0.712:0.0:0.1514:0.1367	.	222;222;222	O95405-2;O95405;O95405-3	.;ZFYV9_HUMAN;.	G	222	ENSP00000349737:E222G;ENSP00000355358:E222G;ENSP00000287727:E222G;ENSP00000360647:E222G	ENSP00000287727:E222G	E	+	2	0	ZFYVE9	52476342	1.000000	0.71417	0.090000	0.20809	0.015000	0.08874	3.211000	0.51137	0.401000	0.25424	0.533000	0.62120	GAG	.	.		0.378	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		G	52703754	A	G	52703754	3	3	111	1	0	0	0	0	1	0	0	0	17686	304	11	2	671	2	ZFYVE9	1	52703754	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	397675	52703754	196546867	14	16254										
FPGT	8790	hgsc.bcm.edu	37	chr1	74670761	74670761	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tatttcatcttcttaaaggaAcatcactaaatgttgttgtt	5	6	4	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:74670761A>G	ENST00000609362.1	+	4	1067	c.1030A>G	c.(1030-1032)Aca>Gca	p.T344A	FPGT-TNNI3K_ENST00000370899.3_Intron|TNNI3K_ENST00000370891.2_Intron|FPGT_ENST00000370894.5_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT_ENST00000370898.3_Missense_Mutation_p.T357A|FPGT_ENST00000534056.1_Intron|FPGT_ENST00000524915.1_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	344					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)			breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						TCTTAAAGGAACATCACTAAA	0.333																																					p.T344A		Atlas-SNP	.											.	FPGT	77	.	0			c.A1030G						.						56	58	57					1																	74670761		2203	4299	6502	SO:0001583	missense	8790	exon4			AAAGGAACATCAC	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.1030A>G	chr1.hg19:g.74670761A>G	ENSP00000476680:p.Thr344Ala	103.0	0.0		87.0	4.0	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Missense_Mutation	SNP	ENST00000609362.1	hg19	CCDS663.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.119137	0.56505	.	.	ENSG00000254685	ENST00000370898	T	0.31769	1.48	5.81	4.67	0.58626	L-fucokinase (1);	.	.	.	.	T	0.21761	0.0524	M	0.64404	1.975	0.50039	D	0.999844	P	0.36712	0.566	B	0.43990	0.438	T	0.07888	-1.0749	8	.	.	.	.	6.7053	0.23246	0.7925:0.0:0.0732:0.1343	.	344	O14772	FPGT_HUMAN	A	344	ENSP00000359935:T344A	.	T	+	1	0	TNNI3K	74443349	1.000000	0.71417	0.984000	0.44739	0.882000	0.50991	4.588000	0.60999	2.217000	0.71921	0.533000	0.62120	ACA	.	.		0.333	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	74670761	A	G	74670761	3	3	111	1	0	0	0	0	1	0	0	0	6045	43	2	2	1044	2	FPGT	1	74670761	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	21967007	74670761	174579860	15	16255										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86904780	86904780	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atttgttcagggcttaagaaAggatttgaggtacagtagag	13	3	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:86904780A>G	ENST00000370565.4	+	7	1356	c.1194A>G	c.(1192-1194)aaA>aaG	p.K398K		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	398	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		GGCTTAAGAAAGGATTTGAGG	0.413																																					p.K398K	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.A1194G						.						104	92	96					1																	86904780		2203	4300	6503	SO:0001819	synonymous_variant	9635	exon7			TAAGAAAGGATTT		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1194A>G	chr1.hg19:g.86904780A>G		136.0	0.0		88.0	4.0	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	hg19	CCDS708.1																																																																																			.	.		0.413	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		G	86904780	A	G	86904780	2	3	111	1	0	0	0	0	0	0	0	1	3460	69	3	2		2	CLCA2	1	86904780	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	12234019	86904780	162345841	16	16256										
GTF2B	2959	hgsc.bcm.edu	37	chr1	89322918	89322918	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcctcttttcagctgatgccTgtgaggccatgtaaatagct	9	10	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:89322918T>C	ENST00000370500.5	-	6	906	c.788A>G	c.(787-789)cAg>cGg	p.Q263R	GTF2B_ENST00000494819.1_5'Flank	NM_001514.5	NP_001505.1	Q00403	TF2B_HUMAN	general transcription factor IIB	263					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)	core promoter binding (GO:0001047)|thyroid hormone receptor binding (GO:0046966)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)		AGCTGATGCCTGTGAGGCCAT	0.483																																					p.Q263R		Atlas-SNP	.											.	GTF2B	32	.	0			c.A788G						.						89	87	88					1																	89322918		2203	4300	6503	SO:0001583	missense	2959	exon6			GATGCCTGTGAGG	M76766	CCDS715.1	1p22-p21	2010-03-23			ENSG00000137947	ENSG00000137947		"General transcription factors"	4648	protein-coding gene	gene with protein product		189963				1876184, 8162052	Standard	NM_001514		Approved	TFIIB	uc001dmo.4	Q00403	OTTHUMG00000010611	ENST00000370500.5:c.788A>G	chr1.hg19:g.89322918T>C	ENSP00000359531:p.Gln263Arg	169.0	0.0		79.0	4.0	NM_001514	A8K1A7|Q5JS30	Missense_Mutation	SNP	ENST00000370500.5	hg19	CCDS715.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.477253	0.84640	.	.	ENSG00000137947	ENST00000370500	T	0.42513	0.97	5.11	5.11	0.69529	Transcription factor TFIIB, cyclin-related (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.35128	0.0921	L	0.34521	1.04	0.80722	D	1	D	0.55605	0.972	P	0.57620	0.824	T	0.06881	-1.0802	10	0.25106	T	0.35	-12.0181	15.2051	0.73173	0.0:0.0:0.0:1.0	.	263	Q00403	TF2B_HUMAN	R	263	ENSP00000359531:Q263R	ENSP00000359531:Q263R	Q	-	2	0	GTF2B	89095506	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.568000	0.82369	2.053000	0.61076	0.459000	0.35465	CAG	.	.		0.483	GTF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029279.1	NM_001514		C	89322918	T	C	89322918	3	2	111	1	0	0	0	0	1	0	0	0	6864	1580	55	2	170	2	GTF2B	1	89322918	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2418138	89322918	159927703	17	16257										
EVI5	7813	hgsc.bcm.edu	37	chr1	93167745	93167745	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agcacttccttgacagtaacCaacctcacgatctactaaag	5	13	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:93167745C>T	ENST00000370331.1	-	5	733	c.724G>A	c.(724-726)Ggt>Agt	p.G242S	EVI5_ENST00000543509.1_Missense_Mutation_p.G242S|EVI5_ENST00000540033.1_Missense_Mutation_p.G242S|RNU4-59P_ENST00000364447.1_RNA	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	242	Dimerization.|Interaction with alpha-tubulin, gamma- tubulin, BIRC5 and FBXO5.|Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		TGACAGTAACCAACCTCACGA	0.299																																					p.G242S		Atlas-SNP	.											.	EVI5	94	.	0			c.G724A						.						71	68	69					1																	93167745		2203	4298	6501	SO:0001583	missense	7813	exon5			AGTAACCAACCTC	AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.724G>A	chr1.hg19:g.93167745C>T	ENSP00000359356:p.Gly242Ser	151.0	0.0		91.0	4.0	NM_005665	A6NKX8|B9A6J0|Q9H1Y9	Missense_Mutation	SNP	ENST00000370331.1	hg19	CCDS30774.1	.	.	.	.	.	.	.	.	.	.	C	34	5.381453	0.95945	.	.	ENSG00000067208	ENST00000370331;ENST00000540033;ENST00000543509	T;T;T	0.10005	2.92;2.92;2.92	5.41	5.41	0.78517	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.25232	0.0613	M	0.88105	2.93	0.80722	D	1	P;P	0.38250	0.571;0.624	P;P	0.48770	0.453;0.589	T	0.02498	-1.1150	10	0.87932	D	0	-15.0775	19.1919	0.93671	0.0:1.0:0.0:0.0	.	242;242	F5H4R0;O60447	.;EVI5_HUMAN	S	242	ENSP00000359356:G242S;ENSP00000440826:G242S;ENSP00000445019:G242S	ENSP00000359356:G242S	G	-	1	0	EVI5	92940333	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.711000	0.84669	2.539000	0.85634	0.650000	0.86243	GGT	.	.		0.299	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665		T	93167745	C	T	93167745	3	4	111	1	0	0	0	0	1	0	0	0	5291	594	21	3	1764	3	EVI5	1	93167745	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	3844827	93167745	156082876	18	16258										
GPSM2	29899	hgsc.bcm.edu	37	chr1	109465167	109465168	+	Missense_Mutation	DNP	TT	TT	AA													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	catacagcttcaacaacaacTtcttccactccccctaaaat					rs374875864|rs79761186|rs35029887|rs201481482	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:109465167_109465168TT>AA	ENST00000406462.2	+	14	2342_2343	c.1569_1570TT>AA	c.(1567-1572)acTTct>acAAct	p.S524T	AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_Missense_Mutation_p.S524T			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	524					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		CAACAACAACTTCTTCCACTCC	0.371																																					p.T523T|p.S524T		Atlas-SNP	.											.	GPSM2	56	.	0			c.T1569A|c.T1570A						.																																			SO:0001583	missense	29899	exon13			AACAACTTCTTCC|ACAACTTCTTCCA	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"Tetratricopeptide (TTC) repeat domain containing"	29501	protein-coding gene	gene with protein product		609245	"G-protein signalling modulator 2 (AGS3-like, C. elegans)", "deafness, autosomal recessive 82"	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	Exception_encountered	chr1.hg19:g.109465167_109465168delinsAA	ENSP00000385510:p.Ser524Thr	94.0|95.0	0.0		37.0	8.0	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	Silent|Missense_Mutation	SNP	ENST00000406462.2	hg19	CCDS792.2																																																																																			.	.		0.371	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296		AA	109465168	TT	AA	109465167	3	1	111	1	0	0	0	0	1	0	0	0	6744	1596	56	4	1615	4	GPSM2	1	109465167	Missense_Mutation	DNP	TT	TCGA-DD-A39X-01A-11D-A20W-10	16297422	109465167	139785454	19	16259										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109793709	109793709	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaggggtctgggggcagcccCtctgaagtctttgagatcga	16	9	3	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:109793709C>T	ENST00000271332.3	+	1	1069	c.1008C>T	c.(1006-1008)ccC>ccT	p.P336P		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	336	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GGGGCAGCCCCTCTGAAGTCT	0.602																																					p.P336P	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.C1008T						.						72	77	75					1																	109793709		2203	4300	6503	SO:0001819	synonymous_variant	1952	exon1			CAGCCCCTCTGAA	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.1008C>T	chr1.hg19:g.109793709C>T		65.0	0.0		56.0	25.0	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	hg19	CCDS796.1																																																																																			.	.		0.602	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		T	109793709	C	T	109793709	2	4	111	1	0	0	0	0	0	0	0	1	3224	668	24	3		3	CELSR2	1	109793709	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	328542	109793709	139456912	20	16260										
GNAI3	2773	hgsc.bcm.edu	37	chr1	110134757	110134757	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccaaggagatctatactcacTtcacctgtgccacagacacg	7	14	3	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:110134757T>C	ENST00000369851.4	+	8	1077	c.967T>C	c.(967-969)Ttc>Ctc	p.F323L	RNU6V_ENST00000384105.1_RNA	NM_006496.3	NP_006487.1	P08754	GNAI3_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 3	323					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|negative regulation of adenylate cyclase activity (GO:0007194)|platelet activation (GO:0030168)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle fusion (GO:0006906)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|midbody (GO:0030496)|plasma membrane (GO:0005886)|zymogen granule (GO:0042588)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	12		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.046)|Colorectal(144;0.119)|Epithelial(280;0.139)|all cancers(265;0.147)|LUSC - Lung squamous cell carcinoma(189;0.237)		CTATACTCACTTCACCTGTGC	0.378																																					p.F323L		Atlas-SNP	.											.	GNAI3	25	.	0			c.T967C						.						131	121	124					1																	110134757		2203	4300	6503	SO:0001583	missense	2773	exon8			ACTCACTTCACCT	M27543	CCDS802.1	1p13	2012-10-02			ENSG00000065135	ENSG00000065135			4387	protein-coding gene	gene with protein product		139370				3109953	Standard	NM_006496		Approved	87U6	uc001dxz.3	P08754	OTTHUMG00000011648	ENST00000369851.4:c.967T>C	chr1.hg19:g.110134757T>C	ENSP00000358867:p.Phe323Leu	171.0	0.0		119.0	5.0	NM_006496	P17539|Q5TZX1	Missense_Mutation	SNP	ENST00000369851.4	hg19	CCDS802.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.207310	0.58343	.	.	ENSG00000065135	ENST00000369851	D	0.89270	-2.49	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.81697	0.4877	L	0.45581	1.43	0.80722	D	1	B	0.15719	0.014	B	0.24155	0.051	T	0.78219	-0.2289	10	0.41790	T	0.15	.	16.3246	0.82970	0.0:0.0:0.0:1.0	.	323	P08754	GNAI3_HUMAN	L	323	ENSP00000358867:F323L	ENSP00000358867:F323L	F	+	1	0	GNAI3	109936280	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.291000	0.72719	2.333000	0.79357	0.482000	0.46254	TTC	.	.		0.378	GNAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032222.1	NM_006496		C	110134757	T	C	110134757	3	2	111	1	0	0	0	0	1	0	0	0	6514	1609	56	2	997	2	GNAI3	1	110134757	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	341048	110134757	139115864	21	16261										
ALX3	257	hgsc.bcm.edu	37	chr1	110607343	110607343	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaaggtcgtgcggttacgacGcttcttgctcttgttcttgg	13	9	3	0	rs535409677		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:110607343G>T	ENST00000369792.4	-	2	547	c.460C>A	c.(460-462)Cgt>Agt	p.R154S	RP4-773N10.4_ENST00000554749.1_RNA	NM_006492.2	NP_006483.2	O95076	ALX3_HUMAN	ALX homeobox 3	154					embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|pattern specification process (GO:0007389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(81;2.35e-05)|all_epithelial(167;7.69e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.015)|all cancers(265;0.0706)|Epithelial(280;0.0758)|Colorectal(144;0.113)|LUSC - Lung squamous cell carcinoma(189;0.135)		CGGTTACGACGCTTCTTGCTC	0.592																																					p.R154S		Atlas-SNP	.											.	ALX3	16	.	0			c.C460A						.						110	109	109					1																	110607343		2203	4300	6503	SO:0001583	missense	257	exon2			TACGACGCTTCTT	AF008203	CCDS819.1	1p13.3	2014-02-04	2008-11-04		ENSG00000156150	ENSG00000156150		"Homeoboxes / PRD class"	449	protein-coding gene	gene with protein product		606014	"aristaless-like homeobox 3", "frontonasal dysplasia"	FND		15226305, 11807986, 19409524	Standard	NM_006492		Approved		uc001dzb.3	O95076	OTTHUMG00000011650	ENST00000369792.4:c.460C>A	chr1.hg19:g.110607343G>T	ENSP00000358807:p.Arg154Ser	344.0	0.0		220.0	118.0	NM_006492	O95075|Q5T8M4	Missense_Mutation	SNP	ENST00000369792.4	hg19	CCDS819.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.368747	0.61624	.	.	ENSG00000156150	ENST00000369792	D	0.97186	-4.28	4.04	4.04	0.47022	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000003	D	0.98966	0.9648	H	0.99325	4.515	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.98737	1.0715	10	0.87932	D	0	.	9.4814	0.38902	0.0:0.0:0.7884:0.2116	.	154	O95076	ALX3_HUMAN	S	154	ENSP00000358807:R154S	ENSP00000358807:R154S	R	-	1	0	ALX3	110408866	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.231000	0.32624	1.940000	0.56252	0.462000	0.41574	CGT	.	.		0.592	ALX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032232.2	NM_006492		T	110607343	G	T	110607343	3	4	111	1	0	0	0	0	1	0	0	0	557	1087	38	1	583	1	ALX3	1	110607343	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	472586	110607343	138643278	22	16262										
SLC16A4	9122	hgsc.bcm.edu	37	chr1	110919677	110919678	+	Frame_Shift_Ins	INS	-	-	CT													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctaaaggagcaagcaggttaINSgtgatgccgcagaggatgag							TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:110919677_110919678insCT	ENST00000369779.4	-	7	1385_1386	c.1136_1137insAG	c.(1135-1137)actfs	p.T379fs	SLC16A4_ENST00000497687.1_5'Flank|SLC16A4_ENST00000541986.1_Frame_Shift_Ins_p.T317fs|SLC16A4_ENST00000369781.4_Frame_Shift_Ins_p.T211fs|SLC16A4_ENST00000472422.2_Frame_Shift_Ins_p.T331fs|SLC16A4_ENST00000437429.2_Frame_Shift_Ins_p.T269fs	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	379					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CAAGCAGGTTAGTGATGCCGCA	0.455																																					p.T379fs		Atlas-INDEL	.											.	SLC16A4	47	.	0			c.1137_1138insAG						.																																			SO:0001589	frameshift_variant	9122	exon7			.	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"Solute carriers"	10925	protein-coding gene	gene with protein product		603878	"solute carrier family 16 (monocarboxylic acid transporters), member 4", "solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.1136_1137insAG	chr1.hg19:g.110919677_110919678insCT	ENSP00000358794:p.Thr379fs	145.0	0.0		98.0	32.0	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Frame_Shift_Ins	INS	ENST00000369779.4	hg19	CCDS823.1																																																																																			.	.		0.455	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696		CT	110919678	-	CT	110919677	7	5	111	1	0	1	1	0	0	0	0	0	14425	407	15	0	338	0	SLC16A4	1	110919677	Frame_Shift_Ins	INS	-	TCGA-DD-A39X-01A-11D-A20W-10	312334	110919677	138330944	23	16263	72	3								
SLC16A4	9122	hgsc.bcm.edu	37	chr1	110919678	110919679	+	Frame_Shift_Ins	INS	-	-	A													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	taaaggagcaagcaggttagINStgatgccgcagaggatgagg					rs147693872		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:110919678_110919679insA	ENST00000369779.4	-	7	1384_1385	c.1135_1136insT	c.(1135-1137)actfs	p.T379fs	SLC16A4_ENST00000497687.1_5'Flank|SLC16A4_ENST00000541986.1_Frame_Shift_Ins_p.T317fs|SLC16A4_ENST00000369781.4_Frame_Shift_Ins_p.T211fs|SLC16A4_ENST00000472422.2_Frame_Shift_Ins_p.T331fs|SLC16A4_ENST00000437429.2_Frame_Shift_Ins_p.T269fs	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	379					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	AAGCAGGTTAGTGATGCCGCAG	0.455																																					p.T379fs		Atlas-INDEL	.											.	SLC16A4	47	.	0			c.1136_1137insT						.																																			SO:0001589	frameshift_variant	9122	exon7			.	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"Solute carriers"	10925	protein-coding gene	gene with protein product		603878	"solute carrier family 16 (monocarboxylic acid transporters), member 4", "solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.1135_1136insT	chr1.hg19:g.110919678_110919679insA	ENSP00000358794:p.Thr379fs	147.0	0.0		98.0	32.0	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Frame_Shift_Ins	INS	ENST00000369779.4	hg19	CCDS823.1																																																																																			.	.		0.455	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696		A	110919679	-	A	110919678	7	5	111	1	0	1	1	0	0	0	0	0	14425	1029	36	0	339	0	SLC16A4	1	110919678	Frame_Shift_Ins	INS	-	TCGA-DD-A39X-01A-11D-A20W-10	1	110919678	138330943	24	16264	72	3								
SLC16A4	9122	hgsc.bcm.edu	37	chr1	110919681	110919682	+	In_Frame_Ins	INS	-	-	TGA													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aggagcaagcaggttagtgaINStgccgcagaggatgaggtaa							TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:110919681_110919682insTGA	ENST00000369779.4	-	7	1381_1382	c.1132_1133insTCA	c.(1132-1134)atc>aTCAtc	p.378_378I>II	SLC16A4_ENST00000497687.1_5'Flank|SLC16A4_ENST00000541986.1_In_Frame_Ins_p.316_316I>II|SLC16A4_ENST00000369781.4_In_Frame_Ins_p.210_210I>II|SLC16A4_ENST00000472422.2_In_Frame_Ins_p.330_330I>II|SLC16A4_ENST00000437429.2_In_Frame_Ins_p.268_268I>II	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	378					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CAGGTTAGTGATGCCGCAGAGG	0.446																																					p.I378delinsII		Pindel	.											.	SLC16A4	47	.	0			c.1133_1134insTCA						.																																			SO:0001652	inframe_insertion	9122	exon7			.	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"Solute carriers"	10925	protein-coding gene	gene with protein product		603878	"solute carrier family 16 (monocarboxylic acid transporters), member 4", "solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.1130_1132dupTCA	chr1.hg19:g.110919679_110919681dupTGA	ENSP00000358794:p.Ile378dup	0.0	0.0		96.0	29.0	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	In_Frame_Ins	INS	ENST00000369779.4	hg19	CCDS823.1																																																																																			.	.		0.446	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696		TGA	110919682	-	TGA	110919681	7	5	111	1	0	1	1	0	0	0	0	0	14425	333	12	0	342	0	SLC16A4	1	110919681	In_Frame_Ins	INS	-	TCGA-DD-A39X-01A-11D-A20W-10	3	110919681	138330940	25	16265	72	3								
MAGI3	260425	hgsc.bcm.edu	37	chr1	114196530	114196530	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccgcctgaaccgggcagaggTcccagccaggcctgcacccc	12	19	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:114196530T>C	ENST00000307546.9	+	15	2594	c.2519T>C	c.(2518-2520)gTc>gCc	p.V840A	MAGI3_ENST00000369611.4_Missense_Mutation_p.V840A|MAGI3_ENST00000369617.4_Missense_Mutation_p.V865A|MAGI3_ENST00000369615.1_Missense_Mutation_p.V840A	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	865					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CGGGCAGAGGTCCCAGCCAGG	0.488																																					p.V840A		Atlas-SNP	.											.	MAGI3	181	.	0			c.T2519C						.						184	199	194					1																	114196530		2203	4300	6503	SO:0001583	missense	260425	exon15			CAGAGGTCCCAGC	AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.2519T>C	chr1.hg19:g.114196530T>C	ENSP00000304604:p.Val840Ala	89.0	0.0		86.0	5.0	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Missense_Mutation	SNP	ENST00000307546.9	hg19	CCDS44196.1	.	.	.	.	.	.	.	.	.	.	T	1.349	-0.592041	0.03799	.	.	ENSG00000081026	ENST00000369617;ENST00000307546;ENST00000369615;ENST00000369611	T;T;T;T	0.15256	2.59;2.44;2.59;2.59	5.41	-1.86	0.07760	.	0.611971	0.17840	N	0.160238	T	0.02970	0.0088	L	0.38175	1.15	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.45687	-0.9244	10	0.16420	T	0.52	-9.1139	7.0519	0.25077	0.0:0.1296:0.3481:0.5223	.	840;840;865	Q5TCQ9-4;Q5TCQ9-3;Q5TCQ9-2	.;.;.	A	865;840;840;840	ENSP00000358630:V865A;ENSP00000304604:V840A;ENSP00000358628:V840A;ENSP00000358624:V840A	ENSP00000304604:V840A	V	+	2	0	MAGI3	113998053	0.001000	0.12720	0.001000	0.08648	0.089000	0.18198	0.495000	0.22483	-0.146000	0.11274	-0.250000	0.11733	GTC	.	.		0.488	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		C	114196530	T	C	114196530	3	2	111	1	0	0	0	0	1	0	0	0	9201	1667	58	2	2577	2	MAGI3	1	114196530	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	3276849	114196530	135054091	26	16266										
MTMR11	10903	hgsc.bcm.edu	37	chr1	149901687	149901687	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tagcaggtcgagggagccaaCgagaagagactgccagcagg	16	9	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:149901687C>T	ENST00000439741.2	-	16	2019	c.1769G>A	c.(1768-1770)cGt>cAt	p.R590H	MTMR11_ENST00000406732.3_3'UTR|SF3B4_ENST00000271628.8_5'Flank|MTMR11_ENST00000369140.3_Missense_Mutation_p.R518H|MTMR11_ENST00000492824.1_5'UTR|MTMR11_ENST00000361405.6_3'UTR	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	590	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.						phosphatase activity (GO:0016791)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			AGGGAGCCAACGAGAAGAGAC	0.597																																					p.R590H		Atlas-SNP	.											MTMR11_ENST00000439741,NS,carcinoma,0,2	MTMR11	136	.	0			c.G1769A						.						58	63	61					1																	149901687		2203	4300	6503	SO:0001583	missense	10903	exon16			AGCCAACGAGAAG	AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	24307	protein-coding gene	gene with protein product	"cisplatin resistance associated"					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.1769G>A	chr1.hg19:g.149901687C>T	ENSP00000391668:p.Arg590His	83.0	0.0		130.0	20.0	NM_001145862	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Missense_Mutation	SNP	ENST00000439741.2	hg19	CCDS53360.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.102395	0.37145	.	.	ENSG00000014914	ENST00000369140;ENST00000439741	T;T	0.40476	1.03;1.03	5.13	4.21	0.49690	Myotubularin phosphatase domain (1);	0.461097	0.23510	N	0.047406	T	0.11067	0.0270	N	0.08118	0	0.80722	D	1	B;B	0.17268	0.017;0.021	B;B	0.12837	0.005;0.008	T	0.05517	-1.0880	10	0.52906	T	0.07	.	9.8951	0.41314	0.0:0.9039:0.0:0.0961	.	518;590	A4FU01-4;A4FU01	.;MTMRB_HUMAN	H	518;590	ENSP00000358136:R518H;ENSP00000391668:R590H	ENSP00000358136:R518H	R	-	2	0	MTMR11	148168311	0.994000	0.37717	1.000000	0.80357	0.994000	0.84299	2.224000	0.42945	1.366000	0.46076	0.655000	0.94253	CGT	.	.		0.597	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873		T	149901687	C	T	149901687	3	4	111	1	0	0	0	0	1	0	0	0	9949	536	19	1	407	1	MTMR11	1	149901687	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	35705157	149901687	99348934	27	16267										
KPRP	448834	hgsc.bcm.edu	37	chr1	152733725	152733725	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tggtgatgtgtttccagagcGgaggggtcaggatggccatg	18	6	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:152733725G>C	ENST00000606109.1	+	1	1689	c.1661G>C	c.(1660-1662)cGg>cCg	p.R554P	KPRP_ENST00000368773.1_Missense_Mutation_p.R554P			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	554						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.R554Q(2)		NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTTCCAGAGCGGAGGGGTCAG	0.542																																					p.R554P		Atlas-SNP	.											KPRP,colon,carcinoma,+1,2	KPRP	152	.	2	Substitution - Missense(2)	ovary(2)	c.G1661C						.						77	71	73					1																	152733725		2203	4300	6503	SO:0001583	missense	448834	exon2			CAGAGCGGAGGGG	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1661G>C	chr1.hg19:g.152733725G>C	ENSP00000475216:p.Arg554Pro	129.0	0.0		259.0	11.0	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	hg19	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	G	0.397	-0.920244	0.02396	.	.	ENSG00000203786	ENST00000368773	T	0.10960	2.82	3.93	3.0	0.34707	.	0.412789	0.17984	N	0.155435	T	0.00875	0.0029	N	0.00583	-1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48885	-0.8995	10	0.23302	T	0.38	-0.1704	9.6976	0.40167	0.0:0.7826:0.2174:0.0	.	554	Q5T749	KPRP_HUMAN	P	554	ENSP00000357762:R554P	ENSP00000357762:R554P	R	+	2	0	KPRP	151000349	0.002000	0.14202	0.078000	0.20375	0.043000	0.13939	0.661000	0.25023	1.013000	0.39391	-0.802000	0.03209	CGG	.	.		0.542	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		C	152733725	G	C	152733725	3	2	111	1	0	0	0	0	1	0	0	0	8445	1116	39	4	1663	4	KPRP	1	152733725	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	2832038	152733725	96516896	28	16268										
PGLYRP4	57115	hgsc.bcm.edu	37	chr1	153317700	153317700	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atgatgggcctgcagttcccGcagtctctggctgcagactg	13	12	1	2	rs554667521		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:153317700G>A	ENST00000359650.5	-	4	362	c.298C>T	c.(298-300)Cgg>Tgg	p.R100W	PGLYRP4_ENST00000490266.1_5'UTR|PGLYRP4_ENST00000368739.3_Missense_Mutation_p.R96W	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	100					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGCAGTTCCCGCAGTCTCTGG	0.552													G|||	1	0.000199681	0	0.0014	5008	,	,		19259	0		0	False		,,,				2504	0				p.R100W		Atlas-SNP	.											.	PGLYRP4	45	.	0			c.C298T						.						103	96	98					1																	153317700		2203	4300	6503	SO:0001583	missense	57115	exon4			GTTCCCGCAGTCT	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I beta precursor"	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.298C>T	chr1.hg19:g.153317700G>A	ENSP00000352672:p.Arg100Trp	65.0	0.0		107.0	10.0	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	hg19	CCDS30871.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.654278	0.29425	.	.	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.27720	1.65;1.65	3.2	1.06	0.20224	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	.	.	.	.	T	0.21347	0.0514	M	0.93420	3.415	0.27233	N	0.959342	P;P	0.36535	0.501;0.557	B;B	0.34093	0.109;0.175	T	0.31364	-0.9946	9	0.87932	D	0	-18.1578	3.3148	0.07029	0.1447:0.0:0.6002:0.255	.	96;100	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	W	96;100	ENSP00000357728:R96W;ENSP00000352672:R100W	ENSP00000352672:R100W	R	-	1	2	PGLYRP4	151584324	0.014000	0.17966	0.997000	0.53966	0.586000	0.36452	0.665000	0.25083	0.691000	0.31592	0.313000	0.20887	CGG	.	.		0.552	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393		A	153317700	G	A	153317700	3	1	111	1	0	0	0	0	1	0	0	0	11805	1086	38	1	847	1	PGLYRP4	1	153317700	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	583975	153317700	95932921	29	16269										
SMG5	23381	hgsc.bcm.edu	37	chr1	156236144	156236144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gatctggctcctcctctttcTccacaggttccttggactct	7	15	4	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:156236144T>C	ENST00000361813.5	-	12	1427	c.1283A>G	c.(1282-1284)gAg>gGg	p.E428G	SMG5_ENST00000368267.5_Intron|SMG5_ENST00000489907.2_5'UTR	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	428					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	48	Hepatocellular(266;0.158)					CTCCTCTTTCTCCACAGGTTC	0.577																																					p.E428G		Atlas-SNP	.											.	SMG5	98	.	0			c.A1283G						.						42	44	43					1																	156236144		2203	4300	6503	SO:0001583	missense	23381	exon12			TCTTTCTCCACAG	AB029012	CCDS1137.1	1q21	2013-07-02	2013-07-02		ENSG00000198952	ENSG00000198952			24644	protein-coding gene	gene with protein product	"EST1 telomerase component homolog B (S. cerevisiae)"	610962	"smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)"			12676087, 12699629	Standard	NM_015327		Approved	KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B	uc001foc.4	Q9UPR3	OTTHUMG00000017491	ENST00000361813.5:c.1283A>G	chr1.hg19:g.156236144T>C	ENSP00000355261:p.Glu428Gly	39.0	0.0		104.0	5.0	NM_015327	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Missense_Mutation	SNP	ENST00000361813.5	hg19	CCDS1137.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.240870	0.39598	.	.	ENSG00000198952	ENST00000361813	T	0.34072	1.38	5.52	4.41	0.53225	.	1.103060	0.06747	N	0.779308	T	0.13798	0.0334	N	0.21373	0.66	0.80722	D	1	P	0.35793	0.521	B	0.31946	0.138	T	0.03433	-1.1037	10	0.52906	T	0.07	-8.2368	9.8528	0.41068	0.0:0.081:0.0:0.919	.	428	Q9UPR3	SMG5_HUMAN	G	428	ENSP00000355261:E428G	ENSP00000355261:E428G	E	-	2	0	SMG5	154502768	1.000000	0.71417	0.524000	0.27887	0.804000	0.45430	2.241000	0.43097	2.097000	0.63578	0.460000	0.39030	GAG	.	.		0.577	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327		C	156236144	T	C	156236144	3	2	111	1	0	0	0	0	1	0	0	0	14811	1551	54	2	1811	2	SMG5	1	156236144	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2918444	156236144	93014477	30	16270										
KLHL20	27252	hgsc.bcm.edu	37	chr1	173720986	173720986	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gatgagctaaacgttcgcagTgaagaacaagtgttcaatgc	11	7	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:173720986T>C	ENST00000209884.4	+	4	817	c.681T>C	c.(679-681)agT>agC	p.S227S	KLHL20_ENST00000546011.1_Silent_p.S38S	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	227	BACK.				cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)			breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						ACGTTCGCAGTGAAGAACAAG	0.403																																					p.S227S	GBM(159;862 2695 6559 23041)	Atlas-SNP	.											.	KLHL20	54	.	0			c.T681C						.						106	93	97					1																	173720986		2203	4300	6503	SO:0001819	synonymous_variant	27252	exon4			TCGCAGTGAAGAA	AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"Kelch-like", "BTB/POZ domain containing"	25056	protein-coding gene	gene with protein product			"kelch-like 20 (Drosophila)"			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.681T>C	chr1.hg19:g.173720986T>C		92.0	0.0		110.0	5.0	NM_014458	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Silent	SNP	ENST00000209884.4	hg19	CCDS1310.1																																																																																			.	.		0.403	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458		C	173720986	T	C	173720986	2	2	111	1	0	0	0	0	0	0	0	1	8384	1693	59	2		2	KLHL20	1	173720986	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	17484842	173720986	75529635	31	16271										
TNR	7143	hgsc.bcm.edu	37	chr1	175323568	175323568	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgatgctgctccacgtggtgTcctgtgctgcctgcaggagc	14	12	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:175323568T>C	ENST00000367674.2	-	18	4049	c.3341A>G	c.(3340-3342)gAc>gGc	p.D1114G	TNR_ENST00000263525.2_Missense_Mutation_p.D1114G			Q92752	TENR_HUMAN	tenascin R	1114	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					CCACGTGGTGTCCTGTGCTGC	0.542																																					p.D1114G		Atlas-SNP	.											.	TNR	399	.	0			c.A3341G						.						177	133	148					1																	175323568		2203	4300	6503	SO:0001583	missense	7143	exon18			GTGGTGTCCTGTG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.3341A>G	chr1.hg19:g.175323568T>C	ENSP00000356646:p.Asp1114Gly	103.0	0.0		88.0	4.0	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	T	0.177	-1.065603	0.01934	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.51817	0.69;0.69	5.3	5.3	0.74995	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.185170	0.46758	D	0.000264	T	0.19366	0.0465	N	0.01454	-0.855	0.33085	D	0.537202	B	0.02656	0.0	B	0.08055	0.003	T	0.17349	-1.0372	10	0.02654	T	1	.	14.9274	0.70890	0.0:0.0:0.0:1.0	.	1114	Q92752	TENR_HUMAN	G	1114;1114;1024	ENSP00000356646:D1114G;ENSP00000263525:D1114G	ENSP00000263525:D1114G	D	-	2	0	TNR	173590191	1.000000	0.71417	0.890000	0.34922	0.044000	0.14063	5.345000	0.65987	2.010000	0.58986	0.528000	0.53228	GAC	.	.		0.542	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		C	175323568	T	C	175323568	3	2	111	1	0	0	0	0	1	0	0	0	16353	1667	58	2	759	2	TNR	1	175323568	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1602582	175323568	73927053	32	16272										
RALGPS2	55103	hgsc.bcm.edu	37	chr1	178854228	178854228	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	taggtcctgaagtaggagcgTctccacagagtggacgaaaa	13	8	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:178854228T>C	ENST00000367635.3	+	12	1260	c.922T>C	c.(922-924)Tct>Cct	p.S308P	RALGPS2_ENST00000477383.1_3'UTR|RALGPS2_ENST00000367634.2_Missense_Mutation_p.S308P	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	308					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						AGTAGGAGCGTCTCCACAGAG	0.423																																					p.S308P		Atlas-SNP	.											.	RALGPS2	69	.	0			c.T922C						.						65	67	66					1																	178854228		2203	4300	6503	SO:0001583	missense	55103	exon12			GGAGCGTCTCCAC	AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"Pleckstrin homology (PH) domain containing"	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.922T>C	chr1.hg19:g.178854228T>C	ENSP00000356607:p.Ser308Pro	115.0	0.0		97.0	4.0	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Missense_Mutation	SNP	ENST00000367635.3	hg19	CCDS1325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.09|13.09	2.132716|2.132716	0.37630|0.37630	.|.	.|.	ENSG00000116191|ENSG00000116191	ENST00000367635;ENST00000367634;ENST00000324778|ENST00000415888	T;T;T|.	0.42900|.	0.96;0.96;0.96|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.731376|.	0.13484|.	N|.	0.384425|.	T|T	0.68155|0.68155	0.2970|0.2970	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	D|D	1|1	B;B|.	0.13145|.	0.007;0.006|.	B;B|.	0.16289|.	0.005;0.015|.	T|T	0.65998|0.65998	-0.6032|-0.6032	10|5	0.54805|.	T|.	0.06|.	.|.	15.4899|15.4899	0.75597|0.75597	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	308;308|.	B7Z7B1;Q86X27|.	.;RGPS2_HUMAN|.	P|A	308;308;273|45	ENSP00000356607:S308P;ENSP00000356606:S308P;ENSP00000313613:S273P|.	ENSP00000313613:S273P|.	S|V	+|+	1|2	0|0	RALGPS2|RALGPS2	177120851|177120851	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.269000|0.269000	0.26545|0.26545	7.329000|7.329000	0.79170|0.79170	2.148000|2.148000	0.66965|0.66965	0.477000|0.477000	0.44152|0.44152	TCT|GTC	.	.		0.423	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663		C	178854228	T	C	178854228	3	2	111	1	0	0	0	0	1	0	0	0	13033	1667	58	2	964	2	RALGPS2	1	178854228	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	3530660	178854228	70396393	33	16273										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179504037	179504037	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gagaagtaaaagaagaagaaGaacaacaagaagaagaagaa	11	2	0	9	rs200097954|rs368406759|rs6425573	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:179504037G>C	ENST00000367618.3	+	25	3358	c.2971G>C	c.(2971-2973)Gaa>Caa	p.E991Q		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	991	Glu-rich.		E -> Q (in dbSNP:rs6425573).					p.E991_Q992delEQ(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agaagaagaagaacaacaaga	0.318													G|||	14	0.00279553	0	0.0058	5008	,	,		17137	0.002		0.004	False		,,,				2504	0.0041				p.E991Q		Atlas-SNP	.											.	AXDND1	142	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2971C						.						49	51	50					1																	179504037		2152	4286	6438	SO:0001583	missense	126859	exon25			GAAGAAGAACAAC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2971G>C	chr1.hg19:g.179504037G>C	ENSP00000356590:p.Glu991Gln	166.0	0.0		146.0	12.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	G	9.300	1.052898	0.19907	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.19105	2.17;2.17	4.89	-6.02	0.02192	.	0.508747	0.16499	N	0.211773	T	0.08980	0.0222	N	0.24115	0.695	0.09310	N	1	B;B	0.24186	0.099;0.099	B;B	0.10450	0.003;0.005	T	0.15838	-1.0423	10	0.28530	T	0.3	-2.8152	6.1976	0.20557	0.4456:0.3814:0.173:0.0	rs6425573	875;991	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	Q	991;875;851	ENSP00000356590:E991Q;ENSP00000391716:E851Q	ENSP00000353471:E875Q	E	+	1	0	AXDND1	177770660	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.365000	0.20348	-1.164000	0.02790	-1.047000	0.02352	GAA	.	G|1.000;|0.000		0.318	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179504037	G	C	179504037	3	2	111	1	0	0	0	0	1	0	0	0	1995	943	33	4	3065	4	C1orf125	1	179504037	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	649809	179504037	69746584	34	16274										
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180905383	180905383	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tggaaattgtctctccttccTccctgcaacagagccatgca	7	14	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:180905383T>C	ENST00000367588.4	+	5	2393	c.2338T>C	c.(2338-2340)Tcc>Ccc	p.S780P	KIAA1614_ENST00000367587.1_Missense_Mutation_p.S401P	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	780										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CTCTCCTTCCTCCCTGCAACA	0.622																																					p.S780P		Atlas-SNP	.											.	KIAA1614	75	.	0			c.T2338C						.						85	90	88					1																	180905383		2051	4191	6242	SO:0001583	missense	57710	exon5			CCTTCCTCCCTGC	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2338T>C	chr1.hg19:g.180905383T>C	ENSP00000356560:p.Ser780Pro	97.0	0.0		97.0	4.0	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	hg19	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.020779	0.35606	.	.	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.50001	0.76;0.76	4.18	1.87	0.25490	.	0.889183	0.09756	N	0.759938	T	0.20455	0.0492	N	0.11560	0.145	0.30945	N	0.725333	B	0.31227	0.314	B	0.31337	0.128	T	0.32955	-0.9887	9	0.02654	T	1	-4.2309	2.4174	0.04439	0.2776:0.2408:0.0:0.4815	.	780	Q5VZ46	K1614_HUMAN	P	780;401	ENSP00000356560:S780P;ENSP00000356559:S401P	ENSP00000356559:S401P	S	+	1	0	KIAA1614	179172006	0.000000	0.05858	0.036000	0.18154	0.806000	0.45545	0.273000	0.18662	0.494000	0.27859	0.459000	0.35465	TCC	.	.		0.622	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		C	180905383	T	C	180905383	3	2	111	1	0	0	0	0	1	0	0	0	8257	1551	54	2	2356	2	KIAA1614	1	180905383	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1401346	180905383	68345238	35	16275										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181767537	181767537	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gccaaagccccggcccctccTttcctacagctccctgattc	6	20	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:181767537T>C	ENST00000367573.2	+	48	6509	c.6509T>C	c.(6508-6510)cTt>cCt	p.L2170P	CACNA1E_ENST00000357570.5_Missense_Mutation_p.L2121P|CACNA1E_ENST00000367567.4_Missense_Mutation_p.L1734P|CACNA1E_ENST00000360108.3_Missense_Mutation_p.L2151P|CACNA1E_ENST00000367570.1_Missense_Mutation_p.L2127P|CACNA1E_ENST00000526775.1_Missense_Mutation_p.L2108P|CACNA1E_ENST00000358338.5_Missense_Mutation_p.L2059P	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2170					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CGGCCCCTCCTTTCCTACAGC	0.632																																					p.L2170P		Atlas-SNP	.											.	CACNA1E	778	.	0			c.T6509C						.						70	81	77					1																	181767537		1983	4164	6147	SO:0001583	missense	777	exon48			CCCTCCTTTCCTA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6509T>C	chr1.hg19:g.181767537T>C	ENSP00000356545:p.Leu2170Pro	90.0	0.0		74.0	4.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.113757	0.77210	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96459	-3.96;-3.96;-4.01;-3.96;-4.02;-4.02;-4.01	5.55	5.55	0.83447	.	0.391255	0.26035	N	0.026732	D	0.95421	0.8513	N	0.22421	0.69	0.80722	D	1	D;P	0.59767	0.986;0.946	P;P	0.57152	0.814;0.777	D	0.96273	0.9200	10	0.72032	D	0.01	.	15.432	0.75108	0.0:0.0:0.0:1.0	.	2108;2127	Q15878-2;Q15878-3	.;.	P	2127;2108;2121;2059;1734;2151;2170	ENSP00000356542:L2127P;ENSP00000434814:L2108P;ENSP00000350183:L2121P;ENSP00000351101:L2059P;ENSP00000356539:L1734P;ENSP00000353222:L2151P;ENSP00000356545:L2170P	ENSP00000350183:L2121P	L	+	2	0	CACNA1E	180034160	1.000000	0.71417	0.966000	0.40874	0.984000	0.73092	7.344000	0.79328	2.117000	0.64856	0.456000	0.33151	CTT	.	.		0.632	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		C	181767537	T	C	181767537	3	2	111	1	0	0	0	0	1	0	0	0	2544	1609	56	2	6566	2	CACNA1E	1	181767537	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	862154	181767537	67483084	36	16276										
DHX9	1660	hgsc.bcm.edu	37	chr1	182822524	182822524	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccaacttgaaggattactacTcaagaaaggaagaacaagaa	8	7	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:182822524T>C	ENST00000367549.3	+	5	558	c.448T>C	c.(448-450)Tca>Cca	p.S150P		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	150	Interaction with CREBBP.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						GGATTACTACTCAAGAAAGGA	0.453																																					p.S150P	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.T448C						.						58	62	61					1																	182822524		1900	4117	6017	SO:0001583	missense	1660	exon5			TACTACTCAAGAA	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.448T>C	chr1.hg19:g.182822524T>C	ENSP00000356520:p.Ser150Pro	83.0	0.0		90.0	4.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	T	12.74	2.029746	0.35797	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	T	0.03745	3.82	5.67	3.14	0.36123	.	0.267312	0.28933	N	0.013679	T	0.03390	0.0098	L	0.31065	0.9	0.38312	D	0.943282	B	0.27594	0.182	B	0.30179	0.112	T	0.51140	-0.8743	10	0.29301	T	0.29	.	9.1942	0.37217	0.2894:0.0:0.0:0.7106	.	150	Q08211	DHX9_HUMAN	P	150	ENSP00000356520:S150P	ENSP00000356520:S150P	S	+	1	0	DHX9	181089147	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.133000	0.42093	0.922000	0.37019	0.528000	0.53228	TCA	.	.		0.453	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		C	182822524	T	C	182822524	3	2	111	1	0	0	0	0	1	0	0	0	4518	1551	54	2	462	2	DHX9	1	182822524	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1054987	182822524	66428097	37	16277										
TROVE2	6738	hgsc.bcm.edu	37	chr1	193060792	193060792	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctttctagccttgcaaaatAccctactaaataaatcattt	2	11	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:193060792A>G	ENST00000367445.3	+	10	1783	c.1596A>G	c.(1594-1596)atA>atG	p.I532M	TROVE2_ENST00000367443.1_3'UTR|TROVE2_ENST00000367444.3_Missense_Mutation_p.T519A|RP11-101E13.5_ENST00000608166.1_RNA	NM_001042370.2	NP_001035829.2	P10155	RO60_HUMAN	TROVE domain family, member 2	0	VWFA-like domain. {ECO:0000250}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)			biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						CTTGCAAAATACCCTACTAAA	0.318																																					p.I532M		Atlas-SNP	.											.	TROVE2	50	.	0			c.A1596G						.						115	108	110					1																	193060792		1847	4095	5942	SO:0001583	missense	6738	exon10			CAAAATACCCTAC	BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367445.3:c.1596A>G	chr1.hg19:g.193060792A>G	ENSP00000356415:p.Ile532Met	89.0	0.0		97.0	4.0	NM_001042370	B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Missense_Mutation	SNP	ENST00000367445.3	hg19	CCDS41450.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.009|0.009	-1.823510|-1.823510	0.00589|0.00589	.|.	.|.	ENSG00000116747|ENSG00000116747	ENST00000367445|ENST00000367444	.|.	.|.	.|.	5.13|5.13	-0.0422|-0.0422	0.13864|0.13864	.|.	.|.	.|.	.|.	.|.	T|T	0.17323|0.17323	0.0416|0.0416	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|B	0.06786|0.02656	0.001|0.0	B|B	0.06405|0.01281	0.002|0.0	T|T	0.20273|0.20273	-1.0280|-1.0280	8|8	0.87932|0.66056	D|D	0|0.02	.|.	5.7028|5.7028	0.17891|0.17891	0.4838:0.3562:0.1601:0.0|0.4838:0.3562:0.1601:0.0	.|.	532|519	Q5LJ99|Q5LJA0	.|.	M|A	532|519	.|.	ENSP00000356415:I532M|ENSP00000356414:T519A	I|T	+|+	3|1	3|0	TROVE2|TROVE2	191327415|191327415	0.780000|0.780000	0.28664|0.28664	0.046000|0.046000	0.18839|0.18839	0.469000|0.469000	0.32828|0.32828	0.447000|0.447000	0.21710|0.21710	-0.097000|-0.097000	0.12307|0.12307	0.533000|0.533000	0.62120|0.62120	ATA|ACC	.	.		0.318	TROVE2-005	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000086692.1	NM_004600		G	193060792	A	G	193060792	3	3	111	1	0	0	0	0	1	0	0	0	16591	391	14	2	1681	2	TROVE2	1	193060792	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	10238268	193060792	56189829	38	16278										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196295981	196295981	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	attagtttatttttgaatccAtaggcttttgcatcctcata	5	7	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:196295981A>G	ENST00000294725.9	-	19	3057	c.2142T>C	c.(2140-2142)taT>taC	p.Y714Y	KCNT2_ENST00000367431.4_Silent_p.Y664Y|KCNT2_ENST00000498426.1_Intron|KCNT2_ENST00000367433.5_Silent_p.Y714Y|KCNT2_ENST00000609185.1_Silent_p.Y664Y|KCNT2_ENST00000451324.2_Silent_p.Y325Y			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	714					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						TTTTGAATCCATAGGCTTTTG	0.323																																					p.Y714Y		Atlas-SNP	.											.	KCNT2	243	.	0			c.T2142C						.						94	98	97					1																	196295981		2203	4293	6496	SO:0001819	synonymous_variant	343450	exon19			GAATCCATAGGCT	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.2142T>C	chr1.hg19:g.196295981A>G		89.0	0.0		78.0	4.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	hg19	CCDS1384.1																																																																																			.	.		0.323	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		G	196295981	A	G	196295981	2	3	111	1	0	0	0	0	0	0	0	1	8101	224	8	2		2	KCNT2	1	196295981	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	3235189	196295981	52954640	39	16279										
NFASC	23114	hgsc.bcm.edu	37	chr1	204978736	204978736	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccagggctggttcattgggcTtatgtgcgccatcgccctcc	12	14	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:204978736T>C	ENST00000401399.1	+	27	3540	c.3341T>C	c.(3340-3342)cTt>cCt	p.L1114P	NFASC_ENST00000339876.6_Missense_Mutation_p.L1114P|NFASC_ENST00000367172.4_Missense_Mutation_p.L1221P|NFASC_ENST00000404076.1_Missense_Mutation_p.L1031P|NFASC_ENST00000360049.4_Missense_Mutation_p.L1043P|NFASC_ENST00000495396.1_3'UTR|NFASC_ENST00000338586.6_Missense_Mutation_p.L1098P|NFASC_ENST00000367170.4_Missense_Mutation_p.L1142P|NFASC_ENST00000404907.1_Missense_Mutation_p.L1048P|NFASC_ENST00000513543.1_Missense_Mutation_p.L1043P|NFASC_ENST00000539706.1_Missense_Mutation_p.L1048P|NFASC_ENST00000338515.6_Missense_Mutation_p.L1131P|NFASC_ENST00000367169.4_Missense_Mutation_p.L945P|NFASC_ENST00000367171.4_Missense_Mutation_p.L1206P			O94856	NFASC_HUMAN	neurofascin	1221	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TTCATTGGGCTTATGTGCGCC	0.587																																					p.L1114P		Atlas-SNP	.											.	NFASC	396	.	0			c.T3341C						.						106	82	90					1																	204978736		2203	4300	6503	SO:0001583	missense	23114	exon28			TTGGGCTTATGTG	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.3341T>C	chr1.hg19:g.204978736T>C	ENSP00000385637:p.Leu1114Pro	67.0	0.0		60.0	5.0	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	hg19	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.716338	0.89205	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393;ENST00000447819	T;T;T;T;T;T;T;T;T;T;T;T;T;T;D	0.82803	-0.77;-0.82;-0.53;-0.57;-0.79;-0.71;-0.42;-0.43;-0.47;-0.52;-0.79;-0.42;-0.43;-0.4;-1.65	5.27	5.27	0.74061	.	0.000000	0.44285	D	0.000480	D	0.91918	0.7441	M	0.87547	2.89	0.53005	D	0.999964	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.997;0.996;0.998;0.996;0.999;0.999	D	0.93338	0.6707	10	0.87932	D	0	.	14.856	0.70338	0.0:0.0:0.0:1.0	.	1221;1063;1048;1098;940;1114;1043	O94856;O94856-11;O94856-8;F8W8X7;O94856-4;O94856-9;O94856-3	NFASC_HUMAN;.;.;.;.;.;.	P	1221;1206;1142;1131;1114;1098;1063;1048;1043;945;1031;1114;1048;1043;1039;92	ENSP00000356140:L1221P;ENSP00000356139:L1206P;ENSP00000356138:L1142P;ENSP00000342128:L1131P;ENSP00000344786:L1114P;ENSP00000343509:L1098P;ENSP00000438614:L1048P;ENSP00000353154:L1043P;ENSP00000356137:L945P;ENSP00000385676:L1031P;ENSP00000385637:L1114P;ENSP00000384061:L1048P;ENSP00000425908:L1043P;ENSP00000415031:L1039P;ENSP00000416891:L92P	ENSP00000295776:L1063P	L	+	2	0	NFASC	203245359	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.988000	0.88194	1.966000	0.57179	0.533000	0.62120	CTT	.	.		0.587	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		C	204978736	T	C	204978736	3	2	111	1	0	0	0	0	1	0	0	0	10368	1609	56	2	3856	2	NFASC	1	204978736	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	8682755	204978736	44271885	40	16280										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208390746	208390746	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttgccatcctcaccctcagaGcgcacaatcaccccgtacat	5	18	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:208390746G>A	ENST00000367033.3	-	2	1279	c.522C>T	c.(520-522)cgC>cgT	p.R174R		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	174	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CACCCTCAGAGCGCACAATCA	0.597																																					p.R174R		Atlas-SNP	.											.	PLXNA2	178	.	0			c.C522T						.						155	157	156					1																	208390746		2203	4300	6503	SO:0001819	synonymous_variant	5362	exon2			CTCAGAGCGCACA	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.522C>T	chr1.hg19:g.208390746G>A		72.0	0.0		94.0	4.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	hg19	CCDS31013.1																																																																																			.	.		0.597	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		A	208390746	G	A	208390746	2	1	111	1	0	0	0	0	0	0	0	1	12129	958	34	3		3	PLXNA2	1	208390746	Silent	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	3412010	208390746	40859875	41	16281										
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222712068	222712068	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gatagacataacctccagtgActgacttccccactgcatgg	8	13	0	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:222712068A>G	ENST00000343410.6	-	5	1557	c.1499T>C	c.(1498-1500)gTc>gCc	p.V500A		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	500					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		ACCTCCAGTGACTGACTTCCC	0.468																																					p.V500A		Atlas-SNP	.											.	HHIPL2	122	.	0			c.T1499C						.						136	111	119					1																	222712068		2203	4300	6503	SO:0001583	missense	79802	exon5			CCAGTGACTGACT	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"KIAA1822-like"	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1499T>C	chr1.hg19:g.222712068A>G	ENSP00000342118:p.Val500Ala	150.0	0.0		117.0	5.0	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	hg19	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	A	21.5	4.157870	0.78114	.	.	ENSG00000143512	ENST00000343410	T	0.15372	2.43	5.35	5.35	0.76521	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Glucose/Sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.060724	0.64402	D	0.000005	T	0.43144	0.1234	M	0.74546	2.27	0.54753	D	0.999981	D	0.89917	1.0	D	0.85130	0.997	T	0.42137	-0.9469	10	0.87932	D	0	-29.4619	14.9878	0.71362	1.0:0.0:0.0:0.0	.	500	Q6UWX4	HIPL2_HUMAN	A	500	ENSP00000342118:V500A	ENSP00000342118:V500A	V	-	2	0	HHIPL2	220778691	1.000000	0.71417	1.000000	0.80357	0.497000	0.33675	8.704000	0.91351	2.001000	0.58596	0.482000	0.46254	GTC	.	.		0.468	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		G	222712068	A	G	222712068	3	3	111	1	0	0	0	0	1	0	0	0	7103	275	10	2	695	2	HHIPL2	1	222712068	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	14321322	222712068	26538553	42	16282										
NVL	4931	hgsc.bcm.edu	37	chr1	224475603	224475603	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	actgaggatagagcaacaatGaaatcattcagttcaatgca	8	7	3	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:224475603G>T	ENST00000281701.6	-	14	1927	c.1668C>A	c.(1666-1668)ttC>ttA	p.F556L	NVL_ENST00000340871.4_Missense_Mutation_p.F367L|NVL_ENST00000469075.1_Missense_Mutation_p.F465L|NVL_ENST00000361463.3_Missense_Mutation_p.F450L|NVL_ENST00000391875.2_Missense_Mutation_p.F450L|NVL_ENST00000482491.1_Missense_Mutation_p.F280L	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	556						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.F556L(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		GAGCAACAATGAAATCATTCA	0.478																																					p.F556L		Atlas-SNP	.											NVL,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	NVL	74	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.C1668A						.						101	84	90					1																	224475603		2203	4300	6503	SO:0001583	missense	4931	exon14			AACAATGAAATCA	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"ATPases / AAA-type"	8070	protein-coding gene	gene with protein product	"Nuclear valosin-containing protein-like", "nuclear VCP-like protein"	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.1668C>A	chr1.hg19:g.224475603G>T	ENSP00000281701:p.Phe556Leu	163.0	0.0		108.0	26.0	NM_002533	B4DMC4|B4DP98|Q96EM7	Missense_Mutation	SNP	ENST00000281701.6	hg19	CCDS1541.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.8|23.8	4.454570|4.454570	0.84209|0.84209	.|.	.|.	ENSG00000143748|ENSG00000143748	ENST00000281701;ENST00000391875;ENST00000469075;ENST00000482491;ENST00000340871;ENST00000361463|ENST00000469968	D;D;D;D;D;D|.	0.96104|.	-3.9;-3.84;-3.81;-3.7;-3.71;-3.91|.	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	0.047995|.	0.85682|.	D|.	0.000000|.	T|T	0.73273|0.73273	0.3566|0.3566	M|M	0.69523|0.69523	2.12|2.12	0.58432|0.58432	D|D	0.999998|0.999998	D;D;D|.	0.89917|.	0.985;0.985;1.0|.	P;P;D|.	0.91635|.	0.728;0.831;0.999|.	T|T	0.72554|0.72554	-0.4258|-0.4258	10|5	0.87932|.	D|.	0|.	-14.9811|-14.9811	14.7518|14.7518	0.69530|0.69530	0.0709:0.0:0.9291:0.0|0.0709:0.0:0.9291:0.0	.|.	367;465;556|.	B4DMC4;B4DP98;O15381|.	.;.;NVL_HUMAN|.	L|N	556;450;465;280;367;450|439	ENSP00000281701:F556L;ENSP00000375747:F450L;ENSP00000417826:F465L;ENSP00000417213:F280L;ENSP00000341362:F367L;ENSP00000354779:F450L|.	ENSP00000281701:F556L|.	F|H	-|-	3|1	2|0	NVL|NVL	222542226|222542226	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.093000|1.093000	0.30939|0.30939	2.624000|2.624000	0.88883|0.88883	0.655000|0.655000	0.94253|0.94253	TTC|CAT	.	.		0.478	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533		T	224475603	G	T	224475603	3	4	111	1	0	0	0	0	1	0	0	0	10789	1281	45	3	942	3	NVL	1	224475603	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	1763535	224475603	24775018	43	16283										
WDR26	80232	hgsc.bcm.edu	37	chr1	224588733	224588733	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gccacacttgtcaaactgtcTtcatgagactggctcatttt	7	11	4	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:224588733T>C	ENST00000414423.2	-	9	1531	c.1338A>G	c.(1336-1338)gaA>gaG	p.E446E	WDR26_ENST00000295024.6_Silent_p.E299E|WDR26_ENST00000366852.2_3'UTR|WDR26_ENST00000479727.1_5'Flank|MIR4742_ENST00000581069.1_RNA	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	446						cytoplasm (GO:0005737)|nucleus (GO:0005634)				biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		TCAAACTGTCTTCATGAGACT	0.443																																					p.E446E		Atlas-SNP	.											.	WDR26	104	.	0			c.A1338G						.						97	83	88					1																	224588733		2203	4300	6503	SO:0001819	synonymous_variant	80232	exon9			ACTGTCTTCATGA	AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"WD repeat domain containing"	21208	protein-coding gene	gene with protein product	"GID complex subunit 7 homolog (S. cerevisiae)"						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.1338A>G	chr1.hg19:g.224588733T>C		79.0	0.0		78.0	5.0	NM_025160	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Silent	SNP	ENST00000414423.2	hg19	CCDS31037.2	.	.	.	.	.	.	.	.	.	.	T	10.58	1.390187	0.25118	.	.	ENSG00000162923	ENST00000480676	.	.	.	5.73	3.39	0.38822	.	.	.	.	.	T	0.59266	0.2181	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52726	-0.8537	4	.	.	.	.	9.5525	0.39319	0.0:0.1475:0.0:0.8525	.	.	.	.	G	80	.	.	R	-	1	2	WDR26	222655356	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.794000	0.26958	0.447000	0.26695	0.477000	0.44152	AGA	.	.		0.443	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160		C	224588733	T	C	224588733	2	2	111	1	0	0	0	0	0	0	0	1	17298	1606	56	2		2	WDR26	1	224588733	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	113130	224588733	24661888	44	16284										
SDCCAG8	10806	hgsc.bcm.edu	37	chr1	243652338	243652338	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	taaggcagctggataagcacAgccaggccacagcccagcag	12	13	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr1:243652338A>G	ENST00000366541.3	+	17	2126	c.2008A>G	c.(2008-2010)Agc>Ggc	p.S670G	AKT3_ENST00000336199.5_Intron|SDCCAG8_ENST00000343783.6_Missense_Mutation_p.S525G|SDCCAG8_ENST00000355875.4_Missense_Mutation_p.S627G	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	670	Gln-rich.|Mediates interaction with OFD1.|Sufficient for homodimerization. {ECO:0000250}.				establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		GGATAAGCACAGCCAGGCCAC	0.582																																					p.S670G		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.A2008G						.						33	35	34					1																	243652338		2203	4300	6503	SO:0001583	missense	10806	exon17			AAGCACAGCCAGG	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.2008A>G	chr1.hg19:g.243652338A>G	ENSP00000355499:p.Ser670Gly	105.0	0.0		122.0	5.0	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	hg19	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	A	13.85	2.360719	0.41801	.	.	ENSG00000054282	ENST00000355875;ENST00000366541;ENST00000343783;ENST00000435549	T;T;T;T	0.44083	0.93;0.95;0.95;0.94	5.63	1.79	0.24919	.	0.287075	0.37761	N	0.001957	T	0.16981	0.0408	N	0.08118	0	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.05131	-1.0904	10	0.22109	T	0.4	-2.5105	3.1947	0.06629	0.5307:0.0:0.2075:0.2619	.	627;670	E9PFS7;Q86SQ7	.;SDCG8_HUMAN	G	627;670;525;371	ENSP00000348137:S627G;ENSP00000355499:S670G;ENSP00000341260:S525G;ENSP00000410200:S371G	ENSP00000341260:S525G	S	+	1	0	SDCCAG8	241718961	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.661000	0.37408	0.403000	0.25479	0.528000	0.53228	AGC	.	.		0.582	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		G	243652338	A	G	243652338	3	3	111	1	0	0	0	0	1	0	0	0	13974	188	7	2	2074	2	SDCCAG8	1	243652338	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	19063605	243652338	5598283	45	16285										
OSR1	130497	hgsc.bcm.edu	37	chr2	19552914	19552914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgccgcacctgtggtctcgcAggtggtcttgcctccggaag	14	13	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:19552914A>G	ENST00000272223.2	-	2	997	c.653T>C	c.(652-654)cTg>cCg	p.L218P	OSR1_ENST00000536433.1_Missense_Mutation_p.L218P	NM_145260.2	NP_660303.1	Q8TAX0	OSR1_HUMAN	odd-skipped related transciption factor 1	218					cell differentiation (GO:0030154)|cell proliferation involved in kidney development (GO:0072111)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|gonad development (GO:0008406)|heart development (GO:0007507)|intermediate mesoderm development (GO:0048389)|mesangial cell development (GO:0072143)|mesonephric duct morphogenesis (GO:0072180)|mesonephros development (GO:0001823)|metanephric cap mesenchymal cell proliferation involved in metanephros development (GO:0090094)|metanephric epithelium development (GO:0072207)|metanephric glomerulus vasculature development (GO:0072239)|metanephric interstitial fibroblast development (GO:0072259)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephric nephron tubule development (GO:0072234)|metanephric smooth muscle tissue development (GO:0072208)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of nephron tubule epithelial cell differentiation (GO:0072183)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|palate development (GO:0060021)|pattern specification involved in metanephros development (GO:0072268)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posterior mesonephric tubule development (GO:0072166)|pronephros development (GO:0048793)|renal vesicle progenitor cell differentiation (GO:0072184)|specification of anterior mesonephric tubule identity (GO:0072168)|specification of posterior mesonephric tubule identity (GO:0072169)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)|ureter urothelium development (GO:0072190)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|large_intestine(2)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)				GTGGTCTCGCAGGTGGTCTTG	0.592																																					p.L218P		Atlas-SNP	.											.	OSR1	29	.	0			c.T653C						.						73	75	74					2																	19552914		2203	4300	6503	SO:0001583	missense	130497	exon2			TCTCGCAGGTGGT	BC025712	CCDS1694.1	2p24.1	2013-10-17	2013-10-17	2004-11-26	ENSG00000143867	ENSG00000143867		"Zinc fingers, C2H2-type"	8111	protein-coding gene	gene with protein product		608891	"odd-skipped (Drosophila) homolog", "odd-skipped related 1 (Drosophila)"	ODD		2120051, 12119563	Standard	XM_006711942		Approved		uc002rdc.3	Q8TAX0	OTTHUMG00000088793	ENST00000272223.2:c.653T>C	chr2.hg19:g.19552914A>G	ENSP00000272223:p.Leu218Pro	78.0	0.0		59.0	4.0	NM_145260	B3KV97|D6W521	Missense_Mutation	SNP	ENST00000272223.2	hg19	CCDS1694.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.281002	0.80692	.	.	ENSG00000143867	ENST00000272223;ENST00000536433	T;T	0.53857	0.6;0.6	6.04	6.04	0.98038	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.78227	0.4250	M	0.90705	3.14	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82550	-0.0401	9	.	.	.	-10.3202	16.289	0.82738	1.0:0.0:0.0:0.0	.	218	Q8TAX0	OSR1_HUMAN	P	218	ENSP00000272223:L218P;ENSP00000441801:L218P	.	L	-	2	0	OSR1	19416395	1.000000	0.71417	0.999000	0.59377	0.812000	0.45895	9.339000	0.96797	2.330000	0.79161	0.529000	0.55759	CTG	.	.		0.592	OSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000201432.2	NM_145260		G	19552914	A	G	19552914	3	3	111	1	0	0	0	0	1	0	0	0	11302	188	7	2	155	2	OSR1	2	19552914	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10		19552914	223646459	46	16286										
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37455988	37455988	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	attttaggtatttttacttcTtttttgctggaattttcttt	5	4	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:37455988T>C	ENST00000234170.5	-	2	493	c.348A>G	c.(346-348)aaA>aaG	p.K116K	NDUFAF7_ENST00000002125.4_5'Flank|NDUFAF7_ENST00000336237.6_5'Flank	NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	116					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				TTTTTACTTCTTTTTTGCTGG	0.299																																					p.K116K		Atlas-SNP	.											.	CEBPZ	68	.	0			c.A348G						.						46	47	47					2																	37455988		2191	4297	6488	SO:0001819	synonymous_variant	10153	exon2			TACTTCTTTTTTG	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.348A>G	chr2.hg19:g.37455988T>C		36.0	0.0		41.0	5.0	NM_005760	Q8NE75	Silent	SNP	ENST00000234170.5	hg19	CCDS1787.1																																																																																			.	.		0.299	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		C	37455988	T	C	37455988	2	2	111	1	0	0	0	0	0	0	0	1	3206	1606	56	2		2	CEBPZ	2	37455988	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	17903074	37455988	205743385	47	16287										
EPAS1	2034	hgsc.bcm.edu	37	chr2	46611704	46611704	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctacctgctgcccgaactgAccagatatgactgtgaggtg	11	12	0	4	rs371184501		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:46611704A>G	ENST00000263734.3	+	16	3028	c.2518A>G	c.(2518-2520)Acc>Gcc	p.T840A		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	840	CTAD.				angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			GCCCGAACTGACCAGATATGA	0.587																																					p.T840A		Atlas-SNP	.											.	EPAS1	83	.	0			c.A2518G						.	A	ALA/THR	0,4406		0,0,2203	84	84	84		2518	5	1	2		84	1,8599	1.2+/-3.3	0,1,4299	no	missense	EPAS1	NM_001430.4	58	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging	840/871	46611704	1,13005	2203	4300	6503	SO:0001583	missense	2034	exon16			GAACTGACCAGAT	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"Basic helix-loop-helix proteins"	3374	protein-coding gene	gene with protein product	"HIF-1 alpha-like factor"	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.2518A>G	chr2.hg19:g.46611704A>G	ENSP00000263734:p.Thr840Ala	100.0	0.0		96.0	4.0	NM_001430	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	hg19	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.745470	0.89663	0.0	1.16E-4	ENSG00000116016	ENST00000263734	T	0.64803	-0.12	5.0	5.0	0.66597	HIF-1 alpha, transactivation domain, C-terminal (1);	0.578264	0.18606	N	0.136288	T	0.80732	0.4679	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83578	0.0116	10	0.87932	D	0	.	14.9966	0.71436	1.0:0.0:0.0:0.0	.	840	Q99814	EPAS1_HUMAN	A	840	ENSP00000263734:T840A	ENSP00000263734:T840A	T	+	1	0	EPAS1	46465208	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.279000	0.95777	1.975000	0.57531	0.533000	0.62120	ACC	.	.		0.587	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430		G	46611704	A	G	46611704	3	3	111	1	0	0	0	0	1	0	0	0	5152	275	10	2	2580	2	EPAS1	2	46611704	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	9155716	46611704	196587669	48	16288										
SMYD5	10322	hgsc.bcm.edu	37	chr2	73452974	73452974	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	caaatgcctggcagaggctgAtgaacccaatgtgacctcag	11	11	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:73452974A>G	ENST00000389501.4	+	13	1202	c.1157A>G	c.(1156-1158)gAt>gGt	p.D386G	PRADC1_ENST00000480093.1_5'Flank	NM_006062.2	NP_006053.2	Q6GMV2	SMYD5_HUMAN	SMYD family member 5	386	Glu-rich.						metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13						GCAGAGGCTGATGAACCCAAT	0.542																																					p.D386G		Atlas-SNP	.											.	SMYD5	58	.	0			c.A1157G						.						133	130	131					2																	73452974		2203	4300	6503	SO:0001583	missense	10322	exon13			AGGCTGATGAACC	U50383	CCDS33221.2	2p12	2007-02-09	2003-05-14	2003-05-16	ENSG00000135632	ENSG00000135632		"Zinc fingers, MYND-type"	16258	protein-coding gene	gene with protein product			"retinoic acid induced 15"	RAI15		8754834	Standard	NM_006062		Approved	RRG1, NN8-4AG, ZMYND23	uc002siw.2	Q6GMV2	OTTHUMG00000150482	ENST00000389501.4:c.1157A>G	chr2.hg19:g.73452974A>G	ENSP00000374152:p.Asp386Gly	83.0	0.0		70.0	4.0	NM_006062	D6W5H3|Q13558	Missense_Mutation	SNP	ENST00000389501.4	hg19	CCDS33221.2	.	.	.	.	.	.	.	.	.	.	A	17.84	3.489039	0.64074	.	.	ENSG00000135632	ENST00000389501	T	0.48522	0.81	4.73	4.73	0.59995	.	0.057123	0.64402	D	0.000003	T	0.46405	0.1391	L	0.59436	1.845	0.53688	D	0.999975	P	0.40970	0.734	B	0.40329	0.326	T	0.48490	-0.9031	10	0.42905	T	0.14	-17.5422	13.4899	0.61388	1.0:0.0:0.0:0.0	.	386	Q6GMV2	SMYD5_HUMAN	G	386	ENSP00000374152:D386G	ENSP00000374152:D386G	D	+	2	0	SMYD5	73306482	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.839000	0.75364	2.131000	0.65755	0.533000	0.62120	GAT	.	.		0.542	SMYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318301.1	NM_006062		G	73452974	A	G	73452974	3	3	111	1	0	0	0	0	1	0	0	0	14840	333	12	2	1207	2	SMYD5	2	73452974	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	26841270	73452974	169746399	49	16289										
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74883799	74883799	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atccctgcccttctcaggggAgagaccccgcagggtgagag	14	13	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:74883799A>G	ENST00000357877.2	+	2	433	c.284A>G	c.(283-285)gAg>gGg	p.E95G	SEMA4F_ENST00000339773.5_Missense_Mutation_p.E95G	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	95	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						TTCTCAGGGGAGAGACCCCGC	0.502																																					p.E95G		Atlas-SNP	.											.	SEMA4F	89	.	0			c.A284G						.						82	78	79					2																	74883799		2203	4300	6503	SO:0001583	missense	10505	exon2			CAGGGGAGAGACC	AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.284A>G	chr2.hg19:g.74883799A>G	ENSP00000350547:p.Glu95Gly	109.0	0.0		88.0	4.0	NM_001271662	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	hg19	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.031987	0.35893	.	.	ENSG00000135622	ENST00000357877;ENST00000339773;ENST00000434486;ENST00000453930	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	4.9	2.44	0.29823	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.568065	0.17331	N	0.178121	T	0.05868	0.0153	N	0.04724	-0.175	0.21256	N	0.999748	B;B;B;B	0.12630	0.006;0.005;0.001;0.0	B;B;B;B	0.11329	0.006;0.005;0.002;0.002	T	0.28267	-1.0049	10	0.87932	D	0	.	3.7857	0.08700	0.659:0.2249:0.1161:0.0	.	95;95;95;95	B7Z931;C9K0A1;O95754-2;O95754	.;.;.;SEM4F_HUMAN	G	95	ENSP00000350547:E95G;ENSP00000342675:E95G;ENSP00000407698:E95G;ENSP00000409141:E95G	ENSP00000342675:E95G	E	+	2	0	SEMA4F	74737307	0.998000	0.40836	0.860000	0.33809	0.981000	0.71138	1.100000	0.31025	0.872000	0.35775	0.529000	0.55759	GAG	.	.		0.502	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		G	74883799	A	G	74883799	3	3	111	1	0	0	0	0	1	0	0	0	14050	304	11	2	290	2	SEMA4F	2	74883799	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1430825	74883799	168315574	50	16290										
KIAA1310	55683	hgsc.bcm.edu	37	chr2	97268497	97268497	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggcagatgtgcacctgtgggGctggtcctggggagggattt	19	7	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:97268497G>A	ENST00000431828.1	-	18	2328	c.2252C>T	c.(2251-2253)gCc>gTc	p.A751V	KANSL3_ENST00000487070.1_5'UTR|KANSL3_ENST00000441706.2_Intron|KANSL3_ENST00000599854.1_Missense_Mutation_p.A664V|KANSL3_ENST00000440133.1_Missense_Mutation_p.A571V			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	777	Ser-rich.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CACCTGTGGGGCTGGTCCTGG	0.597																																					p.A751V		Atlas-SNP	.											.	.	.	.	0			c.C2252T						.						84	90	88					2																	97268497		2015	4195	6210	SO:0001583	missense	55683	exon18			TGTGGGGCTGGTC	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.2252C>T	chr2.hg19:g.97268497G>A	ENSP00000396749:p.Ala751Val	113.0	0.0		89.0	4.0	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	hg19	CCDS46361.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.350346	0.24512	.	.	ENSG00000114982	ENST00000354204;ENST00000447759;ENST00000431828;ENST00000440133;ENST00000444759	T;T	0.45276	0.9;0.9	5.95	2.22	0.28083	.	0.729315	0.13511	N	0.382523	T	0.22781	0.0550	N	0.08118	0	0.22819	N	0.998691	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.001;0.001	T	0.19877	-1.0292	10	0.59425	D	0.04	.	8.9033	0.35507	0.303:0.0:0.697:0.0	.	545;777;751;662;637	B4E1W4;Q9P2N6;Q9P2N6-3;Q9P2N6-5;Q9P2N6-6	.;K1310_HUMAN;.;.;.	V	664;637;751;571;545	ENSP00000396749:A751V;ENSP00000406207:A571V	ENSP00000346144:A664V	A	-	2	0	KIAA1310	96632224	0.820000	0.29190	0.229000	0.23960	0.620000	0.37586	3.428000	0.52792	0.432000	0.26286	-0.793000	0.03317	GCC	.	.		0.597	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		A	97268497	G	A	97268497	3	1	111	1	0	0	0	0	1	0	0	0	8231	1203	42	3	400	3	KIAA1310	2	97268497	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	22384698	97268497	145930876	51	16291										
BUB1	699	hgsc.bcm.edu	37	chr2	111408295	111408295	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctgcagcaggctggctcagAcgaagtaaggatgctgaata	13	9	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:111408295A>G	ENST00000302759.6	-	18	2149	c.2031T>C	c.(2029-2031)cgT>cgC	p.R677R	BUB1_ENST00000535254.1_Silent_p.R657R|BUB1_ENST00000409311.1_Silent_p.R677R	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	677					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		GCTGGCTCAGACGAAGTAAGG	0.498																																					p.R677R		Atlas-SNP	.											.	BUB1	91	.	0			c.T2031C						.						84	74	77					2																	111408295		2203	4300	6503	SO:0001819	synonymous_variant	699	exon18			GCTCAGACGAAGT	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"budding uninhibited by benzimidazoles 1 (yeast homolog)", "budding uninhibited by benzimidazoles 1 homolog (yeast)"	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.2031T>C	chr2.hg19:g.111408295A>G		110.0	0.0		101.0	5.0	NM_004336	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Silent	SNP	ENST00000302759.6	hg19	CCDS33273.1																																																																																			.	.		0.498	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		G	111408295	A	G	111408295	2	3	111	1	0	0	0	0	0	0	0	1	1572	262	10	2		2	BUB1	2	111408295	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	14139798	111408295	131791078	52	16292										
MGAT5	4249	hgsc.bcm.edu	37	chr2	135170467	135170467	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttggacttgggttcccttacGagggcccagctcccctggaa	12	13	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:135170467G>A	ENST00000409645.1	+	13	1810	c.1558G>A	c.(1558-1560)Gag>Aag	p.E520K	MGAT5_ENST00000281923.2_Missense_Mutation_p.E520K			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	520					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|pancreas(1)|skin(3)	36				BRCA - Breast invasive adenocarcinoma(221;0.0964)		GTTCCCTTACGAGGGCCCAGC	0.493																																					p.E520K		Atlas-SNP	.											.	MGAT5	84	.	0			c.G1558A						.						168	151	157					2																	135170467		2203	4300	6503	SO:0001583	missense	4249	exon12			CCTTACGAGGGCC	D17716	CCDS2171.1	2q21	2013-02-25			ENSG00000152127	ENSG00000152127	2.4.1.155	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7049	protein-coding gene	gene with protein product		601774				8292036	Standard	NM_002410		Approved	GNT-V	uc002ttw.4	Q09328	OTTHUMG00000131681	ENST00000409645.1:c.1558G>A	chr2.hg19:g.135170467G>A	ENSP00000386377:p.Glu520Lys	250.0	0.0		231.0	28.0	NM_002410	D3DP70	Missense_Mutation	SNP	ENST00000409645.1	hg19	CCDS2171.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.981741	0.93044	.	.	ENSG00000152127	ENST00000409645;ENST00000281923	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.83617	0.5293	M	0.80982	2.52	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.84896	0.0839	9	0.72032	D	0.01	-27.3571	19.8251	0.96614	0.0:0.0:1.0:0.0	.	520	Q09328	MGT5A_HUMAN	K	520	.	ENSP00000281923:E520K	E	+	1	0	MGAT5	134886937	1.000000	0.71417	0.965000	0.40720	0.988000	0.76386	9.785000	0.99042	2.685000	0.91497	0.655000	0.94253	GAG	.	.		0.493	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410		A	135170467	G	A	135170467	3	1	111	1	0	0	0	0	1	0	0	0	9557	1059	37	1	1604	1	MGAT5	2	135170467	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	23762172	135170467	108028906	53	16293										
BBS5	129880	hgsc.bcm.edu	37	chr2	170349443	170349443	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aagaagtgcactaattcagaAcaagcaactaagactgttgc	8	8	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:170349443A>G	ENST00000295240.3	+	6	822	c.446A>G	c.(445-447)aAc>aGc	p.N149S	RP11-724O16.1_ENST00000513963.1_Missense_Mutation_p.N149S|BBS5_ENST00000392663.2_Missense_Mutation_p.N149S|BBS5_ENST00000554017.1_Missense_Mutation_p.N149S	NM_152384.2	NP_689597.1	Q8N3I7	BBS5_HUMAN	Bardet-Biedl syndrome 5	149					cilium assembly (GO:0042384)|heart looping (GO:0001947)|melanosome transport (GO:0032402)|motile cilium assembly (GO:0044458)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphate binding (GO:0032266)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						CTAATTCAGAACAAGCAACTA	0.313									Bardet-Biedl syndrome																												p.N149S		Atlas-SNP	.											.	BBS5	27	.	0			c.A446G						.						92	90	91					2																	170349443		2203	4298	6501	SO:0001583	missense	129880	exon6	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TTCAGAACAAGCA	AY604003	CCDS2233.1	2q31	2011-08-02			ENSG00000163093	ENSG00000163093			970	protein-coding gene	gene with protein product		603650				9888993, 10053027	Standard	NM_152384		Approved	DKFZp762I194		Q8N3I7	OTTHUMG00000132207	ENST00000295240.3:c.446A>G	chr2.hg19:g.170349443A>G	ENSP00000295240:p.Asn149Ser	91.0	0.0		89.0	4.0	NM_152384	D3DPC3|Q6PKN0	Missense_Mutation	SNP	ENST00000295240.3	hg19	CCDS2233.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.157685	0.78114	.	.	ENSG00000163093;ENSG00000163093;ENSG00000163093;ENSG00000251569	ENST00000295240;ENST00000554017;ENST00000392663;ENST00000513963	T;T;T;T	0.74002	1.4;1.4;-0.8;1.4	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.77711	0.4171	L	0.45698	1.435	0.80722	D	1	P;B;B	0.50066	0.931;0.29;0.124	P;B;B	0.54270	0.747;0.082;0.133	T	0.74355	-0.3692	10	0.24483	T	0.36	-14.9331	16.099	0.81152	1.0:0.0:0.0:0.0	.	149;149;149	E9PBE3;Q8N3I7-2;Q8N3I7	.;.;BBS5_HUMAN	S	149	ENSP00000295240:N149S;ENSP00000452313:N149S;ENSP00000376431:N149S;ENSP00000424363:N149S	ENSP00000295240:N149S	N	+	2	0	BBS5;RP11-724O16.1	170057689	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.201000	0.95017	2.210000	0.71456	0.482000	0.46254	AAC	.	.		0.313	BBS5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255265.2	NM_152384		G	170349443	A	G	170349443	3	3	111	1	0	0	0	0	1	0	0	0	1340	43	2	2	468	2	BBS5	2	170349443	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	35178976	170349443	72849930	54	16294										
HOXD4	3233	hgsc.bcm.edu	37	chr2	177017387	177017387	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcggtcccgaacggcctacaCccggcagcaagtcctagaac	11	16	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:177017387C>T	ENST00000306324.3	+	2	897	c.485C>T	c.(484-486)aCc>aTc	p.T162I	HOXD3_ENST00000468418.3_Intron|MIR10B_ENST00000385011.1_RNA	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	162					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		ACGGCCTACACCCGGCAGCAA	0.557																																					p.T162I		Atlas-SNP	.											.,1	HOXD4	32	.	0			c.C485T						.						42	47	46					2																	177017387		2203	4300	6503	SO:0001583	missense	3233	exon2			CCTACACCCGGCA		CCDS2269.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170166	ENSG00000170166		"Homeoboxes / ANTP class : HOXL subclass"	5138	protein-coding gene	gene with protein product		142981	"homeo box D4"	HOX4B, HOX4		1973146, 1358459	Standard	NM_014621		Approved		uc002uks.3	P09016	OTTHUMG00000132515	ENST00000306324.3:c.485C>T	chr2.hg19:g.177017387C>T	ENSP00000302548:p.Thr162Ile	54.0	0.0		49.0	3.0	NM_014621	B2R9R3|Q96AU0	Missense_Mutation	SNP	ENST00000306324.3	hg19	CCDS2269.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.172606	0.78452	.	.	ENSG00000170166	ENST00000306324	D	0.97016	-4.21	5.38	5.38	0.77491	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99074	0.9682	H	0.98754	4.32	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99056	1.0829	10	0.87932	D	0	.	19.1342	0.93420	0.0:1.0:0.0:0.0	.	162	P09016	HXD4_HUMAN	I	162	ENSP00000302548:T162I	ENSP00000302548:T162I	T	+	2	0	HOXD4	176725633	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.811000	0.86092	2.516000	0.84829	0.643000	0.83706	ACC	.	.		0.557	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2			T	177017387	C	T	177017387	3	4	111	1	0	0	0	0	1	0	0	0	7333	507	18	3	491	3	HOXD4	2	177017387	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	6667944	177017387	66181986	55	16295										
TTN	7273	hgsc.bcm.edu	37	chr2	179506015	179506015	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttttaggttctactttaggtTcttcttcttcaggtcttttt	6	7	6	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:179506015T>C	ENST00000591111.1	-	170	35887	c.35663A>G	c.(35662-35664)gAa>gGa	p.E11888G	TTN_ENST00000589042.1_Missense_Mutation_p.E13529G|TTN_ENST00000342175.6_Missense_Mutation_p.E4656G|TTN-AS1_ENST00000418062.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E10961G|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E4589G|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E4464G			Q8WZ42	TITIN_HUMAN	titin	11888	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACTTTAGGTTCTTCTTCTTC	0.294																																					p.E13529G		Atlas-SNP	.											.	TTN	18412	.	0			c.A40586G						.						101	88	92					2																	179506015		1754	3994	5748	SO:0001583	missense	7273	exon220			TTAGGTTCTTCTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.35663A>G	chr2.hg19:g.179506015T>C	ENSP00000465570:p.Glu11888Gly	82.0	0.0		67.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.02	2.708096	0.48412	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000414766	T;T;T;T	0.69435	-0.4;0.06;0.04;0.04	5.51	5.51	0.81932	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.74230	0.3689	L	0.43923	1.385	0.33545	D	0.595423	P;P;P;P;D	0.76494	0.849;0.849;0.849;0.849;0.999	P;P;P;P;D	0.71414	0.478;0.478;0.478;0.478;0.973	T	0.81675	-0.0825	9	0.87932	D	0	.	11.2668	0.49114	0.1365:0.0:0.0:0.8635	.	4464;4589;4656;11888;10655	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-5	.;.;.;TITIN_HUMAN;.	G	10961;4464;4656;4589;4464;850	ENSP00000343764:E10961G;ENSP00000434586:E4464G;ENSP00000340554:E4656G;ENSP00000352154:E4589G	ENSP00000340554:E4656G	E	-	2	0	TTN	179214260	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	3.635000	0.54309	2.105000	0.64084	0.482000	0.46254	GAA	.	.		0.294	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179506015	T	C	179506015	3	2	111	1	0	0	0	0	1	0	0	0	16750	1783	62	2	67679	2	TTN	2	179506015	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2488628	179506015	63693358	56	16296										
ITGA4	3676	hgsc.bcm.edu	37	chr2	182358065	182358065	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tggatagatgttgctatcggAgctccacaagaagatgactt	11	7	0	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:182358065A>G	ENST00000397033.2	+	11	1597	c.1167A>G	c.(1165-1167)ggA>ggG	p.G389G		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	389					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	TTGCTATCGGAGCTCCACAAG	0.348																																					p.G389G		Atlas-SNP	.											.	ITGA4	142	.	0			c.A1167G						.						104	96	98					2																	182358065		1853	4099	5952	SO:0001819	synonymous_variant	3676	exon11			TATCGGAGCTCCA		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.1167A>G	chr2.hg19:g.182358065A>G		76.0	0.0		86.0	4.0	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	hg19	CCDS42788.1																																																																																			.	.		0.348	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			G	182358065	A	G	182358065	2	3	111	1	0	0	0	0	0	0	0	1	7887	291	11	2		2	ITGA4	2	182358065	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	2852050	182358065	60841308	57	16297										
GTF3C3	9330	hgsc.bcm.edu	37	chr2	197634689	197634689	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atacttctgagatgccatatGaataaaggttaggcctatac	8	7	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:197634689G>A	ENST00000263956.3	-	16	2424	c.2335C>T	c.(2335-2337)Cat>Tat	p.H779Y		NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	779					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GATGCCATATGAATAAAGGTT	0.388																																					p.H779Y		Atlas-SNP	.											.	GTF3C3	96	.	0			c.C2335T						.						100	96	97					2																	197634689		2203	4300	6503	SO:0001583	missense	9330	exon16			CCATATGAATAAA	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.2335C>T	chr2.hg19:g.197634689G>A	ENSP00000263956:p.His779Tyr	99.0	0.0		90.0	17.0	NM_012086	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	hg19	CCDS2316.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.069214	0.76301	.	.	ENSG00000119041	ENST00000263956	T	0.28666	1.6	5.27	4.4	0.53042	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.57169	0.2035	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.66716	0.946	T	0.63337	-0.6660	10	0.48119	T	0.1	-23.271	14.0128	0.64507	0.0725:0.0:0.9275:0.0	.	779	Q9Y5Q9	TF3C3_HUMAN	Y	779	ENSP00000263956:H779Y	ENSP00000263956:H779Y	H	-	1	0	GTF3C3	197342934	1.000000	0.71417	0.707000	0.30419	0.644000	0.38419	9.081000	0.94049	1.451000	0.47736	0.563000	0.77884	CAT	.	.		0.388	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			A	197634689	G	A	197634689	3	1	111	1	0	0	0	0	1	0	0	0	6883	1290	45	3	337	3	GTF3C3	2	197634689	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	15276624	197634689	45564684	58	16298										
CPS1	1373	hgsc.bcm.edu	37	chr2	211476885	211476885	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaggagagtttccagaaagcTttacggatgtgccacccatc	11	10	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:211476885T>C	ENST00000233072.5	+	20	2632	c.2436T>C	c.(2434-2436)gcT>gcC	p.A812A	CPS1_ENST00000430249.2_Silent_p.A818A|CPS1_ENST00000451903.2_Silent_p.A361A	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	812					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TCCAGAAAGCTTTACGGATGT	0.388																																					p.A818A		Atlas-SNP	.											.	CPS1	485	.	0			c.T2454C						.						148	148	148					2																	211476885		2203	4300	6503	SO:0001819	synonymous_variant	1373	exon21			GAAAGCTTTACGG	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2436T>C	chr2.hg19:g.211476885T>C		81.0	0.0		97.0	4.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	hg19	CCDS2393.1																																																																																			.	.		0.388	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			C	211476885	T	C	211476885	2	2	111	1	0	0	0	0	0	0	0	1	3825	1596	56	2		2	CPS1	2	211476885	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	13842196	211476885	31722488	59	16299										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212295715	212295715	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttttcatctccttccaagagTctggctagcccaaaatctgt	6	12	4	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:212295715T>C	ENST00000342788.4	-	21	2908	c.2598A>G	c.(2596-2598)agA>agG	p.R866R	ERBB4_ENST00000402597.1_Silent_p.R856R|ERBB4_ENST00000436443.1_Silent_p.R866R	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	866	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	CTTCCAAGAGTCTGGCTAGCC	0.403										TSP Lung(8;0.080)																											p.R866R		Atlas-SNP	.											.	ERBB4	480	.	0			c.A2598G						.						141	135	137					2																	212295715		2203	4300	6503	SO:0001819	synonymous_variant	2066	exon21			CAAGAGTCTGGCT	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2598A>G	chr2.hg19:g.212295715T>C		134.0	0.0		115.0	5.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	hg19	CCDS2394.1																																																																																			.	.		0.403	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		C	212295715	T	C	212295715	2	2	111	1	0	0	0	0	0	0	0	1	5211	1664	58	2		2	ERBB4	2	212295715	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	818830	212295715	30903658	60	16300										
TNS1	7145	hgsc.bcm.edu	37	chr2	218713178	218713178	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aggccccgcccggctggcagActcgtaggggtagcctcctc	14	16	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:218713178A>G	ENST00000171887.4	-	17	2139	c.1687T>C	c.(1687-1689)Tct>Cct	p.S563P	TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000419504.1_Missense_Mutation_p.S563P|TNS1_ENST00000430930.1_Missense_Mutation_p.S563P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	563					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CGGCTGGCAGACTCGTAGGGG	0.667																																					p.S563P		Atlas-SNP	.											.	TNS1	251	.	0			c.T1687C						.						33	38	36					2																	218713178		2203	4299	6502	SO:0001583	missense	7145	exon17			TGGCAGACTCGTA	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1687T>C	chr2.hg19:g.218713178A>G	ENSP00000171887:p.Ser563Pro	114.0	0.0		125.0	5.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	A	8.614	0.889925	0.17540	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903	D;D;D;D	0.94092	-2.82;-2.82;-2.82;-3.35	4.79	-9.58	0.00559	.	1.246840	0.05476	N	0.553969	T	0.71117	0.3302	N	0.01576	-0.805	0.36093	D	0.843619	B;B;B;B;B	0.34226	0.0;0.443;0.357;0.167;0.167	B;B;B;B;B	0.28784	0.0;0.094;0.094;0.092;0.063	T	0.63350	-0.6657	10	0.21540	T	0.41	.	1.0618	0.01602	0.1773:0.2392:0.3263:0.2571	.	563;617;563;563;563	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	P	563;563;563;688	ENSP00000171887:S563P;ENSP00000408724:S563P;ENSP00000406016:S563P;ENSP00000405460:S688P	ENSP00000171887:S563P	S	-	1	0	TNS1	218421423	0.310000	0.24527	0.288000	0.24862	0.236000	0.25371	-0.491000	0.06474	-1.320000	0.02283	-0.366000	0.07423	TCT	.	.		0.667	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		G	218713178	A	G	218713178	3	3	111	1	0	0	0	0	1	0	0	0	16358	275	10	2	3588	2	TNS1	2	218713178	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	6417463	218713178	24486195	61	16301										
SPEG	10290	hgsc.bcm.edu	37	chr2	220333960	220333960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgtccattcctgacttcctgCggccactgcaggacctggag	11	14	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr2:220333960C>T	ENST00000312358.7	+	13	3706	c.3574C>T	c.(3574-3576)Cgg>Tgg	p.R1192W	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1192	Ig-like 6.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TGACTTCCTGCGGCCACTGCA	0.622																																					p.R1192W		Atlas-SNP	.											.	SPEG	272	.	0			c.C3574T						.						33	42	39					2																	220333960		2149	4262	6411	SO:0001583	missense	10290	exon13			TTCCTGCGGCCAC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.3574C>T	chr2.hg19:g.220333960C>T	ENSP00000311684:p.Arg1192Trp	174.0	0.0		169.0	58.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.783430	0.49891	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.68624	-0.34	4.94	3.99	0.46301	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37955	N	0.001873	T	0.81054	0.4743	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.83667	0.0164	10	0.72032	D	0.01	.	15.1123	0.72368	0.1788:0.8211:0.0:0.0	.	1192	Q15772	SPEG_HUMAN	W	1192	ENSP00000311684:R1192W	ENSP00000265327:R1192W	R	+	1	2	SPEG	220042204	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.476000	0.35420	2.573000	0.86826	0.655000	0.94253	CGG	.	.		0.622	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220333960	C	T	220333960	3	4	111	1	0	0	0	0	1	0	0	0	15051	759	27	1	3636	1	SPEG	2	220333960	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	1620782	220333960	22865413	62	16302										
SLC6A1	6529	hgsc.bcm.edu	37	chr3	11064104	11064104	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccatcacgctggccatcgccTggatccttgtgtatttctgt	9	13	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:11064104T>C	ENST00000287766.4	+	7	1085	c.664T>C	c.(664-666)Tgg>Cgg	p.W222R	SLC6A1_ENST00000536032.1_Missense_Mutation_p.W44R	NM_003042.3	NP_003033.3	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 1	222					gamma-aminobutyric acid import (GO:0051939)|learning (GO:0007612)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neurotransmitter secretion (GO:0007269)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|protein homooligomerization (GO:0051260)|response to calcium ion (GO:0051592)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to lead ion (GO:0010288)|response to purine-containing compound (GO:0014074)|response to sucrose (GO:0009744)|response to toxic substance (GO:0009636)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	26		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Clobazam(DB00349)|Tiagabine(DB00906)	GGCCATCGCCTGGATCCTTGT	0.557																																					p.W222R		Atlas-SNP	.											.	SLC6A1	88	.	0			c.T664C						.						97	85	89					3																	11064104		2203	4300	6503	SO:0001583	missense	6529	exon7			ATCGCCTGGATCC		CCDS2603.1	3p25.3	2013-07-19	2013-07-19		ENSG00000157103	ENSG00000157103		"Solute carriers"	11042	protein-coding gene	gene with protein product	"GABA transporter 1"	137165	"solute carrier family 6 (neurotransmitter transporter, GABA), member 1"			8530094	Standard	NM_003042		Approved	GAT1, GABATR, GABATHG	uc010hdq.3	P30531	OTTHUMG00000044208	ENST00000287766.4:c.664T>C	chr3.hg19:g.11064104T>C	ENSP00000287766:p.Trp222Arg	133.0	0.0		143.0	6.0	NM_003042	Q8N4K8	Missense_Mutation	SNP	ENST00000287766.4	hg19	CCDS2603.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.641613	0.87859	.	.	ENSG00000157103	ENST00000287766;ENST00000536032	T;T	0.78003	-1.14;-1.14	5.02	5.02	0.67125	.	0.000000	0.64402	D	0.000002	D	0.93357	0.7882	H	0.99464	4.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96092	0.9062	10	0.87932	D	0	.	14.9138	0.70778	0.0:0.0:0.0:1.0	.	222	P30531	SC6A1_HUMAN	R	222;44	ENSP00000287766:W222R;ENSP00000445171:W44R	ENSP00000287766:W222R	W	+	1	0	SLC6A1	11039104	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.757000	0.85209	2.107000	0.64212	0.459000	0.35465	TGG	.	.		0.557	SLC6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102767.2	NM_003042		C	11064104	T	C	11064104	3	2	111	1	0	0	0	0	1	0	0	0	14688	1580	55	2	682	2	SLC6A1	3	11064104	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		11064104	186958326	63	16303										
NKIRAS1	28512	hgsc.bcm.edu	37	chr3	23942421	23942421	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaatgaaaaataatgctttgGcagctccacgccttcctgta	7	10	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:23942421G>C	ENST00000443659.2	-	3	991	c.214C>G	c.(214-216)Cca>Gca	p.P72A	NKIRAS1_ENST00000388759.3_Missense_Mutation_p.P72A|NKIRAS1_ENST00000415901.2_Missense_Mutation_p.P72A|NKIRAS1_ENST00000437230.1_Missense_Mutation_p.P72A|NKIRAS1_ENST00000416026.2_Missense_Mutation_p.P72A|NKIRAS1_ENST00000425478.2_Missense_Mutation_p.P72A|NKIRAS1_ENST00000412028.1_Missense_Mutation_p.P72A|NKIRAS1_ENST00000421515.2_Missense_Mutation_p.P72A			Q9NYS0	KBRS1_HUMAN	NFKB inhibitor interacting Ras-like 1	72	Interactions with NFKBIA and NFKBIB.				I-kappaB kinase/NF-kappaB signaling (GO:0007249)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	7						TAATGCTTTGGCAGCTCCACG	0.408																																					p.P72A		Atlas-SNP	.											.	NKIRAS1	18	.	0			c.C214G						.						162	157	159					3																	23942421		2203	4300	6503	SO:0001583	missense	28512	exon4			GCTTTGGCAGCTC	AF229839	CCDS33717.1	3p24.1	2014-05-09	2004-05-20		ENSG00000197885	ENSG00000197885			17899	protein-coding gene	gene with protein product		604496	"NFKB inhibitor interacting Ras-like protein 1"			10657303	Standard	NM_020345		Approved	KBRAS1, kappaB-Ras1	uc003ccj.3	Q9NYS0	OTTHUMG00000155605	ENST00000443659.2:c.214C>G	chr3.hg19:g.23942421G>C	ENSP00000393785:p.Pro72Ala	130.0	0.0		155.0	19.0	NM_020345	Q96K18	Missense_Mutation	SNP	ENST00000443659.2	hg19	CCDS33717.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.723394	0.89298	.	.	ENSG00000197885	ENST00000388759;ENST00000443659;ENST00000421515;ENST00000425478;ENST00000437230;ENST00000412028;ENST00000415901;ENST00000416026	T;T;T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.56	4.69	0.59074	Small GTP-binding protein domain (1);	0.052646	0.85682	D	0.000000	T	0.79678	0.4487	L	0.52266	1.64	0.80722	D	1	P;P	0.48503	0.911;0.877	P;P	0.50617	0.646;0.627	T	0.81645	-0.0839	10	0.72032	D	0.01	-14.2805	14.1746	0.65532	0.0729:0.0:0.9271:0.0	.	72;72	G5E9P3;Q9NYS0	.;KBRS1_HUMAN	A	72	ENSP00000373411:P72A;ENSP00000393785:P72A;ENSP00000392307:P72A;ENSP00000400385:P72A;ENSP00000406543:P72A;ENSP00000396063:P72A;ENSP00000415225:P72A;ENSP00000394214:P72A	ENSP00000373411:P72A	P	-	1	0	NKIRAS1	23917425	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.771000	0.98977	1.354000	0.45846	0.491000	0.48974	CCA	.	.		0.408	NKIRAS1-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340876.2	NM_020345		C	23942421	G	C	23942421	3	2	111	1	0	0	0	0	1	0	0	0	10453	1203	42	4	372	4	NKIRAS1	3	23942421	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	12878317	23942421	174080009	64	16304										
LTF	4057	hgsc.bcm.edu	37	chr3	46501284	46501284	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acggcgcaccactgaacactCctcctacggccagccagaca	8	18	0	2	rs55665884|rs76787706|rs10662431	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:46501284C>T	ENST00000231751.4	-	2	364	c.69G>A	c.(67-69)agG>agA	p.R23R	LTF_ENST00000426532.2_5'UTR|LTF_ENST00000417439.1_Silent_p.R23R	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	23	Bactericidal and antifungal activity.|Critical for glycosaminoglycan, lipid A, lysozyme and DNA binding.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		ACTGAACACTCCTCCTACGGC	0.562																																					p.R23R		Atlas-SNP	.											.	LTF	98	.	0			c.G69A						.						82	66	72					3																	46501284		2203	4300	6503	SO:0001819	synonymous_variant	4057	exon2			AACACTCCTCCTA		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.69G>A	chr3.hg19:g.46501284C>T		181.0	0.0		145.0	7.0	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	hg19	CCDS33747.1																																																																																			.	.		0.562	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		T	46501284	C	T	46501284	2	4	111	1	0	0	0	0	0	0	0	1	9088	854	30	3		3	LTF	3	46501284	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	22558863	46501284	151521146	65	16305										
APEH	327	hgsc.bcm.edu	37	chr3	49713569	49713569	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agaagcgccccaaggccgagTccttctttcagaccaaagcc	9	15	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:49713569T>C	ENST00000296456.5	+	6	923	c.523T>C	c.(523-525)Tcc>Ccc	p.S175P	APEH_ENST00000438011.1_Missense_Mutation_p.S175P	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	175					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CAAGGCCGAGTCCTTCTTTCA	0.572																																					p.S175P		Atlas-SNP	.											.	APEH	45	.	0			c.T523C						.						61	62	62					3																	49713569		2203	4300	6503	SO:0001583	missense	327	exon6			GCCGAGTCCTTCT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.523T>C	chr3.hg19:g.49713569T>C	ENSP00000296456:p.Ser175Pro	86.0	0.0		91.0	6.0	NM_001640	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	T	12.53	1.965575	0.34659	.	.	ENSG00000164062	ENST00000296456;ENST00000449966;ENST00000442186;ENST00000438011;ENST00000457042	T;T;T	0.44482	0.92;0.99;0.92	4.9	4.9	0.64082	Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (1);	0.054422	0.85682	D	0.000000	T	0.28532	0.0706	N	0.20881	0.62	0.36862	D	0.888476	B;B	0.12013	0.001;0.005	B;B	0.09377	0.002;0.004	T	0.18999	-1.0319	10	0.29301	T	0.29	-4.2863	11.798	0.52110	0.0:0.0:0.1463:0.8537	.	175;175	C9JIF9;P13798	.;ACPH_HUMAN	P	175;74;100;175;172	ENSP00000296456:S175P;ENSP00000402365:S100P;ENSP00000415862:S175P	ENSP00000296456:S175P	S	+	1	0	APEH	49688573	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.984000	0.63838	1.839000	0.53478	0.402000	0.26972	TCC	.	.		0.572	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			C	49713569	T	C	49713569	3	2	111	1	0	0	0	0	1	0	0	0	768	1667	58	2	545	2	APEH	3	49713569	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	3212285	49713569	148308861	66	16306										
PARP3	10039	hgsc.bcm.edu	37	chr3	51978115	51978115	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tctggcccaggtgtatgaggActacaactgcaccctgaacc	10	13	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:51978115A>G	ENST00000417220.2	+	4	682	c.194A>G	c.(193-195)gAc>gGc	p.D65G	RRP9_ENST00000232888.6_5'Flank|PARP3_ENST00000431474.1_Missense_Mutation_p.D65G|PARP3_ENST00000398755.3_Missense_Mutation_p.D72G			Q9Y6F1	PARP3_HUMAN	poly (ADP-ribose) polymerase family, member 3	65					DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|positive regulation of DNA ligation (GO:0051106)|protein ADP-ribosylation (GO:0006471)|protein localization to site of double-strand break (GO:1990166)|regulation of mitotic spindle organization (GO:0060236)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	catalytic activity (GO:0003824)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GTGTATGAGGACTACAACTGC	0.587																																					p.D72G		Atlas-SNP	.											.	PARP3	90	.	0			c.A215G						.						120	128	126					3																	51978115		2040	4193	6233	SO:0001583	missense	10039	exon3			ATGAGGACTACAA	AF083068	CCDS43097.1, CCDS46839.1	3p22.2-p21.1	2010-07-14	2004-08-20	2004-08-26	ENSG00000041880	ENSG00000041880	2.4.2.30	"Poly (ADP-ribose) polymerases"	273	protein-coding gene	gene with protein product	"poly(ADP-ribose) synthetase-3", "NAD+ ADP-ribosyltransferase 3", "poly(ADP-ribose) polymerase 3"	607726	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 3"	ADPRTL3		10329013	Standard	NM_001003931		Approved	ADPRT3, IRT1, hPARP-3, pADPRT-3	uc003dbz.3	Q9Y6F1	OTTHUMG00000156931	ENST00000417220.2:c.194A>G	chr3.hg19:g.51978115A>G	ENSP00000395951:p.Asp65Gly	107.0	0.0		97.0	6.0	NM_001003931	Q8NER9|Q96CG2|Q9UG81	Missense_Mutation	SNP	ENST00000417220.2	hg19	CCDS43097.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.913576	0.52439	.	.	ENSG00000041880	ENST00000417220;ENST00000431474;ENST00000398755;ENST00000498510	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	4.87	4.87	0.63330	WGR domain (2);	0.000000	0.85682	D	0.000000	T	0.43678	0.1258	M	0.80332	2.49	0.54753	D	0.999983	P;P	0.42409	0.738;0.779	P;P	0.58721	0.758;0.844	T	0.30179	-0.9987	10	0.35671	T	0.21	-29.0442	11.7039	0.51587	0.8525:0.1475:0.0:0.0	.	72;65	Q9Y6F1-2;Q9Y6F1	.;PARP3_HUMAN	G	65;65;72;65	ENSP00000395951:D65G;ENSP00000401511:D65G;ENSP00000381740:D72G;ENSP00000417625:D65G	ENSP00000381740:D72G	D	+	2	0	PARP3	51953155	1.000000	0.71417	0.995000	0.50966	0.237000	0.25408	6.146000	0.71777	1.813000	0.52934	0.533000	0.62120	GAC	.	.		0.587	PARP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348612.2	NM_005485.4		G	51978115	A	G	51978115	3	3	111	1	0	0	0	0	1	0	0	0	11471	275	10	2	225	2	PARP3	3	51978115	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	2264546	51978115	146044315	67	16307										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52395766	52395766	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcagatcaccaccatccagaAggcgcagcagcagcgggtga	13	13	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:52395766A>G	ENST00000420323.2	+	30	5225	c.4964A>G	c.(4963-4965)aAg>aGg	p.K1655R	DNAH1_ENST00000466628.1_Intron	NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1655	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ACCATCCAGAAGGCGCAGCAG	0.627																																					p.K1655R		Atlas-SNP	.											.	DNAH1	534	.	0			c.A4964G						.						28	33	32					3																	52395766		2185	4290	6475	SO:0001583	missense	25981	exon30			TCCAGAAGGCGCA	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.4964A>G	chr3.hg19:g.52395766A>G	ENSP00000401514:p.Lys1655Arg	173.0	0.0		173.0	7.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	16.05	3.011930	0.54468	.	.	ENSG00000114841	ENST00000420323	T	0.09538	2.97	5.1	5.1	0.69264	.	0.000000	0.52532	D	0.000068	T	0.03871	0.0109	N	0.00750	-1.22	0.49389	D	0.99978	B	0.33777	0.425	B	0.36289	0.221	T	0.50524	-0.8818	10	0.09338	T	0.73	.	14.8904	0.70604	1.0:0.0:0.0:0.0	.	1655	C9JXH6	.	R	1655	ENSP00000401514:K1655R	ENSP00000401514:K1655R	K	+	2	0	DNAH1	52370806	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.089000	0.64492	1.922000	0.55676	0.460000	0.39030	AAG	.	.		0.627	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52395766	A	G	52395766	3	3	111	1	0	0	0	0	1	0	0	0	4599	72	3	2	5078	2	DNAH1	3	52395766	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	417651	52395766	145626664	68	16308										
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113684024	113684024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	attcgttcaccagacttgtcTtactcaaggaccaagtatct	6	11	4	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:113684024T>C	ENST00000295878.3	-	17	2935	c.2789A>G	c.(2788-2790)aAg>aGg	p.K930R		NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	930										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						CAGACTTGTCTTACTCAAGGA	0.448																																					p.K930R		Atlas-SNP	.											.	KIAA1407	80	.	0			c.A2789G						.						124	125	124					3																	113684024		2203	4300	6503	SO:0001583	missense	57577	exon17			CTTGTCTTACTCA	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2789A>G	chr3.hg19:g.113684024T>C	ENSP00000295878:p.Lys930Arg	116.0	0.0		86.0	4.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.150448	0.57151	.	.	ENSG00000163617	ENST00000295878	T	0.32753	1.44	3.55	-2.67	0.06059	.	1.993840	0.02806	N	0.123696	T	0.14485	0.0350	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.19943	-1.0290	10	0.87932	D	0	.	0.62	0.00776	0.3691:0.1115:0.1732:0.3462	.	930	Q8NCU4	K1407_HUMAN	R	930	ENSP00000295878:K930R	ENSP00000295878:K930R	K	-	2	0	KIAA1407	115166714	0.000000	0.05858	0.000000	0.03702	0.320000	0.28249	-0.231000	0.09069	-0.620000	0.05641	0.528000	0.53228	AAG	.	.		0.448	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		C	113684024	T	C	113684024	3	2	111	1	0	0	0	0	1	0	0	0	8238	1609	56	2	25	2	KIAA1407	3	113684024	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	61288258	113684024	84338406	69	16309										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	120941904	120941904	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tatgacaaagcttgtagaagAccaagtttaaccatcatgca	7	8	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:120941904A>G	ENST00000273666.6	+	11	1282	c.1011A>G	c.(1009-1011)agA>agG	p.R337R	STXBP5L_ENST00000471454.1_Silent_p.R337R|STXBP5L_ENST00000497029.1_Silent_p.R337R|STXBP5L_ENST00000472879.1_Silent_p.R337R|STXBP5L_ENST00000492541.1_Silent_p.R337R	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	337					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		CTTGTAGAAGACCAAGTTTAA	0.363																																					p.R337R		Atlas-SNP	.											.	STXBP5L	159	.	0			c.A1011G						.						160	151	154					3																	120941904		1878	4102	5980	SO:0001819	synonymous_variant	9515	exon11			TAGAAGACCAAGT	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.1011A>G	chr3.hg19:g.120941904A>G		132.0	0.0		114.0	5.0	NM_014980	Q4G1B4|Q6PIC3	Silent	SNP	ENST00000273666.6	hg19	CCDS43137.1																																																																																			.	.		0.363	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			G	120941904	A	G	120941904	2	3	111	1	0	0	0	0	0	0	0	1	15372	272	10	2		2	STXBP5L	3	120941904	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	7257880	120941904	77080526	70	16310										
H1FX	8971	hgsc.bcm.edu	37	chr3	129034735	129034735	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctggcagggcctcctcgagcTccacggacatggtagcaaga	13	13	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:129034735T>C	ENST00000333762.4	-	1	385	c.11A>G	c.(10-12)gAg>gGg	p.E4G	H1FX-AS1_ENST00000502789.2_RNA|H1FX-AS1_ENST00000537780.1_RNA|H1FX-AS1_ENST00000433902.2_RNA|H1FX-AS1_ENST00000511998.1_RNA|H1FX-AS1_ENST00000383461.2_RNA	NM_006026.3	NP_006017.1	Q92522	H1X_HUMAN	H1 histone family, member X	4					nucleosome assembly (GO:0006334)	nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			kidney(1)|ovary(1)|urinary_tract(2)	4						CTCCTCGAGCTCCACGGACAT	0.701																																					p.E4G		Atlas-SNP	.											.	H1FX	13	.	0			c.A11G						.						8	8	8					3																	129034735		2192	4291	6483	SO:0001583	missense	8971	exon1			TCGAGCTCCACGG	D64142	CCDS3057.1	3q21.3	2011-08-16			ENSG00000184897	ENSG00000184897		"Histones / Replication-independent"	4722	protein-coding gene	gene with protein product		602785				8964515, 9439656	Standard	NM_006026		Approved	MGC15959, MGC8350, H1X	uc003elx.3	Q92522	OTTHUMG00000159450	ENST00000333762.4:c.11A>G	chr3.hg19:g.129034735T>C	ENSP00000329662:p.Glu4Gly	77.0	0.0		55.0	5.0	NM_006026		Missense_Mutation	SNP	ENST00000333762.4	hg19	CCDS3057.1	.	.	.	.	.	.	.	.	.	.	T	11.34	1.610775	0.28712	.	.	ENSG00000184897	ENST00000333762	T	0.07444	3.19	3.42	3.42	0.39159	.	1.272630	0.05746	U	0.602174	T	0.09291	0.0229	N	0.14661	0.345	0.29847	N	0.82872	D	0.58268	0.982	P	0.49421	0.61	T	0.26155	-1.0111	10	0.49607	T	0.09	-28.5182	8.263	0.31797	0.0:0.0:0.0:1.0	.	4	Q92522	H1X_HUMAN	G	4	ENSP00000329662:E4G	ENSP00000329662:E4G	E	-	2	0	H1FX	130517425	0.995000	0.38212	0.996000	0.52242	0.127000	0.20565	1.174000	0.31932	1.190000	0.43042	0.459000	0.35465	GAG	.	.		0.701	H1FX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355455.2	NM_006026		C	129034735	T	C	129034735	3	2	111	1	0	0	0	0	1	0	0	0	6932	1551	54	2	634	2	H1FX	3	129034735	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	8092831	129034735	68987695	71	16311										
RASA2	5922	hgsc.bcm.edu	37	chr3	141305546	141305546	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaaaaaagaattttaagaaaCgatggttctgcttaacaagc	8	5	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:141305546C>T	ENST00000452898.1	+	19	1920	c.1885C>T	c.(1885-1887)Cga>Tga	p.R629*	RASA2_ENST00000286364.3_Nonsense_Mutation_p.R629*|RASA2_ENST00000509118.1_3'UTR	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	629	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						TTTTAAGAAACGATGGTTCTG	0.373																																					p.R629X		Atlas-SNP	.											.	RASA2	169	.	0			c.C1885T						.						54	58	57					3																	141305546		2203	4300	6503	SO:0001587	stop_gained	5922	exon19			AAGAAACGATGGT	AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"Pleckstrin homology (PH) domain containing"	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.1885C>T	chr3.hg19:g.141305546C>T	ENSP00000391677:p.Arg629*	149.0	0.0		150.0	7.0	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Nonsense_Mutation	SNP	ENST00000452898.1	hg19		.	.	.	.	.	.	.	.	.	.	C	41	8.987938	0.99027	.	.	ENSG00000155903	ENST00000286364;ENST00000452898;ENST00000423660	.	.	.	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.5786	0.95455	0.0:1.0:0.0:0.0	.	.	.	.	X	629;629;221	.	ENSP00000286364:R629X	R	+	1	2	RASA2	142788236	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.697000	0.47060	2.711000	0.92665	0.655000	0.94253	CGA	.	.		0.373	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506		T	141305546	C	T	141305546	4	4	111	1	0	0	0	0	0	1	0	0	13076	528	19	1	1959	1	RASA2	3	141305546	Nonsense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	12270811	141305546	56716884	72	16312										
NMD3	51068	hgsc.bcm.edu	37	chr3	160968077	160968077	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tttcttgaagatcttgaagaAgatgaggcaattcgaaaaaa	9	4	2	6			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:160968077A>G	ENST00000460469.1	+	14	1799	c.1344A>G	c.(1342-1344)gaA>gaG	p.E448E	NMD3_ENST00000351193.2_Silent_p.E448E|NMD3_ENST00000472947.1_Silent_p.E448E			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	448	Necessary for the nuclear export of the 60S ribosomal subunit.				protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			ATCTTGAAGAAGATGAGGCAA	0.279																																					p.E448E		Atlas-SNP	.											.	NMD3	49	.	0			c.A1344G						.						85	87	86					3																	160968077		2203	4296	6499	SO:0001819	synonymous_variant	51068	exon15			TGAAGAAGATGAG	BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"NMD3 homolog (S. cerevisiae)"			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.1344A>G	chr3.hg19:g.160968077A>G		69.0	0.0		69.0	4.0	NM_015938	D3DNM7|Q9Y2Z6	Silent	SNP	ENST00000460469.1	hg19	CCDS3194.1																																																																																			.	.		0.279	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938		G	160968077	A	G	160968077	2	3	111	1	0	0	0	0	0	0	0	1	10497	69	3	2		2	NMD3	3	160968077	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	19662531	160968077	37054353	73	16313										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164907099	164907099	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tattattgaggaatagcagcTtcaagttgggcatgaggctg	13	5	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:164907099T>C	ENST00000475390.1	-	2	1963	c.1520A>G	c.(1519-1521)aAg>aGg	p.K507R	SLITRK3_ENST00000241274.3_Missense_Mutation_p.K507R			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	507					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						GAATAGCAGCTTCAAGTTGGG	0.512										HNSCC(40;0.11)																											p.K507R		Atlas-SNP	.											.	SLITRK3	263	.	0			c.A1520G						.						65	69	68					3																	164907099		2203	4300	6503	SO:0001583	missense	22865	exon2			AGCAGCTTCAAGT	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1520A>G	chr3.hg19:g.164907099T>C	ENSP00000420091:p.Lys507Arg	89.0	0.0		88.0	4.0	NM_014926	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	hg19	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	T	12.31	1.901069	0.33535	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.52295	0.67;0.67	5.18	5.18	0.71444	.	0.000000	0.39687	N	0.001295	T	0.35970	0.0950	N	0.20445	0.575	0.47698	D	0.999499	B	0.29481	0.245	B	0.31946	0.138	T	0.18745	-1.0327	10	0.35671	T	0.21	-14.8971	15.1424	0.72620	0.0:0.0:0.0:1.0	.	507	O94933	SLIK3_HUMAN	R	507	ENSP00000420091:K507R;ENSP00000241274:K507R	ENSP00000241274:K507R	K	-	2	0	SLITRK3	166389793	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.825000	0.86693	2.297000	0.77311	0.533000	0.62120	AAG	.	.		0.512	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		C	164907099	T	C	164907099	3	2	111	1	0	0	0	0	1	0	0	0	14759	1609	56	2	1417	2	SLITRK3	3	164907099	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	3939022	164907099	33115331	74	16314										
YEATS2	55689	hgsc.bcm.edu	37	chr3	183472104	183472104	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	caggttcctaatcctgagtcAcctggaaaatccttccagcc	7	14	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:183472104A>G	ENST00000305135.5	+	11	1536	c.1341A>G	c.(1339-1341)tcA>tcG	p.S447S		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	447					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ATCCTGAGTCACCTGGAAAAT	0.438																																					p.S447S		Atlas-SNP	.											.	YEATS2	111	.	0			c.A1341G						.						101	95	97					3																	183472104		1909	4121	6030	SO:0001819	synonymous_variant	55689	exon11			TGAGTCACCTGGA	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.1341A>G	chr3.hg19:g.183472104A>G		76.0	0.0		81.0	4.0	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Silent	SNP	ENST00000305135.5	hg19	CCDS43175.1																																																																																			.	.		0.438	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023		G	183472104	A	G	183472104	2	3	111	1	0	0	0	0	0	0	0	1	17487	146	6	2		2	YEATS2	3	183472104	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	18565005	183472104	14550326	75	16315										
TBCCD1	55171	hgsc.bcm.edu	37	chr3	186282013	186282013	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gatttgcacataggtggataTcttcctgagatagtgaagac	11	6	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr3:186282013T>C	ENST00000424280.1	-	2	585	c.106A>G	c.(106-108)Ata>Gta	p.I36V	TBCCD1_ENST00000338733.5_Missense_Mutation_p.I36V|TBCCD1_ENST00000446782.1_Intron	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	36					cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		TAGGTGGATATCTTCCTGAGA	0.532																																					p.I36V		Atlas-SNP	.											.	TBCCD1	42	.	0			c.A106G						.						76	72	73					3																	186282013		2203	4300	6503	SO:0001583	missense	55171	exon2			TGGATATCTTCCT	BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.106A>G	chr3.hg19:g.186282013T>C	ENSP00000411253:p.Ile36Val	92.0	0.0		78.0	4.0	NM_001134415	B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	hg19	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.612740	0.28712	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000413695;ENST00000430560	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	5.82	2.12	0.27331	.	0.077706	0.85682	N	0.000000	T	0.50463	0.1617	N	0.19112	0.55	0.30410	N	0.779198	B	0.09022	0.002	B	0.09377	0.004	T	0.43212	-0.9405	10	0.30854	T	0.27	-10.3422	8.1772	0.31289	0.0:0.2378:0.0:0.7622	.	36	Q9NVR7	TBCC1_HUMAN	V	36	ENSP00000411253:I36V;ENSP00000341652:I36V;ENSP00000391109:I36V;ENSP00000407506:I36V	ENSP00000341652:I36V	I	-	1	0	TBCCD1	187764707	1.000000	0.71417	0.969000	0.41365	0.975000	0.68041	3.067000	0.50010	0.441000	0.26529	0.459000	0.35465	ATA	.	.		0.532	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138		C	186282013	T	C	186282013	3	2	111	1	0	0	0	0	1	0	0	0	15647	1435	50	2	1591	2	TBCCD1	3	186282013	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2809909	186282013	11740417	76	16316										
GAK	2580	hgsc.bcm.edu	37	chr4	864601	864601	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccatggtggggcttcccggcTcggcctgtccctgggctcca	14	16	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:864601T>C	ENST00000314167.4	-	19	2256	c.2146A>G	c.(2146-2148)Agc>Ggc	p.S716G	GAK_ENST00000511163.1_Missense_Mutation_p.S637G|GAK_ENST00000509566.1_5'UTR	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	716					cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		GCTTCCCGGCTCGGCCTGTCC	0.542																																					p.S716G		Atlas-SNP	.											.	GAK	104	.	0			c.A2146G						.						70	73	72					4																	864601		2203	4300	6503	SO:0001583	missense	2580	exon19			CCCGGCTCGGCCT	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"Heat shock proteins / DNAJ (HSP40)"	4113	protein-coding gene	gene with protein product	"auxilin-2"	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.2146A>G	chr4.hg19:g.864601T>C	ENSP00000314499:p.Ser716Gly	112.0	0.0		92.0	4.0	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	hg19	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	T	6.947	0.544531	0.13312	.	.	ENSG00000178950	ENST00000314167;ENST00000511163	T;T	0.79033	-0.77;-1.23	5.6	0.209	0.15226	.	0.082759	0.85682	N	0.000000	T	0.59115	0.2170	L	0.31294	0.92	0.39697	D	0.971135	B;B;B;B	0.11235	0.004;0.004;0.002;0.002	B;B;B;B	0.11329	0.005;0.006;0.003;0.003	T	0.34850	-0.9812	10	0.29301	T	0.29	-19.1389	4.4256	0.11501	0.1353:0.2377:0.0:0.627	.	637;637;716;612	Q5U4P5;E9PGR2;O14976;Q59HA5	.;.;GAK_HUMAN;.	G	716;637	ENSP00000314499:S716G;ENSP00000421361:S637G	ENSP00000314499:S716G	S	-	1	0	GAK	854601	0.976000	0.34144	0.111000	0.21465	0.011000	0.07611	2.048000	0.41278	-0.166000	0.10890	0.523000	0.50628	AGC	.	.		0.542	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255		C	864601	T	C	864601	3	2	111	1	0	0	0	0	1	0	0	0	6203	1551	54	2	1829	2	GAK	4	864601	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		864601	190289675	77	16317										
WHSC1	7468	hgsc.bcm.edu	37	chr4	1932357	1932357	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tctcccgttcccacaggtggTagctgagcacccagatgctt	10	14	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:1932357T>C	ENST00000382895.3	+	8	1846	c.1415T>C	c.(1414-1416)gTa>gCa	p.V472A	WHSC1_ENST00000420906.2_Missense_Mutation_p.V472A|WHSC1_ENST00000508803.1_Missense_Mutation_p.V472A|WHSC1_ENST00000382892.2_Missense_Mutation_p.V472A|WHSC1_ENST00000382891.5_Missense_Mutation_p.V472A|WHSC1_ENST00000398261.1_Missense_Mutation_p.V472A|WHSC1_ENST00000503128.1_Missense_Mutation_p.V472A|WHSC1_ENST00000514045.1_Missense_Mutation_p.V472A	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	472					anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		CCACAGGTGGTAGCTGAGCAC	0.483			T	IGH@	MM																																p.V472A		Atlas-SNP	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.T1415C						.						70	61	64					4																	1932357		2203	4300	6503	SO:0001583	missense	7468	exon6			AGGTGGTAGCTGA	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"Zinc fingers, PHD-type"	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.1415T>C	chr4.hg19:g.1932357T>C	ENSP00000372351:p.Val472Ala	112.0	0.0		91.0	4.0	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	hg19	CCDS33940.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.706955	0.48412	.	.	ENSG00000109685	ENST00000508803;ENST00000514045;ENST00000382891;ENST00000382892;ENST00000420906;ENST00000382895;ENST00000503128;ENST00000398261	D;D;D;D;D;D;D;D	0.97888	-4.59;-4.59;-4.59;-4.59;-4.59;-4.59;-4.59;-4.59	5.76	5.76	0.90799	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.249544	0.27991	N	0.017031	D	0.93413	0.7899	N	0.21324	0.655	0.80722	D	1	B;B;B	0.32040	0.353;0.009;0.353	B;B;B	0.28385	0.089;0.021;0.089	D	0.92680	0.6157	10	0.07175	T	0.84	.	16.1249	0.81386	0.0:0.0:0.0:1.0	.	472;472;472	O96028-3;O96028;O96028-5	.;NSD2_HUMAN;.	A	472	ENSP00000423972:V472A;ENSP00000421681:V472A;ENSP00000372347:V472A;ENSP00000372348:V472A;ENSP00000399251:V472A;ENSP00000372351:V472A;ENSP00000425761:V472A;ENSP00000381311:V472A	ENSP00000308780:V472A	V	+	2	0	WHSC1	1902155	0.994000	0.37717	0.005000	0.12908	0.222000	0.24845	5.440000	0.66563	2.213000	0.71641	0.397000	0.26171	GTA	.	.		0.483	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		C	1932357	T	C	1932357	3	2	111	1	0	0	0	0	1	0	0	0	17377	1638	57	2	1433	2	WHSC1	4	1932357	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1067756	1932357	189221919	78	16318										
WDR19	57728	hgsc.bcm.edu	37	chr4	39191330	39191330	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gatgtcctagcagtgattgcTgagaaatctagctgcattta	10	7	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:39191330T>C	ENST00000399820.3	+	4	373	c.219T>C	c.(217-219)gcT>gcC	p.A73A	WDR19_ENST00000288634.7_5'UTR|WDR19_ENST00000506503.1_Silent_p.A73A	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	73					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						CAGTGATTGCTGAGAAATCTA	0.348																																					p.A73A		Atlas-SNP	.											.	WDR19	96	.	0			c.T219C						.						109	107	108					4																	39191330		1850	4114	5964	SO:0001819	synonymous_variant	57728	exon4			GATTGCTGAGAAA	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"WD repeat domain containing", "Intraflagellar transport homologs"	18340	protein-coding gene	gene with protein product	"intraflagellar transport 144 homolog (Chlamydomonas)"	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.219T>C	chr4.hg19:g.39191330T>C		152.0	0.0		103.0	5.0	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.		0.348	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			C	39191330	T	C	39191330	2	2	111	1	0	0	0	0	0	0	0	1	17294	1567	55	2		2	WDR19	4	39191330	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	37258973	39191330	151962946	79	16319										
GNPDA2	132789	hgsc.bcm.edu	37	chr4	44705132	44705132	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcatactgaatagtggatccAcaagtttattgtgcacatgc	8	8	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:44705132A>G	ENST00000295448.3	-	7	953	c.797T>C	c.(796-798)gTg>gCg	p.V266A	GNPDA2_ENST00000507534.1_Missense_Mutation_p.V196A|GNPDA2_ENST00000507917.1_Missense_Mutation_p.V232A|RP11-700J17.2_ENST00000610267.1_RNA	NM_138335.2	NP_612208.1	Q8TDQ7	GNPI2_HUMAN	glucosamine-6-phosphate deaminase 2	266					carbohydrate metabolic process (GO:0005975)|N-acetylglucosamine metabolic process (GO:0006044)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	glucosamine-6-phosphate deaminase activity (GO:0004342)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(1)|lung(7)|ovary(1)	11						TAGTGGATCCACAAGTTTATT	0.318																																					p.V266A	Colon(54;743 1010 7604 16453 19544)	Atlas-SNP	.											.	GNPDA2	28	.	0			c.T797C						.						113	110	111					4																	44705132		2202	4299	6501	SO:0001583	missense	132789	exon7			GGATCCACAAGTT	AF247786	CCDS3469.1, CCDS59472.1, CCDS59473.1	4p13	2006-04-12			ENSG00000163281	ENSG00000163281	3.5.99.6		21526	protein-coding gene	gene with protein product	"glucosamine-6-phosphate isomerase"	613222				12965206	Standard	NM_001270880		Approved	SB52	uc003gwy.4	Q8TDQ7	OTTHUMG00000099415	ENST00000295448.3:c.797T>C	chr4.hg19:g.44705132A>G	ENSP00000295448:p.Val266Ala	74.0	0.0		61.0	4.0	NM_138335	B4DJF3|Q2VYF1|Q59EA7|Q8NCZ8|Q96BJ4|Q96NC6	Missense_Mutation	SNP	ENST00000295448.3	hg19	CCDS3469.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.020068	0.54576	.	.	ENSG00000163281	ENST00000507917;ENST00000295448;ENST00000507534	T;T;T	0.46819	0.86;0.86;0.86	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.36468	0.0968	N	0.25647	0.755	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.19148	0.005;0.024	T	0.15607	-1.0431	10	0.41790	T	0.15	-12.5196	13.9246	0.63955	1.0:0.0:0.0:0.0	.	232;266	Q2VYF1;Q8TDQ7	.;GNPI2_HUMAN	A	232;266;196	ENSP00000425868:V232A;ENSP00000295448:V266A;ENSP00000427423:V196A	ENSP00000295448:V266A	V	-	2	0	GNPDA2	44399889	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.135000	0.89608	2.125000	0.65367	0.482000	0.46254	GTG	.	.		0.318	GNPDA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216874.3	NM_138335		G	44705132	A	G	44705132	3	3	111	1	0	0	0	0	1	0	0	0	6551	159	6	2	37	2	GNPDA2	4	44705132	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	5513802	44705132	146449144	80	16320										
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54325504	54325504	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccatgaaagtgaagaaggagAtagtcacaggagacacaaac	11	7	1	5			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:54325504A>G	ENST00000337488.6	+	18	1867	c.1673A>G	c.(1672-1674)gAt>gGt	p.D558G	FIP1L1_ENST00000358575.5_Missense_Mutation_p.D552G|FIP1L1_ENST00000306932.6_Missense_Mutation_p.D484G|LNX1_ENST00000306888.2_3'UTR|FIP1L1_ENST00000507166.1_Intron	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	558	Arg-rich.|Glu-rich.|Sufficient for interaction with CPSF1 and CSTF3.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			GAAGAAGGAGATAGTCACAGG	0.393			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.D558G		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.A1673G						.						47	44	45					4																	54325504		2203	4300	6503	SO:0001583	missense	81608	exon18			AAGGAGATAGTCA	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.1673A>G	chr4.hg19:g.54325504A>G	ENSP00000336752:p.Asp558Gly	85.0	0.0		83.0	4.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Missense_Mutation	SNP	ENST00000337488.6	hg19	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443265	0.83993	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000306932;ENST00000504094	D;T;T	0.93712	-3.27;-0.13;1.96	5.41	5.41	0.78517	.	0.065900	0.64402	D	0.000009	D	0.95284	0.8470	L	0.50333	1.59	0.80722	D	1	B;D;B;B	0.63880	0.229;0.993;0.229;0.088	B;D;B;B	0.68192	0.081;0.956;0.081;0.055	D	0.95820	0.8849	10	0.87932	D	0	-23.9542	15.7383	0.77863	1.0:0.0:0.0:0.0	.	552;552;484;558	G3XAD6;B4DIR3;Q6UN15-3;Q6UN15	.;.;.;FIP1_HUMAN	G	558;552;484;218	ENSP00000336752:D558G;ENSP00000351383:D552G;ENSP00000302993:D484G	ENSP00000302993:D484G	D	+	2	0	FIP1L1	54020261	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.113000	0.89568	2.174000	0.68829	0.528000	0.53228	GAT	.	.		0.393	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		G	54325504	A	G	54325504	3	3	111	1	0	0	0	0	1	0	0	0	5904	333	12	2	1774	2	FIP1L1	4	54325504	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	9620372	54325504	136828772	81	16321										
CEP135	9662	hgsc.bcm.edu	37	chr4	56847463	56847463	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	accccataatattgttagtcTtatggaaaaggaaaaagaac	7	6	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:56847463T>C	ENST00000257287.4	+	13	1821	c.1697T>C	c.(1696-1698)cTt>cCt	p.L566P		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	566					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					ATTGTTAGTCTTATGGAAAAG	0.333																																					p.L566P		Atlas-SNP	.											.	CEP135	115	.	0			c.T1697C						.						102	106	105					4																	56847463		2203	4299	6502	SO:0001583	missense	9662	exon13			TTAGTCTTATGGA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.1697T>C	chr4.hg19:g.56847463T>C	ENSP00000257287:p.Leu566Pro	110.0	0.0		92.0	4.0	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	hg19	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.332580	0.41297	.	.	ENSG00000174799	ENST00000257287	T	0.44482	0.92	4.79	2.09	0.27110	.	0.712882	0.13627	N	0.374029	T	0.32615	0.0835	L	0.36672	1.1	0.39041	D	0.960133	P	0.48016	0.904	P	0.44811	0.461	T	0.14062	-1.0486	10	0.41790	T	0.15	.	5.4824	0.16731	0.1623:0.0:0.3594:0.4783	.	566	Q66GS9	CP135_HUMAN	P	566	ENSP00000257287:L566P	ENSP00000257287:L566P	L	+	2	0	CEP135	56542220	0.993000	0.37304	0.947000	0.38551	0.946000	0.59487	1.784000	0.38674	0.770000	0.33336	0.383000	0.25322	CTT	.	.		0.333	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		C	56847463	T	C	56847463	3	2	111	1	0	0	0	0	1	0	0	0	3249	1609	56	2	1743	2	CEP135	4	56847463	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2521959	56847463	134306813	82	16322										
GRSF1	2926	hgsc.bcm.edu	37	chr4	71691022	71691022	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcaggacttacgaacgtgggAccgatccttgagcatcgctg	13	11	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:71691022A>G	ENST00000254799.6	-	8	1501	c.1384T>C	c.(1384-1386)Tcc>Ccc	p.S462P	GRSF1_ENST00000439371.1_Missense_Mutation_p.S300P|GRSF1_ENST00000545193.1_Missense_Mutation_p.S344P|GRSF1_ENST00000508091.1_Intron|GRSF1_ENST00000502323.1_Missense_Mutation_p.S300P	NM_002092.3	NP_002083	Q12849	GRSF1_HUMAN	G-rich RNA sequence binding factor 1	462	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anterior/posterior pattern specification (GO:0009952)|morphogenesis of embryonic epithelium (GO:0016331)|mRNA polyadenylation (GO:0006378)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(2)	17		all_hematologic(202;0.21)	Lung(101;0.235)			CGAACGTGGGACCGATCCTTG	0.448																																					p.S462P		Atlas-SNP	.											.	GRSF1	35	.	0			c.T1384C						.						69	69	69					4																	71691022		2017	4196	6213	SO:0001583	missense	2926	exon8			CGTGGGACCGATC	BC040485	CCDS47069.1, CCDS47070.1	4q13	2013-07-16				ENSG00000132463		"RNA binding motif (RRM) containing"	4610	protein-coding gene	gene with protein product		604851				8036161	Standard	NM_001098477		Approved		uc010iia.1	Q12849		ENST00000254799.6:c.1384T>C	chr4.hg19:g.71691022A>G	ENSP00000254799:p.Ser462Pro	154.0	0.0		81.0	5.0	NM_002092	B3KPW0|Q4W5S5|Q6ZST3|Q8IWD6|Q8NBD2	Missense_Mutation	SNP	ENST00000254799.6	hg19	CCDS47069.1	.	.	.	.	.	.	.	.	.	.	A	13.51	2.260216	0.39995	.	.	ENSG00000132463	ENST00000254799;ENST00000439371;ENST00000540657;ENST00000499044;ENST00000502323;ENST00000545193	T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18	5.97	4.79	0.61399	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.660495	0.16615	N	0.206721	T	0.12646	0.0307	M	0.64404	1.975	0.27494	N	0.952197	B;B	0.30793	0.295;0.153	B;B	0.37267	0.245;0.162	T	0.13415	-1.0510	10	0.56958	D	0.05	-2.8195	7.8339	0.29360	0.68:0.2525:0.0675:0.0	.	375;462	B7Z5F9;Q12849	.;GRSF1_HUMAN	P	462;300;394;435;300;344	ENSP00000254799:S462P;ENSP00000389219:S300P;ENSP00000427354:S435P;ENSP00000425430:S300P;ENSP00000443380:S344P	ENSP00000254799:S462P	S	-	1	0	GRSF1	71909886	1.000000	0.71417	1.000000	0.80357	0.562000	0.35680	1.412000	0.34714	1.076000	0.40961	0.533000	0.62120	TCC	.	.		0.448	GRSF1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362642.1	NM_002092		G	71691022	A	G	71691022	3	3	111	1	0	0	0	0	1	0	0	0	6818	275	10	2	66	2	GRSF1	4	71691022	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	14843559	71691022	119463254	83	16323										
ALB	213	hgsc.bcm.edu	37	chr4	74283258	74283259	+	Frame_Shift_Del	DEL	CG	CG	-													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tttttttcaggctattagttCgttacaccaagaaagtaccc					rs78575701		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:74283258_74283259delCG	ENST00000503124.1	+	9	1057_1058	c.850_851delCG	c.(850-852)cgtfs	p.R284fs	ALB_ENST00000295897.4_Frame_Shift_Del_p.R434fs|ALB_ENST00000415165.2_Frame_Shift_Del_p.R242fs|ALB_ENST00000505649.1_Intron|ALB_ENST00000509063.1_Frame_Shift_Del_p.R434fs|ALB_ENST00000401494.3_Frame_Shift_Del_p.R319fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GCTATTAGTTCGTTACACCAAG	0.401																																					p.433_434del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.1299_1300del	GRCh37	CM984718	ALB	M	rs78575701	.																																			SO:0001589	frameshift_variant	213	exon11			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.850_851delCG	chr4.hg19:g.74283258_74283259delCG	ENSP00000421027:p.Arg284fs	105.0	0.0		97.0	15.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.401	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74283259	CG	-	74283258	7	5	111	1	0	1	0	1	0	0	0	0	486	884	31	0	1342	0	ALB	4	74283258	Frame_Shift_Del	DEL	CG	TCGA-DD-A39X-01A-11D-A20W-10	2592236	74283258	116871018	84	16324										
PPEF2	5470	hgsc.bcm.edu	37	chr4	76793207	76793207	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atggtgagtgtgtgggtcacCttgttagcttgatactgcac	13	7	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:76793207C>T	ENST00000286719.7	-	13	1976	c.1620G>A	c.(1618-1620)aaG>aaA	p.K540K		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	540	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TGTGGGTCACCTTGTTAGCTT	0.433																																					p.K540K	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.G1620A						.						137	124	128					4																	76793207		2203	4300	6503	SO:0001819	synonymous_variant	5470	exon13			GGTCACCTTGTTA	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9244	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, beta isozyme"	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.1620G>A	chr4.hg19:g.76793207C>T		126.0	0.0		99.0	4.0	NM_006239	O14831	Silent	SNP	ENST00000286719.7	hg19	CCDS34013.1																																																																																			.	.		0.433	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		T	76793207	C	T	76793207	2	4	111	1	0	0	0	0	0	0	0	1	12317	680	24	3		3	PPEF2	4	76793207	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	2509949	76793207	114361069	85	16325										
PPEF2	5470	hgsc.bcm.edu	37	chr4	76797570	76797570	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gctgccggcaccgctctagcTccagttccacggagctccgc	11	18	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:76797570T>C	ENST00000286719.7	-	11	1546	c.1190A>G	c.(1189-1191)gAg>gGg	p.E397G		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	397	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			CCGCTCTAGCTCCAGTTCCAC	0.657																																					p.E397G	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.A1190G						.						27	30	29					4																	76797570		2203	4300	6503	SO:0001583	missense	5470	exon11			TCTAGCTCCAGTT	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9244	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, beta isozyme"	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.1190A>G	chr4.hg19:g.76797570T>C	ENSP00000286719:p.Glu397Gly	74.0	0.0		90.0	4.0	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	hg19	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	T	15.80	2.940316	0.52972	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.43294	0.95	5.09	2.47	0.30058	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);Metallophosphoesterase domain (1);	2.254190	0.02416	N	0.082082	T	0.45074	0.1324	M	0.68317	2.08	0.31947	N	0.610223	P;P	0.38078	0.617;0.474	B;B	0.37833	0.173;0.259	T	0.45818	-0.9235	10	0.54805	T	0.06	-8.7218	6.0339	0.19694	0.0:0.0896:0.1641:0.7463	.	397;397	O14830-2;O14830	.;PPE2_HUMAN	G	397	ENSP00000286719:E397G	ENSP00000286719:E397G	E	-	2	0	PPEF2	77016594	1.000000	0.71417	0.998000	0.56505	0.618000	0.37518	3.036000	0.49767	0.795000	0.33922	0.402000	0.26972	GAG	.	.		0.657	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		C	76797570	T	C	76797570	3	2	111	1	0	0	0	0	1	0	0	0	12317	1551	54	2	1099	2	PPEF2	4	76797570	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	4363	76797570	114356706	86	16326										
NAAA	27163	hgsc.bcm.edu	37	chr4	76861242	76861242	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gccgcggatctcgccggtgaAgggctggggcaggaagcgct	19	11	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:76861242A>G	ENST00000286733.4	-	2	384	c.283T>C	c.(283-285)Ttc>Ctc	p.F95L	NAAA_ENST00000399497.3_Missense_Mutation_p.F95L|NAAA_ENST00000507956.1_Missense_Mutation_p.F95L|NAAA_ENST00000505594.1_5'UTR|NAAA_ENST00000507187.2_Missense_Mutation_p.F95L	NM_014435.3	NP_055250.2	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase	95					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	11						TCGCCGGTGAAGGGCTGGGGC	0.597																																					p.F95L		Atlas-SNP	.											.	NAAA	26	.	0			c.T283C						.						52	60	57					4																	76861242		2035	4186	6221	SO:0001583	missense	27163	exon2			CGGTGAAGGGCTG	M92449	CCDS43239.1	4q21.1	2011-09-23	2008-04-24	2008-04-24	ENSG00000138744	ENSG00000138744	3.5.1.-		736	protein-coding gene	gene with protein product		607469	"N-acylsphingosine amidohydrolase (acid ceramidase)-like"	ASAHL		10610717, 1446826	Standard	NM_001042402		Approved		uc003hjb.3	Q02083	OTTHUMG00000160855	ENST00000286733.4:c.283T>C	chr4.hg19:g.76861242A>G	ENSP00000286733:p.Phe95Leu	132.0	0.0		105.0	5.0	NM_014435	Q5KTF2|Q96EY2|Q9BRA8	Missense_Mutation	SNP	ENST00000286733.4	hg19	CCDS43239.1	.	.	.	.	.	.	.	.	.	.	A	18.07	3.541104	0.65085	.	.	ENSG00000138744	ENST00000399497;ENST00000286733;ENST00000507956;ENST00000399490;ENST00000507187	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.1	3.91	0.45181	.	0.131674	0.53938	D	0.000047	T	0.42899	0.1223	M	0.70275	2.135	0.22803	N	0.998714	P;B	0.46952	0.887;0.376	B;B	0.40825	0.341;0.114	T	0.34204	-0.9838	10	0.27785	T	0.31	-6.1781	7.5806	0.27963	0.9044:0.0:0.0956:0.0	.	95;95	D6R9S9;Q02083	.;NAAA_HUMAN	L	95	ENSP00000382420:F95L;ENSP00000286733:F95L;ENSP00000427641:F95L;ENSP00000423142:F95L	ENSP00000286733:F95L	F	-	1	0	NAAA	77080266	1.000000	0.71417	0.199000	0.23439	0.990000	0.78478	4.680000	0.61656	0.960000	0.38005	0.477000	0.44152	TTC	.	.		0.597	NAAA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362843.4			G	76861242	A	G	76861242	3	3	111	1	0	0	0	0	1	0	0	0	10136	72	3	2	839	2	NAAA	4	76861242	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	63672	76861242	114293034	87	16327										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79353651	79353651	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tggaggtgagagtagaggtgTccctgtcagaagaccgaggg	18	6	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:79353651T>C	ENST00000325942.6	+	38	5550	c.5110T>C	c.(5110-5112)Tcc>Ccc	p.S1704P	FRAS1_ENST00000264895.6_Missense_Mutation_p.S1704P	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1704					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AGTAGAGGTGTCCCTGTCAGA	0.522																																					p.S1704P		Atlas-SNP	.											.	FRAS1	779	.	0			c.T5110C						.						66	72	70					4																	79353651		2036	4177	6213	SO:0001583	missense	80144	exon38			GAGGTGTCCCTGT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.5110T>C	chr4.hg19:g.79353651T>C	ENSP00000326330:p.Ser1704Pro	145.0	0.0		118.0	5.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.43|13.43	2.235200|2.235200	0.39498|0.39498	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000545316|ENST00000510944	T;T|T	0.52983|0.35605	0.64;0.64|1.3	5.96|5.96	4.75|4.75	0.60458|0.60458	.|.	0.354493|.	0.28555|.	N|.	0.014937|.	T|T	0.41236|0.41236	0.1150|0.1150	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	P;D|.	0.55800|.	0.954;0.973|.	P;P|.	0.50754|.	0.556;0.649|.	T|T	0.26883|0.26883	-1.0090|-1.0090	10|7	0.32370|0.62326	T|D	0.25|0.03	.|.	10.851|10.851	0.46769|0.46769	0.2514:0.0:0.0:0.7486|0.2514:0.0:0.0:0.7486	.|.	1704;1704|.	E9PHH6;A2RRR8|.	.;.|.	P|A	1704;1704;124|153	ENSP00000326330:S1704P;ENSP00000264895:S1704P|ENSP00000422221:V153A	ENSP00000264895:S1704P|ENSP00000422221:V153A	S|V	+|+	1|2	0|0	FRAS1|FRAS1	79572675|79572675	0.995000|0.995000	0.38212|0.38212	0.968000|0.968000	0.41197|0.41197	0.012000|0.012000	0.07955|0.07955	0.916000|0.916000	0.28651|0.28651	1.027000|1.027000	0.39758|0.39758	0.533000|0.533000	0.62120|0.62120	TCC|GTC	.	.		0.522	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			C	79353651	T	C	79353651	3	2	111	1	0	0	0	0	1	0	0	0	6050	1667	58	2	5260	2	FRAS1	4	79353651	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2492409	79353651	111800625	88	16328										
MEPE	56955	hgsc.bcm.edu	37	chr4	88767270	88767270	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgtagatcattctaataggaAccaagcaaccttaaatgaaa	6	7	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:88767270A>G	ENST00000424957.3	+	4	1323	c.1250A>G	c.(1249-1251)aAc>aGc	p.N417S	MEPE_ENST00000361056.3_Missense_Mutation_p.N417S|MEPE_ENST00000560249.1_Missense_Mutation_p.N304S|MEPE_ENST00000497649.2_Missense_Mutation_p.N393S|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000395102.4_Missense_Mutation_p.N448S|MEPE_ENST00000540395.1_Missense_Mutation_p.N304S	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	417					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		TCTAATAGGAACCAAGCAACC	0.393																																					p.N417S		Atlas-SNP	.											.	MEPE	86	.	0			c.A1250G						.						84	80	81					4																	88767270		2203	4300	6503	SO:0001583	missense	56955	exon4			ATAGGAACCAAGC	AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.1250A>G	chr4.hg19:g.88767270A>G	ENSP00000416984:p.Asn417Ser	113.0	0.0		94.0	4.0	NM_020203	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	hg19	CCDS3625.1	.	.	.	.	.	.	.	.	.	.	A	10.29	1.310199	0.23821	.	.	ENSG00000152595	ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.54071	4.34;0.61;0.59;0.62;4.34	5.08	2.71	0.32032	.	0.496943	0.18671	N	0.134457	T	0.38612	0.1047	L	0.44542	1.39	0.09310	N	1	B	0.34255	0.445	B	0.31614	0.133	T	0.18935	-1.0321	10	0.38643	T	0.18	-8.3568	6.1238	0.20167	0.8024:0.0:0.1976:0.0	.	417	Q9NQ76	MEPE_HUMAN	S	417;448;393;304;417	ENSP00000416984:N417S;ENSP00000378534:N448S;ENSP00000422747:N393S;ENSP00000443491:N304S;ENSP00000354341:N417S	ENSP00000354341:N417S	N	+	2	0	MEPE	88986294	0.001000	0.12720	0.001000	0.08648	0.063000	0.16089	0.592000	0.23984	0.439000	0.26476	0.460000	0.39030	AAC	.	.		0.393	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1			G	88767270	A	G	88767270	3	3	111	1	0	0	0	0	1	0	0	0	9487	43	2	2	1260	2	MEPE	4	88767270	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	9413619	88767270	102387006	89	16329										
METAP1	23173	hgsc.bcm.edu	37	chr4	99960538	99960538	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	attccaggaatgtctgaatcTgaacaggctcttaaaggtac	9	8	3	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:99960538T>C	ENST00000296411.6	+	5	488	c.354T>C	c.(352-354)tcT>tcC	p.S118S	METAP1_ENST00000544031.1_Silent_p.S68S	NM_015143.2	NP_055958.2	P53582	MAP11_HUMAN	methionyl aminopeptidase 1	118					N-terminal protein amino acid modification (GO:0031365)|peptidyl-methionine modification (GO:0018206)|phototransduction, visible light (GO:0007603)|platelet aggregation (GO:0070527)|protein initiator methionine removal (GO:0070084)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of translation (GO:0006417)|rhodopsin mediated signaling pathway (GO:0016056)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic ribosome (GO:0022626)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metalloaminopeptidase activity (GO:0070006)|metalloexopeptidase activity (GO:0008235)			endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(123;3.12e-07)		TGTCTGAATCTGAACAGGCTC	0.333																																					p.S118S		Atlas-SNP	.											.	METAP1	40	.	0			c.T354C						.						121	114	116					4																	99960538		1811	4074	5885	SO:0001819	synonymous_variant	23173	exon5			TGAATCTGAACAG	D42084	CCDS47110.1	4q23	2010-08-20			ENSG00000164024	ENSG00000164024	3.4.11.18		15789	protein-coding gene	gene with protein product	"Peptidase M"	610151				7788527, 12144506	Standard	NM_015143		Approved	KIAA0094, MetAP1A, MAP1A	uc003huf.4	P53582	OTTHUMG00000161231	ENST00000296411.6:c.354T>C	chr4.hg19:g.99960538T>C		72.0	0.0		75.0	4.0	NM_015143	B4E2E6	Silent	SNP	ENST00000296411.6	hg19	CCDS47110.1																																																																																			.	.		0.333	METAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364237.1	NM_015143		C	99960538	T	C	99960538	2	2	111	1	0	0	0	0	0	0	0	1	9495	1567	55	2		2	METAP1	4	99960538	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	11193268	99960538	91193738	90	16330										
NDST4	64579	hgsc.bcm.edu	37	chr4	115856381	115856381	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctgggtttagaaggattgtgAgaaaaagttcacctcctctg	11	7	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:115856381A>G	ENST00000264363.2	-	6	2195	c.1517T>C	c.(1516-1518)cTc>cCc	p.L506P		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	506	Heparan sulfate N-deacetylase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		AAGGATTGTGAGAAAAAGTTC	0.348																																					p.L506P		Atlas-SNP	.											.	NDST4	193	.	0			c.T1517C						.						192	194	194					4																	115856381		2203	4300	6503	SO:0001583	missense	64579	exon6			ATTGTGAGAAAAA	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.1517T>C	chr4.hg19:g.115856381A>G	ENSP00000264363:p.Leu506Pro	140.0	0.0		82.0	4.0	NM_022569	Q2KHM8	Missense_Mutation	SNP	ENST00000264363.2	hg19	CCDS3706.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.858431	0.51376	.	.	ENSG00000138653	ENST00000264363	T	0.38401	1.14	5.12	5.12	0.69794	.	0.059132	0.64402	D	0.000001	T	0.48960	0.1529	M	0.75447	2.3	0.80722	D	1	P	0.40250	0.709	P	0.46510	0.519	T	0.52071	-0.8624	10	0.49607	T	0.09	.	14.9199	0.70829	1.0:0.0:0.0:0.0	.	506	Q9H3R1	NDST4_HUMAN	P	506	ENSP00000264363:L506P	ENSP00000264363:L506P	L	-	2	0	NDST4	116075830	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.248000	0.95456	1.912000	0.55364	0.482000	0.46254	CTC	.	.		0.348	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		G	115856381	A	G	115856381	3	3	111	1	0	0	0	0	1	0	0	0	10267	304	11	2	1137	2	NDST4	4	115856381	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	15895843	115856381	75297895	91	16331										
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119948231	119948231	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agaccctaacttgtcacatgAcaggattgtccacataaatt	6	10	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:119948231A>G	ENST00000429713.2	+	3	889	c.707A>G	c.(706-708)gAc>gGc	p.D236G	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.D236G|SYNPO2_ENST00000434046.2_Missense_Mutation_p.D236G	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	236						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TTGTCACATGACAGGATTGTC	0.488																																					p.D236G		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A707G						.						46	51	49					4																	119948231		2203	4300	6503	SO:0001583	missense	171024	exon3			CACATGACAGGAT	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.707A>G	chr4.hg19:g.119948231A>G	ENSP00000395143:p.Asp236Gly	81.0	0.0		84.0	4.0	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.575|0.575	-0.839559|-0.839559	0.02692|0.02692	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.08370|.	3.1;3.11;3.1|.	5.21|5.21	-0.747|-0.747	0.11091|0.11091	.|.	0.719811|.	0.12666|.	N|.	0.449207|.	T|.	0.29158|.	0.0725|.	L|L	0.31294|0.31294	0.92|0.92	0.09310|0.09310	N|N	0.999992|0.999992	B;B;B;B|.	0.11235|.	0.002;0.004;0.001;0.001|.	B;B;B;B|.	0.06405|.	0.001;0.002;0.002;0.002|.	T|.	0.30090|.	-0.9990|.	10|.	0.20519|.	T|.	0.43|.	-2.9747|-2.9747	6.1596|6.1596	0.20356|0.20356	0.5402:0.1319:0.3279:0.0|0.5402:0.1319:0.3279:0.0	.|.	236;236;236;236|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	G|W	236|187	ENSP00000306015:D236G;ENSP00000395143:D236G;ENSP00000390965:D236G|.	ENSP00000306015:D236G|.	D|X	+|+	2|3	0|0	SYNPO2|SYNPO2	120167679|120167679	0.005000|0.005000	0.15991|0.15991	0.000000|0.000000	0.03702|0.03702	0.007000|0.007000	0.05969|0.05969	0.752000|0.752000	0.26362|0.26362	0.033000|0.033000	0.15463|0.15463	0.455000|0.455000	0.32223|0.32223	GAC|TGA	.	.		0.488	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			G	119948231	A	G	119948231	3	3	111	1	0	0	0	0	1	0	0	0	15472	275	10	2	717	2	SYNPO2	4	119948231	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	4091850	119948231	71206045	92	16332										
FAT4	79633	hgsc.bcm.edu	37	chr4	126238284	126238284	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	accttcaggtaaacgtgactGtgcaagacattaatgacaac	8	9	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:126238284G>T	ENST00000394329.3	+	1	731	c.718G>T	c.(718-720)Gtg>Ttg	p.V240L		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	240	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AAACGTGACTGTGCAAGACAT	0.607											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V240L		Atlas-SNP	.											.	FAT4	1752	.	0			c.G718T						.						29	33	32					4																	126238284		2030	4181	6211	SO:0001583	missense	79633	exon1			GTGACTGTGCAAG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.718G>T	chr4.hg19:g.126238284G>T	ENSP00000377862:p.Val240Leu	138.0	0.0	1548	98.0	8.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	10.07	1.250437	0.22880	.	.	ENSG00000196159	ENST00000394329	T	0.63913	-0.07	5.13	5.13	0.70059	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.31233	U	0.008019	T	0.64853	0.2636	M	0.73319	2.225	0.80722	D	1	B	0.29212	0.237	B	0.35278	0.199	T	0.66221	-0.5978	10	0.49607	T	0.09	.	13.8954	0.63768	0.0754:0.0:0.9246:0.0	.	240	Q6V0I7	FAT4_HUMAN	L	240	ENSP00000377862:V240L	ENSP00000377862:V240L	V	+	1	0	FAT4	126457734	1.000000	0.71417	0.997000	0.53966	0.018000	0.09664	5.185000	0.65076	2.364000	0.80123	0.655000	0.94253	GTG	.	.		0.607	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126238284	G	T	126238284	3	4	111	1	0	0	0	0	1	0	0	0	5700	1377	48	3	720	3	FAT4	4	126238284	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	6290053	126238284	64915992	93	16333										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148778702	148778702	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atagttttttttttatttgtAggaagaaaaaaagaagtttg	8	0	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:148778702A>G	ENST00000336498.3	+	5	623		c.e5-1			NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10						establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		TTTTATTTGTAGGAAGAAAAA	0.254																																					.		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.385-2A>G						.						16	17	16					4																	148778702		2074	4159	6233	SO:0001630	splice_region_variant	79658	exon5			ATTTGTAGGAAGA	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.385-1A>G	chr4.hg19:g.148778702A>G		43.0	0.0		38.0	17.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Splice_Site	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	A	18.42	3.619763	0.66787	.	.	ENSG00000071205	ENST00000336498	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8857	0.70567	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGAP10	148998152	1.000000	0.71417	0.949000	0.38748	0.745000	0.42441	8.319000	0.89992	2.206000	0.71126	0.528000	0.53228	.	.	.		0.254	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605	Intron	G	148778702	A	G	148778702	5	3	111	1	0	0	0	0	0	0	1	0	862	434	15	2	401	2	ARHGAP10	4	148778702	Splice_Site	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	22540418	148778702	42375574	94	16334										
LRBA	987	hgsc.bcm.edu	37	chr4	151727552	151727552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agcgtgttcaagcctctctgTaatactaaggaaaagacatt	8	8	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:151727552T>C	ENST00000357115.3	-	33	5632	c.5389A>G	c.(5389-5391)Aca>Gca	p.T1797A	LRBA_ENST00000535741.1_Missense_Mutation_p.T1797A|LRBA_ENST00000507224.1_Missense_Mutation_p.T1797A|LRBA_ENST00000510413.1_Missense_Mutation_p.T1797A	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1797						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AGCCTCTCTGTAATACTAAGG	0.338																																					p.T1797A		Atlas-SNP	.											.	LRBA	253	.	0			c.A5389G						.						39	41	40					4																	151727552		2203	4300	6503	SO:0001583	missense	987	exon33			TCTCTGTAATACT	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.5389A>G	chr4.hg19:g.151727552T>C	ENSP00000349629:p.Thr1797Ala	97.0	0.0		70.0	4.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	T	19.95	3.922047	0.73213	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.59638	0.68;0.83;0.69;0.25	5.55	5.55	0.83447	.	0.253838	0.40728	N	0.001023	T	0.62122	0.2402	M	0.81802	2.56	0.80722	D	1	B;P	0.34615	0.451;0.459	B;B	0.33960	0.137;0.173	T	0.67461	-0.5665	10	0.66056	D	0.02	.	15.692	0.77461	0.0:0.0:0.0:1.0	.	1797;1797	P50851;P50851-2	LRBA_HUMAN;.	A	1797	ENSP00000446299:T1797A;ENSP00000421552:T1797A;ENSP00000349629:T1797A;ENSP00000422180:T1797A	ENSP00000349629:T1797A	T	-	1	0	LRBA	151947002	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	4.856000	0.62932	2.104000	0.64026	0.533000	0.62120	ACA	.	.		0.338	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			C	151727552	T	C	151727552	3	2	111	1	0	0	0	0	1	0	0	0	8940	1638	57	2	3306	2	LRBA	4	151727552	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2948850	151727552	39426724	95	16335										
PDGFC	56034	hgsc.bcm.edu	37	chr4	157693868	157693868	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcttccaaaaacaaaagcctTgccaagaagttgccaagttg	7	10	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:157693868T>C	ENST00000502773.1	-	4	1163	c.673A>G	c.(673-675)Aag>Gag	p.K225E	PDGFC_ENST00000542208.1_Missense_Mutation_p.K70E|PDGFC_ENST00000504672.1_5'UTR|PDGFC_ENST00000541126.1_Missense_Mutation_p.K62E|PDGFC_ENST00000422544.2_Missense_Mutation_p.K225E	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	225		Cleavage.			activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		ACAAAAGCCTTGCCAAGAAGT	0.393																																					p.K225E		Atlas-SNP	.											.	PDGFC	46	.	0			c.A673G						.						54	54	54					4																	157693868		2203	4300	6503	SO:0001583	missense	56034	exon4			AAGCCTTGCCAAG	AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.673A>G	chr4.hg19:g.157693868T>C	ENSP00000422464:p.Lys225Glu	95.0	0.0		68.0	4.0	NM_016205	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Missense_Mutation	SNP	ENST00000502773.1	hg19	CCDS3795.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.959656	0.92791	.	.	ENSG00000145431	ENST00000502773;ENST00000541126;ENST00000542208;ENST00000422544	T;T;T;T	0.44881	2.42;0.91;0.91;2.27	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.64864	0.2637	M	0.75447	2.3	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.75020	0.98;0.985	T	0.69022	-0.5255	10	0.72032	D	0.01	-34.1448	15.7997	0.78443	0.0:0.0:0.0:1.0	.	70;225	B4E3A5;Q9NRA1	.;PDGFC_HUMAN	E	225;62;70;225	ENSP00000422464:K225E;ENSP00000442943:K62E;ENSP00000439728:K70E;ENSP00000410048:K225E	ENSP00000410048:K225E	K	-	1	0	PDGFC	157913318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.189000	0.69895	0.460000	0.39030	AAG	.	.		0.393	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1			C	157693868	T	C	157693868	3	2	111	1	0	0	0	0	1	0	0	0	11668	1821	63	2	376	2	PDGFC	4	157693868	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	5966316	157693868	33460408	96	16336										
GALNTL6	442117	hgsc.bcm.edu	37	chr4	173930373	173930373	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgtgtggacagcaagcatggAgccaccggaacagagctgag	15	9	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:173930373A>G	ENST00000506823.1	+	11	2073	c.1416A>G	c.(1414-1416)ggA>ggG	p.G472G	GALNTL6_ENST00000508122.1_Silent_p.G455G	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	472	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						GCAAGCATGGAGCCACCGGAA	0.493																																					p.G472G		Atlas-SNP	.											.	GALNTL6	102	.	0			c.A1416G						.						93	93	93					4																	173930373		2203	4300	6503	SO:0001819	synonymous_variant	442117	exon11			GCATGGAGCCACC		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.1416A>G	chr4.hg19:g.173930373A>G		136.0	0.0		92.0	5.0	NM_001034845	Q2L4S6	Silent	SNP	ENST00000506823.1	hg19	CCDS34104.1																																																																																			.	.		0.493	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		G	173930373	A	G	173930373	2	3	111	1	0	0	0	0	0	0	0	1	6233	291	11	2		2	GALNTL6	4	173930373	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	16236505	173930373	17223903	97	16337										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183575041	183575041	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgtgtcattaccttctggagAcaatggtaagcgaaagaatt	10	6	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:183575041A>G	ENST00000511685.1	+	6	1229	c.1106A>G	c.(1105-1107)gAc>gGc	p.D369G	TENM3_ENST00000406950.2_Missense_Mutation_p.D369G			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	369					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CCTTCTGGAGACAATGGTAAG	0.368																																					p.D369G		Atlas-SNP	.											.	.	.	.	0			c.A1106G						.						110	105	106					4																	183575041		1903	4129	6032	SO:0001583	missense	55714	exon5			CTGGAGACAATGG	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.1106A>G	chr4.hg19:g.183575041A>G	ENSP00000424226:p.Asp369Gly	115.0	0.0		92.0	4.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	A	10.78	1.447647	0.26074	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86164	-2.08;-2.08	5.95	5.95	0.96441	.	.	.	.	.	T	0.76463	0.3991	N	0.00729	-1.24	0.47153	D	0.999339	P	0.49447	0.924	P	0.59424	0.857	T	0.77373	-0.2612	9	0.02654	T	1	.	16.4323	0.83853	1.0:0.0:0.0:0.0	.	369	Q9P273	TEN3_HUMAN	G	369	ENSP00000424226:D369G;ENSP00000385276:D369G	ENSP00000385276:D369G	D	+	2	0	ODZ3	183812035	1.000000	0.71417	0.999000	0.59377	0.866000	0.49608	6.778000	0.75043	2.281000	0.76405	0.528000	0.53228	GAC	.	.		0.368	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			G	183575041	A	G	183575041	3	3	111	1	0	0	0	0	1	0	0	0	10845	275	10	2	1124	2	ODZ3	4	183575041	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	9644668	183575041	7579235	98	16338										
C4orf41	60684	hgsc.bcm.edu	37	chr4	184589187	184589187	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	attgcttcagaaagggctgcAgctttatgcaatgcatgtga	11	7	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr4:184589187A>G	ENST00000334690.6	+	5	679	c.477A>G	c.(475-477)gcA>gcG	p.A159A	TRAPPC11_ENST00000357207.4_Silent_p.A159A|TRAPPC11_ENST00000511409.1_3'UTR	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	159					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											AAAGGGCTGCAGCTTTATGCA	0.378																																					p.A159A		Atlas-SNP	.											.	.	.	.	0			c.A477G						.						144	144	144					4																	184589187		2203	4300	6503	SO:0001819	synonymous_variant	60684	exon5			GGCTGCAGCTTTA		CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"Trafficking protein particle complex"	25751	protein-coding gene	gene with protein product	"gryzun homolog (Drosophila)", "foie gras homolog (zebrafish)"	614138	"chromosome 4 open reading frame 41"	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.477A>G	chr4.hg19:g.184589187A>G		76.0	0.0		60.0	4.0	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Silent	SNP	ENST00000334690.6	hg19	CCDS34112.1																																																																																			.	.		0.378	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942		G	184589187	A	G	184589187	2	3	111	1	0	0	0	0	0	0	0	1	2272	175	7	2		2	C4orf41	4	184589187	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1014146	184589187	6565089	99	16339										
TERT	7015	hgsc.bcm.edu	37	chr5	1293886	1293886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acctgcggggagtccctggcAtccagggcctggaacccaga	14	14	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:1293886A>G	ENST00000310581.5	-	2	1172	c.1115T>C	c.(1114-1116)aTg>aCg	p.M372T	TERT_ENST00000522877.1_5'Flank|TERT_ENST00000334602.6_Missense_Mutation_p.M372T|TERT_ENST00000508104.2_Missense_Mutation_p.M372T|TERT_ENST00000296820.5_Missense_Mutation_p.M372T	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	372	RNA-interacting domain 2.|Required for oligomerization.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	AGTCCCTGGCATCCAGGGCCT	0.667									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.M372T		Atlas-SNP	.											.	TERT	2594	.	0			c.T1115C						.						16	18	17					5																	1293886		2132	4211	6343	SO:0001583	missense	7015	exon2	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	CCTGGCATCCAGG	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.1115T>C	chr5.hg19:g.1293886A>G	ENSP00000309572:p.Met372Thr	91.0	0.0		82.0	4.0	NM_001193376	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	hg19	CCDS3861.2	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.358819	0.00214	.	.	ENSG00000164362	ENST00000310581;ENST00000296820;ENST00000334602;ENST00000508104	D;D;D;D	0.96168	-3.93;-3.9;-3.83;-3.9	3.99	-7.98	0.01135	.	2.236320	0.02476	N	0.088030	T	0.81503	0.4836	N	0.01168	-0.975	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.79969	-0.1579	10	0.13853	T	0.58	-21.0764	4.858	0.13570	0.086:0.2156:0.4544:0.244	.	372;372;372	O14746-3;O14746;Q8NG38	.;TERT_HUMAN;.	T	372	ENSP00000309572:M372T;ENSP00000296820:M372T;ENSP00000334346:M372T;ENSP00000426042:M372T	ENSP00000296820:M372T	M	-	2	0	TERT	1346886	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.669000	0.00845	-2.827000	0.00341	-0.738000	0.03535	ATG	.	.		0.667	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			G	1293886	A	G	1293886	3	3	111	1	0	0	0	0	1	0	0	0	15779	217	8	2	2343	2	TERT	5	1293886	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10		1293886	179621374	100	16340										
LPCAT1	79888	hgsc.bcm.edu	37	chr5	1467007	1467007	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctcttgcgctccgtacatcTgcaaggcaaactgggtgtca	10	13	3	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:1467007T>C	ENST00000283415.3	-	13	1411		c.e13-2		LPCAT1_ENST00000503252.1_Splice_Site	NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1						cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		TCCGTACATCTGCAAGGCAAA	0.667																																					.		Atlas-SNP	.											.	LPCAT1	70	.	0			c.1279-2A>G						.						105	86	92					5																	1467007		2203	4300	6503	SO:0001630	splice_region_variant	79888	exon14			TACATCTGCAAGG	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"EF-hand domain containing"	25718	protein-coding gene	gene with protein product		610472	"acyltransferase like 2"	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.1279-2A>G	chr5.hg19:g.1467007T>C		107.0	0.0		98.0	4.0	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Splice_Site	SNP	ENST00000283415.3	hg19	CCDS3864.1	.	.	.	.	.	.	.	.	.	.	T	10.65	1.408484	0.25378	.	.	ENSG00000153395	ENST00000283415	.	.	.	4.47	4.47	0.54385	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.0333	0.53410	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LPCAT1	1520007	1.000000	0.71417	0.960000	0.40013	0.110000	0.19582	6.282000	0.72639	1.793000	0.52555	0.459000	0.35465	.	.	.		0.667	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830	Intron	C	1467007	T	C	1467007	5	2	111	1	0	0	0	0	0	0	1	0	8919	1594	55	2	335	2	LPCAT1	5	1467007	Splice_Site	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	173121	1467007	179448253	101	16341										
ITGA2	3673	hgsc.bcm.edu	37	chr5	52371092	52371092	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggctgataatttggtcaaccTcaaaattcctctcctgtatg	7	10	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:52371092T>C	ENST00000296585.5	+	23	2926	c.2783T>C	c.(2782-2784)cTc>cCc	p.L928P		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	928					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				TTGGTCAACCTCAAAATTCCT	0.368																																					p.L928P		Atlas-SNP	.											.	ITGA2	211	.	0			c.T2783C						.						68	69	69					5																	52371092		2203	4300	6503	SO:0001583	missense	3673	exon23			TCAACCTCAAAAT		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2783T>C	chr5.hg19:g.52371092T>C	ENSP00000296585:p.Leu928Pro	89.0	0.0		99.0	4.0	NM_002203	Q14595	Missense_Mutation	SNP	ENST00000296585.5	hg19	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	T	18.60	3.658821	0.67586	.	.	ENSG00000164171	ENST00000296585	T	0.56611	0.45	6.16	5.01	0.66863	Integrin alpha-2 (1);	0.421494	0.25830	N	0.028022	T	0.55433	0.1920	N	0.19112	0.55	0.26756	N	0.970107	D;D	0.59767	0.977;0.986	D;P	0.64410	0.925;0.857	T	0.53070	-0.8490	10	0.72032	D	0.01	.	12.0881	0.53708	0.0:0.0662:0.0:0.9338	.	928;928	E7ESP4;P17301	.;ITA2_HUMAN	P	928	ENSP00000296585:L928P	ENSP00000296585:L928P	L	+	2	0	ITGA2	52406849	0.993000	0.37304	0.012000	0.15200	0.934000	0.57294	7.043000	0.76572	1.162000	0.42619	0.528000	0.53228	CTC	.	.		0.368	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		C	52371092	T	C	52371092	3	2	111	1	0	0	0	0	1	0	0	0	7884	1551	54	2	2873	2	ITGA2	5	52371092	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	50904085	52371092	128544168	102	16342										
DHX29	54505	hgsc.bcm.edu	37	chr5	54570765	54570765	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcatgtatagaatagcatgcTgagtgcggctgctgtacttt	11	7	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:54570765T>C	ENST00000251636.5	-	15	2649	c.2501A>G	c.(2500-2502)cAg>cGg	p.Q834R	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	834						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				AATAGCATGCTGAGTGCGGCT	0.388																																					p.Q834R		Atlas-SNP	.											.	DHX29	116	.	0			c.A2501G						.						104	108	107					5																	54570765		2203	4300	6503	SO:0001583	missense	54505	exon15			GCATGCTGAGTGC	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"DEAH-boxes"	15815	protein-coding gene	gene with protein product		612720	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.2501A>G	chr5.hg19:g.54570765T>C	ENSP00000251636:p.Gln834Arg	109.0	0.0		79.0	16.0	NM_019030	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Missense_Mutation	SNP	ENST00000251636.5	hg19	CCDS34158.1	.	.	.	.	.	.	.	.	.	.	T	10.75	1.437022	0.25900	.	.	ENSG00000067248	ENST00000251636	T	0.13420	2.59	5.1	5.1	0.69264	.	0.059769	0.64402	D	0.000002	T	0.04407	0.0121	N	0.02802	-0.49	0.43390	D	0.995508	B	0.02656	0.0	B	0.04013	0.001	T	0.26916	-1.0089	10	0.02654	T	1	.	7.8895	0.29669	0.0:0.1558:0.0:0.8442	.	834	Q7Z478	DHX29_HUMAN	R	834	ENSP00000251636:Q834R	ENSP00000251636:Q834R	Q	-	2	0	DHX29	54606522	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.460000	0.60108	2.054000	0.61138	0.460000	0.39030	CAG	.	.		0.388	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030		C	54570765	T	C	54570765	3	2	111	1	0	0	0	0	1	0	0	0	4505	1580	55	2	1660	2	DHX29	5	54570765	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2199673	54570765	126344495	103	16343										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54603859	54603859	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaaatggcggacgcattcggAgatgagctgttcagcgtgtt	14	7	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:54603859A>G	ENST00000230640.5	+	1	272	c.18A>G	c.(16-18)ggA>ggG	p.G6G	SKIV2L2_ENST00000545714.1_5'UTR|SKIV2L2_ENST00000504388.1_3'UTR|DHX29_ENST00000251636.5_5'Flank	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	6					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.G6G(1)		NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				ACGCATTCGGAGATGAGCTGT	0.572																																					p.G6G	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											SKIV2L2,NS,carcinoma,0,1	SKIV2L2	104	.	1	Substitution - coding silent(1)	endometrium(1)	c.A18G						.						100	91	94					5																	54603859		2203	4300	6503	SO:0001819	synonymous_variant	23517	exon1			ATTCGGAGATGAG	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.18A>G	chr5.hg19:g.54603859A>G		132.0	1.0		120.0	7.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	hg19	CCDS3967.1																																																																																			.	.		0.572	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			G	54603859	A	G	54603859	2	3	111	1	0	0	0	0	0	0	0	1	14375	291	11	2		2	SKIV2L2	5	54603859	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	33094	54603859	126311401	104	16344										
PDE4D	5144	hgsc.bcm.edu	37	chr5	58270500	58270500	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tttttgcactgttacgtgtcAggagaacgatcatctatgac	9	8	3	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:58270500A>G	ENST00000340635.6	-	15	2596	c.2421T>C	c.(2419-2421)ccT>ccC	p.P807P	PDE4D_ENST00000546160.1_Silent_p.P746P|PDE4D_ENST00000317118.8_Silent_p.P516P|PDE4D_ENST00000405755.2_Silent_p.P685P|PDE4D_ENST00000507116.1_Silent_p.P743P|PDE4D_ENST00000502484.2_Silent_p.P746P|PDE4D_ENST00000358923.6_Silent_p.P505P|PDE4D_ENST00000503258.1_Silent_p.P677P|PDE4D_ENST00000360047.5_Silent_p.P671P	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	807					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	GTTACGTGTCAGGAGAACGAT	0.433																																					p.P807P		Atlas-SNP	.											.	PDE4D	345	.	0			c.T2421C						.						168	164	165					5																	58270500		1920	4142	6062	SO:0001819	synonymous_variant	5144	exon15			CGTGTCAGGAGAA		CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"Phosphodiesterases"	8783	protein-coding gene	gene with protein product	"phosphodiesterase E3 dunce homolog (Drosophila)"	600129	"phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.2421T>C	chr5.hg19:g.58270500A>G		122.0	0.0		131.0	6.0	NM_001104631	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Silent	SNP	ENST00000340635.6	hg19	CCDS47213.1																																																																																			.	.		0.433	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3			G	58270500	A	G	58270500	2	3	111	1	0	0	0	0	0	0	0	1	11651	175	7	2		2	PDE4D	5	58270500	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	3666641	58270500	122644760	105	16345										
CWC27	10283	hgsc.bcm.edu	37	chr5	64079686	64079686	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaatttcattcacggttgcgTtttaatcggagaggactggt	12	6	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:64079686T>C	ENST00000381070.3	+	4	493	c.276T>C	c.(274-276)cgT>cgC	p.R92R	CWC27_ENST00000508024.1_Silent_p.R92R	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	92	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						CACGGTTGCGTTTTAATCGGA	0.403																																					p.R92R		Atlas-SNP	.											.	CWC27	47	.	0			c.T276C						.						202	195	197					5																	64079686		2203	4300	6503	SO:0001819	synonymous_variant	10283	exon4			GTTGCGTTTTAAT	AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"serologically defined colon cancer antigen 10"	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.276T>C	chr5.hg19:g.64079686T>C		62.0	0.0		91.0	4.0	NM_005869	O60529|O60530|Q96EM3	Silent	SNP	ENST00000381070.3	hg19	CCDS3982.2																																																																																			.	.		0.403	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869		C	64079686	T	C	64079686	2	2	111	1	0	0	0	0	0	0	0	1	4072	1712	60	2		2	CWC27	5	64079686	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	5809186	64079686	116835574	106	16346										
MCCC2	64087	hgsc.bcm.edu	37	chr5	70942047	70942047	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tttgcttatagggtactcacTttgtccagttatgctgccaa	8	9	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:70942047T>C	ENST00000340941.6	+	13	1288	c.1159T>C	c.(1159-1161)Ttt>Ctt	p.F387L	MCCC2_ENST00000323375.8_Missense_Mutation_p.F349L	NM_022132.4	NP_071415.1	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-CoA carboxylase 2 (beta)	387	Carboxyltransferase.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|coenzyme A metabolic process (GO:0015936)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			endometrium(2)|kidney(15)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	30		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	GGGTACTCACTTTGTCCAGTT	0.338																																					p.F387L		Atlas-SNP	.											.	MCCC2	47	.	0			c.T1159C						.						116	118	118					5																	70942047		2203	4299	6502	SO:0001583	missense	64087	exon13			ACTCACTTTGTCC	AF310971	CCDS34184.1	5q12-q13	2010-04-30	2010-04-30		ENSG00000131844	ENSG00000131844	6.4.1.4		6937	protein-coding gene	gene with protein product		609014	"methylcrotonoyl-Coenzyme A carboxylase 2 (beta)"				Standard	NM_022132		Approved	MCCB	uc003kbs.4	Q9HCC0	OTTHUMG00000162505	ENST00000340941.6:c.1159T>C	chr5.hg19:g.70942047T>C	ENSP00000343657:p.Phe387Leu	94.0	0.0		91.0	4.0	NM_022132	A6NIY9|Q96C27|Q9Y4L7	Missense_Mutation	SNP	ENST00000340941.6	hg19	CCDS34184.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.151009	0.78001	.	.	ENSG00000131844	ENST00000340941;ENST00000323375;ENST00000509539	D;D;D	0.98178	-4.77;-4.77;-4.77	5.42	5.42	0.78866	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.045076	0.85682	D	0.000000	D	0.99363	0.9776	H	0.98525	4.255	0.80722	D	1	D	0.65815	0.995	D	0.69142	0.962	D	0.98391	1.0563	10	0.87932	D	0	-21.2728	14.4504	0.67382	0.0:0.0:0.0:1.0	.	387	Q9HCC0	MCCB_HUMAN	L	387;349;159	ENSP00000343657:F387L;ENSP00000327308:F349L;ENSP00000425474:F159L	ENSP00000327308:F349L	F	+	1	0	MCCC2	70977803	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	6.793000	0.75130	2.055000	0.61198	0.455000	0.32223	TTT	.	.		0.338	MCCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369243.4			C	70942047	T	C	70942047	3	2	111	1	0	0	0	0	1	0	0	0	9384	1609	56	2	1209	2	MCCC2	5	70942047	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	6862361	70942047	109973213	107	16347										
COL4A3BP	10087	hgsc.bcm.edu	37	chr5	74685511	74685511	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggttctgcaccatctcttcaAccttgagaagggaggaaaaa	10	9	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:74685511A>G	ENST00000405807.4	-	12	1611	c.1190T>C	c.(1189-1191)gTt>gCt	p.V397A	COL4A3BP_ENST00000261415.7_Splice_Site_p.V371A|COL4A3BP_ENST00000380494.5_Splice_Site_p.V525A	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	397	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)			breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		CATCTCTTCAACCTTGAGAAG	0.408																																					p.V525A		Atlas-SNP	.											.	COL4A3BP	72	.	0			c.T1574C						.						108	96	100					5																	74685511		2203	4300	6503	SO:0001630	splice_region_variant	10087	exon13			TCTTCAACCTTGA	AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"StAR-related lipid transfer (START) domain containing", "Pleckstrin homology (PH) domain containing"	2205	protein-coding gene	gene with protein product	"ceramide transporter", "StAR-related lipid transfer (START) domain containing 11"	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.1189-1T>C	chr5.hg19:g.74685511A>G		93.0	0.0		77.0	4.0	NM_001130105	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Missense_Mutation	SNP	ENST00000405807.4	hg19	CCDS4028.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.627862	0.87560	.	.	ENSG00000113163	ENST00000357457;ENST00000405807;ENST00000380494;ENST00000261415	D;D;D	0.83673	-1.75;-1.75;-1.75	5.14	5.14	0.70334	START-like domain (1);	0.000000	0.85682	D	0.000000	D	0.87164	0.6109	L	0.47716	1.5	0.58432	D	0.999994	D;D;D	0.64830	0.98;0.994;0.989	P;D;D	0.66084	0.874;0.941;0.921	D	0.86563	0.1842	10	0.39692	T	0.17	-3.1345	15.2562	0.73588	1.0:0.0:0.0:0.0	.	397;525;371	Q9Y5P4;Q9Y5P4-3;Q9Y5P4-2	C43BP_HUMAN;.;.	A	2;397;525;371	ENSP00000383996:V397A;ENSP00000369862:V525A;ENSP00000261415:V371A	ENSP00000261415:V371A	V	-	2	0	COL4A3BP	74721267	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.158000	0.94723	2.071000	0.62044	0.460000	0.39030	GTT	.	.		0.408	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713	Missense_Mutation	G	74685511	A	G	74685511	5	3	111	1	0	0	0	0	0	0	1	0	3694	57	2	2	708	2	COL4A3BP	5	74685511	Splice_Site	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	3743464	74685511	106229749	108	16348										
RASA1	5921	hgsc.bcm.edu	37	chr5	86659274	86659274	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaaccaaaaggattaatagaTctcagtgtatgttctgtcta	7	6	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:86659274T>C	ENST00000274376.6	+	11	2127	c.1563T>C	c.(1561-1563)gaT>gaC	p.D521D	RASA1_ENST00000506290.1_Silent_p.D355D|RASA1_ENST00000512763.1_Silent_p.D354D|RASA1_ENST00000456692.2_Silent_p.D344D	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	521	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		GATTAATAGATCTCAGTGTAT	0.328																																					p.D521D		Atlas-SNP	.											.	RASA1	213	.	0			c.T1563C						.						105	105	105					5																	86659274		2203	4300	6503	SO:0001819	synonymous_variant	5921	exon11			AATAGATCTCAGT		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.1563T>C	chr5.hg19:g.86659274T>C		83.0	0.0		69.0	4.0	NM_002890	B2R6W3|Q9UDI1	Silent	SNP	ENST00000274376.6	hg19	CCDS34200.1																																																																																			.	.		0.328	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		C	86659274	T	C	86659274	2	2	111	1	0	0	0	0	0	0	0	1	13075	1432	50	2		2	RASA1	5	86659274	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	11973763	86659274	94255986	109	16349										
CCNH	902	hgsc.bcm.edu	37	chr5	86703825	86703825	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaggaagccctcaaatggtcTgtaaggattgtggacaataa	12	6	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:86703825T>C	ENST00000256897.4	-	4	717	c.493A>G	c.(493-495)Aga>Gga	p.R165G	CCNH_ENST00000504878.1_Missense_Mutation_p.R91G|CCNH_ENST00000513499.1_Splice_Site|CCNH_ENST00000508855.1_Missense_Mutation_p.R91G	NM_001239.3	NP_001230.1	P51946	CCNH_HUMAN	cyclin H	165					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cyclin-dependent protein kinase activating kinase holoenzyme complex (GO:0019907)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|TFIIK complex (GO:0070985)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|kinase activity (GO:0016301)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(2)|ovary(2)	15		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;9.01e-39)|Epithelial(54;5.08e-33)|all cancers(79;4.28e-28)		TCAAATGGTCTGTAAGGATTG	0.358								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																													p.R165G		Atlas-SNP	.											.	CCNH	40	.	0			c.A493G						.						126	121	123					5																	86703825		2203	4300	6503	SO:0001583	missense	902	exon4			ATGGTCTGTAAGG	U12685	CCDS4064.1	5q13.3-q14	2014-03-28			ENSG00000134480	ENSG00000134480		"General transcription factor IIH complex subunits"	1594	protein-coding gene	gene with protein product	"CDK-activating kinase complex subunit", "cyclin-dependent kinase-activating kinase complex subunit", "MO15-associated protein", "CAK complex subunit"	601953				9465303	Standard	NM_001239		Approved	p34, p37, CycH	uc003kjb.3	P51946	OTTHUMG00000119077	ENST00000256897.4:c.493A>G	chr5.hg19:g.86703825T>C	ENSP00000256897:p.Arg165Gly	96.0	0.0		82.0	4.0	NM_001239	Q53X72|Q8TBL9	Missense_Mutation	SNP	ENST00000256897.4	hg19	CCDS4064.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.692857	0.48202	.	.	ENSG00000134480	ENST00000508855;ENST00000256897;ENST00000504878	T;T;T	0.64991	-0.13;-0.13;-0.13	5.29	4.07	0.47477	Cyclin-like (2);	0.000000	0.85682	D	0.000000	T	0.81494	0.4834	M	0.90369	3.11	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.77004	0.989;0.983	D	0.85764	0.1351	10	0.87932	D	0	-17.7492	13.4681	0.61268	0.0:0.0:0.1393:0.8607	.	165;112	P51946;E9PDB6	CCNH_HUMAN;.	G	91;165;91	ENSP00000426454:R91G;ENSP00000256897:R165G;ENSP00000426075:R91G	ENSP00000256897:R165G	R	-	1	2	CCNH	86739581	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	3.028000	0.49705	2.005000	0.58758	0.533000	0.62120	AGA	.	.		0.358	CCNH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239291.3	NM_001239		C	86703825	T	C	86703825	3	2	111	1	0	0	0	0	1	0	0	0	2927	1588	55	2	502	2	CCNH	5	86703825	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	44551	86703825	94211435	110	16350										
C5orf36	285600	hgsc.bcm.edu	37	chr5	93807341	93807341	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gccactttacaacaggcctcCaccaagtttgctctaatttc	5	14	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:93807341C>A	ENST00000513200.3	-	8	1623	c.1551G>T	c.(1549-1551)gtG>gtT	p.V517V	KIAA0825_ENST00000312498.7_Silent_p.V517V|KIAA0825_ENST00000427991.2_Silent_p.V517V	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	517										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						AACAGGCCTCCACCAAGTTTG	0.468																																					p.V517V		Atlas-SNP	.											.	KIAA0825	172	.	0			c.G1551T						.						149	123	131					5																	93807341		692	1591	2283	SO:0001819	synonymous_variant	285600	exon9			GGCCTCCACCAAG	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.1551G>T	chr5.hg19:g.93807341C>A		150.0	0.0		173.0	13.0	NM_001145678	O94914|Q6ZNN2	Silent	SNP	ENST00000513200.3	hg19																																																																																				.	.		0.468	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665		A	93807341	C	A	93807341	2	1	111	1	0	0	0	0	0	0	0	1	2297	581	21	3		3	C5orf36	5	93807341	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	7103516	93807341	87107919	111	16351										
ETF1	2107	hgsc.bcm.edu	37	chr5	137844500	137844500	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcgataagctcatgttcctgTccggtctacagggatgacca	10	11	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:137844500T>C	ENST00000360541.5	-	10	1310	c.1089A>G	c.(1087-1089)ggA>ggG	p.G363G	ETF1_ENST00000503014.1_Silent_p.G349G|ETF1_ENST00000499810.2_Silent_p.G330G	NM_004730.3	NP_004721.1	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	363					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)|translation termination factor activity (GO:0008079)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CATGTTCCTGTCCGGTCTACA	0.438																																					p.G363G		Atlas-SNP	.											.	ETF1	38	.	0			c.A1089G						.						87	86	87					5																	137844500		2203	4300	6503	SO:0001819	synonymous_variant	2107	exon10			TTCCTGTCCGGTC	AF095901	CCDS4207.1, CCDS75313.1, CCDS75314.1	5q31.2	2008-02-05			ENSG00000120705	ENSG00000120705			3477	protein-coding gene	gene with protein product	"sup45 (yeast omnipotent suppressor 45) homolog-like 1", "polypeptide chain release factor 1"	600285		SUP45L1, ERF1, ERF		1546371, 7990965	Standard	NM_004730		Approved	eRF1, TB3-1, RF1	uc003ldc.5	P62495	OTTHUMG00000129199	ENST00000360541.5:c.1089A>G	chr5.hg19:g.137844500T>C		85.0	0.0		69.0	4.0	NM_004730	B2R6B4|D3DQC1|P46055|Q5M7Z7|Q96CG1	Silent	SNP	ENST00000360541.5	hg19	CCDS4207.1																																																																																			.	.		0.438	ETF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251276.2	NM_004730		C	137844500	T	C	137844500	2	2	111	1	0	0	0	0	0	0	0	1	5270	1654	58	2		2	ETF1	5	137844500	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	44037159	137844500	43070760	112	16352										
DND1	373863	hgsc.bcm.edu	37	chr5	140052948	140052948	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctccagcgccgccttgttcTctggattcaccctctcacac	6	19	3	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:140052948T>C	ENST00000542735.1	-	2	93	c.50A>G	c.(49-51)gAg>gGg	p.E17G	HARS_ENST00000504156.1_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	17					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCCTTGTTCTCTGGATTCAC	0.637																																					p.E17G		Atlas-SNP	.											.	DND1	15	.	0			c.A50G						.						58	58	58					5																	140052948		2203	4300	6503	SO:0001583	missense	373863	exon2			TTGTTCTCTGGAT	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"RNA binding motif (RRM) containing"	23799	protein-coding gene	gene with protein product		609385	"dead end homolog 1 (zebrafish)"			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.50A>G	chr5.hg19:g.140052948T>C	ENSP00000445366:p.Glu17Gly	91.0	0.0		103.0	5.0	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	hg19	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307720	0.40795	.	.	ENSG00000256453	ENST00000542735	T	0.34275	1.37	4.58	3.34	0.38264	.	0.101126	0.39834	N	0.001254	T	0.21186	0.0510	L	0.33485	1.01	0.80722	D	1	P	0.37466	0.596	B	0.29353	0.101	T	0.04693	-1.0933	10	0.40728	T	0.16	-19.6412	7.7588	0.28940	0.1403:0.0:0.1292:0.7305	.	17	Q8IYX4	DND1_HUMAN	G	17	ENSP00000445366:E17G	ENSP00000445366:E17G	E	-	2	0	DND1	140033132	0.999000	0.42202	0.999000	0.59377	0.966000	0.64601	1.988000	0.40697	1.910000	0.55303	0.379000	0.24179	GAG	.	.		0.637	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249		C	140052948	T	C	140052948	3	2	111	1	0	0	0	0	1	0	0	0	4668	1551	54	2	1023	2	DND1	5	140052948	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2208448	140052948	40862312	113	16353										
PCDHA1	9752	hgsc.bcm.edu	37	chr5	140389506	140389506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaaagggaacagcacgactgAcaacagtgaccagtgaggtc	13	9	0	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:140389506A>G	ENST00000532602.1	+	4	3870	c.2837A>G	c.(2836-2838)gAc>gGc	p.D946G	PCDHA10_ENST00000506939.2_Missense_Mutation_p.D681G|PCDHA1_ENST00000394633.3_Missense_Mutation_p.D682G|PCDHA3_ENST00000522353.2_Missense_Mutation_p.D946G|PCDHA6_ENST00000529310.1_Missense_Mutation_p.D946G|PCDHA13_ENST00000289272.2_Missense_Mutation_p.D946G|PCDHAC1_ENST00000253807.2_Missense_Mutation_p.D959G|PCDHA4_ENST00000512229.2_Intron|PCDHA11_ENST00000398640.2_Missense_Mutation_p.D945G|PCDHA2_ENST00000526136.1_Missense_Mutation_p.D944G|PCDHA12_ENST00000398631.2_Missense_Mutation_p.D937G|PCDHA8_ENST00000531613.1_Missense_Mutation_p.D946G|PCDHAC2_ENST00000289269.5_Missense_Mutation_p.D1003G|PCDHA13_ENST00000409494.1_Intron|PCDHA1_ENST00000504120.2_Missense_Mutation_p.D946G|PCDHA4_ENST00000530339.1_Missense_Mutation_p.D943G|PCDHA5_ENST00000529859.1_Missense_Mutation_p.D932G|PCDHA7_ENST00000525929.1_Missense_Mutation_p.D933G|PCDHA6_ENST00000527624.1_Missense_Mutation_p.D682G|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Missense_Mutation_p.D944G	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	946					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCACGACTGACAACAGTGAC	0.423																																					p.D1003G	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.A3008G						.						106	115	112					5																	140389506		2203	4300	6503	SO:0001583	missense	56134	exon4			CGACTGACAACAG	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.2837A>G	chr5.hg19:g.140389506A>G	ENSP00000436042:p.Asp946Gly	73.0	0.0		91.0	4.0	NM_018899	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	hg19	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	A	18.00	3.524892	0.64747	.	.	ENSG00000204970;ENSG00000204970;ENSG00000204969;ENSG00000255408;ENSG00000204967;ENSG00000204965;ENSG00000081842;ENSG00000081842;ENSG00000204963;ENSG00000204962;ENSG00000204961;ENSG00000250120;ENSG00000250120;ENSG00000249158;ENSG00000251664;ENSG00000239389;ENSG00000248383;ENSG00000243232	ENST00000504120;ENST00000394633;ENST00000526136;ENST00000522353;ENST00000530339;ENST00000529859;ENST00000529310;ENST00000527624;ENST00000525929;ENST00000531613;ENST00000532602;ENST00000506939;ENST00000307360;ENST00000398640;ENST00000398631;ENST00000289272;ENST00000253807;ENST00000289269	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58060	0.57;0.39;0.6;0.61;0.6;0.59;0.61;0.36;0.54;0.66;0.64;0.36;0.53;0.59;0.62;0.71;0.44;0.64	5.87	5.87	0.94306	.	0.000000	0.35708	N	0.003030	T	0.63343	0.2503	L	0.29908	0.895	0.54753	D	0.999983	D;D;D;D;D;D;D;D;B;P;D;P;D;D;D;D;D;D	0.89917	0.993;1.0;0.989;0.999;0.999;1.0;1.0;1.0;0.19;0.502;0.998;0.708;0.999;0.999;1.0;1.0;1.0;1.0	P;D;P;D;D;D;D;D;B;B;D;B;D;D;D;D;D;D	0.91635	0.859;0.965;0.802;0.954;0.979;0.991;0.984;0.995;0.118;0.134;0.961;0.319;0.964;0.971;0.977;0.985;0.999;0.984	T	0.66763	-0.5841	10	0.87932	D	0	.	16.5764	0.84681	1.0:0.0:0.0:0.0	.	1003;959;946;937;945;944;681;946;946;933;946;682;932;943;946;944;946;682	Q9Y5I4;Q9H158;Q9Y5I0;Q9UN75;Q9Y5I1;Q9Y5I2;Q9Y5I2-2;Q9Y5H5;Q9Y5H6;Q9UN72;Q9UN73;Q9UN73-2;Q9Y5H7;Q9UN74;Q9Y5H8;Q9Y5H9;Q9Y5I3;Q9Y5I3-2	PCDC2_HUMAN;PCDC1_HUMAN;PCDAD_HUMAN;PCDAC_HUMAN;PCDAB_HUMAN;PCDAA_HUMAN;.;PCDA9_HUMAN;PCDA8_HUMAN;PCDA7_HUMAN;PCDA6_HUMAN;.;PCDA5_HUMAN;PCDA4_HUMAN;PCDA3_HUMAN;PCDA2_HUMAN;PCDA1_HUMAN;.	G	946;682;944;946;943;932;946;682;933;946;946;681;944;945;937;946;959;1003	ENSP00000420840:D946G;ENSP00000378129:D682G;ENSP00000431748:D944G;ENSP00000429808:D946G;ENSP00000435300:D943G;ENSP00000436557:D932G;ENSP00000433378:D946G;ENSP00000434113:D682G;ENSP00000436426:D933G;ENSP00000434655:D946G;ENSP00000436042:D946G;ENSP00000421030:D681G;ENSP00000304234:D944G;ENSP00000381636:D945G;ENSP00000381628:D937G;ENSP00000289272:D946G;ENSP00000253807:D959G;ENSP00000289269:D1003G	ENSP00000304234:D944G	D	+	2	0	PCDHA6;PCDHA7;PCDHA8;PCDHA9;PCDHA2;PCDHA3;PCDHA4;PCDHA5;PCDHA10;PCDHA11;PCDHA12;PCDHA1;PCDHA13;PCDHAC2;PCDHAC1	140369690	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.163000	0.89659	2.371000	0.80710	0.533000	0.62120	GAC	.	.		0.423	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		G	140389506	A	G	140389506	3	3	111	1	0	0	0	0	1	0	0	0	11528	275	10	2	2881	2	PCDHA1	5	140389506	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	336558	140389506	40525754	114	16354										
PCDHB15	56121	hgsc.bcm.edu	37	chr5	140626124	140626124	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaggcatctgatggcgggggActttctggaaaatgctctgt	15	7	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:140626124A>G	ENST00000231173.3	+	1	978	c.978A>G	c.(976-978)ggA>ggG	p.G326G		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	326	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATGGCGGGGGACTTTCTGGAA	0.408																																					p.G326G		Atlas-SNP	.											.	PCDHB15	138	.	0			c.A978G						.						139	142	141					5																	140626124		2203	4300	6503	SO:0001819	synonymous_variant	56121	exon1			CGGGGGACTTTCT	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.978A>G	chr5.hg19:g.140626124A>G		210.0	0.0		207.0	9.0	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	hg19	CCDS4257.1																																																																																			.	.		0.408	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		G	140626124	A	G	140626124	2	3	111	1	0	0	0	0	0	0	0	1	11549	262	10	2		2	PCDHB15	5	140626124	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	236618	140626124	40289136	115	16355										
PCDHGB3	56102	hgsc.bcm.edu	37	chr5	140750296	140750296	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atttgaaatggttgctgaaaAgcctttaaacttttttcatg	7	5	1	2	rs73265845	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:140750296A>G	ENST00000576222.1	+	1	466	c.335A>G	c.(334-336)aAg>aGg	p.K112R	PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	112	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTGCTGAAAAGCCTTTAAAC	0.438																																					p.K112R		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.A335G						.						131	134	133					5																	140750296		1880	4115	5995	SO:0001583	missense	56102	exon1			CTGAAAAGCCTTT	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.335A>G	chr5.hg19:g.140750296A>G	ENSP00000461862:p.Lys112Arg	66.0	0.0		68.0	4.0	NM_018924	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	A|0.993;T|0.007		0.438	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		G	140750296	A	G	140750296	3	3	111	1	0	0	0	0	1	0	0	0	11573	72	3	2	337	2	PCDHGB3	5	140750296	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	124172	140750296	40164964	116	16356										
PCDHGB3	56102	hgsc.bcm.edu	37	chr5	140750845	140750845	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gagacaactgttcaagctggAcagtaaaacgggggaactca	12	8	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:140750845A>G	ENST00000576222.1	+	1	1015	c.884A>G	c.(883-885)gAc>gGc	p.D295G	PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	295	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCAAGCTGGACAGTAAAACG	0.448																																					p.D295G		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.A884G						.						143	145	144					5																	140750845		2000	4177	6177	SO:0001583	missense	56102	exon1			AGCTGGACAGTAA	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.884A>G	chr5.hg19:g.140750845A>G	ENSP00000461862:p.Asp295Gly	85.0	0.0		98.0	32.0	NM_018924	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.		0.448	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		G	140750845	A	G	140750845	3	3	111	1	0	0	0	0	1	0	0	0	11573	275	10	2	886	2	PCDHGB3	5	140750845	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	549	140750845	40164415	117	16357										
WWC1	23286	hgsc.bcm.edu	37	chr5	167881041	167881041	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggaggaggtggaggaggaggAgggagaagaggatgttttca	22	1	1	2	rs140933524		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:167881041A>G	ENST00000265293.4	+	18	3096	c.2594A>G	c.(2593-2595)gAg>gGg	p.E865G	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Missense_Mutation_p.E865G	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	865	Glu-rich.|Interaction with histone H3.			Missing (in Ref. 6; AAO73817). {ECO:0000305}.	cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		gaggaggaggagggagaagag	0.547																																					p.E865G		Atlas-SNP	.											.	WWC1	98	.	0			c.A2594G						.						116	106	109					5																	167881041		2203	4300	6503	SO:0001583	missense	23286	exon18			AGGAGGAGGGAGA	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2594A>G	chr5.hg19:g.167881041A>G	ENSP00000265293:p.Glu865Gly	167.0	0.0		151.0	12.0	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	hg19	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	A	9.968	1.224627	0.22457	.	.	ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000524038	T;T;T	0.55413	0.52;0.52;0.52	4.64	3.47	0.39725	.	1.031930	0.07651	N	0.932040	T	0.31857	0.0810	N	0.08118	0	0.39367	D	0.966026	B;B	0.20988	0.05;0.03	B;B	0.21151	0.033;0.033	T	0.09335	-1.0679	10	0.24483	T	0.36	.	7.2113	0.25935	0.8962:0.0:0.1038:0.0	.	865;865	Q8IX03-2;Q8IX03	.;KIBRA_HUMAN	G	865;865;191	ENSP00000265293:E865G;ENSP00000427772:E865G;ENSP00000428084:E191G	ENSP00000265293:E865G	E	+	2	0	WWC1	167813619	0.711000	0.27906	0.201000	0.23476	0.005000	0.04900	0.857000	0.27831	0.748000	0.32831	-0.276000	0.10085	GAG	.	.		0.547	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		G	167881041	A	G	167881041	3	3	111	1	0	0	0	0	1	0	0	0	17426	304	11	2	2664	2	WWC1	5	167881041	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	27130196	167881041	13034219	118	16358										
STK10	6793	hgsc.bcm.edu	37	chr5	171509502	171509502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	attccgtgtcaaagaacttcTtcttggcctgaaaggagcag	10	9	3	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:171509502T>C	ENST00000176763.5	-	12	2160	c.1817A>G	c.(1816-1818)aAg>aGg	p.K606R	AC113342.1_ENST00000579783.1_RNA	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	606					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AAAGAACTTCTTCTTGGCCTG	0.522																																					p.K606R		Atlas-SNP	.											.	STK10	100	.	0			c.A1817G						.						69	67	68					5																	171509502		2203	4300	6503	SO:0001583	missense	6793	exon12			AACTTCTTCTTGG	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.1817A>G	chr5.hg19:g.171509502T>C	ENSP00000176763:p.Lys606Arg	88.0	0.0		100.0	4.0	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	hg19	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.433464	0.43224	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.30981	1.51	5.11	5.11	0.69529	.	0.058352	0.64402	D	0.000002	T	0.38321	0.1036	L	0.52206	1.635	0.41599	D	0.988849	P	0.38455	0.632	P	0.50825	0.651	T	0.24048	-1.0171	10	0.40728	T	0.16	.	7.6222	0.28191	0.0:0.0946:0.0:0.9054	.	606	O94804	STK10_HUMAN	R	606	ENSP00000176763:K606R	ENSP00000176763:K606R	K	-	2	0	STK10	171442107	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	5.118000	0.64673	1.932000	0.55993	0.533000	0.62120	AAG	.	.		0.522	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		C	171509502	T	C	171509502	3	2	111	1	0	0	0	0	1	0	0	0	15301	1609	56	2	1121	2	STK10	5	171509502	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	3628461	171509502	9405758	119	16359										
TRIM7	81786	hgsc.bcm.edu	37	chr5	180622632	180622632	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cgcccttaagatccagagagAggatgaggcgcgggttggcc	16	10	0	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr5:180622632A>G	ENST00000274773.7	-	7	1131	c.1070T>C	c.(1069-1071)cTc>cCc	p.L357P	CTC-338M12.6_ENST00000509080.1_RNA|CTC-338M12.5_ENST00000508877.1_RNA|CTC-338M12.6_ENST00000502812.2_RNA|TRIM7_ENST00000393319.3_Missense_Mutation_p.L175P|TRIM7_ENST00000393315.1_Missense_Mutation_p.L149P|TRIM7_ENST00000422067.2_Missense_Mutation_p.L149P|TRIM7_ENST00000361809.3_Missense_Mutation_p.L149P|CTC-338M12.6_ENST00000512508.1_RNA|TRIM7_ENST00000504241.1_5'UTR|CTC-338M12.5_ENST00000514487.1_RNA	NM_203293.1	NP_976038.1	Q9C029	TRIM7_HUMAN	tripartite motif containing 7	357	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|stomach(1)	17	all_cancers(89;6.03e-06)|all_epithelial(37;7.1e-07)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000172)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;2e-06)|Epithelial(171;1.35e-05)|OV - Ovarian serous cystadenocarcinoma(192;0.000128)|Kidney(146;0.0674)|GBM - Glioblastoma multiforme(465;0.0802)		ATCCAGAGAGAGGATGAGGCG	0.672																																					p.L357P	Esophageal Squamous(128;2258 2308 35507 48647)	Atlas-SNP	.											.	TRIM7	56	.	0			c.T1070C						.						46	52	50					5																	180622632		2179	4226	6405	SO:0001583	missense	81786	exon7			AGAGAGAGGATGA	AF220032	CCDS4462.1, CCDS4463.1, CCDS4464.1, CCDS43414.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146054	ENSG00000146054		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16278	protein-coding gene	gene with protein product	"glycogenin-interacting protein", "tripartite motif protein TRIM7"	609315	"tripartite motif-containing 7"			11331580	Standard	NM_203294		Approved	RNF90, GNIP	uc003mmz.1	Q9C029	OTTHUMG00000130963	ENST00000274773.7:c.1070T>C	chr5.hg19:g.180622632A>G	ENSP00000274773:p.Leu357Pro	114.0	0.0		121.0	5.0	NM_203293	A2RUE4|D3DWR7|Q969F5|Q96F67|Q96J89|Q96J90	Missense_Mutation	SNP	ENST00000274773.7	hg19	CCDS4462.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.028853	0.54790	.	.	ENSG00000146054	ENST00000274773;ENST00000393315;ENST00000361809;ENST00000393319;ENST00000422067	T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81	4.57	4.57	0.56435	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (2);B30.2/SPRY domain (1);	0.000000	0.44902	D	0.000414	T	0.62429	0.2427	H	0.95850	3.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.74160	-0.3755	10	0.87932	D	0	.	11.9119	0.52743	1.0:0.0:0.0:0.0	.	357;175	Q9C029;Q9C029-4	TRIM7_HUMAN;.	P	357;149;149;175;149	ENSP00000274773:L357P;ENSP00000376991:L149P;ENSP00000355059:L149P;ENSP00000376994:L175P;ENSP00000391458:L149P	ENSP00000274773:L357P	L	-	2	0	TRIM7	180555238	1.000000	0.71417	1.000000	0.80357	0.258000	0.26162	6.373000	0.73128	1.693000	0.51124	0.448000	0.29417	CTC	.	.		0.672	TRIM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253569.3	NM_203296		G	180622632	A	G	180622632	3	3	111	1	0	0	0	0	1	0	0	0	16558	304	11	2	469	2	TRIM7	5	180622632	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	9113130	180622632	292628	120	16360										
RIOK1	83732	hgsc.bcm.edu	37	chr6	7405539	7405539	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcgggagctctttgaatttgTcacagatccatccattacac	8	11	2	2	rs373917793		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:7405539T>C	ENST00000379834.2	+	12	1661	c.1154T>C	c.(1153-1155)gTc>gCc	p.V385A		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	385	Protein kinase.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					TTTGAATTTGTCACAGATCCA	0.418																																					p.V385A		Atlas-SNP	.											.	RIOK1	36	.	0			c.T1154C						.	T	ALA/VAL,ALA/VAL	0,4406		0,0,2203	97	82	87		1154,431	5.6	1	6		87	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RIOK1	NM_031480.2,NM_153005.1	64,64	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	385/569,144/328	7405539	1,13005	2203	4300	6503	SO:0001583	missense	83732	exon12			AATTTGTCACAGA	BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"RIO kinase 1 (yeast)"				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.1154T>C	chr6.hg19:g.7405539T>C	ENSP00000369162:p.Val385Ala	93.0	0.0		100.0	4.0	NM_031480	B2RB28|Q8NDC8|Q96NV9	Missense_Mutation	SNP	ENST00000379834.2	hg19	CCDS4500.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.182120	0.78677	0.0	1.16E-4	ENSG00000124784	ENST00000379834	T	0.08720	3.06	5.57	5.57	0.84162	RIO kinase (1);	0.155205	0.53938	D	0.000041	T	0.12008	0.0292	M	0.86420	2.815	0.51767	D	0.999936	B	0.27910	0.193	B	0.35899	0.213	T	0.00785	-1.1567	10	0.87932	D	0	-15.8581	14.9078	0.70733	0.0:0.0:0.0:1.0	.	385	Q9BRS2	RIOK1_HUMAN	A	385	ENSP00000369162:V385A	ENSP00000369162:V385A	V	+	2	0	RIOK1	7350538	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	7.369000	0.79578	2.114000	0.64651	0.455000	0.32223	GTC	.	.		0.418	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480		C	7405539	T	C	7405539	3	2	111	1	0	0	0	0	1	0	0	0	13392	1667	58	2	1200	2	RIOK1	6	7405539	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		7405539	163709528	121	16361										
ACOT13	55856	hgsc.bcm.edu	37	chr6	24698153	24698153	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctgggaaagtgatttgtgaaAtgaaagtagaagaagagcat	13	2	0	6			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:24698153A>G	ENST00000230048.4	+	2	317	c.124A>G	c.(124-126)Atg>Gtg	p.M42V	ACOT13_ENST00000537591.1_Missense_Mutation_p.M19V|ACOT13_ENST00000476436.1_3'UTR|RP1-30M3.5_ENST00000607014.1_RNA	NM_018473.3	NP_060943.1	Q9NPJ3	ACO13_HUMAN	acyl-CoA thioesterase 13	42					metabolic process (GO:0008152)|protein homotetramerization (GO:0051289)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA hydrolase activity (GO:0047617)			large_intestine(1)	1						GATTTGTGAAATGAAAGTAGA	0.388																																					p.M42V		Atlas-SNP	.											.	ACOT13	12	.	0			c.A124G						.						106	98	100					6																	24698153		2203	4300	6503	SO:0001583	missense	55856	exon2			TGTGAAATGAAAG	AF220186	CCDS4558.1, CCDS54972.1	6p22.1	2009-11-20	2009-05-05	2009-05-05	ENSG00000112304	ENSG00000112304		"Acyl CoA thioesterases"	20999	protein-coding gene	gene with protein product		615652	"thioesterase superfamily member 2"	THEM2		16934754, 19405909	Standard	NM_018473		Approved	HT012	uc003nek.3	Q9NPJ3	OTTHUMG00000014359	ENST00000230048.4:c.124A>G	chr6.hg19:g.24698153A>G	ENSP00000230048:p.Met42Val	103.0	0.0		90.0	34.0	NM_018473	F5H2L4|O95549	Missense_Mutation	SNP	ENST00000230048.4	hg19	CCDS4558.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.281601	0.40394	.	.	ENSG00000112304	ENST00000537591;ENST00000230048	.	.	.	5.03	1.13	0.20643	Phenylacetic acid degradation-related protein (1);	0.185780	0.56097	D	0.000027	T	0.28267	0.0698	M	0.62016	1.91	0.40470	D	0.980332	B;B	0.31241	0.315;0.15	B;B	0.28638	0.092;0.018	T	0.06023	-1.0850	9	0.35671	T	0.21	-19.9186	4.2242	0.10572	0.4079:0.4044:0.0701:0.1175	.	19;42	F5H2L4;Q9NPJ3	.;ACO13_HUMAN	V	19;42	.	ENSP00000230048:M42V	M	+	1	0	ACOT13	24806132	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	2.010000	0.40913	0.036000	0.15547	0.533000	0.62120	ATG	.	.		0.388	ACOT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040010.2	NM_018473		G	24698153	A	G	24698153	3	3	111	1	0	0	0	0	1	0	0	0	151	101	4	2	146	2	ACOT13	6	24698153	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	17292614	24698153	146416914	122	16362										
KIAA1949	170954	hgsc.bcm.edu	37	chr6	30653159	30653159	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cacctcttttctcctggggcTttgctctcgagactctgcta	8	14	4	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:30653159T>C	ENST00000274853.3	-	1	2513	c.637A>G	c.(637-639)Agc>Ggc	p.S213G	PPP1R18_ENST00000399199.3_Missense_Mutation_p.S213G|NRM_ENST00000470733.1_5'Flank|PPP1R18_ENST00000488324.1_Intron	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	213						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CTCCTGGGGCTTTGCTCTCGA	0.562																																					p.S213G		Atlas-SNP	.											.	.	.	.	0			c.A637G						.						249	266	260					6																	30653159		1193	2530	3723	SO:0001583	missense	170954	exon2			TGGGGCTTTGCTC	AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29413	protein-coding gene	gene with protein product	"protein phosphatase 1 F-actin cytoskeleton targeting subunit"	610990	"KIAA1949"	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.637A>G	chr6.hg19:g.30653159T>C	ENSP00000274853:p.Ser213Gly	114.0	0.0		115.0	5.0	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	hg19	CCDS43444.1	.	.	.	.	.	.	.	.	.	.	T	11.68	1.711881	0.30322	.	.	ENSG00000146112	ENST00000274853;ENST00000399199;ENST00000376424	T;T	0.27557	1.66;1.66	5.66	4.5	0.54988	.	0.171323	0.36134	N	0.002761	T	0.08626	0.0214	L	0.29908	0.895	0.09310	N	1	B	0.16166	0.016	B	0.15870	0.014	T	0.17899	-1.0354	10	0.54805	T	0.06	-11.7841	7.0933	0.25295	0.0:0.0782:0.1483:0.7734	.	213	Q6NYC8	PPR18_HUMAN	G	213	ENSP00000274853:S213G;ENSP00000382150:S213G	ENSP00000274853:S213G	S	-	1	0	KIAA1949	30761138	0.948000	0.32251	0.905000	0.35620	0.497000	0.33675	2.788000	0.47806	0.979000	0.38497	0.533000	0.62120	AGC	.	.		0.562	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471		C	30653159	T	C	30653159	3	2	111	1	0	0	0	0	1	0	0	0	8272	1609	56	2	1216	2	KIAA1949	6	30653159	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	5955006	30653159	140461908	123	16363										
EHMT2	10919	hgsc.bcm.edu	37	chr6	31847967	31847967	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	caatggcttcggctgagtgcTtgcacttctcagagccacat	10	12	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:31847967T>C	ENST00000375537.4	-	28	3533	c.3527A>G	c.(3526-3528)aAg>aGg	p.K1176R	SLC44A4_ENST00000465707.1_5'Flank|EHMT2_ENST00000395728.3_Missense_Mutation_p.K1233R|EHMT2_ENST00000375530.4_Missense_Mutation_p.K1142R|EHMT2_ENST00000480912.1_5'UTR|SLC44A4_ENST00000229729.6_5'Flank|SLC44A4_ENST00000544672.1_5'Flank|SLC44A4_ENST00000375562.4_5'Flank|EHMT2_ENST00000375528.4_Missense_Mutation_p.K1199R	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	1176	Post-SET.				DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						GGCTGAGTGCTTGCACTTCTC	0.587																																					p.K1176R		Atlas-SNP	.											.	EHMT2	45	.	0			c.A3527G						.						63	57	59					6																	31847967		1511	2708	4219	SO:0001583	missense	10919	exon28			GAGTGCTTGCACT	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.3527A>G	chr6.hg19:g.31847967T>C	ENSP00000364687:p.Lys1176Arg	107.0	0.0		119.0	5.0	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	hg19	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	T	13.69	2.313461	0.40996	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537;ENST00000442298	T;T;T;T	0.64260	-0.05;-0.09;-0.03;-0.05	4.75	4.75	0.60458	Post-SET domain (1);	0.000000	0.85682	D	0.000000	T	0.16342	0.0393	N	0.01751	-0.74	0.80722	D	1	B;B;B;B	0.23891	0.003;0.033;0.093;0.019	B;B;B;B	0.26969	0.009;0.042;0.075;0.023	T	0.21314	-1.0249	10	0.07813	T	0.8	.	13.5594	0.61779	0.0:0.0:0.0:1.0	.	1199;1142;1176;997	A2ABF8;Q96KQ7-2;Q96KQ7;Q59FM7	.;.;EHMT2_HUMAN;.	R	1233;1199;1142;1176;997	ENSP00000379078:K1233R;ENSP00000364678:K1199R;ENSP00000364680:K1142R;ENSP00000364687:K1176R	ENSP00000364678:K1199R	K	-	2	0	EHMT2	31955946	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.472000	0.80996	1.915000	0.55452	0.459000	0.35465	AAG	.	.		0.587	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		C	31847967	T	C	31847967	3	2	111	1	0	0	0	0	1	0	0	0	4986	1609	56	2	109	2	EHMT2	6	31847967	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1194808	31847967	139267100	124	16364										
SLC39A7	7922	hgsc.bcm.edu	37	chr6	33169120	33169120	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tggactcgggggtcatgacgAcctgcacgacgatctgcaag	14	11	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:33169120A>G	ENST00000374677.3	+	1	471	c.98A>G	c.(97-99)gAc>gGc	p.D33G	SLC39A7_ENST00000374675.3_Missense_Mutation_p.D33G|RXRB_ENST00000413614.2_5'Flank|RXRB_ENST00000374680.3_5'Flank|RNY4P10_ENST00000365571.1_RNA|RXRB_ENST00000374685.4_5'Flank|RXRB_ENST00000544186.1_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	33	His-rich.				transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						GGTCATGACGACCTGCACGAC	0.647																																					p.D33G		Atlas-SNP	.											.	SLC39A7	32	.	0			c.A98G						.						63	71	68					6																	33169120		2117	4237	6354	SO:0001583	missense	7922	exon1			ATGACGACCTGCA	AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"Solute carriers"	4927	protein-coding gene	gene with protein product		601416	"HLA class II region expressed gene KE4"	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.98A>G	chr6.hg19:g.33169120A>G	ENSP00000363809:p.Asp33Gly	113.0	0.0		132.0	6.0	NM_006979	B0UXF6|Q5STP8|Q9UIQ0	Missense_Mutation	SNP	ENST00000374677.3	hg19	CCDS43453.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.731053	0.48939	.	.	ENSG00000112473	ENST00000374675;ENST00000446283;ENST00000445037;ENST00000374677	T;T	0.59906	0.23;0.23	4.3	4.3	0.51218	.	0.795685	0.11695	N	0.538527	T	0.33089	0.0851	N	0.24115	0.695	0.32460	N	0.544196	P	0.51791	0.948	P	0.45610	0.487	T	0.21075	-1.0256	10	0.72032	D	0.01	-4.2727	9.828	0.40923	1.0:0.0:0.0:0.0	.	33	Q92504	S39A7_HUMAN	G	33	ENSP00000363807:D33G;ENSP00000363809:D33G	ENSP00000363807:D33G	D	+	2	0	SLC39A7	33277098	1.000000	0.71417	0.998000	0.56505	0.781000	0.44180	2.838000	0.48199	1.828000	0.53243	0.241000	0.17934	GAC	.	.		0.647	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979		G	33169120	A	G	33169120	3	3	111	1	0	0	0	0	1	0	0	0	14638	275	10	2	100	2	SLC39A7	6	33169120	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1321153	33169120	137945947	125	16365										
CUL9	23113	hgsc.bcm.edu	37	chr6	43153709	43153709	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acagatcccaggaaagctgcTtttctccttggtgaagcgct	10	11	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:43153709T>C	ENST00000252050.4	+	4	851	c.767T>C	c.(766-768)cTt>cCt	p.L256P	CUL9_ENST00000372647.2_Missense_Mutation_p.L256P|CUL9_ENST00000354495.3_Missense_Mutation_p.L256P	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	256					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GGAAAGCTGCTTTTCTCCTTG	0.527																																					p.L256P		Atlas-SNP	.											.	CUL9	248	.	0			c.T767C						.						60	58	59					6																	43153709		2203	4300	6503	SO:0001583	missense	23113	exon4			AGCTGCTTTTCTC	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.767T>C	chr6.hg19:g.43153709T>C	ENSP00000252050:p.Leu256Pro	96.0	0.0		111.0	6.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	T	12.47	1.946699	0.34377	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.44482	0.92;0.92;0.92	4.59	4.59	0.56863	.	0.149506	0.46442	D	0.000285	T	0.55242	0.1908	M	0.71036	2.16	0.47123	D	0.999327	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.942;0.942;0.999	T	0.62263	-0.6891	10	0.87932	D	0	-20.1468	14.1283	0.65235	0.0:0.0:0.0:1.0	.	256;256;256	E9PEZ1;Q8IWT3;Q05C85	.;CUL9_HUMAN;.	P	256	ENSP00000252050:L256P;ENSP00000346490:L256P;ENSP00000361730:L256P	ENSP00000252050:L256P	L	+	2	0	CUL9	43261687	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	4.730000	0.62015	1.938000	0.56188	0.379000	0.24179	CTT	.	.		0.527	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		C	43153709	T	C	43153709	3	2	111	1	0	0	0	0	1	0	0	0	4063	1609	56	2	777	2	CUL9	6	43153709	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	9984589	43153709	127961358	126	16366										
TTBK1	84630	hgsc.bcm.edu	37	chr6	43250734	43250734	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaagaggatgaggaagaagaAgaggaggaagaggaagagga	20	0	0	7	rs368934924		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:43250734A>G	ENST00000259750.4	+	14	2339	c.2256A>G	c.(2254-2256)gaA>gaG	p.E752E		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	752	Glu-rich.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			aggaagaagaagaggaggaag	0.582																																					p.E752E		Atlas-SNP	.											.	TTBK1	124	.	0			c.A2256G						.						16	16	16					6																	43250734		2202	4297	6499	SO:0001819	synonymous_variant	84630	exon14			AGAAGAAGAGGAG	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.2256A>G	chr6.hg19:g.43250734A>G		59.0	0.0		77.0	5.0	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	hg19	CCDS34455.1																																																																																			.	.		0.582	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			G	43250734	A	G	43250734	2	3	111	1	0	0	0	0	0	0	0	1	16691	69	3	2		2	TTBK1	6	43250734	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	97025	43250734	127864333	127	16367										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51524434	51524434	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggagctcatggtagaatacaGccaagagaagcttggaggta	14	6	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:51524434G>A	ENST00000371117.3	-	61	10765	c.10490C>T	c.(10489-10491)gCt>gTt	p.A3497V		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3497					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GTAGAATACAGCCAAGAGAAG	0.453																																					p.A3497V		Atlas-SNP	.											PKHD1,rectum,carcinoma,0,1	PKHD1	927	.	0			c.C10490T						.						64	65	65					6																	51524434		2203	4300	6503	SO:0001583	missense	5314	exon61			AATACAGCCAAGA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10490C>T	chr6.hg19:g.51524434G>A	ENSP00000360158:p.Ala3497Val	97.0	0.0		84.0	4.0	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.636101	0.67130	.	.	ENSG00000170927	ENST00000371117	D	0.86432	-2.12	5.72	5.72	0.89469	.	0.158779	0.42821	D	0.000641	D	0.88142	0.6357	L	0.32530	0.975	0.80722	D	1	D	0.65815	0.995	D	0.63381	0.914	D	0.89460	0.3736	10	0.87932	D	0	.	18.8671	0.92296	0.0:0.0:1.0:0.0	.	3497	P08F94	PKHD1_HUMAN	V	3497	ENSP00000360158:A3497V	ENSP00000360158:A3497V	A	-	2	0	PKHD1	51632393	0.901000	0.30685	0.966000	0.40874	0.945000	0.59286	3.822000	0.55708	2.695000	0.91970	0.655000	0.94253	GCT	.	.		0.453	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51524434	G	A	51524434	3	1	111	1	0	0	0	0	1	0	0	0	11980	971	34	3	1762	3	PKHD1	6	51524434	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	8273700	51524434	119590633	128	16368										
OGFRL1	79627	hgsc.bcm.edu	37	chr6	72003034	72003034	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcaactgccaaaccaaagagAagtttttatgctgccaggga	10	9	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:72003034A>G	ENST00000370435.4	+	2	407	c.273A>G	c.(271-273)agA>agG	p.R91R	RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000587253.1_RNA|OGFRL1_ENST00000467503.1_3'UTR|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	91						membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						AACCAAAGAGAAGTTTTTATG	0.373																																					p.R91R		Atlas-SNP	.											.	OGFRL1	44	.	0			c.A273G						.						116	119	118					6																	72003034		2203	4300	6503	SO:0001819	synonymous_variant	79627	exon2			AAAGAGAAGTTTT		CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.273A>G	chr6.hg19:g.72003034A>G		127.0	0.0		143.0	22.0	NM_024576	Q2TAC1|Q8NEQ4|Q9H7B5	Silent	SNP	ENST00000370435.4	hg19	CCDS34482.1																																																																																			.	.		0.373	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		G	72003034	A	G	72003034	2	3	111	1	0	0	0	0	0	0	0	1	10853	243	9	2		2	OGFRL1	6	72003034	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	20478600	72003034	99112033	129	16369										
CD109	135228	hgsc.bcm.edu	37	chr6	74516714	74516714	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccaggaagagtgattcatagTgagcttcaaggtggcaataa	12	6	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:74516714T>C	ENST00000287097.5	+	25	3220	c.3108T>C	c.(3106-3108)agT>agC	p.S1036S	CD109_ENST00000422508.2_Silent_p.S959S|CD109_ENST00000437994.2_Silent_p.S1036S			Q6YHK3	CD109_HUMAN	CD109 molecule	1036					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGATTCATAGTGAGCTTCAAG	0.363																																					p.S1036S		Atlas-SNP	.											.	CD109	170	.	0			c.T3108C						.						103	99	101					6																	74516714		2203	4300	6503	SO:0001819	synonymous_variant	135228	exon25			TCATAGTGAGCTT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.3108T>C	chr6.hg19:g.74516714T>C		102.0	0.0		67.0	4.0	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	hg19	CCDS4982.1																																																																																			.	.		0.363	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		C	74516714	T	C	74516714	2	2	111	1	0	0	0	0	0	0	0	1	2965	1693	59	2		2	CD109	6	74516714	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2513680	74516714	96598353	130	16370										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76022124	76022124	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tctactcaccactgactgggTtcctcgagcagatgacgttg	10	12	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:76022124T>C	ENST00000237172.7	-	5	3754	c.3424A>G	c.(3424-3426)Acc>Gcc	p.T1142A	FILIP1_ENST00000393004.2_Missense_Mutation_p.T1142A|FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Missense_Mutation_p.T1043A	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1142										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						ACTGACTGGGTTCCTCGAGCA	0.572																																					p.T1142A		Atlas-SNP	.											.	FILIP1	173	.	0			c.A3424G						.						144	131	135					6																	76022124		2203	4300	6503	SO:0001583	missense	27145	exon5			ACTGGGTTCCTCG	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.3424A>G	chr6.hg19:g.76022124T>C	ENSP00000237172:p.Thr1142Ala	76.0	0.0		47.0	5.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	hg19	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	T	17.74	3.463112	0.63513	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.20332	2.09;2.08;2.09	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.15782	0.0380	L	0.59436	1.845	0.54753	D	0.999986	D;P;P	0.54397	0.966;0.91;0.946	P;B;P	0.48598	0.583;0.294;0.488	T	0.05289	-1.0894	10	0.09843	T	0.71	-15.3761	16.0766	0.80971	0.0:0.0:0.0:1.0	.	1142;1142;1142	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	A	1142;1142;1043	ENSP00000376728:T1142A;ENSP00000237172:T1142A;ENSP00000359037:T1043A	ENSP00000237172:T1142A	T	-	1	0	FILIP1	76078844	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.838000	0.55828	2.202000	0.70862	0.533000	0.62120	ACC	.	.		0.572	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		C	76022124	T	C	76022124	3	2	111	1	0	0	0	0	1	0	0	0	5902	1725	60	2	225	2	FILIP1	6	76022124	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1505410	76022124	95092943	131	16371										
ELOVL4	6785	hgsc.bcm.edu	37	chr6	80635991	80635991	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acgcatctgaaaaggttctcGgtccttcatccattttggac	8	11	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:80635991G>T	ENST00000369816.4	-	2	508	c.208C>A	c.(208-210)Cga>Aga	p.R70R		NM_022726.3	NP_073563.1	Q9GZR5	ELOV4_HUMAN	ELOVL fatty acid elongase 4	70					cellular lipid metabolic process (GO:0044255)|detection of visible light (GO:0009584)|fatty acid biosynthetic process (GO:0006633)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)	G-protein coupled photoreceptor activity (GO:0008020)|transferase activity (GO:0016740)	p.R70G(1)		central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;1.83e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.011)		BRCA - Breast invasive adenocarcinoma(397;0.0168)	Alpha-Linolenic Acid(DB00132)	AAAGGTTCTCGGTCCTTCATC	0.408																																					p.R70R		Atlas-SNP	.											ELOVL4,NS,carcinoma,0,1	ELOVL4	46	.	1	Substitution - Missense(1)	prostate(1)	c.C208A						.						89	77	81					6																	80635991		2203	4300	6503	SO:0001819	synonymous_variant	6785	exon2			GTTCTCGGTCCTT	AF277094	CCDS4992.1	6q14	2013-01-08	2011-05-25		ENSG00000118402	ENSG00000118402			14415	protein-coding gene	gene with protein product	"cancer/testis antigen 118"	605512	"elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4"	STGD2, STGD3		11138005	Standard	NM_022726		Approved	CT118	uc003pja.4	Q9GZR5	OTTHUMG00000015087	ENST00000369816.4:c.208C>A	chr6.hg19:g.80635991G>T		66.0	0.0		45.0	2.0	NM_022726	B2R6B5|Q5TCS2|Q86YJ1|Q9H139	Silent	SNP	ENST00000369816.4	hg19	CCDS4992.1																																																																																			.	.		0.408	ELOVL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041315.1			T	80635991	G	T	80635991	2	4	111	1	0	0	0	0	0	0	0	1	5078	1124	39	1		1	ELOVL4	6	80635991	Silent	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	4613867	80635991	90479076	132	16372										
C6orf162	57150	hgsc.bcm.edu	37	chr6	88046871	88046871	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcgtgctgtgaatccagagcTcttcattaaacctgtaagaa	8	9	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:88046871T>C	ENST00000392863.1	+	3	211	c.122T>C	c.(121-123)cTc>cCc	p.L41P	RP1-102H19.8_ENST00000448282.2_Missense_Mutation_p.L41P|SMIM8_ENST00000608525.1_Missense_Mutation_p.L41P|SMIM8_ENST00000229570.5_Missense_Mutation_p.L41P|SMIM8_ENST00000608868.1_Missense_Mutation_p.L41P|SMIM8_ENST00000608353.1_Missense_Mutation_p.L41P	NM_001042493.1	NP_001035958.1	Q96KF7	SMIM8_HUMAN	small integral membrane protein 8	41						integral component of membrane (GO:0016021)		p.L41P(1)									AATCCAGAGCTCTTCATTAAA	0.393																																					p.L41P		Atlas-SNP	.											C6orf162,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	kidney(1)	c.T122C						.						101	103	103					6																	88046871		2203	4300	6503	SO:0001583	missense	57150	exon3			CAGAGCTCTTCAT	AL050201	CCDS34496.1, CCDS75493.1	6q15	2013-06-21	2012-11-20	2012-11-20	ENSG00000111850	ENSG00000111850			21401	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 162"	C6orf162			Standard	NM_001287445		Approved	DKFZP586E1923, dJ102H19.2	uc003plq.1	Q96KF7	OTTHUMG00000015168	ENST00000392863.1:c.122T>C	chr6.hg19:g.88046871T>C	ENSP00000376603:p.Leu41Pro	88.0	0.0		41.0	3.0	NM_001042493	B2R4V6|E1P505|Q5TEZ3|Q6NSD2|Q8IZ10	Missense_Mutation	SNP	ENST00000392863.1	hg19	CCDS34496.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.557036	0.86231	.	.	ENSG00000111850	ENST00000392863;ENST00000229570	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.76835	0.4043	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80837	-0.1204	8	0.87932	D	0	-8.2011	16.3453	0.83126	0.0:0.0:0.0:1.0	.	41	Q96KF7	CF162_HUMAN	P	41	.	ENSP00000229570:L41P	L	+	2	0	C6orf162	88103590	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.914000	0.75764	2.261000	0.74972	0.533000	0.62120	CTC	.	.		0.393	SMIM8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472479.2	NM_020425		C	88046871	T	C	88046871	3	2	111	1	0	0	0	0	1	0	0	0	2342	1551	54	2	124	2	C6orf162	6	88046871	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	7410880	88046871	83068196	133	16373										
MDN1	23195	hgsc.bcm.edu	37	chr6	90440507	90440507	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttccagtgaattctttggccTtcattctgtcataaatcttc	5	10	5	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:90440507T>C	ENST00000369393.3	-	35	5193	c.5078A>G	c.(5077-5079)aAg>aGg	p.K1693R	MDN1_ENST00000428876.1_Missense_Mutation_p.K1693R			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1693					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TTCTTTGGCCTTCATTCTGTC	0.323																																					p.K1693R		Atlas-SNP	.											.	MDN1	478	.	0			c.A5078G						.						105	97	100					6																	90440507		2203	4300	6503	SO:0001583	missense	23195	exon35			TTGGCCTTCATTC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.5078A>G	chr6.hg19:g.90440507T>C	ENSP00000358400:p.Lys1693Arg	142.0	0.0		86.0	4.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	9.734	1.162964	0.21538	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03242	4.0;4.0	5.62	4.42	0.53409	.	0.260616	0.38663	N	0.001604	T	0.00784	0.0026	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.48896	-0.8994	10	0.13108	T	0.6	.	5.9008	0.18965	0.0:0.144:0.1399:0.7161	.	1693	Q9NU22	MDN1_HUMAN	R	1693	ENSP00000358400:K1693R;ENSP00000413970:K1693R	ENSP00000358400:K1693R	K	-	2	0	MDN1	90497228	0.971000	0.33674	0.954000	0.39281	0.964000	0.63967	1.837000	0.39201	0.912000	0.36772	0.477000	0.44152	AAG	.	.		0.323	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90440507	T	C	90440507	3	2	111	1	0	0	0	0	1	0	0	0	9424	1609	56	2	11984	2	MDN1	6	90440507	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2393636	90440507	80674560	134	16374										
MDN1	23195	hgsc.bcm.edu	37	chr6	90461216	90461216	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aagatgtcagaatgtacgtcTcatctattgtaggctccttg	9	8	3	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:90461216T>C	ENST00000369393.3	-	23	3276	c.3161A>G	c.(3160-3162)gAg>gGg	p.E1054G	MDN1_ENST00000428876.1_Missense_Mutation_p.E1054G			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1054					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AATGTACGTCTCATCTATTGT	0.498																																					p.E1054G		Atlas-SNP	.											.	MDN1	478	.	0			c.A3161G						.						157	135	142					6																	90461216		2203	4300	6503	SO:0001583	missense	23195	exon23			TACGTCTCATCTA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.3161A>G	chr6.hg19:g.90461216T>C	ENSP00000358400:p.Glu1054Gly	164.0	0.0		109.0	5.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	15.42	2.829792	0.50845	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.42900	0.96;0.96;0.96	5.71	5.71	0.89125	.	0.185062	0.47852	D	0.000213	T	0.24431	0.0592	L	0.46819	1.47	0.41553	D	0.988584	B;B	0.25390	0.041;0.125	B;B	0.24394	0.017;0.053	T	0.05599	-1.0875	10	0.32370	T	0.25	.	15.9883	0.80179	0.0:0.0:0.0:1.0	.	981;1054	Q5T795;Q9NU22	.;MDN1_HUMAN	G	1054;1054;981	ENSP00000358400:E1054G;ENSP00000413970:E1054G;ENSP00000409664:E981G	ENSP00000358400:E1054G	E	-	2	0	MDN1	90517937	1.000000	0.71417	0.996000	0.52242	0.899000	0.52679	5.020000	0.64066	2.172000	0.68678	0.533000	0.62120	GAG	.	.		0.498	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90461216	T	C	90461216	3	2	111	1	0	0	0	0	1	0	0	0	9424	1551	54	2	13949	2	MDN1	6	90461216	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	20709	90461216	80653851	135	16375										
CDC40	51362	hgsc.bcm.edu	37	chr6	110540651	110540651	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agataagcaaaatctctttgTggctgggatgtctgataaga	11	5	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:110540651T>C	ENST00000368932.1	+	12	1276	c.1175T>C	c.(1174-1176)gTg>gCg	p.V392A	CDC40_ENST00000307731.1_Missense_Mutation_p.V392A|CDC40_ENST00000368930.1_Missense_Mutation_p.V392A			O60508	PRP17_HUMAN	cell division cycle 40	392					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		AATCTCTTTGTGGCTGGGATG	0.343																																					p.V392A		Atlas-SNP	.											.	CDC40	39	.	0			c.T1175C						.						127	124	125					6																	110540651		2203	4300	6503	SO:0001583	missense	51362	exon11			TCTTTGTGGCTGG	AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438		"WD repeat domain containing"	17350	protein-coding gene	gene with protein product		605585	"cell division cycle 40 homolog (yeast)", "cell division cycle 40 homolog (S. cerevisiae)"			9769104, 9830021	Standard	NM_015891		Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368932.1:c.1175T>C	chr6.hg19:g.110540651T>C	ENSP00000357928:p.Val392Ala	114.0	0.0		86.0	4.0	NM_015891	B2RBC5|O75471|Q5SRN0|Q9UPG1	Missense_Mutation	SNP	ENST00000368932.1	hg19	CCDS5081.1	.	.	.	.	.	.	.	.	.	.	T	31	5.085433	0.94100	.	.	ENSG00000168438	ENST00000368932;ENST00000368933;ENST00000368930;ENST00000307731	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	5.81	5.81	0.92471	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.85013	0.5600	M	0.85859	2.78	0.80722	D	1	P	0.48294	0.908	P	0.58620	0.842	D	0.84033	0.0360	10	0.15066	T	0.55	-11.2631	16.1773	0.81862	0.0:0.0:0.0:1.0	.	392	O60508	PRP17_HUMAN	A	392	ENSP00000357928:V392A;ENSP00000357929:V392A;ENSP00000357926:V392A;ENSP00000304370:V392A	ENSP00000304370:V392A	V	+	2	0	CDC40	110647344	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.217000	0.71921	0.482000	0.46254	GTG	.	.		0.343	CDC40-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041791.1	NM_015891		C	110540651	T	C	110540651	3	2	111	1	0	0	0	0	1	0	0	0	3072	1696	59	2	1217	2	CDC40	6	110540651	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	20079435	110540651	60574416	136	16376										
CDC40	51362	hgsc.bcm.edu	37	chr6	110540992	110540992	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tatgatcggcatttgggagcTgtcaacaccattgtttttgt	10	7	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:110540992T>C	ENST00000368932.1	+	13	1361	c.1260T>C	c.(1258-1260)gcT>gcC	p.A420A	CDC40_ENST00000307731.1_Silent_p.A420A|CDC40_ENST00000368930.1_Silent_p.A420A			O60508	PRP17_HUMAN	cell division cycle 40	420					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		ATTTGGGAGCTGTCAACACCA	0.408																																					p.A420A		Atlas-SNP	.											.	CDC40	39	.	0			c.T1260C						.						209	188	195					6																	110540992		2203	4300	6503	SO:0001819	synonymous_variant	51362	exon12			GGGAGCTGTCAAC	AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438		"WD repeat domain containing"	17350	protein-coding gene	gene with protein product		605585	"cell division cycle 40 homolog (yeast)", "cell division cycle 40 homolog (S. cerevisiae)"			9769104, 9830021	Standard	NM_015891		Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368932.1:c.1260T>C	chr6.hg19:g.110540992T>C		181.0	0.0		106.0	5.0	NM_015891	B2RBC5|O75471|Q5SRN0|Q9UPG1	Silent	SNP	ENST00000368932.1	hg19	CCDS5081.1																																																																																			.	.		0.408	CDC40-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041791.1	NM_015891		C	110540992	T	C	110540992	2	2	111	1	0	0	0	0	0	0	0	1	3072	1567	55	2		2	CDC40	6	110540992	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	341	110540992	60574075	137	16377										
UTRN	7402	hgsc.bcm.edu	37	chr6	144801024	144801024	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaaagacttggcagagatgcAggaatggatgacccaggccg	15	8	0	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:144801024A>G	ENST00000367545.3	+	25	3413	c.3413A>G	c.(3412-3414)cAg>cGg	p.Q1138R		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1138					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GCAGAGATGCAGGAATGGATG	0.468																																					p.Q1138R		Atlas-SNP	.											.	UTRN	327	.	0			c.A3413G						.						112	113	113					6																	144801024		2203	4300	6503	SO:0001583	missense	7402	exon25			AGATGCAGGAATG	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.3413A>G	chr6.hg19:g.144801024A>G	ENSP00000356515:p.Gln1138Arg	55.0	0.0		50.0	5.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.093745	0.76870	.	.	ENSG00000152818	ENST00000367545	T	0.50548	0.74	5.95	5.95	0.96441	.	0.000000	0.49916	D	0.000124	T	0.47192	0.1432	L	0.27053	0.805	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	T	0.48186	-0.9057	10	0.39692	T	0.17	.	16.4237	0.83790	1.0:0.0:0.0:0.0	.	1138	P46939	UTRO_HUMAN	R	1138	ENSP00000356515:Q1138R	ENSP00000356515:Q1138R	Q	+	2	0	UTRN	144842717	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.219000	0.78000	2.279000	0.76181	0.533000	0.62120	CAG	.	.		0.468	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			G	144801024	A	G	144801024	3	3	111	1	0	0	0	0	1	0	0	0	17118	188	7	2	3511	2	UTRN	6	144801024	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	34260032	144801024	26314043	138	16378										
STXBP5	134957	hgsc.bcm.edu	37	chr6	147680286	147680286	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aagcattgacaaagaatcccGagaagcgatctccgctcttc	8	12	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:147680286G>T	ENST00000321680.6	+	23	2372	c.2372G>T	c.(2371-2373)cGa>cTa	p.R791L	STXBP5_ENST00000367480.3_Missense_Mutation_p.R738L|STXBP5_ENST00000179882.6_Missense_Mutation_p.R446L|STXBP5_ENST00000367481.3_Missense_Mutation_p.R755L	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	791					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		AAAGAATCCCGAGAAGCGATC	0.443																																					p.R791L		Atlas-SNP	.											.	STXBP5	163	.	0			c.G2372T						.						94	93	93					6																	147680286		2203	4300	6503	SO:0001583	missense	134957	exon23			AATCCCGAGAAGC	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.2372G>T	chr6.hg19:g.147680286G>T	ENSP00000321826:p.Arg791Leu	92.0	0.0		58.0	24.0	NM_001127715	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	hg19	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.280085	0.59758	.	.	ENSG00000164506	ENST00000367479;ENST00000367481;ENST00000321680;ENST00000367480;ENST00000179882;ENST00000392291	T;T;T;T;T	0.26660	1.72;1.72;1.72;1.72;1.72	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.41743	0.1172	L	0.60455	1.87	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.80764	0.994;0.992;0.991	T	0.15292	-1.0442	10	0.49607	T	0.09	.	19.3349	0.94312	0.0:0.0:1.0:0.0	.	755;791;446	Q5T5C0-2;Q5T5C0;B3KXX0	.;STXB5_HUMAN;.	L	130;755;791;738;446;115	ENSP00000356451:R755L;ENSP00000321826:R791L;ENSP00000356450:R738L;ENSP00000179882:R446L;ENSP00000376112:R115L	ENSP00000179882:R446L	R	+	2	0	STXBP5	147721979	1.000000	0.71417	0.996000	0.52242	0.431000	0.31685	9.476000	0.97823	2.570000	0.86706	0.655000	0.94253	CGA	.	.		0.443	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			T	147680286	G	T	147680286	3	4	111	1	0	0	0	0	1	0	0	0	15371	1058	37	1	2462	1	STXBP5	6	147680286	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	2879262	147680286	23434781	139	16379										
EZR	7430	hgsc.bcm.edu	37	chr6	159190397	159190397	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acttcatcctccttgcgcctCcgcgcctcttccaggagggc	9	18	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:159190397C>T	ENST00000367075.3	-	12	1473	c.1305G>A	c.(1303-1305)cgG>cgA	p.R435R	EZR_ENST00000337147.7_Silent_p.R435R|EZR_ENST00000392177.4_Silent_p.R403R	NM_001111077.1	NP_001104547.1	P15311	EZRI_HUMAN	ezrin	435	Interaction with SCYL3.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of endothelial barrier (GO:0061028)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|filopodium assembly (GO:0046847)|leukocyte cell-cell adhesion (GO:0007159)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|receptor internalization (GO:0031623)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|astrocyte projection (GO:0097449)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell tip (GO:0051286)|ciliary basal body (GO:0036064)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|microspike (GO:0044393)|microvillus (GO:0005902)|microvillus membrane (GO:0031528)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|Schwann cell microvillus (GO:0097454)|T-tubule (GO:0030315)|uropod (GO:0001931)|vesicle (GO:0031982)	actin filament binding (GO:0051015)|cell adhesion molecule binding (GO:0050839)|poly(A) RNA binding (GO:0044822)		EZR/ROS1(4)	breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	15		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)		CCTTGCGCCTCCGCGCCTCTT	0.592			T	ROS1	NSCLC																																p.R435R		Atlas-SNP	.		Dom	yes		6	6q25.3	7430	ezrin		E	.	EZR	44	.	0			c.G1305A						.						82	70	74					6																	159190397		2203	4300	6503	SO:0001819	synonymous_variant	7430	exon11			GCGCCTCCGCGCC	AF187552	CCDS5258.1	6q25.3	2010-12-10	2007-11-29	2007-11-29	ENSG00000092820	ENSG00000092820		"A-kinase anchor proteins"	12691	protein-coding gene	gene with protein product	"cytovillin 2"	123900	"villin 2 (ezrin)"	VIL2			Standard	NM_003379		Approved		uc003qrt.4	P15311	OTTHUMG00000015917	ENST00000367075.3:c.1305G>A	chr6.hg19:g.159190397C>T		45.0	0.0		34.0	4.0	NM_003379	E1P5A8|P23714|Q4VX75|Q96CU8|Q9NSJ4	Silent	SNP	ENST00000367075.3	hg19	CCDS5258.1																																																																																			.	.		0.592	EZR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042878.1	NM_003379		T	159190397	C	T	159190397	2	4	111	1	0	0	0	0	0	0	0	1	5337	842	30	3		3	EZR	6	159190397	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	11510111	159190397	11924670	140	16380										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161455479	161455479	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agccagtcggtctaatttgaAaggtgagtcttgtacttgaa	11	6	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:161455479A>G	ENST00000392142.4	+	2	489	c.341A>G	c.(340-342)aAa>aGa	p.K114R	MAP3K4_ENST00000348824.7_Missense_Mutation_p.K114R|MAP3K4_ENST00000446500.1_3'UTR|MAP3K4_ENST00000366919.2_Missense_Mutation_p.K114R|MAP3K4_ENST00000366920.2_Missense_Mutation_p.K114R	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	114					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		TCTAATTTGAAAGGTGAGTCT	0.413																																					p.K114R		Atlas-SNP	.											.	MAP3K4	364	.	0			c.A341G						.						50	54	53					6																	161455479		2203	4300	6503	SO:0001583	missense	4216	exon2			ATTTGAAAGGTGA	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.341A>G	chr6.hg19:g.161455479A>G	ENSP00000375986:p.Lys114Arg	104.0	0.0		67.0	4.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.316897	0.81469	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824;ENST00000544209;ENST00000448119	T;T;T;T	0.75260	-0.9;-0.92;-0.91;-0.9	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.58409	0.2120	L	0.43152	1.355	0.39588	D	0.969533	P;P	0.44627	0.804;0.839	B;B	0.41571	0.36;0.276	T	0.60757	-0.7200	10	0.28530	T	0.3	-35.8541	16.1616	0.81721	1.0:0.0:0.0:0.0	.	114;114	Q9Y6R4-2;Q9Y6R4	.;M3K4_HUMAN	R	114;114;114;114;114;93;23	ENSP00000355886:K114R;ENSP00000375986:K114R;ENSP00000355887:K114R;ENSP00000297332:K114R	ENSP00000297332:K114R	K	+	2	0	MAP3K4	161375469	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	3.975000	0.56859	2.275000	0.75901	0.529000	0.55759	AAA	.	.		0.413	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			G	161455479	A	G	161455479	3	3	111	1	0	0	0	0	1	0	0	0	9261	14	1	2	347	2	MAP3K4	6	161455479	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	2265082	161455479	9659588	141	16381										
PSMB1	5689	hgsc.bcm.edu	37	chr6	170844336	170844336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tccttaaggaaacagtttccTccctgatgccctctttggtc	7	13	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr6:170844336T>C	ENST00000262193.6	-	6	796	c.698A>G	c.(697-699)gAg>gGg	p.E233G	PSMB1_ENST00000462957.1_5'UTR	NM_002793.3	NP_002784.1	P20618	PSB1_HUMAN	proteasome (prosome, macropain) subunit, beta type, 1	233					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	5		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)|Carfilzomib(DB08889)	AACAGTTTCCTCCCTGATGCC	0.478																																					p.E233G		Atlas-SNP	.											.	PSMB1	12	.	0			c.A698G						.						233	204	214					6																	170844336		2203	4300	6503	SO:0001583	missense	5689	exon6			GTTTCCTCCCTGA	D00761	CCDS34577.1	6q27	2008-02-05			ENSG00000008018	ENSG00000008018		"Proteasome (prosome, macropain) subunits"	9537	protein-coding gene	gene with protein product		602017				2025653	Standard	NM_002793		Approved	PMSB1, HC5	uc011ehe.2	P20618	OTTHUMG00000016087	ENST00000262193.6:c.698A>G	chr6.hg19:g.170844336T>C	ENSP00000262193:p.Glu233Gly	252.0	0.0		147.0	6.0	NM_002793	B5BU76|Q9BWA8	Missense_Mutation	SNP	ENST00000262193.6	hg19	CCDS34577.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.459199	0.63401	.	.	ENSG00000008018	ENST00000262193	T	0.44083	0.93	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.45175	0.1329	M	0.93854	3.465	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.54323	-0.8311	10	0.51188	T	0.08	-34.1252	16.3322	0.83039	0.0:0.0:0.0:1.0	.	233	P20618	PSB1_HUMAN	G	233	ENSP00000262193:E233G	ENSP00000262193:E233G	E	-	2	0	PSMB1	170686261	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	7.238000	0.78173	2.251000	0.74343	0.528000	0.53228	GAG	.	.		0.478	PSMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043278.2	NM_002793		C	170844336	T	C	170844336	3	2	111	1	0	0	0	0	1	0	0	0	12686	1551	54	2	31	2	PSMB1	6	170844336	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	9388857	170844336	270731	142	16382										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5396833	5396833	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttcaacttgtcctgcttggtGagggagagggccttgtcgag	15	8	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:5396833G>T	ENST00000430969.1	-	16	5256	c.4908C>A	c.(4906-4908)ctC>ctA	p.L1636L	TNRC18_ENST00000399537.4_Silent_p.L1636L	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1636							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CCTGCTTGGTGAGGGAGAGGG	0.552																																					p.L1636L		Atlas-SNP	.											.	TNRC18	311	.	0			c.C4908A						.						48	48	48					7																	5396833		2027	4185	6212	SO:0001819	synonymous_variant	84629	exon16			CTTGGTGAGGGAG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4908C>A	chr7.hg19:g.5396833G>T		118.0	0.0		93.0	4.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	hg19	CCDS47534.1																																																																																			.	.		0.552	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	5396833	G	T	5396833	2	4	111	1	0	0	0	0	0	0	0	1	16354	1277	45	3		3	TNRC18	7	5396833	Silent	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10		5396833	153741830	143	16383										
ANKMY2	57037	hgsc.bcm.edu	37	chr7	16640522	16640522	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gagagatacctacttcagccTctggttgctcttcattaaca	7	11	4	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:16640522T>A	ENST00000306999.2	-	10	1433	c.1190A>T	c.(1189-1191)gAg>gTg	p.E397V		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	397						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TACTTCAGCCTCTGGTTGCTC	0.403																																					p.E397V		Atlas-SNP	.											.	ANKMY2	46	.	0			c.A1190T						.						100	95	97					7																	16640522		2203	4300	6503	SO:0001583	missense	57037	exon10			TCAGCCTCTGGTT	AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.1190A>T	chr7.hg19:g.16640522T>A	ENSP00000303570:p.Glu397Val	63.0	0.0		65.0	21.0	NM_020319	A4D124|Q659G1|Q96BL3	Missense_Mutation	SNP	ENST00000306999.2	hg19	CCDS5361.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.284409	0.23392	.	.	ENSG00000106524	ENST00000306999	T	0.71579	-0.58	5.4	0.0896	0.14460	.	1.061010	0.07184	N	0.854515	T	0.52533	0.1740	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43196	-0.9406	10	0.66056	D	0.02	0.8445	1.0465	0.01571	0.1526:0.1712:0.1587:0.5175	.	397	Q8IV38	ANKY2_HUMAN	V	397	ENSP00000303570:E397V	ENSP00000303570:E397V	E	-	2	0	ANKMY2	16607047	0.000000	0.05858	0.044000	0.18714	0.617000	0.37484	0.416000	0.21198	-0.144000	0.11314	0.533000	0.62120	GAG	.	.		0.403	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319		A	16640522	T	A	16640522	3	1	111	1	0	0	0	0	1	0	0	0	635	1551	54	4	139	4	ANKMY2	7	16640522	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	11243689	16640522	142498141	144	16384										
DFNA5	1687	hgsc.bcm.edu	37	chr7	24749890	24749890	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctgggaagatatcccatgcGcagcatctggcatgtctatg	11	11	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:24749890G>C	ENST00000342947.3	-	6	1240	c.815C>G	c.(814-816)gCg>gGg	p.A272G	DFNA5_ENST00000409970.1_Missense_Mutation_p.A108G|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000409775.3_Missense_Mutation_p.A272G|DFNA5_ENST00000545231.1_Missense_Mutation_p.A108G|DFNA5_ENST00000419307.1_Missense_Mutation_p.A108G	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	272					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						TATCCCATGCGCAGCATCTGG	0.512																																					p.A272G	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.C815G						.						140	132	135					7																	24749890		2203	4300	6503	SO:0001583	missense	1687	exon6			CCATGCGCAGCAT	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.815C>G	chr7.hg19:g.24749890G>C	ENSP00000339587:p.Ala272Gly	59.0	0.0		67.0	13.0	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	hg19	CCDS5389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.121|6.121	0.390527|0.390527	0.11581|0.11581	.|.	.|.	ENSG00000105928|ENSG00000105928	ENST00000342947;ENST00000419307;ENST00000545231;ENST00000409970;ENST00000409775|ENST00000415480;ENST00000446822	T;T;T;T;T|.	0.20738|.	2.05;2.05;2.05;2.05;2.05|.	5.47|5.47	-0.583|-0.583	0.11706|0.11706	.|.	1.340530|.	0.04814|.	N|.	0.435804|.	T|T	0.04048|0.04048	0.0113|0.0113	N|N	0.00162|0.00162	-1.95|-1.95	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.40572|0.40572	-0.9556|-0.9556	10|5	0.24483|.	T|.	0.36|.	-0.396|-0.396	3.1868|3.1868	0.06603|0.06603	0.2317:0.312:0.3638:0.0924|0.2317:0.312:0.3638:0.0924	.|.	272|.	O60443|.	DFNA5_HUMAN|.	G|G	272;108;108;108;272|61;97	ENSP00000339587:A272G;ENSP00000401332:A108G;ENSP00000442661:A108G;ENSP00000387119:A108G;ENSP00000386670:A272G|.	ENSP00000339587:A272G|.	A|R	-|-	2|1	0|0	DFNA5|DFNA5	24716415|24716415	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.133000|0.133000	0.20885|0.20885	-0.249000|-0.249000	0.08842|0.08842	-0.019000|-0.019000	0.14055|0.14055	-0.256000|-0.256000	0.11100|0.11100	GCG|CGC	.	.		0.512	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		C	24749890	G	C	24749890	3	2	111	1	0	0	0	0	1	0	0	0	4456	1087	38	4	695	4	DFNA5	7	24749890	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	8109368	24749890	134388773	145	16385										
PDE1C	5137	hgsc.bcm.edu	37	chr7	31912954	31912954	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgagtagttcatagaaaataAatttcagtgcatgatcccca	7	7	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:31912954A>G	ENST00000396191.1	-	6	1015	c.560T>C	c.(559-561)tTt>tCt	p.F187S	PDE1C_ENST00000396182.2_Missense_Mutation_p.F187S|PDE1C_ENST00000396193.1_Missense_Mutation_p.F247S|PDE1C_ENST00000396184.3_Missense_Mutation_p.F187S|PDE1C_ENST00000321453.7_Missense_Mutation_p.F187S	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	187					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.F187S(2)|p.F247S(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	ATAGAAAATAAATTTCAGTGC	0.398																																					p.F247S		Atlas-SNP	.											PDE1C_ENST00000396193,bladder,carcinoma,0,3	PDE1C	465	.	3	Substitution - Missense(3)	urinary_tract(3)	c.T740C						.						86	82	84					7																	31912954		2203	4300	6503	SO:0001583	missense	5137	exon7			AAAATAAATTTCA	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.560T>C	chr7.hg19:g.31912954A>G	ENSP00000379494:p.Phe187Ser	113.0	0.0		66.0	3.0	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	hg19	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.837457	0.91117	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98	5.14	5.14	0.70334	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	D	0.83381	0.5242	M	0.70595	2.14	0.80722	D	1	P;D;D	0.63046	0.779;0.992;0.965	P;P;P	0.61477	0.511;0.889;0.549	D	0.85330	0.1089	10	0.62326	D	0.03	.	14.6161	0.68549	1.0:0.0:0.0:0.0	.	187;247;187	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	S	247;187;187;187;187	ENSP00000379496:F247S;ENSP00000379494:F187S;ENSP00000318105:F187S;ENSP00000379487:F187S;ENSP00000379485:F187S	ENSP00000318105:F187S	F	-	2	0	PDE1C	31879479	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.300000	0.96151	1.921000	0.55644	0.383000	0.25322	TTT	.	.		0.398	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			G	31912954	A	G	31912954	3	3	111	1	0	0	0	0	1	0	0	0	11644	14	1	2	1392	2	PDE1C	7	31912954	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	7163064	31912954	127225709	146	16386										
AVL9	23080	hgsc.bcm.edu	37	chr7	32590989	32590989	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaaacttcaactcattacacAtgcatattttgaagagaagg	6	7	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:32590989A>G	ENST00000318709.4	+	5	637	c.416A>G	c.(415-417)cAt>cGt	p.H139R	AVL9_ENST00000409301.1_Missense_Mutation_p.H139R|AVL9_ENST00000404479.1_Missense_Mutation_p.H139R	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	139					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						CTCATTACACATGCATATTTT	0.303																																					p.H139R		Atlas-SNP	.											.	AVL9	66	.	0			c.A416G						.						107	110	109					7																	32590989		2203	4294	6497	SO:0001583	missense	23080	exon5			TTACACATGCATA	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"KIAA0241"	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.416A>G	chr7.hg19:g.32590989A>G	ENSP00000315568:p.His139Arg	85.0	0.0		68.0	4.0	NM_015060	Q92573	Missense_Mutation	SNP	ENST00000318709.4	hg19	CCDS34613.1	.	.	.	.	.	.	.	.	.	.	A	18.22	3.575568	0.65878	.	.	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000404479;ENST00000446718	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.52208	0.1720	L	0.39326	1.205	0.80722	D	1	D;D	0.63880	0.979;0.993	D;D	0.65233	0.933;0.909	T	0.41378	-0.9512	10	0.19590	T	0.45	-15.3642	15.785	0.78294	1.0:0.0:0.0:0.0	.	139;139	Q8N6Z3;Q8NBF6	.;AVL9_HUMAN	R	139;139;139;139;70	ENSP00000315568:H139R;ENSP00000387011:H139R;ENSP00000385242:H139R;ENSP00000395134:H70R	ENSP00000315568:H139R	H	+	2	0	AVL9	32557514	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.339000	0.96797	2.136000	0.66102	0.383000	0.25322	CAT	.	.		0.303	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		G	32590989	A	G	32590989	3	3	111	1	0	0	0	0	1	0	0	0	1228	217	8	2	434	2	AVL9	7	32590989	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	678035	32590989	126547674	147	16387										
VPS41	27072	hgsc.bcm.edu	37	chr7	38869928	38869928	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctgatttatcttcacaggacTctaaaaagaaaaagacaaaa	5	7	3	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:38869928T>C	ENST00000310301.4	-	5	301	c.247A>G	c.(247-249)Agt>Ggt	p.S83G	VPS41_ENST00000395969.2_Intron	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	83					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						TTCACAGGACTCTAAAAAGAA	0.358																																					p.S83G		Atlas-SNP	.											.	VPS41	102	.	0			c.A247G						.						245	250	248					7																	38869928		2203	4300	6503	SO:0001630	splice_region_variant	27072	exon5			CAGGACTCTAAAA	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"vacuolar protein sorting 41 (yeast homolog)", "vacuolar protein sorting 41 (yeast)"			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.247-1A>G	chr7.hg19:g.38869928T>C		81.0	0.0		80.0	4.0	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	hg19	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	T	16.28	3.080004	0.55753	.	.	ENSG00000006715	ENST00000310301;ENST00000413141;ENST00000414632;ENST00000418457;ENST00000457055	T;T;T;T;T	0.54479	2.32;0.74;3.34;0.57;2.32	5.29	5.29	0.74685	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.56804	0.2010	M	0.72353	2.195	0.80722	D	1	P;P	0.47762	0.9;0.9	B;B	0.44224	0.444;0.444	T	0.64765	-0.6330	10	0.87932	D	0	-16.3791	14.1004	0.65051	0.0:0.0:0.0:1.0	.	83;83	B2RB94;P49754	.;VPS41_HUMAN	G	83;9;70;33;33	ENSP00000309457:S83G;ENSP00000412974:S9G;ENSP00000411919:S70G;ENSP00000407835:S33G;ENSP00000398584:S33G	ENSP00000265745:S83G	S	-	1	0	VPS41	38836453	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.978000	0.63799	2.111000	0.64477	0.528000	0.53228	AGT	.	.		0.358	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		Missense_Mutation	C	38869928	T	C	38869928	5	2	111	1	0	0	0	0	0	0	1	0	17225	1565	54	2	2417	2	VPS41	7	38869928	Splice_Site	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	6278939	38869928	120268735	148	16388										
AEBP1	165	hgsc.bcm.edu	37	chr7	44150363	44150363	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttcttcgtgggcttcagcaaTgacagccagacatgggtgat	12	9	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:44150363T>A	ENST00000223357.3	+	12	1745	c.1440T>A	c.(1438-1440)aaT>aaA	p.N480K	AEBP1_ENST00000450684.2_5'UTR|MIR4649_ENST00000582839.1_RNA	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	480	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.|Interaction with MAPK1 and MAPK3. {ECO:0000250}.|Required for DNA-binding and interaction with NFKBIA. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						GCTTCAGCAATGACAGCCAGA	0.592																																					p.N480K		Atlas-SNP	.											.	AEBP1	102	.	0			c.T1440A						.						168	159	162					7																	44150363		2203	4300	6503	SO:0001583	missense	165	exon12			CAGCAATGACAGC	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"aortic carboxypeptidase-like protein", "adipocyte enhancer binding protein 1"	602981	"AE-binding protein 1"			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.1440T>A	chr7.hg19:g.44150363T>A	ENSP00000223357:p.Asn480Lys	119.0	0.0		92.0	27.0	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	hg19	CCDS5476.1	.	.	.	.	.	.	.	.	.	.	T	19.80	3.895451	0.72639	.	.	ENSG00000106624	ENST00000223357	D	0.98280	-4.84	5.4	-9.63	0.00544	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.97860	0.9297	M	0.73372	2.23	0.80722	D	1	P	0.42908	0.793	P	0.55615	0.78	D	0.96321	0.9236	10	0.87932	D	0	-34.1631	19.0228	0.92921	0.0:0.607:0.0:0.393	.	480	Q8IUX7	AEBP1_HUMAN	K	480	ENSP00000223357:N480K	ENSP00000223357:N480K	N	+	3	2	AEBP1	44116888	0.035000	0.19736	0.657000	0.29651	0.928000	0.56348	-0.887000	0.04152	-2.067000	0.00885	-1.621000	0.00791	AAT	.	.		0.592	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		A	44150363	T	A	44150363	3	1	111	1	0	0	0	0	1	0	0	0	349	1461	51	4	1486	4	AEBP1	7	44150363	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	5280435	44150363	114988300	149	16389										
FGL2	10875	hgsc.bcm.edu	37	chr7	76826056	76826056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tggtcagaagatgaattttaTcgttccccagccaaaattcc	7	10	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:76826056T>C	ENST00000248598.5	-	2	892	c.860A>G	c.(859-861)gAt>gGt	p.D287G	CCDC146_ENST00000285871.4_Intron|RP11-467H10.2_ENST00000459742.1_RNA|CCDC146_ENST00000431197.1_Intron	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	287	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						ATGAATTTTATCGTTCCCCAG	0.423																																					p.D287G		Atlas-SNP	.											.	FGL2	40	.	0			c.A860G						.						119	124	122					7																	76826056		2203	4300	6503	SO:0001583	missense	10875	exon2			ATTTTATCGTTCC	Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"Fibrinogen C domain containing"	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.860A>G	chr7.hg19:g.76826056T>C	ENSP00000248598:p.Asp287Gly	192.0	0.0		125.0	5.0	NM_006682		Missense_Mutation	SNP	ENST00000248598.5	hg19	CCDS5591.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.222273	0.79464	.	.	ENSG00000127951	ENST00000248598	D	0.83250	-1.7	6.03	6.03	0.97812	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.041868	0.85682	D	0.000000	D	0.91758	0.7393	M	0.87097	2.86	0.80722	D	1	D	0.56746	0.977	D	0.64776	0.929	D	0.92972	0.6398	10	0.87932	D	0	.	16.2196	0.82251	0.0:0.0:0.0:1.0	.	287	Q14314	FGL2_HUMAN	G	287	ENSP00000248598:D287G	ENSP00000248598:D287G	D	-	2	0	FGL2	76663992	1.000000	0.71417	0.983000	0.44433	0.950000	0.60333	7.698000	0.84413	2.308000	0.77769	0.533000	0.62120	GAT	.	.		0.423	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682		C	76826056	T	C	76826056	3	2	111	1	0	0	0	0	1	0	0	0	5881	1435	50	2	463	2	FGL2	7	76826056	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	32675693	76826056	82312607	150	16390										
CCDC132	55610	hgsc.bcm.edu	37	chr7	92952972	92952972	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aagccaattgcctttgatgtTattcatttcatgtctcaact	5	9	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:92952972T>A	ENST00000305866.5	+	21	2033	c.1905T>A	c.(1903-1905)gtT>gtA	p.V635V	CCDC132_ENST00000535481.1_Silent_p.V355V|CCDC132_ENST00000541136.1_Silent_p.V446V|CCDC132_ENST00000544910.1_Silent_p.V605V	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	635						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			CCTTTGATGTTATTCATTTCA	0.279																																					p.V635V		Atlas-SNP	.											.	CCDC132	136	.	0			c.T1905A						.						79	74	75					7																	92952972		1802	4062	5864	SO:0001819	synonymous_variant	55610	exon21			TGATGTTATTCAT	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1905T>A	chr7.hg19:g.92952972T>A		59.0	0.0		39.0	9.0	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Silent	SNP	ENST00000305866.5	hg19	CCDS43617.1																																																																																			.	.		0.279	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		A	92952972	T	A	92952972	2	1	111	1	0	0	0	0	0	0	0	1	2769	1741	61	4		4	CCDC132	7	92952972	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	16126916	92952972	66185691	151	16391										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98508787	98508787	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aggagaaggaggtattggagCatttcgctggtgtgttcaca	15	5	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:98508787C>T	ENST00000359863.4	+	17	2109	c.1900C>T	c.(1900-1902)Cat>Tat	p.H634Y	TRRAP_ENST00000446306.3_Missense_Mutation_p.H633Y|TRRAP_ENST00000355540.3_Missense_Mutation_p.H634Y	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	634					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GGTATTGGAGCATTTCGCTGG	0.443																																					p.H634Y		Atlas-SNP	.											.	TRRAP	863	.	0			c.C1900T						.						130	115	120					7																	98508787		2203	4300	6503	SO:0001583	missense	8295	exon17			TTGGAGCATTTCG	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.1900C>T	chr7.hg19:g.98508787C>T	ENSP00000352925:p.His634Tyr	136.0	0.0		100.0	4.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.540478	0.65085	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.43294	0.95;0.95	5.96	5.96	0.96718	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.33411	0.0862	L	0.31294	0.92	0.80722	D	1	P;B;B	0.41080	0.737;0.174;0.299	B;B;B	0.40329	0.326;0.062;0.052	T	0.10132	-1.0643	10	0.02654	T	1	.	20.422	0.99049	0.0:1.0:0.0:0.0	.	634;348;634	Q9Y4A5-2;Q59FH1;Q9Y4A5	.;.;TRRAP_HUMAN	Y	634;634;632	ENSP00000352925:H634Y;ENSP00000347733:H634Y	ENSP00000347733:H634Y	H	+	1	0	TRRAP	98346723	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	7.677000	0.84024	2.832000	0.97577	0.655000	0.94253	CAT	.	.		0.443	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		T	98508787	C	T	98508787	3	4	111	1	0	0	0	0	1	0	0	0	16616	710	25	3	1962	3	TRRAP	7	98508787	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	5555815	98508787	60629876	152	16392										
MUC17	140453	hgsc.bcm.edu	37	chr7	100696684	100696684	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acagtggaccagctcctgggAccttccaaaacattggcttt	9	12	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:100696684A>G	ENST00000306151.4	+	11	13394	c.13330A>G	c.(13330-13332)Acc>Gcc	p.T4444A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4444					cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AGCTCCTGGGACCTTCCAAAA	0.488																																					p.T4444A		Atlas-SNP	.											.	MUC17	804	.	0			c.A13330G						.						96	93	94					7																	100696684		2203	4300	6503	SO:0001583	missense	140453	exon11			CCTGGGACCTTCC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.13330A>G	chr7.hg19:g.100696684A>G	ENSP00000302716:p.Thr4444Ala	106.0	0.0		105.0	6.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	6.086	0.384094	0.11524	.	.	ENSG00000169876	ENST00000306151	T	0.02140	4.43	5.49	1.53	0.23141	.	.	.	.	.	T	0.01765	0.0056	L	0.42245	1.32	0.22378	N	0.999153	P	0.50156	0.932	B	0.38954	0.286	T	0.37820	-0.9689	9	0.10377	T	0.69	.	3.3769	0.07241	0.6159:0.0:0.1799:0.2042	.	4444	Q685J3	MUC17_HUMAN	A	4444	ENSP00000302716:T4444A	ENSP00000302716:T4444A	T	+	1	0	MUC17	100483404	0.870000	0.30015	0.972000	0.41901	0.347000	0.29111	0.450000	0.21762	0.001000	0.14605	-0.280000	0.10049	ACC	.	.		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100696684	A	G	100696684	3	3	111	1	0	0	0	0	1	0	0	0	9983	275	10	2	13372	2	MUC17	7	100696684	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	2187897	100696684	58441979	153	16393										
LRRC17	10234	hgsc.bcm.edu	37	chr7	102575006	102575006	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aacagttgtgtaatgaagaaGaaaaggaacaattggacccg	11	5	0	3	rs80100722		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:102575006G>A	ENST00000339431.4	+	2	941	c.646G>A	c.(646-648)Gaa>Aaa	p.E216K	FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000393772.2_Intron|LRRC17_ENST00000249377.4_Missense_Mutation_p.E216K|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000455112.2_Intron	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	216					bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						TAATGAAGAAGAAAAGGAACA	0.433																																					p.E216K		Atlas-SNP	.											.	LRRC17	45	.	0			c.G646A						.						38	39	39					7																	102575006		2157	4282	6439	SO:0001583	missense	10234	exon2			GAAGAAGAAAAGG	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.646G>A	chr7.hg19:g.102575006G>A	ENSP00000344242:p.Glu216Lys	43.0	0.0		32.0	5.0	NM_005824	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	hg19	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.553100	0.45487	.	.	ENSG00000128606	ENST00000339431;ENST00000249377	T;T	0.63096	0.27;-0.02	5.28	4.33	0.51752	.	0.223034	0.31031	N	0.008387	T	0.50069	0.1594	L	0.55481	1.735	0.09310	N	1	B;B	0.28933	0.146;0.228	B;B	0.30855	0.038;0.121	T	0.41574	-0.9501	10	0.05959	T	0.93	-21.2297	9.2511	0.37555	0.0765:0.1469:0.7766:0.0	.	216;216	Q8N6Y2;Q8N6Y2-2	LRC17_HUMAN;.	K	216	ENSP00000344242:E216K;ENSP00000249377:E216K	ENSP00000249377:E216K	E	+	1	0	LRRC17	102362242	0.526000	0.26298	0.605000	0.28930	0.985000	0.73830	1.553000	0.36255	2.617000	0.88574	0.563000	0.77884	GAA	.	.		0.433	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824		A	102575006	G	A	102575006	3	1	111	1	0	0	0	0	1	0	0	0	8982	943	33	3	648	3	LRRC17	7	102575006	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	1878322	102575006	56563657	154	16394										
DLD	1738	hgsc.bcm.edu	37	chr7	107533711	107533711	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cagtgcctctgagaacttacGcagatcagccgagtaagtac	10	11	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:107533711G>A	ENST00000205402.5	+	2	387	c.106G>A	c.(106-108)Gca>Aca	p.A36T	DLD_ENST00000440410.1_Missense_Mutation_p.A36T|DLD_ENST00000537148.1_5'UTR|DLD_ENST00000494441.1_3'UTR|DLD_ENST00000437604.2_Missense_Mutation_p.A36T	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	36					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	GAGAACTTACGCAGATCAGCC	0.358																																					p.A36T		Atlas-SNP	.											.	DLD	72	.	0			c.G106A						.						102	99	100					7																	107533711		2203	4300	6503	SO:0001583	missense	1738	exon2			ACTTACGCAGATC	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.106G>A	chr7.hg19:g.107533711G>A	ENSP00000205402:p.Ala36Thr	78.0	0.0		65.0	4.0	NM_000108	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Missense_Mutation	SNP	ENST00000205402.5	hg19	CCDS5749.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.059091	0.36373	.	.	ENSG00000091140	ENST00000205402;ENST00000417551;ENST00000440410;ENST00000437604	T;T;T;T	0.70045	-0.4;-0.4;-0.41;-0.45	5.03	2.23	0.28157	.	0.240755	0.41294	N	0.000910	T	0.40094	0.1103	N	0.08118	0	0.80722	D	1	B;B;B	0.15141	0.012;0.012;0.012	B;B;B	0.08055	0.003;0.002;0.003	T	0.09840	-1.0656	10	0.44086	T	0.13	-16.0112	5.0545	0.14525	0.1588:0.0:0.5504:0.2907	.	36;36;36	E9PEX6;B4DT69;P09622	.;.;DLDH_HUMAN	T	36	ENSP00000205402:A36T;ENSP00000390667:A36T;ENSP00000417016:A36T;ENSP00000387542:A36T	ENSP00000205402:A36T	A	+	1	0	DLD	107320947	0.970000	0.33590	0.589000	0.28718	0.410000	0.31052	1.287000	0.33284	0.289000	0.22422	0.467000	0.42956	GCA	.	.		0.358	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108		A	107533711	G	A	107533711	3	1	111	1	0	0	0	0	1	0	0	0	4553	1087	38	1	112	1	DLD	7	107533711	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	4958705	107533711	51604952	155	16395										
LRRN3	54674	hgsc.bcm.edu	37	chr7	110764889	110764889	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ataaatctctgggaagcaggAaaagaaaaaagtacatcact	8	6	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:110764889A>G	ENST00000422987.3	+	2	2892	c.2061A>G	c.(2059-2061)ggA>ggG	p.G687G	LRRN3_ENST00000451085.1_Silent_p.G687G|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000452895.1_Intron|LRRN3_ENST00000308478.5_Silent_p.G687G|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000405709.2_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	687					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		GGGAAGCAGGAAAAGAAAAAA	0.378																																					p.G687G		Atlas-SNP	.											.	LRRN3	132	.	0			c.A2061G						.						67	72	70					7																	110764889		2203	4300	6503	SO:0001819	synonymous_variant	54674	exon2			AGCAGGAAAAGAA	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17200	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 5"					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.2061A>G	chr7.hg19:g.110764889A>G		14.0	0.0		22.0	4.0	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	hg19	CCDS5754.1																																																																																			.	.		0.378	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		G	110764889	A	G	110764889	2	3	111	1	0	0	0	0	0	0	0	1	9045	233	9	2		2	LRRN3	7	110764889	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	3231178	110764889	48373774	156	16396										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121636505	121636505	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cagccttcttgttacatgggAaagacctcgagtcgtttatg	10	9	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:121636505A>G	ENST00000393386.2	+	9	1409	c.998A>G	c.(997-999)gAa>gGa	p.E333G	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.E333G	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	333	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GTTACATGGGAAAGACCTCGA	0.398																																					p.E333G		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.A998G						.						118	113	115					7																	121636505		2203	4300	6503	SO:0001583	missense	5803	exon9			CATGGGAAAGACC	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.998A>G	chr7.hg19:g.121636505A>G	ENSP00000377047:p.Glu333Gly	99.0	0.0		93.0	4.0	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	A	14.59	2.582125	0.46006	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.59364	0.27;0.27	5.92	5.92	0.95590	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.150633	0.46442	D	0.000283	T	0.62575	0.2439	L	0.27053	0.805	0.34971	D	0.753186	D;D	0.76494	0.999;0.999	D;D	0.75020	0.961;0.985	T	0.73291	-0.4029	10	0.72032	D	0.01	.	10.6656	0.45728	0.929:0.0:0.071:0.0	.	333;333	C9JFM0;P23471	.;PTPRZ_HUMAN	G	333	ENSP00000377047:E333G;ENSP00000410000:E333G	ENSP00000377047:E333G	E	+	2	0	PTPRZ1	121423741	1.000000	0.71417	0.997000	0.53966	0.501000	0.33797	5.812000	0.69194	2.266000	0.75297	0.533000	0.62120	GAA	.	.		0.398	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		G	121636505	A	G	121636505	3	3	111	1	0	0	0	0	1	0	0	0	12829	246	9	2	1032	2	PTPRZ1	7	121636505	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	10871616	121636505	37502158	157	16397										
MKLN1	4289	hgsc.bcm.edu	37	chr7	131084062	131084062	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agacaacacaactatacagaAgcttttgagtcactgcaaaa	6	9	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:131084062A>G	ENST00000352689.6	+	6	613	c.573A>G	c.(571-573)gaA>gaG	p.E191E	MKLN1_ENST00000429546.1_3'UTR|MKLN1_ENST00000421797.2_Silent_p.E99E	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	191	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					ACTATACAGAAGCTTTTGAGT	0.393																																					p.E191E		Atlas-SNP	.											.	MKLN1	67	.	0			c.A573G						.						147	148	148					7																	131084062		2203	4300	6503	SO:0001819	synonymous_variant	4289	exon6			TACAGAAGCTTTT	AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.573A>G	chr7.hg19:g.131084062A>G		120.0	0.0		100.0	4.0	NM_013255	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Silent	SNP	ENST00000352689.6	hg19	CCDS34754.1																																																																																			.	.		0.393	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255		G	131084062	A	G	131084062	2	3	111	1	0	0	0	0	0	0	0	1	9612	69	3	2		2	MKLN1	7	131084062	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	9447557	131084062	28054601	158	16398										
CLCN1	1180	hgsc.bcm.edu	37	chr7	143043238	143043238	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tactcttccttacagcttccTccttcccttgctctccaccc	2	20	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:143043238T>C	ENST00000343257.2	+	18	2265	c.2178T>C	c.(2176-2178)ccT>ccC	p.P726P		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	726					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					TACAGCTTCCTCCTTCCCTTG	0.577																																					p.P726P		Atlas-SNP	.											.	CLCN1	141	.	0			c.T2178C						.						105	96	99					7																	143043238		2203	4300	6503	SO:0001819	synonymous_variant	1180	exon18			GCTTCCTCCTTCC	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.2178T>C	chr7.hg19:g.143043238T>C		153.0	0.0		113.0	5.0	NM_000083	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	hg19	CCDS5881.1																																																																																			.	.		0.577	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		C	143043238	T	C	143043238	2	2	111	1	0	0	0	0	0	0	0	1	3464	1538	54	2		2	CLCN1	7	143043238	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	11959176	143043238	16095425	159	16399										
LMBR1	64327	hgsc.bcm.edu	37	chr7	156685632	156685632	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccccacgcaccgtggactccCgcacttggctgtggaagtgc	12	16	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr7:156685632C>A	ENST00000353442.5	-	1	292	c.56G>T	c.(55-57)cGg>cTg	p.R19L	LMBR1_ENST00000540390.1_Silent_p.A22A|LMBR1_ENST00000354505.4_Missense_Mutation_p.R19L	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	19					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		CGTGGACTCCCGCACTTGGCT	0.776																																					p.R19L		Atlas-SNP	.											.	LMBR1	35	.	0			c.G56T						.						21	18	19					7																	156685632		2182	4284	6466	SO:0001583	missense	64327	exon1			GACTCCCGCACTT	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"chromosome 7 open reading frame 2", "limb region 1 homolog (mouse)"	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.56G>T	chr7.hg19:g.156685632C>A	ENSP00000326604:p.Arg19Leu	46.0	0.0		18.0	4.0	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Missense_Mutation	SNP	ENST00000353442.5	hg19	CCDS5945.1	.	.	.	.	.	.	.	.	.	.	C	18.26	3.585764	0.66105	.	.	ENSG00000105983	ENST00000353442;ENST00000415428;ENST00000354505;ENST00000347571	T;T;T	0.59906	0.27;0.24;0.23	3.29	3.29	0.37713	.	0.210739	0.30800	U	0.008846	T	0.50803	0.1637	L	0.46819	1.47	0.80722	D	1	B;B	0.23128	0.08;0.001	B;B	0.25506	0.061;0.002	T	0.57365	-0.7824	10	0.87932	D	0	-0.9976	12.5562	0.56254	0.0:1.0:0.0:0.0	.	19;19	Q8WVP7-3;Q8WVP7	.;LMBR1_HUMAN	L	19;17;19;19	ENSP00000326604:R19L;ENSP00000408256:R17L;ENSP00000346500:R19L	ENSP00000337803:R19L	R	-	2	0	LMBR1	156378393	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.259000	0.51515	1.676000	0.50930	0.298000	0.19748	CGG	.	.		0.776	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458		A	156685632	C	A	156685632	3	1	111	1	0	0	0	0	1	0	0	0	8849	652	23	1	1484	1	LMBR1	7	156685632	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	13642394	156685632	2453031	160	16400										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52287209	52287209	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aacaaacaggcacataagtgTtggtcccactcttgtaccag	8	11	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr8:52287209T>C	ENST00000356297.4	-	18	3740	c.3640A>G	c.(3640-3642)Aca>Gca	p.T1214A	PXDNL_ENST00000543296.1_Missense_Mutation_p.T1214A	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1214					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CACATAAGTGTTGGTCCCACT	0.443																																					p.T1214A		Atlas-SNP	.											.	PXDNL	414	.	0			c.A3640G						.						85	86	86					8																	52287209		1956	4149	6105	SO:0001583	missense	137902	exon18			TAAGTGTTGGTCC		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.3640A>G	chr8.hg19:g.52287209T>C	ENSP00000348645:p.Thr1214Ala	52.0	0.0		56.0	4.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.157073	0.38119	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.79247	-1.25;-1.25	4.63	4.63	0.57726	.	0.131624	0.33631	N	0.004705	D	0.90307	0.6968	H	0.95224	3.64	0.39215	D	0.963384	D	0.76494	0.999	D	0.76575	0.988	D	0.91827	0.5472	10	0.37606	T	0.19	.	11.974	0.53081	0.0:0.0:0.0:1.0	.	1214	A1KZ92	PXDNL_HUMAN	A	1214	ENSP00000348645:T1214A;ENSP00000444865:T1214A	ENSP00000348645:T1214A	T	-	1	0	PXDNL	52449762	1.000000	0.71417	0.057000	0.19452	0.029000	0.11900	6.932000	0.75869	1.732000	0.51606	0.459000	0.35465	ACA	.	.		0.443	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		C	52287209	T	C	52287209	3	2	111	1	0	0	0	0	1	0	0	0	12863	1725	60	2	775	2	PXDNL	8	52287209	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		52287209	94076813	161	16401										
NKAIN3	286183	hgsc.bcm.edu	37	chr8	63492222	63492222	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaccattcagtacagacctcGatacataatggtggtaagtc	9	9	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr8:63492222G>A	ENST00000523211.1	+	2	311	c.179G>A	c.(178-180)cGa>cAa	p.R60Q	NKAIN3_ENST00000519049.1_3'UTR|NKAIN3_ENST00000328472.5_Missense_Mutation_p.R60Q	NM_173688.2	NP_775959.1	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(3)|large_intestine(2)|lung(8)	13	Breast(64;0.127)	Lung NSC(129;0.187)				TACAGACCTCGATACATAATG	0.323																																					p.R60Q		Atlas-SNP	.											NKAIN3,caecum,carcinoma,0,1	NKAIN3	32	.	0			c.G179A						.						149	135	140					8																	63492222		1808	4080	5888	SO:0001583	missense	286183	exon2			GACCTCGATACAT	AK096949	CCDS55239.1	8q12.3	2014-08-12	2007-10-04	2007-10-04	ENSG00000185942	ENSG00000185942		"Na+/K+ transporting ATPase interacting"	26829	protein-coding gene	gene with protein product		612872	"family with sequence similarity 77, member D"	FAM77D		17606467	Standard	NM_173688		Approved	FLJ39630	uc010lyq.1	Q8N8D7	OTTHUMG00000164361	ENST00000523211.1:c.179G>A	chr8.hg19:g.63492222G>A	ENSP00000429073:p.Arg60Gln	46.0	0.0		61.0	3.0	NM_173688		Missense_Mutation	SNP	ENST00000523211.1	hg19	CCDS55239.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475329	0.63737	.	.	ENSG00000185942	ENST00000545532;ENST00000523211;ENST00000524201;ENST00000328472	T;T;T	0.17854	2.25;2.25;2.25	6.01	5.14	0.70334	.	0.000000	0.64402	D	0.000011	T	0.47746	0.1462	M	0.87682	2.9	0.46542	D	0.999091	D	0.89917	1.0	D	0.87578	0.998	T	0.56697	-0.7936	10	0.72032	D	0.01	-24.0867	14.5325	0.67936	0.0699:0.0:0.9301:0.0	.	60	Q8N8D7	NKAI3_HUMAN	Q	60	ENSP00000429073:R60Q;ENSP00000429393:R60Q;ENSP00000333627:R60Q	ENSP00000333627:R60Q	R	+	2	0	NKAIN3	63654776	1.000000	0.71417	0.991000	0.47740	0.008000	0.06430	7.993000	0.88291	1.557000	0.49525	0.650000	0.86243	CGA	.	.		0.323	NKAIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378447.2	NM_173688		A	63492222	G	A	63492222	3	1	111	1	0	0	0	0	1	0	0	0	10446	1058	37	1	185	1	NKAIN3	8	63492222	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	11205013	63492222	82871800	162	16402										
TMEM67	91147	hgsc.bcm.edu	37	chr8	94827602	94827602	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcttcttatttttgatctgcTgttcttctgtgttgtggatt	8	6	5	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr8:94827602T>C	ENST00000453321.3	+	27	2892	c.2834T>C	c.(2833-2835)cTg>cCg	p.L945P	TMEM67_ENST00000409623.3_Missense_Mutation_p.L864P	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	945					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			TTTGATCTGCTGTTCTTCTGT	0.284																																					p.L945P		Atlas-SNP	.											.	TMEM67	187	.	0			c.T2834C						.						127	113	118					8																	94827602		2203	4295	6498	SO:0001583	missense	91147	exon27			ATCTGCTGTTCTT	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.2834T>C	chr8.hg19:g.94827602T>C	ENSP00000389998:p.Leu945Pro	78.0	0.0		86.0	4.0	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	SNP	ENST00000453321.3	hg19	CCDS6258.2	.	.	.	.	.	.	.	.	.	.	T	22.7	4.322436	0.81580	.	.	ENSG00000164953	ENST00000453321;ENST00000409623	D;D	0.97924	-4.61;-4.61	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000002	D	0.98751	0.9580	M	0.84585	2.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.984;0.988	D	0.99816	1.1044	10	0.87932	D	0	-6.1695	16.0711	0.80936	0.0:0.0:0.0:1.0	.	945;864	Q5HYA8;G5E9H2	MKS3_HUMAN;.	P	945;864	ENSP00000389998:L945P;ENSP00000386966:L864P	ENSP00000314488:L935P	L	+	2	0	TMEM67	94896778	1.000000	0.71417	0.980000	0.43619	0.976000	0.68499	7.670000	0.83925	2.197000	0.70478	0.482000	0.46254	CTG	.	.		0.284	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		C	94827602	T	C	94827602	3	2	111	1	0	0	0	0	1	0	0	0	16211	1580	55	2	3078	2	TMEM67	8	94827602	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	31335380	94827602	51536420	163	16403										
CDH17	1015	hgsc.bcm.edu	37	chr8	95161099	95161099	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cttgtgtctcccctcagtgaAtagcttcatcaaatgaaaag	7	10	4	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr8:95161099A>G	ENST00000027335.3	-	14	1924	c.1800T>C	c.(1798-1800)taT>taC	p.Y600Y	CDH17_ENST00000450165.2_Silent_p.Y600Y|CDH17_ENST00000441892.2_Silent_p.Y386Y	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	600	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			CCCTCAGTGAATAGCTTCATC	0.423																																					p.Y600Y		Atlas-SNP	.											.	CDH17	119	.	0			c.T1800C						.						104	88	93					8																	95161099		2203	4300	6503	SO:0001819	synonymous_variant	1015	exon14			CAGTGAATAGCTT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1800T>C	chr8.hg19:g.95161099A>G		118.0	0.0		97.0	4.0	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	hg19	CCDS6260.1																																																																																			.	.		0.423	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		G	95161099	A	G	95161099	2	3	111	1	0	0	0	0	0	0	0	1	3104	108	4	2		2	CDH17	8	95161099	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	333497	95161099	51202923	164	16404										
LRRC24	441381	hgsc.bcm.edu	37	chr8	145748075	145748075	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tagtcgttgacgaacagcgcTccctcccccggaggcccccg	11	18	0	1	rs112652028	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr8:145748075T>C	ENST00000529415.2	-	5	1443	c.1326A>G	c.(1324-1326)ggA>ggG	p.G442G	LRRC14_ENST00000292524.1_3'UTR|LRRC24_ENST00000533758.1_Silent_p.G439G|LRRC14_ENST00000528528.1_3'UTR			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	442						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CGAACAGCGCTCCCTCCCCCG	0.682																																					p.G442G		Atlas-SNP	.											.	LRRC24	11	.	0			c.A1326G						.						13	14	14					8																	145748075		2172	4286	6458	SO:0001819	synonymous_variant	441381	exon5			CAGCGCTCCCTCC	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"Immunoglobulin superfamily / I-set domain containing"	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.1326A>G	chr8.hg19:g.145748075T>C		64.0	0.0		153.0	8.0	NM_001024678		Silent	SNP	ENST00000529415.2	hg19	CCDS34969.1																																																																																			.	T|0.986;G|0.014		0.682	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678		C	145748075	T	C	145748075	2	2	111	1	0	0	0	0	0	0	0	1	8988	1538	54	2		2	LRRC24	8	145748075	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	50586976	145748075	615947	165	16405										
SLC1A1	6505	hgsc.bcm.edu	37	chr9	4490708	4490708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	accggcgaggaaaggatgcgAgtggaagcgcttcctgaaga	16	8	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:4490708A>G	ENST00000262352.3	+	1	265	c.29A>G	c.(28-30)gAg>gGg	p.E10G		NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	10				E -> PS (in Ref. 3; AAA50430). {ECO:0000305}.	D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	AAAGGATGCGAGTGGAAGCGC	0.692																																					p.E10G		Atlas-SNP	.											.	SLC1A1	43	.	0			c.A29G						.						139	113	122					9																	4490708		2203	4300	6503	SO:0001583	missense	6505	exon1			GATGCGAGTGGAA		CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"Solute carriers"	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.29A>G	chr9.hg19:g.4490708A>G	ENSP00000262352:p.Glu10Gly	145.0	0.0		83.0	4.0	NM_004170	O75587|Q5VZ24|Q8N199|Q9UEW2	Missense_Mutation	SNP	ENST00000262352.3	hg19	CCDS6452.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.044083	0.55110	.	.	ENSG00000106688	ENST00000262352	T	0.56444	0.46	5.38	5.38	0.77491	.	0.281433	0.38436	N	0.001687	T	0.37517	0.1006	N	0.19112	0.55	0.31135	N	0.707303	B	0.02656	0.0	B	0.04013	0.001	T	0.39396	-0.9616	10	0.42905	T	0.14	.	11.7645	0.51922	1.0:0.0:0.0:0.0	.	10	P43005	EAA3_HUMAN	G	10	ENSP00000262352:E10G	ENSP00000262352:E10G	E	+	2	0	SLC1A1	4480708	1.000000	0.71417	0.993000	0.49108	0.759000	0.43091	4.010000	0.57117	2.026000	0.59711	0.459000	0.35465	GAG	.	.		0.692	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1			G	4490708	A	G	4490708	3	3	111	1	0	0	0	0	1	0	0	0	14446	304	11	2	31	2	SLC1A1	9	4490708	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10		4490708	136722723	166	16406										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5920644	5920644	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggtgaatggaactggagtgaAgtccgagattgtcttttaga	14	4	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:5920644A>G	ENST00000399933.3	-	8	5351	c.5352T>C	c.(5350-5352)acT>acC	p.T1784T	KIAA2026_ENST00000381461.2_Silent_p.T1754T	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1784										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		ACTGGAGTGAAGTCCGAGATT	0.423																																					p.T1784T		Atlas-SNP	.											.	KIAA2026	231	.	0			c.T5352C						.						359	352	355					9																	5920644		1943	4133	6076	SO:0001819	synonymous_variant	158358	exon8			GAGTGAAGTCCGA	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.5352T>C	chr9.hg19:g.5920644A>G		140.0	0.0		89.0	5.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	hg19																																																																																				.	.		0.423	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		G	5920644	A	G	5920644	2	3	111	1	0	0	0	0	0	0	0	1	8279	59	3	2		2	KIAA2026	9	5920644	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1429936	5920644	135292787	167	16407										
IFNW1	3467	hgsc.bcm.edu	37	chr9	21141108	21141108	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcgctgtatttcttctctttCaggtagacacggattccctg	8	11	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:21141108C>T	ENST00000380229.2	-	1	1036	c.462G>A	c.(460-462)ctG>ctA	p.L154L		NM_002177.1	NP_002168.1	P05000	IFNW1_HUMAN	interferon, omega 1	154					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cell cycle arrest (GO:0007050)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|lung(2)|ovary(1)	5				GBM - Glioblastoma multiforme(5;2.35e-185)|Lung(24;2.24e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		TCTTCTCTTTCAGGTAGACAC	0.473																																					p.L154L		Atlas-SNP	.											.	IFNW1	20	.	0			c.G462A						.						98	93	94					9																	21141108		2203	4300	6503	SO:0001819	synonymous_variant	3467	exon1			CTCTTTCAGGTAG		CCDS6496.1	9p22	2010-12-10			ENSG00000177047	ENSG00000177047		"Interferons"	5448	protein-coding gene	gene with protein product	"IFN-omega 1, interferon omega-1"	147553				1385305	Standard	NM_002177		Approved		uc003zol.1	P05000	OTTHUMG00000019656	ENST00000380229.2:c.462G>A	chr9.hg19:g.21141108C>T		77.0	0.0		80.0	4.0	NM_002177	Q13168|Q5U802|Q5VWD0|Q7M4P5	Silent	SNP	ENST00000380229.2	hg19	CCDS6496.1																																																																																			.	.		0.473	IFNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051885.1	NM_002177		T	21141108	C	T	21141108	2	4	111	1	0	0	0	0	0	0	0	1	7561	813	29	3		3	IFNW1	9	21141108	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	15220464	21141108	120072323	168	16408										
C9orf72	203228	hgsc.bcm.edu	37	chr9	27548315	27548315	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaagagtgtaggcctggtttAattttctcagccagagccat	10	8	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:27548315A>C	ENST00000380003.3	-	11	1428	c.1365T>G	c.(1363-1365)atT>atG	p.I455M	C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	455					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		GGCCTGGTTTAATTTTCTCAG	0.378																																					p.I455M		Atlas-SNP	.											.	C9orf72	48	.	0			c.T1365G						.						110	111	111					9																	27548315		2203	4300	6503	SO:0001583	missense	203228	exon11			TGGTTTAATTTTC	AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.1365T>G	chr9.hg19:g.27548315A>C	ENSP00000369339:p.Ile455Met	64.0	0.0		61.0	15.0	NM_018325	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Missense_Mutation	SNP	ENST00000380003.3	hg19	CCDS6522.1	.	.	.	.	.	.	.	.	.	.	A	12.41	1.929733	0.34096	.	.	ENSG00000147894	ENST00000380003	T	0.47528	0.84	5.75	2.13	0.27403	.	0.158723	0.56097	D	0.000023	T	0.21186	0.0510	N	0.08118	0	0.80722	D	1	P	0.39157	0.662	B	0.34180	0.177	T	0.03296	-1.1051	9	.	.	.	.	7.9488	0.30001	0.5824:0.0:0.4176:0.0	.	455	Q96LT7	CI072_HUMAN	M	455	ENSP00000369339:I455M	.	I	-	3	3	C9orf72	27538315	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.279000	0.33191	0.465000	0.27167	0.374000	0.22700	ATT	.	.		0.378	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325		C	27548315	A	C	27548315	3	2	111	1	0	0	0	0	1	0	0	0	2497	358	13	5	84	5	C9orf72	9	27548315	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	6407207	27548315	113665116	169	16409										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35378361	35378361	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cccttacgtgactgtgcaagTcagcaaaactaagaagcgta	9	10	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:35378361T>C	ENST00000378495.3	+	16	2108	c.1886T>C	c.(1885-1887)gTc>gCc	p.V629A	UNC13B_ENST00000396787.1_Missense_Mutation_p.V641A|UNC13B_ENST00000378496.4_Missense_Mutation_p.V629A	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	629	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			ACTGTGCAAGTCAGCAAAACT	0.473																																					p.V629A		Atlas-SNP	.											.	UNC13B	153	.	0			c.T1886C						.						162	146	152					9																	35378361		2203	4300	6503	SO:0001583	missense	10497	exon16			TGCAAGTCAGCAA	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.1886T>C	chr9.hg19:g.35378361T>C	ENSP00000367756:p.Val629Ala	109.0	0.0		93.0	4.0	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	hg19	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.760325	0.89932	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.71222	-0.55;-0.55;-0.55	5.54	5.54	0.83059	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.80270	0.4592	L	0.48935	1.535	0.80722	D	1	D;D	0.76494	0.957;0.999	P;D	0.91635	0.764;0.999	T	0.82252	-0.0549	10	0.87932	D	0	-16.0502	15.6673	0.77238	0.0:0.0:0.0:1.0	.	629;629	F8W8M9;O14795	.;UN13B_HUMAN	A	641;629;629;216	ENSP00000380006:V641A;ENSP00000367756:V629A;ENSP00000367757:V629A	ENSP00000367756:V629A	V	+	2	0	UNC13B	35368361	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	7.945000	0.87732	2.119000	0.64992	0.477000	0.44152	GTC	.	.		0.473	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		C	35378361	T	C	35378361	3	2	111	1	0	0	0	0	1	0	0	0	17000	1667	58	2	1948	2	UNC13B	9	35378361	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	7830046	35378361	105835070	170	16410										
RECK	8434	hgsc.bcm.edu	37	chr9	36052297	36052297	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atcattcaaaggataaccaaAtgtgccgtgatgtatgtgaa	9	6	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:36052297A>G	ENST00000377966.3	+	2	702	c.136A>G	c.(136-138)Atg>Gtg	p.M46V	RECK_ENST00000479053.1_3'UTR	NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	46	5 X Knot repeats.				blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			GGATAACCAAATGTGCCGTGA	0.398																																					p.M46V		Atlas-SNP	.											.	RECK	73	.	0			c.A136G						.						167	142	150					9																	36052297		2203	4300	6503	SO:0001583	missense	8434	exon2			AACCAAATGTGCC	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.136A>G	chr9.hg19:g.36052297A>G	ENSP00000367202:p.Met46Val	133.0	0.0		97.0	4.0	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Missense_Mutation	SNP	ENST00000377966.3	hg19	CCDS6597.1	.	.	.	.	.	.	.	.	.	.	A	14.35	2.508913	0.44660	.	.	ENSG00000122707	ENST00000377966	T	0.41065	1.01	5.42	5.42	0.78866	.	0.109107	0.64402	D	0.000007	T	0.42449	0.1203	N	0.14661	0.345	0.37086	D	0.899205	P;B;B	0.40332	0.713;0.165;0.452	P;B;P	0.54815	0.761;0.031;0.455	T	0.54741	-0.8248	10	0.66056	D	0.02	-18.4722	11.8478	0.52395	1.0:0.0:0.0:0.0	.	46;46;46	B2RCE6;O95980;Q6P9E2	.;RECK_HUMAN;.	V	46	ENSP00000367202:M46V	ENSP00000367202:M46V	M	+	1	0	RECK	36042297	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.061000	0.64319	2.067000	0.61834	0.533000	0.62120	ATG	.	.		0.398	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1			G	36052297	A	G	36052297	3	3	111	1	0	0	0	0	1	0	0	0	13215	101	4	2	142	2	RECK	9	36052297	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	673936	36052297	105161134	171	16411										
PCSK5	5125	hgsc.bcm.edu	37	chr9	78790032	78790032	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cccacagacgactatggcacAgaggattatgcaggtgagct	12	10	0	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:78790032A>G	ENST00000545128.1	+	14	2425	c.1887A>G	c.(1885-1887)acA>acG	p.T629T	PCSK5_ENST00000376752.4_Silent_p.T629T|PCSK5_ENST00000376767.3_Silent_p.T629T	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	629					anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						ACTATGGCACAGAGGATTATG	0.517																																					p.T629T		Atlas-SNP	.											.	PCSK5	329	.	0			c.A1887G						.						107	102	104					9																	78790032		2203	4300	6503	SO:0001819	synonymous_variant	5125	exon14			TGGCACAGAGGAT		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1887A>G	chr9.hg19:g.78790032A>G		105.0	0.0		83.0	4.0	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	hg19	CCDS55320.1																																																																																			.	.		0.517	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	78790032	A	G	78790032	2	3	111	1	0	0	0	0	0	0	0	1	11612	175	7	2		2	PCSK5	9	78790032	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	42737735	78790032	62423399	172	16412										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87475992	87475992	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tttgggaaagtaaaatcaagAcaaggtgttggtaagtagtt	12	2	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:87475992A>G	ENST00000323115.4	+	12	1749				NTRK2_ENST00000304053.6_Silent_p.R478R|NTRK2_ENST00000376213.1_Intron|NTRK2_ENST00000376208.1_Intron|NTRK2_ENST00000277120.3_Silent_p.R478R|NTRK2_ENST00000376214.1_Silent_p.R478R			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	TAAAATCAAGACAAGGTGTTG	0.358										TSP Lung(25;0.17)																											p.R478R		Atlas-SNP	.											.	NTRK2	331	.	0			c.A1434G						.						170	152	158					9																	87475992		2203	4300	6503	SO:0001627	intron_variant	4915	exon13			ATCAAGACAAGGT	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.1397-6166A>G	chr9.hg19:g.87475992A>G		131.0	0.0		92.0	4.0	NM_001018065	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Silent	SNP	ENST00000323115.4	hg19	CCDS35050.1																																																																																			.	.		0.358	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			G	87475992	A	G	87475992	1	3	111	0	1	0	0	0	0	0	0	0	10716	272	10	2		2	NTRK2	9	87475992	Intron	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	8685960	87475992	53737439	173	16413										
SEMA4D	10507	hgsc.bcm.edu	37	chr9	92020314	92020314	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gggtgcaaatgccatcgctgTcccaaacatcactgcaaggg	11	12	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:92020314T>C	ENST00000450295.1	-	3	834	c.58A>G	c.(58-60)Aca>Gca	p.T20A	SEMA4D_ENST00000339861.4_Missense_Mutation_p.T20A|SEMA4D_ENST00000420987.1_Missense_Mutation_p.T20A|SEMA4D_ENST00000438547.2_Missense_Mutation_p.T20A|SEMA4D_ENST00000422704.2_Missense_Mutation_p.T20A|SEMA4D_ENST00000455551.2_Missense_Mutation_p.T20A|SEMA4D_ENST00000343780.4_Missense_Mutation_p.T20A|SEMA4D_ENST00000356444.2_Missense_Mutation_p.T20A			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	20					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						GCCATCGCTGTCCCAAACATC	0.607																																					p.T20A		Atlas-SNP	.											.	SEMA4D	81	.	0			c.A58G						.						105	95	98					9																	92020314		2203	4300	6503	SO:0001583	missense	10507	exon5			TCGCTGTCCCAAA	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"Semaphorins", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10732	protein-coding gene	gene with protein product	"M-sema G"	601866	"chromosome 9 open reading frame 164"	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.58A>G	chr9.hg19:g.92020314T>C	ENSP00000416523:p.Thr20Ala	88.0	0.0		76.0	4.0	NM_006378	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	hg19	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	T	6.807	0.518052	0.13005	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704;ENST00000420681;ENST00000433650;ENST00000540475;ENST00000418828	T;T;T;T;T;T;T;T;T;T	0.44881	2.14;2.14;2.14;2.14;2.12;2.12;2.12;2.12;0.98;0.91	4.51	0.873	0.19118	Semaphorin/CD100 antigen (1);	0.625976	0.14283	N	0.329384	T	0.25938	0.0632	L	0.41236	1.265	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.14023	0.01;0.002	T	0.32214	-0.9915	10	0.06625	T	0.88	.	6.2697	0.20947	0.0:0.3113:0.0:0.6887	.	20;20	Q92854-2;Q92854	.;SEM4D_HUMAN	A	20	ENSP00000344923:T20A;ENSP00000391733:T20A;ENSP00000411981:T20A;ENSP00000343418:T20A;ENSP00000416523:T20A;ENSP00000405102:T20A;ENSP00000348822:T20A;ENSP00000388768:T20A;ENSP00000390754:T20A;ENSP00000413352:T20A	ENSP00000344923:T20A	T	-	1	0	SEMA4D	91210134	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	0.436000	0.21526	-0.003000	0.14444	0.374000	0.22700	ACA	.	.		0.607	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378		C	92020314	T	C	92020314	3	2	111	1	0	0	0	0	1	0	0	0	14049	1667	58	2	3156	2	SEMA4D	9	92020314	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	4544322	92020314	49193117	174	16414										
FAM22F	54754	hgsc.bcm.edu	37	chr9	97080944	97080944	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cttcttggacttgctggcagGagaaggtgatgggctgaggc	17	7	1	3	rs150455117	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:97080944G>C	ENST00000253262.4	-	7	2094	c.2074C>G	c.(2074-2076)Cct>Gct	p.P692A	NUTM2F_ENST00000335456.7_Intron|NUTM2F_ENST00000341207.4_Missense_Mutation_p.P677A	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	692																	TTGCTGGCAGGAGAAGGTGAT	0.607																																					p.P692A		Atlas-SNP	.											.	FAM22F	72	.	0			c.C2074G						.						21	19	20					9																	97080944		1843	4069	5912	SO:0001583	missense	54754	exon7			TGGCAGGAGAAGG		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"family with sequence similarity 22, member F"	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.2074C>G	chr9.hg19:g.97080944G>C	ENSP00000253262:p.Pro692Ala	352.0	0.0		326.0	17.0	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Missense_Mutation	SNP	ENST00000253262.4	hg19	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.581686	0.00879	.	.	ENSG00000130950	ENST00000253262;ENST00000341207;ENST00000375347	T;T	0.14640	2.49;2.52	1.52	-3.04	0.05412	Nuclear Testis protein, C-terminal (1);	2.077270	0.02242	N	0.065820	T	0.12561	0.0305	L	0.56769	1.78	0.09310	N	1	B	0.13594	0.008	B	0.16289	0.015	T	0.30621	-0.9972	10	0.09084	T	0.74	.	5.0244	0.14378	0.1751:0.5512:0.2738:0.0	.	692	A1L443	FA22F_HUMAN	A	692;677;526	ENSP00000253262:P692A;ENSP00000343865:P677A	ENSP00000253262:P692A	P	-	1	0	FAM22F	96120765	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.495000	0.06443	-1.287000	0.02381	-0.518000	0.04402	CCT	.	.		0.607	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561		C	97080944	G	C	97080944	3	2	111	1	0	0	0	0	1	0	0	0	5550	1174	41	4	200	4	FAM22F	9	97080944	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	5060630	97080944	44132487	175	16415										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113169740	113169740	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aggcaagtcacattcaattgAaatgcaggatggtgcactgc	11	8	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:113169740A>G	ENST00000401783.2	-	38	8476	c.8140T>C	c.(8140-8142)Tca>Cca	p.S2714P	SVEP1_ENST00000374469.1_Missense_Mutation_p.S2691P|SVEP1_ENST00000297826.5_Missense_Mutation_p.S640P	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2714	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CATTCAATTGAAATGCAGGAT	0.463																																					p.S2714P		Atlas-SNP	.											.	SVEP1	326	.	0			c.T8140C						.						140	138	139					9																	113169740		1963	4173	6136	SO:0001583	missense	79987	exon38			CAATTGAAATGCA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8140T>C	chr9.hg19:g.113169740A>G	ENSP00000384917:p.Ser2714Pro	109.0	0.0		131.0	7.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	A	8.616	0.890207	0.17613	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	T;T;T	0.22539	1.95;1.95;1.95	5.87	5.87	0.94306	Sushi/SCR/CCP (1);	0.061117	0.64402	D	0.000002	T	0.08492	0.0211	N	0.01809	-0.71	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.28744	-1.0034	10	0.29301	T	0.29	.	10.5898	0.45304	0.9285:0.0:0.0715:0.0	.	2714	Q4LDE5	SVEP1_HUMAN	P	2714;2691;640;386	ENSP00000384917:S2714P;ENSP00000363593:S2691P;ENSP00000297826:S640P	ENSP00000297826:S640P	S	-	1	0	SVEP1	112209561	1.000000	0.71417	0.996000	0.52242	0.907000	0.53573	5.099000	0.64554	2.247000	0.74100	0.477000	0.44152	TCA	.	.		0.463	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	113169740	A	G	113169740	3	3	111	1	0	0	0	0	1	0	0	0	15435	246	9	2	2619	2	SVEP1	9	113169740	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	16088796	113169740	28043691	176	16416										
C5	727	hgsc.bcm.edu	37	chr9	123738976	123738976	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaacaagacaaagaaatgttAcctgggttgaataaaagcca	8	6	0	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:123738976A>G	ENST00000223642.1	-	29	3894		c.e29+1			NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5						activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	AAGAAATGTTACCTGGGTTGA	0.423																																					.		Atlas-SNP	.											.	C5	124	.	0			c.3864+2T>C						.						117	117	117					9																	123738976		2203	4300	6503	SO:0001630	splice_region_variant	727	exon30			AATGTTACCTGGG	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.3864+1T>C	chr9.hg19:g.123738976A>G		95.0	0.0		80.0	4.0	NM_001735	Q14CJ0|Q27I61	Splice_Site	SNP	ENST00000223642.1	hg19	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.858801	0.71834	.	.	ENSG00000106804	ENST00000223642	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5733	0.68226	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C5	122778797	1.000000	0.71417	0.980000	0.43619	0.818000	0.46254	6.503000	0.73699	2.024000	0.59613	0.460000	0.39030	.	.	.		0.423	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	Intron	G	123738976	A	G	123738976	5	3	111	1	0	0	0	0	0	0	1	0	2282	405	14	2	1216	2	C5	9	123738976	Splice_Site	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	10569236	123738976	17474455	177	16417										
C5	727	hgsc.bcm.edu	37	chr9	123776212	123776212	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cggagctggcttgcgacgacAcaacattcagtgaaagcttt	11	10	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:123776212A>G	ENST00000223642.1	-	17	2225	c.2196T>C	c.(2194-2196)tgT>tgC	p.C732C		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	732	Anaphylatoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00022}.				activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	TTGCGACGACACAACATTCAG	0.438																																					p.C732C		Atlas-SNP	.											.	C5	124	.	0			c.T2196C						.						169	145	153					9																	123776212		2203	4300	6503	SO:0001819	synonymous_variant	727	exon17			GACGACACAACAT	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.2196T>C	chr9.hg19:g.123776212A>G		129.0	0.0		87.0	4.0	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	hg19	CCDS6826.1																																																																																			.	.		0.438	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		G	123776212	A	G	123776212	2	3	111	1	0	0	0	0	0	0	0	1	2282	157	6	2		2	C5	9	123776212	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	37236	123776212	17437219	178	16418										
RAB14	51552	hgsc.bcm.edu	37	chr9	123952841	123952841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttatctcttacctagtgataTcatagaccataagagctccc	5	11	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:123952841T>C	ENST00000373840.4	-	4	512	c.275A>G	c.(274-276)gAt>gGt	p.D92G		NM_016322.3	NP_057406.2	P61106	RAB14_HUMAN	RAB14, member RAS oncogene family	92					embryo development (GO:0009790)|endocytic recycling (GO:0032456)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi to endosome transport (GO:0006895)|GTP catabolic process (GO:0006184)|intracellular transport (GO:0046907)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|rough endoplasmic reticulum (GO:0005791)|trans-Golgi network transport vesicle (GO:0030140)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						CCTAGTGATATCATAGACCAT	0.373																																					p.D92G		Atlas-SNP	.											.	RAB14	14	.	0			c.A275G						.						72	76	75					9																	123952841		2203	4300	6503	SO:0001583	missense	51552	exon4			GTGATATCATAGA	AF152463	CCDS6827.1	9q32-q34.11	2008-07-21			ENSG00000119396	ENSG00000119396		"RAB, member RAS oncogene"	16524	protein-coding gene	gene with protein product	"F protein-binding protein 1", "bA165P4.3 (member RAS oncogene family)", "small GTP binding protein RAB14"	612673				9792283, 15004230	Standard	NM_016322		Approved	FBP, RAB-14	uc004blc.3	P61106	OTTHUMG00000020582	ENST00000373840.4:c.275A>G	chr9.hg19:g.123952841T>C	ENSP00000362946:p.Asp92Gly	72.0	0.0		70.0	4.0	NM_016322	B3KR31|P35287|Q5JVD4|Q6Q7K5|Q969L0|Q9UI11	Missense_Mutation	SNP	ENST00000373840.4	hg19	CCDS6827.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.723595	0.89298	.	.	ENSG00000119396	ENST00000373840;ENST00000451303	D;T	0.87179	-2.22;-1.39	5.26	5.26	0.73747	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95984	0.8692	H	0.97962	4.115	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97465	1.0037	10	0.87932	D	0	.	14.3488	0.66685	0.0:0.0:0.0:1.0	.	92	P61106	RAB14_HUMAN	G	92	ENSP00000362946:D92G;ENSP00000400107:D92G	ENSP00000362946:D92G	D	-	2	0	RAB14	122992662	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	1.985000	0.57927	0.528000	0.53228	GAT	.	.		0.373	RAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053857.1	NM_016322		C	123952841	T	C	123952841	3	2	111	1	0	0	0	0	1	0	0	0	12915	1435	50	2	392	2	RAB14	9	123952841	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	176629	123952841	17260590	179	16419										
OR1L6	392390	hgsc.bcm.edu	37	chr9	125512279	125512279	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctcatcatcccggccatctaCtctgaccccaggctccacac	5	20	4	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:125512279C>T	ENST00000373684.1	+	1	261	c.261C>T	c.(259-261)taC>taT	p.Y87Y	OR1L6_ENST00000304720.2_Silent_p.Y51Y			Q8NGR2	OR1L6_HUMAN	olfactory receptor, family 1, subfamily L, member 6	87						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	12						CGGCCATCTACTCTGACCCCA	0.502																																					p.Y51Y		Atlas-SNP	.											.	OR1L6	31	.	0			c.C153T						.						142	132	135					9																	125512279		2203	4300	6503	SO:0001819	synonymous_variant	392390	exon1			CATCTACTCTGAC		CCDS35130.1, CCDS35130.2	9q33.2	2013-09-20			ENSG00000171459	ENSG00000171459		"GPCR / Class A : Olfactory receptors"	8218	protein-coding gene	gene with protein product				OR1L7			Standard	NM_001004453		Approved		uc022bna.1	Q8NGR2	OTTHUMG00000020621	ENST00000373684.1:c.261C>T	chr9.hg19:g.125512279C>T		311.0	0.0		228.0	45.0	NM_001004453	Q6IFM8|Q96R80	Silent	SNP	ENST00000373684.1	hg19																																																																																				.	.		0.502	OR1L6-201	KNOWN	basic	protein_coding	protein_coding				T	125512279	C	T	125512279	2	4	111	1	0	0	0	0	0	0	0	1	10975	576	20	3		3	OR1L6	9	125512279	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	1559438	125512279	15701152	180	16420										
HSPA5	3309	hgsc.bcm.edu	37	chr9	128000515	128000515	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccactgtgttccttggaatcAgtttggtcatgacacctccc	8	13	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:128000515A>G	ENST00000324460.6	-	7	1510	c.1307T>C	c.(1306-1308)cTg>cCg	p.L436P		NM_005347.4	NP_005338.1	P11021	GRP78_HUMAN	heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)	436					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|cellular response to glucose starvation (GO:0042149)|cellular response to interleukin-4 (GO:0071353)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum structural organization (GO:0021589)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|maintenance of protein localization in endoplasmic reticulum (GO:0035437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell migration (GO:0030335)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein folding in endoplasmic reticulum (GO:0060904)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|chaperone binding (GO:0051087)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|misfolded protein binding (GO:0051787)|protein domain specific binding (GO:0019904)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|prostate(2)|skin(1)	23					Acetylsalicylic acid(DB00945)|Antihemophilic Factor(DB00025)	CCTTGGAATCAGTTTGGTCAT	0.398										Prostate(1;0.17)																											p.L436P		Atlas-SNP	.											.	HSPA5	41	.	0			c.T1307C						.						134	122	126					9																	128000515		2203	4300	6503	SO:0001583	missense	3309	exon7			GGAATCAGTTTGG		CCDS6863.1	9q33.3	2011-09-02	2002-08-29		ENSG00000044574	ENSG00000044574		"Heat shock proteins / HSP70"	5238	protein-coding gene	gene with protein product		138120	"heat shock 70kD protein 5 (glucose-regulated protein, 78kD)"	GRP78			Standard	NM_005347		Approved	BiP	uc004bpn.3	P11021	OTTHUMG00000020672	ENST00000324460.6:c.1307T>C	chr9.hg19:g.128000515A>G	ENSP00000324173:p.Leu436Pro	77.0	0.0		69.0	4.0	NM_005347	B0QZ61|Q2EF78|Q9NPF1|Q9UK02	Missense_Mutation	SNP	ENST00000324460.6	hg19	CCDS6863.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.466116	0.84425	.	.	ENSG00000044574	ENST00000324460	T	0.08102	3.13	4.61	4.61	0.57282	.	0.000000	0.64402	D	0.000001	T	0.51007	0.1649	H	0.99914	4.94	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74569	-0.3622	10	0.87932	D	0	-14.4956	13.1949	0.59732	1.0:0.0:0.0:0.0	.	436	P11021	GRP78_HUMAN	P	436	ENSP00000324173:L436P	ENSP00000324173:L436P	L	-	2	0	HSPA5	127040336	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	1.701000	0.51217	0.455000	0.32223	CTG	.	.		0.398	HSPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054062.1			G	128000515	A	G	128000515	3	3	111	1	0	0	0	0	1	0	0	0	7423	188	7	2	665	2	HSPA5	9	128000515	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	2488236	128000515	13212916	181	16421										
GPSM1	26086	hgsc.bcm.edu	37	chr9	139244074	139244074	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agccaccattcaggggactgGcgggggcccagcagggactc	16	13	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:139244074G>A	ENST00000440944.1	+	11	1534	c.1314G>A	c.(1312-1314)tgG>tgA	p.W438*		NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	438	Interaction with STK11/LKB1. {ECO:0000250}.|Mediates association with membranes. {ECO:0000250}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		CAGGGGACTGGCGGGGGCCCA	0.672																																					p.W438X		Atlas-SNP	.											.	GPSM1	50	.	0			c.G1314A						.						10	8	9					9																	139244074		1799	3685	5484	SO:0001587	stop_gained	26086	exon11			GGACTGGCGGGGG	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"Tetratricopeptide (TTC) repeat domain containing"	17858	protein-coding gene	gene with protein product	"AGS3 homolog (C. elegans)"	609491	"G-protein signalling modulator 1 (AGS3-like, C. elegans)"			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1314G>A	chr9.hg19:g.139244074G>A	ENSP00000392828:p.Trp438*	115.0	0.0		86.0	30.0	NM_001145638	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Nonsense_Mutation	SNP	ENST00000440944.1	hg19	CCDS48055.1	.	.	.	.	.	.	.	.	.	.	G	39	7.514064	0.98332	.	.	ENSG00000160360	ENST00000440944;ENST00000354753	.	.	.	4.62	3.71	0.42584	.	1.552250	0.03955	N	0.289137	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-21.9443	10.0713	0.42335	0.1004:0.0:0.8996:0.0	.	.	.	.	X	438;415	.	ENSP00000346797:W415X	W	+	3	0	GPSM1	138363895	0.894000	0.30519	1.000000	0.80357	0.994000	0.84299	2.672000	0.46850	2.268000	0.75426	0.655000	0.94253	TGG	.	.		0.672	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		A	139244074	G	A	139244074	4	1	111	1	0	0	0	0	0	1	0	0	6743	1212	42	3	1523	3	GPSM1	9	139244074	Nonsense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	11243559	139244074	1969357	182	16422										
ABCA2	20	hgsc.bcm.edu	37	chr9	139910249	139910249	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aggcgatggccacggacagcTtgcgcttcatgccacccgac	12	15	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr9:139910249T>C	ENST00000371605.3	-	22	3536	c.3389A>G	c.(3388-3390)aAg>aGg	p.K1130R	ABCA2_ENST00000341511.6_Missense_Mutation_p.K1131R|ABCA2_ENST00000265662.5_Missense_Mutation_p.K1131R|ABCA2_ENST00000492260.1_5'Flank			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1130	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CACGGACAGCTTGCGCTTCAT	0.672																																					p.K1161R		Atlas-SNP	.											.	ABCA2	113	.	0			c.A3482G						.						40	45	44					9																	139910249		2184	4284	6468	SO:0001583	missense	20	exon23			GACAGCTTGCGCT	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.3389A>G	chr9.hg19:g.139910249T>C	ENSP00000360666:p.Lys1130Arg	247.0	0.0		192.0	8.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Missense_Mutation	SNP	ENST00000371605.3	hg19		.	.	.	.	.	.	.	.	.	.	T	16.96	3.265931	0.59540	.	.	ENSG00000107331	ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	D;D;D	0.99709	-6.48;-6.48;-6.48	4.2	4.2	0.49525	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	U	0.000000	D	0.98782	0.9590	N	0.04320	-0.23	0.52501	D	0.999955	D;D	0.58970	0.984;0.972	P;D	0.64877	0.866;0.93	D	0.99308	1.0903	10	0.54805	T	0.06	.	13.2433	0.60010	0.0:0.0:0.0:1.0	.	1130;1161	Q9BZC7;E7ETC3	ABCA2_HUMAN;.	R	1131;1130;1161;1131	ENSP00000265662:K1131R;ENSP00000360666:K1130R;ENSP00000344155:K1131R	ENSP00000265662:K1131R	K	-	2	0	ABCA2	139030070	1.000000	0.71417	1.000000	0.80357	0.139000	0.21198	6.113000	0.71553	1.531000	0.49152	0.260000	0.18958	AAG	.	.		0.672	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		C	139910249	T	C	139910249	3	2	111	1	0	0	0	0	1	0	0	0	32	1609	56	2	4026	2	ABCA2	9	139910249	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	666175	139910249	1303182	183	16423										
BMI1	648	hgsc.bcm.edu	37	chr10	22616563	22616563	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gatattgtatacaaattagtTccagggcttttcaaaagtga	8	5	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:22616563T>C	ENST00000376663.3	+	4	754	c.249T>C	c.(247-249)gtT>gtC	p.V83V	COMMD3-BMI1_ENST00000602390.1_Silent_p.V226V	NM_005180.8	NP_005171.4	P35226	BMI1_HUMAN	BMI1 proto-oncogene, polycomb ring finger	83					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|regulation of gene expression (GO:0010468)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|ubiquitin ligase complex (GO:0000151)	RING-like zinc finger domain binding (GO:0071535)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|urinary_tract(1)	12						ACAAATTAGTTCCAGGGCTTT	0.279																																					p.V226V		Atlas-SNP	.											BMI1,NS,carcinoma,0,1	.	.	.	0			c.T678C						.						53	61	59					10																	22616563		2195	4291	6486	SO:0001819	synonymous_variant	0	exon8			ATTAGTTCCAGGG	BC011652	CCDS7138.1	10p13	2014-06-26	2014-06-26	2006-04-26	ENSG00000168283	ENSG00000168283		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	1066	protein-coding gene	gene with protein product		164831	"polycomb group ring finger 4", "B lymphoma Mo-MLV insertion region 1 homolog (mouse)"	PCGF4		8268912	Standard	NM_005180		Approved	RNF51		P35226	OTTHUMG00000017807	ENST00000376663.3:c.249T>C	chr10.hg19:g.22616563T>C		66.0	0.0		41.0	3.0	NM_001204062	Q16030|Q5T8Z3|Q96F37	Silent	SNP	ENST00000376663.3	hg19	CCDS7138.1																																																																																			.	.		0.279	BMI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047176.1	NM_005180		C	22616563	T	C	22616563	2	2	111	1	0	0	0	0	0	0	0	1	1455	1770	62	2		2	BMI1	10	22616563	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		22616563	112918184	184	16424										
ERCC6	2074	hgsc.bcm.edu	37	chr10	50690818	50690818	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	caggcaacgtgcctaactttCccgggaagatgaagtcaaag	11	10	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:50690818C>A	ENST00000355832.5	-	10	2162	c.2084G>T	c.(2083-2085)gGa>gTa	p.G695V	ERCC6_ENST00000542458.1_Missense_Mutation_p.G65V	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	695	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						GCCTAACTTTCCCGGGAAGAT	0.488								Direct reversal of damage;Nucleotide excision repair (NER)																													p.C695F		Atlas-SNP	.											.	ERCC6	162	.	0			c.G2084T						.						104	96	99					10																	50690818		2203	4300	6503	SO:0001583	missense	2074	exon10			AACTTTCCCGGGA	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.2084G>T	chr10.hg19:g.50690818C>A	ENSP00000348089:p.Gly695Val	95.0	0.0		77.0	6.0	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	hg19	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	C	30	5.052049	0.93793	.	.	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;D	0.94576	-3.46;-3.46	5.68	5.68	0.88126	DEAD-like helicase (2);SNF2-related (1);	.	.	.	.	D	0.98201	0.9405	H	0.95504	3.68	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.99069	1.0833	9	0.72032	D	0.01	-25.5945	17.9728	0.89118	0.0:1.0:0.0:0.0	.	695;104	Q03468;Q59FF6	ERCC6_HUMAN;.	V	695;104;65	ENSP00000348089:G695V;ENSP00000445134:G65V	ENSP00000348089:G695V	G	-	2	0	ERCC6	50360824	1.000000	0.71417	0.655000	0.29622	0.991000	0.79684	7.796000	0.85898	2.693000	0.91896	0.655000	0.94253	GGA	.	.		0.488	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		A	50690818	C	A	50690818	3	1	111	1	0	0	0	0	1	0	0	0	5219	855	30	3	2445	3	ERCC6	10	50690818	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	28074255	50690818	84843929	185	16425										
CDH23	64072	hgsc.bcm.edu	37	chr10	73567345	73567345	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gctgcgggacctggaccgggAgcgagaagccatcttctcct	14	13	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:73567345A>G	ENST00000224721.6	+	58	8401	c.8396A>G	c.(8395-8397)gAg>gGg	p.E2799G	CDH23_ENST00000398788.3_Missense_Mutation_p.E554G|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2794	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CTGGACCGGGAGCGAGAAGCC	0.622																																					p.E2794G		Atlas-SNP	.											.	CDH23	365	.	0			c.A8381G						.						37	42	40					10																	73567345		2104	4224	6328	SO:0001583	missense	64072	exon57			ACCGGGAGCGAGA	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.8396A>G	chr10.hg19:g.73567345A>G	ENSP00000224721:p.Glu2799Gly	105.0	0.0		94.0	4.0	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	A	28.1	4.894188	0.91889	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.73047	-0.71	5.61	5.61	0.85477	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.88514	0.6457	H	0.94886	3.595	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91715	0.5384	10	0.87932	D	0	.	15.7813	0.78264	1.0:0.0:0.0:0.0	.	2794;2794	E9PEX1;Q9H251	.;CAD23_HUMAN	G	2799;2794;2797;554	ENSP00000381768:E554G	ENSP00000224721:E2799G	E	+	2	0	CDH23	73237351	1.000000	0.71417	0.970000	0.41538	0.980000	0.70556	9.300000	0.96151	2.138000	0.66242	0.450000	0.29827	GAG	.	.		0.622	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		G	73567345	A	G	73567345	3	3	111	1	0	0	0	0	1	0	0	0	3110	304	11	2	8956	2	CDH23	10	73567345	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	22876527	73567345	61967402	186	16426										
MYST4	23522	hgsc.bcm.edu	37	chr10	76602779	76602779	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgaacagctggaactcagtgTtcaggatggctcagttctca	11	9	4	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:76602779T>C	ENST00000287239.4	+	3	653	c.164T>C	c.(163-165)gTt>gCt	p.V55A	KAT6B_ENST00000372711.1_Missense_Mutation_p.V55A|KAT6B_ENST00000372725.1_Missense_Mutation_p.V55A|KAT6B_ENST00000372724.1_Missense_Mutation_p.V55A|KAT6B_ENST00000372714.1_Missense_Mutation_p.V55A	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	55					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GAACTCAGTGTTCAGGATGGC	0.488																																					p.V55A		Atlas-SNP	.											.	.	.	.	0			c.T164C						.						113	107	109					10																	76602779		2203	4300	6503	SO:0001583	missense	23522	exon3			TCAGTGTTCAGGA	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.164T>C	chr10.hg19:g.76602779T>C	ENSP00000287239:p.Val55Ala	101.0	0.0		101.0	5.0	NM_001256469	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	hg19	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.380571	0.61845	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	D;D;D;D;D	0.83250	-1.54;-1.54;-1.7;-1.54;-1.61	6.17	6.17	0.99709	.	0.000000	0.41500	D	0.000879	D	0.91771	0.7397	M	0.83223	2.63	0.40395	D	0.979587	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.77557	0.99;0.99;0.978	D	0.93029	0.6447	10	0.87932	D	0	-9.2844	16.8222	0.85835	0.0:0.0:0.0:1.0	.	55;55;55	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	A	55	ENSP00000361810:V55A;ENSP00000361809:V55A;ENSP00000287239:V55A;ENSP00000361799:V55A;ENSP00000361796:V55A	ENSP00000287239:V55A	V	+	2	0	KAT6B	76272785	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	GTT	.	.		0.488	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		C	76602779	T	C	76602779	3	2	111	1	0	0	0	0	1	0	0	0	10114	1725	60	2	166	2	MYST4	10	76602779	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	3035434	76602779	58931968	187	16427										
KCNMA1	3778	hgsc.bcm.edu	37	chr10	78832856	78832856	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	taataagacgagacgttaccTttatgaatgacctcatggag	9	7	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:78832856T>C	ENST00000286628.8	-	14	1747	c.1748A>G	c.(1747-1749)aAg>aGg	p.K583R	KCNMA1_ENST00000286627.5_Splice_Site_p.K583R|KCNMA1_ENST00000354353.5_Splice_Site_p.K583R|KCNMA1_ENST00000484507.1_5'UTR|KCNMA1_ENST00000372443.1_Splice_Site_p.K583R|KCNMA1_ENST00000406533.3_Splice_Site_p.K583R|KCNMA1_ENST00000404857.1_Splice_Site_p.K583R|KCNMA1_ENST00000372440.1_Splice_Site_p.K583R|KCNMA1_ENST00000404771.3_Splice_Site_p.K583R	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	583					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	AGACGTTACCTTTATGAATGA	0.507																																					p.K583R		Atlas-SNP	.											.	KCNMA1	370	.	0			c.A1748G						.						97	81	86					10																	78832856		2203	4300	6503	SO:0001630	splice_region_variant	3778	exon14			GTTACCTTTATGA	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.1749+1A>G	chr10.hg19:g.78832856T>C		124.0	0.0		99.0	5.0	NM_001161352	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Missense_Mutation	SNP	ENST00000286628.8	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.39|17.39	3.377367|3.377367	0.61735|0.61735	.|.	.|.	ENSG00000156113|ENSG00000156113	ENST00000372440;ENST00000372408;ENST00000372437;ENST00000457953;ENST00000404771;ENST00000372443;ENST00000286627;ENST00000286628;ENST00000406533;ENST00000354353;ENST00000404857;ENST00000412708|ENST00000372403;ENST00000428546	T;T;T;T;T;T;T;T;T|.	0.44482|.	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92|.	5.87|5.87	5.87|5.87	0.94306|0.94306	Potassium channel, calcium-activated, BK, alpha subunit (1);|.	0.094303|.	0.64402|.	D|.	0.000001|.	T|T	0.59307|0.59307	0.2184|0.2184	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	B;B;B;B;B;B;B;B|.	0.25486|.	0.127;0.004;0.001;0.037;0.003;0.009;0.102;0.001|.	B;B;B;B;B;B;B;B|.	0.31812|.	0.136;0.026;0.004;0.046;0.009;0.028;0.126;0.006|.	T|T	0.55386|0.55386	-0.8149|-0.8149	10|5	0.33940|.	T|.	0.23|.	-16.0588|-16.0588	16.2806|16.2806	0.82678|0.82678	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	583;583;583;583;583;365;583;583|.	Q12791-4;B7ZMF5;Q12791-2;Q12791;Q12791-5;C9JFZ9;F8WA96;Q5SVJ7|.	.;.;.;KCMA1_HUMAN;.;.;.;.|.	R|G	583;520;518;557;520;583;583;557;583;583;583;365|534;67	ENSP00000361517:K583R;ENSP00000361485:K520R;ENSP00000361514:K518R;ENSP00000396608:K557R;ENSP00000361520:K583R;ENSP00000286627:K583R;ENSP00000385552:K583R;ENSP00000346321:K583R;ENSP00000385806:K583R|.	ENSP00000286627:K583R|.	K|R	-|-	2|1	0|2	KCNMA1|KCNMA1	78502862|78502862	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	8.040000|8.040000	0.89188|0.89188	2.248000|2.248000	0.74166|0.74166	0.533000|0.533000	0.62120|0.62120	AAG|AGA	.	.		0.507	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247	Missense_Mutation	C	78832856	T	C	78832856	5	2	111	1	0	0	0	0	0	0	1	0	8082	1623	56	2	2194	2	KCNMA1	10	78832856	Splice_Site	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2230077	78832856	56701891	188	16428										
POLR3A	11128	hgsc.bcm.edu	37	chr10	79752965	79752965	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	taaatcttactttgatgttgTccagaacccttttaaactcc	4	10	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:79752965T>C	ENST00000372371.3	-	20	2914	c.2777A>G	c.(2776-2778)gAc>gGc	p.D926G		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	926					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			TTTGATGTTGTCCAGAACCCT	0.383																																					p.D926G		Atlas-SNP	.											.	POLR3A	104	.	0			c.A2777G						.						130	131	131					10																	79752965		2203	4300	6503	SO:0001583	missense	11128	exon20			ATGTTGTCCAGAA	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"RNA polymerase subunits"	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.2777A>G	chr10.hg19:g.79752965T>C	ENSP00000361446:p.Asp926Gly	76.0	0.0		57.0	4.0	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	hg19	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.372988	0.61624	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.67171	-0.25	5.74	5.74	0.90152	RNA polymerase Rpb1, domain 5 (1);	0.000000	0.85682	D	0.000000	T	0.66636	0.2809	M	0.67625	2.065	0.80722	D	1	B	0.24675	0.109	B	0.27170	0.077	T	0.62723	-0.6794	9	.	.	.	-42.5692	16.3426	0.83092	0.0:0.0:0.0:1.0	.	926	O14802	RPC1_HUMAN	G	926	ENSP00000361446:D926G	.	D	-	2	0	POLR3A	79422971	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.655000	0.83696	2.317000	0.78254	0.460000	0.39030	GAC	.	.		0.383	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		C	79752965	T	C	79752965	3	2	111	1	0	0	0	0	1	0	0	0	12237	1667	58	2	1443	2	POLR3A	10	79752965	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	920109	79752965	55781782	189	16429										
LDB3	11155	hgsc.bcm.edu	37	chr10	88459081	88459081	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcccacgttttgccaaattgCgcaactggcaccatggcctt	9	14	0	0	rs121908335		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:88459081C>T	ENST00000372066.3	+	8	881	c.802C>T	c.(802-804)Cgc>Tgc	p.R268C	LDB3_ENST00000361373.4_Intron|LDB3_ENST00000372056.4_Missense_Mutation_p.R383C|LDB3_ENST00000429277.2_Intron|LDB3_ENST00000458213.2_Intron|LDB3_ENST00000352360.5_Intron|LDB3_ENST00000310944.6_Missense_Mutation_p.R315C|LDB3_ENST00000263066.6_Intron|LDB3_ENST00000542786.1_3'UTR	NM_001080116.1	NP_001073585.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						TGCCAAATTGCGCAACTGGCA	0.512																																					p.R383C		Atlas-SNP	.											.	LDB3	164	.	0			c.C1147T	GRCh37	CM050286	LDB3	M	rs121908335	.	C	,CYS/ARG,CYS/ARG,,CYS/ARG,	0,3846		0,0,1923	162	173	169	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,943,802,,1147,	5.1	1	10	dbSNP_133	169	1,8283		0,1,4141	no	intron,missense,missense,intron,missense,intron	LDB3	NM_001080114.1,NM_001080115.1,NM_001080116.1,NM_001171610.1,NM_001171611.1,NM_007078.2	,180,180,,180,	0,1,6064	TT,TC,CC		0.0121,0.0,0.0082	,,,,,	,315/331,268/284,,383/399,	88459081	1,12129	1923	4142	6065	SO:0001583	missense	11155	exon8			AAATTGCGCAACT	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"cypher", "oracle", "Z-band alternatively spliced PDZ motif protein"	605906	"cardiomyopathy, dilated 1C (autosomal dominant)"	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000372066.3:c.802C>T	chr10.hg19:g.88459081C>T	ENSP00000361136:p.Arg268Cys	72.0	0.0		104.0	19.0	NM_001171611		Missense_Mutation	SNP	ENST00000372066.3	hg19	CCDS41545.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.478303	0.84747	0.0	1.21E-4	ENSG00000122367	ENST00000372066;ENST00000372056;ENST00000310944	T;T;T	0.50548	0.86;0.74;0.95	5.06	5.06	0.68205	.	.	.	.	.	T	0.65831	0.2729	L	0.55990	1.75	0.80722	A	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;P	0.76071	0.966;0.987;0.809	T	0.68161	-0.5482	8	0.87932	D	0	.	18.6293	0.91354	0.0:1.0:0.0:0.0	.	383;315;268	O75112-4;O75112-5;O75112-6	.;.;.	C	268;383;315	ENSP00000361136:R268C;ENSP00000361126:R383C;ENSP00000311913:R315C	ENSP00000311913:R315C	R	+	1	0	LDB3	88449061	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.468000	0.60162	2.642000	0.89623	0.561000	0.74099	CGC	.	.		0.512	LDB3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049161.1			T	88459081	C	T	88459081	3	4	111	1	0	0	0	0	1	0	0	0	8706	768	27	1	1204	1	LDB3	10	88459081	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	8706116	88459081	47075666	190	16430										
ATAD1	84896	hgsc.bcm.edu	37	chr10	89550120	89550120	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acaaatgtttctttttgataGgtaagatgactgtgtctttc	8	5	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:89550120G>A	ENST00000308448.7	-	4	707	c.329C>T	c.(328-330)cCt>cTt	p.P110L	ATAD1_ENST00000328142.3_Missense_Mutation_p.P110L|ATAD1_ENST00000541004.1_Missense_Mutation_p.P110L|ATAD1_ENST00000495903.1_5'UTR|ATAD1_ENST00000400215.3_Missense_Mutation_p.P52L	NM_032810.2	NP_116199.2	Q8NBU5	ATAD1_HUMAN	ATPase family, AAA domain containing 1	110					ATP catabolic process (GO:0006200)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|positive regulation of receptor internalization (GO:0002092)	cell junction (GO:0030054)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			kidney(1)|large_intestine(4)|lung(4)|ovary(1)	10		all_cancers(4;6.78e-12)|Prostate(4;3.56e-12)|all_epithelial(4;5.58e-09)|Melanoma(5;0.0273)|Breast(4;0.0424)|all_hematologic(4;0.0846)|Colorectal(252;0.207)|Glioma(4;0.217)|all_neural(4;0.224)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00131)|GBM - Glioblastoma multiforme(1;1.1e-32)|Lung(2;1.4e-05)|LUSC - Lung squamous cell carcinoma(2;2.69e-05)|Colorectal(12;7.09e-05)|COAD - Colon adenocarcinoma(12;0.000261)|STAD - Stomach adenocarcinoma(243;0.235)		CTTTTTGATAGGTAAGATGAC	0.358																																					p.P110L		Atlas-SNP	.											.	ATAD1	32	.	0			c.C329T						.						120	113	115					10																	89550120		2203	4300	6503	SO:0001583	missense	84896	exon4			TTGATAGGTAAGA	AL834370	CCDS7386.1	10q23.31	2010-04-21		2007-02-08	ENSG00000138138	ENSG00000138138		"ATPases / AAA-type"	25903	protein-coding gene	gene with protein product		614452				12477932	Standard	NM_032810		Approved	FLJ14600	uc001kez.1	Q8NBU5	OTTHUMG00000018685	ENST00000308448.7:c.329C>T	chr10.hg19:g.89550120G>A	ENSP00000339017:p.Pro110Leu	80.0	0.0		79.0	25.0	NM_032810	D3DR26|Q6DKG1|Q6P4B9|Q8N3G1|Q8WYR9|Q969Y3	Missense_Mutation	SNP	ENST00000308448.7	hg19	CCDS7386.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.529721	0.85706	.	.	ENSG00000138138	ENST00000308448;ENST00000328142;ENST00000400215;ENST00000541004	D;D;D;D	0.97688	-4.02;-4.02;-4.49;-4.23	5.4	4.5	0.54988	.	0.047500	0.85682	D	0.000000	D	0.99013	0.9663	H	0.94964	3.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	D	0.99410	1.0930	9	.	.	.	-10.6677	14.1714	0.65512	0.0725:0.0:0.9275:0.0	.	52;110	B4E2J1;Q8NBU5	.;ATAD1_HUMAN	L	110;110;52;110	ENSP00000339017:P110L;ENSP00000339016:P110L;ENSP00000412968:P52L;ENSP00000445500:P110L	.	P	-	2	0	ATAD1	89540100	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	1.404000	0.46819	0.563000	0.77884	CCT	.	.		0.358	ATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049235.1	NM_032810		A	89550120	G	A	89550120	3	1	111	1	0	0	0	0	1	0	0	0	1070	1000	35	3	784	3	ATAD1	10	89550120	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	1091039	89550120	45984627	191	16431										
PCGF5	84333	hgsc.bcm.edu	37	chr10	93021180	93021180	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaaacttccaagttcttatgAggtaagttaaataatatcta	5	5	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:93021180A>G	ENST00000336126.5	+	7	804	c.572A>G	c.(571-573)gAg>gGg	p.E191G	PCGF5_ENST00000543648.1_Splice_Site_p.E191G	NM_001257101.1|NM_032373.4	NP_001244030.1|NP_115749.2	Q86SE9	PCGF5_HUMAN	polycomb group ring finger 5	191					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)	12						AGTTCTTATGAGGTAAGTTAA	0.249																																					p.E191G	Colon(178;732 2696 46441 50370)	Atlas-SNP	.											.	PCGF5	29	.	0			c.A572G						.						18	20	19					10																	93021180		2162	4250	6412	SO:0001630	splice_region_variant	84333	exon7			CTTATGAGGTAAG	AL832003	CCDS7413.1	10q23.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000180628	ENSG00000180628		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	28264	protein-coding gene	gene with protein product			"ring finger protein (C3HC4 type) 159"	RNF159		8076819	Standard	NM_001256549		Approved	MGC16202	uc001khh.4	Q86SE9	OTTHUMG00000018740	ENST00000336126.5:c.573+1A>G	chr10.hg19:g.93021180A>G		101.0	0.0		82.0	4.0	NM_001256549	B7Z892|D3DR33|Q6PK47|Q86TD0	Missense_Mutation	SNP	ENST00000336126.5	hg19	CCDS7413.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.647610	0.87958	.	.	ENSG00000180628	ENST00000543648;ENST00000336126	T;T	0.51071	0.72;0.72	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.64951	0.2645	M	0.74881	2.28	0.80722	D	1	D	0.67145	0.996	P	0.58331	0.837	T	0.69694	-0.5076	10	0.66056	D	0.02	-19.9095	15.5816	0.76448	1.0:0.0:0.0:0.0	.	191	Q86SE9	PCGF5_HUMAN	G	191	ENSP00000445704:E191G;ENSP00000337500:E191G	ENSP00000337500:E191G	E	+	2	0	PCGF5	93011160	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.962000	0.93254	2.068000	0.61886	0.459000	0.35465	GAG	.	.		0.249	PCGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049363.1	NM_032373	Missense_Mutation	G	93021180	A	G	93021180	5	3	111	1	0	0	0	0	0	0	1	0	11586	318	11	2	594	2	PCGF5	10	93021180	Splice_Site	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	3471060	93021180	42513567	192	16432										
CYP2C18	1562	hgsc.bcm.edu	37	chr10	96447910	96447910	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttcagcaatggaaagagatgGaaggagatccggcgtttctg	14	6	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:96447910G>A	ENST00000285979.6	+	3	559	c.360G>A	c.(358-360)tgG>tgA	p.W120*	CYP2C18_ENST00000339022.5_Nonsense_Mutation_p.W120*	NM_000772.2	NP_000763.1	P33260	CP2CI_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 18	120					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	26		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Aminophenazone(DB01424)|Antipyrine(DB01435)|Buprenorphine(DB00921)|Clobazam(DB00349)|Clotiazepam(DB01559)|Cyclophosphamide(DB00531)|Dapsone(DB00250)|Desipramine(DB01151)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Ifosfamide(DB01181)|Imipramine(DB00458)|Lansoprazole(DB00448)|Lidocaine(DB00281)|Methadone(DB00333)|Omeprazole(DB00338)|Pegvisomant(DB00082)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Propofol(DB00818)|Tolbutamide(DB01124)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vilazodone(DB06684)|Warfarin(DB00682)	GAAAGAGATGGAAGGAGATCC	0.522																																					p.W120X		Atlas-SNP	.											.	CYP2C18	79	.	0			c.G360A						.						107	97	101					10																	96447910		2203	4300	6503	SO:0001587	stop_gained	1562	exon3			GAGATGGAAGGAG	M61853	CCDS7435.1, CCDS44460.1	10q24	2003-11-12	2003-01-14		ENSG00000108242	ENSG00000108242		"Cytochrome P450s"	2620	protein-coding gene	gene with protein product		601131	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18"	CYP2C17		1896026, 2009263	Standard	NM_000772		Approved	P450IIC17, CPCI, CYP2C		P33260	OTTHUMG00000018796	ENST00000285979.6:c.360G>A	chr10.hg19:g.96447910G>A	ENSP00000285979:p.Trp120*	240.0	0.0		187.0	57.0	NM_000772	B2R8K2|Q16703|Q16751|Q4VAT5|Q6GRG1	Nonsense_Mutation	SNP	ENST00000285979.6	hg19	CCDS7435.1	.	.	.	.	.	.	.	.	.	.	g	41	8.602818	0.98881	.	.	ENSG00000108242	ENST00000339022;ENST00000285979	.	.	.	4.63	3.72	0.42706	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.5565	0.45121	0.0964:0.0:0.9035:0.0	.	.	.	.	X	120	.	ENSP00000285979:W120X	W	+	3	0	CYP2C18	96437900	1.000000	0.71417	0.618000	0.29105	0.786000	0.44442	6.855000	0.75445	0.934000	0.37316	0.306000	0.20318	TGG	.	.		0.522	CYP2C18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049486.1	NM_000772		A	96447910	G	A	96447910	4	1	111	1	0	0	0	0	0	1	0	0	4167	1183	41	3	370	3	CYP2C18	10	96447910	Nonsense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	3426730	96447910	39086837	193	16433										
CNNM2	54805	hgsc.bcm.edu	37	chr10	104679481	104679481	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctataaccgggaaaaactgcTggagatgctccgggtcaccg	12	11	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:104679481T>C	ENST00000369878.4	+	1	1432	c.1244T>C	c.(1243-1245)cTg>cCg	p.L415P	CNNM2_ENST00000433628.2_Missense_Mutation_p.L415P|CNNM2_ENST00000369875.3_Missense_Mutation_p.L415P	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	415	DUF21.				magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GAAAAACTGCTGGAGATGCTC	0.587																																					p.L415P		Atlas-SNP	.											.	CNNM2	119	.	0			c.T1244C						.						83	83	83					10																	104679481		2203	4300	6503	SO:0001583	missense	54805	exon1			AACTGCTGGAGAT	AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"cyclin M2"	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1244T>C	chr10.hg19:g.104679481T>C	ENSP00000358894:p.Leu415Pro	38.0	0.0		61.0	4.0	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Missense_Mutation	SNP	ENST00000369878.4	hg19	CCDS44474.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.132250	0.56828	.	.	ENSG00000148842	ENST00000457502;ENST00000433628;ENST00000369875;ENST00000369878;ENST00000345419;ENST00000541201	D;D;D	0.88431	-2.38;-2.38;-2.38	4.44	4.44	0.53790	Domain of unknown function DUF21 (1);	0.000000	0.64402	D	0.000001	D	0.93831	0.8027	M	0.80183	2.485	0.80722	D	1	D;D;D	0.69078	0.958;0.966;0.997	P;P;D	0.72075	0.759;0.884;0.976	D	0.93853	0.7147	10	0.48119	T	0.1	.	13.7183	0.62712	0.0:0.0:0.0:1.0	.	415;415;415	Q9H8M5-2;Q9H8M5;F5H1I3	.;CNNM2_HUMAN;.	P	415	ENSP00000392875:L415P;ENSP00000358891:L415P;ENSP00000358894:L415P	ENSP00000286899:L415P	L	+	2	0	CNNM2	104669471	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.027000	0.88791	1.620000	0.50308	0.459000	0.35465	CTG	.	.		0.587	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		C	104679481	T	C	104679481	3	2	111	1	0	0	0	0	1	0	0	0	3615	1580	55	2	1246	2	CNNM2	10	104679481	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	8231571	104679481	30855266	194	16434										
ADD3	120	hgsc.bcm.edu	37	chr10	111883829	111883829	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcattcgagagaagcctaggCacaagagtgatgtggaaatc	12	7	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:111883829C>T	ENST00000356080.4	+	10	1565	c.1198C>T	c.(1198-1200)Cac>Tac	p.H400Y	ADD3_ENST00000360162.3_Missense_Mutation_p.H400Y|ADD3_ENST00000277900.8_Missense_Mutation_p.H400Y	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	400						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		GAAGCCTAGGCACAAGAGTGA	0.463																																					p.H400Y		Atlas-SNP	.											.	ADD3	89	.	0			c.C1198T						.						120	102	108					10																	111883829		2203	4300	6503	SO:0001583	missense	120	exon10			CCTAGGCACAAGA	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.1198C>T	chr10.hg19:g.111883829C>T	ENSP00000348381:p.His400Tyr	87.0	0.0		81.0	4.0	NM_001121	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Missense_Mutation	SNP	ENST00000356080.4	hg19	CCDS7561.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.444614	0.83993	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	T;T;T	0.19105	2.17;2.17;2.17	6.03	6.03	0.97812	.	0.088845	0.85682	D	0.000000	T	0.47303	0.1438	M	0.67953	2.075	0.58432	D	0.999999	D;D	0.71674	0.995;0.998	D;D	0.66847	0.922;0.947	T	0.19614	-1.0300	10	0.52906	T	0.07	-12.5626	20.5568	0.99304	0.0:1.0:0.0:0.0	.	400;400	Q9UEY8;Q9UEY8-2	ADDG_HUMAN;.	Y	400	ENSP00000353286:H400Y;ENSP00000348381:H400Y;ENSP00000277900:H400Y	ENSP00000277900:H400Y	H	+	1	0	ADD3	111873819	1.000000	0.71417	0.989000	0.46669	0.989000	0.77384	1.976000	0.40579	2.861000	0.98227	0.655000	0.94253	CAC	.	.		0.463	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903		T	111883829	C	T	111883829	3	4	111	1	0	0	0	0	1	0	0	0	306	710	25	3	1232	3	ADD3	10	111883829	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	7204348	111883829	23650918	195	16435										
PLEKHA1	59338	hgsc.bcm.edu	37	chr10	124189346	124189346	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccaagagaaccagcttccaaAgtgactgaacaagctctgtt	8	11	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:124189346A>G	ENST00000368990.3	+	12	1238	c.1107A>G	c.(1105-1107)aaA>aaG	p.K369K	PLEKHA1_ENST00000433307.1_Silent_p.K369K|PLEKHA1_ENST00000368988.1_Missense_Mutation_p.K383R|PLEKHA1_ENST00000368989.2_Missense_Mutation_p.K383R|PLEKHA1_ENST00000538022.1_3'UTR	NM_001001974.2	NP_001001974.1	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	369					androgen metabolic process (GO:0008209)|B cell receptor signaling pathway (GO:0050853)|cellular response to hydrogen peroxide (GO:0070301)|establishment of protein localization (GO:0045184)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|multicellular organism growth (GO:0035264)|negative regulation of protein kinase B signaling (GO:0051898)|palate development (GO:0060021)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|ruffle organization (GO:0031529)|skeletal system morphogenesis (GO:0048705)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CAGCTTCCAAAGTGACTGAAC	0.483																																					p.K369K		Atlas-SNP	.											.	PLEKHA1	33	.	0			c.A1107G						.						88	84	86					10																	124189346		2203	4300	6503	SO:0001819	synonymous_variant	59338	exon12			TTCCAAAGTGACT	AF286160	CCDS7629.1, CCDS55730.1	10q26.3	2013-01-10	2002-01-14		ENSG00000107679	ENSG00000107679		"Pleckstrin homology (PH) domain containing"	14335	protein-coding gene	gene with protein product	"tandem PH domain containing protein-1"	607772	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 1"			11001876, 15485858	Standard	NM_001001974		Approved	TAPP1	uc001lge.2	Q9HB21	OTTHUMG00000019184	ENST00000368990.3:c.1107A>G	chr10.hg19:g.124189346A>G		73.0	0.0		78.0	4.0	NM_021622	B3KQ55|D3DRE2|Q9BVK0	Silent	SNP	ENST00000368990.3	hg19	CCDS7629.1	.	.	.	.	.	.	.	.	.	.	A	18.94	3.729278	0.69074	.	.	ENSG00000107679	ENST00000368989;ENST00000368988	T;T	0.08984	3.03;3.03	5.71	5.71	0.89125	.	0.845137	0.11289	N	0.579490	T	0.25791	0.0628	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00186	-1.1942	7	0.87932	D	0	-15.2412	16.2826	0.82703	1.0:0.0:0.0:0.0	.	.	.	.	R	383	ENSP00000357985:K383R;ENSP00000357984:K383R	ENSP00000357984:K383R	K	+	2	0	PLEKHA1	124179336	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.536000	0.82023	2.307000	0.77673	0.528000	0.53228	AAG	.	.		0.483	PLEKHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050783.1	NM_001001974		G	124189346	A	G	124189346	2	3	111	1	0	0	0	0	0	0	0	1	12064	69	3	2		2	PLEKHA1	10	124189346	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	12305517	124189346	11345401	196	16436										
CUZD1	50624	hgsc.bcm.edu	37	chr10	124595749	124595749	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaaattccacaacatttgatAattttggtctgcaagttggg	8	6	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:124595749A>G	ENST00000368904.1	-	8	1884	c.935T>C	c.(934-936)tTa>tCa	p.L312S	CUZD1_ENST00000545804.1_Missense_Mutation_p.L312S|CUZD1_ENST00000392790.1_Missense_Mutation_p.L312S					CUB and zona pellucida-like domains 1											NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|stomach(1)	39		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		AACATTTGATAATTTTGGTCT	0.368																																					p.L312S		Atlas-SNP	.											.	CUZD1	82	.	0			c.T935C						.						149	149	149					10																	124595749		2203	4300	6503	SO:0001583	missense	50624	exon6			TTTGATAATTTTG	AF305835	CCDS7631.1	10q26.13	2003-11-18			ENSG00000138161	ENSG00000138161			17937	protein-coding gene	gene with protein product						10542259	Standard	NM_022034		Approved	ERG-1, UO-44		Q86UP6	OTTHUMG00000019195	ENST00000368904.1:c.935T>C	chr10.hg19:g.124595749A>G	ENSP00000357900:p.Leu312Ser	129.0	0.0		94.0	4.0	NM_022034		Missense_Mutation	SNP	ENST00000368904.1	hg19	CCDS7631.1	.	.	.	.	.	.	.	.	.	.	A	6.746	0.506385	0.12883	.	.	ENSG00000138161	ENST00000368904;ENST00000368901;ENST00000368900;ENST00000368899;ENST00000545804;ENST00000392790	T;T;T	0.80994	-1.44;-1.44;-1.44	5.07	5.07	0.68467	Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);	0.440893	0.24332	N	0.039454	T	0.54727	0.1876	N	0.04260	-0.245	0.09310	N	1	B	0.18610	0.029	B	0.13407	0.009	T	0.41251	-0.9519	10	0.10636	T	0.68	-4.5698	5.8441	0.18652	0.78:0.0:0.22:0.0	.	312	Q86UP6	CUZD1_HUMAN	S	312;31;31;31;312;312	ENSP00000357900:L312S;ENSP00000441590:L312S;ENSP00000376540:L312S	ENSP00000357895:L31S	L	-	2	0	CUZD1	124585739	0.017000	0.18338	0.105000	0.21289	0.707000	0.40811	2.525000	0.45598	1.902000	0.55061	0.533000	0.62120	TTA	.	.		0.368	CUZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050829.2	NM_022034		G	124595749	A	G	124595749	3	3	111	1	0	0	0	0	1	0	0	0	4068	372	13	2	904	2	CUZD1	10	124595749	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	406403	124595749	10938998	197	16437										
INPP5A	3632	hgsc.bcm.edu	37	chr10	134563079	134563079	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cgccgacaccaatgaagtggTgaagctcatatttcgtgagt	11	9	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr10:134563079T>C	ENST00000368594.3	+	10	1068	c.791T>C	c.(790-792)gTg>gCg	p.V264A	INPP5A_ENST00000368593.3_Missense_Mutation_p.V264A	NM_005539.3	NP_005530.3	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase, 40kDa	264					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|PH domain binding (GO:0042731)			cervix(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		AATGAAGTGGTGAAGCTCATA	0.617																																					p.V264A	Pancreas(63;823 1267 11107 20380 51626)	Atlas-SNP	.											.	INPP5A	77	.	0			c.T791C						.						78	68	71					10																	134563079		2203	4300	6503	SO:0001583	missense	3632	exon10			AAGTGGTGAAGCT	X77567	CCDS7669.2	10q26.3	2008-08-07	2002-08-29		ENSG00000068383	ENSG00000068383	3.1.3.56		6076	protein-coding gene	gene with protein product	"CTCL tumor antigen HD-CL-02", "43 kDa inositol polyphosphate 5-phophatase", "inositol polyphosphate 5-phophatase, 40kDa", "InsP3 5-phosphatase", "type I inositol-1,4,5-trisphosphate 5-phosphatase"	600106	"inositol polyphosphate-5-phosphatase, 40kD"			8013665	Standard	NM_005539		Approved	5PTASE	uc001llp.3	Q14642	OTTHUMG00000019293	ENST00000368594.3:c.791T>C	chr10.hg19:g.134563079T>C	ENSP00000357583:p.Val264Ala	81.0	0.0		97.0	4.0	NM_005539	D3DXI3|Q14640|Q5JSF1	Missense_Mutation	SNP	ENST00000368594.3	hg19	CCDS7669.2	.	.	.	.	.	.	.	.	.	.	T	9.235	1.036697	0.19669	.	.	ENSG00000068383	ENST00000368594;ENST00000368593;ENST00000432898	T;T	0.43688	0.94;0.95	4.92	4.92	0.64577	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.117705	0.56097	D	0.000034	T	0.27134	0.0665	N	0.19112	0.55	0.39337	D	0.965516	P;P	0.38280	0.625;0.625	B;B	0.39971	0.315;0.315	T	0.08576	-1.0715	10	0.11485	T	0.65	-3.3339	10.186	0.42998	0.1484:0.0:0.0:0.8516	.	264;264	Q14642;Q5T1B5	I5P1_HUMAN;.	A	264;264;181	ENSP00000357583:V264A;ENSP00000357582:V264A	ENSP00000357582:V264A	V	+	2	0	INPP5A	134413069	1.000000	0.71417	0.997000	0.53966	0.895000	0.52256	5.492000	0.66893	1.981000	0.57761	0.533000	0.62120	GTG	.	.		0.617	INPP5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051085.1	NM_005539		C	134563079	T	C	134563079	3	2	111	1	0	0	0	0	1	0	0	0	7763	1696	59	2	829	2	INPP5A	10	134563079	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	9967330	134563079	971668	198	16438										
KRTAP5-1	387264	hgsc.bcm.edu	37	chr11	1606421	1606421	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cggagccacagcccccacagCcggagccacagcccccacag	10	21	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:1606421C>G	ENST00000382171.2	-	1	92	c.59G>C	c.(58-60)gGc>gCc	p.G20A	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	20						keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GCCCCCACAGCCGGAGCCACA	0.677																																					p.G20A		Atlas-SNP	.											.	KRTAP5-1	74	.	0			c.G59C						.						39	50	47					11																	1606421		2172	4259	6431	SO:0001583	missense	387264	exon1			CCACAGCCGGAGC	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"Keratin associated proteins"	23596	protein-coding gene	gene with protein product		148022	"keratin, cuticle, ultrahigh sulphur 1-like"	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.59G>C	chr11.hg19:g.1606421C>G	ENSP00000371606:p.Gly20Ala	190.0	0.0		145.0	62.0	NM_001005922		Missense_Mutation	SNP	ENST00000382171.2	hg19	CCDS31330.1	.	.	.	.	.	.	.	.	.	.	C	0.885	-0.727559	0.03158	.	.	ENSG00000205869	ENST00000382171	T	0.04317	3.65	2.84	2.84	0.33178	.	.	.	.	.	T	0.07143	0.0181	L	0.60455	1.87	0.25427	N	0.98821	B	0.29612	0.251	B	0.35114	0.196	T	0.31971	-0.9924	9	0.10902	T	0.67	.	11.8714	0.52523	0.0:1.0:0.0:0.0	.	20	Q6L8H4	KRA51_HUMAN	A	20	ENSP00000371606:G20A	ENSP00000371606:G20A	G	-	2	0	KRTAP5-1	1562997	0.000000	0.05858	0.988000	0.46212	0.046000	0.14306	0.505000	0.22642	1.535000	0.49220	0.313000	0.20887	GGC	.	.		0.677	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922		G	1606421	C	G	1606421	3	3	111	1	0	0	0	0	1	0	0	0	8567	739	26	4	781	4	KRTAP5-1	11	1606421	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10		1606421	133400095	199	16439										
CARS	833	hgsc.bcm.edu	37	chr11	3059341	3059341	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcacagctttctcaagtggcTctgtggcaagctgcactgcg	12	12	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:3059341T>C	ENST00000397111.5	-	6	736	c.491A>G	c.(490-492)gAg>gGg	p.E164G	CARS_ENST00000380525.4_Missense_Mutation_p.E247G|CARS-AS1_ENST00000499962.1_RNA|CARS_ENST00000397114.3_Missense_Mutation_p.E154G|CARS_ENST00000278224.9_Missense_Mutation_p.E164G|CARS_ENST00000401769.3_Missense_Mutation_p.E177G			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	164					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)		CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	CTCAAGTGGCTCTGTGGCAAG	0.517			T	ALK	ALCL						OREG0020690	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E247G	Ovarian(61;932 1157 5961 20446 52152)	Atlas-SNP	.		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	.	CARS	114	.	0			c.A740G						.						165	145	152					11																	3059341		2202	4298	6500	SO:0001583	missense	833	exon7			AGTGGCTCTGTGG	AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"Aminoacyl tRNA synthetases / Class I"	1493	protein-coding gene	gene with protein product	"cysteine tRNA ligase 1, cytoplasmic"	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.491A>G	chr11.hg19:g.3059341T>C	ENSP00000380300:p.Glu164Gly	111.0	0.0	608	94.0	4.0	NM_001014437	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Missense_Mutation	SNP	ENST00000397111.5	hg19	CCDS7742.1	.	.	.	.	.	.	.	.	.	.	T	10.87	1.471278	0.26423	.	.	ENSG00000110619	ENST00000380525;ENST00000397111;ENST00000278224;ENST00000397114;ENST00000401769	T;T;T;T;T	0.46063	0.89;0.89;0.89;0.89;0.88	3.86	2.73	0.32206	.	0.537151	0.19577	N	0.110958	T	0.33847	0.0877	L	0.54965	1.715	0.31284	N	0.690211	B;B;B;B;B;B	0.12013	0.005;0.002;0.003;0.004;0.001;0.005	B;B;B;B;B;B	0.15870	0.014;0.013;0.013;0.005;0.008;0.008	T	0.29852	-0.9998	10	0.25106	T	0.35	-26.438	7.6555	0.28373	0.0:0.0986:0.0:0.9014	.	177;247;164;164;247;154	B4DKY1;B4DPV7;P49589;P49589-2;Q5HYE4;A8MVQ3	.;.;SYCC_HUMAN;.;.;.	G	247;164;164;154;177	ENSP00000369897:E247G;ENSP00000380300:E164G;ENSP00000278224:E164G;ENSP00000380303:E154G;ENSP00000384069:E177G	ENSP00000278224:E164G	E	-	2	0	CARS	3015917	0.076000	0.21285	0.009000	0.14445	0.021000	0.10359	0.563000	0.23547	0.557000	0.29117	0.459000	0.35465	GAG	.	.		0.517	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751		C	3059341	T	C	3059341	3	2	111	1	0	0	0	0	1	0	0	0	2659	1551	54	2	1831	2	CARS	11	3059341	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1452920	3059341	131947175	200	16440										
RRM1	6240	hgsc.bcm.edu	37	chr11	4127341	4127341	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	accacagtggaactagatacTttggctgctgaaacagctgc	10	10	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:4127341T>C	ENST00000300738.5	+	3	378	c.174T>C	c.(172-174)acT>acC	p.T58T	RRM1_ENST00000423050.2_Intron	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	58	ATP-cone. {ECO:0000255|PROSITE- ProRule:PRU00492}.				cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	AACTAGATACTTTGGCTGCTG	0.443																																					p.T58T	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.T174C						.						98	84	89					11																	4127341		2201	4298	6499	SO:0001819	synonymous_variant	6240	exon3			AGATACTTTGGCT	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"ribonucleotide reductase M1 polypeptide"			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.174T>C	chr11.hg19:g.4127341T>C		71.0	0.0		65.0	4.0	NM_001033	Q9UNN2	Silent	SNP	ENST00000300738.5	hg19	CCDS7750.1																																																																																			.	.		0.443	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		C	4127341	T	C	4127341	2	2	111	1	0	0	0	0	0	0	0	1	13696	1596	56	2		2	RRM1	11	4127341	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1068000	4127341	130879175	201	16441										
SBF2	81846	hgsc.bcm.edu	37	chr11	9871706	9871706	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccatcaggatccagcaagacTcgaagaccctcacagacaat	7	14	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:9871706T>C	ENST00000256190.8	-	22	2807	c.2670A>G	c.(2668-2670)cgA>cgG	p.R890R	RP11-1H15.2_ENST00000533659.1_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	890	GRAM.				cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		CCAGCAAGACTCGAAGACCCT	0.473																																					p.R890R		Atlas-SNP	.											.	SBF2	146	.	0			c.A2670G						.						99	99	99					11																	9871706		2201	4294	6495	SO:0001819	synonymous_variant	81846	exon22			CAAGACTCGAAGA	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.2670A>G	chr11.hg19:g.9871706T>C		97.0	0.0		99.0	4.0	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Silent	SNP	ENST00000256190.8	hg19	CCDS31427.1																																																																																			.	.		0.473	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		C	9871706	T	C	9871706	2	2	111	1	0	0	0	0	0	0	0	1	13874	1538	54	2		2	SBF2	11	9871706	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	5744365	9871706	125134810	202	16442										
PDE3B	5140	hgsc.bcm.edu	37	chr11	14666012	14666012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcatcgcctgtgccttcttcTtcctcacctgcttcctcacc	5	19	4	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:14666012T>C	ENST00000282096.4	+	1	744	c.391T>C	c.(391-393)Ttc>Ctc	p.F131L	PDE3B_ENST00000455098.2_Missense_Mutation_p.F131L|PSMA1_ENST00000418988.2_5'Flank|PDE3B_ENST00000534317.1_3'UTR	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	131					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	TGCCTTCTTCTTCCTCACCTG	0.706																																					p.F131L		Atlas-SNP	.											.	PDE3B	98	.	0			c.T391C						.						34	37	36					11																	14666012		2199	4294	6493	SO:0001583	missense	5140	exon1			TTCTTCTTCCTCA	U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"Phosphodiesterases"	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.391T>C	chr11.hg19:g.14666012T>C	ENSP00000282096:p.Phe131Leu	139.0	0.0		100.0	4.0	NM_000922	B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	ENST00000282096.4	hg19	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	T	34	5.346196	0.95807	.	.	ENSG00000152270	ENST00000282096;ENST00000455098	T;T	0.69926	-0.28;-0.44	3.92	3.92	0.45320	.	4.099390	0.00447	N	0.000085	T	0.66761	0.2822	L	0.43152	1.355	0.49389	D	0.999781	P;P;P	0.52842	0.793;0.793;0.956	B;B;B	0.43123	0.283;0.283;0.409	T	0.58781	-0.7576	10	0.66056	D	0.02	.	12.4706	0.55785	0.0:0.0:0.0:1.0	.	131;131;131	B7ZM37;Q13370;A7E2E5	.;PDE3B_HUMAN;.	L	131	ENSP00000282096:F131L;ENSP00000388644:F131L	ENSP00000282096:F131L	F	+	1	0	PDE3B	14622588	1.000000	0.71417	0.996000	0.52242	0.859000	0.49053	6.931000	0.75863	1.433000	0.47394	0.260000	0.18958	TTC	.	.		0.706	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922		C	14666012	T	C	14666012	3	2	111	1	0	0	0	0	1	0	0	0	11647	1609	56	2	393	2	PDE3B	11	14666012	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	4794306	14666012	120340504	203	16443										
GTF2H1	2965	hgsc.bcm.edu	37	chr11	18373439	18373439	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	taattataggcgaaattacaAgagtccattgaatatgaaga	8	4	0	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:18373439A>G	ENST00000265963.4	+	10	1225	c.1065A>G	c.(1063-1065)caA>caG	p.Q355Q	GTF2H1_ENST00000453096.2_Silent_p.Q355Q|GTF2H1_ENST00000534641.1_Silent_p.Q239Q|GTF2H1_ENST00000526630.2_5'UTR|GTF2H1_ENST00000530496.2_Silent_p.Q43Q	NM_005316.3	NP_005307.1	P32780	TF2H1_HUMAN	general transcription factor IIH, polypeptide 1, 62kDa	355					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	20						CGAAATTACAAGAGTCCATTG	0.313								Nucleotide excision repair (NER)																													p.Q355Q		Atlas-SNP	.											.	GTF2H1	35	.	0			c.A1065G						.						80	91	87					11																	18373439		2199	4292	6491	SO:0001819	synonymous_variant	2965	exon11			ATTACAAGAGTCC		CCDS7838.1	11p15.1-p14	2012-11-05	2002-08-29		ENSG00000110768	ENSG00000110768		"General transcription factors", "General transcription factor IIH complex subunits"	4655	protein-coding gene	gene with protein product		189972	"general transcription factor IIH, polypeptide 1 (62kD subunit)"			1529339, 8162052	Standard	NM_005316		Approved	BTF2, P62, TFIIH	uc001moh.2	P32780	OTTHUMG00000167690	ENST00000265963.4:c.1065A>G	chr11.hg19:g.18373439A>G		89.0	0.0		78.0	4.0	NM_001142307	B3KXE0|D3DQY2|Q6I9Y7|Q9H5K5|Q9NQD9	Silent	SNP	ENST00000265963.4	hg19	CCDS7838.1																																																																																			.	.		0.313	GTF2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395627.2	NM_005316		G	18373439	A	G	18373439	2	3	111	1	0	0	0	0	0	0	0	1	6869	69	3	2		2	GTF2H1	11	18373439	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	3707427	18373439	116633077	204	16444										
NAV2	89797	hgsc.bcm.edu	37	chr11	20066708	20066708	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agagtggttccgccgccggcCtggccatgatcacagccagc	13	15	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:20066708C>G	ENST00000396087.3	+	15	3562	c.3463C>G	c.(3463-3465)Ctg>Gtg	p.L1155V	NAV2_ENST00000360655.4_Missense_Mutation_p.L1068V|NAV2_ENST00000349880.4_Missense_Mutation_p.L1132V|NAV2_ENST00000540292.1_Missense_Mutation_p.L1086V|NAV2_ENST00000396085.1_Missense_Mutation_p.L1132V|NAV2-AS2_ENST00000533767.1_RNA|NAV2_ENST00000311043.8_Missense_Mutation_p.L218V|NAV2_ENST00000533917.1_Missense_Mutation_p.L218V|NAV2_ENST00000527559.2_Missense_Mutation_p.L1084V	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1155					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CGCCGCCGGCCTGGCCATGAT	0.587																																					p.L1155V		Atlas-SNP	.											.	NAV2	255	.	0			c.C3463G						.						73	71	72					11																	20066708		2203	4300	6503	SO:0001583	missense	89797	exon15			GCCGGCCTGGCCA	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.3463C>G	chr11.hg19:g.20066708C>G	ENSP00000379396:p.Leu1155Val	78.0	0.0		54.0	12.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	hg19	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	C	0.147	-1.095834	0.01858	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000525322;ENST00000311043;ENST00000536595	T;T;T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6	5.9	4.05	0.47172	.	0.124126	0.36591	N	0.002504	T	0.13200	0.0320	N	0.08118	0	0.31055	N	0.71483	B;B;B;B;B	0.14012	0.009;0.005;0.007;0.004;0.007	B;B;B;B;B	0.09377	0.003;0.002;0.004;0.004;0.004	T	0.16188	-1.0411	9	.	.	.	.	6.2904	0.21057	0.2349:0.6146:0.0:0.1505	.	1155;218;218;1132;1068	Q8IVL1;Q8IVL1-5;E9PNV5;Q8IVL1-3;Q8IVL1-4	NAV2_HUMAN;.;.;.;.	V	1068;1132;1132;1155;1084;1086;218;218;218;218	ENSP00000353871:L1068V;ENSP00000379394:L1132V;ENSP00000309577:L1132V;ENSP00000379396:L1155V;ENSP00000435395:L1084V;ENSP00000443489:L1086V;ENSP00000437316:L218V;ENSP00000437136:L218V;ENSP00000312169:L218V	.	L	+	1	2	NAV2	20023284	0.914000	0.31030	0.963000	0.40424	0.647000	0.38526	1.702000	0.37836	0.844000	0.35094	0.650000	0.86243	CTG	.	.		0.587	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		G	20066708	C	G	20066708	3	3	111	1	0	0	0	0	1	0	0	0	10193	680	24	4	3557	4	NAV2	11	20066708	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	1693269	20066708	114939808	205	16445										
NAV2	89797	hgsc.bcm.edu	37	chr11	20066858	20066858	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aggatgacgggtatctagccCtaagctcccggacaaacctt	10	12	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:20066858C>T	ENST00000396087.3	+	15	3712	c.3613C>T	c.(3613-3615)Cta>Tta	p.L1205L	NAV2_ENST00000360655.4_Silent_p.L1118L|NAV2_ENST00000349880.4_Silent_p.L1182L|NAV2_ENST00000540292.1_Silent_p.L1136L|NAV2_ENST00000396085.1_Silent_p.L1182L|NAV2-AS2_ENST00000533767.1_RNA|NAV2_ENST00000311043.8_Silent_p.L268L|NAV2_ENST00000533917.1_Silent_p.L268L|NAV2_ENST00000527559.2_Silent_p.L1134L	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1205					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						GTATCTAGCCCTAAGCTCCCG	0.557																																					p.L1205L		Atlas-SNP	.											.	NAV2	255	.	0			c.C3613T						.						68	64	66					11																	20066858		2203	4300	6503	SO:0001819	synonymous_variant	89797	exon15			CTAGCCCTAAGCT	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.3613C>T	chr11.hg19:g.20066858C>T		139.0	0.0		98.0	4.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	hg19	CCDS58126.1																																																																																			.	.		0.557	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		T	20066858	C	T	20066858	2	4	111	1	0	0	0	0	0	0	0	1	10193	680	24	3		3	NAV2	11	20066858	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	150	20066858	114939658	206	16446										
ANO5	203859	hgsc.bcm.edu	37	chr11	22271814	22271814	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gagaaaaaattggtatctatTttgtctttcttggattttac	7	4	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:22271814T>C	ENST00000324559.8	+	10	1227	c.910T>C	c.(910-912)Ttt>Ctt	p.F304L		NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	304					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGGTATCTATTTTGTCTTTCT	0.308																																					p.F304L		Atlas-SNP	.											.	ANO5	162	.	0			c.T910C						.						110	100	103					11																	22271814		2203	4300	6503	SO:0001583	missense	203859	exon10			ATCTATTTTGTCT	AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.910T>C	chr11.hg19:g.22271814T>C	ENSP00000315371:p.Phe304Leu	151.0	0.0		93.0	4.0	NM_213599		Missense_Mutation	SNP	ENST00000324559.8	hg19	CCDS31444.1	.	.	.	.	.	.	.	.	.	.	T	32	5.118758	0.94385	.	.	ENSG00000171714	ENST00000324559	D	0.84298	-1.83	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.93930	0.8057	H	0.96691	3.865	0.80722	D	1	P	0.51791	0.948	P	0.56563	0.801	D	0.95785	0.8820	10	0.87932	D	0	.	15.4423	0.75195	0.0:0.0:0.0:1.0	.	304	Q75V66	ANO5_HUMAN	L	304	ENSP00000315371:F304L	ENSP00000315371:F304L	F	+	1	0	ANO5	22228390	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.641000	0.83368	2.044000	0.60594	0.455000	0.32223	TTT	.	.		0.308	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599		C	22271814	T	C	22271814	3	2	111	1	0	0	0	0	1	0	0	0	700	1841	64	2	948	2	ANO5	11	22271814	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2204956	22271814	112734702	207	16447										
ANO3	63982	hgsc.bcm.edu	37	chr11	26664762	26664762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttttaccaccatctttgttgCggcttttcctctagcccctc	5	15	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:26664762C>T	ENST00000256737.3	+	23	3161	c.2309C>T	c.(2308-2310)gCg>gTg	p.A770V	ANO3_ENST00000531568.1_Missense_Mutation_p.A624V|ANO3_ENST00000537978.1_Missense_Mutation_p.A754V|ANO3_ENST00000525139.1_Missense_Mutation_p.A754V	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	770					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						ATCTTTGTTGCGGCTTTTCCT	0.378																																					p.A770V		Atlas-SNP	.											.	ANO3	145	.	0			c.C2309T						.						122	110	114					11																	26664762		2203	4299	6502	SO:0001583	missense	63982	exon23			TTGTTGCGGCTTT	AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	14004	protein-coding gene	gene with protein product	"transmembrane protein 16C (eight membrane-spanning domains)"	610110	"chromosome 11 open reading frame 25", "transmembrane protein 16C"	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.2309C>T	chr11.hg19:g.26664762C>T	ENSP00000256737:p.Ala770Val	171.0	0.0		137.0	41.0	NM_031418	B7Z3F5	Missense_Mutation	SNP	ENST00000256737.3	hg19	CCDS31447.1	.	.	.	.	.	.	.	.	.	.	C	34	5.400902	0.96030	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.81451	0.4825	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	T	0.81035	-0.1115	10	0.52906	T	0.07	.	19.7537	0.96281	0.0:1.0:0.0:0.0	.	672;770	B7Z7Y6;Q9BYT9	.;ANO3_HUMAN	V	754;754;770;672;624	ENSP00000440737:A754V;ENSP00000432576:A754V;ENSP00000256737:A770V;ENSP00000432394:A624V	ENSP00000256737:A770V	A	+	2	0	ANO3	26621338	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	7.764000	0.85297	2.676000	0.91093	0.655000	0.94253	GCG	.	.		0.378	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		T	26664762	C	T	26664762	3	4	111	1	0	0	0	0	1	0	0	0	698	768	27	1	2399	1	ANO3	11	26664762	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	4392948	26664762	108341754	208	16448										
FBXO3	26273	hgsc.bcm.edu	37	chr11	33790501	33790501	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggtcaatgtatcttcctacaTcagagtaagtatctatgaag	8	7	4	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:33790501T>C	ENST00000265651.3	-	3	272	c.254A>G	c.(253-255)gAt>gGt	p.D85G	FBXO3_ENST00000448981.2_Missense_Mutation_p.D85G|FBXO3_ENST00000534136.1_Missense_Mutation_p.D85G|FBXO3_ENST00000526785.1_5'UTR|FBXO3_ENST00000530401.1_Missense_Mutation_p.D80G|FBXO3_ENST00000533103.1_5'UTR	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	85					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		TCTTCCTACATCAGAGTAAGT	0.353																																					p.D85G		Atlas-SNP	.											.	FBXO3	37	.	0			c.A254G						.						192	186	188					11																	33790501		2202	4298	6500	SO:0001583	missense	26273	exon3			CCTACATCAGAGT	AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"F-boxes /  "other""	13582	protein-coding gene	gene with protein product		609089	"F-box only protein 3"			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.254A>G	chr11.hg19:g.33790501T>C	ENSP00000265651:p.Asp85Gly	110.0	0.0		64.0	4.0	NM_012175	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	hg19	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.225980	0.58668	.	.	ENSG00000110429	ENST00000265651;ENST00000321458;ENST00000530401;ENST00000534136;ENST00000448981	T;T;T;T	0.47177	0.85;0.86;0.88;0.89	5.99	5.99	0.97316	F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	T	0.63908	0.2551	M	0.62723	1.935	0.80722	D	1	D;D;D	0.67145	0.996;0.996;0.985	D;P;P	0.62955	0.909;0.794;0.643	T	0.66131	-0.6000	10	0.62326	D	0.03	-26.0063	14.7241	0.69329	0.0:0.0:0.0:1.0	.	80;85;85	Q9UK99-3;Q9UK99-2;Q9UK99	.;.;FBX3_HUMAN	G	85;82;80;85;85	ENSP00000265651:D85G;ENSP00000433781:D80G;ENSP00000431745:D85G;ENSP00000408836:D85G	ENSP00000265651:D85G	D	-	2	0	FBXO3	33747077	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.919000	0.70005	2.291000	0.77112	0.533000	0.62120	GAT	.	.		0.353	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175		C	33790501	T	C	33790501	3	2	111	1	0	0	0	0	1	0	0	0	5747	1435	50	2	1206	2	FBXO3	11	33790501	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	7125739	33790501	101216015	209	16449										
NAT10	55226	hgsc.bcm.edu	37	chr11	34158255	34158255	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctcctttactcctcaaattgAatgagaggcctgccgaacgc	8	13	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:34158255A>G	ENST00000257829.3	+	20	2301	c.2095A>G	c.(2095-2097)Aat>Gat	p.N699D	NAT10_ENST00000527971.1_Intron|NAT10_ENST00000531159.2_Missense_Mutation_p.N627D	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	699	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.					membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				CCTCAAATTGAATGAGAGGCC	0.552																																					p.N699D		Atlas-SNP	.											.	NAT10	78	.	0			c.A2095G						.						105	104	104					11																	34158255		2202	4298	6500	SO:0001583	missense	55226	exon20			AAATTGAATGAGA	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.2095A>G	chr11.hg19:g.34158255A>G	ENSP00000257829:p.Asn699Asp	142.0	0.0		117.0	5.0	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	SNP	ENST00000257829.3	hg19	CCDS7889.1	.	.	.	.	.	.	.	.	.	.	A	16.05	3.013960	0.54468	.	.	ENSG00000135372	ENST00000257829;ENST00000531159	T;T	0.29142	1.58;1.59	5.4	5.4	0.78164	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (1);	0.200002	0.64402	D	0.000010	T	0.23289	0.0563	N	0.24115	0.695	0.80722	D	1	B	0.02656	0.0	B	0.10450	0.005	T	0.03202	-1.1061	10	0.31617	T	0.26	-19.4285	15.4304	0.75092	1.0:0.0:0.0:0.0	.	699	Q9H0A0	NAT10_HUMAN	D	699;627	ENSP00000257829:N699D;ENSP00000433011:N627D	ENSP00000257829:N699D	N	+	1	0	NAT10	34114831	1.000000	0.71417	0.848000	0.33437	0.662000	0.39071	7.493000	0.81493	2.052000	0.61016	0.459000	0.35465	AAT	.	.		0.552	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		G	34158255	A	G	34158255	3	3	111	1	0	0	0	0	1	0	0	0	10183	246	9	2	2169	2	NAT10	11	34158255	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	367754	34158255	100848261	210	16450										
SPI1	6688	hgsc.bcm.edu	37	chr11	47380449	47380449	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	caggccatccgcctcgccgtCagacacctccagtggggggc	13	17	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:47380449C>T	ENST00000378538.3	-	4	661	c.439G>A	c.(439-441)Gac>Aac	p.D147N	SPI1_ENST00000533030.1_Intron|SPI1_ENST00000533968.1_Missense_Mutation_p.D147N|SPI1_ENST00000227163.4_Missense_Mutation_p.D148N	NM_001080547.1|NM_003120.2	NP_001074016.1|NP_003111.2	P17947	SPI1_HUMAN	Spi-1 proto-oncogene	147					anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|histone H3 acetylation (GO:0043966)|hypermethylation of CpG island (GO:0044027)|lymphocyte differentiation (GO:0030098)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of erythrocyte differentiation (GO:0045646)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somatic stem cell maintenance (GO:0035019)	nuclear chromatin (GO:0000790)	core promoter binding (GO:0001047)|NFAT protein binding (GO:0051525)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(4)|ovary(1)	8				Lung(87;0.0967)		GCCTCGCCGTCAGACACCTCC	0.726																																					p.D148N		Atlas-SNP	.											.	SPI1	21	.	0			c.G442A						.						10	11	11					11																	47380449		2179	4268	6447	SO:0001583	missense	6688	exon4			CGCCGTCAGACAC	X52056	CCDS7933.2, CCDS44591.1	11p12-p11.22	2014-06-25	2014-06-25		ENSG00000066336	ENSG00000066336			11241	protein-coding gene	gene with protein product	"hematopoietic transcription factor PU.1", "31 kDa transforming protein"	165170	"spleen focus forming virus (SFFV) proviral integration oncogene"			1693183	Standard	NM_003120		Approved	PU.1, SPI-A, OF, SFPI1, SPI-1	uc001nfb.1	P17947	OTTHUMG00000150150	ENST00000378538.3:c.439G>A	chr11.hg19:g.47380449C>T	ENSP00000367799:p.Asp147Asn	171.0	0.0		124.0	5.0	NM_001080547		Missense_Mutation	SNP	ENST00000378538.3	hg19	CCDS7933.2	.	.	.	.	.	.	.	.	.	.	C	31	5.075186	0.94000	.	.	ENSG00000066336	ENST00000378538;ENST00000227163;ENST00000533968	T;T;T	0.39787	1.06;1.06;1.06	4.34	4.34	0.51931	.	0.000000	0.85682	D	0.000000	T	0.66934	0.2840	M	0.79926	2.475	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.992;1.0	T	0.72620	-0.4238	10	0.56958	D	0.05	-25.5606	17.2182	0.86950	0.0:1.0:0.0:0.0	.	147;147;148	F5H3K6;P17947;P17947-2	.;SPI1_HUMAN;.	N	147;148;147	ENSP00000367799:D147N;ENSP00000227163:D148N;ENSP00000438846:D147N	ENSP00000227163:D148N	D	-	1	0	SPI1	47337025	1.000000	0.71417	0.863000	0.33907	0.870000	0.49936	7.246000	0.78247	2.117000	0.64856	0.561000	0.74099	GAC	.	.		0.726	SPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316571.1	NM_003120		T	47380449	C	T	47380449	3	4	111	1	0	0	0	0	1	0	0	0	15064	826	29	3	381	3	SPI1	11	47380449	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	13222194	47380449	87626067	211	16451										
OR5I1	10798	hgsc.bcm.edu	37	chr11	55702999	55702999	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttacatctttatttctcaaaCtataaatcaacggattcagc	3	9	4	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:55702999C>T	ENST00000301532.3	-	1	877	c.878G>A	c.(877-879)aGt>aAt	p.S293N		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	293					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						ATTTCTCAAACTATAAATCAA	0.353																																					p.S293N		Atlas-SNP	.											OR5I1,NS,chondrosarcoma,0,1	OR5I1	110	.	0			c.G878A						.						65	63	64					11																	55702999		2200	4294	6494	SO:0001583	missense	10798	exon1			CTCAAACTATAAA	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"GPCR / Class A : Olfactory receptors"	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.878G>A	chr11.hg19:g.55702999C>T	ENSP00000301532:p.Ser293Asn	81.0	0.0		49.0	2.0	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	hg19	CCDS7949.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.746736	0.30955	.	.	ENSG00000167825	ENST00000301532	T	0.39056	1.1	4.96	4.96	0.65561	.	0.112392	0.40144	N	0.001161	T	0.62245	0.2412	H	0.99299	4.505	0.27187	N	0.960529	P	0.36282	0.546	B	0.29353	0.101	T	0.71550	-0.4559	10	0.87932	D	0	.	16.0689	0.80909	0.0:1.0:0.0:0.0	.	293	Q13606	OR5I1_HUMAN	N	293	ENSP00000301532:S293N	ENSP00000301532:S293N	S	-	2	0	OR5I1	55459575	0.000000	0.05858	0.094000	0.20943	0.486000	0.33341	1.129000	0.31381	2.442000	0.82660	0.643000	0.83706	AGT	.	.		0.353	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637		T	55702999	C	T	55702999	3	4	111	1	0	0	0	0	1	0	0	0	11173	565	20	3	69	3	OR5I1	11	55702999	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	8322550	55702999	79303517	212	16452										
SMTNL1	219537	hgsc.bcm.edu	37	chr11	57310650	57310650	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agacagcctctcaggaggagAcaggccagaggaaagagtgc	15	9	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:57310650A>G	ENST00000399154.2	+	1	535	c.535A>G	c.(535-537)Aca>Gca	p.T179A	SMTNL1_ENST00000457912.1_Missense_Mutation_p.T197A|SMTNL1_ENST00000527972.1_Missense_Mutation_p.T179A			A8MU46	SMTL1_HUMAN	smoothelin-like 1	179	Glu-rich.				negative regulation of vasodilation (GO:0045908)|positive regulation of vasoconstriction (GO:0045907)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	8						TCAGGAGGAGACAGGCCAGAG	0.542																																					p.T179A		Atlas-SNP	.											.	SMTNL1	68	.	0			c.A535G						.						48	53	51					11																	57310650		2091	4216	6307	SO:0001583	missense	219537	exon1			GAGGAGACAGGCC	BX116227		11q12.1	2006-02-02				ENSG00000214872			32394	protein-coding gene	gene with protein product	"calponin homology-associated smooth muscle protein"	613664				15327999	Standard	NM_001105565		Approved	CHASM	uc021qjh.1	A8MU46		ENST00000399154.2:c.535A>G	chr11.hg19:g.57310650A>G	ENSP00000382108:p.Thr179Ala	91.0	0.0		77.0	4.0	NM_001105565		Missense_Mutation	SNP	ENST00000399154.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.029	-1.350853	0.01256	.	.	ENSG00000214872	ENST00000457912;ENST00000527972;ENST00000399154	T;T;T	0.02552	4.25;4.25;4.28	3.99	-3.59	0.04583	.	1.595290	0.05188	N	0.502618	T	0.01320	0.0043	N	0.03050	-0.425	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48958	-0.8988	10	0.09843	T	0.71	.	8.4473	0.32849	0.2327:0.1592:0.6081:0.0	.	197	C9J621	.	A	197;179;179	ENSP00000406485:T197A;ENSP00000432651:T179A;ENSP00000382108:T179A	ENSP00000382108:T179A	T	+	1	0	SMTNL1	57067226	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.429000	0.21412	-0.538000	0.06281	-0.256000	0.11100	ACA	.	.		0.542	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203		G	57310650	A	G	57310650	3	3	111	1	0	0	0	0	1	0	0	0	14830	275	10	2	595	2	SMTNL1	11	57310650	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1607651	57310650	77695866	213	16453										
OR5A1	219982	hgsc.bcm.edu	37	chr11	59211305	59211305	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tccaactccttatctcctatGgttacatagtgtctgcggtc	7	12	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:59211305G>T	ENST00000302030.2	+	1	689	c.664G>T	c.(664-666)Ggt>Tgt	p.G222C		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	222						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						TATCTCCTATGGTTACATAGT	0.532																																					p.G222C		Atlas-SNP	.											.	OR5A1	72	.	0			c.G664T						.						225	204	211					11																	59211305		2201	4295	6496	SO:0001583	missense	219982	exon1			TCCTATGGTTACA	AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"GPCR / Class A : Olfactory receptors"	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.664G>T	chr11.hg19:g.59211305G>T	ENSP00000303096:p.Gly222Cys	201.0	0.0		135.0	24.0	NM_001004728	B9EH58|Q6IFF2|Q96RB1	Missense_Mutation	SNP	ENST00000302030.2	hg19	CCDS31561.1	.	.	.	.	.	.	.	.	.	.	G	7.376	0.627884	0.14257	.	.	ENSG00000172320	ENST00000302030	T	0.00107	8.72	5.98	-4.11	0.03928	GPCR, rhodopsin-like superfamily (1);	0.819845	0.10903	N	0.621456	T	0.00300	0.0009	M	0.66439	2.03	0.09310	N	1	D	0.53312	0.959	P	0.61800	0.894	T	0.27806	-1.0063	10	0.28530	T	0.3	-0.0131	9.6614	0.39958	0.3212:0.0:0.5648:0.114	.	222	Q8NGJ0	OR5A1_HUMAN	C	222	ENSP00000303096:G222C	ENSP00000303096:G222C	G	+	1	0	OR5A1	58967881	0.000000	0.05858	0.419000	0.26584	0.002000	0.02628	-0.846000	0.04336	-0.648000	0.05437	-0.781000	0.03364	GGT	.	.		0.532	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728		T	59211305	G	T	59211305	3	4	111	1	0	0	0	0	1	0	0	0	11148	1348	47	3	666	3	OR5A1	11	59211305	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	1900655	59211305	75795211	214	16454										
PATL1	219988	hgsc.bcm.edu	37	chr11	59415324	59415324	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tggagaggaaaggaagaataCgggcaaccattctcttccct	11	9	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:59415324C>T	ENST00000300146.9	-	15	1880	c.1796G>A	c.(1795-1797)cGt>cAt	p.R599H		NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	599	Involved in nuclear spleckles localization.|Region C.				cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						AGGAAGAATACGGGCAACCAT	0.468																																					p.R599H		Atlas-SNP	.											PATL1_ENST00000300146,NS,carcinoma,0,2	PATL1	92	.	0			c.G1796A						.						121	112	115					11																	59415324		1939	4145	6084	SO:0001583	missense	219988	exon15			AGAATACGGGCAA	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.1796G>A	chr11.hg19:g.59415324C>T	ENSP00000300146:p.Arg599His	96.0	0.0		76.0	4.0	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Missense_Mutation	SNP	ENST00000300146.9	hg19	CCDS44613.1	.	.	.	.	.	.	.	.	.	.	C	35	5.510461	0.96386	.	.	ENSG00000166889	ENST00000300146;ENST00000428532	T	0.79247	-1.25	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.88738	0.6518	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.88305	0.2952	10	0.66056	D	0.02	-12.6748	20.2312	0.98350	0.0:1.0:0.0:0.0	.	569;599	Q86TB9-4;Q86TB9	.;PATL1_HUMAN	H	599;569	ENSP00000300146:R599H	ENSP00000300146:R599H	R	-	2	0	PATL1	59171900	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.380000	0.79704	2.882000	0.98803	0.655000	0.94253	CGT	.	.		0.468	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716		T	59415324	C	T	59415324	3	4	111	1	0	0	0	0	1	0	0	0	11484	536	19	1	536	1	PATL1	11	59415324	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	204019	59415324	75591192	215	16455										
SNX32	254122	hgsc.bcm.edu	37	chr11	65618862	65618862	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tctgggaacacaggaagtcaAccagctaaggacgtgaggac	13	9	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:65618862A>G	ENST00000308342.6	+	8	1198	c.773A>G	c.(772-774)aAc>aGc	p.N258S		NM_152760.2	NP_689973.2	Q86XE0	SNX32_HUMAN	sorting nexin 32	258					intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				READ - Rectum adenocarcinoma(159;0.171)		CAGGAAGTCAACCAGCTAAGG	0.557											OREG0021087	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N258S		Atlas-SNP	.											.	SNX32	46	.	0			c.A773G						.						100	86	91					11																	65618862		2201	4297	6498	SO:0001583	missense	254122	exon8			AAGTCAACCAGCT	AK055496	CCDS8113.2	11q13.1	2008-03-11	2008-03-11	2008-03-11	ENSG00000172803	ENSG00000172803		"Sorting nexins"	26423	protein-coding gene	gene with protein product			"sorting nexin 6B"	SNX6B		16782399	Standard	XM_005273871		Approved	FLJ30934	uc001ofr.3	Q86XE0	OTTHUMG00000128491	ENST00000308342.6:c.773A>G	chr11.hg19:g.65618862A>G	ENSP00000310620:p.Asn258Ser	65.0	0.0	1085	51.0	4.0	NM_152760	Q8IW53|Q96NG4	Missense_Mutation	SNP	ENST00000308342.6	hg19	CCDS8113.2	.	.	.	.	.	.	.	.	.	.	A	10.29	1.310563	0.23821	.	.	ENSG00000172803	ENST00000308342	T	0.26518	1.73	5.73	3.39	0.38822	Vps5 C-terminal (1);	0.114234	0.39407	N	0.001369	T	0.10465	0.0256	N	0.10972	0.075	0.25035	N	0.991241	B	0.22604	0.072	B	0.23419	0.046	T	0.26467	-1.0102	10	0.17832	T	0.49	-17.0534	2.6412	0.04971	0.6167:0.1546:0.0803:0.1484	.	258	Q86XE0	SNX32_HUMAN	S	258	ENSP00000310620:N258S	ENSP00000310620:N258S	N	+	2	0	SNX32	65375438	0.042000	0.20092	0.629000	0.29254	0.998000	0.95712	0.561000	0.23515	0.424000	0.26061	0.533000	0.62120	AAC	.	.		0.557	SNX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250295.3	NM_152760		G	65618862	A	G	65618862	3	3	111	1	0	0	0	0	1	0	0	0	14917	43	2	2	803	2	SNX32	11	65618862	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	6203538	65618862	69387654	216	16456										
ACY3	91703	hgsc.bcm.edu	37	chr11	67412312	67412312	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acgcccacgggtctataggcTtccatctcaaaggcaggaaa	10	12	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:67412312T>C	ENST00000255082.3	-	7	833	c.663A>G	c.(661-663)gaA>gaG	p.E221E	ACY3_ENST00000529256.1_Silent_p.E100E	NM_080658.1	NP_542389.1	Q96HD9	ACY3_HUMAN	aspartoacylase (aminocyclase) 3	221	Shielding domain. {ECO:0000250}.				viral process (GO:0016032)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			endometrium(1)|lung(5)|prostate(2)	8					L-Aspartic Acid(DB00128)	GTCTATAGGCTTCCATCTCAA	0.647																																					p.E221E	GBM(56;346 1011 27014 29495 46841)	Atlas-SNP	.											.	ACY3	27	.	0			c.A663G						.						50	38	42					11																	67412312		2193	4289	6482	SO:0001819	synonymous_variant	91703	exon7			ATAGGCTTCCATC	BC008689	CCDS8175.1	11q13.2	2014-08-08			ENSG00000132744	ENSG00000132744			24104	protein-coding gene	gene with protein product		614413				14656720	Standard	NM_080658		Approved	HCBP1, MGC9740, ACY-3	uc001omq.3	Q96HD9	OTTHUMG00000167283	ENST00000255082.3:c.663A>G	chr11.hg19:g.67412312T>C		130.0	0.0		93.0	4.0	NM_080658		Silent	SNP	ENST00000255082.3	hg19	CCDS8175.1																																																																																			.	.		0.647	ACY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394002.1	NM_080658		C	67412312	T	C	67412312	2	2	111	1	0	0	0	0	0	0	0	1	227	1606	56	2		2	ACY3	11	67412312	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1793450	67412312	67594204	217	16457										
GAL	51083	hgsc.bcm.edu	37	chr11	68453108	68453108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaacagcgcgggctacctgcTgggcccacgtaagtgactga	14	12	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:68453108T>C	ENST00000265643.3	+	3	386	c.128T>C	c.(127-129)cTg>cCg	p.L43P		NM_015973.3	NP_057057.2	P22466	GALA_HUMAN	galanin/GMAP prepropeptide	43					cAMP-mediated signaling (GO:0019933)|feeding behavior (GO:0007631)|inflammatory response (GO:0006954)|insulin secretion (GO:0030073)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of root hair elongation (GO:1902891)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catagen (GO:0051795)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of large conductance calcium-activated potassium channel activity (GO:1902608)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein kinase A signaling (GO:0010737)|regulation of glucocorticoid metabolic process (GO:0031943)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to insulin (GO:0032868)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|secretory granule (GO:0030141)	neuropeptide hormone activity (GO:0005184)|type 1 galanin receptor binding (GO:0031764)|type 2 galanin receptor binding (GO:0031765)|type 3 galanin receptor binding (GO:0031766)			lung(4)	4	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)		GGCTACCTGCTGGGCCCACGT	0.642																																					p.L43P		Atlas-SNP	.											.	GAL	11	.	0			c.T128C						.						74	60	65					11																	68453108		2200	4294	6494	SO:0001583	missense	51083	exon3			ACCTGCTGGGCCC	L11144	CCDS8183.1	11q13.2	2013-02-26	2012-10-23		ENSG00000069482	ENSG00000069482		"Endogenous ligands"	4114	protein-coding gene	gene with protein product	"galanin-message-associated peptide", "galanin/GMAP prepropeptide"	137035	"galanin", "galanin prepropeptide"	GALN		7508413	Standard	XM_006718580		Approved	GMAP, GAL-GMAP, GLNN	uc001oob.3	P22466	OTTHUMG00000167890	ENST00000265643.3:c.128T>C	chr11.hg19:g.68453108T>C	ENSP00000265643:p.Leu43Pro	65.0	0.0		60.0	4.0	NM_015973	Q14413	Missense_Mutation	SNP	ENST00000265643.3	hg19	CCDS8183.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.486515	0.44249	.	.	ENSG00000069482	ENST00000265643	T	0.60672	0.17	3.36	3.36	0.38483	Galanin (4);	0.000000	0.64402	D	0.000010	T	0.72137	0.3423	M	0.78801	2.425	0.26695	N	0.971273	D	0.89917	1.0	D	0.91635	0.999	T	0.63005	-0.6733	10	0.87932	D	0	-22.3649	8.0973	0.30835	0.0:0.0:0.0:1.0	.	43	P22466	GALA_HUMAN	P	43	ENSP00000265643:L43P	ENSP00000265643:L43P	L	+	2	0	GAL	68209684	0.778000	0.28640	0.386000	0.26170	0.841000	0.47740	4.018000	0.57174	1.397000	0.46682	0.459000	0.35465	CTG	.	.		0.642	GAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396843.2	NM_001479		C	68453108	T	C	68453108	3	2	111	1	0	0	0	0	1	0	0	0	6204	1580	55	2	134	2	GAL	11	68453108	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1040796	68453108	66553408	218	16458										
FCHSD2	9873	hgsc.bcm.edu	37	chr11	72551974	72551974	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tatgccttgatgcctgtgagAatcctggtgactcagcatga	11	9	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:72551974A>G	ENST00000409418.4	-	19	2470	c.2087T>C	c.(2086-2088)tTc>tCc	p.F696S	FCHSD2_ENST00000409314.1_Missense_Mutation_p.F720S|ATG16L2_ENST00000534905.1_Intron|FCHSD2_ENST00000409263.1_Missense_Mutation_p.F57S|FCHSD2_ENST00000311172.7_Missense_Mutation_p.F640S|FCHSD2_ENST00000458644.2_Missense_Mutation_p.F560S	NM_014824.2	NP_055639.2	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	696										endometrium(2)|large_intestine(11)|lung(5)|ovary(2)|prostate(1)|skin(1)	22			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			TGCCTGTGAGAATCCTGGTGA	0.433																																					p.F696S		Atlas-SNP	.											.	FCHSD2	106	.	0			c.T2087C						.						116	103	108					11																	72551974		2200	4293	6493	SO:0001583	missense	9873	exon19			TGTGAGAATCCTG	AB018312	CCDS8218.2	11q13.3	2008-02-05	2004-04-14	2004-04-16	ENSG00000137478	ENSG00000137478			29114	protein-coding gene	gene with protein product			"SH3 multiple domains 3"	SH3MD3		9872452, 15067381	Standard	NM_014824		Approved	KIAA0769	uc009ytl.3	O94868	OTTHUMG00000153082	ENST00000409418.4:c.2087T>C	chr11.hg19:g.72551974A>G	ENSP00000386722:p.Phe696Ser	74.0	0.0		67.0	4.0	NM_014824	B4DNI3|Q7L8J9|Q8WVM2|Q96FV7|Q9UF77	Missense_Mutation	SNP	ENST00000409418.4	hg19	CCDS8218.2	.	.	.	.	.	.	.	.	.	.	A	19.08	3.757369	0.69648	.	.	ENSG00000137478	ENST00000311172;ENST00000409314;ENST00000409418;ENST00000409263;ENST00000458644	T;T;T;T	0.14144	2.56;2.67;2.68;2.53	5.3	4.16	0.48862	.	0.442270	0.24307	N	0.039674	T	0.07863	0.0197	N	0.24115	0.695	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.24621	-1.0155	10	0.15499	T	0.54	-24.1839	6.5325	0.22334	0.7643:0.1581:0.0776:0.0	.	560;696	E7ENZ2;O94868	.;FCSD2_HUMAN	S	640;720;696;57;560	ENSP00000308978:F640S;ENSP00000386987:F720S;ENSP00000386722:F696S;ENSP00000402972:F560S	ENSP00000308978:F640S	F	-	2	0	FCHSD2	72229622	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	3.613000	0.54152	1.011000	0.39340	0.460000	0.39030	TTC	.	.		0.433	FCHSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329429.2	NM_014824		G	72551974	A	G	72551974	3	3	111	1	0	0	0	0	1	0	0	0	5798	246	9	2	143	2	FCHSD2	11	72551974	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	4098866	72551974	62454542	219	16459										
TYR	7299	hgsc.bcm.edu	37	chr11	88911210	88911210	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctgtgtctcctctaagaaccTgatggagaaggaatgctgtc	11	9	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:88911210T>C	ENST00000263321.5	+	1	591	c.89T>C	c.(88-90)cTg>cCg	p.L30P	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	30					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	TCTAAGAACCTGATGGAGAAG	0.542																																					p.L30P		Atlas-SNP	.											.	TYR	130	.	0			c.T89C						.						78	77	77					11																	88911210		2201	4299	6500	SO:0001583	missense	7299	exon1			AGAACCTGATGGA	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"oculocutaneous albinism IA"	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.89T>C	chr11.hg19:g.88911210T>C	ENSP00000263321:p.Leu30Pro	114.0	0.0		100.0	4.0	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	hg19	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.028925	0.75504	.	.	ENSG00000077498	ENST00000263321	D	0.99405	-5.84	6.07	6.07	0.98685	.	0.151799	0.46145	D	0.000319	D	0.99606	0.9857	M	0.92459	3.31	0.80722	D	1	D	0.56746	0.977	D	0.64506	0.926	D	0.97914	1.0310	9	.	.	.	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	30	P14679	TYRO_HUMAN	P	30	ENSP00000263321:L30P	.	L	+	2	0	TYR	88550858	1.000000	0.71417	0.985000	0.45067	0.829000	0.46940	7.571000	0.82399	2.326000	0.78906	0.533000	0.62120	CTG	.	.		0.542	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		C	88911210	T	C	88911210	3	2	111	1	0	0	0	0	1	0	0	0	16828	1580	55	2	91	2	TYR	11	88911210	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	16359236	88911210	46095306	220	16460										
PGR	5241	hgsc.bcm.edu	37	chr11	100933405	100933405	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gggcttggctttcatttggaAcgcccactggctgtgggaga	15	9	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:100933405A>G	ENST00000325455.5	-	4	3438	c.1985T>C	c.(1984-1986)gTt>gCt	p.V662A	PGR_ENST00000263463.5_Intron|PGR_ENST00000534013.1_Missense_Mutation_p.V68A	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	662					cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	TTCATTTGGAACGCCCACTGG	0.418																																					p.V662A	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.T1985C						.						138	120	126					11																	100933405		2203	4300	6503	SO:0001583	missense	5241	exon4			TTTGGAACGCCCA	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"Nuclear hormone receptors"	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.1985T>C	chr11.hg19:g.100933405A>G	ENSP00000325120:p.Val662Ala	86.0	0.0		97.0	4.0	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	hg19	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	A	12.43	1.936824	0.34189	.	.	ENSG00000082175	ENST00000325455;ENST00000534013	D;D	0.86562	-1.71;-2.14	5.41	4.26	0.50523	Nuclear hormone receptor, ligand-binding (1);	0.567138	0.17572	N	0.169458	T	0.73337	0.3574	N	0.04203	-0.255	0.80722	D	1	B;B	0.13145	0.006;0.007	B;B	0.06405	0.002;0.001	T	0.65335	-0.6193	10	0.39692	T	0.17	.	12.4565	0.55708	0.8597:0.1402:0.0:0.0	.	662;43	P06401;A7LQ08	PRGR_HUMAN;.	A	662;68	ENSP00000325120:V662A;ENSP00000436561:V68A	ENSP00000325120:V662A	V	-	2	0	PGR	100438615	1.000000	0.71417	0.470000	0.27216	0.668000	0.39293	8.421000	0.90259	0.852000	0.35287	0.482000	0.46254	GTT	.	.		0.418	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			G	100933405	A	G	100933405	3	3	111	1	0	0	0	0	1	0	0	0	11814	43	2	2	836	2	PGR	11	100933405	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	12022195	100933405	34073111	221	16461										
CWF19L2	143884	hgsc.bcm.edu	37	chr11	107260852	107260852	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gattttctgctgttcccatcTtttcatttttgactaaatca	4	9	4	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:107260852T>C	ENST00000282251.5	-	12	1847	c.1820A>G	c.(1819-1821)aAg>aGg	p.K607R	CWF19L2_ENST00000433523.1_Missense_Mutation_p.K607R	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	607							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		TGTTCCCATCTTTTCATTTTT	0.333																																					p.K607R		Atlas-SNP	.											CWF19L2_ENST00000282251,right_upper_lobe,carcinoma,0,2	CWF19L2	135	.	0			c.A1820G						.						149	122	131					11																	107260852		2201	4296	6497	SO:0001583	missense	143884	exon12			CCCATCTTTTCAT	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1820A>G	chr11.hg19:g.107260852T>C	ENSP00000282251:p.Lys607Arg	132.0	0.0		100.0	4.0	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	hg19	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	T	17.36	3.369677	0.61624	.	.	ENSG00000152404	ENST00000282251;ENST00000433523	T;T	0.29142	1.58;1.58	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.33498	0.0865	M	0.65320	2	0.58432	D	0.999997	P	0.46327	0.876	P	0.44897	0.463	T	0.13255	-1.0516	10	0.08837	T	0.75	-21.41	14.1054	0.65085	0.0:0.0:0.0:1.0	.	607	Q2TBE0	C19L2_HUMAN	R	607	ENSP00000282251:K607R;ENSP00000387533:K607R	ENSP00000282251:K607R	K	-	2	0	CWF19L2	106766062	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.828000	0.69307	2.211000	0.71520	0.460000	0.39030	AAG	.	.		0.333	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		C	107260852	T	C	107260852	3	2	111	1	0	0	0	0	1	0	0	0	4074	1609	56	2	892	2	CWF19L2	11	107260852	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	6327447	107260852	27745664	222	16462										
ALKBH8	91801	hgsc.bcm.edu	37	chr11	107403057	107403057	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaggtatctagattctcctgTcatcaccagcaaactccgac	6	13	4	1	rs202093339		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:107403057T>C	ENST00000428149.2	-	8	998	c.847A>G	c.(847-849)Aca>Gca	p.T283A	ALKBH8_ENST00000389568.3_Missense_Mutation_p.T283A|ALKBH8_ENST00000417449.2_Missense_Mutation_p.T286A|ALKBH8_ENST00000429370.1_Intron	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	283	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cellular response to DNA damage stimulus (GO:0006974)|tRNA methylation (GO:0030488)	cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|RNA binding (GO:0003723)|tRNA (uracil) methyltransferase activity (GO:0016300)			breast(2)|large_intestine(2)|lung(5)	9		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)		GATTCTCCTGTCATCACCAGC	0.408																																					p.T283A		Atlas-SNP	.											.	ALKBH8	88	.	0			c.A847G						.						113	96	101					11																	107403057		692	1591	2283	SO:0001583	missense	91801	exon8			CTCCTGTCATCAC	AF086489	CCDS8337.2, CCDS73376.1	11q22.3	2013-10-04			ENSG00000137760	ENSG00000137760	2.1.1.229	"Alkylation repair homologs", "RNA binding motif (RRM) containing"	25189	protein-coding gene	gene with protein product		613306				20123966	Standard	NM_138775		Approved	MGC10235	uc009yxp.3	Q96BT7	OTTHUMG00000157008	ENST00000428149.2:c.847A>G	chr11.hg19:g.107403057T>C	ENSP00000415885:p.Thr283Ala	188.0	0.0		174.0	7.0	NM_138775	B1Q2M0|B4DEF6|Q8N989	Missense_Mutation	SNP	ENST00000428149.2	hg19	CCDS8337.2	.	.	.	.	.	.	.	.	.	.	T	17.18	3.324084	0.60634	.	.	ENSG00000137760	ENST00000428149;ENST00000389568;ENST00000417449	T;T;T	0.29397	1.57;1.57;1.57	5.01	5.01	0.66863	Oxoglutarate/iron-dependent oxygenase (2);	0.351918	0.30920	N	0.008611	T	0.31263	0.0791	L	0.42632	1.34	0.47065	D	0.9993	P;B	0.36483	0.555;0.313	B;B	0.40982	0.345;0.165	T	0.05852	-1.0860	10	0.35671	T	0.21	-16.0709	13.8922	0.63747	0.0:0.0:0.0:1.0	.	283;286	Q96BT7;Q96BT7-4	ALKB8_HUMAN;.	A	283;283;286	ENSP00000415885:T283A;ENSP00000374219:T283A;ENSP00000397673:T286A	ENSP00000374219:T283A	T	-	1	0	ALKBH8	106908267	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	1.448000	0.35112	1.883000	0.54544	0.533000	0.62120	ACA	.	T|1.000;A|0.000		0.408	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775		C	107403057	T	C	107403057	3	2	111	1	0	0	0	0	1	0	0	0	533	1667	58	2	1167	2	ALKBH8	11	107403057	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	142205	107403057	27603459	223	16463										
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120312472	120312472	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttactaaaatctcgcccggcTcatttggctgttttcttaca	6	11	3	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:120312472T>C	ENST00000397843.2	+	14	1315	c.1149T>C	c.(1147-1149)gcT>gcC	p.A383A	ARHGEF12_ENST00000356641.3_Silent_p.A364A|ARHGEF12_ENST00000532993.1_Silent_p.A280A	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	383	RGSL.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		CTCGCCCGGCTCATTTGGCTG	0.378			T	MLL	AML																																p.A383A		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.T1149C						.						163	149	154					11																	120312472		1843	4081	5924	SO:0001819	synonymous_variant	23365	exon14			CCCGGCTCATTTG	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.1149T>C	chr11.hg19:g.120312472T>C		131.0	0.0		88.0	4.0	NM_015313	O15086|Q6P526	Silent	SNP	ENST00000397843.2	hg19	CCDS41727.1																																																																																			.	.		0.378	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		C	120312472	T	C	120312472	2	2	111	1	0	0	0	0	0	0	0	1	897	1538	54	2		2	ARHGEF12	11	120312472	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	12909415	120312472	14694044	224	16464										
TECTA	7007	hgsc.bcm.edu	37	chr11	121060537	121060537	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acgagccgggtggatgggccTctctgcagctgtgtaacagg	16	10	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:121060537T>C	ENST00000392793.1	+	23	6586	c.6315T>C	c.(6313-6315)ccT>ccC	p.P2105P	TECTA_ENST00000264037.2_Silent_p.P2105P			O75443	TECTA_HUMAN	tectorin alpha	2105					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGGATGGGCCTCTCTGCAGCT	0.567																																					p.P2105P		Atlas-SNP	.											.	TECTA	329	.	0			c.T6315C						.						125	116	119					11																	121060537		2203	4299	6502	SO:0001819	synonymous_variant	7007	exon22			TGGGCCTCTCTGC	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.6315T>C	chr11.hg19:g.121060537T>C		102.0	0.0		88.0	4.0	NM_005422		Silent	SNP	ENST00000392793.1	hg19	CCDS8434.1																																																																																			.	.		0.567	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		C	121060537	T	C	121060537	2	2	111	1	0	0	0	0	0	0	0	1	15762	1538	54	2		2	TECTA	11	121060537	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	748065	121060537	13945979	225	16465										
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126326264	126326264	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctgtactgggtgacagctggGttggcctttgcagagcagtg	16	8	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:126326264G>A	ENST00000525144.2	-	7	1077	c.828C>T	c.(826-828)aaC>aaT	p.N276N	KIRREL3_ENST00000525704.2_Silent_p.N276N|KIRREL3_ENST00000529097.2_Silent_p.N276N	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	276	Ig-like C2-type 3.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		TGACAGCTGGGTTGGCCTTTG	0.637																																					p.N276N		Atlas-SNP	.											.	KIRREL3	183	.	0			c.C828T						.						57	64	62					11																	126326264		2064	4204	6268	SO:0001819	synonymous_variant	84623	exon7			AGCTGGGTTGGCC	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.828C>T	chr11.hg19:g.126326264G>A		154.0	0.0		96.0	4.0	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Silent	SNP	ENST00000525144.2	hg19	CCDS53723.1																																																																																			.	.		0.637	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		A	126326264	G	A	126326264	2	1	111	1	0	0	0	0	0	0	0	1	8335	1252	44	3		3	KIRREL3	11	126326264	Silent	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	5265727	126326264	8680252	226	16466										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133815970	133815970	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccttacctgcatactcagggTccacgtgcggcgggtagtag	13	12	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr11:133815970T>C	ENST00000321016.8	-	2	478	c.248A>G	c.(247-249)gAc>gGc	p.D83G	IGSF9B_ENST00000533871.2_Missense_Mutation_p.D83G			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	83	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		ATACTCAGGGTCCACGTGCGG	0.622																																					p.D83G		Atlas-SNP	.											.	IGSF9B	290	.	0			c.A248G						.						47	59	55					11																	133815970		2140	4237	6377	SO:0001583	missense	22997	exon2			TCAGGGTCCACGT	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.248A>G	chr11.hg19:g.133815970T>C	ENSP00000317980:p.Asp83Gly	128.0	0.0		95.0	4.0	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	T	24.5	4.539690	0.85917	.	.	ENSG00000080854	ENST00000321016;ENST00000527648;ENST00000533160;ENST00000526663	T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0	5.68	5.68	0.88126	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	T	0.74366	0.3707	L	0.53561	1.675	0.58432	D	0.999998	D	0.67145	0.996	D	0.71870	0.975	T	0.73300	-0.4026	10	0.38643	T	0.18	.	15.926	0.79618	0.0:0.0:0.0:1.0	.	83	Q9UPX0	TUTLB_HUMAN	G	83;83;73;130	ENSP00000317980:D83G;ENSP00000436576:D83G;ENSP00000434026:D73G;ENSP00000435989:D130G	ENSP00000317980:D83G	D	-	2	0	IGSF9B	133321180	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.938000	0.87678	2.175000	0.68902	0.533000	0.62120	GAC	.	.		0.622	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		C	133815970	T	C	133815970	3	2	111	1	0	0	0	0	1	0	0	0	7615	1667	58	2	3873	2	IGSF9B	11	133815970	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	7489706	133815970	1190546	227	16467										
ATN1	1822	hgsc.bcm.edu	37	chr12	7050122	7050122	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atcccctacccagctggaacTctccctaaccccctgcttcc	4	21	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:7050122T>C	ENST00000356654.4	+	8	3531	c.3294T>C	c.(3292-3294)acT>acC	p.T1098T	C12orf57_ENST00000544681.1_5'Flank|RNU7-1_ENST00000458811.1_RNA|U47924.31_ENST00000607421.1_RNA|ATN1_ENST00000396684.2_Silent_p.T1098T|C12orf57_ENST00000537087.1_5'Flank	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	1098					cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						CAGCTGGAACTCTCCCTAACC	0.587																																					p.T1098T		Atlas-SNP	.											.	ATN1	95	.	0			c.T3294C						.						144	114	124					12																	7050122		2203	4300	6503	SO:0001819	synonymous_variant	1822	exon8			TGGAACTCTCCCT	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"dentatorubral-pallidoluysian atrophy (atrophin-1)"	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.3294T>C	chr12.hg19:g.7050122T>C		103.0	0.0		65.0	5.0	NM_001007026	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	hg19	CCDS31734.1																																																																																			.	.		0.587	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		C	7050122	T	C	7050122	2	2	111	1	0	0	0	0	0	0	0	1	1111	1538	54	2		2	ATN1	12	7050122	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		7050122	126801773	228	16468										
PTPRO	5800	hgsc.bcm.edu	37	chr12	15668472	15668472	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tattgaaaatctggttcctgGtgcccagtaccaggttgtaa	10	8	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:15668472G>A	ENST00000281171.4	+	8	1835	c.1505G>A	c.(1504-1506)gGt>gAt	p.G502D	PTPRO_ENST00000348962.2_Missense_Mutation_p.G502D|PTPRO_ENST00000543886.1_Missense_Mutation_p.G502D	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	502	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				CTGGTTCCTGGTGCCCAGTAC	0.403																																					p.G502D		Atlas-SNP	.											.	PTPRO	148	.	0			c.G1505A						.						113	105	108					12																	15668472		2203	4300	6503	SO:0001583	missense	5800	exon8			TTCCTGGTGCCCA	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9678	protein-coding gene	gene with protein product	"osteoclastic transmembrane protein-tyrosine phosphatase"	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.1505G>A	chr12.hg19:g.15668472G>A	ENSP00000281171:p.Gly502Asp	151.0	0.0		95.0	4.0	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	hg19	CCDS8675.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.788610	0.90367	.	.	ENSG00000151490	ENST00000281171;ENST00000543886;ENST00000348962	T;T;T	0.61742	0.08;0.08;0.08	4.93	4.93	0.64822	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000068	T	0.65196	0.2668	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	0.984;0.987;1.0	P;P;D	0.97110	0.77;0.852;1.0	T	0.66428	-0.5926	10	0.48119	T	0.1	.	16.561	0.84566	0.0:0.0:1.0:0.0	.	502;502;502	Q16827-2;Q16827;Q8IYG3	.;PTPRO_HUMAN;.	D	502	ENSP00000281171:G502D;ENSP00000444173:G502D;ENSP00000343434:G502D	ENSP00000281171:G502D	G	+	2	0	PTPRO	15559739	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.839000	0.92120	2.578000	0.87016	0.650000	0.86243	GGT	.	.		0.403	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			A	15668472	G	A	15668472	3	1	111	1	0	0	0	0	1	0	0	0	12824	1261	44	3	1535	3	PTPRO	12	15668472	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	8618350	15668472	118183423	229	16469										
ANO6	196527	hgsc.bcm.edu	37	chr12	45803139	45803139	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ataaattgttctttttggcaGctggatcatgaatctaattg	8	5	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:45803139G>A	ENST00000320560.8	+	16	2082		c.e16-1		ANO6_ENST00000423947.3_Splice_Site|ANO6_ENST00000426898.2_Splice_Site|ANO6_ENST00000435642.1_Splice_Site|ANO6_ENST00000425752.2_Splice_Site|ANO6_ENST00000441606.2_Splice_Site	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6						activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						CTTTTTGGCAGCTGGATCATG	0.393																																					.		Atlas-SNP	.											.	ANO6	163	.	0			c.1944-1G>A						.						88	90	89					12																	45803139		2203	4300	6503	SO:0001630	splice_region_variant	196527	exon17			TTGGCAGCTGGAT	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.1881-1G>A	chr12.hg19:g.45803139G>A		75.0	0.0		53.0	4.0	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Splice_Site	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.362933	0.82353	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9209	0.79570	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ANO6	44089406	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.390000	0.90175	2.596000	0.87737	0.655000	0.94253	.	.	.		0.393	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743	Intron	A	45803139	G	A	45803139	5	1	111	1	0	0	0	0	0	0	1	0	701	985	34	3	1962	3	ANO6	12	45803139	Splice_Site	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	30134667	45803139	88048756	230	16470										
LASS5	91012	hgsc.bcm.edu	37	chr12	50529757	50529757	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tctgagacatcatgtagacaCatgatcagagttcccactcg	8	11	3	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:50529757C>T	ENST00000317551.6	-	7	856	c.732G>A	c.(730-732)atG>atA	p.M244I	CERS5_ENST00000422340.2_Missense_Mutation_p.M186I	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	244	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										CATGTAGACACATGATCAGAG	0.428																																					p.M244I		Atlas-SNP	.											.	.	.	.	0			c.G732A						.						132	122	125					12																	50529757		2203	4300	6503	SO:0001583	missense	91012	exon7			TAGACACATGATC		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"Homeoboxes / CERS class"	23749	protein-coding gene	gene with protein product		615335	"LAG1 longevity assurance homolog 5 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 5"	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.732G>A	chr12.hg19:g.50529757C>T	ENSP00000325485:p.Met244Ile	107.0	0.0		77.0	4.0	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	hg19	CCDS8801.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	15.75|15.75|15.75	2.925636|2.925636|2.925636	0.52759|0.52759|0.52759	.|.|.	.|.|.	ENSG00000139624|ENSG00000139624|ENSG00000139624	ENST00000550547;ENST00000547800|ENST00000551005;ENST00000317551;ENST00000422340|ENST00000550919	.|D;D;D|.	.|0.85773|.	.|-2.03;-2.03;-2.03|.	4.35|4.35|4.35	2.43|2.43|2.43	0.29744|0.29744|0.29744	.|TRAM/LAG1/CLN8 homology domain (3);|.	.|0.234996|.	.|0.47455|.	.|D|.	.|0.000232|.	T|T|T	0.67915|0.67915|0.67915	0.2944|0.2944|0.2944	M|M|M	0.69248|0.69248|0.69248	2.105|2.105|2.105	0.42608|0.42608|0.42608	D|D|D	0.993304|0.993304|0.993304	.|B;B;B|.	.|0.27192|.	.|0.013;0.171;0.036|.	.|B;B;B|.	.|0.25759|.	.|0.038;0.063;0.036|.	T|T|T	0.65651|0.65651|0.65651	-0.6116|-0.6116|-0.6116	5|10|5	.|0.54805|.	.|T|.	.|0.06|.	-2.1121|-2.1121|-2.1121	11.1144|11.1144|11.1144	0.48252|0.48252|0.48252	0.1437:0.7178:0.1385:0.0|0.1437:0.7178:0.1385:0.0|0.1437:0.7178:0.1385:0.0	.|.|.	.|186;244;163|.	.|B4DV54;Q8N5B7;F8W0U5|.	.|.;CERS5_HUMAN;.|.	Y|I|M	46;148|163;244;186|14	.|ENSP00000447556:M163I;ENSP00000325485:M244I;ENSP00000389050:M186I|.	.|ENSP00000325485:M244I|.	C|M|V	-|-|-	2|3|1	0|0|0	CERS5|CERS5|CERS5	48816024|48816024|48816024	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.990000|0.990000|0.990000	0.78478|0.78478|0.78478	2.590000|2.590000|2.590000	0.46154|0.46154|0.46154	0.526000|0.526000|0.526000	0.28541|0.28541|0.28541	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	TGT|ATG|GTG	.	.		0.428	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190		T	50529757	C	T	50529757	3	4	111	1	0	0	0	0	1	0	0	0	8651	478	17	3	462	3	LASS5	12	50529757	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	4726618	50529757	83322138	231	16471										
KRT2	3849	hgsc.bcm.edu	37	chr12	53039093	53039093	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcctctggagccagactgtcGgcctccagagccataactgc	11	15	1	2	rs571471637		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:53039093G>A	ENST00000309680.3	-	9	1651	c.1630C>T	c.(1630-1632)Cga>Tga	p.R544*		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	544	Tail.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		CCAGACTGTCGGCCTCCAGAG	0.572													G|||	1	0.000199681	0	0	5008	,	,		19460	0		0.001	False		,,,				2504	0				p.R544X		Atlas-SNP	.											.	KRT2	94	.	0			c.C1630T						.						117	122	120					12																	53039093		2203	4300	6503	SO:0001587	stop_gained	3849	exon9			ACTGTCGGCCTCC		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.1630C>T	chr12.hg19:g.53039093G>A	ENSP00000310861:p.Arg544*	74.0	0.0		67.0	13.0	NM_000423	Q4VAQ2	Nonsense_Mutation	SNP	ENST00000309680.3	hg19	CCDS8835.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.158842	0.57368	.	.	ENSG00000172867	ENST00000309680	.	.	.	4.06	-2.84	0.05751	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	4.008	0.09610	0.1189:0.1732:0.5177:0.1902	.	.	.	.	X	544	.	ENSP00000310861:R544X	R	-	1	2	KRT2	51325360	0.000000	0.05858	0.410000	0.26471	0.327000	0.28475	-0.305000	0.08188	-0.359000	0.08150	-0.397000	0.06425	CGA	.	.		0.572	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		A	53039093	G	A	53039093	4	1	111	1	0	0	0	0	0	1	0	0	8466	1124	39	1	293	1	KRT2	12	53039093	Nonsense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	2509336	53039093	80812802	232	16472										
HOXC13	3229	hgsc.bcm.edu	37	chr12	54338925	54338925	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	caaagagaagcgccggcgcaTctccgccaccacgaacctct	9	17	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:54338925T>C	ENST00000243056.3	+	2	1034	c.878T>C	c.(877-879)aTc>aCc	p.I293T		NM_017410.2	NP_059106.2	P31276	HXC13_HUMAN	homeobox C13	293					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|hair follicle development (GO:0001942)|nail development (GO:0035878)|tongue morphogenesis (GO:0043587)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			breast(1)|large_intestine(1)|skin(1)	3						CGCCGGCGCATCTCCGCCACC	0.567			T	NUP98	AML																																p.I293T		Atlas-SNP	.		Dom	yes		12	12q13.3	3229	homeo box C13		L	.	HOXC13	24	.	0			c.T878C						.						67	73	71					12																	54338925		2203	4300	6503	SO:0001583	missense	3229	exon2			GGCGCATCTCCGC		CCDS8865.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123364	ENSG00000123364		"Homeoboxes / ANTP class : HOXL subclass"	5125	protein-coding gene	gene with protein product		142976	"homeo box C13"	HOX3, HOX3G		1973146, 1358459	Standard	NM_017410		Approved		uc001sei.3	P31276	OTTHUMG00000160008	ENST00000243056.3:c.878T>C	chr12.hg19:g.54338925T>C	ENSP00000243056:p.Ile293Thr	125.0	0.0		97.0	4.0	NM_017410	Q5BL02|Q96J32|Q9NR24|Q9NYD5	Missense_Mutation	SNP	ENST00000243056.3	hg19	CCDS8865.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.495089	0.85069	.	.	ENSG00000123364	ENST00000243056	D	0.96619	-4.07	4.95	4.95	0.65309	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98422	0.9475	M	0.92459	3.31	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99478	1.0947	10	0.87932	D	0	.	14.0373	0.64654	0.0:0.0:0.0:1.0	.	293	P31276	HXC13_HUMAN	T	293	ENSP00000243056:I293T	ENSP00000243056:I293T	I	+	2	0	HOXC13	52625192	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.797000	0.85911	2.224000	0.72417	0.533000	0.62120	ATC	.	.		0.567	HOXC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358865.2			C	54338925	T	C	54338925	3	2	111	1	0	0	0	0	1	0	0	0	7321	1435	50	2	884	2	HOXC13	12	54338925	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1299832	54338925	79512970	233	16473										
ITGA7	3679	hgsc.bcm.edu	37	chr12	56091488	56091488	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaggggctcacctgaagagcActgcggtgtcagccagggag	17	10	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:56091488A>G	ENST00000555728.1	-	10	1560	c.1532T>C	c.(1531-1533)gTg>gCg	p.V511A	ITGA7_ENST00000394230.2_Missense_Mutation_p.V471A|ITGA7_ENST00000452168.2_Missense_Mutation_p.V374A|ITGA7_ENST00000257879.6_Missense_Mutation_p.V467A|ITGA7_ENST00000394229.2_Missense_Mutation_p.V467A|ITGA7_ENST00000257880.7_Missense_Mutation_p.V511A|ITGA7_ENST00000553804.1_Missense_Mutation_p.V471A|ITGA7_ENST00000347027.6_Missense_Mutation_p.V467A			Q13683	ITA7_HUMAN	integrin, alpha 7	511					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CCTGAAGAGCACTGCGGTGTC	0.592																																					p.V471A		Atlas-SNP	.											.	ITGA7	194	.	0			c.T1412C						.						71	70	71					12																	56091488		2203	4300	6503	SO:0001583	missense	3679	exon9			AAGAGCACTGCGG		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.1532T>C	chr12.hg19:g.56091488A>G	ENSP00000452387:p.Val511Ala	86.0	0.0		52.0	4.0	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Missense_Mutation	SNP	ENST00000555728.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.49	1.365605	0.24684	.	.	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000353687;ENST00000555728	T;T;T;T;T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64;-0.64;-0.64;-0.64;-0.64	4.28	0.256	0.15567	.	0.187105	0.34338	N	0.004060	T	0.51787	0.1695	L	0.38175	1.15	0.39978	D	0.974879	B;B;B;B	0.12630	0.001;0.001;0.0;0.006	B;B;B;B	0.16289	0.012;0.008;0.005;0.015	T	0.27839	-1.0062	10	0.14656	T	0.56	.	6.8805	0.24170	0.6017:0.0:0.3983:0.0	.	374;511;471;530	Q13683-13;Q13683;Q13683-3;Q4LE35	.;ITA7_HUMAN;.;.	A	471;467;467;374;511;471;467;511;511	ENSP00000452120:V471A;ENSP00000257879:V467A;ENSP00000343009:V467A;ENSP00000393844:V374A;ENSP00000257880:V511A;ENSP00000377777:V471A;ENSP00000377776:V467A;ENSP00000452387:V511A	ENSP00000257879:V467A	V	-	2	0	ITGA7	54377755	0.000000	0.05858	0.597000	0.28824	0.129000	0.20672	0.225000	0.17757	0.202000	0.20498	0.459000	0.35465	GTG	.	.		0.592	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		G	56091488	A	G	56091488	3	3	111	1	0	0	0	0	1	0	0	0	7890	159	6	2	2081	2	ITGA7	12	56091488	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1752563	56091488	77760407	234	16474										
SDR9C7	121214	hgsc.bcm.edu	37	chr12	57327766	57327766	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttgttcgcccactttgtcccTcacccactgggccgccgcct	8	19	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:57327766T>C	ENST00000293502.1	-	1	423	c.280A>G	c.(280-282)Agg>Ggg	p.R94G		NM_148897.2	NP_683695.1	Q8NEX9	DR9C7_HUMAN	short chain dehydrogenase/reductase family 9C, member 7	94					oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	retinol dehydrogenase activity (GO:0004745)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)	7						ACTTTGTCCCTCACCCACTGG	0.542																																					p.R94G		Atlas-SNP	.											.	SDR9C7	31	.	0			c.A280G						.						99	91	94					12																	57327766		2203	4300	6503	SO:0001583	missense	121214	exon1			TGTCCCTCACCCA	AY044434	CCDS8926.1	12q13.3	2014-09-04			ENSG00000170426	ENSG00000170426	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	29958	protein-coding gene	gene with protein product		609769				12234675, 19027726	Standard	NM_148897		Approved	SDR-O, RDHS	uc010sqw.2	Q8NEX9	OTTHUMG00000171004	ENST00000293502.1:c.280A>G	chr12.hg19:g.57327766T>C	ENSP00000293502:p.Arg94Gly	51.0	0.0		50.0	5.0	NM_148897	B3KVB4	Missense_Mutation	SNP	ENST00000293502.1	hg19	CCDS8926.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.534619	0.27475	.	.	ENSG00000170426	ENST00000293502	D	0.88046	-2.33	5.17	5.17	0.71159	NAD(P)-binding domain (1);	0.311338	0.28403	N	0.015476	T	0.80243	0.4587	N	0.25245	0.725	0.34565	D	0.712806	B	0.02656	0.0	B	0.10450	0.005	T	0.81998	-0.0675	10	0.66056	D	0.02	.	14.1369	0.65293	0.0:0.0:0.0:1.0	.	94	Q8NEX9	DR9C7_HUMAN	G	94	ENSP00000293502:R94G	ENSP00000293502:R94G	R	-	1	2	SDR9C7	55614033	0.970000	0.33590	1.000000	0.80357	0.196000	0.23810	2.201000	0.42734	2.182000	0.69389	0.528000	0.53228	AGG	.	.		0.542	SDR9C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411211.1	NM_148897		C	57327766	T	C	57327766	3	2	111	1	0	0	0	0	1	0	0	0	13989	1550	54	2	677	2	SDR9C7	12	57327766	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1236278	57327766	76524129	235	16475										
C12orf66	144577	hgsc.bcm.edu	37	chr12	64588106	64588106	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttgctgtcaacgttttcattTctgaagcagtcgtttgtcgg	10	8	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:64588106T>C	ENST00000398055.3	-	3	907	c.854A>G	c.(853-855)gAa>gGa	p.E285G	C12orf66_ENST00000311915.8_Missense_Mutation_p.E285G|C12orf66_ENST00000544871.1_Missense_Mutation_p.E232G	NM_152440.4	NP_689653	Q96MD2	CL066_HUMAN	chromosome 12 open reading frame 66	285										central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)	5						CGTTTTCATTTCTGAAGCAGT	0.398																																					p.E285G		Atlas-SNP	.											.	C12orf66	28	.	0			c.A854G						.						89	83	85					12																	64588106		1840	4086	5926	SO:0001583	missense	144577	exon3			TTCATTTCTGAAG		CCDS41803.1, CCDS73490.1	12q14.2	2008-08-08			ENSG00000174206	ENSG00000174206			26517	protein-coding gene	gene with protein product						12477932	Standard	NM_152440		Approved	FLJ32549	uc001srw.4	Q96MD2	OTTHUMG00000168763	ENST00000398055.3:c.854A>G	chr12.hg19:g.64588106T>C	ENSP00000381132:p.Glu285Gly	117.0	0.0		97.0	4.0	NM_152440	C9JX54|Q8IYA0	Missense_Mutation	SNP	ENST00000398055.3	hg19	CCDS41803.1	.	.	.	.	.	.	.	.	.	.	T	15.74	2.923479	0.52653	.	.	ENSG00000174206	ENST00000311915;ENST00000544871;ENST00000398055	T;T;T	0.56611	0.45;0.45;0.45	5.94	5.94	0.96194	.	0.043376	0.85682	D	0.000000	T	0.60431	0.2268	M	0.70275	2.135	0.80722	D	1	B;B	0.33512	0.241;0.415	B;B	0.41440	0.075;0.357	T	0.58340	-0.7653	9	.	.	.	-20.112	16.3947	0.83586	0.0:0.0:0.0:1.0	.	232;285	F5H2Q3;Q96MD2	.;CL066_HUMAN	G	285;232;285	ENSP00000311486:E285G;ENSP00000445481:E232G;ENSP00000381132:E285G	.	E	-	2	0	C12orf66	62874373	1.000000	0.71417	1.000000	0.80357	0.546000	0.35178	7.975000	0.88055	2.272000	0.75746	0.459000	0.35465	GAA	.	.		0.398	C12orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400921.1	NM_152440		C	64588106	T	C	64588106	3	2	111	1	0	0	0	0	1	0	0	0	1711	1783	62	2	487	2	C12orf66	12	64588106	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	7260340	64588106	69263789	236	16476										
MDM1	56890	hgsc.bcm.edu	37	chr12	68696473	68696473	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgccagtaggatggaacatgTggtggagaaggcaactgtcc	15	7	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:68696473T>C	ENST00000303145.7	-	12	1985	c.1899A>G	c.(1897-1899)ccA>ccG	p.P633P	MDM1_ENST00000411698.2_Silent_p.P598P|MDM1_ENST00000540418.1_Silent_p.P353P	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	633					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		ATGGAACATGTGGTGGAGAAG	0.408																																					p.P633P		Atlas-SNP	.											.	MDM1	74	.	0			c.A1899G						.						125	126	126					12																	68696473		2203	4300	6503	SO:0001819	synonymous_variant	56890	exon12			AACATGTGGTGGA	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.1899A>G	chr12.hg19:g.68696473T>C		82.0	0.0		67.0	4.0	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Silent	SNP	ENST00000303145.7	hg19	CCDS8983.1																																																																																			.	.		0.408	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		C	68696473	T	C	68696473	2	2	111	1	0	0	0	0	0	0	0	1	9421	1683	59	2		2	MDM1	12	68696473	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	4108367	68696473	65155422	237	16477										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85277565	85277565	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gatttgcccacagaaatctgTaacagaatttgagagaggga	11	6	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:85277565T>C	ENST00000266682.5	-	5	1298				SLC6A15_ENST00000450363.3_Missense_Mutation_p.T277A|SLC6A15_ENST00000552192.1_Intron|SLC6A15_ENST00000551388.1_Intron	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15						amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						CAGAAATCTGTAACAGAATTT	0.358																																					p.T277A		Atlas-SNP	.											.	SLC6A15	159	.	0			c.A829G						.						74	71	72					12																	85277565		2203	4300	6503	SO:0001627	intron_variant	55117	exon5			AATCTGTAACAGA	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.756+72A>G	chr12.hg19:g.85277565T>C		118.0	0.0		111.0	5.0	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	hg19	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	T	0.315	-0.965489	0.02249	.	.	ENSG00000072041	ENST00000450363	T	0.68624	-0.34	0.893	-0.338	0.12651	.	.	.	.	.	T	0.33990	0.0882	N	0.02674	-0.535	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.16070	-1.0415	9	0.39692	T	0.17	.	2.9139	0.05746	0.0:0.3183:0.0:0.6817	.	277	Q9H9F5	.	A	277	ENSP00000390706:T277A	ENSP00000390706:T277A	T	-	1	0	SLC6A15	83801696	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.715000	0.01880	-0.128000	0.11641	-0.256000	0.11100	ACA	.	.		0.358	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		C	85277565	T	C	85277565	1	2	111	0	1	0	0	0	0	0	0	0	14693	1638	57	2		2	SLC6A15	12	85277565	Intron	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	16581092	85277565	48574330	238	16478										
C12orf12	196477	hgsc.bcm.edu	37	chr12	91348442	91348442	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctcaaggaggccgagtgtgcCcagccacagccacagccgcc	12	17	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:91348442C>T	ENST00000358859.2	-	1	511	c.78G>A	c.(76-78)tgG>tgA	p.W26*	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	26																	CCGAGTGTGCCCAgccacagc	0.652																																					p.W26X		Atlas-SNP	.											.	.	.	.	0			c.G78A						.						9	8	8					12																	91348442		2147	4220	6367	SO:0001587	stop_gained	196477	exon1			GTGTGCCCAGCCA	BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 12"	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.78G>A	chr12.hg19:g.91348442C>T	ENSP00000351727:p.Trp26*	86.0	0.0		54.0	10.0	NM_152638	Q8TC47	Nonsense_Mutation	SNP	ENST00000358859.2	hg19	CCDS9036.1	.	.	.	.	.	.	.	.	.	.	C	38	6.668357	0.97747	.	.	ENSG00000197651	ENST00000358859	.	.	.	5.08	4.2	0.49525	.	0.000000	0.32328	N	0.006251	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.4946	9.5742	0.39447	0.0:0.9051:0.0:0.0949	.	.	.	.	X	26	.	ENSP00000351727:W26X	W	-	3	0	C12orf12	89872573	0.880000	0.30214	0.790000	0.31976	0.054000	0.15201	1.208000	0.32345	1.381000	0.46364	-0.448000	0.05591	TGG	.	.		0.652	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		T	91348442	C	T	91348442	4	4	111	1	0	0	0	0	0	1	0	0	1678	624	22	3	1146	3	C12orf12	12	91348442	Nonsense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	6070877	91348442	42503453	239	16479										
SLC17A8	246213	hgsc.bcm.edu	37	chr12	100813891	100813891	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gacccttgatgaggaagagcTgacatcctaccagaatgaag	11	9	0	6			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:100813891T>C	ENST00000323346.5	+	12	2037	c.1724T>C	c.(1723-1725)cTg>cCg	p.L575P	SLC17A8_ENST00000392989.3_Missense_Mutation_p.L525P	NM_001145288.1|NM_139319.2	NP_001138760.1|NP_647480.1	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 8	575					ion transport (GO:0006811)|neurotransmitter transport (GO:0006836)|sensory perception of sound (GO:0007605)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	44						GAGGAAGAGCTGACATCCTAC	0.433																																					p.L575P		Atlas-SNP	.											.	SLC17A8	89	.	0			c.T1724C						.						79	69	73					12																	100813891		2203	4300	6503	SO:0001583	missense	246213	exon12			AAGAGCTGACATC	AJ459241	CCDS9077.1, CCDS44957.1	12q23.1	2013-07-18	2013-07-18		ENSG00000179520	ENSG00000179520		"Solute carriers"	20151	protein-coding gene	gene with protein product	"vesicular glutamate transporter 3"	607557	"deafness, autosomal dominant 25", "solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"	DFNA25		12151341	Standard	NM_139319		Approved	VGLUT3	uc010svi.2	Q8NDX2	OTTHUMG00000170358	ENST00000323346.5:c.1724T>C	chr12.hg19:g.100813891T>C	ENSP00000316909:p.Leu575Pro	49.0	0.0		51.0	4.0	NM_139319	B3KXZ6|B7ZKV4|Q17RQ8	Missense_Mutation	SNP	ENST00000323346.5	hg19	CCDS9077.1	.	.	.	.	.	.	.	.	.	.	T	1.997	-0.430302	0.04669	.	.	ENSG00000179520	ENST00000323346;ENST00000392989	T;T	0.68903	0.06;-0.36	4.8	-9.61	0.00550	.	1.005600	0.07999	N	0.988509	T	0.31857	0.0810	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45498	-0.9257	10	0.29301	T	0.29	.	13.0811	0.59114	0.1253:0.6085:0.0:0.2662	.	575;525	Q8NDX2;Q8NDX2-2	VGLU3_HUMAN;.	P	575;525	ENSP00000316909:L575P;ENSP00000376715:L525P	ENSP00000316909:L575P	L	+	2	0	SLC17A8	99338022	0.068000	0.21057	0.000000	0.03702	0.449000	0.32228	0.151000	0.16283	-2.478000	0.00525	-2.300000	0.00261	CTG	.	.		0.433	SLC17A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408673.2	NM_139319		C	100813891	T	C	100813891	3	2	111	1	0	0	0	0	1	0	0	0	14438	1580	55	2	1770	2	SLC17A8	12	100813891	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	9465449	100813891	33038004	240	16480										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112667541	112667541	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttgattgtctctttgaagccTccaagtgcacacagtgcggc	10	11	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:112667541T>C	ENST00000430131.2	-	40	6359	c.5214A>G	c.(5212-5214)ggA>ggG	p.G1738G	HECTD4_ENST00000550722.1_Silent_p.G2014G|HECTD4_ENST00000377560.5_Silent_p.G1988G			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1738					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CTTTGAAGCCTCCAAGTGCAC	0.478																																					p.G2026G		Atlas-SNP	.											.	.	.	.	0			c.A6078G						.						180	181	181					12																	112667541		1951	4127	6078	SO:0001819	synonymous_variant	283450	exon41			GAAGCCTCCAAGT	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.5214A>G	chr12.hg19:g.112667541T>C		112.0	0.0		88.0	4.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19																																																																																				.	.		0.478	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		C	112667541	T	C	112667541	2	2	111	1	0	0	0	0	0	0	0	1	1698	1538	54	2		2	C12orf51	12	112667541	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	11853650	112667541	21184354	241	16481										
TBX5	6910	hgsc.bcm.edu	37	chr12	114793494	114793494	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tctgaggcccacactgcctgAccacaggctggtgggccacg	13	15	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:114793494A>G	ENST00000310346.4	-	9	2066	c.1400T>C	c.(1399-1401)gTc>gCc	p.V467A	TBX5_ENST00000405440.2_Missense_Mutation_p.V467A|TBX5_ENST00000349716.5_Missense_Mutation_p.V417A	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	467					apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		ACACTGCCTGACCACAGGCTG	0.647																																					p.V467A	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											.	TBX5	188	.	0			c.T1400C						.						28	30	30					12																	114793494		2203	4300	6503	SO:0001583	missense	6910	exon9			TGCCTGACCACAG	U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"T-boxes"	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.1400T>C	chr12.hg19:g.114793494A>G	ENSP00000309913:p.Val467Ala	101.0	0.0		67.0	4.0	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	hg19	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	A	5.661	0.306532	0.10733	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000448888;ENST00000405440	T;T;T	0.55234	0.53;0.53;0.53	5.42	3.12	0.35913	.	1.094470	0.06828	N	0.793444	T	0.37433	0.1003	L	0.27053	0.805	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.10941	-1.0608	10	0.08599	T	0.76	.	8.972	0.35912	0.8514:0.0:0.1486:0.0	.	467	Q99593	TBX5_HUMAN	A	417;467;364;467	ENSP00000337723:V417A;ENSP00000309913:V467A;ENSP00000384152:V467A	ENSP00000309913:V467A	V	-	2	0	TBX5	113277877	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.974000	0.49272	0.912000	0.36772	0.533000	0.62120	GTC	.	.		0.647	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		G	114793494	A	G	114793494	3	3	111	1	0	0	0	0	1	0	0	0	15676	275	10	2	160	2	TBX5	12	114793494	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	2125953	114793494	19058401	242	16482										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120587839	120587839	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcagagcatctcgaaggcaaAgagggctcctaggggaaaag	15	8	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:120587839A>G	ENST00000300648.6	-	35	4330	c.4318T>C	c.(4318-4320)Ttt>Ctt	p.F1440L		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1440					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCGAAGGCAAAGAGGGCTCCT	0.572																																					p.F1440L		Atlas-SNP	.											.	GCN1L1	207	.	0			c.T4318C						.						45	46	45					12																	120587839		1962	4164	6126	SO:0001583	missense	10985	exon35			AGGCAAAGAGGGC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.4318T>C	chr12.hg19:g.120587839A>G	ENSP00000300648:p.Phe1440Leu	94.0	0.0		76.0	4.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	A	18.72	3.683371	0.68157	.	.	ENSG00000089154	ENST00000300648	T	0.62105	0.05	5.41	5.41	0.78517	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.46132	0.1377	N	0.13003	0.285	0.80722	D	1	B	0.30033	0.266	B	0.30401	0.115	T	0.41610	-0.9499	10	0.23891	T	0.37	.	15.4394	0.75171	1.0:0.0:0.0:0.0	.	1440	Q92616	GCN1L_HUMAN	L	1440	ENSP00000300648:F1440L	ENSP00000300648:F1440L	F	-	1	0	GCN1L1	119072222	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.055000	0.93873	2.038000	0.60285	0.459000	0.35465	TTT	.	.		0.572	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			G	120587839	A	G	120587839	3	3	111	1	0	0	0	0	1	0	0	0	6307	72	3	2	3793	2	GCN1L1	12	120587839	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	5794345	120587839	13264056	243	16483										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124824721	124824721	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gctgctgctgcccccaccccCgccgctgctgccgctgctct	10	22	1	0	rs61519723|rs112797765|rs143952466	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr12:124824721C>T	ENST00000405201.1	-	37	5518	c.5518G>A	c.(5518-5520)Ggg>Agg	p.G1840R	NCOR2_ENST00000397355.1_Missense_Mutation_p.G1831R|NCOR2_ENST00000404621.1_Missense_Mutation_p.G1830R|NCOR2_ENST00000429285.2_Missense_Mutation_p.G1830R|NCOR2_ENST00000356219.3_Missense_Mutation_p.G1847R|NCOR2_ENST00000404121.2_Missense_Mutation_p.G1401R			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1851					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		cccccacccccgccgctgctg	0.711																																					p.G1840R		Atlas-SNP	.											.,32	NCOR2	475	.	0			c.G5518A						.						14	20	18					12																	124824721		1941	4120	6061	SO:0001583	missense	9612	exon39			CACCCCCGCCGCT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5518G>A	chr12.hg19:g.124824721C>T	ENSP00000384018:p.Gly1840Arg	28.0	0.0		24.0	2.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.12|12.12	1.844110|1.844110	0.32606|0.32606	.|.	.|.	ENSG00000196498|ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285|ENST00000440187;ENST00000453428	T;T;T;T;T;T|.	0.21191|.	2.03;2.29;2.02;2.29;2.04;2.29|.	2.64|2.64	2.64|2.64	0.31445|0.31445	.|.	0.074331|.	0.53938|.	U|.	0.000049|.	T|T	0.32704|0.32704	0.0838|0.0838	L|L	0.29908|0.29908	0.895|0.895	0.23855|0.23855	N|N	0.996651|0.996651	D;P|.	0.71674|.	0.998;0.929|.	P;B|.	0.51297|.	0.665;0.088|.	T|T	0.18650|0.18650	-1.0330|-1.0330	10|5	0.13470|.	T|.	0.59|.	.|.	8.4775|8.4775	0.33023|0.33023	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1831;1840|.	C9J239;C9JFD3|.	.;.|.	R|Q	1840;1830;1847;1831;1839;1401;1830|74;169	ENSP00000384018:G1840R;ENSP00000384202:G1830R;ENSP00000348551:G1847R;ENSP00000380513:G1831R;ENSP00000385618:G1401R;ENSP00000400281:G1830R|.	ENSP00000348551:G1847R|.	G|R	-|-	1|2	0|0	NCOR2|NCOR2	123390674|123390674	0.931000|0.931000	0.31567|0.31567	0.959000|0.959000	0.39883|0.39883	0.993000|0.993000	0.82548|0.82548	-0.026000|-0.026000	0.12392|0.12392	1.307000|1.307000	0.44944|0.44944	0.491000|0.491000	0.48974|0.48974	GGG|CGG	.	.		0.711	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		T	124824721	C	T	124824721	3	4	111	1	0	0	0	0	1	0	0	0	10245	652	23	1	2070	1	NCOR2	12	124824721	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	4236882	124824721	9027174	244	16484										
FLT1	2321	hgsc.bcm.edu	37	chr13	28942736	28942736	+	Intron	SNP	C	C	T													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tatgatgatgatgatgatgaCgatgatgatgatgatgacaa					rs371573097|rs200627038|rs558386334	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr13:28942736C>T	ENST00000282397.4	-	15	2368				FLT1_ENST00000541932.1_Silent_p.S727S	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1						blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)	p.S727S(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	atgatgatgacgatgatgatg	0.338																																					p.S727S		Atlas-SNP	.											.	FLT1	393	.	1	Substitution - coding silent(1)	kidney(1)	c.G2181A						.						289	299	296					13																	28942736		692	1591	2283	SO:0001627	intron_variant	2321	exon15			TGATGACGATGAT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2117-10914G>A	chr13.hg19:g.28942736C>T		91.0	0.0		96.0	24.0	NM_001160030	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.		0.338	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			T	28942736	C	T	28942736	1	4	111	0	1	0	0	0	0	0	0	0	5949	523	19	1		1	FLT1	13	28942736	Intron	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10		28942736	86227142	245	16485	73	2								
FLT1	2321	hgsc.bcm.edu	37	chr13	28942739	28942739	+	Intron	SNP	T	T	C													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gatgatgatgatgatgacgaTgatgatgatgatgacaatgg					rs371573097|rs558386334	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr13:28942739T>C	ENST00000282397.4	-	15	2368				FLT1_ENST00000541932.1_Silent_p.S726S	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1						blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	atgatgacgatgatgatgatg	0.343																																					p.S726S		Atlas-SNP	.											.	FLT1	393	.	0			c.A2178G						.						289	303	299					13																	28942739		692	1591	2283	SO:0001627	intron_variant	2321	exon15			TGACGATGATGAT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2117-10917A>G	chr13.hg19:g.28942739T>C		52.0	0.0		58.0	31.0	NM_001160030	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.		0.343	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	28942739	T	C	28942739	1	2	111	0	1	0	0	0	0	0	0	0	5949	1451	51	2		2	FLT1	13	28942739	Intron	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	3	28942739	86227139	246	16486	73	2								
MRPS31	10240	hgsc.bcm.edu	37	chr13	41323319	41323319	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccatagtttcccctcttttgTccactggatcagctcttcaa	5	14	4	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr13:41323319T>C	ENST00000323563.6	-	6	949	c.913A>G	c.(913-915)Aca>Gca	p.T305A	MRPS31_ENST00000498078.1_5'UTR	NM_005830.3	NP_005821.2	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31	305						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)		CCCTCTTTTGTCCACTGGATC	0.398																																					p.T305A		Atlas-SNP	.											.	MRPS31	30	.	0			c.A913G						.						129	123	125					13																	41323319		2203	4300	6503	SO:0001583	missense	10240	exon6			CTTTTGTCCACTG	Z68747	CCDS9372.1	13q14.11	2012-09-13			ENSG00000102738	ENSG00000102738		"Mitochondrial ribosomal proteins / small subunits"	16632	protein-coding gene	gene with protein product		611992				11279123, 8567980	Standard	NM_005830		Approved	IMOGN38	uc001uxm.4	Q92665	OTTHUMG00000016777	ENST00000323563.6:c.913A>G	chr13.hg19:g.41323319T>C	ENSP00000315397:p.Thr305Ala	146.0	0.0		67.0	4.0	NM_005830	B2RCS3|Q5VYC8|Q8WTV8	Missense_Mutation	SNP	ENST00000323563.6	hg19	CCDS9372.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.201477	0.79015	.	.	ENSG00000102738	ENST00000323563	T	0.55052	0.54	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.76169	0.3950	M	0.90309	3.105	0.80722	D	1	D	0.71674	0.998	D	0.74348	0.983	T	0.81890	-0.0725	10	0.87932	D	0	.	13.4195	0.60989	0.0:0.0:0.0:1.0	.	305	Q92665	RT31_HUMAN	A	305	ENSP00000315397:T305A	ENSP00000315397:T305A	T	-	1	0	MRPS31	40221319	1.000000	0.71417	0.998000	0.56505	0.953000	0.61014	6.864000	0.75494	1.854000	0.53819	0.524000	0.50904	ACA	.	.		0.398	MRPS31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044640.2			C	41323319	T	C	41323319	3	2	111	1	0	0	0	0	1	0	0	0	9850	1667	58	2	282	2	MRPS31	13	41323319	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	12380580	41323319	73846559	247	16487										
SLC25A30	253512	hgsc.bcm.edu	37	chr13	45978525	45978525	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccagacagaattccacatatCacatttatcggtagagtttc	6	10	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr13:45978525C>T	ENST00000539591.1	-	4	340	c.177G>A	c.(175-177)gtG>gtA	p.V59V				Q5SVS4	KMCP1_HUMAN	solute carrier family 25, member 30	110					mitochondrial transport (GO:0006839)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.95e-05)		TTCCACATATCACATTTATCG	0.348																																					p.V110V		Atlas-SNP	.											.	SLC25A30	24	.	0			c.G330A						.						165	156	159					13																	45978525		2203	4300	6503	SO:0001819	synonymous_variant	253512	exon5			ACATATCACATTT	AK074457	CCDS31967.1, CCDS66539.1	13q14	2013-05-22			ENSG00000174032	ENSG00000174032		"Solute carriers"	27371	protein-coding gene	gene with protein product		610793					Standard	XM_005266321		Approved		uc001vag.3	Q5SVS4	OTTHUMG00000016853	ENST00000539591.1:c.177G>A	chr13.hg19:g.45978525C>T		85.0	0.0		42.0	4.0	NM_001010875	B2RN96|B4DZK3|F5H8H8	Silent	SNP	ENST00000539591.1	hg19																																																																																				.	.		0.348	SLC25A30-201	KNOWN	basic	protein_coding	protein_coding		XM_170736		T	45978525	C	T	45978525	2	4	111	1	0	0	0	0	0	0	0	1	14509	813	29	3		3	SLC25A30	13	45978525	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	4655206	45978525	69191353	248	16488										
OR11G2	390439	hgsc.bcm.edu	37	chr14	20666184	20666184	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	actctcacttgcaaaaaaggCcctgtgatagagcttgtctt	8	10	2	2	rs74538160		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:20666184C>G	ENST00000357366.3	+	1	690	c.690C>G	c.(688-690)ggC>ggG	p.G230G		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		GCAAAAAAGGCCCTGTGATAG	0.458																																					p.G230G		Atlas-SNP	.											.	OR11G2	73	.	0			c.C690G						.						140	139	139					14																	20666184		2203	4300	6503	SO:0001819	synonymous_variant	390439	exon1			AAAAGGCCCTGTG		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"GPCR / Class A : Olfactory receptors"	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.690C>G	chr14.hg19:g.20666184C>G		185.0	0.0		148.0	10.0	NM_001005503	Q6IF09|Q96R33	Silent	SNP	ENST00000357366.3	hg19	CCDS32032.1																																																																																			.	.		0.458	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1			G	20666184	C	G	20666184	2	3	111	1	0	0	0	0	0	0	0	1	10934	726	26	4		4	OR11G2	14	20666184	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10		20666184	86683356	249	16489										
HNRNPC	3183	hgsc.bcm.edu	37	chr14	21699222	21699222	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcacttttggctctgcagccAggttaatatctgaaaaacaa	7	9	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:21699222A>C	ENST00000320084.7	-	3	490	c.251T>G	c.(250-252)cTg>cGg	p.L84R	HNRNPC_ENST00000557201.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000556513.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000556142.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000554969.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000553300.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000420743.2_Missense_Mutation_p.L84R|HNRNPC_ENST00000336053.6_Missense_Mutation_p.L84R|HNRNPC_ENST00000555309.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000556628.1_Intron|HNRNPC_ENST00000555914.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000449098.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000556897.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000555883.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000553753.1_Missense_Mutation_p.L84R|HNRNPC_ENST00000430246.2_Missense_Mutation_p.L84R|HNRNPC_ENST00000554455.1_Missense_Mutation_p.L84R	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	84	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		CTCTGCAGCCAGGTTAATATC	0.388																																					p.L84R	NSCLC(108;607 2244 12726 38757)	Atlas-SNP	.											.	HNRNPC	31	.	0			c.T251G						.						73	75	74					14																	21699222		2199	4293	6492	SO:0001583	missense	3183	exon3			GCAGCCAGGTTAA		CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"RNA binding motif (RRM) containing"	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.251T>G	chr14.hg19:g.21699222A>C	ENSP00000319690:p.Leu84Arg	64.0	0.0		60.0	14.0	NM_001077443	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Missense_Mutation	SNP	ENST00000320084.7	hg19	CCDS41915.1	.	.	.	.	.	.	.	.	.	.	A	16.98	3.272549	0.59649	.	.	ENSG00000092199	ENST00000336053;ENST00000320084;ENST00000449098;ENST00000554969;ENST00000556142;ENST00000554455;ENST00000430246;ENST00000553753;ENST00000555914;ENST00000555309;ENST00000452166;ENST00000555883;ENST00000556513;ENST00000557201;ENST00000553300;ENST00000556897;ENST00000420743;ENST00000557157;ENST00000445284;ENST00000554383;ENST00000555215;ENST00000555137;ENST00000554891;ENST00000556226;ENST00000555176	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;2.13;0.89;0.89;0.89;0.89;0.89;0.89	5.88	5.88	0.94601	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.275952	0.22837	U	0.055036	T	0.35941	0.0949	L	0.31294	0.92	0.80722	D	1	B;B;B;B;B	0.27316	0.175;0.012;0.152;0.103;0.1	B;B;B;B;B	0.28139	0.052;0.016;0.086;0.036;0.049	T	0.20472	-1.0274	10	0.87932	D	0	.	15.2723	0.73712	1.0:0.0:0.0:0.0	.	84;84;84;84;84	B4DY08;P07910-4;G3V4C1;P07910;P07910-2	.;.;.;HNRPC_HUMAN;.	R	84;84;84;84;84;84;84;84;84;84;84;84;84;84;84;84;84;5;84;84;84;84;84;84;84	ENSP00000338095:L84R;ENSP00000319690:L84R;ENSP00000404559:L84R;ENSP00000450725:L84R;ENSP00000451187:L84R;ENSP00000451291:L84R;ENSP00000442816:L84R;ENSP00000450548:L84R;ENSP00000451708:L84R;ENSP00000450790:L84R;ENSP00000450629:L84R;ENSP00000452214:L84R;ENSP00000452276:L84R;ENSP00000450544:L84R;ENSP00000451176:L84R;ENSP00000404848:L84R;ENSP00000450601:L5R;ENSP00000452021:L84R;ENSP00000452213:L84R;ENSP00000452185:L84R;ENSP00000450467:L84R;ENSP00000451292:L84R;ENSP00000452573:L84R	ENSP00000319690:L84R	L	-	2	0	HNRNPC	20769062	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.865000	0.87049	2.250000	0.74265	0.482000	0.46254	CTG	.	.		0.388	HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1			C	21699222	A	C	21699222	3	2	111	1	0	0	0	0	1	0	0	0	7271	188	7	5	693	5	HNRNPC	14	21699222	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1033038	21699222	85650318	250	16490										
TGM1	7051	hgsc.bcm.edu	37	chr14	24729674	24729674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acctgggcaccaggggttgaAgaggatgtagatctcattgc	14	8	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:24729674A>G	ENST00000206765.6	-	4	862	c.739T>C	c.(739-741)Ttc>Ctc	p.F247L	TGM1_ENST00000544573.1_Intron	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	247					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	CAGGGGTTGAAGAGGATGTAG	0.592																																					p.F247L		Atlas-SNP	.											.	TGM1	73	.	0			c.T739C						.						82	73	76					14																	24729674		2203	4300	6503	SO:0001583	missense	7051	exon4			GGTTGAAGAGGAT	D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"Transglutaminases"	11777	protein-coding gene	gene with protein product	"K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"	190195	"transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.739T>C	chr14.hg19:g.24729674A>G	ENSP00000206765:p.Phe247Leu	90.0	0.0		57.0	21.0	NM_000359	B4DWR7|Q197M4	Missense_Mutation	SNP	ENST00000206765.6	hg19	CCDS9622.1	.	.	.	.	.	.	.	.	.	.	A	34	5.397022	0.96009	.	.	ENSG00000092295	ENST00000206765	D	0.94613	-3.47	5.49	5.49	0.81192	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.98002	0.9342	H	0.95328	3.655	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	D	0.99153	1.0859	10	0.87932	D	0	-30.3127	14.7155	0.69265	1.0:0.0:0.0:0.0	.	247	P22735	TGM1_HUMAN	L	247	ENSP00000206765:F247L	ENSP00000206765:F247L	F	-	1	0	TGM1	23799514	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.599000	0.90856	2.311000	0.77944	0.533000	0.62120	TTC	.	.		0.592	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359		G	24729674	A	G	24729674	3	3	111	1	0	0	0	0	1	0	0	0	15844	72	3	2	1762	2	TGM1	14	24729674	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	3030452	24729674	82619866	251	16491										
KLHL28	54813	hgsc.bcm.edu	37	chr14	45414969	45414969	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tttgaaatacgggctgacgcTggcaagtaccactttgtgag	12	8	0	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:45414969T>C	ENST00000396128.4	-	2	282	c.163A>G	c.(163-165)Agc>Ggc	p.S55G	KLHL28_ENST00000355081.2_Missense_Mutation_p.S69G	NM_017658.3	NP_060128.2	Q9NXS3	KLH28_HUMAN	kelch-like family member 28	55	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									breast(2)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GGGCTGACGCTGGCAAGTACC	0.438																																					p.S55G		Atlas-SNP	.											.	KLHL28	53	.	0			c.A163G						.						95	89	91					14																	45414969		2203	4300	6503	SO:0001583	missense	54813	exon2			TGACGCTGGCAAG	AK000088	CCDS9680.1	14q21.1	2013-02-22	2013-02-22	2007-01-09	ENSG00000179454	ENSG00000179454		"Kelch-like", "BTB/POZ domain containing"	19741	protein-coding gene	gene with protein product			"BTB (POZ) domain containing 5", "kelch-like 28 (Drosophila)"	BTBD5			Standard	NM_017658		Approved	FLJ20081	uc001wvr.3	Q9NXS3	OTTHUMG00000140263	ENST00000396128.4:c.163A>G	chr14.hg19:g.45414969T>C	ENSP00000379434:p.Ser55Gly	115.0	0.0		85.0	5.0	NM_017658	Q0VAL5	Missense_Mutation	SNP	ENST00000396128.4	hg19	CCDS9680.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.054061	0.55218	.	.	ENSG00000179454	ENST00000396128;ENST00000355081;ENST00000556500;ENST00000556239	T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37	5.81	5.81	0.92471	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.070640	0.85682	D	0.000000	T	0.73133	0.3548	M	0.78285	2.405	0.48040	D	0.999573	B;B	0.29481	0.178;0.245	B;B	0.37550	0.18;0.253	T	0.74337	-0.3698	10	0.66056	D	0.02	.	15.8323	0.78764	0.0:0.0:0.0:1.0	.	55;55	Q9NXS3-2;Q9NXS3	.;KLH28_HUMAN	G	55;69;55;55	ENSP00000379434:S55G;ENSP00000347193:S69G;ENSP00000452061:S55G;ENSP00000452591:S55G	ENSP00000347193:S69G	S	-	1	0	KLHL28	44484719	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.796000	0.69080	2.225000	0.72522	0.533000	0.62120	AGC	.	.		0.438	KLHL28-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276790.3			C	45414969	T	C	45414969	3	2	111	1	0	0	0	0	1	0	0	0	8391	1580	55	2	1568	2	KLHL28	14	45414969	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	20685295	45414969	61934571	252	16492										
MDGA2	161357	hgsc.bcm.edu	37	chr14	47342700	47342700	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcagtgtttgtgggtccataAgggtttttgggagctatgct	15	5	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:47342700A>G	ENST00000399232.2	-	14	2845	c.2481T>C	c.(2479-2481)ccT>ccC	p.P827P	MDGA2_ENST00000426342.1_Silent_p.P598P|MDGA2_ENST00000357362.3_Silent_p.P598P|MDGA2_ENST00000399222.3_Silent_p.P29P|MDGA2_ENST00000439988.3_Silent_p.P896P	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	827	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						TGGGTCCATAAGGGTTTTTGG	0.378																																					p.P896P		Atlas-SNP	.											MDGA2_ENST00000439988,colon,carcinoma,0,3	MDGA2	470	.	0			c.T2688C						.						163	157	158					14																	47342700		1855	4108	5963	SO:0001819	synonymous_variant	161357	exon14			TCCATAAGGGTTT	AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.2481T>C	chr14.hg19:g.47342700A>G		76.0	0.0		66.0	3.0	NM_001113498	F6W3S7|J3KPX6	Silent	SNP	ENST00000399232.2	hg19																																																																																				.	.		0.378	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		G	47342700	A	G	47342700	2	3	111	1	0	0	0	0	0	0	0	1	9416	59	3	2		2	MDGA2	14	47342700	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1927731	47342700	60006840	253	16493										
KLHDC2	23588	hgsc.bcm.edu	37	chr14	50249607	50249607	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agccaactcatggaactgccTtccaaaacacttacttcaca	4	14	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:50249607T>C	ENST00000298307.5	+	13	2018	c.1157T>C	c.(1156-1158)cTt>cCt	p.L386P	KLHDC2_ENST00000554589.1_3'UTR|KLHDC2_ENST00000557247.1_3'UTR|NEMF_ENST00000556925.1_5'Flank	NM_014315.2	NP_055130.1	Q9Y2U9	KLDC2_HUMAN	kelch domain containing 2	386						nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	all_epithelial(31;0.000959)|Breast(41;0.0117)					TGGAACTGCCTTCCAAAACAC	0.378																																					p.L386P		Atlas-SNP	.											.	KLHDC2	33	.	0			c.T1157C						.						100	85	90					14																	50249607		2203	4300	6503	SO:0001583	missense	23588	exon13			ACTGCCTTCCAAA	AK001771	CCDS9693.1	14q21.3	2003-01-15			ENSG00000165516	ENSG00000165516			20231	protein-coding gene	gene with protein product		611280				11384994	Standard	NM_014315		Approved	HCLP-1, LCP	uc001wwx.3	Q9Y2U9	OTTHUMG00000140288	ENST00000298307.5:c.1157T>C	chr14.hg19:g.50249607T>C	ENSP00000298307:p.Leu386Pro	112.0	0.0		90.0	4.0	NM_014315	B3KPF9|Q6IAF0|Q86TY9	Missense_Mutation	SNP	ENST00000298307.5	hg19	CCDS9693.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.362451	0.82353	.	.	ENSG00000165516	ENST00000298307	T	0.07021	3.23	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.29321	0.0730	M	0.72118	2.19	0.80722	D	1	D	0.71674	0.998	D	0.81914	0.995	T	0.00812	-1.1556	10	0.87932	D	0	-23.877	15.7905	0.78357	0.0:0.0:0.0:1.0	.	386	Q9Y2U9	KLDC2_HUMAN	P	386	ENSP00000298307:L386P	ENSP00000298307:L386P	L	+	2	0	KLHDC2	49319357	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.340000	0.72973	2.324000	0.78689	0.533000	0.62120	CTT	.	.		0.378	KLHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276869.1			C	50249607	T	C	50249607	3	2	111	1	0	0	0	0	1	0	0	0	8365	1609	56	2	1207	2	KLHDC2	14	50249607	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2906907	50249607	57099933	254	16494										
L2HGDH	79944	hgsc.bcm.edu	37	chr14	50769676	50769676	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gtgatggatgtcgcaggatgAgtgctctggcagaggcaagc	17	7	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:50769676A>G	ENST00000267436.4	-	2	597	c.200T>C	c.(199-201)cTc>cCc	p.L67P	L2HGDH_ENST00000261699.4_Missense_Mutation_p.L67P|L2HGDH_ENST00000421284.3_Missense_Mutation_p.L67P|L2HGDH_ENST00000555423.1_Missense_Mutation_p.L67P|L2HGDH_ENST00000555610.1_Missense_Mutation_p.L67P|L2HGDH_ENST00000556393.1_5'UTR			Q9H9P8	L2HDH_HUMAN	L-2-hydroxyglutarate dehydrogenase	67					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2-hydroxyglutarate dehydrogenase activity (GO:0047545)			kidney(1)|large_intestine(4)|lung(3)|ovary(2)	10	all_epithelial(31;0.000599)|Breast(41;0.0102)					TCGCAGGATGAGTGCTCTGGC	0.398																																					p.L67P		Atlas-SNP	.											.	L2HGDH	33	.	0			c.T200C						.						132	132	132					14																	50769676		2203	4300	6503	SO:0001583	missense	79944	exon2			AGGATGAGTGCTC		CCDS9698.1	14q22.1	2006-04-28	2005-05-25	2005-05-25	ENSG00000087299	ENSG00000087299	1.1.99.2		20499	protein-coding gene	gene with protein product	"2-hydroxyglutarate dehydrogenase"	609584	"chromosome 14 open reading frame 160"	C14orf160		16005139	Standard	NM_024884		Approved	FLJ12618	uc001wxu.3	Q9H9P8	OTTHUMG00000140289	ENST00000267436.4:c.200T>C	chr14.hg19:g.50769676A>G	ENSP00000267436:p.Leu67Pro	45.0	0.0		52.0	4.0	NM_024884	Q9BRR1	Missense_Mutation	SNP	ENST00000267436.4	hg19	CCDS9698.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.636752	0.87760	.	.	ENSG00000087299	ENST00000261699;ENST00000267436;ENST00000421284;ENST00000557131;ENST00000555423;ENST00000555610	D;D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55;-3.55	5.35	5.35	0.76521	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.98327	0.9445	H	0.97564	4.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.99755	1.1019	10	0.87932	D	0	-10.2049	16.0475	0.80731	1.0:0.0:0.0:0.0	.	67;67	C9JVN9;Q9H9P8	.;L2HDH_HUMAN	P	67	ENSP00000261699:L67P;ENSP00000267436:L67P;ENSP00000405559:L67P;ENSP00000450494:L67P;ENSP00000452483:L67P	ENSP00000261699:L67P	L	-	2	0	L2HGDH	49839426	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.784000	0.91818	2.333000	0.79357	0.533000	0.62120	CTC	.	.		0.398	L2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276870.2	NM_024884		G	50769676	A	G	50769676	3	3	111	1	0	0	0	0	1	0	0	0	8599	304	11	2	1227	2	L2HGDH	14	50769676	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	520069	50769676	56579864	255	16495										
DAAM1	23002	hgsc.bcm.edu	37	chr14	59793328	59793328	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggacaggaccctgactccacAcctttggaaaactttaatat	7	11	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:59793328A>G	ENST00000395125.1	+	10	1298	c.1275A>G	c.(1273-1275)acA>acG	p.T425T	DAAM1_ENST00000351081.1_Silent_p.T425T|DAAM1_ENST00000360909.3_Silent_p.T425T	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	425					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		CTGACTCCACACCTTTGGAAA	0.368																																					p.T425T		Atlas-SNP	.											.	DAAM1	95	.	0			c.A1275G						.						83	84	84					14																	59793328		2203	4300	6503	SO:0001819	synonymous_variant	23002	exon11			CTCCACACCTTTG	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.1275A>G	chr14.hg19:g.59793328A>G		210.0	0.0		145.0	6.0	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	hg19	CCDS9737.1																																																																																			.	.		0.368	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		G	59793328	A	G	59793328	2	3	111	1	0	0	0	0	0	0	0	1	4217	146	6	2		2	DAAM1	14	59793328	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	9023652	59793328	47556212	256	16496										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64496677	64496677	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ataccaggtttgcgtcacagAcctgaatactacattggaca	8	10	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:64496677A>G	ENST00000344113.4	+	44	6991	c.6779A>G	c.(6778-6780)gAc>gGc	p.D2260G	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.D2260G|SYNE2_ENST00000358025.3_Missense_Mutation_p.D2260G	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2260					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGCGTCACAGACCTGAATACT	0.383																																					p.D2260G		Atlas-SNP	.											.	SYNE2	577	.	0			c.A6779G						.						88	85	86					14																	64496677		1828	4088	5916	SO:0001583	missense	23224	exon44			TCACAGACCTGAA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.6779A>G	chr14.hg19:g.64496677A>G	ENSP00000341781:p.Asp2260Gly	119.0	0.0		80.0	4.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	9.367	1.069510	0.20147	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.37752	1.18;1.18;1.18	5.24	5.24	0.73138	.	0.317042	0.26955	N	0.021648	T	0.31827	0.0809	L	0.29908	0.895	0.80722	D	1	P;P	0.49961	0.884;0.93	B;P	0.46758	0.326;0.526	T	0.09015	-1.0694	10	0.62326	D	0.03	.	9.6554	0.39923	0.8251:0.1749:0.0:0.0	.	2260;2260	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	G	2260	ENSP00000350719:D2260G;ENSP00000341781:D2260G;ENSP00000452570:D2260G	ENSP00000261678:D2260G	D	+	2	0	SYNE2	63566430	0.966000	0.33281	0.266000	0.24541	0.131000	0.20780	0.694000	0.25512	2.108000	0.64289	0.533000	0.62120	GAC	.	.		0.383	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64496677	A	G	64496677	3	3	111	1	0	0	0	0	1	0	0	0	15461	275	10	2	6949	2	SYNE2	14	64496677	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	4703349	64496677	42852863	257	16497										
MTHFD1	4522	hgsc.bcm.edu	37	chr14	64898578	64898578	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	catccaaatccgaaggttaaAggtaagctttttttcttcca	6	9	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:64898578A>G	ENST00000545908.1	+	15	1890	c.1661A>G	c.(1660-1662)aAg>aGg	p.K554R	CTD-2555O16.2_ENST00000556640.1_RNA|MTHFD1_ENST00000216605.8_Splice_Site_p.K498R			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	498	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	CGAAGGTTAAAGGTAAGCTTT	0.348																																					p.K498R	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.A1493G						.						83	78	80					14																	64898578		2203	4300	6503	SO:0001630	splice_region_variant	4522	exon15			GGTTAAAGGTAAG	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.1662+1A>G	chr14.hg19:g.64898578A>G		87.0	0.0		87.0	4.0	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.45	2.240767	0.39598	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605;ENST00000555252	T;T;T;T	0.24151	2.69;2.7;2.7;1.87	5.73	-5.62	0.02481	.	0.575440	0.19437	N	0.114293	T	0.12603	0.0306	N	0.11651	0.15	0.23685	N	0.997114	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.10450	0.005;0.005;0.002	T	0.05084	-1.0907	10	0.35671	T	0.21	0.0482	17.0195	0.86429	0.7364:0.0:0.2636:0.0	.	554;498;498	F5H2F4;P11586;G3V2B8	.;C1TC_HUMAN;.	R	554;498;554;478	ENSP00000438588:K554R;ENSP00000450560:K498R;ENSP00000216605:K554R;ENSP00000451309:K478R	ENSP00000216605:K498R	K	+	2	0	MTHFD1	63968331	0.010000	0.17322	0.539000	0.28077	0.961000	0.63080	0.049000	0.14099	-1.240000	0.02529	-0.375000	0.07067	AAG	.	.		0.348	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1		Missense_Mutation	G	64898578	A	G	64898578	5	3	111	1	0	0	0	0	0	0	1	0	9936	86	3	2	1551	2	MTHFD1	14	64898578	Splice_Site	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	401901	64898578	42450962	258	16498										
ENTPD5	957	hgsc.bcm.edu	37	chr14	74443063	74443063	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aacgtgatttgggtggaggcTccccctaggtccaaggtccc	13	12	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:74443063T>C	ENST00000334696.6	-	9	925	c.606A>G	c.(604-606)ggA>ggG	p.G202G	ENTPD5_ENST00000557325.1_Silent_p.G202G	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	202					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		GGGTGGAGGCTCCCCCTAGGT	0.537																																					p.G202G		Atlas-SNP	.											.	ENTPD5	26	.	0			c.A606G						.						110	92	98					14																	74443063		2203	4300	6503	SO:0001819	synonymous_variant	957	exon9			GGAGGCTCCCCCT	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"proto-oncogene CPH"	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.606A>G	chr14.hg19:g.74443063T>C		122.0	0.0		103.0	5.0	NM_001249	A1L4C5|Q96RX0	Silent	SNP	ENST00000334696.6	hg19	CCDS9825.1																																																																																			.	.		0.537	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249		C	74443063	T	C	74443063	2	2	111	1	0	0	0	0	0	0	0	1	5144	1538	54	2		2	ENTPD5	14	74443063	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	9544485	74443063	32906477	259	16499										
YLPM1	56252	hgsc.bcm.edu	37	chr14	75265057	75265057	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aatagaggcaacagctcatcTtacagaggtcctgggcaaag	11	9	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:75265057T>C	ENST00000325680.7	+	5	3181	c.3057T>C	c.(3055-3057)tcT>tcC	p.S1019S	YLPM1_ENST00000552421.1_Intron|YLPM1_ENST00000238571.3_Silent_p.S824S	NM_019589.2	NP_062535.2	P49750	YLPM1_HUMAN	YLP motif containing 1	824	Arg-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		ACAGCTCATCTTACAGAGGTC	0.483																																					p.S1019S		Atlas-SNP	.											.	YLPM1	298	.	0			c.T3057C						.						60	60	60					14																	75265057		1935	4132	6067	SO:0001819	synonymous_variant	56252	exon5			CTCATCTTACAGA	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000325680.7:c.3057T>C	chr14.hg19:g.75265057T>C		83.0	0.0		75.0	4.0	NM_019589	P49752|Q96I64|Q9P1V7	Silent	SNP	ENST00000325680.7	hg19	CCDS45135.1																																																																																			.	.		0.483	YLPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404451.1	NM_019589		C	75265057	T	C	75265057	2	2	111	1	0	0	0	0	0	0	0	1	17501	1596	56	2		2	YLPM1	14	75265057	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	821994	75265057	32084483	260	16500										
GTF2A1	2957	hgsc.bcm.edu	37	chr14	81670411	81670411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gctcttctgaatgaaatccaTctactgccctggactgcatt	7	12	3	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:81670411T>C	ENST00000553612.1	-	3	573	c.170A>G	c.(169-171)gAt>gGt	p.D57G	SNORA79_ENST00000408376.1_RNA|GTF2A1_ENST00000434192.2_Missense_Mutation_p.D18G	NM_001278940.1|NM_015859.3	NP_001265869.1|NP_056943.1	P52655	TF2AA_HUMAN	general transcription factor IIA, 1, 19/37kDa	57					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(234;0.0287)		ATGAAATCCATCTACTGCCCT	0.428																																					p.D57G		Atlas-SNP	.											.	GTF2A1	34	.	0			c.A170G						.						147	97	114					14																	81670411		2203	4300	6503	SO:0001583	missense	2957	exon3			AATCCATCTACTG	X75383	CCDS9873.1, CCDS9874.1	14q31	2010-03-23	2002-08-29					"General transcription factors"	4646	protein-coding gene	gene with protein product		600520	"glucose regulated protein, 58kD pseudogene"			8224848	Standard	NM_015859		Approved	TFIIA	uc001xvf.2	P52655		ENST00000553612.1:c.170A>G	chr14.hg19:g.81670411T>C	ENSP00000452454:p.Asp57Gly	178.0	0.0		114.0	5.0	NM_015859	Q3KNQ9	Missense_Mutation	SNP	ENST00000553612.1	hg19	CCDS9873.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.643700	0.87859	.	.	ENSG00000165417	ENST00000553612;ENST00000344860;ENST00000434192	T;T	0.44482	0.92;0.92	5.55	5.55	0.83447	Transcription factor IIA, alpha subunit, N-terminal (1);	0.097919	0.64402	D	0.000002	T	0.51787	0.1695	M	0.64997	1.995	0.80722	D	1	D;P	0.54207	0.965;0.924	P;P	0.50270	0.636;0.554	T	0.53648	-0.8409	10	0.48119	T	0.1	-16.9599	15.6979	0.77515	0.0:0.0:0.0:1.0	.	18;57	P52655-2;P52655	.;TF2AA_HUMAN	G	57;18;18	ENSP00000452454:D57G;ENSP00000409492:D18G	ENSP00000298173:D57G	D	-	2	0	GTF2A1	80740164	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.260000	0.78391	2.108000	0.64289	0.460000	0.39030	GAT	.	.		0.428	GTF2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413309.1	NM_015859		C	81670411	T	C	81670411	3	2	111	1	0	0	0	0	1	0	0	0	6861	1435	50	2	988	2	GTF2A1	14	81670411	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	6405354	81670411	25679129	261	16501										
SERPINA4	5267	hgsc.bcm.edu	37	chr14	95033451	95033451	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cagatacttgccctgctcggTgctacggatggattacaaag	11	10	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:95033451T>C	ENST00000557004.1	+	3	1215	c.794T>C	c.(793-795)gTg>gCg	p.V265A	SERPINA4_ENST00000555095.1_Missense_Mutation_p.V265A|SERPINA4_ENST00000298841.5_Missense_Mutation_p.V265A|SERPINA5_ENST00000553780.1_Intron			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	265					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		CCCTGCTCGGTGCTACGGATG	0.488																																					p.V265A		Atlas-SNP	.											.	SERPINA4	81	.	0			c.T794C						.						117	101	107					14																	95033451		2203	4300	6503	SO:0001583	missense	5267	exon3			GCTCGGTGCTACG	L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"Serine (or cysteine) peptidase inhibitors"	8948	protein-coding gene	gene with protein product		147935	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.794T>C	chr14.hg19:g.95033451T>C	ENSP00000450838:p.Val265Ala	147.0	0.0		118.0	5.0	NM_006215	Q53XB5|Q86TR9|Q96BZ5	Missense_Mutation	SNP	ENST00000557004.1	hg19	CCDS9927.1	.	.	.	.	.	.	.	.	.	.	T	17.28	3.350113	0.61183	.	.	ENSG00000100665	ENST00000557004;ENST00000555095;ENST00000298841	D;D;D	0.85861	-2.04;-2.04;-2.04	4.56	4.56	0.56223	Serpin domain (3);	0.000000	0.48767	D	0.000172	D	0.90923	0.7147	M	0.71920	2.185	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.73380	0.951;0.98	D	0.91972	0.5587	10	0.87932	D	0	.	13.4119	0.60948	0.0:0.0:0.0:1.0	.	265;265	B2R815;P29622	.;KAIN_HUMAN	A	265	ENSP00000450838:V265A;ENSP00000451172:V265A;ENSP00000298841:V265A	ENSP00000298841:V265A	V	+	2	0	SERPINA4	94103204	0.970000	0.33590	0.327000	0.25402	0.155000	0.21991	4.254000	0.58798	1.814000	0.52955	0.459000	0.35465	GTG	.	.		0.488	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215		C	95033451	T	C	95033451	3	2	111	1	0	0	0	0	1	0	0	0	14106	1696	59	2	800	2	SERPINA4	14	95033451	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	13363040	95033451	12316089	262	16502										
SERPINA4	5267	hgsc.bcm.edu	37	chr14	95034486	95034486	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaatttttacaagaagctagAgttgcatcttcccaagttct	7	8	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:95034486A>G	ENST00000557004.1	+	4	1365	c.944A>G	c.(943-945)gAg>gGg	p.E315G	SERPINA4_ENST00000555095.1_Missense_Mutation_p.E315G|SERPINA4_ENST00000298841.5_Missense_Mutation_p.E315G|SERPINA5_ENST00000553780.1_Intron			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	315					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		AAGAAGCTAGAGTTGCATCTT	0.478																																					p.E315G		Atlas-SNP	.											.	SERPINA4	81	.	0			c.A944G						.						133	133	133					14																	95034486		2203	4300	6503	SO:0001583	missense	5267	exon4			AGCTAGAGTTGCA	L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"Serine (or cysteine) peptidase inhibitors"	8948	protein-coding gene	gene with protein product		147935	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.944A>G	chr14.hg19:g.95034486A>G	ENSP00000450838:p.Glu315Gly	103.0	0.0		68.0	4.0	NM_006215	Q53XB5|Q86TR9|Q96BZ5	Missense_Mutation	SNP	ENST00000557004.1	hg19	CCDS9927.1	.	.	.	.	.	.	.	.	.	.	A	10.87	1.472865	0.26423	.	.	ENSG00000100665	ENST00000557004;ENST00000555095;ENST00000298841	D;D;D	0.85411	-1.98;-1.98;-1.98	4.92	-2.1	0.07210	Serpin domain (3);	0.723224	0.11723	N	0.535656	T	0.80507	0.4636	M	0.69823	2.125	0.09310	N	1	B;B	0.24963	0.02;0.115	B;B	0.32149	0.033;0.141	T	0.70741	-0.4789	10	0.66056	D	0.02	.	1.2779	0.02034	0.4214:0.2839:0.1578:0.1369	.	315;315	B2R815;P29622	.;KAIN_HUMAN	G	315	ENSP00000450838:E315G;ENSP00000451172:E315G;ENSP00000298841:E315G	ENSP00000298841:E315G	E	+	2	0	SERPINA4	94104239	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	1.746000	0.38288	-0.565000	0.06061	0.533000	0.62120	GAG	.	.		0.478	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215		G	95034486	A	G	95034486	3	3	111	1	0	0	0	0	1	0	0	0	14106	304	11	2	954	2	SERPINA4	14	95034486	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1035	95034486	12315054	263	16503										
RTL1	388015	hgsc.bcm.edu	37	chr14	101350675	101350676	+	Missense_Mutation	DNP	GA	GA	CT													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctcggtctggttttgctcttGaggagtctcctcccttcccg							TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:101350675_101350676GA>CT	ENST00000534062.1	-	1	508_509	c.450_451TC>AG	c.(448-453)ccTCaa>ccAGaa	p.Q151E	MIR136_ENST00000385207.1_RNA|MIR432_ENST00000606207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR433_ENST00000384837.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	151					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TTTTGCTCTTGAGGAGTCTCCT	0.515																																					p.Q151E|p.P150P		Atlas-SNP	.											.	RTL1	120	.	0			c.C451G|c.T450A						.																																			SO:0001583	missense	388015	exon1			GCTCTTGAGGAGT|CTCTTGAGGAGTC		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.450_451delinsCT	chr14.hg19:g.101350675_101350676delinsCT	ENSP00000435342:p.Gln151Glu	188.0|186.0	0.0		134.0	6.0	NM_001134888	E9PKS8	Missense_Mutation|Silent	SNP	ENST00000534062.1	hg19	CCDS53910.1																																																																																			.	.		0.515	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		CT	101350676	GA	CT	101350675	3	2	111	1	0	0	0	0	1	0	0	0	13739	1299	45	4	3629	4	RTL1	14	101350675	Missense_Mutation	DNP	GA	TCGA-DD-A39X-01A-11D-A20W-10	6316189	101350675	5998865	264	16504										
RTL1	388015	hgsc.bcm.edu	37	chr14	101351059	101351059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgagccctcggaggactccaTttgttttgatgatggattct	11	8	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:101351059T>C	ENST00000534062.1	-	1	125	c.67A>G	c.(67-69)Atg>Gtg	p.M23V	MIR136_ENST00000385207.1_RNA|MIR432_ENST00000606207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR433_ENST00000384837.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	23					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						GAGGACTCCATTTGTTTTGAT	0.532																																					p.M23V		Atlas-SNP	.											.	RTL1	120	.	0			c.A67G						.						36	34	35					14																	101351059		1568	3582	5150	SO:0001583	missense	388015	exon1			ACTCCATTTGTTT		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.67A>G	chr14.hg19:g.101351059T>C	ENSP00000435342:p.Met23Val	87.0	0.0		72.0	4.0	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	hg19	CCDS53910.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.757753	0.49468	.	.	ENSG00000254656	ENST00000534062	T	0.24350	1.86	3.48	3.48	0.39840	.	.	.	.	.	T	0.29458	0.0734	N	0.24115	0.695	0.21325	N	0.999728	P	0.52842	0.956	P	0.62184	0.899	T	0.07947	-1.0746	9	0.25751	T	0.34	.	8.659	0.34081	0.0:0.0:0.0:1.0	.	23	E9PKS8	.	V	23	ENSP00000435342:M23V	ENSP00000435342:M23V	M	-	1	0	RTL1	100420812	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.050000	0.41297	1.819000	0.53055	0.459000	0.35465	ATG	.	.		0.532	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		C	101351059	T	C	101351059	3	2	111	1	0	0	0	0	1	0	0	0	13739	1493	52	2	4013	2	RTL1	14	101351059	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	384	101351059	5998481	265	16505										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102515840	102515840	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	catgaccgtcatccagtgggTgtccgacttcagcgagagga	13	11	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:102515840T>C	ENST00000360184.4	+	75	13600	c.13436T>C	c.(13435-13437)gTg>gCg	p.V4479A	RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557242.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4479					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ATCCAGTGGGTGTCCGACTTC	0.607																																					p.V4479A		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.T13436C						.						68	60	63					14																	102515840		2203	4300	6503	SO:0001583	missense	1778	exon75			AGTGGGTGTCCGA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.13436T>C	chr14.hg19:g.102515840T>C	ENSP00000348965:p.Val4479Ala	138.0	0.0		116.0	5.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.683070	0.88542	.	.	ENSG00000197102	ENST00000360184	T	0.09911	2.93	5.54	5.54	0.83059	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.16471	0.0396	L	0.42686	1.345	0.80722	D	1	P	0.45634	0.863	P	0.46718	0.525	T	0.00463	-1.1724	10	0.66056	D	0.02	.	15.6827	0.77385	0.0:0.0:0.0:1.0	.	4479	Q14204	DYHC1_HUMAN	A	4479	ENSP00000348965:V4479A	ENSP00000348965:V4479A	V	+	2	0	DYNC1H1	101585593	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.986000	0.88173	2.093000	0.63338	0.533000	0.62120	GTG	.	.		0.607	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		C	102515840	T	C	102515840	3	2	111	1	0	0	0	0	1	0	0	0	4843	1696	59	2	13734	2	DYNC1H1	14	102515840	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1164781	102515840	4833700	266	16506										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105407781	105407781	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcaccttcatgaacaacagaTtccacaatgggaaatgtgga	8	9	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr14:105407781T>C	ENST00000333244.5	-	7	14126	c.14007A>G	c.(14005-14007)gaA>gaG	p.E4669E	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4669						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GAACAACAGATTCCACAATGG	0.418																																					p.E4669E		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A14007G						.						46	48	47					14																	105407781		1910	4116	6026	SO:0001819	synonymous_variant	113146	exon7			AACAGATTCCACA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.14007A>G	chr14.hg19:g.105407781T>C		124.0	0.0		74.0	4.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.418	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105407781	T	C	105407781	2	2	111	1	0	0	0	0	0	0	0	1	415	1490	52	2		2	AHNAK2	14	105407781	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2891941	105407781	1941759	267	16507										
EXD1	161829	hgsc.bcm.edu	37	chr15	41483691	41483691	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gagagatatttaggggctacTtgaaggtgtttgattaaact	12	3	0	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:41483691T>C	ENST00000314992.5	-	8	829	c.639A>G	c.(637-639)caA>caG	p.Q213Q	RN7SL497P_ENST00000476341.2_RNA|EXD1_ENST00000458580.2_Silent_p.Q271Q	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	213							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						TAGGGGCTACTTGAAGGTGTT	0.383																																					p.Q213Q		Atlas-SNP	.											.	EXD1	52	.	0			c.A639G						.						95	98	97					15																	41483691		2203	4300	6503	SO:0001819	synonymous_variant	161829	exon8			GGCTACTTGAAGG	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"exonuclease 3'-5' domain-like 1"	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.639A>G	chr15.hg19:g.41483691T>C		57.0	0.0		83.0	4.0	NM_152596	A8K909|B7Z839|Q6ZW94	Silent	SNP	ENST00000314992.5	hg19	CCDS10072.1																																																																																			.	.		0.383	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596		C	41483691	T	C	41483691	2	2	111	1	0	0	0	0	0	0	0	1	5299	1606	56	2		2	EXD1	15	41483691	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		41483691	61047701	268	16508										
ZFP106	64397	hgsc.bcm.edu	37	chr15	42742306	42742306	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tttttgaagctctgcatccaAgctagcactctcaaagcctt	6	12	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:42742306A>C	ENST00000263805.4	-	2	2421	c.2095T>G	c.(2095-2097)Ttg>Gtg	p.L699V	ZNF106_ENST00000565611.1_Intron|ZNF106_ENST00000565380.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	699					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TCTGCATCCAAGCTAGCACTC	0.448																																					p.L699V		Atlas-SNP	.											.	ZFP106	117	.	0			c.T2095G						.						116	117	117					15																	42742306		2203	4299	6502	SO:0001583	missense	64397	exon2			CATCCAAGCTAGC	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"Zinc fingers, C2H2-type"	12886	protein-coding gene	gene with protein product	"SH3-domain binding protein 3"		"zinc finger protein 106 homolog (mouse)"	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.2095T>G	chr15.hg19:g.42742306A>C	ENSP00000263805:p.Leu699Val	104.0	0.0		106.0	26.0	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	hg19	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	A	16.72	3.201313	0.58234	.	.	ENSG00000103994	ENST00000263805	T	0.66280	-0.2	5.52	2.61	0.31194	.	0.534263	0.18523	N	0.138708	T	0.52175	0.1718	L	0.50333	1.59	0.80722	D	1	B;B	0.20550	0.046;0.012	B;B	0.19946	0.027;0.006	T	0.42783	-0.9431	10	0.45353	T	0.12	-2.2957	7.1598	0.25657	0.7653:0.1355:0.0992:0.0	.	482;699	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	V	699	ENSP00000263805:L699V	ENSP00000263805:L699V	L	-	1	2	ZFP106	40529598	0.996000	0.38824	0.402000	0.26371	0.972000	0.66771	3.602000	0.54066	0.268000	0.21939	0.528000	0.53228	TTG	.	.		0.448	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		C	42742306	A	C	42742306	3	2	111	1	0	0	0	0	1	0	0	0	17652	69	3	5	3628	5	ZFP106	15	42742306	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1258615	42742306	59789086	269	16509										
GATM	2628	hgsc.bcm.edu	37	chr15	45658283	45658283	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gggttggaaagcacaataccAggtccaatgatgttgaaggt	13	6	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:45658283A>G	ENST00000396659.3	-	6	1278	c.939T>C	c.(937-939)ccT>ccC	p.P313P	GATM_ENST00000558336.1_Silent_p.P313P	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	313					cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|embryo development (GO:0009790)|response to mercury ion (GO:0046689)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	glycine amidinotransferase activity (GO:0015068)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines (GO:0016813)			biliary_tract(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	15		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Glycine(DB00145)|L-Ornithine(DB00129)	GCACAATACCAGGTCCAATGA	0.438																																					p.P313P		Atlas-SNP	.											.	GATM	34	.	0			c.T939C						.						178	158	165					15																	45658283		2198	4298	6496	SO:0001819	synonymous_variant	2628	exon6			AATACCAGGTCCA	S68805	CCDS10122.1	15q15.1	2007-12-06			ENSG00000171766	ENSG00000171766	2.1.4.1		4175	protein-coding gene	gene with protein product		602360				8313955	Standard	NM_001482		Approved	AGAT	uc001zvc.3	P50440	OTTHUMG00000131427	ENST00000396659.3:c.939T>C	chr15.hg19:g.45658283A>G		117.0	0.0		84.0	4.0	NM_001482	B4DH99|B4DPI3|Q53EQ4	Silent	SNP	ENST00000396659.3	hg19	CCDS10122.1																																																																																			.	.		0.438	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482		G	45658283	A	G	45658283	2	3	111	1	0	0	0	0	0	0	0	1	6271	175	7	2		2	GATM	15	45658283	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	2915977	45658283	56873109	270	16510										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48056059	48056059	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttgggcaggctgtgtattccCgcgtggcccgcatatgtaaa	13	10	0	0	rs543020539		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:48056059C>T	ENST00000316364.5	+	10	1199	c.760C>T	c.(760-762)Cgc>Tgc	p.R254C	SEMA6D_ENST00000558816.1_Missense_Mutation_p.R254C|SEMA6D_ENST00000536845.2_Missense_Mutation_p.R254C|SEMA6D_ENST00000558014.1_Missense_Mutation_p.R254C|SEMA6D_ENST00000355997.3_Missense_Mutation_p.R254C|SEMA6D_ENST00000389428.3_Missense_Mutation_p.R254C|SEMA6D_ENST00000389433.2_Missense_Mutation_p.R254C|SEMA6D_ENST00000354744.4_Missense_Mutation_p.R254C|SEMA6D_ENST00000537942.1_Missense_Mutation_p.R254C|SEMA6D_ENST00000389425.3_Missense_Mutation_p.R254C|SEMA6D_ENST00000389432.2_Missense_Mutation_p.R254C|SEMA6D_ENST00000358066.4_Missense_Mutation_p.R254C	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	254	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TGTGTATTCCCGCGTGGCCCG	0.488													C|||	1	0.000199681	8e-04	0	5008	,	,		19135	0		0	False		,,,				2504	0				p.R254C		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C760T						.						132	131	131					15																	48056059		2198	4297	6495	SO:0001583	missense	80031	exon10			TATTCCCGCGTGG	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.760C>T	chr15.hg19:g.48056059C>T	ENSP00000324857:p.Arg254Cys	125.0	0.0		116.0	37.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.559209	0.86335	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44	5.87	5.87	0.94306	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.71913	0.3396	H	0.96916	3.905	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.81219	-0.1032	10	0.87932	D	0	.	20.206	0.98277	0.0:1.0:0.0:0.0	.	254;254;254;254;254	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	C	254	ENSP00000442040:R254C;ENSP00000446152:R254C;ENSP00000324857:R254C;ENSP00000374084:R254C;ENSP00000374083:R254C;ENSP00000346786:R254C;ENSP00000350770:R254C;ENSP00000374079:R254C;ENSP00000348276:R254C;ENSP00000374076:R254C	ENSP00000324857:R254C	R	+	1	0	SEMA6D	45843351	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.809000	0.55606	2.785000	0.95823	0.655000	0.94253	CGC	.	.		0.488	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		T	48056059	C	T	48056059	3	4	111	1	0	0	0	0	1	0	0	0	14057	652	23	1	794	1	SEMA6D	15	48056059	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	2397776	48056059	54475333	271	16511										
CEP152	22995	hgsc.bcm.edu	37	chr15	49083508	49083508	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agcttcaagctgtatctctcTttcttttccattctgaaaga	5	10	5	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:49083508T>C	ENST00000380950.2	-	8	1085	c.898A>G	c.(898-900)Aga>Gga	p.R300G	CEP152_ENST00000399334.3_Missense_Mutation_p.R300G|CEP152_ENST00000325747.5_Missense_Mutation_p.R207G	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	300					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TGTATCTCTCTTTCTTTTCCA	0.333																																					p.R300G		Atlas-SNP	.											.	CEP152	145	.	0			c.A898G						.						133	119	124					15																	49083508		1822	4078	5900	SO:0001583	missense	22995	exon8			TCTCTCTTTCTTT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.898A>G	chr15.hg19:g.49083508T>C	ENSP00000370337:p.Arg300Gly	101.0	0.0		72.0	4.0	NM_014985	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	hg19	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.992539	0.74703	.	.	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334;ENST00000541880	T;T;T	0.80214	-1.35;-1.35;-1.35	5.56	5.56	0.83823	.	0.090108	0.85682	D	0.000000	D	0.87111	0.6096	M	0.72894	2.215	0.37710	D	0.924546	P;D;D	0.76494	0.952;0.997;0.999	P;P;D	0.63283	0.461;0.866;0.913	D	0.89686	0.3894	10	0.59425	D	0.04	-21.5976	12.4834	0.55856	0.0:0.0:0.1489:0.8511	.	207;300;300	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	G	300;207;300;300	ENSP00000370337:R300G;ENSP00000321000:R207G;ENSP00000382271:R300G	ENSP00000321000:R207G	R	-	1	2	CEP152	46870800	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	3.816000	0.55658	2.112000	0.64535	0.533000	0.62120	AGA	.	.		0.333	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		C	49083508	T	C	49083508	3	2	111	1	0	0	0	0	1	0	0	0	3250	1617	56	2	4142	2	CEP152	15	49083508	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1027449	49083508	53447884	272	16512										
MYO5C	55930	hgsc.bcm.edu	37	chr15	52548896	52548896	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atgcaaaattgttcaaagctGttcacatcaaaggtttcaaa	6	7	4	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:52548896G>A	ENST00000261839.7	-	11	1496	c.1335C>T	c.(1333-1335)aaC>aaT	p.N445N	MYO5C_ENST00000443683.2_3'UTR	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	445	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		GTTCAAAGCTGTTCACATCAA	0.328											OREG0023130	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N445N		Atlas-SNP	.											.	MYO5C	162	.	0			c.C1335T						.						130	126	128					15																	52548896		1846	4093	5939	SO:0001819	synonymous_variant	55930	exon11			AAAGCTGTTCACA	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.1335C>T	chr15.hg19:g.52548896G>A		93.0	0.0	985	80.0	4.0	NM_018728	Q6P1W8	Silent	SNP	ENST00000261839.7	hg19	CCDS42036.1																																																																																			.	.		0.328	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		A	52548896	G	A	52548896	2	1	111	1	0	0	0	0	0	0	0	1	10089	1368	48	3		3	MYO5C	15	52548896	Silent	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	3465388	52548896	49982496	273	16513										
KIAA1370	56204	hgsc.bcm.edu	37	chr15	52874394	52874394	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggtttgttggtgattcagtgTaagatttgagttcatatgca	12	3	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:52874394T>C	ENST00000261844.7	-	13	3340	c.3188A>G	c.(3187-3189)tAc>tGc	p.Y1063C	RP11-23N2.4_ENST00000566344.1_RNA|FAM214A_ENST00000546305.2_Missense_Mutation_p.Y1070C|RP11-23N2.4_ENST00000562062.1_RNA	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	1063																	TGATTCAGTGTAAGATTTGAG	0.388																																					p.Y1063C		Atlas-SNP	.											.	.	.	.	0			c.A3188G						.						105	100	101					15																	52874394		1882	4098	5980	SO:0001583	missense	56204	exon13			TCAGTGTAAGATT	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"KIAA1370"	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.3188A>G	chr15.hg19:g.52874394T>C	ENSP00000261844:p.Tyr1063Cys	105.0	0.0		99.0	4.0	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	hg19	CCDS45263.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.017203	0.54576	.	.	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000546305	T;T	0.33216	1.42;1.42	5.83	5.83	0.93111	.	0.234874	0.44483	D	0.000446	T	0.43322	0.1242	L	0.29908	0.895	0.44366	D	0.997266	D;D	0.67145	0.995;0.996	P;D	0.64506	0.879;0.926	T	0.37526	-0.9702	10	0.66056	D	0.02	.	16.2028	0.82102	0.0:0.0:0.0:1.0	.	1070;1063	F5H8G0;Q32MH5	.;K1370_HUMAN	C	1063;1063;1070	ENSP00000261844:Y1063C;ENSP00000443598:Y1070C	ENSP00000261844:Y1063C	Y	-	2	0	KIAA1370	50661686	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.875000	0.63072	2.230000	0.72887	0.467000	0.42956	TAC	.	.		0.388	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		C	52874394	T	C	52874394	3	2	111	1	0	0	0	0	1	0	0	0	8235	1638	57	2	46	2	KIAA1370	15	52874394	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	325498	52874394	49656998	274	16514										
GLCE	26035	hgsc.bcm.edu	37	chr15	69553621	69553621	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gggctgctttatggcgaatgTggctgataagtctagattca	13	6	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:69553621T>C	ENST00000261858.2	+	4	1010	c.782T>C	c.(781-783)gTg>gCg	p.V261A	GLCE_ENST00000559500.1_3'UTR|GLCE_ENST00000559420.2_Missense_Mutation_p.V197A	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	261					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						ATGGCGAATGTGGCTGATAAG	0.403																																					p.V261A		Atlas-SNP	.											.	GLCE	48	.	0			c.T782C						.						158	154	155					15																	69553621		2200	4298	6498	SO:0001583	missense	26035	exon4			CGAATGTGGCTGA	AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"heparan sulfate epimerase"	612134	"D-glucuronyl C5-epimerase", "UDP-glucuronic acid epimerase"			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.782T>C	chr15.hg19:g.69553621T>C	ENSP00000261858:p.Val261Ala	125.0	0.0		90.0	4.0	NM_015554	Q6GUQ2	Missense_Mutation	SNP	ENST00000261858.2	hg19	CCDS32277.1	.	.	.	.	.	.	.	.	.	.	T	15.33	2.802042	0.50315	.	.	ENSG00000138604	ENST00000261858	T	0.32515	1.45	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.31888	0.0811	L	0.50333	1.59	0.80722	D	1	P	0.36027	0.533	B	0.36959	0.237	T	0.06023	-1.0850	10	0.40728	T	0.16	-22.1109	14.8343	0.70172	0.0:0.0:0.0:1.0	.	261	O94923	GLCE_HUMAN	A	261	ENSP00000261858:V261A	ENSP00000261858:V261A	V	+	2	0	GLCE	67340675	1.000000	0.71417	0.997000	0.53966	0.767000	0.43475	6.141000	0.71744	2.174000	0.68829	0.482000	0.46254	GTG	.	.		0.403	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		C	69553621	T	C	69553621	3	2	111	1	0	0	0	0	1	0	0	0	6440	1696	59	2	788	2	GLCE	15	69553621	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	16679227	69553621	32977771	275	16515										
HCN4	10021	hgsc.bcm.edu	37	chr15	73615722	73615722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tggaagtggccaaacccggcTatggtggtggcggctacgcc	16	11	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:73615722T>C	ENST00000261917.3	-	8	3705	c.2712A>G	c.(2710-2712)atA>atG	p.I904M		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	904					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		CAAACCCGGCTATGGTGGTGG	0.716																																					p.I904M		Atlas-SNP	.											.	HCN4	150	.	0			c.A2712G						.						8	11	10					15																	73615722		2087	4074	6161	SO:0001583	missense	10021	exon8			CCCGGCTATGGTG	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.2712A>G	chr15.hg19:g.73615722T>C	ENSP00000261917:p.Ile904Met	118.0	0.0		94.0	4.0	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	hg19	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	T	6.051	0.377834	0.11466	.	.	ENSG00000138622	ENST00000261917	D	0.97303	-4.33	2.39	-2.69	0.06022	.	.	.	.	.	D	0.89553	0.6748	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.08055	0.003	T	0.80908	-0.1172	9	0.35671	T	0.21	.	6.8321	0.23915	0.1433:0.0:0.6333:0.2234	.	904	Q9Y3Q4	HCN4_HUMAN	M	904	ENSP00000261917:I904M	ENSP00000261917:I904M	I	-	3	3	HCN4	71402775	.	.	0.018000	0.16275	0.694000	0.40290	.	.	-0.229000	0.09854	0.368000	0.22195	ATA	.	.		0.716	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		C	73615722	T	C	73615722	3	2	111	1	0	0	0	0	1	0	0	0	7008	1512	53	2	903	2	HCN4	15	73615722	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	4062101	73615722	28915670	276	16516										
SEMA7A	8482	hgsc.bcm.edu	37	chr15	74709008	74709008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaagtagtagatcttgtcatCgtaagcctggtcttggtgca	12	7	3	1	rs140707085		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:74709008C>T	ENST00000261918.4	-	7	1257	c.709G>A	c.(709-711)Gat>Aat	p.D237N	SEMA7A_ENST00000542748.1_Missense_Mutation_p.D72N|SEMA7A_ENST00000543145.2_Missense_Mutation_p.D223N	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	237	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						ATCTTGTCATCGTAAGCCTGG	0.567																																					p.D237N		Atlas-SNP	.											.	SEMA7A	58	.	0			c.G709A						.	C	ASN/ASP,ASN/ASP,ASN/ASP	0,4394		0,0,2197	335	290	306		667,214,709	1.2	0.9	15	dbSNP_134	306	3,8589	3.0+/-9.4	0,3,4293	yes	missense,missense,missense	SEMA7A	NM_001146029.1,NM_001146030.1,NM_003612.3	23,23,23	0,3,6490	TT,TC,CC		0.0349,0.0,0.0231	benign,benign,benign	223/653,72/502,237/667	74709008	3,12983	2197	4296	6493	SO:0001583	missense	8482	exon7			TGTCATCGTAAGC	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"Semaphorins", "CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10741	protein-coding gene	gene with protein product	"John Milton Hagen blood group", "H-Sema K1"	607961	"sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A", "sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.709G>A	chr15.hg19:g.74709008C>T	ENSP00000261918:p.Asp237Asn	315.0	0.0		248.0	19.0	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	hg19	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.396710	0.25205	0.0	3.49E-4	ENSG00000138623	ENST00000261918;ENST00000543145;ENST00000542748	T;T;T	0.15718	2.4;2.4;2.4	5.39	1.22	0.21188	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.284277	0.37906	N	0.001891	T	0.11367	0.0277	L	0.37750	1.13	0.32117	N	0.588474	B;B	0.16802	0.009;0.019	B;B	0.12837	0.005;0.008	T	0.06127	-1.0844	10	0.87932	D	0	-10.0158	4.6518	0.12598	0.0:0.4045:0.1593:0.4362	.	223;237	F5H1S0;O75326	.;SEM7A_HUMAN	N	237;223;72	ENSP00000261918:D237N;ENSP00000438966:D223N;ENSP00000441493:D72N	ENSP00000261918:D237N	D	-	1	0	SEMA7A	72496061	0.153000	0.22777	0.907000	0.35723	0.991000	0.79684	0.533000	0.23082	0.573000	0.29400	0.655000	0.94253	GAT	.	C|1.000;T|0.000		0.567	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		T	74709008	C	T	74709008	3	4	111	1	0	0	0	0	1	0	0	0	14058	884	31	1	1323	1	SEMA7A	15	74709008	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	1093286	74709008	27822384	277	16517										
CYP1A1	1543	hgsc.bcm.edu	37	chr15	75015354	75015354	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tttggggacctgaggtcttgAggccctgattacccagaata	12	9	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:75015354A>G	ENST00000379727.3	-	2	283	c.85T>C	c.(85-87)Tca>Cca	p.S29P	CYP1A1_ENST00000395049.4_Missense_Mutation_p.S29P|CYP1A1_ENST00000567032.1_Missense_Mutation_p.S29P|CYP1A1_ENST00000395048.2_Missense_Mutation_p.S29P|CYP1A1_ENST00000564596.1_Intron			P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 1	29					9-cis-retinoic acid biosynthetic process (GO:0042904)|aging (GO:0007568)|amine metabolic process (GO:0009308)|arachidonic acid metabolic process (GO:0019369)|camera-type eye development (GO:0043010)|cell proliferation (GO:0008283)|cellular lipid metabolic process (GO:0044255)|cellular response to organic cyclic compound (GO:0071407)|coumarin metabolic process (GO:0009804)|dibenzo-p-dioxin catabolic process (GO:0019341)|digestive tract development (GO:0048565)|drug metabolic process (GO:0017144)|embryo development ending in birth or egg hatching (GO:0009792)|epoxygenase P450 pathway (GO:0019373)|flavonoid metabolic process (GO:0009812)|hepatocyte differentiation (GO:0070365)|hydrogen peroxide biosynthetic process (GO:0050665)|insecticide metabolic process (GO:0017143)|maternal process involved in parturition (GO:0060137)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|response to antibiotic (GO:0046677)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to food (GO:0032094)|response to herbicide (GO:0009635)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to iron(III) ion (GO:0010041)|response to lipopolysaccharide (GO:0032496)|response to nematode (GO:0009624)|response to virus (GO:0009615)|response to vitamin A (GO:0033189)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|demethylase activity (GO:0032451)|flavonoid 3'-monooxygenase activity (GO:0016711)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on diphenols and related substances as donors (GO:0016679)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)|vitamin D 24-hydroxylase activity (GO:0070576)			autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(7)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Acetaminophen(DB00316)|Albendazole(DB00518)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Caffeine(DB00201)|Carvedilol(DB01136)|Chloroquine(DB00608)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Clenbuterol(DB01407)|Clobetasol propionate(DB01013)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonidine(DB00575)|Clozapine(DB00363)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Dexamethasone(DB01234)|Dexmedetomidine(DB00633)|Diclofenac(DB00586)|Dicyclomine(DB00804)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Ethanol(DB00898)|Flunarizine(DB04841)|Fluorescein(DB00693)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Granisetron(DB00889)|Haloperidol(DB00502)|Isoprenaline(DB01064)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lorcaserin(DB04871)|Mebendazole(DB00643)|Melatonin(DB01065)|Menadione(DB00170)|Methoxsalen(DB00553)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitroprusside(DB00325)|Norfloxacin(DB01059)|Omeprazole(DB00338)|Ouabain(DB01092)|Oxaliplatin(DB00526)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Prazosin(DB00457)|Primaquine(DB01087)|Progesterone(DB00396)|Propofol(DB00818)|Propranolol(DB00571)|Pyridoxine(DB00165)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Riluzole(DB00740)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiabendazole(DB00730)|Ticlopidine(DB00208)|Toremifene(DB00539)|Tretinoin(DB00755)|Vitamin A(DB00162)|Warfarin(DB00682)	TGAGGTCTTGAGGCCCTGATT	0.562									Endometrial Cancer, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.S29P		Atlas-SNP	.											.	CYP1A1	60	.	0			c.T85C						.																																			SO:0001583	missense	1543	exon2	Familial Cancer Database	;AIMAH, Cushing disease, Adrenal, Familial	GTCTTGAGGCCCT	BC023019	CCDS10268.1	15q24.1	2007-12-14	2003-01-14		ENSG00000140465	ENSG00000140465	1.14.14.1	"Cytochrome P450s"	2595	protein-coding gene	gene with protein product		108330	"cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1"	CYP1		15128046	Standard	NM_000499		Approved	P450DX, P1-450, P450-C, CP11	uc002ayp.4	P04798	OTTHUMG00000142812	ENST00000379727.3:c.85T>C	chr15.hg19:g.75015354A>G	ENSP00000369050:p.Ser29Pro	123.0	0.0		91.0	4.0	NM_000499	A4F3V9|A4F3W0|Q53G18	Missense_Mutation	SNP	ENST00000379727.3	hg19	CCDS10268.1	.	.	.	.	.	.	.	.	.	.	A	3.531	-0.095786	0.07010	.	.	ENSG00000140465	ENST00000379727;ENST00000395048;ENST00000395049;ENST00000268062	T;T;T	0.72051	-0.62;-0.62;-0.48	5.31	0.186	0.15105	.	0.934912	0.09279	N	0.824002	T	0.49389	0.1554	N	0.19112	0.55	0.09310	N	1	P;P	0.44478	0.836;0.529	B;B	0.39738	0.308;0.139	T	0.37865	-0.9687	10	0.36615	T	0.2	.	3.232	0.06751	0.42:0.0:0.2825:0.2975	.	29;29	E7EMT5;P04798	.;CP1A1_HUMAN	P	29	ENSP00000369050:S29P;ENSP00000378488:S29P;ENSP00000378489:S29P	ENSP00000268062:S29P	S	-	1	0	CYP1A1	72802407	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.564000	0.23563	-0.007000	0.14345	0.533000	0.62120	TCA	.	.		0.562	CYP1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286396.1	NM_000499		G	75015354	A	G	75015354	3	3	111	1	0	0	0	0	1	0	0	0	4151	304	11	2	1477	2	CYP1A1	15	75015354	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	306346	75015354	27516038	278	16518										
C15orf17	57184	hgsc.bcm.edu	37	chr15	75197055	75197055	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggatcccagctccccatcacTaggagaagaggaaaacagtc	10	12	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:75197055T>C	ENST00000357635.5	-	4	701		c.e4-2		FAM219B_ENST00000563119.1_Splice_Site|FAM219B_ENST00000565772.1_Splice_Site|FAM219B_ENST00000563706.1_Splice_Site	NM_020447.3	NP_065180.1	Q5XKK7	F219B_HUMAN	family with sequence similarity 219, member B																		TCCCCATCACTAGGAGAAGAG	0.537																																					.		Atlas-SNP	.											.	.	.	.	0			c.381-2A>G						.						131	125	127					15																	75197055		2197	4295	6492	SO:0001630	splice_region_variant	57184	exon5			CATCACTAGGAGA	AK000005	CCDS32295.1	15q23	2012-03-06	2012-03-06	2012-03-06	ENSG00000178761	ENSG00000178761			24695	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 17"	C15orf17		11214971	Standard	NM_020447		Approved	FLJ00005	uc002azh.4	Q5XKK7	OTTHUMG00000172715	ENST00000357635.5:c.381-2A>G	chr15.hg19:g.75197055T>C		87.0	0.0		68.0	4.0	NM_020447	A8K4Q5|B4DK57|Q9NXY0	Splice_Site	SNP	ENST00000357635.5	hg19	CCDS32295.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.020476	0.75275	.	.	ENSG00000178761	ENST00000357635	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8914	0.70611	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	C15orf17	72984108	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.304000	0.72800	2.111000	0.64477	0.449000	0.29647	.	.	.		0.537	FAM219B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420165.1	NM_020447	Intron	C	75197055	T	C	75197055	5	2	111	1	0	0	0	0	0	0	1	0	1785	1536	53	2	225	2	C15orf17	15	75197055	Splice_Site	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	181701	75197055	27334337	279	16519										
TBC1D2B	23102	hgsc.bcm.edu	37	chr15	78305187	78305187	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gtttaggccttgacagtagcCgatatctggattccgccagg	12	10	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:78305187C>G	ENST00000300584.3	-	9	2247	c.2248G>C	c.(2248-2250)Ggc>Cgc	p.G750R	TBC1D2B_ENST00000409931.3_Missense_Mutation_p.G750R	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	750	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						TGACAGTAGCCGATATCTGGA	0.537																																					p.G750R		Atlas-SNP	.											.	TBC1D2B	104	.	0			c.G2248C						.						95	80	85					15																	78305187		2196	4293	6489	SO:0001583	missense	23102	exon9			AGTAGCCGATATC	AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.2248G>C	chr15.hg19:g.78305187C>G	ENSP00000300584:p.Gly750Arg	234.0	0.0		232.0	16.0	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Missense_Mutation	SNP	ENST00000300584.3	hg19	CCDS45314.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.141177	0.77775	.	.	ENSG00000167202	ENST00000409931;ENST00000300584	T;T	0.10763	2.84;2.84	5.47	5.47	0.80525	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.45337	0.1337	M	0.92970	3.365	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.56523	-0.7965	10	0.87932	D	0	.	18.6826	0.91551	0.0:1.0:0.0:0.0	.	750;202;750	Q9UPU7-2;Q9UPU7-3;Q9UPU7	.;.;TBD2B_HUMAN	R	750	ENSP00000387165:G750R;ENSP00000300584:G750R	ENSP00000300584:G750R	G	-	1	0	TBC1D2B	76092242	1.000000	0.71417	0.984000	0.44739	0.473000	0.32948	7.631000	0.83237	2.723000	0.93209	0.655000	0.94253	GGC	.	.		0.537	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079		G	78305187	C	G	78305187	3	3	111	1	0	0	0	0	1	0	0	0	15634	652	23	4	663	4	TBC1D2B	15	78305187	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	3108132	78305187	24226205	280	16520										
BLM	641	hgsc.bcm.edu	37	chr15	91292851	91292851	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cttgcagactccgaaggaagTtgtatgcactacccaaaaca	8	11	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:91292851T>C	ENST00000355112.3	+	3	471	c.353T>C	c.(352-354)gTt>gCt	p.V118A	BLM_ENST00000560509.1_Missense_Mutation_p.V118A	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	118					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			CCGAAGGAAGTTGTATGCACT	0.408			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.V118A		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	.	BLM	122	.	0			c.T353C						.						70	69	70					15																	91292851		2198	4298	6496	SO:0001583	missense	641	exon3	Familial Cancer Database		AGGAAGTTGTATG	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"Bloom syndrome"			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.353T>C	chr15.hg19:g.91292851T>C	ENSP00000347232:p.Val118Ala	67.0	0.0		83.0	4.0	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	hg19	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	T	8.900	0.956159	0.18507	.	.	ENSG00000197299	ENST00000355112	T	0.47869	0.83	6.02	-2.49	0.06403	.	1.400750	0.04428	N	0.368798	T	0.31702	0.0805	L	0.41824	1.3	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.002	T	0.07986	-1.0744	10	0.15499	T	0.54	-2.1436	2.0399	0.03548	0.1329:0.3815:0.1355:0.3502	.	118;118	B2RAN0;P54132	.;BLM_HUMAN	A	118	ENSP00000347232:V118A	ENSP00000347232:V118A	V	+	2	0	BLM	89093855	0.000000	0.05858	0.000000	0.03702	0.795000	0.44927	-0.739000	0.04866	-0.340000	0.08388	0.533000	0.62120	GTT	.	.		0.408	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			C	91292851	T	C	91292851	3	2	111	1	0	0	0	0	1	0	0	0	1445	1725	60	2	359	2	BLM	15	91292851	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	12987664	91292851	11238541	281	16521										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94841577	94841577	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	caacttgagcaagaagaaggTgaaaaagaacccaagtaagc	10	7	0	5			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr15:94841577T>C	ENST00000357742.4	+	1	83	c.83T>C	c.(82-84)gTg>gCg	p.V28A	MCTP2_ENST00000451018.3_Missense_Mutation_p.V28A|MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000543482.1_Missense_Mutation_p.V28A	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	28					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			AAGAAGAAGGTGAAAAAGAAC	0.522																																					p.V28A		Atlas-SNP	.											.	MCTP2	122	.	0			c.T83C						.						89	90	90					15																	94841577		2197	4298	6495	SO:0001583	missense	55784	exon1			AGAAGGTGAAAAA	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.83T>C	chr15.hg19:g.94841577T>C	ENSP00000350377:p.Val28Ala	63.0	0.0		96.0	4.0	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	hg19	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	T	7.644	0.681423	0.14907	.	.	ENSG00000140563	ENST00000543482;ENST00000556363;ENST00000451018;ENST00000357742	T;T;T	0.68765	-0.35;-0.11;0.05	4.98	1.23	0.21249	.	0.874162	0.09714	N	0.765375	T	0.38427	0.1040	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B	0.09022	0.0;0.0;0.0;0.0;0.002	B;B;B;B;B	0.06405	0.001;0.002;0.001;0.0;0.002	T	0.38134	-0.9675	10	0.08179	T	0.78	.	0.1219	0.00065	0.2958:0.2096:0.1525:0.3422	.	28;28;28;28;28	F5H415;Q6DN12-2;Q6DN12;B7Z6H2;G3V2J2	.;.;MCTP2_HUMAN;.;.	A	28	ENSP00000438521:V28A;ENSP00000395109:V28A;ENSP00000350377:V28A	ENSP00000350377:V28A	V	+	2	0	MCTP2	92642581	0.000000	0.05858	0.988000	0.46212	0.366000	0.29705	-0.194000	0.09559	-0.034000	0.13713	-0.320000	0.08662	GTG	.	.		0.522	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		C	94841577	T	C	94841577	3	2	111	1	0	0	0	0	1	0	0	0	9410	1696	59	2	85	2	MCTP2	15	94841577	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	3548726	94841577	7689815	282	16522										
TEKT5	146279	hgsc.bcm.edu	37	chr16	10729745	10729745	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctttccagcagcatgatggTgttctcggcctggaagatct	11	11	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:10729745T>C	ENST00000283025.2	-	6	1188	c.1117A>G	c.(1117-1119)Acc>Gcc	p.T373A	TEKT5_ENST00000574923.1_5'UTR	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	373						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						AGCATGATGGTGTTCTCGGCC	0.647																																					p.T373A		Atlas-SNP	.											.	TEKT5	66	.	0			c.A1117G						.						134	131	132					16																	10729745		2197	4300	6497	SO:0001583	missense	146279	exon6			TGATGGTGTTCTC		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.1117A>G	chr16.hg19:g.10729745T>C	ENSP00000283025:p.Thr373Ala	114.0	0.0		99.0	4.0	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	hg19	CCDS10542.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.141508	0.37825	.	.	ENSG00000153060	ENST00000283025	T	0.02395	4.31	4.28	4.28	0.50868	.	0.105342	0.41823	D	0.000811	T	0.05318	0.0141	L	0.58810	1.83	0.31807	N	0.62761	B	0.27997	0.197	B	0.37943	0.261	T	0.06197	-1.0840	10	0.14656	T	0.56	-25.6163	12.2505	0.54595	0.0:0.0:0.0:1.0	.	373	Q96M29	TEKT5_HUMAN	A	373	ENSP00000283025:T373A	ENSP00000283025:T373A	T	-	1	0	TEKT5	10637246	1.000000	0.71417	1.000000	0.80357	0.552000	0.35366	3.885000	0.56182	1.570000	0.49709	0.454000	0.30748	ACC	.	.		0.647	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674		C	10729745	T	C	10729745	3	2	111	1	0	0	0	0	1	0	0	0	15771	1696	59	2	348	2	TEKT5	16	10729745	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		10729745	79625008	283	16523										
C16orf62	57020	hgsc.bcm.edu	37	chr16	19619534	19619534	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gagaatgcaaatgacacggcCaaggaaacatgcctaaattg	10	8	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:19619534C>T	ENST00000251143.5	+	10	831	c.819C>T	c.(817-819)gcC>gcT	p.A273A	C16orf62_ENST00000538853.1_3'UTR|C16orf62_ENST00000542263.1_Silent_p.A362A|C16orf62_ENST00000448695.1_Silent_p.A123A|C16orf62_ENST00000543152.1_Silent_p.A22A|C16orf62_ENST00000438132.3_Silent_p.A362A|C16orf62_ENST00000417362.2_Silent_p.A273A			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	273						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						ATGACACGGCCAAGGAAACAT	0.388																																					p.A362A		Atlas-SNP	.											.	C16orf62	164	.	0			c.C1086T						.						139	134	136					16																	19619534		2197	4300	6497	SO:0001819	synonymous_variant	57020	exon10			CACGGCCAAGGAA		CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.819C>T	chr16.hg19:g.19619534C>T		127.0	0.0		98.0	4.0	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Silent	SNP	ENST00000251143.5	hg19																																																																																				.	.		0.388	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314		T	19619534	C	T	19619534	2	4	111	1	0	0	0	0	0	0	0	1	1827	581	21	3		3	C16orf62	16	19619534	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	8889789	19619534	70735219	284	16524										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21011556	21011556	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aatgccttacccacaaacacCactgctttcttccctatggg	5	15	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:21011556C>T	ENST00000261383.3	-	43	6410	c.6411G>A	c.(6409-6411)gtG>gtA	p.V2137V	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2137	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CCACAAACACCACTGCTTTCT	0.527																																					p.V2137V		Atlas-SNP	.											.	DNAH3	1142	.	0			c.G6411A						.						100	78	86					16																	21011556		2201	4300	6501	SO:0001819	synonymous_variant	55567	exon43			AAACACCACTGCT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.6411G>A	chr16.hg19:g.21011556C>T		122.0	0.0		92.0	4.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	hg19	CCDS10594.1																																																																																			.	.		0.527	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	21011556	C	T	21011556	2	4	111	1	0	0	0	0	0	0	0	1	4605	581	21	3		3	DNAH3	16	21011556	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	1392022	21011556	69343197	285	16525										
OTOA	146183	hgsc.bcm.edu	37	chr16	21716543	21716543	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggaattgctggatgccactgTggctcaagtcctgctttacc	11	11	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:21716543T>C	ENST00000286149.4	+	11	1077	c.1076T>C	c.(1075-1077)gTg>gCg	p.V359A	OTOA_ENST00000388958.3_Missense_Mutation_p.V345A|OTOA_ENST00000388956.4_Missense_Mutation_p.V266A|OTOA_ENST00000388957.3_Missense_Mutation_p.V21A|OTOA_ENST00000569064.1_3'UTR			Q7RTW8	OTOAN_HUMAN	otoancorin	359					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		GATGCCACTGTGGCTCAAGTC	0.577																																					p.V345A		Atlas-SNP	.											.	OTOA	144	.	0			c.T1034C						.						114	105	108					16																	21716543		2199	4300	6499	SO:0001583	missense	146183	exon11			CCACTGTGGCTCA	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.1076T>C	chr16.hg19:g.21716543T>C	ENSP00000286149:p.Val359Ala	103.0	0.0		103.0	5.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	hg19		.	.	.	.	.	.	.	.	.	.	T	14.15	2.450277	0.43531	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956;ENST00000388957	T;T;T;T	0.77098	2.43;-1.07;2.43;-1.07	5.3	4.21	0.49690	.	0.315795	0.29233	N	0.012745	T	0.74527	0.3728	M	0.61703	1.905	0.22366	N	0.999163	P;P;P	0.50943	0.897;0.783;0.94	B;B;B	0.43990	0.335;0.307;0.438	T	0.66901	-0.5806	10	0.48119	T	0.1	-0.9756	9.3397	0.38071	0.0:0.0856:0.0:0.9144	.	266;21;345	B3KWU3;Q7RTW8-2;E9PF51	.;.;.	A	345;359;266;21	ENSP00000373610:V345A;ENSP00000286149:V359A;ENSP00000373608:V266A;ENSP00000373609:V21A	ENSP00000286149:V359A	V	+	2	0	OTOA	21624044	0.955000	0.32602	0.461000	0.27105	0.811000	0.45836	1.673000	0.37534	0.851000	0.35264	0.459000	0.35465	GTG	.	.		0.577	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			C	21716543	T	C	21716543	3	2	111	1	0	0	0	0	1	0	0	0	11311	1696	59	2	1122	2	OTOA	16	21716543	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	704987	21716543	68638210	286	16526										
SCNN1G	6340	hgsc.bcm.edu	37	chr16	23223435	23223435	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agccagcctctacctcctgcAgccaactactgcaactacca	5	18	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:23223435A>G	ENST00000300061.2	+	8	1400	c.1257A>G	c.(1255-1257)gcA>gcG	p.A419A	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	419					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	TACCTCCTGCAGCCAACTACT	0.562																																					p.A419A		Atlas-SNP	.											.	SCNN1G	82	.	0			c.A1257G						.						112	87	95					16																	23223435		2197	4300	6497	SO:0001819	synonymous_variant	6340	exon8			TCCTGCAGCCAAC	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.1257A>G	chr16.hg19:g.23223435A>G		77.0	0.0		68.0	4.0	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Silent	SNP	ENST00000300061.2	hg19	CCDS10608.1																																																																																			.	.		0.562	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		G	23223435	A	G	23223435	2	3	111	1	0	0	0	0	0	0	0	1	13945	175	7	2		2	SCNN1G	16	23223435	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1506892	23223435	67131318	287	16527										
DCTN5	84516	hgsc.bcm.edu	37	chr16	23654296	23654296	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcatctgggaacaaagtcagTcgccagtcagtgttgtgtgg	14	8	3	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:23654296T>C	ENST00000300087.2	+	2	220	c.69T>C	c.(67-69)agT>agC	p.S23S	DCTN5_ENST00000568272.1_Silent_p.S23S|DCTN5_ENST00000568589.1_Silent_p.S23S|DCTN5_ENST00000563998.1_Silent_p.S23S|PALB2_ENST00000261584.4_5'Flank	NM_001199743.1|NM_032486.3	NP_001186672.1|NP_115875.1	Q9BTE1	DCTN5_HUMAN	dynactin 5 (p25)	23					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)				endometrium(2)|lung(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	10				GBM - Glioblastoma multiforme(48;0.0156)		ACAAAGTCAGTCGCCAGTCAG	0.473																																					p.S23S		Atlas-SNP	.											.	DCTN5	21	.	0			c.T69C						.						120	113	116					16																	23654296		2197	4300	6497	SO:0001819	synonymous_variant	84516	exon2			AGTCAGTCGCCAG		CCDS10615.1, CCDS58435.1, CCDS58436.1	16p12.1	2008-02-05			ENSG00000166847	ENSG00000166847			24594	protein-coding gene	gene with protein product		612962				10525537, 15043994	Standard	NM_032486		Approved	MGC3248, p25	uc002dly.2	Q9BTE1	OTTHUMG00000131610	ENST00000300087.2:c.69T>C	chr16.hg19:g.23654296T>C		73.0	0.0		64.0	4.0	NM_001199011	A8K9X8|H3BN51|H3BQA4	Silent	SNP	ENST00000300087.2	hg19	CCDS10615.1																																																																																			.	.		0.473	DCTN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254497.1	NM_032486		C	23654296	T	C	23654296	2	2	111	1	0	0	0	0	0	0	0	1	4312	1664	58	2		2	DCTN5	16	23654296	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	430861	23654296	66700457	288	16528										
NLRC5	84166	hgsc.bcm.edu	37	chr16	57065327	57065327	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atcctgcagggaggcggaccTcatcttccttctttccccgc	9	16	3	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:57065327T>C	ENST00000262510.6	+	11	2654	c.2429T>C	c.(2428-2430)cTc>cCc	p.L810P	NLRC5_ENST00000308149.7_Missense_Mutation_p.L810P|NLRC5_ENST00000436936.1_Missense_Mutation_p.L810P|NLRC5_ENST00000539144.1_Missense_Mutation_p.L810P	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	810				ADL -> RTI (in Ref. 1; AAO59377 and 2; ABO40479). {ECO:0000305}.	defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GAGGCGGACCTCATCTTCCTT	0.557																																					p.L810P		Atlas-SNP	.											NLRC5,rectum,carcinoma,0,1	NLRC5	186	.	0			c.T2429C						.						138	114	122					16																	57065327		2198	4300	6498	SO:0001583	missense	84166	exon10			CGGACCTCATCTT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2429T>C	chr16.hg19:g.57065327T>C	ENSP00000262510:p.Leu810Pro	231.0	1.0		222.0	12.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	hg19	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.138040	0.56936	.	.	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000327982;ENST00000539144;ENST00000538110;ENST00000543030	T;T;T;T;T;T	0.75260	-0.71;-0.74;-0.92;-0.74;2.26;0.24	4.18	4.18	0.49190	.	.	.	.	.	T	0.65811	0.2727	L	0.29908	0.895	0.54753	D	0.999983	B;B;B;B	0.31503	0.119;0.174;0.326;0.063	B;B;B;B	0.38458	0.072;0.143;0.274;0.068	T	0.68074	-0.5505	9	0.62326	D	0.03	.	9.9174	0.41444	0.0:0.0:0.0:1.0	.	810;810;810;810	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3	.;.;.;NLRC5_HUMAN	P	810;810;810;284;810;317;109	ENSP00000262510:L810P;ENSP00000308886:L810P;ENSP00000389739:L810P;ENSP00000441727:L810P;ENSP00000441597:L317P;ENSP00000440153:L109P	ENSP00000262510:L810P	L	+	2	0	NLRC5	55622828	0.173000	0.23056	0.997000	0.53966	0.787000	0.44495	3.042000	0.49815	2.127000	0.65507	0.459000	0.35465	CTC	.	.		0.557	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		C	57065327	T	C	57065327	3	2	111	1	0	0	0	0	1	0	0	0	10479	1551	54	2	2463	2	NLRC5	16	57065327	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	33411031	57065327	33289426	289	16529										
SLC38A7	55238	hgsc.bcm.edu	37	chr16	58712696	58712696	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acatagcacacctgtcagctTgccacacacagcccatacca	5	17	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:58712696T>C	ENST00000570101.1	-	3	1256	c.373A>G	c.(373-375)Aag>Gag	p.K125E	SLC38A7_ENST00000564100.1_Missense_Mutation_p.K125E|SLC38A7_ENST00000566953.1_Intron|SLC38A7_ENST00000564010.1_Missense_Mutation_p.K36E|SLC38A7_ENST00000219320.4_Missense_Mutation_p.K125E			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	125					sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)			endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						CCTGTCAGCTTGCCACACACA	0.542																																					p.K125E		Atlas-SNP	.											.	SLC38A7	26	.	0			c.A373G						.						215	128	158					16																	58712696		2198	4300	6498	SO:0001583	missense	55238	exon4			TCAGCTTGCCACA	BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042		"Solute carriers"	25582	protein-coding gene	gene with protein product		614236					Standard	XM_006721229		Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000570101.1:c.373A>G	chr16.hg19:g.58712696T>C	ENSP00000454646:p.Lys125Glu	124.0	0.0		84.0	4.0	NM_018231	Q53GJ9|Q9H9I5	Missense_Mutation	SNP	ENST00000570101.1	hg19	CCDS10800.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.414777	0.42817	.	.	ENSG00000103042	ENST00000219320	T	0.02421	4.3	5.79	4.64	0.57946	.	0.098334	0.64402	D	0.000002	T	0.04497	0.0123	L	0.50333	1.59	0.80722	D	1	P;B	0.35468	0.503;0.241	B;B	0.39617	0.305;0.085	T	0.51317	-0.8721	9	.	.	.	.	11.0297	0.47765	0.0:0.0:0.2809:0.7191	.	125;125	Q9NVC3;Q9NVC3-2	S38A7_HUMAN;.	E	125	ENSP00000219320:K125E	.	K	-	1	0	SLC38A7	57270197	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.741000	0.55090	2.220000	0.72140	0.528000	0.53228	AAG	.	.		0.542	SLC38A7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422206.2	NM_018231		C	58712696	T	C	58712696	3	2	111	1	0	0	0	0	1	0	0	0	14624	1821	63	2	1051	2	SLC38A7	16	58712696	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1647369	58712696	31642057	290	16530										
CDH8	1006	hgsc.bcm.edu	37	chr16	61687550	61687550	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttcaccaacagagtagagttCgcccagtctcttaaagcggg	10	11	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:61687550C>T	ENST00000577390.1	-	12	3316	c.2362G>A	c.(2362-2364)Gaa>Aaa	p.E788K	CDH8_ENST00000577730.1_Intron|CDH8_ENST00000299345.6_Intron	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	788					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)	p.E788K(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		GAGTAGAGTTCGCCCAGTCTC	0.473																																					p.E788K		Atlas-SNP	.											CDH8,NS,malignant_melanoma,0,3	CDH8	273	.	1	Substitution - Missense(1)	skin(1)	c.G2362A						.						56	59	58					16																	61687550		2202	4300	6502	SO:0001583	missense	1006	exon12			AGAGTTCGCCCAG	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.2362G>A	chr16.hg19:g.61687550C>T	ENSP00000462701:p.Glu788Lys	179.0	0.0		138.0	30.0	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	hg19	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.032742	0.75504	.	.	ENSG00000150394	ENST00000299345	.	.	.	5.7	5.7	0.88788	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.72137	0.3423	L	0.48877	1.53	0.80722	D	1	D	0.61697	0.99	P	0.59012	0.85	T	0.73401	-0.3994	9	0.66056	D	0.02	.	18.8311	0.92139	0.0:1.0:0.0:0.0	.	788	P55286	CADH8_HUMAN	K	788	.	ENSP00000299345:E788K	E	-	1	0	CDH8	60245051	1.000000	0.71417	0.995000	0.50966	0.999000	0.98932	7.770000	0.85390	2.679000	0.91253	0.655000	0.94253	GAA	.	.		0.473	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		T	61687550	C	T	61687550	3	4	111	1	0	0	0	0	1	0	0	0	3118	893	31	1	41	1	CDH8	16	61687550	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	2974854	61687550	28667203	291	16531										
ZDHHC1	29800	hgsc.bcm.edu	37	chr16	67434899	67434899	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgcagtgcaggtcttcaatgAcatgtgcgtgctggcttcgg	14	9	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:67434899A>G	ENST00000348579.2	-	4	730	c.389T>C	c.(388-390)gTc>gCc	p.V130A		NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	130					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		GTCTTCAATGACATGTGCGTG	0.597																																					p.V130A		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.T389C						.						129	112	118					16																	67434899		2198	4300	6498	SO:0001583	missense	29800	exon4			TCAATGACATGTG	U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"Zinc fingers, DHHC-type"	17916	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 1"	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.389T>C	chr16.hg19:g.67434899A>G	ENSP00000340299:p.Val130Ala	176.0	0.0		148.0	6.0	NM_013304	O15461	Missense_Mutation	SNP	ENST00000348579.2	hg19	CCDS10836.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.096311	0.76870	.	.	ENSG00000159714	ENST00000348579	T	0.38722	1.12	6.06	6.06	0.98353	.	0.000000	0.30020	U	0.010620	T	0.59959	0.2232	L	0.56124	1.755	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.55573	-0.8120	10	0.33940	T	0.23	.	15.7905	0.78357	1.0:0.0:0.0:0.0	.	130	Q8WTX9	ZDHC1_HUMAN	A	130	ENSP00000340299:V130A	ENSP00000340299:V130A	V	-	2	0	ZDHHC1	65992400	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.864000	0.92294	2.324000	0.78689	0.533000	0.62120	GTC	.	.		0.597	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304		G	67434899	A	G	67434899	3	3	111	1	0	0	0	0	1	0	0	0	17615	275	10	2	1100	2	ZDHHC1	16	67434899	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	5747349	67434899	22919854	292	16532										
CIRH1A	84916	hgsc.bcm.edu	37	chr16	69187545	69187545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctcttccagtttgctcatcActtagaactttggcgactgg	8	12	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:69187545A>G	ENST00000314423.7	+	9	1238	c.1061A>G	c.(1060-1062)cAc>cGc	p.H354R	CIRH1A_ENST00000563094.1_Missense_Mutation_p.H354R|CIRH1A_ENST00000352319.4_Missense_Mutation_p.H354R			Q969X6	CIR1A_HUMAN	cirrhosis, autosomal recessive 1A (cirhin)	354					maturation of SSU-rRNA (GO:0030490)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(108;0.125)		TTTGCTCATCACTTAGAACTT	0.408																																					p.H354R	Melanoma(69;1156 1278 4951 8715 52012)	Atlas-SNP	.											.	CIRH1A	48	.	0			c.A1061G						.						95	81	86					16																	69187545		2198	4300	6498	SO:0001583	missense	84916	exon9			CTCATCACTTAGA	AB075868	CCDS10872.1	16q22	2014-04-07			ENSG00000141076	ENSG00000141076		"WD repeat domain containing"	1983	protein-coding gene	gene with protein product	"UTP4, small subunit (SSU) processome component, homolog (yeast)"	607456				10820129, 20385600	Standard	NM_032830		Approved	NAIC, FLJ14728, KIAA1988, TEX292, CIRHIN, UTP4	uc002ews.4	Q969X6	OTTHUMG00000137570	ENST00000314423.7:c.1061A>G	chr16.hg19:g.69187545A>G	ENSP00000327179:p.His354Arg	97.0	0.0		89.0	4.0	NM_032830	Q8NCD9|Q8TF14|Q96SP0|Q96SR9|Q96SZ9|Q96T13|Q9BWK6	Missense_Mutation	SNP	ENST00000314423.7	hg19	CCDS10872.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.710637	0.30322	.	.	ENSG00000141076	ENST00000314423;ENST00000352319	T;T	0.27890	1.64;2.37	5.46	4.18	0.49190	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.165338	0.56097	D	0.000038	T	0.16171	0.0389	N	0.21097	0.63	0.45747	D	0.998642	B;B;B	0.20459	0.045;0.001;0.002	B;B;B	0.16289	0.015;0.001;0.004	T	0.10405	-1.0631	10	0.15952	T	0.53	.	5.6183	0.17444	0.8517:0.0:0.1483:0.0	.	354;354;354	Q969X6-2;Q969X6;Q969X6-3	.;CIR1A_HUMAN;.	R	354	ENSP00000327179:H354R;ENSP00000339164:H354R	ENSP00000327179:H354R	H	+	2	0	CIRH1A	67745046	0.997000	0.39634	0.996000	0.52242	0.946000	0.59487	3.176000	0.50863	2.185000	0.69588	0.460000	0.39030	CAC	.	.		0.408	CIRH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268950.2	NM_032830		G	69187545	A	G	69187545	3	3	111	1	0	0	0	0	1	0	0	0	3436	159	6	2	1091	2	CIRH1A	16	69187545	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1752646	69187545	21167208	293	16533										
NFAT5	10725	hgsc.bcm.edu	37	chr16	69718852	69718852	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctagtccagcaagaccttgcTcttttgaagaggccatgaaa	9	10	1	4			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:69718852T>C	ENST00000354436.2	+	10	2017	c.1699T>C	c.(1699-1701)Tct>Cct	p.S567P	NFAT5_ENST00000393742.2_Missense_Mutation_p.S491P|NFAT5_ENST00000432919.1_Missense_Mutation_p.S585P|NFAT5_ENST00000566899.1_Missense_Mutation_p.S491P|NFAT5_ENST00000349945.1_Missense_Mutation_p.S491P|NFAT5_ENST00000567239.1_Missense_Mutation_p.S584P	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	567					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						AAGACCTTGCTCTTTTGAAGA	0.343																																					p.S585P		Atlas-SNP	.											.	NFAT5	184	.	0			c.T1753C						.						66	71	69					16																	69718852		2198	4300	6498	SO:0001583	missense	10725	exon11			CCTTGCTCTTTTG	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.1699T>C	chr16.hg19:g.69718852T>C	ENSP00000346420:p.Ser567Pro	103.0	0.0		103.0	5.0	NM_138713	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Missense_Mutation	SNP	ENST00000354436.2	hg19	CCDS10881.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.268392	0.80469	.	.	ENSG00000102908	ENST00000432919;ENST00000426654;ENST00000349945;ENST00000354436;ENST00000393742	T;T;T;T	0.48836	0.81;0.81;0.8;0.81	5.32	5.32	0.75619	Immunoglobulin E-set (1);	0.113037	0.64402	D	0.000007	T	0.52805	0.1757	L	0.51422	1.61	0.58432	D	0.999996	D;D;D;D	0.60575	0.98;0.98;0.978;0.988	P;P;P;P	0.54706	0.578;0.578;0.585;0.759	T	0.52087	-0.8622	10	0.40728	T	0.16	.	10.5188	0.44907	0.1445:0.0:0.0:0.8555	.	584;567;585;491	A2RRB4;O94916;E9PHR7;O94916-2	.;NFAT5_HUMAN;.;.	P	585;584;491;567;491	ENSP00000396538:S585P;ENSP00000338806:S491P;ENSP00000346420:S567P;ENSP00000377343:S491P	ENSP00000338806:S491P	S	+	1	0	NFAT5	68276353	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.953000	0.63624	2.014000	0.59158	0.533000	0.62120	TCT	.	.		0.343	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		C	69718852	T	C	69718852	3	2	111	1	0	0	0	0	1	0	0	0	10369	1551	54	2	1795	2	NFAT5	16	69718852	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	531307	69718852	20635901	294	16534										
GLG1	2734	hgsc.bcm.edu	37	chr16	74528659	74528659	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gtttcaaaataatacttaccTtttcactcatggattcttca	3	9	5	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:74528659T>C	ENST00000422840.2	-	6	1048	c.1049A>G	c.(1048-1050)aAg>aGg	p.K350R	GLG1_ENST00000447066.2_Splice_Site_p.K339R|GLG1_ENST00000205061.5_Splice_Site_p.K350R	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	350					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						AATACTTACCTTTTCACTCAT	0.363																																					p.K350R		Atlas-SNP	.											.	GLG1	106	.	0			c.A1049G						.						78	78	78					16																	74528659		2198	4300	6498	SO:0001630	splice_region_variant	2734	exon6			CTTACCTTTTCAC		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.1050+1A>G	chr16.hg19:g.74528659T>C		76.0	0.0		91.0	4.0	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	hg19	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.980583	0.53827	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.94	5.94	0.96194	.	0.052465	0.85682	D	0.000000	T	0.47619	0.1455	L	0.40543	1.245	0.58432	D	0.999998	B;B;B	0.15141	0.002;0.012;0.002	B;B;B	0.16289	0.015;0.009;0.003	T	0.40850	-0.9541	9	0.35671	T	0.21	-0.0085	10.6992	0.45918	0.0:0.0707:0.0:0.9293	.	350;350;339	Q92896;Q92896-2;B7Z8Y4	GSLG1_HUMAN;.;.	R	350;339;350	.	ENSP00000205061:K350R	K	-	2	0	GLG1	73086160	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.601000	0.61090	2.275000	0.75901	0.528000	0.53228	AAG	.	.		0.363	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201	Missense_Mutation	C	74528659	T	C	74528659	5	2	111	1	0	0	0	0	0	0	1	0	6444	1623	56	2	2654	2	GLG1	16	74528659	Splice_Site	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	4809807	74528659	15826094	295	16535										
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76523688	76523688	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tttcgagtatgtggccagcaTggagcaacttcaggccacta	11	10	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr16:76523688T>C	ENST00000476707.1	+	12	2136	c.1997T>C	c.(1996-1998)aTg>aCg	p.M666T	CNTNAP4_ENST00000377504.4_Missense_Mutation_p.M614T|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.M590T|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.M662T			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	663	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						GTGGCCAGCATGGAGCAACTT	0.453																																					p.M590T		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.T1769C						.						55	43	47					16																	76523688		2198	4300	6498	SO:0001583	missense	85445	exon12			CCAGCATGGAGCA	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.1997T>C	chr16.hg19:g.76523688T>C	ENSP00000417628:p.Met666Thr	145.0	0.0		109.0	5.0	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	hg19		.	.	.	.	.	.	.	.	.	.	T	4.787	0.146293	0.09134	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.14766	2.48;2.48;2.48;2.48	4.55	1.13	0.20643	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (1);	.	.	.	.	T	0.08268	0.0206	.	.	.	0.32735	N	0.508424	B;B;B;B	0.09022	0.0;0.002;0.001;0.0	B;B;B;B	0.09377	0.002;0.002;0.004;0.001	T	0.29792	-1.0000	8	0.19590	T	0.45	.	8.8403	0.35137	0.0:0.2388:0.0:0.7612	.	590;666;638;663	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	T	662;614;590;666	ENSP00000306893:M662T;ENSP00000439733:M614T;ENSP00000418741:M590T;ENSP00000417628:M666T	ENSP00000306893:M662T	M	+	2	0	CNTNAP4	75081189	0.079000	0.21365	0.999000	0.59377	0.997000	0.91878	0.377000	0.20552	0.360000	0.24265	0.455000	0.32223	ATG	.	.		0.453	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		C	76523688	T	C	76523688	3	2	111	1	0	0	0	0	1	0	0	0	3651	1464	51	2	2051	2	CNTNAP4	16	76523688	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1995029	76523688	13831065	296	16536										
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3920939	3920939	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gctgcttggcatagctctgcTgcagttcgctctctgtgctg	12	12	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:3920939T>C	ENST00000381638.2	-	48	7851	c.7727A>G	c.(7726-7728)cAg>cGg	p.Q2576R		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2576							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						ATAGCTCTGCTGCAGTTCGCT	0.597																																					p.Q2576R		Atlas-SNP	.											.	ZZEF1	195	.	0			c.A7727G						.						80	77	78					17																	3920939		2203	4300	6503	SO:0001583	missense	23140	exon48			CTCTGCTGCAGTT	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.7727A>G	chr17.hg19:g.3920939T>C	ENSP00000371051:p.Gln2576Arg	130.0	0.0		98.0	4.0	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	hg19	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	T	14.84	2.656663	0.47467	.	.	ENSG00000074755	ENST00000381638	T	0.21361	2.01	5.29	4.2	0.49525	.	0.062472	0.64402	D	0.000003	T	0.12135	0.0295	N	0.19112	0.55	0.53688	D	0.99997	B	0.14012	0.009	B	0.12156	0.007	T	0.12344	-1.0551	10	0.18710	T	0.47	-13.6364	9.4366	0.38643	0.0:0.1425:0.0:0.8575	.	2576	O43149	ZZEF1_HUMAN	R	2576	ENSP00000371051:Q2576R	ENSP00000371051:Q2576R	Q	-	2	0	ZZEF1	3867688	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.997000	0.57016	2.009000	0.58944	0.528000	0.53228	CAG	.	.		0.597	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		C	3920939	T	C	3920939	3	2	111	1	0	0	0	0	1	0	0	0	18270	1580	55	2	1190	2	ZZEF1	17	3920939	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		3920939	77274271	297	16537										
ZNF232	7775	hgsc.bcm.edu	37	chr17	5009622	5009622	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttcctcctgggcaggggaccAcctcagtctctccgctttgg	11	15	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:5009622A>G	ENST00000250076.3	-	5	1486	c.832T>C	c.(832-834)Tgg>Cgg	p.W278R	ZNF232_ENST00000575538.1_5'Flank|ZNF232_ENST00000575898.1_Missense_Mutation_p.W269R|ZNF232_ENST00000416429.2_3'UTR	NM_014519.2	NP_055334.2	Q9UNY5	ZN232_HUMAN	zinc finger protein 232	251					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|prostate(2)	11						GCAGGGGACCACCTCAGTCTC	0.468																																					p.W278R		Atlas-SNP	.											.	ZNF232	42	.	0			c.T832C						.						102	101	101					17																	5009622		2203	4300	6503	SO:0001583	missense	7775	exon5			GGGACCACCTCAG	AF080169	CCDS11068.1	17p13.2	2013-01-09			ENSG00000167840	ENSG00000167840		"-", "Zinc fingers, C2H2-type"	13026	protein-coding gene	gene with protein product						11311944	Standard	NM_014519		Approved	ZSCAN11	uc002gat.3	Q9UNY5	OTTHUMG00000099450	ENST00000250076.3:c.832T>C	chr17.hg19:g.5009622A>G	ENSP00000250076:p.Trp278Arg	80.0	0.0		78.0	4.0	NM_014519		Missense_Mutation	SNP	ENST00000250076.3	hg19	CCDS11068.1	.	.	.	.	.	.	.	.	.	.	A	6.227	0.410026	0.11812	.	.	ENSG00000167840	ENST00000250076	T	0.00912	5.55	2.99	-5.98	0.02220	.	3.492970	0.01390	N	0.013220	T	0.00724	0.0024	N	0.24115	0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48115	-0.9063	10	0.22109	T	0.4	.	2.9235	0.05777	0.5675:0.1174:0.1756:0.1394	.	251;242	Q9UNY5;Q9UNY5-2	ZN232_HUMAN;.	R	278	ENSP00000250076:W278R	ENSP00000250076:W278R	W	-	1	0	ZNF232	4950346	0.000000	0.05858	0.000000	0.03702	0.566000	0.35808	-1.363000	0.02592	-1.665000	0.01477	-0.242000	0.12053	TGG	.	.		0.468	ZNF232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216915.1	NM_014519		G	5009622	A	G	5009622	3	3	111	1	0	0	0	0	1	0	0	0	17800	159	6	2	506	2	ZNF232	17	5009622	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1088683	5009622	76185588	298	16538										
RABEP1	9135	hgsc.bcm.edu	37	chr17	5235279	5235279	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaaatgcagtattacaagctGcacaagatgatttgggacac	9	7	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:5235279G>A	ENST00000546142.2	+	3	386	c.199G>A	c.(199-201)Gca>Aca	p.A67T	RABEP1_ENST00000262477.6_Missense_Mutation_p.A67T|RABEP1_ENST00000537505.1_Missense_Mutation_p.A24T|RABEP1_ENST00000341923.6_Missense_Mutation_p.A67T|RABEP1_ENST00000408982.2_Missense_Mutation_p.A67T			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	67					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						ATTACAAGCTGCACAAGATGA	0.433																																					p.A67T		Atlas-SNP	.											.	RABEP1	59	.	0			c.G199A						.						116	105	109					17																	5235279		1910	4123	6033	SO:0001583	missense	9135	exon3			CAAGCTGCACAAG	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.199G>A	chr17.hg19:g.5235279G>A	ENSP00000437701:p.Ala67Thr	38.0	0.0		41.0	4.0	NM_004703	B2RAG7|O95369|Q8IVX3	Missense_Mutation	SNP	ENST00000546142.2	hg19	CCDS45592.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903509	0.72754	.	.	ENSG00000029725	ENST00000262477;ENST00000408982;ENST00000539669;ENST00000546142;ENST00000341923;ENST00000537505	T;T;T;T;T	0.48836	0.84;0.85;0.84;0.85;0.8	6.17	6.17	0.99709	.	0.047483	0.85682	D	0.000000	T	0.42314	0.1197	L	0.47716	1.5	0.58432	D	0.99999	B;B;B;B;B;B	0.31318	0.141;0.214;0.214;0.087;0.141;0.319	B;B;B;B;B;B	0.26416	0.041;0.056;0.031;0.018;0.041;0.069	T	0.24119	-1.0169	10	0.13470	T	0.59	-12.8487	19.8676	0.96824	0.0:0.0:1.0:0.0	.	24;24;67;67;67;67	F5H355;B4DMM4;Q05BX6;Q15276;Q15276-2;F5GZU7	.;.;.;RABE1_HUMAN;.;.	T	67;67;67;67;67;24	ENSP00000262477:A67T;ENSP00000386150:A67T;ENSP00000437701:A67T;ENSP00000339569:A67T;ENSP00000445408:A24T	ENSP00000262477:A67T	A	+	1	0	RABEP1	5176003	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.295000	0.59049	2.941000	0.99782	0.655000	0.94253	GCA	.	.		0.433	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703		A	5235279	G	A	5235279	3	1	111	1	0	0	0	0	1	0	0	0	12976	1319	46	3	209	3	RABEP1	17	5235279	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	225657	5235279	75959931	299	16539										
POLR2A	5430	hgsc.bcm.edu	37	chr17	7416450	7416450	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cccccacttcaccctcctacTcccctacctctccatcctat	0	24	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:7416450T>C	ENST00000322644.6	+	29	5266	c.4867T>C	c.(4867-4869)Tcc>Ccc	p.S1623P		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1623	C-terminal domain (CTD); 52 X 7 AA approximate tandem repeats of Y-[ST]-P- [STQ]-[ST]-P-[SRTEVKGN].				7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				ACCCTCCTACTCCCCTACCTC	0.592																																					p.S1623P		Atlas-SNP	.											.	POLR2A	157	.	0			c.T4867C						.						283	282	282					17																	7416450		2203	4300	6503	SO:0001583	missense	5430	exon29			TCCTACTCCCCTA			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.4867T>C	chr17.hg19:g.7416450T>C	ENSP00000314949:p.Ser1623Pro	213.0	0.0		190.0	9.0	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.581869	0.28180	.	.	ENSG00000181222	ENST00000535204;ENST00000545644;ENST00000322644	T	0.73469	-0.75	3.71	3.71	0.42584	.	0.300781	0.26304	N	0.025148	D	0.83207	0.5204	M	0.93978	3.48	0.80722	D	1	P	0.43826	0.818	P	0.50314	0.637	D	0.85166	0.0995	10	0.87932	D	0	-16.3469	6.626	0.22830	0.34:0.0:0.0:0.66	.	1623	P24928	RPB1_HUMAN	P	1579;522;1623	ENSP00000314949:S1623P	ENSP00000314949:S1623P	S	+	1	0	SLC35G6	7357174	1.000000	0.71417	0.998000	0.56505	0.756000	0.42949	2.156000	0.42310	1.682000	0.51000	0.374000	0.22700	TCC	.	.		0.592	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		C	7416450	T	C	7416450	3	2	111	1	0	0	0	0	1	0	0	0	12223	1551	54	2	4981	2	POLR2A	17	7416450	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2181171	7416450	73778760	300	16540										
CHD3	1107	hgsc.bcm.edu	37	chr17	7804563	7804563	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctctctcctcccttttcaggAgtcccccaaactccccagtg	5	19	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:7804563A>G	ENST00000330494.7	+	20	3272	c.3122A>G	c.(3121-3123)gAg>gGg	p.E1041G	CHD3_ENST00000358181.4_Splice_Site_p.E1041G|CHD3_ENST00000380358.4_Splice_Site_p.E1100G	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1041					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				CCTTTTCAGGAGTCCCCCAAA	0.562																																					p.E1100G		Atlas-SNP	.											.	CHD3	169	.	0			c.A3299G						.						72	77	75					17																	7804563		2203	4300	6503	SO:0001630	splice_region_variant	1107	exon20			TTCAGGAGTCCCC	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.3121-1A>G	chr17.hg19:g.7804563A>G		64.0	0.0		71.0	4.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	A	18.50	3.638377	0.67130	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	D;D;D	0.92249	-3.0;-2.91;-2.93	5.14	5.14	0.70334	.	0.000000	0.46758	D	0.000263	D	0.96722	0.8930	M	0.90870	3.155	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.78314	0.991;0.979;0.986	D	0.97628	1.0140	10	0.87932	D	0	-34.5159	15.122	0.72450	1.0:0.0:0.0:0.0	.	1041;1041;1100	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	G	1100;1041;1041	ENSP00000369716:E1100G;ENSP00000350907:E1041G;ENSP00000332628:E1041G	ENSP00000332628:E1041G	E	+	2	0	CHD3	7745288	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.139000	0.94554	2.169000	0.68431	0.459000	0.35465	GAG	.	.		0.562	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	Missense_Mutation	G	7804563	A	G	7804563	5	3	111	1	0	0	0	0	0	0	1	0	3328	318	11	2	3481	2	CHD3	17	7804563	Splice_Site	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	388113	7804563	73390647	301	16541										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11757692	11757692	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aggcactgaacaaagccaccGcggacctcacagctgcccag	10	16	1	1	rs368607572		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:11757692G>A	ENST00000262442.4	+	50	9948	c.9880G>A	c.(9880-9882)Gcg>Acg	p.A3294T	DNAH9_ENST00000454412.2_Missense_Mutation_p.A3294T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3294	Stalk. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CAAAGCCACCGCGGACCTCAC	0.572													G|||	1	0.000199681	8e-04	0	5008	,	,		16213	0		0	False		,,,				2504	0				p.A3294T		Atlas-SNP	.											.	DNAH9	695	.	0			c.G9880A						.	G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	53	55	54		9880	-5.5	0	17		54	0,8600		0,0,4300	no	missense	DNAH9	NM_001372.3	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	3294/4487	11757692	1,13005	2203	4300	6503	SO:0001583	missense	1770	exon50			GCCACCGCGGACC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.9880G>A	chr17.hg19:g.11757692G>A	ENSP00000262442:p.Ala3294Thr	113.0	0.0		115.0	44.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	6.821	0.520661	0.13005	2.27E-4	0.0	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.76578	-1.03;-1.03	5.44	-5.49	0.02584	Dynein heavy chain, coiled coil stalk (1);	1.599710	0.03137	N	0.166106	T	0.79753	0.4500	M	0.73753	2.245	0.09310	N	1	B	0.21753	0.06	B	0.28991	0.097	T	0.62891	-0.6758	10	0.19147	T	0.46	.	19.8505	0.96738	0.0774:0.0:0.7888:0.1339	.	3294	Q9NYC9	DYH9_HUMAN	T	3294;3294;1876	ENSP00000262442:A3294T;ENSP00000414874:A3294T	ENSP00000262442:A3294T	A	+	1	0	DNAH9	11698417	0.000000	0.05858	0.005000	0.12908	0.231000	0.25187	0.225000	0.17757	-1.336000	0.02238	-0.274000	0.10170	GCG	.	.		0.572	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11757692	G	A	11757692	3	1	111	1	0	0	0	0	1	0	0	0	4610	1087	38	1	10078	1	DNAH9	17	11757692	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	3953129	11757692	69437518	302	16542										
COX10	1352	hgsc.bcm.edu	37	chr17	13972945	13972945	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggccgcatctccgcacactcTctcctcacgcctcctgacag	7	20	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:13972945T>C	ENST00000261643.3	+	1	100	c.23T>C	c.(22-24)cTc>cCc	p.L8P	COX10-AS1_ENST00000449363.1_RNA|COX10_ENST00000536205.1_5'UTR|COX10-AS1_ENST00000602539.1_RNA|COX10_ENST00000537334.1_5'UTR|COX10_ENST00000429152.2_Missense_Mutation_p.L8P|COX10-AS1_ENST00000602743.1_RNA	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	8					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		CCGCACACTCTCTCCTCACGC	0.622																																					p.L8P		Atlas-SNP	.											.	COX10	36	.	0			c.T23C						.						61	55	57					17																	13972945		2203	4300	6503	SO:0001583	missense	1352	exon1			ACACTCTCTCCTC	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.23T>C	chr17.hg19:g.13972945T>C	ENSP00000261643:p.Leu8Pro	127.0	0.0		137.0	7.0	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	hg19	CCDS11166.1	.	.	.	.	.	.	.	.	.	.	T	8.606	0.887998	0.17540	.	.	ENSG00000006695	ENST00000261643	T	0.48836	0.8	4.32	4.32	0.51571	.	0.918277	0.09389	N	0.808761	T	0.44008	0.1273	L	0.57536	1.79	0.28085	N	0.932045	B	0.10296	0.003	B	0.06405	0.002	T	0.39375	-0.9617	10	0.72032	D	0.01	-3.2653	6.6186	0.22790	0.0:0.1035:0.0:0.8965	.	8	Q12887	COX10_HUMAN	P	8	ENSP00000261643:L8P	ENSP00000261643:L8P	L	+	2	0	COX10	13913670	0.007000	0.16637	0.014000	0.15608	0.002000	0.02628	1.421000	0.34815	2.164000	0.68074	0.528000	0.53228	CTC	.	.		0.622	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		C	13972945	T	C	13972945	3	2	111	1	0	0	0	0	1	0	0	0	3764	1551	54	2	25	2	COX10	17	13972945	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2215253	13972945	67222265	303	16543										
NCOR1	9611	hgsc.bcm.edu	37	chr17	15973506	15973506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agttctgttcatcatgggtgAgcctctggacatggtgtttt	12	7	4	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:15973506A>G	ENST00000268712.3	-	31	4743	c.4486T>C	c.(4486-4488)Tca>Cca	p.S1496P	NCOR1_ENST00000395851.1_Missense_Mutation_p.S1512P|NCOR1_ENST00000395857.3_Missense_Mutation_p.S80P	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1496	Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ATCATGGGTGAGCCTCTGGAC	0.408																																					p.S1512P		Atlas-SNP	.											.	NCOR1	240	.	0			c.T4534C						.						213	207	209					17																	15973506		2203	4300	6503	SO:0001583	missense	9611	exon30			TGGGTGAGCCTCT	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.4486T>C	chr17.hg19:g.15973506A>G	ENSP00000268712:p.Ser1496Pro	116.0	0.0		101.0	5.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.596464	0.86953	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.67345	-0.26;0.37;-0.13	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.82089	0.4961	M	0.79475	2.455	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.999;0.998;0.999	D;D;P;D	0.83275	0.996;0.993;0.852;0.929	D	0.84463	0.0595	10	0.87932	D	0	-8.4663	15.3508	0.74384	1.0:0.0:0.0:0.0	.	307;1403;1496;1512	B4DZ48;E7EVK1;O75376;O75376-2	.;.;NCOR1_HUMAN;.	P	1496;1512;1403;80	ENSP00000268712:S1496P;ENSP00000379192:S1512P;ENSP00000379198:S80P	ENSP00000268712:S1496P	S	-	1	0	NCOR1	15914231	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.650000	0.91073	2.221000	0.72209	0.533000	0.62120	TCA	.	.		0.408	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		G	15973506	A	G	15973506	3	3	111	1	0	0	0	0	1	0	0	0	10244	304	11	2	2900	2	NCOR1	17	15973506	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	2000561	15973506	65221704	304	16544										
SMCR8	140775	hgsc.bcm.edu	37	chr17	18219495	18219495	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gctgggagattctaaggaggGcgcctttgcatacgtgcacc	14	10	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:18219495G>A	ENST00000406438.3	+	1	872	c.392G>A	c.(391-393)gGc>gAc	p.G131D	TOP3A_ENST00000542570.1_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	131						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						TCTAAGGAGGGCGCCTTTGCA	0.557																																					p.G131D		Atlas-SNP	.											.	SMCR8	62	.	0			c.G392A						.						89	91	90					17																	18219495		2203	4300	6503	SO:0001583	missense	140775	exon1			AGGAGGGCGCCTT	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.392G>A	chr17.hg19:g.18219495G>A	ENSP00000385025:p.Gly131Asp	42.0	0.0		61.0	4.0	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	hg19	CCDS11195.2	.	.	.	.	.	.	.	.	.	.	G	16.51	3.143160	0.57044	.	.	ENSG00000176994	ENST00000406438	D	0.98684	-5.07	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.98005	0.9343	L	0.35723	1.085	0.58432	D	0.999999	D	0.56035	0.974	P	0.53912	0.737	D	0.97766	1.0223	10	0.36615	T	0.2	-45.2015	20.073	0.97731	0.0:0.0:1.0:0.0	.	131	Q8TEV9	SMCR8_HUMAN	D	131	ENSP00000385025:G131D	ENSP00000385025:G131D	G	+	2	0	SMCR8	18160220	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.794000	0.62482	2.750000	0.94351	0.655000	0.94253	GGC	.	.		0.557	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		A	18219495	G	A	18219495	3	1	111	1	0	0	0	0	1	0	0	0	14807	1203	42	3	394	3	SMCR8	17	18219495	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	2245989	18219495	62975715	305	16545										
PSMD3	5709	hgsc.bcm.edu	37	chr17	38142922	38142922	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agtggaagcctatctccaacTcctcgtggtcatcttcatga	8	12	4	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:38142922T>C	ENST00000264639.4	+	3	680	c.506T>C	c.(505-507)cTc>cCc	p.L169P	PSMD3_ENST00000541736.1_Missense_Mutation_p.L31P	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	169					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Colorectal(19;0.000442)					TATCTCCAACTCCTCGTGGTC	0.542																																					p.L169P	Ovarian(186;531 2051 6385 19668 48409)	Atlas-SNP	.											.	PSMD3	56	.	0			c.T506C						.						163	150	155					17																	38142922		2203	4300	6503	SO:0001583	missense	5709	exon3			TCCAACTCCTCGT	D67025	CCDS11356.1	17q21.2	2010-07-23			ENSG00000108344	ENSG00000108344		"Proteasome (prosome, macropain) subunits"	9560	protein-coding gene	gene with protein product			"tissue specific transplantation antigen 2"	TSTA2		9017604	Standard	NM_002809		Approved	S3, P58, Rpn3	uc002htn.2	O43242	OTTHUMG00000133251	ENST00000264639.4:c.506T>C	chr17.hg19:g.38142922T>C	ENSP00000264639:p.Leu169Pro	124.0	0.0		97.0	4.0	NM_002809	B3KMW9|B4DT72|Q96EI2|Q9BQA4	Missense_Mutation	SNP	ENST00000264639.4	hg19	CCDS11356.1	.	.	.	.	.	.	.	.	.	.	T	15.62	2.887581	0.52014	.	.	ENSG00000108344	ENST00000264639;ENST00000415039;ENST00000541736	D;D	0.87809	-2.3;-2.3	5.35	5.35	0.76521	.	0.066703	0.64402	D	0.000007	D	0.92625	0.7657	M	0.72479	2.2	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.93482	0.6828	10	0.87932	D	0	-19.474	15.0207	0.71630	0.0:0.0:0.0:1.0	.	169	O43242	PSMD3_HUMAN	P	169;156;31	ENSP00000264639:L169P;ENSP00000442508:L31P	ENSP00000264639:L169P	L	+	2	0	PSMD3	35396448	1.000000	0.71417	0.747000	0.31113	0.138000	0.21146	5.868000	0.69605	2.020000	0.59435	0.379000	0.24179	CTC	.	.		0.542	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1	NM_002809		C	38142922	T	C	38142922	3	2	111	1	0	0	0	0	1	0	0	0	12711	1551	54	2	516	2	PSMD3	17	38142922	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	19923427	38142922	43052288	306	16546										
BECN1	8678	hgsc.bcm.edu	37	chr17	40970263	40970263	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cttcctcctgatccagtctcTcagcctcagcctggaccttc	6	18	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:40970263T>C	ENST00000361523.4	-	7	791	c.659A>G	c.(658-660)gAg>gGg	p.E220G	BECN1_ENST00000438274.3_Missense_Mutation_p.E144G|BECN1_ENST00000590099.1_Missense_Mutation_p.E220G	NM_003766.3	NP_003757.1	Q14457	BECN1_HUMAN	beclin 1, autophagy related	220					autophagic vacuole assembly (GO:0000045)|beta-amyloid metabolic process (GO:0050435)|cellular defense response (GO:0006968)|cellular response to aluminum ion (GO:0071275)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokinesis (GO:0000910)|defense response to virus (GO:0051607)|lysosome organization (GO:0007040)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|positive regulation of macroautophagy (GO:0016239)|regulation of catalytic activity (GO:0050790)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to vitamin E (GO:0033197)|viral process (GO:0016032)	dendrite (GO:0030425)|membrane (GO:0016020)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	13		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		ATCCAGTCTCTCAGCCTCAGC	0.537																																					p.E220G		Atlas-SNP	.											.	BECN1	23	.	0			c.A659G						.						151	136	141					17																	40970263		2203	4300	6503	SO:0001583	missense	8678	exon7			AGTCTCTCAGCCT	AF077301	CCDS11441.1	17q21	2014-02-12	2008-01-14		ENSG00000126581	ENSG00000126581			1034	protein-coding gene	gene with protein product	"ATG6 autophagy related 6 homolog (S. cerevisiae)"	604378	"beclin 1 (coiled-coil, moesin-like BCL2 interacting protein)"			9765397	Standard	NM_003766		Approved	ATG6, VPS30	uc002ibn.2	Q14457		ENST00000361523.4:c.659A>G	chr17.hg19:g.40970263T>C	ENSP00000355231:p.Glu220Gly	245.0	0.0		199.0	8.0	NM_003766	B2R6N7|O75595|Q9UNA8	Missense_Mutation	SNP	ENST00000361523.4	hg19	CCDS11441.1	.	.	.	.	.	.	.	.	.	.	T	19.68	3.872225	0.72180	.	.	ENSG00000126581	ENST00000361523;ENST00000438274;ENST00000543382	T;T	0.48522	0.81;0.81	5.82	5.82	0.92795	.	0.103982	0.64402	D	0.000003	T	0.60818	0.2298	M	0.64404	1.975	0.51233	D	0.999912	D;D	0.55800	0.973;0.962	P;P	0.55824	0.785;0.784	T	0.60052	-0.7338	10	0.40728	T	0.16	.	16.1917	0.81992	0.0:0.0:0.0:1.0	.	144;220	E7EV84;Q14457	.;BECN1_HUMAN	G	220;144;133	ENSP00000355231:E220G;ENSP00000416173:E144G	ENSP00000355231:E220G	E	-	2	0	BECN1	38223789	1.000000	0.71417	0.983000	0.44433	0.994000	0.84299	5.503000	0.66962	2.216000	0.71823	0.533000	0.62120	GAG	.	.		0.537	BECN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452405.1	NM_003766		C	40970263	T	C	40970263	3	2	111	1	0	0	0	0	1	0	0	0	1396	1551	54	2	717	2	BECN1	17	40970263	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2827341	40970263	40224947	307	16547										
SPAG9	9043	hgsc.bcm.edu	37	chr17	49043633	49043633	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tccacctgtttcccatgggcTcactcattgccatacatcac	5	16	3	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:49043633T>C	ENST00000262013.7	-	30	4174	c.3966A>G	c.(3964-3966)tgA>tgG	p.*1322W	SPAG9_ENST00000510283.1_Nonstop_Mutation_p.*1178W|SPAG9_ENST00000509724.1_5'Flank|SPAG9_ENST00000505279.1_Nonstop_Mutation_p.*1312W|SPAG9_ENST00000357122.4_Nonstop_Mutation_p.*1308W	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	0					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			TCCCATGGGCTCACTCATTGC	0.433																																					p.X1322W		Atlas-SNP	.											.	SPAG9	151	.	0			c.A3966G						.						192	181	185					17																	49043633		2203	4300	6503	SO:0001578	stop_lost	9043	exon30			ATGGGCTCACTCA	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.3966A>G	chr17.hg19:g.49043633T>C	ENSP00000262013:p.*1322Cysext*25	93.0	0.0		85.0	5.0	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	hg19	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	T	9.014	0.983260	0.18889	.	.	ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	.	.	.	5.65	4.57	0.56435	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9178	0.52776	0.0:0.0682:0.0:0.9318	.	.	.	.	W	1322;1079;1069;1178;1312;1308;920	.	.	X	-	3	0	SPAG9	46398632	1.000000	0.71417	0.986000	0.45419	0.001000	0.01503	6.729000	0.74775	1.073000	0.40885	-0.297000	0.09499	TGA	.	.		0.433	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		C	49043633	T	C	49043633	4	2	111	1	0	0	0	0	0	0	0	0	15000	1564	54	2	3	2	SPAG9	17	49043633	Nonstop_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	8073370	49043633	32151577	308	16548										
MRPS23	51649	hgsc.bcm.edu	37	chr17	55918549	55918549	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tataaaatggcttaccgttgAcaggtagacttgaagtttgg	11	5	0	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:55918549A>G	ENST00000313608.8	-	3	333	c.288T>C	c.(286-288)tgT>tgC	p.C96C	MRPS23_ENST00000578444.1_Silent_p.C96C	NM_016070.3	NP_057154.2	Q9Y3D9	RT23_HUMAN	mitochondrial ribosomal protein S23	96					translation (GO:0006412)	intermediate filament cytoskeleton (GO:0045111)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|large_intestine(1)|lung(2)	5	Breast(9;8.75e-08)					CTTACCGTTGACAGGTAGACT	0.318																																					p.C96C		Atlas-SNP	.											.	MRPS23	16	.	0			c.T288C						.						105	107	106					17																	55918549		2203	4300	6503	SO:0001819	synonymous_variant	51649	exon3			CCGTTGACAGGTA	AB061206	CCDS11598.1	17q22-q23	2012-09-13				ENSG00000181610		"Mitochondrial ribosomal proteins / small subunits"	14509	protein-coding gene	gene with protein product		611985				11279123	Standard	NM_016070		Approved	MRP-S23, CGI-138, HSPC329	uc002ivc.3	Q9Y3D9		ENST00000313608.8:c.288T>C	chr17.hg19:g.55918549A>G		72.0	0.0		64.0	4.0	NM_016070	B2R6V3|Q96Q24|Q9BWH8|Q9P053	Silent	SNP	ENST00000313608.8	hg19	CCDS11598.1																																																																																			.	.		0.318	MRPS23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443301.1	NM_016070		G	55918549	A	G	55918549	2	3	111	1	0	0	0	0	0	0	0	1	9843	273	10	2		2	MRPS23	17	55918549	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	6874916	55918549	25276661	309	16549										
MED13	9969	hgsc.bcm.edu	37	chr17	60050201	60050201	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	catcctgaagaactggctgaAgagagaggagcattcgaagt	13	7	0	5			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:60050201A>G	ENST00000397786.2	-	17	3930	c.3854T>C	c.(3853-3855)cTt>cCt	p.L1285P		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1285					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AACTGGCTGAAGAGAGAGGAG	0.403																																					p.L1285P		Atlas-SNP	.											.	MED13	181	.	0			c.T3854C						.						203	200	201					17																	60050201		1869	4108	5977	SO:0001583	missense	9969	exon17			GGCTGAAGAGAGA	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.3854T>C	chr17.hg19:g.60050201A>G	ENSP00000380888:p.Leu1285Pro	75.0	0.0		81.0	4.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.634984	0.87760	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.74421	-0.84	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.86489	0.5945	M	0.77313	2.365	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.88129	0.2837	10	0.87932	D	0	-19.1759	16.1839	0.81934	1.0:0.0:0.0:0.0	.	1285	Q9UHV7	MED13_HUMAN	P	1285;1284	ENSP00000380888:L1285P	ENSP00000262436:L1284P	L	-	2	0	MED13	57404983	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.222000	0.72286	0.533000	0.62120	CTT	.	.		0.403	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		G	60050201	A	G	60050201	3	3	111	1	0	0	0	0	1	0	0	0	9439	72	3	2	2726	2	MED13	17	60050201	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	4131652	60050201	21145009	310	16550										
MRC2	9902	hgsc.bcm.edu	37	chr17	60766239	60766239	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgtgcagtggtcctgcacagCccctcagcccacttcactgg	10	16	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:60766239C>A	ENST00000303375.5	+	23	3654	c.3252C>A	c.(3250-3252)agC>agA	p.S1084R	MRC2_ENST00000580916.1_3'UTR|MRC2_ENST00000446119.2_Missense_Mutation_p.A30D	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1084	C-type lectin 6. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						TCCTGCACAGCCCCTCAGCCC	0.647																																					p.S1084R		Atlas-SNP	.											.	MRC2	126	.	0			c.C3252A						.						33	29	30					17																	60766239		2203	4300	6503	SO:0001583	missense	9902	exon23			GCACAGCCCCTCA	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3252C>A	chr17.hg19:g.60766239C>A	ENSP00000307513:p.Ser1084Arg	127.0	0.0		124.0	42.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	hg19	CCDS11634.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.88|11.88	1.770068|1.770068	0.31320|0.31320	.|.	.|.	ENSG00000011028|ENSG00000011028	ENST00000446119|ENST00000303375	T|T	0.03301|0.18657	3.98|2.2	4.46|4.46	3.48|3.48	0.39840|0.39840	.|C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.|0.049850	.|0.85682	.|D	.|0.000000	T|T	0.20170|0.20170	0.0485|0.0485	L|L	0.34521|0.34521	1.04|1.04	0.25380|0.25380	N|N	0.988623|0.988623	D|P	0.58268|0.43938	0.982|0.822	P|P	0.50708|0.48400	0.648|0.576	T|T	0.09443|0.09443	-1.0674|-1.0674	9|10	0.40728|0.14656	T|T	0.16|0.56	-37.4987|-37.4987	10.8344|10.8344	0.46679|0.46679	0.0:0.7893:0.1319:0.0788|0.0:0.7893:0.1319:0.0788	.|.	30|1084	E7EME3|Q9UBG0	.|MRC2_HUMAN	D|R	30|1084	ENSP00000400445:A30D|ENSP00000307513:S1084R	ENSP00000400445:A30D|ENSP00000307513:S1084R	A|S	+|+	2|3	0|2	MRC2|MRC2	58119971|58119971	0.990000|0.990000	0.36364|0.36364	1.000000|1.000000	0.80357|0.80357	0.657000|0.657000	0.38888|0.38888	0.865000|0.865000	0.27940|0.27940	0.500000|0.500000	0.27991|0.27991	-1.598000|-1.598000	0.00824|0.00824	GCC|AGC	.	.		0.647	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			A	60766239	C	A	60766239	3	1	111	1	0	0	0	0	1	0	0	0	9767	738	26	3	3342	3	MRC2	17	60766239	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	716038	60766239	20428971	311	16551										
PSMD12	5718	hgsc.bcm.edu	37	chr17	65338310	65338310	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	attactacttacatcaacagAtagatccagaagctgtgcca	6	10	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:65338310A>G	ENST00000356126.3	-	10	1260	c.1153T>C	c.(1153-1155)Tct>Cct	p.S385P	PSMD12_ENST00000357146.4_Missense_Mutation_p.S365P	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	385	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					ACATCAACAGATAGATCCAGA	0.343																																					p.S385P		Atlas-SNP	.											.	PSMD12	32	.	0			c.T1153C						.						157	151	153					17																	65338310		2203	4300	6503	SO:0001583	missense	5718	exon10			CAACAGATAGATC	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.1153T>C	chr17.hg19:g.65338310A>G	ENSP00000348442:p.Ser385Pro	90.0	0.0		80.0	4.0	NM_002816	A6NP15|Q53HA2|Q6P053	Missense_Mutation	SNP	ENST00000356126.3	hg19	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	A	11.80	1.745742	0.30955	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	T;T	0.45668	0.89;0.89	4.91	4.91	0.64330	Winged helix-turn-helix transcription repressor DNA-binding (1);Proteasome component (PCI) domain (2);	0.096735	0.64402	D	0.000001	T	0.34774	0.0909	L	0.39467	1.215	0.80722	D	1	B;B	0.15473	0.013;0.013	B;B	0.24006	0.029;0.05	T	0.12811	-1.0533	10	0.13108	T	0.6	-1.7845	14.8495	0.70286	1.0:0.0:0.0:0.0	.	365;385	A6NP15;O00232	.;PSD12_HUMAN	P	385;365	ENSP00000348442:S385P;ENSP00000349667:S365P	ENSP00000348442:S385P	S	-	1	0	PSMD12	62768772	1.000000	0.71417	0.904000	0.35570	0.769000	0.43574	5.920000	0.70017	1.980000	0.57719	0.454000	0.30748	TCT	.	.		0.343	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		G	65338310	A	G	65338310	3	3	111	1	0	0	0	0	1	0	0	0	12707	333	12	2	225	2	PSMD12	17	65338310	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	4572071	65338310	15856900	312	16552										
BPTF	2186	hgsc.bcm.edu	37	chr17	65971931	65971931	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gtacaaagacgatattatgaAaagctgacggaatttgtggc	11	5	0	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:65971931A>G	ENST00000321892.4	+	29	9022	c.8961A>G	c.(8959-8961)gaA>gaG	p.E2987E	RN7SL622P_ENST00000585292.1_RNA|BPTF_ENST00000424123.3_Silent_p.E2705E|BPTF_ENST00000335221.5_Silent_p.E2844E|BPTF_ENST00000306378.6_Silent_p.E2861E			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2987	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GATATTATGAAAAGCTGACGG	0.363																																					p.E2861E		Atlas-SNP	.											BPTF_ENST00000335221,caecum,carcinoma,0,2	BPTF	415	.	0			c.A8583G						.						91	89	90					17																	65971931		2203	4300	6503	SO:0001819	synonymous_variant	2186	exon27			TTATGAAAAGCTG	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.8961A>G	chr17.hg19:g.65971931A>G		74.0	0.0		56.0	3.0	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	hg19																																																																																				.	.		0.363	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65971931	A	G	65971931	2	3	111	1	0	0	0	0	0	0	0	1	1497	11	1	2		2	BPTF	17	65971931	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	633621	65971931	15223279	313	16553										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67096941	67096941	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gtaaatccaatacttacaagAggaaatgggcttgactcaat	8	7	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:67096941A>G	ENST00000284425.2	-	22	3183	c.3009T>C	c.(3007-3009)ccT>ccC	p.P1003P	MIR4524B_ENST00000581569.1_RNA|ABCA6_ENST00000446604.2_5'Flank	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1003					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					TACTTACAAGAGGAAATGGGC	0.313																																					p.P1003P		Atlas-SNP	.											.	ABCA6	210	.	0			c.T3009C						.						90	88	88					17																	67096941		2201	4298	6499	SO:0001819	synonymous_variant	23460	exon22			TACAAGAGGAAAT	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.3009T>C	chr17.hg19:g.67096941A>G		125.0	0.0		89.0	4.0	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	hg19	CCDS11683.1																																																																																			.	.		0.313	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		G	67096941	A	G	67096941	2	3	111	1	0	0	0	0	0	0	0	1	36	291	11	2		2	ABCA6	17	67096941	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1125010	67096941	14098269	314	16554										
ABCA10	10349	hgsc.bcm.edu	37	chr17	67190540	67190540	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tctcaccttctgtagaaacaGacaatccactaagaatgttt	5	10	2	3	rs113082690|rs200155538	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:67190540G>A	ENST00000269081.4	-	13	2240	c.1331C>T	c.(1330-1332)tCt>tTt	p.S444F	ABCA10_ENST00000416101.2_Missense_Mutation_p.S444F	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	444	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					TGTAGAAACAGACAATCCACT	0.328																																					p.S444F		Atlas-SNP	.											.,5	ABCA10	209	.	0			c.C1331T						.						116	111	113					17																	67190540		2192	4289	6481	SO:0001583	missense	10349	exon13			GAAACAGACAATC	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.1331C>T	chr17.hg19:g.67190540G>A	ENSP00000269081:p.Ser444Phe	39.0	0.0		44.0	8.0	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	hg19	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.497627	0.44455	.	.	ENSG00000154263	ENST00000269081;ENST00000416101	T;D	0.93247	1.12;-3.19	3.8	-0.228	0.13098	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.30118	U	0.010364	D	0.84915	0.5578	N	0.11845	0.185	0.24712	N	0.993191	B;B	0.30146	0.27;0.116	B;B	0.31245	0.126;0.118	T	0.66536	-0.5899	10	0.09338	T	0.73	.	18.3875	0.90471	0.0:0.741:0.259:0.0	.	444;444	E5RFN6;Q8WWZ4	.;ABCAA_HUMAN	F	444	ENSP00000269081:S444F;ENSP00000407772:S444F	ENSP00000269081:S444F	S	-	2	0	ABCA10	64702135	0.000000	0.05858	0.000000	0.03702	0.611000	0.37282	0.017000	0.13399	-0.209000	0.10156	0.557000	0.71058	TCT	.	.		0.328	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		A	67190540	G	A	67190540	3	1	111	1	0	0	0	0	1	0	0	0	29	942	33	3	3412	3	ABCA10	17	67190540	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	93599	67190540	14004670	315	16555										
RNF213	57674	hgsc.bcm.edu	37	chr17	78280933	78280933	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttttctctgccttaggatgtTcaggatgttcagaacgttca	9	8	4	1	rs577690513	byFrequency	TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:78280933T>C	ENST00000582970.1	+	13	2576	c.2433T>C	c.(2431-2433)gtT>gtC	p.V811V	RNF213_ENST00000508628.2_Silent_p.V860V|RNF213_ENST00000319921.4_Silent_p.V811V|RNF213_ENST00000456466.1_Silent_p.V811V	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	811					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CTTAGGATGTTCAGGATGTTC	0.408																																					p.V811V		Atlas-SNP	.											.	RNF213	766	.	0			c.T2433C						.						152	155	154					17																	78280933		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon13			GGATGTTCAGGAT	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.2433T>C	chr17.hg19:g.78280933T>C		93.0	0.0		121.0	5.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.		0.408	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		C	78280933	T	C	78280933	2	2	111	1	0	0	0	0	0	0	0	1	13492	1770	62	2		2	RNF213	17	78280933	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	11090393	78280933	2914277	316	16556										
RNF213	57674	hgsc.bcm.edu	37	chr17	78346832	78346832	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	caagcagttctgtatccgggTggagaacgactggcaccggg	15	10	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr17:78346832T>C	ENST00000582970.1	+	49	12952	c.12809T>C	c.(12808-12810)gTg>gCg	p.V4270A	CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.V2343A|RNF213_ENST00000508628.2_Missense_Mutation_p.V4319A|CTD-2047H16.4_ENST00000575034.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4270					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TGTATCCGGGTGGAGAACGAC	0.627																																					p.V4270A		Atlas-SNP	.											.	RNF213	766	.	0			c.T12809C						.						80	78	79					17																	78346832		2203	4300	6503	SO:0001583	missense	57674	exon49			TCCGGGTGGAGAA	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.12809T>C	chr17.hg19:g.78346832T>C	ENSP00000464087:p.Val4270Ala	135.0	0.0		95.0	6.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	T	4.010	-0.000795	0.07819	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.20463	2.07	5.5	-11.0	0.00169	.	1.235040	0.05478	N	0.554278	T	0.08313	0.0207	N	0.16478	0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.30387	-0.9980	10	0.02654	T	1	.	9.9204	0.41462	0.0:0.5989:0.3196:0.0815	.	4319;2343	C9JCP4;Q63HN8	.;RN213_HUMAN	A	4270;4319;2343	ENSP00000338218:V2343A	ENSP00000338218:V2343A	V	+	2	0	RNF213	75961427	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.828000	0.04419	-2.486000	0.00520	-0.291000	0.09656	GTG	.	.		0.627	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		C	78346832	T	C	78346832	3	2	111	1	0	0	0	0	1	0	0	0	13492	1696	59	2	13318	2	RNF213	17	78346832	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	65899	78346832	2848378	317	16557										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3090725	3090725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aagctggaaagtgtacgttcCctcatcctcatcctgtagct	8	12	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr18:3090725C>T	ENST00000356443.4	-	27	4273	c.3940G>A	c.(3940-3942)Gga>Aga	p.G1314R	RNU7-25P_ENST00000516544.1_RNA|MYOM1_ENST00000400569.3_Missense_Mutation_p.G1314R|MYOM1_ENST00000261606.7_Missense_Mutation_p.G1218R	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1314					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GTGTACGTTCCCTCATCCTCA	0.403																																					p.G1314R		Atlas-SNP	.											.	MYOM1	192	.	0			c.G3940A						.						201	197	198					18																	3090725		1967	4154	6121	SO:0001583	missense	8736	exon27			ACGTTCCCTCATC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.3940G>A	chr18.hg19:g.3090725C>T	ENSP00000348821:p.Gly1314Arg	216.0	0.0		165.0	30.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.426311	0.83667	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.17054	2.3;2.3;2.3	5.7	4.83	0.62350	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.42966	0.1226	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.41627	-0.9498	10	0.20046	T	0.44	.	14.4195	0.67173	0.0:0.9295:0.0:0.0704	.	1218;1314	P52179-2;P52179	.;MYOM1_HUMAN	R	1314;1314;1218	ENSP00000348821:G1314R;ENSP00000383413:G1314R;ENSP00000261606:G1218R	ENSP00000261606:G1218R	G	-	1	0	MYOM1	3080725	1.000000	0.71417	0.988000	0.46212	0.977000	0.68977	7.818000	0.86416	1.412000	0.46977	0.591000	0.81541	GGA	.	.		0.403	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3090725	C	T	3090725	3	4	111	1	0	0	0	0	1	0	0	0	10100	632	22	3	1165	3	MYOM1	18	3090725	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10		3090725	74986523	318	16558										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9254527	9254527	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaaacaaaagccatctagggTcttatattcaagtactgaaa	6	7	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr18:9254527T>C	ENST00000262126.4	+	9	1502	c.1262T>C	c.(1261-1263)gTc>gCc	p.V421A	ANKRD12_ENST00000383440.2_Missense_Mutation_p.V398A|ANKRD12_ENST00000400020.3_Missense_Mutation_p.V398A	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	421						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CCATCTAGGGTCTTATATTCA	0.323																																					p.V421A		Atlas-SNP	.											.	ANKRD12	167	.	0			c.T1262C						.						70	81	77					18																	9254527		2203	4291	6494	SO:0001583	missense	23253	exon9			CTAGGGTCTTATA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.1262T>C	chr18.hg19:g.9254527T>C	ENSP00000262126:p.Val421Ala	80.0	0.0		76.0	4.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	T	13.38	2.219622	0.39201	.	.	ENSG00000101745	ENST00000383440;ENST00000262126;ENST00000359158	T;T	0.04970	3.53;3.52	5.86	5.86	0.93980	.	0.064020	0.64402	D	0.000008	T	0.22126	0.0533	L	0.60455	1.87	0.44754	D	0.997754	D;D;D	0.69078	0.997;0.995;0.997	P;P;D	0.72625	0.826;0.648;0.978	T	0.00112	-1.2043	10	0.54805	T	0.06	-11.1792	16.2507	0.82485	0.0:0.0:0.0:1.0	.	48;398;421	Q9NXU3;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	A	398;421;128	ENSP00000372932:V398A;ENSP00000262126:V421A	ENSP00000262126:V421A	V	+	2	0	ANKRD12	9244527	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.396000	0.79891	2.237000	0.73441	0.528000	0.53228	GTC	.	.		0.323	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		C	9254527	T	C	9254527	3	2	111	1	0	0	0	0	1	0	0	0	640	1667	58	2	1292	2	ANKRD12	18	9254527	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	6163802	9254527	68822721	319	16559										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30517978	30517978	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atacattggttgtttgcttaAccatcgttttcgcatgtgcc	8	9	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr18:30517978A>G	ENST00000383096.3	-	23	2783	c.2601T>C	c.(2599-2601)ggT>ggC	p.G867G	CCDC178_ENST00000300227.8_Silent_p.G829G|CCDC178_ENST00000581852.1_Silent_p.G72G|CCDC178_ENST00000403303.1_Silent_p.G867G|RP11-746B8.1_ENST00000580366.1_RNA|CCDC178_ENST00000406524.2_Silent_p.G891G|CCDC178_ENST00000402325.1_Silent_p.G817G|CCDC178_ENST00000583930.1_Silent_p.G891G|CCDC178_ENST00000579916.1_Silent_p.G187G			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	867																	TGTTTGCTTAACCATCGTTTT	0.373																																					p.G867G		Atlas-SNP	.											.	.	.	.	0			c.T2601C						.						176	156	163					18																	30517978		2203	4300	6503	SO:0001819	synonymous_variant	374864	exon22			TGCTTAACCATCG	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.2601T>C	chr18.hg19:g.30517978A>G		144.0	0.0		87.0	4.0	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Silent	SNP	ENST00000383096.3	hg19	CCDS42424.1																																																																																			.	.		0.373	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		G	30517978	A	G	30517978	2	3	111	1	0	0	0	0	0	0	0	1	1904	30	2	2		2	C18orf34	18	30517978	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	21263451	30517978	47559270	320	16560										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43496028	43496028	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcttcctgcatcagctgaaaAgctgctttacacaagtggtc	8	11	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr18:43496028A>G	ENST00000282041.5	-	19	3562	c.3528T>C	c.(3526-3528)gcT>gcC	p.A1176A	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1176					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TCAGCTGAAAAGCTGCTTTAC	0.423																																					p.A1176A		Atlas-SNP	.											.	EPG5	199	.	0			c.T3528C						.						63	60	61					18																	43496028		1914	4128	6042	SO:0001819	synonymous_variant	57724	exon19			CTGAAAAGCTGCT	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.3528T>C	chr18.hg19:g.43496028A>G		82.0	0.0		55.0	4.0	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	hg19	CCDS11926.2																																																																																			.	.		0.423	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		G	43496028	A	G	43496028	2	3	111	1	0	0	0	0	0	0	0	1	8258	59	3	2		2	KIAA1632	18	43496028	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	12978050	43496028	34581220	321	16561										
MYO5B	4645	hgsc.bcm.edu	37	chr18	47402100	47402100	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gttctctcttctccagctgcActtgcagctttttcctctcc	5	16	4	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr18:47402100A>G	ENST00000285039.7	-	26	3793	c.3494T>C	c.(3493-3495)gTg>gCg	p.V1165A	MYO5B_ENST00000324581.6_Missense_Mutation_p.V306A|MYO5B_ENST00000587895.1_5'UTR	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1165					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		CTCCAGCTGCACTTGCAGCTT	0.527																																					p.V1165A		Atlas-SNP	.											.	MYO5B	178	.	0			c.T3494C						.						197	202	200					18																	47402100		2068	4197	6265	SO:0001583	missense	4645	exon26			AGCTGCACTTGCA	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.3494T>C	chr18.hg19:g.47402100A>G	ENSP00000285039:p.Val1165Ala	155.0	0.0		98.0	4.0	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	hg19	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	A	5.754	0.323586	0.10900	.	.	ENSG00000167306	ENST00000285039;ENST00000324581	T;T	0.16457	2.34;2.34	5.28	-1.97	0.07503	.	0.967479	0.08524	N	0.932958	T	0.09335	0.0230	L	0.27053	0.805	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43130	-0.9410	10	0.08837	T	0.75	.	7.2826	0.26320	0.209:0.3943:0.3967:0.0	.	1165;306	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	A	1165;306	ENSP00000285039:V1165A;ENSP00000315531:V306A	ENSP00000285039:V1165A	V	-	2	0	MYO5B	45656098	0.001000	0.12720	0.962000	0.40283	0.991000	0.79684	-0.109000	0.10840	-0.261000	0.09405	0.459000	0.35465	GTG	.	.		0.527	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			G	47402100	A	G	47402100	3	3	111	1	0	0	0	0	1	0	0	0	10088	159	6	2	2112	2	MYO5B	18	47402100	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	3906072	47402100	30675148	322	16562										
TCF4	6925	hgsc.bcm.edu	37	chr18	53018227	53018227	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tatccatgtcacctccaaggAgactctgctaaaaggttaaa	7	10	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr18:53018227A>G	ENST00000356073.4	-	7	988	c.377T>C	c.(376-378)cTc>cCc	p.L126P	TCF4_ENST00000544241.2_Missense_Mutation_p.L55P|TCF4_ENST00000537578.1_Missense_Mutation_p.L102P|TCF4_ENST00000565018.2_Missense_Mutation_p.L126P|TCF4_ENST00000566286.1_Missense_Mutation_p.L124P|TCF4_ENST00000568740.1_Missense_Mutation_p.L101P|TCF4_ENST00000540999.1_Missense_Mutation_p.L102P|TCF4_ENST00000537856.3_5'UTR|TCF4_ENST00000564999.1_Missense_Mutation_p.L126P|TCF4_ENST00000564228.1_Missense_Mutation_p.L55P|TCF4_ENST00000567880.1_Intron|TCF4_ENST00000561992.1_5'UTR|TCF4_ENST00000543082.1_Missense_Mutation_p.L84P|TCF4_ENST00000570177.2_5'UTR|TCF4_ENST00000566279.1_Intron|TCF4_ENST00000564403.2_Missense_Mutation_p.L126P|TCF4_ENST00000354452.3_Missense_Mutation_p.L126P|TCF4_ENST00000568673.1_Missense_Mutation_p.L102P|TCF4_ENST00000398339.1_Missense_Mutation_p.L228P	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	126					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		ACCTCCAAGGAGACTCTGCTA	0.418																																					p.L228P		Atlas-SNP	.											.	TCF4	178	.	0			c.T683C						.						90	87	88					18																	53018227		2203	4300	6503	SO:0001583	missense	6925	exon8			CCAAGGAGACTCT	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.377T>C	chr18.hg19:g.53018227A>G	ENSP00000348374:p.Leu126Pro	125.0	0.0		100.0	4.0	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	A	13.35	2.211818	0.39102	.	.	ENSG00000196628	ENST00000354452;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000398339	T;T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94;0.94	5.57	5.57	0.84162	.	0.078741	0.51477	D	0.000096	T	0.58935	0.2157	L	0.54323	1.7	0.80722	D	1	B;D;D;D;D;B;B	0.89917	0.051;0.997;0.999;1.0;0.993;0.051;0.051	B;D;D;D;P;B;B	0.74674	0.04;0.969;0.984;0.972;0.788;0.04;0.04	T	0.61758	-0.6997	10	0.87932	D	0	-28.8421	13.5428	0.61684	1.0:0.0:0.0:0.0	.	102;126;102;228;126;84;55	B7Z5M6;G0LNT9;B7Z6Y1;E9PH57;P15884;B3KUC0;B3KT62	.;.;.;.;ITF2_HUMAN;.;.	P	126;126;84;102;102;55;228	ENSP00000346440:L126P;ENSP00000348374:L126P;ENSP00000439656:L84P;ENSP00000445202:L102P;ENSP00000440731:L102P;ENSP00000441562:L55P;ENSP00000381382:L228P	ENSP00000346440:L126P	L	-	2	0	TCF4	51169225	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.350000	0.79385	2.244000	0.73946	0.533000	0.62120	CTC	.	.		0.418	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		G	53018227	A	G	53018227	3	3	111	1	0	0	0	0	1	0	0	0	15710	304	11	2	1690	2	TCF4	18	53018227	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	5616127	53018227	25059021	323	16563										
MED16	10025	hgsc.bcm.edu	37	chr19	873468	873468	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctggttgggtaggctggccAgcaggtacagcacgaagtcg	16	10	0	0	rs367567945		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:873468A>G	ENST00000589119.1	-	10	1885	c.1886T>C	c.(1885-1887)cTg>cCg	p.L629P	MED16_ENST00000325464.1_Missense_Mutation_p.L629P|MED16_ENST00000606828.1_5'Flank|MED16_ENST00000395808.3_Missense_Mutation_p.L629P|MED16_ENST00000312090.6_Missense_Mutation_p.L629P|MED16_ENST00000269814.4_Missense_Mutation_p.L629P			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	629					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TAGGCTGGCCAGCAGGTACAG	0.642																																					p.L629P		Atlas-SNP	.											.	MED16	61	.	0			c.T1886C						.						98	76	84					19																	873468		2202	4296	6498	SO:0001583	missense	10025	exon11			CTGGCCAGCAGGT	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"WD repeat domain containing"	17556	protein-coding gene	gene with protein product		604062	"thyroid hormone receptor associated protein 5"	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1886T>C	chr19.hg19:g.873468A>G	ENSP00000464810:p.Leu629Pro	66.0	0.0		88.0	5.0	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	hg19	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	a	18.67	3.673050	0.67928	.	.	ENSG00000175221	ENST00000325464;ENST00000312090;ENST00000395808;ENST00000269814;ENST00000424039	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	4.44	4.44	0.53790	.	0.000000	0.64402	D	0.000006	T	0.49201	0.1543	M	0.67397	2.05	0.80722	D	1	B;B;B;B;P	0.35192	0.23;0.149;0.433;0.433;0.489	B;B;B;B;B	0.38106	0.124;0.065;0.11;0.172;0.265	T	0.53606	-0.8415	10	0.51188	T	0.08	-25.8475	12.866	0.57939	1.0:0.0:0.0:0.0	.	629;629;629;629;629	Q9Y2X0-2;E7ETV0;Q9Y2X0-4;Q9Y2X0-3;Q9Y2X0	.;.;.;.;MED16_HUMAN	P	629	ENSP00000325612:L629P;ENSP00000308528:L629P;ENSP00000379153:L629P;ENSP00000269814:L629P	ENSP00000269814:L629P	L	-	2	0	MED16	824468	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.592000	0.90828	1.627000	0.50400	0.454000	0.30748	CTG	.	.		0.642	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481		G	873468	A	G	873468	3	3	111	1	0	0	0	0	1	0	0	0	9443	188	7	2	771	2	MED16	19	873468	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10		873468	58255515	324	16564										
SBNO2	22904	hgsc.bcm.edu	37	chr19	1112458	1112458	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctccaaggtcatgtgcacgcGgcgccgctggttctggacac	13	14	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:1112458G>A	ENST00000361757.3	-	21	2695	c.2458C>T	c.(2458-2460)Cgc>Tgc	p.R820C	SBNO2_ENST00000438103.2_Missense_Mutation_p.R763C|SBNO2_ENST00000587024.1_Missense_Mutation_p.R810C	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	820					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGTGCACGCGGCGCCGCTGG	0.721																																					p.R820C		Atlas-SNP	.											.	SBNO2	112	.	0			c.C2458T						.						14	20	18					19																	1112458		2020	4148	6168	SO:0001583	missense	22904	exon21			GCACGCGGCGCCG	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.2458C>T	chr19.hg19:g.1112458G>A	ENSP00000354733:p.Arg820Cys	104.0	0.0		49.0	15.0	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Missense_Mutation	SNP	ENST00000361757.3	hg19	CCDS45894.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.402718	0.83230	.	.	ENSG00000064932	ENST00000361757;ENST00000438103;ENST00000250872	.	.	.	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.87346	0.6154	H	0.95645	3.7	0.52099	D	0.999943	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.91392	0.5136	9	0.87932	D	0	-31.7737	17.2654	0.87085	0.0:0.0:1.0:0.0	.	820;763	Q9Y2G9;Q9Y2G9-3	SBNO2_HUMAN;.	C	820;763;827	.	ENSP00000250872:R827C	R	-	1	0	SBNO2	1063458	1.000000	0.71417	0.931000	0.37212	0.771000	0.43674	2.526000	0.45607	2.323000	0.78572	0.448000	0.29417	CGC	.	.		0.721	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		A	1112458	G	A	1112458	3	1	111	1	0	0	0	0	1	0	0	0	13878	1116	39	1	1690	1	SBNO2	19	1112458	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	238990	1112458	58016525	325	16565										
ZNF562	54811	hgsc.bcm.edu	37	chr19	9768758	9768758	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttctgagttgtgtccagtaaAgcccactcctctggggtgaa	11	10	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:9768758A>G	ENST00000448622.1	-	4	330	c.168T>C	c.(166-168)gcT>gcC	p.A56A	ZNF562_ENST00000541032.1_Silent_p.A19A|ZNF562_ENST00000293648.4_Intron|ZNF562_ENST00000453372.2_Silent_p.A56A|ZNF562_ENST00000453792.2_5'UTR|ZNF562_ENST00000537617.1_Intron|ZNF562_ENST00000587392.1_Silent_p.A56A|ZNF562_ENST00000590155.1_Silent_p.A56A	NM_001130031.1|NM_001130032.1	NP_001123503.1|NP_001123504.1	Q6V9R5	ZN562_HUMAN	zinc finger protein 562	56	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	17						TGTCCAGTAAAGCCCACTCCT	0.473																																					p.A56A		Atlas-SNP	.											.	ZNF562	72	.	0			c.T168C						.						96	88	90					19																	9768758		692	1591	2283	SO:0001819	synonymous_variant	54811	exon4			CAGTAAAGCCCAC	AK000086	CCDS12217.1, CCDS45956.1, CCDS74280.1	19p13.2	2013-09-20			ENSG00000171466	ENSG00000171466		"Zinc fingers, C2H2-type", "-"	25950	protein-coding gene	gene with protein product							Standard	NM_001130031		Approved	FLJ20079	uc010xks.2	Q6V9R5	OTTHUMG00000180205	ENST00000448622.1:c.168T>C	chr19.hg19:g.9768758A>G		142.0	0.0		69.0	4.0	NM_001130032	Q32MN2|Q9NXS5	Silent	SNP	ENST00000448622.1	hg19	CCDS45956.1																																																																																			.	.		0.473	ZNF562-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450239.1	NM_017656		G	9768758	A	G	9768758	2	3	111	1	0	0	0	0	0	0	0	1	18008	59	3	2		2	ZNF562	19	9768758	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	8656300	9768758	49360225	326	16566										
OLFM2	93145	hgsc.bcm.edu	37	chr19	9965137	9965137	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agcgctgcgcttggggtagcCggtgtcccaggaccgcatga	16	12	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:9965137C>T	ENST00000264833.4	-	6	1275	c.1090G>A	c.(1090-1092)Ggc>Agc	p.G364S	OLFM2_ENST00000590841.1_Missense_Mutation_p.G286S|AC008752.3_ENST00000582439.1_RNA	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	364	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						TTGGGGTAGCCGGTGTCCCAG	0.642																																					p.G364S		Atlas-SNP	.											.	OLFM2	42	.	0			c.G1090A						.						81	76	78					19																	9965137		2203	4300	6503	SO:0001583	missense	93145	exon6			GGTAGCCGGTGTC	AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"noelin 2"						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.1090G>A	chr19.hg19:g.9965137C>T	ENSP00000264833:p.Gly364Ser	126.0	0.0		86.0	4.0	NM_058164	Q6IMJ3|Q96FC2	Missense_Mutation	SNP	ENST00000264833.4	hg19	CCDS12221.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.321952	0.60634	.	.	ENSG00000105088	ENST00000264833	D	0.88277	-2.36	4.36	4.36	0.52297	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	T	0.80899	0.4712	L	0.28014	0.82	0.80722	D	1	P	0.47484	0.896	B	0.38616	0.277	T	0.80863	-0.1192	9	.	.	.	.	14.4229	0.67196	0.0:1.0:0.0:0.0	.	364	O95897	NOE2_HUMAN	S	364	ENSP00000264833:G364S	.	G	-	1	0	OLFM2	9826137	0.937000	0.31787	1.000000	0.80357	0.991000	0.79684	2.523000	0.45580	2.239000	0.73571	0.561000	0.74099	GGC	.	.		0.642	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1			T	9965137	C	T	9965137	3	4	111	1	0	0	0	0	1	0	0	0	10862	652	23	1	278	1	OLFM2	19	9965137	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	196379	9965137	49163846	327	16567										
PDE4A	5141	hgsc.bcm.edu	37	chr19	10572599	10572599	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	catgaccctcctggctgaccTgaagaccatggtggagacca	11	13	0	5			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:10572599T>C	ENST00000352831.6	+	13	1777	c.1667T>C	c.(1666-1668)cTg>cCg	p.L556P	PDE4A_ENST00000592685.1_Missense_Mutation_p.L534P|PDE4A_ENST00000440014.2_Missense_Mutation_p.L495P|PDE4A_ENST00000344979.3_Missense_Mutation_p.L317P|PDE4A_ENST00000380702.2_Missense_Mutation_p.L534P|PDE4A_ENST00000293683.5_Missense_Mutation_p.L530P	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	556	Catalytic.				cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Caffeine(DB00201)|Dipyridamole(DB00975)|Drotaverine(DB06751)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theophylline(DB00277)|Tofisopam(DB08811)	CTGGCTGACCTGAAGACCATG	0.632																																					p.L556P		Atlas-SNP	.											.	PDE4A	236	.	0			c.T1667C						.						115	96	103					19																	10572599		2203	4300	6503	SO:0001583	missense	5141	exon13			CTGACCTGAAGAC		CCDS12238.1, CCDS45961.1, CCDS45962.1, CCDS45963.1, CCDS58649.1	19p13.2	2010-06-24	2010-06-24			ENSG00000065989	3.1.4.17	"Phosphodiesterases"	8780	protein-coding gene	gene with protein product	"phosphodiesterase E2 dunce homolog (Drosophila)"	600126	"phosphodiesterase 4A, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E2)"	DPDE2		8009369	Standard	NM_006202		Approved		uc002moj.2	P27815		ENST00000352831.6:c.1667T>C	chr19.hg19:g.10572599T>C	ENSP00000270474:p.Leu556Pro	50.0	0.0		30.0	4.0	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Missense_Mutation	SNP	ENST00000352831.6	hg19	CCDS45961.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.288532	0.80914	.	.	ENSG00000065989	ENST00000380702;ENST00000352831;ENST00000293683;ENST00000440014;ENST00000344979;ENST00000380686	D;D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1;-2.1	3.73	3.73	0.42828	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.64402	D	0.000001	D	0.94295	0.8167	M	0.94021	3.485	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.98;1.0;0.999;0.999;1.0	D	0.94703	0.7885	10	0.87932	D	0	.	10.4073	0.44272	0.0:0.0:0.0:1.0	.	222;317;495;530;556	P27815-5;P27815-4;P27815-6;P27815-2;P27815	.;.;.;.;PDE4A_HUMAN	P	534;556;530;495;317;222	ENSP00000370078:L534P;ENSP00000270474:L556P;ENSP00000293683:L530P;ENSP00000394754:L495P;ENSP00000341007:L317P	ENSP00000293683:L530P	L	+	2	0	PDE4A	10433599	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.770000	0.85390	1.576000	0.49790	0.397000	0.26171	CTG	.	.		0.632	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			C	10572599	T	C	10572599	3	2	111	1	0	0	0	0	1	0	0	0	11648	1580	55	2	2174	2	PDE4A	19	10572599	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	607462	10572599	48556384	328	16568										
ATG4D	84971	hgsc.bcm.edu	37	chr19	10659671	10659671	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctggtgcccgtgcgactgggTggcgagactctcaaccccgt	14	14	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:10659671T>C	ENST00000309469.4	+	6	1100	c.927T>C	c.(925-927)ggT>ggC	p.G309G	ATG4D_ENST00000540862.1_Intron|RNU7-140P_ENST00000459546.1_RNA	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase	309					apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			TGCGACTGGGTGGCGAGACTC	0.602																																					p.G309G		Atlas-SNP	.											.	ATG4D	47	.	0			c.T927C						.						126	94	105					19																	10659671		2203	4300	6503	SO:0001819	synonymous_variant	84971	exon6			ACTGGGTGGCGAG	AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"AUT-like 4, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog D (S. cerevisiae)", "ATG4 autophagy related 4 homolog D (S. cerevisiae)"	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582	ENST00000309469.4:c.927T>C	chr19.hg19:g.10659671T>C		138.0	0.0		117.0	5.0	NM_032885	Q969K0	Silent	SNP	ENST00000309469.4	hg19	CCDS12241.1																																																																																			.	.		0.602	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885		C	10659671	T	C	10659671	2	2	111	1	0	0	0	0	0	0	0	1	1099	1683	59	2		2	ATG4D	19	10659671	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	87072	10659671	48469312	329	16569										
HSH2D	84941	hgsc.bcm.edu	37	chr19	16268213	16268213	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggtccggcagcagctaaaaaAgccacctcgccactgtgaac	10	14	0	1	rs375451762		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:16268213A>G	ENST00000253680.6	+	9	1198	c.667A>G	c.(667-669)Agc>Ggc	p.S223G	HSH2D_ENST00000588246.1_Missense_Mutation_p.K223R|HSH2D_ENST00000397372.4_Missense_Mutation_p.S133G|HSH2D_ENST00000593154.2_Missense_Mutation_p.K223R			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	223					negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(2)	4						CAGCTAAAAAAGCCACCTCGC	0.587																																					p.S223G		Atlas-SNP	.											.	HSH2D	16	.	0			c.A667G						.						62	70	67					19																	16268213		1973	4154	6127	SO:0001583	missense	84941	exon9			TAAAAAAGCCACC	AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684		"SH2 domain containing"	24920	protein-coding gene	gene with protein product		608349				11700021	Standard	NM_032855		Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000253680.6:c.667A>G	chr19.hg19:g.16268213A>G	ENSP00000253680:p.Ser223Gly	93.0	0.0		163.0	7.0	NM_032855	B5ME72|Q6ZNG7	Missense_Mutation	SNP	ENST00000253680.6	hg19		.	.	.	.	.	.	.	.	.	.	A	3.608	-0.080131	0.07141	.	.	ENSG00000196684	ENST00000397372;ENST00000253680	T	0.57595	0.39	.	.	.	.	7739.210000	0.00166	N	0.000000	T	0.40839	0.1133	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.36237	-0.9756	7	0.72032	D	0.01	.	.	.	.	.	223	Q96JZ2	HSH2D_HUMAN	G	133;223	ENSP00000253680:S223G	ENSP00000253680:S223G	S	+	1	0	HSH2D	16129213	0.000000	0.05858	0.033000	0.17914	0.002000	0.02628	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	AGC	.	.		0.587	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855		G	16268213	A	G	16268213	3	3	111	1	0	0	0	0	1	0	0	0	7409	72	3	2	686	2	HSH2D	19	16268213	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	5608542	16268213	42860770	330	16570										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23556628	23556628	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agtaatcaggtctggcttagAgagagcaatacctgttttat	10	6	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:23556628A>G	ENST00000300619.7	-	3	374	c.169T>C	c.(169-171)Tct>Cct	p.S57P	ZNF91_ENST00000397082.2_Intron|ZNF91_ENST00000599743.1_Missense_Mutation_p.S57P	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	57	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TCTGGCTTAGAGAGAGCAATA	0.398																																					p.S57P		Atlas-SNP	.											.	ZNF91	349	.	0			c.T169C						.						74	78	76					19																	23556628		2202	4299	6501	SO:0001583	missense	7644	exon3			GCTTAGAGAGAGC	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.169T>C	chr19.hg19:g.23556628A>G	ENSP00000300619:p.Ser57Pro	117.0	0.0		71.0	4.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	A	0.178	-1.065310	0.01934	.	.	ENSG00000167232	ENST00000300619	T	0.00824	5.65	0.158	0.158	0.14942	Krueppel-associated box (3);	.	.	.	.	T	0.01061	0.0035	L	0.45470	1.425	0.09310	N	1	B	0.21147	0.052	B	0.24269	0.052	T	0.45512	-0.9256	8	0.23891	T	0.37	.	.	.	.	.	57	Q05481	ZNF91_HUMAN	P	57	ENSP00000300619:S57P	ENSP00000300619:S57P	S	-	1	0	ZNF91	23348468	0.363000	0.24989	0.080000	0.20451	0.079000	0.17450	0.149000	0.16243	0.175000	0.19841	0.172000	0.16884	TCT	.	.		0.398	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		G	23556628	A	G	23556628	3	3	111	1	0	0	0	0	1	0	0	0	18215	304	11	2	3414	2	ZNF91	19	23556628	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	7288415	23556628	35572355	331	16571										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31769301	31769301	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tccttcttgacctccacattCagttttggggagatgctggc	10	11	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:31769301C>G	ENST00000240587.4	-	2	1725	c.1398G>C	c.(1396-1398)ctG>ctC	p.L466L		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	466					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CCTCCACATTCAGTTTTGGGG	0.542																																					p.L466L		Atlas-SNP	.											.	TSHZ3	549	.	0			c.G1398C						.						142	144	143					19																	31769301		2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CACATTCAGTTTT	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1398G>C	chr19.hg19:g.31769301C>G		191.0	0.0		177.0	34.0	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	hg19	CCDS12421.2																																																																																			.	.		0.542	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		G	31769301	C	G	31769301	2	3	111	1	0	0	0	0	0	0	0	1	16640	813	29	4		4	TSHZ3	19	31769301	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	8212673	31769301	27359682	332	16572										
KIAA0355	9710	hgsc.bcm.edu	37	chr19	34818735	34818735	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tatgcaatgaaagccggcttCcacctgaatccaaaggcgat	9	11	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:34818735C>T	ENST00000299505.6	+	5	1779	c.906C>T	c.(904-906)ttC>ttT	p.F302F		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	302										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					AAGCCGGCTTCCACCTGAATC	0.433																																					p.F302F		Atlas-SNP	.											.	KIAA0355	105	.	0			c.C906T						.						86	92	90					19																	34818735		2203	4300	6503	SO:0001819	synonymous_variant	9710	exon5			CGGCTTCCACCTG		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.906C>T	chr19.hg19:g.34818735C>T		99.0	0.0		88.0	13.0	NM_014686	Q2M3W4	Silent	SNP	ENST00000299505.6	hg19	CCDS12436.1																																																																																			.	.		0.433	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686		T	34818735	C	T	34818735	2	4	111	1	0	0	0	0	0	0	0	1	8179	854	30	3		3	KIAA0355	19	34818735	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	3049434	34818735	24310248	333	16573										
C19orf55	148137	hgsc.bcm.edu	37	chr19	36258938	36258938	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcggaggccctgcttgcccaGggccgccctgctgctgcagg	15	16	0	0	rs398034467|rs5827939		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:36258938G>A	ENST00000396908.4	+	9	1264	c.1191G>A	c.(1189-1191)caG>caA	p.Q397Q	AC002398.13_ENST00000589397.1_RNA|C19orf55_ENST00000544099.1_Silent_p.Q397Q	NM_001039887.2	NP_001034976.2	Q2NL68	PRSR3_HUMAN		398										cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGCTTGCCCAGGGCCGCCCTG	0.731																																					.		Atlas-SNP	.											.,11	C19orf55	39	.	0			c.1190+1G>A						.						1	1	1					19																	36258938		567	1236	1803	SO:0001630	splice_region_variant	148137	exon9			TGCCCAGGGCCGC																												ENST00000396908.4:c.1191+1G>A	chr19.hg19:g.36258938G>A		16.0	0.0		16.0	2.0	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Splice_Site	SNP	ENST00000396908.4	hg19																																																																																				.	.		0.731	C19orf55-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			Silent	A	36258938	G	A	36258938	5	1	111	1	0	0	0	0	0	0	1	0	1939	991	35	3	1225	3	C19orf55	19	36258938	Splice_Site	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	1440203	36258938	22870045	334	16574										
NPHS1	4868	hgsc.bcm.edu	37	chr19	36330220	36330220	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	actggccagcagccagacccTgtatcttgtagaaggctgta	11	11	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:36330220T>C	ENST00000378910.5	-	22	3027	c.3028A>G	c.(3028-3030)Agg>Ggg	p.R1010G	NPHS1_ENST00000353632.6_Missense_Mutation_p.R1010G	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	1010	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AGCCAGACCCTGTATCTTGTA	0.597																																					p.R1010G		Atlas-SNP	.											.	NPHS1	165	.	0			c.A3028G						.						97	89	92					19																	36330220		2203	4300	6503	SO:0001583	missense	4868	exon22			AGACCCTGTATCT		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.3028A>G	chr19.hg19:g.36330220T>C	ENSP00000368190:p.Arg1010Gly	88.0	0.0		76.0	4.0	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	hg19	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	T	9.941	1.217397	0.22373	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.57752	0.38;0.38	4.61	3.53	0.40419	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.447401	0.24949	N	0.034313	T	0.37785	0.1016	L	0.28649	0.875	0.24027	N	0.996121	B	0.22346	0.068	B	0.26770	0.073	T	0.16482	-1.0401	10	0.23891	T	0.37	-8.4248	9.5549	0.39332	0.0:0.0:0.1884:0.8116	.	1010	O60500	NPHN_HUMAN	G	1010	ENSP00000368190:R1010G;ENSP00000343634:R1010G	ENSP00000343634:R1010G	R	-	1	2	NPHS1	41022060	0.993000	0.37304	0.998000	0.56505	0.962000	0.63368	2.126000	0.42026	1.943000	0.56356	0.477000	0.44152	AGG	.	.		0.597	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			C	36330220	T	C	36330220	3	2	111	1	0	0	0	0	1	0	0	0	10591	1579	55	2	729	2	NPHS1	19	36330220	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	71282	36330220	22798763	335	16575										
SAMD4B	55095	hgsc.bcm.edu	37	chr19	39868421	39868421	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctgccccggctcccgtcgcCgacggagacatccccagcca	10	21	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:39868421C>G	ENST00000314471.6	+	10	2436	c.1401C>G	c.(1399-1401)gcC>gcG	p.A467A	SAMD4B_ENST00000598913.1_Silent_p.A467A|SAMD4B_ENST00000596368.1_Intron	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	467					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(5)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(2)	15	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			CTCCCGTCGCCGACGGAGACA	0.617																																					p.A467A		Atlas-SNP	.											.	SAMD4B	48	.	0			c.C1401G						.						38	40	39					19																	39868421		2203	4299	6502	SO:0001819	synonymous_variant	55095	exon10			CGTCGCCGACGGA		CCDS33020.1	19q13.2	2013-01-10				ENSG00000179134		"Sterile alpha motif (SAM) domain containing"	25492	protein-coding gene	gene with protein product	"smaug homolog B (Drosophila)"					16221671	Standard	XM_005259029		Approved	FLJ10211, MGC99832, SMGB, hSmaug2	uc002olb.3	Q5PRF9		ENST00000314471.6:c.1401C>G	chr19.hg19:g.39868421C>G		88.0	0.0		78.0	12.0	NM_018028	A5Z0M6|Q6P194	Silent	SNP	ENST00000314471.6	hg19	CCDS33020.1																																																																																			.	.		0.617	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028		G	39868421	C	G	39868421	2	3	111	1	0	0	0	0	0	0	0	1	13837	639	23	4		4	SAMD4B	19	39868421	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	3538201	39868421	19260562	336	16576										
ADCK4	79934	hgsc.bcm.edu	37	chr19	41220249	41220249	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atgtcctcctcacccaggccTctcccaggcccatcctggta	7	19	2	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:41220249T>C	ENST00000324464.3	-	3	457	c.156A>G	c.(154-156)agA>agG	p.R52R	ADCK4_ENST00000243583.6_Silent_p.R52R|ADCK4_ENST00000450541.1_Silent_p.R52R|ITPKC_ENST00000263370.2_5'Flank	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	52						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CACCCAGGCCTCTCCCAGGCC	0.597																																					p.R52R		Atlas-SNP	.											.	ADCK4	92	.	0			c.A156G						.						65	70	68					19																	41220249		2203	4300	6503	SO:0001819	synonymous_variant	79934	exon3			CAGGCCTCTCCCA	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.156A>G	chr19.hg19:g.41220249T>C		60.0	0.0		52.0	4.0	NM_001142555	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	hg19	CCDS12562.1																																																																																			.	.		0.597	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876		C	41220249	T	C	41220249	2	2	111	1	0	0	0	0	0	0	0	1	290	1548	54	2		2	ADCK4	19	41220249	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	1351828	41220249	17908734	337	16577										
LMTK3	114783	hgsc.bcm.edu	37	chr19	49003158	49003158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggcaggtggccgccagcaggActgaagaatgtcatacctgg	15	10	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:49003158A>G	ENST00000600059.1	-	11	1395	c.1168T>C	c.(1168-1170)Tcc>Ccc	p.S390P	LMTK3_ENST00000270238.3_Missense_Mutation_p.S419P			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	390	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		CGCCAGCAGGACTGAAGAATG	0.652																																					p.S419P		Atlas-SNP	.											.	LMTK3	125	.	0			c.T1255C						.						7	8	7					19																	49003158		1945	4024	5969	SO:0001583	missense	114783	exon12			AGCAGGACTGAAG	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 101"						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.1168T>C	chr19.hg19:g.49003158A>G	ENSP00000472020:p.Ser390Pro	116.0	0.0		100.0	4.0	NM_001080434	Q4G0U1	Missense_Mutation	SNP	ENST00000600059.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.12	2.439806	0.43326	.	.	ENSG00000142235	ENST00000270238	D	0.83419	-1.72	3.72	2.68	0.31781	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.077128	0.51477	D	0.000085	D	0.84338	0.5450	L	0.46947	1.48	0.40970	D	0.984698	D	0.63046	0.992	D	0.65443	0.935	T	0.80594	-0.1313	10	0.32370	T	0.25	.	7.8702	0.29561	0.8152:0.0:0.0:0.1847	.	390	Q96Q04	LMTK3_HUMAN	P	419	ENSP00000270238:S419P	ENSP00000270238:S419P	S	-	1	0	LMTK3	53694970	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	6.544000	0.73878	0.592000	0.29728	0.329000	0.21502	TCC	.	.		0.652	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895		G	49003158	A	G	49003158	3	3	111	1	0	0	0	0	1	0	0	0	8869	275	10	2	3234	2	LMTK3	19	49003158	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	7782909	49003158	10125825	338	16578										
HRC	3270	hgsc.bcm.edu	37	chr19	49657916	49657916	+	Silent	SNP	T	T	C													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcctcctcctcctcctcctcTtctccttcatcatcttcccc					rs7409255		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:49657916T>C	ENST00000252825.4	-	1	765	c.579A>G	c.(577-579)gaA>gaG	p.E193E	HRC_ENST00000595625.1_Silent_p.E193E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	193	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cctcctcctcttcTCCTTCAT	0.557																																					p.E193E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A579G						.						119	95	103					19																	49657916		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCTCCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.579A>G	chr19.hg19:g.49657916T>C		126.0	0.0		175.0	15.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.557	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657916	T	C	49657916	2	2	111	1	0	0	0	0	0	0	0	1	7361	1606	56	2		2	HRC	19	49657916	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	654758	49657916	9471067	339	16579	74	2								
HRC	3270	hgsc.bcm.edu	37	chr19	49657920	49657920	+	Missense_Mutation	SNP	C	C	T													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctcctcctcctcctcttctCcttcatcatcttccccatca					rs200730671		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:49657920C>T	ENST00000252825.4	-	1	761	c.575G>A	c.(574-576)gGa>gAa	p.G192E	HRC_ENST00000595625.1_Missense_Mutation_p.G192E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	192	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		ctcctcttcTCCTTCATCATC	0.562																																					p.G192E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G575A						.						124	98	107					19																	49657920		2203	4300	6503	SO:0001583	missense	3270	exon1			TCTTCTCCTTCAT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.575G>A	chr19.hg19:g.49657920C>T	ENSP00000252825:p.Gly192Glu	130.0	0.0		177.0	13.0	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	hg19	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	c	0.009	-1.835792	0.00579	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.05717	3.4	2.59	-1.01	0.10169	.	.	.	.	.	T	0.02156	0.0067	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.46289	-0.9202	9	0.02654	T	1	4.5523	7.8184	0.29274	0.0:0.7009:0.0:0.2991	.	192	P23327	SRCH_HUMAN	E	192;162	ENSP00000252825:G192E	ENSP00000252825:G192E	G	-	2	0	HRC	54349732	0.005000	0.15991	0.001000	0.08648	0.082000	0.17680	-0.740000	0.04861	-0.145000	0.11294	-0.389000	0.06534	GGA	.	.		0.562	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		T	49657920	C	T	49657920	3	4	111	1	0	0	0	0	1	0	0	0	7361	855	30	3	1548	3	HRC	19	49657920	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	4	49657920	9471063	340	16580	74	2								
ZNF28	7576	hgsc.bcm.edu	37	chr19	53303761	53303761	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttgattgttgattaaaaaccTtgccacattcattacacttg	5	8	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:53303761T>C	ENST00000457749.2	-	4	1456	c.1337A>G	c.(1336-1338)aAg>aGg	p.K446R	ZNF28_ENST00000360272.4_Missense_Mutation_p.K393R|ZNF28_ENST00000438150.2_Missense_Mutation_p.K393R|ZNF28_ENST00000414252.2_Missense_Mutation_p.K393R	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	446					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		ATTAAAAACCTTGCCACATTC	0.368																																					p.K446R		Atlas-SNP	.											.	ZNF28	191	.	0			c.A1337G						.						111	115	114					19																	53303761		2203	4300	6503	SO:0001583	missense	7576	exon4			AAAACCTTGCCAC	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.1337A>G	chr19.hg19:g.53303761T>C	ENSP00000397693:p.Lys446Arg	53.0	0.0		70.0	4.0	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	hg19	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	14.80	2.644985	0.47258	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75	1.74	1.74	0.24563	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.34077	0.0885	L	0.28458	0.855	0.25343	N	0.988933	D	0.57571	0.98	D	0.70935	0.971	T	0.09618	-1.0666	9	0.62326	D	0.03	.	8.2975	0.31995	0.0:0.0:0.0:1.0	.	446	P17035	ZNF28_HUMAN	R	393;446;393;393;393	ENSP00000412143:K393R;ENSP00000397693:K446R;ENSP00000353410:K393R;ENSP00000444965:K393R;ENSP00000375661:K393R	ENSP00000353410:K393R	K	-	2	0	ZNF28	57995573	0.935000	0.31712	0.037000	0.18230	0.023000	0.10783	2.740000	0.47418	0.792000	0.33850	0.156000	0.16432	AAG	.	.		0.368	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		C	53303761	T	C	53303761	3	2	111	1	0	0	0	0	1	0	0	0	17828	1609	56	2	823	2	ZNF28	19	53303761	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	3645841	53303761	5825222	341	16581										
LILRB5	10990	hgsc.bcm.edu	37	chr19	54759311	54759311	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctgctggccagagccctggaCgaggtcatgttccccctcct	11	16	1	1	rs376519844		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:54759311C>T	ENST00000316219.5	-	5	897	c.790G>A	c.(790-792)Gtc>Atc	p.V264I	LILRB5_ENST00000450632.1_Missense_Mutation_p.V255I|LILRB5_ENST00000345866.6_Missense_Mutation_p.V164I|LILRB5_ENST00000449561.2_Missense_Mutation_p.V264I	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	264	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GAGCCCTGGACGAGGTCATGT	0.652																																					p.V264I		Atlas-SNP	.											.	LILRB5	176	.	0			c.G790A						.	C	ILE/VAL,ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	50	49	49		790,490,790	0.2	0	19		49	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	29,29,29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign,benign,benign	264/592,164/492,264/591	54759311	2,13004	2203	4300	6503	SO:0001583	missense	10990	exon5			CCTGGACGAGGTC	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.790G>A	chr19.hg19:g.54759311C>T	ENSP00000320390:p.Val264Ile	217.0	0.0		228.0	28.0	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	hg19	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	C	2.988	-0.208894	0.06140	2.27E-4	1.16E-4	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.10382	2.88;2.88;2.88;2.88	2.62	0.214	0.15249	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	2.098760	0.02459	N	0.086366	T	0.05640	0.0148	N	0.16130	0.375	0.09310	N	1	B;P;B;B;B	0.41597	0.197;0.756;0.136;0.078;0.054	B;B;B;B;B	0.34038	0.067;0.174;0.035;0.015;0.046	T	0.27400	-1.0075	10	0.21540	T	0.41	.	4.7798	0.13197	0.0:0.2451:0.5056:0.2493	.	255;155;164;264;264	C9JMK7;Q8NF80;O75023-2;O75023-3;O75023	.;.;.;.;LIRB5_HUMAN	I	264;255;264;164	ENSP00000320390:V264I;ENSP00000414225:V255I;ENSP00000406478:V264I;ENSP00000263430:V164I	ENSP00000320390:V264I	V	-	1	0	LILRB5	59451123	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-0.659000	0.05323	0.136000	0.18733	-0.428000	0.05917	GTC	.	.		0.652	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			T	54759311	C	T	54759311	3	4	111	1	0	0	0	0	1	0	0	0	8803	536	19	1	1021	1	LILRB5	19	54759311	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	1455550	54759311	4369672	342	16582										
ZNF71	58491	hgsc.bcm.edu	37	chr19	57133319	57133319	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgtgcgacgtgtgtggcaagGccttccggaagacttcctct	13	11	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr19:57133319G>A	ENST00000328070.6	+	3	898	c.664G>A	c.(664-666)Gcc>Acc	p.A222T		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	222					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		GTGTGGCAAGGCCTTCCGGAA	0.647																																					p.A222T		Atlas-SNP	.											.	ZNF71	69	.	0			c.G664A						.						55	46	49					19																	57133319		2203	4300	6503	SO:0001583	missense	58491	exon3			GGCAAGGCCTTCC	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"Zinc fingers, C2H2-type"	13141	protein-coding gene	gene with protein product		194545	"zinc finger protein 71 (Cos26)"			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.664G>A	chr19.hg19:g.57133319G>A	ENSP00000328245:p.Ala222Thr	100.0	0.0		118.0	18.0	NM_021216	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	hg19	CCDS12947.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.694000	0.30052	.	.	ENSG00000197951	ENST00000328070	T	0.13778	2.56	3.47	2.39	0.29439	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04407	0.0121	N	0.01817	-0.705	0.21861	N	0.999505	B	0.33883	0.43	B	0.31869	0.137	T	0.30650	-0.9971	9	0.27785	T	0.31	.	5.6102	0.17400	0.1098:0.0:0.6973:0.1929	.	222	Q9NQZ8	ZNF71_HUMAN	T	222	ENSP00000328245:A222T	ENSP00000328245:A222T	A	+	1	0	ZNF71	61825131	0.000000	0.05858	0.993000	0.49108	0.457000	0.32468	-0.946000	0.03905	1.777000	0.52277	0.561000	0.74099	GCC	.	.		0.647	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		A	57133319	G	A	57133319	3	1	111	1	0	0	0	0	1	0	0	0	18129	1203	42	3	666	3	ZNF71	19	57133319	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	2374008	57133319	1995664	343	16583										
DEFB126	81623	hgsc.bcm.edu	37	chr20	126206	126206	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cagacgtgctaattatcctgTtttctgtgtccagacaaaga	8	9	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:126206T>C	ENST00000382398.3	+	2	469	c.209T>C	c.(208-210)gTt>gCt	p.V70A	DEFB126_ENST00000542572.1_Intron	NM_030931.3	NP_112193.1	Q9BYW3	DB126_HUMAN	defensin, beta 126	70					defense response to bacterium (GO:0042742)	cell surface (GO:0009986)|extracellular region (GO:0005576)|glycocalyx (GO:0030112)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			AATTATCCTGTTTTCTGTGTC	0.433																																					p.V70A		Atlas-SNP	.											.	DEFB126	52	.	0			c.T209C						.						169	142	151					20																	126206		2203	4300	6503	SO:0001583	missense	81623	exon2			ATCCTGTTTTCTG		CCDS12990.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125788	ENSG00000125788		"Defensins, beta"	15900	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 8"	C20orf8		11854508	Standard	NM_030931		Approved	bA530N10.1, DEFB-26	uc002wcx.3	Q9BYW3	OTTHUMG00000031616	ENST00000382398.3:c.209T>C	chr20.hg19:g.126206T>C	ENSP00000371835:p.Val70Ala	109.0	0.0		134.0	6.0	NM_030931	Q562G3|Q9H1M5	Missense_Mutation	SNP	ENST00000382398.3	hg19	CCDS12990.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.739998	0.00675	.	.	ENSG00000125788	ENST00000382398	T	0.38077	1.16	3.02	-6.04	0.02178	.	17.788600	0.00166	N	0.000000	T	0.12689	0.0308	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23476	-1.0187	10	0.07990	T	0.79	.	2.9649	0.05905	0.2486:0.1201:0.0933:0.5379	.	70	Q9BYW3	DB126_HUMAN	A	70	ENSP00000371835:V70A	ENSP00000371835:V70A	V	+	2	0	DEFB126	74206	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.305000	0.01133	-3.271000	0.00199	-1.329000	0.01275	GTT	.	.		0.433	DEFB126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077428.2	NM_030931		C	126206	T	C	126206	3	2	111	1	0	0	0	0	1	0	0	0	4414	1725	60	2	215	2	DEFB126	20	126206	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		126206	62899314	344	16584										
SIRPB2	284759	hgsc.bcm.edu	37	chr20	1460431	1460431	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcacacagtggtaggttccaGtgtgctccctggtgacattg	12	10	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:1460431G>A	ENST00000359801.3	-	2	401	c.365C>T	c.(364-366)aCt>aTt	p.T122I	SIRPB2_ENST00000444444.2_Intron|SIRPB2_ENST00000537284.1_5'UTR|SIRPB2_ENST00000608747.1_Intron	NM_001122962.1	NP_001116434.1	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein beta 2	114	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GTAGGTTCCAGTGTGCTCCCT	0.488																																					p.T122I		Atlas-SNP	.											.	SIRPB2	50	.	0			c.C365T						.						134	119	124					20																	1460431		1568	3582	5150	SO:0001583	missense	284759	exon2			GTTCCAGTGTGCT	AL109658	CCDS42849.1, CCDS46570.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000196209	ENSG00000196209		"Signal-regulatory proteins", "Immunoglobulin superfamily / V-set domain containing"	16247	protein-coding gene	gene with protein product			"protein tyrosine phosphatase, non-receptor type 1-like", "protein tyrosine phosphatase, non-receptor type substrate 1-like 3"	PTPN1L, PTPNS1L3		16339511	Standard	NM_001122962		Approved	dJ776F14.2	uc002wfg.2	Q5JXA9	OTTHUMG00000031670	ENST00000359801.3:c.365C>T	chr20.hg19:g.1460431G>A	ENSP00000352849:p.Thr122Ile	233.0	0.0		217.0	61.0	NM_001122962	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000359801.3	hg19	CCDS42849.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.742104	0.30865	.	.	ENSG00000196209	ENST00000359801	T	0.68331	-0.32	4.13	2.12	0.27331	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.927056	0.09011	N	0.861546	T	0.56702	0.2003	L	0.46819	1.47	0.30217	N	0.797182	B	0.29862	0.259	B	0.28232	0.087	T	0.56763	-0.7925	10	0.72032	D	0.01	-1.7633	5.0834	0.14668	0.109:0.0:0.6862:0.2048	.	122	Q5JXA9	SIRB2_HUMAN	I	122	ENSP00000352849:T122I	ENSP00000352849:T122I	T	-	2	0	SIRPB2	1408431	0.082000	0.21442	0.739000	0.30968	0.880000	0.50808	0.075000	0.14686	0.492000	0.27815	0.655000	0.94253	ACT	.	.		0.488	SIRPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077544.1	NM_178459		A	1460431	G	A	1460431	3	1	111	1	0	0	0	0	1	0	0	0	14349	1029	36	3	679	3	SIRPB2	20	1460431	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	1334225	1460431	61565089	345	16585										
CHGB	1114	hgsc.bcm.edu	37	chr20	5903684	5903684	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aggtcctctcaaggagggagTcttccctctgaggaaaaggg	14	9	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:5903684T>C	ENST00000378961.4	+	4	1098	c.894T>C	c.(892-894)agT>agC	p.S298S		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	298						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						AAGGAGGGAGTCTTCCCTCTG	0.582																																					p.S298S		Atlas-SNP	.											.	CHGB	112	.	0			c.T894C						.						28	30	29					20																	5903684		2203	4300	6503	SO:0001819	synonymous_variant	1114	exon4			AGGGAGTCTTCCC		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.894T>C	chr20.hg19:g.5903684T>C		79.0	0.0		72.0	4.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Silent	SNP	ENST00000378961.4	hg19	CCDS13092.1																																																																																			.	.		0.582	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		C	5903684	T	C	5903684	2	2	111	1	0	0	0	0	0	0	0	1	3341	1664	58	2		2	CHGB	20	5903684	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	4443253	5903684	57121836	346	16586										
FERMT1	55612	hgsc.bcm.edu	37	chr20	6057869	6057869	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	acaagtcctcatcgagtgttTcattctggtccttggagcgg	11	10	3	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:6057869T>A	ENST00000217289.4	-	15	2773	c.1985A>T	c.(1984-1986)gAa>gTa	p.E662V	FERMT1_ENST00000536936.1_Missense_Mutation_p.E405V|FERMT1_ENST00000478194.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	662					cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						ATCGAGTGTTTCATTCTGGTC	0.527											OREG0025763	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E662V		Atlas-SNP	.											.	FERMT1	106	.	0			c.A1985T						.						103	93	97					20																	6057869		2203	4300	6503	SO:0001583	missense	55612	exon15			AGTGTTTCATTCT	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"Fermitins", "Pleckstrin homology (PH) domain containing"	15889	protein-coding gene	gene with protein product	"kindlin-1", "kinderlin"	607900	"chromosome 20 open reading frame 42", "fermitin family homolog 1 (Drosophila)"	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1985A>T	chr20.hg19:g.6057869T>A	ENSP00000217289:p.Glu662Val	167.0	0.0	631	137.0	23.0	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Missense_Mutation	SNP	ENST00000217289.4	hg19	CCDS13098.1	.	.	.	.	.	.	.	.	.	.	T	33	5.218220	0.95104	.	.	ENSG00000101311	ENST00000217289;ENST00000536936	T;T	0.38077	1.16;1.16	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.60470	0.2271	M	0.73598	2.24	0.80722	D	1	D	0.71674	0.998	D	0.68765	0.96	T	0.64219	-0.6459	10	0.66056	D	0.02	-5.3488	16.1008	0.81169	0.0:0.0:0.0:1.0	.	662	Q9BQL6	FERM1_HUMAN	V	662;405	ENSP00000217289:E662V;ENSP00000441063:E405V	ENSP00000217289:E662V	E	-	2	0	FERMT1	6005869	1.000000	0.71417	0.996000	0.52242	0.971000	0.66376	7.930000	0.87610	2.206000	0.71126	0.533000	0.62120	GAA	.	.		0.527	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671		A	6057869	T	A	6057869	3	1	111	1	0	0	0	0	1	0	0	0	5825	1783	62	4	52	4	FERMT1	20	6057869	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	154185	6057869	56967651	347	16587										
TPX2	22974	hgsc.bcm.edu	37	chr20	30366726	30366726	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gtgccccttgcacagcaagtTgaagacttccataaacgaac	8	12	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:30366726T>C	ENST00000300403.6	+	10	1521	c.993T>C	c.(991-993)gtT>gtC	p.V331V	TPX2_ENST00000340513.4_Silent_p.V331V	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	331					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			CACAGCAAGTTGAAGACTTCC	0.403																																					p.V331V		Atlas-SNP	.											.	TPX2	61	.	0			c.T993C						.						120	111	114					20																	30366726		2203	4300	6503	SO:0001819	synonymous_variant	22974	exon10			GCAAGTTGAAGAC	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"chromosome 20 open reading frame 1", "TPX2, microtubule-associated, homolog (Xenopus laevis)"	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.993T>C	chr20.hg19:g.30366726T>C		96.0	0.0		92.0	4.0	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Silent	SNP	ENST00000300403.6	hg19	CCDS13190.1																																																																																			.	.		0.403	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2			C	30366726	T	C	30366726	2	2	111	1	0	0	0	0	0	0	0	1	16447	1799	63	2		2	TPX2	20	30366726	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	24308857	30366726	32658794	348	16588										
C20orf185	359710	hgsc.bcm.edu	37	chr20	31644372	31644372	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccagaactcactggttggggAgcccattctgcagaatgtgc	12	11	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:31644372A>G	ENST00000375494.3	+	2	149	c.149A>G	c.(148-150)gAg>gGg	p.E50G	AL121756.1_ENST00000579962.1_RNA	NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	50	Leu-rich.				innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										CTGGTTGGGGAGCCCATTCTG	0.607																																					p.E50G		Atlas-SNP	.											.	.	.	.	0			c.A149G						.						95	96	96					20																	31644372		2203	4300	6503	SO:0001583	missense	359710	exon2			TTGGGGAGCCCAT	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"BPI fold containing"	16178	protein-coding gene	gene with protein product		615717	"chromosome 20 open reading frame 185"	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.149A>G	chr20.hg19:g.31644372A>G	ENSP00000364643:p.Glu50Gly	101.0	0.0		91.0	4.0	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	hg19	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	A	0.430	-0.903634	0.02453	.	.	ENSG00000186190	ENST00000375494	T	0.05580	3.42	4.57	2.63	0.31362	.	0.224806	0.31061	N	0.008337	T	0.01320	0.0043	N	0.00182	-1.905	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.46400	-0.9194	10	0.14252	T	0.57	-7.6424	7.1807	0.25770	0.2043:0.0:0.7957:0.0	.	50	P59826	BPIB3_HUMAN	G	50	ENSP00000364643:E50G	ENSP00000364643:E50G	E	+	2	0	BPIFB3	31108033	0.993000	0.37304	0.472000	0.27241	0.830000	0.47004	2.689000	0.46993	0.538000	0.28769	-0.146000	0.13790	GAG	.	.		0.607	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		G	31644372	A	G	31644372	3	3	111	1	0	0	0	0	1	0	0	0	2099	304	11	2	155	2	C20orf185	20	31644372	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1277646	31644372	31381148	349	16589										
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42157387	42157387	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agtcagcctcttccaggacgTgagttggacaatttccccgt	10	12	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:42157387T>C	ENST00000427442.2	+	8	1044		c.e8+2		L3MBTL1_ENST00000444063.1_Splice_Site|L3MBTL1_ENST00000457824.1_Splice_Site|L3MBTL1_ENST00000373135.3_Splice_Site|L3MBTL1_ENST00000373134.1_Splice_Site|L3MBTL1_ENST00000418998.1_Splice_Site			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)						chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						TTCCAGGACGTGAGTTGGACA	0.542																																					.		Atlas-SNP	.											.	L3MBTL1	105	.	0			c.885+2T>C						.						93	82	86					20																	42157387		2203	4300	6503	SO:0001630	splice_region_variant	26013	exon8			AGGACGTGAGTTG	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.885+2T>C	chr20.hg19:g.42157387T>C		146.0	0.0		118.0	5.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Splice_Site	SNP	ENST00000427442.2	hg19	CCDS46602.2	.	.	.	.	.	.	.	.	.	.	T	20.9	4.068361	0.76301	.	.	ENSG00000185513	ENST00000427442;ENST00000418998;ENST00000373135;ENST00000444063;ENST00000373134;ENST00000422861	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6845	0.69040	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	L3MBTL1	41590801	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.108000	0.71522	2.122000	0.65172	0.455000	0.32223	.	.	.		0.542	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107	Intron	C	42157387	T	C	42157387	5	2	111	1	0	0	0	0	0	0	1	0	8600	1710	59	2	701	2	L3MBTL	20	42157387	Splice_Site	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	10513015	42157387	20868133	350	16590										
IFT52	51098	hgsc.bcm.edu	37	chr20	42252541	42252541	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tggctttcagatttctgactAcatgatgctgccctacacag	8	11	2	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:42252541A>G	ENST00000373030.3	+	10	909	c.779A>G	c.(778-780)tAc>tGc	p.Y260C	IFT52_ENST00000373039.4_Missense_Mutation_p.Y260C	NM_016004.2	NP_057088.2	Q9Y366	IFT52_HUMAN	intraflagellar transport 52	260					cilium morphogenesis (GO:0060271)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube formation (GO:0001841)|regulation of protein processing (GO:0070613)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)	protein C-terminus binding (GO:0008022)			endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			ATTTCTGACTACATGATGCTG	0.483																																					p.Y260C		Atlas-SNP	.											.	IFT52	40	.	0			c.A779G						.						123	113	116					20																	42252541		2203	4300	6503	SO:0001583	missense	51098	exon10			CTGACTACATGAT	AF151811	CCDS33470.1	20q12-q13.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000101052	ENSG00000101052		"Intraflagellar transport homologs"	15901	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 9", "intraflagellar transport 52 homolog (Chlamydomonas)"	C20orf9		10810093	Standard	NM_016004		Approved	CGI-53, NGD5, dJ1028D15.1, NGD2	uc002xkw.3	Q9Y366	OTTHUMG00000032513	ENST00000373030.3:c.779A>G	chr20.hg19:g.42252541A>G	ENSP00000362121:p.Tyr260Cys	126.0	0.0		94.0	4.0	NM_016004	B3KMA1|E1P5W9|Q5H8Z0|Q9H1G3|Q9H1G4|Q9H1H2	Missense_Mutation	SNP	ENST00000373030.3	hg19	CCDS33470.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.934048	0.73442	.	.	ENSG00000101052	ENST00000373030;ENST00000373039	.	.	.	5.58	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.79902	0.4526	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.81627	-0.0847	9	0.59425	D	0.04	-15.1853	11.2533	0.49039	0.8626:0.0:0.0:0.1374	.	260	Q9Y366	IFT52_HUMAN	C	260	.	ENSP00000362121:Y260C	Y	+	2	0	IFT52	41685955	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.720000	0.91442	1.034000	0.39945	0.533000	0.62120	TAC	.	.		0.483	IFT52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079317.1	NM_016004		G	42252541	A	G	42252541	3	3	111	1	0	0	0	0	1	0	0	0	7570	391	14	2	813	2	IFT52	20	42252541	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	95154	42252541	20772979	351	16591										
PCIF1	63935	hgsc.bcm.edu	37	chr20	44574501	44574501	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggagagatggtcaaggtcagCcgcaactacttcagcaagct	12	10	3	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:44574501C>T	ENST00000372409.3	+	12	1684	c.1320C>T	c.(1318-1320)agC>agT	p.S440S	PCIF1_ENST00000479348.1_3'UTR	NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	440					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						TCAAGGTCAGCCGCAACTACT	0.587																																					p.S440S		Atlas-SNP	.											.	PCIF1	51	.	0			c.C1320T						.						91	86	88					20																	44574501		2203	4300	6503	SO:0001819	synonymous_variant	63935	exon12			GGTCAGCCGCAAC	AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 121"		"chromosome 20 open reading frame 67"	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.1320C>T	chr20.hg19:g.44574501C>T		112.0	0.0		90.0	4.0	NM_022104	E1P5P1|Q54AB9|Q9NT85	Silent	SNP	ENST00000372409.3	hg19	CCDS13388.1																																																																																			.	.		0.587	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104		T	44574501	C	T	44574501	2	4	111	1	0	0	0	0	0	0	0	1	11589	738	26	3		3	PCIF1	20	44574501	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	2321960	44574501	18451019	352	16592										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46271003	46271003	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	atcttgttgggccaccttccAacctggaaggccagagtgac	11	12	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:46271003A>G	ENST00000371998.3	+	17	3318	c.3127A>G	c.(3127-3129)Aac>Gac	p.N1043D	NCOA3_ENST00000372004.3_Missense_Mutation_p.N1043D|NCOA3_ENST00000341724.6_Missense_Mutation_p.N973D|NCOA3_ENST00000371997.3_Missense_Mutation_p.N1038D			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1043	Interaction with CREBBP.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GCCACCTTCCAACCTGGAAGG	0.448																																					p.N1043D		Atlas-SNP	.											.	NCOA3	156	.	0			c.A3127G						.						155	145	148					20																	46271003		2203	4300	6503	SO:0001583	missense	8202	exon17			CCTTCCAACCTGG	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3127A>G	chr20.hg19:g.46271003A>G	ENSP00000361066:p.Asn1043Asp	72.0	0.0		40.0	4.0	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	hg19	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.289902	0.80914	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.02050	4.48;4.66;4.66;4.48	5.62	5.62	0.85841	.	0.130948	0.52532	D	0.000062	T	0.03608	0.0103	L	0.56769	1.78	0.37633	D	0.921752	B;P;B;B;B;B	0.47762	0.243;0.9;0.243;0.243;0.356;0.243	B;B;B;B;B;B	0.39258	0.09;0.295;0.09;0.09;0.185;0.09	T	0.59685	-0.7408	10	0.22109	T	0.4	-24.9681	16.1146	0.81295	1.0:0.0:0.0:0.0	.	1043;1038;1047;1043;1043;1043	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	D	1043;973;1043;1043;1038	ENSP00000342123:N973D;ENSP00000361073:N1043D;ENSP00000361066:N1043D;ENSP00000361065:N1038D	ENSP00000345671:N1043D	N	+	1	0	NCOA3	45704410	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.910000	0.92685	2.260000	0.74910	0.528000	0.53228	AAC	.	.		0.448	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		G	46271003	A	G	46271003	3	3	111	1	0	0	0	0	1	0	0	0	10239	130	5	2	3215	2	NCOA3	20	46271003	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1696502	46271003	16754517	353	16593										
RAE1	8480	hgsc.bcm.edu	37	chr20	55949682	55949682	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggtaaatggaatcgcgttccAtcctgttcatggcacccttg	10	11	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:55949682A>G	ENST00000395841.2	+	11	1265	c.845A>G	c.(844-846)cAt>cGt	p.H282R	RAE1_ENST00000395840.2_Missense_Mutation_p.H282R|RAE1_ENST00000527947.1_Missense_Mutation_p.H282R|RAE1_ENST00000371242.2_Missense_Mutation_p.H282R	NM_003610.3	NP_003601.1	P78406	RAE1L_HUMAN	ribonucleic acid export 1	282					carbohydrate metabolic process (GO:0005975)|cellular response to organic cyclic compound (GO:0071407)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|nuclear pore (GO:0005643)|nucleolus (GO:0005730)|nucleus (GO:0005634)	microtubule binding (GO:0008017)|RNA binding (GO:0003723)			breast(1)|endometrium(5)|large_intestine(4)|lung(6)|prostate(3)|skin(2)	21	Lung NSC(12;0.00263)|all_lung(29;0.00828)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;3.7e-14)|Epithelial(14;1.07e-09)|all cancers(14;1.11e-08)			ATCGCGTTCCATCCTGTTCAT	0.493																																					p.H282R		Atlas-SNP	.											.	RAE1	54	.	0			c.A845G						.						205	195	199					20																	55949682		2203	4300	6503	SO:0001583	missense	8480	exon11			CGTTCCATCCTGT	U84720	CCDS13458.1	20q13.31	2013-08-28	2013-08-28		ENSG00000101146	ENSG00000101146		"WD repeat domain containing"	9828	protein-coding gene	gene with protein product		603343	"RAE1 (RNA export 1, S.pombe) homolog", "RAE1 RNA export 1 homolog (S. pombe)"			9370289, 9256445	Standard	XM_005260582		Approved	Mnrp41	uc002xyi.3	P78406	OTTHUMG00000032819	ENST00000395841.2:c.845A>G	chr20.hg19:g.55949682A>G	ENSP00000379182:p.His282Arg	80.0	0.0		79.0	4.0	NM_003610	A8K882|O15306|Q3SYL7|Q5TCH8|Q6V708|Q9H100|Q9NQM6	Missense_Mutation	SNP	ENST00000395841.2	hg19	CCDS13458.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.720938	0.89205	.	.	ENSG00000101146	ENST00000395841;ENST00000371242;ENST00000527947;ENST00000395840	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.91	5.91	0.95273	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.89701	0.6791	H	0.96943	3.91	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.987;0.987	D	0.93028	0.6446	10	0.87932	D	0	-15.6787	16.3483	0.83171	1.0:0.0:0.0:0.0	.	282;282;282	E9PQ57;A8K882;P78406	.;.;RAE1L_HUMAN	R	282	ENSP00000379182:H282R;ENSP00000360286:H282R;ENSP00000432609:H282R;ENSP00000379181:H282R	ENSP00000360286:H282R	H	+	2	0	RAE1	55383089	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.952000	0.93031	2.254000	0.74563	0.533000	0.62120	CAT	.	.		0.493	RAE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079842.2			G	55949682	A	G	55949682	3	3	111	1	0	0	0	0	1	0	0	0	13013	217	8	2	883	2	RAE1	20	55949682	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	9678679	55949682	7075838	354	16594										
SLC2A4RG	56731	hgsc.bcm.edu	37	chr20	62373927	62373927	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cgccccctgtcctgagcaccGttgctaacccccagtcctgt	8	19	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr20:62373927G>A	ENST00000266077.2	+	6	971	c.919G>A	c.(919-921)Gtt>Att	p.V307I	RP4-583P15.10_ENST00000433905.2_RNA|RP4-583P15.10_ENST00000447343.2_RNA|SLC2A4RG_ENST00000493772.1_3'UTR	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					CCTGAGCACCGTTGCTAACCC	0.721																																					p.V307I		Atlas-SNP	.											.	SLC2A4RG	20	.	0			c.G919A						.						6	8	7					20																	62373927		1855	3904	5759	SO:0001583	missense	56731	exon6			AGCACCGTTGCTA	AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"GLUT4 enhancer factor", "Huntington's disease gene regulatory region-binding protein 1"	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.919G>A	chr20.hg19:g.62373927G>A	ENSP00000266077:p.Val307Ile	40.0	0.0		39.0	6.0	NM_020062	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Missense_Mutation	SNP	ENST00000266077.2	hg19	CCDS13537.1	.	.	.	.	.	.	.	.	.	.	G	6.082	0.383377	0.11524	.	.	ENSG00000125520	ENST00000266077	T	0.44482	0.92	3.07	-3.4	0.04853	.	.	.	.	.	T	0.14830	0.0358	N	0.14661	0.345	0.09310	N	1	P	0.38863	0.65	B	0.26614	0.071	T	0.09907	-1.0653	9	0.39692	T	0.17	.	0.4685	0.00528	0.2102:0.2887:0.2089:0.2922	.	307	Q9NR83	S2A4R_HUMAN	I	307	ENSP00000266077:V307I	ENSP00000266077:V307I	V	+	1	0	SLC2A4RG	61844371	0.004000	0.15560	0.000000	0.03702	0.041000	0.13682	0.412000	0.21131	-1.174000	0.02754	0.313000	0.20887	GTT	.	.		0.721	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1	NM_020062		A	62373927	G	A	62373927	3	1	111	1	0	0	0	0	1	0	0	0	14562	1145	40	1	941	1	SLC2A4RG	20	62373927	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	6424245	62373927	651593	355	16595										
NRIP1	8204	hgsc.bcm.edu	37	chr21	16339695	16339695	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaatactgctgcaaatgggcTtcgcttgacagaagtaatgc	11	8	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr21:16339695T>C	ENST00000400202.1	-	3	1531	c.819A>G	c.(817-819)gaA>gaG	p.E273E	NRIP1_ENST00000400199.1_Silent_p.E273E|NRIP1_ENST00000318948.4_Silent_p.E273E			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	273	Interaction with ZNF366.|Repression domain 1.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		GCAAATGGGCTTCGCTTGACA	0.453																																					p.E273E		Atlas-SNP	.											.	NRIP1	103	.	0			c.A819G						.						153	140	144					21																	16339695		2203	4300	6503	SO:0001819	synonymous_variant	8204	exon4			ATGGGCTTCGCTT	X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"receptor interacting protein 140", "nuclear factor RIP140"	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.819A>G	chr21.hg19:g.16339695T>C		105.0	0.0		99.0	4.0	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	hg19	CCDS13568.1																																																																																			.	.		0.453	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489		C	16339695	T	C	16339695	2	2	111	1	0	0	0	0	0	0	0	1	10661	1606	56	2		2	NRIP1	21	16339695	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10		16339695	31790200	356	16596										
IL10RB	3588	hgsc.bcm.edu	37	chr21	34660496	34660496	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cctcggctgcttcgccttgcTgtggtgcgtttacaagaaga	12	11	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr21:34660496T>C	ENST00000290200.2	+	6	842	c.734T>C	c.(733-735)cTg>cCg	p.L245P		NM_000628.4	NP_000619.3	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta	245					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	14						TTCGCCTTGCTGTGGTGCGTT	0.552																																					p.L245P	Melanoma(67;315 1275 21667 21943 44564)	Atlas-SNP	.											.	IL10RB	37	.	0			c.T734C						.						201	149	167					21																	34660496		2203	4300	6503	SO:0001583	missense	3588	exon6			CCTTGCTGTGGTG	U08988	CCDS13623.1	21q22.11	2014-09-17			ENSG00000243646	ENSG00000243646		"Interleukins and interleukin receptors", "CD molecules"	5965	protein-coding gene	gene with protein product		123889		CRFB4, D21S58, D21S66		8314576, 9312047	Standard	NM_000628		Approved	CRF2-4, CDW210B, IL-10R2		Q08334	OTTHUMG00000065128	ENST00000290200.2:c.734T>C	chr21.hg19:g.34660496T>C	ENSP00000290200:p.Leu245Pro	99.0	0.0		93.0	4.0	NM_000628	Q9BUU4	Missense_Mutation	SNP	ENST00000290200.2	hg19	CCDS13623.1	.	.	.	.	.	.	.	.	.	.	T	15.04	2.716252	0.48622	.	.	ENSG00000243646	ENST00000290200;ENST00000539894	T	0.46451	0.87	5.71	4.57	0.56435	.	0.908051	0.09343	N	0.815180	T	0.55353	0.1915	M	0.73598	2.24	0.38374	D	0.94495	D;D	0.57899	0.981;0.981	P;P	0.54174	0.744;0.643	T	0.48670	-0.9015	10	0.36615	T	0.2	-0.1263	8.4551	0.32895	0.0:0.088:0.0:0.912	.	247;245	Q6ZVU9;Q08334	.;I10R2_HUMAN	P	245	ENSP00000290200:L245P	ENSP00000290200:L245P	L	+	2	0	IL10RB	33582366	0.909000	0.30893	0.267000	0.24556	0.384000	0.30261	1.822000	0.39052	0.994000	0.38892	0.533000	0.62120	CTG	.	.		0.552	IL10RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139831.3			C	34660496	T	C	34660496	3	2	111	1	0	0	0	0	1	0	0	0	7630	1580	55	2	756	2	IL10RB	21	34660496	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	18320801	34660496	13469399	357	16597										
IFNGR2	3460	hgsc.bcm.edu	37	chr21	34805151	34805151	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	aaatactggtttcacactccAccaagcatcccattacagat	4	13	1	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr21:34805151A>G	ENST00000290219.6	+	6	1500	c.852A>G	c.(850-852)ccA>ccG	p.P284P	IFNGR2_ENST00000405436.1_Silent_p.P205P|IFNGR2_ENST00000381995.1_Silent_p.P303P	NM_005534.3	NP_005525.2	P38484	INGR2_HUMAN	interferon gamma receptor 2 (interferon gamma transducer 1)	284					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	interferon-gamma receptor activity (GO:0004906)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	13					Interferon gamma-1b(DB00033)	TTCACACTCCACCAAGCATCC	0.478																																					p.P284P		Atlas-SNP	.											.	IFNGR2	30	.	0			c.A852G						.						92	88	89					21																	34805151		2203	4300	6503	SO:0001819	synonymous_variant	3460	exon6			CACTCCACCAAGC		CCDS33544.1	21q22.1	2014-09-17			ENSG00000159128	ENSG00000159128		"Interferons", "Fibronectin type III domain containing"	5440	protein-coding gene	gene with protein product		147569		IFNGT1		3136170	Standard	NM_005534		Approved	AF-1	uc002yrp.4	P38484	OTTHUMG00000065188	ENST00000290219.6:c.852A>G	chr21.hg19:g.34805151A>G		99.0	0.0		97.0	5.0	NM_005534	Q9BTL5	Silent	SNP	ENST00000290219.6	hg19	CCDS33544.1	.	.	.	.	.	.	.	.	.	.	A	3.905	-0.021319	0.07634	.	.	ENSG00000159128	ENST00000421802	.	.	.	5.53	-8.93	0.00771	.	.	.	.	.	T	0.50000	0.1590	.	.	.	0.37879	D	0.930328	.	.	.	.	.	.	T	0.59129	-0.7512	4	.	.	.	-4.0195	10.986	0.47523	0.6734:0.1008:0.2257:0.0	.	.	.	.	R	50	.	.	H	+	2	0	IFNGR2	33727021	0.000000	0.05858	0.061000	0.19648	0.402000	0.30811	-2.876000	0.00717	-1.642000	0.01521	-0.371000	0.07208	CAC	.	.		0.478	IFNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139916.1			G	34805151	A	G	34805151	2	3	111	1	0	0	0	0	0	0	0	1	7559	146	6	2		2	IFNGR2	21	34805151	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	144655	34805151	13324744	358	16598										
SIM2	6493	hgsc.bcm.edu	37	chr21	38095410	38095410	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttggcgaaaaggaacgcgggCctgacctgcagcggatacaa	14	10	0	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr21:38095410C>A	ENST00000290399.6	+	5	1135	c.522C>A	c.(520-522)ggC>ggA	p.G174G	SIM2_ENST00000430056.3_Silent_p.G174G	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	174					cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						GGAACGCGGGCCTGACCTGCA	0.527																																					p.G174G		Atlas-SNP	.											.	SIM2	55	.	0			c.C522A						.						133	121	126					21																	38095410		2203	4300	6503	SO:0001819	synonymous_variant	6493	exon5			CGCGGGCCTGACC		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"Basic helix-loop-helix proteins"	10883	protein-coding gene	gene with protein product	"transcription factor SIM2"	600892	"single-minded (Drosophila) homolog 2", "single-minded homolog 2 (Drosophila)"	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.522C>A	chr21.hg19:g.38095410C>A		80.0	0.0		58.0	14.0	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Silent	SNP	ENST00000290399.6	hg19	CCDS13646.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.361190	0.24684	.	.	ENSG00000159263	ENST00000431229	.	.	.	5.24	3.21	0.36854	.	.	.	.	.	T	0.57651	0.2068	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53627	-0.8412	4	.	.	.	.	8.7021	0.34332	0.3174:0.5033:0.1793:0.0	.	.	.	.	T	112	.	.	P	+	1	0	SIM2	37017280	0.001000	0.12720	1.000000	0.80357	0.950000	0.60333	-0.375000	0.07475	2.445000	0.82738	0.655000	0.94253	CCT	.	.		0.527	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586		A	38095410	C	A	38095410	2	1	111	1	0	0	0	0	0	0	0	1	14339	726	26	3		3	SIM2	21	38095410	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	3290259	38095410	10034485	359	16599										
CBS	875	hgsc.bcm.edu	37	chr21	44480560	44480560	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccgtgtcttacatgtagttcCgcactgagtcgggcagaatg	12	10	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr21:44480560C>T	ENST00000398165.3	-	12	1395	c.1136G>A	c.(1135-1137)cGg>cAg	p.R379Q	CBS_ENST00000398158.1_Missense_Mutation_p.R379Q|CBS_ENST00000544202.1_Missense_Mutation_p.R291Q|CBS_ENST00000359624.3_Missense_Mutation_p.R379Q|CBS_ENST00000352178.5_Missense_Mutation_p.R379Q|CBS_ENST00000398168.1_Missense_Mutation_p.R379Q	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	379			R -> Q (in CBSD; exhibits an activity lower than 4% of the wild-type enzyme; absent capacity to form multimeric quaternary structure). {ECO:0000269|PubMed:12815602}.|R -> W (in CBSD). {ECO:0000269|PubMed:15365998}.		cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	CATGTAGTTCCGCACTGAGTC	0.662																																					p.R379Q		Atlas-SNP	.											.	CBS	85	.	0			c.G1136A	GRCh37	CM031652	CBS	M		.						95	67	76					21																	44480560		2203	4300	6503	SO:0001583	missense	875	exon12			TAGTTCCGCACTG	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.1136G>A	chr21.hg19:g.44480560C>T	ENSP00000381231:p.Arg379Gln	58.0	0.0		54.0	4.0	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Missense_Mutation	SNP	ENST00000398165.3	hg19	CCDS13693.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	4.005806|4.005806	0.74932|0.74932	.|.	.|.	ENSG00000160200|ENSG00000160200	ENST00000430013|ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000398168;ENST00000539520;ENST00000544202	.|D;D;D;D;D;D	.|0.99207	.|-5.56;-5.56;-5.56;-5.56;-5.56;-5.56	4.9|4.9	4.01|4.01	0.46588|0.46588	.|Pyridoxal phosphate-dependent enzyme, beta subunit (1);	.|0.123875	.|0.53938	.|D	.|0.000051	D|D	0.99048|0.99048	0.9674|0.9674	M|M	0.84846|0.84846	2.72|2.72	0.58432|0.58432	D|D	0.999996|0.999996	.|P;D	.|0.63046	.|0.708;0.992	.|B;P	.|0.53649	.|0.238;0.731	D|D	0.98701|0.98701	1.0700|1.0700	5|10	.|0.72032	.|D	.|0.01	-33.6255|-33.6255	12.2822|12.2822	0.54771|0.54771	0.0:0.9166:0.0:0.0834|0.0:0.9166:0.0:0.0834	.|.	.|379;336	.|P35520;B7Z2D6	.|CBS_HUMAN;.	R|Q	33|379;379;379;379;379;336;291	.|ENSP00000381225:R379Q;ENSP00000381231:R379Q;ENSP00000352643:R379Q;ENSP00000344460:R379Q;ENSP00000381234:R379Q;ENSP00000439332:R291Q	.|ENSP00000344460:R379Q	G|R	-|-	1|2	0|0	CBS|CBS	43353629|43353629	1.000000|1.000000	0.71417|0.71417	0.541000|0.541000	0.28102|0.28102	0.718000|0.718000	0.41266|0.41266	5.609000|5.609000	0.67661|0.67661	2.262000|2.262000	0.75019|0.75019	0.591000|0.591000	0.81541|0.81541	GGA|CGG	.	.		0.662	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071		T	44480560	C	T	44480560	3	4	111	1	0	0	0	0	1	0	0	0	2713	652	23	1	543	1	CBS	21	44480560	Missense_Mutation	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	6385150	44480560	3649335	360	16600										
FTCD	10841	hgsc.bcm.edu	37	chr21	47575400	47575401	+	In_Frame_Ins	INS	-	-	CCATAA													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cacctcctggttcttcccctINSccgaaaagttggggacgcat							TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr21:47575400_47575401insCCATAA	ENST00000291670.5	-	1	80_81	c.37_38insTTATGG	c.(37-39)gag>gTTATGGag	p.12_13insVM	FTCD_ENST00000359679.2_In_Frame_Ins_p.12_13insVM|FTCD_ENST00000498355.2_De_novo_Start_OutOfFrame|FTCD_ENST00000397746.3_In_Frame_Ins_p.12_13insVM|FTCD-AS1_ENST00000446649.1_RNA|FTCD_ENST00000397748.1_In_Frame_Ins_p.12_13insVM|FTCD_ENST00000355384.2_In_Frame_Ins_p.12_13insVM|FTCD_ENST00000397743.1_In_Frame_Ins_p.12_13insVM	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	12	Formiminotransferase N-subdomain. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	GTTCTTCCCCTCCGAAAAGTTG	0.619																																					p.E13delinsVME		Atlas-Indel,Pindel	.											.	FTCD	59	.	0			c.38_39insTTATGG						.																																			SO:0001652	inframe_insertion	10841	exon1			.	U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"formiminotransferase cyclodeaminase"			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.37_38insTTATGG	chr21.hg19:g.47575400_47575401insCCATAA	ENSP00000291670:p.Ser12_Glu13insValMet	100.0	0.0		82.0	11.0	NM_206965	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	In_Frame_Ins	INS	ENST00000291670.5	hg19	CCDS13731.1																																																																																			.	.		0.619	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657		CCATAA	47575401	-	CCATAA	47575400	7	5	111	1	0	1	1	0	0	0	0	0	6089	1551	54	0	1643	0	FTCD	21	47575400	In_Frame_Ins	INS	-	TCGA-DD-A39X-01A-11D-A20W-10	3094840	47575400	554495	361	16601										
PCNT	5116	hgsc.bcm.edu	37	chr21	47817283	47817283	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cccagatgaagattttggagTctgagttagaagaacagctg	12	6	1	6			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr21:47817283T>G	ENST00000359568.5	+	22	4428	c.4321T>G	c.(4321-4323)Tct>Gct	p.S1441A	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1441					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GATTTTGGAGTCTGAGTTAGA	0.567																																					p.S1441A		Atlas-SNP	.											.	PCNT	283	.	0			c.T4321G						.						74	73	73					21																	47817283		2203	4300	6503	SO:0001583	missense	5116	exon22			TTGGAGTCTGAGT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.4321T>G	chr21.hg19:g.47817283T>G	ENSP00000352572:p.Ser1441Ala	95.0	0.0		78.0	4.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	T	1.323	-0.598815	0.03744	.	.	ENSG00000160299	ENST00000359568	T	0.56941	0.43	5.46	-3.1	0.05315	.	1.087950	0.07372	N	0.885968	T	0.16342	0.0393	N	0.02111	-0.68	0.09310	N	1	B;B	0.12630	0.001;0.006	B;B	0.08055	0.003;0.001	T	0.23511	-1.0186	10	0.06625	T	0.88	.	0.7064	0.00917	0.2208:0.2678:0.2895:0.2219	.	1323;1441	O95613-2;O95613	.;PCNT_HUMAN	A	1441	ENSP00000352572:S1441A	ENSP00000352572:S1441A	S	+	1	0	PCNT	46641711	0.009000	0.17119	0.011000	0.14972	0.001000	0.01503	-0.062000	0.11674	-0.172000	0.10779	-0.444000	0.05651	TCT	.	.		0.567	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		G	47817283	T	G	47817283	3	3	111	1	0	0	0	0	1	0	0	0	11599	1667	58	5	4407	5	PCNT	21	47817283	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	241883	47817283	312612	362	16602										
EIF4ENIF1	56478	hgsc.bcm.edu	37	chr22	31846327	31846327	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gaatctcagcaggggacatcAaatggctttcaaggtttcgc	11	9	3	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr22:31846327A>G	ENST00000397525.1	-	11	1755	c.1532T>C	c.(1531-1533)tTg>tCg	p.L511S	EIF4ENIF1_ENST00000344710.5_Missense_Mutation_p.L336S|EIF4ENIF1_ENST00000330125.5_Missense_Mutation_p.L511S|EIF4ENIF1_ENST00000382180.2_Intron|EIF4ENIF1_ENST00000397523.1_Intron	NM_001164501.1	NP_001157973.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	511						cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AGGGGACATCAAATGGCTTTC	0.423																																					p.L511S		Atlas-SNP	.											.	EIF4ENIF1	80	.	0			c.T1532C						.						132	133	132					22																	31846327		2203	4300	6503	SO:0001583	missense	56478	exon11			GACATCAAATGGC	AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708			16687	protein-coding gene	gene with protein product		607445				10856257	Standard	NM_019843		Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000397525.1:c.1532T>C	chr22.hg19:g.31846327A>G	ENSP00000380659:p.Leu511Ser	99.0	0.0		83.0	4.0	NM_019843	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	Missense_Mutation	SNP	ENST00000397525.1	hg19	CCDS13898.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.943527	0.73672	.	.	ENSG00000184708	ENST00000344710;ENST00000397525;ENST00000330125;ENST00000418321	.	.	.	5.74	5.74	0.90152	.	0.312066	0.30076	N	0.010468	T	0.65291	0.2677	L	0.48642	1.525	0.80722	D	1	D;D;D	0.61697	0.99;0.959;0.974	P;P;P	0.62491	0.903;0.783;0.647	T	0.59511	-0.7441	9	0.13108	T	0.6	-7.4625	15.2313	0.73390	1.0:0.0:0.0:0.0	.	336;511;336	B1AKL3;Q9NRA8;Q9NRA8-2	.;4ET_HUMAN;.	S	336;511;511;109	.	ENSP00000328103:L511S	L	-	2	0	EIF4ENIF1	30176327	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.156000	0.71840	2.197000	0.70478	0.528000	0.53228	TTG	.	.		0.423	EIF4ENIF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127926.1	NM_019843		G	31846327	A	G	31846327	3	3	111	1	0	0	0	0	1	0	0	0	5037	131	5	2	1464	2	EIF4ENIF1	22	31846327	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10		31846327	19458239	363	16603										
KCTD17	79734	hgsc.bcm.edu	37	chr22	37453518	37453518	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gtctccaccatgtctgatggCtggcgcttcgagcaggtgcg	14	12	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr22:37453518C>T	ENST00000403888.3	+	4	493	c.492C>T	c.(490-492)ggC>ggT	p.G164G	RN7SKP214_ENST00000364208.1_RNA|KCTD17_ENST00000402077.3_Silent_p.G164G	NM_001282684.1	NP_001269613.1	Q8N5Z5	KCD17_HUMAN	potassium channel tetramerization domain containing 17	164					protein homooligomerization (GO:0051260)		identical protein binding (GO:0042802)			NS(1)|breast(1)|endometrium(1)|lung(1)|prostate(1)	5						TGTCTGATGGCTGGCGCTTCG	0.652																																					p.G164G		Atlas-SNP	.											.	KCTD17	17	.	0			c.C492T						.						82	63	69					22																	37453518		2203	4300	6503	SO:0001819	synonymous_variant	79734	exon4			TGATGGCTGGCGC	BC025403	CCDS13940.2, CCDS74854.1, CCDS74855.1	22q12.3	2013-06-20	2013-06-20		ENSG00000100379	ENSG00000100379			25705	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 17"			12477932	Standard	XM_005261741		Approved	FLJ12242	uc011amv.2	Q8N5Z5	OTTHUMG00000150532	ENST00000403888.3:c.492C>T	chr22.hg19:g.37453518C>T		75.0	0.0		46.0	4.0	NM_024681	B0QYA9|B0QYB0|O95517	Silent	SNP	ENST00000403888.3	hg19		.	.	.	.	.	.	.	.	.	.	C	10.04	1.242295	0.22796	.	.	ENSG00000100379	ENST00000456470	.	.	.	4.46	2.28	0.28536	.	.	.	.	.	T	0.55689	0.1936	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49771	-0.8904	4	.	.	.	-0.2577	7.7435	0.28856	0.3389:0.5772:0.0:0.0839	.	.	.	.	V	119	.	.	A	+	2	0	KCTD17	35783464	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	2.135000	0.42112	0.837000	0.34925	0.407000	0.27541	GCT	.	.		0.652	KCTD17-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318781.1	NM_024681		T	37453518	C	T	37453518	2	4	111	1	0	0	0	0	0	0	0	1	8113	784	28	3		3	KCTD17	22	37453518	Silent	SNP	C	TCGA-DD-A39X-01A-11D-A20W-10	5607191	37453518	13851048	364	16604										
KLHDC7B	113730	hgsc.bcm.edu	37	chr22	50987911	50987911	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gccactccccgcaggcacctTccctgtggcccacgaggctg	11	19	0	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chr22:50987911T>C	ENST00000395676.2	+	1	1450	c.1316T>C	c.(1315-1317)tTc>tCc	p.F439S	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	439										central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	14		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GCAGGCACCTTCCCTGTGGCC	0.657																																					p.F439S		Atlas-SNP	.											.	KLHDC7B	39	.	0			c.T1316C						.						69	72	71					22																	50987911		2200	4299	6499	SO:0001583	missense	113730	exon1			GCACCTTCCCTGT	BC009980	CCDS14097.2	22q13.33	2006-11-29		2005-12-13	ENSG00000130487	ENSG00000130487			25145	protein-coding gene	gene with protein product							Standard	NM_138433		Approved	MGC16635	uc003bmi.3	Q96G42	OTTHUMG00000150250	ENST00000395676.2:c.1316T>C	chr22.hg19:g.50987911T>C	ENSP00000379034:p.Phe439Ser	97.0	0.0		73.0	4.0	NM_138433		Missense_Mutation	SNP	ENST00000395676.2	hg19	CCDS14097.2	.	.	.	.	.	.	.	.	.	.	T	23.7	4.446523	0.84101	.	.	ENSG00000130487	ENST00000395676	T	0.65178	-0.14	5.35	5.35	0.76521	Kelch-type beta propeller (1);	0.000000	0.43747	U	0.000535	T	0.77418	0.4127	M	0.80183	2.485	0.39199	D	0.963114	D	0.89917	1.0	D	0.83275	0.996	T	0.76849	-0.2807	10	0.17832	T	0.49	.	13.277	0.60191	0.0:0.0:0.0:1.0	.	439	Q96G42	KLD7B_HUMAN	S	439	ENSP00000379034:F439S	ENSP00000379034:F439S	F	+	2	0	KLHDC7B	49334777	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.330000	0.52068	2.044000	0.60594	0.402000	0.26972	TTC	.	.		0.657	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433		C	50987911	T	C	50987911	3	2	111	1	0	0	0	0	1	0	0	0	8370	1783	62	2	1318	2	KLHDC7B	22	50987911	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	13534393	50987911	316655	365	16605										
TLR7	51284	hgsc.bcm.edu	37	chrX	12904278	12904278	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctgaaagataacaatgtcacAgccgtccctactgttttgcc	7	12	1	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:12904278A>G	ENST00000380659.3	+	3	790	c.651A>G	c.(649-651)acA>acG	p.T217T		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	217					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	ACAATGTCACAGCCGTCCCTA	0.338																																					p.T217T		Atlas-SNP	.											.	TLR7	125	.	0			c.A651G						.						66	62	63					X																	12904278		2203	4300	6503	SO:0001819	synonymous_variant	51284	exon3			TGTCACAGCCGTC	AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.651A>G	chrX.hg19:g.12904278A>G		134.0	0.0		97.0	4.0	NM_016562	D1CS69|Q9NR98	Silent	SNP	ENST00000380659.3	hg19	CCDS14151.1																																																																																			.	.		0.338	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		G	12904278	A	G	12904278	2	3	111	1	0	0	0	0	0	0	0	1	15971	175	7	2		2	TLR7	23	12904278	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10		12904278	142366282	366	16606										
TLR7	51284	hgsc.bcm.edu	37	chrX	12905003	12905003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	agaaagttatgaaccccaggTcctggaacaattacattatt	7	8	0	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:12905003T>C	ENST00000380659.3	+	3	1515	c.1376T>C	c.(1375-1377)gTc>gCc	p.V459A		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	459					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	GAACCCCAGGTCCTGGAACAA	0.368																																					p.V459A		Atlas-SNP	.											.	TLR7	125	.	0			c.T1376C						.						75	80	78					X																	12905003		2199	4294	6493	SO:0001583	missense	51284	exon3			CCCAGGTCCTGGA	AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.1376T>C	chrX.hg19:g.12905003T>C	ENSP00000370034:p.Val459Ala	69.0	0.0		69.0	4.0	NM_016562	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	hg19	CCDS14151.1	.	.	.	.	.	.	.	.	.	.	T	0.516	-0.864165	0.02590	.	.	ENSG00000196664	ENST00000380659	T	0.39406	1.08	5.51	4.34	0.51931	.	0.491077	0.19300	N	0.117675	T	0.36054	0.0953	L	0.52759	1.655	0.09310	N	1	B	0.15930	0.015	B	0.14578	0.011	T	0.32052	-0.9921	10	0.56958	D	0.05	.	8.0509	0.30577	0.0:0.1593:0.0:0.8407	.	459	Q9NYK1	TLR7_HUMAN	A	459	ENSP00000370034:V459A	ENSP00000370034:V459A	V	+	2	0	TLR7	12814924	0.213000	0.23551	0.006000	0.13384	0.007000	0.05969	3.543000	0.53633	0.833000	0.34828	0.486000	0.48141	GTC	.	.		0.368	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		C	12905003	T	C	12905003	3	2	111	1	0	0	0	0	1	0	0	0	15971	1667	58	2	1382	2	TLR7	23	12905003	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	725	12905003	142365557	367	16607										
ZFX	7543	hgsc.bcm.edu	37	chrX	24197777	24197777	+	Missense_Mutation	SNP	A	A	T													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	taccgacgtagtttcagaagAagtattggtagcagactgtg							TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:24197777A>T	ENST00000379177.1	+	6	963	c.536A>T	c.(535-537)gAa>gTa	p.E179V	ZFX_ENST00000379188.3_Missense_Mutation_p.E179V|ZFX_ENST00000459724.1_Intron|ZFX_ENST00000539115.1_Intron|ZFX_ENST00000304543.5_Missense_Mutation_p.E179V|ZFX_ENST00000540034.1_Missense_Mutation_p.E218V|ZFX_ENST00000338565.3_Missense_Mutation_p.E179V	NM_001178085.1|NM_003410.3	NP_001171556.1|NP_003401.2	P17010	ZFX_HUMAN	zinc finger protein, X-linked	179					death (GO:0016265)|fertilization (GO:0009566)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|parental behavior (GO:0060746)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|prostate(1)	24						GTTTCAGAAGAAGTATTGGTA	0.463																																					p.E179V	Esophageal Squamous(20;306 562 7346 32868 37983)	Atlas-SNP	.											.	ZFX	61	.	0			c.A536T						.						191	165	174					X																	24197777		2203	4300	6503	SO:0001583	missense	7543	exon5			CAGAAGAAGTATT		CCDS14211.1, CCDS55390.1	Xp22.1-p21.3	2013-01-08			ENSG00000005889	ENSG00000005889		"Zinc fingers, C2H2-type"	12869	protein-coding gene	gene with protein product		314980					Standard	NM_003410		Approved	ZNF926	uc022bua.1	P17010	OTTHUMG00000021264	ENST00000379177.1:c.536A>T	chrX.hg19:g.24197777A>T	ENSP00000368475:p.Glu179Val	129.0	0.0		89.0	7.0	NM_003410	B9EG97|O43668|Q8WYJ8	Missense_Mutation	SNP	ENST00000379177.1	hg19	CCDS14211.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.157264	0.78114	.	.	ENSG00000005889	ENST00000379188;ENST00000536464;ENST00000379177;ENST00000304543;ENST00000540034;ENST00000338565	T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48	5.97	5.97	0.96955	Transcriptional activator, Zfx / Zfy domain (1);	0.000000	0.64402	D	0.000001	T	0.72120	0.3421	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.997;1.0	D;D;D;D	0.80764	0.98;0.982;0.994;0.985	T	0.73490	-0.3966	9	.	.	.	-7.0613	15.388	0.74718	1.0:0.0:0.0:0.0	.	218;179;179;183	B9EG97;F5H6Z8;P17010;Q59EB9	.;.;ZFX_HUMAN;.	V	179;179;179;179;218;179	ENSP00000368486:E179V;ENSP00000368475:E179V;ENSP00000304985:E179V;ENSP00000441382:E218V;ENSP00000343384:E179V	.	E	+	2	0	ZFX	24107698	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.402000	0.73260	2.018000	0.59344	0.486000	0.48141	GAA	.	.		0.463	ZFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056084.1	NM_003410		T	24197777	A	T	24197777	3	4	111	1	0	0	0	0	1	0	0	0	17676	246	9	4	542	4	ZFX	23	24197777	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	11292774	24197777	131072783	368	16608	75	2								
ZFX	7543	hgsc.bcm.edu	37	chrX	24197779	24197779	+	Missense_Mutation	SNP	G	G	T													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccgacgtagtttcagaagaaGtattggtagcagactgtgcc							TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:24197779G>T	ENST00000379177.1	+	6	965	c.538G>T	c.(538-540)Gta>Tta	p.V180L	ZFX_ENST00000379188.3_Missense_Mutation_p.V180L|ZFX_ENST00000459724.1_Intron|ZFX_ENST00000539115.1_Intron|ZFX_ENST00000304543.5_Missense_Mutation_p.V180L|ZFX_ENST00000540034.1_Missense_Mutation_p.V219L|ZFX_ENST00000338565.3_Missense_Mutation_p.V180L	NM_001178085.1|NM_003410.3	NP_001171556.1|NP_003401.2	P17010	ZFX_HUMAN	zinc finger protein, X-linked	180					death (GO:0016265)|fertilization (GO:0009566)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|parental behavior (GO:0060746)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|prostate(1)	24						TTCAGAAGAAGTATTGGTAGC	0.458																																					p.V180L	Esophageal Squamous(20;306 562 7346 32868 37983)	Atlas-SNP	.											.	ZFX	61	.	0			c.G538T						.						191	166	174					X																	24197779		2203	4300	6503	SO:0001583	missense	7543	exon5			GAAGAAGTATTGG		CCDS14211.1, CCDS55390.1	Xp22.1-p21.3	2013-01-08			ENSG00000005889	ENSG00000005889		"Zinc fingers, C2H2-type"	12869	protein-coding gene	gene with protein product		314980					Standard	NM_003410		Approved	ZNF926	uc022bua.1	P17010	OTTHUMG00000021264	ENST00000379177.1:c.538G>T	chrX.hg19:g.24197779G>T	ENSP00000368475:p.Val180Leu	130.0	0.0		88.0	6.0	NM_003410	B9EG97|O43668|Q8WYJ8	Missense_Mutation	SNP	ENST00000379177.1	hg19	CCDS14211.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.119223	0.77323	.	.	ENSG00000005889	ENST00000379188;ENST00000536464;ENST00000379177;ENST00000304543;ENST00000540034;ENST00000338565	T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49	5.97	5.12	0.69794	Transcriptional activator, Zfx / Zfy domain (1);	0.000000	0.64402	D	0.000012	T	0.68375	0.2994	L	0.61387	1.9	0.80722	D	1	P;D;D;D	0.56521	0.934;0.976;0.967;0.959	P;P;D;P	0.70716	0.677;0.793;0.97;0.734	T	0.68183	-0.5476	9	.	.	.	-9.7366	14.2222	0.65836	0.0728:0.0:0.9272:0.0	.	219;180;180;184	B9EG97;F5H6Z8;P17010;Q59EB9	.;.;ZFX_HUMAN;.	L	180;180;180;180;219;180	ENSP00000368486:V180L;ENSP00000368475:V180L;ENSP00000304985:V180L;ENSP00000441382:V219L;ENSP00000343384:V180L	.	V	+	1	0	ZFX	24107700	1.000000	0.71417	0.987000	0.45799	0.998000	0.95712	6.766000	0.74970	1.284000	0.44531	0.600000	0.82982	GTA	.	.		0.458	ZFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056084.1	NM_003410		T	24197779	G	T	24197779	3	4	111	1	0	0	0	0	1	0	0	0	17676	1029	36	3	544	3	ZFX	23	24197779	Missense_Mutation	SNP	G	TCGA-DD-A39X-01A-11D-A20W-10	2	24197779	131072781	369	16609	75	2								
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53310699	53310699	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tgctgctcctcccggggggcTccatgggtctggacctgtcc	14	15	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:53310699T>C	ENST00000375368.5	-	2	908				IQSEC2_ENST00000396435.3_Intron|IQSEC2_ENST00000375365.2_Missense_Mutation_p.E2G|IQSEC2_ENST00000462054.1_5'UTR			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2						actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						CCCGGGGGGCTCCATGGGTCT	0.697																																					p.E2G		Atlas-SNP	.											.	IQSEC2	195	.	0			c.A5G						.						7	7	7					X																	53310699		1842	3610	5452	SO:0001627	intron_variant	23096	exon1			GGGGGCTCCATGG	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.708-25456A>G	chrX.hg19:g.53310699T>C		211.0	0.0		113.0	6.0	NM_015075	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	t	18.77	3.695070	0.68386	.	.	ENSG00000124313	ENST00000375365	T	0.11712	2.75	4.79	4.79	0.61399	.	.	.	.	.	T	0.09598	0.0236	.	.	.	0.80722	D	1	B	0.30281	0.275	B	0.24848	0.056	T	0.08534	-1.0717	8	0.62326	D	0.03	.	9.7252	0.40328	0.0:0.0:0.0:1.0	.	2	Q5JU85-3	.	G	2	ENSP00000364514:E2G	ENSP00000364514:E2G	E	-	2	0	IQSEC2	53327424	0.989000	0.36119	0.899000	0.35326	0.705000	0.40729	1.948000	0.40303	1.899000	0.54978	0.483000	0.47432	GAG	.	.		0.697	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		C	53310699	T	C	53310699	1	2	111	0	1	0	0	0	0	0	0	0	7827	1551	54	2		2	IQSEC2	23	53310699	Intron	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	29112920	53310699	101959861	370	16610										
AR	367	hgsc.bcm.edu	37	chrX	66765176	66765176	+	Missense_Mutation	SNP	A	A	T													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gctgcagcagcagcagcagcAgcagcagcagcagcagcagc					rs62636527		TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:66765176A>T	ENST00000374690.3	+	1	712	c.188A>T	c.(187-189)cAg>cTg	p.Q63L	AR_ENST00000396044.3_Missense_Mutation_p.Q63L|AR_ENST00000513847.1_3'UTR|AR_ENST00000504326.1_Missense_Mutation_p.Q63L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	63	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.672									Androgen Insensitivity Syndrome																												p.Q63L		Atlas-SNP	.											.	AR	249	.	0			c.A188T						.						5	8	7					X																	66765176		1640	3236	4876	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.188A>T	chrX.hg19:g.66765176A>T	ENSP00000363822:p.Gln63Leu	72.0	0.0		62.0	10.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.08	1.532203	0.27387	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.78246	-1.16;-1.16;-1.16	.	.	.	.	0.479323	0.15343	U	0.267412	T	0.62624	0.2443	N	0.19112	0.55	0.09310	N	0.999992	P;D;.	0.58268	0.755;0.982;.	B;P;.	0.48627	0.089;0.584;.	T	0.56408	-0.7984	8	0.17832	T	0.49	.	.	.	.	rs62636527	63;63;61	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	63	ENSP00000363822:Q63L;ENSP00000421155:Q63L;ENSP00000379359:Q63L	ENSP00000363822:Q63L	Q	+	2	0	AR	66681901	0.810000	0.29049	0.871000	0.34182	0.555000	0.35460	1.078000	0.30754	0.000000	0.14550	0.000000	0.15137	CAG	.	A|0.982;T|0.018		0.672	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765176	A	T	66765176	3	4	111	1	0	0	0	0	1	0	0	0	836	188	7	4	190	4	AR	23	66765176	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	13454477	66765176	88505384	371	16611	76	2								
AR	367	hgsc.bcm.edu	37	chrX	66765179	66765179	+	Missense_Mutation	SNP	A	A	T													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gcagcagcagcagcagcagcAgcagcagcagcagcagcagc							TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:66765179A>T	ENST00000374690.3	+	1	715	c.191A>T	c.(190-192)cAg>cTg	p.Q64L	AR_ENST00000396044.3_Missense_Mutation_p.Q64L|AR_ENST00000513847.1_3'UTR|AR_ENST00000504326.1_Missense_Mutation_p.Q64L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	64	Gln-rich.|Modulating.|Poly-Gln.		Q -> R (in prostate cancer).		androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q64L		Atlas-SNP	.											.	AR	249	.	0			c.A191T						.						4	8	7					X																	66765179		1590	3143	4733	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.191A>T	chrX.hg19:g.66765179A>T	ENSP00000363822:p.Gln64Leu	69.0	0.0		69.0	14.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.28	1.591655	0.28357	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.67865	-0.29;-0.29;-0.29	.	.	.	.	1.847110	0.03494	N	0.217131	T	0.56124	0.1964	N	0.19112	0.55	0.09310	N	0.999991	P;D;.	0.58268	0.755;0.982;.	B;P;.	0.48627	0.089;0.584;.	T	0.50381	-0.8835	8	0.38643	T	0.18	.	.	.	.	.	64;64;62	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	64	ENSP00000363822:Q64L;ENSP00000421155:Q64L;ENSP00000379359:Q64L	ENSP00000363822:Q64L	Q	+	2	0	AR	66681904	0.024000	0.19004	0.883000	0.34634	0.574000	0.36063	-0.145000	0.10265	0.000000	0.14550	0.000000	0.15137	CAG	.	.		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765179	A	T	66765179	3	4	111	1	0	0	0	0	1	0	0	0	836	188	7	4	193	4	AR	23	66765179	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	3	66765179	88505381	372	16612	76	2								
STARD8	9754	hgsc.bcm.edu	37	chrX	67936251	67936251	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ttgtgcctcgatgaaactggAggttcattttcaaagcaagc	10	8	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:67936251A>G	ENST00000252336.6	+	4	407	c.35A>G	c.(34-36)gAg>gGg	p.E12G	STARD8_ENST00000374599.3_Missense_Mutation_p.E92G|STARD8_ENST00000374597.3_Missense_Mutation_p.E12G	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	12					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	50						ATGAAACTGGAGGTTCATTTT	0.488																																					p.E92G		Atlas-SNP	.											.	STARD8	282	.	0			c.A275G						.						142	114	124					X																	67936251		2203	4300	6503	SO:0001583	missense	9754	exon5			AACTGGAGGTTCA	D80011	CCDS14390.1, CCDS48134.1	Xq13.1	2011-09-13	2007-08-16		ENSG00000130052	ENSG00000130052		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19161	protein-coding gene	gene with protein product		300689	"START domain containing 8"			8724849	Standard	NM_001142504		Approved	KIAA0189, ARHGAP38	uc004dxb.3	Q92502	OTTHUMG00000021748	ENST00000252336.6:c.35A>G	chrX.hg19:g.67936251A>G	ENSP00000252336:p.Glu12Gly	117.0	0.0		94.0	4.0	NM_001142503	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Missense_Mutation	SNP	ENST00000252336.6	hg19	CCDS14390.1	.	.	.	.	.	.	.	.	.	.	a	22.6	4.307817	0.81247	.	.	ENSG00000130052	ENST00000252336;ENST00000374599;ENST00000374597	T;T;T	0.41758	2.52;0.99;2.52	3.79	3.79	0.43588	.	0.000000	0.64402	D	0.000001	T	0.47728	0.1461	M	0.82630	2.6	0.37676	D	0.923312	P;P	0.40534	0.72;0.455	B;B	0.41036	0.346;0.188	T	0.61476	-0.7055	10	0.87932	D	0	.	9.8886	0.41276	1.0:0.0:0.0:0.0	.	92;12	Q92502-2;Q92502	.;STAR8_HUMAN	G	12;92;12	ENSP00000252336:E12G;ENSP00000363727:E92G;ENSP00000363725:E12G	ENSP00000252336:E12G	E	+	2	0	STARD8	67852976	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.857000	0.75455	1.524000	0.49035	0.483000	0.47432	GAG	.	.		0.488	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725		G	67936251	A	G	67936251	3	3	111	1	0	0	0	0	1	0	0	0	15278	304	11	2	293	2	STARD8	23	67936251	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1171072	67936251	87334309	373	16613										
ABCB7	22	hgsc.bcm.edu	37	chrX	74295254	74295254	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ggaagaagattaaataccaaAgcactcaggacaaaactgat	8	7	1	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:74295254A>G	ENST00000373394.3	-	6	805	c.798T>C	c.(796-798)gcT>gcC	p.A266A	ABCB7_ENST00000339447.4_Silent_p.A226A|ABCB7_ENST00000253577.3_Silent_p.A267A|ABCB7_ENST00000534570.1_5'Flank			O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 7	266	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)			breast(1)|endometrium(5)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)	20						TAAATACCAAAGCACTCAGGA	0.388																																					p.A267A		Atlas-SNP	.											.	ABCB7	69	.	0			c.T801C						.						110	93	99					X																	74295254		2203	4300	6503	SO:0001819	synonymous_variant	22	exon6			TACCAAAGCACTC	AF038950	CCDS14428.1, CCDS65290.1, CCDS65291.1, CCDS75994.1	Xq13.3	2012-03-14			ENSG00000131269	ENSG00000131269		"ATP binding cassette transporters / subfamily B"	48	protein-coding gene	gene with protein product		300135		ABC7		9143506	Standard	NM_004299		Approved	EST140535, Atm1p, ASAT	uc004ebz.4	O75027	OTTHUMG00000021862	ENST00000373394.3:c.798T>C	chrX.hg19:g.74295254A>G		157.0	0.0		137.0	6.0	NM_004299	G3XAC4|O75345|Q5VWY7|Q5VWY8|Q9BRE1|Q9UND1|Q9UP01	Silent	SNP	ENST00000373394.3	hg19																																																																																				.	.		0.388	ABCB7-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000057274.1	NM_004299		G	74295254	A	G	74295254	2	3	111	1	0	0	0	0	0	0	0	1	46	59	3	2		2	ABCB7	23	74295254	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	6359003	74295254	80975306	374	16614										
HMGN5	79366	hgsc.bcm.edu	37	chrX	80371833	80371833	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ccatcatatcactttttgtcTtcattttctgccaagcaata	3	11	5	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:80371833T>C	ENST00000358130.2	-	6	465	c.137A>G	c.(136-138)aAg>aGg	p.K46R	HMGN5_ENST00000491275.1_5'UTR	NM_030763.2	NP_110390.1	P82970	HMGN5_HUMAN	high mobility group nucleosome binding domain 5	46					chromatin modification (GO:0016568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	10						ACTTTTTGTCTTCATTTTCTG	0.318																																					p.K46R		Atlas-SNP	.											.	HMGN5	29	.	0			c.A137G						.						106	81	89					X																	80371833		2202	4298	6500	SO:0001583	missense	79366	exon6			TTTGTCTTCATTT	AF250329	CCDS14448.1	Xq13.3	2011-07-01	2011-04-05	2009-09-15	ENSG00000198157	ENSG00000198157		"High-mobility group / Canonical"	8013	protein-coding gene	gene with protein product		300385	"nucleosomal binding protein 1", "high-mobility group nucleosome binding domain 5"	NSBP1		11161810, 19748358	Standard	NM_030763		Approved		uc004eee.1	P82970	OTTHUMG00000021911	ENST00000358130.2:c.137A>G	chrX.hg19:g.80371833T>C	ENSP00000350848:p.Lys46Arg	102.0	0.0		81.0	4.0	NM_030763	Q5JSL1	Missense_Mutation	SNP	ENST00000358130.2	hg19	CCDS14448.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.857822	0.32791	.	.	ENSG00000198157	ENST00000358130;ENST00000447319;ENST00000373250;ENST00000430960;ENST00000436386;ENST00000451455	.	.	.	4.64	3.43	0.39272	.	0.000000	0.34291	U	0.004091	T	0.63558	0.2521	M	0.73598	2.24	0.09310	N	1	D	0.89917	1.0	D	0.75020	0.985	T	0.55147	-0.8186	9	0.87932	D	0	.	7.9301	0.29897	0.1855:0.0:0.0:0.8145	.	46	P82970	HMGN5_HUMAN	R	46;26;36;46;46;46	.	ENSP00000350848:K46R	K	-	2	0	HMGN5	80258489	1.000000	0.71417	0.109000	0.21407	0.014000	0.08584	2.414000	0.44627	0.672000	0.31204	0.441000	0.28932	AAG	.	.		0.318	HMGN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057354.1	NM_030763		C	80371833	T	C	80371833	3	2	111	1	0	0	0	0	1	0	0	0	7247	1609	56	2	719	2	HMGN5	23	80371833	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	6076579	80371833	74898727	375	16615										
BHLHB9	80823	hgsc.bcm.edu	37	chrX	102004756	102004756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	tcgctcatgctcacagcctaTccctgagtgtcgttttgatt	8	12	2	2			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:102004756T>C	ENST00000372735.1	+	4	1418	c.833T>C	c.(832-834)aTc>aCc	p.I278T	BHLHB9_ENST00000361229.4_Missense_Mutation_p.I278T|BHLHB9_ENST00000457056.1_Missense_Mutation_p.I278T|BHLHB9_ENST00000448867.1_Missense_Mutation_p.I278T|BHLHB9_ENST00000447531.1_Missense_Mutation_p.I278T			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	278					learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TCACAGCCTATCCCTGAGTGT	0.483																																					p.I278T		Atlas-SNP	.											.	BHLHB9	60	.	0			c.T833C						.						74	67	69					X																	102004756		2203	4300	6503	SO:0001583	missense	80823	exon2			AGCCTATCCCTGA	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"Basic helix-loop-helix proteins", "Armadillo repeat containing"	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.833T>C	chrX.hg19:g.102004756T>C	ENSP00000361820:p.Ile278Thr	122.0	0.0		87.0	4.0	NM_001142530	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	hg19	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.731761	0.00687	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77	4.47	2.02	0.26589	.	0.848237	0.10046	N	0.722893	T	0.08802	0.0218	L	0.44542	1.39	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.40831	-0.9542	9	.	.	.	-2.8756	3.9496	0.09363	0.0:0.1123:0.2117:0.6759	.	278	Q6PI77	BHLH9_HUMAN	T	278	ENSP00000403226:I278T;ENSP00000354675:I278T;ENSP00000405893:I278T;ENSP00000391722:I278T;ENSP00000361820:I278T	.	I	+	2	0	BHLHB9	101891412	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.886000	0.28241	0.289000	0.22422	-0.360000	0.07572	ATC	.	.		0.483	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639		C	102004756	T	C	102004756	3	2	111	1	0	0	0	0	1	0	0	0	1420	1435	50	2	835	2	BHLHB9	23	102004756	Missense_Mutation	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	21632923	102004756	53265804	376	16616										
RBM41	55285	hgsc.bcm.edu	37	chrX	106358785	106358785	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gagttgccctcagttttgtcTtctgaaaccagaggaatgag	11	8	3	3			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:106358785T>C	ENST00000372479.3	-	4	350	c.320A>G	c.(319-321)aAg>aGg	p.K107R	RBM41_ENST00000471079.1_5'UTR|RBM41_ENST00000203616.8_Splice_Site_p.K107R|RBM41_ENST00000372487.1_Splice_Site_p.K107R	NM_018301.3	NP_060771.3	Q96IZ5	RBM41_HUMAN	RNA binding motif protein 41	107							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	13						CAGTTTTGTCTTCTGAAACCA	0.453																																					p.K107R		Atlas-SNP	.											.	RBM41	34	.	0			c.A320G						.						88	75	80					X																	106358785		2203	4299	6502	SO:0001630	splice_region_variant	55285	exon4			TTTGTCTTCTGAA	BC006986	CCDS14526.1, CCDS55472.1	Xq22.3	2013-02-12			ENSG00000089682	ENSG00000089682		"RNA binding motif (RRM) containing"	25617	protein-coding gene	gene with protein product						12477932	Standard	NM_001171080		Approved	FLJ11016	uc004emz.3	Q96IZ5	OTTHUMG00000022156	ENST00000372479.3:c.319-1A>G	chrX.hg19:g.106358785T>C		127.0	0.0		99.0	4.0	NM_001171080	Q5JSN7|Q5JSN8|Q9H8F7|Q9NV04	Missense_Mutation	SNP	ENST00000372479.3	hg19	CCDS14526.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.907961	0.00508	.	.	ENSG00000089682	ENST00000372487;ENST00000372479;ENST00000203616;ENST00000372482	T;T	0.22336	1.96;1.96	5.33	1.18	0.20946	.	0.774613	0.12942	N	0.426559	T	0.06917	0.0176	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40831	-0.9542	10	0.05525	T	0.97	.	7.1784	0.25757	0.0:0.5384:0.0:0.4616	.	107	Q96IZ5	RBM41_HUMAN	R	107	ENSP00000361565:K107R;ENSP00000361557:K107R	ENSP00000203616:K107R	K	-	2	0	RBM41	106245441	0.919000	0.31177	0.230000	0.23976	0.307000	0.27823	1.022000	0.30052	-0.220000	0.09988	0.381000	0.24937	AAG	.	.		0.453	RBM41-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057819.1	NM_018301	Missense_Mutation	C	106358785	T	C	106358785	5	2	111	1	0	0	0	0	0	0	1	0	13150	1623	56	2	946	2	RBM41	23	106358785	Splice_Site	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	4354029	106358785	48911775	377	16617										
GUCY2F	2986	hgsc.bcm.edu	37	chrX	108619161	108619161	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	ctcaccaactgcctttctgcTtttcttctttggaaggctgc	7	13	4	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:108619161T>C	ENST00000218006.2	-	19	3585	c.3294A>G	c.(3292-3294)aaA>aaG	p.K1098K		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	1098					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						GCCTTTCTGCTTTTCTTCTTT	0.502																																					p.K1098K		Atlas-SNP	.											.	GUCY2F	178	.	0			c.A3294G						.						177	143	155					X																	108619161		2203	4300	6503	SO:0001819	synonymous_variant	2986	exon19			TTCTGCTTTTCTT	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.3294A>G	chrX.hg19:g.108619161T>C		155.0	0.0		113.0	5.0	NM_001522	Q9UJF1	Silent	SNP	ENST00000218006.2	hg19	CCDS14545.1																																																																																			.	.		0.502	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		C	108619161	T	C	108619161	2	2	111	1	0	0	0	0	0	0	0	1	6907	1606	56	2		2	GUCY2F	23	108619161	Silent	SNP	T	TCGA-DD-A39X-01A-11D-A20W-10	2260376	108619161	46651399	378	16618										
CAPN6	827	hgsc.bcm.edu	37	chrX	110490683	110490683	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	actgtattcttctggacaggAgaacggacttcctcctttcc	8	12	2	1			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:110490683A>G	ENST00000324068.1	-	12	1823	c.1656T>C	c.(1654-1656)tcT>tcC	p.S552S	CAPN6_ENST00000541758.1_Silent_p.S297S	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	552	C2.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						TCTGGACAGGAGAACGGACTT	0.393																																					p.S552S		Atlas-SNP	.											.	CAPN6	120	.	0			c.T1656C						.						152	129	137					X																	110490683		2203	4300	6503	SO:0001819	synonymous_variant	827	exon12			GACAGGAGAACGG	AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.1656T>C	chrX.hg19:g.110490683A>G		148.0	0.0		113.0	5.0	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Silent	SNP	ENST00000324068.1	hg19	CCDS14555.1																																																																																			.	.		0.393	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			G	110490683	A	G	110490683	2	3	111	1	0	0	0	0	0	0	0	1	2632	291	11	2		2	CAPN6	23	110490683	Silent	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	1871522	110490683	44779877	379	16619										
LDOC1	23641	hgsc.bcm.edu	37	chrX	140270987	140270987	+	Frame_Shift_Del	DEL	A	A	-													0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	gttctcgttcacgagcatgtAagacgccgtctgcacgataa							TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:140270987delA	ENST00000370526.2	-	1	323	c.220delT	c.(220-222)tacfs	p.Y74fs	LDOC1_ENST00000460721.1_Intron	NM_012317.2	NP_036449.1	O95751	LDOC1_HUMAN	leucine zipper, down-regulated in cancer 1	74					negative regulation of cell proliferation (GO:0008285)	nucleus (GO:0005634)				endometrium(6)|large_intestine(1)|lung(6)|ovary(1)	14	Acute lymphoblastic leukemia(192;7.65e-05)					ACGAGCATGTAAGACGCCGTC	0.617																																					p.Y74fs		Atlas-Indel,Pindel	.											.	LDOC1	26	.	0			c.221delA						.						98	81	86					X																	140270987		2203	4300	6503	SO:0001589	frameshift_variant	23641	exon1			.	AB019527	CCDS14672.1	Xq27	2008-02-05			ENSG00000182195	ENSG00000182195			6548	protein-coding gene	gene with protein product		300402		BCUR1		10403563, 15716091, 16093683	Standard	NM_012317		Approved	Mar7, Mart7	uc004fbj.3	O95751	OTTHUMG00000022558	ENST00000370526.2:c.220delT	chrX.hg19:g.140270987delA	ENSP00000359557:p.Tyr74fs	95.0	0.0		75.0	28.0	NM_012317	Q6IAR6	Frame_Shift_Del	DEL	ENST00000370526.2	hg19	CCDS14672.1																																																																																			.	.		0.617	LDOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058592.1	NM_012317		-	140270987	A	-	140270987	7	5	111	1	0	1	0	1	0	0	0	0	8718	362	13	0	224	0	LDOC1	23	140270987	Frame_Shift_Del	DEL	A	TCGA-DD-A39X-01A-11D-A20W-10	29780304	140270987	14999573	380	16620										
HCFC1	3054	hgsc.bcm.edu	37	chrX	153225829	153225829	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0213333333333333	8	1	0.71401188422465	1.100768321513	0.639155799588195	0.169802333889021	0.751940625889747	0	cacgggggatgttgtcctccAgtgtatccatcaggatggtc	13	10	1	0			TCGA-DD-A39X-01A-11D-A20W-10	TCGA-DD-A39X-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d48a532-df89-439c-8c4f-4b284cfdbb79	c27b95f8-bb8d-429a-b193-81f1caf006ee	g.chrX:153225829A>G	ENST00000310441.7	-	7	1907	c.941T>C	c.(940-942)cTg>cCg	p.L314P	HCFC1_ENST00000369984.4_Missense_Mutation_p.L314P|HCFC1_ENST00000461098.1_5'UTR|HCFC1_ENST00000354233.3_Missense_Mutation_p.L314P	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	314					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GTTGTCCTCCAGTGTATCCAT	0.632																																					p.L314P		Atlas-SNP	.											.	HCFC1	284	.	0			c.T941C						.						28	30	29					X																	153225829		2102	4185	6287	SO:0001583	missense	3054	exon7			TCCTCCAGTGTAT		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"VP16-accessory protein", "protein phosphatase 1, regulatory subunit 89"	300019	"mental retardation, X-linked 3", "host cell factor C1 (VP16-accessory protein)"	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.941T>C	chrX.hg19:g.153225829A>G	ENSP00000309555:p.Leu314Pro	177.0	0.0		124.0	5.0	NM_005334	Q6P4G5	Missense_Mutation	SNP	ENST00000310441.7	hg19	CCDS44020.1	.	.	.	.	.	.	.	.	.	.	A	18.77	3.693859	0.68386	.	.	ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233	T;T;T	0.03242	4.0;4.0;4.07	5.39	5.39	0.77823	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.09113	0.0225	L	0.31065	0.9	0.80722	D	1	D	0.58970	0.984	P	0.61533	0.89	T	0.12372	-1.0550	10	0.66056	D	0.02	.	13.3608	0.60654	1.0:0.0:0.0:0.0	.	314	P51610	HCFC1_HUMAN	P	314	ENSP00000309555:L314P;ENSP00000359001:L314P;ENSP00000346174:L314P	ENSP00000309555:L314P	L	-	2	0	HCFC1	152879023	1.000000	0.71417	0.985000	0.45067	0.968000	0.65278	3.618000	0.54188	1.796000	0.52611	0.486000	0.48141	CTG	.	.		0.632	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		G	153225829	A	G	153225829	3	3	111	1	0	0	0	0	1	0	0	0	7000	188	7	2	5246	2	HCFC1	23	153225829	Missense_Mutation	SNP	A	TCGA-DD-A39X-01A-11D-A20W-10	12954842	153225829	2044731	381	16621										
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1887022	1887022	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttaacatcgaaggcctaggAaaattctctactttccagcc	6	12	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:1887022A>G								TMEM52 (36310 upstream) : C1orf222 (32540 downstream)																							AAGGCCTAGGAAAATTCTCTA	0.537																																					p.S762P		Atlas-SNP	.											.	KIAA1751	92	.	0			c.T2284C						.						74	79	78					1																	1887022		1887	4091	5978	SO:0001628	intergenic_variant	85452	exon18			CCTAGGAAAATTC																													chr1.hg19:g.1887022A>G		95.0	0.0		179.0	8.0	NM_001080484		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	A	9.318	1.057357	0.19907	.	.	ENSG00000142609	ENST00000270720	.	.	.	1.45	-1.37	0.09056	.	0.228496	0.26556	N	0.023701	T	0.15565	0.0375	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08452	-1.0721	9	0.87932	D	0	.	6.1345	0.20223	0.7187:0.0:0.2813:0.0	.	762	Q9C0B2	K1751_HUMAN	P	762	.	ENSP00000270720:S762P	S	-	1	0	C1orf222	1876882	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.572000	0.05881	-1.085000	0.03088	-1.489000	0.00976	TCC	.	.	0	0.537									G	1887022	A	G	1887022	1	3	112	0	1	0	0	0	0	0	0	0	8265	246	9	2		2	KIAA1751	1	1887022	IGR	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10		1887022	247363599	1	16622										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12433904	12433904	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagacacaaagagtcattttAaaaaagaaggtaagagagct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:12433904delA	ENST00000358136.3	+	55	11038	c.10908delA	c.(10906-10908)ttafs	p.L3636fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.L3611fs|VPS13D_ENST00000496628.1_3'UTR	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		GAGTCATTTTAAAAAAGAAGG	0.468																																					p.L3636X		Atlas-INDEL	.											.	VPS13D	316	.	0			c.10907delT						.						37	38	38					1																	12433904		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon55			.	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.10908delA	chr1.hg19:g.12433904delA	ENSP00000350854:p.Leu3636fs	191.0	0.0		268.0	17.0	NM_015378		Frame_Shift_Del	DEL	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.468	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		-	12433904	A	-	12433904	7	5	112	1	0	1	0	1	0	0	0	0	17207	359	13	0	11122	0	VPS13D	1	12433904	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	10546882	12433904	236816717	2	16623										
PRDM2	7799	hgsc.bcm.edu	37	chr1	14108857	14108857	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggacagcggatgcggagattAaaatgcaaagcatgcagact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:14108857delA	ENST00000235372.7	+	8	5423	c.4567delA	c.(4567-4569)aaafs	p.K1523fs	PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000343137.4_Frame_Shift_Del_p.K1322fs|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000311066.5_Frame_Shift_Del_p.K1523fs|PRDM2_ENST00000413440.1_Frame_Shift_Del_p.K1322fs|PRDM2_ENST00000376048.5_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1523					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TGCGGAGATTAAAATGCAAAG	0.522																																					p.I1522fs		Atlas-INDEL	.											.	PRDM2	147	.	0			c.4566delT						.						65	72	70					1																	14108857		2203	4300	6503	SO:0001589	frameshift_variant	7799	exon8			.	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"Chromatin-modifying enzymes / K-methyltransferases"	9347	protein-coding gene	gene with protein product	"retinoblastoma protein-binding zinc finger protein", "retinoblastoma protein-interacting zinc finger protein", "MTE-binding protein", "zinc-finger DNA-binding protein", "GATA-3 binding protein G3B"	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.4567delA	chr1.hg19:g.14108857delA	ENSP00000235372:p.Lys1523fs	85.0	0.0		125.0	10.0	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Frame_Shift_Del	DEL	ENST00000235372.7	hg19	CCDS150.1																																																																																			.	.		0.522	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		-	14108857	A	-	14108857	7	5	112	1	0	1	0	1	0	0	0	0	12470	363	13	0	4593	0	PRDM2	1	14108857	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1674953	14108857	235141764	3	16624										
DDI2	84301	hgsc.bcm.edu	37	chr1	15959967	15959967	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtcctggtggagcagcagcAggaccgagcccggagagagc	17	11	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:15959967A>G	ENST00000480945.1	+	4	710	c.539A>G	c.(538-540)cAg>cGg	p.Q180R		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	180							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		GAGCAGCAGCAGGACCGAGCC	0.398																																					p.Q180R		Atlas-SNP	.											.	DDI2	38	.	0			c.A539G						.						171	205	194					1																	15959967		2203	4300	6503	SO:0001583	missense	84301	exon4			AGCAGCAGGACCG		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.539A>G	chr1.hg19:g.15959967A>G	ENSP00000417748:p.Gln180Arg	67.0	0.0		118.0	5.0	NM_032341	A8KAE1|Q7RTZ0|Q9BRT1	Missense_Mutation	SNP	ENST00000480945.1	hg19	CCDS30607.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.568994	0.28003	.	.	ENSG00000197312	ENST00000480945	T	0.23348	1.91	5.64	5.64	0.86602	.	0.000000	0.85682	U	0.000000	T	0.16685	0.0401	N	0.21324	0.655	0.58432	D	0.999997	B	0.06786	0.001	B	0.10450	0.005	T	0.05402	-1.0887	10	0.05721	T	0.95	-10.7207	15.5299	0.75952	1.0:0.0:0.0:0.0	.	180	Q5TDH0	DDI2_HUMAN	R	180	ENSP00000417748:Q180R	ENSP00000449475:Q65R	Q	+	2	0	DDI2	15832554	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.890000	0.92477	2.147000	0.66899	0.533000	0.62120	CAG	.	.		0.398	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341		G	15959967	A	G	15959967	3	3	112	1	0	0	0	0	1	0	0	0	4331	188	7	2	553	2	DDI2	1	15959967	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1851110	15959967	233290654	4	16625										
C1orf64	149563	hgsc.bcm.edu	37	chr1	16332618	16332618	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccccatctgactcgggtgaCccccatgggtgggggatgcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:16332618delC	ENST00000329454.2	+	2	355	c.287delC	c.(286-288)accfs	p.T96fs	RP11-5P18.5_ENST00000437156.1_RNA	NM_178840.2	NP_849162.1	Q8NEQ6	CA064_HUMAN	chromosome 1 open reading frame 64	96										breast(2)|endometrium(1)|lung(3)	6		Colorectal(325;0.000435)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;2.08e-05)|BRCA - Breast invasive adenocarcinoma(304;9.19e-05)|Kidney(64;0.000165)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0114)|READ - Rectum adenocarcinoma(331;0.0649)		ACTCGGGTGACCCCCATGGGT	0.652																																					p.T96fs		Atlas-INDEL	.											.	C1orf64	16	.	0			c.286delA						.						67	66	66					1																	16332618		2203	4300	6503	SO:0001589	frameshift_variant	149563	exon2			.	AK127425	CCDS166.1	1p36.13	2013-10-11			ENSG00000183888	ENSG00000183888			28339	protein-coding gene	gene with protein product	"ER-related factor"					22341523	Standard	NM_178840		Approved	MGC24047, ERRF	uc001axn.3	Q8NEQ6	OTTHUMG00000009523	ENST00000329454.2:c.287delC	chr1.hg19:g.16332618delC	ENSP00000332162:p.Thr96fs	104.0	0.0		148.0	10.0	NM_178840	B3KXI9	Frame_Shift_Del	DEL	ENST00000329454.2	hg19	CCDS166.1																																																																																			.	.		0.652	C1orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026317.1	NM_178840		-	16332618	C	-	16332618	7	5	112	1	0	1	0	1	0	0	0	0	2056	507	18	0	293	0	C1orf64	1	16332618	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	372651	16332618	232918003	5	16626										
PLA2G2F	64600	hgsc.bcm.edu	37	chr1	20465957	20465957	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggccaaccccaaagggttcAaaaagaaggtgctggataga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:20465957delA	ENST00000375102.3	+	1	139	c.37delA	c.(37-39)aaafs	p.K15fs		NM_022819.3	NP_073730.3	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	0					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CAAAGGGTTCAAAAAGAAGGT	0.592																																					p.F12fs		Atlas-INDEL	.											.	PLA2G2F	28	.	0			c.36delC						.						35	41	39					1																	20465957		1873	4103	5976	SO:0001589	frameshift_variant	64600	exon1			.	AL158172	CCDS204.2	1p35	2008-09-19			ENSG00000158786	ENSG00000158786	3.1.1.4		30040	protein-coding gene	gene with protein product						11112443	Standard	NM_022819		Approved		uc009vpp.1	Q9BZM2	OTTHUMG00000002704	ENST00000375102.3:c.37delA	chr1.hg19:g.20465957delA	ENSP00000364243:p.Lys15fs	87.0	0.0		146.0	10.0	NM_022819	Q5R385|Q8N217|Q9H506	Frame_Shift_Del	DEL	ENST00000375102.3	hg19	CCDS204.2																																																																																			.	.		0.592	PLA2G2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007687.1	NM_022819		-	20465957	A	-	20465957	7	5	112	1	0	1	0	1	0	0	0	0	12008	131	5	0	39	0	PLA2G2F	1	20465957	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4133339	20465957	228784664	6	16627										
RAP1GAP	5909	hgsc.bcm.edu	37	chr1	21936094	21936094	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaacacagcggggtccgggaGggggggtccaaagaagggca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:21936094delG	ENST00000374765.4	-	15	1245	c.1045delC	c.(1045-1047)ctcfs	p.L349fs	RAP1GAP_ENST00000290101.4_Frame_Shift_Del_p.L413fs|RAP1GAP_ENST00000542643.2_Frame_Shift_Del_p.L349fs|RAP1GAP_ENST00000374761.2_Frame_Shift_Del_p.L380fs|RAP1GAP_ENST00000374763.2_Frame_Shift_Del_p.L349fs	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	349	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		GGGTCCGGGAGGGGGGGTCCA	0.632																																					p.L413fs		Atlas-INDEL	.											.	RAP1GAP	119	.	0			c.1238delT						.						71	76	74					1																	21936094		2203	4300	6503	SO:0001589	frameshift_variant	5909	exon15			.	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"RAP1, GTPase activating protein 1"	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1045delC	chr1.hg19:g.21936094delG	ENSP00000363897:p.Leu349fs	82.0	0.0		162.0	10.0	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Frame_Shift_Del	DEL	ENST00000374765.4	hg19	CCDS218.1																																																																																			.	.		0.632	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885		-	21936094	G	-	21936094	7	5	112	1	0	1	0	1	0	0	0	0	13052	1000	35	0	1068	0	RAP1GAP	1	21936094	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1470137	21936094	227314527	7	16628										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22168836	22168836	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catactcgcctgagtcggcaGgggagacgaggtggagccgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:22168836delG	ENST00000374695.3	-	68	9027	c.8948delC	c.(8947-8949)cctfs	p.P2983fs		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2983	Ig-like C2-type 15.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGAGTCGGCAGGGGAGACGAG	0.637																																					p.P2983fs		Atlas-INDEL	.											.	HSPG2	311	.	0			c.8949delT						.						29	27	28					1																	22168836		2203	4300	6503	SO:0001589	frameshift_variant	3339	exon68			.	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.8948delC	chr1.hg19:g.22168836delG	ENSP00000363827:p.Pro2983fs	113.0	0.0		174.0	11.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Frame_Shift_Del	DEL	ENST00000374695.3	hg19	CCDS30625.1																																																																																			.	.		0.637	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		-	22168836	G	-	22168836	7	5	112	1	0	1	0	1	0	0	0	0	7439	1000	35	0	4347	0	HSPG2	1	22168836	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	232742	22168836	227081785	8	16629										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22178628	22178628	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acgcttgtaccatgtgacctGggcgtgggcctgccctgcca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:22178628delG	ENST00000374695.3	-	53	6902	c.6823delC	c.(6823-6825)cagfs	p.Q2275fs	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2275	Ig-like C2-type 8.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CATGTGACCTGGGCGTGGGCC	0.652																																					p.Q2275fs		Atlas-INDEL	.											.	HSPG2	311	.	0			c.6824delA						.						49	48	48					1																	22178628		2203	4299	6502	SO:0001589	frameshift_variant	3339	exon53			.	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6823delC	chr1.hg19:g.22178628delG	ENSP00000363827:p.Gln2275fs	114.0	0.0		243.0	15.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Frame_Shift_Del	DEL	ENST00000374695.3	hg19	CCDS30625.1																																																																																			.	.		0.652	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		-	22178628	G	-	22178628	7	5	112	1	0	1	0	1	0	0	0	0	7439	1357	47	0	6532	0	HSPG2	1	22178628	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	9792	22178628	227071993	9	16630										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22217107	22217107	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacagcctcggacacctctcGgaactctctggagcctgcat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:22217107delG	ENST00000374695.3	-	4	404	c.325delC	c.(325-327)cgafs	p.R109fs		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	109	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GACACCTCTCGGAACTCTCTG	0.592																																					p.R109fs		Atlas-INDEL	.											HSPG2,leg,malignant_melanoma,0,1	HSPG2	311	.	0			c.326delG						.						101	104	103					1																	22217107		2203	4300	6503	SO:0001589	frameshift_variant	3339	exon4			.	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.325delC	chr1.hg19:g.22217107delG	ENSP00000363827:p.Arg109fs	105.0	0.0		174.0	11.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Frame_Shift_Del	DEL	ENST00000374695.3	hg19	CCDS30625.1																																																																																			.	.		0.592	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		-	22217107	G	-	22217107	7	5	112	1	0	1	0	1	0	0	0	0	7439	1124	39	0	13226	0	HSPG2	1	22217107	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	38479	22217107	227033514	10	16631										
CELA3B	23436	hgsc.bcm.edu	37	chr1	22310726	22310726	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcaggaggccctgctgccgGtggtggactatgaacactgc	15	11	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:22310726G>C	ENST00000337107.6	+	6	563	c.544G>C	c.(544-546)Gtg>Ctg	p.V182L		NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	182	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.V182M(1)		breast(2)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						CCTGCTGCCGGTGGTGGACTA	0.627																																					p.V182L		Atlas-SNP	.											CELA3B,NS,carcinoma,0,1	CELA3B	24	.	1	Substitution - Missense(1)	kidney(1)	c.G544C						.						82	79	80					1																	22310726		2203	4300	6503	SO:0001583	missense	23436	exon6			CTGCCGGTGGTGG	M18692	CCDS219.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000219073	ENSG00000219073	3.4.21.70		15945	protein-coding gene	gene with protein product	"proteinase E", "elastase 1", "cholesterol-binding pancreatic protease", "pancreatic endopeptidase E"		"elastase 3B, pancreatic"	ELA3B		2826474, 2460440	Standard	NM_007352		Approved	CBPP	uc001bfk.3	P08861	OTTHUMG00000002758	ENST00000337107.6:c.544G>C	chr1.hg19:g.22310726G>C	ENSP00000338369:p.Val182Leu	184.0	1.0		282.0	0.0	NM_007352	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	Missense_Mutation	SNP	ENST00000337107.6	hg19	CCDS219.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.784915	0.70222	.	.	ENSG00000219073	ENST00000337107;ENST00000400277	D;D	0.89050	-2.46;-2.46	4.53	4.53	0.55603	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.88232	0.6381	N	0.11255	0.115	0.58432	D	0.999991	P	0.35363	0.497	P	0.55824	0.785	D	0.89830	0.3995	10	0.66056	D	0.02	-19.876	15.0932	0.72211	0.0:0.0:1.0:0.0	.	182	P08861	CEL3B_HUMAN	L	182;85	ENSP00000338369:V182L;ENSP00000383135:V85L	ENSP00000338369:V182L	V	+	1	0	CELA3B	22183313	1.000000	0.71417	0.976000	0.42696	0.313000	0.28021	5.358000	0.66064	2.232000	0.73038	0.650000	0.86243	GTG	.	.		0.627	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007797.1	NM_007352		C	22310726	G	C	22310726	3	2	112	1	0	0	0	0	1	0	0	0	3216	1261	44	4	566	4	CELA3B	1	22310726	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	93619	22310726	226939895	11	16632										
CDC42	998	hgsc.bcm.edu	37	chr1	22413358	22413358	+	Splice_Site	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggagtgttctgcacttacacAggtaagaatggcatgaaacc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:22413358delA	ENST00000344548.3	+	6	736	c.485delA	c.(484-486)cag>cg	p.Q162fs	CDC42_ENST00000315554.8_Splice_Site_p.Q162fs|CDC42_ENST00000421089.2_Splice_Site_p.Q204fs|CDC42_ENST00000400259.1_Splice_Site_p.Q162fs|CDC42_ENST00000498236.1_3'UTR	NM_001039802.1	NP_001034891.1	P60953	CDC42_HUMAN	cell division cycle 42	162					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cellular protein localization (GO:0034613)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell-cell adhesion (GO:0090136)|epithelial-mesenchymal cell signaling (GO:0060684)|establishment of Golgi localization (GO:0051683)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|keratinization (GO:0031424)|keratinocyte development (GO:0003334)|macrophage differentiation (GO:0030225)|multicellular organism growth (GO:0035264)|muscle cell differentiation (GO:0042692)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of gene expression (GO:0010629)|negative regulation of protein complex assembly (GO:0031333)|neuron fate determination (GO:0048664)|nuclear migration (GO:0007097)|nucleus localization (GO:0051647)|organelle transport along microtubule (GO:0072384)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of JNK cascade (GO:0046330)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of synapse structural plasticity (GO:0051835)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of filopodium assembly (GO:0051489)|regulation of mitosis (GO:0007088)|regulation of protein catabolic process (GO:0042176)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein kinase activity (GO:0045859)|regulation of protein stability (GO:0031647)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|sprouting angiogenesis (GO:0002040)|submandibular salivary gland formation (GO:0060661)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	apical part of cell (GO:0045177)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|spindle midzone (GO:0051233)	apolipoprotein A-I receptor binding (GO:0034191)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)	12		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		GCACTTACACAGGTAAGAATG	0.443																																					p.Q162fs		Pindel	.											.	CDC42	26	.	0			c.484delC						.						123	123	123					1																	22413358		2203	4300	6503	SO:0001630	splice_region_variant	998	exon6			.	BC018266	CCDS221.1, CCDS222.1	1p36.1	2013-01-17	2013-01-17		ENSG00000070831	ENSG00000070831			1736	protein-coding gene	gene with protein product	"GTP binding protein, 25kDa"	116952	"cell division cycle 42 (GTP-binding protein, 25kD)", "cell division cycle 42 (GTP binding protein, 25kDa)"			2124704, 2122236	Standard	NM_001039802		Approved	G25K, CDC42Hs	uc001bfr.3	P60953	OTTHUMG00000002753	ENST00000344548.3:c.486+1A>-	chr1.hg19:g.22413358delA		47.0	0.0		97.0	22.0	NM_001039802	P21181|P25763|Q7L8R5|Q9UDI2	Frame_Shift_Del	DEL	ENST00000344548.3	hg19	CCDS221.1																																																																																			.	.		0.443	CDC42-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007787.1	NM_001791	Frame_Shift_Del	-	22413358	A	-	22413358	8	5	112	1	0	1	0	1	0	0	1	0	3073	202	7	0	499	0	CDC42	1	22413358	Splice_Site	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	102632	22413358	226837263	12	16633										
RPL11	6135	hgsc.bcm.edu	37	chr1	24022333	24022333	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcgcagacaagaagcgcaggAcaggctgcattggggccaaa	14	10	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:24022333A>G	ENST00000374550.3	+	5	487	c.442A>G	c.(442-444)Aca>Gca	p.T148A	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	148					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		GAAGCGCAGGACAGGCTGCAT	0.527																																					p.T148A		Atlas-SNP	.											.	RPL11	21	.	0			c.A442G						.						73	62	66					1																	24022333		2202	4299	6501	SO:0001583	missense	6135	exon5			CGCAGGACAGGCT	L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"L ribosomal proteins"	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.442A>G	chr1.hg19:g.24022333A>G	ENSP00000363676:p.Thr148Ala	88.0	0.0		165.0	7.0	NM_000975	P25121|P39026|Q8TDH2|Q9Y674	Missense_Mutation	SNP	ENST00000374550.3	hg19	CCDS238.1	.	.	.	.	.	.	.	.	.	.	A	16.93	3.257612	0.59321	.	.	ENSG00000142676	ENST00000374550;ENST00000458455	T;T	0.74632	-0.86;-0.86	5.7	5.7	0.88788	Ribosomal protein L5 domain (2);	0.102168	0.64402	D	0.000003	T	0.71065	0.3296	L	0.52823	1.66	0.50467	D	0.999872	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.66567	-0.5891	10	0.41790	T	0.15	-12.3044	15.9514	0.79843	1.0:0.0:0.0:0.0	.	147;148	P62913-2;P62913	.;RL11_HUMAN	A	148;146	ENSP00000363676:T148A;ENSP00000398888:T146A	ENSP00000363676:T148A	T	+	1	0	RPL11	23894920	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.779000	0.68948	2.171000	0.68590	0.482000	0.46254	ACA	.	.		0.527	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975		G	24022333	A	G	24022333	3	3	112	1	0	0	0	0	1	0	0	0	13572	275	10	2	460	2	RPL11	1	24022333	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1608975	24022333	225228288	13	16634										
TCEB3	6924	hgsc.bcm.edu	37	chr1	24077422	24077422	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagaaggaggaggagatggaGggggactaccaagaaacctg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:24077422delG	ENST00000418390.2	+	4	676	c.405delG	c.(403-405)gagfs	p.E135fs	TCEB3_ENST00000487554.1_3'UTR|TCEB3_ENST00000609199.1_Frame_Shift_Del_p.E109fs	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	135					gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		AGGAGATGGAGGGGGACTACC	0.527																																					p.E135fs		Atlas-INDEL	.											.	TCEB3	61	.	0			c.404delA						.						47	52	51					1																	24077422		2203	4300	6503	SO:0001589	frameshift_variant	6924	exon4			.	L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.405delG	chr1.hg19:g.24077422delG	ENSP00000395574:p.Glu135fs	70.0	0.0		128.0	10.0	NM_003198	B2R7Q8|Q8IXH1	Frame_Shift_Del	DEL	ENST00000418390.2	hg19	CCDS239.2																																																																																			.	.		0.527	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198		-	24077422	G	-	24077422	7	5	112	1	0	1	0	1	0	0	0	0	15696	991	35	0	419	0	TCEB3	1	24077422	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	55089	24077422	225173199	14	16635										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27087916	27087916	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacccagtggccagtcggacAgcatcatgcatccttccatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:27087916delA	ENST00000324856.7	+	6	2574	c.2203delA	c.(2203-2205)agcfs	p.S735fs	ARID1A_ENST00000457599.2_Frame_Shift_Del_p.S735fs|RN7SL501P_ENST00000578818.1_RNA|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.S352fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	735					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCAGTCGGACAGCATCATGCA	0.537			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.D734fs		Atlas-Indel,Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.2202delC						.						92	84	86					1																	27087916		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon6			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2203delA	chr1.hg19:g.27087916delA	ENSP00000320485:p.Ser735fs	326.0	0.0		505.0	34.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.537	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27087916	A	-	27087916	7	5	112	1	0	1	0	1	0	0	0	0	913	188	7	0	2225	0	ARID1A	1	27087916	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3010494	27087916	222162705	15	16636										
C1orf172	126695	hgsc.bcm.edu	37	chr1	27278443	27278443	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgctggccatcccgccggctGgggggtgcacgatcagggct					rs535449942		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:27278443delG	ENST00000320567.5	-	2	517	c.429delC	c.(427-429)cccfs	p.P143fs		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		143					developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		CCCGCCGGCTGGGGGGTGCAC	0.632																																					p.S144fs		Atlas-INDEL	.											.	C1orf172	38	.	0			c.430delA						.						24	27	26					1																	27278443		2203	4300	6503	SO:0001589	frameshift_variant	126695	exon2			.																												ENST00000320567.5:c.429delC	chr1.hg19:g.27278443delG	ENSP00000319179:p.Pro143fs	181.0	0.0		351.0	22.0	NM_152365	Q5QP32|Q8N0S7	Frame_Shift_Del	DEL	ENST00000320567.5	hg19	CCDS293.1																																																																																			.	.		0.632	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1			-	27278443	G	-	27278443	7	5	112	1	0	1	0	1	0	0	0	0	2015	1335	47	0	779	0	C1orf172	1	27278443	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	190527	27278443	221972178	16	16637										
AHDC1	27245	hgsc.bcm.edu	37	chr1	27875231	27875231	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggctcgctgacgtggcagtcAaaactgggattgtagagctg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:27875231delA	ENST00000247087.5	-	5	3992	c.3396delT	c.(3394-3396)tttfs	p.F1132fs	AHDC1_ENST00000374011.2_Frame_Shift_Del_p.F1132fs			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1132							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CGTGGCAGTCAAAACTGGGAT	0.587																																					p.D1133fs		Atlas-INDEL	.											.	AHDC1	98	.	0			c.3397delG						.						81	80	80					1																	27875231		2203	4299	6502	SO:0001589	frameshift_variant	27245	exon6			.	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.3396delT	chr1.hg19:g.27875231delA	ENSP00000247087:p.Phe1132fs	88.0	0.0		154.0	10.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Frame_Shift_Del	DEL	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.		0.587	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			-	27875231	A	-	27875231	7	5	112	1	0	1	0	1	0	0	0	0	412	127	5	0	1419	0	AHDC1	1	27875231	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	596788	27875231	221375390	17	16638										
AHDC1	27245	hgsc.bcm.edu	37	chr1	27876439	27876439	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccagtcacagcgtctacctCcccccggccccgtttgcgtg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:27876439delC	ENST00000247087.5	-	5	2784	c.2188delG	c.(2188-2190)gagfs	p.E730fs	AHDC1_ENST00000374011.2_Frame_Shift_Del_p.E730fs			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	730	Gly-rich.						DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GCGTCTACCTCCCCCCGGCCC	0.662																																					p.E730fs		Atlas-INDEL	.											.	AHDC1	98	.	0			c.2189delA						.						36	34	34					1																	27876439		2203	4300	6503	SO:0001589	frameshift_variant	27245	exon6			.	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.2188delG	chr1.hg19:g.27876439delC	ENSP00000247087:p.Glu730fs	195.0	0.0		348.0	22.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Frame_Shift_Del	DEL	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.		0.662	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			-	27876439	C	-	27876439	7	5	112	1	0	1	0	1	0	0	0	0	412	864	30	0	2627	0	AHDC1	1	27876439	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1208	27876439	221374182	18	16639										
YTHDF2	51441	hgsc.bcm.edu	37	chr1	29069727	29069727	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagcaggctaacaatagcccAccagtggctcaggcatcagt	10	13	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:29069727A>G	ENST00000373812.3	+	4	1307	c.945A>G	c.(943-945)ccA>ccG	p.P315P	YTHDF2_ENST00000542507.1_Silent_p.P315P|YTHDF2_ENST00000541996.1_Silent_p.P265P|YTHDF2_ENST00000478283.1_3'UTR	NM_016258.2	NP_057342.2	Q9Y5A9	YTHD2_HUMAN	YTH domain family, member 2	315	Localization to mRNA processing bodies (P-bodies).				humoral immune response (GO:0006959)|regulation of mRNA stability (GO:0043488)	cytoplasmic mRNA processing body (GO:0000932)	N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		ACAATAGCCCACCAGTGGCTC	0.577																																					p.P315P		Atlas-SNP	.											.	YTHDF2	47	.	0			c.A945G						.						47	48	47					1																	29069727		1985	4151	6136	SO:0001819	synonymous_variant	51441	exon4			TAGCCCACCAGTG	AF155095	CCDS41296.1, CCDS53287.1	1p35	2008-02-05	2004-11-16		ENSG00000198492	ENSG00000198492			31675	protein-coding gene	gene with protein product		610640	"YTH domain family 2"			10508479	Standard	NM_016258		Approved	HGRG8, NY-REN-2	uc021okf.1	Q9Y5A9	OTTHUMG00000003648	ENST00000373812.3:c.945A>G	chr1.hg19:g.29069727A>G		196.0	0.0		373.0	48.0	NM_016258	A6NKG4|A8K966|B4E1G7|D3DPM8|Q5VSZ9|Q8TDH0|Q9BUJ5	Silent	SNP	ENST00000373812.3	hg19	CCDS41296.1																																																																																			.	.		0.577	YTHDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010335.1	NM_016258		G	29069727	A	G	29069727	2	3	112	1	0	0	0	0	0	0	0	1	17514	146	6	2		2	YTHDF2	1	29069727	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1193288	29069727	220180894	19	16640										
SFRS4	6429	hgsc.bcm.edu	37	chr1	29475675	29475675	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctggggctcctgcttttctcTttcttgctccggctccgact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:29475675delT	ENST00000373795.4	-	6	966	c.732delA	c.(730-732)aaafs	p.K244fs	SRSF4_ENST00000546138.1_Frame_Shift_Del_p.R143fs|SRSF4_ENST00000466448.1_5'UTR|RP11-242O24.3_ENST00000413004.1_lincRNA	NM_005626.4	NP_005617.2	Q08170	SRSF4_HUMAN	serine/arginine-rich splicing factor 4	244	Arg/Ser-rich (RS domain).				gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						TGCTTTTCTCTTTCTTgctcc	0.597																																					p.E245fs		Atlas-INDEL	.											.	SRSF4	44	.	0			c.733delG						.						66	77	73					1																	29475675		2202	4300	6502	SO:0001589	frameshift_variant	6429	exon6			.	BC002781	CCDS333.1	1p35.3	2013-02-12	2010-06-22	2010-06-22	ENSG00000116350	ENSG00000116350		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10786	protein-coding gene	gene with protein product	"SR splicing factor 4"	601940	"splicing factor, arginine/serine-rich 4"	SFRS4		8321209, 20516191	Standard	NM_005626		Approved	SRP75	uc001bro.3	Q08170	OTTHUMG00000003663	ENST00000373795.4:c.732delA	chr1.hg19:g.29475675delT	ENSP00000362900:p.Lys244fs	106.0	0.0		166.0	10.0	NM_005626	Q5VXP1|Q9BUA4|Q9UEB5	Frame_Shift_Del	DEL	ENST00000373795.4	hg19	CCDS333.1																																																																																			.	.		0.597	SRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010392.1	NM_005626		-	29475675	T	-	29475675	7	5	112	1	0	1	0	1	0	0	0	0	14194	1606	56	0	756	0	SFRS4	1	29475675	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	405948	29475675	219774946	20	16641										
PUM1	9698	hgsc.bcm.edu	37	chr1	31441332	31441332	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacgttggctggctcctccaCggagaacctgggaaaggaag	15	10	0	1	rs551662997		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:31441332C>T	ENST00000257075.5	-	11	1607	c.1514G>A	c.(1513-1515)cGt>cAt	p.R505H	PUM1_ENST00000423018.2_Missense_Mutation_p.R409H|PUM1_ENST00000424085.2_Missense_Mutation_p.R263H|PUM1_ENST00000373741.4_Missense_Mutation_p.R541H|PUM1_ENST00000373742.2_Missense_Mutation_p.R446H|PUM1_ENST00000426105.2_Missense_Mutation_p.R505H|SNORD85_ENST00000363311.1_RNA|PUM1_ENST00000440538.2_Missense_Mutation_p.R506H|PUM1_ENST00000490546.1_5'UTR|PUM1_ENST00000373747.3_Missense_Mutation_p.R506H	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	505	Ala-rich.|Gln-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		GGCTCCTCCACGGAGAACCTG	0.493													C|||	1	0.000199681	0	0	5008	,	,		19035	0		0	False		,,,				2504	0.001				p.R505H		Atlas-SNP	.											.	PUM1	107	.	0			c.G1514A						.						89	83	85					1																	31441332		2203	4300	6503	SO:0001583	missense	9698	exon11			CCTCCACGGAGAA	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.1514G>A	chr1.hg19:g.31441332C>T	ENSP00000257075:p.Arg505His	87.0	0.0		180.0	22.0	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	hg19	CCDS338.1	.	.	.	.	.	.	.	.	.	.	C	36	5.706510	0.96821	.	.	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742	T;T;T;T;T;T;T;T	0.25579	1.94;1.92;2.04;2.04;1.99;2.02;2.24;1.79	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.52158	0.1717	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.998;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.83275	0.996;0.976;0.996;0.989;0.996;0.996;0.996;0.996	T	0.47623	-0.9103	10	0.72032	D	0.01	-7.3314	20.3627	0.98863	0.0:1.0:0.0:0.0	.	446;409;541;506;505;505;506;505	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.;.;.;.;PUM1_HUMAN;.;.;.	H	263;505;506;243;505;506;541;409;446	ENSP00000400141:R263H;ENSP00000257075:R505H;ENSP00000362852:R506H;ENSP00000391723:R505H;ENSP00000401777:R506H;ENSP00000362846:R541H;ENSP00000399440:R409H;ENSP00000362847:R446H	ENSP00000257075:R505H	R	-	2	0	PUM1	31213919	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.701000	0.84566	2.885000	0.99019	0.655000	0.94253	CGT	.	.		0.493	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			T	31441332	C	T	31441332	3	4	112	1	0	0	0	0	1	0	0	0	12840	536	19	1	2100	1	PUM1	1	31441332	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1965657	31441332	217809289	21	16642										
C1orf94	84970	hgsc.bcm.edu	37	chr1	34643426	34643426	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggttgtgttctagccctgggTggacagaggggcttccagaa	16	8	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:34643426T>C	ENST00000488417.1	+	1	156	c.36T>C	c.(34-36)ggT>ggC	p.G12G	C1orf94_ENST00000373374.3_Intron|AC115286.1_ENST00000408126.1_RNA	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	12										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				TAGCCCTGGGTGGACAGAGGG	0.622																																					p.G12G		Atlas-SNP	.											.	C1orf94	156	.	0			c.T36C						.						9	11	10					1																	34643426		692	1587	2279	SO:0001819	synonymous_variant	84970	exon1			CCTGGGTGGACAG	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.36T>C	chr1.hg19:g.34643426T>C		80.0	0.0		119.0	5.0	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	hg19	CCDS44108.1																																																																																			.	.		0.622	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884		C	34643426	T	C	34643426	2	2	112	1	0	0	0	0	0	0	0	1	2073	1683	59	2		2	C1orf94	1	34643426	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3202094	34643426	214607195	22	16643										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35835675	35835675	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaactcaagagggggaactgAaaattagtgctgtgttttca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:35835675delA	ENST00000314607.6	+	6	966	c.886delA	c.(886-888)aaafs	p.K296fs	ZMYM4_ENST00000482131.1_3'UTR|ZMYM4_ENST00000373297.2_Frame_Shift_Del_p.K296fs	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	296					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GGGGGAACTGAAAATTAGTGC	0.343																																					p.L295fs		Atlas-INDEL	.											.	ZMYM4	143	.	0			c.885delG						.						76	76	76					1																	35835675		2203	4300	6503	SO:0001589	frameshift_variant	9202	exon6			.	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.886delA	chr1.hg19:g.35835675delA	ENSP00000322915:p.Lys296fs	102.0	0.0		161.0	12.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Frame_Shift_Del	DEL	ENST00000314607.6	hg19	CCDS389.1																																																																																			.	.		0.343	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		-	35835675	A	-	35835675	7	5	112	1	0	1	0	1	0	0	0	0	17717	247	9	0	908	0	ZMYM4	1	35835675	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1192249	35835675	213414946	23	16644										
PSMB2	5690	hgsc.bcm.edu	37	chr1	36101937	36101937	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcatcttataaagttgcacgTttttctgaatatattctgca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:36101937delT	ENST00000373237.3	-	2	599	c.188delA	c.(187-189)aacfs	p.N63fs		NM_002794.4	NP_002785.1	P49721	PSB2_HUMAN	proteasome (prosome, macropain) subunit, beta type, 2	63					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|large_intestine(2)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)|Carfilzomib(DB08889)	AAGTTGCACGTTTTTCTGAAT	0.398																																					p.N63fs		Atlas-INDEL	.											.	PSMB2	9	.	0			c.189delC						.						139	132	134					1																	36101937		2202	4300	6502	SO:0001589	frameshift_variant	5690	exon2			.	D26599	CCDS394.1, CCDS72755.1	1p34.2	2008-02-05			ENSG00000126067	ENSG00000126067		"Proteasome (prosome, macropain) subunits"	9539	protein-coding gene	gene with protein product		602175				7918633	Standard	NM_002794		Approved	HC7-I	uc001bzf.2	P49721	OTTHUMG00000004169	ENST00000373237.3:c.188delA	chr1.hg19:g.36101937delT	ENSP00000362334:p.Asn63fs	170.0	0.0		344.0	26.0	NM_002794	D3DPS0|P31145|Q9BWZ9	Frame_Shift_Del	DEL	ENST00000373237.3	hg19	CCDS394.1																																																																																			.	.		0.398	PSMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012016.1	NM_002794		-	36101937	T	-	36101937	7	5	112	1	0	1	0	1	0	0	0	0	12689	1725	60	0	437	0	PSMB2	1	36101937	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	266262	36101937	213148684	24	16645										
CLSPN	63967	hgsc.bcm.edu	37	chr1	36228077	36228077	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccactctccaaagatggttcTtttttctaaaagaaatggca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:36228077delT	ENST00000318121.3	-	5	807	c.750delA	c.(748-750)aaafs	p.K250fs	CLSPN_ENST00000520551.1_Frame_Shift_Del_p.K250fs|CLSPN_ENST00000251195.5_Frame_Shift_Del_p.K250fs|CLSPN_ENST00000373220.3_Frame_Shift_Del_p.K250fs	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	250					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AAGATGGTTCTTTTTTCTAAA	0.398																																					p.E251fs		Atlas-INDEL	.											.	CLSPN	248	.	0			c.751delG						.						87	83	84					1																	36228077		2203	4300	6503	SO:0001589	frameshift_variant	63967	exon5			.	AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"claspin homolog (Xenopus laevis)"			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.750delA	chr1.hg19:g.36228077delT	ENSP00000312995:p.Lys250fs	100.0	0.0		141.0	11.0	NM_001190481	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Frame_Shift_Del	DEL	ENST00000318121.3	hg19	CCDS396.1																																																																																			.	.		0.398	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111		-	36228077	T	-	36228077	7	5	112	1	0	1	0	1	0	0	0	0	3562	1606	56	0	3353	0	CLSPN	1	36228077	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	126140	36228077	213022544	25	16646										
EIF2C4	192670	hgsc.bcm.edu	37	chr1	36306817	36306817	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgggagcggatgtcacacaCcccccagcaggggatgggaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:36306817delC	ENST00000373210.3	+	14	2021	c.1776delC	c.(1774-1776)cacfs	p.H592fs		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	592	Piwi. {ECO:0000255|HAMAP-Rule:MF_03033}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										ATGTCACACACCCCCCAGCAG	0.557																																					p.H592fs		Atlas-INDEL	.											.	.	.	.	0			c.1775delA						.						47	45	46					1																	36306817		2203	4300	6503	SO:0001589	frameshift_variant	192670	exon14			.	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"Argonaute/PIWI family"	18424	protein-coding gene	gene with protein product	"argonaute 4"	607356	"eukaryotic translation initiation factor 2C, 4"	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.1776delC	chr1.hg19:g.36306817delC	ENSP00000362306:p.His592fs	113.0	0.0		154.0	10.0	NM_017629	A7MD27	Frame_Shift_Del	DEL	ENST00000373210.3	hg19	CCDS397.1																																																																																			.	.		0.557	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629		-	36306817	C	-	36306817	7	5	112	1	0	1	0	1	0	0	0	0	5010	506	18	0	1830	0	EIF2C4	1	36306817	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	78740	36306817	212943804	26	16647										
MEAF6	64769	hgsc.bcm.edu	37	chr1	37961495	37961495	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgatacttacagctcgtggTtttttgtttaacttcagatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:37961495delT	ENST00000296214.5	-	6	585	c.558delA	c.(556-558)aaafs	p.K186fs	MEAF6_ENST00000373073.4_Intron|MEAF6_ENST00000373075.2_Frame_Shift_Del_p.K196fs|MEAF6_ENST00000373074.1_Frame_Shift_Del_p.K164fs|MEAF6_ENST00000475828.1_5'UTR|MEAF6_ENST00000448519.2_3'UTR	NM_001270875.1	NP_001257804.1	Q9HAF1	EAF6_HUMAN	MYST/Esa1-associated factor 6	186					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)	7						CAGCTCGTGGTTTTTTGTTTA	0.378																																					p.P197fs		Atlas-INDEL	.											.	MEAF6	25	.	0			c.589delC						.						95	99	98					1																	37961495		2203	4300	6503	SO:0001589	frameshift_variant	64769	exon7			.	BC016328	CCDS418.1, CCDS59195.1, CCDS59196.1	1p35.3-p33	2011-08-12	2009-07-13	2009-07-13	ENSG00000163875	ENSG00000163875			25674	protein-coding gene	gene with protein product	"Esa1p-associated factor 6 homolog (S. cerevisiae)", "centromere protein 28"	611001	"chromosome 1 open reading frame 149"	C1orf149		8619474, 9110174, 12963728, 14966270, 16387653	Standard	NM_022756		Approved	NY-SAR-91, FLJ11730, Eaf6, CENP-28	uc001cbe.2	Q9HAF1	OTTHUMG00000004223	ENST00000296214.5:c.558delA	chr1.hg19:g.37961495delT	ENSP00000296214:p.Lys186fs	132.0	0.0		200.0	12.0	NM_022756	B1AK64|Q4F967|Q7Z311|Q86WE3	Frame_Shift_Del	DEL	ENST00000296214.5	hg19	CCDS59196.1																																																																																			.	.		0.378	MEAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012161.1	NM_022756		-	37961495	T	-	37961495	7	5	112	1	0	1	0	1	0	0	0	0	9430	1722	60	0	25	0	MEAF6	1	37961495	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1654678	37961495	211289126	27	16648										
MTF1	4520	hgsc.bcm.edu	37	chr1	38288327	38288327	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gataaagatgctgaatttccTgtggatggcggaacatcact	11	7	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:38288327T>C	ENST00000373036.4	-	9	1373	c.1233A>G	c.(1231-1233)acA>acG	p.T411T		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	411					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CTGAATTTCCTGTGGATGGCG	0.478																																					p.T411T		Atlas-SNP	.											.	MTF1	67	.	0			c.A1233G						.						71	79	76					1																	38288327		2203	4300	6503	SO:0001819	synonymous_variant	4520	exon9			ATTTCCTGTGGAT	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1233A>G	chr1.hg19:g.38288327T>C		32.0	0.0		63.0	4.0	NM_005955	B2RAK6|Q96CB1	Silent	SNP	ENST00000373036.4	hg19	CCDS30676.1																																																																																			.	.		0.478	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955		C	38288327	T	C	38288327	2	2	112	1	0	0	0	0	0	0	0	1	9931	1567	55	2		2	MTF1	1	38288327	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	326832	38288327	210962294	28	16649										
UTP11L	51118	hgsc.bcm.edu	37	chr1	38483393	38483393	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcttcggaagaaggctcttgAaaaaaatccagatgaattct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:38483393delA	ENST00000373014.4	+	3	240	c.179delA	c.(178-180)gaafs	p.E60fs	UTP11L_ENST00000537711.1_Frame_Shift_Del_p.E60fs|UTP11L_ENST00000488453.1_3'UTR	NM_016037.3	NP_057121.2	Q9Y3A2	UTP11_HUMAN	UTP11-like, U3 small nucleolar ribonucleoprotein (yeast)	60					nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleolus (GO:0005730)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				AAGGCTCTTGAAAAAAATCCA	0.378																																					p.E60fs		Atlas-INDEL	.											.	UTP11L	17	.	0			c.178delG						.						74	84	81					1																	38483393		2201	4300	6501	SO:0001589	frameshift_variant	51118	exon3			.	AF151852	CCDS429.1	1p34.3	2014-03-06	2014-03-06		ENSG00000183520	ENSG00000183520			24329	protein-coding gene	gene with protein product		609440				11860508, 10810093	Standard	NM_016037		Approved	CGI-94	uc001ccn.4	Q9Y3A2	OTTHUMG00000004435	ENST00000373014.4:c.179delA	chr1.hg19:g.38483393delA	ENSP00000362105:p.Glu60fs	160.0	0.0		262.0	16.0	NM_016037	A8K785|B4DJC6|D3DPT7|Q5VT93|Q9BS98|Q9NS31	Frame_Shift_Del	DEL	ENST00000373014.4	hg19	CCDS429.1																																																																																			.	.		0.378	UTP11L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012962.1	NM_016037		-	38483393	A	-	38483393	7	5	112	1	0	1	0	1	0	0	0	0	17109	246	9	0	189	0	UTP11L	1	38483393	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	195066	38483393	210767228	29	16650										
MACF1	23499	hgsc.bcm.edu	37	chr1	39908507	39908507	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttaaggagccgtttggaagCcatgaaccaatgctgggagt	13	8	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:39908507C>A	ENST00000372915.3	+	77	19010	c.18923C>A	c.(18922-18924)gCc>gAc	p.A6308D	MACF1_ENST00000539005.1_Missense_Mutation_p.A4220D|MACF1_ENST00000361689.2_Missense_Mutation_p.A4350D|MACF1_ENST00000564288.1_Missense_Mutation_p.A6409D|MACF1_ENST00000317713.7_Missense_Mutation_p.A4350D|MACF1_ENST00000289893.4_Missense_Mutation_p.A4852D|MACF1_ENST00000567887.1_Missense_Mutation_p.A6446D|MACF1_ENST00000545844.1_Missense_Mutation_p.A4350D			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6308			A -> T (in dbSNP:rs587404).		ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CGTTTGGAAGCCATGAACCAA	0.498																																					p.A4350D		Atlas-SNP	.											MACF1_ENST00000361689,NS,carcinoid-endocrine_tumour,0,2	MACF1	909	.	0			c.C13049A						.						63	54	57					1																	39908507		2203	4300	6503	SO:0001583	missense	23499	exon75			TGGAAGCCATGAA	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18923C>A	chr1.hg19:g.39908507C>A	ENSP00000362006:p.Ala6308Asp	108.0	1.0		186.0	0.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.747|8.747	0.920321|0.920321	0.17982|0.17982	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.49432|.	1.41;0.78;1.41;1.41;1.41;0.78|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.195229|.	0.36066|.	N|.	0.002819|.	T|T	0.42086|0.42086	0.1187|0.1187	N|N	0.14661|0.14661	0.345|0.345	0.45183|0.45183	D|D	0.998192|0.998192	B;B|.	0.21821|.	0.061;0.061|.	B;B|.	0.28011|.	0.039;0.085|.	T|T	0.28902|0.28902	-1.0029|-1.0029	10|5	0.17369|.	T|.	0.5|.	.|.	12.8167|12.8167	0.57669|0.57669	0.1283:0.748:0.1237:0.0|0.1283:0.748:0.1237:0.0	.|.	6308;4350|.	Q9UPN3;F8W8Q1|.	MACF1_HUMAN;.|.	D|R	4350;6308;4350;4350;4220;4852|3353	ENSP00000439537:A4350D;ENSP00000362006:A6308D;ENSP00000354573:A4350D;ENSP00000313438:A4350D;ENSP00000444364:A4220D;ENSP00000289893:A4852D|.	ENSP00000289893:A4852D|.	A|S	+|+	2|3	0|2	MACF1|MACF1	39681094|39681094	0.999000|0.999000	0.42202|0.42202	0.996000|0.996000	0.52242|0.52242	0.979000|0.979000	0.70002|0.70002	3.775000|3.775000	0.55349|0.55349	2.752000|2.752000	0.94435|0.94435	0.655000|0.655000	0.94253|0.94253	GCC|AGC	.	.		0.498	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39908507	C	A	39908507	3	1	112	1	0	0	0	0	1	0	0	0	9153	739	26	3	19494	3	MACF1	1	39908507	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1425114	39908507	209342114	30	16651										
PABPC4	8761	hgsc.bcm.edu	37	chr1	40028016	40028016	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagcatctgcttctgttcctGggggggtgctgcagccagca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:40028016delG	ENST00000372857.3	-	13	2485	c.1693delC	c.(1693-1695)cagfs	p.Q565fs	PABPC4_ENST00000372856.3_Frame_Shift_Del_p.Q552fs|RP11-69E11.8_ENST00000415255.1_RNA|PABPC4_ENST00000372858.3_Frame_Shift_Del_p.Q581fs|PABPC4_ENST00000372862.3_Frame_Shift_Del_p.Q536fs	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	565	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.				blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TTCTGTTCCTGGGGGGGTGCT	0.602																																					p.Q581fs		Atlas-INDEL	.											.	PABPC4	56	.	0			c.1742delA						.						50	54	53					1																	40028016		2203	4300	6503	SO:0001589	frameshift_variant	8761	exon13			.	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"RNA binding motif (RRM) containing"	8557	protein-coding gene	gene with protein product		603407	"poly(A)-binding protein, cytoplasmic 4 (inducible form)"			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.1693delC	chr1.hg19:g.40028016delG	ENSP00000361948:p.Gln565fs	135.0	0.0		248.0	16.0	NM_001135653	B1ANQ8|Q4VC03|Q6P0N3	Frame_Shift_Del	DEL	ENST00000372857.3	hg19	CCDS438.1																																																																																			.	.		0.602	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653		-	40028016	G	-	40028016	7	5	112	1	0	1	0	1	0	0	0	0	11375	1357	47	0	253	0	PABPC4	1	40028016	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	119509	40028016	209222605	31	16652										
MYCL1	4610	hgsc.bcm.edu	37	chr1	40366859	40366859	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgatggaggcgtagttcctgCcccagcctttcgagtggccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:40366859delC	ENST00000372816.2	-	1	695	c.248delG	c.(247-249)ggcfs	p.G83fs	MYCL_ENST00000372815.1_Frame_Shift_Del_p.G113fs|MYCL_ENST00000429311.1_Frame_Shift_Del_p.G83fs|MYCL_ENST00000397332.2_Frame_Shift_Del_p.G113fs|RP1-118J21.5_ENST00000418255.1_RNA			P12524	MYCL_HUMAN	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog	83						nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GTAGTTCCTGCCCCAGCCTTT	0.711																																					p.G113fs		Atlas-INDEL	.											.	MYCL1	36	.	0			c.339delC						.						26	25	26					1																	40366859		2200	4293	6493	SO:0001589	frameshift_variant	4610	exon2			.		CCDS30682.1, CCDS44117.1, CCDS44117.2, CCDS53300.1	1p34.3	2013-07-09	2013-07-09	2013-07-09	ENSG00000116990	ENSG00000116990		"Basic helix-loop-helix proteins"	7555	protein-coding gene	gene with protein product	"l-myc protein", "myc-related gene from lung cancer", "oncogene lmyc"	164850	"v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"	MYCL1		8978772	Standard	NM_001033082		Approved	LMYC, bHLHe38	uc001cer.2	P12524	OTTHUMG00000009243	ENST00000372816.2:c.248delG	chr1.hg19:g.40366859delC	ENSP00000361903:p.Gly83fs	176.0	0.0		302.0	19.0	NM_005376	A2A2C9|B4DJH2|Q14897|Q5QPL0|Q5QPL1|Q9NUE9	Frame_Shift_Del	DEL	ENST00000372816.2	hg19	CCDS30682.1																																																																																			.	.		0.711	MYCL-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277004.1	NM_001033082		-	40366859	C	-	40366859	7	5	112	1	0	1	0	1	0	0	0	0	10029	739	26	0	979	0	MYCL1	1	40366859	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	338843	40366859	208883762	32	16653										
COL9A2	1298	hgsc.bcm.edu	37	chr1	40776921	40776921	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccttcactccctgcagccctGggggacctttcattccgggt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:40776921delG	ENST00000372748.3	-	11	653	c.557delC	c.(556-558)ccafs	p.P186fs		NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	186	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			CTGCAGCCCTGGGGGACCTTT	0.587																																					p.P186fs		Atlas-INDEL	.											.	COL9A2	63	.	0			c.558delA						.						77	78	78					1																	40776921		2203	4300	6503	SO:0001589	frameshift_variant	1298	exon11			.	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.557delC	chr1.hg19:g.40776921delG	ENSP00000361834:p.Pro186fs	77.0	0.0		147.0	11.0	NM_001852	B2RMP9	Frame_Shift_Del	DEL	ENST00000372748.3	hg19	CCDS450.1																																																																																			.	.		0.587	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852		-	40776921	G	-	40776921	7	5	112	1	0	1	0	1	0	0	0	0	3710	1348	47	0	1600	0	COL9A2	1	40776921	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	410062	40776921	208473700	33	16654										
NFYC	4802	hgsc.bcm.edu	37	chr1	41204559	41204559	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggtactagcagcagtgatgCccagcaaagcctacagtcgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:41204559delC	ENST00000308733.5	+	1	50	c.44delC	c.(43-45)gccfs	p.A15fs	NFYC_ENST00000456393.2_Frame_Shift_Del_p.A15fs|NFYC_ENST00000440226.3_Frame_Shift_Del_p.A15fs|NFYC_ENST00000425457.2_Frame_Shift_Del_p.A15fs|NFYC_ENST00000372654.1_Frame_Shift_Del_p.A15fs|NFYC_ENST00000427410.2_Frame_Shift_Del_p.A15fs|NFYC_ENST00000372652.1_Frame_Shift_Del_p.A15fs|NFYC_ENST00000372653.1_Frame_Shift_Del_p.A15fs|NFYC_ENST00000372651.1_Frame_Shift_Del_p.A15fs|NFYC_ENST00000447388.3_Frame_Shift_Del_p.A15fs			Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma	15					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription, DNA-templated (GO:0045893)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(1)|prostate(1)|skin(2)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)			AGCAGTGATGCCCAGCAAAGC	0.403																																					p.A15fs		Atlas-INDEL	.											.	NFYC	39	.	0			c.43delG						.						118	119	118					1																	41204559		2203	4300	6503	SO:0001589	frameshift_variant	4802	exon2			.	U78774	CCDS455.1, CCDS44120.1, CCDS44121.1, CCDS44122.1, CCDS44123.1	1p32	2008-11-11			ENSG00000066136	ENSG00000066136			7806	protein-coding gene	gene with protein product		605344				8921405, 9249075	Standard	NM_014223		Approved	CBF-C, NF-YC	uc009vwd.3	Q13952	OTTHUMG00000007729	ENST00000308733.5:c.44delC	chr1.hg19:g.41204559delC	ENSP00000312617:p.Ala15fs	96.0	0.0		194.0	12.0	NM_001142587	B4DUS6|B4DW63|D3DPV9|F8VWM3|Q59GY4|Q5T6K8|Q5T6K9|Q5T6L1|Q5TZR6|Q92869|Q9HBX1|Q9NXB5|Q9UM67|Q9UML0|Q9UMT7	Frame_Shift_Del	DEL	ENST00000308733.5	hg19																																																																																				.	.		0.403	NFYC-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000020802.1	NM_014223		-	41204559	C	-	41204559	7	5	112	1	0	1	0	1	0	0	0	0	10400	739	26	0	46	0	NFYC	1	41204559	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	427638	41204559	208046062	34	16655										
MPL	4352	hgsc.bcm.edu	37	chr1	43812586	43812586	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcaactccgatacacaggagAaggccatcaggactggaagg	12	10	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:43812586A>G	ENST00000372470.3	+	8	1331	c.1289A>G	c.(1288-1290)gAa>gGa	p.E430G	MPL_ENST00000413998.2_Missense_Mutation_p.E430G	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	430	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	TACACAGGAGAAGGCCATCAG	0.562			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														p.E430G	NSCLC(52;534 1204 10016 41452 44427)	Atlas-SNP	.	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"myeloproliferative leukemia virus oncogene, thrombopoietin receptor"	yes	L	.	MPL	651	.	0			c.A1289G						.						51	47	48					1																	43812586		2203	4300	6503	SO:0001583	missense	4352	exon8			CAGGAGAAGGCCA	M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"CD molecules", "Fibronectin type III domain containing"	7217	protein-coding gene	gene with protein product		159530	"myeloproliferative leukemia virus oncogene"			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.1289A>G	chr1.hg19:g.43812586A>G	ENSP00000361548:p.Glu430Gly	39.0	0.0		85.0	4.0	NM_005373	Q5JUZ0	Missense_Mutation	SNP	ENST00000372470.3	hg19	CCDS483.1	.	.	.	.	.	.	.	.	.	.	a	19.68	3.872859	0.72180	.	.	ENSG00000117400	ENST00000372468;ENST00000372470;ENST00000413998	D;D	0.86627	-2.15;-2.15	5.3	5.3	0.74995	Fibronectin, type III (4);Long hematopoietin receptor, single chain, conserved site (1);Immunoglobulin-like fold (1);	1.167460	0.06230	N	0.688550	D	0.92410	0.7591	L	0.54323	1.7	0.30547	N	0.765804	D;D;D	0.89917	1.0;0.987;0.999	D;D;D	0.87578	0.998;0.912;0.979	T	0.82977	-0.0189	10	0.72032	D	0.01	-5.739	11.6301	0.51168	1.0:0.0:0.0:0.0	.	423;430;430	Q308M1;P40238;Q5JUY5	.;TPOR_HUMAN;.	G	430	ENSP00000361548:E430G;ENSP00000414004:E430G	ENSP00000361546:E430G	E	+	2	0	MPL	43585173	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.671000	0.61590	1.993000	0.58246	0.454000	0.30748	GAA	.	.		0.562	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373		G	43812586	A	G	43812586	3	3	112	1	0	0	0	0	1	0	0	0	9739	246	9	2	1319	2	MPL	1	43812586	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2608027	43812586	205438035	35	16656										
NASP	4678	hgsc.bcm.edu	37	chr1	46073055	46073055	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgggagaaaaagaagaagccAaaaaaacagaagacaagtct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:46073055delA	ENST00000350030.3	+	6	559	c.472delA	c.(472-474)aaafs	p.K159fs	NASP_ENST00000537798.1_Frame_Shift_Del_p.K95fs|NASP_ENST00000372052.4_Intron|NASP_ENST00000402363.3_Frame_Shift_Del_p.K161fs|NASP_ENST00000351223.3_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	159	Glu-rich (acidic).			K -> T (in Ref. 3; BAD96536). {ECO:0000305}.	blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					AGAAGAAGCCAAAAAAACAGA	0.393																																					p.A157fs		Atlas-INDEL	.											.	NASP	77	.	0			c.471delC						.						55	56	56					1																	46073055		2203	4300	6503	SO:0001589	frameshift_variant	4678	exon6			.	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"Tetratricopeptide (TTC) repeat domain containing"	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.472delA	chr1.hg19:g.46073055delA	ENSP00000255120:p.Lys159fs	138.0	0.0		238.0	17.0	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Frame_Shift_Del	DEL	ENST00000350030.3	hg19	CCDS524.1																																																																																			.	.		0.393	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		-	46073055	A	-	46073055	7	5	112	1	0	1	0	1	0	0	0	0	10181	131	5	0	571	0	NASP	1	46073055	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2260469	46073055	203177566	36	16657										
CCDC17	149483	hgsc.bcm.edu	37	chr1	46088658	46088658	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgcagctcctgaatgcgggCccccaacacctctagagctc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:46088658delC	ENST00000528266.1	-	4	772	c.625delG	c.(625-627)gccfs	p.A209fs	CCDC17_ENST00000464739.1_5'Flank|CCDC17_ENST00000343901.2_Frame_Shift_Del_p.A177fs|CCDC17_ENST00000421127.2_Frame_Shift_Del_p.A200fs|CCDC17_ENST00000445048.2_Intron			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	209										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					TGAATGCGGGCCCCCAACACC	0.692																																					p.A209fs		Atlas-INDEL	.											.	CCDC17	54	.	0			c.626delC						.						24	29	28					1																	46088658		2203	4298	6501	SO:0001589	frameshift_variant	149483	exon4			.		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.625delG	chr1.hg19:g.46088658delC	ENSP00000432172:p.Ala209fs	97.0	0.0		188.0	13.0	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Frame_Shift_Del	DEL	ENST00000528266.1	hg19	CCDS44131.2																																																																																			.	.		0.692	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500		-	46088658	C	-	46088658	7	5	112	1	0	1	0	1	0	0	0	0	2795	739	26	0	1283	0	CCDC17	1	46088658	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	15603	46088658	203161963	37	16658										
LDLRAD1	388633	hgsc.bcm.edu	37	chr1	54476004	54476004	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagttgttagtgccatcacaTttttggtctgagtagatcca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:54476004delT	ENST00000371360.1	-	5	437	c.420delA	c.(418-420)aaafs	p.K140fs	LDLRAD1_ENST00000420619.1_Frame_Shift_Del_p.K101fs|LDLRAD1_ENST00000545928.1_Frame_Shift_Del_p.K97fs|LDLRAD1_ENST00000371362.3_Frame_Shift_Del_p.K51fs	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1	140	LDL-receptor class A 2; atypical. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						TGCCATCACATTTTTGGTCTG	0.607																																					p.C141fs		Atlas-INDEL	.											.	LDLRAD1	22	.	0			c.421delT						.						74	72	73					1																	54476004		2203	4300	6503	SO:0001589	frameshift_variant	388633	exon5			.		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"low density lipoprotein receptor A domain containing 1"				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.420delA	chr1.hg19:g.54476004delT	ENSP00000360411:p.Lys140fs	90.0	0.0		164.0	11.0	NM_001010978	A0PJY0|B7ZME3|Q5T6Z9	Frame_Shift_Del	DEL	ENST00000371360.1	hg19	CCDS30725.1																																																																																			.	.		0.607	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978		-	54476004	T	-	54476004	7	5	112	1	0	1	0	1	0	0	0	0	8714	1490	52	0	205	0	LDLRAD1	1	54476004	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	8387346	54476004	194774617	38	16659										
CDCP2	200008	hgsc.bcm.edu	37	chr1	54605317	54605317	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggagctggagaagaccattcAtggggggggcaggacaaact	17	7	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:54605317A>T	ENST00000371330.1	-	4	2073	c.1226T>A	c.(1225-1227)aTg>aAg	p.M409K	RP11-446E24.4_ENST00000525949.1_5'Flank|CDCP2_ENST00000530059.1_Intron	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	409						extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						AAGACCATTCATGGGGGGGGC	0.597																																					p.M409K		Atlas-SNP	.											.	CDCP2	52	.	0			c.T1226A						.						52	54	53					1																	54605317		2203	4300	6503	SO:0001583	missense	200008	exon4			CCATTCATGGGGG		CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.1226T>A	chr1.hg19:g.54605317A>T	ENSP00000360381:p.Met409Lys	104.0	0.0		137.0	6.0	NM_201546	Q6ZWJ3	Missense_Mutation	SNP	ENST00000371330.1	hg19	CCDS588.2	.	.	.	.	.	.	.	.	.	.	A	8.959	0.970117	0.18659	.	.	ENSG00000157211	ENST00000371330	T	0.26810	1.71	1.84	-3.68	0.04463	.	4.591200	0.01848	U	0.035750	T	0.12817	0.0311	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.16424	-1.0403	10	0.07644	T	0.81	0.2877	3.6798	0.08306	0.3471:0.3485:0.3044:0.0	.	409	Q5VXM1	CDCP2_HUMAN	K	409	ENSP00000360381:M409K	ENSP00000360381:M409K	M	-	2	0	CDCP2	54377905	0.000000	0.05858	0.001000	0.08648	0.097000	0.18754	-1.482000	0.02320	-1.230000	0.02561	-0.648000	0.03929	ATG	.	.		0.597	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546		T	54605317	A	T	54605317	3	4	112	1	0	0	0	0	1	0	0	0	3096	217	8	4	127	4	CDCP2	1	54605317	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	129313	54605317	194645304	39	16660										
FAM151A	338094	hgsc.bcm.edu	37	chr1	55078303	55078303	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttgggtgtacgtcctgtttGgggacgtggacatgtagaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:55078303delG	ENST00000302250.2	-	5	816	c.656delC	c.(655-657)ccafs	p.P219fs	FAM151A_ENST00000371304.2_Frame_Shift_Del_p.P219fs|ACOT11_ENST00000371316.3_Intron	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	219						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						CGTCCTGTTTGGGGACGTGGA	0.572																																					p.P219fs		Atlas-INDEL	.											.	FAM151A	58	.	0			c.657delA						.						128	108	115					1																	55078303		2203	4300	6503	SO:0001589	frameshift_variant	338094	exon5			.	AK091901	CCDS594.1	1p32.3	2008-02-05	2007-12-18	2007-12-18	ENSG00000162391	ENSG00000162391			25032	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 179"	C1orf179		17273976	Standard	NM_176782		Approved	MGC27169	uc001cxn.3	Q8WW52	OTTHUMG00000009888	ENST00000302250.2:c.656delC	chr1.hg19:g.55078303delG	ENSP00000306888:p.Pro219fs	101.0	0.0		156.0	10.0	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Frame_Shift_Del	DEL	ENST00000302250.2	hg19	CCDS594.1																																																																																			.	.		0.572	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782		-	55078303	G	-	55078303	7	5	112	1	0	1	0	1	0	0	0	0	5463	1348	47	0	1117	0	FAM151A	1	55078303	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	472986	55078303	194172318	40	16661										
TACSTD2	4070	hgsc.bcm.edu	37	chr1	59041883	59041883	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctcggttcctttctcaactCccccagttccttgatctcca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:59041883delC	ENST00000371225.2	-	1	1283	c.946delG	c.(946-948)gagfs	p.E316fs		NM_002353.2	NP_002344.2	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	316					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell motility (GO:2000146)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of stem cell differentiation (GO:2000738)|regulation of epithelial cell proliferation (GO:0050678)|ureteric bud morphogenesis (GO:0060675)|visual perception (GO:0007601)	basal plasma membrane (GO:0009925)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)					all_cancers(7;6.54e-05)					TTTCTCAACTCCCCCAGTTCC	0.612																																					p.E316fs		Atlas-INDEL	.											.	TACSTD2	6	.	0			c.947delA						.						71	67	68					1																	59041883		2203	4300	6503	SO:0001589	frameshift_variant	4070	exon1			.	X77753	CCDS609.1	1p32	2008-02-05			ENSG00000184292	ENSG00000184292			11530	protein-coding gene	gene with protein product		137290		M1S1		8382772, 11306819	Standard	NM_002353		Approved	TROP2, GA733-1, EGP-1	uc001cyz.4	P09758	OTTHUMG00000010067	ENST00000371225.2:c.946delG	chr1.hg19:g.59041883delC	ENSP00000360269:p.Glu316fs	64.0	0.0		121.0	10.0	NM_002353	Q15658|Q6FG48|Q7Z7Q4|Q96QD2	Frame_Shift_Del	DEL	ENST00000371225.2	hg19	CCDS609.1																																																																																			.	.		0.612	TACSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027818.1	NM_002353		-	59041883	C	-	59041883	7	5	112	1	0	1	0	1	0	0	0	0	15523	864	30	0	29	0	TACSTD2	1	59041883	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	3963580	59041883	190208738	41	16662										
JAK1	3716	hgsc.bcm.edu	37	chr1	65310468	65310468	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcaccgtaatggggatgccGgggtcactgagcttgatgaa					rs548872770		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:65310468delG	ENST00000342505.4	-	16	2468	c.2220delC	c.(2218-2220)cccfs	p.P740fs	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	740	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TGGGGATGCCGGGGTCACTGA	0.577			Mis		ALL																																p.G741fs		Atlas-INDEL	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.2221delG						.						92	108	103					1																	65310468		2124	4232	6356	SO:0001589	frameshift_variant	3716	exon16			.	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2220delC	chr1.hg19:g.65310468delG	ENSP00000343204:p.Pro740fs	116.0	0.0		187.0	13.0	NM_002227	Q59GQ2|Q9UD26	Frame_Shift_Del	DEL	ENST00000342505.4	hg19	CCDS41346.1																																																																																			.	.		0.577	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		-	65310468	G	-	65310468	7	5	112	1	0	1	0	1	0	0	0	0	7946	1103	39	0	1284	0	JAK1	1	65310468	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	6268585	65310468	183940153	42	16663										
LEPROT	54741	hgsc.bcm.edu	37	chr1	65897552	65897552	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttttccttacaattcaagggTttttccttatatttggaaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:65897552delT	ENST00000371065.4	+	4	484	c.346delT	c.(346-348)tttfs	p.F117fs	LEPR_ENST00000371060.3_Intron|LEPR_ENST00000371059.3_Intron|LEPR_ENST00000344610.8_Intron|LEPR_ENST00000349533.6_Intron|LEPR_ENST00000406510.3_Intron	NM_001198681.1|NM_017526.4	NP_001185610.1|NP_059996.1	O15243	OBRG_HUMAN	leptin receptor overlapping transcript	117					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			kidney(1)|large_intestine(1)|lung(5)	7				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		AATTCAAGGGTTTTTCCTTAT	0.393																																					p.G124fs		Atlas-INDEL	.											.	LEPROT	16	.	0			c.372delG						.						136	131	132					1																	65897552		2203	4300	6503	SO:0001589	frameshift_variant	54741	exon5			.	Y12670	CCDS630.1, CCDS72801.1	1p31.2	2008-02-05			ENSG00000213625	ENSG00000213625			29477	protein-coding gene	gene with protein product	"leptin receptor gene related protein"	613461				9207021	Standard	NM_001198681		Approved	OBRGRP, OB-RGRP, VPS55, FLJ90360	uc001dcf.3	O15243	OTTHUMG00000009065	ENST00000371065.4:c.346delT	chr1.hg19:g.65897552delT	ENSP00000360104:p.Phe117fs	110.0	0.0		205.0	13.0	NM_001198681	Q6FHL5	Frame_Shift_Del	DEL	ENST00000371065.4	hg19	CCDS630.1																																																																																			.	.		0.393	LEPROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025132.4	NM_017526		-	65897552	T	-	65897552	7	5	112	1	0	1	0	1	0	0	0	0	8741	1725	60	0	360	0	LEPROT	1	65897552	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	587084	65897552	183353069	43	16664										
RPE65	6121	hgsc.bcm.edu	37	chr1	68910348	68910348	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctctactcctcgaaagtaagAaaaaaacctgtagaaacaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:68910348delA	ENST00000262340.5	-	5	414	c.361delT	c.(361-363)tctfs	p.S121fs		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	121					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						CGAAAGTAAGAAAAAAACCTG	0.368																																					p.S121fs		Atlas-INDEL	.											.	RPE65	87	.	0			c.362delC						.						50	53	52					1																	68910348		2201	4300	6501	SO:0001589	frameshift_variant	6121	exon5			.	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.361delT	chr1.hg19:g.68910348delA	ENSP00000262340:p.Ser121fs	80.0	0.0		169.0	13.0	NM_000329	A8K1L0|Q5T9U3	Frame_Shift_Del	DEL	ENST00000262340.5	hg19	CCDS643.1																																																																																			.	.		0.368	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		-	68910348	A	-	68910348	7	5	112	1	0	1	0	1	0	0	0	0	13560	246	9	0	1280	0	RPE65	1	68910348	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3012796	68910348	180340273	44	16665										
SFRS11	9295	hgsc.bcm.edu	37	chr1	70687464	70687464	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgagcgctagctctgagcagAtgcggactctcttcggtttc	12	12	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:70687464A>G	ENST00000370950.3	+	2	227	c.145A>G	c.(145-147)Atg>Gtg	p.M49V	SRSF11_ENST00000370951.1_Missense_Mutation_p.M49V|SRSF11_ENST00000436161.2_Missense_Mutation_p.M49V|SRSF11_ENST00000405432.1_Missense_Mutation_p.M49V|RP4-677H15.4_ENST00000422107.1_RNA|SRSF11_ENST00000454435.2_Missense_Mutation_p.M49V			Q05519	SRS11_HUMAN	serine/arginine-rich splicing factor 11	49	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(3)|ovary(2)|skin(1)	6						CTCTGAGCAGATGCGGACTCT	0.647																																					p.M49V		Atlas-SNP	.											.	SRSF11	68	.	0			c.A145G						.						80	81	81					1																	70687464		2203	4300	6503	SO:0001583	missense	9295	exon2			GAGCAGATGCGGA	M74002	CCDS647.1, CCDS53332.1	1p31.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000116754	ENSG00000116754		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10782	protein-coding gene	gene with protein product	"SR splicing factor 11"	602010	"splicing factor, arginine/serine-rich 11"	SFRS11		1896467, 20516191	Standard	NM_004768		Approved	p54, NET2	uc001des.3	Q05519	OTTHUMG00000009342	ENST00000370950.3:c.145A>G	chr1.hg19:g.70687464A>G	ENSP00000359988:p.Met49Val	52.0	0.0		80.0	4.0	NM_001190987	Q5T758|Q8IWE6	Missense_Mutation	SNP	ENST00000370950.3	hg19	CCDS647.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.919128	0.73098	.	.	ENSG00000116754	ENST00000370951;ENST00000370950;ENST00000405432;ENST00000454435;ENST00000395136;ENST00000436161	T;T;T;T;T;T	0.14893	2.47;2.47;2.47;2.47;2.47;2.47	5.29	5.29	0.74685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.25568	0.0622	L	0.47016	1.485	0.80722	D	1	P;P;P;P;P;P	0.44776	0.726;0.677;0.843;0.843;0.843;0.843	P;B;P;D;D;D	0.64506	0.762;0.322;0.893;0.926;0.926;0.926	T	0.01305	-1.1390	10	0.87932	D	0	.	14.8872	0.70579	1.0:0.0:0.0:0.0	.	49;49;49;49;49;49	B4DTC1;B4DWT1;Q05BU6;Q6PJB9;Q8IWE6;Q05519	.;.;.;.;.;SRS11_HUMAN	V	49	ENSP00000359989:M49V;ENSP00000359988:M49V;ENSP00000384357:M49V;ENSP00000411159:M49V;ENSP00000378568:M49V;ENSP00000405120:M49V	ENSP00000359988:M49V	M	+	1	0	SRSF11	70460052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.573000	0.90759	1.995000	0.58328	0.379000	0.24179	ATG	.	.		0.647	SRSF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025889.1	NM_004768		G	70687464	A	G	70687464	3	3	112	1	0	0	0	0	1	0	0	0	14181	333	12	2	147	2	SFRS11	1	70687464	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1777116	70687464	178563157	45	16666										
TTLL7	79739	hgsc.bcm.edu	37	chr1	84386998	84386998	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgaggagcctggtaagagccTtttaattgaattttgaccat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:84386998delT	ENST00000260505.8	-	11	1599	c.1222delA	c.(1222-1224)aggfs	p.R408fs	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	408					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		GGTAAGAGCCTTTTAATTGAA	0.408																																					p.R408fs		Atlas-INDEL	.											.	TTLL7	93	.	0			c.1223delG						.						83	84	84					1																	84386998		2203	4299	6502	SO:0001589	frameshift_variant	79739	exon11			.	AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"Tubulin tyrosine ligase-like family"	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.1222delA	chr1.hg19:g.84386998delT	ENSP00000260505:p.Arg408fs	91.0	0.0		189.0	12.0	NM_024686	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Frame_Shift_Del	DEL	ENST00000260505.8	hg19	CCDS690.2																																																																																			.	.		0.408	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686		-	84386998	T	-	84386998	7	5	112	1	0	1	0	1	0	0	0	0	16747	1608	56	0	1485	0	TTLL7	1	84386998	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	13699534	84386998	164863623	46	16667										
ODF2L	57489	hgsc.bcm.edu	37	chr1	86850466	86850466	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgttcagaaatcttcaaatTcaatgcagaaagattcgcct	6	9	4	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:86850466T>C	ENST00000359242.3	-	4	546	c.265A>G	c.(265-267)Aat>Gat	p.N89D	ODF2L_ENST00000317336.7_Missense_Mutation_p.N89D|ODF2L_ENST00000394731.1_5'UTR|ODF2L_ENST00000370566.3_Missense_Mutation_p.N89D|ODF2L_ENST00000370567.1_Missense_Mutation_p.N89D|ODF2L_ENST00000294678.2_Missense_Mutation_p.N89D	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	89						centrosome (GO:0005813)		p.N89H(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		ATCTTCAAATTCAATGCAGAA	0.279																																					p.N89D		Atlas-SNP	.											ODF2L,colon,carcinoma,0,1	ODF2L	53	.	1	Substitution - Missense(1)	large_intestine(1)	c.A265G						.						54	53	53					1																	86850466		2202	4284	6486	SO:0001583	missense	57489	exon4			TCAAATTCAATGC		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.265A>G	chr1.hg19:g.86850466T>C	ENSP00000359600:p.Asn89Asp	47.0	0.0		63.0	3.0	NM_001184766	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Missense_Mutation	SNP	ENST00000359242.3	hg19	CCDS41354.2	.	.	.	.	.	.	.	.	.	.	T	0.634	-0.815961	0.02776	.	.	ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000317336;ENST00000370567;ENST00000294678;ENST00000465959	T;T;T;T;T	0.22336	1.97;1.98;1.98;1.96;1.97	5.17	1.43	0.22495	.	2.459430	0.01409	N	0.013911	T	0.03390	0.0098	N	0.24115	0.695	0.09310	N	0.999998	B;B;B;P;P	0.43352	0.001;0.024;0.003;0.634;0.804	B;B;B;B;B	0.36719	0.003;0.012;0.005;0.085;0.231	T	0.19321	-1.0309	10	0.12103	T	0.63	-1.0E-4	4.0073	0.09607	0.3218:0.0891:0.0:0.5892	.	89;89;89;89;89	B4E037;Q9ULJ1-2;Q9ULJ1-4;Q9ULJ1-3;Q9ULJ1	.;.;.;.;ODF2L_HUMAN	D	89	ENSP00000359597:N89D;ENSP00000359600:N89D;ENSP00000320165:N89D;ENSP00000359598:N89D;ENSP00000294678:N89D	ENSP00000294678:N89D	N	-	1	0	ODF2L	86623054	0.001000	0.12720	0.022000	0.16811	0.364000	0.29643	0.762000	0.26503	0.048000	0.15891	0.451000	0.29950	AAT	.	.		0.279	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			C	86850466	T	C	86850466	3	2	112	1	0	0	0	0	1	0	0	0	10837	1783	62	2	1881	2	ODF2L	1	86850466	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2463468	86850466	162400155	47	16668										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86900229	86900229	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attttgtaatgcaagtacccAcaaccaagaagcaccaaacc	5	12	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:86900229A>G	ENST00000370565.4	+	6	935	c.773A>G	c.(772-774)cAc>cGc	p.H258R		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	258					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		GCAAGTACCCACAACCAAGAA	0.428																																					p.H258R	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.A773G						.						121	112	115					1																	86900229		2203	4300	6503	SO:0001583	missense	9635	exon6			GTACCCACAACCA		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.773A>G	chr1.hg19:g.86900229A>G	ENSP00000359596:p.His258Arg	75.0	0.0		122.0	5.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.558641	0.86231	.	.	ENSG00000137975	ENST00000370565	T	0.19938	2.11	6.17	6.17	0.99709	Chloride channel calcium-activated (1);	0.000000	0.85682	D	0.000000	T	0.48660	0.1512	M	0.91196	3.185	0.49687	D	0.999819	D	0.76494	0.999	D	0.71656	0.974	T	0.61143	-0.7122	10	0.87932	D	0	-9.4266	16.4837	0.84171	1.0:0.0:0.0:0.0	.	258	Q9UQC9	CLCA2_HUMAN	R	258	ENSP00000359596:H258R	ENSP00000359596:H258R	H	+	2	0	CLCA2	86672817	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.997000	0.76270	2.371000	0.80710	0.533000	0.62120	CAC	.	.		0.428	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		G	86900229	A	G	86900229	3	3	112	1	0	0	0	0	1	0	0	0	3460	159	6	2	795	2	CLCA2	1	86900229	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	49763	86900229	162350392	48	16669										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86920818	86920818	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtctacagaatatccaagatGactttaacaatgctatttta	5	7	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:86920818G>A	ENST00000370565.4	+	14	2602	c.2440G>A	c.(2440-2442)Gac>Aac	p.D814N		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	814					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TATCCAAGATGACTTTAACAA	0.318																																					p.D814N	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.G2440A						.						42	42	42					1																	86920818		2203	4300	6503	SO:0001583	missense	9635	exon14			CAAGATGACTTTA		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2440G>A	chr1.hg19:g.86920818G>A	ENSP00000359596:p.Asp814Asn	72.0	0.0		100.0	4.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	G	9.007	0.981460	0.18812	.	.	ENSG00000137975	ENST00000370565	T	0.02472	4.28	5.78	3.9	0.45041	.	0.266861	0.33854	N	0.004492	T	0.00906	0.0030	L	0.34521	1.04	0.33416	D	0.579243	P	0.49090	0.919	P	0.47015	0.534	T	0.26087	-1.0113	10	0.02654	T	1	-17.7009	5.6904	0.17827	0.3612:0.0:0.6388:0.0	.	814	Q9UQC9	CLCA2_HUMAN	N	814	ENSP00000359596:D814N	ENSP00000359596:D814N	D	+	1	0	CLCA2	86693406	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.061000	0.49963	1.444000	0.47605	0.585000	0.79938	GAC	.	.		0.318	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		A	86920818	G	A	86920818	3	1	112	1	0	0	0	0	1	0	0	0	3460	1290	45	3	2494	3	CLCA2	1	86920818	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	20589	86920818	162329803	49	16670										
PKN2	5586	hgsc.bcm.edu	37	chr1	89270151	89270151	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaatttctgaggttagaagaTtttttagacaaccaacggca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:89270151delT	ENST00000370521.3	+	9	1718	c.1359delT	c.(1357-1359)gatfs	p.D453fs	PKN2_ENST00000544045.1_Frame_Shift_Del_p.D127fs|PKN2_ENST00000370513.5_Intron|PKN2_ENST00000370505.3_Frame_Shift_Del_p.D296fs|PKN2_ENST00000316005.7_Frame_Shift_Del_p.D453fs	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	453	C2.|Necessary to rescue apical junction formation. {ECO:0000250}.				apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		GGTTAGAAGATTTTTTAGACA	0.343																																					p.D453fs		Atlas-INDEL	.											.	PKN2	109	.	0			c.1358delA						.						110	104	106					1																	89270151		1843	4088	5931	SO:0001589	frameshift_variant	5586	exon9			.	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"cardiolipin-activated protein kinase Pak2"	602549	"protein kinase C-like 2"	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1359delT	chr1.hg19:g.89270151delT	ENSP00000359552:p.Asp453fs	176.0	0.0		223.0	14.0	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Frame_Shift_Del	DEL	ENST00000370521.3	hg19	CCDS714.1																																																																																			.	.		0.343	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		-	89270151	T	-	89270151	7	5	112	1	0	1	0	1	0	0	0	0	11989	1490	52	0	1393	0	PKN2	1	89270151	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2349333	89270151	159980470	50	16671										
LRRC8B	23507	hgsc.bcm.edu	37	chr1	90049043	90049043	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atcataacttatgttccataTtttttaacccacatcactct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:90049043delT	ENST00000330947.2	+	5	1194	c.834delT	c.(832-834)tatfs	p.Y278fs	RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Frame_Shift_Del_p.Y278fs|LRRC8B_ENST00000439853.1_Frame_Shift_Del_p.Y278fs	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	278					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	26		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		ATGTTCCATATTTTTTAACCC	0.373																																					p.Y278fs		Atlas-INDEL	.											.	LRRC8B	49	.	0			c.833delA						.						121	118	119					1																	90049043		2203	4300	6503	SO:0001589	frameshift_variant	23507	exon5			.	AF385436	CCDS724.1	1p22.2	2008-02-05			ENSG00000197147	ENSG00000197147			30692	protein-coding gene	gene with protein product	"T cell activation leucine repeat rich protein"	612888				9039502	Standard	NM_015350		Approved	TA-LRRP, KIAA0231	uc001dni.3	Q6P9F7	OTTHUMG00000010129	ENST00000330947.2:c.834delT	chr1.hg19:g.90049043delT	ENSP00000332674:p.Tyr278fs	113.0	0.0		178.0	11.0	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Frame_Shift_Del	DEL	ENST00000330947.2	hg19	CCDS724.1																																																																																			.	.		0.373	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350		-	90049043	T	-	90049043	7	5	112	1	0	1	0	1	0	0	0	0	9031	1500	52	0	836	0	LRRC8B	1	90049043	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	778892	90049043	159201578	51	16672										
LRRC8D	55144	hgsc.bcm.edu	37	chr1	90399470	90399470	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atcctggataaaaaggatggAgagcaggccaaagccctgtt	12	8	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:90399470A>G	ENST00000337338.5	+	3	1250	c.843A>G	c.(841-843)ggA>ggG	p.G281G	LRRC8D_ENST00000394593.3_Silent_p.G281G	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	281					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		AAAAGGATGGAGAGCAGGCCA	0.428																																					p.G281G		Atlas-SNP	.											.	LRRC8D	78	.	0			c.A843G						.						40	40	40					1																	90399470		2203	4300	6503	SO:0001819	synonymous_variant	55144	exon3			GGATGGAGAGCAG	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.843A>G	chr1.hg19:g.90399470A>G		68.0	0.0		111.0	5.0	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Silent	SNP	ENST00000337338.5	hg19	CCDS726.1																																																																																			.	.		0.428	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		G	90399470	A	G	90399470	2	3	112	1	0	0	0	0	0	0	0	1	9033	291	11	2		2	LRRC8D	1	90399470	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	350427	90399470	158851151	52	16673										
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94670628	94670628	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcaactcacccaagttaagcTttttttcaacccatgaaact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:94670628delT	ENST00000260526.6	-	7	868	c.686delA	c.(685-687)aagfs	p.K229fs	ARHGAP29_ENST00000370217.3_Frame_Shift_Del_p.K229fs	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	229					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		CAAGTTAAGCTTTTTTTCAAC	0.318																																					p.K229fs		Atlas-INDEL	.											.	ARHGAP29	132	.	0			c.687delG						.						84	84	84					1																	94670628		2202	4298	6500	SO:0001589	frameshift_variant	9411	exon7			.		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.686delA	chr1.hg19:g.94670628delT	ENSP00000260526:p.Lys229fs	153.0	0.0		232.0	16.0	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Frame_Shift_Del	DEL	ENST00000260526.6	hg19	CCDS748.1																																																																																			.	.		0.318	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		-	94670628	T	-	94670628	7	5	112	1	0	1	0	1	0	0	0	0	878	1609	56	0	3167	0	ARHGAP29	1	94670628	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	4271158	94670628	154579993	53	16674										
VCAM1	7412	hgsc.bcm.edu	37	chr1	101197977	101197977	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgtctctgccttttcagttgCccccagagatacaaccgtct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:101197977delC	ENST00000294728.2	+	7	1630	c.1529delC	c.(1528-1530)gccfs	p.A510fs	VCAM1_ENST00000347652.2_Frame_Shift_Del_p.A418fs|VCAM1_ENST00000370119.4_Frame_Shift_Del_p.A448fs|VCAM1_ENST00000370115.1_Frame_Shift_Del_p.A311fs	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	510					acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	TTTTCAGTTGCCCCCAGAGAT	0.483																																					p.A510fs		Atlas-INDEL	.											.	VCAM1	111	.	0			c.1528delG						.						84	86	86					1																	101197977		2203	4300	6503	SO:0001589	frameshift_variant	7412	exon7			.	M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.1529delC	chr1.hg19:g.101197977delC	ENSP00000294728:p.Ala510fs	57.0	0.0		101.0	11.0	NM_001078	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Frame_Shift_Del	DEL	ENST00000294728.2	hg19	CCDS773.1																																																																																			.	.		0.483	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078		-	101197977	C	-	101197977	7	5	112	1	0	1	0	1	0	0	0	0	17152	739	26	0	1555	0	VCAM1	1	101197977	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	6527349	101197977	148052644	54	16675										
FNDC7	163479	hgsc.bcm.edu	37	chr1	109260509	109260509	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acctcctcacggctgaagacGgggacacagtcattgaaacc	10	13	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:109260509G>T	ENST00000370017.3	+	3	470	c.193G>T	c.(193-195)Ggg>Tgg	p.G65W	FNDC7_ENST00000271311.2_Missense_Mutation_p.G66W	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	65	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		GGCTGAAGACGGGGACACAGT	0.522																																					p.G65W		Atlas-SNP	.											FNDC7_ENST00000370017,colon,carcinoma,0,1	FNDC7	113	.	0			c.G193T						.						106	85	92					1																	109260509		692	1591	2283	SO:0001583	missense	163479	exon3			GAAGACGGGGACA		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"Fibronectin type III domain containing"	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.193G>T	chr1.hg19:g.109260509G>T	ENSP00000359034:p.Gly65Trp	147.0	0.0		221.0	0.0	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	hg19	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.186653	0.57909	.	.	ENSG00000143107	ENST00000370017;ENST00000271311	T;T	0.57273	0.41;0.41	5.78	5.78	0.91487	.	.	.	.	.	T	0.67767	0.2928	M	0.63428	1.95	0.44780	D	0.997789	D	0.89917	1.0	D	0.97110	1.0	T	0.69113	-0.5231	9	0.87932	D	0	.	20.0065	0.97435	0.0:0.0:1.0:0.0	.	65	E9PAZ5	.	W	65;66	ENSP00000359034:G65W;ENSP00000271311:G66W	ENSP00000271311:G66W	G	+	1	0	FNDC7	109062032	1.000000	0.71417	0.875000	0.34327	0.303000	0.27691	4.733000	0.62036	2.731000	0.93534	0.655000	0.94253	GGG	.	.		0.522	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532		T	109260509	G	T	109260509	3	4	112	1	0	0	0	0	1	0	0	0	5981	1116	39	1	203	1	FNDC7	1	109260509	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	8062532	109260509	139990112	55	16676										
PSRC1	84722	hgsc.bcm.edu	37	chr1	109823047	109823047	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctgggactgccactttcctGgggggctgcagattgctgcg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:109823047delG	ENST00000438534.2	-	6	1197	c.1059delC	c.(1057-1059)cccfs	p.P353fs	PSRC1_ENST00000409138.2_Frame_Shift_Del_p.P353fs|PSRC1_ENST00000369903.2_Frame_Shift_Del_p.P323fs|PSRC1_ENST00000369904.3_Frame_Shift_Del_p.Q290fs|PSRC1_ENST00000369907.3_Frame_Shift_Del_p.P323fs|PSRC1_ENST00000409267.1_Frame_Shift_Del_p.P323fs|PSRC1_ENST00000369909.2_Frame_Shift_Del_p.P323fs	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	353	Pro/Ser-rich.				microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		CCACTTTCCTGGGGGGCTGCA	0.547																																					p.R324fs		Atlas-INDEL	.											.	PSRC1	12	.	0			c.970delA						.						38	43	42					1																	109823047		2203	4300	6503	SO:0001589	frameshift_variant	84722	exon7			.		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"differential display and activated by p53"	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.1059delC	chr1.hg19:g.109823047delG	ENSP00000413591:p.Pro353fs	87.0	0.0		159.0	13.0	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Frame_Shift_Del	DEL	ENST00000438534.2	hg19																																																																																				.	.		0.547	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636		-	109823047	G	-	109823047	7	5	112	1	0	1	0	1	0	0	0	0	12731	1357	47	0	72	0	PSRC1	1	109823047	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	562538	109823047	139427574	56	16677										
PSRC1	84722	hgsc.bcm.edu	37	chr1	109824582	109824582	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taggctgagcctcacaccctGgggggcaggtgccactgcat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:109824582delG	ENST00000438534.2	-	4	316	c.178delC	c.(178-180)cagfs	p.Q60fs	PSRC1_ENST00000409138.2_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369903.2_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369904.3_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369907.3_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000409267.1_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369909.2_Frame_Shift_Del_p.Q60fs	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	60					microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		CTCACACCCTGGGGGGCAGGT	0.622																																					p.Q60fs		Atlas-INDEL	.											.	PSRC1	12	.	0			c.179delA						.						16	15	16					1																	109824582		2188	4287	6475	SO:0001589	frameshift_variant	84722	exon4			.		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"differential display and activated by p53"	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.178delC	chr1.hg19:g.109824582delG	ENSP00000413591:p.Gln60fs	74.0	0.0		165.0	11.0	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Frame_Shift_Del	DEL	ENST00000438534.2	hg19																																																																																				.	.		0.622	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636		-	109824582	G	-	109824582	7	5	112	1	0	1	0	1	0	0	0	0	12731	1357	47	0	904	0	PSRC1	1	109824582	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1535	109824582	139426039	57	16678										
CSDE1	7812	hgsc.bcm.edu	37	chr1	115272999	115272999	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaaccgtgcccttgggaagTtttttaatcctaatagcatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:115272999delT	ENST00000358528.4	-	12	1662	c.1236delA	c.(1234-1236)aaafs	p.K412fs	CSDE1_ENST00000339438.6_Frame_Shift_Del_p.K381fs|CSDE1_ENST00000534699.1_Frame_Shift_Del_p.K412fs|CSDE1_ENST00000261443.5_Frame_Shift_Del_p.K381fs|CSDE1_ENST00000369530.1_Frame_Shift_Del_p.K427fs|CSDE1_ENST00000530886.1_Frame_Shift_Del_p.K282fs|CSDE1_ENST00000438362.2_Frame_Shift_Del_p.K458fs|Y_RNA_ENST00000365030.1_RNA	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	412					male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCTTGGGAAGTTTTTTAATCC	0.358																																					p.L459fs		Atlas-INDEL	.											.	CSDE1	145	.	0			c.1375delC						.						81	86	85					1																	115272999		2203	4300	6503	SO:0001589	frameshift_variant	7812	exon13			.		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"upstream of NRAS"	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1236delA	chr1.hg19:g.115272999delT	ENSP00000351329:p.Lys412fs	72.0	0.0		116.0	10.0	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Frame_Shift_Del	DEL	ENST00000358528.4	hg19	CCDS30812.1																																																																																			.	.		0.358	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		-	115272999	T	-	115272999	7	5	112	1	0	1	0	1	0	0	0	0	3931	1722	60	0	1196	0	CSDE1	1	115272999	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	5448417	115272999	133977622	58	16679										
TTF2	8458	hgsc.bcm.edu	37	chr1	117618310	117618310	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtttcctctaagcctgggagCcccctactctttgactcgac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:117618310delC	ENST00000369466.4	+	5	1148	c.1104delC	c.(1102-1104)agcfs	p.S368fs		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	368					ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		AGCCTGGGAGCCCCCTACTCT	0.527																																					p.S368fs		Atlas-INDEL	.											.	TTF2	92	.	0			c.1103delG						.			6,4260		2,2,2129	67	61	63			0.6	0	1		63	17,8237		7,3,4117	no	frameshift	TTF2	NM_003594.3		9,5,6246	A1A1,A1R,RR		0.206,0.1406,0.1837			117618310	23,12497	2203	4300	6503	SO:0001589	frameshift_variant	8458	exon5			.	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 6"	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.1104delC	chr1.hg19:g.117618310delC	ENSP00000358478:p.Ser368fs	191.0	0.0		382.0	23.0	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Frame_Shift_Del	DEL	ENST00000369466.4	hg19	CCDS892.1																																																																																			.	.		0.527	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			-	117618310	C	-	117618310	7	5	112	1	0	1	0	1	0	0	0	0	16734	738	26	0	1122	0	TTF2	1	117618310	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	2345311	117618310	131632311	59	16680										
HMGCS2	3158	hgsc.bcm.edu	37	chr1	120301762	120301762	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgcttccactgattctggaTttttttacggtatgatgtgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:120301762delT	ENST00000369406.3	-	4	878	c.829delA	c.(829-831)atcfs	p.I277fs	HMGCS2_ENST00000544913.2_Frame_Shift_Del_p.I235fs|HMGCS2_ENST00000476640.1_Intron	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	277					cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)	p.I277F(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		TGATTCTGGATTTTTTTACGG	0.478																																					p.I277fs		Atlas-Indel,Pindel	.											.	HMGCS2	58	.	1	Substitution - Missense(1)	NS(1)	c.830delT						.						131	131	131					1																	120301762		2203	4300	6503	SO:0001589	frameshift_variant	3158	exon4			.	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.829delA	chr1.hg19:g.120301762delT	ENSP00000358414:p.Ile277fs	140.0	0.0		197.0	13.0	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Frame_Shift_Del	DEL	ENST00000369406.3	hg19	CCDS905.1																																																																																			.	.		0.478	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518		-	120301762	T	-	120301762	7	5	112	1	0	1	0	1	0	0	0	0	7242	1493	52	0	721	0	HMGCS2	1	120301762	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2683452	120301762	128948859	60	16681										
GJA8	2703	hgsc.bcm.edu	37	chr1	147380686	147380686	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcgtgtcccggcccacggagAaaaccatcttcatcctgttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:147380686delA	ENST00000369235.1	+	1	604	c.604delA	c.(604-606)aaafs	p.K202fs	GJA8_ENST00000240986.4_Frame_Shift_Del_p.K202fs			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	202					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GCCCACGGAGAAAACCATCTT	0.602																																					p.E201fs	Melanoma(76;1255 1795 8195 52096)	Atlas-INDEL	.											.	GJA8	108	.	0			c.603delG						.						119	102	108					1																	147380686		2203	4300	6503	SO:0001589	frameshift_variant	2703	exon2			.	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.604delA	chr1.hg19:g.147380686delA	ENSP00000358238:p.Lys202fs	89.0	0.0		148.0	10.0	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Frame_Shift_Del	DEL	ENST00000369235.1	hg19	CCDS30834.1																																																																																			.	.		0.602	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		-	147380686	A	-	147380686	7	5	112	1	0	1	0	1	0	0	0	0	6413	247	9	0	606	0	GJA8	1	147380686	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	27078924	147380686	101869935	61	16682										
PLEKHO1	51177	hgsc.bcm.edu	37	chr1	150131502	150131502	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggaagcgaaaggccaaggaCccccctcggtctccgccgga					rs587674656		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:150131502delC	ENST00000369124.4	+	6	1292	c.1014delC	c.(1012-1014)gacfs	p.D338fs	PLEKHO1_ENST00000025469.6_Frame_Shift_Del_p.D304fs|PLEKHO1_ENST00000369126.1_Frame_Shift_Del_p.D155fs	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	338	Negative regulator of AP-1 activity.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGCCAAGGACCCCCCTCGGT	0.607																																					p.D338fs		Atlas-INDEL	.											.	PLEKHO1	37	.	0			c.1013delA						.						52	57	56					1																	150131502		2203	4300	6503	SO:0001589	frameshift_variant	51177	exon6			.	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.1014delC	chr1.hg19:g.150131502delC	ENSP00000358120:p.Asp338fs	126.0	0.0		233.0	16.0	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Frame_Shift_Del	DEL	ENST00000369124.4	hg19	CCDS945.1																																																																																			.	.		0.607	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		-	150131502	C	-	150131502	7	5	112	1	0	1	0	1	0	0	0	0	12093	506	18	0	1036	0	PLEKHO1	1	150131502	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	2750816	150131502	99119119	62	16683										
RPRD2	23248	hgsc.bcm.edu	37	chr1	150429791	150429791	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaacctttgctaaccgagtaAacaatttaaagaagaagttg	7	6	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:150429791A>G	ENST00000369068.4	+	8	902	c.898A>G	c.(898-900)Aac>Gac	p.N300D	RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.N274D|RPRD2_ENST00000539519.1_Missense_Mutation_p.N274D	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	300						DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TAACCGAGTAAACAATTTAAA	0.408																																					p.N300D		Atlas-SNP	.											.	RPRD2	189	.	0			c.A898G						.						84	80	82					1																	150429791		1851	4098	5949	SO:0001583	missense	23248	exon8			CGAGTAAACAATT	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.898A>G	chr1.hg19:g.150429791A>G	ENSP00000358064:p.Asn300Asp	68.0	0.0		83.0	4.0	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	hg19	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.802671	0.50315	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.45668	0.89;0.9;0.9	5.18	5.18	0.71444	.	0.247869	0.47852	D	0.000201	T	0.16514	0.0397	L	0.29908	0.895	0.28767	N	0.900554	B;P;P	0.36535	0.255;0.495;0.557	B;B;B	0.30716	0.053;0.119;0.116	T	0.08086	-1.0739	10	0.42905	T	0.14	-14.3218	15.4834	0.75545	1.0:0.0:0.0:0.0	.	274;300;274	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	D	274;274;300	ENSP00000383785:N274D;ENSP00000445482:N274D;ENSP00000358064:N300D	ENSP00000358064:N300D	N	+	1	0	RPRD2	148696415	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.933000	0.56545	2.291000	0.77112	0.519000	0.50382	AAC	.	.		0.408	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		G	150429791	A	G	150429791	3	3	112	1	0	0	0	0	1	0	0	0	13632	14	1	2	928	2	RPRD2	1	150429791	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	298289	150429791	98820830	63	16684										
TARS2	80222	hgsc.bcm.edu	37	chr1	150469064	150469064	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagggtctgggaagcatggaGggaggaagcagaattgcggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:150469064delG	ENST00000369064.3	+	8	915	c.881delG	c.(880-882)aggfs	p.R294fs	TARS2_ENST00000463555.1_Intron|TARS2_ENST00000438568.2_3'UTR|TARS2_ENST00000606933.1_Intron|TARS2_ENST00000369054.2_Intron	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	294					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	GAAGCATGGAGGGAGGAAGCA	0.542																																					p.R294fs		Atlas-INDEL	.											.	TARS2	91	.	0			c.880delA						.						131	125	127					1																	150469064		2203	4300	6503	SO:0001589	frameshift_variant	80222	exon8			.	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	30740	protein-coding gene	gene with protein product	"threonine tRNA ligase 2, mitochondrial"	612805	"threonyl-tRNA synthetase-like 1"	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.881delG	chr1.hg19:g.150469064delG	ENSP00000358060:p.Arg294fs	121.0	0.0		216.0	14.0	NM_025150	Q53GW7|Q96I50|Q9H9V2	Frame_Shift_Del	DEL	ENST00000369064.3	hg19	CCDS952.1																																																																																			.	.		0.542	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150		-	150469064	G	-	150469064	7	5	112	1	0	1	0	1	0	0	0	0	15575	1000	35	0	911	0	TARS2	1	150469064	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	39273	150469064	98781557	64	16685										
BNIPL	149428	hgsc.bcm.edu	37	chr1	151019162	151019162	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccatggctcaggagggacatAgcacaggactggataaaagg	14	8	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:151019162A>G	ENST00000368931.3	+	10	1229	c.1073A>G	c.(1072-1074)tAg>tGg	p.*358W	C1orf56_ENST00000368926.5_5'Flank|BNIPL_ENST00000295294.7_Nonstop_Mutation_p.*276W	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	0					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GGAGGGACATAGCACAGGACT	0.498																																					p.X358W		Atlas-SNP	.											.	BNIPL	45	.	0			c.A1073G						.						125	109	115					1																	151019162		2203	4300	6503	SO:0001578	stop_lost	149428	exon10			GGACATAGCACAG	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.1073A>G	chr1.hg19:g.151019162A>G	ENSP00000357927:p.*358Trpext*5	90.0	0.0		122.0	5.0	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Missense_Mutation	SNP	ENST00000368931.3	hg19	CCDS978.2	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082695	0.76528	.	.	ENSG00000163141	ENST00000368931;ENST00000361277;ENST00000295294	.	.	.	5.85	0.493	0.16878	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.5308	0.04703	0.6024:0.1253:0.0785:0.1939	.	.	.	.	W	358;356;276	.	.	X	+	2	0	BNIPL	149285786	0.718000	0.27976	0.003000	0.11579	0.671000	0.39405	1.073000	0.30691	-0.150000	0.11195	0.533000	0.62120	TAG	.	.		0.498	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279		G	151019162	A	G	151019162	4	3	112	1	0	0	0	0	0	0	0	0	1480	433	15	2	1111	2	BNIPL	1	151019162	Nonstop_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	550098	151019162	98231459	65	16686										
SELENBP1	8991	hgsc.bcm.edu	37	chr1	151339214	151339214	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcaccagcctccacatcagcGgggttgaagccatctcgtaa					rs375401678		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:151339214delG	ENST00000368868.5	-	6	739	c.648delC	c.(646-648)cccfs	p.P216fs	SELENBP1_ENST00000435071.1_Frame_Shift_Del_p.P152fs|SELENBP1_ENST00000473693.1_5'Flank|SELENBP1_ENST00000426705.2_Frame_Shift_Del_p.P258fs|SELENBP1_ENST00000447402.3_Frame_Shift_Del_p.P154fs	NM_003944.3	NP_003935.2	Q13228	SBP1_HUMAN	selenium binding protein 1	216					protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	selenium binding (GO:0008430)	p.P216P(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|urinary_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CCACATCAGCGGGGTTGAAGC	0.572																																					p.A259fs		Atlas-INDEL	.											.	SELENBP1	44	.	1	Substitution - coding silent(1)	lung(1)	c.775delG						.						175	153	160					1																	151339214		2203	4300	6503	SO:0001589	frameshift_variant	8991	exon6			.	U29091	CCDS995.1, CCDS58027.1, CCDS60266.1	1q21.3	2014-05-19			ENSG00000143416	ENSG00000143416			10719	protein-coding gene	gene with protein product		604188				9027582	Standard	NM_003944		Approved	hSP56, hSBP, LPSB	uc010pcy.3	Q13228	OTTHUMG00000012498	ENST00000368868.5:c.648delC	chr1.hg19:g.151339214delG	ENSP00000357861:p.Pro216fs	88.0	0.0		163.0	10.0	NM_001258289	A6NML9|A6PVW9|B2RDR3|B4DKP6|B4E1F3|Q49AQ8|Q96GX7	Frame_Shift_Del	DEL	ENST00000368868.5	hg19	CCDS995.1																																																																																			.	.		0.572	SELENBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034904.4			-	151339214	G	-	151339214	7	5	112	1	0	1	0	1	0	0	0	0	14029	1103	39	0	798	0	SELENBP1	1	151339214	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	320052	151339214	97911407	66	16687										
LCE2D	353141	hgsc.bcm.edu	37	chr1	152636615	152636615	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaaccagcagcagtgccagCcccctcccaaatgtcctccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:152636615delC	ENST00000368784.1	+	2	89	c.34delC	c.(34-36)cccfs	p.P14fs		NM_178430.2	NP_848517.1	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	14	Cys-rich.				keratinization (GO:0031424)					large_intestine(1)|lung(7)|prostate(2)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCAGTGCCAGCCCCCTCCCAA	0.493																																					p.Q11fs		Atlas-INDEL	.											.	LCE2D	26	.	0			c.33delG						.						106	112	110					1																	152636615		2203	4300	6503	SO:0001589	frameshift_variant	353141	exon2			.	BI670513	CCDS1018.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000187223	ENSG00000187223		"Late cornified envelopes"	16518	protein-coding gene	gene with protein product		612612	"small proline rich-like (epidermal differentiation complex) 1A"	SPRL1A		11698679	Standard	NM_178430		Approved	LEP12	uc001fag.4	Q5TA82	OTTHUMG00000014400	ENST00000368784.1:c.34delC	chr1.hg19:g.152636615delC	ENSP00000357773:p.Pro14fs	113.0	0.0		146.0	10.0	NM_178430	A1L4M8	Frame_Shift_Del	DEL	ENST00000368784.1	hg19	CCDS1018.1																																																																																			.	.		0.493	LCE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040058.1	NM_178430		-	152636615	C	-	152636615	7	5	112	1	0	1	0	1	0	0	0	0	8677	739	26	0	36	0	LCE2D	1	152636615	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1297401	152636615	96614006	67	16688										
SPRR2G	6706	hgsc.bcm.edu	37	chr1	153122487	153122487	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggaggaggcaggtaaggctCagggcacttcgggggtggac	20	7	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:153122487C>T	ENST00000368748.4	-	2	138	c.100G>A	c.(100-102)Gag>Aag	p.E34K		NM_001014291.3	NP_001014313.1	Q9BYE4	SPR2G_HUMAN	small proline-rich protein 2G	34	3 X 9 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				endometrium(1)|lung(1)|skin(1)	3	all_lung(78;1.78e-30)|Lung NSC(65;7.29e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGTAAGGCTCAGGGCACTTC	0.612																																					p.E34K		Atlas-SNP	.											.	SPRR2G	20	.	0			c.G100A						.						151	115	127					1																	153122487		2203	4300	6503	SO:0001583	missense	6706	exon2			AAGGCTCAGGGCA	AF333957	CCDS30868.1	1q21-q22	2008-02-05			ENSG00000159516	ENSG00000159516			11267	protein-coding gene	gene with protein product						8325635, 11279051	Standard	NM_001014291		Approved		uc009wod.2	Q9BYE4	OTTHUMG00000014399	ENST00000368748.4:c.100G>A	chr1.hg19:g.153122487C>T	ENSP00000357737:p.Glu34Lys	66.0	0.0		141.0	75.0	NM_001014291		Missense_Mutation	SNP	ENST00000368748.4	hg19	CCDS30868.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687891	0.29962	.	.	ENSG00000159516	ENST00000368748	T	0.43688	0.94	4.64	3.68	0.42216	.	.	.	.	.	T	0.40372	0.1114	.	.	.	0.09310	N	1	P	0.52061	0.95	P	0.55391	0.775	T	0.11446	-1.0587	8	0.87932	D	0	-15.1488	10.7082	0.45966	0.0:0.8074:0.1925:0.0	.	34	Q9BYE4	SPR2G_HUMAN	K	34	ENSP00000357737:E34K	ENSP00000357737:E34K	E	-	1	0	SPRR2G	151389111	0.000000	0.05858	0.055000	0.19348	0.062000	0.15995	-0.303000	0.08210	2.414000	0.81942	0.609000	0.83330	GAG	.	.		0.612	SPRR2G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040057.1			T	153122487	C	T	153122487	3	4	112	1	0	0	0	0	1	0	0	0	15117	835	29	3	125	3	SPRR2G	1	153122487	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	485872	153122487	96128134	68	16689										
CREB3L4	148327	hgsc.bcm.edu	37	chr1	153941909	153941909	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcccagagcaggcaccgtagCcccagtgccctgtacaaccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:153941909delC	ENST00000368607.3	+	4	787	c.521delC	c.(520-522)gccfs	p.A174fs	CREB3L4_ENST00000468845.1_3'UTR|CREB3L4_ENST00000405694.3_Frame_Shift_Del_p.A27fs|CREB3L4_ENST00000368600.3_Frame_Shift_Del_p.A154fs|SLC39A1_ENST00000310483.6_5'Flank|CREB3L4_ENST00000271889.4_Frame_Shift_Del_p.A174fs|CREB3L4_ENST00000368601.1_Frame_Shift_Del_p.A174fs|CREB3L4_ENST00000368603.1_Frame_Shift_Del_p.A174fs|RP11-422P24.10_ENST00000608147.1_RNA	NM_001255978.1|NM_001255980.1|NM_130898.3	NP_001242907.1|NP_001242909.1|NP_570968.1	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like 4	174					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(3)	13	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGCACCGTAGCCCCAGTGCCC	0.532																																					p.A174fs		Atlas-INDEL	.											.	CREB3L4	36	.	0			c.520delG						.						104	88	93					1																	153941909		2203	4300	6503	SO:0001589	frameshift_variant	148327	exon4			.	AF394167	CCDS1056.1, CCDS58029.1	1q21.2	2013-01-10			ENSG00000143578	ENSG00000143578		"basic leucine zipper proteins"	18854	protein-coding gene	gene with protein product		607138					Standard	NM_130898		Approved	AIbZIP, CREB4, CREB3, hJAL, ATCE1	uc001fdr.3	Q8TEY5	OTTHUMG00000037159	ENST00000368607.3:c.521delC	chr1.hg19:g.153941909delC	ENSP00000357596:p.Ala174fs	90.0	0.0		165.0	10.0	NM_001255978	D3DV62|Q5T4L0|Q86YW6	Frame_Shift_Del	DEL	ENST00000368607.3	hg19	CCDS1056.1																																																																																			.	.		0.532	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090291.1	NM_130898		-	153941909	C	-	153941909	7	5	112	1	0	1	0	1	0	0	0	0	3861	739	26	0	531	0	CREB3L4	1	153941909	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	819422	153941909	95308712	69	16690										
TRIM46	80128	hgsc.bcm.edu	37	chr1	155156381	155156381	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcaagatcctgctggggtcGggggcaagctcaaacgcagg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:155156381delG	ENST00000334634.4	+	10	1995	c.1995delG	c.(1993-1995)tcgfs	p.S665fs	TRIM46_ENST00000392451.2_3'UTR|MUC1_ENST00000462215.1_5'Flank|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000545012.1_Frame_Shift_Del_p.S539fs|TRIM46_ENST00000368382.1_Frame_Shift_Del_p.S642fs	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	665	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGCTGGGGTCGGGGGCAAGCT	0.672																																					p.S665fs		Atlas-INDEL	.											.	TRIM46	79	.	0			c.1994delC						.						59	61	60					1																	155156381		2203	4300	6503	SO:0001589	frameshift_variant	80128	exon10			.		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19019	protein-coding gene	gene with protein product		600986	"tripartite motif-containing 46"				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.1995delG	chr1.hg19:g.155156381delG	ENSP00000334657:p.Ser665fs	78.0	0.0		133.0	11.0	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Frame_Shift_Del	DEL	ENST00000334634.4	hg19	CCDS1097.1																																																																																			.	.		0.672	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058		-	155156381	G	-	155156381	7	5	112	1	0	1	0	1	0	0	0	0	16536	1103	39	0	2033	0	TRIM46	1	155156381	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1214472	155156381	94094240	70	16691										
SCAMP3	10067	hgsc.bcm.edu	37	chr1	155227359	155227359	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaaaggaggacccagaggaTagaaagcccaaagcctgcgc	13	10	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:155227359T>C	ENST00000302631.3	-	6	714	c.607A>G	c.(607-609)Atc>Gtc	p.I203V	SCAMP3_ENST00000355379.3_Missense_Mutation_p.I177V|FAM189B_ENST00000472550.1_5'Flank|FAM189B_ENST00000368368.3_5'Flank|FAM189B_ENST00000361361.2_5'Flank|SCAMP3_ENST00000472397.1_5'UTR|FAM189B_ENST00000350210.2_5'Flank	NM_005698.3	NP_005689.2	O14828	SCAM3_HUMAN	secretory carrier membrane protein 3	203					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|response to retinoic acid (GO:0032526)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|large_intestine(3)|lung(7)|ovary(4)|urinary_tract(1)	19	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			ACCCAGAGGATAGAAAGCCCA	0.562																																					p.I203V		Atlas-SNP	.											.	SCAMP3	33	.	0			c.A607G						.						73	74	74					1																	155227359		2203	4300	6503	SO:0001583	missense	10067	exon6			AGAGGATAGAAAG	AF005039	CCDS1105.1, CCDS1106.1	1q21	2013-02-21			ENSG00000116521	ENSG00000116521		"Secretory carrier membrane proteins"	10565	protein-coding gene	gene with protein product	"Propin 1"	606913		C1orf3		9331372, 9658162	Standard	NM_005698		Approved		uc001fjs.3	O14828	OTTHUMG00000035874	ENST00000302631.3:c.607A>G	chr1.hg19:g.155227359T>C	ENSP00000307275:p.Ile203Val	125.0	0.0		283.0	176.0	NM_005698	A9Z1W6|B1AVS6|O15128|Q96FR8|Q9BPY0	Missense_Mutation	SNP	ENST00000302631.3	hg19	CCDS1105.1	.	.	.	.	.	.	.	.	.	.	.	14.96	2.692259	0.48202	.	.	ENSG00000116521	ENST00000302631;ENST00000355379	T;T	0.20200	2.09;2.09	4.92	1.05	0.20165	.	0.167506	0.50627	D	0.000115	T	0.18635	0.0447	M	0.71036	2.16	0.46874	D	0.999233	P;B;B	0.39352	0.669;0.099;0.23	P;B;B	0.46320	0.512;0.3;0.149	T	0.04413	-1.0953	10	0.62326	D	0.03	-10.7064	12.6247	0.56623	0.0:0.0:0.315:0.685	.	203;177;203	Q6FHJ5;O14828-2;O14828	.;.;SCAM3_HUMAN	V	203;177	ENSP00000307275:I203V;ENSP00000347540:I177V	ENSP00000307275:I203V	I	-	1	0	SCAMP3	153493983	1.000000	0.71417	0.983000	0.44433	0.889000	0.51656	4.098000	0.57748	0.003000	0.14656	-0.396000	0.06452	ATC	.	.		0.562	SCAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087399.1	NM_005698		C	155227359	T	C	155227359	3	2	112	1	0	0	0	0	1	0	0	0	13887	1406	49	2	452	2	SCAMP3	1	155227359	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	70978	155227359	94023262	71	16692										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155307895	155307895	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttaccattttttccagggaTtttttcaaggagattgagca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:155307895delT	ENST00000368346.3	-	27	9442	c.8803delA	c.(8803-8805)atcfs	p.I2935fs	ASH1L_ENST00000392403.3_Frame_Shift_Del_p.I2930fs			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2935					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTTCCAGGGATTTTTTCAAGG	0.418																																					p.I2930fs		Atlas-INDEL	.											.	ASH1L	279	.	0			c.8789delT						.						99	92	94					1																	155307895		2203	4300	6503	SO:0001589	frameshift_variant	55870	exon27			.	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.8803delA	chr1.hg19:g.155307895delT	ENSP00000357330:p.Ile2935fs	102.0	0.0		165.0	10.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Frame_Shift_Del	DEL	ENST00000368346.3	hg19																																																																																				.	.		0.418	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		-	155307895	T	-	155307895	7	5	112	1	0	1	0	1	0	0	0	0	1041	1493	52	0	114	0	ASH1L	1	155307895	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	80536	155307895	93942726	72	16693										
PEAR1	375033	hgsc.bcm.edu	37	chr1	156883056	156883056	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgtcgcagtgctccccaaaCcccccaccccctaacaaggt					rs147826153		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:156883056delC	ENST00000338302.3	+	20	2718	c.2493delC	c.(2491-2493)aacfs	p.N831fs	PEAR1_ENST00000292357.7_Frame_Shift_Del_p.N831fs			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	831	Pro-rich.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCTCCCCAAACCCCCCACCCC	0.607																																					p.N831fs		Atlas-INDEL	.											.	PEAR1	118	.	0			c.2492delA						.						103	102	103					1																	156883056		2203	4300	6503	SO:0001589	frameshift_variant	375033	exon19			.	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"multiple EGF-like-domains 12"	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.2493delC	chr1.hg19:g.156883056delC	ENSP00000344465:p.Asn831fs	91.0	0.0		212.0	14.0	NM_001080471	Q8TEK2	Frame_Shift_Del	DEL	ENST00000338302.3	hg19	CCDS30892.1																																																																																			.	.		0.607	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		-	156883056	C	-	156883056	7	5	112	1	0	1	0	1	0	0	0	0	11721	506	18	0	2563	0	PEAR1	1	156883056	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1575161	156883056	92367565	73	16694										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158641962	158641962	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccacagttccagcagggcagTccagttgttgtcaagtattt	10	10	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:158641962T>C	ENST00000368147.4	-	11	1555	c.1375A>G	c.(1375-1377)Act>Gct	p.T459A		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	459					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGCAGGGCAGTCCAGTTGTTG	0.378																																					p.T459A		Atlas-SNP	.											.	SPTA1	720	.	0			c.A1375G						.						97	90	92					1																	158641962		1902	4136	6038	SO:0001583	missense	6708	exon11			GGGCAGTCCAGTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1375A>G	chr1.hg19:g.158641962T>C	ENSP00000357129:p.Thr459Ala	69.0	0.0		97.0	4.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	0.117	-1.130297	0.01756	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.33654	1.4;1.4	5.0	-0.203	0.13204	.	0.554250	0.13585	N	0.377056	T	0.02119	0.0066	N	0.01081	-1.03	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45101	-0.9284	10	0.05620	T	0.96	.	5.6186	0.17446	0.2081:0.5034:0.0:0.2886	.	459	P02549	SPTA1_HUMAN	A	459	ENSP00000357130:T459A;ENSP00000357129:T459A	ENSP00000357129:T459A	T	-	1	0	SPTA1	156908586	0.000000	0.05858	0.039000	0.18376	0.012000	0.07955	-0.788000	0.04614	-0.158000	0.11040	-0.716000	0.03619	ACT	.	.		0.378	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158641962	T	C	158641962	3	2	112	1	0	0	0	0	1	0	0	0	15131	1667	58	2	6052	2	SPTA1	1	158641962	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1758906	158641962	90608659	74	16695										
MNDA	4332	hgsc.bcm.edu	37	chr1	158813107	158813107	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacaagaaaaagctccagtgAaaaaaataaaccaggaagaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:158813107delA	ENST00000368141.4	+	3	565	c.304delA	c.(304-306)aaafs	p.K103fs		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	103					B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					AGCTCCAGTGAAAAAAATAAA	0.433																																					p.V101fs		Atlas-INDEL	.											.	MNDA	147	.	0			c.303delG						.						34	36	36					1																	158813107		2203	4299	6502	SO:0001589	frameshift_variant	4332	exon3			.	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.304delA	chr1.hg19:g.158813107delA	ENSP00000357123:p.Lys103fs	75.0	0.0		116.0	12.0	NM_002432		Frame_Shift_Del	DEL	ENST00000368141.4	hg19	CCDS1177.1																																																																																			.	.		0.433	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		-	158813107	A	-	158813107	7	5	112	1	0	1	0	1	0	0	0	0	9685	247	9	0	310	0	MNDA	1	158813107	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	171145	158813107	90437514	75	16696										
IGSF9	57549	hgsc.bcm.edu	37	chr1	159900106	159900106	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtctcttagggaccagctctGggggatcccaatgcaggagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:159900106delG	ENST00000368094.1	-	15	2134	c.1937delC	c.(1936-1938)ccafs	p.P646fs	IGSF9_ENST00000493195.1_5'UTR|IGSF9_ENST00000361509.3_Frame_Shift_Del_p.P630fs	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	646	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GACCAGCTCTGGGGGATCCCA	0.667																																					p.P646fs		Atlas-INDEL	.											.	IGSF9	123	.	0			c.1938delA						.						83	90	87					1																	159900106		2203	4300	6503	SO:0001589	frameshift_variant	57549	exon15			.	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.1937delC	chr1.hg19:g.159900106delG	ENSP00000357073:p.Pro646fs	62.0	0.0		154.0	10.0	NM_001135050		Frame_Shift_Del	DEL	ENST00000368094.1	hg19	CCDS44254.1																																																																																			.	.		0.667	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		-	159900106	G	-	159900106	7	5	112	1	0	1	0	1	0	0	0	0	7614	1348	47	0	1630	0	IGSF9	1	159900106	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1086999	159900106	89350515	76	16697										
USP21	27005	hgsc.bcm.edu	37	chr1	161130443	161130443	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtccacaatgccccaggccTctgagcaccgcctgggccgt	11	17	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:161130443T>C	ENST00000289865.8	+	2	234	c.13T>C	c.(13-15)Tct>Cct	p.S5P	USP21_ENST00000368001.1_Missense_Mutation_p.S5P|RP11-297K8.2_ENST00000420498.1_RNA|USP21_ENST00000368002.3_Missense_Mutation_p.S5P	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	5					histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			GCCCCAGGCCTCTGAGCACCG	0.607																																					p.S5P		Atlas-SNP	.											.	USP21	63	.	0			c.T13C						.						47	50	49					1																	161130443		2203	4300	6503	SO:0001583	missense	27005	exon2			CAGGCCTCTGAGC	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"Ubiquitin-specific peptidases"	12620	protein-coding gene	gene with protein product		604729	"ubiquitin specific protease 21"	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.13T>C	chr1.hg19:g.161130443T>C	ENSP00000289865:p.Ser5Pro	54.0	0.0		91.0	4.0	NM_012475	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Missense_Mutation	SNP	ENST00000289865.8	hg19	CCDS30920.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.020729	0.54576	.	.	ENSG00000143258	ENST00000368002;ENST00000289865;ENST00000368001	T;T;T	0.21191	2.19;2.19;2.02	5.14	5.14	0.70334	.	0.474172	0.19882	N	0.103944	T	0.12902	0.0313	N	0.14661	0.345	0.33985	D	0.64838	D	0.65815	0.995	P	0.53185	0.72	T	0.05209	-1.0899	10	0.87932	D	0	.	14.0799	0.64914	0.0:0.0:0.0:1.0	.	5	Q9UK80	UBP21_HUMAN	P	5	ENSP00000356981:S5P;ENSP00000289865:S5P;ENSP00000356980:S5P	ENSP00000289865:S5P	S	+	1	0	USP21	159397067	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.621000	0.61233	2.155000	0.67459	0.459000	0.35465	TCT	.	.		0.607	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1			C	161130443	T	C	161130443	3	2	112	1	0	0	0	0	1	0	0	0	17068	1551	54	2	15	2	USP21	1	161130443	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1230337	161130443	88120178	77	16698										
USP21	27005	hgsc.bcm.edu	37	chr1	161134345	161134345	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtgtgaccgatgtcggcagAaaactcgaagtaccaaaaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:161134345delA	ENST00000289865.8	+	10	1548	c.1327delA	c.(1327-1329)aaafs	p.K443fs	PPOX_ENST00000432542.2_5'Flank|USP21_ENST00000368001.1_Frame_Shift_Del_p.K443fs|USP21_ENST00000493054.1_3'UTR|PPOX_ENST00000544598.1_5'Flank|PPOX_ENST00000352210.5_5'Flank|PPOX_ENST00000367999.4_5'Flank|USP21_ENST00000368002.3_Frame_Shift_Del_p.K443fs|PPOX_ENST00000535223.1_5'Flank	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	443	USP.				histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			ATGTCGGCAGAAAACTCGAAG	0.428																																					p.Q442fs		Atlas-INDEL	.											.	USP21	63	.	0			c.1326delG						.						102	89	94					1																	161134345		2203	4300	6503	SO:0001589	frameshift_variant	27005	exon11			.	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"Ubiquitin-specific peptidases"	12620	protein-coding gene	gene with protein product		604729	"ubiquitin specific protease 21"	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.1327delA	chr1.hg19:g.161134345delA	ENSP00000289865:p.Lys443fs	157.0	0.0		236.0	15.0	NM_001014443	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Frame_Shift_Del	DEL	ENST00000289865.8	hg19	CCDS30920.1																																																																																			.	.		0.428	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1			-	161134345	A	-	161134345	7	5	112	1	0	1	0	1	0	0	0	0	17068	247	9	0	1361	0	USP21	1	161134345	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3902	161134345	88116276	78	16699										
PPOX	5498	hgsc.bcm.edu	37	chr1	161140706	161140706	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctcttctcagaactgcattCcccagtatacactaggtcac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:161140706delC	ENST00000367999.4	+	12	1524	c.1258delC	c.(1258-1260)cccfs	p.P420fs	PPOX_ENST00000432542.2_Intron|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000544598.1_Frame_Shift_Del_p.P128fs|PPOX_ENST00000352210.5_Frame_Shift_Del_p.P420fs|B4GALT3_ENST00000470882.1_5'Flank|PPOX_ENST00000535223.1_Intron	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	420			P -> R (in VP). {ECO:0000269|PubMed:24073655}.		heme biosynthetic process (GO:0006783)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound biosynthetic process (GO:0006779)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of mitochondrial inner membrane (GO:0031304)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)	flavin adenine dinucleotide binding (GO:0050660)|oxygen-dependent protoporphyrinogen oxidase activity (GO:0004729)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			GAACTGCATTCCCCAGTATAC	0.473																																					p.I419fs		Atlas-INDEL	.											.	PPOX	34	.	0			c.1257delT						.						132	133	133					1																	161140706		2203	4300	6503	SO:0001589	frameshift_variant	5498	exon12			.	BC002357	CCDS1221.1	1q22	2008-02-05			ENSG00000143224	ENSG00000143224	1.3.3.4		9280	protein-coding gene	gene with protein product		600923	"variegate porphyria"	VP		8575762, 10457135	Standard	NM_000309		Approved	PPO	uc001fyg.2	P50336	OTTHUMG00000034342	ENST00000367999.4:c.1258delC	chr1.hg19:g.161140706delC	ENSP00000356978:p.Pro420fs	87.0	0.0		120.0	10.0	NM_001122764	D3DVG0|Q5VTW8	Frame_Shift_Del	DEL	ENST00000367999.4	hg19	CCDS1221.1																																																																																			.	.		0.473	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309		-	161140706	C	-	161140706	7	5	112	1	0	1	0	1	0	0	0	0	12360	855	30	0	1300	0	PPOX	1	161140706	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	6361	161140706	88109915	79	16700										
DUSP12	11266	hgsc.bcm.edu	37	chr1	161726728	161726728	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gttttgggatcacaaacaggAaaaatatgaacatgatattt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:161726728delA	ENST00000367943.4	+	6	1046	c.1014delA	c.(1012-1014)ggafs	p.G338fs		NM_007240.1	NP_009171.1	Q9UNI6	DUS12_HUMAN	dual specificity phosphatase 12	338					cellular protein modification process (GO:0006464)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of glucokinase activity (GO:0033133)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|lung(1)	5	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			CACAAACAGGAAAAATATGAA	0.358																																					p.G338fs		Atlas-INDEL	.											.	DUSP12	20	.	0			c.1013delG						.						49	49	49					1																	161726728		2203	4300	6503	SO:0001589	frameshift_variant	11266	exon6			.	AF119226	CCDS1234.1	1q21-q22	2011-06-09			ENSG00000081721	ENSG00000081721		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3067	protein-coding gene	gene with protein product	"serine/threonine specific protein phosphatase", "YVH1 protein-tyrosine phosphatase (S. cerevisiae) ortholog"	604835				10446167	Standard	XM_005244862		Approved	YVH1, DUSP1	uc001gbo.3	Q9UNI6	OTTHUMG00000034540	ENST00000367943.4:c.1014delA	chr1.hg19:g.161726728delA	ENSP00000356920:p.Gly338fs	76.0	0.0		140.0	10.0	NM_007240	Q5VXA8	Frame_Shift_Del	DEL	ENST00000367943.4	hg19	CCDS1234.1																																																																																			.	.		0.358	DUSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083588.1	NM_007240		-	161726728	A	-	161726728	7	5	112	1	0	1	0	1	0	0	0	0	4814	233	9	0	1036	0	DUSP12	1	161726728	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	586022	161726728	87523893	80	16701										
ADCY10	55811	hgsc.bcm.edu	37	chr1	167780125	167780125	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaagacagggccagtggtaTtttgagccaccagattctcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:167780125delT	ENST00000367851.4	-	32	4692	c.4508delA	c.(4507-4509)aatfs	p.N1503fs	ADCY10_ENST00000367848.1_Frame_Shift_Del_p.N1411fs|ADCY10_ENST00000545172.1_Frame_Shift_Del_p.N1350fs	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	1503					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						GCCAGTGGTATTTTGAGCCAC	0.428																																					p.N1503fs		Atlas-INDEL	.											.	ADCY10	175	.	0			c.4509delT						.						65	66	65					1																	167780125		2203	4300	6503	SO:0001589	frameshift_variant	55811	exon32			.	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.4508delA	chr1.hg19:g.167780125delT	ENSP00000356825:p.Asn1503fs	141.0	0.0		216.0	13.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Frame_Shift_Del	DEL	ENST00000367851.4	hg19	CCDS1265.1																																																																																			.	.		0.428	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		-	167780125	T	-	167780125	7	5	112	1	0	1	0	1	0	0	0	0	293	1493	52	0	332	0	ADCY10	1	167780125	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	6053397	167780125	81470496	81	16702										
FMO4	2329	hgsc.bcm.edu	37	chr1	171310877	171310877	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggcacctgtcctacttgccTctcttctacttatctgtaaa	6	13	3	0	rs569945058		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:171310877T>C	ENST00000367749.3	+	10	1906	c.1576T>C	c.(1576-1578)Tct>Cct	p.S526P		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	526					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					CCTACTTGCCTCTCTTCTACT	0.423																																					p.S526P	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											.	FMO4	64	.	0			c.T1576C						.						48	47	47					1																	171310877		2203	4300	6503	SO:0001583	missense	2329	exon10			CTTGCCTCTCTTC	BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.1576T>C	chr1.hg19:g.171310877T>C	ENSP00000356723:p.Ser526Pro	79.0	0.0		150.0	6.0	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	hg19	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	T	18.73	3.686586	0.68157	.	.	ENSG00000076258	ENST00000367749	T	0.55760	0.5	5.76	3.44	0.39384	.	0.537430	0.18577	N	0.137151	T	0.38108	0.1028	L	0.45137	1.4	0.33823	D	0.629235	P	0.52463	0.953	P	0.53266	0.722	T	0.41016	-0.9532	10	0.62326	D	0.03	-11.6813	5.9074	0.19008	0.1346:0.0:0.3172:0.5482	.	526	P31512	FMO4_HUMAN	P	526	ENSP00000356723:S526P	ENSP00000356723:S526P	S	+	1	0	FMO4	169577501	0.298000	0.24417	0.840000	0.33206	0.839000	0.47603	0.296000	0.19083	0.961000	0.38030	0.533000	0.62120	TCT	.	.		0.423	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		C	171310877	T	C	171310877	3	2	112	1	0	0	0	0	1	0	0	0	5965	1551	54	2	1606	2	FMO4	1	171310877	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3530752	171310877	77939744	82	16703										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172558537	172558537	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atataccatcaccagtgattCcccaagagagttctgttgag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:172558537delC	ENST00000263688.3	+	18	2515	c.2296delC	c.(2296-2298)cccfs	p.P766fs	SUCO_ENST00000608151.1_Frame_Shift_Del_p.P918fs|SUCO_ENST00000367723.4_Frame_Shift_Del_p.P917fs|SUCO_ENST00000610051.1_Intron	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	766					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											ACCAGTGATTCCCCAAGAGAG	0.358																																					p.I765fs		Atlas-INDEL	.											.	.	.	.	0			c.2295delT						.						62	62	62					1																	172558537		2195	4291	6486	SO:0001589	frameshift_variant	51430	exon18			.	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.2296delC	chr1.hg19:g.172558537delC	ENSP00000263688:p.Pro766fs	76.0	0.0		138.0	10.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Frame_Shift_Del	DEL	ENST00000263688.3	hg19	CCDS1303.1																																																																																			.	.		0.358	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		-	172558537	C	-	172558537	7	5	112	1	0	1	0	1	0	0	0	0	2069	855	30	0	2366	0	C1orf9	1	172558537	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1247660	172558537	76692084	83	16704										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172571330	172571330	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attatatttcaaaacttcctAaaagtaatcagtatccaagc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:172571330delA	ENST00000263688.3	+	21	3364	c.3145delA	c.(3145-3147)aaafs	p.K1049fs	SUCO_ENST00000608151.1_Frame_Shift_Del_p.K1201fs|SUCO_ENST00000367723.4_Frame_Shift_Del_p.K1200fs|SUCO_ENST00000610051.1_Frame_Shift_Del_p.K678fs	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	1049					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											AAAACTTCCTAAAAGTAATCA	0.299																																					p.P1048fs		Atlas-INDEL	.											.	.	.	.	0			c.3144delT						.						78	72	74					1																	172571330		2201	4300	6501	SO:0001589	frameshift_variant	51430	exon21			.	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.3145delA	chr1.hg19:g.172571330delA	ENSP00000263688:p.Lys1049fs	84.0	0.0		159.0	12.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Frame_Shift_Del	DEL	ENST00000263688.3	hg19	CCDS1303.1																																																																																			.	.		0.299	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		-	172571330	A	-	172571330	7	5	112	1	0	1	0	1	0	0	0	0	2069	363	13	0	3227	0	C1orf9	1	172571330	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	12793	172571330	76679291	84	16705										
ABL2	27	hgsc.bcm.edu	37	chr1	179086622	179086622	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttttaccacatggttttctCccactaggcagttacgagct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:179086622delC	ENST00000502732.1	-	8	1456	c.1253delG	c.(1252-1254)ggafs	p.G418fs	ABL2_ENST00000367623.4_Frame_Shift_Del_p.G397fs|ABL2_ENST00000512653.1_Frame_Shift_Del_p.G403fs|ABL2_ENST00000504405.1_Frame_Shift_Del_p.G382fs|ABL2_ENST00000511413.1_Frame_Shift_Del_p.G418fs|ABL2_ENST00000408940.3_Frame_Shift_Del_p.G382fs|ABL2_ENST00000344730.3_Frame_Shift_Del_p.G403fs|ABL2_ENST00000392043.3_Frame_Shift_Del_p.G397fs|ABL2_ENST00000507173.1_Frame_Shift_Del_p.G397fs	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	ATGGTTTTCTCCCACTAGGCA	0.428			T	ETV6	AML																																p.G418fs		Atlas-INDEL	.		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	ABL2	307	.	0			c.1254delA						.						118	105	110					1																	179086622		2203	4300	6503	SO:0001589	frameshift_variant	27	exon8			.	M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.1253delG	chr1.hg19:g.179086622delC	ENSP00000427562:p.Gly418fs	94.0	0.0		182.0	12.0	NM_007314	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Frame_Shift_Del	DEL	ENST00000502732.1	hg19	CCDS30947.1																																																																																			.	.		0.428	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		-	179086622	C	-	179086622	7	5	112	1	0	1	0	1	0	0	0	0	93	855	30	0	2360	0	ABL2	1	179086622	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	6515292	179086622	70163999	85	16706										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181701779	181701779	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggaggagcgcatcagccgtGgggggtccctcaagggggat					rs556292815	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:181701779delG	ENST00000367573.2	+	20	2557	c.2557delG	c.(2557-2559)gggfs	p.G854fs	CACNA1E_ENST00000360108.3_Frame_Shift_Del_p.G835fs|CACNA1E_ENST00000367567.4_Frame_Shift_Del_p.G461fs|CACNA1E_ENST00000358338.5_Frame_Shift_Del_p.G786fs|CACNA1E_ENST00000367570.1_Frame_Shift_Del_p.G854fs|CACNA1E_ENST00000526775.1_Frame_Shift_Del_p.G835fs|CACNA1E_ENST00000357570.5_Frame_Shift_Del_p.G805fs	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	854					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CATCAGCCGTGGGGGGTCCCT	0.682																																					p.R852fs		Atlas-INDEL	.											.	CACNA1E	778	.	0			c.2556delT						.						11	14	13					1																	181701779		1882	4083	5965	SO:0001589	frameshift_variant	777	exon20			.	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2557delG	chr1.hg19:g.181701779delG	ENSP00000356545:p.Gly854fs	153.0	0.0		249.0	15.0	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Frame_Shift_Del	DEL	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.682	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		-	181701779	G	-	181701779	7	5	112	1	0	1	0	1	0	0	0	0	2544	1348	47	0	2635	0	CACNA1E	1	181701779	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2615157	181701779	67548842	86	16707										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183109548	183109548	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcccttacaggcttcacagGctgctcaagaagccgagatc	9	13	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:183109548G>A	ENST00000258341.4	+	27	4740	c.4483G>A	c.(4483-4485)Gct>Act	p.A1495T	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1495	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GGCTTCACAGGCTGCTCAAGA	0.423																																					p.A1495T		Atlas-SNP	.											.	LAMC1	176	.	0			c.G4483A						.						52	54	53					1																	183109548		2203	4300	6503	SO:0001583	missense	3915	exon27			TCACAGGCTGCTC	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4483G>A	chr1.hg19:g.183109548G>A	ENSP00000258341:p.Ala1495Thr	58.0	0.0		81.0	4.0	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.094192	0.56075	.	.	ENSG00000135862	ENST00000258341	T	0.78481	-1.18	5.31	5.31	0.75309	.	0.106561	0.64402	D	0.000006	T	0.64659	0.2618	N	0.24115	0.695	0.46901	D	0.999249	P	0.39282	0.666	B	0.33339	0.162	T	0.65899	-0.6056	10	0.31617	T	0.26	.	17.1486	0.86772	0.0:0.0:1.0:0.0	.	1495	P11047	LAMC1_HUMAN	T	1495	ENSP00000258341:A1495T	ENSP00000258341:A1495T	A	+	1	0	LAMC1	181376171	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.654000	0.74387	2.484000	0.83849	0.655000	0.94253	GCT	.	.		0.423	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		A	183109548	G	A	183109548	3	1	112	1	0	0	0	0	1	0	0	0	8623	1203	42	3	4589	3	LAMC1	1	183109548	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	1407769	183109548	66141073	87	16708										
C1orf26	54823	hgsc.bcm.edu	37	chr1	185175808	185175808	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tacatttactacagtgctttAaaaaacattggttggctgta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:185175808delA	ENST00000367500.4	+	13	2050	c.1885delA	c.(1885-1887)aaafs	p.K630fs	SWT1_ENST00000367501.3_Frame_Shift_Del_p.K630fs	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	630										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						ACAGTGCTTTAAAAAACATTG	0.313																																					p.F628fs		Atlas-INDEL	.											.	SWT1	88	.	0			c.1884delT						.						67	70	69					1																	185175808		2202	4295	6497	SO:0001589	frameshift_variant	54823	exon13			.	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.1885delA	chr1.hg19:g.185175808delA	ENSP00000356470:p.Lys630fs	109.0	0.0		176.0	11.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Frame_Shift_Del	DEL	ENST00000367500.4	hg19	CCDS1367.1																																																																																			.	.		0.313	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		-	185175808	A	-	185175808	7	5	112	1	0	1	0	1	0	0	0	0	2037	363	13	0	1931	0	C1orf26	1	185175808	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2066260	185175808	64074813	88	16709										
TPR	7175	hgsc.bcm.edu	37	chr1	186319458	186319458	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgagcattttttaatagttcTtttgtgttaagatgaagatt	8	2	1	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:186319458T>G	ENST00000367478.4	-	21	2969	c.2673A>C	c.(2671-2673)aaA>aaC	p.K891N	TPR_ENST00000474852.1_5'Flank	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	891					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TTAATAGTTCTTTTGTGTTAA	0.323			T	NTRK1	papillary thyroid																																p.K891N		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A2673C						.						186	170	175					1																	186319458		1821	4081	5902	SO:0001583	missense	7175	exon21			TAGTTCTTTTGTG	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2673A>C	chr1.hg19:g.186319458T>G	ENSP00000356448:p.Lys891Asn	138.0	0.0		234.0	108.0	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	hg19	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	18.66	3.671956	0.67928	.	.	ENSG00000047410	ENST00000367478	T	0.28454	1.61	5.88	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.47173	0.1431	M	0.65498	2.005	0.58432	D	0.999995	D	0.89917	1.0	D	0.69307	0.963	T	0.42616	-0.9441	10	0.46703	T	0.11	.	6.3881	0.21572	0.0:0.3132:0.0:0.6868	.	891	P12270	TPR_HUMAN	N	891	ENSP00000356448:K891N	ENSP00000356448:K891N	K	-	3	2	TPR	184586081	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.793000	0.47845	1.015000	0.39444	-0.366000	0.07423	AAA	.	.		0.323	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		G	186319458	T	G	186319458	3	3	112	1	0	0	0	0	1	0	0	0	16431	1606	56	5	4542	5	TPR	1	186319458	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1143650	186319458	62931163	89	16710										
TPR	7175	hgsc.bcm.edu	37	chr1	186324639	186324639	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcaagctgctcattttgtaTtttttcattttctgcttttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:186324639delT	ENST00000367478.4	-	17	2370	c.2074delA	c.(2074-2076)atafs	p.I692fs	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	692					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TCATTTTGTATTTTTTCATTT	0.318			T	NTRK1	papillary thyroid																																p.I692fs		Atlas-INDEL	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.2075delT						.						107	96	100					1																	186324639		1788	4066	5854	SO:0001589	frameshift_variant	7175	exon17			.	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2074delA	chr1.hg19:g.186324639delT	ENSP00000356448:p.Ile692fs	87.0	0.0		196.0	12.0	NM_003292	Q15655|Q5SWY0|Q99968	Frame_Shift_Del	DEL	ENST00000367478.4	hg19	CCDS41446.1																																																																																			.	.		0.318	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		-	186324639	T	-	186324639	7	5	112	1	0	1	0	1	0	0	0	0	16431	1493	52	0	5157	0	TPR	1	186324639	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	5181	186324639	62925982	90	16711										
TPR	7175	hgsc.bcm.edu	37	chr1	186340145	186340145	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagcaatttcaagttctttgTttttctcagttagtgccttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:186340145delT	ENST00000367478.4	-	3	583	c.287delA	c.(286-288)aacfs	p.N96fs	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	96	Necessary for interaction with HSF1.				carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		AAGTTCTTTGTTTTTCTCAGT	0.328			T	NTRK1	papillary thyroid																																p.N96fs		Atlas-INDEL	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.288delC						.						196	178	184					1																	186340145		1831	4082	5913	SO:0001589	frameshift_variant	7175	exon3			.	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.287delA	chr1.hg19:g.186340145delT	ENSP00000356448:p.Asn96fs	125.0	0.0		174.0	11.0	NM_003292	Q15655|Q5SWY0|Q99968	Frame_Shift_Del	DEL	ENST00000367478.4	hg19	CCDS41446.1																																																																																			.	.		0.328	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		-	186340145	T	-	186340145	7	5	112	1	0	1	0	1	0	0	0	0	16431	1725	60	0	7000	0	TPR	1	186340145	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	15506	186340145	62910476	91	16712										
ASPM	259266	hgsc.bcm.edu	37	chr1	197102505	197102505	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctttccataggtgtctatcTtttcgaacaattaaccgcct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:197102505delT	ENST00000367409.4	-	6	2650	c.2394delA	c.(2392-2394)aaafs	p.K798fs	ASPM_ENST00000367408.1_Frame_Shift_Del_p.K48fs|ASPM_ENST00000294732.7_Frame_Shift_Del_p.K798fs	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	798					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						GGTGTCTATCTTTTCGAACAA	0.353																																					p.D799fs		Atlas-INDEL	.											.	ASPM	444	.	0			c.2395delG						.						66	66	66					1																	197102505		2203	4300	6503	SO:0001589	frameshift_variant	259266	exon6			.	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.2394delA	chr1.hg19:g.197102505delT	ENSP00000356379:p.Lys798fs	100.0	0.0		179.0	11.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Frame_Shift_Del	DEL	ENST00000367409.4	hg19	CCDS1389.1																																																																																			.	.		0.353	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		-	197102505	T	-	197102505	7	5	112	1	0	1	0	1	0	0	0	0	1056	1606	56	0	8131	0	ASPM	1	197102505	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	10762360	197102505	52148116	92	16713										
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200818368	200818368	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcaaaagaaaaggaatcacAaaaaactgatggacaaagga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:200818368delA	ENST00000236925.4	+	12	2553	c.2504delA	c.(2503-2505)caafs	p.Q835fs	CAMSAP2_ENST00000358823.2_Frame_Shift_Del_p.Q824fs|CAMSAP2_ENST00000413307.2_Frame_Shift_Del_p.Q808fs			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	835					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										AAGGAATCACAAAAAACTGAT	0.428																																					p.Q824fs		Atlas-INDEL	.											.	.	.	.	0			c.2470delC						.						104	111	109					1																	200818368		2203	4298	6501	SO:0001589	frameshift_variant	23271	exon11			.	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.2504delA	chr1.hg19:g.200818368delA	ENSP00000236925:p.Gln835fs	100.0	0.0		197.0	12.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Frame_Shift_Del	DEL	ENST00000236925.4	hg19																																																																																				.	.		0.428	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		-	200818368	A	-	200818368	7	5	112	1	0	1	0	1	0	0	0	0	2614	130	5	0	2513	0	CAMSAP1L1	1	200818368	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3715863	200818368	48432253	93	16714										
C4BPA	722	hgsc.bcm.edu	37	chr1	207317164	207317164	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaatatgtttccattacagcTctgtgtcggaaaccagaatt	7	8	1	1	rs562681258		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:207317164T>C	ENST00000367070.3	+	11	1640	c.1446T>C	c.(1444-1446)gcT>gcC	p.A482A		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	482	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						CCATTACAGCTCTGTGTCGGA	0.363																																					p.A482A		Atlas-SNP	.											.	C4BPA	70	.	0			c.T1446C						.						144	133	136					1																	207317164		2203	4300	6503	SO:0001630	splice_region_variant	722	exon11			TACAGCTCTGTGT	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.1445-1T>C	chr1.hg19:g.207317164T>C		94.0	0.0		126.0	6.0	NM_000715	Q5VVQ8	Silent	SNP	ENST00000367070.3	hg19	CCDS1477.1																																																																																			.	.		0.363	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		Silent	C	207317164	T	C	207317164	5	2	112	1	0	0	0	0	0	0	1	0	2251	1565	54	2	1484	2	C4BPA	1	207317164	Splice_Site	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	6498796	207317164	41933457	94	16715										
CR1	1378	hgsc.bcm.edu	37	chr1	207700165	207700165	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacaaggacaacttttcaccTgggcaggaagtgttctacag					rs3866235		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:207700165delT	ENST00000367049.4	+	6	954	c.954delT	c.(952-954)cctfs	p.P318fs	CR1_ENST00000400960.2_Frame_Shift_Del_p.P318fs|CR1_ENST00000367053.1_Frame_Shift_Del_p.P318fs|CR1_ENST00000367050.4_Intron|CR1_ENST00000367052.1_Frame_Shift_Del_p.P318fs|CR1_ENST00000367051.1_Intron	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	318	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ACTTTTCACCTGGGCAGGAAG	0.572																																					p.P318fs		Atlas-INDEL	.											.	CR1	354	.	0			c.953delC						.						69	108	98					1																	207700165		1396	4008	5404	SO:0001589	frameshift_variant	1378	exon6			.	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.954delT	chr1.hg19:g.207700165delT	ENSP00000356016:p.Pro318fs	5.0	0.0		17.0	11.0	NM_000573	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Frame_Shift_Del	DEL	ENST00000367049.4	hg19	CCDS44308.1																																																																																			.	.		0.572	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		-	207700165	T	-	207700165	7	5	112	1	0	1	0	1	0	0	0	0	3842	1567	55	0	976	0	CR1	1	207700165	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	383001	207700165	41550456	95	16716										
ATF3	467	hgsc.bcm.edu	37	chr1	212788594	212788594	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccctcggggtgtccatcacAaaagccgaggtgggttctat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:212788594delA	ENST00000341491.4	+	2	496	c.231delA	c.(229-231)acafs	p.T77fs	ATF3_ENST00000336937.4_Frame_Shift_Del_p.T48fs|RN7SL512P_ENST00000578962.1_RNA|ATF3_ENST00000366987.2_Frame_Shift_Del_p.T77fs|ATF3_ENST00000366985.1_Frame_Shift_Del_p.T20fs|ATF3_ENST00000492118.1_Intron|ATF3_ENST00000366983.1_Frame_Shift_Del_p.T77fs	NM_001040619.2|NM_001206488.2|NM_001674.3	NP_001035709.1|NP_001193417.2|NP_001665.1	P18847	ATF3_HUMAN	activating transcription factor 3	77					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gluconeogenesis (GO:0006094)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)	Pseudoephedrine(DB00852)	TGTCCATCACAAAAGCCGAGG	0.552																																					p.T77fs		Atlas-INDEL	.											.	ATF3	22	.	0			c.230delC						.						42	44	43					1																	212788594		2203	4300	6503	SO:0001589	frameshift_variant	467	exon2			.	L19871	CCDS1506.1, CCDS41464.1, CCDS55688.1, CCDS58059.1	1q32.3	2013-01-10			ENSG00000162772	ENSG00000162772		"basic leucine zipper proteins"	785	protein-coding gene	gene with protein product		603148				7515060	Standard	NM_001674		Approved		uc021pit.1	P18847	OTTHUMG00000036747	ENST00000341491.4:c.231delA	chr1.hg19:g.212788594delA	ENSP00000344352:p.Thr77fs	89.0	0.0		147.0	14.0	NM_001030287	Q5VTZ2|Q6ICQ9|Q7Z566|Q8WYM6	Frame_Shift_Del	DEL	ENST00000341491.4	hg19	CCDS1506.1																																																																																			.	.		0.552	ATF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089296.1	NM_001674		-	212788594	A	-	212788594	7	5	112	1	0	1	0	1	0	0	0	0	1081	117	5	0	233	0	ATF3	1	212788594	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5088429	212788594	36462027	96	16717										
ANGEL2	90806	hgsc.bcm.edu	37	chr1	213181561	213181561	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttgcacttacgtctgcatcAaaatgtttaatttctttcag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:213181561delA	ENST00000366962.3	-	3	787	c.633delT	c.(631-633)tttfs	p.F211fs	ANGEL2_ENST00000540642.1_Frame_Shift_Del_p.F85fs|ANGEL2_ENST00000544555.1_Frame_Shift_Del_p.F42fs|ANGEL2_ENST00000360506.2_Frame_Shift_Del_p.F42fs|ANGEL2_ENST00000535388.1_Frame_Shift_Del_p.F42fs	NM_144567.3	NP_653168.2	Q5VTE6	ANGE2_HUMAN	angel homolog 2 (Drosophila)	211										central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(1)	24				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		CGTCTGCATCAAAATGTTTAA	0.398																																					p.D212fs		Atlas-INDEL	.											.	ANGEL2	45	.	0			c.634delG						.						35	37	37					1																	213181561		2203	4300	6503	SO:0001589	frameshift_variant	90806	exon3			.	AL079275	CCDS1512.1, CCDS73027.1	1q32.3	2014-06-17			ENSG00000174606	ENSG00000174606			30534	protein-coding gene	gene with protein product						11943475	Standard	XM_005273344		Approved	KIAA0759L, FLJ12793, Ccr4d	uc001hjz.3	Q5VTE6	OTTHUMG00000036927	ENST00000366962.3:c.633delT	chr1.hg19:g.213181561delA	ENSP00000355929:p.Phe211fs	126.0	0.0		219.0	14.0	NM_144567	B7Z2U4|D3DTA3|Q86X13|Q8NHH3	Frame_Shift_Del	DEL	ENST00000366962.3	hg19	CCDS1512.1																																																																																			.	.		0.398	ANGEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089693.1	NM_144567		-	213181561	A	-	213181561	7	5	112	1	0	1	0	1	0	0	0	0	609	127	5	0	1029	0	ANGEL2	1	213181561	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	392967	213181561	36069060	97	16718										
MARK1	4139	hgsc.bcm.edu	37	chr1	220792019	220792019	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgagggaagtaccgtattccCttctatatgtccacagactg	9	11	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:220792019C>T	ENST00000366917.4	+	9	1097	c.831C>T	c.(829-831)ccC>ccT	p.P277P	MARK1_ENST00000366918.4_Silent_p.P255P|MARK1_ENST00000402574.1_Silent_p.P142P					MAP/microtubule affinity-regulating kinase 1											central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		ACCGTATTCCCTTCTATATGT	0.368																																					p.P277P		Atlas-SNP	.											.	MARK1	161	.	0			c.C831T						.						98	99	99					1																	220792019		2203	4300	6503	SO:0001819	synonymous_variant	4139	exon9			TATTCCCTTCTAT	AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.831C>T	chr1.hg19:g.220792019C>T		62.0	0.0		87.0	4.0	NM_018650		Silent	SNP	ENST00000366917.4	hg19	CCDS31029.2																																																																																			.	.		0.368	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			T	220792019	C	T	220792019	2	4	112	1	0	0	0	0	0	0	0	1	9321	668	24	3		3	MARK1	1	220792019	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	7610458	220792019	28458602	98	16719										
MIA3	375056	hgsc.bcm.edu	37	chr1	222824154	222824154	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggataaaatcaagacacttgAaaaaaatcaggaaattctgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:222824154delA	ENST00000344922.5	+	11	3843	c.3818delA	c.(3817-3819)gaafs	p.E1273fs	MIA3_ENST00000344441.6_Frame_Shift_Del_p.E1273fs|MIA3_ENST00000344507.1_Intron|MIA3_ENST00000340535.7_Frame_Shift_Del_p.E151fs	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1273					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		AAGACACTTGAAAAAAATCAG	0.303																																					p.E1273fs		Atlas-INDEL	.											.	MIA3	167	.	0			c.3817delG						.						53	52	53					1																	222824154		1800	4067	5867	SO:0001589	frameshift_variant	375056	exon11			.		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.3818delA	chr1.hg19:g.222824154delA	ENSP00000340900:p.Glu1273fs	143.0	0.0		250.0	17.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Frame_Shift_Del	DEL	ENST00000344922.5	hg19	CCDS41470.1																																																																																			.	.		0.303	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		-	222824154	A	-	222824154	7	5	112	1	0	1	0	1	0	0	0	0	9574	246	9	0	3860	0	MIA3	1	222824154	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2032135	222824154	26426467	99	16720										
DISP1	84976	hgsc.bcm.edu	37	chr1	223177971	223177971	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagtgatcttctctctgagtCgcgtgggctctgcgatggcc	13	11	4	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:223177971C>A	ENST00000284476.6	+	8	3396	c.3232C>A	c.(3232-3234)Cgc>Agc	p.R1078S		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1078					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		CTCTCTGAGTCGCGTGGGCTC	0.592																																					p.R1078S		Atlas-SNP	.											.	DISP1	145	.	0			c.C3232A						.						73	70	71					1																	223177971		2203	4300	6503	SO:0001583	missense	84976	exon10			CTGAGTCGCGTGG	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.3232C>A	chr1.hg19:g.223177971C>A	ENSP00000284476:p.Arg1078Ser	131.0	0.0		237.0	23.0	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	hg19	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752065	0.89753	.	.	ENSG00000154309	ENST00000284476	T	0.15256	2.44	5.95	5.95	0.96441	.	0.190252	0.56097	D	0.000039	T	0.34366	0.0895	L	0.44542	1.39	0.80722	D	1	D	0.65815	0.995	D	0.66497	0.944	T	0.00400	-1.1763	10	0.23302	T	0.38	-38.7962	20.3719	0.98893	0.0:1.0:0.0:0.0	.	1078	Q96F81	DISP1_HUMAN	S	1078	ENSP00000284476:R1078S	ENSP00000284476:R1078S	R	+	1	0	DISP1	221244594	1.000000	0.71417	0.971000	0.41717	0.927000	0.56198	5.829000	0.69316	2.826000	0.97356	0.491000	0.48974	CGC	.	.		0.592	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		A	223177971	C	A	223177971	3	1	112	1	0	0	0	0	1	0	0	0	4541	884	31	1	3258	1	DISP1	1	223177971	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	353817	223177971	26072650	100	16721										
ZNF678	339500	hgsc.bcm.edu	37	chr1	227843072	227843072	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taaaagaattcatactggagAgaaaccctacaaatgcaaag	7	7	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:227843072A>G	ENST00000343776.5	+	4	1466	c.1121A>G	c.(1120-1122)gAg>gGg	p.E374G	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.E429G	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	374					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				CATACTGGAGAGAAACCCTAC	0.383																																					p.E429G		Atlas-SNP	.											.	ZNF678	137	.	0			c.A1286G						.						34	38	37					1																	227843072		2198	4294	6492	SO:0001583	missense	339500	exon4			CTGGAGAGAAACC	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"Zinc fingers, C2H2-type", "-"	28652	protein-coding gene	gene with protein product	"hypothetical protein MGC42493"					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.1121A>G	chr1.hg19:g.227843072A>G	ENSP00000344828:p.Glu374Gly	45.0	0.0		81.0	4.0	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	hg19		.	.	.	.	.	.	.	.	.	.	A	14.94	2.685045	0.47991	.	.	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.27557	1.66;1.66	1.5	1.5	0.22942	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40546	0.1121	L	0.56124	1.755	0.34319	D	0.686384	P	0.46656	0.882	P	0.56916	0.809	T	0.53158	-0.8478	9	0.72032	D	0.01	.	6.9712	0.24650	1.0:0.0:0.0:0.0	.	374	Q5SXM1	ZN678_HUMAN	G	374;429	ENSP00000344828:E374G;ENSP00000440403:E429G	ENSP00000344828:E374G	E	+	2	0	ZNF678	225909695	1.000000	0.71417	0.017000	0.16124	0.009000	0.06853	3.033000	0.49743	0.591000	0.29711	0.418000	0.28097	GAG	.	.		0.383	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		G	227843072	A	G	227843072	3	3	112	1	0	0	0	0	1	0	0	0	18100	304	11	2	1300	2	ZNF678	1	227843072	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	4665101	227843072	21407549	101	16722										
ZNF678	339500	hgsc.bcm.edu	37	chr1	227843509	227843509	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagaggaacctgacaaatgtAaaaaatgtggcagtctttaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:227843509delA	ENST00000343776.5	+	4	1903	c.1558delA	c.(1558-1560)aaafs	p.K521fs	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Frame_Shift_Del_p.K576fs	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	521					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				TGACAAATGTAAAAAATGTGG	0.323																																					p.C574X		Atlas-INDEL	.											.	ZNF678	137	.	0			c.1722delT						.						40	44	43					1																	227843509		2202	4295	6497	SO:0001589	frameshift_variant	339500	exon4			.	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"Zinc fingers, C2H2-type", "-"	28652	protein-coding gene	gene with protein product	"hypothetical protein MGC42493"					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.1558delA	chr1.hg19:g.227843509delA	ENSP00000344828:p.Lys521fs	120.0	0.0		189.0	12.0	NM_178549	Q8IVQ9	Frame_Shift_Del	DEL	ENST00000343776.5	hg19																																																																																				.	.		0.323	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		-	227843509	A	-	227843509	7	5	112	1	0	1	0	1	0	0	0	0	18100	363	13	0	1737	0	ZNF678	1	227843509	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	437	227843509	21407112	102	16723										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228430955	228430955	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgaggcaggggccagtgccAcgctgagctgcgaggtggcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:228430955delA	ENST00000422127.1	+	10	3045	c.3001delA	c.(3001-3003)acgfs	p.T1001fs	OBSCN_ENST00000284548.11_Frame_Shift_Del_p.T1001fs|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Frame_Shift_Del_p.T1093fs	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1001	Ig-like 10.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGCCAGTGCCACGCTGAGCTG	0.612																																					p.A1092fs		Atlas-INDEL	.											.	OBSCN	2142	.	0			c.3276delC						.						27	27	27					1																	228430955		2014	4169	6183	SO:0001589	frameshift_variant	84033	exon11			.	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3001delA	chr1.hg19:g.228430955delA	ENSP00000409493:p.Thr1001fs	112.0	0.0		216.0	13.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Del	DEL	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		-	228430955	A	-	228430955	7	5	112	1	0	1	0	1	0	0	0	0	10821	159	6	0	3035	0	OBSCN	1	228430955	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	587446	228430955	20819666	103	16724										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228434396	228434396	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgaaagtgcgcatagaggctGcgggctgcatgcggcagctg	17	10	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:228434396G>C	ENST00000422127.1	+	13	3969	c.3925G>C	c.(3925-3927)Gcg>Ccg	p.A1309P	OBSCN_ENST00000284548.11_Missense_Mutation_p.A1309P|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.A1401P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1309	Ig-like 13.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CATAGAGGCTGCGGGCTGCAT	0.637																																					p.A1401P		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,-2,2	OBSCN	2142	.	0			c.G4201C						.						78	83	81					1																	228434396		2055	4204	6259	SO:0001583	missense	84033	exon14			GAGGCTGCGGGCT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3925G>C	chr1.hg19:g.228434396G>C	ENSP00000409493:p.Ala1309Pro	189.0	0.0		366.0	0.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	2.050	-0.417834	0.04766	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.67523	-0.27;-0.27	5.01	-10.0	0.00425	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.320640	0.05001	N	0.469196	T	0.51346	0.1669	L	0.41415	1.275	0.09310	N	0.999999	P;P	0.40266	0.584;0.71	B;B	0.43623	0.425;0.18	T	0.54200	-0.8329	10	0.32370	T	0.25	.	2.8128	0.05446	0.1971:0.2173:0.3853:0.2003	.	1309;1309	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	P	1309	ENSP00000284548:A1309P;ENSP00000409493:A1309P	ENSP00000284548:A1309P	A	+	1	0	OBSCN	226501019	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.133000	0.15912	-3.413000	0.00168	-2.284000	0.00269	GCG	.	.		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228434396	G	C	228434396	3	2	112	1	0	0	0	0	1	0	0	0	10821	1319	46	4	3971	4	OBSCN	1	228434396	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	3441	228434396	20816225	104	16725										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228434468	228434468	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggagtacacctgtgaggctGggggccagcggctctccttc	16	12	1	1	rs372487722		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:228434468G>C	ENST00000422127.1	+	13	4041	c.3997G>C	c.(3997-3999)Ggg>Cgg	p.G1333R	OBSCN_ENST00000284548.11_Missense_Mutation_p.G1333R|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.G1425R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1333	Ig-like 13.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.G1334fs*37(2)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CTGTGAGGCTGGGGGCCAGCG	0.592																																					p.G1425R		Atlas-SNP	.											.,2	OBSCN	2142	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.G4273C						.						71	80	77					1																	228434468		2004	4180	6184	SO:0001583	missense	84033	exon14			GAGGCTGGGGGCC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3997G>C	chr1.hg19:g.228434468G>C	ENSP00000409493:p.Gly1333Arg	158.0	0.0		293.0	0.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	7.104	0.574764	0.13623	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.11930	2.73;2.73	5.07	4.15	0.48705	Immunoglobulin subtype (1);	0.070770	0.53938	D	0.000044	T	0.17408	0.0418	L	0.49256	1.55	0.80722	D	1	P;D	0.54964	0.536;0.969	B;P	0.46796	0.398;0.527	T	0.01162	-1.1432	10	0.48119	T	0.1	.	11.4416	0.50100	0.1512:0.0:0.8488:0.0	.	1333;1333	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	R	1333	ENSP00000284548:G1333R;ENSP00000409493:G1333R	ENSP00000284548:G1333R	G	+	1	0	OBSCN	226501091	1.000000	0.71417	0.896000	0.35187	0.062000	0.15995	5.366000	0.66122	1.115000	0.41800	0.557000	0.71058	GGG	.	.		0.592	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228434468	G	C	228434468	3	2	112	1	0	0	0	0	1	0	0	0	10821	1348	47	4	4043	4	OBSCN	1	228434468	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	72	228434468	20816153	105	16726										
COG2	22796	hgsc.bcm.edu	37	chr1	230800279	230800279	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcggtcagttgagaaaattgAaaaaatcttaaactctcaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:230800279delA	ENST00000366669.4	+	5	546	c.431delA	c.(430-432)gaafs	p.E144fs	COG2_ENST00000366668.3_Frame_Shift_Del_p.E144fs|COG2_ENST00000535166.1_Frame_Shift_Del_p.E28fs|COG2_ENST00000534989.1_Frame_Shift_Del_p.E85fs	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	144					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GAGAAAATTGAAAAAATCTTA	0.269																																					p.E144fs		Atlas-INDEL	.											.	COG2	61	.	0			c.430delG						.						28	30	29					1																	230800279		2196	4274	6470	SO:0001589	frameshift_variant	22796	exon5			.	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"Components of oligomeric golgi complex"	6546	protein-coding gene	gene with protein product		606974	"low density lipoprotein receptor defect C complementing"	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.431delA	chr1.hg19:g.230800279delA	ENSP00000355629:p.Glu144fs	114.0	0.0		183.0	13.0	NM_007357	Q86U99	Frame_Shift_Del	DEL	ENST00000366669.4	hg19	CCDS1584.1																																																																																			.	.		0.269	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357		-	230800279	A	-	230800279	7	5	112	1	0	1	0	1	0	0	0	0	3660	246	9	0	449	0	COG2	1	230800279	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2365811	230800279	18450342	106	16727										
SLC35F3	148641	hgsc.bcm.edu	37	chr1	234041422	234041422	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaggatctcaccagcgggccGgtggggctcacgtccatcga					rs57010808	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:234041422delG	ENST00000366618.3	+	2	346	c.201delG	c.(199-201)ccgfs	p.P67fs		NM_173508.2	NP_775779.1	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	408					thiamine transport (GO:0015888)	integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			CCAGCGGGCCGGTGGGGCTCA	0.622																																					p.P67fs		Atlas-INDEL	.											.	SLC35F3	81	.	0			c.200delC						.						69	69	69					1																	234041422		2203	4300	6503	SO:0001589	frameshift_variant	148641	exon2			.		CCDS1600.1, CCDS73050.1	1q42.3	2013-05-22			ENSG00000183780	ENSG00000183780		"Solute carriers"	23616	protein-coding gene	gene with protein product							Standard	XM_005273070		Approved	FLJ37712	uc001hvy.1	Q8IY50	OTTHUMG00000037929	ENST00000366618.3:c.201delG	chr1.hg19:g.234041422delG	ENSP00000355577:p.Pro67fs	90.0	0.0		159.0	11.0	NM_173508	Q5TDD6|Q8N9C9	Frame_Shift_Del	DEL	ENST00000366618.3	hg19	CCDS1600.1																																																																																			.	.		0.622	SLC35F3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092579.2	NM_173508		-	234041422	G	-	234041422	7	5	112	1	0	1	0	1	0	0	0	0	14605	1103	39	0	207	0	SLC35F3	1	234041422	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	3241143	234041422	15209199	107	16728										
RYR2	6262	hgsc.bcm.edu	37	chr1	237604620	237604620	+	Splice_Site	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttcctcctctccccttaggAaaaattggatgtaggggtga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:237604620delA	ENST00000366574.2	+	13	1324	c.1007delA	c.(1006-1008)gaa>ga	p.E336fs	RYR2_ENST00000360064.6_Splice_Site_p.E334fs|RYR2_ENST00000542537.1_Splice_Site_p.E320fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	336	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TCCCCTTAGGAAAAATTGGAT	0.358																																					p.E336fs		Atlas-INDEL	.											.	RYR2	1273	.	0			c.1006delG						.						111	106	107					1																	237604620		1830	4085	5915	SO:0001630	splice_region_variant	6262	exon13			.	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.1006-1A>-	chr1.hg19:g.237604620delA		100.0	0.0		152.0	10.0	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Del	DEL	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.358	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	Frame_Shift_Del	-	237604620	A	-	237604620	8	5	112	1	0	1	0	1	0	0	1	0	13784	260	9	0	1057	0	RYR2	1	237604620	Splice_Site	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3563198	237604620	11646001	108	16729										
RYR2	6262	hgsc.bcm.edu	37	chr1	237711798	237711798	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttatcaaactcaccccatcaCaagaagcaatggtggacaag	7	11	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:237711798C>G	ENST00000366574.2	+	26	3291	c.2974C>G	c.(2974-2976)Caa>Gaa	p.Q992E	RYR2_ENST00000360064.6_Missense_Mutation_p.Q990E|RYR2_ENST00000542537.1_Missense_Mutation_p.Q976E	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	992	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CACCCCATCACAAGAAGCAAT	0.473																																					p.Q992E		Atlas-SNP	.											RYR2,NS,carcinoma,0,1	RYR2	1273	.	0			c.C2974G						.						62	58	59					1																	237711798		1919	4129	6048	SO:0001583	missense	6262	exon26			CCATCACAAGAAG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2974C>G	chr1.hg19:g.237711798C>G	ENSP00000355533:p.Gln992Glu	142.0	0.0		248.0	0.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.320888	0.81469	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.91237	-2.81;-2.81;-2.81	5.51	5.51	0.81932	Ryanodine receptor Ryr (1);	0.000000	0.64402	D	0.000009	D	0.91845	0.7419	M	0.66939	2.045	0.80722	D	1	P	0.42827	0.791	P	0.44673	0.457	D	0.92329	0.5872	10	0.66056	D	0.02	.	19.7837	0.96428	0.0:1.0:0.0:0.0	.	992	Q92736	RYR2_HUMAN	E	992;990;976	ENSP00000355533:Q992E;ENSP00000353174:Q990E;ENSP00000443798:Q976E	ENSP00000353174:Q990E	Q	+	1	0	RYR2	235778421	1.000000	0.71417	0.964000	0.40570	0.548000	0.35241	7.645000	0.83430	2.738000	0.93877	0.655000	0.94253	CAA	.	.		0.473	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237711798	C	G	237711798	3	3	112	1	0	0	0	0	1	0	0	0	13784	479	17	4	3076	4	RYR2	1	237711798	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	107178	237711798	11538823	109	16730										
RYR2	6262	hgsc.bcm.edu	37	chr1	237957192	237957192	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attggttatttttaagcgagAaaaggaagtggcacggaaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:237957192delA	ENST00000366574.2	+	95	14125	c.13808delA	c.(13807-13809)gaafs	p.E4603fs	RYR2_ENST00000360064.6_Frame_Shift_Del_p.E4609fs|RYR2_ENST00000542537.1_Frame_Shift_Del_p.E4587fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4603					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTTAAGCGAGAAAAGGAAGTG	0.348																																					p.E4603fs		Atlas-INDEL	.											.	RYR2	1273	.	0			c.13807delG						.						62	58	59					1																	237957192		1808	4071	5879	SO:0001589	frameshift_variant	6262	exon95			.	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.13808delA	chr1.hg19:g.237957192delA	ENSP00000355533:p.Glu4603fs	114.0	0.0		200.0	12.0	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Del	DEL	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.348	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		-	237957192	A	-	237957192	7	5	112	1	0	1	0	1	0	0	0	0	13784	246	9	0	14186	0	RYR2	1	237957192	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	245394	237957192	11293429	110	16731										
WDR64	128025	hgsc.bcm.edu	37	chr1	241875143	241875143	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgccaagaggagccaacacTttttgctactgtgttaaggc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:241875143delT	ENST00000366552.2	+	8	1191	c.984delT	c.(982-984)actfs	p.T328fs	WDR64_ENST00000437684.2_Frame_Shift_Del_p.T328fs	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	328										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GAGCCAACACTTTTTGCTACT	0.393																																					p.T328fs		Atlas-INDEL	.											.	WDR64	234	.	0			c.983delC						.						118	111	113					1																	241875143		2203	4300	6503	SO:0001589	frameshift_variant	128025	exon8			.	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.984delT	chr1.hg19:g.241875143delT	ENSP00000355510:p.Thr328fs	92.0	0.0		194.0	15.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Frame_Shift_Del	DEL	ENST00000366552.2	hg19																																																																																				.	.		0.393	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		-	241875143	T	-	241875143	7	5	112	1	0	1	0	1	0	0	0	0	17330	1596	56	0	1014	0	WDR64	1	241875143	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3917951	241875143	7375478	111	16732										
WDR64	128025	hgsc.bcm.edu	37	chr1	241936138	241936138	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaagcaacagccaatggacAaaaaacaccctggaattgcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:241936138delA	ENST00000366552.2	+	19	2512	c.2305delA	c.(2305-2307)aaafs	p.K770fs	WDR64_ENST00000437684.2_Intron	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	770										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GCCAATGGACAAAAAACACCC	0.478																																					p.D768fs		Atlas-INDEL	.											.	WDR64	234	.	0			c.2304delC						.						108	106	107					1																	241936138		692	1591	2283	SO:0001589	frameshift_variant	128025	exon19			.	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.2305delA	chr1.hg19:g.241936138delA	ENSP00000355510:p.Lys770fs	110.0	0.0		164.0	12.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Frame_Shift_Del	DEL	ENST00000366552.2	hg19																																																																																				.	.		0.478	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		-	241936138	A	-	241936138	7	5	112	1	0	1	0	1	0	0	0	0	17330	131	5	0	2379	0	WDR64	1	241936138	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	60995	241936138	7314483	112	16733										
EXO1	9156	hgsc.bcm.edu	37	chr1	242042452	242042452	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gttccgaagaaagagcgattCccccacctctttgcctgaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:242042452delC	ENST00000366548.3	+	13	2509	c.1916delC	c.(1915-1917)tccfs	p.S639fs	EXO1_ENST00000348581.5_Frame_Shift_Del_p.S639fs|EXO1_ENST00000518483.1_Frame_Shift_Del_p.S639fs	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	639	Interaction with MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			AAGAGCGATTCCCCCACCTCT	0.488								Editing and processing nucleases																													p.S639fs		Atlas-INDEL	.											.	EXO1	103	.	0			c.1915delT						.						78	73	75					1																	242042452		2203	4300	6503	SO:0001589	frameshift_variant	9156	exon13			.	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1916delC	chr1.hg19:g.242042452delC	ENSP00000355506:p.Ser639fs	136.0	0.0		226.0	17.0	NM_130398	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Frame_Shift_Del	DEL	ENST00000366548.3	hg19	CCDS1620.1																																																																																			.	.		0.488	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027		-	242042452	C	-	242042452	7	5	112	1	0	1	0	1	0	0	0	0	5302	855	30	0	1954	0	EXO1	1	242042452	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	106314	242042452	7208169	113	16734										
ZNF670	93474	hgsc.bcm.edu	37	chr1	247200789	247200789	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcatgctttcgaagggaacTggaacaactgaaggctttac	10	8	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:247200789T>G	ENST00000366503.2	-	4	1290	c.1132A>C	c.(1132-1134)Agt>Cgt	p.S378R		NM_001204220.1|NM_033213.4	NP_001191149.1|NP_149990.1	Q9BS34	ZN670_HUMAN	zinc finger protein 670	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00427)			CGAAGGGAACTGGAACAACTG	0.388																																					p.S378R		Atlas-SNP	.											.	ZNF670	52	.	0			c.A1132C						.						77	75	76					1																	247200789		2203	4300	6503	SO:0001583	missense	93474	exon4			GGGAACTGGAACA		CCDS31087.1	1q44	2013-01-08			ENSG00000135747	ENSG00000135747		"Zinc fingers, C2H2-type", "-"	28167	protein-coding gene	gene with protein product						12477932	Standard	NM_033213		Approved	MGC12466	uc001icd.2	Q9BS34	OTTHUMG00000040868	ENST00000366503.2:c.1132A>C	chr1.hg19:g.247200789T>G	ENSP00000355459:p.Ser378Arg	58.0	0.0		100.0	5.0	NM_033213		Missense_Mutation	SNP	ENST00000366503.2	hg19	CCDS31087.1	.	.	.	.	.	.	.	.	.	.	T	15.31	2.795187	0.50208	.	.	ENSG00000135747	ENST00000366503	T	0.01145	5.27	0.641	0.641	0.17759	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01661	0.0053	M	0.72118	2.19	0.09310	N	1	P	0.38020	0.615	B	0.34385	0.181	T	0.42137	-0.9469	9	0.54805	T	0.06	.	5.5163	0.16908	0.0:1.0E-4:0.0:0.9999	.	378	Q9BS34	ZN670_HUMAN	R	378	ENSP00000355459:S378R	ENSP00000355459:S378R	S	-	1	0	ZNF670	245267412	0.000000	0.05858	0.692000	0.30179	0.816000	0.46133	-1.011000	0.03652	0.508000	0.28173	0.383000	0.25322	AGT	.	.		0.388	ZNF670-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098183.3	NM_033213		G	247200789	T	G	247200789	3	3	112	1	0	0	0	0	1	0	0	0	18092	1580	55	5	41	5	ZNF670	1	247200789	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	5158337	247200789	2049832	114	16735										
OR2T11	127077	hgsc.bcm.edu	37	chr1	248790265	248790265	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgactgagcagaaagtacatGggggtgtggaggcgagagtc					rs537122223		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:248790265delG	ENST00000330803.2	-	1	226	c.165delC	c.(163-165)cccfs	p.P55fs		NM_001001964.1	NP_001001964.1	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T, member 11 (gene/pseudogene)	55						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(5)|lung(20)|skin(2)	28	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GAAAGTACATGGGGGTGTGGA	0.468																																					p.M56fs		Atlas-INDEL	.											.,1	OR2T11	64	.	0			c.166delA						.						65	72	70					1																	248790265		2052	4235	6287	SO:0001589	frameshift_variant	127077	exon1			.	BK004476	CCDS31122.1	1q44	2013-10-10	2013-10-10		ENSG00000183130	ENSG00000183130		"GPCR / Class A : Olfactory receptors"	19574	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily T, member 11"				Standard	NM_001001964		Approved	OR2T11Q	uc001ier.1	Q8NH01	OTTHUMG00000040384	ENST00000330803.2:c.165delC	chr1.hg19:g.248790265delG	ENSP00000328934:p.Pro55fs	102.0	0.0		196.0	12.0	NM_001001964	Q6IEY6	Frame_Shift_Del	DEL	ENST00000330803.2	hg19	CCDS31122.1																																																																																			.	.		0.468	OR2T11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097134.1	NM_001001964		-	248790265	G	-	248790265	7	5	112	1	0	1	0	1	0	0	0	0	11027	1335	47	0	789	0	OR2T11	1	248790265	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1589476	248790265	460356	115	16736										
KIDINS220	57498	hgsc.bcm.edu	37	chr2	8872078	8872078	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tactggaatcctgggaattgAgactcgaaagacttggggtt	13	6	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:8872078A>G	ENST00000256707.3	-	30	4269	c.4088T>C	c.(4087-4089)cTc>cCc	p.L1363P	KIDINS220_ENST00000418530.1_Missense_Mutation_p.L1264P|KIDINS220_ENST00000473731.1_Missense_Mutation_p.L1344P|KIDINS220_ENST00000427284.1_Missense_Mutation_p.L1344P	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1363					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CTGGGAATTGAGACTCGAAAG	0.373																																					p.L1363P		Atlas-SNP	.											.	KIDINS220	136	.	0			c.T4088C						.						80	76	78					2																	8872078		1824	4097	5921	SO:0001583	missense	57498	exon30			GAATTGAGACTCG	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4088T>C	chr2.hg19:g.8872078A>G	ENSP00000256707:p.Leu1363Pro	80.0	0.0		109.0	5.0	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.254122	0.80135	.	.	ENSG00000134313	ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731	T;T;T;T	0.78595	-1.18;-1.19;-1.18;-1.19	5.86	5.86	0.93980	.	0.059447	0.64402	D	0.000002	D	0.82756	0.5106	L	0.34521	1.04	0.80722	D	1	D;D;D	0.76494	0.997;0.997;0.999	D;D;D	0.74023	0.979;0.954;0.982	D	0.84849	0.0812	10	0.87932	D	0	.	16.2644	0.82568	1.0:0.0:0.0:0.0	.	1264;1363;217	Q9ULH0-2;Q9ULH0;B4DG84	.;KDIS_HUMAN;.	P	1363;1344;1264;1344	ENSP00000256707:L1363P;ENSP00000411849:L1344P;ENSP00000414923:L1264P;ENSP00000418974:L1344P	ENSP00000256707:L1363P	L	-	2	0	KIDINS220	8789529	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.730000	0.91510	2.244000	0.73946	0.528000	0.53228	CTC	.	.		0.373	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		G	8872078	A	G	8872078	3	3	112	1	0	0	0	0	1	0	0	0	8280	304	11	2	1231	2	KIDINS220	2	8872078	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10		8872078	234327295	116	16737										
ASAP2	8853	hgsc.bcm.edu	37	chr2	9515031	9515031	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgctccaagcttatgctgaTggtgtggatcttacggaaaa	11	7	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:9515031T>C	ENST00000281419.3	+	17	2044	c.1704T>C	c.(1702-1704)gaT>gaC	p.D568D	ASAP2_ENST00000315273.4_Silent_p.D568D	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	568					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						CTTATGCTGATGGTGTGGATC	0.483																																					p.D568D		Atlas-SNP	.											.	ASAP2	91	.	0			c.T1704C						.						96	97	96					2																	9515031		2203	4300	6503	SO:0001819	synonymous_variant	8853	exon17			TGCTGATGGTGTG	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1704T>C	chr2.hg19:g.9515031T>C		61.0	0.0		69.0	4.0	NM_001135191	D6W4Y8	Silent	SNP	ENST00000281419.3	hg19	CCDS1661.1																																																																																			.	.		0.483	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		C	9515031	T	C	9515031	2	2	112	1	0	0	0	0	0	0	0	1	1011	1461	51	2		2	ASAP2	2	9515031	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	642953	9515031	233684342	117	16738										
TAF1B	9014	hgsc.bcm.edu	37	chr2	9994472	9994472	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tagaacgatgttttacataaTttttggaagcgctaccttca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:9994472delT	ENST00000263663.5	+	5	509	c.321delT	c.(319-321)aatfs	p.N107fs	TAF1B_ENST00000396242.3_5'UTR|TAF1B_ENST00000402170.1_3'UTR	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	107	N-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTTTACATAATTTTTGGAAGC	0.423																																					p.N107fs		Atlas-INDEL	.											.	TAF1B	62	.	0			c.320delA						.						135	129	131					2																	9994472		2203	4300	6503	SO:0001589	frameshift_variant	9014	exon5			.	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.321delT	chr2.hg19:g.9994472delT	ENSP00000263663:p.Asn107fs	151.0	0.0		163.0	10.0	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Frame_Shift_Del	DEL	ENST00000263663.5	hg19	CCDS33143.1																																																																																			.	.		0.423	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		-	9994472	T	-	9994472	7	5	112	1	0	1	0	1	0	0	0	0	15535	1490	52	0	339	0	TAF1B	2	9994472	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	479441	9994472	233204901	118	16739										
ATP6V1C2	245973	hgsc.bcm.edu	37	chr2	10894153	10894153	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggtggaagtcatggaggacTcaaaggggaaggtccaggag	18	5	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:10894153T>C	ENST00000272238.4	+	4	353	c.244T>C	c.(244-246)Tca>Cca	p.S82P	ATP6V1C2_ENST00000381661.3_Missense_Mutation_p.S82P	NM_001039362.1	NP_001034451.1	Q8NEY4	VATC2_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2	82					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|protein dimerization activity (GO:0046983)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		CATGGAGGACTCAAAGGGGAA	0.547																																					p.S82P	NSCLC(188;1042 2136 10807 16813 47705)	Atlas-SNP	.											.	ATP6V1C2	73	.	0			c.T244C						.						73	52	59					2																	10894153		2203	4299	6502	SO:0001583	missense	245973	exon4			GAGGACTCAAAGG	AY039759	CCDS1674.1, CCDS42653.1	2p25.1	2010-04-21	2006-01-13		ENSG00000143882	ENSG00000143882		"ATPases / V-type"	18264	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal 42kD, V1 subunit C isoform 2", "ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C isoform 2"			12384298	Standard	XR_426949		Approved	VMA5, ATP6C2	uc002ras.3	Q8NEY4	OTTHUMG00000090459	ENST00000272238.4:c.244T>C	chr2.hg19:g.10894153T>C	ENSP00000272238:p.Ser82Pro	99.0	0.0		106.0	6.0	NM_001039362	Q96EL8	Missense_Mutation	SNP	ENST00000272238.4	hg19	CCDS42653.1	.	.	.	.	.	.	.	.	.	.	T	12.07	1.826934	0.32329	.	.	ENSG00000143882	ENST00000272238;ENST00000381661	T;T	0.44881	0.91;0.91	5.72	1.45	0.22620	.	0.442738	0.25065	N	0.033416	T	0.36524	0.0970	L	0.49350	1.555	0.19300	N	0.99998	B;B	0.16802	0.002;0.019	B;B	0.25759	0.008;0.063	T	0.31943	-0.9925	10	0.48119	T	0.1	-4.0E-4	10.5921	0.45316	0.079:0.0:0.1955:0.7255	.	82;82	Q8NEY4-2;Q8NEY4	.;VATC2_HUMAN	P	82	ENSP00000272238:S82P;ENSP00000371077:S82P	ENSP00000272238:S82P	S	+	1	0	ATP6V1C2	10811604	0.013000	0.17824	0.015000	0.15790	0.836000	0.47400	0.354000	0.20146	-0.030000	0.13804	0.482000	0.46254	TCA	.	.		0.547	ATP6V1C2-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323555.1	NM_144583		C	10894153	T	C	10894153	3	2	112	1	0	0	0	0	1	0	0	0	1181	1551	54	2	254	2	ATP6V1C2	2	10894153	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	899681	10894153	232305220	119	16740										
WDR35	57539	hgsc.bcm.edu	37	chr2	20188946	20188946	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgtctgcgtctctaatttcAaaactttcagtaatccatct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:20188946delA	ENST00000345530.3	-	2	237	c.122delT	c.(121-123)ttgfs	p.L41fs	AC079145.4_ENST00000416575.1_RNA|WDR35_ENST00000281405.4_Frame_Shift_Del_p.L41fs	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	41					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCTAATTTCAAAACTTTCAG	0.413																																					p.L41fs		Atlas-INDEL	.											.	WDR35	92	.	0			c.123delG						.						252	227	235					2																	20188946		2203	4300	6503	SO:0001589	frameshift_variant	57539	exon2			.	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"WD repeat domain containing", "Intraflagellar transport homologs"	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.122delT	chr2.hg19:g.20188946delA	ENSP00000314444:p.Leu41fs	137.0	0.0		160.0	10.0	NM_020779	B3KVI5|Q4ZG01|Q8NE11	Frame_Shift_Del	DEL	ENST00000345530.3	hg19	CCDS33152.1																																																																																			.	.		0.413	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779		-	20188946	A	-	20188946	7	5	112	1	0	1	0	1	0	0	0	0	17304	131	5	0	3531	0	WDR35	2	20188946	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	9294793	20188946	223010427	120	16741										
MATN3	4148	hgsc.bcm.edu	37	chr2	20202988	20202988	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcacagtggtgcttgccttCcccatcactgatgcagacgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:20202988delC	ENST00000407540.3	-	3	912	c.850delG	c.(850-852)gaafs	p.E284fs	MATN3_ENST00000421259.2_Intron|AC079145.4_ENST00000416575.1_RNA	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	284	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTTGCCTTCCCCATCACTG	0.537																																					p.E284fs		Atlas-INDEL	.											.	MATN3	28	.	0			c.851delA						.						114	107	109					2																	20202988		2039	4196	6235	SO:0001589	frameshift_variant	4148	exon3			.	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.850delG	chr2.hg19:g.20202988delC	ENSP00000383894:p.Glu284fs	144.0	0.0		137.0	10.0	NM_002381	B2CPU0|Q4ZG02	Frame_Shift_Del	DEL	ENST00000407540.3	hg19	CCDS46226.1																																																																																			.	.		0.537	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381		-	20202988	C	-	20202988	7	5	112	1	0	1	0	1	0	0	0	0	9344	864	30	0	634	0	MATN3	2	20202988	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	14042	20202988	222996385	121	16742										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	24033288	24033288	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agagtgtgcaaaagtgctggAgcaaggtgagaagtttgacc	15	5	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:24033288A>G	ENST00000238789.5	-	18	2695	c.2352T>C	c.(2350-2352)gcT>gcC	p.A784A	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	784						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAAGTGCTGGAGCAAGGTGAG	0.463																																					p.A784A		Atlas-SNP	.											.	ATAD2B	110	.	0			c.T2352C						.						89	91	91					2																	24033288		1964	4158	6122	SO:0001819	synonymous_variant	54454	exon18			TGCTGGAGCAAGG	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.2352T>C	chr2.hg19:g.24033288A>G		120.0	0.0		118.0	5.0	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Silent	SNP	ENST00000238789.5	hg19	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	A	11.06	1.529099	0.27387	.	.	ENSG00000119778	ENST00000381024	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	T	0.72003	0.3407	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71244	-0.4650	4	.	.	.	.	15.9297	0.79648	1.0:0.0:0.0:0.0	.	.	.	.	P	65	.	.	L	-	2	0	ATAD2B	23886792	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.887000	0.39698	2.219000	0.72066	0.533000	0.62120	CTC	.	.		0.463	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		G	24033288	A	G	24033288	2	3	112	1	0	0	0	0	0	0	0	1	1072	291	11	2		2	ATAD2B	2	24033288	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	3830300	24033288	219166085	122	16743										
ASXL2	55252	hgsc.bcm.edu	37	chr2	25966582	25966582	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagccactggcacactagcaTctgtctttgatgaggctgaa	10	11	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:25966582T>C	ENST00000435504.4	-	13	2917	c.2624A>G	c.(2623-2625)gAt>gGt	p.D875G	ASXL2_ENST00000404843.1_Intron|ASXL2_ENST00000336112.4_Missense_Mutation_p.D847G|ASXL2_ENST00000272341.4_Intron			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	875					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACACTAGCATCTGTCTTTGA	0.478																																					p.D875G		Atlas-SNP	.											.	ASXL2	217	.	0			c.A2624G						.						110	112	112					2																	25966582		2041	4181	6222	SO:0001583	missense	55252	exon12			CTAGCATCTGTCT			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.2624A>G	chr2.hg19:g.25966582T>C	ENSP00000391447:p.Asp875Gly	66.0	0.0		72.0	4.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	hg19		.	.	.	.	.	.	.	.	.	.	T	5.275	0.236102	0.10023	.	.	ENSG00000143970	ENST00000435504;ENST00000336112	T;T	0.21932	1.98;1.98	5.57	-2.32	0.06745	.	1.214150	0.05505	N	0.559175	T	0.09992	0.0245	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32693	-0.9897	10	0.87932	D	0	0.9626	3.481	0.07602	0.0847:0.4337:0.3188:0.1628	.	875	Q76L83	ASXL2_HUMAN	G	875;847	ENSP00000391447:D875G;ENSP00000337250:D847G	ENSP00000337250:D847G	D	-	2	0	ASXL2	25820086	0.000000	0.05858	0.045000	0.18777	0.321000	0.28281	-0.452000	0.06787	-0.876000	0.04017	0.460000	0.39030	GAT	.	.		0.478	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		C	25966582	T	C	25966582	3	2	112	1	0	0	0	0	1	0	0	0	1067	1435	50	2	1687	2	ASXL2	2	25966582	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1933294	25966582	217232791	123	16744										
CENPA	1058	hgsc.bcm.edu	37	chr2	27016084	27016084	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttacatgcaggccgagttacTctcttcccaaaggatgtgca	9	11	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:27016084T>C	ENST00000335756.4	+	4	560	c.360T>C	c.(358-360)acT>acC	p.T120T	CENPA_ENST00000233505.8_Silent_p.T94T|CENPA_ENST00000475662.1_3'UTR	NM_001809.3	NP_001800.1	P49450	CENPA_HUMAN	centromere protein A	120	H3-like.				CENP-A containing nucleosome assembly (GO:0034080)|establishment of mitotic spindle orientation (GO:0000132)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|protein localization to chromosome, centromeric region (GO:0071459)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|condensed chromosome inner kinetochore (GO:0000939)|condensed nuclear chromosome kinetochore (GO:0000778)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(3)|lung(3)|urinary_tract(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCGAGTTACTCTCTTCCCAA	0.537																																					p.T120T	Pancreas(28;769 878 30250 30578 41330)	Atlas-SNP	.											.	CENPA	13	.	0			c.T360C						.						174	180	178					2																	27016084		2203	4300	6503	SO:0001819	synonymous_variant	1058	exon4			AGTTACTCTCTTC	U14518	CCDS1729.1, CCDS42662.1	2p23.3	2013-11-05	2006-06-16		ENSG00000115163	ENSG00000115163			1851	protein-coding gene	gene with protein product	"centromere-specific histone", "histone H3-like centromeric protein A"	117139	"centromere protein A (17kD)", "centromere protein A, 17kDa"				Standard	NM_001042426		Approved	CENP-A, CenH3	uc002rhr.3	P49450	OTTHUMG00000097073	ENST00000335756.4:c.360T>C	chr2.hg19:g.27016084T>C		82.0	0.0		97.0	5.0	NM_001809	D6W544|Q53T74|Q9BVW2	Silent	SNP	ENST00000335756.4	hg19	CCDS1729.1																																																																																			.	.		0.537	CENPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214190.2	NM_001809		C	27016084	T	C	27016084	2	2	112	1	0	0	0	0	0	0	0	1	3228	1538	54	2		2	CENPA	2	27016084	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1049502	27016084	216183289	124	16745										
SLC30A3	7781	hgsc.bcm.edu	37	chr2	27480186	27480186	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcccctagacccgtggctgtGggggggcccagcctggtgca					rs148758588		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:27480186delG	ENST00000233535.4	-	5	965	c.613delC	c.(613-615)cacfs	p.H205fs	SLC30A3_ENST00000447008.2_Frame_Shift_Del_p.H200fs	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	205					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCGTGGCTGTGGGGGGGCCCA	0.657																																					p.H205fs		Atlas-INDEL	.											.	SLC30A3	39	.	0			c.614delA						.						16	18	17					2																	27480186		2202	4299	6501	SO:0001589	frameshift_variant	7781	exon5			.	U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"Solute carriers"	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.613delC	chr2.hg19:g.27480186delG	ENSP00000233535:p.His205fs	136.0	0.0		163.0	11.0	NM_003459	Q8TC03	Frame_Shift_Del	DEL	ENST00000233535.4	hg19	CCDS1743.1																																																																																			.	.		0.657	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2			-	27480186	G	-	27480186	7	5	112	1	0	1	0	1	0	0	0	0	14571	1348	47	0	569	0	SLC30A3	2	27480186	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	464102	27480186	215719187	125	16746										
BRE	9577	hgsc.bcm.edu	37	chr2	28210936	28210936	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaagatgctgaattcctgccAgacccctcagctttgcaggt	10	12	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:28210936A>G	ENST00000342045.2	+	5	423	c.282A>G	c.(280-282)ccA>ccG	p.P94P	BRE_ENST00000379624.1_Silent_p.P94P|BRE_ENST00000379632.2_Silent_p.P94P|BRE_ENST00000361704.2_Silent_p.P94P|BRE_ENST00000603461.1_3'UTR|BRE_ENST00000344773.2_Silent_p.P94P	NM_199194.2	NP_954664.1			brain and reproductive organ-expressed (TNFRSF1A modulator)											NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23	Acute lymphoblastic leukemia(172;0.155)					AATTCCTGCCAGACCCCTCAG	0.413																																					p.P94P		Atlas-SNP	.											.	BRE	164	.	0			c.A282G						.						247	269	262					2																	28210936		2203	4300	6503	SO:0001819	synonymous_variant	9577	exon4			CCTGCCAGACCCC	AF015767	CCDS1763.1, CCDS1764.1, CCDS1765.1	2p23	2008-02-05			ENSG00000158019	ENSG00000158019			1106	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 4"	610497				9737713, 7826398	Standard	NM_004899		Approved	BRCC45, BRCC4	uc002rls.3	Q9NXR7	OTTHUMG00000097831	ENST00000342045.2:c.282A>G	chr2.hg19:g.28210936A>G		45.0	0.0		60.0	4.0	NM_199191		Silent	SNP	ENST00000342045.2	hg19	CCDS1763.1																																																																																			.	.		0.413	BRE-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215114.1			G	28210936	A	G	28210936	2	3	112	1	0	0	0	0	0	0	0	1	1511	175	7	2		2	BRE	2	28210936	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	730750	28210936	214988437	126	16747										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29293880	29293880	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atggggagggaatcgagaaaGgggggcttgcttctgggtgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:29293880delG	ENST00000331664.5	-	1	3247	c.3248delC	c.(3247-3249)cctfs	p.P1083fs		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1083	Pro-rich.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						AATCGAGAAAGGGGGGCTTGC	0.602																																					p.P1083fs		Atlas-INDEL	.											.	C2orf71	146	.	0			c.3249delT						.						57	65	63					2																	29293880		1891	4089	5980	SO:0001589	frameshift_variant	388939	exon1			.		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3248delC	chr2.hg19:g.29293880delG	ENSP00000332809:p.Pro1083fs	57.0	0.0		102.0	10.0	NM_001029883		Frame_Shift_Del	DEL	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.		0.602	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		-	29293880	G	-	29293880	7	5	112	1	0	1	0	1	0	0	0	0	2193	1000	35	0	626	0	C2orf71	2	29293880	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1082944	29293880	213905493	127	16748										
XDH	7498	hgsc.bcm.edu	37	chr2	31587070	31587070	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccacattgctgaagtggtccAcctcaagagccacaactgtc	8	14	1	2	rs371816841		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:31587070A>G	ENST00000379416.3	-	24	2633	c.2585T>C	c.(2584-2586)gTg>gCg	p.V862A		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	862					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GAAGTGGTCCACCTCAAGAGC	0.542																																					p.V862A	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.T2585C						.						158	142	148					2																	31587070		2203	4300	6503	SO:0001583	missense	7498	exon24			TGGTCCACCTCAA	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.2585T>C	chr2.hg19:g.31587070A>G	ENSP00000368727:p.Val862Ala	93.0	0.0		90.0	4.0	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	hg19	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	A	32	5.144226	0.94603	.	.	ENSG00000158125	ENST00000379416	T	0.39592	1.07	6.17	6.17	0.99709	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.000000	0.85682	D	0.000000	T	0.50888	0.1642	L	0.38953	1.18	0.80722	D	1	D	0.55800	0.973	P	0.57152	0.814	T	0.48636	-0.9018	10	0.52906	T	0.07	.	16.4957	0.84242	1.0:0.0:0.0:0.0	.	862	P47989	XDH_HUMAN	A	862	ENSP00000368727:V862A	ENSP00000368727:V862A	V	-	2	0	XDH	31440574	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.964000	0.93389	2.371000	0.80710	0.533000	0.62120	GTG	.	.		0.542	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		G	31587070	A	G	31587070	3	3	112	1	0	0	0	0	1	0	0	0	17441	159	6	2	1468	2	XDH	2	31587070	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2293190	31587070	211612303	128	16749										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37217794	37217794	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtaacgtgtaacttacccaTgggtcgcatgaatttaatgc	9	8	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:37217794T>C	ENST00000233099.5	-	34	5789	c.5694A>G	c.(5692-5694)ccA>ccG	p.P1898P	HEATR5B_ENST00000354531.2_Silent_p.P1809P	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1898						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				AACTTACCCATGGGTCGCATG	0.343																																					p.P1898P		Atlas-SNP	.											.	HEATR5B	185	.	0			c.A5694G						.						107	99	102					2																	37217794		2203	4300	6503	SO:0001819	synonymous_variant	54497	exon34			TACCCATGGGTCG	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.5694A>G	chr2.hg19:g.37217794T>C		98.0	0.0		96.0	4.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	hg19	CCDS33181.1																																																																																			.	.		0.343	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		C	37217794	T	C	37217794	2	2	112	1	0	0	0	0	0	0	0	1	7041	1451	51	2		2	HEATR5B	2	37217794	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	5630724	37217794	205981579	129	16750										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37234290	37234290	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaattgacagatgtagaacgTttttgtaaaccagatattgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:37234290delT	ENST00000233099.5	-	29	4775	c.4680delA	c.(4678-4680)aaafs	p.K1560fs	HEATR5B_ENST00000354531.2_Frame_Shift_Del_p.K1560fs	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1560						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				ATGTAGAACGTTTTTGTAAAC	0.428																																					p.R1561fs		Atlas-INDEL	.											.	HEATR5B	185	.	0			c.4681delC						.						143	131	135					2																	37234290		2203	4300	6503	SO:0001589	frameshift_variant	54497	exon29			.	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.4680delA	chr2.hg19:g.37234290delT	ENSP00000233099:p.Lys1560fs	119.0	0.0		152.0	12.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Frame_Shift_Del	DEL	ENST00000233099.5	hg19	CCDS33181.1																																																																																			.	.		0.428	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		-	37234290	T	-	37234290	7	5	112	1	0	1	0	1	0	0	0	0	7041	1722	60	0	1567	0	HEATR5B	2	37234290	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	16496	37234290	205965083	130	16751										
SOS1	6654	hgsc.bcm.edu	37	chr2	39262357	39262357	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taaagagttttcttaccttcAaaagttcaaagtaatggaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:39262357delA	ENST00000426016.1	-	9	1156	c.1070delT	c.(1069-1071)ttgfs	p.L357fs	SOS1_ENST00000428721.2_Frame_Shift_Del_p.L300fs|SOS1_ENST00000402219.2_Frame_Shift_Del_p.L357fs|SOS1_ENST00000395038.2_Frame_Shift_Del_p.L357fs			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	357	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				TCTTACCTTCAAAAGTTCAAA	0.353									Noonan syndrome																												p.L357fs		Atlas-INDEL	.											.	SOS1	134	.	0			c.1071delG						.						43	46	45					2																	39262357		2203	4300	6503	SO:0001589	frameshift_variant	6654	exon8	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	.	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1070delT	chr2.hg19:g.39262357delA	ENSP00000387784:p.Leu357fs	163.0	0.0		173.0	11.0	NM_005633	A8K2G3|B4DXG2	Frame_Shift_Del	DEL	ENST00000426016.1	hg19	CCDS1802.1																																																																																			.	.		0.353	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		-	39262357	A	-	39262357	7	5	112	1	0	1	0	1	0	0	0	0	14951	131	5	0	2995	0	SOS1	2	39262357	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2028067	39262357	203937016	131	16752										
SOS1	6654	hgsc.bcm.edu	37	chr2	39262585	39262585	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgactaaggaaacgatcatgAaaaccaggtcgcaaaatatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:39262585delA	ENST00000426016.1	-	8	1007	c.921delT	c.(919-921)tttfs	p.F307fs	SOS1_ENST00000428721.2_Frame_Shift_Del_p.F250fs|SOS1_ENST00000402219.2_Frame_Shift_Del_p.F307fs|SOS1_ENST00000395038.2_Frame_Shift_Del_p.F307fs			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	307	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				AACGATCATGAAAACCAGGTC	0.333									Noonan syndrome																												p.H308fs		Atlas-INDEL	.											.	SOS1	134	.	0			c.922delC						.						75	78	77					2																	39262585		2203	4300	6503	SO:0001589	frameshift_variant	6654	exon7	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	.	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.921delT	chr2.hg19:g.39262585delA	ENSP00000387784:p.Phe307fs	177.0	0.0		165.0	11.0	NM_005633	A8K2G3|B4DXG2	Frame_Shift_Del	DEL	ENST00000426016.1	hg19	CCDS1802.1																																																																																			.	.		0.333	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		-	39262585	A	-	39262585	7	5	112	1	0	1	0	1	0	0	0	0	14951	243	9	0	3148	0	SOS1	2	39262585	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	228	39262585	203936788	132	16753										
KCNG3	170850	hgsc.bcm.edu	37	chr2	42671493	42671493	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acgggcaagcttaatcacccAaaaaatcctcatcattctaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:42671493delA	ENST00000306078.1	-	2	1487	c.892delT	c.(892-894)tggfs	p.W298fs	KCNG3_ENST00000394973.4_Frame_Shift_Del_p.W287fs	NM_133329.5|NM_172344.2	NP_579875.1|NP_758847.1	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G, member 3	298					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	6						TTAATCACCCAAAAAATCCTC	0.443																																					p.W298fs		Atlas-INDEL	.											.	KCNG3	19	.	0			c.893delG						.						100	94	96					2																	42671493		2203	4300	6503	SO:0001589	frameshift_variant	170850	exon2			.	AB070604	CCDS1809.1, CCDS42674.1	2p21	2011-07-05			ENSG00000171126	ENSG00000171126		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18306	protein-coding gene	gene with protein product		606767				11852086, 16382104	Standard	NM_133329		Approved	Kv6.3	uc002rsn.3	Q8TAE7	OTTHUMG00000128604	ENST00000306078.1:c.892delT	chr2.hg19:g.42671493delA	ENSP00000304127:p.Trp298fs	116.0	0.0		173.0	12.0	NM_133329	Q53SC1	Frame_Shift_Del	DEL	ENST00000306078.1	hg19	CCDS1809.1																																																																																			.	.		0.443	KCNG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250464.2	NM_172344		-	42671493	A	-	42671493	7	5	112	1	0	1	0	1	0	0	0	0	8038	130	5	0	422	0	KCNG3	2	42671493	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3408908	42671493	200527880	133	16754										
C2orf63	130162	hgsc.bcm.edu	37	chr2	55445059	55445059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agttcttcggtctttctttaTtgtctcaataaaggcatcat	6	8	5	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:55445059T>C	ENST00000401408.1	-	4	598	c.253A>G	c.(253-255)Ata>Gta	p.I85V	CLHC1_ENST00000494539.1_Intron|AC012358.7_ENST00000366153.2_RNA|CLHC1_ENST00000407122.1_Missense_Mutation_p.I85V|CLHC1_ENST00000406437.2_Intron|CLHC1_ENST00000406076.1_5'UTR	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	85																	TCTTTCTTTATTGTCTCAATA	0.333																																					p.I85V		Atlas-SNP	.											.	.	.	.	0			c.A253G						.						105	103	104					2																	55445059		2203	4299	6502	SO:0001583	missense	130162	exon4			TCTTTATTGTCTC		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 63"	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.253A>G	chr2.hg19:g.55445059T>C	ENSP00000384869:p.Ile85Val	95.0	0.0		78.0	4.0	NM_152385	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	hg19	CCDS33201.1	.	.	.	.	.	.	.	.	.	.	T	9.958	1.221918	0.22457	.	.	ENSG00000162994	ENST00000407122;ENST00000401408	T;T	0.22336	1.96;1.96	5.96	-8.28	0.01013	.	0.862446	0.10359	N	0.684170	T	0.13670	0.0331	L	0.47716	1.5	0.48571	D	0.999674	B	0.06786	0.001	B	0.09377	0.004	T	0.09079	-1.0691	10	0.45353	T	0.12	-1.8293	7.3007	0.26418	0.0878:0.1115:0.5389:0.2618	.	85	Q8NHS4	CB063_HUMAN	V	85	ENSP00000385778:I85V;ENSP00000384869:I85V	ENSP00000384869:I85V	I	-	1	0	C2orf63	55298563	0.002000	0.14202	0.336000	0.25522	0.538000	0.34931	-0.372000	0.07504	-1.243000	0.02519	-1.139000	0.01908	ATA	.	.		0.333	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385		C	55445059	T	C	55445059	3	2	112	1	0	0	0	0	1	0	0	0	2184	1493	52	2	1547	2	C2orf63	2	55445059	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	12773566	55445059	187754314	134	16755										
PNPT1	87178	hgsc.bcm.edu	37	chr2	55907883	55907883	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggaatatctgataatgagaGggctacggaagcttaaaaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:55907883delG	ENST00000447944.2	-	7	615	c.529delC	c.(529-531)ctcfs	p.L177fs		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	177					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GATAATGAGAGGGCTACGGAA	0.284																																					p.L177fs		Atlas-INDEL	.											.	PNPT1	68	.	0			c.530delT						.						48	53	51					2																	55907883		2202	4300	6502	SO:0001589	frameshift_variant	87178	exon7			.	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.529delC	chr2.hg19:g.55907883delG	ENSP00000400646:p.Leu177fs	139.0	0.0		180.0	11.0	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Frame_Shift_Del	DEL	ENST00000447944.2	hg19	CCDS1856.1																																																																																			.	.		0.284	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		-	55907883	G	-	55907883	7	5	112	1	0	1	0	1	0	0	0	0	12182	1000	35	0	1910	0	PNPT1	2	55907883	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	462824	55907883	187291490	135	16756										
XPO1	7514	hgsc.bcm.edu	37	chr2	61719275	61719275	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgaacgaaatgcctgcggcaTttttgggctattttaatgaa					rs3816341	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:61719275delT	ENST00000401558.2	-	16	2509	c.1782delA	c.(1780-1782)aaafs	p.K594fs	XPO1_ENST00000406957.1_Frame_Shift_Del_p.K594fs|XPO1_ENST00000404992.2_Frame_Shift_Del_p.K594fs	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	594	Necessary for HTLV-1 Rex-mediated mRNA export.				gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			GCCTGCGGCATTTTTGGGCTA	0.373			Mis		CLL																																p.C595fs		Atlas-INDEL	.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1	108	.	0			c.1783delT						.						76	77	77					2																	61719275		2203	4300	6503	SO:0001589	frameshift_variant	7514	exon16			.	Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.1782delA	chr2.hg19:g.61719275delT	ENSP00000384863:p.Lys594fs	138.0	0.0		146.0	10.0	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Frame_Shift_Del	DEL	ENST00000401558.2	hg19	CCDS33205.1																																																																																			.	.		0.373	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		-	61719275	T	-	61719275	7	5	112	1	0	1	0	1	0	0	0	0	17460	1490	52	0	1473	0	XPO1	2	61719275	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	5811392	61719275	181480098	136	16757										
TMEM17	200728	hgsc.bcm.edu	37	chr2	62729911	62729911	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgacatctgcagtgccaaaCtggagaccatttcattttct	8	10	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:62729911C>T	ENST00000335390.5	-	2	330	c.119G>A	c.(118-120)aGt>aAt	p.S40N		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	40					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			CAGTGCCAAACTGGAGACCAT	0.358																																					p.S40N		Atlas-SNP	.											.	TMEM17	19	.	0			c.G119A						.						75	77	76					2																	62729911		2203	4300	6503	SO:0001583	missense	200728	exon2			GCCAAACTGGAGA		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.119G>A	chr2.hg19:g.62729911C>T	ENSP00000335094:p.Ser40Asn	207.0	0.0		199.0	9.0	NM_198276	Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	hg19	CCDS1871.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.883387	0.72410	.	.	ENSG00000186889	ENST00000335390	T	0.54866	0.55	6.07	5.2	0.72013	.	0.190536	0.64402	N	0.000003	T	0.39733	0.1089	N	0.19112	0.55	0.54753	D	0.999985	B	0.16396	0.017	B	0.15052	0.012	T	0.15206	-1.0445	10	0.38643	T	0.18	-9.5686	15.2691	0.73686	0.0:0.933:0.0:0.067	.	40	Q86X19	TMM17_HUMAN	N	40	ENSP00000335094:S40N	ENSP00000335094:S40N	S	-	2	0	TMEM17	62583415	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.586000	0.60984	1.567000	0.49668	0.655000	0.94253	AGT	.	.		0.358	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276		T	62729911	C	T	62729911	3	4	112	1	0	0	0	0	1	0	0	0	16100	565	20	3	489	3	TMEM17	2	62729911	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1010636	62729911	180469462	137	16758										
SLC1A4	6509	hgsc.bcm.edu	37	chr2	65237733	65237733	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctctctgatcctgcagatCcccataggcactgagataga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:65237733delC	ENST00000234256.3	+	4	879	c.636delC	c.(634-636)atcfs	p.I212fs	SLC1A4_ENST00000493121.1_3'UTR|SLC1A4_ENST00000531327.1_5'UTR	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	212					amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	TCCTGCAGATCCCCATAGGCA	0.448																																					p.I212fs		Atlas-INDEL	.											.	SLC1A4	33	.	0			c.635delT						.						161	153	155					2																	65237733		2203	4300	6503	SO:0001589	frameshift_variant	6509	exon4			.		CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"Solute carriers"	10942	protein-coding gene	gene with protein product	"alanine/serine/cysteine/threonine transporter"	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.636delC	chr2.hg19:g.65237733delC	ENSP00000234256:p.Ile212fs	161.0	0.0		164.0	10.0	NM_003038	B7Z3C0|D6W5F0	Frame_Shift_Del	DEL	ENST00000234256.3	hg19	CCDS1879.1																																																																																			.	.		0.448	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038		-	65237733	C	-	65237733	7	5	112	1	0	1	0	1	0	0	0	0	14449	845	30	0	650	0	SLC1A4	2	65237733	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	2507822	65237733	177961640	138	16759										
ADD2	119	hgsc.bcm.edu	37	chr2	70890579	70890579	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggactccactttctccttcTttttgctctttttcaggaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:70890579delT	ENST00000264436.4	-	16	2603	c.2159delA	c.(2158-2160)aagfs	p.K721fs	ADD2_ENST00000407644.2_Frame_Shift_Del_p.K721fs	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	721	Interaction with calmodulin. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						TTTCTCCTTCTTTTTGCTCTT	0.547																																					p.K720fs		Atlas-INDEL	.											.	ADD2	261	.	0			c.2160delG						.						157	153	155					2																	70890579		2203	4300	6503	SO:0001589	frameshift_variant	119	exon16			.	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.2159delA	chr2.hg19:g.70890579delT	ENSP00000264436:p.Lys721fs	107.0	0.0		120.0	11.0	NM_001617	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Frame_Shift_Del	DEL	ENST00000264436.4	hg19	CCDS1906.1																																																																																			.	.		0.547	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		-	70890579	T	-	70890579	7	5	112	1	0	1	0	1	0	0	0	0	305	1609	56	0	25	0	ADD2	2	70890579	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	5652846	70890579	172308794	139	16760										
NAGK	55577	hgsc.bcm.edu	37	chr2	71302707	71302707	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccagatcggctagggatacTcactcacctgtatagggact	11	11	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:71302707T>C	ENST00000244204.6	+	7	664	c.602T>C	c.(601-603)cTc>cCc	p.L201P	NAGK_ENST00000443872.2_Missense_Mutation_p.L53P|NAGK_ENST00000455662.2_Missense_Mutation_p.L247P|NAGK_ENST00000443938.2_Missense_Mutation_p.L201P|NAGK_ENST00000418807.3_Missense_Mutation_p.L150P			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	201					carbohydrate phosphorylation (GO:0046835)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|N-acetylglucosamine kinase activity (GO:0045127)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|urinary_tract(1)	18					N-Acetyl-D-glucosamine(DB00141)	CTAGGGATACTCACTCACCTG	0.498																																					p.L247P		Atlas-SNP	.											.	NAGK	34	.	0			c.T740C						.						94	90	91					2																	71302707		2203	4300	6503	SO:0001583	missense	55577	exon7			GGATACTCACTCA	AJ242910	CCDS33220.1, CCDS33220.2	2p24.3-p24.1	2008-02-05			ENSG00000124357	ENSG00000124357	2.7.1.59		17174	protein-coding gene	gene with protein product		606828				10824116	Standard	NM_017567		Approved	GNK	uc002shp.4	Q9UJ70	OTTHUMG00000153239	ENST00000244204.6:c.602T>C	chr2.hg19:g.71302707T>C	ENSP00000244204:p.Leu201Pro	118.0	0.0		96.0	4.0	NM_017567	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Missense_Mutation	SNP	ENST00000244204.6	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.3|23.3	4.399084|4.399084	0.83120|0.83120	.|.	.|.	ENSG00000124357|ENSG00000124357	ENST00000244204;ENST00000455662;ENST00000531934;ENST00000418807;ENST00000529236|ENST00000443938	T;T;T|.	0.56444|.	1.09;1.05;0.46|.	5.35|5.35	5.35|5.35	0.76521|0.76521	ATPase, BadF/BadG/BcrA/BcrD type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79644|0.79644	0.4481|0.4481	M|M	0.88310|0.88310	2.945|2.945	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.83031|0.83031	-0.0162|-0.0162	10|5	0.66056|.	D|.	0.02|.	-18.7632|-18.7632	13.5719|13.5719	0.61851|0.61851	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	201|.	Q9UJ70|.	NAGK_HUMAN|.	P|P	201;247;53;150;95|223	ENSP00000244204:L201P;ENSP00000389087:L247P;ENSP00000396070:L150P|.	ENSP00000244204:L201P|.	L|S	+|+	2|1	0|0	NAGK|NAGK	71156215|71156215	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.976000|0.976000	0.68499|0.68499	7.037000|7.037000	0.76531|0.76531	2.155000|2.155000	0.67459|0.67459	0.533000|0.533000	0.62120|0.62120	CTC|TCA	.	.		0.498	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1			C	71302707	T	C	71302707	3	2	112	1	0	0	0	0	1	0	0	0	10151	1551	54	2	766	2	NAGK	2	71302707	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	412128	71302707	171896666	140	16761										
DYSF	8291	hgsc.bcm.edu	37	chr2	71801370	71801370	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcgagggctgggagtacgccTctctttttggctggaagttc	15	9	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:71801370T>C	ENST00000258104.3	+	30	3494	c.3217T>C	c.(3217-3219)Tct>Cct	p.S1073P	DYSF_ENST00000409744.1_Missense_Mutation_p.S1060P|DYSF_ENST00000394120.2_Missense_Mutation_p.S1074P|DYSF_ENST00000409582.3_Missense_Mutation_p.S1090P|DYSF_ENST00000409651.1_Missense_Mutation_p.S1105P|DYSF_ENST00000410020.3_Missense_Mutation_p.S1091P|DYSF_ENST00000429174.2_Missense_Mutation_p.S1073P|DYSF_ENST00000410041.1_Missense_Mutation_p.S1091P|DYSF_ENST00000413539.2_Missense_Mutation_p.S1104P|DYSF_ENST00000409366.1_Missense_Mutation_p.S1074P|DYSF_ENST00000409762.1_Missense_Mutation_p.S1090P	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1073	Arg-rich.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GGAGTACGCCTCTCTTTTTGG	0.667																																					p.S1105P		Atlas-SNP	.											.	DYSF	536	.	0			c.T3313C						.						68	80	76					2																	71801370		2203	4300	6503	SO:0001583	missense	8291	exon31			TACGCCTCTCTTT	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.3217T>C	chr2.hg19:g.71801370T>C	ENSP00000258104:p.Ser1073Pro	66.0	0.0		97.0	4.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.398940	0.83120	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.83837	-1.76;-1.77;-1.77;-1.77;-1.77;-1.76;-1.77;-1.77;-1.77;-1.77;-1.77	5.6	4.41	0.53225	Ferlin/Peroxisome membrane (1);	0.062797	0.64402	D	0.000003	D	0.86322	0.5905	L	0.48642	1.525	0.41765	D	0.989734	D;D;D;D;D;D;D;P;D;B;B;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.746;1.0;0.017;0.313;0.999;1.0;1.0	D;D;D;D;D;D;D;P;D;B;B;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.994;0.991;0.994;0.535;0.999;0.054;0.261;0.999;0.999;0.998	D	0.83801	0.0236	10	0.33141	T	0.24	-14.8294	10.1355	0.42704	0.1498:0.0:0.0:0.8502	.	1105;1091;1074;1060;1091;1060;1090;1059;1104;1090;1073;1059;1074;1073	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	P	1104;1090;1090;1073;1073;1105;1074;1060;1074;1091;1091	ENSP00000407046:S1104P;ENSP00000387137:S1090P;ENSP00000386547:S1090P;ENSP00000398305:S1073P;ENSP00000258104:S1073P;ENSP00000386683:S1105P;ENSP00000377678:S1074P;ENSP00000386285:S1060P;ENSP00000386512:S1074P;ENSP00000386881:S1091P;ENSP00000386617:S1091P	ENSP00000258104:S1073P	S	+	1	0	DYSF	71654878	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	7.661000	0.83786	0.907000	0.36646	0.528000	0.53228	TCT	.	.		0.667	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		C	71801370	T	C	71801370	3	2	112	1	0	0	0	0	1	0	0	0	4861	1551	54	2	3527	2	DYSF	2	71801370	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	498663	71801370	171398003	141	16762										
WDR54	84058	hgsc.bcm.edu	37	chr2	74652051	74652051	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgactcaggcttgctgtgtgTctggcggtcagggccagaat	15	9	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:74652051T>C	ENST00000348227.4	+	7	672	c.584T>C	c.(583-585)gTc>gCc	p.V195A	WDR54_ENST00000461531.1_3'UTR|WDR54_ENST00000409791.1_Missense_Mutation_p.V143A	NM_032118.2	NP_115494.1	Q9H977	WDR54_HUMAN	WD repeat domain 54	195										breast(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9						TTGCTGTGTGTCTGGCGGTCA	0.537																																					p.V195A		Atlas-SNP	.											.	WDR54	17	.	0			c.T584C						.						236	186	203					2																	74652051		2203	4300	6503	SO:0001583	missense	84058	exon7			TGTGTGTCTGGCG	AK023015	CCDS1940.1	2p13.1	2013-01-09			ENSG00000005448	ENSG00000005448		"WD repeat domain containing"	25770	protein-coding gene	gene with protein product						12477932	Standard	NM_032118		Approved	FLJ12953	uc002slb.3	Q9H977	OTTHUMG00000129951	ENST00000348227.4:c.584T>C	chr2.hg19:g.74652051T>C	ENSP00000006526:p.Val195Ala	186.0	0.0		204.0	11.0	NM_032118	D6W5I3|Q53H85|Q86V45	Missense_Mutation	SNP	ENST00000348227.4	hg19	CCDS1940.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433301	0.83776	.	.	ENSG00000005448	ENST00000409791;ENST00000348227	T;T	0.56776	0.44;0.44	5.13	5.13	0.70059	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.070433	0.56097	D	0.000025	T	0.58323	0.2114	L	0.47716	1.5	0.42214	D	0.991828	D	0.60575	0.988	P	0.54759	0.76	T	0.62863	-0.6764	10	0.72032	D	0.01	-20.9254	12.5647	0.56304	0.0:0.0:0.0:1.0	.	195	Q9H977	WDR54_HUMAN	A	143;195	ENSP00000387236:V143A;ENSP00000006526:V195A	ENSP00000006526:V195A	V	+	2	0	WDR54	74505559	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.196000	0.72094	2.158000	0.67659	0.459000	0.35465	GTC	.	.		0.537	WDR54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252213.1	NM_032118		C	74652051	T	C	74652051	3	2	112	1	0	0	0	0	1	0	0	0	17321	1667	58	2	606	2	WDR54	2	74652051	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2850681	74652051	168547322	142	16763										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84954804	84954804	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcacacagttgttcaatacCaccattgaaacttctgtaaa	4	10	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:84954804C>T	ENST00000237449.6	+	60	9992	c.9984C>T	c.(9982-9984)acC>acT	p.T3328T	DNAH6_ENST00000389394.3_Silent_p.T3328T			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3328					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TGTTCAATACCACCATTGAAA	0.393																																					p.T3328T		Atlas-SNP	.											.	DNAH6	194	.	0			c.C9984T						.						103	84	90					2																	84954804		692	1591	2283	SO:0001819	synonymous_variant	1768	exon61			CAATACCACCATT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.9984C>T	chr2.hg19:g.84954804C>T		222.0	0.0		192.0	65.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.393	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84954804	C	T	84954804	2	4	112	1	0	0	0	0	0	0	0	1	4607	581	21	3		3	DNAH6	2	84954804	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	10302753	84954804	158244569	143	16764										
RETSAT	54884	hgsc.bcm.edu	37	chr2	85578072	85578072	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acaggggagcccagtccagcTgcccttcagtgatctggtcc	12	14	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:85578072T>C	ENST00000295802.4	-	3	540	c.428A>G	c.(427-429)cAg>cGg	p.Q143R	RETSAT_ENST00000263854.6_Missense_Mutation_p.Q143R|RETSAT_ENST00000457495.2_Missense_Mutation_p.Q82R	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	143					oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	CCAGTCCAGCTGCCCTTCAGT	0.517																																					p.Q143R		Atlas-SNP	.											.	RETSAT	56	.	0			c.A428G						.						70	68	69					2																	85578072		2203	4300	6503	SO:0001583	missense	54884	exon3			TCCAGCTGCCCTT	AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	1.3.99.23		25991	protein-coding gene	gene with protein product						12975309, 15358783	Standard	NM_017750		Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.428A>G	chr2.hg19:g.85578072T>C	ENSP00000295802:p.Gln143Arg	191.0	0.0		158.0	7.0	NM_017750	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Missense_Mutation	SNP	ENST00000295802.4	hg19	CCDS1972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	33|33	5.205535|5.205535	0.95033|0.95033	.|.	.|.	ENSG00000042445|ENSG00000042445	ENST00000295802;ENST00000263854;ENST00000457495|ENST00000409984	T;T|.	0.58358|.	2.0;0.34|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77658|0.77658	0.4163|0.4163	M|M	0.83384|0.83384	2.64|2.64	0.58432|0.58432	D|D	0.999999|0.999999	P;P|.	0.46784|.	0.537;0.884|.	B;B|.	0.43155|.	0.236;0.41|.	T|T	0.79460|0.79460	-0.1794|-0.1794	9|5	.|.	.|.	.|.	-25.9613|-25.9613	14.4967|14.4967	0.67694|0.67694	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	82;143|.	G5E9N3;Q6NUM9|.	.;RETST_HUMAN|.	R|G	143;143;82|82	ENSP00000295802:Q143R;ENSP00000405040:Q82R|.	.|.	Q|S	-|-	2|1	0|0	RETSAT|RETSAT	85431583|85431583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.914000|7.914000	0.87478|0.87478	2.311000|2.311000	0.77944|0.77944	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.517	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750		C	85578072	T	C	85578072	3	2	112	1	0	0	0	0	1	0	0	0	13253	1580	55	2	1440	2	RETSAT	2	85578072	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	623268	85578072	157621301	144	16765										
MRPS5	64969	hgsc.bcm.edu	37	chr2	95767468	95767468	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tagctttcccaatagaaaaaCctttaaacaaaaaagcaaaa	3	8	0	1	rs199914429		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:95767468C>A	ENST00000272418.2	-	8	972	c.764G>T	c.(763-765)gGt>gTt	p.G255V		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	255	S5 DRBM. {ECO:0000255|PROSITE- ProRule:PRU00268}.				translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						AATAGAAAAACCTTTAAACAA	0.323																																					p.G255V		Atlas-SNP	.											.	MRPS5	52	.	0			c.G764T						.						36	34	35					2																	95767468		2202	4299	6501	SO:0001630	splice_region_variant	64969	exon8			GAAAAACCTTTAA	AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"Mitochondrial ribosomal proteins / small subunits"	14498	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S5"	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.764-1G>T	chr2.hg19:g.95767468C>A		91.0	0.0		110.0	23.0	NM_031902	Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Missense_Mutation	SNP	ENST00000272418.2	hg19	CCDS2010.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319758	0.60524	.	.	ENSG00000144029	ENST00000272418	.	.	.	5.32	5.32	0.75619	Ribosomal protein S5, N-terminal, conserved site (1);Ribosomal protein S5, N-terminal (2);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.88347	0.6412	H	0.98027	4.13	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92102	0.5689	9	0.87932	D	0	.	14.8467	0.70264	0.0:1.0:0.0:0.0	.	255	P82675	RT05_HUMAN	V	255	.	ENSP00000272418:G255V	G	-	2	0	MRPS5	95131195	1.000000	0.71417	1.000000	0.80357	0.342000	0.28953	5.298000	0.65710	2.634000	0.89283	0.591000	0.81541	GGT	.	C|1.000;G|0.000		0.323	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902	Missense_Mutation	A	95767468	C	A	95767468	5	1	112	1	0	0	0	0	0	0	1	0	9855	521	18	3	548	3	MRPS5	2	95767468	Splice_Site	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	10189396	95767468	147431905	145	16766										
SNRNP200	23020	hgsc.bcm.edu	37	chr2	96958714	96958714	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taaaccacgggcaaacctgaTtttttccagcatgttccatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:96958714delT	ENST00000323853.5	-	16	2233	c.2156delA	c.(2155-2157)aatfs	p.N719fs	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	719	Helicase C-terminal 1. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						GCAAACCTGATTTTTTCCAGC	0.368																																					p.N719fs		Atlas-INDEL	.											.	SNRNP200	195	.	0			c.2157delT						.						113	102	106					2																	96958714		2203	4300	6503	SO:0001589	frameshift_variant	23020	exon16			.	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.2156delA	chr2.hg19:g.96958714delT	ENSP00000317123:p.Asn719fs	160.0	0.0		175.0	13.0	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Frame_Shift_Del	DEL	ENST00000323853.5	hg19	CCDS2020.1																																																																																			.	.		0.368	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		-	96958714	T	-	96958714	7	5	112	1	0	1	0	1	0	0	0	0	14867	1493	52	0	4374	0	SNRNP200	2	96958714	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1191246	96958714	146240659	146	16767										
IL18RAP	8807	hgsc.bcm.edu	37	chr2	103067460	103067460	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atagcctgtgtttgcttgaaAgagatgtggctccaggagga	14	6	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:103067460A>G	ENST00000264260.2	+	11	1952	c.1363A>G	c.(1363-1365)Aga>Gga	p.R455G	IL18RAP_ENST00000409369.1_Missense_Mutation_p.R313G	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	455	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						TTTGCTTGAAAGAGATGTGGC	0.423																																					p.R455G		Atlas-SNP	.											.	IL18RAP	102	.	0			c.A1363G						.						84	85	85					2																	103067460		2203	4300	6503	SO:0001583	missense	8807	exon11			CTTGAAAGAGATG	AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.1363A>G	chr2.hg19:g.103067460A>G	ENSP00000264260:p.Arg455Gly	59.0	0.0		77.0	4.0	NM_003853	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Missense_Mutation	SNP	ENST00000264260.2	hg19	CCDS2061.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.008323	0.75046	.	.	ENSG00000115607	ENST00000264260;ENST00000409369	T;T	0.12147	2.71;2.71	5.66	3.2	0.36748	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.64402	D	0.000002	T	0.43344	0.1243	M	0.89904	3.07	0.46078	D	0.99885	D	0.89917	1.0	D	0.91635	0.999	T	0.50259	-0.8849	10	0.87932	D	0	.	12.928	0.58270	0.7721:0.2279:0.0:0.0	.	455	O95256	I18RA_HUMAN	G	455;313	ENSP00000264260:R455G;ENSP00000387201:R313G	ENSP00000264260:R455G	R	+	1	2	IL18RAP	102433892	1.000000	0.71417	0.975000	0.42487	0.958000	0.62258	5.769000	0.68865	0.383000	0.24910	0.528000	0.53228	AGA	.	.		0.423	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853		G	103067460	A	G	103067460	3	3	112	1	0	0	0	0	1	0	0	0	7657	64	3	2	1397	2	IL18RAP	2	103067460	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	6108746	103067460	140131913	147	16768										
GCC2	9648	hgsc.bcm.edu	37	chr2	109086500	109086500	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaatattaatagtttgcagGaagagcttttacagttgaaa	8	3	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:109086500G>A	ENST00000309863.6	+	6	1429	c.715G>A	c.(715-717)Gaa>Aaa	p.E239K	GCC2_ENST00000485546.1_3'UTR	NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	239					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						TAGTTTGCAGGAAGAGCTTTT	0.363																																					p.E239K		Atlas-SNP	.											.	GCC2	129	.	0			c.G715A						.						82	93	89					2																	109086500		2200	4300	6500	SO:0001583	missense	9648	exon6			TTGCAGGAAGAGC	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.715G>A	chr2.hg19:g.109086500G>A	ENSP00000307939:p.Glu239Lys	86.0	0.0		93.0	4.0	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	hg19	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195700	0.38806	.	.	ENSG00000135968	ENST00000435553;ENST00000309863;ENST00000409821;ENST00000409896	T	0.52526	0.66	4.93	4.93	0.64822	.	0.206931	0.39834	N	0.001260	T	0.37945	0.1022	L	0.32530	0.975	0.33117	D	0.54135	P	0.37781	0.608	B	0.32980	0.156	T	0.50717	-0.8795	10	0.32370	T	0.25	.	18.5148	0.90931	0.0:0.0:1.0:0.0	.	239	Q8IWJ2	GCC2_HUMAN	K	239;239;242;202	ENSP00000307939:E239K	ENSP00000307939:E239K	E	+	1	0	GCC2	108452932	1.000000	0.71417	0.928000	0.36995	0.276000	0.26787	4.873000	0.63057	2.432000	0.82394	0.460000	0.39030	GAA	.	.		0.363	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		A	109086500	G	A	109086500	3	1	112	1	0	0	0	0	1	0	0	0	6294	1175	41	3	737	3	GCC2	2	109086500	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	6019040	109086500	134112873	148	16769										
BUB1	699	hgsc.bcm.edu	37	chr2	111430402	111430402	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccatggttgtacagaaactcAaaaaattgatggaggtcact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:111430402delA	ENST00000302759.6	-	4	376	c.258delT	c.(256-258)tttfs	p.F86fs	BUB1_ENST00000535254.1_Frame_Shift_Del_p.F66fs|BUB1_ENST00000409311.1_Frame_Shift_Del_p.F86fs	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	86	BUB1 N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00822}.|Necessary for kinetochore localization.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		ACAGAAACTCAAAAAATTGAT	0.478																																					p.E87fs		Atlas-INDEL	.											.	BUB1	91	.	0			c.259delG						.						101	104	103					2																	111430402		2203	4300	6503	SO:0001589	frameshift_variant	699	exon4			.	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"budding uninhibited by benzimidazoles 1 (yeast homolog)", "budding uninhibited by benzimidazoles 1 homolog (yeast)"	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.258delT	chr2.hg19:g.111430402delA	ENSP00000302530:p.Phe86fs	124.0	0.0		123.0	10.0	NM_004336	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Frame_Shift_Del	DEL	ENST00000302759.6	hg19	CCDS33273.1																																																																																			.	.		0.478	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		-	111430402	A	-	111430402	7	5	112	1	0	1	0	1	0	0	0	0	1572	127	5	0	3087	0	BUB1	2	111430402	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2343902	111430402	131768971	149	16770										
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113089974	113089974	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccaggacaggggagcccgaCcccagataatgatcccggta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:113089974delC	ENST00000409871.1	+	12	3880	c.3479delC	c.(3478-3480)accfs	p.T1160fs	AC115115.2_ENST00000607612.1_RNA|ZC3H6_ENST00000343936.4_Frame_Shift_Del_p.T1160fs	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	1160							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						GGGAGCCCGACCCCAGATAAT	0.473																																					p.T1160fs		Atlas-INDEL	.											.	ZC3H6	93	.	0			c.3478delA						.						50	59	56					2																	113089974		1908	4119	6027	SO:0001589	frameshift_variant	376940	exon12			.	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.3479delC	chr2.hg19:g.113089974delC	ENSP00000386764:p.Thr1160fs	112.0	0.0		166.0	11.0	NM_198581	A9JR71|Q6ZW96	Frame_Shift_Del	DEL	ENST00000409871.1	hg19	CCDS46393.1																																																																																			.	.		0.473	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		-	113089974	C	-	113089974	7	5	112	1	0	1	0	1	0	0	0	0	17586	507	18	0	3525	0	ZC3H6	2	113089974	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1659572	113089974	130109399	150	16771										
MKI67IP	84365	hgsc.bcm.edu	37	chr2	122485457	122485457	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttgagattttcgcctctccAaaaatgttggtgtacaaact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:122485457delA	ENST00000285814.4	-	7	797	c.725delT	c.(724-726)ttgfs	p.L242fs	AC018737.1_ENST00000419902.1_RNA	NM_032390.4	NP_115766.3	Q9BYG3	MK67I_HUMAN		242	Interaction with MKI67.				negative regulation of phosphatase activity (GO:0010923)|protein complex assembly (GO:0006461)|rRNA metabolic process (GO:0016072)|rRNA transcription (GO:0009303)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|pancreas(1)|urinary_tract(1)	12						TCGCCTCTCCAAAAATGTTGG	0.338																																					p.L242fs		Atlas-INDEL	.											.	MKI67IP	27	.	0			c.726delG						.						68	67	67					2																	122485457		2203	4300	6503	SO:0001589	frameshift_variant	84365	exon7			.																												ENST00000285814.4:c.725delT	chr2.hg19:g.122485457delA	ENSP00000285814:p.Leu242fs	166.0	0.0		198.0	12.0	NM_032390	A8K788|Q8TB66|Q96ED4	Frame_Shift_Del	DEL	ENST00000285814.4	hg19	CCDS2135.1																																																																																			.	.		0.338	MKI67IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254239.2			-	122485457	A	-	122485457	7	5	112	1	0	1	0	1	0	0	0	0	9608	131	5	0	160	0	MKI67IP	2	122485457	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	9395483	122485457	120713916	151	16772										
SAP130	79595	hgsc.bcm.edu	37	chr2	128712861	128712861	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttttgattggatacagtctcCatggacacagtgaccggagt	11	8	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:128712861C>A	ENST00000259235.3	-	15	2223	c.2094G>T	c.(2092-2094)atG>atT	p.M698I	SAP130_ENST00000357702.5_Missense_Mutation_p.M733I|SAP130_ENST00000259234.6_Missense_Mutation_p.M706I	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	698					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)	p.M733I(1)|p.M698I(1)		NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		ATACAGTCTCCATGGACACAG	0.468																																					p.M733I		Atlas-SNP	.											SAP130_ENST00000357702,NS,carcinoma,0,2	SAP130	169	.	2	Substitution - Missense(2)	lung(2)	c.G2199T						.						97	105	102					2																	128712861		2203	4300	6503	SO:0001583	missense	79595	exon16			AGTCTCCATGGAC	BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"sin3A-associated protein, 130kDa"			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.2094G>T	chr2.hg19:g.128712861C>A	ENSP00000259235:p.Met698Ile	188.0	0.0		190.0	60.0	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation	SNP	ENST00000259235.3	hg19	CCDS2153.1	.	.	.	.	.	.	.	.	.	.	C	7.865	0.726937	0.15439	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234	.	.	.	5.33	4.44	0.53790	.	0.593501	0.18602	N	0.136411	T	0.24275	0.0588	N	0.08118	0	0.28868	N	0.895108	B;B;B;B;B	0.18166	0.013;0.001;0.001;0.026;0.0	B;B;B;B;B	0.17979	0.006;0.001;0.001;0.02;0.0	T	0.07424	-1.0773	9	0.24483	T	0.36	-0.3078	14.3007	0.66346	0.0:0.9271:0.0:0.0729	.	733;706;698;263;335	B7ZLM3;Q96DP1;Q9H0E3;Q9H0E3-2;B3KRT9	.;.;SP130_HUMAN;.;.	I	733;698;706	.	ENSP00000259234:M706I	M	-	3	0	SAP130	128429331	1.000000	0.71417	0.998000	0.56505	0.242000	0.25591	1.559000	0.36320	2.502000	0.84385	0.632000	0.83419	ATG	.	.		0.468	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545		A	128712861	C	A	128712861	3	1	112	1	0	0	0	0	1	0	0	0	13846	594	21	3	1076	3	SAP130	2	128712861	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	6227404	128712861	114486512	152	16773										
POTEF	728378	hgsc.bcm.edu	37	chr2	130865619	130865619	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaagagatttttagcatctgTttttctttgtagtcagaaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:130865619delT	ENST00000409914.2	-	8	1488	c.1089delA	c.(1087-1089)aaafs	p.K363fs	POTEF_ENST00000361163.4_Frame_Shift_Del_p.K373fs|POTEF_ENST00000360967.5_Frame_Shift_Del_p.K363fs|AC018804.3_ENST00000433507.1_RNA|RNU6-1049P_ENST00000516414.1_RNA|POTEF_ENST00000357462.5_Frame_Shift_Del_p.K363fs	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	363					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						TTAGCATCTGTTTTTCTTTGT	0.308																																					p.Q364fs		Atlas-INDEL	.											.	POTEF	140	.	0			c.1090delC						.						2	3	3					2																	130865619		863	1896	2759	SO:0001589	frameshift_variant	728378	exon8			.	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33905	protein-coding gene	gene with protein product			"ANKRD26-like family C, member 1B"	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.1089delA	chr2.hg19:g.130865619delT	ENSP00000386786:p.Lys363fs	238.0	0.0		247.0	17.0	NM_001099771	A6NC34	Frame_Shift_Del	DEL	ENST00000409914.2	hg19	CCDS46409.1																																																																																			.	.		0.308	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		-	130865619	T	-	130865619	7	5	112	1	0	1	0	1	0	0	0	0	12274	1722	60	0	2178	0	POTEF	2	130865619	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2152758	130865619	112333754	153	16774										
LYPD1	116372	hgsc.bcm.edu	37	chr2	133403775	133403775	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaactgagttcagtttccctGgggagcagaaggactggtac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:133403775delG	ENST00000397463.2	-	3	541	c.269delC	c.(268-270)ccafs	p.P90fs	GPR39_ENST00000329321.3_3'UTR|LYPD1_ENST00000345008.6_Frame_Shift_Del_p.P38fs|GPR39_ENST00000470071.1_3'UTR	NM_144586.5	NP_653187.3	Q8N2G4	LYPD1_HUMAN	LY6/PLAUR domain containing 1	90	UPAR/Ly6.					anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				lung(2)	2						CAGTTTCCCTGGGGAGCAGAA	0.572																																					p.P90fs		Atlas-INDEL	.											.	LYPD1	11	.	0			c.270delA						.						54	61	59					2																	133403775		2082	4208	6290	SO:0001589	frameshift_variant	116372	exon3			.	AK075487	CCDS42759.1, CCDS46416.1	2q21.2	2008-02-05		2005-08-30	ENSG00000150551	ENSG00000150551			28431	protein-coding gene	gene with protein product		610450		LYPDC1		12477932	Standard	NM_144586		Approved	MGC29643	uc002ttn.3	Q8N2G4	OTTHUMG00000153609	ENST00000397463.2:c.269delC	chr2.hg19:g.133403775delG	ENSP00000380605:p.Pro90fs	117.0	0.0		156.0	10.0	NM_144586	H7BXW6|Q6ZP52|Q6ZWI4|Q96AC2	Frame_Shift_Del	DEL	ENST00000397463.2	hg19	CCDS42759.1																																																																																			.	.		0.572	LYPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331821.1	NM_144586		-	133403775	G	-	133403775	7	5	112	1	0	1	0	1	0	0	0	0	9118	1348	47	0	160	0	LYPD1	2	133403775	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2538156	133403775	109795598	154	16775										
ACMSD	130013	hgsc.bcm.edu	37	chr2	135621155	135621155	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtccaaattggcacccacgTcaacgagtgggacctgaacg	12	12	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:135621155T>C	ENST00000356140.5	+	5	576	c.440T>C	c.(439-441)gTc>gCc	p.V147A	ACMSD_ENST00000283054.4_Missense_Mutation_p.V89A|AC016725.4_ENST00000392929.2_RNA|ACMSD_ENST00000392928.1_Missense_Mutation_p.V89A	NM_138326.2	NP_612199.2	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	147					cellular nitrogen compound metabolic process (GO:0034641)|quinolinate metabolic process (GO:0046874)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminocarboxymuconate-semialdehyde decarboxylase activity (GO:0001760)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(4)|lung(6)|skin(1)	14				BRCA - Breast invasive adenocarcinoma(221;0.115)		GGCACCCACGTCAACGAGTGG	0.657																																					p.V147A		Atlas-SNP	.											.	ACMSD	43	.	0			c.T440C						.						66	53	58					2																	135621155		2203	4300	6503	SO:0001583	missense	130013	exon5			CCCACGTCAACGA	AB071418	CCDS2173.2	2q21.3	2008-03-11			ENSG00000153086	ENSG00000153086	4.1.1.45		19288	protein-coding gene	gene with protein product		608889				12140278	Standard	NM_138326		Approved		uc002ttz.3	Q8TDX5	OTTHUMG00000131711	ENST00000356140.5:c.440T>C	chr2.hg19:g.135621155T>C	ENSP00000348459:p.Val147Ala	94.0	0.0		91.0	5.0	NM_138326	Q3B7X3|Q53SR5|Q96KY2	Missense_Mutation	SNP	ENST00000356140.5	hg19	CCDS2173.2	.	.	.	.	.	.	.	.	.	.	T	32	5.172638	0.94807	.	.	ENSG00000153086	ENST00000356140;ENST00000283054;ENST00000392928	.	.	.	5.74	5.74	0.90152	.	0.226724	0.51477	D	0.000099	T	0.74450	0.3718	M	0.67517	2.055	0.45899	D	0.998745	B;P	0.38922	0.131;0.651	B;P	0.55260	0.336;0.772	T	0.70439	-0.4871	9	0.25751	T	0.34	-7.4584	16.042	0.80691	0.0:0.0:0.0:1.0	.	89;147	Q53SR5;Q8TDX5	.;ACMSD_HUMAN	A	147;89;89	.	ENSP00000283054:V89A	V	+	2	0	ACMSD	135337625	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.691000	0.84191	2.188000	0.69820	0.459000	0.35465	GTC	.	.		0.657	ACMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254627.1			C	135621155	T	C	135621155	3	2	112	1	0	0	0	0	1	0	0	0	144	1667	58	2	458	2	ACMSD	2	135621155	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2217380	135621155	107578218	155	16776										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141806696	141806696	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taccagattttctatggggaTcatgtattcatcagctatct	7	8	5	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:141806696T>C	ENST00000389484.3	-	11	2619	c.1648A>G	c.(1648-1650)Atc>Gtc	p.I550V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	550					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCTATGGGGATCATGTATTCA	0.433										TSP Lung(27;0.18)																											p.I550V	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A1648G						.						183	179	180					2																	141806696		2203	4300	6503	SO:0001583	missense	53353	exon11			TGGGGATCATGTA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1648A>G	chr2.hg19:g.141806696T>C	ENSP00000374135:p.Ile550Val	270.0	0.0		186.0	8.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	3.098	-0.185487	0.06340	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90676	-2.71	5.49	5.49	0.81192	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.257041	0.31257	U	0.007966	T	0.81259	0.4785	N	0.17082	0.46	0.28702	N	0.904	B	0.14438	0.01	B	0.10450	0.005	T	0.67377	-0.5686	10	0.13108	T	0.6	.	11.5754	0.50858	0.0:0.0:0.1491:0.8509	.	550	Q9NZR2	LRP1B_HUMAN	V	550;488	ENSP00000374135:I550V	ENSP00000374135:I550V	I	-	1	0	LRP1B	141523166	1.000000	0.71417	1.000000	0.80357	0.412000	0.31113	3.163000	0.50763	2.074000	0.62210	0.460000	0.39030	ATC	.	.		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141806696	T	C	141806696	3	2	112	1	0	0	0	0	1	0	0	0	8964	1435	50	2	12475	2	LRP1B	2	141806696	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	6185541	141806696	101392677	156	16777										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141812812	141812812	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attccatatggatcgacttcAcatgcatggcttctgactac	7	11	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:141812812A>G	ENST00000389484.3	-	10	2396	c.1425T>C	c.(1423-1425)tgT>tgC	p.C475C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	475	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.C475C(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GATCGACTTCACATGCATGGC	0.413										TSP Lung(27;0.18)																											p.C475C	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,0,1	LRP1B	1315	.	1	Substitution - coding silent(1)	endometrium(1)	c.T1425C						.						93	83	86					2																	141812812		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon10			GACTTCACATGCA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1425T>C	chr2.hg19:g.141812812A>G		110.0	1.0		89.0	4.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.		0.413	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141812812	A	G	141812812	2	3	112	1	0	0	0	0	0	0	0	1	8964	157	6	2		2	LRP1B	2	141812812	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	6116	141812812	101386561	157	16778										
RBM43	375287	hgsc.bcm.edu	37	chr2	152107917	152107917	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acttctctgtagattcctctGgggattttgtctattccact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:152107917delG	ENST00000331426.5	-	4	728	c.577delC	c.(577-579)cagfs	p.Q193fs		NM_198557.2	NP_940959.1	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	193							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.131)		AGATTCCTCTGGGGATTTTGT	0.418																																					p.Q193fs		Atlas-INDEL	.											.	RBM43	35	.	0			c.578delA						.						139	144	142					2																	152107917		2203	4300	6503	SO:0001589	frameshift_variant	375287	exon4			.	AK127552	CCDS2191.1	2q23.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000184898	ENSG00000184898		"RNA binding motif (RRM) containing"	24790	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 38"	C2orf38			Standard	NM_198557		Approved	FLJ45645	uc002txh.3	Q6ZSC3	OTTHUMG00000131866	ENST00000331426.5:c.577delC	chr2.hg19:g.152107917delG	ENSP00000331211:p.Gln193fs	226.0	0.0		231.0	14.0	NM_198557	B2RMT5	Frame_Shift_Del	DEL	ENST00000331426.5	hg19	CCDS2191.1																																																																																			.	.		0.418	RBM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254816.2	NM_198557		-	152107917	G	-	152107917	7	5	112	1	0	1	0	1	0	0	0	0	13152	1357	47	0	500	0	RBM43	2	152107917	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	10295105	152107917	91091456	158	16779										
CACNB4	785	hgsc.bcm.edu	37	chr2	152709963	152709963	+	Splice_Site	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaaaatgatcatacttactGgggggcattgtgcaagttta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:152709963delG	ENST00000539935.1	-	12	1182	c.1115delC	c.(1114-1116)cca>ca	p.P372fs	CACNB4_ENST00000201943.5_Splice_Site_p.P372fs|CACNB4_ENST00000397327.2_Splice_Site_p.P325fs|CACNB4_ENST00000534999.1_Splice_Site_p.P338fs|CACNB4_ENST00000360283.6_Splice_Site_p.P339fs|CACNB4_ENST00000427385.1_Splice_Site_p.P354fs	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	372					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CATACTTACTGGGGGGCATTG	0.358																																					p.P372fs		Atlas-INDEL	.											CACNB4_ENST00000539935,NS,carcinoma,0,2	CACNB4	108	.	0			c.1116delA						.						74	69	71					2																	152709963		1853	4095	5948	SO:0001630	splice_region_variant	785	exon12			.	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"Calcium channel subunits"	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.1116+1C>-	chr2.hg19:g.152709963delG		89.0	0.0		115.0	10.0	NM_001145798	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Frame_Shift_Del	DEL	ENST00000539935.1	hg19	CCDS46426.1																																																																																			.	.		0.358	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3	Frame_Shift_Del	-	152709963	G	-	152709963	8	5	112	1	0	1	0	1	0	0	1	0	2557	1362	47	0	459	0	CACNB4	2	152709963	Splice_Site	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	602046	152709963	90489410	159	16780										
GALNT13	114805	hgsc.bcm.edu	37	chr2	155252538	155252538	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attatggagatgtgtcagtcAgaaaaacactaagagaaaat	9	4	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:155252538A>G	ENST00000392825.3	+	10	1759	c.1192A>G	c.(1192-1194)Aga>Gga	p.R398G	GALNT13_ENST00000487047.1_3'UTR|GALNT13_ENST00000409237.1_Missense_Mutation_p.R398G	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	398					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						TGTGTCAGTCAGAAAAACACT	0.373																																					p.R398G		Atlas-SNP	.											.	GALNT13	170	.	0			c.A1192G						.						88	84	85					2																	155252538		2203	4300	6503	SO:0001583	missense	114805	exon10			TCAGTCAGAAAAA	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23242	protein-coding gene	gene with protein product	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13", "polypeptide GalNAc transferase 13"	608369	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.1192A>G	chr2.hg19:g.155252538A>G	ENSP00000376570:p.Arg398Gly	80.0	0.0		104.0	5.0	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Missense_Mutation	SNP	ENST00000392825.3	hg19	CCDS2199.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.1|21.1	4.103010|4.103010	0.76983|0.76983	.|.	.|.	ENSG00000144278|ENSG00000144278	ENST00000450838|ENST00000392825;ENST00000409237	.|T;T	.|0.58652	.|0.32;0.32	5.02|5.02	5.02|5.02	0.67125|0.67125	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.83202|0.83202	0.5203|0.5203	H|H	0.96996|0.96996	3.92|3.92	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.999;0.998;0.997;0.998	.|D;D;D;D	.|0.78314	.|0.991;0.967;0.937;0.967	D|D	0.88786|0.88786	0.3274|0.3274	5|10	.|0.87932	.|D	.|0	.|.	13.8582|13.8582	0.63542|0.63542	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|398;398;398;398	.|Q8IUC8-2;B3KY85;Q08ER7;Q8IUC8	.|.;.;.;GLT13_HUMAN	R|G	16|398	.|ENSP00000376570:R398G;ENSP00000387239:R398G	.|ENSP00000376570:R398G	Q|R	+|+	2|1	0|2	GALNT13|GALNT13	154960784|154960784	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.223000|5.223000	0.65283|0.65283	2.016000|2.016000	0.59253|0.59253	0.528000|0.528000	0.53228|0.53228	CAG|AGA	.	.		0.373	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917		G	155252538	A	G	155252538	3	3	112	1	0	0	0	0	1	0	0	0	6219	180	7	2	1222	2	GALNT13	2	155252538	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2542575	155252538	87946835	160	16781										
GALNT13	114805	hgsc.bcm.edu	37	chr2	155295237	155295237	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gttatgggaatatgatgctgAggtatagtattttcttaatt	10	2	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:155295237A>G	ENST00000392825.3	+	12	2096	c.1529A>G	c.(1528-1530)gAg>gGg	p.E510G	GALNT13_ENST00000409237.1_Splice_Site_p.E510G|AC009227.2_ENST00000434635.1_RNA	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	510	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						TATGATGCTGAGGTATAGTAT	0.313																																					p.E510G		Atlas-SNP	.											.	GALNT13	170	.	0			c.A1529G						.						104	109	107					2																	155295237		2203	4300	6503	SO:0001630	splice_region_variant	114805	exon12			ATGCTGAGGTATA	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23242	protein-coding gene	gene with protein product	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13", "polypeptide GalNAc transferase 13"	608369	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.1530+1A>G	chr2.hg19:g.155295237A>G		63.0	0.0		72.0	4.0	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Missense_Mutation	SNP	ENST00000392825.3	hg19	CCDS2199.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.10|18.10	3.547727|3.547727	0.65311|0.65311	.|.	.|.	ENSG00000144278|ENSG00000144278	ENST00000392825;ENST00000409237;ENST00000453715|ENST00000450838	T;T|.	0.76448|.	-1.02;1.99|.	5.76|5.76	5.76|5.76	0.90799|0.90799	Ricin B-related lectin (1);Ricin B lectin (3);|.	0.693058|.	0.15449|.	N|.	0.261796|.	T|.	0.45438|.	0.1342|.	L|L	0.41710|0.41710	1.295|1.295	0.32964|0.32964	D|D	0.521388|0.521388	P;P|.	0.37731|.	0.607;0.464|.	P;B|.	0.45913|.	0.497;0.395|.	T|.	0.57289|.	-0.7837|.	10|.	0.38643|.	T|.	0.18|.	.|.	9.3359|9.3359	0.38049|0.38049	0.8402:0.0:0.0:0.1598|0.8402:0.0:0.0:0.1598	.|.	510;510|.	Q08ER7;Q8IUC8|.	.;GLT13_HUMAN|.	G|W	510;510;45|95	ENSP00000376570:E510G;ENSP00000387239:E510G|.	ENSP00000376570:E510G|.	E|X	+|+	2|3	0|0	GALNT13|GALNT13	155003483|155003483	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	7.210000|7.210000	0.77924|0.77924	2.197000|2.197000	0.70478|0.70478	0.533000|0.533000	0.62120|0.62120	GAG|TGA	.	.		0.313	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917	Missense_Mutation	G	155295237	A	G	155295237	5	3	112	1	0	0	0	0	0	0	1	0	6219	318	11	2	1567	2	GALNT13	2	155295237	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	42699	155295237	87904136	161	16782										
NR4A2	4929	hgsc.bcm.edu	37	chr2	157186374	157186374	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cggcatcatctcctcagactGggggggcaggtggctgtgtt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:157186374delG	ENST00000339562.4	-	3	687	c.325delC	c.(325-327)cagfs	p.Q109fs	NR4A2_ENST00000409108.2_Frame_Shift_Del_p.Q109fs|NR4A2_ENST00000409572.1_Frame_Shift_Del_p.Q109fs|NR4A2_ENST00000426264.1_Frame_Shift_Del_p.Q46fs|NR4A2_ENST00000539077.1_Frame_Shift_Del_p.Q120fs|NR4A2_ENST00000429376.1_Frame_Shift_Del_p.Q46fs	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	109	Gln-rich.				adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.Q109fs*3(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						TCCTCAGACTGGGGGGGCAGG	0.602																																					p.Q109fs		Atlas-INDEL	.											.,2	NR4A2	82	.	1	Insertion - Frameshift(1)	ovary(1)	c.326delA						.						83	83	83					2																	157186374		2203	4300	6503	SO:0001589	frameshift_variant	4929	exon3			.	X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"Nuclear hormone receptors"	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.325delC	chr2.hg19:g.157186374delG	ENSP00000344479:p.Gln109fs	143.0	0.0		172.0	11.0	NM_006186	Q16311|Q53RZ2|Q6NXU0	Frame_Shift_Del	DEL	ENST00000339562.4	hg19	CCDS2201.1																																																																																			.	.		0.602	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2			-	157186374	G	-	157186374	7	5	112	1	0	1	0	1	0	0	0	0	10642	1357	47	0	1495	0	NR4A2	2	157186374	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1891137	157186374	86012999	162	16783										
ACVR1	90	hgsc.bcm.edu	37	chr2	158622477	158622477	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cattcttcttaaccagaataTttttgctctttaaatctcga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:158622477delT	ENST00000263640.3	-	8	1451	c.1022delA	c.(1021-1023)aatfs	p.N341fs	ACVR1_ENST00000410057.2_Frame_Shift_Del_p.N341fs|ACVR1_ENST00000434821.1_Frame_Shift_Del_p.N341fs|ACVR1_ENST00000409283.2_Frame_Shift_Del_p.N341fs	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	341	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.N341I(1)		endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	AACCAGAATATTTTTGCTCTT	0.363																																					p.N341fs		Atlas-INDEL	.											.	ACVR1	52	.	1	Substitution - Missense(1)	large_intestine(1)	c.1023delT						.						90	90	90					2																	158622477		2203	4300	6503	SO:0001589	frameshift_variant	90	exon8			.		CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.1022delA	chr2.hg19:g.158622477delT	ENSP00000263640:p.Asn341fs	141.0	0.0		160.0	10.0	NM_001105		Frame_Shift_Del	DEL	ENST00000263640.3	hg19	CCDS2206.1																																																																																			.	.		0.363	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105		-	158622477	T	-	158622477	7	5	112	1	0	1	0	1	0	0	0	0	220	1493	52	0	523	0	ACVR1	2	158622477	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1436103	158622477	84576896	163	16784										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160182380	160182380	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctttctttgactcattagtcTtttttcctttgacatgaagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:160182380delT	ENST00000392783.2	-	35	6488	c.5993delA	c.(5992-5994)aagfs	p.K1998fs	BAZ2B_ENST00000392782.1_Frame_Shift_Del_p.K1962fs|BAZ2B_ENST00000343439.5_Frame_Shift_Del_p.K1898fs|BAZ2B_ENST00000355831.2_Frame_Shift_Del_p.K1964fs	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1998					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CTCATTAGTCTTTTTTCCTTT	0.323																																					p.K1998fs		Atlas-INDEL	.											.	BAZ2B	196	.	0			c.5994delG						.						95	85	88					2																	160182380		1820	4079	5899	SO:0001589	frameshift_variant	29994	exon35			.	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.5993delA	chr2.hg19:g.160182380delT	ENSP00000376534:p.Lys1998fs	133.0	0.0		173.0	13.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Frame_Shift_Del	DEL	ENST00000392783.2	hg19	CCDS2209.2																																																																																			.	.		0.323	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			-	160182380	T	-	160182380	7	5	112	1	0	1	0	1	0	0	0	0	1332	1609	56	0	525	0	BAZ2B	2	160182380	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1559903	160182380	83016993	164	16785										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160229687	160229687	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catcaaagagcttccttctgTactgactctgttgctgttaa	7	10	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:160229687T>C	ENST00000392783.2	-	27	4577	c.4082A>G	c.(4081-4083)tAc>tGc	p.Y1361C	BAZ2B_ENST00000392782.1_Missense_Mutation_p.Y1325C|BAZ2B_ENST00000343439.5_Missense_Mutation_p.Y1261C|BAZ2B_ENST00000355831.2_Missense_Mutation_p.Y1327C	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1361					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CTTCCTTCTGTACTGACTCTG	0.383																																					p.Y1361C		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A4082G						.						89	82	84					2																	160229687		1871	4112	5983	SO:0001583	missense	29994	exon27			CTTCTGTACTGAC	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.4082A>G	chr2.hg19:g.160229687T>C	ENSP00000376534:p.Tyr1361Cys	83.0	0.0		99.0	4.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	T	10.83	1.459757	0.26248	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.31769	1.48;1.48;1.48;4.31	5.48	5.48	0.80851	.	0.000000	0.33834	U	0.004501	T	0.45538	0.1347	L	0.39898	1.24	0.42852	D	0.994088	D;D	0.76494	0.999;0.999	D;P	0.64595	0.927;0.894	T	0.41574	-0.9501	10	0.56958	D	0.05	-5.9942	15.5721	0.76349	0.0:0.0:0.0:1.0	.	1325;1361	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	C	1325;1361;1327;1261	ENSP00000376533:Y1325C;ENSP00000376534:Y1361C;ENSP00000348087:Y1327C;ENSP00000339670:Y1261C	ENSP00000339670:Y1261C	Y	-	2	0	BAZ2B	159937933	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.091000	0.57700	2.081000	0.62600	0.383000	0.25322	TAC	.	.		0.383	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			C	160229687	T	C	160229687	3	2	112	1	0	0	0	0	1	0	0	0	1332	1638	57	2	2468	2	BAZ2B	2	160229687	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	47307	160229687	82969686	165	16786										
LY75	4065	hgsc.bcm.edu	37	chr2	160732083	160732083	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aattgaaagtgctttgaagcTtctgcagtccttcacctccc	7	12	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:160732083T>C	ENST00000263636.4	-	12	1873	c.1846A>G	c.(1846-1848)Agc>Ggc	p.S616G	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.S616G|LY75_ENST00000553424.1_Missense_Mutation_p.S616G|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.S616G|LY75_ENST00000554112.1_Missense_Mutation_p.S616G	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	616	C-type lectin 3. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GCTTTGAAGCTTCTGCAGTCC	0.517																																					p.S616G		Atlas-SNP	.											.	LY75	151	.	0			c.A1846G						.						129	137	134					2																	160732083		2203	4300	6503	SO:0001583	missense	4065	exon12			TGAAGCTTCTGCA	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.1846A>G	chr2.hg19:g.160732083T>C	ENSP00000263636:p.Ser616Gly	83.0	0.0		105.0	5.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	T	16.69	3.193623	0.58017	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.20463	2.07;2.07;2.07;2.07;2.07	5.07	5.07	0.68467	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.352983	0.20491	N	0.091293	T	0.28400	0.0702	M	0.64404	1.975	0.37230	D	0.905635	B;P;P;B	0.36483	0.27;0.499;0.555;0.264	B;B;B;B	0.40982	0.232;0.234;0.345;0.085	T	0.19128	-1.0315	10	0.41790	T	0.15	-0.6067	14.1143	0.65142	0.0:0.0:0.0:1.0	.	234;616;616;616	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	G	616	ENSP00000451511:S616G;ENSP00000451446:S616G;ENSP00000263636:S616G;ENSP00000423463:S616G;ENSP00000421035:S616G	ENSP00000423463:S616G	S	-	1	0	LY75;LY75-CD302	160440329	0.634000	0.27190	0.644000	0.29465	0.982000	0.71751	2.598000	0.46223	2.029000	0.59856	0.460000	0.39030	AGC	.	.		0.517	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			C	160732083	T	C	160732083	3	2	112	1	0	0	0	0	1	0	0	0	9108	1609	56	2	3418	2	LY75	2	160732083	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	502396	160732083	82467290	166	16787										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160806244	160806244	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctcatctttccaaaaagtgAaagaagatttggtgccatca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:160806244delA	ENST00000283243.7	-	25	3790	c.3584delT	c.(3583-3585)ttcfs	p.F1195fs	PLA2R1_ENST00000392771.1_Frame_Shift_Del_p.F1195fs	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	1195	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CCAAAAAGTGAAAGAAGATTT	0.502																																					p.F1195fs		Atlas-INDEL	.											.	PLA2R1	153	.	0			c.3585delC						.						93	89	90					2																	160806244		2203	4300	6503	SO:0001589	frameshift_variant	22925	exon25			.	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.3584delT	chr2.hg19:g.160806244delA	ENSP00000283243:p.Phe1195fs	129.0	0.0		135.0	10.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Frame_Shift_Del	DEL	ENST00000283243.7	hg19	CCDS33309.1																																																																																			.	.		0.502	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			-	160806244	A	-	160806244	7	5	112	1	0	1	0	1	0	0	0	0	12019	246	9	0	839	0	PLA2R1	2	160806244	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	74161	160806244	82393129	167	16788										
DPP4	1803	hgsc.bcm.edu	37	chr2	162875361	162875361	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatagtcactaagttggattCtgtaaaaccaacggtggaaa	9	6	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:162875361C>T	ENST00000360534.3	-	16	1859		c.e16-1		DPP4_ENST00000491591.1_5'Flank	NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4						cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	AAGTTGGATTCTGTAAAACCA	0.403																																					.		Atlas-SNP	.											DPP4,NS,carcinoma,0,1	DPP4	90	.	0			c.1299-1G>A						.						116	108	111					2																	162875361		2203	4300	6503	SO:0001630	splice_region_variant	1803	exon17			TGGATTCTGTAAA	M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"CD molecules"	3009	protein-coding gene	gene with protein product		102720	"dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)", "adenosine deaminase complexing protein 2"	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.1299-1G>A	chr2.hg19:g.162875361C>T		94.0	0.0		107.0	5.0	NM_001935	Q53TN1	Splice_Site	SNP	ENST00000360534.3	hg19	CCDS2216.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.857580	0.71834	.	.	ENSG00000197635	ENST00000360534	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7997	0.92011	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DPP4	162583607	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	5.486000	0.66856	2.756000	0.94617	0.563000	0.77884	.	.	.		0.403	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2		Intron	T	162875361	C	T	162875361	5	4	112	1	0	0	0	0	0	0	1	0	4731	927	32	3	1046	3	DPP4	2	162875361	Splice_Site	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	2069117	162875361	80324012	168	16789										
GRB14	2888	hgsc.bcm.edu	37	chr2	165476321	165476321	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccggaacatcaagatctttcTtttttctcctacagtaagag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:165476321delT	ENST00000263915.3	-	2	738	c.200delA	c.(199-201)aagfs	p.K68fs		NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	68					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.K67M(1)		breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						AAGATCTTTCTTTTTTCTCCT	0.368																																					p.K67fs		Atlas-INDEL	.											.	GRB14	73	.	1	Substitution - Missense(1)	ovary(1)	c.201delG						.						134	138	137					2																	165476321		2203	4300	6503	SO:0001589	frameshift_variant	2888	exon2			.		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.200delA	chr2.hg19:g.165476321delT	ENSP00000263915:p.Lys68fs	271.0	0.0		253.0	16.0	NM_004490	B7Z7F9|Q7Z6I1	Frame_Shift_Del	DEL	ENST00000263915.3	hg19	CCDS2222.1																																																																																			.	.		0.368	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			-	165476321	T	-	165476321	7	5	112	1	0	1	0	1	0	0	0	0	6766	1609	56	0	1474	0	GRB14	2	165476321	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2600960	165476321	77723052	169	16790										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166852565	166852565	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcggttttttcgatcctaaTtttttcattgcattatagta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:166852565delT	ENST00000303395.4	-	24	4538	c.4539delA	c.(4537-4539)aaafs	p.K1513fs	SCN1A_ENST00000423058.2_Frame_Shift_Del_p.K1513fs|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000409050.1_Frame_Shift_Del_p.K1485fs|SCN1A_ENST00000375405.3_Frame_Shift_Del_p.K1502fs			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1513					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCGATCCTAATTTTTTCATTG	0.333																																					p.L1514X		Atlas-INDEL	.											SCN1A_ENST00000303395,caecum,carcinoma,0,2	SCN1A	641	.	0			c.4540delT						.						132	127	129					2																	166852565		2202	4300	6502	SO:0001589	frameshift_variant	6323	exon24			.	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.4539delA	chr2.hg19:g.166852565delT	ENSP00000303540:p.Lys1513fs	142.0	0.0		148.0	10.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Frame_Shift_Del	DEL	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.333	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		-	166852565	T	-	166852565	7	5	112	1	0	1	0	1	0	0	0	0	13929	1490	52	0	1502	0	SCN1A	2	166852565	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1376244	166852565	76346808	170	16791										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167141203	167141203	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttctgctctcattgtctccAaaaatgctgtgctcatcatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:167141203delA	ENST00000409435.1	-	11	1733	c.1734delT	c.(1732-1734)tttfs	p.F578fs	SCN9A_ENST00000375387.4_Frame_Shift_Del_p.F579fs|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.F579fs|SCN9A_ENST00000409672.1_Frame_Shift_Del_p.F578fs			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	578					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CATTGTCTCCAAAAATGCTGT	0.507																																					p.G579fs		Atlas-INDEL	.											SCN9A_ENST00000375387,right_upper_lobe,carcinoma,+1,1	SCN9A	296	.	0			c.1735delG						.						99	103	102					2																	167141203		2071	4227	6298	SO:0001589	frameshift_variant	6335	exon12			.	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1734delT	chr2.hg19:g.167141203delA	ENSP00000386330:p.Phe578fs	146.0	0.0		152.0	11.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	hg19	CCDS46441.1																																																																																			.	.		0.507	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		-	167141203	A	-	167141203	7	5	112	1	0	1	0	1	0	0	0	0	13940	127	5	0	4263	0	SCN9A	2	167141203	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	288638	167141203	76058170	171	16792										
TLK1	9874	hgsc.bcm.edu	37	chr2	171862754	171862754	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accaaaatcagtgattttgaTttcaccacatgctgttccat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:171862754delT	ENST00000431350.2	-	18	2211	c.1807delA	c.(1807-1809)atcfs	p.I603fs	TLK1_ENST00000434911.2_Frame_Shift_Del_p.I507fs|TLK1_ENST00000442919.2_Frame_Shift_Del_p.I555fs|TLK1_ENST00000521943.1_Frame_Shift_Del_p.I555fs|TLK1_ENST00000360843.3_Frame_Shift_Del_p.I624fs			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	603	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						GTGATTTTGATTTCACCACAT	0.353																																					p.I603fs		Atlas-INDEL	.											.	TLK1	134	.	0			c.1808delT						.						126	118	121					2																	171862754		2203	4300	6503	SO:0001589	frameshift_variant	9874	exon18			.	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.1807delA	chr2.hg19:g.171862754delT	ENSP00000411099:p.Ile603fs	174.0	0.0		195.0	12.0	NM_012290	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Frame_Shift_Del	DEL	ENST00000431350.2	hg19	CCDS2241.1																																																																																			.	.		0.353	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		-	171862754	T	-	171862754	7	5	112	1	0	1	0	1	0	0	0	0	15958	1493	52	0	509	0	TLK1	2	171862754	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	4721551	171862754	71336619	172	16793										
ITGA6	3655	hgsc.bcm.edu	37	chr2	173355995	173355995	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaacatcagatgcccgctgcGggggctggacagcaaggcgt					rs377077160		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:173355995delG	ENST00000264106.6	+	23	3145	c.2942delG	c.(2941-2943)cggfs	p.R981fs	ITGA6_ENST00000375221.2_Frame_Shift_Del_p.R981fs|ITGA6_ENST00000409532.1_Frame_Shift_Del_p.R823fs|ITGA6_ENST00000343713.4_Frame_Shift_Del_p.R937fs|ITGA6_ENST00000409080.1_Frame_Shift_Del_p.R942fs|ITGA6_ENST00000264107.7_Frame_Shift_Del_p.R942fs|AC093818.1_ENST00000442417.1_RNA			P23229	ITA6_HUMAN	integrin, alpha 6	981					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TGCCCGCTGCGGGGGCTGGAC	0.468																																					p.R942fs		Atlas-INDEL	.											.	ITGA6	171	.	0			c.2824delC						.						132	137	135					2																	173355995		2203	4300	6503	SO:0001589	frameshift_variant	3655	exon22			.		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"CD molecules", "Integrins"	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.2942delG	chr2.hg19:g.173355995delG	ENSP00000264106:p.Arg981fs	152.0	0.0		183.0	11.0	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Frame_Shift_Del	DEL	ENST00000264106.6	hg19																																																																																				.	.		0.468	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				-	173355995	G	-	173355995	7	5	112	1	0	1	0	1	0	0	0	0	7889	1116	39	0	2911	0	ITGA6	2	173355995	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1493241	173355995	69843378	173	16794										
KIAA1715	80856	hgsc.bcm.edu	37	chr2	176804341	176804341	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atccaaagcacctcgttctcGggggagaataggtcttgcta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:176804341delG	ENST00000272748.4	-	10	998	c.751delC	c.(751-753)cgafs	p.R251fs	KIAA1715_ENST00000535310.1_Frame_Shift_Del_p.R176fs|KIAA1715_ENST00000544803.1_Frame_Shift_Del_p.R282fs	NM_030650.1	NP_085153.1	Q9C0E8	LNP_HUMAN	KIAA1715	251					blood coagulation (GO:0007596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|limb development (GO:0060173)|regulation of chondrocyte differentiation (GO:0032330)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)	20			OV - Ovarian serous cystadenocarcinoma(117;0.0793)			CCTCGTTCTCGGGGGAGAATA	0.323																																					p.R251fs		Atlas-INDEL	.											KIAA1715,caecum,carcinoma,-1,1	KIAA1715	61	.	0			c.752delG						.						85	83	84					2																	176804341		2203	4300	6503	SO:0001589	frameshift_variant	80856	exon10			.	AB051502	CCDS33332.1	2q31	2014-06-27			ENSG00000144320	ENSG00000144320			21610	protein-coding gene	gene with protein product	"lunapark", "limb and neural patterns"	610236				11214970, 22729086	Standard	NM_030650		Approved	ulnaless, Ul, LNP1, LNP	uc002ukc.1	Q9C0E8	OTTHUMG00000154112	ENST00000272748.4:c.751delC	chr2.hg19:g.176804341delG	ENSP00000272748:p.Arg251fs	184.0	0.0		200.0	12.0	NM_030650	B7ZLA8|Q2M2V8|Q2YD99|Q658W8|Q8N5V9|Q96MS5	Frame_Shift_Del	DEL	ENST00000272748.4	hg19	CCDS33332.1																																																																																			.	.		0.323	KIAA1715-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333949.3	XM_042834		-	176804341	G	-	176804341	7	5	112	1	0	1	0	1	0	0	0	0	8263	1124	39	0	551	0	KIAA1715	2	176804341	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	3448346	176804341	66395032	174	16795										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179226415	179226415	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttctccccacccagtgcattCtcttttgaagtctgcattta	5	13	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:179226415C>G	ENST00000190611.4	+	13	1536	c.1160C>G	c.(1159-1161)tCt>tGt	p.S387C	OSBPL6_ENST00000409045.3_Missense_Mutation_p.S356C|OSBPL6_ENST00000357080.4_Missense_Mutation_p.S356C|OSBPL6_ENST00000359685.3_Missense_Mutation_p.S387C|OSBPL6_ENST00000409631.1_Missense_Mutation_p.S387C|OSBPL6_ENST00000315022.2_Missense_Mutation_p.S391C|OSBPL6_ENST00000392505.2_Missense_Mutation_p.S412C	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	387					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			CCAGTGCATTCTCTTTTGAAG	0.413																																					p.S412C		Atlas-SNP	.											.	OSBPL6	178	.	0			c.C1235G						.						101	97	98					2																	179226415		2203	4300	6503	SO:0001583	missense	114880	exon14			TGCATTCTCTTTT	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1160C>G	chr2.hg19:g.179226415C>G	ENSP00000190611:p.Ser387Cys	258.0	0.0		234.0	92.0	NM_001201480	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	hg19	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.087567	0.76642	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.14391	2.6;2.62;2.51;2.63;2.62;2.62;2.6	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.37210	0.0995	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;1.0;0.999;1.0;0.999;1.0	D;D;D;D;D;D	0.91635	0.96;0.999;0.987;0.999;0.993;0.997	T	0.01468	-1.1347	10	0.59425	D	0.04	-12.2188	19.6657	0.95891	0.0:1.0:0.0:0.0	.	356;391;387;412;387;356	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	C	412;387;356;356;387;387;391	ENSP00000376293:S412C;ENSP00000352713:S387C;ENSP00000349591:S356C;ENSP00000387248:S356C;ENSP00000190611:S387C;ENSP00000386885:S387C;ENSP00000318723:S391C	ENSP00000190611:S387C	S	+	2	0	OSBPL6	178934661	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.262000	0.72514	2.744000	0.94065	0.655000	0.94253	TCT	.	.		0.413	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		G	179226415	C	G	179226415	3	3	112	1	0	0	0	0	1	0	0	0	11290	913	32	4	1324	4	OSBPL6	2	179226415	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	2422074	179226415	63972958	175	16796										
TTN	7273	hgsc.bcm.edu	37	chr2	179427959	179427959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtgttttctttaagcttggTcactgtgaactgctttcctt	8	8	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:179427959T>C	ENST00000591111.1	-	276	78201	c.77977A>G	c.(77977-77979)Acc>Gcc	p.T25993A	TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T18694A|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T18569A|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T27634A|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T18761A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T25066A|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25993	Fibronectin type-III 89. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTAAGCTTGGTCACTGTGAAC	0.448																																					p.T27634A		Atlas-SNP	.											.	TTN	18412	.	0			c.A82900G						.						123	124	123					2																	179427959		2011	4186	6197	SO:0001583	missense	7273	exon326			GCTTGGTCACTGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.77977A>G	chr2.hg19:g.179427959T>C	ENSP00000465570:p.Thr25993Ala	304.0	0.0		321.0	111.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.10	3.548853	0.65311	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59364	0.27;0.27;0.27;0.27	5.65	5.65	0.86999	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.59348	0.2187	L	0.50993	1.605	0.49582	D	0.999803	P;P;P;P	0.44090	0.826;0.826;0.826;0.826	P;P;P;P	0.45195	0.473;0.473;0.473;0.473	T	0.64402	-0.6416	9	0.87932	D	0	.	15.861	0.79021	0.0:0.0:0.0:1.0	.	18569;18694;18761;25993	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	25066;18569;18761;18694;18567	ENSP00000343764:T25066A;ENSP00000434586:T18569A;ENSP00000340554:T18761A;ENSP00000352154:T18694A	ENSP00000340554:T18761A	T	-	1	0	TTN	179136205	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.991000	0.88244	2.152000	0.67230	0.379000	0.24179	ACC	.	.		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179427959	T	C	179427959	3	2	112	1	0	0	0	0	1	0	0	0	16750	1667	58	2	25227	2	TTN	2	179427959	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	201544	179427959	63771414	176	16797										
TTN	7273	hgsc.bcm.edu	37	chr2	179429759	179429759	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcctgttttcagtttggttaTtttaattgttgttcttgcaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:179429759delT	ENST00000591111.1	-	276	76401	c.76177delA	c.(76177-76179)atafs	p.I25393fs	TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.I18094fs|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.I17969fs|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.I27034fs|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.I18161fs|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.I24466fs|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25393	Fibronectin type-III 84. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTTTGGTTATTTTAATTGTT	0.413																																					p.I27034fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.81101delT						.						135	133	134					2																	179429759		1904	4115	6019	SO:0001589	frameshift_variant	7273	exon326			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.76177delA	chr2.hg19:g.179429759delT	ENSP00000465570:p.Ile25393fs	163.0	0.0		176.0	11.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179429759	T	-	179429759	7	5	112	1	0	1	0	1	0	0	0	0	16750	1493	52	0	27027	0	TTN	2	179429759	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1800	179429759	63769614	177	16798										
TTN	7273	hgsc.bcm.edu	37	chr2	179500233	179500233	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcatactcagcaatatcttCtggcatagcattcttaattt	5	9	4	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:179500233C>T	ENST00000591111.1	-	177	37119	c.36895G>A	c.(36895-36897)Gaa>Aaa	p.E12299K	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E5000K|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E4875K|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E13940K|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E5067K|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E11372K|TTN-AS1_ENST00000418062.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12299	Ig-like 82.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCAATATCTTCTGGCATAGCA	0.353																																					p.E13940K		Atlas-SNP	.											.	TTN	18412	.	0			c.G41818A						.						91	79	83					2																	179500233		1849	4088	5937	SO:0001583	missense	7273	exon227			TATCTTCTGGCAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.36895G>A	chr2.hg19:g.179500233C>T	ENSP00000465570:p.Glu12299Lys	153.0	0.0		165.0	50.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	18.12	3.552617	0.65425	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.48522	0.81;0.81;0.81;0.81	5.94	5.94	0.96194	Immunoglobulin subtype (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46268	0.1384	L	0.50333	1.59	0.48830	D	0.999713	P;P;P;P	0.38922	0.651;0.651;0.651;0.651	B;B;B;B	0.33521	0.165;0.165;0.165;0.165	T	0.50591	-0.8810	9	0.87932	D	0	.	20.3658	0.98878	0.0:1.0:0.0:0.0	.	4875;5000;5067;12299	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	11372;4875;5067;5000;4875	ENSP00000343764:E11372K;ENSP00000434586:E4875K;ENSP00000340554:E5067K;ENSP00000352154:E5000K	ENSP00000340554:E5067K	E	-	1	0	TTN	179208478	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.866000	0.63005	2.820000	0.97059	0.650000	0.86243	GAA	.	.		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179500233	C	T	179500233	3	4	112	1	0	0	0	0	1	0	0	0	16750	922	32	3	66419	3	TTN	2	179500233	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	70474	179500233	63699140	178	16799										
TTN	7273	hgsc.bcm.edu	37	chr2	179554548	179554548	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagccactgtacctttagctGggggagcttcctttttcttt					rs186731979		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:179554548delG	ENST00000591111.1	-	120	31111	c.30887delC	c.(30886-30888)ccafs	p.P10296fs	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Frame_Shift_Del_p.P10613fs|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.P9369fs			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACCTTTAGCTGGGGGAGCTTC	0.373																																					p.P10613fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.31839delA						.						160	154	156					2																	179554548		1836	4086	5922	SO:0001589	frameshift_variant	7273	exon122			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30887delC	chr2.hg19:g.179554548delG	ENSP00000465570:p.Pro10296fs	101.0	0.0		131.0	11.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179554548	G	-	179554548	7	5	112	1	0	1	0	1	0	0	0	0	16750	1348	47	0	72655	0	TTN	2	179554548	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	54315	179554548	63644825	179	16800										
PDE1A	5136	hgsc.bcm.edu	37	chr2	183387041	183387041	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacattttttcagtctgttcTcctgtaagatacttaaaagt	5	8	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:183387041T>C	ENST00000410103.1	-	2	146	c.63A>G	c.(61-63)ggA>ggG	p.G21G	PDE1A_ENST00000435564.1_Silent_p.G21G|PDE1A_ENST00000456212.1_Silent_p.G21G|PDE1A_ENST00000331935.6_Silent_p.G21G|PDE1A_ENST00000536095.1_5'UTR|PDE1A_ENST00000358139.2_Silent_p.G21G	NM_001003683.2	NP_001003683.1	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	21					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	CAGTCTGTTCTCCTGTAAGAT	0.393																																					p.G25G		Atlas-SNP	.											.	PDE1A	184	.	0			c.A75G						.						146	147	146					2																	183387041		2202	4300	6502	SO:0001819	synonymous_variant	5136	exon2			CTGTTCTCCTGTA		CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	3.1.4.17	"Phosphodiesterases"	8774	protein-coding gene	gene with protein product		171890				8557689, 11342109	Standard	NM_005019		Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000410103.1:c.63A>G	chr2.hg19:g.183387041T>C		78.0	0.0		82.0	4.0	NM_001258312	D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	Silent	SNP	ENST00000410103.1	hg19	CCDS33344.1																																																																																			.	.		0.393	PDE1A-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334356.1			C	183387041	T	C	183387041	2	2	112	1	0	0	0	0	0	0	0	1	11642	1538	54	2		2	PDE1A	2	183387041	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3832493	183387041	59812332	180	16801										
NCKAP1	10787	hgsc.bcm.edu	37	chr2	183822266	183822266	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccctttcttaccagtctgcTtttttgatttcttattcact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:183822266delT	ENST00000361354.4	-	19	2312	c.1940delA	c.(1939-1941)aagfs	p.K647fs	NCKAP1_ENST00000360982.2_Frame_Shift_Del_p.K653fs	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	647					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			ACCAGTCTGCTTTTTTGATTT	0.378																																					p.K653fs		Atlas-INDEL	.											.	NCKAP1	105	.	0			c.1959delG						.						172	154	160					2																	183822266		2203	4300	6503	SO:0001589	frameshift_variant	10787	exon20			.	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.1940delA	chr2.hg19:g.183822266delT	ENSP00000355348:p.Lys647fs	162.0	0.0		152.0	10.0	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Frame_Shift_Del	DEL	ENST00000361354.4	hg19	CCDS2287.1																																																																																			.	.		0.378	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		-	183822266	T	-	183822266	7	5	112	1	0	1	0	1	0	0	0	0	10230	1609	56	0	1498	0	NCKAP1	2	183822266	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	435225	183822266	59377107	181	16802										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189852856	189852856	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tacatctggtcatcctggttCccctgtaagtatagccattg					rs374532486		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:189852856delC	ENST00000304636.3	+	6	748	c.578delC	c.(577-579)tccfs	p.S193fs	COL3A1_ENST00000317840.5_Frame_Shift_Del_p.S193fs	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	193	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	CATCCTGGTTCCCCTGTAAGT	0.398																																					p.S193fs		Atlas-INDEL	.											.	COL3A1	292	.	0			c.577delT						.						103	106	105					2																	189852856		2203	4300	6503	SO:0001589	frameshift_variant	1281	exon6			.	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.578delC	chr2.hg19:g.189852856delC	ENSP00000304408:p.Ser193fs	276.0	0.0		321.0	20.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Frame_Shift_Del	DEL	ENST00000304636.3	hg19	CCDS2297.1																																																																																			.	.		0.398	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		-	189852856	C	-	189852856	7	5	112	1	0	1	0	1	0	0	0	0	3690	855	30	0	600	0	COL3A1	2	189852856	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	6030590	189852856	53346517	182	16803										
COL5A2	1290	hgsc.bcm.edu	37	chr2	189904144	189904144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgggtccgttttgtttttgTcatcaggagccgcctgatct	11	10	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:189904144T>C	ENST00000374866.3	-	51	4053	c.3779A>G	c.(3778-3780)gAc>gGc	p.D1260G		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1260					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			TTTGTTTTTGTCATCAGGAGC	0.522																																					p.D1260G		Atlas-SNP	.											.	COL5A2	230	.	0			c.A3779G						.						85	76	79					2																	189904144		2203	4300	6503	SO:0001583	missense	1290	exon51			TTTTTGTCATCAG	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.3779A>G	chr2.hg19:g.189904144T>C	ENSP00000364000:p.Asp1260Gly	119.0	0.0		137.0	8.0	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	hg19	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.841703	0.32513	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.83506	-1.73	5.28	5.28	0.74379	.	0.000000	0.50627	D	0.000106	T	0.68815	0.3042	N	0.16602	0.42	0.43122	D	0.994847	B;P	0.38767	0.243;0.646	B;B	0.31442	0.079;0.13	T	0.70403	-0.4881	10	0.28530	T	0.3	.	15.1969	0.73100	0.0:0.0:0.0:1.0	.	900;1260	Q5PR22;P05997	.;CO5A2_HUMAN	G	1260;900	ENSP00000364000:D1260G	ENSP00000364000:D1260G	D	-	2	0	COL5A2	189612389	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	2.733000	0.47360	1.983000	0.57843	0.533000	0.62120	GAC	.	.		0.522	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		C	189904144	T	C	189904144	3	2	112	1	0	0	0	0	1	0	0	0	3699	1667	58	2	736	2	COL5A2	2	189904144	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	51288	189904144	53295229	183	16804										
ANKAR	150709	hgsc.bcm.edu	37	chr2	190569759	190569759	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccattctaggtccaacaccTctacaccttgctgcacaggc	6	16	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:190569759T>C	ENST00000520309.1	+	8	1807	c.1719T>C	c.(1717-1719)ccT>ccC	p.P573P	ANKAR_ENST00000281412.6_Silent_p.P337P|ANKAR_ENST00000438402.2_Silent_p.P573P|ANKAR_ENST00000313581.4_Silent_p.P573P|ANKAR_ENST00000431575.2_Silent_p.P502P	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	573						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			GTCCAACACCTCTACACCTTG	0.428																																					p.P573P		Atlas-SNP	.											.	ANKAR	184	.	0			c.T1719C						.						146	120	129					2																	190569759		2203	4300	6503	SO:0001819	synonymous_variant	150709	exon8			AACACCTCTACAC	AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"Ankyrin repeat domain containing", "Armadillo repeat containing"	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.1719T>C	chr2.hg19:g.190569759T>C		83.0	0.0		85.0	4.0	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Silent	SNP	ENST00000520309.1	hg19	CCDS33351.2																																																																																			.	.		0.428	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		C	190569759	T	C	190569759	2	2	112	1	0	0	0	0	0	0	0	1	623	1538	54	2		2	ANKAR	2	190569759	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	665615	190569759	52629614	184	16805										
ANKAR	150709	hgsc.bcm.edu	37	chr2	190569839	190569839	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agctgattacacgctttctgAaaaaagaggctggatgccga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:190569839delA	ENST00000520309.1	+	8	1887	c.1799delA	c.(1798-1800)gaafs	p.E600fs	ANKAR_ENST00000281412.6_Frame_Shift_Del_p.E364fs|ANKAR_ENST00000438402.2_Frame_Shift_Del_p.E600fs|ANKAR_ENST00000313581.4_Frame_Shift_Del_p.E600fs|ANKAR_ENST00000431575.2_Frame_Shift_Del_p.E529fs	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	600						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			ACGCTTTCTGAAAAAAGAGGC	0.443																																					p.E600fs		Atlas-INDEL	.											.	ANKAR	184	.	0			c.1798delG						.						158	145	149					2																	190569839		2203	4300	6503	SO:0001589	frameshift_variant	150709	exon8			.	AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"Ankyrin repeat domain containing", "Armadillo repeat containing"	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.1799delA	chr2.hg19:g.190569839delA	ENSP00000427882:p.Glu600fs	144.0	0.0		152.0	10.0	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Frame_Shift_Del	DEL	ENST00000520309.1	hg19	CCDS33351.2																																																																																			.	.		0.443	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		-	190569839	A	-	190569839	7	5	112	1	0	1	0	1	0	0	0	0	623	246	9	0	1825	0	ANKAR	2	190569839	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	80	190569839	52629534	185	16806										
PMS1	5378	hgsc.bcm.edu	37	chr2	190719511	190719511	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggagcaggggaaatatacttAaaaattcagtgggagagaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:190719511delA	ENST00000441310.2	+	9	1746	c.1513delA	c.(1513-1515)aaafs	p.K505fs	PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000418224.3_Frame_Shift_Del_p.K329fs|PMS1_ENST00000432292.3_Frame_Shift_Del_p.K329fs|PMS1_ENST00000447232.2_Frame_Shift_Del_p.K505fs|PMS1_ENST00000409823.3_Frame_Shift_Del_p.K466fs	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	505					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			AAATATACTTAAAAATTCAGT	0.353			"Mis, N"			"colorectal, endometrial, ovarian"		Direct reversal of damage;Mismatch excision repair (MMR)																													p.L504fs		Atlas-INDEL	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	.	PMS1	78	.	0			c.1512delT						.						35	40	38					2																	190719511		2191	4289	6480	SO:0001589	frameshift_variant	5378	exon9			.		CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"postmeiotic segregation increased (S. cerevisiae) 1"	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.1513delA	chr2.hg19:g.190719511delA	ENSP00000406490:p.Lys505fs	145.0	0.0		162.0	11.0	NM_001128144	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Frame_Shift_Del	DEL	ENST00000441310.2	hg19	CCDS2302.1																																																																																			.	.		0.353	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2			-	190719511	A	-	190719511	7	5	112	1	0	1	0	1	0	0	0	0	12151	363	13	0	1543	0	PMS1	2	190719511	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	149672	190719511	52479862	186	16807										
GLS	2744	hgsc.bcm.edu	37	chr2	191765310	191765310	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgtgttcagagcaacattgTtttgttgacacaagcattta	8	6	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:191765310T>C	ENST00000320717.3	+	4	884	c.626T>C	c.(625-627)gTt>gCt	p.V209A	GLS_ENST00000338435.4_Missense_Mutation_p.V209A	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	209					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate secretion (GO:0014047)|glutamine catabolic process (GO:0006543)|neurotransmitter secretion (GO:0007269)|protein homotetramerization (GO:0051289)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|small molecule metabolic process (GO:0044281)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamine(DB00130)	AGCAACATTGTTTTGTTGACA	0.308																																					p.V209A		Atlas-SNP	.											.	GLS	47	.	0			c.T626C						.						113	106	108					2																	191765310		2203	4298	6501	SO:0001583	missense	2744	exon4			ACATTGTTTTGTT	AB020645	CCDS2308.1, CCDS58744.1	2q32-q34	2013-01-10			ENSG00000115419	ENSG00000115419	3.5.1.2	"Ankyrin repeat domain containing"	4331	protein-coding gene	gene with protein product		138280				10048485	Standard	NM_014905		Approved	KIAA0838, GLS1	uc002usf.3	O94925	OTTHUMG00000132701	ENST00000320717.3:c.626T>C	chr2.hg19:g.191765310T>C	ENSP00000317379:p.Val209Ala	63.0	0.0		55.0	4.0	NM_014905	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	hg19	CCDS2308.1	.	.	.	.	.	.	.	.	.	.	T	16.93	3.256801	0.59321	.	.	ENSG00000115419	ENST00000320717;ENST00000338435	T;T	0.46819	0.98;0.86	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.52208	0.1720	M	0.79475	2.455	0.80722	D	1	B;B	0.21821	0.008;0.061	B;B	0.25140	0.01;0.058	T	0.50338	-0.8840	10	0.32370	T	0.25	-18.3999	15.9423	0.79768	0.0:0.0:0.0:1.0	.	209;209	O94925;O94925-3	GLSK_HUMAN;.	A	209	ENSP00000317379:V209A;ENSP00000340689:V209A	ENSP00000317379:V209A	V	+	2	0	GLS	191473555	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.980000	0.88113	2.223000	0.72356	0.455000	0.32223	GTT	.	.		0.308	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			C	191765310	T	C	191765310	3	2	112	1	0	0	0	0	1	0	0	0	6471	1725	60	2	640	2	GLS	2	191765310	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1045799	191765310	51434063	187	16808										
STAT1	6772	hgsc.bcm.edu	37	chr2	191835434	191835434	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaaaaattcatgctctataCtgtgttcatctgtaaaaaga	5	6	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:191835434C>T	ENST00000361099.3	-	25	2635	c.2248G>A	c.(2248-2250)Gta>Ata	p.V750I	STAT1_ENST00000540176.1_3'UTR|STAT1_ENST00000409465.1_Missense_Mutation_p.V750I	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	750					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			ATGCTCTATACTGTGTTCATC	0.368																																					p.V750I		Atlas-SNP	.											.	STAT1	93	.	0			c.G2248A						.						133	122	125					2																	191835434		2203	4300	6503	SO:0001583	missense	6772	exon25			TCTATACTGTGTT		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"SH2 domain containing"	11362	protein-coding gene	gene with protein product	"transcription factor ISGF-3 components p91/p84"	600555	"signal transducer and activator of transcription 1, 91kD"			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.2248G>A	chr2.hg19:g.191835434C>T	ENSP00000354394:p.Val750Ile	63.0	0.0		65.0	5.0	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	hg19	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.284187	0.40394	.	.	ENSG00000115415	ENST00000361099;ENST00000409465	D;D	0.88046	-2.33;-2.33	4.84	3.88	0.44766	.	2.274050	0.01934	N	0.041451	D	0.83266	0.5217	L	0.36672	1.1	0.32343	N	0.55943	B	0.14012	0.009	B	0.17098	0.017	T	0.71672	-0.4522	10	0.54805	T	0.06	.	7.2042	0.25897	0.0:0.8776:0.0:0.1224	.	750	P42224	STAT1_HUMAN	I	750	ENSP00000354394:V750I;ENSP00000386244:V750I	ENSP00000354394:V750I	V	-	1	0	STAT1	191543679	0.760000	0.28428	0.524000	0.27887	0.848000	0.48234	1.920000	0.40025	2.483000	0.83821	0.655000	0.94253	GTA	.	.		0.368	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		T	191835434	C	T	191835434	3	4	112	1	0	0	0	0	1	0	0	0	15279	565	20	3	8	3	STAT1	2	191835434	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	70124	191835434	51363939	188	16809										
SDPR	8436	hgsc.bcm.edu	37	chr2	192701068	192701068	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaaaccttgaagggggagcTttttcctgaggatattttct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:192701068delT	ENST00000304141.4	-	2	1188	c.859delA	c.(859-861)agcfs	p.S288fs		NM_004657.5	NP_004648.1			serum deprivation response											NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			AAGGGGGAGCTTTTTCCTGAG	0.463																																					p.S287fs		Atlas-INDEL	.											.	SDPR	67	.	0			c.860delG						.						134	151	145					2																	192701068		2203	4300	6503	SO:0001589	frameshift_variant	8436	exon2			.	AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"phosphatidylserine binding protein"	606728	"serum deprivation response (phosphatidylserine-binding protein)", "serum deprivation response (phosphatidylserine binding protein)"			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.859delA	chr2.hg19:g.192701068delT	ENSP00000305675:p.Ser288fs	170.0	0.0		209.0	13.0	NM_004657		Frame_Shift_Del	DEL	ENST00000304141.4	hg19	CCDS2313.1																																																																																			.	.		0.463	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657		-	192701068	T	-	192701068	7	5	112	1	0	1	0	1	0	0	0	0	13985	1609	56	0	422	0	SDPR	2	192701068	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	865634	192701068	50498305	189	16810										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196753679	196753679	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actgcatctactgggccatcAaaaattaaccatttcctatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:196753679delA	ENST00000312428.6	-	32	5173	c.5073delT	c.(5071-5073)tttfs	p.F1691fs		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1691	AAA 2. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CTGGGCCATCAAAAATTAACC	0.368																																					p.D1692fs		Atlas-INDEL	.											.	DNAH7	512	.	0			c.5074delG						.						127	119	121					2																	196753679		1909	4135	6044	SO:0001589	frameshift_variant	56171	exon32			.	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.5073delT	chr2.hg19:g.196753679delA	ENSP00000311273:p.Phe1691fs	228.0	0.0		264.0	16.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Frame_Shift_Del	DEL	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.368	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		-	196753679	A	-	196753679	7	5	112	1	0	1	0	1	0	0	0	0	4608	127	5	0	7137	0	DNAH7	2	196753679	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4052611	196753679	46445694	190	16811										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198281517	198281517	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagtggcaccaggagtctgaTcagctgtttgatcccaacgc	12	11	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:198281517T>C	ENST00000335508.6	-	6	705	c.614A>G	c.(613-615)gAt>gGt	p.D205G		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	205	U2AF homology region; mediates interaction with RMB39.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AGGAGTCTGATCAGCTGTTTG	0.413			Mis		myelodysplastic syndrome																																p.D205G		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.A614G						.						171	169	170					2																	198281517		2203	4300	6503	SO:0001583	missense	23451	exon6			GTCTGATCAGCTG	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.614A>G	chr2.hg19:g.198281517T>C	ENSP00000335321:p.Asp205Gly	147.0	0.0		157.0	7.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	15.58	2.875995	0.51695	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.55016	0.1894	L	0.48642	1.525	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.50516	-0.8819	9	0.22109	T	0.4	.	15.3288	0.74190	0.0:0.0:0.0:1.0	.	205	O75533	SF3B1_HUMAN	G	205	.	ENSP00000335321:D205G	D	-	2	0	SF3B1	197989762	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	7.776000	0.85560	2.209000	0.71365	0.472000	0.43445	GAT	.	.		0.413	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198281517	T	C	198281517	3	2	112	1	0	0	0	0	1	0	0	0	14164	1435	50	2	3380	2	SF3B1	2	198281517	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1527838	198281517	44917856	191	16812										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198285793	198285793	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatcattaagcaatgccacaGgggcatgatatcctggcttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:198285793delG	ENST00000335508.6	-	3	351	c.260delC	c.(259-261)cctfs	p.P87fs	SF3B1_ENST00000487698.1_Frame_Shift_Del_p.P87fs|SF3B1_ENST00000409915.4_Frame_Shift_Del_p.P87fs|SF3B1_ENST00000414963.2_Frame_Shift_Del_p.P87fs	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	87					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CAATGCCACAGGGGCATGATA	0.388			Mis		myelodysplastic syndrome																																p.P87fs		Atlas-INDEL	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.261delT						.						157	162	160					2																	198285793		2203	4300	6503	SO:0001589	frameshift_variant	23451	exon3			.	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.260delC	chr2.hg19:g.198285793delG	ENSP00000335321:p.Pro87fs	151.0	0.0		153.0	10.0	NM_001005526	E9PCH3	Frame_Shift_Del	DEL	ENST00000335508.6	hg19	CCDS33356.1																																																																																			.	.		0.388	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			-	198285793	G	-	198285793	7	5	112	1	0	1	0	1	0	0	0	0	14164	1000	35	0	3770	0	SF3B1	2	198285793	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	4276	198285793	44913580	192	16813										
AOX1	316	hgsc.bcm.edu	37	chr2	201485931	201485931	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgacgtcaactccttctgcTtttttactgaagctgagaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:201485931delT	ENST00000374700.2	+	18	2204	c.1963delT	c.(1963-1965)tttfs	p.F656fs	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	656					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	CTCCTTCTGCTTTTTTACTGA	0.393																																					p.C654fs		Atlas-INDEL	.											.	AOX1	152	.	0			c.1962delC						.						156	149	152					2																	201485931		2203	4300	6503	SO:0001589	frameshift_variant	316	exon18			.	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.1963delT	chr2.hg19:g.201485931delT	ENSP00000363832:p.Phe656fs	169.0	0.0		186.0	12.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Frame_Shift_Del	DEL	ENST00000374700.2	hg19	CCDS33360.1																																																																																			.	.		0.393	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		-	201485931	T	-	201485931	7	5	112	1	0	1	0	1	0	0	0	0	729	1609	56	0	2033	0	AOX1	2	201485931	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3200138	201485931	41713442	193	16814										
ORC2L	4999	hgsc.bcm.edu	37	chr2	201778021	201778021	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caatagtggagtcttaccttCtttgttcttataagcttgtg	8	7	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:201778021C>T	ENST00000234296.2	-	17	1893	c.1644G>A	c.(1642-1644)aaG>aaA	p.K548K		NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	548					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						GTCTTACCTTCTTTGTTCTTA	0.408																																					p.K548K		Atlas-SNP	.											.	ORC2	48	.	0			c.G1644A						.						115	105	109					2																	201778021		2203	4300	6503	SO:0001819	synonymous_variant	4999	exon17			TACCTTCTTTGTT		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"origin recognition complex, subunit 2 (yeast homolog)-like", "origin recognition complex, subunit 2-like (yeast)", "origin recognition complex, subunit 2 homolog (yeast)"	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1644G>A	chr2.hg19:g.201778021C>T		70.0	0.0		77.0	4.0	NM_006190	Q13204|Q53TX5	Silent	SNP	ENST00000234296.2	hg19	CCDS2334.1																																																																																			.	.		0.408	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190		T	201778021	C	T	201778021	2	4	112	1	0	0	0	0	0	0	0	1	11271	912	32	3		3	ORC2L	2	201778021	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	292090	201778021	41421352	194	16815										
ALS2CR4	65062	hgsc.bcm.edu	37	chr2	202503720	202503720	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ataacgtcttacctggtgtgTtttttgttctgggcttcttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:202503720delT	ENST00000409883.2	-	4	244	c.128delA	c.(127-129)aacfs	p.N43fs	TMEM237_ENST00000409444.2_Frame_Shift_Del_p.N35fs	NM_001044385.2	NP_001037850.1	Q96Q45	TM237_HUMAN	transmembrane protein 237	43					cilium assembly (GO:0042384)|regulation of Wnt signaling pathway (GO:0030111)	ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)	7						ACCTGGTGTGTTTTTTGTTCT	0.403																																					p.N43fs		Atlas-INDEL	.											.	TMEM237	21	.	0			c.129delC						.						125	107	113					2																	202503720		1833	4089	5922	SO:0001589	frameshift_variant	65062	exon3			.	AB053301	CCDS46489.1, CCDS46490.1	2q33	2012-05-08	2011-05-20	2011-05-20	ENSG00000155755	ENSG00000155755			14432	protein-coding gene	gene with protein product		614423	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 4"	ALS2CR4		11586298, 20375344	Standard	NM_001044385		Approved	JBTS14	uc021vvg.2	Q96Q45	OTTHUMG00000154526	ENST00000409883.2:c.128delA	chr2.hg19:g.202503720delT	ENSP00000386264:p.Asn43fs	224.0	0.0		220.0	16.0	NM_001044385	B4E1R8|B4E2R8|E9PAR8|E9PBF8|E9PG24|E9PGX0|Q53TS9|Q53TT2|Q7Z3B6|Q8IZ18|Q8NBF8|Q96CY1	Frame_Shift_Del	DEL	ENST00000409883.2	hg19	CCDS46489.1																																																																																			.	.		0.403	TMEM237-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335753.1	NM_152388		-	202503720	T	-	202503720	7	5	112	1	0	1	0	1	0	0	0	0	554	1725	60	0	1138	0	ALS2CR4	2	202503720	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	725699	202503720	40695653	195	16816										
FAM117B	150864	hgsc.bcm.edu	37	chr2	203621969	203621969	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagatggccatcgtgctccaCccccccttgtacagagaagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:203621969delC	ENST00000392238.2	+	6	1138	c.1138delC	c.(1138-1140)cccfs	p.P381fs	FAM117B_ENST00000303116.6_Frame_Shift_Del_p.P137fs			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	381										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						TCGTGCTCCACCCCCCCTTGT	0.488																																					p.P379fs		Atlas-INDEL	.											.	FAM117B	73	.	0			c.1137delA						.						55	55	55					2																	203621969		2203	4300	6503	SO:0001589	frameshift_variant	150864	exon6			.	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.1138delC	chr2.hg19:g.203621969delC	ENSP00000376071:p.Pro381fs	222.0	0.0		295.0	19.0	NM_173511	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Frame_Shift_Del	DEL	ENST00000392238.2	hg19	CCDS33362.2																																																																																			.	.		0.488	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511		-	203621969	C	-	203621969	7	5	112	1	0	1	0	1	0	0	0	0	5415	507	18	0	1160	0	FAM117B	2	203621969	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1118249	203621969	39577404	196	16817										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204045127	204045127	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgactgtgcagatcgacagTtccattctattcctgctacc	7	12	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:204045127T>C	ENST00000449802.1	+	42	6733	c.6400T>C	c.(6400-6402)Ttc>Ctc	p.F2134L		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2134	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.									NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AGATCGACAGTTCCATTCTAT	0.338																																					p.F2134L		Atlas-SNP	.											.	NBEAL1	266	.	0			c.T6400C						.						127	120	122					2																	204045127		1842	4098	5940	SO:0001583	missense	65065	exon42			CGACAGTTCCATT	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.6400T>C	chr2.hg19:g.204045127T>C	ENSP00000399903:p.Phe2134Leu	83.0	0.0		89.0	4.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.911492	0.92178	.	.	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	D;D	0.83419	-1.72;-1.72	5.85	5.85	0.93711	BEACH domain (4);	0.000000	0.85682	D	0.000000	D	0.94255	0.8155	H	0.96833	3.89	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.995;0.996	D	0.95931	0.8938	10	0.72032	D	0.01	.	15.9036	0.79403	0.0:0.0:0.0:1.0	.	2134;2123	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	L	2134;2134;149	ENSP00000399903:F2134L;ENSP00000388466:F149L	ENSP00000344985:F2134L	F	+	1	0	NBEAL1	203753372	1.000000	0.71417	0.996000	0.52242	0.773000	0.43773	7.841000	0.86834	2.234000	0.73211	0.533000	0.62120	TTC	.	.		0.338	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			C	204045127	T	C	204045127	3	2	112	1	0	0	0	0	1	0	0	0	10197	1725	60	2	6562	2	NBEAL1	2	204045127	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	423158	204045127	39154246	197	16818										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212248737	212248737	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccaatgcttgaaggtctccaTtttttctccgagaaacaaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:212248737delT	ENST00000342788.4	-	28	3840	c.3530delA	c.(3529-3531)aatfs	p.N1177fs	ERBB4_ENST00000436443.1_Frame_Shift_Del_p.N1161fs|ERBB4_ENST00000402597.1_Frame_Shift_Del_p.N1167fs	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1177					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	AAGGTCTCCATTTTTTCTCCG	0.403										TSP Lung(8;0.080)																											p.N1177fs		Atlas-INDEL	.											ERBB4,NS,carcinoma,0,2	ERBB4	480	.	0			c.3531delT						.						111	113	112					2																	212248737		2203	4300	6503	SO:0001589	frameshift_variant	2066	exon28			.	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3530delA	chr2.hg19:g.212248737delT	ENSP00000342235:p.Asn1177fs	108.0	0.0		113.0	11.0	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Frame_Shift_Del	DEL	ENST00000342788.4	hg19	CCDS2394.1																																																																																			.	.		0.403	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		-	212248737	T	-	212248737	7	5	112	1	0	1	0	1	0	0	0	0	5211	1493	52	0	400	0	ERBB4	2	212248737	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	8203610	212248737	30950636	198	16819										
VWC2L	402117	hgsc.bcm.edu	37	chr2	215279116	215279116	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatacaagttgggagaacgaTttttccctgggcattccaac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:215279116delT	ENST00000312504.5	+	2	1001	c.199delT	c.(199-201)tttfs	p.F68fs	AC107218.3_ENST00000437883.1_RNA|VWC2L_ENST00000427124.1_Frame_Shift_Del_p.F68fs|AC107218.3_ENST00000412896.1_RNA	NM_001080500.2	NP_001073969.1	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain containing protein 2-like	68	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				breast(1)|endometrium(1)|large_intestine(3)|lung(10)|prostate(1)	16						GGGAGAACGATTTTTCCCTGG	0.458																																					p.R66fs		Atlas-INDEL	.											.	VWC2L	40	.	0			c.198delA						.						118	124	122					2																	215279116		1961	4149	6110	SO:0001589	frameshift_variant	402117	exon2			.	AB374231	CCDS46509.1	2q34-q35	2011-01-25	2011-01-25		ENSG00000174453	ENSG00000174453			37203	protein-coding gene	gene with protein product			"von Willebrand factor C domain-containing protein 2-like"				Standard	NM_001080500		Approved		uc002vet.2	B2RUY7	OTTHUMG00000154811	ENST00000312504.5:c.199delT	chr2.hg19:g.215279116delT	ENSP00000308976:p.Phe68fs	121.0	0.0		115.0	10.0	NM_001080500	A6NC69|B2RUW7|B7X8X1	Frame_Shift_Del	DEL	ENST00000312504.5	hg19	CCDS46509.1																																																																																			.	.		0.458	VWC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337175.1	NM_001080500		-	215279116	T	-	215279116	7	5	112	1	0	1	0	1	0	0	0	0	17259	1493	52	0	201	0	VWC2L	2	215279116	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3030379	215279116	27920257	199	16820										
XRCC5	7520	hgsc.bcm.edu	37	chr2	217057430	217057430	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaagtggaaattaaacaattAaatcatttctgggaaattgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:217057430delA	ENST00000392133.3	+	20	2474	c.2013delA	c.(2011-2013)ttafs	p.L671fs	XRCC5_ENST00000392132.2_Frame_Shift_Del_p.L671fs			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	671					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to fatty acid (GO:0071398)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|hematopoietic stem cell differentiation (GO:0060218)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of type I interferon production (GO:0032481)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|kidney(3)|large_intestine(8)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		TTAAACAATTAAATCATTTCT	0.338								Non-homologous end-joining																													p.L671X		Atlas-INDEL	.											.	XRCC5	64	.	0			c.2012delT						.						48	48	48					2																	217057430		2202	4300	6502	SO:0001589	frameshift_variant	7520	exon18			.	AF039597	CCDS2402.1	2q35	2008-07-31	2008-07-31		ENSG00000079246	ENSG00000079246			12833	protein-coding gene	gene with protein product	"Ku autoantigen, 80kDa"	194364	"X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)"			9636207, 9214634	Standard	NM_021141		Approved	KU80, KARP-1, Ku86, KUB2	uc002vfy.3	P13010	OTTHUMG00000133059	ENST00000392133.3:c.2013delA	chr2.hg19:g.217057430delA	ENSP00000375978:p.Leu671fs	205.0	0.0		280.0	21.0	NM_021141	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Frame_Shift_Del	DEL	ENST00000392133.3	hg19	CCDS2402.1																																																																																			.	.		0.338	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141		-	217057430	A	-	217057430	7	5	112	1	0	1	0	1	0	0	0	0	17471	359	13	0	2083	0	XRCC5	2	217057430	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1778314	217057430	26141943	200	16821										
VIL1	7429	hgsc.bcm.edu	37	chr2	219292980	219292980	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctggaagagtttcaaccgaGgggatgttttcctcctggac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:219292980delG	ENST00000248444.5	+	6	575	c.487delG	c.(487-489)gggfs	p.G163fs	VIL1_ENST00000440053.1_Frame_Shift_Del_p.G163fs|VIL1_ENST00000392114.2_Intron	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	163	Core.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTTCAACCGAGGGGATGTTTT	0.547																																					p.R162fs		Atlas-INDEL	.											.	VIL1	65	.	0			c.486delA						.						140	128	132					2																	219292980		2203	4300	6503	SO:0001589	frameshift_variant	7429	exon6			.	X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.487delG	chr2.hg19:g.219292980delG	ENSP00000248444:p.Gly163fs	213.0	0.0		186.0	12.0	NM_007127	B2R9A7|Q53S11|Q96AC8	Frame_Shift_Del	DEL	ENST00000248444.5	hg19	CCDS2417.1																																																																																			.	.		0.547	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127		-	219292980	G	-	219292980	7	5	112	1	0	1	0	1	0	0	0	0	17179	1000	35	0	505	0	VIL1	2	219292980	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2235550	219292980	23906393	201	16822										
USP37	57695	hgsc.bcm.edu	37	chr2	219350428	219350428	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcctgacaagagcacacttCccaccacacttctcacaaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:219350428delC	ENST00000258399.3	-	16	2041	c.1629delG	c.(1627-1629)gggfs	p.G543fs	USP37_ENST00000418019.1_Frame_Shift_Del_p.G543fs|USP37_ENST00000475553.1_5'UTR|USP37_ENST00000415516.1_Frame_Shift_Del_p.G471fs|USP37_ENST00000454775.1_Frame_Shift_Del_p.G543fs	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	543	USP.				G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		GAGCACACTTCCCACCACACT	0.338																																					p.K544fs		Atlas-INDEL	.											.	USP37	76	.	0			c.1630delA						.						117	117	117					2																	219350428		2203	4300	6503	SO:0001589	frameshift_variant	57695	exon16			.	AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"Ubiquitin-specific peptidases"	20063	protein-coding gene	gene with protein product			"ubiquitin specific protease 37"			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.1629delG	chr2.hg19:g.219350428delC	ENSP00000258399:p.Gly543fs	160.0	0.0		179.0	11.0	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Frame_Shift_Del	DEL	ENST00000258399.3	hg19	CCDS2418.1																																																																																			.	.		0.338	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		-	219350428	C	-	219350428	7	5	112	1	0	1	0	1	0	0	0	0	17083	842	30	0	1354	0	USP37	2	219350428	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	57448	219350428	23848945	202	16823										
ABCB6	10058	hgsc.bcm.edu	37	chr2	220075719	220075719	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcagcagcctccacctcatCattcccagctgtgacacggc	8	17	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:220075719C>A	ENST00000265316.3	-	15	2396	c.2080G>T	c.(2080-2082)Gat>Tat	p.D694Y	ABCB6_ENST00000439002.2_Missense_Mutation_p.D648Y	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	694	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCCACCTCATCATTCCCAGCT	0.547																																					p.D694Y		Atlas-SNP	.											.	ABCB6	76	.	0			c.G2080T						.						86	76	79					2																	220075719		2203	4300	6503	SO:0001583	missense	10058	exon15			CCTCATCATTCCC	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.2080G>T	chr2.hg19:g.220075719C>A	ENSP00000265316:p.Asp694Tyr	115.0	0.0		149.0	42.0	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	SNP	ENST00000265316.3	hg19	CCDS2436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.411|6.411	0.444004|0.444004	0.12164|0.12164	.|.	.|.	ENSG00000115657|ENSG00000115657	ENST00000265316;ENST00000439002|ENST00000295750	D;D|.	0.91068|.	-2.78;-2.78|.	4.7|4.7	-1.52|-1.52	0.08637|0.08637	ATPase, AAA+ type, core (1);ABC transporter-like (2);|.	0.915309|.	0.09535|.	N|.	0.789071|.	T|T	0.47192|0.47192	0.1432|0.1432	M|M	0.83852|0.83852	2.665|2.665	0.09310|0.09310	N|N	0.999999|0.999999	B;P|.	0.34892|.	0.297;0.474|.	B;B|.	0.40506|.	0.105;0.331|.	T|T	0.48175|0.48175	-0.9058|-0.9058	10|5	0.87932|.	D|.	0|.	0.686|0.686	2.4059|2.4059	0.04413|0.04413	0.1079:0.4165:0.2131:0.2625|0.1079:0.4165:0.2131:0.2625	.|.	648;694|.	Q9NP58-4;Q9NP58|.	.;ABCB6_HUMAN|.	Y|I	694;648|541	ENSP00000265316:D694Y;ENSP00000394333:D648Y|.	ENSP00000265316:D694Y|.	D|M	-|-	1|3	0|0	ABCB6|ABCB6	219783963|219783963	0.010000|0.010000	0.17322|0.17322	0.000000|0.000000	0.03702|0.03702	0.022000|0.022000	0.10575|0.10575	0.588000|0.588000	0.23924|0.23924	-0.096000|-0.096000	0.12329|0.12329	-0.903000|-0.903000	0.02851|0.02851	GAT|ATG	.	.		0.547	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		A	220075719	C	A	220075719	3	1	112	1	0	0	0	0	1	0	0	0	45	826	29	3	468	3	ABCB6	2	220075719	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	725291	220075719	23123654	203	16824										
SPEG	10290	hgsc.bcm.edu	37	chr2	220354172	220354172	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccacccctagctcctgctgCccccacacccccgtcagtca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:220354172delC	ENST00000312358.7	+	36	8564	c.8432delC	c.(8431-8433)gccfs	p.A2811fs	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2811	Pro-rich.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GCTCCTGCTGCCCCCACACCC	0.672																																					p.A2811fs		Atlas-INDEL	.											.	SPEG	272	.	0			c.8431delG						.						29	31	31					2																	220354172		1885	4089	5974	SO:0001589	frameshift_variant	10290	exon36			.	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.8432delC	chr2.hg19:g.220354172delC	ENSP00000311684:p.Ala2811fs	154.0	0.0		205.0	13.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Frame_Shift_Del	DEL	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.672	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		-	220354172	C	-	220354172	7	5	112	1	0	1	0	1	0	0	0	0	15051	739	26	0	8586	0	SPEG	2	220354172	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	278453	220354172	22845201	204	16825										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225695297	225695297	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atcaagtgctgtgccatcgaTtttaggataattgcaaagaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:225695297delT	ENST00000258390.7	-	27	3064	c.2997delA	c.(2995-2997)aaafs	p.K999fs	DOCK10_ENST00000409592.3_Frame_Shift_Del_p.K993fs	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	999					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GTGCCATCGATTTTAGGATAA	0.284																																					p.S1000fs		Atlas-INDEL	.											.	DOCK10	308	.	0			c.2998delT						.																																			SO:0001589	frameshift_variant	55619	exon27			.	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.2997delA	chr2.hg19:g.225695297delT	ENSP00000258390:p.Lys999fs	182.0	0.0		163.0	11.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Frame_Shift_Del	DEL	ENST00000258390.7	hg19	CCDS46528.1																																																																																			.	.		0.284	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			-	225695297	T	-	225695297	7	5	112	1	0	1	0	1	0	0	0	0	4687	1490	52	0	3683	0	DOCK10	2	225695297	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	5341125	225695297	17504076	205	16826										
ECEL1	9427	hgsc.bcm.edu	37	chr2	233350834	233350834	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaaggcgcgcaccttgcgcTgggccgcgccgccaggccca	15	17	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:233350834T>C	ENST00000304546.1	-	2	740	c.530A>G	c.(529-531)cAg>cGg	p.Q177R	ECEL1_ENST00000409941.1_Missense_Mutation_p.Q177R	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	177					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		CACCTTGCGCTgggccgcgcc	0.716																																					p.Q177R		Atlas-SNP	.											.	ECEL1	73	.	0			c.A530G						.						4	5	5					2																	233350834		1993	3987	5980	SO:0001583	missense	9427	exon2			TTGCGCTGGGCCG	Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.530A>G	chr2.hg19:g.233350834T>C	ENSP00000302051:p.Gln177Arg	9.0	0.0		9.0	5.0	NM_004826	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Missense_Mutation	SNP	ENST00000304546.1	hg19	CCDS2493.1	.	.	.	.	.	.	.	.	.	.	T	17.49	3.403395	0.62288	.	.	ENSG00000171551	ENST00000304546;ENST00000409941	T;T	0.73897	-0.79;-0.79	5.33	4.13	0.48395	Peptidase M13 (1);	0.135808	0.47455	D	0.000230	T	0.56247	0.1972	N	0.11255	0.115	0.35224	D	0.776337	B;B	0.31153	0.31;0.025	B;B	0.29862	0.108;0.016	T	0.64980	-0.6279	10	0.87932	D	0	-17.2238	12.0726	0.53626	0.0:0.0:0.1442:0.8557	.	177;177	O95672-2;O95672	.;ECEL1_HUMAN	R	177	ENSP00000302051:Q177R;ENSP00000386333:Q177R	ENSP00000302051:Q177R	Q	-	2	0	ECEL1	233059078	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.682000	0.68182	0.822000	0.34565	0.528000	0.53228	CAG	.	.		0.716	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		C	233350834	T	C	233350834	3	2	112	1	0	0	0	0	1	0	0	0	4893	1580	55	2	1865	2	ECEL1	2	233350834	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	7655537	233350834	9848539	206	16827										
CHRNG	1146	hgsc.bcm.edu	37	chr2	233408309	233408309	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgacaggtacctgaccttccTcctggtggtgaccatcctca	9	14	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:233408309T>C	ENST00000389494.3	+	9	956	c.935T>C	c.(934-936)cTc>cCc	p.L312P	CHRNG_ENST00000389492.3_Missense_Mutation_p.L260P	NM_005199.4	NP_005190.4	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma (muscle)	312					muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)			breast(2)|endometrium(3)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)	Galantamine(DB00674)	CTGACCTTCCTCCTGGTGGTG	0.622																																					p.L312P		Atlas-SNP	.											.	CHRNG	54	.	0			c.T935C						.						174	129	144					2																	233408309		2203	4300	6503	SO:0001583	missense	1146	exon9			CCTTCCTCCTGGT	X01715	CCDS33400.1	2q37.1	2012-10-02	2012-02-07		ENSG00000196811	ENSG00000196811		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1967	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, gamma (muscle)"	100730	"cholinergic receptor, nicotinic, gamma"	ACHRG			Standard	NM_005199		Approved		uc002vsx.1	P07510	OTTHUMG00000153327	ENST00000389494.3:c.935T>C	chr2.hg19:g.233408309T>C	ENSP00000374145:p.Leu312Pro	129.0	0.0		169.0	7.0	NM_005199	B3KWM8|Q14DU4|Q53RG2	Missense_Mutation	SNP	ENST00000389494.3	hg19	CCDS33400.1	.	.	.	.	.	.	.	.	.	.	T	16.84	3.234536	0.58886	.	.	ENSG00000196811	ENST00000389494;ENST00000541596;ENST00000389492	D;D	0.84944	-1.92;-1.92	5.22	5.22	0.72569	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.077174	0.51477	D	0.000087	D	0.91229	0.7236	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.85130	0.997;0.974	D	0.92169	0.5742	10	0.72032	D	0.01	.	15.0989	0.72256	0.0:0.0:0.0:1.0	.	260;312	Q14DU4;P07510	.;ACHG_HUMAN	P	312;312;260	ENSP00000374145:L312P;ENSP00000374143:L260P	ENSP00000374143:L260P	L	+	2	0	CHRNG	233116553	1.000000	0.71417	1.000000	0.80357	0.697000	0.40408	5.540000	0.67205	1.973000	0.57446	0.260000	0.18958	CTC	.	.		0.622	CHRNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330743.1	NM_005199		C	233408309	T	C	233408309	3	2	112	1	0	0	0	0	1	0	0	0	3398	1551	54	2	969	2	CHRNG	2	233408309	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	57475	233408309	9791064	207	16828										
EIF4E2	9470	hgsc.bcm.edu	37	chr2	233421124	233421124	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attgtgttgcctttccattcAgtttgaaagatgatgacagt	9	6	1	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:233421124A>G	ENST00000258416.3	+	2	693		c.e2-1		EIF4E2_ENST00000409167.3_Splice_Site|EIF4E2_ENST00000409394.1_Splice_Site|EIF4E2_ENST00000409322.1_Splice_Site|EIF4E2_ENST00000409098.1_Splice_Site|EIF4E2_ENST00000479834.1_Splice_Site|EIF4E2_ENST00000409514.1_Splice_Site|EIF4E2_ENST00000409495.1_Splice_Site	NM_004846.2	NP_004837.1	O60573	IF4E2_HUMAN	eukaryotic translation initiation factor 4E family member 2						cytokine-mediated signaling pathway (GO:0019221)|in utero embryonic development (GO:0001701)|negative regulation of translation (GO:0017148)	cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;2.3e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000912)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CTTTCCATTCAGTTTGAAAGA	0.413																																					.		Atlas-SNP	.											.	EIF4E2	23	.	0			c.21-2A>G						.						135	116	122					2																	233421124		2203	4300	6503	SO:0001630	splice_region_variant	9470	exon2			CCATTCAGTTTGA	AF038957	CCDS2496.1, CCDS63158.1, CCDS63159.1, CCDS74671.1	2q37.1	2008-02-05	2006-11-13	2004-10-30	ENSG00000135930	ENSG00000135930			3293	protein-coding gene	gene with protein product		605895	"eukaryotic translation initiation factor 4E-like 3"	EIF4EL3		9653160, 9582349	Standard	XM_005246975		Approved	IF4e, 4EHP	uc002vta.3	O60573	OTTHUMG00000133256	ENST00000258416.3:c.21-1A>G	chr2.hg19:g.233421124A>G		107.0	0.0		99.0	4.0	NM_004846	B8ZZJ9|O75349	Splice_Site	SNP	ENST00000258416.3	hg19	CCDS2496.1	.	.	.	.	.	.	.	.	.	.	A	15.92	2.976699	0.53720	.	.	ENSG00000135930	ENST00000258416;ENST00000409514;ENST00000409098;ENST00000409495;ENST00000409167;ENST00000409322;ENST00000409394;ENST00000454501	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0662	0.64831	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF4E2	233129368	1.000000	0.71417	0.916000	0.36221	0.505000	0.33919	8.714000	0.91412	2.214000	0.71695	0.528000	0.53228	.	.	.		0.413	EIF4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257033.2	NM_004846	Intron	G	233421124	A	G	233421124	5	3	112	1	0	0	0	0	0	0	1	0	5032	202	7	2	25	2	EIF4E2	2	233421124	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	12815	233421124	9778249	208	16829										
UGT1A1	54658	hgsc.bcm.edu	37	chr2	234668947	234668947	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggcgccatggctgtggagtCccagggcggacgcccacttg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:234668947delC	ENST00000608383.1	+	1	14	c.14delC	c.(13-15)tccfs	p.S5fs	UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A3_ENST00000482026.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A8_ENST00000305208.5_Frame_Shift_Del_p.S5fs|UGT1A1_ENST00000360418.3_Frame_Shift_Del_p.S5fs|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000406651.1_Intron			P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	5					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	GCTGTGGAGTCCCAGGGCGGA	0.542											OREG0003837	type=REGULATORY REGION|Gene=UGT1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.S5fs		Atlas-INDEL	.											.	UGT1A1	81	.	0			c.13delT						.						31	30	30					2																	234668947		2203	4300	6503	SO:0001589	frameshift_variant	54658	exon1			.	M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"UDP glucuronosyltransferases"	12530	other	complex locus constituent		191740	"UDP glycosyltransferase 1 family, polypeptide A1"	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	ENST00000608383.1:c.14delC	chr2.hg19:g.234668947delC	ENSP00000476741:p.Ser5fs	135.0	0.0	2375	159.0	10.0	NM_000463	A6NJC3|B8K286	Frame_Shift_Del	DEL	ENST00000608383.1	hg19	CCDS2510.1																																																																																			.	.		0.542	UGT1A1-203	KNOWN	basic|CCDS	protein_coding	protein_coding				-	234668947	C	-	234668947	7	5	112	1	0	1	0	1	0	0	0	0	16959	855	30	0	16	0	UGT1A1	2	234668947	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1247823	234668947	8530426	209	16830										
LRRFIP1	9208	hgsc.bcm.edu	37	chr2	238666189	238666189	+	Intron	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtggaaagacaaaaagataGgggtaggattcccaagtctt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:238666189delG	ENST00000392000.4	+	9	864				LRRFIP1_ENST00000289175.6_Intron|LRRFIP1_ENST00000308482.9_Frame_Shift_Del_p.G408fs|LRRFIP1_ENST00000244815.5_Intron	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1						innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		CAAAAAGATAGGGGTAGGATT	0.423																																					p.I407fs		Atlas-INDEL	.											.	LRRFIP1	171	.	0			c.1221delA						.						46	44	45					2																	238666189		1566	3573	5139	SO:0001627	intron_variant	9208	exon17			.	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"GC-binding factor 2"	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.747+1359G>-	chr2.hg19:g.238666189delG		248.0	0.0		240.0	16.0	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Frame_Shift_Del	DEL	ENST00000392000.4	hg19	CCDS46552.1																																																																																			.	.		0.423	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		-	238666189	G	-	238666189	6	5	112	0	1	1	0	1	0	0	0	0	9036	1000	35	0		0	LRRFIP1	2	238666189	Intron	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	3997242	238666189	4533184	210	16831										
TRAF3IP1	26146	hgsc.bcm.edu	37	chr2	239237915	239237915	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acagggacagacggagagtgAaaaacggggagcactcctgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:239237915delA	ENST00000373327.4	+	5	1069	c.847delA	c.(847-849)aaafs	p.K283fs	TRAF3IP1_ENST00000391994.2_Frame_Shift_Del_p.K283fs|TRAF3IP1_ENST00000391993.3_Frame_Shift_Del_p.K283fs	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	283	Abolishes microtubules-binding when missing.|DISC1-interaction domain.				cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		acggagagtgaaaaacgggga	0.542																																					p.V282fs		Atlas-INDEL	.											TRAF3IP1,right_upper_lobe,carcinoma,0,1	TRAF3IP1	58	.	0			c.846delG						.						77	89	85					2																	239237915		2200	4299	6499	SO:0001589	frameshift_variant	26146	exon5			.	AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"Intraflagellar transport homologs"	17861	protein-coding gene	gene with protein product	"microtubule interacting protein that associates with TRAF3"	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.847delA	chr2.hg19:g.239237915delA	ENSP00000362424:p.Lys283fs	100.0	0.0		152.0	12.0	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Frame_Shift_Del	DEL	ENST00000373327.4	hg19	CCDS33415.1																																																																																			.	.		0.542	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650		-	239237915	A	-	239237915	7	5	112	1	0	1	0	1	0	0	0	0	16455	247	9	0	865	0	TRAF3IP1	2	239237915	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	571726	239237915	3961458	211	16832										
HDAC4	9759	hgsc.bcm.edu	37	chr2	240111545	240111545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcaccttgatgtgctcgtggAgctgcgcctcgtgctgccgg	14	13	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:240111545A>G	ENST00000345617.3	-	4	1114	c.323T>C	c.(322-324)cTc>cCc	p.L108P	HDAC4_ENST00000541256.1_Missense_Mutation_p.L77P	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	108					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GTGCTCGTGGAGCTGCGCCTC	0.682																																					p.L108P		Atlas-SNP	.											.	HDAC4	127	.	0			c.T323C						.						26	24	24					2																	240111545		2203	4300	6503	SO:0001583	missense	9759	exon4			TCGTGGAGCTGCG	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.323T>C	chr2.hg19:g.240111545A>G	ENSP00000264606:p.Leu108Pro	74.0	0.0		87.0	4.0	NM_006037	Q9UND6	Missense_Mutation	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.702272	0.68501	.	.	ENSG00000068024	ENST00000345617;ENST00000541256;ENST00000454542;ENST00000446876	T;T;T;T	0.66995	0.99;0.99;-0.24;-0.18	4.29	4.29	0.51040	Histone deacetylase, glutamine rich N-terminal domain (1);	0.000000	0.64402	D	0.000007	T	0.79598	0.4473	M	0.71206	2.165	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.995;0.999	D;D;D;D;D	0.91635	0.999;0.977;0.987;0.929;0.977	T	0.80542	-0.1336	9	.	.	.	.	13.7561	0.62937	1.0:0.0:0.0:0.0	.	103;77;77;76;108	B7Z8G5;F5H5W4;B7Z8I2;Q53SM2;P56524	.;.;.;.;HDAC4_HUMAN	P	108;77;77;81	ENSP00000264606:L108P;ENSP00000443057:L77P;ENSP00000405226:L77P;ENSP00000392912:L81P	.	L	-	2	0	HDAC4	239776482	1.000000	0.71417	0.958000	0.39756	0.665000	0.39181	8.779000	0.91792	1.736000	0.51660	0.460000	0.39030	CTC	.	.		0.682	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		G	240111545	A	G	240111545	3	3	112	1	0	0	0	0	1	0	0	0	7018	304	11	2	3027	2	HDAC4	2	240111545	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	873630	240111545	3087828	212	16833										
SNED1	25992	hgsc.bcm.edu	37	chr2	241988110	241988110	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gactgtgagtgccgcaacggAggcagatgcctgggcgccaa	16	11	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:241988110A>G	ENST00000310397.8	+	10	1431	c.1431A>G	c.(1429-1431)ggA>ggG	p.G477G	AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000342631.6_Silent_p.G477G|SNED1_ENST00000401884.1_Silent_p.G477G|SNED1_ENST00000405547.3_Silent_p.G477G|SNED1_ENST00000469006.1_3'UTR	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	477	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GCCGCAACGGAGGCAGATGCC	0.632																																					p.G477G		Atlas-SNP	.											.	SNED1	76	.	0			c.A1431G						.						50	62	58					2																	241988110		2062	4198	6260	SO:0001819	synonymous_variant	25992	exon10			CAACGGAGGCAGA	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"Fibronectin type III domain containing"	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.1431A>G	chr2.hg19:g.241988110A>G		111.0	0.0		121.0	5.0	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	hg19	CCDS46562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.043|5.043	0.193556|0.193556	0.09599|0.09599	.|.	.|.	ENSG00000162804|ENSG00000162804	ENST00000431690|ENST00000401644	.|.	.|.	.|.	4.81|4.81	-4.89|-4.89	0.03103|0.03103	.|.	.|.	.|.	.|.	.|.	T|T	0.48554|0.48554	0.1506|0.1506	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.48399|0.48399	-0.9039|-0.9039	4|4	.|.	.|.	.|.	.|.	7.2522|7.2522	0.26156|0.26156	0.4664:0.0:0.4121:0.1215|0.4664:0.0:0.4121:0.1215	.|.	.|.	.|.	.|.	G|G	135|174	.|.	.|.	E|R	+|+	2|1	0|2	SNED1|SNED1	241636783|241636783	0.192000|0.192000	0.23301|0.23301	0.831000|0.831000	0.32960|0.32960	0.338000|0.338000	0.28826|0.28826	-0.758000|-0.758000	0.04766|0.04766	-0.784000|-0.784000	0.04528|0.04528	-0.376000|-0.376000	0.06991|0.06991	GAG|AGG	.	.		0.632	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		G	241988110	A	G	241988110	2	3	112	1	0	0	0	0	0	0	0	1	14860	291	11	2		2	SNED1	2	241988110	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1876565	241988110	1211263	213	16834										
MTERFD2	130916	hgsc.bcm.edu	37	chr2	242039228	242039228	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcgcaacaaagaagctgtcgTccttctctgttctccaagat	8	12	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:242039228T>C	ENST00000391980.2	-	2	161	c.103A>G	c.(103-105)Acg>Gcg	p.T35A	MTERFD2_ENST00000495694.1_Missense_Mutation_p.T35A|MTERFD2_ENST00000407095.3_Missense_Mutation_p.T35A|MTERFD2_ENST00000406593.1_Intron|MTERFD2_ENST00000464344.2_Intron	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		35					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		GAAGCTGTCGTCCTTCTCTGT	0.507																																					p.T35A		Atlas-SNP	.											.	MTERFD2	33	.	0			c.A103G						.						50	51	51					2																	242039228		2203	4300	6503	SO:0001583	missense	130916	exon2			CTGTCGTCCTTCT																												ENST00000391980.2:c.103A>G	chr2.hg19:g.242039228T>C	ENSP00000375840:p.Thr35Ala	103.0	0.0		103.0	5.0	NM_182501	A8K6K0|Q9P0E0	Missense_Mutation	SNP	ENST00000391980.2	hg19	CCDS2544.1	.	.	.	.	.	.	.	.	.	.	T	10.72	1.428513	0.25726	.	.	ENSG00000122085	ENST00000495694;ENST00000401626;ENST00000391980;ENST00000424798;ENST00000407095;ENST00000434791	T;T;T;T;T;T	0.48201	0.82;0.88;2.7;1.47;1.49;0.92	4.39	0.138	0.14793	.	0.949254	0.08630	N	0.917139	T	0.29749	0.0743	L	0.29908	0.895	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.22487	-1.0215	10	0.32370	T	0.25	0.8672	2.2603	0.04065	0.2226:0.2928:0.0:0.4845	.	35;35	B4DKD5;Q7Z6M4	.;MTER2_HUMAN	A	35;35;35;28;35;14	ENSP00000419315:T35A;ENSP00000385183:T35A;ENSP00000375840:T35A;ENSP00000409023:T28A;ENSP00000385630:T35A;ENSP00000393063:T14A	ENSP00000241527:T35A	T	-	1	0	MTERFD2	241687901	0.008000	0.16893	0.001000	0.08648	0.025000	0.11179	0.979000	0.29500	0.175000	0.19841	0.482000	0.46254	ACG	.	.		0.507	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4			C	242039228	T	C	242039228	3	2	112	1	0	0	0	0	1	0	0	0	9929	1667	58	2	1054	2	MTERFD2	2	242039228	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	51118	242039228	1160145	214	16835										
STK25	10494	hgsc.bcm.edu	37	chr2	242440926	242440926	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccaaagtagcgggtgatgtaGgggctgtcgcactgactgag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:242440926delG	ENST00000316586.4	-	3	577	c.228delC	c.(226-228)cccfs	p.P76fs	STK25_ENST00000478403.1_5'Flank|STK25_ENST00000405883.3_Intron|STK25_ENST00000405585.1_Intron|STK25_ENST00000401869.1_Frame_Shift_Del_p.P76fs|STK25_ENST00000535007.1_5'UTR|STK25_ENST00000543554.1_5'UTR|STK25_ENST00000403346.3_Frame_Shift_Del_p.P76fs	NM_001271977.1|NM_001271978.1|NM_001282308.1	NP_001258906.1|NP_001258907.1|NP_001269237.1	O00506	STK25_HUMAN	serine/threonine kinase 25	76	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				establishment or maintenance of cell polarity (GO:0007163)|Golgi localization (GO:0051645)|positive regulation of axonogenesis (GO:0050772)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	10		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		GGGTGATGTAGGGGCTGTCGC	0.602																																					p.Y77fs	NSCLC(99;1100 1566 7679 28647 48345)	Atlas-INDEL	.											.	STK25	32	.	0			c.229delT						.						128	101	110					2																	242440926		2203	4300	6503	SO:0001589	frameshift_variant	10494	exon3			.	D63780	CCDS2549.1, CCDS63199.1, CCDS63200.1	2q37.3	2010-06-25	2010-06-25		ENSG00000115694	ENSG00000115694			11404	protein-coding gene	gene with protein product		602255	"serine/threonine kinase 25 (Ste20, yeast homolog)"			8887545, 9160885, 15037601	Standard	NM_001271977		Approved	SOK1, YSK1	uc002wbp.4	O00506	OTTHUMG00000133408	ENST00000316586.4:c.228delC	chr2.hg19:g.242440926delG	ENSP00000325748:p.Pro76fs	98.0	0.0		119.0	10.0	NM_001271977	A8K6Z3|A8K7D2|B7Z9K1|Q15522|Q5BJF1	Frame_Shift_Del	DEL	ENST00000316586.4	hg19	CCDS2549.1																																																																																			.	.		0.602	STK25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257265.4	NM_006374		-	242440926	G	-	242440926	7	5	112	1	0	1	0	1	0	0	0	0	15309	987	35	0	1092	0	STK25	2	242440926	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	401698	242440926	758447	215	16836										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1367497	1367497	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcacttgcctttttgaaacAgctcctccagaatgggaaca	9	11	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:1367497A>G	ENST00000446702.2	+	9	1573		c.e9-1		CNTN6_ENST00000350110.2_Splice_Site|CNTN6_ENST00000539053.1_Splice_Site			Q9UQ52	CNTN6_HUMAN	contactin 6						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TTTTTGAAACAGCTCCTCCAG	0.428																																					.		Atlas-SNP	.											.	CNTN6	245	.	0			c.947-2A>G						.						99	93	95					3																	1367497		2203	4300	6503	SO:0001630	splice_region_variant	27255	exon9			TGAAACAGCTCCT	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.947-1A>G	chr3.hg19:g.1367497A>G		42.0	0.0		66.0	5.0	NM_014461	Q2KHM2	Splice_Site	SNP	ENST00000446702.2	hg19	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.249872	0.80024	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7897	0.63133	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNTN6	1342497	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	5.614000	0.67695	1.997000	0.58415	0.533000	0.62120	.	.	.		0.428	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	Intron	G	1367497	A	G	1367497	5	3	112	1	0	0	0	0	0	0	1	0	3647	202	7	2	975	2	CNTN6	3	1367497	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10		1367497	196654933	216	16837										
CRELD1	78987	hgsc.bcm.edu	37	chr3	9976237	9976237	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctccacctccccagtcttctCccccgcctcagccccatccg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:9976237delC	ENST00000383811.3	+	1	714	c.115delC	c.(115-117)cccfs	p.P41fs	CRELD1_ENST00000397170.3_Frame_Shift_Del_p.P41fs|CRELD1_ENST00000326434.5_Frame_Shift_Del_p.P41fs|CRELD1_ENST00000452070.1_Frame_Shift_Del_p.P41fs|RP11-1020A11.1_ENST00000602411.1_RNA	NM_015513.4	NP_056328	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1	41	Pro-rich.				cardiac septum development (GO:0003279)|endocardial cushion development (GO:0003197)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|urinary_tract(1)	14						CCAGTCTTCTCCCCCGCCTCA	0.627																																					p.S38fs		Atlas-INDEL	.											.	CRELD1	48	.	0			c.114delT						.						55	45	48					3																	9976237		2203	4300	6503	SO:0001589	frameshift_variant	78987	exon2			.	AF452623	CCDS2593.1, CCDS33693.1	3p25.3	2005-12-08	2004-02-13		ENSG00000163703	ENSG00000163703			14630	protein-coding gene	gene with protein product		607170	"atrioventricular septal defect 2"	AVSD2		10922384, 12137942	Standard	NM_015513		Approved		uc003buf.3	Q96HD1	OTTHUMG00000128653	ENST00000383811.3:c.115delC	chr3.hg19:g.9976237delC	ENSP00000373322:p.Pro41fs	139.0	0.0		167.0	11.0	NM_001077415	A8MX90|B2RAA9|Q6I9X5|Q8NFT4|Q9Y409	Frame_Shift_Del	DEL	ENST00000383811.3	hg19	CCDS2593.1																																																																																			.	.		0.627	CRELD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250533.1	NM_015513		-	9976237	C	-	9976237	7	5	112	1	0	1	0	1	0	0	0	0	3868	855	30	0	117	0	CRELD1	3	9976237	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	8608740	9976237	188046193	217	16838										
FANCD2	2177	hgsc.bcm.edu	37	chr3	10108949	10108949	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgaaggggaaggtgctcacTcggttaaagcacattgtaga	13	6	1	2	rs201487858		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:10108949T>C	ENST00000419585.1	+	26	2603	c.2442T>C	c.(2440-2442)acT>acC	p.T814T	FANCD2_ENST00000287647.3_Silent_p.T814T|FANCD2_ENST00000383806.1_Silent_p.T814T|FANCD2_ENST00000383807.1_Silent_p.T814T			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	814					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		AGGTGCTCACTCGGTTAAAGC	0.413			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.T814T		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.T2442C						.						96	83	87					3																	10108949		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon26	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GCTCACTCGGTTA	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.2442T>C	chr3.hg19:g.10108949T>C		61.0	0.0		115.0	7.0	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	hg19	CCDS33696.1																																																																																			.	T|0.998;C|0.002		0.413	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			C	10108949	T	C	10108949	2	2	112	1	0	0	0	0	0	0	0	1	5673	1538	54	2		2	FANCD2	3	10108949	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	132712	10108949	187913481	218	16839										
IQSEC1	9922	hgsc.bcm.edu	37	chr3	12942773	12942773	+	Intron	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcatggcggcctgcggcagCccctctgggggccccaggtg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:12942773delC	ENST00000273221.4	-	13	3064					NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1						actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CCTGCGGCAGCCCCTCTGGGG	0.701																																					p.L1019fs		Atlas-INDEL	.											.	IQSEC1	88	.	0			c.3055delC						.						1	2	1					3																	12942773		276	894	1170	SO:0001627	intron_variant	9922	exon15			.	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"brefeldin A-resistant ARF-GEF2"	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.2847+1499G>-	chr3.hg19:g.12942773delC		133.0	0.0		183.0	11.0	NM_001134382	O94863|Q96D85	Frame_Shift_Del	DEL	ENST00000273221.4	hg19	CCDS33703.1																																																																																			.	.		0.701	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869		-	12942773	C	-	12942773	6	5	112	0	1	1	0	1	0	0	0	0	7826	739	26	0		0	IQSEC1	3	12942773	Intron	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	2833824	12942773	185079657	219	16840										
GALNTL2	117248	hgsc.bcm.edu	37	chr3	16268877	16268877	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttagaatgggatgattgtccAcattctttctgggaaatgca	10	6	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:16268877A>G	ENST00000339732.5	+	10	2293	c.1790A>G	c.(1789-1791)cAc>cGc	p.H597R	GALNT15_ENST00000437509.1_Intron	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	597	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										ATGATTGTCCACATTCTTTCT	0.398																																					p.H597R		Atlas-SNP	.											.	.	.	.	0			c.A1790G						.						102	104	103					3																	16268877		2203	4300	6503	SO:0001583	missense	117248	exon10			TTGTCCACATTCT	AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"Glycosyltransferase family 2 domain containing"	21531	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 15"	615131	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.1790A>G	chr3.hg19:g.16268877A>G	ENSP00000344260:p.His597Arg	57.0	0.0		87.0	4.0	NM_054110	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	hg19	CCDS33711.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.949686	0.73787	.	.	ENSG00000131386	ENST00000339732;ENST00000543679	T	0.29917	1.55	5.62	5.62	0.85841	Ricin B-related lectin (1);Ricin B lectin (3);	0.000000	0.85682	D	0.000000	T	0.58380	0.2118	M	0.85041	2.73	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.64960	-0.6284	10	0.87932	D	0	.	12.4983	0.55942	1.0:0.0:0.0:0.0	.	597	Q8N3T1	GLTL2_HUMAN	R	597;127	ENSP00000344260:H597R	ENSP00000344260:H597R	H	+	2	0	GALNTL2	16243881	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.013000	0.64023	2.266000	0.75297	0.533000	0.62120	CAC	.	.		0.398	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110		G	16268877	A	G	16268877	3	3	112	1	0	0	0	0	1	0	0	0	6230	159	6	2	1828	2	GALNTL2	3	16268877	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	3326104	16268877	181753553	220	16841										
SATB1	6304	hgsc.bcm.edu	37	chr3	18427925	18427925	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgggtggtgtgctgatgaggGgggcaggacccatggccgag	21	7	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:18427925G>T	ENST00000338745.6	-	8	3119	c.1385C>A	c.(1384-1386)cCc>cAc	p.P462H	TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000417717.2_Missense_Mutation_p.P462H|SATB1_ENST00000454909.2_Missense_Mutation_p.P462H	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	462					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						GCTGATGAGGGGGGCAGGACC	0.512																																					p.P462H		Atlas-SNP	.											.	SATB1	96	.	0			c.C1385A						.						161	172	168					3																	18427925		2203	4300	6503	SO:0001583	missense	6304	exon8			ATGAGGGGGGCAG		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.1385C>A	chr3.hg19:g.18427925G>T	ENSP00000341024:p.Pro462His	131.0	0.0		191.0	9.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	G	11.98	1.801329	0.31869	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	T;T;T	0.48522	0.81;0.81;0.81	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.57592	0.2064	N	0.19112	0.55	0.80722	D	1	D;B	0.71674	0.998;0.059	D;B	0.69824	0.966;0.038	T	0.58901	-0.7554	10	0.59425	D	0.04	-0.8987	20.8794	0.99867	0.0:0.0:1.0:0.0	.	462;462	Q01826-2;Q01826	.;SATB1_HUMAN	H	462	ENSP00000341024:P462H;ENSP00000399708:P462H;ENSP00000399518:P462H	ENSP00000341024:P462H	P	-	2	0	SATB1	18402929	1.000000	0.71417	0.996000	0.52242	0.229000	0.25112	7.876000	0.87215	2.941000	0.99782	0.655000	0.94253	CCC	.	.		0.512	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		T	18427925	G	T	18427925	3	4	112	1	0	0	0	0	1	0	0	0	13868	1232	43	3	922	3	SATB1	3	18427925	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	2159048	18427925	179594505	221	16842										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19559532	19559532	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctcttcatcaaagcagaggAgaccaagcagcagataaaca	8	10	3	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:19559532A>G	ENST00000328405.2	+	15	2851	c.2585A>G	c.(2584-2586)gAg>gGg	p.E862G		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	862					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						AAAGCAGAGGAGACCAAGCAG	0.408																																					p.E862G	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.A2585G						.						114	113	113					3																	19559532		2203	4300	6503	SO:0001583	missense	131096	exon15			CAGAGGAGACCAA	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2585A>G	chr3.hg19:g.19559532A>G	ENSP00000328813:p.Glu862Gly	96.0	0.0		131.0	7.0	NM_144633	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	hg19	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	A	17.67	3.447487	0.63178	.	.	ENSG00000183960	ENST00000328405	D	0.99105	-5.43	5.66	5.66	0.87406	.	0.000000	0.31976	U	0.006779	D	0.97558	0.9200	L	0.54323	1.7	0.80722	D	1	B	0.21606	0.058	B	0.23852	0.049	D	0.96921	0.9674	9	.	.	.	.	14.7558	0.69564	1.0:0.0:0.0:0.0	.	862	Q96L42	KCNH8_HUMAN	G	862	ENSP00000328813:E862G	.	E	+	2	0	KCNH8	19534536	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.652000	0.67959	2.277000	0.76020	0.528000	0.53228	GAG	.	.		0.408	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		G	19559532	A	G	19559532	3	3	112	1	0	0	0	0	1	0	0	0	8047	304	11	2	2643	2	KCNH8	3	19559532	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1131607	19559532	178462898	222	16843										
EFHB	151651	hgsc.bcm.edu	37	chr3	19924173	19924173	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtcactgatgcgacgaattcGgggagcaggaatgtcagatc					rs370616437		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:19924173delG	ENST00000295824.9	-	12	2358	c.2197delC	c.(2197-2199)cgafs	p.R733fs	EFHB_ENST00000344838.4_Frame_Shift_Del_p.R603fs	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	733							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						CGACGAATTCGGGGAGCAGGA	0.423																																					p.R733fs		Atlas-INDEL	.											EFHB_ENST00000295824,NS,carcinoma,0,4	EFHB	186	.	0			c.2198delG						.						97	80	85					3																	19924173		2203	4300	6503	SO:0001589	frameshift_variant	151651	exon12			.	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"EF-hand domain containing"	26330	protein-coding gene	gene with protein product	"cilia and flagella associated protein 21"					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.2197delC	chr3.hg19:g.19924173delG	ENSP00000295824:p.Arg733fs	91.0	0.0		144.0	10.0	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Frame_Shift_Del	DEL	ENST00000295824.9	hg19	CCDS33715.2																																																																																			.	.		0.423	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715		-	19924173	G	-	19924173	7	5	112	1	0	1	0	1	0	0	0	0	4947	1124	39	0	312	0	EFHB	3	19924173	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	364641	19924173	178098257	223	16844										
TOP2B	7155	hgsc.bcm.edu	37	chr3	25679663	25679663	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attcagactttacctgtaacTtttttctcatcatcatcata							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:25679663delT	ENST00000264331.4	-	5	533	c.534delA	c.(532-534)aaafs	p.K178fs	TOP2B_ENST00000435706.2_Frame_Shift_Del_p.K173fs	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	178					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	TACCTGTAACTTTTTTCTCAT	0.313																																					p.V174fs		Atlas-INDEL	.											.	TOP2B	98	.	0			c.520delG						.						70	62	65					3																	25679663		1788	4049	5837	SO:0001589	frameshift_variant	7155	exon5			.	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.534delA	chr3.hg19:g.25679663delT	ENSP00000264331:p.Lys178fs	192.0	0.0		275.0	20.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Frame_Shift_Del	DEL	ENST00000264331.4	hg19																																																																																				.	.		0.313	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				-	25679663	T	-	25679663	7	5	112	1	0	1	0	1	0	0	0	0	16381	1606	56	0	4474	0	TOP2B	3	25679663	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	5755490	25679663	172342767	224	16845										
NEK10	152110	hgsc.bcm.edu	37	chr3	27335088	27335088	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taacctcataccttttaaagAgtggtctgtttctttccata	5	9	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:27335088A>G	ENST00000429845.2	-	17	1726	c.1364T>C	c.(1363-1365)cTc>cCc	p.L455P	NEK10_ENST00000357467.2_5'Flank|NEK10_ENST00000341435.5_Missense_Mutation_p.L455P			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	455					positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CCTTTTAAAGAGTGGTCTGTT	0.348																																					p.L455P		Atlas-SNP	.											.	NEK10	271	.	0			c.T1364C						.						77	67	70					3																	27335088		1568	3582	5150	SO:0001583	missense	152110	exon17			TTAAAGAGTGGTC	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)- related kinase 10"			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1364T>C	chr3.hg19:g.27335088A>G	ENSP00000395849:p.Leu455Pro	59.0	0.0		101.0	5.0	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Missense_Mutation	SNP	ENST00000429845.2	hg19		.	.	.	.	.	.	.	.	.	.	A	18.11	3.551171	0.65311	.	.	ENSG00000163491	ENST00000341435;ENST00000396636	T	0.52526	0.66	5.44	5.44	0.79542	Armadillo-like helical (1);	0.305868	0.31335	N	0.007823	T	0.59459	0.2195	L	0.43152	1.355	0.80722	D	1	D	0.69078	0.997	P	0.62649	0.905	T	0.63056	-0.6722	10	0.87932	D	0	.	15.4989	0.75680	1.0:0.0:0.0:0.0	.	455	Q6ZWH5	NEK10_HUMAN	P	455	ENSP00000343847:L455P	ENSP00000343847:L455P	L	-	2	0	NEK10	27310092	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.591000	0.74090	2.052000	0.61016	0.528000	0.53228	CTC	.	.		0.348	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534		G	27335088	A	G	27335088	3	3	112	1	0	0	0	0	1	0	0	0	10331	304	11	2	810	2	NEK10	3	27335088	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1655425	27335088	170687342	225	16846										
ZCWPW2	152098	hgsc.bcm.edu	37	chr3	28557110	28557110	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgccttatcaaaggagaacaGgggtatgtgaaagcctgtcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:28557110delG	ENST00000383768.2	+	8	970	c.782delG	c.(781-783)aggfs	p.R261fs	ZCWPW2_ENST00000421010.1_Frame_Shift_Del_p.R261fs			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	261							zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						AAGGAGAACAGGGGTATGTGA	0.318																																					p.R261fs		Atlas-INDEL	.											.	ZCWPW2	49	.	0			c.781delA						.						46	48	47					3																	28557110		2203	4296	6499	SO:0001589	frameshift_variant	152098	exon7			.	BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.782delG	chr3.hg19:g.28557110delG	ENSP00000373278:p.Arg261fs	126.0	0.0		200.0	12.0	NM_001040432		Frame_Shift_Del	DEL	ENST00000383768.2	hg19	CCDS33723.1																																																																																			.	.		0.318	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384		-	28557110	G	-	28557110	7	5	112	1	0	1	0	1	0	0	0	0	17613	1000	35	0	804	0	ZCWPW2	3	28557110	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1222022	28557110	169465320	226	16847										
RBMS3	27303	hgsc.bcm.edu	37	chr3	29628669	29628669	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcggtagcatctctcaaggcAaatggcgtgcaggcacagat					rs199714122		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:29628669delA	ENST00000383767.2	+	4	708	c.372delA	c.(370-372)gcafs	p.A124fs	RBMS3_ENST00000452462.1_Frame_Shift_Del_p.A124fs|RBMS3_ENST00000383766.2_Frame_Shift_Del_p.A123fs|RBMS3_ENST00000396583.3_Frame_Shift_Del_p.A124fs|RBMS3_ENST00000273139.9_Frame_Shift_Del_p.A124fs|RBMS3_ENST00000434693.2_Frame_Shift_Del_p.A123fs|RBMS3_ENST00000445033.1_Frame_Shift_Del_p.A124fs|RBMS3_ENST00000456853.1_Frame_Shift_Del_p.A124fs			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	124	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				CTCTCAAGGCAAATGGCGTGC	0.408																																					p.A124fs		Atlas-INDEL	.											.	RBMS3	62	.	0			c.371delC						.						133	137	135					3																	29628669		2203	4300	6503	SO:0001589	frameshift_variant	27303	exon4			.	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"RNA binding motif (RRM) containing"	13427	protein-coding gene	gene with protein product	"RNA-binding protein"	605786	"RNA binding motif, single stranded interacting protein"			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.372delA	chr3.hg19:g.29628669delA	ENSP00000373277:p.Ala124fs	91.0	0.0		143.0	10.0	NM_001177712	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Frame_Shift_Del	DEL	ENST00000383767.2	hg19	CCDS33724.1																																																																																			.	.		0.408	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792		-	29628669	A	-	29628669	7	5	112	1	0	1	0	1	0	0	0	0	13165	117	5	0	386	0	RBMS3	3	29628669	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1071559	29628669	168393761	227	16848										
STT3B	201595	hgsc.bcm.edu	37	chr3	31656646	31656646	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atattatcaatgcagataccTtttgtgggattccagccaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:31656646delT	ENST00000295770.2	+	6	1136	c.927delT	c.(925-927)cctfs	p.P309fs	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	309					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						TGCAGATACCTTTTGTGGGAT	0.338																																					p.P309fs		Atlas-INDEL	.											.	STT3B	52	.	0			c.926delC						.						105	100	102					3																	31656646		2203	4299	6502	SO:0001589	frameshift_variant	201595	exon6			.	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"source of immunodominant MHC associated peptides", "dolichyl-diphosphooligosaccharide protein glycotransferase"	608605	"STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.927delT	chr3.hg19:g.31656646delT	ENSP00000295770:p.Pro309fs	130.0	0.0		155.0	12.0	NM_178862	Q96JZ4|Q96KY7	Frame_Shift_Del	DEL	ENST00000295770.2	hg19	CCDS2650.1																																																																																			.	.		0.338	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862		-	31656646	T	-	31656646	7	5	112	1	0	1	0	1	0	0	0	0	15349	1596	56	0	949	0	STT3B	3	31656646	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2027977	31656646	166365784	228	16849										
STT3B	201595	hgsc.bcm.edu	37	chr3	31665200	31665200	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaacatgcaactgaacaggAaaaaactgaagagggattag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:31665200delA	ENST00000295770.2	+	11	1783	c.1574delA	c.(1573-1575)gaafs	p.E525fs		NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	525					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						ACTGAACAGGAAAAAACTGAA	0.358																																					p.E525fs		Atlas-INDEL	.											.	STT3B	52	.	0			c.1573delG						.						166	144	152					3																	31665200		2203	4300	6503	SO:0001589	frameshift_variant	201595	exon11			.	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"source of immunodominant MHC associated peptides", "dolichyl-diphosphooligosaccharide protein glycotransferase"	608605	"STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.1574delA	chr3.hg19:g.31665200delA	ENSP00000295770:p.Glu525fs	133.0	0.0		156.0	10.0	NM_178862	Q96JZ4|Q96KY7	Frame_Shift_Del	DEL	ENST00000295770.2	hg19	CCDS2650.1																																																																																			.	.		0.358	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862		-	31665200	A	-	31665200	7	5	112	1	0	1	0	1	0	0	0	0	15349	246	9	0	1616	0	STT3B	3	31665200	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	8554	31665200	166357230	229	16850										
STT3B	201595	hgsc.bcm.edu	37	chr3	31674442	31674442	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcagctggattttcgtacaCccccaggttttgaccgaaca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:31674442delC	ENST00000295770.2	+	15	2412	c.2203delC	c.(2203-2205)cccfs	p.P736fs		NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	736					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						TTTTCGTACACCCCCAGGTTT	0.363																																					p.T734fs		Atlas-INDEL	.											.	STT3B	52	.	0			c.2202delA						.						126	127	126					3																	31674442		2203	4300	6503	SO:0001589	frameshift_variant	201595	exon15			.	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"source of immunodominant MHC associated peptides", "dolichyl-diphosphooligosaccharide protein glycotransferase"	608605	"STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.2203delC	chr3.hg19:g.31674442delC	ENSP00000295770:p.Pro736fs	133.0	0.0		174.0	11.0	NM_178862	Q96JZ4|Q96KY7	Frame_Shift_Del	DEL	ENST00000295770.2	hg19	CCDS2650.1																																																																																			.	.		0.363	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862		-	31674442	C	-	31674442	7	5	112	1	0	1	0	1	0	0	0	0	15349	507	18	0	2261	0	STT3B	3	31674442	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	9242	31674442	166347988	230	16851										
OSBPL10	114884	hgsc.bcm.edu	37	chr3	31712394	31712394	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcctccgagctccacccacGggatggtgagaatggaccgg	13	13	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:31712394G>T	ENST00000396556.2	-	9	1930	c.1808C>A	c.(1807-1809)cCg>cAg	p.P603Q	OSBPL10_ENST00000438237.2_Missense_Mutation_p.P539Q	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	603					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)	p.P603L(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		CTCCACCCACGGGATGGTGAG	0.567																																					p.P603Q		Atlas-SNP	.											OSBPL10_ENST00000396556,extremity,malignant_melanoma,0,6	OSBPL10	160	.	2	Substitution - Missense(2)	skin(2)	c.C1808A						.						131	115	120					3																	31712394		2203	4300	6503	SO:0001583	missense	114884	exon9			ACCCACGGGATGG	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.1808C>A	chr3.hg19:g.31712394G>T	ENSP00000379804:p.Pro603Gln	140.0	0.0		197.0	0.0	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	hg19	CCDS2651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.72|17.72	3.458058|3.458058	0.63401|0.63401	.|.	.|.	ENSG00000144645|ENSG00000144645	ENST00000396556;ENST00000438237|ENST00000429492	T;T|.	0.32753|.	1.44;1.44|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87565|0.87565	0.6209|0.6209	H|H	0.95004|0.95004	3.61|3.61	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	D|D	0.90774|0.90774	0.4674|0.4674	10|5	0.72032|.	D|.	0.01|.	-18.8515|-18.8515	19.3207|19.3207	0.94237|0.94237	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	539;603;371|.	B4E212;Q9BXB5;Q59ED9|.	.;OSB10_HUMAN;.|.	Q|S	603;539|372	ENSP00000379804:P603Q;ENSP00000406124:P539Q|.	ENSP00000379804:P603Q|.	P|R	-|-	2|1	0|0	OSBPL10|OSBPL10	31687398|31687398	1.000000|1.000000	0.71417|0.71417	0.841000|0.841000	0.33234|0.33234	0.009000|0.009000	0.06853|0.06853	9.869000|9.869000	0.99810|0.99810	2.550000|2.550000	0.86006|0.86006	0.557000|0.557000	0.71058|0.71058	CCG|CGT	.	.		0.567	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			T	31712394	G	T	31712394	3	4	112	1	0	0	0	0	1	0	0	0	11284	1116	39	1	502	1	OSBPL10	3	31712394	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	37952	31712394	166310036	231	16852										
TRANK1	9881	hgsc.bcm.edu	37	chr3	36897154	36897154	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcctcaaaagaaccctttagAaaagattttatttctttcca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:36897154delA	ENST00000429976.2	-	12	4174	c.3927delT	c.(3925-3927)tttfs	p.F1309fs	TRANK1_ENST00000301807.6_Frame_Shift_Del_p.F759fs|TRANK1_ENST00000428977.2_Frame_Shift_Del_p.F759fs	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1309							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						AACCCTTTAGAAAAGATTTTA	0.433																																					p.L1310X		Atlas-INDEL	.											.	TRANK1	398	.	0			c.3928delC						.						118	116	117					3																	36897154		1829	4083	5912	SO:0001589	frameshift_variant	9881	exon12			.	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.3927delT	chr3.hg19:g.36897154delA	ENSP00000416168:p.Phe1309fs	118.0	0.0		170.0	12.0	NM_014831	Q8N8K0	Frame_Shift_Del	DEL	ENST00000429976.2	hg19	CCDS46789.2																																																																																			.	.		0.433	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		-	36897154	A	-	36897154	7	5	112	1	0	1	0	1	0	0	0	0	16469	243	9	0	4898	0	TRANK1	3	36897154	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5184760	36897154	161125276	232	16853										
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37149563	37149563	+	Splice_Site	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcagagactagacagctcaCccctggactgcttcgggctg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:37149563delC	ENST00000336686.4	-	13	795		c.e13+1		LRRFIP2_ENST00000421307.1_Splice_Site|LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000396428.2_Intron|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000440230.1_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2						Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						AGACAGCTCACCCCTGGACTG	0.378																																					.		Atlas-INDEL	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.714+2G>-						.						88	84	85					3																	37149563		2203	4300	6503	SO:0001630	splice_region_variant	9209	exon15			.	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.714+1G>-	chr3.hg19:g.37149563delC		110.0	0.0		154.0	10.0	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Splice_Site	DEL	ENST00000336686.4	hg19	CCDS2664.1																																																																																			.	.		0.378	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	Intron	-	37149563	C	-	37149563	8	5	112	1	0	1	0	1	0	0	1	0	9037	521	18	0	1514	0	LRRFIP2	3	37149563	Splice_Site	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	252409	37149563	160872867	233	16854										
OXSR1	9943	hgsc.bcm.edu	37	chr3	38207429	38207429	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggacgattacgagctgcaggAggtgatcggtgagagcaggc	18	7	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:38207429A>G	ENST00000446845.1	+	1	434	c.62A>G	c.(61-63)gAg>gGg	p.E21G	OXSR1_ENST00000311806.3_Missense_Mutation_p.E21G|OXSR1_ENST00000492714.1_Intron					oxidative stress responsive 1											skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GAGCTGCAGGAGGTGATCGGT	0.716																																					p.E21G		Atlas-SNP	.											.	OXSR1	74	.	0			c.A62G						.						22	23	22					3																	38207429		2202	4298	6500	SO:0001583	missense	9943	exon1			TGCAGGAGGTGAT	AB017642	CCDS2675.1	3p22.2	2013-05-17	2013-05-17	2004-11-26	ENSG00000172939	ENSG00000172939			8508	protein-coding gene	gene with protein product		604046	"oxidative-stress responsive 1"	OSR1		10083736	Standard	XM_005265638		Approved	KIAA1101	uc003chy.3	O95747	OTTHUMG00000131084	ENST00000446845.1:c.62A>G	chr3.hg19:g.38207429A>G	ENSP00000415851:p.Glu21Gly	130.0	0.0		189.0	8.0	NM_005109		Missense_Mutation	SNP	ENST00000446845.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.6	4.172832	0.78452	.	.	ENSG00000172939	ENST00000446845;ENST00000311806	T;T	0.23754	1.89;1.89	3.89	2.72	0.32119	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.051096	0.85682	N	0.000000	T	0.28699	0.0711	L	0.59436	1.845	0.80722	D	1	P	0.41498	0.752	P	0.45119	0.47	T	0.03840	-1.0999	10	0.87932	D	0	-5.6688	7.5008	0.27516	0.8933:0.0:0.1067:0.0	.	21	O95747	OXSR1_HUMAN	G	21	ENSP00000415851:E21G;ENSP00000311713:E21G	ENSP00000311713:E21G	E	+	2	0	OXSR1	38182433	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.387000	0.73191	0.674000	0.31244	0.454000	0.30748	GAG	.	.		0.716	OXSR1-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000342708.1	NM_005109		G	38207429	A	G	38207429	3	3	112	1	0	0	0	0	1	0	0	0	11345	304	11	2	64	2	OXSR1	3	38207429	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1057866	38207429	159815001	234	16855										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266867	41266867	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttatggtccatcagctttctAaaaaggaagcttccagacac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:41266867delA	ENST00000349496.5	+	5	818	c.538delA	c.(538-540)aaafs	p.K181fs	CTNNB1_ENST00000396185.3_Frame_Shift_Del_p.K181fs|CTNNB1_ENST00000396183.3_Frame_Shift_Del_p.K181fs|CTNNB1_ENST00000453024.1_Frame_Shift_Del_p.K174fs|CTNNB1_ENST00000405570.1_Frame_Shift_Del_p.K181fs	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	181					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCAGCTTTCTAAAAAGGAAGC	0.418		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S179fs	Colon(6;3 56 14213 18255)	Atlas-INDEL	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	0			c.537delT						.						65	67	66					3																	41266867		2203	4300	6503	SO:0001589	frameshift_variant	1499	exon5	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	.	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.538delA	chr3.hg19:g.41266867delA	ENSP00000344456:p.Lys181fs	122.0	0.0		182.0	12.0	NM_001098210	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Frame_Shift_Del	DEL	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.418	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		-	41266867	A	-	41266867	7	5	112	1	0	1	0	1	0	0	0	0	4018	363	13	0	552	0	CTNNB1	3	41266867	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3059438	41266867	156755563	235	16856										
VIPR1	7433	hgsc.bcm.edu	37	chr3	42573788	42573788	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctgcttcagaaactgcggCccccagatatcaggaagagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:42573788delC	ENST00000325123.4	+	10	1086	c.973delC	c.(973-975)cccfs	p.P326fs	VIPR1-AS1_ENST00000593621.1_RNA|VIPR1-AS1_ENST00000602176.1_RNA|VIPR1_ENST00000433647.1_Frame_Shift_Del_p.P285fs|VIPR1-AS1_ENST00000608869.1_RNA|VIPR1_ENST00000543411.1_Frame_Shift_Del_p.P278fs|VIPR1_ENST00000438259.2_Frame_Shift_Del_p.P116fs|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000610022.1_RNA|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000593611.1_RNA	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	326					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		GAAACTGCGGCCCCCAGATAT	0.557																																					p.R324fs		Atlas-INDEL	.											.	VIPR1	45	.	0			c.972delG						.						143	134	137					3																	42573788		2203	4300	6503	SO:0001589	frameshift_variant	7433	exon10			.	AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12694	protein-coding gene	gene with protein product	"VIP and PACAP receptor 1"	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.973delC	chr3.hg19:g.42573788delC	ENSP00000327246:p.Pro326fs	135.0	0.0		215.0	14.0	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Frame_Shift_Del	DEL	ENST00000325123.4	hg19	CCDS2698.1																																																																																			.	.		0.557	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624		-	42573788	C	-	42573788	7	5	112	1	0	1	0	1	0	0	0	0	17184	739	26	0	1011	0	VIPR1	3	42573788	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1306921	42573788	155448642	236	16857										
KIF15	56992	hgsc.bcm.edu	37	chr3	44835775	44835775	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgaacagagaatcgtctaggTctcatgccgtctttacaatt	8	9	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:44835775T>C	ENST00000326047.4	+	8	855	c.706T>C	c.(706-708)Tct>Cct	p.S236P	AC098649.1_ENST00000459037.1_RNA	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	236	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		ATCGTCTAGGTCTCATGCCGT	0.403																																					p.S236P		Atlas-SNP	.											.	KIF15	103	.	0			c.T706C						.						158	139	145					3																	44835775		2203	4300	6503	SO:0001583	missense	56992	exon8			TCTAGGTCTCATG	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.706T>C	chr3.hg19:g.44835775T>C	ENSP00000324020:p.Ser236Pro	114.0	0.0		165.0	7.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	hg19	CCDS33744.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.436083	0.83885	.	.	ENSG00000163808	ENST00000326047;ENST00000481166;ENST00000396031	D;D	0.87966	-2.32;-2.32	5.1	5.1	0.69264	Kinesin, motor domain (5);	0.000000	0.51477	D	0.000094	D	0.96163	0.8749	H	0.98646	4.29	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97817	1.0254	10	0.87932	D	0	.	14.882	0.70540	0.0:0.0:0.0:1.0	.	236	Q9NS87	KIF15_HUMAN	P	236;8;235	ENSP00000324020:S236P;ENSP00000425499:S8P	ENSP00000324020:S236P	S	+	1	0	KIF15	44810779	1.000000	0.71417	0.937000	0.37676	0.738000	0.42128	7.698000	0.84413	1.926000	0.55796	0.533000	0.62120	TCT	.	.		0.403	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			C	44835775	T	C	44835775	3	2	112	1	0	0	0	0	1	0	0	0	8286	1667	58	2	736	2	KIF15	3	44835775	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2261987	44835775	153186655	237	16858										
TREX1	11277	hgsc.bcm.edu	37	chr3	48508447	48508447	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aatggtgaccgctacgacttCcccctgctccaagcagagct					rs78762691		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:48508447delC	ENST00000422277.2	+	1	1219	c.558delC	c.(556-558)ttcfs	p.F186fs	TREX1_ENST00000436480.2_Frame_Shift_Del_p.F131fs|TREX1_ENST00000444177.1_Frame_Shift_Del_p.F121fs|TREX1_ENST00000433541.1_5'UTR|SHISA5_ENST00000465449.1_5'Flank|TREX1_ENST00000456089.1_Intron|TREX1_ENST00000296443.9_Frame_Shift_Del_p.F131fs|TREX1_ENST00000492235.1_3'UTR	NM_016381.4	NP_057465.1	Q9NSU2	TREX1_HUMAN	three prime repair exonuclease 1	186					cell death (GO:0008219)|cellular response to interferon-beta (GO:0035458)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|innate immune response (GO:0045087)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	endoplasmic reticulum membrane (GO:0005789)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|3'-5'-exodeoxyribonuclease activity (GO:0008296)|adenyl deoxyribonucleotide binding (GO:0032558)|double-stranded DNA binding (GO:0003690)|exodeoxyribonuclease III activity (GO:0008853)|metal ion binding (GO:0046872)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein homodimerization activity (GO:0042803)|single-stranded DNA binding (GO:0003697)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|skin(3)	9				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GCTACGACTTCCCCCTGCTCC	0.607																																					p.F186fs		Atlas-INDEL	.											.	TREX1	17	.	0			c.557delT						.						72	70	71					3																	48508447		2203	4300	6503	SO:0001589	frameshift_variant	11277	exon1			.	AF151105	CCDS2769.1, CCDS59451.1	3p21.31	2014-09-17			ENSG00000213689	ENSG00000213689			12269	protein-coding gene	gene with protein product		606609	"Aicardi-Goutieres syndrome 1"	AGS1		10391904, 10393201, 16845398	Standard	NM_033629		Approved	DRN3	uc010hka.4	Q9NSU2	OTTHUMG00000156205	ENST00000422277.2:c.558delC	chr3.hg19:g.48508447delC	ENSP00000390478:p.Phe186fs	111.0	0.0		152.0	10.0	NM_016381	B2RCN9|Q8TEU2|Q9BPW1|Q9Y4X2	Frame_Shift_Del	DEL	ENST00000422277.2	hg19	CCDS43086.1																																																																																			.	.		0.607	TREX1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_016381		-	48508447	C	-	48508447	7	5	112	1	0	1	0	1	0	0	0	0	16491	854	30	0	560	0	TREX1	3	48508447	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	3672672	48508447	149513983	238	16859										
PFKFB4	5210	hgsc.bcm.edu	37	chr3	48561220	48561220	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cattctcttgcctctccagcTccatgatgacaggctccagt	7	15	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:48561220T>C	ENST00000232375.3	-	11	1248	c.1136A>G	c.(1135-1137)gAg>gGg	p.E379G	PFKFB4_ENST00000536104.1_Missense_Mutation_p.E368G|PFKFB4_ENST00000383734.2_Missense_Mutation_p.E344G|PFKFB4_ENST00000490115.1_5'UTR|PFKFB4_ENST00000416568.1_Missense_Mutation_p.E372G|PFKFB4_ENST00000541519.1_Missense_Mutation_p.E345G	NM_004567.2	NP_004558.1	Q16877	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	379	Fructose-2,6-bisphosphatase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		CCTCTCCAGCTCCATGATGAC	0.627																																					p.E379G		Atlas-SNP	.											.	PFKFB4	39	.	0			c.A1136G						.						116	98	104					3																	48561220		2203	4300	6503	SO:0001583	missense	5210	exon11			TCCAGCTCCATGA	BC010269	CCDS2771.1	3p22-p21	2004-03-02			ENSG00000114268	ENSG00000114268			8875	protein-coding gene	gene with protein product		605320				8830046, 10095107	Standard	NM_004567		Approved		uc003ctv.3	Q16877	OTTHUMG00000133528	ENST00000232375.3:c.1136A>G	chr3.hg19:g.48561220T>C	ENSP00000232375:p.Glu379Gly	143.0	0.0		198.0	8.0	NM_004567	Q5S3G5|Q5XLC2|Q64EX5	Missense_Mutation	SNP	ENST00000232375.3	hg19	CCDS2771.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.686400	0.88639	.	.	ENSG00000114268	ENST00000232375;ENST00000536104;ENST00000416568;ENST00000383734;ENST00000541519	T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84	4.71	4.71	0.59529	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	D	0.000000	D	0.88001	0.6320	M	0.91768	3.24	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.87578	0.998;0.986;0.998;0.992	D	0.90273	0.4309	10	0.87932	D	0	-1.8298	12.1756	0.54184	0.0:0.0:0.0:1.0	.	368;344;372;379	B7Z5C3;Q5XLC2;Q66S35;Q16877	.;.;.;F264_HUMAN	G	379;368;372;344;345	ENSP00000232375:E379G;ENSP00000438908:E368G;ENSP00000388394:E372G;ENSP00000437446:E345G	ENSP00000232375:E379G	E	-	2	0	PFKFB4	48536224	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.825000	0.86693	1.961000	0.56991	0.460000	0.39030	GAG	.	.		0.627	PFKFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257503.2	NM_004567		C	48561220	T	C	48561220	3	2	112	1	0	0	0	0	1	0	0	0	11772	1551	54	2	289	2	PFKFB4	3	48561220	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	52773	48561220	149461210	239	16860										
MST1	327	hgsc.bcm.edu	37	chr3	49722913	49722913	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caactcctaacctggggggtCcaggattgatggcggctggt	15	10	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:49722913C>T	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000449682.2_Missense_Mutation_p.D472N|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCTGGGGGGTCCAGGATTGAT	0.592																																					p.D472N		Atlas-SNP	.											.	MST1	84	.	0			c.G1414A						.						29	32	31					3																	49722913		2202	4299	6501	SO:0001628	intergenic_variant	4485	exon12			GGGGGTCCAGGAT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		chr3.hg19:g.49722913C>T		262.0	0.0		552.0	46.0	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	C	10.90	1.481708	0.26598	.	.	ENSG00000173531	ENST00000449682	T	0.79940	-1.32	4.78	2.98	0.34508	.	0.707688	0.11995	N	0.509451	T	0.60392	0.2265	N	0.08118	0	0.80722	D	1	B	0.21753	0.06	B	0.26094	0.066	T	0.44436	-0.9328	10	0.10636	T	0.68	.	8.1354	0.31052	0.0:0.8059:0.0:0.1941	.	472	G3XAK1	.	N	472	ENSP00000414287:D472N	ENSP00000414287:D472N	D	-	1	0	MST1	49697917	1.000000	0.71417	0.995000	0.50966	0.784000	0.44337	3.079000	0.50104	0.689000	0.31550	0.655000	0.94253	GAC	.	.		0.592	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			T	49722913	C	T	49722913	1	4	112	0	1	0	0	0	0	0	0	0	9899	855	30	3		3	MST1	3	49722913	IGR	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1161693	49722913	148299517	240	16861										
CDHR4	389118	hgsc.bcm.edu	37	chr3	49830724	49830724	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgaaatgggggctcacactcGggggcatggtcattcacatc					rs368005921		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:49830724delG	ENST00000412678.2	-	13	1652	c.1644delC	c.(1642-1644)cccfs	p.P548fs	CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	548	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						GCTCACACTCGGGGGCATGGT	0.572																																					p.E549fs		Atlas-INDEL	.											.	CDHR4	37	.	0			c.1645delG						.						55	58	57					3																	49830724		692	1591	2283	SO:0001589	frameshift_variant	389118	exon13			.		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"Cadherins / Cadherin-related"	34527	protein-coding gene	gene with protein product			"cadherin-like 29"	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.1644delC	chr3.hg19:g.49830724delG	ENSP00000391409:p.Pro548fs	52.0	0.0		107.0	10.0	NM_001007540	Q6UXT0	Frame_Shift_Del	DEL	ENST00000412678.2	hg19	CCDS46829.1																																																																																			.	.		0.572	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540		-	49830724	G	-	49830724	7	5	112	1	0	1	0	1	0	0	0	0	3123	1103	39	0	750	0	CDHR4	3	49830724	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	107811	49830724	148191706	241	16862										
CDHR4	389118	hgsc.bcm.edu	37	chr3	49836290	49836290	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggagttctaggcctgggaggAgcagagtgtacagccgagcc	17	9	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:49836290A>G	ENST00000412678.2	-	4	472	c.464T>C	c.(463-465)cTc>cCc	p.L155P	CDHR4_ENST00000343366.4_Silent_p.A180A|CDHR4_ENST00000487256.1_Missense_Mutation_p.L155P	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	155					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						GCCTGGGAGGAGCAGAGTGTA	0.597																																					p.L155P		Atlas-SNP	.											.	CDHR4	37	.	0			c.T464C						.						36	41	39					3																	49836290		2024	4179	6203	SO:0001583	missense	389118	exon4			GGGAGGAGCAGAG		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"Cadherins / Cadherin-related"	34527	protein-coding gene	gene with protein product			"cadherin-like 29"	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.464T>C	chr3.hg19:g.49836290A>G	ENSP00000391409:p.Leu155Pro	115.0	0.0		142.0	7.0	NM_001007540	Q6UXT0	Missense_Mutation	SNP	ENST00000412678.2	hg19	CCDS46829.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.484399	0.44147	.	.	ENSG00000187492	ENST00000412678;ENST00000487256	T;T	0.57907	0.37;0.58	4.81	4.81	0.61882	.	.	.	.	.	T	0.59004	0.2162	L	0.32530	0.975	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.54715	-0.8252	9	0.25751	T	0.34	-7.2563	12.0308	0.53396	1.0:0.0:0.0:0.0	.	155;155	E9PFE8;A6H8M9	.;CDHR4_HUMAN	P	155	ENSP00000391409:L155P;ENSP00000420677:L155P	ENSP00000391409:L155P	L	-	2	0	CDHR4	49811294	0.985000	0.35326	1.000000	0.80357	0.162000	0.22319	4.665000	0.61547	1.932000	0.55993	0.482000	0.46254	CTC	.	.		0.597	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540		G	49836290	A	G	49836290	3	3	112	1	0	0	0	0	1	0	0	0	3123	304	11	2	1966	2	CDHR4	3	49836290	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	5566	49836290	148186140	242	16863										
RBM6	10180	hgsc.bcm.edu	37	chr3	50095987	50095987	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atggctttattgacctcgacTcccatgcggtgagtttcctc	9	12	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:50095987T>C	ENST00000266022.4	+	10	2381	c.2122T>C	c.(2122-2124)Tcc>Ccc	p.S708P	RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000539992.1_Missense_Mutation_p.S50P|RBM6_ENST00000442092.1_Missense_Mutation_p.S186P|RBM6_ENST00000443081.1_Missense_Mutation_p.S576P|RBM6_ENST00000422955.1_Missense_Mutation_p.S186P	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	708					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TGACCTCGACTCCCATGCGGT	0.542																																					p.S708P		Atlas-SNP	.											.	RBM6	85	.	0			c.T2122C						.						156	139	145					3																	50095987		2203	4300	6503	SO:0001583	missense	10180	exon10			CTCGACTCCCATG	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"RNA binding motif (RRM) containing", "G patch domain containing"	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.2122T>C	chr3.hg19:g.50095987T>C	ENSP00000266022:p.Ser708Pro	51.0	0.0		86.0	4.0	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	hg19	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.824828	0.90955	.	.	ENSG00000004534	ENST00000442092;ENST00000266022;ENST00000443081;ENST00000539992;ENST00000422955	T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75	5.71	5.71	0.89125	Nucleotide-binding, alpha-beta plait (1);	0.982328	0.08318	N	0.964376	T	0.31827	0.0809	L	0.55990	1.75	0.48830	D	0.999712	D;D	0.76494	0.999;0.995	D;P	0.70487	0.969;0.874	T	0.00080	-1.2110	9	.	.	.	-1.9563	16.0336	0.80603	0.0:0.0:0.0:1.0	.	576;708	E9PGM9;P78332	.;RBM6_HUMAN	P	186;708;576;50;186	ENSP00000393530:S186P;ENSP00000266022:S708P;ENSP00000396466:S576P;ENSP00000443165:S50P;ENSP00000392939:S186P	.	S	+	1	0	RBM6	50070991	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.086000	0.57664	2.189000	0.69895	0.529000	0.55759	TCC	.	.		0.542	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		C	50095987	T	C	50095987	3	2	112	1	0	0	0	0	1	0	0	0	13159	1551	54	2	2156	2	RBM6	3	50095987	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	259697	50095987	147926443	243	16864										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51198017	51198017	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgaacgactcaaagaaaggTcctcctcacctgcactacag	7	14	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:51198017T>C	ENST00000266037.9	+	12	944	c.921T>C	c.(919-921)ggT>ggC	p.G307G		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	307					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		CAAAGAAAGGTCCTCCTCACC	0.493																																					p.G307G		Atlas-SNP	.											.	DOCK3	397	.	0			c.T921C						.						66	67	66					3																	51198017		2054	4192	6246	SO:0001819	synonymous_variant	1795	exon12			GAAAGGTCCTCCT	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.921T>C	chr3.hg19:g.51198017T>C		72.0	0.0		127.0	6.0	NM_004947	O15017	Silent	SNP	ENST00000266037.9	hg19	CCDS46835.1																																																																																			.	.		0.493	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		C	51198017	T	C	51198017	2	2	112	1	0	0	0	0	0	0	0	1	4690	1654	58	2		2	DOCK3	3	51198017	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1102030	51198017	146824413	244	16865										
NT5DC2	64943	hgsc.bcm.edu	37	chr3	52562508	52562508	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atagtgggatgtgctgggtaCccccatacagctcaatcacc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:52562508delC	ENST00000307076.4	-	5	885	c.485delG	c.(484-486)ggtfs	p.G162fs	NT5DC2_ENST00000459839.1_Frame_Shift_Del_p.G174fs|NT5DC2_ENST00000490681.1_5'Flank|NT5DC2_ENST00000307092.4_Frame_Shift_Del_p.G103fs|NT5DC2_ENST00000422318.2_Frame_Shift_Del_p.G199fs	NM_022908.2	NP_075059.1	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2	162							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(1)|lung(3)|prostate(1)|stomach(1)	6				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)		GTGCTGGGTACCCCCATACAG	0.577																																					p.G199fs		Atlas-INDEL	.											.	NT5DC2	35	.	0			c.597delT						.						105	94	98					3																	52562508		2203	4300	6503	SO:0001589	frameshift_variant	64943	exon5			.	AF131781	CCDS2858.1, CCDS46843.1	3p21.1	2006-02-03			ENSG00000168268	ENSG00000168268			25717	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_022908		Approved	FLJ12442	uc003den.3	Q9H857	OTTHUMG00000158626	ENST00000307076.4:c.485delG	chr3.hg19:g.52562508delC	ENSP00000302468:p.Gly162fs	250.0	0.0		406.0	26.0	NM_001134231	C9JTZ6|E9PAL9|O95888|Q96C80|Q9H9Z8	Frame_Shift_Del	DEL	ENST00000307076.4	hg19	CCDS2858.1																																																																																			.	.		0.577	NT5DC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000351509.1	NM_022908		-	52562508	C	-	52562508	7	5	112	1	0	1	0	1	0	0	0	0	10700	507	18	0	1117	0	NT5DC2	3	52562508	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1364491	52562508	145459922	245	16866										
ITIH4	3700	hgsc.bcm.edu	37	chr3	52860860	52860860	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttcagcagcagctcgtacaCccccaaacgccgcttgagca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:52860860delC	ENST00000266041.4	-	4	562	c.466delG	c.(466-468)gtgfs	p.V156fs	ITIH4_ENST00000406595.1_Frame_Shift_Del_p.V156fs|ITIH4_ENST00000485816.1_Frame_Shift_Del_p.V156fs|ITIH4-AS1_ENST00000478366.1_RNA|RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000434759.3_Frame_Shift_Del_p.V68fs|ITIH4_ENST00000346281.5_Frame_Shift_Del_p.V156fs	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	156					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		AGCTCGTACACCCCCAAACGC	0.592																																					p.V156fs		Atlas-INDEL	.											.	ITIH4	74	.	0			c.467delT						.						60	59	59					3																	52860860		2203	4300	6503	SO:0001589	frameshift_variant	3700	exon4			.	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"plasma Kallikrein-sensitive glycoprotein"	600564	"inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.466delG	chr3.hg19:g.52860860delC	ENSP00000266041:p.Val156fs	143.0	0.0		196.0	12.0	NM_002218	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Frame_Shift_Del	DEL	ENST00000266041.4	hg19	CCDS2865.1																																																																																			.	.		0.592	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218		-	52860860	C	-	52860860	7	5	112	1	0	1	0	1	0	0	0	0	7915	507	18	0	2410	0	ITIH4	3	52860860	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	298352	52860860	145161570	246	16867										
CHDH	55349	hgsc.bcm.edu	37	chr3	53852175	53852175	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagggcttcctgtgcaaaaaTttctctggtgagcttcacac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:53852175delT	ENST00000315251.6	-	9	1851	c.1414delA	c.(1414-1416)attfs	p.I472fs		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	472					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	TGTGCAAAAATTTCTCTGGTG	0.517																																					p.I472fs		Atlas-INDEL	.											.	CHDH	34	.	0			c.1415delT						.						48	47	47					3																	53852175		2203	4300	6503	SO:0001589	frameshift_variant	55349	exon9			.	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.1414delA	chr3.hg19:g.53852175delT	ENSP00000319851:p.Ile472fs	105.0	0.0		155.0	11.0	NM_018397	Q9NY17	Frame_Shift_Del	DEL	ENST00000315251.6	hg19	CCDS2873.1																																																																																			.	.		0.517	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		-	53852175	T	-	53852175	7	5	112	1	0	1	0	1	0	0	0	0	3335	1493	52	0	374	0	CHDH	3	53852175	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	991315	53852175	144170255	247	16868										
C3orf63	23272	hgsc.bcm.edu	37	chr3	56694990	56694990	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ataaaacagtgctggagggaTtttctgtttcagatgatcaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:56694990delT	ENST00000493960.2	-	10	1226	c.1216delA	c.(1216-1218)atcfs	p.I406fs	FAM208A_ENST00000355628.5_Frame_Shift_Del_p.I406fs|FAM208A_ENST00000431842.2_Frame_Shift_Del_p.I10fs	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	406							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						GCTGGAGGGATTTTCTGTTTC	0.303																																					p.I406fs		Atlas-INDEL	.											.	FAM208A	113	.	0			c.1217delT						.						111	111	111					3																	56694990		2202	4299	6501	SO:0001589	frameshift_variant	23272	exon10			.	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 63"	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1216delA	chr3.hg19:g.56694990delT	ENSP00000417509:p.Ile406fs	131.0	0.0		230.0	16.0	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Frame_Shift_Del	DEL	ENST00000493960.2	hg19	CCDS46853.1																																																																																			.	.		0.303	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		-	56694990	T	-	56694990	7	5	112	1	0	1	0	1	0	0	0	0	2241	1493	52	0	3916	0	C3orf63	3	56694990	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2842815	56694990	141327440	248	16869										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57399487	57399487	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agttaccaatgtccacagtcAaaaaactgtcgtaataattc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:57399487delA	ENST00000351747.2	-	39	6129	c.5949delT	c.(5947-5949)tttfs	p.F1983fs		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1983	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						GTCCACAGTCAAAAAACTGTC	0.294																																					p.D1984fs		Atlas-INDEL	.											.	DNAH12	182	.	0			c.5950delG						.						97	85	89					3																	57399487		692	1590	2282	SO:0001589	frameshift_variant	201625	exon39			.	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.5949delT	chr3.hg19:g.57399487delA	ENSP00000295937:p.Phe1983fs	192.0	0.0		270.0	20.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Frame_Shift_Del	DEL	ENST00000351747.2	hg19																																																																																				.	.		0.294	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		-	57399487	A	-	57399487	7	5	112	1	0	1	0	1	0	0	0	0	4602	127	5	0	3413	0	DNAH12	3	57399487	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	704497	57399487	140622943	249	16870										
FAM116A	201627	hgsc.bcm.edu	37	chr3	57644895	57644895	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccaggcttgtcatgacatgTgggaatccgtacctaaaaga	10	10	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:57644895T>C	ENST00000311128.5	-	8	782	c.712A>G	c.(712-714)Aca>Gca	p.T238A		NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	238					positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										TCATGACATGTGGGAATCCGT	0.393																																					p.T238A		Atlas-SNP	.											.	.	.	.	0			c.A712G						.						173	163	166					3																	57644895		2203	4300	6503	SO:0001583	missense	201627	exon8			GACATGTGGGAAT	AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839		"DENN/MADD domain containing"	26635	protein-coding gene	gene with protein product			"family with sequence similarity 116, member A"	FAM116A		21330364	Standard	NM_152678		Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.712A>G	chr3.hg19:g.57644895T>C	ENSP00000311401:p.Thr238Ala	67.0	0.0		94.0	4.0	NM_152678	Q7Z5T4|Q8N235|Q8TEG8	Missense_Mutation	SNP	ENST00000311128.5	hg19	CCDS33773.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.564656	0.65651	.	.	ENSG00000174839	ENST00000311128	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.43964	0.1271	N	0.25647	0.755	0.58432	D	0.999995	B	0.17038	0.02	B	0.20955	0.032	T	0.37267	-0.9713	9	0.07813	T	0.8	-15.4435	16.0684	0.80907	0.0:0.0:0.0:1.0	.	238	Q8IWF6	F116A_HUMAN	A	238	.	ENSP00000311401:T238A	T	-	1	0	FAM116A	57619935	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.985000	0.70556	2.272000	0.75746	0.460000	0.39030	ACA	.	.		0.393	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351594.1	NM_152678		C	57644895	T	C	57644895	3	2	112	1	0	0	0	0	1	0	0	0	5412	1696	59	2	1166	2	FAM116A	3	57644895	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	245408	57644895	140377535	250	16871										
FLNB	2317	hgsc.bcm.edu	37	chr3	58107010	58107010	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggagttcaccgttgataccaGgggggcaggaggccagggga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:58107010delG	ENST00000295956.4	+	20	3071	c.2906delG	c.(2905-2907)aggfs	p.R969fs	FLNB_ENST00000490882.1_Frame_Shift_Del_p.R969fs|FLNB_ENST00000357272.4_Frame_Shift_Del_p.R969fs|FLNB_ENST00000429972.2_Frame_Shift_Del_p.R969fs|FLNB_ENST00000358537.3_Frame_Shift_Del_p.R969fs|FLNB_ENST00000493452.1_Frame_Shift_Del_p.R800fs|FLNB_ENST00000348383.5_Frame_Shift_Del_p.R969fs|FLNB_ENST00000419752.2_Frame_Shift_Del_p.R800fs	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	969					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GTTGATACCAGGGGGGCAGGA	0.572																																					p.R969fs		Atlas-INDEL	.											.	FLNB	430	.	0			c.2905delA						.						135	126	129					3																	58107010		2203	4300	6503	SO:0001589	frameshift_variant	2317	exon20			.	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.2906delG	chr3.hg19:g.58107010delG	ENSP00000295956:p.Arg969fs	134.0	0.0		166.0	10.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Frame_Shift_Del	DEL	ENST00000295956.4	hg19	CCDS2885.1																																																																																			.	.		0.572	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		-	58107010	G	-	58107010	7	5	112	1	0	1	0	1	0	0	0	0	5942	1000	35	0	2984	0	FLNB	3	58107010	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	462115	58107010	139915420	251	16872										
RPP14	11102	hgsc.bcm.edu	37	chr3	58296091	58296091	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgccacatatgaaagagtagTttacaaaaacccttccgagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:58296091delT	ENST00000445193.3	+	2	446	c.35delT	c.(34-36)gttfs	p.V12fs	RPP14_ENST00000477305.1_Intron|RPP14_ENST00000466547.1_Frame_Shift_Del_p.V12fs|RPP14_ENST00000295959.5_Frame_Shift_Del_p.V12fs	NM_001098783.2	NP_001092253.1	O95059	RPP14_HUMAN	ribonuclease P/MRP 14kDa subunit	12					tRNA processing (GO:0008033)	nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)|RNA binding (GO:0003723)			large_intestine(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.000187)|KIRC - Kidney renal clear cell carcinoma(10;0.0102)|Kidney(10;0.0118)|OV - Ovarian serous cystadenocarcinoma(275;0.191)		GAAAGAGTAGTTTACAAAAAC	0.398																																					p.V12fs		Atlas-INDEL	.											.	RPP14	6	.	0			c.34delG						.						119	115	116					3																	58296091		2203	4300	6503	SO:0001589	frameshift_variant	11102	exon2			.	AF001175	CCDS2888.1	3p21.2	2012-05-21	2007-06-26		ENSG00000163684	ENSG00000163684			30327	protein-coding gene	gene with protein product		606112	"ribonuclease P 14kDa subunit"			10024167, 11929972	Standard	NM_001098783		Approved	P14	uc031sah.1	O95059	OTTHUMG00000159152	ENST00000445193.3:c.35delT	chr3.hg19:g.58296091delT	ENSP00000412894:p.Val12fs	117.0	0.0		157.0	10.0	NM_007042	Q53X97	Frame_Shift_Del	DEL	ENST00000445193.3	hg19	CCDS2888.1																																																																																			.	.		0.398	RPP14-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353527.2	NM_007042		-	58296091	T	-	58296091	7	5	112	1	0	1	0	1	0	0	0	0	13624	1725	60	0	37	0	RPP14	3	58296091	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	189081	58296091	139726339	252	16873										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64085551	64085551	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttgctgaggtcaggcatggAaaatcgggataggtgctcct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:64085551delA	ENST00000295902.6	-	8	2296	c.1711delT	c.(1711-1713)tccfs	p.S571fs	PRICKLE2-AS1_ENST00000476308.1_RNA|PRICKLE2-AS1_ENST00000460946.1_RNA|RP11-129B22.1_ENST00000482609.1_RNA|PRICKLE2_ENST00000564377.1_Frame_Shift_Del_p.S627fs	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	571					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		TCAGGCATGGAAAATCGGGAT	0.537																																					p.S571fs		Atlas-INDEL	.											.	PRICKLE2	88	.	0			c.1712delC						.						133	137	135					3																	64085551		2203	4300	6503	SO:0001589	frameshift_variant	166336	exon8			.	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.1711delT	chr3.hg19:g.64085551delA	ENSP00000295902:p.Ser571fs	99.0	0.0		137.0	10.0	NM_198859	Q0VF44	Frame_Shift_Del	DEL	ENST00000295902.6	hg19	CCDS2902.1																																																																																			.	.		0.537	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		-	64085551	A	-	64085551	7	5	112	1	0	1	0	1	0	0	0	0	12499	246	9	0	827	0	PRICKLE2	3	64085551	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5789460	64085551	133936879	253	16874										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78710322	78710322	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttggctggcgtcctcacttcAaaaactaaccagtctgattc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:78710322delA	ENST00000464233.1	-	16	2291	c.2178delT	c.(2176-2178)tttfs	p.F726fs	ROBO1_ENST00000467549.1_Frame_Shift_Del_p.F690fs|ROBO1_ENST00000495273.1_Frame_Shift_Del_p.F690fs|ROBO1_ENST00000436010.2_Frame_Shift_Del_p.F687fs	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	726	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TCCTCACTTCAAAAACTAACC	0.398																																					p.E727fs		Atlas-INDEL	.											.	ROBO1	833	.	0			c.2179delG						.						103	100	101					3																	78710322		1826	4092	5918	SO:0001589	frameshift_variant	6091	exon16			.	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2178delT	chr3.hg19:g.78710322delA	ENSP00000420321:p.Phe726fs	127.0	0.0		165.0	10.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Frame_Shift_Del	DEL	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.		0.398	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		-	78710322	A	-	78710322	7	5	112	1	0	1	0	1	0	0	0	0	13528	127	5	0	2841	0	ROBO1	3	78710322	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	14624771	78710322	119312108	254	16875										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78719381	78719381	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccacacagctgaggacgaaAgtgccatccacggctacagt	11	13	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:78719381A>G	ENST00000464233.1	-	11	1526	c.1413T>C	c.(1411-1413)acT>acC	p.T471T	ROBO1_ENST00000467549.1_Silent_p.T435T|ROBO1_ENST00000495273.1_Silent_p.T435T|ROBO1_ENST00000436010.2_Silent_p.T432T	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	471	Ig-like C2-type 5.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TGAGGACGAAAGTGCCATCCA	0.507																																					p.T471T		Atlas-SNP	.											.	ROBO1	833	.	0			c.T1413C						.						45	44	44					3																	78719381		1963	4173	6136	SO:0001819	synonymous_variant	6091	exon11			GACGAAAGTGCCA	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.1413T>C	chr3.hg19:g.78719381A>G		48.0	0.0		95.0	4.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.		0.507	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		G	78719381	A	G	78719381	2	3	112	1	0	0	0	0	0	0	0	1	13528	59	3	2		2	ROBO1	3	78719381	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	9059	78719381	119303049	255	16876										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89480505	89480505	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccagaagctgcttatacaaCaagagtgagtaacttagatt	8	8	0	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:89480505C>G	ENST00000336596.2	+	13	2567	c.2342C>G	c.(2341-2343)aCa>aGa	p.T781R	EPHA3_ENST00000494014.1_Missense_Mutation_p.T781R	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	781	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		GCTTATACAACAAGAGTGAGT	0.388										TSP Lung(6;0.00050)																											p.T781R		Atlas-SNP	.											.	EPHA3	501	.	0			c.C2342G						.						94	90	92					3																	89480505		2203	4300	6503	SO:0001583	missense	2042	exon13			ATACAACAAGAGT	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2342C>G	chr3.hg19:g.89480505C>G	ENSP00000337451:p.Thr781Arg	121.0	0.0		141.0	83.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.279726	0.80692	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	D;D	0.82081	-1.57;-1.57	5.33	5.33	0.75918	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.88702	0.6508	L	0.48362	1.52	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87033	0.2136	9	.	.	.	.	19.3726	0.94495	0.0:1.0:0.0:0.0	.	781	P29320	EPHA3_HUMAN	R	781	ENSP00000337451:T781R;ENSP00000419190:T781R	.	T	+	2	0	EPHA3	89563195	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	7.776000	0.85560	2.648000	0.89879	0.585000	0.79938	ACA	.	.		0.388	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		G	89480505	C	G	89480505	3	3	112	1	0	0	0	0	1	0	0	0	5170	478	17	4	2418	4	EPHA3	3	89480505	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	10761124	89480505	108541925	256	16877										
IMPG2	50939	hgsc.bcm.edu	37	chr3	101023118	101023118	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acgcccaggaagtcgatcccAaaaagtcctgaaggcttccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:101023118delA	ENST00000193391.7	-	3	560	c.373delT	c.(373-375)tggfs	p.W125fs		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	125					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	AGTCGATCCCAAAAAGTCCTG	0.403																																					p.W125fs		Atlas-INDEL	.											.	IMPG2	164	.	0			c.374delG						.						80	78	79					3																	101023118		2203	4300	6503	SO:0001589	frameshift_variant	50939	exon3			.	AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.373delT	chr3.hg19:g.101023118delA	ENSP00000193391:p.Trp125fs	134.0	0.0		151.0	11.0	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Frame_Shift_Del	DEL	ENST00000193391.7	hg19	CCDS2940.1																																																																																			.	.		0.403	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			-	101023118	A	-	101023118	7	5	112	1	0	1	0	1	0	0	0	0	7738	130	5	0	3420	0	IMPG2	3	101023118	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	11542613	101023118	96999312	257	16878										
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101371772	101371772	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atctctagcttcaaagaaacTtttttcacatctgcaataaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:101371772delT	ENST00000312938.4	-	9	2900	c.2320delA	c.(2320-2322)agtfs	p.S774fs		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	774					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TCAAAGAAACTTTTTTCACAT	0.338																																					p.S774fs		Atlas-INDEL	.											.	ZBTB11	77	.	0			c.2321delG						.						103	96	99					3																	101371772		2203	4300	6503	SO:0001589	frameshift_variant	27107	exon9			.	U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.2320delA	chr3.hg19:g.101371772delT	ENSP00000326200:p.Ser774fs	115.0	0.0		189.0	12.0	NM_014415	Q2NKP9	Frame_Shift_Del	DEL	ENST00000312938.4	hg19	CCDS2943.1																																																																																			.	.		0.338	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		-	101371772	T	-	101371772	7	5	112	1	0	1	0	1	0	0	0	0	17539	1609	56	0	853	0	ZBTB11	3	101371772	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	348654	101371772	96650658	258	16879										
ALCAM	214	hgsc.bcm.edu	37	chr3	105243184	105243184	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccttcagatcctctacaaagAaaagtgtgcagtacgacgat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:105243184delA	ENST00000306107.5	+	3	726	c.226delA	c.(226-228)aaafs	p.K76fs	ALCAM_ENST00000472644.2_Frame_Shift_Del_p.K76fs|ALCAM_ENST00000481337.1_3'UTR|ALCAM_ENST00000486979.2_Frame_Shift_Del_p.K25fs	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	76	Ig-like V-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CTCTACAAAGAAAAGTGTGCA	0.353																																					p.K75fs		Atlas-INDEL	.											.	ALCAM	71	.	0			c.225delG						.						111	107	108					3																	105243184		2203	4300	6503	SO:0001589	frameshift_variant	214	exon3			.	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	400	protein-coding gene	gene with protein product		601662	"activated leucocyte cell adhesion molecule"			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.226delA	chr3.hg19:g.105243184delA	ENSP00000305988:p.Lys76fs	97.0	0.0		159.0	10.0	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Frame_Shift_Del	DEL	ENST00000306107.5	hg19	CCDS33810.1																																																																																			.	.		0.353	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627		-	105243184	A	-	105243184	7	5	112	1	0	1	0	1	0	0	0	0	487	247	9	0	236	0	ALCAM	3	105243184	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3871412	105243184	92779246	259	16880										
BBX	56987	hgsc.bcm.edu	37	chr3	107497314	107497314	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaatgtgtacctgtcccaagAaaaaagaagaagactggaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:107497314delA	ENST00000325805.8	+	13	2438	c.2151delA	c.(2149-2151)agafs	p.R717fs	BBX_ENST00000473542.1_3'UTR|BBX_ENST00000402543.1_Frame_Shift_Del_p.R717fs|BBX_ENST00000416476.2_Frame_Shift_Del_p.E381fs|BBX_ENST00000406780.1_Frame_Shift_Del_p.R717fs|BBX_ENST00000415149.2_Frame_Shift_Del_p.R717fs			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	717	Lys-rich.				bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			CTGTCCCAAGAAAAAAGAAGA	0.428																																					p.R717fs		Atlas-INDEL	.											.	BBX	156	.	0			c.2150delG						.						101	98	99					3																	107497314		2203	4300	6503	SO:0001589	frameshift_variant	56987	exon13			.	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.2151delA	chr3.hg19:g.107497314delA	ENSP00000319974:p.Arg717fs	187.0	0.0		275.0	20.0	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Frame_Shift_Del	DEL	ENST00000325805.8	hg19	CCDS46881.1																																																																																			.	.		0.428	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		-	107497314	A	-	107497314	7	5	112	1	0	1	0	1	0	0	0	0	1343	243	9	0	2189	0	BBX	3	107497314	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2254130	107497314	90525116	260	16881										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111888153	111888153	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctcaaaagcatcatacaagTgagttttgggaataaaacat	8	6	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:111888153T>C	ENST00000305815.5	-	24	3194	c.2942A>G	c.(2941-2943)cAc>cGc	p.H981R	SLC9C1_ENST00000487372.1_Missense_Mutation_p.H933R	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	981					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										ATCATACAAGTGAGTTTTGGG	0.318																																					p.H981R		Atlas-SNP	.											.	.	.	.	0			c.A2942G						.						88	87	87					3																	111888153		2203	4300	6503	SO:0001583	missense	285335	exon24			TACAAGTGAGTTT	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2942A>G	chr3.hg19:g.111888153T>C	ENSP00000306627:p.His981Arg	74.0	0.0		84.0	4.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	T	13.95	2.389764	0.42410	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	D;D	0.92348	-3.02;-3.02	5.83	4.65	0.58169	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.499344	0.19936	N	0.102757	D	0.90655	0.7069	L	0.52364	1.645	0.09310	N	1	P;D	0.54397	0.713;0.966	P;P	0.52109	0.596;0.69	T	0.81206	-0.1038	10	0.15066	T	0.55	-0.562	9.0919	0.36617	0.1632:0.0:0.0:0.8368	.	933;981	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	R	981;933	ENSP00000306627:H981R;ENSP00000420688:H933R	ENSP00000306627:H981R	H	-	2	0	SLC9A10	113370843	0.981000	0.34729	0.003000	0.11579	0.008000	0.06430	2.740000	0.47418	0.993000	0.38866	0.491000	0.48974	CAC	.	.		0.318	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		C	111888153	T	C	111888153	3	2	112	1	0	0	0	0	1	0	0	0	14725	1696	59	2	615	2	SLC9A10	3	111888153	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4390839	111888153	86134277	261	16882										
ZNF80	7634	hgsc.bcm.edu	37	chr3	113955740	113955740	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gatgtcgaacaaggaggctgTttttgttaaacacgctccca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:113955740delT	ENST00000482457.2	-	1	685	c.182delA	c.(181-183)aacfs	p.N61fs	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	61					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				AAGGAGGCTGTTTTTGTTAAA	0.473																																					p.N61fs	GBM(23;986 1114 21716)	Atlas-INDEL	.											.	ZNF80	75	.	0			c.183delC						.						120	104	109					3																	113955740		2203	4300	6503	SO:0001589	frameshift_variant	7634	exon1			.	X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"Zinc fingers, C2H2-type"	13155	protein-coding gene	gene with protein product		194553	"zinc finger protein 80 (pT17)"			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.182delA	chr3.hg19:g.113955740delT	ENSP00000417192:p.Asn61fs	84.0	0.0		136.0	11.0	NM_007136	Q6NSW4|Q6NT14	Frame_Shift_Del	DEL	ENST00000482457.2	hg19	CCDS2979.1																																																																																			.	.		0.473	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136		-	113955740	T	-	113955740	7	5	112	1	0	1	0	1	0	0	0	0	18183	1725	60	0	643	0	ZNF80	3	113955740	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2067587	113955740	84066690	262	16883										
C3orf30	152405	hgsc.bcm.edu	37	chr3	118867142	118867142	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtttcactccaatacatggAaaaacaccacattctgcaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:118867142delA	ENST00000295622.1	+	2	1554	c.1514delA	c.(1513-1515)gaafs	p.E505fs	RP11-484M3.5_ENST00000490594.1_Intron|IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	505										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		CAATACATGGAAAAACACCAC	0.333																																					p.E505fs		Atlas-INDEL	.											.	C3orf30	64	.	0			c.1513delG						.						66	70	69					3																	118867142		2203	4300	6503	SO:0001589	frameshift_variant	152405	exon2			.	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.1514delA	chr3.hg19:g.118867142delA	ENSP00000295622:p.Glu505fs	170.0	0.0		279.0	18.0	NM_152539	A1L4B7	Frame_Shift_Del	DEL	ENST00000295622.1	hg19	CCDS2984.1																																																																																			.	.		0.333	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539		-	118867142	A	-	118867142	7	5	112	1	0	1	0	1	0	0	0	0	2222	246	9	0	1520	0	C3orf30	3	118867142	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4911402	118867142	79155288	263	16884										
LRRC58	116064	hgsc.bcm.edu	37	chr3	120054700	120054700	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgaggaggtatgctttggaTtttgttgtcacataatacca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:120054700delT	ENST00000295628.3	-	2	696	c.601delA	c.(601-603)atcfs	p.I201fs		NM_001099678.1	NP_001093148.1	Q96CX6	LRC58_HUMAN	leucine rich repeat containing 58	201										large_intestine(2)|lung(5)	7				GBM - Glioblastoma multiforme(114;0.147)		ATGCTTTGGATTTTGTTGTCA	0.343																																					p.I201fs		Atlas-INDEL	.											.	LRRC58	18	.	0			c.602delT						.						166	157	160					3																	120054700		1828	4097	5925	SO:0001589	frameshift_variant	116064	exon2			.	BC013757	CCDS46892.1	3q13.33	2006-01-06			ENSG00000163428	ENSG00000163428			26968	protein-coding gene	gene with protein product							Standard	NM_001099678		Approved		uc003edr.2	Q96CX6	OTTHUMG00000159407	ENST00000295628.3:c.601delA	chr3.hg19:g.120054700delT	ENSP00000295628:p.Ile201fs	127.0	0.0		156.0	12.0	NM_001099678		Frame_Shift_Del	DEL	ENST00000295628.3	hg19	CCDS46892.1																																																																																			.	.		0.343	LRRC58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355142.1	XM_057296		-	120054700	T	-	120054700	7	5	112	1	0	1	0	1	0	0	0	0	9023	1493	52	0	526	0	LRRC58	3	120054700	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1187558	120054700	77967730	264	16885										
IQCB1	9657	hgsc.bcm.edu	37	chr3	121527845	121527845	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaaagtgtagtaattcatcTttttcttcagccttaacata							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:121527845delT	ENST00000310864.6	-	6	619	c.405delA	c.(403-405)aaafs	p.K135fs	IQCB1_ENST00000349820.6_Frame_Shift_Del_p.K135fs	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	135					cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)			NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		GTAATTCATCTTTTTCTTCAG	0.328																																					p.D136fs		Atlas-INDEL	.											IQCB1,NS,carcinoma,0,1	IQCB1	50	.	0			c.406delG						.						57	63	61					3																	121527845		2203	4300	6503	SO:0001589	frameshift_variant	9657	exon6			.	D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"nephrocystin-5"	609237	"IQ calmodulin-binding motif containing 1"			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.405delA	chr3.hg19:g.121527845delT	ENSP00000311505:p.Lys135fs	181.0	0.0		221.0	14.0	NM_001023571	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Frame_Shift_Del	DEL	ENST00000310864.6	hg19	CCDS33837.1																																																																																			.	.		0.328	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642		-	121527845	T	-	121527845	7	5	112	1	0	1	0	1	0	0	0	0	7812	1606	56	0	1431	0	IQCB1	3	121527845	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1473145	121527845	76494585	265	16886										
SLC15A2	6565	hgsc.bcm.edu	37	chr3	121613348	121613348	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atcctttccagaaaaatgagTccaaggaaactcttttttca	5	9	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:121613348T>C	ENST00000489711.1	+	1	413	c.25T>C	c.(25-27)Tcc>Ccc	p.S9P	SLC15A2_ENST00000295605.2_Missense_Mutation_p.S9P	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	9					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	GAAAAATGAGTCCAAGGAAAC	0.483																																					p.S9P		Atlas-SNP	.											.	SLC15A2	92	.	0			c.T25C						.						167	179	175					3																	121613348		2203	4300	6503	SO:0001583	missense	6565	exon1			AATGAGTCCAAGG	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.25T>C	chr3.hg19:g.121613348T>C	ENSP00000417085:p.Ser9Pro	68.0	0.0		93.0	4.0	NM_001145998	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	hg19	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.003908	0.74932	.	.	ENSG00000163406	ENST00000489711;ENST00000295605	T;T	0.03553	4.3;3.89	5.1	5.1	0.69264	Major facilitator superfamily domain, general substrate transporter (1);	0.102776	0.43919	D	0.000505	T	0.11410	0.0278	L	0.42245	1.32	0.35790	D	0.82235	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.06391	-1.0829	10	0.66056	D	0.02	-4.6463	11.2128	0.48808	0.0:0.0:0.0:1.0	.	9;9	B4E2A7;Q16348	.;S15A2_HUMAN	P	9	ENSP00000417085:S9P;ENSP00000295605:S9P	ENSP00000295605:S9P	S	+	1	0	SLC15A2	123096038	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.163000	0.58183	2.141000	0.66446	0.455000	0.32223	TCC	.	.		0.483	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		C	121613348	T	C	121613348	3	2	112	1	0	0	0	0	1	0	0	0	14414	1667	58	2	27	2	SLC15A2	3	121613348	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	85503	121613348	76409082	266	16887										
PARP14	54625	hgsc.bcm.edu	37	chr3	122423544	122423544	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcaagaatcagctgaaaacTttacaagaggttcactttct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:122423544delT	ENST00000474629.2	+	8	3755	c.3489delT	c.(3487-3489)actfs	p.T1163fs		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1163	Macro 2. {ECO:0000255|PROSITE- ProRule:PRU00490}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		AGCTGAAAACTTTACAAGAGG	0.373																																					p.T1163fs		Atlas-INDEL	.											.	PARP14	242	.	0			c.3488delC						.						38	35	36					3																	122423544		1826	4068	5894	SO:0001589	frameshift_variant	54625	exon8			.	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.3489delT	chr3.hg19:g.122423544delT	ENSP00000418194:p.Thr1163fs	204.0	0.0		225.0	14.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Frame_Shift_Del	DEL	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.		0.373	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		-	122423544	T	-	122423544	7	5	112	1	0	1	0	1	0	0	0	0	11467	1596	56	0	3519	0	PARP14	3	122423544	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	810196	122423544	75598886	267	16888										
MYLK	4638	hgsc.bcm.edu	37	chr3	123419119	123419119	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttaacgtctttcttgagttCttctttgctagcggatttca	7	9	5	1	rs372794395|rs72491150|rs75967604	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:123419119C>G	ENST00000475616.1	-	15	3195	c.3196G>C	c.(3196-3198)Gaa>Caa	p.E1066Q	MYLK_ENST00000359169.1_Missense_Mutation_p.E1066Q|MYLK_ENST00000360772.3_Missense_Mutation_p.E1066Q|MYLK_ENST00000360304.3_Missense_Mutation_p.E1066Q|MYLK_ENST00000346322.5_Missense_Mutation_p.E997Q|MYLK_ENST00000510775.1_5'Flank			Q15746	MYLK_HUMAN	myosin light chain kinase	1066	Actin-binding (calcium/calmodulin- insensitive). {ECO:0000250}.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)	p.E1066K(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TTCTTGAGTTCTTCTTTGCTA	0.527																																					p.E1066Q		Atlas-SNP	.											MYLK,bladder,carcinoma,0,1	MYLK	224	.	1	Substitution - Missense(1)	urinary_tract(1)	c.G3196C						.						262	266	265					3																	123419119		2203	4300	6503	SO:0001583	missense	4638	exon18			TGAGTTCTTCTTT	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7590	protein-coding gene	gene with protein product	"smooth muscle myosin light chain kinase"	600922	"myosin, light polypeptide kinase"			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.3196G>C	chr3.hg19:g.123419119C>G	ENSP00000418335:p.Glu1066Gln	133.0	2.0		163.0	9.0	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	hg19	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	C	11.12	1.544986	0.27652	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.67523	-0.27;-0.22;-0.27;-0.2;-0.22	5.69	5.69	0.88448	.	.	.	.	.	T	0.69726	0.3143	M	0.68952	2.095	0.80722	D	1	B;B;P;P;P;B	0.47106	0.404;0.008;0.89;0.709;0.89;0.282	B;B;B;B;B;B	0.44224	0.353;0.014;0.444;0.353;0.444;0.192	T	0.71451	-0.4589	9	0.44086	T	0.13	.	17.998	0.89189	0.0:1.0:0.0:0.0	.	1066;144;997;1066;997;1066	Q15746-6;Q15746-7;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;.;MYLK_HUMAN	Q	1066;1066;1066;997;1066	ENSP00000354004:E1066Q;ENSP00000353452:E1066Q;ENSP00000352088:E1066Q;ENSP00000320622:E997Q;ENSP00000418335:E1066Q	ENSP00000320622:E997Q	E	-	1	0	MYLK	124901809	0.997000	0.39634	1.000000	0.80357	0.169000	0.22640	1.326000	0.33735	2.692000	0.91855	0.505000	0.49811	GAA	.	.		0.527	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		G	123419119	C	G	123419119	3	3	112	1	0	0	0	0	1	0	0	0	10065	922	32	4	2616	4	MYLK	3	123419119	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	995575	123419119	74603311	268	16889										
KALRN	8997	hgsc.bcm.edu	37	chr3	124210240	124210240	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgccttgtggtctgggcgcaCcccatcctcagacaataaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:124210240delC	ENST00000240874.3	+	31	4809	c.4652delC	c.(4651-4653)accfs	p.T1551fs	KALRN_ENST00000360013.3_Frame_Shift_Del_p.T1551fs|KALRN_ENST00000460856.1_Frame_Shift_Del_p.T1542fs	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1551	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TCTGGGCGCACCCCATCCTCA	0.542																																					p.T1551fs		Atlas-INDEL	.											.	KALRN	556	.	0			c.4651delA						.						84	75	78					3																	124210240		2203	4300	6503	SO:0001589	frameshift_variant	8997	exon31			.	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4652delC	chr3.hg19:g.124210240delC	ENSP00000240874:p.Thr1551fs	68.0	0.0		151.0	10.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Frame_Shift_Del	DEL	ENST00000240874.3	hg19	CCDS3027.1																																																																																			.	.		0.542	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		-	124210240	C	-	124210240	7	5	112	1	0	1	0	1	0	0	0	0	7984	507	18	0	4774	0	KALRN	3	124210240	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	791121	124210240	73812190	269	16890										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129277345	129277345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gactgaaaggcaggcgtcgaTgtggtctgtcttgtcgatgt	15	7	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:129277345T>C	ENST00000324093.4	-	33	5549	c.5371A>G	c.(5371-5373)Atc>Gtc	p.I1791V	PLXND1_ENST00000393239.1_3'UTR|PLXND1_ENST00000504689.1_5'Flank	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1791					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						CAGGCGTCGATGTGGTCTGTC	0.577																																					p.I1791V	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.A5371G						.						81	74	77					3																	129277345		2203	4300	6503	SO:0001583	missense	23129	exon33			CGTCGATGTGGTC	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.5371A>G	chr3.hg19:g.129277345T>C	ENSP00000317128:p.Ile1791Val	70.0	0.0		130.0	6.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	5.814|5.814	0.334382|0.334382	0.11013|0.11013	.|.	.|.	ENSG00000004399|ENSG00000004399	ENST00000506979|ENST00000324093	T|T	0.11277|0.10477	2.79|2.87	4.68|4.68	4.68|4.68	0.58851|0.58851	.|Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	.|0.110120	.|0.64402	.|D	.|0.000010	T|T	0.03959|0.03959	0.0111|0.0111	N|N	0.01015|0.01015	-1.05|-1.05	0.80722|0.80722	D|D	1|1	.|B;P	.|0.35551	.|0.018;0.509	.|B;B	.|0.35607	.|0.018;0.206	T|T	0.54938|0.54938	-0.8218|-0.8218	7|10	0.44086|0.23891	T|T	0.13|0.37	.|.	13.3343|13.3343	0.60507|0.60507	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|387;1791	.|B4DRU3;Q9Y4D7	.|.;PLXD1_HUMAN	R|V	134|1791	ENSP00000427696:H134R|ENSP00000317128:I1791V	ENSP00000427696:H134R|ENSP00000317128:I1791V	H|I	-|-	2|1	0|0	PLXND1|PLXND1	130760035|130760035	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	4.010000|4.010000	0.57117|0.57117	1.737000|1.737000	0.51674|0.51674	0.459000|0.459000	0.35465|0.35465	CAT|ATC	.	.		0.577	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		C	129277345	T	C	129277345	3	2	112	1	0	0	0	0	1	0	0	0	12136	1464	51	2	422	2	PLXND1	3	129277345	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	5067105	129277345	68745085	270	16891										
TRH	7200	hgsc.bcm.edu	37	chr3	129695643	129695643	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagaagaggaagaggaagaaGggggggctgtgggaccccac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:129695643delG	ENST00000302649.3	+	3	840	c.313delG	c.(313-315)gggfs	p.G106fs	TRH_ENST00000507066.1_Frame_Shift_Del_p.G102fs	NM_007117.3	NP_009048.1	P20396	TRH_HUMAN	thyrotropin-releasing hormone	106					adult walking behavior (GO:0007628)|cell-cell signaling (GO:0007267)|eating behavior (GO:0042755)|histamine metabolic process (GO:0001692)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of feeding behavior (GO:2000252)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of insulin secretion (GO:0032024)|response to cold (GO:0009409)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	thyrotropin-releasing hormone activity (GO:0008437)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)	14						agaggaagaagggggggCTGT	0.567																																					p.E104fs	Esophageal Squamous(60;321 1330 17401 41911)	Atlas-INDEL	.											.	TRH	30	.	0			c.312delA						.						52	49	50					3																	129695643		2203	4300	6503	SO:0001589	frameshift_variant	7200	exon3			.		CCDS3066.1	3q13.3-q21	2013-02-28				ENSG00000170893		"Endogenous ligands"	12298	protein-coding gene	gene with protein product	"prothyroliberin"	613879				2126343, 1900134	Standard	NM_007117		Approved		uc003enc.4	P20396		ENST00000302649.3:c.313delG	chr3.hg19:g.129695643delG	ENSP00000303452:p.Gly106fs	70.0	0.0		142.0	10.0	NM_007117	B2R8R1|Q2TB83	Frame_Shift_Del	DEL	ENST00000302649.3	hg19	CCDS3066.1																																																																																			.	.		0.567	TRH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356592.1	NM_007117		-	129695643	G	-	129695643	7	5	112	1	0	1	0	1	0	0	0	0	16493	1000	35	0	319	0	TRH	3	129695643	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	418298	129695643	68326787	271	16892										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130300684	130300684	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agttaaaggaccatctcttcTcaatgcaaacctcttggatt	6	10	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:130300684T>C	ENST00000358511.6	+	8	3858	c.3827T>C	c.(3826-3828)cTc>cCc	p.L1276P	COL6A6_ENST00000453409.2_Missense_Mutation_p.L1276P	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1276	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CCATCTCTTCTCAATGCAAAC	0.363																																					p.L1276P		Atlas-SNP	.											.	COL6A6	497	.	0			c.T3827C						.						173	167	169					3																	130300684		1873	4094	5967	SO:0001583	missense	131873	exon8			CTCTTCTCAATGC	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3827T>C	chr3.hg19:g.130300684T>C	ENSP00000351310:p.Leu1276Pro	88.0	0.0		149.0	6.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.32|13.32	2.201236|2.201236	0.38905|0.38905	.|.	.|.	ENSG00000206384|ENSG00000206384	ENST00000358511;ENST00000453409|ENST00000511332	T;T|.	0.38560|.	1.13;1.13|.	6.06|6.06	6.06|6.06	0.98353|0.98353	von Willebrand factor, type A (2);|.	.|.	.|.	.|.	.|.	T|T	0.75302|0.75302	0.3831|0.3831	M|M	0.76170|0.76170	2.325|2.325	0.58432|0.58432	D|D	0.999999|0.999999	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|T	0.75499|0.75499	-0.3296|-0.3296	9|5	0.46703|.	T|.	0.11|.	.|.	15.5919|15.5919	0.76537|0.76537	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1276|.	A6NMZ7|.	CO6A6_HUMAN|.	P|P	1276|34	ENSP00000351310:L1276P;ENSP00000399236:L1276P|.	ENSP00000351310:L1276P|.	L|S	+|+	2|1	0|0	COL6A6|COL6A6	131783374|131783374	0.994000|0.994000	0.37717|0.37717	0.394000|0.394000	0.26270|0.26270	0.009000|0.009000	0.06853|0.06853	5.297000|5.297000	0.65704|0.65704	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	CTC|TCA	.	.		0.363	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		C	130300684	T	C	130300684	3	2	112	1	0	0	0	0	1	0	0	0	3705	1551	54	2	3857	2	COL6A6	3	130300684	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	605041	130300684	67721746	272	16893										
MRPL3	11222	hgsc.bcm.edu	37	chr3	131188575	131188575	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtcctgtatatgtttcccaTttttccaggcattttagttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:131188575delT	ENST00000264995.3	-	8	928	c.781delA	c.(781-783)atgfs	p.M261fs	MRPL3_ENST00000425847.2_Frame_Shift_Del_p.M288fs	NM_007208.3	NP_009139.1	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	261			M -> T (in dbSNP:rs2291381).		translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						ATGTTTCCCATTTTTCCAGGC	0.348																																					p.M261fs		Atlas-INDEL	.											.,1	MRPL3	32	.	0			c.782delT						.						128	112	117					3																	131188575		2203	4300	6503	SO:0001589	frameshift_variant	11222	exon8			.	X06323	CCDS3071.1	3q21-q23	2012-09-13			ENSG00000114686	ENSG00000114686		"Mitochondrial ribosomal proteins / large subunits"	10379	protein-coding gene	gene with protein product		607118		RPML3		2891103	Standard	NM_007208		Approved	MRL3	uc003eoh.3	P09001	OTTHUMG00000159607	ENST00000264995.3:c.781delA	chr3.hg19:g.131188575delT	ENSP00000264995:p.Met261fs	119.0	0.0		153.0	10.0	NM_007208	Q6IBT2	Frame_Shift_Del	DEL	ENST00000264995.3	hg19	CCDS3071.1																																																																																			.	.		0.348	MRPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356471.3	NM_007208		-	131188575	T	-	131188575	7	5	112	1	0	1	0	1	0	0	0	0	9802	1493	52	0	277	0	MRPL3	3	131188575	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	887891	131188575	66833855	273	16894										
ACPP	55	hgsc.bcm.edu	37	chr3	132075605	132075605	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcatgctacctggctgcagCcccagctgtcctctggagag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:132075605delC	ENST00000336375.5	+	10	1134	c.1044delC	c.(1042-1044)agcfs	p.S348fs	ACPP_ENST00000475741.1_Frame_Shift_Del_p.S315fs|ACPP_ENST00000351273.7_Frame_Shift_Del_p.S348fs	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	348					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						CTGGCTGCAGCCCCAGCTGTC	0.557																																					p.S348fs		Atlas-INDEL	.											ACPP_ENST00000351273,NS,carcinoma,0,2	ACPP	118	.	0			c.1043delG						.						161	141	148					3																	132075605		2203	4300	6503	SO:0001589	frameshift_variant	55	exon10			.		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.1044delC	chr3.hg19:g.132075605delC	ENSP00000337471:p.Ser348fs	115.0	0.0		165.0	10.0	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Frame_Shift_Del	DEL	ENST00000336375.5	hg19	CCDS3073.1																																																																																			.	.		0.557	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099		-	132075605	C	-	132075605	7	5	112	1	0	1	0	1	0	0	0	0	167	738	26	0	1082	0	ACPP	3	132075605	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	887030	132075605	65946825	274	16895										
MRPS22	56945	hgsc.bcm.edu	37	chr3	139074572	139074572	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgtatcacgtgctccatccAgatggccagtcggctcaagg	11	13	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:139074572A>G	ENST00000495075.1	+	9	1359	c.927A>G	c.(925-927)ccA>ccG	p.P309P	MRPS22_ENST00000310776.4_Silent_p.P309P|MRPS22_ENST00000465056.1_Silent_p.P308P|MRPS22_ENST00000478464.1_Silent_p.P268P			P82650	RT22_HUMAN	mitochondrial ribosomal protein S22	309						mitochondrial ribosome (GO:0005761)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12						TGCTCCATCCAGATGGCCAGT	0.418																																					p.P309P		Atlas-SNP	.											.	MRPS22	40	.	0			c.A927G						.						76	75	75					3																	139074572		2203	4300	6503	SO:0001819	synonymous_variant	56945	exon7			CCATCCAGATGGC	AF226045	CCDS3107.1	3q23	2012-09-13			ENSG00000175110	ENSG00000175110		"Mitochondrial ribosomal proteins / small subunits"	14508	protein-coding gene	gene with protein product		605810				11175783	Standard	NM_020191		Approved	MRP-S22, GK002, C3orf5, GIBT	uc003etb.3	P82650	OTTHUMG00000159910	ENST00000495075.1:c.927A>G	chr3.hg19:g.139074572A>G		154.0	0.0		243.0	10.0	NM_020191	Q9H3I1	Silent	SNP	ENST00000495075.1	hg19	CCDS3107.1																																																																																			.	.		0.418	MRPS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358120.1	NM_020191		G	139074572	A	G	139074572	2	3	112	1	0	0	0	0	0	0	0	1	9842	175	7	2		2	MRPS22	3	139074572	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	6998967	139074572	58947858	275	16896										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140178605	140178605	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccatcctctgcaactcagacAaaaccggtgagtctctagcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:140178605delA	ENST00000458420.3	+	7	1406	c.1216delA	c.(1216-1218)aaafs	p.K406fs	RP11-68L1.1_ENST00000483759.2_RNA|RP11-68L1.2_ENST00000503357.1_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	406					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						CAACTCAGACAAAACCGGTGA	0.567										HNSCC(16;0.037)																											p.D405fs	GBM(45;858 913 3709 36904 37282)	Atlas-INDEL	.											.	CLSTN2	190	.	0			c.1215delC						.						75	68	70					3																	140178605		2203	4300	6503	SO:0001589	frameshift_variant	64084	exon7			.	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1216delA	chr3.hg19:g.140178605delA	ENSP00000402460:p.Lys406fs	102.0	0.0		211.0	15.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Frame_Shift_Del	DEL	ENST00000458420.3	hg19	CCDS3112.1																																																																																			.	.		0.567	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		-	140178605	A	-	140178605	7	5	112	1	0	1	0	1	0	0	0	0	3564	131	5	0	1242	0	CLSTN2	3	140178605	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1104033	140178605	57843825	276	16897										
CHST2	9435	hgsc.bcm.edu	37	chr3	142840446	142840446	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtggtgtgctcgtcaccacTctgccccgcctaccgcaagg	12	16	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:142840446T>C	ENST00000309575.3	+	2	2172	c.788T>C	c.(787-789)cTc>cCc	p.L263P		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	263					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						TCGTCACCACTCTGCCCCGCC	0.677																																					p.L263P		Atlas-SNP	.											.	CHST2	67	.	0			c.T788C						.						20	24	23					3																	142840446		2201	4299	6500	SO:0001583	missense	9435	exon2			CACCACTCTGCCC	BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"Sulfotransferases, membrane-bound"	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.788T>C	chr3.hg19:g.142840446T>C	ENSP00000307911:p.Leu263Pro	90.0	0.0		120.0	5.0	NM_004267	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	hg19	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	T	14.86	2.660842	0.47572	.	.	ENSG00000175040	ENST00000309575	D	0.96856	-4.15	4.17	4.17	0.49024	Sulfotransferase domain (1);	0.000000	0.56097	U	0.000026	D	0.97467	0.9171	M	0.70275	2.135	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.97825	1.0259	10	0.62326	D	0.03	-16.2734	13.3769	0.60743	0.0:0.0:0.0:1.0	.	263	Q9Y4C5	CHST2_HUMAN	P	263	ENSP00000307911:L263P	ENSP00000307911:L263P	L	+	2	0	CHST2	144323136	1.000000	0.71417	0.795000	0.32087	0.439000	0.31926	5.778000	0.68940	1.747000	0.51819	0.334000	0.21626	CTC	.	.		0.677	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		C	142840446	T	C	142840446	3	2	112	1	0	0	0	0	1	0	0	0	3406	1551	54	2	790	2	CHST2	3	142840446	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2661841	142840446	55181984	277	16898										
PLOD2	5352	hgsc.bcm.edu	37	chr3	145804616	145804616	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttgacttagattttcttctGgtcctactatttttatagtt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:145804616delG	ENST00000360060.3	-	10	1262	c.1085delC	c.(1084-1086)ccafs	p.P362fs	PLOD2_ENST00000282903.5_Frame_Shift_Del_p.P362fs|PLOD2_ENST00000461497.1_5'Flank|PLOD2_ENST00000494950.1_Frame_Shift_Del_p.P307fs|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	362					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	ATTTTCTTCTGGTCCTACTAT	0.259																																					p.P362fs		Atlas-INDEL	.											.	PLOD2	81	.	0			c.1086delA						.						57	51	53					3																	145804616		2176	4274	6450	SO:0001589	frameshift_variant	5352	exon10			.	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"lysyl hydroxlase 2"	601865	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.1085delC	chr3.hg19:g.145804616delG	ENSP00000353170:p.Pro362fs	114.0	0.0		159.0	10.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Frame_Shift_Del	DEL	ENST00000360060.3	hg19	CCDS3131.1																																																																																			.	.		0.259	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		-	145804616	G	-	145804616	7	5	112	1	0	1	0	1	0	0	0	0	12111	1348	47	0	1235	0	PLOD2	3	145804616	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2964170	145804616	52217814	278	16899										
P2RY12	64805	hgsc.bcm.edu	37	chr3	151055960	151055960	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctggggactttacctacaCccctcgttcttacgtatgac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:151055960delC	ENST00000302632.3	-	3	973	c.674delG	c.(673-675)ggtfs	p.G225fs	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron|MED12L_ENST00000474524.1_Intron	NM_022788.4|NM_176876.2	NP_073625.1|NP_795345.1	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y, G-protein coupled, 12	225					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell projection organization (GO:0030030)|G-protein coupled purinergic nucleotide receptor signaling pathway (GO:0035589)|G-protein coupled receptor signaling pathway (GO:0007186)|hemostasis (GO:0007599)|negative regulation of cell differentiation (GO:0045596)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of GTPase activity (GO:0043547)|positive regulation of ion transport (GO:0043270)|potassium ion transmembrane transport (GO:0071805)|protein kinase B signaling (GO:0043491)|regulation of calcium ion transport (GO:0051924)	basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	ADP receptor activity (GO:0001621)|G-protein coupled adenosine receptor activity (GO:0001609)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	17			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Prasugrel(DB06209)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Treprostinil(DB00374)	TTTACCTACACCCCTCGTTCT	0.348																																					p.G225fs		Atlas-INDEL	.											.	P2RY12	36	.	0			c.675delT						.						73	75	75					3																	151055960		2203	4300	6503	SO:0001589	frameshift_variant	64805	exon3			.	AJ320495	CCDS3159.1	3q24-q25	2014-09-17			ENSG00000169313	ENSG00000169313		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	18124	protein-coding gene	gene with protein product		600515				11502873, 11104774	Standard	NM_022788		Approved	P2Y12, SP1999, HORK3	uc003eyw.1	Q9H244	OTTHUMG00000159863	ENST00000302632.3:c.674delG	chr3.hg19:g.151055960delC	ENSP00000307259:p.Gly225fs	109.0	0.0		166.0	13.0	NM_022788	D3DNJ5|Q546J7	Frame_Shift_Del	DEL	ENST00000302632.3	hg19	CCDS3159.1																																																																																			.	.		0.348	P2RY12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357796.1			-	151055960	C	-	151055960	7	5	112	1	0	1	0	1	0	0	0	0	11358	507	18	0	358	0	P2RY12	3	151055960	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	5251344	151055960	46966470	279	16900										
AADAC	13	hgsc.bcm.edu	37	chr3	151542580	151542580	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagagaatcggtatttctggAgatagtgcaggagggaattt	15	3	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:151542580A>G	ENST00000232892.7	+	4	687	c.561A>G	c.(559-561)ggA>ggG	p.G187G	RP11-454C18.2_ENST00000483843.2_RNA|AADAC_ENST00000488869.1_Silent_p.G187G|RP11-454C18.2_ENST00000475855.1_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	187					positive regulation of triglyceride catabolic process (GO:0010898)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|deacetylase activity (GO:0019213)|lipase activity (GO:0016298)|serine hydrolase activity (GO:0017171)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(5)|skin(2)	19		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			GTATTTCTGGAGATAGTGCAG	0.353																																					p.G187G	Ovarian(30;839 841 2699 32801 46334)	Atlas-SNP	.											.	AADAC	49	.	0			c.A561G						.						84	82	83					3																	151542580		2203	4300	6503	SO:0001819	synonymous_variant	13	exon4			TTCTGGAGATAGT	L32179	CCDS33877.1	3q25.1	2014-03-18	2012-07-13		ENSG00000114771	ENSG00000114771	3.1.1.3		17	protein-coding gene	gene with protein product		600338	"arylacetamide deacetylase (esterase)"			8063807	Standard	XM_005247103		Approved	DAC, CES5A1	uc003eze.3	P22760	OTTHUMG00000159876	ENST00000232892.7:c.561A>G	chr3.hg19:g.151542580A>G		105.0	0.0		164.0	7.0	NM_001086	A8K3L3|D3DNJ6|Q8N1A9	Silent	SNP	ENST00000232892.7	hg19	CCDS33877.1																																																																																			.	.		0.353	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086		G	151542580	A	G	151542580	2	3	112	1	0	0	0	0	0	0	0	1	10	291	11	2		2	AADAC	3	151542580	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	486620	151542580	46479850	280	16901										
SGEF	26084	hgsc.bcm.edu	37	chr3	153839867	153839867	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gattcctcagccccaccaggTtctgggccggagcaagccga	12	15	2	0	rs200926651	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:153839867T>C	ENST00000356448.4	+	2	370	c.86T>C	c.(85-87)gTt>gCt	p.V29A	ARHGEF26_ENST00000465817.1_Missense_Mutation_p.V29A|ARHGEF26-AS1_ENST00000467912.1_RNA|ARHGEF26-AS1_ENST00000479270.1_RNA|ARHGEF26-AS1_ENST00000491862.1_RNA|ARHGEF26-AS1_ENST00000480639.1_RNA|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.V29A	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	29			V -> L (in dbSNP:rs12493885). {ECO:0000269|PubMed:12697679, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15133129, ECO:0000269|PubMed:15221005, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21406692}.		endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						CCCCACCAGGTTCTGGGCCGG	0.627																																					p.V29A	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.T86C						.						19	22	21					3																	153839867		1948	4153	6101	SO:0001583	missense	26084	exon2			ACCAGGTTCTGGG	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.86T>C	chr3.hg19:g.153839867T>C	ENSP00000348828:p.Val29Ala	146.0	0.0		231.0	11.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	hg19	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	T	12.15	1.851263	0.32699	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.55234	0.53;0.53;2.31	4.49	0.538	0.17150	.	1.110460	0.06940	N	0.812561	T	0.30230	0.0758	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24297	-1.0164	10	0.51188	T	0.08	-4.6961	5.2467	0.15500	0.0:0.196:0.2513:0.5526	.	29;29	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	A	29	ENSP00000348828:V29A;ENSP00000423418:V29A;ENSP00000423295:V29A	ENSP00000348828:V29A	V	+	2	0	ARHGEF26	155322557	0.088000	0.21588	0.872000	0.34217	0.713000	0.41058	0.303000	0.19210	0.555000	0.29079	0.459000	0.35465	GTT	.	.		0.627	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		C	153839867	T	C	153839867	3	2	112	1	0	0	0	0	1	0	0	0	14220	1725	60	2	88	2	SGEF	3	153839867	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2297287	153839867	44182563	281	16902										
IFT80	57560	hgsc.bcm.edu	37	chr3	160037585	160037585	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcgttaatgttacttgaaaaTttttccactcccaatgttgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:160037585delT	ENST00000326448.7	-	9	1352	c.920delA	c.(919-921)aatfs	p.N307fs	IFT80_ENST00000483465.1_Frame_Shift_Del_p.N170fs|IFT80_ENST00000496589.1_Frame_Shift_Del_p.N170fs|RP11-432B6.3_ENST00000483754.1_Frame_Shift_Del_p.N478fs	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	307					bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TACTTGAAAATTTTTCCACTC	0.378																																					p.N307fs		Atlas-INDEL	.											.	IFT80	68	.	0			c.921delT						.						129	127	128					3																	160037585		2203	4300	6503	SO:0001589	frameshift_variant	57560	exon9			.	AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"Intraflagellar transport homologs", "WD repeat domain containing"	29262	protein-coding gene	gene with protein product		611177	"WD repeat domain 56", "intraflagellar transport 80 homolog (Chlamydomonas)"	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.920delA	chr3.hg19:g.160037585delT	ENSP00000312778:p.Asn307fs	127.0	0.0		162.0	10.0	NM_020800	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Frame_Shift_Del	DEL	ENST00000326448.7	hg19	CCDS3188.1																																																																																			.	.		0.378	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800		-	160037585	T	-	160037585	7	5	112	1	0	1	0	1	0	0	0	0	7573	1493	52	0	1461	0	IFT80	3	160037585	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	6197718	160037585	37984845	282	16903										
SMC4	10051	hgsc.bcm.edu	37	chr3	160131299	160131299	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aattgctgaaatggaaactcAaaaggaaaaaattcatgaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:160131299delA	ENST00000357388.3	+	8	1470	c.1019delA	c.(1018-1020)caafs	p.Q340fs	RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000462787.1_Frame_Shift_Del_p.Q340fs|SMC4_ENST00000360111.2_Frame_Shift_Del_p.Q340fs|SMC4_ENST00000469762.1_Frame_Shift_Del_p.Q315fs|SMC4_ENST00000344722.5_Frame_Shift_Del_p.Q340fs	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	340					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ATGGAAACTCAAAAGGAAAAA	0.289																																					p.Q340fs		Atlas-INDEL	.											.	SMC4	135	.	0			c.1018delC						.						36	37	36					3																	160131299		2174	4267	6441	SO:0001589	frameshift_variant	10051	exon7			.	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.1019delA	chr3.hg19:g.160131299delA	ENSP00000349961:p.Gln340fs	109.0	0.0		183.0	13.0	NM_005496	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Frame_Shift_Del	DEL	ENST00000357388.3	hg19	CCDS3189.1																																																																																			.	.		0.289	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			-	160131299	A	-	160131299	7	5	112	1	0	1	0	1	0	0	0	0	14800	130	5	0	1045	0	SMC4	3	160131299	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	93714	160131299	37891131	283	16904										
SI	6476	hgsc.bcm.edu	37	chr3	164758754	164758754	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaactggtcttgctactgtTtctccaaacacatgggcttt	8	10	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:164758754T>C	ENST00000264382.3	-	18	2195	c.2133A>G	c.(2131-2133)gaA>gaG	p.E711E		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	711	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TTGCTACTGTTTCTCCAAACA	0.328										HNSCC(35;0.089)																											p.E711E		Atlas-SNP	.											.	SI	500	.	0			c.A2133G						.						138	137	138					3																	164758754		2203	4300	6503	SO:0001819	synonymous_variant	6476	exon18			TACTGTTTCTCCA	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.2133A>G	chr3.hg19:g.164758754T>C		89.0	0.0		83.0	4.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	hg19	CCDS3196.1																																																																																			.	.		0.328	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		C	164758754	T	C	164758754	2	2	112	1	0	0	0	0	0	0	0	1	14312	1838	64	2		2	SI	3	164758754	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4627455	164758754	33263676	284	16905										
MECOM	2122	hgsc.bcm.edu	37	chr3	169099249	169099249	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggagggagtgctggctactCcatctgcatctggcatttct	13	10	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:169099249C>T	ENST00000494292.1	-	2	198	c.101G>A	c.(100-102)gGa>gAa	p.G34E	MECOM_ENST00000485957.1_5'UTR	NM_004991.3	NP_004982.2	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	34					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						GCTGGCTACTCCATCTGCATC	0.448																																					p.G34E		Atlas-SNP	.											.	MECOM	216	.	0			c.G101A						.						58	59	58					3																	169099249		1929	4136	6065	SO:0001583	missense	2122	exon2			GCTACTCCATCTG	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000494292.1:c.101G>A	chr3.hg19:g.169099249C>T	ENSP00000417899:p.Gly34Glu	92.0	0.0		151.0	51.0	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000494292.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.78	3.218032	0.58560	.	.	ENSG00000085276	ENST00000494292;ENST00000486748	T	0.06687	3.27	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000012	T	0.28732	0.0712	M	0.63428	1.95	0.80722	D	1	D;P	0.76494	0.999;0.72	D;B	0.71656	0.974;0.346	T	0.00068	-1.2139	10	0.54805	T	0.06	.	20.1184	0.97949	0.0:1.0:0.0:0.0	.	34;34	Q13465;Q03112-3	MDS1_HUMAN;.	E	34;58	ENSP00000417899:G34E	ENSP00000419537:G58E	G	-	2	0	MECOM	170581943	1.000000	0.71417	0.982000	0.44146	0.033000	0.12548	5.030000	0.64128	2.775000	0.95449	0.650000	0.86243	GGA	.	.		0.448	MECOM-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000351517.3	NM_005241, NM_004991		T	169099249	C	T	169099249	3	4	112	1	0	0	0	0	1	0	0	0	9431	855	30	3	3692	3	MECOM	3	169099249	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	4340495	169099249	28923181	285	16906										
LRRIQ4	344657	hgsc.bcm.edu	37	chr3	169540116	169540116	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctgaaggaaattcccgtcgTcatctttaaaaacctccacc	5	14	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:169540116T>C	ENST00000340806.6	+	1	407	c.407T>C	c.(406-408)gTc>gCc	p.V136A		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	136										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						ATTCCCGTCGTCATCTTTAAA	0.552																																					p.V136A		Atlas-SNP	.											.	LRRIQ4	68	.	0			c.T407C						.						56	60	59					3																	169540116		2049	4194	6243	SO:0001583	missense	344657	exon1			CCGTCGTCATCTT		CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"leucine rich repeat containing 64"						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.407T>C	chr3.hg19:g.169540116T>C	ENSP00000342188:p.Val136Ala	65.0	0.0		94.0	4.0	NM_001080460		Missense_Mutation	SNP	ENST00000340806.6	hg19	CCDS46951.1	.	.	.	.	.	.	.	.	.	.	T	7.594	0.671289	0.14776	.	.	ENSG00000188306	ENST00000340806	T	0.55760	0.5	5.56	-10.7	0.00240	.	1.401490	0.04370	N	0.358914	T	0.16557	0.0398	N	0.03016	-0.435	0.09310	N	1	B	0.17268	0.021	B	0.13407	0.009	T	0.09335	-1.0679	10	0.09843	T	0.71	.	1.5474	0.02568	0.3988:0.2921:0.1674:0.1417	.	136	A6NIV6	LRIQ4_HUMAN	A	136	ENSP00000342188:V136A	ENSP00000342188:V136A	V	+	2	0	LRRIQ4	171022810	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.539000	0.06113	-1.422000	0.02004	-0.609000	0.04063	GTC	.	.		0.552	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460		C	169540116	T	C	169540116	3	2	112	1	0	0	0	0	1	0	0	0	9040	1667	58	2	409	2	LRRIQ4	3	169540116	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	440867	169540116	28482314	286	16907										
SEC62	7095	hgsc.bcm.edu	37	chr3	169700648	169700648	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aatataaaggatgagaagacAaaaaaagaaaaagagaaaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:169700648delA	ENST00000337002.4	+	4	463	c.405delA	c.(403-405)acafs	p.T135fs	SEC62-AS1_ENST00000479626.1_RNA|SEC62_ENST00000480708.1_Frame_Shift_Del_p.T135fs	NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	135					cotranslational protein targeting to membrane (GO:0006613)|posttranslational protein targeting to membrane (GO:0006620)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.E138fs*9(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	9						atgagaagacaaaaaaagaaa	0.254																																					p.T135fs		Atlas-INDEL	.											.,1	SEC62	27	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.404delC						.						17	19	19					3																	169700648		2082	4215	6297	SO:0001589	frameshift_variant	7095	exon4			.	D87127	CCDS3210.1	3q26.2	2008-04-22	2008-04-22	2008-04-22	ENSG00000008952	ENSG00000008952			11846	protein-coding gene	gene with protein product		602173	"translocation protein 1"	TLOC1		9020021, 10799540	Standard	NM_003262		Approved	Dtrp1, HTP1	uc003fgh.3	Q99442	OTTHUMG00000158753	ENST00000337002.4:c.405delA	chr3.hg19:g.169700648delA	ENSP00000337688:p.Thr135fs	68.0	0.0		126.0	10.0	NM_003262	D3DNQ0|O00682|O00729	Frame_Shift_Del	DEL	ENST00000337002.4	hg19	CCDS3210.1																																																																																			.	.		0.254	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352043.1			-	169700648	A	-	169700648	7	5	112	1	0	1	0	1	0	0	0	0	14019	117	5	0	419	0	SEC62	3	169700648	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	160532	169700648	28321782	287	16908										
DCUN1D1	54165	hgsc.bcm.edu	37	chr3	182665124	182665124	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgatcgtttatgatgttccTatttaaaaaacaaaaacaaa	4	5	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:182665124T>C	ENST00000292782.4	-	6	757		c.e6-2		DCUN1D1_ENST00000469954.1_Splice_Site	NM_020640.2	NP_065691.2	Q96GG9	DCNL1_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 1							ubiquitin ligase complex (GO:0000151)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			ATGATGTTCCTATTTAAAAAA	0.294																																					.		Atlas-SNP	.											.	DCUN1D1	27	.	0			c.604-2A>G						.						103	98	99					3																	182665124		2199	4298	6497	SO:0001630	splice_region_variant	54165	exon7			TGTTCCTATTTAA	AF292100, AK056335	CCDS3240.1	3q26.3	2013-06-10	2013-06-10		ENSG00000043093	ENSG00000043093			18184	protein-coding gene	gene with protein product	"squamous cell carcinoma related oncogene"	605905	"DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)"			10777668, 15988528	Standard	NM_020640		Approved	RP42, SCRO, DCUN1L1, Tes3, SCCRO	uc003fld.1	Q96GG9	OTTHUMG00000158314	ENST00000292782.4:c.604-2A>G	chr3.hg19:g.182665124T>C		36.0	0.0		63.0	4.0	NM_020640	B2RB37|Q7L3G9|Q8TEX7|Q9H6M1|Q9HCT3	Splice_Site	SNP	ENST00000292782.4	hg19	CCDS3240.1	.	.	.	.	.	.	.	.	.	.	T	19.59	3.855373	0.71719	.	.	ENSG00000043093	ENST00000292782;ENST00000458486;ENST00000469954	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4861	0.75569	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DCUN1D1	184147818	1.000000	0.71417	0.995000	0.50966	0.840000	0.47671	7.671000	0.83941	2.048000	0.60808	0.460000	0.39030	.	.	.		0.294	DCUN1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350658.1	NM_020640	Intron	C	182665124	T	C	182665124	5	2	112	1	0	0	0	0	0	0	1	0	4315	1536	53	2	185	2	DCUN1D1	3	182665124	Splice_Site	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	12964476	182665124	15357306	288	16909										
MCCC1	56922	hgsc.bcm.edu	37	chr3	182751818	182751818	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtcatgtttctggtatacgAgatattcagtcttcttccac	7	9	5	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:182751818A>G	ENST00000265594.4	-	14	1788	c.1642T>C	c.(1642-1644)Tcg>Ccg	p.S548P	MCCC1_ENST00000539926.1_Missense_Mutation_p.S413P|MCCC1_ENST00000489909.1_5'UTR|MCCC1_ENST00000492597.1_Missense_Mutation_p.S439P	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	548					biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	CTGGTATACGAGATATTCAGT	0.299																																					p.S548P		Atlas-SNP	.											.	MCCC1	87	.	0			c.T1642C						.						96	98	97					3																	182751818		2203	4300	6503	SO:0001583	missense	56922	exon14			TATACGAGATATT	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1642T>C	chr3.hg19:g.182751818A>G	ENSP00000265594:p.Ser548Pro	67.0	0.0		110.0	5.0	NM_020166	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	hg19	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	A	1.508	-0.550372	0.03996	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176	D;D;D;D	0.95588	-3.75;-3.7;-3.55;-3.48	5.39	-1.99	0.07457	.	1.075510	0.07135	U	0.846277	D	0.89132	0.6628	L	0.34521	1.04	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.75909	-0.3151	10	0.27082	T	0.32	.	2.1764	0.03863	0.3659:0.2321:0.0654:0.3366	.	501;439;548	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	P	548;439;398;413;501	ENSP00000265594:S548P;ENSP00000419898:S439P;ENSP00000441253:S413P;ENSP00000420433:S501P	ENSP00000265594:S548P	S	-	1	0	MCCC1	184234512	0.413000	0.25400	0.001000	0.08648	0.776000	0.43924	1.453000	0.35167	-0.225000	0.09913	-0.438000	0.05819	TCG	.	.		0.299	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		G	182751818	A	G	182751818	3	3	112	1	0	0	0	0	1	0	0	0	9383	304	11	2	559	2	MCCC1	3	182751818	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	86694	182751818	15270612	289	16910										
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184040193	184040193	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agacggaaaattaaggagctAaataagaaggaggctgttgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:184040193delA	ENST00000346169.2	+	11	1834	c.1563delA	c.(1561-1563)ctafs	p.L521fs	EIF4G1_ENST00000424196.1_Frame_Shift_Del_p.L528fs|EIF4G1_ENST00000392537.2_Frame_Shift_Del_p.L434fs|EIF4G1_ENST00000382330.3_Frame_Shift_Del_p.L528fs|EIF4G1_ENST00000342981.4_Frame_Shift_Del_p.L521fs|EIF4G1_ENST00000434061.2_Frame_Shift_Del_p.L325fs|EIF4G1_ENST00000414031.1_Frame_Shift_Del_p.L481fs|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000427845.1_Frame_Shift_Del_p.L434fs|EIF4G1_ENST00000435046.2_Frame_Shift_Del_p.L325fs|EIF4G1_ENST00000350481.5_Frame_Shift_Del_p.L357fs|EIF4G1_ENST00000319274.6_Frame_Shift_Del_p.L521fs|EIF4G1_ENST00000352767.3_Frame_Shift_Del_p.L528fs|EIF4G1_ENST00000441154.1_Frame_Shift_Del_p.L357fs|EIF4G1_ENST00000411531.1_Frame_Shift_Del_p.L481fs	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	521					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TTAAGGAGCTAAATAAGAAGG	0.433																																					p.L528fs		Atlas-INDEL	.											.	EIF4G1	151	.	0			c.1583delT						.						63	60	61					3																	184040193		2203	4300	6503	SO:0001589	frameshift_variant	1981	exon11			.	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1563delA	chr3.hg19:g.184040193delA	ENSP00000316879:p.Leu521fs	114.0	0.0		183.0	16.0	NM_001194947	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Frame_Shift_Del	DEL	ENST00000346169.2	hg19	CCDS3259.1																																																																																			.	.		0.433	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		-	184040193	A	-	184040193	7	5	112	1	0	1	0	1	0	0	0	0	5038	349	13	0	1597	0	EIF4G1	3	184040193	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1288375	184040193	13982237	290	16911										
POLR2H	5437	hgsc.bcm.edu	37	chr3	184084588	184084588	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tactgaagcagcaacacgccTgtaagttacgtaatcttgtg	9	9	1	1	rs138482713		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:184084588T>C	ENST00000456318.1	+	5	1384	c.335T>C	c.(334-336)cTc>cCc	p.L112P	POLR2H_ENST00000452961.1_Splice_Site_p.L76P|POLR2H_ENST00000443489.1_Intron|POLR2H_ENST00000429568.1_Splice_Site_p.L112P|POLR2H_ENST00000296223.3_Splice_Site_p.L112P|EIF2B5_ENST00000444495.1_Intron|POLR2H_ENST00000430783.1_Intron|POLR2H_ENST00000438240.1_Splice_Site_p.L76P	NM_001278699.1	NP_001265628.1	P52434	RPAB3_HUMAN	polymerase (RNA) II (DNA directed) polypeptide H	112					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase II, core complex (GO:0005665)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.L112P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GCAACACGCCTGTAAGTTACG	0.458																																					p.L112P		Atlas-SNP	.											POLR2H,NS,carcinoma,0,1	POLR2H	17	.	1	Substitution - Missense(1)	breast(1)	c.T335C						.						165	141	149					3																	184084588		2203	4300	6503	SO:0001630	splice_region_variant	5437	exon4			CACGCCTGTAAGT		CCDS3264.1, CCDS63861.1, CCDS63862.1, CCDS63859.1, CCDS63860.1	3q28	2013-01-21			ENSG00000163882	ENSG00000163882		"RNA polymerase subunits"	9195	protein-coding gene	gene with protein product		606023					Standard	NM_001278698		Approved	RPB8	uc003fok.2	P52434	OTTHUMG00000156746	ENST00000456318.1:c.335+1T>C	chr3.hg19:g.184084588T>C		88.0	0.0		94.0	4.0	NM_006232	C9J413|C9JBJ6|C9JCU7|C9JUA8|P53802|Q969R0	Missense_Mutation	SNP	ENST00000456318.1	hg19	CCDS3264.1	.	.	.	.	.	.	.	.	.	.	t	23.2	4.386562	0.82902	.	.	ENSG00000163882	ENST00000456318;ENST00000438240;ENST00000455712;ENST00000452961;ENST00000296223;ENST00000429568	.	.	.	5.91	5.91	0.95273	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	T	0.80798	0.4692	M	0.86178	2.8	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.83499	0.0074	9	0.62326	D	0.03	-9.4653	14.291	0.66278	0.0:0.0:0.0:1.0	.	112	P52434	RPAB3_HUMAN	P	112;76;112;76;112;112	.	ENSP00000296223:L112P	L	+	2	0	POLR2H	185567282	1.000000	0.71417	0.999000	0.59377	0.818000	0.46254	7.678000	0.84035	2.263000	0.75096	0.529000	0.55759	CTC;CTC;CTC;CTC;CTC;CTG	.	T|1.000;G|0.000		0.458	POLR2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345558.1	NM_006232	Missense_Mutation	C	184084588	T	C	184084588	5	2	112	1	0	0	0	0	0	0	1	0	12230	1594	55	2	349	2	POLR2H	3	184084588	Splice_Site	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	44395	184084588	13937842	291	16912										
C3orf59	151963	hgsc.bcm.edu	37	chr3	192516280	192516280	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcagtcactagctgctgcagTttttttgccaaacggtcatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:192516280delT	ENST00000392452.2	-	2	1691	c.1371delA	c.(1369-1371)aaafs	p.K457fs		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	457							protein complex binding (GO:0032403)			endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						GCTGCTGCAGTTTTTTTGCCA	0.512																																					p.L458fs		Atlas-INDEL	.											.	MB21D2	75	.	0			c.1372delC						.						108	113	111					3																	192516280		2203	4300	6503	SO:0001589	frameshift_variant	151963	exon2			.	AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 59"	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.1371delA	chr3.hg19:g.192516280delT	ENSP00000376246:p.Lys457fs	147.0	0.0		197.0	14.0	NM_178496	Q86VD8	Frame_Shift_Del	DEL	ENST00000392452.2	hg19	CCDS3302.2																																																																																			.	.		0.512	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496		-	192516280	T	-	192516280	7	5	112	1	0	1	0	1	0	0	0	0	2239	1722	60	0	108	0	C3orf59	3	192516280	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	8431692	192516280	5506150	292	16913										
PCYT1A	5130	hgsc.bcm.edu	37	chr3	195968954	195968954	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctgtcctctgtgttggagcAaacatgcctaactcagaaac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:195968954delA	ENST00000292823.2	-	8	745	c.573delT	c.(571-573)tttfs	p.F191fs	PCYT1A_ENST00000431016.1_Frame_Shift_Del_p.F191fs|PCYT1A_ENST00000419333.1_Frame_Shift_Del_p.F191fs	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	191			F -> L (in SMDCRD). {ECO:0000269|PubMed:24387990}.		CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	GTGTTGGAGCAAACATGCCTA	0.468																																					p.A192fs		Atlas-INDEL	.											.	PCYT1A	34	.	0			c.574delG						.						117	104	108					3																	195968954		2203	4300	6503	SO:0001589	frameshift_variant	5130	exon8			.	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"phosphate cytidylyltransferase 1, choline, alpha isoform"	123695	"phosphate cytidylyltransferase 1, choline, alpha isoform"	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.573delT	chr3.hg19:g.195968954delA	ENSP00000292823:p.Phe191fs	82.0	0.0		132.0	10.0	NM_005017	A9LYK9|D3DXB1|Q86Y88	Frame_Shift_Del	DEL	ENST00000292823.2	hg19	CCDS3315.1																																																																																			.	.		0.468	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017		-	195968954	A	-	195968954	7	5	112	1	0	1	0	1	0	0	0	0	11619	127	5	0	542	0	PCYT1A	3	195968954	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3452674	195968954	2053476	293	16914										
PIGZ	80235	hgsc.bcm.edu	37	chr3	196674974	196674975	+	Missense_Mutation	DNP	GC	GC	CG													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acaccgctgctgtgagggctGccccagggagcagcaccagg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:196674974_196674975GC>CG	ENST00000412723.1	-	3	939_940	c.793_794GC>CG	c.(793-795)GCa>CGa	p.A265R	PIGZ_ENST00000443835.1_3'UTR	NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	265					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		TGTGAGGGCTGCCCCAGGGAGC	0.614																																					p.A265G|p.A265P		Atlas-SNP	.											.	PIGZ	34	.	0			c.C794G|c.G793C						.																																			SO:0001583	missense	80235	exon3			AGGGCTGCCCCAG|GGGCTGCCCCAGG	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	30596	protein-coding gene	gene with protein product	"GPI mannosyltransferase 4", "dol-P-Man dependent GPI mannosyltransferase"	611671	"phosphatidylinositol glycan, class Z"			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.793_794delinsCG	chr3.hg19:g.196674974_196674975delinsCG	ENSP00000413405:p.Ala265Arg	51.0|52.0	0.0		88.0	5.0|4.0	NM_025163	Q9H9G6	Missense_Mutation	SNP	ENST00000412723.1	hg19	CCDS3324.1																																																																																			.	.		0.614	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163		CG	196674975	GC	CG	196674974	3	2	112	1	0	0	0	0	1	0	0	0	11914	1319	46	4	949	4	PIGZ	3	196674974	Missense_Mutation	DNP	GC	TCGA-DD-A39Y-01A-11D-A20W-10	706020	196674974	1347456	294	16915										
LRCH3	84859	hgsc.bcm.edu	37	chr3	197566229	197566229	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtagccattagggagtttcAaaaaacagaagatatgagaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:197566229delA	ENST00000425562.2	+	10	1289	c.1289delA	c.(1288-1290)caafs	p.Q430fs	LRCH3_ENST00000441090.2_Frame_Shift_Del_p.Q276fs|LRCH3_ENST00000414675.2_Frame_Shift_Del_p.Q402fs|LRCH3_ENST00000334859.4_Frame_Shift_Del_p.Q430fs|LRCH3_ENST00000536618.1_Frame_Shift_Del_p.Q25fs|LRCH3_ENST00000438796.2_Frame_Shift_Del_p.Q430fs			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	430						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		AGGGAGTTTCAAAAAACAGAA	0.328																																					p.Q430fs		Atlas-INDEL	.											.	LRCH3	96	.	0			c.1288delC						.						52	53	53					3																	197566229		2203	4299	6502	SO:0001589	frameshift_variant	84859	exon10			.	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1289delA	chr3.hg19:g.197566229delA	ENSP00000393579:p.Gln430fs	96.0	0.0		155.0	11.0	NM_032773	B4E0T7|Q96FP9|Q9NT52	Frame_Shift_Del	DEL	ENST00000425562.2	hg19																																																																																				.	.		0.328	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773		-	197566229	A	-	197566229	7	5	112	1	0	1	0	1	0	0	0	0	8943	130	5	0	1327	0	LRCH3	3	197566229	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	891255	197566229	456201	295	16916										
PDE6B	5158	hgsc.bcm.edu	37	chr4	660330	660330	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcccaccagcctatgatggAccggaacaaggcggccgagc	12	15	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:660330A>G	ENST00000496514.1	+	20	2300	c.2279A>G	c.(2278-2280)gAc>gGc	p.D760G	PDE6B_ENST00000429163.2_Missense_Mutation_p.D481G|PDE6B_ENST00000255622.6_Missense_Mutation_p.D760G			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	760					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	CCTATGATGGACCGGAACAAG	0.637																																					p.D760G	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.A2279G						.						89	75	80					4																	660330		2203	4300	6503	SO:0001583	missense	5158	exon20			TGATGGACCGGAA	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"Phosphodiesterases"	8786	protein-coding gene	gene with protein product	"congenital stationary night blindness 3, autosomal dominant"	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.2279A>G	chr4.hg19:g.660330A>G	ENSP00000420295:p.Asp760Gly	71.0	0.0		106.0	5.0	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	hg19	CCDS33932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.5|22.5	4.295859|4.295859	0.81025|0.81025	.|.	.|.	ENSG00000133256|ENSG00000133256	ENST00000255622;ENST00000496514;ENST00000429163;ENST00000471824|ENST00000461490	D;D;D;D|.	0.82619|.	-1.63;-1.63;-1.63;-1.63|.	4.22|4.22	4.22|4.22	0.49857|0.49857	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84419|0.84419	0.5468|0.5468	H|H	0.94698|0.94698	3.57|3.57	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.998|.	D|D	0.88109|0.88109	0.2824|0.2824	10|5	0.87932|.	D|.	0|.	.|.	11.6112|11.6112	0.51059|0.51059	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	760;760|.	P35913;P35913-2|.	PDE6B_HUMAN;.|.	G|A	760;760;481;120|41	ENSP00000255622:D760G;ENSP00000420295:D760G;ENSP00000406334:D481G;ENSP00000417852:D120G|.	ENSP00000255622:D760G|.	D|T	+|+	2|1	0|0	PDE6B|PDE6B	650330|650330	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.926000|0.926000	0.56050|0.56050	6.872000|6.872000	0.75536|0.75536	1.687000|1.687000	0.51057|0.51057	0.524000|0.524000	0.50904|0.50904	GAC|ACC	.	.		0.637	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		G	660330	A	G	660330	3	3	112	1	0	0	0	0	1	0	0	0	11655	275	10	2	2357	2	PDE6B	4	660330	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10		660330	190493946	296	16917										
SPON2	10417	hgsc.bcm.edu	37	chr4	1165676	1165676	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgcgcaggggggcggaacaGggggtactgcttggggaagg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:1165676delG	ENST00000290902.5	-	2	516	c.184delC	c.(184-186)ctgfs	p.L62fs	SPON2_ENST00000431380.1_Frame_Shift_Del_p.L62fs	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	62	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		GGGCGGAACAGGGGGTACTGC	0.672																																					p.L62fs		Atlas-INDEL	.											.	SPON2	22	.	0			c.185delT						.						55	76	69					4																	1165676		2189	4287	6476	SO:0001589	frameshift_variant	10417	exon2			.	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"Mindin", "M-spondin"	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.184delC	chr4.hg19:g.1165676delG	ENSP00000290902:p.Leu62fs	95.0	0.0		159.0	10.0	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Frame_Shift_Del	DEL	ENST00000290902.5	hg19	CCDS3347.1																																																																																			.	.		0.672	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2			-	1165676	G	-	1165676	7	5	112	1	0	1	0	1	0	0	0	0	15098	991	35	0	831	0	SPON2	4	1165676	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	505346	1165676	189988600	297	16918										
CTBP1	1487	hgsc.bcm.edu	37	chr4	1206096	1206096	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttggccaggagaaggggcgtGgggcgggtgggccacagggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:1206096delG	ENST00000290921.6	-	9	1436	c.1255delC	c.(1255-1257)cacfs	p.H419fs	CTBP1_ENST00000382952.3_Frame_Shift_Del_p.H408fs	NM_001328.2	NP_001319.1	Q13363	CTBP1_HUMAN	C-terminal binding protein 1	419					Golgi organization (GO:0007030)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone deacetylation (GO:0031065)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of transcription by chromatin organization (GO:0034401)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.00818)	Colorectal(103;0.2)		GAAGGGGCGTGGGGCGGGTGG	0.701																																					p.H419fs		Atlas-INDEL	.											.	CTBP1	30	.	0			c.1256delA						.						10	11	11					4																	1206096		2152	4257	6409	SO:0001589	frameshift_variant	1487	exon9			.	U37408	CCDS3348.1, CCDS43203.1	4p16	2008-02-05			ENSG00000159692	ENSG00000159692			2494	protein-coding gene	gene with protein product	"brefeldin A-ribosylated substrate"	602618				9479502	Standard	XM_005272261		Approved	BARS	uc003gcv.1	Q13363	OTTHUMG00000089259	ENST00000290921.6:c.1255delC	chr4.hg19:g.1206096delG	ENSP00000290921:p.His419fs	177.0	0.0		180.0	11.0	NM_001328	Q4W5N3|Q7Z2Q5	Frame_Shift_Del	DEL	ENST00000290921.6	hg19	CCDS3348.1																																																																																			.	.		0.701	CTBP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000202938.1	NM_001328		-	1206096	G	-	1206096	7	5	112	1	0	1	0	1	0	0	0	0	3999	1348	47	0	71	0	CTBP1	4	1206096	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	40420	1206096	189948180	298	16919										
SORCS2	57537	hgsc.bcm.edu	37	chr4	7716932	7716932	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actacggatttgagcgctccTcctcctcagagtccagcacc					rs6816604	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:7716932delT	ENST00000507866.2	+	17	2255	c.2146delT	c.(2146-2148)tccfs	p.S718fs	SORCS2_ENST00000329016.9_Frame_Shift_Del_p.S546fs	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	718					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						TGAGCGCTCCTCCTCCTCAGA	0.592																																					p.S715fs		Atlas-INDEL	.											.	SORCS2	98	.	0			c.2145delC						.						145	153	151					4																	7716932		2012	4155	6167	SO:0001589	frameshift_variant	57537	exon17			.	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2146delT	chr4.hg19:g.7716932delT	ENSP00000422185:p.Ser718fs	153.0	0.0		150.0	11.0	NM_020777	Q9P2L7	Frame_Shift_Del	DEL	ENST00000507866.2	hg19	CCDS47008.1																																																																																			.	.		0.592	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		-	7716932	T	-	7716932	7	5	112	1	0	1	0	1	0	0	0	0	14946	1551	54	0	2212	0	SORCS2	4	7716932	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	6510836	7716932	183437344	299	16920										
HTRA3	94031	hgsc.bcm.edu	37	chr4	8307696	8307696	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accccgtctctcctgttggcAgaggcggcatccaagatggt	12	13	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:8307696A>G	ENST00000307358.2	+	9	1400		c.e9-1			NM_053044.3	NP_444272.1	P83110	HTRA3_HUMAN	HtrA serine peptidase 3						negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|prostate(1)|urinary_tract(1)	18						TCCTGTTGGCAGAGGCGGCAT	0.622																																					.		Atlas-SNP	.											.	HTRA3	39	.	0			c.1197-2A>G						.						89	83	85					4																	8307696		2203	4300	6503	SO:0001630	splice_region_variant	94031	exon9			GTTGGCAGAGGCG	AY040094	CCDS3400.1, CCDS75105.1	4p16.1	2008-02-05			ENSG00000170801	ENSG00000170801			30406	protein-coding gene	gene with protein product	"pregnancy-related serine protease"	608785				12513693, 14500695	Standard	XM_005248040		Approved	Tasp, Prsp	uc003gla.3	P83110	OTTHUMG00000090561	ENST00000307358.2:c.1197-1A>G	chr4.hg19:g.8307696A>G		99.0	0.0		96.0	5.0	NM_053044	Q7Z7A2	Splice_Site	SNP	ENST00000307358.2	hg19	CCDS3400.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.005216	0.74932	.	.	ENSG00000170801	ENST00000307358	.	.	.	4.08	4.08	0.47627	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3595	0.60648	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HTRA3	8358596	1.000000	0.71417	0.998000	0.56505	0.879000	0.50718	7.408000	0.80041	1.635000	0.50512	0.248000	0.18094	.	.	.		0.622	HTRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092669.1	NM_053044	Intron	G	8307696	A	G	8307696	5	3	112	1	0	0	0	0	0	0	1	0	7464	202	7	2	1229	2	HTRA3	4	8307696	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	590764	8307696	182846580	300	16921										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13601642	13601642	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacccttcagaggtgcttgtGgaaatcatggcggtgtcacc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:13601642delG	ENST00000040738.5	-	10	7017	c.6882delC	c.(6880-6882)tccfs	p.S2294fs		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2294						nucleus (GO:0005634)	DNA binding (GO:0003677)										AGGTGCTTGTGGAAATCATGG	0.552																																					p.T2295fs		Atlas-INDEL	.											.	.	.	.	0			c.6883delA						.						61	52	55					4																	13601642		2203	4300	6503	SO:0001589	frameshift_variant	259282	exon10			.	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.6882delC	chr4.hg19:g.13601642delG	ENSP00000040738:p.Ser2294fs	169.0	0.0		179.0	11.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Frame_Shift_Del	DEL	ENST00000040738.5	hg19	CCDS3411.2																																																																																			.	.		0.552	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		-	13601642	G	-	13601642	7	5	112	1	0	1	0	1	0	0	0	0	1483	1335	47	0	2341	0	BOD1L	4	13601642	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	5293946	13601642	177552634	301	16922										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13602811	13602811	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacagtaccaatctgactgtCcccttctgcactttcacaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:13602811delC	ENST00000040738.5	-	10	5848	c.5713delG	c.(5713-5715)gacfs	p.D1905fs		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1905						nucleus (GO:0005634)	DNA binding (GO:0003677)										ATCTGACTGTCCCCTTCTGCA	0.453																																					p.D1905fs		Atlas-INDEL	.											.	.	.	.	0			c.5714delA						.						132	132	132					4																	13602811		2203	4300	6503	SO:0001589	frameshift_variant	259282	exon10			.	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.5713delG	chr4.hg19:g.13602811delC	ENSP00000040738:p.Asp1905fs	153.0	0.0		149.0	10.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Frame_Shift_Del	DEL	ENST00000040738.5	hg19	CCDS3411.2																																																																																			.	.		0.453	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		-	13602811	C	-	13602811	7	5	112	1	0	1	0	1	0	0	0	0	1483	855	30	0	3510	0	BOD1L	4	13602811	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1169	13602811	177551465	302	16923										
FGFBP1	9982	hgsc.bcm.edu	37	chr4	15938186	15938186	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccattcttcacttttttttTcccctccaccaggagcacct	3	16	2	0	rs201240184	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:15938186T>C	ENST00000382333.1	-	3	364	c.70A>G	c.(70-72)Aaa>Gaa	p.K24E	FGFBP1_ENST00000259988.2_Missense_Mutation_p.K24E	NM_005130.4	NP_005121.1	Q14512	FGFP1_HUMAN	fibroblast growth factor binding protein 1	24					cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|prostate(2)|skin(1)	10						ACTTTTTTTTTCCCCTCCACC	0.517													T|||	366	0.0730831	0.0227	0.072	5008	,	,		20082	0.1895		0.0885	False		,,,				2504	0.0061				p.K24E		Atlas-SNP	.											.	FGFBP1	26	.	0			c.A70G						.						67	71	70					4																	15938186		2200	4294	6494	SO:0001583	missense	9982	exon3			TTTTTTTCCCCTC	M60047	CCDS3418.1	4p15.32	2008-02-05			ENSG00000137440	ENSG00000137440			19695	protein-coding gene	gene with protein product		607737				11148217, 1885605	Standard	NM_005130		Approved	HBP17, FGFBP	uc003gom.3	Q14512	OTTHUMG00000097745	ENST00000382333.1:c.70A>G	chr4.hg19:g.15938186T>C	ENSP00000371770:p.Lys24Glu	145.0	0.0		152.0	7.0	NM_005130	A8K5J2	Missense_Mutation	SNP	ENST00000382333.1	hg19	CCDS3418.1	.	.	.	.	.	.	.	.	.	.	T	9.070	0.996742	0.19043	.	.	ENSG00000137440	ENST00000382333;ENST00000259988	T;T	0.15487	2.42;2.42	5.68	-4.23	0.03789	.	0.827902	0.11485	N	0.559298	T	0.12390	0.0301	L	0.42245	1.32	0.09310	N	1	B	0.21520	0.057	B	0.20955	0.032	T	0.25537	-1.0129	10	0.49607	T	0.09	.	7.7466	0.28873	0.0:0.2911:0.1875:0.5215	.	24	Q14512	FGFP1_HUMAN	E	24	ENSP00000371770:K24E;ENSP00000259988:K24E	ENSP00000259988:K24E	K	-	1	0	FGFBP1	15547284	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	-0.357000	0.07651	-0.795000	0.04462	-1.475000	0.01000	AAA	.	.		0.517	FGFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214974.1	NM_005130		C	15938186	T	C	15938186	3	2	112	1	0	0	0	0	1	0	0	0	5868	1792	62	2	638	2	FGFBP1	4	15938186	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2335375	15938186	175216090	303	16924										
TLR10	81793	hgsc.bcm.edu	37	chr4	38777029	38777029	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaatctgaactctggagttgAaaaaggaggttataggataa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:38777029delA	ENST00000308973.4	-	4	788	c.183delT	c.(181-183)tttfs	p.F61fs	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000508334.1_Frame_Shift_Del_p.F61fs|TLR10_ENST00000361424.2_Frame_Shift_Del_p.F61fs|TLR10_ENST00000506111.1_Frame_Shift_Del_p.F61fs	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	61					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						TCTGGAGTTGAAAAAGGAGGT	0.423																																					p.Q62fs		Atlas-INDEL	.											.	TLR10	87	.	0			c.184delC						.						73	70	71					4																	38777029		2203	4300	6503	SO:0001589	frameshift_variant	81793	exon4			.	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.183delT	chr4.hg19:g.38777029delA	ENSP00000308925:p.Phe61fs	166.0	0.0		200.0	13.0	NM_030956	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Frame_Shift_Del	DEL	ENST00000308973.4	hg19	CCDS3445.1																																																																																			.	.		0.423	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			-	38777029	A	-	38777029	7	5	112	1	0	1	0	1	0	0	0	0	15965	243	9	0	2256	0	TLR10	4	38777029	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	22838843	38777029	152377247	304	16925										
TLR1	7096	hgsc.bcm.edu	37	chr4	38800352	38800352	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taggaacgtggatgagaccgTtttttgacctatcaactaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:38800352delT	ENST00000502213.2	-	3	330	c.101delA	c.(100-102)aacfs	p.N34fs	TLR1_ENST00000308979.2_Frame_Shift_Del_p.N34fs			Q15399	TLR1_HUMAN	toll-like receptor 1	34					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						GATGAGACCGTTTTTTGACCT	0.323																																					p.N34fs	GBM(5;216 373 40795 46382)	Atlas-INDEL	.											.	TLR1	70	.	0			c.102delC						.						63	68	67					4																	38800352		2197	4299	6496	SO:0001589	frameshift_variant	7096	exon4			.	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.101delA	chr4.hg19:g.38800352delT	ENSP00000421259:p.Asn34fs	127.0	0.0		151.0	11.0	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Frame_Shift_Del	DEL	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.		0.323	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			-	38800352	T	-	38800352	7	5	112	1	0	1	0	1	0	0	0	0	15964	1725	60	0	2263	0	TLR1	4	38800352	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	23323	38800352	152353924	305	16926										
N4BP2	55728	hgsc.bcm.edu	37	chr4	40123872	40123872	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actgtctggaattggcattaCcccctgaactggcttttcaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:40123872delC	ENST00000261435.6	+	9	4557	c.4141delC	c.(4141-4143)cccfs	p.P1382fs		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1382					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						ATTGGCATTACCCCCTGAACT	0.413																																					p.L1380fs		Atlas-INDEL	.											.	N4BP2	166	.	0			c.4140delA						.						129	138	135					4																	40123872		2203	4300	6503	SO:0001589	frameshift_variant	55728	exon9			.	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.4141delC	chr4.hg19:g.40123872delC	ENSP00000261435:p.Pro1382fs	197.0	0.0		248.0	16.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Frame_Shift_Del	DEL	ENST00000261435.6	hg19	CCDS3457.1																																																																																			.	.		0.413	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		-	40123872	C	-	40123872	7	5	112	1	0	1	0	1	0	0	0	0	10119	507	18	0	4167	0	N4BP2	4	40123872	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1323520	40123872	151030404	306	16927										
CORIN	10699	hgsc.bcm.edu	37	chr4	47695047	47695047	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccattacattgcagtttccCggggatgcagattccactgg	11	11	0	1	rs143738568		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:47695047C>T	ENST00000273857.4	-	6	852	c.853G>A	c.(853-855)Ggg>Agg	p.G285R	CORIN_ENST00000505909.1_Missense_Mutation_p.G285R|CORIN_ENST00000508498.1_Missense_Mutation_p.G146R|CORIN_ENST00000504584.1_Missense_Mutation_p.G285R|CORIN_ENST00000502252.1_Missense_Mutation_p.G218R	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	285	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						TGCAGTTTCCCGGGGATGCAG	0.463																																					p.G285R		Atlas-SNP	.											.	CORIN	154	.	0			c.G853A						.						143	129	133					4																	47695047		2203	4300	6503	SO:0001583	missense	10699	exon6			GTTTCCCGGGGAT	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"Serine peptidases / Transmembrane"	19012	protein-coding gene	gene with protein product		605236	"corin, serine protease"			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.853G>A	chr4.hg19:g.47695047C>T	ENSP00000273857:p.Gly285Arg	100.0	0.0		127.0	48.0	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	hg19	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	T	6.621	0.483004	0.12581	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252;ENST00000505909;ENST00000504584	D;D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64;-3.64	5.54	-1.94	0.07571	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.695685	0.14811	N	0.297050	T	0.79257	0.4415	N	0.02775	-0.495	0.09310	N	1	B;B;B;B;B	0.10296	0.0;0.001;0.003;0.001;0.0	B;B;B;B;B	0.13407	0.001;0.001;0.009;0.005;0.001	T	0.70070	-0.4973	10	0.14656	T	0.56	.	2.4803	0.04586	0.0963:0.2274:0.3147:0.3616	.	285;285;218;146;285	B7Z4R1;B4E2W9;B4E1Y7;B4DZA3;Q9Y5Q5	.;.;.;.;CORIN_HUMAN	R	285;146;218;285;285	ENSP00000273857:G285R;ENSP00000425597:G146R;ENSP00000424212:G218R;ENSP00000425401:G285R;ENSP00000423216:G285R	ENSP00000273857:G285R	G	-	1	0	CORIN	47389804	0.190000	0.23276	0.499000	0.27577	0.955000	0.61496	0.181000	0.16880	-0.467000	0.06932	-0.530000	0.04314	GGG	.	C|1.000;G|0.000		0.463	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2			T	47695047	C	T	47695047	3	4	112	1	0	0	0	0	1	0	0	0	3754	652	23	1	2343	1	CORIN	4	47695047	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	7571175	47695047	143459229	307	16928										
SLAIN2	57606	hgsc.bcm.edu	37	chr4	48384604	48384604	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtctccggcaagaatatgcAgccaccacgtctcggcgcag	12	14	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:48384604A>G	ENST00000264313.6	+	5	1300	c.882A>G	c.(880-882)gcA>gcG	p.A294A	SLAIN2_ENST00000512093.1_Silent_p.A101A	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	294					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						AAGAATATGCAGCCACCACGT	0.338																																					p.A294A		Atlas-SNP	.											.	SLAIN2	31	.	0			c.A882G						.						50	45	47					4																	48384604		1936	4123	6059	SO:0001819	synonymous_variant	57606	exon5			ATATGCAGCCACC	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"KIAA1458"	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.882A>G	chr4.hg19:g.48384604A>G		29.0	0.0		45.0	4.0	NM_020846	A8K4P1|Q8N5R3	Silent	SNP	ENST00000264313.6	hg19	CCDS47051.1																																																																																			.	.		0.338	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846		G	48384604	A	G	48384604	2	3	112	1	0	0	0	0	0	0	0	1	14381	175	7	2		2	SLAIN2	4	48384604	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	689557	48384604	142769672	308	16929										
POLR2B	5431	hgsc.bcm.edu	37	chr4	57877166	57877166	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcattgtagtgcaaccaagaTttttgttaatggctgctggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:57877166delT	ENST00000381227.1	+	14	2113	c.1700delT	c.(1699-1701)attfs	p.I567fs	POLR2B_ENST00000441246.2_Frame_Shift_Del_p.I560fs|POLR2B_ENST00000510355.1_3'UTR|POLR2B_ENST00000431623.2_Frame_Shift_Del_p.I492fs|POLR2B_ENST00000314595.5_Frame_Shift_Del_p.I567fs			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	567					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					GCAACCAAGATTTTTGTTAAT	0.333																																					p.I567fs		Atlas-INDEL	.											.	POLR2B	108	.	0			c.1699delA						.						108	104	105					4																	57877166		2203	4300	6503	SO:0001589	frameshift_variant	5431	exon13			.		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1700delT	chr4.hg19:g.57877166delT	ENSP00000370625:p.Ile567fs	161.0	0.0		145.0	11.0	NM_000938	A8K1A8|Q8IZ61	Frame_Shift_Del	DEL	ENST00000381227.1	hg19	CCDS3511.1																																																																																			.	.		0.333	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		-	57877166	T	-	57877166	7	5	112	1	0	1	0	1	0	0	0	0	12224	1493	52	0	1750	0	POLR2B	4	57877166	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	9492562	57877166	133277110	309	16930										
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69962593	69962593	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tacaggaaatcatgtcaataTttggtgacataactagaaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:69962593delT	ENST00000508661.1	+	1	382	c.355delT	c.(355-357)tttfs	p.F119fs	UGT2B7_ENST00000305231.7_Frame_Shift_Del_p.F119fs|UGT2B7_ENST00000509763.1_Intron			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	119					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CATGTCAATATTTGGTGACAT	0.313																																					p.I118fs		Atlas-INDEL	.											.	UGT2B7	79	.	0			c.354delA						.						49	49	49					4																	69962593		2185	4294	6479	SO:0001589	frameshift_variant	7364	exon1			.	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"UDP glucuronosyltransferases"	12554	protein-coding gene	gene with protein product		600068	"UDP glycosyltransferase 2 family, polypeptide B7"			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.355delT	chr4.hg19:g.69962593delT	ENSP00000427659:p.Phe119fs	132.0	0.0		164.0	10.0	NM_001074	B2R810|Q6GTW0	Frame_Shift_Del	DEL	ENST00000508661.1	hg19																																																																																				.	.		0.313	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		-	69962593	T	-	69962593	7	5	112	1	0	1	0	1	0	0	0	0	16977	1493	52	0	357	0	UGT2B7	4	69962593	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	12085427	69962593	121191683	310	16931										
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72432766	72432766	+	3'UTR	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acgccacacatcatgctgatAaaattcctttccttcagtca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:72432766delA	ENST00000264485.5	+	0	3359				SLC4A4_ENST00000340595.3_3'UTR|SLC4A4_ENST00000351898.6_3'UTR|SLC4A4_ENST00000425175.1_Frame_Shift_Del_p.K1049fs	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4						bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	TCATGCTGATAAAATTCCTTT	0.358																																					p.D1048fs		Atlas-INDEL	.											SLC4A4_ENST00000425175,NS,carcinoma,0,1	SLC4A4	269	.	0			c.3144delT						.						147	134	139					4																	72432766		2203	4300	6503	SO:0001624	3_prime_UTR_variant	8671	exon24			.	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.*2A>-	chr4.hg19:g.72432766delA		124.0	0.0		100.0	10.0	NM_001134742	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Frame_Shift_Del	DEL	ENST00000264485.5	hg19	CCDS43236.1																																																																																			.	.		0.358	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		-	72432766	A	-	72432766	6	5	112	0	1	1	0	1	0	0	0	0	14671	363	13	0		0	SLC4A4	4	72432766	3'UTR	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2470173	72432766	118721510	311	16932										
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73280611	73280611	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tagacaacatgaatccttccTttttcttcctccatctgttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:73280611delT	ENST00000286657.4	-	4	618	c.582delA	c.(580-582)aaafs	p.K194fs		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	194					collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GAATCCTTCCTTTTTCTTCCT	0.403																																					p.G195fs	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-INDEL	.											.	ADAMTS3	164	.	0			c.583delG						.						173	166	168					4																	73280611		2203	4300	6503	SO:0001589	frameshift_variant	9508	exon4			.	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.582delA	chr4.hg19:g.73280611delT	ENSP00000286657:p.Lys194fs	124.0	0.0		156.0	10.0	NM_014243	A1L3U9|Q9BXZ8	Frame_Shift_Del	DEL	ENST00000286657.4	hg19	CCDS3553.1																																																																																			.	.		0.403	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			-	73280611	T	-	73280611	7	5	112	1	0	1	0	1	0	0	0	0	267	1606	56	0	3111	0	ADAMTS3	4	73280611	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	847845	73280611	117873665	312	16933										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	73957752	73957752	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attcactgggttcttaatggTtttgtgagtggatgcagaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:73957752delT	ENST00000358602.4	-	29	5709	c.5593delA	c.(5593-5595)accfs	p.T1865fs	ANKRD17_ENST00000509867.2_Frame_Shift_Del_p.T1752fs|ANKRD17_ENST00000330838.6_Frame_Shift_Del_p.T1614fs	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1865					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTCTTAATGGTTTTGTGAGTG	0.433																																					p.T1865fs		Atlas-INDEL	.											.	ANKRD17	214	.	0			c.5594delC						.						175	183	180					4																	73957752		2203	4300	6503	SO:0001589	frameshift_variant	26057	exon29			.	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.5593delA	chr4.hg19:g.73957752delT	ENSP00000351416:p.Thr1865fs	189.0	0.0		197.0	14.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Frame_Shift_Del	DEL	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.433	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		-	73957752	T	-	73957752	7	5	112	1	0	1	0	1	0	0	0	0	646	1725	60	0	2242	0	ANKRD17	4	73957752	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	677141	73957752	117196524	313	16934										
ANTXR2	118429	hgsc.bcm.edu	37	chr4	80957125	80957125	+	Splice_Site	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttttaaattctaaacacttaCcccccacacagacacttgag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:80957125delC	ENST00000307333.7	-	8	700		c.e8+1		ANTXR2_ENST00000346652.6_Intron|ANTXR2_ENST00000404191.1_Splice_Site|ANTXR2_ENST00000403729.2_Splice_Site|ANTXR2_ENST00000295465.4_Splice_Site	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2						reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						TAAACACTTACCCCCCACACA	0.299									Juvenile Hyaline Fibromatosis																												.		Atlas-INDEL	.											.	ANTXR2	97	.	0			c.697+2G>-	GRCh37	CS033827	ANTXR2	S		.						26	25	26					4																	80957125		1784	4032	5816	SO:0001630	splice_region_variant	118429	exon9	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	.	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297			21732	protein-coding gene	gene with protein product	"capillary morphogenesis protein 2"	608041				11683410, 12700348	Standard	NM_058172		Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000307333.7:c.697+1G>-	chr4.hg19:g.80957125delC		159.0	0.0		213.0	13.0	NM_058172	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Splice_Site	DEL	ENST00000307333.7	hg19	CCDS47086.1																																																																																			.	.		0.299	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172	Intron	-	80957125	C	-	80957125	8	5	112	1	0	1	0	1	0	0	1	0	712	521	18	0	850	0	ANTXR2	4	80957125	Splice_Site	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	6999373	80957125	110197151	314	16935										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85614081	85614081	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcaagttgtctagatgatgAaaaaagatcttgtcacttgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:85614081delA	ENST00000295888.4	-	59	9413	c.9006delT	c.(9004-9006)tttfs	p.F3002fs	WDFY3_ENST00000322366.6_Frame_Shift_Del_p.F2985fs	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	3002	Interaction with ATG5.|Interaction with SQSTM1.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CTAGATGATGAAAAAAGATCT	0.358																																					p.H3003fs		Atlas-INDEL	.											.	WDFY3	314	.	0			c.9007delC						.						116	112	113					4																	85614081		2203	4300	6503	SO:0001589	frameshift_variant	23001	exon59			.	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.9006delT	chr4.hg19:g.85614081delA	ENSP00000295888:p.Phe3002fs	103.0	0.0		164.0	10.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Frame_Shift_Del	DEL	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.		0.358	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		-	85614081	A	-	85614081	7	5	112	1	0	1	0	1	0	0	0	0	17285	243	9	0	1614	0	WDFY3	4	85614081	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4656956	85614081	105540195	315	16936										
AFF1	4299	hgsc.bcm.edu	37	chr4	88026981	88026981	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccccagagaagcctccctccTcatctgcacctccaaggtac	6	19	2	1	rs141434206		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:88026981T>C	ENST00000307808.6	+	9	1759	c.1339T>C	c.(1339-1341)Tca>Cca	p.S447P	AFF1_ENST00000395146.4_Missense_Mutation_p.S454P|AFF1_ENST00000544085.1_Missense_Mutation_p.S85P	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	447					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		GCCTCCCTCCTCATCTGCACC	0.423																																					p.S454P		Atlas-SNP	.											.	AFF1	102	.	0			c.T1360C						.						195	185	188					4																	88026981		2203	4300	6503	SO:0001583	missense	4299	exon10			CCCTCCTCATCTG	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.1339T>C	chr4.hg19:g.88026981T>C	ENSP00000305689:p.Ser447Pro	176.0	0.0		112.0	5.0	NM_001166693	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	hg19	CCDS3616.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.47|13.47	2.247952|2.247952	0.39697|0.39697	.|.	.|.	ENSG00000172493|ENSG00000172493	ENST00000541943|ENST00000395146;ENST00000307808;ENST00000511722;ENST00000544085;ENST00000514970	.|T;T;T;T;T	.|0.63744	.|-0.06;-0.06;-0.06;-0.06;-0.06	5.91|5.91	-1.59|-1.59	0.08453|0.08453	.|.	.|0.809745	.|0.11469	.|N	.|0.560997	.|T	.|0.30198	.|0.0757	N|N	0.03000|0.03000	-0.44|-0.44	0.38468|0.38468	D|D	0.947388|0.947388	.|B;B;B	.|0.22541	.|0.071;0.071;0.071	.|B;B;B	.|0.29663	.|0.105;0.105;0.105	.|T	.|0.09164	.|-1.0687	.|10	.|0.22706	.|T	.|0.39	.|0.0102	2.4099|2.4099	0.04421|0.04421	0.3915:0.0658:0.1458:0.3969|0.3915:0.0658:0.1458:0.3969	.|.	.|454;447;447	.|E9PBM3;Q14C88;P51825	.|.;.;AFF1_HUMAN	.|P	-1|454;447;85;85;138	.|ENSP00000378578:S454P;ENSP00000305689:S447P;ENSP00000424766:S85P;ENSP00000440843:S85P;ENSP00000424881:S138P	.|ENSP00000305689:S447P	.|S	+|+	.|1	.|0	AFF1|AFF1	88246005|88246005	0.214000|0.214000	0.23563|0.23563	0.129000|0.129000	0.21949|0.21949	0.976000|0.976000	0.68499|0.68499	0.101000|0.101000	0.15251|0.15251	-0.491000|-0.491000	0.06697|0.06697	0.533000|0.533000	0.62120|0.62120	.|TCA	.	T|1.000;A|0.000		0.423	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		C	88026981	T	C	88026981	3	2	112	1	0	0	0	0	1	0	0	0	356	1551	54	2	1415	2	AFF1	4	88026981	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2412900	88026981	103127295	316	16937										
FAM13A	10144	hgsc.bcm.edu	37	chr4	89702436	89702436	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtaccttttcgacttcctgAgtattcaaaatacaatcatc	4	10	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:89702436A>G	ENST00000264344.5	-	11	1545	c.1338T>C	c.(1336-1338)acT>acC	p.T446T	FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000513837.1_Silent_p.T92T|FAM13A_ENST00000508369.1_Silent_p.T120T|FAM13A_ENST00000395002.2_Silent_p.T120T|FAM13A_ENST00000511976.1_Intron|FAM13A_ENST00000503556.1_Silent_p.T106T	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	446					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						CGACTTCCTGAGTATTCAAAA	0.353																																					p.T446T		Atlas-SNP	.											.	FAM13A	181	.	0			c.T1338C						.						98	98	98					4																	89702436		2203	4300	6503	SO:0001819	synonymous_variant	10144	exon11			TTCCTGAGTATTC	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.1338T>C	chr4.hg19:g.89702436A>G		134.0	0.0		97.0	4.0	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Silent	SNP	ENST00000264344.5	hg19	CCDS34029.1																																																																																			.	.		0.353	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			G	89702436	A	G	89702436	2	3	112	1	0	0	0	0	0	0	0	1	5457	291	11	2		2	FAM13A	4	89702436	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1675455	89702436	101451840	317	16938										
GRID2	2895	hgsc.bcm.edu	37	chr4	94690497	94690497	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggacataaagagctttgcaGgggtcttttgtatcctggct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:94690497delG	ENST00000282020.4	+	15	2755	c.2497delG	c.(2497-2499)gggfs	p.G833fs	GRID2_ENST00000510992.1_Frame_Shift_Del_p.G738fs	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	833					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		GAGCTTTGCAGGGGTCTTTTG	0.527																																					p.A832fs		Atlas-INDEL	.											.	GRID2	233	.	0			c.2496delA						.						114	124	121					4																	94690497		2203	4300	6503	SO:0001589	frameshift_variant	2895	exon15			.	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.2497delG	chr4.hg19:g.94690497delG	ENSP00000282020:p.Gly833fs	182.0	0.0		143.0	10.0	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Frame_Shift_Del	DEL	ENST00000282020.4	hg19	CCDS3637.1																																																																																			.	.		0.527	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			-	94690497	G	-	94690497	7	5	112	1	0	1	0	1	0	0	0	0	6781	1000	35	0	2555	0	GRID2	4	94690497	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	4988061	94690497	96463779	318	16939										
RAP1GDS1	5910	hgsc.bcm.edu	37	chr4	99313179	99313179	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgggcatccactgccaaaaTgcagctcttacagaaatgtg	9	11	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:99313179T>C	ENST00000408927.3	+	6	698	c.585T>C	c.(583-585)aaT>aaC	p.N195N	RAP1GDS1_ENST00000380158.4_Silent_p.N147N|RAP1GDS1_ENST00000453712.2_Silent_p.N196N|RAP1GDS1_ENST00000339360.5_Silent_p.N196N|RAP1GDS1_ENST00000408900.3_Silent_p.N146N|RAP1GDS1_ENST00000264572.7_Intron	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	195					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		ACTGCCAAAATGCAGCTCTTA	0.348			T	NUP98	T-ALL																																p.N196N		Atlas-SNP	.		Dom	yes		4	4q21-q25	5910	"RAP1, GTP-GDP dissociation stimulator 1"		L	.	RAP1GDS1	61	.	0			c.T588C						.						101	97	98					4																	99313179		1847	4080	5927	SO:0001819	synonymous_variant	5910	exon6			CCAAAATGCAGCT		CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"Armadillo repeat containing"	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	ENST00000408927.3:c.585T>C	chr4.hg19:g.99313179T>C		126.0	0.0		77.0	33.0	NM_001100426	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Silent	SNP	ENST00000408927.3	hg19	CCDS43253.1	.	.	.	.	.	.	.	.	.	.	T	10.10	1.256495	0.22965	.	.	ENSG00000138698	ENST00000509501	.	.	.	5.75	3.3	0.37823	.	.	.	.	.	T	0.57888	0.2084	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53373	-0.8448	4	.	.	.	-18.1237	8.3318	0.32191	0.0:0.2137:0.0:0.7863	.	.	.	.	R	47	.	.	C	+	1	0	RAP1GDS1	99532202	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.469000	0.35343	0.966000	0.38159	0.374000	0.22700	TGC	.	.		0.348	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363273.2	NM_001100426		C	99313179	T	C	99313179	2	2	112	1	0	0	0	0	0	0	0	1	13054	1461	51	2		2	RAP1GDS1	4	99313179	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4622682	99313179	91841097	319	16940										
ADH4	127	hgsc.bcm.edu	37	chr4	100060247	100060247	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaatttgtgagtggactcagAcaaaacttgcattttctaca	7	7	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:100060247A>G	ENST00000265512.7	-	4	389	c.315T>C	c.(313-315)tgT>tgC	p.C105C	ADH4_ENST00000504581.1_5'Flank|ADH4_ENST00000508393.1_Silent_p.C124C|ADH4_ENST00000423445.1_Silent_p.C124C|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000505590.1_Silent_p.C124C	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	105					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		GTGGACTCAGACAAAACTTGC	0.348																																					p.C105C		Atlas-SNP	.											.	ADH4	35	.	0			c.T315C						.						94	88	90					4																	100060247		2203	4300	6503	SO:0001819	synonymous_variant	127	exon4			ACTCAGACAAAAC	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"Alcohol dehydrogenases"	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.315T>C	chr4.hg19:g.100060247A>G		119.0	0.0		100.0	4.0	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Silent	SNP	ENST00000265512.7	hg19	CCDS34032.1																																																																																			.	.		0.348	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670		G	100060247	A	G	100060247	2	3	112	1	0	0	0	0	0	0	0	1	310	273	10	2		2	ADH4	4	100060247	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	747068	100060247	91094029	320	16941										
SLC39A8	64116	hgsc.bcm.edu	37	chr4	103226251	103226251	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcaacataactgtcgactttGggatcaaatccaaatgccta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:103226251delG	ENST00000394833.2	-	4	1046	c.570delC	c.(568-570)cccfs	p.P190fs	SLC39A8_ENST00000510255.1_5'UTR|SLC39A8_ENST00000356736.4_Frame_Shift_Del_p.P190fs|SLC39A8_ENST00000424970.2_Frame_Shift_Del_p.P190fs	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	190					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		TGTCGACTTTGGGATCAAATC	0.333																																					p.K191fs		Atlas-INDEL	.											.	SLC39A8	24	.	0			c.571delA						.						64	63	63					4																	103226251		2203	4300	6503	SO:0001589	frameshift_variant	64116	exon4			.		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"Solute carriers"	20862	protein-coding gene	gene with protein product		608732	"solute carrier family 39 (metal ion transporter), member 8"			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.570delC	chr4.hg19:g.103226251delG	ENSP00000378310:p.Pro190fs	276.0	0.0		129.0	10.0	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Frame_Shift_Del	DEL	ENST00000394833.2	hg19	CCDS3656.1																																																																																			.	.		0.333	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154		-	103226251	G	-	103226251	7	5	112	1	0	1	0	1	0	0	0	0	14639	1335	47	0	909	0	SLC39A8	4	103226251	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	3166004	103226251	87928025	321	16942										
CENPE	1062	hgsc.bcm.edu	37	chr4	104066439	104066439	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cattcactttttcctgaaccTcactaatttgttttatatta	2	9	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:104066439T>C	ENST00000265148.3	-	32	4714	c.4625A>G	c.(4624-4626)gAg>gGg	p.E1542G	CENPE_ENST00000380026.3_Missense_Mutation_p.E1517G	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1542					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TTCCTGAACCTCACTAATTTG	0.303																																					p.E1542G		Atlas-SNP	.											.	CENPE	253	.	0			c.A4625G						.						75	70	72					4																	104066439		2202	4299	6501	SO:0001583	missense	1062	exon32			TGAACCTCACTAA	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.4625A>G	chr4.hg19:g.104066439T>C	ENSP00000265148:p.Glu1542Gly	119.0	0.0		86.0	5.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	T	7.302	0.613262	0.14066	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	D;T	0.81659	-1.52;-1.33	4.34	3.08	0.35506	.	.	.	.	.	D	0.86632	0.5979	M	0.75777	2.31	0.09310	N	1	D;D	0.76494	0.993;0.999	D;D	0.64144	0.91;0.922	T	0.75393	-0.3333	9	0.62326	D	0.03	.	8.9898	0.36017	0.0:0.0:0.1852:0.8148	.	1517;1542	Q02224-3;Q02224	.;CENPE_HUMAN	G	1542;1542;1517	ENSP00000265148:E1542G;ENSP00000369365:E1517G	ENSP00000265148:E1542G	E	-	2	0	CENPE	104285888	0.006000	0.16342	0.020000	0.16555	0.006000	0.05464	1.032000	0.30178	1.813000	0.52934	0.448000	0.29417	GAG	.	.		0.303	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	104066439	T	C	104066439	3	2	112	1	0	0	0	0	1	0	0	0	3232	1551	54	2	3552	2	CENPE	4	104066439	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	840188	104066439	87087837	322	16943										
TBCK	93627	hgsc.bcm.edu	37	chr4	107156504	107156504	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttgcttctttccagatttgGttttttttatatggataagc	7	6	1	1	rs532862191		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:107156504G>T	ENST00000273980.5	-	16	1818	c.1371C>A	c.(1369-1371)aaC>aaA	p.N457K	TBCK_ENST00000361687.4_Missense_Mutation_p.N394K|TBCK_ENST00000432496.2_Missense_Mutation_p.N457K|TBCK_ENST00000394708.2_Missense_Mutation_p.N457K|TBCK_ENST00000394706.3_Missense_Mutation_p.N418K					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TCCAGATTTGGTTTTTTTTAT	0.363													G|||	1	0.000199681	8e-04	0	5008	,	,		14482	0		0	False		,,,				2504	0				p.N457K		Atlas-SNP	.											.,1	TBCK	89	.	0			c.C1371A						.																																			SO:0001583	missense	93627	exon15			GATTTGGTTTTTT		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1371C>A	chr4.hg19:g.107156504G>T	ENSP00000273980:p.Asn457Lys	53.0	0.0		34.0	2.0	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	hg19	CCDS54788.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.104986	0.37145	.	.	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394706;ENST00000394708	T;T;T;T;T	0.09817	2.94;2.94;2.94;2.94;2.94	5.9	0.724	0.18236	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.06645	0.0170	L	0.34521	1.04	0.48087	D	0.999586	B;P;B	0.43094	0.013;0.799;0.012	B;B;B	0.33620	0.003;0.167;0.022	T	0.39396	-0.9616	10	0.34782	T	0.22	.	10.6525	0.45657	0.6634:0.0:0.3366:0.0	.	457;418;394	Q8TEA7;Q8TEA7-2;Q8TEA7-3	TBCK_HUMAN;.;.	K	457;457;394;418;457	ENSP00000273980:N457K;ENSP00000405847:N457K;ENSP00000355338:N394K;ENSP00000378196:N418K;ENSP00000378198:N457K	ENSP00000273980:N457K	N	-	3	2	TBCK	107375953	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.665000	0.46791	0.157000	0.19338	-1.027000	0.02421	AAC	.	.		0.363	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		T	107156504	G	T	107156504	3	4	112	1	0	0	0	0	1	0	0	0	15651	1252	44	3	1358	3	TBCK	4	107156504	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	3090065	107156504	83997772	323	16944										
CYP2U1	113612	hgsc.bcm.edu	37	chr4	108866756	108866756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatgtcgctgaaccccgatgTacaaggtaattaataggtgt	10	7	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:108866756T>C	ENST00000332884.6	+	2	1396	c.1121T>C	c.(1120-1122)gTa>gCa	p.V374A	RP11-286E11.1_ENST00000513071.1_RNA|CYP2U1_ENST00000508453.1_Missense_Mutation_p.V165A	NM_183075.2	NP_898898.1	Q7Z449	CP2U1_HUMAN	cytochrome P450, family 2, subfamily U, polypeptide 1	374					arachidonic acid metabolic process (GO:0019369)|cell death (GO:0008219)|omega-hydroxylase P450 pathway (GO:0097267)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|large_intestine(2)|lung(4)|skin(2)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000128)		AACCCCGATGTACAAGGTAAT	0.408																																					p.V374A		Atlas-SNP	.											.	CYP2U1	20	.	0			c.T1121C						.						127	124	125					4																	108866756		2203	4300	6503	SO:0001583	missense	113612	exon2			CCGATGTACAAGG	BC012027	CCDS34047.1	4q25	2012-11-23			ENSG00000155016	ENSG00000155016		"Cytochrome P450s"	20582	protein-coding gene	gene with protein product	"spastic paraplegia 49"	610670				14975754, 14660610	Standard	XM_005262717		Approved	SPG49	uc003hyp.3	Q7Z449	OTTHUMG00000161084	ENST00000332884.6:c.1121T>C	chr4.hg19:g.108866756T>C	ENSP00000333212:p.Val374Ala	84.0	0.0		68.0	4.0	NM_183075	B2RMV7|Q96EQ6	Missense_Mutation	SNP	ENST00000332884.6	hg19	CCDS34047.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.286053	0.23478	.	.	ENSG00000155016	ENST00000332884;ENST00000424249;ENST00000508453	T;T	0.72394	-0.65;-0.65	5.83	4.62	0.57501	.	0.392414	0.28659	N	0.014563	T	0.75027	0.3794	L	0.60012	1.86	0.09310	N	1	B	0.30709	0.291	P	0.45712	0.491	T	0.70103	-0.4964	10	0.87932	D	0	.	10.507	0.44839	0.2581:0.0:0.0:0.7419	.	374	Q7Z449	CP2U1_HUMAN	A	374;331;165	ENSP00000333212:V374A;ENSP00000423667:V165A	ENSP00000333212:V374A	V	+	2	0	CYP2U1	109086205	0.930000	0.31532	0.001000	0.08648	0.162000	0.22319	4.747000	0.62141	0.989000	0.38761	0.459000	0.35465	GTA	.	.		0.408	CYP2U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363691.2	NM_183075		C	108866756	T	C	108866756	3	2	112	1	0	0	0	0	1	0	0	0	4177	1638	57	2	1127	2	CYP2U1	4	108866756	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1710252	108866756	82287520	324	16945										
CCDC109B	55013	hgsc.bcm.edu	37	chr4	110605773	110605773	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catttgcaaattctatggtcTtttttgcatactttatagtc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:110605773delT	ENST00000394650.4	+	6	920	c.787delT	c.(787-789)tttfs	p.F264fs		NM_017918.4	NP_060388.2	Q9NWR8	MCUB_HUMAN	coiled-coil domain containing 109B	264					mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)	calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of membrane (GO:0031224)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium channel inhibitor activity (GO:0019855)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(1)	9				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)		TTCTATGGTCTTTTTTGCATA	0.423																																					p.V262fs		Atlas-INDEL	.											.	CCDC109B	47	.	0			c.786delC						.						189	175	180					4																	110605773		2203	4300	6503	SO:0001589	frameshift_variant	55013	exon6			.	BC002633	CCDS3683.2	4q25	2011-05-24			ENSG00000005059	ENSG00000005059			26076	protein-coding gene	gene with protein product						12477932	Standard	NM_017918		Approved	FLJ20647	uc011cfs.2	Q9NWR8	OTTHUMG00000161103	ENST00000394650.4:c.787delT	chr4.hg19:g.110605773delT	ENSP00000378145:p.Phe264fs	156.0	0.0		107.0	10.0	NM_017918	A8K4Y3|Q6IAC1	Frame_Shift_Del	DEL	ENST00000394650.4	hg19	CCDS3683.2																																																																																			.	.		0.423	CCDC109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254865.1	NM_017918		-	110605773	T	-	110605773	7	5	112	1	0	1	0	1	0	0	0	0	2747	1609	56	0	809	0	CCDC109B	4	110605773	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1739017	110605773	80548503	325	16946										
LARP7	51574	hgsc.bcm.edu	37	chr4	113567545	113567545	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgtgtcttttaacaaaatgAaaaaattgactactgatggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:113567545delA	ENST00000344442.5	+	3	519	c.241delA	c.(241-243)aaafs	p.K82fs	MIR302B_ENST00000362188.1_RNA|MIR367_ENST00000362299.1_RNA|MIR302C_ENST00000362232.1_RNA|MIR302D_ENST00000362275.1_RNA|MIR302B_ENST00000505215.1_RNA|MIR302A_ENST00000385192.1_RNA|LARP7_ENST00000509061.1_Frame_Shift_Del_p.K89fs|MIR302B_ENST00000510655.1_RNA|LARP7_ENST00000324052.6_Frame_Shift_Del_p.K82fs|MIR302B_ENST00000509938.1_RNA	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	82	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.				RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		TAACAAAATGAAAAAATTGAC	0.289																																					p.M87fs		Atlas-INDEL	.											.,1	LARP7	54	.	0			c.261delG						.																																			SO:0001589	frameshift_variant	51574	exon5			.	AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	24912	protein-coding gene	gene with protein product	"P-TEFb-interaction protein for 7SK stability"	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.241delA	chr4.hg19:g.113567545delA	ENSP00000344950:p.Lys82fs	259.0	0.0		179.0	11.0	NM_001267039	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Frame_Shift_Del	DEL	ENST00000344442.5	hg19	CCDS3701.2																																																																																			.	.		0.289	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648		-	113567545	A	-	113567545	7	5	112	1	0	1	0	1	0	0	0	0	8642	247	9	0	247	0	LARP7	4	113567545	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2961772	113567545	77586731	326	16947										
ANK2	287	hgsc.bcm.edu	37	chr4	114276005	114276005	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctccataggagttaagaaAgaagatgcagctggaggaaa	12	6	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:114276005A>G	ENST00000357077.4	+	38	6284	c.6231A>G	c.(6229-6231)aaA>aaG	p.K2077K	ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Silent_p.K2044K|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000509550.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2077					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GAGTTAAGAAAGAAGATGCAG	0.478																																					p.K2077K		Atlas-SNP	.											.	ANK2	576	.	0			c.A6231G						.						77	83	81					4																	114276005		2203	4300	6503	SO:0001819	synonymous_variant	287	exon38			TAAGAAAGAAGAT	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.6231A>G	chr4.hg19:g.114276005A>G		108.0	0.0		92.0	5.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.		0.478	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114276005	A	G	114276005	2	3	112	1	0	0	0	0	0	0	0	1	621	69	3	2		2	ANK2	4	114276005	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	708460	114276005	76878271	327	16948										
NDST3	9348	hgsc.bcm.edu	37	chr4	118975821	118975821	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccttccatctctaaaggtgcTttttatgccactattataca					rs35086179		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:118975821delT	ENST00000296499.5	+	2	1159	c.756delT	c.(754-756)gctfs	p.A252fs	NDST3_ENST00000433996.2_Frame_Shift_Del_p.A252fs	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	252	Heparan sulfate N-deacetylase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						CTAAAGGTGCTTTTTATGCCA	0.393																																					p.A252fs		Atlas-INDEL	.											.	NDST3	107	.	0			c.755delC						.						130	126	127					4																	118975821		2203	4299	6502	SO:0001589	frameshift_variant	9348	exon2			.	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.756delT	chr4.hg19:g.118975821delT	ENSP00000296499:p.Ala252fs	173.0	0.0		180.0	11.0	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Frame_Shift_Del	DEL	ENST00000296499.5	hg19	CCDS3708.1																																																																																			.	.		0.393	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		-	118975821	T	-	118975821	7	5	112	1	0	1	0	1	0	0	0	0	10266	1596	56	0	758	0	NDST3	4	118975821	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	4699816	118975821	72178455	328	16949										
CCNA2	890	hgsc.bcm.edu	37	chr4	122742218	122742218	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcttttcatcttctaatatAattgacatgtccatagtatg	6	7	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:122742218A>C	ENST00000274026.5	-	3	789	c.486T>G	c.(484-486)atT>atG	p.I162M		NM_001237.3	NP_001228	P20248	CCNA2_HUMAN	cyclin A2	162					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|organ regeneration (GO:0031100)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|response to estradiol (GO:0032355)|response to glucagon (GO:0033762)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	12						CTTCTAATATAATTGACATGT	0.343																																					p.I162M		Atlas-SNP	.											CCNA2,colon,carcinoma,0,1	CCNA2	30	.	0			c.T486G						.						196	187	190					4																	122742218		2203	4299	6502	SO:0001583	missense	890	exon3			TAATATAATTGAC		CCDS3723.1	4q27	2012-07-12			ENSG00000145386	ENSG00000145386			1578	protein-coding gene	gene with protein product		123835		CCNA, CCN1		1675006	Standard	NM_001237		Approved		uc003iec.4	P20248	OTTHUMG00000133072	ENST00000274026.5:c.486T>G	chr4.hg19:g.122742218A>C	ENSP00000274026:p.Ile162Met	166.0	0.0		135.0	0.0	NM_001237	A8K7B6|Q2M3U6|Q4W5P4|Q6LER8	Missense_Mutation	SNP	ENST00000274026.5	hg19	CCDS3723.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.121146	0.37436	.	.	ENSG00000145386	ENST00000274026	T	0.15256	2.44	5.86	3.55	0.40652	.	0.665471	0.12795	U	0.438573	T	0.14787	0.0357	L	0.58101	1.795	0.32550	N	0.532438	B	0.12630	0.006	B	0.12156	0.007	T	0.18429	-1.0337	10	0.33940	T	0.23	.	1.6245	0.02720	0.5393:0.1859:0.0894:0.1854	.	162	P20248	CCNA2_HUMAN	M	162	ENSP00000274026:I162M	ENSP00000274026:I162M	I	-	3	3	CCNA2	122961668	0.997000	0.39634	0.569000	0.28460	0.977000	0.68977	1.504000	0.35726	1.038000	0.40049	0.482000	0.46254	ATT	.	.		0.343	CCNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256712.2	NM_001237		C	122742218	A	C	122742218	3	2	112	1	0	0	0	0	1	0	0	0	2912	358	13	5	836	5	CCNA2	4	122742218	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	3766397	122742218	68412058	329	16950										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123145811	123145811	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgcaggctggaagtcttacAgctaaggtcacagcaccaca	11	11	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:123145811A>G	ENST00000264501.4	+	23	3145	c.2772A>G	c.(2770-2772)acA>acG	p.T924T	KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000455637.1_Silent_p.T924T|KIAA1109_ENST00000388738.3_Silent_p.T924T			Q2LD37	K1109_HUMAN	KIAA1109	924					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GAAGTCTTACAGCTAAGGTCA	0.433																																					p.T924T		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A2772G						.						121	122	121					4																	123145811		1952	4149	6101	SO:0001819	synonymous_variant	84162	exon21			TCTTACAGCTAAG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.2772A>G	chr4.hg19:g.123145811A>G		209.0	0.0		168.0	7.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	A	9.136	1.012639	0.19277	.	.	ENSG00000138688	ENST00000424425	.	.	.	5.23	2.75	0.32379	.	.	.	.	.	T	0.45337	0.1337	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30416	-0.9979	4	.	.	.	.	2.2057	0.03935	0.6008:0.1327:0.1393:0.1271	.	.	.	.	G	756	.	.	S	+	1	0	KIAA1109	123365261	0.908000	0.30866	1.000000	0.80357	0.981000	0.71138	0.122000	0.15687	0.387000	0.25024	-0.389000	0.06534	AGC	.	.		0.433	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123145811	A	G	123145811	2	3	112	1	0	0	0	0	0	0	0	1	8217	175	7	2		2	KIAA1109	4	123145811	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	403593	123145811	68008465	330	16951										
SPRY1	10252	hgsc.bcm.edu	37	chr4	124322782	124322782	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caacatggcagtggcagttcGttagttgtgatccagcagcc	12	10	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:124322782G>A	ENST00000394339.2	+	2	376	c.36G>A	c.(34-36)tcG>tcA	p.S12S	SPRY1_ENST00000339241.1_Silent_p.S12S	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)	12					epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				NS(1)|large_intestine(4)|lung(2)|ovary(1)|skin(3)	11						GTGGCAGTTCGTTAGTTGTGA	0.453																																					p.S12S		Atlas-SNP	.											.	SPRY1	28	.	0			c.G36A						.						172	181	178					4																	124322782		2203	4300	6503	SO:0001819	synonymous_variant	10252	exon2			CAGTTCGTTAGTT	AF041037	CCDS3731.1	4q	2009-04-17	2001-11-28		ENSG00000164056	ENSG00000164056			11269	protein-coding gene	gene with protein product		602465	"sprouty (Drosophila) homolog 1 (antagonist of FGF signaling)"			9458049, 15962011	Standard	NM_001258038		Approved	hSPRY1	uc003ifa.4	O43609	OTTHUMG00000133071	ENST00000394339.2:c.36G>A	chr4.hg19:g.124322782G>A		143.0	0.0		188.0	60.0	NM_001258039	D3DNX6|Q6PNE0	Silent	SNP	ENST00000394339.2	hg19	CCDS3731.1																																																																																			.	.		0.453	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1			A	124322782	G	A	124322782	2	1	112	1	0	0	0	0	0	0	0	1	15120	1132	40	1		1	SPRY1	4	124322782	Silent	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	1176971	124322782	66831494	331	16952										
SPRY1	10252	hgsc.bcm.edu	37	chr4	124323707	124323707	+	3'UTR	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtcagggtaaaccatcatgaTttttggaggtgggttgtacc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:124323707delT	ENST00000394339.2	+	0	1301				SPRY1_ENST00000339241.1_3'UTR	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)						epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				NS(1)|large_intestine(4)|lung(2)|ovary(1)|skin(3)	11						ACCATCATGATTTTTGGAGGT	0.433																																					p.X320C		Atlas-INDEL	.											.	SPRY1	28	.	0			c.960delA						.						64	68	67					4																	124323707		2173	4277	6450	SO:0001624	3_prime_UTR_variant	10252	exon3			.	AF041037	CCDS3731.1	4q	2009-04-17	2001-11-28		ENSG00000164056	ENSG00000164056			11269	protein-coding gene	gene with protein product		602465	"sprouty (Drosophila) homolog 1 (antagonist of FGF signaling)"			9458049, 15962011	Standard	NM_001258038		Approved	hSPRY1	uc003ifa.4	O43609	OTTHUMG00000133071	ENST00000394339.2:c.*1T>-	chr4.hg19:g.124323707delT		148.0	0.0		168.0	13.0	NM_001258038	D3DNX6|Q6PNE0	Frame_Shift_Del	DEL	ENST00000394339.2	hg19	CCDS3731.1																																																																																			.	.		0.433	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1			-	124323707	T	-	124323707	6	5	112	0	1	1	0	1	0	0	0	0	15120	1508	52	0		0	SPRY1	4	124323707	3'UTR	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	925	124323707	66830569	332	16953										
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125591535	125591535	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctacgtttgcaccattttctAaaaaatattcggccattgta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:125591535delA	ENST00000504087.1	-	4	3934	c.2897delT	c.(2896-2898)ttafs	p.L966fs	ANKRD50_ENST00000515641.1_Frame_Shift_Del_p.L787fs	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	966										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						ACCATTTTCTAAAAAATATTC	0.428																																					p.L966fs		Atlas-INDEL	.											.	ANKRD50	136	.	0			c.2898delA						.						65	60	62					4																	125591535		2203	4300	6503	SO:0001589	frameshift_variant	57182	exon4			.	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.2897delT	chr4.hg19:g.125591535delA	ENSP00000425658:p.Leu966fs	159.0	0.0		178.0	15.0	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Frame_Shift_Del	DEL	ENST00000504087.1	hg19	CCDS34060.1																																																																																			.	.		0.428	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		-	125591535	A	-	125591535	7	5	112	1	0	1	0	1	0	0	0	0	677	372	13	0	1396	0	ANKRD50	4	125591535	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1267828	125591535	65562741	333	16954										
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125593315	125593315	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgacatgtttttggtccataCtgcgtgatataattccgtta	8	8	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:125593315C>T	ENST00000504087.1	-	4	2154	c.1117G>A	c.(1117-1119)Gta>Ata	p.V373I	ANKRD50_ENST00000515641.1_Missense_Mutation_p.V194I	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	373								p.V373I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TTGGTCCATACTGCGTGATAT	0.363																																					p.V373I		Atlas-SNP	.											ANKRD50,NS,carcinoma,0,1	ANKRD50	136	.	1	Substitution - Missense(1)	endometrium(1)	c.G1117A						.						136	136	136					4																	125593315		2203	4300	6503	SO:0001583	missense	57182	exon4			TCCATACTGCGTG	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1117G>A	chr4.hg19:g.125593315C>T	ENSP00000425658:p.Val373Ile	119.0	1.0		95.0	4.0	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	hg19	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.039880	0.55003	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.65364	-0.15;-0.13	5.29	5.29	0.74685	.	0.148679	0.46145	D	0.000307	T	0.42359	0.1199	N	0.16602	0.42	0.58432	D	0.999998	B	0.30824	0.296	B	0.19946	0.027	T	0.44802	-0.9304	10	0.05525	T	0.97	.	19.1267	0.93388	0.0:1.0:0.0:0.0	.	373	Q9ULJ7	ANR50_HUMAN	I	373;194	ENSP00000425658:V373I;ENSP00000425355:V194I	ENSP00000425658:V373I	V	-	1	0	ANKRD50	125812765	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.164000	0.77533	2.753000	0.94483	0.555000	0.69702	GTA	.	.		0.363	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		T	125593315	C	T	125593315	3	4	112	1	0	0	0	0	1	0	0	0	677	565	20	3	3176	3	ANKRD50	4	125593315	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1780	125593315	65560961	334	16955										
FAT4	79633	hgsc.bcm.edu	37	chr4	126329790	126329790	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcactgttcgagcagaagatGgtgggggacaatttactacc	12	8	1	2	rs370906656		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:126329790G>C	ENST00000394329.3	+	4	5774	c.5761G>C	c.(5761-5763)Ggt>Cgt	p.G1921R	FAT4_ENST00000335110.5_Missense_Mutation_p.G219R	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1921	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G1921C(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AGCAGAAGATGGTGGGGGACA	0.333																																					p.G1921R		Atlas-SNP	.											FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	.	2	Substitution - Missense(2)	lung(2)	c.G5761C						.						88	90	89					4																	126329790		2203	4300	6503	SO:0001583	missense	79633	exon4			GAAGATGGTGGGG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.5761G>C	chr4.hg19:g.126329790G>C	ENSP00000377862:p.Gly1921Arg	82.0	0.0		97.0	0.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	18.24	3.580005	0.65992	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01787	4.64;4.64	5.2	5.2	0.72013	Cadherin (4);Cadherin-like (1);	0.000000	0.34853	U	0.003632	T	0.06872	0.0175	L	0.39397	1.21	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.97110	0.994;1.0	T	0.55921	-0.8064	10	0.27082	T	0.32	.	18.7437	0.91784	0.0:0.0:1.0:0.0	.	219;1921	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	R	1921;219	ENSP00000377862:G1921R;ENSP00000335169:G219R	ENSP00000335169:G219R	G	+	1	0	FAT4	126549240	1.000000	0.71417	0.991000	0.47740	0.328000	0.28507	9.231000	0.95317	2.420000	0.82092	0.591000	0.81541	GGT	.	.		0.333	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126329790	G	C	126329790	3	2	112	1	0	0	0	0	1	0	0	0	5700	1348	47	4	5775	4	FAT4	4	126329790	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	736475	126329790	64824486	335	16956										
PLK4	10733	hgsc.bcm.edu	37	chr4	128814719	128814719	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taatttcagaagaggaaaggAaaactaggagtgctcccttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:128814719delA	ENST00000270861.5	+	12	2648	c.2374delA	c.(2374-2376)aaafs	p.K792fs	PLK4_ENST00000515069.1_Frame_Shift_Del_p.K714fs|RNU6-583P_ENST00000516012.1_RNA|PLK4_ENST00000513090.1_Frame_Shift_Del_p.K760fs|PLK4_ENST00000514379.1_Frame_Shift_Del_p.K751fs|PLK4_ENST00000507249.1_Frame_Shift_Del_p.K731fs	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	792					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						AGAGGAAAGGAAAACTAGGAG	0.323																																					p.R791fs	Colon(135;508 1718 19061 31832 42879)	Atlas-INDEL	.											.	PLK4	65	.	0			c.2373delG						.						78	81	80					4																	128814719		2203	4300	6503	SO:0001589	frameshift_variant	10733	exon12			.	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.2374delA	chr4.hg19:g.128814719delA	ENSP00000270861:p.Lys792fs	126.0	0.0		169.0	13.0	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Frame_Shift_Del	DEL	ENST00000270861.5	hg19	CCDS3735.1																																																																																			.	.		0.323	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			-	128814719	A	-	128814719	7	5	112	1	0	1	0	1	0	0	0	0	12107	247	9	0	2420	0	PLK4	4	128814719	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2484929	128814719	62339557	336	16957										
RNF150	57484	hgsc.bcm.edu	37	chr4	141868832	141868832	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agggcaggatccggacaacgTcattgggcttgtacccttca	12	11	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:141868832T>C	ENST00000515673.2	-	4	899	c.866A>G	c.(865-867)gAc>gGc	p.D289G	RNF150_ENST00000507500.1_Missense_Mutation_p.D289G|RNF150_ENST00000306799.3_Missense_Mutation_p.D247G|RNF150_ENST00000420921.2_Missense_Mutation_p.D148G|RNF150_ENST00000379512.2_Missense_Mutation_p.D148G|RNF150_ENST00000515057.1_5'UTR			Q9ULK6	RN150_HUMAN	ring finger protein 150	289						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					CCGGACAACGTCATTGGGCTT	0.537																																					p.D289G		Atlas-SNP	.											.	RNF150	94	.	0			c.A866G						.						152	119	130					4																	141868832		2203	4300	6503	SO:0001583	missense	57484	exon4			ACAACGTCATTGG	AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"RING-type (C3HC4) zinc fingers"	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.866A>G	chr4.hg19:g.141868832T>C	ENSP00000425840:p.Asp289Gly	251.0	0.0		264.0	11.0	NM_020724	Q3T1D0|Q6ZNW6	Missense_Mutation	SNP	ENST00000515673.2	hg19	CCDS34065.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.724036	0.89298	.	.	ENSG00000170153	ENST00000379512;ENST00000420921;ENST00000306799;ENST00000515673;ENST00000507500;ENST00000506101	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	5.95	5.95	0.96441	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.000000	0.85682	D	0.000000	T	0.66790	0.2825	M	0.62016	1.91	0.80722	D	1	D;P;D	0.89917	0.969;0.862;1.0	P;P;D	0.91635	0.796;0.746;0.999	T	0.69472	-0.5136	10	0.87932	D	0	.	15.4149	0.74960	0.0:0.0:0.0:1.0	.	247;289;289	Q9ULK6-2;Q9ULK6-3;Q9ULK6	.;.;RN150_HUMAN	G	148;148;247;289;289;120	ENSP00000368827:D148G;ENSP00000394581:D148G;ENSP00000304321:D247G;ENSP00000425840:D289G;ENSP00000425568:D289G;ENSP00000425947:D120G	ENSP00000304321:D247G	D	-	2	0	RNF150	142088282	1.000000	0.71417	0.916000	0.36221	0.984000	0.73092	7.336000	0.79245	2.281000	0.76405	0.528000	0.53228	GAC	.	.		0.537	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090		C	141868832	T	C	141868832	3	2	112	1	0	0	0	0	1	0	0	0	13466	1667	58	2	466	2	RNF150	4	141868832	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	13054113	141868832	49285444	337	16958										
USP38	84640	hgsc.bcm.edu	37	chr4	144135539	144135539	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttacttctttctcttcattgTcagaaagttggtctgtagat	7	7	5	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:144135539T>C	ENST00000307017.4	+	9	2916	c.2410T>C	c.(2410-2412)Tca>Cca	p.S804P	USP38_ENST00000510377.1_Missense_Mutation_p.S804P	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	804	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					CTCTTCATTGTCAGAAAGTTG	0.368																																					p.S804P		Atlas-SNP	.											.	USP38	92	.	0			c.T2410C						.						76	74	75					4																	144135539		2203	4300	6503	SO:0001583	missense	84640	exon9			TCATTGTCAGAAA	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2410T>C	chr4.hg19:g.144135539T>C	ENSP00000303434:p.Ser804Pro	112.0	0.0		130.0	6.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	T	9.491	1.100690	0.20552	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	T;T	0.73681	-0.77;-0.77	5.48	4.26	0.50523	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.280229	0.35555	N	0.003132	T	0.57388	0.2050	N	0.21545	0.675	0.36598	D	0.874492	B;B	0.10296	0.003;0.002	B;B	0.12156	0.006;0.007	T	0.55315	-0.8160	10	0.33141	T	0.24	-9.7229	7.2722	0.26262	0.0:0.0729:0.1469:0.7801	.	804;804	Q8NB14;Q3ZCV1	UBP38_HUMAN;.	P	804	ENSP00000427647:S804P;ENSP00000303434:S804P	ENSP00000303434:S804P	S	+	1	0	USP38	144354989	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	0.980000	0.29513	0.967000	0.38186	0.482000	0.46254	TCA	.	.		0.368	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		C	144135539	T	C	144135539	3	2	112	1	0	0	0	0	1	0	0	0	17084	1667	58	2	2444	2	USP38	4	144135539	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2266707	144135539	47018737	338	16959										
USP38	84640	hgsc.bcm.edu	37	chr4	144135649	144135649	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcacaaaattggtgccctaTctattaagttccgttgtggt	9	8	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:144135649T>C	ENST00000307017.4	+	9	3026	c.2520T>C	c.(2518-2520)taT>taC	p.Y840Y	USP38_ENST00000510377.1_Silent_p.Y840Y	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	840	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					TGGTGCCCTATCTATTAAGTT	0.403																																					p.Y840Y		Atlas-SNP	.											.	USP38	92	.	0			c.T2520C						.						104	98	100					4																	144135649		2203	4300	6503	SO:0001819	synonymous_variant	84640	exon9			GCCCTATCTATTA	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2520T>C	chr4.hg19:g.144135649T>C		66.0	0.0		82.0	4.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Silent	SNP	ENST00000307017.4	hg19	CCDS3758.1																																																																																			.	.		0.403	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		C	144135649	T	C	144135649	2	2	112	1	0	0	0	0	0	0	0	1	17084	1442	50	2		2	USP38	4	144135649	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	110	144135649	47018627	339	16960										
ABCE1	6059	hgsc.bcm.edu	37	chr4	146033436	146033436	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tacctagatgtcaagcagcgTttaaaggctgctattactat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:146033436delT	ENST00000296577.4	+	9	1271	c.756delT	c.(754-756)cgtfs	p.R252fs	ABCE1_ENST00000502803.1_Intron|OTUD4_ENST00000455611.2_Intron	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	252	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					TCAAGCAGCGTTTAAAGGCTG	0.313																																					p.R252fs		Atlas-INDEL	.											.	ABCE1	47	.	0			c.755delG						.						62	59	60					4																	146033436		2202	4300	6502	SO:0001589	frameshift_variant	6059	exon9			.	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"ATP binding cassette transporters / subfamily E"	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.756delT	chr4.hg19:g.146033436delT	ENSP00000296577:p.Arg252fs	139.0	0.0		152.0	12.0	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Frame_Shift_Del	DEL	ENST00000296577.4	hg19	CCDS34071.1																																																																																			.	.		0.313	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940		-	146033436	T	-	146033436	7	5	112	1	0	1	0	1	0	0	0	0	64	1712	60	0	786	0	ABCE1	4	146033436	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1897787	146033436	45120840	340	16961										
LRBA	987	hgsc.bcm.edu	37	chr4	151829842	151829842	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtgcatgtggtgaatgaacAaaaattgaagggttgtcctt					rs373877713		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:151829842delA	ENST00000357115.3	-	10	1572	c.1329delT	c.(1327-1329)tttfs	p.F443fs	LRBA_ENST00000507224.1_Frame_Shift_Del_p.F443fs|LRBA_ENST00000535741.1_Frame_Shift_Del_p.F443fs|LRBA_ENST00000510413.1_Frame_Shift_Del_p.F443fs	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	443						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					GTGAATGAACAAAAATTGAAG	0.388																																					p.V444fs		Atlas-INDEL	.											.	LRBA	253	.	0			c.1330delG						.						150	141	144					4																	151829842		2203	4300	6503	SO:0001589	frameshift_variant	987	exon10			.	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.1329delT	chr4.hg19:g.151829842delA	ENSP00000349629:p.Phe443fs	144.0	0.0		147.0	10.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Frame_Shift_Del	DEL	ENST00000357115.3	hg19	CCDS3773.1																																																																																			.	.		0.388	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			-	151829842	A	-	151829842	7	5	112	1	0	1	0	1	0	0	0	0	8940	127	5	0	7458	0	LRBA	4	151829842	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5796406	151829842	39324434	341	16962										
RPS3A	6189	hgsc.bcm.edu	37	chr4	152025347	152025347	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggattccagacagcattggAaaagacatagaaaaggcttg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:152025347delA	ENST00000509736.1	+	3	319	c.225delA	c.(223-225)ggafs	p.G75fs	RPS3A_ENST00000506126.1_Frame_Shift_Del_p.G157fs|RPS3A_ENST00000514682.1_Frame_Shift_Del_p.G157fs|SNORD73A_ENST00000386062.1_RNA|RPS3A_ENST00000274065.4_Frame_Shift_Del_p.G194fs|SNORD73_ENST00000364394.1_RNA|RPS3A_ENST00000512690.1_Frame_Shift_Del_p.K192fs					ribosomal protein S3A											endometrium(1)|lung(1)|ovary(1)|pancreas(1)	4	all_hematologic(180;0.093)					ACAGCATTGGAAAAGACATAG	0.358																																					p.G194fs		Atlas-INDEL	.											.	RPS3A	11	.	0			c.581delG						.						52	54	53					4																	152025347		2203	4300	6503	SO:0001589	frameshift_variant	6189	exon5			.	X87373	CCDS3775.1	4q31.2-q31.3	2011-04-05			ENSG00000145425	ENSG00000145425		"S ribosomal proteins"	10421	protein-coding gene	gene with protein product		180478		MFTL		8647443, 1398113	Standard	NM_001006		Approved	S3A	uc003ilz.4	P61247	OTTHUMG00000161445	ENST00000509736.1:c.225delA	chr4.hg19:g.152025347delA	ENSP00000422994:p.Gly75fs	153.0	0.0		159.0	10.0	NM_001006		Frame_Shift_Del	DEL	ENST00000509736.1	hg19																																																																																				.	.		0.358	RPS3A-006	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000364962.2			-	152025347	A	-	152025347	7	5	112	1	0	1	0	1	0	0	0	0	13659	233	9	0	600	0	RPS3A	4	152025347	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	195505	152025347	39128929	342	16963										
ARFIP1	27236	hgsc.bcm.edu	37	chr4	153803996	153803996	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtgaataaaaccattgaagAtacattaatgactgtgaaac	8	5	0	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:153803996A>G	ENST00000451320.2	+	7	919	c.755A>G	c.(754-756)gAt>gGt	p.D252G	ARFIP1_ENST00000429148.2_Missense_Mutation_p.D72G|ARFIP1_ENST00000405727.2_Missense_Mutation_p.D220G|ARFIP1_ENST00000356064.3_Missense_Mutation_p.D220G|ARFIP1_ENST00000353617.2_Missense_Mutation_p.D252G			P53367	ARFP1_HUMAN	ADP-ribosylation factor interacting protein 1	252	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				intracellular protein transport (GO:0006886)|regulation of protein secretion (GO:0050708)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)			ARFIP1/FHDC1(2)	cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(180;0.093)					ACCATTGAAGATACATTAATG	0.348																																					p.D252G		Atlas-SNP	.											.	ARFIP1	69	.	0			c.A755G						.						89	91	90					4																	153803996		2203	4300	6503	SO:0001583	missense	27236	exon7			TTGAAGATACATT	U52521	CCDS3780.1, CCDS34080.1	4q31.3	2008-08-01	2008-08-01			ENSG00000164144			21496	protein-coding gene	gene with protein product	"arfaptin 1"	605928				9038142, 10413101	Standard	NM_001025595		Approved	HSU52521	uc003imz.3	P53367		ENST00000451320.2:c.755A>G	chr4.hg19:g.153803996A>G	ENSP00000395083:p.Asp252Gly	60.0	0.0		65.0	4.0	NM_001025595	Q2M2X4|Q3SYL4|Q9Y2X6	Missense_Mutation	SNP	ENST00000451320.2	hg19	CCDS34080.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.737579	0.89482	.	.	ENSG00000164144	ENST00000451320;ENST00000429148;ENST00000353617;ENST00000405727;ENST00000356064	D;D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11;-3.11	6.17	6.17	0.99709	Arfaptin-like (3);	0.000000	0.85682	D	0.000000	D	0.96476	0.8850	M	0.84948	2.725	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.96901	0.9660	10	0.87932	D	0	-24.5395	16.8222	0.85835	1.0:0.0:0.0:0.0	.	72;220;252	B4DS69;Q2M2X4;P53367	.;.;ARFP1_HUMAN	G	252;72;252;220;220	ENSP00000395083:D252G;ENSP00000396653:D72G;ENSP00000296557:D252G;ENSP00000384189:D220G;ENSP00000348360:D220G	ENSP00000296557:D252G	D	+	2	0	ARFIP1	154023446	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	GAT	.	.		0.348	ARFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365032.1	NM_014447		G	153803996	A	G	153803996	3	3	112	1	0	0	0	0	1	0	0	0	854	333	12	2	777	2	ARFIP1	4	153803996	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1778649	153803996	37350280	343	16964										
FGA	2243	hgsc.bcm.edu	37	chr4	155507905	155507905	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caagtctggaactggtttcaTttttatcagtggtaagtgtt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:155507905delT	ENST00000302053.3	-	5	754	c.676delA	c.(676-678)atgfs	p.M226fs	FGA_ENST00000403106.3_Frame_Shift_Del_p.M226fs	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	226					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	ACTGGTTTCATTTTTATCAGT	0.443																																					p.M226fs	NSCLC(143;340 1922 20892 22370 48145)	Atlas-INDEL	.											.	FGA	179	.	0			c.677delT						.						134	138	137					4																	155507905		2203	4300	6503	SO:0001589	frameshift_variant	2243	exon5			.		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.676delA	chr4.hg19:g.155507905delT	ENSP00000306361:p.Met226fs	147.0	0.0		154.0	13.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Frame_Shift_Del	DEL	ENST00000302053.3	hg19	CCDS3787.1																																																																																			.	.		0.443	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		-	155507905	T	-	155507905	7	5	112	1	0	1	0	1	0	0	0	0	5838	1493	52	0	1976	0	FGA	4	155507905	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1703909	155507905	35646371	344	16965										
C4orf45	152940	hgsc.bcm.edu	37	chr4	159894380	159894380	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taaatatctgagatctccagTtttttctaacgccagatgct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:159894380delT	ENST00000434826.2	-	2	232	c.148delA	c.(148-150)actfs	p.T50fs	C4orf45_ENST00000508011.1_5'UTR	NM_152543.2	NP_689756.2	Q96LM5	CD045_HUMAN	chromosome 4 open reading frame 45	50										large_intestine(2)|lung(3)	5						AGATCTCCAGTTTTTTCTAAC	0.388																																					p.T50fs		Atlas-INDEL	.											.	C4orf45	8	.	0			c.149delC						.						97	83	87					4																	159894380		1824	4088	5912	SO:0001589	frameshift_variant	152940	exon2			.		CCDS47156.1	4q32.1	2012-03-02			ENSG00000164123	ENSG00000164123			26342	protein-coding gene	gene with protein product							Standard	NM_152543		Approved	FLJ25371	uc003iqf.1	Q96LM5	OTTHUMG00000161988	ENST00000434826.2:c.148delA	chr4.hg19:g.159894380delT	ENSP00000412215:p.Thr50fs	136.0	0.0		134.0	10.0	NM_152543	A8MPU3|C9J0T8	Frame_Shift_Del	DEL	ENST00000434826.2	hg19	CCDS47156.1																																																																																			.	.		0.388	C4orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366636.1	NM_152543		-	159894380	T	-	159894380	7	5	112	1	0	1	0	1	0	0	0	0	2275	1725	60	0	428	0	C4orf45	4	159894380	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	4386475	159894380	31259896	345	16966										
NPY1R	4886	hgsc.bcm.edu	37	chr4	164246487	164246487	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attatcatcattgttgttgaTttttttaaatgcgactgggc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:164246487delT	ENST00000296533.2	-	3	1654	c.1123delA	c.(1123-1125)atcfs	p.I375fs	NPY1R_ENST00000509586.1_Frame_Shift_Del_p.I132fs	NM_000909.5	NP_000900.1	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1	375					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose metabolic process (GO:0006006)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|regulation of blood pressure (GO:0008217)|regulation of multicellular organism growth (GO:0040014)|sensory perception of pain (GO:0019233)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			breast(1)|cervix(1)|large_intestine(4)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)	30	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TTGTTGTTGATTTTTTTAAAT	0.378																																					p.I375fs		Atlas-INDEL	.											.	NPY1R	72	.	0			c.1124delT						.						138	140	139					4																	164246487		2203	4300	6503	SO:0001589	frameshift_variant	4886	exon3			.		CCDS34089.1	4q31.3-q32	2012-08-08				ENSG00000164128		"GPCR / Class A : Neuropeptide receptors : Y"	7956	protein-coding gene	gene with protein product		162641		NPYR		8095935	Standard	NM_000909		Approved		uc003iqm.2	P25929		ENST00000296533.2:c.1123delA	chr4.hg19:g.164246487delT	ENSP00000354652:p.Ile375fs	204.0	0.0		191.0	12.0	NM_000909	B2R6H5	Frame_Shift_Del	DEL	ENST00000296533.2	hg19	CCDS34089.1																																																																																			.	.		0.378	NPY1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364685.1			-	164246487	T	-	164246487	7	5	112	1	0	1	0	1	0	0	0	0	10617	1493	52	0	35	0	NPY1R	4	164246487	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	4352107	164246487	26907789	346	16967										
DDX60	55601	hgsc.bcm.edu	37	chr4	169195111	169195111	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggtgcaacgtacacgaccaCcccgtcgtcgctctccttca	9	17	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:169195111C>A	ENST00000393743.3	-	17	2719	c.2428G>T	c.(2428-2430)Gtg>Ttg	p.V810L		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	810	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		TACACGACCACCCCGTCGTCG	0.443																																					p.V810L		Atlas-SNP	.											.	DDX60	304	.	0			c.G2428T						.						150	140	143					4																	169195111		2203	4300	6503	SO:0001583	missense	55601	exon17			CGACCACCCCGTC	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.2428G>T	chr4.hg19:g.169195111C>A	ENSP00000377344:p.Val810Leu	82.0	0.0		88.0	6.0	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	hg19	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	C	15.96	2.985995	0.53934	.	.	ENSG00000137628	ENST00000393743	T	0.14516	2.5	4.98	4.98	0.66077	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.52532	D	0.000073	T	0.29458	0.0734	L	0.47190	1.495	0.44539	D	0.997495	D	0.55385	0.971	P	0.60286	0.872	T	0.01178	-1.1427	10	0.66056	D	0.02	.	18.2063	0.89855	0.0:1.0:0.0:0.0	.	810	Q8IY21	DDX60_HUMAN	L	810	ENSP00000377344:V810L	ENSP00000377344:V810L	V	-	1	0	DDX60	169431686	0.984000	0.35163	1.000000	0.80357	0.019000	0.09904	2.353000	0.44089	2.467000	0.83353	0.557000	0.71058	GTG	.	.		0.443	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		A	169195111	C	A	169195111	3	1	112	1	0	0	0	0	1	0	0	0	4380	507	18	3	2798	3	DDX60	4	169195111	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	4948624	169195111	21959165	347	16968										
DDX60	55601	hgsc.bcm.edu	37	chr4	169223484	169223484	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttattccattttaaacttccAaaaagaggtgctaatgctga					rs34458540		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:169223484delA	ENST00000393743.3	-	6	981	c.690delT	c.(688-690)tttfs	p.F230fs		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	230					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		TTAAACTTCCAAAAAGAGGTG	0.279																																					p.G231fs		Atlas-INDEL	.											.	DDX60	304	.	0			c.691delG						.						39	39	39					4																	169223484		2197	4291	6488	SO:0001589	frameshift_variant	55601	exon6			.	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.690delT	chr4.hg19:g.169223484delA	ENSP00000377344:p.Phe230fs	158.0	0.0		152.0	12.0	NM_017631	Q6PK35|Q9NVE3	Frame_Shift_Del	DEL	ENST00000393743.3	hg19	CCDS34097.1																																																																																			.	.		0.279	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		-	169223484	A	-	169223484	7	5	112	1	0	1	0	1	0	0	0	0	4380	127	5	0	4580	0	DDX60	4	169223484	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	28373	169223484	21930792	348	16969										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169348237	169348237	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ataccttcacctcggcaatgTtttttccatgctttaaagca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:169348237delT	ENST00000511577.1	-	14	2161	c.1914delA	c.(1912-1914)aaafs	p.K638fs	DDX60L_ENST00000260184.7_Frame_Shift_Del_p.K638fs|DDX60L_ENST00000505890.1_Frame_Shift_Del_p.K638fs			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	638							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CTCGGCAATGTTTTTTCCATG	0.338																																					p.H639fs		Atlas-INDEL	.											.	DDX60L	116	.	0			c.1915delC						.						64	57	59					4																	169348237		1846	4095	5941	SO:0001589	frameshift_variant	91351	exon14			.	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.1914delA	chr4.hg19:g.169348237delT	ENSP00000422423:p.Lys638fs	153.0	0.0		135.0	10.0	NM_001012967	Q96ND6	Frame_Shift_Del	DEL	ENST00000511577.1	hg19																																																																																				.	.		0.338	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		-	169348237	T	-	169348237	7	5	112	1	0	1	0	1	0	0	0	0	4381	1722	60	0	3306	0	DDX60L	4	169348237	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	124753	169348237	21806039	349	16970										
KIAA1712	80817	hgsc.bcm.edu	37	chr4	175224892	175224892	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aattataaaccaattttgacAaaaaagcagtttatccaatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:175224892delA	ENST00000503780.1	+	5	690	c.276delA	c.(274-276)acafs	p.T92fs	CEP44_ENST00000296519.4_Frame_Shift_Del_p.T92fs|CEP44_ENST00000457424.2_Frame_Shift_Del_p.T92fs|CEP44_ENST00000426172.1_Frame_Shift_Del_p.T92fs	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	92						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)				endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						CAATTTTGACAAAAAAGCAGT	0.313																																					p.T92fs		Atlas-INDEL	.											.	CEP44	35	.	0			c.275delC						.						63	66	65					4																	175224892		2202	4299	6501	SO:0001589	frameshift_variant	80817	exon5			.	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"KIAA1712"	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.276delA	chr4.hg19:g.175224892delA	ENSP00000423153:p.Thr92fs	182.0	0.0		178.0	11.0	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Frame_Shift_Del	DEL	ENST00000503780.1	hg19	CCDS34106.1																																																																																			.	.		0.313	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633		-	175224892	A	-	175224892	7	5	112	1	0	1	0	1	0	0	0	0	8262	117	5	0	286	0	KIAA1712	4	175224892	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5876655	175224892	15929384	350	16971										
WDR17	116966	hgsc.bcm.edu	37	chr4	177093632	177093632	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttgttaagtcaagaacctgAaaaagcccttcctattggta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:177093632delA	ENST00000280190.4	+	26	3482	c.3326delA	c.(3325-3327)gaafs	p.E1109fs	WDR17_ENST00000508596.1_Frame_Shift_Del_p.E1070fs|WDR17_ENST00000393643.2_Frame_Shift_Del_p.E1085fs|WDR17_ENST00000507824.2_Frame_Shift_Del_p.E1084fs			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1109										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CAAGAACCTGAAAAAGCCCTT	0.333																																					p.E1109fs		Atlas-INDEL	.											.	WDR17	198	.	0			c.3325delG						.						69	73	72					4																	177093632		2203	4300	6503	SO:0001589	frameshift_variant	116966	exon26			.	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3326delA	chr4.hg19:g.177093632delA	ENSP00000280190:p.Glu1109fs	204.0	0.0		195.0	15.0	NM_170710	E7EQX0|Q0QD35	Frame_Shift_Del	DEL	ENST00000280190.4	hg19	CCDS3825.1																																																																																			.	.		0.333	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			-	177093632	A	-	177093632	7	5	112	1	0	1	0	1	0	0	0	0	17292	246	9	0	3424	0	WDR17	4	177093632	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1868740	177093632	14060644	351	16972										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183713573	183713573	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tactaccgcaacatatacaaCcccccggaaagcaacgcctc					rs80197208	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:183713573delC	ENST00000511685.1	+	26	5871	c.5748delC	c.(5746-5748)aacfs	p.N1916fs	TENM3_ENST00000406950.2_Frame_Shift_Del_p.N1916fs			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1916					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.E1919fs*37(1)									ACATATACAACCCCCCGGAAA	0.532																																					p.N1916fs		Atlas-INDEL	.											.,1	.	.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.5747delA						.						70	73	72					4																	183713573		2022	4170	6192	SO:0001589	frameshift_variant	55714	exon25			.	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5748delC	chr4.hg19:g.183713573delC	ENSP00000424226:p.Asn1916fs	139.0	0.0		175.0	11.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Frame_Shift_Del	DEL	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.		0.532	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			-	183713573	C	-	183713573	7	5	112	1	0	1	0	1	0	0	0	0	10845	506	18	0	5846	0	ODZ3	4	183713573	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	6619941	183713573	7440703	352	16973										
CCDC110	256309	hgsc.bcm.edu	37	chr4	186382237	186382237	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcgcgtgccaaacaccagaTttttttctgagctaaattgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:186382237delT	ENST00000307588.3	-	5	389	c.314delA	c.(313-315)aatfs	p.N105fs	CCDC110_ENST00000507501.1_5'UTR|CCDC110_ENST00000510617.1_Frame_Shift_Del_p.N105fs|CCDC110_ENST00000393540.3_Intron	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	105						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		AAACACCAGATTTTTTTCTGA	0.318																																					p.N105fs		Atlas-INDEL	.											.	CCDC110	78	.	0			c.315delT						.						141	137	138					4																	186382237		2203	4299	6502	SO:0001589	frameshift_variant	256309	exon5			.	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"cancer/testis antigen 52"	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.314delA	chr4.hg19:g.186382237delT	ENSP00000306776:p.Asn105fs	139.0	0.0		154.0	12.0	NM_152775	Q86YI9|Q8N7W0	Frame_Shift_Del	DEL	ENST00000307588.3	hg19	CCDS3843.1																																																																																			.	.		0.318	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775		-	186382237	T	-	186382237	7	5	112	1	0	1	0	1	0	0	0	0	2749	1493	52	0	2199	0	CCDC110	4	186382237	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2668664	186382237	4772039	353	16974										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186583322	186583322	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctgggagagaatatgccgaGggggaaaacggcctctgata							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:186583322delG	ENST00000284776.7	-	5	539	c.30delC	c.(28-30)cccfs	p.P10fs	SORBS2_ENST00000431808.1_Frame_Shift_Del_p.P10fs|SORBS2_ENST00000449407.2_Frame_Shift_Del_p.P96fs|SORBS2_ENST00000355634.5_Frame_Shift_Del_p.P110fs|SORBS2_ENST00000319471.9_Frame_Shift_Del_p.P96fs|SORBS2_ENST00000393528.3_Frame_Shift_Del_p.P56fs|SORBS2_ENST00000448662.2_Frame_Shift_Del_p.P79fs|SORBS2_ENST00000437304.2_Frame_Shift_Del_p.P189fs	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	10					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		AATATGCCGAGGGGGAAAACG	0.512																																					p.S190fs	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-INDEL	.											.	SORBS2	300	.	0			c.568delT						.						117	101	107					4																	186583322		2203	4300	6503	SO:0001589	frameshift_variant	8470	exon6			.		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.30delC	chr4.hg19:g.186583322delG	ENSP00000284776:p.Pro10fs	209.0	0.0		225.0	15.0	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Frame_Shift_Del	DEL	ENST00000284776.7	hg19	CCDS3845.1																																																																																			.	.		0.512	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		-	186583322	G	-	186583322	7	5	112	1	0	1	0	1	0	0	0	0	14943	987	35	0	3680	0	SORBS2	4	186583322	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	201085	186583322	4570954	354	16975										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186598318	186598318	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggaaagagatgctgtgtgtgTctcaggcactggattagggg	17	5	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:186598318T>C	ENST00000284776.7	-	4	465				SORBS2_ENST00000431808.1_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000355634.5_Intron|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000448662.2_Intron|RP11-626E13.1_ENST00000447277.1_RNA|SORBS2_ENST00000437304.2_Missense_Mutation_p.T109A	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2						actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GCTGTGTGTGTCTCAGGCACT	0.488																																					p.T109A	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.A325G						.						137	132	134					4																	186598318		692	1591	2283	SO:0001627	intron_variant	8470	exon5			TGTGTGTCTCAGG		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.44+1258A>G	chr4.hg19:g.186598318T>C		133.0	0.0		139.0	6.0	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	hg19	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	T	9.763	1.170512	0.21621	.	.	ENSG00000154556	ENST00000437304	T	0.32023	1.47	5.91	4.54	0.55810	.	.	.	.	.	T	0.17238	0.0414	N	0.08118	0	0.58432	D	0.999999	B	0.14012	0.009	B	0.16289	0.015	T	0.05386	-1.0888	9	0.62326	D	0.03	.	11.1936	0.48700	0.0:0.0801:0.0:0.9199	.	109	E9PAW4	.	A	109	ENSP00000396008:T109A	ENSP00000396008:T109A	T	-	1	0	SORBS2	186835312	0.963000	0.33076	0.955000	0.39395	0.749000	0.42624	1.292000	0.33342	2.254000	0.74563	0.533000	0.62120	ACA	.	.		0.488	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		C	186598318	T	C	186598318	1	2	112	0	1	0	0	0	0	0	0	0	14943	1667	58	2		2	SORBS2	4	186598318	Intron	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	14996	186598318	4555958	355	16976										
FAT1	2195	hgsc.bcm.edu	37	chr4	187517698	187517698	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaaagtggctcttactgtcAtagtcaaagtcccagctagg	9	9	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:187517698A>G	ENST00000441802.2	-	25	13205	c.12996T>C	c.(12994-12996)taT>taC	p.Y4332Y	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4332					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TCTTACTGTCATAGTCAAAGT	0.488										HNSCC(5;0.00058)																											p.Y4332Y	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T12996C						.						46	48	47					4																	187517698		1987	4163	6150	SO:0001819	synonymous_variant	2195	exon25			ACTGTCATAGTCA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.12996T>C	chr4.hg19:g.187517698A>G		83.0	0.0		99.0	4.0	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	1.177	-0.639369	0.03557	.	.	ENSG00000083857	ENST00000512772	.	.	.	5.37	-2.77	0.05877	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4738	0.55801	0.5168:0.0:0.4832:0.0	.	.	.	.	R	100	.	.	X	-	1	0	FAT1	187754692	0.652000	0.27349	0.827000	0.32855	0.248000	0.25809	-0.012000	0.12699	-0.604000	0.05760	-0.256000	0.11100	TGA	.	.		0.488	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187517698	A	G	187517698	2	3	112	1	0	0	0	0	0	0	0	1	5697	224	8	2		2	FAT1	4	187517698	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	919380	187517698	3636578	356	16977										
ADCY2	108	hgsc.bcm.edu	37	chr5	7396594	7396594	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggctcctgcctcgccctgcTcgccgtcttcttcgcgctcg	11	19	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:7396594T>C	ENST00000338316.4	+	1	274	c.185T>C	c.(184-186)cTc>cCc	p.L62P		NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	62					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CTCGCCCTGCTCGCCGTCTTC	0.701																																					p.L62P		Atlas-SNP	.											.	ADCY2	337	.	0			c.T185C						.						48	41	43					5																	7396594		2203	4300	6503	SO:0001583	missense	108	exon1			CCCTGCTCGCCGT	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.185T>C	chr5.hg19:g.7396594T>C	ENSP00000342952:p.Leu62Pro	63.0	0.0		150.0	6.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	T	14.70	2.614340	0.46631	.	.	ENSG00000078295	ENST00000338316	T	0.79749	-1.3	3.67	3.67	0.42095	.	0.098199	0.42172	U	0.000754	T	0.70971	0.3285	L	0.36672	1.1	0.80722	D	1	B	0.15930	0.015	B	0.18263	0.021	T	0.67597	-0.5630	10	0.49607	T	0.09	.	10.0639	0.42292	0.0:0.0:0.0:1.0	.	62	Q08462	ADCY2_HUMAN	P	62	ENSP00000342952:L62P	ENSP00000342952:L62P	L	+	2	0	ADCY2	7449594	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	4.709000	0.61867	1.279000	0.44446	0.254000	0.18369	CTC	.	.		0.701	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		C	7396594	T	C	7396594	3	2	112	1	0	0	0	0	1	0	0	0	294	1551	54	2	187	2	ADCY2	5	7396594	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10		7396594	173518666	357	16978										
FAM173B	134145	hgsc.bcm.edu	37	chr5	10239279	10239279	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcgtagttgcaggtacaaacGgcaaacagacttttcgaagg	11	8	0	1	rs367602123		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:10239279G>T	ENST00000511437.1	-	2	218	c.206C>A	c.(205-207)cCg>cAg	p.P69Q	FAM173B_ENST00000510052.1_5'UTR|FAM173B_ENST00000280330.8_5'UTR|FAM173B_ENST00000510047.1_Missense_Mutation_p.P69Q	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	69						integral component of membrane (GO:0016021)		p.P69L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						AGGTACAAACGGCAAACAGAC	0.527																																					p.P69Q		Atlas-SNP	.											FAM173B,NS,carcinoma,0,1	FAM173B	24	.	1	Substitution - Missense(1)	lung(1)	c.C206A						.						114	112	113					5																	10239279		2037	4176	6213	SO:0001583	missense	134145	exon2			ACAAACGGCAAAC		CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.206C>A	chr5.hg19:g.10239279G>T	ENSP00000422338:p.Pro69Gln	110.0	1.0		236.0	0.0	NM_199133	B4DT41|B4DXK2|E9PBZ4	Missense_Mutation	SNP	ENST00000511437.1	hg19	CCDS43301.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.987143	0.74589	.	.	ENSG00000150756	ENST00000511437;ENST00000510047	T;T	0.25912	1.77;1.77	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.59376	0.2189	M	0.88241	2.94	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.68179	-0.5477	10	0.87932	D	0	-16.8539	17.7316	0.88379	0.0:0.0:1.0:0.0	.	69;69	E9PBZ4;Q6P4H8	.;F173B_HUMAN	Q	69	ENSP00000422338:P69Q;ENSP00000420876:P69Q	ENSP00000424210:P69Q	P	-	2	0	FAM173B	10292279	1.000000	0.71417	0.927000	0.36925	0.361000	0.29550	8.798000	0.91888	2.430000	0.82344	0.655000	0.94253	CCG	.	.		0.527	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133		T	10239279	G	T	10239279	3	4	112	1	0	0	0	0	1	0	0	0	5499	1116	39	1	511	1	FAM173B	5	10239279	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	2842685	10239279	170675981	358	16979										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11159822	11159822	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtactgctagggcatcctgGatgattggcattttgagtgc	13	7	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:11159822G>A	ENST00000304623.8	-	12	2214	c.2025C>T	c.(2023-2025)atC>atT	p.I675I	CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000458100.2_Silent_p.I242I|CTNND2_ENST00000359640.2_Silent_p.I675I|CTNND2_ENST00000511377.1_Silent_p.I584I|CTNND2_ENST00000503622.1_Silent_p.I338I	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	675					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GGGCATCCTGGATGATTGGCA	0.483																																					p.I675I		Atlas-SNP	.											.	CTNND2	289	.	0			c.C2025T						.						177	163	168					5																	11159822		2203	4300	6503	SO:0001819	synonymous_variant	1501	exon12			ATCCTGGATGATT	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.2025C>T	chr5.hg19:g.11159822G>A		185.0	0.0		323.0	66.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Silent	SNP	ENST00000304623.8	hg19	CCDS3881.1																																																																																			.	.		0.483	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11159822	G	A	11159822	2	1	112	1	0	0	0	0	0	0	0	1	4022	1164	41	3		3	CTNND2	5	11159822	Silent	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	920543	11159822	169755438	359	16980										
MYO10	4651	hgsc.bcm.edu	37	chr5	16762178	16762178	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccagcatagtgcttcactccAaaattgttaactgcaactct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:16762178delA	ENST00000513610.1	-	16	2086	c.1632delT	c.(1630-1632)tttfs	p.F544fs		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	544	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GCTTCACTCCAAAATTGTTAA	0.313																																					p.G545fs		Atlas-INDEL	.											.	MYO10	198	.	0			c.1633delG						.						41	37	38					5																	16762178		1813	4065	5878	SO:0001589	frameshift_variant	4651	exon16			.	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.1632delT	chr5.hg19:g.16762178delA	ENSP00000421280:p.Phe544fs	101.0	0.0		192.0	13.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Frame_Shift_Del	DEL	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.313	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		-	16762178	A	-	16762178	7	5	112	1	0	1	0	1	0	0	0	0	10071	127	5	0	4648	0	MYO10	5	16762178	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5602356	16762178	164153082	360	16981										
CDH10	1008	hgsc.bcm.edu	37	chr5	24487952	24487952	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taggttgcaagtgagtcgtaGgggggtgcggtggggtcaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:24487952delG	ENST00000264463.4	-	12	2694	c.2187delC	c.(2185-2187)cccfs	p.P729fs	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	729					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		GTGAGTCGTAGGGGGGTGCGG	0.463										HNSCC(23;0.051)																											p.Y730fs		Atlas-INDEL	.											.	CDH10	391	.	0			c.2188delT						.						105	108	107					5																	24487952		2203	4300	6503	SO:0001589	frameshift_variant	1008	exon12			.	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.2187delC	chr5.hg19:g.24487952delG	ENSP00000264463:p.Pro729fs	80.0	0.0		132.0	10.0	NM_006727	Q9ULB3	Frame_Shift_Del	DEL	ENST00000264463.4	hg19	CCDS3892.1																																																																																			.	.		0.463	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		-	24487952	G	-	24487952	7	5	112	1	0	1	0	1	0	0	0	0	3098	987	35	0	183	0	CDH10	5	24487952	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	7725774	24487952	156427308	361	16982										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33881513	33881513	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gatagtgcaagccatatgacAaaaaatgcccactggcatct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:33881513delA	ENST00000504830.1	-	2	535	c.200delT	c.(199-201)ttgfs	p.L67fs	ADAMTS12_ENST00000352040.3_Frame_Shift_Del_p.L67fs|ADAMTS12_ENST00000515401.1_Frame_Shift_Del_p.L67fs	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	67					cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GCCATATGACAAAAAATGCCC	0.483										HNSCC(64;0.19)																											p.L67fs		Atlas-INDEL	.											.,2	ADAMTS12	464	.	0			c.201delG						.						124	126	125					5																	33881513		2203	4300	6503	SO:0001589	frameshift_variant	81792	exon2			.	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.200delT	chr5.hg19:g.33881513delA	ENSP00000422554:p.Leu67fs	122.0	0.0		143.0	10.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Frame_Shift_Del	DEL	ENST00000504830.1	hg19	CCDS34140.1																																																																																			.	.		0.483	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		-	33881513	A	-	33881513	7	5	112	1	0	1	0	1	0	0	0	0	257	131	5	0	4676	0	ADAMTS12	5	33881513	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	9393561	33881513	147033747	362	16983										
C1QTNF3	114899	hgsc.bcm.edu	37	chr5	34035781	34035781	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caggagggcccggtggcccaGgggggccttggtagcctcga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:34035781delG	ENST00000231338.7	-	2	254	c.167delC	c.(166-168)cctfs	p.P56fs	RP11-1084J3.4_ENST00000382079.3_Frame_Shift_Del_p.P40fs|C1QTNF3_ENST00000382065.3_Frame_Shift_Del_p.P129fs|C1QTNF3_ENST00000513065.1_5'Flank	NM_030945.3	NP_112207.1	Q9BXJ4	C1QT3_HUMAN	C1q and tumor necrosis factor related protein 3	56	Collagen-like.				cellular triglyceride homeostasis (GO:0035356)|fat cell differentiation (GO:0045444)|negative regulation of gene expression (GO:0010629)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of cytokine secretion (GO:0050715)|protein trimerization (GO:0070206)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|prostate(3)|stomach(1)|urinary_tract(1)	17	all_lung(31;0.0207)					CGGTGGCCCAGGGGGGCCTTG	0.522																																					p.P129fs		Atlas-INDEL	.											.	C1QTNF3	31	.	0			c.387delT						.						42	45	44					5																	34035781		2203	4300	6503	SO:0001589	frameshift_variant	114899	exon2			.	AF329837	CCDS3904.1, CCDS34141.1	5p13	2009-05-20			ENSG00000082196	ENSG00000082196			14326	protein-coding gene	gene with protein product	"cartonectin"	612045				18421280	Standard	NM_030945		Approved	CTRP3, Cors, Corcs, 2310005P21Rik, Cors-26	uc003jio.3	Q9BXJ4	OTTHUMG00000090735	ENST00000231338.7:c.167delC	chr5.hg19:g.34035781delG	ENSP00000231338:p.Pro56fs	95.0	0.0		152.0	10.0	NM_181435	Q0VAN4|Q542Y2|Q6MZN1|Q96KY1	Frame_Shift_Del	DEL	ENST00000231338.7	hg19	CCDS3904.1																																																																																			.	.		0.522	C1QTNF3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207469.1	NM_030945		-	34035781	G	-	34035781	7	5	112	1	0	1	0	1	0	0	0	0	1966	1000	35	0	593	0	C1QTNF3	5	34035781	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	154268	34035781	146879479	363	16984										
AGXT2	64902	hgsc.bcm.edu	37	chr5	35025928	35025928	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcaaaggcttcctttagaaaCccctttgggtactggacaac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:35025928delC	ENST00000231420.6	-	9	1103	c.903delG	c.(901-903)gggfs	p.G301fs		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	301					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	CCTTTAGAAACCCCTTTGGGT	0.463																																					p.F302fs		Atlas-INDEL	.											.	AGXT2	89	.	0			c.904delT						.						88	84	85					5																	35025928		2203	4300	6503	SO:0001589	frameshift_variant	64902	exon9			.	AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"beta-alanine-pyruvate aminotransferase", "beta-ALAAT II"	612471	"alanine-glyoxylate aminotransferase 2"			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.903delG	chr5.hg19:g.35025928delC	ENSP00000231420:p.Gly301fs	89.0	0.0		139.0	12.0	NM_031900	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Frame_Shift_Del	DEL	ENST00000231420.6	hg19	CCDS3908.1																																																																																			.	.		0.463	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900		-	35025928	C	-	35025928	7	5	112	1	0	1	0	1	0	0	0	0	405	494	18	0	665	0	AGXT2	5	35025928	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	990147	35025928	145889332	364	16985										
RANBP3L	202151	hgsc.bcm.edu	37	chr5	36270074	36270074	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggttctgctgcttcatacaGggtgtcttctgcaggtctct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:36270074delG	ENST00000296604.3	-	3	654	c.169delC	c.(169-171)ctgfs	p.L57fs	RANBP3L_ENST00000502994.1_Frame_Shift_Del_p.L57fs|RANBP3L_ENST00000515759.1_Frame_Shift_Del_p.L57fs	NM_145000.3	NP_659437.3	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like	57					intracellular transport (GO:0046907)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	16	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			GCTTCATACAGGGTGTCTTCT	0.388																																					p.L57fs		Atlas-INDEL	.											.	RANBP3L	41	.	0			c.170delT						.						178	195	189					5																	36270074		2203	4300	6503	SO:0001589	frameshift_variant	202151	exon3			.	BC047660	CCDS3918.1, CCDS54843.1	5p13.2	2008-02-05			ENSG00000164188	ENSG00000164188			26353	protein-coding gene	gene with protein product						12477932	Standard	NM_145000		Approved	FLJ25422	uc011cow.2	Q86VV4	OTTHUMG00000131110	ENST00000296604.3:c.169delC	chr5.hg19:g.36270074delG	ENSP00000296604:p.Leu57fs	116.0	0.0		172.0	11.0	NM_001161429	B7Z866|E9PGP9|Q96LK2	Frame_Shift_Del	DEL	ENST00000296604.3	hg19	CCDS3918.1																																																																																			.	.		0.388	RANBP3L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253773.2	NM_145000		-	36270074	G	-	36270074	7	5	112	1	0	1	0	1	0	0	0	0	13045	991	35	0	1355	0	RANBP3L	5	36270074	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1244146	36270074	144645186	365	16986										
NUP155	9631	hgsc.bcm.edu	37	chr5	37309279	37309279	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaggtccacttgattgctaaTtttttgatattcctttaatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:37309279delT	ENST00000231498.3	-	24	2922	c.2719delA	c.(2719-2721)attfs	p.I907fs	NUP155_ENST00000513532.1_Frame_Shift_Del_p.I843fs|NUP155_ENST00000381843.2_Frame_Shift_Del_p.I848fs|NUP155_ENST00000502533.1_5'UTR	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	907					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGATTGCTAATTTTTTGATAT	0.343																																					p.I907fs		Atlas-INDEL	.											.	NUP155	116	.	0			c.2720delT						.						159	152	154					5																	37309279		2203	4300	6503	SO:0001589	frameshift_variant	9631	exon24			.	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.2719delA	chr5.hg19:g.37309279delT	ENSP00000231498:p.Ile907fs	175.0	0.0		198.0	12.0	NM_153485	Q9UBE9|Q9UFL5	Frame_Shift_Del	DEL	ENST00000231498.3	hg19	CCDS3921.1																																																																																			.	.		0.343	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		-	37309279	T	-	37309279	7	5	112	1	0	1	0	1	0	0	0	0	10765	1493	52	0	1504	0	NUP155	5	37309279	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1039205	37309279	143605981	366	16987										
NUP155	9631	hgsc.bcm.edu	37	chr5	37352917	37352917	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaccaggaggtgtcgcacatGaggttgaaagatgcctaaga	13	7	0	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:37352917G>A	ENST00000231498.3	-	5	681	c.478C>T	c.(478-480)Cat>Tat	p.H160Y	NUP155_ENST00000513532.1_Missense_Mutation_p.H160Y|NUP155_ENST00000381843.2_Missense_Mutation_p.H101Y	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	160					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGTCGCACATGAGGTTGAAAG	0.418																																					p.H160Y		Atlas-SNP	.											.	NUP155	116	.	0			c.C478T						.						90	84	86					5																	37352917		2203	4300	6503	SO:0001583	missense	9631	exon5			GCACATGAGGTTG	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.478C>T	chr5.hg19:g.37352917G>A	ENSP00000231498:p.His160Tyr	67.0	0.0		102.0	6.0	NM_153485	Q9UBE9|Q9UFL5	Missense_Mutation	SNP	ENST00000231498.3	hg19	CCDS3921.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.926367	0.34002	.	.	ENSG00000113569	ENST00000231498;ENST00000381843;ENST00000434056;ENST00000513532	T;T;T	0.44083	0.93;0.93;0.93	5.85	5.85	0.93711	Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.087367	0.85682	D	0.000000	T	0.42832	0.1220	L	0.55213	1.73	0.80722	D	1	B;B	0.13145	0.004;0.007	B;B	0.19666	0.008;0.026	T	0.16100	-1.0414	10	0.28530	T	0.3	.	18.3541	0.90351	0.0:0.0:1.0:0.0	.	160;160	E9PF10;O75694	.;NU155_HUMAN	Y	160;101;122;160	ENSP00000231498:H160Y;ENSP00000371265:H101Y;ENSP00000422019:H160Y	ENSP00000231498:H160Y	H	-	1	0	NUP155	37388674	1.000000	0.71417	0.997000	0.53966	0.712000	0.41017	6.022000	0.70839	2.767000	0.95098	0.557000	0.71058	CAT	.	.		0.418	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		A	37352917	G	A	37352917	3	1	112	1	0	0	0	0	1	0	0	0	10765	1290	45	3	3821	3	NUP155	5	37352917	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	43638	37352917	143562343	367	16988										
OXCT1	5019	hgsc.bcm.edu	37	chr5	41862804	41862804	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcttctactggatctgtatAaaacttggtatggcgatgag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:41862804delA	ENST00000196371.5	-	2	287	c.127delT	c.(127-129)tatfs	p.Y43fs		NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	43					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	GGATCTGTATAAAACTTGGTA	0.373																																					p.Y43fs		Atlas-INDEL	.											.	OXCT1	54	.	0			c.128delA						.						128	114	119					5																	41862804		2203	4300	6503	SO:0001589	frameshift_variant	5019	exon2			.	U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"3-oxoacid CoA transferase"	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.127delT	chr5.hg19:g.41862804delA	ENSP00000196371:p.Tyr43fs	161.0	0.0		211.0	15.0	NM_000436	B2R5V2|B7Z528	Frame_Shift_Del	DEL	ENST00000196371.5	hg19	CCDS3937.1																																																																																			.	.		0.373	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436		-	41862804	A	-	41862804	7	5	112	1	0	1	0	1	0	0	0	0	11338	362	13	0	1499	0	OXCT1	5	41862804	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4509887	41862804	139052456	368	16989										
NNT	23530	hgsc.bcm.edu	37	chr5	43644296	43644296	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttctttgattttattaggtAaaaaagctccagttttattt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:43644296delA	ENST00000264663.5	+	8	1188	c.967delA	c.(967-969)aaafs	p.K324fs	NNT_ENST00000344920.4_Frame_Shift_Del_p.K324fs|NNT_ENST00000512996.2_Frame_Shift_Del_p.K193fs	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	324					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					TTTATTAGGTAAAAAAGCTCC	0.328																																					p.G322fs		Atlas-INDEL	.											.	NNT	92	.	0			c.966delT						.						52	58	56					5																	43644296		2203	4300	6503	SO:0001589	frameshift_variant	23530	exon8			.	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.967delA	chr5.hg19:g.43644296delA	ENSP00000264663:p.Lys324fs	109.0	0.0		178.0	11.0	NM_182977	Q16796|Q2TB60|Q8N3V4	Frame_Shift_Del	DEL	ENST00000264663.5	hg19	CCDS3949.1																																																																																			.	.		0.328	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		-	43644296	A	-	43644296	7	5	112	1	0	1	0	1	0	0	0	0	10519	363	13	0	993	0	NNT	5	43644296	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1781492	43644296	137270964	369	16990										
SNX18	112574	hgsc.bcm.edu	37	chr5	53813856	53813856	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gatctcgctgcgagagcacgAggtgctgagcctgtgcagcg	16	11	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:53813856A>G	ENST00000326277.3	+	1	264	c.74A>G	c.(73-75)gAg>gGg	p.E25G	SNX18_ENST00000381410.4_Missense_Mutation_p.E25G|SNX18_ENST00000343017.6_Missense_Mutation_p.E25G	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	25	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				CGAGAGCACGAGGTGCTGAGC	0.706																																					p.E25G		Atlas-SNP	.											.	SNX18	102	.	0			c.A74G						.						7	8	8					5																	53813856		2148	4207	6355	SO:0001583	missense	112574	exon1			AGCACGAGGTGCT	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"Sorting nexins"	19245	protein-coding gene	gene with protein product			"sorting nexin associated golgi protein 1"	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.74A>G	chr5.hg19:g.53813856A>G	ENSP00000317332:p.Glu25Gly	33.0	0.0		48.0	5.0	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Missense_Mutation	SNP	ENST00000326277.3	hg19	CCDS3962.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.835950	0.71373	.	.	ENSG00000178996	ENST00000343017;ENST00000381410;ENST00000326277	T;T;T	0.58506	0.33;0.33;0.33	3.82	3.82	0.43975	Src homology-3 domain (4);	0.142348	0.51477	D	0.000099	T	0.77164	0.4090	M	0.86805	2.84	0.58432	D	0.999998	D;D	0.71674	0.998;0.982	D;P	0.81914	0.995;0.82	T	0.81671	-0.0827	10	0.87932	D	0	-26.2397	12.4182	0.55506	1.0:0.0:0.0:0.0	.	25;25	Q96RF0;Q96RF0-2	SNX18_HUMAN;.	G	25	ENSP00000342276:E25G;ENSP00000370817:E25G;ENSP00000317332:E25G	ENSP00000317332:E25G	E	+	2	0	SNX18	53849613	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	6.472000	0.73567	1.589000	0.49982	0.254000	0.18369	GAG	.	.		0.706	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2			G	53813856	A	G	53813856	3	3	112	1	0	0	0	0	1	0	0	0	14904	304	11	2	76	2	SNX18	5	53813856	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	10169560	53813856	127101404	370	16991										
GZMA	3001	hgsc.bcm.edu	37	chr5	54403626	54403626	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgtgtctgttctcaggaacAaaaggtcccaggtcattctt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:54403626delA	ENST00000274306.6	+	3	255	c.220delA	c.(220-222)aaafs	p.K74fs		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	74	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				TCTCAGGAACAAAAGGTCCCA	0.378																																					p.N73fs		Atlas-INDEL	.											.	GZMA	60	.	0			c.219delC						.						105	101	103					5																	54403626		2203	4300	6503	SO:0001589	frameshift_variant	3001	exon3			.		CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"CTL tryptase", "Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.220delA	chr5.hg19:g.54403626delA	ENSP00000274306:p.Lys74fs	85.0	0.0		163.0	10.0	NM_006144	A4PHN1|Q6IB36	Frame_Shift_Del	DEL	ENST00000274306.6	hg19	CCDS3965.1																																																																																			.	.		0.378	GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144		-	54403626	A	-	54403626	7	5	112	1	0	1	0	1	0	0	0	0	6924	131	5	0	230	0	GZMA	5	54403626	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	589770	54403626	126511634	371	16992										
DDX4	54514	hgsc.bcm.edu	37	chr5	55110940	55110940	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atactggcagagcaatttccTtttttgatcttgaatcggat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:55110940delT	ENST00000505374.1	+	20	2019	c.1927delT	c.(1927-1929)tttfs	p.F644fs	DDX4_ENST00000511853.1_Frame_Shift_Del_p.F495fs|DDX4_ENST00000353507.5_Frame_Shift_Del_p.F610fs|DDX4_ENST00000514278.2_Frame_Shift_Del_p.F624fs|DDX4_ENST00000354991.5_Frame_Shift_Del_p.F610fs	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	644	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				AGCAATTTCCTTTTTTGATCT	0.358																																					p.S642fs		Atlas-INDEL	.											.	DDX4	194	.	0			c.1926delC						.						178	173	175					5																	55110940		2203	4300	6503	SO:0001589	frameshift_variant	54514	exon20			.	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.1927delT	chr5.hg19:g.55110940delT	ENSP00000424838:p.Phe644fs	295.0	0.0		466.0	29.0	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Frame_Shift_Del	DEL	ENST00000505374.1	hg19	CCDS3969.1																																																																																			.	.		0.358	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		-	55110940	T	-	55110940	7	5	112	1	0	1	0	1	0	0	0	0	4362	1609	56	0	2042	0	DDX4	5	55110940	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	707314	55110940	125804320	372	16993										
IL31RA	133396	hgsc.bcm.edu	37	chr5	55168109	55168109	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctttcaaagcgcttttggagAaaaacatgataattgtacaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:55168109delA	ENST00000447346.2	+	4	349	c.284delA	c.(283-285)gaafs	p.E95fs	IL31RA_ENST00000490985.1_5'UTR|IL31RA_ENST00000354961.4_Frame_Shift_Del_p.E76fs|IL31RA_ENST00000396834.1_Frame_Shift_Del_p.E76fs|IL31RA_ENST00000297015.3_5'UTR|IL31RA_ENST00000359040.5_Frame_Shift_Del_p.E95fs|IL31RA_ENST00000396836.2_Frame_Shift_Del_p.E95fs	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	63	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				GCTTTTGGAGAAAAACATGAT	0.313																																					p.E95fs		Atlas-INDEL	.											.	IL31RA	84	.	0			c.283delG						.						53	57	55					5																	55168109		2203	4299	6502	SO:0001589	frameshift_variant	133396	exon4			.	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.284delA	chr5.hg19:g.55168109delA	ENSP00000415900:p.Glu95fs	106.0	0.0		164.0	11.0	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Frame_Shift_Del	DEL	ENST00000447346.2	hg19	CCDS3970.2																																																																																			.	.		0.313	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		-	55168109	A	-	55168109	7	5	112	1	0	1	0	1	0	0	0	0	7700	246	9	0	298	0	IL31RA	5	55168109	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	57169	55168109	125747151	373	16994										
ERCC8	1161	hgsc.bcm.edu	37	chr5	60214181	60214181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgaggataccactgtacagTctccacactgtatctgtgaa	8	10	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:60214181T>C	ENST00000265038.5	-	4	352	c.310A>G	c.(310-312)Act>Gct	p.T104A	AC104113.3_ENST00000457499.1_RNA|ERCC8_ENST00000543101.1_5'UTR|ERCC8_ENST00000426742.2_Missense_Mutation_p.T46A	NM_000082.3	NP_000073.1	Q13216	ERCC8_HUMAN	excision repair cross-complementation group 8	104					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|positive regulation of DNA repair (GO:0045739)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|transcription-coupled nucleotide-excision repair (GO:0006283)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|protein complex (GO:0043234)	protein complex binding (GO:0032403)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)				CACTGTACAGTCTCCACACTG	0.343																																					p.T104A		Atlas-SNP	.											.	ERCC8	31	.	0			c.A310G						.						122	116	118					5																	60214181		2203	4299	6502	SO:0001583	missense	1161	exon4			GTACAGTCTCCAC	U28413	CCDS3978.1	5q12.1	2014-09-17	2014-03-07		ENSG00000049167	ENSG00000049167		"WD repeat domain containing"	3439	protein-coding gene	gene with protein product		609412	"Cockayne syndrome 1 (classical)", "excision repair cross-complementing rodent repair deficiency, complementation group 8"	CKN1		8596535	Standard	NM_000082		Approved	CSA	uc003jsm.3	Q13216	OTTHUMG00000097741	ENST00000265038.5:c.310A>G	chr5.hg19:g.60214181T>C	ENSP00000265038:p.Thr104Ala	77.0	0.0		115.0	5.0	NM_000082	B2RB64|Q6FHX5|Q96GB9	Missense_Mutation	SNP	ENST00000265038.5	hg19	CCDS3978.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.497119	0.85069	.	.	ENSG00000049167	ENST00000426742;ENST00000265038;ENST00000536596;ENST00000439176	T;T;T	0.58060	0.36;0.36;0.36	4.74	4.74	0.60224	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.34919	0.0914	N	0.05012	-0.13	0.80722	D	1	B;B	0.31351	0.084;0.32	B;B	0.36719	0.163;0.231	T	0.27191	-1.0081	10	0.27785	T	0.31	-28.586	14.4087	0.67101	0.0:0.0:0.0:1.0	.	104;104	Q13216-2;Q13216	.;ERCC8_HUMAN	A	46;104;103;46	ENSP00000400110:T46A;ENSP00000265038:T104A;ENSP00000408344:T46A	ENSP00000265038:T104A	T	-	1	0	ERCC8	60249938	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.608000	0.82898	1.995000	0.58328	0.533000	0.62120	ACT	.	.		0.343	ERCC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214971.2	NM_000082		C	60214181	T	C	60214181	3	2	112	1	0	0	0	0	1	0	0	0	5221	1667	58	2	916	2	ERCC8	5	60214181	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	5046072	60214181	120701079	374	16995										
BDP1	55814	hgsc.bcm.edu	37	chr5	70806693	70806693	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attgatttgaaagaaactggAaaaagagacattcccatcat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:70806693delA	ENST00000358731.4	+	17	4037	c.3774delA	c.(3772-3774)ggafs	p.G1258fs	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	1258	9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		AAGAAACTGGAAAAAGAGACA	0.363																																					p.G1258fs		Atlas-INDEL	.											.	BDP1	204	.	0			c.3773delG						.						142	142	142					5																	70806693		1833	4081	5914	SO:0001589	frameshift_variant	55814	exon17			.	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.3774delA	chr5.hg19:g.70806693delA	ENSP00000351575:p.Gly1258fs	71.0	0.0		175.0	11.0	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Frame_Shift_Del	DEL	ENST00000358731.4	hg19	CCDS43328.1																																																																																			.	.		0.363	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		-	70806693	A	-	70806693	7	5	112	1	0	1	0	1	0	0	0	0	1395	233	9	0	3840	0	BDP1	5	70806693	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	10592512	70806693	110108567	375	16996										
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79732785	79732785	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acttacttctatacaaaatgAaaaaaatgtaacaggacttg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:79732785delA	ENST00000338008.5	+	3	461	c.281delA	c.(280-282)gaafs	p.E94fs	ZFYVE16_ENST00000510158.1_Frame_Shift_Del_p.E94fs|ZFYVE16_ENST00000505560.1_Frame_Shift_Del_p.E94fs	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	94					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		ATACAAAATGAAAAAAATGTA	0.378																																					p.E94fs	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-Indel,Pindel	.											ZFYVE16,colon,carcinoma,0,1	ZFYVE16	100	.	0			c.280delG						.						77	81	79					5																	79732785		2203	4300	6503	SO:0001589	frameshift_variant	9765	exon4			.	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"Zinc fingers, FYVE domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20756	protein-coding gene	gene with protein product	"endofin", "protein phosphatase 1, regulatory subunit 69"	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.281delA	chr5.hg19:g.79732785delA	ENSP00000337159:p.Glu94fs	125.0	0.0		263.0	16.0	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Frame_Shift_Del	DEL	ENST00000338008.5	hg19	CCDS4050.1																																																																																			.	.		0.378	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		-	79732785	A	-	79732785	7	5	112	1	0	1	0	1	0	0	0	0	17679	246	9	0	287	0	ZFYVE16	5	79732785	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	8926092	79732785	101182475	376	16997										
ZCCHC9	84240	hgsc.bcm.edu	37	chr5	80608475	80608475	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaatacctaaagttgttaaTttttgataacagctagcact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:80608475delT	ENST00000254037.2	+	5	3965	c.810delT	c.(808-810)aatfs	p.N270fs	ZCCHC9_ENST00000380199.5_Frame_Shift_Del_p.N270fs|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000407610.3_Frame_Shift_Del_p.N270fs|ZCCHC9_ENST00000438268.2_Frame_Shift_Del_p.N270fs			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	270					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		AAGTTGTTAATTTTTGATAAC	0.418																																					p.N270fs		Atlas-INDEL	.											.	ZCCHC9	26	.	0			c.809delA						.						81	78	79					5																	80608475		2203	4300	6503	SO:0001589	frameshift_variant	84240	exon6			.	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"Zinc fingers, CCHC domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25424	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 41"					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.810delT	chr5.hg19:g.80608475delT	ENSP00000254037:p.Asn270fs	105.0	0.0		212.0	13.0	NM_001131036	B2RAE7|Q9H027	Frame_Shift_Del	DEL	ENST00000254037.2	hg19	CCDS4054.1																																																																																			.	.		0.418	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280		-	80608475	T	-	80608475	7	5	112	1	0	1	0	1	0	0	0	0	17610	1490	52	0	828	0	ZCCHC9	5	80608475	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	875690	80608475	100306785	377	16998										
HAPLN1	1404	hgsc.bcm.edu	37	chr5	82948593	82948593	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aacattgccacctctgtgtgAaaacaccttggcttgctctg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:82948593delA	ENST00000274341.4	-	3	1001	c.151delT	c.(151-153)tcafs	p.S51fs	HAPLN1_ENST00000514416.1_Frame_Shift_Del_p.S51fs	NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	51	Ig-like V-type.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	CCTCTGTGTGAAAACACCTTG	0.373																																					p.S51fs		Atlas-INDEL	.											.	HAPLN1	79	.	0			c.152delC						.						56	56	56					5																	82948593		2203	4300	6503	SO:0001589	frameshift_variant	1404	exon3			.		CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"Immunoglobulin superfamily / V-set domain containing"	2380	protein-coding gene	gene with protein product	"Cartilage link protein", "hyaluronan and proteoglycan link protein 1"	115435	"cartilage linking protein 1"	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.151delT	chr5.hg19:g.82948593delA	ENSP00000274341:p.Ser51fs	77.0	0.0		162.0	10.0	NM_001884	B2R9A9	Frame_Shift_Del	DEL	ENST00000274341.4	hg19	CCDS4061.1																																																																																			.	.		0.373	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884		-	82948593	A	-	82948593	7	5	112	1	0	1	0	1	0	0	0	0	6963	246	9	0	925	0	HAPLN1	5	82948593	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2340118	82948593	97966667	378	16999										
GPR98	84059	hgsc.bcm.edu	37	chr5	89968413	89968413	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtggttgagagaaccagaggAgctctggattatgtgcatgt	15	5	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:89968413A>G	ENST00000405460.2	+	22	4899	c.4803A>G	c.(4801-4803)ggA>ggG	p.G1601G	GPR98_ENST00000450321.2_3'UTR	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1601	Calx-beta 11. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GAACCAGAGGAGCTCTGGATT	0.368																																					p.G1601G		Atlas-SNP	.											.	GPR98	605	.	0			c.A4803G						.						174	158	163					5																	89968413		1866	4103	5969	SO:0001819	synonymous_variant	84059	exon22			CAGAGGAGCTCTG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.4803A>G	chr5.hg19:g.89968413A>G		177.0	0.0		372.0	87.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	hg19	CCDS47246.1																																																																																			.	.		0.368	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	89968413	A	G	89968413	2	3	112	1	0	0	0	0	0	0	0	1	6730	291	11	2		2	GPR98	5	89968413	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	7019820	89968413	90946847	379	17000										
TTC37	9652	hgsc.bcm.edu	37	chr5	94856440	94856440	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caagtaaaatattccagtgcTttttctatgtagtctacggc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:94856440delT	ENST00000358746.2	-	20	2392	c.2094delA	c.(2092-2094)aaafs	p.K698fs	RNU6-308P_ENST00000390957.1_RNA	NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	698						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						ATTCCAGTGCTTTTTCTATGT	0.289																																					p.A699fs		Atlas-INDEL	.											.	TTC37	128	.	0			c.2095delG						.						63	65	64					5																	94856440		2203	4297	6500	SO:0001589	frameshift_variant	9652	exon20			.	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"Tetratricopeptide (TTC) repeat domain containing"	23639	protein-coding gene	gene with protein product		614589	"KIAA0372"	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.2094delA	chr5.hg19:g.94856440delT	ENSP00000351596:p.Lys698fs	113.0	0.0		237.0	16.0	NM_014639	O15077|Q6PJI3	Frame_Shift_Del	DEL	ENST00000358746.2	hg19	CCDS4072.1																																																																																			.	.		0.289	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639		-	94856440	T	-	94856440	7	5	112	1	0	1	0	1	0	0	0	0	16720	1606	56	0	2696	0	TTC37	5	94856440	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	4888027	94856440	86058820	380	17001										
ERAP2	64167	hgsc.bcm.edu	37	chr5	96232481	96232481	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggattttctgggtgaggagAaattccagaaaggaataatt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:96232481delA	ENST00000437043.3	+	9	2128	c.1417delA	c.(1417-1419)aaafs	p.K473fs	ERAP2_ENST00000515095.1_3'UTR|ERAP2_ENST00000379904.4_Frame_Shift_Del_p.K428fs|CTD-2260A17.2_ENST00000501338.1_Intron	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	473					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		GGGTGAGGAGAAATTCCAGAA	0.323																																					p.E472fs		Atlas-INDEL	.											.	ERAP2	77	.	0			c.1416delG						.						78	86	83					5																	96232481		2200	4299	6499	SO:0001589	frameshift_variant	64167	exon9			.	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"leukocyte-derived arginine aminopeptidase"	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1417delA	chr5.hg19:g.96232481delA	ENSP00000400376:p.Lys473fs	119.0	0.0		171.0	11.0	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Frame_Shift_Del	DEL	ENST00000437043.3	hg19	CCDS4086.1																																																																																			.	.		0.323	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350		-	96232481	A	-	96232481	7	5	112	1	0	1	0	1	0	0	0	0	5206	247	9	0	1447	0	ERAP2	5	96232481	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1376041	96232481	84682779	381	17002										
CHD1	1105	hgsc.bcm.edu	37	chr5	98194094	98194094	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctcttttaatctttccacaTctgttagataagtacaactt	3	9	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:98194094T>C	ENST00000284049.3	-	34	4726	c.4577A>G	c.(4576-4578)gAt>gGt	p.D1526G		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1526					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TCTTTCCACATCTGTTAGATA	0.323																																					p.D1526G		Atlas-SNP	.											.	CHD1	137	.	0			c.A4577G						.						158	154	155					5																	98194094		2203	4300	6503	SO:0001630	splice_region_variant	1105	exon34			TCCACATCTGTTA	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.4577-1A>G	chr5.hg19:g.98194094T>C		111.0	0.0		170.0	7.0	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.559636	0.45590	.	.	ENSG00000153922	ENST00000422663;ENST00000284049	D	0.89810	-2.57	5.12	5.12	0.69794	.	0.000000	0.34555	U	0.003862	D	0.86066	0.5844	L	0.51422	1.61	0.58432	D	0.999999	B	0.19200	0.034	B	0.17722	0.019	T	0.82520	-0.0416	10	0.37606	T	0.19	.	15.1902	0.73038	0.0:0.0:0.0:1.0	.	1526	O14646	CHD1_HUMAN	G	116;1526	ENSP00000284049:D1526G	ENSP00000284049:D1526G	D	-	2	0	CHD1	98221994	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.460000	0.80816	2.046000	0.60703	0.397000	0.26171	GAT	.	.		0.323	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	Missense_Mutation	C	98194094	T	C	98194094	5	2	112	1	0	0	0	0	0	0	1	0	3325	1449	50	2	563	2	CHD1	5	98194094	Splice_Site	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1961613	98194094	82721166	382	17003										
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109190938	109190938	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccaatggcaaataagttctCctcacctacccttgagctgc	6	14	2	1	rs3217225|rs200723635	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:109190938C>T	ENST00000261483.4	+	20	4126	c.3074C>T	c.(3073-3075)tCc>tTc	p.S1025F	MAN2A1_ENST00000505313.1_3'UTR	NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	1025					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		AATAAGTTCTCCTCACCTACC	0.403																																					p.S1025F		Atlas-SNP	.											MAN2A1,colon,carcinoma,0,1	MAN2A1	136	.	0			c.C3074T						.						163	117	132					5																	109190938		2202	4295	6497	SO:0001583	missense	4124	exon20			AGTTCTCCTCACC		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.3074C>T	chr5.hg19:g.109190938C>T	ENSP00000261483:p.Ser1025Phe	48.0	2.0		81.0	8.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	C	9.575	1.122145	0.20877	.	.	ENSG00000112893	ENST00000261483	T	0.80738	-1.41	5.07	1.88	0.25563	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	1.184260	0.05825	N	0.616516	T	0.71609	0.3360	L	0.34521	1.04	0.09310	N	1	B	0.10296	0.003	B	0.19666	0.026	T	0.58521	-0.7622	10	0.56958	D	0.05	1.7459	5.1539	0.15025	0.5166:0.3102:0.0:0.1732	.	1025	Q16706	MA2A1_HUMAN	F	1025	ENSP00000261483:S1025F	ENSP00000261483:S1025F	S	+	2	0	MAN2A1	109218837	0.407000	0.25352	0.001000	0.08648	0.007000	0.05969	3.958000	0.56737	0.412000	0.25729	-0.373000	0.07131	TCC	.	.		0.403	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			T	109190938	C	T	109190938	3	4	112	1	0	0	0	0	1	0	0	0	9223	855	30	3	3152	3	MAN2A1	5	109190938	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	10996844	109190938	71724322	383	17004										
KCNN2	3781	hgsc.bcm.edu	37	chr5	113698631	113698631	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctccccgtctgcagccgcTgccgccgccgccgctgtttc	10	21	1	0	rs151038013|rs111266015|rs76852708|rs34641516		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:113698631T>C	ENST00000512097.3	+	2	1177	c.159T>C	c.(157-159)gcT>gcC	p.A53A	KCNN2_ENST00000264773.3_Silent_p.A53A			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	53	Poly-Ala.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	CTGCAGCCGCTGCCGCCGCCG	0.701																																					p.A53A		Atlas-SNP	.											.,4	KCNN2	144	.	0			c.T159C						.						7	7	7					5																	113698631		2067	4071	6138	SO:0001819	synonymous_variant	3781	exon1			AGCCGCTGCCGCC	AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.159T>C	chr5.hg19:g.113698631T>C		2.0	0.0		17.0	4.0	NM_021614	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Silent	SNP	ENST00000512097.3	hg19	CCDS4114.1																																																																																			.	.		0.701	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614		C	113698631	T	C	113698631	2	2	112	1	0	0	0	0	0	0	0	1	8088	1567	55	2		2	KCNN2	5	113698631	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4507693	113698631	67216629	384	17005										
PRR16	51334	hgsc.bcm.edu	37	chr5	120022115	120022115	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaacgagttcggtttaatgAaaaagtacagtaccatggct					rs35167981		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:120022115delA	ENST00000407149.2	+	2	835	c.626delA	c.(625-627)gaafs	p.E209fs	PRR16_ENST00000446965.1_Frame_Shift_Del_p.E139fs|PRR16_ENST00000379551.2_Frame_Shift_Del_p.E186fs|PRR16_ENST00000505123.1_Frame_Shift_Del_p.E139fs			Q569H4	LARGN_HUMAN	proline rich 16	209	Pro-rich.				positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CGGTTTAATGAAAAAGTACAG	0.483																																					p.E186fs		Atlas-INDEL	.											.	PRR16	71	.	0			c.556delG						.						74	75	75					5																	120022115		2203	4300	6503	SO:0001589	frameshift_variant	51334	exon3			.	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.626delA	chr5.hg19:g.120022115delA	ENSP00000385118:p.Glu209fs	107.0	0.0		167.0	11.0	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Frame_Shift_Del	DEL	ENST00000407149.2	hg19																																																																																				.	.		0.483	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644		-	120022115	A	-	120022115	7	5	112	1	0	1	0	1	0	0	0	0	12601	246	9	0	563	0	PRR16	5	120022115	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	6323484	120022115	60893145	385	17006										
SNX2	6643	hgsc.bcm.edu	37	chr5	122137589	122137589	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaagaagcaaatggagacaTttttgacatagaaattggtg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:122137589delT	ENST00000379516.2	+	4	524	c.416delT	c.(415-417)attfs	p.I139fs	SNX2_ENST00000510372.1_3'UTR|SNX2_ENST00000514949.1_Frame_Shift_Del_p.I22fs	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	139					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		AATGGAGACATTTTTGACATA	0.239																																					p.I139fs		Atlas-INDEL	.											.	SNX2	42	.	0			c.415delA						.						72	82	78					5																	122137589		2174	4287	6461	SO:0001589	frameshift_variant	6643	exon4			.	AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"Sorting nexins"	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.416delT	chr5.hg19:g.122137589delT	ENSP00000368831:p.Ile139fs	154.0	0.0		316.0	19.0	NM_003100	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Frame_Shift_Del	DEL	ENST00000379516.2	hg19	CCDS34217.1																																																																																			.	.		0.239	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100		-	122137589	T	-	122137589	7	5	112	1	0	1	0	1	0	0	0	0	14906	1493	52	0	430	0	SNX2	5	122137589	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2115474	122137589	58777671	386	17007										
PHAX	51808	hgsc.bcm.edu	37	chr5	125960441	125960441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acacgaatgaggccttggccTctcttgatgagtcacaggaa	11	10	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:125960441T>C	ENST00000297540.4	+	5	1785	c.1090T>C	c.(1090-1092)Tct>Cct	p.S364P		NM_032177.3	NP_115553.2	Q9H814	PHAX_HUMAN	phosphorylated adaptor for RNA export	364					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein transport (GO:0015031)|RNA metabolic process (GO:0016070)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA binding (GO:0003723)|toxic substance binding (GO:0015643)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	8						GGCCTTGGCCTCTCTTGATGA	0.403																																					p.S364P		Atlas-SNP	.											.	PHAX	20	.	0			c.T1090C						.						107	106	106					5																	125960441		2203	4300	6503	SO:0001583	missense	51808	exon5			TTGGCCTCTCTTG	AK023255	CCDS4138.1	5q23.2	2011-05-24	2008-10-01	2008-10-01	ENSG00000164902	ENSG00000164902			10241	protein-coding gene	gene with protein product		604924	"RNA U, small nuclear RNA export adaptor (phosphorylation regulated)"	RNUXA		10786834	Standard	NM_032177		Approved	FLJ13193	uc003kua.2	Q9H814	OTTHUMG00000163273	ENST00000297540.4:c.1090T>C	chr5.hg19:g.125960441T>C	ENSP00000297540:p.Ser364Pro	103.0	0.0		160.0	7.0	NM_032177	Q9H8W1	Missense_Mutation	SNP	ENST00000297540.4	hg19	CCDS4138.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.993292	0.74703	.	.	ENSG00000164902	ENST00000297540	T	0.54675	0.56	5.62	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.39963	0.1098	L	0.32530	0.975	0.58432	D	0.999998	B	0.21753	0.06	B	0.14578	0.011	T	0.28839	-1.0031	10	0.40728	T	0.16	-26.0387	10.994	0.47565	0.0:0.0723:0.0:0.9277	.	364	Q9H814	PHAX_HUMAN	P	364	ENSP00000297540:S364P	ENSP00000297540:S364P	S	+	1	0	PHAX	125988340	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.457000	0.66672	2.146000	0.66826	0.460000	0.39030	TCT	.	.		0.403	PHAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250924.1	NM_032177		C	125960441	T	C	125960441	3	2	112	1	0	0	0	0	1	0	0	0	11822	1551	54	2	1108	2	PHAX	5	125960441	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3822852	125960441	54954819	387	17008										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128994381	128994381	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtgtatgcaatggcaatggAaaatcatgcaagatcattaa					rs552521438		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:128994381delA	ENST00000274487.4	+	15	2503	c.2358delA	c.(2356-2358)ggafs	p.G786fs	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	786	Cys-rich.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		ATGGCAATGGAAAATCATGCA	0.363																																					p.G786fs		Atlas-INDEL	.											.	ADAMTS19	216	.	0			c.2357delG						.						167	166	167					5																	128994381		2203	4300	6503	SO:0001589	frameshift_variant	171019	exon15			.	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.2358delA	chr5.hg19:g.128994381delA	ENSP00000274487:p.Gly786fs	78.0	0.0		164.0	10.0	NM_133638		Frame_Shift_Del	DEL	ENST00000274487.4	hg19	CCDS4146.1																																																																																			.	.		0.363	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		-	128994381	A	-	128994381	7	5	112	1	0	1	0	1	0	0	0	0	264	233	9	0	2416	0	ADAMTS19	5	128994381	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3033940	128994381	51920879	388	17009										
SEC24A	10802	hgsc.bcm.edu	37	chr5	134059335	134059335	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcttagagagcagagaccaTttttcccaatactttatgta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:134059335delT	ENST00000398844.2	+	22	3430	c.3142delT	c.(3142-3144)tttfs	p.F1049fs		NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	1049					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCAGAGACCATTTTTCCCAAT	0.373																																					p.P1047fs		Atlas-INDEL	.											.	SEC24A	77	.	0			c.3141delA						.						157	146	149					5																	134059335		1835	4081	5916	SO:0001589	frameshift_variant	10802	exon22			.	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.3142delT	chr5.hg19:g.134059335delT	ENSP00000381823:p.Phe1049fs	99.0	0.0		177.0	11.0	NM_021982	A8MVW3|Q8WUV2|Q96GP7	Frame_Shift_Del	DEL	ENST00000398844.2	hg19	CCDS43363.1																																																																																			.	.		0.373	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			-	134059335	T	-	134059335	7	5	112	1	0	1	0	1	0	0	0	0	14009	1493	52	0	3228	0	SEC24A	5	134059335	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	5064954	134059335	46855925	389	17010										
SRA1	10307	hgsc.bcm.edu	37	chr5	139936736	139936736	+	IGR	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caggggccccacgcacctctGggggatccatcctggggtgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:139936736delG	ENST00000357560.4	-	0	2218				SRA1_ENST00000336283.6_Frame_Shift_Del_p.P61fs|SRA1_ENST00000520427.1_5'UTR	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGCACCTCTGGGGGATCCAT	0.662																																					p.P101fs		Atlas-INDEL	.											.	SRA1	24	.	0			c.303delA						.						37	44	42					5																	139936736		2188	4283	6471	SO:0001628	intergenic_variant	10011	exon1			.	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504		chr5.hg19:g.139936736delG		103.0	0.0		189.0	15.0	NM_001253764	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Frame_Shift_Del	DEL	ENST00000357560.4	hg19	CCDS4229.1																																																																																			.	.		0.662	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051		-	139936736	G	-	139936736	6	5	112	0	1	1	0	1	0	0	0	0	15147	1335	47	0		0	SRA1	5	139936736	IGR	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	5877401	139936736	40978524	390	17011										
PCDHB15	56121	hgsc.bcm.edu	37	chr5	140627002	140627002	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgggctgttcggcgtgtgggCgcacaatggcgaggtgcgca	19	10	0	0	rs17844634	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:140627002C>G	ENST00000231173.3	+	1	1856	c.1856C>G	c.(1855-1857)gCg>gGg	p.A619G		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	619	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A619E(1)|p.A619V(1)		NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCGTGTGGGCGCACAATGGC	0.692													C|||	2	0.000399361	0	0	5008	,	,		15365	0.002		0	False		,,,				2504	0				p.A619G		Atlas-SNP	.											PCDHB15,NS,carcinoma,0,2	PCDHB15	138	.	2	Substitution - Missense(2)	lung(1)|endometrium(1)	c.C1856G						.						25	27	26					5																	140627002		2064	4076	6140	SO:0001583	missense	56121	exon1			TGTGGGCGCACAA	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1856C>G	chr5.hg19:g.140627002C>G	ENSP00000231173:p.Ala619Gly	7.0	1.0		35.0	11.0	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	hg19	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.055284	0.55325	.	.	ENSG00000113248	ENST00000231173	T	0.52983	0.64	4.11	3.21	0.36854	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.42494	0.1205	L	0.55017	1.72	0.20563	N	0.999889	B	0.18968	0.032	B	0.30782	0.12	T	0.29912	-0.9996	9	0.35671	T	0.21	.	5.7793	0.18297	0.0:0.6715:0.0:0.3285	rs17844634	619	Q9Y5E8	PCDBF_HUMAN	G	619	ENSP00000231173:A619G	ENSP00000231173:A619G	A	+	2	0	PCDHB15	140607186	0.000000	0.05858	1.000000	0.80357	0.980000	0.70556	-1.729000	0.01856	2.032000	0.59987	0.549000	0.68633	GCG	.	.		0.692	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		G	140627002	C	G	140627002	3	3	112	1	0	0	0	0	1	0	0	0	11549	768	27	4	1858	4	PCDHB15	5	140627002	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	690266	140627002	40288258	391	17012										
TCERG1	10915	hgsc.bcm.edu	37	chr5	145890008	145890008	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctttttcttatttcagatccAaaaaattaatccaagaatca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:145890008delA	ENST00000296702.5	+	22	3138	c.3100delA	c.(3100-3102)aaafs	p.K1035fs	TCERG1_ENST00000394421.2_Frame_Shift_Del_p.K1014fs	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	1035	FF 6.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTTCAGATCCAAAAAATTAAT	0.368																																					p.S1033fs		Atlas-INDEL	.											.	TCERG1	148	.	0			c.3099delC						.						48	52	51					5																	145890008		2203	4300	6503	SO:0001589	frameshift_variant	10915	exon22			.	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.3100delA	chr5.hg19:g.145890008delA	ENSP00000296702:p.Lys1035fs	69.0	0.0		119.0	10.0	NM_006706	Q2NKN2|Q59EA1	Frame_Shift_Del	DEL	ENST00000296702.5	hg19	CCDS4282.1																																																																																			.	.		0.368	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		-	145890008	A	-	145890008	7	5	112	1	0	1	0	1	0	0	0	0	15700	131	5	0	3186	0	TCERG1	5	145890008	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5263006	145890008	35025252	392	17013										
CSNK1A1	1452	hgsc.bcm.edu	37	chr5	148889476	148889476	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caacaggcgtggacatcttcTtttcactaatcttttcatat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:148889476delT	ENST00000377843.2	-	7	1195	c.716delA	c.(715-717)aagfs	p.K240fs	CSNK1A1_ENST00000606299.1_5'UTR|CSNK1A1_ENST00000515435.1_Frame_Shift_Del_p.K179fs|CSNK1A1_ENST00000261798.5_Frame_Shift_Del_p.K240fs|CSNK1A1_ENST00000504676.1_Frame_Shift_Del_p.K151fs|CSNK1A1_ENST00000606719.1_Frame_Shift_Del_p.K37fs|CSNK1A1_ENST00000515768.1_Frame_Shift_Del_p.K268fs	NM_001025105.1|NM_001892.4	NP_001020276.1|NP_001883.4	P48729	KC1A_HUMAN	casein kinase 1, alpha 1	240	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(4)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GGACATCTTCTTTTCACTAAT	0.333																																					p.K267fs	Colon(5;64 69 1309 10383)	Atlas-INDEL	.											.	CSNK1A1	63	.	0			c.801delG						.						111	107	109					5																	148889476		1973	4213	6186	SO:0001589	frameshift_variant	1452	exon8			.	AF119911	CCDS47303.1, CCDS47304.1, CCDS64291.1	5q32	2013-01-17			ENSG00000113712	ENSG00000113712			2451	protein-coding gene	gene with protein product	"clock regulator kinase"	600505				8050587	Standard	NM_001025105		Approved	CK1, CK1a, CK1alpha, CKIa, CKIalpha	uc003lqw.2	P48729	OTTHUMG00000163463	ENST00000377843.2:c.716delA	chr5.hg19:g.148889476delT	ENSP00000367074:p.Lys240fs	73.0	0.0		225.0	15.0	NM_001025105	D3DQG0|D3DQG1|Q4JJA0|Q5U046|Q5U047|Q6FGA2|Q71TU5|Q96HD2|Q9UDK3	Frame_Shift_Del	DEL	ENST00000377843.2	hg19	CCDS47303.1																																																																																			.	.		0.333	CSNK1A1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001892		-	148889476	T	-	148889476	7	5	112	1	0	1	0	1	0	0	0	0	3952	1609	56	0	313	0	CSNK1A1	5	148889476	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2999468	148889476	32025784	393	17014										
ARHGEF37	389337	hgsc.bcm.edu	37	chr5	149006643	149006643	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctcctcctctcccagccgcTccttccagggtctgaacgcc	8	20	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:149006643T>C	ENST00000333677.6	+	11	1632	c.1469T>C	c.(1468-1470)cTc>cCc	p.L490P		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	490						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						TCCCAGCCGCTCCTTCCAGGG	0.552																																					p.L490P		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.T1469C						.						91	100	97					5																	149006643		2061	4206	6267	SO:0001583	missense	389337	exon11			AGCCGCTCCTTCC	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"Rho guanine nucleotide exchange factors"	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1469T>C	chr5.hg19:g.149006643T>C	ENSP00000328083:p.Leu490Pro	94.0	0.0		208.0	9.0	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	hg19	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.260430	0.80246	.	.	ENSG00000183111	ENST00000333677	T	0.57907	0.37	5.39	5.39	0.77823	.	0.063201	0.64402	D	0.000004	T	0.67998	0.2953	L	0.58101	1.795	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.70226	-0.4930	10	0.59425	D	0.04	.	13.6429	0.62263	0.0:0.0:0.0:1.0	.	490	A1IGU5	ARH37_HUMAN	P	490	ENSP00000328083:L490P	ENSP00000328083:L490P	L	+	2	0	ARHGEF37	148986836	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	5.468000	0.66743	2.036000	0.60181	0.459000	0.35465	CTC	.	.		0.552	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669		C	149006643	T	C	149006643	3	2	112	1	0	0	0	0	1	0	0	0	906	1551	54	2	1507	2	ARHGEF37	5	149006643	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	117167	149006643	31908617	394	17015										
TIGD6	81789	hgsc.bcm.edu	37	chr5	149375707	149375707	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ataaagagcgctcctcatccTtttccgctggggtcccacgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:149375707delT	ENST00000296736.3	-	2	979	c.205delA	c.(205-207)aggfs	p.R69fs	TIGD6_ENST00000515406.2_Frame_Shift_Del_p.R69fs	NM_030953.3	NP_112215.1	Q17RP2	TIGD6_HUMAN	tigger transposable element derived 6	69	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|stomach(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CTCCTCATCCTTTTCCGCTGG	0.433																																					p.R69fs		Atlas-INDEL	.											.	TIGD6	29	.	0			c.206delG						.						111	112	112					5																	149375707		2203	4300	6503	SO:0001589	frameshift_variant	81789	exon2			.	AK056604	CCDS4301.1	5q33.1	2008-02-05			ENSG00000164296	ENSG00000164296			18332	protein-coding gene	gene with protein product						11230166	Standard	NM_030953		Approved	DKFZp761E2110	uc003lrj.3	Q17RP2	OTTHUMG00000130045	ENST00000296736.3:c.205delA	chr5.hg19:g.149375707delT	ENSP00000296736:p.Arg69fs	63.0	0.0		143.0	13.0	NM_001243253	B3KTZ8|Q96MQ4|Q9H0X7	Frame_Shift_Del	DEL	ENST00000296736.3	hg19	CCDS4301.1																																																																																			.	.		0.433	TIGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252324.1	NM_030953		-	149375707	T	-	149375707	7	5	112	1	0	1	0	1	0	0	0	0	15915	1608	56	0	1364	0	TIGD6	5	149375707	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	369064	149375707	31539553	395	17016										
CCDC69	26112	hgsc.bcm.edu	37	chr5	150563972	150563972	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcctgttgcagggtcgtaaTtttttcctccaatatcagat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:150563972delT	ENST00000355417.2	-	8	820	c.646delA	c.(646-648)attfs	p.I216fs	CCDC69_ENST00000521308.1_5'UTR	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	216										haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGGTCGTAATTTTTTCCTCC	0.488																																					p.I216fs		Atlas-INDEL	.											.	CCDC69	30	.	0			c.647delT						.						129	120	123					5																	150563972		2203	4300	6503	SO:0001589	frameshift_variant	26112	exon8			.		CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.646delA	chr5.hg19:g.150563972delT	ENSP00000347586:p.Ile216fs	139.0	0.0		231.0	14.0	NM_015621	A8K9X6	Frame_Shift_Del	DEL	ENST00000355417.2	hg19	CCDS4312.1																																																																																			.	.		0.488	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621		-	150563972	T	-	150563972	7	5	112	1	0	1	0	1	0	0	0	0	2843	1493	52	0	252	0	CCDC69	5	150563972	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1188265	150563972	30351288	396	17017										
FAT2	2196	hgsc.bcm.edu	37	chr5	150924388	150924388	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatgtaacagccccatttgtCcccaagtcctcatcagtggc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:150924388delC	ENST00000261800.5	-	9	6312	c.6300delG	c.(6298-6300)gggfs	p.G2100fs		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2100	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCCATTTGTCCCCAAGTCCT	0.443																																					p.T2101fs		Atlas-INDEL	.											.	FAT2	465	.	0			c.6301delA						.						123	127	126					5																	150924388		2203	4300	6503	SO:0001589	frameshift_variant	2196	exon9			.	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.6300delG	chr5.hg19:g.150924388delC	ENSP00000261800:p.Gly2100fs	110.0	0.0		208.0	14.0	NM_001447	O75091|Q9NSR7	Frame_Shift_Del	DEL	ENST00000261800.5	hg19	CCDS4317.1																																																																																			.	.		0.443	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		-	150924388	C	-	150924388	7	5	112	1	0	1	0	1	0	0	0	0	5698	842	30	0	6809	0	FAT2	5	150924388	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	360416	150924388	29990872	397	17018										
THG1L	54974	hgsc.bcm.edu	37	chr5	157161681	157161681	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccttctgtatcccccaggcTttgacggaagagtcgtggtg	12	12	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:157161681T>C	ENST00000231198.7	+	3	710	c.466T>C	c.(466-468)Ttt>Ctt	p.F156L	AC026407.1_ENST00000599823.1_Silent_p.K15K	NM_017872.3	NP_060342.2	Q9NWX6	THG1_HUMAN	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	156					protein homotetramerization (GO:0051289)|tRNA modification (GO:0006400)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|tRNA binding (GO:0000049)|tRNA guanylyltransferase activity (GO:0008193)			NS(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)	13	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCCCCCAGGCTTTGACGGAAG	0.498																																					p.F156L		Atlas-SNP	.											.	THG1L	31	.	0			c.T466C						.						126	118	121					5																	157161681		2203	4300	6503	SO:0001583	missense	54974	exon3			CCAGGCTTTGACG	AK223119	CCDS4341.1	5q33.3	2008-02-05			ENSG00000113272	ENSG00000113272			26053	protein-coding gene	gene with protein product	"interphase cytoplasmic foci protein 45"					11230166	Standard	XM_005265939		Approved	ICF45, FLJ11601, FLJ20546	uc003lxd.3	Q9NWX6	OTTHUMG00000130254	ENST00000231198.7:c.466T>C	chr5.hg19:g.157161681T>C	ENSP00000231198:p.Phe156Leu	99.0	0.0		191.0	8.0	NM_017872	D3DQJ5|Q53G12|Q7L5R3|Q9H0S2	Missense_Mutation	SNP	ENST00000231198.7	hg19	CCDS4341.1	.	.	.	.	.	.	.	.	.	.	T	19.20	3.781232	0.70222	.	.	ENSG00000113272	ENST00000231198;ENST00000448153	T	0.70749	-0.51	5.95	5.95	0.96441	.	0.042575	0.85682	N	0.000000	D	0.85894	0.5803	H	0.96430	3.82	0.80722	D	1	P;P	0.48016	0.888;0.904	P;P	0.51135	0.489;0.66	D	0.90196	0.4253	10	0.87932	D	0	-36.0233	16.4208	0.83758	0.0:0.0:0.0:1.0	.	24;156	B4E366;Q9NWX6	.;THG1_HUMAN	L	156;31	ENSP00000231198:F156L	ENSP00000231198:F156L	F	+	1	0	THG1L	157094259	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.001000	0.88508	2.274000	0.75844	0.528000	0.53228	TTT	.	.		0.498	THG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252579.2	NM_017872		C	157161681	T	C	157161681	3	2	112	1	0	0	0	0	1	0	0	0	15876	1609	56	2	476	2	THG1L	5	157161681	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	6237293	157161681	23753579	398	17019										
PTTG1	9232	hgsc.bcm.edu	37	chr5	159851311	159851311	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgatgcctatccagaaatagAaaaattctttcccttcaatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:159851311delA	ENST00000393964.1	+	3	747	c.344delA	c.(343-345)gaafs	p.E115fs	PTTG1_ENST00000352433.5_Frame_Shift_Del_p.E115fs|PTTG1_ENST00000520452.1_Frame_Shift_Del_p.E115fs|PTTG1_ENST00000519287.1_3'UTR	NM_001282382.1	NP_001269311.1	O95997	PTTG1_HUMAN	pituitary tumor-transforming 1	115					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|DNA repair (GO:0006281)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of endopeptidase activity (GO:0010951)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(1)|lung(4)	6	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.00219)|Epithelial(171;0.00348)|all cancers(165;0.0104)		CCAGAAATAGAAAAATTCTTT	0.383																																					p.E115fs		Atlas-INDEL	.											.	PTTG1	15	.	0			c.343delG						.						112	118	116					5																	159851311		2203	4300	6503	SO:0001589	frameshift_variant	9232	exon4			.	AF062649	CCDS4353.1	5q35.1	2014-08-04			ENSG00000164611	ENSG00000164611			9690	protein-coding gene	gene with protein product	"ESP1-associated protein 1", "tumor-transforming protein 1"	604147		TUTR1		9811450, 9892021	Standard	NM_004219		Approved	PTTG, HPTTG, EAP1, securin	uc003lyj.3	O95997	OTTHUMG00000130328	ENST00000393964.1:c.344delA	chr5.hg19:g.159851311delA	ENSP00000377536:p.Glu115fs	104.0	0.0		173.0	11.0	NM_004219		Frame_Shift_Del	DEL	ENST00000393964.1	hg19	CCDS4353.1																																																																																			.	.		0.383	PTTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252677.1	NM_004219		-	159851311	A	-	159851311	7	5	112	1	0	1	0	1	0	0	0	0	12834	246	9	0	354	0	PTTG1	5	159851311	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2689630	159851311	21063949	399	17020										
GABRA1	2554	hgsc.bcm.edu	37	chr5	161277851	161277851	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggtctgtctgactgtctttGggcctggatcctccttctga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:161277851delG	ENST00000428797.2	+	3	390	c.35delG	c.(34-36)tggfs	p.W12fs	GABRA1_ENST00000420560.1_Frame_Shift_Del_p.W12fs|GABRA1_ENST00000437025.2_Frame_Shift_Del_p.W12fs|GABRA1_ENST00000393943.4_Frame_Shift_Del_p.W12fs|GABRA1_ENST00000444819.1_Frame_Shift_Del_p.W12fs|GABRA1_ENST00000023897.6_Frame_Shift_Del_p.W12fs	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	12					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	GACTGTCTTTGGGCCTGGATC	0.423																																					p.W12fs		Atlas-INDEL	.											.	GABRA1	132	.	0			c.34delT						.						111	106	107					5																	161277851		2203	4300	6503	SO:0001589	frameshift_variant	2554	exon2			.		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.35delG	chr5.hg19:g.161277851delG	ENSP00000393097:p.Trp12fs	139.0	0.0		235.0	15.0	NM_001127644	D3DQK6|Q8N629	Frame_Shift_Del	DEL	ENST00000428797.2	hg19	CCDS4357.1																																																																																			.	.		0.423	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		-	161277851	G	-	161277851	7	5	112	1	0	1	0	1	0	0	0	0	6168	1357	47	0	37	0	GABRA1	5	161277851	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1426540	161277851	19637409	400	17021										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168127640	168127640	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caggtgcctccatgctgacaGgggttctggatgcaggtgtt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:168127640delG	ENST00000519560.1	-	27	3308	c.2889delC	c.(2887-2889)cccfs	p.P963fs	SLIT3_ENST00000332966.8_Frame_Shift_Del_p.P970fs|SLIT3_ENST00000404867.3_Frame_Shift_Del_p.P963fs	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	963	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CATGCTGACAGGGGTTCTGGA	0.572																																					p.C971fs	Ovarian(29;311 847 10864 17279 24903)	Atlas-INDEL	.											.	SLIT3	224	.	0			c.2911delT						.						111	93	99					5																	168127640		2203	4300	6503	SO:0001589	frameshift_variant	6586	exon27			.	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.2889delC	chr5.hg19:g.168127640delG	ENSP00000430333:p.Pro963fs	140.0	0.0		273.0	18.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Frame_Shift_Del	DEL	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.572	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		-	168127640	G	-	168127640	7	5	112	1	0	1	0	1	0	0	0	0	14756	987	35	0	1722	0	SLIT3	5	168127640	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	6849789	168127640	12787620	401	17022										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168212944	168212944	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacaccagcccatcaaacagTcccttgacaatctcggtgat	7	14	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:168212944T>C	ENST00000519560.1	-	12	1538	c.1119A>G	c.(1117-1119)ggA>ggG	p.G373G	SLIT3_ENST00000332966.8_Silent_p.G373G|SLIT3_ENST00000404867.3_Silent_p.G373G	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	373					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CATCAAACAGTCCCTTGACAA	0.512																																					p.G373G	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.A1119G						.						156	130	139					5																	168212944		2203	4300	6503	SO:0001819	synonymous_variant	6586	exon12			AAACAGTCCCTTG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.1119A>G	chr5.hg19:g.168212944T>C		66.0	0.0		132.0	6.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.512	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		C	168212944	T	C	168212944	2	2	112	1	0	0	0	0	0	0	0	1	14756	1654	58	2		2	SLIT3	5	168212944	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	85304	168212944	12702316	402	17023										
HMP19	51617	hgsc.bcm.edu	37	chr5	173473819	173473819	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agccgccttcagttgaggatGgcttccagaccgtccctctc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:173473819delG	ENST00000303177.3	+	2	323	c.61delG	c.(61-63)ggcfs	p.G21fs	NSG2_ENST00000521585.1_Frame_Shift_Del_p.G21fs	NM_015980.4	NP_057064.1	Q9Y328	NSG2_HUMAN		21					clathrin coat assembly (GO:0048268)|dopamine receptor signaling pathway (GO:0007212)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.G21S(1)									AGTTGAGGATGGCTTCCAGAC	0.537																																					p.D20fs		Atlas-INDEL	.											.	HMP19	21	.	1	Substitution - Missense(1)	lung(1)	c.60delT						.						219	198	205					5																	173473819		2203	4300	6503	SO:0001589	frameshift_variant	0	exon2			.																												ENST00000303177.3:c.61delG	chr5.hg19:g.173473819delG	ENSP00000307722:p.Gly21fs	98.0	0.0		161.0	10.0	NM_015980	B2R5Y0|D3DQN0|Q9UHX8	Frame_Shift_Del	DEL	ENST00000303177.3	hg19	CCDS4391.1																																																																																			.	.		0.537	NSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252966.2			-	173473819	G	-	173473819	7	5	112	1	0	1	0	1	0	0	0	0	7254	1348	47	0	63	0	HMP19	5	173473819	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	5260875	173473819	7441441	403	17024										
THOC3	84321	hgsc.bcm.edu	37	chr5	175394993	175394993	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctggccgtcttgtcgaaggaCcccgaggctaggcgacgccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:175394993delC	ENST00000265097.4	-	1	309	c.219delG	c.(217-219)gggfs	p.G73fs	THOC3_ENST00000514861.1_Intron|THOC3_ENST00000510300.1_5'Flank|THOC3_ENST00000513482.1_Frame_Shift_Del_p.G73fs	NM_032361.2	NP_115737.1	Q96J01	THOC3_HUMAN	THO complex 3	73					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)	4	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		TGTCGAAGGACCCCGAGGCTA	0.672																																					p.S74fs		Atlas-INDEL	.											.	THOC3	11	.	0			c.220delT						.						9	10	10					5																	175394993		2002	3986	5988	SO:0001589	frameshift_variant	84321	exon1			.	BC006849	CCDS4397.1	5q35.3	2013-02-11			ENSG00000051596	ENSG00000051596		"WD repeat domain containing", "THO complex subunits"	19072	protein-coding gene	gene with protein product		606929				11979277	Standard	NM_032361		Approved	TEX1, MGC5469	uc003mdg.5	Q96J01	OTTHUMG00000130658	ENST00000265097.4:c.219delG	chr5.hg19:g.175394993delC	ENSP00000265097:p.Gly73fs	83.0	0.0		169.0	13.0	NM_032361	Q6NZ53	Frame_Shift_Del	DEL	ENST00000265097.4	hg19	CCDS4397.1																																																																																			.	.		0.672	THOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253148.1			-	175394993	C	-	175394993	7	5	112	1	0	1	0	1	0	0	0	0	15881	494	18	0	860	0	THOC3	5	175394993	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1921174	175394993	5520267	404	17025										
C5orf25	375484	hgsc.bcm.edu	37	chr5	175740835	175740835	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgctttcctgtgacaagcagCcccacaatgtcaggtaagca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:175740835delC	ENST00000443967.1	+	7	2226	c.1819delC	c.(1819-1821)cccfs	p.P607fs	SIMC1_ENST00000332772.4_Frame_Shift_Del_p.P68fs|SIMC1_ENST00000341199.6_Frame_Shift_Del_p.P192fs|SIMC1_ENST00000430704.2_Frame_Shift_Del_p.P192fs			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	607							SUMO polymer binding (GO:0032184)										TGACAAGCAGCCCCACAATGT	0.542																																					p.Q191fs		Atlas-INDEL	.											.	.	.	.	0			c.573delG						.						85	79	81					5																	175740835		2203	4300	6503	SO:0001589	frameshift_variant	375484	exon4			.	BC037298	CCDS4398.2	5q35.2	2013-08-14	2012-11-14	2012-11-14	ENSG00000170085	ENSG00000170085			24779	protein-coding gene	gene with protein product	"oocyte maturation associated 1", "platform element for inhibition of autolytic degradation"		"chromosome 5 open reading frame 25"	C5orf25		23086935, 23707407	Standard	NM_198567		Approved	FLJ44216, OOMA1, PLEIAD	uc003mds.4	Q8NDZ2	OTTHUMG00000130663	ENST00000443967.1:c.1819delC	chr5.hg19:g.175740835delC	ENSP00000406571:p.Pro607fs	113.0	0.0		171.0	11.0	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Frame_Shift_Del	DEL	ENST00000443967.1	hg19																																																																																				.	.		0.542	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567		-	175740835	C	-	175740835	7	5	112	1	0	1	0	1	0	0	0	0	2290	739	26	0	588	0	C5orf25	5	175740835	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	345842	175740835	5174425	405	17026										
HK3	3101	hgsc.bcm.edu	37	chr5	176309024	176309024	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catggccagagagccatcgtCcccaaaggcgccccactcca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:176309024delC	ENST00000292432.5	-	16	2249	c.2158delG	c.(2158-2160)gacfs	p.D721fs		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	721	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGCCATCGTCCCCAAAGGCG	0.647																																					p.D720fs		Atlas-INDEL	.											.	HK3	210	.	0			c.2159delA						.						82	81	81					5																	176309024		2203	4300	6503	SO:0001589	frameshift_variant	3101	exon16			.		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.2158delG	chr5.hg19:g.176309024delC	ENSP00000292432:p.Asp721fs	97.0	0.0		193.0	15.0	NM_002115	Q8N1E7	Frame_Shift_Del	DEL	ENST00000292432.5	hg19	CCDS4407.1																																																																																			.	.		0.647	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			-	176309024	C	-	176309024	7	5	112	1	0	1	0	1	0	0	0	0	7201	855	30	0	629	0	HK3	5	176309024	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	568189	176309024	4606236	406	17027										
CLK4	57396	hgsc.bcm.edu	37	chr5	178032333	178032333	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgaatcatgtgttgtggtatGggtcctaatattcgttccat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:178032333delG	ENST00000316308.4	-	11	1353	c.1185delC	c.(1183-1185)cccfs	p.P395fs		NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	395	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		GTTGTGGTATGGGTCCTAATA	0.343																																					p.I396fs		Atlas-INDEL	.											.	CLK4	103	.	0			c.1186delA						.						163	147	153					5																	178032333		2203	4299	6502	SO:0001589	frameshift_variant	57396	exon11			.	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.1185delC	chr5.hg19:g.178032333delG	ENSP00000316948:p.Pro395fs	120.0	0.0		214.0	13.0	NM_020666		Frame_Shift_Del	DEL	ENST00000316308.4	hg19	CCDS4437.1																																																																																			.	.		0.343	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			-	178032333	G	-	178032333	7	5	112	1	0	1	0	1	0	0	0	0	3541	1335	47	0	272	0	CLK4	5	178032333	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1723309	178032333	2882927	407	17028										
RUFY1	80230	hgsc.bcm.edu	37	chr5	179023590	179023590	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cactcggagcgggcgaggcaGggggctgaggagcggagcca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:179023590delG	ENST00000319449.4	+	13	1551	c.1539delG	c.(1537-1539)cagfs	p.Q513fs	RUFY1_ENST00000393438.2_Frame_Shift_Del_p.Q405fs|RUFY1_ENST00000437570.2_Frame_Shift_Del_p.Q405fs|RUFY1_ENST00000377001.2_3'UTR|RP11-1379J22.2_ENST00000500262.1_RNA	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	513					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGGCGAGGCAGGGGGCTGAGG	0.607										HNSCC(44;0.11)																											p.Q513fs		Atlas-INDEL	.											.	RUFY1	101	.	0			c.1538delA						.						81	97	92					5																	179023590		2182	4267	6449	SO:0001589	frameshift_variant	80230	exon13			.	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"Zinc fingers, FYVE domain containing"	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.1539delG	chr5.hg19:g.179023590delG	ENSP00000325594:p.Gln513fs	101.0	0.0		182.0	11.0	NM_025158	Q59FF3|Q71S93|Q9H6I3	Frame_Shift_Del	DEL	ENST00000319449.4	hg19	CCDS4445.2																																																																																			.	.		0.607	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451		-	179023590	G	-	179023590	7	5	112	1	0	1	0	1	0	0	0	0	13753	991	35	0	1589	0	RUFY1	5	179023590	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	991257	179023590	1891670	408	17029										
MAML1	9794	hgsc.bcm.edu	37	chr5	179193024	179193024	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcccctgtgagtacagattCccccagcctagggggctccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:179193024delC	ENST00000292599.3	+	2	1276	c.1013delC	c.(1012-1014)tccfs	p.S338fs	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGTACAGATTCCCCCAGCCTA	0.617																																					p.S338fs		Atlas-INDEL	.											.	MAML1	118	.	0			c.1012delT						.						31	34	33					5																	179193024		2203	4300	6503	SO:0001589	frameshift_variant	9794	exon2			.	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1013delC	chr5.hg19:g.179193024delC	ENSP00000292599:p.Ser338fs	69.0	0.0		144.0	10.0	NM_014757		Frame_Shift_Del	DEL	ENST00000292599.3	hg19	CCDS34315.1																																																																																			.	.		0.617	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		-	179193024	C	-	179193024	7	5	112	1	0	1	0	1	0	0	0	0	9214	855	30	0	1019	0	MAML1	5	179193024	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	169434	179193024	1722236	409	17030										
EXOC2	55770	hgsc.bcm.edu	37	chr6	532529	532529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ataaattccaggttctaaggAgccaacgatgggatctgctt	10	8	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:532529A>G	ENST00000230449.4	-	23	2455	c.2320T>C	c.(2320-2322)Tcc>Ccc	p.S774P	EXOC2_ENST00000448181.3_Missense_Mutation_p.S369P	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	774					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.S774P(1)		breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GGTTCTAAGGAGCCAACGATG	0.378																																					p.S774P		Atlas-SNP	.											EXOC2,NS,carcinoma,0,1	EXOC2	81	.	1	Substitution - Missense(1)	kidney(1)	c.T2320C						.						125	119	121					6																	532529		2203	4300	6503	SO:0001583	missense	55770	exon23			CTAAGGAGCCAAC	AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"SEC5-like 1 (S. cerevisiae)"	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.2320T>C	chr6.hg19:g.532529A>G	ENSP00000230449:p.Ser774Pro	144.0	0.0		217.0	9.0	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Missense_Mutation	SNP	ENST00000230449.4	hg19	CCDS34327.1	.	.	.	.	.	.	.	.	.	.	A	19.44	3.828161	0.71143	.	.	ENSG00000112685	ENST00000230449;ENST00000448181	T;T	0.28255	1.62;1.62	5.67	5.67	0.87782	.	0.052488	0.85682	D	0.000000	T	0.19604	0.0471	M	0.63428	1.95	0.80722	D	1	P	0.40875	0.731	B	0.32533	0.147	T	0.08106	-1.0738	10	0.59425	D	0.04	-0.0072	16.2014	0.82084	1.0:0.0:0.0:0.0	.	774	Q96KP1	EXOC2_HUMAN	P	774;369	ENSP00000230449:S774P;ENSP00000398113:S369P	ENSP00000230449:S774P	S	-	1	0	EXOC2	477529	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.880000	0.92407	2.281000	0.76405	0.533000	0.62120	TCC	.	.		0.378	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303		G	532529	A	G	532529	3	3	112	1	0	0	0	0	1	0	0	0	5304	304	11	2	478	2	EXOC2	6	532529	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10		532529	170582538	410	17031										
SNRNP48	154007	hgsc.bcm.edu	37	chr6	7594353	7594353	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgaaatgtataatcctgagTttttctatgaaaatgtgaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:7594353delT	ENST00000342415.5	+	3	351	c.292delT	c.(292-294)tttfs	p.F99fs		NM_152551.3	NP_689764.3	Q6IEG0	SNR48_HUMAN	small nuclear ribonucleoprotein 48kDa (U11/U12)	99					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)			kidney(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						TAATCCTGAGTTTTTCTATGA	0.234																																					p.E97fs		Atlas-INDEL	.											.	SNRNP48	32	.	0			c.291delG						.						23	24	24					6																	7594353		2134	4195	6329	SO:0001589	frameshift_variant	154007	exon3			.	AK056796	CCDS4502.1	6p24.3	2011-10-11	2008-10-29	2008-10-29	ENSG00000168566	ENSG00000168566			21368	protein-coding gene	gene with protein product	"U11/U12 snRNP 48K"		"chromosome 6 open reading frame 151"	C6orf151		15146077	Standard	XR_427825		Approved	FLJ32234, dJ512B11.2, dJ336K20B.1	uc003mxr.3	Q6IEG0	OTTHUMG00000014213	ENST00000342415.5:c.292delT	chr6.hg19:g.7594353delT	ENSP00000339834:p.Phe99fs	98.0	0.0		176.0	11.0	NM_152551	A8K8P4|Q14C91|Q5T339|Q5THM1|Q5THM2|Q96MK1	Frame_Shift_Del	DEL	ENST00000342415.5	hg19	CCDS4502.1																																																																																			.	.		0.234	SNRNP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039787.3	NM_152551		-	7594353	T	-	7594353	7	5	112	1	0	1	0	1	0	0	0	0	14872	1725	60	0	302	0	SNRNP48	6	7594353	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	7061824	7594353	163520714	411	17032										
SOX4	6659	hgsc.bcm.edu	37	chr6	21595211	21595211	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcctcggccgccgcctcctCcaagccgggggagaagggag	15	16	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:21595211C>T	ENST00000244745.1	+	1	1240	c.446C>T	c.(445-447)tCc>tTc	p.S149F	SOX4_ENST00000543472.1_Missense_Mutation_p.S149F	NM_003107.2	NP_003098.1	Q06945	SOX4_HUMAN	SRY (sex determining region Y)-box 4	149					ascending aorta morphogenesis (GO:0035910)|atrial septum primum morphogenesis (GO:0003289)|canonical Wnt signaling pathway (GO:0060070)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle formation (GO:0003211)|cellular response to glucose stimulus (GO:0071333)|DNA damage response, detection of DNA damage (GO:0042769)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endocrine pancreas development (GO:0031018)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|kidney morphogenesis (GO:0060993)|limb bud formation (GO:0060174)|mitral valve morphogenesis (GO:0003183)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein ubiquitination (GO:0031397)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|noradrenergic neuron differentiation (GO:0003357)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin secretion (GO:0032024)|positive regulation of N-terminal peptidyl-lysine acetylation (GO:2000761)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of Wnt signaling pathway (GO:0030177)|pro-B cell differentiation (GO:0002328)|protein stabilization (GO:0050821)|regulation of protein stability (GO:0031647)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spinal cord development (GO:0021510)|spinal cord motor neuron differentiation (GO:0021522)|sympathetic nervous system development (GO:0048485)|T cell differentiation (GO:0030217)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.S149Y(1)		kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	6	Ovarian(93;0.163)		all cancers(50;0.0751)|Epithelial(50;0.155)			GCCGCCTCCTCCAAGCCGGGG	0.716																																					p.S149F		Atlas-SNP	.											SOX4,mouth,carcinoma,0,1	SOX4	11	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C446T						.						9	11	10					6																	21595211		2180	4278	6458	SO:0001583	missense	6659	exon1			CCTCCTCCAAGCC	AF070669	CCDS4547.1	6p22.3	2008-02-05			ENSG00000124766	ENSG00000124766		"SRY (sex determining region Y)-boxes"	11200	protein-coding gene	gene with protein product		184430				8268656, 9730625	Standard	NM_003107		Approved		uc003ndi.3	Q06945	OTTHUMG00000016101	ENST00000244745.1:c.446C>T	chr6.hg19:g.21595211C>T	ENSP00000244745:p.Ser149Phe	29.0	0.0		62.0	3.0	NM_003107		Missense_Mutation	SNP	ENST00000244745.1	hg19	CCDS4547.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.332285	0.24167	.	.	ENSG00000124766	ENST00000244745;ENST00000543472	T;T	0.20332	2.08;2.08	3.43	2.54	0.30619	.	.	.	.	.	T	0.07324	0.0185	L	0.48642	1.525	0.35912	D	0.831198	P	0.38565	0.637	B	0.41813	0.367	T	0.12811	-1.0533	9	0.09338	T	0.73	.	7.8342	0.29360	0.2467:0.7532:0.0:0.0	.	149	Q06945	SOX4_HUMAN	F	149	ENSP00000244745:S149F;ENSP00000438412:S149F	ENSP00000244745:S149F	S	+	2	0	SOX4	21703190	0.003000	0.15002	0.788000	0.31933	0.314000	0.28054	1.614000	0.36911	0.591000	0.29711	0.305000	0.20034	TCC	.	.		0.716	SOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043301.1	NM_003107		T	21595211	C	T	21595211	3	4	112	1	0	0	0	0	1	0	0	0	14968	855	30	3	448	3	SOX4	6	21595211	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	14000858	21595211	149519856	412	17033										
DCDC2	51473	hgsc.bcm.edu	37	chr6	24278359	24278359	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttttctgaattcacgtcttcTtttttccctttcctcttcag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:24278359delT	ENST00000378454.3	-	7	1141	c.840delA	c.(838-840)aaafs	p.K280fs		NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	280					cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TCACGTCTTCTTTTTTCCCTT	0.358																																					p.E281fs		Atlas-INDEL	.											DCDC2,colon,carcinoma,0,1	DCDC2	53	.	0			c.841delG						.						148	139	142					6																	24278359		2203	4300	6503	SO:0001589	frameshift_variant	51473	exon8			.	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.840delA	chr6.hg19:g.24278359delT	ENSP00000367715:p.Lys280fs	148.0	0.0		230.0	16.0	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Frame_Shift_Del	DEL	ENST00000378454.3	hg19	CCDS4550.1																																																																																			.	.		0.358	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356		-	24278359	T	-	24278359	7	5	112	1	0	1	0	1	0	0	0	0	4287	1606	56	0	606	0	DCDC2	6	24278359	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2683148	24278359	146836708	413	17034										
FAM65B	9750	hgsc.bcm.edu	37	chr6	24806664	24806664	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttaacacagtctcgaggaaaTttgtccaattgttcatatgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:24806664delT	ENST00000259698.4	-	23	3319	c.3144delA	c.(3142-3144)aaafs	p.K1048fs	FAM65B_ENST00000538035.1_Frame_Shift_Del_p.K1027fs	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	1048					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						CTCGAGGAAATTTGTCCAATT	0.378																																					p.F1049fs		Atlas-INDEL	.											.	FAM65B	134	.	0			c.3145delT						.						152	129	136					6																	24806664		692	1591	2283	SO:0001589	frameshift_variant	9750	exon23			.	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.3144delA	chr6.hg19:g.24806664delT	ENSP00000259698:p.Lys1048fs	81.0	0.0		106.0	12.0	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Frame_Shift_Del	DEL	ENST00000259698.4	hg19	CCDS47383.1																																																																																			.	.		0.378	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			-	24806664	T	-	24806664	7	5	112	1	0	1	0	1	0	0	0	0	5608	1490	52	0	66	0	FAM65B	6	24806664	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	528305	24806664	146308403	414	17035										
LRRC16A	55604	hgsc.bcm.edu	37	chr6	25619801	25619801	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaagcagaaaaagagtttaTttttgtgtaaaggtcaccca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:25619801delT	ENST00000329474.6	+	37	4474	c.4106delT	c.(4105-4107)attfs	p.I1369fs	LRRC16A_ENST00000476458.1_3'UTR	NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1369					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						AAAGAGTTTATTTTTGTGTAA	0.483																																					p.I1369fs		Atlas-INDEL	.											.	LRRC16A	168	.	0			c.4105delA						.						94	96	96					6																	25619801		1923	4123	6046	SO:0001589	frameshift_variant	55604	exon37			.	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"	609593	"leucine rich repeat containing 16"	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.4106delT	chr6.hg19:g.25619801delT	ENSP00000331983:p.Ile1369fs	116.0	0.0		149.0	11.0	NM_017640	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Frame_Shift_Del	DEL	ENST00000329474.6	hg19	CCDS54973.1																																																																																			.	.		0.483	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640		-	25619801	T	-	25619801	7	5	112	1	0	1	0	1	0	0	0	0	8980	1493	52	0	4252	0	LRRC16A	6	25619801	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	813137	25619801	145495266	415	17036										
HMGN4	10473	hgsc.bcm.edu	37	chr6	26545644	26545644	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaggatgggaacaaccctgcAaaaaaccgagatgcctctac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:26545644delA	ENST00000377575.2	+	2	387	c.210delA	c.(208-210)gcafs	p.A70fs		NM_006353.2	NP_006344.1	O00479	HMGN4_HUMAN	high mobility group nucleosomal binding domain 4	70						chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)			lung(2)|skin(1)	3						ACAACCCTGCAAAAAACCGAG	0.498																																					p.A70fs		Atlas-INDEL	.											.	HMGN4	4	.	0			c.209delC						.						92	105	100					6																	26545644		2203	4300	6503	SO:0001589	frameshift_variant	10473	exon2			.	U90549	CCDS4615.1	6p21.3	2011-07-01	2002-07-25	2002-07-26	ENSG00000182952	ENSG00000182952		"High-mobility group / Canonical"	4989	protein-coding gene	gene with protein product			"high-mobility group (nonhistone chromosomal) protein 17-like 3"	HMG17L3		9149941, 11410162	Standard	NM_006353		Approved	NHC	uc003nig.3	O00479	OTTHUMG00000014458	ENST00000377575.2:c.210delA	chr6.hg19:g.26545644delA	ENSP00000366798:p.Ala70fs	114.0	0.0		154.0	10.0	NM_006353	B2R4I6|Q53XL9	Frame_Shift_Del	DEL	ENST00000377575.2	hg19	CCDS4615.1																																																																																			.	.		0.498	HMGN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040123.2			-	26545644	A	-	26545644	7	5	112	1	0	1	0	1	0	0	0	0	7246	117	5	0	212	0	HMGN4	6	26545644	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	925843	26545644	144569423	416	17037										
ZNF184	7738	hgsc.bcm.edu	37	chr6	27420023	27420023	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggtttctccccagtatgagTtttttgatgctgagtgaggt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:27420023delT	ENST00000211936.6	-	6	1599	c.1315delA	c.(1315-1317)actfs	p.T439fs	ZNF184_ENST00000377419.1_Frame_Shift_Del_p.T439fs	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	439					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						CCAGTATGAGTTTTTTGATGC	0.408																																					p.T439fs		Atlas-INDEL	.											.	ZNF184	89	.	0			c.1316delC						.						87	87	87					6																	27420023		2203	4300	6503	SO:0001589	frameshift_variant	7738	exon6			.	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1315delA	chr6.hg19:g.27420023delT	ENSP00000211936:p.Thr439fs	87.0	0.0		130.0	10.0	NM_007149	B2R715|O60792|Q8TBA9	Frame_Shift_Del	DEL	ENST00000211936.6	hg19	CCDS4624.1																																																																																			.	.		0.408	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		-	27420023	T	-	27420023	7	5	112	1	0	1	0	1	0	0	0	0	17766	1725	60	0	944	0	ZNF184	6	27420023	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	874379	27420023	143695044	417	17038										
HLA-G	3135	hgsc.bcm.edu	37	chr6	29797196	29797196	+	Splice_Site	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttctgactcttcctttcagaCccccccaagacacacgtgac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:29797196delC	ENST00000360323.6	+	4	645	c.621delC	c.(619-621)gac>ga	p.D207fs	HLA-G_ENST00000376818.3_Splice_Site_p.N115fs|HLA-G_ENST00000376828.2_Splice_Site_p.D212fs|HLA-G_ENST00000428701.1_Splice_Site_p.D207fs|HLA-G_ENST00000376815.3_Intron			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	207	Alpha-3.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						TCCTTTCAGACCCCCCCAAGA	0.537																																					p.D207fs		Pindel	.											.,1	HLA-G	90	.	0			c.620delA						.						91	98	95					6																	29797196		2203	4300	6503	SO:0001630	splice_region_variant	3135	exon5			.		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4964	protein-coding gene	gene with protein product	"b2 microglobulin"	142871	"HLA-G histocompatibility antigen, class I, G"				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.620-1C>-	chr6.hg19:g.29797196delC		150.0	0.0		227.0	10.0	NM_002127		Frame_Shift_Del	DEL	ENST00000360323.6	hg19	CCDS4668.1																																																																																			.	.		0.537	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	Frame_Shift_Del	-	29797196	C	-	29797196	8	5	112	1	0	1	0	1	0	0	1	0	7221	521	18	0	635	0	HLA-G	6	29797196	Splice_Site	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	2377173	29797196	141317871	418	17039										
MRPS18B	28973	hgsc.bcm.edu	37	chr6	30587360	30587360	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttataaggatgagccctggAaatatctggaatcagaaggt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:30587360delA	ENST00000259873.4	+	2	326	c.169delA	c.(169-171)aaafs	p.K57fs	MRPS18B_ENST00000472229.1_3'UTR|PPP1R10_ENST00000484449.1_5'Flank|MRPS18B_ENST00000506373.2_Frame_Shift_Del_p.K57fs|PPP1R10_ENST00000376511.2_5'Flank	NM_014046.3	NP_054765.1	Q9Y676	RT18B_HUMAN	mitochondrial ribosomal protein S18B	57					translation (GO:0006412)	cell junction (GO:0030054)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(2)	13						TGAGCCCTGGAAATATCTGGA	0.488																																					p.W56X		Atlas-INDEL	.											.	MRPS18B	22	.	0			c.168delG						.						65	78	74					6																	30587360		1508	2709	4217	SO:0001589	frameshift_variant	28973	exon2			.	AF100761	CCDS4682.1	6p21	2012-09-13			ENSG00000204568	ENSG00000204568		"Mitochondrial ribosomal proteins / small subunits"	14516	protein-coding gene	gene with protein product		611982				11279123	Standard	NM_014046		Approved	MRPS18-2, PTD017, C6orf14, HSPC183	uc003nqo.2	Q9Y676	OTTHUMG00000031268	ENST00000259873.4:c.169delA	chr6.hg19:g.30587360delA	ENSP00000259873:p.Lys57fs	102.0	0.0		151.0	10.0	NM_014046	A6NDQ0|Q659G4|Q9BS27	Frame_Shift_Del	DEL	ENST00000259873.4	hg19	CCDS4682.1																																																																																			.	.		0.488	MRPS18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076584.2			-	30587360	A	-	30587360	7	5	112	1	0	1	0	1	0	0	0	0	9838	247	9	0	175	0	MRPS18B	6	30587360	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	790164	30587360	140527707	419	17040										
HSPA1B	3304	hgsc.bcm.edu	37	chr6	31796253	31796253	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgctgcggatcatcaacgagCccacggccgccgccatcgcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:31796253delC	ENST00000375650.3	+	1	742	c.526delC	c.(526-528)cccfs	p.P176fs	HSPA1B_ENST00000545241.1_Frame_Shift_Del_p.P85fs	NM_005346.4	NP_005337.2	P08107	HSP71_HUMAN	heat shock 70kDa protein 1B	176					ATP catabolic process (GO:0006200)|cellular heat acclimation (GO:0070370)|cellular response to heat (GO:0034605)|gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of inclusion body assembly (GO:0090084)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of erythrocyte differentiation (GO:0045648)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)	aggresome (GO:0016235)|blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|inclusion body (GO:0016234)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|protein N-terminus binding (GO:0047485)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|virus receptor activity (GO:0001618)			breast(1)|large_intestine(1)|prostate(1)	3						CATCAACGAGCCCACGGCCGC	0.662																																					p.E175fs		Atlas-INDEL	.											.	HSPA1B	5	.	0			c.525delG						.						1	1	1					6																	31796253		5	12	17	SO:0001589	frameshift_variant	3304	exon1			.		CCDS34415.1	6p21.3	2011-09-02	2002-08-29		ENSG00000204388	ENSG00000204388		"Heat shock proteins / HSP70"	5233	protein-coding gene	gene with protein product		603012	"heat shock 70kD protein 1B"			1700760	Standard	NM_005346		Approved	HSP70-2	uc003nxk.2	P08107	OTTHUMG00000031202	ENST00000375650.3:c.526delC	chr6.hg19:g.31796253delC	ENSP00000364801:p.Pro176fs	117.0	0.0		153.0	10.0	NM_005346	B4E3B6|P19790|Q5JQI4|Q5SP17|Q9UQL9|Q9UQM0	Frame_Shift_Del	DEL	ENST00000375650.3	hg19	CCDS34415.1																																																																																			.	.		0.662	HSPA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076402.2			-	31796253	C	-	31796253	7	5	112	1	0	1	0	1	0	0	0	0	7418	739	26	0	528	0	HSPA1B	6	31796253	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1208893	31796253	139318814	420	17041										
EHMT2	10919	hgsc.bcm.edu	37	chr6	31864543	31864543	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccagcaggctccagggagtcGggggtggccttgggcagggt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:31864543delG	ENST00000375537.4	-	3	174	c.168delC	c.(166-168)cccfs	p.P56fs	EHMT2_ENST00000480912.1_5'Flank|C2_ENST00000469372.1_5'Flank|EHMT2_ENST00000375528.4_Frame_Shift_Del_p.P113fs|EHMT2_ENST00000395728.3_Frame_Shift_Del_p.P113fs|EHMT2_ENST00000375530.4_Frame_Shift_Del_p.P56fs	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	56					DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						CCAGGGAGTCGGGGGTGGCCT	0.582																																					p.D57fs		Atlas-INDEL	.											.	EHMT2	45	.	0			c.169delG						.						55	65	62					6																	31864543		1509	2709	4218	SO:0001589	frameshift_variant	10919	exon3			.	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.168delC	chr6.hg19:g.31864543delG	ENSP00000364687:p.Pro56fs	97.0	0.0		161.0	10.0	NM_025256	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Frame_Shift_Del	DEL	ENST00000375537.4	hg19	CCDS4725.1																																																																																			.	.		0.582	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		-	31864543	G	-	31864543	7	5	112	1	0	1	0	1	0	0	0	0	4986	1103	39	0	3568	0	EHMT2	6	31864543	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	68290	31864543	139250524	421	17042										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32191665	32191665	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccactgagacacatagcagcAgcagcagcagcagcagcagc	11	14	0	1	rs543450919|rs150280230	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:32191665A>G	ENST00000375023.3	-	1	179	c.41T>C	c.(40-42)cTg>cCg	p.L14P		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	14					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						ACATagcagcagcagcagcag	0.637																																					p.L14P		Atlas-SNP	.											.	NOTCH4	201	.	0			c.T41C						.						74	56	62					6																	32191665		1510	2709	4219	SO:0001583	missense	4855	exon1			AGCAGCAGCAGCA		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.41T>C	chr6.hg19:g.32191665A>G	ENSP00000364163:p.Leu14Pro	59.0	0.0		93.0	4.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	A	12.18	1.861685	0.32884	.	.	ENSG00000204301	ENST00000375023	D	0.82711	-1.64	2.85	-1.26	0.09376	.	3.622260	0.01980	N	0.044758	T	0.46328	0.1387	N	0.19112	0.55	0.09310	N	0.999996	B;B	0.25667	0.131;0.063	B;B	0.15870	0.014;0.006	T	0.35276	-0.9795	10	0.30078	T	0.28	.	2.9781	0.05945	0.482:0.2361:0.2819:0.0	.	14;14	Q6P3V5;Q99466	.;NOTC4_HUMAN	P	14	ENSP00000364163:L14P	ENSP00000364163:L14P	L	-	2	0	NOTCH4	32299643	0.008000	0.16893	0.005000	0.12908	0.016000	0.09150	-0.129000	0.10515	-0.207000	0.10187	0.372000	0.22366	CTG	.	.		0.637	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			G	32191665	A	G	32191665	3	3	112	1	0	0	0	0	1	0	0	0	10560	188	7	2	6090	2	NOTCH4	6	32191665	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	327122	32191665	138923402	422	17043										
HLA-DRA	3122	hgsc.bcm.edu	37	chr6	32411036	32411036	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acgtcctcatctgtttcataGacaagttcaccccaccagtg	6	14	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:32411036G>C	ENST00000395388.2	+	3	512	c.403G>C	c.(403-405)Gac>Cac	p.D135H	HLA-DRA_ENST00000374982.5_Splice_Site	NM_019111.4	NP_061984.2	P01903	DRA_HUMAN	major histocompatibility complex, class II, DR alpha	135	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002504)|cognition (GO:0050890)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|polysaccharide assembly with MHC class II protein complex (GO:0002506)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)	p.D135N(1)		NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19						CTGTTTCATAGACAAGTTCAC	0.522									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Kaposi Sarcoma, Familial Clustering of																												p.D135H		Atlas-SNP	.											HLA-DRA,NS,carcinoma,0,1	HLA-DRA	34	.	1	Substitution - Missense(1)	breast(1)	c.G403C						.						137	109	119					6																	32411036		1511	2709	4220	SO:0001583	missense	3122	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;	TTCATAGACAAGT		CCDS4750.1	6p21.3	2013-01-11			ENSG00000204287	ENSG00000204287		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4947	protein-coding gene	gene with protein product		142860		HLA-DRA1			Standard	NM_019111		Approved		uc003obh.3	P01903	OTTHUMG00000031269	ENST00000395388.2:c.403G>C	chr6.hg19:g.32411036G>C	ENSP00000378786:p.Asp135His	157.0	0.0		264.0	0.0	NM_019111	A2BET4|Q30160|Q6IAZ1|Q861I2|Q9TP70	Missense_Mutation	SNP	ENST00000395388.2	hg19	CCDS4750.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|.	7.137|7.137	0.581116|0.581116	0.13686|0.13686	.|.	.|.	ENSG00000204287|ENSG00000204287	ENST00000374982|ENST00000395388	.|T	.|0.02944	.|4.1	5.59|5.59	3.83|3.83	0.44106|0.44106	.|Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	.|0.164111	.|0.56097	.|D	.|0.000038	.|T	.|0.06600	.|0.0169	M|M	0.75085|0.75085	2.285|2.285	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	.|T	.|0.02751	.|-1.1115	.|10	.|0.87932	.|D	.|0	.|.	7.8337|7.8337	0.29358|0.29358	0.2453:0.0:0.7547:0.0|0.2453:0.0:0.7547:0.0	.|.	.|135	.|P01903	.|DRA_HUMAN	.|H	-1|135	.|ENSP00000378786:D135H	.|ENSP00000378786:D135H	.|D	+|+	.|1	.|0	HLA-DRA|HLA-DRA	32519014|32519014	0.993000|0.993000	0.37304|0.37304	0.707000|0.707000	0.30419|0.30419	0.151000|0.151000	0.21798|0.21798	2.330000|2.330000	0.43885|0.43885	0.939000|0.939000	0.37446|0.37446	0.638000|0.638000	0.83543|0.83543	.|GAC	.	.		0.522	HLA-DRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076586.2	NM_019111		C	32411036	G	C	32411036	3	2	112	1	0	0	0	0	1	0	0	0	7216	942	33	4	413	4	HLA-DRA	6	32411036	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	219371	32411036	138704031	423	17044										
BRD2	6046	hgsc.bcm.edu	37	chr6	32945598	32945598	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaaccagggcctttaccagTctctactgccatgccccctg	8	16	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:32945598T>C	ENST00000374825.4	+	9	3095	c.1394T>C	c.(1393-1395)gTc>gCc	p.V465A	BRD2_ENST00000395289.2_Missense_Mutation_p.V465A|BRD2_ENST00000374831.4_Missense_Mutation_p.V465A|BRD2_ENST00000443797.2_Missense_Mutation_p.V345A|BRD2_ENST00000449085.2_Missense_Mutation_p.V418A|BRD2_ENST00000395287.1_Missense_Mutation_p.V465A	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	465					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						CCTTTACCAGTCTCTACTGCC	0.488																																					p.V465A		Atlas-SNP	.											.	BRD2	70	.	0			c.T1394C						.						126	135	132					6																	32945598		1511	2708	4219	SO:0001583	missense	6046	exon9			TACCAGTCTCTAC	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"bromodomain-containing 2"			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1394T>C	chr6.hg19:g.32945598T>C	ENSP00000363958:p.Val465Ala	205.0	0.0		288.0	22.0	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Missense_Mutation	SNP	ENST00000374825.4	hg19	CCDS4762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.34|11.34	1.609980|1.609980	0.28712|0.28712	.|.	.|.	ENSG00000204256|ENSG00000204256	ENST00000449025|ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085	.|T;T;T;T;T;T	.|0.06933	.|3.41;3.41;3.39;3.24;3.39;3.37	5.63|5.63	4.47|4.47	0.54385|0.54385	.|Bromodomain (1);	.|0.305062	.|0.23670	.|N	.|0.045736	T|T	0.01320|0.01320	0.0043|0.0043	N|N	0.16478|0.16478	0.41|0.41	0.42077|0.42077	D|D	0.991233|0.991233	.|B;B	.|0.15141	.|0.005;0.012	.|B;B	.|0.15870	.|0.014;0.014	T|T	0.42430|0.42430	-0.9452|-0.9452	5|10	.|0.06891	.|T	.|0.86	-9.8783|-9.8783	5.5595|5.5595	0.17135|0.17135	0.0:0.1763:0.0:0.8237|0.0:0.1763:0.0:0.8237	.|.	.|465;465	.|A2AAU0;P25440	.|.;BRD2_HUMAN	P|A	471|465;465;465;345;465;418	.|ENSP00000363958:V465A;ENSP00000363964:V465A;ENSP00000378704:V465A;ENSP00000413495:V345A;ENSP00000378702:V465A;ENSP00000409145:V418A	.|ENSP00000363958:V465A	S|V	+|+	1|2	0|0	BRD2|BRD2	33053576|33053576	0.410000|0.410000	0.25376|0.25376	0.975000|0.975000	0.42487|0.42487	0.990000|0.990000	0.78478|0.78478	0.895000|0.895000	0.28363|0.28363	2.363000|2.363000	0.80096|0.80096	0.523000|0.523000	0.50628|0.50628	TCT|GTC	.	.		0.488	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			C	32945598	T	C	32945598	3	2	112	1	0	0	0	0	1	0	0	0	1504	1667	58	2	1424	2	BRD2	6	32945598	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	534562	32945598	138169469	424	17045										
TCP11	6954	hgsc.bcm.edu	37	chr6	35096919	35096919	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgctctttaagatggtcccAaaaggcattgtgcactgtct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:35096919delA	ENST00000512012.1	-	3	433	c.277delT	c.(277-279)tggfs	p.W93fs	TCP11_ENST00000412155.2_Frame_Shift_Del_p.W55fs|TCP11_ENST00000510465.1_5'UTR|TCP11_ENST00000311875.5_Frame_Shift_Del_p.W106fs|TCP11_ENST00000418521.2_Frame_Shift_Del_p.W30fs|TCP11_ENST00000244645.3_Frame_Shift_Del_p.W31fs|TCP11_ENST00000444780.2_Frame_Shift_Del_p.W101fs|TCP11_ENST00000373979.2_Frame_Shift_Del_p.W31fs|TCP11_ENST00000373974.4_Frame_Shift_Del_p.W60fs			Q8WWU5	TCP11_HUMAN	t-complex 11, testis-specific	93					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				breast(1)|kidney(5)|large_intestine(3)|lung(10)|ovary(3)|prostate(1)|skin(4)	27						AGATGGTCCCAAAAGGCATTG	0.428																																					p.W106fs		Atlas-INDEL	.											.	TCP11	94	.	0			c.317delG						.						159	133	142					6																	35096919		2203	4300	6503	SO:0001589	frameshift_variant	6954	exon4			.		CCDS4799.1, CCDS47413.1, CCDS59015.1, CCDS59016.1, CCDS59017.1, CCDS59018.1	6p21.31	2012-09-20	2012-09-20		ENSG00000124678	ENSG00000124678			11658	protein-coding gene	gene with protein product	"fertilization-promoting peptide receptor"	186982	"t-complex 11 (a murine tcp homolog)", "t-complex 11 homolog (mouse)"	D6S230E		1427894, 11756566, 21597245	Standard	NM_001093728		Approved	KIAA0229, FPPR	uc003okd.2	Q8WWU5	OTTHUMG00000014560	ENST00000512012.1:c.277delT	chr6.hg19:g.35096919delA	ENSP00000425995:p.Trp93fs	135.0	0.0		181.0	12.0	NM_001093728	B2RCE9|B3KQ27|B7Z7B5|B7Z7G1|B7Z7H4|B7Z7S8|E7EP29|J3KNG1|Q8NF85|Q9NQZ9|Q9NR39	Frame_Shift_Del	DEL	ENST00000512012.1	hg19																																																																																				.	.		0.428	TCP11-014	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000370354.1	NM_001093728		-	35096919	A	-	35096919	7	5	112	1	0	1	0	1	0	0	0	0	15728	130	5	0	1262	0	TCP11	6	35096919	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2151321	35096919	136018148	425	17046										
SCUBE3	222663	hgsc.bcm.edu	37	chr6	35216340	35216340	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccatcctttgcaggacaagaAgctcatcaaggccttctttg	8	12	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:35216340A>G	ENST00000274938.7	+	22	2840	c.2840A>G	c.(2839-2841)aAg>aGg	p.K947R	SCUBE3_ENST00000394681.1_Missense_Mutation_p.K963R	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						CAGGACAAGAAGCTCATCAAG	0.512																																					p.K947R		Atlas-SNP	.											.	SCUBE3	99	.	0			c.A2840G						.						141	130	134					6																	35216340		2203	4300	6503	SO:0001583	missense	222663	exon22			ACAAGAAGCTCAT	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"CUB domain and EGF-like repeat containing 3"	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.2840A>G	chr6.hg19:g.35216340A>G	ENSP00000274938:p.Lys947Arg	56.0	0.0		86.0	4.0	NM_152753		Missense_Mutation	SNP	ENST00000274938.7	hg19	CCDS4800.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.391521	0.83011	.	.	ENSG00000146197	ENST00000394681;ENST00000274938	T;D	0.83837	-1.35;-1.77	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.71719	0.3373	N	0.24115	0.695	0.80722	D	1	P;P	0.49559	0.925;0.877	P;B	0.47162	0.54;0.339	T	0.77029	-0.2739	10	0.51188	T	0.08	.	15.9698	0.80004	1.0:0.0:0.0:0.0	.	963;947	Q8IX30-2;Q8IX30	.;SCUB3_HUMAN	R	963;947	ENSP00000378174:K963R;ENSP00000274938:K947R	ENSP00000274938:K947R	K	+	2	0	SCUBE3	35324318	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.910000	0.92685	2.183000	0.69458	0.533000	0.62120	AAG	.	.		0.512	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753		G	35216340	A	G	35216340	3	3	112	1	0	0	0	0	1	0	0	0	13961	72	3	2	2926	2	SCUBE3	6	35216340	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	119421	35216340	135898727	426	17047										
TULP1	7287	hgsc.bcm.edu	37	chr6	35473878	35473878	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcagcgcaccgtgcggccctGgggggcaggccggagcacaa					rs201070350|rs62636292		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:35473878delG	ENST00000229771.6	-	10	980	c.901delC	c.(901-903)cagfs	p.Q301fs	TULP1_ENST00000322263.4_Frame_Shift_Del_p.Q248fs	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	301					dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						GTGCGGCCCTGGGGGGCAGGC	0.667																																					p.Q301fs	GBM(55;1027 1091 11115 23439)	Atlas-INDEL	.											.	TULP1	51	.	0			c.902delA	GRCh37	CD004592	TULP1	D		.						39	45	43					6																	35473878		2202	4298	6500	SO:0001589	frameshift_variant	7287	exon10			.	U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.901delC	chr6.hg19:g.35473878delG	ENSP00000229771:p.Gln301fs	36.0	0.0		83.0	11.0	NM_003322	O43536|Q5TGM5|Q8N571	Frame_Shift_Del	DEL	ENST00000229771.6	hg19	CCDS4807.1																																																																																			.	.		0.667	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2			-	35473878	G	-	35473878	7	5	112	1	0	1	0	1	0	0	0	0	16788	1357	47	0	751	0	TULP1	6	35473878	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	257538	35473878	135641189	427	17048										
GLO1	2739	hgsc.bcm.edu	37	chr6	38654690	38654690	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cattccaagaactctagtatAaaaatccagtgacttcttag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:38654690delA	ENST00000373365.4	-	2	231	c.145delT	c.(145-147)tatfs	p.Y49fs		NM_006708.2	NP_006699.2	Q04760	LGUL_HUMAN	glyoxalase I	49					carbohydrate metabolic process (GO:0005975)|glutathione metabolic process (GO:0006749)|methylglyoxal metabolic process (GO:0009438)|negative regulation of apoptotic process (GO:0043066)|osteoclast differentiation (GO:0030316)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lactoylglutathione lyase activity (GO:0004462)|zinc ion binding (GO:0008270)			lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	6					Glutathione(DB00143)|Indomethacin(DB00328)	ACTCTAGTATAAAAATCCAGT	0.333																																					p.Y49fs		Atlas-INDEL	.											.	GLO1	12	.	0			c.146delA						.						68	74	72					6																	38654690		2203	4300	6503	SO:0001589	frameshift_variant	2739	exon2			.	L07837	CCDS4837.1	6p21.3-p21.1	2012-10-02			ENSG00000124767	ENSG00000124767	4.4.1.5		4323	protein-coding gene	gene with protein product	"glyoxalase domain containing 1"	138750				8449929, 7684374	Standard	NM_006708		Approved	GLOD1	uc003ooc.3	Q04760	OTTHUMG00000014636	ENST00000373365.4:c.145delT	chr6.hg19:g.38654690delA	ENSP00000362463:p.Tyr49fs	218.0	0.0		333.0	20.0	NM_006708	B2R6P7|B4DDV0|P78375|Q59EL0|Q5TZW3|Q96FC0|Q96J41	Frame_Shift_Del	DEL	ENST00000373365.4	hg19	CCDS4837.1																																																																																			.	.		0.333	GLO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040438.2	NM_006708		-	38654690	A	-	38654690	7	5	112	1	0	1	0	1	0	0	0	0	6457	362	13	0	429	0	GLO1	6	38654690	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3180812	38654690	132460377	428	17049										
TREML4	285852	hgsc.bcm.edu	37	chr6	41196606	41196606	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtcaccagctccaagccctGgacagcagttcagaagtctc	9	14	3	1	rs549544699	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:41196606G>C	ENST00000341495.2	+	2	322	c.218G>C	c.(217-219)tGg>tCg	p.W73S	TREML4_ENST00000448827.2_Missense_Mutation_p.W73S	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	73	Ig-like V-type.		W -> R (in dbSNP:rs9369265).			extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					TCCAAGCCCTGGACAGCAGTT	0.512																																					p.W73S		Atlas-SNP	.											TREML4,NS,carcinoma,0,1	TREML4	25	.	0			c.G218C						.						83	77	79					6																	41196606		2203	4300	6503	SO:0001583	missense	285852	exon2			AGCCCTGGACAGC	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"Immunoglobulin superfamily / V-set domain containing"	30807	protein-coding gene	gene with protein product	"TREM like transcript 4"	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.218G>C	chr6.hg19:g.41196606G>C	ENSP00000342570:p.Trp73Ser	95.0	0.0		138.0	0.0	NM_198153	B7ZL92	Missense_Mutation	SNP	ENST00000341495.2	hg19	CCDS34446.1	.	.	.	.	.	.	.	.	.	.	.	4.856	0.159171	0.09236	.	.	ENSG00000188056	ENST00000341495;ENST00000445267;ENST00000448827	T;T	0.03889	3.77;3.77	4.16	-8.32	0.00996	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00496	0.0016	N	0.03608	-0.345	0.09310	N	1	B	0.31893	0.345	B	0.30251	0.113	T	0.48031	-0.9070	9	0.56958	D	0.05	-0.0212	3.7754	0.08657	0.5171:0.1297:0.2579:0.0953	.	73	Q6UXN2	TRML4_HUMAN	S	73	ENSP00000342570:W73S;ENSP00000418078:W73S	ENSP00000342570:W73S	W	+	2	0	TREML4	41304584	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.226000	0.00270	-2.913000	0.00307	-1.915000	0.00519	TGG	.	.		0.512	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2			C	41196606	G	C	41196606	3	2	112	1	0	0	0	0	1	0	0	0	16489	1357	47	4	224	4	TREML4	6	41196606	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	2541916	41196606	129918461	429	17050										
TREM1	54210	hgsc.bcm.edu	37	chr6	41250470	41250470	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcatacttttcctcagttaaTttagttgcagctcggagttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:41250470delT	ENST00000244709.4	-	2	132	c.69delA	c.(67-69)aaafs	p.K23fs	TREM1_ENST00000591620.1_Frame_Shift_Del_p.K23fs|TREM1_ENST00000589614.1_Frame_Shift_Del_p.K23fs|TREM1_ENST00000334475.6_Frame_Shift_Del_p.K23fs	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	23					blood coagulation (GO:0007596)|chemokine metabolic process (GO:0050755)|cytokine secretion involved in immune response (GO:0002374)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|neutrophil mediated killing of gram-negative bacterium (GO:0070945)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			NS(1)|breast(2)|endometrium(2)|large_intestine(5)|lung(5)|skin(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					CCTCAGTTAATTTAGTTGCAG	0.468																																					p.L24X		Atlas-INDEL	.											.	TREM1	38	.	0			c.70delT						.						93	101	98					6																	41250470		2203	4300	6503	SO:0001589	frameshift_variant	54210	exon2			.	AF196329	CCDS4854.1, CCDS56427.1, CCDS59499.1	6p21.1	2013-01-11			ENSG00000124731	ENSG00000124731		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	17760	protein-coding gene	gene with protein product		605085				11922939, 10799849	Standard	NM_018643		Approved	TREM-1, CD354	uc003oqf.2	Q9NP99	OTTHUMG00000014674	ENST00000244709.4:c.69delA	chr6.hg19:g.41250470delT	ENSP00000244709:p.Lys23fs	136.0	0.0		225.0	14.0	NM_001242590	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Frame_Shift_Del	DEL	ENST00000244709.4	hg19	CCDS4854.1																																																																																			.	.		0.468	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040505.2	NM_018643		-	41250470	T	-	41250470	7	5	112	1	0	1	0	1	0	0	0	0	16485	1490	52	0	647	0	TREM1	6	41250470	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	53864	41250470	129864597	430	17051										
CUL7	9820	hgsc.bcm.edu	37	chr6	43017756	43017756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctcctgatggtcaggtccaTccagcttcttgatgaagaag	10	11	2	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:43017756T>C	ENST00000265348.3	-	6	1599	c.1514A>G	c.(1513-1515)gAt>gGt	p.D505G	CUL7_ENST00000478630.1_5'Flank|CUL7_ENST00000535468.1_Missense_Mutation_p.D589G			Q14999	CUL7_HUMAN	cullin 7	505					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			GTCAGGTCCATCCAGCTTCTT	0.557																																					p.D589G		Atlas-SNP	.											.	CUL7	133	.	0			c.A1766G						.						121	112	115					6																	43017756		2203	4300	6503	SO:0001583	missense	9820	exon6			GGTCCATCCAGCT	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"KIAA0076"	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.1514A>G	chr6.hg19:g.43017756T>C	ENSP00000265348:p.Asp505Gly	70.0	0.0		97.0	5.0	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	hg19	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.461565	0.43736	.	.	ENSG00000044090	ENST00000265348;ENST00000535468	T;T	0.66280	-0.2;-0.2	5.12	-0.858	0.10689	.	0.861913	0.10357	N	0.684436	T	0.36413	0.0966	L	0.61218	1.895	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42599	-0.9442	10	0.45353	T	0.12	-19.4144	6.1451	0.20280	0.0:0.1394:0.2509:0.6097	.	589;505	F5H0L1;Q14999	.;CUL7_HUMAN	G	505;589	ENSP00000265348:D505G;ENSP00000438788:D589G	ENSP00000265348:D505G	D	-	2	0	CUL7	43125734	0.698000	0.27777	0.032000	0.17829	0.923000	0.55619	1.018000	0.30002	-0.047000	0.13423	0.533000	0.62120	GAT	.	.		0.557	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780		C	43017756	T	C	43017756	3	2	112	1	0	0	0	0	1	0	0	0	4062	1435	50	2	3666	2	CUL7	6	43017756	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1767286	43017756	128097311	431	17052										
ZNF318	24149	hgsc.bcm.edu	37	chr6	43320194	43320194	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcttcccggtcattctttagTttttccctctcttcaataac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:43320194delT	ENST00000361428.2	-	5	2768	c.2691delA	c.(2689-2691)aaafs	p.K897fs	ZNF318_ENST00000318149.3_Frame_Shift_Del_p.K897fs	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	897					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			CATTCTTTAGTTTTTCCCTCT	0.433																																					p.L898X		Atlas-INDEL	.											.	ZNF318	175	.	0			c.2692delC						.						116	105	108					6																	43320194		2203	4300	6503	SO:0001589	frameshift_variant	24149	exon5			.	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.2691delA	chr6.hg19:g.43320194delT	ENSP00000354964:p.Lys897fs	118.0	0.0		182.0	13.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Frame_Shift_Del	DEL	ENST00000361428.2	hg19	CCDS4895.2																																																																																			.	.		0.433	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		-	43320194	T	-	43320194	7	5	112	1	0	1	0	1	0	0	0	0	17851	1722	60	0	4172	0	ZNF318	6	43320194	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	302438	43320194	127794873	432	17053										
XPO5	57510	hgsc.bcm.edu	37	chr6	43496599	43496599	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgaaaagaggtccgaggatGggggataccagggcttcata							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:43496599delG	ENST00000265351.7	-	24	2952	c.2742delC	c.(2740-2742)cccfs	p.P914fs	POLR1C_ENST00000304004.3_Intron	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	914					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			GTCCGAGGATGGGGGATACCA	0.473																																					p.I915fs		Atlas-INDEL	.											.	XPO5	79	.	0			c.2743delA						.						55	56	56					6																	43496599		1873	4104	5977	SO:0001589	frameshift_variant	57510	exon24			.	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.2742delC	chr6.hg19:g.43496599delG	ENSP00000265351:p.Pro914fs	106.0	0.0		156.0	11.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Frame_Shift_Del	DEL	ENST00000265351.7	hg19	CCDS47430.1																																																																																			.	.		0.473	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		-	43496599	G	-	43496599	7	5	112	1	0	1	0	1	0	0	0	0	17462	1335	47	0	908	0	XPO5	6	43496599	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	176405	43496599	127618468	433	17054										
CAPN11	11131	hgsc.bcm.edu	37	chr6	44145022	44145022	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttaagatctctcttcctgaGggggatgacccagaggatga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:44145022delG	ENST00000398776.1	+	12	1319	c.1281delG	c.(1279-1281)gagfs	p.E427fs	CAPN11_ENST00000542245.1_Frame_Shift_Del_p.E427fs	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	427	Domain III.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTCTTCCTGAGGGGGATGACC	0.607																																					p.E427fs		Atlas-INDEL	.											.	CAPN11	66	.	0			c.1280delA						.						29	32	31					6																	44145022		2122	4241	6363	SO:0001589	frameshift_variant	11131	exon12			.	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1281delG	chr6.hg19:g.44145022delG	ENSP00000381758:p.Glu427fs	121.0	0.0		174.0	11.0	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Frame_Shift_Del	DEL	ENST00000398776.1	hg19	CCDS47436.1																																																																																			.	.		0.607	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			-	44145022	G	-	44145022	7	5	112	1	0	1	0	1	0	0	0	0	2626	991	35	0	1327	0	CAPN11	6	44145022	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	648423	44145022	126970045	434	17055										
CYP39A1	51302	hgsc.bcm.edu	37	chr6	46604172	46604172	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgcttttatatctggaatgTttttctcaaacagttccagg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:46604172delT	ENST00000275016.2	-	5	889	c.686delA	c.(685-687)aacfs	p.N229fs		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	229					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						ATCTGGAATGTTTTTCTCAAA	0.274																																					p.N229fs		Atlas-INDEL	.											.	CYP39A1	41	.	0			c.687delC						.						50	52	51					6																	46604172		2202	4293	6495	SO:0001589	frameshift_variant	51302	exon5			.	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"Cytochrome P450s"	17449	protein-coding gene	gene with protein product		605994	"cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.686delA	chr6.hg19:g.46604172delT	ENSP00000275016:p.Asn229fs	94.0	0.0		144.0	11.0	NM_016593	Q5VTT0|Q96FW5	Frame_Shift_Del	DEL	ENST00000275016.2	hg19	CCDS4916.1																																																																																			.	.		0.274	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1			-	46604172	T	-	46604172	7	5	112	1	0	1	0	1	0	0	0	0	4179	1725	60	0	755	0	CYP39A1	6	46604172	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2459150	46604172	124510895	435	17056										
GPR115	221393	hgsc.bcm.edu	37	chr6	47680293	47680293	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcatttatagtggagttattAaaaaatatttctacagactt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:47680293delA	ENST00000283303.2	+	5	759	c.501delA	c.(499-501)ttafs	p.L167fs	GPR115_ENST00000371220.1_Frame_Shift_Del_p.L224fs|GPR115_ENST00000327753.3_Frame_Shift_Del_p.L167fs|RN7SKP116_ENST00000516902.1_RNA	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	167					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						TGGAGTTATTAAAAAATATTT	0.303																																					p.L167X	GBM(22;431 510 9010 26644 32828)	Atlas-INDEL	.											.	GPR115	140	.	0			c.500delT						.						61	66	64					6																	47680293		2203	4299	6502	SO:0001589	frameshift_variant	221393	exon5			.	AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.501delA	chr6.hg19:g.47680293delA	ENSP00000283303:p.Leu167fs	133.0	0.0		176.0	13.0	NM_153838	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Frame_Shift_Del	DEL	ENST00000283303.2	hg19	CCDS4922.2																																																																																			.	.		0.303	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		-	47680293	A	-	47680293	7	5	112	1	0	1	0	1	0	0	0	0	6640	359	13	0	515	0	GPR115	6	47680293	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1076121	47680293	123434774	436	17057										
FAM83B	222584	hgsc.bcm.edu	37	chr6	54735393	54735393	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgtgatgcccggactcttaGggggcacccatatagatctc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:54735393delG	ENST00000306858.7	+	2	465	c.349delG	c.(349-351)gggfs	p.G118fs		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	118										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					CGGACTCTTAGGGGGCACCCA	0.433																																					p.L116fs		Atlas-INDEL	.											.	FAM83B	186	.	0			c.348delA						.						84	87	86					6																	54735393		2203	4300	6503	SO:0001589	frameshift_variant	222584	exon2			.	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 143"	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.349delG	chr6.hg19:g.54735393delG	ENSP00000304078:p.Gly118fs	124.0	0.0		184.0	12.0	NM_001010872	Q2M1P3|Q96DQ2	Frame_Shift_Del	DEL	ENST00000306858.7	hg19	CCDS34479.1																																																																																			.	.		0.433	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		-	54735393	G	-	54735393	7	5	112	1	0	1	0	1	0	0	0	0	5642	1000	35	0	351	0	FAM83B	6	54735393	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	7055100	54735393	116379674	437	17058										
KHDRBS2	202559	hgsc.bcm.edu	37	chr6	62688078	62688078	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgaagctcatcactcaagtGggcatatttggcttccccac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:62688078delG	ENST00000281156.4	-	4	654	c.376delC	c.(376-378)cacfs	p.H126fs		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	126	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		TCACTCAAGTGGGCATATTTG	0.353																																					p.H126fs		Atlas-INDEL	.											.	KHDRBS2	103	.	0			c.377delA						.						123	109	114					6																	62688078		2203	4300	6503	SO:0001589	frameshift_variant	202559	exon4			.	BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"Sam68-like mammalian protein 1"	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.376delC	chr6.hg19:g.62688078delG	ENSP00000281156:p.His126fs	144.0	0.0		163.0	10.0	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Frame_Shift_Del	DEL	ENST00000281156.4	hg19	CCDS4963.1																																																																																			.	.		0.353	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688		-	62688078	G	-	62688078	7	5	112	1	0	1	0	1	0	0	0	0	8156	1348	47	0	697	0	KHDRBS2	6	62688078	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	7952685	62688078	108426989	438	17059										
EYS	346007	hgsc.bcm.edu	37	chr6	64574091	64574091	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctcttaccatcagtgcagaGgggtccagacctcccatatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:64574091delG	ENST00000370621.3	-	36	7742	c.7216delC	c.(7216-7218)ctcfs	p.L2406fs	EYS_ENST00000370616.2_Frame_Shift_Del_p.L2406fs|EYS_ENST00000503581.1_Frame_Shift_Del_p.L2406fs			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2406	EGF-like 23. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TCAGTGCAGAGGGGTCCAGAC	0.448																																					p.L2406fs		Atlas-INDEL	.											.	EYS	527	.	0			c.7217delT						.						107	89	94					6																	64574091		692	1591	2283	SO:0001589	frameshift_variant	346007	exon36			.		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.7216delC	chr6.hg19:g.64574091delG	ENSP00000359655:p.Leu2406fs	97.0	0.0		184.0	12.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Frame_Shift_Del	DEL	ENST00000370621.3	hg19																																																																																				.	.		0.448	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		-	64574091	G	-	64574091	7	5	112	1	0	1	0	1	0	0	0	0	5334	1000	35	0	2250	0	EYS	6	64574091	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1886013	64574091	106540976	439	17060										
EYS	346007	hgsc.bcm.edu	37	chr6	66094287	66094287	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taaattacttactttgaatcTtccaattatattgaaacacc	2	8	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:66094287T>C	ENST00000370621.3	-	8	1817	c.1291A>G	c.(1291-1293)Aga>Gga	p.R431G	EYS_ENST00000393380.2_Missense_Mutation_p.R431G|EYS_ENST00000370618.3_Missense_Mutation_p.R431G|EYS_ENST00000370616.2_Missense_Mutation_p.R431G|EYS_ENST00000342421.5_Missense_Mutation_p.R431G|EYS_ENST00000503581.1_Missense_Mutation_p.R431G			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	431					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						ACTTTGAATCTTCCAATTATA	0.313																																					p.R431G		Atlas-SNP	.											.	EYS	527	.	0			c.A1291G						.						88	87	87					6																	66094287		2202	4293	6495	SO:0001583	missense	346007	exon8			TGAATCTTCCAAT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1291A>G	chr6.hg19:g.66094287T>C	ENSP00000359655:p.Arg431Gly	42.0	0.0		77.0	4.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	T	14.87	2.664843	0.47572	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	T;T;T;T;T;T	0.10477	2.87;2.87;2.87;2.87;2.87;2.87	6.07	-1.86	0.07760	.	.	.	.	.	T	0.00906	0.0030	N	0.05280	-0.08	0.22675	N	0.998868	B;B;B	0.18166	0.009;0.009;0.026	B;B;B	0.14578	0.007;0.007;0.011	T	0.47861	-0.9084	9	0.10636	T	0.68	.	2.1204	0.03724	0.1229:0.306:0.126:0.4451	.	431;431;431	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	G	431	ENSP00000424243:R431G;ENSP00000359655:R431G;ENSP00000359650:R431G;ENSP00000377042:R431G;ENSP00000341818:R431G;ENSP00000359652:R431G	ENSP00000341818:R431G	R	-	1	2	EYS	66151008	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.504000	0.35726	-0.071000	0.12886	0.533000	0.62120	AGA	.	.		0.313	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		C	66094287	T	C	66094287	3	2	112	1	0	0	0	0	1	0	0	0	5334	1617	56	2	8249	2	EYS	6	66094287	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1520196	66094287	105020780	440	17061										
LMBRD1	55788	hgsc.bcm.edu	37	chr6	70490443	70490443	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctgacattagcattagcccAgtcctaggataaaaggaaac	9	9	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:70490443A>G	ENST00000370577.3	-	3	479	c.250T>C	c.(250-252)Tgg>Cgg	p.W84R	LMBRD1_ENST00000370570.1_Missense_Mutation_p.W11R	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	84					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						GCATTAGCCCAGTCCTAGGAT	0.338																																					p.W84R		Atlas-SNP	.											.	LMBRD1	61	.	0			c.T250C						.						112	108	109					6																	70490443		2203	4300	6503	SO:0001583	missense	55788	exon3			TAGCCCAGTCCTA	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.250T>C	chr6.hg19:g.70490443A>G	ENSP00000359609:p.Trp84Arg	40.0	0.0		52.0	4.0	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Missense_Mutation	SNP	ENST00000370577.3	hg19	CCDS4969.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.012555	0.75161	.	.	ENSG00000168216	ENST00000370577;ENST00000370570	T;T	0.35973	1.28;1.99	5.67	5.67	0.87782	LMBR1-like membrane protein (1);	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.66444	-0.5922	10	0.87932	D	0	-4.874	15.0854	0.72148	1.0:0.0:0.0:0.0	.	84	Q9NUN5	LMBD1_HUMAN	R	84;11	ENSP00000359609:W84R;ENSP00000359602:W11R	ENSP00000359602:W11R	W	-	1	0	LMBRD1	70547164	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.469000	0.73555	2.149000	0.67028	0.379000	0.24179	TGG	.	.		0.338	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		G	70490443	A	G	70490443	3	3	112	1	0	0	0	0	1	0	0	0	8851	188	7	2	1428	2	LMBRD1	6	70490443	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	4396156	70490443	100624624	441	17062										
KCNQ5	56479	hgsc.bcm.edu	37	chr6	73787525	73787525	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cataggatttttggttcttaTtttttcgtctttccttgtct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:73787525delT	ENST00000370398.1	+	5	942	c.833delT	c.(832-834)attfs	p.I278fs	KCNQ5_ENST00000403813.2_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000370392.1_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000355635.3_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000402622.2_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000355194.4_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000414165.2_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000342056.2_Frame_Shift_Del_p.I278fs	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	278					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	TTGGTTCTTATTTTTTCGTCT	0.338																																					p.I278fs	GBM(142;1375 1859 14391 23261 44706)	Atlas-INDEL	.											.	KCNQ5	153	.	0			c.832delA						.						143	121	128					6																	73787525		2203	4300	6503	SO:0001589	frameshift_variant	56479	exon5			.	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.833delT	chr6.hg19:g.73787525delT	ENSP00000359425:p.Ile278fs	114.0	0.0		183.0	11.0	NM_001160132	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Frame_Shift_Del	DEL	ENST00000370398.1	hg19	CCDS4976.1																																																																																			.	.		0.338	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		-	73787525	T	-	73787525	7	5	112	1	0	1	0	1	0	0	0	0	8095	1493	52	0	851	0	KCNQ5	6	73787525	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3297082	73787525	97327542	442	17063										
DPPA5	340168	hgsc.bcm.edu	37	chr6	74063604	74063604	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggcgctggcggtgccactcAgccatggactggagcatcca	14	13	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:74063604A>G	ENST00000370370.3	-	2	333	c.264T>C	c.(262-264)gcT>gcC	p.A88A		NM_001025290.2	NP_001020461.1	A6NC42	DPPA5_HUMAN	developmental pluripotency associated 5	88					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|endometrium(1)|lung(5)	7						GGTGCCACTCAGCCATGGACT	0.637																																					p.A88A		Atlas-SNP	.											.	DPPA5	23	.	0			c.T264C						.						33	31	32					6																	74063604		2203	4300	6503	SO:0001819	synonymous_variant	340168	exon2			CCACTCAGCCATG		CCDS34483.1	6q13	2014-01-28			ENSG00000203909	ENSG00000203909			19201	protein-coding gene	gene with protein product		611111					Standard	NM_001025290		Approved	Esg1	uc003pgs.2	A6NC42	OTTHUMG00000015025	ENST00000370370.3:c.264T>C	chr6.hg19:g.74063604A>G		97.0	0.0		134.0	6.0	NM_001025290	B2RPQ7	Silent	SNP	ENST00000370370.3	hg19	CCDS34483.1																																																																																			.	.		0.637	DPPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041203.3	NM_001025290		G	74063604	A	G	74063604	2	3	112	1	0	0	0	0	0	0	0	1	4739	175	7	2		2	DPPA5	6	74063604	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	276079	74063604	97051463	443	17064										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76124598	76124598	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttttgcatcttctgagagacTtttttcaccagcattgccga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:76124598delT	ENST00000237172.7	-	2	421	c.91delA	c.(91-93)agtfs	p.S31fs	FILIP1_ENST00000393004.2_Frame_Shift_Del_p.S31fs	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	31										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						TCTGAGAGACTTTTTTCACCA	0.453																																					p.S31fs		Atlas-INDEL	.											.	FILIP1	173	.	0			c.92delG						.						181	174	177					6																	76124598		2203	4300	6503	SO:0001589	frameshift_variant	27145	exon2			.	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.91delA	chr6.hg19:g.76124598delT	ENSP00000237172:p.Ser31fs	133.0	0.0		192.0	13.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Frame_Shift_Del	DEL	ENST00000237172.7	hg19	CCDS4984.1																																																																																			.	.		0.453	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		-	76124598	T	-	76124598	7	5	112	1	0	1	0	1	0	0	0	0	5902	1609	56	0	3570	0	FILIP1	6	76124598	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2060994	76124598	94990469	444	17065										
SENP6	26054	hgsc.bcm.edu	37	chr6	76331286	76331286	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctaagagagatggaggttttAaaaataattggagctttgat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:76331286delA	ENST00000447266.2	+	2	569	c.91delA	c.(91-93)aaafs	p.K31fs	SENP6_ENST00000370010.2_Frame_Shift_Del_p.K31fs|SENP6_ENST00000370014.3_Frame_Shift_Del_p.K31fs|SENP6_ENST00000327284.8_Frame_Shift_Del_p.K31fs	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	31					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				TGGAGGTTTTAAAAATAATTG	0.289																																					p.F30fs		Atlas-INDEL	.											.	SENP6	189	.	0			c.90delT						.						99	99	99					6																	76331286		1786	4060	5846	SO:0001589	frameshift_variant	26054	exon2			.		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.91delA	chr6.hg19:g.76331286delA	ENSP00000402527:p.Lys31fs	157.0	0.0		256.0	16.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Frame_Shift_Del	DEL	ENST00000447266.2	hg19	CCDS47454.1																																																																																			.	.		0.289	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		-	76331286	A	-	76331286	7	5	112	1	0	1	0	1	0	0	0	0	14065	363	13	0	97	0	SENP6	6	76331286	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	206688	76331286	94783781	445	17066										
LCA5	167691	hgsc.bcm.edu	37	chr6	80197095	80197095	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttggaaatccaaaaaactacTtttttgactaaatggatttg					rs34176430		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:80197095delT	ENST00000392959.1	-	9	2331	c.1720delA	c.(1720-1722)agtfs	p.S575fs	LCA5_ENST00000369846.4_Frame_Shift_Del_p.S575fs	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	575					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		AAAAAACTACTTTTTTGACTA	0.343																																					p.S574fs		Atlas-INDEL	.											.	LCA5	71	.	0			c.1721delG						.						65	69	68					6																	80197095		2203	4299	6502	SO:0001589	frameshift_variant	167691	exon8			.		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.1720delA	chr6.hg19:g.80197095delT	ENSP00000376686:p.Ser575fs	109.0	0.0		159.0	10.0	NM_001122769	E1P542|Q9BWX7	Frame_Shift_Del	DEL	ENST00000392959.1	hg19	CCDS4990.1																																																																																			.	.		0.343	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		-	80197095	T	-	80197095	7	5	112	1	0	1	0	1	0	0	0	0	8665	1609	56	0	377	0	LCA5	6	80197095	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3865809	80197095	90917972	446	17067										
FAM46A	55603	hgsc.bcm.edu	37	chr6	82459741	82459741	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caaataggactccagttttcTctgctgctctccaatgtctg	7	12	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:82459741T>C	ENST00000320172.6	-	3	1314	c.1000A>G	c.(1000-1002)Aga>Gga	p.R334G	FAM46A_ENST00000369754.3_Missense_Mutation_p.R353G|FAM46A_ENST00000369756.3_Missense_Mutation_p.R415G	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	334					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		TCCAGTTTTCTCTGCTGCTCT	0.468																																					p.R334G		Atlas-SNP	.											.	FAM46A	37	.	0			c.A1000G						.						92	88	90					6																	82459741		2203	4300	6503	SO:0001583	missense	55603	exon3			GTTTTCTCTGCTG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.1000A>G	chr6.hg19:g.82459741T>C	ENSP00000318298:p.Arg334Gly	116.0	0.0		139.0	6.0	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Missense_Mutation	SNP	ENST00000320172.6	hg19	CCDS34489.1	.	.	.	.	.	.	.	.	.	.	T	8.059	0.767657	0.15983	.	.	ENSG00000112773	ENST00000369754;ENST00000320172;ENST00000369756;ENST00000423467	T;T;T	0.26223	1.75;1.75;1.75	5.95	4.78	0.61160	Domain of unknown function DUF1693 (1);	0.000000	0.85682	D	0.000000	T	0.41511	0.1162	M	0.80028	2.48	0.80722	D	1	D;D	0.62365	0.991;0.989	D;D	0.78314	0.991;0.985	T	0.45101	-0.9284	10	0.54805	T	0.06	-1.3331	12.5901	0.56437	0.0:0.0:0.2617:0.7383	.	334;353	Q96IP4;Q96IP4-2	FA46A_HUMAN;.	G	353;334;415;68	ENSP00000358769:R353G;ENSP00000318298:R334G;ENSP00000358771:R415G	ENSP00000318298:R334G	R	-	1	2	FAM46A	82516460	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	4.959000	0.63666	1.057000	0.40506	-0.313000	0.08912	AGA	.	.		0.468	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			C	82459741	T	C	82459741	3	2	112	1	0	0	0	0	1	0	0	0	5573	1559	54	2	332	2	FAM46A	6	82459741	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2262646	82459741	88655326	447	17068										
UBE2CBP	90025	hgsc.bcm.edu	37	chr6	83733743	83733743	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aataattatctctgtcatatAaaacttggtggtttctagaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:83733743delA	ENST00000369747.3	-	6	804	c.682delT	c.(682-684)tatfs	p.Y228fs		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	228					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										TCTGTCATATAAAACTTGGTG	0.284																																					p.Y228fs		Atlas-INDEL	.											.	.	.	.	0			c.683delA						.						38	43	41					6																	83733743		2199	4279	6478	SO:0001589	frameshift_variant	90025	exon6			.	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"UBCH10 binding protein with a hect-like domain"	612495	"chromosome 6 open reading frame 157", "ubiquitin-conjugating enzyme E2C binding protein"	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.682delT	chr6.hg19:g.83733743delA	ENSP00000358762:p.Tyr228fs	147.0	0.0		215.0	15.0	NM_198920	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Frame_Shift_Del	DEL	ENST00000369747.3	hg19	CCDS34491.1																																																																																			.	.		0.284	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920		-	83733743	A	-	83733743	7	5	112	1	0	1	0	1	0	0	0	0	16862	362	13	0	507	0	UBE2CBP	6	83733743	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1274002	83733743	87381324	448	17069										
TBX18	9096	hgsc.bcm.edu	37	chr6	85446613	85446613	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcaggactggcagccagtttGggggatgtggagaagttata							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:85446613delG	ENST00000369663.5	-	8	1951	c.1614delC	c.(1612-1614)cccfs	p.P538fs	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	538					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		CAGCCAGTTTGGGGGATGTGG	0.502																																					p.K539fs		Atlas-INDEL	.											.	TBX18	131	.	0			c.1615delA						.						84	98	94					6																	85446613		2203	4300	6503	SO:0001589	frameshift_variant	9096	exon8			.	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"T-boxes"	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1614delC	chr6.hg19:g.85446613delG	ENSP00000358677:p.Pro538fs	127.0	0.0		191.0	12.0	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Frame_Shift_Del	DEL	ENST00000369663.5	hg19	CCDS34495.1																																																																																			.	.		0.502	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508		-	85446613	G	-	85446613	7	5	112	1	0	1	0	1	0	0	0	0	15668	1335	47	0	213	0	TBX18	6	85446613	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1712870	85446613	85668454	449	17070										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87970974	87970974	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaaaaatgtctcacaaaatAaaaaaaggaaagttgaaaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:87970974delA	ENST00000369577.3	+	8	7670	c.7627delA	c.(7627-7629)aaafs	p.K2544fs	ZNF292_ENST00000339907.4_Frame_Shift_Del_p.K2539fs	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2544						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		CTCACAAAATAAAAAAAGGAA	0.358																																					p.N2542fs		Atlas-INDEL	.											.	ZNF292	479	.	0			c.7626delT						.						42	41	41					6																	87970974		1820	4073	5893	SO:0001589	frameshift_variant	23036	exon8			.	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.7627delA	chr6.hg19:g.87970974delA	ENSP00000358590:p.Lys2544fs	76.0	0.0		100.0	11.0	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Frame_Shift_Del	DEL	ENST00000369577.3	hg19	CCDS47457.1																																																																																			.	.		0.358	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		-	87970974	A	-	87970974	7	5	112	1	0	1	0	1	0	0	0	0	17841	363	13	0	7657	0	ZNF292	6	87970974	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2524361	87970974	83144093	450	17071										
RARS2	57038	hgsc.bcm.edu	37	chr6	88229963	88229963	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgctgaaaatgctttttttgTcctttatctgtcttgggaag	9	6	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:88229963T>C	ENST00000369536.5	-	13	1092	c.1047A>G	c.(1045-1047)ggA>ggG	p.G349G	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	349					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		GCTTTTTTTGTCCTTTATCTG	0.313																																					p.G349G		Atlas-SNP	.											.	RARS2	61	.	0			c.A1047G						.						172	165	167					6																	88229963		2203	4300	6503	SO:0001819	synonymous_variant	57038	exon13			TTTTTGTCCTTTA	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	21406	protein-coding gene	gene with protein product	"arginine tRNA ligase 2, mitochondrial (putative)"	611524	"arginyl-tRNA synthetase-like"	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.1047A>G	chr6.hg19:g.88229963T>C		30.0	0.0		67.0	4.0	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Silent	SNP	ENST00000369536.5	hg19	CCDS5011.1																																																																																			.	.		0.313	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		C	88229963	T	C	88229963	2	2	112	1	0	0	0	0	0	0	0	1	13074	1654	58	2		2	RARS2	6	88229963	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	258989	88229963	82885104	451	17072										
UBE2J1	51465	hgsc.bcm.edu	37	chr6	90048232	90048232	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcctgagatgctcaaacagaTtttcttgcccacttcaaatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:90048232delT	ENST00000435041.2	-	4	546	c.268delA	c.(268-270)atcfs	p.I90fs		NM_016021.2	NP_057105.2	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1	90					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(11)|stomach(1)	18		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)		CTCAAACAGATTTTCTTGCCC	0.333																																					p.I90fs		Atlas-INDEL	.											.	UBE2J1	28	.	0			c.269delT						.						94	94	94					6																	90048232		2203	4300	6503	SO:0001589	frameshift_variant	51465	exon4			.	AJ245898	CCDS5021.1	6q15	2014-01-28	2012-06-08		ENSG00000198833	ENSG00000198833		"Ubiquitin-conjugating enzymes E2"	17598	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)"			10708578	Standard	NM_016021		Approved	HSPC153, CGI-76, NCUBE1, UBC6	uc003pnc.3	Q9Y385	OTTHUMG00000016337	ENST00000435041.2:c.268delA	chr6.hg19:g.90048232delT	ENSP00000451261:p.Ile90fs	145.0	0.0		195.0	13.0	NM_016021	A8K3F9|Q53F25|Q5W0N4|Q9BZ32|Q9NQL3|Q9NY66|Q9P011|Q9P0S0|Q9UF10	Frame_Shift_Del	DEL	ENST00000435041.2	hg19	CCDS5021.1																																																																																			.	.		0.333	UBE2J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043742.2	NM_016021		-	90048232	T	-	90048232	7	5	112	1	0	1	0	1	0	0	0	0	16875	1493	52	0	708	0	UBE2J1	6	90048232	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1818269	90048232	81066835	452	17073										
MDN1	23195	hgsc.bcm.edu	37	chr6	90382309	90382309	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggtcagtgttctcctctgcTttttcattctttctttcttc					rs201481158		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:90382309delT	ENST00000369393.3	-	81	13702	c.13587delA	c.(13585-13587)aaafs	p.K4529fs	MDN1_ENST00000468568.1_5'Flank|RP1-122O8.7_ENST00000438877.1_RNA|MDN1_ENST00000428876.1_Frame_Shift_Del_p.K4529fs			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4529					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCTCCTCTGCTTTTTCATTCT	0.393																																					p.A4530fs		Atlas-INDEL	.											.	MDN1	478	.	0			c.13588delG						.						108	112	110					6																	90382309		2203	4300	6503	SO:0001589	frameshift_variant	23195	exon81			.	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.13587delA	chr6.hg19:g.90382309delT	ENSP00000358400:p.Lys4529fs	149.0	0.0		193.0	12.0	NM_014611	O15019|Q5T794	Frame_Shift_Del	DEL	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.393	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			-	90382309	T	-	90382309	7	5	112	1	0	1	0	1	0	0	0	0	9424	1606	56	0	3291	0	MDN1	6	90382309	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	334077	90382309	80732758	453	17074										
MDN1	23195	hgsc.bcm.edu	37	chr6	90504517	90504517	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccttgaaatatctcagggcAaaccttcaaacacaaagaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:90504517delA	ENST00000369393.3	-	3	448	c.333delT	c.(331-333)tttfs	p.F111fs	MDN1_ENST00000428876.1_Frame_Shift_Del_p.F111fs			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	111					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		ATCTCAGGGCAAACCTTCAAA	0.383																																					p.A112fs		Atlas-INDEL	.											.	MDN1	478	.	0			c.334delG						.						51	49	50					6																	90504517		2203	4300	6503	SO:0001589	frameshift_variant	23195	exon3			.	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.333delT	chr6.hg19:g.90504517delA	ENSP00000358400:p.Phe111fs	94.0	0.0		156.0	10.0	NM_014611	O15019|Q5T794	Frame_Shift_Del	DEL	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.383	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			-	90504517	A	-	90504517	7	5	112	1	0	1	0	1	0	0	0	0	9424	127	5	0	16857	0	MDN1	6	90504517	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	122208	90504517	80610550	454	17075										
SFRS18	25957	hgsc.bcm.edu	37	chr6	99848584	99848584	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctagaatcagagcctgaatgTtttttactatctttggtagt					rs201782750		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:99848584delT	ENST00000369239.5	-	12	2454	c.2250delA	c.(2248-2250)aaafs	p.K750fs	PNISR_ENST00000438806.1_Frame_Shift_Del_p.K750fs	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	750	Ser-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						AGCCTGAATGTTTTTTACTAT	0.383																																					p.H751fs		Atlas-INDEL	.											.,1	PNISR	74	.	0			c.2251delC						.						193	196	195					6																	99848584		2203	4300	6503	SO:0001589	frameshift_variant	25957	exon11			.	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 111", "splicing factor, arginine/serine-rich 18"	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.2250delA	chr6.hg19:g.99848584delT	ENSP00000358242:p.Lys750fs	146.0	0.0		241.0	16.0	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Frame_Shift_Del	DEL	ENST00000369239.5	hg19	CCDS5043.1																																																																																			.	.		0.383	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870		-	99848584	T	-	99848584	7	5	112	1	0	1	0	1	0	0	0	0	14189	1722	60	0	171	0	SFRS18	6	99848584	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	9344067	99848584	71266483	455	17076										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101312035	101312035	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cattcaaaaattttattatcTtcttccatgtcaggcccaaa	3	10	4	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:101312035T>C	ENST00000369162.2	-	3	490	c.146A>G	c.(145-147)aAg>aGg	p.K49R	ASCC3_ENST00000369143.2_Missense_Mutation_p.K49R|ASCC3_ENST00000522650.1_Missense_Mutation_p.K49R	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	49					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TTTTATTATCTTCTTCCATGT	0.294																																					p.K49R		Atlas-SNP	.											.	ASCC3	205	.	0			c.A146G						.						99	110	107					6																	101312035		2201	4298	6499	SO:0001583	missense	10973	exon3			ATTATCTTCTTCC	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.146A>G	chr6.hg19:g.101312035T>C	ENSP00000358159:p.Lys49Arg	75.0	0.0		112.0	5.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.609906	0.46527	.	.	ENSG00000112249	ENST00000369162;ENST00000522650;ENST00000324723;ENST00000369143	T;T;T	0.58506	0.42;0.33;0.79	5.32	4.16	0.48862	.	0.108694	0.64402	D	0.000009	T	0.55955	0.1953	L	0.59436	1.845	0.26722	N	0.970765	B;D;B;B	0.71674	0.022;0.998;0.022;0.003	B;D;B;B	0.78314	0.018;0.991;0.018;0.005	T	0.51748	-0.8666	10	0.41790	T	0.15	.	9.1586	0.37007	0.0:0.0868:0.0:0.9132	.	49;49;49;49	Q4G1A0;Q9H5A2;E7EW23;Q8N3C0	.;.;.;HELC1_HUMAN	R	49	ENSP00000358159:K49R;ENSP00000430769:K49R;ENSP00000320777:K49R	ENSP00000320777:K49R	K	-	2	0	ASCC3	101418756	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	5.069000	0.64370	0.861000	0.35504	0.533000	0.62120	AAG	.	.		0.294	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		C	101312035	T	C	101312035	3	2	112	1	0	0	0	0	1	0	0	0	1033	1609	56	2	6721	2	ASCC3	6	101312035	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1463451	101312035	69803032	456	17077										
BEND3	57673	hgsc.bcm.edu	37	chr6	107389947	107389947	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctttcttgaggatgtcgcaTtttttcctgttggggcggcg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:107389947delT	ENST00000369042.1	-	4	2638	c.2448delA	c.(2446-2448)aaafs	p.K816fs	BEND3_ENST00000429433.2_Frame_Shift_Del_p.K816fs			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	816	BEN 4. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						GGATGTCGCATTTTTTCCTGT	0.577																																					p.C817fs		Atlas-Indel,Pindel	.											.	BEND3	70	.	0			c.2449delT						.						59	61	60					6																	107389947		2203	4299	6502	SO:0001589	frameshift_variant	57673	exon5			.	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"BEN domain containing"	23040	protein-coding gene	gene with protein product			"KIAA1553"	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.2448delA	chr6.hg19:g.107389947delT	ENSP00000358038:p.Lys816fs	119.0	0.0		231.0	14.0	NM_001080450	A2RRH2|Q9HCL9	Frame_Shift_Del	DEL	ENST00000369042.1	hg19	CCDS34507.1																																																																																			.	.		0.577	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913		-	107389947	T	-	107389947	7	5	112	1	0	1	0	1	0	0	0	0	1399	1490	52	0	42	0	BEND3	6	107389947	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	6077912	107389947	63725120	457	17078										
SOBP	55084	hgsc.bcm.edu	37	chr6	107956410	107956410	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acctggacggggaggcggccAaaaagctgatgggcgaggag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:107956410delA	ENST00000317357.5	+	6	3021	c.2362delA	c.(2362-2364)aaafs	p.K789fs	SOBP_ENST00000494935.1_3'UTR	NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)											endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		GGAGGCGGCCAAAAAGCTGAT	0.617																																					p.A787fs		Atlas-INDEL	.											.	SOBP	53	.	0			c.2361delC						.						42	52	49					6																	107956410		2006	4173	6179	SO:0001589	frameshift_variant	55084	exon6			.	AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.2362delA	chr6.hg19:g.107956410delA	ENSP00000318900:p.Lys789fs	108.0	0.0		137.0	10.0	NM_018013		Frame_Shift_Del	DEL	ENST00000317357.5	hg19	CCDS43488.1																																																																																			.	.		0.617	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013		-	107956410	A	-	107956410	7	5	112	1	0	1	0	1	0	0	0	0	14927	131	5	0	2384	0	SOBP	6	107956410	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	566463	107956410	63158657	458	17079										
PPIL6	285755	hgsc.bcm.edu	37	chr6	109757309	109757309	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accccaaatatcctttacccTttttttctcctgtagatatt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:109757309delT	ENST00000521072.2	-	2	809	c.229delA	c.(229-231)aggfs	p.R77fs	PPIL6_ENST00000440797.2_Frame_Shift_Del_p.R77fs|PPIL6_ENST00000424445.2_Intron|AL109947.1_ENST00000459391.1_RNA	NM_173672.4	NP_775943.1	Q8IXY8	PPIL6_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 6	77					protein folding (GO:0006457)		peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.00684)|BRCA - Breast invasive adenocarcinoma(108;0.00889)|all cancers(137;0.0106)|OV - Ovarian serous cystadenocarcinoma(136;0.0259)		TCCTTTACCCTTTTTTTCTCC	0.338																																					p.R77fs		Atlas-INDEL	.											.	PPIL6	20	.	0			c.230delG						.						112	120	117					6																	109757309		2203	4300	6503	SO:0001589	frameshift_variant	285755	exon2			.		CCDS5074.1, CCDS47466.1, CCDS47466.2, CCDS69169.1	6q21	2009-11-18			ENSG00000185250	ENSG00000185250			21557	protein-coding gene	gene with protein product	"radial spoke 12 homolog (Chlamydomonas)"						Standard	NM_173672		Approved	bA425D10.6, MGC41939, dJ919F19.1, RSPH12	uc010kdp.3	Q8IXY8	OTTHUMG00000036593	ENST00000521072.2:c.229delA	chr6.hg19:g.109757309delT	ENSP00000427929:p.Arg77fs	198.0	0.0		286.0	18.0	NM_001111298	A9NIU0|A9NIU9|E7EX15	Frame_Shift_Del	DEL	ENST00000521072.2	hg19	CCDS5074.1																																																																																			.	.		0.338	PPIL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089003.4			-	109757309	T	-	109757309	7	5	112	1	0	1	0	1	0	0	0	0	12343	1608	56	0	816	0	PPIL6	6	109757309	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1800899	109757309	61357758	459	17080										
FIG4	9896	hgsc.bcm.edu	37	chr6	110098164	110098164	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cattaatctcttcctgggagTtttccatcccactgaaggga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:110098164delT	ENST00000230124.3	+	16	1914	c.1790delT	c.(1789-1791)gttfs	p.V597fs	FIG4_ENST00000441478.2_Frame_Shift_Del_p.V320fs	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	597					cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		TTCCTGGGAGTTTTCCATCCC	0.368																																					p.V597fs		Atlas-INDEL	.											.	FIG4	77	.	0			c.1789delG						.						61	66	64					6																	110098164		2203	4300	6503	SO:0001589	frameshift_variant	9896	exon16			.	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"KIAA0274", "FIG4 homolog (S. cerevisiae)", "FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.1790delT	chr6.hg19:g.110098164delT	ENSP00000230124:p.Val597fs	155.0	0.0		200.0	12.0	NM_014845	Q53H49|Q5TCS6	Frame_Shift_Del	DEL	ENST00000230124.3	hg19	CCDS5078.1																																																																																			.	.		0.368	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845		-	110098164	T	-	110098164	7	5	112	1	0	1	0	1	0	0	0	0	5896	1725	60	0	1852	0	FIG4	6	110098164	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	340855	110098164	61016903	460	17081										
FIG4	9896	hgsc.bcm.edu	37	chr6	110112750	110112750	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccgtgaagatgactgatgcAggagacagtgccaaagtgac	13	9	0	6			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:110112750A>G	ENST00000230124.3	+	20	2476	c.2352A>G	c.(2350-2352)gcA>gcG	p.A784A	FIG4_ENST00000441478.2_Silent_p.A507A	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	784					cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		TGACTGATGCAGGAGACAGTG	0.557																																					p.A784A		Atlas-SNP	.											.	FIG4	77	.	0			c.A2352G						.						44	45	44					6																	110112750		2203	4300	6503	SO:0001819	synonymous_variant	9896	exon20			TGATGCAGGAGAC	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"KIAA0274", "FIG4 homolog (S. cerevisiae)", "FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.2352A>G	chr6.hg19:g.110112750A>G		54.0	0.0		55.0	4.0	NM_014845	Q53H49|Q5TCS6	Silent	SNP	ENST00000230124.3	hg19	CCDS5078.1																																																																																			.	.		0.557	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845		G	110112750	A	G	110112750	2	3	112	1	0	0	0	0	0	0	0	1	5896	175	7	2		2	FIG4	6	110112750	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	14586	110112750	61002317	461	17082										
HS3ST5	222537	hgsc.bcm.edu	37	chr6	114383906	114383906	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgttttaagcacccacctaTccaagctcccaactctggcg	7	15	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:114383906T>C	ENST00000312719.5	-	4	1292	c.104A>G	c.(103-105)gAt>gGt	p.D35G	RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000519270.1_RNA|HS3ST5_ENST00000411826.1_Missense_Mutation_p.D35G|RP3-399L15.3_ENST00000523087.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	35					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		CACCCACCTATCCAAGCTCCC	0.463																																					p.D35G		Atlas-SNP	.											.	HS3ST5	80	.	0			c.A104G						.						150	148	149					6																	114383906		2203	4300	6503	SO:0001583	missense	222537	exon1			CACCTATCCAAGC	AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"Sulfotransferases, membrane-bound"	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.104A>G	chr6.hg19:g.114383906T>C	ENSP00000427888:p.Asp35Gly	77.0	0.0		117.0	6.0	NM_153612	A8K1J2|Q52LI2|Q8N285	Missense_Mutation	SNP	ENST00000312719.5	hg19	CCDS34517.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.673016	0.88445	.	.	ENSG00000249853	ENST00000312719;ENST00000411826	T;T	0.48522	0.81;0.81	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.41419	0.1158	N	0.19112	0.55	0.58432	D	0.999999	D	0.57571	0.98	D	0.68192	0.956	T	0.32161	-0.9917	10	0.20046	T	0.44	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	35	Q8IZT8	HS3S5_HUMAN	G	35	ENSP00000427888:D35G;ENSP00000440332:D35G	ENSP00000427888:D35G	D	-	2	0	HS3ST5	114490599	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.218000	0.77991	2.326000	0.78906	0.533000	0.62120	GAT	.	.		0.463	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612		C	114383906	T	C	114383906	3	2	112	1	0	0	0	0	1	0	0	0	7377	1435	50	2	944	2	HS3ST5	6	114383906	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4271156	114383906	56731161	462	17083										
NT5DC1	221294	hgsc.bcm.edu	37	chr6	116565118	116565118	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agattctcttcaagcaattcAaaaacagctggctactatcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:116565118delA	ENST00000319550.4	+	12	1381	c.1299delA	c.(1297-1299)tcafs	p.S433fs	RP3-486I3.5_ENST00000457319.1_RNA	NM_152729.2	NP_689942.2	Q5TFE4	NT5D1_HUMAN	5'-nucleotidase domain containing 1	433							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|stomach(1)	8		all_cancers(87;0.00367)|all_epithelial(87;0.00449)|Colorectal(196;0.0469)		all cancers(137;0.0327)|OV - Ovarian serous cystadenocarcinoma(136;0.0445)|GBM - Glioblastoma multiforme(226;0.0719)|Epithelial(106;0.112)		CAAGCAATTCAAAAACAGCTG	0.358																																					p.S433X	Colon(128;1440 1664 38087 41475 42869)	Atlas-INDEL	.											.	NT5DC1	32	.	0			c.1298delC						.						53	54	54					6																	116565118		2202	4294	6496	SO:0001589	frameshift_variant	221294	exon12			.	BC015138	CCDS5104.1	6q22.31	2008-02-05	2006-01-27	2006-01-27	ENSG00000178425	ENSG00000178425			21556	protein-coding gene	gene with protein product			"5'-nucleotidase, cytosolic II-like 1"	NT5C2L1			Standard	NM_152729		Approved	dJ486I3.1, MGC24302	uc003pwj.3	Q5TFE4	OTTHUMG00000015428	ENST00000319550.4:c.1299delA	chr6.hg19:g.116565118delA	ENSP00000326858:p.Ser433fs	191.0	0.0		255.0	17.0	NM_152729	B2RND9|B3KR35|Q6XYD5	Frame_Shift_Del	DEL	ENST00000319550.4	hg19	CCDS5104.1																																																																																			.	.		0.358	NT5DC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041931.3	NM_152729		-	116565118	A	-	116565118	7	5	112	1	0	1	0	1	0	0	0	0	10699	117	5	0	1345	0	NT5DC1	6	116565118	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2181212	116565118	54549949	463	17084										
RWDD1	51389	hgsc.bcm.edu	37	chr6	116901503	116901503	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caccattactgtgacgtctgAggctggagaaaatgatgaaa	11	7	1	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:116901503A>G	ENST00000466444.2	+	2	335	c.119A>G	c.(118-120)gAg>gGg	p.E40G	RWDD1_ENST00000392526.1_5'UTR|RWDD1_ENST00000487832.2_5'UTR|RWDD1_ENST00000517800.1_3'UTR	NM_015952.2	NP_057036.2	Q9H446	RWDD1_HUMAN	RWD domain containing 1	40	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.									NS(1)|breast(2)|central_nervous_system(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)	12		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.0312)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)|Epithelial(106;0.161)		GTGACGTCTGAGGCTGGAGAA	0.348																																					p.E40G		Atlas-SNP	.											.	RWDD1	21	.	0			c.A119G						.						52	49	50					6																	116901503		2203	4300	6503	SO:0001583	missense	51389	exon2			CGTCTGAGGCTGG	AF092134	CCDS34520.1, CCDS43496.1	6q13-q22.33	2012-12-07			ENSG00000111832	ENSG00000111832			20993	protein-coding gene	gene with protein product						10810093	Standard	NM_016104		Approved	PTD013	uc003pxd.3	Q9H446	OTTHUMG00000015441	ENST00000466444.2:c.119A>G	chr6.hg19:g.116901503A>G	ENSP00000420357:p.Glu40Gly	41.0	0.0		68.0	4.0	NM_015952	A8K3W2|A8MT24|Q9Y313|Q9Y6B3	Missense_Mutation	SNP	ENST00000466444.2	hg19	CCDS34520.1	.	.	.	.	.	.	.	.	.	.	A	19.98	3.926828	0.73327	.	.	ENSG00000111832	ENST00000466444	T	0.44881	0.91	5.95	5.95	0.96441	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.049815	0.85682	D	0.000000	T	0.40791	0.1131	M	0.71581	2.175	0.80722	D	1	B	0.22983	0.078	B	0.36922	0.236	T	0.41910	-0.9482	10	0.54805	T	0.06	-29.7264	16.4116	0.83717	1.0:0.0:0.0:0.0	.	40	Q9H446	RWDD1_HUMAN	G	40	ENSP00000420357:E40G	ENSP00000420357:E40G	E	+	2	0	RWDD1	117008196	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.649000	0.91067	2.276000	0.75962	0.528000	0.53228	GAG	.	.		0.348	RWDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041952.2	NM_015952		G	116901503	A	G	116901503	3	3	112	1	0	0	0	0	1	0	0	0	13769	304	11	2	125	2	RWDD1	6	116901503	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	336385	116901503	54213564	464	17085										
C6orf204	387119	hgsc.bcm.edu	37	chr6	118803074	118803074	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagcctcttgtaaattcttaTttttttcttccagaatctgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:118803074delT	ENST00000368491.3	-	8	2234	c.1613delA	c.(1612-1614)aatfs	p.N538fs	CEP85L_ENST00000368488.5_Frame_Shift_Del_p.N541fs	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	538						centrosome (GO:0005813)|cytoplasm (GO:0005737)											TAAATTCTTATTTTTTTCTTC	0.313																																					p.N541fs		Atlas-Indel,Pindel	.											.	CEP85L	26	.	0			c.1623delT						.						69	61	63					6																	118803074		1789	4061	5850	SO:0001589	frameshift_variant	387119	exon9			.	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 204"	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.1613delA	chr6.hg19:g.118803074delT	ENSP00000357477:p.Asn538fs	75.0	0.0		120.0	12.0	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Frame_Shift_Del	DEL	ENST00000368491.3	hg19	CCDS43498.1																																																																																			.	.		0.313	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		-	118803074	T	-	118803074	7	5	112	1	0	1	0	1	0	0	0	0	2355	1493	52	0	828	0	C6orf204	6	118803074	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1901571	118803074	52311993	465	17086										
MCM9	254394	hgsc.bcm.edu	37	chr6	119238756	119238756	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atcgctcttatagtattcccAaaaatcttcgaattcctttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:119238756delA	ENST00000316316.6	-	5	1160	c.874delT	c.(874-876)tggfs	p.W292fs	MCM9_ENST00000316068.3_Frame_Shift_Del_p.W292fs	NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	292					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		TAGTATTCCCAAAAATCTTCG	0.368																																					p.W292fs		Atlas-INDEL	.											.	MCM9	73	.	0			c.875delG						.						110	103	106					6																	119238756		2203	4300	6503	SO:0001589	frameshift_variant	254394	exon4			.	BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"minichromosome maintenance deficient domain containing 1", "chromosome 6 open reading frame 61"	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.874delT	chr6.hg19:g.119238756delA	ENSP00000314505:p.Trp292fs	103.0	0.0		202.0	13.0	NM_017696	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Frame_Shift_Del	DEL	ENST00000316316.6	hg19	CCDS56447.1																																																																																			.	.		0.368	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255		-	119238756	A	-	119238756	7	5	112	1	0	1	0	1	0	0	0	0	9403	130	5	0	313	0	MCM9	6	119238756	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	435682	119238756	51876311	466	17087										
TRDN	10345	hgsc.bcm.edu	37	chr6	123594509	123594510	+	Splice_Site	DNP	CT	CT	TA													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgcactttttcagatatagCtaaaataaataaataacata					rs147062785|rs386359375|rs535166955	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:123594509_123594510CT>TA	ENST00000398178.3	-	28	1619		c.e28-1		TRDN_ENST00000334268.4_Splice_Site	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin						cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		TCAGATATAGCTAAAATAAATA	0.233																																					.		Atlas-SNP	.											.	TRDN	88	.	0			c.1598-1G>A|c.1598-2A>T						.																																			SO:0001630	splice_region_variant	10345	exon29			ATATAGCTAAAAT|TATAGCTAAAATA	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1598_1598delinsTA	chr6.hg19:g.123594509_123594510delinsTA		33.0|32.0	0.0		76.0|74.0	6.0|5.0	NM_006073	A5D6W5|F5H2W7|Q6NSB8	Splice_Site	SNP	ENST00000398178.3	hg19	CCDS55053.1																																																																																			.	.		0.233	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			Intron	TA	123594510	CT	TA	123594509	5	4	112	1	0	0	0	0	0	0	1	0	16483	811	28	3	648	3	TRDN	6	123594509	Splice_Site	DNP	CT	TCGA-DD-A39Y-01A-11D-A20W-10	4355753	123594509	47520558	467	17088										
TPD52L1	7164	hgsc.bcm.edu	37	chr6	125541327	125541327	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaaaggaagagttaaaagcAgagttagttcaggtatgttt	12	2	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:125541327A>G	ENST00000534000.1	+	2	419	c.123A>G	c.(121-123)gcA>gcG	p.A41A	TPD52L1_ENST00000392482.2_Silent_p.A12A|TPD52L1_ENST00000534199.1_Silent_p.A12A|TPD52L1_ENST00000527711.1_Silent_p.A41A|TPD52L1_ENST00000304877.13_Silent_p.A41A|TPD52L1_ENST00000524679.1_Silent_p.A12A|TPD52L1_ENST00000368402.5_Silent_p.A41A|TPD52L1_ENST00000528193.1_Silent_p.A41A|TPD52L1_ENST00000532429.1_Silent_p.A12A|HDDC2_ENST00000608456.1_Intron|TPD52L1_ENST00000368388.2_Silent_p.A41A	NM_003287.2	NP_003278.1	Q16890	TPD53_HUMAN	tumor protein D52-like 1	41					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|prostate(1)	5			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)		AGTTAAAAGCAGAGTTAGTTC	0.368																																					p.A41A		Atlas-SNP	.											.	TPD52L1	14	.	0			c.A123G						.						128	124	125					6																	125541327		2203	4300	6503	SO:0001819	synonymous_variant	7164	exon2			AAAAGCAGAGTTA	U44427	CCDS5130.1, CCDS34527.1, CCDS34528.1, CCDS43502.1, CCDS75513.1, CCDS75514.1	6q22-q23	2008-07-29			ENSG00000111907	ENSG00000111907			12006	protein-coding gene	gene with protein product		604069				8812487, 16112108	Standard	NM_003287		Approved	D53, hD53	uc003pzu.1	Q16890	OTTHUMG00000015505	ENST00000534000.1:c.123A>G	chr6.hg19:g.125541327A>G		95.0	0.0		121.0	5.0	NM_001003396	A8K757|A8K772|A8MUD2|A8MUJ7|A8MW70|F6V707|O43397|Q5TC99|Q5TDQ0|Q9BUQ6|Q9C054	Silent	SNP	ENST00000534000.1	hg19	CCDS5130.1																																																																																			.	.		0.368	TPD52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042065.2			G	125541327	A	G	125541327	2	3	112	1	0	0	0	0	0	0	0	1	16413	175	7	2		2	TPD52L1	6	125541327	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1946818	125541327	45573740	468	17089										
HINT3	135114	hgsc.bcm.edu	37	chr6	126278229	126278229	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggggacctgtgaagccgctGgcaagtcaccagagcccaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:126278229delG	ENST00000229633.5	+	1	303	c.106delG	c.(106-108)ggcfs	p.G36fs		NM_138571.4	NP_612638.3	Q9NQE9	HINT3_HUMAN	histidine triad nucleotide binding protein 3	36			G -> A (2.5-fold increase in affinity for indolepropinoic acyl-adenylate and cytosine; 2-fold decrease in hypoxanthine affinity; nearly no change in affinity for adenine, guanine and uracil; dbSNP:rs2295005). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17870088, ECO:0000269|Ref.1}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)			endometrium(1)|large_intestine(1)|lung(1)|stomach(1)	4				UCEC - Uterine corpus endometrioid carcinoma (4;0.153)|GBM - Glioblastoma multiforme(226;0.0321)		TGAAGCCGCTGGCAAGTCACC	0.672											OREG0017649	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A35fs		Atlas-INDEL	.											.	HINT3	14	.	0			c.105delT						.						27	21	23					6																	126278229		1869	3644	5513	SO:0001589	frameshift_variant	135114	exon1			.	AK057688	CCDS5133.1	6q22.33	2007-12-04			ENSG00000111911	ENSG00000111911			18468	protein-coding gene	gene with protein product		609998				11805111	Standard	NM_138571		Approved	FLJ33126	uc003qal.4	Q9NQE9	OTTHUMG00000015514	ENST00000229633.5:c.106delG	chr6.hg19:g.126278229delG	ENSP00000229633:p.Gly36fs	111.0	0.0	1548	184.0	12.0	NM_138571	B3KQ91|Q8N0Y9	Frame_Shift_Del	DEL	ENST00000229633.5	hg19	CCDS5133.1																																																																																			.	.		0.672	HINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042090.1	NM_138571		-	126278229	G	-	126278229	7	5	112	1	0	1	0	1	0	0	0	0	7122	1348	47	0	108	0	HINT3	6	126278229	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	736902	126278229	44836838	469	17090	77	2								
HINT3	135114	hgsc.bcm.edu	37	chr6	126278232	126278232	+	Missense_Mutation	SNP	A	A	C													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggacctgtgaagccgctggcAagtcaccagagcccaaggac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:126278232A>C	ENST00000229633.5	+	1	306	c.109A>C	c.(109-111)Aag>Cag	p.K37Q		NM_138571.4	NP_612638.3	Q9NQE9	HINT3_HUMAN	histidine triad nucleotide binding protein 3	37						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)			endometrium(1)|large_intestine(1)|lung(1)|stomach(1)	4				UCEC - Uterine corpus endometrioid carcinoma (4;0.153)|GBM - Glioblastoma multiforme(226;0.0321)		AGCCGCTGGCAAGTCACCAGA	0.677											OREG0017649	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K37Q		Atlas-SNP	.											.	HINT3	14	.	0			c.A109C						.						27	21	23					6																	126278232		1869	3645	5514	SO:0001583	missense	135114	exon1			GCTGGCAAGTCAC	AK057688	CCDS5133.1	6q22.33	2007-12-04			ENSG00000111911	ENSG00000111911			18468	protein-coding gene	gene with protein product		609998				11805111	Standard	NM_138571		Approved	FLJ33126	uc003qal.4	Q9NQE9	OTTHUMG00000015514	ENST00000229633.5:c.109A>C	chr6.hg19:g.126278232A>C	ENSP00000229633:p.Lys37Gln	117.0	0.0	1548	187.0	8.0	NM_138571	B3KQ91|Q8N0Y9	Missense_Mutation	SNP	ENST00000229633.5	hg19	CCDS5133.1	.	.	.	.	.	.	.	.	.	.	A	9.072	0.997150	0.19043	.	.	ENSG00000111911	ENST00000229633	D	0.91351	-2.83	4.51	-1.37	0.09056	Histidine triad-like motif (1);	1.335400	0.04646	N	0.406141	T	0.63861	0.2547	N	0.19112	0.55	0.09310	N	1	B	0.23806	0.091	B	0.19148	0.024	T	0.56111	-0.8033	10	0.19147	T	0.46	-33.9008	4.8889	0.13717	0.3582:0.2836:0.3582:0.0	.	37	Q9NQE9	HINT3_HUMAN	Q	37	ENSP00000229633:K37Q	ENSP00000229633:K37Q	K	+	1	0	HINT3	126319925	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.402000	0.07223	-0.523000	0.06409	0.374000	0.22700	AAG	.	.		0.677	HINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042090.1	NM_138571		C	126278232	A	C	126278232	3	2	112	1	0	0	0	0	1	0	0	0	7122	131	5	5	111	5	HINT3	6	126278232	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	3	126278232	44836835	470	17091	77	2								
TRMT11	60487	hgsc.bcm.edu	37	chr6	126319442	126319442	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taagacattgacacaagaagAgaaaatcaagcgaatagatg	9	5	1	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:126319442A>G	ENST00000334379.5	+	5	489	c.368A>G	c.(367-369)gAg>gGg	p.E123G	TRMT11_ENST00000368332.3_Missense_Mutation_p.E123G|TRMT11_ENST00000450358.1_Missense_Mutation_p.E123G	NM_001031712.2	NP_001026882.2	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	123					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)|tRNA binding (GO:0000049)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(226;0.0356)		ACACAAGAAGAGAAAATCAAG	0.299																																					p.E123G		Atlas-SNP	.											.	TRMT11	43	.	0			c.A368G						.						39	38	39					6																	126319442		2175	4293	6468	SO:0001583	missense	60487	exon5			AAGAAGAGAAAAT	AF182423	CCDS35496.1	6q11.1-q22.33	2009-06-15	2006-11-28	2006-11-28	ENSG00000066651	ENSG00000066651			21080	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 75"	C6orf75			Standard	XM_006715546		Approved	MDS024, dJ187J11.2, TRM11, TRMT11-1	uc003qam.3	Q7Z4G4	OTTHUMG00000015515	ENST00000334379.5:c.368A>G	chr6.hg19:g.126319442A>G	ENSP00000333934:p.Glu123Gly	54.0	0.0		64.0	4.0	NM_001031712	E1P570|Q5JY11|Q6PGQ5|Q9HC13	Missense_Mutation	SNP	ENST00000334379.5	hg19	CCDS35496.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.164128	0.78339	.	.	ENSG00000066651	ENST00000334379;ENST00000450358;ENST00000368332;ENST00000444121;ENST00000446681	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	5.95	5.95	0.96441	.	0.135400	0.64402	D	0.000003	T	0.62588	0.2440	M	0.86502	2.82	0.53688	D	0.999974	P;P	0.52577	0.954;0.514	P;B	0.56700	0.804;0.106	T	0.69935	-0.5010	10	0.62326	D	0.03	-24.7641	16.4237	0.83790	1.0:0.0:0.0:0.0	.	123;123	Q7Z4G4-2;Q7Z4G4	.;TRM11_HUMAN	G	123;123;123;60;60	ENSP00000333934:E123G;ENSP00000405140:E123G;ENSP00000357316:E123G;ENSP00000406230:E60G;ENSP00000415724:E60G	ENSP00000333934:E123G	E	+	2	0	TRMT11	126361135	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.137000	0.94496	2.279000	0.76181	0.533000	0.62120	GAG	.	.		0.299	TRMT11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_021820		G	126319442	A	G	126319442	3	3	112	1	0	0	0	0	1	0	0	0	16577	304	11	2	386	2	TRMT11	6	126319442	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	41210	126319442	44795625	471	17092										
C6orf174	387104	hgsc.bcm.edu	37	chr6	127834044	127834044	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcaaatactaacctctttcaTtttttccagttcattctgta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:127834044delT	ENST00000525778.1	-	4	2222	c.1477delA	c.(1477-1479)atgfs	p.M493fs	SOGA3_ENST00000465909.2_Frame_Shift_Del_p.M493fs|SOGA3_ENST00000481848.2_Frame_Shift_Del_p.M493fs|SOGA3_ENST00000368268.2_Frame_Shift_Del_p.M493fs|SOGA3_ENST00000556132.1_Frame_Shift_Del_p.M493fs			Q5TF21	SOGA3_HUMAN	SOGA family member 3	493					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											ACCTCTTTCATTTTTTCCAGT	0.308																																					p.M493fs		Atlas-INDEL	.											.	.	.	.	0			c.1478delT						.						124	108	113					6																	127834044		1812	4070	5882	SO:0001589	frameshift_variant	387104	exon4			.	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1477delA	chr6.hg19:g.127834044delT	ENSP00000434570:p.Met493fs	172.0	0.0		245.0	16.0	NM_001012279		Frame_Shift_Del	DEL	ENST00000525778.1	hg19	CCDS43505.1																																																																																			.	.		0.308	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		-	127834044	T	-	127834044	7	5	112	1	0	1	0	1	0	0	0	0	2347	1493	52	0	1382	0	C6orf174	6	127834044	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1514602	127834044	43281023	472	17093										
C6orf58	352999	hgsc.bcm.edu	37	chr6	127902409	127902409	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcaaccttggcagataataTcaaaagttttgaagacaggt	8	6	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:127902409T>C	ENST00000329722.7	+	4	668	c.656T>C	c.(655-657)aTc>aCc	p.I219T		NM_001010905.1	NP_001010905.1	Q6P5S2	CF058_HUMAN	chromosome 6 open reading frame 58	219						extracellular vesicular exosome (GO:0070062)				kidney(3)|large_intestine(3)|liver(1)|lung(7)|pancreas(1)	15				GBM - Glioblastoma multiforme(226;0.0405)|all cancers(137;0.156)		GCAGATAATATCAAAAGTTTT	0.299																																					p.I219T		Atlas-SNP	.											.	C6orf58	35	.	0			c.T656C						.						89	86	87					6																	127902409		2203	4296	6499	SO:0001583	missense	352999	exon4			ATAATATCAAAAG	BC062712	CCDS34533.1	6q22.33	2011-12-13			ENSG00000184530	ENSG00000184530			20960	protein-coding gene	gene with protein product							Standard	NM_001010905		Approved		uc003qbh.4	Q6P5S2	OTTHUMG00000015530	ENST00000329722.7:c.656T>C	chr6.hg19:g.127902409T>C	ENSP00000328069:p.Ile219Thr	43.0	0.0		59.0	4.0	NM_001010905	B4E1I0|Q5VUP2	Missense_Mutation	SNP	ENST00000329722.7	hg19	CCDS34533.1	.	.	.	.	.	.	.	.	.	.	T	6.420	0.445667	0.12164	.	.	ENSG00000184530	ENST00000329722	T	0.40225	1.04	4.07	-7.47	0.01365	.	2.424140	0.01919	N	0.040386	T	0.05044	0.0135	N	0.11927	0.2	0.09310	N	1	B	0.29481	0.245	B	0.24006	0.05	T	0.08269	-1.0730	10	0.20046	T	0.44	3.7749	0.7466	0.00983	0.2647:0.2924:0.2581:0.1848	.	219	Q6P5S2	CF058_HUMAN	T	219	ENSP00000328069:I219T	ENSP00000328069:I219T	I	+	2	0	C6orf58	127944102	0.000000	0.05858	0.000000	0.03702	0.385000	0.30292	-0.210000	0.09345	-1.308000	0.02318	0.477000	0.44152	ATC	.	.		0.299	C6orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042152.1	NM_001010905		C	127902409	T	C	127902409	3	2	112	1	0	0	0	0	1	0	0	0	2369	1435	50	2	670	2	C6orf58	6	127902409	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	68365	127902409	43212658	473	17094										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128388715	128388715	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgttgtatcctttgcgcggAgccaaaggagggttccaaaa	12	8	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:128388715A>G	ENST00000368215.3	-	12	2105	c.2106T>C	c.(2104-2106)gcT>gcC	p.A702A	PTPRK_ENST00000368226.4_Silent_p.A702A|PTPRK_ENST00000368227.3_Silent_p.A702A|RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000532331.1_Silent_p.A702A|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368210.3_Silent_p.A702A|PTPRK_ENST00000368207.3_Silent_p.A702A|PTPRK_ENST00000368213.5_Silent_p.A702A			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	702					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		CTTTGCGCGGAGCCAAAGGAG	0.527																																					p.A702A		Atlas-SNP	.											.	PTPRK	330	.	0			c.T2106C						.						71	70	71					6																	128388715		2203	4300	6503	SO:0001819	synonymous_variant	5796	exon12			GCGCGGAGCCAAA	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2106T>C	chr6.hg19:g.128388715A>G		45.0	0.0		82.0	4.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Silent	SNP	ENST00000368215.3	hg19																																																																																				.	.		0.527	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			G	128388715	A	G	128388715	2	3	112	1	0	0	0	0	0	0	0	1	12820	291	11	2		2	PTPRK	6	128388715	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	486306	128388715	42726352	474	17095										
L3MBTL3	84456	hgsc.bcm.edu	37	chr6	130425608	130425608	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attcagaaatcaatttgaatAaagaccgtatttttccagac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:130425608delA	ENST00000529410.1	+	21	2253	c.1774delA	c.(1774-1776)aaafs	p.K592fs	L3MBTL3_ENST00000361794.2_Frame_Shift_Del_p.K592fs|L3MBTL3_ENST00000526019.1_Frame_Shift_Del_p.K567fs|L3MBTL3_ENST00000533560.1_Frame_Shift_Del_p.K567fs|L3MBTL3_ENST00000368139.2_Frame_Shift_Del_p.K567fs|L3MBTL3_ENST00000368136.2_Frame_Shift_Del_p.K592fs			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	592					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		CAATTTGAATAAAGACCGTAT	0.373																																					p.N591fs		Atlas-INDEL	.											.	L3MBTL3	99	.	0			c.1773delT						.						96	98	97					6																	130425608		2202	4300	6502	SO:0001589	frameshift_variant	84456	exon19			.	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"Sterile alpha motif (SAM) domain containing"	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.1774delA	chr6.hg19:g.130425608delA	ENSP00000431962:p.Lys592fs	156.0	0.0		194.0	13.0	NM_032438	Q4VXE1|Q5VUM9|Q6P9B5	Frame_Shift_Del	DEL	ENST00000529410.1	hg19	CCDS34537.1																																																																																			.	.		0.373	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074		-	130425608	A	-	130425608	7	5	112	1	0	1	0	1	0	0	0	0	8602	363	13	0	1840	0	L3MBTL3	6	130425608	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2036893	130425608	40689459	475	17096										
CTGF	1490	hgsc.bcm.edu	37	chr6	132270568	132270568	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cggcagggtggtggttctgtGgggggtgcagcatcggccgt					rs15960		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:132270568delG	ENST00000367976.3	-	5	1086	c.886delC	c.(886-888)cacfs	p.H296fs	RP11-69I8.3_ENST00000435287.1_RNA	NM_001901.2	NP_001892	P29279	CTGF_HUMAN	connective tissue growth factor	296	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.|Heparin-binding.				angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|chondrocyte proliferation (GO:0035988)|cytosolic calcium ion transport (GO:0060401)|DNA replication (GO:0006260)|epidermis development (GO:0008544)|extracellular matrix constituent secretion (GO:0070278)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of gene expression (GO:0010629)|organ senescence (GO:0010260)|ossification (GO:0001503)|positive regulation of cardiac muscle contraction (GO:0060452)|positive regulation of cell activation (GO:0050867)|positive regulation of cell death (GO:0010942)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G0 to G1 transition (GO:0070318)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|regulation of cell growth (GO:0001558)|regulation of chondrocyte differentiation (GO:0032330)|response to amino acid (GO:0043200)|response to anoxia (GO:0034059)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to glucose (GO:0009749)|response to mineralocorticoid (GO:0051385)|response to peptide hormone (GO:0043434)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell cortex (GO:0005938)|cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|insulin-like growth factor binding (GO:0005520)			breast(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	13	Breast(56;0.0602)			GBM - Glioblastoma multiforme(226;0.015)|OV - Ovarian serous cystadenocarcinoma(155;0.0169)		GTGGTTCTGTGGGGGGTGCAG	0.532																																					p.H296fs	Esophageal Squamous(127;510 1660 12817 24400 38449)	Atlas-INDEL	.											.	CTGF	36	.	0			c.887delA						.						167	164	165					6																	132270568		2203	4300	6503	SO:0001589	frameshift_variant	1490	exon5			.	X78947	CCDS5151.1	6q23.2	2008-02-05			ENSG00000118523	ENSG00000118523			2500	protein-coding gene	gene with protein product		121009				1654338	Standard	NM_001901		Approved	IGFBP8, CCN2	uc003qcz.3	P29279	OTTHUMG00000015573	ENST00000367976.3:c.886delC	chr6.hg19:g.132270568delG	ENSP00000356954:p.His296fs	102.0	0.0		179.0	14.0	NM_001901	E1P578|Q6LCY0|Q96A79|Q96QX2|Q9UDL6	Frame_Shift_Del	DEL	ENST00000367976.3	hg19	CCDS5151.1																																																																																			.	.		0.532	CTGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042239.2	NM_001901		-	132270568	G	-	132270568	7	5	112	1	0	1	0	1	0	0	0	0	4010	1348	47	0	167	0	CTGF	6	132270568	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1844960	132270568	38844499	476	17097										
EYA4	2070	hgsc.bcm.edu	37	chr6	133783807	133783807	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacagagagtggactttcccAaactcagtccccattacaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:133783807delA	ENST00000367895.5	+	9	1093	c.629delA	c.(628-630)caafs	p.Q210fs	EYA4_ENST00000452339.2_Frame_Shift_Del_p.Q156fs|EYA4_ENST00000355286.6_Frame_Shift_Del_p.Q187fs|EYA4_ENST00000355167.3_Frame_Shift_Del_p.Q210fs|EYA4_ENST00000431403.2_Frame_Shift_Del_p.Q210fs|EYA4_ENST00000531901.1_Frame_Shift_Del_p.Q210fs|EYA4_ENST00000525849.1_Frame_Shift_Del_p.Q187fs|EYA4_ENST00000430974.2_Frame_Shift_Del_p.Q156fs	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	210					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		GGACTTTCCCAAACTCAGTCC	0.453																																					p.Q210fs	Melanoma(57;398 1237 3528 4702 7415)	Atlas-INDEL	.											.	EYA4	196	.	0			c.628delC						.						94	88	90					6																	133783807		2203	4300	6503	SO:0001589	frameshift_variant	2070	exon9			.	Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"Protein tyrosine phosphatases / Asp-based PTPs"	3522	protein-coding gene	gene with protein product		603550	"eyes absent (Drosophila) homolog 4", "eyes absent homolog 4 (Drosophila)"	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.629delA	chr6.hg19:g.133783807delA	ENSP00000356870:p.Gln210fs	99.0	0.0		116.0	10.0	NM_172105	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Frame_Shift_Del	DEL	ENST00000367895.5	hg19	CCDS5165.1																																																																																			.	.		0.453	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100		-	133783807	A	-	133783807	7	5	112	1	0	1	0	1	0	0	0	0	5333	130	5	0	659	0	EYA4	6	133783807	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1513239	133783807	37331260	477	17098										
IL20RA	53832	hgsc.bcm.edu	37	chr6	137322699	137322699	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaggaagtgttggcatcagTtttccatctgcacatataac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:137322699delT	ENST00000316649.5	-	7	1893	c.1658delA	c.(1657-1659)aacfs	p.N553fs	IL20RA_ENST00000541547.1_Frame_Shift_Del_p.N504fs|RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000367748.1_Frame_Shift_Del_p.N442fs	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha	553					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		TTGGCATCAGTTTTCCATCTG	0.453																																					p.N553fs		Atlas-INDEL	.											.	IL20RA	54	.	0			c.1659delC						.						163	159	161					6																	137322699		2203	4300	6503	SO:0001589	frameshift_variant	53832	exon7			.	AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"Interleukins and interleukin receptors"	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.1658delA	chr6.hg19:g.137322699delT	ENSP00000314976:p.Asn553fs	194.0	0.0		225.0	14.0	NM_014432	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Frame_Shift_Del	DEL	ENST00000316649.5	hg19	CCDS5181.1																																																																																			.	.		0.453	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432		-	137322699	T	-	137322699	7	5	112	1	0	1	0	1	0	0	0	0	7677	1725	60	0	7	0	IL20RA	6	137322699	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3538892	137322699	33792368	478	17099										
PBOV1	59351	hgsc.bcm.edu	37	chr6	138539188	138539188	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagcattccagacctagggtCtgagttaactgcaaagtcaa	9	10	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:138539188C>T	ENST00000527246.2	-	1	439	c.345G>A	c.(343-345)caG>caA	p.Q115Q	KIAA1244_ENST00000251691.4_Intron	NM_021635.2	NP_067648.1	Q9GZY1	PBOV1_HUMAN	prostate and breast cancer overexpressed 1	115						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)	1	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00055)|GBM - Glioblastoma multiforme(68;0.000674)		GACCTAGGGTCTGAGTTAACT	0.403																																					p.Q115Q		Atlas-SNP	.											.	PBOV1	12	.	0			c.G345A						.						159	162	161					6																	138539188		2203	4300	6503	SO:0001819	synonymous_variant	59351	exon1			TAGGGTCTGAGTT	AF189269	CCDS5190.1	6q23.3	2012-02-09			ENSG00000254440	ENSG00000254440			21079	protein-coding gene	gene with protein product		605669				12553037, 11156405	Standard	NM_021635		Approved	UC28, UROC28	uc003qhv.3	Q9GZY1	OTTHUMG00000167040	ENST00000527246.2:c.345G>A	chr6.hg19:g.138539188C>T		205.0	0.0		274.0	15.0	NM_021635		Silent	SNP	ENST00000527246.2	hg19	CCDS5190.1																																																																																			.	.		0.403	PBOV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392617.1	NM_021635		T	138539188	C	T	138539188	2	4	112	1	0	0	0	0	0	0	0	1	11499	912	32	3		3	PBOV1	6	138539188	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1216489	138539188	32575879	479	17100										
PHACTR2	9749	hgsc.bcm.edu	37	chr6	144086851	144086851	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctctgccttagacccaagtcAgcttctttgggctgaagagc	10	12	3	3	rs372509172		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:144086851A>G	ENST00000427704.2	+	6	1245	c.1115A>G	c.(1114-1116)cAg>cGg	p.Q372R	PHACTR2_ENST00000305766.6_Missense_Mutation_p.Q292R|PHACTR2_ENST00000367584.4_Missense_Mutation_p.Q360R|PHACTR2_ENST00000367582.3_Missense_Mutation_p.Q303R|PHACTR2_ENST00000440869.2_Missense_Mutation_p.Q383R	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	372							protein phosphatase inhibitor activity (GO:0004864)			NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		GACCCAAGTCAGCTTCTTTGG	0.517																																					p.Q383R	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)	Atlas-SNP	.											.	PHACTR2	99	.	0			c.A1148G						.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	1,3903		0,1,1951	86	84	85		1148,908,875,1115	-2.1	0.1	6		85	1,8285		0,1,4142	no	missense,missense,missense,missense	PHACTR2	NM_001100164.1,NM_001100165.1,NM_001100166.1,NM_014721.2	43,43,43,43	0,2,6093	GG,GA,AA		0.0121,0.0256,0.0164	benign,benign,benign,benign	383/646,303/566,292/555,372/635	144086851	2,12188	1952	4143	6095	SO:0001583	missense	9749	exon6			CAAGTCAGCTTCT	AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"Phosphatase and actin regulators"	20956	protein-coding gene	gene with protein product		608724	"chromosome 6 open reading frame 56"	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.1115A>G	chr6.hg19:g.144086851A>G	ENSP00000391763:p.Gln372Arg	60.0	0.0		73.0	4.0	NM_001100164	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Missense_Mutation	SNP	ENST00000427704.2	hg19	CCDS47492.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.290420	0.40494	2.56E-4	1.21E-4	ENSG00000112419	ENST00000367584;ENST00000427704;ENST00000305766;ENST00000440869;ENST00000367582	T;T;T;T;T	0.30981	1.51;1.95;1.53;1.95;1.53	5.22	-2.09	0.07232	.	1.212500	0.05664	N	0.587411	T	0.07593	0.0191	L	0.34521	1.04	0.09310	N	0.999991	B;B;B;B	0.26258	0.145;0.0;0.0;0.0	B;B;B;B	0.26864	0.074;0.001;0.001;0.0	T	0.34900	-0.9810	10	0.19590	T	0.45	.	8.4382	0.32799	0.2972:0.5516:0.1512:0.0	.	383;292;303;372	O75167-4;O75167-5;O75167-2;O75167	.;.;.;PHAR2_HUMAN	R	360;372;292;383;303	ENSP00000356556:Q360R;ENSP00000391763:Q372R;ENSP00000305530:Q292R;ENSP00000417038:Q383R;ENSP00000356554:Q303R	ENSP00000305530:Q292R	Q	+	2	0	PHACTR2	144128544	0.926000	0.31397	0.118000	0.21660	0.977000	0.68977	0.054000	0.14205	-0.633000	0.05545	-0.290000	0.09829	CAG	.	.		0.517	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721		G	144086851	A	G	144086851	3	3	112	1	0	0	0	0	1	0	0	0	11819	188	7	2	1187	2	PHACTR2	6	144086851	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	5547663	144086851	27028216	480	17101										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146254194	146254194	+	Splice_Site	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taaagcaatcaccttctaccTttaataatatgaatgcctgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:146254194delT	ENST00000367505.2	-	14	3375	c.3111delA	c.(3109-3111)aaa>aa	p.K1037fs	SHPRH_ENST00000367503.3_Splice_Site_p.K1046fs|SHPRH_ENST00000438092.2_Splice_Site_p.K1046fs|SHPRH_ENST00000275233.7_Splice_Site_p.K1037fs			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1037					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		ACCTTCTACCTTTAATAATAT	0.373																																					p.G1047fs		Atlas-INDEL	.											.	SHPRH	169	.	0			c.3139delG						.						93	87	89					6																	146254194		1845	4093	5938	SO:0001630	splice_region_variant	257218	exon14			.	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.3112+1A>-	chr6.hg19:g.146254194delT		85.0	0.0		125.0	10.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Frame_Shift_Del	DEL	ENST00000367505.2	hg19	CCDS43513.2																																																																																			.	.		0.373	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	Frame_Shift_Del	-	146254194	T	-	146254194	8	5	112	1	0	1	0	1	0	0	1	0	14306	1623	56	0	2025	0	SHPRH	6	146254194	Splice_Site	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2167343	146254194	24860873	481	17102										
RAET1L	154064	hgsc.bcm.edu	37	chr6	150343212	150343212	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gttctgtgctttccaggccaTtgtgacatttagtttcttcc	8	10	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:150343212T>G	ENST00000367341.1	-	2	252	c.253A>C	c.(253-255)Atg>Ctg	p.M85L	RAET1L_ENST00000286380.2_Missense_Mutation_p.M85L			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	85	MHC class I alpha-1 like. {ECO:0000250}.		M -> T (in dbSNP:rs912565). {ECO:0000269|PubMed:11827464, ECO:0000269|PubMed:15489334}.		antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		TTCCAGGCCATTGTGACATTT	0.483																																					p.M85L		Atlas-SNP	.											RAET1L,NS,carcinoma,0,2	RAET1L	21	.	0			c.A253C						.																																			SO:0001583	missense	154064	exon2			AGGCCATTGTGAC	AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918			16798	protein-coding gene	gene with protein product		611047				11827464	Standard	NM_130900		Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.253A>C	chr6.hg19:g.150343212T>G	ENSP00000356310:p.Met85Leu	208.0	1.0		354.0	0.0	NM_130900	A3KME4|Q8TE74	Missense_Mutation	SNP	ENST00000367341.1	hg19	CCDS5224.1	.	.	.	.	.	.	.	.	.	.	t	6.430	0.447513	0.12223	.	.	ENSG00000155918	ENST00000367341;ENST00000286380	T;T	0.06218	3.33;3.33	1.91	-2.05	0.07321	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00967	0.0032	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.47548	-0.9109	9	0.87932	D	0	.	5.9233	0.19094	0.0:0.5665:0.0:0.4335	.	85	Q5VY80	RET1L_HUMAN	L	85	ENSP00000356310:M85L;ENSP00000286380:M85L	ENSP00000286380:M85L	M	-	1	0	RAET1L	150384905	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.287000	0.01151	-0.549000	0.06191	0.402000	0.26972	ATG	.	.		0.483	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042676.1	NM_130900		G	150343212	T	G	150343212	3	3	112	1	0	0	0	0	1	0	0	0	13016	1493	52	5	498	5	RAET1L	6	150343212	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4089018	150343212	20771855	482	17103										
MTHFD1L	25902	hgsc.bcm.edu	37	chr6	151198808	151198808	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgcaggaaatcaaccagaaTttggctgaggaggtgaggac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:151198808delT	ENST00000367321.3	+	3	625	c.351delT	c.(349-351)aatfs	p.N117fs	MTHFD1L_ENST00000367307.4_Frame_Shift_Del_p.N117fs	NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	117	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		TCAACCAGAATTTGGCTGAGG	0.353																																					p.N117fs		Atlas-INDEL	.											.	MTHFD1L	75	.	0			c.350delA						.						119	116	117					6																	151198808		2203	4300	6503	SO:0001589	frameshift_variant	25902	exon3			.	BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"10-formyl-THF synthetase", "mitochondrial C1-tetrahydrofolate synthase", "monofunctional C1-tetrahydrofolate synthase, mitochondrial"	611427	"formyltetrahydrofolate synthetase domain containing 1"	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.351delT	chr6.hg19:g.151198808delT	ENSP00000356290:p.Asn117fs	117.0	0.0		154.0	11.0	NM_001242767	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Frame_Shift_Del	DEL	ENST00000367321.3	hg19	CCDS5228.1																																																																																			.	.		0.353	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440		-	151198808	T	-	151198808	7	5	112	1	0	1	0	1	0	0	0	0	9937	1490	52	0	361	0	MTHFD1L	6	151198808	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	855596	151198808	19916259	483	17104										
AKAP12	9590	hgsc.bcm.edu	37	chr6	151672185	151672185	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtccaaggagctcagcgagAgtcaggttcatatgatggca	13	8	3	2	rs61748676	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:151672185A>G	ENST00000253332.1	+	3	2848	c.2659A>G	c.(2659-2661)Agt>Ggt	p.S887G	AKAP12_ENST00000359755.5_Missense_Mutation_p.S782G|AKAP12_ENST00000354675.6_Missense_Mutation_p.S789G|AKAP12_ENST00000402676.2_Missense_Mutation_p.S887G			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	887					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GCTCAGCGAGAGTCAGGTTCA	0.532																																					p.S887G	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.A2659G						.						73	80	78					6																	151672185		2203	4300	6503	SO:0001583	missense	9590	exon4			AGCGAGAGTCAGG	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.2659A>G	chr6.hg19:g.151672185A>G	ENSP00000253332:p.Ser887Gly	84.0	0.0		123.0	6.0	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	hg19	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	A	4.061	0.009112	0.07912	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.06687	3.27;3.27;3.28;3.28	5.4	3.03	0.35002	.	1.136460	0.06613	N	0.755988	T	0.01905	0.0060	L	0.33485	1.01	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.11329	0.006;0.006;0.003	T	0.46261	-0.9204	10	0.20046	T	0.44	.	4.6169	0.12432	0.5207:0.0:0.4793:0.0	.	782;789;887	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	G	887;887;789;782	ENSP00000384537:S887G;ENSP00000253332:S887G;ENSP00000346702:S789G;ENSP00000352794:S782G	ENSP00000253332:S887G	S	+	1	0	AKAP12	151713878	0.348000	0.24861	0.192000	0.23308	0.015000	0.08874	0.815000	0.27253	0.888000	0.36160	0.459000	0.35465	AGT	.	A|0.978;T|0.022		0.532	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			G	151672185	A	G	151672185	3	3	112	1	0	0	0	0	1	0	0	0	448	304	11	2	2698	2	AKAP12	6	151672185	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	473377	151672185	19442882	484	17105										
C6orf97	80129	hgsc.bcm.edu	37	chr6	151907220	151907220	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caacttgaattttgagaaacAaaaagtaatgacccgagggc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:151907220delA	ENST00000239374.7	+	7	1388	c.1289delA	c.(1288-1290)caafs	p.Q430fs	CCDC170_ENST00000367290.5_Frame_Shift_Del_p.Q430fs	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	430																	TTTGAGAAACAAAAAGTAATG	0.408																																					p.Q430fs		Atlas-INDEL	.											.	.	.	.	0			c.1288delC						.						54	53	53					6																	151907220		1863	4113	5976	SO:0001589	frameshift_variant	80129	exon7			.	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 97"	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1289delA	chr6.hg19:g.151907220delA	ENSP00000239374:p.Gln430fs	73.0	0.0		145.0	12.0	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Frame_Shift_Del	DEL	ENST00000239374.7	hg19	CCDS43515.1																																																																																			.	.		0.408	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		-	151907220	A	-	151907220	7	5	112	1	0	1	0	1	0	0	0	0	2376	130	5	0	1315	0	C6orf97	6	151907220	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	235035	151907220	19207847	485	17106										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152589207	152589207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atacccagcatcaccagaggTctctgccgccgaatgttgaa	9	13	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:152589207T>C	ENST00000367255.5	-	100	19400	c.18799A>G	c.(18799-18801)Acc>Gcc	p.T6267A	SYNE1_ENST00000341594.5_Missense_Mutation_p.T5879A|SYNE1_ENST00000423061.1_Missense_Mutation_p.T6196A|SYNE1_ENST00000356820.4_Missense_Mutation_p.T791A|SYNE1_ENST00000265368.4_Missense_Mutation_p.T6267A|SYNE1_ENST00000448038.1_Missense_Mutation_p.T6196A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6267					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCACCAGAGGTCTCTGCCGCC	0.428										HNSCC(10;0.0054)																											p.T6267A		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A18799G						.						101	98	99					6																	152589207		2203	4300	6503	SO:0001583	missense	23345	exon100			CAGAGGTCTCTGC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.18799A>G	chr6.hg19:g.152589207T>C	ENSP00000356224:p.Thr6267Ala	92.0	0.0		112.0	5.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	0.032	-1.326150	0.01309	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.53206	0.72;0.71;0.63;0.71;0.82;2.73	5.74	-0.38	0.12490	.	0.819818	0.11015	N	0.609069	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.42103	-0.9471	10	0.07813	T	0.8	.	7.0886	0.25272	0.0:0.4353:0.1405:0.4242	.	6267;6267;6196	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	A	6267;6196;6267;6196;5879;791	ENSP00000356224:T6267A;ENSP00000396024:T6196A;ENSP00000265368:T6267A;ENSP00000390975:T6196A;ENSP00000341887:T5879A;ENSP00000349276:T791A	ENSP00000265368:T6267A	T	-	1	0	SYNE1	152630900	0.000000	0.05858	0.127000	0.21898	0.122000	0.20287	-1.644000	0.02002	-0.010000	0.14271	0.460000	0.39030	ACC	.	.		0.428	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152589207	T	C	152589207	3	2	112	1	0	0	0	0	1	0	0	0	15460	1667	58	2	7855	2	SYNE1	6	152589207	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	681987	152589207	18525860	486	17107										
MTRF1L	54516	hgsc.bcm.edu	37	chr6	153323592	153323592	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgctcagtctcccgcagctCccgctccttctcgttcagca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:153323592delC	ENST00000367233.5	-	1	228	c.229delG	c.(229-231)gagfs	p.E77fs	MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367230.1_Frame_Shift_Del_p.E77fs|MTRF1L_ENST00000367231.5_Frame_Shift_Del_p.E77fs	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	77						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		TCCCGCAGCTCCCGCTCCTTC	0.617																																					p.E77fs		Atlas-INDEL	.											.	MTRF1L	21	.	0			c.230delA						.						30	31	31					6																	153323592		2203	4300	6503	SO:0001589	frameshift_variant	54516	exon1			.	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.229delG	chr6.hg19:g.153323592delC	ENSP00000356202:p.Glu77fs	190.0	0.0		227.0	14.0	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Frame_Shift_Del	DEL	ENST00000367233.5	hg19	CCDS5243.1																																																																																			.	.		0.617	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041		-	153323592	C	-	153323592	7	5	112	1	0	1	0	1	0	0	0	0	9969	864	30	0	941	0	MTRF1L	6	153323592	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	734385	153323592	17791475	487	17108										
CLDN20	49861	hgsc.bcm.edu	37	chr6	155596902	155596902	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctttcatcctggccttatctGgggtctctggagtgctcaca	10	12	4	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:155596902G>C	ENST00000367165.3	+	2	429	c.49G>C	c.(49-51)Ggg>Cgg	p.G17R	TFB1M_ENST00000367166.4_Intron	NM_001001346.3	NP_001001346.1	P56880	CLD20_HUMAN	claudin 20	17					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.G17R(1)		endometrium(1)|lung(2)	3				OV - Ovarian serous cystadenocarcinoma(155;7.82e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0114)		GGCCTTATCTGGGGTCTCTGG	0.493																																					p.G17R		Atlas-SNP	.											CLDN20,NS,carcinoma,0,1	CLDN20	10	.	1	Substitution - Missense(1)	endometrium(1)	c.G49C						.						99	103	102					6																	155596902		2203	4300	6503	SO:0001583	missense	49861	exon2			TTATCTGGGGTCT	BC020838	CCDS5249.1	6q25	2008-08-01			ENSG00000171217	ENSG00000171217		"Claudins"	2042	protein-coding gene	gene with protein product						16836752	Standard	NM_001001346		Approved		uc003qql.2	P56880	OTTHUMG00000015882	ENST00000367165.3:c.49G>C	chr6.hg19:g.155596902G>C	ENSP00000356133:p.Gly17Arg	177.0	0.0		231.0	0.0	NM_001001346		Missense_Mutation	SNP	ENST00000367165.3	hg19	CCDS5249.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.001899	0.93227	.	.	ENSG00000171217	ENST00000367165	D	0.89681	-2.55	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.96476	0.8850	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97406	0.9999	10	0.87932	D	0	.	19.451	0.94867	0.0:0.0:1.0:0.0	.	17	P56880	CLD20_HUMAN	R	17	ENSP00000356133:G17R	ENSP00000356133:G17R	G	+	1	0	CLDN20	155638594	1.000000	0.71417	0.942000	0.38095	0.906000	0.53458	9.624000	0.98398	2.593000	0.87608	0.655000	0.94253	GGG	.	.		0.493	CLDN20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042818.1	NM_001001346		C	155596902	G	C	155596902	3	2	112	1	0	0	0	0	1	0	0	0	3484	1348	47	4	51	4	CLDN20	6	155596902	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	2273310	155596902	15518165	488	17109										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157099949	157099949	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtaccccaacagccagtgcAaccattatccgggctacagc	9	15	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:157099949A>G	ENST00000350026.5	+	1	887	c.886A>G	c.(886-888)Aac>Gac	p.N296D	ARID1B_ENST00000275248.4_Missense_Mutation_p.N238D|RP11-230C9.2_ENST00000603191.1_lincRNA|ARID1B_ENST00000367148.1_Missense_Mutation_p.N296D|RP11-230C9.3_ENST00000604792.1_RNA|ARID1B_ENST00000346085.5_Missense_Mutation_p.N296D|MIR4466_ENST00000606121.1_RNA	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	296	Gly-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CAGCCAGTGCAACCATTATCC	0.746																																					p.N296D		Atlas-SNP	.											.	ARID1B	320	.	0			c.A886G						.						2	3	2					6																	157099949		1113	2290	3403	SO:0001583	missense	57492	exon1			CAGTGCAACCATT	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.886A>G	chr6.hg19:g.157099949A>G	ENSP00000055163:p.Asn296Asp	23.0	0.0		37.0	4.0	NM_017519	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	a	4.021	0.001387	0.07819	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248	T;T;T;T	0.02103	4.45;4.5;4.48;4.48	2.12	2.12	0.27331	.	0.340062	0.18727	U	0.132842	T	0.00440	0.0014	N	0.08118	0	0.23425	N	0.997701	P;P;P	0.48694	0.86;0.914;0.914	B;B;B	0.34418	0.089;0.182;0.182	T	0.52689	-0.8542	10	0.87932	D	0	.	7.4066	0.26993	1.0:0.0:0.0:0.0	.	296;296;238	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	D	296;296;296;238	ENSP00000344546:N296D;ENSP00000055163:N296D;ENSP00000356116:N296D;ENSP00000275248:N238D	ENSP00000275248:N238D	N	+	1	0	ARID1B	157141641	1.000000	0.71417	0.933000	0.37362	0.635000	0.38103	1.408000	0.34668	0.726000	0.32339	0.128000	0.15822	AAC	.	.		0.746	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		G	157099949	A	G	157099949	3	3	112	1	0	0	0	0	1	0	0	0	914	130	5	2	888	2	ARID1B	6	157099949	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1503047	157099949	14015118	489	17110										
SYTL3	94120	hgsc.bcm.edu	37	chr6	159103969	159103969	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttttcaggaatgtcaaaatAaaaactggagaatggttcta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:159103969delA	ENST00000297239.9	+	5	536	c.342delA	c.(340-342)atafs	p.I114fs	SYTL3_ENST00000367081.3_5'UTR|SYTL3_ENST00000360448.3_Frame_Shift_Del_p.I114fs			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	114	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	calcium-dependent phospholipid binding (GO:0005544)			endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		ATGTCAAAATAAAAACTGGAG	0.348																																					p.I114fs		Atlas-INDEL	.											.	SYTL3	49	.	0			c.341delT						.						56	57	57					6																	159103969		2203	4300	6503	SO:0001589	frameshift_variant	94120	exon7			.	AK055750	CCDS34563.1, CCDS56458.1	6q25.3	2008-07-04			ENSG00000164674	ENSG00000164674			15587	protein-coding gene	gene with protein product						11773082	Standard	NM_001242384		Approved	SLP3, exophilin-6	uc003qrp.3	Q4VX76	OTTHUMG00000015916	ENST00000297239.9:c.342delA	chr6.hg19:g.159103969delA	ENSP00000297239:p.Ile114fs	154.0	0.0		176.0	14.0	NM_001009991	Q496J4|Q496J6|Q5U3B9	Frame_Shift_Del	DEL	ENST00000297239.9	hg19	CCDS56458.1																																																																																			.	.		0.348	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042876.1			-	159103969	A	-	159103969	7	5	112	1	0	1	0	1	0	0	0	0	15499	352	13	0	352	0	SYTL3	6	159103969	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2004020	159103969	12011098	490	17111										
TAGAP	117289	hgsc.bcm.edu	37	chr6	159464683	159464683	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acaggggatgttccttgataTcaccctaaaaacatttttat	6	8	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:159464683T>C	ENST00000367066.3	-	4	417	c.86A>G	c.(85-87)gAt>gGt	p.D29G	TAGAP_ENST00000338313.5_Missense_Mutation_p.D29G|RP1-111C20.4_ENST00000606466.1_RNA|TAGAP_ENST00000326965.6_5'UTR|RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	29					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TTCCTTGATATCACCCTAAAA	0.348																																					p.D29G		Atlas-SNP	.											.	TAGAP	75	.	0			c.A86G						.						156	159	158					6																	159464683		2203	4300	6503	SO:0001583	missense	117289	exon4			TTGATATCACCCT	AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.86A>G	chr6.hg19:g.159464683T>C	ENSP00000356033:p.Asp29Gly	103.0	0.0		159.0	7.0	NM_138810	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	hg19	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	T	14.14	2.447965	0.43429	.	.	ENSG00000164691	ENST00000367066;ENST00000338313	T;T	0.26373	1.74;1.85	5.52	5.52	0.82312	.	0.224065	0.37761	N	0.001951	T	0.09158	0.0226	L	0.32530	0.975	0.45502	D	0.998466	B;P	0.44429	0.037;0.835	B;B	0.39119	0.046;0.291	T	0.10917	-1.0609	10	0.15952	T	0.53	-18.011	13.0162	0.58759	0.0:0.0:0.0:1.0	.	29;29	Q8N103-4;Q8N103	.;TAGAP_HUMAN	G	29	ENSP00000356033:D29G;ENSP00000340217:D29G	ENSP00000340217:D29G	D	-	2	0	TAGAP	159384671	0.266000	0.24112	0.907000	0.35723	0.925000	0.55904	3.660000	0.54496	2.100000	0.63781	0.533000	0.62120	GAT	.	.		0.348	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		C	159464683	T	C	159464683	3	2	112	1	0	0	0	0	1	0	0	0	15552	1435	50	2	2155	2	TAGAP	6	159464683	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	360714	159464683	11650384	491	17112										
SLC22A2	6582	hgsc.bcm.edu	37	chr6	160671613	160671613	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tattaaccagcctgctttgcTgaccagtccttggattaagc	8	11	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:160671613T>C	ENST00000366953.3	-	3	898	c.640A>G	c.(640-642)Agc>Ggc	p.S214G	SLC22A2_ENST00000366952.1_Missense_Mutation_p.S193G|SLC22A2_ENST00000491092.1_5'UTR	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	214					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	CCTGCTTTGCTGACCAGTCCT	0.458																																					p.S214G		Atlas-SNP	.											.	SLC22A2	78	.	0			c.A640G						.						126	117	120					6																	160671613		2203	4300	6503	SO:0001583	missense	6582	exon3			CTTTGCTGACCAG	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"Solute carriers"	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.640A>G	chr6.hg19:g.160671613T>C	ENSP00000355920:p.Ser214Gly	125.0	0.0		87.0	4.0	NM_003058	Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Missense_Mutation	SNP	ENST00000366953.3	hg19	CCDS5276.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268361	0.40095	.	.	ENSG00000112499	ENST00000366953;ENST00000366952	T;T	0.74209	-0.82;-0.82	5.43	5.43	0.79202	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.103676	0.64402	D	0.000002	T	0.69628	0.3132	M	0.70275	2.135	0.36461	D	0.866699	P;B;B	0.36330	0.548;0.337;0.315	P;B;B	0.44673	0.457;0.261;0.169	T	0.69888	-0.5023	10	0.20046	T	0.44	.	15.6414	0.77006	0.0:0.0:0.0:1.0	.	214;214;214	O15244-3;O15244;O15244-2	.;S22A2_HUMAN;.	G	214;193	ENSP00000355920:S214G;ENSP00000355919:S193G	ENSP00000355919:S193G	S	-	1	0	SLC22A2	160591603	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.767000	0.62286	2.279000	0.76181	0.533000	0.62120	AGC	.	.		0.458	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058		C	160671613	T	C	160671613	3	2	112	1	0	0	0	0	1	0	0	0	14465	1580	55	2	1063	2	SLC22A2	6	160671613	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1206930	160671613	10443454	492	17113										
LPA	4018	hgsc.bcm.edu	37	chr6	161022116	161022116	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gatctggatttcggcagtagTtcttgatcaagccactggaa	11	8	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:161022116T>C	ENST00000316300.5	-	19	3004	c.2960A>G	c.(2959-2961)aAc>aGc	p.N987S	LPA_ENST00000447678.1_Missense_Mutation_p.N987S			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3495	Kringle 9. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TCGGCAGTAGTTCTTGATCAA	0.443																																					p.N987S		Atlas-SNP	.											.	LPA	237	.	0			c.A2960G						.						67	70	69					6																	161022116		2164	4289	6453	SO:0001583	missense	4018	exon20			CAGTAGTTCTTGA	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.2960A>G	chr6.hg19:g.161022116T>C	ENSP00000321334:p.Asn987Ser	136.0	0.0		73.0	4.0	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	hg19	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	t	15.59	2.877383	0.51801	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.71934	-0.61;-0.61	2.31	2.31	0.28768	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.79143	0.4396	M	0.92691	3.335	0.20489	N	0.999899	P	0.50156	0.932	D	0.67103	0.949	T	0.67910	-0.5548	9	0.72032	D	0.01	.	6.4002	0.21634	0.0:0.0:0.0:1.0	.	3495	P08519	APOA_HUMAN	S	987	ENSP00000321334:N987S;ENSP00000395608:N987S	ENSP00000321334:N987S	N	-	2	0	LPA	160942106	1.000000	0.71417	0.726000	0.30738	0.371000	0.29859	4.141000	0.58038	1.041000	0.40125	0.172000	0.16884	AAC	.	.		0.443	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		C	161022116	T	C	161022116	3	2	112	1	0	0	0	0	1	0	0	0	8912	1725	60	2	3246	2	LPA	6	161022116	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	350503	161022116	10092951	493	17114										
THBS2	7058	hgsc.bcm.edu	37	chr6	169646335	169646336	+	Frame_Shift_Del	DEL	CA	CA	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcttgcttagaatatcttcCacagagttttcaaacactag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:169646335_169646336delCA	ENST00000366787.3	-	5	899_900	c.650_651delTG	c.(649-651)gtgfs	p.V217fs		NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	217	Heparin-binding. {ECO:0000255}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.V217A(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		GAATATCTTCCACAGAGTTTTC	0.406																																					p.217_218del	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-INDEL	.											.	THBS2	230	.	1	Substitution - Missense(1)	lung(1)	c.651_652del						.																																			SO:0001589	frameshift_variant	7058	exon5			.		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.650_651delTG	chr6.hg19:g.169646337_169646338delCA	ENSP00000355751:p.Val217fs	87.0	0.0		111.0	17.0	NM_003247	A6H8N1|A7E232|Q5RI52	Frame_Shift_Del	DEL	ENST00000366787.3	hg19	CCDS34574.1																																																																																			.	.		0.406	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		-	169646336	CA	-	169646335	7	5	112	1	0	1	0	1	0	0	0	0	15869	581	21	0	2943	0	THBS2	6	169646335	Frame_Shift_Del	DEL	CA	TCGA-DD-A39Y-01A-11D-A20W-10	8624219	169646335	1468732	494	17115										
DLL1	28514	hgsc.bcm.edu	37	chr6	170592565	170592565	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgatgatgctgactgagatgTccttctcacgctggcagttg	12	10	1	3	rs573197356	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:170592565T>C	ENST00000366756.3	-	9	2135	c.1802A>G	c.(1801-1803)gAc>gGc	p.D601G		NM_005618.3	NP_005609.3	O00548	DLL1_HUMAN	delta-like 1 (Drosophila)	601					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|cell-cell signaling (GO:0007267)|compartment pattern specification (GO:0007386)|determination of left/right symmetry (GO:0007368)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|inner ear development (GO:0048839)|left/right axis specification (GO:0070986)|loop of Henle development (GO:0072070)|negative regulation of auditory receptor cell differentiation (GO:0045608)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of myeloid cell differentiation (GO:0045638)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|regulation of cell adhesion (GO:0030155)|somite specification (GO:0001757)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)			NS(2)|breast(1)|endometrium(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	33		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		GACTGAGATGTCCTTCTCACG	0.632																																					p.D601G		Atlas-SNP	.											DLL1,caecum,carcinoma,0,1	DLL1	72	.	0			c.A1802G						.						210	185	193					6																	170592565		2203	4300	6503	SO:0001583	missense	28514	exon9			GAGATGTCCTTCT	AF003522	CCDS5313.1	6q13-q22.33	2008-07-28	2001-12-03		ENSG00000198719	ENSG00000198719			2908	protein-coding gene	gene with protein product		606582	"delta (Drosophila)-like 1"				Standard	NM_005618		Approved		uc003qxm.3	O00548	OTTHUMG00000016078	ENST00000366756.3:c.1802A>G	chr6.hg19:g.170592565T>C	ENSP00000355718:p.Asp601Gly	44.0	0.0		108.0	5.0	NM_005618	B2RAK7|B5M0B3|Q9NU41|Q9UJV2	Missense_Mutation	SNP	ENST00000366756.3	hg19	CCDS5313.1	.	.	.	.	.	.	.	.	.	.	T	18.62	3.663252	0.67700	.	.	ENSG00000198719	ENST00000366756	D	0.86497	-2.13	5.38	2.88	0.33553	.	0.138436	0.64402	D	0.000004	D	0.86556	0.5961	M	0.77616	2.38	0.58432	D	0.999995	D	0.55385	0.971	P	0.57324	0.818	D	0.84563	0.0651	10	0.44086	T	0.13	.	7.5209	0.27626	0.1265:0.0694:0.0:0.804	.	601	O00548	DLL1_HUMAN	G	601	ENSP00000355718:D601G	ENSP00000355718:D601G	D	-	2	0	DLL1	170434490	1.000000	0.71417	0.497000	0.27552	0.992000	0.81027	7.932000	0.87634	0.389000	0.25086	0.533000	0.62120	GAC	.	.		0.632	DLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043254.1			C	170592565	T	C	170592565	3	2	112	1	0	0	0	0	1	0	0	0	4568	1667	58	2	381	2	DLL1	6	170592565	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	946230	170592565	522502	495	17116										
PDCD2	5134	hgsc.bcm.edu	37	chr6	170886715	170886715	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccagtacccaagctgcagcTctcagcacaggtgaagacag	11	13	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:170886715T>C	ENST00000541970.1	-	6	1045	c.967A>G	c.(967-969)Agc>Ggc	p.S323G	PDCD2_ENST00000392090.2_Missense_Mutation_p.S290G	NM_001199462.1|NM_002598.3	NP_001186391.1|NP_002589.2	Q16342	PDCD2_HUMAN	programmed cell death 2	323					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(5)	9		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)		AAGCTGCAGCTCTCAGCACAG	0.473																																					p.S323G	Colon(60;1476 1726 39478)	Atlas-SNP	.											.	PDCD2	13	.	0			c.A967G						.						96	87	90					6																	170886715		2203	4300	6503	SO:0001583	missense	5134	exon6			TGCAGCTCTCAGC	AJ420535	CCDS5316.1, CCDS47521.1, CCDS56460.1, CCDS56461.1, CCDS56462.1, CCDS75557.1	6q27	2008-02-05			ENSG00000071994	ENSG00000071994		"Zinc fingers, MYND-type"	8762	protein-coding gene	gene with protein product		600866				7606924	Standard	NM_002598		Approved	ZMYND7, RP8	uc003qxw.3	Q16342	OTTHUMG00000016083	ENST00000541970.1:c.967A>G	chr6.hg19:g.170886715T>C	ENSP00000439467:p.Ser323Gly	103.0	0.0		167.0	7.0	NM_002598	E9PCU7|F5GYS7|Q58HM9|Q58HN0|Q9UH12	Missense_Mutation	SNP	ENST00000541970.1	hg19	CCDS5316.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.933045	0.92458	.	.	ENSG00000071994	ENST00000541970;ENST00000392090	.	.	.	5.48	5.48	0.80851	Programmed cell death protein 2, C-terminal (1);	0.074954	0.85682	D	0.000000	D	0.83635	0.5297	M	0.93375	3.41	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.966	D	0.88443	0.3043	8	.	.	.	-22.8436	15.5971	0.76595	0.0:0.0:0.0:1.0	.	323;290	Q16342;Q58HN0	PDCD2_HUMAN;.	G	323;290	.	.	S	-	1	0	PDCD2	170728640	1.000000	0.71417	0.969000	0.41365	0.974000	0.67602	7.576000	0.82467	2.072000	0.62099	0.528000	0.53228	AGC	.	.		0.473	PDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043269.2	NM_002598		C	170886715	T	C	170886715	3	2	112	1	0	0	0	0	1	0	0	0	11628	1551	54	2	71	2	PDCD2	6	170886715	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	294150	170886715	228352	496	17117										
C7orf27	221927	hgsc.bcm.edu	37	chr7	2583461	2583461	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggcacacgcgggccagtcaCcccccggcaggcagggctgc					rs531827528		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:2583461delC	ENST00000340611.4	-	5	822	c.566delG	c.(565-567)ggtfs	p.G189fs	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	189					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						GGGCCAGTCACCCCCCGGCAG	0.662																																					p.G189fs		Atlas-INDEL	.											.	BRAT1	57	.	0			c.567delT						.						46	55	52					7																	2583461		2203	4300	6503	SO:0001589	frameshift_variant	221927	exon5			.	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"BRCA1-associated protein required for ATM activation protein 1"	614506	"chromosome 7 open reading frame 27"	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.566delG	chr7.hg19:g.2583461delC	ENSP00000339637:p.Gly189fs	116.0	0.0		163.0	10.0	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Frame_Shift_Del	DEL	ENST00000340611.4	hg19	CCDS5334.1																																																																																			.	.		0.662	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		-	2583461	C	-	2583461	7	5	112	1	0	1	0	1	0	0	0	0	2384	507	18	0	1939	0	C7orf27	7	2583461	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10		2583461	156555202	497	17118										
FOXK1	221937	hgsc.bcm.edu	37	chr7	4722303	4722303	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agttcctcatgcgccagcccAgcgtcaccatcggccgcaac	9	18	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:4722303A>G	ENST00000328914.4	+	1	364	c.364A>G	c.(364-366)Agc>Ggc	p.S122G	FOXK1_ENST00000446823.1_Intron	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GCGCCAGCCCAGCGTCACCAT	0.726																																					p.S122G		Atlas-SNP	.											.	FOXK1	64	.	0			c.A364G						.						18	16	17					7																	4722303		2196	4295	6491	SO:0001583	missense	221937	exon1			CAGCCCAGCGTCA	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.364A>G	chr7.hg19:g.4722303A>G	ENSP00000328720:p.Ser122Gly	66.0	0.0		78.0	5.0	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	hg19	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	a	15.04	2.716642	0.48622	.	.	ENSG00000164916	ENST00000328914;ENST00000545598	T	0.35973	1.28	2.93	-0.257	0.12979	Forkhead-associated (FHA) domain (2);SMAD/FHA domain (1);	0.308602	0.29066	U	0.013244	T	0.18841	0.0452	L	0.32530	0.975	0.80722	D	1	B;B	0.19331	0.035;0.013	B;B	0.19391	0.018;0.025	T	0.06643	-1.0815	10	0.19147	T	0.46	.	2.0879	0.03650	0.3237:0.0:0.2029:0.4735	.	122;5	P85037;F5H8G8	FOXK1_HUMAN;.	G	122;5	ENSP00000328720:S122G	ENSP00000328720:S122G	S	+	1	0	FOXK1	4688829	0.993000	0.37304	0.997000	0.53966	0.967000	0.64934	1.459000	0.35234	0.167000	0.19631	0.228000	0.17796	AGC	.	.		0.726	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			G	4722303	A	G	4722303	3	3	112	1	0	0	0	0	1	0	0	0	6022	188	7	2	366	2	FOXK1	7	4722303	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2138842	4722303	154416360	498	17119										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20698161	20698161	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttggtaggggaaaaaggagcTcaaatgagtggagggcagaa	17	3	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:20698161T>C	ENST00000404938.2	+	14	2221	c.1569T>C	c.(1567-1569)gcT>gcC	p.A523A	ABCB5_ENST00000443026.2_Silent_p.A78A|ABCB5_ENST00000258738.6_Silent_p.A78A|ABCB5_ENST00000406935.1_Silent_p.A78A	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	523	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						AAAAAGGAGCTCAAATGAGTG	0.423																																					p.A523A		Atlas-SNP	.											.	ABCB5	357	.	0			c.T1569C						.						102	93	96					7																	20698161		2203	4300	6503	SO:0001819	synonymous_variant	340273	exon14			AGGAGCTCAAATG	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.1569T>C	chr7.hg19:g.20698161T>C		89.0	0.0		83.0	6.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent	SNP	ENST00000404938.2	hg19	CCDS55090.1																																																																																			.	.		0.423	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		C	20698161	T	C	20698161	2	2	112	1	0	0	0	0	0	0	0	1	44	1538	54	2		2	ABCB5	7	20698161	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	15975858	20698161	138440502	499	17120										
HOXA4	3201	hgsc.bcm.edu	37	chr7	27170333	27170333	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgatgtagttggagtttatcAaaaacgagctcatggtcatt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:27170333delA	ENST00000360046.5	-	1	85	c.20delT	c.(19-21)ttgfs	p.L7fs	HOXA4_ENST00000428284.2_Frame_Shift_Del_p.L7fs|HOXA-AS2_ENST00000521159.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS2_ENST00000521687.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS2_ENST00000517550.1_RNA|HOXA3_ENST00000521401.1_Intron	NM_002141.4	NP_002132.3	Q00056	HXA4_HUMAN	homeobox A4	7					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)	12						GGAGTTTATCAAAAACGAGCT	0.582																																					p.L7fs		Atlas-INDEL	.											.	HOXA4	21	.	0			c.21delG						.						16	16	16					7																	27170333		2201	4291	6492	SO:0001589	frameshift_variant	3201	exon1			.		CCDS5405.1	7p15.2	2011-06-20	2005-12-22		ENSG00000197576	ENSG00000197576		"Homeoboxes / ANTP class : HOXL subclass"	5105	protein-coding gene	gene with protein product		142953	"homeo box A4"	HOX1D, HOX1		1973146, 1358459	Standard	NM_002141		Approved		uc003sym.4	Q00056	OTTHUMG00000023213	ENST00000360046.5:c.20delT	chr7.hg19:g.27170333delA	ENSP00000353151:p.Leu7fs	170.0	0.0		213.0	14.0	NM_002141	A4D180|O43366	Frame_Shift_Del	DEL	ENST00000360046.5	hg19	CCDS5405.1																																																																																			.	.		0.582	HOXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059534.4			-	27170333	A	-	27170333	7	5	112	1	0	1	0	1	0	0	0	0	7303	131	5	0	950	0	HOXA4	7	27170333	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	6472172	27170333	131968330	500	17121										
HOXA9	3205	hgsc.bcm.edu	37	chr7	27204507	27204507	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agacacttactgggatcgatGgggggcttgtctccgccgct					rs370679767		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:27204507delG	ENST00000343483.6	-	1	642	c.570delC	c.(568-570)cccfs	p.P190fs	RP1-170O19.20_ENST00000470747.4_Frame_Shift_Del_p.P30fs|RP1-170O19.20_ENST00000465941.1_Intron|HOXA9_ENST00000497089.1_Intron|HOXA9_ENST00000396345.1_3'UTR	NM_152739.3	NP_689952.1	P31269	HXA9_HUMAN	homeobox A9	190					endothelial cell activation (GO:0042118)|multicellular organismal development (GO:0007275)|negative regulation of myeloid cell differentiation (GO:0045638)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)	p.P190P(1)		central_nervous_system(1)|endometrium(1)|lung(5)|prostate(1)	8						TGGGATCGATGGGGGGCTTGT	0.587			T	"NUP98, MSI2"	AML*																																p.I191fs		Atlas-INDEL	.		Dom	yes		7	7p15-p14.2	3205	homeo box A9		L	.	HOXA9	20	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.571delA						.						45	52	50					7																	27204507		2203	4300	6503	SO:0001589	frameshift_variant	3205	exon1			.		CCDS5409.1	7p15.2	2011-06-20	2005-12-22		ENSG00000078399	ENSG00000078399		"Homeoboxes / ANTP class : HOXL subclass"	5109	protein-coding gene	gene with protein product		142956	"homeo box A9"	HOX1G, HOX1		1973146, 1358459	Standard	NM_152739		Approved		uc003syt.3	P31269	OTTHUMG00000023220	ENST00000343483.6:c.570delC	chr7.hg19:g.27204507delG	ENSP00000343619:p.Pro190fs	88.0	0.0		157.0	11.0	NM_152739	O43369|O43429|Q99820	Frame_Shift_Del	DEL	ENST00000343483.6	hg19	CCDS5409.1																																																																																			.	.		0.587	HOXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358706.2			-	27204507	G	-	27204507	7	5	112	1	0	1	0	1	0	0	0	0	7307	1335	47	0	256	0	HOXA9	7	27204507	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	34174	27204507	131934156	501	17122										
TAX1BP1	8887	hgsc.bcm.edu	37	chr7	27827096	27827096	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgtcagaggtccagactttAaaaaatttagatgggaacaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:27827096delA	ENST00000396319.2	+	8	1000	c.912delA	c.(910-912)ttafs	p.L304fs	TAX1BP1_ENST00000265393.6_Frame_Shift_Del_p.L304fs|TAX1BP1_ENST00000543117.1_Frame_Shift_Del_p.L304fs|TAX1BP1_ENST00000433216.2_Frame_Shift_Del_p.L147fs|TAX1BP1_ENST00000409980.1_Frame_Shift_Del_p.L304fs	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	304					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			TCCAGACTTTAAAAAATTTAG	0.343																																					p.L304X		Atlas-INDEL	.											.	TAX1BP1	71	.	0			c.911delT						.						72	77	75					7																	27827096		2203	4300	6503	SO:0001589	frameshift_variant	8887	exon8			.	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.912delA	chr7.hg19:g.27827096delA	ENSP00000379612:p.Leu304fs	116.0	0.0		171.0	14.0	NM_001206901	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Frame_Shift_Del	DEL	ENST00000396319.2	hg19	CCDS5415.1																																																																																			.	.		0.343	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		-	27827096	A	-	27827096	7	5	112	1	0	1	0	1	0	0	0	0	15609	359	13	0	938	0	TAX1BP1	7	27827096	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	622589	27827096	131311567	502	17123										
BBS9	27241	hgsc.bcm.edu	37	chr7	33217199	33217199	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatggatcatttggtggtgtAaaaggtaatttgcttttaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:33217199delA	ENST00000242067.6	+	5	959	c.438delA	c.(436-438)gtafs	p.V146fs	RNA5SP229_ENST00000410809.1_RNA|BBS9_ENST00000396127.2_Frame_Shift_Del_p.V146fs|BBS9_ENST00000425508.2_Frame_Shift_Del_p.V101fs|BBS9_ENST00000355070.2_Frame_Shift_Del_p.V146fs|BBS9_ENST00000354265.4_Frame_Shift_Del_p.V146fs|BBS9_ENST00000350941.3_Frame_Shift_Del_p.V146fs	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	146					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			TTGGTGGTGTAAAAGGTAATT	0.343									Bardet-Biedl syndrome																												p.V146fs		Atlas-INDEL	.											.	BBS9	194	.	0			c.437delT						.						151	141	145					7																	33217199		2203	4300	6503	SO:0001589	frameshift_variant	27241	exon5	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	.		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"parathyroid hormone responsive B1 gene"	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.438delA	chr7.hg19:g.33217199delA	ENSP00000242067:p.Val146fs	75.0	0.0		99.0	11.0	NM_014451	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Frame_Shift_Del	DEL	ENST00000242067.6	hg19	CCDS43566.1																																																																																			.	.		0.343	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1			-	33217199	A	-	33217199	7	5	112	1	0	1	0	1	0	0	0	0	1342	349	13	0	452	0	BBS9	7	33217199	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5390103	33217199	125921464	503	17124										
ELMO1	9844	hgsc.bcm.edu	37	chr7	37252948	37252948	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgagcactcacctggtcctGggggtccattttggtcatca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:37252948delG	ENST00000310758.4	-	12	1593	c.946delC	c.(946-948)cagfs	p.Q316fs	ELMO1_ENST00000448602.1_Frame_Shift_Del_p.Q316fs|ELMO1_ENST00000442504.1_Frame_Shift_Del_p.Q316fs	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	316					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						ACCTGGTCCTGGGGGTCCATT	0.488																																					p.Q316fs		Atlas-INDEL	.											.	ELMO1	141	.	0			c.947delA						.						136	122	127					7																	37252948		2203	4300	6503	SO:0001589	frameshift_variant	9844	exon12			.	AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"Engulfment and cell motility proteins"	16286	protein-coding gene	gene with protein product		606420	"engulfment and cell motility 1 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.946delC	chr7.hg19:g.37252948delG	ENSP00000312185:p.Gln316fs	142.0	0.0		232.0	15.0	NM_014800	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Frame_Shift_Del	DEL	ENST00000310758.4	hg19	CCDS5449.1																																																																																			.	.		0.488	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442		-	37252948	G	-	37252948	7	5	112	1	0	1	0	1	0	0	0	0	5067	1357	47	0	1281	0	ELMO1	7	37252948	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	4035749	37252948	121885715	504	17125										
RALA	5898	hgsc.bcm.edu	37	chr7	39745787	39745787	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacagcaaagaaaagaatggAaaaaagaagaggaaaagttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:39745787delA	ENST00000005257.2	+	5	944	c.564delA	c.(562-564)ggafs	p.G188fs	AC004837.5_ENST00000435766.1_RNA|RALA_ENST00000468201.1_3'UTR	NM_005402.3	NP_005393.2	P11233	RALA_HUMAN	v-ral simian leukemia viral oncogene homolog A (ras related)	188					actin cytoskeleton reorganization (GO:0031532)|chemotaxis (GO:0006935)|cytokinesis (GO:0000910)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|membrane raft localization (GO:0051665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of filopodium assembly (GO:0051491)|Ras protein signal transduction (GO:0007265)|regulation of exocytosis (GO:0017157)|signal transduction (GO:0007165)|viral process (GO:0016032)	cell surface (GO:0009986)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(9)|skin(3)	16						AAAAGAATGGAAAAAAGAAGA	0.308																																					p.G188fs		Atlas-INDEL	.											.	RALA	39	.	0			c.563delG						.						89	99	96					7																	39745787		2203	4296	6499	SO:0001589	frameshift_variant	5898	exon5			.		CCDS5460.1	7p22-p15	2014-05-09			ENSG00000006451	ENSG00000006451			9839	protein-coding gene	gene with protein product	"RAS-like protein A", "Ras-related protein Ral-A", "Ras family small GTP binding protein RALA", "ras related GTP binding protein A"	179550		RAL		3292391	Standard	NM_005402		Approved		uc003thd.3	P11233	OTTHUMG00000128775	ENST00000005257.2:c.564delA	chr7.hg19:g.39745787delA	ENSP00000005257:p.Gly188fs	228.0	0.0		330.0	23.0	NM_005402	A4D1W3	Frame_Shift_Del	DEL	ENST00000005257.2	hg19	CCDS5460.1																																																																																			.	.		0.308	RALA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250696.2	NM_005402		-	39745787	A	-	39745787	7	5	112	1	0	1	0	1	0	0	0	0	13025	233	9	0	578	0	RALA	7	39745787	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2492839	39745787	119392876	505	17126										
URGCP	55665	hgsc.bcm.edu	37	chr7	43916637	43916637	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtagttgggcatgtgccccgTtttttctaacctcagaaatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:43916637delT	ENST00000453200.1	-	6	2918	c.2425delA	c.(2425-2427)acgfs	p.T809fs	URGCP_ENST00000443736.1_Frame_Shift_Del_p.T766fs|URGCP_ENST00000497914.1_5'UTR|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000447717.3_Frame_Shift_Del_p.T766fs|URGCP_ENST00000223341.7_Frame_Shift_Del_p.T766fs|URGCP_ENST00000402306.3_Frame_Shift_Del_p.T800fs|URGCP_ENST00000336086.6_Frame_Shift_Del_p.T766fs			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	809	VLIG-type G.				cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						ATGTGCCCCGTTTTTTCTAAC	0.502																																					p.T809fs		Atlas-INDEL	.											.	URGCP	170	.	0			c.2426delC						.						112	107	109					7																	43916637		1955	4143	6098	SO:0001589	frameshift_variant	55665	exon6			.		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.2425delA	chr7.hg19:g.43916637delT	ENSP00000396918:p.Thr809fs	103.0	0.0		196.0	12.0	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Frame_Shift_Del	DEL	ENST00000453200.1	hg19	CCDS47578.1																																																																																			.	.		0.502	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		-	43916637	T	-	43916637	7	5	112	1	0	1	0	1	0	0	0	0	17041	1725	60	0	374	0	URGCP	7	43916637	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	4170850	43916637	115222026	506	17127										
FIGNL1	63979	hgsc.bcm.edu	37	chr7	50514614	50514614	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccaacagagagtctttgaaTtttttgccagcttgcatcat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:50514614delT	ENST00000419119.1	-	2	1925	c.372delA	c.(370-372)aaafs	p.K124fs	FIGNL1_ENST00000395556.2_Frame_Shift_Del_p.K124fs|FIGNL1_ENST00000433017.1_Frame_Shift_Del_p.K124fs|FIGNL1_ENST00000356889.4_Frame_Shift_Del_p.K124fs|FIGNL1_ENST00000435566.1_3'UTR			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	124					ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				AGTCTTTGAATTTTTTGCCAG	0.388																																					p.F125fs		Atlas-Indel,Pindel	.											.	FIGNL1	73	.	0			c.373delT						.						95	96	96					7																	50514614		2203	4300	6503	SO:0001589	frameshift_variant	63979	exon4			.	AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"ATPases / AAA-type"	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.372delA	chr7.hg19:g.50514614delT	ENSP00000410811:p.Lys124fs	102.0	0.0		157.0	10.0	NM_022116	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Frame_Shift_Del	DEL	ENST00000419119.1	hg19	CCDS5510.1																																																																																			.	.		0.388	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762		-	50514614	T	-	50514614	7	5	112	1	0	1	0	1	0	0	0	0	5900	1490	52	0	1656	0	FIGNL1	7	50514614	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	6597977	50514614	108624049	507	17128										
GUSB	2990	hgsc.bcm.edu	37	chr7	65429409	65429409	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atggtactgctctagcagacTtttctggtactcttcagtga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:65429409delT	ENST00000304895.4	-	11	1820	c.1690delA	c.(1690-1692)agtfs	p.S564fs	GUSB_ENST00000421103.1_Frame_Shift_Del_p.S418fs|GUSB_ENST00000345660.6_Frame_Shift_Del_p.S513fs	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	564					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TCTAGCAGACTTTTCTGGTAC	0.413																																					p.S564fs		Atlas-INDEL	.											.	GUSB	52	.	0			c.1691delG						.						55	49	51					7																	65429409		2203	4299	6502	SO:0001589	frameshift_variant	2990	exon11			.	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1690delA	chr7.hg19:g.65429409delT	ENSP00000302728:p.Ser564fs	122.0	0.0		155.0	11.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Frame_Shift_Del	DEL	ENST00000304895.4	hg19	CCDS5530.1																																																																																			.	.		0.413	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		-	65429409	T	-	65429409	7	5	112	1	0	1	0	1	0	0	0	0	6911	1609	56	0	273	0	GUSB	7	65429409	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	14914795	65429409	93709254	508	17129										
LIMK1	3984	hgsc.bcm.edu	37	chr7	73521482	73521482	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggccgtcggacctcatccacGgggaggtgctgggcaagggc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:73521482delG	ENST00000336180.2	+	8	1075	c.1024delG	c.(1024-1026)gggfs	p.G342fs	LIMK1_ENST00000418310.1_Frame_Shift_Del_p.G372fs|LIMK1_ENST00000538333.3_Frame_Shift_Del_p.G308fs	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	342	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	CCTCATCCACGGGGAGGTGCT	0.677																																					p.H341fs		Atlas-INDEL	.											LIMK1,NS,carcinoma,0,1	LIMK1	55	.	0			c.1023delC						.						49	48	49					7																	73521482		2203	4300	6503	SO:0001589	frameshift_variant	3984	exon8			.	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.1024delG	chr7.hg19:g.73521482delG	ENSP00000336740:p.Gly342fs	151.0	0.0		169.0	11.0	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Frame_Shift_Del	DEL	ENST00000336180.2	hg19	CCDS5563.1																																																																																			.	.		0.677	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		-	73521482	G	-	73521482	7	5	112	1	0	1	0	1	0	0	0	0	8810	1116	39	0	1054	0	LIMK1	7	73521482	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	8092073	73521482	85617181	509	17130										
RFC2	5982	hgsc.bcm.edu	37	chr7	73651756	73651756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctcctttaccagcagtgggTggggctcgtcacagacctgg	13	12	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:73651756T>C	ENST00000055077.3	-	9	836	c.776A>G	c.(775-777)cAc>cGc	p.H259R	RFC2_ENST00000352131.3_Missense_Mutation_p.H225R	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	259					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						CAGCAGTGGGTGGGGCTCGTC	0.592																																					p.H259R		Atlas-SNP	.											.	RFC2	27	.	0			c.A776G						.						77	55	62					7																	73651756		2203	4299	6502	SO:0001583	missense	5982	exon9			AGTGGGTGGGGCT		CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"ATPases / AAA-type"	9970	protein-coding gene	gene with protein product	"activator 1"	600404	"replication factor C (activator 1) 2 (40kD)"			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.776A>G	chr7.hg19:g.73651756T>C	ENSP00000055077:p.His259Arg	63.0	0.0		123.0	5.0	NM_181471	B5BU07|D3DXG3|P32846|Q9BU93	Missense_Mutation	SNP	ENST00000055077.3	hg19	CCDS5568.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.972365	0.74246	.	.	ENSG00000049541	ENST00000352131;ENST00000055077	T;T	0.42900	0.96;0.96	5.16	5.16	0.70880	Replication factor C (1);DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.58736	0.2143	L	0.59436	1.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.54807	-0.8238	10	0.27082	T	0.32	.	14.1544	0.65407	0.0:0.0:0.0:1.0	.	225;225;259	P35250-2;Q75MT5;P35250	.;.;RFC2_HUMAN	R	225;259	ENSP00000275627:H225R;ENSP00000055077:H259R	ENSP00000055077:H259R	H	-	2	0	RFC2	73289692	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	7.578000	0.82498	2.081000	0.62600	0.533000	0.62120	CAC	.	.		0.592	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471		C	73651756	T	C	73651756	3	2	112	1	0	0	0	0	1	0	0	0	13260	1696	59	2	300	2	RFC2	7	73651756	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	130274	73651756	85486907	510	17131										
HIP1	3092	hgsc.bcm.edu	37	chr7	75221727	75221727	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggaggagtttgtggaacacaTggcagaacttccagcagagc	14	8	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:75221727T>C	ENST00000336926.6	-	3	316	c.290A>G	c.(289-291)cAt>cGt	p.H97R	HIP1_ENST00000434438.2_Missense_Mutation_p.H97R	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	97	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GTGGAACACATGGCAGAACTT	0.577			T	PDGFRB	CMML																																p.H97R		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A290G						.						83	67	73					7																	75221727		2203	4300	6503	SO:0001583	missense	3092	exon3			AACACATGGCAGA	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.290A>G	chr7.hg19:g.75221727T>C	ENSP00000336747:p.His97Arg	77.0	0.0		92.0	4.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	hg19	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.817059	0.90790	.	.	ENSG00000127946	ENST00000336926;ENST00000434438;ENST00000420909	T;T;T	0.31510	1.49;1.49;1.49	5.78	5.78	0.91487	ENTH/VHS (2);ANTH (1);Epsin-like, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.54351	0.1853	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51148	-0.8742	10	0.23891	T	0.37	-27.4743	14.9254	0.70875	0.0:0.0:0.0:1.0	.	97	O00291	HIP1_HUMAN	R	97;97;68	ENSP00000336747:H97R;ENSP00000410300:H97R;ENSP00000414280:H68R	ENSP00000336747:H97R	H	-	2	0	HIP1	75059663	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	7.698000	0.84413	2.208000	0.71279	0.455000	0.32223	CAT	.	.		0.577	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		C	75221727	T	C	75221727	3	2	112	1	0	0	0	0	1	0	0	0	7123	1464	51	2	2939	2	HIP1	7	75221727	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1569971	75221727	83916936	511	17132										
GNAI1	2770	hgsc.bcm.edu	37	chr7	79842146	79842146	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atctctttgaagaaaaaatcAaaaagagccctctcactata							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:79842146delA	ENST00000351004.3	+	7	1208	c.835delA	c.(835-837)aaafs	p.K280fs	GNAI1_ENST00000457358.2_Frame_Shift_Del_p.K228fs	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	280					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						AGAAAAAATCAAAAAGAGCCC	0.328																																					p.I278fs		Atlas-INDEL	.											.	GNAI1	44	.	0			c.834delC						.						66	74	71					7																	79842146		2203	4294	6497	SO:0001589	frameshift_variant	2770	exon7			.	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"Gi1 protein alpha subunit"	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.835delA	chr7.hg19:g.79842146delA	ENSP00000343027:p.Lys280fs	183.0	0.0		246.0	15.0	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Frame_Shift_Del	DEL	ENST00000351004.3	hg19	CCDS5595.1																																																																																			.	.		0.328	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		-	79842146	A	-	79842146	7	5	112	1	0	1	0	1	0	0	0	0	6512	131	5	0	861	0	GNAI1	7	79842146	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4620419	79842146	79296517	512	17133										
GNAT3	346562	hgsc.bcm.edu	37	chr7	80103636	80103636	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttttcactcgagaatggagaAcatcttgttcatttggcaca	8	8	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:80103636A>G	ENST00000398291.3	-	5	614	c.521T>C	c.(520-522)gTt>gCt	p.V174A	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	174					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						AGAATGGAGAACATCTTGTTC	0.313																																					p.V174A		Atlas-SNP	.											.	GNAT3	65	.	0			c.T521C						.						67	62	64					7																	80103636		1835	4106	5941	SO:0001583	missense	346562	exon5			TGGAGAACATCTT		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.521T>C	chr7.hg19:g.80103636A>G	ENSP00000381339:p.Val174Ala	90.0	0.0		95.0	4.0	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Missense_Mutation	SNP	ENST00000398291.3	hg19	CCDS47625.1	.	.	.	.	.	.	.	.	.	.	A	32	5.115798	0.94339	.	.	ENSG00000214415	ENST00000398291	D	0.90385	-2.66	5.99	5.99	0.97316	G protein alpha subunit, helical insertion (1);	0.069591	0.56097	U	0.000026	D	0.96119	0.8735	M	0.92219	3.285	0.80722	D	1	P	0.52061	0.95	P	0.62014	0.897	D	0.96744	0.9549	9	.	.	.	.	16.1526	0.81632	1.0:0.0:0.0:0.0	.	174	A8MTJ3	GNAT3_HUMAN	A	174	ENSP00000381339:V174A	.	V	-	2	0	GNAT3	79941572	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	8.987000	0.93497	2.300000	0.77407	0.533000	0.62120	GTT	.	.		0.313	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370		G	80103636	A	G	80103636	3	3	112	1	0	0	0	0	1	0	0	0	6521	43	2	2	557	2	GNAT3	7	80103636	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	261490	80103636	79035027	513	17134										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84644405	84644405	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taggagcatatcgagagcatGcatttccatcccaggcacag	10	11	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:84644405G>A	ENST00000284136.6	-	14	1716	c.1673C>T	c.(1672-1674)gCa>gTa	p.A558V	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	558	PSI.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						TCGAGAGCATGCATTTCCATC	0.453																																					p.A558V	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.C1673T						.						126	114	118					7																	84644405		2203	4300	6503	SO:0001583	missense	223117	exon14			GAGCATGCATTTC	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1673C>T	chr7.hg19:g.84644405G>A	ENSP00000284136:p.Ala558Val	148.0	0.0		157.0	34.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	hg19	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.760243	0.69763	.	.	ENSG00000153993	ENST00000284136	T	0.21932	1.98	5.75	5.75	0.90469	.	0.381500	0.32935	N	0.005473	T	0.23054	0.0557	L	0.50993	1.605	0.80722	D	1	B	0.33583	0.418	B	0.24394	0.053	T	0.02610	-1.1134	10	0.72032	D	0.01	.	19.9361	0.97143	0.0:0.0:1.0:0.0	.	558	O95025	SEM3D_HUMAN	V	558	ENSP00000284136:A558V	ENSP00000284136:A558V	A	-	2	0	SEMA3D	84482341	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	7.674000	0.83992	2.720000	0.93068	0.561000	0.74099	GCA	.	.		0.453	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		A	84644405	G	A	84644405	3	1	112	1	0	0	0	0	1	0	0	0	14042	1319	46	3	676	3	SEMA3D	7	84644405	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	4540769	84644405	74494258	514	17135										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91726097	91726097	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actactgaacgaatcccagcAaaaaatagaatcacagagaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:91726097delA	ENST00000359028.2	+	41	10061	c.9836delA	c.(9835-9837)caafs	p.Q3279fs	AKAP9_ENST00000356239.3_Frame_Shift_Del_p.Q3275fs|AKAP9_ENST00000358100.2_Frame_Shift_Del_p.Q3225fs			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3279					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAATCCCAGCAAAAAATAGAA	0.383			T	BRAF	papillary thyroid																																p.Q3275fs		Atlas-INDEL	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	AKAP9_ENST00000356239,NS,carcinoma,0,2	AKAP9	788	.	0			c.9823delC						.						70	73	72					7																	91726097		2203	4300	6503	SO:0001589	frameshift_variant	10142	exon41			.	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.9836delA	chr7.hg19:g.91726097delA	ENSP00000351922:p.Gln3279fs	104.0	0.0		152.0	10.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Frame_Shift_Del	DEL	ENST00000359028.2	hg19																																																																																				.	.		0.383	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		-	91726097	A	-	91726097	7	5	112	1	0	1	0	1	0	0	0	0	459	130	5	0	9986	0	AKAP9	7	91726097	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	7081692	91726097	67412566	515	17136										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91726654	91726654	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagaaagtagaagaattctgTatcagaaccttaatgaggta	10	4	2	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:91726654T>A	ENST00000359028.2	+	41	10618	c.10393T>A	c.(10393-10395)Tat>Aat	p.Y3465N	AKAP9_ENST00000356239.3_Missense_Mutation_p.Y3461N|AKAP9_ENST00000358100.2_Missense_Mutation_p.Y3411N			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3465					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAGAATTCTGTATCAGAACCT	0.343			T	BRAF	papillary thyroid																																p.Y3461N		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.T10381A						.						27	28	28					7																	91726654		2156	4283	6439	SO:0001583	missense	10142	exon41			ATTCTGTATCAGA	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.10393T>A	chr7.hg19:g.91726654T>A	ENSP00000351922:p.Tyr3465Asn	40.0	0.0		56.0	4.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	T	10.60	1.395114	0.25205	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.03386	4.04;4.04;4.05;3.95	5.47	2.87	0.33458	.	0.418583	0.17737	N	0.163696	T	0.04815	0.0130	L	0.57536	1.79	0.21220	N	0.999752	B;B;B;B;B	0.27416	0.035;0.178;0.112;0.178;0.178	B;B;B;B;B	0.33521	0.021;0.165;0.05;0.107;0.107	T	0.40270	-0.9572	10	0.09084	T	0.74	.	8.0957	0.30826	0.127:0.0:0.2348:0.6382	.	736;3465;3465;3461;3453	B3KQF9;Q99996-6;Q99996;Q99996-2;Q99996-3	.;.;AKAP9_HUMAN;.;.	N	3461;3465;3411;3465;1307	ENSP00000348573:Y3461N;ENSP00000351922:Y3465N;ENSP00000350813:Y3411N;ENSP00000378042:Y1307N	ENSP00000348573:Y3461N	Y	+	1	0	AKAP9	91564590	0.636000	0.27207	0.999000	0.59377	0.989000	0.77384	0.696000	0.25541	0.975000	0.38392	0.533000	0.62120	TAT	.	.		0.343	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		A	91726654	T	A	91726654	3	1	112	1	0	0	0	0	1	0	0	0	459	1638	57	4	10543	4	AKAP9	7	91726654	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	557	91726654	67412009	516	17137										
SGCE	8910	hgsc.bcm.edu	37	chr7	94232644	94232644	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgtaaaattgagtacgaaaTtttttatcacatgttattac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:94232644delT	ENST00000265735.7	-	6	893	c.783delA	c.(781-783)aaafs	p.K261fs	SGCE_ENST00000415788.2_Frame_Shift_Del_p.K297fs|SGCE_ENST00000447873.1_Frame_Shift_Del_p.K261fs|SGCE_ENST00000445866.2_Frame_Shift_Del_p.K261fs|SGCE_ENST00000428696.2_Frame_Shift_Del_p.K261fs|SGCE_ENST00000437425.2_Frame_Shift_Del_p.K220fs	NM_003919.2	NP_003910.1	O43556	SGCE_HUMAN	sarcoglycan, epsilon	261	Cys-rich.				cell-matrix adhesion (GO:0007160)|muscle organ development (GO:0007517)	cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|dystrophin-associated glycoprotein complex (GO:0016010)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	14	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GAGTACGAAATTTTTTATCAC	0.318																																					p.F262fs		Atlas-INDEL	.											.	SGCE	68	.	0			c.784delT						.						83	80	81					7																	94232644		2203	4300	6503	SO:0001589	frameshift_variant	8910	exon6			.	AF036364	CCDS5637.1, CCDS47642.1, CCDS47643.1, CCDS75634.1	7q21.3	2014-09-17			ENSG00000127990	ENSG00000127990			10808	protein-coding gene	gene with protein product		604149		DYT11		9475163, 9405466	Standard	NM_001099401		Approved		uc003unn.2	O43556	OTTHUMG00000022828	ENST00000265735.7:c.783delA	chr7.hg19:g.94232644delT	ENSP00000265735:p.Lys261fs	142.0	0.0		166.0	12.0	NM_001099401	B2R8N2|D6W5Q8|E9PF60|G5E9K6|Q6L8P0|Q75MH8|Q8NFG8|Q8WW28	Frame_Shift_Del	DEL	ENST00000265735.7	hg19	CCDS5637.1																																																																																			.	.		0.318	SGCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255251.2			-	94232644	T	-	94232644	7	5	112	1	0	1	0	1	0	0	0	0	14217	1490	52	0	706	0	SGCE	7	94232644	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2505990	94232644	64906019	517	17138										
ZNF498	221785	hgsc.bcm.edu	37	chr7	99219096	99219096	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtggaggtcaagcctgaatGggggatgccccctggggaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:99219096delG	ENST00000394152.2	+	5	815	c.488delG	c.(487-489)tggfs	p.W163fs	ZSCAN25_ENST00000334715.3_Frame_Shift_Del_p.W163fs|ZSCAN25_ENST00000262941.6_Frame_Shift_Del_p.W163fs|ZSCAN25_ENST00000466948.1_Intron	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	163					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AAGCCTGAATGGGGGATGCCC	0.622																																					p.W163fs		Atlas-INDEL	.											.	.	.	.	0			c.487delT						.						65	61	63					7																	99219096		2203	4300	6503	SO:0001589	frameshift_variant	221785	exon5			.	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"-", "Zinc fingers, C2H2-type"	21961	protein-coding gene	gene with protein product			"zinc finger protein 498"	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.488delG	chr7.hg19:g.99219096delG	ENSP00000377708:p.Trp163fs	120.0	0.0		159.0	10.0	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Frame_Shift_Del	DEL	ENST00000394152.2	hg19	CCDS5671.2																																																																																			.	.		0.622	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		-	99219096	G	-	99219096	7	5	112	1	0	1	0	1	0	0	0	0	17962	1357	47	0	494	0	ZNF498	7	99219096	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	4986452	99219096	59919567	518	17139										
CYP3A4	1576	hgsc.bcm.edu	37	chr7	99364063	99364063	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagctgaaggaaatccactcGgtgctagaagcaaaaagaga	11	8	0	3	rs138105638		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:99364063G>A	ENST00000336411.2	-	9	985	c.802C>T	c.(802-804)Cga>Tga	p.R268*	CYP3A4_ENST00000354593.2_Nonsense_Mutation_p.R118*|RP11-757A13.1_ENST00000608397.1_RNA	NM_001202855.2|NM_017460.5	NP_001189784.1|NP_059488.2	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 4	268					alkaloid catabolic process (GO:0009822)|androgen metabolic process (GO:0008209)|calcitriol biosynthetic process from calciol (GO:0036378)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|lipid metabolic process (GO:0006629)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	albendazole monooxygenase activity (GO:0047638)|caffeine oxidase activity (GO:0034875)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)|quinine 3-monooxygenase activity (GO:0050591)|steroid binding (GO:0005496)|steroid hydroxylase activity (GO:0008395)|taurochenodeoxycholate 6alpha-hydroxylase activity (GO:0033780)|testosterone 6-beta-hydroxylase activity (GO:0050649)|vitamin D 24-hydroxylase activity (GO:0070576)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(3)|central_nervous_system(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Abiraterone(DB05812)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetazolamide(DB00819)|Adinazolam(DB00546)|ado-trastuzumab emtansine(DB05773)|Albendazole(DB00518)|Alclometasone(DB00240)|Aldesleukin(DB00041)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Alimemazine(DB01246)|Aliskiren(DB01258)|Allylestrenol(DB01431)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alosetron(DB00969)|Alprazolam(DB00404)|Ambroxol(DB06742)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Arsenic trioxide(DB01169)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atazanavir(DB01072)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Avanafil(DB06237)|Axitinib(DB06626)|Azatadine(DB00719)|Azelastine(DB00972)|Azithromycin(DB00207)|Bedaquiline(DB08903)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bezafibrate(DB01393)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bisoprolol(DB00612)|Boceprevir(DB08873)|Bortezomib(DB00188)|Bosentan(DB00559)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Brinzolamide(DB01194)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Brompheniramine(DB00835)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Busulfan(DB01008)|Cabazitaxel(DB06772)|Cabergoline(DB00248)|Cabozantinib(DB08875)|Caffeine(DB00201)|Calcitriol(DB00136)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Caspofungin(DB00520)|Cefradine(DB01333)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chenodeoxycholic acid(DB06777)|Chloramphenicol(DB00446)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clemastine(DB00283)|Clevidipine(DB04920)|Clindamycin(DB01190)|Clobazam(DB00349)|Clofazimine(DB00845)|Clofibrate(DB00636)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonazepam(DB01068)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Colchicine(DB01394)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cortisone acetate(DB01380)|Crizotinib(DB08865)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Cytarabine(DB00987)|Dabrafenib(DB08912)|Dalfopristin(DB01764)|Danazol(DB01406)|Dantrolene(DB01219)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Deferasirox(DB01609)|Delavirdine(DB00705)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Dicloxacillin(DB00485)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydrocodeine(DB01551)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Disopyramide(DB00280)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dofetilide(DB00204)|Dolasetron(DB00757)|Dolutegravir(DB08930)|Domperidone(DB01184)|Donepezil(DB00843)|Dorzolamide(DB00869)|Doxepin(DB01142)|Doxorubicin(DB00997)|Doxycycline(DB00254)|Dronabinol(DB00470)|Dronedarone(DB04855)|Dutasteride(DB01126)|Econazole(DB01127)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Epinephrine(DB00668)|Eplerenone(DB00700)|Ergocalciferol(DB00153)|Ergoloid mesylate(DB01049)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Estradiol valerate/Dienogest(DB08866)|Estradiol(DB00783)|Estramustine(DB01196)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Etravirine(DB06414)|Everolimus(DB01590)|Exemestane(DB00990)|Ezetimibe(DB00973)|Famciclovir(DB00426)|Felbamate(DB00949)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Finasteride(DB01216)|Fingolimod(DB08868)|Flucloxacillin(DB00301)|Fluconazole(DB00196)|Flunisolide(DB00180)|Flunitrazepam(DB01544)|Fluorometholone(DB00324)|Fluoxetine(DB00472)|Flurazepam(DB00690)|Flutamide(DB00499)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosamprenavir(DB01319)|Fosphenytoin(DB01320)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Glipizide(DB01067)|Glyburide(DB01016)|Granisetron(DB00889)|Griseofulvin(DB00400)|Guanethidine(DB01170)|Guanfacine(DB01018)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Hydralazine(DB01275)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|Indacaterol(DB05039)|Indapamide(DB00808)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Irinotecan(DB00762)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ixabepilone(DB04845)|Josamycin(DB01321)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Levomethadyl Acetate(DB01227)|Levomilnacipran(DB08918)|Levonorgestrel(DB00367)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Lisuride(DB00589)|Lomitapide(DB08827)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumefantrine(DB06708)|Lurasidone(DB08815)|MACITENTAN(DB08932)|Maraviroc(DB04835)|Mebendazole(DB00643)|Medroxyprogesterone Acetate(DB00603)|Mefloquine(DB00358)|Meloxicam(DB00814)|Mequitazine(DB01071)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Methylergometrine(DB00353)|Methylprednisolone(DB00959)|Methyltestosterone(DB06710)|Metronidazole(DB00916)|Metyrapone(DB01011)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Mitoxantrone(DB01204)|Modafinil(DB00745)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nafcillin(DB00607)|Naloxone(DB01183)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nitric Oxide(DB00435)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Omeprazole(DB00338)|Ondansetron(DB00904)|Orlistat(DB01083)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paramethasone(DB01384)|Paricalcitol(DB00910)|Pazopanib(DB06589)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perampanel(DB08883)|Pergolide(DB01186)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenoxybenzamine(DB00925)|Phenprocoumon(DB00946)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pilocarpine(DB01085)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Prazepam(DB01588)|Praziquantel(DB01058)|Prednisolone(DB00860)|Prednisone(DB00635)|Primaquine(DB01087)|Primidone(DB00794)|Probenecid(DB01032)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Pyridostigmine(DB00545)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Quinupristin(DB01369)|Rabeprazole(DB01129)|Raloxifene(DB00481)|Ramelteon(DB00980)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Regorafenib(DB08896)|Repaglinide(DB00912)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rifapentine(DB01201)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Rimonabant(DB06155)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rivastigmine(DB00989)|Rolitetracycline(DB01301)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosuvastatin(DB01098)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Rufinamide(DB06201)|Ruxolitinib(DB08877)|Salbutamol(DB01001)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sevoflurane(DB01236)|Sibutramine(DB01105)|Sildenafil(DB00203)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Sitaxentan(DB06268)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sufentanil(DB00708)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfanilamide(DB00259)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tasosartan(DB01349)|Telaprevir(DB05521)|Telithromycin(DB00976)|Temazepam(DB00231)|Temozolomide(DB00853)|Temsirolimus(DB06287)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Thiopental(DB00599)|Thiotepa(DB04572)|Tiagabine(DB00906)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tioconazole(DB01007)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tofisopam(DB08811)|Tolterodine(DB01036)|Tolvaptan(DB06212)|Topiramate(DB00273)|Topotecan(DB01030)|Toremifene(DB00539)|Trabectedin(DB05109)|Tramadol(DB00193)|Trametinib(DB08911)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Tretinoin(DB00755)|Triamcinolone(DB00620)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vandetanib(DB05294)|Vardenafil(DB00862)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Zidovudine(DB00495)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)|Zopiclone(DB01198)	AAATCCACTCGGTGCTAGAAG	0.448																																					p.R268X		Atlas-SNP	.											.	CYP3A4	56	.	0			c.C802T						.	G	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	94	92	93		799,802	1.9	0.2	7	dbSNP_134	93	0,8600		0,0,4300	no	stop-gained,stop-gained	CYP3A4	NM_001202855.2,NM_017460.5	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	267/503,268/504	99364063	1,13005	2203	4300	6503	SO:0001587	stop_gained	1576	exon9			CCACTCGGTGCTA	AF280107	CCDS5674.1	7q21.1	2011-06-21	2003-01-14		ENSG00000160868	ENSG00000160868	1.1.1.161	"Cytochrome P450s"	2637	protein-coding gene	gene with protein product		124010	"cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 4"	CYP3A3		8269949, 1391968	Standard	NM_001202855		Approved		uc003urv.2	P08684	OTTHUMG00000156651	ENST00000336411.2:c.802C>T	chr7.hg19:g.99364063G>A	ENSP00000337915:p.Arg268*	159.0	0.0		187.0	26.0	NM_017460	P05184|Q16757|Q9UK50	Nonsense_Mutation	SNP	ENST00000336411.2	hg19	CCDS5674.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267773	0.80469	2.27E-4	0.0	ENSG00000160868	ENST00000354593;ENST00000336411	.	.	.	3.87	1.92	0.25849	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.6971	0.12809	0.1102:0.0:0.5124:0.3773	.	.	.	.	X	118;268	.	ENSP00000337915:R268X	R	-	1	2	CYP3A4	99201999	0.290000	0.24343	0.204000	0.23530	0.958000	0.62258	0.489000	0.22387	0.193000	0.20303	0.491000	0.48974	CGA	.	G|1.000;A|0.000		0.448	CYP3A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345059.1			A	99364063	G	A	99364063	4	1	112	1	0	0	0	0	0	1	0	0	4180	1124	39	1	729	1	CYP3A4	7	99364063	Nonsense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	144967	99364063	59774600	519	17140										
C7orf61	402573	hgsc.bcm.edu	37	chr7	100061288	100061288	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctgagatggttggtttaaTtttttgcctccagaagaaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:100061288delT	ENST00000332375.3	-	2	330	c.85delA	c.(85-87)attfs	p.I29fs	TSC22D4_ENST00000496728.1_5'UTR|RN7SL161P_ENST00000582642.1_RNA	NM_001004323.1	NP_001004323.1	Q8IZ16	CG061_HUMAN	chromosome 7 open reading frame 61	29						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|prostate(1)|skin(1)	4						GTTGGTTTAATTTTTTGCCTC	0.488																																					p.I29fs		Pindel	.											.	C7orf61	12	.	0			c.86delT						.						57	63	61					7																	100061288		2027	4210	6237	SO:0001589	frameshift_variant	402573	exon2			.		CCDS47661.1	7q22.1	2013-10-11			ENSG00000185955	ENSG00000185955			22135	protein-coding gene	gene with protein product						12690205	Standard	NM_001004323		Approved	IMAGE:4839025	uc003uuz.1	Q8IZ16	OTTHUMG00000150234	ENST00000332375.3:c.85delA	chr7.hg19:g.100061288delT	ENSP00000327732:p.Ile29fs	167.0	0.0		243.0	11.0	NM_001004323		Frame_Shift_Del	DEL	ENST00000332375.3	hg19	CCDS47661.1																																																																																			.	.		0.488	C7orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316976.2	NM_001004323		-	100061288	T	-	100061288	7	5	112	1	0	1	0	1	0	0	0	0	2410	1493	52	0	543	0	C7orf61	7	100061288	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	697225	100061288	59077375	520	17141										
FBXL13	222235	hgsc.bcm.edu	37	chr7	102665640	102665640	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcttttgagtattaacctaTttttccattttttcaattga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:102665640delT	ENST00000313221.4	-	6	791	c.365delA	c.(364-366)aatfs	p.N122fs	FBXL13_ENST00000379308.3_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000456695.1_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000379305.3_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000455112.2_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000436908.1_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000379306.3_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000471074.1_5'UTR|FBXL13_ENST00000393772.2_Frame_Shift_Del_p.N122fs	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	122										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						TATTAACCTATTTTTCCATTT	0.323																																					p.N122fs		Atlas-INDEL	.											.	FBXL13	65	.	0			c.366delT						.						44	42	43					7																	102665640		2201	4297	6498	SO:0001589	frameshift_variant	222235	exon6			.	BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"F-boxes / Leucine-rich repeats"	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.365delA	chr7.hg19:g.102665640delT	ENSP00000321927:p.Asn122fs	103.0	0.0		163.0	11.0	NM_145032	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Frame_Shift_Del	DEL	ENST00000313221.4	hg19	CCDS5726.1																																																																																			.	.		0.323	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032		-	102665640	T	-	102665640	7	5	112	1	0	1	0	1	0	0	0	0	5717	1493	52	0	1902	0	FBXL13	7	102665640	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2604352	102665640	56473023	521	17142										
MLL5	55904	hgsc.bcm.edu	37	chr7	104715257	104715257	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aacaacacatttcaaaatgtAaaaaggtacgtttttgcttg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:104715257delA	ENST00000311117.3	+	8	1269	c.724delA	c.(724-726)aaafs	p.K243fs	KMT2E_ENST00000476671.1_Frame_Shift_Del_p.K243fs|KMT2E_ENST00000257745.4_Frame_Shift_Del_p.K243fs|KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000334877.4_Frame_Shift_Del_p.K243fs	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	243					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										TTCAAAATGTAAAAAGGTACG	0.353																																					p.C241X		Atlas-INDEL	.											.	MLL5	173	.	0			c.723delT						.						49	50	50					7																	104715257		2202	4300	6502	SO:0001589	frameshift_variant	55904	exon8			.	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.724delA	chr7.hg19:g.104715257delA	ENSP00000312379:p.Lys243fs	130.0	0.0		167.0	12.0	NM_182931	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Frame_Shift_Del	DEL	ENST00000311117.3	hg19	CCDS34723.1																																																																																			.	.		0.353	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			-	104715257	A	-	104715257	7	5	112	1	0	1	0	1	0	0	0	0	9633	363	13	0	746	0	MLL5	7	104715257	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2049617	104715257	54423406	522	17143										
MLL5	55904	hgsc.bcm.edu	37	chr7	104745930	104745930	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagaagaatgagaagacaggAaaaccttcagatggcctttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:104745930delA	ENST00000311117.3	+	18	2786	c.2241delA	c.(2239-2241)ggafs	p.G747fs	KMT2E_ENST00000257745.4_Frame_Shift_Del_p.G747fs|KMT2E_ENST00000334914.7_5'UTR|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334877.4_Frame_Shift_Del_p.G747fs	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	747					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										AGAAGACAGGAAAACCTTCAG	0.378																																					p.G747fs		Atlas-INDEL	.											.	MLL5	173	.	0			c.2240delG						.						89	90	90					7																	104745930		2203	4300	6503	SO:0001589	frameshift_variant	55904	exon18			.	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2241delA	chr7.hg19:g.104745930delA	ENSP00000312379:p.Gly747fs	66.0	0.0		120.0	10.0	NM_182931	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Frame_Shift_Del	DEL	ENST00000311117.3	hg19	CCDS34723.1																																																																																			.	.		0.378	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			-	104745930	A	-	104745930	7	5	112	1	0	1	0	1	0	0	0	0	9633	233	9	0	2303	0	MLL5	7	104745930	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	30673	104745930	54392733	523	17144										
ATXN7L1	222255	hgsc.bcm.edu	37	chr7	105283324	105283324	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttgttgctgtttttggtgcCattttggtgtttcttgtcta	10	6	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:105283324C>G	ENST00000419735.3	-	5	868	c.823G>C	c.(823-825)Ggc>Cgc	p.G275R	ATXN7L1_ENST00000472910.1_5'UTR|ATXN7L1_ENST00000477775.1_Missense_Mutation_p.G151R	NM_020725.1	NP_065776.1	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1	275										endometrium(1)|large_intestine(4)|lung(5)	10						TTTTTGGTGCCATTTTGGTGT	0.463																																					p.G275R		Atlas-SNP	.											.	ATXN7L1	56	.	0			c.G823C						.						446	342	373					7																	105283324		692	1591	2283	SO:0001583	missense	222255	exon5			TGGTGCCATTTTG	AB033044	CCDS34727.1, CCDS47682.1, CCDS47683.1	7q22.1	2007-11-13			ENSG00000146776	ENSG00000146776			22210	protein-coding gene	gene with protein product			"ataxin 7-like 4"	ATXN7L4		15115762	Standard	NM_152749		Approved	KIAA1218, MGC33190	uc003vde.2	Q9ULK2	OTTHUMG00000157521	ENST00000419735.3:c.823G>C	chr7.hg19:g.105283324C>G	ENSP00000410759:p.Gly275Arg	309.0	0.0		475.0	126.0	NM_020725	A4D0Q2|B4DTS1|Q8N2T0	Missense_Mutation	SNP	ENST00000419735.3	hg19	CCDS47682.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.285886	0.80803	.	.	ENSG00000146776	ENST00000419735;ENST00000477775;ENST00000472195	T;T;T	0.15487	2.46;2.43;2.42	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000001	T	0.36441	0.0967	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.961;1.0	T	0.00802	-1.1560	10	0.52906	T	0.07	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	59;151;275	A4D0Q3;Q9ULK2-3;Q9ULK2	.;.;AT7L1_HUMAN	R	275;151;151	ENSP00000410759:G275R;ENSP00000418476:G151R;ENSP00000419566:G151R	ENSP00000410759:G275R	G	-	1	0	ATXN7L1	105070560	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.546000	0.60705	2.941000	0.99782	0.655000	0.94253	GGC	.	.		0.463	ATXN7L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349037.2			G	105283324	C	G	105283324	3	3	112	1	0	0	0	0	1	0	0	0	1216	594	21	4	1797	4	ATXN7L1	7	105283324	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	537394	105283324	53855339	524	17145										
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107340574	107340574	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcttagattttccagtcctaTtttctatggcaatgtcgatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:107340574delT	ENST00000265715.3	+	15	1885	c.1661delT	c.(1660-1662)attfs	p.I554fs	SLC26A4_ENST00000541474.1_Frame_Shift_Del_p.I115fs|SLC26A4_ENST00000544569.1_Frame_Shift_Del_p.I141fs|SLC26A4_ENST00000543100.1_Frame_Shift_Del_p.I123fs|SLC26A4_ENST00000480841.1_3'UTR	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	554	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						TCCAGTCCTATTTTCTATGGC	0.318									Pendred syndrome																												p.I554fs		Atlas-INDEL	.											.	SLC26A4	117	.	0			c.1660delA						.						116	120	119					7																	107340574		2202	4299	6501	SO:0001589	frameshift_variant	5172	exon15	Familial Cancer Database	Goiter-Deafness syndrome	.	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.1661delT	chr7.hg19:g.107340574delT	ENSP00000265715:p.Ile554fs	136.0	0.0		197.0	12.0	NM_000441	B7Z266|O43170	Frame_Shift_Del	DEL	ENST00000265715.3	hg19	CCDS5746.1																																																																																			.	.		0.318	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		-	107340574	T	-	107340574	7	5	112	1	0	1	0	1	0	0	0	0	14534	1493	52	0	1715	0	SLC26A4	7	107340574	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2057250	107340574	51798089	525	17146										
DLD	1738	hgsc.bcm.edu	37	chr7	107555996	107555996	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagatgtgacagcagttgaaTttttaggtcatgtaggtgga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:107555996delT	ENST00000205402.5	+	9	1011	c.730delT	c.(730-732)tttfs	p.F244fs	DLD_ENST00000537148.1_Frame_Shift_Del_p.F145fs|DLD_ENST00000437604.2_Frame_Shift_Del_p.F196fs|DLD_ENST00000440410.1_Frame_Shift_Del_p.F221fs	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	244					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	AGCAGTTGAATTTTTAGGTCA	0.318																																					p.E243fs		Atlas-INDEL	.											.	DLD	72	.	0			c.729delA						.						118	119	118					7																	107555996		2203	4300	6503	SO:0001589	frameshift_variant	1738	exon9			.	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.730delT	chr7.hg19:g.107555996delT	ENSP00000205402:p.Phe244fs	112.0	0.0		155.0	13.0	NM_000108	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Frame_Shift_Del	DEL	ENST00000205402.5	hg19	CCDS5749.1																																																																																			.	.		0.318	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108		-	107555996	T	-	107555996	7	5	112	1	0	1	0	1	0	0	0	0	4553	1493	52	0	764	0	DLD	7	107555996	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	215422	107555996	51582667	526	17147										
CAV2	858	hgsc.bcm.edu	37	chr7	116140387	116140387	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtgtggatctgcagccatgCcctctttgaaatcagcaaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:116140387delC	ENST00000222693.4	+	2	616	c.224delC	c.(223-225)gccfs	p.A75fs	AC002066.1_ENST00000446355.2_RNA|CAV2_ENST00000343213.2_Intron|CAV2_ENST00000393480.2_Frame_Shift_Del_p.A75fs|CAV2_ENST00000462876.1_3'UTR	NM_001206747.1|NM_001206748.1|NM_001233.4	NP_001193676.1|NP_001193677.1|NP_001224.1	P51636	CAV2_HUMAN	caveolin 2	75					caveola assembly (GO:0070836)|endoplasmic reticulum organization (GO:0007029)|mitochondrion organization (GO:0007005)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of endothelial cell proliferation (GO:0001938)|protein oligomerization (GO:0051259)|regulation of mitosis (GO:0007088)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)|vesicle docking (GO:0048278)|vesicle fusion (GO:0006906)|vesicle organization (GO:0016050)	acrosomal membrane (GO:0002080)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	D1 dopamine receptor binding (GO:0031748)|protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(1)|skin(1)	3	all_epithelial(6;1.53e-06)|Lung NSC(10;0.00592)|all_lung(10;0.00642)		STAD - Stomach adenocarcinoma(10;0.00878)			TGCAGCCATGCCCTCTTTGAA	0.552																																					p.A75fs		Atlas-INDEL	.											.	CAV2	10	.	0			c.223delG						.						180	147	158					7																	116140387		2203	4300	6503	SO:0001589	frameshift_variant	858	exon2			.	AF035752	CCDS5765.1, CCDS5766.1	7q31	2006-02-09			ENSG00000105971	ENSG00000105971			1528	protein-coding gene	gene with protein product		601048				8552590, 10087206	Standard	NM_001233		Approved	CAV	uc003vid.3	P51636	OTTHUMG00000023414	ENST00000222693.4:c.224delC	chr7.hg19:g.116140387delC	ENSP00000222693:p.Ala75fs	101.0	0.0		157.0	11.0	NM_001233	A4D0U2|Q9UGM7	Frame_Shift_Del	DEL	ENST00000222693.4	hg19	CCDS5766.1																																																																																			.	.		0.552	CAV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059735.4	NM_001233		-	116140387	C	-	116140387	7	5	112	1	0	1	0	1	0	0	0	0	2696	739	26	0	230	0	CAV2	7	116140387	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	8584391	116140387	42998276	527	17148										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128455707	128455707	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actacaaggccagccagaggAaattagatggactagcaaaa	10	8	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:128455707A>C	ENST00000297788.4	+	16	3452	c.3085A>C	c.(3085-3087)Aaa>Caa	p.K1029Q	CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000471729.1_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000378685.4_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	1029						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CAGCCAGAGGAAATTAGATGG	0.507																																					p.K1029Q		Atlas-SNP	.											.	CCDC136	170	.	0			c.A3085C						.						34	34	34					7																	128455707		1946	4129	6075	SO:0001583	missense	64753	exon16			CAGAGGAAATTAG		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.3085A>C	chr7.hg19:g.128455707A>C	ENSP00000297788:p.Lys1029Gln	102.0	0.0		146.0	73.0	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	A	7.458	0.644011	0.14451	.	.	ENSG00000128596	ENST00000297788;ENST00000397697	T	0.31510	1.49	4.82	0.68	0.17980	.	1.619910	0.03252	N	0.181948	T	0.19327	0.0464	L	0.34521	1.04	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.10450	0.005;0.003	T	0.10086	-1.0645	10	0.08837	T	0.75	0.8604	1.0683	0.01616	0.222:0.2189:0.3982:0.1609	.	1029;1029	Q96JN2-4;Q96JN2	.;CC136_HUMAN	Q	1029	ENSP00000297788:K1029Q	ENSP00000297788:K1029Q	K	+	1	0	CCDC136	128242943	0.000000	0.05858	0.000000	0.03702	0.057000	0.15508	0.216000	0.17585	0.004000	0.14682	-0.468000	0.05107	AAA	.	.		0.507	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		C	128455707	A	C	128455707	3	2	112	1	0	0	0	0	1	0	0	0	2772	247	9	5	3147	5	CCDC136	7	128455707	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	12315320	128455707	30682956	528	17149										
EXOC4	60412	hgsc.bcm.edu	37	chr7	133580480	133580480	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tacaaggacacctgcactgcAgcttacaggtagagcttctg	10	11	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:133580480A>G	ENST00000253861.4	+	12	1892	c.1863A>G	c.(1861-1863)gcA>gcG	p.A621A	EXOC4_ENST00000539845.1_Silent_p.A520A|EXOC4_ENST00000545148.1_Silent_p.A231A|EXOC4_ENST00000460346.1_3'UTR	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	621					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				CCTGCACTGCAGCTTACAGGT	0.453																																					p.A621A		Atlas-SNP	.											.	EXOC4	118	.	0			c.A1863G						.						129	110	117					7																	133580480		2203	4300	6503	SO:0001819	synonymous_variant	60412	exon12			CACTGCAGCTTAC	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"SEC8-like 1 (S. cerevisiae)"	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.1863A>G	chr7.hg19:g.133580480A>G		87.0	0.0		131.0	6.0	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	hg19	CCDS5829.1																																																																																			.	.		0.453	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		G	133580480	A	G	133580480	2	3	112	1	0	0	0	0	0	0	0	1	5308	175	7	2		2	EXOC4	7	133580480	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	5124773	133580480	25558183	529	17150										
ARHGEF5	7984	hgsc.bcm.edu	37	chr7	144075858	144075858	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actcttctcttccaaagactCcccccaggtacagtgccttc					rs201067947		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:144075858delC	ENST00000056217.5	+	14	4709	c.4535delC	c.(4534-4536)tccfs	p.S1512fs	ARHGEF5_ENST00000471847.2_Frame_Shift_Del_p.S434fs	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	1512					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					TCCAAAGACTCCCCCCAGGTA	0.557																																					p.S1512fs		Atlas-INDEL	.											.	ARHGEF5	73	.	0			c.4534delT						.						161	156	158					7																	144075858		2203	4300	6503	SO:0001589	frameshift_variant	7984	exon14			.	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"Rho guanine nucleotide exchange factors"	13209	protein-coding gene	gene with protein product	"transforming immortalized mammary oncogene", "guanine nucleotide regulatory protein TIM"	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.4535delC	chr7.hg19:g.144075858delC	ENSP00000056217:p.Ser1512fs	158.0	0.0		227.0	14.0	NM_005435	A6NNJ2|Q6ZML7	Frame_Shift_Del	DEL	ENST00000056217.5	hg19	CCDS34771.1																																																																																			.	.		0.557	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435		-	144075858	C	-	144075858	7	5	112	1	0	1	0	1	0	0	0	0	909	855	30	0	4585	0	ARHGEF5	7	144075858	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	10495378	144075858	15062805	530	17151										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	147844667	147844667	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accaacccctctcaacgatgAccagtggcaccgggtcactg	9	16	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:147844667A>G	ENST00000361727.3	+	17	3155	c.2639A>G	c.(2638-2640)gAc>gGc	p.D880G	CNTNAP2_ENST00000538075.1_5'UTR	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	880	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CTCAACGATGACCAGTGGCAC	0.567										HNSCC(39;0.1)																											p.D880G		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.A2639G						.						130	120	124					7																	147844667		2203	4300	6503	SO:0001583	missense	26047	exon17			ACGATGACCAGTG	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.2639A>G	chr7.hg19:g.147844667A>G	ENSP00000354778:p.Asp880Gly	87.0	0.0		117.0	5.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	hg19	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.615335	0.87359	.	.	ENSG00000174469	ENST00000361727	T	0.71341	-0.56	5.34	5.34	0.76211	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	T	0.56441	0.1985	N	0.04018	-0.295	0.80722	D	1	B	0.34103	0.437	P	0.44422	0.449	T	0.57207	-0.7851	10	0.17832	T	0.49	.	14.1814	0.65577	1.0:0.0:0.0:0.0	.	880	Q9UHC6	CNTP2_HUMAN	G	880	ENSP00000354778:D880G	ENSP00000354778:D880G	D	+	2	0	CNTNAP2	147475600	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.233000	0.95337	2.029000	0.59856	0.459000	0.35465	GAC	.	.		0.567	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			G	147844667	A	G	147844667	3	3	112	1	0	0	0	0	1	0	0	0	3649	275	10	2	2705	2	CNTNAP2	7	147844667	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	3768809	147844667	11293996	531	17152										
ZNF777	27153	hgsc.bcm.edu	37	chr7	149152609	149152609	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttccttctggactgcagaagAgatctggaaaggggtgtcct	13	8	2	2	rs3823695		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:149152609A>G	ENST00000247930.4	-	2	828	c.505T>C	c.(505-507)Tct>Cct	p.S169P		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			ACTGCAGAAGAGATCTGGAAA	0.607																																					p.S169P		Atlas-SNP	.											.	ZNF777	63	.	0			c.T505C						.						74	84	81					7																	149152609		2011	4178	6189	SO:0001583	missense	27153	exon2			CAGAAGAGATCTG	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"Zinc fingers, C2H2-type", "-"	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.505T>C	chr7.hg19:g.149152609A>G	ENSP00000247930:p.Ser169Pro	66.0	0.0		103.0	5.0	NM_015694	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	hg19	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.145832	0.57044	.	.	ENSG00000196453	ENST00000247930	T	0.05717	3.4	4.57	3.43	0.39272	.	0.000000	0.44097	D	0.000494	T	0.04452	0.0122	L	0.27053	0.805	0.31089	N	0.711009	B	0.12013	0.005	B	0.12156	0.007	T	0.08207	-1.0733	10	0.36615	T	0.2	-9.9234	6.0597	0.19830	0.8861:0.0:0.1139:0.0	.	169	Q9ULD5-2	.	P	169	ENSP00000247930:S169P	ENSP00000247930:S169P	S	-	1	0	ZNF777	148783542	0.999000	0.42202	0.997000	0.53966	0.925000	0.55904	1.474000	0.35398	1.708000	0.51301	0.460000	0.39030	TCT	.	.		0.607	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694		G	149152609	A	G	149152609	3	3	112	1	0	0	0	0	1	0	0	0	18165	304	11	2	2010	2	ZNF777	7	149152609	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1307942	149152609	9986054	532	17153										
ABCB8	11194	hgsc.bcm.edu	37	chr7	150739104	150739104	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atccgctttgggaagctggaAgcttccgatgaagaggtgta	14	7	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:150739104A>G	ENST00000297504.6	+	15	1791	c.1725A>G	c.(1723-1725)gaA>gaG	p.E575E	ABCB8_ENST00000542328.1_Silent_p.E470E|ABCB8_ENST00000356058.4_3'UTR|ABCB8_ENST00000358849.4_Silent_p.E558E|ABCB8_ENST00000498578.1_Silent_p.E558E			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	575	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	GGAAGCTGGAAGCTTCCGATG	0.562																																					p.E558E		Atlas-SNP	.											.	ABCB8	65	.	0			c.A1674G						.						61	64	63					7																	150739104		2203	4300	6503	SO:0001819	synonymous_variant	11194	exon14			GCTGGAAGCTTCC	AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"ATP binding cassette transporters / subfamily B"	49	protein-coding gene	gene with protein product	"mitochondrial ABC protein"	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.1725A>G	chr7.hg19:g.150739104A>G		51.0	0.0		95.0	4.0	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Silent	SNP	ENST00000297504.6	hg19																																																																																				.	.		0.562	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188		G	150739104	A	G	150739104	2	3	112	1	0	0	0	0	0	0	0	1	47	69	3	2		2	ABCB8	7	150739104	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1586495	150739104	8399559	533	17154										
MLL3	58508	hgsc.bcm.edu	37	chr7	151848557	151848557	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agggtcagatctttgaaagaTttccgcacaccacttccaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:151848557delT	ENST00000262189.6	-	50	12854	c.12636delA	c.(12634-12636)aaafs	p.K4212fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.K4269fs|KMT2C_ENST00000485241.1_5'Flank	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4212					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CTTTGAAAGATTTCCGCACAC	0.448																																					p.S4213fs		Atlas-INDEL	.											.	MLL3	1564	.	0			c.12637delT						.						104	88	94					7																	151848557		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon50			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.12636delA	chr7.hg19:g.151848557delT	ENSP00000262189:p.Lys4212fs	92.0	0.0		157.0	11.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151848557	T	-	151848557	7	5	112	1	0	1	0	1	0	0	0	0	9631	1490	52	0	2139	0	MLL3	7	151848557	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1109453	151848557	7290106	534	17155										
RBM33	155435	hgsc.bcm.edu	37	chr7	155511123	155511123	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agccgagacctgccgtgggaCcccagagattcccagtgagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:155511123delC	ENST00000401878.3	+	9	1444	c.1246delC	c.(1246-1248)cccfs	p.P416fs	RBM33_ENST00000486747.1_3'UTR	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	416	Pro-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		TGCCGTGGGACCCCAGAGATT	0.483																																					p.G415fs		Atlas-INDEL	.											.	RBM33	157	.	0			c.1245delA						.						81	85	84					7																	155511123		1880	4130	6010	SO:0001589	frameshift_variant	155435	exon9			.	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"RNA binding motif (RRM) containing"	27223	protein-coding gene	gene with protein product			"proline rich 8"	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.1246delC	chr7.hg19:g.155511123delC	ENSP00000384160:p.Pro416fs	129.0	0.0		166.0	10.0	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Frame_Shift_Del	DEL	ENST00000401878.3	hg19	CCDS5941.2																																																																																			.	.		0.483	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		-	155511123	C	-	155511123	7	5	112	1	0	1	0	1	0	0	0	0	13145	507	18	0	1280	0	RBM33	7	155511123	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	3662566	155511123	3627540	535	17156										
WDR60	55112	hgsc.bcm.edu	37	chr7	158719144	158719144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttggatgagagtggggttcTcaatgtatgggtgagtagtg	17	3	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:158719144T>C	ENST00000407559.3	+	19	2581	c.2423T>C	c.(2422-2424)cTc>cCc	p.L808P		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	808					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		AGTGGGGTTCTCAATGTATGG	0.542																																					p.L808P		Atlas-SNP	.											.	WDR60	94	.	0			c.T2423C						.						38	36	36					7																	158719144		1925	4130	6055	SO:0001583	missense	55112	exon19			GGGTTCTCAATGT		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"WD repeat domain containing"	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.2423T>C	chr7.hg19:g.158719144T>C	ENSP00000384290:p.Leu808Pro	134.0	0.0		195.0	8.0	NM_018051	Q9NW58	Missense_Mutation	SNP	ENST00000407559.3	hg19	CCDS47757.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.974786	0.74360	.	.	ENSG00000126870	ENST00000407559	T	0.69926	-0.44	5.95	5.95	0.96441	WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000001	D	0.82540	0.5059	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.987;0.994	D	0.84970	0.0882	10	0.87932	D	0	-19.656	15.6048	0.76658	0.0:0.0:0.0:1.0	.	291;808	A4D230;Q8WVS4	.;WDR60_HUMAN	P	808	ENSP00000384290:L808P	ENSP00000384290:L808P	L	+	2	0	WDR60	158411905	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	6.194000	0.72082	2.279000	0.76181	0.533000	0.62120	CTC	.	.		0.542	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051		C	158719144	T	C	158719144	3	2	112	1	0	0	0	0	1	0	0	0	17326	1551	54	2	2497	2	WDR60	7	158719144	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3208021	158719144	419519	536	17157										
ZDHHC2	51201	hgsc.bcm.edu	37	chr8	17067945	17067945	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgccttgttaaccaggatccTgaacaagcatctactcctgc	7	13	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:17067945T>C	ENST00000262096.8	+	10	1601	c.906T>C	c.(904-906)ccT>ccC	p.P302P		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	302					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|recycling endosome membrane (GO:0055038)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|pancreas(1)|stomach(1)	8				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		ACCAGGATCCTGAACAAGCAT	0.348																																					p.P302P		Atlas-SNP	.											.	ZDHHC2	25	.	0			c.T906C						.						77	72	73					8																	17067945		1835	4094	5929	SO:0001819	synonymous_variant	51201	exon10			GGATCCTGAACAA	AB023584	CCDS47810.1	8p22	2008-05-15			ENSG00000104219	ENSG00000104219		"Zinc fingers, DHHC-type"	18469	protein-coding gene	gene with protein product						10918388	Standard	NM_016353		Approved	ZNF372	uc003wxe.3	Q9UIJ5	OTTHUMG00000163860	ENST00000262096.8:c.906T>C	chr8.hg19:g.17067945T>C		74.0	0.0		63.0	4.0	NM_016353	D3DSP5	Silent	SNP	ENST00000262096.8	hg19	CCDS47810.1																																																																																			.	.		0.348	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	NM_016353		C	17067945	T	C	17067945	2	2	112	1	0	0	0	0	0	0	0	1	17625	1567	55	2		2	ZDHHC2	8	17067945	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10		17067945	129296077	537	17158										
INTS10	55174	hgsc.bcm.edu	37	chr8	19675087	19675087	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcgagttcctggtgcagcgAgcccgggagttggtgccgca	17	11	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:19675087A>G	ENST00000397977.3	+	1	437	c.39A>G	c.(37-39)cgA>cgG	p.R13R	INTS10_ENST00000521758.1_3'UTR	NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	13					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	20				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		TGGTGCAGCGAGCCCGGGAGT	0.677																																					p.R13R		Atlas-SNP	.											.	INTS10	46	.	0			c.A39G						.						18	26	24					8																	19675087		2036	4179	6215	SO:0001819	synonymous_variant	55174	exon1			GCAGCGAGCCCGG	AK001431	CCDS6011.2	8p21.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000104613	ENSG00000104613			25548	protein-coding gene	gene with protein product		611353	"chromosome 8 open reading frame 35"	C8orf35		16239144	Standard	XM_005273558		Approved	FLJ10569, INT10	uc003wzj.3	Q9NVR2	OTTHUMG00000131065	ENST00000397977.3:c.39A>G	chr8.hg19:g.19675087A>G		89.0	0.0		61.0	4.0	NM_018142	Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Silent	SNP	ENST00000397977.3	hg19	CCDS6011.2																																																																																			.	.		0.677	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253724.2	NM_018142		G	19675087	A	G	19675087	2	3	112	1	0	0	0	0	0	0	0	1	7785	291	11	2		2	INTS10	8	19675087	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2607142	19675087	126688935	538	17159										
PDLIM2	64236	hgsc.bcm.edu	37	chr8	22452076	22452076	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctatggagggaatgagattgTcactggaagctttggagggg	17	4	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:22452076T>C	ENST00000397760.4	+	0	1837				PDLIM2_ENST00000265810.4_Missense_Mutation_p.S339P|AC037459.4_ENST00000430850.2_Intron			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		AATGAGATTGTCACTGGAAGC	0.527																																					p.S339P		Atlas-SNP	.											.	PDLIM2	42	.	0			c.T1015C						.						168	169	169					8																	22452076		2203	4300	6503	SO:0001628	intergenic_variant	64236	exon10			AGATTGTCACTGG	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270		chr8.hg19:g.22452076T>C		85.0	0.0		57.0	4.0	NM_176871	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	hg19		.	.	.	.	.	.	.	.	.	.	T	12.83	2.054956	0.36277	.	.	ENSG00000120913	ENST00000265810	T	0.13901	2.55	1.84	1.84	0.25277	.	.	.	.	.	T	0.08980	0.0222	.	.	.	0.09310	N	0.999999	B	0.13145	0.007	B	0.06405	0.002	T	0.25467	-1.0131	8	0.45353	T	0.12	.	5.7188	0.17974	0.0:0.0:0.0:1.0	.	339	Q96JY6-3	.	P	339	ENSP00000265810:S339P	ENSP00000265810:S339P	S	+	1	0	PDLIM2	22508021	0.021000	0.18746	0.007000	0.13788	0.015000	0.08874	0.862000	0.27899	1.108000	0.41662	0.402000	0.26972	TCA	.	.		0.527	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1			C	22452076	T	C	22452076	1	2	112	0	1	0	0	0	0	0	0	0	11689	1667	58	2		2	PDLIM2	8	22452076	IGR	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2776989	22452076	123911946	539	17160										
DOCK5	80005	hgsc.bcm.edu	37	chr8	25182970	25182970	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaaagagcttcaagcatccAaaaacctggtcaccttcacc	5	13	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:25182970A>T	ENST00000276440.7	+	18	1854	c.1810A>T	c.(1810-1812)Aaa>Taa	p.K604*		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	604	DHR-1.				positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TCAAGCATCCAAAAACCTGGT	0.458																																					p.K604X	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.A1810T						.						135	124	128					8																	25182970		2203	4300	6503	SO:0001587	stop_gained	80005	exon18			GCATCCAAAAACC		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.1810A>T	chr8.hg19:g.25182970A>T	ENSP00000276440:p.Lys604*	167.0	0.0		137.0	7.0	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Nonsense_Mutation	SNP	ENST00000276440.7	hg19	CCDS6047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	40|40	7.961131|7.961131	0.98583|0.98583	.|.	.|.	ENSG00000147459|ENSG00000147459	ENST00000276440|ENST00000444569	.|.	.|.	.|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	2.143080|.	0.01481|.	N|.	0.016688|.	.|T	.|0.65770	.|0.2723	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70781	.|-0.4779	.|3	0.02654|.	T|.	1|.	.|.	14.3564|14.3564	0.66740|0.66740	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	604|375	.|.	ENSP00000276440:K604X|.	K|Q	+|+	1|2	0|0	DOCK5|DOCK5	25238887|25238887	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.362000|0.362000	0.29581|0.29581	4.167000|4.167000	0.58209|0.58209	2.129000|2.129000	0.65627|0.65627	0.533000|0.533000	0.62120|0.62120	AAA|CAA	.	.		0.458	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		T	25182970	A	T	25182970	4	4	112	1	0	0	0	0	0	1	0	0	4692	131	5	4	1880	4	DOCK5	8	25182970	Nonsense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2730894	25182970	121181052	540	17161										
PBK	55872	hgsc.bcm.edu	37	chr8	27668599	27668599	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acaccattctcctccacagcTtctttgggtttccatggctc	6	15	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:27668599T>C	ENST00000301905.4	-	7	1111	c.648A>G	c.(646-648)gaA>gaG	p.E216E	PBK_ENST00000522944.1_Silent_p.E227E|ESCO2_ENST00000397418.2_Intron	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	216	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		CCTCCACAGCTTCTTTGGGTT	0.433																																					p.E216E		Atlas-SNP	.											.	PBK	29	.	0			c.A648G						.						127	110	116					8																	27668599		2203	4300	6503	SO:0001819	synonymous_variant	55872	exon7			CACAGCTTCTTTG	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"T-LAK cell-originated protein kinase", "cancer/testis antigen 84"	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.648A>G	chr8.hg19:g.27668599T>C		139.0	0.0		94.0	4.0	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Silent	SNP	ENST00000301905.4	hg19	CCDS6063.1																																																																																			.	.		0.433	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492		C	27668599	T	C	27668599	2	2	112	1	0	0	0	0	0	0	0	1	11497	1606	56	2		2	PBK	8	27668599	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2485629	27668599	118695423	541	17162										
ELP3	55140	hgsc.bcm.edu	37	chr8	27995291	27995291	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtgattcgtgggaccgggcTttatgagctttggaaatcag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:27995291delT	ENST00000256398.8	+	10	1360	c.983delT	c.(982-984)cttfs	p.L328fs	ELP3_ENST00000380353.4_Frame_Shift_Del_p.L236fs|ELP3_ENST00000537665.1_Frame_Shift_Del_p.L209fs|ELP3_ENST00000542181.1_Frame_Shift_Del_p.L199fs|ELP3_ENST00000524103.1_Frame_Shift_Del_p.L256fs|ELP3_ENST00000521015.1_Frame_Shift_Del_p.L314fs	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3	328					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		GGGACCGGGCTTTATGAGCTT	0.483																																					p.L328fs		Atlas-INDEL	.											.	ELP3	36	.	0			c.982delC						.						111	110	110					8																	27995291		2203	4300	6503	SO:0001589	frameshift_variant	55140	exon10			.		CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"Chromatin-modifying enzymes / K-acetyltransferases", "Elongator acetyltransferase complex subunits"	20696	protein-coding gene	gene with protein product		612722	"elongation protein 3 homolog (S. cerevisiae)"			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.983delT	chr8.hg19:g.27995291delT	ENSP00000256398:p.Leu328fs	153.0	0.0		111.0	10.0	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Frame_Shift_Del	DEL	ENST00000256398.8	hg19	CCDS6065.1																																																																																			.	.		0.483	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091		-	27995291	T	-	27995291	7	5	112	1	0	1	0	1	0	0	0	0	5083	1609	56	0	1021	0	ELP3	8	27995291	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	326692	27995291	118368731	542	17163										
KIF13B	23303	hgsc.bcm.edu	37	chr8	28928094	28928094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggccagggcagctgtcagcGaggccaggttggtggcggag	20	9	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:28928094G>A	ENST00000524189.1	-	40	5446	c.5408C>T	c.(5407-5409)tCg>tTg	p.S1803L	KIF13B_ENST00000404075.3_Missense_Mutation_p.S322L|CTD-2647L4.5_ENST00000560714.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1803					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		AGCTGTCAGCGAGGCCAGGTT	0.706																																					p.S1803L		Atlas-SNP	.											.	KIF13B	192	.	0			c.C5408T						.						11	14	13					8																	28928094		1957	4149	6106	SO:0001583	missense	23303	exon40			GTCAGCGAGGCCA	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.5408C>T	chr8.hg19:g.28928094G>A	ENSP00000427900:p.Ser1803Leu	78.0	0.0		47.0	4.0	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	hg19	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.321783	0.81580	.	.	ENSG00000197892	ENST00000524189;ENST00000523130;ENST00000404075	T;D;D	0.82619	-1.25;-1.63;-1.62	4.63	3.76	0.43208	.	0.169623	0.36740	N	0.002423	T	0.67116	0.2859	N	0.14661	0.345	0.40215	D	0.977676	P;B	0.34412	0.453;0.054	B;B	0.23716	0.048;0.007	T	0.69760	-0.5058	10	0.54805	T	0.06	.	12.7104	0.57086	0.0797:0.0:0.9203:0.0	.	322;1803	B4DGY5;F8VPJ2	.;.	L	1803;395;322	ENSP00000427900:S1803L;ENSP00000429106:S395L;ENSP00000384054:S322L	ENSP00000384054:S322L	S	-	2	0	KIF13B	28984013	1.000000	0.71417	0.962000	0.40283	0.736000	0.42039	6.729000	0.74775	1.179000	0.42884	0.561000	0.74099	TCG	.	.		0.706	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			A	28928094	G	A	28928094	3	1	112	1	0	0	0	0	1	0	0	0	8284	1059	37	1	76	1	KIF13B	8	28928094	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	932803	28928094	117435928	543	17164										
KIF13B	23303	hgsc.bcm.edu	37	chr8	28999714	28999714	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctttccactcctgataaaggTctctcatatccaacagcctg	5	14	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:28999714T>C	ENST00000524189.1	-	19	2332	c.2294A>G	c.(2293-2295)gAc>gGc	p.D765G	CTD-2647L4.1_ENST00000523661.1_RNA|RN7SL781P_ENST00000582428.1_RNA|CTD-2647L4.1_ENST00000517632.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	765					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		CTGATAAAGGTCTCTCATATC	0.398																																					p.D765G		Atlas-SNP	.											.	KIF13B	192	.	0			c.A2294G						.						168	148	154					8																	28999714		1835	4093	5928	SO:0001583	missense	23303	exon19			TAAAGGTCTCTCA	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.2294A>G	chr8.hg19:g.28999714T>C	ENSP00000427900:p.Asp765Gly	97.0	0.0		78.0	5.0	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	hg19	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.581706	0.65992	.	.	ENSG00000197892	ENST00000524189	T	0.80653	-1.4	5.28	5.28	0.74379	.	0.044544	0.85682	D	0.000000	T	0.78641	0.4315	L	0.49778	1.585	0.80722	D	1	B	0.27679	0.185	B	0.32090	0.14	T	0.78555	-0.2159	10	0.87932	D	0	.	15.3876	0.74714	0.0:0.0:0.0:1.0	.	765	F8VPJ2	.	G	765	ENSP00000427900:D765G	ENSP00000427900:D765G	D	-	2	0	KIF13B	29055633	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.436000	0.80404	2.217000	0.71921	0.533000	0.62120	GAC	.	.		0.398	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			C	28999714	T	C	28999714	3	2	112	1	0	0	0	0	1	0	0	0	8284	1667	58	2	3274	2	KIF13B	8	28999714	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	71620	28999714	117364308	544	17165										
TEX15	56154	hgsc.bcm.edu	37	chr8	30703400	30703400	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagaactataaccttgaaggTcacaactttcccagaaatta	5	10	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:30703400T>C	ENST00000256246.2	-	1	3208	c.3134A>G	c.(3133-3135)gAc>gGc	p.D1045G	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1045					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		ACCTTGAAGGTCACAACTTTC	0.333																																					p.D1045G		Atlas-SNP	.											.	TEX15	350	.	0			c.A3134G						.						66	70	68					8																	30703400		2203	4295	6498	SO:0001583	missense	56154	exon1			TGAAGGTCACAAC	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.3134A>G	chr8.hg19:g.30703400T>C	ENSP00000256246:p.Asp1045Gly	99.0	0.0		69.0	4.0	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	18.15	3.560018	0.65538	.	.	ENSG00000133863	ENST00000256246	T	0.26957	1.7	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000005	T	0.46054	0.1373	L	0.55481	1.735	0.43766	D	0.99628	D	0.89917	1.0	D	0.81914	0.995	T	0.42682	-0.9437	10	0.87932	D	0	.	13.5087	0.61499	0.0:0.0:0.0:1.0	.	1045	Q9BXT5	TEX15_HUMAN	G	1045	ENSP00000256246:D1045G	ENSP00000256246:D1045G	D	-	2	0	TEX15	30822942	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	4.331000	0.59273	2.180000	0.69256	0.383000	0.25322	GAC	.	.		0.333	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30703400	T	C	30703400	3	2	112	1	0	0	0	0	1	0	0	0	15794	1667	58	2	5251	2	TEX15	8	30703400	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1703686	30703400	115660622	545	17166										
WHSC1L1	54904	hgsc.bcm.edu	37	chr8	38178646	38178646	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtggatttctctgattcagAacgagttctaattgatcttc	8	7	4	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:38178646A>G	ENST00000317025.8	-	8	2270	c.1753T>C	c.(1753-1755)Tct>Cct	p.S585P	WHSC1L1_ENST00000525081.1_5'Flank|WHSC1L1_ENST00000316985.3_Missense_Mutation_p.S585P|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.S585P|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.S585P	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	585					histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			TCTGATTCAGAACGAGTTCTA	0.358			T	NUP98	AML																																p.S585P		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.T1753C						.						176	159	165					8																	38178646		2203	4300	6503	SO:0001583	missense	54904	exon8			ATTCAGAACGAGT	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.1753T>C	chr8.hg19:g.38178646A>G	ENSP00000313983:p.Ser585Pro	83.0	0.0		82.0	4.0	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	hg19	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.770502	0.90108	.	.	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985;ENST00000528627	D;D;D;T	0.95238	-3.65;-3.65;-3.65;-0.9	5.71	5.71	0.89125	.	0.000000	0.47455	U	0.000226	D	0.96175	0.8753	L	0.50333	1.59	0.58432	D	0.999995	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.91635	0.994;0.997;0.999;0.994	D	0.96409	0.9303	10	0.56958	D	0.05	.	15.9628	0.79945	1.0:0.0:0.0:0.0	.	585;585;585;585	B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95	.;.;.;NSD3_HUMAN	P	585;585;522;585;585;51	ENSP00000393284:S585P;ENSP00000313983:S585P;ENSP00000434730:S585P;ENSP00000313410:S585P	ENSP00000313410:S585P	S	-	1	0	WHSC1L1	38297803	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.060000	0.89464	2.166000	0.68216	0.482000	0.46254	TCT	.	.		0.358	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		G	38178646	A	G	38178646	3	3	112	1	0	0	0	0	1	0	0	0	17378	246	9	2	2715	2	WHSC1L1	8	38178646	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	7475246	38178646	108185376	546	17167										
ADAM9	8754	hgsc.bcm.edu	37	chr8	38880753	38880753	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaacctgatcaacatagttGggggtgctggtgatgtgctg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:38880753delG	ENST00000487273.2	+	9	901	c.823delG	c.(823-825)gggfs	p.G276fs		NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	276	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			CAACATAGTTGGGGGTGCTGG	0.423																																					p.V274fs		Atlas-INDEL	.											.	ADAM9	66	.	0			c.822delT						.						153	139	144					8																	38880753		2203	4300	6503	SO:0001589	frameshift_variant	8754	exon9			.	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"ADAM metallopeptidase domain containing"	216	protein-coding gene	gene with protein product	"meltrin gamma"	602713	"a disintegrin and metalloproteinase domain 9 (meltrin gamma)", "cone rod dystrophy 9"	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.823delG	chr8.hg19:g.38880753delG	ENSP00000419446:p.Gly276fs	196.0	0.0		157.0	10.0	NM_003816	B7ZLN7|Q10718|Q8NFM6	Frame_Shift_Del	DEL	ENST00000487273.2	hg19	CCDS6112.1																																																																																			.	.		0.423	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			-	38880753	G	-	38880753	7	5	112	1	0	1	0	1	0	0	0	0	253	1348	47	0	857	0	ADAM9	8	38880753	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	702107	38880753	107483269	547	17168										
MYST3	7994	hgsc.bcm.edu	37	chr8	41832291	41832291	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtcatgatttcctggctcccAaaaagtcgctcctcattttc					rs141739124		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:41832291delA	ENST00000396930.3	-	9	1956	c.1413delT	c.(1411-1413)tttfs	p.F471fs	KAT6A_ENST00000406337.1_Frame_Shift_Del_p.F471fs|KAT6A_ENST00000265713.2_Frame_Shift_Del_p.F471fs|KAT6A_ENST00000485568.1_Frame_Shift_Del_p.F471fs	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	471	Interaction with PML.|Interaction with RUNX1-1.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CCTGGCTCCCAAAAAGTCGCT	0.388																																					p.G472fs		Atlas-INDEL	.											.	.	.	.	0			c.1414delG						.						143	129	134					8																	41832291		2203	4300	6503	SO:0001589	frameshift_variant	7994	exon8			.	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.1413delT	chr8.hg19:g.41832291delA	ENSP00000380136:p.Phe471fs	215.0	0.0		182.0	12.0	NM_006766	Q76L81	Frame_Shift_Del	DEL	ENST00000396930.3	hg19	CCDS6124.1																																																																																			.	.		0.388	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		-	41832291	A	-	41832291	7	5	112	1	0	1	0	1	0	0	0	0	10113	127	5	0	4641	0	MYST3	8	41832291	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2951538	41832291	104531731	548	17169										
POLB	5423	hgsc.bcm.edu	37	chr8	42213041	42213041	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atcttctatacagatctcagAaaaaatgaagataaattgaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:42213041delA	ENST00000265421.4	+	7	548	c.378delA	c.(376-378)agafs	p.R126fs	POLB_ENST00000538005.1_5'UTR	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	126					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	CAGATCTCAGAAAAAATGAAG	0.303								DNA polymerases (catalytic subunits)																													p.R126fs		Atlas-INDEL	.											.	POLB	60	.	0			c.377delG						.						65	69	67					8																	42213041		2203	4298	6501	SO:0001589	frameshift_variant	5423	exon7			.		CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	2.7.7.7	"DNA polymerases"	9174	protein-coding gene	gene with protein product		174760					Standard	NM_002690		Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.378delA	chr8.hg19:g.42213041delA	ENSP00000265421:p.Arg126fs	264.0	0.0		158.0	10.0	NM_002690	B2RC78|Q3KP48|Q6FI34	Frame_Shift_Del	DEL	ENST00000265421.4	hg19	CCDS6129.1																																																																																			.	.		0.303	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377242.1	NM_002690		-	42213041	A	-	42213041	7	5	112	1	0	1	0	1	0	0	0	0	12198	243	9	0	404	0	POLB	8	42213041	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	380750	42213041	104150981	549	17170										
PCMTD1	115294	hgsc.bcm.edu	37	chr8	52773460	52773460	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gttccacttcccaggttaagAaaagacaatcctggttgaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:52773460delA	ENST00000360540.5	-	3	658	c.252delT	c.(250-252)tttfs	p.F84fs	PCMTD1_ENST00000519559.1_Intron|PCMTD1_ENST00000522514.1_Frame_Shift_Del_p.F84fs|PCMTD1_ENST00000544451.1_Intron|PCMTD1_ENST00000521344.1_Frame_Shift_Del_p.F84fs	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	84						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				CCAGGTTAAGAAAAGACAATC	0.338																																					p.L85fs		Atlas-INDEL	.											.	PCMTD1	73	.	0			c.253delC						.						87	83	85					8																	52773460		2203	4300	6503	SO:0001589	frameshift_variant	115294	exon2			.		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.252delT	chr8.hg19:g.52773460delA	ENSP00000353739:p.Phe84fs	93.0	0.0		202.0	15.0	NM_052937	Q96FK9	Frame_Shift_Del	DEL	ENST00000360540.5	hg19	CCDS6148.1																																																																																			.	.		0.338	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937		-	52773460	A	-	52773460	7	5	112	1	0	1	0	1	0	0	0	0	11595	243	9	0	841	0	PCMTD1	8	52773460	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	10560419	52773460	93590562	550	17171										
PLAG1	5324	hgsc.bcm.edu	37	chr8	57078932	57078932	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctgaagatcctgtgtttgtGgggggagctgggaaacagaa					rs144552372		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:57078932delG	ENST00000316981.3	-	5	1852	c.1373delC	c.(1372-1374)ccafs	p.P458fs	PLAG1_ENST00000429357.2_Frame_Shift_Del_p.P458fs|PLAG1_ENST00000423799.2_Frame_Shift_Del_p.P376fs	NM_001114634.1|NM_002655.2	NP_001108106.1|NP_002646.2	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1	458	Activates transcription; Inhibition of nuclear import due to lack of NLS and KPNA2 interaction.|Massively activates transcription.		P -> T (in dbSNP:rs35883156). {ECO:0000269|PubMed:9020842}.		gland morphogenesis (GO:0022612)|multicellular organism growth (GO:0035264)|negative regulation of gene expression (GO:0010629)|organ growth (GO:0035265)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		CTNNB1/PLAG1(60)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|FGFR1_ENST00000447712/PLAG1(28)|COL1A2/PLAG1(3)|CHCHD7/PLAG1(12)|TCEA1_ENST00000521604/PLAG1(3)	breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			CTGTGTTTGTGGGGGGAGCTG	0.488			T	"TCEA1, LIFR, CTNNB1, CHCHD7"	salivary adenoma																																p.P458fs		Atlas-INDEL	.		Dom	yes		8	8q12	5324	pleiomorphic adenoma gene 1		E	.	PLAG1	123	.	0			c.1374delA						.						127	129	129					8																	57078932		2203	4300	6503	SO:0001589	frameshift_variant	5324	exon5			.	U65002	CCDS6165.1, CCDS47860.1	8q12	2010-07-30				ENSG00000181690		"Zinc fingers, C2H2-type"	9045	protein-coding gene	gene with protein product		603026				9268638	Standard	NM_002655		Approved	ZNF912	uc010lyi.3	Q6DJT9		ENST00000316981.3:c.1373delC	chr8.hg19:g.57078932delG	ENSP00000325546:p.Pro458fs	88.0	0.0		229.0	15.0	NM_002655	B4DLC2|Q59GH8|Q9Y4L2	Frame_Shift_Del	DEL	ENST00000316981.3	hg19	CCDS6165.1																																																																																			.	.		0.488	PLAG1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378212.1	NM_002655		-	57078932	G	-	57078932	7	5	112	1	0	1	0	1	0	0	0	0	12027	1348	47	0	133	0	PLAG1	8	57078932	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	4305472	57078932	89285090	551	17172										
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68113709	68113709	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcaaaagtcttacttcaaaaGcctctgctggacctcctccc	5	15	4	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:68113709G>C	ENST00000262215.3	-	37	5649	c.5260C>G	c.(5260-5262)Ctt>Gtt	p.L1754V	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.L1208V|ARFGEF1_ENST00000518230.1_Missense_Mutation_p.L592V|ARFGEF1_ENST00000517955.1_5'UTR	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1754					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TACTTCAAAAGCCTCTGCTGG	0.587																																					p.L1754V		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.C5260G						.						63	58	59					8																	68113709		2203	4300	6503	SO:0001583	missense	10565	exon37			TCAAAAGCCTCTG	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.5260C>G	chr8.hg19:g.68113709G>C	ENSP00000262215:p.Leu1754Val	106.0	0.0		349.0	17.0	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	hg19	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.514446	0.64522	.	.	ENSG00000066777	ENST00000520381;ENST00000262215;ENST00000518789;ENST00000518230	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.42	5.42	0.78866	.	0.144113	0.48286	D	0.000193	T	0.71779	0.3380	M	0.88842	2.985	0.58432	D	0.99999	D;P;B;P	0.89917	1.0;0.89;0.435;0.89	D;P;B;P	0.87578	0.998;0.486;0.266;0.486	T	0.74973	-0.3481	10	0.51188	T	0.08	.	12.5629	0.56293	0.0772:0.0:0.9228:0.0	.	1754;1232;578;1208	Q9Y6D6;Q59FY5;B3KMS9;E5RIF2	BIG1_HUMAN;.;.;.	V	1208;1754;85;592	ENSP00000428429:L1208V;ENSP00000262215:L1754V;ENSP00000429560:L85V;ENSP00000430891:L592V	ENSP00000262215:L1754V	L	-	1	0	ARFGEF1	68276263	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.826000	0.62715	2.717000	0.92951	0.650000	0.86243	CTT	.	.		0.587	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		C	68113709	G	C	68113709	3	2	112	1	0	0	0	0	1	0	0	0	852	971	34	4	301	4	ARFGEF1	8	68113709	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	11034777	68113709	78250313	552	17173										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77775609	77775609	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaacaccccaaaaaagaggAaaaaatctcatctgctcttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:77775609delA	ENST00000521891.2	+	11	10107	c.9659delA	c.(9658-9660)gaafs	p.E3220fs	ZFHX4_ENST00000050961.6_Frame_Shift_Del_p.E3171fs|ZFHX4_ENST00000455469.2_Frame_Shift_Del_p.E3175fs|ZFHX4_ENST00000518282.1_Frame_Shift_Del_p.E3194fs	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAAAAAGAGGAAAAAATCTCA	0.403										HNSCC(33;0.089)																											p.E3220fs		Atlas-INDEL	.											.	ZFHX4	878	.	0			c.9658delG						.						130	126	128					8																	77775609		1864	4098	5962	SO:0001589	frameshift_variant	79776	exon11			.		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.9659delA	chr8.hg19:g.77775609delA	ENSP00000430497:p.Glu3220fs	67.0	0.0		246.0	15.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Frame_Shift_Del	DEL	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.403	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		-	77775609	A	-	77775609	7	5	112	1	0	1	0	1	0	0	0	0	17650	246	9	0	9697	0	ZFHX4	8	77775609	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	9661900	77775609	68588413	553	17174										
RBM12B	389677	hgsc.bcm.edu	37	chr8	94746023	94746023	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaatcatcaggcgggctcctAaaatcctcaccaggaggtct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:94746023delA	ENST00000399300.2	-	3	2829	c.2616delT	c.(2614-2616)tttfs	p.F872fs	RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000517700.1_Frame_Shift_Del_p.F752fs	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	872							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			GCGGGCTCCTAAAATCCTCAC	0.488																																					p.R873fs		Atlas-INDEL	.											.	RBM12B	78	.	0			c.2617delA						.						114	117	116					8																	94746023		1806	4077	5883	SO:0001589	frameshift_variant	389677	exon3			.		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.2616delT	chr8.hg19:g.94746023delA	ENSP00000382239:p.Phe872fs	54.0	0.0		163.0	10.0	NM_203390	A8MYB5	Frame_Shift_Del	DEL	ENST00000399300.2	hg19	CCDS43755.1																																																																																			.	.		0.488	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		-	94746023	A	-	94746023	7	5	112	1	0	1	0	1	0	0	0	0	13129	359	13	0	393	0	RBM12B	8	94746023	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	16970414	94746023	51617999	554	17175										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95531264	95531264	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagtaataagactttggagaTttttctccagactaaaaaca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:95531264delT	ENST00000297591.5	-	9	2537	c.2462delA	c.(2461-2463)aatfs	p.N821fs	KIAA1429_ENST00000437199.1_Frame_Shift_Del_p.N821fs|KIAA1429_ENST00000421249.2_Frame_Shift_Del_p.N821fs	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	821					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ACTTTGGAGATTTTTCTCCAG	0.363																																					p.N821fs		Atlas-INDEL	.											.	KIAA1429	176	.	0			c.2463delT						.						54	59	57					8																	95531264		2203	4300	6503	SO:0001589	frameshift_variant	25962	exon9			.	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.2462delA	chr8.hg19:g.95531264delT	ENSP00000297591:p.Asn821fs	51.0	0.0		160.0	10.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Frame_Shift_Del	DEL	ENST00000297591.5	hg19	CCDS34923.1																																																																																			.	.		0.363	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		-	95531264	T	-	95531264	7	5	112	1	0	1	0	1	0	0	0	0	8240	1493	52	0	3094	0	KIAA1429	8	95531264	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	785241	95531264	50832758	555	17176										
FZD6	8323	hgsc.bcm.edu	37	chr8	104330820	104330820	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcttgatgtctttaatagcaTtttcttcctctcgcaaatct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:104330820delT	ENST00000358755.4	+	3	497	c.180delT	c.(178-180)catfs	p.H60fs	FZD6_ENST00000540287.1_Intron|FZD6_ENST00000522566.1_Frame_Shift_Del_p.H60fs|FZD6_ENST00000523739.1_Frame_Shift_Del_p.H28fs	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	60	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			TTTAATAGCATTTTCTTCCTC	0.299																																					p.H60fs		Atlas-INDEL	.											.	FZD6	61	.	0			c.179delA						.						70	70	70					8																	104330820		2203	4300	6503	SO:0001589	frameshift_variant	8323	exon3			.	AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"GPCR / Class F : Frizzled receptors"	4044	protein-coding gene	gene with protein product		603409	"frizzled (Drosophila) homolog 6", "frizzled homolog 6 (Drosophila)", "frizzled 6, seven transmembrane spanning receptor", "frizzled family receptor 6"			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.180delT	chr8.hg19:g.104330820delT	ENSP00000351605:p.His60fs	98.0	0.0		299.0	18.0	NM_003506	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Frame_Shift_Del	DEL	ENST00000358755.4	hg19	CCDS6298.1																																																																																			.	.		0.299	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506		-	104330820	T	-	104330820	7	5	112	1	0	1	0	1	0	0	0	0	6142	1490	52	0	186	0	FZD6	8	104330820	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	8799556	104330820	42033202	556	17177										
LRP12	29967	hgsc.bcm.edu	37	chr8	105503191	105503191	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atcatcttctcttccacttaCcccattatcaagttgtctca					rs370769936		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:105503191delC	ENST00000276654.5	-	7	2398	c.2290delG	c.(2290-2292)gtafs	p.V764fs	LRP12_ENST00000424843.2_Frame_Shift_Del_p.V745fs|LRP12_ENST00000518375.1_5'UTR	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	764					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CTTCCACTTACCCCATTATCA	0.428																																					p.V764fs		Atlas-INDEL	.											.	LRP12	124	.	0			c.2291delT						.						116	114	115					8																	105503191		2203	4300	6503	SO:0001589	frameshift_variant	29967	exon7			.	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.2290delG	chr8.hg19:g.105503191delC	ENSP00000276654:p.Val764fs	24.0	0.0		182.0	11.0	NM_013437	A8K137|B4DRQ2	Frame_Shift_Del	DEL	ENST00000276654.5	hg19	CCDS6303.1																																																																																			.	.		0.428	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		-	105503191	C	-	105503191	7	5	112	1	0	1	0	1	0	0	0	0	8963	507	18	0	293	0	LRP12	8	105503191	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1172371	105503191	40860831	557	17178										
ZHX2	22882	hgsc.bcm.edu	37	chr8	123965336	123965336	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcatgcgtacccagactttgCcccccagaagttcaaagaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:123965336delC	ENST00000314393.4	+	3	2421	c.1586delC	c.(1585-1587)gccfs	p.A529fs		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	529					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CCAGACTTTGCCCCCCAGAAG	0.517																																					p.A529fs	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-INDEL	.											.	ZHX2	106	.	0			c.1585delG						.						61	56	57					8																	123965336		2203	4300	6503	SO:0001589	frameshift_variant	22882	exon3			.	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1586delC	chr8.hg19:g.123965336delC	ENSP00000314709:p.Ala529fs	69.0	0.0		257.0	18.0	NM_014943		Frame_Shift_Del	DEL	ENST00000314393.4	hg19	CCDS6336.1																																																																																			.	.		0.517	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		-	123965336	C	-	123965336	7	5	112	1	0	1	0	1	0	0	0	0	17691	739	26	0	1588	0	ZHX2	8	123965336	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	18462145	123965336	22398686	558	17179										
OC90	729330	hgsc.bcm.edu	37	chr8	133036828	133036828	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtggagggtcctcctcgctgTcctcctcagagctggagccc	13	15	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:133036828T>C	ENST00000443356.2	-	15	1468	c.1382A>G	c.(1381-1383)gAc>gGc	p.D461G	OC90_ENST00000603859.1_Missense_Mutation_p.D445G|OC90_ENST00000262283.5_Missense_Mutation_p.D657G|OC90_ENST00000254627.3_Missense_Mutation_p.D445G			Q02509	OC90_HUMAN	otoconin 90	461					lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			CTCCTCGCTGTCCTCCTCAGA	0.652																																					p.D445G		Atlas-SNP	.											OC90_ENST00000262283,caecum,carcinoma,0,2	OC90	163	.	0			c.A1334G						.						22	25	24					8																	133036828		1933	4127	6060	SO:0001583	missense	729330	exon14			TCGCTGTCCTCCT	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.1382A>G	chr8.hg19:g.133036828T>C	ENSP00000390050:p.Asp461Gly	52.0	0.0		187.0	10.0	NM_001080399	B4DNG8	Missense_Mutation	SNP	ENST00000443356.2	hg19		.	.	.	.	.	.	.	.	.	.	T	11.74	1.729548	0.30684	.	.	ENSG00000253117;ENSG00000253117;ENSG00000258417	ENST00000254627;ENST00000443356;ENST00000262283	T;T;T	0.31769	1.51;1.51;1.48	5.85	2.04	0.26737	.	0.704021	0.14765	N	0.299776	T	0.13798	0.0334	N	0.14661	0.345	0.22541	N	0.999008	B;B	0.33171	0.4;0.278	B;B	0.30855	0.121;0.057	T	0.17531	-1.0366	10	0.56958	D	0.05	-5.1902	0.9521	0.01378	0.1744:0.1368:0.1819:0.5069	.	445;461	Q02509-2;Q02509	.;OC90_HUMAN	G	445;461;657	ENSP00000254627:D445G;ENSP00000390050:D461G;ENSP00000262283:D657G	ENSP00000254627:D445G	D	-	2	0	RP11-240B13.2;OC90	133106010	0.988000	0.35896	0.976000	0.42696	0.071000	0.16799	0.804000	0.27098	0.407000	0.25591	0.533000	0.62120	GAC	.	.		0.652	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399		C	133036828	T	C	133036828	3	2	112	1	0	0	0	0	1	0	0	0	10823	1667	58	2	103	2	OC90	8	133036828	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	9071492	133036828	13327194	559	17180										
PTK2	5747	hgsc.bcm.edu	37	chr8	141749131	141749131	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actcaccaaacatccatacgTcactagctgaggtaaaacgt	6	12	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:141749131T>C	ENST00000522684.1	-	21	2040	c.1811A>G	c.(1810-1812)gAc>gGc	p.D604G	PTK2_ENST00000538769.1_Missense_Mutation_p.D272G|PTK2_ENST00000521059.1_Missense_Mutation_p.D604G|PTK2_ENST00000519465.1_Missense_Mutation_p.D232G|PTK2_ENST00000519419.1_Missense_Mutation_p.D648G|PTK2_ENST00000340930.3_Missense_Mutation_p.D604G|PTK2_ENST00000535192.1_Missense_Mutation_p.D604G|PTK2_ENST00000517887.1_Missense_Mutation_p.D648G|PTK2_ENST00000395218.2_Missense_Mutation_p.D604G	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	604	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			CATCCATACGTCACTAGCTGA	0.279																																					p.D626G		Atlas-SNP	.											.	PTK2	311	.	0			c.A1877G						.						61	60	60					8																	141749131		2203	4300	6503	SO:0001583	missense	5747	exon21			CATACGTCACTAG	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9611	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 71"	600758	"PTK2 protein tyrosine kinase 2"			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.1811A>G	chr8.hg19:g.141749131T>C	ENSP00000429911:p.Asp604Gly	26.0	0.0		116.0	5.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.23|18.23	3.577129|3.577129	0.65878|0.65878	.|.	.|.	ENSG00000169398|ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000521986;ENST00000342207|ENST00000519654	D;D;D;D;D;D;D;D;D;D;D|.	0.88818|.	-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43|.	5.07|5.07	3.91|3.91	0.45181|0.45181	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);|.	0.046536|.	0.85682|.	N|.	0.000000|.	D|.	0.87633|.	0.6226|.	H|H	0.98629|0.98629	4.285|4.285	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0|.	D;D;D;D;D;D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0|.	D|.	0.89457|.	0.3734|.	10|.	0.87932|.	D|.	0|.	.|.	10.7871|10.7871	0.46411|0.46411	0.0:0.0746:0.0:0.9254|0.0:0.0746:0.0:0.9254	.|.	604;299;524;604;626;604;556;452;272;232|.	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4|.	.;.;.;FAK1_HUMAN;.;.;.;.;.;.|.	G|W	604;604;232;648;604;556;604;525;299;276;604;272;648;302;450|614	ENSP00000429911:D604G;ENSP00000438009:D604G;ENSP00000429170:D232G;ENSP00000429082:D648G;ENSP00000429474:D604G;ENSP00000378644:D604G;ENSP00000428492:D276G;ENSP00000341189:D604G;ENSP00000445742:D272G;ENSP00000429129:D648G;ENSP00000430603:D302G|.	ENSP00000341189:D604G|.	D|X	-|-	2|3	0|0	PTK2|PTK2	141818313|141818313	1.000000|1.000000	0.71417|0.71417	0.880000|0.880000	0.34516|0.34516	0.777000|0.777000	0.43975|0.43975	7.859000|7.859000	0.86982|0.86982	0.782000|0.782000	0.33613|0.33613	-0.290000|-0.290000	0.09829|0.09829	GAC|TGA	.	.		0.279	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		C	141749131	T	C	141749131	3	2	112	1	0	0	0	0	1	0	0	0	12775	1667	58	2	1395	2	PTK2	8	141749131	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	8712303	141749131	4614891	560	17181										
ZFP41	286128	hgsc.bcm.edu	37	chr8	144332034	144332034	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atggagaagcctgcaggcagAaaaaagaagacgccgacccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:144332034delA	ENST00000330701.4	+	2	390	c.21delA	c.(19-21)agafs	p.R7fs	ZFP41_ENST00000520584.1_Frame_Shift_Del_p.R7fs|ZFP41_ENST00000522452.1_Frame_Shift_Del_p.R7fs	NM_173832.4	NP_776193.1	Q8N8Y5	ZFP41_HUMAN	ZFP41 zinc finger protein	7					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|lung(4)|ovary(1)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CTGCAGGCAGAAAAAAGAAGA	0.587																																					p.R7fs		Atlas-INDEL	.											.	ZFP41	25	.	0			c.20delG						.						24	27	26					8																	144332034		2201	4299	6500	SO:0001589	frameshift_variant	286128	exon2			.		CCDS6397.1	8q24.3	2013-01-08	2012-11-27		ENSG00000181638	ENSG00000181638		"Zinc fingers, C2H2-type"	26786	protein-coding gene	gene with protein product			"zinc finger protein 41 homolog (mouse)"			11214971	Standard	NM_173832		Approved	FLJ38705, FLJ00028, ZNF753	uc003yxw.4	Q8N8Y5	OTTHUMG00000164951	ENST00000330701.4:c.21delA	chr8.hg19:g.144332034delA	ENSP00000327427:p.Arg7fs	47.0	0.0		198.0	13.0	NM_173832	D3DWJ5	Frame_Shift_Del	DEL	ENST00000330701.4	hg19	CCDS6397.1																																																																																			.	.		0.587	ZFP41-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381114.2	NM_173832		-	144332034	A	-	144332034	7	5	112	1	0	1	0	1	0	0	0	0	17664	243	9	0	23	0	ZFP41	8	144332034	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2582903	144332034	2031988	561	17182										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144940597	144940597	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacagcctcaggttgcgcacGgggtcgatgacgaagccggt	16	11	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:144940597G>A	ENST00000525985.1	-	2	6896	c.6825C>T	c.(6823-6825)ccC>ccT	p.P2275P				P58107	EPIPL_HUMAN	epiplakin 1	2275						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGTTGCGCACGGGGTCGATGA	0.721																																					p.P2275P		Atlas-SNP	.											.	EPPK1	199	.	0			c.C6825T						.						50	47	48					8																	144940597		2163	4239	6402	SO:0001819	synonymous_variant	83481	exon1			GCGCACGGGGTCG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6825C>T	chr8.hg19:g.144940597G>A		1.0	0.0		39.0	4.0	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	hg19																																																																																				.	.		0.721	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144940597	G	A	144940597	2	1	112	1	0	0	0	0	0	0	0	1	5192	1103	39	1		1	EPPK1	8	144940597	Silent	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	608563	144940597	1423425	562	17183										
CYC1	1537	hgsc.bcm.edu	37	chr8	145150814	145150814	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgctgggcatgctggcggcaGggggtgcggggctggccatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:145150814delG	ENST00000318911.4	+	2	281	c.208delG	c.(208-210)gggfs	p.G71fs		NM_001916.3	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	71					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to glucagon (GO:0033762)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|respiratory chain (GO:0070469)	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity (GO:0045155)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	15	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCTGGCGGCAGGGGGTGCGGG	0.662											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A69fs		Atlas-INDEL	.											.	CYC1	34	.	0			c.207delA						.						58	60	60					8																	145150814		2203	4299	6502	SO:0001589	frameshift_variant	1537	exon2			.	BC001006	CCDS6415.1	8q24	2011-07-04			ENSG00000179091	ENSG00000179091		"Mitochondrial respiratory chain complex / Complex III"	2579	protein-coding gene	gene with protein product		123980					Standard	NM_001916		Approved	UQCR4	uc003zaz.4	P08574	OTTHUMG00000165242	ENST00000318911.4:c.208delG	chr8.hg19:g.145150814delG	ENSP00000317159:p.Gly71fs	62.0	0.0	1692	239.0	15.0	NM_001916	Q5U062|Q6FHS7	Frame_Shift_Del	DEL	ENST00000318911.4	hg19	CCDS6415.1																																																																																			.	.		0.662	CYC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382895.1	NM_001916		-	145150814	G	-	145150814	7	5	112	1	0	1	0	1	0	0	0	0	4137	1000	35	0	214	0	CYC1	8	145150814	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	210217	145150814	1213208	563	17184										
CPSF1	29894	hgsc.bcm.edu	37	chr8	145619169	145619169	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttcagtggccccccggcacGgggtcctccagaacgtgttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:145619169delG	ENST00000349769.3	-	35	4038	c.3944delC	c.(3943-3945)ccgfs	p.P1315fs	CPSF1_ENST00000531727.1_5'UTR|MIR939_ENST00000401314.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	1315					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CCCCCGGCACGGGGTCCTCCA	0.622																																					p.P1315fs	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-INDEL	.											.	CPSF1	92	.	0			c.3945delG						.						56	55	55					8																	145619169		2201	4300	6501	SO:0001589	frameshift_variant	29894	exon35			.	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.3944delC	chr8.hg19:g.145619169delG	ENSP00000339353:p.Pro1315fs	87.0	0.0		274.0	17.0	NM_013291	Q96AF0	Frame_Shift_Del	DEL	ENST00000349769.3	hg19	CCDS34966.1																																																																																			.	.		0.622	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		-	145619169	G	-	145619169	7	5	112	1	0	1	0	1	0	0	0	0	3826	1116	39	0	403	0	CPSF1	8	145619169	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	468355	145619169	744853	564	17185										
KIFC2	90990	hgsc.bcm.edu	37	chr8	145693366	145693366	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgggccccccatcagggctcCgcaggtactctgctcccgag	12	18	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:145693366C>T	ENST00000301332.2	+	7	1183	c.806C>T	c.(805-807)cCg>cTg	p.P269L	CYHR1_ENST00000306145.5_5'Flank|KIFC2_ENST00000301331.5_Missense_Mutation_p.P17L|CYHR1_ENST00000403000.2_5'Flank|CYHR1_ENST00000424149.2_5'Flank|CYHR1_ENST00000438911.2_5'Flank|CTD-2517M22.16_ENST00000525461.1_RNA	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	269	Gln-rich.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			ATCAGGGCTCCGCAGGTACTC	0.677																																					p.P269L		Atlas-SNP	.											.	KIFC2	53	.	0			c.C806T						.						12	15	14					8																	145693366		2178	4270	6448	SO:0001583	missense	90990	exon7			GGGCTCCGCAGGT	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"Kinesins"	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.806C>T	chr8.hg19:g.145693366C>T	ENSP00000301332:p.Pro269Leu	42.0	0.0		218.0	25.0	NM_145754	E9PHB2|Q96NN6	Missense_Mutation	SNP	ENST00000301332.2	hg19	CCDS6427.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.755500	0.49362	.	.	ENSG00000167702	ENST00000301332;ENST00000301331	T;T	0.71461	-0.57;-0.51	4.22	2.34	0.29019	.	0.251086	0.21037	N	0.081232	T	0.49236	0.1545	N	0.24115	0.695	0.23640	N	0.997228	B	0.16802	0.019	B	0.14578	0.011	T	0.23762	-1.0179	10	0.14252	T	0.57	-9.219	6.5852	0.22616	0.1789:0.7215:0.0:0.0996	.	269	Q96AC6	KIFC2_HUMAN	L	269;17	ENSP00000301332:P269L;ENSP00000301331:P17L	ENSP00000301331:P17L	P	+	2	0	KIFC2	145664174	0.000000	0.05858	0.331000	0.25455	0.036000	0.12997	0.282000	0.18829	0.486000	0.27676	0.655000	0.94253	CCG	.	.		0.677	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754		T	145693366	C	T	145693366	3	4	112	1	0	0	0	0	1	0	0	0	8322	652	23	1	832	1	KIFC2	8	145693366	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	74197	145693366	670656	565	17186										
RFX3	5991	hgsc.bcm.edu	37	chr9	3275558	3275558	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatcctcaaaggtagtaccaTctggcagagaagagatttca	9	8	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:3275558T>C	ENST00000382004.3	-	10	1339	c.1028A>G	c.(1027-1029)gAt>gGt	p.D343G	RFX3_ENST00000358730.2_Missense_Mutation_p.D343G|RFX3_ENST00000302303.1_Missense_Mutation_p.D343G	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	343					cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		GGTAGTACCATCTGGCAGAGA	0.418																																					p.D343G		Atlas-SNP	.											.	RFX3	156	.	0			c.A1028G						.						120	114	116					9																	3275558		2203	4300	6503	SO:0001583	missense	5991	exon10			GTACCATCTGGCA	AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.1028A>G	chr9.hg19:g.3275558T>C	ENSP00000371434:p.Asp343Gly	88.0	0.0		68.0	4.0	NM_134428	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	hg19	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.460186	0.63401	.	.	ENSG00000080298	ENST00000382004;ENST00000358730;ENST00000302303	T;T;T	0.58797	0.32;0.31;0.31	5.83	5.83	0.93111	.	0.048134	0.85682	D	0.000000	T	0.61565	0.2357	L	0.39147	1.195	0.80722	D	1	D;B;B	0.58970	0.984;0.003;0.001	P;B;B	0.56042	0.79;0.011;0.003	T	0.55872	-0.8072	10	0.17369	T	0.5	-14.9945	16.2141	0.82191	0.0:0.0:0.0:1.0	.	343;343;343	P48380-3;P48380-2;P48380	.;.;RFX3_HUMAN	G	343	ENSP00000371434:D343G;ENSP00000351574:D343G;ENSP00000303847:D343G	ENSP00000303847:D343G	D	-	2	0	RFX3	3265558	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.186000	0.72026	2.224000	0.72417	0.528000	0.53228	GAT	.	.		0.418	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		C	3275558	T	C	3275558	3	2	112	1	0	0	0	0	1	0	0	0	13279	1435	50	2	1413	2	RFX3	9	3275558	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10		3275558	137937873	566	17187										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5921058	5921058	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcacatttactgctcttgcTgaagaaaccactgattcatt	6	10	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:5921058T>C	ENST00000399933.3	-	8	4937	c.4938A>G	c.(4936-4938)tcA>tcG	p.S1646S	KIAA2026_ENST00000381461.2_Silent_p.S1616S	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1646										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		CTGCTCTTGCTGAAGAAACCA	0.428																																					p.S1646S		Atlas-SNP	.											.	KIAA2026	231	.	0			c.A4938G						.						99	94	96					9																	5921058		1856	4100	5956	SO:0001819	synonymous_variant	158358	exon8			TCTTGCTGAAGAA	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.4938A>G	chr9.hg19:g.5921058T>C		51.0	0.0		72.0	5.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	hg19																																																																																				.	.		0.428	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		C	5921058	T	C	5921058	2	2	112	1	0	0	0	0	0	0	0	1	8279	1567	55	2		2	KIAA2026	9	5921058	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2645500	5921058	135292373	567	17188										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5954073	5954073	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcctcttctttgtgattgcTtttttagagacggatttttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:5954073delT	ENST00000399933.3	-	4	2234	c.2235delA	c.(2233-2235)aaafs	p.K745fs	KIAA2026_ENST00000381461.2_Frame_Shift_Del_p.K745fs	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	745	Lys-rich.									breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TTGTGATTGCTTTTTTAGAGA	0.308																																					p.A746fs		Atlas-INDEL	.											.	KIAA2026	231	.	0			c.2236delG						.						164	145	151					9																	5954073		1798	4061	5859	SO:0001589	frameshift_variant	158358	exon4			.	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.2235delA	chr9.hg19:g.5954073delT	ENSP00000382815:p.Lys745fs	138.0	0.0		135.0	10.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Frame_Shift_Del	DEL	ENST00000399933.3	hg19																																																																																				.	.		0.308	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		-	5954073	T	-	5954073	7	5	112	1	0	1	0	1	0	0	0	0	8279	1606	56	0	4096	0	KIAA2026	9	5954073	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	33015	5954073	135259358	568	17189										
KDM4C	23081	hgsc.bcm.edu	37	chr9	6805725	6805725	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcactcagtacaacatccagAaaaaagcgatgactgtgaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:6805725delA	ENST00000381309.3	+	3	836	c.271delA	c.(271-273)aaafs	p.K92fs	KDM4C_ENST00000535193.1_Frame_Shift_Del_p.K114fs|KDM4C_ENST00000489243.1_3'UTR|KDM4C_ENST00000381306.3_Frame_Shift_Del_p.K92fs|KDM4C_ENST00000536108.1_5'UTR|KDM4C_ENST00000543771.1_Frame_Shift_Del_p.K92fs|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000401787.3_Frame_Shift_Del_p.K92fs	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	92					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						CAACATCCAGAAAAAAGCGAT	0.423																																					p.Q112fs		Atlas-INDEL	.											.	KDM4C	186	.	0			c.336delG						.						124	118	120					9																	6805725		2203	4300	6503	SO:0001589	frameshift_variant	23081	exon3			.	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	17071	protein-coding gene	gene with protein product	"tudor domain containing 14C"	605469	"jumonji domain containing 2C"	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.271delA	chr9.hg19:g.6805725delA	ENSP00000370710:p.Lys92fs	193.0	0.0		199.0	12.0	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Frame_Shift_Del	DEL	ENST00000381309.3	hg19	CCDS6471.1																																																																																			.	.		0.423	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		-	6805725	A	-	6805725	7	5	112	1	0	1	0	1	0	0	0	0	8139	247	9	0	347	0	KDM4C	9	6805725	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	851652	6805725	134407706	569	17190										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13125334	13125334	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagcctgggaatctggattcTcagcatggatggtaagtttt	12	7	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:13125334T>C	ENST00000319217.7	-	35	4935	c.4688A>G	c.(4687-4689)gAg>gGg	p.E1563G	MPDZ_ENST00000536827.1_Missense_Mutation_p.E1530G|MPDZ_ENST00000381022.2_Missense_Mutation_p.E1563G|MPDZ_ENST00000541093.1_5'UTR|MPDZ_ENST00000541718.1_Missense_Mutation_p.E1563G|MPDZ_ENST00000546205.1_Missense_Mutation_p.E1577G|MPDZ_ENST00000381015.4_Missense_Mutation_p.E1563G|MPDZ_ENST00000447879.1_Missense_Mutation_p.E1530G|MPDZ_ENST00000538841.1_Missense_Mutation_p.E422G	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1563	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		ATCTGGATTCTCAGCATGGAT	0.473																																					p.E1563G		Atlas-SNP	.											.	MPDZ	324	.	0			c.A4688G						.						115	111	112					9																	13125334		1883	4118	6001	SO:0001583	missense	8777	exon35			GGATTCTCAGCAT	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.4688A>G	chr9.hg19:g.13125334T>C	ENSP00000320006:p.Glu1563Gly	135.0	0.0		114.0	6.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	T	12.59	1.983258	0.35036	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000438511;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.83	5.83	0.93111	PDZ/DHR/GLGF (3);	0.139426	0.32719	N	0.005734	T	0.33933	0.0880	L	0.46614	1.455	0.80722	D	1	B;B;B;B;B;B;B	0.25235	0.121;0.0;0.018;0.089;0.054;0.089;0.032	B;B;B;B;B;B;B	0.26969	0.034;0.001;0.021;0.075;0.05;0.075;0.028	T	0.16778	-1.0391	10	0.22109	T	0.4	.	8.4452	0.32838	0.1222:0.0:0.1424:0.7354	.	1530;422;268;1530;1443;1563;1563	B7ZMI4;B7ZB24;B4DGX5;O75970-3;E7EPZ1;O75970-2;O75970	.;.;.;.;.;.;MPDZ_HUMAN	G	1563;1563;1563;132;499;422;1530;1530;1563;1443;1577	ENSP00000320006:E1563G;ENSP00000439807:E1563G;ENSP00000370410:E1563G;ENSP00000415964:E132G;ENSP00000444230:E499G;ENSP00000444717:E422G;ENSP00000444151:E1530G;ENSP00000415208:E1530G;ENSP00000370403:E1563G;ENSP00000446358:E1577G	ENSP00000320006:E1563G	E	-	2	0	MPDZ	13115334	0.986000	0.35501	0.980000	0.43619	0.403000	0.30841	1.508000	0.35769	2.228000	0.72767	0.528000	0.53228	GAG	.	.		0.473	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		C	13125334	T	C	13125334	3	2	112	1	0	0	0	0	1	0	0	0	9731	1551	54	2	1485	2	MPDZ	9	13125334	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	6319609	13125334	128088097	570	17191										
FREM1	158326	hgsc.bcm.edu	37	chr9	14863881	14863881	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acatacttgacttcgttgggAaggaaatggcagtcaaagac	11	7	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:14863881A>G	ENST00000380880.3	-	3	1038	c.255T>C	c.(253-255)ctT>ctC	p.L85L	FREM1_ENST00000380881.4_Silent_p.L85L|FREM1_ENST00000422223.2_Silent_p.L85L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	85					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		CTTCGTTGGGAAGGAAATGGC	0.413																																					p.L85L		Atlas-SNP	.											.	FREM1	261	.	0			c.T255C						.						108	103	105					9																	14863881		1935	4139	6074	SO:0001819	synonymous_variant	158326	exon4			GTTGGGAAGGAAA	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.255T>C	chr9.hg19:g.14863881A>G		112.0	0.0		100.0	4.0	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	hg19	CCDS47952.1																																																																																			.	.		0.413	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		G	14863881	A	G	14863881	2	3	112	1	0	0	0	0	0	0	0	1	6052	233	9	2		2	FREM1	9	14863881	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1738547	14863881	126349550	571	17192										
DENND4C	55667	hgsc.bcm.edu	37	chr9	19346888	19346888	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcataaagaacgttcaacttCtttgtcagcactggtgcgtt	8	9	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:19346888C>T	ENST00000380432.2	+	18	3299	c.3266C>T	c.(3265-3267)tCt>tTt	p.S1089F	DENND4C_ENST00000434457.2_Missense_Mutation_p.S1374F|DENND4C_ENST00000602925.1_Missense_Mutation_p.S1325F			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1089					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CGTTCAACTTCTTTGTCAGCA	0.468																																					p.S1325F		Atlas-SNP	.											DENND4C,colon,carcinoma,0,1	DENND4C	120	.	0			c.C3974T						.						64	63	63					9																	19346888		2203	4300	6503	SO:0001583	missense	55667	exon22			CAACTTCTTTGTC	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.3266C>T	chr9.hg19:g.19346888C>T	ENSP00000369797:p.Ser1089Phe	36.0	0.0		72.0	4.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	C	22.4	4.285076	0.80803	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T	0.57752	0.38;0.38	5.31	5.31	0.75309	.	2.141580	0.01702	N	0.027243	T	0.74535	0.3729	L	0.59436	1.845	0.80722	D	1	P;D;D;P	0.54397	0.768;0.966;0.959;0.943	B;P;P;P	0.61397	0.396;0.873;0.888;0.75	T	0.58634	-0.7602	10	0.87932	D	0	-16.8913	18.9763	0.92738	0.0:1.0:0.0:0.0	.	419;1089;271;1089	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	F	1089;562;271;419;562;271;86	ENSP00000305795:S562F;ENSP00000443804:S419F	ENSP00000305795:S562F	S	+	2	0	DENND4C	19336888	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.263000	0.78421	2.483000	0.83821	0.585000	0.79938	TCT	.	.		0.468	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		T	19346888	C	T	19346888	3	4	112	1	0	0	0	0	1	0	0	0	4437	913	32	3	3336	3	DENND4C	9	19346888	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	4483007	19346888	121866543	572	17193										
C9orf82	79886	hgsc.bcm.edu	37	chr9	26886160	26886160	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctaactgttcctggcatagTtttttaatttcttctattga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:26886160delT	ENST00000333916.5	-	3	619	c.531delA	c.(529-531)aaafs	p.K177fs	CAAP1_ENST00000520187.1_Intron|CAAP1_ENST00000495958.1_Intron|CAAP1_ENST00000535437.1_Frame_Shift_Del_p.K32fs	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	177					apoptotic process (GO:0006915)												CCTGGCATAGTTTTTTAATTT	0.294																																					p.L178fs		Atlas-INDEL	.											.	.	.	.	0			c.532delC						.						30	32	32					9																	26886160		2186	4269	6455	SO:0001589	frameshift_variant	79886	exon3			.	BC014658	CCDS6516.1	9p21.2	2012-04-20	2012-04-20	2012-04-20	ENSG00000120159	ENSG00000120159			25834	protein-coding gene	gene with protein product	"conserved anti-apoptotic protein"		"chromosome 9 open reading frame 82"	C9orf82		21980415	Standard	NM_024828		Approved	FLJ13657, CAAP	uc003zqc.3	Q9H8G2	OTTHUMG00000019706	ENST00000333916.5:c.531delA	chr9.hg19:g.26886160delT	ENSP00000369431:p.Lys177fs	194.0	0.0		197.0	12.0	NM_024828	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Frame_Shift_Del	DEL	ENST00000333916.5	hg19	CCDS6516.1																																																																																			.	.		0.294	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051954.1	NM_024828		-	26886160	T	-	26886160	7	5	112	1	0	1	0	1	0	0	0	0	2501	1722	60	0	570	0	C9orf82	9	26886160	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	7539272	26886160	114327271	573	17194										
ACO1	48	hgsc.bcm.edu	37	chr9	32425907	32425907	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acctttatctatgataacacTgaattcacccttgctcatgg	5	11	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:32425907T>G	ENST00000309951.6	+	11	1398	c.1260T>G	c.(1258-1260)acT>acG	p.T420T	ACO1_ENST00000379923.1_Silent_p.T420T|ACO1_ENST00000541043.1_Silent_p.T321T	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	420					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		ATGATAACACTGAATTCACCC	0.383																																					p.T420T		Atlas-SNP	.											ACO1_ENST00000379923,NS,carcinoma,0,2	ACO1	149	.	0			c.T1260G						.						137	107	117					9																	32425907		2203	4300	6503	SO:0001819	synonymous_variant	48	exon11			TAACACTGAATTC	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1260T>G	chr9.hg19:g.32425907T>G		121.0	0.0		97.0	4.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	hg19	CCDS6525.1																																																																																			.	.		0.383	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		G	32425907	T	G	32425907	2	3	112	1	0	0	0	0	0	0	0	1	146	1567	55	5		5	ACO1	9	32425907	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	5539747	32425907	108787524	574	17195										
CHMP5	51510	hgsc.bcm.edu	37	chr9	33271180	33271180	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgaaactgggagtaaaggaaAtgaagaaggcatacaagcaa	12	4	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:33271180A>G	ENST00000223500.8	+	5	483	c.346A>G	c.(346-348)Atg>Gtg	p.M116V	CHMP5_ENST00000419016.2_Missense_Mutation_p.M116V	NM_016410.5	NP_057494.3	Q9NZZ3	CHMP5_HUMAN	charged multivesicular body protein 5	116					endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of receptor recycling (GO:0001919)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10			LUSC - Lung squamous cell carcinoma(29;0.00506)			AGTAAAGGAAATGAAGAAGGC	0.353																																					p.M116V		Atlas-SNP	.											.	CHMP5	15	.	0			c.A346G						.						164	144	151					9																	33271180		2203	4300	6503	SO:0001583	missense	51510	exon5			AAGGAAATGAAGA	AF132968	CCDS6537.1, CCDS56569.1	9p13.3	2011-09-21	2011-09-21	2005-08-09	ENSG00000086065	ENSG00000086065		"Charged multivesicular body proteins"	26942	protein-coding gene	gene with protein product		610900	"chromosome 9 open reading frame 83", "chromatin modifying protein 5"	C9orf83, SNF7DC2		15644320, 11559748	Standard	NM_016410		Approved	HSPC177, CGI-34, Vps60	uc003zsm.4	Q9NZZ3	OTTHUMG00000019765	ENST00000223500.8:c.346A>G	chr9.hg19:g.33271180A>G	ENSP00000223500:p.Met116Val	64.0	0.0		82.0	6.0	NM_016410	B2RD95|B4DIR6|Q5VXW2|Q96AV2|Q9HB68|Q9NYS4|Q9Y323	Missense_Mutation	SNP	ENST00000223500.8	hg19	CCDS6537.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172728	0.78452	.	.	ENSG00000086065	ENST00000223500;ENST00000419016	T;T	0.79653	-1.29;-1.29	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.86222	0.5881	M	0.87328	2.875	0.58432	D	0.999999	P;B	0.36712	0.566;0.416	B;B	0.43990	0.438;0.403	D	0.88094	0.2815	10	0.87932	D	0	-9.9225	14.049	0.64725	1.0:0.0:0.0:0.0	.	116;116	B4DIR6;Q9NZZ3	.;CHMP5_HUMAN	V	116	ENSP00000223500:M116V;ENSP00000442725:M116V	ENSP00000223500:M116V	M	+	1	0	CHMP5	33261180	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.879000	0.92398	2.259000	0.74868	0.529000	0.55759	ATG	.	.		0.353	CHMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052040.3	NM_016410		G	33271180	A	G	33271180	3	3	112	1	0	0	0	0	1	0	0	0	3361	101	4	2	364	2	CHMP5	9	33271180	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	845273	33271180	107942251	575	17196										
NFX1	4799	hgsc.bcm.edu	37	chr9	33295418	33295418	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgctaaagaatgtggaaacGcacacaggtaaacctaccta	9	9	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:33295418G>A	ENST00000379540.3	+	2	1088	c.1026G>A	c.(1024-1026)acG>acA	p.T342T	NFX1_ENST00000379521.4_Silent_p.T342T|NFX1_ENST00000318524.6_Silent_p.T342T	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	342					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		ATGTGGAAACGCACACAGGTA	0.363																																					p.T342T		Atlas-SNP	.											.	NFX1	85	.	0			c.G1026A						.						57	55	56					9																	33295418		2203	4300	6503	SO:0001819	synonymous_variant	4799	exon2			GGAAACGCACACA	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1026G>A	chr9.hg19:g.33295418G>A		27.0	0.0		33.0	14.0	NM_147134	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Silent	SNP	ENST00000379540.3	hg19	CCDS6538.1																																																																																			.	.		0.363	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			A	33295418	G	A	33295418	2	1	112	1	0	0	0	0	0	0	0	1	10396	1074	38	1		1	NFX1	9	33295418	Silent	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	24238	33295418	107918013	576	17197										
C9orf24	84688	hgsc.bcm.edu	37	chr9	34385753	34385753	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcagggcttcgggatccacAtgtcgctccatggtatgagt	13	10	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:34385753A>G	ENST00000297623.2	-	2	360	c.162T>C	c.(160-162)caT>caC	p.H54H		NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	54					cell differentiation (GO:0030154)|cellular protein complex assembly (GO:0043623)|spermatogenesis (GO:0007283)	manchette (GO:0002177)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)		CGGGATCCACATGTCGCTCCA	0.557																																					p.H54H		Atlas-SNP	.											.	C9orf24	15	.	0			c.T162C						.						104	99	101					9																	34385753		2203	4300	6503	SO:0001819	synonymous_variant	84688	exon2			ATCCACATGTCGC	BC029484	CCDS6553.1, CCDS6554.1, CCDS6555.1, CCDS59121.1	9p11.2	2013-01-11			ENSG00000164972	ENSG00000164972			19919	protein-coding gene	gene with protein product	"ciliated bronchial epithelium 1", "spermatid-specific manchette-related protein 1"					12029067	Standard	NM_147168		Approved	bA573M23.4, NYD-SP22, MGC32921, MGC33614, CBE1, SMRP1	uc003zuh.1	Q8NCR6	OTTHUMG00000000437	ENST00000297623.2:c.162T>C	chr9.hg19:g.34385753A>G		95.0	0.0		95.0	4.0	NM_032596	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Silent	SNP	ENST00000297623.2	hg19	CCDS6554.1	.	.	.	.	.	.	.	.	.	.	A	0.144	-1.098945	0.01843	.	.	ENSG00000164972	ENST00000444429	.	.	.	5.89	-11.8	0.00035	.	.	.	.	.	T	0.26738	0.0654	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.25984	-1.0116	4	.	.	.	-6.9167	11.3006	0.49302	0.1352:0.171:0.6092:0.0846	.	.	.	.	R	20	.	.	C	-	1	0	C9orf24	34375753	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-1.545000	0.02190	-2.668000	0.00415	-0.250000	0.11733	TGT	.	.		0.557	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169		G	34385753	A	G	34385753	2	3	112	1	0	0	0	0	0	0	0	1	2477	214	8	2		2	C9orf24	9	34385753	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1090335	34385753	106827678	577	17198										
SIGMAR1	10280	hgsc.bcm.edu	37	chr9	34635688	34635688	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccggaggccccgagcataggAgcgaagagtatagaagaggg	17	8	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:34635688A>G	ENST00000277010.4	-	4	686	c.613T>C	c.(613-615)Tcc>Ccc	p.S205P	SIGMAR1_ENST00000477726.1_Missense_Mutation_p.S174P|SIGMAR1_ENST00000461426.1_5'UTR|SIGMAR1_ENST00000378892.1_Missense_Mutation_p.S116P	NM_001282208.1|NM_005866.2	NP_001269137.1|NP_005857.1	Q99720	SGMR1_HUMAN	sigma non-opioid intracellular receptor 1	205					cell death (GO:0008219)|lipid transport (GO:0006869)|nervous system development (GO:0007399)|regulation of neuron apoptotic process (GO:0043523)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|nuclear envelope (GO:0005635)	drug binding (GO:0008144)|opioid receptor activity (GO:0004985)			large_intestine(1)|lung(1)	2					Amitriptyline(DB00321)|Dextromethorphan(DB00514)|Nortriptyline(DB00540)|Pentazocine(DB00652)|Remoxipride(DB00409)	CGAGCATAGGAGCGAAGAGTA	0.627																																					p.S205P		Atlas-SNP	.											.	SIGMAR1	6	.	0			c.T613C						.						108	95	100					9																	34635688		2203	4300	6503	SO:0001583	missense	10280	exon4			CATAGGAGCGAAG	BC004899	CCDS6562.1, CCDS6563.1	9p13.3	2008-12-18	2008-12-18	2008-12-18	ENSG00000147955	ENSG00000147955			8157	protein-coding gene	gene with protein product		601978	"opioid receptor, sigma 1"	OPRS1		8954936, 9453537	Standard	NM_005866		Approved	SR-BP1	uc003zvb.3	Q99720	OTTHUMG00000019829	ENST00000277010.4:c.613T>C	chr9.hg19:g.34635688A>G	ENSP00000277010:p.Ser205Pro	134.0	0.0		161.0	7.0	NM_005866	D3DRM7|O00673|O00725|Q0Z9W6|Q153Z1|Q2TSD1|Q53GN2|Q7Z653|Q8N7H3|Q9NYX0	Missense_Mutation	SNP	ENST00000277010.4	hg19	CCDS6562.1	.	.	.	.	.	.	.	.	.	.	A	14.82	2.649224	0.47362	.	.	ENSG00000147955	ENST00000378892;ENST00000277010;ENST00000360710;ENST00000477726	T;T;T	0.63255	-0.03;-0.03;-0.03	4.43	1.08	0.20341	.	0.278543	0.34750	N	0.003713	T	0.37376	0.1001	N	0.08118	0	0.25052	N	0.991129	B;B;P	0.38420	0.202;0.119;0.63	B;B;B	0.32289	0.072;0.143;0.131	T	0.21586	-1.0241	10	0.42905	T	0.14	-10.9058	14.248	0.66001	0.1673:0.8327:0.0:0.0	.	174;205;185	A2A3U5;Q99720;Q99720-2	.;SGMR1_HUMAN;.	P	116;205;171;174	ENSP00000368170:S116P;ENSP00000277010:S205P;ENSP00000420022:S174P	ENSP00000277010:S205P	S	-	1	0	SIGMAR1	34625688	0.903000	0.30736	0.812000	0.32479	0.995000	0.86356	1.916000	0.39986	0.006000	0.14734	0.379000	0.24179	TCC	.	.		0.627	SIGMAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052204.1	NM_005866		G	34635688	A	G	34635688	3	3	112	1	0	0	0	0	1	0	0	0	14331	304	11	2	62	2	SIGMAR1	9	34635688	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	249935	34635688	106577743	578	17199										
TLN1	7094	hgsc.bcm.edu	37	chr9	35717439	35717439	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgattgtaggtgccaccaccTgtaggtaaagtgaatgtcag	12	7	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:35717439T>C	ENST00000314888.9	-	19	2517		c.e19-2		TLN1_ENST00000540444.1_Splice_Site	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TGCCACCACCTGTAGGTAAAG	0.557																																					.		Atlas-SNP	.											.	TLN1	185	.	0			c.2164-2A>G						.						64	59	61					9																	35717439		2203	4300	6503	SO:0001630	splice_region_variant	7094	exon20			ACCACCTGTAGGT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.2164-2A>G	chr9.hg19:g.35717439T>C		66.0	0.0		73.0	4.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Splice_Site	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.044061	0.75732	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7766	0.78224	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TLN1	35707439	1.000000	0.71417	0.967000	0.41034	0.795000	0.44927	8.040000	0.89188	2.143000	0.66587	0.459000	0.35465	.	.	.		0.557	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	Intron	C	35717439	T	C	35717439	5	2	112	1	0	0	0	0	0	0	1	0	15962	1594	55	2	5619	2	TLN1	9	35717439	Splice_Site	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1081751	35717439	105495992	579	17200										
HRCT1	646962	hgsc.bcm.edu	37	chr9	35906303	35906303	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agatgctgggcctcctggggAgcacagccctcgtgggatgg	17	11	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:35906303A>G	ENST00000354323.2	+	1	115	c.19A>G	c.(19-21)Agc>Ggc	p.S7G		NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	7						integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						CCTCCTGGGGAGCACAGCCCT	0.652																																					p.S7G		Atlas-SNP	.											.	HRCT1	14	.	0			c.A19G						.						22	24	23					9																	35906303		2202	4300	6502	SO:0001583	missense	646962	exon1			CTGGGGAGCACAG		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.19A>G	chr9.hg19:g.35906303A>G	ENSP00000346283:p.Ser7Gly	68.0	0.0		100.0	7.0	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	hg19	CCDS35012.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.481596	0.44147	.	.	ENSG00000196196	ENST00000354323	.	.	.	3.83	2.69	0.31865	.	0.379917	0.19341	N	0.116648	T	0.24314	0.0589	N	0.19112	0.55	0.22866	N	0.998639	B	0.17667	0.023	B	0.14023	0.01	T	0.12889	-1.0530	9	0.41790	T	0.15	-13.1954	5.9057	0.19001	0.8813:0.0:0.1187:0.0	.	7	Q6UXD1	HRCT1_HUMAN	G	7	.	ENSP00000346283:S7G	S	+	1	0	HRCT1	35896303	0.999000	0.42202	0.989000	0.46669	0.649000	0.38597	1.385000	0.34408	0.827000	0.34685	0.533000	0.62120	AGC	.	.		0.652	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792		G	35906303	A	G	35906303	3	3	112	1	0	0	0	0	1	0	0	0	7362	304	11	2	21	2	HRCT1	9	35906303	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	188864	35906303	105307128	580	17201										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37707505	37707505	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaagatagacaaagacacccTcctccaggactatggatttc	7	11	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:37707505T>C	ENST00000539465.1	+	3	787	c.194T>C	c.(193-195)cTc>cCc	p.L65P	FRMPD1_ENST00000377765.3_Missense_Mutation_p.L65P|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	65	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		AAAGACACCCTCCTCCAGGAC	0.527																																					p.L65P		Atlas-SNP	.											.	FRMPD1	237	.	0			c.T194C						.						126	124	125					9																	37707505		2203	4300	6503	SO:0001583	missense	22844	exon3			ACACCCTCCTCCA	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.194T>C	chr9.hg19:g.37707505T>C	ENSP00000444411:p.Leu65Pro	72.0	0.0		86.0	4.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	hg19	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	T	19.80	3.895589	0.72639	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.26957	1.7;1.7	5.97	4.82	0.62117	PDZ/DHR/GLGF (3);	0.757041	0.12892	N	0.430536	T	0.31918	0.0812	L	0.27053	0.805	0.80722	D	1	D	0.57257	0.979	P	0.58331	0.837	T	0.01935	-1.1244	10	0.54805	T	0.06	-4.9713	9.1518	0.36967	0.0:0.0828:0.0:0.9172	.	65	Q5SYB0	FRPD1_HUMAN	P	65	ENSP00000366995:L65P;ENSP00000444411:L65P	ENSP00000366995:L65P	L	+	2	0	FRMPD1	37697505	0.899000	0.30636	0.923000	0.36655	0.985000	0.73830	2.208000	0.42797	1.062000	0.40625	0.533000	0.62120	CTC	.	.		0.527	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		C	37707505	T	C	37707505	3	2	112	1	0	0	0	0	1	0	0	0	6065	1551	54	2	200	2	FRMPD1	9	37707505	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1801202	37707505	103505926	581	17202										
RG9MTD3	158234	hgsc.bcm.edu	37	chr9	37762657	37762657	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagcaagaaaaagaacgaagAaaagccaatcgtgcagaaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:37762657delA	ENST00000297994.3	+	3	335	c.270delA	c.(268-270)agafs	p.R90fs	TRMT10B_ENST00000377753.2_Intron|RP11-613M10.9_ENST00000540557.1_Intron|TRMT10B_ENST00000377754.2_Intron|TRMT10B_ENST00000537911.1_Frame_Shift_Del_p.R90fs	NM_144964.2	NP_659401.2	Q6PF06	TM10B_HUMAN	tRNA methyltransferase 10 homolog B (S. cerevisiae)	90							methyltransferase activity (GO:0008168)										AAGAACGAAGAAAAGCCAATC	0.343																																					p.R90fs		Atlas-INDEL	.											.	.	.	.	0			c.269delG						.						45	47	46					9																	37762657		1824	4082	5906	SO:0001589	frameshift_variant	158234	exon3			.	BC057774	CCDS43804.1, CCDS69598.1, CCDS69600.1, CCDS69601.1	9p13.1	2012-06-28	2012-06-28	2012-06-28	ENSG00000165275	ENSG00000165275			26454	protein-coding gene	gene with protein product			"RNA (guanine-9-) methyltransferase domain containing 3"	RG9MTD3		14702039	Standard	XM_005251373		Approved	FLJ31455, bA3J10.9	uc004aai.3	Q6PF06	OTTHUMG00000019933	ENST00000297994.3:c.270delA	chr9.hg19:g.37762657delA	ENSP00000297994:p.Arg90fs	190.0	0.0		158.0	10.0	NM_144964	B7Z216|B7Z3D3|Q05DJ4|Q5QP83|Q8NAG2|Q96N36	Frame_Shift_Del	DEL	ENST00000297994.3	hg19	CCDS43804.1																																																																																			.	.		0.343	TRMT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052482.1	NM_144964		-	37762657	A	-	37762657	7	5	112	1	0	1	0	1	0	0	0	0	13288	243	9	0	276	0	RG9MTD3	9	37762657	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	55152	37762657	103450774	582	17203										
ZFAND5	7763	hgsc.bcm.edu	37	chr9	74974352	74974352	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acctggctctgacacctctgTtttcggggtagttattttgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:74974352delT	ENST00000237937.3	-	4	906	c.349delA	c.(349-351)acafs	p.T117fs	ZFAND5_ENST00000376960.4_Frame_Shift_Del_p.T117fs|ZFAND5_ENST00000376962.5_Frame_Shift_Del_p.T117fs|ZFAND5_ENST00000343431.2_Frame_Shift_Del_p.T117fs|ZFAND5_ENST00000488164.1_5'UTR	NM_001102421.1|NM_001278243.1|NM_001278244.1|NM_001278245.1|NM_006007.2	NP_001095891.1|NP_001265172.1|NP_001265173.1|NP_001265174.1|NP_005998.1	O76080	ZFAN5_HUMAN	zinc finger, AN1-type domain 5	117					face development (GO:0060324)|fibroblast migration (GO:0010761)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|respiratory system process (GO:0003016)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|kidney(2)|lung(2)|prostate(1)	6						GACACCTCTGTTTTCGGGGTA	0.418																																					p.T117fs		Atlas-INDEL	.											.	ZFAND5	14	.	0			c.350delC						.						89	87	87					9																	74974352		2203	4299	6502	SO:0001589	frameshift_variant	7763	exon5			.	AF062072	CCDS6642.1	9q13-q21	2008-05-02	2006-07-07	2006-07-07	ENSG00000107372	ENSG00000107372		"Zinc fingers, AN1-type domain containing"	13008	protein-coding gene	gene with protein product		604761	"zinc finger protein 216", "zinc finger, A20 domain containing 2"	ZNF216, ZA20D2		9758550	Standard	NM_001278243		Approved	ZFAND5A	uc004aiy.2	O76080	OTTHUMG00000020008	ENST00000237937.3:c.349delA	chr9.hg19:g.74974352delT	ENSP00000237937:p.Thr117fs	105.0	0.0		116.0	10.0	NM_001102420	A8K484	Frame_Shift_Del	DEL	ENST00000237937.3	hg19	CCDS6642.1																																																																																			.	.		0.418	ZFAND5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052644.1			-	74974352	T	-	74974352	7	5	112	1	0	1	0	1	0	0	0	0	17645	1725	60	0	304	0	ZFAND5	9	74974352	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	37211695	74974352	66239079	583	17204										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79318977	79318977	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggctctttggtaggaattgTtttttcttcttccaattctg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:79318977delT	ENST00000376718.3	-	9	7675	c.7552delA	c.(7552-7554)acafs	p.T2518fs	PRUNE2_ENST00000428286.1_Frame_Shift_Del_p.T2159fs	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2518					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GTAGGAATTGTTTTTTCTTCT	0.363																																					p.T2518fs		Atlas-INDEL	.											.	PRUNE2	331	.	0			c.7553delC						.						140	130	133					9																	79318977		1568	3582	5150	SO:0001589	frameshift_variant	158471	exon9			.	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.7552delA	chr9.hg19:g.79318977delT	ENSP00000365908:p.Thr2518fs	127.0	0.0		170.0	11.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Frame_Shift_Del	DEL	ENST00000376718.3	hg19	CCDS47982.1																																																																																			.	.		0.363	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		-	79318977	T	-	79318977	7	5	112	1	0	1	0	1	0	0	0	0	12653	1725	60	0	1758	0	PRUNE2	9	79318977	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	4344625	79318977	61894454	584	17205										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79465566	79465566	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagcactggtaaacacagaaCccctggtggactgacctacc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:79465566delC	ENST00000376718.3	-	3	280	c.157delG	c.(157-159)gttfs	p.V53fs	PRUNE2_ENST00000376713.3_Frame_Shift_Del_p.V53fs|PRUNE2_ENST00000428286.1_5'UTR	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	53					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AAACACAGAACCCCTGGTGGA	0.403																																					p.V53fs		Atlas-INDEL	.											.	PRUNE2	331	.	0			c.158delT						.						102	106	105					9																	79465566		2203	4300	6503	SO:0001589	frameshift_variant	158471	exon3			.	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.157delG	chr9.hg19:g.79465566delC	ENSP00000365908:p.Val53fs	148.0	0.0		153.0	10.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Frame_Shift_Del	DEL	ENST00000376718.3	hg19	CCDS47982.1																																																																																			.	.		0.403	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		-	79465566	C	-	79465566	7	5	112	1	0	1	0	1	0	0	0	0	12653	507	18	0	9177	0	PRUNE2	9	79465566	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	146589	79465566	61747865	585	17206										
PSAT1	29968	hgsc.bcm.edu	37	chr9	80923403	80923403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgtggtgattgtccgtgatgAcctgctggggtttgccctcc	14	11	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:80923403A>G	ENST00000376588.3	+	6	712	c.644A>G	c.(643-645)gAc>gGc	p.D215G	PSAT1_ENST00000347159.2_Missense_Mutation_p.D215G	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1	215					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-serine biosynthetic process (GO:0006564)|pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	O-phospho-L-serine:2-oxoglutarate aminotransferase activity (GO:0004648)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						GTCCGTGATGACCTGCTGGGG	0.517																																					p.D215G	Colon(34;187 791 10662 18313 37609)	Atlas-SNP	.											.	PSAT1	33	.	0			c.A644G						.						141	119	127					9																	80923403		2203	4300	6503	SO:0001583	missense	29968	exon6			GTGATGACCTGCT	BC004863	CCDS6659.1, CCDS6660.1	9q21.2	2008-08-11			ENSG00000135069	ENSG00000135069			19129	protein-coding gene	gene with protein product		610936				12633500, 3651428	Standard	NM_058179		Approved	PSA	uc004ala.3	Q9Y617	OTTHUMG00000020066	ENST00000376588.3:c.644A>G	chr9.hg19:g.80923403A>G	ENSP00000365773:p.Asp215Gly	192.0	0.0		145.0	6.0	NM_021154	Q5T7G5|Q5T7G6|Q96AW2|Q9BQ12	Missense_Mutation	SNP	ENST00000376588.3	hg19	CCDS6660.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.929233	0.92389	.	.	ENSG00000135069	ENST00000421149;ENST00000347159;ENST00000376588	T;T	0.65732	-0.17;-0.17	5.59	5.59	0.84812	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	D	0.83083	0.5177	M	0.91717	3.235	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.73380	0.945;0.98	D	0.87222	0.2254	10	0.87932	D	0	-13.1243	15.7658	0.78126	1.0:0.0:0.0:0.0	.	215;215	Q9Y617-2;Q9Y617	.;SERC_HUMAN	G	39;215;215	ENSP00000317606:D215G;ENSP00000365773:D215G	ENSP00000317606:D215G	D	+	2	0	PSAT1	80113223	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.899000	0.92544	2.131000	0.65755	0.455000	0.32223	GAC	.	.		0.517	PSAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052777.1	NM_021154		G	80923403	A	G	80923403	3	3	112	1	0	0	0	0	1	0	0	0	12656	275	10	2	666	2	PSAT1	9	80923403	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1457837	80923403	60290028	586	17207										
UBQLN1	29979	hgsc.bcm.edu	37	chr9	86284243	86284243	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggtgtgttgaacatactagCtgaaagtttgtttttaaaaa	9	3	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:86284243C>T	ENST00000376395.4	-	7	1629		c.e7-1		UBQLN1_ENST00000257468.7_Splice_Site	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1						cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)			breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						AACATACTAGCTGAAAGTTTG	0.328																																					.	Melanoma(186;1284 2073 12755 14558 18426)	Atlas-SNP	.											.	UBQLN1	49	.	0			c.1106-1G>A						.						97	87	91					9																	86284243		2203	4300	6503	SO:0001630	splice_region_variant	29979	exon8			TACTAGCTGAAAG	AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"Ubiquilin family"	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1106-1G>A	chr9.hg19:g.86284243C>T		78.0	0.0		80.0	5.0	NM_013438	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Splice_Site	SNP	ENST00000376395.4	hg19	CCDS6663.1	.	.	.	.	.	.	.	.	.	.	C	19.68	3.872873	0.72180	.	.	ENSG00000135018	ENST00000376395;ENST00000257468	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8548	0.96752	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBQLN1	85474063	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.054000	0.57434	2.687000	0.91594	0.655000	0.94253	.	.	.		0.328	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438	Intron	T	86284243	C	T	86284243	5	4	112	1	0	0	0	0	0	0	1	0	16911	811	28	3	684	3	UBQLN1	9	86284243	Splice_Site	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	5360840	86284243	54929188	587	17208										
SLC28A3	64078	hgsc.bcm.edu	37	chr9	86920237	86920237	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctacagaaaccacatactGtgtcatacctcctttccaaa	3	14	1	1	rs570175390		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:86920237G>C	ENST00000376238.4	-	4	315	c.266C>G	c.(265-267)aCa>aGa	p.T89R	SLC28A3_ENST00000495823.1_5'UTR|SLC28A3_ENST00000537648.1_Missense_Mutation_p.T20R	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	89					pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)	p.T89I(1)		endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	ACCACATACTGTGTCATACCT	0.398																																					p.T89R	Ovarian(106;425 1539 34835 42413 43572)	Atlas-SNP	.											SLC28A3,NS,carcinoma,0,1	SLC28A3	72	.	1	Substitution - Missense(1)	endometrium(1)	c.C266G						.						138	126	130					9																	86920237		2203	4300	6503	SO:0001583	missense	64078	exon4			CATACTGTGTCAT	AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"Solute carriers"	16484	protein-coding gene	gene with protein product		608269	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.266C>G	chr9.hg19:g.86920237G>C	ENSP00000365413:p.Thr89Arg	114.0	0.0		145.0	0.0	NM_001199633	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Missense_Mutation	SNP	ENST00000376238.4	hg19	CCDS6670.1	.	.	.	.	.	.	.	.	.	.	G	0.037	-1.300979	0.01364	.	.	ENSG00000197506	ENST00000376238;ENST00000537648	T;T	0.01838	4.8;4.61	5.49	-5.3	0.02738	.	1.406730	0.04062	N	0.306495	T	0.01222	0.0040	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.46303	-0.9201	10	0.08381	T	0.77	6.5937	2.532	0.04705	0.1242:0.2813:0.2153:0.3792	.	20;89	B4E2S8;Q9HAS3	.;S28A3_HUMAN	R	89;20	ENSP00000365413:T89R;ENSP00000446438:T20R	ENSP00000365413:T89R	T	-	2	0	SLC28A3	86110057	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.234000	0.09028	-0.818000	0.04329	-0.140000	0.14226	ACA	.	.		0.398	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127		C	86920237	G	C	86920237	3	2	112	1	0	0	0	0	1	0	0	0	14548	1377	48	4	1869	4	SLC28A3	9	86920237	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	635994	86920237	54293194	588	17209										
TSTD2	158427	hgsc.bcm.edu	37	chr9	100389705	100389705	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctttgcaaacgagtatttcTtttttgtactgccatctaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:100389705delT	ENST00000341170.4	-	2	522	c.140delA	c.(139-141)aagfs	p.K48fs	TSTD2_ENST00000354801.2_5'UTR	NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	48										large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						CGAGTATTTCTTTTTTGTACT	0.343																																					p.K47fs		Atlas-INDEL	.											.	TSTD2	42	.	0			c.141delG						.						177	163	167					9																	100389705		2203	4300	6503	SO:0001589	frameshift_variant	158427	exon2			.	AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925			30087	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 97"	C9orf97		12477932	Standard	NM_139246		Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.140delA	chr9.hg19:g.100389705delT	ENSP00000342499:p.Lys48fs	163.0	0.0		188.0	13.0	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Frame_Shift_Del	DEL	ENST00000341170.4	hg19	CCDS6727.2																																																																																			.	.		0.343	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246		-	100389705	T	-	100389705	7	5	112	1	0	1	0	1	0	0	0	0	16690	1609	56	0	1446	0	TSTD2	9	100389705	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	13469468	100389705	40823726	589	17210										
NCBP1	4686	hgsc.bcm.edu	37	chr9	100410326	100410326	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggcccagattcagaaattgAaaaaggatcgctggcaggaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:100410326delA	ENST00000375147.3	+	8	974	c.718delA	c.(718-720)aaafs	p.K241fs		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	241					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				TCAGAAATTGAAAAAGGATCG	0.378																																					p.L239fs	Ovarian(36;879 898 2893 44212 50307)	Atlas-INDEL	.											.	NCBP1	64	.	0			c.717delG						.						63	56	59					9																	100410326		2203	4300	6503	SO:0001589	frameshift_variant	4686	exon8			.	BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.718delA	chr9.hg19:g.100410326delA	ENSP00000364289:p.Lys241fs	167.0	0.0		146.0	11.0	NM_002486	B2R718|Q59G76|Q5T1V0|Q5T7X2	Frame_Shift_Del	DEL	ENST00000375147.3	hg19	CCDS6728.1																																																																																			.	.		0.378	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		-	100410326	A	-	100410326	7	5	112	1	0	1	0	1	0	0	0	0	10220	247	9	0	748	0	NCBP1	9	100410326	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	20621	100410326	40803105	590	17211										
C9orf156	51531	hgsc.bcm.edu	37	chr9	100672401	100672401	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggccatgggctgtgtctctgCcctgcttccttgcaagactg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:100672401delC	ENST00000375119.3	-	4	983	c.907delG	c.(907-909)gcafs	p.A303fs	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	303					viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				TGTGTCTCTGCCCTGCTTCCT	0.572																																					p.A303fs		Atlas-INDEL	.											.	C9orf156	35	.	0			c.908delC						.						114	97	102					9																	100672401		2203	4300	6503	SO:0001589	frameshift_variant	51531	exon4			.	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"Nef (lentivirus myristoylated factor) associated protein 1"						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.907delG	chr9.hg19:g.100672401delC	ENSP00000364260:p.Ala303fs	141.0	0.0		181.0	12.0	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Frame_Shift_Del	DEL	ENST00000375119.3	hg19	CCDS6730.1																																																																																			.	.		0.572	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481		-	100672401	C	-	100672401	7	5	112	1	0	1	0	1	0	0	0	0	2467	739	26	0	426	0	C9orf156	9	100672401	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	262075	100672401	40541030	591	17212										
COL15A1	1306	hgsc.bcm.edu	37	chr9	101765842	101765842	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccaaccctctctatgtccacGgagaacccagaggaaggggt	11	13	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:101765842G>T	ENST00000375001.3	+	8	1596	c.1173G>T	c.(1171-1173)acG>acT	p.T391T		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	391	4 X tandem repeats.|Nonhelical region 1 (NC1).		T -> M (in dbSNP:rs10988532).		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.T391T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CTATGTCCACGGAGAACCCAG	0.622																																					p.T391T		Atlas-SNP	.											COL15A1,NS,carcinoma,0,1	COL15A1	211	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1173T						.						57	61	60					9																	101765842		2203	4300	6503	SO:0001819	synonymous_variant	1306	exon8			GTCCACGGAGAAC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1173G>T	chr9.hg19:g.101765842G>T		180.0	1.0		196.0	0.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	hg19	CCDS35081.1																																																																																			.	.		0.622	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		T	101765842	G	T	101765842	2	4	112	1	0	0	0	0	0	0	0	1	3674	1103	39	1		1	COL15A1	9	101765842	Silent	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	1093441	101765842	39447589	592	17213										
TMEFF1	8577	hgsc.bcm.edu	37	chr9	103279042	103279042	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctgagtgtgatgaagatgcAgaaaatgttgggtgagttgg	17	2	0	6			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:103279042A>G	ENST00000374879.4	+	5	981	c.549A>G	c.(547-549)gcA>gcG	p.A183A	TMEFF1_ENST00000334943.6_Silent_p.A144A|MSANTD3-TMEFF1_ENST00000502978.1_Missense_Mutation_p.R147G	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	183					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				ATGAAGATGCAGAAAATGTTG	0.393																																					p.A257A		Atlas-SNP	.											.	.	.	.	0			c.A771G						.						123	104	111					9																	103279042		2203	4300	6503	SO:0001819	synonymous_variant	100526694	exon5			AGATGCAGAAAAT	U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"tomoregulin-1", "cancer/testis antigen family 120, member 1"	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.549A>G	chr9.hg19:g.103279042A>G		86.0	0.0		113.0	5.0	NM_001198812	Q13086|Q8N3T8	Silent	SNP	ENST00000374879.4	hg19	CCDS6750.1	.	.	.	.	.	.	.	.	.	.	A	8.992	0.977907	0.18812	.	.	ENSG00000251349	ENST00000502978	.	.	.	5.74	1.96	0.26148	.	.	.	.	.	T	0.45994	0.1370	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29731	-1.0002	4	.	.	.	-30.1287	3.3496	0.07147	0.568:0.0:0.2675:0.1644	.	.	.	.	G	147	.	.	R	+	1	2	C9orf30-TMEFF1	102318863	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	1.435000	0.34969	0.552000	0.29026	0.460000	0.39030	AGA	.	.		0.393	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692		G	103279042	A	G	103279042	2	3	112	1	0	0	0	0	0	0	0	1	16028	175	7	2		2	TMEFF1	9	103279042	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1513200	103279042	37934389	593	17214										
RNF20	56254	hgsc.bcm.edu	37	chr9	104323165	104323165	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cattggcacaggggagaaagAgctgggtcttaggacccaag	15	8	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:104323165A>G	ENST00000389120.3	+	17	2555	c.2465A>G	c.(2464-2466)gAg>gGg	p.E822G		NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	822					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		GGGGAGAAAGAGCTGGGTCTT	0.418																																					p.E822G		Atlas-SNP	.											.	RNF20	110	.	0			c.A2465G						.						83	85	84					9																	104323165		2203	4300	6503	SO:0001583	missense	56254	exon17			AGAAAGAGCTGGG	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.2465A>G	chr9.hg19:g.104323165A>G	ENSP00000373772:p.Glu822Gly	101.0	0.0		134.0	6.0	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	hg19	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.680329	0.88542	.	.	ENSG00000155827	ENST00000389120	T	0.38887	1.11	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.66076	0.2753	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.70230	-0.4929	10	0.66056	D	0.02	-24.4215	15.5321	0.75970	1.0:0.0:0.0:0.0	.	822	Q5VTR2	BRE1A_HUMAN	G	822	ENSP00000373772:E822G	ENSP00000373772:E822G	E	+	2	0	RNF20	103362986	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	8.962000	0.93254	2.204000	0.70986	0.528000	0.53228	GAG	.	.		0.418	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		G	104323165	A	G	104323165	3	3	112	1	0	0	0	0	1	0	0	0	13488	304	11	2	2527	2	RNF20	9	104323165	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1044123	104323165	36890266	594	17215										
RAD23B	5887	hgsc.bcm.edu	37	chr9	110091920	110091920	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccaattttcttctacagcagAactttgatgaagattgaaag	7	7	2	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:110091920A>G	ENST00000358015.3	+	10	1564	c.1213A>G	c.(1213-1215)Aac>Gac	p.N405D	RAD23B_ENST00000416373.2_Missense_Mutation_p.N333D	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	405					DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						TCTACAGCAGAACTTTGATGA	0.398								Direct reversal of damage;Nucleotide excision repair (NER)																													p.N405D		Atlas-SNP	.											.	RAD23B	31	.	0			c.A1213G						.						77	77	77					9																	110091920		2203	4300	6503	SO:0001583	missense	5887	exon10			CAGCAGAACTTTG		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"XP-C repair complementing protein", "XP-C repair complementing complex 58 kDa"	600062	"RAD23 (S. cerevisiae) homolog B"			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.1213A>G	chr9.hg19:g.110091920A>G	ENSP00000350708:p.Asn405Asp	85.0	0.0		71.0	4.0	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	hg19	CCDS6769.1	.	.	.	.	.	.	.	.	.	.	A	16.99	3.272855	0.59649	.	.	ENSG00000119318	ENST00000358015;ENST00000416373	T;T	0.55052	0.54;0.54	4.85	4.85	0.62838	UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.62356	0.2421	L	0.38531	1.155	0.80722	D	1	D;P	0.63880	0.993;0.609	D;B	0.70935	0.971;0.168	T	0.64106	-0.6485	10	0.51188	T	0.08	-2.3866	14.7172	0.69277	1.0:0.0:0.0:0.0	.	384;405	B7Z4W4;P54727	.;RD23B_HUMAN	D	405;333	ENSP00000350708:N405D;ENSP00000405623:N333D	ENSP00000350708:N405D	N	+	1	0	RAD23B	109131741	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.943000	0.63554	1.942000	0.56320	0.460000	0.39030	AAC	.	.		0.398	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874		G	110091920	A	G	110091920	3	3	112	1	0	0	0	0	1	0	0	0	12998	246	9	2	1251	2	RAD23B	9	110091920	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	5768755	110091920	31121511	595	17216										
PTGR1	22949	hgsc.bcm.edu	37	chr9	114355220	114355220	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aattacttggccacttgctgCcccatcattgtatcaccttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:114355220delC	ENST00000407693.2	-	4	457	c.195delG	c.(193-195)gggfs	p.G65fs	PTGR1_ENST00000538962.1_Frame_Shift_Del_p.G65fs|PTGR1_ENST00000309195.5_Frame_Shift_Del_p.G65fs|PTGR1_ENST00000238248.3_5'UTR	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	65					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						CCACTTGCTGCCCCATCATTG	0.368																																					p.Q66fs	Ovarian(200;132 2151 7551 19220 46064)	Atlas-INDEL	.											.	PTGR1	23	.	0			c.196delC						.						109	99	102					9																	114355220		2203	4300	6503	SO:0001589	frameshift_variant	22949	exon4			.	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.195delG	chr9.hg19:g.114355220delC	ENSP00000385763:p.Gly65fs	118.0	0.0		153.0	10.0	NM_001146108	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Frame_Shift_Del	DEL	ENST00000407693.2	hg19	CCDS6779.1																																																																																			.	.		0.368	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			-	114355220	C	-	114355220	7	5	112	1	0	1	0	1	0	0	0	0	12766	726	26	0	853	0	PTGR1	9	114355220	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	4263300	114355220	26858211	596	17217										
TRIM32	22954	hgsc.bcm.edu	37	chr9	119461528	119461528	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcacagttgatcgaggatcaGgggtggtcaaatacagctgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:119461528delG	ENST00000450136.1	+	2	1668	c.1507delG	c.(1507-1509)gggfs	p.G503fs	ASTN2_ENST00000361477.3_Intron|ASTN2_ENST00000313400.4_Intron|ASTN2_ENST00000373996.3_Intron|ASTN2_ENST00000361209.2_Intron|TRIM32_ENST00000373983.2_Frame_Shift_Del_p.G503fs	NM_001099679.1|NM_012210.3	NP_001093149.1|NP_036342.2	Q13049	TRI32_HUMAN	tripartite motif containing 32	503					fat cell differentiation (GO:0045444)|innate immune response (GO:0045087)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of proteolysis (GO:0045862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of type I interferon production (GO:0032479)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|striated muscle myosin thick filament (GO:0005863)	ligase activity (GO:0016874)|myosin binding (GO:0017022)|protein self-association (GO:0043621)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|translation initiation factor binding (GO:0031369)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	26						TCGAGGATCAGGGGTGGTCAA	0.522																																					p.S502fs	Esophageal Squamous(92;212 1916 19711 26951)	Atlas-INDEL	.											.	TRIM32	67	.	0			c.1506delA						.						84	70	75					9																	119461528		2203	4300	6503	SO:0001589	frameshift_variant	22954	exon2			.	U18543	CCDS6817.1	9q33.1	2014-09-17	2011-01-25		ENSG00000119401	ENSG00000119401		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16380	protein-coding gene	gene with protein product		602290	"limb girdle muscular dystrophy 2H (autosomal recessive)", "tripartite motif-containing 32"	LGMD2H		11331580, 7778269, 16606853	Standard	NM_001099679		Approved	HT2A, TATIP, BBS11	uc004bjx.2	Q13049	OTTHUMG00000021026	ENST00000450136.1:c.1507delG	chr9.hg19:g.119461528delG	ENSP00000408292:p.Gly503fs	161.0	0.0		171.0	11.0	NM_012210	Q9NQP8	Frame_Shift_Del	DEL	ENST00000450136.1	hg19	CCDS6817.1																																																																																			.	.		0.522	TRIM32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055466.2	NM_012210		-	119461528	G	-	119461528	7	5	112	1	0	1	0	1	0	0	0	0	16521	1000	35	0	1509	0	TRIM32	9	119461528	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	5106308	119461528	21751903	597	17218										
TTLL11	158135	hgsc.bcm.edu	37	chr9	124736391	124736391	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctggggacattttcaaacaCccctggagaaagcttgaacg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:124736391delC	ENST00000321582.5	-	6	1835	c.1648delG	c.(1648-1650)gtgfs	p.V550fs	TTLL11_ENST00000474723.1_5'UTR	NM_001139442.1	NP_001132914.1	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	0					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						TTTTCAAACACCCCTGGAGAA	0.493																																					p.V550fs		Atlas-INDEL	.											.	TTLL11	67	.	0			c.1649delT						.						138	123	128					9																	124736391		692	1591	2283	SO:0001589	frameshift_variant	158135	exon6			.	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"Tubulin tyrosine ligase-like family"	18113	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 20"	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000321582.5:c.1648delG	chr9.hg19:g.124736391delC	ENSP00000321346:p.Val550fs	110.0	0.0		159.0	10.0	NM_001139442		Frame_Shift_Del	DEL	ENST00000321582.5	hg19	CCDS48012.1																																																																																			.	.		0.493	TTLL11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_088486		-	124736391	C	-	124736391	7	5	112	1	0	1	0	1	0	0	0	0	16739	507	18	0	770	0	TTLL11	9	124736391	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	5274863	124736391	16477040	598	17219										
RC3H2	54542	hgsc.bcm.edu	37	chr9	125652757	125652757	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcttcctccaccagttgacaGtttacaagtgtcaccagttt					rs10818759	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:125652757delG	ENST00000373670.1	-	3	1017	c.417delC	c.(415-417)aacfs	p.N139fs	RC3H2_ENST00000471874.2_Frame_Shift_Del_p.N139fs|RC3H2_ENST00000357244.2_Frame_Shift_Del_p.N139fs|RC3H2_ENST00000478216.1_5'UTR|RC3H2_ENST00000373665.2_Frame_Shift_Del_p.N139fs|RC3H2_ENST00000335387.5_Frame_Shift_Del_p.N139fs|RC3H2_ENST00000423239.2_Frame_Shift_Del_p.N139fs			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	139					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						CCAGTTGACAGTTTACAAGTG	0.473																																					p.C140fs		Atlas-INDEL	.											.	RC3H2	150	.	0			c.418delT						.						99	99	99					9																	125652757		1941	4155	6096	SO:0001589	frameshift_variant	54542	exon4			.	AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"RING-type (C3HC4) zinc fingers", "Zinc fingers, CCCH-type domain containing"	21461	protein-coding gene	gene with protein product		615231	"membrane associated DNA binding protein", "ring finger and CCCH-type zinc finger domains 2"	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.417delC	chr9.hg19:g.125652757delG	ENSP00000362774:p.Asn139fs	137.0	0.0		173.0	11.0	NM_018835	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Frame_Shift_Del	DEL	ENST00000373670.1	hg19	CCDS43874.1																																																																																			.	.		0.473	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835		-	125652757	G	-	125652757	7	5	112	1	0	1	0	1	0	0	0	0	13182	1020	36	0	3308	0	RC3H2	9	125652757	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	916366	125652757	15560674	599	17220										
RABGAP1	23637	hgsc.bcm.edu	37	chr9	125835865	125835865	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcattcagtgttctggtcaAgatcatgtttgactatgggc	12	7	4	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:125835865A>G	ENST00000373647.4	+	16	2152	c.2018A>G	c.(2017-2019)aAg>aGg	p.K673R	RABGAP1_ENST00000493854.1_3'UTR|RABGAP1_ENST00000373643.5_Missense_Mutation_p.K12R	NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	673	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						GTTCTGGTCAAGATCATGTTT	0.443																																					p.K673R		Atlas-SNP	.											.	RABGAP1	164	.	0			c.A2018G						.						173	164	167					9																	125835865		2203	4300	6503	SO:0001583	missense	23637	exon16			TGGTCAAGATCAT	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"rab6 GTPase activating protein (GAP and centrosome-associated)", "TBC1 domain family, member 11"	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.2018A>G	chr9.hg19:g.125835865A>G	ENSP00000362751:p.Lys673Arg	126.0	0.0		96.0	4.0	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Missense_Mutation	SNP	ENST00000373647.4	hg19	CCDS6848.2	.	.	.	.	.	.	.	.	.	.	A	28.6	4.930181	0.92389	.	.	ENSG00000011454	ENST00000373647;ENST00000373643	T;T	0.11495	2.77;2.77	6.17	6.17	0.99709	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.12561	0.0305	L	0.37800	1.135	0.80722	D	1	B	0.31026	0.304	B	0.36244	0.22	T	0.18840	-1.0324	10	0.20046	T	0.44	-24.4333	16.8222	0.85835	1.0:0.0:0.0:0.0	.	673	Q9Y3P9	RBGP1_HUMAN	R	673;12	ENSP00000362751:K673R;ENSP00000362747:K12R	ENSP00000362747:K12R	K	+	2	0	RABGAP1	124875686	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.443	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197		G	125835865	A	G	125835865	3	3	112	1	0	0	0	0	1	0	0	0	12979	72	3	2	2076	2	RABGAP1	9	125835865	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	183108	125835865	15377566	600	17221										
WDR38	401551	hgsc.bcm.edu	37	chr9	127619900	127619900	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccaaatcacccagggacccTcaaacctaacaccaaccacc	3	19	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:127619900T>C	ENST00000373574.1	+	9	992	c.936T>C	c.(934-936)ccT>ccC	p.P312P		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	312					hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CCAGGGACCCTCAAACCTAAC	0.567																																					p.P313P		Atlas-SNP	.											.	WDR38	21	.	0			c.T939C						.						63	69	67					9																	127619900		2135	4240	6375	SO:0001819	synonymous_variant	401551	exon9			GGACCCTCAAACC		CCDS43876.1, CCDS75898.1, CCDS75899.1	9q33.3	2013-01-09			ENSG00000136918	ENSG00000136918		"WD repeat domain containing"	23745	protein-coding gene	gene with protein product							Standard	NM_001276375		Approved		uc011lzo.3	Q5JTN6	OTTHUMG00000020664	ENST00000373574.1:c.936T>C	chr9.hg19:g.127619900T>C		50.0	0.0		95.0	4.0	NM_001276374	A0PK24	Silent	SNP	ENST00000373574.1	hg19	CCDS43876.1																																																																																			.	.		0.567	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476		C	127619900	T	C	127619900	2	2	112	1	0	0	0	0	0	0	0	1	17307	1538	54	2		2	WDR38	9	127619900	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1784035	127619900	13593531	601	17222										
TOR1B	27348	hgsc.bcm.edu	37	chr9	132571650	132571650	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcacagtggactgatcgacAaaaacctcattgattacttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:132571650delA	ENST00000259339.2	+	5	859	c.799delA	c.(799-801)aaafs	p.K267fs		NM_014506.1	NP_055321.1	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B)	267					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum organization (GO:0007029)|nuclear membrane organization (GO:0071763)|protein homooligomerization (GO:0051260)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)	12		Ovarian(14;0.0586)				ACTGATCGACAAAAACCTCAT	0.552																																					p.D266fs		Atlas-INDEL	.											.	TOR1B	20	.	0			c.798delC						.						99	83	89					9																	132571650		2203	4300	6503	SO:0001589	frameshift_variant	27348	exon5			.	AF007872	CCDS6929.1	9q34	2008-07-21			ENSG00000136816	ENSG00000136816			11995	protein-coding gene	gene with protein product		608050				9288096, 10644435	Standard	NM_014506		Approved	DQ1, MGC4386	uc004byk.1	O14657	OTTHUMG00000020795	ENST00000259339.2:c.799delA	chr9.hg19:g.132571650delA	ENSP00000259339:p.Lys267fs	146.0	0.0		177.0	17.0	NM_014506		Frame_Shift_Del	DEL	ENST00000259339.2	hg19	CCDS6929.1																																																																																			.	.		0.552	TOR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054615.1	NM_014506		-	132571650	A	-	132571650	7	5	112	1	0	1	0	1	0	0	0	0	16389	131	5	0	817	0	TOR1B	9	132571650	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4951750	132571650	8641781	602	17223										
GPR107	57720	hgsc.bcm.edu	37	chr9	132863470	132863470	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acatcctttctgataaagacAaaaagatcttcatgattgtc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:132863470delA	ENST00000372406.1	+	12	1606	c.1099delA	c.(1099-1101)aaafs	p.K368fs	GPR107_ENST00000372410.3_Frame_Shift_Del_p.K368fs|GPR107_ENST00000347136.6_Frame_Shift_Del_p.K368fs	NM_001136557.1	NP_001130029.1	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107	368						integral component of membrane (GO:0016021)				endometrium(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	11		Ovarian(14;0.000531)				TGATAAAGACAAAAAGATCTT	0.458																																					p.D366fs		Atlas-INDEL	.											.	GPR107	30	.	0			c.1098delC						.						182	174	177					9																	132863470		2203	4300	6503	SO:0001589	frameshift_variant	57720	exon12			.	AF376725	CCDS35162.1, CCDS48041.1, CCDS48042.1	9q34.2	2014-01-30			ENSG00000148358	ENSG00000148358		"GPCR / Unclassified : 7TM orphan receptors"	17830	protein-coding gene	gene with protein product							Standard	NM_020960		Approved	KIAA1624, RP11-88G17, FLJ20998, LUSTR1	uc004bzd.2	Q5VW38	OTTHUMG00000020804	ENST00000372406.1:c.1099delA	chr9.hg19:g.132863470delA	ENSP00000361483:p.Lys368fs	184.0	0.0		190.0	12.0	NM_001136557	A6NJ53|Q2TB81|Q5JPA3|Q5VW39|Q96T26|Q9H658|Q9HCE8	Frame_Shift_Del	DEL	ENST00000372406.1	hg19	CCDS48041.1																																																																																			.	.		0.458	GPR107-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054643.2			-	132863470	A	-	132863470	7	5	112	1	0	1	0	1	0	0	0	0	6631	131	5	0	1145	0	GPR107	9	132863470	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	291820	132863470	8349961	603	17224										
NUP214	8021	hgsc.bcm.edu	37	chr9	134015961	134015961	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaaagactcttcctcctgcTccagttctcatgttactttc	5	13	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:134015961T>C	ENST00000359428.5	+	11	1302	c.1158T>C	c.(1156-1158)gcT>gcC	p.A386A	RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|NUP214_ENST00000451030.1_Silent_p.A386A|RP11-544A12.4_ENST00000586290.1_RNA|NUP214_ENST00000411637.2_Silent_p.A386A|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	386	Seven-bladed beta propeller.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTCCTCCTGCTCCAGTTCTCA	0.393			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.A386A	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.T1158C						.						130	132	132					9																	134015961		2203	4300	6503	SO:0001819	synonymous_variant	8021	exon11			TCCTGCTCCAGTT	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.1158T>C	chr9.hg19:g.134015961T>C		88.0	0.0		112.0	5.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	T	11.52	1.664693	0.29604	.	.	ENSG00000126883	ENST00000530863	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	T	0.59348	0.2187	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59558	-0.7432	4	.	.	.	-25.847	7.8314	0.29344	0.1356:0.0:0.1413:0.723	.	.	.	.	P	58	.	.	S	+	1	0	NUP214	133005782	0.992000	0.36948	1.000000	0.80357	0.995000	0.86356	0.143000	0.16115	2.206000	0.71126	0.533000	0.62120	TCC	.	.		0.393	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		C	134015961	T	C	134015961	2	2	112	1	0	0	0	0	0	0	0	1	10771	1538	54	2		2	NUP214	9	134015961	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1152491	134015961	7197470	604	17225										
POMT1	10585	hgsc.bcm.edu	37	chr9	134390827	134390827	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttccaggcatgatgttgcagCccccctgagcccccattcac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:134390827delC	ENST00000372228.3	+	13	1435	c.1256delC	c.(1255-1257)gccfs	p.A419fs	POMT1_ENST00000419118.2_Frame_Shift_Del_p.A245fs|POMT1_ENST00000423007.1_Frame_Shift_Del_p.A397fs|POMT1_ENST00000341012.7_Frame_Shift_Del_p.A343fs|POMT1_ENST00000404875.2_Frame_Shift_Del_p.A280fs|POMT1_ENST00000354713.4_Frame_Shift_Del_p.A367fs|POMT1_ENST00000485278.1_3'UTR|POMT1_ENST00000402686.3_Frame_Shift_Del_p.A397fs|RP11-334J6.6_ENST00000415423.1_RNA|POMT1_ENST00000541219.1_Frame_Shift_Del_p.A175fs	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	419	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|mannosylation (GO:0097502)|multicellular organismal development (GO:0007275)|protein O-linked glycosylation (GO:0006493)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|sarcoplasmic reticulum (GO:0016529)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannosyltransferase activity (GO:0000030)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	31		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		GATGTTGCAGCCCCCCTGAGC	0.507																																					p.A419fs		Atlas-INDEL	.											.	POMT1	59	.	0			c.1255delG						.						120	119	119					9																	134390827		2203	4300	6503	SO:0001589	frameshift_variant	10585	exon13			.	AF095136	CCDS6943.1, CCDS43894.1, CCDS43895.1, CCDS48045.1	9q34.1	2014-09-17			ENSG00000130714	ENSG00000130714	2.4.1.109	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	9202	protein-coding gene	gene with protein product	"dolichyl-phosphate-mannose-protein mannosyltransferase"	607423				10366449	Standard	NM_001077366		Approved	LGMD2K	uc004cav.3	Q9Y6A1	OTTHUMG00000020826	ENST00000372228.3:c.1256delC	chr9.hg19:g.134390827delC	ENSP00000361302:p.Ala419fs	137.0	0.0		156.0	11.0	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Frame_Shift_Del	DEL	ENST00000372228.3	hg19	CCDS6943.1																																																																																			.	.		0.507	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171		-	134390827	C	-	134390827	7	5	112	1	0	1	0	1	0	0	0	0	12254	739	26	0	1302	0	POMT1	9	134390827	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	374866	134390827	6822604	605	17226										
C9orf171	389799	hgsc.bcm.edu	37	chr9	135374145	135374145	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcattaattttaattatggaCtctacatccgagggcttgac	8	8	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:135374145C>T	ENST00000343036.2	+	3	415	c.367C>T	c.(367-369)Ctc>Ttc	p.L123F	C9orf171_ENST00000393215.3_Missense_Mutation_p.L87F|C9orf171_ENST00000393216.2_Missense_Mutation_p.L87F	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	123										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						TAATTATGGACTCTACATCCG	0.577																																					p.L123F		Atlas-SNP	.											.	C9orf171	53	.	0			c.C367T						.						30	30	30					9																	135374145		2203	4300	6503	SO:0001583	missense	389799	exon3			TATGGACTCTACA	AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.367C>T	chr9.hg19:g.135374145C>T	ENSP00000343290:p.Leu123Phe	51.0	0.0		52.0	5.0	NM_207417	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	hg19	CCDS6949.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648559	0.47258	.	.	ENSG00000188523	ENST00000393215;ENST00000343036;ENST00000393216	T;T;T	0.23754	1.89;1.89;1.89	5.14	4.22	0.49857	.	0.265059	0.31507	N	0.007537	T	0.35941	0.0949	L	0.46157	1.445	0.31780	N	0.631044	P;D	0.71674	0.794;0.998	B;D	0.67548	0.31;0.952	T	0.26224	-1.0109	10	0.30854	T	0.27	.	7.5683	0.27892	0.1656:0.7478:0.0:0.0866	.	87;123	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	F	87;123;87	ENSP00000376908:L87F;ENSP00000343290:L123F;ENSP00000376909:L87F	ENSP00000343290:L123F	L	+	1	0	C9orf171	134363966	0.976000	0.34144	0.999000	0.59377	0.505000	0.33919	0.449000	0.21744	2.545000	0.85829	0.655000	0.94253	CTC	.	.		0.577	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417		T	135374145	C	T	135374145	3	4	112	1	0	0	0	0	1	0	0	0	2472	565	20	3	377	3	C9orf171	9	135374145	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	983318	135374145	5839286	606	17227										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137593113	137593113	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcctcgaccgcagcgaccaCcccatgatcgacatcaatgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:137593113delC	ENST00000371817.3	+	4	1002	c.588delC	c.(586-588)cacfs	p.H196fs	COL5A1_ENST00000464187.1_3'UTR	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	196	Laminin G-like.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GCAGCGACCACCCCATGATCG	0.542																																					p.H196fs		Atlas-INDEL	.											.	COL5A1	323	.	0			c.587delA						.						169	124	139					9																	137593113		2203	4300	6503	SO:0001589	frameshift_variant	1289	exon4			.	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.588delC	chr9.hg19:g.137593113delC	ENSP00000360882:p.His196fs	178.0	0.0		192.0	13.0	NM_000093	Q15094|Q5SUX4	Frame_Shift_Del	DEL	ENST00000371817.3	hg19	CCDS6982.1																																																																																			.	.		0.542	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		-	137593113	C	-	137593113	7	5	112	1	0	1	0	1	0	0	0	0	3698	506	18	0	602	0	COL5A1	9	137593113	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	2218968	137593113	3620318	607	17228										
SDCCAG3	10807	hgsc.bcm.edu	37	chr9	139301956	139301956	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgatactccaggccataccCgccggtttgggagggtgggg	16	11	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:139301956C>T	ENST00000357365.3	-	5	589	c.460G>A	c.(460-462)Ggg>Agg	p.G154R	SDCCAG3_ENST00000371725.3_Missense_Mutation_p.G81R|SDCCAG3_ENST00000298537.7_Missense_Mutation_p.G131R|SDCCAG3_ENST00000461693.1_5'Flank	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	154						cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		AGGCCATACCCGCCGGTTTGG	0.537																																					p.G154R		Atlas-SNP	.											.	SDCCAG3	41	.	0			c.G460A						.						24	30	28					9																	139301956		1887	4104	5991	SO:0001583	missense	10807	exon5			CATACCCGCCGGT	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.460G>A	chr9.hg19:g.139301956C>T	ENSP00000349929:p.Gly154Arg	50.0	0.0		72.0	4.0	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Missense_Mutation	SNP	ENST00000357365.3	hg19	CCDS43904.1	.	.	.	.	.	.	.	.	.	.	C	8.678	0.904540	0.17760	.	.	ENSG00000165689	ENST00000357365;ENST00000298537;ENST00000371725;ENST00000371723	T;T;T;T	0.34072	2.46;2.53;2.52;1.38	5.27	4.36	0.52297	.	0.059281	0.64402	D	0.000004	T	0.34948	0.0915	L	0.56769	1.78	0.09310	N	1	B;P;B	0.35600	0.324;0.511;0.324	B;B;B	0.35770	0.119;0.21;0.158	T	0.39941	-0.9589	10	0.66056	D	0.02	-14.9586	11.2499	0.49020	0.0:0.9119:0.0:0.0881	.	81;131;154	Q96C92-4;Q96C92-2;Q96C92	.;.;SDCG3_HUMAN	R	154;131;81;104	ENSP00000349929:G154R;ENSP00000298537:G131R;ENSP00000360790:G81R;ENSP00000360788:G104R	ENSP00000298537:G131R	G	-	1	0	SDCCAG3	138421777	0.031000	0.19500	0.126000	0.21872	0.026000	0.11368	2.663000	0.46774	2.454000	0.82982	0.650000	0.86243	GGG	.	.		0.537	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643		T	139301956	C	T	139301956	3	4	112	1	0	0	0	0	1	0	0	0	13973	652	23	1	871	1	SDCCAG3	9	139301956	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1708843	139301956	1911475	608	17229										
ABCA2	20	hgsc.bcm.edu	37	chr9	139906582	139906582	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagggagaggctggcgctggTcttattcatggggtggttgg	19	6	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:139906582T>C	ENST00000371605.3	-	33	5476	c.5329A>G	c.(5329-5331)Acc>Gcc	p.T1777A	ABCA2_ENST00000341511.6_Missense_Mutation_p.T1778A|ABCA2_ENST00000265662.5_Missense_Mutation_p.T1778A			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1777					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CTGGCGCTGGTCTTATTCATG	0.692																																					p.T1808A		Atlas-SNP	.											.	ABCA2	113	.	0			c.A5422G						.						88	90	89					9																	139906582		2021	4172	6193	SO:0001583	missense	20	exon34			CGCTGGTCTTATT	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.5329A>G	chr9.hg19:g.139906582T>C	ENSP00000360666:p.Thr1777Ala	56.0	0.0		83.0	6.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Missense_Mutation	SNP	ENST00000371605.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.52|14.52	2.561208|2.561208	0.45590|0.45590	.|.	.|.	ENSG00000107331|ENSG00000107331	ENST00000477420|ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	.|D;D;D	.|0.87887	.|-2.31;-2.31;-2.31	4.31|4.31	4.31|4.31	0.51392|0.51392	.|.	.|0.332898	.|0.33813	.|N	.|0.004537	D|D	0.86301|0.86301	0.5900|0.5900	M|M	0.68317|0.68317	2.08|2.08	0.58432|0.58432	D|D	0.999996|0.999996	.|P;P	.|0.45634	.|0.773;0.863	.|B;B	.|0.42495	.|0.389;0.389	D|D	0.88115|0.88115	0.2828|0.2828	5|10	.|0.72032	.|D	.|0.01	.|.	13.2697|13.2697	0.60153|0.60153	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1777;1808	.|Q9BZC7;E7ETC3	.|ABCA2_HUMAN;.	G|A	189|1778;1777;1808;1778	.|ENSP00000265662:T1778A;ENSP00000360666:T1777A;ENSP00000344155:T1778A	.|ENSP00000265662:T1778A	D|T	-|-	2|1	0|0	ABCA2|ABCA2	139026403|139026403	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.183000|0.183000	0.23260|0.23260	5.318000|5.318000	0.65829|0.65829	1.807000|1.807000	0.52817|0.52817	0.254000|0.254000	0.18369|0.18369	GAC|ACC	.	.		0.692	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		C	139906582	T	C	139906582	3	2	112	1	0	0	0	0	1	0	0	0	32	1667	58	2	2042	2	ABCA2	9	139906582	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	604626	139906582	1306849	609	17230										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140772543	140772543	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcaatcgatcgcgcagcgcgCgcggaccatggcgctgtaca	14	14	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:140772543C>T	ENST00000371372.1	+	1	303	c.158C>T	c.(157-159)gCg>gTg	p.A53V	CACNA1B_ENST00000277551.2_Missense_Mutation_p.A53V|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371363.1_Missense_Mutation_p.A53V|CACNA1B_ENST00000371355.4_Missense_Mutation_p.A53V|CACNA1B_ENST00000371357.1_Missense_Mutation_p.A53V|CACNA1B_ENST00000277549.5_5'UTR	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	53					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GCGCAGCGCGCGCGGACCATG	0.721																																					p.A53V		Atlas-SNP	.											.	CACNA1B	266	.	0			c.C158T						.						24	28	27					9																	140772543		2013	4175	6188	SO:0001583	missense	774	exon1			AGCGCGCGCGGAC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.158C>T	chr9.hg19:g.140772543C>T	ENSP00000360423:p.Ala53Val	99.0	0.0		170.0	75.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708039	0.89018	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.97404	-4.36;-4.37;-4.32;-4.34;-4.35	3.46	3.46	0.39613	.	0.000000	0.64402	U	0.000003	D	0.96219	0.8767	M	0.83953	2.67	0.80722	D	1	B	0.24533	0.105	B	0.11329	0.006	D	0.95823	0.8851	10	0.87932	D	0	.	13.975	0.64268	0.0:1.0:0.0:0.0	.	53	B1AQK6	.	V	53	ENSP00000360423:A53V;ENSP00000277551:A53V;ENSP00000360414:A53V;ENSP00000360408:A53V;ENSP00000360406:A53V	ENSP00000277551:A53V	A	+	2	0	CACNA1B	139892364	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.994000	0.63901	1.497000	0.48584	0.298000	0.19748	GCG	.	.		0.721	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		T	140772543	C	T	140772543	3	4	112	1	0	0	0	0	1	0	0	0	2541	768	27	1	160	1	CACNA1B	9	140772543	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	865961	140772543	440888	610	17231										
C10orf18	54906	hgsc.bcm.edu	37	chr10	5803302	5803302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taatgttgaagtcatttcagAgtgcaaatatcattgaattg	8	4	3	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:5803302A>G	ENST00000328090.5	+	19	7667	c.7042A>G	c.(7042-7044)Agt>Ggt	p.S2348G		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2348																	GTCATTTCAGAGTGCAAATAT	0.328																																					p.S2348G		Atlas-SNP	.											.	.	.	.	0			c.A7042G						.						118	111	113					10																	5803302		1877	4113	5990	SO:0001583	missense	54906	exon19			TTTCAGAGTGCAA	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.7042A>G	chr10.hg19:g.5803302A>G	ENSP00000328426:p.Ser2348Gly	127.0	0.0		113.0	5.0	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	hg19	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	A	7.721	0.697098	0.15106	.	.	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.42131	0.98	6.06	2.48	0.30137	.	0.223507	0.40908	N	0.000991	T	0.28034	0.0691	L	0.41027	1.25	0.26465	N	0.975389	B	0.14012	0.009	B	0.14578	0.011	T	0.13710	-1.0499	10	0.30854	T	0.27	.	4.5273	0.11988	0.5083:0.1643:0.3274:0.0	.	2348	Q5VWN6	F208B_HUMAN	G	2348;1543	ENSP00000328426:S2348G	ENSP00000328426:S2348G	S	+	1	0	C10orf18	5843308	1.000000	0.71417	0.994000	0.49952	0.207000	0.24258	2.952000	0.49097	0.514000	0.28300	-0.256000	0.11100	AGT	.	.		0.328	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		G	5803302	A	G	5803302	3	3	112	1	0	0	0	0	1	0	0	0	1598	304	11	2	7104	2	C10orf18	10	5803302	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10		5803302	129731445	611	17232										
GDI2	2665	hgsc.bcm.edu	37	chr10	5836890	5836890	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtggaaggaaccttgtagaTttttccacccttatagacaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:5836890delT	ENST00000380191.4	-	4	636	c.346delA	c.(346-348)atcfs	p.I116fs	GDI2_ENST00000380181.3_Intron|GDI2_ENST00000380132.4_Frame_Shift_Del_p.I120fs	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2	116					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|Rab GDP-dissociation inhibitor activity (GO:0005093)|Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|large_intestine(1)|lung(6)|urinary_tract(1)	10						ACCTTGTAGATTTTTCCACCC	0.368																																					p.I116fs		Atlas-INDEL	.											.	GDI2	26	.	0			c.347delT						.						95	92	93					10																	5836890		2203	4300	6503	SO:0001589	frameshift_variant	2665	exon4			.	D13988	CCDS7071.1, CCDS44352.1	10p15	2010-03-16			ENSG00000057608	ENSG00000057608			4227	protein-coding gene	gene with protein product	"rab GDP-dissociation"	600767				9434952	Standard	NM_001494		Approved	RABGDIB	uc001iil.4	P50395	OTTHUMG00000017607	ENST00000380191.4:c.346delA	chr10.hg19:g.5836890delT	ENSP00000369538:p.Ile116fs	173.0	0.0		160.0	10.0	NM_001494	O43928|Q5SX88|Q9UQM6	Frame_Shift_Del	DEL	ENST00000380191.4	hg19	CCDS7071.1																																																																																			.	.		0.368	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	NM_001494		-	5836890	T	-	5836890	7	5	112	1	0	1	0	1	0	0	0	0	6329	1493	52	0	1023	0	GDI2	10	5836890	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	33588	5836890	129697857	612	17233										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7214583	7214583	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcggggttgctttccccgatGgggggcttggagatcttctt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:7214583delG	ENST00000361972.4	-	18	2115	c.2025delC	c.(2023-2025)cccfs	p.P675fs	SFMBT2_ENST00000397167.1_Frame_Shift_Del_p.P675fs	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	675			P -> R (in dbSNP:rs3740212).		negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						TTTCCCCGATGGGGGGCTTGG	0.517																																					p.I676fs		Atlas-INDEL	.											.	SFMBT2	209	.	0			c.2026delA						.						48	58	54					10																	7214583		2203	4300	6503	SO:0001589	frameshift_variant	57713	exon18			.	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.2025delC	chr10.hg19:g.7214583delG	ENSP00000355109:p.Pro675fs	203.0	0.0		217.0	17.0	NM_001029880	A7MD09|Q9HCF5	Frame_Shift_Del	DEL	ENST00000361972.4	hg19	CCDS31138.1																																																																																			.	.		0.517	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		-	7214583	G	-	7214583	7	5	112	1	0	1	0	1	0	0	0	0	14173	1335	47	0	675	0	SFMBT2	10	7214583	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1377693	7214583	128320164	613	17234										
TAF3	83860	hgsc.bcm.edu	37	chr10	8007022	8007022	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggagaaaaccaagctgcctTcctccgtggaggtaaagaag	12	9	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:8007022T>C	ENST00000344293.5	+	3	1755	c.1549T>C	c.(1549-1551)Tcc>Ccc	p.S517P		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	517	Lys-rich.				maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						CAAGCTGCCTTCCTCCGTGGA	0.433																																					p.S517P		Atlas-SNP	.											.	TAF3	93	.	0			c.T1549C						.						73	69	70					10																	8007022		1854	4100	5954	SO:0001583	missense	83860	exon3			CTGCCTTCCTCCG	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"Zinc fingers, PHD-type"	17303	protein-coding gene	gene with protein product		606576	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.1549T>C	chr10.hg19:g.8007022T>C	ENSP00000340271:p.Ser517Pro	82.0	0.0		85.0	4.0	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	hg19	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	T	0.779	-0.763054	0.02996	.	.	ENSG00000165632	ENST00000344293	T	0.19669	2.13	5.82	0.777	0.18538	.	0.449719	0.20668	N	0.087889	T	0.10723	0.0262	L	0.28504	0.86	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.27088	-1.0084	10	0.19147	T	0.46	-1.1284	2.9263	0.05785	0.1143:0.1303:0.1274:0.6279	.	517	Q5VWG9	TAF3_HUMAN	P	517	ENSP00000340271:S517P	ENSP00000340271:S517P	S	+	1	0	TAF3	8047028	0.254000	0.23992	0.000000	0.03702	0.147000	0.21601	0.768000	0.26590	0.100000	0.17581	-0.341000	0.08007	TCC	.	.		0.433	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		C	8007022	T	C	8007022	3	2	112	1	0	0	0	0	1	0	0	0	15540	1783	62	2	1559	2	TAF3	10	8007022	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	792439	8007022	127527725	614	17235										
TAF3	83860	hgsc.bcm.edu	37	chr10	8007368	8007368	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggcaagaaagataaagataAgagagagaaagaaaaagtga	12	1	0	7			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:8007368A>G	ENST00000344293.5	+	3	2101	c.1895A>G	c.(1894-1896)aAg>aGg	p.K632R		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	632	Lys-rich.				maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						gataaagataagagagagaaa	0.423																																					p.K632R		Atlas-SNP	.											TAF3,NS,carcinoma,0,1	TAF3	93	.	0			c.A1895G						.						44	47	46					10																	8007368		1855	4095	5950	SO:0001583	missense	83860	exon3			AAGATAAGAGAGA	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"Zinc fingers, PHD-type"	17303	protein-coding gene	gene with protein product		606576	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.1895A>G	chr10.hg19:g.8007368A>G	ENSP00000340271:p.Lys632Arg	28.0	0.0		37.0	2.0	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	hg19	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	A	18.30	3.592708	0.66219	.	.	ENSG00000165632	ENST00000344293	T	0.23552	1.9	5.82	4.68	0.58851	.	0.093307	0.44483	N	0.000459	T	0.30759	0.0775	M	0.80183	2.485	0.58432	D	0.999995	B	0.25390	0.125	B	0.24848	0.056	T	0.06338	-1.0832	10	0.22109	T	0.4	-18.2116	11.3896	0.49806	0.9288:0.0:0.0712:0.0	.	632	Q5VWG9	TAF3_HUMAN	R	632	ENSP00000340271:K632R	ENSP00000340271:K632R	K	+	2	0	TAF3	8047374	1.000000	0.71417	0.737000	0.30932	0.903000	0.53119	6.895000	0.75660	1.034000	0.39945	0.528000	0.53228	AAG	.	.		0.423	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		G	8007368	A	G	8007368	3	3	112	1	0	0	0	0	1	0	0	0	15540	72	3	2	1905	2	TAF3	10	8007368	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	346	8007368	127527379	615	17236										
OPTN	10133	hgsc.bcm.edu	37	chr10	13152401	13152401	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaagcaaaagagcgtctaatGgccttgagtcatgagaatga	12	6	2	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:13152401G>A	ENST00000378748.3	+	5	656	c.294G>A	c.(292-294)atG>atA	p.M98I	OPTN_ENST00000378764.2_Missense_Mutation_p.M98I|OPTN_ENST00000378747.3_Missense_Mutation_p.M98I|OPTN_ENST00000378752.3_Missense_Mutation_p.M98I|OPTN_ENST00000378757.2_Missense_Mutation_p.M98I|OPTN_ENST00000482140.1_Intron|OPTN_ENST00000263036.5_Missense_Mutation_p.M98I	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	98	Interaction with Rab8.		M -> K (may modify intraocular pressure and increase risk of GLC1E and NPG, induces TFRC degradation leading to autophagic death in retinal ganglion cells; may be a common polymorphism; dbSNP:rs11258194). {ECO:0000269|PubMed:11834836, ECO:0000269|PubMed:14627677, ECO:0000269|PubMed:15498064, ECO:0000269|PubMed:15557444}.		cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)	p.M98I(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						AGCGTCTAATGGCCTTGAGTC	0.438																																					p.M98I		Atlas-SNP	.											OPTN,NS,carcinoma,0,1	OPTN	57	.	1	Substitution - Missense(1)	lung(1)	c.G294A						.						105	118	113					10																	13152401		2203	4300	6503	SO:0001583	missense	10133	exon4			TCTAATGGCCTTG	AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"glaucoma 1, open angle, E (adult-onset)"	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.294G>A	chr10.hg19:g.13152401G>A	ENSP00000368022:p.Met98Ile	149.0	0.0		155.0	0.0	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Missense_Mutation	SNP	ENST00000378748.3	hg19	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.308852	0.23821	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000430081;ENST00000378747	D;D;D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58	5.98	1.37	0.22104	NF-kappa-B essential modulator NEMO, N-terminal (1);	0.586858	0.21037	N	0.081226	T	0.63861	0.2547	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.11329	0.004;0.006	T	0.53802	-0.8387	10	0.38643	T	0.18	-3.4751	8.4113	0.32644	0.5199:0.0:0.4801:0.0	.	98;98	Q96CV9-2;Q96CV9	.;OPTN_HUMAN	I	98;98;98;98;98;41;98	ENSP00000263036:M98I;ENSP00000368040:M98I;ENSP00000368032:M98I;ENSP00000368027:M98I;ENSP00000368022:M98I;ENSP00000414747:M41I;ENSP00000368021:M98I	ENSP00000263036:M98I	M	+	3	0	OPTN	13192407	0.000000	0.05858	0.644000	0.29465	0.643000	0.38383	-0.333000	0.07894	0.376000	0.24707	0.655000	0.94253	ATG	.	.		0.438	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980		A	13152401	G	A	13152401	3	1	112	1	0	0	0	0	1	0	0	0	10898	1348	47	3	300	3	OPTN	10	13152401	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	5145033	13152401	122382346	616	17237										
FRMD4A	55691	hgsc.bcm.edu	37	chr10	13838525	13838525	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagtataaaaccacgggtccTgactttttagggaagtcatg	10	7	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:13838525T>C	ENST00000357447.2	-	5	638	c.270A>G	c.(268-270)tcA>tcG	p.S90S	FRMD4A_ENST00000358621.4_Silent_p.S75S|FRMD4A_ENST00000378503.1_Silent_p.S90S|FRMD4A_ENST00000342409.2_Silent_p.S106S	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	90	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)				breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						CCACGGGTCCTGACTTTTTAG	0.428																																					p.S90S		Atlas-SNP	.											.	FRMD4A	108	.	0			c.A270G						.						150	148	149					10																	13838525		2203	4300	6503	SO:0001819	synonymous_variant	55691	exon5			GGGTCCTGACTTT	AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"FERM domain containing 4"	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.270A>G	chr10.hg19:g.13838525T>C		64.0	0.0		84.0	4.0	NM_018027	A7E2Y3|Q5T377	Silent	SNP	ENST00000357447.2	hg19	CCDS7101.1																																																																																			.	.		0.428	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027		C	13838525	T	C	13838525	2	2	112	1	0	0	0	0	0	0	0	1	6059	1567	55	2		2	FRMD4A	10	13838525	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	686124	13838525	121696222	617	17238										
MRC1	4360	hgsc.bcm.edu	37	chr10	17917243	17917243	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttctattcaaagtgaaagtgAaaagaagtttctatggaaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:17917243delA	ENST00000331429.2	+	17	2631	c.2528delA	c.(2527-2529)gaafs	p.E843fs																	breast(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						AGTGAAAGTGAAAAGAAGTTT	0.333																																					p.E843fs		Atlas-INDEL	.											.	MRC1	13	.	0			c.2527delG						.						1	1	1					10																	17917243		34	89	123	SO:0001589	frameshift_variant	4360	exon17			.																												ENST00000331429.2:c.2528delA	chr10.hg19:g.17917243delA	ENSP00000332124:p.Glu843fs	138.0	0.0		175.0	11.0	NM_002438		Frame_Shift_Del	DEL	ENST00000331429.2	hg19																																																																																				.	.		0.333	MRC1L1-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047054.1			-	17917243	A	-	17917243	7	5	112	1	0	1	0	1	0	0	0	0	9765	246	9	0	2594	0	MRC1	10	17917243	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4078718	17917243	117617504	618	17239										
NSUN6	221078	hgsc.bcm.edu	37	chr10	18837156	18837156	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcacaccctctggcttcagcAgctgaaccgcctaaagaaaa	8	14	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:18837156A>G	ENST00000377304.4	-	10	1500	c.1082T>C	c.(1081-1083)cTg>cCg	p.L361P	NSUN6_ENST00000493816.1_5'UTR|RP11-499P20.2_ENST00000425669.1_RNA	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	361							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						TGGCTTCAGCAGCTGAACCGC	0.433																																					p.L361P		Atlas-SNP	.											.	NSUN6	46	.	0			c.T1082C						.						61	57	58					10																	18837156		2203	4300	6503	SO:0001583	missense	221078	exon10			TTCAGCAGCTGAA	BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"NOP2/Sun domain containing"	23529	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 6", "NOL1/NOP2/Sun domain family, member 6", "ARL5B antisense RNA 1"	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.1082T>C	chr10.hg19:g.18837156A>G	ENSP00000366519:p.Leu361Pro	105.0	0.0		92.0	4.0	NM_182543	B0YJ54	Missense_Mutation	SNP	ENST00000377304.4	hg19	CCDS7130.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.516697	0.85495	.	.	ENSG00000241058	ENST00000377304	T	0.26223	1.75	5.87	5.87	0.94306	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.000000	0.85682	D	0.000000	T	0.64659	0.2618	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.76049	-0.3101	10	0.66056	D	0.02	.	16.2813	0.82687	1.0:0.0:0.0:0.0	.	361	Q8TEA1	NSUN6_HUMAN	P	361	ENSP00000366519:L361P	ENSP00000366519:L361P	L	-	2	0	NSUN6	18877162	1.000000	0.71417	0.975000	0.42487	0.991000	0.79684	8.737000	0.91562	2.244000	0.73946	0.533000	0.62120	CTG	.	.		0.433	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543		G	18837156	A	G	18837156	3	3	112	1	0	0	0	0	1	0	0	0	10691	188	7	2	335	2	NSUN6	10	18837156	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	919913	18837156	116697591	619	17240										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26462846	26462846	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagccccaaacagaagtctgTcaaagacctggaagagaaca	9	10	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:26462846T>C	ENST00000265944.5	+	30	3819	c.3653T>C	c.(3652-3654)gTc>gCc	p.V1218A	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1218					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CAGAAGTCTGTCAAAGACCTG	0.413																																					p.V1218A		Atlas-SNP	.											.	MYO3A	371	.	0			c.T3653C						.						96	99	98					10																	26462846		2203	4300	6503	SO:0001583	missense	53904	exon30			AGTCTGTCAAAGA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3653T>C	chr10.hg19:g.26462846T>C	ENSP00000265944:p.Val1218Ala	90.0	0.0		106.0	5.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	T	3.997	-0.003383	0.07773	.	.	ENSG00000095777	ENST00000265944	T	0.77098	-1.07	5.18	-1.67	0.08238	.	1.632550	0.02541	N	0.094604	T	0.54224	0.1845	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.44081	-0.9351	10	0.07644	T	0.81	.	1.2475	0.01975	0.304:0.1362:0.1072:0.4527	.	1218	Q8NEV4	MYO3A_HUMAN	A	1218	ENSP00000265944:V1218A	ENSP00000265944:V1218A	V	+	2	0	MYO3A	26502852	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.373000	0.07494	0.058000	0.16222	-0.301000	0.09380	GTC	.	.		0.413	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		C	26462846	T	C	26462846	3	2	112	1	0	0	0	0	1	0	0	0	10085	1667	58	2	3763	2	MYO3A	10	26462846	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	7625690	26462846	109071901	620	17241										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27303455	27303455	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttgacaaagattttctaacTtttaattcttctagatagag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:27303455delT	ENST00000376087.4	-	31	4857	c.4692delA	c.(4690-4692)aaafs	p.K1564fs	ANKRD26_ENST00000436985.2_Frame_Shift_Del_p.K1580fs|ANKRD26_ENST00000376070.3_Frame_Shift_Del_p.K1121fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1563					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						ATTTTCTAACTTTTAATTCTT	0.274																																					p.V1565fs		Atlas-INDEL	.											.	ANKRD26	179	.	0			c.4693delG						.						42	40	41					10																	27303455		1779	4038	5817	SO:0001589	frameshift_variant	22852	exon31			.	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.4692delA	chr10.hg19:g.27303455delT	ENSP00000365255:p.Lys1564fs	146.0	0.0		152.0	10.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Del	DEL	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.274	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			-	27303455	T	-	27303455	7	5	112	1	0	1	0	1	0	0	0	0	654	1606	56	0	456	0	ANKRD26	10	27303455	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	840609	27303455	108231292	621	17242										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27317833	27317833	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctcaattttgtccatttgcTttttgactgtaacttttaac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:27317833delT	ENST00000376087.4	-	27	4085	c.3920delA	c.(3919-3921)aagfs	p.K1307fs	ANKRD26_ENST00000436985.2_Frame_Shift_Del_p.K1323fs|ANKRD26_ENST00000376070.3_Frame_Shift_Del_p.K864fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1306					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						GTCCATTTGCTTTTTGACTGT	0.284																																					p.K1307fs		Atlas-INDEL	.											.	ANKRD26	179	.	0			c.3921delG						.						117	108	110					10																	27317833		1800	4060	5860	SO:0001589	frameshift_variant	22852	exon27			.	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3920delA	chr10.hg19:g.27317833delT	ENSP00000365255:p.Lys1307fs	218.0	0.0		240.0	16.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Del	DEL	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.284	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			-	27317833	T	-	27317833	7	5	112	1	0	1	0	1	0	0	0	0	654	1609	56	0	1244	0	ANKRD26	10	27317833	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	14378	27317833	108216914	622	17243										
WAC	51322	hgsc.bcm.edu	37	chr10	28908473	28908473	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttttttttttcaggatactaTttttgagacaacaaattaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:28908473delT	ENST00000354911.4	+	14	2043	c.1882delT	c.(1882-1884)tttfs	p.F628fs	WAC_ENST00000375646.1_Frame_Shift_Del_p.F476fs|WAC_ENST00000347934.4_Frame_Shift_Del_p.F525fs|WAC_ENST00000375664.4_Frame_Shift_Del_p.F583fs	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	628					cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						CAGGATACTATTTTTGAGACA	0.284																																					p.L627fs		Atlas-INDEL	.											.	WAC	77	.	0			c.1881delA						.						40	42	41					10																	28908473		2200	4300	6500	SO:0001589	frameshift_variant	51322	exon14			.	AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"WW domain-containing adaptor with coiled coil"			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.1882delT	chr10.hg19:g.28908473delT	ENSP00000346986:p.Phe628fs	133.0	0.0		163.0	10.0	NM_016628	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Frame_Shift_Del	DEL	ENST00000354911.4	hg19	CCDS7159.1																																																																																			.	.		0.284	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264		-	28908473	T	-	28908473	7	5	112	1	0	1	0	1	0	0	0	0	17262	1493	52	0	1936	0	WAC	10	28908473	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1590640	28908473	106626274	623	17244										
SVIL	6840	hgsc.bcm.edu	37	chr10	29839664	29839664	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtctcgcccagagaaagagAaggtcgaggaactctcggct	13	10	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:29839664A>G	ENST00000355867.4	-	6	1441	c.689T>C	c.(688-690)tTc>tCc	p.F230S	SVIL_ENST00000375400.3_Missense_Mutation_p.F230S|SVIL_ENST00000375398.2_Missense_Mutation_p.F230S	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	230					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				AGAGAAAGAGAAGGTCGAGGA	0.627																																					p.F230S		Atlas-SNP	.											.	SVIL	226	.	0			c.T689C						.						76	77	77					10																	29839664		2203	4300	6503	SO:0001583	missense	6840	exon8			AAAGAGAAGGTCG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.689T>C	chr10.hg19:g.29839664A>G	ENSP00000348128:p.Phe230Ser	70.0	0.0		81.0	5.0	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	A	9.667	1.145566	0.21288	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.50277	0.75;0.75;0.75	5.35	1.71	0.24356	.	0.674623	0.16241	N	0.223158	T	0.40040	0.1101	M	0.64997	1.995	0.80722	D	1	B;B	0.20887	0.013;0.049	B;B	0.19666	0.022;0.026	T	0.11227	-1.0596	9	.	.	.	-1.7418	6.397	0.21618	0.7264:0.1332:0.1404:0.0	.	230;230	O95425-2;O95425	.;SVIL_HUMAN	S	230	ENSP00000364549:F230S;ENSP00000364547:F230S;ENSP00000348128:F230S	.	F	-	2	0	SVIL	29879670	0.895000	0.30542	0.033000	0.17914	0.035000	0.12851	1.543000	0.36147	0.040000	0.15660	0.533000	0.62120	TTC	.	.		0.627	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			G	29839664	A	G	29839664	3	3	112	1	0	0	0	0	1	0	0	0	15436	246	9	2	6087	2	SVIL	10	29839664	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	931191	29839664	105695083	624	17245										
CCDC7	79741	hgsc.bcm.edu	37	chr10	32832279	32832279	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagctgtgaaaacagtgaagAaaaaagacaaaggaaaatct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:32832279delA	ENST00000362006.5	+	13	1588	c.1045delA	c.(1045-1047)aaafs	p.K350fs	CCDC7_ENST00000277657.6_Frame_Shift_Del_p.K350fs	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	350										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				AACAGTGAAGAAAAAAGACAA	0.264																																					p.K348fs		Atlas-INDEL	.											.	CCDC7	47	.	0			c.1044delG						.						30	31	30					10																	32832279		2186	4267	6453	SO:0001589	frameshift_variant	221016	exon13			.	BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 68"	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.1045delA	chr10.hg19:g.32832279delA	ENSP00000355078:p.Lys350fs	126.0	0.0		230.0	17.0	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Frame_Shift_Del	DEL	ENST00000362006.5	hg19	CCDS7173.1																																																																																			.	.		0.264	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023		-	32832279	A	-	32832279	7	5	112	1	0	1	0	1	0	0	0	0	2844	247	9	0	1091	0	CCDC7	10	32832279	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2992615	32832279	102702468	625	17246										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37505286	37505286	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaatcacagttagagaaccAaaaagttaaatgggaacaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:37505286delA	ENST00000602533.1	+	32	2978	c.2879delA	c.(2878-2880)caafs	p.Q960fs	ANKRD30A_ENST00000374660.1_Frame_Shift_Del_p.Q1079fs|ANKRD30A_ENST00000361713.1_Frame_Shift_Del_p.Q960fs			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1016					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						TTAGAGAACCAAAAAGTTAAA	0.313																																					p.Q960fs		Atlas-INDEL	.											.	ANKRD30A	448	.	0			c.2878delC						.						75	76	76					10																	37505286		1831	4079	5910	SO:0001589	frameshift_variant	91074	exon32			.	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.2879delA	chr10.hg19:g.37505286delA	ENSP00000473551:p.Gln960fs	325.0	0.0		339.0	22.0	NM_052997	Q5W025	Frame_Shift_Del	DEL	ENST00000602533.1	hg19																																																																																				.	.		0.313	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		-	37505286	A	-	37505286	7	5	112	1	0	1	0	1	0	0	0	0	658	130	5	0	3005	0	ANKRD30A	10	37505286	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4673007	37505286	98029461	626	17247										
PARG	119016	hgsc.bcm.edu	37	chr10	51363013	51363013	+	Intron	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttagtagagtaccgtttcctGaattcaatgtcagcgtctct					rs112991319		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:51363013delG	ENST00000602930.1	-	1	468				RP11-592B15.3_ENST00000432221.2_RNA	NM_001276343.1	NP_001263272.1	Q5SRD3	AGAP8_HUMAN							regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(2)|ovary(2)	6						ACCGTTTCCTGAATTCAATGT	0.408																																					p.R354fs		Atlas-INDEL	.											.	PARG	46	.	0			c.1060delA						.						79	83	82					10																	51363013		233	1110	1343	SO:0001627	intron_variant	8505	exon3			.																												ENST00000602930.1:c.81+7840C>-	chr10.hg19:g.51363013delG		5.0	0.0		11.0	10.0	NM_003631		Frame_Shift_Del	DEL	ENST00000602930.1	hg19																																																																																				.	.		0.408	AGAP8-006	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000467541.1			-	51363013	G	-	51363013	6	5	112	0	1	1	0	1	0	0	0	0	11457	1281	45	0		0	PARG	10	51363013	Intron	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	13857727	51363013	84171734	627	17248										
FAM21A	387680	hgsc.bcm.edu	37	chr10	51829353	51829353	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acagcaaactatctctaggaCccatgaaatcaagaaacaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:51829353delC	ENST00000282633.5	+	3	218	c.173delC	c.(172-174)accfs	p.T58fs	RP11-324H6.5_ENST00000456967.1_RNA|FAM21A_ENST00000351071.6_Frame_Shift_Del_p.T58fs|FAM21A_ENST00000314664.7_Frame_Shift_Del_p.T58fs|FAM21A_ENST00000492914.1_3'UTR	NM_001005751.1	NP_001005751.1	Q641Q2	FA21A_HUMAN	family with sequence similarity 21, member A	58					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)				breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	15						ATCTCTAGGACCCATGAAATC	0.368																																					p.T58fs		Atlas-INDEL	.											.	FAM21A	32	.	0			c.172delA						.						121	117	118					10																	51829353		1823	4080	5903	SO:0001589	frameshift_variant	387680	exon3			.	BC082258	CCDS41527.1	10q11.23	2014-06-19			ENSG00000099290	ENSG00000099290			23416	protein-coding gene	gene with protein product			"family with sequence similarity 21, member B"	FAM21B			Standard	XM_005269805		Approved	bA56A21.1, bA98I6.1, FLJ10824	uc001jjb.3	Q641Q2	OTTHUMG00000018225	ENST00000282633.5:c.173delC	chr10.hg19:g.51829353delC	ENSP00000282633:p.Thr58fs	187.0	0.0		191.0	12.0	NM_001005751	A2A3S2|A2A3U6|Q6DHY0	Frame_Shift_Del	DEL	ENST00000282633.5	hg19	CCDS41527.1																																																																																			.	.		0.368	FAM21A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276917.2	NM_001005751		-	51829353	C	-	51829353	7	5	112	1	0	1	0	1	0	0	0	0	5545	507	18	0	183	0	FAM21A	10	51829353	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	466340	51829353	83705394	628	17249										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55582820	55582820	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agacttactcttggcttgtaTtttgggtgaaaatgggtcta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:55582820delT	ENST00000320301.6	-	33	5060	c.4666delA	c.(4666-4668)atafs	p.I1556fs	PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395430.1_Frame_Shift_Del_p.I1553fs|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000437009.1_Frame_Shift_Del_p.I1487fs|PCDH15_ENST00000395432.2_Frame_Shift_Del_p.I1516fs|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395433.1_Frame_Shift_Del_p.I1533fs|PCDH15_ENST00000361849.3_Frame_Shift_Del_p.I1558fs	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1556					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TTGGCTTGTATTTTGGGTGAA	0.428										HNSCC(58;0.16)																											p.I1563fs		Atlas-INDEL	.											.	PCDH15	1715	.	0			c.4688delT						.						85	89	87					10																	55582820		2203	4299	6502	SO:0001589	frameshift_variant	65217	exon35			.	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4666delA	chr10.hg19:g.55582820delT	ENSP00000322604:p.Ile1556fs	164.0	0.0		180.0	11.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Frame_Shift_Del	DEL	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.		0.428	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		-	55582820	T	-	55582820	7	5	112	1	0	1	0	1	0	0	0	0	11520	1493	52	0	2811	0	PCDH15	10	55582820	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3753467	55582820	79951927	629	17250										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64967219	64967219	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctggaaacactggtagtatCggcagcagatgtgattacat	12	7	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:64967219C>T	ENST00000399262.2	-	10	4428	c.4210G>A	c.(4210-4212)Gat>Aat	p.D1404N	JMJD1C_ENST00000399251.1_Missense_Mutation_p.D1185N|JMJD1C_ENST00000402544.1_Missense_Mutation_p.D1185N|JMJD1C_ENST00000542921.1_Missense_Mutation_p.D1222N	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1404					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					CTGGTAGTATCGGCAGCAGAT	0.418																																					p.D1404N		Atlas-SNP	.											.	JMJD1C	347	.	0			c.G4210A						.						125	123	124					10																	64967219		1923	4129	6052	SO:0001583	missense	221037	exon10			TAGTATCGGCAGC	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.4210G>A	chr10.hg19:g.64967219C>T	ENSP00000382204:p.Asp1404Asn	113.0	0.0		100.0	4.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	C	6.132	0.392627	0.11638	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.52754	1.0;0.65;2.57;1.0	5.72	1.98	0.26296	.	0.606592	0.18492	N	0.139603	T	0.19604	0.0471	N	0.08118	0	0.21290	N	0.999736	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.04013	0.001;0.001;0.001	T	0.17806	-1.0357	10	0.11794	T	0.64	-1.5356	2.8573	0.05576	0.2438:0.069:0.1268:0.5604	.	945;1404;1222	A6PW35;Q15652;A0T124	.;JHD2C_HUMAN;.	N	1404;1185;1185;1222	ENSP00000382204:D1404N;ENSP00000384990:D1185N;ENSP00000382195:D1185N;ENSP00000444682:D1222N	ENSP00000382195:D1185N	D	-	1	0	JMJD1C	64637225	0.000000	0.05858	0.995000	0.50966	0.582000	0.36321	-0.354000	0.07681	0.070000	0.16634	-0.469000	0.05056	GAT	.	.		0.418	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		T	64967219	C	T	64967219	3	4	112	1	0	0	0	0	1	0	0	0	7959	884	31	1	3480	1	JMJD1C	10	64967219	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	9384399	64967219	70567528	630	17251										
VPS26A	9559	hgsc.bcm.edu	37	chr10	70928313	70928313	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caacaatgagagatgtgaacAaaaaattttcagtaaggtac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:70928313delA	ENST00000373382.1	+	9	1449	c.796delA	c.(796-798)aaafs	p.K267fs	VPS26A_ENST00000395098.1_Intron|VPS26A_ENST00000489794.1_Intron|VPS26A_ENST00000263559.6_Frame_Shift_Del_p.K267fs|VPS26A_ENST00000546041.1_Frame_Shift_Del_p.K250fs|VPS26A_ENST00000541711.1_Frame_Shift_Del_p.K156fs|VPS26A_ENST00000490696.1_3'UTR			O75436	VP26A_HUMAN	vacuolar protein sorting 26 homolog A (S. pombe)	267					retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|vesicle (GO:0031982)	protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)	8						AGATGTGAACAAAAAATTTTC	0.368																																					p.N265fs	Colon(90;545 1358 4729 6702 16773)	Atlas-INDEL	.											.	VPS26A	24	.	0			c.795delC						.						93	98	96					10																	70928313		2203	4300	6503	SO:0001589	frameshift_variant	9559	exon8			.	AF054179	CCDS7286.1, CCDS41536.1	10q21.1	2007-01-12	2007-01-12	2005-10-11	ENSG00000122958	ENSG00000122958			12711	protein-coding gene	gene with protein product		605506	"vacuolar protein sorting 26 (yeast homolog)", "vacuolar protein sorting 26 (yeast)", "vacuolar protein sorting 26 homolog A (yeast)"	VPS26		1638986, 9653160	Standard	NM_004896		Approved	Hbeta58, PEP8A	uc001jpb.3	O75436	OTTHUMG00000018376	ENST00000373382.1:c.796delA	chr10.hg19:g.70928313delA	ENSP00000362480:p.Lys267fs	142.0	0.0		168.0	13.0	NM_004896	A8MZ56|B2RDD3|Q8TBH4|Q9H982	Frame_Shift_Del	DEL	ENST00000373382.1	hg19	CCDS7286.1																																																																																			.	.		0.368	VPS26A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048403.1	NM_004896		-	70928313	A	-	70928313	7	5	112	1	0	1	0	1	0	0	0	0	17212	131	5	0	826	0	VPS26A	10	70928313	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5961094	70928313	64606434	631	17252										
PPA1	5464	hgsc.bcm.edu	37	chr10	71969413	71969413	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acagtagcttctaagtagccAggtttcagccgtttgacatc	9	10	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:71969413A>G	ENST00000373232.3	-	7	639	c.540T>C	c.(538-540)ccT>ccC	p.P180P		NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	180					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						CTAAGTAGCCAGGTTTCAGCC	0.348																																					p.P180P		Atlas-SNP	.											.	PPA1	24	.	0			c.T540C						.						104	107	106					10																	71969413		2203	4300	6503	SO:0001819	synonymous_variant	5464	exon7			GTAGCCAGGTTTC	AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	3.6.1.1		9226	protein-coding gene	gene with protein product	"cytosolic inorganic pyrophosphatase", "inorganic pyrophosphatase 1", "pyrophosphate phospho-hydrolase"	179030	"pyrophosphatase (inorganic)"	PP		10542310, 975879	Standard	NM_021129		Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.540T>C	chr10.hg19:g.71969413A>G		211.0	0.0		238.0	18.0	NM_021129	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	Silent	SNP	ENST00000373232.3	hg19	CCDS7299.1																																																																																			.	.		0.348	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048490.2	NM_021129		G	71969413	A	G	71969413	2	3	112	1	0	0	0	0	0	0	0	1	12295	175	7	2		2	PPA1	10	71969413	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1041100	71969413	63565334	632	17253										
PPA1	5464	hgsc.bcm.edu	37	chr10	71977640	71977640	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcaacatagcgaagttttccTtttttcacatcttgtttaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:71977640delT	ENST00000373232.3	-	4	324	c.225delA	c.(223-225)aaafs	p.K75fs	PPA1_ENST00000608321.1_Frame_Shift_Del_p.K75fs|PPA1_ENST00000495346.1_5'Flank	NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	75					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						GAAGTTTTCCTTTTTTCACAT	0.353																																					p.G76fs		Atlas-INDEL	.											.	PPA1	24	.	0			c.226delG						.						100	93	96					10																	71977640		2203	4300	6503	SO:0001589	frameshift_variant	5464	exon4			.	AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	3.6.1.1		9226	protein-coding gene	gene with protein product	"cytosolic inorganic pyrophosphatase", "inorganic pyrophosphatase 1", "pyrophosphate phospho-hydrolase"	179030	"pyrophosphatase (inorganic)"	PP		10542310, 975879	Standard	NM_021129		Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.225delA	chr10.hg19:g.71977640delT	ENSP00000362329:p.Lys75fs	137.0	0.0		148.0	11.0	NM_021129	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	Frame_Shift_Del	DEL	ENST00000373232.3	hg19	CCDS7299.1																																																																																			.	.		0.353	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048490.2	NM_021129		-	71977640	T	-	71977640	7	5	112	1	0	1	0	1	0	0	0	0	12295	1606	56	0	676	0	PPA1	10	71977640	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	8227	71977640	63557107	633	17254										
PLA2G12B	84647	hgsc.bcm.edu	37	chr10	74702445	74702445	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagacccaggaaataggagcCgcagccattgggctcttggg	15	10	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:74702445C>A	ENST00000373032.3	-	2	357	c.265G>T	c.(265-267)Ggc>Tgc	p.G89C		NM_032562.2	NP_115951.2	Q9BX93	PG12B_HUMAN	phospholipase A2, group XIIB	89					cholesterol homeostasis (GO:0042632)|lipid catabolic process (GO:0016042)|triglyceride homeostasis (GO:0070328)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|skin(2)	9	Prostate(51;0.0198)					AAATAGGAGCCGCAGCCATTG	0.468																																					p.G89C		Atlas-SNP	.											.	PLA2G12B	19	.	0			c.G265T						.						49	49	49					10																	74702445		2203	4300	6503	SO:0001583	missense	84647	exon2			AGGAGCCGCAGCC	AF349540	CCDS7319.1	10q22.1	2008-09-19	2004-01-13	2004-01-14	ENSG00000138308	ENSG00000138308	3.1.1.4		18555	protein-coding gene	gene with protein product		611653	"phospholipase A2, group XIII"	PLA2G13			Standard	NM_032562		Approved		uc001jtf.1	Q9BX93	OTTHUMG00000018446	ENST00000373032.3:c.265G>T	chr10.hg19:g.74702445C>A	ENSP00000362123:p.Gly89Cys	58.0	0.0		61.0	27.0	NM_032562	B7ZL23|Q52LB2|Q96Q99	Missense_Mutation	SNP	ENST00000373032.3	hg19	CCDS7319.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.595133	0.66219	.	.	ENSG00000138308	ENST00000373032	.	.	.	5.17	1.18	0.20946	Phospholipase A2 (1);	0.114987	0.85682	D	0.000000	T	0.58424	0.2121	L	0.56280	1.765	0.36214	D	0.851564	P;D	0.55172	0.949;0.97	P;P	0.57846	0.828;0.776	T	0.64525	-0.6387	9	0.87932	D	0	-8.8295	9.261	0.37612	0.0:0.2118:0.0:0.7882	.	89;89	B7ZL23;Q9BX93	.;PG12B_HUMAN	C	89	.	ENSP00000362123:G89C	G	-	1	0	PLA2G12B	74372451	1.000000	0.71417	0.999000	0.59377	0.936000	0.57629	1.490000	0.35573	0.046000	0.15833	-0.459000	0.05422	GGC	.	.		0.468	PLA2G12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048598.1	NM_032562		A	74702445	C	A	74702445	3	1	112	1	0	0	0	0	1	0	0	0	12000	652	23	1	334	1	PLA2G12B	10	74702445	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	2724805	74702445	60832302	634	17255										
SEC24C	9632	hgsc.bcm.edu	37	chr10	75525560	75525560	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgccatgcttcccacagttCccccccagtattttcagcac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:75525560delC	ENST00000339365.2	+	11	1531	c.1369delC	c.(1369-1371)cccfs	p.P458fs	SEC24C_ENST00000411652.2_Frame_Shift_Del_p.P339fs|SEC24C_ENST00000546025.1_Intron|SEC24C_ENST00000345254.4_Frame_Shift_Del_p.P458fs|SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000535742.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	458					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					TCCCACAGTTCCCCCCCAGTA	0.507																																					p.V456fs		Atlas-INDEL	.											.,1	SEC24C	86	.	0			c.1368delT						.						195	176	182					10																	75525560		2203	4300	6503	SO:0001589	frameshift_variant	9632	exon11			.	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"SEC24 (S. cerevisiae) related gene family, member C", "SEC24 family, member C (S. cerevisiae)"			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.1369delC	chr10.hg19:g.75525560delC	ENSP00000343405:p.Pro458fs	184.0	0.0		173.0	12.0	NM_004922	B4DZT4|Q8WV25	Frame_Shift_Del	DEL	ENST00000339365.2	hg19	CCDS7332.1																																																																																			.	.		0.507	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			-	75525560	C	-	75525560	7	5	112	1	0	1	0	1	0	0	0	0	14011	855	30	0	1403	0	SEC24C	10	75525560	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	823115	75525560	60009187	635	17256										
KCNMA1	3778	hgsc.bcm.edu	37	chr10	78799310	78799310	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaacagtagggaaggacagaCccacgaaggcactggagaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:78799310delC	ENST00000286628.8	-	15	1834	c.1835delG	c.(1834-1836)ggtfs	p.G612fs	KCNMA1_ENST00000354353.5_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000372440.1_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000286627.5_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000404771.3_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000406533.3_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000404857.1_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000372443.1_Frame_Shift_Del_p.G612fs	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	612					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	GAAGGACAGACCCACGAAGGC	0.453																																					p.G612fs		Atlas-INDEL	.											.	KCNMA1	370	.	0			c.1836delT						.						228	192	204					10																	78799310		2203	4300	6503	SO:0001589	frameshift_variant	3778	exon15			.	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.1835delG	chr10.hg19:g.78799310delC	ENSP00000286628:p.Gly612fs	117.0	0.0		157.0	10.0	NM_002247	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Frame_Shift_Del	DEL	ENST00000286628.8	hg19																																																																																				.	.		0.453	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247		-	78799310	C	-	78799310	7	5	112	1	0	1	0	1	0	0	0	0	8082	507	18	0	2103	0	KCNMA1	10	78799310	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	3273750	78799310	56735437	636	17257										
POLR3A	11128	hgsc.bcm.edu	37	chr10	79745906	79745906	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcagagacccccttaatgaaTttttttatttcctgaaagat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:79745906delT	ENST00000372371.3	-	22	3050	c.2913delA	c.(2911-2913)aaafs	p.K971fs		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	971					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			CCTTAATGAATTTTTTTATTT	0.358																																					p.F972fs		Atlas-INDEL	.											.	POLR3A	104	.	0			c.2914delT						.						117	120	119					10																	79745906		2203	4300	6503	SO:0001589	frameshift_variant	11128	exon22			.	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"RNA polymerase subunits"	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.2913delA	chr10.hg19:g.79745906delT	ENSP00000361446:p.Lys971fs	97.0	0.0		160.0	10.0	NM_007055	Q8IW34|Q8TCW5	Frame_Shift_Del	DEL	ENST00000372371.3	hg19	CCDS7354.1																																																																																			.	.		0.358	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		-	79745906	T	-	79745906	7	5	112	1	0	1	0	1	0	0	0	0	12237	1490	52	0	1299	0	POLR3A	10	79745906	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	946596	79745906	55788841	637	17258										
ZMIZ1	57178	hgsc.bcm.edu	37	chr10	81058316	81058316	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgacatcaagccaaatatgAgcgctctgccaccaccccca	6	17	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:81058316A>G	ENST00000334512.5	+	15	2217	c.1645A>G	c.(1645-1647)Agc>Ggc	p.S549G		NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	549	Pro-rich.				artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			GCCAAATATGAGCGCTCTGCC	0.672																																					p.S549G		Atlas-SNP	.											ZMIZ1,right_upper_lobe,carcinoma,0,1	ZMIZ1	101	.	0			c.A1645G						.						95	95	95					10																	81058316		2203	4300	6503	SO:0001583	missense	57178	exon15			AATATGAGCGCTC	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"Zinc fingers, MIZ-type"	16493	protein-coding gene	gene with protein product		607159	"retinoic acid induced 17"	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.1645A>G	chr10.hg19:g.81058316A>G	ENSP00000334474:p.Ser549Gly	73.0	0.0		77.0	4.0	NM_020338	Q5JSH9|Q7Z7E6	Missense_Mutation	SNP	ENST00000334512.5	hg19	CCDS7357.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.451507	0.63290	.	.	ENSG00000108175	ENST00000334512;ENST00000360331;ENST00000372347	T	0.49139	0.79	5.12	5.12	0.69794	.	0.130904	0.33309	N	0.005050	T	0.43787	0.1263	L	0.51422	1.61	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.30650	-0.9971	10	0.37606	T	0.19	-22.1592	14.9189	0.70818	1.0:0.0:0.0:0.0	.	549	Q9ULJ6	ZMIZ1_HUMAN	G	549;479;456	ENSP00000334474:S549G	ENSP00000334474:S549G	S	+	1	0	ZMIZ1	80728322	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	8.882000	0.92420	1.936000	0.56123	0.379000	0.24179	AGC	.	.		0.672	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338		G	81058316	A	G	81058316	3	3	112	1	0	0	0	0	1	0	0	0	17711	304	11	2	1687	2	ZMIZ1	10	81058316	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1312410	81058316	54476431	638	17259										
PCGF5	84333	hgsc.bcm.edu	37	chr10	93000241	93000241	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aacatcttctttcttcttagTctgtaagacttgtattgttc	5	8	5	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:93000241T>C	ENST00000336126.5	+	3	345	c.113T>C	c.(112-114)tTc>tCc	p.F38S	PCGF5_ENST00000543648.1_Splice_Site_p.F38S	NM_001257101.1|NM_032373.4	NP_001244030.1|NP_115749.2	Q86SE9	PCGF5_HUMAN	polycomb group ring finger 5	38					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)	12						TTCTTCTTAGTCTGTAAGACT	0.348																																					p.F38S	Colon(178;732 2696 46441 50370)	Atlas-SNP	.											.	PCGF5	29	.	0			c.T113C						.						125	133	131					10																	93000241		2203	4300	6503	SO:0001630	splice_region_variant	84333	exon3			TCTTAGTCTGTAA	AL832003	CCDS7413.1	10q23.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000180628	ENSG00000180628		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	28264	protein-coding gene	gene with protein product			"ring finger protein (C3HC4 type) 159"	RNF159		8076819	Standard	NM_001256549		Approved	MGC16202	uc001khh.4	Q86SE9	OTTHUMG00000018740	ENST00000336126.5:c.113-1T>C	chr10.hg19:g.93000241T>C		76.0	0.0		58.0	4.0	NM_001256549	B7Z892|D3DR33|Q6PK47|Q86TD0	Missense_Mutation	SNP	ENST00000336126.5	hg19	CCDS7413.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735227	0.69189	.	.	ENSG00000180628	ENST00000543648;ENST00000336126	T;T	0.33865	1.39;1.39	6.0	6.0	0.97389	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type, conserved site (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	T	0.62490	0.2432	H	0.98866	4.355	0.80722	D	1	B	0.18968	0.032	B	0.26614	0.071	T	0.68945	-0.5275	9	.	.	.	.	16.5561	0.84485	0.0:0.0:0.0:1.0	.	38	Q86SE9	PCGF5_HUMAN	S	38	ENSP00000445704:F38S;ENSP00000337500:F38S	.	F	+	2	0	PCGF5	92990221	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.951000	0.87819	2.310000	0.77875	0.451000	0.29950	TTC	.	.		0.348	PCGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049363.1	NM_032373	Missense_Mutation	C	93000241	T	C	93000241	5	2	112	1	0	0	0	0	0	0	1	0	11586	1681	58	2	119	2	PCGF5	10	93000241	Splice_Site	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	11941925	93000241	42534506	639	17260										
MYOF	26509	hgsc.bcm.edu	37	chr10	95157188	95157188	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gattccactctgggtttgcaTttttctcaattatgtttgta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:95157188delT	ENST00000359263.4	-	14	1246	c.1247delA	c.(1246-1248)aatfs	p.N416fs	MYOF_ENST00000371502.4_Frame_Shift_Del_p.N416fs|MYOF_ENST00000371501.4_Frame_Shift_Del_p.N416fs|MYOF_ENST00000358334.5_Frame_Shift_Del_p.N416fs|MYOF_ENST00000371489.1_Frame_Shift_Del_p.N416fs	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	416	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TGGGTTTGCATTTTTCTCAAT	0.294																																					p.N416fs		Atlas-INDEL	.											.	MYOF	177	.	0			c.1248delT						.						139	128	132					10																	95157188		1812	4076	5888	SO:0001589	frameshift_variant	26509	exon14			.	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.1247delA	chr10.hg19:g.95157188delT	ENSP00000352208:p.Asn416fs	126.0	0.0		156.0	10.0	NM_133337	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Frame_Shift_Del	DEL	ENST00000359263.4	hg19	CCDS41551.1																																																																																			.	.		0.294	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		-	95157188	T	-	95157188	7	5	112	1	0	1	0	1	0	0	0	0	10098	1493	52	0	5102	0	MYOF	10	95157188	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2156947	95157188	40377559	640	17261										
HELLS	3070	hgsc.bcm.edu	37	chr10	96336531	96336531	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtggtaatcacgtcatttgAaatagccatgagagaccgaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:96336531delA	ENST00000348459.5	+	10	1106	c.1001delA	c.(1000-1002)gaafs	p.E334fs	RP11-119K6.6_ENST00000432120.1_RNA|HELLS_ENST00000239026.6_3'UTR|HELLS_ENST00000371332.4_Frame_Shift_Del_p.E334fs|HELLS_ENST00000394045.1_Frame_Shift_Del_p.E334fs|HELLS_ENST00000394044.1_Intron|HELLS_ENST00000394036.1_3'UTR	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		ACGTCATTTGAAATAGCCATG	0.348																																					p.E334fs		Atlas-INDEL	.											.	HELLS	63	.	0			c.1000delG						.						141	129	133					10																	96336531		2203	4300	6503	SO:0001589	frameshift_variant	3070	exon10			.	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6", "proliferation-associated SNF2-like protein"	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.1001delA	chr10.hg19:g.96336531delA	ENSP00000239027:p.Glu334fs	157.0	0.0		184.0	12.0	NM_018063		Frame_Shift_Del	DEL	ENST00000348459.5	hg19	CCDS7434.1																																																																																			.	.		0.348	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		-	96336531	A	-	96336531	7	5	112	1	0	1	0	1	0	0	0	0	7055	246	9	0	1039	0	HELLS	10	96336531	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1179343	96336531	39198216	641	17262										
ARHGAP19	84986	hgsc.bcm.edu	37	chr10	99025639	99025639	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttcgcttgagagacatgagAgaccggaagaatcctgatgc	12	8	0	6			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:99025639A>G	ENST00000358531.4	-	2	328	c.300T>C	c.(298-300)tcT>tcC	p.S100S	ARHGAP19_ENST00000371027.1_Silent_p.S91S|ARHGAP19-SLIT1_ENST00000316676.8_Silent_p.S100S|ARHGAP19_ENST00000355366.5_Silent_p.S91S|ARHGAP19-SLIT1_ENST00000358308.3_Silent_p.S100S|ARHGAP19-SLIT1_ENST00000453547.2_Silent_p.S100S	NM_001204300.1|NM_032900.5	NP_001191229.1|NP_116289.4	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	100					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|urinary_tract(1)	13		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		GAGACATGAGAGACCGGAAGA	0.557																																					p.S100S		Atlas-SNP	.											.	ARHGAP19	72	.	0			c.T300C						.						92	88	89					10																	99025639		2203	4300	6503	SO:0001819	synonymous_variant	84986	exon2			CATGAGAGACCGG	AK074122	CCDS7454.2, CCDS58092.1, CCDS73175.1	10q24.2	2011-06-29			ENSG00000213390	ENSG00000213390		"Rho GTPase activating proteins"	23724	protein-coding gene	gene with protein product		611587					Standard	NM_032900		Approved	FLJ00194, MGC14258	uc001knb.3	Q14CB8	OTTHUMG00000018845	ENST00000358531.4:c.300T>C	chr10.hg19:g.99025639A>G		62.0	0.0		84.0	4.0	NM_001204300	A1XCP1|B4DZR1|Q14CF2|Q5J8M2|Q5T460|Q5T462|Q68DG6|Q8N9X1|Q8NF34|Q8TEK1	Silent	SNP	ENST00000358531.4	hg19	CCDS7454.2																																																																																			.	.		0.557	ARHGAP19-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049647.2	NM_032900		G	99025639	A	G	99025639	2	3	112	1	0	0	0	0	0	0	0	1	869	291	11	2		2	ARHGAP19	10	99025639	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2689108	99025639	36509108	642	17263										
PI4K2A	55361	hgsc.bcm.edu	37	chr10	99426199	99426199	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttttcctcttttcagatccTttttactgggcctggttgcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:99426199delT	ENST00000370631.3	+	7	1146	c.1089delT	c.(1087-1089)cctfs	p.P363fs	PI4K2A_ENST00000555577.1_Frame_Shift_Del_p.P333fs|PI4K2A_ENST00000370649.3_Frame_Shift_Del_p.P333fs	NM_018425.2	NP_060895.1	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	363	PI3K/PI4K.				basophil degranulation (GO:0002561)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endosome (GO:0005768)|exocytic vesicle (GO:0070382)|Golgi apparatus (GO:0005794)|growing cell tip (GO:0035838)|host cell presynaptic membrane (GO:0044231)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|AP-3 adaptor complex binding (GO:0035651)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		TTTCAGATCCTTTTTACTGGG	0.478																																					p.P363fs		Atlas-INDEL	.											.	PI4K2A	57	.	0			c.1088delC						.						76	73	74					10																	99426199		2203	4300	6503	SO:0001589	frameshift_variant	55361	exon7			.	AF070611	CCDS7469.1	10q24	2011-02-09			ENSG00000155252	ENSG00000155252			30031	protein-coding gene	gene with protein product		609763				11244087, 11279162	Standard	NM_018425		Approved	PI4KII, DKFZP761G1923, PIK42A	uc001kog.1	Q9BTU6	OTTHUMG00000018863	ENST00000370631.3:c.1089delT	chr10.hg19:g.99426199delT	ENSP00000359665:p.Pro363fs	119.0	0.0		139.0	10.0	NM_018425	D3DR59|Q9NSG8	Frame_Shift_Del	DEL	ENST00000370631.3	hg19	CCDS7469.1																																																																																			.	.		0.478	PI4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049735.1	NM_018425		-	99426199	T	-	99426199	7	5	112	1	0	1	0	1	0	0	0	0	11880	1596	56	0	1115	0	PI4K2A	10	99426199	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	400560	99426199	36108548	643	17264										
CRTAC1	55118	hgsc.bcm.edu	37	chr10	99640100	99640100	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccataggtgttgacacatacGggcttgtctcgagggcacac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:99640100delG	ENST00000370597.3	-	14	2080	c.1725delC	c.(1723-1725)cccfs	p.P575fs	CRTAC1_ENST00000298819.4_Frame_Shift_Del_p.P561fs|CRTAC1_ENST00000370591.2_Frame_Shift_Del_p.P575fs|CRTAC1_ENST00000468549.1_5'Flank	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	575	EGF-like.					extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		TGACACATACGGGCTTGTCTC	0.577																																					p.V576fs		Atlas-INDEL	.											.	CRTAC1	86	.	0			c.1726delG						.						145	111	122					10																	99640100		2203	4300	6503	SO:0001589	frameshift_variant	55118	exon14			.	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.1725delC	chr10.hg19:g.99640100delG	ENSP00000359629:p.Pro575fs	144.0	0.0		152.0	10.0	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Frame_Shift_Del	DEL	ENST00000370597.3	hg19	CCDS31266.1																																																																																			.	.		0.577	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058		-	99640100	G	-	99640100	7	5	112	1	0	1	0	1	0	0	0	0	3898	1103	39	0	268	0	CRTAC1	10	99640100	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	213901	99640100	35894647	644	17265										
PKD2L1	9033	hgsc.bcm.edu	37	chr10	102054379	102054379	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgtcgatagcattgtagtcAaagtccccgaggattatccg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:102054379delA	ENST00000318222.3	-	9	1954	c.1572delT	c.(1570-1572)tttfs	p.F524fs	PKD2L1_ENST00000338519.3_Frame_Shift_Del_p.F449fs|PKD2L1_ENST00000353274.3_Frame_Shift_Del_p.F524fs	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	524					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)			NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		CATTGTAGTCAAAGTCCCCGA	0.522																																					p.D525fs		Atlas-INDEL	.											.	PKD2L1	103	.	0			c.1573delG						.						172	160	164					10																	102054379		2203	4300	6503	SO:0001589	frameshift_variant	9033	exon9			.	AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"Voltage-gated ion channels / Transient receptor potential cation channels"	9011	protein-coding gene	gene with protein product	"transient receptor potential cation channel, subfamily P, member 3"	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.1572delT	chr10.hg19:g.102054379delA	ENSP00000325296:p.Phe524fs	128.0	0.0		157.0	10.0	NM_016112	O75972|Q5W039|Q9UP35|Q9UPA2	Frame_Shift_Del	DEL	ENST00000318222.3	hg19	CCDS7492.1																																																																																			.	.		0.522	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112		-	102054379	A	-	102054379	7	5	112	1	0	1	0	1	0	0	0	0	11976	127	5	0	877	0	PKD2L1	10	102054379	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2414279	102054379	33480368	645	17266										
SEC31B	25956	hgsc.bcm.edu	37	chr10	102275905	102275905	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caagtccagagaagggtcccTgaaatcaacctcaaatattt	7	10	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:102275905T>C	ENST00000370345.3	-	3	248	c.151A>G	c.(151-153)Agg>Ggg	p.R51G	SEC31B_ENST00000451524.1_Missense_Mutation_p.R51G|SEC31B_ENST00000370329.5_Missense_Mutation_p.R51G|NDUFB8_ENST00000557395.1_3'UTR|NDUFB8_ENST00000531258.1_3'UTR|SEC31B_ENST00000535773.1_5'UTR	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	51					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GAAGGGTCCCTGAAATCAACC	0.458																																					p.R51G		Atlas-SNP	.											.	SEC31B	84	.	0			c.A151G						.						93	88	89					10																	102275905		2203	4300	6503	SO:0001583	missense	25956	exon3			GGTCCCTGAAATC	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.151A>G	chr10.hg19:g.102275905T>C	ENSP00000359370:p.Arg51Gly	116.0	0.0		91.0	4.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	hg19	CCDS7495.1	.	.	.	.	.	.	.	.	.	.	T	12.44	1.938920	0.34189	.	.	ENSG00000075826	ENST00000370345;ENST00000451524;ENST00000370329	T;T;T	0.57595	0.76;0.39;0.49	5.89	3.53	0.40419	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.215458	0.49916	D	0.000121	T	0.32376	0.0827	N	0.19112	0.55	0.80722	D	1	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.001;0.001	T	0.06643	-1.0815	10	0.33141	T	0.24	-12.9283	5.7669	0.18231	0.0:0.1432:0.1424:0.7144	.	51;51;51;51	B4DGE3;Q9NQW1-5;E9PKR7;Q9NQW1	.;.;.;SC31B_HUMAN	G	51	ENSP00000359370:R51G;ENSP00000391178:R51G;ENSP00000359354:R51G	ENSP00000359354:R51G	R	-	1	2	SEC31B	102265895	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.025000	0.30090	0.473000	0.27368	0.454000	0.30748	AGG	.	.		0.458	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		C	102275905	T	C	102275905	3	2	112	1	0	0	0	0	1	0	0	0	14014	1579	55	2	3484	2	SEC31B	10	102275905	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	221526	102275905	33258842	646	17267										
PDZD7	79955	hgsc.bcm.edu	37	chr10	102777929	102777929	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtccaggcctctctgcgcccGtcccgcgctagcctcccctg	10	21	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:102777929G>A	ENST00000370215.3	-	9	1674	c.1449C>T	c.(1447-1449)gaC>gaT	p.D483D		NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	483						cilium (GO:0005929)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		CTCTGCGCCCGTCCCGCGCTA	0.617																																					p.D483D		Atlas-SNP	.											.	PDZD7	101	.	0			c.C1449T						.						81	77	79					10																	102777929		2203	4300	6503	SO:0001819	synonymous_variant	79955	exon9			GCGCCCGTCCCGC	AK026862	CCDS31269.1, CCDS73182.1	10q24.32	2006-01-24		2006-01-24	ENSG00000186862	ENSG00000186862			26257	protein-coding gene	gene with protein product		612971		PDZK7		12477932	Standard	NM_024895		Approved	FLJ23209, bA108L7.8	uc021pxc.1	Q9H5P4	OTTHUMG00000018916	ENST00000370215.3:c.1449C>T	chr10.hg19:g.102777929G>A		104.0	0.0		138.0	39.0	NM_001195263	D5FJ77|Q8N321	Silent	SNP	ENST00000370215.3	hg19	CCDS31269.1	.	.	.	.	.	.	.	.	.	.	G	0.204	-1.042112	0.01997	.	.	ENSG00000186862	ENST00000433616	.	.	.	4.12	-4.62	0.03370	.	.	.	.	.	T	0.35278	0.0926	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.34079	-0.9843	4	.	.	.	.	13.4053	0.60908	0.6497:0.0:0.3503:0.0	.	.	.	.	M	58	.	.	T	-	2	0	PDZD7	102767919	0.000000	0.05858	0.003000	0.11579	0.079000	0.17450	-1.754000	0.01816	-1.446000	0.01945	-1.164000	0.01763	ACG	.	.		0.617	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895		A	102777929	G	A	102777929	2	1	112	1	0	0	0	0	0	0	0	1	11713	1136	40	1		1	PDZD7	10	102777929	Silent	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	502024	102777929	32756818	647	17268										
FBXW4	6468	hgsc.bcm.edu	37	chr10	103433426	103433426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctctagctgcatccagggcaTctgactgaaatgatggaaaa	10	9	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:103433426T>C	ENST00000331272.7	-	3	979	c.361A>G	c.(361-363)Atg>Gtg	p.M121V		NM_022039.3	NP_071322.1	P57775	FBXW4_HUMAN	F-box and WD repeat domain containing 4	121					cartilage development (GO:0051216)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|positive regulation of mesenchymal cell proliferation (GO:0002053)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	ubiquitin ligase complex (GO:0000151)				breast(3)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	15		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)		ATCCAGGGCATCTGACTGAAA	0.428																																					p.M121V		Atlas-SNP	.											.	FBXW4	39	.	0			c.A361G						.						59	60	60					10																	103433426		2203	4300	6503	SO:0001583	missense	6468	exon3			AGGGCATCTGACT	AF281859	CCDS31271.1	10q24	2013-01-09	2007-02-08	2005-03-12	ENSG00000107829	ENSG00000107829		"F-boxes / WD-40 domains", "WD repeat domain containing"	10847	protein-coding gene	gene with protein product		608071	"split hand/foot malformation (ectrodactyly) type 3", "F-box and WD-40 domain protein 4"	SHFM3		8723077, 7912888	Standard	XM_005270053		Approved	Fbw4, dactylin	uc001kto.3	P57775	OTTHUMG00000018938	ENST00000331272.7:c.361A>G	chr10.hg19:g.103433426T>C	ENSP00000359149:p.Met121Val	85.0	0.0		90.0	4.0	NM_022039	Q5SVS1|Q96IM6	Missense_Mutation	SNP	ENST00000331272.7	hg19	CCDS31271.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.637031	0.47049	.	.	ENSG00000107829	ENST00000331272;ENST00000389046;ENST00000457105;ENST00000431477	T	0.72505	-0.66	5.23	5.23	0.72850	.	0.043313	0.85682	D	0.000000	T	0.56920	0.2018	L	0.29908	0.895	0.42535	D	0.993059	B	0.26195	0.144	B	0.26969	0.075	T	0.54166	-0.8334	10	0.07175	T	0.84	-19.5873	15.4089	0.74902	0.0:0.0:0.0:1.0	.	121	P57775	FBXW4_HUMAN	V	121;121;34;77	ENSP00000359149:M121V	ENSP00000359149:M121V	M	-	1	0	FBXW4	103423416	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	4.676000	0.61627	2.103000	0.63969	0.397000	0.26171	ATG	.	.		0.428	FBXW4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049979.2	NM_022039		C	103433426	T	C	103433426	3	2	112	1	0	0	0	0	1	0	0	0	5775	1435	50	2	905	2	FBXW4	10	103433426	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	655497	103433426	32101321	648	17269										
TMEM180	79847	hgsc.bcm.edu	37	chr10	104230585	104230585	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcctctatgatggcttcctgAcgctcgtggacctgcaccac	10	15	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:104230585A>G	ENST00000238936.4	+	5	652	c.415A>G	c.(415-417)Acg>Gcg	p.T139A	TMEM180_ENST00000366277.2_Intron|TMEM180_ENST00000369931.3_Intron	NM_024789.3	NP_079065.2	Q14CX5	TM180_HUMAN	transmembrane protein 180	139						integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|skin(1)	13		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TGGCTTCCTGACGCTCGTGGA	0.662																																					p.T139A		Atlas-SNP	.											.	TMEM180	33	.	0			c.A415G						.						96	93	94					10																	104230585		2203	4300	6503	SO:0001583	missense	79847	exon5			TTCCTGACGCTCG	AK026182	CCDS7535.1	10q24.32	2011-02-09	2006-10-12	2006-10-12	ENSG00000138111	ENSG00000138111			26196	protein-coding gene	gene with protein product				C10orf77		12477932	Standard	XM_006717971		Approved	FLJ22529, bA18I14.8	uc001kvt.3	Q14CX5	OTTHUMG00000018961	ENST00000238936.4:c.415A>G	chr10.hg19:g.104230585A>G	ENSP00000238936:p.Thr139Ala	103.0	0.0		123.0	5.0	NM_024789	Q6NWM8|Q6NWM9|Q6PEZ7|Q9H679	Missense_Mutation	SNP	ENST00000238936.4	hg19	CCDS7535.1	.	.	.	.	.	.	.	.	.	.	A	32	5.138864	0.94560	.	.	ENSG00000138111	ENST00000238936	T	0.78003	-1.14	5.74	5.74	0.90152	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.88485	0.6449	M	0.81341	2.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89522	0.3779	10	0.59425	D	0.04	.	16.0229	0.80512	1.0:0.0:0.0:0.0	.	139	Q14CX5	TM180_HUMAN	A	139	ENSP00000238936:T139A	ENSP00000238936:T139A	T	+	1	0	TMEM180	104220575	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.339000	0.96797	2.189000	0.69895	0.459000	0.35465	ACG	.	.		0.662	TMEM180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050075.2	NM_024789		G	104230585	A	G	104230585	3	3	112	1	0	0	0	0	1	0	0	0	16114	275	10	2	425	2	TMEM180	10	104230585	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	797159	104230585	31304162	649	17270										
ARL3	403	hgsc.bcm.edu	37	chr10	104449670	104449670	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgacccgtctcttcaaatcTttttctgtctgcactgtcga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:104449670delT	ENST00000260746.5	-	4	426	c.295delA	c.(295-297)agafs	p.R99fs		NM_004311.3	NP_004302.1	P36405	ARL3_HUMAN	ADP-ribosylation factor-like 3	99					cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|intraciliary transport (GO:0042073)|kidney development (GO:0001822)|photoreceptor cell development (GO:0042461)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|spindle microtubule (GO:0005876)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			large_intestine(2)	2		Colorectal(252;0.122)		Epithelial(162;4.88e-09)|all cancers(201;1.29e-07)|BRCA - Breast invasive adenocarcinoma(275;0.22)		TCTTCAAATCTTTTTCTGTCT	0.313																																					p.R99fs		Atlas-INDEL	.											.	ARL3	13	.	0			c.296delG						.						50	55	54					10																	104449670		2203	4298	6501	SO:0001589	frameshift_variant	403	exon4			.	U07151	CCDS7538.1	10q23.3	2014-05-09			ENSG00000138175	ENSG00000138175		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	694	protein-coding gene	gene with protein product		604695				8034651, 10072593	Standard	NM_004311		Approved	ARFL3	uc001kwa.3	P36405	OTTHUMG00000018965	ENST00000260746.5:c.295delA	chr10.hg19:g.104449670delT	ENSP00000260746:p.Arg99fs	147.0	0.0		157.0	10.0	NM_004311	B2R6C7|Q53X83|Q5JSM2	Frame_Shift_Del	DEL	ENST00000260746.5	hg19	CCDS7538.1																																																																																			.	.		0.313	ARL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050088.2	NM_004311		-	104449670	T	-	104449670	7	5	112	1	0	1	0	1	0	0	0	0	935	1617	56	0	265	0	ARL3	10	104449670	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	219085	104449670	31085077	650	17271										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105174798	105174798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taaagtcatatgggatgctgGtgaaggtgggcgagcagatg	17	4	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:105174798G>A	ENST00000369797.3	+	12	1502	c.1408G>A	c.(1408-1410)Gtg>Atg	p.V470M		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	470	S1 motif 5. {ECO:0000255|PROSITE- ProRule:PRU00180}.				mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		TGGGATGCTGGTGAAGGTGGG	0.517																																					p.V470M		Atlas-SNP	.											.	PDCD11	160	.	0			c.G1408A						.						109	92	98					10																	105174798		2203	4300	6503	SO:0001583	missense	22984	exon12			ATGCTGGTGAAGG	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.1408G>A	chr10.hg19:g.105174798G>A	ENSP00000358812:p.Val470Met	110.0	0.0		151.0	48.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	hg19	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	G	18.59	3.656309	0.67586	.	.	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.71103	-0.54	5.35	2.44	0.29823	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (2);	0.115848	0.64402	D	0.000018	D	0.84848	0.5563	H	0.95260	3.645	0.58432	D	0.999998	D	0.58268	0.982	P	0.59761	0.863	D	0.84585	0.0663	10	0.34782	T	0.22	-8.7672	11.3229	0.49433	0.0:0.1226:0.6225:0.2549	.	470	Q14690	RRP5_HUMAN	M	470	ENSP00000358812:V470M	ENSP00000358812:V470M	V	+	1	0	PDCD11	105164788	1.000000	0.71417	0.997000	0.53966	0.769000	0.43574	5.224000	0.65288	0.324000	0.23333	-0.183000	0.12914	GTG	.	.		0.517	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			A	105174798	G	A	105174798	3	1	112	1	0	0	0	0	1	0	0	0	11626	1261	44	3	1450	3	PDCD11	10	105174798	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	725128	105174798	30359949	651	17272										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105205170	105205170	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtcattcatctgagcttggCccccaagagaatgaagttct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:105205170delC	ENST00000369797.3	+	36	5574	c.5480delC	c.(5479-5481)gccfs	p.A1827fs		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1827					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CTGAGCTTGGCCCCCAAGAGA	0.547																																					p.A1827fs		Atlas-INDEL	.											.	PDCD11	160	.	0			c.5479delG						.						160	139	146					10																	105205170		2203	4300	6503	SO:0001589	frameshift_variant	22984	exon36			.	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5480delC	chr10.hg19:g.105205170delC	ENSP00000358812:p.Ala1827fs	174.0	0.0		175.0	12.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Frame_Shift_Del	DEL	ENST00000369797.3	hg19	CCDS31276.1																																																																																			.	.		0.547	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			-	105205170	C	-	105205170	7	5	112	1	0	1	0	1	0	0	0	0	11626	739	26	0	5618	0	PDCD11	10	105205170	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	30372	105205170	30329577	652	17273										
C10orf79	80217	hgsc.bcm.edu	37	chr10	105971830	105971830	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagtggcagcacgggaccatAgatgagatctttcggcaacg	13	10	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:105971830A>G	ENST00000278064.2	-	5	785	c.460T>C	c.(460-462)Tat>Cat	p.Y154H	WDR96_ENST00000357060.3_Missense_Mutation_p.Y224H|WDR96_ENST00000369719.1_Missense_Mutation_p.Y154H|WDR96_ENST00000369720.1_Missense_Mutation_p.Y154H|WDR96_ENST00000428666.1_Missense_Mutation_p.Y224H																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ACGGGACCATAGATGAGATCT	0.493																																					p.Y224H		Atlas-SNP	.											.	WDR96	183	.	0			c.T670C						.						86	79	82					10																	105971830		2203	4300	6503	SO:0001583	missense	80217	exon5			GACCATAGATGAG																												ENST00000278064.2:c.460T>C	chr10.hg19:g.105971830A>G	ENSP00000278064:p.Tyr154His	72.0	0.0		64.0	4.0	NM_025145		Missense_Mutation	SNP	ENST00000278064.2	hg19		.	.	.	.	.	.	.	.	.	.	A	14.99	2.699136	0.48307	.	.	ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064;ENST00000369720;ENST00000369719	T;T;T;T;T	0.48201	2.41;2.4;2.39;1.41;0.82	5.51	5.51	0.81932	WD40 repeat-like-containing domain (1);	0.000000	0.34676	N	0.003774	T	0.57330	0.2046	M	0.74258	2.255	0.31682	N	0.642947	B;P;P	0.51653	0.41;0.947;0.786	B;P;B	0.50270	0.113;0.636;0.321	T	0.65446	-0.6166	10	0.27082	T	0.32	.	14.6028	0.68453	1.0:0.0:0.0:0.0	.	224;224;224	Q8NDM7-5;B4DHB6;Q8NDM7	.;.;WDR96_HUMAN	H	224;224;154;154;154	ENSP00000349568:Y224H;ENSP00000400289:Y224H;ENSP00000278064:Y154H;ENSP00000358734:Y154H;ENSP00000358733:Y154H	ENSP00000278064:Y154H	Y	-	1	0	WDR96	105961820	1.000000	0.71417	1.000000	0.80357	0.565000	0.35776	3.888000	0.56204	2.101000	0.63845	0.533000	0.62120	TAT	.	.		0.493	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			G	105971830	A	G	105971830	3	3	112	1	0	0	0	0	1	0	0	0	1620	420	15	2	4463	2	C10orf79	10	105971830	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	766660	105971830	29562917	653	17274										
CCDC147	159686	hgsc.bcm.edu	37	chr10	106121791	106121791	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcccatctaggaaattgaaaAggcctggaagatggtggact	13	7	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:106121791A>G	ENST00000369704.3	+	3	436	c.302A>G	c.(301-303)aAg>aGg	p.K101R	CCDC147_ENST00000312902.5_5'UTR	NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		101						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		GAAATTGAAAAGGCCTGGAAG	0.438																																					p.K101R		Atlas-SNP	.											.	CCDC147	137	.	0			c.A302G						.						84	79	81					10																	106121791		2203	4300	6503	SO:0001583	missense	159686	exon3			TTGAAAAGGCCTG																												ENST00000369704.3:c.302A>G	chr10.hg19:g.106121791A>G	ENSP00000358718:p.Lys101Arg	56.0	0.0		90.0	4.0	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	hg19	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.859253	0.91433	.	.	ENSG00000120051	ENST00000369704	T	0.36699	1.24	6.17	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.53449	0.1797	M	0.76328	2.33	0.80722	D	1	D	0.55605	0.972	P	0.58130	0.833	T	0.53662	-0.8407	10	0.40728	T	0.16	-24.7135	12.297	0.54854	0.9345:0.0:0.0655:0.0	.	101	Q5T655	CC147_HUMAN	R	101	ENSP00000358718:K101R	ENSP00000358718:K101R	K	+	2	0	CCDC147	106111781	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.347000	0.79356	1.158000	0.42547	0.533000	0.62120	AAG	.	.		0.438	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			G	106121791	A	G	106121791	3	3	112	1	0	0	0	0	1	0	0	0	2783	72	3	2	312	2	CCDC147	10	106121791	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	149961	106121791	29412956	654	17275										
XPNPEP1	7511	hgsc.bcm.edu	37	chr10	111635319	111635319	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccgagtcaataaggtacaccTcatccagggacaaggtccta	9	12	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:111635319T>C	ENST00000502935.1	-	15	1477	c.1358A>G	c.(1357-1359)gAg>gGg	p.E453G	XPNPEP1_ENST00000322238.8_Intron|XPNPEP1_ENST00000369683.1_Missense_Mutation_p.E339G|XPNPEP1_ENST00000369680.4_Missense_Mutation_p.E410G					X-prolyl aminopeptidase (aminopeptidase P) 1, soluble											endometrium(2)|kidney(9)|large_intestine(4)|lung(9)|ovary(3)|pancreas(2)|skin(1)|urinary_tract(1)	31		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)		AAGGTACACCTCATCCAGGGA	0.438																																					p.E453G		Atlas-SNP	.											.	XPNPEP1	110	.	0			c.A1358G						.						127	103	111					10																	111635319		2203	4300	6503	SO:0001583	missense	7511	exon15			TACACCTCATCCA		CCDS7560.1, CCDS7560.2, CCDS53576.1	10q25.3	2006-01-16	2002-07-17		ENSG00000108039	ENSG00000108039	3.4.11.9		12822	protein-coding gene	gene with protein product		602443	"X-prolyl aminopeptidase (aminopeptidase P)-like"	XPNPEP, XPNPEPL1, XPNPEPL			Standard	NM_020383		Approved		uc001kyp.2	Q9NQW7	OTTHUMG00000019029	ENST00000502935.1:c.1358A>G	chr10.hg19:g.111635319T>C	ENSP00000421566:p.Glu453Gly	112.0	0.0		90.0	5.0	NM_020383		Missense_Mutation	SNP	ENST00000502935.1	hg19	CCDS7560.2	.	.	.	.	.	.	.	.	.	.	T	25.6	4.659386	0.88154	.	.	ENSG00000108039	ENST00000502935;ENST00000369683;ENST00000369680	T;T;T	0.77358	-1.09;-1.09;-1.09	5.43	5.43	0.79202	Peptidase M24, structural domain (3);	0.000000	0.85682	D	0.000000	T	0.77425	0.4128	N	0.24115	0.695	0.54753	D	0.999988	D	0.89917	1.0	D	0.77557	0.99	T	0.71813	-0.4479	10	0.06891	T	0.86	-23.1133	14.3486	0.66685	0.0:0.0:0.0:1.0	.	410	Q9NQW7	XPP1_HUMAN	G	453;339;410	ENSP00000421566:E453G;ENSP00000358697:E339G;ENSP00000358694:E410G	ENSP00000358694:E410G	E	-	2	0	XPNPEP1	111625309	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	5.682000	0.68182	2.179000	0.69175	0.533000	0.62120	GAG	.	.		0.438	XPNPEP1-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050264.2			C	111635319	T	C	111635319	3	2	112	1	0	0	0	0	1	0	0	0	17457	1551	54	2	670	2	XPNPEP1	10	111635319	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	5513528	111635319	23899428	655	17276										
GPAM	57678	hgsc.bcm.edu	37	chr10	113935417	113935417	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aacatgcccttatgcacatcTcgctcttgaataaaaagaac	5	11	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:113935417T>C	ENST00000348367.4	-	6	551	c.354A>G	c.(352-354)cgA>cgG	p.R118R	GPAM_ENST00000423155.1_Silent_p.R118R|GPAM_ENST00000369425.1_Silent_p.R118R			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	118					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		TATGCACATCTCGCTCTTGAA	0.473																																					p.R118R	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.A354G						.						167	148	154					10																	113935417		2203	4300	6503	SO:0001819	synonymous_variant	57678	exon6			CACATCTCGCTCT	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"glycerol-3-phosphate acyltransferase 1, mitochondrial"	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.354A>G	chr10.hg19:g.113935417T>C		73.0	0.0		60.0	4.0	NM_001244949	Q5VW51|Q86TA3	Silent	SNP	ENST00000348367.4	hg19	CCDS7570.1																																																																																			.	.		0.473	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		C	113935417	T	C	113935417	2	2	112	1	0	0	0	0	0	0	0	1	6596	1538	54	2		2	GPAM	10	113935417	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2300098	113935417	21599330	656	17277										
NHLRC2	374354	hgsc.bcm.edu	37	chr10	115657964	115657964	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actctggcaaactgccaaagAaaaagtaagtgacagcctct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:115657964delA	ENST00000369301.3	+	6	1347	c.1135delA	c.(1135-1137)aaafs	p.K379fs		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	379										breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		ACTGCCAAAGAAAAAGTAAGT	0.428																																					p.K378fs		Atlas-INDEL	.											NHLRC2,colon,carcinoma,0,1	NHLRC2	56	.	0			c.1134delG						.						36	36	36					10																	115657964		2203	4300	6503	SO:0001589	frameshift_variant	374354	exon6			.	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.1135delA	chr10.hg19:g.115657964delA	ENSP00000358307:p.Lys379fs	222.0	0.0		265.0	16.0	NM_198514	Q8N1H1|Q8N5A6	Frame_Shift_Del	DEL	ENST00000369301.3	hg19	CCDS7585.1																																																																																			.	.		0.428	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514		-	115657964	A	-	115657964	7	5	112	1	0	1	0	1	0	0	0	0	10415	247	9	0	1157	0	NHLRC2	10	115657964	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1722547	115657964	19876783	657	17278										
FAM160B1	57700	hgsc.bcm.edu	37	chr10	116608429	116608429	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctctgtctggtaccggatgAcgcaaaatcctcctaccatg	8	13	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:116608429A>G	ENST00000369248.4	+	13	2071	c.1736A>G	c.(1735-1737)gAc>gGc	p.D579G	FAM160B1_ENST00000369250.3_Missense_Mutation_p.D579G	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	579										NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						GTACCGGATGACGCAAAATCC	0.403																																					p.D579G		Atlas-SNP	.											.	FAM160B1	107	.	0			c.A1736G						.						112	88	96					10																	116608429		2203	4300	6503	SO:0001583	missense	57700	exon13			CGGATGACGCAAA	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"KIAA1600"	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.1736A>G	chr10.hg19:g.116608429A>G	ENSP00000358251:p.Asp579Gly	94.0	0.0		99.0	4.0	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Missense_Mutation	SNP	ENST00000369248.4	hg19	CCDS31290.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.803348	0.70682	.	.	ENSG00000151553	ENST00000369248;ENST00000369250	T;T	0.66460	-0.21;-0.21	5.58	5.58	0.84498	.	0.083461	0.85682	D	0.000000	T	0.47801	0.1465	N	0.08118	0	0.80722	D	1	B;B	0.11235	0.002;0.004	B;B	0.18561	0.022;0.005	T	0.41502	-0.9505	10	0.21540	T	0.41	-13.1897	16.0529	0.80775	1.0:0.0:0.0:0.0	.	579;579	Q5W0V3-2;Q5W0V3	.;F16B1_HUMAN	G	579	ENSP00000358251:D579G;ENSP00000358253:D579G	ENSP00000358251:D579G	D	+	2	0	FAM160B1	116598419	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.971000	0.93419	2.257000	0.74773	0.459000	0.35465	GAC	.	.		0.403	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351		G	116608429	A	G	116608429	3	3	112	1	0	0	0	0	1	0	0	0	5475	275	10	2	1786	2	FAM160B1	10	116608429	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	950465	116608429	18926318	658	17279										
TRUB1	142940	hgsc.bcm.edu	37	chr10	116698055	116698055	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggtgtcttcgccgtctttgAaaacagacacatcccctgtc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:116698055delA	ENST00000298746.3	+	1	104	c.43delA	c.(43-45)aaafs	p.K15fs		NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase family member 1	15					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		GCCGTCTTTGAAAACAGACAC	0.602																																					p.L14fs		Atlas-INDEL	.											.	TRUB1	30	.	0			c.42delG						.						48	47	48					10																	116698055		2203	4300	6503	SO:0001589	frameshift_variant	142940	exon1			.	AF448144	CCDS7591.1	10q25.3	2013-09-02	2013-09-02		ENSG00000165832	ENSG00000165832			16060	protein-coding gene	gene with protein product		610726	"TruB pseudouridine (psi) synthase homolog 1 (E. coli)"			12736709	Standard	NM_139169		Approved	PUS4	uc001lcd.3	Q8WWH5	OTTHUMG00000019094	ENST00000298746.3:c.43delA	chr10.hg19:g.116698055delA	ENSP00000298746:p.Lys15fs	175.0	0.0		186.0	14.0	NM_139169	B2R716|Q53ES2	Frame_Shift_Del	DEL	ENST00000298746.3	hg19	CCDS7591.1																																																																																			.	.		0.602	TRUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050504.1	NM_139169		-	116698055	A	-	116698055	7	5	112	1	0	1	0	1	0	0	0	0	16617	247	9	0	45	0	TRUB1	10	116698055	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	89626	116698055	18836692	659	17280										
PNLIPRP3	119548	hgsc.bcm.edu	37	chr10	118231366	118231366	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgtaggcggggcagttaggAaaactggggagtttgccatt	17	5	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:118231366A>G	ENST00000369230.3	+	10	1293	c.1147A>G	c.(1147-1149)Aaa>Gaa	p.K383E		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	383	PLAT.				lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		GGCAGTTAGGAAAACTGGGGA	0.483																																					p.K383E		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.A1147G						.						128	136	133					10																	118231366		2203	4300	6503	SO:0001583	missense	119548	exon10			GTTAGGAAAACTG	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1147A>G	chr10.hg19:g.118231366A>G	ENSP00000358232:p.Lys383Glu	132.0	0.0		118.0	6.0	NM_001011709		Missense_Mutation	SNP	ENST00000369230.3	hg19	CCDS31292.1	.	.	.	.	.	.	.	.	.	.	A	12.17	1.858868	0.32884	.	.	ENSG00000203837	ENST00000369230	T	0.64991	-0.13	4.18	1.81	0.25067	Lipoxygenase, LH2 (2);Lipase/lipooxygenase, PLAT/LH2 (1);	0.871930	0.09589	N	0.781766	T	0.54838	0.1883	L	0.47716	1.5	0.09310	N	1	B	0.16396	0.017	B	0.26614	0.071	T	0.51426	-0.8707	10	0.62326	D	0.03	.	6.8165	0.23833	0.8008:0.0:0.1992:0.0	.	383	Q17RR3	LIPR3_HUMAN	E	383	ENSP00000358232:K383E	ENSP00000358232:K383E	K	+	1	0	PNLIPRP3	118221356	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.003000	0.12901	0.252000	0.21531	0.482000	0.46254	AAA	.	.		0.483	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		G	118231366	A	G	118231366	3	3	112	1	0	0	0	0	1	0	0	0	12161	247	9	2	1185	2	PNLIPRP3	10	118231366	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1533311	118231366	17303381	660	17281										
KIAA1598	57698	hgsc.bcm.edu	37	chr10	118728182	118728182	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttttctgaaattcttccagTtttttaacggcttcatctcg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:118728182delT	ENST00000355371.4	-	3	650	c.153delA	c.(151-153)aaafs	p.K51fs	KIAA1598_ENST00000497044.1_5'UTR|KIAA1598_ENST00000392901.4_5'UTR|KIAA1598_ENST00000392903.2_Frame_Shift_Del_p.K51fs|KIAA1598_ENST00000260777.10_Frame_Shift_Del_p.K51fs	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	51					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		ATTCTTCCAGTTTTTTAACGG	0.313																																					p.L52fs		Atlas-INDEL	.											.	KIAA1598	74	.	0			c.154delC						.						132	118	123					10																	118728182		2200	4298	6498	SO:0001589	frameshift_variant	57698	exon3			.	BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.153delA	chr10.hg19:g.118728182delT	ENSP00000347532:p.Lys51fs	123.0	0.0		150.0	10.0	NM_001127211	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Frame_Shift_Del	DEL	ENST00000355371.4	hg19	CCDS44482.1																																																																																			.	.		0.313	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330		-	118728182	T	-	118728182	7	5	112	1	0	1	0	1	0	0	0	0	8255	1722	60	0	1802	0	KIAA1598	10	118728182	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	496816	118728182	16806565	661	17282										
TACC2	10579	hgsc.bcm.edu	37	chr10	124008566	124008566	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctctgccctgctgtgtcagaAtgaagaggtgttgaagagat	13	7	2	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:124008566A>G	ENST00000369005.1	+	21	8895	c.8555A>G	c.(8554-8556)aAt>aGt	p.N2852S	TACC2_ENST00000368999.1_Splice_Site_p.N942S|TACC2_ENST00000453444.2_Splice_Site_p.N2779S|TACC2_ENST00000515273.1_Splice_Site_p.N2779S|TACC2_ENST00000369001.1_Splice_Site_p.N479S|TACC2_ENST00000369004.3_Splice_Site_p.N912S|TACC2_ENST00000513429.1_Splice_Site_p.N998S|TACC2_ENST00000369000.1_Splice_Site_p.N475S|TACC2_ENST00000260733.3_Splice_Site_p.N930S|TACC2_ENST00000334433.3_Splice_Site_p.N2852S|TACC2_ENST00000515603.1_Splice_Site_p.N2730S|TACC2_ENST00000358010.1_Splice_Site_p.N998S|TACC2_ENST00000360561.3_Splice_Site_p.N900S	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2852					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CTGTGTCAGAATGAAGAGGTG	0.587																																					p.N2852S		Atlas-SNP	.											.	TACC2	271	.	0			c.A8555G						.						76	73	74					10																	124008566		2203	4300	6503	SO:0001630	splice_region_variant	10579	exon21			GTCAGAATGAAGA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.8554-1A>G	chr10.hg19:g.124008566A>G		87.0	0.0		77.0	4.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	hg19	CCDS7626.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.41|17.41	3.382677|3.382677	0.61845|0.61845	.|.	.|.	ENSG00000138162|ENSG00000138162	ENST00000490979|ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000369001;ENST00000369000;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733	.|T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.68025	.|-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.04|5.04	3.91|3.91	0.45181|0.45181	.|.	.|0.000000	.|0.39341	.|N	.|0.001387	T|T	0.78742|0.78742	0.4331|0.4331	M|M	0.70842|0.70842	2.15|2.15	0.49213|0.49213	D|D	0.999767|0.999767	.|D;D;D;D;D;D;D;D;D	.|0.89917	.|0.998;0.999;1.0;0.999;1.0;0.984;1.0;0.984;1.0	.|D;D;D;D;D;D;D;D;D	.|0.91635	.|0.999;0.996;0.999;0.999;0.999;0.973;0.999;0.973;0.999	T|T	0.78841|0.78841	-0.2045|-0.2045	5|10	.|0.59425	.|D	.|0.04	-16.0554|-16.0554	10.8205|10.8205	0.46601|0.46601	0.9252:0.0:0.0748:0.0|0.9252:0.0:0.0748:0.0	.|.	.|2779;912;2730;2779;900;930;475;998;2852	.|E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-2;O95359-5;O95359	.|.;.;.;.;.;.;.;.;TACC2_HUMAN	V|S	96|2852;998;2779;2730;2852;998;2779;2765;479;475;900;942;912;930	.|ENSP00000358001:N2852S;ENSP00000425062:N998S;ENSP00000424467:N2779S;ENSP00000427618:N2730S;ENSP00000334280:N2852S;ENSP00000350701:N998S;ENSP00000395048:N2779S;ENSP00000357997:N479S;ENSP00000357996:N475S;ENSP00000353763:N900S;ENSP00000357995:N942S;ENSP00000422815:N912S;ENSP00000260733:N930S	.|ENSP00000260733:N930S	M|N	+|+	1|2	0|0	TACC2|TACC2	123998556|123998556	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.469000|0.469000	0.32828|0.32828	9.197000|9.197000	0.94985|0.94985	0.875000|0.875000	0.35847|0.35847	-0.256000|-0.256000	0.11100|0.11100	ATG|AAT	.	.		0.587	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		Missense_Mutation	G	124008566	A	G	124008566	5	3	112	1	0	0	0	0	0	0	1	0	15517	115	4	2	8705	2	TACC2	10	124008566	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	5280384	124008566	11526181	662	17283										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124402895	124402895	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctgcagacccccccacgccGagaagaggagcctcggtagg	14	15	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:124402895G>A	ENST00000338354.3	+	53	7329	c.7223G>A	c.(7222-7224)cGa>cAa	p.R2408Q	DMBT1_ENST00000368956.2_Missense_Mutation_p.R1780Q|DMBT1_ENST00000368955.3_Missense_Mutation_p.R2398Q|DMBT1_ENST00000359586.6_Missense_Mutation_p.R1128Q|DMBT1_ENST00000330163.4_Missense_Mutation_p.R1780Q|DMBT1_ENST00000344338.3_Missense_Mutation_p.R2398Q|DMBT1_ENST00000368909.3_Missense_Mutation_p.R2408Q			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	2408					defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCCCCACGCCGAGAAGAGGAG	0.622																																					p.R2408Q	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,colon,carcinoma,0,3	DMBT1	677	.	0			c.G7223A						.						29	32	31					10																	124402895		1942	4134	6076	SO:0001583	missense	1755	exon53			CACGCCGAGAAGA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.7223G>A	chr10.hg19:g.124402895G>A	ENSP00000342210:p.Arg2408Gln	117.0	0.0		165.0	50.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	G	10.20	1.284184	0.23392	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000344467;ENST00000359586	T;T;T;T;T;T;T	0.23950	1.93;1.92;1.88;1.93;1.92;1.88;1.91	4.38	-8.09	0.01090	.	0.736603	0.10817	U	0.630867	T	0.06234	0.0161	N	0.08118	0	0.09310	N	1	B;P;B;B;B;B;B	0.39717	0.013;0.684;0.013;0.013;0.013;0.013;0.007	B;B;B;B;B;B;B	0.26094	0.003;0.066;0.002;0.004;0.004;0.004;0.002	T	0.19128	-1.0315	10	0.49607	T	0.09	.	1.2818	0.02042	0.2559:0.1826:0.3749:0.1866	.	1128;2388;1657;2537;1780;2398;2408	F8WEF7;Q9UGM3-5;Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;.;DMBT1_HUMAN	Q	2408;2537;2408;2408;2408;2407;1780;2398;1780;1780;2408;2398;1780;554;1128	ENSP00000342210:R2408Q;ENSP00000343175:R2398Q;ENSP00000327747:R1780Q;ENSP00000357905:R2408Q;ENSP00000357951:R2398Q;ENSP00000357952:R1780Q;ENSP00000352593:R1128Q	ENSP00000331522:R1780Q	R	+	2	0	DMBT1	124392885	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.977000	0.03782	-2.400000	0.00579	-2.511000	0.00188	CGA	.	.		0.622	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124402895	G	A	124402895	3	1	112	1	0	0	0	0	1	0	0	0	4579	1058	37	1	7433	1	DMBT1	10	124402895	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	394329	124402895	11131852	663	17284										
PSTK	118672	hgsc.bcm.edu	37	chr10	124742793	124742793	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttaaactgttttcagattcgTtgggcttttgccagctcttt	8	8	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:124742793T>A	ENST00000368887.3	+	3	954	c.514T>A	c.(514-516)Ttg>Atg	p.L172M	PSTK_ENST00000405485.1_Missense_Mutation_p.L172M|PSTK_ENST00000497219.1_3'UTR	NM_153336.2	NP_699167.2	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	172					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|tRNA binding (GO:0000049)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|skin(1)|stomach(2)	13		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		TTCAGATTCGTTGGGCTTTTG	0.378																																					p.L172M		Atlas-SNP	.											PSTK,NS,lymphoid_neoplasm,0,1	PSTK	34	.	0			c.T514A						.						52	51	52					10																	124742793		2203	4300	6503	SO:0001583	missense	118672	exon3			GATTCGTTGGGCT	AK127173	CCDS7633.1	10q26.13	2007-04-17	2007-04-17	2007-04-17	ENSG00000179988	ENSG00000179988			28578	protein-coding gene	gene with protein product		611310	"chromosome 10 open reading frame 89"	C10orf89		15317934	Standard	NM_153336		Approved	MGC35392	uc001lgy.1	Q8IV42	OTTHUMG00000019191	ENST00000368887.3:c.514T>A	chr10.hg19:g.124742793T>A	ENSP00000357882:p.Leu172Met	94.0	0.0		104.0	0.0	NM_153336	Q6ZSS9	Missense_Mutation	SNP	ENST00000368887.3	hg19	CCDS7633.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.987176	0.53934	.	.	ENSG00000179988	ENST00000368887;ENST00000405485	T;T	0.30448	1.53;1.53	5.86	0.849	0.18972	.	0.153654	0.41605	D	0.000841	T	0.45175	0.1329	M	0.73962	2.25	0.09310	N	1	P	0.52692	0.955	P	0.57244	0.816	T	0.34900	-0.9810	10	0.52906	T	0.07	-19.4718	9.706	0.40216	0.0:0.3732:0.0:0.6268	.	172	Q8IV42	PSTK_HUMAN	M	172	ENSP00000357882:L172M;ENSP00000384764:L172M	ENSP00000357882:L172M	L	+	1	2	PSTK	124732783	0.114000	0.22134	0.002000	0.10522	0.932000	0.56968	0.517000	0.22832	-0.087000	0.12528	0.460000	0.39030	TTG	.	.		0.378	PSTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050811.1	NM_153336		A	124742793	T	A	124742793	3	1	112	1	0	0	0	0	1	0	0	0	12732	1722	60	4	524	4	PSTK	10	124742793	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	339898	124742793	10791954	664	17285										
ZRANB1	54764	hgsc.bcm.edu	37	chr10	126670335	126670335	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctcagagctttggtttacaTttttccttgagagaagaaca					rs367624249		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:126670335delT	ENST00000359653.4	+	6	1856	c.1485delT	c.(1483-1485)catfs	p.H495fs	ZRANB1_ENST00000471421.1_3'UTR	NM_017580.2	NP_060050.2	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1	495	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.				cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|positive regulation of Wnt signaling pathway (GO:0030177)|protein deubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0071947)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell morphogenesis (GO:0022604)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	23		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)		TTGGTTTACATTTTTCCTTGA	0.368																																					p.H495fs		Atlas-INDEL	.											.	ZRANB1	60	.	0			c.1484delA						.						130	134	132					10																	126670335		2203	4300	6503	SO:0001589	frameshift_variant	54764	exon6			.	AJ252060	CCDS7642.1	10q26.12	2014-02-24			ENSG00000019995	ENSG00000019995		"Zinc fingers, RAN-binding domain containing", "OTU domain containing"	18224	protein-coding gene	gene with protein product		611749				11463333	Standard	NM_017580		Approved	TRABID	uc001lic.3	Q9UGI0	OTTHUMG00000019223	ENST00000359653.4:c.1485delT	chr10.hg19:g.126670335delT	ENSP00000352676:p.His495fs	145.0	0.0		179.0	11.0	NM_017580	B4DZ98|D3DRF4|Q5SQP6|Q69YK3	Frame_Shift_Del	DEL	ENST00000359653.4	hg19	CCDS7642.1																																																																																			.	.		0.368	ZRANB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050898.1	NM_017580		-	126670335	T	-	126670335	7	5	112	1	0	1	0	1	0	0	0	0	18237	1490	52	0	1507	0	ZRANB1	10	126670335	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1927542	126670335	8864412	665	17286										
NPS	594857	hgsc.bcm.edu	37	chr10	129350732	129350732	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgaattgccaggtgtctggAaaatctgattactttctcat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:129350732delA	ENST00000398023.1	+	3	119	c.99delA	c.(97-99)ggafs	p.G33fs		NM_001030013.1	NP_001025184.1	P0C0P6	NPS_HUMAN	neuropeptide S	33					neuropeptide signaling pathway (GO:0007218)|positive regulation of action potential (GO:0045760)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|visual learning (GO:0008542)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						AGGTGTCTGGAAAATCTGATT	0.393																																					p.G33fs		Atlas-INDEL	.											.	NPS	14	.	0			c.98delG						.						317	315	316					10																	129350732		1827	4092	5919	SO:0001589	frameshift_variant	594857	exon3			.	BC148465	CCDS41577.1	10q26.2	2013-02-26			ENSG00000214285	ENSG00000214285		"Endogenous ligands"	33940	protein-coding gene	gene with protein product	"prepro-neuropeptide S"	609513				18181564, 15312648	Standard	NM_001030013		Approved		uc001ljx.1	P0C0P6		ENST00000398023.1:c.99delA	chr10.hg19:g.129350732delA	ENSP00000381105:p.Gly33fs	128.0	0.0		118.0	10.0	NM_001030013		Frame_Shift_Del	DEL	ENST00000398023.1	hg19	CCDS41577.1																																																																																			.	.		0.393	NPS-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001030013		-	129350732	A	-	129350732	7	5	112	1	0	1	0	1	0	0	0	0	10608	233	9	0	109	0	NPS	10	129350732	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2680397	129350732	6184015	666	17287										
TCERG1L	256536	hgsc.bcm.edu	37	chr10	132891517	132891517	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaatgctcctggtcctttcTtttttgaacaagtcggaacc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:132891517delT	ENST00000368642.4	-	12	1754	c.1669delA	c.(1669-1671)agafs	p.R557fs	RP11-462G8.3_ENST00000436942.1_RNA	NM_174937.3	NP_777597.2	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	557	FF 2.									cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	31		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		TGGTCCTTTCTTTTTTGAACA	0.418																																					p.R557fs		Atlas-INDEL	.											.	TCERG1L	91	.	0			c.1670delG						.						100	102	101					10																	132891517		2203	4300	6503	SO:0001589	frameshift_variant	256536	exon12			.	AK096269	CCDS7662.2	10q26.3	2006-04-12			ENSG00000176769	ENSG00000176769			23533	protein-coding gene	gene with protein product							Standard	NM_174937		Approved	FLJ38950	uc001lkp.3	Q5VWI1	OTTHUMG00000019276	ENST00000368642.4:c.1669delA	chr10.hg19:g.132891517delT	ENSP00000357631:p.Arg557fs	126.0	0.0		134.0	10.0	NM_174937	Q5VWI2|Q86XM8	Frame_Shift_Del	DEL	ENST00000368642.4	hg19	CCDS7662.2																																																																																			.	.		0.418	TCERG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091619.2	NM_174937		-	132891517	T	-	132891517	7	5	112	1	0	1	0	1	0	0	0	0	15701	1617	56	0	95	0	TCERG1L	10	132891517	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3540785	132891517	2643230	667	17288										
CDHR5	53841	hgsc.bcm.edu	37	chr11	618994	618994	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggtgctgttttctgcacccGggggccccccgggtgtggac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:618994delG	ENST00000358353.3	-	14	1887	c.1565delC	c.(1564-1566)ccgfs	p.P522fs	CDHR5_ENST00000397542.2_Frame_Shift_Del_p.P522fs|CDHR5_ENST00000349570.7_Intron|IRF7_ENST00000397570.1_5'Flank|IRF7_ENST00000397574.2_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	522					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						TTCTGCACCCGGGGGCCCCCC	0.677																																					p.P522fs		Atlas-INDEL	.											.	CDHR5	77	.	0			c.1566delG						.						55	72	66					11																	618994		2203	4299	6502	SO:0001589	frameshift_variant	53841	exon13			.	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.1565delC	chr11.hg19:g.618994delG	ENSP00000351118:p.Pro522fs	91.0	0.0		166.0	11.0	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Frame_Shift_Del	DEL	ENST00000358353.3	hg19	CCDS7707.1																																																																																			.	.		0.677	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		-	618994	G	-	618994	7	5	112	1	0	1	0	1	0	0	0	0	3124	1116	39	0	984	0	CDHR5	11	618994	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10		618994	134387522	668	17289										
MUC2	4583	hgsc.bcm.edu	37	chr11	1094691	1094691	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccactcgcggtaccacgaccGggtcatcttcagcccccacc	8	20	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:1094691G>T	ENST00000441003.2	+	31	5806	c.5779G>T	c.(5779-5781)Ggg>Tgg	p.G1927W	MUC2_ENST00000361558.6_Missense_Mutation_p.G65W|MUC2_ENST00000333592.6_Missense_Mutation_p.G215W	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4289					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TACCACGACCGGGTCATCTTC	0.632																																					p.G1923W		Atlas-SNP	.											.	MUC2	614	.	0			c.G5767T						.						78	97	90					11																	1094691		2117	4220	6337	SO:0001583	missense	4583	exon32			ACGACCGGGTCAT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5779G>T	chr11.hg19:g.1094691G>T	ENSP00000415183:p.Gly1927Trp	101.0	0.0		164.0	7.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	G	10.79	1.449554	0.26074	.	.	ENSG00000198788	ENST00000441003;ENST00000361558;ENST00000333592	T;T;T	0.41758	2.56;0.99;2.9	1.97	-1.24	0.09435	.	.	.	.	.	T	0.40171	0.1106	L	0.51422	1.61	0.09310	N	1	D	0.63880	0.993	P	0.49665	0.618	T	0.31613	-0.9937	9	0.66056	D	0.02	.	5.8132	0.18477	0.5036:0.0:0.4964:0.0	.	1927	E7EUV1	.	W	1927;65;215	ENSP00000415183:G1927W;ENSP00000354885:G65W;ENSP00000331373:G215W	ENSP00000331373:G215W	G	+	1	0	MUC2	1084691	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.996000	0.00655	-0.225000	0.09913	0.479000	0.44913	GGG	.	.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1094691	G	T	1094691	3	4	112	1	0	0	0	0	1	0	0	0	9984	1116	39	1	5893	1	MUC2	11	1094691	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	475697	1094691	133911825	669	17290										
MOB2	81532	hgsc.bcm.edu	37	chr11	1492622	1492622	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccgtgcacttgaccttcttCccccgctcgtcataccagta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:1492622delC	ENST00000329957.6	-	4	582	c.393delG	c.(391-393)gggfs	p.G131fs	MOB2_ENST00000526462.1_5'UTR	NM_001172223.1	NP_001165694.1	Q70IA6	MOB2_HUMAN	MOB kinase activator 2	100					actin cytoskeleton organization (GO:0030036)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein phosphorylation (GO:0001934)	cytoplasm (GO:0005737)|neuron projection terminus (GO:0044306)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|kidney(2)|lung(1)	4						TGACCTTCTTCCCCCGCTCGT	0.597																																					p.K132fs		Atlas-INDEL	.											.	MOB2	23	.	0			c.394delA						.						116	130	125					11																	1492622		2163	4243	6406	SO:0001589	frameshift_variant	81532	exon4			.		CCDS53591.1	11p15.5	2011-09-28			ENSG00000182208	ENSG00000182208		"MOB kinase activators"	24904	protein-coding gene	gene with protein product	"MOB2 Mps One Binder homolog (yeast)"	611969				11223154, 15067004	Standard	NM_053005		Approved	HCCA2	uc010qwz.2	Q70IA6	OTTHUMG00000165545	ENST00000329957.6:c.393delG	chr11.hg19:g.1492622delC	ENSP00000328694:p.Gly131fs	132.0	0.0		177.0	12.0	NM_001172223	B4DKP3|Q96M67	Frame_Shift_Del	DEL	ENST00000329957.6	hg19	CCDS53591.1																																																																																			.	.		0.597	MOB2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000384770.1	NM_053005		-	1492622	C	-	1492622	7	5	112	1	0	1	0	1	0	0	0	0	9690	842	30	0	421	0	MOB2	11	1492622	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	397931	1492622	133513894	670	17291										
OR51A7	119687	hgsc.bcm.edu	37	chr11	4929062	4929062	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tagccattaggagcattctcTtagtgattccatttcccttc	6	11	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:4929062T>G	ENST00000359350.4	+	1	463	c.463T>G	c.(463-465)Tta>Gta	p.L155V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		GAGCATTCTCTTAGTGATTCC	0.393																																					p.L155V		Atlas-SNP	.											OR51A7,NS,carcinoma,0,1	OR51A7	86	.	0			c.T463G						.						99	98	98					11																	4929062		2201	4298	6499	SO:0001583	missense	119687	exon1			ATTCTCTTAGTGA	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"GPCR / Class A : Olfactory receptors"	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.463T>G	chr11.hg19:g.4929062T>G	ENSP00000352305:p.Leu155Val	94.0	0.0		149.0	0.0	NM_001004749	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	hg19	CCDS31364.1	.	.	.	.	.	.	.	.	.	.	T	5.845	0.340128	0.11069	.	.	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.72282	-0.64	5.02	2.68	0.31781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37095	N	0.002254	T	0.64670	0.2619	L	0.41710	1.295	0.09310	N	1	P	0.44195	0.828	P	0.54924	0.764	T	0.53648	-0.8409	10	0.09590	T	0.72	.	3.7568	0.08588	0.157:0.1825:0.0:0.6605	.	155	Q8NH64	O51A7_HUMAN	V	155;155;144	ENSP00000352305:L155V	ENSP00000352305:L155V	L	+	1	2	OR51A7	4885638	0.000000	0.05858	0.059000	0.19551	0.360000	0.29518	-1.244000	0.02902	0.379000	0.24794	-0.250000	0.11733	TTA	.	.		0.393	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749		G	4929062	T	G	4929062	3	3	112	1	0	0	0	0	1	0	0	0	11097	1606	56	5	465	5	OR51A7	11	4929062	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3436440	4929062	130077454	671	17292										
OR52B6	340980	hgsc.bcm.edu	37	chr11	5602546	5602546	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccgctatgtggccatctgctCccccctgcgatatgtcacaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:5602546delC	ENST00000345043.2	+	1	440	c.440delC	c.(439-441)tccfs	p.S147fs	HBG2_ENST00000380259.2_Intron|AC015691.13_ENST00000394793.2_RNA	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	147						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCCATCTGCTCCCCCCTGCGA	0.507																																					p.S147fs		Atlas-INDEL	.											.	OR52B6	37	.	0			c.439delT						.						140	146	144					11																	5602546		2201	4297	6498	SO:0001589	frameshift_variant	340980	exon1			.	AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"GPCR / Class A : Olfactory receptors"	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.440delC	chr11.hg19:g.5602546delC	ENSP00000341581:p.Ser147fs	102.0	0.0		157.0	11.0	NM_001005162	Q6IFI7	Frame_Shift_Del	DEL	ENST00000345043.2	hg19	CCDS41611.1																																																																																			.	.		0.507	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162		-	5602546	C	-	5602546	7	5	112	1	0	1	0	1	0	0	0	0	11122	855	30	0	442	0	OR52B6	11	5602546	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	673484	5602546	129403970	672	17293										
OR52E8	390079	hgsc.bcm.edu	37	chr11	5878820	5878820	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgcaacaagatacacaaagAaaaaagggactccaatccaa					rs374161114		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:5878820delA	ENST00000537935.1	-	1	144	c.113delT	c.(112-114)ttcfs	p.F39fs	TRIM5_ENST00000380027.1_Intron	NM_001005168.1	NP_001005168.1	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E, member 8	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATACACAAAGAAAAAAGGGAC	0.468																																					p.F38fs		Atlas-INDEL	.											.	OR52E8	54	.	0			c.114delC						.						110	132	124					11																	5878820		2144	4296	6440	SO:0001589	frameshift_variant	390079	exon1			.	BK004301	CCDS31400.1	11p15.4	2012-08-09	2003-12-15		ENSG00000183269	ENSG00000183269		"GPCR / Class A : Olfactory receptors"	15217	protein-coding gene	gene with protein product			"olfactory receptor, family 52, subfamily E, member 8 pseudogene"				Standard	NM_001005168		Approved		uc010qzr.2	Q6IFG1	OTTHUMG00000168803	ENST00000537935.1:c.113delT	chr11.hg19:g.5878820delA	ENSP00000444054:p.Phe39fs	128.0	0.0		213.0	19.0	NM_001005168	B9EH38	Frame_Shift_Del	DEL	ENST00000537935.1	hg19	CCDS31400.1																																																																																			.	.		0.468	OR52E8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401145.1	NM_001005168		-	5878820	A	-	5878820	7	5	112	1	0	1	0	1	0	0	0	0	11127	246	9	0	842	0	OR52E8	11	5878820	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	276274	5878820	129127696	673	17294										
CNGA4	1262	hgsc.bcm.edu	37	chr11	6265177	6265177	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catctctgcccatgagccacAgggaacatgtctgggaaccg	11	13	2	1	rs34385295		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:6265177A>G	ENST00000379936.2	+	6	1382		c.e6-1			NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4						phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATGAGCCACAGGGAACATGT	0.552																																					.		Atlas-SNP	.											.	CNGA4	96	.	0			c.1268-2A>G						.						50	49	50					11																	6265177		2201	4296	6497	SO:0001630	splice_region_variant	1262	exon6			AGCCACAGGGAAC	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2152	protein-coding gene	gene with protein product		609472	"cyclic nucleotide gated channel beta 2"	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.1268-1A>G	chr11.hg19:g.6265177A>G		32.0	0.0		46.0	4.0	NM_001037329		Splice_Site	SNP	ENST00000379936.2	hg19	CCDS31408.1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.585347	0.66105	.	.	ENSG00000132259	ENST00000379936	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5724	0.56344	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNGA4	6221753	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.111000	0.71541	2.185000	0.69588	0.514000	0.50259	.	.	.		0.552	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329	Intron	G	6265177	A	G	6265177	5	3	112	1	0	0	0	0	0	0	1	0	3601	202	7	2	1288	2	CNGA4	11	6265177	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	386357	6265177	128741339	674	17295										
TRIM3	10612	hgsc.bcm.edu	37	chr11	6472208	6472208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggtaaagacgcagcaagacTtgttgtcgaccacaatgata	10	8	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:6472208T>C	ENST00000525074.1	-	9	2178	c.1784A>G	c.(1783-1785)aAg>aGg	p.K595R	TRIM3_ENST00000345851.3_Missense_Mutation_p.K595R|TRIM3_ENST00000537602.1_Missense_Mutation_p.K517R|TRIM3_ENST00000536344.1_Missense_Mutation_p.K476R|TRIM3_ENST00000359518.3_Missense_Mutation_p.K595R	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	595					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCAGCAAGACTTGTTGTCGAC	0.572																																					p.K595R	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.A1784G						.						78	75	76					11																	6472208		2201	4296	6497	SO:0001583	missense	10612	exon9			CAAGACTTGTTGT	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10064	protein-coding gene	gene with protein product	"ring finger protein 22", "brain expressed ring finger", "tripartite motif protein TRIM3"	605493	"tripartite motif-containing 3"	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.1784A>G	chr11.hg19:g.6472208T>C	ENSP00000433102:p.Lys595Arg	55.0	0.0		93.0	4.0	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Missense_Mutation	SNP	ENST00000525074.1	hg19	CCDS7764.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.884841	0.91814	.	.	ENSG00000110171	ENST00000530899;ENST00000525074;ENST00000545029;ENST00000345851;ENST00000336043;ENST00000537602;ENST00000359518;ENST00000536344	T;T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6;-0.6	5.14	5.14	0.70334	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.67382	0.2887	L	0.39020	1.185	0.80722	D	1	P;P	0.48911	0.917;0.833	P;P	0.51055	0.657;0.6	T	0.62492	-0.6843	10	0.12430	T	0.62	-20.4211	13.9521	0.64123	0.0:0.0:0.0:1.0	.	476;595	F5H2Q8;O75382	.;TRIM3_HUMAN	R	595;595;595;595;584;517;595;476	ENSP00000433102:K595R;ENSP00000340797:K595R;ENSP00000441091:K517R;ENSP00000352508:K595R;ENSP00000445460:K476R	ENSP00000337094:K584R	K	-	2	0	TRIM3	6428784	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	7.868000	0.87116	2.155000	0.67459	0.460000	0.39030	AAG	.	.		0.572	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458		C	6472208	T	C	6472208	3	2	112	1	0	0	0	0	1	0	0	0	16519	1609	56	2	466	2	TRIM3	11	6472208	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	207031	6472208	128534308	675	17296										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6649903	6649903	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcccacatctggatcagaggCccgaagcatggtaagggtct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:6649903delC	ENST00000299441.3	-	13	5731	c.5320delG	c.(5320-5322)gccfs	p.A1774fs	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1774	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGATCAGAGGCCCGAAGCATG	0.572																																					p.A1774fs		Atlas-INDEL	.											.	DCHS1	277	.	0			c.5321delC						.						106	97	100					11																	6649903		2201	4296	6497	SO:0001589	frameshift_variant	8642	exon13			.	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.5320delG	chr11.hg19:g.6649903delC	ENSP00000299441:p.Ala1774fs	107.0	0.0		161.0	10.0	NM_003737	O15098	Frame_Shift_Del	DEL	ENST00000299441.3	hg19	CCDS7771.1																																																																																			.	.		0.572	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		-	6649903	C	-	6649903	7	5	112	1	0	1	0	1	0	0	0	0	4289	739	26	0	4612	0	DCHS1	11	6649903	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	177695	6649903	128356613	676	17297										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6653852	6653852	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggcctccagctccagctcaTgggctggccctcctgagggc	14	16	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:6653852T>C	ENST00000299441.3	-	6	3302	c.2891A>G	c.(2890-2892)cAt>cGt	p.H964R	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	964	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTCCAGCTCATGGGCTGGCCC	0.662																																					p.H964R		Atlas-SNP	.											.	DCHS1	277	.	0			c.A2891G						.						10	10	10					11																	6653852		2177	4263	6440	SO:0001583	missense	8642	exon6			AGCTCATGGGCTG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.2891A>G	chr11.hg19:g.6653852T>C	ENSP00000299441:p.His964Arg	38.0	0.0		86.0	4.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.678686	0.29783	.	.	ENSG00000166341	ENST00000299441	T	0.52295	0.67	4.34	4.34	0.51931	Cadherin (4);Cadherin-like (1);	0.146542	0.31542	N	0.007479	T	0.46927	0.1418	M	0.71581	2.175	0.38604	D	0.95072	P	0.35821	0.523	B	0.33846	0.171	T	0.57659	-0.7773	10	0.52906	T	0.07	.	13.1399	0.59428	0.0:0.0:0.0:1.0	.	964	Q96JQ0	PCD16_HUMAN	R	964	ENSP00000299441:H964R	ENSP00000299441:H964R	H	-	2	0	DCHS1	6610428	1.000000	0.71417	0.992000	0.48379	0.442000	0.32017	3.518000	0.53451	1.952000	0.56665	0.459000	0.35465	CAT	.	.		0.662	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		C	6653852	T	C	6653852	3	2	112	1	0	0	0	0	1	0	0	0	4289	1464	51	2	7069	2	DCHS1	11	6653852	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3949	6653852	128352664	677	17298										
OR10A3	26496	hgsc.bcm.edu	37	chr11	7960747	7960747	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaaaacattcagtcccaccAaaaagaaggatgaaatacat					rs35194212		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:7960747delA	ENST00000360759.3	-	1	394	c.321delT	c.(319-321)tttfs	p.F107fs		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	107					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAGTCCCACCAAAAAGAAGGA	0.443																																					p.G108fs		Atlas-INDEL	.											.	OR10A3	54	.	0			c.322delG						.						94	87	89					11																	7960747		2201	4296	6497	SO:0001589	frameshift_variant	26496	exon1			.	BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"GPCR / Class A : Olfactory receptors"	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.321delT	chr11.hg19:g.7960747delA	ENSP00000353988:p.Phe107fs	87.0	0.0		161.0	13.0	NM_001003745	B9EH39|Q6IF58|Q96R11	Frame_Shift_Del	DEL	ENST00000360759.3	hg19	CCDS31421.1																																																																																			.	.		0.443	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745		-	7960747	A	-	7960747	7	5	112	1	0	1	0	1	0	0	0	0	10900	127	5	0	626	0	OR10A3	11	7960747	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1306895	7960747	127045769	678	17299										
ST5	6764	hgsc.bcm.edu	37	chr11	8736195	8736195	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caatgctggacatagacaacTtttttaatctcttctttcct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:8736195delT	ENST00000534127.1	-	10	2289	c.1904delA	c.(1903-1905)aagfs	p.K635fs	ST5_ENST00000313726.6_Frame_Shift_Del_p.K635fs|ST5_ENST00000526757.1_Frame_Shift_Del_p.K215fs|ST5_ENST00000530991.1_Frame_Shift_Del_p.K107fs|ST5_ENST00000530438.1_Frame_Shift_Del_p.K215fs|ST5_ENST00000526099.1_Frame_Shift_Del_p.K148fs|ST5_ENST00000357665.1_Frame_Shift_Del_p.K635fs|RPL27A_ENST00000531102.1_Intron	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	635					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		CATAGACAACTTTTTTAATCT	0.468																																					p.K635fs		Atlas-INDEL	.											.	ST5	85	.	0			c.1905delG						.						258	231	240					11																	8736195		2201	4296	6497	SO:0001589	frameshift_variant	6764	exon7			.	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"DENN/MADD domain containing"	11350	protein-coding gene	gene with protein product	"DENN/MADD domain containing 2B"	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.1904delA	chr11.hg19:g.8736195delT	ENSP00000433528:p.Lys635fs	134.0	0.0		186.0	15.0	NM_213618	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Frame_Shift_Del	DEL	ENST00000534127.1	hg19	CCDS7791.1																																																																																			.	.		0.468	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		-	8736195	T	-	8736195	7	5	112	1	0	1	0	1	0	0	0	0	15235	1609	56	0	1565	0	ST5	11	8736195	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	775448	8736195	126270321	679	17300										
AMPD3	272	hgsc.bcm.edu	37	chr11	10524339	10524339	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctcctcttagcaacaacagTttgttcctcgaatattccaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:10524339delT	ENST00000396554.3	+	13	2282	c.1941delT	c.(1939-1941)agtfs	p.S647fs	AMPD3_ENST00000530864.1_3'UTR|AMPD3_ENST00000444303.2_Frame_Shift_Del_p.S479fs	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	638					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		GCAACAACAGTTTGTTCCTCG	0.478																																					p.S647fs		Atlas-INDEL	.											.	AMPD3	68	.	0			c.1940delG						.						216	203	207					11																	10524339		2201	4294	6495	SO:0001589	frameshift_variant	272	exon13			.	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"erythrocyte-specific AMP deaminase"	102772	"adenosine monophosphate deaminase (isoform E)"			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.1941delT	chr11.hg19:g.10524339delT	ENSP00000379802:p.Ser647fs	141.0	0.0		152.0	10.0	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Frame_Shift_Del	DEL	ENST00000396554.3	hg19	CCDS7802.1																																																																																			.	.		0.478	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480		-	10524339	T	-	10524339	7	5	112	1	0	1	0	1	0	0	0	0	587	1722	60	0	2011	0	AMPD3	11	10524339	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1788144	10524339	124482177	680	17301										
SOX6	55553	hgsc.bcm.edu	37	chr11	16208476	16208476	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atggtggagagctgccgttcTttttctgccaggctctcagg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:16208476delT	ENST00000352083.6	-	5	638	c.561delA	c.(559-561)aaafs	p.K187fs	SOX6_ENST00000528429.1_Frame_Shift_Del_p.K187fs|SOX6_ENST00000316399.6_Frame_Shift_Del_p.K187fs|SOX6_ENST00000527619.1_Frame_Shift_Del_p.K190fs|SOX6_ENST00000528252.1_Frame_Shift_Del_p.K187fs|SOX6_ENST00000396356.3_Frame_Shift_Del_p.K187fs			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	187					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						GCTGCCGTTCTTTTTCTGCCA	0.473																																					p.E201fs		Atlas-INDEL	.											.	SOX6	149	.	0			c.601delG						.						118	119	119					11																	16208476		2200	4294	6494	SO:0001589	frameshift_variant	55553	exon5			.	AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"SRY (sex determining region Y)-boxes"	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.561delA	chr11.hg19:g.16208476delT	ENSP00000339876:p.Lys187fs	114.0	0.0		175.0	11.0	NM_001145819	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Frame_Shift_Del	DEL	ENST00000352083.6	hg19																																																																																				.	.		0.473	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326		-	16208476	T	-	16208476	7	5	112	1	0	1	0	1	0	0	0	0	14970	1606	56	0	2015	0	SOX6	11	16208476	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	5684137	16208476	118798040	681	17302										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17113160	17113160	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taagagatggataatttcacAgctcctcctatttggcctgg	9	9	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:17113160A>G	ENST00000265970.7	-	30	4685	c.4686T>C	c.(4684-4686)gcT>gcC	p.A1562A	PIK3C2A_ENST00000531428.1_5'UTR|PIK3C2A_ENST00000540361.1_Silent_p.A1182A	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1562	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						ATAATTTCACAGCTCCTCCTA	0.378																																					p.A1562A		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T4686C						.						104	97	99					11																	17113160		2200	4294	6494	SO:0001819	synonymous_variant	5286	exon30			TTTCACAGCTCCT	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.4686T>C	chr11.hg19:g.17113160A>G		134.0	0.0		170.0	7.0	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Silent	SNP	ENST00000265970.7	hg19	CCDS7824.1																																																																																			.	.		0.378	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17113160	A	G	17113160	2	3	112	1	0	0	0	0	0	0	0	1	11918	175	7	2		2	PIK3C2A	11	17113160	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	904684	17113160	117893356	682	17303										
HPS5	11234	hgsc.bcm.edu	37	chr11	18305405	18305405	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attggtgaaggcctctcttcTtctctccagctccaaacaga	7	13	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:18305405T>C	ENST00000349215.3	-	21	3272	c.2995A>G	c.(2995-2997)Aga>Gga	p.R999G	HPS5_ENST00000438420.2_Missense_Mutation_p.R885G|HPS5_ENST00000396253.3_Missense_Mutation_p.R885G|HPS5_ENST00000537258.1_Missense_Mutation_p.R106G|HPS5_ENST00000352460.3_5'UTR	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	999					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						GCCTCTCTTCTTCTCTCCAGC	0.408									Hermansky-Pudlak syndrome																												p.R999G		Atlas-SNP	.											.	HPS5	70	.	0			c.A2995G						.						132	128	129					11																	18305405		2199	4293	6492	SO:0001583	missense	11234	exon21	Familial Cancer Database	HPS, HPS1-8	CTCTTCTTCTCTC	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.2995A>G	chr11.hg19:g.18305405T>C	ENSP00000265967:p.Arg999Gly	47.0	0.0		89.0	4.0	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	hg19	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.345007	0.82022	.	.	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000537258	T;T;T	0.63913	-0.07;-0.07;-0.0	5.98	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.74680	0.3748	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76176	-0.3055	10	0.72032	D	0.01	.	12.2493	0.54589	0.0:0.0664:0.0:0.9336	.	999	Q9UPZ3	HPS5_HUMAN	G	885;885;999;106	ENSP00000379552:R885G;ENSP00000399590:R885G;ENSP00000265967:R999G	ENSP00000265967:R999G	R	-	1	2	HPS5	18261981	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.345000	0.59360	1.078000	0.41014	0.482000	0.46254	AGA	.	.		0.408	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507		C	18305405	T	C	18305405	3	2	112	1	0	0	0	0	1	0	0	0	7351	1617	56	2	406	2	HPS5	11	18305405	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1192245	18305405	116701111	683	17304										
PTPN5	84867	hgsc.bcm.edu	37	chr11	18763990	18763990	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctggcggctcactgactggcGcctgtcctcagggggcagtg	16	13	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:18763990G>A	ENST00000358540.2	-	7	974	c.544C>T	c.(544-546)Cgc>Tgc	p.R182C	PTPN5_ENST00000477854.1_5'UTR|PTPN5_ENST00000396167.2_Missense_Mutation_p.R150C|PTPN5_ENST00000496201.2_5'UTR|PTPN5_ENST00000396168.1_Missense_Mutation_p.R158C|PTPN5_ENST00000396170.1_Missense_Mutation_p.R150C|PTPN5_ENST00000396171.4_Missense_Mutation_p.R182C|RP11-1081L13.4_ENST00000527285.1_RNA	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	182					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						ACTGACTGGCGCCTGTCCTCA	0.632																																					p.R182C		Atlas-SNP	.											PTPN5_ENST00000358540,NS,carcinoma,0,2	PTPN5	163	.	0			c.C544T						.						47	50	49					11																	18763990		2199	4293	6492	SO:0001583	missense	84867	exon7			ACTGGCGCCTGTC	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.544C>T	chr11.hg19:g.18763990G>A	ENSP00000351342:p.Arg182Cys	95.0	0.0		120.0	59.0	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Missense_Mutation	SNP	ENST00000358540.2	hg19	CCDS7845.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.699138	0.88830	.	.	ENSG00000110786	ENST00000358540;ENST00000396170;ENST00000396171;ENST00000396167;ENST00000396168	T;T;T;T;T	0.05025	3.51;3.68;3.51;3.68;3.54	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.15565	0.0375	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.02797	-1.1109	10	0.87932	D	0	.	16.3618	0.83270	0.0:0.0:1.0:0.0	.	182;150	P54829;B3KXG7	PTN5_HUMAN;.	C	182;150;182;150;158	ENSP00000351342:R182C;ENSP00000379473:R150C;ENSP00000379474:R182C;ENSP00000379470:R150C;ENSP00000379471:R158C	ENSP00000351342:R182C	R	-	1	0	PTPN5	18720566	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.080000	0.94040	2.290000	0.77057	0.561000	0.74099	CGC	.	.		0.632	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970		A	18763990	G	A	18763990	3	1	112	1	0	0	0	0	1	0	0	0	12806	1087	38	1	1189	1	PTPN5	11	18763990	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	458585	18763990	116242526	684	17305										
HTATIP2	10553	hgsc.bcm.edu	37	chr11	20398242	20398242	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggagctgataaatcaagcaaTtttttatatctacaagttaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:20398242delT	ENST00000451739.2	+	3	861	c.420delT	c.(418-420)aatfs	p.N140fs	HTATIP2_ENST00000443524.2_Frame_Shift_Del_p.N140fs|HTATIP2_ENST00000531058.1_Intron|HTATIP2_ENST00000421577.2_Frame_Shift_Del_p.N140fs|HTATIP2_ENST00000419348.2_Frame_Shift_Del_p.N174fs	NM_001098522.1	NP_001091992.1			HIV-1 Tat interactive protein 2, 30kDa											large_intestine(2)|lung(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	8						AATCAAGCAATTTTTTATATC	0.358																																					p.N174fs		Atlas-INDEL	.											HTATIP2_ENST00000419348,NS,carcinoma,0,3	HTATIP2	30	.	0			c.521delA						.						86	89	88					11																	20398242		2203	4300	6503	SO:0001589	frameshift_variant	10553	exon4			.	AF039103	CCDS7852.1, CCDS44553.1, CCDS53613.1	11p15.1	2011-09-14	2002-08-29		ENSG00000109854	ENSG00000109854	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	16637	protein-coding gene	gene with protein product	"Tat-interacting protein (30kD)", "short chain dehydrogenase/reductase family 44U, member 1"	605628	"HIV-1 Tat interactive protein 2, 30 kDa"			9482853, 9174052, 19027726	Standard	NM_006410		Approved	TIP30, CC3, FLJ26963, SDR44U1	uc001mpx.2	Q9BUP3	OTTHUMG00000166015	ENST00000451739.2:c.420delT	chr11.hg19:g.20398242delT	ENSP00000394259:p.Asn140fs	127.0	0.0		167.0	13.0	NM_001098520		Frame_Shift_Del	DEL	ENST00000451739.2	hg19	CCDS7852.1																																																																																			.	.		0.358	HTATIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387445.2	NM_001098521		-	20398242	T	-	20398242	7	5	112	1	0	1	0	1	0	0	0	0	7441	1490	52	0	635	0	HTATIP2	11	20398242	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1634252	20398242	114608274	685	17306										
IMMP1L	196294	hgsc.bcm.edu	37	chr11	31477911	31477911	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgattttggatcacttgggcTttttgcaatcacaatgtcac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:31477911delT	ENST00000278200.1	-	5	412	c.217delA	c.(217-219)agcfs	p.S73fs	IMMP1L_ENST00000533642.1_Intron|IMMP1L_ENST00000528161.1_5'UTR|IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000532287.1_Frame_Shift_Del_p.S73fs|IMMP1L_ENST00000526776.1_Intron	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	73					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	serine-type peptidase activity (GO:0008236)			breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					TCACTTGGGCTTTTTGCAATC	0.348																																					p.S73fs		Atlas-INDEL	.											.	IMMP1L	16	.	0			c.218delG						.						57	54	55					11																	31477911		2202	4295	6497	SO:0001589	frameshift_variant	196294	exon5			.		CCDS7874.1	11p13	2014-07-30			ENSG00000148950	ENSG00000148950			26317	protein-coding gene	gene with protein product		612323					Standard	NM_144981		Approved	FLJ25059	uc001msy.1	Q96LU5	OTTHUMG00000166226	ENST00000278200.1:c.217delA	chr11.hg19:g.31477911delT	ENSP00000278200:p.Ser73fs	133.0	0.0		161.0	12.0	NM_144981	D3DQZ7|Q96SH9	Frame_Shift_Del	DEL	ENST00000278200.1	hg19	CCDS7874.1																																																																																			.	.		0.348	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981		-	31477911	T	-	31477911	7	5	112	1	0	1	0	1	0	0	0	0	7725	1609	56	0	295	0	IMMP1L	11	31477911	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	11079669	31477911	103528605	686	17307										
TCP11L1	55346	hgsc.bcm.edu	37	chr11	33079469	33079469	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgtgttctcttgtagactcTcttatctttcttgctgcctg	7	11	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:33079469T>C	ENST00000334274.4	+	5	822	c.422T>C	c.(421-423)cTc>cCc	p.L141P	TCP11L1_ENST00000530171.1_3'UTR|TCP11L1_ENST00000531632.2_Missense_Mutation_p.L141P|TCP11L1_ENST00000324357.9_5'Flank|TCP11L1_ENST00000432887.1_Missense_Mutation_p.L141P	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	141						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						TTGTAGACTCTCTTATCTTTC	0.368																																					p.L141P		Atlas-SNP	.											.	TCP11L1	40	.	0			c.T422C						.						56	55	55					11																	33079469		2202	4298	6500	SO:0001583	missense	55346	exon5			AGACTCTCTTATC	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 1"				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.422T>C	chr11.hg19:g.33079469T>C	ENSP00000335595:p.Leu141Pro	77.0	0.0		96.0	4.0	NM_001145541	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	hg19	CCDS7882.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.263626	0.80358	.	.	ENSG00000176148	ENST00000530419;ENST00000334274;ENST00000531632;ENST00000432887	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.63628	0.2527	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72557	-0.4257	10	0.87932	D	0	-20.0459	15.5323	0.75974	0.0:0.0:0.0:1.0	.	141	Q9NUJ3	T11L1_HUMAN	P	141	ENSP00000436428:L141P;ENSP00000335595:L141P;ENSP00000433067:L141P;ENSP00000395070:L141P	ENSP00000335595:L141P	L	+	2	0	TCP11L1	33036045	1.000000	0.71417	0.704000	0.30370	0.917000	0.54804	8.040000	0.89188	2.074000	0.62210	0.402000	0.26972	CTC	.	.		0.368	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393		C	33079469	T	C	33079469	3	2	112	1	0	0	0	0	1	0	0	0	15729	1551	54	2	436	2	TCP11L1	11	33079469	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1601558	33079469	101927047	687	17308										
TCP11L1	55346	hgsc.bcm.edu	37	chr11	33083146	33083146	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgactcagaagtataaacaCgccctgccagtggggggaat	12	9	1	2	rs145755006		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:33083146C>T	ENST00000334274.4	+	7	1246	c.846C>T	c.(844-846)caC>caT	p.H282H	TCP11L1_ENST00000531632.2_Silent_p.H282H|TCP11L1_ENST00000324357.9_Silent_p.H61H|TCP11L1_ENST00000432887.1_Silent_p.H282H	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	282						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						AGTATAAACACGCCCTGCCAG	0.532																																					p.H282H		Atlas-SNP	.											TCP11L1_ENST00000324357,NS,carcinoma,0,2	TCP11L1	40	.	0			c.C846T						.	C	,	0,4404		0,0,2202	56	56	56		846,846	-2.5	0.5	11	dbSNP_134	56	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous,coding-synonymous	TCP11L1	NM_001145541.1,NM_018393.3	,	0,2,6498	TT,TC,CC		0.0233,0.0,0.0154	,	282/510,282/510	33083146	2,12998	2202	4298	6500	SO:0001819	synonymous_variant	55346	exon7			TAAACACGCCCTG	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 1"				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.846C>T	chr11.hg19:g.33083146C>T		92.0	0.0		123.0	29.0	NM_001145541	D3DR01|Q8IVX4	Silent	SNP	ENST00000334274.4	hg19	CCDS7882.1																																																																																			.	C|1.000;T|0.000		0.532	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393		T	33083146	C	T	33083146	2	4	112	1	0	0	0	0	0	0	0	1	15729	535	19	1		1	TCP11L1	11	33083146	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	3677	33083146	101923370	688	17309										
ELF5	2001	hgsc.bcm.edu	37	chr11	34511593	34511593	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgctttcttcagcgtcattAaaaaaggagtaacctgggaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:34511593delA	ENST00000312319.2	-	4	628	c.399delT	c.(397-399)tttfs	p.F133fs	ELF5_ENST00000257832.2_Frame_Shift_Del_p.F123fs|ELF5_ENST00000528709.1_5'UTR|ELF5_ENST00000429939.2_Intron	NM_001243081.1|NM_198381.1	NP_001230010.1|NP_938195.1	Q9UKW6	ELF5_HUMAN	E74-like factor 5 (ets domain transcription factor)	133					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|ectoderm development (GO:0007398)|mammary gland epithelial cell differentiation (GO:0060644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			large_intestine(4)|skin(1)	5		Acute lymphoblastic leukemia(5;0.0087)|all_hematologic(20;0.0384)				CAGCGTCATTAAAAAAGGAGT	0.488																																					p.N134fs	Melanoma(61;202 1660 4348 21594)	Atlas-INDEL	.											.	ELF5	21	.	0			c.400delA						.						242	235	237					11																	34511593		2202	4298	6500	SO:0001589	frameshift_variant	2001	exon4			.	AF049703	CCDS7892.1, CCDS7893.1, CCDS58129.1, CCDS73273.1	11p13-p12	2008-05-14			ENSG00000135374	ENSG00000135374			3320	protein-coding gene	gene with protein product		605169				9840936	Standard	NM_001422		Approved		uc001mvp.2	Q9UKW6	OTTHUMG00000166451	ENST00000312319.2:c.399delT	chr11.hg19:g.34511593delA	ENSP00000311010:p.Phe133fs	97.0	0.0		156.0	10.0	NM_198381	A6XAE6|A8K452|O95175|Q8N2K9|Q96QY3|Q9UKW5	Frame_Shift_Del	DEL	ENST00000312319.2	hg19	CCDS7892.1																																																																																			.	.		0.488	ELF5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389845.1	NM_198381		-	34511593	A	-	34511593	7	5	112	1	0	1	0	1	0	0	0	0	5059	359	13	0	414	0	ELF5	11	34511593	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1428447	34511593	100494923	689	17310										
LDLRAD3	143458	hgsc.bcm.edu	37	chr11	36119988	36119988	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgtcaagacaacagtgatgAggaaagctgtgaaagttctc	11	7	2	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:36119988A>G	ENST00000315571.5	+	4	452	c.431A>G	c.(430-432)gAg>gGg	p.E144G	LDLRAD3_ENST00000524419.1_Missense_Mutation_p.E95G|LDLRAD3_ENST00000528989.1_Missense_Mutation_p.E95G	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	144	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				receptor-mediated endocytosis (GO:0006898)|regulation of protein processing (GO:0070613)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(7)|skin(1)	28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				AACAGTGATGAGGAAAGCTGT	0.468																																					p.E144G		Atlas-SNP	.											.	LDLRAD3	52	.	0			c.A431G						.						97	83	88					11																	36119988		2202	4298	6500	SO:0001583	missense	143458	exon4			GTGATGAGGAAAG	AK075546	CCDS31462.1	11p13	2014-06-05			ENSG00000179241	ENSG00000179241			27046	protein-coding gene	gene with protein product						21795536	Standard	NM_174902		Approved	LRAD3	uc001mwk.1	Q86YD5	OTTHUMG00000166313	ENST00000315571.5:c.431A>G	chr11.hg19:g.36119988A>G	ENSP00000318607:p.Glu144Gly	56.0	0.0		123.0	5.0	NM_174902	B7Z1U3|B9EG81|Q8NBJ0	Missense_Mutation	SNP	ENST00000315571.5	hg19	CCDS31462.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.430084	0.83776	.	.	ENSG00000179241	ENST00000528989;ENST00000524419;ENST00000545142;ENST00000315571	D;D;D	0.98876	-5.2;-5.2;-5.2	4.97	4.97	0.65823	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99513	0.9826	H	0.98721	4.31	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.992	D	0.97862	1.0281	10	0.87932	D	0	.	14.1219	0.65192	1.0:0.0:0.0:0.0	.	95;144	B7Z1U3;Q86YD5	.;LRAD3_HUMAN	G	95;95;130;144	ENSP00000433954:E95G;ENSP00000434313:E95G;ENSP00000318607:E144G	ENSP00000318607:E144G	E	+	2	0	LDLRAD3	36076564	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	8.190000	0.89714	1.996000	0.58369	0.533000	0.62120	GAG	.	.		0.468	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902		G	36119988	A	G	36119988	3	3	112	1	0	0	0	0	1	0	0	0	8716	304	11	2	445	2	LDLRAD3	11	36119988	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1608395	36119988	98886528	690	17311										
RAG1	5896	hgsc.bcm.edu	37	chr11	36594873	36594873	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcatggcagcctctttcccaCccaccttgggactcagttct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:36594873delC	ENST00000299440.5	+	2	131	c.19delC	c.(19-21)cccfs	p.P7fs		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	7	Interaction with importin alpha-1.				adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				CTCTTTCCCACCCACCTTGGG	0.403									Familial Hemophagocytic Lymphohistiocytosis																												p.P6fs	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-INDEL	.											.	RAG1	151	.	0			c.18delA						.						64	65	65					11																	36594873		2202	4298	6500	SO:0001589	frameshift_variant	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	.	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.19delC	chr11.hg19:g.36594873delC	ENSP00000299440:p.Pro7fs	133.0	0.0		183.0	11.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Frame_Shift_Del	DEL	ENST00000299440.5	hg19	CCDS7902.1																																																																																			.	.		0.403	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		-	36594873	C	-	36594873	7	5	112	1	0	1	0	1	0	0	0	0	13018	507	18	0	21	0	RAG1	11	36594873	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	474885	36594873	98411643	691	17312										
ACCSL	390110	hgsc.bcm.edu	37	chr11	44077622	44077622	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caacaggacccatgtgatctGgggtaccagtaaggtgagcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:44077622delG	ENST00000378832.1	+	10	1228	c.1172delG	c.(1171-1173)tggfs	p.W391fs		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	391					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						CATGTGATCTGGGGTACCAGT	0.438																																					p.W391fs		Atlas-INDEL	.											.	ACCSL	57	.	0			c.1171delT						.						145	136	138					11																	44077622		1913	4127	6040	SO:0001589	frameshift_variant	390110	exon10			.		CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.1172delG	chr11.hg19:g.44077622delG	ENSP00000368109:p.Trp391fs	97.0	0.0		188.0	12.0	NM_001031854		Frame_Shift_Del	DEL	ENST00000378832.1	hg19	CCDS41636.1																																																																																			.	.		0.438	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854		-	44077622	G	-	44077622	7	5	112	1	0	1	0	1	0	0	0	0	134	1357	47	0	1210	0	ACCSL	11	44077622	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	7482749	44077622	90928894	692	17313										
DGKZ	8525	hgsc.bcm.edu	37	chr11	46394213	46394213	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acctgcggatcctggcgtgcGggggcgacggcacggtgagc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:46394213delG	ENST00000454345.1	+	13	1746	c.1621delG	c.(1621-1623)gggfs	p.G542fs	DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000532868.2_Frame_Shift_Del_p.G358fs|DGKZ_ENST00000395574.3_Frame_Shift_Del_p.G320fs|DGKZ_ENST00000343674.6_Frame_Shift_Del_p.G370fs|DGKZ_ENST00000421244.2_Frame_Shift_Del_p.G354fs|DGKZ_ENST00000527911.1_Frame_Shift_Del_p.G354fs|DGKZ_ENST00000318201.8_Frame_Shift_Del_p.G331fs|DGKZ_ENST00000456247.2_Frame_Shift_Del_p.G353fs|DGKZ_ENST00000528615.1_Frame_Shift_Del_p.G132fs	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	542	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.|Mediates interaction with RASGRP1.				blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)	p.G369R(1)|p.G541R(1)|p.G353R(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		CCTGGCGTGCGGGGGCGACGG	0.662																																					p.C540fs		Atlas-INDEL	.											.	DGKZ	199	.	3	Substitution - Missense(3)	lung(3)	c.1620delC						.						48	44	45					11																	46394213		2202	4299	6501	SO:0001589	frameshift_variant	8525	exon13			.	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"diacylglycerol kinase, zeta 104kDa"			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.1621delG	chr11.hg19:g.46394213delG	ENSP00000412178:p.Gly542fs	51.0	0.0		132.0	10.0	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Frame_Shift_Del	DEL	ENST00000454345.1	hg19	CCDS41640.1																																																																																			.	.		0.662	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540		-	46394213	G	-	46394213	7	5	112	1	0	1	0	1	0	0	0	0	4476	1116	39	0	2114	0	DGKZ	11	46394213	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2316591	46394213	88612303	693	17314										
OR4X1	390113	hgsc.bcm.edu	37	chr11	48286313	48286313	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgccatgaggagatttattGggggaaaagtaatttgagaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:48286313delG	ENST00000320048.1	+	1	901	c.901delG	c.(901-903)gggfs	p.G302fs		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						GAGATTTATTGGGGGAAAAGT	0.398																																					p.I300fs		Atlas-INDEL	.											.	OR4X1	75	.	0			c.900delT						.						35	35	35					11																	48286313		2201	4296	6497	SO:0001589	frameshift_variant	390113	exon1			.	AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"GPCR / Class A : Olfactory receptors"	14854	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily X, member 1"				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.901delG	chr11.hg19:g.48286313delG	ENSP00000321506:p.Gly302fs	114.0	0.0		152.0	11.0	NM_001004726	Q6IF74	Frame_Shift_Del	DEL	ENST00000320048.1	hg19	CCDS31487.1																																																																																			.	.		0.398	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726		-	48286313	G	-	48286313	7	5	112	1	0	1	0	1	0	0	0	0	11093	1348	47	0	903	0	OR4X1	11	48286313	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1892100	48286313	86720203	694	17315										
OR4A5	81318	hgsc.bcm.edu	37	chr11	51411652	51411652	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatatgaaaatacagggtacAaaaaagaggacaacaacggt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:51411652delA	ENST00000319760.6	-	1	796	c.744delT	c.(742-744)tttfs	p.F248fs		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				TACAGGGTACAAAAAAGAGGA	0.408																																					p.V249fs		Atlas-INDEL	.											.	OR4A5	116	.	0			c.745delG						.						55	54	54					11																	51411652		2201	4296	6497	SO:0001589	frameshift_variant	81318	exon1			.	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"GPCR / Class A : Olfactory receptors"	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.744delT	chr11.hg19:g.51411652delA	ENSP00000367664:p.Phe248fs	86.0	0.0		143.0	13.0	NM_001005272	Q6IF84	Frame_Shift_Del	DEL	ENST00000319760.6	hg19	CCDS31497.1																																																																																			.	.		0.408	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		-	51411652	A	-	51411652	7	5	112	1	0	1	0	1	0	0	0	0	11052	127	5	0	207	0	OR4A5	11	51411652	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3125339	51411652	83594864	695	17316										
OR8I2	120586	hgsc.bcm.edu	37	chr11	55861691	55861691	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaaaatgctcttctgagagTcatacatagaaaactttttc	6	7	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:55861691T>C	ENST00000302124.2	+	1	939	c.908T>C	c.(907-909)gTc>gCc	p.V303A		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	303						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					CTTCTGAGAGTCATACATAGA	0.373																																					p.V303A		Atlas-SNP	.											.	OR8I2	119	.	0			c.T908C						.						23	23	23					11																	55861691		2200	4275	6475	SO:0001583	missense	120586	exon1			TGAGAGTCATACA	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.908T>C	chr11.hg19:g.55861691T>C	ENSP00000303864:p.Val303Ala	24.0	0.0		48.0	4.0	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	hg19	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	T	8.935	0.964439	0.18583	.	.	ENSG00000172154	ENST00000302124	T	0.38240	1.15	4.0	4.0	0.46444	.	0.440276	0.16412	U	0.215536	T	0.19046	0.0457	N	0.16368	0.405	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.19614	-1.0300	10	0.13470	T	0.59	-4.5772	7.0122	0.24869	0.2033:0.0:0.0:0.7967	.	303	Q8N0Y5	OR8I2_HUMAN	A	303	ENSP00000303864:V303A	ENSP00000303864:V303A	V	+	2	0	OR8I2	55618267	.	.	0.002000	0.10522	0.234000	0.25298	.	.	1.580000	0.49851	0.367000	0.22151	GTC	.	.		0.373	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		C	55861691	T	C	55861691	3	2	112	1	0	0	0	0	1	0	0	0	11249	1667	58	2	910	2	OR8I2	11	55861691	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4450039	55861691	79144825	696	17317										
OR8K1	390157	hgsc.bcm.edu	37	chr11	56114060	56114060	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggctcaaacataatcagctaTttttactgtgactgtatccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:56114060delT	ENST00000279783.2	+	1	640	c.546delT	c.(544-546)tatfs	p.Y182fs		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					TAATCAGCTATTTTTACTGTG	0.348										HNSCC(65;0.19)																											p.Y182fs		Atlas-INDEL	.											.	OR8K1	93	.	0			c.545delA						.						144	146	145					11																	56114060		2201	4296	6497	SO:0001589	frameshift_variant	390157	exon1			.	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.546delT	chr11.hg19:g.56114060delT	ENSP00000279783:p.Tyr182fs	126.0	0.0		192.0	13.0	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Frame_Shift_Del	DEL	ENST00000279783.2	hg19	CCDS31528.1																																																																																			.	.		0.348	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		-	56114060	T	-	56114060	7	5	112	1	0	1	0	1	0	0	0	0	11252	1500	52	0	548	0	OR8K1	11	56114060	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	252369	56114060	78892456	697	17318										
OR8J1	219477	hgsc.bcm.edu	37	chr11	56128630	56128630	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggatgtgaagactgctctacAgagattcatgacaaatctgt	10	7	3	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:56128630A>G	ENST00000303039.3	+	1	940	c.908A>G	c.(907-909)cAg>cGg	p.Q303R		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	303						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					ACTGCTCTACAGAGATTCATG	0.358																																					p.Q303R		Atlas-SNP	.											.	OR8J1	87	.	0			c.A908G						.						71	65	67					11																	56128630		2201	4296	6497	SO:0001583	missense	219477	exon1			CTCTACAGAGATT	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"GPCR / Class A : Olfactory receptors"	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.908A>G	chr11.hg19:g.56128630A>G	ENSP00000304060:p.Gln303Arg	76.0	0.0		125.0	5.0	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	hg19	CCDS31529.1	.	.	.	.	.	.	.	.	.	.	A	1.442	-0.567393	0.03910	.	.	ENSG00000172487	ENST00000303039	T	0.34072	1.38	4.02	2.89	0.33648	.	0.477293	0.21088	N	0.080372	T	0.11793	0.0287	N	0.01679	-0.765	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20706	-1.0267	10	0.25751	T	0.34	.	5.5946	0.17319	0.6885:0.0:0.3114:0.0	.	303	Q8NGP2	OR8J1_HUMAN	R	303	ENSP00000304060:Q303R	ENSP00000304060:Q303R	Q	+	2	0	OR8J1	55885206	0.000000	0.05858	0.925000	0.36789	0.053000	0.15095	-0.480000	0.06559	0.711000	0.32018	0.448000	0.29417	CAG	.	.		0.358	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205		G	56128630	A	G	56128630	3	3	112	1	0	0	0	0	1	0	0	0	11250	188	7	2	910	2	OR8J1	11	56128630	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	14570	56128630	78877886	698	17319										
OR5M11	219487	hgsc.bcm.edu	37	chr11	56310222	56310222	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtagaagtggttgatgacaCtggatctacagaaggtcagg					rs628524	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:56310222delC	ENST00000528616.2	-	1	535	c.512delG	c.(511-513)agtfs	p.S171fs		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	171			S -> N (in dbSNP:rs628524). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)	18						GTTGATGACACTGGATCTACA	0.483																																					p.S171fs		Atlas-INDEL	.											.	OR5M11	60	.	0			c.513delT						.						45	47	47					11																	56310222		2092	4229	6321	SO:0001589	frameshift_variant	219487	exon1			.	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"GPCR / Class A : Olfactory receptors"	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.512delG	chr11.hg19:g.56310222delC	ENSP00000432417:p.Ser171fs	84.0	0.0		130.0	12.0	NM_001005245	B2RNL5|B2RNL7	Frame_Shift_Del	DEL	ENST00000528616.2	hg19	CCDS53629.1																																																																																			.	.		0.483	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245		-	56310222	C	-	56310222	7	5	112	1	0	1	0	1	0	0	0	0	11183	565	20	0	408	0	OR5M11	11	56310222	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	181592	56310222	78696294	699	17320	78	2								
OR5M11	219487	hgsc.bcm.edu	37	chr11	56310224	56310224	+	Silent	SNP	G	G	T													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tagaagtggttgatgacactGgatctacagaaggtcaggcg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:56310224G>T	ENST00000528616.2	-	1	533	c.510C>A	c.(508-510)tcC>tcA	p.S170S		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	170						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)	18						TGATGACACTGGATCTACAGA	0.488																																					p.S170S		Atlas-SNP	.											.	OR5M11	60	.	0			c.C510A						.						45	47	46					11																	56310224		2091	4226	6317	SO:0001819	synonymous_variant	219487	exon1			GACACTGGATCTA	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"GPCR / Class A : Olfactory receptors"	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.510C>A	chr11.hg19:g.56310224G>T		84.0	0.0		131.0	7.0	NM_001005245	B2RNL5|B2RNL7	Silent	SNP	ENST00000528616.2	hg19	CCDS53629.1																																																																																			.	.		0.488	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245		T	56310224	G	T	56310224	2	4	112	1	0	0	0	0	0	0	0	1	11183	1335	47	3		3	OR5M11	11	56310224	Silent	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	2	56310224	78696292	700	17321	78	2								
P2RX3	5024	hgsc.bcm.edu	37	chr11	57118235	57118235	+	Splice_Site	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atacccggcccgtttcttcaGgggggagttctgggcattaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:57118235delG	ENST00000263314.2	+	8	739		c.e8-1			NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3						behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						CGTTTCTTCAGGGGGGAGTTC	0.607																																					.		Atlas-INDEL	.											.	P2RX3	55	.	0			c.706-2G>-						.						65	57	59					11																	57118235		2201	4296	6497	SO:0001630	splice_region_variant	5024	exon8			.	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.706-1G>-	chr11.hg19:g.57118235delG		145.0	0.0		195.0	14.0	NM_002559	Q6DK37|Q9UQB6	Splice_Site	DEL	ENST00000263314.2	hg19	CCDS7953.1																																																																																			.	.		0.607	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	Intron	-	57118235	G	-	57118235	8	5	112	1	0	1	0	1	0	0	1	0	11350	1014	35	0	735	0	P2RX3	11	57118235	Splice_Site	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	808011	57118235	77888281	701	17322										
SLC43A3	29015	hgsc.bcm.edu	37	chr11	57193097	57193097	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgaagttgttcatgaaggaCcccagggtgaagatgagtga					rs571852590		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:57193097delC	ENST00000395123.2	-	4	535	c.231delG	c.(229-231)gggfs	p.G77fs	SLC43A3_ENST00000529554.1_Frame_Shift_Del_p.G77fs|SLC43A3_ENST00000352187.1_Frame_Shift_Del_p.G77fs|SLC43A3_ENST00000528098.1_5'UTR|SLC43A3_ENST00000395124.1_Frame_Shift_Del_p.G77fs|SLC43A3_ENST00000533524.1_Frame_Shift_Del_p.G90fs	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	77					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						TCATGAAGGACCCCAGGGTGA	0.522																																					p.S78fs		Atlas-INDEL	.											.	SLC43A3	54	.	0			c.232delT						.						116	104	108					11																	57193097		2201	4296	6497	SO:0001589	frameshift_variant	29015	exon4			.	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"Solute carriers"	17466	protein-coding gene	gene with protein product	"likely ortholog of mouse embryonic epithelial gene 1"					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.231delG	chr11.hg19:g.57193097delC	ENSP00000378555:p.Gly77fs	134.0	0.0		155.0	13.0	NM_014096	B4DNR8|E7EQD2|Q9NSS4	Frame_Shift_Del	DEL	ENST00000395123.2	hg19	CCDS7956.1																																																																																			.	.		0.522	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611		-	57193097	C	-	57193097	7	5	112	1	0	1	0	1	0	0	0	0	14649	494	18	0	1288	0	SLC43A3	11	57193097	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	74862	57193097	77813419	702	17323										
SERPING1	710	hgsc.bcm.edu	37	chr11	57367406	57367406	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccagctcccaggatccagagAgtttgcaagacagaggcgaa	12	11	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:57367406A>G	ENST00000278407.4	+	3	333	c.106A>G	c.(106-108)Agt>Ggt	p.S36G	SERPING1_ENST00000378323.4_Missense_Mutation_p.S41G|SERPING1_ENST00000378324.2_5'UTR|SERPING1_ENST00000340687.6_Missense_Mutation_p.S36G|SERPING1_ENST00000403558.1_Missense_Mutation_p.S70G	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	36					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						GGATCCAGAGAGTTTGCAAGA	0.478																																					p.S36G		Atlas-SNP	.											.	SERPING1	57	.	0			c.A106G	GRCh37	CD961868	SERPING1	D		.						115	115	115					11																	57367406		2201	4296	6497	SO:0001583	missense	710	exon2			CCAGAGAGTTTGC	X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"Serine (or cysteine) peptidase inhibitors"	1228	protein-coding gene	gene with protein product	"plasma protease C1 inhibitor", "angioedema, hereditary"	606860	"serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.106A>G	chr11.hg19:g.57367406A>G	ENSP00000278407:p.Ser36Gly	96.0	0.0		156.0	7.0	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	hg19	CCDS7962.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.663237	0.29515	.	.	ENSG00000149131	ENST00000405496;ENST00000278407;ENST00000457869;ENST00000340687;ENST00000378323;ENST00000403558;ENST00000433668	D;D;T;D;D;D	0.89875	-2.58;-1.93;-1.42;-1.98;-1.99;-2.03	4.76	-0.369	0.12534	.	1.223870	0.05423	N	0.544623	T	0.81403	0.4815	L	0.46157	1.445	0.09310	N	1	B;P;B;B	0.39480	0.118;0.675;0.118;0.118	B;B;B;B	0.28553	0.026;0.091;0.037;0.026	T	0.69716	-0.5070	10	0.59425	D	0.04	.	4.704	0.12841	0.5712:0.1563:0.2725:0.0	.	41;70;36;36	B4E1F0;E9PGN7;E9KL26;P05155	.;.;.;IC1_HUMAN	G	36;36;70;36;41;70;36	ENSP00000384561:S36G;ENSP00000278407:S36G;ENSP00000399746:S70G;ENSP00000341861:S36G;ENSP00000367574:S41G;ENSP00000384420:S70G	ENSP00000278407:S36G	S	+	1	0	SERPING1	57123982	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.428000	0.21395	-0.144000	0.11314	0.402000	0.26972	AGT	.	.		0.478	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062		G	57367406	A	G	57367406	3	3	112	1	0	0	0	0	1	0	0	0	14131	304	11	2	112	2	SERPING1	11	57367406	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	174309	57367406	77639110	703	17324										
FADS3	3995	hgsc.bcm.edu	37	chr11	61658711	61658711	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccgctgtgcccagcggctgAtgtcgtagacgcggcgctcg	16	14	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:61658711A>G	ENST00000278829.2	-	1	295	c.143T>C	c.(142-144)aTc>aCc	p.I48T	FADS3_ENST00000529525.1_5'UTR|FADS3_ENST00000540820.1_Missense_Mutation_p.I48T|FADS3_ENST00000527697.1_Intron|FADS3_ENST00000525588.1_Missense_Mutation_p.I48T	NM_021727.3	NP_068373.1	Q9Y5Q0	FADS3_HUMAN	fatty acid desaturase 3	48	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				unsaturated fatty acid biosynthetic process (GO:0006636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water (GO:0016717)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CCAGCGGCTGATGTCGTAGAC	0.711																																					p.I48T		Atlas-SNP	.											.	FADS3	29	.	0			c.T143C						.						5	6	6					11																	61658711		2043	4012	6055	SO:0001583	missense	3995	exon1			CGGCTGATGTCGT		CCDS8013.1	11q12-q13.1	2013-01-25			ENSG00000221968	ENSG00000221968	1.14.19.3	"Fatty acid desaturases"	3576	protein-coding gene	gene with protein product	"delta-9-desaturase"	606150		LLCDL3			Standard	NM_021727		Approved	CYB5RP	uc001nsm.3	Q9Y5Q0	OTTHUMG00000167500	ENST00000278829.2:c.143T>C	chr11.hg19:g.61658711A>G	ENSP00000278829:p.Ile48Thr	43.0	0.0		96.0	4.0	NM_021727	O60426	Missense_Mutation	SNP	ENST00000278829.2	hg19	CCDS8013.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.626385	0.66901	.	.	ENSG00000221968	ENST00000278829;ENST00000540820;ENST00000525588	T;T;T	0.81330	-1.48;-1.48;-1.48	3.65	3.65	0.41850	Cytochrome b5 (4);	0.117094	0.34555	U	0.003864	D	0.85371	0.5681	M	0.79123	2.44	0.39950	D	0.974528	B	0.31318	0.319	P	0.46339	0.513	D	0.87215	0.2250	10	0.66056	D	0.02	-8.2834	11.5368	0.50641	1.0:0.0:0.0:0.0	.	48	Q9Y5Q0	FADS3_HUMAN	T	48	ENSP00000278829:I48T;ENSP00000439308:I48T;ENSP00000432206:I48T	ENSP00000278829:I48T	I	-	2	0	FADS3	61415287	1.000000	0.71417	0.993000	0.49108	0.999000	0.98932	7.106000	0.77039	1.657000	0.50732	0.533000	0.62120	ATC	.	.		0.711	FADS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394836.1			G	61658711	A	G	61658711	3	3	112	1	0	0	0	0	1	0	0	0	5372	333	12	2	1242	2	FADS3	11	61658711	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	4291305	61658711	73347805	704	17325										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62288216	62288216	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagtgtcaatgcccactttaGggcctttgacatccactttg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:62288216delG	ENST00000378024.4	-	5	13947	c.13673delC	c.(13672-13674)cctfs	p.P4558fs	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4558					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GCCCACTTTAGGGCCTTTGAC	0.443																																					p.P4558fs		Atlas-INDEL	.											.	AHNAK	532	.	0			c.13674delT						.						82	80	81					11																	62288216		2202	4299	6501	SO:0001589	frameshift_variant	79026	exon5			.	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.13673delC	chr11.hg19:g.62288216delG	ENSP00000367263:p.Pro4558fs	126.0	0.0		202.0	13.0	NM_001620	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.443	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		-	62288216	G	-	62288216	7	5	112	1	0	1	0	1	0	0	0	0	414	1000	35	0	4119	0	AHNAK	11	62288216	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	629505	62288216	72718300	705	17326										
FERMT3	83706	hgsc.bcm.edu	37	chr11	63988014	63988014	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcaggccatcctggccttccTcagcctgcagcgcacgggca	12	17	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:63988014T>C	ENST00000279227.5	+	12	1525	c.1430T>C	c.(1429-1431)cTc>cCc	p.L477P	FERMT3_ENST00000345728.5_Missense_Mutation_p.L473P	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	477	FERM.				integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						CTGGCCTTCCTCAGCCTGCAG	0.711																																					p.L477P		Atlas-SNP	.											.	FERMT3	51	.	0			c.T1430C						.						12	14	13					11																	63988014		2184	4270	6454	SO:0001583	missense	83706	exon12			CCTTCCTCAGCCT	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"Fermitins", "Pleckstrin homology (PH) domain containing"	23151	protein-coding gene	gene with protein product	"kindlin-3"	607901	"fermitin family homolog 3 (Drosophila)"				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.1430T>C	chr11.hg19:g.63988014T>C	ENSP00000279227:p.Leu477Pro	46.0	0.0		94.0	4.0	NM_178443	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	hg19	CCDS8060.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.1|22.1	4.249925|4.249925	0.80024|0.80024	.|.	.|.	ENSG00000149781|ENSG00000149781	ENST00000345728;ENST00000279227|ENST00000545896	T;T|T	0.77098|0.56941	-1.07;-1.07|0.43	4.31|4.31	4.31|4.31	0.51392|0.51392	Band 4.1 domain (1);FERM central domain (2);|.	0.000000|.	0.64402|.	D|.	0.000004|.	T|T	0.65059|0.65059	0.2655|0.2655	M|M	0.73598|0.73598	2.24|2.24	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.66654|0.66654	-0.5869|-0.5869	10|6	0.87932|.	D|.	0|.	-34.5898|-34.5898	12.87|12.87	0.57960|0.57960	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	473;477|.	Q86UX7-2;Q86UX7|.	.;URP2_HUMAN|.	P|P	473;477|36	ENSP00000339950:L473P;ENSP00000279227:L477P|ENSP00000440209:S36P	ENSP00000279227:L477P|.	L|S	+|+	2|1	0|0	FERMT3|FERMT3	63744590|63744590	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.915000|0.915000	0.54546|0.54546	5.707000|5.707000	0.68370|0.68370	1.940000|1.940000	0.56252|0.56252	0.459000|0.459000	0.35465|0.35465	CTC|TCA	.	.		0.711	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471		C	63988014	T	C	63988014	3	2	112	1	0	0	0	0	1	0	0	0	5827	1551	54	2	1472	2	FERMT3	11	63988014	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1699798	63988014	71018502	706	17327										
SYVN1	84447	hgsc.bcm.edu	37	chr11	64897763	64897763	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccacagcctctcctgagctGgggggaggcgggacaggtgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:64897763delG	ENST00000377190.3	-	12	1288	c.1194delC	c.(1192-1194)cccfs	p.P398fs	SYVN1_ENST00000526060.1_Frame_Shift_Del_p.P398fs|SYVN1_ENST00000307289.6_Frame_Shift_Del_p.P347fs|SYVN1_ENST00000294256.8_Frame_Shift_Del_p.P398fs|SYVN1_ENST00000526121.1_5'Flank	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	398	Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						CTCCTGAGCTGGGGGGAGGCG	0.642																																					p.S399fs		Atlas-INDEL	.											.	SYVN1	55	.	0			c.1195delA						.						11	14	13					11																	64897763		2195	4280	6475	SO:0001589	frameshift_variant	84447	exon12			.	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"RING-type (C3HC4) zinc fingers"	20738	protein-coding gene	gene with protein product	"HMG-coA reductase degradation 1 homolog (S. cerevisiae)"	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.1194delC	chr11.hg19:g.64897763delG	ENSP00000366395:p.Pro398fs	107.0	0.0		153.0	10.0	NM_032431	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Frame_Shift_Del	DEL	ENST00000377190.3	hg19	CCDS31605.1																																																																																			.	.		0.642	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431		-	64897763	G	-	64897763	7	5	112	1	0	1	0	1	0	0	0	0	15502	1335	47	0	679	0	SYVN1	11	64897763	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	909749	64897763	70108753	707	17328										
SCYL1	57410	hgsc.bcm.edu	37	chr11	65294460	65294460	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaacgctggtgccccattacTgtgagctggtgggagcaaac	13	10	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:65294460T>C	ENST00000270176.5	+	6	798	c.721T>C	c.(721-723)Tgt>Cgt	p.C241R	SCYL1_ENST00000533862.1_Missense_Mutation_p.C241R|SCYL1_ENST00000527009.1_Missense_Mutation_p.C98R|SCYL1_ENST00000420247.2_Missense_Mutation_p.C241R|SCYL1_ENST00000279270.6_Missense_Mutation_p.C241R|SCYL1_ENST00000524944.1_Missense_Mutation_p.C241R|SCYL1_ENST00000525364.1_Missense_Mutation_p.C241R	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	241	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						GCCCCATTACTGTGAGCTGGT	0.627																																					p.C241R		Atlas-SNP	.											.	SCYL1	76	.	0			c.T721C						.						39	43	42					11																	65294460		1941	4131	6072	SO:0001583	missense	57410	exon6			CATTACTGTGAGC	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"teratoma-associated tyrosine kinase", "telomerase transcriptional elements-interacting factor", "telomerase regulation-associated protein"	607982	"N-terminal kinase-like"	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.721T>C	chr11.hg19:g.65294460T>C	ENSP00000270176:p.Cys241Arg	120.0	0.0		143.0	6.0	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Missense_Mutation	SNP	ENST00000270176.5	hg19	CCDS41672.1	.	.	.	.	.	.	.	.	.	.	T	11.65	1.700715	0.30142	.	.	ENSG00000142186	ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000417543;ENST00000527009	T;T;T;T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63	4.64	4.64	0.57946	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047838	0.85682	D	0.000000	T	0.53318	0.1789	N	0.21508	0.67	0.80722	D	1	B;B;B;B	0.28470	0.004;0.009;0.009;0.213	B;B;B;B	0.30401	0.055;0.032;0.032;0.115	T	0.48833	-0.9000	10	0.07325	T	0.83	-5.9943	12.3316	0.55043	0.0:0.0:0.0:1.0	.	241;241;241;241	E9PS17;Q96KG9-6;Q96KG9-2;Q96KG9	.;.;.;NTKL_HUMAN	R	241;241;241;241;241;241;241;241;241;98	ENSP00000270176:C241R;ENSP00000431635:C241R;ENSP00000408192:C241R;ENSP00000437254:C241R;ENSP00000433450:C241R;ENSP00000279270:C241R;ENSP00000432175:C241R;ENSP00000436993:C98R	ENSP00000270176:C241R	C	+	1	0	SCYL1	65051036	1.000000	0.71417	0.998000	0.56505	0.935000	0.57460	6.943000	0.75934	1.870000	0.54199	0.459000	0.35465	TGT	.	.		0.627	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		C	65294460	T	C	65294460	3	2	112	1	0	0	0	0	1	0	0	0	13962	1580	55	2	743	2	SCYL1	11	65294460	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	396697	65294460	69712056	708	17329										
CNIH2	254263	hgsc.bcm.edu	37	chr11	66050215	66050215	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccccaacagcgcgagcgtttAaaaaacatcgaacgcatctg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:66050215delA	ENST00000311445.6	+	3	420	c.162delA	c.(160-162)ttafs	p.L54fs	YIF1A_ENST00000526497.1_5'Flank|CNIH2_ENST00000528852.1_Frame_Shift_Del_p.L54fs|CNIH2_ENST00000530519.1_3'UTR	NM_182553.2	NP_872359.1	Q6PI25	CNIH2_HUMAN	cornichon family AMPA receptor auxiliary protein 2	54					intracellular signal transduction (GO:0035556)|localization within membrane (GO:0051668)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	5						GCGAGCGTTTAAAAAACATCG	0.647											OREG0021100	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L54X		Atlas-INDEL	.											.	CNIH2	15	.	0			c.161delT						.						31	30	30					11																	66050215		2200	4294	6494	SO:0001589	frameshift_variant	254263	exon3			.	BC047953	CCDS8131.1	11q13.2	2013-08-28	2013-08-28		ENSG00000174871	ENSG00000174871			28744	protein-coding gene	gene with protein product		611288	"cornichon homolog 2 (Drosophila)"			12477932	Standard	NM_182553		Approved	MGC50896, Cnil, CNIH-2	uc001ohi.2	Q6PI25	OTTHUMG00000166919	ENST00000311445.6:c.162delA	chr11.hg19:g.66050215delA	ENSP00000310003:p.Leu54fs	107.0	0.0	1088	176.0	11.0	NM_182553		Frame_Shift_Del	DEL	ENST00000311445.6	hg19	CCDS8131.1																																																																																			.	.		0.647	CNIH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391892.1	NM_182553		-	66050215	A	-	66050215	7	5	112	1	0	1	0	1	0	0	0	0	3605	359	13	0	172	0	CNIH2	11	66050215	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	755755	66050215	68956301	709	17330										
LRFN4	78999	hgsc.bcm.edu	37	chr11	66627324	66627324	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggaccctgaccgtggccgtGgggggtgtgctggtggctgc					rs142190580		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:66627324delG	ENST00000309602.4	+	2	1809	c.1566delG	c.(1564-1566)gtgfs	p.V522fs	PC_ENST00000393960.1_Intron|LRFN4_ENST00000393952.3_Intron|PC_ENST00000393958.2_Intron|PC_ENST00000393955.2_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	522						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						CCGTGGCCGTGGGGGGTGTGC	0.716																																					p.V522fs		Atlas-INDEL	.											.	LRFN4	25	.	0			c.1565delT						.						28	22	24					11																	66627324		2187	4280	6467	SO:0001589	frameshift_variant	78999	exon2			.	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28456	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 6"	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.1566delG	chr11.hg19:g.66627324delG	ENSP00000312535:p.Val522fs	76.0	0.0		149.0	10.0	NM_024036	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Frame_Shift_Del	DEL	ENST00000309602.4	hg19	CCDS8153.1																																																																																			.	.		0.716	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		-	66627324	G	-	66627324	7	5	112	1	0	1	0	1	0	0	0	0	8949	1335	47	0	1572	0	LRFN4	11	66627324	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	577109	66627324	68379192	710	17331										
TBX10	347853	hgsc.bcm.edu	37	chr11	67402373	67402373	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccaggatcttcacctggaaGggggggaacatcctcctgcg					rs144542807		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:67402373delG	ENST00000335385.3	-	3	378	c.291delC	c.(289-291)cccfs	p.P97fs		NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	97					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						TCACCTGGAAGGGGGGGAACA	0.677																																					p.F98fs		Atlas-INDEL	.											.	TBX10	25	.	0			c.292delT						.						50	49	49					11																	67402373		2200	4294	6494	SO:0001589	frameshift_variant	347853	exon3			.	AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"T-boxes"	11593	protein-coding gene	gene with protein product		604648	"T-box 7"	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.291delC	chr11.hg19:g.67402373delG	ENSP00000335191:p.Pro97fs	109.0	0.0		188.0	16.0	NM_005995	Q14D64|Q86XS3	Frame_Shift_Del	DEL	ENST00000335385.3	hg19	CCDS31621.1																																																																																			.	.		0.677	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995		-	67402373	G	-	67402373	7	5	112	1	0	1	0	1	0	0	0	0	15666	987	35	0	890	0	TBX10	11	67402373	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	775049	67402373	67604143	711	17332										
MYEOV	26579	hgsc.bcm.edu	37	chr11	69063723	69063723	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgttgtgactgttgaggcccTgggggggtggcgcatgggag	21	6	0	2	rs552116583	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:69063723T>C	ENST00000308946.3	+	3	1256	c.806T>C	c.(805-807)cTg>cCg	p.L269P	MYEOV_ENST00000535407.1_Missense_Mutation_p.L211P|MYEOV_ENST00000441339.2_Missense_Mutation_p.L269P	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	269										endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|urinary_tract(1)	24	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		GTTGAGGCCCTGGGGGGGTGG	0.677																																					p.L269P		Atlas-SNP	.											.,1	MYEOV	42	.	0			c.T806C						.						46	49	48					11																	69063723		2200	4294	6494	SO:0001583	missense	26579	exon3			AGGCCCTGGGGGG	AJ223366	CCDS8190.1, CCDS73340.1	11q13.2	2013-03-27	2013-03-27			ENSG00000172927			7563	protein-coding gene	gene with protein product		605625	"myeloma overexpressed (in a subset of t(11;14) positive multiple myelomas)"			10753852	Standard	XM_005273908		Approved	OCIM	uc001oov.3	Q96EZ4		ENST00000308946.3:c.806T>C	chr11.hg19:g.69063723T>C	ENSP00000308330:p.Leu269Pro	86.0	2.0		145.0	8.0	NM_138768	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	hg19	CCDS8190.1	.	.	.	.	.	.	.	.	.	.	T	2.171	-0.389831	0.04932	.	.	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.27402	1.68;1.68;1.67	1.59	-3.17	0.05202	.	.	.	.	.	T	0.13200	0.0320	N	0.08118	0	0.09310	N	1	P	0.47910	0.902	B	0.41135	0.348	T	0.16335	-1.0406	9	0.87932	D	0	.	4.1225	0.10112	0.1762:0.0:0.3642:0.4596	.	269	Q96EZ4	MYEOV_HUMAN	P	269;269;211	ENSP00000412482:L269P;ENSP00000308330:L269P;ENSP00000438100:L211P	ENSP00000308330:L269P	L	+	2	0	MYEOV	68820299	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.789000	0.04609	-2.394000	0.00583	-2.303000	0.00259	CTG	.	.		0.677	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1			C	69063723	T	C	69063723	3	2	112	1	0	0	0	0	1	0	0	0	10034	1580	55	2	812	2	MYEOV	11	69063723	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1661350	69063723	65942793	712	17333										
RNF121	55298	hgsc.bcm.edu	37	chr11	71671841	71671841	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagcaccgtggccatgaagcTatgcatgctgaaatggtcct	11	10	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:71671841T>C	ENST00000361756.3	+	3	508	c.147T>C	c.(145-147)gcT>gcC	p.A49A	RNF121_ENST00000545854.1_5'UTR|RNF121_ENST00000490867.1_3'UTR|RNF121_ENST00000393713.3_Silent_p.A17A|RNF121_ENST00000533380.1_Silent_p.A17A|RNF121_ENST00000530137.1_Silent_p.A17A	NM_018320.4	NP_060790.2	Q9H920	RN121_HUMAN	ring finger protein 121	49						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|urinary_tract(1)	13						GCCATGAAGCTATGCATGCTG	0.552																																					p.A49A		Atlas-SNP	.											.	RNF121	19	.	0			c.T147C						.						143	102	116					11																	71671841		2200	4293	6493	SO:0001819	synonymous_variant	55298	exon3			TGAAGCTATGCAT	AK001961	CCDS8203.1, CCDS73343.1	11q13.3	2008-02-05			ENSG00000137522	ENSG00000137522		"RING-type (C3HC4) zinc fingers"	21070	protein-coding gene	gene with protein product							Standard	NM_018320		Approved	FLJ11099	uc001ora.3	Q9H920	OTTHUMG00000157023	ENST00000361756.3:c.147T>C	chr11.hg19:g.71671841T>C		85.0	0.0		119.0	5.0	NM_018320	B3KSW8|Q6IA57|Q6P449|Q96DB4	Silent	SNP	ENST00000361756.3	hg19	CCDS8203.1																																																																																			.	.		0.552	RNF121-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347132.1	NM_018320		C	71671841	T	C	71671841	2	2	112	1	0	0	0	0	0	0	0	1	13446	1509	53	2		2	RNF121	11	71671841	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2608118	71671841	63334675	713	17334										
PRKRIR	5612	hgsc.bcm.edu	37	chr11	76066662	76066662	+	Splice_Site	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcattaacactatcacttacTttttttctgtttcagtgtcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76066662delT	ENST00000260045.3	-	4	460	c.355delA	c.(355-357)att>tt	p.I119fs	PRKRIR_ENST00000531878.1_5'UTR	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	119					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						TATCACTTACTTTTTTTCTGT	0.318																																					.		Atlas-INDEL	.											.	PRKRIR	65	.	0			c.355+1A>-						.						172	157	162					11																	76066662		2196	4291	6487	SO:0001630	splice_region_variant	5612	exon5			.	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"THAP (C2CH-type zinc finger) domain containing"	9440	protein-coding gene	gene with protein product	"THAP domain containing 12"	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.355+1A>-	chr11.hg19:g.76066662delT		82.0	0.0		120.0	12.0	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Splice_Site	DEL	ENST00000260045.3	hg19	CCDS8243.1																																																																																			.	.		0.318	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705	Frame_Shift_Del	-	76066662	T	-	76066662	8	5	112	1	0	1	0	1	0	0	1	0	12538	1623	56	0	1938	0	PRKRIR	11	76066662	Splice_Site	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	4394821	76066662	58939854	714	17335										
C11orf30	56946	hgsc.bcm.edu	37	chr11	76255832	76255832	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccccagagccaaatgtcgcTcccagcttcttcagagaaac	7	16	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76255832T>C	ENST00000529032.1	+	18	3239	c.3239T>C	c.(3238-3240)cTc>cCc	p.L1080P	C11orf30_ENST00000525919.1_Missense_Mutation_p.L1081P|C11orf30_ENST00000524767.1_Missense_Mutation_p.L1095P|C11orf30_ENST00000334736.3_Missense_Mutation_p.L1080P|C11orf30_ENST00000524490.1_Missense_Mutation_p.L982P|C11orf30_ENST00000525038.1_Missense_Mutation_p.L1081P|C11orf30_ENST00000343878.3_Missense_Mutation_p.L1080P|C11orf30_ENST00000533248.1_Missense_Mutation_p.L989P			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	1080	Gln-rich.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						CAAATGTCGCTCCCAGCTTCT	0.478																																					p.L1080P		Atlas-SNP	.											.	C11orf30	123	.	0			c.T3239C						.						64	77	73					11																	76255832		2200	4292	6492	SO:0001583	missense	56946	exon19			TGTCGCTCCCAGC	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.3239T>C	chr11.hg19:g.76255832T>C	ENSP00000432327:p.Leu1080Pro	55.0	0.0		63.0	4.0	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Missense_Mutation	SNP	ENST00000529032.1	hg19	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.121128	0.37436	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000343878;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032;ENST00000532719	.	.	.	5.24	4.1	0.47936	.	0.183972	0.49916	D	0.000136	T	0.53786	0.1818	N	0.19112	0.55	0.58432	D	0.999998	D;P;P;D;D;D;D	0.69078	0.996;0.94;0.94;0.99;0.976;0.997;0.976	D;P;P;P;P;P;P	0.67725	0.953;0.462;0.462;0.836;0.454;0.879;0.454	T	0.50923	-0.8770	9	0.36615	T	0.2	-1.3643	11.4725	0.50278	0.1349:0.0:0.0:0.8651	.	989;1081;1095;434;1081;982;1080	B7ZKT8;B7ZKU2;B7ZKU0;B3KWW8;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;.;EMSY_HUMAN	P	982;1080;1080;762;1095;989;1081;1081;1080;220	.	ENSP00000334130:L1080P	L	+	2	0	C11orf30	75933480	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.574000	0.53863	0.815000	0.34398	0.383000	0.25322	CTC	.	.		0.478	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193		C	76255832	T	C	76255832	3	2	112	1	0	0	0	0	1	0	0	0	1638	1551	54	2	3309	2	C11orf30	11	76255832	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	189170	76255832	58750684	715	17336										
C11orf30	56946	hgsc.bcm.edu	37	chr11	76257129	76257129	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctggtgaagcaggatcattaCcctccacccacatggtggtg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76257129delC	ENST00000529032.1	+	19	3562	c.3562delC	c.(3562-3564)cccfs	p.P1188fs	C11orf30_ENST00000525919.1_Frame_Shift_Del_p.P1189fs|C11orf30_ENST00000524767.1_Frame_Shift_Del_p.P1203fs|C11orf30_ENST00000334736.3_Frame_Shift_Del_p.P1188fs|C11orf30_ENST00000524490.1_Frame_Shift_Del_p.P1090fs|C11orf30_ENST00000525038.1_Frame_Shift_Del_p.P1189fs|C11orf30_ENST00000343878.3_Intron|C11orf30_ENST00000533248.1_Frame_Shift_Del_p.P1097fs			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	1188					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						AGGATCATTACCCTCCACCCA	0.502																																					p.L1187fs		Atlas-INDEL	.											.	C11orf30	123	.	0			c.3561delA						.						89	89	89					11																	76257129		2200	4292	6492	SO:0001589	frameshift_variant	56946	exon20			.	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.3562delC	chr11.hg19:g.76257129delC	ENSP00000432327:p.Pro1188fs	139.0	0.0		178.0	11.0	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Frame_Shift_Del	DEL	ENST00000529032.1	hg19	CCDS8244.1																																																																																			.	.		0.502	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193		-	76257129	C	-	76257129	7	5	112	1	0	1	0	1	0	0	0	0	1638	507	18	0	3636	0	C11orf30	11	76257129	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1297	76257129	58749387	716	17337										
LRRC32	2615	hgsc.bcm.edu	37	chr11	76370772	76370772	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgaggttgatgttcttcagtCcccccttctcacagtcctca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76370772delC	ENST00000407242.2	-	3	2107	c.1865delG	c.(1864-1866)ggafs	p.G622fs	AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000260061.5_Frame_Shift_Del_p.G622fs|LRRC32_ENST00000464145.1_Intron|LRRC32_ENST00000404995.1_Frame_Shift_Del_p.G622fs	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	622					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cytokine secretion (GO:0050710)|positive regulation of gene expression (GO:0010628)	integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						GTTCTTCAGTCCCCCCTTCTC	0.622																																					p.G622fs		Atlas-INDEL	.											.	LRRC32	74	.	0			c.1866delA						.						145	132	136					11																	76370772		2200	4292	6492	SO:0001589	frameshift_variant	2615	exon3			.	Z24680	CCDS8245.1	11q13.5-q14	2008-02-05	2005-02-25	2005-02-25	ENSG00000137507	ENSG00000137507			4161	protein-coding gene	gene with protein product		137207	"glycoprotein A repetitions predominant"	D11S833E, GARP		8180135, 1543912	Standard	NM_005512		Approved		uc001oxq.4	Q14392	OTTHUMG00000133687	ENST00000407242.2:c.1865delG	chr11.hg19:g.76370772delC	ENSP00000384126:p.Gly622fs	93.0	0.0		137.0	12.0	NM_001128922	Q86V06	Frame_Shift_Del	DEL	ENST00000407242.2	hg19	CCDS8245.1																																																																																			.	.		0.622	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512		-	76370772	C	-	76370772	7	5	112	1	0	1	0	1	0	0	0	0	8996	855	30	0	127	0	LRRC32	11	76370772	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	113643	76370772	58635744	717	17338										
TSKU	25987	hgsc.bcm.edu	37	chr11	76507185	76507185	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attcaccgcctcgtgccccaCcccacgagggccggcctgcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76507185delC	ENST00000527881.1	+	2	1551	c.525delC	c.(523-525)cacfs	p.H175fs	TSKU_ENST00000333090.4_Frame_Shift_Del_p.H175fs			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	175					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					TCGTGCCCCACCCCACGAGGG	0.672																																					p.H175fs		Atlas-INDEL	.											.	TSKU	26	.	0			c.524delA						.						63	72	69					11																	76507185		2200	4292	6492	SO:0001589	frameshift_variant	25987	exon2			.	AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"leucine rich repeat containing 54", "tsukushin", "tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.525delC	chr11.hg19:g.76507185delC	ENSP00000434847:p.His175fs	102.0	0.0		159.0	10.0	NM_015516	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Frame_Shift_Del	DEL	ENST00000527881.1	hg19	CCDS8246.1																																																																																			.	.		0.672	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516		-	76507185	C	-	76507185	7	5	112	1	0	1	0	1	0	0	0	0	16642	506	18	0	527	0	TSKU	11	76507185	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	136413	76507185	58499331	718	17339										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76867058	76867058	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acaagaagattggggagatgCccccccacatctttgccatt					rs377214759		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76867058delC	ENST00000409709.3	+	5	663	c.391delC	c.(391-393)cccfs	p.P132fs	MYO7A_ENST00000409893.1_Frame_Shift_Del_p.P132fs|MYO7A_ENST00000409619.2_Frame_Shift_Del_p.P121fs|MYO7A_ENST00000458637.2_Frame_Shift_Del_p.P132fs	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	132	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TGGGGAGATGCCCCCCCACAT	0.567																																					p.M130fs		Atlas-INDEL	.											.,1	MYO7A	164	.	0			c.390delG						.						49	52	51					11																	76867058		2076	4226	6302	SO:0001589	frameshift_variant	4647	exon5			.	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.391delC	chr11.hg19:g.76867058delC	ENSP00000386331:p.Pro132fs	92.0	0.0		139.0	11.0	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Frame_Shift_Del	DEL	ENST00000409709.3	hg19	CCDS53683.1																																																																																			.	.		0.567	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		-	76867058	C	-	76867058	7	5	112	1	0	1	0	1	0	0	0	0	10091	739	26	0	405	0	MYO7A	11	76867058	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	359873	76867058	58139458	719	17340										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76917218	76917218	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaccacccagattttccacAaagtctacttccctgatgac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76917218delA	ENST00000409709.3	+	41	5985	c.5713delA	c.(5713-5715)aaafs	p.K1905fs	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Frame_Shift_Del_p.K1856fs|MYO7A_ENST00000458637.2_Frame_Shift_Del_p.K1867fs	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1905	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GATTTTCCACAAAGTCTACTT	0.602																																					p.H1904fs		Atlas-INDEL	.											.	MYO7A	164	.	0			c.5712delC						.						79	90	87					11																	76917218		2009	4162	6171	SO:0001589	frameshift_variant	4647	exon41			.	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.5713delA	chr11.hg19:g.76917218delA	ENSP00000386331:p.Lys1905fs	88.0	0.0		127.0	10.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Frame_Shift_Del	DEL	ENST00000409709.3	hg19	CCDS53683.1																																																																																			.	.		0.602	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		-	76917218	A	-	76917218	7	5	112	1	0	1	0	1	0	0	0	0	10091	131	5	0	5905	0	MYO7A	11	76917218	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	50160	76917218	58089298	720	17341										
NARS2	79731	hgsc.bcm.edu	37	chr11	78154722	78154722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtacctggctaagcgctccTctaagaaatggtatcgttct	9	10	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:78154722T>C	ENST00000281038.5	-	12	1622	c.1247A>G	c.(1246-1248)gAg>gGg	p.E416G	RP11-452H21.1_ENST00000534168.1_RNA|NARS2_ENST00000528850.1_Missense_Mutation_p.E189G	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	416					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	TAAGCGCTCCTCTAAGAAATG	0.438																																					p.E416G		Atlas-SNP	.											.	NARS2	62	.	0			c.A1247G						.						96	91	92					11																	78154722		2200	4292	6492	SO:0001583	missense	79731	exon12			CGCTCCTCTAAGA	BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"Aminoacyl tRNA synthetases / Class II"	26274	protein-coding gene	gene with protein product	"asparagine tRNA ligase 2, mitochondrial (putative)"	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.1247A>G	chr11.hg19:g.78154722T>C	ENSP00000281038:p.Glu416Gly	75.0	0.0		82.0	4.0	NM_024678	G3V178	Missense_Mutation	SNP	ENST00000281038.5	hg19	CCDS8261.1	.	.	.	.	.	.	.	.	.	.	T	15.87	2.961013	0.53400	.	.	ENSG00000137513	ENST00000281038;ENST00000528850	T;T	0.80480	-1.38;-1.38	4.96	3.8	0.43715	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.452209	0.27572	N	0.018770	D	0.83275	0.5219	M	0.86953	2.85	0.38088	D	0.93686	P	0.39920	0.695	B	0.41374	0.355	D	0.85761	0.1349	10	0.59425	D	0.04	-7.8818	12.1094	0.53830	0.0:0.0:0.1439:0.8561	.	416	Q96I59	SYNM_HUMAN	G	416;189	ENSP00000281038:E416G;ENSP00000432635:E189G	ENSP00000281038:E416G	E	-	2	0	NARS2	77832370	0.891000	0.30450	1.000000	0.80357	0.991000	0.79684	3.084000	0.50143	0.992000	0.38840	0.482000	0.46254	GAG	.	.		0.438	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		C	78154722	T	C	78154722	3	2	112	1	0	0	0	0	1	0	0	0	10180	1551	54	2	198	2	NARS2	11	78154722	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1237504	78154722	56851794	721	17342										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78423720	78423720	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggaagacggccccactcatGgggtctgtggccaggtagta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:78423720delG	ENST00000278550.7	-	26	4323	c.3861delC	c.(3859-3861)cccfs	p.P1287fs		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1287					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CCCCACTCATGGGGTCTGTGG	0.502																																					p.M1288X		Atlas-INDEL	.											.	.	.	.	0			c.3862delA						.						54	55	55					11																	78423720		1887	4099	5986	SO:0001589	frameshift_variant	26011	exon26			.	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.3861delC	chr11.hg19:g.78423720delG	ENSP00000278550:p.Pro1287fs	77.0	0.0		148.0	10.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Frame_Shift_Del	DEL	ENST00000278550.7	hg19	CCDS44688.1																																																																																			.	.		0.502	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			-	78423720	G	-	78423720	7	5	112	1	0	1	0	1	0	0	0	0	10846	1335	47	0	4484	0	ODZ4	11	78423720	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	268998	78423720	56582796	722	17343										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78614323	78614323	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggccgcgcacctggtctccaGggggatgttgctgttgagca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:78614323delG	ENST00000278550.7	-	7	1201	c.739delC	c.(739-741)ctgfs	p.L247fs		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	247	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CTGGTCTCCAGGGGGATGTTG	0.721																																					p.L247fs		Atlas-INDEL	.											.	.	.	.	0			c.740delT						.						10	14	12					11																	78614323		689	1588	2277	SO:0001589	frameshift_variant	26011	exon7			.	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.739delC	chr11.hg19:g.78614323delG	ENSP00000278550:p.Leu247fs	94.0	0.0		165.0	10.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Frame_Shift_Del	DEL	ENST00000278550.7	hg19	CCDS44688.1																																																																																			.	.		0.721	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			-	78614323	G	-	78614323	7	5	112	1	0	1	0	1	0	0	0	0	10846	991	35	0	7682	0	ODZ4	11	78614323	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	190603	78614323	56392193	723	17344										
PCF11	51585	hgsc.bcm.edu	37	chr11	82877693	82877693	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cactgaaccaaaggagaatgTagaaaactggcaaagttcca	9	8	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:82877693T>C	ENST00000298281.4	+	5	2206	c.1754T>C	c.(1753-1755)gTa>gCa	p.V585A		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	585					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AAGGAGAATGTAGAAAACTGG	0.393																																					p.V585A		Atlas-SNP	.											.	PCF11	220	.	0			c.T1754C						.						67	66	66					11																	82877693		1815	4038	5853	SO:0001583	missense	51585	exon5			AGAATGTAGAAAA	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1754T>C	chr11.hg19:g.82877693T>C	ENSP00000298281:p.Val585Ala	100.0	0.0		122.0	58.0	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	T	4.321	0.058962	0.08339	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.50548	1.75;0.74;0.76	6.07	6.07	0.98685	.	0.819345	0.10731	N	0.640597	T	0.28797	0.0714	N	0.08118	0	0.09310	N	0.999999	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.001	T	0.15578	-1.0432	9	.	.	.	.	11.1894	0.48677	0.0:0.0761:0.0:0.9239	.	585;585	E9PQ01;O94913	.;PCF11_HUMAN	A	585	ENSP00000298281:V585A;ENSP00000434540:V585A;ENSP00000431567:V585A	.	V	+	2	0	PCF11	82555341	1.000000	0.71417	0.653000	0.29593	0.954000	0.61252	4.381000	0.59587	2.326000	0.78906	0.533000	0.62120	GTA	.	.		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		C	82877693	T	C	82877693	3	2	112	1	0	0	0	0	1	0	0	0	11582	1638	57	2	1772	2	PCF11	11	82877693	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4263370	82877693	52128823	724	17345										
CCDC83	220047	hgsc.bcm.edu	37	chr11	85622356	85622356	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggaaggaagttgaagaattAaaaaatgctattcatgaact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:85622356delA	ENST00000342404.3	+	8	921	c.705delA	c.(703-705)ttafs	p.L235fs	CCDC83_ENST00000280245.4_Frame_Shift_Del_p.L235fs|CCDC83_ENST00000376067.1_Frame_Shift_Del_p.L136fs|CCDC83_ENST00000529676.2_3'UTR			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	235										breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				TTGAAGAATTAAAAAATGCTA	0.338																																					p.L235X		Atlas-INDEL	.											.	CCDC83	48	.	0			c.704delT						.						101	112	108					11																	85622356		2203	4299	6502	SO:0001589	frameshift_variant	220047	exon8			.	AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.705delA	chr11.hg19:g.85622356delA	ENSP00000344512:p.Leu235fs	133.0	0.0		182.0	11.0	NM_173556	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Frame_Shift_Del	DEL	ENST00000342404.3	hg19																																																																																				.	.		0.338	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556		-	85622356	A	-	85622356	7	5	112	1	0	1	0	1	0	0	0	0	2859	359	13	0	731	0	CCDC83	11	85622356	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2744663	85622356	49384160	725	17346										
NAALAD2	10003	hgsc.bcm.edu	37	chr11	89883695	89883695	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcgcactgaagactttttcAaactagaaagagagatgggc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:89883695delA	ENST00000534061.1	+	5	759	c.529delA	c.(529-531)aaafs	p.K177fs	NAALAD2_ENST00000321955.4_Frame_Shift_Del_p.K177fs|NAALAD2_ENST00000375944.3_Frame_Shift_Del_p.K177fs|NAALAD2_ENST00000525171.1_Frame_Shift_Del_p.K177fs	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	177					neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				AGACTTTTTCAAACTAGAAAG	0.299																																					p.F176fs		Atlas-INDEL	.											.	NAALAD2	113	.	0			c.528delC						.						87	93	91					11																	89883695		2201	4299	6500	SO:0001589	frameshift_variant	10003	exon5			.	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.529delA	chr11.hg19:g.89883695delA	ENSP00000432481:p.Lys177fs	136.0	0.0		166.0	11.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Frame_Shift_Del	DEL	ENST00000534061.1	hg19	CCDS8288.1																																																																																			.	.		0.299	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		-	89883695	A	-	89883695	7	5	112	1	0	1	0	1	0	0	0	0	10137	131	5	0	547	0	NAALAD2	11	89883695	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4261339	89883695	45122821	726	17347										
CCDC67	159989	hgsc.bcm.edu	37	chr11	93104240	93104240	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accaaactcaactaaatggtAaaaaacagtgcttagaagac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:93104240delA	ENST00000298050.3	+	7	683	c.583delA	c.(583-585)aaafs	p.K196fs		NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	196					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				ACTAAATGGTAAAAAACAGTG	0.333																																					p.G194fs		Atlas-INDEL	.											.,1	CCDC67	57	.	0			c.582delT						.						58	55	56					11																	93104240		1821	4083	5904	SO:0001589	frameshift_variant	159989	exon7			.	AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.583delA	chr11.hg19:g.93104240delA	ENSP00000298050:p.Lys196fs	152.0	0.0		241.0	16.0	NM_181645	Q8NEF1|Q96LL7	Frame_Shift_Del	DEL	ENST00000298050.3	hg19	CCDS44707.1																																																																																			.	.		0.333	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645		-	93104240	A	-	93104240	7	5	112	1	0	1	0	1	0	0	0	0	2841	363	13	0	605	0	CCDC67	11	93104240	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3220545	93104240	41902276	727	17348										
C11orf54	28970	hgsc.bcm.edu	37	chr11	93492928	93492928	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctgcagaattttcttcctgCcccttgaactctgatgaaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:93492928delC	ENST00000331239.4	+	8	857	c.678delC	c.(676-678)tgcfs	p.C226fs	C11orf54_ENST00000540113.1_Frame_Shift_Del_p.C207fs|C11orf54_ENST00000528099.1_Frame_Shift_Del_p.C226fs|C11orf54_ENST00000354421.3_Frame_Shift_Del_p.C226fs|C11orf54_ENST00000528288.1_Frame_Shift_Del_p.C176fs			Q9H0W9	CK054_HUMAN	chromosome 11 open reading frame 54	226					metabolic process (GO:0008152)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(5)	8		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TTTCTTCCTGCCCCTTGAACT	0.303																																					p.C176fs		Atlas-INDEL	.											.	C11orf54	23	.	0			c.527delG						.						126	137	133					11																	93492928		2201	4298	6499	SO:0001589	frameshift_variant	28970	exon7			.	AF092133	CCDS8294.1, CCDS66204.1, CCDS73365.1, CCDS73366.1	11q21	2012-08-09			ENSG00000182919	ENSG00000182919			30204	protein-coding gene	gene with protein product		615810				16522806	Standard	NM_014039		Approved	PTD012	uc001pef.3	Q9H0W9	OTTHUMG00000167452	ENST00000331239.4:c.678delC	chr11.hg19:g.93492928delC	ENSP00000331209:p.Cys226fs	102.0	0.0		165.0	11.0	NM_014039	A8K850|Q6FI88|Q6XYB0|Q96EI3|Q96IX1|Q9Y6B4	Frame_Shift_Del	DEL	ENST00000331239.4	hg19																																																																																				.	.		0.303	C11orf54-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394671.1	NM_014039		-	93492928	C	-	93492928	7	5	112	1	0	1	0	1	0	0	0	0	1651	747	26	0	550	0	C11orf54	11	93492928	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	388688	93492928	41513588	728	17349										
PANX1	24145	hgsc.bcm.edu	37	chr11	93912932	93912932	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctgggctattacttcagccTctcctcactctcagacgagt	7	15	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:93912932T>C	ENST00000227638.3	+	4	1095	c.710T>C	c.(709-711)cTc>cCc	p.L237P	PANX1_ENST00000436171.2_Missense_Mutation_p.L237P	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	237					calcium ion transport (GO:0006816)|cation transport (GO:0006812)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|protein hexamerization (GO:0034214)|response to ATP (GO:0033198)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	bleb (GO:0032059)|endoplasmic reticulum (GO:0005783)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium channel activity (GO:0005262)|gap junction hemi-channel activity (GO:0055077)|leak channel activity (GO:0022840)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Probenecid(DB01032)	TACTTCAGCCTCTCCTCACTC	0.448																																					p.L237P		Atlas-SNP	.											.	PANX1	38	.	0			c.T710C						.						124	110	115					11																	93912932		2201	4298	6499	SO:0001583	missense	24145	exon4			TCAGCCTCTCCTC	AF093239	CCDS8296.1	11q14-q21	2011-12-02			ENSG00000110218	ENSG00000110218		"Ion channels / Pannexins"	8599	protein-coding gene	gene with protein product	"innexin"	608420				14597722	Standard	NM_015368		Approved	MRS1, UNQ2529, PX1	uc001per.3	Q96RD7	OTTHUMG00000167757	ENST00000227638.3:c.710T>C	chr11.hg19:g.93912932T>C	ENSP00000227638:p.Leu237Pro	90.0	0.0		117.0	7.0	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Missense_Mutation	SNP	ENST00000227638.3	hg19	CCDS8296.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.312663	0.60414	.	.	ENSG00000110218	ENST00000227638;ENST00000436171	T;T	0.20598	2.07;2.06	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	M	0.83483	2.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.49643	-0.8918	10	0.35671	T	0.21	-30.008	16.0852	0.81042	0.0:0.0:0.0:1.0	.	237;237	Q96RD7;Q96RD7-2	PANX1_HUMAN;.	P	237	ENSP00000227638:L237P;ENSP00000411461:L237P	ENSP00000227638:L237P	L	+	2	0	PANX1	93552580	1.000000	0.71417	0.949000	0.38748	0.564000	0.35744	7.538000	0.82048	2.279000	0.76181	0.533000	0.62120	CTC	.	.		0.448	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368		C	93912932	T	C	93912932	3	2	112	1	0	0	0	0	1	0	0	0	11429	1551	54	2	724	2	PANX1	11	93912932	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	420004	93912932	41093584	729	17350										
BIRC2	329	hgsc.bcm.edu	37	chr11	102221110	102221110	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atctcttcatcgaggactaaCccctacagttatgcaatgag					rs139349997		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:102221110delC	ENST00000227758.2	+	2	1924	c.525delC	c.(523-525)aacfs	p.N175fs	BIRC2_ENST00000530675.1_Frame_Shift_Del_p.N126fs|BIRC2_ENST00000532672.1_Frame_Shift_Del_p.N154fs|BIRC2_ENST00000527910.1_3'UTR	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	175					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		CGAGGACTAACCCCTACAGTT	0.423																																					p.N175fs		Atlas-INDEL	.											.	BIRC2	51	.	0			c.524delA						.						128	125	126					11																	102221110		2203	4299	6502	SO:0001589	frameshift_variant	329	exon2			.	L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	590	protein-coding gene	gene with protein product	"NFR2-TRAF signalling complex protein", "apoptosis inhibitor 1"	601712	"baculoviral IAP repeat-containing 2"	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.525delC	chr11.hg19:g.102221110delC	ENSP00000227758:p.Asn175fs	85.0	0.0		133.0	11.0	NM_001256163	B4E026|Q16516|Q4TTG0	Frame_Shift_Del	DEL	ENST00000227758.2	hg19	CCDS8316.1																																																																																			.	.		0.423	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166		-	102221110	C	-	102221110	7	5	112	1	0	1	0	1	0	0	0	0	1435	506	18	0	527	0	BIRC2	11	102221110	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	8308178	102221110	32785406	730	17351										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	102991458	102991458	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtctcaatatgaaaagattaTtgcacctgcggaacaaaaaa	7	7	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:102991458T>C	ENST00000375735.2	+	8	1319	c.1175T>C	c.(1174-1176)aTt>aCt	p.I392T	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.I392T|DYNC2H1_ENST00000334267.7_Missense_Mutation_p.I392T	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	392	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GAAAAGATTATTGCACCTGCG	0.308																																					p.I392T		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T1175C						.						37	36	36					11																	102991458		1807	4061	5868	SO:0001583	missense	79659	exon8			AGATTATTGCACC	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.1175T>C	chr11.hg19:g.102991458T>C	ENSP00000364887:p.Ile392Thr	38.0	0.0		72.0	4.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	18.15	3.560736	0.65538	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.56776	0.44;0.44;0.44	5.2	4.08	0.47627	Dynein heavy chain, domain-1 (1);	0.537912	0.15256	U	0.272042	T	0.66416	0.2787	M	0.73598	2.24	0.53688	D	0.999979	B;P;P	0.41188	0.084;0.741;0.734	B;P;P	0.53809	0.022;0.735;0.617	T	0.66460	-0.5918	10	0.87932	D	0	.	10.8046	0.46509	0.0:0.0744:0.0:0.9256	.	392;392;392	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	T	392	ENSP00000364887:I392T;ENSP00000334021:I392T;ENSP00000381167:I392T	ENSP00000334021:I392T	I	+	2	0	DYNC2H1	102496668	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.790000	0.62453	0.939000	0.37446	0.528000	0.53228	ATT	.	.		0.308	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	102991458	T	C	102991458	3	2	112	1	0	0	0	0	1	0	0	0	4848	1493	52	2	1205	2	DYNC2H1	11	102991458	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	770348	102991458	32015058	731	17352										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103153740	103153740	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aattgcttttattaaaggacTctcaacaaaaaatacgtgat	5	6	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:103153740T>C	ENST00000375735.2	+	73	10960	c.10816T>C	c.(10816-10818)Tct>Cct	p.S3606P	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.S3613P|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3606					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		ATTAAAGGACTCTCAACAAAA	0.313																																					p.S3613P		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10837C						.						60	59	59					11																	103153740		1810	4063	5873	SO:0001583	missense	79659	exon74			AAGGACTCTCAAC	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.10816T>C	chr11.hg19:g.103153740T>C	ENSP00000364887:p.Ser3606Pro	81.0	0.0		175.0	7.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	11.75	1.732659	0.30684	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.28454	1.61;1.61	5.14	2.55	0.30701	.	0.647467	0.15994	N	0.234658	T	0.34716	0.0907	L	0.40543	1.245	0.37071	D	0.898524	P;P	0.52316	0.952;0.941	P;P	0.54815	0.761;0.648	T	0.18935	-1.0321	10	0.28530	T	0.3	.	9.7604	0.40528	0.272:0.0:0.0:0.728	.	3606;3613	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	P	3606;3613	ENSP00000364887:S3606P;ENSP00000381167:S3613P	ENSP00000364887:S3606P	S	+	1	0	DYNC2H1	102658950	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.010000	0.40913	0.842000	0.35045	0.377000	0.23210	TCT	.	.		0.313	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103153740	T	C	103153740	3	2	112	1	0	0	0	0	1	0	0	0	4848	1551	54	2	11131	2	DYNC2H1	11	103153740	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	162282	103153740	31852776	732	17353										
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110454273	110454273	+	Splice_Site	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaatgaaaaacttcattaccTtttttgtaaattcgttttct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:110454273delT	ENST00000260283.4	-	14	1888	c.1604delA	c.(1603-1605)aag>ag	p.K535fs	ARHGAP20_ENST00000357139.3_Splice_Site_p.K509fs|ARHGAP20_ENST00000529591.1_Splice_Site_p.K78fs|ARHGAP20_ENST00000533353.1_Splice_Site_p.K509fs|ARHGAP20_ENST00000527598.1_Splice_Site_p.K499fs|ARHGAP20_ENST00000528829.1_Splice_Site_p.K499fs|ARHGAP20_ENST00000524756.1_Splice_Site_p.K512fs	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	535	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		CTTCATTACCTTTTTTGTAAA	0.368																																					p.K535fs		Atlas-INDEL	.											.	ARHGAP20	150	.	0			c.1605delG						.						80	76	77					11																	110454273		2201	4298	6499	SO:0001630	splice_region_variant	57569	exon14			.	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.1605+1A>-	chr11.hg19:g.110454273delT		90.0	0.0		141.0	10.0	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Frame_Shift_Del	DEL	ENST00000260283.4	hg19	CCDS31673.1																																																																																			.	.		0.368	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809	Frame_Shift_Del	-	110454273	T	-	110454273	8	5	112	1	0	1	0	1	0	0	1	0	870	1623	56	0	1983	0	ARHGAP20	11	110454273	Splice_Site	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	7300533	110454273	24552243	733	17354										
POU2AF1	5450	hgsc.bcm.edu	37	chr11	111225126	111225126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaggactggctctgggatagAgatggggagctggacaaact	16	6	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:111225126A>G	ENST00000393067.3	-	5	1145	c.631T>C	c.(631-633)Tct>Cct	p.S211P		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	211					humoral immune response (GO:0006959)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(2)|lung(2)	5		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		TCTGGGATAGAGATGGGGAGC	0.622			T	BCL6	NHL																																p.S211P		Atlas-SNP	.		Dom	yes		11	11q23.1	5450	"POU domain, class 2, associating factor 1 (OBF1)"		L	.	POU2AF1	23	.	0			c.T631C						.						55	58	57					11																	111225126		2201	4297	6498	SO:0001583	missense	5450	exon5			GGATAGAGATGGG		CCDS31675.1	11q23.1	2011-06-01	2007-07-13			ENSG00000110777			9211	protein-coding gene	gene with protein product		601206	"POU domain class 2, associating factor 1"			8617501	Standard	NM_006235		Approved	OBF1	uc001plg.4	Q16633		ENST00000393067.3:c.631T>C	chr11.hg19:g.111225126A>G	ENSP00000376786:p.Ser211Pro	155.0	0.0		199.0	8.0	NM_006235	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	hg19	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.167841	0.78339	.	.	ENSG00000110777	ENST00000393067	T	0.32023	1.47	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.45397	0.1340	L	0.41710	1.295	0.44880	D	0.997894	D	0.89917	1.0	D	0.91635	0.999	T	0.24584	-1.0156	10	0.33141	T	0.24	-3.9004	14.4288	0.67236	1.0:0.0:0.0:0.0	.	211	Q16633	OBF1_HUMAN	P	211	ENSP00000376786:S211P	ENSP00000376786:S211P	S	-	1	0	POU2AF1	110730336	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	4.228000	0.58619	2.067000	0.61834	0.460000	0.39030	TCT	.	.		0.622	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235		G	111225126	A	G	111225126	3	3	112	1	0	0	0	0	1	0	0	0	12279	304	11	2	143	2	POU2AF1	11	111225126	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	770853	111225126	23781390	734	17355										
SIK3	23387	hgsc.bcm.edu	37	chr11	116744713	116744713	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccacctgcaggaatggagccTgggggttgactccaggaaag	15	10	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:116744713T>C	ENST00000292055.4	-	12	1348	c.1313A>G	c.(1312-1314)cAg>cGg	p.Q438R	SIK3_ENST00000375288.1_5'UTR|SIK3_ENST00000542607.1_Missense_Mutation_p.Q390R|SIK3_ENST00000446921.2_Missense_Mutation_p.Q448R|SIK3_ENST00000375300.1_Missense_Mutation_p.Q496R|SIK3_ENST00000434315.2_Missense_Mutation_p.Q337R	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	438					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						GAATGGAGCCTGGGGGTTGAC	0.478																																					p.Q438R		Atlas-SNP	.											.	SIK3	112	.	0			c.A1313G						.						99	101	100					11																	116744713		2201	4296	6497	SO:0001583	missense	23387	exon12			GGAGCCTGGGGGT	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.1313A>G	chr11.hg19:g.116744713T>C	ENSP00000292055:p.Gln438Arg	90.0	0.0		127.0	31.0	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	hg19	CCDS8379.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.506538	0.64410	.	.	ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000542607;ENST00000434315	T;T;T;T	0.72835	-0.56;-0.6;-0.69;-0.18	5.33	4.18	0.49190	Protein kinase-like domain (1);	0.000000	0.37530	U	0.002048	T	0.75287	0.3829	L	0.38531	1.155	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.75020	0.985;0.918;0.985	T	0.72679	-0.4220	10	0.36615	T	0.2	.	12.3471	0.55126	0.0:0.0:0.1415:0.8585	.	390;337;438	A1A5A8;A1A5A9;Q9Y2K2	.;.;SIK3_HUMAN	R	496;438;390;337	ENSP00000364449:Q496R;ENSP00000292055:Q438R;ENSP00000438108:Q390R;ENSP00000415873:Q337R	ENSP00000292055:Q438R	Q	-	2	0	SIK3	116249923	1.000000	0.71417	0.409000	0.26459	0.484000	0.33280	7.503000	0.81632	0.843000	0.35070	-0.321000	0.08615	CAG	.	.		0.478	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164		C	116744713	T	C	116744713	3	2	112	1	0	0	0	0	1	0	0	0	14334	1580	55	2	2526	2	SIK3	11	116744713	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	5519587	116744713	18261803	735	17356										
PAFAH1B2	5049	hgsc.bcm.edu	37	chr11	117038299	117038299	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccatctcctgccacgacatgTttgattttctgcatctgaca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:117038299delT	ENST00000527958.1	+	6	733	c.574delT	c.(574-576)tttfs	p.F192fs	PAFAH1B2_ENST00000529887.2_Intron|PAFAH1B2_ENST00000530272.1_Intron|PAFAH1B2_ENST00000526888.1_Intron|PAFAH1B2_ENST00000419197.2_Intron	NM_002572.3	NP_002563.1	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa)	192					brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|positive regulation of macroautophagy (GO:0016239)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)		CCACGACATGTTTGATTTTCT	0.532			T	IGH@	MLCLS																																p.M191fs		Atlas-INDEL	.		Dom	yes		11	11q23	5049	"platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa"		L	.	PAFAH1B2	19	.	0			c.573delG						.						84	69	74					11																	117038299		2201	4296	6497	SO:0001589	frameshift_variant	5049	exon6			.	D63390	CCDS8380.1, CCDS53713.1, CCDS53714.1, CCDS53715.1	11q23	2011-10-24	2010-02-10			ENSG00000168092			8575	protein-coding gene	gene with protein product	"PAF-AH1b alpha 2 subunit"	602508	"platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa", "platelet-activating factor acetylhydrolase, isoform Ib, subunit 2 (30kDa)"			9144386, 9693049	Standard	NM_002572		Approved		uc001pqe.2	P68402		ENST00000527958.1:c.574delT	chr11.hg19:g.117038299delT	ENSP00000435289:p.Phe192fs	123.0	0.0		171.0	11.0	NM_002572	A8DPS5|A8DPS6|A8DPS7|E9PEJ5|E9PLP3|O00687|Q29459|Q6IBR6	Frame_Shift_Del	DEL	ENST00000527958.1	hg19	CCDS8380.1																																																																																			.	.		0.532	PAFAH1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392826.1	NM_002572		-	117038299	T	-	117038299	7	5	112	1	0	1	0	1	0	0	0	0	11394	1725	60	0	592	0	PAFAH1B2	11	117038299	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	293586	117038299	17968217	736	17357										
CEP164	22897	hgsc.bcm.edu	37	chr11	117222658	117222658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taagaagaagaaaaaaaaaaAggaaaagaaagacaagaagg	10	1	0	6			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:117222658A>G	ENST00000278935.3	+	5	494	c.347A>G	c.(346-348)aAg>aGg	p.K116R		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	116	Interaction with ATRIP.|Lys-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		aaaaaaaaaaaggaaaagaaa	0.502																																					p.K116R		Atlas-SNP	.											CEP164,caecum,carcinoma,0,1	CEP164	121	.	0			c.A347G						.						33	34	34					11																	117222658		2201	4296	6497	SO:0001583	missense	22897	exon4			AAAAAAAGGAAAA	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.347A>G	chr11.hg19:g.117222658A>G	ENSP00000278935:p.Lys116Arg	38.0	0.0		70.0	6.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	hg19	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744661	0.49151	.	.	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000533570;ENST00000529538	T;T;T;T	0.76060	-0.34;-0.03;-0.29;-0.99	5.95	4.82	0.62117	.	0.243999	0.29172	N	0.012934	T	0.80221	0.4583	M	0.62723	1.935	0.34770	D	0.733632	D;P;B;D	0.56521	0.959;0.482;0.023;0.976	P;B;B;P	0.56960	0.65;0.11;0.01;0.81	D	0.85776	0.1358	10	0.62326	D	0.03	-27.2573	11.2799	0.49188	0.9276:0.0:0.0724:0.0	.	116;70;116;116	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	R	70;116;70;70;116;116	ENSP00000436034:K70R;ENSP00000278935:K116R;ENSP00000435759:K70R;ENSP00000431302:K116R	ENSP00000278935:K116R	K	+	2	0	CEP164	116727868	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.713000	0.91408	1.068000	0.40764	0.533000	0.62120	AAG	.	.		0.502	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		G	117222658	A	G	117222658	3	3	112	1	0	0	0	0	1	0	0	0	3251	72	3	2	357	2	CEP164	11	117222658	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	184359	117222658	17783858	737	17358										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117306420	117306420	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tacgatgaagagcagtgccaCccccagtgtggccaggatga					rs138082991		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:117306420delC	ENST00000321322.6	-	27	4997	c.4996delG	c.(4996-4998)gtgfs	p.V1666fs	DSCAML1_ENST00000527706.1_Frame_Shift_Del_p.V1396fs	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1606					axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		AGCAGTGCCACCCCCAGTGTG	0.577																																					p.V1666fs		Atlas-INDEL	.											.	DSCAML1	286	.	0			c.4997delT						.						129	100	110					11																	117306420		2201	4296	6497	SO:0001589	frameshift_variant	57453	exon27			.		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.4996delG	chr11.hg19:g.117306420delC	ENSP00000315465:p.Val1666fs	86.0	0.0		144.0	10.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Frame_Shift_Del	DEL	ENST00000321322.6	hg19	CCDS8384.1																																																																																			.	.		0.577	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		-	117306420	C	-	117306420	7	5	112	1	0	1	0	1	0	0	0	0	4771	507	18	0	1373	0	DSCAML1	11	117306420	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	83762	117306420	17700096	738	17359										
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117782565	117782565	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctgtgggcaacctcggttgTccggtgagcactacaaggga	14	11	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:117782565T>C	ENST00000430170.2	-	6	907	c.820A>G	c.(820-822)Aca>Gca	p.T274A	TMPRSS13_ENST00000445164.2_Missense_Mutation_p.T274A|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.T274A|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.T239A|TMPRSS13_ENST00000524993.1_Missense_Mutation_p.T274A	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	274	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		ACCTCGGTTGTCCGGTGAGCA	0.582																																					p.T274A		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.A820G						.						65	69	68					11																	117782565		1944	4141	6085	SO:0001583	missense	84000	exon6			CGGTTGTCCGGTG	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"Serine peptidases / Transmembrane"	29808	protein-coding gene	gene with protein product		610050	"transmembrane protease, serine 11"	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.820A>G	chr11.hg19:g.117782565T>C	ENSP00000387702:p.Thr274Ala	52.0	0.0		86.0	4.0	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	hg19	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336595	0.60963	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81	5.35	5.35	0.76521	.	0.366933	0.26535	N	0.023832	T	0.43964	0.1271	L	0.53729	1.69	0.39913	D	0.974055	B;B	0.33637	0.234;0.42	B;B	0.35240	0.198;0.061	T	0.39860	-0.9593	10	0.25751	T	0.34	.	12.7014	0.57035	0.0:0.0:0.0:1.0	.	269;274	Q9BYE2-4;E9PRA0	.;.	A	239;269;274;274;274;274	ENSP00000435813:T239A;ENSP00000434279:T274A;ENSP00000387702:T274A;ENSP00000394114:T274A;ENSP00000436502:T274A	ENSP00000337113:T269A	T	-	1	0	TMPRSS13	117287775	1.000000	0.71417	0.995000	0.50966	0.508000	0.34012	4.419000	0.59835	2.024000	0.59613	0.459000	0.35465	ACA	.	.		0.582	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		C	117782565	T	C	117782565	3	2	112	1	0	0	0	0	1	0	0	0	16260	1667	58	2	915	2	TMPRSS13	11	117782565	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	476145	117782565	17223951	739	17360										
MLL	4297	hgsc.bcm.edu	37	chr11	118347674	118347674	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgggaagaacgagaaaagaTtttgtcttccatggggaatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:118347674delT	ENST00000389506.5	+	4	3311	c.3311delT	c.(3310-3312)attfs	p.I1104fs	KMT2A_ENST00000534358.1_Frame_Shift_Del_p.I1104fs|KMT2A_ENST00000354520.4_Frame_Shift_Del_p.I1104fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1104					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CGAGAAAAGATTTTGTCTTCC	0.478																																					p.I1104fs		Atlas-INDEL	.											.	MLL	548	.	0			c.3310delA						.						108	100	103					11																	118347674		2200	4296	6496	SO:0001589	frameshift_variant	4297	exon4			.	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.3311delT	chr11.hg19:g.118347674delT	ENSP00000374157:p.Ile1104fs	157.0	0.0		161.0	10.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Del	DEL	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.478	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		-	118347674	T	-	118347674	7	5	112	1	0	1	0	1	0	0	0	0	9629	1493	52	0	3325	0	MLL	11	118347674	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	565109	118347674	16658842	740	17361										
ASAM	79827	hgsc.bcm.edu	37	chr11	122968546	122968546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cggtgagcagccattcaataTccagagtgtctttttctgga	10	9	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:122968546T>C	ENST00000448775.2	-	2	483	c.143A>G	c.(142-144)gAt>gGt	p.D48G		NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein	48	Ig-like C2-type 1.				digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						CCATTCAATATCCAGAGTGTC	0.502																																					p.D48G		Atlas-SNP	.											.	CLMP	39	.	0			c.A143G						.						152	147	149					11																	122968546		2202	4299	6501	SO:0001583	missense	79827	exon2			TCAATATCCAGAG	BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24039	protein-coding gene	gene with protein product	"adipocyte-specific adhesion molecule", "coxsackie- and adenovirus receptor-like membrane protein", "adipocyte adhesion molecule"	611693				12851705, 14573622	Standard	NM_024769		Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.143A>G	chr11.hg19:g.122968546T>C	ENSP00000405577:p.Asp48Gly	97.0	0.0		127.0	6.0	NM_024769		Missense_Mutation	SNP	ENST00000448775.2	hg19	CCDS8441.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.280885	0.80692	.	.	ENSG00000166250	ENST00000448775	T	0.66638	-0.22	5.34	5.34	0.76211	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.80110	0.4563	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78919	-0.2014	10	0.32370	T	0.25	.	13.8471	0.63474	0.0:0.0:0.0:1.0	.	48	Q9H6B4	CLMP_HUMAN	G	48	ENSP00000405577:D48G	ENSP00000405577:D48G	D	-	2	0	CLMP	122473756	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.069000	0.64370	2.161000	0.67846	0.379000	0.24179	GAT	.	.		0.502	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387542.1	NM_024769		C	122968546	T	C	122968546	3	2	112	1	0	0	0	0	1	0	0	0	1009	1435	50	2	1002	2	ASAM	11	122968546	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4620872	122968546	12037970	741	17362										
NTM	50863	hgsc.bcm.edu	37	chr11	132177637	132177637	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aattcagggcatcaccagggAgcagtcaggggactacgagt	14	9	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:132177637A>G	ENST00000374786.1	+	4	1060	c.581A>G	c.(580-582)gAg>gGg	p.E194G	NTM_ENST00000374791.3_Missense_Mutation_p.E194G|NTM_ENST00000474900.1_3'UTR|NTM_ENST00000539799.1_Missense_Mutation_p.E194G|NTM_ENST00000425719.2_Missense_Mutation_p.E194G|NTM_ENST00000427481.2_Missense_Mutation_p.E185G|NTM_ENST00000374784.1_Missense_Mutation_p.E194G	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	194	Ig-like C2-type 2.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						ATCACCAGGGAGCAGTCAGGG	0.527																																					p.E194G		Atlas-SNP	.											.	NTM	253	.	0			c.A581G						.						97	87	90					11																	132177637		2201	4297	6498	SO:0001583	missense	50863	exon4			CCAGGGAGCAGTC	AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"Immunoglobulin superfamily / I-set domain containing"	17941	protein-coding gene	gene with protein product	"neurotrimin", "IgLON family member 2"	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.581A>G	chr11.hg19:g.132177637A>G	ENSP00000363918:p.Glu194Gly	50.0	0.0		115.0	5.0	NM_001144059	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	hg19	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	A	12.94	2.087205	0.36855	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000550167;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T;T	0.39406	1.44;1.44;1.08;1.44;1.44;1.44;1.44	5.62	4.43	0.53597	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.089217	0.85682	D	0.000000	T	0.30603	0.0770	L	0.28776	0.89	0.52501	D	0.99995	B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B	0.15484	0.013;0.004;0.003;0.002;0.003;0.001	T	0.07404	-1.0774	10	0.22706	T	0.39	-29.9428	13.2973	0.60305	0.8689:0.1311:0.0:0.0	.	194;185;194;194;194;194	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;NTRI_HUMAN;.;.	G	194;194;185;185;194;194;194	ENSP00000363923:E194G;ENSP00000437668:E194G;ENSP00000448104:E185G;ENSP00000416320:E185G;ENSP00000363918:E194G;ENSP00000396722:E194G;ENSP00000363916:E194G	ENSP00000363916:E194G	E	+	2	0	NTM	131682847	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.007000	0.76335	2.267000	0.75376	0.383000	0.25322	GAG	.	.		0.527	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		G	132177637	A	G	132177637	3	3	112	1	0	0	0	0	1	0	0	0	10708	304	11	2	681	2	NTM	11	132177637	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	9209091	132177637	2828879	742	17363										
TEAD4	7004	hgsc.bcm.edu	37	chr12	3128311	3128311	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttctctcagcaaacctatgcTgtccagcctccgctgcctct	6	17	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:3128311T>C	ENST00000397122.2	+	6	456	c.171T>C	c.(169-171)gcT>gcC	p.A57A	TEAD4_ENST00000358409.2_Silent_p.A143A|TEAD4_ENST00000359864.2_Silent_p.A186A	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4	186					gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			AAACCTATGCTGTCCAGCCTC	0.682																																					p.A186A		Atlas-SNP	.											.	TEAD4	45	.	0			c.T558C						.						93	76	81					12																	3128311		2203	4300	6503	SO:0001819	synonymous_variant	7004	exon8			CTATGCTGTCCAG	X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561		ENST00000397122.2:c.171T>C	chr12.hg19:g.3128311T>C		115.0	0.0		92.0	5.0	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Silent	SNP	ENST00000397122.2	hg19	CCDS41737.1	.	.	.	.	.	.	.	.	.	.	T	10.85	1.467103	0.26335	.	.	ENSG00000197905	ENST00000544666	.	.	.	5.0	3.86	0.44501	.	.	.	.	.	T	0.57257	0.2041	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52071	-0.8624	4	.	.	.	0.4751	7.3544	0.26711	0.0:0.1698:0.0:0.8302	.	.	.	.	R	109	.	.	C	+	1	0	TEAD4	2998572	0.993000	0.37304	0.979000	0.43373	0.925000	0.55904	0.744000	0.26245	0.759000	0.33084	0.459000	0.35465	TGT	.	.		0.682	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213		C	3128311	T	C	3128311	2	2	112	1	0	0	0	0	0	0	0	1	15756	1567	55	2		2	TEAD4	12	3128311	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10		3128311	130723584	743	17364										
CDCA3	83461	hgsc.bcm.edu	37	chr12	6958537	6958537	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtcatcctgcaggatggtgaGgggggatctccctagtacct					rs142590132		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:6958537delG	ENST00000538862.2	-	5	1502	c.601delC	c.(601-603)ctcfs	p.L201fs	CDCA3_ENST00000422785.3_Intron|USP5_ENST00000389231.5_5'Flank|CDCA3_ENST00000604599.1_5'Flank|CDCA3_ENST00000540683.1_Intron|CDCA3_ENST00000229265.6_Frame_Shift_Del_p.L176fs|CDCA3_ENST00000535406.1_Frame_Shift_Del_p.L201fs|USP5_ENST00000229268.8_5'Flank			Q99618	CDCA3_HUMAN	cell division cycle associated 3	201					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|large_intestine(4)|lung(1)|stomach(1)	8						AGGATGGTGAGGGGGGATCTC	0.512																																					p.L201fs		Atlas-INDEL	.											.	CDCA3	17	.	0			c.602delT						.						164	158	160					12																	6958537		2203	4300	6503	SO:0001589	frameshift_variant	83461	exon5			.	BG354576	CCDS8565.1, CCDS73428.1	12p13.31	2010-07-20				ENSG00000111665			14624	protein-coding gene	gene with protein product	"trigger of mitotic entry 1"	607749				9074930, 12188893	Standard	XR_242988		Approved	TOME-1, GRCC8	uc001qrg.2	Q99618		ENST00000538862.2:c.601delC	chr12.hg19:g.6958537delG	ENSP00000442068:p.Leu201fs	247.0	0.0		200.0	13.0	NM_031299	A8K5V6|D3DUS6	Frame_Shift_Del	DEL	ENST00000538862.2	hg19	CCDS8565.1																																																																																			.	.		0.512	CDCA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401940.2	NM_031299		-	6958537	G	-	6958537	7	5	112	1	0	1	0	1	0	0	0	0	3089	1000	35	0	213	0	CDCA3	12	6958537	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	3830226	6958537	126893358	744	17365										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7527201	7527201	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcagagaccgtggcattgaaGgccactccacagcccagctt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:7527201delG	ENST00000313599.3	-	13	3303	c.3246delC	c.(3244-3246)gccfs	p.A1082fs	CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000396630.1_Frame_Shift_Del_p.A1082fs|CD163L1_ENST00000416109.2_Frame_Shift_Del_p.A1092fs			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1082	SRCR 10. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TGGCATTGAAGGCCACTCCAC	0.592											OREG0021653	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F1083fs		Atlas-INDEL	.											.	CD163L1	238	.	0			c.3247delT						.						93	83	86					12																	7527201		2203	4300	6503	SO:0001589	frameshift_variant	283316	exon13			.	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.3246delC	chr12.hg19:g.7527201delG	ENSP00000315945:p.Ala1082fs	218.0	0.0	642	163.0	10.0	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Frame_Shift_Del	DEL	ENST00000313599.3	hg19	CCDS8577.1																																																																																			.	.		0.592	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		-	7527201	G	-	7527201	7	5	112	1	0	1	0	1	0	0	0	0	2970	987	35	0	1143	0	CD163L1	12	7527201	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	568664	7527201	126324694	745	17366										
PZP	5858	hgsc.bcm.edu	37	chr12	9349247	9349247	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taatctggagcattttggtgTgtacttgttgggtgatgcag	14	4	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:9349247T>C	ENST00000261336.2	-	9	930	c.902A>G	c.(901-903)cAc>cGc	p.H301R	PZP_ENST00000381997.2_Missense_Mutation_p.H170R	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	301					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CATTTTGGTGTGTACTTGTTG	0.398																																					p.H301R	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A902G						.						146	141	143					12																	9349247		2203	4300	6503	SO:0001583	missense	5858	exon9			TTGGTGTGTACTT	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.902A>G	chr12.hg19:g.9349247T>C	ENSP00000261336:p.His301Arg	84.0	0.0		68.0	4.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	5.429	0.264282	0.10294	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.32753	1.64;1.44	3.57	2.4	0.29515	.	0.940200	0.08770	N	0.896414	T	0.10937	0.0267	N	0.01352	-0.895	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.26258	-1.0108	10	0.34782	T	0.22	.	5.8195	0.18520	0.0:0.1321:0.0:0.8679	.	170;301	P20742-2;P20742	.;PZP_HUMAN	R	301;170	ENSP00000261336:H301R;ENSP00000371427:H170R	ENSP00000261336:H301R	H	-	2	0	PZP	9240514	0.003000	0.15002	0.016000	0.15963	0.006000	0.05464	0.144000	0.16135	0.546000	0.28920	0.374000	0.22700	CAC	.	.		0.398	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		C	9349247	T	C	9349247	3	2	112	1	0	0	0	0	1	0	0	0	12884	1696	59	2	3658	2	PZP	12	9349247	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1822046	9349247	124502648	746	17367										
CLEC1B	51266	hgsc.bcm.edu	37	chr12	10147781	10147781	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catcctcccacttccagaccTcattcgacttctggcgagat	6	16	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:10147781T>C	ENST00000298527.6	-	5	682	c.503A>G	c.(502-504)gAg>gGg	p.E168G	CLEC1B_ENST00000348658.4_Missense_Mutation_p.E135G|CLEC1B_ENST00000428126.2_Missense_Mutation_p.E135G	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	168	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						CTTCCAGACCTCATTCGACTT	0.408																																					p.E168G		Atlas-SNP	.											.	CLEC1B	39	.	0			c.A503G						.						270	262	265					12																	10147781		1869	4096	5965	SO:0001583	missense	51266	exon5			CAGACCTCATTCG	AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"C-type lectin domain containing"	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.503A>G	chr12.hg19:g.10147781T>C	ENSP00000298527:p.Glu168Gly	56.0	0.0		36.0	4.0	NM_016509	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	hg19	CCDS41752.1	.	.	.	.	.	.	.	.	.	.	T	7.016	0.557656	0.13436	.	.	ENSG00000165682	ENST00000398937;ENST00000428126;ENST00000298527;ENST00000348658;ENST00000398939	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	3.83	2.78	0.32641	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.888420	0.09391	N	0.808501	T	0.05777	0.0151	N	0.05177	-0.1	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.43196	-0.9406	10	0.22109	T	0.4	.	3.0056	0.06027	0.0:0.3524:0.0:0.6476	.	135;168	Q9P126-2;Q9P126	.;CLC1B_HUMAN	G	75;135;168;135;75	ENSP00000381910:E75G;ENSP00000406338:E135G;ENSP00000298527:E168G;ENSP00000327169:E135G	ENSP00000298527:E168G	E	-	2	0	CLEC1B	10039048	0.001000	0.12720	0.001000	0.08648	0.470000	0.32858	0.827000	0.27421	0.560000	0.29169	0.248000	0.18094	GAG	.	.		0.408	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509		C	10147781	T	C	10147781	3	2	112	1	0	0	0	0	1	0	0	0	3508	1551	54	2	194	2	CLEC1B	12	10147781	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	798534	10147781	123704114	747	17368										
TAS2R8	50836	hgsc.bcm.edu	37	chr12	10958681	10958681	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggcaatttttctacatgtcAgcattctgacaaatgtctgc	7	9	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:10958681A>G	ENST00000240615.2	-	1	1211	c.899T>C	c.(898-900)cTg>cCg	p.L300P		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	300					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TCTACATGTCAGCATTCTGAC	0.318																																					p.L300P		Atlas-SNP	.											.	TAS2R8	42	.	0			c.T899C						.						27	28	28					12																	10958681		2197	4291	6488	SO:0001583	missense	50836	exon1			CATGTCAGCATTC	AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.899T>C	chr12.hg19:g.10958681A>G	ENSP00000240615:p.Leu300Pro	127.0	0.0		127.0	7.0	NM_023918	Q4KN29|Q645Y2	Missense_Mutation	SNP	ENST00000240615.2	hg19	CCDS8632.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.797846	0.31777	.	.	ENSG00000121314	ENST00000240615	T	0.01323	5.01	3.95	1.51	0.23008	.	0.699272	0.11364	N	0.571658	T	0.09291	0.0229	M	0.91768	3.24	0.09310	N	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.10520	-1.0626	10	0.87932	D	0	.	5.7189	0.17976	0.7703:0.0:0.2297:0.0	.	300	Q9NYW2	TA2R8_HUMAN	P	300	ENSP00000240615:L300P	ENSP00000240615:L300P	L	-	2	0	TAS2R8	10849948	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.519000	0.22862	0.207000	0.20607	-0.256000	0.11100	CTG	.	.		0.318	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1			G	10958681	A	G	10958681	3	3	112	1	0	0	0	0	1	0	0	0	15602	188	7	2	33	2	TAS2R8	12	10958681	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	810900	10958681	122893214	748	17369										
PLBD1	79887	hgsc.bcm.edu	37	chr12	14693776	14693776	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccatcacatagcctgtatgTctccaaaatgaatcagtctt	6	11	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:14693776T>C	ENST00000240617.5	-	4	1132	c.480A>G	c.(478-480)agA>agG	p.R160R		NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	160					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						AGCCTGTATGTCTCCAAAATG	0.393																																					p.R160R		Atlas-SNP	.											.	PLBD1	36	.	0			c.A480G						.						205	198	200					12																	14693776		2203	4300	6503	SO:0001819	synonymous_variant	79887	exon4			TGTATGTCTCCAA	BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"PLB homolog 1 (Dictyostelium)"					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.480A>G	chr12.hg19:g.14693776T>C		170.0	0.0		116.0	5.0	NM_024829	A8K4E9|Q9BVV3|Q9H625	Silent	SNP	ENST00000240617.5	hg19	CCDS31751.1																																																																																			.	.		0.393	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829		C	14693776	T	C	14693776	2	2	112	1	0	0	0	0	0	0	0	1	12034	1664	58	2		2	PLBD1	12	14693776	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3735095	14693776	119158119	749	17370										
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18872429	18872429	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taccaaatatgtgttatgtgAagatgaaataaaataatcat	6	3	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:18872429A>G	ENST00000266505.7	-	5	768	c.505T>C	c.(505-507)Tca>Cca	p.S169P	PLCZ1_ENST00000435379.1_Intron|PLCZ1_ENST00000447925.2_Missense_Mutation_p.S167P|PLCZ1_ENST00000539875.1_Intron|PLCZ1_ENST00000541695.1_Missense_Mutation_p.S32P|RP11-361I14.2_ENST00000536931.1_RNA					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					GTGTTATGTGAAGATGAAATA	0.264																																					p.S169P		Atlas-SNP	.											.	PLCZ1	107	.	0			c.T505C						.						56	58	57					12																	18872429		2202	4289	6491	SO:0001583	missense	89869	exon5			TATGTGAAGATGA	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000266505.7:c.505T>C	chr12.hg19:g.18872429A>G	ENSP00000266505:p.Ser169Pro	104.0	0.0		80.0	4.0	NM_033123		Missense_Mutation	SNP	ENST00000266505.7	hg19	CCDS8680.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443784	0.83993	.	.	ENSG00000139151	ENST00000266505;ENST00000447925;ENST00000541695;ENST00000541966	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.28	5.28	0.74379	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.000000	0.64402	D	0.000001	D	0.86973	0.6062	H	0.98407	4.225	0.54753	D	0.999988	D	0.89917	1.0	D	0.97110	1.0	D	0.91848	0.5489	10	0.87932	D	0	.	14.3734	0.66857	1.0:0.0:0.0:0.0	.	169	Q86YW0	PLCZ1_HUMAN	P	169;167;32;65	ENSP00000266505:S169P;ENSP00000402358:S167P;ENSP00000443349:S32P;ENSP00000444383:S65P	ENSP00000266505:S169P	S	-	1	0	PLCZ1	18763696	1.000000	0.71417	0.993000	0.49108	0.937000	0.57800	8.664000	0.91139	1.994000	0.58287	0.482000	0.46254	TCA	.	.		0.264	PLCZ1-001	KNOWN	NAGNAG_splice_site|non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401667.3	NM_033123		G	18872429	A	G	18872429	3	3	112	1	0	0	0	0	1	0	0	0	12053	246	9	2	1365	2	PLCZ1	12	18872429	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	4178653	18872429	114979466	750	17371										
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18876315	18876315	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcatctcagctgcatattgTtcttgtgtcagaaattgagc	8	9	4	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:18876315T>C	ENST00000266505.7	-	4	560	c.297A>G	c.(295-297)gaA>gaG	p.E99E	PLCZ1_ENST00000435379.1_Intron|PLCZ1_ENST00000447925.2_Silent_p.E97E|PLCZ1_ENST00000539875.1_Intron|RP11-361I14.2_ENST00000536931.1_RNA					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					CTGCATATTGTTCTTGTGTCA	0.343																																					p.E99E		Atlas-SNP	.											.	PLCZ1	107	.	0			c.A297G						.						89	85	87					12																	18876315		2202	4299	6501	SO:0001819	synonymous_variant	89869	exon4			ATATTGTTCTTGT	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000266505.7:c.297A>G	chr12.hg19:g.18876315T>C		119.0	0.0		88.0	4.0	NM_033123		Silent	SNP	ENST00000266505.7	hg19	CCDS8680.1																																																																																			.	.		0.343	PLCZ1-001	KNOWN	NAGNAG_splice_site|non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401667.3	NM_033123		C	18876315	T	C	18876315	2	2	112	1	0	0	0	0	0	0	0	1	12053	1722	60	2		2	PLCZ1	12	18876315	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3886	18876315	114975580	751	17372										
AEBP2	121536	hgsc.bcm.edu	37	chr12	19667647	19667647	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaagtgaacgacatcagttAaaaactaaagtagttcattt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:19667647delA	ENST00000398864.3	+	7	1436	c.1410delA	c.(1408-1410)ttafs	p.L470fs	AEBP2_ENST00000360995.4_Frame_Shift_Del_p.L254fs|AEBP2_ENST00000541908.1_Frame_Shift_Del_p.L241fs|AEBP2_ENST00000266508.9_Frame_Shift_Del_p.L470fs	NM_001114176.1	NP_001107648.1	Q6ZN18	AEBP2_HUMAN	AE binding protein 2	470	Interaction with SUZ12.				chromatin modification (GO:0016568)	ESC/E(Z) complex (GO:0035098)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			ovary(1)	1	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)|Esophageal squamous(101;0.143)					GACATCAGTTAAAAACTAAAG	0.313																																					p.L470X		Atlas-INDEL	.											.	AEBP2	21	.	0			c.1409delT						.						81	77	78					12																	19667647		1828	4089	5917	SO:0001589	frameshift_variant	121536	exon7			.		CCDS44841.1, CCDS44842.1, CCDS58215.1	12p12.3	2012-10-02			ENSG00000139154	ENSG00000139154			24051	protein-coding gene	gene with protein product						10329662	Standard	NM_153207		Approved	MGC17922	uc001ref.2	Q6ZN18	OTTHUMG00000168906	ENST00000398864.3:c.1410delA	chr12.hg19:g.19667647delA	ENSP00000381840:p.Leu470fs	194.0	0.0		163.0	10.0	NM_001114176	Q59FS5|Q6ZN62|Q96BG3	Frame_Shift_Del	DEL	ENST00000398864.3	hg19	CCDS44841.1																																																																																			.	.		0.313	AEBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401575.1	NM_153207		-	19667647	A	-	19667647	7	5	112	1	0	1	0	1	0	0	0	0	350	359	13	0	1436	0	AEBP2	12	19667647	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	791332	19667647	114184248	752	17373										
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21375253	21375253	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaattgttcaacctgaattgAaatcacttgcactgggtttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:21375253delA	ENST00000256958.2	+	13	1798	c.1702delA	c.(1702-1704)aaafs	p.K568fs		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	568					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	ACCTGAATTGAAATCACTTGC	0.264																																					p.L567fs		Atlas-INDEL	.											.	SLCO1B1	151	.	0			c.1701delG						.						110	106	107					12																	21375253		2203	4300	6503	SO:0001589	frameshift_variant	10599	exon13			.		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1702delA	chr12.hg19:g.21375253delA	ENSP00000256958:p.Lys568fs	165.0	0.0		140.0	10.0	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Frame_Shift_Del	DEL	ENST00000256958.2	hg19	CCDS8685.1																																																																																			.	.		0.264	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		-	21375253	A	-	21375253	7	5	112	1	0	1	0	1	0	0	0	0	14738	247	9	0	1748	0	SLCO1B1	12	21375253	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1707606	21375253	112476642	753	17374										
PYROXD1	79912	hgsc.bcm.edu	37	chr12	21605042	21605042	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaaacagcttactaaagctAaaagaataatgatcataggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:21605042delA	ENST00000240651.9	+	5	496	c.442delA	c.(442-444)aaafs	p.K148fs	PYROXD1_ENST00000545178.1_Intron|PYROXD1_ENST00000538582.1_Frame_Shift_Del_p.K77fs	NM_024854.3	NP_079130.2	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 1	148							oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|soft_tissue(1)	18						TACTAAAGCTAAAAGAATAAT	0.264																																					p.A147fs		Atlas-INDEL	.											.	PYROXD1	38	.	0			c.441delT						.						31	34	33					12																	21605042		2197	4281	6478	SO:0001589	frameshift_variant	79912	exon5			.	AL832441	CCDS31755.1	12p12.1	2014-02-12			ENSG00000121350	ENSG00000121350			26162	protein-coding gene	gene with protein product						12477932	Standard	NM_024854		Approved	DKFZp762G094, FLJ22028	uc001rew.3	Q8WU10	OTTHUMG00000169129	ENST00000240651.9:c.442delA	chr12.hg19:g.21605042delA	ENSP00000240651:p.Lys148fs	230.0	0.0		156.0	11.0	NM_024854	A6NKI6|B3KWN8|Q9H6P1	Frame_Shift_Del	DEL	ENST00000240651.9	hg19	CCDS31755.1																																																																																			.	.		0.264	PYROXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402363.1	NM_024854		-	21605042	A	-	21605042	7	5	112	1	0	1	0	1	0	0	0	0	12881	363	13	0	460	0	PYROXD1	12	21605042	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	229789	21605042	112246853	754	17375										
PYROXD1	79912	hgsc.bcm.edu	37	chr12	21620538	21620538	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtttgctcatgtgacaaaaTtttttaactataaggtaaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:21620538delT	ENST00000240651.9	+	11	1294	c.1240delT	c.(1240-1242)tttfs	p.F415fs	PYROXD1_ENST00000538582.1_Frame_Shift_Del_p.F344fs	NM_024854.3	NP_079130.2	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 1	415							oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|soft_tissue(1)	18						TGTGACAAAATTTTTTAACTA	0.358																																					p.K413fs		Atlas-INDEL	.											.	PYROXD1	38	.	0			c.1239delA						.						90	91	91					12																	21620538		2203	4300	6503	SO:0001589	frameshift_variant	79912	exon11			.	AL832441	CCDS31755.1	12p12.1	2014-02-12			ENSG00000121350	ENSG00000121350			26162	protein-coding gene	gene with protein product						12477932	Standard	NM_024854		Approved	DKFZp762G094, FLJ22028	uc001rew.3	Q8WU10	OTTHUMG00000169129	ENST00000240651.9:c.1240delT	chr12.hg19:g.21620538delT	ENSP00000240651:p.Phe415fs	243.0	0.0		209.0	13.0	NM_024854	A6NKI6|B3KWN8|Q9H6P1	Frame_Shift_Del	DEL	ENST00000240651.9	hg19	CCDS31755.1																																																																																			.	.		0.358	PYROXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402363.1	NM_024854		-	21620538	T	-	21620538	7	5	112	1	0	1	0	1	0	0	0	0	12881	1493	52	0	1282	0	PYROXD1	12	21620538	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	15496	21620538	112231357	755	17376										
ABCC9	10060	hgsc.bcm.edu	37	chr12	22001144	22001144	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atacatggcccgtcggagagTtttcctctctaaagtagttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:22001144delT	ENST00000261201.4	-	23	2805	c.2806delA	c.(2806-2808)actfs	p.T936fs	ABCC9_ENST00000345162.2_Frame_Shift_Del_p.T900fs|RP11-729I10.2_ENST00000539874.1_RNA|ABCC9_ENST00000261200.4_Frame_Shift_Del_p.T936fs	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	936					defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	CGTCGGAGAGTTTTCCTCTCT	0.413																																					p.T936fs		Atlas-INDEL	.											.	ABCC9	411	.	0			c.2807delC						.						133	121	125					12																	22001144		2203	4300	6503	SO:0001589	frameshift_variant	10060	exon23			.	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.2806delA	chr12.hg19:g.22001144delT	ENSP00000261201:p.Thr936fs	328.0	0.0		187.0	12.0	NM_005691	O60707	Frame_Shift_Del	DEL	ENST00000261201.4	hg19	CCDS8694.1																																																																																			.	.		0.413	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		-	22001144	T	-	22001144	7	5	112	1	0	1	0	1	0	0	0	0	59	1725	60	0	2049	0	ABCC9	12	22001144	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	380606	22001144	111850751	756	17377										
ABCC9	10060	hgsc.bcm.edu	37	chr12	22012588	22012588	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctctgcctctgtcccccacTcaggttgatgccctagagaa	8	15	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:22012588T>C	ENST00000261201.4	-	20	2436	c.2437A>G	c.(2437-2439)Agt>Ggt	p.S813G	ABCC9_ENST00000345162.2_Missense_Mutation_p.S777G|RP11-729I10.2_ENST00000539874.1_RNA|ABCC9_ENST00000261200.4_Missense_Mutation_p.S813G	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	813	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	TGTCCCCCACTCAGGTTGATG	0.383																																					p.S813G		Atlas-SNP	.											.	ABCC9	411	.	0			c.A2437G						.						170	171	170					12																	22012588		2203	4300	6503	SO:0001583	missense	10060	exon20			CCCCACTCAGGTT	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.2437A>G	chr12.hg19:g.22012588T>C	ENSP00000261201:p.Ser813Gly	78.0	0.0		62.0	5.0	NM_005691	O60707	Missense_Mutation	SNP	ENST00000261201.4	hg19	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.169044	0.78339	.	.	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	D;D;D;D	0.98822	-5.16;-5.16;-5.16;-5.16	4.71	4.71	0.59529	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	H	0.99211	4.47	0.80722	D	1	P;D	0.89917	0.941;1.0	P;D	0.91635	0.766;0.999	D	0.97698	1.0183	10	0.87932	D	0	-17.5591	14.3377	0.66603	0.0:0.0:0.0:1.0	.	813;813	O60706;O60706-2	ABCC9_HUMAN;.	G	813;440;813;777	ENSP00000261200:S813G;ENSP00000440521:S440G;ENSP00000261201:S813G;ENSP00000261202:S777G	ENSP00000261200:S813G	S	-	1	0	ABCC9	21903855	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.854000	0.86942	1.982000	0.57802	0.383000	0.25322	AGT	.	.		0.383	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		C	22012588	T	C	22012588	3	2	112	1	0	0	0	0	1	0	0	0	59	1551	54	2	2430	2	ABCC9	12	22012588	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	11444	22012588	111839307	757	17378										
KRAS	3845	hgsc.bcm.edu	37	chr12	25368464	25368464	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctgtattgtcggatctcccTcaccaatgtataaaaagcat	6	10	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:25368464T>C	ENST00000256078.4	-	5	544	c.481A>G	c.(481-483)Agg>Ggg	p.R161G	KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Intron	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	161					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CGGATCTCCCTCACCAATGTA	0.348		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.R161G	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	.	KRAS	30930	.	0			c.A481G						.						119	114	116					12																	25368464		2203	4300	6503	SO:0001583	missense	3845	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TCTCCCTCACCAA	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.481A>G	chr12.hg19:g.25368464T>C	ENSP00000256078:p.Arg161Gly	138.0	0.0		67.0	4.0	NM_033360	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	T	19.90	3.913542	0.72983	.	.	ENSG00000133703	ENST00000256078	T	0.71579	-0.58	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.85225	0.5648	M	0.88906	2.99	0.80722	D	1	D	0.71674	0.998	D	0.70016	0.967	D	0.87762	0.2599	10	0.87932	D	0	.	12.0477	0.53489	0.0:0.0:0.1538:0.8462	.	161	P01116	RASK_HUMAN	G	161	ENSP00000256078:R161G	ENSP00000256078:R161G	R	-	1	2	KRAS	25259731	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.695000	0.54749	2.254000	0.74563	0.482000	0.46254	AGG	.	.		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		C	25368464	T	C	25368464	3	2	112	1	0	0	0	0	1	0	0	0	8447	1550	54	2	213	2	KRAS	12	25368464	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3355876	25368464	108483431	758	17379										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26809378	26809378	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaacggcaggctctcatccgAcacacaccgcaggatcaggt	11	14	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:26809378A>G	ENST00000381340.3	-	19	2712	c.2296T>C	c.(2296-2298)Tcg>Ccg	p.S766P		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	766					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CTCTCATCCGACACACACCGC	0.567																																					p.S766P		Atlas-SNP	.											.	ITPR2	270	.	0			c.T2296C						.						67	73	71					12																	26809378		2066	4200	6266	SO:0001583	missense	3709	exon19			CATCCGACACACA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.2296T>C	chr12.hg19:g.26809378A>G	ENSP00000370744:p.Ser766Pro	104.0	0.0		83.0	4.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.598181	0.66332	.	.	ENSG00000123104	ENST00000381340	D	0.92348	-3.02	4.62	4.62	0.57501	.	0.056272	0.64402	D	0.000001	D	0.91703	0.7377	M	0.76574	2.34	0.80722	D	1	P	0.37330	0.59	B	0.38880	0.284	D	0.92449	0.5968	10	0.59425	D	0.04	.	14.4962	0.67688	1.0:0.0:0.0:0.0	.	766	Q14571	ITPR2_HUMAN	P	766	ENSP00000370744:S766P	ENSP00000370744:S766P	S	-	1	0	ITPR2	26700645	1.000000	0.71417	0.966000	0.40874	0.432000	0.31715	4.744000	0.62118	2.059000	0.61396	0.533000	0.62120	TCG	.	.		0.567	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		G	26809378	A	G	26809378	3	3	112	1	0	0	0	0	1	0	0	0	7930	275	10	2	5965	2	ITPR2	12	26809378	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1440914	26809378	107042517	759	17380										
PUS7L	83448	hgsc.bcm.edu	37	chr12	44124292	44124292	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atcaatgtgggaacctttcgTtttgacatcaatgtcatgat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:44124292delT	ENST00000416848.2	-	9	2481	c.1993delA	c.(1993-1995)acgfs	p.T665fs	PUS7L_ENST00000431332.3_Frame_Shift_Del_p.T352fs|PUS7L_ENST00000344862.5_Frame_Shift_Del_p.T665fs|PUS7L_ENST00000551923.1_Frame_Shift_Del_p.T665fs	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	665					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		GAACCTTTCGTTTTGACATCA	0.363																																					p.T665fs		Atlas-INDEL	.											PUS7L,colon,carcinoma,+1,1	PUS7L	73	.	0			c.1994delC						.						153	140	144					12																	44124292		2203	4300	6503	SO:0001589	frameshift_variant	83448	exon9			.	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.1993delA	chr12.hg19:g.44124292delT	ENSP00000415899:p.Thr665fs	226.0	0.0		243.0	15.0	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Frame_Shift_Del	DEL	ENST00000416848.2	hg19	CCDS8743.1																																																																																			.	.		0.363	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		-	44124292	T	-	44124292	7	5	112	1	0	1	0	1	0	0	0	0	12849	1725	60	0	116	0	PUS7L	12	44124292	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	17314914	44124292	89727603	760	17381										
IRAK4	51135	hgsc.bcm.edu	37	chr12	44180517	44180517	+	Stop_Codon_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcaagagatgacagcttcttAaaactttattggaaaagact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:44180517delA	ENST00000448290.2	+	0	1453				IRAK4_ENST00000551736.1_Stop_Codon_Del|IRAK4_ENST00000440781.2_Stop_Codon_Del|IRAK4_ENST00000431837.1_Stop_Codon_Del	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4						cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		ACAGCTTCTTAAAACTTTATT	0.289																																					p.X461K		Atlas-INDEL	.											.	IRAK4	77	.	0			c.1381delT						.						57	63	61					12																	44180517		2202	4299	6501	SO:0001567	stop_retained_variant	51135	exon12			.	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		Exception_encountered	chr12.hg19:g.44180517delA		127.0	0.0		145.0	10.0	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Frame_Shift_Del	DEL	ENST00000448290.2	hg19	CCDS8744.1																																																																																			.	.		0.289	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1			-	44180517	A	-	44180517	7	5	112	1	0	1	0	1	0	0	0	0	7834	369	13	0	1424	0	IRAK4	12	44180517	Stop_Codon_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	56225	44180517	89671378	761	17382										
SENP1	29843	hgsc.bcm.edu	37	chr12	48477423	48477423	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagttttcttggggctcaaaAgacttcgacgacatgaacca	10	9	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:48477423A>G	ENST00000004980.5	-	6	981	c.503T>C	c.(502-504)cTt>cCt	p.L168P	SENP1_ENST00000547886.1_5'UTR|SENP1_ENST00000549518.1_Missense_Mutation_p.L168P|SENP1_ENST00000551330.1_Missense_Mutation_p.L168P|RNU6-1203P_ENST00000410703.1_RNA|SENP1_ENST00000448372.1_Missense_Mutation_p.L168P|SENP1_ENST00000549595.1_Missense_Mutation_p.L168P|SENP1_ENST00000339976.6_3'UTR			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	168	Ser-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				GGGGCTCAAAAGACTTCGACG	0.413																																					p.L168P		Atlas-SNP	.											.	SENP1	44	.	0			c.T503C						.						121	112	115					12																	48477423		1855	4091	5946	SO:0001583	missense	29843	exon6			CTCAAAAGACTTC	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"SUMO1/sentrin specific protease 1"			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.503T>C	chr12.hg19:g.48477423A>G	ENSP00000004980:p.Leu168Pro	124.0	0.0		100.0	4.0	NM_001267594	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	hg19	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	A	17.78	3.472698	0.63737	.	.	ENSG00000079387	ENST00000004980;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518	T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99	4.2	3.01	0.34805	.	0.610158	0.15739	N	0.247034	T	0.24005	0.0581	N	0.24115	0.695	0.80722	D	1	D;D	0.58620	0.971;0.983	P;P	0.56700	0.641;0.804	T	0.02546	-1.1143	10	0.72032	D	0.01	-11.7182	9.0643	0.36453	0.8359:0.0:0.0:0.1641	.	168;168	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	P	168	ENSP00000004980:L168P;ENSP00000394791:L168P;ENSP00000446681:L168P;ENSP00000450076:L168P;ENSP00000447328:L168P	ENSP00000004980:L168P	L	-	2	0	SENP1	46763690	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.478000	0.53158	0.900000	0.36469	0.533000	0.62120	CTT	.	.		0.413	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554		G	48477423	A	G	48477423	3	3	112	1	0	0	0	0	1	0	0	0	14061	72	3	2	1480	2	SENP1	12	48477423	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	4296906	48477423	85374472	762	17383										
DDX23	9416	hgsc.bcm.edu	37	chr12	49224336	49224336	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctgggtggttggctagttcGgggggacaggaagacactgg					rs146973565	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:49224336delG	ENST00000308025.3	-	17	2458	c.2379delC	c.(2377-2379)cccfs	p.P793fs		NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	793	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)	p.P793P(1)		NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						TGGCTAGTTCGGGGGGACAGG	0.562																																					p.E794fs		Atlas-Indel,Pindel	.											DDX23,NS,carcinoma,0,1	DDX23	82	.	1	Substitution - coding silent(1)	lung(1)	c.2380delG						.						114	101	105					12																	49224336		2203	4300	6503	SO:0001589	frameshift_variant	9416	exon17			.	AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"DEAD-boxes"	17347	protein-coding gene	gene with protein product		612172	"PRP28 homolog, yeast"			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.2379delC	chr12.hg19:g.49224336delG	ENSP00000310723:p.Pro793fs	203.0	0.0		262.0	18.0	NM_004818	B2R600|B4DH15|O43188	Frame_Shift_Del	DEL	ENST00000308025.3	hg19	CCDS8770.1																																																																																			.	.		0.562	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818		-	49224336	G	-	49224336	7	5	112	1	0	1	0	1	0	0	0	0	4352	1103	39	0	87	0	DDX23	12	49224336	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	746913	49224336	84627559	763	17384										
DNAJC22	79962	hgsc.bcm.edu	37	chr12	49743396	49743396	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cggatctggaggctactgatGggggagactggcttcaacag					rs148896963		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:49743396delG	ENST00000549441.2	+	3	1945	c.741delG	c.(739-741)atgfs	p.M247fs	DNAJC22_ENST00000395069.3_Frame_Shift_Del_p.M247fs			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	247						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						GGCTACTGATGGGGGAGACTG	0.532																																					p.M247fs		Atlas-INDEL	.											.	DNAJC22	29	.	0			c.740delT						.						116	120	119					12																	49743396		2203	4300	6503	SO:0001589	frameshift_variant	79962	exon2			.	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"Heat shock proteins / DNAJ (HSP40)"	25802	protein-coding gene	gene with protein product	"wurst homolog (Drosophila)"					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.741delG	chr12.hg19:g.49743396delG	ENSP00000446830:p.Met247fs	135.0	0.0		155.0	10.0	NM_024902	B3KP54	Frame_Shift_Del	DEL	ENST00000549441.2	hg19	CCDS8785.1																																																																																			.	.		0.532	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902		-	49743396	G	-	49743396	7	5	112	1	0	1	0	1	0	0	0	0	4643	1348	47	0	743	0	DNAJC22	12	49743396	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	519060	49743396	84108499	764	17385										
LASS5	91012	hgsc.bcm.edu	37	chr12	50532384	50532384	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatgccagcactgtcggatgTcccagaaccaaggtgactaa	10	11	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:50532384T>C	ENST00000317551.6	-	5	633	c.509A>G	c.(508-510)gAc>gGc	p.D170G	CERS5_ENST00000422340.2_Missense_Mutation_p.D112G	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	170	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										CTGTCGGATGTCCCAGAACCA	0.453																																					p.D170G		Atlas-SNP	.											.	.	.	.	0			c.A509G						.						216	203	207					12																	50532384		2203	4300	6503	SO:0001583	missense	91012	exon5			CGGATGTCCCAGA		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"Homeoboxes / CERS class"	23749	protein-coding gene	gene with protein product		615335	"LAG1 longevity assurance homolog 5 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 5"	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.509A>G	chr12.hg19:g.50532384T>C	ENSP00000325485:p.Asp170Gly	101.0	0.0		109.0	5.0	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	hg19	CCDS8801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.0|27.0	4.794249|4.794249	0.90453|0.90453	.|.	.|.	ENSG00000139624|ENSG00000139624	ENST00000551005;ENST00000317551;ENST00000422340|ENST00000547800	T;T;T|.	0.27402|.	1.67;2.66;2.48|.	5.12|5.12	5.12|5.12	0.69794|0.69794	TRAM/LAG1/CLN8 homology domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80768|0.80768	0.4686|0.4686	M|M	0.88512|0.88512	2.96|2.96	0.80722|0.80722	D|D	1|1	P;D;D|.	0.71674|.	0.881;0.957;0.998|.	P;P;D|.	0.68192|.	0.794;0.833;0.956|.	D|D	0.85025|0.85025	0.0914|0.0914	10|6	0.87932|0.87932	D|D	0|0	-17.9584|-17.9584	15.4003|15.4003	0.74834|0.74834	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	112;170;89|.	B4DV54;Q8N5B7;F8W0U5|.	.;CERS5_HUMAN;.|.	G|A	89;170;112|105	ENSP00000447556:D89G;ENSP00000325485:D170G;ENSP00000389050:D112G|.	ENSP00000325485:D170G|ENSP00000369536:T151A	D|T	-|-	2|1	0|0	CERS5|CERS5	48818651|48818651	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	7.787000|7.787000	0.85759|0.85759	2.288000|2.288000	0.76882|0.76882	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.		0.453	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190		C	50532384	T	C	50532384	3	2	112	1	0	0	0	0	1	0	0	0	8651	1667	58	2	693	2	LASS5	12	50532384	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	788988	50532384	83319511	765	17386										
KRT7	3855	hgsc.bcm.edu	37	chr12	52639299	52639299	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctggaagccgccctgcagcGgggcaagcaggatatggcac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:52639299delG	ENST00000331817.5	+	7	1271	c.1088delG	c.(1087-1089)cggfs	p.R363fs	KRT7_ENST00000552322.1_3'UTR|RP3-416H24.1_ENST00000546686.1_RNA	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	363	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	GCCCTGCAGCGGGGCAAGCAG	0.647																																					p.R363fs		Atlas-INDEL	.											.	KRT7	48	.	0			c.1087delC						.						47	48	48					12																	52639299		2203	4300	6503	SO:0001589	frameshift_variant	3855	exon7			.		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"-", "Intermediate filaments type II, keratins (basic)"	6445	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 7", "cytokeratin 7", "sarcolectin", "keratin, 55K type II cytoskeletal"	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.1088delG	chr12.hg19:g.52639299delG	ENSP00000329243:p.Arg363fs	106.0	0.0		127.0	13.0	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Frame_Shift_Del	DEL	ENST00000331817.5	hg19	CCDS8822.1																																																																																			.	.		0.647	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556		-	52639299	G	-	52639299	7	5	112	1	0	1	0	1	0	0	0	0	8492	1116	39	0	1114	0	KRT7	12	52639299	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2106915	52639299	81212596	766	17387										
EIF4B	1975	hgsc.bcm.edu	37	chr12	53427592	53427592	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagtttcatttaacttaggtCccccccaaagacccaaactg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:53427592delC	ENST00000262056.9	+	9	1308	c.982delC	c.(982-984)cccfs	p.P329fs	EIF4B_ENST00000416762.3_Frame_Shift_Del_p.P290fs|RP11-983P16.4_ENST00000552905.1_RNA|EIF4B_ENST00000420463.3_Frame_Shift_Del_p.P329fs	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	329	Arg-rich.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						TAACTTAGGTCCCCCCCAAAG	0.423																																					p.G327fs		Atlas-INDEL	.											.	EIF4B	38	.	0			c.981delT						.						60	56	57					12																	53427592		1816	4081	5897	SO:0001589	frameshift_variant	1975	exon9			.	X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"RNA binding motif (RRM) containing"	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.982delC	chr12.hg19:g.53427592delC	ENSP00000262056:p.Pro329fs	328.0	0.0		389.0	26.0	NM_001417	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Frame_Shift_Del	DEL	ENST00000262056.9	hg19	CCDS41788.1																																																																																			.	.		0.423	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404852.2	NM_001417		-	53427592	C	-	53427592	7	5	112	1	0	1	0	1	0	0	0	0	5029	855	30	0	1016	0	EIF4B	12	53427592	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	788293	53427592	80424303	767	17388										
CSAD	51380	hgsc.bcm.edu	37	chr12	53553669	53553669	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acaaaatagaaaggggtcctAcctccatgactagctcaaac	7	11	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:53553669A>G	ENST00000444623.1	-	15	1486		c.e15+1		CSAD_ENST00000379843.3_Splice_Site|CSAD_ENST00000453446.2_Splice_Site|CSAD_ENST00000379846.1_Splice_Site|RP11-1136G11.8_ENST00000550908.1_lincRNA|CSAD_ENST00000267085.4_Splice_Site	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase						cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	AAGGGGTCCTACCTCCATGAC	0.552											OREG0021859	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.	Ovarian(109;252 1546 16882 28524 44645)	Atlas-SNP	.											.	CSAD	66	.	0			c.519+2T>C						.						48	48	48					12																	53553669		2203	4300	6503	SO:0001630	splice_region_variant	51380	exon7			GGTCCTACCTCCA	AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"P-selectin cytoplasmic tail-associated protein"					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.1218+1T>C	chr12.hg19:g.53553669A>G		107.0	0.0	993	101.0	5.0	NM_001244706	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Splice_Site	SNP	ENST00000444623.1	hg19	CCDS58235.1	.	.	.	.	.	.	.	.	.	.	A	11.02	1.514972	0.27123	.	.	ENSG00000139631	ENST00000308926;ENST00000379843;ENST00000267085;ENST00000379850;ENST00000379846;ENST00000444623;ENST00000398047;ENST00000453446	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.554	0.61749	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CSAD	51839936	1.000000	0.71417	0.945000	0.38365	0.089000	0.18198	7.633000	0.83260	2.101000	0.63845	0.533000	0.62120	.	.	.		0.552	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343697.1	NM_015989	Intron	G	53553669	A	G	53553669	5	3	112	1	0	0	0	0	0	0	1	0	3927	405	14	2	273	2	CSAD	12	53553669	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	126077	53553669	80298226	768	17389										
ATP5G2	517	hgsc.bcm.edu	37	chr12	54063089	54063089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctgcggctagagacaagtgAggtaaggggacatgagactg	17	6	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:54063089A>G	ENST00000549164.1	-	4	341	c.154T>C	c.(154-156)Tca>Cca	p.S52P	ATP5G2_ENST00000602871.1_Missense_Mutation_p.S52P|ATP5G2_ENST00000394349.3_Missense_Mutation_p.S109P|ATP5G2_ENST00000338662.5_Missense_Mutation_p.S68P|ATP5G2_ENST00000550241.1_5'Flank			Q06055	AT5G2_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)	52					ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986)|response to ethanol (GO:0045471)	integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)			kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6						GAGACAAGTGAGGTAAGGGGA	0.498																																					p.S109P		Atlas-SNP	.											.	ATP5G2	16	.	0			c.T325C						.						46	44	44					12																	54063089		2203	4300	6503	SO:0001583	missense	517	exon4			CAAGTGAGGTAAG	X69908	CCDS8863.2, CCDS31812.1	12q13.13	2012-10-12	2010-06-11		ENSG00000135390	ENSG00000135390		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	842	protein-coding gene	gene with protein product		603193	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 2", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)"			8328972	Standard	NM_005176		Approved		uc001sec.3	Q06055	OTTHUMG00000133442	ENST00000549164.1:c.154T>C	chr12.hg19:g.54063089A>G	ENSP00000447317:p.Ser52Pro	62.0	0.0		69.0	4.0	NM_005176	B3KQQ6	Missense_Mutation	SNP	ENST00000549164.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.44	1.937443	0.34189	.	.	ENSG00000135390	ENST00000394349;ENST00000549164;ENST00000338662	T;T;T	0.26373	1.74;1.79;1.76	5.26	4.08	0.47627	.	0.477592	0.22598	N	0.058000	T	0.25195	0.0612	M	0.69358	2.11	0.27892	N	0.939296	B;B;B	0.18310	0.009;0.004;0.027	B;B;B	0.23275	0.016;0.015;0.045	T	0.16837	-1.0389	10	0.31617	T	0.26	0.0319	6.6517	0.22965	0.7525:0.0:0.2475:0.0	.	52;68;109	Q06055;Q06055-3;Q06055-2	AT5G2_HUMAN;.;.	P	109;52;68	ENSP00000377878:S109P;ENSP00000447317:S52P;ENSP00000340315:S68P	ENSP00000340315:S68P	S	-	1	0	ATP5G2	52349356	0.973000	0.33851	0.990000	0.47175	0.737000	0.42083	1.442000	0.35046	1.096000	0.41439	0.533000	0.62120	TCA	.	.		0.498	ATP5G2-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000407403.1	NM_005176		G	54063089	A	G	54063089	3	3	112	1	0	0	0	0	1	0	0	0	1154	304	11	2	279	2	ATP5G2	12	54063089	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	509420	54063089	79788806	769	17390										
ITGA5	3678	hgsc.bcm.edu	37	chr12	54796806	54796806	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtcaggcacacagatgttgTcttctccacagtccagcaag	10	12	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:54796806T>C	ENST00000293379.4	-	19	2204	c.1943A>G	c.(1942-1944)gAc>gGc	p.D648G	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	648					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						ACAGATGTTGTCTTCTCCACA	0.547																																					p.D648G		Atlas-SNP	.											.	ITGA5	99	.	0			c.A1943G						.						111	97	102					12																	54796806		2203	4300	6503	SO:0001583	missense	3678	exon19			ATGTTGTCTTCTC		CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"CD molecules", "Integrins"	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.1943A>G	chr12.hg19:g.54796806T>C	ENSP00000293379:p.Asp648Gly	108.0	0.0		113.0	5.0	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	hg19	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.517798	0.85495	.	.	ENSG00000161638	ENST00000293379	T	0.72725	-0.68	4.94	4.94	0.65067	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	D	0.84620	0.5512	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87017	0.2126	10	0.72032	D	0.01	.	12.8536	0.57871	0.0:0.0:0.0:1.0	.	648	P08648	ITA5_HUMAN	G	648	ENSP00000293379:D648G	ENSP00000293379:D648G	D	-	2	0	ITGA5	53083073	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.680000	0.84062	2.006000	0.58801	0.454000	0.30748	GAC	.	.		0.547	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			C	54796806	T	C	54796806	3	2	112	1	0	0	0	0	1	0	0	0	7888	1667	58	2	1254	2	ITGA5	12	54796806	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	733717	54796806	79055089	770	17391										
MUCL1	118430	hgsc.bcm.edu	37	chr12	55251994	55251994	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagttttacccaaatgggttGgggatctcccgaatggtaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:55251994delG	ENST00000308796.6	+	4	287	c.241delG	c.(241-243)gggfs	p.G81fs	MUCL1_ENST00000547990.1_3'UTR|MUCL1_ENST00000546809.1_Frame_Shift_Del_p.G76fs	NM_058173.2	NP_477521.1	Q96DR8	MUCL1_HUMAN	mucin-like 1	81					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|membrane (GO:0016020)				breast(1)|kidney(1)|lung(1)	3						CAAATGGGTTGGGGATCTCCC	0.413																																					p.V80fs		Atlas-INDEL	.											.	MUCL1	11	.	0			c.240delT						.						172	163	166					12																	55251994		2203	4300	6503	SO:0001589	frameshift_variant	118430	exon4			.	AF414087	CCDS8885.1	12q13.2	2007-07-02							30588	protein-coding gene	gene with protein product	"small breast epithelial mucin"	610857				12019145	Standard	NM_058173		Approved	SBEM	uc001sgk.3	Q96DR8		ENST00000308796.6:c.241delG	chr12.hg19:g.55251994delG	ENSP00000311364:p.Gly81fs	179.0	0.0		196.0	12.0	NM_058173	Q0VG95|Q32ZB5	Frame_Shift_Del	DEL	ENST00000308796.6	hg19	CCDS8885.1																																																																																			.	.		0.413	MUCL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406062.1	NM_058173		-	55251994	G	-	55251994	7	5	112	1	0	1	0	1	0	0	0	0	9991	1348	47	0	255	0	MUCL1	12	55251994	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	455188	55251994	78599901	771	17392										
OR6C68	403284	hgsc.bcm.edu	37	chr12	55886489	55886489	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acctctttggggtaactgaaTtttttcttttggctaccatg					rs7304753	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:55886489delT	ENST00000548615.1	+	1	328	c.328delT	c.(328-330)tttfs	p.F111fs	RP11-110A12.2_ENST00000556750.1_RNA|OR6C68_ENST00000379662.1_Frame_Shift_Del_p.F116fs|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005519.2	NP_001005519.2	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C, member 68	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15						GGTAACTGAATTTTTTCTTTT	0.373																																					p.E109fs		Atlas-INDEL	.											.	OR6C68	36	.	0			c.327delA						.						163	153	156					12																	55886489		2203	4300	6503	SO:0001589	frameshift_variant	403284	exon1			.		CCDS31826.1, CCDS31826.2	12q13.2	2013-09-23			ENSG00000205327	ENSG00000205327		"GPCR / Class A : Olfactory receptors"	31297	protein-coding gene	gene with protein product							Standard	NM_001005519		Approved		uc031qhq.1	A6NDL8	OTTHUMG00000169958	ENST00000548615.1:c.328delT	chr12.hg19:g.55886489delT	ENSP00000448811:p.Phe111fs	145.0	0.0		153.0	11.0	NM_001005519		Frame_Shift_Del	DEL	ENST00000548615.1	hg19	CCDS31826.2																																																																																			.	.		0.373	OR6C68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406677.1			-	55886489	T	-	55886489	7	5	112	1	0	1	0	1	0	0	0	0	11205	1493	52	0	345	0	OR6C68	12	55886489	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	634495	55886489	77965406	772	17393										
MMP19	4327	hgsc.bcm.edu	37	chr12	56233389	56233389	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaatatcgggagtgcccaagCcccagagcatggcccacttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56233389delC	ENST00000322569.4	-	5	748	c.657delG	c.(655-657)gggfs	p.G219fs	MMP19_ENST00000547487.1_5'Flank|MMP19_ENST00000548629.1_Frame_Shift_Del_p.G196fs|MMP19_ENST00000409200.3_Intron|MMP19_ENST00000394182.1_5'Flank	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	219					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	AGTGCCCAAGCCCCAGAGCAT	0.612																																					p.L220fs		Atlas-INDEL	.											.	MMP19	61	.	0			c.658delC						.						73	59	64					12																	56233389		2203	4300	6503	SO:0001589	frameshift_variant	4327	exon5			.	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"matrix metalloproteinase 19"	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.657delG	chr12.hg19:g.56233389delC	ENSP00000313437:p.Gly219fs	184.0	0.0		180.0	12.0	NM_002429	B4E030|O15278|O95606|Q99580	Frame_Shift_Del	DEL	ENST00000322569.4	hg19	CCDS8895.1																																																																																			.	.		0.612	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429		-	56233389	C	-	56233389	7	5	112	1	0	1	0	1	0	0	0	0	9666	726	26	0	889	0	MMP19	12	56233389	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	346900	56233389	77618506	773	17394										
WIBG	84305	hgsc.bcm.edu	37	chr12	56296053	56296053	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caccaccttcaggcctggatGgggtgacaggagcagtggcc					rs201814214		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56296053delG	ENST00000408946.2	-	3	369	c.218delC	c.(217-219)ccafs	p.P73fs	WIBG_ENST00000557259.1_3'UTR|WIBG_ENST00000302533.6_5'UTR|WIBG_ENST00000398213.4_Frame_Shift_Del_p.P72fs|WIBG_ENST00000547925.1_3'UTR	NM_032345.2	NP_115721.1	Q9BRP8	WIBG_HUMAN	within bgcn homolog (Drosophila)	73					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|exon-exon junction complex (GO:0035145)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						AGGCCTGGATGGGGTGACAGG	0.522																																					p.P73fs		Atlas-INDEL	.											.	WIBG	11	.	0			c.219delA						.						60	57	58					12																	56296053		1905	4131	6036	SO:0001589	frameshift_variant	84305	exon3			.	BC014976	CCDS41795.1, CCDS44916.1	12q13.2	2008-02-05				ENSG00000170473			30258	protein-coding gene	gene with protein product						12438415, 12483225	Standard	NM_032345		Approved	PYM	uc001sif.1	Q9BRP8	OTTHUMG00000170220	ENST00000408946.2:c.218delC	chr12.hg19:g.56296053delG	ENSP00000386156:p.Pro73fs	100.0	0.0		139.0	11.0	NM_032345	B6ZDM5|Q8IXJ8|Q8N8E7	Frame_Shift_Del	DEL	ENST00000408946.2	hg19	CCDS41795.1																																																																																			.	.		0.522	WIBG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408079.1	NM_032345		-	56296053	G	-	56296053	7	5	112	1	0	1	0	1	0	0	0	0	17380	1348	47	0	400	0	WIBG	12	56296053	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	62664	56296053	77555842	774	17395										
DGKA	1606	hgsc.bcm.edu	37	chr12	56346858	56346858	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agactggaagtggttgggctGgagggtgcaattgagatggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56346858delG	ENST00000331886.5	+	22	2431	c.1977delG	c.(1975-1977)ctgfs	p.L659fs	DGKA_ENST00000551156.1_Frame_Shift_Del_p.L659fs|DGKA_ENST00000394147.1_Frame_Shift_Del_p.L659fs|DGKA_ENST00000549079.2_3'UTR	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	659					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	TGGTTGGGCTGGAGGGTGCAA	0.502																																					p.L659fs		Atlas-INDEL	.											.	DGKA	70	.	0			c.1976delT						.						117	116	116					12																	56346858		2203	4300	6503	SO:0001589	frameshift_variant	1606	exon22			.	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"EF-hand domain containing"	2849	protein-coding gene	gene with protein product		125855	"diacylglycerol kinase, alpha (80kD)"	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.1977delG	chr12.hg19:g.56346858delG	ENSP00000328405:p.Leu659fs	180.0	0.0		149.0	10.0	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Frame_Shift_Del	DEL	ENST00000331886.5	hg19	CCDS8896.1																																																																																			.	.		0.502	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1			-	56346858	G	-	56346858	7	5	112	1	0	1	0	1	0	0	0	0	4467	1335	47	0	2059	0	DGKA	12	56346858	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	50805	56346858	77505037	775	17396										
DGKA	1606	hgsc.bcm.edu	37	chr12	56346928	56346928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacgtcggctggccaagtgcTctgagatcaccttccagtaa	11	12	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56346928T>C	ENST00000331886.5	+	22	2501	c.2047T>C	c.(2047-2049)Tct>Cct	p.S683P	DGKA_ENST00000551156.1_Missense_Mutation_p.S683P|DGKA_ENST00000394147.1_Missense_Mutation_p.S683P|DGKA_ENST00000549079.2_3'UTR	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	683					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	GGCCAAGTGCTCTGAGATCAC	0.567																																					p.S683P		Atlas-SNP	.											.	DGKA	70	.	0			c.T2047C						.						86	84	85					12																	56346928		2203	4300	6503	SO:0001583	missense	1606	exon22			AAGTGCTCTGAGA	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"EF-hand domain containing"	2849	protein-coding gene	gene with protein product		125855	"diacylglycerol kinase, alpha (80kD)"	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.2047T>C	chr12.hg19:g.56346928T>C	ENSP00000328405:p.Ser683Pro	86.0	0.0		99.0	6.0	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Missense_Mutation	SNP	ENST00000331886.5	hg19	CCDS8896.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.968503	0.74131	.	.	ENSG00000065357	ENST00000331886;ENST00000394147;ENST00000551156	T;T;T	0.46063	0.88;0.88;0.88	4.83	3.64	0.41730	Diacylglycerol kinase, accessory domain (2);	0.057410	0.64402	D	0.000001	T	0.68348	0.2991	M	0.91459	3.21	0.53005	D	0.999968	D	0.67145	0.996	D	0.75020	0.985	T	0.73353	-0.4009	10	0.87932	D	0	.	10.8775	0.46919	0.0:0.0:0.1583:0.8417	.	683	P23743	DGKA_HUMAN	P	683	ENSP00000328405:S683P;ENSP00000377703:S683P;ENSP00000450359:S683P	ENSP00000328405:S683P	S	+	1	0	DGKA	54633195	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.875000	0.69660	0.752000	0.32923	0.459000	0.35465	TCT	.	.		0.567	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1			C	56346928	T	C	56346928	3	2	112	1	0	0	0	0	1	0	0	0	4467	1551	54	2	2129	2	DGKA	12	56346928	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	70	56346928	77504967	776	17397										
PA2G4	5036	hgsc.bcm.edu	37	chr12	56503708	56503708	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accattatccagaatcccacAgaccagcagaagtaggtgcc	8	13	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56503708A>G	ENST00000303305.6	+	7	1037	c.618A>G	c.(616-618)acA>acG	p.T206T	PA2G4_ENST00000552766.1_Silent_p.T206T|RP11-603J24.17_ENST00000548595.1_RNA	NM_006191.2	NP_006182.2	Q9UQ80	PA2G4_HUMAN	proliferation-associated 2G4, 38kDa	206					cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of translation (GO:0006417)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(18;0.0739)			AGAATCCCACAGACCAGCAGA	0.438																																					p.T206T		Atlas-SNP	.											.	PA2G4	24	.	0			c.A618G						.						106	97	100					12																	56503708		2203	4300	6503	SO:0001819	synonymous_variant	5036	exon7			TCCCACAGACCAG	U59435, BC007561	CCDS8902.1	12q13.2	2008-09-05	2002-08-29		ENSG00000170515	ENSG00000170515			8550	protein-coding gene	gene with protein product		602145	"proliferation-associated 2G4, 38kD"			9345902	Standard	NM_006191		Approved		uc001sjm.3	Q9UQ80	OTTHUMG00000170173	ENST00000303305.6:c.618A>G	chr12.hg19:g.56503708A>G		105.0	0.0		113.0	5.0	NM_006191	O43846|Q9UM59	Silent	SNP	ENST00000303305.6	hg19	CCDS8902.1																																																																																			.	.		0.438	PA2G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407767.1	NM_006191		G	56503708	A	G	56503708	2	3	112	1	0	0	0	0	0	0	0	1	11370	175	7	2		2	PA2G4	12	56503708	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	156780	56503708	77348187	777	17398										
ESYT1	23344	hgsc.bcm.edu	37	chr12	56531342	56531342	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attgccaaagaccgtttcttGgggggactggtgaagggcaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56531342delG	ENST00000394048.5	+	18	2262	c.1998delG	c.(1996-1998)ttgfs	p.L666fs	ESYT1_ENST00000541590.1_Frame_Shift_Del_p.L676fs|ESYT1_ENST00000267113.4_Frame_Shift_Del_p.L676fs	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	666	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						ACCGTTTCTTGGGGGGACTGG	0.552																																					p.L676fs		Pindel	.											.	ESYT1	84	.	0			c.2027delT						.						154	158	157					12																	56531342		2203	4300	6503	SO:0001589	frameshift_variant	23344	exon18			.	AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"Synaptotagmins"	29534	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member A"	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.1998delG	chr12.hg19:g.56531342delG	ENSP00000377612:p.Leu666fs	100.0	0.0		141.0	10.0	NM_001184796	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Frame_Shift_Del	DEL	ENST00000394048.5	hg19	CCDS8904.1																																																																																			.	.		0.552	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292		-	56531342	G	-	56531342	7	5	112	1	0	1	0	1	0	0	0	0	5266	1339	47	0	2098	0	ESYT1	12	56531342	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	27634	56531342	77320553	778	17399										
MYL6	4637	hgsc.bcm.edu	37	chr12	56553921	56553921	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgctgaaatccggcatgttcTtgtcacactgggtaaggttc	11	9	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56553921T>C	ENST00000550697.1	+	4	579	c.338T>C	c.(337-339)cTt>cCt	p.L113P	MYL6_ENST00000547649.1_Missense_Mutation_p.L113P|MYL6_ENST00000548293.1_Missense_Mutation_p.L113P|MYL6_ENST00000348108.4_Missense_Mutation_p.L114P|MYL6_ENST00000536128.1_Missense_Mutation_p.L206P|MYL6_ENST00000549566.1_Missense_Mutation_p.L158P|RP11-977G19.5_ENST00000553176.1_RNA|MYL6_ENST00000551589.1_Missense_Mutation_p.L113P|MYL6_ENST00000293422.5_Missense_Mutation_p.L114P|MYL6_ENST00000548400.1_Missense_Mutation_p.L77P|MYL6_ENST00000548580.1_Missense_Mutation_p.L65P|RP11-603J24.14_ENST00000548731.1_RNA|MYL6_ENST00000547408.1_Missense_Mutation_p.L113P|MYL6_ENST00000549017.1_Missense_Mutation_p.L9P	NM_021019.4	NP_066299.2	P60660	MYL6_HUMAN	myosin, light chain 6, alkali, smooth muscle and non-muscle	113	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle tissue development (GO:0007519)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|unconventional myosin complex (GO:0016461)|vesicle (GO:0031982)	actin-dependent ATPase activity (GO:0030898)|calcium ion binding (GO:0005509)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			large_intestine(1)|lung(1)|ovary(1)|prostate(3)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(18;0.0979)			CGGCATGTTCTTGTCACACTG	0.502																																					p.L113P		Atlas-SNP	.											.	MYL6	16	.	0			c.T338C						.						75	71	72					12																	56553921		2203	4300	6503	SO:0001583	missense	4637	exon4			ATGTTCTTGTCAC	AB046613	CCDS8906.1, CCDS31834.1	12q13.13	2013-01-10	2006-09-29			ENSG00000092841		"Myosins / Light chain", "EF-hand domain containing"	7587	protein-coding gene	gene with protein product		609931	"myosin, light polypeptide 6, alkali, smooth muscle and non-muscle"			8188229, 2304459, 2722814	Standard	NM_021019		Approved	ESMLC, MLC3NM, MLC1SM	uc001sjx.2	P60660		ENST00000550697.1:c.338T>C	chr12.hg19:g.56553921T>C	ENSP00000446955:p.Leu113Pro	75.0	0.0		84.0	4.0	NM_079423	P16475|P24572|P24573|Q12790|Q561V9|Q6IAZ0|Q6IPY5	Missense_Mutation	SNP	ENST00000550697.1	hg19	CCDS8906.1	.	.	.	.	.	.	.	.	.	.	T	19.39	3.818926	0.71028	.	.	ENSG00000092841	ENST00000550697;ENST00000548580;ENST00000293422;ENST00000348108;ENST00000549017;ENST00000549566;ENST00000536128;ENST00000547649;ENST00000547408;ENST00000551589;ENST00000553056;ENST00000549392;ENST00000548400;ENST00000548293	D;D;D;D;T;D;D;D;D;D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87;0.37;-2.87;-2.87;-2.87;-2.87;-2.87;-2.87;-2.87;-2.87	4.19	4.19	0.49359	EF-hand-like domain (1);	0.000000	0.64402	D	0.000001	D	0.97365	0.9138	H	0.99600	4.65	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98068	1.0397	10	0.87932	D	0	.	12.662	0.56820	0.0:0.0:0.0:1.0	.	206;113;113;113	B7Z6Z4;P60660-2;P60660;F8W1R7	.;.;MYL6_HUMAN;.	P	113;65;114;114;9;158;206;113;113;113;113;101;77;113	ENSP00000446955:L113P;ENSP00000446640:L65P;ENSP00000293422:L114P;ENSP00000301540:L114P;ENSP00000449086:L9P;ENSP00000446709:L158P;ENSP00000441750:L206P;ENSP00000446714:L113P;ENSP00000446721:L113P;ENSP00000446687:L113P;ENSP00000450116:L101P;ENSP00000448859:L77P;ENSP00000448101:L113P	ENSP00000293422:L114P	L	+	2	0	MYL6	54840188	1.000000	0.71417	0.966000	0.40874	0.988000	0.76386	7.856000	0.86956	1.898000	0.54952	0.379000	0.24179	CTT	.	.		0.502	MYL6-003	KNOWN	NAGNAG_splice_site|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407928.3			C	56553921	T	C	56553921	3	2	112	1	0	0	0	0	1	0	0	0	10060	1609	56	2	352	2	MYL6	12	56553921	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	22579	56553921	77297974	779	17400										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56997486	56997486	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggccagaacagttttcagccTtgaaatagatggagaaagat	11	6	1	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56997486T>C	ENST00000551812.1	-	17	3238		c.e17-2		BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000379441.3_Splice_Site|BAZ2A_ENST00000179765.5_Splice_Site|BAZ2A_ENST00000549884.1_Splice_Site	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A						chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						GTTTTCAGCCTTGAAATAGAT	0.542																																					.		Atlas-SNP	.											.	BAZ2A	263	.	0			c.3045-2A>G						.						42	40	41					12																	56997486		1932	4135	6067	SO:0001630	splice_region_variant	11176	exon18			TCAGCCTTGAAAT	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.3045-2A>G	chr12.hg19:g.56997486T>C		67.0	0.0		77.0	4.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Splice_Site	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	T	13.93	2.385176	0.42308	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0842	0.48078	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	BAZ2A	55283753	1.000000	0.71417	0.985000	0.45067	0.517000	0.34286	4.145000	0.58065	1.940000	0.56252	0.533000	0.62120	.	.	.		0.542	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	Intron	C	56997486	T	C	56997486	5	2	112	1	0	0	0	0	0	0	1	0	1331	1623	56	2	2726	2	BAZ2A	12	56997486	Splice_Site	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	443565	56997486	76854409	780	17401										
KIF5A	3798	hgsc.bcm.edu	37	chr12	57974761	57974761	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtacgtgacaatgcagatcTgcgttgtgagcttcctaaat	11	8	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:57974761T>C	ENST00000455537.2	+	24	2835	c.2561T>C	c.(2560-2562)cTg>cCg	p.L854P	KIF5A_ENST00000286452.5_Missense_Mutation_p.L765P	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	854					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						AATGCAGATCTGCGTTGTGAG	0.557																																					p.L854P		Atlas-SNP	.											.	KIF5A	143	.	0			c.T2561C						.						66	58	61					12																	57974761		2203	4300	6503	SO:0001583	missense	3798	exon24			CAGATCTGCGTTG	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.2561T>C	chr12.hg19:g.57974761T>C	ENSP00000408979:p.Leu854Pro	74.0	0.0		92.0	4.0	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.431502	0.83776	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	D;D	0.87729	-2.29;-2.29	4.97	4.97	0.65823	.	0.000000	0.64402	D	0.000005	D	0.94291	0.8166	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	D	0.95266	0.8373	10	0.87932	D	0	.	14.0734	0.64874	0.0:0.0:0.0:1.0	.	765;854	B7Z2M7;Q12840	.;KIF5A_HUMAN	P	854;765	ENSP00000408979:L854P;ENSP00000286452:L765P	ENSP00000286452:L765P	L	+	2	0	KIF5A	56261028	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.700000	0.84556	2.225000	0.72522	0.533000	0.62120	CTG	.	.		0.557	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		C	57974761	T	C	57974761	3	2	112	1	0	0	0	0	1	0	0	0	8314	1580	55	2	2655	2	KIF5A	12	57974761	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	977275	57974761	75877134	781	17402										
SRGAP1	57522	hgsc.bcm.edu	37	chr12	64472776	64472776	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gactatgatgtttctgaatgCttccagcacagtcgttccac	8	11	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:64472776C>T	ENST00000355086.3	+	9	1727	c.1203C>T	c.(1201-1203)tgC>tgT	p.C401C	SRGAP1_ENST00000543397.1_Silent_p.C361C|SRGAP1_ENST00000357825.3_Silent_p.C401C|RP11-196H14.2_ENST00000535594.1_RNA	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	401	F-BAR domain.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		TTTCTGAATGCTTCCAGCACA	0.458																																					p.C401C		Atlas-SNP	.											.	SRGAP1	146	.	0			c.C1203T						.						118	99	105					12																	64472776		2203	4300	6503	SO:0001819	synonymous_variant	57522	exon9			TGAATGCTTCCAG	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.1203C>T	chr12.hg19:g.64472776C>T		78.0	0.0		83.0	4.0	NM_020762	Q9H8A3|Q9P2P2	Silent	SNP	ENST00000355086.3	hg19	CCDS8967.1																																																																																			.	.		0.458	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			T	64472776	C	T	64472776	2	4	112	1	0	0	0	0	0	0	0	1	15160	805	28	3		3	SRGAP1	12	64472776	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	6498015	64472776	69379119	782	17403										
C12orf66	144577	hgsc.bcm.edu	37	chr12	64609570	64609570	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atagaagtctgccatctccaTccgagcctgaacaaagaagc	8	12	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:64609570T>C	ENST00000398055.3	-	2	462	c.409A>G	c.(409-411)Atg>Gtg	p.M137V	C12orf66_ENST00000311915.8_Missense_Mutation_p.M137V|C12orf66_ENST00000544871.1_Missense_Mutation_p.M84V	NM_152440.4	NP_689653	Q96MD2	CL066_HUMAN	chromosome 12 open reading frame 66	137										central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)	5						GCCATCTCCATCCGAGCCTGA	0.527																																					p.M137V		Atlas-SNP	.											.	C12orf66	28	.	0			c.A409G						.						64	64	64					12																	64609570		2024	4203	6227	SO:0001583	missense	144577	exon2			TCTCCATCCGAGC		CCDS41803.1, CCDS73490.1	12q14.2	2008-08-08			ENSG00000174206	ENSG00000174206			26517	protein-coding gene	gene with protein product						12477932	Standard	NM_152440		Approved	FLJ32549	uc001srw.4	Q96MD2	OTTHUMG00000168763	ENST00000398055.3:c.409A>G	chr12.hg19:g.64609570T>C	ENSP00000381132:p.Met137Val	117.0	0.0		115.0	5.0	NM_152440	C9JX54|Q8IYA0	Missense_Mutation	SNP	ENST00000398055.3	hg19	CCDS41803.1	.	.	.	.	.	.	.	.	.	.	T	11.49	1.653358	0.29425	.	.	ENSG00000174206	ENST00000311915;ENST00000544871;ENST00000398055	T;T;T	0.34859	1.34;1.34;1.34	5.95	4.82	0.62117	.	0.188542	0.64402	D	0.000003	T	0.26738	0.0654	L	0.38838	1.175	0.46542	D	0.999091	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.06356	-1.0831	9	.	.	.	-21.9238	10.6315	0.45538	0.0:0.1006:0.0:0.8994	.	84;137	F5H2Q3;Q96MD2	.;CL066_HUMAN	V	137;84;137	ENSP00000311486:M137V;ENSP00000445481:M84V;ENSP00000381132:M137V	.	M	-	1	0	C12orf66	62895837	1.000000	0.71417	0.997000	0.53966	0.912000	0.54170	3.179000	0.50887	2.279000	0.76181	0.402000	0.26972	ATG	.	.		0.527	C12orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400921.1	NM_152440		C	64609570	T	C	64609570	3	2	112	1	0	0	0	0	1	0	0	0	1711	1435	50	2	936	2	C12orf66	12	64609570	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	136794	64609570	69242325	783	17404										
XPOT	11260	hgsc.bcm.edu	37	chr12	64827209	64827209	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcagatacaggtatccccgTttttacaacagatgttcatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:64827209delT	ENST00000332707.5	+	19	2807	c.2278delT	c.(2278-2280)tttfs	p.F760fs		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	760	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		GGTATCCCCGTTTTTACAACA	0.363																																					p.P759fs		Atlas-INDEL	.											.	XPOT	105	.	0			c.2277delG						.						133	131	132					12																	64827209		2203	4300	6503	SO:0001589	frameshift_variant	11260	exon19			.	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.2278delT	chr12.hg19:g.64827209delT	ENSP00000327821:p.Phe760fs	128.0	0.0		138.0	12.0	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Frame_Shift_Del	DEL	ENST00000332707.5	hg19	CCDS31852.1																																																																																			.	.		0.363	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		-	64827209	T	-	64827209	7	5	112	1	0	1	0	1	0	0	0	0	17465	1725	60	0	2348	0	XPOT	12	64827209	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	217639	64827209	69024686	784	17405										
IFNG	3458	hgsc.bcm.edu	37	chr12	68551987	68551987	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttacctctttccaattcttcAaaatgcctaagaaaagagtt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:68551987delA	ENST00000229135.3	-	2	298	c.167delT	c.(166-168)ttgfs	p.L56fs	IFNG-AS1_ENST00000536914.1_RNA	NM_000619.2	NP_000610.2	P01579	IFNG_HUMAN	interferon, gamma	56					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell cycle arrest (GO:0007050)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to interleukin-18 (GO:0071351)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|extrinsic apoptotic signaling pathway (GO:0097191)|humoral immune response (GO:0006959)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of myelination (GO:0031642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil apoptotic process (GO:0001781)|neutrophil chemotaxis (GO:0030593)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity (GO:0060550)|positive regulation of fructose 1,6-bisphosphate metabolic process (GO:0060552)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|regulation of insulin secretion (GO:0050796)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of the force of heart contraction (GO:0002026)|response to drug (GO:0042493)|response to virus (GO:0009615)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|interferon-gamma receptor binding (GO:0005133)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Glucosamine(DB01296)|Olsalazine(DB01250)	CCAATTCTTCAAAATGCCTAA	0.338																																					p.L56fs		Atlas-INDEL	.											.	IFNG	38	.	0			c.168delG						.						97	98	98					12																	68551987		2203	4300	6503	SO:0001589	frameshift_variant	3458	exon2			.		CCDS8980.1	12q14	2007-10-17			ENSG00000111537	ENSG00000111537		"Interferons"	5438	protein-coding gene	gene with protein product		147570					Standard	NM_000619		Approved		uc001stw.1	P01579	OTTHUMG00000169113	ENST00000229135.3:c.167delT	chr12.hg19:g.68551987delA	ENSP00000229135:p.Leu56fs	106.0	0.0		76.0	11.0	NM_000619	B5BU88|Q53ZV4	Frame_Shift_Del	DEL	ENST00000229135.3	hg19	CCDS8980.1																																																																																			.	.		0.338	IFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402301.1			-	68551987	A	-	68551987	7	5	112	1	0	1	0	1	0	0	0	0	7557	131	5	0	345	0	IFNG	12	68551987	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3724778	68551987	65299908	785	17406										
CPSF6	11052	hgsc.bcm.edu	37	chr12	69650513	69650513	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gttggatctgaagcatcttcAaaaaagttaatggatctgtt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:69650513delA	ENST00000435070.2	+	4	521	c.411delA	c.(409-411)tcafs	p.S137fs	CPSF6_ENST00000551516.1_Intron|CPSF6_ENST00000456847.3_Frame_Shift_Del_p.S137fs|CPSF6_ENST00000266679.8_Frame_Shift_Del_p.S137fs	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa	137	Necessary for interaction with NUDT21/CPSF5.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(7)|lung(8)	16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			AAGCATCTTCAAAAAAGTTAA	0.348																																					p.S137X		Atlas-INDEL	.											.	CPSF6	96	.	0			c.410delC						.						124	125	125					12																	69650513		2203	4300	6503	SO:0001589	frameshift_variant	11052	exon4			.	X67336	CCDS8988.1, CCDS73494.1	12q15	2013-06-18	2002-08-29			ENSG00000111605		"RNA binding motif (RRM) containing"	13871	protein-coding gene	gene with protein product	"cleavage factor Im complex 68 kDa subunit"	604979	"cleavage and polyadenylation specific factor 6, 68kD subunit"			9659921, 17267687	Standard	NM_007007		Approved	CFIM, HPBRII-4, HPBRII-7, CFIM68	uc001sut.4	Q16630		ENST00000435070.2:c.411delA	chr12.hg19:g.69650513delA	ENSP00000391774:p.Ser137fs	178.0	0.0		194.0	13.0	NM_007007	A8K7K9|Q53ES1|Q9BSJ7|Q9BW18	Frame_Shift_Del	DEL	ENST00000435070.2	hg19	CCDS8988.1																																																																																			.	.		0.348	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	NM_007007		-	69650513	A	-	69650513	7	5	112	1	0	1	0	1	0	0	0	0	3831	117	5	0	425	0	CPSF6	12	69650513	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1098526	69650513	64201382	786	17407										
CPSF6	11052	hgsc.bcm.edu	37	chr12	69652587	69652587	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctccagttccaggctacggCccccctcctggcccaccacc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:69652587delC	ENST00000435070.2	+	6	1022	c.912delC	c.(910-912)ggcfs	p.G304fs	CPSF6_ENST00000551516.1_Intron|CPSF6_ENST00000456847.3_Frame_Shift_Del_p.G231fs|CPSF6_ENST00000266679.8_Frame_Shift_Del_p.G341fs	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa	304	Pro-rich.				mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(7)|lung(8)	16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			CAGGCTACGGCCCCCCTCCTG	0.632																																					p.G304fs		Atlas-INDEL	.											.	CPSF6	96	.	0			c.911delG						.						104	85	91					12																	69652587		2203	4300	6503	SO:0001589	frameshift_variant	11052	exon6			.	X67336	CCDS8988.1, CCDS73494.1	12q15	2013-06-18	2002-08-29			ENSG00000111605		"RNA binding motif (RRM) containing"	13871	protein-coding gene	gene with protein product	"cleavage factor Im complex 68 kDa subunit"	604979	"cleavage and polyadenylation specific factor 6, 68kD subunit"			9659921, 17267687	Standard	NM_007007		Approved	CFIM, HPBRII-4, HPBRII-7, CFIM68	uc001sut.4	Q16630		ENST00000435070.2:c.912delC	chr12.hg19:g.69652587delC	ENSP00000391774:p.Gly304fs	79.0	0.0		133.0	11.0	NM_007007	A8K7K9|Q53ES1|Q9BSJ7|Q9BW18	Frame_Shift_Del	DEL	ENST00000435070.2	hg19	CCDS8988.1																																																																																			.	.		0.632	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	NM_007007		-	69652587	C	-	69652587	7	5	112	1	0	1	0	1	0	0	0	0	3831	726	26	0	934	0	CPSF6	12	69652587	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	2074	69652587	64199308	787	17408										
TBC1D15	64786	hgsc.bcm.edu	37	chr12	72300901	72300901	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cattttgatgacctactgtaTgtatgattttgatttaggta	8	4	0	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:72300901T>C	ENST00000550746.1	+	12	1398	c.1334T>C	c.(1333-1335)aTg>aCg	p.M445T	TBC1D15_ENST00000548679.1_3'UTR|TBC1D15_ENST00000319106.8_Missense_Mutation_p.M436T|TBC1D15_ENST00000485960.2_Missense_Mutation_p.M428T|TBC1D15_ENST00000393309.3_Missense_Mutation_p.M199T	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	445	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ACCTACTGTATGTATGATTTT	0.289																																					p.M445T		Atlas-SNP	.											.	TBC1D15	99	.	0			c.T1334C						.						177	159	165					12																	72300901		2202	4298	6500	SO:0001583	missense	64786	exon12			ACTGTATGTATGA	AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.1334T>C	chr12.hg19:g.72300901T>C	ENSP00000448182:p.Met445Thr	89.0	0.0		97.0	4.0	NM_022771	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Missense_Mutation	SNP	ENST00000550746.1	hg19	CCDS31858.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.673062	0.67928	.	.	ENSG00000121749	ENST00000550746;ENST00000319106;ENST00000485960;ENST00000393309	T;T;T;T	0.04234	3.67;3.67;3.67;3.67	5.09	5.09	0.68999	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.19604	0.0471	M	0.68317	2.08	0.80722	D	1	D;D;D	0.65815	0.995;0.994;0.993	D;D;P	0.77004	0.989;0.981;0.901	T	0.00256	-1.1873	10	0.72032	D	0.01	-13.8343	14.8798	0.70522	0.0:0.0:0.0:1.0	.	436;428;445	E9PH93;Q8TC07-2;Q8TC07	.;.;TBC15_HUMAN	T	445;436;428;199	ENSP00000448182:M445T;ENSP00000318262:M436T;ENSP00000420678:M428T;ENSP00000376986:M199T	ENSP00000318262:M436T	M	+	2	0	TBC1D15	70587168	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	1.919000	0.55581	0.528000	0.53228	ATG	.	.		0.289	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771		C	72300901	T	C	72300901	3	2	112	1	0	0	0	0	1	0	0	0	15619	1464	51	2	1504	2	TBC1D15	12	72300901	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2648314	72300901	61550994	788	17409										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85264404	85264404	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agatgcaggaaaatgtgtcaTcgcttctgtaaaggcaataa	10	6	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:85264404T>C	ENST00000266682.5	-	9	1889	c.1348A>G	c.(1348-1350)Atg>Gtg	p.M450V	SLC6A15_ENST00000551388.1_5'Flank|SLC6A15_ENST00000552192.1_Missense_Mutation_p.M343V|SLC6A15_ENST00000309283.7_Missense_Mutation_p.M158V	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	450					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						AAATGTGTCATCGCTTCTGTA	0.418																																					p.M450V		Atlas-SNP	.											.	SLC6A15	159	.	0			c.A1348G						.						143	133	136					12																	85264404		2203	4300	6503	SO:0001583	missense	55117	exon9			GTGTCATCGCTTC	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.1348A>G	chr12.hg19:g.85264404T>C	ENSP00000266682:p.Met450Val	97.0	0.0		80.0	4.0	NM_182767	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	hg19	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.945403	0.73672	.	.	ENSG00000072041	ENST00000309283;ENST00000266682;ENST00000318721;ENST00000552192;ENST00000551818	T;T;T	0.73152	-0.72;-0.72;-0.72	5.7	5.7	0.88788	.	0.070578	0.85682	D	0.000000	T	0.71728	0.3374	N	0.20530	0.585	0.80722	D	1	D;D	0.62365	0.991;0.985	P;D	0.63877	0.835;0.919	T	0.69950	-0.5006	10	0.25106	T	0.35	.	15.9735	0.80040	0.0:0.0:0.0:1.0	.	158;450	F8WJN6;Q9H2J7	.;S6A15_HUMAN	V	158;450;166;343;158	ENSP00000311645:M158V;ENSP00000266682:M450V;ENSP00000450145:M343V	ENSP00000266682:M450V	M	-	1	0	SLC6A15	83788535	1.000000	0.71417	0.918000	0.36340	0.993000	0.82548	7.603000	0.82811	2.159000	0.67721	0.533000	0.62120	ATG	.	.		0.418	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		C	85264404	T	C	85264404	3	2	112	1	0	0	0	0	1	0	0	0	14693	1435	50	2	860	2	SLC6A15	12	85264404	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	12963503	85264404	48587491	789	17410										
TSPAN19	144448	hgsc.bcm.edu	37	chr12	85411267	85411267	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcattcagtggctcatcacAaaaccattttcttaaagttg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:85411267delA	ENST00000532498.2	-	7	642	c.562delT	c.(562-564)tgtfs	p.C188fs	TSPAN19_ENST00000547403.2_5'Flank	NM_001100917.1	NP_001094387.1	P0C672	TSN19_HUMAN	tetraspanin 19	188						integral component of membrane (GO:0016021)				ovary(1)	1						GGCTCATCACAAAACCATTTT	0.328																																					p.C188fs		Atlas-INDEL	.											.	TSPAN19	23	.	0			c.563delG						.						92	87	88					12																	85411267		1843	4092	5935	SO:0001589	frameshift_variant	144448	exon7			.		CCDS44949.1	12q21.31	2013-02-14			ENSG00000231738	ENSG00000231738		"Tetraspanins"	31886	protein-coding gene	gene with protein product							Standard	NM_001100917		Approved		uc009zsj.3	P0C672	OTTHUMG00000166181	ENST00000532498.2:c.562delT	chr12.hg19:g.85411267delA	ENSP00000433816:p.Cys188fs	123.0	0.0		139.0	11.0	NM_001100917		Frame_Shift_Del	DEL	ENST00000532498.2	hg19	CCDS44949.1																																																																																			.	.		0.328	TSPAN19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388240.2	NM_001100917		-	85411267	A	-	85411267	7	5	112	1	0	1	0	1	0	0	0	0	16658	130	5	0	196	0	TSPAN19	12	85411267	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	146863	85411267	48440628	790	17411										
MGAT4C	25834	hgsc.bcm.edu	37	chr12	86383211	86383211	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcttcaatgtacaagttcatAaaaaggagaaaaatgacaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:86383211delA	ENST00000604798.1	-	6	1318	c.114delT	c.(112-114)tttfs	p.F38fs	MGAT4C_ENST00000549405.2_Frame_Shift_Del_p.F38fs|MGAT4C_ENST00000332156.1_Frame_Shift_Del_p.F38fs|MGAT4C_ENST00000552435.2_Frame_Shift_Del_p.F38fs|MGAT4C_ENST00000552808.2_Frame_Shift_Del_p.F38fs|MGAT4C_ENST00000548651.1_Frame_Shift_Del_p.F38fs|MGAT4C_ENST00000393205.2_Frame_Shift_Del_p.F67fs			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	38					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ACAAGTTCATAAAAAGGAGAA	0.323																																					p.M39X		Atlas-INDEL	.											.	MGAT4C	110	.	0			c.115delA						.						86	75	79					12																	86383211		2203	4299	6502	SO:0001589	frameshift_variant	25834	exon5			.		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	30871	protein-coding gene	gene with protein product		607385	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.114delT	chr12.hg19:g.86383211delA	ENSP00000474896:p.Phe38fs	205.0	0.0		179.0	11.0	NM_013244	B4DRH2|Q4G199|Q9UIU5	Frame_Shift_Del	DEL	ENST00000604798.1	hg19	CCDS9030.1																																																																																			.	.		0.323	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		-	86383211	A	-	86383211	7	5	112	1	0	1	0	1	0	0	0	0	9556	359	13	0	1334	0	MGAT4C	12	86383211	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	971944	86383211	47468684	791	17412										
C12orf50	160419	hgsc.bcm.edu	37	chr12	88383079	88383079	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgatatggtgatttctttcTcttcagttaaagcttcactt	6	7	4	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:88383079T>C	ENST00000298699.2	-	8	842	c.662A>G	c.(661-663)gAg>gGg	p.E221G	C12orf50_ENST00000550553.1_Missense_Mutation_p.E221G	NM_152589.1	NP_689802.1	Q8NA57	CL050_HUMAN	chromosome 12 open reading frame 50	221										NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|urinary_tract(2)	34						GATTTCTTTCTCTTCAGTTAA	0.338																																					p.E221G		Atlas-SNP	.											.	C12orf50	70	.	0			c.A662G						.						69	67	68					12																	88383079		2203	4300	6503	SO:0001583	missense	160419	exon8			TCTTTCTCTTCAG	AK093140	CCDS9031.1	12q21.32	2006-02-03				ENSG00000165805			26665	protein-coding gene	gene with protein product						12477932	Standard	NM_152589		Approved	FLJ35821	uc001tam.1	Q8NA57	OTTHUMG00000169869	ENST00000298699.2:c.662A>G	chr12.hg19:g.88383079T>C	ENSP00000298699:p.Glu221Gly	44.0	0.0		60.0	4.0	NM_152589	Q6P674	Missense_Mutation	SNP	ENST00000298699.2	hg19	CCDS9031.1	.	.	.	.	.	.	.	.	.	.	T	11.78	1.742198	0.30865	.	.	ENSG00000165805	ENST00000298699;ENST00000550553;ENST00000551944	T;T	0.35421	1.31;1.31	4.96	3.81	0.43845	.	0.344430	0.24539	N	0.037650	T	0.27731	0.0682	L	0.41824	1.3	0.23731	N	0.996992	B;B	0.10296	0.003;0.001	B;B	0.09377	0.004;0.003	T	0.18053	-1.0349	10	0.44086	T	0.13	.	8.3575	0.32340	0.0:0.0924:0.0:0.9076	.	275;221	G3V208;Q8NA57	.;CL050_HUMAN	G	221;221;275	ENSP00000298699:E221G;ENSP00000448344:E221G	ENSP00000298699:E221G	E	-	2	0	C12orf50	86907210	0.852000	0.29690	0.936000	0.37596	0.615000	0.37417	1.020000	0.30027	0.758000	0.33059	-0.379000	0.06801	GAG	.	.		0.338	C12orf50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406328.1	NM_152589		C	88383079	T	C	88383079	3	2	112	1	0	0	0	0	1	0	0	0	1697	1551	54	2	606	2	C12orf50	12	88383079	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1999868	88383079	45468816	792	17413										
EEA1	8411	hgsc.bcm.edu	37	chr12	93251072	93251072	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgctgctgcagcccttgataTttttctaattccttctttaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:93251072delT	ENST00000322349.8	-	5	609	c.345delA	c.(343-345)aaafs	p.K115fs	EEA1_ENST00000547833.1_5'Flank	NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	115					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						GCCCTTGATATTTTTCTAATT	0.254																																					p.Y116fs		Atlas-INDEL	.											.	EEA1	104	.	0			c.346delT						.						29	29	29					12																	93251072		2200	4289	6489	SO:0001589	frameshift_variant	8411	exon5			.	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.345delA	chr12.hg19:g.93251072delT	ENSP00000317955:p.Lys115fs	209.0	0.0		276.0	20.0	NM_003566	Q14221	Frame_Shift_Del	DEL	ENST00000322349.8	hg19	CCDS31874.1																																																																																			.	.		0.254	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		-	93251072	T	-	93251072	7	5	112	1	0	1	0	1	0	0	0	0	4923	1490	52	0	3990	0	EEA1	12	93251072	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	4867993	93251072	40600823	793	17414										
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94692436	94692436	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcattctgtgcttgaaaaacTttttagaagcatttggagtt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:94692436delT	ENST00000258526.4	+	27	4352	c.4103delT	c.(4102-4104)cttfs	p.L1368fs	PLXNC1_ENST00000545312.1_Frame_Shift_Del_p.L107fs|PLXNC1_ENST00000547057.1_Frame_Shift_Del_p.L415fs	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1368					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CTTGAAAAACTTTTTAGAAGC	0.348																																					p.L1368fs		Atlas-INDEL	.											.	PLXNC1	135	.	0			c.4102delC						.						74	75	75					12																	94692436		2203	4300	6503	SO:0001589	frameshift_variant	10154	exon27			.	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.4103delT	chr12.hg19:g.94692436delT	ENSP00000258526:p.Leu1368fs	120.0	0.0		165.0	11.0	NM_005761	Q59H25	Frame_Shift_Del	DEL	ENST00000258526.4	hg19	CCDS9049.1																																																																																			.	.		0.348	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			-	94692436	T	-	94692436	7	5	112	1	0	1	0	1	0	0	0	0	12135	1609	56	0	4209	0	PLXNC1	12	94692436	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1441364	94692436	39159459	794	17415										
VEZT	55591	hgsc.bcm.edu	37	chr12	95694123	95694123	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgaaaactctctagaaggtAaaaataaagataattcttca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:95694123delA	ENST00000436874.1	+	12	2119	c.2014delA	c.(2014-2016)aaafs	p.K672fs	VEZT_ENST00000261219.6_Frame_Shift_Del_p.K624fs|VEZT_ENST00000356859.4_3'UTR	NM_017599.3	NP_060069.3	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane protein	672					chordate embryonic development (GO:0043009)|single organismal cell-cell adhesion (GO:0016337)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stereocilia ankle link complex (GO:0002142)				endometrium(2)|kidney(3)|large_intestine(1)|lung(14)|ovary(2)|upper_aerodigestive_tract(1)	23						TCTAGAAGGTAAAAATAAAGA	0.358																																					p.G671fs		Atlas-INDEL	.											.	VEZT	106	.	0			c.2013delT						.						39	37	38					12																	95694123		1848	4093	5941	SO:0001589	frameshift_variant	55591	exon12			.	AF216644	CCDS44954.1	12q22	2011-02-15			ENSG00000028203	ENSG00000028203			18258	protein-coding gene	gene with protein product						11080149, 16199027, 21156161	Standard	NM_017599		Approved	DKFZP761C241	uc001tdz.2	Q9HBM0	OTTHUMG00000170182	ENST00000436874.1:c.2014delA	chr12.hg19:g.95694123delA	ENSP00000410083:p.Lys672fs	93.0	0.0		193.0	12.0	NM_017599	Q6P1Q3|Q9H2F4|Q9H2U5|Q9NT70|Q9NVW0|Q9UF91	Frame_Shift_Del	DEL	ENST00000436874.1	hg19	CCDS44954.1																																																																																			.	.		0.358	VEZT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407804.2	NM_017599		-	95694123	A	-	95694123	7	5	112	1	0	1	0	1	0	0	0	0	17171	363	13	0	2060	0	VEZT	12	95694123	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1001687	95694123	38157772	795	17416										
IKBIP	121457	hgsc.bcm.edu	37	chr12	99020228	99020228	+	Intron	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcttagtgtgctatcttccAaatcttttagccgttcagtg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:99020228delA	ENST00000342502.2	-	2	709				IKBIP_ENST00000420861.1_Intron|IKBIP_ENST00000299157.4_Frame_Shift_Del_p.L205fs|IKBIP_ENST00000393042.3_Intron	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein						response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						GCTATCTTCCAAATCTTTTAG	0.363																																					p.L205fs		Atlas-INDEL	.											.	IKBIP	46	.	0			c.615delG						.						143	136	139					12																	99020228		2203	4300	6503	SO:0001627	intron_variant	121457	exon3			.	AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"I kappa B kinase interacting protein"	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.297+7845T>-	chr12.hg19:g.99020228delA		97.0	0.0		165.0	10.0	NM_153687	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Frame_Shift_Del	DEL	ENST00000342502.2	hg19	CCDS9067.1																																																																																			.	.		0.363	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687		-	99020228	A	-	99020228	6	5	112	0	1	1	0	1	0	0	0	0	7618	131	5	0		0	IKBIP	12	99020228	Intron	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3326105	99020228	34831667	796	17417										
UTP20	27340	hgsc.bcm.edu	37	chr12	101746865	101746865	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagcattccactttgaccacAaaactcttgaagaacaaatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:101746865delA	ENST00000261637.4	+	40	5239	c.5065delA	c.(5065-5067)aaafs	p.K1689fs		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1689					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CTTTGACCACAAAACTCTTGA	0.274																																					p.H1688fs		Atlas-INDEL	.											.	UTP20	222	.	0			c.5064delC						.						49	52	51					12																	101746865		2200	4293	6493	SO:0001589	frameshift_variant	27340	exon40			.	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.5065delA	chr12.hg19:g.101746865delA	ENSP00000261637:p.Lys1689fs	141.0	0.0		186.0	13.0	NM_014503	Q9H3H4	Frame_Shift_Del	DEL	ENST00000261637.4	hg19	CCDS9081.1																																																																																			.	.		0.274	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		-	101746865	A	-	101746865	7	5	112	1	0	1	0	1	0	0	0	0	17114	131	5	0	5223	0	UTP20	12	101746865	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2726637	101746865	32105030	797	17418										
C12orf48	55010	hgsc.bcm.edu	37	chr12	102589882	102589882	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acaggtggatttggatggtgAaaatattctctgtgataata							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:102589882delA	ENST00000358383.5	+	11	1598	c.1553delA	c.(1552-1554)gaafs	p.E518fs	PARPBP_ENST00000392911.2_Frame_Shift_Del_p.E437fs|PARPBP_ENST00000541394.1_Frame_Shift_Del_p.E595fs|PARPBP_ENST00000543784.1_3'UTR|PARPBP_ENST00000378128.3_3'UTR|PARPBP_ENST00000535811.1_3'UTR|PARPBP_ENST00000327680.2_Frame_Shift_Del_p.E437fs			Q9NWS1	PARI_HUMAN	PARP1 binding protein	518					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(8)|urinary_tract(2)	11						TTGGATGGTGAAAATATTCTC	0.323																																					p.E518fs		Atlas-INDEL	.											.	PARPBP	40	.	0			c.1552delG						.						62	63	63					12																	102589882		2203	4300	6503	SO:0001589	frameshift_variant	55010	exon11			.	AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"PARP-1 binding protein"	613687	"chromosome 12 open reading frame 48"	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.1553delA	chr12.hg19:g.102589882delA	ENSP00000351153:p.Glu518fs	138.0	0.0		210.0	14.0	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Frame_Shift_Del	DEL	ENST00000358383.5	hg19	CCDS9090.2																																																																																			.	.		0.323	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915		-	102589882	A	-	102589882	7	5	112	1	0	1	0	1	0	0	0	0	1694	246	9	0	1344	0	C12orf48	12	102589882	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	843017	102589882	31262013	798	17419										
ATP2A2	488	hgsc.bcm.edu	37	chr12	110720572	110720572	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgaagacttgctagttaggaTtttattactggcagcatgta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:110720572delT	ENST00000539276.2	+	3	300	c.191delT	c.(190-192)attfs	p.I64fs	ATP2A2_ENST00000395494.2_Frame_Shift_Del_p.I64fs|ATP2A2_ENST00000308664.6_Frame_Shift_Del_p.I64fs|ATP2A2_ENST00000552636.1_5'UTR			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	64					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						CTAGTTAGGATTTTATTACTG	0.323																																					p.I64fs		Atlas-INDEL	.											.	ATP2A2	78	.	0			c.190delA						.						113	109	111					12																	110720572		2203	4300	6503	SO:0001589	frameshift_variant	488	exon3			.		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.191delT	chr12.hg19:g.110720572delT	ENSP00000440045:p.Ile64fs	104.0	0.0		156.0	11.0	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Frame_Shift_Del	DEL	ENST00000539276.2	hg19	CCDS9144.1																																																																																			.	.		0.323	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		-	110720572	T	-	110720572	7	5	112	1	0	1	0	1	0	0	0	0	1137	1493	52	0	201	0	ATP2A2	12	110720572	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	8130690	110720572	23131323	799	17420										
GPN3	51184	hgsc.bcm.edu	37	chr12	110895351	110895351	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgaactgagaatcaacaagAaaaactccacagactcggaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:110895351delA	ENST00000228827.3	-	4	476	c.414delT	c.(412-414)tttfs	p.F138fs	GPN3_ENST00000543199.1_Frame_Shift_Del_p.F177fs|GPN3_ENST00000552180.1_5'Flank|GPN3_ENST00000537466.2_Frame_Shift_Del_p.F148fs	NM_016301.3	NP_057385.3			GPN-loop GTPase 3											endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|urinary_tract(1)	8						AATCAACAAGAAAAACTCCAC	0.403																																					p.L178fs		Atlas-INDEL	.											.	GPN3	37	.	0			c.532delC						.						56	52	53					12																	110895351		2203	4300	6503	SO:0001589	frameshift_variant	51184	exon4			.	BC008416	CCDS9147.1, CCDS53830.1, CCDS53831.1	12q24.11	2012-12-18	2008-04-30	2008-04-30	ENSG00000111231	ENSG00000111231		"GPN-loop GTPases"	30186	protein-coding gene	gene with protein product			"ATP binding domain 1 family, member C"	ATPBD1C		12975309	Standard	NM_016301		Approved	MGC14560	uc021rdu.1	Q9UHW5	OTTHUMG00000169524	ENST00000228827.3:c.414delT	chr12.hg19:g.110895351delA	ENSP00000228827:p.Phe138fs	129.0	0.0		194.0	13.0	NM_001164372		Frame_Shift_Del	DEL	ENST00000228827.3	hg19	CCDS9147.1																																																																																			.	.		0.403	GPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404607.1	NM_016301		-	110895351	A	-	110895351	7	5	112	1	0	1	0	1	0	0	0	0	6627	243	9	0	460	0	GPN3	12	110895351	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	174779	110895351	22956544	800	17421										
VPS29	51699	hgsc.bcm.edu	37	chr12	110933940	110933940	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atttttcctggcaccaggagTtttttgaatttagctggcaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:110933940delT	ENST00000549578.1	-	2	137	c.72delA	c.(70-72)aaafs	p.K24fs	VPS29_ENST00000552130.2_5'UTR|SNORD50_ENST00000365465.1_RNA|VPS29_ENST00000549970.1_5'UTR|VPS29_ENST00000447578.2_5'UTR|VPS29_ENST00000551655.1_5'Flank|VPS29_ENST00000360579.7_Frame_Shift_Del_p.K28fs|VPS29_ENST00000546588.1_Frame_Shift_Del_p.K56fs	NM_016226.3	NP_057310.1	Q9UBQ0	VPS29_HUMAN	vacuolar protein sorting 29 homolog (S. cerevisiae)	24					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphoserine phosphatase activity (GO:0004647)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						GCACCAGGAGTTTTTTGAATT	0.423																																					p.L29fs		Atlas-INDEL	.											.	VPS29	10	.	0			c.85delC						.						140	126	130					12																	110933940		1864	4101	5965	SO:0001589	frameshift_variant	51699	exon3			.	AF193795	CCDS41832.1, CCDS53832.1, CCDS73525.1	12q24	2006-12-19	2006-12-19			ENSG00000111237			14340	protein-coding gene	gene with protein product		606932	"vacuolar protein sorting 29 (yeast homolog)", "vacuolar protein sorting 29 (yeast)"			11062004	Standard	NM_001282151		Approved	PEP11, DC7, DC15	uc001tqx.3	Q9UBQ0	OTTHUMG00000169527	ENST00000549578.1:c.72delA	chr12.hg19:g.110933940delT	ENSP00000447058:p.Lys24fs	103.0	0.0		144.0	11.0	NM_057180	Q502Y5|Q6FIF8|Q6IAH3|Q9H0W0|Q9NRP1|Q9NRU7	Frame_Shift_Del	DEL	ENST00000549578.1	hg19	CCDS41832.1																																																																																			.	.		0.423	VPS29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404623.1			-	110933940	T	-	110933940	7	5	112	1	0	1	0	1	0	0	0	0	17215	1722	60	0	488	0	VPS29	12	110933940	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	38589	110933940	22917955	801	17422										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112622648	112622648	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcgtcactcgtcacgcccagCccctgtgggtccttcctggt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:112622648delC	ENST00000430131.2	-	60	10001	c.8856delG	c.(8854-8856)gggfs	p.G2952fs	HECTD4_ENST00000377560.5_Frame_Shift_Del_p.G3202fs|HECTD4_ENST00000550722.1_Frame_Shift_Del_p.G3228fs			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2952					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TCACGCCCAGCCCCTGTGGGT	0.682																																					p.L3241fs		Atlas-INDEL	.											.	.	.	.	0			c.9721delC						.						72	87	82					12																	112622648		2196	4278	6474	SO:0001589	frameshift_variant	283450	exon61			.	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.8856delG	chr12.hg19:g.112622648delC	ENSP00000404379:p.Gly2952fs	84.0	0.0		183.0	11.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Frame_Shift_Del	DEL	ENST00000430131.2	hg19																																																																																				.	.		0.682	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		-	112622648	C	-	112622648	7	5	112	1	0	1	0	1	0	0	0	0	1698	726	26	0	3198	0	C12orf51	12	112622648	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1688708	112622648	21229247	802	17423										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112630422	112630422	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaggggtactggtcagcggtGgggggaggtgcaagcccagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:112630422delG	ENST00000430131.2	-	58	9113	c.7968delC	c.(7966-7968)cccfs	p.P2656fs	HECTD4_ENST00000377560.5_Frame_Shift_Del_p.P2906fs|HECTD4_ENST00000550722.1_Frame_Shift_Del_p.P2932fs			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2656					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GGTCAGCGGTGGGGGGAGGTG	0.607																																					p.T2945fs		Atlas-INDEL	.											C12orf51_ENST00000377560,NS,carcinoma,0,2	.	.	.	0			c.8833delA						.						26	30	28					12																	112630422		2006	4160	6166	SO:0001589	frameshift_variant	283450	exon59			.	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.7968delC	chr12.hg19:g.112630422delG	ENSP00000404379:p.Pro2656fs	70.0	0.0		152.0	11.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Frame_Shift_Del	DEL	ENST00000430131.2	hg19																																																																																				.	.		0.607	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		-	112630422	G	-	112630422	7	5	112	1	0	1	0	1	0	0	0	0	1698	1335	47	0	4094	0	C12orf51	12	112630422	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	7774	112630422	21221473	803	17424										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112694221	112694221	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttctttaaatttatagttgTctctgacggggtggactgtt	10	5	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:112694221T>C	ENST00000430131.2	-	20	3079	c.1934A>G	c.(1933-1935)gAc>gGc	p.D645G	RP3-521E19.2_ENST00000547401.1_RNA|HECTD4_ENST00000377560.5_Missense_Mutation_p.D895G|HECTD4_ENST00000550722.1_Missense_Mutation_p.D931G			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	645					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TTTATAGTTGTCTCTGACGGG	0.448																																					p.D933G		Atlas-SNP	.											.	.	.	.	0			c.A2798G						.						89	91	90					12																	112694221		2203	4300	6503	SO:0001583	missense	283450	exon21			TAGTTGTCTCTGA	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.1934A>G	chr12.hg19:g.112694221T>C	ENSP00000404379:p.Asp645Gly	87.0	0.0		123.0	5.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	T	29.6	5.016303	0.93404	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.56444	0.46;0.47;0.64	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.60051	0.2239	N	0.24115	0.695	0.58432	D	0.999992	D;D;D	0.67145	0.996;0.993;0.996	D;D;D	0.73708	0.981;0.971;0.981	T	0.65084	-0.6254	10	0.87932	D	0	.	15.3801	0.74648	0.0:0.0:0.0:1.0	.	645;645;645	Q9Y4D8-2;Q9Y4D8;Q9Y4D8-3	.;K0614_HUMAN;.	G	895;645;931	ENSP00000366783:D895G;ENSP00000404379:D645G;ENSP00000449784:D931G	ENSP00000366783:D895G	D	-	2	0	C12orf51	111178604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.459000	0.80802	2.275000	0.75901	0.533000	0.62120	GAC	.	.		0.448	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		C	112694221	T	C	112694221	3	2	112	1	0	0	0	0	1	0	0	0	1698	1667	58	2	10280	2	C12orf51	12	112694221	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	63799	112694221	21157674	804	17425										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112888306	112888306	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctctgaactgtgcagatcctAcctctgaaaggtcagtaaca	8	11	3	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:112888306A>G	ENST00000351677.2	+	3	520	c.322A>G	c.(322-324)Acc>Gcc	p.T108A	PTPN11_ENST00000392597.1_Missense_Mutation_p.T108A	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	108					abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						TGCAGATCCTACCTCTGAAAG	0.448			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																												p.T108A		Atlas-SNP	.		Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	.	PTPN11	623	.	0			c.A322G						.						95	89	91					12																	112888306		2203	4300	6503	SO:0001583	missense	5781	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	GATCCTACCTCTG	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.322A>G	chr12.hg19:g.112888306A>G	ENSP00000340944:p.Thr108Ala	70.0	0.0		97.0	4.0	NM_080601	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	hg19	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.552427	0.86127	.	.	ENSG00000179295	ENST00000392597;ENST00000351677;ENST00000392596	T;T	0.73047	-0.71;2.88	6.05	4.87	0.63330	.	0.045464	0.85682	D	0.000000	T	0.79052	0.4381	M	0.83953	2.67	0.58432	D	0.999998	P;B	0.43542	0.81;0.196	P;B	0.48952	0.596;0.199	T	0.81150	-0.1064	10	0.87932	D	0	.	12.5001	0.55950	0.8747:0.0:0.0:0.1253	.	108;108	Q06124-2;Q06124-3	.;.	A	108	ENSP00000376376:T108A;ENSP00000340944:T108A	ENSP00000340944:T108A	T	+	1	0	PTPN11	111372689	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.568000	0.82369	1.055000	0.40461	0.528000	0.53228	ACC	.	.		0.448	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			G	112888306	A	G	112888306	3	3	112	1	0	0	0	0	1	0	0	0	12793	391	14	2	332	2	PTPN11	12	112888306	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	194085	112888306	20963589	805	17426										
RASAL1	8437	hgsc.bcm.edu	37	chr12	113553545	113553545	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcaaggtcctggcggcagtCccccaaggtcagctcttcca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:113553545delC	ENST00000261729.5	-	11	1213	c.898delG	c.(898-900)gacfs	p.D300fs	RASAL1_ENST00000446861.3_Frame_Shift_Del_p.D300fs|RASAL1_ENST00000546530.1_Frame_Shift_Del_p.D300fs|RASAL1_ENST00000548055.1_Frame_Shift_Del_p.D300fs|RASAL1_ENST00000418411.2_5'UTR			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	300					intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						TGGCGGCAGTCCCCCAAGGTC	0.637																																					p.D300fs		Atlas-INDEL	.											.	RASAL1	89	.	0			c.899delA						.						56	62	60					12																	113553545		2203	4300	6503	SO:0001589	frameshift_variant	8437	exon11			.	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"Pleckstrin homology (PH) domain containing"	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.898delG	chr12.hg19:g.113553545delC	ENSP00000261729:p.Asp300fs	119.0	0.0		194.0	12.0	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Frame_Shift_Del	DEL	ENST00000261729.5	hg19	CCDS9165.1																																																																																			.	.		0.637	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658		-	113553545	C	-	113553545	7	5	112	1	0	1	0	1	0	0	0	0	13078	855	30	0	1564	0	RASAL1	12	113553545	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	665239	113553545	20298350	806	17427										
MSI1	4440	hgsc.bcm.edu	37	chr12	120784098	120784098	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggctgggagtcgaacctggaGggggagccatcgtccagggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:120784098delG	ENST00000257552.2	-	13	975	c.887delC	c.(886-888)cctfs	p.P297fs		NM_002442.3	NP_002433.1	O43347	MSI1H_HUMAN	musashi RNA-binding protein 1	297					epithelial cell differentiation (GO:0030855)|nervous system development (GO:0007399)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(4)|central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGAACCTGGAGGGGGAGCCAT	0.697																																					p.P296fs		Atlas-INDEL	.											.	MSI1	40	.	0			c.888delT						.						11	9	10					12																	120784098		2124	4206	6330	SO:0001589	frameshift_variant	4440	exon13			.	AB012851	CCDS9196.1	12q24	2013-07-16	2012-12-13					"RNA binding motif (RRM) containing"	7330	protein-coding gene	gene with protein product		603328	"Musashi (Drosophila) homolog 1", "musashi homolog 1 (Drosophila)"			9790759	Standard	NM_002442		Approved		uc001tye.2	O43347	OTTHUMG00000169344	ENST00000257552.2:c.887delC	chr12.hg19:g.120784098delG	ENSP00000257552:p.Pro297fs	64.0	0.0		151.0	11.0	NM_002442	Q96PU0|Q96PU1|Q96PU2|Q96PU3	Frame_Shift_Del	DEL	ENST00000257552.2	hg19	CCDS9196.1																																																																																			.	.		0.697	MSI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403629.1	NM_002442		-	120784098	G	-	120784098	7	5	112	1	0	1	0	1	0	0	0	0	9884	1000	35	0	209	0	MSI1	12	120784098	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	7230553	120784098	13067797	807	17428										
KDM2B	84678	hgsc.bcm.edu	37	chr12	122018773	122018773	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgctgcatgtctttttcgtGgggggtgatcctctgcagat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:122018773delG	ENST00000377071.4	-	1	116	c.44delC	c.(43-45)ccafs	p.P15fs	KDM2B_ENST00000538046.2_Frame_Shift_Del_p.P15fs|RP13-941N14.1_ENST00000541574.1_lincRNA|KDM2B_ENST00000377069.4_5'Flank|KDM2B_ENST00000536437.1_5'UTR	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	15					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						TCTTTTTCGTGGGGGGTGATC	0.483																																					p.P15fs		Atlas-INDEL	.											.	KDM2B	218	.	0			c.45delA						.						128	128	128					12																	122018773		1842	4084	5926	SO:0001589	frameshift_variant	84678	exon1			.	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.44delC	chr12.hg19:g.122018773delG	ENSP00000366271:p.Pro15fs	172.0	0.0		224.0	14.0	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Frame_Shift_Del	DEL	ENST00000377071.4	hg19	CCDS41850.1																																																																																			.	.		0.483	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		-	122018773	G	-	122018773	7	5	112	1	0	1	0	1	0	0	0	0	8134	1348	47	0	4147	0	KDM2B	12	122018773	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1234675	122018773	11833122	808	17429										
BCL7A	605	hgsc.bcm.edu	37	chr12	122473237	122473237	+	Splice_Site	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgctccattttcccctgcagAaaaacaagaataagaaaaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:122473237delA	ENST00000261822.4	+	3	381	c.175delA	c.(175-177)aaa>aa	p.K59fs	BCL7A_ENST00000538010.1_Splice_Site_p.K59fs	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	59					negative regulation of transcription, DNA-templated (GO:0045892)					haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		TCCCCTGCAGAAAAACAAGAA	0.498			T	MYC	BNHL																																.	GBM(17;197 467 16477 23242 44349)	Atlas-INDEL	.		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	BCL7A,mouth,carcinoma,0,1	BCL7A	31	.	0			c.175-1A>-						.						79	73	75					12																	122473237		2203	4300	6503	SO:0001630	splice_region_variant	605	exon3			.	X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.175-1A>-	chr12.hg19:g.122473237delA		187.0	0.0		216.0	13.0	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Splice_Site	DEL	ENST00000261822.4	hg19	CCDS53841.1																																																																																			.	.		0.498	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1		Frame_Shift_Del	-	122473237	A	-	122473237	8	5	112	1	0	1	0	1	0	0	1	0	1378	260	9	0	185	0	BCL7A	12	122473237	Splice_Site	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	454464	122473237	11378658	809	17430										
KNTC1	9735	hgsc.bcm.edu	37	chr12	123014679	123014679	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tacctgagtgtcggttcaagAaaagaacatggaactgcttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:123014679delA	ENST00000333479.7	+	2	246	c.69delA	c.(67-69)agafs	p.R23fs	KNTC1_ENST00000450485.2_Frame_Shift_Del_p.R23fs	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	23					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		TCGGTTCAAGAAAAGAACATG	0.388																																					p.R23fs		Atlas-INDEL	.											.	KNTC1	182	.	0			c.68delG						.						126	130	128					12																	123014679		1863	4108	5971	SO:0001589	frameshift_variant	9735	exon2			.		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.69delA	chr12.hg19:g.123014679delA	ENSP00000328236:p.Arg23fs	103.0	0.0		154.0	10.0	NM_014708	A7E2C4|B3KSG2	Frame_Shift_Del	DEL	ENST00000333479.7	hg19	CCDS45002.1																																																																																			.	.		0.388	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			-	123014679	A	-	123014679	7	5	112	1	0	1	0	1	0	0	0	0	8437	243	9	0	71	0	KNTC1	12	123014679	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	541442	123014679	10837216	810	17431										
HIP1R	9026	hgsc.bcm.edu	37	chr12	123340451	123340452	+	Splice_Site	DNP	GT	GT	TG													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggagaagatcaagctggagGtgcggggtggggatgggtgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:123340451_123340452GT>TG	ENST00000253083.4	+	13	1253		c.e13+1			NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related						receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		CAAGCTGGAGGTGCGGGGTGGG	0.649																																					.		Atlas-SNP	.											.	HIP1R	68	.	0			c.1128+1G>T|c.1128+2T>G						.																																			SO:0001630	splice_region_variant	9026	exon13			CTGGAGGTGCGGG|TGGAGGTGCGGGG	AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	Exception_encountered	chr12.hg19:g.123340451_123340452delinsTG		85.0|84.0	0.0		118.0|115.0	7.0|9.0	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Splice_Site	SNP	ENST00000253083.4	hg19	CCDS31922.1																																																																																			.	.		0.649	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959	Intron	TG	123340452	GT	TG	123340451	5	4	112	1	0	0	0	0	0	0	1	0	7124	1275	44	3	1179	3	HIP1R	12	123340451	Splice_Site	DNP	GT	TCGA-DD-A39Y-01A-11D-A20W-10	325772	123340451	10511444	811	17432										
VPS37B	79720	hgsc.bcm.edu	37	chr12	123352099	123352099	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtttccgtttgctctgatagAcatcaatgaaggaatccaga	9	8	2	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:123352099A>G	ENST00000267202.2	-	4	803	c.422T>C	c.(421-423)gTc>gCc	p.V141A	RP11-463O12.3_ENST00000537827.2_lincRNA	NM_024667.2	NP_078943.1	Q9H9H4	VP37B_HUMAN	vacuolar protein sorting 37 homolog B (S. cerevisiae)	141	Interaction with IST1.|VPS37 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00646}.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)				breast(1)|central_nervous_system(1)|large_intestine(1)|skin(1)|urinary_tract(1)	5	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.08e-05)|Epithelial(86;0.000197)|BRCA - Breast invasive adenocarcinoma(302;0.205)		GCTCTGATAGACATCAATGAA	0.532																																					p.V141A		Atlas-SNP	.											.	VPS37B	26	.	0			c.T422C						.						107	111	109					12																	123352099		2203	4300	6503	SO:0001583	missense	79720	exon4			TGATAGACATCAA	AK022812	CCDS9239.1	12q24.31	2008-02-05	2006-04-04		ENSG00000139722	ENSG00000139722			25754	protein-coding gene	gene with protein product		610037	"vacuolar protein sorting 37B (yeast)"			15218037	Standard	NM_024667		Approved	FLJ12750	uc001udl.3	Q9H9H4	OTTHUMG00000168767	ENST00000267202.2:c.422T>C	chr12.hg19:g.123352099A>G	ENSP00000267202:p.Val141Ala	80.0	0.0		86.0	4.0	NM_024667		Missense_Mutation	SNP	ENST00000267202.2	hg19	CCDS9239.1	.	.	.	.	.	.	.	.	.	.	A	5.165	0.216049	0.09810	.	.	ENSG00000139722	ENST00000267202;ENST00000535765;ENST00000371248	T;T;T	0.75154	-0.91;-0.91;-0.91	5.59	0.21	0.15231	Modifier of rudimentary, Modr (2);	0.625852	0.16458	N	0.213530	T	0.44829	0.1312	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.23476	-1.0187	10	0.10377	T	0.69	-17.7843	4.1147	0.10076	0.395:0.0:0.2805:0.3245	.	141	Q9H9H4	VP37B_HUMAN	A	141;139;139	ENSP00000267202:V141A;ENSP00000446075:V139A;ENSP00000360294:V139A	ENSP00000267202:V141A	V	-	2	0	VPS37B	121918052	0.652000	0.27349	0.181000	0.23098	0.744000	0.42396	1.600000	0.36762	0.093000	0.17368	0.533000	0.62120	GTC	.	.		0.532	VPS37B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400946.1	NM_024667		G	123352099	A	G	123352099	3	3	112	1	0	0	0	0	1	0	0	0	17221	275	10	2	439	2	VPS37B	12	123352099	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	11648	123352099	10499796	812	17433										
MMP17	4326	hgsc.bcm.edu	37	chr12	132335715	132335715	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcacctctggggcatcctctCccccgggggccccaggccca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:132335715delC	ENST00000360564.1	+	10	1810	c.1708delC	c.(1708-1710)cccfs	p.P571fs	MMP17_ENST00000535004.1_Frame_Shift_Del_p.P111fs|MMP17_ENST00000535291.1_Frame_Shift_Del_p.P487fs	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	571					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	GGCATCCTCTCCCCCGGGGGC	0.716																																					p.S569fs		Atlas-INDEL	.											.	MMP17	77	.	0			c.1707delT						.						12	13	12					12																	132335715		2154	4241	6395	SO:0001589	frameshift_variant	4326	exon10			.	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"matrix metalloproteinase 17 (membrane-inserted)"			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.1708delC	chr12.hg19:g.132335715delC	ENSP00000353767:p.Pro571fs	81.0	0.0		152.0	10.0	NM_016155	Q14850	Frame_Shift_Del	DEL	ENST00000360564.1	hg19	CCDS31927.1																																																																																			.	.		0.716	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155		-	132335715	C	-	132335715	7	5	112	1	0	1	0	1	0	0	0	0	9665	855	30	0	1746	0	MMP17	12	132335715	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	8983616	132335715	1516180	813	17434										
ANKLE2	23141	hgsc.bcm.edu	37	chr12	133312071	133312071	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgctttctctcgaggtggagTtttccagagcttgcgaaaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:133312071delT	ENST00000357997.5	-	9	1710	c.1621delA	c.(1621-1623)actfs	p.T541fs	ANKLE2_ENST00000542374.1_5'Flank|ANKLE2_ENST00000337516.5_Frame_Shift_Del_p.T541fs|ANKLE2_ENST00000539605.1_Frame_Shift_Del_p.T479fs	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	541					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		CGAGGTGGAGTTTTCCAGAGC	0.522																																					p.T541fs		Atlas-INDEL	.											.	ANKLE2	76	.	0			c.1622delC						.						123	126	125					12																	133312071		1979	4169	6148	SO:0001589	frameshift_variant	23141	exon9			.	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"Ankyrin repeat domain containing"	29101	protein-coding gene	gene with protein product	"LEM domain containing 7"		"KIAA0692"	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.1621delA	chr12.hg19:g.133312071delT	ENSP00000350686:p.Thr541fs	118.0	0.0		178.0	11.0	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Frame_Shift_Del	DEL	ENST00000357997.5	hg19	CCDS41869.1																																																																																			.	.		0.522	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1			-	133312071	T	-	133312071	7	5	112	1	0	1	0	1	0	0	0	0	633	1725	60	0	1215	0	ANKLE2	12	133312071	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	976356	133312071	539824	814	17435										
CENPJ	55835	hgsc.bcm.edu	37	chr13	25480336	25480336	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agctttgacaggggtggaagAcatccggtgacctttgcaga	14	8	0	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:25480336A>G	ENST00000381884.4	-	7	2025	c.1840T>C	c.(1840-1842)Tct>Cct	p.S614P	CENPJ_ENST00000545981.1_Missense_Mutation_p.S614P	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	614					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		GGGGTGGAAGACATCCGGTGA	0.433																																					p.S614P		Atlas-SNP	.											.	CENPJ	116	.	0			c.T1840C						.						94	92	93					13																	25480336		2203	4300	6503	SO:0001583	missense	55835	exon7			TGGAAGACATCCG	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"centrosomal P4.1-associated protein"	609279	"microcephaly, primary autosomal recessive 6"	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.1840T>C	chr13.hg19:g.25480336A>G	ENSP00000371308:p.Ser614Pro	103.0	0.0		87.0	6.0	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Missense_Mutation	SNP	ENST00000381884.4	hg19	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.091830	0.76756	.	.	ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729	T;T	0.67698	-0.28;0.25	6.02	6.02	0.97574	.	0.135337	0.49916	D	0.000122	T	0.81683	0.4874	M	0.76574	2.34	0.48901	D	0.999729	D	0.89917	1.0	D	0.85130	0.997	D	0.83582	0.0118	10	0.72032	D	0.01	.	15.5319	0.75970	1.0:0.0:0.0:0.0	.	614	Q9HC77	CENPJ_HUMAN	P	614	ENSP00000371308:S614P;ENSP00000441090:S614P	ENSP00000371308:S614P	S	-	1	0	CENPJ	24378336	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.924000	0.70054	2.299000	0.77371	0.528000	0.53228	TCT	.	.		0.433	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		G	25480336	A	G	25480336	3	3	112	1	0	0	0	0	1	0	0	0	3236	275	10	2	2220	2	CENPJ	13	25480336	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10		25480336	89689542	815	17436										
STARD13	90627	hgsc.bcm.edu	37	chr13	33684128	33684128	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgcacaaagtcctcgtcccAcaggtggcgctctctcagca	9	16	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:33684128A>G	ENST00000336934.5	-	12	3045	c.2929T>C	c.(2929-2931)Tgg>Cgg	p.W977R	STARD13_ENST00000255486.4_Missense_Mutation_p.W969R|STARD13_ENST00000399365.3_Missense_Mutation_p.W859R	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	977	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		TCCTCGTCCCACAGGTGGCGC	0.587											OREG0022359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W977R		Atlas-SNP	.											.	STARD13	100	.	0			c.T2929C						.						163	139	147					13																	33684128		2203	4300	6503	SO:0001583	missense	90627	exon12			CGTCCCACAGGTG	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19164	protein-coding gene	gene with protein product		609866	"START domain containing 13", "long intergenic non-protein coding RNA 464"	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.2929T>C	chr13.hg19:g.33684128A>G	ENSP00000338785:p.Trp977Arg	145.0	0.0	841	114.0	5.0	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	hg19	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.589348	0.86851	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934	D;D;D	0.94457	-3.43;-3.43;-3.43	5.34	5.34	0.76211	Lipid-binding START (3);START-like domain (1);	0.000000	0.85682	D	0.000000	D	0.97751	0.9262	M	0.91717	3.235	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98813	1.0744	10	0.87932	D	0	.	15.6106	0.76713	1.0:0.0:0.0:0.0	.	942;977;969	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	R	859;969;977	ENSP00000382300:W859R;ENSP00000255486:W969R;ENSP00000338785:W977R	ENSP00000255486:W969R	W	-	1	0	STARD13	32582128	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.181000	0.94874	2.147000	0.66899	0.533000	0.62120	TGG	.	.		0.587	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		G	33684128	A	G	33684128	3	3	112	1	0	0	0	0	1	0	0	0	15271	159	6	2	424	2	STARD13	13	33684128	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	8203792	33684128	81485750	816	17437										
TRPC4	7223	hgsc.bcm.edu	37	chr13	38213437	38213437	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagttatcagcagctcgcctCtgaaaaggaaaaggacattc	9	9	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:38213437C>T	ENST00000379705.3	-	9	2937		c.e9-1		TRPC4_ENST00000447043.1_Splice_Site|TRPC4_ENST00000379673.2_Splice_Site|TRPC4_ENST00000379681.3_Splice_Site|TRPC4_ENST00000355779.2_Splice_Site|TRPC4_ENST00000426868.2_Splice_Site|TRPC4_ENST00000338947.5_Splice_Site|TRPC4_ENST00000379679.1_Splice_Site|TRPC4_ENST00000358477.2_Splice_Site			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4						axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CAGCTCGCCTCTGAAAAGGAA	0.303																																					.		Atlas-SNP	.											TRPC4_ENST00000379681,NS,carcinoma,0,2	TRPC4	389	.	0			c.1885-1G>A						.						118	122	121					13																	38213437		2203	4300	6503	SO:0001630	splice_region_variant	7223	exon9			TCGCCTCTGAAAA	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2080-1G>A	chr13.hg19:g.38213437C>T		39.0	0.0		54.0	3.0	NM_001135956	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Splice_Site	SNP	ENST00000379705.3	hg19	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.699269	0.88830	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1041	0.97884	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TRPC4	37111437	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.982000	0.70532	2.826000	0.97356	0.655000	0.94253	.	.	.		0.303	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	Intron	T	38213437	C	T	38213437	5	4	112	1	0	0	0	0	0	0	1	0	16595	927	32	3	866	3	TRPC4	13	38213437	Splice_Site	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	4529309	38213437	76956441	817	17438										
COG6	57511	hgsc.bcm.edu	37	chr13	40297514	40297514	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ataaatgagcaagcctcttaTgttttaactagggtaggctt	9	6	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:40297514T>G	ENST00000455146.3	+	16	1679	c.1629T>G	c.(1627-1629)taT>taG	p.Y543*	COG6_ENST00000416691.1_Nonsense_Mutation_p.Y543*	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	543					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		AAGCCTCTTATGTTTTAACTA	0.343																																					p.Y543X		Atlas-SNP	.											.	COG6	49	.	0			c.T1629G						.						114	107	110					13																	40297514		2203	4300	6503	SO:0001587	stop_gained	57511	exon16			CTCTTATGTTTTA	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"Components of oligomeric golgi complex"	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.1629T>G	chr13.hg19:g.40297514T>G	ENSP00000397441:p.Tyr543*	98.0	0.0		83.0	5.0	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Nonsense_Mutation	SNP	ENST00000455146.3	hg19	CCDS9370.1	.	.	.	.	.	.	.	.	.	.	T	36	5.716747	0.96830	.	.	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000455146	.	.	.	5.66	-6.93	0.01638	.	0.055567	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.4576	16.8685	0.86035	0.0:0.5934:0.0:0.4066	.	.	.	.	X	543;574;543	.	ENSP00000255468:Y574X	Y	+	3	2	COG6	39195514	0.173000	0.23056	0.634000	0.29324	0.990000	0.78478	-0.518000	0.06267	-1.658000	0.01490	-0.280000	0.10049	TAT	.	.		0.343	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3			G	40297514	T	G	40297514	4	3	112	1	0	0	0	0	0	1	0	0	3664	1471	51	5	1691	5	COG6	13	40297514	Nonsense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2084077	40297514	74872364	818	17439										
ELF1	1997	hgsc.bcm.edu	37	chr13	41523943	41523943	+	Splice_Site	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aacaaagtaacccacctaccTtttttcctcttaggctgttc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:41523943delT	ENST00000239882.3	-	5	842	c.528delA	c.(526-528)aaa>aa	p.K176fs	ELF1_ENST00000442101.1_Splice_Site_p.K152fs|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	176					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		CCCACCTACCTTTTTTCCTCT	0.423																																					p.G177fs		Atlas-INDEL	.											.	ELF1	65	.	0			c.529delG						.						197	194	195					13																	41523943		2203	4300	6503	SO:0001630	splice_region_variant	1997	exon5			.	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.529+1A>-	chr13.hg19:g.41523943delT		245.0	0.0		169.0	13.0	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Frame_Shift_Del	DEL	ENST00000239882.3	hg19	CCDS9374.1																																																																																			.	.		0.423	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	Frame_Shift_Del	-	41523943	T	-	41523943	8	5	112	1	0	1	0	1	0	0	1	0	5055	1623	56	0	1351	0	ELF1	13	41523943	Splice_Site	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1226429	41523943	73645935	819	17440										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42877272	42877272	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttcaacctctctggttcacAgcataacaaaagatgctaag	6	10	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:42877272A>G	ENST00000025301.2	+	8	4565	c.4390A>G	c.(4390-4392)Agc>Ggc	p.S1464G		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1464				LDPYRNEVSQLYSFSTSLVHSITKDA -> CGPSVELSPWK WQTRCGREGNSWKRE (in Ref. 5; BAA92117). {ECO:0000305}.	intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TCTGGTTCACAGCATAACAAA	0.378																																					p.S1464G		Atlas-SNP	.											.	AKAP11	146	.	0			c.A4390G						.						71	77	75					13																	42877272		2203	4300	6503	SO:0001583	missense	11215	exon8			GTTCACAGCATAA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.4390A>G	chr13.hg19:g.42877272A>G	ENSP00000025301:p.Ser1464Gly	95.0	0.0		64.0	5.0	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	12.66	2.005396	0.35415	.	.	ENSG00000023516	ENST00000025301	T	0.51817	0.69	5.99	4.79	0.61399	.	0.168669	0.50627	D	0.000116	T	0.41811	0.1175	M	0.62723	1.935	0.32309	N	0.56396	P	0.34724	0.465	B	0.31101	0.124	T	0.50725	-0.8794	10	0.18710	T	0.47	.	12.4499	0.55671	0.8743:0.0:0.0:0.1257	.	1464	Q9UKA4	AKA11_HUMAN	G	1464	ENSP00000025301:S1464G	ENSP00000025301:S1464G	S	+	1	0	AKAP11	41775272	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	4.885000	0.63142	1.049000	0.40321	0.533000	0.62120	AGC	.	.		0.378	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		G	42877272	A	G	42877272	3	3	112	1	0	0	0	0	1	0	0	0	447	188	7	2	4412	2	AKAP11	13	42877272	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1353329	42877272	72292606	820	17441										
PHF11	51131	hgsc.bcm.edu	37	chr13	50098318	50098318	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacaaagttcattcaattccAgaaaaactcatggatgagac	7	8	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:50098318A>G	ENST00000378319.3	+	8	776	c.735A>G	c.(733-735)ccA>ccG	p.P245P	PHF11_ENST00000357596.3_Silent_p.P206P|PHF11_ENST00000488958.1_Silent_p.P206P	NM_001040443.1	NP_001035533.1	Q9UIL8	PHF11_HUMAN	PHD finger protein 11	245					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(3)|lung(1)	4		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		ATTCAATTCCAGAAAAACTCA	0.333																																					p.P245P		Atlas-SNP	.											.	PHF11	20	.	0			c.A735G						.						51	55	54					13																	50098318		2203	4296	6499	SO:0001819	synonymous_variant	51131	exon8			AATTCCAGAAAAA	AB011031	CCDS31975.1, CCDS41887.1	13q14.11	2014-05-20			ENSG00000136147	ENSG00000136147		"Zinc fingers, PHD-type"	17024	protein-coding gene	gene with protein product	"IgE responsiveness (atopic)"	607796				10508479, 15057823	Standard	XM_005266417		Approved	NY-REN-34, BCAP, IGER	uc001vdb.3	Q9UIL8	OTTHUMG00000016916	ENST00000378319.3:c.735A>G	chr13.hg19:g.50098318A>G		145.0	0.0		88.0	4.0	NM_001040443	Q5W0A4|Q5W0A6|Q9Y5A2	Silent	SNP	ENST00000378319.3	hg19	CCDS31975.1	.	.	.	.	.	.	.	.	.	.	A	0.020	-1.433803	0.01108	.	.	ENSG00000136147	ENST00000426879	.	.	.	4.27	-8.53	0.00916	.	.	.	.	.	T	0.14743	0.0356	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.20672	-1.0268	4	.	.	.	-1.7604	1.0353	0.01547	0.2341:0.1021:0.3428:0.321	.	.	.	.	R	200	.	.	Q	+	2	0	PHF11	48996319	0.020000	0.18652	0.001000	0.08648	0.000000	0.00434	-0.837000	0.04377	-1.470000	0.01888	-1.286000	0.01371	CAG	.	.		0.333	PHF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044915.1	NM_016119		G	50098318	A	G	50098318	2	3	112	1	0	0	0	0	0	0	0	1	11831	175	7	2		2	PHF11	13	50098318	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	7221046	50098318	65071560	821	17442										
LECT1	11061	hgsc.bcm.edu	37	chr13	53277943	53277943	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtcatgctttccccttcctgCtgctgtgaaataaaagataa	7	10	1	2	rs368102754		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:53277943C>T	ENST00000377962.3	-	7	870	c.792G>A	c.(790-792)caG>caA	p.Q264Q	LECT1_ENST00000448904.2_Splice_Site			O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1	264					cartilage development (GO:0051216)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|proteoglycan metabolic process (GO:0006029)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)		CCCCTTCCTGCTGCTGTGAAA	0.403																																					p.Q264Q		Atlas-SNP	.											.	LECT1	44	.	0			c.G792A						.	C	,	0,4406		0,0,2203	68	65	66		,792	4.3	1	13		66	1,8599	1.2+/-3.3	0,1,4299	no	splice-3,coding-synonymous	LECT1	NM_001011705.1,NM_007015.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	,264/335	53277943	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11061	exon7			TTCCTGCTGCTGT	AB006000	CCDS9437.1, CCDS45051.1	13q14.3	2012-10-10			ENSG00000136110	ENSG00000136110		"BRICHOS domain containing"	17005	protein-coding gene	gene with protein product	"BRICHOS domain containing 3"	605147	"multiple myeloma tumor suppressor 1"	MYETS1		9731231, 10103018	Standard	XM_006719760		Approved	CHM-I, CHM1, chondromodulin, BRICD3	uc001vhf.2	O75829	OTTHUMG00000016980	ENST00000377962.3:c.792G>A	chr13.hg19:g.53277943C>T		74.0	0.0		77.0	4.0	NM_007015	Q5TAM4|Q8TAY6|Q9UM18	Silent	SNP	ENST00000377962.3	hg19	CCDS9437.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.235196	0.58886	0.0	1.16E-4	ENSG00000136110	ENST00000448904	.	.	.	5.23	4.3	0.51218	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2671	0.60139	0.0:0.8717:0.0:0.1283	.	.	.	.	.	-1	.	.	.	-	.	.	LECT1	52175944	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.554000	0.23407	2.717000	0.92951	0.585000	0.79938	.	.	.		0.403	LECT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045110.3			T	53277943	C	T	53277943	2	4	112	1	0	0	0	0	0	0	0	1	8721	811	28	3		3	LECT1	13	53277943	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	3179625	53277943	61891935	822	17443										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88328344	88328344	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtggagctacagctggaggAaaacccttggaattgttctt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:88328344delA	ENST00000325089.6	+	2	920	c.701delA	c.(700-702)gaafs	p.E234fs	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	234					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					CAGCTGGAGGAAAACCCTTGG	0.532																																					p.E234fs		Atlas-INDEL	.											.	SLITRK5	192	.	0			c.700delG						.						84	87	86					13																	88328344		2203	4300	6503	SO:0001589	frameshift_variant	26050	exon2			.	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.701delA	chr13.hg19:g.88328344delA	ENSP00000366283:p.Glu234fs	98.0	0.0		189.0	12.0	NM_015567	B3KNB8|B4DSH5|Q5VT81	Frame_Shift_Del	DEL	ENST00000325089.6	hg19	CCDS9465.1																																																																																			.	.		0.532	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			-	88328344	A	-	88328344	7	5	112	1	0	1	0	1	0	0	0	0	14761	246	9	0	703	0	SLITRK5	13	88328344	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	35050401	88328344	26841534	823	17444										
UGGT2	55757	hgsc.bcm.edu	37	chr13	96684195	96684195	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtttccaaaaactgccaaaaTttttcattactttcttctgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:96684195delT	ENST00000376747.3	-	2	259	c.189delA	c.(187-189)aaafs	p.K63fs	UGGT2_ENST00000376714.3_Frame_Shift_Del_p.K63fs|UGGT2_ENST00000376712.4_Frame_Shift_Del_p.K63fs|UGGT2_ENST00000397618.3_Frame_Shift_Del_p.K63fs	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	63					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						ACTGCCAAAATTTTTCATTAC	0.269																																					p.F64fs		Atlas-INDEL	.											.	UGGT2	127	.	0			c.190delT						.						54	57	56					13																	96684195		2199	4279	6478	SO:0001589	frameshift_variant	55757	exon2			.	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.189delA	chr13.hg19:g.96684195delT	ENSP00000365938:p.Lys63fs	140.0	0.0		203.0	13.0	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Frame_Shift_Del	DEL	ENST00000376747.3	hg19	CCDS9480.1																																																																																			.	.		0.269	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		-	96684195	T	-	96684195	7	5	112	1	0	1	0	1	0	0	0	0	16957	1490	52	0	4513	0	UGGT2	13	96684195	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	8355851	96684195	18485683	824	17445										
IPO5	3843	hgsc.bcm.edu	37	chr13	98658548	98658548	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaagaactgagacttctgagAggaaaaactattgaatgcat	9	5	1	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:98658548A>G	ENST00000490680.1	+	14	1727	c.1662A>G	c.(1660-1662)agA>agG	p.R554R	IPO5_ENST00000493492.2_3'UTR|IPO5_ENST00000539640.1_Silent_p.R429R|IPO5_ENST00000261574.5_Silent_p.R572R			O00410	IPO5_HUMAN	importin 5	554					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						GACTTCTGAGAGGAAAAACTA	0.313																																					p.R572R		Atlas-SNP	.											.	IPO5	90	.	0			c.A1716G						.						78	78	78					13																	98658548		2203	4300	6503	SO:0001819	synonymous_variant	3843	exon17			TCTGAGAGGAAAA	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"Importins"	6402	protein-coding gene	gene with protein product		602008	"karyopherin (importin) beta 3", "RAN binding protein 5"	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.1662A>G	chr13.hg19:g.98658548A>G		113.0	0.0		211.0	12.0	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Silent	SNP	ENST00000490680.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.07	1.249378	0.22880	.	.	ENSG00000065150	ENST00000469360	.	.	.	5.1	2.65	0.31530	.	.	.	.	.	T	0.58293	0.2112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51172	-0.8739	4	.	.	.	-2.596	9.2079	0.37300	0.8505:0.0:0.1495:0.0	.	.	.	.	G	556	.	.	E	+	2	0	IPO5	97456549	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	1.071000	0.30666	0.358000	0.24211	0.377000	0.23210	GAG	.	.		0.313	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271		G	98658548	A	G	98658548	2	3	112	1	0	0	0	0	0	0	0	1	7805	301	11	2		2	IPO5	13	98658548	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1974353	98658548	16511330	825	17446										
TPP2	7174	hgsc.bcm.edu	37	chr13	103326668	103326668	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaatccaccctcgtagatgCcctttgtaggaaaggttgtg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:103326668delC	ENST00000376065.4	+	27	3404	c.3368delC	c.(3367-3369)gccfs	p.A1123fs	TPP2_ENST00000466153.1_3'UTR|TPP2_ENST00000376052.3_Frame_Shift_Del_p.A1136fs	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	1123					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)			breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTCGTAGATGCCCTTTGTAGG	0.413																																					p.A1123fs		Atlas-INDEL	.											.	TPP2	124	.	0			c.3367delG						.						103	95	98					13																	103326668		2203	4300	6503	SO:0001589	frameshift_variant	7174	exon27			.	M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.3368delC	chr13.hg19:g.103326668delC	ENSP00000365233:p.Ala1123fs	91.0	0.0		162.0	10.0	NM_003291	Q5VZU8	Frame_Shift_Del	DEL	ENST00000376065.4	hg19	CCDS9502.1																																																																																			.	.		0.413	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			-	103326668	C	-	103326668	7	5	112	1	0	1	0	1	0	0	0	0	16427	739	26	0	3474	0	TPP2	13	103326668	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	4668120	103326668	11843210	826	17447										
COL4A1	1282	hgsc.bcm.edu	37	chr13	110827094	110827094	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaacccgctatcccttgatcTccctgcaagtaaaagtcagg	7	13	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:110827094T>C	ENST00000375820.4	-	38	3322	c.3201A>G	c.(3199-3201)ggA>ggG	p.G1067G		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1067	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TCCCTTGATCTCCCTGCAAGT	0.463																																					p.G1067G		Atlas-SNP	.											.	COL4A1	372	.	0			c.A3201G						.						147	159	155					13																	110827094		2203	4300	6503	SO:0001819	synonymous_variant	1282	exon38			TTGATCTCCCTGC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.3201A>G	chr13.hg19:g.110827094T>C		62.0	0.0		94.0	6.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	hg19	CCDS9511.1																																																																																			.	.		0.463	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			C	110827094	T	C	110827094	2	2	112	1	0	0	0	0	0	0	0	1	3691	1538	54	2		2	COL4A1	13	110827094	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	7500426	110827094	4342784	827	17448										
OR4Q3	441669	hgsc.bcm.edu	37	chr14	20215940	20215940	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagatgtttttgctgacagtCatggcctatgacaggtatgt	12	6	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:20215940C>T	ENST00000331723.1	+	1	354	c.354C>T	c.(352-354)gtC>gtT	p.V118V		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V118V(1)		NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TGCTGACAGTCATGGCCTATG	0.498																																					p.V118V		Atlas-SNP	.											OR4Q3,NS,carcinoma,0,1	OR4Q3	117	.	1	Substitution - coding silent(1)	lung(1)	c.C354T						.						93	94	94					14																	20215940		2203	4299	6502	SO:0001819	synonymous_variant	441669	exon1			GACAGTCATGGCC	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"GPCR / Class A : Olfactory receptors"	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.354C>T	chr14.hg19:g.20215940C>T		139.0	0.0		145.0	10.0	NM_172194	Q6IEX4	Silent	SNP	ENST00000331723.1	hg19	CCDS32020.1																																																																																			.	.		0.498	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2			T	20215940	C	T	20215940	2	4	112	1	0	0	0	0	0	0	0	1	11090	813	29	3		3	OR4Q3	14	20215940	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10		20215940	87133600	828	17449										
METT11D1	64745	hgsc.bcm.edu	37	chr14	21462740	21462740	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agccttatattccaggtgtcTttttcagacagtttctacct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:21462740delT	ENST00000339374.6	+	8	969	c.736delT	c.(736-738)tttfs	p.F247fs	RP11-84C10.4_ENST00000557335.1_RNA|METTL17_ENST00000556670.2_Frame_Shift_Del_p.F247fs|METTL17_ENST00000382985.4_Frame_Shift_Del_p.F247fs	NM_001029991.1|NM_022734.2	NP_001025162.1|NP_073571.1	Q9H7H0	MET17_HUMAN	methyltransferase like 17	247					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	copper ion binding (GO:0005507)|methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20						TCCAGGTGTCTTTTTCAGACA	0.418																																					p.V245fs		Atlas-INDEL	.											METTL17,NS,carcinoma,0,1	METTL17	46	.	0			c.735delC						.						148	149	149					14																	21462740		2203	4300	6503	SO:0001589	frameshift_variant	64745	exon8			.	AK024512	CCDS9562.1, CCDS41913.1	14q11.2	2011-03-03	2011-03-02	2011-03-02	ENSG00000165792	ENSG00000165792			19280	protein-coding gene	gene with protein product			"methyltransferase 11 domain containing 1"	METT11D1		11278769	Standard	XM_006720235		Approved	FLJ20859	uc001vyn.3	Q9H7H0	OTTHUMG00000029610	ENST00000339374.6:c.736delT	chr14.hg19:g.21462740delT	ENSP00000343041:p.Phe247fs	162.0	0.0		172.0	11.0	NM_022734	Q9BSH1|Q9BZH2|Q9BZH3	Frame_Shift_Del	DEL	ENST00000339374.6	hg19	CCDS9562.1																																																																																			.	.		0.418	METTL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073804.4	NM_022734		-	21462740	T	-	21462740	7	5	112	1	0	1	0	1	0	0	0	0	9500	1609	56	0	766	0	METT11D1	14	21462740	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1246800	21462740	85886800	829	17450										
TOX4	9878	hgsc.bcm.edu	37	chr14	21957371	21957371	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagtcgtggtggaagcagggAaaaagcagaaggccccaaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:21957371delA	ENST00000405508.1	+	6	895	c.619delA	c.(619-621)aaafs	p.K208fs	TOX4_ENST00000262709.3_Frame_Shift_Del_p.K208fs|TOX4_ENST00000448790.2_Frame_Shift_Del_p.K185fs			O94842	TOX4_HUMAN	TOX high mobility group box family member 4	208						chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)			large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		GGAAGCAGGGAAAAAGCAGAA	0.418																																					p.G206fs		Atlas-INDEL	.											.	TOX4	50	.	0			c.618delG						.						91	100	97					14																	21957371		2203	4300	6503	SO:0001589	frameshift_variant	9878	exon5			.	AB018280	CCDS32043.1	14q11.2	2007-03-20	2007-03-20	2007-03-20	ENSG00000092203	ENSG00000092203			20161	protein-coding gene	gene with protein product		614032	"chromosome 14 open reading frame 92", "KIAA0737"	C14orf92, KIAA0737			Standard	NM_014828		Approved	LCP1	uc001waz.3	O94842	OTTHUMG00000150278	ENST00000405508.1:c.619delA	chr14.hg19:g.21957371delA	ENSP00000385102:p.Lys208fs	111.0	0.0		120.0	11.0	NM_014828	B4DPY8|B4DSM0|E7EV69	Frame_Shift_Del	DEL	ENST00000405508.1	hg19	CCDS32043.1																																																																																			.	.		0.418	TOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317287.2	NM_014828		-	21957371	A	-	21957371	7	5	112	1	0	1	0	1	0	0	0	0	16395	247	9	0	637	0	TOX4	14	21957371	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	494631	21957371	85392169	830	17451										
SALL2	6297	hgsc.bcm.edu	37	chr14	21991715	21991715	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taccaccgttggggatctggCcccccaggtgcatccggaca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:21991715delC	ENST00000327430.3	-	2	2441	c.2147delG	c.(2146-2148)ggcfs	p.G716fs	SALL2_ENST00000538754.1_Intron|SALL2_ENST00000317492.5_Intron|AE000658.22_ENST00000535893.1_RNA|SALL2_ENST00000450879.2_Frame_Shift_Del_p.G579fs	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	716					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		GGGGATCTGGCCCCCCAGGTG	0.612																																					p.G716fs		Atlas-INDEL	.											.	SALL2	95	.	0			c.2148delC						.						65	60	61					14																	21991715		2203	4300	6503	SO:0001589	frameshift_variant	6297	exon2			.	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"Zinc fingers, C2H2-type"	10526	protein-coding gene	gene with protein product		602219	"sal (Drosophila)-like 2", "sal-like 2 (Drosophila)"			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.2147delG	chr14.hg19:g.21991715delC	ENSP00000333537:p.Gly716fs	86.0	0.0		115.0	11.0	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Frame_Shift_Del	DEL	ENST00000327430.3	hg19	CCDS32045.1																																																																																			.	.		0.612	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407		-	21991715	C	-	21991715	7	5	112	1	0	1	0	1	0	0	0	0	13826	739	26	0	880	0	SALL2	14	21991715	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	34344	21991715	85357825	831	17452										
PRMT5	10419	hgsc.bcm.edu	37	chr14	23393312	23393312	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgacaatgatgtctgctttcTctggagccacccattccctc	7	14	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:23393312T>C	ENST00000324366.8	-	12	1503	c.1280A>G	c.(1279-1281)gAg>gGg	p.E427G	PRMT5_ENST00000538452.1_Missense_Mutation_p.E321G|PRMT5-AS1_ENST00000457443.2_RNA|PRMT5_ENST00000553897.1_Missense_Mutation_p.E383G|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5-AS1_ENST00000424245.2_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000553641.1_5'Flank|PRMT5_ENST00000397440.4_Missense_Mutation_p.E256G|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000397441.2_Missense_Mutation_p.E410G|PRMT5_ENST00000216350.8_Missense_Mutation_p.E366G|PRMT5-AS1_ENST00000609885.1_RNA|PRMT5-AS1_ENST00000587245.2_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	427	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		GTCTGCTTTCTCTGGAGCCAC	0.502																																					p.E427G		Atlas-SNP	.											.	PRMT5	101	.	0			c.A1280G						.						91	81	85					14																	23393312		2203	4300	6503	SO:0001583	missense	10419	exon12			GCTTTCTCTGGAG	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"Protein arginine methyltransferases"	10894	protein-coding gene	gene with protein product		604045	"skb1 (S. pombe) homolog", "SKB1 homolog (S. pombe)"	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.1280A>G	chr14.hg19:g.23393312T>C	ENSP00000319169:p.Glu427Gly	110.0	0.0		117.0	5.0	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Missense_Mutation	SNP	ENST00000324366.8	hg19	CCDS9579.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.567072	0.86439	.	.	ENSG00000100462	ENST00000324366;ENST00000397441;ENST00000397440;ENST00000216350;ENST00000555454;ENST00000538452;ENST00000553897	T;T;T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87;1.87;1.87	5.5	5.5	0.81552	.	0.089755	0.85682	D	0.000000	T	0.53867	0.1823	M	0.83692	2.655	0.80722	D	1	D;D;D;D;D	0.71674	0.997;0.986;0.998;0.998;0.996	D;D;D;D;D	0.75020	0.974;0.944;0.985;0.956;0.978	T	0.59043	-0.7528	10	0.59425	D	0.04	-23.0779	14.731	0.69383	0.0:0.0:0.0:1.0	.	383;366;256;427;410	G3V5W5;B4DX49;A8MTP3;O14744;A8MZ91	.;.;.;ANM5_HUMAN;.	G	427;410;256;366;26;321;383	ENSP00000319169:E427G;ENSP00000380583:E410G;ENSP00000380582:E256G;ENSP00000216350:E366G;ENSP00000451245:E26G;ENSP00000444915:E321G;ENSP00000452555:E383G	ENSP00000216350:E366G	E	-	2	0	PRMT5	22463152	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.304000	0.78882	2.313000	0.78055	0.454000	0.30748	GAG	.	.		0.502	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3			C	23393312	T	C	23393312	3	2	112	1	0	0	0	0	1	0	0	0	12551	1551	54	2	657	2	PRMT5	14	23393312	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1401597	23393312	83956228	832	17453										
C14orf93	60686	hgsc.bcm.edu	37	chr14	23457145	23457145	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttcgaagtttcttctcctcTttttccttcaggcctttaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:23457145delT	ENST00000299088.6	-	6	1593	c.1164delA	c.(1162-1164)aaafs	p.K388fs	RP11-298I3.4_ENST00000555294.1_RNA|C14orf93_ENST00000397377.1_Frame_Shift_Del_p.K208fs|C14orf93_ENST00000341470.4_Frame_Shift_Del_p.K388fs|C14orf93_ENST00000397382.4_Frame_Shift_Del_p.K388fs|RP11-298I3.4_ENST00000556503.1_RNA|C14orf93_ENST00000406429.2_Frame_Shift_Del_p.K388fs|RP11-298I3.4_ENST00000557615.1_RNA|C14orf93_ENST00000397379.3_Frame_Shift_Del_p.K388fs	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93	388						extracellular region (GO:0005576)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	17	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		TCTTCTCCTCTTTTTCCTTCA	0.507																																					p.E389fs		Atlas-INDEL	.											.	C14orf93	33	.	0			c.1165delG						.						108	105	106					14																	23457145		2203	4300	6503	SO:0001589	frameshift_variant	60686	exon6			.	AK023026	CCDS9583.1, CCDS61399.1, CCDS61400.1	14q11.1	2012-09-25			ENSG00000100802	ENSG00000100802			20162	protein-coding gene	gene with protein product							Standard	XM_005267971		Approved	FLJ12154	uc001wih.3	Q9H972	OTTHUMG00000028712	ENST00000299088.6:c.1164delA	chr14.hg19:g.23457145delT	ENSP00000299088:p.Lys388fs	115.0	0.0		148.0	11.0	NM_021944	B7WP03|D3DS38|D3DS39|Q86SE6|Q96CF7|Q9HA68	Frame_Shift_Del	DEL	ENST00000299088.6	hg19	CCDS9583.1																																																																																			.	.		0.507	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	NM_021944		-	23457145	T	-	23457145	7	5	112	1	0	1	0	1	0	0	0	0	1784	1606	56	0	460	0	C14orf93	14	23457145	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	63833	23457145	83892395	833	17454										
MYH7	4625	hgsc.bcm.edu	37	chr14	23894966	23894966	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggagctgagcagcttctctgCccccttcctgctatcaatga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:23894966delC	ENST00000355349.3	-	20	2386	c.2224delG	c.(2224-2226)gcafs	p.A742fs		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	742	Myosin motor.		A -> E (in CMH1). {ECO:0000269|PubMed:16199542}.		adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		AGCTTCTCTGCCCCCTTCCTG	0.517																																					p.A742fs		Atlas-INDEL	.											.	MYH7	349	.	0			c.2225delC						.						121	102	109					14																	23894966		2203	4300	6503	SO:0001589	frameshift_variant	4625	exon20			.	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.2224delG	chr14.hg19:g.23894966delC	ENSP00000347507:p.Ala742fs	118.0	0.0		164.0	11.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Frame_Shift_Del	DEL	ENST00000355349.3	hg19	CCDS9601.1																																																																																			.	.		0.517	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		-	23894966	C	-	23894966	7	5	112	1	0	1	0	1	0	0	0	0	10048	739	26	0	3667	0	MYH7	14	23894966	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	437821	23894966	83454574	834	17455										
IPO4	79711	hgsc.bcm.edu	37	chr14	24653232	24653232	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctcggtggaacgcagtgacAgcagcatgagcgtggtgatc	15	10	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:24653232A>G	ENST00000354464.6	-	18	2017	c.1841T>C	c.(1840-1842)cTg>cCg	p.L614P	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	614					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		ACGCAGTGACAGCAGCATGAG	0.612																																					p.L614P		Atlas-SNP	.											.	IPO4	74	.	0			c.T1841C						.						44	44	44					14																	24653232		1978	4148	6126	SO:0001583	missense	79711	exon18			AGTGACAGCAGCA	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"Importins"	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1841T>C	chr14.hg19:g.24653232A>G	ENSP00000346453:p.Leu614Pro	80.0	0.0		100.0	4.0	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	hg19	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.698050	0.30142	.	.	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.04654	3.58	5.93	3.28	0.37604	Armadillo-like helical (1);Armadillo-type fold (1);	0.240418	0.33457	N	0.004891	T	0.05502	0.0145	L	0.48642	1.525	0.80722	D	1	B;B	0.25904	0.084;0.137	B;B	0.33339	0.106;0.162	T	0.36383	-0.9750	10	0.30854	T	0.27	-2.2341	5.7616	0.18203	0.7089:0.0:0.1599:0.1312	.	614;614	Q8TEX9;Q8TEX9-2	IPO4_HUMAN;.	P	614;290	ENSP00000346453:L614P	ENSP00000346453:L614P	L	-	2	0	IPO4	23723072	0.052000	0.20516	0.980000	0.43619	0.984000	0.73092	1.876000	0.39588	1.076000	0.40961	0.533000	0.62120	CTG	.	.		0.612	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		G	24653232	A	G	24653232	3	3	112	1	0	0	0	0	1	0	0	0	7804	188	7	2	1456	2	IPO4	14	24653232	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	758266	24653232	82696308	835	17456										
TM9SF1	10548	hgsc.bcm.edu	37	chr14	24662001	24662001	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accagaacctgcagaggtggTctcctcatctaagttgtacc	9	12	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:24662001T>C	ENST00000261789.4	-	3	1178	c.820A>G	c.(820-822)Acc>Gcc	p.T274A	RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000528669.1_Missense_Mutation_p.T274A|TM9SF1_ENST00000524835.1_Missense_Mutation_p.T187A|TM9SF1_ENST00000530611.1_Missense_Mutation_p.T483A|TM9SF1_ENST00000396854.4_Missense_Mutation_p.T274A|TM9SF1_ENST00000556387.1_Missense_Mutation_p.T483A	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	274					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		GCAGAGGTGGTCTCCTCATCT	0.498																																					p.T274A		Atlas-SNP	.											.	TM9SF1	58	.	0			c.A820G						.						141	130	134					14																	24662001		2203	4300	6503	SO:0001583	missense	10548	exon3			AGGTGGTCTCCTC	U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.820A>G	chr14.hg19:g.24662001T>C	ENSP00000261789:p.Thr274Ala	137.0	0.0		123.0	5.0	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	hg19	CCDS9617.1	.	.	.	.	.	.	.	.	.	.	T	4.994	0.184632	0.09495	.	.	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000528895;ENST00000530563;ENST00000530611	T;T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02	5.1	3.94	0.45596	.	0.451250	0.24580	N	0.037304	T	0.14485	0.0350	N	0.02708	-0.52	0.31439	N	0.672171	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.20042	-1.0287	10	0.09590	T	0.72	-6.1289	4.8739	0.13646	0.0:0.0982:0.2058:0.696	.	274;274;274	E9PJM1;Q86SZ6;O15321	.;.;TM9S1_HUMAN	A	274;274;483;187;274;274;187;483	ENSP00000261789:T274A;ENSP00000432997:T274A;ENSP00000451949:T483A;ENSP00000434387:T187A;ENSP00000380063:T274A;ENSP00000431447:T274A;ENSP00000437127:T187A;ENSP00000433967:T483A	ENSP00000433967:T483A	T	-	1	0	TM9SF1;RP11-468E2.1	23731841	1.000000	0.71417	0.929000	0.37066	0.889000	0.51656	4.087000	0.57671	2.137000	0.66172	0.533000	0.62120	ACC	.	.		0.498	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405		C	24662001	T	C	24662001	3	2	112	1	0	0	0	0	1	0	0	0	15992	1667	58	2	1059	2	TM9SF1	14	24662001	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	8769	24662001	82687539	836	17457										
RIPK3	11035	hgsc.bcm.edu	37	chr14	24805506	24805506	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttgcccgaaggtgccaagcCccatgtgggcaaggcagttg	14	12	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:24805506C>T	ENST00000216274.5	-	10	1650	c.1432G>A	c.(1432-1434)Ggc>Agc	p.G478S	ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000554068.2_5'Flank|RP11-934B9.3_ENST00000555591.1_Intron|ADCY4_ENST00000396747.3_5'Flank|ADCY4_ENST00000558563.1_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000418030.2_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	478					activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		GGTGCCAAGCCCCATGTGGGC	0.567																																					p.G478S	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.G1432A						.						89	91	90					14																	24805506		2203	4300	6503	SO:0001583	missense	11035	exon10			CCAAGCCCCATGT	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.1432G>A	chr14.hg19:g.24805506C>T	ENSP00000216274:p.Gly478Ser	88.0	0.0		98.0	37.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	hg19	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.524751	0.44969	.	.	ENSG00000129465	ENST00000216274	T	0.77098	-1.07	4.2	-2.27	0.06846	.	1.815640	0.02715	N	0.113376	T	0.62539	0.2436	L	0.27053	0.805	0.09310	N	1	B	0.26363	0.147	B	0.18263	0.021	T	0.43653	-0.9378	10	0.29301	T	0.29	1.2926	5.4134	0.16360	0.0:0.2791:0.4437:0.2772	.	478	Q9Y572	RIPK3_HUMAN	S	478	ENSP00000216274:G478S	ENSP00000216274:G478S	G	-	1	0	RIPK3	23875346	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.006000	0.03671	-0.484000	0.06763	-0.176000	0.13171	GGC	.	.		0.567	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		T	24805506	C	T	24805506	3	4	112	1	0	0	0	0	1	0	0	0	13397	623	22	3	128	3	RIPK3	14	24805506	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	143505	24805506	82544034	837	17458										
PRKD1	5587	hgsc.bcm.edu	37	chr14	30095706	30095706	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctacctccataaacaattccAaactgtccagaacccagtac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:30095706delA	ENST00000331968.5	-	12	2011	c.1782delT	c.(1780-1782)tttfs	p.F594fs	PRKD1_ENST00000415220.2_Frame_Shift_Del_p.F602fs	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	594	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		AAACAATTCCAAACTGTCCAG	0.323																																					p.G595fs		Atlas-INDEL	.											.	PRKD1	316	.	0			c.1783delG						.						56	58	57					14																	30095706		2203	4299	6502	SO:0001589	frameshift_variant	5587	exon12			.		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.1782delT	chr14.hg19:g.30095706delA	ENSP00000333568:p.Phe594fs	193.0	0.0		193.0	12.0	NM_002742	A6NL64|B2RAF6	Frame_Shift_Del	DEL	ENST00000331968.5	hg19	CCDS9637.1																																																																																			.	.		0.323	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		-	30095706	A	-	30095706	7	5	112	1	0	1	0	1	0	0	0	0	12530	127	5	0	984	0	PRKD1	14	30095706	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5290200	30095706	77253834	838	17459										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31617960	31617960	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttttctaacttagatttcagTtttctgcctcttttgccagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:31617960delT	ENST00000399332.1	-	15	2951	c.2463delA	c.(2461-2463)aaafs	p.K821fs	HECTD1_ENST00000553700.1_Frame_Shift_Del_p.K821fs	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	821					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TAGATTTCAGTTTTCTGCCTC	0.323																																					p.L822X		Atlas-INDEL	.											.	HECTD1	159	.	0			c.2464delC						.						99	89	92					14																	31617960		1803	4065	5868	SO:0001589	frameshift_variant	25831	exon15			.	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.2463delA	chr14.hg19:g.31617960delT	ENSP00000382269:p.Lys821fs	189.0	0.0		178.0	11.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Frame_Shift_Del	DEL	ENST00000399332.1	hg19	CCDS41939.1																																																																																			.	.		0.323	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			-	31617960	T	-	31617960	7	5	112	1	0	1	0	1	0	0	0	0	7048	1722	60	0	5485	0	HECTD1	14	31617960	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1522254	31617960	75731580	839	17460										
CFL2	1073	hgsc.bcm.edu	37	chr14	35182277	35182277	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtttgtacctgtaaatttcTttttaatggcatctttagag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:35182277delT	ENST00000341223.3	-	3	528	c.377delA	c.(376-378)aagfs	p.K127fs	CFL2_ENST00000555765.1_Frame_Shift_Del_p.K110fs|CFL2_ENST00000298159.6_Frame_Shift_Del_p.K127fs|CFL2_ENST00000556161.1_Frame_Shift_Del_p.K110fs	NM_001243645.1|NM_021914.7	NP_001230574.1|NP_068733.1	Q9Y281	COF2_HUMAN	cofilin 2 (muscle)	127	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin filament depolymerization (GO:0030042)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of actin filament depolymerization (GO:0030836)|regulation of dendritic spine morphogenesis (GO:0061001)|sarcomere organization (GO:0045214)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|nucleus (GO:0005634)				breast(3)|endometrium(2)|lung(3)	8	Breast(36;0.0361)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;6.07e-06)|Lung(238;2.23e-05)|Epithelial(34;0.0387)|all cancers(34;0.0814)	GBM - Glioblastoma multiforme(112;0.0424)		TGTAAATTTCTTTTTAATGGC	0.264																																					p.K126fs		Atlas-INDEL	.											.	CFL2	22	.	0			c.378delG						.						23	21	22					14																	35182277		2196	4281	6477	SO:0001589	frameshift_variant	1073	exon3			.	AF087867	CCDS9649.1, CCDS9650.1, CCDS58311.1	14q13.2	2014-09-17			ENSG00000165410	ENSG00000165410			1875	protein-coding gene	gene with protein product	"nemaline myopathy type 7"	601443				8800436	Standard	NM_138638		Approved	NEM7	uc001wsh.3	Q9Y281	OTTHUMG00000029536	ENST00000341223.3:c.377delA	chr14.hg19:g.35182277delT	ENSP00000340635:p.Lys127fs	146.0	0.0		195.0	12.0	NM_021914	G3V5P4	Frame_Shift_Del	DEL	ENST00000341223.3	hg19	CCDS9650.1																																																																																			.	.		0.264	CFL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276639.1	NM_138638		-	35182277	T	-	35182277	7	5	112	1	0	1	0	1	0	0	0	0	3293	1609	56	0	131	0	CFL2	14	35182277	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3564317	35182277	72167263	840	17461										
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39788448	39788448	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcttaaatttgaacttttagAaaaagatccttatgcactcg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:39788448delA	ENST00000280083.3	+	18	1810	c.1496delA	c.(1495-1497)gaafs	p.E499fs	CTAGE5_ENST00000556148.1_Frame_Shift_Del_p.E424fs|CTAGE5_ENST00000553352.1_Frame_Shift_Del_p.E470fs|CTAGE5_ENST00000348007.3_Frame_Shift_Del_p.E499fs|CTAGE5_ENST00000396165.4_Frame_Shift_Del_p.E470fs|CTAGE5_ENST00000396158.2_Frame_Shift_Del_p.E504fs|CTAGE5_ENST00000341502.5_Frame_Shift_Del_p.E499fs|CTAGE5_ENST00000557038.1_Frame_Shift_Del_p.E419fs|CTAGE5_ENST00000341749.3_Frame_Shift_Del_p.E487fs|RP11-407N17.3_ENST00000603904.1_Frame_Shift_Del_p.E470fs|RP11-407N17.3_ENST00000553728.1_Frame_Shift_Del_p.E1034fs			O15320	CTGE5_HUMAN	CTAGE family, member 5	499					positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		GAACTTTTAGAAAAAGATCCT	0.308																																					p.E504fs		Atlas-INDEL	.											CTAGE5,colon,carcinoma,0,1	CTAGE5	75	.	0			c.1510delG						.						83	84	83					14																	39788448		2203	4300	6503	SO:0001589	frameshift_variant	4253	exon18			.	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"meningioma expressed antigen 6 (coiled-coil proline-rich)"	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.1496delA	chr14.hg19:g.39788448delA	ENSP00000280083:p.Glu499fs	70.0	0.0		114.0	10.0	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Frame_Shift_Del	DEL	ENST00000280083.3	hg19	CCDS9674.1																																																																																			.	.		0.308	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		-	39788448	A	-	39788448	7	5	112	1	0	1	0	1	0	0	0	0	3996	246	9	0	1597	0	CTAGE5	14	39788448	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4606171	39788448	67561092	841	17462										
PRPF39	55015	hgsc.bcm.edu	37	chr14	45571779	45571779	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggaacagatttccgttctgAcagactgtgggaaatgtata	11	6	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:45571779A>G	ENST00000355765.6	+	5	787	c.617A>G	c.(616-618)gAc>gGc	p.D206G		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	206					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						TTCCGTTCTGACAGACTGTGG	0.358																																					p.D206G		Atlas-SNP	.											.	PRPF39	46	.	0			c.A617G						.						101	105	104					14																	45571779		2203	4300	6503	SO:0001583	missense	55015	exon5			GTTCTGACAGACT	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"PRP39 pre-mRNA processing factor 39 homolog (yeast)", "PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.617A>G	chr14.hg19:g.45571779A>G	ENSP00000348010:p.Asp206Gly	98.0	0.0		90.0	4.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	A	26.8	4.770121	0.90108	.	.	ENSG00000185246	ENST00000355765;ENST00000355846	T	0.29655	1.56	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.48277	0.1491	L	0.50993	1.605	0.80722	D	1	P;D	0.89917	0.86;1.0	P;D	0.87578	0.661;0.998	T	0.30416	-0.9979	10	0.20046	T	0.44	-8.4025	15.4843	0.75551	1.0:0.0:0.0:0.0	.	206;85	Q86UA1;F5H1P0	PRP39_HUMAN;.	G	206;85	ENSP00000348010:D206G	ENSP00000348010:D206G	D	+	2	0	PRPF39	44641529	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.137000	0.66172	0.533000	0.62120	GAC	.	.		0.358	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			G	45571779	A	G	45571779	3	3	112	1	0	0	0	0	1	0	0	0	12581	275	10	2	631	2	PRPF39	14	45571779	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	5783331	45571779	61777761	842	17463										
FANCM	57697	hgsc.bcm.edu	37	chr14	45645902	45645902	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catttgccactgagtgcagcAaaaaatgaagaattgttatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:45645902delA	ENST00000267430.5	+	14	4030	c.3945delA	c.(3943-3945)gcafs	p.A1315fs	FANCM_ENST00000542564.2_Frame_Shift_Del_p.A1289fs	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1315					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TGAGTGCAGCAAAAAATGAAG	0.323								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.A1315fs		Atlas-INDEL	.											.	FANCM	225	.	0			c.3944delC						.						75	74	74					14																	45645902		2202	4296	6498	SO:0001589	frameshift_variant	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.3945delA	chr14.hg19:g.45645902delA	ENSP00000267430:p.Ala1315fs	183.0	0.0		172.0	12.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Frame_Shift_Del	DEL	ENST00000267430.5	hg19	CCDS32070.1																																																																																			.	.		0.323	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		-	45645902	A	-	45645902	7	5	112	1	0	1	0	1	0	0	0	0	5679	117	5	0	3999	0	FANCM	14	45645902	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	74123	45645902	61703638	843	17464										
SOS2	6655	hgsc.bcm.edu	37	chr14	50647366	50647366	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actctggtgaaagaatgtccTgtgataatgtttcataagga	10	5	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:50647366T>C	ENST00000216373.5	-	7	1167	c.893A>G	c.(892-894)cAg>cGg	p.Q298R	SOS2_ENST00000555794.1_5'UTR|SOS2_ENST00000543680.1_Missense_Mutation_p.Q298R	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	298	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					AAGAATGTCCTGTGATAATGT	0.313																																					p.Q298R		Atlas-SNP	.											.	SOS2	195	.	0			c.A893G						.						77	77	77					14																	50647366		2203	4300	6503	SO:0001583	missense	6655	exon7			ATGTCCTGTGATA	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11188	protein-coding gene	gene with protein product		601247	"son of sevenless (Drosophilia) homolog 2"			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.893A>G	chr14.hg19:g.50647366T>C	ENSP00000216373:p.Gln298Arg	48.0	0.0		56.0	4.0	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	hg19	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	T	8.883	0.952136	0.18431	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.62941	-0.01;-0.01	5.6	5.6	0.85130	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.46833	0.1413	N	0.25485	0.75	0.80722	D	1	B;B	0.14805	0.011;0.002	B;B	0.16289	0.015;0.01	T	0.43196	-0.9406	10	0.06099	T	0.92	.	15.829	0.78736	0.0:0.0:0.0:1.0	.	298;298	B7ZKT6;Q07890	.;SOS2_HUMAN	R	298	ENSP00000216373:Q298R;ENSP00000445328:Q298R	ENSP00000216373:Q298R	Q	-	2	0	SOS2	49717116	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.033000	0.88852	2.122000	0.65172	0.529000	0.55759	CAG	.	.		0.313	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2			C	50647366	T	C	50647366	3	2	112	1	0	0	0	0	1	0	0	0	14952	1580	55	2	3173	2	SOS2	14	50647366	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	5001464	50647366	56702174	844	17465										
ABHD12B	145447	hgsc.bcm.edu	37	chr14	51368597	51368597	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acacttatggatgccctgagAaaagacaaaataatctttcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:51368597delA	ENST00000337334.2	+	10	846	c.831delA	c.(829-831)agafs	p.R277fs	PYGL_ENST00000532462.1_Intron|ABHD12B_ENST00000395752.1_Frame_Shift_Del_p.R170fs|ABHD12B_ENST00000353130.1_Frame_Shift_Del_p.R200fs	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	277							hydrolase activity (GO:0016787)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					ATGCCCTGAGAAAAGACAAAA	0.313																																					p.R277fs		Atlas-INDEL	.											.	ABHD12B	53	.	0			c.830delG						.						77	73	74					14																	51368597		2203	4296	6499	SO:0001589	frameshift_variant	145447	exon10			.	BG698443	CCDS9702.1, CCDS55916.1	14q21.3	2009-10-09	2007-04-03	2007-04-03	ENSG00000131969	ENSG00000131969		"Abhydrolase domain containing"	19837	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 29"	C14orf29			Standard	NM_181814		Approved	BEM46L3	uc001wys.3	Q7Z5M8	OTTHUMG00000140286	ENST00000337334.2:c.831delA	chr14.hg19:g.51368597delA	ENSP00000336693:p.Arg277fs	85.0	0.0		113.0	11.0	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Frame_Shift_Del	DEL	ENST00000337334.2	hg19	CCDS55916.1																																																																																			.	.		0.313	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1			-	51368597	A	-	51368597	7	5	112	1	0	1	0	1	0	0	0	0	77	243	9	0	648	0	ABHD12B	14	51368597	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	721231	51368597	55980943	845	17466										
PYGL	5836	hgsc.bcm.edu	37	chr14	51375542	51375542	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcttatgggaactcacctgTcatgataaaatagcatgttg	8	7	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:51375542T>C	ENST00000216392.7	-	18	2641	c.2309A>G	c.(2308-2310)gAc>gGc	p.D770G	PYGL_ENST00000532462.1_Missense_Mutation_p.D770G|PYGL_ENST00000544180.2_Missense_Mutation_p.D736G	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	770					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|necroptotic process (GO:0070266)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	AMP binding (GO:0016208)|ATP binding (GO:0005524)|bile acid binding (GO:0032052)|drug binding (GO:0008144)|glucose binding (GO:0005536)|glycogen phosphorylase activity (GO:0008184)|protein homodimerization activity (GO:0042803)|purine nucleobase binding (GO:0002060)|pyridoxal phosphate binding (GO:0030170)|vitamin binding (GO:0019842)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)	AACTCACCTGTCATGATAAAA	0.383																																					p.D770G		Atlas-SNP	.											.	PYGL	77	.	0			c.A2309G						.						237	251	247					14																	51375542		2203	4300	6503	SO:0001583	missense	5836	exon18			CACCTGTCATGAT		CCDS32080.1, CCDS53894.1	14q11.2-q24.3	2013-03-01	2008-07-31		ENSG00000100504	ENSG00000100504	2.4.1.1	"Glycogen phosphorylases"	9725	protein-coding gene	gene with protein product	"Hers disease", "glycogen storage disease type VI", "glycogen phosphorylase, liver form"	613741	"phosphorylase, glycogen; liver"			2877458	Standard	NM_002863		Approved		uc001wyu.3	P06737	OTTHUMG00000166596	ENST00000216392.7:c.2309A>G	chr14.hg19:g.51375542T>C	ENSP00000216392:p.Asp770Gly	109.0	0.0		93.0	5.0	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Missense_Mutation	SNP	ENST00000216392.7	hg19	CCDS32080.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.808688	0.90707	.	.	ENSG00000100504	ENST00000532462;ENST00000544180;ENST00000216392	D;D;D	0.96265	-3.96;-3.96;-3.96	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.98833	0.9606	H	0.97491	4.015	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.83275	0.992;0.996;0.996	D	0.99585	1.0974	10	0.87932	D	0	.	14.8423	0.70235	0.0:0.0:0.0:1.0	.	736;736;770	F5H816;B4DUB7;P06737	.;.;PYGL_HUMAN	G	770;736;770	ENSP00000431657:D770G;ENSP00000443787:D736G;ENSP00000216392:D770G	ENSP00000216392:D770G	D	-	2	0	PYGL	50445292	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	8.040000	0.89188	2.187000	0.69744	0.533000	0.62120	GAC	.	.		0.383	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863		C	51375542	T	C	51375542	3	2	112	1	0	0	0	0	1	0	0	0	12876	1667	58	2	246	2	PYGL	14	51375542	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	6945	51375542	55973998	846	17467										
STYX	6815	hgsc.bcm.edu	37	chr14	53213189	53213189	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcccatattcatctgctatgAaaagcaaggtatgaactttg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:53213189delA	ENST00000354586.4	+	3	429	c.136delA	c.(136-138)aaafs	p.K46fs	STYX_ENST00000442123.2_Frame_Shift_Del_p.K46fs|STYX_ENST00000556861.1_Intron	NM_145251.3	NP_660294.1	Q8WUJ0	STYX_HUMAN	serine/threonine/tyrosine interacting protein	46					MAPK export from nucleus (GO:0045204)|protein dephosphorylation (GO:0006470)|regulation of ERK1 and ERK2 cascade (GO:0070372)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5	Breast(41;0.176)					ATCTGCTATGAAAAGCAAGGT	0.294																																					p.M45fs		Atlas-INDEL	.											.	STYX	14	.	0			c.135delG						.						61	63	62					14																	53213189		2202	4298	6500	SO:0001589	frameshift_variant	6815	exon4			.		CCDS9711.1	14q22.1	2011-06-09	2001-11-29		ENSG00000198252	ENSG00000198252		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	11447	protein-coding gene	gene with protein product		615814	"serine/threonine/tyrosine-interacting protein"			7592916	Standard	NM_145251		Approved		uc010tqy.2	Q8WUJ0	OTTHUMG00000140306	ENST00000354586.4:c.136delA	chr14.hg19:g.53213189delA	ENSP00000346599:p.Lys46fs	180.0	0.0		203.0	14.0	NM_001130701	B9EJG0|Q99850	Frame_Shift_Del	DEL	ENST00000354586.4	hg19	CCDS9711.1																																																																																			.	.		0.294	STYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276902.1	NM_145251		-	53213189	A	-	53213189	7	5	112	1	0	1	0	1	0	0	0	0	15375	247	9	0	146	0	STYX	14	53213189	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1837647	53213189	54136351	847	17468										
FERMT2	10979	hgsc.bcm.edu	37	chr14	53326414	53326414	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcaattccaataagttcttcTtttttgcccccttggaacct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:53326414delT	ENST00000395631.2	-	14	1962	c.1746delA	c.(1744-1746)aaafs	p.K582fs	FERMT2_ENST00000553373.1_Frame_Shift_Del_p.K589fs|FERMT2_ENST00000341590.3_Frame_Shift_Del_p.K582fs|FERMT2_ENST00000343279.4_Frame_Shift_Del_p.K589fs|FERMT2_ENST00000557255.1_5'UTR|FERMT2_ENST00000399304.3_Frame_Shift_Del_p.K589fs			Q96AC1	FERM2_HUMAN	fermitin family member 2	582	FERM.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					TAAGTTCTTCTTTTTTGCCCC	0.398																																					p.E590fs		Atlas-INDEL	.											.	FERMT2	59	.	0			c.1768delG						.						118	103	108					14																	53326414		2203	4298	6501	SO:0001589	frameshift_variant	10979	exon15			.	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"Fermitins", "Pleckstrin homology (PH) domain containing"	15767	protein-coding gene	gene with protein product	"kindlin-2"	607746	"pleckstrin homology domain containing, family C (with FERM domain) member 1", "fermitin family homolog 2 (Drosophila)"	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.1746delA	chr14.hg19:g.53326414delT	ENSP00000378993:p.Lys582fs	229.0	0.0		269.0	18.0	NM_001135000	B5TJY2|Q14840|Q86TY7	Frame_Shift_Del	DEL	ENST00000395631.2	hg19	CCDS9713.1																																																																																			.	.		0.398	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832		-	53326414	T	-	53326414	7	5	112	1	0	1	0	1	0	0	0	0	5826	1606	56	0	316	0	FERMT2	14	53326414	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	113225	53326414	54023126	848	17469										
DLGAP5	9787	hgsc.bcm.edu	37	chr14	55625371	55625371	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taattctctctctcattgcaTtttttatggcagctaggcga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:55625371delT	ENST00000247191.2	-	14	1958	c.1742delA	c.(1741-1743)aatfs	p.N581fs	DLGAP5_ENST00000395425.2_Frame_Shift_Del_p.N581fs	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	581					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TCTCATTGCATTTTTTATGGC	0.393																																					p.N581fs		Atlas-INDEL	.											.	DLGAP5	84	.	0			c.1743delT						.						116	103	107					14																	55625371		2202	4300	6502	SO:0001589	frameshift_variant	9787	exon14			.	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.1742delA	chr14.hg19:g.55625371delT	ENSP00000247191:p.Asn581fs	180.0	0.0		205.0	13.0	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Frame_Shift_Del	DEL	ENST00000247191.2	hg19	CCDS9723.1																																																																																			.	.		0.393	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		-	55625371	T	-	55625371	7	5	112	1	0	1	0	1	0	0	0	0	4565	1493	52	0	917	0	DLGAP5	14	55625371	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2298957	55625371	51724169	849	17470										
KTN1	3895	hgsc.bcm.edu	37	chr14	56126388	56126388	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttaactcttttgataggcatCttcttttccccctcatgaag	5	11	4	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:56126388C>T	ENST00000395314.3	+	31	3034	c.2966C>T	c.(2965-2967)tCt>tTt	p.S989F	KTN1_ENST00000395309.3_Missense_Mutation_p.S989F|KTN1_ENST00000555573.1_5'Flank|KTN1_ENST00000438792.2_Missense_Mutation_p.S989F|KTN1_ENST00000416613.1_Missense_Mutation_p.S989F|KTN1_ENST00000413890.2_Missense_Mutation_p.S966F|KTN1_ENST00000554507.1_Missense_Mutation_p.S284F|KTN1_ENST00000395311.1_Missense_Mutation_p.S966F|KTN1_ENST00000395308.1_Missense_Mutation_p.S966F	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	989					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TGATAGGCATCTTCTTTTCCC	0.274			T	RET	papillary thryoid																																p.S989F		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.C2966T						.						70	81	77					14																	56126388		2199	4283	6482	SO:0001583	missense	3895	exon31			AGGCATCTTCTTT		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.2966C>T	chr14.hg19:g.56126388C>T	ENSP00000378725:p.Ser989Phe	59.0	0.0		97.0	5.0	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.409650	0.62399	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613;ENST00000554507	T;T;T;T;T;T;T;T	0.37411	1.39;1.38;1.2;1.38;1.39;1.39;1.38;1.2	4.68	4.68	0.58851	.	0.000000	0.43579	D	0.000546	T	0.48114	0.1482	L	0.50333	1.59	0.34812	D	0.737796	B;D;B;B;P	0.52996	0.429;0.957;0.429;0.343;0.744	B;P;B;B;P	0.56127	0.421;0.792;0.323;0.311;0.503	T	0.61431	-0.7064	10	0.56958	D	0.05	-0.0373	15.1455	0.72647	0.0:1.0:0.0:0.0	.	989;284;989;966;989	B4DZ88;G3V4Y7;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;.;KTN1_HUMAN	F	966;989;989;989;966;966;989;284	ENSP00000394992:S966F;ENSP00000378720:S989F;ENSP00000391964:S989F;ENSP00000378725:S989F;ENSP00000378719:S966F;ENSP00000378722:S966F;ENSP00000388807:S989F;ENSP00000452073:S284F	ENSP00000378719:S966F	S	+	2	0	KTN1	55196141	0.982000	0.34865	0.998000	0.56505	0.993000	0.82548	1.978000	0.40598	2.418000	0.82041	0.563000	0.77884	TCT	.	.		0.274	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			T	56126388	C	T	56126388	3	4	112	1	0	0	0	0	1	0	0	0	8594	913	32	3	3084	3	KTN1	14	56126388	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	501017	56126388	51223152	850	17471										
MUDENG	55745	hgsc.bcm.edu	37	chr14	57741096	57741096	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgatgataaagacttcgttgAgagtcgtgatagctgttcac	11	6	1	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:57741096A>G	ENST00000261558.3	+	2	615	c.209A>G	c.(208-210)gAg>gGg	p.E70G	AP5M1_ENST00000431972.2_Missense_Mutation_p.E84G	NM_018229.3	NP_060699.3	Q9H0R1	AP5M1_HUMAN	adaptor-related protein complex 5, mu 1 subunit	70					endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytosol (GO:0005829)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)											GACTTCGTTGAGAGTCGTGAT	0.408																																					p.E70G		Atlas-SNP	.											.	.	.	.	0			c.A209G						.						109	101	104					14																	57741096		2203	4300	6503	SO:0001583	missense	55745	exon2			TCGTTGAGAGTCG	AF094583	CCDS9729.1	14q22.2	2012-03-20	2012-03-20	2012-03-20	ENSG00000053770	ENSG00000053770			20192	protein-coding gene	gene with protein product	"Mu-2 related death-inducing gene"	614368	"chromosome 14 open reading frame 108", "MU-2/AP1M2 domain containing, death-inducing"	C14orf108, MUDENG		18395520	Standard	NM_018229		Approved	FLJ10813, MuD, mu5	uc001xcv.3	Q9H0R1	OTTHUMG00000140318	ENST00000261558.3:c.209A>G	chr14.hg19:g.57741096A>G	ENSP00000261558:p.Glu70Gly	105.0	0.0		114.0	5.0	NM_018229	O95354|Q6ZMD7|Q96DX3|Q9NVC5	Missense_Mutation	SNP	ENST00000261558.3	hg19	CCDS9729.1	.	.	.	.	.	.	.	.	.	.	A	9.012	0.982620	0.18889	.	.	ENSG00000053770	ENST00000261558;ENST00000431972	T;T	0.36878	1.24;1.23	5.56	4.4	0.53042	.	0.136995	0.64402	D	0.000004	T	0.38374	0.1038	M	0.67953	2.075	0.48830	D	0.999715	B;P	0.38078	0.038;0.617	B;B	0.37144	0.045;0.242	T	0.32640	-0.9899	10	0.62326	D	0.03	.	12.9714	0.58515	0.8647:0.1353:0.0:0.0	.	70;70	Q9H0R1;Q9H0R1-2	MUDEN_HUMAN;.	G	70;84	ENSP00000261558:E70G;ENSP00000390531:E84G	ENSP00000261558:E70G	E	+	2	0	MUDENG	56810849	0.999000	0.42202	0.010000	0.14722	0.091000	0.18340	4.322000	0.59215	1.026000	0.39733	-0.438000	0.05819	GAG	.	.		0.408	AP5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276922.1	NM_018229		G	57741096	A	G	57741096	3	3	112	1	0	0	0	0	1	0	0	0	9992	304	11	2	215	2	MUDENG	14	57741096	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1614708	57741096	49608444	851	17472										
C14orf135	64430	hgsc.bcm.edu	37	chr14	60592492	60592492	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgaaaagtggaaggaagcaaTtttacaagaaaagccatact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:60592492delT	ENST00000406854.1	+	10	3772	c.3218delT	c.(3217-3219)attfs	p.I1073fs	PCNXL4_ENST00000317623.4_Frame_Shift_Del_p.I839fs|PCNXL4_ENST00000406949.1_Frame_Shift_Del_p.I839fs|PCNXL4_ENST00000535349.1_Frame_Shift_Del_p.I280fs|PCNXL4_ENST00000404681.2_Frame_Shift_Del_p.I1073fs			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	1073						integral component of membrane (GO:0016021)											AAGGAAGCAATTTTACAAGAA	0.323																																					p.I839fs		Atlas-INDEL	.											.	.	.	.	0			c.2515delA						.						67	70	69					14																	60592492		2203	4300	6503	SO:0001589	frameshift_variant	64430	exon9			.	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 135"	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.3218delT	chr14.hg19:g.60592492delT	ENSP00000384801:p.Ile1073fs	98.0	0.0		115.0	10.0	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Frame_Shift_Del	DEL	ENST00000406854.1	hg19																																																																																				.	.		0.323	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495		-	60592492	T	-	60592492	7	5	112	1	0	1	0	1	0	0	0	0	1747	1493	52	0	2546	0	C14orf135	14	60592492	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2851396	60592492	46757048	852	17473										
SLC38A6	145389	hgsc.bcm.edu	37	chr14	61497161	61497161	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aacactatttattcttttgcAgctatgtcatcttatctttt	3	8	4	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:61497161A>G	ENST00000267488.4	+	6	519		c.e6-1		SLC38A6_ENST00000456840.2_Splice_Site|SLC38A6_ENST00000354886.2_Splice_Site	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6						amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		ATTCTTTTGCAGCTATGTCAT	0.303																																					.		Atlas-SNP	.											.	SLC38A6	87	.	0			c.404-2A>G						.						56	58	57					14																	61497161		2202	4294	6496	SO:0001630	splice_region_variant	145389	exon6			TTTTGCAGCTATG	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"Solute carriers"	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000267488.4:c.404-1A>G	chr14.hg19:g.61497161A>G		112.0	0.0		97.0	5.0	NM_153811	C9JWA6|Q86SY5	Splice_Site	SNP	ENST00000267488.4	hg19	CCDS9751.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.908374	0.52333	.	.	ENSG00000139974	ENST00000354886;ENST00000267488;ENST00000451406;ENST00000456840;ENST00000526105;ENST00000533744	.	.	.	5.08	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3669	0.55234	0.8589:0.1411:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC38A6	60566914	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	5.449000	0.66619	0.874000	0.35823	-0.291000	0.09656	.	.	.		0.303	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1		Intron	G	61497161	A	G	61497161	5	3	112	1	0	0	0	0	0	0	1	0	14623	202	7	2	424	2	SLC38A6	14	61497161	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	904669	61497161	45852379	853	17474										
SNAPC1	6617	hgsc.bcm.edu	37	chr14	62245598	62245598	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcagaatcattagcgaaaatAaaatcaaaggccttttcagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:62245598delA	ENST00000216294.4	+	7	899	c.795delA	c.(793-795)atafs	p.I265fs	RP11-618G20.1_ENST00000555937.1_RNA	NM_003082.3	NP_003073.1	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex, polypeptide 1, 43kDa	265	SNAPC4-binding.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		TAGCGAAAATAAAATCAAAGG	0.284																																					p.I265fs	NSCLC(27;223 907 37180 39193 46568)	Atlas-INDEL	.											.	SNAPC1	32	.	0			c.794delT						.						76	81	79					14																	62245598		2203	4298	6501	SO:0001589	frameshift_variant	6617	exon7			.	Z47542	CCDS9755.1	14q22	2008-08-11	2002-08-29		ENSG00000023608	ENSG00000023608			11134	protein-coding gene	gene with protein product		600591	"small nuclear RNA activating complex, polypeptide 1, 43kD"			9644240	Standard	NM_003082		Approved	SNAP43, PTFgamma	uc001xft.3	Q16533	OTTHUMG00000140343	ENST00000216294.4:c.795delA	chr14.hg19:g.62245598delA	ENSP00000216294:p.Ile265fs	152.0	0.0		186.0	12.0	NM_003082		Frame_Shift_Del	DEL	ENST00000216294.4	hg19	CCDS9755.1																																																																																			.	.		0.284	SNAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276976.2	NM_003082		-	62245598	A	-	62245598	7	5	112	1	0	1	0	1	0	0	0	0	14849	352	13	0	821	0	SNAPC1	14	62245598	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	748437	62245598	45103942	854	17475										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63174612	63174612	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccactgtcacaagaatctgTttttcttagtgggtttttgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:63174612delT	ENST00000322893.7	-	11	2849	c.2581delA	c.(2581-2583)acafs	p.T861fs	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	861					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CAAGAATCTGTTTTTCTTAGT	0.478																																					p.T861fs		Atlas-INDEL	.											.	KCNH5	320	.	0			c.2582delC						.						159	142	148					14																	63174612		2203	4300	6503	SO:0001589	frameshift_variant	27133	exon11			.	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2581delA	chr14.hg19:g.63174612delT	ENSP00000321427:p.Thr861fs	193.0	0.0		183.0	14.0	NM_139318	C9JP98	Frame_Shift_Del	DEL	ENST00000322893.7	hg19	CCDS9756.1																																																																																			.	.		0.478	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		-	63174612	T	-	63174612	7	5	112	1	0	1	0	1	0	0	0	0	8044	1725	60	0	389	0	KCNH5	14	63174612	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	929014	63174612	44174928	855	17476										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64556329	64556329	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atctgaagtaaaatcaatggAaaaaagagtttcaaaaatca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:64556329delA	ENST00000344113.4	+	59	11920	c.11708delA	c.(11707-11709)gaafs	p.E3903fs	SYNE2_ENST00000554584.1_Frame_Shift_Del_p.E3936fs|SYNE2_ENST00000555002.1_Frame_Shift_Del_p.E537fs|SYNE2_ENST00000357395.3_Frame_Shift_Del_p.E288fs|SYNE2_ENST00000358025.3_Frame_Shift_Del_p.E3903fs|SYNE2_ENST00000394768.2_Frame_Shift_Del_p.E288fs|ESR2_ENST00000542956.1_Intron	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3903					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAATCAATGGAAAAAAGAGTT	0.284																																					p.E3903fs		Atlas-INDEL	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	.	0			c.11707delG						.						32	34	33					14																	64556329		2194	4264	6458	SO:0001589	frameshift_variant	23224	exon59			.	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.11708delA	chr14.hg19:g.64556329delA	ENSP00000341781:p.Glu3903fs	185.0	0.0		211.0	13.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Frame_Shift_Del	DEL	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.284	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		-	64556329	A	-	64556329	7	5	112	1	0	1	0	1	0	0	0	0	15461	246	9	0	11938	0	SYNE2	14	64556329	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1381717	64556329	42793211	856	17477										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64593150	64593150	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggaggagatgctggagatgCccagactttacagggaggat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:64593150delC	ENST00000344113.4	+	72	13872	c.13660delC	c.(13660-13662)cccfs	p.P4554fs	SYNE2_ENST00000554584.1_Frame_Shift_Del_p.P4505fs|SYNE2_ENST00000555002.1_Frame_Shift_Del_p.P1188fs|SYNE2_ENST00000357395.3_Frame_Shift_Del_p.P939fs|SYNE2_ENST00000358025.3_Frame_Shift_Del_p.P4554fs|SYNE2_ENST00000394768.2_Frame_Shift_Del_p.P939fs|ESR2_ENST00000542956.1_Intron	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4554					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GCTGGAGATGCCCAGACTTTA	0.498																																					p.M4553fs		Atlas-INDEL	.											.	SYNE2	577	.	0			c.13659delG						.						95	92	93					14																	64593150		2203	4300	6503	SO:0001589	frameshift_variant	23224	exon72			.	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.13660delC	chr14.hg19:g.64593150delC	ENSP00000341781:p.Pro4554fs	165.0	0.0		201.0	13.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Frame_Shift_Del	DEL	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.498	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		-	64593150	C	-	64593150	7	5	112	1	0	1	0	1	0	0	0	0	15461	739	26	0	13942	0	SYNE2	14	64593150	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	36821	64593150	42756390	857	17478										
HSPA2	3306	hgsc.bcm.edu	37	chr14	65008143	65008143	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctggacaagaagggctgcgcGggcggcgagaagaacgtgct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:65008143delG	ENST00000394709.1	+	2	652	c.576delG	c.(574-576)gcgfs	p.A192fs	HSPA2_ENST00000554883.1_3'UTR|HSPA2_ENST00000247207.6_Frame_Shift_Del_p.A192fs|RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	192					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		AGGGCTGCGCGGGCGGCGAGA	0.632																																					p.A192fs	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-INDEL	.											HSPA2,NS,carcinoma,0,1	HSPA2	83	.	0			c.575delC						.						83	91	88					14																	65008143		2203	4300	6503	SO:0001589	frameshift_variant	3306	exon1			.	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"Heat shock proteins / HSP70"	5235	protein-coding gene	gene with protein product		140560	"heat shock 70kD protein 2"				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.576delG	chr14.hg19:g.65008143delG	ENSP00000378199:p.Ala192fs	133.0	0.0		162.0	10.0	NM_021979	Q15508|Q53XM3|Q9UE78	Frame_Shift_Del	DEL	ENST00000394709.1	hg19	CCDS9766.1																																																																																			.	.		0.632	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			-	65008143	G	-	65008143	7	5	112	1	0	1	0	1	0	0	0	0	7420	1103	39	0	578	0	HSPA2	14	65008143	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	414993	65008143	42341397	858	17479										
GALNTL1	57452	hgsc.bcm.edu	37	chr14	69795179	69795179	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcttgtagggctgatccggtCccgagtgcgtggggcggacg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:69795179delC	ENST00000337827.4	+	6	908	c.581delC	c.(580-582)tccfs	p.S194fs	GALNT16_ENST00000448469.3_Frame_Shift_Del_p.S194fs|GALNT16_ENST00000553669.1_Frame_Shift_Del_p.S194fs	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	194	Catalytic subdomain A.				protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										CTGATCCGGTCCCGAGTGCGT	0.632																																					p.S194fs		Atlas-INDEL	.											.	GALNT16	8	.	0			c.580delT						.						97	88	91					14																	69795179		2203	4300	6503	SO:0001589	frameshift_variant	57452	exon6			.	AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23233	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 16"	615132	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.581delC	chr14.hg19:g.69795179delC	ENSP00000336729:p.Ser194fs	76.0	0.0		103.0	10.0	NM_001168368	Q4KMG3|Q58A55|Q9ULT9	Frame_Shift_Del	DEL	ENST00000337827.4	hg19	CCDS32107.1																																																																																			.	.		0.632	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368		-	69795179	C	-	69795179	7	5	112	1	0	1	0	1	0	0	0	0	6229	855	30	0	603	0	GALNTL1	14	69795179	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	4787036	69795179	37554361	859	17480										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72152235	72152235	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtcccgtcccaggtgcagagTcccatgacctcgcggctgaa	12	15	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:72152235T>C	ENST00000555818.1	+	10	3609	c.3261T>C	c.(3259-3261)agT>agC	p.S1087S	SIPA1L1_ENST00000358550.2_Silent_p.S1087S|SIPA1L1_ENST00000537413.1_Silent_p.S562S|SIPA1L1_ENST00000381232.3_Silent_p.S1087S	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1087					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AGGTGCAGAGTCCCATGACCT	0.547																																					p.S1087S		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.T3261C						.						52	50	51					14																	72152235		2203	4300	6503	SO:0001819	synonymous_variant	26037	exon10			GCAGAGTCCCATG	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.3261T>C	chr14.hg19:g.72152235T>C		88.0	0.0		97.0	5.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	hg19	CCDS9807.1																																																																																			.	.		0.547	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		C	72152235	T	C	72152235	2	2	112	1	0	0	0	0	0	0	0	1	14344	1664	58	2		2	SIPA1L1	14	72152235	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2357056	72152235	35197305	860	17481										
FAM161B	145483	hgsc.bcm.edu	37	chr14	74409383	74409383	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctggagcatgtccagggctcTcatttggatgcgaattttcc	11	10	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:74409383T>C	ENST00000534936.1	-	4	1066	c.961A>G	c.(961-963)Aga>Gga	p.R321G	FAM161B_ENST00000286544.3_Missense_Mutation_p.R384G			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	321										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						TCCAGGGCTCTCATTTGGATG	0.537																																					p.R384G		Atlas-SNP	.											.	FAM161B	67	.	0			c.A1150G						.						68	74	72					14																	74409383		2203	4300	6503	SO:0001583	missense	145483	exon4			GGGCTCTCATTTG	AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 44"	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.961A>G	chr14.hg19:g.74409383T>C	ENSP00000445326:p.Arg321Gly	68.0	0.0		70.0	4.0	NM_152445	B7Z882|J3KNA2	Missense_Mutation	SNP	ENST00000534936.1	hg19		.	.	.	.	.	.	.	.	.	.	T	20.7	4.035816	0.75617	.	.	ENSG00000156050	ENST00000286544;ENST00000534936	T;T	0.37915	1.17;1.17	5.5	-0.0292	0.13919	.	0.061993	0.64402	D	0.000016	T	0.62196	0.2408	M	0.86953	2.85	0.51012	D	0.999902	D	0.89917	1.0	D	0.91635	0.999	T	0.71130	-0.4682	10	0.87932	D	0	-14.4659	14.7771	0.69738	0.0:0.0:0.507:0.493	.	321	Q96MY7	F161B_HUMAN	G	384;321	ENSP00000286544:R384G;ENSP00000445326:R321G	ENSP00000286544:R384G	R	-	1	2	FAM161B	73479136	1.000000	0.71417	0.994000	0.49952	0.969000	0.65631	1.711000	0.37930	0.134000	0.18681	0.533000	0.62120	AGA	.	.		0.537	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445		C	74409383	T	C	74409383	3	2	112	1	0	0	0	0	1	0	0	0	5478	1559	54	2	1006	2	FAM161B	14	74409383	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2257148	74409383	32940157	861	17482										
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493060	77493060	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cggcgcggttgcgcaggctcTcgctcagctcggccagggcc	16	16	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:77493060T>C	ENST00000238647.3	-	1	1974	c.1076A>G	c.(1075-1077)gAg>gGg	p.E359G		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	359					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						GCGCAGGCTCTCGCTCAGCTC	0.682																																					p.E359G		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.A1076G						.						31	29	30					14																	77493060		2200	4299	6499	SO:0001583	missense	64207	exon1			AGGCTCTCGCTCA	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.1076A>G	chr14.hg19:g.77493060T>C	ENSP00000238647:p.Glu359Gly	66.0	0.0		100.0	5.0	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Missense_Mutation	SNP	ENST00000238647.3	hg19	CCDS9854.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.980023	0.74474	.	.	ENSG00000119669	ENST00000238647	T	0.20463	2.07	4.03	4.03	0.46877	.	0.083770	0.45606	U	0.000343	T	0.34890	0.0913	L	0.58810	1.83	0.52099	D	0.999942	D	0.60575	0.988	P	0.57204	0.815	T	0.15607	-1.0431	10	0.87932	D	0	7.8519	11.9534	0.52968	0.0:0.0:0.0:1.0	.	359	Q9H1B7	I2BPL_HUMAN	G	359	ENSP00000238647:E359G	ENSP00000238647:E359G	E	-	2	0	IRF2BPL	76562813	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.635000	0.67841	1.696000	0.51158	0.379000	0.24179	GAG	.	.		0.682	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		C	77493060	T	C	77493060	3	2	112	1	0	0	0	0	1	0	0	0	1775	1551	54	2	1318	2	C14orf4	14	77493060	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3083677	77493060	29856480	862	17483										
AHSA1	10598	hgsc.bcm.edu	37	chr14	77935521	77935521	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcctgaggaagagcggacgCgacagggctggcagcggtac	17	11	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:77935521C>A	ENST00000216479.3	+	9	1106	c.946C>A	c.(946-948)Cga>Aga	p.R316R	SNORA46_ENST00000391069.1_RNA|AHSA1_ENST00000555457.1_3'UTR	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	316					positive regulation of ATPase activity (GO:0032781)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		AGAGCGGACGCGACAGGGCTG	0.572																																					p.R316R		Atlas-SNP	.											AHSA1,NS,carcinoma,0,1	AHSA1	24	.	0			c.C946A						.						170	159	162					14																	77935521		2203	4300	6503	SO:0001819	synonymous_variant	10598	exon9			CGGACGCGACAGG	AJ243310	CCDS9863.1	14q	2008-02-05	2003-04-04	2003-04-11		ENSG00000100591			1189	protein-coding gene	gene with protein product		608466	"chromosome 14 open reading frame 3"	C14orf3			Standard	NM_012111		Approved	p38	uc001xtw.3	O95433		ENST00000216479.3:c.946C>A	chr14.hg19:g.77935521C>A		163.0	0.0		166.0	0.0	NM_012111	B2R9L2|B4DUR9|Q96IL6|Q9P060	Silent	SNP	ENST00000216479.3	hg19	CCDS9863.1	.	.	.	.	.	.	.	.	.	.	C	6.398	0.441552	0.12164	.	.	ENSG00000100591	ENST00000555729	.	.	.	5.46	2.44	0.29823	.	.	.	.	.	T	0.33059	0.0850	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.19679	-1.0298	4	.	.	.	-4.2088	7.4374	0.27164	0.5001:0.4161:0.0:0.0837	.	.	.	.	E	110	.	.	A	+	2	0	AHSA1	77005274	0.801000	0.28930	0.972000	0.41901	0.782000	0.44232	1.616000	0.36933	0.865000	0.35603	-0.229000	0.12294	GCG	.	.		0.572	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111		A	77935521	C	A	77935521	2	1	112	1	0	0	0	0	0	0	0	1	418	760	27	1		1	AHSA1	14	77935521	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	442461	77935521	29414019	863	17484										
SEL1L	6400	hgsc.bcm.edu	37	chr14	81970628	81970628	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctgcttcctgcatctgccgTctcttagcagcctcttcttc	6	16	5	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:81970628T>C	ENST00000336735.4	-	5	647	c.531A>G	c.(529-531)agA>agG	p.R177R	SEL1L_ENST00000555824.1_Silent_p.R177R	NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	177	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		GCATCTGCCGTCTCTTAGCAG	0.353																																					p.R177R		Atlas-SNP	.											.	SEL1L	67	.	0			c.A531G						.						205	182	190					14																	81970628		2203	4300	6503	SO:0001819	synonymous_variant	6400	exon5			CTGCCGTCTCTTA		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.531A>G	chr14.hg19:g.81970628T>C		146.0	0.0		142.0	6.0	NM_001244984	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	hg19	CCDS9876.1																																																																																			.	.		0.353	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		C	81970628	T	C	81970628	2	2	112	1	0	0	0	0	0	0	0	1	14025	1664	58	2		2	SEL1L	14	81970628	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4035107	81970628	25378912	864	17485										
GALC	2581	hgsc.bcm.edu	37	chr14	88429767	88429767	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgaggttccctaagccatcAgtcagagctacgtagcttcc	10	12	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:88429767A>G	ENST00000261304.2	-	10	1228	c.1122T>C	c.(1120-1122)acT>acC	p.T374T	GALC_ENST00000393569.2_Silent_p.T348T|GALC_ENST00000393568.4_Silent_p.T351T|GALC_ENST00000544807.2_Silent_p.T318T	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	374					carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTAAGCCATCAGTCAGAGCTA	0.383																																					p.T374T		Atlas-SNP	.											.	GALC	48	.	0			c.T1122C						.						139	130	132					14																	88429767		1897	4114	6011	SO:0001819	synonymous_variant	2581	exon10			GCCATCAGTCAGA	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"Krabbe disease"	606890	"galactosylceramidase (Krabbe disease)"				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.1122T>C	chr14.hg19:g.88429767A>G		90.0	0.0		102.0	6.0	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Silent	SNP	ENST00000261304.2	hg19	CCDS9878.2																																																																																			.	.		0.383	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2			G	88429767	A	G	88429767	2	3	112	1	0	0	0	0	0	0	0	1	6209	175	7	2		2	GALC	14	88429767	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	6459139	88429767	18919773	865	17486										
EML5	161436	hgsc.bcm.edu	37	chr14	89172628	89172628	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtgctatgtgaacagcatcTttcagttttctttcaggaat	9	7	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:89172628T>C	ENST00000380664.5	-	11	1799	c.1800A>G	c.(1798-1800)aaA>aaG	p.K600K	EML5_ENST00000352093.5_Silent_p.K600K|EML5_ENST00000554922.1_Silent_p.K600K			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	600						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GAACAGCATCTTTCAGTTTTC	0.368																																					p.K600K		Atlas-SNP	.											.	EML5	141	.	0			c.A1800G						.						108	105	106					14																	89172628		1841	4086	5927	SO:0001819	synonymous_variant	161436	exon11			AGCATCTTTCAGT	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.1800A>G	chr14.hg19:g.89172628T>C		96.0	0.0		87.0	4.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Silent	SNP	ENST00000380664.5	hg19	CCDS45148.1																																																																																			.	.		0.368	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			C	89172628	T	C	89172628	2	2	112	1	0	0	0	0	0	0	0	1	5102	1606	56	2		2	EML5	14	89172628	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	742861	89172628	18176912	866	17487										
BTBD7	55727	hgsc.bcm.edu	37	chr14	93712578	93712578	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctcccaggctgtctcattgTcaagagtggactttcatccc	8	13	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:93712578T>C	ENST00000334746.5	-	10	2483	c.2176A>G	c.(2176-2178)Aca>Gca	p.T726A	BTBD7_ENST00000554565.1_Missense_Mutation_p.T375A|BTBD7_ENST00000393170.2_Missense_Mutation_p.T300A	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	726					multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		TGTCTCATTGTCAAGAGTGGA	0.403																																					p.T726A		Atlas-SNP	.											.	BTBD7	112	.	0			c.A2176G						.						106	106	106					14																	93712578		2203	4300	6503	SO:0001583	missense	55727	exon10			TCATTGTCAAGAG	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"BTB/POZ domain containing"	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.2176A>G	chr14.hg19:g.93712578T>C	ENSP00000335615:p.Thr726Ala	113.0	0.0		130.0	6.0	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.821766	0.50633	.	.	ENSG00000011114	ENST00000334746;ENST00000554565;ENST00000553975;ENST00000393170	T;T	0.39997	1.41;1.05	5.75	5.75	0.90469	.	0.044520	0.85682	D	0.000000	T	0.24812	0.0602	N	0.08118	0	0.53688	D	0.999978	B;B;B	0.27625	0.183;0.1;0.002	B;B;B	0.22601	0.04;0.022;0.004	T	0.09037	-1.0693	10	0.23891	T	0.37	.	16.0605	0.80836	0.0:0.0:0.0:1.0	.	300;375;726	E7ERI4;Q9P203-5;Q9P203	.;.;BTBD7_HUMAN	A	726;375;341;300	ENSP00000335615:T726A;ENSP00000451010:T375A	ENSP00000335615:T726A	T	-	1	0	BTBD7	92782331	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.126000	0.57937	2.193000	0.70182	0.528000	0.53228	ACA	.	.		0.403	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		C	93712578	T	C	93712578	3	2	112	1	0	0	0	0	1	0	0	0	1548	1667	58	2	1230	2	BTBD7	14	93712578	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4539950	93712578	13636962	867	17488										
DDX24	57062	hgsc.bcm.edu	37	chr14	94519409	94519409	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctgctcaatccaagagttgTgcaggcaagcctggaagttc	11	11	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:94519409T>C	ENST00000330836.5	-	8	2374	c.2243A>G	c.(2242-2244)cAc>cGc	p.H748R	DDX24_ENST00000555054.1_Missense_Mutation_p.H705R|DDX24_ENST00000544005.1_Missense_Mutation_p.H498R|DDX24_ENST00000553400.1_5'Flank	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	748					RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		CCAAGAGTTGTGCAGGCAAGC	0.483																																					p.H748R		Atlas-SNP	.											.	DDX24	82	.	0			c.A2243G						.						68	66	67					14																	94519409		2203	4300	6503	SO:0001583	missense	57062	exon8			GAGTTGTGCAGGC	AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"DEAD-boxes"	13266	protein-coding gene	gene with protein product		606181	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.2243A>G	chr14.hg19:g.94519409T>C	ENSP00000328690:p.His748Arg	106.0	0.0		81.0	4.0	NM_020414	E7EMJ4|Q4V9L5	Missense_Mutation	SNP	ENST00000330836.5	hg19	CCDS9918.1	.	.	.	.	.	.	.	.	.	.	T	19.34	3.807978	0.70797	.	.	ENSG00000089737	ENST00000330836;ENST00000544005;ENST00000440370;ENST00000543787;ENST00000555054;ENST00000542247	T;T;T	0.03358	4.05;3.96;4.05	5.61	5.61	0.85477	.	0.047415	0.85682	D	0.000000	T	0.06325	0.0163	L	0.43152	1.355	0.58432	D	0.999993	B	0.30146	0.27	B	0.34489	0.184	T	0.28776	-1.0033	10	0.59425	D	0.04	-10.2535	16.0977	0.81139	0.0:0.0:0.0:1.0	.	748	Q9GZR7	DDX24_HUMAN	R	748;498;693;374;705;705	ENSP00000328690:H748R;ENSP00000440623:H498R;ENSP00000452145:H705R	ENSP00000328690:H748R	H	-	2	0	DDX24	93589162	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	8.029000	0.88807	2.269000	0.75478	0.533000	0.62120	CAC	.	.		0.483	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		C	94519409	T	C	94519409	3	2	112	1	0	0	0	0	1	0	0	0	4353	1696	59	2	344	2	DDX24	14	94519409	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	806831	94519409	12830131	868	17489										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96761480	96761480	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccttggcaaactgcaggtgAcatcagctccaggagacttt	11	11	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:96761480A>G	ENST00000359933.4	-	36	6136	c.5243T>C	c.(5242-5244)gTc>gCc	p.V1748A	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1748					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		ACTGCAGGTGACATCAGCTCC	0.373																																					p.V1748A		Atlas-SNP	.											.	ATG2B	169	.	0			c.T5243C						.						73	70	71					14																	96761480		2203	4300	6503	SO:0001583	missense	55102	exon36			CAGGTGACATCAG	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.5243T>C	chr14.hg19:g.96761480A>G	ENSP00000353010:p.Val1748Ala	110.0	0.0		89.0	5.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	17.89	3.500390	0.64298	.	.	ENSG00000066739	ENST00000359933	T	0.10005	2.92	5.52	5.52	0.82312	.	0.089600	0.44285	D	0.000476	T	0.11665	0.0284	L	0.42245	1.32	0.49483	D	0.999796	P	0.47302	0.893	B	0.44315	0.446	T	0.04840	-1.0923	10	0.06099	T	0.92	.	15.9319	0.79668	1.0:0.0:0.0:0.0	.	1748	Q96BY7	ATG2B_HUMAN	A	1748	ENSP00000353010:V1748A	ENSP00000261834:V392A	V	-	2	0	ATG2B	95831233	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.927000	0.75840	2.225000	0.72522	0.459000	0.35465	GTC	.	.		0.373	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96761480	A	G	96761480	3	3	112	1	0	0	0	0	1	0	0	0	1094	275	10	2	1021	2	ATG2B	14	96761480	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2242071	96761480	10588060	869	17490										
CCNK	8812	hgsc.bcm.edu	37	chr14	99976694	99976694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccaccaccagctcctacatgTctggagagggctaccagagc	10	15	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:99976694T>C	ENST00000389879.5	+	11	1441	c.1318T>C	c.(1318-1320)Tct>Cct	p.S440P	CCNK_ENST00000555049.1_Intron|RP11-688G15.3_ENST00000557733.1_RNA	NM_001099402.1	NP_001092872.1	O75909	CCNK_HUMAN	cyclin K	440					cellular response to DNA damage stimulus (GO:0006974)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of cell cycle arrest (GO:0071157)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cyclin K-CDK12 complex (GO:0002944)|cyclin K-CDK13 complex (GO:0002945)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase binding (GO:0019901)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|endometrium(2)|lung(3)	6		all_cancers(154;0.224)|all_epithelial(191;0.0643)|Melanoma(154;0.0866)				CTCCTACATGTCTGGAGAGGG	0.697																																					p.S440P		Atlas-SNP	.											.	CCNK	32	.	0			c.T1318C						.						20	22	22					14																	99976694		1957	4123	6080	SO:0001583	missense	8812	exon11			TACATGTCTGGAG	AF060515	CCDS45160.1	14q32.2	2014-07-03			ENSG00000090061	ENSG00000090061			1596	protein-coding gene	gene with protein product		603544				9632813, 10574912	Standard	NM_001099402		Approved	CPR4	uc001ygi.4	O75909	OTTHUMG00000171495	ENST00000389879.5:c.1318T>C	chr14.hg19:g.99976694T>C	ENSP00000374529:p.Ser440Pro	130.0	0.0		139.0	6.0	NM_001099402	Q59FT6|Q86U16|Q96B63|Q9NNY9	Missense_Mutation	SNP	ENST00000389879.5	hg19	CCDS45160.1	.	.	.	.	.	.	.	.	.	.	T	15.81	2.944018	0.53079	.	.	ENSG00000090061	ENST00000437596;ENST00000389879	T	0.27720	1.65	3.96	3.96	0.45880	.	0.292105	0.33496	N	0.004854	T	0.30541	0.0768	N	0.24115	0.695	0.80722	D	1	D	0.65815	0.995	P	0.54889	0.763	T	0.02596	-1.1136	10	0.21014	T	0.42	-6.8107	13.0066	0.58707	0.0:0.0:0.0:1.0	.	440	O75909	CCNK_HUMAN	P	460;440	ENSP00000374529:S440P	ENSP00000374529:S440P	S	+	1	0	CCNK	99046447	1.000000	0.71417	0.994000	0.49952	0.985000	0.73830	7.023000	0.76437	1.665000	0.50811	0.397000	0.26171	TCT	.	.		0.697	CCNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413721.1			C	99976694	T	C	99976694	3	2	112	1	0	0	0	0	1	0	0	0	2932	1667	58	2	1356	2	CCNK	14	99976694	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3215214	99976694	7372846	870	17491										
DLK1	8788	hgsc.bcm.edu	37	chr14	101200644	101200644	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgacggcgtctgcactgacaTtgggggcgacttccgctgcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:101200644delT	ENST00000341267.4	+	5	805	c.563delT	c.(562-564)attfs	p.I188fs	DLK1_ENST00000331224.6_Frame_Shift_Del_p.I188fs	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	188	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				TGCACTGACATTGGGGGCGAC	0.667																																					p.I188fs		Atlas-INDEL	.											.	DLK1	57	.	0			c.562delA						.						52	57	55					14																	101200644		2203	4300	6503	SO:0001589	frameshift_variant	8788	exon5			.	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"delta-like homolog (Drosophila)"			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.563delT	chr14.hg19:g.101200644delT	ENSP00000340292:p.Ile188fs	190.0	0.0		211.0	13.0	NM_003836	P15803|Q96DW5	Frame_Shift_Del	DEL	ENST00000341267.4	hg19	CCDS9963.1																																																																																			.	.		0.667	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1			-	101200644	T	-	101200644	7	5	112	1	0	1	0	1	0	0	0	0	4566	1493	52	0	581	0	DLK1	14	101200644	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1223950	101200644	6148896	871	17492										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102431079	102431079	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacggctcggccggattggaAgtgtcggccgtgcagaatgt	17	9	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:102431079A>G	ENST00000360184.4	+	1	215	c.51A>G	c.(49-51)gaA>gaG	p.E17E		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	17					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						CCGGATTGGAAGTGTCGGCCG	0.726																																					p.E17E		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A51G						.						7	9	8					14																	102431079		1982	3991	5973	SO:0001819	synonymous_variant	1778	exon1			ATTGGAAGTGTCG	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.51A>G	chr14.hg19:g.102431079A>G		25.0	0.0		43.0	4.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	hg19	CCDS9966.1																																																																																			.	.		0.726	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		G	102431079	A	G	102431079	2	3	112	1	0	0	0	0	0	0	0	1	4843	69	3	2		2	DYNC1H1	14	102431079	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1230435	102431079	4918461	872	17493										
TRAF3	7187	hgsc.bcm.edu	37	chr14	103371834	103371834	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggggacgcacttgtcgctgTtttttgtcatcatgcgtgga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:103371834delT	ENST00000560371.1	+	11	1637	c.1420delT	c.(1420-1422)tttfs	p.F475fs	TRAF3_ENST00000351691.5_Frame_Shift_Del_p.F450fs|TRAF3_ENST00000347662.4_Frame_Shift_Del_p.F450fs|TRAF3_ENST00000392745.2_Frame_Shift_Del_p.F475fs|TRAF3_ENST00000539721.1_Frame_Shift_Del_p.F392fs	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	475	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		CTTGTCGCTGTTTTTTGTCAT	0.517																																					p.L473fs		Atlas-INDEL	.											.	TRAF3	60	.	0			c.1419delG						.						229	203	212					14																	103371834		2203	4300	6503	SO:0001589	frameshift_variant	7187	exon12			.	U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.1420delT	chr14.hg19:g.103371834delT	ENSP00000454207:p.Phe475fs	154.0	0.0		177.0	11.0	NM_145725	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Frame_Shift_Del	DEL	ENST00000560371.1	hg19	CCDS9975.1																																																																																			.	.		0.517	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725		-	103371834	T	-	103371834	7	5	112	1	0	1	0	1	0	0	0	0	16454	1725	60	0	1458	0	TRAF3	14	103371834	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	940755	103371834	3977706	873	17494										
AMN	81693	hgsc.bcm.edu	37	chr14	103395267	103395267	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttccgcgtggggctcggcccTggcgctagccccgtgcgtgt	16	15	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:103395267T>C	ENST00000299155.5	+	5	501	c.468T>C	c.(466-468)ccT>ccC	p.P156P		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	156					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|excretion (GO:0007588)|Golgi to plasma membrane protein transport (GO:0043001)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GGCTCGGCCCTGGCGCTAGCC	0.721																																					p.P156P		Atlas-SNP	.											.	AMN	13	.	0			c.T468C						.						25	25	25					14																	103395267		2199	4296	6495	SO:0001819	synonymous_variant	81693	exon5			CGGCCCTGGCGCT	AF328788	CCDS9977.1	14q32.32	2014-09-17	2012-12-07		ENSG00000166126	ENSG00000166126			14604	protein-coding gene	gene with protein product		605799	"amnionless homolog (mouse)"			11279523	Standard	NM_030943		Approved	amnionless	uc001ymg.4	Q9BXJ7		ENST00000299155.5:c.468T>C	chr14.hg19:g.103395267T>C		32.0	0.0		53.0	4.0	NM_030943	Q6UX83	Silent	SNP	ENST00000299155.5	hg19	CCDS9977.1																																																																																			.	.		0.721	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1			C	103395267	T	C	103395267	2	2	112	1	0	0	0	0	0	0	0	1	580	1567	55	2		2	AMN	14	103395267	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	23433	103395267	3954273	874	17495										
CDC42BPB	9578	hgsc.bcm.edu	37	chr14	103414077	103414077	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccctgaatatacatggaataTctcggcgtgtagcatgaatg	10	8	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:103414077T>C	ENST00000361246.2	-	27	3800	c.3512A>G	c.(3511-3513)gAt>gGt	p.D1171G		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		ACATGGAATATCTCGGCGTGT	0.443																																					p.D1171G		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.A3512G						.						113	114	113					14																	103414077		2200	4293	6493	SO:0001583	missense	9578	exon27			GGAATATCTCGGC	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"CDC42-binding protein kinase beta (DMPK-like)"			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.3512A>G	chr14.hg19:g.103414077T>C	ENSP00000355237:p.Asp1171Gly	65.0	0.0		96.0	4.0	NM_006035		Missense_Mutation	SNP	ENST00000361246.2	hg19	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.165233	0.78339	.	.	ENSG00000198752	ENST00000361246;ENST00000541396	T	0.40476	1.03	5.63	5.63	0.86233	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.046925	0.85682	D	0.000000	T	0.71459	0.3342	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.78352	-0.2237	10	0.87932	D	0	.	16.1721	0.81825	0.0:0.0:0.0:1.0	.	1171;1171	A9JR72;Q9Y5S2	.;MRCKB_HUMAN	G	1171;282	ENSP00000355237:D1171G	ENSP00000355237:D1171G	D	-	2	0	CDC42BPB	102483830	1.000000	0.71417	0.955000	0.39395	0.671000	0.39405	7.483000	0.81158	2.281000	0.76405	0.524000	0.50904	GAT	.	.		0.443	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		C	103414077	T	C	103414077	3	2	112	1	0	0	0	0	1	0	0	0	3075	1435	50	2	1667	2	CDC42BPB	14	103414077	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	18810	103414077	3935463	875	17496										
MARK3	4140	hgsc.bcm.edu	37	chr14	103934485	103934485	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccacaaagtgcagagaagtgTtttttcaagccaaaagcaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:103934485delT	ENST00000429436.2	+	12	1736	c.1226delT	c.(1225-1227)gttfs	p.V409fs	MARK3_ENST00000216288.7_Frame_Shift_Del_p.V393fs|MARK3_ENST00000303622.9_Frame_Shift_Del_p.V409fs|MARK3_ENST00000561071.1_Intron|MARK3_ENST00000440884.3_Frame_Shift_Del_p.V330fs|MARK3_ENST00000416682.2_Frame_Shift_Del_p.V432fs|MARK3_ENST00000335102.5_Frame_Shift_Del_p.V432fs|MARK3_ENST00000553942.1_Frame_Shift_Del_p.V409fs	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	409						plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			CAGAGAAGTGTTTTTTCAAGC	0.478																																					p.V409fs		Atlas-INDEL	.											.	MARK3	86	.	0			c.1225delG						.						128	116	120					14																	103934485		1962	4159	6121	SO:0001589	frameshift_variant	4140	exon12			.	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.1226delT	chr14.hg19:g.103934485delT	ENSP00000411397:p.Val409fs	157.0	0.0		179.0	11.0	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Frame_Shift_Del	DEL	ENST00000429436.2	hg19	CCDS45165.1																																																																																			.	.		0.478	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		-	103934485	T	-	103934485	7	5	112	1	0	1	0	1	0	0	0	0	9323	1725	60	0	1272	0	MARK3	14	103934485	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	520408	103934485	3415055	876	17497										
CDCA4	55038	hgsc.bcm.edu	37	chr14	105477749	105477749	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctcttccatgcagctggggTttttagtctccagcgtttca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:105477749delT	ENST00000336219.3	-	2	673	c.518delA	c.(517-519)aacfs	p.N173fs	CDCA4_ENST00000392590.3_Frame_Shift_Del_p.N173fs	NM_017955.3	NP_060425.2	Q9BXL8	CDCA4_HUMAN	cell division cycle associated 4	173						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.142)		GCAGCTGGGGTTTTTAGTCTC	0.562																																					p.N173fs		Atlas-INDEL	.											.	CDCA4	18	.	0			c.519delC						.						86	83	84					14																	105477749		2203	4300	6503	SO:0001589	frameshift_variant	55038	exon2			.	BG354577	CCDS9996.1	14q32.33	2014-02-14			ENSG00000170779	ENSG00000170779			14625	protein-coding gene	gene with protein product	"hematopoietic progenitor protein"	612270				12188893	Standard	NM_145701		Approved	FLJ20764, Hepp	uc001yqb.2	Q9BXL8	OTTHUMG00000170767	ENST00000336219.3:c.518delA	chr14.hg19:g.105477749delT	ENSP00000337226:p.Asn173fs	133.0	0.0		174.0	12.0	NM_017955	Q8TB18|Q9NWK7	Frame_Shift_Del	DEL	ENST00000336219.3	hg19	CCDS9996.1																																																																																			.	.		0.562	CDCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410311.1	NM_145701		-	105477749	T	-	105477749	7	5	112	1	0	1	0	1	0	0	0	0	3090	1725	60	0	211	0	CDCA4	14	105477749	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1543264	105477749	1871791	877	17498										
JAG2	3714	hgsc.bcm.edu	37	chr14	105618518	105618518	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctttgtcacagagcaggccgCcccagttggtctcacagttg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:105618518delC	ENST00000331782.3	-	6	1302	c.899delG	c.(898-900)ggcfs	p.G301fs	RP11-44N21.4_ENST00000548203.1_RNA|JAG2_ENST00000347004.2_Frame_Shift_Del_p.G301fs	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	301	EGF-like 2; atypical. {ECO:0000255|PROSITE-ProRule:PRU00076}.				auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		GAGCAGGCCGCCCCAGTTGGT	0.642																																					p.G300fs		Atlas-INDEL	.											.	JAG2	69	.	0			c.900delC						.						80	71	74					14																	105618518		2203	4300	6503	SO:0001589	frameshift_variant	3714	exon6			.	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.899delG	chr14.hg19:g.105618518delC	ENSP00000328169:p.Gly301fs	196.0	0.0		220.0	14.0	NM_145159	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Frame_Shift_Del	DEL	ENST00000331782.3	hg19	CCDS9998.1																																																																																			.	.		0.642	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			-	105618518	C	-	105618518	7	5	112	1	0	1	0	1	0	0	0	0	7944	739	26	0	2901	0	JAG2	14	105618518	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	140769	105618518	1731022	878	17499										
MTA1	9112	hgsc.bcm.edu	37	chr14	105916421	105916421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tagaagaggaaatggagaacCcggaaatggtggacctgccc	14	8	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:105916421C>T	ENST00000331320.7	+	5	482	c.268C>T	c.(268-270)Ccg>Tcg	p.P90S	MTA1_ENST00000406191.1_Missense_Mutation_p.P90S|MTA1_ENST00000405646.1_Missense_Mutation_p.P73S	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	90	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		AATGGAGAACCCGGAAATGGT	0.627																																					p.P90S		Atlas-SNP	.											MTA1,NS,carcinoma,0,1	MTA1	61	.	0			c.C268T						.						61	66	64					14																	105916421		2203	4300	6503	SO:0001583	missense	9112	exon5			GAGAACCCGGAAA	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"GATA zinc finger domain containing"	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.268C>T	chr14.hg19:g.105916421C>T	ENSP00000333633:p.Pro90Ser	179.0	0.0		157.0	0.0	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	19.02	3.746070	0.69418	.	.	ENSG00000182979	ENST00000331320;ENST00000406191;ENST00000405646;ENST00000498644	D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02	4.14	4.14	0.48551	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	U	0.000000	D	0.83367	0.5239	L	0.56396	1.775	0.80722	D	1	P	0.38250	0.624	B	0.39465	0.3	D	0.83910	0.0295	10	0.41790	T	0.15	-11.5496	14.9627	0.71169	0.0:1.0:0.0:0.0	.	90	Q13330	MTA1_HUMAN	S	90;90;73;4	ENSP00000333633:P90S;ENSP00000385702:P90S;ENSP00000384180:P73S;ENSP00000448146:P4S	ENSP00000333633:P90S	P	+	1	0	MTA1	104987466	1.000000	0.71417	0.914000	0.36105	0.674000	0.39518	3.448000	0.52943	1.839000	0.53478	0.306000	0.20318	CCG	.	.		0.627	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			T	105916421	C	T	105916421	3	4	112	1	0	0	0	0	1	0	0	0	9917	623	22	3	286	3	MTA1	14	105916421	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	297903	105916421	1433119	879	17500										
SNRPN	6638	hgsc.bcm.edu	37	chr15	25221497	25221497	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgtgaagaaaagcgggttttGggtctggtgttgctgcgtgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:25221497delG	ENST00000400100.1	+	9	1091	c.201delG	c.(199-201)ttgfs	p.L67fs	SNRPN_ENST00000554227.2_Frame_Shift_Del_p.L71fs|SNRPN_ENST00000400098.1_Frame_Shift_Del_p.L67fs|SNRPN_ENST00000444203.2_Frame_Shift_Del_p.L71fs|SNURF_ENST00000551312.2_Intron|SNURF_ENST00000338094.6_3'UTR|SNRPN_ENST00000577565.1_Frame_Shift_Del_p.L67fs|SNRPN_ENST00000400097.1_Frame_Shift_Del_p.L67fs|SNRPN_ENST00000346403.6_Frame_Shift_Del_p.L67fs|SNRPN_ENST00000390687.4_Frame_Shift_Del_p.L67fs	NM_022807.2	NP_073718.1	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	67					response to hormone (GO:0009725)|RNA splicing (GO:0008380)	small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U2 snRNP (GO:0005686)	RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(2)	24		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		AGCGGGTTTTGGGTCTGGTGT	0.453									Prader-Willi syndrome																												p.L67fs		Atlas-INDEL	.											.	SNRPN	58	.	0			c.200delT						.						94	99	97					15																	25221497		1909	4127	6036	SO:0001589	frameshift_variant	6638	exon9	Familial Cancer Database	Prader-Labhart-Willi syndrome	.	L80005	CCDS10017.1	15q11.2	2013-07-16			ENSG00000128739	ENSG00000128739			11164	protein-coding gene	gene with protein product	"tissue-specific splicing protein", "SM protein N", "small nuclear ribonucleoprotein N"	182279	"Prader-Willi syndrome chromosome region"	PWCR		1533223	Standard	NM_022805		Approved	SMN, SM-D, HCERN3, SNRNP-N, SNURF-SNRPN, RT-LI	uc001ywt.1	P63162	OTTHUMG00000129180	ENST00000400100.1:c.201delG	chr15.hg19:g.25221497delG	ENSP00000382972:p.Leu67fs	86.0	0.0		128.0	10.0	NM_022807	B3KVR1|P14648|P17135|Q0D2Q5	Frame_Shift_Del	DEL	ENST00000400100.1	hg19	CCDS10017.1																																																																																			.	.		0.453	SNRPN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413849.10	NM_003097		-	25221497	G	-	25221497	7	5	112	1	0	1	0	1	0	0	0	0	14885	1339	47	0	211	0	SNRPN	15	25221497	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10		25221497	77309895	880	17501										
APBA2	321	hgsc.bcm.edu	37	chr15	29397672	29397672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcatcaaccccgaagacttgAgccagaaggaatacagcgac	10	12	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:29397672A>G	ENST00000558402.1	+	12	2214	c.1615A>G	c.(1615-1617)Agc>Ggc	p.S539G	APBA2_ENST00000561069.1_Missense_Mutation_p.S539G|APBA2_ENST00000558259.1_Missense_Mutation_p.S539G|APBA2_ENST00000411764.1_Missense_Mutation_p.S527G|APBA2_ENST00000558330.1_Missense_Mutation_p.S527G			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	539	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CGAAGACTTGAGCCAGAAGGA	0.562																																					p.S539G		Atlas-SNP	.											.	APBA2	132	.	0			c.A1615G						.						160	113	129					15																	29397672		2202	4300	6502	SO:0001583	missense	321	exon10			GACTTGAGCCAGA	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1615A>G	chr15.hg19:g.29397672A>G	ENSP00000453293:p.Ser539Gly	86.0	0.0		123.0	5.0	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	hg19	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.155937	0.57259	.	.	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.06218	3.33	4.23	4.23	0.50019	Phosphotyrosine interaction domain (1);PDZ/DHR/GLGF (1);	0.159368	0.51477	D	0.000082	T	0.15478	0.0373	L	0.41492	1.28	0.80722	D	1	P;D;B	0.71674	0.856;0.998;0.089	B;D;B	0.73380	0.352;0.98;0.042	T	0.01884	-1.1254	10	0.39692	T	0.17	.	12.9273	0.58266	1.0:0.0:0.0:0.0	.	527;527;539	Q5XKC0;E9PGI4;Q99767	.;.;APBA2_HUMAN	G	527;539	ENSP00000409312:S527G	ENSP00000219865:S539G	S	+	1	0	APBA2	27184964	1.000000	0.71417	1.000000	0.80357	0.321000	0.28281	5.828000	0.69307	1.880000	0.54463	0.402000	0.26972	AGC	.	.		0.562	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		G	29397672	A	G	29397672	3	3	112	1	0	0	0	0	1	0	0	0	757	304	11	2	1645	2	APBA2	15	29397672	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	4176175	29397672	73133720	881	17502										
FMN1	342184	hgsc.bcm.edu	37	chr15	33069072	33069072	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgattttctttgtctccacTttcttctctgaagtcaactt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:33069072delT	ENST00000559047.1	-	17	4178	c.4179delA	c.(4177-4179)aaafs	p.K1393fs	FMN1_ENST00000561249.1_Frame_Shift_Del_p.K1295fs|FMN1_ENST00000334528.9_Frame_Shift_Del_p.K1170fs			Q68DA7	FMN1_HUMAN	formin 1	1393					actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TTGTCTCCACTTTCTTCTCTG	0.413																																					p.V1171fs		Atlas-INDEL	.											FMN1_ENST00000334528,brain,glioma,0,2	FMN1	174	.	0			c.3511delG						.						90	79	82					15																	33069072		1837	4093	5930	SO:0001589	frameshift_variant	342184	exon16			.	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.4179delA	chr15.hg19:g.33069072delT	ENSP00000454047:p.Lys1393fs	150.0	0.0		142.0	10.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Frame_Shift_Del	DEL	ENST00000559047.1	hg19																																																																																				.	.		0.413	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		-	33069072	T	-	33069072	7	5	112	1	0	1	0	1	0	0	0	0	5957	1606	56	0	88	0	FMN1	15	33069072	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3671400	33069072	69462320	882	17503										
C15orf55	256646	hgsc.bcm.edu	37	chr15	34649310	34649310	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggccaaaggaaaggagaaaaAgaaaaaggaagcagaggaag	15	3	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:34649310A>G	ENST00000333756.4	+	7	3172	c.3017A>G	c.(3016-3018)aAg>aGg	p.K1006R	NUTM1_ENST00000438749.3_Missense_Mutation_p.K1024R|NUTM1_ENST00000537011.1_Missense_Mutation_p.K1034R	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	1006						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.K1006M(1)									AAGGAGAAAAAGAAAAAGGAA	0.478																																					p.K1006R		Atlas-SNP	.											C15orf55_ENST00000333756,lymph_node,lymphoid_neoplasm,0,1	C15orf55	110	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A3017G						.						53	45	47					15																	34649310		2201	4298	6499	SO:0001583	missense	256646	exon7			AGAAAAAGAAAAA	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"nuclear protein in testis"	608963	"chromosome 15 open reading frame 55"	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.3017A>G	chr15.hg19:g.34649310A>G	ENSP00000329448:p.Lys1006Arg	55.0	0.0		56.0	3.0	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	hg19	CCDS32190.1	.	.	.	.	.	.	.	.	.	.	A	4.528	0.097981	0.08681	.	.	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.08807	3.05;3.05;3.06	4.06	-1.03	0.10102	.	2.094490	0.02876	N	0.132249	T	0.04679	0.0127	N	0.14661	0.345	0.09310	N	1	B;B;B	0.11235	0.003;0.004;0.003	B;B;B	0.08055	0.001;0.003;0.001	T	0.35773	-0.9775	10	0.12766	T	0.61	.	3.9357	0.09305	0.4982:0.1883:0.3135:0.0	.	1024;1034;1006	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	R	1034;1024;1006	ENSP00000444896:K1034R;ENSP00000407031:K1024R;ENSP00000329448:K1006R	ENSP00000329448:K1006R	K	+	2	0	C15orf55	32436602	0.013000	0.17824	0.000000	0.03702	0.016000	0.09150	1.969000	0.40510	-0.188000	0.10499	0.533000	0.62120	AAG	.	.		0.478	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		G	34649310	A	G	34649310	3	3	112	1	0	0	0	0	1	0	0	0	1805	72	3	2	3043	2	C15orf55	15	34649310	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1580238	34649310	67882082	883	17504										
AQR	9716	hgsc.bcm.edu	37	chr15	35174733	35174733	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcttgaccaagtcatgtcgTtttaaggcagcatgagtaca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:35174733delT	ENST00000156471.5	-	27	3360	c.3135delA	c.(3133-3135)aaafs	p.K1045fs		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1045					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		AGTCATGTCGTTTTAAGGCAG	0.358																																					p.R1046fs		Atlas-INDEL	.											.	AQR	139	.	0			c.3136delC						.						79	73	75					15																	35174733		1832	4088	5920	SO:0001589	frameshift_variant	9716	exon27			.	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.3135delA	chr15.hg19:g.35174733delT	ENSP00000156471:p.Lys1045fs	161.0	0.0		149.0	10.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Frame_Shift_Del	DEL	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.		0.358	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		-	35174733	T	-	35174733	7	5	112	1	0	1	0	1	0	0	0	0	835	1722	60	0	1358	0	AQR	15	35174733	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	525423	35174733	67356659	884	17505										
ATPBD4	89978	hgsc.bcm.edu	37	chr15	35742950	35742950	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atcatctctctgagcaaatcTtcctggtttctctgccaaag	6	12	5	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:35742950T>C	ENST00000256538.4	-	5	467	c.441A>G	c.(439-441)gaA>gaG	p.E147E		NM_080650.3	NP_542381.1	Q7L8W6	DPH6_HUMAN	diphthamine biosynthesis 6	147					peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		ATP binding (GO:0005524)|diphthine-ammonia ligase activity (GO:0017178)										TGAGCAAATCTTCCTGGTTTC	0.378																																					p.E147E		Atlas-SNP	.											.	ATPBD4	30	.	0			c.A441G						.						145	129	134					15																	35742950		2201	4298	6499	SO:0001819	synonymous_variant	89978	exon5			CAAATCTTCCTGG		CCDS10043.1, CCDS45213.1	15q14	2013-06-19	2013-06-19	2013-05-02	ENSG00000134146	ENSG00000134146	6.3.1.14		30543	protein-coding gene	gene with protein product	"diphthine--ammonia ligase"		"ATP binding domain 4", "DPH6 homolog (S. cerevisiae)"	ATPBD4		23169644, 23468660	Standard	NM_080650		Approved	MGC14798		Q7L8W6	OTTHUMG00000129759	ENST00000256538.4:c.441A>G	chr15.hg19:g.35742950T>C		112.0	0.0		96.0	4.0	NM_080650	B3KWG1|Q96HJ6	Silent	SNP	ENST00000256538.4	hg19	CCDS10043.1																																																																																			.	.		0.378	DPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251973.1	NM_080650		C	35742950	T	C	35742950	2	2	112	1	0	0	0	0	0	0	0	1	1202	1606	56	2		2	ATPBD4	15	35742950	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	568217	35742950	66788442	885	17506										
RASGRP1	10125	hgsc.bcm.edu	37	chr15	38810590	38810590	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtctgtcaagctggcgtccaTtttaaacatgacccagaatt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:38810590delT	ENST00000310803.5	-	5	601	c.424delA	c.(424-426)atgfs	p.M142fs	RASGRP1_ENST00000558164.1_Frame_Shift_Del_p.M142fs|RASGRP1_ENST00000539159.1_Frame_Shift_Del_p.M94fs|RASGRP1_ENST00000450598.2_Frame_Shift_Del_p.M142fs|RASGRP1_ENST00000561180.1_Frame_Shift_Del_p.M193fs|RASGRP1_ENST00000559830.1_Frame_Shift_Del_p.M142fs	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	142	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		CTGGCGTCCATTTTAAACATG	0.433																																					p.M142fs		Atlas-INDEL	.											.	RASGRP1	50	.	0			c.425delT						.						87	77	80					15																	38810590		1878	4112	5990	SO:0001589	frameshift_variant	10125	exon5			.	AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"EF-hand domain containing"	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.424delA	chr15.hg19:g.38810590delT	ENSP00000310244:p.Met142fs	105.0	0.0		135.0	10.0	NM_001128602	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Frame_Shift_Del	DEL	ENST00000310803.5	hg19	CCDS45222.1																																																																																			.	.		0.433	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739		-	38810590	T	-	38810590	7	5	112	1	0	1	0	1	0	0	0	0	13089	1493	52	0	2021	0	RASGRP1	15	38810590	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3067640	38810590	63720802	886	17507										
NDUFAF1	51103	hgsc.bcm.edu	37	chr15	41688824	41688824	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaacacttcacttctgcctCcaatcgtcttatcagaagtc	4	13	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:41688824C>A	ENST00000260361.4	-	2	815	c.434G>T	c.(433-435)gGa>gTa	p.G145V		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	145					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		ACTTCTGCCTCCAATCGTCTT	0.488																																					p.G145V		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.G434T						.						91	86	88					15																	41688824		2203	4300	6503	SO:0001583	missense	51103	exon2			CTGCCTCCAATCG	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"Mitochondrial respiratory chain complex assembly factors"	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.434G>T	chr15.hg19:g.41688824C>A	ENSP00000260361:p.Gly145Val	250.0	0.0		270.0	94.0	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	hg19	CCDS10075.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487384	0.84854	.	.	ENSG00000137806	ENST00000260361	D	0.88741	-2.42	4.7	4.7	0.59300	NADH:ubiquinone oxidoreductase intermediate-associated protein 30 (1);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.95544	0.8552	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96545	0.9403	10	0.87932	D	0	-13.2143	18.0656	0.89389	0.0:1.0:0.0:0.0	.	145	Q9Y375	CIA30_HUMAN	V	145	ENSP00000260361:G145V	ENSP00000260361:G145V	G	-	2	0	NDUFAF1	39476116	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.624000	0.83124	2.334000	0.79466	0.449000	0.29647	GGA	.	.		0.488	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013		A	41688824	C	A	41688824	3	1	112	1	0	0	0	0	1	0	0	0	10283	855	30	3	565	3	NDUFAF1	15	41688824	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	2878234	41688824	60842568	887	17508										
ITPKA	3706	hgsc.bcm.edu	37	chr15	41794627	41794627	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acggctcctgcagcaccgacTtcaagactacgcgaagccga	10	15	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:41794627T>C	ENST00000260386.5	+	5	1089	c.1036T>C	c.(1036-1038)Ttc>Ctc	p.F346L		NM_002220.2	NP_002211.1	P23677	IP3KA_HUMAN	inositol-trisphosphate 3-kinase A	346					actin cytoskeleton organization (GO:0030036)|dendritic spine maintenance (GO:0097062)|inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|positive regulation of dendritic spine morphogenesis (GO:0061003)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendritic spine (GO:0043197)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			kidney(1)|lung(3)|skin(1)	5		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;7.63e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CAGCACCGACTTCAAGACTAC	0.612																																					p.F346L		Atlas-SNP	.											.	ITPKA	19	.	0			c.T1036C						.						60	65	63					15																	41794627		2203	4300	6503	SO:0001583	missense	3706	exon5			ACCGACTTCAAGA	X54938	CCDS10076.1	15q15.1	2011-04-28	2011-04-28		ENSG00000137825	ENSG00000137825	2.7.1.127		6178	protein-coding gene	gene with protein product		147521	"inositol 1,4,5-trisphosphate 3-kinase A"			1330886, 2175886	Standard	NM_002220		Approved	IP3KA, IP3-3KA	uc001znz.3	P23677	OTTHUMG00000130343	ENST00000260386.5:c.1036T>C	chr15.hg19:g.41794627T>C	ENSP00000260386:p.Phe346Leu	79.0	0.0		96.0	5.0	NM_002220	Q8TAN3	Missense_Mutation	SNP	ENST00000260386.5	hg19	CCDS10076.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.888794	0.91814	.	.	ENSG00000137825	ENST00000425927;ENST00000260386	T;T	0.17370	2.28;2.28	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.39545	0.1082	M	0.71920	2.185	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.19353	-1.0308	10	0.54805	T	0.06	-3.0312	12.219	0.54423	0.0:0.0:0.0:1.0	.	346	P23677	IP3KA_HUMAN	L	241;346	ENSP00000396560:F241L;ENSP00000260386:F346L	ENSP00000260386:F346L	F	+	1	0	ITPKA	39581919	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.791000	0.69045	2.020000	0.59435	0.533000	0.62120	TTC	.	.		0.612	ITPKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252695.3	NM_002220		C	41794627	T	C	41794627	3	2	112	1	0	0	0	0	1	0	0	0	7926	1609	56	2	1054	2	ITPKA	15	41794627	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	105803	41794627	60736765	888	17509										
LTK	4058	hgsc.bcm.edu	37	chr15	41797008	41797008	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtgaagatgccctccaggaAggcctctgggggcatccact	13	12	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:41797008A>G	ENST00000263800.6	-	17	2179	c.2083T>C	c.(2083-2085)Ttc>Ctc	p.F695L	LTK_ENST00000453182.2_Missense_Mutation_p.F565L|LTK_ENST00000355166.5_Missense_Mutation_p.F634L|LTK_ENST00000561619.1_Missense_Mutation_p.F393L	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	695	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CCCTCCAGGAAGGCCTCTGGG	0.582										TSP Lung(18;0.14)																											p.F695L		Atlas-SNP	.											.	LTK	117	.	0			c.T2083C						.						52	58	56					15																	41797008		2203	4300	6503	SO:0001583	missense	4058	exon17			CCAGGAAGGCCTC	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.2083T>C	chr15.hg19:g.41797008A>G	ENSP00000263800:p.Phe695Leu	76.0	0.0		99.0	4.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.371410	0.42003	.	.	ENSG00000062524	ENST00000355166;ENST00000263800;ENST00000453182	T;T;T	0.79940	-1.32;-1.32;-1.32	4.6	2.28	0.28536	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.245905	0.21107	N	0.080057	T	0.45975	0.1369	N	0.00313	-1.665	0.43234	D	0.995131	B;B;B;B	0.30763	0.02;0.028;0.107;0.294	B;B;B;B	0.35470	0.043;0.017;0.052;0.203	T	0.22347	-1.0219	10	0.18276	T	0.48	.	6.5018	0.22174	0.7502:0.0:0.2498:0.0	.	565;565;634;695	E9PFX4;B4DL89;P29376-4;P29376	.;.;.;LTK_HUMAN	L	634;695;565	ENSP00000347293:F634L;ENSP00000263800:F695L;ENSP00000392196:F565L	ENSP00000263800:F695L	F	-	1	0	LTK	39584300	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.712000	0.54875	0.306000	0.22856	0.533000	0.62120	TTC	.	.		0.582	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			G	41797008	A	G	41797008	3	3	112	1	0	0	0	0	1	0	0	0	9089	72	3	2	527	2	LTK	15	41797008	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2381	41797008	60734384	889	17510										
UBR1	197131	hgsc.bcm.edu	37	chr15	43314950	43314950	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttcttcttcaggagcttttTgaagctgttgcttctcttct	7	10	5	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:43314950T>C	ENST00000290650.4	-	26	2867	c.2789A>G	c.(2788-2790)cAa>cGa	p.Q930R	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	930					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		AGGAGCTTTTTGAAGCTGTTG	0.348																																					p.Q930R		Atlas-SNP	.											.	UBR1	124	.	0			c.A2789G						.						98	99	99					15																	43314950		2203	4298	6501	SO:0001583	missense	197131	exon26			GCTTTTTGAAGCT		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.2789A>G	chr15.hg19:g.43314950T>C	ENSP00000290650:p.Gln930Arg	54.0	0.0		65.0	4.0	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	hg19	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	T	18.32	3.597076	0.66332	.	.	ENSG00000159459	ENST00000290650;ENST00000546274	T	0.58506	0.33	4.77	4.77	0.60923	.	0.125005	0.53938	D	0.000041	T	0.51058	0.1652	L	0.53249	1.67	0.80722	D	1	P;P	0.38922	0.57;0.651	B;B	0.35114	0.196;0.165	T	0.51996	-0.8634	10	0.29301	T	0.29	-13.5412	14.7539	0.69549	0.0:0.0:0.0:1.0	.	930;930	B4DYL2;Q8IWV7	.;UBR1_HUMAN	R	930	ENSP00000290650:Q930R	ENSP00000290650:Q930R	Q	-	2	0	UBR1	41102242	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.280000	0.65603	2.134000	0.65973	0.528000	0.53228	CAA	.	.		0.348	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		C	43314950	T	C	43314950	3	2	112	1	0	0	0	0	1	0	0	0	16916	1812	63	2	2548	2	UBR1	15	43314950	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1517942	43314950	59216442	890	17511										
CASC4	113201	hgsc.bcm.edu	37	chr15	44673029	44673029	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacataaaccacaatggaaaCcccggtacttcaaaacagaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:44673029delC	ENST00000345795.2	+	8	1197	c.927delC	c.(925-927)aacfs	p.N309fs	CASC4_ENST00000299957.6_Frame_Shift_Del_p.N309fs|CASC4_ENST00000360824.3_3'UTR	NM_177974.2	NP_816929.1	Q6P4E1	CASC4_HUMAN	cancer susceptibility candidate 4	309						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(2)	17		all_cancers(109;1.69e-13)|all_epithelial(112;3.94e-11)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.027)		all cancers(107;2.91e-20)|GBM - Glioblastoma multiforme(94;1.57e-06)|COAD - Colon adenocarcinoma(120;0.217)|Colorectal(105;0.237)		ACAATGGAAACCCCGGTACTT	0.343																																					p.N309fs		Atlas-INDEL	.											.	CASC4	34	.	0			c.926delA						.						63	61	62					15																	44673029		2198	4298	6496	SO:0001589	frameshift_variant	113201	exon8			.	AF103804	CCDS10108.1, CCDS10109.1	15q15.1	2010-11-24			ENSG00000166734	ENSG00000166734			24892	protein-coding gene	gene with protein product						10497265	Standard	NM_138423		Approved	H63, DKFZp459F1927	uc001ztp.3	Q6P4E1	OTTHUMG00000131133	ENST00000345795.2:c.927delC	chr15.hg19:g.44673029delC	ENSP00000335063:p.Asn309fs	130.0	0.0		156.0	13.0	NM_138423	B4DPZ6|G5E934|Q6UY45|Q96EM1	Frame_Shift_Del	DEL	ENST00000345795.2	hg19	CCDS10109.1																																																																																			.	.		0.343	CASC4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253816.1	NM_138423		-	44673029	C	-	44673029	7	5	112	1	0	1	0	1	0	0	0	0	2664	506	18	0	957	0	CASC4	15	44673029	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1358079	44673029	57858363	891	17512										
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48539132	48539132	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcatggtatcagggttcggCcccctcatcactgcgggaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:48539132delC	ENST00000558405.1	+	11	1493	c.1479delC	c.(1477-1479)ggcfs	p.G493fs	SLC12A1_ENST00000396577.3_Frame_Shift_Del_p.G493fs|SLC12A1_ENST00000380993.3_Frame_Shift_Del_p.G493fs			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	493					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CAGGGTTCGGCCCCCTCATCA	0.498																																					p.G493fs		Atlas-INDEL	.											.	SLC12A1	243	.	0			c.1478delG						.						281	247	259					15																	48539132		2198	4297	6495	SO:0001589	frameshift_variant	6557	exon12			.		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1479delC	chr15.hg19:g.48539132delC	ENSP00000453409:p.Gly493fs	100.0	0.0		135.0	10.0	NM_001184832	A8JYA2|E9PDW4	Frame_Shift_Del	DEL	ENST00000558405.1	hg19	CCDS10129.2																																																																																			.	.		0.498	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			-	48539132	C	-	48539132	7	5	112	1	0	1	0	1	0	0	0	0	14397	726	26	0	1621	0	SLC12A1	15	48539132	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	3866103	48539132	53992260	892	17513										
DUT	1854	hgsc.bcm.edu	37	chr15	48634251	48634251	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accgaaaggggttcaggaggTtttggttccactggaaagaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:48634251delT	ENST00000331200.3	+	7	828	c.735delT	c.(733-735)ggtfs	p.G245fs	DUT_ENST00000455976.2_Frame_Shift_Del_p.G157fs|DUT_ENST00000559540.1_3'UTR|DUT_ENST00000559416.1_Frame_Shift_Del_p.G160fs|DUT_ENST00000558813.1_Frame_Shift_Del_p.G134fs	NM_001025248.1|NM_001025249.1	NP_001020419.1|NP_001020420.1	P33316	DUT_HUMAN	deoxyuridine triphosphatase	245					DNA replication (GO:0006260)|dUMP biosynthetic process (GO:0006226)|dUTP catabolic process (GO:0046081)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotrimerization (GO:0070207)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of protein heterodimerization activity (GO:0043497)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dUTP diphosphatase activity (GO:0004170)|poly(A) RNA binding (GO:0044822)|pyrimidine deoxyribonucleotide binding (GO:0032556)|receptor inhibitor activity (GO:0030547)			kidney(2)	2		all_lung(180;0.00265)		all cancers(107;2.66e-09)|GBM - Glioblastoma multiforme(94;6.76e-07)		GTTCAGGAGGTTTTGGTTCCA	0.358								Modulation of nucleotide pools																													p.G245fs		Atlas-INDEL	.											.	DUT	9	.	0			c.734delG						.						77	82	80					15																	48634251		2198	4297	6495	SO:0001589	frameshift_variant	1854	exon7			.	M89913	CCDS32231.1, CCDS45255.1, CCDS45256.1	15q21.1	2010-06-24	2007-12-17		ENSG00000128951	ENSG00000128951	3.6.1.23		3078	protein-coding gene	gene with protein product		601266	"dUTP pyrophosphatase"			1325640, 9070952	Standard	XM_005254211		Approved	dUTPase	uc001zws.3	P33316		ENST00000331200.3:c.735delT	chr15.hg19:g.48634251delT	ENSP00000370376:p.Gly245fs	165.0	0.0		198.0	12.0	NM_001025248	A8K650|B4DPR5|O14785|Q16708|Q16860|Q6FHN1|Q6NSA3|Q96Q81	Frame_Shift_Del	DEL	ENST00000331200.3	hg19	CCDS32231.1																																																																																			.	.		0.358	DUT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417142.2			-	48634251	T	-	48634251	7	5	112	1	0	1	0	1	0	0	0	0	4835	1712	60	0	777	0	DUT	15	48634251	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	95119	48634251	53897141	893	17514										
SECISBP2L	9728	hgsc.bcm.edu	37	chr15	49293086	49293086	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcgcataccttttgactggaTtttttcacagtttggagaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:49293086delT	ENST00000559471.1	-	15	2499	c.2236delA	c.(2236-2238)atcfs	p.I746fs	SECISBP2L_ENST00000261847.3_Frame_Shift_Del_p.I701fs|SECISBP2L_ENST00000559122.1_5'UTR	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	746							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTTGACTGGATTTTTTCACAG	0.343																																					p.I746fs		Atlas-INDEL	.											.	SECISBP2L	118	.	0			c.2237delT						.						92	87	89					15																	49293086		2196	4295	6491	SO:0001589	frameshift_variant	9728	exon15			.	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2236delA	chr15.hg19:g.49293086delT	ENSP00000453854:p.Ile746fs	193.0	0.0		214.0	14.0	NM_001193489	Q8N767	Frame_Shift_Del	DEL	ENST00000559471.1	hg19	CCDS53942.1																																																																																			.	.		0.343	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		-	49293086	T	-	49293086	7	5	112	1	0	1	0	1	0	0	0	0	14022	1493	52	0	1085	0	SECISBP2L	15	49293086	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	658835	49293086	53238306	894	17515										
MYO5C	55930	hgsc.bcm.edu	37	chr15	52571842	52571842	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggattccgaagtggaggcagAgattctggattgacagaata	14	5	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:52571842A>G	ENST00000261839.7	-	3	329	c.168T>C	c.(166-168)tcT>tcC	p.S56S	MYO5C_ENST00000541028.1_5'UTR|MYO5C_ENST00000443683.2_5'UTR|MIR1266_ENST00000408125.1_RNA	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	56						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		GTGGAGGCAGAGATTCTGGAT	0.468																																					p.S56S		Atlas-SNP	.											.	MYO5C	162	.	0			c.T168C						.						47	46	46					15																	52571842		1862	4110	5972	SO:0001819	synonymous_variant	55930	exon3			AGGCAGAGATTCT	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.168T>C	chr15.hg19:g.52571842A>G		61.0	0.0		78.0	6.0	NM_018728	Q6P1W8	Silent	SNP	ENST00000261839.7	hg19	CCDS42036.1																																																																																			.	.		0.468	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		G	52571842	A	G	52571842	2	3	112	1	0	0	0	0	0	0	0	1	10089	291	11	2		2	MYO5C	15	52571842	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	3278756	52571842	49959550	895	17516										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52645812	52645812	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccccattaccttgagtgacTcatattccagttctgcacct	5	14	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:52645812T>C	ENST00000399231.3	-	27	3854	c.3611A>G	c.(3610-3612)gAg>gGg	p.E1204G	MYO5A_ENST00000399233.2_Missense_Mutation_p.E1204G|MYO5A_ENST00000358212.6_Missense_Mutation_p.E1204G|MYO5A_ENST00000553916.1_Missense_Mutation_p.E1204G|MYO5A_ENST00000356338.6_Missense_Mutation_p.E1204G	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1204					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		CTTGAGTGACTCATATTCCAG	0.348																																					p.E1204G		Atlas-SNP	.											.	MYO5A	145	.	0			c.A3611G						.						113	110	111					15																	52645812		1818	4078	5896	SO:0001583	missense	4644	exon27			AGTGACTCATATT		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.3611A>G	chr15.hg19:g.52645812T>C	ENSP00000382177:p.Glu1204Gly	139.0	0.0		151.0	7.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	hg19	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.817687	0.90790	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.39091	0.1065	L	0.40543	1.245	0.80722	D	1	B;D	0.89917	0.012;1.0	B;D	0.85130	0.015;0.997	T	0.06935	-1.0799	10	0.48119	T	0.1	.	16.3631	0.83280	0.0:0.0:0.0:1.0	.	1204;1204	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	G	1204;738;1204;1204;1204;834;1204	ENSP00000382177:E1204G;ENSP00000382179:E1204G;ENSP00000348693:E1204G;ENSP00000350945:E1204G;ENSP00000451109:E1204G	ENSP00000348693:E1204G	E	-	2	0	MYO5A	50433104	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.138000	0.77305	2.266000	0.75297	0.533000	0.62120	GAG	.	.		0.348	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		C	52645812	T	C	52645812	3	2	112	1	0	0	0	0	1	0	0	0	10087	1551	54	2	2016	2	MYO5A	15	52645812	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	73970	52645812	49885580	896	17517										
GCOM1	100820829	hgsc.bcm.edu	37	chr15	57967220	57967220	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagaaacccaggccaagactGaagtggaaaccagagagata	11	9	0	5	rs146505887	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:57967220G>C	ENST00000267853.5	+	12	1352	c.1258G>C	c.(1258-1260)Gaa>Caa	p.E420Q	GCOM1_ENST00000380561.2_Missense_Mutation_p.E361Q|GCOM1_ENST00000380568.3_Missense_Mutation_p.E420Q|GCOM1_ENST00000574161.1_Missense_Mutation_p.E420Q|GCOM1_ENST00000572390.1_Missense_Mutation_p.E392Q|GCOM1_ENST00000380560.2_Missense_Mutation_p.E351Q|GCOM1_ENST00000396180.1_Missense_Mutation_p.E389Q|GCOM1_ENST00000380569.2_Missense_Mutation_p.E420Q|POLR2M_ENST00000380563.2_5'UTR|MYZAP_ENST00000380565.4_Missense_Mutation_p.E392Q|GCOM1_ENST00000587652.1_Missense_Mutation_p.E420Q			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	420					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											GGCCAAGACTGAAGTGGAAAC	0.378																																					p.E420Q		Atlas-SNP	.											GCOM1_ENST00000574161,NS,carcinoma,0,2	GCOM1	66	.	0			c.G1258C						.						99	102	101					15																	57967220		2192	4292	6484	SO:0001583	missense	145781	exon12			AAGACTGAAGTGG	FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"myocardium-enriched zonula adherens protein"	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.1258G>C	chr15.hg19:g.57967220G>C	ENSP00000267853:p.Glu420Gln	104.0	0.0		104.0	0.0	NM_001018090	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	hg19	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.325088	0.41197	.	.	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T;T;T;T	0.26373	1.85;1.82;1.87;1.87;1.84;1.74;1.85	5.55	4.64	0.57946	.	0.474041	0.25222	N	0.032236	T	0.20292	0.0488	L	0.27053	0.805	0.80722	D	1	P;B;B;B	0.39903	0.694;0.374;0.385;0.015	B;B;B;B	0.42422	0.387;0.334;0.387;0.043	T	0.03433	-1.1037	10	0.27082	T	0.32	-6.0611	10.3407	0.43877	0.0905:0.0:0.9095:0.0	.	420;420;392;420	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	Q	420;361;389;351;420;392;420	ENSP00000369943:E420Q;ENSP00000369935:E361Q;ENSP00000379483:E389Q;ENSP00000369933:E351Q;ENSP00000267853:E420Q;ENSP00000369939:E392Q;ENSP00000369942:E420Q	ENSP00000267853:E420Q	E	+	1	0	GCOM1	55754512	0.849000	0.29639	0.974000	0.42286	0.747000	0.42532	2.916000	0.48813	1.342000	0.45619	-0.136000	0.14681	GAA	.	G|0.999;A|0.001		0.378	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100		C	57967220	G	C	57967220	3	2	112	1	0	0	0	0	1	0	0	0	6312	1291	45	4	1304	4	GCOM1	15	57967220	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	5321408	57967220	44564172	897	17518										
GCNT3	9245	hgsc.bcm.edu	37	chr15	59910958	59910958	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtccccagaaactttcaaagAggcggtcaaagcaattattt	8	9	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:59910958A>G	ENST00000396065.1	+	3	969	c.521A>G	c.(520-522)gAg>gGg	p.E174G	GCNT3_ENST00000560585.1_Missense_Mutation_p.E174G	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	174					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ACTTTCAAAGAGGCGGTCAAA	0.473																																					p.E174G		Atlas-SNP	.											.	GCNT3	42	.	0			c.A521G						.						104	101	102					15																	59910958		2190	4290	6480	SO:0001583	missense	9245	exon3			TCAAAGAGGCGGT	AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.521A>G	chr15.hg19:g.59910958A>G	ENSP00000379377:p.Glu174Gly	93.0	0.0		93.0	4.0	NM_004751		Missense_Mutation	SNP	ENST00000396065.1	hg19	CCDS10172.1	.	.	.	.	.	.	.	.	.	.	A	9.148	1.015453	0.19355	.	.	ENSG00000140297	ENST00000396065	T	0.13089	2.62	6.16	3.76	0.43208	.	0.485335	0.23151	N	0.051359	T	0.13286	0.0322	L	0.51914	1.62	0.35243	D	0.778048	B	0.31459	0.324	B	0.31390	0.129	T	0.13522	-1.0506	10	0.34782	T	0.22	.	9.4683	0.38826	0.7526:0.1268:0.0:0.1206	.	174	O95395	GCNT3_HUMAN	G	174	ENSP00000379377:E174G	ENSP00000379377:E174G	E	+	2	0	GCNT3	57698250	0.600000	0.26899	0.521000	0.27850	0.374000	0.29953	2.343000	0.44001	0.505000	0.28104	0.528000	0.53228	GAG	.	.		0.473	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1	NM_004751		G	59910958	A	G	59910958	3	3	112	1	0	0	0	0	1	0	0	0	6310	304	11	2	523	2	GCNT3	15	59910958	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1943738	59910958	42620434	898	17519										
RORA	6095	hgsc.bcm.edu	37	chr15	60803793	60803793	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catacaagctgtctctctgcTtttttgacattcggccaaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:60803793delT	ENST00000335670.6	-	5	552	c.452delA	c.(451-453)aagfs	p.K151fs	RORA_ENST00000261523.5_Frame_Shift_Del_p.K184fs|RORA_ENST00000309157.4_Frame_Shift_Del_p.K176fs|RP11-219B17.1_ENST00000501579.2_RNA|RORA_ENST00000449337.2_Frame_Shift_Del_p.K96fs|RP11-219B17.1_ENST00000558235.1_RNA|RP11-219B17.1_ENST00000559824.1_RNA|RP11-219B17.1_ENST00000559902.1_RNA|RP11-219B17.1_ENST00000558140.1_RNA|RORA_ENST00000560004.1_5'UTR	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	151	Hinge.				angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						GTCTCTCTGCTTTTTTGACAT	0.507																																					p.K184fs		Atlas-INDEL	.											.	RORA	114	.	0			c.552delG						.						51	47	48					15																	60803793		2203	4300	6503	SO:0001589	frameshift_variant	6095	exon6			.	U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"Nuclear hormone receptors"	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.452delA	chr15.hg19:g.60803793delT	ENSP00000335087:p.Lys151fs	156.0	0.0		159.0	10.0	NM_134260	P35397|P35399|P45445|Q495X4|Q96H83	Frame_Shift_Del	DEL	ENST00000335670.6	hg19	CCDS10177.1																																																																																			.	.		0.507	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2			-	60803793	T	-	60803793	7	5	112	1	0	1	0	1	0	0	0	0	13543	1609	56	0	1147	0	RORA	15	60803793	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	892835	60803793	41727599	899	17520										
TLN2	83660	hgsc.bcm.edu	37	chr15	62948266	62948266	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcgagagaccccgtgcagcTgaacttgctttatgttcagg	11	10	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:62948266T>G	ENST00000561311.1	+	7	871	c.641T>G	c.(640-642)cTg>cGg	p.L214R	TLN2_ENST00000306829.6_Missense_Mutation_p.L214R			Q9Y4G6	TLN2_HUMAN	talin 2	214	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CCCGTGCAGCTGAACTTGCTT	0.468																																					p.L214R		Atlas-SNP	.											.	TLN2	253	.	0			c.T641G						.						108	92	97					15																	62948266		2203	4300	6503	SO:0001583	missense	83660	exon5			TGCAGCTGAACTT	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.641T>G	chr15.hg19:g.62948266T>G	ENSP00000453508:p.Leu214Arg	133.0	0.0		146.0	6.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.583538	0.86748	.	.	ENSG00000171914	ENST00000306829	T	0.77620	-1.11	5.47	5.47	0.80525	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	D	0.000000	D	0.87900	0.6294	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89418	0.3708	10	0.87932	D	0	-13.9128	15.0304	0.71701	0.0:0.0:0.0:1.0	.	214	Q9Y4G6	TLN2_HUMAN	R	214	ENSP00000303476:L214R	ENSP00000303476:L214R	L	+	2	0	TLN2	60735558	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.988000	0.88194	2.199000	0.70637	0.533000	0.62120	CTG	.	.		0.468	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			G	62948266	T	G	62948266	3	3	112	1	0	0	0	0	1	0	0	0	15963	1580	55	5	659	5	TLN2	15	62948266	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2144473	62948266	39583126	900	17521										
RBPMS2	348093	hgsc.bcm.edu	37	chr15	65040685	65040685	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acgcagcatgggagatggctGgggtcagctctgtggtgtac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:65040685delG	ENST00000300069.4	-	6	767	c.500delC	c.(499-501)ccafs	p.P167fs	RBPMS2_ENST00000560606.1_Frame_Shift_Del_p.P56fs	NM_194272.1	NP_919248.1	Q6ZRY4	RBPS2_HUMAN	RNA binding protein with multiple splicing 2	167							nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)			breast(1)|large_intestine(3)|lung(3)|prostate(1)	8						GGAGATGGCTGGGGTCAGCTC	0.617																																					p.P167fs		Atlas-INDEL	.											.	RBPMS2	14	.	0			c.501delA						.						83	72	76					15																	65040685		2202	4299	6501	SO:0001589	frameshift_variant	348093	exon6			.	AY369207	CCDS32271.1	15q22.31	2014-05-15			ENSG00000166831	ENSG00000166831		"RNA binding motif (RRM) containing"	19098	protein-coding gene	gene with protein product							Standard	NM_194272		Approved		uc002anq.3	Q6ZRY4	OTTHUMG00000172423	ENST00000300069.4:c.500delC	chr15.hg19:g.65040685delG	ENSP00000300069:p.Pro167fs	124.0	0.0		149.0	10.0	NM_194272	A2RRG0	Frame_Shift_Del	DEL	ENST00000300069.4	hg19	CCDS32271.1																																																																																			.	.		0.617	RBPMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418466.1			-	65040685	G	-	65040685	7	5	112	1	0	1	0	1	0	0	0	0	13179	1348	47	0	137	0	RBPMS2	15	65040685	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2092419	65040685	37490707	901	17522										
IGDCC3	9543	hgsc.bcm.edu	37	chr15	65623433	65623433	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggcacagaggctgagctggCcccccttggtgtgtaggcct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:65623433delC	ENST00000327987.4	-	9	1767	c.1516delG	c.(1516-1518)gccfs	p.A506fs	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	506	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GCTGAGCTGGCCCCCCTTGGT	0.597																																					p.A506fs		Atlas-INDEL	.											.	IGDCC3	82	.	0			c.1517delC						.						109	111	110					15																	65623433		2201	4299	6500	SO:0001589	frameshift_variant	9543	exon9			.	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9700	protein-coding gene	gene with protein product		604184	"putative neuronal cell adhesion molecule"	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.1516delG	chr15.hg19:g.65623433delC	ENSP00000332773:p.Ala506fs	151.0	0.0		168.0	15.0	NM_004884	O95215	Frame_Shift_Del	DEL	ENST00000327987.4	hg19	CCDS10205.1																																																																																			.	.		0.597	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884		-	65623433	C	-	65623433	7	5	112	1	0	1	0	1	0	0	0	0	7577	739	26	0	952	0	IGDCC3	15	65623433	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	582748	65623433	36907959	902	17523										
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65689174	65689174	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccttcggcccgcctcacccAgcacacggagctcagcggct	10	20	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:65689174A>G	ENST00000352385.2	-	6	1204	c.995T>C	c.(994-996)cTg>cCg	p.L332P		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	332						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						CGCCTCACCCAGCACACGGAG	0.701																																					p.L332P		Atlas-SNP	.											.	IGDCC4	95	.	0			c.T995C						.						10	11	11					15																	65689174		2179	4274	6453	SO:0001583	missense	57722	exon6			TCACCCAGCACAC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.995T>C	chr15.hg19:g.65689174A>G	ENSP00000319623:p.Leu332Pro	36.0	0.0		82.0	4.0	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.074015	0.36566	.	.	ENSG00000103742	ENST00000352385	T	0.31247	1.5	4.04	4.04	0.47022	.	0.377432	0.24396	N	0.038897	T	0.37348	0.1000	M	0.79011	2.435	0.80722	D	1	B	0.20988	0.05	B	0.24394	0.053	T	0.36065	-0.9763	10	0.59425	D	0.04	-4.2363	12.9927	0.58630	1.0:0.0:0.0:0.0	.	332	Q8TDY8	IGDC4_HUMAN	P	332	ENSP00000319623:L332P	ENSP00000319623:L332P	L	-	2	0	IGDCC4	63476227	1.000000	0.71417	1.000000	0.80357	0.395000	0.30598	7.138000	0.77305	1.455000	0.47813	0.379000	0.24179	CTG	.	.		0.701	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		G	65689174	A	G	65689174	3	3	112	1	0	0	0	0	1	0	0	0	7578	188	7	2	2817	2	IGDCC4	15	65689174	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	65741	65689174	36842218	903	17524										
C15orf44	81556	hgsc.bcm.edu	37	chr15	65871932	65871932	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cattccctttccagcatgtcAgccacccctttcagcaggtc	6	17	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:65871932A>G	ENST00000395644.4	-	12	1706	c.1371T>C	c.(1369-1371)gcT>gcC	p.A457A	VWA9_ENST00000569491.1_Silent_p.A407A|VWA9_ENST00000567744.1_Silent_p.A493A|VWA9_ENST00000420799.2_Silent_p.A400A|VWA9_ENST00000442903.3_Silent_p.A421A|VWA9_ENST00000431261.2_Silent_p.A378A|VWA9_ENST00000313182.2_Silent_p.A457A			Q96SY0	VWA9_HUMAN	von Willebrand factor A domain containing 9	457																	CCAGCATGTCAGCCACCCCTT	0.552																																					p.A439A		Atlas-SNP	.											.	VWA9	15	.	0			c.T1317C						.						70	61	64					15																	65871932		2201	4299	6500	SO:0001819	synonymous_variant	81556	exon12			CATGTCAGCCACC	AL136662	CCDS55969.1, CCDS45283.1	15q22.31	2012-09-27	2012-09-27	2012-09-27	ENSG00000138614	ENSG00000138614			25372	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 44"	C15orf44		11230166	Standard	NM_001136043		Approved	DKFZP564O1664	uc010uja.2	Q96SY0	OTTHUMG00000133159	ENST00000395644.4:c.1371T>C	chr15.hg19:g.65871932A>G		98.0	0.0		110.0	5.0	NM_001207058	B4DDI6|B4DVD5|Q49AH8|Q96HX5|Q9H0S5	Silent	SNP	ENST00000395644.4	hg19																																																																																				.	.		0.552	VWA9-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420604.3	NM_030800		G	65871932	A	G	65871932	2	3	112	1	0	0	0	0	0	0	0	1	1800	175	7	2		2	C15orf44	15	65871932	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	182758	65871932	36659460	904	17525										
SMAD3	4088	hgsc.bcm.edu	37	chr15	67482771	67482771	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagacagactgtgaccagtaCcccctgctggattgagctgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:67482771delC	ENST00000327367.4	+	9	1485	c.1175delC	c.(1174-1176)accfs	p.T392fs	SMAD3_ENST00000439724.3_Frame_Shift_Del_p.T348fs|SMAD3_ENST00000540846.2_Frame_Shift_Del_p.T287fs|SMAD3_ENST00000537194.2_Frame_Shift_Del_p.T197fs	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	392	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		GTGACCAGTACCCCCTGCTGG	0.532																																					p.T392fs		Atlas-INDEL	.											.	SMAD3	119	.	0			c.1174delA						.						62	59	60					15																	67482771		2201	4299	6500	SO:0001589	frameshift_variant	4088	exon9			.	BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"SMADs"	6769	protein-coding gene	gene with protein product		603109	"MAD, mothers against decapentaplegic homolog 3 (Drosophila)", "SMAD, mothers against DPP homolog 3 (Drosophila)"	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.1175delC	chr15.hg19:g.67482771delC	ENSP00000332973:p.Thr392fs	133.0	0.0		147.0	10.0	NM_005902	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Frame_Shift_Del	DEL	ENST00000327367.4	hg19	CCDS10222.1																																																																																			.	.		0.532	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902		-	67482771	C	-	67482771	7	5	112	1	0	1	0	1	0	0	0	0	14774	507	18	0	1287	0	SMAD3	15	67482771	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1610839	67482771	35048621	905	17526										
NOX5	79400	hgsc.bcm.edu	37	chr15	69331259	69331259	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agacctggtgactacttgtaTctgaacatccccaccattgc	7	13	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:69331259T>C	ENST00000388866.3	+	9	1475	c.1434T>C	c.(1432-1434)taT>taC	p.Y478Y	NOX5_ENST00000530406.2_Silent_p.Y450Y|NOX5_ENST00000455873.3_Silent_p.Y443Y|NOX5_ENST00000448182.3_Silent_p.Y432Y|NOX5_ENST00000260364.5_Silent_p.Y460Y|RP11-809H16.4_ENST00000559495.1_RNA	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	478	C-terminal catalytic region.|FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						ACTACTTGTATCTGAACATCC	0.522																																					p.Y478Y		Atlas-SNP	.											.	NOX5	60	.	0			c.T1434C						.						230	217	221					15																	69331259		2200	4298	6498	SO:0001819	synonymous_variant	79400	exon9			CTTGTATCTGAAC	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"EF-hand domain containing"	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.1434T>C	chr15.hg19:g.69331259T>C		148.0	0.0		165.0	7.0	NM_024505	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Silent	SNP	ENST00000388866.3	hg19	CCDS32276.2																																																																																			.	.		0.522	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505		C	69331259	T	C	69331259	2	2	112	1	0	0	0	0	0	0	0	1	10568	1442	50	2		2	NOX5	15	69331259	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1848488	69331259	33200133	906	17527										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72193622	72193622	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcaacaatatgattctgcgGagcacctcttggtgaagcag	11	9	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:72193622G>A	ENST00000356056.5	-	23	3532	c.3060C>T	c.(3058-3060)ctC>ctT	p.L1020L	MYO9A_ENST00000444904.1_Silent_p.L1001L|MYO9A_ENST00000564571.1_Silent_p.L1020L|MYO9A_ENST00000424560.1_Silent_p.L1020L|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000566885.1_Silent_p.L640L	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1020					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TGATTCTGCGGAGCACCTCTT	0.458																																					p.L1020L		Atlas-SNP	.											.	MYO9A	203	.	0			c.C3060T						.						114	97	102					15																	72193622		2199	4297	6496	SO:0001819	synonymous_variant	4649	exon23			TCTGCGGAGCACC	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.3060C>T	chr15.hg19:g.72193622G>A		132.0	0.0		141.0	57.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	hg19	CCDS10239.1																																																																																			.	.		0.458	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		A	72193622	G	A	72193622	2	1	112	1	0	0	0	0	0	0	0	1	10093	1161	41	3		3	MYO9A	15	72193622	Silent	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	2862363	72193622	30337770	907	17528										
STRA6	64220	hgsc.bcm.edu	37	chr15	74473791	74473791	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaagaaaggtggctgcatagAgcactcgcctaggatgggag	16	7	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:74473791A>G	ENST00000323940.5	-	17	1774	c.1529T>C	c.(1528-1530)cTc>cCc	p.L510P	STRA6_ENST00000563965.1_Missense_Mutation_p.L549P|STRA6_ENST00000574278.1_Missense_Mutation_p.L525P|STRA6_ENST00000449139.2_Missense_Mutation_p.L510P|STRA6_ENST00000395105.4_Missense_Mutation_p.L510P|STRA6_ENST00000574439.1_5'UTR|STRA6_ENST00000416286.3_Missense_Mutation_p.L502P|STRA6_ENST00000423167.2_Missense_Mutation_p.L501P|STRA6_ENST00000535552.1_Missense_Mutation_p.L547P|RP11-665J16.1_ENST00000561647.1_RNA	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	510					adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						GGCTGCATAGAGCACTCGCCT	0.602																																					p.L549P		Atlas-SNP	.											.	STRA6	66	.	0			c.T1646C						.						64	56	59					15																	74473791		2198	4297	6495	SO:0001583	missense	64220	exon17			GCATAGAGCACTC	AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"retinol binding protein 4 receptor"	610745	"stimulated by retinoic acid gene 6 homolog (mouse)", "stimulated by retinoic acid 6 homolog (mouse)"			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.1529T>C	chr15.hg19:g.74473791A>G	ENSP00000326085:p.Leu510Pro	67.0	0.0		100.0	4.0	NM_001199042	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Missense_Mutation	SNP	ENST00000323940.5	hg19	CCDS10261.1	.	.	.	.	.	.	.	.	.	.	A	17.99	3.522404	0.64747	.	.	ENSG00000137868	ENST00000395105;ENST00000323940;ENST00000416286;ENST00000545137;ENST00000449139;ENST00000423167;ENST00000535552;ENST00000536129	D;D;T;D;D	0.83755	-1.76;-1.76;-1.47;-1.76;-1.76	4.72	4.72	0.59763	.	0.068022	0.64402	D	0.000012	D	0.89952	0.6864	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.85130	0.996;0.996;0.996;0.997;0.996;0.996	D	0.91199	0.4990	10	0.87932	D	0	-37.6285	14.2323	0.65901	1.0:0.0:0.0:0.0	.	547;548;501;510;549;319	F5GYI8;B7Z5G7;Q9BX79-3;Q9BX79;Q9BX79-4;B3KRT6	.;.;.;STRA6_HUMAN;.;.	P	510;510;442;319;549;501;547;400	ENSP00000378537:L510P;ENSP00000326085:L510P;ENSP00000410221:L549P;ENSP00000413012:L501P;ENSP00000440238:L547P	ENSP00000326085:L510P	L	-	2	0	STRA6	72260844	1.000000	0.71417	0.040000	0.18447	0.257000	0.26127	7.603000	0.82811	1.769000	0.52152	0.459000	0.35465	CTC	.	.		0.602	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1			G	74473791	A	G	74473791	3	3	112	1	0	0	0	0	1	0	0	0	15337	304	11	2	486	2	STRA6	15	74473791	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2280169	74473791	28057601	908	17529										
CHRNB4	1143	hgsc.bcm.edu	37	chr15	78921420	78921420	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaccgcagccagaaatccctGgggatagccaccggggtaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:78921420delG	ENST00000261751.3	-	5	1338	c.1227delC	c.(1225-1227)cccfs	p.P409fs	RP11-335K5.2_ENST00000559120.1_RNA|CHRNB4_ENST00000560511.1_5'Flank|CHRNB4_ENST00000412074.2_Intron	NM_000750.3	NP_000741.1	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4 (neuronal)	409					action potential (GO:0001508)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|regulation of neurotransmitter secretion (GO:0046928)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			endometrium(7)|kidney(1)|lung(13)|prostate(1)	22					Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)	AGAAATCCCTGGGGATAGCCA	0.577																																					p.R410fs		Atlas-INDEL	.											.	CHRNB4	59	.	0			c.1228delA						.						52	55	54					15																	78921420		2196	4293	6489	SO:0001589	frameshift_variant	1143	exon5			.	U48861	CCDS10306.1, CCDS58392.1	15q24	2012-02-11	2012-02-07		ENSG00000117971	ENSG00000117971		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1964	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 4 (neuronal)"	118509	"cholinergic receptor, nicotinic, beta polypeptide 4"			2004777	Standard	NM_000750		Approved		uc002bed.1	P30926	OTTHUMG00000143860	ENST00000261751.3:c.1227delC	chr15.hg19:g.78921420delG	ENSP00000261751:p.Pro409fs	130.0	0.0		138.0	10.0	NM_000750	A4FTX5|E9PHE8|Q16607|Q4VBA5|Q8WXC8|Q9BQR4	Frame_Shift_Del	DEL	ENST00000261751.3	hg19	CCDS10306.1																																																																																			.	.		0.577	CHRNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290108.1			-	78921420	G	-	78921420	7	5	112	1	0	1	0	1	0	0	0	0	3395	1335	47	0	277	0	CHRNB4	15	78921420	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	4447629	78921420	23609972	909	17530										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86124122	86124122	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctctattaaggaaaatgcTctctcttcaggaactttgca	6	10	4	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:86124122T>C	ENST00000394518.2	+	7	2918	c.2823T>C	c.(2821-2823)gcT>gcC	p.A941A	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Silent_p.A941A	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	941					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						AGGAAAATGCTCTCTCTTCAG	0.438																																					p.A941A	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.T2823C						.						77	80	79					15																	86124122		2202	4299	6501	SO:0001819	synonymous_variant	11214	exon7			AAATGCTCTCTCT	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.2823T>C	chr15.hg19:g.86124122T>C		100.0	0.0		89.0	4.0	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	hg19	CCDS32319.1																																																																																			.	.		0.438	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		C	86124122	T	C	86124122	2	2	112	1	0	0	0	0	0	0	0	1	449	1538	54	2		2	AKAP13	15	86124122	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	7202702	86124122	16407270	910	17531										
KLHL25	64410	hgsc.bcm.edu	37	chr15	86312123	86312123	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacctggtagatcttgtcacAcatgaaggtctggcccccca	9	14	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:86312123A>G	ENST00000337975.5	-	2	1193	c.919T>C	c.(919-921)Tgt>Cgt	p.C307R	MIR1276_ENST00000408707.1_RNA|KLHL25_ENST00000559131.1_Intron|KLHL25_ENST00000536947.1_Missense_Mutation_p.C307R	NM_022480.3	NP_071925.2	Q9H0H3	KLH25_HUMAN	kelch-like family member 25	307					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of translational initiation (GO:0006446)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)				breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	25						ATCTTGTCACACATGAAGGTC	0.642																																					p.C307R		Atlas-SNP	.											.	KLHL25	58	.	0			c.T919C						.						74	58	63					15																	86312123		2202	4299	6501	SO:0001583	missense	64410	exon2			TGTCACACATGAA		CCDS10339.1	15q25.3	2013-02-22	2013-02-22		ENSG00000183655	ENSG00000183655		"Kelch-like", "BTB/POZ domain containing"	25732	protein-coding gene	gene with protein product	"ectodermal-neural cortex 2"		"kelch-like 25 (Drosophila)"				Standard	XM_006720635		Approved	FLJ12587, ENC2, ENC-2	uc002bly.3	Q9H0H3	OTTHUMG00000148672	ENST00000337975.5:c.919T>C	chr15.hg19:g.86312123A>G	ENSP00000336800:p.Cys307Arg	140.0	0.0		123.0	5.0	NM_022480	B2RDH2|B3KRT7	Missense_Mutation	SNP	ENST00000337975.5	hg19	CCDS10339.1	.	.	.	.	.	.	.	.	.	.	A	17.09	3.301136	0.60195	.	.	ENSG00000183655	ENST00000337975;ENST00000538153;ENST00000536947	T;T	0.65178	-0.14;-0.14	5.13	5.13	0.70059	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.69842	0.3156	L	0.61218	1.895	0.80722	D	1	D	0.53619	0.961	P	0.53224	0.721	T	0.73110	-0.4086	10	0.56958	D	0.05	.	14.1137	0.65139	1.0:0.0:0.0:0.0	.	307	Q9H0H3	ENC2_HUMAN	R	307;276;307	ENSP00000336800:C307R;ENSP00000444739:C307R	ENSP00000336800:C307R	C	-	1	0	KLHL25	84113127	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	1.933000	0.56026	0.379000	0.24179	TGT	.	.		0.642	KLHL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309023.1	NM_022480		G	86312123	A	G	86312123	3	3	112	1	0	0	0	0	1	0	0	0	8389	159	6	2	854	2	KLHL25	15	86312123	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	188001	86312123	16219269	911	17532										
AGBL1	123624	hgsc.bcm.edu	37	chr15	87531281	87531281	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taccacttttttgccattacAaactttttcaagatgaacct					rs1006030	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:87531281delA	ENST00000441037.2	+	23	3242	c.3147delA	c.(3145-3147)acafs	p.T1049fs	AGBL1_ENST00000389298.3_Frame_Shift_Del_p.T780fs|AGBL1_ENST00000421325.2_Frame_Shift_Del_p.T1049fs|RP11-133L19.1_ENST00000558587.1_RNA	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	1049			Missing (in FECD8; enriched in the nucleus, decreased TCF4-binding). {ECO:0000269|PubMed:24094747}.		C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						ttgccattacaaactttttca	0.403																																					p.T1049fs		Atlas-INDEL	.											.	AGBL1	151	.	0			c.3146delC						.						274	256	261					15																	87531281		1860	4087	5947	SO:0001589	frameshift_variant	123624	exon23			.	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.3147delA	chr15.hg19:g.87531281delA	ENSP00000413001:p.Thr1049fs	180.0	0.0		138.0	11.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Frame_Shift_Del	DEL	ENST00000441037.2	hg19	CCDS58398.1																																																																																			.	.		0.403	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		-	87531281	A	-	87531281	7	5	112	1	0	1	0	1	0	0	0	0	375	117	5	0	3233	0	AGBL1	15	87531281	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1219158	87531281	15000111	912	17533										
ACAN	176	hgsc.bcm.edu	37	chr15	89386594	89386594	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtccttcacaggtgaggtcTtttatgcaacatctccagag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:89386594delT	ENST00000561243.1	+	5	766	c.766delT	c.(766-768)tttfs	p.F256fs	ACAN_ENST00000439576.2_Frame_Shift_Del_p.F256fs|ACAN_ENST00000559004.1_Frame_Shift_Del_p.F256fs|ACAN_ENST00000352105.7_Frame_Shift_Del_p.F256fs|ACAN_ENST00000558207.1_Frame_Shift_Del_p.F256fs			P16112	PGCA_HUMAN	aggrecan	256	G1-B'.|Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			AGGTGAGGTCTTTTATGCAAC	0.602																																					p.V255fs		Atlas-INDEL	.											.	ACAN	220	.	0			c.765delC						.						32	35	34					15																	89386594		1974	4160	6134	SO:0001589	frameshift_variant	176	exon6			.	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.766delT	chr15.hg19:g.89386594delT	ENSP00000453342:p.Phe256fs	151.0	0.0		182.0	12.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Frame_Shift_Del	DEL	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.602	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		-	89386594	T	-	89386594	7	5	112	1	0	1	0	1	0	0	0	0	117	1609	56	0	784	0	ACAN	15	89386594	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1855313	89386594	13144798	913	17534										
ACAN	176	hgsc.bcm.edu	37	chr15	89400592	89400592	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcagtgggttgccttctggAaaagaagacttggtggggtc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:89400592delA	ENST00000561243.1	+	11	4776	c.4776delA	c.(4774-4776)ggafs	p.G1592fs	ACAN_ENST00000439576.2_Frame_Shift_Del_p.G1592fs|ACAN_ENST00000559004.1_Frame_Shift_Del_p.G1592fs|ACAN_ENST00000352105.7_Frame_Shift_Del_p.G1592fs			P16112	PGCA_HUMAN	aggrecan	1626	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TGCCTTCTGGAAAAGAAGACT	0.532																																					p.G1592fs		Atlas-INDEL	.											.	ACAN	220	.	0			c.4775delG						.						101	106	105					15																	89400592		1886	4126	6012	SO:0001589	frameshift_variant	176	exon12			.	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.4776delA	chr15.hg19:g.89400592delA	ENSP00000453342:p.Gly1592fs	115.0	0.0		165.0	10.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Frame_Shift_Del	DEL	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.532	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		-	89400592	A	-	89400592	7	5	112	1	0	1	0	1	0	0	0	0	117	233	9	0	4818	0	ACAN	15	89400592	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	13998	89400592	13130800	914	17535										
FANCI	55215	hgsc.bcm.edu	37	chr15	89828374	89828374	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aattctgtcgccaatgaaacTttttgccttgagatcatgga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:89828374delT	ENST00000310775.7	+	18	1832	c.1746delT	c.(1744-1746)actfs	p.T582fs	FANCI_ENST00000300027.8_Frame_Shift_Del_p.T582fs	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	582					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CCAATGAAACTTTTTGCCTTG	0.418								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.T582fs		Atlas-INDEL	.											.	FANCI	129	.	0			c.1745delC						.						220	188	199					15																	89828374		2200	4299	6499	SO:0001589	frameshift_variant	55215	exon18	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.1746delT	chr15.hg19:g.89828374delT	ENSP00000310842:p.Thr582fs	135.0	0.0		161.0	10.0	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Frame_Shift_Del	DEL	ENST00000310775.7	hg19	CCDS45346.1																																																																																			.	.		0.418	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		-	89828374	T	-	89828374	7	5	112	1	0	1	0	1	0	0	0	0	5677	1596	56	0	1812	0	FANCI	15	89828374	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	427782	89828374	12703018	915	17536										
CRTC3	64784	hgsc.bcm.edu	37	chr15	91185296	91185296	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acccctgagcctggacggacTcaacatgttaagtgactcca	9	13	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:91185296T>C	ENST00000268184.6	+	15	1788	c.1784T>C	c.(1783-1785)cTc>cCc	p.L595P	RP11-387D10.2_ENST00000559531.1_RNA|CRTC3_ENST00000420329.2_Missense_Mutation_p.L594P			Q6UUV7	CRTC3_HUMAN	CREB regulated transcription coactivator 3	595					energy homeostasis (GO:0097009)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of lipid catabolic process (GO:0050995)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)		CRTC3/MAML2(26)	breast(1)|endometrium(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			CTGGACGGACTCAACATGTTA	0.552			T	MAML2	salivary gland mucoepidermoid																																p.L595P		Atlas-SNP	.		Dom	yes		15	15q26.1	64784	CREB regulated transcription coactivator 3		E	.	CRTC3	47	.	0			c.T1784C						.						79	69	73					15																	91185296		2198	4298	6496	SO:0001583	missense	64784	exon15			ACGGACTCAACAT		CCDS32331.1, CCDS45348.1	15q26.1	2005-11-24				ENSG00000140577			26148	protein-coding gene	gene with protein product		608986				14536081, 14506290	Standard	NM_022769		Approved	FLJ21868	uc002bpp.4	Q6UUV7		ENST00000268184.6:c.1784T>C	chr15.hg19:g.91185296T>C	ENSP00000268184:p.Leu595Pro	173.0	0.0		162.0	7.0	NM_022769	Q6DK61|Q6DK62|Q8NF38|Q9H6U2	Missense_Mutation	SNP	ENST00000268184.6	hg19	CCDS32331.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.331247	0.81690	.	.	ENSG00000140577	ENST00000437186;ENST00000268184;ENST00000420329	T;T	0.29142	1.58;1.59	4.93	4.93	0.64822	Transducer of regulated CREB activity, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.53481	0.1799	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.57740	-0.7759	10	0.87932	D	0	-23.2149	12.578	0.56375	0.0:0.0:0.0:1.0	.	595;594	Q6UUV7;Q6UUV7-3	CRTC3_HUMAN;.	P	558;595;594	ENSP00000268184:L595P;ENSP00000416573:L594P	ENSP00000268184:L595P	L	+	2	0	CRTC3	88986300	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.146000	0.77373	2.079000	0.62486	0.533000	0.62120	CTC	.	.		0.552	CRTC3-001	KNOWN	NAGNAG_splice_site|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417716.2	NM_022769		C	91185296	T	C	91185296	3	2	112	1	0	0	0	0	1	0	0	0	3903	1551	54	2	1842	2	CRTC3	15	91185296	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1356922	91185296	11346096	916	17537										
CHD2	1106	hgsc.bcm.edu	37	chr15	93540530	93540530	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcacattttgatgtagagtGgggggtggaagatgattctc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:93540530delG	ENST00000394196.4	+	30	4850	c.3782delG	c.(3781-3783)tggfs	p.W1261fs	CHD2_ENST00000557381.1_Frame_Shift_Del_p.W1261fs	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1261					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GATGTAGAGTGGGGGGTGGAA	0.413																																					p.W1261fs		Atlas-INDEL	.											.	CHD2	280	.	0			c.3781delT						.						139	138	138					15																	93540530		2197	4298	6495	SO:0001589	frameshift_variant	1106	exon30			.	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.3782delG	chr15.hg19:g.93540530delG	ENSP00000377747:p.Trp1261fs	159.0	0.0		161.0	11.0	NM_001271	C6G482|Q96IP5	Frame_Shift_Del	DEL	ENST00000394196.4	hg19	CCDS10374.2																																																																																			.	.		0.413	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		-	93540530	G	-	93540530	7	5	112	1	0	1	0	1	0	0	0	0	3327	1357	47	0	3900	0	CHD2	15	93540530	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2355234	93540530	8990862	917	17538										
LASS3	204219	hgsc.bcm.edu	37	chr15	101009634	101009634	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaaatatggtggagaagatgAaaaacagggtgttacaggtc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:101009634delA	ENST00000394113.1	-	12	1484	c.794delT	c.(793-795)ttcfs	p.F265fs	CERS3_ENST00000538112.2_Frame_Shift_Del_p.F265fs|CERS3_ENST00000284382.4_Frame_Shift_Del_p.F265fs|CERS3_ENST00000560944.1_Intron			Q8IU89	CERS3_HUMAN	ceramide synthase 3	265	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GGAGAAGATGAAAAACAGGGT	0.448																																					p.F265fs		Atlas-INDEL	.											.	.	.	.	0			c.795delC						.						113	110	111					15																	101009634		2203	4300	6503	SO:0001589	frameshift_variant	204219	exon11			.		CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"Homeoboxes / CERS class"	23752	protein-coding gene	gene with protein product		615276	"LAG1 longevity assurance homolog 3 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 3"	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.794delT	chr15.hg19:g.101009634delA	ENSP00000377672:p.Phe265fs	151.0	0.0		138.0	10.0	NM_178842	Q8NE64|Q8NEN6	Frame_Shift_Del	DEL	ENST00000394113.1	hg19	CCDS10384.1																																																																																			.	.		0.448	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842		-	101009634	A	-	101009634	7	5	112	1	0	1	0	1	0	0	0	0	8649	246	9	0	369	0	LASS3	15	101009634	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	7469104	101009634	1521758	918	17539										
ZNF598	90850	hgsc.bcm.edu	37	chr16	2053113	2053113	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accgcgggcactcgtgctgcAgcagctgcctaggaagacac	13	14	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:2053113A>G	ENST00000563630.1	-	3	421	c.179T>C	c.(178-180)cTg>cCg	p.L60P	ZNF598_ENST00000562103.1_Missense_Mutation_p.L60P|ZNF598_ENST00000431526.1_Missense_Mutation_p.L115P			Q86UK7	ZN598_HUMAN	zinc finger protein 598	115							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						CTCGTGCTGCAGCAGCTGCCT	0.687																																					p.L115P		Atlas-SNP	.											.	ZNF598	55	.	0			c.T344C						.						8	11	10					16																	2053113		2009	4154	6163	SO:0001583	missense	90850	exon5			TGCTGCAGCAGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.179T>C	chr16.hg19:g.2053113A>G	ENSP00000455882:p.Leu60Pro	52.0	0.0		59.0	4.0	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	hg19		.	.	.	.	.	.	.	.	.	.	.	20.4	3.991751	0.74703	.	.	ENSG00000167962	ENST00000431526	T	0.32272	1.46	4.73	3.65	0.41850	.	0.000000	0.64402	D	0.000002	T	0.55417	0.1919	M	0.86097	2.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60870	-0.7177	10	0.87932	D	0	-15.1366	8.9718	0.35910	0.912:0.0:0.088:0.0	.	115	Q86UK7	ZN598_HUMAN	P	115	ENSP00000411409:L115P	ENSP00000411409:L115P	L	-	2	0	ZNF598	1993114	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.552000	0.67281	1.773000	0.52216	0.533000	0.62120	CTG	.	.		0.687	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167		G	2053113	A	G	2053113	3	3	112	1	0	0	0	0	1	0	0	0	18043	188	7	2	2410	2	ZNF598	16	2053113	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10		2053113	88301640	919	17540										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2812846	2812846	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtccaaagcaaaatctcgcTtgtctttgaggcgcagcctt	10	11	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:2812846T>C	ENST00000301740.8	+	11	2866	c.2317T>C	c.(2317-2319)Ttg>Ctg	p.L773L		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	773	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						AAAATCTCGCTTGTCTTTGAG	0.517																																					p.L773L		Atlas-SNP	.											.	SRRM2	263	.	0			c.T2317C						.						160	164	163					16																	2812846		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			TCTCGCTTGTCTT	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2317T>C	chr16.hg19:g.2812846T>C		67.0	0.0		63.0	4.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.		0.517	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			C	2812846	T	C	2812846	2	2	112	1	0	0	0	0	0	0	0	1	15184	1606	56	2		2	SRRM2	16	2812846	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	759733	2812846	87541907	920	17541										
FLYWCH1	84256	hgsc.bcm.edu	37	chr16	2979748	2979748	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaggccggccaggagccatCccccaagccaggcacggacg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:2979748delC	ENST00000253928.9	+	3	467	c.62delC	c.(61-63)tccfs	p.S21fs	FLYWCH1_ENST00000399667.2_Frame_Shift_Del_p.S21fs|FLYWCH1_ENST00000416288.2_Frame_Shift_Del_p.S21fs			Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1	21						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|lung(3)	4						CAGGAGCCATCCCCCAAGCCA	0.687																																					p.S21fs		Atlas-INDEL	.											.	FLYWCH1	27	.	0			c.61delT						.						42	49	47					16																	2979748		2198	4299	6497	SO:0001589	frameshift_variant	84256	exon3			.	AL136585	CCDS45390.1	16p13.3	2013-01-10	2007-06-21	2007-06-21	ENSG00000059122	ENSG00000059122		"Zinc fingers"	25404	protein-coding gene	gene with protein product						11230166, 10997877	Standard	XM_006720959		Approved	DKFZp761A132	uc002csc.3	Q4VC44		ENST00000253928.9:c.62delC	chr16.hg19:g.2979748delC	ENSP00000253928:p.Ser21fs	128.0	0.0		142.0	12.0	NM_020912	D3DUA1|Q6ZSQ1|Q8WV62|Q9BQG6|Q9BUS5|Q9HCM0	Frame_Shift_Del	DEL	ENST00000253928.9	hg19																																																																																				.	.		0.687	FLYWCH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000436479.1	NM_032296		-	2979748	C	-	2979748	7	5	112	1	0	1	0	1	0	0	0	0	5955	855	30	0	64	0	FLYWCH1	16	2979748	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	166902	2979748	87375005	921	17542										
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3079412	3079412	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggggctggacgcctttcgggTctttggggaccgggtggtct	19	9	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:3079412T>C	ENST00000572449.1	-	7	1038	c.976A>G	c.(976-978)Acc>Gcc	p.T326A	CCDC64B_ENST00000573514.1_Missense_Mutation_p.T119A|CCDC64B_ENST00000389347.4_Missense_Mutation_p.T326A			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	326										breast(1)|endometrium(2)|large_intestine(1)	4						GCCTTTCGGGTCTTTGGGGAC	0.587																																					p.T326A		Atlas-SNP	.											.	CCDC64B	19	.	0			c.A976G						.						34	35	35					16																	3079412		1881	4111	5992	SO:0001583	missense	146439	exon6			TTCGGGTCTTTGG	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.976A>G	chr16.hg19:g.3079412T>C	ENSP00000459043:p.Thr326Ala	32.0	0.0		57.0	4.0	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	T	6.735	0.504396	0.12822	.	.	ENSG00000162069	ENST00000389347	T	0.32023	1.47	4.07	1.75	0.24633	.	1.015660	0.07866	N	0.967158	T	0.21387	0.0515	L	0.44542	1.39	0.09310	N	1	B	0.15930	0.015	B	0.13407	0.009	T	0.35943	-0.9768	10	0.09338	T	0.73	-6.8936	4.0812	0.09927	0.0:0.1167:0.2332:0.65	.	326	A1A5D9	BICR2_HUMAN	A	326	ENSP00000373998:T326A	ENSP00000373998:T326A	T	-	1	0	CCDC64B	3019413	0.049000	0.20398	0.031000	0.17742	0.089000	0.18198	0.192000	0.17096	0.251000	0.21505	0.418000	0.28097	ACC	.	.		0.587	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1			C	3079412	T	C	3079412	3	2	112	1	0	0	0	0	1	0	0	0	2838	1667	58	2	566	2	CCDC64B	16	3079412	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	99664	3079412	87275341	922	17543										
ZNF205	7755	hgsc.bcm.edu	37	chr16	3163480	3163480	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acacccaggacaaggagacaCccccggaggtacagatgggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:3163480delC	ENST00000382192.3	+	2	254	c.49delC	c.(49-51)cccfs	p.P18fs	ZNF205-AS1_ENST00000576943.1_RNA|ZNF205_ENST00000219091.4_Frame_Shift_Del_p.P18fs|RP11-473M20.14_ENST00000576490.1_RNA|RP11-473M20.14_ENST00000575139.1_RNA|ZNF205-AS1_ENST00000572691.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	18					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hydrogen peroxide biosynthetic process (GO:0010729)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20						CAAGGAGACACCCCCGGAGGT	0.552																																					p.T16fs		Atlas-INDEL	.											.	ZNF205	42	.	0			c.48delA						.						68	68	68					16																	3163480		2197	4300	6497	SO:0001589	frameshift_variant	7755	exon2			.	AF060865	CCDS10494.2	16p13.3	2013-01-08			ENSG00000122386	ENSG00000122386		"Zinc fingers, C2H2-type", "-"	12996	protein-coding gene	gene with protein product		603436		ZNF210		9787081	Standard	NM_003456		Approved	Zfp13	uc002cub.3	O95201	OTTHUMG00000148676	ENST00000382192.3:c.49delC	chr16.hg19:g.3163480delC	ENSP00000371627:p.Pro18fs	119.0	0.0		162.0	10.0	NM_003456	A8MZK0|D3DUB4|Q9BU95	Frame_Shift_Del	DEL	ENST00000382192.3	hg19	CCDS10494.2																																																																																			.	.		0.552	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456		-	3163480	C	-	3163480	7	5	112	1	0	1	0	1	0	0	0	0	17779	507	18	0	51	0	ZNF205	16	3163480	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	84068	3163480	87191273	923	17544										
ZNF597	146434	hgsc.bcm.edu	37	chr16	3486565	3486565	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcaagttctgagtccaaagcAaaactttcctcgcatgtttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:3486565delA	ENST00000301744.4	-	4	1369	c.1134delT	c.(1132-1134)tttfs	p.F378fs		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						AGTCCAAAGCAAAACTTTCCT	0.438																																					p.A379fs		Atlas-INDEL	.											.	ZNF597	41	.	0			c.1135delG						.						74	65	68					16																	3486565		2197	4299	6496	SO:0001589	frameshift_variant	146434	exon4			.	AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"Zinc fingers, C2H2-type", "-"	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.1134delT	chr16.hg19:g.3486565delA	ENSP00000301744:p.Phe378fs	135.0	0.0		163.0	10.0	NM_152457		Frame_Shift_Del	DEL	ENST00000301744.4	hg19	CCDS10505.1																																																																																			.	.		0.438	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457		-	3486565	A	-	3486565	7	5	112	1	0	1	0	1	0	0	0	0	18042	127	5	0	144	0	ZNF597	16	3486565	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	323085	3486565	86868188	924	17545										
ADCY9	115	hgsc.bcm.edu	37	chr16	4016885	4016885	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caagagcaggagaaagaagaCgagaaccacctcctggccga	12	11	0	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:4016885C>T	ENST00000294016.3	-	11	3491	c.2953G>A	c.(2953-2955)Gtc>Atc	p.V985I		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	985					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AGAAAGAAGACGAGAACCACC	0.592																																					p.V985I		Atlas-SNP	.											ADCY9,NS,carcinoma,0,1	ADCY9	151	.	0			c.G2953A						.						69	76	74					16																	4016885		2197	4300	6497	SO:0001583	missense	115	exon11			AGAAGACGAGAAC	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2953G>A	chr16.hg19:g.4016885C>T	ENSP00000294016:p.Val985Ile	60.0	0.0		69.0	3.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	hg19	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	C	7.751	0.703434	0.15172	.	.	ENSG00000162104	ENST00000294016	D	0.82526	-1.62	5.48	3.5	0.40072	.	0.521749	0.21639	N	0.071363	T	0.65037	0.2653	N	0.08118	0	0.28252	N	0.925232	B	0.19817	0.039	B	0.18263	0.021	T	0.52548	-0.8561	10	0.20519	T	0.43	.	10.7456	0.46179	0.0:0.7952:0.1324:0.0724	.	985	O60503	ADCY9_HUMAN	I	985	ENSP00000294016:V985I	ENSP00000294016:V985I	V	-	1	0	ADCY9	3956886	0.992000	0.36948	0.508000	0.27688	0.023000	0.10783	3.024000	0.49674	0.768000	0.33290	-0.304000	0.09214	GTC	.	.		0.592	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			T	4016885	C	T	4016885	3	4	112	1	0	0	0	0	1	0	0	0	301	536	19	1	1112	1	ADCY9	16	4016885	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	530320	4016885	86337868	925	17546										
ATF7IP2	80063	hgsc.bcm.edu	37	chr16	10551340	10551340	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acccttccgaaaaaggaagtAaaaaaattaatttgtcatca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:10551340delA	ENST00000396560.2	+	7	1533	c.1306delA	c.(1306-1308)aaafs	p.K437fs	ATF7IP2_ENST00000324570.5_Frame_Shift_Del_p.K437fs|ATF7IP2_ENST00000356427.2_Frame_Shift_Del_p.K437fs|ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Frame_Shift_Del_p.K437fs	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	437					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AAAAGGAAGTAAAAAAATTAA	0.294																																					p.S435fs		Atlas-INDEL	.											.	ATF7IP2	40	.	0			c.1305delT						.						93	105	101					16																	10551340		2196	4295	6491	SO:0001589	frameshift_variant	80063	exon7			.	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.1306delA	chr16.hg19:g.10551340delA	ENSP00000379808:p.Lys437fs	140.0	0.0		139.0	10.0	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Frame_Shift_Del	DEL	ENST00000396560.2	hg19	CCDS10540.1																																																																																			.	.		0.294	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997		-	10551340	A	-	10551340	7	5	112	1	0	1	0	1	0	0	0	0	1088	363	13	0	1324	0	ATF7IP2	16	10551340	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	6534455	10551340	79803413	926	17547										
TEKT5	146279	hgsc.bcm.edu	37	chr16	10788409	10788409	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccggctggcccacagccgggAggcctcggccccacgcacct	13	20	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:10788409A>G	ENST00000283025.2	-	1	393	c.322T>C	c.(322-324)Tcc>Ccc	p.S108P	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	108						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						CACAGCCGGGAGGCCTCGGCC	0.667																																					p.S108P		Atlas-SNP	.											.	TEKT5	66	.	0			c.T322C						.						60	70	67					16																	10788409		2197	4300	6497	SO:0001583	missense	146279	exon1			GCCGGGAGGCCTC		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.322T>C	chr16.hg19:g.10788409A>G	ENSP00000283025:p.Ser108Pro	53.0	0.0		79.0	5.0	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	hg19	CCDS10542.1	.	.	.	.	.	.	.	.	.	.	.	26.1	4.705016	0.88924	.	.	ENSG00000153060	ENST00000283025	T	0.02682	4.2	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000020	T	0.11537	0.0281	M	0.74881	2.28	0.80722	D	1	P	0.51537	0.946	P	0.56163	0.793	T	0.00254	-1.1874	10	0.62326	D	0.03	-28.5225	14.5344	0.67950	1.0:0.0:0.0:0.0	.	108	Q96M29	TEKT5_HUMAN	P	108	ENSP00000283025:S108P	ENSP00000283025:S108P	S	-	1	0	TEKT5	10695910	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.516000	0.67055	2.161000	0.67846	0.528000	0.53228	TCC	.	.		0.667	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674		G	10788409	A	G	10788409	3	3	112	1	0	0	0	0	1	0	0	0	15771	304	11	2	1163	2	TEKT5	16	10788409	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	237069	10788409	79566344	927	17548										
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11272336	11272336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagcctgtcccccagcctcgTccctgcccggcagcccacca	8	23	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:11272336T>C	ENST00000409790.1	+	24	3181	c.2951T>C	c.(2950-2952)gTc>gCc	p.V984A	CLEC16A_ENST00000381822.2_Missense_Mutation_p.V71A	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CCCAGCCTCGTCCCTGCCCGG	0.637																																					p.V984A		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.T2951C						.						61	74	70					16																	11272336		2154	4250	6404	SO:0001583	missense	23274	exon23			GCCTCGTCCCTGC	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2951T>C	chr16.hg19:g.11272336T>C	ENSP00000387122:p.Val984Ala	67.0	0.0		94.0	4.0	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	hg19	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.158172	0.38119	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.46819	0.86	4.64	2.36	0.29203	.	0.333921	0.31381	N	0.007755	T	0.22781	0.0550	N	0.08118	0	0.18873	N	0.999989	B;B	0.33777	0.425;0.001	B;B	0.28385	0.089;0.004	T	0.11966	-1.0566	10	0.56958	D	0.05	-8.071	7.2849	0.26333	0.0:0.1785:0.0:0.8215	.	71;984	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	A	984;984;71	ENSP00000387122:V984A	ENSP00000371244:V71A	V	+	2	0	CLEC16A	11179837	0.994000	0.37717	0.144000	0.22314	0.801000	0.45260	0.743000	0.26231	0.254000	0.21573	0.533000	0.62120	GTC	.	.		0.637	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		C	11272336	T	C	11272336	3	2	112	1	0	0	0	0	1	0	0	0	3502	1667	58	2	3041	2	CLEC16A	16	11272336	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	483927	11272336	79082417	928	17549										
MKL2	57496	hgsc.bcm.edu	37	chr16	14346343	14346343	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caagcagacacgcagcacacAggcccctctgccagaggtaa	10	15	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:14346343A>G	ENST00000341243.5	+	13	2654	c.2654A>G	c.(2653-2655)cAg>cGg	p.Q885R	MKL2_ENST00000574045.1_Missense_Mutation_p.Q846R|MKL2_ENST00000571589.1_Missense_Mutation_p.Q896R|MKL2_ENST00000318282.5_Missense_Mutation_p.Q846R			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	885					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CGCAGCACACAGGCCCCTCTG	0.552																																					p.Q846R		Atlas-SNP	.											.	MKL2	103	.	0			c.A2537G						.						59	62	61					16																	14346343		2197	4300	6497	SO:0001583	missense	57496	exon15			GCACACAGGCCCC	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.2654A>G	chr16.hg19:g.14346343A>G	ENSP00000345841:p.Gln885Arg	85.0	0.0		82.0	4.0	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Missense_Mutation	SNP	ENST00000341243.5	hg19		.	.	.	.	.	.	.	.	.	.	A	16.85	3.237921	0.58886	.	.	ENSG00000186260	ENST00000318282;ENST00000341243	.	.	.	5.84	3.53	0.40419	.	0.463978	0.25619	N	0.029421	T	0.40473	0.1118	M	0.68317	2.08	0.25544	N	0.987155	P;P	0.41848	0.651;0.763	B;B	0.39840	0.081;0.311	T	0.19877	-1.0292	9	0.23302	T	0.38	-1.6222	12.2411	0.54541	0.5843:0.4157:0.0:0.0	.	896;846	B4DGT8;Q9ULH7-4	.;.	R	846;885	.	ENSP00000339086:Q846R	Q	+	2	0	MKL2	14253844	0.995000	0.38212	0.007000	0.13788	0.431000	0.31685	3.515000	0.53429	0.434000	0.26340	0.533000	0.62120	CAG	.	.		0.552	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		G	14346343	A	G	14346343	3	3	112	1	0	0	0	0	1	0	0	0	9611	188	7	2	2587	2	MKL2	16	14346343	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	3074007	14346343	76008410	929	17550										
MYH11	4629	hgsc.bcm.edu	37	chr16	15876271	15876271	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggagttgtcgttcttcactgTtttggcgttgccgaaagcct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:15876271delT	ENST00000300036.5	-	6	806	c.697delA	c.(697-699)acafs	p.T233fs	MYH11_ENST00000576790.2_Frame_Shift_Del_p.T233fs|MYH11_ENST00000452625.2_Frame_Shift_Del_p.T240fs|MYH11_ENST00000396324.3_Frame_Shift_Del_p.T240fs	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	233	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TTCTTCACTGTTTTGGCGTTG	0.463			T	CBFB	AML																																p.T240fs		Atlas-INDEL	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.719delC						.						171	155	160					16																	15876271		2197	4300	6497	SO:0001589	frameshift_variant	4629	exon7			.	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.697delA	chr16.hg19:g.15876271delT	ENSP00000300036:p.Thr233fs	146.0	0.0		142.0	11.0	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Frame_Shift_Del	DEL	ENST00000300036.5	hg19	CCDS10565.1																																																																																			.	.		0.463	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		-	15876271	T	-	15876271	7	5	112	1	0	1	0	1	0	0	0	0	10040	1725	60	0	5400	0	MYH11	16	15876271	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1529928	15876271	74478482	930	17551										
SMG1	23049	hgsc.bcm.edu	37	chr16	18841357	18841357	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgccggtgattatcatcatcAaaaaaattaacttgagtact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:18841357delA	ENST00000446231.2	-	53	9436	c.9024delT	c.(9022-9024)tttfs	p.F3008fs	SMG1_ENST00000389467.3_Frame_Shift_Del_p.F3008fs			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	3008					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TATCATCATCAAAAAAATTAA	0.363																																					p.D3009fs		Atlas-INDEL	.											.	SMG1	401	.	0			c.9025delG						.						34	31	32					16																	18841357		1816	4073	5889	SO:0001589	frameshift_variant	23049	exon53			.	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.9024delT	chr16.hg19:g.18841357delA	ENSP00000402515:p.Phe3008fs	123.0	0.0		157.0	11.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Frame_Shift_Del	DEL	ENST00000446231.2	hg19	CCDS45430.1																																																																																			.	.		0.363	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		-	18841357	A	-	18841357	7	5	112	1	0	1	0	1	0	0	0	0	14810	127	5	0	2005	0	SMG1	16	18841357	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2965086	18841357	71513396	931	17552										
ACSM1	116285	hgsc.bcm.edu	37	chr16	20682956	20682956	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gatgaccattgggtccaaggTctttgacttaacacaggtgt	11	8	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:20682956T>C	ENST00000307493.4	-	4	716	c.649A>G	c.(649-651)Acc>Gcc	p.T217A	ACSM1_ENST00000520010.1_Missense_Mutation_p.T217A|ACSM1_ENST00000219151.4_5'UTR	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	217					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						GGGTCCAAGGTCTTTGACTTA	0.488																																					p.T217A		Atlas-SNP	.											.	ACSM1	118	.	0			c.A649G						.						136	115	122					16																	20682956		2201	4300	6501	SO:0001583	missense	116285	exon4			CCAAGGTCTTTGA	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"Acyl-CoA synthetase family"	18049	protein-coding gene	gene with protein product		614357	"butyryl Coenzyme A synthetase 1"	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.649A>G	chr16.hg19:g.20682956T>C	ENSP00000301956:p.Thr217Ala	81.0	0.0		114.0	5.0	NM_052956	Q08AH2|Q96A20	Missense_Mutation	SNP	ENST00000307493.4	hg19	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	T	10.56	1.383779	0.25031	.	.	ENSG00000166743	ENST00000307493;ENST00000520010	T;T	0.37915	1.17;1.17	5.19	1.58	0.23477	AMP-dependent synthetase/ligase (1);	0.535492	0.17171	N	0.184277	T	0.17408	0.0418	N	0.10645	0.015	0.36941	D	0.892402	P	0.38617	0.64	B	0.40602	0.334	T	0.10337	-1.0634	10	0.34782	T	0.22	.	4.4887	0.11803	0.1446:0.166:0.0:0.6894	.	217	Q08AH1	ACSM1_HUMAN	A	217	ENSP00000301956:T217A;ENSP00000428047:T217A	ENSP00000301956:T217A	T	-	1	0	ACSM1	20590457	0.702000	0.27816	0.543000	0.28128	0.627000	0.37826	1.033000	0.30191	0.450000	0.26774	0.491000	0.48974	ACC	.	.		0.488	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956		C	20682956	T	C	20682956	3	2	112	1	0	0	0	0	1	0	0	0	182	1667	58	2	1124	2	ACSM1	16	20682956	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1841599	20682956	69671797	932	17553										
ACSM1	116285	hgsc.bcm.edu	37	chr16	20696513	20696513	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggtccctcttgcatcactgAcctgttcgcatgcagcccac	8	16	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:20696513A>G	ENST00000307493.4	-	2	471		c.e2+1		ACSM1_ENST00000520010.1_Splice_Site|ACSM1_ENST00000219151.4_Splice_Site	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1						benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						TGCATCACTGACCTGTTCGCA	0.582																																					.		Atlas-SNP	.											.	ACSM1	118	.	0			c.403+2T>C						.						119	92	101					16																	20696513		2201	4300	6501	SO:0001630	splice_region_variant	116285	exon3			TCACTGACCTGTT	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"Acyl-CoA synthetase family"	18049	protein-coding gene	gene with protein product		614357	"butyryl Coenzyme A synthetase 1"	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.403+1T>C	chr16.hg19:g.20696513A>G		100.0	0.0		96.0	4.0	NM_052956	Q08AH2|Q96A20	Splice_Site	SNP	ENST00000307493.4	hg19	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	.	17.04	3.287478	0.59976	.	.	ENSG00000166743	ENST00000307493;ENST00000520010;ENST00000523065	.	.	.	4.38	4.38	0.52667	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4282	0.61039	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ACSM1	20604014	1.000000	0.71417	1.000000	0.80357	0.675000	0.39556	7.258000	0.78371	1.835000	0.53391	0.496000	0.49642	.	.	.		0.582	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956	Intron	G	20696513	A	G	20696513	5	3	112	1	0	0	0	0	0	0	1	0	182	289	10	2	1376	2	ACSM1	16	20696513	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	13557	20696513	69658240	933	17554										
ACSM3	6296	hgsc.bcm.edu	37	chr16	20808252	20808252	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagactatcagtgggaagacAaaaagaaatgaactgaggaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:20808252delA	ENST00000289416.5	+	14	2194	c.1719delA	c.(1717-1719)acafs	p.T573fs	ACSM3_ENST00000450120.2_Frame_Shift_Del_p.T565fs|ERI2_ENST00000564349.1_3'UTR|ERI2_ENST00000569729.1_3'UTR|ERI2_ENST00000357967.4_3'UTR|ERI2_ENST00000300005.3_Intron|ACSM3_ENST00000567387.1_3'UTR	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3	573					cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						GTGGGAAGACAAAAAGAAATG	0.323																																					p.T573fs		Atlas-INDEL	.											.	ACSM3	113	.	0			c.1718delC						.						79	85	83					16																	20808252		2201	4300	6501	SO:0001589	frameshift_variant	6296	exon14			.	D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"Acyl-CoA synthetase family"	10522	protein-coding gene	gene with protein product		145505	"SA (rat hypertension-associated) homolog", "SA hypertension-associated homolog (rat)"	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.1719delA	chr16.hg19:g.20808252delA	ENSP00000289416:p.Thr573fs	209.0	0.0		205.0	13.0	NM_005622	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Frame_Shift_Del	DEL	ENST00000289416.5	hg19	CCDS10589.1																																																																																			.	.		0.323	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622		-	20808252	A	-	20808252	7	5	112	1	0	1	0	1	0	0	0	0	185	117	5	0	1862	0	ACSM3	16	20808252	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	111739	20808252	69546501	934	17555										
DNAH3	55567	hgsc.bcm.edu	37	chr16	20994094	20994094	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctctagaaatttgttagccAccaactctagggcatctgtg	8	11	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:20994094A>G	ENST00000261383.3	-	49	7807	c.7808T>C	c.(7807-7809)gTg>gCg	p.V2603A	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2603	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TTTGTTAGCCACCAACTCTAG	0.468																																					p.V2603A		Atlas-SNP	.											DNAH3_ENST00000261383,caecum,carcinoma,0,2	DNAH3	1142	.	0			c.T7808C						.						83	80	81					16																	20994094		2201	4300	6501	SO:0001583	missense	55567	exon49			TTAGCCACCAACT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.7808T>C	chr16.hg19:g.20994094A>G	ENSP00000261383:p.Val2603Ala	46.0	1.0		64.0	3.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.910029	0.92107	.	.	ENSG00000158486	ENST00000261383	T	0.42900	0.96	5.83	5.83	0.93111	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.64402	D	0.000002	T	0.80681	0.4669	H	0.99404	4.55	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89364	0.3670	10	0.87932	D	0	.	16.2159	0.82217	1.0:0.0:0.0:0.0	.	2603	Q8TD57	DYH3_HUMAN	A	2603	ENSP00000261383:V2603A	ENSP00000261383:V2603A	V	-	2	0	DNAH3	20901595	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	8.831000	0.92068	2.235000	0.73313	0.533000	0.62120	GTG	.	.		0.468	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		G	20994094	A	G	20994094	3	3	112	1	0	0	0	0	1	0	0	0	4605	159	6	2	4597	2	DNAH3	16	20994094	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	185842	20994094	69360659	935	17556										
COG7	91949	hgsc.bcm.edu	37	chr16	23404640	23404640	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcacaaatggctcaagattcAgggggagggacatgatgtac	13	7	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:23404640A>G	ENST00000307149.5	-	15	2101	c.1916T>C	c.(1915-1917)cTg>cCg	p.L639P	COG7_ENST00000569635.1_Intron	NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	639					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		CTCAAGATTCAGGGGGAGGGA	0.498																																					p.L639P		Atlas-SNP	.											.	COG7	62	.	0			c.T1916C						.						83	70	74					16																	23404640		2197	4300	6497	SO:0001583	missense	91949	exon15			AGATTCAGGGGGA	AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"Components of oligomeric golgi complex"	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1916T>C	chr16.hg19:g.23404640A>G	ENSP00000305442:p.Leu639Pro	51.0	0.0		66.0	4.0	NM_153603	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	hg19	CCDS10610.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.238246	0.79800	.	.	ENSG00000168434	ENST00000307149	T	0.49432	0.78	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.61615	0.2361	L	0.55481	1.735	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.59091	-0.7519	10	0.31617	T	0.26	-16.3661	13.8458	0.63466	1.0:0.0:0.0:0.0	.	639	P83436	COG7_HUMAN	P	639	ENSP00000305442:L639P	ENSP00000305442:L639P	L	-	2	0	COG7	23312141	1.000000	0.71417	0.997000	0.53966	0.941000	0.58515	9.307000	0.96226	1.866000	0.54105	0.533000	0.62120	CTG	.	.		0.498	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1			G	23404640	A	G	23404640	3	3	112	1	0	0	0	0	1	0	0	0	3665	188	7	2	408	2	COG7	16	23404640	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2410546	23404640	66950113	936	17557										
GGA2	23062	hgsc.bcm.edu	37	chr16	23481435	23481435	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcccgtctgggagaagtggAgcagaattctgaatccattc	11	10	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:23481435A>G	ENST00000309859.4	-	15	1584	c.1502T>C	c.(1501-1503)cTc>cCc	p.L501P	GGA2_ENST00000567468.1_Intron	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	501	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		GGAGAAGTGGAGCAGAATTCT	0.552																																					p.L501P		Atlas-SNP	.											.	GGA2	49	.	0			c.T1502C						.						69	70	69					16																	23481435		2197	4300	6497	SO:0001583	missense	23062	exon15			AAGTGGAGCAGAA	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.1502T>C	chr16.hg19:g.23481435A>G	ENSP00000311962:p.Leu501Pro	87.0	0.0		71.0	5.0	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	hg19	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.182572	0.78677	.	.	ENSG00000103365	ENST00000309859	T	0.51071	0.72	4.93	4.93	0.64822	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, gamma-adaptin, appendage (2);Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain (2);	0.156761	0.42053	D	0.000762	T	0.69006	0.3063	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.74047	-0.3790	10	0.87932	D	0	-21.3672	12.8236	0.57707	1.0:0.0:0.0:0.0	.	501	Q9UJY4	GGA2_HUMAN	P	501	ENSP00000311962:L501P	ENSP00000311962:L501P	L	-	2	0	GGA2	23388936	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.094000	0.89533	1.958000	0.56883	0.459000	0.35465	CTC	.	.		0.552	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1			G	23481435	A	G	23481435	3	3	112	1	0	0	0	0	1	0	0	0	6361	304	11	2	351	2	GGA2	16	23481435	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	76795	23481435	66873318	937	17558										
ARHGAP17	55114	hgsc.bcm.edu	37	chr16	24950880	24950880	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttctatttagagtgccacccCgccggtgggcctggaagtcc	12	13	1	1	rs78457529	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:24950880C>A	ENST00000289968.6	-	17	1598	c.1529G>T	c.(1528-1530)cGg>cTg	p.R510L	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000303665.5_Intron	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	510					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		AGTGCCACCCCGCCGGTGGGC	0.582																																					p.R510L		Atlas-SNP	.											.	ARHGAP17	138	.	0			c.G1529T						.						29	26	27					16																	24950880		2194	4300	6494	SO:0001583	missense	55114	exon17			CCACCCCGCCGGT	AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"Rho GTPase activating proteins"	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.1529G>T	chr16.hg19:g.24950880C>A	ENSP00000289968:p.Arg510Leu	63.0	0.0		81.0	4.0	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Missense_Mutation	SNP	ENST00000289968.6	hg19	CCDS32409.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906595	0.92107	.	.	ENSG00000140750	ENST00000289968;ENST00000455311	T	0.23552	1.9	5.0	5.0	0.66597	.	0.000000	0.40144	N	0.001163	T	0.48447	0.1500	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	0.965;1.0	P;D	0.87578	0.545;0.998	T	0.39583	-0.9607	10	0.48119	T	0.1	.	15.8573	0.78989	0.0:1.0:0.0:0.0	.	510;43	Q68EM7;Q68EM7-7	RHG17_HUMAN;.	L	510	ENSP00000289968:R510L	ENSP00000289968:R510L	R	-	2	0	ARHGAP17	24858381	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	6.289000	0.72696	2.595000	0.87683	0.655000	0.94253	CGG	.	C|0.992;T|0.008		0.582	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054		A	24950880	C	A	24950880	3	1	112	1	0	0	0	0	1	0	0	0	867	652	23	1	1132	1	ARHGAP17	16	24950880	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1469445	24950880	65403873	938	17559										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30735727	30735727	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gttggctccatcatcaactcAaactatgctaccagccccgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:30735727delA	ENST00000262518.4	+	25	5367	c.4982delA	c.(4981-4983)caafs	p.Q1661fs	SRCAP_ENST00000344771.4_Frame_Shift_Del_p.Q1503fs|SRCAP_ENST00000395059.2_Frame_Shift_Del_p.Q1599fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1661	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TCATCAACTCAAACTATGCTA	0.582																																					p.Q1661fs		Atlas-INDEL	.											SRCAP,NS,carcinoma,0,2	SRCAP	298	.	0			c.4981delC						.						143	147	146					16																	30735727		2197	4300	6497	SO:0001589	frameshift_variant	10847	exon25			.	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.4982delA	chr16.hg19:g.30735727delA	ENSP00000262518:p.Gln1661fs	116.0	0.0		163.0	10.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.		0.582	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		-	30735727	A	-	30735727	7	5	112	1	0	1	0	1	0	0	0	0	15150	130	5	0	5072	0	SRCAP	16	30735727	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5784847	30735727	59619026	939	17560										
SETD1A	9739	hgsc.bcm.edu	37	chr16	30976976	30976976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctccgacgacgaccggggtGgctcaccccctccggccccg	12	20	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:30976976G>A	ENST00000262519.8	+	8	2460	c.1774G>A	c.(1774-1776)Ggc>Agc	p.G592S		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	592	Pro-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CGACCGGGGTGGCTCACCCCC	0.677																																					p.G592S		Atlas-SNP	.											.	SETD1A	143	.	0			c.G1774A						.						23	27	25					16																	30976976		2194	4289	6483	SO:0001583	missense	9739	exon8			CGGGGTGGCTCAC	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.1774G>A	chr16.hg19:g.30976976G>A	ENSP00000262519:p.Gly592Ser	55.0	0.0		83.0	34.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.446036	0.43429	.	.	ENSG00000099381	ENST00000262519	D	0.93859	-3.3	4.41	4.41	0.53225	.	0.476082	0.19592	N	0.110587	T	0.80969	0.4726	N	0.11427	0.14	0.20638	N	0.999879	P	0.38473	0.633	B	0.30782	0.12	T	0.71533	-0.4564	10	0.25751	T	0.34	.	5.4932	0.16787	0.1012:0.0:0.6995:0.1993	.	592	O15047	SET1A_HUMAN	S	592	ENSP00000262519:G592S	ENSP00000262519:G592S	G	+	1	0	SETD1A	30884477	0.970000	0.33590	0.997000	0.53966	0.985000	0.73830	2.685000	0.46959	2.269000	0.75478	0.561000	0.74099	GGC	.	.		0.677	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		A	30976976	G	A	30976976	3	1	112	1	0	0	0	0	1	0	0	0	14145	1348	47	3	1800	3	SETD1A	16	30976976	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	241249	30976976	59377777	940	17561										
ZNF646	9726	hgsc.bcm.edu	37	chr16	31088375	31088375	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcggtacaaatgtagtcagTgtggcaagacctacaagcac	12	9	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:31088375T>C	ENST00000394979.2	+	1	1153	c.730T>C	c.(730-732)Tgt>Cgt	p.C244R	ZNF646_ENST00000300850.5_Missense_Mutation_p.C244R|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000300849.4_5'Flank			O15015	ZN646_HUMAN	zinc finger protein 646	244					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						ATGTAGTCAGTGTGGCAAGAC	0.582																																					p.C244R		Atlas-SNP	.											ZNF646,NS,carcinoma,0,1	ZNF646	133	.	0			c.T730C						.						71	67	68					16																	31088375		2197	4300	6497	SO:0001583	missense	9726	exon2			AGTCAGTGTGGCA	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.730T>C	chr16.hg19:g.31088375T>C	ENSP00000378429:p.Cys244Arg	76.0	1.0		99.0	4.0	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.64	3.440009	0.63067	.	.	ENSG00000167395	ENST00000300850;ENST00000394979;ENST00000439353	D;D	0.99974	-10.2;-10.2	5.6	5.6	0.85130	.	.	.	.	.	D	0.99984	0.9995	H	0.98682	4.3	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.98834	1.0752	9	0.87932	D	0	-9.2591	14.7704	0.69671	0.0:0.0:0.0:1.0	.	244	O15015-2	.	R	244;244;9	ENSP00000300850:C244R;ENSP00000378429:C244R	ENSP00000300850:C244R	C	+	1	0	ZNF646	30995876	1.000000	0.71417	0.931000	0.37212	0.890000	0.51754	7.499000	0.81566	2.133000	0.65898	0.533000	0.62120	TGT	.	.		0.582	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		C	31088375	T	C	31088375	3	2	112	1	0	0	0	0	1	0	0	0	18077	1696	59	2	732	2	ZNF646	16	31088375	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	111399	31088375	59266378	941	17562										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31413551	31413551	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctgtcatgggccagtttgaGggcactgacaccctggtgaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:31413551delG	ENST00000389202.2	+	6	592	c.543delG	c.(541-543)gagfs	p.E181fs	RP11-120K18.2_ENST00000567545.1_RNA	NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	181	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GCCAGTTTGAGGGCACTGACA	0.607																																					p.E181fs		Atlas-INDEL	.											.	ITGAD	154	.	0			c.542delA						.						95	88	90					16																	31413551		2197	4300	6497	SO:0001589	frameshift_variant	3681	exon6			.	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.543delG	chr16.hg19:g.31413551delG	ENSP00000373854:p.Glu181fs	143.0	0.0		144.0	10.0	NM_005353	Q15575|Q15576	Frame_Shift_Del	DEL	ENST00000389202.2	hg19	CCDS32438.1																																																																																			.	.		0.607	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		-	31413551	G	-	31413551	7	5	112	1	0	1	0	1	0	0	0	0	7893	991	35	0	565	0	ITGAD	16	31413551	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	325176	31413551	58941202	942	17563										
PHKB	5257	hgsc.bcm.edu	37	chr16	47622844	47622844	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgctgccctgctcccctgcaTcagttatcctgcatttgccc	7	17	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:47622844T>C	ENST00000323584.5	+	10	923	c.899T>C	c.(898-900)aTc>aCc	p.I300T	PHKB_ENST00000566044.1_Missense_Mutation_p.I293T|PHKB_ENST00000455779.1_Missense_Mutation_p.I293T|PHKB_ENST00000299167.8_Missense_Mutation_p.I300T|PHKB_ENST00000567402.1_3'UTR	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	300					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				CTCCCCTGCATCAGTTATCCT	0.423																																					p.I300T		Atlas-SNP	.											.	PHKB	298	.	0			c.T899C						.						92	86	88					16																	47622844		2201	4300	6501	SO:0001583	missense	5257	exon10			CCTGCATCAGTTA		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.899T>C	chr16.hg19:g.47622844T>C	ENSP00000313504:p.Ile300Thr	93.0	0.0		79.0	4.0	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.737779	0.69304	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.93366	-3.21;-3.21	5.58	5.58	0.84498	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.050257	0.85682	D	0.000000	D	0.96156	0.8747	M	0.79805	2.47	0.80722	D	1	P;P	0.43024	0.798;0.554	P;B	0.56474	0.799;0.295	D	0.96638	0.9472	10	0.87932	D	0	-4.5324	15.7677	0.78141	0.0:0.0:0.0:1.0	.	300;293	Q93100;Q93100-4	KPBB_HUMAN;.	T	293;293;300	ENSP00000414345:I293T;ENSP00000313504:I300T	ENSP00000299167:I293T	I	+	2	0	PHKB	46180345	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.875000	0.87205	2.124000	0.65301	0.477000	0.44152	ATC	.	.		0.423	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			C	47622844	T	C	47622844	3	2	112	1	0	0	0	0	1	0	0	0	11854	1435	50	2	996	2	PHKB	16	47622844	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	16209293	47622844	42731909	943	17564										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48596281	48596281	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aacaggctctctgccccaacAaaaatgcagtgcatgtcctt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:48596281delA	ENST00000262384.3	-	2	509	c.273delT	c.(271-273)tttfs	p.F91fs	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	91					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				CTGCCCCAACAAAAATGCAGT	0.418																																					p.V92fs		Atlas-INDEL	.											.	N4BP1	121	.	0			c.274delG						.						51	52	51					16																	48596281		1917	4121	6038	SO:0001589	frameshift_variant	9683	exon2			.	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.273delT	chr16.hg19:g.48596281delA	ENSP00000262384:p.Phe91fs	126.0	0.0		142.0	10.0	NM_153029	A7MD49|Q2YDX1	Frame_Shift_Del	DEL	ENST00000262384.3	hg19	CCDS45479.1																																																																																			.	.		0.418	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		-	48596281	A	-	48596281	7	5	112	1	0	1	0	1	0	0	0	0	10118	127	5	0	2441	0	N4BP1	16	48596281	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	973437	48596281	41758472	944	17565										
ZNF423	23090	hgsc.bcm.edu	37	chr16	49672029	49672029	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgctggagtcgggctgccggTggctgtccaggtggcagtag	19	9	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:49672029T>C	ENST00000561648.1	-	4	1087	c.1034A>G	c.(1033-1035)cAc>cGc	p.H345R	ZNF423_ENST00000562520.1_Missense_Mutation_p.H285R|ZNF423_ENST00000563137.2_Missense_Mutation_p.H285R|ZNF423_ENST00000262383.2_Missense_Mutation_p.H345R|ZNF423_ENST00000535559.1_Missense_Mutation_p.H228R|ZNF423_ENST00000567169.1_Missense_Mutation_p.H228R|ZNF423_ENST00000562871.1_Missense_Mutation_p.H285R	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	345					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GGGCTGCCGGTGGCTGTCCAG	0.632																																					p.H345R		Atlas-SNP	.											.	ZNF423	463	.	0			c.A1034G						.						54	48	50					16																	49672029		2198	4300	6498	SO:0001583	missense	23090	exon4			TGCCGGTGGCTGT	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1034A>G	chr16.hg19:g.49672029T>C	ENSP00000455426:p.His345Arg	72.0	0.0		89.0	6.0	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.417281	0.42918	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	D;D	0.88975	-2.45;-2.45	5.0	5.0	0.66597	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.046152	0.85682	D	0.000000	D	0.94003	0.8079	M	0.89904	3.07	0.44055	D	0.996797	D	0.57899	0.981	P	0.56163	0.793	D	0.94876	0.8034	9	.	.	.	.	14.7223	0.69317	0.0:0.0:0.0:1.0	.	345	Q2M1K9	ZN423_HUMAN	R	345;228	ENSP00000262383:H345R;ENSP00000442321:H228R	.	H	-	2	0	ZNF423	48229530	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.139000	0.71728	1.891000	0.54761	0.459000	0.35465	CAC	.	.		0.632	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		C	49672029	T	C	49672029	3	2	112	1	0	0	0	0	1	0	0	0	17913	1696	59	2	2840	2	ZNF423	16	49672029	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1075748	49672029	40682724	945	17566										
TMEM188	255919	hgsc.bcm.edu	37	chr16	50067341	50067341	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catcattatggaatcacccaTttttcaccattagctgtatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:50067341delT	ENST00000427478.2	+	4	259	c.205delT	c.(205-207)tttfs	p.F70fs	CNEP1R1_ENST00000562576.1_Frame_Shift_Del_p.F70fs|CNEP1R1_ENST00000565556.1_Frame_Shift_Del_p.F38fs|CNEP1R1_ENST00000458059.3_Frame_Shift_Del_p.F87fs	NM_001281789.1	NP_001268718.1	Q8N9A8	NEPR1_HUMAN	CTD nuclear envelope phosphatase 1 regulatory subunit 1	70					lipid metabolic process (GO:0006629)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of triglyceride biosynthetic process (GO:0010867)|protein localization to nucleus (GO:0034504)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|Nem1-Spo7 phosphatase complex (GO:0071595)|nuclear membrane (GO:0031965)											GAATCACCCATTTTTCACCAT	0.358																																					p.P85fs		Atlas-INDEL	.											.	.	.	.	0			c.255delA						.						124	106	112					16																	50067341		1855	4098	5953	SO:0001589	frameshift_variant	255919	exon5			.	AK095420	CCDS45480.1, CCDS61931.1	16q12.1	2012-02-01	2012-02-01	2012-02-01	ENSG00000205423	ENSG00000205423			26759	protein-coding gene	gene with protein product	"nuclear envelope phosphatase 1-regulatory subunit 1"		"chromosome 16 open reading frame 69", "transmembrane protein 188"	C16orf69, TMEM188		22134922	Standard	NM_153261		Approved	FLJ38101, NEP1-R1	uc002eft.3	Q8N9A8		ENST00000427478.2:c.205delT	chr16.hg19:g.50067341delT	ENSP00000394224:p.Phe70fs	148.0	0.0		173.0	11.0	NM_153261	Q4G1A9|Q5H9V0|Q8NE06	Frame_Shift_Del	DEL	ENST00000427478.2	hg19																																																																																				.	.		0.358	CNEP1R1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153261		-	50067341	T	-	50067341	7	5	112	1	0	1	0	1	0	0	0	0	16125	1493	52	0	274	0	TMEM188	16	50067341	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	395312	50067341	40287412	946	17567										
PAPD5	64282	hgsc.bcm.edu	37	chr16	50257145	50257145	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atggtgttctcttaatagaaTtttttgaattatatggacga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:50257145delT	ENST00000561678.1	+	6	927	c.853delT	c.(853-855)tttfs	p.F286fs	PAPD5_ENST00000357464.3_Frame_Shift_Del_p.F317fs|PAPD5_ENST00000436909.3_Frame_Shift_Del_p.F396fs|PAPD5_ENST00000573002.1_3'UTR			Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5	317					histone mRNA catabolic process (GO:0071044)|mitotic nuclear division (GO:0007067)|mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652)			endometrium(1)|kidney(1)|lung(2)	4		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		CTTAATAGAATTTTTTGAATT	0.338																																					p.E394fs		Atlas-INDEL	.											.	PAPD5	57	.	0			c.1182delA						.						79	78	78					16																	50257145		1803	4071	5874	SO:0001589	frameshift_variant	64282	exon8			.	AF089897	CCDS54006.1	16q12.1	2010-11-18				ENSG00000121274			30758	protein-coding gene	gene with protein product	"TUTase3"	605540				10066793	Standard	NM_001040284		Approved	TRF4-2	uc010vgo.2	Q8NDF8		ENST00000561678.1:c.853delT	chr16.hg19:g.50257145delT	ENSP00000455837:p.Phe286fs	147.0	0.0		163.0	11.0	NM_001040284	B4DV38|Q9NW67|Q9Y6C0	Frame_Shift_Del	DEL	ENST00000561678.1	hg19																																																																																				.	.		0.338	PAPD5-002	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000423150.1	NM_022447		-	50257145	T	-	50257145	7	5	112	1	0	1	0	1	0	0	0	0	11434	1493	52	0	1213	0	PAPD5	16	50257145	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	189804	50257145	40097608	947	17568										
SALL1	6299	hgsc.bcm.edu	37	chr16	51173561	51173561	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcgatgctcgacatctcgaGgggcaaaggcgaagaggata	15	8	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:51173561G>A	ENST00000251020.4	-	2	2605	c.2572C>T	c.(2572-2574)Ctc>Ttc	p.L858F	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.L761F	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	858					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GACATCTCGAGGGGCAAAGGC	0.527																																					p.L858F	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C2572T						.						98	95	96					16																	51173561		2198	4300	6498	SO:0001583	missense	6299	exon2			TCTCGAGGGGCAA	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2572C>T	chr16.hg19:g.51173561G>A	ENSP00000251020:p.Leu858Phe	155.0	0.0		183.0	8.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	6.849	0.525946	0.13066	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.57107	0.42;0.42	5.37	5.37	0.77165	.	0.382264	0.26784	N	0.022518	T	0.47691	0.1459	L	0.55990	1.75	0.37039	D	0.897036	P	0.48162	0.906	B	0.38378	0.272	T	0.53599	-0.8416	10	0.17369	T	0.5	.	19.1142	0.93331	0.0:0.0:1.0:0.0	.	858	Q9NSC2	SALL1_HUMAN	F	858;761;822	ENSP00000251020:L858F;ENSP00000407914:L761F	ENSP00000251020:L858F	L	-	1	0	SALL1	49731062	1.000000	0.71417	0.966000	0.40874	0.016000	0.09150	5.613000	0.67688	2.515000	0.84797	0.460000	0.39030	CTC	.	.		0.527	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51173561	G	A	51173561	3	1	112	1	0	0	0	0	1	0	0	0	13825	1000	35	3	1410	3	SALL1	16	51173561	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	916416	51173561	39181192	948	17569										
AMFR	267	hgsc.bcm.edu	37	chr16	56441911	56441911	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agccaaggtgtgcattccgtGggtgtagccggtgatggagc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:56441911delG	ENST00000290649.5	-	4	841	c.631delC	c.(631-633)cacfs	p.H211fs	RP11-413H22.2_ENST00000563090.1_RNA	NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	211					aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						TGCATTCCGTGGGTGTAGCCG	0.557																																					p.H211fs	Pancreas(2;144 323 39528)	Atlas-INDEL	.											.	AMFR	40	.	0			c.632delA						.						78	74	76					16																	56441911		2198	4300	6498	SO:0001589	frameshift_variant	267	exon4			.	L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"RING-type (C3HC4) zinc fingers"	463	protein-coding gene	gene with protein product		603243	"autocrine motility factor receptor"			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.631delC	chr16.hg19:g.56441911delG	ENSP00000290649:p.His211fs	196.0	0.0		196.0	12.0	NM_001144	P26442|Q8IZ70	Frame_Shift_Del	DEL	ENST00000290649.5	hg19	CCDS10758.1																																																																																			.	.		0.557	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2			-	56441911	G	-	56441911	7	5	112	1	0	1	0	1	0	0	0	0	571	1348	47	0	1344	0	AMFR	16	56441911	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	5268350	56441911	33912842	949	17570										
NUP93	9688	hgsc.bcm.edu	37	chr16	56867148	56867148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgagtcccactttacggtgaAccagcaacccttcctctact	6	16	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:56867148A>G	ENST00000308159.5	+	13	1488	c.1367A>G	c.(1366-1368)aAc>aGc	p.N456S	NUP93_ENST00000569842.1_Missense_Mutation_p.N456S|NUP93_ENST00000542526.1_Missense_Mutation_p.N333S|NUP93_ENST00000564887.1_Missense_Mutation_p.N333S	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	456					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TTTACGGTGAACCAGCAACCC	0.562																																					p.N456S	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.A1367G						.						147	127	134					16																	56867148		2198	4300	6498	SO:0001583	missense	9688	exon13			CGGTGAACCAGCA	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.1367A>G	chr16.hg19:g.56867148A>G	ENSP00000310668:p.Asn456Ser	127.0	0.0		150.0	6.0	NM_014669	B3KPQ8|Q14705	Missense_Mutation	SNP	ENST00000308159.5	hg19	CCDS10769.1	.	.	.	.	.	.	.	.	.	.	A	12.63	1.996597	0.35226	.	.	ENSG00000102900	ENST00000308159;ENST00000542526	T;T	0.40225	1.04;1.04	5.53	5.53	0.82687	.	0.078415	0.85682	D	0.000000	T	0.24661	0.0598	N	0.08118	0	0.48452	D	0.999656	B	0.10296	0.003	B	0.14578	0.011	T	0.09552	-1.0669	10	0.15952	T	0.53	-15.9651	15.6915	0.77457	1.0:0.0:0.0:0.0	.	456	Q8N1F7	NUP93_HUMAN	S	456;333	ENSP00000310668:N456S;ENSP00000440235:N333S	ENSP00000310668:N456S	N	+	2	0	NUP93	55424649	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	5.315000	0.65810	2.107000	0.64212	0.533000	0.62120	AAC	.	.		0.562	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669		G	56867148	A	G	56867148	3	3	112	1	0	0	0	0	1	0	0	0	10781	43	2	2	1413	2	NUP93	16	56867148	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	425237	56867148	33487605	950	17571										
RSPRY1	89970	hgsc.bcm.edu	37	chr16	57254758	57254758	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gatctcacctcatggcttagAggtaggtaatgcttctacag	10	9	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:57254758A>G	ENST00000537866.1	+	9	1889	c.1016A>G	c.(1015-1017)gAg>gGg	p.E339G	RSPRY1_ENST00000394420.4_Splice_Site_p.E339G			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	339	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular region (GO:0005576)	zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						CATGGCTTAGAGGTAGGTAAT	0.463																																					p.E339G		Atlas-SNP	.											.	RSPRY1	49	.	0			c.A1016G						.						162	131	141					16																	57254758		2198	4300	6498	SO:0001630	splice_region_variant	89970	exon9			GCTTAGAGGTAGG	AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"RING-type (C3HC4) zinc fingers"	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.1017+1A>G	chr16.hg19:g.57254758A>G		128.0	0.0		125.0	5.0	NM_133368	Q6UX21|Q8ND53	Missense_Mutation	SNP	ENST00000537866.1	hg19	CCDS10775.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.919567	0.73098	.	.	ENSG00000159579	ENST00000394420;ENST00000537866	T;T	0.73681	-0.77;-0.77	5.33	5.33	0.75918	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.051956	0.85682	D	0.000000	T	0.76371	0.3978	M	0.79805	2.47	0.80722	D	1	B	0.31752	0.338	B	0.31547	0.132	T	0.77973	-0.2386	10	0.56958	D	0.05	.	15.3204	0.74117	1.0:0.0:0.0:0.0	.	339	Q96DX4	RSPRY_HUMAN	G	339	ENSP00000377942:E339G;ENSP00000443176:E339G	ENSP00000377942:E339G	E	+	2	0	RSPRY1	55812259	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	9.236000	0.95360	2.014000	0.59158	0.533000	0.62120	GAG	.	.		0.463	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368	Missense_Mutation	G	57254758	A	G	57254758	5	3	112	1	0	0	0	0	0	0	1	0	13728	318	11	2	1046	2	RSPRY1	16	57254758	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	387610	57254758	33099995	951	17572										
DOK4	55715	hgsc.bcm.edu	37	chr16	57507902	57507902	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacgcgctggtaaatctgctCcccctcttgtgtctggaagg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:57507902delC	ENST00000340099.4	-	7	1020	c.649delG	c.(649-651)gagfs	p.E217fs	DOK4_ENST00000569548.1_Frame_Shift_Del_p.E217fs|DOK4_ENST00000566936.1_Frame_Shift_Del_p.E217fs|DOK4_ENST00000561918.1_5'Flank	NM_018110.3	NP_060580.2	Q8TEW6	DOK4_HUMAN	docking protein 4	217	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				MAPK cascade (GO:0000165)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)		receptor signaling protein activity (GO:0005057)			kidney(1)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	6						TAAATCTGCTCCCCCTCTTGT	0.597																																					p.E217fs		Atlas-INDEL	.											.	DOK4	19	.	0			c.650delA						.						101	90	94					16																	57507902		2198	4300	6498	SO:0001589	frameshift_variant	55715	exon7			.	BC003541	CCDS10783.1	16q13	2013-01-10			ENSG00000125170	ENSG00000125170		"Pleckstrin homology (PH) domain containing"	19868	protein-coding gene	gene with protein product		608333				10493829	Standard	NM_018110		Approved	FLJ10488	uc002elv.4	Q8TEW6	OTTHUMG00000133460	ENST00000340099.4:c.649delG	chr16.hg19:g.57507902delC	ENSP00000344277:p.Glu217fs	155.0	0.0		159.0	11.0	NM_018110	O75209|Q9BTP2|Q9NVV3	Frame_Shift_Del	DEL	ENST00000340099.4	hg19	CCDS10783.1																																																																																			.	.		0.597	DOK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257335.3			-	57507902	C	-	57507902	7	5	112	1	0	1	0	1	0	0	0	0	4701	864	30	0	343	0	DOK4	16	57507902	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	253144	57507902	32846851	952	17573										
GPR97	222487	hgsc.bcm.edu	37	chr16	57707239	57707239	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cattccttccttaggtcaggAaaagcccaccgaagggccaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:57707239delA	ENST00000333493.4	+	2	226	c.65delA	c.(64-66)gaafs	p.E22fs	GPR97_ENST00000327655.6_5'UTR|GPR97_ENST00000450388.3_5'UTR	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	22					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTAGGTCAGGAAAAGCCCACC	0.537																																					p.E22fs		Atlas-INDEL	.											.	GPR97	74	.	0			c.64delG						.						79	72	74					16																	57707239		2198	4300	6498	SO:0001589	frameshift_variant	222487	exon2			.	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"-", "GPCR / Class B : Orphans"	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.65delA	chr16.hg19:g.57707239delA	ENSP00000332900:p.Glu22fs	168.0	0.0		165.0	11.0	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Frame_Shift_Del	DEL	ENST00000333493.4	hg19	CCDS10786.1																																																																																			.	.		0.537	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776		-	57707239	A	-	57707239	7	5	112	1	0	1	0	1	0	0	0	0	6729	246	9	0	71	0	GPR97	16	57707239	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	199337	57707239	32647514	953	17574										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58562491	58562491	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcacatcacagaacccataaTggtaatcacaaaggaactct	5	11	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:58562491T>C	ENST00000317147.5	-	44	6673	c.6341A>G	c.(6340-6342)cAt>cGt	p.H2114R	CNOT1_ENST00000245138.4_Missense_Mutation_p.H965R|CNOT1_ENST00000569240.1_Missense_Mutation_p.H2109R	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	2114					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GAACCCATAATGGTAATCACA	0.398																																					p.H2114R		Atlas-SNP	.											.	CNOT1	359	.	0			c.A6341G						.						93	94	94					16																	58562491		2198	4300	6498	SO:0001583	missense	23019	exon44			CCATAATGGTAAT	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.6341A>G	chr16.hg19:g.58562491T>C	ENSP00000320949:p.His2114Arg	61.0	0.0		71.0	4.0	NM_016284	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.811403	0.90707	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000546037;ENST00000245138;ENST00000394200	T	0.56776	0.44	5.73	5.73	0.89815	CCR4-Not complex component, Not1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80502	0.4635	H	0.94925	3.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.998;0.997	D	0.86096	0.1553	10	0.72032	D	0.01	.	16.0096	0.80391	0.0:0.0:0.0:1.0	.	965;2114;2109	B5MDN3;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	R	2114;808;119;965;2109	ENSP00000320949:H2114R	ENSP00000245138:H965R	H	-	2	0	CNOT1	57119992	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.015000	0.88690	2.184000	0.69523	0.477000	0.44152	CAT	.	.		0.398	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		C	58562491	T	C	58562491	3	2	112	1	0	0	0	0	1	0	0	0	3619	1464	51	2	813	2	CNOT1	16	58562491	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	855252	58562491	31792262	954	17575										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58608980	58608980	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcacgacgtgaagcaagtgcAgcaaggtcaataacaaaggc	11	9	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:58608980A>G	ENST00000317147.5	-	15	2090	c.1758T>C	c.(1756-1758)gcT>gcC	p.A586A	CNOT1_ENST00000569240.1_Silent_p.A586A|CNOT1_ENST00000441024.2_Silent_p.A586A	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	586					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		AAGCAAGTGCAGCAAGGTCAA	0.393																																					p.A586A		Atlas-SNP	.											.	CNOT1	359	.	0			c.T1758C						.						131	115	121					16																	58608980		2198	4300	6498	SO:0001819	synonymous_variant	23019	exon15			AAGTGCAGCAAGG	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.1758T>C	chr16.hg19:g.58608980A>G		82.0	0.0		90.0	4.0	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	hg19	CCDS10799.1																																																																																			.	.		0.393	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		G	58608980	A	G	58608980	2	3	112	1	0	0	0	0	0	0	0	1	3619	175	7	2		2	CNOT1	16	58608980	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	46489	58608980	31745773	955	17576										
CDH11	1009	hgsc.bcm.edu	37	chr16	64981570	64981570	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctagtttcttaaaacgaggtCcccagttctgtagataatca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:64981570delC	ENST00000268603.4	-	13	2942	c.2327delG	c.(2326-2328)ggafs	p.G776fs	CDH11_ENST00000394156.3_3'UTR|CDH11_ENST00000566827.1_Frame_Shift_Del_p.G650fs	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	776					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		AAAACGAGGTCCCCAGTTCTG	0.453			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.G776fs		Atlas-INDEL	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	.	CDH11	260	.	0			c.2328delA						.						77	79	78					16																	64981570		2203	4300	6503	SO:0001589	frameshift_variant	1009	exon13			.	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.2327delG	chr16.hg19:g.64981570delC	ENSP00000268603:p.Gly776fs	178.0	0.0		153.0	13.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Frame_Shift_Del	DEL	ENST00000268603.4	hg19	CCDS10803.1																																																																																			.	.		0.453	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		-	64981570	C	-	64981570	7	5	112	1	0	1	0	1	0	0	0	0	3099	855	30	0	67	0	CDH11	16	64981570	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	6372590	64981570	25373183	956	17577										
CES3	23491	hgsc.bcm.edu	37	chr16	66995238	66995238	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagcagtgagagtggagtccGgggtcctggtcggggtggtc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:66995238delG	ENST00000303334.4	+	1	99	c.28delG	c.(28-30)gggfs	p.G10fs	RP11-361L15.4_ENST00000566869.1_RNA|CES3_ENST00000394037.1_Frame_Shift_Del_p.G10fs	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	10						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		AGTGGAGTCCGGGGTCCTGGT	0.582											OREG0023869	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S9fs		Atlas-INDEL	.											.	CES3	56	.	0			c.27delC						.						101	88	92					16																	66995238		2200	4300	6500	SO:0001589	frameshift_variant	23491	exon1			.	AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"Carboxylesterases"	1865	protein-coding gene	gene with protein product	"esterase 31", "brain carboxylesterase BR3"	605279	"carboxylesterase 3 (brain)"			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.28delG	chr16.hg19:g.66995238delG	ENSP00000304782:p.Gly10fs	162.0	0.0	1096	191.0	12.0	NM_024922	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Frame_Shift_Del	DEL	ENST00000303334.4	hg19	CCDS10826.1																																																																																			.	.		0.582	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922		-	66995238	G	-	66995238	7	5	112	1	0	1	0	1	0	0	0	0	3273	1116	39	0	30	0	CES3	16	66995238	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2013668	66995238	23359515	957	17578										
CBFB	865	hgsc.bcm.edu	37	chr16	67116231	67116231	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtgagagtttcacagctgcTggcagtaactggttagtact	13	7	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:67116231T>C	ENST00000290858.6	+	5	776	c.515T>C	c.(514-516)cTg>cCg	p.L172P	CBFB_ENST00000561924.2_Missense_Mutation_p.L72P|CBFB_ENST00000412916.2_Intron	NM_001755.2|NM_022845.2	NP_001746.1|NP_074036.1	Q13951	PEBB_HUMAN	core-binding factor, beta subunit	172					cell maturation (GO:0048469)|definitive hemopoiesis (GO:0060216)|lymphocyte differentiation (GO:0030098)|myeloid cell differentiation (GO:0030099)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|large_intestine(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)		TCACAGCTGCTGGCAGTAACT	0.428			T	MYH11	AML																																p.L172P		Atlas-SNP	.		Dom	yes		16	16q22	865	"core-binding factor, beta subunit"		L	.	CBFB	52	.	0			c.T515C						.						143	140	141					16																	67116231		2200	4300	6500	SO:0001583	missense	865	exon5			AGCTGCTGGCAGT	BC018509	CCDS10827.1, CCDS45508.1	16q22.1	2008-02-05			ENSG00000067955	ENSG00000067955			1539	protein-coding gene	gene with protein product		121360				8351518, 7587111	Standard	NM_001755		Approved	PEBP2B	uc002erb.3	Q13951	OTTHUMG00000137520	ENST00000290858.6:c.515T>C	chr16.hg19:g.67116231T>C	ENSP00000290858:p.Leu172Pro	86.0	0.0		96.0	4.0	NM_001755	A8K347|Q13124|Q9HCT2	Missense_Mutation	SNP	ENST00000290858.6	hg19	CCDS10827.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.811884	0.70797	.	.	ENSG00000067955	ENST00000290858	.	.	.	5.64	5.64	0.86602	.	0.504996	0.22835	N	0.055046	T	0.42245	0.1194	N	0.19112	0.55	0.80722	D	1	P	0.38440	0.631	B	0.39119	0.291	T	0.47812	-0.9088	9	0.72032	D	0.01	.	14.6719	0.68951	0.0:0.0:0.0:1.0	.	172	Q13951	PEBB_HUMAN	P	172	.	ENSP00000290858:L172P	L	+	2	0	CBFB	65673732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.868000	0.56055	2.145000	0.66743	0.477000	0.44152	CTG	.	.		0.428	CBFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268843.2	NM_001755		C	67116231	T	C	67116231	3	2	112	1	0	0	0	0	1	0	0	0	2701	1580	55	2	533	2	CBFB	16	67116231	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	120993	67116231	23238522	958	17579										
HSF4	3299	hgsc.bcm.edu	37	chr16	67203201	67203201	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gatgcagcccttggttccagAgcggggtgagcctgagctgg	17	10	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:67203201A>G	ENST00000521374.1	+	12	1274	c.1274A>G	c.(1273-1275)gAg>gGg	p.E425G	NOL3_ENST00000432069.2_5'Flank|HSF4_ENST00000264009.8_Missense_Mutation_p.E425G|HSF4_ENST00000584272.1_Missense_Mutation_p.E395G|NOL3_ENST00000564053.1_5'Flank|HSF4_ENST00000421453.1_Missense_Mutation_p.E395G			Q9ULV5	HSF4_HUMAN	heat shock transcription factor 4	425					camera-type eye development (GO:0043010)|cell development (GO:0048468)|histone H3-K9 demethylation (GO:0033169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotrimerization (GO:0070207)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		TTGGTTCCAGAGCGGGGTGAG	0.592																																					p.E425G		Atlas-SNP	.											.	HSF4	33	.	0			c.A1274G						.						33	37	36					16																	67203201		1987	4169	6156	SO:0001583	missense	3299	exon14			TTCCAGAGCGGGG	D87673	CCDS42175.1, CCDS45510.1	16q21	2013-01-22			ENSG00000102878	ENSG00000102878			5227	protein-coding gene	gene with protein product		602438	"cataract, Marner"	CTM		8972228, 10488131, 12089525	Standard	NM_001538		Approved		uc002erl.2	Q9ULV5	OTTHUMG00000178325	ENST00000521374.1:c.1274A>G	chr16.hg19:g.67203201A>G	ENSP00000430947:p.Glu425Gly	59.0	0.0		72.0	4.0	NM_001040667	Q99472|Q9ULV6	Missense_Mutation	SNP	ENST00000521374.1	hg19	CCDS42175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.0|21.0	4.086265|4.086265	0.76642|0.76642	.|.	.|.	ENSG00000102878|ENSG00000102878	ENST00000421453;ENST00000264009;ENST00000517685;ENST00000521374|ENST00000520304	.|.	.|.	.|.	4.73|4.73	4.73|4.73	0.59995|0.59995	.|.	0.000000|.	0.51477|.	D|.	0.000086|.	T|T	0.47673|0.47673	0.1458|0.1458	L|L	0.32530|0.32530	0.975|0.975	0.37856|0.37856	D|D	0.929561|0.929561	D;D|.	0.89917|.	1.0;0.999|.	D;D|.	0.80764|.	0.994;0.986|.	T|T	0.49341|0.49341	-0.8950|-0.8950	9|5	0.27785|.	T|.	0.31|.	-31.7262|-31.7262	10.5258|10.5258	0.44948|0.44948	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	395;425|.	Q9ULV5-2;Q9ULV5|.	.;HSF4_HUMAN|.	G|G	395;425;349;425|101	.|.	ENSP00000264009:E425G|.	E|S	+|+	2|1	0|0	HSF4|HSF4	65760702|65760702	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.946000|0.946000	0.59487|0.59487	2.915000|2.915000	0.48805|0.48805	1.958000|1.958000	0.56883|0.56883	0.533000|0.533000	0.62120|0.62120	GAG|AGC	.	.		0.592	HSF4-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375080.1	NM_001538		G	67203201	A	G	67203201	3	3	112	1	0	0	0	0	1	0	0	0	7407	304	11	2	1334	2	HSF4	16	67203201	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	86970	67203201	23151552	959	17580										
KCTD19	146212	hgsc.bcm.edu	37	chr16	67329298	67329298	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctctctgagggttggacagcAgttctggatactggaggggg	17	7	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:67329298A>G	ENST00000304372.5	-	9	1314	c.1259T>C	c.(1258-1260)cTg>cCg	p.L420P		NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	420	BTB 2.				protein homooligomerization (GO:0051260)					endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		GTTGGACAGCAGTTCTGGATA	0.527																																					p.L420P		Atlas-SNP	.											.	KCTD19	82	.	0			c.T1259C						.						87	81	83					16																	67329298		1948	4145	6093	SO:0001583	missense	146212	exon9			GACAGCAGTTCTG	AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 19"				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.1259T>C	chr16.hg19:g.67329298A>G	ENSP00000305702:p.Leu420Pro	67.0	0.0		82.0	4.0	NM_001100915	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	hg19	CCDS42179.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.933643	0.73442	.	.	ENSG00000168676	ENST00000304372	T	0.52754	0.65	5.5	5.5	0.81552	BTB/POZ fold (2);	0.000000	0.47455	D	0.000237	T	0.62171	0.2406	L	0.49778	1.585	0.58432	D	0.999999	D	0.76494	0.999	D	0.78314	0.991	T	0.64846	-0.6311	10	0.72032	D	0.01	-9.0977	12.9874	0.58599	1.0:0.0:0.0:0.0	.	420	Q17RG1	KCD19_HUMAN	P	420	ENSP00000305702:L420P	ENSP00000305702:L420P	L	-	2	0	KCTD19	65886799	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.001000	0.70685	2.102000	0.63906	0.533000	0.62120	CTG	.	.		0.527	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367		G	67329298	A	G	67329298	3	3	112	1	0	0	0	0	1	0	0	0	8115	188	7	2	1553	2	KCTD19	16	67329298	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	126097	67329298	23025455	960	17581										
NFATC3	4775	hgsc.bcm.edu	37	chr16	68156826	68156826	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaggaaaacttctgaagatcAagctgccatactaccaggaa	8	9	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:68156826A>G	ENST00000346183.3	+	2	1064	c.1040A>G	c.(1039-1041)cAa>cGa	p.Q347R	NFATC3_ENST00000349223.5_Missense_Mutation_p.Q347R|NFATC3_ENST00000329524.4_Missense_Mutation_p.Q347R|NFATC3_ENST00000575270.1_Missense_Mutation_p.Q347R|NFATC3_ENST00000535127.2_3'UTR|RP11-67A1.2_ENST00000548144.1_RNA	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	347					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		TCTGAAGATCAAGCTGCCATA	0.473																																					p.Q347R		Atlas-SNP	.											.	NFATC3	190	.	0			c.A1040G						.						143	143	143					16																	68156826		2198	4300	6498	SO:0001583	missense	4775	exon2			AAGATCAAGCTGC	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"Nuclear factor of activated T-cells"	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.1040A>G	chr16.hg19:g.68156826A>G	ENSP00000300659:p.Gln347Arg	71.0	0.0		75.0	4.0	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	hg19	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	A	11.36	1.615684	0.28801	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524	T;T;T	0.08720	3.06;3.06;3.06	5.39	4.27	0.50696	.	0.261212	0.45361	D	0.000375	T	0.06917	0.0176	L	0.29908	0.895	0.35391	D	0.790771	B;B;B;B	0.28713	0.22;0.0;0.22;0.072	B;B;B;B	0.26864	0.074;0.002;0.045;0.024	T	0.31833	-0.9929	9	.	.	.	-3.8788	12.5522	0.56233	0.8607:0.1393:0.0:0.0	.	347;347;347;347	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	R	347	ENSP00000264008:Q347R;ENSP00000300659:Q347R;ENSP00000331324:Q347R	.	Q	+	2	0	NFATC3	66714327	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.593000	0.61034	0.951000	0.37770	0.460000	0.39030	CAA	.	.		0.473	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		G	68156826	A	G	68156826	3	3	112	1	0	0	0	0	1	0	0	0	10373	130	5	2	1046	2	NFATC3	16	68156826	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	827528	68156826	22197927	961	17582										
COG4	25839	hgsc.bcm.edu	37	chr16	70548316	70548316	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtatgtgctgcagcctgctCataatcttcactcctcaaag	7	12	4	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:70548316C>T	ENST00000323786.5	-	4	487	c.466G>A	c.(466-468)Gag>Aag	p.E156K	COG4_ENST00000564653.1_Missense_Mutation_p.E156K|COG4_ENST00000393612.4_Missense_Mutation_p.E152K	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	152					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				GCAGCCTGCTCATAATCTTCA	0.517																																					p.E156K		Atlas-SNP	.											.	COG4	64	.	0			c.G466A						.						110	94	99					16																	70548316		2198	4300	6498	SO:0001583	missense	25839	exon4			CCTGCTCATAATC	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"Components of oligomeric golgi complex"	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.466G>A	chr16.hg19:g.70548316C>T	ENSP00000315775:p.Glu156Lys	101.0	0.0		107.0	24.0	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	ENST00000323786.5	hg19	CCDS10892.2	.	.	.	.	.	.	.	.	.	.	C	36	5.840835	0.97009	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000393612;ENST00000534772	T;T;T	0.41758	0.99;0.99;0.99	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.69700	0.3140	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.992;0.999	T	0.74003	-0.3804	10	0.87932	D	0	-19.7913	19.4155	0.94694	0.0:1.0:0.0:0.0	.	151;152	Q6PIW8;Q9H9E3	.;COG4_HUMAN	K	156;152;152;79	ENSP00000315775:E156K;ENSP00000377236:E152K;ENSP00000461912:E79K	ENSP00000315775:E156K	E	-	1	0	COG4	69105817	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.342000	0.79310	2.589000	0.87451	0.561000	0.74099	GAG	.	.		0.517	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3			T	70548316	C	T	70548316	3	4	112	1	0	0	0	0	1	0	0	0	3662	835	29	3	1967	3	COG4	16	70548316	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	2391490	70548316	19806437	962	17583										
MARVELD3	91862	hgsc.bcm.edu	37	chr16	71674880	71674880	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acaaaggcagccgagaacagCccggaagttacagtgatgca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:71674880delC	ENST00000299952.4	+	3	1226	c.1183delC	c.(1183-1185)cccfs	p.P395fs	MARVELD3_ENST00000565261.1_3'UTR|PHLPP2_ENST00000540628.1_3'UTR|MARVELD3_ENST00000561682.1_Intron	NM_001017967.3|NM_001271329.1	NP_001017967.2|NP_001258258.1	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	0					cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				CCGAGAACAGCCCGGAAGTTA	0.512																																					p.Q394fs		Atlas-INDEL	.											.	MARVELD3	63	.	0			c.1182delG						.						51	43	46					16																	71674880		2198	4300	6498	SO:0001589	frameshift_variant	91862	exon3			.	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"MARVEL (membrane-associating) domain containing 3"	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000299952.4:c.1183delC	chr16.hg19:g.71674880delC	ENSP00000299952:p.Pro395fs	190.0	0.0		201.0	13.0	NM_001017967	A8K820|H3BQM5|Q96MJ4	Frame_Shift_Del	DEL	ENST00000299952.4	hg19	CCDS32478.1																																																																																			.	.		0.512	MARVELD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268990.1	NM_052858		-	71674880	C	-	71674880	7	5	112	1	0	1	0	1	0	0	0	0	9328	739	26	0	1808	0	MARVELD3	16	71674880	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1126564	71674880	18679873	963	17584										
BCAR1	9564	hgsc.bcm.edu	37	chr16	75269533	75269533	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgacaggcgcttgccctctgCcggggcttcacgttcagctg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:75269533delC	ENST00000162330.5	-	5	1390	c.1264delG	c.(1264-1266)gcafs	p.A422fs	BCAR1_ENST00000546196.1_Frame_Shift_Del_p.A393fs|BCAR1_ENST00000393422.2_Frame_Shift_Del_p.A440fs|BCAR1_ENST00000542031.2_Frame_Shift_Del_p.A420fs|BCAR1_ENST00000393420.6_Frame_Shift_Del_p.A440fs|BCAR1_ENST00000535626.2_Frame_Shift_Del_p.A274fs|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Frame_Shift_Del_p.A440fs|BCAR1_ENST00000538440.2_Frame_Shift_Del_p.A422fs|BCAR1_ENST00000418647.3_Frame_Shift_Del_p.A468fs	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	422	Ser-rich.				actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		TTGCCCTCTGCCGGGGCTTCA	0.687																																					p.A468fs		Atlas-INDEL	.											.	BCAR1	184	.	0			c.1403delC						.						19	25	23					16																	75269533		2197	4298	6495	SO:0001589	frameshift_variant	9564	exon6			.	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"Cas scaffolding proteins"	971	protein-coding gene	gene with protein product	"Crk-associated substrate", "Cas scaffolding protein family member 1"	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.1264delG	chr16.hg19:g.75269533delC	ENSP00000162330:p.Ala422fs	133.0	0.0		151.0	11.0	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Frame_Shift_Del	DEL	ENST00000162330.5	hg19	CCDS10915.1																																																																																			.	.		0.687	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567		-	75269533	C	-	75269533	7	5	112	1	0	1	0	1	0	0	0	0	1348	739	26	0	1360	0	BCAR1	16	75269533	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	3594653	75269533	15085220	964	17585	79	2								
BCAR1	9564	hgsc.bcm.edu	37	chr16	75269535	75269535	+	Missense_Mutation	SNP	G	G	T													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acaggcgcttgccctctgccGgggcttcacgttcagctggg					rs376153187		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:75269535G>T	ENST00000162330.5	-	5	1388	c.1262C>A	c.(1261-1263)cCg>cAg	p.P421Q	BCAR1_ENST00000546196.1_Missense_Mutation_p.P392Q|BCAR1_ENST00000393422.2_Missense_Mutation_p.P439Q|BCAR1_ENST00000542031.2_Missense_Mutation_p.P419Q|BCAR1_ENST00000393420.6_Missense_Mutation_p.P439Q|BCAR1_ENST00000535626.2_Missense_Mutation_p.P273Q|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Missense_Mutation_p.P439Q|BCAR1_ENST00000538440.2_Missense_Mutation_p.P421Q|BCAR1_ENST00000418647.3_Missense_Mutation_p.P467Q	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	421					actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		GCCCTCTGCCGGGGCTTCACG	0.687																																					p.P467Q		Atlas-SNP	.											.	BCAR1	184	.	0			c.C1400A						.						21	26	24					16																	75269535		2197	4298	6495	SO:0001583	missense	9564	exon6			TCTGCCGGGGCTT	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"Cas scaffolding proteins"	971	protein-coding gene	gene with protein product	"Crk-associated substrate", "Cas scaffolding protein family member 1"	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.1262C>A	chr16.hg19:g.75269535G>T	ENSP00000162330:p.Pro421Gln	134.0	0.0		153.0	10.0	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Missense_Mutation	SNP	ENST00000162330.5	hg19	CCDS10915.1	.	.	.	.	.	.	.	.	.	.	G	1.871	-0.460203	0.04508	.	.	ENSG00000050820	ENST00000162330;ENST00000393422;ENST00000420641;ENST00000538440;ENST00000418647;ENST00000535626;ENST00000393420;ENST00000542031;ENST00000546196	T;T;T;T;T;T;T;T;T	0.37584	1.3;1.84;1.61;1.41;1.61;1.19;1.38;1.3;3.11	3.91	0.522	0.17053	.	0.693744	0.12978	N	0.423522	T	0.27697	0.0681	L	0.34521	1.04	0.09310	N	0.999999	P;P;P;P;P;P;P;P;B	0.46952	0.64;0.887;0.819;0.755;0.755;0.64;0.874;0.64;0.33	B;P;B;B;B;B;B;B;B	0.49683	0.238;0.619;0.301;0.299;0.417;0.171;0.394;0.157;0.157	T	0.09796	-1.0658	10	0.28530	T	0.3	-7.8402	0.9398	0.01353	0.2195:0.1783:0.4197:0.1826	.	439;273;467;419;439;439;421;421;211	B4DIW5;F5GXV6;E9PCL5;F5GXA2;F8WA69;E9PCV2;F5H7Z0;P56945;B3KWE2	.;.;.;.;.;.;.;BCAR1_HUMAN;.	Q	421;439;439;421;467;273;439;419;392	ENSP00000162330:P421Q;ENSP00000377074:P439Q;ENSP00000392708:P439Q;ENSP00000443841:P421Q;ENSP00000391669:P467Q;ENSP00000440370:P273Q;ENSP00000377072:P439Q;ENSP00000440415:P419Q;ENSP00000442161:P392Q	ENSP00000162330:P421Q	P	-	2	0	BCAR1	73827036	0.004000	0.15560	0.007000	0.13788	0.002000	0.02628	0.235000	0.17948	0.411000	0.25702	-0.384000	0.06662	CCG	.	.		0.687	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567		T	75269535	G	T	75269535	3	4	112	1	0	0	0	0	1	0	0	0	1348	1116	39	1	1362	1	BCAR1	16	75269535	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	2	75269535	15085218	965	17586	79	2								
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76486452	76486452	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccacaatctatgcccgtgacTtttctgagctccaggagtta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:76486452delT	ENST00000476707.1	+	7	1267	c.1128delT	c.(1126-1128)actfs	p.T376fs	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000377504.4_Frame_Shift_Del_p.T324fs|CNTNAP4_ENST00000478060.1_Frame_Shift_Del_p.T300fs|CNTNAP4_ENST00000307431.8_Frame_Shift_Del_p.T372fs			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	373					cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						TGCCCGTGACTTTTCTGAGCT	0.408																																					p.T300fs		Atlas-INDEL	.											.	CNTNAP4	600	.	0			c.899delC						.						98	98	98					16																	76486452		2198	4300	6498	SO:0001589	frameshift_variant	85445	exon7			.	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.1128delT	chr16.hg19:g.76486452delT	ENSP00000417628:p.Thr376fs	138.0	0.0		127.0	10.0	NM_138994	E9PFZ6|Q86YZ7	Frame_Shift_Del	DEL	ENST00000476707.1	hg19																																																																																				.	.		0.408	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		-	76486452	T	-	76486452	7	5	112	1	0	1	0	1	0	0	0	0	3651	1596	56	0	1162	0	CNTNAP4	16	76486452	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1216917	76486452	13868301	966	17587										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77327037	77327037	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcatcgtccaagcacacagCcctcctgcagctcaggtctg	10	16	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:77327037C>A	ENST00000282849.5	-	20	3543	c.3125G>T	c.(3124-3126)gGc>gTc	p.G1042V	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1042	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						AAGCACACAGCCCTCCTGCAG	0.602																																					p.G1042V		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G3125T						.						88	82	84					16																	77327037		2198	4300	6498	SO:0001583	missense	170692	exon20			ACACAGCCCTCCT	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3125G>T	chr16.hg19:g.77327037C>A	ENSP00000282849:p.Gly1042Val	62.0	0.0		80.0	23.0	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	5.352	0.250201	0.10130	.	.	ENSG00000140873	ENST00000282849	T	0.59638	0.25	6.02	6.02	0.97574	.	0.159420	0.52532	D	0.000077	T	0.38585	0.1046	N	0.11131	0.1	0.58432	D	0.999998	B;B	0.10296	0.003;0.002	B;B	0.14023	0.002;0.01	T	0.25710	-1.0124	10	0.15066	T	0.55	.	15.7552	0.78018	0.0:0.8545:0.1455:0.0	.	1042;1042	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	V	1042	ENSP00000282849:G1042V	ENSP00000282849:G1042V	G	-	2	0	ADAMTS18	75884538	1.000000	0.71417	1.000000	0.80357	0.009000	0.06853	1.304000	0.33482	2.850000	0.98022	0.650000	0.86243	GGC	.	.		0.602	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			A	77327037	C	A	77327037	3	1	112	1	0	0	0	0	1	0	0	0	263	739	26	3	556	3	ADAMTS18	16	77327037	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	840585	77327037	13027716	967	17588										
KIAA1609	57707	hgsc.bcm.edu	37	chr16	84520325	84520325	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcgaggacagccacacagggTccccggtgagtgatgtggcc					rs431389	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:84520325delT	ENST00000343629.6	-	5	1052	c.870delA	c.(868-870)ggafs	p.G290fs	TLDC1_ENST00000535580.1_Frame_Shift_Del_p.G263fs|TLDC1_ENST00000561807.1_5'Flank	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	290	TLD.					lysosomal membrane (GO:0005765)											CCACACAGGGTCCCCGGTGAG	0.587																																					p.P291fs		Atlas-INDEL	.											.	KIAA1609	39	.	0			c.871delC						.						77	69	72					16																	84520325		2200	4300	6500	SO:0001589	frameshift_variant	57707	exon5			.	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"TLD domain containing 1"		"KIAA1609"	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.870delA	chr16.hg19:g.84520325delT	ENSP00000343635:p.Gly290fs	151.0	0.0		156.0	10.0	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Frame_Shift_Del	DEL	ENST00000343629.6	hg19	CCDS32498.1																																																																																			.	.		0.587	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947		-	84520325	T	-	84520325	7	5	112	1	0	1	0	1	0	0	0	0	8256	1654	58	0	516	0	KIAA1609	16	84520325	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	7193288	84520325	5834428	968	17589										
KIAA0513	9764	hgsc.bcm.edu	37	chr16	85112029	85112029	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctctccctcagggaagacgAgaacaaaccccaggagaagc	10	13	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:85112029A>G	ENST00000566428.1	+	7	1422	c.791A>G	c.(790-792)gAg>gGg	p.E264G	KIAA0513_ENST00000258180.3_Missense_Mutation_p.E264G|KIAA0513_ENST00000567328.1_Missense_Mutation_p.E264G|KIAA0513_ENST00000538274.1_Missense_Mutation_p.E264G			O60268	K0513_HUMAN	KIAA0513	264						cytoplasm (GO:0005737)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(9)|pancreas(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.234)		AGGGAAGACGAGAACAAACCC	0.587																																					p.E264G		Atlas-SNP	.											.	KIAA0513	43	.	0			c.A791G						.						59	57	58					16																	85112029		2198	4300	6498	SO:0001583	missense	9764	exon7			AAGACGAGAACAA	AB011085	CCDS32499.1, CCDS67091.1, CCDS73919.1	16q24.1	2012-11-29			ENSG00000135709	ENSG00000135709			29058	protein-coding gene	gene with protein product		611675				9628581	Standard	XM_005256265		Approved		uc002fiu.3	O60268	OTTHUMG00000176597	ENST00000566428.1:c.791A>G	chr16.hg19:g.85112029A>G	ENSP00000457408:p.Glu264Gly	95.0	0.0		121.0	5.0	NM_014732	B4DSS5|D3DUM2|Q8N6G0	Missense_Mutation	SNP	ENST00000566428.1	hg19	CCDS32499.1	.	.	.	.	.	.	.	.	.	.	A	10.72	1.430298	0.25726	.	.	ENSG00000135709	ENST00000538274;ENST00000258180	T;T	0.37058	1.22;1.22	4.97	4.97	0.65823	.	0.206732	0.49305	D	0.000141	T	0.28333	0.0700	L	0.29908	0.895	0.39812	D	0.972725	P;P	0.37370	0.592;0.457	B;B	0.37601	0.254;0.129	T	0.13980	-1.0489	10	0.45353	T	0.12	-17.9317	12.328	0.55022	1.0:0.0:0.0:0.0	.	264;264	B4DSS5;O60268	.;K0513_HUMAN	G	264	ENSP00000446439:E264G;ENSP00000258180:E264G	ENSP00000258180:E264G	E	+	2	0	KIAA0513	83669530	0.994000	0.37717	0.092000	0.20876	0.034000	0.12701	4.876000	0.63079	1.982000	0.57802	0.459000	0.35465	GAG	.	.		0.587	KIAA0513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432736.1	NM_014732		G	85112029	A	G	85112029	3	3	112	1	0	0	0	0	1	0	0	0	8190	304	11	2	813	2	KIAA0513	16	85112029	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	591704	85112029	5242724	969	17590										
ZNF778	197320	hgsc.bcm.edu	37	chr16	89294754	89294754	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaagccttccgtgcctcctcTcacctgcataaacatggaag	7	14	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:89294754T>C	ENST00000433976.2	+	6	2306	c.1974T>C	c.(1972-1974)tcT>tcC	p.S658S	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Silent_p.S616S	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	658					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		GTGCCTCCTCTCACCTGCATA	0.428																																					p.S686S		Atlas-SNP	.											.	ZNF778	67	.	0			c.T2058C						.						53	57	56					16																	89294754		2180	4293	6473	SO:0001819	synonymous_variant	197320	exon7			CTCCTCTCACCTG	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"Zinc fingers, C2H2-type", "-"	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.1974T>C	chr16.hg19:g.89294754T>C		115.0	0.0		114.0	5.0	NM_001201407	Q08AG0	Silent	SNP	ENST00000433976.2	hg19	CCDS45550.1																																																																																			.	.		0.428	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		C	89294754	T	C	89294754	2	2	112	1	0	0	0	0	0	0	0	1	18166	1538	54	2		2	ZNF778	16	89294754	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4182725	89294754	1059999	970	17591										
SPATA2L	124044	hgsc.bcm.edu	37	chr16	89764134	89764134	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttccagcccctcctccaaggCcccatatggtgggctgctgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:89764134delC	ENST00000289805.5	-	3	951	c.883delG	c.(883-885)gccfs	p.A295fs	SPATA2L_ENST00000335360.7_Intron	NM_152339.3	NP_689552.2	Q8IUW3	SPA2L_HUMAN	spermatogenesis associated 2-like	295										breast(1)|cervix(1)|endometrium(1)|lung(2)|skin(1)	6		Lung NSC(15;0.00043)|all_lung(18;0.000665)|all_hematologic(23;0.0355)		BRCA - Breast invasive adenocarcinoma(80;0.0272)		TCCTCCAAGGCCCCATATGGT	0.672																																					p.A295fs		Atlas-INDEL	.											.	SPATA2L	16	.	0			c.884delC						.						22	24	23					16																	89764134		2193	4295	6488	SO:0001589	frameshift_variant	124044	exon3			.	AF070574	CCDS10985.1	16q24.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000158792	ENSG00000158792			28393	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 76"	C16orf76		8619474	Standard	NM_152339		Approved	MGC26885, tamo	uc002foj.3	Q8IUW3	OTTHUMG00000138047	ENST00000289805.5:c.883delG	chr16.hg19:g.89764134delC	ENSP00000289805:p.Ala295fs	92.0	0.0		138.0	10.0	NM_152339	D3DX85|Q8NHV3	Frame_Shift_Del	DEL	ENST00000289805.5	hg19	CCDS10985.1																																																																																			.	.		0.672	SPATA2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269923.1	NM_152339		-	89764134	C	-	89764134	7	5	112	1	0	1	0	1	0	0	0	0	15024	739	26	0	395	0	SPATA2L	16	89764134	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	469380	89764134	590619	971	17592										
FANCA	2175	hgsc.bcm.edu	37	chr16	89839740	89839740	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccagtgcagctgtgagctgTcccaggggctcctcagcaga	13	14	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:89839740T>C	ENST00000389301.3	-	22	1983	c.1953A>G	c.(1951-1953)ggA>ggG	p.G651G	FANCA_ENST00000567284.2_5'UTR|FANCA_ENST00000568369.1_Silent_p.G651G	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	651					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CTGTGAGCTGTCCCAGGGGCT	0.572			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G651G		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.A1953G						.						35	27	30					16																	89839740		2027	3941	5968	SO:0001819	synonymous_variant	2175	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GAGCTGTCCCAGG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"Fanconi anemia, complementation groups"	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1953A>G	chr16.hg19:g.89839740T>C		101.0	0.0		91.0	4.0	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	hg19	CCDS32515.1																																																																																			.	.		0.572	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			C	89839740	T	C	89839740	2	2	112	1	0	0	0	0	0	0	0	1	5670	1654	58	2		2	FANCA	16	89839740	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	75606	89839740	515013	972	17593										
FANCA	2175	hgsc.bcm.edu	37	chr16	89857899	89857899	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acgcagtgaccatgctgtccAgctggcagctctcgaatgcc	11	14	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:89857899A>G	ENST00000389301.3	-	14	1301	c.1271T>C	c.(1270-1272)cTg>cCg	p.L424P	FANCA_ENST00000568369.1_Missense_Mutation_p.L424P	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	424					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CATGCTGTCCAGCTGGCAGCT	0.572			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.L424P		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.T1271C						.						67	53	58					16																	89857899		2198	4300	6498	SO:0001583	missense	2175	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTGTCCAGCTGGC	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"Fanconi anemia, complementation groups"	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1271T>C	chr16.hg19:g.89857899A>G	ENSP00000373952:p.Leu424Pro	62.0	0.0		82.0	4.0	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	hg19	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.411386	0.42817	.	.	ENSG00000187741	ENST00000389301	D	0.98493	-4.96	5.13	2.89	0.33648	.	0.157917	0.29126	N	0.013066	D	0.98232	0.9415	M	0.73598	2.24	0.80722	D	1	D;D	0.56746	0.977;0.977	P;P	0.60236	0.871;0.871	D	0.97490	1.0053	10	0.72032	D	0.01	-4.5933	9.8979	0.41329	0.8946:0.0:0.1054:0.0	.	424;424	B4DRI7;O15360	.;FANCA_HUMAN	P	424	ENSP00000373952:L424P	ENSP00000373952:L424P	L	-	2	0	FANCA	88385400	1.000000	0.71417	0.479000	0.27329	0.150000	0.21749	2.965000	0.49200	0.322000	0.23283	0.529000	0.55759	CTG	.	.		0.572	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			G	89857899	A	G	89857899	3	3	112	1	0	0	0	0	1	0	0	0	5670	188	7	2	3216	2	FANCA	16	89857899	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	18159	89857899	496854	973	17594										
SGSM2	9905	hgsc.bcm.edu	37	chr17	2282488	2282488	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acttcactgacatcatcaagTttttcaatggtacgagctgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:2282488delT	ENST00000426855.2	+	22	3098	c.2923delT	c.(2923-2925)tttfs	p.F976fs	RP1-59D14.5_ENST00000574290.1_RNA|SGSM2_ENST00000574563.1_Frame_Shift_Del_p.F976fs|SGSM2_ENST00000268989.3_Frame_Shift_Del_p.F1021fs|RP1-59D14.5_ENST00000573007.1_RNA	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	976					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		CATCATCAAGTTTTTCAATGG	0.577																																					p.K1019fs		Atlas-INDEL	.											.	SGSM2	60	.	0			c.3057delG						.						189	149	163					17																	2282488		2203	4300	6503	SO:0001589	frameshift_variant	9905	exon23			.	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"Small G protein signaling modulators"	29026	protein-coding gene	gene with protein product		611418	"RUN and TBC1 domain containing 1"	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.2923delT	chr17.hg19:g.2282488delT	ENSP00000415107:p.Phe976fs	244.0	0.0		200.0	12.0	NM_014853	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Frame_Shift_Del	DEL	ENST00000426855.2	hg19	CCDS45570.1																																																																																			.	.		0.577	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853		-	2282488	T	-	2282488	7	5	112	1	0	1	0	1	0	0	0	0	14238	1725	60	0	3148	0	SGSM2	17	2282488	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10		2282488	78912722	974	17595										
C17orf85	55421	hgsc.bcm.edu	37	chr17	3716454	3716454	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctctttctccttaatcagagCcccccatgccctttgcagct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:3716454delC	ENST00000389005.4	-	13	1774	c.1747delG	c.(1747-1749)gctfs	p.A583fs	C17orf85_ENST00000158149.3_Frame_Shift_Del_p.A303fs	NM_001114118.2	NP_001107590.1	Q53F19	CQ085_HUMAN	chromosome 17 open reading frame 85	583							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A303fs*2(1)		endometrium(2)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (3;0.0725)		TTAATCAGAGCCCCCCATGCC	0.507																																					p.A583fs		Atlas-INDEL	.											.	C17orf85	66	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1748delC						.						139	139	139					17																	3716454		2203	4300	6503	SO:0001589	frameshift_variant	55421	exon13			.		CCDS45578.1	17p13.2	2012-10-23			ENSG00000074356	ENSG00000074356			24612	protein-coding gene	gene with protein product	"ELG protein"					11412301	Standard	NM_001114118		Approved	HSA277841, ELG	uc010ckl.2	Q53F19	OTTHUMG00000177672	ENST00000389005.4:c.1747delG	chr17.hg19:g.3716454delC	ENSP00000373657:p.Ala583fs	206.0	0.0		151.0	13.0	NM_001114118	B3KWG7|Q7L406|Q96FK1|Q9NXZ4	Frame_Shift_Del	DEL	ENST00000389005.4	hg19	CCDS45578.1																																																																																			.	.		0.507	C17orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438385.1	NM_018553		-	3716454	C	-	3716454	7	5	112	1	0	1	0	1	0	0	0	0	1890	739	26	0	119	0	C17orf85	17	3716454	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1433966	3716454	77478756	975	17596										
ACADVL	37	hgsc.bcm.edu	37	chr17	7123922	7123922	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aatttgcctctctctgcccaGgaatctaagtcctttgctgt	7	12	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7123922G>A	ENST00000356839.5	+	4	383		c.e4-1		ACADVL_ENST00000543245.2_Splice_Site|ACADVL_ENST00000350303.5_Splice_Site|ACADVL_ENST00000581562.1_Splice_Site|MIR324_ENST00000362183.1_RNA|DLG4_ENST00000399510.2_5'Flank	NM_000018.3|NM_001270448.1	NP_000009.1|NP_001257377.1	P49748	ACADV_HUMAN	acyl-CoA dehydrogenase, very long chain						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy derivation by oxidation of organic compounds (GO:0015980)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(1)|ovary(4)|skin(1)	21						TCTCTGCCCAGGAATCTAAGT	0.562																																					.		Atlas-SNP	.											.	ACADVL	43	.	0			c.274-1G>A						.						96	98	97					17																	7123922		2203	4300	6503	SO:0001630	splice_region_variant	37	exon5			TGCCCAGGAATCT	BC012912	CCDS11090.1, CCDS42249.1, CCDS58509.1	17p13.1	2010-04-30	2010-04-30		ENSG00000072778	ENSG00000072778			92	protein-coding gene	gene with protein product		609575	"acyl-Coenzyme A dehydrogenase, very long chain"			8921384	Standard	NM_000018		Approved	VLCAD, LCACD, ACAD6	uc002gev.4	P49748	OTTHUMG00000102157	ENST00000356839.5:c.205-1G>A	chr17.hg19:g.7123922G>A		93.0	0.0		65.0	4.0	NM_001270447	B4DEB6|F5H2A9|O76056|Q8WUL0	Splice_Site	SNP	ENST00000356839.5	hg19	CCDS11090.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.966479	0.92855	.	.	ENSG00000072778	ENST00000543245;ENST00000356839;ENST00000350303;ENST00000322910;ENST00000542255	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2384	0.73450	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACADVL	7064646	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.412000	0.90232	2.675000	0.91044	0.655000	0.94253	.	.	.		0.562	ACADVL-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220001.5	NM_000018	Intron	A	7123922	G	A	7123922	5	1	112	1	0	0	0	0	0	0	1	0	116	1014	35	3	218	3	ACADVL	17	7123922	Splice_Site	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	3407468	7123922	74071288	976	17597										
NEURL4	84461	hgsc.bcm.edu	37	chr17	7224736	7224736	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccatccaccaggatgtgcaTcgtgtcatctgccccccgac	8	17	2	0	rs117553236	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7224736T>C	ENST00000399464.2	-	19	3157	c.3142A>G	c.(3142-3144)Atg>Gtg	p.M1048V	NEURL4_ENST00000315614.7_Missense_Mutation_p.M1046V|RP11-542C16.2_ENST00000575474.1_5'Flank|NEURL4_ENST00000570460.1_Missense_Mutation_p.M1024V|NEURL4_ENST00000574120.1_5'Flank	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1048	NHR 5. {ECO:0000255|PROSITE- ProRule:PRU00400}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AGGATGTGCATCGTGTCATCT	0.607																																					p.M1048V		Atlas-SNP	.											.	NEURL4	192	.	0			c.A3142G						.						104	113	110					17																	7224736		2147	4233	6380	SO:0001583	missense	84461	exon19			TGTGCATCGTGTC		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"neuralized homolog 4 (Drosophila)"			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.3142A>G	chr17.hg19:g.7224736T>C	ENSP00000382390:p.Met1048Val	106.0	0.0		82.0	6.0	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	hg19	CCDS42251.1	.	.	.	.	.	.	.	.	.	.	T	13.96	2.393743	0.42410	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.33654	1.4;1.48	5.14	5.14	0.70334	NEUZ (1);	0.046596	0.85682	D	0.000000	T	0.42017	0.1184	M	0.74647	2.275	0.37491	D	0.916388	P;B	0.36712	0.566;0.275	B;B	0.41135	0.348;0.051	T	0.49466	-0.8937	10	0.38643	T	0.18	-27.0231	10.1661	0.42882	0.0:0.0:0.1675:0.8325	.	1046;1048	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	V	1046;1048	ENSP00000319826:M1046V;ENSP00000382390:M1048V	ENSP00000319826:M1046V	M	-	1	0	NEURL4	7165460	1.000000	0.71417	0.976000	0.42696	0.994000	0.84299	4.065000	0.57513	1.911000	0.55334	0.460000	0.39030	ATG	.	T|0.996;G|0.004		0.607	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442		C	7224736	T	C	7224736	3	2	112	1	0	0	0	0	1	0	0	0	10356	1435	50	2	1590	2	NEURL4	17	7224736	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	100814	7224736	73970474	977	17598										
POLR2A	5430	hgsc.bcm.edu	37	chr17	7416095	7416095	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcttctctcactctatagggAgtggaatgaccccaggggca	12	11	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7416095A>G	ENST00000322644.6	+	28	5008	c.4609A>G	c.(4609-4611)Agt>Ggt	p.S1537G		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1537					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				CTCTATAGGGAGTGGAATGAC	0.622																																					p.S1537G		Atlas-SNP	.											.	POLR2A	157	.	0			c.A4609G						.						64	74	71					17																	7416095		2203	4300	6503	SO:0001583	missense	5430	exon28			ATAGGGAGTGGAA			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.4609A>G	chr17.hg19:g.7416095A>G	ENSP00000314949:p.Ser1537Gly	57.0	0.0		48.0	4.0	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	A	8.797	0.931934	0.18131	.	.	ENSG00000181222	ENST00000535204;ENST00000545644;ENST00000322644	T	0.71103	-0.54	4.04	4.04	0.47022	.	0.822365	0.10722	N	0.641652	T	0.53594	0.1806	N	0.11201	0.11	0.80722	D	1	B	0.15719	0.014	B	0.15484	0.013	T	0.47142	-0.9140	10	0.44086	T	0.13	-2.128	12.4264	0.55548	1.0:0.0:0.0:0.0	.	1537	P24928	RPB1_HUMAN	G	1493;436;1537	ENSP00000314949:S1537G	ENSP00000314949:S1537G	S	+	1	0	SLC35G6	7356819	1.000000	0.71417	0.992000	0.48379	0.254000	0.26022	8.174000	0.89682	1.819000	0.53055	0.374000	0.22700	AGT	.	.		0.622	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		G	7416095	A	G	7416095	3	3	112	1	0	0	0	0	1	0	0	0	12223	304	11	2	4719	2	POLR2A	17	7416095	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	191359	7416095	73779115	978	17599										
SHBG	6462	hgsc.bcm.edu	37	chr17	7536255	7536255	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgggccaagcctcaagggcgTctcttcctgggggctttacc	13	13	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7536255T>C	ENST00000380450.4	+	7	1069	c.1038T>C	c.(1036-1038)cgT>cgC	p.R346R	SHBG_ENST00000570547.1_Intron|SHBG_ENST00000575903.1_Silent_p.R328R|SHBG_ENST00000572262.1_Silent_p.R234R|SHBG_ENST00000575314.1_Silent_p.R288R|SHBG_ENST00000576478.1_Intron|SHBG_ENST00000574539.1_Intron|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000416273.3_Intron|SHBG_ENST00000340624.5_Intron|SHBG_ENST00000441599.2_Intron|SHBG_ENST00000576728.1_Intron	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	346	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.0?(1)|p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	CTCAAGGGCGTCTCTTCCTGG	0.562											OREG0024140	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R346R		Atlas-SNP	.											.	SHBG	21	.	2	Unknown(1)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)|bone(1)	c.T1038C						.						38	37	38					17																	7536255		2203	4300	6503	SO:0001819	synonymous_variant	6462	exon7			AGGGCGTCTCTTC		CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"androgen binding protein"	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.1038T>C	chr17.hg19:g.7536255T>C		63.0	0.0	642	43.0	4.0	NM_001040	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Silent	SNP	ENST00000380450.4	hg19	CCDS11117.1																																																																																			.	.		0.562	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040		C	7536255	T	C	7536255	2	2	112	1	0	0	0	0	0	0	0	1	14284	1654	58	2		2	SHBG	17	7536255	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	120160	7536255	73658955	979	17600										
TP53	7157	hgsc.bcm.edu	37	chr17	7578457	7578457	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcttgtagatggccatggcgCggacgcgggtgccgggcggg	21	10	0	1	rs587782144		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7578457C>T	ENST00000269305.4	-	5	662	c.473G>A	c.(472-474)cGc>cAc	p.R158H	TP53_ENST00000359597.4_Missense_Mutation_p.R158H|TP53_ENST00000455263.2_Missense_Mutation_p.R158H|TP53_ENST00000420246.2_Missense_Mutation_p.R158H|TP53_ENST00000413465.2_Missense_Mutation_p.R158H|TP53_ENST00000445888.2_Missense_Mutation_p.R158H|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	158	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R158L(77)|p.R158H(74)|p.R158P(9)|p.R65L(8)|p.0?(8)|p.R26L(8)|p.R158fs(6)|p.R158fs*11(6)|p.R65H(5)|p.R26H(5)|p.R158_A159insX(4)|p.R65fs(2)|p.R158_A159delRA(2)|p.R156_I162delRVRAMAI(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.R26fs(2)|p.V157fs*22(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.R158F(1)|p.P151_V173del23(1)|p.R156_R158delRVR(1)|p.R156fs*18(1)|p.R26fs*11(1)|p.R156_A161del(1)|p.V157_M160delVRAM(1)|p.V157_R158delVR(1)|p.S149fs*72(1)|p.A159fs*21(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R65fs*11(1)|p.R156fs*20(1)|p.R158C(1)|p.V157_I162delVRAMAI(1)|p.V157fs*21(1)|p.R158fs*8(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCCATGGCGCGGACGCGGGT	0.627		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R158H	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,0,2	TP53	33396	.	244	Substitution - Missense(188)|Deletion - Frameshift(19)|Deletion - In frame(13)|Complex(10)|Whole gene deletion(8)|Insertion - In frame(4)|Complex - frameshift(2)	lung(78)|central_nervous_system(33)|oesophagus(20)|haematopoietic_and_lymphoid_tissue(19)|large_intestine(18)|upper_aerodigestive_tract(12)|stomach(12)|urinary_tract(9)|prostate(7)|kidney(6)|liver(6)|breast(5)|bone(4)|soft_tissue(3)|ovary(3)|pancreas(3)|thyroid(2)|biliary_tract(2)|vulva(1)|thymus(1)	c.G473A	GRCh37	CM994513	TP53	M		.						49	51	50					17																	7578457		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ATGGCGCGGACGC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.473G>A	chr17.hg19:g.7578457C>T	ENSP00000269305:p.Arg158His	153.0	0.0		90.0	55.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.306299	0.40795	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	5.59	4.63	0.57726	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.110116	0.64402	D	0.000010	D	0.99809	0.9917	M	0.77486	2.375	0.58432	D	0.999999	D;P;D;D;P;P;D	0.89917	0.998;0.631;0.984;0.982;0.831;0.48;1.0	P;B;P;P;P;B;D	0.97110	0.907;0.274;0.76;0.751;0.516;0.242;1.0	D	0.96738	0.9544	10	0.87932	D	0	-10.4795	12.6491	0.56751	0.0:0.9196:0.0:0.0804	.	119;158;158;65;158;158;158	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	158;158;158;158;158;158;147;65;26;65;26;158	ENSP00000410739:R158H;ENSP00000352610:R158H;ENSP00000269305:R158H;ENSP00000398846:R158H;ENSP00000391127:R158H;ENSP00000391478:R158H;ENSP00000425104:R26H;ENSP00000423862:R65H;ENSP00000424104:R158H	ENSP00000269305:R158H	R	-	2	0	TP53	7519182	1.000000	0.71417	0.034000	0.17996	0.175000	0.22909	7.775000	0.85489	1.514000	0.48869	-0.140000	0.14226	CGC	.	.		0.627	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578457	C	T	7578457	3	4	112	1	0	0	0	0	1	0	0	0	16396	768	27	1	825	1	TP53	17	7578457	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	42202	7578457	73616753	980	17601										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7674122	7674122	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gataaccaggtagctctgtcTaccatgaaggcatcacgctt	9	11	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7674122T>C	ENST00000572933.1	+	27	5693	c.4233T>C	c.(4231-4233)tcT>tcC	p.S1411S	DNAH2_ENST00000389173.2_Silent_p.S1411S			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1411	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TAGCTCTGTCTACCATGAAGG	0.488																																					p.S1411S		Atlas-SNP	.											.	DNAH2	498	.	0			c.T4233C						.						181	164	170					17																	7674122		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon26			TCTGTCTACCATG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.4233T>C	chr17.hg19:g.7674122T>C		124.0	0.0		99.0	4.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.		0.488	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		C	7674122	T	C	7674122	2	2	112	1	0	0	0	0	0	0	0	1	4604	1509	53	2		2	DNAH2	17	7674122	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	95665	7674122	73521088	981	17602										
CHD3	1107	hgsc.bcm.edu	37	chr17	7802659	7802659	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgcccccattcttgactcccAgggccacacaaaaggtccct	7	17	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7802659A>G	ENST00000330494.7	+	15	2493		c.e15-1		CHD3_ENST00000380358.4_Splice_Site|CHD3_ENST00000358181.4_Splice_Site	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3						centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				CTTGACTCCCAGGGCCACACA	0.557																																					.		Atlas-SNP	.											.	CHD3	169	.	0			c.2521-2A>G						.						95	94	94					17																	7802659		2203	4300	6503	SO:0001630	splice_region_variant	1107	exon15			ACTCCCAGGGCCA	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.2344-1A>G	chr17.hg19:g.7802659A>G		120.0	0.0		86.0	4.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Splice_Site	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	A	16.26	3.072821	0.55646	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3149	0.74065	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CHD3	7743384	1.000000	0.71417	0.996000	0.52242	0.704000	0.40688	9.139000	0.94554	2.266000	0.75297	0.454000	0.30748	.	.	.		0.557	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	Intron	G	7802659	A	G	7802659	5	3	112	1	0	0	0	0	0	0	1	0	3328	202	7	2	2681	2	CHD3	17	7802659	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	128537	7802659	73392551	982	17603										
MYH8	4626	hgsc.bcm.edu	37	chr17	10318665	10318665	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attgccaaaggcctccagtaGgggattggcgctgatgattt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:10318665delG	ENST00000403437.2	-	8	779	c.685delC	c.(685-687)ctafs	p.L230fs	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	230	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GCCTCCAGTAGGGGATTGGCG	0.512									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.L229fs		Atlas-INDEL	.											.	MYH8	346	.	0			c.686delT						.						128	130	129					17																	10318665		2203	4300	6503	SO:0001589	frameshift_variant	4626	exon8	Familial Cancer Database	Carney Complex Variant	.		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.685delC	chr17.hg19:g.10318665delG	ENSP00000384330:p.Leu230fs	166.0	0.0		130.0	10.0	NM_002472	Q14910	Frame_Shift_Del	DEL	ENST00000403437.2	hg19	CCDS11153.1																																																																																			.	.		0.512	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		-	10318665	G	-	10318665	7	5	112	1	0	1	0	1	0	0	0	0	10050	991	35	0	5260	0	MYH8	17	10318665	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2516006	10318665	70876545	983	17604										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11572530	11572530	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccagcatttttaggataccaTctctggtgccacggctttcc	8	13	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:11572530T>C	ENST00000262442.4	+	16	2949	c.2881T>C	c.(2881-2883)Tct>Cct	p.S961P	DNAH9_ENST00000454412.2_Missense_Mutation_p.S961P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	961	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TAGGATACCATCTCTGGTGCC	0.532																																					p.S961P		Atlas-SNP	.											.	DNAH9	695	.	0			c.T2881C						.						126	119	121					17																	11572530		2203	4300	6503	SO:0001583	missense	1770	exon16			ATACCATCTCTGG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.2881T>C	chr17.hg19:g.11572530T>C	ENSP00000262442:p.Ser961Pro	149.0	0.0		105.0	5.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.146753	0.57151	.	.	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.27557	1.7;1.66	5.6	4.51	0.55191	.	0.143325	0.48767	D	0.000168	T	0.51941	0.1704	M	0.85041	2.73	0.80722	D	1	D	0.54601	0.967	P	0.59948	0.866	T	0.54296	-0.8315	10	0.59425	D	0.04	.	8.0065	0.30327	0.1357:0.0:0.1421:0.7222	.	961	Q9NYC9	DYH9_HUMAN	P	961	ENSP00000262442:S961P;ENSP00000414874:S961P	ENSP00000262442:S961P	S	+	1	0	DNAH9	11513255	0.990000	0.36364	0.743000	0.31040	0.601000	0.36947	2.384000	0.44362	0.924000	0.37069	0.533000	0.62120	TCT	.	.		0.532	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		C	11572530	T	C	11572530	3	2	112	1	0	0	0	0	1	0	0	0	4610	1435	50	2	2943	2	DNAH9	17	11572530	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1253865	11572530	69622680	984	17605										
RAI1	10743	hgsc.bcm.edu	37	chr17	17700882	17700882	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tattccaagcggaagcgcctCactcggggccgggccaagaa	13	13	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:17700882C>A	ENST00000353383.1	+	3	5089	c.4620C>A	c.(4618-4620)ctC>ctA	p.L1540L	RAI1_ENST00000261641.6_Silent_p.L1540L	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1540					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GGAAGCGCCTCACTCGGGGCC	0.667																																					p.L1540L		Atlas-SNP	.											.	RAI1	121	.	0			c.C4620A						.						57	69	65					17																	17700882		2203	4300	6503	SO:0001819	synonymous_variant	10743	exon3			GCGCCTCACTCGG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"Smith-Magenis syndrome chromosome region"	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.4620C>A	chr17.hg19:g.17700882C>A		227.0	0.0		256.0	89.0	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	hg19	CCDS11188.1																																																																																			.	.		0.667	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		A	17700882	C	A	17700882	2	1	112	1	0	0	0	0	0	0	0	1	13022	813	29	3		3	RAI1	17	17700882	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	6128352	17700882	63494328	985	17606										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18077149	18077149	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtcgacgcggacccagcggCccacggccaactccagctac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:18077149delC	ENST00000205890.5	+	65	10743	c.10405delC	c.(10405-10407)cccfs	p.P3469fs	RP11-258F1.1_ENST00000583062.1_RNA|MYO15A_ENST00000418233.3_Frame_Shift_Del_p.P733fs|RP11-258F1.1_ENST00000577847.1_RNA|MYO15A_ENST00000451725.2_Intron	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3469	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					GACCCAGCGGCCCACGGCCAA	0.662																																					p.R3468fs		Atlas-INDEL	.											.	MYO15A	268	.	0			c.10404delG						.						40	44	43					17																	18077149		1958	4137	6095	SO:0001589	frameshift_variant	51168	exon64			.	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.10405delC	chr17.hg19:g.18077149delC	ENSP00000205890:p.Pro3469fs	214.0	0.0		228.0	14.0	NM_016239	B4DFC7	Frame_Shift_Del	DEL	ENST00000205890.5	hg19	CCDS42271.1																																																																																			.	.		0.662	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		-	18077149	C	-	18077149	7	5	112	1	0	1	0	1	0	0	0	0	10072	739	26	0	10655	0	MYO15A	17	18077149	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	376267	18077149	63118061	986	17607										
TOP3A	7156	hgsc.bcm.edu	37	chr17	18217965	18217965	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgatccccttggccgcgtcgTttttttcggccacacagagg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:18217965delT	ENST00000321105.5	-	1	342	c.128delA	c.(127-129)aacfs	p.N43fs	SMCR8_ENST00000406438.3_5'Flank|TOP3A_ENST00000582230.1_5'UTR|TOP3A_ENST00000542570.1_5'UTR	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	43	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						GGCCGCGTCGTTTTTTTCGGC	0.652																																					p.N43fs		Atlas-INDEL	.											.	TOP3A	85	.	0			c.129delC						.						53	42	46					17																	18217965		2203	4300	6503	SO:0001589	frameshift_variant	7156	exon1			.	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 7"	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.128delA	chr17.hg19:g.18217965delT	ENSP00000321636:p.Asn43fs	132.0	0.0		156.0	13.0	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Frame_Shift_Del	DEL	ENST00000321105.5	hg19	CCDS11194.1																																																																																			.	.		0.652	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			-	18217965	T	-	18217965	7	5	112	1	0	1	0	1	0	0	0	0	16382	1725	60	0	2953	0	TOP3A	17	18217965	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	140816	18217965	62977245	987	17608										
SMCR8	140775	hgsc.bcm.edu	37	chr17	18221365	18221365	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actgcactggctatctttgtCcccagctatggctgctacgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:18221365delC	ENST00000406438.3	+	1	2742	c.2262delC	c.(2260-2262)gtcfs	p.V754fs		NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	754						nucleus (GO:0005634)		p.V754V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						CTATCTTTGTCCCCAGCTATG	0.532																																					p.V754fs		Atlas-INDEL	.											.	SMCR8	62	.	1	Substitution - coding silent(1)	lung(1)	c.2261delT						.						129	108	115					17																	18221365		2203	4300	6503	SO:0001589	frameshift_variant	140775	exon1			.	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.2262delC	chr17.hg19:g.18221365delC	ENSP00000385025:p.Val754fs	113.0	0.0		147.0	12.0	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Frame_Shift_Del	DEL	ENST00000406438.3	hg19	CCDS11195.2																																																																																			.	.		0.532	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		-	18221365	C	-	18221365	7	5	112	1	0	1	0	1	0	0	0	0	14807	842	30	0	2264	0	SMCR8	17	18221365	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	3400	18221365	62973845	988	17609										
ZNF286B	729288	hgsc.bcm.edu	37	chr17	18566149	18566149	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtttgatttttgtttcaagcTtttttcaagtgtatggaagg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:18566149delT	ENST00000545289.1	-	5	920	c.670delA	c.(670-672)agcfs	p.S224fs	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	224					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						TGTTTCAAGCTTTTTTCAAGT	0.348																																					p.S224fs		Atlas-INDEL	.											.	ZNF286B	75	.	0			c.671delG						.						8	7	7					17																	18566149		683	1545	2228	SO:0001589	frameshift_variant	729288	exon5			.		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"Zinc fingers, C2H2-type"	33241	protein-coding gene	gene with protein product	"zinc finger protein 590"		"zinc finger protein 286-like", "zinc finger 286C pseudogene"	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.670delA	chr17.hg19:g.18566149delT	ENSP00000461413:p.Ser224fs	233.0	0.0		220.0	14.0	NM_001145045		Frame_Shift_Del	DEL	ENST00000545289.1	hg19	CCDS58523.1																																																																																			.	.		0.348	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047		-	18566149	T	-	18566149	7	5	112	1	0	1	0	1	0	0	0	0	17839	1609	56	0	902	0	ZNF286B	17	18566149	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	344784	18566149	62629061	989	17610										
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19451395	19451395	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccctgctgggcgctctttcTcaacacccagcacatcctgc	7	19	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:19451395T>C	ENST00000270570.4	+	4	490	c.404T>C	c.(403-405)cTc>cCc	p.L135P	SLC47A1_ENST00000571335.1_5'UTR|SLC47A1_ENST00000584348.1_3'UTR|SLC47A1_ENST00000457293.1_Missense_Mutation_p.L135P|SLC47A1_ENST00000395585.1_Missense_Mutation_p.L135P|SLC47A1_ENST00000575023.1_Missense_Mutation_p.L135P|SLC47A1_ENST00000436810.2_Missense_Mutation_p.L112P|SLC47A1_ENST00000542886.1_Missense_Mutation_p.L135P	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	135					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	GCGCTCTTTCTCAACACCCAG	0.617																																					p.L135P		Atlas-SNP	.											.	SLC47A1	55	.	0			c.T404C						.						114	93	100					17																	19451395		2203	4300	6503	SO:0001583	missense	55244	exon4			TCTTTCTCAACAC		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"Solute carriers"	25588	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 1"	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.404T>C	chr17.hg19:g.19451395T>C	ENSP00000270570:p.Leu135Pro	77.0	0.0		95.0	4.0	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	hg19	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.127766	0.77549	.	.	ENSG00000142494	ENST00000436810;ENST00000270570;ENST00000457293;ENST00000542886;ENST00000395585	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	4.99	4.99	0.66335	.	0.285709	0.37219	N	0.002181	T	0.59335	0.2186	M	0.76002	2.32	0.54753	D	0.999981	D;D;D;D	0.69078	0.997;0.997;0.993;0.982	D;D;D;P	0.73380	0.98;0.974;0.976;0.891	T	0.64698	-0.6346	10	0.87932	D	0	-12.738	13.8392	0.63428	0.0:0.0:0.0:1.0	.	112;135;135;135	E7EX57;B4DYV3;Q96FL8;Q96FL8-3	.;.;S47A1_HUMAN;.	P	112;135;135;135;135	ENSP00000407155:L112P;ENSP00000270570:L135P;ENSP00000415586:L135P;ENSP00000440435:L135P;ENSP00000378951:L135P	ENSP00000270570:L135P	L	+	2	0	SLC47A1	19391987	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	7.403000	0.79983	1.879000	0.54435	0.379000	0.24179	CTC	.	.		0.617	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		C	19451395	T	C	19451395	3	2	112	1	0	0	0	0	1	0	0	0	14662	1551	54	2	418	2	SLC47A1	17	19451395	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	885246	19451395	61743815	990	17611										
SLC47A2	146802	hgsc.bcm.edu	37	chr17	19583316	19583316	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctggttgcagtgctctctgCtctctgctgctgctgccggc	12	14	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:19583316C>A	ENST00000325411.5	-	16	1587	c.1537G>T	c.(1537-1539)Gca>Tca	p.A513S	SLC47A2_ENST00000350657.5_Missense_Mutation_p.A491S|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	513					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	GTGCTCTCTGCTCTCTGCTGC	0.493																																					p.A513S		Atlas-SNP	.											.	SLC47A2	61	.	0			c.G1537T						.						107	89	95					17																	19583316		2203	4300	6503	SO:0001583	missense	146802	exon16			TCTCTGCTCTCTG	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"Solute carriers"	26439	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 2"	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.1537G>T	chr17.hg19:g.19583316C>A	ENSP00000326671:p.Ala513Ser	64.0	0.0		86.0	28.0	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Missense_Mutation	SNP	ENST00000325411.5	hg19	CCDS11211.1	.	.	.	.	.	.	.	.	.	.	C	4.854	0.158712	0.09236	.	.	ENSG00000180638	ENST00000350657;ENST00000325411	T;T	0.29397	1.57;1.59	4.04	-8.08	0.01094	.	2.099700	0.02651	U	0.106463	T	0.12008	0.0292	N	0.14661	0.345	0.09310	N	1	B;B;B	0.24186	0.099;0.037;0.001	B;B;B	0.25405	0.06;0.048;0.002	T	0.24584	-1.0156	10	0.06891	T	0.86	1.1802	1.9074	0.03280	0.2094:0.2109:0.1039:0.4758	.	477;491;513	Q86VL8-3;Q86VL8-4;Q86VL8	.;.;S47A2_HUMAN	S	491;513	ENSP00000338084:A491S;ENSP00000326671:A513S	ENSP00000326671:A513S	A	-	1	0	SLC47A2	19523908	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.977000	0.01495	-2.180000	0.00766	-0.251000	0.11542	GCA	.	.		0.493	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908		A	19583316	C	A	19583316	3	1	112	1	0	0	0	0	1	0	0	0	14663	797	28	3	279	3	SLC47A2	17	19583316	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	131921	19583316	61611894	991	17612										
FOXN1	8456	hgsc.bcm.edu	37	chr17	26857795	26857795	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcttcatggcccttaagaacAgtaaaactgggagccttccc	8	12	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:26857795A>G	ENST00000226247.2	+	5	888	c.859A>G	c.(859-861)Agt>Ggt	p.S287G	FOXN1_ENST00000579795.1_Missense_Mutation_p.S287G	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	287					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					CCTTAAGAACAGTAAAACTGG	0.537																																					p.S287G		Atlas-SNP	.											.	FOXN1	51	.	0			c.A859G						.						104	101	102					17																	26857795		2203	4300	6503	SO:0001583	missense	8456	exon5			AAGAACAGTAAAA	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"Forkhead boxes"	12765	protein-coding gene	gene with protein product		600838	"winged-helix nude", "Rowett nude"	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.859A>G	chr17.hg19:g.26857795A>G	ENSP00000226247:p.Ser287Gly	143.0	0.0		158.0	9.0	NM_003593	B2R9Q7|O15352	Missense_Mutation	SNP	ENST00000226247.2	hg19	CCDS11232.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.006365	0.93287	.	.	ENSG00000109101	ENST00000226247	D	0.96554	-4.05	5.84	5.84	0.93424	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.98707	0.9566	H	0.95645	3.7	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	D	0.99719	1.1009	10	0.87932	D	0	.	16.2045	0.82114	1.0:0.0:0.0:0.0	.	287	O15353	FOXN1_HUMAN	G	287	ENSP00000226247:S287G	ENSP00000226247:S287G	S	+	1	0	FOXN1	23881922	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.339000	0.96797	2.234000	0.73211	0.459000	0.35465	AGT	.	.		0.537	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1			G	26857795	A	G	26857795	3	3	112	1	0	0	0	0	1	0	0	0	6027	188	7	2	877	2	FOXN1	17	26857795	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	7274479	26857795	54337415	992	17613										
ERAL1	26284	hgsc.bcm.edu	37	chr17	27182148	27182148	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcgagggagcgggtgatcccTttttcctcactcttaggctt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:27182148delT	ENST00000254928.5	+	1	193	c.96delT	c.(94-96)cctfs	p.P32fs	ERAL1_ENST00000578001.1_3'UTR|FAM222B_ENST00000583953.1_5'Flank	NM_005702.2	NP_005693.1	O75616	ERAL1_HUMAN	Era-like 12S mitochondrial rRNA chaperone 1	32					ribosomal small subunit assembly (GO:0000028)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	11	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.12e-05)|all cancers(11;5.32e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.105)			GGGTGATCCCTTTTTCCTCAC	0.627																																					p.P32fs		Atlas-INDEL	.											ERAL1,NS,carcinoma,0,1	ERAL1	28	.	0			c.95delC						.						89	77	81					17																	27182148		2203	4300	6503	SO:0001589	frameshift_variant	26284	exon1			.	AF082657	CCDS11244.1	17q11.2	2013-05-22	2013-05-22		ENSG00000132591	ENSG00000132591			3424	protein-coding gene	gene with protein product		607435	"Era (E. coli G-protein homolog)-like 1", "Era G-protein-like 1 (E. coli)"			10945472, 20604745	Standard	NM_005702		Approved	HERA-B	uc002hcy.1	O75616	OTTHUMG00000132675	ENST00000254928.5:c.96delT	chr17.hg19:g.27182148delT	ENSP00000254928:p.Pro32fs	115.0	0.0		175.0	11.0	NM_005702	B3KN21|C9JEC6|O75617|Q8WUY4|Q96LE2|Q96TC0	Frame_Shift_Del	DEL	ENST00000254928.5	hg19	CCDS11244.1																																																																																			.	.		0.627	ERAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255937.2			-	27182148	T	-	27182148	7	5	112	1	0	1	0	1	0	0	0	0	5204	1596	56	0	98	0	ERAL1	17	27182148	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	324353	27182148	54013062	993	17614										
TAOK1	57551	hgsc.bcm.edu	37	chr17	27805327	27805327	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attacacatggtgctcttcaGggattagcctacttacattc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:27805327delG	ENST00000261716.3	+	6	930	c.411delG	c.(409-411)cagfs	p.Q137fs	TAOK1_ENST00000536202.1_Frame_Shift_Del_p.Q137fs	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	137	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|execution phase of apoptosis (GO:0097194)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of cytoskeleton organization (GO:0051493)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28			Colorectal(6;0.198)			GTGCTCTTCAGGGATTAGCCT	0.299																																					p.Q137fs		Atlas-INDEL	.											.	TAOK1	151	.	0			c.410delA						.						109	114	112					17																	27805327		2203	4290	6493	SO:0001589	frameshift_variant	57551	exon6			.	AB037782	CCDS32601.1, CCDS56024.1	17q11.2	2014-01-28				ENSG00000160551			29259	protein-coding gene	gene with protein product		610266				10718198, 14517247	Standard	NM_020791		Approved	KIAA1361, MARKK, PSK2, MAP3K16, FLJ14314, TAO1	uc002hdz.2	Q7L7X3		ENST00000261716.3:c.411delG	chr17.hg19:g.27805327delG	ENSP00000261716:p.Gln137fs	213.0	0.0		234.0	15.0	NM_025142	A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Frame_Shift_Del	DEL	ENST00000261716.3	hg19	CCDS32601.1																																																																																			.	.		0.299	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791		-	27805327	G	-	27805327	7	5	112	1	0	1	0	1	0	0	0	0	15562	991	35	0	429	0	TAOK1	17	27805327	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	623179	27805327	53389883	994	17615										
SSH2	85464	hgsc.bcm.edu	37	chr17	27959313	27959313	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggacagtgagccagcctcagAcccactgtatttccctttgc	9	14	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:27959313A>G	ENST00000269033.3	-	15	2969	c.2818T>C	c.(2818-2820)Tct>Cct	p.S940P	RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Missense_Mutation_p.S967P	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	940					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCAGCCTCAGACCCACTGTAT	0.532																																					p.S940P		Atlas-SNP	.											.	SSH2	107	.	0			c.T2818C						.						136	135	136					17																	27959313		2203	4300	6503	SO:0001583	missense	85464	exon15			CCTCAGACCCACT	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.2818T>C	chr17.hg19:g.27959313A>G	ENSP00000269033:p.Ser940Pro	63.0	0.0		98.0	4.0	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	hg19	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	A	1.170	-0.641203	0.03557	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.10477	2.87;2.87	5.47	-4.85	0.03142	.	0.751587	0.12524	N	0.461421	T	0.07683	0.0193	L	0.60455	1.87	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.37174	-0.9717	10	0.24483	T	0.36	-0.0038	2.7204	0.05199	0.37:0.2765:0.2626:0.0909	.	967;940	F5H527;Q76I76	.;SSH2_HUMAN	P	940;967	ENSP00000269033:S940P;ENSP00000444743:S967P	ENSP00000269033:S940P	S	-	1	0	SSH2	24983439	0.000000	0.05858	0.030000	0.17652	0.234000	0.25298	-0.060000	0.11712	-0.938000	0.03714	-1.139000	0.01908	TCT	.	.		0.532	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		G	27959313	A	G	27959313	3	3	112	1	0	0	0	0	1	0	0	0	15200	275	10	2	1457	2	SSH2	17	27959313	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	153986	27959313	53235897	995	17616										
CPD	1362	hgsc.bcm.edu	37	chr17	28791765	28791765	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taccggctccaagaagtcccTcctaagccatgagttccagg	9	14	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:28791765T>C	ENST00000225719.4	+	21	4152	c.4076T>C	c.(4075-4077)cTc>cCc	p.L1359P	CPD_ENST00000543464.2_Missense_Mutation_p.L1112P	NM_001304.4	NP_001295.2	O75976	CBPD_HUMAN	carboxypeptidase D	1359						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metallocarboxypeptidase activity (GO:0004181)|serine-type carboxypeptidase activity (GO:0004185)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						AAGAAGTCCCTCCTAAGCCAT	0.413																																					p.L1359P		Atlas-SNP	.											.	CPD	89	.	0			c.T4076C						.						147	139	142					17																	28791765		2203	4300	6503	SO:0001583	missense	1362	exon21			AGTCCCTCCTAAG	U65090	CCDS11257.1, CCDS56025.1	17q11.2	2012-02-10			ENSG00000108582	ENSG00000108582	3.4.17.22		2301	protein-coding gene	gene with protein product	"metallocarboxypeptidase D"	603102				9628828, 9355738	Standard	NM_001304		Approved	GP180	uc002hfb.2	O75976	OTTHUMG00000132797	ENST00000225719.4:c.4076T>C	chr17.hg19:g.28791765T>C	ENSP00000225719:p.Leu1359Pro	80.0	0.0		97.0	6.0	NM_001304	B7Z7T9|B7ZAU4|F5GZH6|O15377|Q86SH9|Q86XE6	Missense_Mutation	SNP	ENST00000225719.4	hg19	CCDS11257.1	.	.	.	.	.	.	.	.	.	.	T	16.26	3.074156	0.55646	.	.	ENSG00000108582	ENST00000225719;ENST00000543464	T;T	0.25250	1.81;2.93	5.6	5.6	0.85130	.	1.657100	0.02876	N	0.132188	T	0.42404	0.1201	N	0.14661	0.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.05683	-1.0870	10	0.87932	D	0	-22.1691	15.0117	0.71555	0.0:0.0:0.0:1.0	.	1112;1359	F5GZH6;O75976	.;CBPD_HUMAN	P	1359;1112	ENSP00000225719:L1359P;ENSP00000444443:L1112P	ENSP00000225719:L1359P	L	+	2	0	CPD	25815891	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.282000	0.78630	2.118000	0.64928	0.529000	0.55759	CTC	.	.		0.413	CPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256214.3	NM_001304		C	28791765	T	C	28791765	3	2	112	1	0	0	0	0	1	0	0	0	3800	1551	54	2	4158	2	CPD	17	28791765	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	832452	28791765	52403445	996	17617										
ACCN1	40	hgsc.bcm.edu	37	chr17	31439005	31439005	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atctccagcccgttgcctgtCccccccttgaccgtggtgag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:31439005delC	ENST00000359872.6	-	2	1397	c.636delG	c.(634-636)gggfs	p.G212fs	RP11-40A13.1_ENST00000584688.1_RNA|ASIC2_ENST00000448983.1_5'UTR|ASIC2_ENST00000225823.2_Frame_Shift_Del_p.G263fs	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	212					central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	CGTTGCCTGTCCCCCCCTTGA	0.552																																					p.T264fs		Atlas-INDEL	.											.,2	.	.	.	0			c.790delA						.						146	120	129					17																	31439005		2203	4300	6503	SO:0001589	frameshift_variant	40	exon2			.	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.636delG	chr17.hg19:g.31439005delC	ENSP00000352934:p.Gly212fs	146.0	0.0		153.0	10.0	NM_183377	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Frame_Shift_Del	DEL	ENST00000359872.6	hg19	CCDS42296.1																																																																																			.	.		0.552	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		-	31439005	C	-	31439005	7	5	112	1	0	1	0	1	0	0	0	0	128	842	30	0	938	0	ACCN1	17	31439005	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	2647240	31439005	49756205	997	17618										
NLE1	54475	hgsc.bcm.edu	37	chr17	33460449	33460449	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cactgctgccgctgaccaggAgccgactgtcagctgaccac	11	16	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:33460449A>G	ENST00000442241.4	-	11	1322	c.1283T>C	c.(1282-1284)cTc>cCc	p.L428P	NLE1_ENST00000360831.5_Missense_Mutation_p.L386P|NLE1_ENST00000586869.1_Missense_Mutation_p.L136P	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	428					hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				GCTGACCAGGAGCCGACTGTC	0.617																																					p.L428P		Atlas-SNP	.											.	NLE1	42	.	0			c.T1283C						.						41	36	38					17																	33460449		2203	4300	6503	SO:0001583	missense	54475	exon11			ACCAGGAGCCGAC		CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"WD repeat domain containing"	19889	protein-coding gene	gene with protein product	"Notchless gene homolog, (Drosophila)"						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.1283T>C	chr17.hg19:g.33460449A>G	ENSP00000413572:p.Leu428Pro	97.0	0.0		102.0	6.0	NM_018096	O60868|Q59GJ8|Q9BU54	Missense_Mutation	SNP	ENST00000442241.4	hg19	CCDS11291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.5|23.5	4.428386|4.428386	0.83667|0.83667	.|.	.|.	ENSG00000073536|ENSG00000073536	ENST00000442241;ENST00000360831;ENST00000537697|ENST00000436188	T|.	0.63255|.	-0.03|.	5.14|5.14	5.14|5.14	0.70334|0.70334	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86176|0.86176	0.5870|0.5870	H|H	0.95402|0.95402	3.665|3.665	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.997;1.0|.	D|D	0.89897|0.89897	0.4041|0.4041	10|5	0.72032|.	D|.	0.01|.	-15.3864|-15.3864	12.9593|12.9593	0.58449|0.58449	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	404;428|.	B4E074;Q9NVX2|.	.;NLE1_HUMAN|.	P|P	428;136;404|247	ENSP00000413572:L428P|.	ENSP00000354075:L136P|.	L|S	-|-	2|1	0|0	NLE1|NLE1	30484562|30484562	1.000000|1.000000	0.71417|0.71417	0.922000|0.922000	0.36590|0.36590	0.987000|0.987000	0.75469|0.75469	8.531000|8.531000	0.90610|0.90610	2.144000|2.144000	0.66660|0.66660	0.460000|0.460000	0.39030|0.39030	CTC|TCC	.	.		0.617	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096		G	33460449	A	G	33460449	3	3	112	1	0	0	0	0	1	0	0	0	10469	304	11	2	186	2	NLE1	17	33460449	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2021444	33460449	47734761	998	17619										
SLFN13	146857	hgsc.bcm.edu	37	chr17	33772591	33772591	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctctcttggtctctctgagTtttctgtagcttttttctgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:33772591delT	ENST00000285013.6	-	3	384	c.109delA	c.(109-111)actfs	p.T37fs	SLFN13_ENST00000542635.1_Frame_Shift_Del_p.T37fs|SLFN13_ENST00000360502.2_Intron|SLFN13_ENST00000526861.1_Frame_Shift_Del_p.T37fs|SLFN13_ENST00000534689.1_Intron|SLFN13_ENST00000533791.1_Frame_Shift_Del_p.T37fs	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	37						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TCTCTCTGAGTTTTCTGTAGC	0.483																																					p.T37fs		Atlas-INDEL	.											.	SLFN13	79	.	0			c.110delC						.						98	97	97					17																	33772591		2203	4300	6503	SO:0001589	frameshift_variant	146857	exon3			.	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.109delA	chr17.hg19:g.33772591delT	ENSP00000285013:p.Thr37fs	188.0	0.0		174.0	11.0	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Frame_Shift_Del	DEL	ENST00000285013.6	hg19	CCDS32620.1																																																																																			.	.		0.483	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		-	33772591	T	-	33772591	7	5	112	1	0	1	0	1	0	0	0	0	14751	1725	60	0	2600	0	SLFN13	17	33772591	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	312142	33772591	47422619	999	17620										
SLFN12L	100506736	hgsc.bcm.edu	37	chr17	33806378	33806378	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caggcagtttcccaatggaaTtttttgttacttcttctaac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:33806378delT	ENST00000260908.7	-	2	968	c.851delA	c.(850-852)aatfs	p.N284fs	SLFN12L_ENST00000449046.1_Frame_Shift_Del_p.N315fs|RP11-686D22.9_ENST00000587076.1_RNA|SLFN12L_ENST00000361112.4_Frame_Shift_Del_p.N313fs	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	284						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						CCCAATGGAATTTTTTGTTAC	0.353																																					p.N284fs		Atlas-INDEL	.											.	SLFN12L	140	.	0			c.852delT						.						126	104	110					17																	33806378		692	1591	2283	SO:0001589	frameshift_variant	100506736	exon2			.	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.851delA	chr17.hg19:g.33806378delT	ENSP00000437635:p.Asn284fs	140.0	0.0		157.0	10.0	NM_001195790	F5H6G3	Frame_Shift_Del	DEL	ENST00000260908.7	hg19	CCDS56026.1																																																																																			.	.		0.353	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206		-	33806378	T	-	33806378	7	5	112	1	0	1	0	1	0	0	0	0	14750	1493	52	0	927	0	SLFN12L	17	33806378	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	33787	33806378	47388832	1000	17621										
LHX1	3975	hgsc.bcm.edu	37	chr17	35300095	35300095	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggggcaactacgacttcttCccgcaaggccccccgtcctc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:35300095delC	ENST00000254457.5	+	5	2299	c.888delC	c.(886-888)ttcfs	p.F296fs	RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	296					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				ACGACTTCTTCCCGCAAGGCC	0.731																																					p.F296fs		Atlas-INDEL	.											.	LHX1	48	.	0			c.887delT						.						15	17	16					17																	35300095		2199	4296	6495	SO:0001589	frameshift_variant	3975	exon5			.	U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"Homeoboxes / LIM class"	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.888delC	chr17.hg19:g.35300095delC	ENSP00000254457:p.Phe296fs	119.0	0.0		153.0	10.0	NM_005568	Q3MIW0	Frame_Shift_Del	DEL	ENST00000254457.5	hg19	CCDS11316.1																																																																																			.	.		0.731	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3	NM_005568		-	35300095	C	-	35300095	7	5	112	1	0	1	0	1	0	0	0	0	8779	854	30	0	906	0	LHX1	17	35300095	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1493717	35300095	45895115	1001	17622										
THRA	7067	hgsc.bcm.edu	37	chr17	38230771	38230771	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagccaagcaaggtggagtgTgggtcagacccagaggagaa	16	7	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:38230771T>C	ENST00000264637.4	+	2	610	c.30T>C	c.(28-30)tgT>tgC	p.C10C	THRA_ENST00000546243.1_Silent_p.C10C|THRA_ENST00000394121.4_Silent_p.C10C|THRA_ENST00000450525.2_Silent_p.C10C|THRA_ENST00000584985.1_Silent_p.C10C	NM_003250.5	NP_003241.2	P10827	THA_HUMAN	thyroid hormone receptor, alpha	10	Modulating.				cartilage condensation (GO:0001502)|cytoplasmic sequestering of transcription factor (GO:0042994)|erythrocyte differentiation (GO:0030218)|female courtship behavior (GO:0008050)|gene expression (GO:0010467)|hormone-mediated signaling pathway (GO:0009755)|learning or memory (GO:0007611)|negative regulation of DNA-templated transcription, initiation (GO:2000143)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of female receptivity (GO:0045925)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|regulation of lipid catabolic process (GO:0050994)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cold (GO:0009409)|thyroid gland development (GO:0030878)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Type I pneumocyte differentiation (GO:0060509)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|steroid receptor RNA activator RNA binding (GO:0002153)|TBP-class protein binding (GO:0017025)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)	11	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)			Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	AGGTGGAGTGTGGGTCAGACC	0.582																																					p.C10C		Atlas-SNP	.											.	THRA	88	.	0			c.T30C						.						191	161	171					17																	38230771		2203	4300	6503	SO:0001819	synonymous_variant	7067	exon2			GGAGTGTGGGTCA	J03239	CCDS11360.1, CCDS42316.1, CCDS58546.1	17q21.1	2013-01-16	2011-05-19		ENSG00000126351	ENSG00000126351		"Nuclear hormone receptors"	11796	protein-coding gene	gene with protein product		190120	"thyroid hormone receptor, alpha (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog)", "thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian)"	THRA1, THRA2, ERBA1		6323162, 6589608	Standard	NM_003250		Approved	EAR-7.1/EAR-7.2, THRA3, AR7, ERBA, NR1A1	uc002htw.3	P10827	OTTHUMG00000133332	ENST00000264637.4:c.30T>C	chr17.hg19:g.38230771T>C		83.0	0.0		117.0	6.0	NM_001190918	A8K3B5|P21205|Q8N6A1|Q96H73	Silent	SNP	ENST00000264637.4	hg19	CCDS11360.1																																																																																			.	.		0.582	THRA-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257160.2			C	38230771	T	C	38230771	2	2	112	1	0	0	0	0	0	0	0	1	15888	1702	59	2		2	THRA	17	38230771	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2930676	38230771	42964439	1002	17623										
WIPF2	147179	hgsc.bcm.edu	37	chr17	38430226	38430226	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggaatggccacagagattcTatcaccactgtccggtcttt	9	11	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:38430226T>C	ENST00000323571.4	+	6	1395	c.1155T>C	c.(1153-1155)tcT>tcC	p.S385S	WIPF2_ENST00000585043.1_Silent_p.S385S|WIPF2_ENST00000536600.1_Silent_p.S127S|WIPF2_ENST00000394103.3_Silent_p.S127S|WIPF2_ENST00000583130.1_Silent_p.S385S|WIPF2_ENST00000494757.1_3'UTR	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	385					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						ACAGAGATTCTATCACCACTG	0.602										HNSCC(43;0.11)																											p.S385S		Atlas-SNP	.											.	WIPF2	55	.	0			c.T1155C						.						136	114	121					17																	38430226		2203	4300	6503	SO:0001819	synonymous_variant	147179	exon6			AGATTCTATCACC	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.1155T>C	chr17.hg19:g.38430226T>C		52.0	0.0		68.0	24.0	NM_133264	A8K0L3|Q658J8|Q71RE1|Q8TE44	Silent	SNP	ENST00000323571.4	hg19	CCDS11364.1																																																																																			.	.		0.602	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264		C	38430226	T	C	38430226	2	2	112	1	0	0	0	0	0	0	0	1	17383	1509	53	2		2	WIPF2	17	38430226	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	199455	38430226	42764984	1003	17624										
KRT20	54474	hgsc.bcm.edu	37	chr17	39041106	39041106	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtagtcgcgaccagccctcGgggcgttggtttcgtaccac					rs547778667		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:39041106delG	ENST00000167588.3	-	1	373	c.332delC	c.(331-333)ccgfs	p.P111fs		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	111	Linker 1.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)	p.P111Q(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				ACCAGCCCTCGGGGCGTTGGT	0.498																																					p.P111fs		Atlas-INDEL	.											.	KRT20	38	.	1	Substitution - Missense(1)	lung(1)	c.333delG						.						98	92	94					17																	39041106		2203	4300	6503	SO:0001589	frameshift_variant	54474	exon1			.	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"-", "Intermediate filaments type I, keratins (acidic)"	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.332delC	chr17.hg19:g.39041106delG	ENSP00000167588:p.Pro111fs	172.0	0.0		157.0	10.0	NM_019010	B2R6W7	Frame_Shift_Del	DEL	ENST00000167588.3	hg19	CCDS11379.1																																																																																			.	.		0.498	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2			-	39041106	G	-	39041106	7	5	112	1	0	1	0	1	0	0	0	0	8467	1116	39	0	974	0	KRT20	17	39041106	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	610880	39041106	42154104	1004	17625										
KRT16	3868	hgsc.bcm.edu	37	chr17	39766478	39766478	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggattggccagatgcttgctGggaggaaaggctgtgggaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:39766478delG	ENST00000301653.4	-	7	1355	c.1291delC	c.(1291-1293)cagfs	p.Q432fs		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	432	Tail.				aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				GATGCTTGCTGGGAGGAAAGG	0.617																																					p.Q431fs		Atlas-INDEL	.											.	KRT16	45	.	0			c.1292delA						.						39	41	40					17																	39766478		2203	4300	6503	SO:0001589	frameshift_variant	3868	exon7			.	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"-", "Intermediate filaments type I, keratins (acidic)"	6423	protein-coding gene	gene with protein product	"focal non-epidermolytic palmoplantar keratoderma"	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.1291delC	chr17.hg19:g.39766478delG	ENSP00000301653:p.Gln432fs	187.0	0.0		173.0	11.0	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Frame_Shift_Del	DEL	ENST00000301653.4	hg19	CCDS11401.1																																																																																			.	.		0.617	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557		-	39766478	G	-	39766478	7	5	112	1	0	1	0	1	0	0	0	0	8462	1357	47	0	138	0	KRT16	17	39766478	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	725372	39766478	41428732	1005	17626										
EZH1	2145	hgsc.bcm.edu	37	chr17	40860046	40860046	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caggggcaggtgctgtcacaGgggcggtctgggtggtcgca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:40860046delG	ENST00000428826.2	-	15	1711	c.1590delC	c.(1588-1590)cccfs	p.P530fs	EZH1_ENST00000590783.1_5'UTR|EZH1_ENST00000415827.2_Frame_Shift_Del_p.P521fs|EZH1_ENST00000590078.1_Frame_Shift_Del_p.P460fs|EZH1_ENST00000592743.1_Frame_Shift_Del_p.P530fs|EZH1_ENST00000435174.1_Frame_Shift_Del_p.P391fs|EZH1_ENST00000585893.1_Frame_Shift_Del_p.P490fs			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	530	CXC. {ECO:0000255|PROSITE- ProRule:PRU00970}.|Cys-rich.				anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)			breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		TGCTGTCACAGGGGCGGTCTG	0.498																																					p.C531fs		Atlas-INDEL	.											.	EZH1	62	.	0			c.1591delT						.						149	137	141					17																	40860046		2203	4300	6503	SO:0001589	frameshift_variant	2145	exon15			.		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.1590delC	chr17.hg19:g.40860046delG	ENSP00000404658:p.Pro530fs	98.0	0.0		161.0	10.0	NM_001991	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Frame_Shift_Del	DEL	ENST00000428826.2	hg19	CCDS32659.1																																																																																			.	.		0.498	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		-	40860046	G	-	40860046	7	5	112	1	0	1	0	1	0	0	0	0	5335	987	35	0	681	0	EZH1	17	40860046	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1093568	40860046	40335164	1006	17627										
AARSD1	80755	hgsc.bcm.edu	37	chr17	41113229	41113229	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgaatgctgctgcatgtggTcaaacctccgctcccaatct	8	14	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:41113229T>C	ENST00000427569.2	-	3	346	c.311A>G	c.(310-312)gAc>gGc	p.D104G	AARSD1_ENST00000416949.1_5'UTR|PTGES3L-AARSD1_ENST00000421990.2_Missense_Mutation_p.D278G|PTGES3L-AARSD1_ENST00000409399.1_Missense_Mutation_p.D278G|PTGES3L-AARSD1_ENST00000360221.4_Missense_Mutation_p.D217G|PTGES3L-AARSD1_ENST00000409103.1_Missense_Mutation_p.D187G	NM_001261434.1	NP_001248363.1	Q9BTE6	AASD1_HUMAN	alanyl-tRNA synthetase domain containing 1	104					alanyl-tRNA aminoacylation (GO:0006419)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	alanine-tRNA ligase activity (GO:0004813)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|Ser-tRNA(Ala) hydrolase activity (GO:0002196)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|skin(1)	17		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		CTGCATGTGGTCAAACCTCCG	0.562																																					p.D278G		Atlas-SNP	.											.	PTGES3L-AARSD1	15	.	0			c.A833G						.						232	221	225					17																	41113229		2203	4300	6503	SO:0001583	missense	100885850	exon8			ATGTGGTCAAACC	BC004172	CCDS11447.1, CCDS45691.1, CCDS58552.1	17q21.31	2012-10-05			ENSG00000266967	ENSG00000266967			28417	protein-coding gene	gene with protein product		613212					Standard	NM_001261434		Approved	MGC2744		Q9BTE6	OTTHUMG00000153515	ENST00000427569.2:c.311A>G	chr17.hg19:g.41113229T>C	ENSP00000400870:p.Asp104Gly	114.0	0.0		156.0	8.0	NM_001136042	B4DI73	Missense_Mutation	SNP	ENST00000427569.2	hg19	CCDS58552.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.8|24.8	4.565951|4.565951	0.86439|0.86439	.|.	.|.	ENSG00000108825|ENSG00000108825	ENST00000360221;ENST00000409399;ENST00000421990;ENST00000427569;ENST00000409103|ENST00000441280;ENST00000430739	T;T|.	0.50548|.	0.74;0.74|.	4.18|4.18	4.18|4.18	0.49190|0.49190	Alanyl-tRNA synthetase, class IIc, core domain (1);Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80722|0.80722	0.4677|0.4677	M|M	0.91459|0.91459	3.21|3.21	.|.	.|.	.|.	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	0.999;0.999;1.0;0.999;1.0|.	D|D	0.87911|0.87911	0.2697|0.2697	9|4	0.41790|.	T|.	0.15|.	-22.4336|-22.4336	13.4037|13.4037	0.60898|0.60898	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	217;278;187;235;104|.	Q9BTE6-2;B4DI73;C9J5N1;B3KSP9;Q9BTE6|.	.;.;.;.;AASD1_HUMAN|.	G|A	217;278;278;104;187|110	ENSP00000386621:D278G;ENSP00000409924:D278G|.	ENSP00000353355:D217G|.	D|T	-|-	2|1	0|0	AARSD1|AARSD1	38366755|38366755	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.688000|7.688000	0.84153|0.84153	1.752000|1.752000	0.51891|0.51891	0.443000|0.443000	0.29094|0.29094	GAC|ACC	.	.		0.562	AARSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467729.1	NM_001261434		C	41113229	T	C	41113229	3	2	112	1	0	0	0	0	1	0	0	0	21	1667	58	2	967	2	AARSD1	17	41113229	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	253183	41113229	40081981	1007	17628										
DHX8	1659	hgsc.bcm.edu	37	chr17	41582118	41582118	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcaacaaagcctcttacggAaaaaagacccagatgtcaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:41582118delA	ENST00000262415.3	+	12	1725	c.1653delA	c.(1651-1653)ggafs	p.G551fs	DHX8_ENST00000540306.1_Frame_Shift_Del_p.G551fs	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	551					ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		CCTCTTACGGAAAAAAGACCC	0.478																																					p.G551fs	NSCLC(56;1548 1661 49258 49987)	Atlas-INDEL	.											.	DHX8	98	.	0			c.1652delG						.						126	128	127					17																	41582118		2203	4300	6503	SO:0001589	frameshift_variant	1659	exon12			.	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"DEAH-boxes"	2749	protein-coding gene	gene with protein product		600396	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.1653delA	chr17.hg19:g.41582118delA	ENSP00000262415:p.Gly551fs	82.0	0.0		117.0	10.0	NM_004941		Frame_Shift_Del	DEL	ENST00000262415.3	hg19	CCDS11464.1																																																																																			.	.		0.478	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			-	41582118	A	-	41582118	7	5	112	1	0	1	0	1	0	0	0	0	4517	233	9	0	1699	0	DHX8	17	41582118	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	468889	41582118	39613092	1008	17629										
DHX8	1659	hgsc.bcm.edu	37	chr17	41582144	41582144	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gacccagatgtcaatccttgAgcagagggagagcctgccca	12	12	1	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:41582144A>G	ENST00000262415.3	+	12	1751	c.1679A>G	c.(1678-1680)gAg>gGg	p.E560G	DHX8_ENST00000540306.1_Missense_Mutation_p.E560G	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	560					ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		TCAATCCTTGAGCAGAGGGAG	0.463																																					p.E560G	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.A1679G						.						108	107	107					17																	41582144		2203	4300	6503	SO:0001583	missense	1659	exon12			TCCTTGAGCAGAG	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"DEAH-boxes"	2749	protein-coding gene	gene with protein product		600396	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.1679A>G	chr17.hg19:g.41582144A>G	ENSP00000262415:p.Glu560Gly	97.0	0.0		116.0	5.0	NM_004941		Missense_Mutation	SNP	ENST00000262415.3	hg19	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.913858	0.72983	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.08634	3.07;3.07	5.36	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.25975	0.0633	M	0.84511	2.7	0.80722	D	1	D;P	0.62365	0.991;0.95	P;P	0.58721	0.844;0.703	T	0.01982	-1.1235	10	0.87932	D	0	.	10.3646	0.44015	0.9228:0.0:0.0772:0.0	.	560;560	F5H658;Q14562	.;DHX8_HUMAN	G	560	ENSP00000437886:E560G;ENSP00000262415:E560G	ENSP00000262415:E560G	E	+	2	0	DHX8	38937670	1.000000	0.71417	0.990000	0.47175	0.557000	0.35523	9.237000	0.95368	0.884000	0.36064	0.454000	0.30748	GAG	.	.		0.463	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			G	41582144	A	G	41582144	3	3	112	1	0	0	0	0	1	0	0	0	4517	304	11	2	1725	2	DHX8	17	41582144	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	26	41582144	39613066	1009	17630										
ATXN7L3	56970	hgsc.bcm.edu	37	chr17	42273429	42273429	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgttttaatgacttggatcTtcgaggggaattggggttct	14	4	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:42273429T>C	ENST00000454077.2	-	6	516	c.517A>G	c.(517-519)Aga>Gga	p.R173G	CTB-175E5.7_ENST00000586560.1_RNA|ATXN7L3_ENST00000593073.1_Intron|ATXN7L3_ENST00000389384.4_Missense_Mutation_p.R166G	NM_020218.1	NP_064603.1			ataxin 7-like 3											kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	12		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GACTTGGATCTTCGAGGGGAA	0.502																																					p.R173G		Atlas-SNP	.											.	ATXN7L3	31	.	0			c.A517G						.						91	89	90					17																	42273429		1852	4093	5945	SO:0001583	missense	56970	exon6			TGGATCTTCGAGG	AK056002	CCDS42345.1, CCDS45697.1	17q21	2010-03-10			ENSG00000087152	ENSG00000087152			25416	protein-coding gene	gene with protein product						15115762	Standard	NM_001098833		Approved	DKFZp761G2113	uc002ifz.3	Q14CW9		ENST00000454077.2:c.517A>G	chr17.hg19:g.42273429T>C	ENSP00000397259:p.Arg173Gly	95.0	0.0		76.0	4.0	NM_020218		Missense_Mutation	SNP	ENST00000454077.2	hg19	CCDS45697.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.674091	0.47781	.	.	ENSG00000087152	ENST00000454077;ENST00000389384	.	.	.	4.95	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.66499	0.2795	L	0.46157	1.445	0.58432	D	0.999999	D;D	0.61080	0.982;0.989	P;D	0.75020	0.715;0.985	T	0.67975	-0.5531	9	0.59425	D	0.04	.	10.5191	0.44907	0.0:0.0:0.1623:0.8377	.	166;173	Q14CW9;Q14CW9-2	AT7L3_HUMAN;.	G	173;166	.	ENSP00000374035:R166G	R	-	1	2	ATXN7L3	39628955	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.526000	0.60566	1.858000	0.53909	0.454000	0.30748	AGA	.	.		0.502	ATXN7L3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457724.1			C	42273429	T	C	42273429	3	2	112	1	0	0	0	0	1	0	0	0	1218	1617	56	2	575	2	ATXN7L3	17	42273429	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	691285	42273429	38921781	1010	17631										
OSBPL7	114881	hgsc.bcm.edu	37	chr17	45888158	45888158	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttgccagaaggcgaagttcTcagactctgcatggcaggcc	12	12	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:45888158T>C	ENST00000007414.3	-	17	1972	c.1781A>G	c.(1780-1782)gAg>gGg	p.E594G	OSBPL7_ENST00000392507.3_Missense_Mutation_p.E594G	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	594					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						GGCGAAGTTCTCAGACTCTGC	0.592																																					p.E594G		Atlas-SNP	.											.	OSBPL7	65	.	0			c.A1781G						.						39	38	38					17																	45888158		2203	4300	6503	SO:0001583	missense	114881	exon17			AAGTTCTCAGACT	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.1781A>G	chr17.hg19:g.45888158T>C	ENSP00000007414:p.Glu594Gly	63.0	0.0		87.0	5.0	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	hg19	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	T	16.38	3.107490	0.56291	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.31510	1.49;1.49	4.49	4.49	0.54785	.	0.235041	0.42294	D	0.000726	T	0.28732	0.0712	L	0.48935	1.535	0.52501	D	0.999959	P	0.34587	0.458	B	0.35413	0.202	T	0.07501	-1.0769	10	0.42905	T	0.14	-22.3097	12.7769	0.57453	0.0:0.0:0.0:1.0	.	594	Q9BZF2	OSBL7_HUMAN	G	594	ENSP00000007414:E594G;ENSP00000376295:E594G	ENSP00000007414:E594G	E	-	2	0	OSBPL7	43243157	0.728000	0.28080	1.000000	0.80357	0.924000	0.55760	2.838000	0.48199	1.650000	0.50662	0.402000	0.26972	GAG	.	.		0.592	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		C	45888158	T	C	45888158	3	2	112	1	0	0	0	0	1	0	0	0	11291	1551	54	2	775	2	OSBPL7	17	45888158	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3614729	45888158	35307052	1011	17632										
HLF	3131	hgsc.bcm.edu	37	chr17	53345191	53345191	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtcccccagtcggcattcctGgggcctaccttatgggacaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:53345191delG	ENST00000226067.5	+	2	668	c.195delG	c.(193-195)ctgfs	p.L65fs	HLF_ENST00000573945.1_5'UTR|HLF_ENST00000430986.2_5'UTR|HLF_ENST00000575345.1_5'UTR	NM_002126.4	NP_002117.1	Q16534	HLF_HUMAN	hepatic leukemia factor	65					multicellular organismal development (GO:0007275)|rhythmic process (GO:0048511)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|ovary(2)	3						CGGCATTCCTGGGGCCTACCT	0.483			T	TCF3	ALL																																p.L65fs		Atlas-INDEL	.		Dom	yes		17	17q22	3131	hepatic leukemia factor		L	.	HLF	39	.	0			c.194delT						.						91	91	91					17																	53345191		2203	4300	6503	SO:0001589	frameshift_variant	3131	exon2			.		CCDS11585.1	17q22	2011-05-19			ENSG00000108924	ENSG00000108924			4977	protein-coding gene	gene with protein product		142385				1386162	Standard	XM_005257269		Approved	MGC33822	uc002iug.1	Q16534		ENST00000226067.5:c.195delG	chr17.hg19:g.53345191delG	ENSP00000226067:p.Leu65fs	96.0	0.0		145.0	10.0	NM_002126	A8K1X8|Q6FHS9	Frame_Shift_Del	DEL	ENST00000226067.5	hg19	CCDS11585.1																																																																																			.	.		0.483	HLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439185.1	NM_002126		-	53345191	G	-	53345191	7	5	112	1	0	1	0	1	0	0	0	0	7223	1335	47	0	201	0	HLF	17	53345191	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	7457033	53345191	27850019	1012	17633										
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56393388	56393388	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccactacattcctaccttcAaaaaagccatcctcatccat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:56393388delA	ENST00000343736.4	-	16	2257	c.2094delT	c.(2092-2094)tttfs	p.F698fs	BZRAP1_ENST00000268893.6_Frame_Shift_Del_p.F638fs|BZRAP1_ENST00000355701.3_Frame_Shift_Del_p.F698fs			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	698	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCCTACCTTCAAAAAAGCCAT	0.502																																					p.E699fs		Atlas-INDEL	.											.	BZRAP1	287	.	0			c.2095delG						.						194	158	170					17																	56393388		2203	4300	6503	SO:0001589	frameshift_variant	9256	exon16			.	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.2094delT	chr17.hg19:g.56393388delA	ENSP00000345824:p.Phe698fs	174.0	0.0		260.0	19.0	NM_004758	O75111|Q8N5W3	Frame_Shift_Del	DEL	ENST00000343736.4	hg19	CCDS11605.1																																																																																			.	.		0.502	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		-	56393388	A	-	56393388	7	5	112	1	0	1	0	1	0	0	0	0	1579	127	5	0	3543	0	BZRAP1	17	56393388	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3048197	56393388	24801822	1013	17634										
RNF43	54894	hgsc.bcm.edu	37	chr17	56448298	56448298	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agccagtgacaggcaggggcGgggggcccgtcgaggactct	19	11	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:56448298G>T	ENST00000584437.1	-	2	2304	c.349C>A	c.(349-351)Cgc>Agc	p.R117S	RNF43_ENST00000407977.2_Missense_Mutation_p.R117S|RNF43_ENST00000577625.1_5'UTR|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_5'UTR|RNF43_ENST00000577716.1_Missense_Mutation_p.R117S|RNF43_ENST00000583753.1_Intron|RNF43_ENST00000500597.2_Intron			Q68DV7	RNF43_HUMAN	ring finger protein 43	117			R -> H (in dbSNP:rs2257205).		negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGGCAGGGGCGGGGGGCCCGT	0.607																																					p.R117S		Atlas-SNP	.											.,6	RNF43	157	.	0			c.C349A						.						55	51	52					17																	56448298		2203	4300	6503	SO:0001583	missense	54894	exon3			AGGGGCGGGGGGC		CCDS11607.1	17q23.2	2013-01-09						"RING-type (C3HC4) zinc fingers"	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.349C>A	chr17.hg19:g.56448298G>T	ENSP00000463069:p.Arg117Ser	82.0	0.0		129.0	0.0	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	hg19	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.673770	0.67928	.	.	ENSG00000108375	ENST00000407977	T	0.41065	1.01	5.45	5.45	0.79879	.	0.368624	0.26753	N	0.022674	T	0.41442	0.1159	N	0.24115	0.695	0.80722	D	1	D	0.58620	0.983	P	0.52267	0.694	T	0.36817	-0.9732	10	0.72032	D	0.01	-4.475	13.8474	0.63477	0.0:0.0:0.8373:0.1627	.	117	Q68DV7	RNF43_HUMAN	S	117	ENSP00000385328:R117S	ENSP00000385328:R117S	R	-	1	0	RNF43	53803297	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.888000	0.63164	2.555000	0.86185	0.655000	0.94253	CGC	.	.		0.607	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763		T	56448298	G	T	56448298	3	4	112	1	0	0	0	0	1	0	0	0	13510	1116	39	1	2034	1	RNF43	17	56448298	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	54910	56448298	24746912	1014	17635										
C17orf47	284083	hgsc.bcm.edu	37	chr17	56620577	56620577	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctcgctgtttcctcggattGgggtcctcacgttggactcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:56620577delG	ENST00000321691.3	-	1	1152	c.971delC	c.(970-972)ccafs	p.P324fs	RP11-112H10.4_ENST00000580769.1_RNA|SEPT4_ENST00000412945.3_5'Flank|RP11-112H10.4_ENST00000578022.1_RNA|SEPT4_ENST00000457347.2_5'Flank|RP11-112H10.4_ENST00000580589.1_RNA	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	324										NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCCTCGGATTGGGGTCCTCAC	0.532																																					p.P324fs		Atlas-INDEL	.											.	C17orf47	59	.	0			c.972delA						.						99	88	92					17																	56620577		2203	4300	6503	SO:0001589	frameshift_variant	284083	exon1			.		CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013			26844	protein-coding gene	gene with protein product							Standard	NM_001038704		Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.971delC	chr17.hg19:g.56620577delG	ENSP00000354874:p.Pro324fs	163.0	0.0		178.0	11.0	NM_001038704	Q8N821	Frame_Shift_Del	DEL	ENST00000321691.3	hg19	CCDS32691.1																																																																																			.	.		0.532	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1	NM_001038704		-	56620577	G	-	56620577	7	5	112	1	0	1	0	1	0	0	0	0	1860	1348	47	0	749	0	C17orf47	17	56620577	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	172279	56620577	24574633	1015	17636										
TMEM49	81671	hgsc.bcm.edu	37	chr17	57808841	57808841	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaaaaattgtgaccagagaCgtgtagcaatgaacaaggaa	11	5	0	3	rs543321998		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:57808841C>T	ENST00000262291.4	+	2	344	c.34C>T	c.(34-36)Cgt>Tgt	p.R12C	VMP1_ENST00000537567.1_5'UTR|VMP1_ENST00000536180.1_5'UTR|VMP1_ENST00000545362.1_Missense_Mutation_p.R12C|VMP1_ENST00000539763.1_5'UTR	NM_030938.3	NP_112200.2	Q96GC9	VMP1_HUMAN	vacuole membrane protein 1	12					autophagy (GO:0006914)|cell junction assembly (GO:0034329)|embryo implantation (GO:0007566)|regulation of autophagy (GO:0010506)|single organismal cell-cell adhesion (GO:0016337)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|pre-autophagosomal structure (GO:0000407)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|skin(2)	16						TGACCAGAGACGTGTAGCAAT	0.348													C|||	1	0.000199681	8e-04	0	5008	,	,		14778	0		0	False		,,,				2504	0				p.R12C		Atlas-SNP	.											.	VMP1	49	.	0			c.C34T						.						107	104	105					17																	57808841		2203	4300	6503	SO:0001583	missense	81671	exon2			CAGAGACGTGTAG		CCDS11619.1	17q23.1	2014-05-20	2011-03-02	2011-03-02	ENSG00000062716	ENSG00000062716			29559	protein-coding gene	gene with protein product	"ectopic P-granules autophagy protein 3 homolog (C. elegans)", "transport and golgi organization 5 homolog (Drosophila)"	611753	"transmembrane protein 49"	TMEM49		11230166, 11785947	Standard	NM_030938		Approved	EPG3, TANGO5	uc002ixu.4	Q96GC9	OTTHUMG00000179882	ENST00000262291.4:c.34C>T	chr17.hg19:g.57808841C>T	ENSP00000262291:p.Arg12Cys	84.0	0.0		120.0	31.0	NM_030938	B4DVV9|Q9H0P4|Q9P089	Missense_Mutation	SNP	ENST00000262291.4	hg19	CCDS11619.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.508102	0.85282	.	.	ENSG00000062716	ENST00000262291;ENST00000545362	.	.	.	5.04	5.04	0.67666	.	0.226055	0.44285	D	0.000464	T	0.60090	0.2242	L	0.40543	1.245	0.80722	D	1	D;D	0.64830	0.994;0.987	P;B	0.50049	0.629;0.409	T	0.64114	-0.6483	9	0.56958	D	0.05	-6.6801	18.4015	0.90518	0.0:1.0:0.0:0.0	.	12;12	F5H2J3;Q96GC9	.;VMP1_HUMAN	C	12	.	ENSP00000262291:R12C	R	+	1	0	VMP1	55163623	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.624000	0.61254	2.320000	0.78422	0.460000	0.39030	CGT	.	.		0.348	VMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448793.1	NM_030938		T	57808841	C	T	57808841	3	4	112	1	0	0	0	0	1	0	0	0	16188	536	19	1	36	1	TMEM49	17	57808841	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1188264	57808841	23386369	1016	17637										
HEATR6	63897	hgsc.bcm.edu	37	chr17	58124746	58124746	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaccagagaactcttcctggAaacttgggtctggtgtttcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:58124746delA	ENST00000184956.6	-	18	2709	c.2693delT	c.(2692-2694)ttcfs	p.F898fs	HEATR6_ENST00000585976.1_Frame_Shift_Del_p.F786fs	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	898							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			CTCTTCCTGGAAACTTGGGTC	0.373																																					p.F898fs		Atlas-INDEL	.											.	HEATR6	98	.	0			c.2694delC						.						177	151	159					17																	58124746		2203	4300	6503	SO:0001589	frameshift_variant	63897	exon18			.	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"amplified in breast cancer 1"					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.2693delT	chr17.hg19:g.58124746delA	ENSP00000184956:p.Phe898fs	151.0	0.0		210.0	13.0	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Frame_Shift_Del	DEL	ENST00000184956.6	hg19	CCDS11623.1																																																																																			.	.		0.373	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070		-	58124746	A	-	58124746	7	5	112	1	0	1	0	1	0	0	0	0	7042	246	9	0	864	0	HEATR6	17	58124746	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	315905	58124746	23070464	1017	17638										
MED13	9969	hgsc.bcm.edu	37	chr17	60087940	60087940	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gatgttacactttcctgtccAaaaggtccaactggatcatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:60087940delA	ENST00000397786.2	-	9	2014	c.1938delT	c.(1936-1938)tttfs	p.F646fs		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	646					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTTCCTGTCCAAAAGGTCCAA	0.348																																					p.G647fs		Atlas-INDEL	.											.	MED13	181	.	0			c.1939delG						.						68	62	64					17																	60087940		1840	4084	5924	SO:0001589	frameshift_variant	9969	exon9			.	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.1938delT	chr17.hg19:g.60087940delA	ENSP00000380888:p.Phe646fs	119.0	0.0		170.0	12.0	NM_005121	B2RU05|O60334	Frame_Shift_Del	DEL	ENST00000397786.2	hg19	CCDS42366.1																																																																																			.	.		0.348	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		-	60087940	A	-	60087940	7	5	112	1	0	1	0	1	0	0	0	0	9439	127	5	0	4674	0	MED13	17	60087940	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1963194	60087940	21107270	1018	17639										
TANC2	26115	hgsc.bcm.edu	37	chr17	61086972	61086972	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctggtgggaaatcaagtcgtAaaaacaggtcaagtggtaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:61086972delA	ENST00000424789.2	+	1	56	c.52delA	c.(52-54)aaafs	p.K18fs	TANC2_ENST00000389520.4_Frame_Shift_Del_p.K18fs	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	18					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						ATCAAGTCGTAAAAACAGGTC	0.343																																					p.R17fs		Atlas-INDEL	.											.	TANC2	266	.	0			c.51delT						.						171	174	173					17																	61086972		1872	4109	5981	SO:0001589	frameshift_variant	26115	exon1			.	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.52delA	chr17.hg19:g.61086972delA	ENSP00000387593:p.Lys18fs	111.0	0.0		161.0	10.0	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Frame_Shift_Del	DEL	ENST00000424789.2	hg19	CCDS45754.1																																																																																			.	.		0.343	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			-	61086972	A	-	61086972	7	5	112	1	0	1	0	1	0	0	0	0	15560	363	13	0	54	0	TANC2	17	61086972	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	999032	61086972	20108238	1019	17640										
ACE	1636	hgsc.bcm.edu	37	chr17	61568576	61568576	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccctctgcttgcagggctggAcgcccaggaggatgtttaag	14	11	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:61568576A>G	ENST00000290866.4	+	19	2770	c.2746A>G	c.(2746-2748)Acg>Gcg	p.T916A	ACE_ENST00000290863.6_Missense_Mutation_p.T342A|ACE_ENST00000413513.3_Missense_Mutation_p.T342A|ACE_ENST00000490216.2_Missense_Mutation_p.T342A|ACE_ENST00000421982.2_Missense_Mutation_p.T162A|ACE_ENST00000428043.1_Missense_Mutation_p.T916A|ACE_ENST00000577647.1_Missense_Mutation_p.T342A	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	916	Peptidase M2 2.		T -> M (in dbSNP:rs3730043).		angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	GCAGGGCTGGACGCCCAGGAG	0.617																																					p.T916A		Atlas-SNP	.											.	ACE	187	.	0			c.A2746G						.						47	47	47					17																	61568576		2203	4300	6503	SO:0001583	missense	1636	exon19			GGCTGGACGCCCA	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.2746A>G	chr17.hg19:g.61568576A>G	ENSP00000290866:p.Thr916Ala	62.0	0.0		82.0	4.0	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	A	12.83	2.054984	0.36277	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863;ENST00000413513;ENST00000421982	T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2	5.28	5.28	0.74379	.	0.101804	0.64402	D	0.000002	T	0.69637	0.3133	H	0.94847	3.59	0.80722	D	1	P;D;P;P	0.56035	0.722;0.974;0.931;0.894	P;D;P;B	0.68765	0.688;0.96;0.681;0.422	T	0.78964	-0.1996	10	0.62326	D	0.03	-10.8333	15.2126	0.73238	1.0:0.0:0.0:0.0	.	162;342;342;916	F6X3S4;B4DXI3;P12821-3;P12821	.;.;.;ACE_HUMAN	A	916;916;342;342;162	ENSP00000290866:T916A;ENSP00000397593:T916A;ENSP00000290863:T342A;ENSP00000392247:T342A;ENSP00000387760:T162A	ENSP00000290863:T342A	T	+	1	0	ACE	58922308	1.000000	0.71417	0.996000	0.52242	0.501000	0.33797	5.279000	0.65597	1.975000	0.57531	0.459000	0.35465	ACG	.	.		0.617	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			G	61568576	A	G	61568576	3	3	112	1	0	0	0	0	1	0	0	0	136	275	10	2	3023	2	ACE	17	61568576	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	481604	61568576	19626634	1020	17641										
CCDC47	57003	hgsc.bcm.edu	37	chr17	61831827	61831827	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggaccagagaactggtctgAaaaatgaacagattcaatct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:61831827delA	ENST00000225726.5	-	9	1382	c.1000delT	c.(1000-1002)tcafs	p.S334fs	CCDC47_ENST00000582252.1_Frame_Shift_Del_p.S334fs|CCDC47_ENST00000403162.3_Frame_Shift_Del_p.S334fs|RP11-51F16.8_ENST00000580553.1_5'Flank	NM_020198.2	NP_064583.2	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47	334					calcium ion homeostasis (GO:0055074)|ER overload response (GO:0006983)|osteoblast differentiation (GO:0001649)|post-embryonic development (GO:0009791)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	18						AACTGGTCTGAAAAATGAACA	0.303																																					p.S334X		Atlas-INDEL	.											.	CCDC47	34	.	0			c.1001delC						.						49	51	51					17																	61831827		2203	4300	6503	SO:0001589	frameshift_variant	57003	exon9			.	AF226054	CCDS11643.1	17q23.3	2005-12-19				ENSG00000108588			24856	protein-coding gene	gene with protein product						12477932	Standard	NM_020198		Approved	GK001	uc002jbs.4	Q96A33		ENST00000225726.5:c.1000delT	chr17.hg19:g.61831827delA	ENSP00000225726:p.Ser334fs	243.0	0.0		326.0	20.0	NM_020198	B2RAS8|D3DU20|Q96D00|Q96JZ7|Q9H3E4|Q9NRG3	Frame_Shift_Del	DEL	ENST00000225726.5	hg19	CCDS11643.1																																																																																			.	.		0.303	CCDC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444016.2	NM_020198		-	61831827	A	-	61831827	7	5	112	1	0	1	0	1	0	0	0	0	2820	246	9	0	471	0	CCDC47	17	61831827	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	263251	61831827	19363383	1021	17642										
SMARCD2	6603	hgsc.bcm.edu	37	chr17	61914354	61914354	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtctggtccagcttccgctcAaaagccaagagatccatgta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:61914354delA	ENST00000448276.2	-	4	760	c.495delT	c.(493-495)tttfs	p.F165fs	RN7SL805P_ENST00000581353.1_RNA|SMARCD2_ENST00000323347.10_Frame_Shift_Del_p.F117fs|SMARCD2_ENST00000225742.9_Frame_Shift_Del_p.F90fs	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	165					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						GCTTCCGCTCAAAAGCCAAGA	0.552																																					p.E166fs		Atlas-INDEL	.											.	SMARCD2	29	.	0			c.496delG						.						88	89	89					17																	61914354		2017	4194	6211	SO:0001589	frameshift_variant	6603	exon4			.	U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60B", "Swp73-like protein", "chromatin remodeling complex BAF60B subunit", "SWI/SNF complex 60 kDa subunit B"	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.495delT	chr17.hg19:g.61914354delA	ENSP00000392617:p.Phe165fs	77.0	0.0		132.0	10.0	NM_001098426	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Frame_Shift_Del	DEL	ENST00000448276.2	hg19	CCDS45756.1																																																																																			.	.		0.552	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426		-	61914354	A	-	61914354	7	5	112	1	0	1	0	1	0	0	0	0	14793	127	5	0	1140	0	SMARCD2	17	61914354	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	82527	61914354	19280856	1022	17643										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62021202	62021202	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccgtcataaagatgtctttCccccctaagtatagtgggat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:62021202delC	ENST00000435607.1	-	22	3997	c.3921delG	c.(3919-3921)gggfs	p.G1307fs	SCN4A_ENST00000578147.1_Frame_Shift_Del_p.G1307fs	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1307					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGATGTCTTTCCCCCCTAAGT	0.537																																					p.K1308fs		Atlas-INDEL	.											.	SCN4A	205	.	0			c.3922delA						.						68	70	69					17																	62021202		2139	4276	6415	SO:0001589	frameshift_variant	6329	exon22			.	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.3921delG	chr17.hg19:g.62021202delC	ENSP00000396320:p.Gly1307fs	176.0	0.0		251.0	17.0	NM_000334	Q15478|Q16447|Q7Z6B1	Frame_Shift_Del	DEL	ENST00000435607.1	hg19	CCDS45761.1																																																																																			.	.		0.537	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		-	62021202	C	-	62021202	7	5	112	1	0	1	0	1	0	0	0	0	13935	842	30	0	1601	0	SCN4A	17	62021202	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	106848	62021202	19174008	1023	17644										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62048557	62048557	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggttttgagggcccgcagcAcccggaaggtcctcagggct	15	12	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:62048557A>G	ENST00000435607.1	-	5	744	c.668T>C	c.(667-669)gTg>gCg	p.V223A	CTC-264K15.6_ENST00000577329.1_lincRNA|SCN4A_ENST00000578147.1_Missense_Mutation_p.V223A	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	223					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGCCCGCAGCACCCGGAAGGT	0.642																																					p.V223A		Atlas-SNP	.											.	SCN4A	205	.	0			c.T668C						.						24	27	26					17																	62048557		1917	4132	6049	SO:0001583	missense	6329	exon5			CGCAGCACCCGGA	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.668T>C	chr17.hg19:g.62048557A>G	ENSP00000396320:p.Val223Ala	42.0	0.0		71.0	5.0	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.228631	0.79576	.	.	ENSG00000007314	ENST00000435607	D	0.98835	-5.17	4.22	4.22	0.49857	Ion transport (1);	0.124247	0.53938	D	0.000053	D	0.98969	0.9649	M	0.83852	2.665	0.54753	D	0.999984	D	0.63880	0.993	D	0.72075	0.976	D	0.99421	1.0933	10	0.72032	D	0.01	.	12.5717	0.56341	1.0:0.0:0.0:0.0	.	223	P35499	SCN4A_HUMAN	A	223	ENSP00000396320:V223A	ENSP00000396320:V223A	V	-	2	0	SCN4A	59402289	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.087000	0.94110	1.894000	0.54839	0.379000	0.24179	GTG	.	.		0.642	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		G	62048557	A	G	62048557	3	3	112	1	0	0	0	0	1	0	0	0	13935	159	6	2	4922	2	SCN4A	17	62048557	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	27355	62048557	19146653	1024	17645										
GNA13	10672	hgsc.bcm.edu	37	chr17	63014373	63014373	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttggtttaaacacttactgGttctccaagtttatccaagt	6	8	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:63014373G>A	ENST00000439174.2	-	3	804	c.559C>T	c.(559-561)Cca>Tca	p.P187S	GNA13_ENST00000541118.1_Missense_Mutation_p.P92S	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	187					activation of phospholipase D activity (GO:0031584)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|in utero embryonic development (GO:0001701)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(14)|kidney(2)|large_intestine(4)|lung(6)|urinary_tract(1)	34						ACACTTACTGGTTCTCCAAGT	0.303																																					p.P187S		Atlas-SNP	.											.	GNA13	69	.	0			c.C559T						.						132	139	137					17																	63014373		2203	4299	6502	SO:0001583	missense	10672	exon3			TTACTGGTTCTCC	L22075	CCDS11661.1, CCDS62302.1	17q24.1	2014-09-04			ENSG00000120063	ENSG00000120063			4381	protein-coding gene	gene with protein product		604406				7791744	Standard	NM_006572		Approved	G13, MGC46138	uc002jfc.3	Q14344	OTTHUMG00000179316	ENST00000439174.2:c.559C>T	chr17.hg19:g.63014373G>A	ENSP00000400717:p.Pro187Ser	200.0	0.0		236.0	57.0	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Missense_Mutation	SNP	ENST00000439174.2	hg19	CCDS11661.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.679744	0.29783	.	.	ENSG00000120063	ENST00000439174;ENST00000541118;ENST00000239138	D;D	0.89123	-2.47;-2.47	4.95	0.565	0.17309	G protein alpha subunit, helical insertion (2);	0.864625	0.10553	N	0.661221	D	0.82921	0.5142	L	0.48260	1.515	0.47009	D	0.999289	B	0.02656	0.0	B	0.01281	0.0	T	0.75048	-0.3455	10	0.37606	T	0.19	.	7.1178	0.25427	0.1565:0.2824:0.5612:0.0	.	187	Q14344	GNA13_HUMAN	S	187;92;162	ENSP00000400717:P187S;ENSP00000439647:P92S	ENSP00000239138:P162S	P	-	1	0	GNA13	60444835	0.839000	0.29477	1.000000	0.80357	0.996000	0.88848	0.044000	0.13992	0.679000	0.31345	0.655000	0.94253	CCA	.	.		0.303	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572		A	63014373	G	A	63014373	3	1	112	1	0	0	0	0	1	0	0	0	6509	1261	44	3	582	3	GNA13	17	63014373	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	965816	63014373	18180837	1025	17646										
PSMD12	5718	hgsc.bcm.edu	37	chr17	65346373	65346373	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cggtaaccattcgtagagtaTcaattaatcgaagtttgata	8	6	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:65346373T>C	ENST00000356126.3	-	4	484	c.377A>G	c.(376-378)gAt>gGt	p.D126G	PSMD12_ENST00000581618.1_Intron|PSMD12_ENST00000357146.4_Missense_Mutation_p.D106G	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	126					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					TCGTAGAGTATCAATTAATCG	0.333																																					p.D126G		Atlas-SNP	.											.	PSMD12	32	.	0			c.A377G						.						84	78	80					17																	65346373		2203	4300	6503	SO:0001583	missense	5718	exon4			AGAGTATCAATTA	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.377A>G	chr17.hg19:g.65346373T>C	ENSP00000348442:p.Asp126Gly	109.0	0.0		131.0	6.0	NM_002816	A6NP15|Q53HA2|Q6P053	Missense_Mutation	SNP	ENST00000356126.3	hg19	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	T	19.74	3.883153	0.72410	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	T;T	0.41758	0.99;0.99	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.55862	0.1947	M	0.80616	2.505	0.80722	D	1	P;P	0.48230	0.907;0.907	P;P	0.49953	0.489;0.627	T	0.61753	-0.6998	10	0.48119	T	0.1	-22.0817	14.4325	0.67259	0.0:0.0:0.0:1.0	.	106;126	A6NP15;O00232	.;PSD12_HUMAN	G	126;106	ENSP00000348442:D126G;ENSP00000349667:D106G	ENSP00000348442:D126G	D	-	2	0	PSMD12	62776835	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.280000	0.78610	1.944000	0.56390	0.383000	0.25322	GAT	.	.		0.333	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		C	65346373	T	C	65346373	3	2	112	1	0	0	0	0	1	0	0	0	12707	1435	50	2	1025	2	PSMD12	17	65346373	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2332000	65346373	15848837	1026	17647										
BPTF	2186	hgsc.bcm.edu	37	chr17	65955903	65955903	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actccagctcaaagtccaagAaaaagaaaatgatctctact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:65955903delA	ENST00000321892.4	+	26	8612	c.8551delA	c.(8551-8553)aaafs	p.K2853fs	BPTF_ENST00000424123.3_Frame_Shift_Del_p.K2571fs|BPTF_ENST00000335221.5_Frame_Shift_Del_p.K2710fs|BPTF_ENST00000306378.6_Frame_Shift_Del_p.K2727fs			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2853	Poly-Lys.				anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAAGTCCAAGAAAAAGAAAAT	0.443																																					p.K2724fs		Atlas-INDEL	.											.	BPTF	415	.	0			c.8172delG						.						68	67	67					17																	65955903		2203	4300	6503	SO:0001589	frameshift_variant	2186	exon24			.	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.8551delA	chr17.hg19:g.65955903delA	ENSP00000315454:p.Lys2853fs	112.0	0.0		178.0	12.0	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Frame_Shift_Del	DEL	ENST00000321892.4	hg19																																																																																				.	.		0.443	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		-	65955903	A	-	65955903	7	5	112	1	0	1	0	1	0	0	0	0	1497	247	9	0	8653	0	BPTF	17	65955903	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	609530	65955903	15239307	1027	17648										
ABCA8	10351	hgsc.bcm.edu	37	chr17	66918423	66918423	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcaggctttcctttatattcTtttgtaacatttctgattct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:66918423delT	ENST00000269080.2	-	11	1598	c.1461delA	c.(1459-1461)aaafs	p.K487fs	ABCA8_ENST00000586539.1_Frame_Shift_Del_p.K487fs|ABCA8_ENST00000430352.2_Frame_Shift_Del_p.K487fs	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	487	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					CTTTATATTCTTTTGTAACAT	0.244																																					p.E488fs		Atlas-INDEL	.											.	ABCA8	213	.	0			c.1462delG						.						37	40	39					17																	66918423		2187	4289	6476	SO:0001589	frameshift_variant	10351	exon11			.	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.1461delA	chr17.hg19:g.66918423delT	ENSP00000269080:p.Lys487fs	92.0	0.0		197.0	14.0	NM_007168	A1L3U3|C9JQE6|Q86WW0	Frame_Shift_Del	DEL	ENST00000269080.2	hg19	CCDS11680.1																																																																																			.	.		0.244	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		-	66918423	T	-	66918423	7	5	112	1	0	1	0	1	0	0	0	0	38	1606	56	0	3396	0	ABCA8	17	66918423	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	962520	66918423	14276787	1028	17649										
ABCA5	23461	hgsc.bcm.edu	37	chr17	67255885	67255885	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttattgatctgcctccataTtttttctcatagtattgtaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:67255885delT	ENST00000392676.3	-	28	3757	c.3693delA	c.(3691-3693)aaafs	p.K1231fs	ABCA5_ENST00000392677.2_Frame_Shift_Del_p.K1232fs|ABCA5_ENST00000588877.1_Frame_Shift_Del_p.K1231fs			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	1231					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TGCCTCCATATTTTTTCTCAT	0.313																																					p.Y1232fs		Atlas-INDEL	.											.	ABCA5	162	.	0			c.3694delT						.						60	59	59					17																	67255885		2203	4299	6502	SO:0001589	frameshift_variant	23461	exon27			.	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.3693delA	chr17.hg19:g.67255885delT	ENSP00000376443:p.Lys1231fs	137.0	0.0		265.0	18.0	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Frame_Shift_Del	DEL	ENST00000392676.3	hg19	CCDS11685.1																																																																																			.	.		0.313	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		-	67255885	T	-	67255885	7	5	112	1	0	1	0	1	0	0	0	0	35	1490	52	0	1283	0	ABCA5	17	67255885	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	337462	67255885	13939325	1029	17650										
ABCA5	23461	hgsc.bcm.edu	37	chr17	67282042	67282042	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttaaagtaagtaatacctgAaaatttgtccatgtccttga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:67282042delA	ENST00000392676.3	-	17	2333	c.2269delT	c.(2269-2271)tcafs	p.S757fs	ABCA5_ENST00000392677.2_Frame_Shift_Del_p.S757fs|ABCA5_ENST00000588877.1_Frame_Shift_Del_p.S757fs			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	757					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	GTAATACCTGAAAATTTGTCC	0.353																																					p.S757X		Atlas-INDEL	.											.	ABCA5	162	.	0			c.2270delC						.						144	142	143					17																	67282042		2203	4300	6503	SO:0001589	frameshift_variant	23461	exon16			.	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.2269delT	chr17.hg19:g.67282042delA	ENSP00000376443:p.Ser757fs	93.0	0.0		178.0	13.0	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Frame_Shift_Del	DEL	ENST00000392676.3	hg19	CCDS11685.1																																																																																			.	.		0.353	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		-	67282042	A	-	67282042	7	5	112	1	0	1	0	1	0	0	0	0	35	246	9	0	2751	0	ABCA5	17	67282042	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	26157	67282042	13913168	1030	17651										
FDXR	2232	hgsc.bcm.edu	37	chr17	72860316	72860316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacctgctgcccgccgcccaTctggtgagggcagcacctgc	12	18	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:72860316T>C	ENST00000293195.5	-	9	1034	c.956A>G	c.(955-957)gAt>gGt	p.D319G	FDXR_ENST00000581969.1_5'Flank|FDXR_ENST00000413947.2_Missense_Mutation_p.D350G|FDXR_ENST00000582944.1_Missense_Mutation_p.D311G|FDXR_ENST00000544854.1_Missense_Mutation_p.D267G|FDXR_ENST00000442102.2_Missense_Mutation_p.D362G|GRIN2C_ENST00000578159.1_5'Flank|FDXR_ENST00000455107.2_Missense_Mutation_p.D275G|FDXR_ENST00000581530.1_Missense_Mutation_p.D325G|FDXR_ENST00000420580.2_Missense_Mutation_p.D279G|FDXR_ENST00000583917.1_Missense_Mutation_p.D291G	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	319					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	CCGCCGCCCATCTGGTGAGGG	0.672																																					p.D362G		Atlas-SNP	.											.	FDXR	68	.	0			c.A1085G						.						22	27	25					17																	72860316		2199	4293	6492	SO:0001583	missense	2232	exon9			CGCCCATCTGGTG	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"adrenodoxin-NADP(+) reductase", "adrenodoxin reductase"	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.956A>G	chr17.hg19:g.72860316T>C	ENSP00000293195:p.Asp319Gly	54.0	0.0		93.0	7.0	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	hg19	CCDS58593.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.864812	0.51482	.	.	ENSG00000161513	ENST00000420580;ENST00000544854;ENST00000293195;ENST00000455107;ENST00000442102;ENST00000413947	T;T;T;T;T	0.26067	1.76;2.72;2.72;2.72;2.72	4.58	4.58	0.56647	.	0.100098	0.64402	D	0.000003	T	0.26593	0.0650	L	0.41236	1.265	0.80722	D	1	B;B;B;B;B;B;B;B;B;B	0.24651	0.043;0.108;0.001;0.012;0.0;0.001;0.0;0.012;0.0;0.006	B;B;B;B;B;B;B;B;B;B	0.33799	0.025;0.17;0.006;0.032;0.002;0.005;0.007;0.032;0.007;0.019	T	0.08289	-1.0729	10	0.52906	T	0.07	-6.4927	13.6354	0.62219	0.0:0.0:0.0:1.0	.	279;362;350;317;267;350;319;311;319;325	B4DQQ4;B4DHX5;E7EQC1;B4DDI9;B7Z7G2;B4DDI7;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;.;.;ADRO_HUMAN;.	G	279;267;325;275;362;350	ENSP00000414172:D279G;ENSP00000445432:D267G;ENSP00000390875:D275G;ENSP00000416515:D362G;ENSP00000408595:D350G	ENSP00000293195:D325G	D	-	2	0	FDXR	70371911	0.569000	0.26643	0.742000	0.31022	0.940000	0.58332	2.017000	0.40981	1.713000	0.51359	0.459000	0.35465	GAT	.	.		0.672	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110		C	72860316	T	C	72860316	3	2	112	1	0	0	0	0	1	0	0	0	5815	1435	50	2	535	2	FDXR	17	72860316	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	5578274	72860316	8334894	1031	17652										
NUP85	79902	hgsc.bcm.edu	37	chr17	73221299	73221299	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcaggcatatgccgaatcatGggggacctgatgaggacaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:73221299delG	ENST00000245544.4	+	8	770	c.699delG	c.(697-699)atgfs	p.M233fs	NUP85_ENST00000579324.1_Frame_Shift_Del_p.M121fs|NUP85_ENST00000541827.1_Frame_Shift_Del_p.M187fs|NUP85_ENST00000447371.2_Frame_Shift_Del_p.M65fs|NUP85_ENST00000579298.1_Intron|NUP85_ENST00000449421.2_3'UTR|NUP85_ENST00000540768.1_5'Flank	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	233					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			GCCGAATCATGGGGGACCTGA	0.562																																					p.M233fs		Atlas-INDEL	.											.	NUP85	44	.	0			c.698delT						.						125	124	124					17																	73221299		2203	4300	6503	SO:0001589	frameshift_variant	79902	exon8			.	AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450			8734	protein-coding gene	gene with protein product		170285				8124707	Standard	XM_005257690		Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000245544.4:c.699delG	chr17.hg19:g.73221299delG	ENSP00000245544:p.Met233fs	93.0	0.0		150.0	10.0	NM_024844	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Frame_Shift_Del	DEL	ENST00000245544.4	hg19	CCDS32730.1																																																																																			.	.		0.562	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844		-	73221299	G	-	73221299	7	5	112	1	0	1	0	1	0	0	0	0	10779	1348	47	0	729	0	NUP85	17	73221299	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	360983	73221299	7973911	1032	17653										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73746239	73746239	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agatgttgtcatcacagccaCcccctcacggcgacctgggc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:73746239delC	ENST00000200181.3	+	28	3551	c.3364delC	c.(3364-3366)cccfs	p.P1123fs	ITGB4_ENST00000339591.3_Frame_Shift_Del_p.P1123fs|ITGB4_ENST00000579662.1_Frame_Shift_Del_p.P1123fs|ITGB4_ENST00000450894.3_Frame_Shift_Del_p.P1123fs|ITGB4_ENST00000449880.2_Frame_Shift_Del_p.P1123fs	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1123					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			ATCACAGCCACCCCCTCACGG	0.612											OREG0024739	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P1121fs		Atlas-INDEL	.											.	ITGB4	165	.	0			c.3363delA						.						59	60	60					17																	73746239		2203	4300	6503	SO:0001589	frameshift_variant	3691	exon27			.		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.3364delC	chr17.hg19:g.73746239delC	ENSP00000200181:p.Pro1123fs	148.0	0.0	1147	171.0	11.0	NM_001005619	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Frame_Shift_Del	DEL	ENST00000200181.3	hg19	CCDS11727.1																																																																																			.	.		0.612	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			-	73746239	C	-	73746239	7	5	112	1	0	1	0	1	0	0	0	0	7906	507	18	0	3470	0	ITGB4	17	73746239	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	524940	73746239	7448971	1033	17654										
QRICH2	84074	hgsc.bcm.edu	37	chr17	74274145	74274145	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggctgctggccttggtggagCccccgaagtggatctgcacc					rs200636552		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:74274145delC	ENST00000262765.5	-	15	4723	c.4544delG	c.(4543-4545)ggcfs	p.G1515fs		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1515										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CTTGGTGGAGCCCCCGAAGTG	0.642																																					p.G1515fs		Atlas-INDEL	.											.	QRICH2	143	.	0			c.4545delC						.						84	86	85					17																	74274145		2203	4300	6503	SO:0001589	frameshift_variant	84074	exon15			.	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.4544delG	chr17.hg19:g.74274145delC	ENSP00000262765:p.Gly1515fs	139.0	0.0		166.0	10.0	NM_032134	A2RRE1|Q96LM3	Frame_Shift_Del	DEL	ENST00000262765.5	hg19	CCDS32741.1																																																																																			.	.		0.642	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		-	74274145	C	-	74274145	7	5	112	1	0	1	0	1	0	0	0	0	12895	739	26	0	467	0	QRICH2	17	74274145	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	527906	74274145	6921065	1034	17655										
SEC14L1	6397	hgsc.bcm.edu	37	chr17	75189591	75189591	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggttttgaaagtacagtggAaaaaattgcaatgaaacaat					rs34381783		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:75189591delA	ENST00000413679.2	+	6	737	c.434delA	c.(433-435)gaafs	p.E145fs	SEC14L1_ENST00000443798.4_Frame_Shift_Del_p.E145fs|SEC14L1_ENST00000591437.1_Frame_Shift_Del_p.E111fs|SEC14L1_ENST00000431431.2_Frame_Shift_Del_p.E111fs|SEC14L1_ENST00000392476.2_Frame_Shift_Del_p.E145fs|SEC14L1_ENST00000430767.4_Frame_Shift_Del_p.E145fs|SEC14L1_ENST00000436233.4_Frame_Shift_Del_p.E145fs|SEC14L1_ENST00000585618.1_Frame_Shift_Del_p.E145fs	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	145	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						AGTACAGTGGAAAAAATTGCA	0.378																																					p.E145fs		Atlas-INDEL	.											.	SEC14L1	81	.	0			c.433delG						.						76	75	75					17																	75189591		2203	4300	6503	SO:0001589	frameshift_variant	6397	exon8			.	D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"SEC14 (S. cerevisiae)-like 1"	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.434delA	chr17.hg19:g.75189591delA	ENSP00000394716:p.Glu145fs	110.0	0.0		174.0	12.0	NM_001204408	A8K4E8|B4DDI5|D5G3K1|Q99780	Frame_Shift_Del	DEL	ENST00000413679.2	hg19	CCDS11752.1																																																																																			.	.		0.378	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003		-	75189591	A	-	75189591	7	5	112	1	0	1	0	1	0	0	0	0	13996	246	9	0	448	0	SEC14L1	17	75189591	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	915446	75189591	6005619	1035	17656										
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76075517	76075517	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgtttggcaatagtggagcAgcacaagccaggaccatgca	12	9	0	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:76075517A>G	ENST00000588061.1	+	12	3979	c.3252A>G	c.(3250-3252)gcA>gcG	p.A1084A	TNRC6C_ENST00000335749.4_Silent_p.A1081A|TNRC6C_ENST00000588847.1_Silent_p.A1081A|TNRC6C_ENST00000301624.4_Silent_p.A1084A|TNRC6C_ENST00000544502.1_Silent_p.A1081A|TNRC6C_ENST00000541771.1_Silent_p.A1084A			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1084					embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			ATAGTGGAGCAGCACAAGCCA	0.527																																					p.A1084A		Atlas-SNP	.											.	TNRC6C	173	.	0			c.A3252G						.						99	108	105					17																	76075517		2153	4260	6413	SO:0001819	synonymous_variant	57690	exon11			TGGAGCAGCACAA	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.3252A>G	chr17.hg19:g.76075517A>G		88.0	0.0		149.0	6.0	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Silent	SNP	ENST00000588061.1	hg19	CCDS45798.1																																																																																			.	.		0.527	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		G	76075517	A	G	76075517	2	3	112	1	0	0	0	0	0	0	0	1	16357	175	7	2		2	TNRC6C	17	76075517	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	885926	76075517	5119693	1036	17657										
USP36	57602	hgsc.bcm.edu	37	chr17	76799861	76799861	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctcttctcagaggggctctGggggggctcactggcctctg	15	13	5	1	rs537129179		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:76799861G>C	ENST00000542802.3	-	16	2859	c.2416C>G	c.(2416-2418)Cag>Gag	p.Q806E	USP36_ENST00000312010.6_Missense_Mutation_p.Q806E|USP36_ENST00000449938.2_Intron			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	806			Q -> R (in dbSNP:rs3088040). {ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			GAGGGGCTCTGGGGGGGCTCA	0.632																																					p.Q806E		Atlas-SNP	.											.,2	USP36	243	.	0			c.C2416G						.						38	46	43					17																	76799861		2167	4248	6415	SO:0001583	missense	57602	exon16			GGCTCTGGGGGGG	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"Ubiquitin-specific peptidases"	20062	protein-coding gene	gene with protein product		612543	"ubiquitin specific protease 36"			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.2416C>G	chr17.hg19:g.76799861G>C	ENSP00000441214:p.Gln806Glu	52.0	0.0		80.0	0.0	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Missense_Mutation	SNP	ENST00000542802.3	hg19	CCDS32755.1	.	.	.	.	.	.	.	.	.	.	G	3.509	-0.100119	0.07010	.	.	ENSG00000055483	ENST00000312010;ENST00000542802	T;T	0.06449	3.3;3.3	5.42	1.16	0.20824	.	2.568530	0.00751	N	0.001065	T	0.06096	0.0158	L	0.44542	1.39	0.09310	N	0.999999	B;B	0.14438	0.006;0.01	B;B	0.15870	0.006;0.014	T	0.42172	-0.9467	10	0.02654	T	1	0.0129	5.3078	0.15813	0.2332:0.0:0.6269:0.1399	.	806;806	Q9P275;Q9P275-2	UBP36_HUMAN;.	E	806	ENSP00000310590:Q806E;ENSP00000441214:Q806E	ENSP00000310590:Q806E	Q	-	1	0	USP36	74311456	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.402000	0.20965	0.268000	0.21939	-0.137000	0.14449	CAG	.	.		0.632	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090		C	76799861	G	C	76799861	3	2	112	1	0	0	0	0	1	0	0	0	17082	1357	47	4	975	4	USP36	17	76799861	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	724344	76799861	4395349	1037	17658										
CBX2	84733	hgsc.bcm.edu	37	chr17	77755868	77755868	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctctctgctgggtggcagggTcaaactgctgcagacaagca	13	11	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:77755868T>C	ENST00000310942.4	+	4	392				CBX2_ENST00000269399.5_Missense_Mutation_p.S186P	NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2						cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GGTGGCAGGGTCAAACTGCTG	0.647																																					p.S186P		Atlas-SNP	.											.	CBX2	50	.	0			c.T556C						.						39	44	42					17																	77755868		2203	4298	6501	SO:0001627	intron_variant	84733	exon4			GCAGGGTCAAACT	BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"Pc class homolog (Drosophila)"	602770	"chromobox homolog 2 (Drosophila Pc class)", "cell division cycle associated 6"	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.288+268T>C	chr17.hg19:g.77755868T>C		72.0	0.0		131.0	6.0	NM_032647	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	hg19	CCDS32757.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.281458	0.40394	.	.	ENSG00000173894	ENST00000269399	.	.	.	3.0	-1.23	0.09465	.	.	.	.	.	T	0.21962	0.0529	.	.	.	0.09310	N	1	B	0.14438	0.01	B	0.13407	0.009	T	0.22977	-1.0201	6	.	.	.	.	4.8624	0.13590	0.0:0.1508:0.554:0.2952	.	186	Q14781-2	.	P	186	.	.	S	+	1	0	CBX2	75370463	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.195000	0.09546	-0.051000	0.13334	0.454000	0.30748	TCA	.	.		0.647	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647		C	77755868	T	C	77755868	1	2	112	0	1	0	0	0	0	0	0	0	2720	1667	58	2		2	CBX2	17	77755868	Intron	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	956007	77755868	3439342	1038	17659										
CBX4	8535	hgsc.bcm.edu	37	chr17	77812826	77812826	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttacttgggcgaccagcctcTccatttcaccagatactcca	6	15	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:77812826T>C	ENST00000269397.4	-	2	274	c.97A>G	c.(97-99)Aga>Gga	p.R33G	CBX4_ENST00000448310.1_Missense_Mutation_p.R33G	NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	33	Chromo. {ECO:0000255|PROSITE- ProRule:PRU00053}.|Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GACCAGCCTCTCCATTTCACC	0.751																																					p.R33G		Atlas-SNP	.											.	CBX4	40	.	0			c.A97G						.						13	12	12					17																	77812826		2137	4199	6336	SO:0001583	missense	8535	exon2			AGCCTCTCCATTT	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"NS5ATP1-binding protein 16", "Pc class 2 homolog (Drosophila)"	603079	"chromobox homolog 4 (Drosophila Pc class)"			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.97A>G	chr17.hg19:g.77812826T>C	ENSP00000269397:p.Arg33Gly	54.0	0.0		91.0	5.0	NM_003655	B1PJR7|Q6TPI8|Q96C04	Missense_Mutation	SNP	ENST00000269397.4	hg19	CCDS32758.1	.	.	.	.	.	.	.	.	.	.	T	7.386	0.629745	0.14257	.	.	ENSG00000141582	ENST00000269397;ENST00000343048	T	0.73469	-0.75	2.41	-0.374	0.12512	Chromo domain (1);Chromo domain subgroup (1);Chromo domain-like (1);Chromo domain/shadow (2);Chromo domain, conserved site (1);	0.075581	0.49305	U	0.000152	T	0.70710	0.3255	M	0.85041	2.73	0.41740	D	0.989608	B	0.09022	0.002	B	0.12837	0.008	T	0.63967	-0.6517	10	0.87932	D	0	-40.4506	5.0543	0.14524	0.0:0.1178:0.1823:0.6999	.	33	O00257	CBX4_HUMAN	G	33	ENSP00000269397:R33G	ENSP00000269397:R33G	R	-	1	2	CBX4	75427421	1.000000	0.71417	0.988000	0.46212	0.149000	0.21700	1.228000	0.32588	-0.020000	0.14032	0.358000	0.22013	AGA	.	.		0.751	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655		C	77812826	T	C	77812826	3	2	112	1	0	0	0	0	1	0	0	0	2722	1559	54	2	1601	2	CBX4	17	77812826	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	56958	77812826	3382384	1039	17660										
BAIAP2	10458	hgsc.bcm.edu	37	chr17	79089623	79089623	+	Intron	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtgaccaacgacaggtctgCccccctcctcagctgatggc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:79089623delC	ENST00000321300.6	+	14	1676				BAIAP2_ENST00000392411.3_Frame_Shift_Del_p.A452fs|BAIAP2_ENST00000435091.3_3'UTR|BAIAP2_ENST00000428708.2_Frame_Shift_Del_p.A530fs|BAIAP2_ENST00000575245.1_3'UTR	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2						actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GACAGGTCTGCCCCCCTCCTC	0.562																																					p.A530fs		Atlas-INDEL	.											.	BAIAP2	74	.	0			c.1588delG						.						79	82	81					17																	79089623		2203	4300	6503	SO:0001627	intron_variant	10458	exon14			.	AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.1583+6C>-	chr17.hg19:g.79089623delC		83.0	0.0		131.0	11.0	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Frame_Shift_Del	DEL	ENST00000321300.6	hg19	CCDS11775.1																																																																																			.	.		0.562	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1			-	79089623	C	-	79089623	6	5	112	0	1	1	0	1	0	0	0	0	1301	739	26	0		0	BAIAP2	17	79089623	Intron	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1276797	79089623	2105587	1040	17661										
AATK	9625	hgsc.bcm.edu	37	chr17	79094085	79094085	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctcgcagaaggtctcggaCagcaggctgggcatcttgag	14	11	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:79094085C>G	ENST00000326724.4	-	11	3675	c.3651G>C	c.(3649-3651)ctG>ctC	p.L1217L	AATK_ENST00000417379.1_Silent_p.L1114L	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1217					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			AGGTCTCGGACAGCAGGCTGG	0.667																																					p.L1217L		Atlas-SNP	.											.	AATK	102	.	0			c.G3651C						.						26	31	30					17																	79094085		2147	4235	6382	SO:0001819	synonymous_variant	9625	exon11			CTCGGACAGCAGG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.3651G>C	chr17.hg19:g.79094085C>G		105.0	0.0		173.0	39.0	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	hg19	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	C	8.746	0.920116	0.17982	.	.	ENSG00000181409	ENST00000417379	.	.	.	3.98	2.9	0.33743	.	.	.	.	.	T	0.56381	0.1981	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50792	-0.8786	4	.	.	.	.	7.9182	0.29831	0.0:0.5191:0.3869:0.094	.	.	.	.	S	1170	.	.	C	-	2	0	AATK	76708680	0.013000	0.17824	0.991000	0.47740	0.832000	0.47134	-0.192000	0.09587	0.843000	0.35070	0.313000	0.20887	TGT	.	.		0.667	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		G	79094085	C	G	79094085	2	3	112	1	0	0	0	0	0	0	0	1	26	465	17	4		4	AATK	17	79094085	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	4462	79094085	2101125	1041	17662										
AZI1	22994	hgsc.bcm.edu	37	chr17	79172711	79172711	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctggaggctgctgtggttctGgggatgagtcggaggtgggc					rs147729628	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:79172711delG	ENST00000269392.4	-	11	1500	c.1253delC	c.(1252-1254)ccafs	p.P418fs	AZI1_ENST00000450824.2_Frame_Shift_Del_p.P418fs|RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000374782.3_Frame_Shift_Del_p.P418fs|AZI1_ENST00000575907.1_Frame_Shift_Del_p.P418fs|AZI1_ENST00000570482.2_5'Flank	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		418					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)	p.P418L(1)		breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CTGTGGTTCTGGGGATGAGTC	0.617																																					p.P418fs		Atlas-INDEL	.											.	AZI1	145	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.1254delA						.						77	57	64					17																	79172711		2181	4292	6473	SO:0001589	frameshift_variant	22994	exon11			.																												ENST00000269392.4:c.1253delC	chr17.hg19:g.79172711delG	ENSP00000269392:p.Pro418fs	78.0	0.0		130.0	10.0	NM_014984	A6NHI8|B2RN11|Q96F50	Frame_Shift_Del	DEL	ENST00000269392.4	hg19																																																																																				.	.		0.617	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			-	79172711	G	-	79172711	7	5	112	1	0	1	0	1	0	0	0	0	1240	1348	47	0	2053	0	AZI1	17	79172711	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	78626	79172711	2022499	1042	17663										
DUS1L	64118	hgsc.bcm.edu	37	chr17	80020818	80020818	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acacggattttgcacgtgacAggaacagagagtttctcgtg	12	8	1	2	rs372985546		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:80020818A>G	ENST00000354321.7	-	4	914	c.429T>C	c.(427-429)ccT>ccC	p.P143P	DUS1L_ENST00000306796.5_Silent_p.P143P			Q6P1R4	DUS1L_HUMAN	dihydrouridine synthase 1-like (S. cerevisiae)	143							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	6	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			TGCACGTGACAGGAACAGAGA	0.612																																					p.P143P		Atlas-SNP	.											.	DUS1L	25	.	0			c.T429C						.						60	59	59					17																	80020818		2202	4300	6502	SO:0001819	synonymous_variant	64118	exon5			CGTGACAGGAACA		CCDS32775.1	17q25.3	2005-08-09				ENSG00000169718			30086	protein-coding gene	gene with protein product						12477932	Standard	NM_022156		Approved	PP3111, DUS1	uc002kdr.4	Q6P1R4		ENST00000354321.7:c.429T>C	chr17.hg19:g.80020818A>G		47.0	0.0		55.0	4.0	NM_022156	A6NHV4|Q96AI3	Silent	SNP	ENST00000354321.7	hg19	CCDS32775.1																																																																																			.	.		0.612	DUS1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442347.1	NM_022156		G	80020818	A	G	80020818	2	3	112	1	0	0	0	0	0	0	0	1	4807	175	7	2		2	DUS1L	17	80020818	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	848107	80020818	1174392	1043	17664										
USP14	9097	hgsc.bcm.edu	37	chr18	198083	198083	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catcggcagcgacaccttctAaaaagaaaagtttaatcgat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:198083delA	ENST00000261601.7	+	9	803	c.712delA	c.(712-714)aaafs	p.K240fs	USP14_ENST00000582707.1_Frame_Shift_Del_p.K205fs|USP14_ENST00000383589.2_Frame_Shift_Del_p.K194fs|USP14_ENST00000400266.3_Frame_Shift_Del_p.K229fs	NM_005151.3	NP_005142.1	P54578	UBP14_HUMAN	ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)	240	USP.				negative regulation of endopeptidase activity (GO:0010951)|protein deubiquitination (GO:0016579)|regulation of chemotaxis (GO:0050920)|regulation of proteasomal protein catabolic process (GO:0061136)|synaptic transmission (GO:0007268)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|synapse (GO:0045202)	cysteine-type endopeptidase activity (GO:0004197)|endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)|tRNA guanylyltransferase activity (GO:0008193)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(2)	11		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				GACACCTTCTAAAAAGAAAAG	0.328																																					p.S237fs		Atlas-INDEL	.											.	USP14	41	.	0			c.711delT						.						66	68	68					18																	198083		2203	4300	6503	SO:0001589	frameshift_variant	9097	exon9			.	U30888	CCDS32780.1, CCDS32781.1	18p11.32	2006-10-06	2005-08-08			ENSG00000101557		"Ubiquitin-specific peptidases"	12612	protein-coding gene	gene with protein product		607274	"ubiquitin specific protease 14 (tRNA-guanine transglycosylase)"			12838346	Standard	NM_001037334		Approved	TGT	uc002kkf.1	P54578		ENST00000261601.7:c.712delA	chr18.hg19:g.198083delA	ENSP00000261601:p.Lys240fs	117.0	0.0		172.0	12.0	NM_005151	J3QRZ5|Q53XY5	Frame_Shift_Del	DEL	ENST00000261601.7	hg19	CCDS32780.1																																																																																			.	.		0.328	USP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440305.3	NM_005151		-	198083	A	-	198083	7	5	112	1	0	1	0	1	0	0	0	0	17060	363	13	0	746	0	USP14	18	198083	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10		198083	77879165	1044	17665										
USP14	9097	hgsc.bcm.edu	37	chr18	210016	210016	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagaagttaagtatgaacccTtttcttttgctgatggtaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:210016delT	ENST00000261601.7	+	14	1301	c.1210delT	c.(1210-1212)tttfs	p.F404fs	USP14_ENST00000582707.1_Frame_Shift_Del_p.F369fs|USP14_ENST00000383589.2_Frame_Shift_Del_p.F358fs|USP14_ENST00000400266.3_Frame_Shift_Del_p.F393fs	NM_005151.3	NP_005142.1	P54578	UBP14_HUMAN	ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)	404	USP.				negative regulation of endopeptidase activity (GO:0010951)|protein deubiquitination (GO:0016579)|regulation of chemotaxis (GO:0050920)|regulation of proteasomal protein catabolic process (GO:0061136)|synaptic transmission (GO:0007268)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|synapse (GO:0045202)	cysteine-type endopeptidase activity (GO:0004197)|endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)|tRNA guanylyltransferase activity (GO:0008193)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(2)	11		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				GTATGAACCCTTTTCTTTTGC	0.279																																					p.P403fs		Atlas-INDEL	.											.	USP14	41	.	0			c.1209delC						.						120	119	119					18																	210016		2203	4297	6500	SO:0001589	frameshift_variant	9097	exon14			.	U30888	CCDS32780.1, CCDS32781.1	18p11.32	2006-10-06	2005-08-08			ENSG00000101557		"Ubiquitin-specific peptidases"	12612	protein-coding gene	gene with protein product		607274	"ubiquitin specific protease 14 (tRNA-guanine transglycosylase)"			12838346	Standard	NM_001037334		Approved	TGT	uc002kkf.1	P54578		ENST00000261601.7:c.1210delT	chr18.hg19:g.210016delT	ENSP00000261601:p.Phe404fs	161.0	0.0		180.0	13.0	NM_005151	J3QRZ5|Q53XY5	Frame_Shift_Del	DEL	ENST00000261601.7	hg19	CCDS32780.1																																																																																			.	.		0.279	USP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440305.3	NM_005151		-	210016	T	-	210016	7	5	112	1	0	1	0	1	0	0	0	0	17060	1609	56	0	1264	0	USP14	18	210016	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	11933	210016	77867232	1045	17666										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2722560	2722560	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttggtcttctggatcttccTtttcgtgttggagttccatt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:2722560delT	ENST00000320876.6	+	20	2840	c.2502delT	c.(2500-2502)cctfs	p.P834fs	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Frame_Shift_Del_p.P834fs	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	834					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TGGATCTTCCTTTTCGTGTTG	0.368																																					p.P834fs		Atlas-INDEL	.											.	SMCHD1	88	.	0			c.2501delC						.						183	165	171					18																	2722560		1816	4080	5896	SO:0001589	frameshift_variant	23347	exon20			.	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.2502delT	chr18.hg19:g.2722560delT	ENSP00000326603:p.Pro834fs	149.0	0.0		162.0	10.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Frame_Shift_Del	DEL	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.		0.368	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			-	2722560	T	-	2722560	7	5	112	1	0	1	0	1	0	0	0	0	14803	1596	56	0	2580	0	SMCHD1	18	2722560	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2512544	2722560	75354688	1046	17667										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2750117	2750117	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtattcagtgtttttgcccCtaggtaagaaccaaaagttt	8	7	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:2750117C>A	ENST00000320876.6	+	31	4342	c.4004C>A	c.(4003-4005)cCt>cAt	p.P1335H	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.P1335H	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1335					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GTTTTTGCCCCTAGGTAAGAA	0.368																																					p.P1335H		Atlas-SNP	.											.	SMCHD1	88	.	0			c.C4004A						.						121	108	112					18																	2750117		1839	4087	5926	SO:0001583	missense	23347	exon31			TTGCCCCTAGGTA	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.4004C>A	chr18.hg19:g.2750117C>A	ENSP00000326603:p.Pro1335His	106.0	0.0		94.0	23.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	C	15.77	2.932066	0.52866	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.28454	1.61;1.62	5.96	5.96	0.96718	.	0.052669	0.85682	D	0.000000	T	0.52484	0.1737	M	0.67953	2.075	0.43133	D	0.994877	D	0.76494	0.999	P	0.60173	0.87	T	0.51942	-0.8641	10	0.72032	D	0.01	-7.2361	18.1738	0.89754	0.0:1.0:0.0:0.0	.	1335	A6NHR9	SMHD1_HUMAN	H	1335	ENSP00000326603:P1335H;ENSP00000261598:P1335H	ENSP00000261598:P1335H	P	+	2	0	SMCHD1	2740117	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.754000	0.62191	2.826000	0.97356	0.655000	0.94253	CCT	.	.		0.368	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			A	2750117	C	A	2750117	3	1	112	1	0	0	0	0	1	0	0	0	14803	681	24	3	4126	3	SMCHD1	18	2750117	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	27557	2750117	75327131	1047	17668										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3151804	3151804	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actcggaagatataggaacgAccttcgatcaatccagtgac	9	10	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:3151804A>G	ENST00000356443.4	-	12	2064	c.1731T>C	c.(1729-1731)ggT>ggC	p.G577G	MYOM1_ENST00000400569.3_Silent_p.G577G|MYOM1_ENST00000261606.7_Silent_p.G577G	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	577	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TATAGGAACGACCTTCGATCA	0.502											OREG0024839	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G577G		Atlas-SNP	.											.	MYOM1	192	.	0			c.T1731C						.						94	92	93					18																	3151804		1923	4144	6067	SO:0001819	synonymous_variant	8736	exon12			GGAACGACCTTCG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.1731T>C	chr18.hg19:g.3151804A>G		91.0	0.0	609	98.0	4.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.502	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		G	3151804	A	G	3151804	2	3	112	1	0	0	0	0	0	0	0	1	10100	262	10	2		2	MYOM1	18	3151804	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	401687	3151804	74925444	1048	17669										
ZFP161	7541	hgsc.bcm.edu	37	chr18	5291325	5291325	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccgtgtggagtttctcatgCttcctcaatctgccttcatc	8	13	4	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:5291325C>A	ENST00000357006.4	-	4	1220	c.882G>T	c.(880-882)aaG>aaT	p.K294N	ZBTB14_ENST00000400143.3_Missense_Mutation_p.K294N	NM_001143823.2|NM_001243704.1	NP_001137295.1|NP_001230633.1	O43829	ZBT14_HUMAN	zinc finger and BTB domain containing 14	294					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)										GTTTCTCATGCTTCCTCAATC	0.478																																					p.K294N		Atlas-SNP	.											.	.	.	.	0			c.G882T						.						98	89	92					18																	5291325		2203	4300	6503	SO:0001583	missense	7541	exon4			CTCATGCTTCCTC	D89859	CCDS11837.1	18p11.31	2013-09-19	2013-01-08	2013-01-08	ENSG00000198081	ENSG00000198081		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12860	protein-coding gene	gene with protein product		602126	"zinc finger protein 161 homolog (mouse)", "zinc finger protein 161", "ZFP161 zinc finger protein"	ZFP161		9244432	Standard	NM_001243702		Approved	ZNF478	uc010dkp.3	O43829	OTTHUMG00000131563	ENST00000357006.4:c.882G>T	chr18.hg19:g.5291325C>A	ENSP00000349503:p.Lys294Asn	115.0	0.0		122.0	43.0	NM_001243702	O00403|Q2TB80	Missense_Mutation	SNP	ENST00000357006.4	hg19	CCDS11837.1	.	.	.	.	.	.	.	.	.	.	C	9.860	1.195990	0.22037	.	.	ENSG00000198081	ENST00000357006;ENST00000400143	T;T	0.20598	2.06;2.06	5.8	3.05	0.35203	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.103499	0.64402	D	0.000006	T	0.18509	0.0444	L	0.33668	1.02	0.54753	D	0.999989	D	0.57257	0.979	P	0.48368	0.575	T	0.02031	-1.1226	10	0.33940	T	0.23	-20.0419	7.9098	0.29785	0.0:0.5701:0.0:0.4299	.	294	O43829	ZF161_HUMAN	N	294	ENSP00000349503:K294N;ENSP00000383009:K294N	ENSP00000349503:K294N	K	-	3	2	ZFP161	5281325	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	0.666000	0.25097	0.361000	0.24292	0.650000	0.86243	AAG	.	.		0.478	ZBTB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254425.1	NM_003409		A	5291325	C	A	5291325	3	1	112	1	0	0	0	0	1	0	0	0	17655	796	28	3	471	3	ZFP161	18	5291325	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	2139521	5291325	72785923	1049	17670										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9257212	9257212	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgtagcatgccttctgtcaTttgtgaacataccaaacaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:9257212delT	ENST00000262126.4	+	9	4187	c.3947delT	c.(3946-3948)attfs	p.I1316fs	ANKRD12_ENST00000400020.3_Frame_Shift_Del_p.I1293fs|ANKRD12_ENST00000383440.2_Frame_Shift_Del_p.I1293fs|RP11-888D10.4_ENST00000609701.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1316						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CCTTCTGTCATTTGTGAACAT	0.403																																					p.I1316fs		Atlas-INDEL	.											.	ANKRD12	167	.	0			c.3946delA						.						133	126	128					18																	9257212		2203	4300	6503	SO:0001589	frameshift_variant	23253	exon9			.	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.3947delT	chr18.hg19:g.9257212delT	ENSP00000262126:p.Ile1316fs	142.0	0.0		134.0	10.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Frame_Shift_Del	DEL	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.403	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		-	9257212	T	-	9257212	7	5	112	1	0	1	0	1	0	0	0	0	640	1493	52	0	3977	0	ANKRD12	18	9257212	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3965887	9257212	68820036	1050	17671										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9279634	9279634	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgtggatgataaatttgacAaattaaaggtatgtatgttt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:9279634delA	ENST00000262126.4	+	12	6235	c.5995delA	c.(5995-5997)aaafs	p.K1999fs	ANKRD12_ENST00000400020.3_Frame_Shift_Del_p.K1976fs|ANKRD12_ENST00000383440.2_Frame_Shift_Del_p.K1976fs|snoU13_ENST00000459594.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1999						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						TAAATTTGACAAATTAAAGGT	0.323																																					p.D1998fs		Atlas-INDEL	.											.	ANKRD12	167	.	0			c.5994delC						.						93	100	98					18																	9279634		2203	4299	6502	SO:0001589	frameshift_variant	23253	exon12			.	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5995delA	chr18.hg19:g.9279634delA	ENSP00000262126:p.Lys1999fs	173.0	0.0		216.0	14.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Frame_Shift_Del	DEL	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.323	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		-	9279634	A	-	9279634	7	5	112	1	0	1	0	1	0	0	0	0	640	131	5	0	6037	0	ANKRD12	18	9279634	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	22422	9279634	68797614	1051	17672										
PPP4R1	9989	hgsc.bcm.edu	37	chr18	9557277	9557277	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgacttcatcgaggtcttttAaaaatccattaaaaattgga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:9557277delA	ENST00000400556.3	-	15	2205	c.2132delT	c.(2131-2133)ttafs	p.L711fs	PPP4R1_ENST00000400555.3_Frame_Shift_Del_p.L694fs	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	711					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						GAGGTCTTTTAAAAATCCATT	0.348																																					p.L711fs	Melanoma(188;1232 2082 5061 11948 35994)	Atlas-INDEL	.											.	PPP4R1	63	.	0			c.2133delA						.						157	152	154					18																	9557277		1821	4076	5897	SO:0001589	frameshift_variant	9989	exon15			.	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.2132delT	chr18.hg19:g.9557277delA	ENSP00000383402:p.Leu711fs	166.0	0.0		149.0	11.0	NM_001042388	Q99774|Q9UNQ7	Frame_Shift_Del	DEL	ENST00000400556.3	hg19	CCDS42412.1																																																																																			.	.		0.348	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134		-	9557277	A	-	9557277	7	5	112	1	0	1	0	1	0	0	0	0	12415	372	13	0	744	0	PPP4R1	18	9557277	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	277643	9557277	68519971	1052	17673										
FAM38B	63895	hgsc.bcm.edu	37	chr18	10671532	10671532	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgttctaaggtttcaatttgTtttttctctagtccatttga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:10671532delT	ENST00000503781.3	-	52	8250	c.8251delA	c.(8251-8253)acafs	p.T2751fs	PIEZO2_ENST00000285141.4_Frame_Shift_Del_p.T543fs|PIEZO2_ENST00000538948.1_Frame_Shift_Del_p.T708fs|PIEZO2_ENST00000581680.1_5'Flank|PIEZO2_ENST00000580640.1_Frame_Shift_Del_p.T2776fs|PIEZO2_ENST00000302079.6_Frame_Shift_Del_p.T2688fs	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2751					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										TTTCAATTTGTTTTTTCTCTA	0.338																																					p.T2751fs		Atlas-INDEL	.											.	.	.	.	0			c.8252delC						.						110	98	102					18																	10671532		2203	4300	6503	SO:0001589	frameshift_variant	63895	exon52			.	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"chromosome 18 open reading frame 30", "chromosome 18 open reading frame 58", "family with sequence similarity 38, member B"	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.8251delA	chr18.hg19:g.10671532delT	ENSP00000421377:p.Thr2751fs	163.0	0.0		184.0	12.0	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Frame_Shift_Del	DEL	ENST00000503781.3	hg19																																																																																				.	.		0.338	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		-	10671532	T	-	10671532	7	5	112	1	0	1	0	1	0	0	0	0	5563	1725	60	0	11	0	FAM38B	18	10671532	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1114255	10671532	67405716	1053	17674										
CEP76	79959	hgsc.bcm.edu	37	chr18	12673464	12673464	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaactgccagtcgcacttggTctccacggcaacagattatt	9	12	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:12673464T>C	ENST00000262127.2	-	12	2105	c.1880A>G	c.(1879-1881)gAc>gGc	p.D627G	PSMG2_ENST00000589405.1_Intron|RP11-973H7.3_ENST00000585877.1_RNA|CEP76_ENST00000423709.2_Missense_Mutation_p.D552G|PSMG2_ENST00000585331.2_Intron	NM_024899.2	NP_079175.2	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	627					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCGCACTTGGTCTCCACGGCA	0.363																																					p.D627G		Atlas-SNP	.											.	CEP76	45	.	0			c.A1880G						.						102	101	102					18																	12673464		2203	4300	6503	SO:0001583	missense	79959	exon12			ACTTGGTCTCCAC	BC026307	CCDS11861.1, CCDS62390.1	18p11.21	2014-02-20	2005-12-01	2005-12-01	ENSG00000101624	ENSG00000101624			25727	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 9"	C18orf9		14654843	Standard	NM_024899		Approved	HsT1705, FLJ12542	uc002kri.4	Q8TAP6	OTTHUMG00000131701	ENST00000262127.2:c.1880A>G	chr18.hg19:g.12673464T>C	ENSP00000262127:p.Asp627Gly	126.0	0.0		150.0	6.0	NM_024899	B0YJB2|B4DXG5|B4DZW1|Q658N5|Q9H9U7	Missense_Mutation	SNP	ENST00000262127.2	hg19	CCDS11861.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.656210	0.88056	.	.	ENSG00000101624	ENST00000262127;ENST00000423709	T;T	0.35048	1.33;1.33	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.55955	0.1953	L	0.60845	1.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	T	0.51268	-0.8727	10	0.33141	T	0.24	-3.0266	16.1307	0.81436	0.0:0.0:0.0:1.0	.	552;627	Q8TAP6-2;Q8TAP6	.;CEP76_HUMAN	G	627;552	ENSP00000262127:D627G;ENSP00000403074:D552G	ENSP00000262127:D627G	D	-	2	0	CEP76	12663464	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.263000	0.75096	0.533000	0.62120	GAC	.	.		0.363	CEP76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254611.1	NM_024899		C	12673464	T	C	12673464	3	2	112	1	0	0	0	0	1	0	0	0	3263	1667	58	2	103	2	CEP76	18	12673464	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2001932	12673464	65403784	1054	17675										
POTEC	388468	hgsc.bcm.edu	37	chr18	14542924	14542924	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccacgttgctcgtgccgctCcccctgcagcaggggaagca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:14542924delC	ENST00000358970.5	-	1	221	c.222delG	c.(220-222)gggfs	p.G74fs	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	74										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TCGTGCCGCTCCCCCTGCAGC	0.567																																					p.S75fs		Atlas-INDEL	.											.	POTEC	129	.	0			c.223delA						.						45	56	53					18																	14542924		692	1591	2283	SO:0001589	frameshift_variant	388468	exon1			.	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33894	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 6"		"ANKRD26-like family B, member 2"	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.222delG	chr18.hg19:g.14542924delC	ENSP00000351856:p.Gly74fs	422.0	0.0		461.0	29.0	NM_001137671		Frame_Shift_Del	DEL	ENST00000358970.5	hg19	CCDS45835.1																																																																																			.	.		0.567	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		-	14542924	C	-	14542924	7	5	112	1	0	1	0	1	0	0	0	0	12271	842	30	0	1450	0	POTEC	18	14542924	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1869460	14542924	63534324	1055	17676										
RBBP8	5932	hgsc.bcm.edu	37	chr18	20573135	20573135	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccgaacatccaaaaggaagAaaactgaggaagaaagtgaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:20573135delA	ENST00000399722.2	+	11	1696	c.1345delA	c.(1345-1347)aaafs	p.K449fs	RBBP8_ENST00000399725.2_Frame_Shift_Del_p.K449fs|RBBP8_ENST00000360790.5_Frame_Shift_Del_p.K449fs|RBBP8_ENST00000327155.5_Frame_Shift_Del_p.K449fs	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	449					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			CAAAAGGAAGAAAACTGAGGA	0.403								Homologous recombination																													p.K448fs		Atlas-INDEL	.											.	RBBP8	138	.	0			c.1344delG						.						49	52	51					18																	20573135		2198	4298	6496	SO:0001589	frameshift_variant	5932	exon11			.	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"CTBP-interacting protein"	604124	"retinoblastoma-binding protein 8", "Seckel syndrome 2"	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.1345delA	chr18.hg19:g.20573135delA	ENSP00000382628:p.Lys449fs	150.0	0.0		136.0	10.0	NM_203292	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Frame_Shift_Del	DEL	ENST00000399722.2	hg19	CCDS11875.1																																																																																			.	.		0.403	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		-	20573135	A	-	20573135	7	5	112	1	0	1	0	1	0	0	0	0	13120	247	9	0	1383	0	RBBP8	18	20573135	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	6030211	20573135	57504113	1056	17677										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21494402	21494402	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggactacatcggcatggcagTtgtggatggccagctcacct	13	11	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:21494402T>C	ENST00000313654.9	+	57	7599	c.7358T>C	c.(7357-7359)gTt>gCt	p.V2453A	LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Missense_Mutation_p.V844A|LAMA3_ENST00000587184.1_Missense_Mutation_p.V788A|LAMA3_ENST00000399516.3_Missense_Mutation_p.V2397A	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2453	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GGCATGGCAGTTGTGGATGGC	0.542																																					p.V2453A		Atlas-SNP	.											.	LAMA3	397	.	0			c.T7358C						.						83	77	79					18																	21494402		2203	4300	6503	SO:0001583	missense	3909	exon57			TGGCAGTTGTGGA	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.7358T>C	chr18.hg19:g.21494402T>C	ENSP00000324532:p.Val2453Ala	63.0	0.0		65.0	4.0	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.852232	0.51270	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.75821	-0.97;-0.97;-0.97	5.25	5.25	0.73442	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.82346	0.5017	M	0.77820	2.39	0.23371	N	0.997819	B;P;P;P	0.49185	0.309;0.549;0.866;0.92	B;B;P;P	0.51657	0.197;0.32;0.676;0.578	T	0.76556	-0.2916	9	0.72032	D	0.01	.	15.1529	0.72717	0.0:0.0:0.0:1.0	.	788;844;2397;2453	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	A	2453;2397;844	ENSP00000324532:V2453A;ENSP00000382432:V2397A;ENSP00000269217:V844A	ENSP00000269217:V844A	V	+	2	0	LAMA3	19748400	0.965000	0.33210	0.009000	0.14445	0.147000	0.21601	6.957000	0.76019	1.977000	0.57605	0.459000	0.35465	GTT	.	.		0.542	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		C	21494402	T	C	21494402	3	2	112	1	0	0	0	0	1	0	0	0	8616	1725	60	2	7759	2	LAMA3	18	21494402	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	921267	21494402	56582846	1057	17678										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21494698	21494698	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggcttaattacaccaaaggAgccacatccagtaaaccaga	7	11	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:21494698A>G	ENST00000313654.9	+	58	7759	c.7518A>G	c.(7516-7518)ggA>ggG	p.G2506G	LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Silent_p.G897G|LAMA3_ENST00000587184.1_Silent_p.G841G|LAMA3_ENST00000399516.3_Silent_p.G2450G	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2506	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					ACACCAAAGGAGCCACATCCA	0.328																																					p.G2506G		Atlas-SNP	.											.	LAMA3	397	.	0			c.A7518G						.						60	60	60					18																	21494698		2203	4300	6503	SO:0001819	synonymous_variant	3909	exon58			CAAAGGAGCCACA	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.7518A>G	chr18.hg19:g.21494698A>G		109.0	0.0		113.0	5.0	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.		0.328	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		G	21494698	A	G	21494698	2	3	112	1	0	0	0	0	0	0	0	1	8616	291	11	2		2	LAMA3	18	21494698	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	296	21494698	56582550	1058	17679										
TTC39C	125488	hgsc.bcm.edu	37	chr18	21662914	21662914	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atcatactgtagtccgcccgTtttttgccttggatggcagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:21662914delT	ENST00000317571.3	+	6	1089	c.853delT	c.(853-855)tttfs	p.F286fs	RP11-403A21.3_ENST00000578443.1_RNA|TTC39C_ENST00000304621.6_Frame_Shift_Del_p.F225fs	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	286										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						AGTCCGCCCGTTTTTTGCCTT	0.413																																					p.P284fs		Atlas-INDEL	.											.	TTC39C	83	.	0			c.852delG						.						186	180	182					18																	21662914		2203	4300	6503	SO:0001589	frameshift_variant	125488	exon6			.	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"Tetratricopeptide (TTC) repeat domain containing"	26595	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 17"	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.853delT	chr18.hg19:g.21662914delT	ENSP00000323645:p.Phe286fs	127.0	0.0		162.0	10.0	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Frame_Shift_Del	DEL	ENST00000317571.3	hg19	CCDS45839.1																																																																																			.	.		0.413	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211		-	21662914	T	-	21662914	7	5	112	1	0	1	0	1	0	0	0	0	16724	1725	60	0	875	0	TTC39C	18	21662914	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	168216	21662914	56414334	1059	17680										
DSG2	1829	hgsc.bcm.edu	37	chr18	29125991	29125991	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatggttaattcagagaataCctactcctctggcagtagct	8	9	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:29125991C>T	ENST00000261590.8	+	15	2851	c.2642C>T	c.(2641-2643)aCc>aTc	p.T881I	RP11-75N4.2_ENST00000583706.1_RNA	NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	881					apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			TCAGAGAATACCTACTCCTCT	0.403																																					p.T881I		Atlas-SNP	.											.	DSG2	115	.	0			c.C2642T						.						70	68	69					18																	29125991		1870	4100	5970	SO:0001583	missense	1829	exon15			AGAATACCTACTC	Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"Cadherins / Major cadherins"	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.2642C>T	chr18.hg19:g.29125991C>T	ENSP00000261590:p.Thr881Ile	65.0	0.0		79.0	4.0	NM_001943	Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	hg19	CCDS42423.1	.	.	.	.	.	.	.	.	.	.	C	8.610	0.888861	0.17540	.	.	ENSG00000046604	ENST00000261590	T	0.59906	0.23	5.63	3.82	0.43975	.	0.971478	0.08457	N	0.943034	T	0.47820	0.1466	L	0.36672	1.1	0.24752	N	0.992975	P	0.42785	0.79	B	0.36719	0.231	T	0.31943	-0.9925	10	0.59425	D	0.04	.	10.6835	0.45828	0.0:0.7952:0.1331:0.0717	.	881	Q14126	DSG2_HUMAN	I	881	ENSP00000261590:T881I	ENSP00000261590:T881I	T	+	2	0	DSG2	27379989	0.001000	0.12720	0.000000	0.03702	0.034000	0.12701	0.662000	0.25038	0.705000	0.31890	0.591000	0.81541	ACC	.	.		0.403	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943		T	29125991	C	T	29125991	3	4	112	1	0	0	0	0	1	0	0	0	4779	507	18	3	2700	3	DSG2	18	29125991	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	7463077	29125991	48951257	1060	17681										
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29429604	29429604	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acagcatcctctgttgactgTttttctgtatgcacaggcaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:29429604delT	ENST00000283351.4	-	25	3995	c.3660delA	c.(3658-3660)aaafs	p.K1220fs	TRAPPC8_ENST00000582539.1_Frame_Shift_Del_p.K1166fs	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	1220					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTGTTGACTGTTTTTCTGTAT	0.358																																					p.Q1221fs		Atlas-INDEL	.											.	TRAPPC8	126	.	0			c.3661delC						.						124	111	116					18																	29429604		2203	4300	6503	SO:0001589	frameshift_variant	22878	exon25			.	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.3660delA	chr18.hg19:g.29429604delT	ENSP00000283351:p.Lys1220fs	146.0	0.0		159.0	10.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Frame_Shift_Del	DEL	ENST00000283351.4	hg19	CCDS11901.1																																																																																			.	.		0.358	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		-	29429604	T	-	29429604	7	5	112	1	0	1	0	1	0	0	0	0	8213	1722	60	0	667	0	KIAA1012	18	29429604	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	303613	29429604	48647644	1061	17682										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31320093	31320093	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tacaggacaagcaatatatcTcatcagtggataaggctcca	8	9	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:31320093T>C	ENST00000269197.5	+	11	2725	c.2725T>C	c.(2725-2727)Tca>Cca	p.S909P		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	909					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						GCAATATATCTCATCAGTGGA	0.393																																					p.S909P		Atlas-SNP	.											.	ASXL3	405	.	0			c.T2725C						.						89	85	86					18																	31320093		1860	4098	5958	SO:0001583	missense	80816	exon11			TATATCTCATCAG	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.2725T>C	chr18.hg19:g.31320093T>C	ENSP00000269197:p.Ser909Pro	108.0	0.0		100.0	4.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	T	0.159	-1.083017	0.01888	.	.	ENSG00000141431	ENST00000269197	T	0.15487	2.42	5.86	2.29	0.28610	.	1.176010	0.06075	N	0.660859	T	0.10165	0.0249	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39418	-0.9615	10	0.21540	T	0.41	.	4.3564	0.11181	0.1347:0.2186:0.0:0.6467	.	909	Q9C0F0	ASXL3_HUMAN	P	909	ENSP00000269197:S909P	ENSP00000269197:S909P	S	+	1	0	ASXL3	29574091	0.083000	0.21467	0.001000	0.08648	0.039000	0.13416	0.095000	0.15127	0.168000	0.19655	0.533000	0.62120	TCA	.	.		0.393	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			C	31320093	T	C	31320093	3	2	112	1	0	0	0	0	1	0	0	0	1068	1551	54	2	2767	2	ASXL3	18	31320093	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1890489	31320093	46757155	1062	17683										
MOCOS	55034	hgsc.bcm.edu	37	chr18	33800091	33800091	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggttgtgaatcacaatggtgTttgcctgagtcagaagcagg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:33800091delT	ENST00000261326.5	+	9	1892	c.1871delT	c.(1870-1872)gttfs	p.V624fs		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CACAATGGTGTTTGCCTGAGT	0.517																																					p.V624fs		Atlas-INDEL	.											.	MOCOS	84	.	0			c.1870delG						.						150	131	138					18																	33800091		2203	4300	6503	SO:0001589	frameshift_variant	55034	exon9			.	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.1871delT	chr18.hg19:g.33800091delT	ENSP00000261326:p.Val624fs	121.0	0.0		135.0	10.0	NM_017947		Frame_Shift_Del	DEL	ENST00000261326.5	hg19	CCDS11919.1																																																																																			.	.		0.517	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			-	33800091	T	-	33800091	7	5	112	1	0	1	0	1	0	0	0	0	9698	1725	60	0	1905	0	MOCOS	18	33800091	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	2479998	33800091	44277157	1063	17684										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34205516	34205516	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcgatgagaccacggagccaCcccccagtgggtgccgggac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:34205516delC	ENST00000359247.4	+	10	1000	c.1000delC	c.(1000-1002)cccfs	p.P335fs	FHOD3_ENST00000590592.1_Frame_Shift_Del_p.P335fs|FHOD3_ENST00000445677.1_Frame_Shift_Del_p.P335fs|FHOD3_ENST00000257209.4_Frame_Shift_Del_p.P335fs|FHOD3_ENST00000591635.1_Frame_Shift_Del_p.H8fs	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	335	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.S336fs*138(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CACGGAGCCACCCCCCAGTGG	0.677																																					p.P333fs		Atlas-INDEL	.											.	FHOD3	210	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.999delA						.						40	44	43					18																	34205516		2203	4299	6502	SO:0001589	frameshift_variant	80206	exon10			.	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.1000delC	chr18.hg19:g.34205516delC	ENSP00000352186:p.Pro335fs	105.0	0.0		144.0	10.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Frame_Shift_Del	DEL	ENST00000359247.4	hg19																																																																																				.	.		0.677	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		-	34205516	C	-	34205516	7	5	112	1	0	1	0	1	0	0	0	0	5891	507	18	0	1038	0	FHOD3	18	34205516	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	405425	34205516	43871732	1064	17685										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43532416	43532416	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcagaacagctgaactactgAgcaatgcatagatgtaagac	9	8	1	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:43532416A>G	ENST00000282041.5	-	3	1236	c.1202T>C	c.(1201-1203)cTc>cCc	p.L401P		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	401					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TGAACTACTGAGCAATGCATA	0.423																																					p.L401P		Atlas-SNP	.											.	EPG5	199	.	0			c.T1202C						.						106	102	103					18																	43532416		1934	4137	6071	SO:0001583	missense	57724	exon3			CTACTGAGCAATG	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.1202T>C	chr18.hg19:g.43532416A>G	ENSP00000282041:p.Leu401Pro	91.0	0.0		100.0	4.0	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	A	18.28	3.588365	0.66105	.	.	ENSG00000152223	ENST00000282041	T	0.80994	-1.44	5.38	5.38	0.77491	.	0.556823	0.18742	N	0.132439	D	0.87517	0.6197	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.68483	0.958;0.958	D	0.88122	0.2832	10	0.66056	D	0.02	-8.0382	15.6912	0.77453	1.0:0.0:0.0:0.0	.	401;401	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	P	401	ENSP00000282041:L401P	ENSP00000282041:L401P	L	-	2	0	EPG5	41786414	1.000000	0.71417	0.784000	0.31847	0.520000	0.34377	8.473000	0.90410	2.170000	0.68504	0.460000	0.39030	CTC	.	.		0.423	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		G	43532416	A	G	43532416	3	3	112	1	0	0	0	0	1	0	0	0	8258	304	11	2	6705	2	KIAA1632	18	43532416	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	9326900	43532416	34544832	1065	17686										
DCC	1630	hgsc.bcm.edu	37	chr18	50278698	50278698	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caatgtgaggcatctttaggAgattctggctcaattattag	10	6	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:50278698A>G	ENST00000442544.2	+	2	982	c.366A>G	c.(364-366)ggA>ggG	p.G122G	DCC_ENST00000412726.1_5'UTR	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	122	Ig-like C2-type 1.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CATCTTTAGGAGATTCTGGCT	0.443																																					p.G122G		Atlas-SNP	.											.	DCC	360	.	0			c.A366G						.						128	119	122					18																	50278698		2203	4300	6503	SO:0001819	synonymous_variant	1630	exon2			TTTAGGAGATTCT	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.366A>G	chr18.hg19:g.50278698A>G		146.0	0.0		163.0	7.0	NM_005215		Silent	SNP	ENST00000442544.2	hg19	CCDS11952.1																																																																																			.	.		0.443	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		G	50278698	A	G	50278698	2	3	112	1	0	0	0	0	0	0	0	1	4284	291	11	2		2	DCC	18	50278698	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	6746282	50278698	27798550	1066	17687										
POLI	11201	hgsc.bcm.edu	37	chr18	51807238	51807238	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acctgaaagttgtcaacatcTtattcatagtttgaatcaca	5	8	4	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:51807238T>C	ENST00000579534.1	+	5	904	c.761T>C	c.(760-762)cTt>cCt	p.L254P	POLI_ENST00000217800.5_Missense_Mutation_p.L128P|POLI_ENST00000406285.3_Intron|POLI_ENST00000579434.1_Missense_Mutation_p.L151P	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	254	UmuC. {ECO:0000255|PROSITE- ProRule:PRU00216}.				DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		TGTCAACATCTTATTCATAGT	0.279								DNA polymerases (catalytic subunits)																													p.L254P		Atlas-SNP	.											.	POLI	132	.	0			c.T761C						.						58	61	60					18																	51807238		2203	4300	6503	SO:0001583	missense	11201	exon5			AACATCTTATTCA		CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"DNA polymerases"	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.761T>C	chr18.hg19:g.51807238T>C	ENSP00000462664:p.Leu254Pro	74.0	0.0		76.0	4.0	NM_007195	Q8N590|Q9H0S1|Q9NYH6	Missense_Mutation	SNP	ENST00000579534.1	hg19	CCDS11954.2	.	.	.	.	.	.	.	.	.	.	T	12.86	2.065191	0.36470	.	.	ENSG00000101751	ENST00000217800	.	.	.	5.72	5.72	0.89469	DNA-repair protein, UmuC-like, N-terminal (1);	0.123680	0.56097	D	0.000032	T	0.81800	0.4899	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85130	0.0974	9	0.72032	D	0.01	-6.7447	13.816	0.63292	0.0:0.0:0.0:1.0	.	254	Q9UNA4	POLI_HUMAN	P	254	.	ENSP00000217800:L254P	L	+	2	0	POLI	50061236	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	4.985000	0.63845	2.304000	0.77564	0.528000	0.53228	CTT	.	.		0.279	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195		C	51807238	T	C	51807238	3	2	112	1	0	0	0	0	1	0	0	0	12212	1609	56	2	779	2	POLI	18	51807238	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1528540	51807238	26270010	1067	17688										
WDR7	23335	hgsc.bcm.edu	37	chr18	54547190	54547190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcaggttgcttatcaagtgTcccacaaatgaaaaaaattt	6	7	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:54547190T>C	ENST00000254442.3	+	21	3531	c.3320T>C	c.(3319-3321)gTc>gCc	p.V1107A	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Missense_Mutation_p.V1074A	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	1107					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TTATCAAGTGTCCCACAAATG	0.363																																					p.V1107A		Atlas-SNP	.											WDR7,colon,carcinoma,0,1	WDR7	166	.	0			c.T3320C						.						73	68	70					18																	54547190		2203	4300	6503	SO:0001583	missense	23335	exon21			CAAGTGTCCCACA	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"WD repeat domain containing"	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.3320T>C	chr18.hg19:g.54547190T>C	ENSP00000254442:p.Val1107Ala	92.0	0.0		131.0	6.0	NM_015285	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Missense_Mutation	SNP	ENST00000254442.3	hg19	CCDS11962.1	.	.	.	.	.	.	.	.	.	.	T	4.589	0.109480	0.08780	.	.	ENSG00000091157	ENST00000254442;ENST00000357574;ENST00000444065;ENST00000398311	T;T	0.69926	-0.44;1.47	5.37	4.21	0.49690	.	0.358804	0.29508	N	0.011960	T	0.44498	0.1296	N	0.14661	0.345	0.30187	N	0.799835	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.32428	-0.9907	10	0.09084	T	0.74	.	10.8785	0.46925	0.0:0.0749:0.0:0.9251	.	1074;1107	Q9Y4E6-2;Q9Y4E6	.;WDR7_HUMAN	A	1107;1074;432;1074	ENSP00000254442:V1107A;ENSP00000350187:V1074A	ENSP00000254442:V1107A	V	+	2	0	WDR7	52698188	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	3.661000	0.54503	0.991000	0.38814	0.533000	0.62120	GTC	.	.		0.363	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			C	54547190	T	C	54547190	3	2	112	1	0	0	0	0	1	0	0	0	17335	1667	58	2	3398	2	WDR7	18	54547190	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2739952	54547190	23530058	1068	17689										
ST8SIA3	51046	hgsc.bcm.edu	37	chr18	55024466	55024466	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaagaaaaaccaatcttaccAccttcaaccccagcatcctg	4	15	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:55024466A>G	ENST00000324000.3	+	3	2659	c.625A>G	c.(625-627)Acc>Gcc	p.T209A		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	209					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		CAATCTTACCACCTTCAACCC	0.403																																					p.T209A		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.A625G						.						66	68	67					18																	55024466		2203	4300	6503	SO:0001583	missense	51046	exon3			CTTACCACCTTCA	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"Sialyltransferases"	14269	protein-coding gene	gene with protein product	"ST8Sia III"	609478	"sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.625A>G	chr18.hg19:g.55024466A>G	ENSP00000320431:p.Thr209Ala	69.0	0.0		92.0	4.0	NM_015879	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	hg19	CCDS32834.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.147013	0.77888	.	.	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.32988	1.43	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.63117	0.2484	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.70799	-0.4774	10	0.87932	D	0	-10.9553	15.897	0.79341	1.0:0.0:0.0:0.0	.	209	O43173	SIA8C_HUMAN	A	316;209	ENSP00000320431:T209A	ENSP00000320431:T209A	T	+	1	0	ST8SIA3	53175464	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.936000	0.92931	2.238000	0.73509	0.533000	0.62120	ACC	.	.		0.403	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879		G	55024466	A	G	55024466	3	3	112	1	0	0	0	0	1	0	0	0	15248	159	6	2	635	2	ST8SIA3	18	55024466	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	477276	55024466	23052782	1069	17690										
ST8SIA3	51046	hgsc.bcm.edu	37	chr18	55027237	55027237	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gttccacaggtactggaaaaAcaaacatttgtcacctaaac	6	10	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:55027237A>G	ENST00000324000.3	+	4	2906	c.872A>G	c.(871-873)aAc>aGc	p.N291S		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	291					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		TACTGGAAAAACAAACATTTG	0.423																																					p.N291S		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.A872G						.						85	81	82					18																	55027237		2203	4300	6503	SO:0001583	missense	51046	exon4			GGAAAAACAAACA	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"Sialyltransferases"	14269	protein-coding gene	gene with protein product	"ST8Sia III"	609478	"sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.872A>G	chr18.hg19:g.55027237A>G	ENSP00000320431:p.Asn291Ser	101.0	0.0		94.0	4.0	NM_015879	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	hg19	CCDS32834.1	.	.	.	.	.	.	.	.	.	.	A	13.27	2.187544	0.38609	.	.	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.28069	1.63	6.11	4.95	0.65309	.	0.084546	0.85682	N	0.000000	T	0.15609	0.0376	N	0.10809	0.05	0.48452	D	0.999657	B	0.26002	0.139	B	0.25506	0.061	T	0.06588	-1.0818	10	0.09843	T	0.71	-12.7948	11.8217	0.52242	0.9313:0.0:0.0687:0.0	.	291	O43173	SIA8C_HUMAN	S	398;291	ENSP00000320431:N291S	ENSP00000320431:N291S	N	+	2	0	ST8SIA3	53178235	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.683000	0.54663	1.125000	0.41998	0.533000	0.62120	AAC	.	.		0.423	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879		G	55027237	A	G	55027237	3	3	112	1	0	0	0	0	1	0	0	0	15248	43	2	2	886	2	ST8SIA3	18	55027237	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2771	55027237	23050011	1070	17691										
ALPK2	115701	hgsc.bcm.edu	37	chr18	56246440	56246440	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccctcttgctccataagtccTttccccccactctcttgtca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:56246440delT	ENST00000361673.3	-	4	1781	c.1568delA	c.(1567-1569)aagfs	p.K523fs	ALPK2_ENST00000587399.1_5'UTR	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	523						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCATAAGTCCTTTCCCCCCAC	0.522											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K523fs		Atlas-INDEL	.											.	ALPK2	487	.	0			c.1569delG						.						227	226	226					18																	56246440		2203	4300	6503	SO:0001589	frameshift_variant	115701	exon4			.	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.1568delA	chr18.hg19:g.56246440delT	ENSP00000354991:p.Lys523fs	105.0	0.0	1014	124.0	10.0	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Frame_Shift_Del	DEL	ENST00000361673.3	hg19	CCDS11966.2																																																																																			.	.		0.522	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		-	56246440	T	-	56246440	7	5	112	1	0	1	0	1	0	0	0	0	545	1609	56	0	4984	0	ALPK2	18	56246440	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1219203	56246440	21830808	1071	17692										
ZNF532	55205	hgsc.bcm.edu	37	chr18	56651255	56651255	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagttctggagttcaggcctCcccgaggagcaatcactcaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:56651255delC	ENST00000336078.4	+	11	4239	c.3463delC	c.(3463-3465)cccfs	p.P1155fs	ZNF532_ENST00000591808.1_Frame_Shift_Del_p.P1155fs|ZNF532_ENST00000591230.1_Frame_Shift_Del_p.P1155fs|ZNF532_ENST00000588956.1_3'UTR|ZNF532_ENST00000589288.1_Frame_Shift_Del_p.P1155fs|ZNF532_ENST00000591083.1_Frame_Shift_Del_p.P1155fs	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	1155					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						GTTCAGGCCTCCCCGAGGAGC	0.493																																					p.P1154fs		Atlas-INDEL	.											.	ZNF532	108	.	0			c.3462delT						.						77	78	78					18																	56651255		2203	4300	6503	SO:0001589	frameshift_variant	55205	exon11			.	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.3463delC	chr18.hg19:g.56651255delC	ENSP00000338217:p.Pro1155fs	223.0	0.0		253.0	16.0	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Frame_Shift_Del	DEL	ENST00000336078.4	hg19	CCDS11969.1																																																																																			.	.		0.493	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		-	56651255	C	-	56651255	7	5	112	1	0	1	0	1	0	0	0	0	17987	855	30	0	3493	0	ZNF532	18	56651255	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	404815	56651255	21425993	1072	17693										
DSEL	92126	hgsc.bcm.edu	37	chr18	65178866	65178866	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aggacgtgcacttggatagtAaaccaggtgtctcctcaaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:65178866delA	ENST00000310045.7	-	2	4483	c.3010delT	c.(3010-3012)tacfs	p.Y1005fs	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	995					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				CTTGGATAGTAAACCAGGTGT	0.418																																					p.Y1004fs		Atlas-INDEL	.											.	DSEL	196	.	0			c.3011delA						.						63	67	66					18																	65178866		2203	4300	6503	SO:0001589	frameshift_variant	92126	exon2			.	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.3010delT	chr18.hg19:g.65178866delA	ENSP00000310565:p.Tyr1005fs	135.0	0.0		147.0	13.0	NM_032160	Q17RH1|Q6P5Z3	Frame_Shift_Del	DEL	ENST00000310045.7	hg19	CCDS11995.1																																																																																			.	.		0.418	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		-	65178866	A	-	65178866	7	5	112	1	0	1	0	1	0	0	0	0	4777	362	13	0	662	0	DSEL	18	65178866	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	8527611	65178866	12898382	1073	17694										
PRSSL1	400668	hgsc.bcm.edu	37	chr19	687117	687117	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cggcaccgtgtccccgctgtGgggggcctggcccttctccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:687117delG	ENST00000329267.7	-	4	482	c.453delC	c.(451-453)cccfs	p.P151fs		NM_214710.3	NP_999875	Q6UWY2	PRS57_HUMAN	protease, serine, 57	151	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|lung(5)	6						TCCCCGCTGTGGGGGGCCTGG	0.682																																					p.T152fs		Atlas-INDEL	.											.	PRSS57	18	.	0			c.454delA						.																																			SO:0001589	frameshift_variant	400668	exon4			.	AY358594	CCDS12041.1	19p13.3	2012-03-26	2011-03-07	2011-03-07		ENSG00000185198		"Serine peptidases / Serine peptidases"	31397	protein-coding gene	gene with protein product			"protease, serine-like 1"	PRSSL1		12975309	Standard	NM_214710		Approved	UNQ782	uc002lpl.1	Q6UWY2		ENST00000329267.7:c.453delC	chr19.hg19:g.687117delG	ENSP00000327386:p.Pro151fs	155.0	0.0		175.0	11.0	NM_214710	B2RNW8	Frame_Shift_Del	DEL	ENST00000329267.7	hg19	CCDS12041.1																																																																																			.	.		0.682	PRSS57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452480.2	NM_214710		-	687117	G	-	687117	7	5	112	1	0	1	0	1	0	0	0	0	12648	1335	47	0	406	0	PRSSL1	19	687117	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10		687117	58441866	1074	17695										
ARID3A	1820	hgsc.bcm.edu	37	chr19	932477	932477	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cggggaggatgaggaggaggAggaggaggattacgaggatg	23	2	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:932477A>G	ENST00000263620.3	+	3	755	c.428A>G	c.(427-429)gAg>gGg	p.E143G		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	143	Acidic.|Glu-rich.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gaggaggaggaggaggaggat	0.652																																					p.E143G	Pancreas(29;54 1022 32760 50921)	Atlas-SNP	.											.	ARID3A	35	.	0			c.A428G						.						13	12	12					19																	932477		2185	4277	6462	SO:0001583	missense	1820	exon3			AGGAGGAGGAGGA	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"-"	3031	protein-coding gene	gene with protein product		603265	"dead ringer-like 1 (Drosophila)", "AT rich interactive domain 3A (BRIGHT- like)"	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.428A>G	chr19.hg19:g.932477A>G	ENSP00000263620:p.Glu143Gly	48.0	0.0		71.0	4.0	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Missense_Mutation	SNP	ENST00000263620.3	hg19	CCDS12050.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.484176	0.44147	.	.	ENSG00000116017	ENST00000263620	T	0.13307	2.6	3.66	3.66	0.41972	.	0.324761	0.26159	N	0.025998	T	0.09686	0.0238	L	0.29908	0.895	0.36972	D	0.893854	P	0.34522	0.455	B	0.31614	0.133	T	0.29518	-1.0009	10	0.30854	T	0.27	.	11.2668	0.49114	1.0:0.0:0.0:0.0	.	143	Q99856	ARI3A_HUMAN	G	143	ENSP00000263620:E143G	ENSP00000263620:E143G	E	+	2	0	ARID3A	883477	0.996000	0.38824	0.184000	0.23157	0.675000	0.39556	3.832000	0.55783	1.527000	0.49086	0.375000	0.23000	GAG	.	.		0.652	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224		G	932477	A	G	932477	3	3	112	1	0	0	0	0	1	0	0	0	916	304	11	2	434	2	ARID3A	19	932477	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	245360	932477	58196506	1075	17696										
MKNK2	2872	hgsc.bcm.edu	37	chr19	2041918	2041918	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgaagggcgggtagccgctgAgtaggatatacaagatgacg	16	7	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:2041918A>G	ENST00000591601.1	-	10	901	c.866T>C	c.(865-867)cTc>cCc	p.L289P	MKNK2_ENST00000250896.3_Missense_Mutation_p.L289P|MKNK2_ENST00000591142.1_Missense_Mutation_p.L33P|MKNK2_ENST00000588014.1_Missense_Mutation_p.L33P|MKNK2_ENST00000309340.7_Missense_Mutation_p.L289P|MKNK2_ENST00000541165.1_Missense_Mutation_p.L158P|MKNK2_ENST00000591588.1_Missense_Mutation_p.L33P			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	289	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTAGCCGCTGAGTAGGATATA	0.687																																					p.L289P		Atlas-SNP	.											.	MKNK2	56	.	0			c.T866C						.						26	22	23					19																	2041918		2129	4174	6303	SO:0001583	missense	2872	exon11			CCGCTGAGTAGGA	AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"Putative map kinase interacting kinase"	605069	"G protein-coupled receptor kinase 7"	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.866T>C	chr19.hg19:g.2041918A>G	ENSP00000467811:p.Leu289Pro	71.0	0.0		54.0	4.0	NM_017572	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	hg19	CCDS12080.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.150244	0.57151	.	.	ENSG00000099875	ENST00000309340;ENST00000250896;ENST00000541165;ENST00000545627	T;T;T	0.53206	0.63;0.63;0.63	4.08	4.08	0.47627	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.79470	0.4451	H	0.98487	4.245	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.998;0.999	D	0.86533	0.1823	10	0.87932	D	0	-9.2055	12.3786	0.55293	1.0:0.0:0.0:0.0	.	94;289;289;191	Q59GN5;Q9HBH9;Q9HBH9-2;Q9NT28	.;MKNK2_HUMAN;.;.	P	289;289;158;229	ENSP00000309485:L289P;ENSP00000250896:L289P;ENSP00000438904:L158P	ENSP00000250896:L289P	L	-	2	0	MKNK2	1992918	1.000000	0.71417	1.000000	0.80357	0.116000	0.19942	8.803000	0.91915	1.712000	0.51347	0.454000	0.30748	CTC	.	.		0.687	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054		G	2041918	A	G	2041918	3	3	112	1	0	0	0	0	1	0	0	0	9614	304	11	2	642	2	MKNK2	19	2041918	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1109441	2041918	57087065	1076	17697										
AP3D1	8943	hgsc.bcm.edu	37	chr19	2123875	2123875	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgccggaggacagcgagatgAgcactgcaacagacagcttg	14	10	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:2123875A>G	ENST00000345016.5	-	10	1091	c.860T>C	c.(859-861)cTc>cCc	p.L287P	AP3D1_ENST00000355272.6_Missense_Mutation_p.L287P|AP3D1_ENST00000350812.6_Missense_Mutation_p.L118P|AP3D1_ENST00000590683.1_5'UTR|AP3D1_ENST00000356926.4_Missense_Mutation_p.L196P	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	287					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCGAGATGAGCACTGCAAC	0.687																																					p.L287P		Atlas-SNP	.											.	AP3D1	81	.	0			c.T860C						.						90	101	97					19																	2123875		2192	4285	6477	SO:0001583	missense	8943	exon10			GAGATGAGCACTG	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.860T>C	chr19.hg19:g.2123875A>G	ENSP00000344055:p.Leu287Pro	136.0	0.0		147.0	8.0	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	hg19	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.673405	0.88445	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	T;T;T;T	0.24538	1.85;1.85;1.85;1.85	5.07	5.07	0.68467	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.47619	0.1455	M	0.63208	1.945	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.43507	-0.9387	10	0.48119	T	0.1	-38.2157	13.9963	0.64405	1.0:0.0:0.0:0.0	.	287;287;196	O14617-5;O14617;G5E988	.;AP3D1_HUMAN;.	P	196;287;287;287;118	ENSP00000349398:L196P;ENSP00000344055:L287P;ENSP00000347416:L287P;ENSP00000342321:L118P	ENSP00000341579:L287P	L	-	2	0	AP3D1	2074875	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	8.755000	0.91646	1.909000	0.55274	0.460000	0.39030	CTC	.	.		0.687	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1			G	2123875	A	G	2123875	3	3	112	1	0	0	0	0	1	0	0	0	746	304	11	2	2843	2	AP3D1	19	2123875	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	81957	2123875	57005108	1077	17698										
JSRP1	126306	hgsc.bcm.edu	37	chr19	2254202	2254202	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccactcgctccggctttcagCctctccttccccgttcctgg	7	20	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:2254202C>T	ENST00000300961.6	-	4	310	c.246G>A	c.(244-246)agG>agA	p.R82R	JSRP1_ENST00000586471.2_Silent_p.R82R	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	82					protein localization to membrane (GO:0072657)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|skeletal muscle contraction (GO:0003009)	membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|pancreas(1)|urinary_tract(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGCTTTCAGCCTCTCCTTCC	0.637											OREG0025137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R82R		Atlas-SNP	.											.	JSRP1	18	.	0			c.G246A						.						133	132	132					19																	2254202		2203	4300	6503	SO:0001819	synonymous_variant	126306	exon4			TTTCAGCCTCTCC	AK056978	CCDS12086.1	19p13.3	2010-03-23			ENSG00000167476	ENSG00000167476			24963	protein-coding gene	gene with protein product	"homolog of mouse skeletal muscle sarcoplasmic reticulum protein JP-45"	608743				12871958	Standard	NM_144616		Approved	JP-45, FLJ32416	uc002lvj.2	Q96MG2		ENST00000300961.6:c.246G>A	chr19.hg19:g.2254202C>T		72.0	0.0	602	89.0	4.0	NM_144616		Silent	SNP	ENST00000300961.6	hg19	CCDS12086.1																																																																																			.	.		0.637	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616		T	2254202	C	T	2254202	2	4	112	1	0	0	0	0	0	0	0	1	7975	738	26	3		3	JSRP1	19	2254202	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	130327	2254202	56874781	1078	17699										
ZNF556	80032	hgsc.bcm.edu	37	chr19	2877368	2877368	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	attgtaatcgtcatctgcgcAagaattgttgtactagtgta	9	6	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:2877368A>G	ENST00000307635.2	+	4	499	c.412A>G	c.(412-414)Aag>Gag	p.K138E	ZNF556_ENST00000586426.1_Missense_Mutation_p.K137E	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	138					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCATCTGCGCAAGAATTGTTG	0.433																																					p.K138E		Atlas-SNP	.											.	ZNF556	73	.	0			c.A412G						.						131	114	120					19																	2877368		2203	4300	6503	SO:0001583	missense	80032	exon4			CTGCGCAAGAATT	BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"Zinc fingers, C2H2-type", "-"	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.412A>G	chr19.hg19:g.2877368A>G	ENSP00000302603:p.Lys138Glu	119.0	0.0		95.0	4.0	NM_024967	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	hg19	CCDS12097.1	.	.	.	.	.	.	.	.	.	.	A	4.609	0.113209	0.08831	.	.	ENSG00000172000	ENST00000307635	T	0.05855	3.38	1.95	0.854	0.19007	.	.	.	.	.	T	0.03695	0.0105	N	0.16708	0.43	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.43228	-0.9404	9	0.62326	D	0.03	.	1.8371	0.03142	0.5443:0.0:0.1805:0.2752	.	138	Q9HAH1	ZN556_HUMAN	E	138	ENSP00000302603:K138E	ENSP00000302603:K138E	K	+	1	0	ZNF556	2828368	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.208000	0.17415	0.058000	0.16222	0.334000	0.21626	AAG	.	.		0.433	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967		G	2877368	A	G	2877368	3	3	112	1	0	0	0	0	1	0	0	0	18002	131	5	2	426	2	ZNF556	19	2877368	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	623166	2877368	56251615	1079	17700										
PTPRS	5802	hgsc.bcm.edu	37	chr19	5231449	5231449	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcaggatctgagtggtggtcGgggggatgccgttcacctcc					rs376058028		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:5231449delG	ENST00000587303.1	-	13	2126	c.2027delC	c.(2026-2028)ccgfs	p.P676fs	PTPRS_ENST00000592099.1_Intron|PTPRS_ENST00000588552.1_Intron|PTPRS_ENST00000348075.2_Frame_Shift_Del_p.P663fs|PTPRS_ENST00000372412.4_Frame_Shift_Del_p.P677fs|PTPRS_ENST00000357368.4_Frame_Shift_Del_p.P676fs|PTPRS_ENST00000262963.6_Frame_Shift_Del_p.P672fs|PTPRS_ENST00000588012.1_Frame_Shift_Del_p.P663fs|PTPRS_ENST00000353284.2_Intron			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	676	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	AGTGGTGGTCGGGGGGATGCC	0.667																																					p.P676fs		Atlas-INDEL	.											.	PTPRS	169	.	0			c.2028delG						.						60	48	52					19																	5231449		2203	4300	6503	SO:0001589	frameshift_variant	5802	exon14			.	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.2027delC	chr19.hg19:g.5231449delG	ENSP00000467537:p.Pro676fs	89.0	0.0		102.0	10.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Frame_Shift_Del	DEL	ENST00000587303.1	hg19	CCDS45930.1																																																																																			.	.		0.667	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			-	5231449	G	-	5231449	7	5	112	1	0	1	0	1	0	0	0	0	12826	1116	39	0	3919	0	PTPRS	19	5231449	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2354081	5231449	53897534	1080	17701										
SH2D3A	10045	hgsc.bcm.edu	37	chr19	6755180	6755180	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagttcgaaggagggtgtccGggggggcttcgttggtgcct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:6755180delG	ENST00000245908.6	-	5	912	c.643delC	c.(643-645)cggfs	p.R215fs	SH2D3A_ENST00000437152.3_Frame_Shift_Del_p.R93fs|SH2D3A_ENST00000599563.1_5'UTR	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	215					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						GAGGGTGTCCGGGGGGGCTTC	0.657																																					p.R215fs		Atlas-INDEL	.											.	SH2D3A	53	.	0			c.644delG						.						97	110	106					19																	6755180		2203	4300	6503	SO:0001589	frameshift_variant	10045	exon5			.	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"SH2 domain containing"	16885	protein-coding gene	gene with protein product		604721	"SH2 domain-containing 3A"			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.643delC	chr19.hg19:g.6755180delG	ENSP00000245908:p.Arg215fs	127.0	0.0		168.0	11.0	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Frame_Shift_Del	DEL	ENST00000245908.6	hg19	CCDS12173.1																																																																																			.	.		0.657	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490		-	6755180	G	-	6755180	7	5	112	1	0	1	0	1	0	0	0	0	14248	1115	39	0	1111	0	SH2D3A	19	6755180	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1523731	6755180	52373803	1081	17702										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10087955	10087955	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtgtccgggggcacccacatCcccctgcagaggaaatggga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:10087955delC	ENST00000264828.3	-	44	3323	c.3238delG	c.(3238-3240)gatfs	p.D1080fs		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1080	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			GCACCCACATCCCCCTGCAGA	0.612																																					p.D1080fs		Atlas-INDEL	.											.	COL5A3	243	.	0			c.3239delA						.						114	87	96					19																	10087955		2203	4300	6503	SO:0001589	frameshift_variant	50509	exon44			.	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3238delG	chr19.hg19:g.10087955delC	ENSP00000264828:p.Asp1080fs	115.0	0.0		129.0	10.0	NM_015719	Q9NZQ6	Frame_Shift_Del	DEL	ENST00000264828.3	hg19	CCDS12222.1																																																																																			.	.		0.612	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		-	10087955	C	-	10087955	7	5	112	1	0	1	0	1	0	0	0	0	3700	855	30	0	2095	0	COL5A3	19	10087955	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	3332775	10087955	49041028	1082	17703										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11150224	11150224	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttcagttctgcacacgtgcgTcaaaggtggggagagttctg	14	8	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:11150224T>C	ENST00000429416.3	+	31	4451				SMARCA4_ENST00000413806.3_Intron|SMARCA4_ENST00000538456.3_3'UTR|SMARCA4_ENST00000590574.1_Intron|SMARCA4_ENST00000589677.1_Intron|SMARCA4_ENST00000541122.2_Intron|SMARCA4_ENST00000358026.2_Missense_Mutation_p.S1421P|SMARCA4_ENST00000344626.4_Intron|SMARCA4_ENST00000444061.3_Intron|SMARCA4_ENST00000450717.3_Intron	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4						aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CACACGTGCGTCAAAGGTGGG	0.527			"F, N, Mis"		NSCLC																																p.S1421P		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.T4261C						.						56	52	53					19																	11150224		1566	3580	5146	SO:0001627	intron_variant	6597	exon30			CGTGCGTCAAAGG	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.4171-1759T>C	chr19.hg19:g.11150224T>C		121.0	0.0		112.0	5.0	NM_001128849	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.53|12.53	1.966007|1.966007	0.34659|0.34659	.|.	.|.	ENSG00000127616|ENSG00000127616	ENST00000358026|ENST00000538456	D|.	0.87256|.	-2.23|.	0.727|0.727	0.727|0.727	0.18254|0.18254	.|.	.|.	.|.	.|.	.|.	T|T	0.16685|0.16685	0.0401|0.0401	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	P|.	0.39520|.	0.676|.	B|.	0.39706|.	0.307|.	T|T	0.28202|0.28202	-1.0051|-1.0051	8|4	0.38643|.	T|.	0.18|.	.|.	.|.	.|.	.|.	.|.	1421|.	Q9HBD4|.	.|.	P|A	1421|157	ENSP00000350720:S1421P|.	ENSP00000350720:S1421P|.	S|V	+|+	1|2	0|0	SMARCA4|SMARCA4	11011224|11011224	0.015000|0.015000	0.18098|0.18098	0.007000|0.007000	0.13788|0.13788	0.981000|0.981000	0.71138|0.71138	0.614000|0.614000	0.24314|0.24314	0.555000|0.555000	0.29079|0.29079	0.260000|0.260000	0.18958|0.18958	TCA|GTC	.	.		0.527	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		C	11150224	T	C	11150224	1	2	112	0	1	0	0	0	0	0	0	0	14785	1667	58	2		2	SMARCA4	19	11150224	Intron	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1062269	11150224	47978759	1083	17704										
ELAVL3	1995	hgsc.bcm.edu	37	chr19	11565448	11565448	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggccgcctcgtcatagttggTcatggtcacgaagccgaaac	12	12	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:11565448T>C	ENST00000359227.3	-	7	1421	c.997A>G	c.(997-999)Acc>Gcc	p.T333A	ELAVL3_ENST00000438662.2_Missense_Mutation_p.T326A	NM_001420.3|NM_032281.2	NP_001411.2|NP_115657.2	Q14576	ELAV3_HUMAN	ELAV like neuron-specific RNA binding protein 3	333	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)		AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15						TCATAGTTGGTCATGGTCACG	0.587																																					p.T333A		Atlas-SNP	.											.	ELAVL3	58	.	0			c.A997G						.						157	112	127					19																	11565448		2203	4300	6503	SO:0001583	missense	1995	exon7			AGTTGGTCATGGT		CCDS32912.1, CCDS45978.1	19p13.2	2013-10-03	2013-10-03			ENSG00000196361		"RNA binding motif (RRM) containing"	3314	protein-coding gene	gene with protein product	"Hu antigen C", "paraneoplastic limbic encephalitis antigen 21", "paraneoplastic cerebellar degeneration-associated antigen", "ELAV-like protein 3"	603458	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)"			9799595	Standard	NM_001420		Approved	HUC, PLE21, DKFZp547J036, HUCL, MGC20653	uc002mry.1	Q14576		ENST00000359227.3:c.997A>G	chr19.hg19:g.11565448T>C	ENSP00000352162:p.Thr333Ala	108.0	0.0		127.0	7.0	NM_001420	Q16135|Q96CL8|Q96QS9	Missense_Mutation	SNP	ENST00000359227.3	hg19	CCDS32912.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.769848	0.49680	.	.	ENSG00000196361	ENST00000359227;ENST00000438662	T;T	0.15487	2.42;2.42	4.59	3.55	0.40652	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.105378	0.64402	D	0.000005	T	0.07999	0.0200	N	0.03115	-0.41	0.53688	D	0.999978	B;B	0.27951	0.195;0.075	B;B	0.31016	0.123;0.051	T	0.30238	-0.9985	10	0.37606	T	0.19	.	9.5834	0.39501	0.1575:0.0:0.0:0.8425	.	333;326	Q14576;Q14576-2	ELAV3_HUMAN;.	A	333;326	ENSP00000352162:T333A;ENSP00000390878:T326A	ENSP00000352162:T333A	T	-	1	0	ELAVL3	11426448	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.576000	0.82467	0.598000	0.29829	0.352000	0.21897	ACC	.	.		0.587	ELAVL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458827.2	NM_001420		C	11565448	T	C	11565448	3	2	112	1	0	0	0	0	1	0	0	0	5053	1667	58	2	110	2	ELAVL3	19	11565448	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	415224	11565448	47563535	1084	17705										
PRDX2	7001	hgsc.bcm.edu	37	chr19	12911076	12911076	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcaagcagggggatgttcaGggggcccaagcctccctctt					rs1056648		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:12911076delG	ENST00000301522.2	-	4	423	c.295delC	c.(295-297)ctgfs	p.L99fs	PRDX2_ENST00000334482.5_Frame_Shift_Del_p.L99fs|CTD-2659N19.10_ENST00000585496.1_RNA	NM_005809.4	NP_005800.3	P32119	PRDX2_HUMAN	peroxiredoxin 2	99	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular response to oxidative stress (GO:0034599)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of apoptotic process (GO:0042981)|removal of superoxide radicals (GO:0019430)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)|thioredoxin peroxidase activity (GO:0008379)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4						GGGATGTTCAGGGGGCCCAAG	0.607																																					p.R99fs		Atlas-INDEL	.											.	PRDX2	20	.	0			c.296delG						.						62	67	65					19																	12911076		2203	4300	6503	SO:0001589	frameshift_variant	7001	exon4			.		CCDS12281.1	19p13.2	2008-07-17			ENSG00000167815	ENSG00000167815			9353	protein-coding gene	gene with protein product	"thioredoxin-dependent peroxide reductase 1", "thiol-specific antioxidant 1", "natural killer-enhancing factor B", "thioredoxin peroxidase 1", "torin"	600538		TDPX1		7607688	Standard	NM_005809		Approved	PRP, NKEFB, TSA, PRXII, PRX2, MGC4104	uc002mvd.4	P32119	OTTHUMG00000134285	ENST00000301522.2:c.295delC	chr19.hg19:g.12911076delG	ENSP00000301522:p.Leu99fs	251.0	0.0		227.0	15.0	NM_005809	A8K0C0|P31945|P32118|P35701|Q6FHG4|Q92763|Q9UC23	Frame_Shift_Del	DEL	ENST00000301522.2	hg19	CCDS12281.1																																																																																			.	.		0.607	PRDX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258950.2	NM_005809		-	12911076	G	-	12911076	7	5	112	1	0	1	0	1	0	0	0	0	12477	991	35	0	313	0	PRDX2	19	12911076	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1345628	12911076	46217907	1085	17706										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14031386	14031386	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acagcagaacagccctgtggCccccacagcccagcccaaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:14031386delC	ENST00000318003.7	+	13	1614	c.1373delC	c.(1372-1374)gccfs	p.A458fs	CC2D1A_ENST00000589606.1_Frame_Shift_Del_p.A458fs	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	458					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			AGCCCTGTGGCCCCCACAGCC	0.587																																					p.A458fs		Atlas-INDEL	.											.	CC2D1A	67	.	0			c.1372delG						.						35	49	45					19																	14031386		1930	4129	6059	SO:0001589	frameshift_variant	54862	exon13			.	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.1373delC	chr19.hg19:g.14031386delC	ENSP00000313601:p.Ala458fs	183.0	0.0		193.0	13.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Frame_Shift_Del	DEL	ENST00000318003.7	hg19	CCDS42512.1																																																																																			.	.		0.587	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		-	14031386	C	-	14031386	7	5	112	1	0	1	0	1	0	0	0	0	2728	739	26	0	1423	0	CC2D1A	19	14031386	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1120310	14031386	45097597	1086	17707										
EMR2	30817	hgsc.bcm.edu	37	chr19	14884853	14884853	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacgaggagtcctgagggcaCcaccgggcacagcctgcaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:14884853delC	ENST00000315576.3	-	4	547	c.96delG	c.(94-96)tggfs	p.W32fs	EMR2_ENST00000353005.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000392965.3_Frame_Shift_Del_p.W32fs|EMR2_ENST00000353876.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000599423.1_5'UTR|EMR2_ENST00000392967.2_Frame_Shift_Del_p.W32fs|EMR2_ENST00000594294.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000601345.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000594076.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000595839.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000346057.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000596991.2_Frame_Shift_Del_p.W32fs|EMR2_ENST00000392964.3_5'Flank	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	32	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						CCTGAGGGCACCACCGGGCAC	0.592																																					p.C33fs		Atlas-INDEL	.											.	EMR2	99	.	0			c.97delT						.						117	110	112					19																	14884853		2203	4300	6503	SO:0001589	frameshift_variant	30817	exon3			.	AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"CD molecules", "-", "GPCR / Class B : Orphans"	3337	protein-coding gene	gene with protein product		606100	"egf-like module containing, mucin-like, hormone receptor-like sequence 2"				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.96delG	chr19.hg19:g.14884853delC	ENSP00000319883:p.Trp32fs	144.0	0.0		178.0	12.0	NM_001271052	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Frame_Shift_Del	DEL	ENST00000315576.3	hg19	CCDS32935.1																																																																																			.	.		0.592	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2			-	14884853	C	-	14884853	7	5	112	1	0	1	0	1	0	0	0	0	5107	508	18	0	2447	0	EMR2	19	14884853	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	853467	14884853	44244130	1087	17708										
OR7A17	26333	hgsc.bcm.edu	37	chr19	14991635	14991635	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgacctgattaagttcacagAaaaagtgggggatttccaag					rs35659165		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:14991635delA	ENST00000327462.2	-	1	629	c.533delT	c.(532-534)ttcfs	p.F178fs		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	178						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					AAGTTCACAGAAAAAGTGGGG	0.483																																					p.F178fs		Atlas-INDEL	.											.	OR7A17	37	.	0			c.534delC						.						90	85	87					19																	14991635		2203	4300	6503	SO:0001589	frameshift_variant	26333	exon1			.	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"GPCR / Class A : Olfactory receptors"	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.533delT	chr19.hg19:g.14991635delA	ENSP00000328144:p.Phe178fs	127.0	0.0		155.0	10.0	NM_030901	Q6IFQ6|Q96R98	Frame_Shift_Del	DEL	ENST00000327462.2	hg19	CCDS12319.1																																																																																			.	.		0.483	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901		-	14991635	A	-	14991635	7	5	112	1	0	1	0	1	0	0	0	0	11224	246	9	0	398	0	OR7A17	19	14991635	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	106782	14991635	44137348	1088	17709										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15292438	15292438	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtggaagcctccgtagcctGgcgggcaggtgcaggtgaag	18	9	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:15292438G>C	ENST00000263388.2	-	17	2816	c.2741C>G	c.(2740-2742)cCa>cGa	p.P914R		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	914	EGF-like 23; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.P914L(1)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TCCGTAGCCTGGCGGGCAGGT	0.697																																					p.P914R		Atlas-SNP	.											NOTCH3,NS,carcinoma,0,1	NOTCH3	340	.	1	Substitution - Missense(1)	lung(1)	c.C2741G						.						13	11	11					19																	15292438		2094	4050	6144	SO:0001583	missense	4854	exon17			TAGCCTGGCGGGC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.2741C>G	chr19.hg19:g.15292438G>C	ENSP00000263388:p.Pro914Arg	281.0	0.0		296.0	0.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.001631	0.54254	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.96200	-3.94	5.45	5.45	0.79879	EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.32015	N	0.006713	D	0.96153	0.8746	L	0.41492	1.28	0.58432	D	0.999999	D;D	0.58620	0.983;0.975	P;P	0.62649	0.88;0.905	D	0.96302	0.9222	10	0.54805	T	0.06	.	18.0459	0.89332	0.0:0.0:1.0:0.0	.	865;914	Q59FL3;Q9UM47	.;NOTC3_HUMAN	R	914;864	ENSP00000263388:P914R	ENSP00000263388:P914R	P	-	2	0	NOTCH3	15153438	1.000000	0.71417	0.035000	0.18076	0.010000	0.07245	5.641000	0.67881	2.569000	0.86673	0.561000	0.74099	CCA	.	.		0.697	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		C	15292438	G	C	15292438	3	2	112	1	0	0	0	0	1	0	0	0	10559	1348	47	4	4292	4	NOTCH3	19	15292438	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	300803	15292438	43836545	1089	17710										
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15807241	15807241	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttctttgtctcacctgcaggTctacgaccccttccgctttg	7	15	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:15807241T>C	ENST00000550308.1	+	12	1696	c.1316T>C	c.(1315-1317)gTc>gCc	p.V439A	CYP4F12_ENST00000324632.10_Splice_Site_p.V439A	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	439					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CACCTGCAGGTCTACGACCCC	0.537																																					p.V439A		Atlas-SNP	.											.	CYP4F12	89	.	0			c.T1316C						.						109	105	107					19																	15807241		2202	4300	6502	SO:0001630	splice_region_variant	66002	exon12			TGCAGGTCTACGA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"Cytochrome P450s"	18857	protein-coding gene	gene with protein product		611485	"cytochrome P450, subfamily IVF, polypeptide 12"			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1315-1T>C	chr19.hg19:g.15807241T>C		95.0	0.0		127.0	6.0	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	hg19	CCDS42517.1	.	.	.	.	.	.	.	.	.	.	.	11.30	1.597846	0.28445	.	.	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.79033	-1.23;-1.23	2.31	2.31	0.28768	.	0.188665	0.32106	U	0.006572	T	0.82038	0.4950	L	0.54863	1.705	0.40773	D	0.983102	D	0.62365	0.991	D	0.70016	0.967	T	0.82418	-0.0467	10	0.72032	D	0.01	.	8.4933	0.33112	0.0:0.0:0.0:1.0	.	439	Q9HCS2	CP4FC_HUMAN	A	439	ENSP00000448998:V439A;ENSP00000321821:V439A	ENSP00000321821:V439A	V	+	2	0	CYP4F12	15668241	1.000000	0.71417	0.998000	0.56505	0.190000	0.23558	4.375000	0.59549	1.308000	0.44962	0.260000	0.18958	GTC	.	.		0.537	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		Missense_Mutation	C	15807241	T	C	15807241	5	2	112	1	0	0	0	0	0	0	1	0	4189	1681	58	2	1358	2	CYP4F12	19	15807241	Splice_Site	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	514803	15807241	43321742	1090	17711										
UNC13A	23025	hgsc.bcm.edu	37	chr19	17758258	17758258	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcaccatgatgatgttctgTgtccggtcctccgccccgtg	11	14	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:17758258T>C	ENST00000519716.2	-	17	1859	c.1860A>G	c.(1858-1860)acA>acG	p.T620T	UNC13A_ENST00000552293.1_Silent_p.T620T|UNC13A_ENST00000550896.1_Silent_p.T618T|UNC13A_ENST00000551649.1_Silent_p.T620T|UNC13A_ENST00000252773.7_Silent_p.T620T|UNC13A_ENST00000428389.2_Silent_p.T708T	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	620					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						TGATGTTCTGTGTCCGGTCCT	0.642																																					p.T620T		Atlas-SNP	.											.	UNC13A	299	.	0			c.A1860G						.						76	79	78					19																	17758258		2153	4284	6437	SO:0001819	synonymous_variant	23025	exon16			GTTCTGTGTCCGG	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.1860A>G	chr19.hg19:g.17758258T>C		117.0	0.0		109.0	5.0	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	hg19	CCDS46013.2																																																																																			.	.		0.642	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		C	17758258	T	C	17758258	2	2	112	1	0	0	0	0	0	0	0	1	16999	1683	59	2		2	UNC13A	19	17758258	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1951017	17758258	41370725	1091	17712										
RPL18A	6142	hgsc.bcm.edu	37	chr19	17973742	17973742	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacagaccgagacatgggtgCccggcaccgcgcccgagccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:17973742delC	ENST00000222247.5	+	4	425	c.344delC	c.(343-345)gccfs	p.A115fs	RPL18A_ENST00000599898.1_Frame_Shift_Del_p.A76fs|SNORA68_ENST00000384437.1_RNA|RPL18A_ENST00000600147.1_Frame_Shift_Del_p.A115fs|RPL18A_ENST00000599870.1_Frame_Shift_Del_p.A86fs	NM_000980.3	NP_000971.1	Q02543	RL18A_HUMAN	ribosomal protein L18a	115					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(1)	5						GACATGGGTGCCCGGCACCGC	0.642																																					p.A115fs		Atlas-INDEL	.											.	RPL18A	15	.	0			c.343delG						.						29	30	30					19																	17973742		2203	4300	6503	SO:0001589	frameshift_variant	6142	exon4			.	AB007175	CCDS12367.1	19p13.11	2011-04-06			ENSG00000105640	ENSG00000105640		"L ribosomal proteins"	10311	protein-coding gene	gene with protein product	"60S ribosomal protein L18a", "ribosomal protein L18a-like protein"	604178				9582194	Standard	NM_000980		Approved	L18A	uc002nhp.3	Q02543		ENST00000222247.5:c.344delC	chr19.hg19:g.17973742delC	ENSP00000222247:p.Ala115fs	112.0	0.0		155.0	10.0	NM_000980		Frame_Shift_Del	DEL	ENST00000222247.5	hg19	CCDS12367.1																																																																																			.	.		0.642	RPL18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466679.1	NM_000980		-	17973742	C	-	17973742	7	5	112	1	0	1	0	1	0	0	0	0	13580	739	26	0	358	0	RPL18A	19	17973742	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	215484	17973742	41155241	1092	17713										
PDE4C	5143	hgsc.bcm.edu	37	chr19	18322644	18322644	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccgactcacgctcgcggtcTccctgctggaagaactcggc	11	17	2	1	rs577328081		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:18322644T>C	ENST00000355502.3	-	18	2587	c.1716A>G	c.(1714-1716)ggA>ggG	p.G572G	PDE4C_ENST00000594465.3_Silent_p.G572G|PDE4C_ENST00000262805.12_Silent_p.G540G|PDE4C_ENST00000447275.3_Silent_p.G466G|PDE4C_ENST00000598111.2_Silent_p.G287G|PDE4C_ENST00000597297.1_Silent_p.G342G|PDE4C_ENST00000594617.3_Silent_p.G572G|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000539010.1_Silent_p.G341G|AC068499.10_ENST00000599416.2_RNA			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	572					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	GCTCGCGGTCTCCCTGCTGGA	0.627																																					p.G572G		Atlas-SNP	.											.	PDE4C	80	.	0			c.A1716G						.						112	93	99					19																	18322644		2203	4300	6503	SO:0001819	synonymous_variant	5143	exon15			GCGGTCTCCCTGC		CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"Phosphodiesterases"	8782	protein-coding gene	gene with protein product	"phosphodiesterase E1 dunce homolog (Drosophila)"	600128	"phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.1716A>G	chr19.hg19:g.18322644T>C		120.0	0.0		135.0	7.0	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Silent	SNP	ENST00000355502.3	hg19	CCDS12373.1																																																																																			.	.		0.627	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1			C	18322644	T	C	18322644	2	2	112	1	0	0	0	0	0	0	0	1	11650	1538	54	2		2	PDE4C	19	18322644	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	348902	18322644	40806339	1093	17714										
PBX4	80714	hgsc.bcm.edu	37	chr19	19681414	19681414	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctgttcatatttctctagcTcagagtggtaaatctgtcgg	9	9	4	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:19681414T>C	ENST00000251203.9	-	3	708	c.422A>G	c.(421-423)gAg>gGg	p.E141G		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	141					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|XY body (GO:0001741)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(4)|ovary(1)|prostate(3)	9						TTTCTCTAGCTCAGAGTGGTA	0.483																																					p.E141G		Atlas-SNP	.											.	PBX4	34	.	0			c.A422G						.						73	68	70					19																	19681414		2203	4300	6503	SO:0001583	missense	80714	exon3			TCTAGCTCAGAGT	AJ300182	CCDS12406.1	19p13.11	2014-09-11	2007-01-30		ENSG00000105717			"Homeoboxes / TALE class"	13403	protein-coding gene	gene with protein product		608127	"pre-B-cell leukemia transcription factor 4"				Standard	NM_025245		Approved		uc002nmy.3	Q9BYU1	OTTHUMG00000172310	ENST00000251203.9:c.422A>G	chr19.hg19:g.19681414T>C	ENSP00000251203:p.Glu141Gly	90.0	0.0		123.0	6.0	NM_025245	A5D8Y0|B3KUK9	Missense_Mutation	SNP	ENST00000251203.9	hg19	CCDS12406.1	.	.	.	.	.	.	.	.	.	.	T	19.16	3.773765	0.69992	.	.	ENSG00000105717	ENST00000251203	T	0.50813	0.73	3.47	3.47	0.39725	PBX (1);	0.000000	0.85682	D	0.000000	T	0.66829	0.2829	M	0.80616	2.505	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.70669	-0.4808	10	0.87932	D	0	-15.0187	10.0195	0.42035	0.0:0.0:0.0:1.0	.	141	Q9BYU1	PBX4_HUMAN	G	141	ENSP00000251203:E141G	ENSP00000251203:E141G	E	-	2	0	PBX4	19542414	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.825000	0.75293	1.451000	0.47736	0.414000	0.27820	GAG	.	.		0.483	PBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417784.6			C	19681414	T	C	19681414	3	2	112	1	0	0	0	0	1	0	0	0	11504	1551	54	2	726	2	PBX4	19	19681414	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1358770	19681414	39447569	1094	17715										
ZNF626	199777	hgsc.bcm.edu	37	chr19	20807353	20807353	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctctccagtatgaattctccTatgtgtagtaaggattgagg	10	7	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:20807353T>C	ENST00000601440.1	-	4	1476	c.1330A>G	c.(1330-1332)Agg>Ggg	p.R444G	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|lung(3)|skin(1)	6						TGAATTCTCCTATGTGTAGTA	0.373																																					p.R444G		Atlas-SNP	.											ZNF626_ENST00000392298,bladder,carcinoma,0,1	ZNF626	121	.	0			c.A1330G						.						65	59	61					19																	20807353		2108	4259	6367	SO:0001583	missense	199777	exon4			TTCTCCTATGTGT	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"Zinc fingers, C2H2-type", "-"	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.1330A>G	chr19.hg19:g.20807353T>C	ENSP00000469958:p.Arg444Gly	24.0	0.0		39.0	4.0	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	hg19	CCDS42535.1	.	.	.	.	.	.	.	.	.	.	N	0.713	-0.786488	0.02907	.	.	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	0.832	0.832	0.18867	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.50718	0.1632	L	0.58101	1.795	0.80722	D	1	B	0.23806	0.091	B	0.33121	0.158	T	0.49447	-0.8939	8	0.87932	D	0	.	3.5311	0.07777	0.0:0.0:0.4169:0.583	.	444	Q68DY1	ZN626_HUMAN	G	444;368;444	.	ENSP00000445201:R444G	R	-	1	2	ZNF626	20599193	0.121000	0.22262	0.006000	0.13384	0.006000	0.05464	0.065000	0.14466	0.148000	0.19059	0.147000	0.16070	AGG	.	.		0.373	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		C	20807353	T	C	20807353	3	2	112	1	0	0	0	0	1	0	0	0	18065	1521	53	2	260	2	ZNF626	19	20807353	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1125939	20807353	38321630	1095	17716										
C19orf12	83636	hgsc.bcm.edu	37	chr19	30193879	30193879	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acctaacagccccccgacagCcccccctagaaaacatggaa					rs398122409		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:30193879delC	ENST00000392278.2	-	3	325	c.199delG	c.(199-201)gctfs	p.A67fs	C19orf12_ENST00000392275.1_5'UTR|C19orf12_ENST00000392276.1_5'UTR|C19orf12_ENST00000323670.9_Frame_Shift_Del_p.A56fs|C19orf12_ENST00000592153.1_Frame_Shift_Del_p.A56fs	NM_001031726.3	NP_001026896.2	Q9NSK7	CS012_HUMAN	chromosome 19 open reading frame 12	67					cell death (GO:0008219)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)						Ovarian(5;0.000567)|Breast(6;0.0203)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0435)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.183)			CCCCCGACAGCCCCCCCTAGA	0.527																																					p.A67fs		Atlas-INDEL	.											.	C19orf12	16	.	0			c.200delC						.						58	66	63					19																	30193879		2203	4300	6503	SO:0001589	frameshift_variant	83636	exon3			.	AK057185	CCDS12418.2, CCDS42542.1, CCDS59373.1, CCDS74325.1	19q13.11	2013-07-24			ENSG00000131943	ENSG00000131943			25443	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 4"	614297	"spastic paraplegia 43 (autosomal recessive)"	SPG43		21981780, 23857908	Standard	NM_031448		Approved	MGC10922, DKFZP762D096, NBIA4	uc002nsj.3	Q9NSK7	OTTHUMG00000149838	ENST00000392278.2:c.199delG	chr19.hg19:g.30193879delC	ENSP00000376103:p.Ala67fs	188.0	0.0		195.0	16.0	NM_001031726	B3KQ16|Q0D2Q0|Q6P4C5|Q9BSL7	Frame_Shift_Del	DEL	ENST00000392278.2	hg19	CCDS42542.1																																																																																			.	.		0.527	C19orf12-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313509.2	NM_031448		-	30193879	C	-	30193879	7	5	112	1	0	1	0	1	0	0	0	0	1911	739	26	0	263	0	C19orf12	19	30193879	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	9386526	30193879	28935104	1096	17717										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935844	30935844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctatggcaagggcgagctgCccatgaaggagaaggaagcg	16	8	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:30935844C>T	ENST00000355537.3	+	2	1522	c.1375C>T	c.(1375-1377)Ccc>Tcc	p.P459S		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	459					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GGGCGAGCTGCCCATGAAGGA	0.647																																					p.P459S		Atlas-SNP	.											.	ZNF536	424	.	0			c.C1375T						.						31	33	32					19																	30935844		2199	4299	6498	SO:0001583	missense	9745	exon2			GAGCTGCCCATGA		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.1375C>T	chr19.hg19:g.30935844C>T	ENSP00000347730:p.Pro459Ser	82.0	0.0		73.0	4.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	2.002	-0.429180	0.04701	.	.	ENSG00000198597	ENST00000355537	T	0.07327	3.2	5.44	1.79	0.24919	.	0.228755	0.45867	D	0.000336	T	0.07503	0.0189	L	0.27053	0.805	0.37911	D	0.931372	B;B	0.24258	0.1;0.1	B;B	0.24541	0.054;0.054	T	0.24764	-1.0151	10	0.45353	T	0.12	-18.4226	15.9244	0.79603	0.0:0.5869:0.4131:0.0	.	459;459	A7E228;O15090	.;ZN536_HUMAN	S	459	ENSP00000347730:P459S	ENSP00000347730:P459S	P	+	1	0	ZNF536	35627684	1.000000	0.71417	0.886000	0.34754	0.033000	0.12548	2.772000	0.47678	0.599000	0.29845	0.591000	0.81541	CCC	.	.		0.647	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30935844	C	T	30935844	3	4	112	1	0	0	0	0	1	0	0	0	17989	739	26	3	1377	3	ZNF536	19	30935844	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	741965	30935844	28193139	1097	17718										
ZNF536	9745	hgsc.bcm.edu	37	chr19	31039960	31039960	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcccactctgaagaggatgTccccatcctgatccccgaaa	9	15	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:31039960T>C	ENST00000355537.3	+	4	3581	c.3434T>C	c.(3433-3435)gTc>gCc	p.V1145A		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1145					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GAAGAGGATGTCCCCATCCTG	0.547																																					p.V1145A		Atlas-SNP	.											ZNF536,colon,carcinoma,0,1	ZNF536	424	.	0			c.T3434C						.						73	70	71					19																	31039960		2203	4300	6503	SO:0001583	missense	9745	exon4			AGGATGTCCCCAT		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3434T>C	chr19.hg19:g.31039960T>C	ENSP00000347730:p.Val1145Ala	97.0	0.0		113.0	6.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	t	0.008	-1.871054	0.00542	.	.	ENSG00000198597	ENST00000355537	T	0.06933	3.24	5.59	1.07	0.20283	.	0.656971	0.15796	N	0.244188	T	0.02688	0.0081	N	0.03608	-0.345	0.19300	N	0.999974	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46512	-0.9186	10	0.02654	T	1	-9.6809	7.7337	0.28802	0.0:0.6861:0.1173:0.1966	.	1145;1145	A7E228;O15090	.;ZN536_HUMAN	A	1145	ENSP00000347730:V1145A	ENSP00000347730:V1145A	V	+	2	0	ZNF536	35731800	0.159000	0.22864	0.250000	0.24296	0.402000	0.30811	1.115000	0.31209	0.047000	0.15862	-0.866000	0.03004	GTC	.	.		0.547	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		C	31039960	T	C	31039960	3	2	112	1	0	0	0	0	1	0	0	0	17989	1667	58	2	3444	2	ZNF536	19	31039960	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	104116	31039960	28089023	1098	17719										
KIAA0355	9710	hgsc.bcm.edu	37	chr19	34832378	34832378	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgcaaagggagatctgtgaTtttggcaaccaggctgacct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:34832378delT	ENST00000299505.6	+	10	2412	c.1539delT	c.(1537-1539)gatfs	p.D513fs		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	513										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					AGATCTGTGATTTTGGCAACC	0.403																																					p.D513fs		Atlas-INDEL	.											.	KIAA0355	105	.	0			c.1538delA						.						76	79	78					19																	34832378		2203	4300	6503	SO:0001589	frameshift_variant	9710	exon10			.		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.1539delT	chr19.hg19:g.34832378delT	ENSP00000299505:p.Asp513fs	152.0	0.0		178.0	12.0	NM_014686	Q2M3W4	Frame_Shift_Del	DEL	ENST00000299505.6	hg19	CCDS12436.1																																																																																			.	.		0.403	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686		-	34832378	T	-	34832378	7	5	112	1	0	1	0	1	0	0	0	0	8179	1490	52	0	1573	0	KIAA0355	19	34832378	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3792418	34832378	24296605	1099	17720										
ATP4A	495	hgsc.bcm.edu	37	chr19	36048637	36048637	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actgctcgtccagcggcagcTcctggcccttgataaggatg	12	13	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:36048637T>C	ENST00000262623.3	-	11	1641	c.1613A>G	c.(1612-1614)gAg>gGg	p.E538G		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	538					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CAGCGGCAGCTCCTGGCCCTT	0.706																																					p.E538G		Atlas-SNP	.											.	ATP4A	123	.	0			c.A1613G						.						13	14	14					19																	36048637		2187	4280	6467	SO:0001583	missense	495	exon11			GGCAGCTCCTGGC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.1613A>G	chr19.hg19:g.36048637T>C	ENSP00000262623:p.Glu538Gly	127.0	0.0		155.0	9.0	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.034699	0.93575	.	.	ENSG00000105675	ENST00000262623	D	0.81659	-1.52	3.8	3.8	0.43715	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.52532	D	0.000061	D	0.84329	0.5448	L	0.49778	1.585	0.53005	D	0.999969	P	0.51240	0.943	D	0.64321	0.924	D	0.84894	0.0838	10	0.62326	D	0.03	.	10.5596	0.45138	0.0:0.0:0.0:1.0	.	538	P20648	ATP4A_HUMAN	G	538	ENSP00000262623:E538G	ENSP00000262623:E538G	E	-	2	0	ATP4A	40740477	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.736000	0.84948	1.598000	0.50083	0.397000	0.26171	GAG	.	.		0.706	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		C	36048637	T	C	36048637	3	2	112	1	0	0	0	0	1	0	0	0	1145	1551	54	2	1542	2	ATP4A	19	36048637	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1216259	36048637	23080346	1100	17721										
MLL4	9757	hgsc.bcm.edu	37	chr19	36223328	36223328	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctacctcaggggagctggctCcccctggcccggccccatct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:36223328delC	ENST00000222270.7	+	28	5878	c.5878delC	c.(5878-5880)cccfs	p.P1961fs	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Frame_Shift_Del_p.P1961fs	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1961					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GGAGCTGGCTCCCCCTGGCCC	0.647																																					p.A1959fs		Atlas-INDEL	.											.	MLL4	229	.	0			c.5877delT						.						31	37	35					19																	36223328		1984	4140	6124	SO:0001589	frameshift_variant	8085	exon28			.	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5878delC	chr19.hg19:g.36223328delC	ENSP00000222270:p.Pro1961fs	160.0	0.0		166.0	10.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Frame_Shift_Del	DEL	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.647	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		-	36223328	C	-	36223328	7	5	112	1	0	1	0	1	0	0	0	0	9632	855	30	0	5988	0	MLL4	19	36223328	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	174691	36223328	22905655	1101	17722										
ARHGAP33	115703	hgsc.bcm.edu	37	chr19	36278689	36278689	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtctggaggagctctctgggCccccctgcaccactcgacag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:36278689delC	ENST00000007510.4	+	21	3366	c.3222delC	c.(3220-3222)ggcfs	p.G1074fs	AC002398.5_ENST00000433059.1_lincRNA|ARHGAP33_ENST00000314737.5_Frame_Shift_Del_p.G913fs|ARHGAP33_ENST00000378944.5_Frame_Shift_Del_p.G910fs			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	1074					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						GCTCTCTGGGCCCCCCTGCAC	0.662																																					p.G913fs		Atlas-INDEL	.											.	ARHGAP33	102	.	0			c.2738delG						.						26	30	29					19																	36278689		2200	4296	6496	SO:0001589	frameshift_variant	115703	exon21			.	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.3222delC	chr19.hg19:g.36278689delC	ENSP00000007510:p.Gly1074fs	136.0	0.0		157.0	10.0	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Frame_Shift_Del	DEL	ENST00000007510.4	hg19																																																																																				.	.		0.662	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		-	36278689	C	-	36278689	7	5	112	1	0	1	0	1	0	0	0	0	882	726	26	0	3304	0	ARHGAP33	19	36278689	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	55361	36278689	22850294	1102	17723										
NPHS1	4868	hgsc.bcm.edu	37	chr19	36333298	36333298	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacatctgacaacaagacggAgcagccgtcgtgctggaggc	13	12	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:36333298A>G	ENST00000378910.5	-	18	2488	c.2489T>C	c.(2488-2490)cTc>cCc	p.L830P	NPHS1_ENST00000353632.6_Missense_Mutation_p.L830P	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	830	Ig-like C2-type 7.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AACAAGACGGAGCAGCCGTCG	0.582																																					p.L830P		Atlas-SNP	.											.	NPHS1	165	.	0			c.T2489C						.						65	58	60					19																	36333298		2203	4300	6503	SO:0001583	missense	4868	exon18			AGACGGAGCAGCC		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.2489T>C	chr19.hg19:g.36333298A>G	ENSP00000368190:p.Leu830Pro	37.0	0.0		71.0	5.0	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	hg19	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	A	11.69	1.712724	0.30413	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.14766	2.48;2.48	4.57	2.39	0.29439	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.512179	0.20255	N	0.095982	T	0.09992	0.0245	L	0.38175	1.15	0.31825	N	0.62543	B	0.18166	0.026	B	0.24269	0.052	T	0.05162	-1.0902	10	0.72032	D	0.01	-18.1196	4.0947	0.09985	0.6786:0.2128:0.1087:0.0	.	830	O60500	NPHN_HUMAN	P	830	ENSP00000368190:L830P;ENSP00000343634:L830P	ENSP00000343634:L830P	L	-	2	0	NPHS1	41025138	0.986000	0.35501	1.000000	0.80357	0.859000	0.49053	2.140000	0.42159	1.936000	0.56123	0.456000	0.33151	CTC	.	.		0.582	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			G	36333298	A	G	36333298	3	3	112	1	0	0	0	0	1	0	0	0	10591	304	11	2	1284	2	NPHS1	19	36333298	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	54609	36333298	22795685	1103	17724										
YIF1B	90522	hgsc.bcm.edu	37	chr19	38796095	38796095	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggttccgggccccacgcaccGggaccccctcagctgctgcg					rs536877708		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:38796095delG	ENST00000339413.6	-	8	887	c.842delC	c.(841-843)ccgfs	p.P281fs	YIF1B_ENST00000592246.1_Frame_Shift_Del_p.P215fs|YIF1B_ENST00000392124.3_Frame_Shift_Del_p.P250fs|YIF1B_ENST00000592694.1_Frame_Shift_Del_p.P250fs|YIF1B_ENST00000337679.8_3'UTR|YIF1B_ENST00000591784.1_Frame_Shift_Del_p.P250fs|YIF1B_ENST00000329420.8_Frame_Shift_Del_p.P266fs	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	281						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CCCACGCACCGGGACCCCCTC	0.642																																					p.P281fs		Atlas-INDEL	.											.	YIF1B	47	.	0			c.843delG						.						15	17	17					19																	38796095		2196	4288	6484	SO:0001589	frameshift_variant	90522	exon8			.	AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05							30511	protein-coding gene	gene with protein product						12975309	Standard	NM_001039672		Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.842delC	chr19.hg19:g.38796095delG	ENSP00000343435:p.Pro281fs	161.0	0.0		162.0	10.0	NM_001039672	H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	Frame_Shift_Del	DEL	ENST00000339413.6	hg19	CCDS33010.1																																																																																			.	.		0.642	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460511.1	NM_033557		-	38796095	G	-	38796095	7	5	112	1	0	1	0	1	0	0	0	0	17491	1116	39	0	106	0	YIF1B	19	38796095	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2462797	38796095	20332888	1104	17725										
IL28B	282617	hgsc.bcm.edu	37	chr19	39734707	39734707	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aaggggctggtccaagacatCccccagggctgggtcagtgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:39734707delC	ENST00000413851.2	-	3	387	c.349delG	c.(349-351)gatfs	p.D117fs		NM_172139.2	NP_742151.2	Q8IZI9	IFNL3_HUMAN	interferon, lambda 3	117					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of viral genome replication (GO:0045071)|positive regulation of immune response (GO:0050778)	extracellular space (GO:0005615)											TCCAAGACATCCCCCAGGGCT	0.662																																					p.D117fs		Atlas-INDEL	.											.	.	.	.	0			c.350delA						.						61	66	64					19																	39734707		2203	4300	6503	SO:0001589	frameshift_variant	282617	exon3			.	AY129149	CCDS12530.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000197110	ENSG00000197110		"Interferons"	18365	protein-coding gene	gene with protein product		607402	"interleukin 28B", "interleukin 28B (interferon, lambda 3)"	IL28B			Standard	NM_172139		Approved	IL-28B, IL28C	uc010xut.2	Q8IZI9	OTTHUMG00000182805	ENST00000413851.2:c.349delG	chr19.hg19:g.39734707delC	ENSP00000409000:p.Asp117fs	108.0	0.0		161.0	10.0	NM_172139	A2BDE1|Q6VN56|Q7Z4J3|Q8IWL6	Frame_Shift_Del	DEL	ENST00000413851.2	hg19	CCDS12530.1																																																																																			.	.		0.662	IFNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463832.1	NM_172139		-	39734707	C	-	39734707	7	5	112	1	0	1	0	1	0	0	0	0	7692	855	30	0	252	0	IL28B	19	39734707	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	938612	39734707	19394276	1105	17726										
GRIK5	2901	hgsc.bcm.edu	37	chr19	42510910	42510910	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catgcgctgcacggtgaggaAggcggccaggttggccgtgt	18	10	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:42510910A>G	ENST00000262895.3	-	15	1923	c.1924T>C	c.(1924-1926)Ttc>Ctc	p.F642L	GRIK5_ENST00000301218.4_Missense_Mutation_p.F642L|GRIK5_ENST00000593562.1_Missense_Mutation_p.F642L	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	642					cellular response to glucose stimulus (GO:0071333)|establishment of localization in cell (GO:0051649)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|positive regulation of neuron apoptotic process (GO:0043525)|protein retention in ER lumen (GO:0006621)|receptor clustering (GO:0043113)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	35		Prostate(69;0.059)				ACGGTGAGGAAGGCGGCCAGG	0.627																																					p.F642L		Atlas-SNP	.											.	GRIK5	220	.	0			c.T1924C						.						68	54	59					19																	42510910		2203	4300	6503	SO:0001583	missense	2901	exon15			TGAGGAAGGCGGC		CCDS12595.1	19q13.2	2012-08-29			ENSG00000105737	ENSG00000105737		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4583	protein-coding gene	gene with protein product		600283		GRIK2		7527545	Standard	NM_002088		Approved	GluK5, KA2	uc002osj.2	Q16478	OTTHUMG00000044573	ENST00000262895.3:c.1924T>C	chr19.hg19:g.42510910A>G	ENSP00000262895:p.Phe642Leu	84.0	0.0		94.0	4.0	NM_002088	Q8WWG8	Missense_Mutation	SNP	ENST00000262895.3	hg19	CCDS12595.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	32|32	5.171401|5.171401	0.94807|0.94807	.|.	.|.	ENSG00000105737|ENSG00000105737	ENST00000262895;ENST00000301218|ENST00000454993	T;T|.	0.56941|.	0.43;0.43|.	5.18|5.18	5.18|5.18	0.71444|0.71444	Ionotropic glutamate receptor (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85940|0.85940	0.5814|0.5814	H|H	0.94886|0.94886	3.595|3.595	0.58432|0.58432	D|D	0.999998|0.999998	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.89859|0.89859	0.4015|0.4015	10|5	0.87932|.	D|.	0|.	.|.	14.0093|14.0093	0.64486|0.64486	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	642|.	Q16478|.	GRIK5_HUMAN|.	L|P	642|18	ENSP00000262895:F642L;ENSP00000301218:F642L|.	ENSP00000262895:F642L|.	F|L	-|-	1|2	0|0	GRIK5|GRIK5	47202750|47202750	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.324000|9.324000	0.96373|0.96373	1.959000|1.959000	0.56917|0.56917	0.460000|0.460000	0.39030|0.39030	TTC|CTT	.	.		0.627	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1			G	42510910	A	G	42510910	3	3	112	1	0	0	0	0	1	0	0	0	6786	72	3	2	1038	2	GRIK5	19	42510910	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2776203	42510910	16618073	1106	17727										
ERCC2	2068	hgsc.bcm.edu	37	chr19	45867515	45867515	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagcaccgtcttctgcagggTctccaggttgccctggcacc	12	15	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:45867515T>C	ENST00000391945.4	-	9	870	c.793A>G	c.(793-795)Acc>Gcc	p.T265A	ERCC2_ENST00000485403.2_Missense_Mutation_p.T241A|ERCC2_ENST00000221481.6_3'UTR|ERCC2_ENST00000391940.4_Missense_Mutation_p.T241A|ERCC2_ENST00000391944.3_Missense_Mutation_p.T187A	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	265	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TTCTGCAGGGTCTCCAGGTTG	0.682			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.T265A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"		E	.	ERCC2	78	.	0			c.A793G						.						35	39	38					19																	45867515		2201	4300	6501	SO:0001583	missense	2068	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GCAGGGTCTCCAG		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"General transcription factor IIH complex subunits"	3434	protein-coding gene	gene with protein product	"excision repair cross-complementing rodent repair deficiency, complementation group 2 protein", "TFIIH basal transcription factor complex helicase XPB subunit"	126340	"xeroderma pigmentosum complementary group D", "excision repair cross-complementing rodent repair deficiency, complementation group 2"	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.793A>G	chr19.hg19:g.45867515T>C	ENSP00000375809:p.Thr265Ala	83.0	0.0		114.0	6.0	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	hg19	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	T	13.32	2.201219	0.38905	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944;ENST00000391940	T;D;T	0.82081	-1.4;-1.57;-0.25	4.72	4.72	0.59763	Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.107907	0.64402	D	0.000010	T	0.70613	0.3244	N	0.21448	0.665	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.12837	0.001;0.008;0.0	T	0.64546	-0.6382	10	0.15499	T	0.54	-54.599	12.4641	0.55749	0.0:0.0:0.0:1.0	.	187;241;265	E7EVE9;Q7KZU6;P18074	.;.;ERCC2_HUMAN	A	215;241;265;187;241	ENSP00000375809:T265A;ENSP00000375808:T187A;ENSP00000375804:T241A	ENSP00000375804:T241A	T	-	1	0	ERCC2	50559355	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	4.054000	0.57434	2.102000	0.63906	0.459000	0.35465	ACC	.	.		0.682	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400		C	45867515	T	C	45867515	3	2	112	1	0	0	0	0	1	0	0	0	5215	1667	58	2	1606	2	ERCC2	19	45867515	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3356605	45867515	13261468	1107	17728										
NOVA2	4858	hgsc.bcm.edu	37	chr19	46464290	46464290	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggtagaagtctttggacttGgagagcttgatggtggctcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:46464290delG	ENST00000263257.5	-	2	401	c.207delC	c.(205-207)tccfs	p.S69fs		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	69	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		CTTTGGACTTGGAGAGCTTGA	0.652																																					p.K70fs		Atlas-INDEL	.											.	NOVA2	38	.	0			c.208delA						.						51	52	52					19																	46464290		2198	4296	6494	SO:0001589	frameshift_variant	4858	exon2			.	U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"neuro-oncological ventral antigen 3"	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.207delC	chr19.hg19:g.46464290delG	ENSP00000263257:p.Ser69fs	116.0	0.0		128.0	10.0	NM_002516	O43267|Q9UEA1	Frame_Shift_Del	DEL	ENST00000263257.5	hg19	CCDS12679.1																																																																																			.	.		0.652	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516		-	46464290	G	-	46464290	7	5	112	1	0	1	0	1	0	0	0	0	10564	1335	47	0	1283	0	NOVA2	19	46464290	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	596775	46464290	12664693	1108	17729										
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47422735	47422735	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agctctcaagcagcagagtcAgcagatagctacagcaaaag	10	10	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:47422735A>G	ENST00000404338.3	+	1	803	c.803A>G	c.(802-804)cAg>cGg	p.Q268R		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	268					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										CAGCAGAGTCAGCAGATAGCT	0.453																																					p.Q268R		Atlas-SNP	.											.	.	.	.	0			c.A803G						.						72	73	72					19																	47422735		2023	4202	6225	SO:0001583	missense	2909	exon1			AGAGTCAGCAGAT	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.803A>G	chr19.hg19:g.47422735A>G	ENSP00000385720:p.Gln268Arg	73.0	0.0		99.0	5.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.646163	0.67358	.	.	ENSG00000160007	ENST00000317082;ENST00000501576;ENST00000404338	T	0.09073	3.02	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.20414	0.0491	L	0.55990	1.75	0.80722	D	1	P	0.48834	0.916	P	0.55345	0.774	T	0.00061	-1.2159	10	0.87932	D	0	-32.9111	15.4607	0.75353	1.0:0.0:0.0:0.0	.	268	Q9NRY4-2	.	R	268	ENSP00000385720:Q268R	ENSP00000324820:Q268R	Q	+	2	0	ARHGAP35	52114575	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.339000	0.96797	2.288000	0.76882	0.528000	0.53228	CAG	.	.		0.453	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		G	47422735	A	G	47422735	3	3	112	1	0	0	0	0	1	0	0	0	6804	188	7	2	805	2	ARHGAP35	19	47422735	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	958445	47422735	11706248	1109	17730										
SLC6A16	28968	hgsc.bcm.edu	37	chr19	49813309	49813309	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcctcaccaaagccactagAgttcatcgttaagggacatt	7	12	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:49813309A>G	ENST00000335875.4	-	4	929	c.688T>C	c.(688-690)Tct>Cct	p.S230P	MIR4324_ENST00000584846.1_RNA|SLC6A16_ENST00000454748.3_Missense_Mutation_p.S230P	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	230					neurotransmitter transport (GO:0006836)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		AAGCCACTAGAGTTCATCGTT	0.473																																					p.S230P		Atlas-SNP	.											.	SLC6A16	62	.	0			c.T688C						.						88	77	80					19																	49813309		1885	4124	6009	SO:0001583	missense	28968	exon4			CACTAGAGTTCAT	AF265578	CCDS42590.1	19q13.33	2013-05-22			ENSG00000063127	ENSG00000063127		"Solute carriers"	13622	protein-coding gene	gene with protein product	"NTT5 protein"	607972	"solute carrier family 6 (neurotransmitter transporter), member 16"			10471414, 11112352	Standard	XM_005258820		Approved	NTT5	uc002pmz.3	Q9GZN6		ENST00000335875.4:c.688T>C	chr19.hg19:g.49813309A>G	ENSP00000338627:p.Ser230Pro	160.0	0.0		147.0	6.0	NM_014037	Q8IYV4|Q9Y5I9	Missense_Mutation	SNP	ENST00000335875.4	hg19	CCDS42590.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.694629	0.30052	.	.	ENSG00000063127	ENST00000335875;ENST00000454748	T;T	0.75477	-0.94;-0.94	4.58	-0.138	0.13464	.	0.788296	0.12019	N	0.507196	D	0.83344	0.5234	M	0.86268	2.805	0.28862	N	0.895465	D;D	0.67145	0.996;0.996	D;D	0.68192	0.956;0.956	T	0.72931	-0.4142	10	0.39692	T	0.17	.	6.9237	0.24403	0.3769:0.4712:0.0:0.1518	.	230;230	Q8IYV4;Q9GZN6	.;S6A16_HUMAN	P	230	ENSP00000338627:S230P;ENSP00000404022:S230P	ENSP00000338627:S230P	S	-	1	0	SLC6A16	54505121	0.913000	0.31002	0.910000	0.35882	0.003000	0.03518	-0.247000	0.08866	-0.127000	0.11661	-0.327000	0.08410	TCT	.	.		0.473	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037		G	49813309	A	G	49813309	3	3	112	1	0	0	0	0	1	0	0	0	14694	304	11	2	1558	2	SLC6A16	19	49813309	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2390574	49813309	9315674	1110	17731										
MYH14	79784	hgsc.bcm.edu	37	chr19	50812903	50812903	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctcctccccacagacgcggCcccctcaccttcaccacccg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:50812903delC	ENST00000596571.1	+	40	5844	c.5844delC	c.(5842-5844)ggcfs	p.G1948fs	MYH14_ENST00000262269.8_Frame_Shift_Del_p.G1989fs|MYH14_ENST00000425460.1_Frame_Shift_Del_p.G1956fs|MYH14_ENST00000376970.2_Frame_Shift_Del_p.G1981fs|CTB-191K22.5_ENST00000595563.1_RNA|MYH14_ENST00000601313.1_Frame_Shift_Del_p.G1989fs|MYH14_ENST00000598205.1_Frame_Shift_Del_p.G1956fs|MYH14_ENST00000440075.2_Frame_Shift_Del_p.G1989fs			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1948					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		ACAGACGCGGCCCCCTCACCT	0.642																																					p.G1989fs		Atlas-INDEL	.											.	MYH14	261	.	0			c.5966delG						.						22	23	23					19																	50812903		1975	4144	6119	SO:0001589	frameshift_variant	79784	exon43			.	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.5844delC	chr19.hg19:g.50812903delC	ENSP00000472819:p.Gly1948fs	154.0	0.0		141.0	10.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Frame_Shift_Del	DEL	ENST00000596571.1	hg19	CCDS59411.1																																																																																			.	.		0.642	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		-	50812903	C	-	50812903	7	5	112	1	0	1	0	1	0	0	0	0	10042	726	26	0	6133	0	MYH14	19	50812903	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	999594	50812903	8316080	1111	17732										
SIGLEC7	27036	hgsc.bcm.edu	37	chr19	51650558	51650558	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaggatgcaaacaccatcaGgggctcagcctctcaggtga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:51650558delG	ENST00000317643.6	+	6	1274	c.1205delG	c.(1204-1206)aggfs	p.R402fs	SIGLEC7_ENST00000600577.1_Intron|SIGLEC7_ENST00000305628.7_Frame_Shift_Del_p.R309fs	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	402					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		AACACCATCAGGGGCTCAGCC	0.557																																					p.R402fs		Atlas-INDEL	.											.	SIGLEC7	74	.	0			c.1204delA						.						123	96	105					19																	51650558		2203	4300	6503	SO:0001589	frameshift_variant	27036	exon6			.	AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10876	protein-coding gene	gene with protein product		604410	"sialic acid binding Ig-like lectin 19, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 2"	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.1205delG	chr19.hg19:g.51650558delG	ENSP00000323328:p.Arg402fs	118.0	0.0		121.0	10.0	NM_014385	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Frame_Shift_Del	DEL	ENST00000317643.6	hg19	CCDS12826.1																																																																																			.	.		0.557	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543		-	51650558	G	-	51650558	7	5	112	1	0	1	0	1	0	0	0	0	14328	1000	35	0	1227	0	SIGLEC7	19	51650558	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	837655	51650558	7478425	1112	17733										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52002448	52002448	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccatctccttggaagacagTcatggtcaagttctgaggag	12	9	4	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:52002448T>C	ENST00000291707.3	-	4	1166	c.1111A>G	c.(1111-1113)Act>Gct	p.T371A	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.T253A	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	371	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		TGGAAGACAGTCATGGTCAAG	0.567																																					p.T371A		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.A1111G						.						120	102	108					19																	52002448		2203	4300	6503	SO:0001583	missense	89858	exon4			AGACAGTCATGGT	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1111A>G	chr19.hg19:g.52002448T>C	ENSP00000291707:p.Thr371Ala	137.0	0.0		141.0	6.0	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	hg19	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	10.75	1.439444	0.25900	.	.	ENSG00000254521	ENST00000291707	T	0.41758	0.99	2.07	2.07	0.26955	Immunoglobulin-like (1);	0.896444	0.09202	N	0.834571	T	0.42607	0.1210	M	0.69248	2.105	0.09310	N	1	P;P	0.37612	0.602;0.567	B;B	0.40901	0.343;0.343	T	0.34625	-0.9821	10	0.41790	T	0.15	.	6.0661	0.19864	0.0:0.0:0.0:1.0	.	371;253	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	A	371	ENSP00000291707:T371A	ENSP00000291707:T371A	T	-	1	0	SIGLEC12	56694260	0.000000	0.05858	0.002000	0.10522	0.591000	0.36615	0.002000	0.13061	0.975000	0.38392	0.329000	0.21502	ACT	.	.		0.567	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		C	52002448	T	C	52002448	3	2	112	1	0	0	0	0	1	0	0	0	14323	1667	58	2	696	2	SIGLEC12	19	52002448	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	351890	52002448	7126535	1113	17734										
ZNF841	284371	hgsc.bcm.edu	37	chr19	52569542	52569542	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctccggtatgaattctctgAtgtacagttagtaatgagcc	9	8	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:52569542A>G	ENST00000426391.2	-	5	1796	c.1245T>C	c.(1243-1245)caT>caC	p.H415H	ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000594295.1_Silent_p.H531H|ZNF841_ENST00000389534.4_Silent_p.H531H|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000359973.2_Intron			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	415					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						GAATTCTCTGATGTACAGTTA	0.398																																					p.H531H		Atlas-SNP	.											.	ZNF841	183	.	0			c.T1593C						.						99	91	94					19																	52569542		692	1591	2283	SO:0001819	synonymous_variant	284371	exon7			TCTCTGATGTACA	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"Zinc fingers, C2H2-type", "-"	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.1245T>C	chr19.hg19:g.52569542A>G		52.0	0.0		36.0	4.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Silent	SNP	ENST00000426391.2	hg19																																																																																				.	.		0.398	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		G	52569542	A	G	52569542	2	3	112	1	0	0	0	0	0	0	0	1	18204	330	12	2		2	ZNF841	19	52569542	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	567094	52569542	6559441	1114	17735										
ZNF701	55762	hgsc.bcm.edu	37	chr19	53085947	53085947	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acgggaagtacacacaagagAaaaatctttccaacgtaatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:53085947delA	ENST00000540331.1	+	5	1058	c.833delA	c.(832-834)gaafs	p.E278fs	CTD-3099C6.7_ENST00000599222.1_RNA|ZNF701_ENST00000391785.3_Frame_Shift_Del_p.E212fs|ZNF701_ENST00000301093.2_Frame_Shift_Del_p.E278fs	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	278					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		CACACAAGAGAAAAATCTTTC	0.348																																					p.E278fs	NSCLC(89;451 1475 9611 20673 52284)	Atlas-INDEL	.											.	ZNF701	44	.	0			c.832delG						.						57	60	59					19																	53085947		2203	4300	6503	SO:0001589	frameshift_variant	55762	exon5			.	AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"Zinc fingers, C2H2-type", "-"	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.833delA	chr19.hg19:g.53085947delA	ENSP00000444339:p.Glu278fs	91.0	0.0		125.0	10.0	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Frame_Shift_Del	DEL	ENST00000540331.1	hg19	CCDS54311.1																																																																																			.	.		0.348	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260		-	53085947	A	-	53085947	7	5	112	1	0	1	0	1	0	0	0	0	18120	246	9	0	847	0	ZNF701	19	53085947	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	516405	53085947	6043036	1115	17736										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53645764	53645764	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atacttctcctgtattactcTtccctttgtgtagtaaatct	4	10	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:53645764T>C	ENST00000334197.7	-	5	385	c.317A>G	c.(316-318)aAg>aGg	p.K106R	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_Missense_Mutation_p.K107R|ZNF347_ENST00000452676.2_Missense_Mutation_p.K107R	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	106					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		TGTATTACTCTTCCCTTTGTG	0.358																																					p.K107R	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.A320G						.						60	53	55					19																	53645764		2203	4299	6502	SO:0001583	missense	84671	exon5			TTACTCTTCCCTT	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.317A>G	chr19.hg19:g.53645764T>C	ENSP00000334146:p.Lys106Arg	118.0	0.0		119.0	5.0	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	hg19	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	T	3.500	-0.102088	0.06967	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.07021	3.23;3.23	2.57	-1.34	0.09143	.	.	.	.	.	T	0.02727	0.0082	N	0.08118	0	0.09310	N	1	P;B	0.42908	0.793;0.316	B;B	0.37780	0.258;0.098	T	0.28138	-1.0053	9	0.18710	T	0.47	.	0.3772	0.00389	0.2189:0.1429:0.2244:0.4138	.	107;106	G5E9N4;Q96SE7	.;ZN347_HUMAN	R	106;107	ENSP00000334146:K106R;ENSP00000405218:K107R	ENSP00000334146:K106R	K	-	2	0	ZNF347	58337576	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.782000	0.04643	-0.596000	0.05821	-0.256000	0.11100	AAG	.	.		0.358	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		C	53645764	T	C	53645764	3	2	112	1	0	0	0	0	1	0	0	0	17876	1609	56	2	2206	2	ZNF347	19	53645764	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	559817	53645764	5483219	1116	17737										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53855284	53855284	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaagctttcagtttcaaatcGaaccttgaaagacataggag	9	7	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:53855284G>A	ENST00000595091.1	+	5	1575	c.1356G>A	c.(1354-1356)tcG>tcA	p.S452S	ZNF845_ENST00000458035.1_Silent_p.S452S			Q96IR2	ZN845_HUMAN	zinc finger protein 845	452					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S452S(2)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						GTTTCAAATCGAACCTTGAAA	0.398																																					p.S452S		Atlas-SNP	.											ZNF845,NS,carcinoma,0,1	ZNF845	101	.	2	Substitution - coding silent(2)	prostate(1)|kidney(1)	c.G1356A						.						26	24	25					19																	53855284		692	1590	2282	SO:0001819	synonymous_variant	91664	exon4			CAAATCGAACCTT	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.1356G>A	chr19.hg19:g.53855284G>A		45.0	1.0		55.0	3.0	NM_138374		Silent	SNP	ENST00000595091.1	hg19	CCDS46170.1																																																																																			.	.		0.398	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		A	53855284	G	A	53855284	2	1	112	1	0	0	0	0	0	0	0	1	18206	1045	37	1		1	ZNF845	19	53855284	Silent	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	209520	53855284	5273699	1117	17738										
ZNF761	388561	hgsc.bcm.edu	37	chr19	53959189	53959189	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaatgtgacaaagctttccgTttcaaatcaaaccttgaaag	7	8	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:53959189T>C	ENST00000454407.1	+	0	1881							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		AAGCTTTCCGTTTCAAATCAA	0.423																																					p.R476R		Atlas-SNP	.											.	ZNF761	104	.	0			c.T1428C						.						76	80	78					19																	53959189		2203	4300	6503			388561	exon7			TTTCCGTTTCAAA	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		chr19.hg19:g.53959189T>C		41.0	0.0		39.0	10.0	NM_001008401	Q6ZNB9	Silent	SNP	ENST00000454407.1	hg19																																																																																				.	.		0.423	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		C	53959189	T	C	53959189	1	2	112	0	1	0	0	0	0	0	0	0	18151	1712	60	2		2	ZNF761	19	53959189	RNA	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	103905	53959189	5169794	1118	17739										
DPRX	503834	hgsc.bcm.edu	37	chr19	54140025	54140025	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgctcacccgatcggcctggTgtacacgggtcatcgagtcc	12	14	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:54140025T>A	ENST00000376650.1	+	3	410	c.359T>A	c.(358-360)gTg>gAg	p.V120E		NM_001012728.1	NP_001012746.1	A6NFQ7	DPRX_HUMAN	divergent-paired related homeobox	120					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(4)|large_intestine(1)|lung(7)	12	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.013)		ATCGGCCTGGTGTACACGGGT	0.562																																					p.V120E		Atlas-SNP	.											.	DPRX	34	.	0			c.T359A						.						133	105	114					19																	54140025		2203	4300	6503	SO:0001583	missense	503834	exon3			GCCTGGTGTACAC		CCDS33103.1	19q13.42	2011-06-20			ENSG00000204595	ENSG00000204595		"Homeoboxes / PRD class"	32166	protein-coding gene	gene with protein product		611165					Standard	NM_001012728		Approved		uc002qcf.1	A6NFQ7		ENST00000376650.1:c.359T>A	chr19.hg19:g.54140025T>A	ENSP00000365838:p.Val120Glu	158.0	0.0		160.0	52.0	NM_001012728		Missense_Mutation	SNP	ENST00000376650.1	hg19	CCDS33103.1	.	.	.	.	.	.	.	.	.	.	t	9.525	1.109197	0.20714	.	.	ENSG00000204595	ENST00000376650	D	0.94376	-3.41	1.45	1.45	0.22620	.	.	.	.	.	D	0.91432	0.7296	N	0.24115	0.695	0.09310	N	1	D	0.76494	0.999	D	0.71184	0.972	T	0.82014	-0.0667	9	0.29301	T	0.29	.	5.0324	0.14417	0.0:0.0:0.0:1.0	.	120	A6NFQ7	DPRX_HUMAN	E	120	ENSP00000365838:V120E	ENSP00000365838:V120E	V	+	2	0	DPRX	58831837	0.014000	0.17966	0.004000	0.12327	0.002000	0.02628	1.273000	0.33121	0.918000	0.36919	0.459000	0.35465	GTG	.	.		0.562	DPRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409880.1	NM_001012728		A	54140025	T	A	54140025	3	1	112	1	0	0	0	0	1	0	0	0	4740	1696	59	4	369	4	DPRX	19	54140025	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	180836	54140025	4988958	1119	17740										
CNOT3	4849	hgsc.bcm.edu	37	chr19	54647778	54647778	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagttgtggaacgagagaccAaaaccaaagcttacagcaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:54647778delA	ENST00000406403.1	+	5	1898	c.295delA	c.(295-297)aaafs	p.K99fs	CNOT3_ENST00000358389.3_5'UTR|CNOT3_ENST00000221232.5_Frame_Shift_Del_p.K99fs			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	99					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(7)|urinary_tract(3)	28	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					ACGAGAGACCAAAACCAAAGC	0.557																																					p.T98fs		Atlas-INDEL	.											.	CNOT3	133	.	0			c.294delC						.						86	84	84					19																	54647778		2203	4300	6503	SO:0001589	frameshift_variant	4849	exon6			.	AF180474	CCDS12880.1	19q13.4	2011-02-14			ENSG00000088038	ENSG00000088038			7879	protein-coding gene	gene with protein product	"NOT3 (negative regulator of transcription 3, yeast) homolog"	604910		NOT3		10637334, 9734811	Standard	NM_014516		Approved	NOT3H, KIAA0691, LENG2	uc002qdj.2	O75175	OTTHUMG00000066468	ENST00000406403.1:c.295delA	chr19.hg19:g.54647778delA	ENSP00000383954:p.Lys99fs	107.0	0.0		122.0	10.0	NM_014516	Q9NZN7|Q9UF76	Frame_Shift_Del	DEL	ENST00000406403.1	hg19	CCDS12880.1																																																																																			.	.		0.557	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516		-	54647778	A	-	54647778	7	5	112	1	0	1	0	1	0	0	0	0	3622	131	5	0	313	0	CNOT3	19	54647778	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	507753	54647778	4481205	1120	17741										
NLRP7	199713	hgsc.bcm.edu	37	chr19	55445101	55445101	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcttctgtaagacgacagttTtccaacctgcaaaaatatga	7	9	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:55445101T>C	ENST00000590030.1	-	7	2518	c.2478A>G	c.(2476-2478)gaA>gaG	p.E826E	NLRP7_ENST00000446217.1_Silent_p.E854E|NLRP7_ENST00000592784.1_Silent_p.E826E|NLRP7_ENST00000328092.5_Silent_p.E798E|NLRP7_ENST00000448121.2_Silent_p.E798E|NLRP7_ENST00000340844.2_Silent_p.E826E|NLRP7_ENST00000588756.1_Silent_p.E826E			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	826							ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		GACGACAGTTTTCCAACCTGC	0.478																																					p.E826E		Atlas-SNP	.											.	NLRP7	411	.	0			c.A2478G						.						81	78	79					19																	55445101		2203	4300	6503	SO:0001819	synonymous_variant	199713	exon8			ACAGTTTTCCAAC	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.2478A>G	chr19.hg19:g.55445101T>C		78.0	0.0		97.0	4.0	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	hg19	CCDS33109.1																																																																																			.	.		0.478	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		C	55445101	T	C	55445101	2	2	112	1	0	0	0	0	0	0	0	1	10491	1838	64	2		2	NLRP7	19	55445101	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	797323	55445101	3683882	1121	17742										
PEG3	5178	hgsc.bcm.edu	37	chr19	57326604	57326604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgctgtgggtctcctccccaTcagtattctcgccttgagac	9	15	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:57326604T>C	ENST00000326441.9	-	10	3569	c.3206A>G	c.(3205-3207)gAt>gGt	p.D1069G	PEG3_ENST00000423103.2_Missense_Mutation_p.D1069G|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000599935.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.D943G|PEG3_ENST00000598410.1_Missense_Mutation_p.D945G|ZIM2_ENST00000601070.1_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1069					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CTCCTCCCCATCAGTATTCTC	0.493																																					p.D1069G		Atlas-SNP	.											.	PEG3	414	.	0			c.A3206G						.						148	134	139					19																	57326604		2203	4300	6503	SO:0001583	missense	5178	exon9			TCCCCATCAGTAT	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.3206A>G	chr19.hg19:g.57326604T>C	ENSP00000326581:p.Asp1069Gly	84.0	0.0		115.0	5.0	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	hg19	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.882305	0.00532	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02737	4.18;4.18	2.5	-0.933	0.10431	.	2.678910	0.01592	N	0.021597	T	0.01905	0.0060	N	0.08118	0	.	.	.	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.44605	-0.9317	9	0.22706	T	0.39	0.3141	5.7766	0.18283	0.0:0.4641:0.0:0.5359	.	945;1069;1004	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	G	1069	ENSP00000326581:D1069G;ENSP00000403051:D1069G	ENSP00000326581:D1069G	D	-	2	0	ZIM2	62018416	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.306000	0.02735	-0.307000	0.08804	-0.290000	0.09829	GAT	.	.		0.493	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			C	57326604	T	C	57326604	3	2	112	1	0	0	0	0	1	0	0	0	11729	1435	50	2	1564	2	PEG3	19	57326604	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1881503	57326604	1802379	1122	17743										
CSNK2A1	1457	hgsc.bcm.edu	37	chr20	469379	469379	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgttgtatttgtcaatatagTcatataaatcttctgtcccc	5	8	4	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:469379T>C	ENST00000217244.3	-	11	1142	c.767A>G	c.(766-768)gAc>gGc	p.D256G	CSNK2A1_ENST00000349736.5_Missense_Mutation_p.D256G|CSNK2A1_ENST00000400217.2_Missense_Mutation_p.D120G|CSNK2A1_ENST00000400227.3_Missense_Mutation_p.D256G	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	256	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			D -> G (in Ref. 3; CAA49758). {ECO:0000305}.	axon guidance (GO:0007411)|chaperone-mediated protein folding (GO:0061077)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	ATP binding (GO:0005524)|Hsp90 protein binding (GO:0051879)|protein N-terminus binding (GO:0047485)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			GTCAATATAGTCATATAAATC	0.338																																					p.D256G		Atlas-SNP	.											.	CSNK2A1	36	.	0			c.A767G						.						139	128	132					20																	469379		2203	4300	6503	SO:0001583	missense	1457	exon10			ATATAGTCATATA	M55265	CCDS13003.1, CCDS13004.1	20p13	2013-01-17			ENSG00000101266	ENSG00000101266			2457	protein-coding gene	gene with protein product		115440				2174700, 1766873	Standard	NM_177559		Approved		uc002wdx.1	P68400	OTTHUMG00000031636	ENST00000217244.3:c.767A>G	chr20.hg19:g.469379T>C	ENSP00000217244:p.Asp256Gly	73.0	0.0		111.0	6.0	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	hg19	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	T	13.52	2.262675	0.39995	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.44	5.44	0.79542	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.086149	0.85682	D	0.000000	T	0.64746	0.2626	M	0.69248	2.105	0.80722	D	1	B	0.06786	0.001	B	0.16722	0.016	T	0.60372	-0.7276	10	0.23302	T	0.38	-3.5424	14.836	0.70183	0.0:0.0:0.0:1.0	.	256	P68400	CSK21_HUMAN	G	256;256;256;256;120	ENSP00000383086:D256G;ENSP00000339247:D256G;ENSP00000217244:D256G;ENSP00000383076:D120G	ENSP00000217244:D256G	D	-	2	0	CSNK2A1	417379	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.978000	0.70501	2.285000	0.76669	0.533000	0.62120	GAC	.	.		0.338	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895		C	469379	T	C	469379	3	2	112	1	0	0	0	0	1	0	0	0	3959	1667	58	2	424	2	CSNK2A1	20	469379	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10		469379	62556141	1123	17744										
SDCBP2	27111	hgsc.bcm.edu	37	chr20	1291473	1291473	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgtgctcgtagatcacactGgggatgatggtcagggtgac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:1291473delG	ENST00000360779.3	-	8	968	c.795delC	c.(793-795)cccfs	p.P265fs	SDCBP2_ENST00000467129.1_5'UTR|SDCBP2_ENST00000381812.1_Frame_Shift_Del_p.P265fs|SDCBP2_ENST00000381808.3_Frame_Shift_Del_p.P180fs|SDCBP2_ENST00000339987.3_Frame_Shift_Del_p.P265fs	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	265	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						AGATCACACTGGGGATGATGG	0.572																																					p.S266fs		Atlas-INDEL	.											.	SDCBP2	78	.	0			c.796delA						.						169	145	153					20																	1291473		2203	4300	6503	SO:0001589	frameshift_variant	27111	exon8			.	AF131809	CCDS13013.1, CCDS42848.1	20p13	2008-07-02			ENSG00000125775	ENSG00000125775			15756	protein-coding gene	gene with protein product						11152476	Standard	NM_080489		Approved	ST-2, SITAC18	uc021vzn.1	Q9H190	OTTHUMG00000031661	ENST00000360779.3:c.795delC	chr20.hg19:g.1291473delG	ENSP00000354013:p.Pro265fs	195.0	0.0		193.0	12.0	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Frame_Shift_Del	DEL	ENST00000360779.3	hg19	CCDS42848.1																																																																																			.	.		0.572	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489		-	1291473	G	-	1291473	7	5	112	1	0	1	0	1	0	0	0	0	13971	1335	47	0	91	0	SDCBP2	20	1291473	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	822094	1291473	61734047	1124	17745										
TGM3	7053	hgsc.bcm.edu	37	chr20	2291043	2291043	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acttgggacgttcatactgcTttttaacccctggctgaatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:2291043delT	ENST00000381458.5	+	3	464	c.401delT	c.(400-402)cttfs	p.L134fs		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	134					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	TTCATACTGCTTTTTAACCCC	0.537																																					p.L134fs		Atlas-INDEL	.											.	TGM3	105	.	0			c.400delC						.						176	169	171					20																	2291043		2203	4300	6503	SO:0001589	frameshift_variant	7053	exon3			.	L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"Transglutaminases"	11779	protein-coding gene	gene with protein product	"E polypeptide, protein-glutamine-gamma-glutamyltransferase"	600238	"transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.401delT	chr20.hg19:g.2291043delT	ENSP00000370867:p.Leu134fs	119.0	0.0		162.0	10.0	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Frame_Shift_Del	DEL	ENST00000381458.5	hg19	CCDS33435.1																																																																																			.	.		0.537	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245		-	2291043	T	-	2291043	7	5	112	1	0	1	0	1	0	0	0	0	15846	1609	56	0	411	0	TGM3	20	2291043	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	999570	2291043	60734477	1125	17746										
ZNF343	79175	hgsc.bcm.edu	37	chr20	2474194	2474194	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggcctttccctcctttttctGggggcagtcagtatcattag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:2474194delG	ENST00000278772.4	-	4	635	c.148delC	c.(148-150)cagfs	p.Q50fs	RP4-734P14.4_ENST00000461548.1_Frame_Shift_Del_p.Q50fs|ZNF343_ENST00000358413.2_Frame_Shift_Del_p.Q50fs|ZNF343_ENST00000381253.1_Frame_Shift_Del_p.Q50fs	NM_001282495.1|NM_001282496.1|NM_024325.4	NP_001269424.1|NP_001269425.1|NP_077301.4	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	50					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|skin(4)|upper_aerodigestive_tract(1)	25						TCCTTTTTCTGGGGGCAGTCA	0.478																																					p.Q50fs		Atlas-INDEL	.											.	ZNF343	47	.	0			c.149delA						.						59	65	63					20																	2474194		2203	4300	6503	SO:0001589	frameshift_variant	79175	exon4			.	AK096911	CCDS13028.1, CCDS74692.1, CCDS74693.1, CCDS74694.1	20p13	2013-01-08			ENSG00000088876	ENSG00000088876		"Zinc fingers, C2H2-type", "-"	16017	protein-coding gene	gene with protein product							Standard	NM_001282498		Approved	MGC10715	uc002wge.1	Q6P1L6	OTTHUMG00000031701	ENST00000278772.4:c.148delC	chr20.hg19:g.2474194delG	ENSP00000278772:p.Gln50fs	146.0	0.0		159.0	10.0	NM_024325	Q5JXU8|Q5JXU9|Q8N8F2|Q96EX8|Q96NA5|Q9BQB0	Frame_Shift_Del	DEL	ENST00000278772.4	hg19	CCDS13028.1																																																																																			.	.		0.478	ZNF343-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077617.1	NM_024325		-	2474194	G	-	2474194	7	5	112	1	0	1	0	1	0	0	0	0	17873	1357	47	0	1663	0	ZNF343	20	2474194	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	183151	2474194	60551326	1126	17747										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9352974	9352974	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgaaattgagcccacagcaTtttcttatgaaaagttctat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:9352974delT	ENST00000378493.1	+	8	625	c.610delT	c.(610-612)tttfs	p.F204fs	PLCB4_ENST00000378501.2_Frame_Shift_Del_p.F204fs|PLCB4_ENST00000378473.3_Frame_Shift_Del_p.F204fs|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000334005.3_Frame_Shift_Del_p.F204fs|PLCB4_ENST00000278655.4_Frame_Shift_Del_p.F204fs|PLCB4_ENST00000414679.2_Frame_Shift_Del_p.F204fs			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	204					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						GCCCACAGCATTTTCTTATGA	0.363																																					p.A203fs		Atlas-INDEL	.											.	PLCB4	204	.	0			c.609delA						.						79	81	80					20																	9352974		2202	4300	6502	SO:0001589	frameshift_variant	5332	exon9			.		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.610delT	chr20.hg19:g.9352974delT	ENSP00000367754:p.Phe204fs	239.0	0.0		215.0	13.0	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Frame_Shift_Del	DEL	ENST00000378493.1	hg19	CCDS13105.1																																																																																			.	.		0.363	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			-	9352974	T	-	9352974	7	5	112	1	0	1	0	1	0	0	0	0	12039	1493	52	0	640	0	PLCB4	20	9352974	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	6878780	9352974	53672546	1127	17748										
PAK7	57144	hgsc.bcm.edu	37	chr20	9538333	9538333	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggttatgaaggtaggagagAgctctcagaactgacaggca	14	6	1	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:9538333A>G	ENST00000378429.3	-	8	2211	c.1665T>C	c.(1663-1665)gcT>gcC	p.A555A	PAK7_ENST00000353224.5_Silent_p.A555A|PAK7_ENST00000378423.1_Silent_p.A555A	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	555	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> S (in dbSNP:rs34102290). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			GGTAGGAGAGAGCTCTCAGAA	0.433																																					p.A555A		Atlas-SNP	.											.	PAK7	194	.	0			c.T1665C						.						141	122	128					20																	9538333		2203	4300	6503	SO:0001819	synonymous_variant	57144	exon7			GGAGAGAGCTCTC	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1665T>C	chr20.hg19:g.9538333A>G		79.0	0.0		96.0	4.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Silent	SNP	ENST00000378429.3	hg19	CCDS13107.1																																																																																			.	.		0.433	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			G	9538333	A	G	9538333	2	3	112	1	0	0	0	0	0	0	0	1	11414	291	11	2		2	PAK7	20	9538333	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	185359	9538333	53487187	1128	17749										
JAG1	182	hgsc.bcm.edu	37	chr20	10622493	10622493	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acagtcatcatcccatttggCcccatctggtatcacactcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:10622493delC	ENST00000254958.5	-	22	3135	c.2620delG	c.(2620-2622)gccfs	p.A874fs	JAG1_ENST00000423891.2_Frame_Shift_Del_p.A715fs	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	874					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						TCCCATTTGGCCCCATCTGGT	0.532									Alagille Syndrome																												p.A874fs		Atlas-INDEL	.											.	JAG1	213	.	0			c.2621delC						.						214	186	195					20																	10622493		2203	4300	6503	SO:0001589	frameshift_variant	182	exon22	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	.	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"CD molecules"	6188	protein-coding gene	gene with protein product		601920	"Alagille syndrome"	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2620delG	chr20.hg19:g.10622493delC	ENSP00000254958:p.Ala874fs	187.0	0.0		188.0	13.0	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Frame_Shift_Del	DEL	ENST00000254958.5	hg19	CCDS13112.1																																																																																			.	.		0.532	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		-	10622493	C	-	10622493	7	5	112	1	0	1	0	1	0	0	0	0	7943	739	26	0	1056	0	JAG1	20	10622493	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1084160	10622493	52403027	1129	17750										
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13899678	13899678	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagacttactcttctttttgTttttggcttttagactgctg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:13899678delT	ENST00000284951.5	-	4	449	c.375delA	c.(373-375)aaafs	p.K125fs	SEL1L2_ENST00000378072.5_Frame_Shift_Del_p.K125fs|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	125						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CTTCTTTTTGTTTTTGGCTTT	0.343																																					p.Q126fs		Atlas-INDEL	.											.	SEL1L2	103	.	0			c.376delC						.						167	151	156					20																	13899678		1823	4085	5908	SO:0001589	frameshift_variant	80343	exon4			.	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.375delA	chr20.hg19:g.13899678delT	ENSP00000284951:p.Lys125fs	138.0	0.0		144.0	11.0	NM_001271539	B4DXX5	Frame_Shift_Del	DEL	ENST00000284951.5	hg19																																																																																				.	.		0.343	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		-	13899678	T	-	13899678	7	5	112	1	0	1	0	1	0	0	0	0	14026	1722	60	0	1759	0	SEL1L2	20	13899678	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	3277185	13899678	49125842	1130	17751										
C20orf72	27131	hgsc.bcm.edu	37	chr20	17950850	17950850	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gataaaccaaatgcaagtgaTccttcagttcctttgaaaat	6	8	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:17950850T>C	ENST00000377768.3	-	0	0				MGME1_ENST00000377704.4_Silent_p.D116D|SNX5_ENST00000606602.1_5'Flank|MGME1_ENST00000377710.5_Silent_p.D116D|MGME1_ENST00000467391.1_3'UTR|MGME1_ENST00000377709.1_Intron|SNX5_ENST00000486039.1_5'Flank|SNX5_ENST00000481323.1_5'Flank|SNX5_ENST00000377759.4_5'Flank|SNX5_ENST00000606557.1_5'Flank	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5						intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						ATGCAAGTGATCCTTCAGTTC	0.448																																					p.D116D		Atlas-SNP	.											.	.	.	.	0			c.T348C						.						84	89	87					20																	17950850		2203	4300	6503	SO:0001631	upstream_gene_variant	92667	exon2			AAGTGATCCTTCA	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"Sorting nexins"	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953		chr20.hg19:g.17950850T>C	Exception_encountered	131.0	0.0		119.0	5.0	NM_052865	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	hg19	CCDS13130.1																																																																																			.	.		0.448	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			C	17950850	T	C	17950850	1	2	112	0	1	0	0	0	0	0	0	0	2120	1432	50	2		2	C20orf72	20	17950850	5'Flank	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	4051172	17950850	45074670	1131	17752										
DNMT3B	1789	hgsc.bcm.edu	37	chr20	31369189	31369189	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagctcgcgactctccaagaGggaggtgtccagtctgctaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:31369189delG	ENST00000328111.2	+	3	494	c.173delG	c.(172-174)aggfs	p.R58fs	DNMT3B_ENST00000201963.3_Frame_Shift_Del_p.R70fs|DNMT3B_ENST00000348286.2_Frame_Shift_Del_p.R58fs|DNMT3B_ENST00000375623.4_Frame_Shift_Del_p.R58fs|DNMT3B_ENST00000443239.3_Frame_Shift_Del_p.R58fs|DNMT3B_ENST00000456297.2_Frame_Shift_Del_p.R58fs|DNMT3B_ENST00000344505.4_Frame_Shift_Del_p.R58fs|DNMT3B_ENST00000353855.2_Frame_Shift_Del_p.R58fs	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	58	Interaction with DNMT1 and DNMT3A.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTCTCCAAGAGGGAGGTGTCC	0.552																																					p.R70fs		Atlas-INDEL	.											.	DNMT3B	196	.	0			c.208delA						.						141	111	121					20																	31369189		2203	4300	6503	SO:0001589	frameshift_variant	1789	exon3			.		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.173delG	chr20.hg19:g.31369189delG	ENSP00000328547:p.Arg58fs	127.0	0.0		144.0	10.0	NM_175850	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Frame_Shift_Del	DEL	ENST00000328111.2	hg19	CCDS13205.1																																																																																			.	.		0.552	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		-	31369189	G	-	31369189	7	5	112	1	0	1	0	1	0	0	0	0	4679	1000	35	0	219	0	DNMT3B	20	31369189	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	13418339	31369189	31656331	1132	17753										
PXMP4	11264	hgsc.bcm.edu	37	chr20	32302502	32302502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccattccggaagagaaaggTcatgaccagcgcgtgagggg	16	9	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:32302502T>C	ENST00000409299.3	-	2	246	c.154A>G	c.(154-156)Acc>Gcc	p.T52A	PXMP4_ENST00000344022.3_Missense_Mutation_p.T52A|PXMP4_ENST00000217398.3_Missense_Mutation_p.T52A	NM_007238.4	NP_009169.3	Q9Y6I8	PXMP4_HUMAN	peroxisomal membrane protein 4, 24kDa	52						integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|large_intestine(2)|lung(8)	13						AAGAGAAAGGTCATGACCAGC	0.502																																					p.T52A		Atlas-SNP	.											.	PXMP4	20	.	0			c.A154G						.						167	151	156					20																	32302502		2203	4300	6503	SO:0001583	missense	11264	exon2			GAAAGGTCATGAC	AF072864	CCDS13225.1, CCDS13226.1	20q11.22	2008-07-02	2002-08-29		ENSG00000101417	ENSG00000101417			15920	protein-coding gene	gene with protein product	"24 kDa peroxisomal intrinsic membrane protein"		"peroxisomal membrane protein 4 (24kD)"			10366717	Standard	NM_183397		Approved	PMP24	uc002wzv.3	Q9Y6I8	OTTHUMG00000032273	ENST00000409299.3:c.154A>G	chr20.hg19:g.32302502T>C	ENSP00000386385:p.Thr52Ala	144.0	0.0		150.0	6.0	NM_183397	A2A2I7|Q9H0T4	Missense_Mutation	SNP	ENST00000409299.3	hg19	CCDS13225.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.694169	0.88735	.	.	ENSG00000101417	ENST00000409299;ENST00000344022;ENST00000217398	T	0.31510	1.49	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.52208	0.1720	M	0.64567	1.98	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.85130	0.997;0.996;0.957	T	0.49735	-0.8908	10	0.39692	T	0.17	-40.2422	14.8622	0.70389	0.0:0.0:0.0:1.0	.	52;52;52	B4DWH1;A2A2I7;Q9Y6I8	.;.;PXMP4_HUMAN	A	52	ENSP00000386385:T52A	ENSP00000217398:T52A	T	-	1	0	PXMP4	31766163	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.943000	0.87716	1.996000	0.58369	0.368000	0.22195	ACC	.	.		0.502	PXMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078739.2	NM_007238		C	32302502	T	C	32302502	3	2	112	1	0	0	0	0	1	0	0	0	12866	1667	58	2	496	2	PXMP4	20	32302502	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	933313	32302502	30723018	1133	17754										
EIF2S2	8894	hgsc.bcm.edu	37	chr20	32686360	32686360	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acttaacattcttctttttcTtctttttattgccaagcata	2	9	4	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:32686360T>C	ENST00000374980.2	-	4	598	c.377A>G	c.(376-378)aAg>aGg	p.K126R		NM_003908.3	NP_003899.2	P20042	IF2B_HUMAN	eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa	126	Poly-Lys.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|male germ cell proliferation (GO:0002176)|male gonad development (GO:0008584)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 2 complex (GO:0005850)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|prostate(3)|upper_aerodigestive_tract(1)	11						CTTCTTTTTCTTCTTTTTATT	0.383																																					p.K126R		Atlas-SNP	.											.	EIF2S2	32	.	0			c.A377G						.						105	101	103					20																	32686360		2203	4300	6503	SO:0001583	missense	8894	exon4			TTTTTCTTCTTTT	M29536	CCDS13231.1	20q11.2	2012-04-17	2002-08-29		ENSG00000125977	ENSG00000125977		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	3266	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 67"	603908	"eukaryotic translation initiation factor 2, subunit 2 (beta, 38kD )"	EIF2		3044606	Standard	XM_005260605		Approved	EIF2beta, PPP1R67	uc031rsu.1	P20042	OTTHUMG00000032287	ENST00000374980.2:c.377A>G	chr20.hg19:g.32686360T>C	ENSP00000364119:p.Lys126Arg	81.0	0.0		72.0	4.0	NM_003908	Q9BVU0|Q9UJE4	Missense_Mutation	SNP	ENST00000374980.2	hg19	CCDS13231.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461514	0.63513	.	.	ENSG00000125977	ENST00000374980	T	0.55588	0.51	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.66470	0.2792	L	0.55017	1.72	0.80722	D	1	B;P;P	0.52842	0.002;0.956;0.956	B;P;P	0.62184	0.003;0.899;0.899	T	0.66073	-0.6014	10	0.46703	T	0.11	-14.8695	16.1549	0.81657	0.0:0.0:0.0:1.0	.	126;126;126	B5BU01;Q6IBR8;P20042	.;.;IF2B_HUMAN	R	126	ENSP00000364119:K126R	ENSP00000364119:K126R	K	-	2	0	EIF2S2	32150021	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.412000	0.73303	2.207000	0.71202	0.528000	0.53228	AAG	.	.		0.383	EIF2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078765.2	NM_003908		C	32686360	T	C	32686360	3	2	112	1	0	0	0	0	1	0	0	0	5012	1609	56	2	648	2	EIF2S2	20	32686360	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	383858	32686360	30339160	1134	17755										
CEP250	11190	hgsc.bcm.edu	37	chr20	34092346	34092346	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	acttgcccagagggatgaagAgctgagacatcagcaggaac	13	9	1	4			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:34092346A>G	ENST00000397527.1	+	30	6869	c.6149A>G	c.(6148-6150)gAg>gGg	p.E2050G	CEP250_ENST00000342580.4_Missense_Mutation_p.E1994G	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	2050	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AGGGATGAAGAGCTGAGACAT	0.557																																					p.E2050G		Atlas-SNP	.											.	CEP250	141	.	0			c.A6149G						.						30	31	31					20																	34092346		2203	4300	6503	SO:0001583	missense	11190	exon30			ATGAAGAGCTGAG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.6149A>G	chr20.hg19:g.34092346A>G	ENSP00000380661:p.Glu2050Gly	71.0	0.0		79.0	4.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	A	18.40	3.616285	0.66672	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.57907	2.42;2.36;0.37	4.83	4.83	0.62350	.	0.000000	0.56097	D	0.000026	T	0.60547	0.2277	M	0.68952	2.095	0.34852	D	0.741764	P	0.49559	0.925	P	0.49752	0.621	T	0.75374	-0.3340	10	0.72032	D	0.01	.	14.2031	0.65716	1.0:0.0:0.0:0.0	.	2050	Q9BV73	CP250_HUMAN	G	2050;1994;538	ENSP00000380661:E2050G;ENSP00000341541:E1994G;ENSP00000395992:E538G	ENSP00000341541:E1994G	E	+	2	0	CEP250	33555760	0.976000	0.34144	0.880000	0.34516	0.991000	0.79684	2.566000	0.45948	2.021000	0.59480	0.533000	0.62120	GAG	.	.		0.557	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		G	34092346	A	G	34092346	3	3	112	1	0	0	0	0	1	0	0	0	3254	304	11	2	6255	2	CEP250	20	34092346	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1405986	34092346	28933174	1135	17756										
PHF20	51230	hgsc.bcm.edu	37	chr20	34526859	34526859	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taccagaagccccgcgcctaTtaccctgccgtggagcagaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:34526859delT	ENST00000374012.3	+	16	2670	c.2541delT	c.(2539-2541)tatfs	p.Y848fs	PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	848					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					CCCGCGCCTATTACCCTGCCG	0.632																																					p.Y847fs		Atlas-INDEL	.											.	PHF20	94	.	0			c.2540delA						.						48	44	45					20																	34526859		2203	4300	6503	SO:0001589	frameshift_variant	51230	exon16			.	AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"Tudor domain containing", "Zinc fingers, PHD-type"	16098	protein-coding gene	gene with protein product	"tudor domain containing 20A"	610335	"chromosome 20 open reading frame 104"	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.2541delT	chr20.hg19:g.34526859delT	ENSP00000363124:p.Tyr848fs	101.0	0.0		128.0	10.0	NM_016436	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Frame_Shift_Del	DEL	ENST00000374012.3	hg19	CCDS13268.1																																																																																			.	.		0.632	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		-	34526859	T	-	34526859	7	5	112	1	0	1	0	1	0	0	0	0	11840	1500	52	0	2599	0	PHF20	20	34526859	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	434513	34526859	28498661	1136	17757										
TGIF2	60436	hgsc.bcm.edu	37	chr20	35219773	35219773	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gatggagcttcagaagcagcAggacccatcactcccattac	9	13	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:35219773A>G	ENST00000373874.2	+	3	852	c.653A>G	c.(652-654)cAg>cGg	p.Q218R	RP5-977B1.11_ENST00000561134.1_RNA|TGIF2_ENST00000373872.4_Missense_Mutation_p.Q218R|TGIF2-C20orf24_ENST00000558530.1_Intron	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	218	Repressive function.				gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway (GO:0038092)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				CAGAAGCAGCAGGACCCATCA	0.577																																					p.Q218R		Atlas-SNP	.											.	TGIF2	26	.	0			c.A653G						.						127	125	125					20																	35219773		2200	4295	6495	SO:0001583	missense	60436	exon3			AGCAGCAGGACCC	AB042646	CCDS13278.1	20q11.23	2012-12-12	2007-02-07		ENSG00000118707	ENSG00000118707		"Homeoboxes / TALE class"	15764	protein-coding gene	gene with protein product		607294	"TGFB-induced factor 2 (TALE family homeobox)"			11006116	Standard	NM_021809		Approved		uc021wcv.1	Q9GZN2	OTTHUMG00000172332	ENST00000373874.2:c.653A>G	chr20.hg19:g.35219773A>G	ENSP00000362981:p.Gln218Arg	112.0	0.0		117.0	6.0	NM_021809	B2R9U3|E1P5T9|H0YNI0	Missense_Mutation	SNP	ENST00000373874.2	hg19	CCDS13278.1	.	.	.	.	.	.	.	.	.	.	A	14.18	2.457346	0.43634	.	.	ENSG00000118707	ENST00000373874;ENST00000373872	T;T	0.65732	-0.17;-0.17	5.5	5.5	0.81552	.	0.750110	0.13143	N	0.410470	T	0.53142	0.1778	L	0.39898	1.24	0.80722	D	1	B	0.11235	0.004	B	0.04013	0.001	T	0.51529	-0.8694	10	0.56958	D	0.05	-22.1275	9.2083	0.37302	0.9107:0.0:0.0893:0.0	.	218	Q9GZN2	TGIF2_HUMAN	R	218	ENSP00000362981:Q218R;ENSP00000362979:Q218R	ENSP00000362979:Q218R	Q	+	2	0	TGIF2	34653187	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.798000	0.55522	2.077000	0.62373	0.459000	0.35465	CAG	.	.		0.577	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809		G	35219773	A	G	35219773	3	3	112	1	0	0	0	0	1	0	0	0	15841	188	7	2	659	2	TGIF2	20	35219773	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	692914	35219773	27805747	1137	17758										
DHX35	60625	hgsc.bcm.edu	37	chr20	37650554	37650554	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atccagaatatctttgtggtCcccccaaaccagaagtctca					rs142673637		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:37650554delC	ENST00000252011.3	+	16	1602	c.1569delC	c.(1567-1569)gtcfs	p.V523fs	DHX35_ENST00000373325.2_Frame_Shift_Del_p.V523fs|DHX35_ENST00000373323.4_Frame_Shift_Del_p.V492fs	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	523					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				TCTTTGTGGTCCCCCCAAACC	0.453																																					p.V523fs		Atlas-INDEL	.											.	DHX35	82	.	0			c.1568delT						.						143	137	139					20																	37650554		2203	4300	6503	SO:0001589	frameshift_variant	60625	exon16			.	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.1569delC	chr20.hg19:g.37650554delC	ENSP00000252011:p.Val523fs	187.0	0.0		179.0	12.0	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Frame_Shift_Del	DEL	ENST00000252011.3	hg19	CCDS13310.1																																																																																			.	.		0.453	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		-	37650554	C	-	37650554	7	5	112	1	0	1	0	1	0	0	0	0	4510	842	30	0	1631	0	DHX35	20	37650554	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	2430781	37650554	25374966	1138	17759										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39798114	39798114	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagcacttggacgagaacagCcccctaggggacttgctgcg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:39798114delC	ENST00000373271.1	+	23	3003	c.2598delC	c.(2596-2598)agcfs	p.S866fs	PLCG1_ENST00000244007.3_Frame_Shift_Del_p.S866fs|PLCG1_ENST00000373272.2_Frame_Shift_Del_p.S866fs	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	866					activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				ACGAGAACAGCCCCCTAGGGG	0.552																																					p.S866fs		Atlas-INDEL	.											.	PLCG1	111	.	0			c.2597delG						.						163	160	161					20																	39798114		2203	4300	6503	SO:0001589	frameshift_variant	5335	exon23			.	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.2598delC	chr20.hg19:g.39798114delC	ENSP00000362368:p.Ser866fs	176.0	0.0		174.0	11.0	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Frame_Shift_Del	DEL	ENST00000373271.1	hg19	CCDS13314.1																																																																																			.	.		0.552	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		-	39798114	C	-	39798114	7	5	112	1	0	1	0	1	0	0	0	0	12044	738	26	0	2688	0	PLCG1	20	39798114	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	2147560	39798114	23227406	1139	17760										
CHD6	84181	hgsc.bcm.edu	37	chr20	40084597	40084597	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccggagtaggtcctccaccTccatttttgagagctgctgt	10	12	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:40084597T>C	ENST00000373233.3	-	19	3029	c.2852A>G	c.(2851-2853)gAg>gGg	p.E951G	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	951	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GTCCTCCACCTCCATTTTTGA	0.448																																					p.E951G		Atlas-SNP	.											.	CHD6	312	.	0			c.A2852G						.						174	164	167					20																	40084597		2203	4300	6503	SO:0001583	missense	84181	exon19			TCCACCTCCATTT	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.2852A>G	chr20.hg19:g.40084597T>C	ENSP00000362330:p.Glu951Gly	137.0	0.0		119.0	5.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736086	0.89482	.	.	ENSG00000124177	ENST00000373233	T	0.75589	-0.95	5.73	5.73	0.89815	Helicase, C-terminal (1);	0.000000	0.64402	D	0.000017	D	0.90707	0.7084	H	0.96080	3.765	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.93516	0.6857	10	0.87932	D	0	-29.5288	16.3123	0.82883	0.0:0.0:0.0:1.0	.	951	Q8TD26	CHD6_HUMAN	G	951	ENSP00000362330:E951G	ENSP00000362330:E951G	E	-	2	0	CHD6	39518011	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.040000	0.89188	2.308000	0.77769	0.533000	0.62120	GAG	.	.		0.448	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			C	40084597	T	C	40084597	3	2	112	1	0	0	0	0	1	0	0	0	3331	1551	54	2	5371	2	CHD6	20	40084597	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	286483	40084597	22940923	1140	17761										
GDAP1L1	78997	hgsc.bcm.edu	37	chr20	42907863	42907863	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggaaacccccatccttcttcGgggcgtccttcctcatgggc					rs201609457		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:42907863delG	ENST00000342560.5	+	6	1115	c.1027delG	c.(1027-1029)gggfs	p.G343fs	GDAP1L1_ENST00000537864.1_Frame_Shift_Del_p.G151fs	NM_001256737.1|NM_024034.4	NP_001243666.1|NP_076939.3	Q96MZ0	GD1L1_HUMAN	ganglioside induced differentiation associated protein 1-like 1	343										endometrium(1)|large_intestine(5)|lung(10)|pancreas(1)|prostate(1)	18		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			ATCCTTCTTCGGGGCGTCCTT	0.587																																					p.F361fs		Atlas-INDEL	.											GDAP1L1,colon,carcinoma,0,1	GDAP1L1	36	.	0			c.1083delC						.						124	113	117					20																	42907863		2203	4300	6503	SO:0001589	frameshift_variant	78997	exon6			.		CCDS13328.1, CCDS74725.1, CCDS74726.1, CCDS74727.1	20q12	2012-02-09	2012-02-09		ENSG00000124194	ENSG00000124194			4213	protein-coding gene	gene with protein product							Standard	NM_024034		Approved		uc010zwl.3	Q96MZ0	OTTHUMG00000032530	ENST00000342560.5:c.1027delG	chr20.hg19:g.42907863delG	ENSP00000341782:p.Gly343fs	162.0	0.0		164.0	10.0	NM_001256737	B7Z621|Q5TE60|Q68CW7|Q9BQJ7|Q9BQV4|Q9BWJ4|Q9H3Y2|Q9H4G5	Frame_Shift_Del	DEL	ENST00000342560.5	hg19	CCDS13328.1																																																																																			.	.		0.587	GDAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079356.1	NM_024034		-	42907863	G	-	42907863	7	5	112	1	0	1	0	1	0	0	0	0	6316	1116	39	0	1049	0	GDAP1L1	20	42907863	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	2823266	42907863	20117657	1141	17762										
R3HDML	140902	hgsc.bcm.edu	37	chr20	42979399	42979399	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aatagcaacatgtgcttcaaGgggctgaaatccaacaagtt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:42979399delG	ENST00000217043.2	+	5	901	c.729delG	c.(727-729)aagfs	p.K243fs	RP5-881L22.5_ENST00000430481.2_RNA|RP5-881L22.5_ENST00000438702.1_RNA	NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	243						extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)	21		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			TGTGCTTCAAGGGGCTGAAAT	0.552																																					p.K243fs		Atlas-INDEL	.											.	R3HDML	33	.	0			c.728delA						.						159	139	146					20																	42979399		2203	4300	6503	SO:0001589	frameshift_variant	140902	exon5			.	BC107048	CCDS13329.1	20q13.12	2007-04-26	2005-09-02		ENSG00000101074	ENSG00000101074			16249	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing-like"				Standard	NM_178491		Approved	dJ881L22.3	uc002xls.2	Q9H3Y0	OTTHUMG00000032524	ENST00000217043.2:c.729delG	chr20.hg19:g.42979399delG	ENSP00000217043:p.Lys243fs	227.0	0.0		245.0	16.0	NM_178491		Frame_Shift_Del	DEL	ENST00000217043.2	hg19	CCDS13329.1																																																																																			.	.		0.552	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491		-	42979399	G	-	42979399	7	5	112	1	0	1	0	1	0	0	0	0	12904	991	35	0	747	0	R3HDML	20	42979399	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	71536	42979399	20046121	1142	17763										
SEMG2	6407	hgsc.bcm.edu	37	chr20	43851552	43851552	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtggagaaaaggatgtacagAaaggtgtatccaaaggcagt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:43851552delA	ENST00000372769.3	+	2	1369	c.1279delA	c.(1279-1281)aaafs	p.K427fs		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	427	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				GGATGTACAGAAAGGTGTATC	0.383																																					p.Q426fs		Atlas-INDEL	.											.	SEMG2	92	.	0			c.1278delG						.						80	76	77					20																	43851552		2203	4300	6503	SO:0001589	frameshift_variant	6407	exon2			.		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"Semenogelin 2"	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.1279delA	chr20.hg19:g.43851552delA	ENSP00000361855:p.Lys427fs	107.0	0.0		158.0	10.0	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Frame_Shift_Del	DEL	ENST00000372769.3	hg19	CCDS13346.1																																																																																			.	.		0.383	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		-	43851552	A	-	43851552	7	5	112	1	0	1	0	1	0	0	0	0	14060	247	9	0	1285	0	SEMG2	20	43851552	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	872153	43851552	19173968	1143	17764										
CTSA	5476	hgsc.bcm.edu	37	chr20	44521908	44521908	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctatgagcagaatgacaactCcctggtctactttgcctact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:44521908delC	ENST00000372459.2	+	6	843	c.650delC	c.(649-651)tccfs	p.S217fs	CTSA_ENST00000354880.5_Frame_Shift_Del_p.S218fs|CTSA_ENST00000191018.5_Frame_Shift_Del_p.S217fs|RP3-337O18.9_ENST00000607703.1_RNA|NEURL2_ENST00000372518.4_5'Flank|CTSA_ENST00000372484.3_Frame_Shift_Del_p.S235fs			P10619	PPGB_HUMAN	cathepsin A	217					glycosphingolipid metabolic process (GO:0006687)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|enzyme activator activity (GO:0008047)|serine-type carboxypeptidase activity (GO:0004185)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				AATGACAACTCCCTGGTCTAC	0.552																																					p.S235fs		Atlas-INDEL	.											CTSA,NS,carcinoma,0,1	CTSA	52	.	0			c.703delT						.						143	122	129					20																	44521908		2203	4300	6503	SO:0001589	frameshift_variant	5476	exon7			.	M22960	CCDS13385.2, CCDS46609.1, CCDS54467.1	20q13.12	2012-02-10	2006-12-05	2006-12-05	ENSG00000064601	ENSG00000064601	3.4.16.5	"Cathepsins"	9251	protein-coding gene	gene with protein product	"carboxypeptidase C", "lysosomal protective protein", "carboxypeptidase-L", "carboxypeptidase Y-like kininase", "deamidase", "lysosomal carboxypeptidase A", "urinary kininase"	613111	"protective protein for beta-galactosidase (galactosialidosis)"	GSL, PPGB		2071143	Standard	NM_000308		Approved		uc002xqh.3	P10619	OTTHUMG00000033078	ENST00000372459.2:c.650delC	chr20.hg19:g.44521908delC	ENSP00000361537:p.Ser217fs	157.0	0.0		155.0	10.0	NM_000308	B2R798|Q561W6|Q5JZH1|Q96KJ2|Q9BR08|Q9BW68	Frame_Shift_Del	DEL	ENST00000372459.2	hg19	CCDS46609.1																																																																																			.	.		0.552	CTSA-012	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471297.2	NM_000308		-	44521908	C	-	44521908	7	5	112	1	0	1	0	1	0	0	0	0	4031	855	30	0	730	0	CTSA	20	44521908	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	670356	44521908	18503612	1144	17765										
PCIF1	63935	hgsc.bcm.edu	37	chr20	44569759	44569759	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggggccttcagaggtgctgCccccgcatcccgaagtggaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:44569759delC	ENST00000372409.3	+	7	950	c.586delC	c.(586-588)cccfs	p.P197fs		NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	197					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						AGAGGTGCTGCCCCCGCATCC	0.612																																					p.L195fs		Atlas-INDEL	.											.	PCIF1	51	.	0			c.585delG						.						50	46	48					20																	44569759		2203	4300	6503	SO:0001589	frameshift_variant	63935	exon7			.	AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 121"		"chromosome 20 open reading frame 67"	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.586delC	chr20.hg19:g.44569759delC	ENSP00000361486:p.Pro197fs	130.0	0.0		166.0	10.0	NM_022104	E1P5P1|Q54AB9|Q9NT85	Frame_Shift_Del	DEL	ENST00000372409.3	hg19	CCDS13388.1																																																																																			.	.		0.612	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104		-	44569759	C	-	44569759	7	5	112	1	0	1	0	1	0	0	0	0	11589	739	26	0	604	0	PCIF1	20	44569759	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	47851	44569759	18455761	1145	17766										
ZNF334	55713	hgsc.bcm.edu	37	chr20	45131438	45131438	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctcattggattgtatctgtaTtttttcattcccaaatgact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:45131438delT	ENST00000347606.4	-	5	722	c.540delA	c.(538-540)aaafs	p.K180fs	ZNF334_ENST00000593880.1_Frame_Shift_Del_p.K203fs|ZNF334_ENST00000457685.2_Frame_Shift_Del_p.K142fs	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				TGTATCTGTATTTTTTCATTC	0.338																																					p.Y181fs		Atlas-INDEL	.											.	ZNF334	101	.	0			c.541delT						.						95	91	92					20																	45131438		2203	4300	6503	SO:0001589	frameshift_variant	55713	exon5			.	AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"Zinc fingers, C2H2-type", "-"	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.540delA	chr20.hg19:g.45131438delT	ENSP00000255129:p.Lys180fs	185.0	0.0		197.0	12.0	NM_018102	Q5T6U2|Q9NVW4	Frame_Shift_Del	DEL	ENST00000347606.4	hg19	CCDS33480.1																																																																																			.	.		0.338	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			-	45131438	T	-	45131438	7	5	112	1	0	1	0	1	0	0	0	0	17866	1490	52	0	1506	0	ZNF334	20	45131438	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	561679	45131438	17894082	1146	17767										
PREX1	57580	hgsc.bcm.edu	37	chr20	47342873	47342873	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctctggatcggagacaacAggtagccttccaaagggatg	12	10	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:47342873A>G	ENST00000371941.3	-	5	597	c.575T>C	c.(574-576)cTg>cCg	p.L192P	PREX1_ENST00000396220.1_Missense_Mutation_p.L192P	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	192	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CGGAGACAACAGGTAGCCTTC	0.512																																					p.L192P		Atlas-SNP	.											.	PREX1	441	.	0			c.T575C						.						101	83	89					20																	47342873		2203	4300	6503	SO:0001583	missense	57580	exon5			GACAACAGGTAGC	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.575T>C	chr20.hg19:g.47342873A>G	ENSP00000361009:p.Leu192Pro	126.0	0.0		89.0	5.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	a	25.4	4.636544	0.87760	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	D;D	0.84298	-1.83;-1.83	5.51	5.51	0.81932	Guanine-nucleotide dissociation stimulator, CDC24, conserved site (1);Dbl homology (DH) domain (5);	0.000000	0.42294	U	0.000728	D	0.95510	0.8541	H	0.98542	4.26	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97213	0.9872	10	0.87932	D	0	.	14.906	0.70718	1.0:0.0:0.0:0.0	.	192	Q8TCU6	PREX1_HUMAN	P	192	ENSP00000361009:L192P;ENSP00000379522:L192P	ENSP00000361009:L192P	L	-	2	0	PREX1	46776280	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.471000	0.90403	2.215000	0.71742	0.529000	0.55759	CTG	.	.		0.512	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		G	47342873	A	G	47342873	3	3	112	1	0	0	0	0	1	0	0	0	12488	188	7	2	4548	2	PREX1	20	47342873	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2211435	47342873	15682647	1147	17768										
ADNP	23394	hgsc.bcm.edu	37	chr20	49508560	49508560	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagattttaggttcaacttcAaaaacagggtcaaaagggct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:49508560delA	ENST00000396029.3	-	5	3258	c.2691delT	c.(2689-2691)tttfs	p.F897fs	ADNP_ENST00000371602.4_Frame_Shift_Del_p.F897fs|ADNP_ENST00000396032.3_Frame_Shift_Del_p.F897fs|ADNP_ENST00000349014.3_Frame_Shift_Del_p.F897fs	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	897					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						GTTCAACTTCAAAAACAGGGT	0.403																																					p.E898fs		Atlas-INDEL	.											.	ADNP	106	.	0			c.2692delG						.						143	144	144					20																	49508560		2203	4300	6503	SO:0001589	frameshift_variant	23394	exon5			.	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.2691delT	chr20.hg19:g.49508560delA	ENSP00000379346:p.Phe897fs	109.0	0.0		144.0	10.0	NM_015339	E1P5Y2|O94881|Q5BKU2|Q9UG34	Frame_Shift_Del	DEL	ENST00000396029.3	hg19	CCDS13433.1																																																																																			.	.		0.403	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		-	49508560	A	-	49508560	7	5	112	1	0	1	0	1	0	0	0	0	323	127	5	0	621	0	ADNP	20	49508560	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2165687	49508560	13516960	1148	17769										
SALL4	57167	hgsc.bcm.edu	37	chr20	50408744	50408744	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caggtggatttttagtgcaaTttttcttatgttccaggaac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:50408744delT	ENST00000217086.4	-	2	389	c.278delA	c.(277-279)aatfs	p.N93fs	SALL4_ENST00000483130.1_5'UTR|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Frame_Shift_Del_p.N93fs	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	93					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTTAGTGCAATTTTTCTTATG	0.522																																					p.N93fs		Atlas-INDEL	.											.	SALL4	168	.	0			c.279delT						.						62	64	63					20																	50408744		2203	4300	6503	SO:0001589	frameshift_variant	57167	exon2			.	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.278delA	chr20.hg19:g.50408744delT	ENSP00000217086:p.Asn93fs	73.0	0.0		103.0	10.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Frame_Shift_Del	DEL	ENST00000217086.4	hg19	CCDS13438.1																																																																																			.	.		0.522	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			-	50408744	T	-	50408744	7	5	112	1	0	1	0	1	0	0	0	0	13828	1493	52	0	2895	0	SALL4	20	50408744	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	900184	50408744	12616776	1149	17770										
BCAS1	8537	hgsc.bcm.edu	37	chr20	52645367	52645367	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caggccgagagagcatcaagAaaaaacgagatttagcagct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:52645367delA	ENST00000395961.3	-	4	453	c.287delT	c.(286-288)ttcfs	p.F96fs	BCAS1_ENST00000371435.2_Frame_Shift_Del_p.F96fs|BCAS1_ENST00000371440.3_Frame_Shift_Del_p.F96fs|BCAS1_ENST00000411563.1_5'UTR	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	96						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			GAGCATCAAGAAAAAACGAGA	0.522																																					p.F96fs		Atlas-INDEL	.											.	BCAS1	77	.	0			c.288delC						.						86	76	79					20																	52645367		2203	4300	6503	SO:0001589	frameshift_variant	8537	exon4			.	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.287delT	chr20.hg19:g.52645367delA	ENSP00000379290:p.Phe96fs	118.0	0.0		140.0	10.0	NM_003657	A0AVG5|Q68CZ3	Frame_Shift_Del	DEL	ENST00000395961.3	hg19	CCDS13444.1																																																																																			.	.		0.522	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657		-	52645367	A	-	52645367	7	5	112	1	0	1	0	1	0	0	0	0	1350	246	9	0	1503	0	BCAS1	20	52645367	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2236623	52645367	10380153	1150	17771										
VAPB	9217	hgsc.bcm.edu	37	chr20	57019177	57019177	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aagacagtgcagagcaacagCcccatttcagcattagcccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:57019177delC	ENST00000475243.1	+	6	956	c.618delC	c.(616-618)agcfs	p.S206fs	VAPB_ENST00000265619.2_3'UTR|VAPB_ENST00000395802.3_Frame_Shift_Del_p.P86fs	NM_004738.4	NP_004729.1	O95292	VAPB_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein B and C	206					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|endoplasmic reticulum unfolded protein response (GO:0030968)|modulation by virus of host morphology or physiology (GO:0019048)|positive regulation of viral genome replication (GO:0045070)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-tubulin binding (GO:0048487)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|structural molecule activity (GO:0005198)			kidney(2)|lung(3)|prostate(1)	6	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)			AGAGCAACAGCCCCATTTCAG	0.507																																					p.S206fs		Atlas-INDEL	.											.	VAPB	21	.	0			c.617delG						.						244	219	227					20																	57019177		2203	4300	6503	SO:0001589	frameshift_variant	9217	exon6			.	AF086628	CCDS33498.1, CCDS56198.1	20q13	2014-09-17			ENSG00000124164	ENSG00000124164			12649	protein-coding gene	gene with protein product		605704				9920726	Standard	NM_004738		Approved	VAP-B, VAP-C, ALS8	uc002xza.3	O95292	OTTHUMG00000032840	ENST00000475243.1:c.618delC	chr20.hg19:g.57019177delC	ENSP00000417175:p.Ser206fs	159.0	0.0		174.0	12.0	NM_004738	A2A2F2|O95293|Q9P0H0	Frame_Shift_Del	DEL	ENST00000475243.1	hg19	CCDS33498.1																																																																																			.	.		0.507	VAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079875.2			-	57019177	C	-	57019177	7	5	112	1	0	1	0	1	0	0	0	0	17137	738	26	0	640	0	VAPB	20	57019177	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	4373810	57019177	6006343	1151	17772										
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57269500	57269500	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtctgcgagcagccggaggTctttgcttccgcctgtgccc	14	14	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:57269500T>C	ENST00000356091.6	+	3	647	c.359T>C	c.(358-360)gTc>gCc	p.V120A	NPEPL1_ENST00000525817.1_Missense_Mutation_p.V72A|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Missense_Mutation_p.V92A	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	120						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			CAGCCGGAGGTCTTTGCTTCC	0.652																																					p.V120A		Atlas-SNP	.											.	NPEPL1	36	.	0			c.T359C						.						69	76	74					20																	57269500		2041	4187	6228	SO:0001583	missense	79716	exon3			CGGAGGTCTTTGC	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.359T>C	chr20.hg19:g.57269500T>C	ENSP00000348395:p.Val120Ala	69.0	0.0		107.0	5.0	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	hg19	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	T	10.51	1.370083	0.24771	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.32023	1.47;1.49;1.48	4.58	3.49	0.39957	.	0.057690	0.64402	N	0.000002	T	0.23370	0.0565	L	0.52206	1.635	0.58432	D	0.99999	B;B;B;B	0.14438	0.0;0.0;0.001;0.01	B;B;B;B	0.22753	0.003;0.007;0.003;0.041	T	0.05937	-1.0855	10	0.14656	T	0.56	-24.6563	5.9423	0.19199	0.0:0.1513:0.0:0.8487	.	120;72;92;120	Q8NDH3;G5EA34;E9PN47;Q8NDH3-3	PEPL1_HUMAN;.;.;.	A	92;72;120	ENSP00000434810:V92A;ENSP00000437112:V72A;ENSP00000348395:V120A	ENSP00000348395:V120A	V	+	2	0	NPEPL1	56702907	1.000000	0.71417	0.319000	0.25293	0.122000	0.20287	3.234000	0.51320	0.693000	0.31634	0.449000	0.29647	GTC	.	.		0.652	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		C	57269500	T	C	57269500	3	2	112	1	0	0	0	0	1	0	0	0	10583	1667	58	2	215	2	NPEPL1	20	57269500	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	250323	57269500	5756020	1152	17773										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58489043	58489043	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtttaccttcttttgtctcCaagcatgccatttacaaggt	6	10	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:58489043C>T	ENST00000357552.3	-	12	1042	c.817G>A	c.(817-819)Gga>Aga	p.G273R	SYCP2_ENST00000371001.2_Missense_Mutation_p.G273R			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	273					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			CTTTTGTCTCCAAGCATGCCA	0.294																																					p.G273R		Atlas-SNP	.											.	SYCP2	204	.	0			c.G817A						.						68	65	66					20																	58489043		2201	4298	6499	SO:0001583	missense	10388	exon11			TGTCTCCAAGCAT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.817G>A	chr20.hg19:g.58489043C>T	ENSP00000350162:p.Gly273Arg	126.0	0.0		148.0	6.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.152350	0.78001	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.04809	3.55;3.55;3.55	4.91	4.91	0.64330	.	0.101773	0.43110	D	0.000601	T	0.24812	0.0602	M	0.80422	2.495	0.44282	D	0.99714	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	T	0.01743	-1.1283	10	0.87932	D	0	-22.4929	18.4759	0.90792	0.0:1.0:0.0:0.0	.	273;273	A2A341;Q9BX26	.;SYCP2_HUMAN	R	273	ENSP00000360040:G273R;ENSP00000350162:G273R;ENSP00000402456:G273R	ENSP00000350162:G273R	G	-	1	0	SYCP2	57922438	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.736000	0.68597	2.430000	0.82344	0.655000	0.94253	GGA	.	.		0.294	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		T	58489043	C	T	58489043	3	4	112	1	0	0	0	0	1	0	0	0	15447	603	21	3	3911	3	SYCP2	20	58489043	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1219543	58489043	4536477	1153	17774										
CDH26	60437	hgsc.bcm.edu	37	chr20	58547020	58547020	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atttttcctccttccagctgTtcaataatatgtcttataac	3	10	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:58547020T>C	ENST00000244047.5	+	4	546	c.235T>C	c.(235-237)Ttc>Ctc	p.F79L	CDH26_ENST00000348616.4_Missense_Mutation_p.F79L			Q8IXH8	CAD26_HUMAN	cadherin 26	79	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			CTTCCAGCTGTTCAATAATAT	0.353																																					p.F79L		Atlas-SNP	.											.	CDH26	229	.	0			c.T235C						.						122	115	117					20																	58547020		2203	4300	6503	SO:0001583	missense	60437	exon4			CAGCTGTTCAATA	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"Cadherins / Major cadherins"	15902	protein-coding gene	gene with protein product			"cadherin-like 26"				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.235T>C	chr20.hg19:g.58547020T>C	ENSP00000244047:p.Phe79Leu	104.0	0.0		70.0	4.0	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	hg19		.	.	.	.	.	.	.	.	.	.	T	16.94	3.261979	0.59431	.	.	ENSG00000124215	ENST00000244047;ENST00000348616	T;T	0.57907	0.37;0.46	5.13	4.03	0.46877	.	0.055201	0.64402	D	0.000001	T	0.63896	0.2550	M	0.75447	2.3	0.46376	D	0.999011	P	0.40602	0.723	P	0.52758	0.708	T	0.62234	-0.6897	10	0.41790	T	0.15	.	10.0199	0.42037	0.0:0.0816:0.0:0.9184	.	79	Q8IXH8-4	.	L	79	ENSP00000244047:F79L;ENSP00000339390:F79L	ENSP00000244047:F79L	F	+	1	0	CDH26	57980415	1.000000	0.71417	0.951000	0.38953	0.718000	0.41266	4.458000	0.60095	0.904000	0.36572	0.528000	0.53228	TTC	.	.		0.353	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980		C	58547020	T	C	58547020	3	2	112	1	0	0	0	0	1	0	0	0	3112	1725	60	2	249	2	CDH26	20	58547020	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	57977	58547020	4478500	1154	17775										
OGFR	11054	hgsc.bcm.edu	37	chr20	61443731	61443731	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtgcggcagagtgccctggActacttcatgttcgccgtgc	14	12	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:61443731A>G	ENST00000290291.6	+	7	789	c.764A>G	c.(763-765)gAc>gGc	p.D255G	OGFR_ENST00000370461.1_Missense_Mutation_p.D203G	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	255					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					AGTGCCCTGGACTACTTCATG	0.706																																					p.D255G		Atlas-SNP	.											.	OGFR	63	.	0			c.A764G						.						12	12	12					20																	61443731		2160	4254	6414	SO:0001583	missense	11054	exon7			CCCTGGACTACTT	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.764A>G	chr20.hg19:g.61443731A>G	ENSP00000290291:p.Asp255Gly	47.0	0.0		78.0	6.0	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	hg19	CCDS13504.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.589434	0.66105	.	.	ENSG00000060491	ENST00000290291;ENST00000370468;ENST00000357163;ENST00000370469;ENST00000370461	T;T;T	0.52754	1.55;0.65;1.08	4.57	4.57	0.56435	Opioid growth factor receptor (OGFr) conserved domain (1);	0.106918	0.64402	N	0.000007	T	0.46639	0.1403	M	0.65975	2.015	0.45490	D	0.998451	B;B;B	0.33171	0.4;0.4;0.4	B;B;B	0.30251	0.113;0.113;0.113	T	0.53620	-0.8413	10	0.72032	D	0.01	-43.7867	13.9168	0.63902	1.0:0.0:0.0:0.0	.	255;238;255	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	G	255;255;255;110;203	ENSP00000290291:D255G;ENSP00000359499:D255G;ENSP00000359491:D203G	ENSP00000290291:D255G	D	+	2	0	OGFR	60914176	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.834000	0.92094	1.664000	0.50801	0.459000	0.35465	GAC	.	.		0.706	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			G	61443731	A	G	61443731	3	3	112	1	0	0	0	0	1	0	0	0	10852	275	10	2	790	2	OGFR	20	61443731	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2896711	61443731	1581789	1155	17776										
COL9A3	1299	hgsc.bcm.edu	37	chr20	61450582	61450582	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctcctgcacagggaccaaaGggggccccaggaaagccggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:61450582delG	ENST00000343916.3	+	4	195	c.192delG	c.(190-192)aagfs	p.K64fs		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	64	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					AGGGACCAAAGGGGGCCCCAG	0.657																																					p.K64fs		Atlas-INDEL	.											.	COL9A3	70	.	0			c.191delA						.						22	32	29					20																	61450582		2197	4298	6495	SO:0001589	frameshift_variant	1299	exon4			.	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2219	protein-coding gene	gene with protein product	"collagen type IX proteoglycan"	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.192delG	chr20.hg19:g.61450582delG	ENSP00000341640:p.Lys64fs	180.0	0.0		199.0	13.0	NM_001853	Q13681|Q9H4G9|Q9UPE2	Frame_Shift_Del	DEL	ENST00000343916.3	hg19	CCDS13505.1																																																																																			.	.		0.657	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853		-	61450582	G	-	61450582	7	5	112	1	0	1	0	1	0	0	0	0	3711	991	35	0	206	0	COL9A3	20	61450582	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	6851	61450582	1574938	1156	17777										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61513462	61513462	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gctgtggctgggctgggggcTgcaggtttgagggatgacag	21	6	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:61513462T>C	ENST00000266070.4	-	16	4171	c.3846A>G	c.(3844-3846)gcA>gcG	p.A1282A	DIDO1_ENST00000395343.1_Silent_p.A1282A	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1282	Pro-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GGCTGGGGGCTGCAGGTTTGA	0.652																																					p.A1282A	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.A3846G						.						62	68	66					20																	61513462		2202	4299	6501	SO:0001819	synonymous_variant	11083	exon16			GGGGGCTGCAGGT	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.3846A>G	chr20.hg19:g.61513462T>C		75.0	0.0		104.0	5.0	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	hg19	CCDS33506.1																																																																																			.	.		0.652	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		C	61513462	T	C	61513462	2	2	112	1	0	0	0	0	0	0	0	1	4524	1567	55	2		2	DIDO1	20	61513462	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	62880	61513462	1512058	1157	17778										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19704485	19704485	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagctcaaaaggtcctccacAgtccgctgaaaaggaaagca	9	12	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:19704485A>G	ENST00000284885.3	-	14	1603	c.1570T>C	c.(1570-1572)Tgt>Cgt	p.C524R		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	524	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						GGTCCTCCACAGTCCGCTGAA	0.383																																					p.C524R		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.T1570C						.						114	112	113					21																	19704485		2203	4300	6503	SO:0001583	missense	5651	exon14			CTCCACAGTCCGC		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1570T>C	chr21.hg19:g.19704485A>G	ENSP00000284885:p.Cys524Arg	73.0	0.0		92.0	5.0	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	hg19	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	A	18.79	3.698574	0.68386	.	.	ENSG00000154646	ENST00000284885	D	0.95377	-3.69	5.43	5.43	0.79202	CUB (5);	0.000000	0.85682	D	0.000000	D	0.98626	0.9540	H	0.97918	4.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99651	1.0991	9	.	.	.	.	14.6004	0.68438	1.0:0.0:0.0:0.0	.	524	P98073	ENTK_HUMAN	R	524	ENSP00000284885:C524R	.	C	-	1	0	TMPRSS15	18626356	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	6.228000	0.72288	2.184000	0.69523	0.528000	0.53228	TGT	.	.		0.383	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		G	19704485	A	G	19704485	3	3	112	1	0	0	0	0	1	0	0	0	16261	188	7	2	1537	2	TMPRSS15	21	19704485	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10		19704485	28425410	1158	17779										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19725327	19725327	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catttagatcctggacccagAaacaaaagccatcctcaaag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:19725327delA	ENST00000284885.3	-	10	1097	c.1064delT	c.(1063-1065)ttcfs	p.F355fs		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	355	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CTGGACCCAGAAACAAAAGCC	0.333																																					p.F355fs		Atlas-INDEL	.											.	TMPRSS15	189	.	0			c.1065delC						.						80	85	83					21																	19725327		2203	4299	6502	SO:0001589	frameshift_variant	5651	exon10			.		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1064delT	chr21.hg19:g.19725327delA	ENSP00000284885:p.Phe355fs	176.0	0.0		176.0	11.0	NM_002772	Q2NKL7	Frame_Shift_Del	DEL	ENST00000284885.3	hg19	CCDS13571.1																																																																																			.	.		0.333	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		-	19725327	A	-	19725327	7	5	112	1	0	1	0	1	0	0	0	0	16261	246	9	0	2059	0	TMPRSS15	21	19725327	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	20842	19725327	28404568	1159	17780										
KRTAP19-8	728299	hgsc.bcm.edu	37	chr21	32410759	32410759	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ataatagcttctgtagtagcTcatggttcagcaactgtaga	9	7	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:32410759T>C	ENST00000382822.2	-	1	36	c.4A>G	c.(4-6)Agc>Ggc	p.S2G		NM_001099219.1	NP_001092689.1	Q3LI54	KR198_HUMAN	keratin associated protein 19-8	2						intermediate filament (GO:0005882)				endometrium(2)|upper_aerodigestive_tract(1)	3						CTGTAGTAGCTCATGGTTCAG	0.507																																					p.S2G		Atlas-SNP	.											.	KRTAP19-8	9	.	0			c.A4G						.						108	121	117					21																	32410759		2203	4300	6503	SO:0001583	missense	728299	exon1			AGTAGCTCATGGT	AB096964	CCDS42917.1	21q22.11	2007-11-23			ENSG00000206102	ENSG00000206102		"Keratin associated proteins"	33898	protein-coding gene	gene with protein product							Standard	NM_001099219		Approved		uc010glt.3	Q3LI54	OTTHUMG00000057787	ENST00000382822.2:c.4A>G	chr21.hg19:g.32410759T>C	ENSP00000372272:p.Ser2Gly	130.0	0.0		139.0	6.0	NM_001099219		Missense_Mutation	SNP	ENST00000382822.2	hg19	CCDS42917.1	.	.	.	.	.	.	.	.	.	.	T	7.608	0.674208	0.14841	.	.	ENSG00000206102	ENST00000382822	T	0.11821	2.74	4.04	-3.48	0.04739	.	1.705140	0.04349	U	0.355326	T	0.09069	0.0224	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.41822	-0.9487	9	0.87932	D	0	.	3.1895	0.06612	0.4744:0.1745:0.0:0.3511	.	2	Q3LI54	KR198_HUMAN	G	2	ENSP00000372272:S2G	ENSP00000372272:S2G	S	-	1	0	KRTAP19-8	31332630	0.014000	0.17966	0.054000	0.19295	0.026000	0.11368	-0.308000	0.08156	-0.357000	0.08175	-0.876000	0.02978	AGC	.	.		0.507	KRTAP19-8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000128239.3	NM_001099219		C	32410759	T	C	32410759	3	2	112	1	0	0	0	0	1	0	0	0	8544	1551	54	2	191	2	KRTAP19-8	21	32410759	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	12685432	32410759	15719136	1160	17781										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32519299	32519299	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagcataatacaggaatgatCcccccagagagaacagcact							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:32519299delC	ENST00000286827.3	-	21	3860	c.3389delG	c.(3388-3390)ggafs	p.G1130fs	TIAM1_ENST00000541036.1_Frame_Shift_Del_p.G1070fs	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1130	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CAGGAATGATCCCCCCAGAGA	0.507																																					p.G1130fs		Atlas-INDEL	.											.	TIAM1	522	.	0			c.3390delA						.						124	99	107					21																	32519299		2203	4300	6503	SO:0001589	frameshift_variant	7074	exon21			.		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.3389delG	chr21.hg19:g.32519299delC	ENSP00000286827:p.Gly1130fs	194.0	0.0		155.0	10.0	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Frame_Shift_Del	DEL	ENST00000286827.3	hg19	CCDS13609.1																																																																																			.	.		0.507	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		-	32519299	C	-	32519299	7	5	112	1	0	1	0	1	0	0	0	0	15905	855	30	0	1422	0	TIAM1	21	32519299	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	108540	32519299	15610596	1161	17782										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34053824	34053824	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accttcgctttcccttcaagAgctccagttcctgcatatat	5	14	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:34053824A>G	ENST00000322229.7	-	10	1334	c.1335T>C	c.(1333-1335)gcT>gcC	p.A445A	SYNJ1_ENST00000433931.2_Silent_p.A484A|SYNJ1_ENST00000382499.2_Silent_p.A484A|SYNJ1_ENST00000357345.3_Silent_p.A445A|SYNJ1_ENST00000382491.3_Silent_p.A445A			O43426	SYNJ1_HUMAN	synaptojanin 1	445					cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						TCCCTTCAAGAGCTCCAGTTC	0.378																																					p.A484A		Atlas-SNP	.											.	SYNJ1	253	.	0			c.T1452C						.						161	159	160					21																	34053824		2203	4300	6503	SO:0001819	synonymous_variant	8867	exon11			TTCAAGAGCTCCA	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.1335T>C	chr21.hg19:g.34053824A>G		104.0	0.0		112.0	5.0	NM_203446	O43425|O94984|Q4KMR1	Silent	SNP	ENST00000322229.7	hg19	CCDS54484.1																																																																																			.	.		0.378	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				G	34053824	A	G	34053824	2	3	112	1	0	0	0	0	0	0	0	1	15467	291	11	2		2	SYNJ1	21	34053824	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1534525	34053824	14076071	1162	17783										
TTC3	7267	hgsc.bcm.edu	37	chr21	38555184	38555184	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gactaaaatcactgaagaagAaaattaaaaaggtttcaaat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:38555184delA	ENST00000399017.2	+	36	7473	c.4726delA	c.(4726-4728)aaafs	p.K1576fs	TTC3_ENST00000355666.1_Frame_Shift_Del_p.K1576fs|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Frame_Shift_Del_p.K1576fs	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1576	Arg/Lys-rich (basic).				negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				ACTGAAGAAGAAAATTAAAAA	0.279																																					p.K1575fs	Ovarian(38;194 1649 35661)	Atlas-INDEL	.											.	TTC3	182	.	0			c.4725delG						.						20	23	22					21																	38555184		2169	4271	6440	SO:0001589	frameshift_variant	7267	exon36			.	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.4726delA	chr21.hg19:g.38555184delA	ENSP00000381981:p.Lys1576fs	178.0	0.0		209.0	13.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Frame_Shift_Del	DEL	ENST00000399017.2	hg19	CCDS13651.1																																																																																			.	.		0.279	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			-	38555184	A	-	38555184	7	5	112	1	0	1	0	1	0	0	0	0	16712	247	9	0	4864	0	TTC3	21	38555184	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4501360	38555184	9574711	1163	17784										
ERG	2078	hgsc.bcm.edu	37	chr21	39755389	39755389	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcctagtgttggggtatataCccccagttggtgaattccag							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:39755389delC	ENST00000417133.2	-	12	1582	c.1397delG	c.(1396-1398)ggtfs	p.G466fs	ERG_ENST00000398907.1_Frame_Shift_Del_p.G436fs|ERG_ENST00000398905.1_Frame_Shift_Del_p.G435fs|ERG_ENST00000398910.1_Frame_Shift_Del_p.G443fs|ERG_ENST00000288319.7_Frame_Shift_Del_p.G459fs|ERG_ENST00000398897.1_Frame_Shift_Del_p.G343fs|ERG_ENST00000398911.1_Frame_Shift_Del_p.G442fs|ERG_ENST00000442448.1_Frame_Shift_Del_p.G442fs|ERG_ENST00000453032.2_Frame_Shift_Del_p.G367fs|ERG_ENST00000398919.2_Frame_Shift_Del_p.G466fs	NM_001136154.1|NM_001243432.1	NP_001129626.1|NP_001230361.1	Q12809	KCNH2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog	0					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)		EWSR1/ERG(178)|NDRG1/ERG(5)|TMPRSS2/ERG(3582)|FUS/ERG(167)|SLC45A3/ERG(50)	lung(2)|ovary(1)|skin(1)	4		Prostate(19;3.6e-06)			Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GGGGTATATACCCCCAGTTGG	0.537			T	"EWSR1, TMPRSS2, ELF4, FUS, HERPUD1, NDRG1"	"Ewing sarcoma, prostate, AML"																																p.G466fs	Esophageal Squamous(130;336 1700 3010 3083 40589)	Atlas-INDEL	.		Dom	yes		21	21q22.3	2078	v-ets erythroblastosis virus E26 oncogene like (avian)		"M, E, L"	.	ERG	78	.	0			c.1398delT						.						34	35	35					21																	39755389		2203	4300	6503	SO:0001589	frameshift_variant	2078	exon12			.		CCDS13657.1, CCDS13658.1, CCDS46648.1, CCDS46649.1, CCDS58789.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157554	ENSG00000157554			3446	protein-coding gene	gene with protein product	"v-ets avian erythroblastosis virus E26 oncogene related", "transcriptional regulator ERG (transforming protein ERG)", "v-ets erythroblastosis virus E26 oncogene like", "TMPRSS2-ERG prostate cancer specific"	165080	"v-ets avian erythroblastosis virus E26 oncogene related"			3274086	Standard	NM_001136154		Approved	erg-3, p55	uc002yxa.3	P11308	OTTHUMG00000090767	ENST00000417133.2:c.1397delG	chr21.hg19:g.39755389delC	ENSP00000414150:p.Gly466fs	145.0	0.0		156.0	14.0	NM_001136154	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Frame_Shift_Del	DEL	ENST00000417133.2	hg19	CCDS46648.1																																																																																			.	.		0.537	ERG-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207532.2	NM_182918		-	39755389	C	-	39755389	7	5	112	1	0	1	0	1	0	0	0	0	5224	507	18	0	67	0	ERG	21	39755389	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1200205	39755389	8374506	1164	17785										
LCA5L	150082	hgsc.bcm.edu	37	chr21	40800338	40800338	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcctgggcttctcttgcatgCtgcagacctcctattgtttt	9	12	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:40800338C>T	ENST00000358268.2	-	4	610	c.82G>A	c.(82-84)Gca>Aca	p.A28T	LCA5L_ENST00000380671.2_Missense_Mutation_p.A28T|LCA5L_ENST00000485895.2_Missense_Mutation_p.A28T|LCA5L_ENST00000288350.3_Missense_Mutation_p.A28T			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	28										breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				CTCTTGCATGCTGCAGACCTC	0.408																																					p.A28T		Atlas-SNP	.											.	LCA5L	57	.	0			c.G82A						.						126	120	122					21																	40800338		2203	4300	6503	SO:0001583	missense	150082	exon4			TGCATGCTGCAGA	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 13"	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.82G>A	chr21.hg19:g.40800338C>T	ENSP00000351008:p.Ala28Thr	150.0	0.0		146.0	6.0	NM_152505	D3DSI0|Q3ZCT0	Missense_Mutation	SNP	ENST00000358268.2	hg19	CCDS13665.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.461870	0.43736	.	.	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268;ENST00000418018;ENST00000448288;ENST00000434281;ENST00000438404;ENST00000411566;ENST00000415863;ENST00000426783;ENST00000456017	T;T;T;T;T;T;T;T;T;T;T	0.68479	0.5;0.5;0.5;0.91;0.9;0.9;0.9;0.9;0.88;0.87;-0.33	5.43	3.57	0.40892	.	0.433618	0.21726	N	0.070045	T	0.45756	0.1358	N	0.14661	0.345	0.09310	N	1	B;B	0.26547	0.02;0.152	B;B	0.20955	0.023;0.032	T	0.40384	-0.9566	10	0.72032	D	0.01	-9.476	7.4124	0.27025	0.0:0.59:0.32:0.09	.	28;28	C9JFB6;O95447	.;LCA5L_HUMAN	T	28	ENSP00000288350:A28T;ENSP00000370046:A28T;ENSP00000351008:A28T;ENSP00000404521:A28T;ENSP00000405598:A28T;ENSP00000400086:A28T;ENSP00000405130:A28T;ENSP00000412691:A28T;ENSP00000395593:A28T;ENSP00000414784:A28T;ENSP00000407065:A28T	ENSP00000288350:A28T	A	-	1	0	LCA5L	39722208	0.000000	0.05858	0.001000	0.08648	0.134000	0.20937	0.328000	0.19681	0.632000	0.30432	0.655000	0.94253	GCA	.	.		0.408	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		T	40800338	C	T	40800338	3	4	112	1	0	0	0	0	1	0	0	0	8666	797	28	3	1958	3	LCA5L	21	40800338	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	1044949	40800338	7329557	1165	17786										
IGSF5	150084	hgsc.bcm.edu	37	chr21	41143130	41143130	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgtaaatctcactgtgattCggtgtccccaaggtaagtga	10	9	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:41143130C>A	ENST00000380588.4	+	4	809	c.706C>A	c.(706-708)Cgg>Agg	p.R236R	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	236					single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.R236W(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				CACTGTGATTCGGTGTCCCCA	0.468																																					p.R236R		Atlas-SNP	.											IGSF5,caecum,carcinoma,0,1	IGSF5	62	.	1	Substitution - Missense(1)	large_intestine(1)	c.C706A						.						70	71	71					21																	41143130		2203	4300	6503	SO:0001819	synonymous_variant	150084	exon4			GTGATTCGGTGTC		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5952	protein-coding gene	gene with protein product	"junctional adhesion molecule 4"	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.706C>A	chr21.hg19:g.41143130C>A		98.0	0.0		70.0	3.0	NM_001080444		Silent	SNP	ENST00000380588.4	hg19	CCDS33562.1																																																																																			.	.		0.468	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1			A	41143130	C	A	41143130	2	1	112	1	0	0	0	0	0	0	0	1	7611	875	31	1		1	IGSF5	21	41143130	Silent	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	342792	41143130	6986765	1166	17787										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41434820	41434820	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgagcatttcagctaaactcTttgcatctggggaaagaaag	10	7	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:41434820T>C	ENST00000400454.1	-	28	5372	c.4895A>G	c.(4894-4896)aAg>aGg	p.K1632R		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1632					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AGCTAAACTCTTTGCATCTGG	0.348																																					p.K1632R	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.A4895G						.						127	117	120					21																	41434820		1865	4102	5967	SO:0001583	missense	1826	exon28			AAACTCTTTGCAT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4895A>G	chr21.hg19:g.41434820T>C	ENSP00000383303:p.Lys1632Arg	96.0	0.0		88.0	4.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845118	0.91197	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.60040	0.22;0.34	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.60869	0.2302	L	0.36672	1.1	0.42313	D	0.992225	D	0.63880	0.993	P	0.54629	0.757	T	0.60677	-0.7216	10	0.38643	T	0.18	.	15.5822	0.76452	0.0:0.0:0.0:1.0	.	1632	O60469	DSCAM_HUMAN	R	1632;1384	ENSP00000383303:K1632R;ENSP00000385342:K1384R	ENSP00000383303:K1632R	K	-	2	0	DSCAM	40356690	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.349000	0.79376	2.210000	0.71456	0.533000	0.62120	AAG	.	.		0.348	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		C	41434820	T	C	41434820	3	2	112	1	0	0	0	0	1	0	0	0	4770	1609	56	2	1167	2	DSCAM	21	41434820	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	291690	41434820	6695075	1167	17788										
ZNF295	49854	hgsc.bcm.edu	37	chr21	43414014	43414014	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaaatacagtttgtgactcaTtttccttatttgtgaataaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:43414014delT	ENST00000310826.5	-	3	374	c.191delA	c.(190-192)aatfs	p.N64fs	ZBTB21_ENST00000398505.3_Frame_Shift_Del_p.N64fs|ZBTB21_ENST00000398511.3_Frame_Shift_Del_p.N64fs|ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398499.1_Frame_Shift_Del_p.N64fs	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	64	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.|Mediates homodimerization.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										TTGTGACTCATTTTCCTTATT	0.383																																					p.N64fs		Atlas-INDEL	.											.	.	.	.	0			c.192delT						.						72	67	69					21																	43414014		2203	4300	6503	SO:0001589	frameshift_variant	49854	exon3			.	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13083	protein-coding gene	gene with protein product			"zinc finger protein 295"	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.191delA	chr21.hg19:g.43414014delT	ENSP00000308759:p.Asn64fs	174.0	0.0		160.0	12.0	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Frame_Shift_Del	DEL	ENST00000310826.5	hg19	CCDS13678.1																																																																																			.	.		0.383	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727		-	43414014	T	-	43414014	7	5	112	1	0	1	0	1	0	0	0	0	17842	1493	52	0	3013	0	ZNF295	21	43414014	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1979194	43414014	4715881	1168	17789										
SLC37A1	54020	hgsc.bcm.edu	37	chr21	43945906	43945906	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtacagagccttcatttttaTtttgacatttctgctgtatg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:43945906delT	ENST00000352133.2	+	3	1059	c.77delT	c.(76-78)attfs	p.I26fs	SLC37A1_ENST00000398341.3_Frame_Shift_Del_p.I26fs			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	26					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						TTCATTTTTATTTTGACATTT	0.378																																					p.I26fs		Atlas-INDEL	.											.	SLC37A1	48	.	0			c.76delA						.						155	136	143					21																	43945906		2203	4300	6503	SO:0001589	frameshift_variant	54020	exon4			.	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"Solute carriers"	11024	protein-coding gene	gene with protein product		608094	"solute carrier family 37 (glycerol-3-phosphate transporter), member 1"			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.77delT	chr21.hg19:g.43945906delT	ENSP00000344648:p.Ile26fs	169.0	0.0		161.0	11.0	NM_018964	D3DSJ7|Q9HAQ1	Frame_Shift_Del	DEL	ENST00000352133.2	hg19	CCDS13689.1																																																																																			.	.		0.378	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1			-	43945906	T	-	43945906	7	5	112	1	0	1	0	1	0	0	0	0	14612	1493	52	0	83	0	SLC37A1	21	43945906	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	531892	43945906	4183989	1169	17790										
AGPAT3	56894	hgsc.bcm.edu	37	chr21	45389012	45389012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctccagagctccaaggtccTcgctaagaaggagctgctct	10	14	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:45389012T>C	ENST00000398063.2	+	4	854	c.362T>C	c.(361-363)cTc>cCc	p.L121P	AGPAT3_ENST00000291572.8_Missense_Mutation_p.L121P|AGPAT3_ENST00000327505.2_Missense_Mutation_p.L121P|AGPAT3_ENST00000546158.1_Missense_Mutation_p.L121P|AGPAT3_ENST00000398061.1_Missense_Mutation_p.L121P|AGPAT3_ENST00000479117.1_3'UTR|AGPAT3_ENST00000398058.1_Missense_Mutation_p.L121P	NM_001037553.1	NP_001032642.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	121					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			large_intestine(4)|lung(5)|ovary(1)|prostate(1)	11				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		TCCAAGGTCCTCGCTAAGAAG	0.637																																					p.L121P	Pancreas(60;623 1650 5574 52796)	Atlas-SNP	.											.	AGPAT3	37	.	0			c.T362C						.						112	87	95					21																	45389012		2203	4300	6503	SO:0001583	missense	56894	exon4			AGGTCCTCGCTAA	AF156774	CCDS13703.1	21q22.3	2013-02-05			ENSG00000160216	ENSG00000160216	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	326	protein-coding gene	gene with protein product		614794					Standard	XM_005261159		Approved	LPAAT-gamma	uc002zdw.3	Q9NRZ7	OTTHUMG00000086892	ENST00000398063.2:c.362T>C	chr21.hg19:g.45389012T>C	ENSP00000381140:p.Leu121Pro	119.0	0.0		119.0	5.0	NM_001037553	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	Missense_Mutation	SNP	ENST00000398063.2	hg19	CCDS13703.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.200300	0.79015	.	.	ENSG00000160216	ENST00000291572;ENST00000398061;ENST00000327505;ENST00000445582;ENST00000398063;ENST00000438598;ENST00000398058;ENST00000457068;ENST00000422850;ENST00000546158	D;D;D;D;D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4;-3.4;-3.4;-3.4;-3.4	4.5	4.5	0.54988	Phospholipid/glycerol acyltransferase (2);	0.000000	0.64402	D	0.000001	D	0.96500	0.8858	M	0.82517	2.595	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.79784	0.993;0.971	D	0.96997	0.9726	10	0.72032	D	0.01	-14.3743	13.8003	0.63196	0.0:0.0:0.0:1.0	.	141;121	Q9NRZ7-3;Q9NRZ7	.;PLCC_HUMAN	P	121	ENSP00000291572:L121P;ENSP00000381138:L121P;ENSP00000332989:L121P;ENSP00000381140:L121P;ENSP00000381135:L121P;ENSP00000413906:L121P;ENSP00000414440:L121P;ENSP00000443510:L121P	ENSP00000291572:L121P	L	+	2	0	AGPAT3	44213440	1.000000	0.71417	0.684000	0.30055	0.948000	0.59901	7.470000	0.80973	1.667000	0.50832	0.402000	0.26972	CTC	.	.		0.637	AGPAT3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195722.1	NM_020132		C	45389012	T	C	45389012	3	2	112	1	0	0	0	0	1	0	0	0	388	1551	54	2	372	2	AGPAT3	21	45389012	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1443106	45389012	2740883	1170	17791										
PWP2	5822	hgsc.bcm.edu	37	chr21	45547852	45547852	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caccacggagggactcctcaTctactccctggacacccgcg	9	18	2	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:45547852T>C	ENST00000291576.7	+	18	2307	c.2180T>C	c.(2179-2181)aTc>aCc	p.I727T	PWP2_ENST00000494310.1_3'UTR	NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	727					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		GGACTCCTCATCTACTCCCTG	0.582																																					p.I727T		Atlas-SNP	.											.	PWP2	64	.	0			c.T2180C						.						42	41	41					21																	45547852		2200	4300	6500	SO:0001583	missense	5822	exon18			TCCTCATCTACTC		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"WD repeat domain containing"	9711	protein-coding gene	gene with protein product		601475	"PWP2 (periodic tryptophan protein, yeast) homolog"	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.2180T>C	chr21.hg19:g.45547852T>C	ENSP00000291576:p.Ile727Thr	69.0	0.0		90.0	4.0	NM_005049	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	hg19	CCDS33579.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.263433	0.59431	.	.	ENSG00000241945	ENST00000291576	T	0.65364	-0.15	4.47	4.47	0.54385	WD40/YVTN repeat-like-containing domain (1);	0.281959	0.38381	N	0.001703	T	0.60612	0.2282	M	0.69248	2.105	0.54753	D	0.999981	B	0.14438	0.01	B	0.10450	0.005	T	0.63269	-0.6675	10	0.72032	D	0.01	-18.2125	13.0243	0.58806	0.0:0.0:0.0:1.0	.	727	Q15269	PWP2_HUMAN	T	727	ENSP00000291576:I727T	ENSP00000291576:I727T	I	+	2	0	PWP2	44372280	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.201000	0.77847	1.956000	0.56807	0.533000	0.62120	ATC	.	.		0.582	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049		C	45547852	T	C	45547852	3	2	112	1	0	0	0	0	1	0	0	0	12859	1435	50	2	2250	2	PWP2	21	45547852	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	158840	45547852	2582043	1171	17792										
ITGB2	3689	hgsc.bcm.edu	37	chr21	46309403	46309403	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacttcccgcagaagcagagCcccctccctggaagacgggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:46309403delC	ENST00000397850.2	-	14	2117	c.1665delG	c.(1663-1665)gggfs	p.G555fs	ITGB2_ENST00000397854.3_Frame_Shift_Del_p.G498fs|ITGB2_ENST00000397852.1_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000302347.5_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000397857.1_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000355153.4_Frame_Shift_Del_p.G555fs			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	555	Cysteine-rich tandem repeats.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	AGAAGCAGAGCCCCCTCCCTG	0.697																																					p.L556fs		Atlas-INDEL	.											.	ITGB2	107	.	0			c.1666delC						.						24	20	22					21																	46309403		2160	4257	6417	SO:0001589	frameshift_variant	3689	exon13			.	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.1665delG	chr21.hg19:g.46309403delC	ENSP00000380948:p.Gly555fs	134.0	0.0		166.0	10.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Frame_Shift_Del	DEL	ENST00000397850.2	hg19	CCDS13716.1																																																																																			.	.		0.697	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		-	46309403	C	-	46309403	7	5	112	1	0	1	0	1	0	0	0	0	7903	726	26	0	660	0	ITGB2	21	46309403	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	761551	46309403	1820492	1172	17793										
CECR1	51816	hgsc.bcm.edu	37	chr22	17662863	17662863	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccatggggtgcccagtggccAtcagagtggctacagggtgg	17	10	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:17662863A>G	ENST00000399839.1	-	9	1559	c.1289T>C	c.(1288-1290)aTg>aCg	p.M430T	CECR1_ENST00000399837.2_Missense_Mutation_p.M430T|CECR1_ENST00000330232.4_Missense_Mutation_p.M189T|CECR1_ENST00000449907.2_Missense_Mutation_p.M388T|CECR1_ENST00000262607.3_Missense_Mutation_p.M430T	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	430					adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				CCCAGTGGCCATCAGAGTGGC	0.512																																					p.M430T		Atlas-SNP	.											.	CECR1	77	.	0			c.T1289C						.						86	76	79					22																	17662863		2203	4300	6503	SO:0001583	missense	51816	exon8			GTGGCCATCAGAG	AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.1289T>C	chr22.hg19:g.17662863A>G	ENSP00000382733:p.Met430Thr	64.0	0.0		72.0	4.0	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Missense_Mutation	SNP	ENST00000399839.1	hg19	CCDS13742.1	.	.	.	.	.	.	.	.	.	.	A	14.53	2.564220	0.45694	.	.	ENSG00000093072	ENST00000399839;ENST00000330232;ENST00000262607;ENST00000449907;ENST00000399837	D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62	3.92	3.92	0.45320	Adenosine/AMP deaminase (1);	0.124034	0.64402	D	0.000001	D	0.90940	0.7152	M	0.86028	2.79	0.49687	D	0.99981	D;D	0.89917	1.0;0.982	D;P	0.81914	0.995;0.875	D	0.92061	0.5656	10	0.72032	D	0.01	.	12.8002	0.57582	1.0:0.0:0.0:0.0	.	430;189	Q9NZK5;Q9NZK5-2	CECR1_HUMAN;.	T	430;189;430;388;430	ENSP00000382733:M430T;ENSP00000332871:M189T;ENSP00000262607:M430T;ENSP00000406443:M388T;ENSP00000382731:M430T	ENSP00000262607:M430T	M	-	2	0	CECR1	16042863	1.000000	0.71417	0.162000	0.22713	0.435000	0.31806	6.006000	0.70724	1.407000	0.46875	0.454000	0.30748	ATG	.	.		0.512	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1			G	17662863	A	G	17662863	3	3	112	1	0	0	0	0	1	0	0	0	3207	217	8	2	254	2	CECR1	22	17662863	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10		17662863	33641703	1173	17794										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19188997	19188998	+	Missense_Mutation	DNP	TC	TC	CT													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttccctcctcgtaacagcggTctccaactacggataatagg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:19188997_19188998TC>CT	ENST00000263200.10	-	23	3679_3680	c.3607_3608GA>AG	c.(3607-3609)GAc>AGc	p.D1203S	CLTCL1_ENST00000442042.2_5'UTR|CLTCL1_ENST00000427926.1_Splice_Site_p.G1203E|CLTCL1_ENST00000353891.5_Missense_Mutation_p.D1203S	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1203	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GTAACAGCGGTCTCCAACTACG	0.485			T	?	ALCL																																p.D1203G|p.D1203N		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.A3608G|c.G3607A						.																																			SO:0001583	missense	8218	exon23			CAGCGGTCTCCAA|AGCGGTCTCCAAC		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.3607_3608delinsCT	chr22.hg19:g.19188997_19188998delinsCT	ENSP00000445677:p.Asp1203Ser	107.0|105.0	0.0		107.0|106.0	5.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1																																																																																			.	.		0.485	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		CT	19188998	TC	CT	19188997	3	2	112	1	0	0	0	0	1	0	0	0	3569	1667	58	2	1354	2	CLTCL1	22	19188997	Missense_Mutation	DNP	TC	TCGA-DD-A39Y-01A-11D-A20W-10	1526134	19188997	32115569	1174	17795										
C22orf25	128989	hgsc.bcm.edu	37	chr22	20024329	20024329	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gccctgcaccaccatgtgcaTcatcttctttaagtttgatc	6	13	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:20024329T>C	ENST00000327374.4	+	2	186	c.8T>C	c.(7-9)aTc>aCc	p.I3T	TANGO2_ENST00000479679.1_3'UTR|TANGO2_ENST00000447208.2_Missense_Mutation_p.I3T|TANGO2_ENST00000432883.1_Missense_Mutation_p.I3T|TANGO2_ENST00000434570.2_5'UTR|TANGO2_ENST00000456048.1_5'Flank|TANGO2_ENST00000401833.1_5'UTR|TANGO2_ENST00000398042.2_Missense_Mutation_p.I3T|TANGO2_ENST00000420290.2_5'UTR|TANGO2_ENST00000401886.1_Missense_Mutation_p.I3T	NM_001283106.1|NM_001283116.1|NM_001283148.1|NM_001283154.1|NM_152906.4	NP_001270035.1|NP_001270045.1|NP_001270077.1|NP_001270083.1|NP_690870.3	Q6ICL3	TNG2_HUMAN	transport and golgi organization 2 homolog (Drosophila)	3																	ACCATGTGCATCATCTTCTTT	0.587																																					p.I3T		Atlas-SNP	.											.	TANGO2	4	.	0			c.T8C						.						197	150	166					22																	20024329		2203	4300	6503	SO:0001583	missense	128989	exon2			TGTGCATCATCTT		CCDS13772.1, CCDS63404.1, CCDS63405.1, CCDS63406.1, CCDS63407.1, CCDS74821.1, CCDS74822.1	22q11.21	2012-12-13	2012-12-13	2012-12-13	ENSG00000183597	ENSG00000183597			25439	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 25"	C22orf25		12477932	Standard	XM_005261222		Approved	DKFZp761P1121	uc002zrc.1	Q6ICL3	OTTHUMG00000150510	ENST00000327374.4:c.8T>C	chr22.hg19:g.20024329T>C	ENSP00000332721:p.Ile3Thr	98.0	0.0		125.0	5.0	NM_152906	A8MUE9|B7WNV6|B7Z583|B7Z730|D3DX23|Q8IW05|Q8NAL0|Q8TCS0|Q96M16	Missense_Mutation	SNP	ENST00000327374.4	hg19	CCDS13772.1	.	.	.	.	.	.	.	.	.	.	T	13.78	2.339307	0.41398	.	.	ENSG00000183597	ENST00000401886;ENST00000432198;ENST00000447208;ENST00000398042;ENST00000450664;ENST00000327374;ENST00000432883;ENST00000434168	T;T;T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39	4.14	3.1	0.35709	.	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	M	0.82630	2.6	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;1.0;1.0;1.0;0.999	T	0.59080	-0.7521	10	0.66056	D	0.02	.	8.083	0.30756	0.0:0.102:0.0:0.898	.	3;3;3;3;3	B7Z9Q5;B7Z4A5;Q6AHY1;Q6ICL3;Q6ICL3-2	.;.;.;CV025_HUMAN;.	T	3	ENSP00000385662:I3T;ENSP00000413850:I3T;ENSP00000389797:I3T;ENSP00000381122:I3T;ENSP00000415450:I3T;ENSP00000332721:I3T;ENSP00000402926:I3T;ENSP00000411602:I3T	ENSP00000332721:I3T	I	+	2	0	C22orf25	18404329	1.000000	0.71417	1.000000	0.80357	0.365000	0.29674	6.609000	0.74173	0.721000	0.32231	-0.415000	0.06103	ATC	.	.		0.587	TANGO2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318689.2	NM_152906		C	20024329	T	C	20024329	3	2	112	1	0	0	0	0	1	0	0	0	2141	1435	50	2	10	2	C22orf25	22	20024329	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	835332	20024329	31280237	1175	17796										
PRAME	23532	hgsc.bcm.edu	37	chr22	22892453	22892453	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atatcctgcatgggcattgcAaaaatcttcagcttcttaca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:22892453delA	ENST00000398741.1	-	5	954	c.648delT	c.(646-648)tttfs	p.F216fs	PRAME_ENST00000402697.1_Frame_Shift_Del_p.F216fs|PRAME_ENST00000539862.1_Frame_Shift_Del_p.F200fs|PRAME_ENST00000405655.3_Frame_Shift_Del_p.F216fs|PRAME_ENST00000398743.2_Frame_Shift_Del_p.F216fs|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000424204.2_Frame_Shift_Del_p.F200fs|PRAME_ENST00000543184.1_Frame_Shift_Del_p.F216fs	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	216					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		TGGGCATTGCAAAAATCTTCA	0.438																																					p.A217fs	Melanoma(73;1707 1838 15168 27201)	Atlas-INDEL	.											.	PRAME	78	.	0			c.649delG						.						119	118	119					22																	22892453		2203	4300	6503	SO:0001589	frameshift_variant	23532	exon5			.	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"-"	9336	protein-coding gene	gene with protein product	"cancer/testis antigen 130"	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.648delT	chr22.hg19:g.22892453delA	ENSP00000381726:p.Phe216fs	169.0	0.0		145.0	10.0	NM_206954	B2R6Y7|O43481|Q8IXN8	Frame_Shift_Del	DEL	ENST00000398741.1	hg19	CCDS13801.1																																																																																			.	.		0.438	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953		-	22892453	A	-	22892453	7	5	112	1	0	1	0	1	0	0	0	0	12436	127	5	0	889	0	PRAME	22	22892453	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2868124	22892453	28412113	1176	17797										
PRAME	23532	hgsc.bcm.edu	37	chr22	22892685	22892685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgagtacagactggccctgTttccagaccatacagtccag	9	12	0	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:22892685T>C	ENST00000398741.1	-	5	722	c.416A>G	c.(415-417)aAc>aGc	p.N139S	PRAME_ENST00000402697.1_Missense_Mutation_p.N139S|PRAME_ENST00000539862.1_Missense_Mutation_p.N123S|PRAME_ENST00000405655.3_Missense_Mutation_p.N139S|PRAME_ENST00000398743.2_Missense_Mutation_p.N139S|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000424204.2_Missense_Mutation_p.N123S|PRAME_ENST00000543184.1_Missense_Mutation_p.N139S	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	139					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		ACTGGCCCTGTTTCCAGACCA	0.493																																					p.N139S	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											.	PRAME	78	.	0			c.A416G						.						77	72	74					22																	22892685		2203	4300	6503	SO:0001583	missense	23532	exon5			GCCCTGTTTCCAG	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"-"	9336	protein-coding gene	gene with protein product	"cancer/testis antigen 130"	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.416A>G	chr22.hg19:g.22892685T>C	ENSP00000381726:p.Asn139Ser	112.0	0.0		78.0	21.0	NM_206954	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	hg19	CCDS13801.1	.	.	.	.	.	.	.	.	.	.	.	0.809	-0.752527	0.03041	.	.	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204;ENST00000439106;ENST00000420709	T;T;T;T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9;0.9;2.56;2.56	3.02	-0.399	0.12415	.	1.549960	0.03983	N	0.293671	T	0.12774	0.0310	N	0.00462	-1.47	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.11817	-1.0572	10	0.27785	T	0.31	.	3.8691	0.09029	0.1273:0.0:0.4273:0.4454	.	139	P78395	PRAME_HUMAN	S	139;139;139;139;123;139;123;139;139	ENSP00000381728:N139S;ENSP00000445675:N139S;ENSP00000381726:N139S;ENSP00000384343:N139S;ENSP00000445097:N123S;ENSP00000385198:N139S;ENSP00000407342:N123S;ENSP00000407320:N139S;ENSP00000412318:N139S	ENSP00000381726:N139S	N	-	2	0	PRAME	21222685	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-1.283000	0.02796	-0.012000	0.14223	-0.396000	0.06452	AAC	.	.		0.493	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953		C	22892685	T	C	22892685	3	2	112	1	0	0	0	0	1	0	0	0	12436	1725	60	2	1121	2	PRAME	22	22892685	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	232	22892685	28411881	1177	17798										
XBP1	7494	hgsc.bcm.edu	37	chr22	29195079	29195079	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctaccacttgctgttccagcTcactcattcgagccttcttt	5	15	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:29195079T>C	ENST00000216037.6	-	2	362	c.290A>G	c.(289-291)gAg>gGg	p.E97G	XBP1_ENST00000403532.3_Missense_Mutation_p.E97G|CTA-292E10.6_ENST00000585003.1_RNA|CTA-292E10.6_ENST00000458080.1_RNA|CTA-292E10.6_ENST00000418292.1_RNA|CTA-292E10.6_ENST00000451486.1_RNA|XBP1_ENST00000405219.3_Missense_Mutation_p.E47G|XBP1_ENST00000344347.5_Missense_Mutation_p.E97G	NM_001079539.1|NM_005080.3	NP_001073007.1|NP_005071.2	P17861	XBP1_HUMAN	X-box binding protein 1	97	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial cell maturation involved in salivary gland development (GO:0060691)|exocrine pancreas development (GO:0031017)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|serotonin secretion, neurotransmission (GO:0060096)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|large_intestine(1)|lung(1)	5						CTGTTCCAGCTCACTCATTCG	0.408																																					p.E97G		Atlas-SNP	.											.	XBP1	37	.	0			c.A290G						.						131	114	120					22																	29195079		2203	4300	6503	SO:0001583	missense	7494	exon2			TCCAGCTCACTCA	M31627	CCDS13847.1	22q12.1	2013-01-10			ENSG00000100219	ENSG00000100219		"basic leucine zipper proteins"	12801	protein-coding gene	gene with protein product		194355		XBP2		1718857, 2196176	Standard	NM_001079539		Approved		uc003aec.3	P17861	OTTHUMG00000151094	ENST00000216037.6:c.290A>G	chr22.hg19:g.29195079T>C	ENSP00000216037:p.Glu97Gly	86.0	0.0		112.0	6.0	NM_001079539	Q8WYK6|Q969P1|Q96BD7	Missense_Mutation	SNP	ENST00000216037.6	hg19	CCDS13847.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.934656	0.92458	.	.	ENSG00000100219	ENST00000216037;ENST00000403532;ENST00000344347;ENST00000405219	.	.	.	5.26	5.26	0.73747	.	0.048750	0.85682	D	0.000000	T	0.70290	0.3207	L	0.53671	1.685	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.977;0.996	T	0.68727	-0.5332	9	0.34782	T	0.22	.	14.0068	0.64468	0.0:0.0:0.0:1.0	.	97;47	P17861-2;B1AHH1	.;.	G	97;97;97;47	.	ENSP00000216037:E97G	E	-	2	0	XBP1	27525079	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.699000	0.74613	1.987000	0.57996	0.533000	0.62120	GAG	.	.		0.408	XBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321274.1	NM_005080		C	29195079	T	C	29195079	3	2	112	1	0	0	0	0	1	0	0	0	17437	1551	54	2	882	2	XBP1	22	29195079	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	6302394	29195079	22109487	1178	17799										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32215113	32215113	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcatgttcgacctggtggatAcacgccccagagagcactga	12	12	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:32215113A>G	ENST00000382112.3	+	21	1842	c.1772A>G	c.(1771-1773)tAc>tGc	p.Y591C	DEPDC5_ENST00000535622.1_Missense_Mutation_p.Y591C|DEPDC5_ENST00000382111.2_Missense_Mutation_p.Y591C|DEPDC5_ENST00000400246.1_Missense_Mutation_p.Y591C|DEPDC5_ENST00000400248.2_Missense_Mutation_p.Y591C|DEPDC5_ENST00000536766.1_Missense_Mutation_p.Y563C|DEPDC5_ENST00000266091.3_Missense_Mutation_p.Y591C|DEPDC5_ENST00000400249.2_Missense_Mutation_p.Y591C|DEPDC5_ENST00000382105.2_Missense_Mutation_p.Y591C	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	591					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CCTGGTGGATACACGCCCCAG	0.562																																					p.Y591C		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A1772G						.						148	152	151					22																	32215113		2115	4226	6341	SO:0001583	missense	9681	exon22			GTGGATACACGCC	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.1772A>G	chr22.hg19:g.32215113A>G	ENSP00000371546:p.Tyr591Cys	130.0	0.0		140.0	8.0	NM_001242897	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	16.48	3.134531	0.56828	.	.	ENSG00000100150	ENST00000535622;ENST00000536766;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	T;T;T;T;T;T;T;T;T	0.31510	1.5;1.49;1.88;1.91;1.86;1.49;1.91;1.86;1.91	5.68	2.25	0.28309	.	0.128121	0.53938	N	0.000042	T	0.33177	0.0854	N	0.22421	0.69	0.80722	D	1	D;B;D;D;D;D	0.76494	0.999;0.003;0.999;0.999;0.997;0.999	P;B;D;D;D;D	0.79784	0.884;0.009;0.993;0.927;0.947;0.965	T	0.07986	-1.0744	10	0.39692	T	0.17	.	5.3509	0.16036	0.7256:0.0:0.1443:0.1301	.	591;563;591;591;591;591	B9EGN9;F5GYZ8;B4DH93;O75140-4;A8MPX9;O75140	.;.;.;.;.;DEPD5_HUMAN	C	591;563;591;591;591;591;591;591;591;591	ENSP00000440210:Y591C;ENSP00000441358:Y563C;ENSP00000266091:Y591C;ENSP00000383108:Y591C;ENSP00000383105:Y591C;ENSP00000371539:Y591C;ENSP00000371546:Y591C;ENSP00000371545:Y591C;ENSP00000383107:Y591C	ENSP00000266091:Y591C	Y	+	2	0	DEPDC5	30545113	1.000000	0.71417	0.364000	0.25888	0.883000	0.51084	3.586000	0.53950	0.436000	0.26393	0.460000	0.39030	TAC	.	.		0.562	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		G	32215113	A	G	32215113	3	3	112	1	0	0	0	0	1	0	0	0	4444	391	14	2	1872	2	DEPDC5	22	32215113	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	3020034	32215113	19089453	1179	17800										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32266729	32266729	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccacaaactccagtgacagcAggtgagattcagagtggcca	11	11	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:32266729A>G	ENST00000382112.3	+	33	3527	c.3457A>G	c.(3457-3459)Agc>Ggc	p.S1153G	DEPDC5_ENST00000535622.1_Splice_Site_p.S1062G|DEPDC5_ENST00000382111.2_Splice_Site_p.S1162G|DEPDC5_ENST00000400248.2_Splice_Site_p.S1131G|DEPDC5_ENST00000539165.1_5'UTR|DEPDC5_ENST00000266091.3_Splice_Site_p.S1140G|DEPDC5_ENST00000400249.2_Splice_Site_p.S1131G|DEPDC5_ENST00000400246.1_Splice_Site_p.S1162G|DEPDC5_ENST00000382105.2_Splice_Site_p.S1084G|DEPDC5_ENST00000494060.1_3'UTR	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1162					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CAGTGACAGCAGGTGAGATTC	0.542																																					p.S1162G		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A3484G						.						80	82	81					22																	32266729		1994	4167	6161	SO:0001630	splice_region_variant	9681	exon34			GACAGCAGGTGAG	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.3458+1A>G	chr22.hg19:g.32266729A>G		143.0	0.0		148.0	6.0	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.95|12.95	2.091620|2.091620	0.36952|0.36952	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000433147|ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	.|T;T;T;T;T;T;T;T	.|0.32272	.|1.52;1.94;1.94;1.89;1.46;1.9;1.89;1.94	5.95|5.95	4.92|4.92	0.64577|0.64577	.|.	.|0.466924	.|0.24573	.|N	.|0.037379	T|T	0.18425|0.18425	0.0442|0.0442	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B;B	.|0.11235	.|0.0;0.003;0.0;0.004;0.0;0.001	.|B;B;B;B;B;B	.|0.13407	.|0.0;0.003;0.0;0.009;0.0;0.002	T|T	0.06770|0.06770	-1.0808|-1.0808	5|10	.|0.15952	.|T	.|0.53	.|.	9.714|9.714	0.40263|0.40263	0.9212:0.0:0.0788:0.0|0.9212:0.0:0.0788:0.0	.|.	.|1162;1062;548;1140;1153;1131	.|B9EGN9;B4DH93;O75140-7;O75140-4;A8MPX9;O75140	.|.;.;.;.;.;DEPD5_HUMAN	R|G	537|1062;1140;1131;1062;1162;1084;1153;1162;1131	.|ENSP00000440210:S1062G;ENSP00000266091:S1140G;ENSP00000383108:S1131G;ENSP00000383105:S1162G;ENSP00000371539:S1084G;ENSP00000371546:S1153G;ENSP00000371545:S1162G;ENSP00000383107:S1131G	.|ENSP00000266091:S1140G	Q|S	+|+	2|1	0|0	DEPDC5|DEPDC5	30596729|30596729	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	1.328000|1.328000	0.33758|0.33758	1.076000|1.076000	0.40961|0.40961	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.542	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	Missense_Mutation	G	32266729	A	G	32266729	5	3	112	1	0	0	0	0	0	0	1	0	4444	202	7	2	3605	2	DEPDC5	22	32266729	Splice_Site	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	51616	32266729	19037837	1180	17801										
SSTR3	6753	hgsc.bcm.edu	37	chr22	37602589	37602590	+	Missense_Mutation	DNP	CA	CA	AC													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctggctttccccaggccctaCaggtagctgatgcgcatcgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:37602589_37602590CA>AC	ENST00000328544.3	-	2	1786_1787	c.1253_1254TG>GT	c.(1252-1254)cTG>cGT	p.L418R	SSTR3_ENST00000402501.1_Missense_Mutation_p.L418R	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	418					cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	CCAGGCCCTACAGGTAGCTGAT	0.639																																					p.L418L|p.L418R		Atlas-SNP	.											.	SSTR3	42	.	0			c.G1254T|c.T1253G						.																																			SO:0001583	missense	6753	exon2			GCCCTACAGGTAG|CCCTACAGGTAGC		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"GPCR / Class A : Somatostatin receptors"	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.1253_1254delinsAC	chr22.hg19:g.37602589_37602590delinsAC	ENSP00000330138:p.Leu418Arg	39.0	0.0		53.0|54.0	4.0	NM_001051	A8K550|Q53ZR7	Silent|Missense_Mutation	SNP	ENST00000328544.3	hg19	CCDS13944.1																																																																																			.	.		0.639	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1			AC	37602590	CA	AC	37602589	3	1	112	1	0	0	0	0	1	0	0	0	15214	465	17	3	6	3	SSTR3	22	37602589	Missense_Mutation	DNP	CA	TCGA-DD-A39Y-01A-11D-A20W-10	5335860	37602589	13701977	1181	17802										
SOX10	6663	hgsc.bcm.edu	37	chr22	38379616	38379616	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	catcgtccgcctcgccgtccTgctgctccttcttgaccttg	8	18	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:38379616T>C	ENST00000396884.2	-	2	458	c.176A>G	c.(175-177)cAg>cGg	p.Q59R	SOX10_ENST00000360880.2_Missense_Mutation_p.Q59R|SOX10_ENST00000470555.1_Intron|POLR2F_ENST00000405557.1_Intron|POLR2F_ENST00000407936.1_Intron	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	59					anatomical structure morphogenesis (GO:0009653)|cell maturation (GO:0048469)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|enteric nervous system development (GO:0048484)|in utero embryonic development (GO:0001701)|melanocyte differentiation (GO:0030318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system development (GO:0007422)|positive regulation of gliogenesis (GO:0014015)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extrinsic component of mitochondrial outer membrane (GO:0031315)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|transcription coactivator activity (GO:0003713)			NS(6)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|skin(2)	20	Melanoma(58;0.045)					CTCGCCGTCCTGCTGCTCCTT	0.731																																					p.Q59R	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)	Atlas-SNP	.											.	SOX10	48	.	0			c.A176G						.						60	37	45					22																	38379616		2203	4300	6503	SO:0001583	missense	6663	exon2			CCGTCCTGCTGCT		CCDS13964.1	22q13.1	2014-09-17			ENSG00000100146	ENSG00000100146		"SRY (sex determining region Y)-boxes"	11190	protein-coding gene	gene with protein product	"dominant megacolon, mouse, human homolog of"	602229				9462749, 10441344, 12944398	Standard	NM_006941		Approved	DOM, WS4, WS2E	uc003aun.1	P56693	OTTHUMG00000149913	ENST00000396884.2:c.176A>G	chr22.hg19:g.38379616T>C	ENSP00000380093:p.Gln59Arg	57.0	0.0		83.0	4.0	NM_006941	B4DV62|Q6FHW7	Missense_Mutation	SNP	ENST00000396884.2	hg19	CCDS13964.1	.	.	.	.	.	.	.	.	.	.	T	9.955	1.221143	0.22457	.	.	ENSG00000100146	ENST00000396884;ENST00000360880;ENST00000416937;ENST00000427770	T;T;T	0.76578	-1.03;-1.03;-1.03	4.39	2.14	0.27477	.	0.545411	0.18672	N	0.134414	T	0.61924	0.2386	N	0.22421	0.69	0.33535	D	0.594119	B	0.15141	0.012	B	0.20384	0.029	T	0.57329	-0.7830	9	.	.	.	.	9.889	0.41279	0.0:0.0:0.3323:0.6677	.	59	P56693	SOX10_HUMAN	R	59	ENSP00000380093:Q59R;ENSP00000354130:Q59R;ENSP00000414853:Q59R	.	Q	-	2	0	SOX10	36709562	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.027000	0.41078	0.186000	0.20125	0.379000	0.24179	CAG	.	.		0.731	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941		C	38379616	T	C	38379616	3	2	112	1	0	0	0	0	1	0	0	0	14956	1580	55	2	1236	2	SOX10	22	38379616	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	777027	38379616	12924950	1182	17803										
PICK1	9463	hgsc.bcm.edu	37	chr22	38470994	38470994	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggtagacctggcgcacaccaCattggcctatggcctcaacc	10	15	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:38470994C>T	ENST00000404072.3	+	13	1450	c.1103C>T	c.(1102-1104)aCa>aTa	p.T368I	PICK1_ENST00000356976.3_Missense_Mutation_p.T368I|RP5-1039K5.13_ENST00000445483.1_RNA	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	368					ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					GCGCACACCACATTGGCCTAT	0.617																																					p.T368I		Atlas-SNP	.											.	PICK1	30	.	0			c.C1103T						.						84	63	70					22																	38470994		2203	4300	6503	SO:0001583	missense	9463	exon13			ACACCACATTGGC	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"protein kinase C, alpha binding protein", "protein interacting with PRKCA"	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.1103C>T	chr22.hg19:g.38470994C>T	ENSP00000385205:p.Thr368Ile	107.0	0.0		116.0	46.0	NM_012407	B3KS52|O95906	Missense_Mutation	SNP	ENST00000404072.3	hg19	CCDS13965.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.863168	0.32884	.	.	ENSG00000100151	ENST00000404072;ENST00000356976	T;T	0.31510	1.49;1.49	4.33	3.21	0.36854	.	0.147994	0.64402	D	0.000013	T	0.24509	0.0594	L	0.47716	1.5	0.37753	D	0.926044	B	0.34103	0.437	B	0.27076	0.076	T	0.23547	-1.0185	10	0.32370	T	0.25	-16.1603	13.831	0.63380	0.0:0.8456:0.1544:0.0	.	368	Q9NRD5	PICK1_HUMAN	I	368	ENSP00000385205:T368I;ENSP00000349465:T368I	ENSP00000349465:T368I	T	+	2	0	PICK1	36800940	0.937000	0.31787	1.000000	0.80357	0.634000	0.38068	2.210000	0.42816	2.124000	0.65301	0.561000	0.74099	ACA	.	.		0.617	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407		T	38470994	C	T	38470994	3	4	112	1	0	0	0	0	1	0	0	0	11890	478	17	3	1149	3	PICK1	22	38470994	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	91378	38470994	12833572	1183	17804										
APOBEC3B	9582	hgsc.bcm.edu	37	chr22	39381926	39381926	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacctggtttgtatcctggaCcccctgcccggactgtgtgg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:39381926delC	ENST00000333467.3	+	3	329	c.284delC	c.(283-285)accfs	p.T95fs	APOBEC3B_ENST00000407298.3_Frame_Shift_Del_p.T95fs|APOBEC3B_ENST00000402182.3_Frame_Shift_Del_p.T95fs	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	95	CMP/dCMP deaminase zinc-binding 1.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|negative regulation of transposition (GO:0010529)	nucleus (GO:0005634)	deoxycytidine deaminase activity (GO:0047844)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	13	Melanoma(58;0.04)					GTATCCTGGACCCCCTGCCCG	0.562																																					p.T95fs		Atlas-INDEL	.											.	APOBEC3B	32	.	0			c.283delA						.						136	128	131					22																	39381926		2202	4297	6499	SO:0001589	frameshift_variant	9582	exon3			.	AK024854	CCDS13982.1, CCDS58807.1	22q13.1-q13.2	2008-05-15			ENSG00000179750	ENSG00000179750		"Apolipoprotein B mRNA editing enzymes"	17352	protein-coding gene	gene with protein product	"phorbolin 3"	607110				11863358, 10469298	Standard	NM_004900		Approved	PHRBNL, FLJ21201	uc003awo.2	Q9UH17	OTTHUMG00000151085	ENST00000333467.3:c.284delC	chr22.hg19:g.39381926delC	ENSP00000327459:p.Thr95fs	126.0	0.0		127.0	10.0	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Frame_Shift_Del	DEL	ENST00000333467.3	hg19	CCDS13982.1																																																																																			.	.		0.562	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900		-	39381926	C	-	39381926	7	5	112	1	0	1	0	1	0	0	0	0	790	507	18	0	294	0	APOBEC3B	22	39381926	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	910932	39381926	11922640	1184	17805										
FAM83F	113828	hgsc.bcm.edu	37	chr22	40417739	40417739	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggatggtctctcacatgcacAgagacctgaagcccaaatcc	9	13	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:40417739A>G	ENST00000333407.6	+	4	1319	c.1225A>G	c.(1225-1227)Aga>Gga	p.R409G	FAM83F_ENST00000473717.1_Missense_Mutation_p.R241G	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	409										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						TCACATGCACAGAGACCTGAA	0.662																																					p.R409G		Atlas-SNP	.											.	FAM83F	29	.	0			c.A1225G						.						32	26	28					22																	40417739		2203	4300	6503	SO:0001583	missense	113828	exon4			ATGCACAGAGACC		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.1225A>G	chr22.hg19:g.40417739A>G	ENSP00000330432:p.Arg409Gly	106.0	0.0		101.0	5.0	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	hg19	CCDS14000.2	.	.	.	.	.	.	.	.	.	.	A	11.94	1.790035	0.31685	.	.	ENSG00000133477	ENST00000333407	T	0.08008	3.14	4.42	-8.83	0.00806	.	2.532400	0.01078	N	0.004933	T	0.03390	0.0098	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.33929	-0.9849	10	0.22109	T	0.4	4.4295	4.758	0.13093	0.2899:0.168:0.452:0.09	.	409	Q8NEG4	FA83F_HUMAN	G	409	ENSP00000330432:R409G	ENSP00000330432:R409G	R	+	1	2	FAM83F	38747685	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-1.758000	0.01810	-1.733000	0.01357	0.379000	0.24179	AGA	.	.		0.662	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435		G	40417739	A	G	40417739	3	3	112	1	0	0	0	0	1	0	0	0	5646	180	7	2	1239	2	FAM83F	22	40417739	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1035813	40417739	10886827	1185	17806										
L3MBTL2	83746	hgsc.bcm.edu	37	chr22	41620044	41620044	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atggtggagagcatgaagtaCccctttaggcagggcatgcg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:41620044delC	ENST00000216237.5	+	9	1121	c.963delC	c.(961-963)tacfs	p.Y321fs		NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	321					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GCATGAAGTACCCCTTTAGGC	0.602																																					p.Y321fs		Atlas-INDEL	.											.	L3MBTL2	61	.	0			c.962delA						.						111	71	85					22																	41620044		2203	4300	6503	SO:0001589	frameshift_variant	83746	exon9			.	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.963delC	chr22.hg19:g.41620044delC	ENSP00000216237:p.Tyr321fs	150.0	0.0		197.0	12.0	NM_031488	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Frame_Shift_Del	DEL	ENST00000216237.5	hg19	CCDS14011.1																																																																																			.	.		0.602	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488		-	41620044	C	-	41620044	7	5	112	1	0	1	0	1	0	0	0	0	8601	518	18	0	997	0	L3MBTL2	22	41620044	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1202305	41620044	9684522	1186	17807										
POLDIP3	84271	hgsc.bcm.edu	37	chr22	42981894	42981894	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgtcagggtccacttcggcaGgggggttggaggaggaggca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:42981894delG	ENST00000252115.5	-	9	1273	c.1169delC	c.(1168-1170)cctfs	p.P390fs	POLDIP3_ENST00000339677.6_Intron|POLDIP3_ENST00000348657.2_Frame_Shift_Del_p.P361fs|POLDIP3_ENST00000491021.1_5'UTR|POLDIP3_ENST00000451060.2_3'UTR	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	390					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						CACTTCGGCAGGGGGGTTGGA	0.572																																					p.P390fs	Ovarian(52;967 1128 5875 19997 42537)	Atlas-INDEL	.											.	POLDIP3	58	.	0			c.1170delT						.						70	63	65					22																	42981894		2203	4300	6503	SO:0001589	frameshift_variant	84271	exon9			.		CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"RNA binding motif (RRM) containing"	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.1169delC	chr22.hg19:g.42981894delG	ENSP00000252115:p.Pro390fs	130.0	0.0		121.0	10.0	NM_032311	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Frame_Shift_Del	DEL	ENST00000252115.5	hg19	CCDS14038.1																																																																																			.	.		0.572	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311		-	42981894	G	-	42981894	7	5	112	1	0	1	0	1	0	0	0	0	12204	1000	35	0	100	0	POLDIP3	22	42981894	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1361850	42981894	8322672	1187	17808										
SAMM50	25813	hgsc.bcm.edu	37	chr22	44379821	44379821	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gttttgtcctaggttttaccTtgggggacccacaagcatcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:44379821delT	ENST00000350028.4	+	12	1173	c.1016delT	c.(1015-1017)cttfs	p.L339fs	SAMM50_ENST00000396202.3_Frame_Shift_Del_p.L129fs	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	339					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)				endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				AGGTTTTACCTTGGGGGACCC	0.552																																					p.L339fs		Atlas-INDEL	.											.	SAMM50	30	.	0			c.1015delC						.						171	156	161					22																	44379821		2203	4300	6503	SO:0001589	frameshift_variant	25813	exon12			.	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"sorting and assembly machinery component 50 homolog (S. cerevisiae)"			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.1016delT	chr22.hg19:g.44379821delT	ENSP00000345445:p.Leu339fs	134.0	0.0		160.0	10.0	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Frame_Shift_Del	DEL	ENST00000350028.4	hg19	CCDS14055.1																																																																																			.	.		0.552	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380		-	44379821	T	-	44379821	7	5	112	1	0	1	0	1	0	0	0	0	13844	1609	56	0	1062	0	SAMM50	22	44379821	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1397927	44379821	6924745	1188	17809										
UPK3A	7380	hgsc.bcm.edu	37	chr22	45681941	45681941	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcaaagaggccctcactggcAcccacgaggtctacctgtat	10	14	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:45681941A>G	ENST00000216211.4	+	2	204	c.172A>G	c.(172-174)Acc>Gcc	p.T58A	UPK3A_ENST00000396082.2_Missense_Mutation_p.T58A	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	58					cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CCTCACTGGCACCCACGAGGT	0.572																																					p.T58A		Atlas-SNP	.											.	UPK3A	14	.	0			c.A172G						.						127	94	105					22																	45681941		2203	4300	6503	SO:0001583	missense	7380	exon2			ACTGGCACCCACG	AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"uroplakin 3"	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.172A>G	chr22.hg19:g.45681941A>G	ENSP00000216211:p.Thr58Ala	101.0	0.0		112.0	7.0	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Missense_Mutation	SNP	ENST00000216211.4	hg19	CCDS14064.1	.	.	.	.	.	.	.	.	.	.	A	13.85	2.360497	0.41801	.	.	ENSG00000100373	ENST00000216211;ENST00000396082	T;D	0.83419	-0.06;-1.72	4.74	-9.49	0.00587	.	1.151650	0.06239	N	0.690140	T	0.65428	0.2690	L	0.36672	1.1	0.09310	N	1	B;B	0.12013	0.0;0.005	B;B	0.11329	0.001;0.006	T	0.50004	-0.8878	10	0.27082	T	0.32	-16.1587	1.1443	0.01772	0.1464:0.3123:0.2092:0.3321	.	58;58	O75631-2;O75631	.;UPK3A_HUMAN	A	58	ENSP00000216211:T58A;ENSP00000379391:T58A	ENSP00000216211:T58A	T	+	1	0	UPK3A	44060605	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.794000	0.04584	-2.021000	0.00939	-1.236000	0.01555	ACC	.	.		0.572	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953		G	45681941	A	G	45681941	3	3	112	1	0	0	0	0	1	0	0	0	17025	159	6	2	178	2	UPK3A	22	45681941	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1302120	45681941	5622625	1189	17810										
SMC1B	27127	hgsc.bcm.edu	37	chr22	45798221	45798221	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttaaaaactcactttaattcTttttctgtttgttgtagttg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:45798221delT	ENST00000357450.4	-	5	845	c.846delA	c.(844-846)aaafs	p.K282fs	SMC1B_ENST00000404354.3_Frame_Shift_Del_p.K282fs	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	282					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		ACTTTAATTCTTTTTCTGTTT	0.299																																					p.E283fs		Atlas-INDEL	.											SMC1B,NS,carcinoma,0,1	SMC1B	215	.	0			c.847delG						.						124	105	111					22																	45798221		1811	4069	5880	SO:0001589	frameshift_variant	27127	exon5			.	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.846delA	chr22.hg19:g.45798221delT	ENSP00000350036:p.Lys282fs	149.0	0.0		192.0	12.0	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Frame_Shift_Del	DEL	ENST00000357450.4	hg19	CCDS43027.1																																																																																			.	.		0.299	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		-	45798221	T	-	45798221	7	5	112	1	0	1	0	1	0	0	0	0	14797	1606	56	0	2945	0	SMC1B	22	45798221	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	116280	45798221	5506345	1190	17811										
CRELD2	79174	hgsc.bcm.edu	37	chr22	50319089	50319089	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggacgagtgctcactagcagAaaaaacctgtgtgaggaaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:50319089delA	ENST00000328268.4	+	9	967	c.893delA	c.(892-894)gaafs	p.E298fs	CRELD2_ENST00000403427.3_Frame_Shift_Del_p.E270fs|CRELD2_ENST00000407217.3_Frame_Shift_Del_p.E266fs|CRELD2_ENST00000404488.3_Frame_Shift_Del_p.E347fs	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	298	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		TCACTAGCAGAAAAAACCTGT	0.438																																					p.E347fs		Atlas-INDEL	.											.	CRELD2	57	.	0			c.1039delG						.						107	108	108					22																	50319089		2203	4300	6503	SO:0001589	frameshift_variant	79174	exon10			.	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.893delA	chr22.hg19:g.50319089delA	ENSP00000332223:p.Glu298fs	123.0	0.0		137.0	10.0	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Frame_Shift_Del	DEL	ENST00000328268.4	hg19	CCDS14082.1																																																																																			.	.		0.438	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324		-	50319089	A	-	50319089	7	5	112	1	0	1	0	1	0	0	0	0	3869	246	9	0	1078	0	CRELD2	22	50319089	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	4520868	50319089	985477	1191	17812										
SBF1	6305	hgsc.bcm.edu	37	chr22	50905072	50905072	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gggccacgctgcagcggctgAcgggcagcgagtcggccagt	18	13	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:50905072A>G	ENST00000390679.3	-	6	801	c.617T>C	c.(616-618)gTc>gCc	p.V206A	SBF1_ENST00000380817.3_Missense_Mutation_p.V206A|SBF1_ENST00000348911.6_Missense_Mutation_p.V207A			O95248	MTMR5_HUMAN	SET binding factor 1	206	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GCAGCGGCTGACGGGCAGCGA	0.632																																					p.V206A		Atlas-SNP	.											.	SBF1	211	.	0			c.T617C						.						6	11	10					22																	50905072		1965	4052	6017	SO:0001583	missense	6305	exon6			CGGCTGACGGGCA	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.617T>C	chr22.hg19:g.50905072A>G	ENSP00000375097:p.Val206Ala	128.0	0.0		124.0	6.0	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	A	12.66	2.004760	0.35320	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000356279;ENST00000337034;ENST00000390679	T;T;T	0.12039	2.72;2.72;2.72	4.28	4.28	0.50868	.	0.580414	0.16662	N	0.204748	T	0.15998	0.0385	L	0.56340	1.77	0.50632	D	0.99988	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.03060	-1.1077	10	0.87932	D	0	.	12.5208	0.56058	1.0:0.0:0.0:0.0	.	207;206	G5E933;O95248-4	.;.	A	206;207;217;216;206	ENSP00000370196:V206A;ENSP00000252027:V207A;ENSP00000375097:V206A	ENSP00000336522:V216A	V	-	2	0	SBF1	49251938	0.998000	0.40836	0.937000	0.37676	0.011000	0.07611	3.884000	0.56175	1.801000	0.52704	0.459000	0.35465	GTC	.	.		0.632	SBF1-201	KNOWN	basic	protein_coding	protein_coding				G	50905072	A	G	50905072	3	3	112	1	0	0	0	0	1	0	0	0	13873	275	10	2	5208	2	SBF1	22	50905072	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	585983	50905072	399494	1192	17813										
NCAPH2	29781	hgsc.bcm.edu	37	chr22	50957703	50957703	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agagcttcctgaggcctcggCccccaaggccgctctggagc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:50957703delC	ENST00000420993.2	+	9	937	c.815delC	c.(814-816)gccfs	p.A272fs	NCAPH2_ENST00000299821.11_Frame_Shift_Del_p.A272fs|NCAPH2_ENST00000395698.3_Frame_Shift_Del_p.A272fs|NCAPH2_ENST00000395701.3_Frame_Shift_Del_p.A272fs	NM_001185011.1|NM_152299.3	NP_001171940.1|NP_689512.2	Q6IBW4	CNDH2_HUMAN	non-SMC condensin II complex, subunit H2	272					chromosome condensation (GO:0030261)|mitotic cell cycle (GO:0000278)	chromosome (GO:0005694)|membrane (GO:0016020)|nucleoplasm (GO:0005654)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|lung(10)|ovary(1)|prostate(2)|skin(3)|stomach(1)	24		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.212)		GAGGCCTCGGCCCCCAAGGCC	0.677																																					p.A272fs		Atlas-INDEL	.											.	NCAPH2	69	.	0			c.814delG						.						22	29	27					22																	50957703		2196	4296	6492	SO:0001589	frameshift_variant	29781	exon9			.	BC001937	CCDS14094.2, CCDS43038.1, CCDS54546.1	22q13.33	2008-02-04			ENSG00000025770	ENSG00000025770			25071	protein-coding gene	gene with protein product	"kleisin beta", "CAP-H2 subunit of the condensin II complex"	611230				10493829	Standard	NM_014551		Approved	384D8-2, hCAP-H2, CAP-H2	uc003blx.4	Q6IBW4	OTTHUMG00000150205	ENST00000420993.2:c.815delC	chr22.hg19:g.50957703delC	ENSP00000410088:p.Ala272fs	175.0	0.0		187.0	12.0	NM_152299	B7WPH1|O43788|Q13391|Q96C14|Q96GJ0|Q9BQ71|Q9BUT3|Q9BVD1	Frame_Shift_Del	DEL	ENST00000420993.2	hg19	CCDS14094.2																																																																																			.	.		0.677	NCAPH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317012.1	NM_152299		-	50957703	C	-	50957703	7	5	112	1	0	1	0	1	0	0	0	0	10219	739	26	0	849	0	NCAPH2	22	50957703	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	52631	50957703	346863	1193	17814										
RABL2B	11158	hgsc.bcm.edu	37	chr22	51207957	51207957	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttcttggcaaaattgaagcTtttttgggtcacgtttatgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:51207957delT	ENST00000395598.3	-	7	641	c.430delA	c.(430-432)agcfs	p.S144fs	RABL2B_ENST00000395593.3_Frame_Shift_Del_p.S144fs|RABL2B_ENST00000435118.1_Frame_Shift_Del_p.S144fs|RABL2B_ENST00000395591.1_Frame_Shift_Del_p.S81fs|RABL2B_ENST00000465063.1_5'UTR|RABL2B_ENST00000354869.3_Frame_Shift_Del_p.S145fs|RABL2B_ENST00000395595.3_Frame_Shift_Del_p.S145fs	NM_001003789.1|NM_001130919.1|NM_001130922.1|NM_007081.2	NP_001003789.1|NP_001124391.1|NP_001124394.1|NP_009012.1	Q9UNT1	RBL2B_HUMAN	RAB, member of RAS oncogene family-like 2B	144					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)			lung(1)	1		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.0539)|LUAD - Lung adenocarcinoma(64;0.247)		AAATTGAAGCTTTTTTGGGTC	0.512																																					p.S145fs	GBM(148;358 1894 4987 13698 40400)	Atlas-INDEL	.											.	RABL2B	8	.	0			c.434delG						.						67	76	73					22																	51207957		2203	4297	6500	SO:0001589	frameshift_variant	11158	exon8			.		CCDS14102.1, CCDS33683.1, CCDS46738.1	22q13.33	2014-05-09			ENSG00000079974	ENSG00000079974		"RAB, member RAS oncogene"	9800	protein-coding gene	gene with protein product		605413				10444334	Standard	NM_001130919		Approved		uc011asg.1	Q9UNT1	OTTHUMG00000150156	ENST00000395598.3:c.430delA	chr22.hg19:g.51207957delT	ENSP00000378962:p.Ser144fs	388.0	0.0		438.0	28.0	NM_001130920	Q5TZT8|Q96C33	Frame_Shift_Del	DEL	ENST00000395598.3	hg19	CCDS14102.1																																																																																			.	.		0.512	RABL2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316606.1	NM_001003789		-	51207957	T	-	51207957	7	5	112	1	0	1	0	1	0	0	0	0	12986	1609	56	0	298	0	RABL2B	22	51207957	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	250254	51207957	96609	1194	17815										
ARSF	416	hgsc.bcm.edu	37	chrX	2994595	2994595	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctctcccccttcaggacgccTcacatcgaccgccttgccag	7	20	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:2994595T>C	ENST00000381127.1	+	4	389	c.168T>C	c.(166-168)ccT>ccC	p.P56P	ARSF_ENST00000359361.2_Silent_p.P56P|ARSF_ENST00000537104.1_Silent_p.P56P	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	56					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				tcAGGACGCCTCACATCGACC	0.612																																					p.P56P		Atlas-SNP	.											.	ARSF	97	.	0			c.T168C						.						40	24	29					X																	2994595		2203	4299	6502	SO:0001819	synonymous_variant	416	exon4			GACGCCTCACATC	X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"Arylsulfatase family"	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.168T>C	chrX.hg19:g.2994595T>C		48.0	0.0		66.0	5.0	NM_004042	Q8TCC5	Silent	SNP	ENST00000381127.1	hg19	CCDS14123.1																																																																																			.	.		0.612	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1			C	2994595	T	C	2994595	2	2	112	1	0	0	0	0	0	0	0	1	991	1538	54	2		2	ARSF	23	2994595	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10		2994595	152275965	1195	17816										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3241039	3241039	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttcagtggaagttatctccTcagtcttctcggaaaggtca	9	10	6	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:3241039T>C	ENST00000217939.6	-	5	2841	c.2687A>G	c.(2686-2688)gAg>gGg	p.E896G		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	896						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				AGTTATCTCCTCAGTCTTCTC	0.463																																					p.E896G		Atlas-SNP	.											.	MXRA5	815	.	0			c.A2687G						.						95	83	87					X																	3241039		2203	4300	6503	SO:0001583	missense	25878	exon5			ATCTCCTCAGTCT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2687A>G	chrX.hg19:g.3241039T>C	ENSP00000217939:p.Glu896Gly	106.0	0.0		112.0	5.0	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	t	6.662	0.490634	0.12702	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.64085	-0.08	3.33	0.722	0.18225	.	1.435640	0.04933	U	0.457118	T	0.38026	0.1025	N	0.08118	0	0.09310	N	1	B	0.23058	0.079	B	0.17098	0.017	T	0.15752	-1.0426	10	0.28530	T	0.3	.	3.2428	0.06787	0.2055:0.1216:0.0:0.6729	.	896	Q9NR99	MXRA5_HUMAN	G	896	ENSP00000217939:E896G	ENSP00000217939:E896G	E	-	2	0	MXRA5	3251039	0.002000	0.14202	0.000000	0.03702	0.014000	0.08584	0.998000	0.29744	-0.136000	0.11475	0.430000	0.28490	GAG	.	.		0.463	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		C	3241039	T	C	3241039	3	2	112	1	0	0	0	0	1	0	0	0	10012	1551	54	2	5811	2	MXRA5	23	3241039	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	246444	3241039	152029521	1196	17817										
PIGA	5277	hgsc.bcm.edu	37	chrX	15349573	15349573	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtaagcaccgagctgacatcAgcaaatccaaaaagggaatg	10	9	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:15349573A>G	ENST00000333590.4	-	2	564	c.480T>C	c.(478-480)gcT>gcC	p.A160A	PIGA_ENST00000428964.1_Intron|PIGA_ENST00000482148.1_Intron|PIGA_ENST00000542278.1_Intron	NM_002641.3	NP_002632.1	P37287	PIGA_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class A	160					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|positive regulation of metabolic process (GO:0009893)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)|UDP-glycosyltransferase activity (GO:0008194)			endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Hepatocellular(33;0.183)					AGCTGACATCAGCAAATCCAA	0.433																																					p.A160A		Atlas-SNP	.											.	PIGA	34	.	0			c.T480C						.						94	73	80					X																	15349573		2203	4300	6503	SO:0001819	synonymous_variant	5277	exon2			GACATCAGCAAAT	BC038236	CCDS14165.1, CCDS48086.1, CCDS48086.2	Xp22.1	2014-09-17	2008-07-31		ENSG00000165195	ENSG00000165195	2.4.1.198	"Glycosyltransferase group 1 domain containing", "Phosphatidylinositol glycan anchor biosynthesis"	8957	protein-coding gene	gene with protein product	"paroxysmal nocturnal hemoglobinuria", "phosphatidylinositol N-acetylglucosaminyltransferase"	311770	"phosphatidylinositol glycan, class A (paroxysmal nocturnal hemoglobinuria)"			8500164	Standard	NM_002641		Approved	GPI3	uc004cwr.3	P37287	OTTHUMG00000021174	ENST00000333590.4:c.480T>C	chrX.hg19:g.15349573A>G		72.0	0.0		89.0	6.0	NM_002641	B4E0V2|Q16025|Q16250	Silent	SNP	ENST00000333590.4	hg19	CCDS14165.1																																																																																			.	.		0.433	PIGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055854.1	NM_002641		G	15349573	A	G	15349573	2	3	112	1	0	0	0	0	0	0	0	1	11893	175	7	2		2	PIGA	23	15349573	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	12108534	15349573	139920987	1197	17818										
TMEM27	57393	hgsc.bcm.edu	37	chrX	15682878	15682878	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcatgaatggcagtcaccagAaaaaagagcagccacaacat							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:15682878delA	ENST00000380342.3	-	1	276	c.21delT	c.(19-21)tttfs	p.F7fs		NM_020665.4	NP_065716.1	Q9HBJ8	TMM27_HUMAN	transmembrane protein 27	7					positive regulation of amino acid transport (GO:0051957)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of SNARE complex assembly (GO:0035543)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)			endometrium(3)|lung(4)|ovary(1)	8	Hepatocellular(33;0.183)					CAGTCACCAGAAAAAAGAGCA	0.398																																					p.L8fs		Atlas-INDEL	.											.	TMEM27	21	.	0			c.22delC						.						53	48	50					X																	15682878		2203	4299	6502	SO:0001589	frameshift_variant	57393	exon1			.	AF229179	CCDS14170.1	Xp22	2012-04-13			ENSG00000147003	ENSG00000147003			29437	protein-coding gene	gene with protein product	"collectrin"	300631				11278314	Standard	NM_020665		Approved	NX17	uc004cxc.2	Q9HBJ8	OTTHUMG00000021181	ENST00000380342.3:c.21delT	chrX.hg19:g.15682878delA	ENSP00000369699:p.Phe7fs	133.0	0.0		149.0	11.0	NM_020665	B2R9M1|Q6UW07	Frame_Shift_Del	DEL	ENST00000380342.3	hg19	CCDS14170.1																																																																																			.	.		0.398	TMEM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055879.1	NM_020665		-	15682878	A	-	15682878	7	5	112	1	0	1	0	1	0	0	0	0	16167	243	9	0	671	0	TMEM27	23	15682878	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	333305	15682878	139587682	1198	17819										
AP1S2	8905	hgsc.bcm.edu	37	chrX	15864073	15864073	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacataacgatgaattatttCcagggtaattagttcattgt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:15864073delC	ENST00000329235.2	-	3	484	c.241delG	c.(241-243)gaafs	p.E81fs	AP1S2_ENST00000479184.1_5'Flank|AP1S2_ENST00000421527.2_Frame_Shift_Del_p.E123fs|AP1S2_ENST00000545766.1_Frame_Shift_Del_p.E123fs|AP1S2_ENST00000380291.1_Frame_Shift_Del_p.E81fs	NM_001272071.1|NM_003916.3	NP_001259000.1|NP_003907.3	P56377	AP1S2_HUMAN	adaptor-related protein complex 1, sigma 2 subunit	81					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)			large_intestine(1)	1	Hepatocellular(33;0.183)					TGAATTATTTCCAGGGTAATT	0.323																																					p.E81fs		Atlas-INDEL	.											.	AP1S2	9	.	0			c.242delA						.						84	87	86					X																	15864073		2203	4292	6495	SO:0001589	frameshift_variant	8905	exon3			.	AB015320	CCDS14173.1, CCDS75958.1	Xp22	2014-01-31			ENSG00000182287	ENSG00000182287			560	protein-coding gene	gene with protein product		300629	"mental retardation, X-linked 59", "mental retardation, X-linked, syndromic 5", "Pettigrew X-linked mental retardation syndrome"	MRX59, MRXS5, PGS		9733768, 17186471, 23756445	Standard	NM_003916		Approved	SIGMA1B	uc010nex.4	P56377	OTTHUMG00000021186	ENST00000329235.2:c.241delG	chrX.hg19:g.15864073delC	ENSP00000328789:p.Glu81fs	130.0	0.0		165.0	10.0	NM_001272071	B4DSU4|O95326|Q9H2N6	Frame_Shift_Del	DEL	ENST00000329235.2	hg19	CCDS14173.1																																																																																			.	.		0.323	AP1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055893.1	NM_003916		-	15864073	C	-	15864073	7	5	112	1	0	1	0	1	0	0	0	0	737	864	30	0	244	0	AP1S2	23	15864073	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	181195	15864073	139406487	1199	17820										
SCML1	6322	hgsc.bcm.edu	37	chrX	17767571	17767571	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agaagattgatgtgattcgtAgaaaggtttcaaaaatccaa	9	4	1	5			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:17767571A>G	ENST00000380041.3	+	5	578	c.250A>G	c.(250-252)Aga>Gga	p.R84G	SCML1_ENST00000398080.1_5'UTR|SCML1_ENST00000380045.3_5'UTR|SCML1_ENST00000380043.3_Missense_Mutation_p.R57G	NM_001037540.1	NP_001032629.1	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 (Drosophila)	84					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)	10	Hepatocellular(33;0.183)					TGTGATTCGTAGAAAGGTTTC	0.308																																					p.R84G		Atlas-SNP	.											.	SCML1	55	.	0			c.A250G						.						101	92	95					X																	17767571		2203	4300	6503	SO:0001583	missense	6322	exon5			ATTCGTAGAAAGG		CCDS14182.2, CCDS35210.1, CCDS35211.1	Xp22	2013-01-10	2001-11-28		ENSG00000047634	ENSG00000047634		"Sterile alpha motif (SAM) domain containing"	10580	protein-coding gene	gene with protein product		300227	"sex comb on midleg (Drosophila)-like 1"			9570953	Standard	XM_005274578		Approved		uc004cyc.3	Q9UN30	OTTHUMG00000021206	ENST00000380041.3:c.250A>G	chrX.hg19:g.17767571A>G	ENSP00000369380:p.Arg84Gly	120.0	0.0		128.0	6.0	NM_001037540	B0FZN6|B2RA08|Q5H968|Q5H969	Missense_Mutation	SNP	ENST00000380041.3	hg19	CCDS35210.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.115816	0.37339	.	.	ENSG00000047634	ENST00000380041;ENST00000380043;ENST00000419185	.	.	.	4.96	-0.356	0.12583	.	1.217200	0.06182	N	0.679576	T	0.16428	0.0395	N	0.03050	-0.425	0.09310	N	0.999999	B;B	0.09022	0.001;0.002	B;B	0.04013	0.001;0.001	T	0.24548	-1.0157	9	0.35671	T	0.21	-0.5909	7.8214	0.29290	0.5618:0.0:0.4382:0.0	.	57;84	Q9UN30-2;Q9UN30	.;SCML1_HUMAN	G	84;57;57	.	ENSP00000369380:R84G	R	+	1	2	SCML1	17677492	0.003000	0.15002	0.000000	0.03702	0.025000	0.11179	0.162000	0.16501	-0.312000	0.08741	-0.438000	0.05819	AGA	.	.		0.308	SCML1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060495.5	NM_006746		G	17767571	A	G	17767571	3	3	112	1	0	0	0	0	1	0	0	0	13924	412	15	2	267	2	SCML1	23	17767571	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1903498	17767571	137502989	1200	17821										
FAM48B2	170067	hgsc.bcm.edu	37	chrX	24329517	24329517	+	IGR	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaccttccggagtatttaggAaaaactgaaggggtgctgga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:24329517delA								AC096509.1 (24723 upstream) : AC004552.1 (37408 downstream)																							AGTATTTAGGAAAAACTGAAG	0.602																																					p.F639fs		Atlas-INDEL	.											.	.	.	.	0			c.1917delC						.						39	39	39					X																	24329517		1568	3581	5149	SO:0001628	intergenic_variant	170067	exon1			.																													chrX.hg19:g.24329517delA		144.0	0.0		210.0	13.0	NM_001136233		Frame_Shift_Del	DEL		hg19																																																																																				.	.	0	0.602									-	24329517	A	-	24329517	6	5	112	0	1	1	0	1	0	0	0	0	5582	246	9	0		0	FAM48B2	23	24329517	IGR	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	6561946	24329517	130941043	1201	17822										
MAGEB16	139604	hgsc.bcm.edu	37	chrX	35820408	35820408	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ggaggttgcacaggtctccaAggctctggagaagaccctcc	13	12	2	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:35820408A>G	ENST00000399989.1	+	2	374	c.95A>G	c.(94-96)aAg>aGg	p.K32R	MAGEB16_ENST00000399988.1_Missense_Mutation_p.K32R|MAGEB16_ENST00000399987.1_Missense_Mutation_p.K32R|MAGEB16_ENST00000399992.1_Missense_Mutation_p.K64R|MAGEB16_ENST00000399985.1_Missense_Mutation_p.K32R	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	32										breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						CAGGTCTCCAAGGCTCTGGAG	0.552																																					p.K32R		Atlas-SNP	.											.	MAGEB16	64	.	0			c.A95G						.						41	42	41					X																	35820408		2022	4171	6193	SO:0001583	missense	139604	exon2			TCTCCAAGGCTCT		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"melanoma antigen family B, 16 (pseudogene)"			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.95A>G	chrX.hg19:g.35820408A>G	ENSP00000382871:p.Lys32Arg	87.0	0.0		87.0	4.0	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	hg19	CCDS43927.1	.	.	.	.	.	.	.	.	.	.	A	3.125	-0.179717	0.06380	.	.	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04317	3.65;3.65;3.65;3.65;3.65	3.02	-6.03	0.02185	Melanoma associated antigen, MAGE, N-terminal (1);	1.111270	0.06703	N	0.771751	T	0.03651	0.0104	L	0.34521	1.04	0.09310	N	1	B	0.18013	0.025	B	0.18263	0.021	T	0.42344	-0.9457	10	0.48119	T	0.1	.	4.6746	0.12706	0.2246:0.0:0.4599:0.3155	.	32	A2A368	MAGBG_HUMAN	R	32;64;32;32;32	ENSP00000382870:K32R;ENSP00000382874:K64R;ENSP00000382869:K32R;ENSP00000382871:K32R;ENSP00000382867:K32R	ENSP00000382867:K32R	K	+	2	0	MAGEB16	35730329	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.720000	0.04969	-1.864000	0.01148	0.423000	0.28283	AAG	.	.		0.552	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1			G	35820408	A	G	35820408	3	3	112	1	0	0	0	0	1	0	0	0	9183	72	3	2	97	2	MAGEB16	23	35820408	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	11490891	35820408	119450152	1202	17823										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37028804	37028804	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tgagactggagtgtcccatcTccacccagagcttcccaagc	9	15	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:37028804T>C	ENST00000358047.3	+	1	2373	c.2321T>C	c.(2320-2322)cTc>cCc	p.L774P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	774										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						GTGTCCCATCTCCACCCAGAG	0.627																																					p.L774P		Atlas-SNP	.											.	FAM47C	267	.	0			c.T2321C						.						40	40	40					X																	37028804		2202	4300	6502	SO:0001583	missense	442444	exon1			CCCATCTCCACCC	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2321T>C	chrX.hg19:g.37028804T>C	ENSP00000367913:p.Leu774Pro	38.0	0.0		49.0	4.0	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	hg19	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	-	5.808	0.333363	0.11013	.	.	ENSG00000198173	ENST00000358047	T	0.23348	1.91	0.118	0.118	0.14667	.	.	.	.	.	T	0.39784	0.1091	M	0.79258	2.445	0.22888	N	0.998603	D	0.62365	0.991	P	0.60609	0.877	T	0.21621	-1.0240	9	0.29301	T	0.29	.	4.6021	0.12359	0.0:5.0E-4:0.0:0.9995	.	774	Q5HY64	FA47C_HUMAN	P	774	ENSP00000367913:L774P	ENSP00000367913:L774P	L	+	2	0	FAM47C	36938725	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	-1.576000	0.02129	0.153000	0.19213	0.151000	0.16131	CTC	.	.		0.627	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		C	37028804	T	C	37028804	3	2	112	1	0	0	0	0	1	0	0	0	5579	1551	54	2	2323	2	FAM47C	23	37028804	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1208396	37028804	118241756	1203	17824										
USP9X	8239	hgsc.bcm.edu	37	chrX	41069767	41069767	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcattcatttcttaggctttGgggtgagcctgttaatctgc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:41069767delG	ENST00000324545.8	+	33	5654	c.5021delG	c.(5020-5022)tggfs	p.W1674fs	USP9X_ENST00000378308.2_Frame_Shift_Del_p.W1674fs	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1674	USP.				axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CTTAGGCTTTGGGGTGAGCCT	0.333																																					p.W1674fs	Ovarian(172;1807 2695 35459 49286)	Atlas-INDEL	.											.	USP9X	385	.	0			c.5020delT						.						113	107	109					X																	41069767		2164	4278	6442	SO:0001589	frameshift_variant	8239	exon33			.	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.5021delG	chrX.hg19:g.41069767delG	ENSP00000316357:p.Trp1674fs	145.0	0.0		148.0	11.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Frame_Shift_Del	DEL	ENST00000324545.8	hg19	CCDS43930.1																																																																																			.	.		0.333	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		-	41069767	G	-	41069767	7	5	112	1	0	1	0	1	0	0	0	0	17105	1357	47	0	5147	0	USP9X	23	41069767	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	4040963	41069767	114200793	1204	17825										
USP9X	8239	hgsc.bcm.edu	37	chrX	41075804	41075804	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagaagtgtacggaaacagaAcgtacaattcatgcataacc	9	8	1	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:41075804A>G	ENST00000324545.8	+	35	6617	c.5984A>G	c.(5983-5985)aAc>aGc	p.N1995S	USP9X_ENST00000378308.2_Missense_Mutation_p.N1995S	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1995					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CGGAAACAGAACGTACAATTC	0.388																																					p.N1995S	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.A5984G						.						115	101	106					X																	41075804		2103	4228	6331	SO:0001583	missense	8239	exon35			AACAGAACGTACA	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.5984A>G	chrX.hg19:g.41075804A>G	ENSP00000316357:p.Asn1995Ser	116.0	0.0		112.0	5.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	hg19	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.047601	0.75846	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.13307	2.6;2.6	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.39545	0.1082	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.983	T	0.31916	-0.9926	10	0.87932	D	0	.	14.9222	0.70847	1.0:0.0:0.0:0.0	.	1995;1995	Q93008-1;Q93008	.;USP9X_HUMAN	S	1995	ENSP00000367558:N1995S;ENSP00000316357:N1995S	ENSP00000316357:N1995S	N	+	2	0	USP9X	40960748	1.000000	0.71417	0.963000	0.40424	0.985000	0.73830	8.952000	0.93031	1.906000	0.55180	0.481000	0.45027	AAC	.	.		0.388	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		G	41075804	A	G	41075804	3	3	112	1	0	0	0	0	1	0	0	0	17105	43	2	2	6118	2	USP9X	23	41075804	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	6037	41075804	114194756	1205	17826										
KDM6A	7403	hgsc.bcm.edu	37	chrX	44941973	44941973	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttttaagttctgggaggaggAggaaaggaccctttaaaacc	12	6	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:44941973A>G	ENST00000377967.4	+	22	3264	c.3223A>G	c.(3223-3225)Agg>Ggg	p.R1075G	KDM6A_ENST00000382899.4_Missense_Mutation_p.R1082G|KDM6A_ENST00000543216.1_Missense_Mutation_p.R996G|KDM6A_ENST00000536777.1_Missense_Mutation_p.R1030G	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1075	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						TGGGAGGAGGAGGAAAGGACC	0.338			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.R1075G	Colon(129;1273 1667 15230 27352 52914)	Atlas-SNP	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A	274	.	6	Whole gene deletion(6)	oesophagus(2)|breast(2)|pancreas(2)	c.A3223G						.						113	103	106					X																	44941973		2203	4300	6503	SO:0001583	missense	7403	exon22			AGGAGGAGGAAAG	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.3223A>G	chrX.hg19:g.44941973A>G	ENSP00000367203:p.Arg1075Gly	78.0	0.0		72.0	5.0	NM_021140	Q52LL9|Q5JVQ7	Missense_Mutation	SNP	ENST00000377967.4	hg19	CCDS14265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.46|14.46	2.543038|2.543038	0.45280|0.45280	.|.	.|.	ENSG00000147050|ENSG00000147050	ENST00000414389;ENST00000433797|ENST00000334516;ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216	.|T;T;T;T	.|0.79554	.|-1.28;-1.28;-1.28;-1.28	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	.|0.042744	.|0.85682	.|D	.|0.000000	T|T	0.76793|0.76793	0.4037|0.4037	N|N	0.25890|0.25890	0.77|0.77	0.80722|0.80722	D|D	1|1	.|P;B;D;B;P	.|0.54047	.|0.816;0.275;0.964;0.027;0.647	.|B;B;P;B;P	.|0.52217	.|0.091;0.109;0.693;0.011;0.653	T|T	0.77493|0.77493	-0.2567|-0.2567	5|10	.|0.46703	.|T	.|0.11	-2.9787|-2.9787	10.5922|10.5922	0.45316|0.45316	0.8411:0.1589:0.0:0.0|0.8411:0.1589:0.0:0.0	.|.	.|714;1082;1030;1127;1075	.|B4E0L8;F8W8R6;F5H6S1;B7ZKN5;O15550	.|.;.;.;.;KDM6A_HUMAN	G|G	672;717|772;1075;1030;1082;996	.|ENSP00000367203:R1075G;ENSP00000437405:R1030G;ENSP00000372355:R1082G;ENSP00000443078:R996G	.|ENSP00000334340:R772G	E|R	+|+	2|1	0|2	KDM6A|KDM6A	44826917|44826917	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.991000|0.991000	0.79684|0.79684	4.667000|4.667000	0.61561|0.61561	1.793000|1.793000	0.52555|0.52555	0.437000|0.437000	0.28790|0.28790	GAG|AGG	.	.		0.338	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		G	44941973	A	G	44941973	3	3	112	1	0	0	0	0	1	0	0	0	8146	295	11	2	3309	2	KDM6A	23	44941973	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	3866169	44941973	110328587	1206	17827										
RBM10	8241	hgsc.bcm.edu	37	chrX	47041607	47041607	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtacctgtactgggatggggAgaggcggacctatgttcccg	16	9	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:47041607A>G	ENST00000377604.3	+	17	2574	c.1832A>G	c.(1831-1833)gAg>gGg	p.E611G	RBM10_ENST00000345781.6_Missense_Mutation_p.E534G|RBM10_ENST00000329236.7_Missense_Mutation_p.E533G	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	611					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						TGGGATGGGGAGAGGCGGACC	0.577																																					p.E676G	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.A2027G						.						92	80	84					X																	47041607		2203	4300	6503	SO:0001583	missense	8241	exon17			ATGGGGAGAGGCG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.1832A>G	chrX.hg19:g.47041607A>G	ENSP00000366829:p.Glu611Gly	99.0	0.0		94.0	4.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	A	19.38	3.815946	0.70912	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	T;T;T	0.22336	2.63;1.96;2.22	4.85	4.85	0.62838	.	0.060824	0.64402	D	0.000006	T	0.45796	0.1360	M	0.79475	2.455	0.40097	D	0.976325	D;D;D;D;D	0.89917	0.99;0.993;0.984;1.0;0.991	P;D;P;D;P	0.80764	0.843;0.926;0.888;0.994;0.837	T	0.50709	-0.8796	10	0.66056	D	0.02	-18.6669	11.6162	0.51092	1.0:0.0:0.0:0.0	.	534;676;610;533;611	P98175-3;Q7Z3D7;P98175-2;P98175-4;P98175	.;.;.;.;RBM10_HUMAN	G	611;533;534	ENSP00000366829:E611G;ENSP00000328848:E533G;ENSP00000329659:E534G	ENSP00000328848:E533G	E	+	2	0	RBM10	46926551	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.086000	0.94088	1.713000	0.51359	0.356000	0.21956	GAG	.	.		0.577	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		G	47041607	A	G	47041607	3	3	112	1	0	0	0	0	1	0	0	0	13126	304	11	2	1894	2	RBM10	23	47041607	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	2099634	47041607	108228953	1207	17828										
SSX4	6759	hgsc.bcm.edu	37	chrX	48244046	48244046	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttctctaagaaagagtgggAaaagatgaaatcctcggaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48244046delA	ENST00000376886.2	+	3	276	c.113delA	c.(112-114)gaafs	p.E38fs	SSX4_ENST00000375517.3_Frame_Shift_Del_p.E38fs	NM_005636.3	NP_005627.1	O60224	SSX4_HUMAN	synovial sarcoma, X breakpoint 4	38	KRAB-related. {ECO:0000255|PROSITE- ProRule:PRU00120}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)		SS18/SSX4(12)	lung(1)	1						AAAGAGTGGGAAAAGATGAAA	0.383			T	SS18	synovial sarcoma																																p.E38fs		Atlas-INDEL	.		Dom	yes		X	Xp11.23	6759	"synovial sarcoma, X breakpoint 4"		M	.	SSX4B	9	.	0			c.112delG						.						8	4	6					X																	48244046		1829	3342	5171	SO:0001589	frameshift_variant	548313	exon3			.		CCDS35240.1, CCDS43934.1	Xp11.23	2009-06-17			ENSG00000204645	ENSG00000268009			11338	protein-coding gene	gene with protein product		300326					Standard	NM_005636		Approved	CT5.4		O60224	OTTHUMG00000022698	ENST00000376886.2:c.113delA	chrX.hg19:g.48244046delA	ENSP00000366083:p.Glu38fs	308.0	0.0		319.0	20.0	NM_001034832	A8MYD4|B2RPE3|Q3SYD4|Q5JQZ0|Q9UJU9	Frame_Shift_Del	DEL	ENST00000376886.2	hg19	CCDS35240.1																																																																																			.	.		0.383	SSX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058902.2			-	48244046	A	-	48244046	7	5	112	1	0	1	0	1	0	0	0	0	15221	246	9	0	119	0	SSX4	23	48244046	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	1202439	48244046	107026514	1208	17829										
FTSJ1	24140	hgsc.bcm.edu	37	chrX	48341394	48341394	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atggaagacaatgaaatgagTtgttcaccttaacccattac	7	8	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48341394T>C	ENST00000348411.2	+	12	1301	c.978T>C	c.(976-978)agT>agC	p.S326S	FTSJ1_ENST00000456787.1_Silent_p.S324S|FTSJ1_ENST00000019019.2_Silent_p.S324S|FTSJ1_ENST00000396894.4_Silent_p.S189S|FTSJ1_ENST00000496365.1_3'UTR	NM_012280.2	NP_036412.1			FtsJ RNA methyltransferase homolog 1 (E. coli)											breast(1)|central_nervous_system(1)|lung(4)|skin(1)	7						ATGAAATGAGTTGTTCACCTT	0.338																																					p.S326S		Atlas-SNP	.											.	FTSJ1	21	.	0			c.T978C						.						156	138	144					X																	48341394		2203	4300	6503	SO:0001819	synonymous_variant	24140	exon12			AATGAGTTGTTCA	AJ005892	CCDS14294.1, CCDS14295.1, CCDS75972.1	Xp11.23	2012-06-12	2012-06-12		ENSG00000068438	ENSG00000068438			13254	protein-coding gene	gene with protein product	"tRNA methyltransferase 7 homolog (S. cerevisiae)"	300499	"mental retardation, X-linked 9", "mental retardation, X-linked 44"	MRX9, MRX44		15342698, 15162322	Standard	XR_246715		Approved	JM23, CDLIV, SPB1, TRM7, TRMT7	uc004djo.1	Q9UET6	OTTHUMG00000024118	ENST00000348411.2:c.978T>C	chrX.hg19:g.48341394T>C		60.0	0.0		60.0	4.0	NM_012280		Silent	SNP	ENST00000348411.2	hg19	CCDS14294.1																																																																																			.	.		0.338	FTSJ1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060726.1			C	48341394	T	C	48341394	2	2	112	1	0	0	0	0	0	0	0	1	6095	1722	60	2		2	FTSJ1	23	48341394	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	97348	48341394	106929166	1209	17830										
WDR13	64743	hgsc.bcm.edu	37	chrX	48458000	48458000	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctggcagcgtggtgcccacgTcagcagcagaggcaagtcgg	16	12	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48458000T>C	ENST00000218056.5	+	4	923	c.418T>C	c.(418-420)Tca>Cca	p.S140P	WDR13_ENST00000492715.1_3'UTR|WDR13_ENST00000376729.5_Missense_Mutation_p.S140P	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	140						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						GGTGCCCACGTCAGCAGCAGA	0.612																																					p.S140P		Atlas-SNP	.											.	WDR13	96	.	0			c.T418C						.						81	70	73					X																	48458000		2203	4300	6503	SO:0001583	missense	64743	exon4			CCCACGTCAGCAG	AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"WD repeat domain containing"	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.418T>C	chrX.hg19:g.48458000T>C	ENSP00000218056:p.Ser140Pro	85.0	0.0		96.0	5.0	NM_017883	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Missense_Mutation	SNP	ENST00000218056.5	hg19	CCDS14302.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.501964	0.44455	.	.	ENSG00000101940	ENST00000376729;ENST00000218056	T;T	0.72167	-0.63;-0.63	5.48	5.48	0.80851	.	0.065767	0.64402	D	0.000005	T	0.52773	0.1755	L	0.27053	0.805	0.48236	D	0.999614	B;B	0.13145	0.007;0.004	B;B	0.09377	0.002;0.004	T	0.48340	-0.9044	10	0.19590	T	0.45	-25.0681	7.2254	0.26012	0.0:0.0991:0.0:0.9008	.	18;140	B4DVQ7;Q9H1Z4	.;WDR13_HUMAN	P	140	ENSP00000365919:S140P;ENSP00000218056:S140P	ENSP00000218056:S140P	S	+	1	0	WDR13	48342944	0.999000	0.42202	0.020000	0.16555	0.854000	0.48673	3.373000	0.52394	1.826000	0.53198	0.430000	0.28490	TCA	.	.		0.612	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2			C	48458000	T	C	48458000	3	2	112	1	0	0	0	0	1	0	0	0	17290	1667	58	2	432	2	WDR13	23	48458000	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	116606	48458000	106812560	1210	17831										
GATA1	2623	hgsc.bcm.edu	37	chrX	48650547	48650547	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctgacttttccagtaccttcTtttctcccaccgggagcccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48650547delT	ENST00000376670.3	+	3	628	c.517delT	c.(517-519)tttfs	p.F173fs	GATA1_ENST00000376665.3_Frame_Shift_Del_p.F173fs	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	173					basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.?(2)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						CAGTACCTTCTTTTCTCCCAC	0.572			"Mis, F"		megakaryoblastic leukemia of Downs Syndrome																																p.F172fs	Pancreas(9;429 505 11287 29617)	Atlas-INDEL	.		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	.	GATA1	342	.	2	Unknown(2)	haematopoietic_and_lymphoid_tissue(2)	c.516delC						.						48	47	48					X																	48650547		2203	4300	6503	SO:0001589	frameshift_variant	2623	exon3			.	X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"GATA zinc finger domain containing"	4170	protein-coding gene	gene with protein product	"nuclear factor, erythroid 1"	305371	"GATA-binding protein 1 (globin transcription factor 1)"	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.517delT	chrX.hg19:g.48650547delT	ENSP00000365858:p.Phe173fs	116.0	0.0		142.0	11.0	NM_002049	Q96GB8	Frame_Shift_Del	DEL	ENST00000376670.3	hg19	CCDS14305.1																																																																																			.	.		0.572	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049		-	48650547	T	-	48650547	7	5	112	1	0	1	0	1	0	0	0	0	6261	1609	56	0	523	0	GATA1	23	48650547	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	192547	48650547	106620013	1211	17832										
HDAC6	10013	hgsc.bcm.edu	37	chrX	48661166	48661166	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gtaggcagaacccccagtcgCcccctcaggactccagtgtc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48661166delC	ENST00000334136.5	+	2	245	c.67delC	c.(67-69)cccfs	p.P24fs	HDAC6_ENST00000469223.1_Intron|HDAC6_ENST00000376619.2_Frame_Shift_Del_p.P24fs|HDAC6_ENST00000413163.2_Intron|HDAC6_ENST00000444343.2_Frame_Shift_Del_p.P38fs			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	24					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	CCCCCAGTCGCCCCCTCAGGA	0.622																																					p.S22fs	Pancreas(112;205 1675 2305 8976 15959)	Atlas-INDEL	.											.	HDAC6	111	.	0			c.66delG						.						46	38	41					X																	48661166		2200	4300	6500	SO:0001589	frameshift_variant	10013	exon2			.	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.67delC	chrX.hg19:g.48661166delC	ENSP00000334061:p.Pro24fs	123.0	0.0		147.0	10.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Frame_Shift_Del	DEL	ENST00000334136.5	hg19	CCDS14306.1																																																																																			.	.		0.622	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		-	48661166	C	-	48661166	7	5	112	1	0	1	0	1	0	0	0	0	7020	739	26	0	69	0	HDAC6	23	48661166	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	10619	48661166	106609394	1212	17833										
HDAC6	10013	hgsc.bcm.edu	37	chrX	48663924	48663924	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tcctagatcgctgcgtgtccTttcaggtaaggcccccaagc	10	14	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48663924T>C	ENST00000334136.5	+	5	569	c.391T>C	c.(391-393)Ttt>Ctt	p.F131L	HDAC6_ENST00000469223.1_3'UTR|HDAC6_ENST00000376619.2_Missense_Mutation_p.F131L|HDAC6_ENST00000413163.2_Missense_Mutation_p.F76L|HDAC6_ENST00000444343.2_Missense_Mutation_p.F145L			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	131	Histone deacetylase 1.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	CTGCGTGTCCTTTCAGGTAAG	0.592																																					p.F131L	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.T391C						.						79	59	65					X																	48663924		2203	4300	6503	SO:0001583	missense	10013	exon5			GTGTCCTTTCAGG	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.391T>C	chrX.hg19:g.48663924T>C	ENSP00000334061:p.Phe131Leu	89.0	0.0		88.0	4.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	hg19	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	T	9.004	0.980811	0.18812	.	.	ENSG00000094631	ENST00000423941;ENST00000376643;ENST00000444343;ENST00000376610;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000413163;ENST00000441703;ENST00000426196;ENST00000443563;ENST00000440653	T;T;T;T	0.61392	0.38;0.38;0.38;0.11	4.16	2.94	0.34122	Histone deacetylase domain (2);	0.379228	0.23422	N	0.048352	T	0.14787	0.0357	N	0.00226	-1.805	0.29091	N	0.882076	B;B;B;P	0.38335	0.321;0.002;0.321;0.627	B;B;B;B	0.36030	0.107;0.002;0.107;0.216	T	0.17776	-1.0358	10	0.10111	T	0.7	-7.3413	4.4811	0.11767	0.1971:0.0:0.2002:0.6027	.	121;76;131;131	B4DZN1;E7EUZ1;Q9UBN7;Q9BRX7	.;.;HDAC6_HUMAN;.	L	131;131;145;131;131;131;131;76;131;131;131;131	ENSP00000398566:F145L;ENSP00000334061:F131L;ENSP00000365804:F131L;ENSP00000398801:F76L	ENSP00000334061:F131L	F	+	1	0	HDAC6	48548868	0.998000	0.40836	0.988000	0.46212	0.880000	0.50808	0.772000	0.26647	0.517000	0.28361	0.242000	0.17961	TTT	.	.		0.592	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		C	48663924	T	C	48663924	3	2	112	1	0	0	0	0	1	0	0	0	7020	1609	56	2	405	2	HDAC6	23	48663924	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2758	48663924	106606636	1213	17834										
CACNA1F	778	hgsc.bcm.edu	37	chrX	49066137	49066137	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcgtcgttgcctagtagcccTttttctttcctccgccggaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:49066137delT	ENST00000376265.2	-	41	4867	c.4806delA	c.(4804-4806)aaafs	p.K1602fs	CACNA1F_ENST00000376251.1_Frame_Shift_Del_p.K1537fs|CACNA1F_ENST00000323022.5_Frame_Shift_Del_p.K1591fs	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1602					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CTAGTAGCCCTTTTTCTTTCC	0.587																																					p.G1603fs		Atlas-INDEL	.											.	CACNA1F	218	.	0			c.4807delG						.						87	66	73					X																	49066137		2203	4300	6503	SO:0001589	frameshift_variant	778	exon41			.	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1393	protein-coding gene	gene with protein product		300110	"Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.4806delA	chrX.hg19:g.49066137delT	ENSP00000365441:p.Lys1602fs	92.0	0.0		123.0	11.0	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Frame_Shift_Del	DEL	ENST00000376265.2	hg19	CCDS35253.1																																																																																			.	.		0.587	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		-	49066137	T	-	49066137	7	5	112	1	0	1	0	1	0	0	0	0	2545	1606	56	0	1159	0	CACNA1F	23	49066137	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	402213	49066137	106204423	1214	17835										
AKAP4	8852	hgsc.bcm.edu	37	chrX	49963345	49963345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttgctgtccttctgggttgTagagatctaccttgcacaca	9	11	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:49963345T>C	ENST00000376056.2	-	2	209	c.59A>G	c.(58-60)tAc>tGc	p.Y20C	AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Missense_Mutation_p.Y20C|AKAP4_ENST00000376064.3_Missense_Mutation_p.Y20C|AKAP4_ENST00000358526.2_Missense_Mutation_p.Y29C					A kinase (PRKA) anchor protein 4											NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					TTCTGGGTTGTAGAGATCTAC	0.423																																					p.Y29C		Atlas-SNP	.											.	AKAP4	131	.	0			c.A86G						.						121	92	102					X																	49963345		2203	4300	6503	SO:0001583	missense	8852	exon2			GGGTTGTAGAGAT	AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"A-kinase anchor proteins"	374	protein-coding gene	gene with protein product	"A-kinase anchor protein 82 kDa", "testis-specific gene HI", "protein kinase A anchoring protein 4", "cancer/testis antigen 99"	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.59A>G	chrX.hg19:g.49963345T>C	ENSP00000365224:p.Tyr20Cys	79.0	0.0		118.0	7.0	NM_003886		Missense_Mutation	SNP	ENST00000376056.2	hg19	CCDS14330.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.251060	0.22880	.	.	ENSG00000147081	ENST00000376056;ENST00000376058;ENST00000358526;ENST00000376064;ENST00000448865;ENST00000437370	T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06	5.02	5.02	0.67125	.	0.000000	0.46442	D	0.000284	T	0.62502	0.2433	M	0.78801	2.425	0.25657	N	0.986043	D;D	0.76494	0.999;0.999	D;D	0.81914	0.994;0.995	T	0.58165	-0.7684	9	.	.	.	-11.9723	10.2373	0.43290	0.0:0.0:0.0:1.0	.	29;20	Q5JQC9;A6ND82	AKAP4_HUMAN;.	C	20;20;29;20;20;20	ENSP00000365224:Y20C;ENSP00000365226:Y20C;ENSP00000351327:Y29C;ENSP00000365232:Y20C;ENSP00000402403:Y20C;ENSP00000412279:Y20C	.	Y	-	2	0	AKAP4	49850085	1.000000	0.71417	0.999000	0.59377	0.052000	0.14988	3.990000	0.56965	1.683000	0.51011	0.486000	0.48141	TAC	.	.		0.423	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		C	49963345	T	C	49963345	3	2	112	1	0	0	0	0	1	0	0	0	453	1638	57	2	2498	2	AKAP4	23	49963345	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	897208	49963345	105307215	1215	17836										
SMC1A	8243	hgsc.bcm.edu	37	chrX	53407993	53407993	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atctcatccaggacgaagaaGggggctggcttgtagctggg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:53407993delG	ENST00000322213.4	-	23	3580	c.3453delC	c.(3451-3453)cccfs	p.P1151fs	SMC1A_ENST00000469129.1_5'Flank	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	1151	Ala/Asp-rich (DA-box).				DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						GGACGAAGAAGGGGGCTGGCT	0.622																																					p.F1152fs		Atlas-INDEL	.											.	SMC1A	112	.	0			c.3454delT						.						68	59	62					X																	53407993		2203	4300	6503	SO:0001589	frameshift_variant	8243	exon23			.	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"Structural maintenance of chromosomes proteins"	11111	protein-coding gene	gene with protein product		300040	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.3453delC	chrX.hg19:g.53407993delG	ENSP00000323421:p.Pro1151fs	125.0	0.0		125.0	10.0	NM_006306	O14995|Q16351|Q2M228	Frame_Shift_Del	DEL	ENST00000322213.4	hg19	CCDS14352.1																																																																																			.	.		0.622	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		-	53407993	G	-	53407993	7	5	112	1	0	1	0	1	0	0	0	0	14796	987	35	0	260	0	SMC1A	23	53407993	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	3444648	53407993	101862567	1216	17837										
TRO	7216	hgsc.bcm.edu	37	chrX	54955827	54955827	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agcaccagcactggctttggAggcatactcagcaccagtgt	11	12	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:54955827A>G	ENST00000173898.7	+	12	2782	c.2670A>G	c.(2668-2670)ggA>ggG	p.G890G	TRO_ENST00000375022.4_Intron|TRO_ENST00000319167.8_Intron|TRO_ENST00000375041.2_Silent_p.G493G|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000420798.2_Silent_p.G421G|TRO_ENST00000399736.1_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	890	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						CTGGCTTTGGAGGCATACTCA	0.547																																					p.G890G		Atlas-SNP	.											.	TRO	246	.	0			c.A2670G						.						70	63	65					X																	54955827		2102	4200	6302	SO:0001819	synonymous_variant	7216	exon12			CTTTGGAGGCATA	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.2670A>G	chrX.hg19:g.54955827A>G		145.0	0.0		119.0	5.0	NM_001039705	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Silent	SNP	ENST00000173898.7	hg19	CCDS43959.1																																																																																			.	.		0.547	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		G	54955827	A	G	54955827	2	3	112	1	0	0	0	0	0	0	0	1	16589	291	11	2		2	TRO	23	54955827	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	1547834	54955827	100314733	1217	17838										
LAS1L	81887	hgsc.bcm.edu	37	chrX	64754546	64754546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	accacgcactccacacgagaTccatcccctgggaacctaga	7	17	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:64754546T>C	ENST00000374811.3	-	1	90	c.50A>G	c.(49-51)gAt>gGt	p.D17G	LAS1L_ENST00000312391.8_Missense_Mutation_p.D17G|LAS1L_ENST00000374804.5_Missense_Mutation_p.D17G|LAS1L_ENST00000374807.5_Missense_Mutation_p.D17G	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	17					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						CCACACGAGATCCATCCCCTG	0.642																																					p.D17G		Atlas-SNP	.											.	LAS1L	72	.	0			c.A50G						.						115	77	90					X																	64754546		2198	4291	6489	SO:0001583	missense	81887	exon1			ACGAGATCCATCC	BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.50A>G	chrX.hg19:g.64754546T>C	ENSP00000363944:p.Asp17Gly	78.0	0.0		104.0	5.0	NM_031206	A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Missense_Mutation	SNP	ENST00000374811.3	hg19	CCDS14381.1	.	.	.	.	.	.	.	.	.	.	t	19.62	3.862209	0.71949	.	.	ENSG00000001497	ENST00000374807;ENST00000374811;ENST00000374804;ENST00000312391	.	.	.	4.39	4.39	0.52855	.	0.453724	0.22209	N	0.063140	T	0.53883	0.1824	L	0.32530	0.975	0.35087	D	0.763914	D;D;D	0.61080	0.964;0.964;0.989	P;P;P	0.57846	0.71;0.71;0.828	T	0.66204	-0.5982	9	0.87932	D	0	.	8.9211	0.35612	0.0:0.0:0.0:1.0	.	17;17;17	Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2	.;.;LAS1L_HUMAN	G	17	.	ENSP00000308649:D17G	D	-	2	0	LAS1L	64671271	0.998000	0.40836	0.994000	0.49952	0.838000	0.47535	1.851000	0.39338	1.928000	0.55862	0.481000	0.45027	GAT	.	.		0.642	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206		C	64754546	T	C	64754546	3	2	112	1	0	0	0	0	1	0	0	0	8645	1435	50	2	2210	2	LAS1L	23	64754546	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	9798719	64754546	90516014	1218	17839										
EDA2R	60401	hgsc.bcm.edu	37	chrX	65822591	65822591	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caacaagtgtggcctcctgaGggggcactgtgggtgtatct							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:65822591delG	ENST00000374719.3	-	5	457	c.401delC	c.(400-402)cctfs	p.P134fs	EDA2R_ENST00000253392.5_Frame_Shift_Del_p.P134fs|EDA2R_ENST00000451436.2_Frame_Shift_Del_p.P40fs|EDA2R_ENST00000450752.1_Frame_Shift_Del_p.P134fs|EDA2R_ENST00000396050.1_Frame_Shift_Del_p.P134fs|EDA2R_ENST00000456230.2_Frame_Shift_Del_p.P134fs	NM_021783.3	NP_068555	Q9HAV5	TNR27_HUMAN	ectodysplasin A2 receptor	134					cell differentiation (GO:0030154)|embryo development (GO:0009790)|epidermis development (GO:0008544)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						GGCCTCCTGAGGGGGCACTGT	0.537																																					p.P134fs		Atlas-INDEL	.											.	EDA2R	30	.	0			c.402delT						.						50	35	40					X																	65822591		2203	4299	6502	SO:0001589	frameshift_variant	60401	exon4			.	AF298812	CCDS14386.1, CCDS56603.1	Xq11.1	2013-05-22			ENSG00000131080	ENSG00000131080		"Tumor necrosis factor receptor superfamily"	17756	protein-coding gene	gene with protein product		300276				11039935	Standard	NM_021783		Approved	XEDAR, EDA-A2R, EDAA2R, TNFRSF27	uc004dwt.2	Q9HAV5	OTTHUMG00000021736	ENST00000374719.3:c.401delC	chrX.hg19:g.65822591delG	ENSP00000363851:p.Pro134fs	109.0	0.0		155.0	12.0	NM_001242310	Q5VYX9|Q5VYY0|Q6UWM2|Q8IZA6	Frame_Shift_Del	DEL	ENST00000374719.3	hg19	CCDS14386.1																																																																																			.	.		0.537	EDA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057002.1	NM_021783		-	65822591	G	-	65822591	7	5	112	1	0	1	0	1	0	0	0	0	4906	1000	35	0	500	0	EDA2R	23	65822591	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	1068045	65822591	89447969	1219	17840										
SLC7A3	84889	hgsc.bcm.edu	37	chrX	70146023	70146023	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agtgggaggagaggcaaagcAggcacctgaaaacaaagtaa	14	6	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:70146023A>G	ENST00000374299.3	-	11	1770	c.1626T>C	c.(1624-1626)ccT>ccC	p.P542P	SLC7A3_ENST00000298085.4_Silent_p.P542P			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	542					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GAGGCAAAGCAGGCACCTGAA	0.463																																					p.P542P		Atlas-SNP	.											.	SLC7A3	76	.	0			c.T1626C						.						59	49	52					X																	70146023		2203	4300	6503	SO:0001819	synonymous_variant	84889	exon11			CAAAGCAGGCACC	AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"Solute carriers"	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.1626T>C	chrX.hg19:g.70146023A>G		69.0	0.0		87.0	4.0	NM_032803	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Silent	SNP	ENST00000374299.3	hg19	CCDS14404.1																																																																																			.	.		0.463	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803		G	70146023	A	G	70146023	2	3	112	1	0	0	0	0	0	0	0	1	14713	175	7	2		2	SLC7A3	23	70146023	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	4323432	70146023	85124537	1220	17841										
MED12	9968	hgsc.bcm.edu	37	chrX	70344673	70344673	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccagtgttctctttgaggaCatggagaagcctgatttctc	10	9	2	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:70344673C>A	ENST00000374080.3	+	14	2066	c.2034C>A	c.(2032-2034)gaC>gaA	p.D678E	MED12_ENST00000374102.1_Missense_Mutation_p.D678E|MED12_ENST00000333646.6_Missense_Mutation_p.D678E			Q93074	MED12_HUMAN	mediator complex subunit 12	678					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					TCTTTGAGGACATGGAGAAGC	0.468			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.D678E		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.C2034A						.						132	112	118					X																	70344673		1943	4114	6057	SO:0001583	missense	9968	exon14			TGAGGACATGGAG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.2034C>A	chrX.hg19:g.70344673C>A	ENSP00000363193:p.Asp678Glu	89.0	0.0		100.0	4.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	hg19	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	8.615	0.889947	0.17540	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.57907	0.37;0.38;0.38;0.38	4.49	2.72	0.32119	Mediator complex, subunit Med12, LCEWAV-domain (1);	0.053172	0.85682	D	0.000000	T	0.36303	0.0962	L	0.33485	1.01	0.47214	D	0.999355	B;B;B;B	0.25048	0.002;0.117;0.005;0.007	B;B;B;B	0.25884	0.006;0.064;0.009;0.007	T	0.07158	-1.0787	10	0.11182	T	0.66	-17.6143	9.9661	0.41725	0.0:0.8301:0.0:0.1699	.	678;525;678;678	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	E	678;678;678;678;646	ENSP00000333125:D678E;ENSP00000363215:D678E;ENSP00000363193:D678E;ENSP00000414203:D646E	ENSP00000333125:D678E	D	+	3	2	MED12	70261398	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.616000	0.24344	0.378000	0.24764	0.529000	0.55759	GAC	.	.		0.468	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		A	70344673	C	A	70344673	3	1	112	1	0	0	0	0	1	0	0	0	9437	477	17	3	2088	3	MED12	23	70344673	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	198650	70344673	84925887	1221	17842										
OGT	8473	hgsc.bcm.edu	37	chrX	70781722	70781722	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	taagggcgctcgaaatgagcTttttgctctcaggccagctc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:70781722delT	ENST00000373719.3	+	15	2166	c.1949delT	c.(1948-1950)cttfs	p.L650fs	OGT_ENST00000373701.3_Frame_Shift_Del_p.L640fs	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	650					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					CGAAATGAGCTTTTTGCTCTC	0.408																																					p.L650fs		Atlas-INDEL	.											.	OGT	207	.	0			c.1948delC						.						68	59	62					X																	70781722		2203	4300	6503	SO:0001589	frameshift_variant	8473	exon15			.	U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"Tetratricopeptide (TTC) repeat domain containing"	8127	protein-coding gene	gene with protein product	"UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"	300255	"O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.1949delT	chrX.hg19:g.70781722delT	ENSP00000362824:p.Leu650fs	173.0	0.0		146.0	10.0	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Frame_Shift_Del	DEL	ENST00000373719.3	hg19	CCDS14414.1																																																																																			.	.		0.408	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		-	70781722	T	-	70781722	7	5	112	1	0	1	0	1	0	0	0	0	10856	1609	56	0	2007	0	OGT	23	70781722	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	437049	70781722	84488838	1222	17843										
ACRC	93953	hgsc.bcm.edu	37	chrX	70800684	70800684	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ctacagacatggatgggtgcAaaaaagagctgccccgcttg							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:70800684delA	ENST00000373695.1	+	1	550	c.13delA	c.(13-15)aaafs	p.K6fs	ACRC_ENST00000373696.3_Frame_Shift_Del_p.K6fs			Q96QF7	ACRC_HUMAN	acidic repeat containing	6						nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1)	54	Renal(35;0.156)					GGATGGGTGCAAAAAAGAGCT	0.468																																					p.C4X		Atlas-INDEL	.											.	ACRC	110	.	0			c.12delC						.						143	130	134					X																	70800684		2203	4299	6502	SO:0001589	frameshift_variant	93953	exon2			.	AJ311392	CCDS35326.1	Xq13.1	2010-08-05			ENSG00000147174	ENSG00000147174			15805	protein-coding gene	gene with protein product		300369					Standard	NM_052957		Approved		uc004eae.2	Q96QF7	OTTHUMG00000033327	ENST00000373695.1:c.13delA	chrX.hg19:g.70800684delA	ENSP00000362799:p.Lys6fs	215.0	0.0		238.0	17.0	NM_052957	B9EG62	Frame_Shift_Del	DEL	ENST00000373695.1	hg19	CCDS35326.1																																																																																			.	.		0.468	ACRC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081856.1			-	70800684	A	-	70800684	7	5	112	1	0	1	0	1	0	0	0	0	171	131	5	0	15	0	ACRC	23	70800684	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	18962	70800684	84469876	1223	17844										
PIN4	5303	hgsc.bcm.edu	37	chrX	71401650	71401650	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tccaagatgccgcccaaaggAaaaagtggttctggaaaagc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:71401650delA	ENST00000373669.2	+	1	122	c.90delA	c.(88-90)ggafs	p.G30fs	PIN4_ENST00000218432.5_Frame_Shift_Del_p.G30fs|PIN4_ENST00000423432.2_Frame_Shift_Del_p.G30fs	NM_006223.3	NP_006214.2	Q9Y237	PIN4_HUMAN	protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)	5	Necessary for association with the pre- rRNP complexes.				protein folding (GO:0006457)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome (GO:0030684)|spindle (GO:0005819)	bent DNA binding (GO:0003681)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(2)	3	Renal(35;0.156)					CGCCCAAAGGAAAAAGTGGTT	0.557																																					p.G30fs		Atlas-INDEL	.											.	PIN4	8	.	0			c.89delG						.						42	35	38					X																	71401650		2203	4300	6503	SO:0001589	frameshift_variant	5303	exon1			.	AB009690	CCDS14417.1, CCDS55447.1	Xq13.1	2008-02-05	2006-01-12		ENSG00000102309	ENSG00000102309			8992	protein-coding gene	gene with protein product		300252	"protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)"			16522211, 17875217	Standard	NM_006223		Approved	PAR14, PAR17, EPVH	uc004eam.3	Q9Y237	OTTHUMG00000021811	ENST00000373669.2:c.90delA	chrX.hg19:g.71401650delA	ENSP00000362773:p.Gly30fs	152.0	0.0		180.0	11.0	NM_001170747	A8E0G6|B3KXM0|F5H1P5|Q0D2H3|Q3MHV0|Q52M21|Q5HYW6|Q6IRW4	Frame_Shift_Del	DEL	ENST00000373669.2	hg19	CCDS14417.1																																																																																			.	.		0.557	PIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057175.2	NM_006223		-	71401650	A	-	71401650	7	5	112	1	0	1	0	1	0	0	0	0	11940	233	9	0	92	0	PIN4	23	71401650	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	600966	71401650	83868910	1224	17845										
PHKA1	5255	hgsc.bcm.edu	37	chrX	71873287	71873287	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tggcactgtctgactcacccTgtcaggaggaacactgtaca	10	12	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:71873287T>C	ENST00000373542.4	-	11	1294	c.1135A>G	c.(1135-1137)Agg>Ggg	p.R379G	PHKA1_ENST00000339490.3_Missense_Mutation_p.R379G|PHKA1_ENST00000373545.3_Missense_Mutation_p.R379G|PHKA1_ENST00000373539.3_Missense_Mutation_p.R379G|PHKA1_ENST00000541944.1_Missense_Mutation_p.R379G	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	379					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					TGACTCACCCTGTCAGGAGGA	0.428																																					p.R379G		Atlas-SNP	.											.	PHKA1	129	.	0			c.A1135G						.						81	65	70					X																	71873287		2203	4300	6503	SO:0001583	missense	5255	exon11			TCACCCTGTCAGG		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.1135A>G	chrX.hg19:g.71873287T>C	ENSP00000362643:p.Arg379Gly	88.0	0.0		85.0	4.0	NM_001172436	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	T	15.44	2.833627	0.50951	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68;-2.68	5.08	5.08	0.68730	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.047373	0.85682	D	0.000000	D	0.84284	0.5438	L	0.29908	0.895	0.41772	D	0.989773	B;B;B	0.22851	0.03;0.014;0.076	B;B;B	0.25759	0.027;0.023;0.063	T	0.79626	-0.1725	10	0.24483	T	0.36	-19.5286	11.8025	0.52135	0.0:0.0:0.0:1.0	.	379;379;379	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	G	379	ENSP00000362646:R379G;ENSP00000362643:R379G;ENSP00000441251:R379G;ENSP00000342469:R379G;ENSP00000362640:R379G	ENSP00000342469:R379G	R	-	1	2	PHKA1	71790012	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	5.416000	0.66417	1.688000	0.51068	0.430000	0.28490	AGG	.	.		0.428	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			C	71873287	T	C	71873287	3	2	112	1	0	0	0	0	1	0	0	0	11852	1579	55	2	2624	2	PHKA1	23	71873287	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	471637	71873287	83397273	1225	17846										
ATP7A	538	hgsc.bcm.edu	37	chrX	77245318	77245318	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctattgagggtgtcatatcAaaaaagccaggtgtaaaatc					rs398123133		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:77245318delA	ENST00000341514.6	+	4	1355	c.1200delA	c.(1198-1200)tcafs	p.S400fs	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Frame_Shift_Del_p.S400fs	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	400	HMA 4. {ECO:0000255|PROSITE- ProRule:PRU00280}.				blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	GTGTCATATCAAAAAAGCCAG	0.423																																					p.S400X		Atlas-INDEL	.											.	ATP7A	248	.	0			c.1199delC						.						140	130	134					X																	77245318		2203	4296	6499	SO:0001589	frameshift_variant	538	exon4			.	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.1200delA	chrX.hg19:g.77245318delA	ENSP00000345728:p.Ser400fs	143.0	0.0		186.0	12.0	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Frame_Shift_Del	DEL	ENST00000341514.6	hg19	CCDS35339.1																																																																																			.	.		0.423	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		-	77245318	A	-	77245318	7	5	112	1	0	1	0	1	0	0	0	0	1190	117	5	0	1210	0	ATP7A	23	77245318	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	5372031	77245318	78025242	1226	17847										
RPS6KA6	27330	hgsc.bcm.edu	37	chrX	83374999	83374999	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacaaaatgagtaagccttcTtttcttgatctactgactcc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:83374999delT	ENST00000262752.2	-	9	690	c.683delA	c.(682-684)aagfs	p.K229fs	RPS6KA6_ENST00000543399.1_Frame_Shift_Del_p.K229fs	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	229	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						GTAAGCCTTCTTTTCTTGATC	0.373																																					p.K228fs		Atlas-INDEL	.											.	RPS6KA6	116	.	0			c.684delG						.						95	82	86					X																	83374999		2203	4300	6503	SO:0001589	frameshift_variant	27330	exon9			.	AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.683delA	chrX.hg19:g.83374999delT	ENSP00000262752:p.Lys229fs	165.0	0.0		166.0	10.0	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Frame_Shift_Del	DEL	ENST00000262752.2	hg19	CCDS14451.1																																																																																			.	.		0.373	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		-	83374999	T	-	83374999	7	5	112	1	0	1	0	1	0	0	0	0	13670	1609	56	0	1610	0	RPS6KA6	23	83374999	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	6129681	83374999	71895561	1227	17848										
HDX	139324	hgsc.bcm.edu	37	chrX	83577009	83577009	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cctctaattcaggaggtaaaTctgacagcagtgcctgaata	9	9	3	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:83577009T>C	ENST00000297977.5	-	10	2072	c.1961A>G	c.(1960-1962)gAt>gGt	p.D654G	HDX_ENST00000373177.2_Missense_Mutation_p.D654G|HDX_ENST00000506585.2_Missense_Mutation_p.D596G	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	654						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						AGGAGGTAAATCTGACAGCAG	0.348																																					p.D654G	Pancreas(53;231 1169 36156 43751 51139)	Atlas-SNP	.											.	HDX	124	.	0			c.A1961G						.						55	45	48					X																	83577009		2203	4298	6501	SO:0001583	missense	139324	exon10			GGTAAATCTGACA	BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"Homeoboxes / POU class"	26411	protein-coding gene	gene with protein product			"chromosome X open reading frame 43"	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.1961A>G	chrX.hg19:g.83577009T>C	ENSP00000297977:p.Asp654Gly	109.0	0.0		97.0	4.0	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	hg19	CCDS35342.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.571720	0.45798	.	.	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.32988	1.45;1.43;1.45	5.52	5.52	0.82312	.	0.201705	0.52532	D	0.000074	T	0.26810	0.0656	L	0.27053	0.805	0.46631	D	0.999133	B	0.29531	0.247	B	0.33392	0.163	T	0.08411	-1.0723	10	0.72032	D	0.01	-21.2483	14.6824	0.69028	0.0:0.0:0.0:1.0	.	654	Q7Z353	HDX_HUMAN	G	654;596;654	ENSP00000297977:D654G;ENSP00000362272:D596G;ENSP00000423670:D654G	ENSP00000297977:D654G	D	-	2	0	HDX	83463665	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.322000	0.65852	1.848000	0.53677	0.486000	0.48141	GAT	.	.		0.348	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		C	83577009	T	C	83577009	3	2	112	1	0	0	0	0	1	0	0	0	7035	1435	50	2	115	2	HDX	23	83577009	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	202010	83577009	71693551	1228	17849										
APOOL	139322	hgsc.bcm.edu	37	chrX	84306506	84306506	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	caactggttgttacattggcTggtgcaaggtaagtcaattc	11	7	1	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:84306506T>G	ENST00000373173.2	+	3	319	c.232T>G	c.(232-234)Tgg>Ggg	p.W78G		NM_198450.5	NP_940852.3	Q6UXV4	MIC27_HUMAN	apolipoprotein O-like	78						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8						TTACATTGGCTGGTGCAAGGT	0.403																																					p.W78G		Atlas-SNP	.											.	APOOL	20	.	0			c.T232G						.						82	73	76					X																	84306506		1869	4098	5967	SO:0001583	missense	139322	exon3			ATTGGCTGGTGCA	AK130506	CCDS48138.1	Xq21.1	2007-01-17	2007-01-17	2007-01-17	ENSG00000155008	ENSG00000155008			24009	protein-coding gene	gene with protein product			"chromosome X open reading frame 33", "family with sequence similarity 121A"	CXorf33, FAM121A		12975309	Standard	NM_198450		Approved	UNQ8193, AAIR8193	uc004eem.3	Q6UXV4	OTTHUMG00000021930	ENST00000373173.2:c.232T>G	chrX.hg19:g.84306506T>G	ENSP00000362268:p.Trp78Gly	67.0	0.0		73.0	4.0	NM_198450	Q3KNU7|Q5H9D1	Missense_Mutation	SNP	ENST00000373173.2	hg19	CCDS48138.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.907132	0.33628	.	.	ENSG00000155008	ENST00000373173;ENST00000373169	.	.	.	4.36	4.36	0.52297	.	0.192534	0.47455	D	0.000225	T	0.59376	0.2189	M	0.69463	2.115	0.43448	D	0.995632	P	0.48162	0.906	P	0.50754	0.649	T	0.56798	-0.7919	9	0.15952	T	0.53	-29.2283	8.5823	0.33637	0.0:0.0:0.1916:0.8084	.	78	Q6UXV4	APOOL_HUMAN	G	78	.	ENSP00000362264:W78G	W	+	1	0	APOOL	84193162	1.000000	0.71417	0.998000	0.56505	0.483000	0.33249	2.022000	0.41030	1.610000	0.50200	0.481000	0.45027	TGG	.	.		0.403	APOOL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057385.2	NM_198450		G	84306506	T	G	84306506	3	3	112	1	0	0	0	0	1	0	0	0	814	1580	55	5	242	5	APOOL	23	84306506	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	729497	84306506	70964054	1229	17850										
DIAPH2	1730	hgsc.bcm.edu	37	chrX	96396689	96396689	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	agatactaaatcagcggatcAaaaaacaacccttttgcatt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:96396689delA	ENST00000324765.8	+	22	2962	c.2615delA	c.(2614-2616)caafs	p.Q872fs	DIAPH2_ENST00000373049.4_Frame_Shift_Del_p.Q872fs|DIAPH2_ENST00000355827.4_Frame_Shift_Del_p.Q872fs|DIAPH2_ENST00000373061.3_Frame_Shift_Del_p.Q872fs|DIAPH2_ENST00000373054.4_Frame_Shift_Del_p.Q868fs			O60879	DIAP2_HUMAN	diaphanous-related formin 2	872	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						TCAGCGGATCAAAAAACAACC	0.313																																					p.Q872fs		Atlas-INDEL	.											.	DIAPH2	148	.	0			c.2614delC						.						64	57	59					X																	96396689		2203	4300	6503	SO:0001589	frameshift_variant	1730	exon22			.	Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"diaphanous (Drosophila, homolog) 2", "diaphanous homolog 2 (Drosophila)"			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.2615delA	chrX.hg19:g.96396689delA	ENSP00000321348:p.Gln872fs	158.0	0.0		148.0	11.0	NM_007309	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Frame_Shift_Del	DEL	ENST00000324765.8	hg19	CCDS14467.1																																																																																			.	.		0.313	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		-	96396689	A	-	96396689	7	5	112	1	0	1	0	1	0	0	0	0	4521	130	5	0	2701	0	DIAPH2	23	96396689	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	12090183	96396689	58873871	1230	17851										
CSTF2	1478	hgsc.bcm.edu	37	chrX	100078882	100078882	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttatcttctcagctctgtgTccagaatagtccccaggagg	9	12	3	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:100078882T>C	ENST00000372972.2	+	5	468	c.452T>C	c.(451-453)gTc>gCc	p.V151A	SNORA9_ENST00000365361.1_RNA|CSTF2_ENST00000415585.2_Missense_Mutation_p.V151A	NM_001325.2	NP_001316.1	P33240	CSTF2_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa	151	Interactions with CSTF3 and SYMPK.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cleavage body (GO:0071920)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	13						CAGCTCTGTGTCCAGAATAGT	0.428																																					p.V151A		Atlas-SNP	.											.	CSTF2	47	.	0			c.T452C						.						131	112	119					X																	100078882		2203	4300	6503	SO:0001583	missense	1478	exon5			TCTGTGTCCAGAA	BC017712	CCDS14473.1	Xq22.1	2013-02-12	2002-08-29		ENSG00000101811	ENSG00000101811		"RNA binding motif (RRM) containing"	2484	protein-coding gene	gene with protein product		300907	"cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kD"			1741396	Standard	XM_006724622		Approved		uc004egh.3	P33240	OTTHUMG00000022709	ENST00000372972.2:c.452T>C	chrX.hg19:g.100078882T>C	ENSP00000362063:p.Val151Ala	53.0	0.0		74.0	4.0	NM_001325	Q5H951|Q6LA74|Q8N502	Missense_Mutation	SNP	ENST00000372972.2	hg19	CCDS14473.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.712235	0.68730	.	.	ENSG00000101811	ENST00000415585;ENST00000372972;ENST00000458320;ENST00000413437	T;T;T	0.14640	2.67;2.72;2.49	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.21347	0.0514	L	0.35414	1.06	0.80722	D	1	B;D;B	0.53619	0.351;0.961;0.351	B;P;B	0.58454	0.444;0.839;0.262	T	0.03566	-1.1024	10	0.20046	T	0.44	-11.164	14.5729	0.68224	0.0:0.0:0.0:1.0	.	151;151;151	E7EWR4;P33240-2;P33240	.;.;CSTF2_HUMAN	A	151;151;151;142	ENSP00000387996:V151A;ENSP00000362063:V151A;ENSP00000415705:V142A	ENSP00000362063:V151A	V	+	2	0	CSTF2	99965538	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.440000	0.80464	1.822000	0.53115	0.486000	0.48141	GTC	.	.		0.428	CSTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058926.1	NM_001325		C	100078882	T	C	100078882	3	2	112	1	0	0	0	0	1	0	0	0	3986	1667	58	2	470	2	CSTF2	23	100078882	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	3682193	100078882	55191678	1231	17852										
TCEAL6	158931	hgsc.bcm.edu	37	chrX	101395773	101395773	+	Missense_Mutation	SNP	G	G	T													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cactcccctgacaccccgttGtccccttgggcgaatggatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:101395773G>T	ENST00000372774.3	-	3	780	c.531C>A	c.(529-531)gaC>gaA	p.D177E	TCEAL6_ENST00000372773.1_Missense_Mutation_p.D177E	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						ACACCCCGTTGTCCCCTTGGG	0.502																																					p.D177E		Atlas-SNP	.											.	TCEAL6	27	.	0			c.C531A						.						22	21	21					X																	101395773		2197	4275	6472	SO:0001583	missense	158931	exon3			CCCGTTGTCCCCT	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.531C>A	chrX.hg19:g.101395773G>T	ENSP00000361860:p.Asp177Glu	79.0	0.0		143.0	6.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.032|0.032	-1.327438|-1.327438	0.01309|0.01309	.|.	.|.	ENSG00000204071|ENSG00000204071	ENST00000372774;ENST00000372773|ENST00000536102	T;T|.	0.21191|.	2.02;2.02|.	2.82|2.82	2.82|2.82	0.32997|0.32997	.|.	0.272209|.	0.20313|.	N|.	0.094788|.	T|T	0.20455|0.20455	0.0492|0.0492	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B|.	0.16396|.	0.017|.	B|.	0.13407|.	0.009|.	T|T	0.20638|0.20638	-1.0269|-1.0269	10|6	0.22706|0.06236	T|T	0.39|0.91	.|.	8.3639|8.3639	0.32374|0.32374	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	177|.	Q6IPX3-2|.	.|.	E|K	177|177	ENSP00000361860:D177E;ENSP00000361859:D177E|.	ENSP00000361859:D177E|ENSP00000437364:Q177K	D|Q	-|-	3|1	2|0	TCEAL6|TCEAL6	101282429|101282429	0.014000|0.014000	0.17966|0.17966	0.012000|0.012000	0.15200|0.15200	0.864000|0.864000	0.49448|0.49448	2.835000|2.835000	0.48175|0.48175	1.692000|1.692000	0.51112|0.51112	0.468000|0.468000	0.43344|0.43344	GAC|CAA	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938		T	101395773	G	T	101395773	3	4	112	1	0	0	0	0	1	0	0	0	15690	1368	48	3	24	3	TCEAL6	23	101395773	Missense_Mutation	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	1316891	101395773	53874787	1232	17853	80	3								
TCEAL6	158931	hgsc.bcm.edu	37	chrX	101395778	101395778	+	Missense_Mutation	SNP	C	C	T													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccctgacaccccgttgtcccCttgggcgaatggatcctgta							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:101395778C>T	ENST00000372774.3	-	3	775	c.526G>A	c.(526-528)Ggg>Agg	p.G176R	TCEAL6_ENST00000372773.1_Missense_Mutation_p.G176R	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						CCGTTGTCCCCTTGGGCGAAT	0.502																																					p.G176R		Atlas-SNP	.											.	TCEAL6	27	.	0			c.G526A						.						13	13	13					X																	101395778		2197	4251	6448	SO:0001583	missense	158931	exon3			TGTCCCCTTGGGC	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.526G>A	chrX.hg19:g.101395778C>T	ENSP00000361860:p.Gly176Arg	74.0	0.0		140.0	19.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.605|9.605	1.129729|1.129729	0.21041|0.21041	.|.	.|.	ENSG00000204071|ENSG00000204071	ENST00000372774;ENST00000372773|ENST00000536102	T;T|.	0.40225|.	1.04;1.04|.	2.82|2.82	2.82|2.82	0.32997|0.32997	.|.	0.000000|.	0.39341|.	N|.	0.001392|.	T|T	0.27832|0.27832	0.0685|0.0685	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	D|.	0.57257|.	0.979|.	P|.	0.56563|.	0.801|.	T|T	0.22243|0.22243	-1.0222|-1.0222	10|6	0.54805|0.06365	T|T	0.06|0.9	.|.	8.3639|8.3639	0.32374|0.32374	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	176|.	Q6IPX3-2|.	.|.	R|K	176|175	ENSP00000361860:G176R;ENSP00000361859:G176R|.	ENSP00000361859:G176R|ENSP00000437364:R175K	G|R	-|-	1|2	0|0	TCEAL6|TCEAL6	101282434|101282434	0.007000|0.007000	0.16637|0.16637	0.089000|0.089000	0.20774|0.20774	0.743000|0.743000	0.42351|0.42351	1.059000|1.059000	0.30517|0.30517	1.692000|1.692000	0.51112|0.51112	0.468000|0.468000	0.43344|0.43344	GGG|AGG	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938		T	101395778	C	T	101395778	3	4	112	1	0	0	0	0	1	0	0	0	15690	681	24	3	29	3	TCEAL6	23	101395778	Missense_Mutation	SNP	C	TCGA-DD-A39Y-01A-11D-A20W-10	5	101395778	53874782	1233	17854	80	3								
TCEAL6	158931	hgsc.bcm.edu	37	chrX	101395786	101395786	+	Missense_Mutation	SNP	A	A	G													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccccgttgtccccttgggcgAatggatcctgtacatctctt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:101395786A>G	ENST00000372774.3	-	3	767	c.518T>C	c.(517-519)tTc>tCc	p.F173S	TCEAL6_ENST00000372773.1_Missense_Mutation_p.F173S	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	173					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						CCCTTGGGCGAATGGATCCTG	0.502																																					p.F173S		Atlas-SNP	.											.	TCEAL6	27	.	0			c.T518C						.						18	16	17					X																	101395786		2188	4247	6435	SO:0001583	missense	158931	exon3			TGGGCGAATGGAT	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.518T>C	chrX.hg19:g.101395786A>G	ENSP00000361860:p.Phe173Ser	89.0	0.0		165.0	7.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.	.	.	.	.	.	.	.	.	.	A	11.02	1.514968	0.27123	.	.	ENSG00000204071	ENST00000372774;ENST00000372773;ENST00000536102	T;T	0.10288	2.89;2.89	2.82	1.57	0.23409	.	0.407517	0.18158	N	0.149877	T	0.23965	0.0580	M	0.65498	2.005	0.09310	N	1	D	0.76494	0.999	D	0.80764	0.994	T	0.04495	-1.0947	10	0.87932	D	0	.	4.5124	0.11917	0.7069:0.0:0.0:0.2931	.	173	Q6IPX3-2	.	S	173	ENSP00000361860:F173S;ENSP00000361859:F173S	ENSP00000361859:F173S	F	-	2	0	TCEAL6	101282442	0.004000	0.15560	0.001000	0.08648	0.524000	0.34500	1.362000	0.34148	0.327000	0.23409	0.381000	0.24937	TTC	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938		G	101395786	A	G	101395786	3	3	112	1	0	0	0	0	1	0	0	0	15690	246	9	2	37	2	TCEAL6	23	101395786	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	8	101395786	53874774	1234	17855	80	3								
GPRASP2	114928	hgsc.bcm.edu	37	chrX	101970497	101970497	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cagatgagacctctacagcgTcttctttctggactggagaa	10	10	4	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:101970497T>C	ENST00000535209.1	+	4	1531	c.700T>C	c.(700-702)Tct>Cct	p.S234P	GPRASP2_ENST00000332262.5_Missense_Mutation_p.S234P|GPRASP2_ENST00000543253.1_Missense_Mutation_p.S234P			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	234						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						CTCTACAGCGTCTTCTTTCTG	0.532																																					p.S234P		Atlas-SNP	.											.	GPRASP2	89	.	0			c.T700C						.						90	97	94					X																	101970497		2203	4299	6502	SO:0001583	missense	114928	exon4			ACAGCGTCTTCTT	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"Armadillo repeat containing"	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.700T>C	chrX.hg19:g.101970497T>C	ENSP00000437394:p.Ser234Pro	92.0	0.0		79.0	4.0	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	hg19	CCDS14501.1	.	.	.	.	.	.	.	.	.	.	T	10.33	1.319545	0.23994	.	.	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.25085	1.82;1.82;1.82	5.05	3.88	0.44766	.	0.144862	0.32753	N	0.005700	T	0.19327	0.0464	L	0.52126	1.63	0.19775	N	0.999954	B	0.25904	0.137	B	0.21151	0.033	T	0.20739	-1.0266	10	0.19147	T	0.46	.	6.8718	0.24125	0.0:0.1088:0.0:0.8912	.	234	Q96D09	GASP2_HUMAN	P	234	ENSP00000437872:S234P;ENSP00000437394:S234P;ENSP00000339057:S234P	ENSP00000339057:S234P	S	+	1	0	GPRASP2	101857153	0.689000	0.27690	0.052000	0.19188	0.002000	0.02628	0.707000	0.25704	0.815000	0.34398	0.486000	0.48141	TCT	.	.		0.532	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		C	101970497	T	C	101970497	3	2	112	1	0	0	0	0	1	0	0	0	6732	1667	58	2	702	2	GPRASP2	23	101970497	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	574711	101970497	53300063	1235	17856										
TCEAL4	79921	hgsc.bcm.edu	37	chrX	102841728	102841728	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tctggaagacaagaagttagAaaacgagggaaagacagaaa							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:102841728delA	ENST00000472745.1	+	3	677	c.125delA	c.(124-126)gaafs	p.E42fs	TCEAL4_ENST00000415568.2_Frame_Shift_Del_p.E42fs|TCEAL4_ENST00000472484.1_Frame_Shift_Del_p.E42fs|TCEAL4_ENST00000372629.4_Frame_Shift_Del_p.E185fs|TCEAL4_ENST00000468024.1_Frame_Shift_Del_p.E42fs|TCEAL4_ENST00000494801.1_Frame_Shift_Del_p.E42fs			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	42	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|skin(2)	6						AAGAAGTTagaaaacgaggga	0.423																																					p.E42fs		Atlas-INDEL	.											.	TCEAL4	18	.	0			c.124delG						.						87	88	88					X																	102841728		2187	4286	6473	SO:0001589	frameshift_variant	79921	exon3			.	AF314542	CCDS14510.2, CCDS76004.1	Xq22.2	2014-03-21			ENSG00000133142	ENSG00000133142			26121	protein-coding gene	gene with protein product						14702039, 16221301	Standard	XM_005262192		Approved	FLJ21174, WEX7	uc004ekn.3	Q96EI5	OTTHUMG00000022103	ENST00000472745.1:c.125delA	chrX.hg19:g.102841728delA	ENSP00000424314:p.Glu42fs	115.0	0.0		142.0	10.0	NM_001006935	Q8WY12|Q9H2H1|Q9H775	Frame_Shift_Del	DEL	ENST00000472745.1	hg19	CCDS14510.2																																																																																			.	.		0.423	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863		-	102841728	A	-	102841728	7	5	112	1	0	1	0	1	0	0	0	0	15688	246	9	0	127	0	TCEAL4	23	102841728	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	871231	102841728	52428832	1236	17857										
NRK	203447	hgsc.bcm.edu	37	chrX	105153617	105153617	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	actcaaagccacttggtccgTtgcaaaccctgatggaaaat	8	11	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:105153617T>C	ENST00000243300.9	+	13	2287	c.1984T>C	c.(1984-1986)Ttg>Ctg	p.L662L	NRK_ENST00000428173.2_Silent_p.L663L	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	662					activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						ACTTGGTCCGTTGCAAACCCT	0.453										HNSCC(51;0.14)																											p.L662L		Atlas-SNP	.											.	NRK	321	.	0			c.T1984C						.						37	34	35					X																	105153617		1884	4089	5973	SO:0001819	synonymous_variant	203447	exon13			GGTCCGTTGCAAA	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.1984T>C	chrX.hg19:g.105153617T>C		73.0	0.0		100.0	4.0	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Silent	SNP	ENST00000243300.9	hg19																																																																																				.	.		0.453	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		C	105153617	T	C	105153617	2	2	112	1	0	0	0	0	0	0	0	1	10664	1722	60	2		2	NRK	23	105153617	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2311889	105153617	50116943	1237	17858										
TBC1D8B	54885	hgsc.bcm.edu	37	chrX	106116905	106116905	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttgtaaccagccttttactcAggatggaagaagttggaagg	12	6	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:106116905A>G	ENST00000357242.5	+	21	3247	c.3073A>G	c.(3073-3075)Agg>Ggg	p.R1025G	TBC1D8B_ENST00000276175.3_Missense_Mutation_p.R1019G	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	1025							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CCTTTTACTCAGGATGGAAGA	0.413																																					p.R1025G		Atlas-SNP	.											.	TBC1D8B	181	.	0			c.A3073G						.						135	131	132					X																	106116905		2203	4300	6503	SO:0001583	missense	54885	exon21			TTACTCAGGATGG	AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"EF-hand domain containing"	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.3073A>G	chrX.hg19:g.106116905A>G	ENSP00000349781:p.Arg1025Gly	94.0	0.0		112.0	5.0	NM_017752	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Missense_Mutation	SNP	ENST00000357242.5	hg19	CCDS14522.1	.	.	.	.	.	.	.	.	.	.	A	10.21	1.287530	0.23478	.	.	ENSG00000133138	ENST00000357242;ENST00000276175	T;T	0.09350	2.99;2.99	5.72	4.51	0.55191	.	0.310822	0.31976	N	0.006768	T	0.14485	0.0350	M	0.68317	2.08	0.35764	D	0.820377	B	0.26147	0.143	B	0.29524	0.103	T	0.08106	-1.0738	10	0.62326	D	0.03	-4.3801	10.1722	0.42917	0.6919:0.3081:0.0:0.0	.	1025	Q0IIM8	TBC8B_HUMAN	G	1025;1019	ENSP00000349781:R1025G;ENSP00000276175:R1019G	ENSP00000276175:R1019G	R	+	1	2	TBC1D8B	106003561	1.000000	0.71417	0.999000	0.59377	0.119000	0.20118	2.883000	0.48554	1.917000	0.55516	0.481000	0.45027	AGG	.	.		0.413	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752		G	106116905	A	G	106116905	3	3	112	1	0	0	0	0	1	0	0	0	15641	179	7	2	3221	2	TBC1D8B	23	106116905	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	963288	106116905	49153655	1238	17859										
GUCY2F	2986	hgsc.bcm.edu	37	chrX	108691369	108691369	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aattctattgggtcctttgaTcaactggattttatttatac	6	6	2	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:108691369T>C	ENST00000218006.2	-	6	1789	c.1498A>G	c.(1498-1500)Atc>Gtc	p.I500V		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	500					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						GGTCCTTTGATCAACTGGATT	0.423																																					p.I500V		Atlas-SNP	.											.	GUCY2F	178	.	0			c.A1498G						.						135	115	121					X																	108691369		2203	4300	6503	SO:0001583	missense	2986	exon6			CTTTGATCAACTG	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.1498A>G	chrX.hg19:g.108691369T>C	ENSP00000218006:p.Ile500Val	45.0	0.0		52.0	5.0	NM_001522	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	hg19	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	T	1.509	-0.550103	0.03996	.	.	ENSG00000101890	ENST00000218006	T	0.77620	-1.11	4.38	3.23	0.37069	.	0.187646	0.46145	D	0.000310	T	0.39860	0.1094	N	0.00554	-1.385	0.34113	D	0.663265	B	0.06786	0.001	B	0.09377	0.004	T	0.33007	-0.9885	10	0.16420	T	0.52	.	5.1422	0.14965	0.0:0.2326:0.0:0.7674	.	500	P51841	GUC2F_HUMAN	V	500	ENSP00000218006:I500V	ENSP00000218006:I500V	I	-	1	0	GUCY2F	108578025	0.994000	0.37717	1.000000	0.80357	0.982000	0.71751	0.993000	0.29680	0.803000	0.34113	0.486000	0.48141	ATC	.	.		0.423	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		C	108691369	T	C	108691369	3	2	112	1	0	0	0	0	1	0	0	0	6907	1435	50	2	1884	2	GUCY2F	23	108691369	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	2574464	108691369	46579191	1239	17860										
DCX	1641	hgsc.bcm.edu	37	chrX	110574142	110574142	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagcactcaccgtcttggtcGttacctgagtcagctggaga	12	11	3	2	rs371447966		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:110574142G>T	ENST00000338081.3	-	5	1346				DCX_ENST00000356915.2_Missense_Mutation_p.N312K|DCX_ENST00000371993.2_Intron|DCX_ENST00000496551.1_5'UTR|DCX_ENST00000488120.1_Intron|DCX_ENST00000356220.3_Missense_Mutation_p.N312K	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin						axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						CGTCTTGGTCGTTACCTGAGT	0.522																																					p.N312K		Atlas-SNP	.											.	DCX	158	.	0			c.C936A						.						322	256	279					X																	110574142		2203	4300	6503	SO:0001627	intron_variant	1641	exon5			TTGGTCGTTACCT	AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"doublecortex"	300121	"doublecortex; lissencephaly, X-linked (doublecortin)"			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.1174+4C>A	chrX.hg19:g.110574142G>T		87.0	0.0		109.0	72.0	NM_001195553	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Missense_Mutation	SNP	ENST00000338081.3	hg19	CCDS14556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.65|14.65	2.600082|2.600082	0.46318|0.46318	.|.	.|.	ENSG00000077279|ENSG00000077279	ENST00000356915;ENST00000356220|ENST00000358070	T;T|.	0.21543|.	2.0;2.0|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.256890|.	0.31797|.	N|.	0.007046|.	T|T	0.40670|0.40670	0.1126|0.1126	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	D|D	1|1	P|.	0.35401|.	0.499|.	B|.	0.31442|.	0.13|.	T|T	0.30238|0.30238	-0.9985|-0.9985	10|5	0.06236|.	T|.	0.91|.	.|.	11.7176|11.7176	0.51663|0.51663	0.0827:0.0:0.9173:0.0|0.0827:0.0:0.9173:0.0	.|.	381|.	B4DM53|.	.|.	K|K	312|385	ENSP00000349385:N312K;ENSP00000348553:N312K|.	ENSP00000348553:N312K|.	N|T	-|-	3|2	2|0	DCX|DCX	110460798|110460798	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.209000|4.209000	0.58493|0.58493	2.238000|2.238000	0.73509|0.73509	0.594000|0.594000	0.82650|0.82650	AAC|ACG	.	.		0.522	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153		T	110574142	G	T	110574142	1	4	112	0	1	0	0	0	0	0	0	0	4320	1136	40	1		1	DCX	23	110574142	Intron	SNP	G	TCGA-DD-A39Y-01A-11D-A20W-10	1882773	110574142	44696418	1240	17861										
LUZP4	51213	hgsc.bcm.edu	37	chrX	114536631	114536631	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ataaaagacagaaccatagtAaaaaggaatcgccttcaaga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:114536631delA	ENST00000371920.3	+	2	173	c.166delA	c.(166-168)aaafs	p.K57fs	LUZP4_ENST00000451986.2_Frame_Shift_Del_p.V13fs	NM_016383.3	NP_057467.1	Q9P127	LUZP4_HUMAN	leucine zipper protein 4	57						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	14						GAACCATAGTAAAAAGGAATC	0.348																																					p.S55fs		Atlas-INDEL	.											.	LUZP4	51	.	0			c.165delT						.						145	136	139					X																	114536631		2203	4300	6503	SO:0001589	frameshift_variant	51213	exon2			.	AF124430	CCDS14567.1	Xq24	2009-03-25			ENSG00000102021	ENSG00000102021			24971	protein-coding gene	gene with protein product	"cancer/testis antigen 28"	300616				12032826, 11051238	Standard	XM_005268343		Approved	HOM-TES-85, CT-8, CT28	uc004eqa.3	Q9P127	OTTHUMG00000022234	ENST00000371920.3:c.166delA	chrX.hg19:g.114536631delA	ENSP00000360988:p.Lys57fs	184.0	0.0		185.0	12.0	NM_016383	B3KSD6	Frame_Shift_Del	DEL	ENST00000371920.3	hg19	CCDS14567.1																																																																																			.	.		0.348	LUZP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057972.1	NM_016383		-	114536631	A	-	114536631	7	5	112	1	0	1	0	1	0	0	0	0	9097	363	13	0	172	0	LUZP4	23	114536631	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	3962489	114536631	40733929	1241	17862										
SLC6A14	11254	hgsc.bcm.edu	37	chrX	115573885	115573885	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tacaatggtcctgatctccaTttttgtgacaatctattaca							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:115573885delT	ENST00000371900.4	+	4	465	c.377delT	c.(376-378)attfs	p.I126fs		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	126					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CTGATCTCCATTTTTGTGACA	0.299																																					p.I126fs		Atlas-INDEL	.											.	SLC6A14	56	.	0			c.376delA						.						139	133	135					X																	115573885		2203	4299	6502	SO:0001589	frameshift_variant	11254	exon4			.	AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"Solute carriers"	11047	protein-coding gene	gene with protein product		300444	"solute carrier family 6 (neurotransmitter transporter), member 14"			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.377delT	chrX.hg19:g.115573885delT	ENSP00000360967:p.Ile126fs	104.0	0.0		121.0	10.0	NM_007231	Q5H942	Frame_Shift_Del	DEL	ENST00000371900.4	hg19	CCDS14570.1																																																																																			.	.		0.299	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			-	115573885	T	-	115573885	7	5	112	1	0	1	0	1	0	0	0	0	14692	1493	52	0	391	0	SLC6A14	23	115573885	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	1037254	115573885	39696675	1242	17863										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117749649	117749649	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aacttgccaatggcatttgcAaaacctaaactgcagcgggt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:117749649delA	ENST00000276202.7	+	30	3330	c.3267delA	c.(3265-3267)gcafs	p.A1089fs	DOCK11_ENST00000276204.6_Frame_Shift_Del_p.A1089fs	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1089					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TGGCATTTGCAAAACCTAAAC	0.363																																					p.A1089fs		Atlas-INDEL	.											.	DOCK11	185	.	0			c.3266delC						.						117	88	98					X																	117749649		2203	4300	6503	SO:0001589	frameshift_variant	139818	exon30			.	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.3267delA	chrX.hg19:g.117749649delA	ENSP00000276202:p.Ala1089fs	162.0	0.0		200.0	13.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Frame_Shift_Del	DEL	ENST00000276202.7	hg19	CCDS35373.1																																																																																			.	.		0.363	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		-	117749649	A	-	117749649	7	5	112	1	0	1	0	1	0	0	0	0	4688	117	5	0	3385	0	DOCK11	23	117749649	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	2175764	117749649	37520911	1243	17864										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128640085	128640085	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	aattaaagacatcaggcaatAaaaagttgagtaaggcccac							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:128640085delA	ENST00000371122.4	-	8	1199	c.1070delT	c.(1069-1071)ttafs	p.L358fs	SMARCA1_ENST00000371121.3_Frame_Shift_Del_p.L358fs|SMARCA1_ENST00000478420.1_5'Flank|SMARCA1_ENST00000371123.1_Frame_Shift_Del_p.L358fs	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	358	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						ATCAGGCAATAAAAAGTTGAG	0.363																																					p.L357fs		Atlas-INDEL	.											.	SMARCA1	126	.	0			c.1071delA						.						190	179	183					X																	128640085		2203	4300	6503	SO:0001589	frameshift_variant	6594	exon8			.	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.1070delT	chrX.hg19:g.128640085delA	ENSP00000360163:p.Leu358fs	128.0	0.0		142.0	11.0	NM_139035	Q5JV41|Q5JV42	Frame_Shift_Del	DEL	ENST00000371122.4	hg19	CCDS14612.1																																																																																			.	.		0.363	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		-	128640085	A	-	128640085	7	5	112	1	0	1	0	1	0	0	0	0	14783	372	13	0	2162	0	SMARCA1	23	128640085	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	10890436	128640085	26630475	1244	17865										
SLC9A6	10479	hgsc.bcm.edu	37	chrX	135080706	135080706	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cttggaacagcaatttcttgTttcgttattgggtaagtatt							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:135080706delT	ENST00000370698.3	+	4	608	c.573delT	c.(571-573)tgtfs	p.C191fs	SLC9A6_ENST00000370701.1_Frame_Shift_Del_p.C171fs|SLC9A6_ENST00000370695.4_Frame_Shift_Del_p.C223fs	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	191					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CAATTTCTTGTTTCGTTATTG	0.274																																					p.C223fs		Atlas-INDEL	.											.	SLC9A6	64	.	0			c.668delG						.						65	66	66					X																	135080706		2202	4290	6492	SO:0001589	frameshift_variant	10479	exon4			.	AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"Solute carriers"	11079	protein-coding gene	gene with protein product		300231	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 6", "solute carrier family 9 (sodium/hydrogen exchanger), member 6"			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.573delT	chrX.hg19:g.135080706delT	ENSP00000359732:p.Cys191fs	138.0	0.0		154.0	11.0	NM_001042537	A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Frame_Shift_Del	DEL	ENST00000370698.3	hg19	CCDS14654.1																																																																																			.	.		0.274	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	NM_006359		-	135080706	T	-	135080706	7	5	112	1	0	1	0	1	0	0	0	0	14733	1731	60	0	683	0	SLC9A6	23	135080706	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	6440621	135080706	20189854	1245	17866										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135313838	135313838	+	Frame_Shift_Del	DEL	G	G	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gaccctttcacactctccttGggggctacttctgcgctccc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:135313838delG	ENST00000316077.9	-	8	1498	c.1278delC	c.(1276-1278)cccfs	p.P426fs	MAP7D3_ENST00000370661.1_Frame_Shift_Del_p.P391fs|MAP7D3_ENST00000495432.1_5'Flank|MAP7D3_ENST00000370663.5_Frame_Shift_Del_p.P408fs	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	426					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					CACTCTCCTTGGGGGCTACTT	0.602																																					p.K427fs		Atlas-INDEL	.											.	MAP7D3	102	.	0			c.1279delA						.						88	82	84					X																	135313838		1938	4115	6053	SO:0001589	frameshift_variant	79649	exon8			.	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1278delC	chrX.hg19:g.135313838delG	ENSP00000318086:p.Pro426fs	141.0	0.0		142.0	10.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Frame_Shift_Del	DEL	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.602	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			-	135313838	G	-	135313838	7	5	112	1	0	1	0	1	0	0	0	0	9278	1335	47	0	1396	0	MAP7D3	23	135313838	Frame_Shift_Del	DEL	G	TCGA-DD-A39Y-01A-11D-A20W-10	233132	135313838	19956722	1246	17867										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135328464	135328464	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cacgattaaccacatcttgcTtcctcctttccttagcaatc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:135328464delT	ENST00000316077.9	-	2	327	c.107delA	c.(106-108)aagfs	p.K36fs	MAP7D3_ENST00000370661.1_Frame_Shift_Del_p.K36fs|MAP7D3_ENST00000370663.5_Frame_Shift_Del_p.K18fs	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	36					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					CACATCTTGCTTCCTCCTTTC	0.383																																					p.K36fs		Atlas-INDEL	.											.	MAP7D3	102	.	0			c.108delG						.						89	80	83					X																	135328464		1986	4153	6139	SO:0001589	frameshift_variant	79649	exon2			.	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.107delA	chrX.hg19:g.135328464delT	ENSP00000318086:p.Lys36fs	140.0	0.0		158.0	10.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Frame_Shift_Del	DEL	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.383	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			-	135328464	T	-	135328464	7	5	112	1	0	1	0	1	0	0	0	0	9278	1609	56	0	2591	0	MAP7D3	23	135328464	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	14626	135328464	19942096	1247	17868										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135328496	135328496	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ttagcaatctcgtttgctgcAgcaactaaaatacagggaga	9	8	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:135328496A>G	ENST00000316077.9	-	2	295	c.75T>C	c.(73-75)gcT>gcC	p.A25A	MAP7D3_ENST00000370661.1_Silent_p.A25A|MAP7D3_ENST00000370663.5_Silent_p.A7A	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	25					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					CGTTTGCTGCAGCAACTAAAA	0.388																																					p.A25A		Atlas-SNP	.											.	MAP7D3	102	.	0			c.T75C						.						61	55	57					X																	135328496		2044	4173	6217	SO:0001819	synonymous_variant	79649	exon2			TGCTGCAGCAACT	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.75T>C	chrX.hg19:g.135328496A>G		122.0	0.0		143.0	6.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Silent	SNP	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.388	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			G	135328496	A	G	135328496	2	3	112	1	0	0	0	0	0	0	0	1	9278	175	7	2		2	MAP7D3	23	135328496	Silent	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	32	135328496	19942064	1248	17869										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140967163	140967163	+	Frame_Shift_Del	DEL	T	T	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gagaggcacaggctacacccTttcccttcctgccgtcagcc					rs372869684		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:140967163delT	ENST00000298296.1	+	3	461	c.461delT	c.(460-462)cttfs	p.L154fs	MAGEC3_ENST00000536088.1_5'Flank|MAGEC3_ENST00000443323.2_5'Flank|MAGEC3_ENST00000448920.1_5'Flank	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	154										NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					GGCTACACCCTTTCCCTTCCT	0.567																																					p.L154fs		Atlas-INDEL	.											.	MAGEC3	228	.	0			c.460delC						.						38	33	35					X																	140967163		2067	4298	6365	SO:0001589	frameshift_variant	139081	exon3			.	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.461delT	chrX.hg19:g.140967163delT	ENSP00000298296:p.Leu154fs	175.0	0.0		193.0	12.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Frame_Shift_Del	DEL	ENST00000298296.1	hg19	CCDS14676.1																																																																																			.	.		0.567	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		-	140967163	T	-	140967163	7	5	112	1	0	1	0	1	0	0	0	0	9191	1609	56	0	471	0	MAGEC3	23	140967163	Frame_Shift_Del	DEL	T	TCGA-DD-A39Y-01A-11D-A20W-10	5638667	140967163	14303397	1249	17870										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151815555	151815555	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tttctgaacagcaaggatgcTttcgtgcatgatgtgactgt	11	7	1	3			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:151815555T>C	ENST00000370306.2	+	4	473	c.453T>C	c.(451-453)gcT>gcC	p.A151A		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	151					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCAAGGATGCTTTCGTGCATG	0.537																																					p.A151A		Atlas-SNP	.											.	GABRQ	131	.	0			c.T453C						.						289	200	230					X																	151815555		2203	4300	6503	SO:0001819	synonymous_variant	55879	exon4			GGATGCTTTCGTG	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.453T>C	chrX.hg19:g.151815555T>C		120.0	0.0		98.0	4.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Silent	SNP	ENST00000370306.2	hg19	CCDS14707.1																																																																																			.	.		0.537	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		C	151815555	T	C	151815555	2	2	112	1	0	0	0	0	0	0	0	1	6183	1596	56	2		2	GABRQ	23	151815555	Silent	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	10848392	151815555	3455005	1250	17871										
PNCK	139728	hgsc.bcm.edu	37	chrX	152937342	152937342	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cccagccaggcaccttgaggTcccggtgcacgatccccagg	12	17	0	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:152937342T>C	ENST00000370150.1	-	5	585	c.407A>G	c.(406-408)gAc>gGc	p.D136G	PNCK_ENST00000447676.2_Missense_Mutation_p.D219G|PNCK_ENST00000370145.4_Missense_Mutation_p.D153G|PNCK_ENST00000370142.1_Missense_Mutation_p.D136G|PNCK_ENST00000340888.3_Missense_Mutation_p.D136G|PNCK_ENST00000475172.1_5'UTR|PNCK_ENST00000393831.2_Missense_Mutation_p.D136G			Q6P2M8	KCC1B_HUMAN	pregnancy up-regulated nonubiquitous CaM kinase	136	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|lung(3)|skin(1)	6	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CACCTTGAGGTCCCGGTGCAC	0.657																																					p.D219G		Atlas-SNP	.											.	PNCK	70	.	0			c.A656G						.						21	21	21					X																	152937342		2203	4292	6495	SO:0001583	missense	139728	exon5			TTGAGGTCCCGGT	BC033746	CCDS35503.2, CCDS48189.1	Xq28	2013-10-14	2013-10-14		ENSG00000130822	ENSG00000130822			13415	protein-coding gene	gene with protein product		300680	"pregnancy upregulated non-ubiquitously expressed CaM kinase", "pregnancy up-regulated non-ubiquitously expressed CaM kinase"			12477932	Standard	NM_001039582		Approved	MGC45419, CaMK1b	uc011myu.2	Q6P2M8	OTTHUMG00000024216	ENST00000370150.1:c.407A>G	chrX.hg19:g.152937342T>C	ENSP00000359169:p.Asp136Gly	132.0	0.0		134.0	8.0	NM_001039582	B4DJR8|B4E1A6|B7WPG0|D3DWU7|Q8N4R0	Missense_Mutation	SNP	ENST00000370150.1	hg19		.	.	.	.	.	.	.	.	.	.	t	23.5	4.428324	0.83667	.	.	ENSG00000130822	ENST00000340888;ENST00000370150;ENST00000393831;ENST00000370142;ENST00000370145;ENST00000447676;ENST00000439087;ENST00000422811	D;D;D;D;D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15;-3.15;-3.15;-3.15;-3.15	5.01	5.01	0.66863	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000017	D	0.97901	0.9310	H	0.98133	4.155	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;0.992;0.992	D;P;D;D	0.87578	0.998;0.863;0.916;0.916	D	0.98715	1.0706	10	0.87932	D	0	-26.4021	12.7717	0.57426	0.0:0.0:0.0:1.0	.	163;219;153;136	B4DJG4;Q6P2M8-5;B4E1A6;Q6P2M8	.;.;.;KCC1B_HUMAN	G	136;136;136;136;153;219;136;136	ENSP00000340586:D136G;ENSP00000359169:D136G;ENSP00000377417:D136G;ENSP00000359161:D136G;ENSP00000359164:D153G;ENSP00000405950:D219G;ENSP00000415770:D136G;ENSP00000391772:D136G	ENSP00000340586:D136G	D	-	2	0	PNCK	152590536	1.000000	0.71417	0.998000	0.56505	0.914000	0.54420	6.153000	0.71819	1.653000	0.50694	0.430000	0.28490	GAC	.	.		0.657	PNCK-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000061044.2	NM_198452		C	152937342	T	C	152937342	3	2	112	1	0	0	0	0	1	0	0	0	12154	1667	58	2	652	2	PNCK	23	152937342	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	1121787	152937342	2333218	1251	17872										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153128287	153128287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	ccaggctgtcgtcactgcccAggggcttgatgtccccgttg	13	14	1	1			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:153128287A>G	ENST00000370060.1	-	29	3794	c.3605T>C	c.(3604-3606)cTg>cCg	p.L1202P	L1CAM_ENST00000361981.3_Missense_Mutation_p.L1193P|L1CAM_ENST00000361699.4_Missense_Mutation_p.L1198P|L1CAM_ENST00000370057.3_Missense_Mutation_p.L1202P|L1CAM_ENST00000543994.1_Missense_Mutation_p.L1204P|L1CAM_ENST00000538883.1_Missense_Mutation_p.L1200P|L1CAM_ENST00000370055.1_Missense_Mutation_p.L1193P	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	1202					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GTCACTGCCCAGGGGCTTGAT	0.592																																					p.L1202P		Atlas-SNP	.											.	L1CAM	189	.	0			c.T3605C						.						74	55	61					X																	153128287		2203	4300	6503	SO:0001583	missense	3897	exon28			CTGCCCAGGGGCT	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.3605T>C	chrX.hg19:g.153128287A>G	ENSP00000359077:p.Leu1202Pro	63.0	0.0		72.0	5.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	hg19	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.428003	0.43122	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000370058;ENST00000361699	D;D;D;D;D;D;D;D	0.86097	-2.07;-2.07;-2.07;-2.07;-2.07;-2.07;-2.07;-2.07	4.6	4.6	0.57074	.	0.000000	0.42053	D	0.000762	D	0.87740	0.6253	L	0.40543	1.245	0.80722	D	1	D;P;D	0.76494	0.999;0.86;0.999	D;P;D	0.77004	0.921;0.535;0.989	D	0.86471	0.1785	10	0.36615	T	0.2	.	12.0976	0.53763	1.0:0.0:0.0:0.0	.	1193;1198;1202	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	P	1202;1204;1202;1200;1193;1193;98;1198	ENSP00000359077:L1202P;ENSP00000438430:L1204P;ENSP00000359074:L1202P;ENSP00000439645:L1200P;ENSP00000354712:L1193P;ENSP00000359072:L1193P;ENSP00000359075:L98P;ENSP00000355380:L1198P	ENSP00000355380:L1198P	L	-	2	0	L1CAM	152781481	0.169000	0.23002	1.000000	0.80357	0.786000	0.44442	0.772000	0.26647	1.697000	0.51169	0.430000	0.28490	CTG	.	.		0.592	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		G	153128287	A	G	153128287	3	3	112	1	0	0	0	0	1	0	0	0	8597	188	7	2	172	2	L1CAM	23	153128287	Missense_Mutation	SNP	A	TCGA-DD-A39Y-01A-11D-A20W-10	190945	153128287	2142273	1252	17873										
ATP6AP1	537	hgsc.bcm.edu	37	chrX	153664091	153664091	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	gcgactgtgccagcttcttcTcccccggcatctggatgggg	13	14	3	0			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:153664091T>C	ENST00000369762.2	+	10	1328	c.1267T>C	c.(1267-1269)Tcc>Ccc	p.S423P	GDI1_ENST00000447750.2_5'Flank	NM_001183.4	NP_001174.2	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1	423					ATP hydrolysis coupled proton transport (GO:0015991)|establishment of organelle localization (GO:0051656)|pH reduction (GO:0045851)|positive regulation of bone resorption (GO:0045780)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoclast development (GO:2001206)|proton transport (GO:0015992)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuole (GO:0005773)	ATP binding (GO:0005524)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(5)	14	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CAGCTTCTTCTCCCCCGGCAT	0.562																																					p.S423P		Atlas-SNP	.											.	ATP6AP1	46	.	0			c.T1267C						.						191	180	184					X																	153664091		2203	4300	6503	SO:0001583	missense	537	exon10			TTCTTCTCCCCCG	D16469	CCDS35451.1	Xq28	2010-03-10	2003-08-28	2003-08-29	ENSG00000071553	ENSG00000071553			868	protein-coding gene	gene with protein product		300197	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1"	ATP6S1, ATP6IP1		8733135, 8281148	Standard	NM_001183		Approved	ORF, XAP-3, VATPS1, 16A, Ac45, XAP3, CF2	uc004flf.1	Q15904	OTTHUMG00000033291	ENST00000369762.2:c.1267T>C	chrX.hg19:g.153664091T>C	ENSP00000358777:p.Ser423Pro	98.0	0.0		104.0	5.0	NM_001183	A6ZKI4|Q8NBT4|Q9H0C7	Missense_Mutation	SNP	ENST00000369762.2	hg19	CCDS35451.1	.	.	.	.	.	.	.	.	.	.	T	19.03	3.747755	0.69533	.	.	ENSG00000071553	ENST00000369762;ENST00000445849	.	.	.	5.4	5.4	0.78164	.	0.161766	0.56097	D	0.000028	T	0.79003	0.4373	M	0.79693	2.465	0.50632	D	0.999889	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.81799	-0.0767	9	0.72032	D	0.01	-30.5053	12.2595	0.54642	0.0:0.0:0.0:1.0	.	383;423	B3KR70;Q15904	.;VAS1_HUMAN	P	423;247	.	ENSP00000358777:S423P	S	+	1	0	ATP6AP1	153317285	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	0.885000	0.28227	1.799000	0.52666	0.486000	0.48141	TCC	.	.		0.562	ATP6AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081639.4	NM_001183		C	153664091	T	C	153664091	3	2	112	1	0	0	0	0	1	0	0	0	1165	1551	54	2	1305	2	ATP6AP1	23	153664091	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10	535804	153664091	1606469	1253	17874										
IL9R	3581	hgsc.bcm.edu	37	chrX	155239775	155239775	+	Frame_Shift_Del	DEL	C	C	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	cgtccctgactaggccggctCccccagactcagagggcagc							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:155239775delC	ENST00000244174.5	+	9	1446	c.1267delC	c.(1267-1269)cccfs	p.P424fs	IL9R_ENST00000424344.3_Frame_Shift_Del_p.P403fs|IL9R_ENST00000369423.2_3'UTR|IL9R_ENST00000540897.1_3'UTR	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	424					cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)			NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TAGGCCGGCTCCCCCAGACTC	0.627																																					p.A422fs		Atlas-INDEL	.											.	IL9R	73	.	0			c.1266delT						.						14	22	19					X																	155239775		2190	4288	6478	SO:0001589	frameshift_variant	3581	exon9			.	M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"Pseudoautosomal regions / PAR2", "Interleukins and interleukin receptors", "CD molecules"	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.1267delC	chrX.hg19:g.155239775delC	ENSP00000244174:p.Pro424fs	114.0	0.0		157.0	10.0	NM_002186	B9ZVT0|Q14634|Q8WWU1|Q96TF0	Frame_Shift_Del	DEL	ENST00000244174.5	hg19	CCDS14771.4																																																																																			.	.		0.627	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	NM_002186		-	155239775	C	-	155239775	7	5	112	1	0	1	0	1	0	0	0	0	7717	855	30	0	1301	0	IL9R	23	155239775	Frame_Shift_Del	DEL	C	TCGA-DD-A39Y-01A-11D-A20W-10	1575684	155239775	30785	1254	17875										
TBL1Y	90665	hgsc.bcm.edu	37	chrY	6938816	6938816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	atgagaatagcaacgggggcTccacccagctcgtgttgaga	13	10	0	2			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrY:6938816T>C	ENST00000383032.1	+	10	1293	c.646T>C	c.(646-648)Tcc>Ccc	p.S216P	TBL1Y_ENST00000346432.3_Missense_Mutation_p.S216P|TBL1Y_ENST00000355162.2_Missense_Mutation_p.S216P	NM_033284.1	NP_150600.1	Q9BQ87	TBL1Y_HUMAN	transducin (beta)-like 1, Y-linked	216					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(1)|large_intestine(4)|lung(2)|skin(1)	8						CAACGGGGGCTCCACCCAGCT	0.478																																					p.S216P		Atlas-SNP	.											.	TBL1Y	15	.	0			c.T646C						.																																			SO:0001583	missense	90665	exon9			GGGGGCTCCACCC	AF332220	CCDS14779.1	Yp11.2	2013-01-10	2009-12-17		ENSG00000092377	ENSG00000092377		"WD repeat domain containing"	18502	protein-coding gene	gene with protein product		400033					Standard	NM_033284		Approved	TBL1	uc004frd.3	Q9BQ87	OTTHUMG00000035299	ENST00000383032.1:c.646T>C	chrY.hg19:g.6938816T>C	ENSP00000372499:p.Ser216Pro	122.0	0.0		95.0	5.0	NM_134258	A1L4B3	Missense_Mutation	SNP	ENST00000383032.1	hg19	CCDS14779.1																																																																																			.	.		0.478	TBL1Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085360.1	NM_033284		C	6938816	T	C	6938816	3	2	112	1	0	0	0	0	1	0	0	0	15656	1551	54	2	664	2	TBL1Y	24	6938816	Missense_Mutation	SNP	T	TCGA-DD-A39Y-01A-11D-A20W-10		6938816	52434750	1255	17876										
RPS4Y2	140032	hgsc.bcm.edu	37	chrY	22921883	22921883	+	Frame_Shift_Del	DEL	A	A	-													0.0127897681854516	16	1	1.30861182884239	1.41192328901415	1.27745440434614	0.0175920837235342	0.284515636918383	0	tatgtatgcaacacttcctcAaaattgatggcaaggttcga							TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrY:22921883delA	ENST00000288666.5	+	3	211	c.211delA	c.(211-213)aaafs	p.K71fs		NM_001039567.2	NP_001034656.1	Q8TD47	RS4Y2_HUMAN	ribosomal protein S4, Y-linked 2	71	S4 RNA-binding.				translation (GO:0006412)	ribosome (GO:0005840)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			lung(2)	2						ACACTTCCTCAAAATTGATGG	0.418																																					p.L70fs		Atlas-INDEL	.											.	RPS4Y2	3	.	0			c.210delC						.																																			SO:0001589	frameshift_variant	140032	exon3			.	AF497481	CCDS44028.1	Yq11.223	2006-02-22	2006-02-22	2006-02-22	ENSG00000157828	ENSG00000157828		"S ribosomal proteins"	18501	protein-coding gene	gene with protein product		400030	"ribosomal protein S4, Y-linked 2 pseudogene"	RPS4Y2P		12815422	Standard	NM_001039567		Approved		uc011nbb.2	Q8TD47	OTTHUMG00000036540	ENST00000288666.5:c.211delA	chrY.hg19:g.22921883delA	ENSP00000288666:p.Lys71fs	143.0	0.0		166.0	10.0	NM_001039567	A6NIR6	Frame_Shift_Del	DEL	ENST00000288666.5	hg19	CCDS44028.1																																																																																			.	.		0.418	RPS4Y2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088873.1			-	22921883	A	-	22921883	7	5	112	1	0	1	0	1	0	0	0	0	13662	131	5	0	221	0	RPS4Y2	24	22921883	Frame_Shift_Del	DEL	A	TCGA-DD-A39Y-01A-11D-A20W-10	15983067	22921883	36451683	1256	17877										
LRRC47	57470	hgsc.bcm.edu	37	chr1	3703707	3703707	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cccttcccgccaccacggccTccgacgcgcaggtactccag	9	21	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:3703707T>C	ENST00000378251.1	-	2	810	c.783A>G	c.(781-783)ggA>ggG	p.G261G	RP1-286D6.5_ENST00000607459.1_RNA	NM_020710.2	NP_065761.1	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	261							phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		CACCACGGCCTCCGACGCGCA	0.637																																					p.G261G		Atlas-SNP	.											.	LRRC47	42	.	0			c.A783G						.						77	61	67					1																	3703707		2203	4300	6503	SO:0001819	synonymous_variant	57470	exon2			ACGGCCTCCGACG	AB033011	CCDS51.1	1p36.32	2008-02-05			ENSG00000130764	ENSG00000130764			29207	protein-coding gene	gene with protein product						10574461	Standard	NM_020710		Approved	KIAA1185, RP1-286D6.3	uc001akx.1	Q8N1G4	OTTHUMG00000003506	ENST00000378251.1:c.783A>G	chr1.hg19:g.3703707T>C		192.0	0.0		70.0	4.0	NM_020710	Q9ULN5	Silent	SNP	ENST00000378251.1	hg19	CCDS51.1																																																																																			.	.		0.637	LRRC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009744.1	NM_020710		C	3703707	T	C	3703707	2	2	113	1	0	0	0	0	0	0	0	1	9013	1538	54	2		2	LRRC47	1	3703707	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10		3703707	245546914	1	17878										
PRAMEF4	400735	hgsc.bcm.edu	37	chr1	12942173	12942173	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcctcttggcattgaggaagCacccatgggccatagcttca	10	12	2	1	rs201789683		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:12942173C>G	ENST00000235349.5	-	3	447	c.377G>C	c.(376-378)tGc>tCc	p.C126S		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	126					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATTGAGGAAGCACCCATGGGC	0.493																																					p.C126S		Atlas-SNP	.											PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	.	0			c.G377C						.						44	56	52					1																	12942173		1381	2629	4010	SO:0001583	missense	400735	exon3			AGGAAGCACCCAT		CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"-"	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.377G>C	chr1.hg19:g.12942173C>G	ENSP00000235349:p.Cys126Ser	38.0	1.0		20.0	4.0	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	hg19	CCDS30592.1	.	.	.	.	.	.	.	.	.	.	c	8.575	0.881031	0.17467	.	.	ENSG00000243073	ENST00000235349	T	0.18016	2.24	1.35	0.315	0.15852	.	1.371720	0.04624	N	0.402516	T	0.19406	0.0466	L	0.53671	1.685	0.09310	N	1	P	0.50272	0.933	P	0.44811	0.461	T	0.23190	-1.0195	10	0.33940	T	0.23	.	5.2546	0.15540	0.0:0.6297:0.3703:0.0	.	126	O60810	PRAM4_HUMAN	S	126	ENSP00000235349:C126S	ENSP00000235349:C126S	C	-	2	0	PRAMEF4	12864760	0.002000	0.14202	0.003000	0.11579	0.008000	0.06430	0.188000	0.17018	0.112000	0.17975	0.194000	0.17425	TGC	.	C|0.500;G|0.500		0.493	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611		G	12942173	C	G	12942173	3	3	113	1	0	0	0	0	1	0	0	0	12449	710	25	4	1067	4	PRAMEF4	1	12942173	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	9238466	12942173	236308448	2	17879										
DDOST	1650	hgsc.bcm.edu	37	chr1	20982026	20982026	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgtcagccacgatgagcgtaTgctgcaaagagtagatggaa	13	7	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:20982026T>C	ENST00000375048.3	-	5	614	c.509A>G	c.(508-510)cAt>cGt	p.H170R	DDOST_ENST00000415136.2_Splice_Site_p.H133R|DDOST_ENST00000602624.2_Splice_Site_p.H153R	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	170					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GATGAGCGTATGCTGCAAAGA	0.522																																					p.H170R		Atlas-SNP	.											.	DDOST	30	.	0			c.A509G						.						107	108	107					1																	20982026		2203	4300	6503	SO:0001630	splice_region_variant	1650	exon5			AGCGTATGCTGCA	D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"oligosaccharyltransferase subunit 48"	602202	"dolichyl-diphosphooligosaccharide-protein glycosyltransferase", "dolichyl-diphosphooligosaccharide--protein glycosyltransferase"			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.508-1A>G	chr1.hg19:g.20982026T>C		135.0	0.0		92.0	4.0	NM_005216	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Missense_Mutation	SNP	ENST00000375048.3	hg19	CCDS212.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.490162	0.64074	.	.	ENSG00000244038	ENST00000375048;ENST00000415136	T;T	0.79141	-1.24;-1.24	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.91219	0.7233	H	0.94183	3.505	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	1.0;1.0;0.989	D	0.93555	0.6890	10	0.72032	D	0.01	-24.3728	15.6348	0.76944	0.0:0.0:0.0:1.0	.	133;152;170	E7EWT1;B4DLI2;P39656	.;.;OST48_HUMAN	R	170;133	ENSP00000364188:H170R;ENSP00000399457:H133R	ENSP00000364188:H170R	H	-	2	0	DDOST	20854613	1.000000	0.71417	0.992000	0.48379	0.210000	0.24377	6.179000	0.71974	2.152000	0.67230	0.383000	0.25322	CAT	.	.		0.522	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216	Missense_Mutation	C	20982026	T	C	20982026	5	2	113	1	0	0	0	0	0	0	1	0	4337	1478	51	2	889	2	DDOST	1	20982026	Splice_Site	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	8039853	20982026	228268595	3	17880										
AIM1L	55057	hgsc.bcm.edu	37	chr1	26663170	26663170	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cgcagttacgatacacgcccTtctccagcacgtactgttcc	7	16	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:26663170T>C	ENST00000308182.5	-	11	1259	c.830A>G	c.(829-831)aAg>aGg	p.K277R	AIM1L_ENST00000527815.1_Missense_Mutation_p.K448R|AIM1L_ENST00000522993.1_5'UTR			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	277	Beta/gamma crystallin 'Greek key' 6. {ECO:0000255|PROSITE-ProRule:PRU00028}.						carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		ATACACGCCCTTCTCCAGCAC	0.706																																					p.K1322R		Atlas-SNP	.											.	AIM1L	98	.	0			c.A3965G						.						16	15	15					1																	26663170		2183	4267	6450	SO:0001583	missense	55057	exon12			ACGCCCTTCTCCA			1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"beta-gamma crystallin domain containing 2"						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490	ENST00000308182.5:c.830A>G	chr1.hg19:g.26663170T>C	ENSP00000310435:p.Lys277Arg	141.0	0.0		70.0	4.0	NM_001039775	B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	hg19		.	.	.	.	.	.	.	.	.	.	T	28.9	4.957733	0.92726	.	.	ENSG00000176092	ENST00000527815;ENST00000308182	T;T	0.76448	-1.02;-1.02	5.36	4.22	0.49857	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.82697	0.5093	L	0.51422	1.61	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.87578	0.951;0.998	T	0.78964	-0.1996	10	0.27082	T	0.32	.	11.3091	0.49353	0.1366:0.0:0.0:0.8634	.	194;277	Q9NTH7;Q8N1P7	.;AIM1L_HUMAN	R	448;277	ENSP00000433931:K448R;ENSP00000310435:K277R	ENSP00000310435:K277R	K	-	2	0	AIM1L	26535757	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	7.402000	0.79972	0.845000	0.35118	0.533000	0.62120	AAG	.	.		0.706	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2		C	26663170	T	C	26663170	3	2	113	1	0	0	0	0	1	0	0	0	431	1609	56	2	1056	2	AIM1L	1	26663170	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	5681144	26663170	222587451	4	17881										
RPA2	6118	hgsc.bcm.edu	37	chr1	28233497	28233497	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgtcatgtcatctattttgTaaacaatgttggttggagcc	9	7	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:28233497T>C	ENST00000373912.3	-	4	574	c.275A>G	c.(274-276)tAc>tGc	p.Y92C	RPA2_ENST00000313433.7_Missense_Mutation_p.Y180C|RPA2_ENST00000373909.3_Missense_Mutation_p.Y100C	NM_002946.3	NP_002937.1	P15927	RFA2_HUMAN	replication protein A2, 32kDa	92					base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of DNA damage checkpoint (GO:2000001)|regulation of double-strand break repair via homologous recombination (GO:0010569)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor A complex (GO:0005662)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|enzyme binding (GO:0019899)|protein phosphatase binding (GO:0019903)|single-stranded DNA binding (GO:0003697)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(3)|skin(1)	11		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.62e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00294)|STAD - Stomach adenocarcinoma(196;0.00308)|BRCA - Breast invasive adenocarcinoma(304;0.00613)|READ - Rectum adenocarcinoma(331;0.0649)		ATCTATTTTGTAAACAATGTT	0.433								Direct reversal of damage;Nucleotide excision repair (NER)																													p.Y92C		Atlas-SNP	.											.	RPA2	34	.	0			c.A275G						.						85	74	78					1																	28233497		2203	4300	6503	SO:0001583	missense	6118	exon4			ATTTTGTAAACAA	BC021257	CCDS314.1, CCDS72740.1	1p35	2008-02-05	2002-08-29		ENSG00000117748	ENSG00000117748			10290	protein-coding gene	gene with protein product		179836	"replication protein A2 (32kD)"			8454588	Standard	XM_005245965		Approved		uc001bpe.1	P15927	OTTHUMG00000003915	ENST00000373912.3:c.275A>G	chr1.hg19:g.28233497T>C	ENSP00000363021:p.Tyr92Cys	127.0	0.0		69.0	4.0	NM_002946	Q52II0|Q5TEI9|Q5TEJ5	Missense_Mutation	SNP	ENST00000373912.3	hg19	CCDS314.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.558191	0.86231	.	.	ENSG00000117748	ENST00000373912;ENST00000373909;ENST00000313433;ENST00000444045	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.83	5.83	0.93111	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);Nucleic acid binding, OB-fold, tRNA/helicase-type (1);	0.000000	0.85682	D	0.000000	T	0.54663	0.1872	M	0.89601	3.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.63620	-0.6596	10	0.62326	D	0.03	-29.0408	15.1763	0.72913	0.0:0.0:0.0:1.0	.	92;100	P15927;P15927-2	RFA2_HUMAN;.	C	92;100;180;96	ENSP00000363021:Y92C;ENSP00000363017:Y100C;ENSP00000363015:Y180C;ENSP00000387649:Y96C	ENSP00000363015:Y180C	Y	-	2	0	RPA2	28106084	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.642000	0.83385	2.225000	0.72522	0.482000	0.46254	TAC	.	.		0.433	RPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011179.1	NM_002946		C	28233497	T	C	28233497	3	2	113	1	0	0	0	0	1	0	0	0	13552	1638	57	2	561	2	RPA2	1	28233497	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1570327	28233497	221017124	5	17882										
DLGAP3	58512	hgsc.bcm.edu	37	chr1	35334624	35334624	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	accgtggccaggcctgccagGccctccagctccaggtctgc	12	18	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:35334624G>A	ENST00000373347.1	-	9	2335	c.2067C>T	c.(2065-2067)ggC>ggT	p.G689G	DLGAP3_ENST00000235180.4_Silent_p.G689G			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	689					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				GGCCTGCCAGGCCCTCCAGCT	0.682																																					p.G689G		Atlas-SNP	.											.	DLGAP3	107	.	0			c.C2067T						.						14	13	13					1																	35334624		2128	4110	6238	SO:0001819	synonymous_variant	58512	exon7			TGCCAGGCCCTCC	AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544			30368	protein-coding gene	gene with protein product		611413				8619474, 9110174	Standard	NM_001080418		Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.2067C>T	chr1.hg19:g.35334624G>A		96.0	0.0		64.0	25.0	NM_001080418	Q5TDD5|Q9H3X7	Silent	SNP	ENST00000373347.1	hg19	CCDS30670.1																																																																																			.	.		0.682	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		A	35334624	G	A	35334624	2	1	113	1	0	0	0	0	0	0	0	1	4563	1190	42	3		3	DLGAP3	1	35334624	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	7101127	35334624	213915997	6	17883										
OSCP1	127700	hgsc.bcm.edu	37	chr1	36889022	36889022	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cccggacaccggcaacacaaAgcgaccgttattattctgaa	8	13	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:36889022A>G	ENST00000356637.5	-	6	655	c.592T>C	c.(592-594)Ttt>Ctt	p.F198L	OSCP1_ENST00000235532.5_Missense_Mutation_p.F188L|OSCP1_ENST00000315643.9_Missense_Mutation_p.F198L|OSCP1_ENST00000433045.2_Missense_Mutation_p.F143L|OSCP1_ENST00000495222.1_5'UTR			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	198					transport (GO:0006810)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						GGCAACACAAAGCGACCGTTA	0.408																																					p.F188L		Atlas-SNP	.											.	OSCP1	48	.	0			c.T562C						.						91	94	93					1																	36889022		2203	4300	6503	SO:0001583	missense	127700	exon5			ACACAAAGCGACC		CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"oxidored nitro domain containing protein"	608854	"chromosome 1 open reading frame 102"	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.592T>C	chr1.hg19:g.36889022A>G	ENSP00000349052:p.Phe198Leu	91.0	0.0		57.0	5.0	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Missense_Mutation	SNP	ENST00000356637.5	hg19		.	.	.	.	.	.	.	.	.	.	a	16.12	3.034298	0.54896	.	.	ENSG00000116885	ENST00000235532;ENST00000356637;ENST00000433045;ENST00000445843;ENST00000315643	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.50735	0.1633	L	0.46157	1.445	0.80722	D	1	B;P	0.52061	0.448;0.95	P;P	0.55303	0.55;0.773	T	0.48043	-0.9069	10	0.42905	T	0.14	.	14.4998	0.67714	1.0:0.0:0.0:0.0	.	188;198	Q8WVF1-3;Q8WVF1	.;OSCP1_HUMAN	L	188;198;143;158;198	ENSP00000235532:F188L;ENSP00000349052:F198L;ENSP00000390820:F143L;ENSP00000396417:F158L;ENSP00000314541:F198L	ENSP00000235532:F188L	F	-	1	0	OSCP1	36661609	1.000000	0.71417	1.000000	0.80357	0.308000	0.27856	8.667000	0.91153	2.032000	0.59987	0.528000	0.53228	TTT	.	.		0.408	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047		G	36889022	A	G	36889022	3	3	113	1	0	0	0	0	1	0	0	0	11295	72	3	2	601	2	OSCP1	1	36889022	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1554398	36889022	212361599	7	17884										
RLF	6018	hgsc.bcm.edu	37	chr1	40656478	40656478	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tactgctttcagtgtctgaaAgtgaactgccatgtgaagtc	10	8	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:40656478A>G	ENST00000372771.4	+	3	454	c.427A>G	c.(427-429)Agt>Ggt	p.S143G		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	143					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			AGTGTCTGAAAGTGAACTGCC	0.343																																					p.S143G		Atlas-SNP	.											.	RLF	152	.	0			c.A427G						.						131	124	127					1																	40656478		2203	4300	6503	SO:0001583	missense	6018	exon3			TCTGAAAGTGAAC		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.427A>G	chr1.hg19:g.40656478A>G	ENSP00000361857:p.Ser143Gly	155.0	0.0		91.0	4.0	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	hg19	CCDS448.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.309168	0.40895	.	.	ENSG00000117000	ENST00000372771	T	0.14640	2.49	5.21	5.21	0.72293	.	0.193874	0.56097	D	0.000029	T	0.13543	0.0328	L	0.36672	1.1	0.38696	D	0.952874	B	0.20261	0.043	B	0.19391	0.025	T	0.04333	-1.0959	10	0.72032	D	0.01	-6.3038	13.7214	0.62730	1.0:0.0:0.0:0.0	.	143	Q13129	RLF_HUMAN	G	143	ENSP00000361857:S143G	ENSP00000361857:S143G	S	+	1	0	RLF	40429065	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.320000	0.79064	1.970000	0.57323	0.456000	0.33151	AGT	.	.		0.343	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		G	40656478	A	G	40656478	3	3	113	1	0	0	0	0	1	0	0	0	13404	72	3	2	437	2	RLF	1	40656478	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3767456	40656478	208594143	8	17885										
RLF	6018	hgsc.bcm.edu	37	chr1	40705106	40705106	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aacgcactcatcagatgagtAgtgcctatttagagcaacag	9	9	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:40705106A>G	ENST00000372771.4	+	8	4759	c.4732A>G	c.(4732-4734)Agt>Ggt	p.S1578G		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1578					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			TCAGATGAGTAGTGCCTATTT	0.448																																					p.S1578G		Atlas-SNP	.											.	RLF	152	.	0			c.A4732G						.						80	78	78					1																	40705106		2203	4300	6503	SO:0001583	missense	6018	exon8			ATGAGTAGTGCCT		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.4732A>G	chr1.hg19:g.40705106A>G	ENSP00000361857:p.Ser1578Gly	110.0	0.0		42.0	13.0	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	hg19	CCDS448.1	.	.	.	.	.	.	.	.	.	.	A	10.36	1.327471	0.24080	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.14266	2.52	6.15	4.97	0.65823	.	0.273633	0.47455	D	0.000240	T	0.10423	0.0255	L	0.36672	1.1	0.31147	N	0.705943	P;P	0.38370	0.628;0.495	B;B	0.31869	0.137;0.065	T	0.07558	-1.0766	10	0.56958	D	0.05	-15.8971	10.5126	0.44870	0.7507:0.0:0.0:0.2493	.	1271;1578	F5H2M5;Q13129	.;RLF_HUMAN	G	1578;1271	ENSP00000361857:S1578G	ENSP00000361857:S1578G	S	+	1	0	RLF	40477693	0.961000	0.32948	1.000000	0.80357	0.999000	0.98932	2.645000	0.46621	2.363000	0.80096	0.523000	0.50628	AGT	.	.		0.448	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		G	40705106	A	G	40705106	3	3	113	1	0	0	0	0	1	0	0	0	13404	420	15	2	4762	2	RLF	1	40705106	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	48628	40705106	208545515	9	17886										
ZNF642	339559	hgsc.bcm.edu	37	chr1	40961639	40961639	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctggagaaaaaccttacgaaTgtaacgaatgtggaaaagcc	10	7	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:40961639T>C	ENST00000372706.1	+	6	2495	c.1489T>C	c.(1489-1491)Tgt>Cgt	p.C497R	ZFP69_ENST00000372705.3_Missense_Mutation_p.C497R|RP11-656D10.3_ENST00000450713.1_RNA			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	497					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										ACCTTACGAATGTAACGAATG	0.393																																					p.C497R		Atlas-SNP	.											.	.	.	.	0			c.T1489C						.						62	63	63					1																	40961639		2203	4300	6503	SO:0001583	missense	339559	exon6			TACGAATGTAACG	AK122618	CCDS30686.1	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187815	ENSG00000187815		"Zinc fingers, C2H2-type", "-", "-", "-"	24708	protein-coding gene	gene with protein product	"ZFP69 zinc finger protein A"		"zinc finger protein 642"	ZNF642			Standard	XM_005270808		Approved	ZKSCAN23A, FLJ16030, ZFP69A, ZSCAN54A	uc001cfo.3	Q49AA0	OTTHUMG00000007303	ENST00000372706.1:c.1489T>C	chr1.hg19:g.40961639T>C	ENSP00000361791:p.Cys497Arg	105.0	0.0		90.0	7.0	NM_198494	Q5SWM5|Q6ZWK8	Missense_Mutation	SNP	ENST00000372706.1	hg19	CCDS30686.1	.	.	.	.	.	.	.	.	.	.	T	18.60	3.658079	0.67586	.	.	ENSG00000187815	ENST00000372706;ENST00000372705	D;D	0.85258	-1.96;-1.96	4.51	4.51	0.55191	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45361	D	0.000380	D	0.95778	0.8626	H	0.99619	4.66	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96792	0.9583	10	0.87932	D	0	-8.8513	12.4448	0.55645	0.0:0.0:0.0:1.0	.	497	Q49AA0	ZN642_HUMAN	R	497	ENSP00000361791:C497R;ENSP00000361790:C497R	ENSP00000361790:C497R	C	+	1	0	ZNF642	40734226	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.104000	0.71498	2.248000	0.74166	0.459000	0.35465	TGT	.	.		0.393	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494		C	40961639	T	C	40961639	3	2	113	1	0	0	0	0	1	0	0	0	18073	1464	51	2	1507	2	ZNF642	1	40961639	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	256533	40961639	208288982	10	17887										
WDR65	149465	hgsc.bcm.edu	37	chr1	43652435	43652435	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgacaaacaggacgttctcTgcctgtgcttcagcccctca	8	15	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:43652435T>C	ENST00000372492.4	+	6	1351	c.1027T>C	c.(1027-1029)Tgc>Cgc	p.C343R	WDR65_ENST00000528956.1_Missense_Mutation_p.C343R	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		343										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GGACGTTCTCTGCCTGTGCTT	0.512																																					p.C343R		Atlas-SNP	.											.	WDR65	76	.	0			c.T1027C						.						123	107	113					1																	43652435		2203	4300	6503	SO:0001583	missense	149465	exon6			GTTCTCTGCCTGT																												ENST00000372492.4:c.1027T>C	chr1.hg19:g.43652435T>C	ENSP00000361570:p.Cys343Arg	145.0	0.0		86.0	4.0	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	hg19		.	.	.	.	.	.	.	.	.	.	T	16.89	3.247482	0.59103	.	.	ENSG00000243710	ENST00000372492;ENST00000528956	T;T	0.43294	0.95;3.39	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat-like-containing domain (1);	0.217301	0.48286	D	0.000190	T	0.56891	0.2016	M	0.67953	2.075	0.58432	D	0.999993	P;P	0.46327	0.515;0.876	B;P	0.55508	0.269;0.777	T	0.52749	-0.8534	10	0.27082	T	0.32	.	15.91	0.79467	0.0:0.0:0.0:1.0	.	343;343	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	R	343	ENSP00000361570:C343R;ENSP00000435310:C343R	ENSP00000361570:C343R	C	+	1	0	WDR65	43425022	0.999000	0.42202	0.999000	0.59377	0.771000	0.43674	3.710000	0.54860	2.141000	0.66446	0.533000	0.62120	TGC	.	.		0.512	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			C	43652435	T	C	43652435	3	2	113	1	0	0	0	0	1	0	0	0	17331	1580	55	2	1045	2	WDR65	1	43652435	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2690796	43652435	205598186	11	17888										
ATPAF1	64756	hgsc.bcm.edu	37	chr1	47118264	47118264	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gaaacttactgttggacaggActgagcccggttccagatca	11	10	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:47118264A>G	ENST00000371937.4	-	6	681	c.577T>C	c.(577-579)Tcc>Ccc	p.S193P	ATPAF1_ENST00000532925.1_Missense_Mutation_p.S105P|ATPAF1_ENST00000576409.1_Missense_Mutation_p.S216P|ATPAF1_ENST00000329231.4_Missense_Mutation_p.S216P|ATPAF1_ENST00000574428.1_Missense_Mutation_p.S193P|ATPAF1_ENST00000542495.1_Missense_Mutation_p.S42P	NM_022745.4	NP_073582.3	Q5TC12	ATPF1_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 1	193					protein complex assembly (GO:0006461)	mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	8	Acute lymphoblastic leukemia(166;0.155)					GTTGGACAGGACTGAGCCCGG	0.408																																					p.S216P	Melanoma(138;107 1777 21672 30337 52312)	Atlas-SNP	.											.	ATPAF1	19	.	0			c.T646C						.						114	102	106					1																	47118264		2203	4300	6503	SO:0001583	missense	64756	exon6			GACAGGACTGAGC	AK026004	CCDS541.1, CCDS41327.1, CCDS541.2, CCDS41327.2, CCDS57997.1, CCDS57998.1	1p33-p32.3	2012-10-12			ENSG00000123472	ENSG00000123472		"Mitochondrial respiratory chain complex assembly factors"	18803	protein-coding gene	gene with protein product		608917				11410595	Standard	NM_022745		Approved	FLJ22351, Atp11p, ATP11	uc001cqh.4	Q5TC12	OTTHUMG00000007988	ENST00000371937.4:c.577T>C	chr1.hg19:g.47118264A>G	ENSP00000361005:p.Ser193Pro	148.0	0.0		81.0	4.0	NM_001042546	B1AQW7|B7Z7D6|B7Z7I6|Q9H6E3	Missense_Mutation	SNP	ENST00000371937.4	hg19		.	.	.	.	.	.	.	.	.	.	A	15.82	2.944712	0.53079	.	.	ENSG00000123472	ENST00000371937;ENST00000526821;ENST00000542495;ENST00000329231;ENST00000532925	T	0.46063	0.88	5.57	4.33	0.51752	.	0.302414	0.36893	N	0.002353	T	0.44435	0.1293	L	0.40543	1.245	0.30840	N	0.735728	P;D;P	0.54397	0.523;0.966;0.822	B;P;P	0.55303	0.305;0.773;0.554	T	0.45818	-0.9235	10	0.40728	T	0.16	-10.5936	9.2861	0.37758	0.7895:0.0:0.0:0.2105	.	105;193;193	B7Z7I6;A8MRA7;Q5TC12	.;.;ATPF1_HUMAN	P	193;107;42;193;105	ENSP00000361005:S193P	ENSP00000330685:S193P	S	-	1	0	ATPAF1	46890851	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.177000	0.42509	2.129000	0.65627	0.454000	0.30748	TCC	.	.		0.408	ATPAF1-201	KNOWN	basic	protein_coding	protein_coding		NM_022745		G	47118264	A	G	47118264	3	3	113	1	0	0	0	0	1	0	0	0	1200	275	10	2	425	2	ATPAF1	1	47118264	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3465829	47118264	202132357	12	17889										
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52705075	52705075	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atctccactagaccatgcctTgcattagctccagatagccc	6	15	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:52705075T>C	ENST00000371591.1	+	3	2117	c.1986T>C	c.(1984-1986)ctT>ctC	p.L662L	ZFYVE9_ENST00000287727.3_Silent_p.L662L|ZFYVE9_ENST00000357206.2_Silent_p.L662L	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	662					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						GACCATGCCTTGCATTAGCTC	0.453																																					p.L662L		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.T1986C						.						113	108	110					1																	52705075		2203	4300	6503	SO:0001819	synonymous_variant	9372	exon4			ATGCCTTGCATTA	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.1986T>C	chr1.hg19:g.52705075T>C		137.0	0.0		90.0	4.0	NM_007323	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Silent	SNP	ENST00000371591.1	hg19	CCDS563.1																																																																																			.	.		0.453	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		C	52705075	T	C	52705075	2	2	113	1	0	0	0	0	0	0	0	1	17686	1799	63	2		2	ZFYVE9	1	52705075	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	5586811	52705075	196545546	13	17890										
MRPL37	51253	hgsc.bcm.edu	37	chr1	54681856	54681856	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agcccgtggtggtgcagagcGtgggcacggatggacgtgtc	19	9	0	1	rs369065705		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:54681856G>A	ENST00000360840.5	+	6	1110	c.1033G>A	c.(1033-1035)Gtg>Atg	p.V345M	MRPL37_ENST00000336230.6_Missense_Mutation_p.V214M|MRPL37_ENST00000605337.1_Missense_Mutation_p.V345M	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	345					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.V345M(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						GGTGCAGAGCGTGGGCACGGA	0.517																																					p.V345M		Atlas-SNP	.											MRPL37,caecum,carcinoma,0,1	MRPL37	36	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1033A						.	G	MET/VAL	0,4406		0,0,2203	176	155	162		1033	3.3	1	1		162	1,8599	1.2+/-3.3	0,1,4299	no	missense	MRPL37	NM_016491.3	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	345/424	54681856	1,13005	2203	4300	6503	SO:0001583	missense	51253	exon6			CAGAGCGTGGGCA	AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221		"Mitochondrial ribosomal proteins / large subunits"	14034	protein-coding gene	gene with protein product		611843				10600119	Standard	NM_016491		Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.1033G>A	chr1.hg19:g.54681856G>A	ENSP00000354086:p.Val345Met	361.0	0.0		170.0	7.0	NM_016491	Q96Q67|Q9BWR1|Q9P0P3	Missense_Mutation	SNP	ENST00000360840.5	hg19	CCDS589.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.514810	0.27123	0.0	1.16E-4	ENSG00000116221	ENST00000360840;ENST00000329505;ENST00000336230	T;T	0.32753	1.44;1.44	5.23	3.33	0.38152	.	0.118458	0.64402	D	0.000020	T	0.49047	0.1534	M	0.77820	2.39	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.991	P;P;P	0.60886	0.88;0.854;0.771	T	0.53034	-0.8495	10	0.87932	D	0	-14.5998	9.371	0.38254	0.2227:0.0:0.7773:0.0	.	214;282;345	A6NHR2;E9PB99;Q9BZE1	.;.;RM37_HUMAN	M	345;282;214	ENSP00000354086:V345M;ENSP00000338526:V214M	ENSP00000328799:V282M	V	+	1	0	MRPL37	54454444	0.989000	0.36119	0.963000	0.40424	0.057000	0.15508	2.009000	0.40903	1.204000	0.43247	-0.391000	0.06502	GTG	.	.		0.517	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022224.1	NM_016491		A	54681856	G	A	54681856	3	1	113	1	0	0	0	0	1	0	0	0	9809	1145	40	1	1055	1	MRPL37	1	54681856	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	1976781	54681856	194568765	14	17891										
CTH	1491	hgsc.bcm.edu	37	chr1	70881689	70881689	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	actaggaattgccttgaaaaAgcagtggcagcactggatgg	13	7	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:70881689A>G	ENST00000370938.3	+	2	363	c.219A>G	c.(217-219)aaA>aaG	p.K73K	CTH_ENST00000346806.2_Silent_p.K73K|CTH_ENST00000411986.2_Silent_p.K73K|CTH_ENST00000464926.1_3'UTR	NM_001902.5	NP_001893.2	Q96IQ7	VSIG2_HUMAN	cystathionine gamma-lyase	0	Ig-like V-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						GCCTTGAAAAAGCAGTGGCAG	0.368																																					p.K73K		Atlas-SNP	.											.	CTH	48	.	0			c.A219G						.						83	90	88					1																	70881689		2203	4300	6503	SO:0001819	synonymous_variant	1491	exon2			TGAAAAAGCAGTG	BC015807	CCDS650.1, CCDS651.1, CCDS53333.1	1p31.1	2014-06-24	2014-06-24		ENSG00000116761	ENSG00000116761	4.4.1.1		2501	protein-coding gene	gene with protein product		607657	"cystathionase (cystathionine gamma-lyase)"			1339280	Standard	NM_001902		Approved		uc001dfd.3	P32929	OTTHUMG00000009352	ENST00000370938.3:c.219A>G	chr1.hg19:g.70881689A>G		115.0	0.0		71.0	4.0	NM_153742	O95791|Q9NX42	Silent	SNP	ENST00000370938.3	hg19	CCDS650.1																																																																																			.	.		0.368	CTH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025918.1	NM_001902		G	70881689	A	G	70881689	2	3	113	1	0	0	0	0	0	0	0	1	4011	69	3	2		2	CTH	1	70881689	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	16199833	70881689	178368932	15	17892										
LRRC8C	84230	hgsc.bcm.edu	37	chr1	90180439	90180439	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttgaaatcctccctcctgaActgggtgactgtcgggctct	10	12	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:90180439A>G	ENST00000370454.4	+	3	2565	c.2310A>G	c.(2308-2310)gaA>gaG	p.E770E	RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	770					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		TCCCTCCTGAACTGGGTGACT	0.418																																					p.E770E		Atlas-SNP	.											.	LRRC8C	73	.	0			c.A2310G						.						82	84	84					1																	90180439		2203	4300	6503	SO:0001819	synonymous_variant	84230	exon3			TCCTGAACTGGGT		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"hypothetical protein AD158"	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.2310A>G	chr1.hg19:g.90180439A>G		118.0	0.0		89.0	4.0	NM_032270	B3KXS9|Q29RV6|Q9H075	Silent	SNP	ENST00000370454.4	hg19	CCDS725.1																																																																																			.	.		0.418	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		G	90180439	A	G	90180439	2	3	113	1	0	0	0	0	0	0	0	1	9032	40	2	2		2	LRRC8C	1	90180439	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	19298750	90180439	159070182	16	17893										
ABCA4	24	hgsc.bcm.edu	37	chr1	94497407	94497407	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcagcgcctgcacatgctggAggaccagctgtgtccccgtg	14	14	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:94497407A>G	ENST00000370225.3	-	27	4141	c.4055T>C	c.(4054-4056)cTc>cCc	p.L1352P		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1352					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CACATGCTGGAGGACCAGCTG	0.647																																					p.L1352P		Atlas-SNP	.											.	ABCA4	275	.	0			c.T4055C						.						78	75	76					1																	94497407		2203	4300	6503	SO:0001583	missense	24	exon27			TGCTGGAGGACCA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.4055T>C	chr1.hg19:g.94497407A>G	ENSP00000359245:p.Leu1352Pro	180.0	0.0		128.0	7.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	A	11.70	1.717146	0.30413	.	.	ENSG00000198691	ENST00000546054;ENST00000370225	D	0.93547	-3.24	5.78	3.5	0.40072	.	0.993436	0.08189	N	0.984138	D	0.84875	0.5569	M	0.67700	2.07	0.09310	N	1	B	0.32543	0.375	B	0.34991	0.193	T	0.76895	-0.2790	10	0.40728	T	0.16	.	2.4174	0.04439	0.5703:0.1495:0.0807:0.1995	.	1352	P78363	ABCA4_HUMAN	P	144;1352	ENSP00000359245:L1352P	ENSP00000359245:L1352P	L	-	2	0	ABCA4	94269995	0.000000	0.05858	0.042000	0.18584	0.288000	0.27193	0.925000	0.28791	1.002000	0.39104	0.528000	0.53228	CTC	.	.		0.647	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		G	94497407	A	G	94497407	3	3	113	1	0	0	0	0	1	0	0	0	34	304	11	2	2862	2	ABCA4	1	94497407	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	4316968	94497407	154753214	17	17894										
ABCA4	24	hgsc.bcm.edu	37	chr1	94502755	94502755	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgagaccaaggtcagccagCgtctcctccagctctctgaa	9	15	3	2	rs147884766	byFrequency	TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:94502755C>A	ENST00000370225.3	-	25	3845	c.3759G>T	c.(3757-3759)acG>acT	p.T1253T		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1253			T -> M (in FFM; unknown pathological significance). {ECO:0000269|PubMed:11385708}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GGTCAGCCAGCGTCTCCTCCA	0.483																																					p.T1253T		Atlas-SNP	.											ABCA4,left_upper_lobe,carcinoma,0,1	ABCA4	275	.	0			c.G3759T						.						106	108	107					1																	94502755		2203	4300	6503	SO:0001819	synonymous_variant	24	exon25			AGCCAGCGTCTCC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.3759G>T	chr1.hg19:g.94502755C>A		132.0	0.0		75.0	35.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	hg19	CCDS747.1																																																																																			.	C|0.998;T|0.002		0.483	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94502755	C	A	94502755	2	1	113	1	0	0	0	0	0	0	0	1	34	755	27	1		1	ABCA4	1	94502755	Silent	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	5348	94502755	154747866	18	17895										
C1orf56	54964	hgsc.bcm.edu	37	chr1	151020559	151020559	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cgacgccgaccgcctggctgGaccagcggctgccgagctct	14	17	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:151020559G>A	ENST00000368926.5	+	1	344	c.236G>A	c.(235-237)gGa>gAa	p.G79E		NM_017860.3	NP_060330.2	Q9BUN1	MENT_HUMAN	chromosome 1 open reading frame 56	79						cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	7	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CGCCTGGCTGGACCAGCGGCT	0.642																																					p.G79E	GBM(146;891 3320 6873)	Atlas-SNP	.											.	C1orf56	25	.	0			c.G236A						.						22	26	25					1																	151020559		2171	4251	6422	SO:0001583	missense	54964	exon1			TGGCTGGACCAGC	BC002469	CCDS980.1	1q21.2	2013-09-20			ENSG00000143443	ENSG00000143443			26045	protein-coding gene	gene with protein product	"methylated in normal thymocytes"					12975309, 22133874	Standard	NM_017860		Approved	FLJ20519, MENT	uc001ewn.3	Q9BUN1	OTTHUMG00000035159	ENST00000368926.5:c.236G>A	chr1.hg19:g.151020559G>A	ENSP00000357922:p.Gly79Glu	155.0	0.0		97.0	4.0	NM_017860	B2RDU8|Q9NWZ4	Missense_Mutation	SNP	ENST00000368926.5	hg19	CCDS980.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.498711	0.44455	.	.	ENSG00000143443	ENST00000368926;ENST00000433087	.	.	.	5.19	1.99	0.26369	.	0.883386	0.09540	N	0.788410	T	0.12944	0.0314	L	0.27053	0.805	0.18873	N	0.999985	P	0.43701	0.815	B	0.43251	0.413	T	0.11372	-1.0590	9	0.56958	D	0.05	-14.3663	6.8085	0.23790	0.0:0.1725:0.4539:0.3736	.	79	Q9BUN1	CA056_HUMAN	E	79	.	ENSP00000357922:G79E	G	+	2	0	C1orf56	149287183	0.510000	0.26171	0.400000	0.26346	0.046000	0.14306	0.700000	0.25601	0.684000	0.31448	0.557000	0.71058	GGA	.	.		0.642	C1orf56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085101.1	NM_017860		A	151020559	G	A	151020559	3	1	113	1	0	0	0	0	1	0	0	0	2050	1174	41	3	238	3	C1orf56	1	151020559	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	56517804	151020559	98230062	19	17896										
SELENBP1	8991	hgsc.bcm.edu	37	chr1	151337178	151337178	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	acctgcagcatcacagagccTtccctggtggaaaagggaat	11	11	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:151337178T>C	ENST00000368868.5	-	12	1351	c.1260A>G	c.(1258-1260)gaA>gaG	p.E420E	SELENBP1_ENST00000435071.1_Silent_p.E356E|SELENBP1_ENST00000473693.1_5'Flank|SELENBP1_ENST00000426705.2_Silent_p.E462E|SELENBP1_ENST00000447402.3_Silent_p.E358E	NM_003944.3	NP_003935.2	Q13228	SBP1_HUMAN	selenium binding protein 1	420					protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	selenium binding (GO:0008430)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|urinary_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TCACAGAGCCTTCCCTGGTGG	0.557																																					p.E462E		Atlas-SNP	.											.	SELENBP1	44	.	0			c.A1386G						.						103	104	104					1																	151337178		2203	4300	6503	SO:0001819	synonymous_variant	8991	exon12			AGAGCCTTCCCTG	U29091	CCDS995.1, CCDS58027.1, CCDS60266.1	1q21.3	2014-05-19			ENSG00000143416	ENSG00000143416			10719	protein-coding gene	gene with protein product		604188				9027582	Standard	NM_003944		Approved	hSP56, hSBP, LPSB	uc010pcy.3	Q13228	OTTHUMG00000012498	ENST00000368868.5:c.1260A>G	chr1.hg19:g.151337178T>C		100.0	0.0		90.0	4.0	NM_001258289	A6NML9|A6PVW9|B2RDR3|B4DKP6|B4E1F3|Q49AQ8|Q96GX7	Silent	SNP	ENST00000368868.5	hg19	CCDS995.1																																																																																			.	.		0.557	SELENBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034904.4			C	151337178	T	C	151337178	2	2	113	1	0	0	0	0	0	0	0	1	14029	1606	56	2		2	SELENBP1	1	151337178	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	316619	151337178	97913443	20	17897										
CD1E	913	hgsc.bcm.edu	37	chr1	158325760	158325760	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agcagcggggcactcagcgaGgggacgtcctgcctaatgct	15	12	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:158325760G>A	ENST00000368167.3	+	4	1008	c.769G>A	c.(769-771)Ggg>Agg	p.G257R	CD1E_ENST00000368157.1_Intron|CD1E_ENST00000368165.3_Missense_Mutation_p.G167R|CD1E_ENST00000444681.2_Missense_Mutation_p.G158R|CD1E_ENST00000368156.1_Missense_Mutation_p.G167R|CD1E_ENST00000368166.3_Missense_Mutation_p.G68R|CD1E_ENST00000368161.3_Missense_Mutation_p.G257R|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368164.3_Missense_Mutation_p.G68R|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368163.3_Intron|CD1E_ENST00000434258.1_Missense_Mutation_p.G255R|CD1E_ENST00000368160.3_Missense_Mutation_p.G257R|CD1E_ENST00000452291.2_Missense_Mutation_p.G68R	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	257	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)	p.G257W(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					CACTCAGCGAGGGGACGTCCT	0.622																																					p.G257R		Atlas-SNP	.											CD1E,NS,carcinoma,-1,1	CD1E	129	.	1	Substitution - Missense(1)	lung(1)	c.G769A						.						114	110	111					1																	158325760		2203	4300	6503	SO:0001583	missense	913	exon4			CAGCGAGGGGACG	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1638	protein-coding gene	gene with protein product		188411	"CD1E antigen, e polypeptide", "CD1e antigen"			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.769G>A	chr1.hg19:g.158325760G>A	ENSP00000357149:p.Gly257Arg	342.0	1.0		251.0	67.0	NM_001042584	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	ENST00000368167.3	hg19	CCDS41417.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.20|11.20	1.569581|1.569581	0.28003|0.28003	.|.	.|.	ENSG00000158488|ENSG00000158488	ENST00000434258;ENST00000444681;ENST00000368167;ENST00000452291;ENST00000368165;ENST00000368166;ENST00000368164;ENST00000368160;ENST00000368161;ENST00000368156|ENST00000368162	T;T;T;T;T;T;T;T;T;T|T	0.02812|0.02579	4.15;4.15;4.15;4.15;4.15;4.15;4.15;4.15;4.15;4.15|4.24	4.6|4.6	2.69|2.69	0.31865|0.31865	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);|.	0.314836|.	0.23782|.	N|.	0.044603|.	T|T	0.03695|0.03695	0.0105|0.0105	M|M	0.83774|0.83774	2.66|2.66	0.09310|0.09310	N|N	1|1	P;D;D;D;P;P;P;P;D;D;D;D;D|.	0.89917|.	0.843;0.998;0.998;0.998;0.929;0.907;0.931;0.914;0.994;0.998;1.0;0.961;0.992|.	P;P;P;P;P;P;P;P;P;D;D;P;P|.	0.91635|.	0.787;0.901;0.901;0.901;0.872;0.877;0.603;0.723;0.864;0.944;0.999;0.797;0.832|.	T|T	0.30268|0.30268	-0.9984|-0.9984	10|7	0.66056|0.49607	D|T	0.02|0.09	-7.087|-7.087	7.2054|7.2054	0.25905|0.25905	0.2087:0.0:0.7913:0.0|0.2087:0.0:0.7913:0.0	.|.	68;158;255;257;158;167;68;68;257;257;257;68;167|.	B4E057;B4E042;E7ET31;A2RRL5;E7EP01;P15812-5;P15812-9;P15812-10;P15812-2;P15812;P15812-3;P15812-8;P15812-6|.	.;.;.;.;.;.;.;.;.;CD1E_HUMAN;.;.;.|.	R|K	255;158;257;68;167;68;68;257;257;167|26	ENSP00000401957:G255R;ENSP00000402906:G158R;ENSP00000357149:G257R;ENSP00000416228:G68R;ENSP00000357147:G167R;ENSP00000357148:G68R;ENSP00000357146:G68R;ENSP00000357142:G257R;ENSP00000357143:G257R;ENSP00000357138:G167R|ENSP00000357144:R26K	ENSP00000357138:G167R|ENSP00000357144:R26K	G|R	+|+	1|2	0|0	CD1E|CD1E	156592384|156592384	0.001000|0.001000	0.12720|0.12720	0.099000|0.099000	0.21106|0.21106	0.019000|0.019000	0.09904|0.09904	0.503000|0.503000	0.22610|0.22610	1.174000|1.174000	0.42811|0.42811	-0.253000|-0.253000	0.11424|0.11424	GGG|AGG	.	.		0.622	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		A	158325760	G	A	158325760	3	1	113	1	0	0	0	0	1	0	0	0	2980	1000	35	3	783	3	CD1E	1	158325760	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	6988582	158325760	90924861	21	17898										
SLAMF7	57823	hgsc.bcm.edu	37	chr1	160719673	160719673	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ataagaatggcacctgtgtgAccaatctgacatgctgcatg	10	9	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:160719673A>G	ENST00000368043.3	+	3	476	c.439A>G	c.(439-441)Acc>Gcc	p.T147A	SLAMF7_ENST00000444090.2_Intron|SLAMF7_ENST00000458104.2_Missense_Mutation_p.T40A|SLAMF7_ENST00000359331.4_Missense_Mutation_p.T147A|SLAMF7_ENST00000368042.3_Missense_Mutation_p.T40A|SLAMF7_ENST00000441662.2_Intron|SLAMF7_ENST00000458602.2_Missense_Mutation_p.T40A	NM_001282595.1|NM_021181.3	NP_001269524.1|NP_067004.3	Q9NQ25	SLAF7_HUMAN	SLAM family member 7	147	Ig-like C2-type.				cell adhesion (GO:0007155)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of natural killer cell activation (GO:0032814)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(4)	24	all_cancers(52;2.63e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			CACCTGTGTGACCAATCTGAC	0.512																																					p.T147A		Atlas-SNP	.											.	SLAMF7	54	.	0			c.A439G						.						120	120	120					1																	160719673		2203	4300	6503	SO:0001583	missense	57823	exon3			TGTGTGACCAATC	AB027233	CCDS1209.1, CCDS60321.1, CCDS60322.1, CCDS60323.1, CCDS60324.1, CCDS60325.1, CCDS72956.1, CCDS72957.1	1q23.1-q24.1	2013-01-11			ENSG00000026751	ENSG00000026751		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	21394	protein-coding gene	gene with protein product		606625				11802771, 11220635	Standard	XM_005245386		Approved	CRACC, 19A, CS1, CD319	uc001fwq.3	Q9NQ25	OTTHUMG00000024008	ENST00000368043.3:c.439A>G	chr1.hg19:g.160719673A>G	ENSP00000357022:p.Thr147Ala	156.0	0.0		95.0	4.0	NM_021181	A8K3U1|B4DPU4|B4DPY3|B4DWA3|Q8N6Y8|Q8ND32|Q9NY08|Q9NY23	Missense_Mutation	SNP	ENST00000368043.3	hg19	CCDS1209.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.524450	0.27299	.	.	ENSG00000026751	ENST00000368043;ENST00000368042;ENST00000458602;ENST00000458104;ENST00000359331	T;T;T;T;T	0.41065	4.13;1.01;1.01;1.01;4.13	5.16	0.103	0.14526	Immunoglobulin-like (1);	0.926254	0.09304	N	0.820567	T	0.30603	0.0770	L	0.39898	1.24	0.09310	N	1	P;D;D;D;D;D	0.76494	0.952;0.993;0.998;0.997;0.992;0.999	P;P;D;D;P;D	0.72625	0.647;0.84;0.947;0.921;0.87;0.978	T	0.07214	-1.0784	10	0.41790	T	0.15	-5.746	3.6683	0.08264	0.5756:0.0:0.2679:0.1565	.	40;40;40;40;147;147	B4DVL7;B4DWA3;B4DW98;Q9NQ25-2;A8K3U1;Q9NQ25	.;.;.;.;.;SLAF7_HUMAN	A	147;40;40;40;147	ENSP00000357022:T147A;ENSP00000357021:T40A;ENSP00000409965:T40A;ENSP00000403294:T40A;ENSP00000352281:T147A	ENSP00000352281:T147A	T	+	1	0	SLAMF7	158986297	0.001000	0.12720	0.006000	0.13384	0.118000	0.20060	0.052000	0.14163	0.097000	0.17492	0.528000	0.53228	ACC	.	.		0.512	SLAMF7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060464.1	NM_021181		G	160719673	A	G	160719673	3	3	113	1	0	0	0	0	1	0	0	0	14384	275	10	2	449	2	SLAMF7	1	160719673	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2393913	160719673	88530948	22	17899										
RGS4	5999	hgsc.bcm.edu	37	chr1	163042190	163042190	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttctcttctgtgcagtgcaaAagatatgaaacatcggctag	9	8	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:163042190A>G	ENST00000367909.6	+	2	390	c.50A>G	c.(49-51)aAa>aGa	p.K17R	RGS4_ENST00000421743.2_Missense_Mutation_p.K114R|RGS4_ENST00000491263.1_3'UTR|RGS4_ENST00000367908.4_Missense_Mutation_p.K17R|RGS4_ENST00000367906.3_5'UTR|RGS4_ENST00000531057.1_Missense_Mutation_p.K17R|RGS4_ENST00000527809.1_5'UTR	NM_001113380.1|NM_005613.5	NP_001106851.1|NP_005604.1	P49798	RGS4_HUMAN	regulator of G-protein signaling 4	17					inactivation of MAPK activity (GO:0000188)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)	21						TGCAGTGCAAAAGATATGAAA	0.368																																					p.K114R	Ovarian(76;1257 1738 3039 6086)	Atlas-SNP	.											.	RGS4	97	.	0			c.A341G						.						56	55	56					1																	163042190		2203	4300	6503	SO:0001583	missense	5999	exon3			GTGCAAAAGATAT	BC051869	CCDS1243.1, CCDS44270.1, CCDS44271.1, CCDS44272.1	1q23.3	2008-05-14	2007-08-14		ENSG00000117152	ENSG00000117152		"Regulators of G-protein signaling"	10000	protein-coding gene	gene with protein product		602516	"regulator of G-protein signalling 4", "schizophrenia disorder 9"	SCZD9		8602223, 8756726	Standard	NM_001102445		Approved		uc001gcl.4	P49798	OTTHUMG00000034417	ENST00000367909.6:c.50A>G	chr1.hg19:g.163042190A>G	ENSP00000356885:p.Lys17Arg	93.0	0.0		71.0	20.0	NM_001102445	A7XA56|A7XA58|A7XA59|A7YVV7|B1APZ3	Missense_Mutation	SNP	ENST00000367909.6	hg19	CCDS1243.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.424432	0.83667	.	.	ENSG00000117152	ENST00000421743;ENST00000367909;ENST00000531057;ENST00000367908	T;T;D	0.88201	0.28;0.35;-2.35	4.52	4.52	0.55395	.	0.000000	0.85682	D	0.000000	D	0.93324	0.7872	M	0.86953	2.85	0.42174	D	0.991651	D;D;D	0.89917	0.996;1.0;1.0	D;D;D	0.80764	0.99;0.991;0.994	D	0.94358	0.7585	9	0.62326	D	0.03	.	11.8394	0.52344	1.0:0.0:0.0:0.0	.	17;17;114	B1APZ3;P49798;A7XA59	.;RGS4_HUMAN;.	R	114;17;17;17	ENSP00000397181:K114R;ENSP00000356885:K17R;ENSP00000436106:K17R	ENSP00000356884:K17R	K	+	2	0	RGS4	161308814	1.000000	0.71417	0.964000	0.40570	0.997000	0.91878	6.310000	0.72830	1.890000	0.54733	0.533000	0.62120	AAA	.	.		0.368	RGS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083197.2	NM_005613		G	163042190	A	G	163042190	3	3	113	1	0	0	0	0	1	0	0	0	13322	14	1	2	351	2	RGS4	1	163042190	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2322517	163042190	86208431	23	17900										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179504037	179504037	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gagaagtaaaagaagaagaaGaacaacaagaagaagaagaa	11	2	0	9	rs200097954|rs368406759|rs6425573	byFrequency	TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:179504037G>C	ENST00000367618.3	+	25	3358	c.2971G>C	c.(2971-2973)Gaa>Caa	p.E991Q		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	991	Glu-rich.		E -> Q (in dbSNP:rs6425573).					p.E991_Q992delEQ(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agaagaagaagaacaacaaga	0.318													G|||	14	0.00279553	0	0.0058	5008	,	,		17137	0.002		0.004	False		,,,				2504	0.0041				p.E991Q		Atlas-SNP	.											.	AXDND1	142	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2971C						.						49	51	50					1																	179504037		2152	4286	6438	SO:0001583	missense	126859	exon25			GAAGAAGAACAAC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2971G>C	chr1.hg19:g.179504037G>C	ENSP00000356590:p.Glu991Gln	240.0	0.0		230.0	33.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	G	9.300	1.052898	0.19907	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.19105	2.17;2.17	4.89	-6.02	0.02192	.	0.508747	0.16499	N	0.211773	T	0.08980	0.0222	N	0.24115	0.695	0.09310	N	1	B;B	0.24186	0.099;0.099	B;B	0.10450	0.003;0.005	T	0.15838	-1.0423	10	0.28530	T	0.3	-2.8152	6.1976	0.20557	0.4456:0.3814:0.173:0.0	rs6425573	875;991	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	Q	991;875;851	ENSP00000356590:E991Q;ENSP00000391716:E851Q	ENSP00000353471:E875Q	E	+	1	0	AXDND1	177770660	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.365000	0.20348	-1.164000	0.02790	-1.047000	0.02352	GAA	.	G|1.000;|0.000		0.318	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179504037	G	C	179504037	3	2	113	1	0	0	0	0	1	0	0	0	1995	943	33	4	3065	4	C1orf125	1	179504037	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	16461847	179504037	69746584	24	17901										
PRG4	10216	hgsc.bcm.edu	37	chr1	186275693	186275693	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtctttgacagtgaataaagAgacaacagttgaaactaaag	9	5	1	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:186275693A>G	ENST00000445192.2	+	7	887	c.842A>G	c.(841-843)gAg>gGg	p.E281G	PRG4_ENST00000367485.4_Missense_Mutation_p.E188G|PRG4_ENST00000367486.3_Missense_Mutation_p.E238G|PRG4_ENST00000367483.4_Missense_Mutation_p.E240G|PRG4_ENST00000367484.3_Missense_Mutation_p.E240G	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	281					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GTGAATAAAGAGACAACAGTT	0.373																																					p.E281G		Atlas-SNP	.											.	PRG4	259	.	0			c.A842G						.						175	189	184					1																	186275693		2203	4300	6503	SO:0001583	missense	10216	exon7			ATAAAGAGACAAC	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.842A>G	chr1.hg19:g.186275693A>G	ENSP00000399679:p.Glu281Gly	112.0	0.0		86.0	5.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	hg19	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	A	4.390	0.072021	0.08436	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.09911	2.93;3.33;3.25;3.09;3.33	3.81	3.81	0.43845	.	0.000000	0.42682	U	0.000665	T	0.27278	0.0669	M	0.67397	2.05	0.22666	N	0.99887	D;D;D;D	0.71674	0.998;0.998;0.997;0.998	D;D;D;D	0.68943	0.961;0.961;0.915;0.961	T	0.02365	-1.1170	9	.	.	.	-11.4708	11.4546	0.50173	1.0:0.0:0.0:0.0	.	147;188;281;240	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	G	238;240;147;240;188;281	ENSP00000356456:E238G;ENSP00000356454:E240G;ENSP00000356453:E240G;ENSP00000356455:E188G;ENSP00000399679:E281G	.	E	+	2	0	PRG4	184542316	0.003000	0.15002	0.935000	0.37517	0.138000	0.21146	1.257000	0.32932	1.512000	0.48834	0.378000	0.23410	GAG	.	.		0.373	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		G	186275693	A	G	186275693	3	3	113	1	0	0	0	0	1	0	0	0	12493	304	11	2	864	2	PRG4	1	186275693	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	6771656	186275693	62974928	25	17902										
C1orf27	54953	hgsc.bcm.edu	37	chr1	186352261	186352261	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aagttggataacttggatgaAgaatgggccacagaacatgc	12	6	0	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:186352261A>G	ENST00000287859.6	+	3	332	c.207A>G	c.(205-207)gaA>gaG	p.E69E	C1orf27_ENST00000432021.3_Silent_p.E69E|C1orf27_ENST00000419367.3_Silent_p.E69E|C1orf27_ENST00000367470.3_Silent_p.E69E	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	69						integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						ACTTGGATGAAGAATGGGCCA	0.368																																					p.E69E		Atlas-SNP	.											.	C1orf27	41	.	0			c.A207G						.						76	76	76					1																	186352261		1930	4130	6060	SO:0001819	synonymous_variant	54953	exon3			GGATGAAGAATGG	BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"transactivated by recombinant transforming growth factor beta"	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.207A>G	chr1.hg19:g.186352261A>G		112.0	0.0		94.0	5.0	NM_001164245	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Silent	SNP	ENST00000287859.6	hg19	CCDS53448.1																																																																																			.	.		0.368	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847		G	186352261	A	G	186352261	2	3	113	1	0	0	0	0	0	0	0	1	2038	69	3	2		2	C1orf27	1	186352261	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	76568	186352261	62898360	26	17903										
GUK1	2987	hgsc.bcm.edu	37	chr1	228333287	228333287	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caccctgctgaagaggctgcTccaggagcacagcggcatct	12	14	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr1:228333287T>C	ENST00000366718.1	+	2	501	c.74T>C	c.(73-75)cTc>cCc	p.L25P	GUK1_ENST00000391865.3_Missense_Mutation_p.L46P|GUK1_ENST00000366728.2_Missense_Mutation_p.L46P|GUK1_ENST00000366726.1_Missense_Mutation_p.L25P|GUK1_ENST00000366723.1_Missense_Mutation_p.L46P|GUK1_ENST00000470040.1_3'UTR|GUK1_ENST00000366721.1_Missense_Mutation_p.L25P|GUK1_ENST00000366722.1_Missense_Mutation_p.L25P|GUK1_ENST00000312726.4_Missense_Mutation_p.L25P|GUK1_ENST00000366716.1_Missense_Mutation_p.L25P|GUK1_ENST00000366730.1_Missense_Mutation_p.L25P	NM_001159391.1	NP_001152863.1	Q16774	KGUA_HUMAN	guanylate kinase 1	25	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				ATP metabolic process (GO:0046034)|dATP metabolic process (GO:0046060)|dGDP biosynthetic process (GO:0006185)|dGMP metabolic process (GO:0046054)|drug metabolic process (GO:0017144)|GDP biosynthetic process (GO:0046711)|GDP-mannose metabolic process (GO:0019673)|glycoprotein transport (GO:0034436)|GMP metabolic process (GO:0046037)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleotide metabolic process (GO:0006163)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			endometrium(2)|lung(5)|prostate(1)|soft_tissue(1)	9		Prostate(94;0.0405)				AAGAGGCTGCTCCAGGAGCAC	0.647																																					p.L46P		Atlas-SNP	.											.	GUK1	34	.	0			c.T137C						.						54	47	50					1																	228333287		2203	4300	6503	SO:0001583	missense	2987	exon2			GGCTGCTCCAGGA	BC006249	CCDS1568.1, CCDS53481.1, CCDS55689.1	1q32-q41	2012-10-02			ENSG00000143774	ENSG00000143774	2.7.4.8		4693	protein-coding gene	gene with protein product		139270				8647247	Standard	NM_000858		Approved		uc021pkf.1	Q16774	OTTHUMG00000039503	ENST00000366718.1:c.74T>C	chr1.hg19:g.228333287T>C	ENSP00000355679:p.Leu25Pro	98.0	0.0		113.0	5.0	NM_001242840	B1ANH1	Missense_Mutation	SNP	ENST00000366718.1	hg19	CCDS1568.1	.	.	.	.	.	.	.	.	.	.	T	16.77	3.215297	0.58452	.	.	ENSG00000143774	ENST00000366730;ENST00000391865;ENST00000366726;ENST00000312726;ENST00000366728;ENST00000453943;ENST00000366723;ENST00000366722;ENST00000366721;ENST00000412265;ENST00000366718;ENST00000366716;ENST00000420445	T;T;T;T;T;T;T;T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22	5.02	3.87	0.44632	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	.	.	.	.	T	0.78729	0.4329	H	0.94222	3.51	0.27438	N	0.953802	P;P	0.47762	0.673;0.9	B;P	0.59171	0.238;0.853	T	0.72087	-0.4396	9	0.72032	D	0.01	.	9.5048	0.39040	0.1576:0.0:0.0:0.8424	.	46;25	B4E1H6;Q16774	.;KGUA_HUMAN	P	25;46;25;25;46;46;46;25;25;91;25;25;25	ENSP00000355691:L25P;ENSP00000375738:L46P;ENSP00000355687:L25P;ENSP00000317659:L25P;ENSP00000355689:L46P;ENSP00000401832:L46P;ENSP00000355684:L46P;ENSP00000355683:L25P;ENSP00000355682:L25P;ENSP00000407604:L91P;ENSP00000355679:L25P;ENSP00000355677:L25P	ENSP00000317659:L25P	L	+	2	0	GUK1	226399910	1.000000	0.71417	0.638000	0.29380	0.886000	0.51366	7.640000	0.83355	0.724000	0.32296	0.260000	0.18958	CTC	.	.		0.647	GUK1-021	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000095944.1	NM_000858		C	228333287	T	C	228333287	3	2	113	1	0	0	0	0	1	0	0	0	6909	1551	54	2	143	2	GUK1	1	228333287	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	41981026	228333287	20917334	27	17904										
GREB1	9687	hgsc.bcm.edu	37	chr2	11725969	11725969	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tccagtggtggcctctggagAaccagtgtctgttcctgaca	12	11	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:11725969A>G	ENST00000381486.2	+	9	1397	c.1097A>G	c.(1096-1098)gAa>gGa	p.E366G	GREB1_ENST00000263834.5_Missense_Mutation_p.E366G|RN7SL674P_ENST00000463397.2_RNA|GREB1_ENST00000381483.2_Missense_Mutation_p.E366G|GREB1_ENST00000234142.5_Missense_Mutation_p.E366G	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	366						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GCCTCTGGAGAACCAGTGTCT	0.537																																					p.E366G	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.A1097G						.						86	74	78					2																	11725969		2203	4300	6503	SO:0001583	missense	9687	exon9			CTGGAGAACCAGT		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.1097A>G	chr2.hg19:g.11725969A>G	ENSP00000370896:p.Glu366Gly	218.0	0.0		120.0	5.0	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.621814	0.87460	.	.	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000381483;ENST00000234142	T;T;T;T	0.21932	2.98;1.98;1.99;2.98	5.46	5.46	0.80206	.	0.153900	0.45126	D	0.000381	T	0.44993	0.1320	M	0.73217	2.22	0.58432	D	0.999999	D;P;D	0.71674	0.971;0.853;0.998	P;P;D	0.65684	0.745;0.584;0.937	T	0.43065	-0.9414	10	0.62326	D	0.03	-38.1138	15.5136	0.75806	1.0:0.0:0.0:0.0	.	366;366;366	Q4ZG55-2;Q4ZG55-3;Q4ZG55	.;.;GREB1_HUMAN	G	366	ENSP00000370896:E366G;ENSP00000263834:E366G;ENSP00000370892:E366G;ENSP00000234142:E366G	ENSP00000234142:E366G	E	+	2	0	GREB1	11643420	1.000000	0.71417	0.924000	0.36721	0.962000	0.63368	5.761000	0.68801	2.075000	0.62263	0.528000	0.53228	GAA	.	.		0.537	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		G	11725969	A	G	11725969	3	3	113	1	0	0	0	0	1	0	0	0	6769	246	9	2	1127	2	GREB1	2	11725969	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10		11725969	231473404	28	17905										
C2orf39	92749	hgsc.bcm.edu	37	chr2	26644239	26644239	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atcagagagattcacaggagAgtcgaagaagaggagataaa	13	4	2	6			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:26644239A>G	ENST00000288710.2	+	3	401	c.327A>G	c.(325-327)agA>agG	p.R109R		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	109					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											TTCACAGGAGAGTCGAAGAAG	0.458																																					p.R109R		Atlas-SNP	.											.	CCDC164	84	.	0			c.A327G						.						84	82	83					2																	26644239		2203	4300	6503	SO:0001819	synonymous_variant	92749	exon3			CAGGAGAGTCGAA	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"chromosome 2 open reading frame 39", "coiled-coil domain containing 164", "dynein regulatory complex subunit 1 homolog (Chlamydomonas)"	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.327A>G	chr2.hg19:g.26644239A>G		136.0	0.0		95.0	4.0	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Silent	SNP	ENST00000288710.2	hg19	CCDS1723.1																																																																																			.	.		0.458	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038		G	26644239	A	G	26644239	2	3	113	1	0	0	0	0	0	0	0	1	2166	301	11	2		2	C2orf39	2	26644239	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	14918270	26644239	216555134	29	17906										
SLC30A3	7781	hgsc.bcm.edu	37	chr2	27481800	27481800	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctctgagggctctgtgaagAgactgaggcaagcaacatgg	15	8	2	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:27481800A>G	ENST00000233535.4	-	2	450	c.98T>C	c.(97-99)cTc>cCc	p.L33P	SLC30A3_ENST00000447008.2_Missense_Mutation_p.L28P	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	33					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCTGTGAAGAGACTGAGGCA	0.632																																					p.L33P		Atlas-SNP	.											.	SLC30A3	39	.	0			c.T98C						.						35	41	39					2																	27481800		2203	4300	6503	SO:0001583	missense	7781	exon2			GTGAAGAGACTGA	U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"Solute carriers"	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.98T>C	chr2.hg19:g.27481800A>G	ENSP00000233535:p.Leu33Pro	134.0	0.0		91.0	4.0	NM_003459	Q8TC03	Missense_Mutation	SNP	ENST00000233535.4	hg19	CCDS1743.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.496416	0.64186	.	.	ENSG00000115194	ENST00000233535;ENST00000447008;ENST00000426924;ENST00000424577	T;T;T;T	0.81163	-0.32;-0.4;-1.18;-1.46	5.02	5.02	0.67125	.	0.000000	0.49305	D	0.000159	T	0.67069	0.2854	N	0.19112	0.55	0.53688	D	0.999975	B;B	0.20550	0.046;0.027	B;B	0.20184	0.028;0.012	T	0.62728	-0.6793	10	0.28530	T	0.3	-25.7601	11.4202	0.49976	1.0:0.0:0.0:0.0	.	28;33	F5H3B7;Q99726	.;ZNT3_HUMAN	P	33;28;20;11	ENSP00000233535:L33P;ENSP00000415226:L28P;ENSP00000393545:L20P;ENSP00000403959:L11P	ENSP00000233535:L33P	L	-	2	0	SLC30A3	27335304	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	3.470000	0.53100	2.008000	0.58898	0.459000	0.35465	CTC	.	.		0.632	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2			G	27481800	A	G	27481800	3	3	113	1	0	0	0	0	1	0	0	0	14571	304	11	2	1096	2	SLC30A3	2	27481800	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	837561	27481800	215717573	30	17907										
CLIP4	79745	hgsc.bcm.edu	37	chr2	29344378	29344378	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttctgcagcaccaatgcctTcagactgtggtatgtgaagt	10	9	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:29344378T>C	ENST00000320081.5	+	2	379	c.124T>C	c.(124-126)Tca>Cca	p.S42P	CLIP4_ENST00000404424.1_Missense_Mutation_p.S42P|CLIP4_ENST00000401617.2_Intron|CLIP4_ENST00000401605.1_Missense_Mutation_p.S42P	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	42										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					ACCAATGCCTTCAGACTGTGG	0.383																																					p.S42P		Atlas-SNP	.											.	CLIP4	69	.	0			c.T124C						.						201	206	205					2																	29344378		2203	4300	6503	SO:0001583	missense	79745	exon2			ATGCCTTCAGACT	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"Ankyrin repeat domain containing"	26108	protein-coding gene	gene with protein product			"restin-like 2"	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.124T>C	chr2.hg19:g.29344378T>C	ENSP00000327009:p.Ser42Pro	145.0	0.0		99.0	4.0	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Missense_Mutation	SNP	ENST00000320081.5	hg19	CCDS1770.1	.	.	.	.	.	.	.	.	.	.	T	19.71	3.877838	0.72294	.	.	ENSG00000115295	ENST00000401605;ENST00000404424;ENST00000402240;ENST00000320081;ENST00000379543;ENST00000449202	T;T;T;T	0.76060	-0.99;-0.67;-0.67;0.82	5.93	5.93	0.95920	.	0.210963	0.41001	D	0.000977	T	0.77177	0.4092	M	0.62723	1.935	0.58432	D	0.999995	P	0.50943	0.94	P	0.46685	0.524	T	0.80144	-0.1505	10	0.66056	D	0.02	.	16.3871	0.83514	0.0:0.0:0.0:1.0	.	42	Q8N3C7	CLIP4_HUMAN	P	42;42;42;42;43;42	ENSP00000384242:S42P;ENSP00000385594:S42P;ENSP00000327009:S42P;ENSP00000393354:S42P	ENSP00000327009:S42P	S	+	1	0	CLIP4	29197882	1.000000	0.71417	0.996000	0.52242	0.836000	0.47400	4.139000	0.58024	2.270000	0.75569	0.482000	0.46254	TCA	.	.		0.383	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		C	29344378	T	C	29344378	3	2	113	1	0	0	0	0	1	0	0	0	3537	1783	62	2	126	2	CLIP4	2	29344378	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1862578	29344378	213854995	31	17908										
XDH	7498	hgsc.bcm.edu	37	chr2	31620567	31620567	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cggaagccctggaggatgggTctgtagcctgtgcagcggca	17	10	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:31620567T>C	ENST00000379416.3	-	6	510	c.462A>G	c.(460-462)agA>agG	p.R154R		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	154					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GGAGGATGGGTCTGTAGCCTG	0.537																																					p.R154R	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.A462G						.						112	118	116					2																	31620567		2203	4300	6503	SO:0001819	synonymous_variant	7498	exon6			GATGGGTCTGTAG	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.462A>G	chr2.hg19:g.31620567T>C		156.0	0.0		90.0	4.0	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	hg19	CCDS1775.1																																																																																			.	.		0.537	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		C	31620567	T	C	31620567	2	2	113	1	0	0	0	0	0	0	0	1	17441	1664	58	2		2	XDH	2	31620567	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2276189	31620567	211578806	32	17909										
NLRC4	58484	hgsc.bcm.edu	37	chr2	32449645	32449645	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcagaaaagttaacttggatAacacttggctaagttttctg	9	6	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:32449645A>G	ENST00000404025.2	-	10	3460	c.2972T>C	c.(2971-2973)tTa>tCa	p.L991S	NLRC4_ENST00000342905.6_Missense_Mutation_p.L326S|NLRC4_ENST00000402280.1_Missense_Mutation_p.L991S|NLRC4_ENST00000360906.5_Missense_Mutation_p.L991S			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	991					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TAACTTGGATAACACTTGGCT	0.353																																					p.L991S		Atlas-SNP	.											.	NLRC4	165	.	0			c.T2972C						.						113	114	114					2																	32449645		2203	4300	6503	SO:0001583	missense	58484	exon9			TTGGATAACACTT	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.2972T>C	chr2.hg19:g.32449645A>G	ENSP00000385090:p.Leu991Ser	135.0	0.0		75.0	4.0	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	hg19	CCDS33174.1	.	.	.	.	.	.	.	.	.	.	A	15.73	2.921008	0.52653	.	.	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000342905;ENST00000404025	T;T;T;T	0.53640	0.61;0.61;0.61;0.61	4.57	1.97	0.26223	.	0.000000	0.29466	N	0.012077	T	0.32585	0.0834	L	0.27053	0.805	0.33133	D	0.543303	P;P	0.48911	0.911;0.917	B;B	0.43728	0.429;0.348	T	0.45234	-0.9275	9	0.72032	D	0.01	-2.3967	6.0271	0.19660	0.6697:0.1686:0.0:0.1618	.	326;991	Q9NPP4-2;Q9NPP4	.;NLRC4_HUMAN	S	991;991;326;991	ENSP00000354159:L991S;ENSP00000385428:L991S;ENSP00000339666:L326S;ENSP00000385090:L991S	ENSP00000339666:L326S	L	-	2	0	NLRC4	32303149	0.226000	0.23696	0.124000	0.21820	0.891000	0.51852	2.179000	0.42528	0.775000	0.33450	0.528000	0.53228	TTA	.	.		0.353	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		G	32449645	A	G	32449645	3	3	113	1	0	0	0	0	1	0	0	0	10478	372	13	2	106	2	NLRC4	2	32449645	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	829078	32449645	210749728	33	17910										
PPM1B	5495	hgsc.bcm.edu	37	chr2	44436409	44436409	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caaatgctcccaaggtctcaGatgaagcggtgaaaaaagat	10	8	1	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:44436409G>A	ENST00000282412.4	+	3	1319	c.907G>A	c.(907-909)Gat>Aat	p.D303N	PPM1B_ENST00000378551.2_Missense_Mutation_p.D303N|PPM1B_ENST00000345249.4_Missense_Mutation_p.D16N|PPM1B_ENST00000378540.4_3'UTR|PPM1B_ENST00000409895.4_Missense_Mutation_p.D303N|PPM1B_ENST00000409432.3_Missense_Mutation_p.D303N	NM_002706.4	NP_002697.1	O75688	PPM1B_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1B	303					cytokine-mediated signaling pathway (GO:0019221)|N-terminal protein myristoylation (GO:0006499)|negative regulation of defense response to virus (GO:0050687)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(4)|large_intestine(3)|lung(7)|skin(2)	16		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CAAGGTCTCAGATGAAGCGGT	0.363																																					p.D303N		Atlas-SNP	.											.	PPM1B	97	.	0			c.G907A						.						90	89	89					2																	44436409		2203	4300	6503	SO:0001583	missense	5495	exon3			GTCTCAGATGAAG	AJ005801	CCDS1816.1, CCDS1817.1, CCDS1818.1, CCDS46271.1	2p22.1	2012-04-17	2010-03-05		ENSG00000138032	ENSG00000138032	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9276	protein-coding gene	gene with protein product	"protein phosphatase 2C, beta isoform"	603770	"protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform"			9684878	Standard	NM_002706		Approved	PPC2BETAX, PP2CB, PP2CBETA	uc002rtt.3	O75688	OTTHUMG00000128757	ENST00000282412.4:c.907G>A	chr2.hg19:g.44436409G>A	ENSP00000282412:p.Asp303Asn	54.0	0.0		25.0	4.0	NM_001033556	Q461Q2|Q4J6C1|Q4J6C2|Q658R4|Q96ER6|Q9HAY8	Missense_Mutation	SNP	ENST00000282412.4	hg19	CCDS1817.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176650	0.78564	.	.	ENSG00000138032	ENST00000419807;ENST00000409895;ENST00000409432;ENST00000282412;ENST00000378551;ENST00000345249;ENST00000409473	T;T;T;T;T;T	0.22539	1.98;1.98;1.98;1.95;1.97;3.0	5.24	5.24	0.73138	Protein serine/threonine phosphatase 2C, C-terminal (3);	0.284278	0.40728	N	0.001024	T	0.21387	0.0515	L	0.27053	0.805	0.46981	D	0.999277	B;B;B;B;B	0.20459	0.045;0.004;0.022;0.018;0.009	B;B;B;B;B	0.32022	0.139;0.038;0.063;0.088;0.063	T	0.05131	-1.0904	10	0.34782	T	0.22	-6.4833	19.1692	0.93570	0.0:0.0:1.0:0.0	.	303;303;303;303;303	Q4J6C0;O75688-2;Q4J6C1;O75688;Q4J6C2	.;.;.;PPM1B_HUMAN;.	N	303;303;303;303;303;16;228	ENSP00000390087:D303N;ENSP00000387341:D303N;ENSP00000387287:D303N;ENSP00000282412:D303N;ENSP00000367813:D303N;ENSP00000386982:D228N	ENSP00000282412:D303N	D	+	1	0	PPM1B	44289913	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.854000	0.86942	2.590000	0.87494	0.655000	0.94253	GAT	.	.		0.363	PPM1B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250672.1	NM_002706		A	44436409	G	A	44436409	3	1	113	1	0	0	0	0	1	0	0	0	12348	942	33	3	913	3	PPM1B	2	44436409	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	11986764	44436409	198762964	34	17911										
GTF2A1L	11036	hgsc.bcm.edu	37	chr2	48872210	48872210	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcaaactttacttttcctggTtatcccattcatgtaccagc	5	12	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:48872210T>C	ENST00000403751.3	+	5	379	c.342T>C	c.(340-342)ggT>ggC	p.G114G	GTF2A1L_ENST00000430487.2_Silent_p.G80G|STON1-GTF2A1L_ENST00000394754.1_Silent_p.G818G|STON1-GTF2A1L_ENST00000309827.2_Silent_p.G818G|STON1-GTF2A1L_ENST00000402114.2_Silent_p.G818G|STON1-GTF2A1L_ENST00000394751.3_Intron|STON1-GTF2A1L_ENST00000405008.1_Silent_p.G818G|LHCGR_ENST00000420913.3_Intron|GTF2A1L_ENST00000468326.1_3'UTR	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	114					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTTTTCCTGGTTATCCCATTC	0.343																																					p.G818G		Atlas-SNP	.											.	STON1-GTF2A1L	180	.	0			c.T2454C						.						116	116	116					2																	48872210		2203	4300	6503	SO:0001819	synonymous_variant	286749	exon7			TCCTGGTTATCCC	AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.342T>C	chr2.hg19:g.48872210T>C		146.0	0.0		78.0	4.0	NM_001198593	B4DY14|Q53FD9|Q5D050	Silent	SNP	ENST00000403751.3	hg19	CCDS46281.1																																																																																			.	.		0.343	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		C	48872210	T	C	48872210	2	2	113	1	0	0	0	0	0	0	0	1	6862	1712	60	2		2	GTF2A1L	2	48872210	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	4435801	48872210	194327163	35	17912										
PSME4	23198	hgsc.bcm.edu	37	chr2	54152693	54152693	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	taccataaatatttctttggAacattgggtgaggattgtac	9	5	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:54152693A>G	ENST00000404125.1	-	14	1847	c.1792T>C	c.(1792-1794)Tcc>Ccc	p.S598P	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	598					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			ATTTCTTTGGAACATTGGGTG	0.338																																					p.S598P		Atlas-SNP	.											.	PSME4	247	.	0			c.T1792C						.						124	116	118					2																	54152693		2203	4300	6503	SO:0001583	missense	23198	exon14			CTTTGGAACATTG	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.1792T>C	chr2.hg19:g.54152693A>G	ENSP00000384211:p.Ser598Pro	226.0	0.0		123.0	5.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	A	27.0	4.792073	0.90453	.	.	ENSG00000068878	ENST00000404125	T	0.03772	3.81	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.24586	0.0596	M	0.83223	2.63	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.00763	-1.1576	10	0.54805	T	0.06	.	16.226	0.82293	1.0:0.0:0.0:0.0	.	598	Q14997	PSME4_HUMAN	P	598	ENSP00000384211:S598P	ENSP00000384211:S598P	S	-	1	0	PSME4	54006197	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.104000	0.94239	2.230000	0.72887	0.528000	0.53228	TCC	.	.		0.338	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		G	54152693	A	G	54152693	3	3	113	1	0	0	0	0	1	0	0	0	12721	246	9	2	3871	2	PSME4	2	54152693	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	5280483	54152693	189046680	36	17913										
PSME4	23198	hgsc.bcm.edu	37	chr2	54159837	54159837	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	attatttgaaggatggtaaaAagatgtgatgctgttaaaca	10	2	0	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:54159837A>G	ENST00000404125.1	-	9	1073	c.1018T>C	c.(1018-1020)Ttt>Ctt	p.F340L	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	340					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			GGATGGTAAAAAGATGTGATG	0.398																																					p.F340L		Atlas-SNP	.											.	PSME4	247	.	0			c.T1018C						.						129	117	121					2																	54159837		2203	4300	6503	SO:0001583	missense	23198	exon9			GGTAAAAAGATGT	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.1018T>C	chr2.hg19:g.54159837A>G	ENSP00000384211:p.Phe340Leu	145.0	0.0		79.0	4.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	A	27.0	4.790439	0.90367	.	.	ENSG00000068878	ENST00000404125	T	0.03496	3.91	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.09423	0.0232	M	0.81497	2.545	0.80722	D	1	P	0.50156	0.932	B	0.42593	0.392	T	0.04140	-1.0974	10	0.46703	T	0.11	.	16.2988	0.82793	1.0:0.0:0.0:0.0	.	340	Q14997	PSME4_HUMAN	L	340	ENSP00000384211:F340L	ENSP00000374643:F340L	F	-	1	0	PSME4	54013341	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.262000	0.95591	2.311000	0.77944	0.533000	0.62120	TTT	.	.		0.398	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		G	54159837	A	G	54159837	3	3	113	1	0	0	0	0	1	0	0	0	12721	14	1	2	4665	2	PSME4	2	54159837	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	7144	54159837	189039536	37	17914										
PNPT1	87178	hgsc.bcm.edu	37	chr2	55906857	55906857	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccagcaaccactaaatttaaAgtactagaagacatttcttt	4	9	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:55906857A>G	ENST00000447944.2	-	8	725	c.639T>C	c.(637-639)acT>acC	p.T213T		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	213					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CTAAATTTAAAGTACTAGAAG	0.328																																					p.T213T		Atlas-SNP	.											.	PNPT1	68	.	0			c.T639C						.						105	107	106					2																	55906857		2201	4299	6500	SO:0001819	synonymous_variant	87178	exon8			ATTTAAAGTACTA	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.639T>C	chr2.hg19:g.55906857A>G		144.0	0.0		59.0	4.0	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Silent	SNP	ENST00000447944.2	hg19	CCDS1856.1																																																																																			.	.		0.328	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		G	55906857	A	G	55906857	2	3	113	1	0	0	0	0	0	0	0	1	12182	59	3	2		2	PNPT1	2	55906857	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1747020	55906857	187292516	38	17915										
PUS10	150962	hgsc.bcm.edu	37	chr2	61175205	61175205	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cctgagttttcaagtggaggCggaagtggtgctcatccacg	14	9	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:61175205C>T	ENST00000316752.6	-	16	1685	c.1424G>A	c.(1423-1425)cGc>cAc	p.R475H	PUS10_ENST00000407787.1_Missense_Mutation_p.R475H	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	475					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			CAAGTGGAGGCGGAAGTGGTG	0.542																																					p.R475H		Atlas-SNP	.											.	PUS10	49	.	0			c.G1424A						.						159	160	160					2																	61175205		2203	4300	6503	SO:0001583	missense	150962	exon16			TGGAGGCGGAAGT	AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"coiled-coil domain containing 139"	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.1424G>A	chr2.hg19:g.61175205C>T	ENSP00000326003:p.Arg475His	208.0	0.0		109.0	5.0	NM_144709	Q5JPJ5|Q96MI8	Missense_Mutation	SNP	ENST00000316752.6	hg19	CCDS1865.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.514692	0.27123	.	.	ENSG00000162927	ENST00000316752;ENST00000407787	D;D	0.88431	-2.38;-2.38	5.86	4.96	0.65561	Pseudouridine synthase, catalytic domain (1);	0.220456	0.49916	N	0.000133	D	0.83982	0.5372	L	0.55834	1.745	0.80722	D	1	P;P	0.34684	0.463;0.463	B;B	0.27076	0.076;0.076	T	0.81165	-0.1057	10	0.15952	T	0.53	8.0589	14.4899	0.67645	0.0:0.9271:0.0:0.0729	.	475;475	A8K6R4;Q3MIT2	.;PUS10_HUMAN	H	475	ENSP00000326003:R475H;ENSP00000386074:R475H	ENSP00000326003:R475H	R	-	2	0	PUS10	61028709	1.000000	0.71417	1.000000	0.80357	0.038000	0.13279	2.736000	0.47385	1.557000	0.49525	0.650000	0.86243	CGC	.	.		0.542	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709		T	61175205	C	T	61175205	3	4	113	1	0	0	0	0	1	0	0	0	12846	768	27	1	177	1	PUS10	2	61175205	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	5268348	61175205	182024168	39	17916										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71592804	71592804	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctttgtcagaatgtaaacagGtgtctgataaagctgtttct	9	6	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:71592804G>T	ENST00000409544.1	+	6	2593	c.1963G>T	c.(1963-1965)Gtg>Ttg	p.V655L	ZNF638_ENST00000377802.2_Missense_Mutation_p.V655L|ZNF638_ENST00000355812.3_Missense_Mutation_p.V655L|ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000264447.4_Missense_Mutation_p.V655L	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	655					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						ATGTAAACAGGTGTCTGATAA	0.363																																					p.V655L		Atlas-SNP	.											.	ZNF638	179	.	0			c.G1963T						.						48	47	47					2																	71592804		2203	4300	6503	SO:0001583	missense	27332	exon6			AAACAGGTGTCTG	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.1963G>T	chr2.hg19:g.71592804G>T	ENSP00000386433:p.Val655Leu	198.0	0.0		118.0	47.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	G	9.344	1.063785	0.20067	.	.	ENSG00000075292	ENST00000410075;ENST00000544512;ENST00000394137;ENST00000355812;ENST00000377802;ENST00000264447;ENST00000409544	T;T;T;T;T;T	0.72505	-0.07;-0.66;0.51;-0.06;1.51;1.51	5.69	-1.65	0.08291	.	1.967430	0.01694	N	0.026819	T	0.55305	0.1912	N	0.24115	0.695	0.09310	N	1	B;B;B;B;B;B	0.23806	0.03;0.091;0.029;0.017;0.022;0.029	B;B;B;B;B;B	0.23574	0.005;0.047;0.012;0.025;0.017;0.011	T	0.36212	-0.9757	10	0.29301	T	0.29	2.5262	5.8202	0.18524	0.4791:0.1386:0.3823:0.0	.	655;761;655;655;655;655	A8K583;F5H330;Q14966-4;Q14966-3;Q14966;Q14966-2	.;.;.;.;ZN638_HUMAN;.	L	655;761;234;655;655;655;655	ENSP00000386669:V655L;ENSP00000438189:V761L;ENSP00000348066:V655L;ENSP00000367033:V655L;ENSP00000264447:V655L;ENSP00000386433:V655L	ENSP00000264447:V655L	V	+	1	0	ZNF638	71446312	0.002000	0.14202	0.014000	0.15608	0.821000	0.46438	-0.248000	0.08854	-0.135000	0.11495	0.563000	0.77884	GTG	.	.		0.363	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		T	71592804	G	T	71592804	3	4	113	1	0	0	0	0	1	0	0	0	18070	1261	44	3	1981	3	ZNF638	2	71592804	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	10417599	71592804	171606569	40	17917										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73716837	73716837	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tattattgagagccatgaaaAgggatgtttccggactctaa	10	6	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:73716837A>G	ENST00000264448.6	+	10	7859	c.7748A>G	c.(7747-7749)aAg>aGg	p.K2583R	AC096546.1_ENST00000408160.1_RNA|ALMS1_ENST00000409009.1_Missense_Mutation_p.K2541R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2583					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AGCCATGAAAAGGGATGTTTC	0.458																																					p.K2583R		Atlas-SNP	.											.	ALMS1	384	.	0			c.A7748G						.						124	118	120					2																	73716837		1918	4116	6034	SO:0001583	missense	7840	exon10			ATGAAAAGGGATG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7748A>G	chr2.hg19:g.73716837A>G	ENSP00000264448:p.Lys2583Arg	118.0	0.0		50.0	22.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.242566	0.39598	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.10860	2.83;2.83	4.45	3.31	0.37934	.	0.000000	0.52532	D	0.000080	T	0.09949	0.0244	L	0.48642	1.525	0.80722	D	1	P;P;P	0.41597	0.756;0.756;0.756	B;B;B	0.39805	0.31;0.31;0.31	T	0.08229	-1.0732	10	0.51188	T	0.08	.	6.6531	0.22973	0.8956:0.0:0.1044:0.0	.	2583;2541;2583	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	R	2541;2583	ENSP00000386627:K2541R;ENSP00000264448:K2583R	ENSP00000264448:K2583R	K	+	2	0	ALMS1	73570345	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	1.674000	0.37544	1.041000	0.40125	0.528000	0.53228	AAG	.	.		0.458	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		G	73716837	A	G	73716837	3	3	113	1	0	0	0	0	1	0	0	0	535	72	3	2	7786	2	ALMS1	2	73716837	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2124033	73716837	169482536	41	17918										
WDR33	55339	hgsc.bcm.edu	37	chr2	128480841	128480841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tctcaccatattctactccaTcttcagacattccaggtaaa	3	13	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:128480841T>C	ENST00000322313.4	-	12	1435	c.1277A>G	c.(1276-1278)gAt>gGt	p.D426G		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	426					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TTCTACTCCATCTTCAGACAT	0.353																																					p.D426G		Atlas-SNP	.											.	WDR33	136	.	0			c.A1277G						.						151	163	158					2																	128480841		2203	4300	6503	SO:0001583	missense	55339	exon12			ACTCCATCTTCAG		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.1277A>G	chr2.hg19:g.128480841T>C	ENSP00000325377:p.Asp426Gly	107.0	0.0		85.0	4.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.447507	0.63178	.	.	ENSG00000136709	ENST00000322313	D	0.90069	-2.61	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.92011	0.7469	L	0.47716	1.5	0.80722	D	1	D	0.63880	0.993	D	0.74674	0.984	D	0.91720	0.5388	10	0.42905	T	0.14	-14.7764	15.4363	0.75149	0.0:0.0:0.0:1.0	.	426	Q9C0J8	WDR33_HUMAN	G	426	ENSP00000325377:D426G	ENSP00000325377:D426G	D	-	2	0	WDR33	128197311	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.259000	0.78381	2.091000	0.63221	0.533000	0.62120	GAT	.	.		0.353	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		C	128480841	T	C	128480841	3	2	113	1	0	0	0	0	1	0	0	0	17302	1435	50	2	2777	2	WDR33	2	128480841	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	54764004	128480841	114718532	42	17919										
KYNU	8942	hgsc.bcm.edu	37	chr2	143799616	143799616	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctttattttttccccacagTgtgacaagcggaatccaaat	7	10	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:143799616T>C	ENST00000264170.4	+	14	1531	c.1273T>C	c.(1273-1275)Tgt>Cgt	p.C425R	KYNU_ENST00000409512.1_Splice_Site_p.C425R	NM_003937.2	NP_003928.1			kynureninase											large_intestine(10)|liver(1)|lung(18)|prostate(3)|skin(4)	36				BRCA - Breast invasive adenocarcinoma(221;0.072)		TTCCCCACAGTGTGACAAGCG	0.348																																					p.C425R		Atlas-SNP	.											.	KYNU	110	.	0			c.T1273C						.						129	127	127					2																	143799616		2203	4299	6502	SO:0001630	splice_region_variant	8942	exon15			CCACAGTGTGACA	U57721	CCDS2183.1, CCDS33299.1	2q22.2	2010-11-23	2010-11-23		ENSG00000115919	ENSG00000115919	3.7.1.3		6469	protein-coding gene	gene with protein product	"L-kynurenine hydrolase"	605197	"kynureninase (L-kynurenine hydrolase)"			8706755, 9180257	Standard	NM_001199241		Approved		uc002tvl.3	Q16719	OTTHUMG00000131829	ENST00000264170.4:c.1273-1T>C	chr2.hg19:g.143799616T>C		158.0	0.0		71.0	4.0	NM_001199241		Missense_Mutation	SNP	ENST00000264170.4	hg19	CCDS2183.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.188161	0.57909	.	.	ENSG00000115919	ENST00000264170;ENST00000409512	T;T	0.54866	0.55;0.55	5.09	5.09	0.68999	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.090646	0.85682	D	0.000000	T	0.75917	0.3915	M	0.91300	3.195	0.80722	D	1	D	0.76494	0.999	D	0.72075	0.976	T	0.80989	-0.1136	9	.	.	.	.	11.4247	0.50003	0.0:0.0:0.0:1.0	.	425	Q16719	KYNU_HUMAN	R	425	ENSP00000264170:C425R;ENSP00000386731:C425R	.	C	+	1	0	KYNU	143516086	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	3.820000	0.55693	2.263000	0.75096	0.528000	0.53228	TGT	.	.		0.348	KYNU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254772.1	NM_001032998	Missense_Mutation	C	143799616	T	C	143799616	5	2	113	1	0	0	0	0	0	0	1	0	8596	1710	59	2	1349	2	KYNU	2	143799616	Splice_Site	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	15318775	143799616	99399757	43	17920										
NEB	4703	hgsc.bcm.edu	37	chr2	152392260	152392260	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tattgatcggagagtcggcaAcatacttgaaatctgacttt	9	7	1	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:152392260A>G	ENST00000172853.10	-	114	16301	c.16154T>C	c.(16153-16155)gTt>gCt	p.V5385A	NEB_ENST00000409198.1_Missense_Mutation_p.V5385A|NEB_ENST00000397345.3_Missense_Mutation_p.V7086A|NEB_ENST00000604864.1_Missense_Mutation_p.V7086A|NEB_ENST00000603639.1_Missense_Mutation_p.V7086A|NEB_ENST00000427231.2_Missense_Mutation_p.V7086A			P20929	NEBU_HUMAN	nebulin	5385					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		AGAGTCGGCAACATACTTGAA	0.343																																					p.V7086A		Atlas-SNP	.											.	NEB	1697	.	0			c.T21257C						.						99	93	95					2																	152392260		1850	4085	5935	SO:0001583	missense	4703	exon142			TCGGCAACATACT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.16154T>C	chr2.hg19:g.152392260A>G	ENSP00000172853:p.Val5385Ala	123.0	0.0		90.0	4.0	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	A	14.02	2.410359	0.42715	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000420924	T;T;T;T;T;T	0.11821	3.32;3.31;3.31;3.18;3.32;2.74	6.17	-5.92	0.02261	.	0.513957	0.21451	N	0.074327	T	0.12220	0.0297	N	0.14661	0.345	0.30100	N	0.807546	B;P	0.46859	0.068;0.885	B;P	0.57244	0.041;0.816	T	0.09207	-1.0685	10	0.48119	T	0.1	.	10.9905	0.47547	0.2316:0.0:0.057:0.7114	.	5385;1816	P20929;Q14215	NEBU_HUMAN;.	A	5385;7086;7086;1434;1816;5385;174	ENSP00000386259:V5385A;ENSP00000380505:V7086A;ENSP00000416578:V7086A;ENSP00000410961:V1816A;ENSP00000172853:V5385A;ENSP00000405167:V174A	ENSP00000172853:V5385A	V	-	2	0	NEB	152100506	0.192000	0.23301	0.007000	0.13788	0.585000	0.36419	0.528000	0.23002	-0.822000	0.04306	0.533000	0.62120	GTT	.	.		0.343	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152392260	A	G	152392260	3	3	113	1	0	0	0	0	1	0	0	0	10311	43	2	2	4593	2	NEB	2	152392260	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	8592644	152392260	90807113	44	17921										
NEB	4703	hgsc.bcm.edu	37	chr2	152534626	152534626	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cacgttcatataatgaaccaGtttagggtcatcttgaagac	8	8	3	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:152534626G>A	ENST00000172853.10	-	33	3478	c.3331C>T	c.(3331-3333)Ctg>Ttg	p.L1111L	NEB_ENST00000409198.1_Silent_p.L1111L|NEB_ENST00000397345.3_Silent_p.L1111L|NEB_ENST00000604864.1_Silent_p.L1111L|NEB_ENST00000603639.1_Silent_p.L1111L|NEB_ENST00000427231.2_Silent_p.L1111L			P20929	NEBU_HUMAN	nebulin	1111					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TAATGAACCAGTTTAGGGTCA	0.378																																					p.L1111L		Atlas-SNP	.											.	NEB	1697	.	0			c.C3331T						.						77	71	73					2																	152534626		1837	4087	5924	SO:0001819	synonymous_variant	4703	exon33			GAACCAGTTTAGG	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.3331C>T	chr2.hg19:g.152534626G>A		382.0	1.0		227.0	94.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	.		0.378	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152534626	G	A	152534626	2	1	113	1	0	0	0	0	0	0	0	1	10311	1020	36	3		3	NEB	2	152534626	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	142366	152534626	90664747	45	17922										
CACNB4	785	hgsc.bcm.edu	37	chr2	152732942	152732942	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gaaaagatgggaacgtacccTccgtgaaaacgtcctctttt	9	10	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:152732942T>C	ENST00000539935.1	-	5	586	c.519A>G	c.(517-519)ggA>ggG	p.G173G	CACNB4_ENST00000360283.6_Silent_p.G139G|CACNB4_ENST00000534999.1_Silent_p.G139G|CACNB4_ENST00000397327.2_Silent_p.G126G|CACNB4_ENST00000427385.1_Silent_p.G155G|CACNB4_ENST00000201943.5_Silent_p.G173G	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	173					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GAACGTACCCTCCGTGAAAAC	0.408																																					p.G173G		Atlas-SNP	.											.	CACNB4	108	.	0			c.A519G						.						129	121	124					2																	152732942		1888	4112	6000	SO:0001819	synonymous_variant	785	exon5			GTACCCTCCGTGA	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"Calcium channel subunits"	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.519A>G	chr2.hg19:g.152732942T>C		124.0	0.0		100.0	5.0	NM_001145798	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Silent	SNP	ENST00000539935.1	hg19	CCDS46426.1																																																																																			.	.		0.408	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3		C	152732942	T	C	152732942	2	2	113	1	0	0	0	0	0	0	0	1	2557	1538	54	2		2	CACNB4	2	152732942	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	198316	152732942	90466431	46	17923										
FMNL2	114793	hgsc.bcm.edu	37	chr2	153435453	153435453	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	acgctgtcaatgagattgcaCtaagcctgaacaacaagaat	8	9	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:153435453C>G	ENST00000288670.9	+	8	1124	c.757C>G	c.(757-759)Cta>Gta	p.L253V		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	253	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						TGAGATTGCACTAAGCCTGAA	0.388																																					p.L253V		Atlas-SNP	.											.	FMNL2	75	.	0			c.C757G						.						81	79	79					2																	153435453		1929	4166	6095	SO:0001583	missense	114793	exon8			ATTGCACTAAGCC	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.757C>G	chr2.hg19:g.153435453C>G	ENSP00000288670:p.Leu253Val	116.0	0.0		50.0	19.0	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	hg19	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.813000	0.70912	.	.	ENSG00000157827	ENST00000288670	D	0.89552	-2.53	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.95162	0.8432	M	0.87180	2.865	0.80722	D	1	D	0.67145	0.996	D	0.75484	0.986	D	0.93768	0.7072	10	0.33141	T	0.24	.	19.4836	0.95020	0.0:1.0:0.0:0.0	.	253	Q96PY5-3	.	V	253	ENSP00000288670:L253V	ENSP00000288670:L253V	L	+	1	2	FMNL2	153143699	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.847000	0.62867	2.700000	0.92200	0.563000	0.77884	CTA	.	.		0.388	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		G	153435453	C	G	153435453	3	3	113	1	0	0	0	0	1	0	0	0	5960	564	20	4	787	4	FMNL2	2	153435453	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	702511	153435453	89763920	47	17924										
FMNL2	114793	hgsc.bcm.edu	37	chr2	153486415	153486415	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atttaaacttcagagtttagAtctggtgagtggactaaaag	10	4	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:153486415A>G	ENST00000475377.2	+	7	871	c.671A>G	c.(670-672)gAt>gGt	p.D224G	FMNL2_ENST00000288670.9_Missense_Mutation_p.D849G			Q96PY5	FMNL2_HUMAN	formin-like 2	849	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						CAGAGTTTAGATCTGGTGAGT	0.388																																					p.D849G		Atlas-SNP	.											.	FMNL2	75	.	0			c.A2546G						.						94	86	89					2																	153486415		1883	4100	5983	SO:0001583	missense	114793	exon20			GTTTAGATCTGGT	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000475377.2:c.671A>G	chr2.hg19:g.153486415A>G	ENSP00000418959:p.Asp224Gly	141.0	0.0		87.0	4.0	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000475377.2	hg19		.	.	.	.	.	.	.	.	.	.	A	20.2	3.942041	0.73557	.	.	ENSG00000157827	ENST00000288670;ENST00000421344;ENST00000475377	T;T	0.63417	-0.04;-0.04	5.61	5.61	0.85477	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	D	0.83769	0.5326	M	0.93763	3.455	0.80722	D	1	D;P;D	0.69078	0.997;0.949;0.991	D;P;D	0.79108	0.992;0.869;0.968	D	0.86461	0.1779	10	0.42905	T	0.14	.	15.759	0.78063	1.0:0.0:0.0:0.0	.	849;330;849	Q96PY5;Q6ZN96;Q96PY5-3	FMNL2_HUMAN;.;.	G	849;330;224	ENSP00000288670:D849G;ENSP00000418959:D224G	ENSP00000288670:D849G	D	+	2	0	FMNL2	153194661	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.231000	0.95317	2.269000	0.75478	0.533000	0.62120	GAT	.	.		0.388	FMNL2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333583.3	NM_052905		G	153486415	A	G	153486415	3	3	113	1	0	0	0	0	1	0	0	0	5960	333	12	2	2624	2	FMNL2	2	153486415	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	50962	153486415	89712958	48	17925										
MARCH7	64844	hgsc.bcm.edu	37	chr2	160615791	160615791	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atgtaaagagaagttggagcTtaacctggaggattttgata	12	3	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:160615791T>C	ENST00000259050.4	+	7	1960	c.1838T>C	c.(1837-1839)cTt>cCt	p.L613P	MARCH7_ENST00000409591.1_Missense_Mutation_p.L575P|MARCH7_ENST00000539065.1_Missense_Mutation_p.L557P|MARCH7_ENST00000409175.1_Missense_Mutation_p.L613P	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	613					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						AAGTTGGAGCTTAACCTGGAG	0.318																																					p.L613P		Atlas-SNP	.											.	MARCH7	48	.	0			c.T1838C						.						132	134	133					2																	160615791		2203	4298	6501	SO:0001583	missense	64844	exon7			TGGAGCTTAACCT	AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	17393	protein-coding gene	gene with protein product		613334	"axotrophin", "membrane-associated ring finger (C3HC4) 7"	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.1838T>C	chr2.hg19:g.160615791T>C	ENSP00000259050:p.Leu613Pro	158.0	0.0		87.0	4.0	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	hg19	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.006535	0.74932	.	.	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000409591;ENST00000420397	T;T;T;T;T	0.50277	2.36;2.39;2.36;2.37;0.75	5.49	5.49	0.81192	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-CH-type (1);	0.000000	0.85682	D	0.000000	T	0.60327	0.2260	L	0.38531	1.155	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.85130	0.996;0.997;0.997	T	0.63453	-0.6634	10	0.72032	D	0.01	-14.4281	15.876	0.79162	0.0:0.0:0.0:1.0	.	557;575;613	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	P	613;557;613;575;46	ENSP00000386830:L613P;ENSP00000442992:L557P;ENSP00000259050:L613P;ENSP00000387238:L575P;ENSP00000391493:L46P	ENSP00000259050:L613P	L	+	2	0	MARCH7	160324037	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.852000	0.86927	2.200000	0.70718	0.454000	0.30748	CTT	.	.		0.318	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826		C	160615791	T	C	160615791	3	2	113	1	0	0	0	0	1	0	0	0	9315	1609	56	2	1860	2	MARCH7	2	160615791	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	7129376	160615791	82583582	49	17926										
SCN3A	6328	hgsc.bcm.edu	37	chr2	166019086	166019086	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgtcatctccaatgtaatccTtccagttaaatgtgctcatt	5	10	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:166019086T>C	ENST00000360093.3	-	8	1438	c.947A>G	c.(946-948)aAg>aGg	p.K316R	SCN3A_ENST00000283254.7_Missense_Mutation_p.K316R|SCN3A_ENST00000409101.3_Missense_Mutation_p.K316R	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	316					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AATGTAATCCTTCCAGTTAAA	0.348																																					p.K316R		Atlas-SNP	.											.	SCN3A	544	.	0			c.A947G						.						120	122	121					2																	166019086		2203	4300	6503	SO:0001583	missense	6328	exon8			TAATCCTTCCAGT	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.947A>G	chr2.hg19:g.166019086T>C	ENSP00000353206:p.Lys316Arg	138.0	0.0		76.0	4.0	NM_001081676	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	hg19		.	.	.	.	.	.	.	.	.	.	T	11.48	1.650437	0.29336	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	D;D;D;D	0.96041	-3.89;-3.88;-3.84;-3.71	5.82	5.82	0.92795	Ion transport (1);	0.234157	0.29980	N	0.010706	D	0.92136	0.7507	L	0.33189	0.99	0.80722	D	1	B;B;B;B;B	0.31485	0.077;0.325;0.001;0.001;0.145	B;B;B;B;B	0.28849	0.042;0.095;0.019;0.019;0.036	D	0.90956	0.4809	10	0.49607	T	0.09	.	16.1839	0.81934	0.0:0.0:0.0:1.0	.	316;316;316;316;316	Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3	SCN3A_HUMAN;.;.;.;.	R	316	ENSP00000353206:K316R;ENSP00000283254:K316R;ENSP00000386726:K316R;ENSP00000403348:K316R	ENSP00000283254:K316R	K	-	2	0	SCN3A	165727332	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.590000	0.46154	2.222000	0.72286	0.533000	0.62120	AAG	.	.		0.348	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		C	166019086	T	C	166019086	3	2	113	1	0	0	0	0	1	0	0	0	13933	1609	56	2	5139	2	SCN3A	2	166019086	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	5403295	166019086	77180287	50	17927										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168099632	168099632	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gaagggagaggtgcagtccaTtagatggatctttgagaatc	14	5	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:168099632T>C	ENST00000409195.1	+	9	1819	c.1730T>C	c.(1729-1731)aTt>aCt	p.I577T	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.I355T|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.I577T	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	402					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GTGCAGTCCATTAGATGGATC	0.388																																					p.I577T		Atlas-SNP	.											.	XIRP2	914	.	0			c.T1730C						.						68	67	68					2																	168099632		1909	4115	6024	SO:0001583	missense	129446	exon9			AGTCCATTAGATG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.1730T>C	chr2.hg19:g.168099632T>C	ENSP00000386840:p.Ile577Thr	191.0	0.0		89.0	5.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.673191	0.47781	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.22743	1.94;1.94;1.94	5.54	4.38	0.52667	.	0.338576	0.34986	N	0.003532	T	0.14960	0.0361	N	0.22421	0.69	0.38926	D	0.957832	P;B;B	0.35226	0.491;0.435;0.01	B;B;B	0.34536	0.185;0.116;0.005	T	0.07385	-1.0775	10	0.66056	D	0.02	-2.2586	11.1645	0.48535	0.0:0.0731:0.0:0.9269	.	402;402;355	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	T	577;577;355	ENSP00000386840:I577T;ENSP00000295237:I577T;ENSP00000387255:I355T	ENSP00000295237:I577T	I	+	2	0	XIRP2	167807878	1.000000	0.71417	0.900000	0.35374	0.979000	0.70002	4.141000	0.58038	0.936000	0.37367	0.533000	0.62120	ATT	.	.		0.388	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		C	168099632	T	C	168099632	3	2	113	1	0	0	0	0	1	0	0	0	17445	1493	52	2	1760	2	XIRP2	2	168099632	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2080546	168099632	75099741	51	17928										
LRP2	4036	hgsc.bcm.edu	37	chr2	170103365	170103365	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttcattggttgggtccccctCgcatgtcaagtgattggaag	12	9	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:170103365C>T	ENST00000263816.3	-	21	3325	c.3040G>A	c.(3040-3042)Gag>Aag	p.E1014K	LRP2_ENST00000443831.1_Missense_Mutation_p.E877K	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1014	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GGGTCCCCCTCGCATGTCAAG	0.517																																					p.E1014K		Atlas-SNP	.											.	LRP2	751	.	0			c.G3040A						.						116	105	109					2																	170103365		2203	4300	6503	SO:0001583	missense	4036	exon21			CCCCCTCGCATGT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.3040G>A	chr2.hg19:g.170103365C>T	ENSP00000263816:p.Glu1014Lys	259.0	0.0		149.0	51.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	4.510	0.094617	0.08681	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	T;T	0.44881	0.91;0.91	6.03	4.22	0.49857	Epidermal growth factor-like (1);	0.250775	0.39615	N	0.001301	T	0.23886	0.0578	L	0.29908	0.895	0.26234	N	0.978977	B;P	0.36412	0.452;0.552	B;B	0.29785	0.107;0.042	T	0.19451	-1.0305	10	0.05721	T	0.95	.	11.8159	0.52211	0.1263:0.6124:0.2613:0.0	.	877;1014	E9PC35;P98164	.;LRP2_HUMAN	K	1014;877	ENSP00000263816:E1014K;ENSP00000409813:E877K	ENSP00000263816:E1014K	E	-	1	0	LRP2	169811611	0.076000	0.21285	0.004000	0.12327	0.081000	0.17604	0.568000	0.23623	0.852000	0.35287	0.655000	0.94253	GAG	.	.		0.517	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170103365	C	T	170103365	3	4	113	1	0	0	0	0	1	0	0	0	8965	893	31	1	11163	1	LRP2	2	170103365	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	2003733	170103365	73096008	52	17929										
KLHL23	151230	hgsc.bcm.edu	37	chr2	170598012	170598012	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gagctacaattccgatatcaAcgaatggagcctcatcacct	7	12	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:170598012A>G	ENST00000392647.2	+	3	1575	c.1331A>G	c.(1330-1332)aAc>aGc	p.N444S	KLHL23_ENST00000272797.4_Missense_Mutation_p.N444S|KLHL23_ENST00000602521.1_5'UTR	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	444										breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						TCCGATATCAACGAATGGAGC	0.433																																					p.N444S		Atlas-SNP	.											.	KLHL23	52	.	0			c.A1331G						.						167	143	151					2																	170598012		2203	4300	6503	SO:0001583	missense	151230	exon3			ATATCAACGAATG	BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160		"Kelch-like", "BTB/POZ domain containing"	27506	protein-coding gene	gene with protein product			"kelch-like 23 (Drosophila)"				Standard	NM_144711		Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000392647.2:c.1331A>G	chr2.hg19:g.170598012A>G	ENSP00000376419:p.Asn444Ser	189.0	0.0		99.0	4.0	NM_144711	Q8N9B9|Q96FT8	Missense_Mutation	SNP	ENST00000392647.2	hg19	CCDS2236.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.68|18.68	3.676295|3.676295	0.67928|0.67928	.|.	.|.	ENSG00000213160|ENSG00000213160	ENST00000272797;ENST00000392647;ENST00000437875|ENST00000448589	D;D;D|.	0.82526|.	-1.62;-1.62;-1.62|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Kelch-type beta propeller (1);|.	0.143602|.	0.64402|.	D|.	0.000012|.	T|T	0.77336|0.77336	0.4115|0.4115	M|M	0.80508|0.80508	2.5|2.5	0.29743|.	N|.	0.836963|.	B|.	0.26445|.	0.149|.	B|.	0.36186|.	0.219|.	T|T	0.79431|0.79431	-0.1806|-0.1806	9|4	0.72032|.	D|.	0.01|.	.|.	16.0977|16.0977	0.81139|0.81139	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	444|.	Q8NBE8|.	KLH23_HUMAN|.	S|A	444;444;265|4	ENSP00000272797:N444S;ENSP00000376419:N444S;ENSP00000394732:N265S|.	ENSP00000272797:N444S|.	N|T	+|+	2|1	0|0	KLHL23|KLHL23	170306258|170306258	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.931000|0.931000	0.56810|0.56810	9.339000|9.339000	0.96797|0.96797	2.216000|2.216000	0.71823|0.71823	0.528000|0.528000	0.53228|0.53228	AAC|ACG	.	.		0.433	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711		G	170598012	A	G	170598012	3	3	113	1	0	0	0	0	1	0	0	0	8387	43	2	2	1337	2	KLHL23	2	170598012	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	494647	170598012	72601361	53	17930										
RAPGEF4	11069	hgsc.bcm.edu	37	chr2	173852991	173852991	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggatcagtgaatgtagtcatTtacggcaaggtatatatatc	10	5	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:173852991T>C	ENST00000397081.3	+	13	1361	c.1218T>C	c.(1216-1218)atT>atC	p.I406I	RAPGEF4_ENST00000538974.1_Silent_p.I235I|RAPGEF4_ENST00000473043.1_3'UTR|RAPGEF4_ENST00000539331.1_Silent_p.I253I|RAPGEF4_ENST00000264111.6_Silent_p.I405I|RAPGEF4_ENST00000540783.1_Silent_p.I253I|RAPGEF4_ENST00000535187.1_Silent_p.I186I|RAPGEF4_ENST00000409036.1_Silent_p.I406I|RAPGEF4_ENST00000397087.3_Silent_p.I262I	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	406					blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			ATGTAGTCATTTACGGCAAGG	0.338																																					p.I406I		Atlas-SNP	.											.	RAPGEF4	103	.	0			c.T1218C						.						124	113	116					2																	173852991		1814	4087	5901	SO:0001819	synonymous_variant	11069	exon13			AGTCATTTACGGC	U78516	CCDS42775.1, CCDS42776.1, CCDS63060.1, CCDS63061.1, CCDS74604.1	2q31-q32	2008-02-05	2004-03-26		ENSG00000091428	ENSG00000091428			16626	protein-coding gene	gene with protein product	"cAMP-regulated guanine nucleotide exchange factor II", " exchange protein directly activated by cAMP 2"	606058	"RAP guanine-nucleotide-exchange factor (GEF) 4"			10777494, 9856955	Standard	NM_007023		Approved	cAMP-GEFII, CGEF2	uc002uhv.4	Q8WZA2	OTTHUMG00000133677	ENST00000397081.3:c.1218T>C	chr2.hg19:g.173852991T>C		74.0	0.0		57.0	4.0	NM_007023	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Silent	SNP	ENST00000397081.3	hg19	CCDS42775.1																																																																																			.	.		0.338	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023		C	173852991	T	C	173852991	2	2	113	1	0	0	0	0	0	0	0	1	13061	1829	64	2		2	RAPGEF4	2	173852991	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	3254979	173852991	69346382	54	17931										
AGPS	8540	hgsc.bcm.edu	37	chr2	178310274	178310274	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tctttcttcctttgcaacagAatcgaattctctgggttgat	7	9	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:178310274A>G	ENST00000264167.4	+	8	936	c.790A>G	c.(790-792)Aat>Gat	p.N264D	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	264	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			TTTGCAACAGAATCGAATTCT	0.363																																					p.N264D		Atlas-SNP	.											.	AGPS	56	.	0			c.A790G						.						88	85	86					2																	178310274		2203	4300	6503	SO:0001630	splice_region_variant	8540	exon8			CAACAGAATCGAA	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.790-1A>G	chr2.hg19:g.178310274A>G		144.0	0.0		79.0	4.0	NM_003659	A5D8U9|Q2TU35	Missense_Mutation	SNP	ENST00000264167.4	hg19	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	A	19.84	3.901825	0.72754	.	.	ENSG00000018510	ENST00000264167;ENST00000536686	D	0.84730	-1.89	5.87	5.87	0.94306	FAD-binding, type 2, subdomain 1 (1);FAD-binding, type 2 (2);FAD linked oxidase, N-terminal (1);	0.145736	0.64402	D	0.000011	D	0.83667	0.5304	L	0.43646	1.37	0.80722	D	1	B	0.31581	0.329	B	0.39738	0.308	T	0.80502	-0.1354	9	.	.	.	.	16.2676	0.82597	1.0:0.0:0.0:0.0	.	264	O00116	ADAS_HUMAN	D	264;134	ENSP00000264167:N264D	.	N	+	1	0	AGPS	178018520	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.815000	0.86186	2.243000	0.73865	0.533000	0.62120	AAT	.	.		0.363	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2		Missense_Mutation	G	178310274	A	G	178310274	5	3	113	1	0	0	0	0	0	0	1	0	394	260	9	2	820	2	AGPS	2	178310274	Splice_Site	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	4457283	178310274	64889099	55	17932										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179247841	179247841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgacaccagtaacattaaccTgtggaatatcttgaggaaca	8	8	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:179247841T>C	ENST00000190611.4	+	17	2088	c.1712T>C	c.(1711-1713)cTg>cCg	p.L571P	OSBPL6_ENST00000409045.3_Missense_Mutation_p.L540P|OSBPL6_ENST00000315022.2_Missense_Mutation_p.L575P|OSBPL6_ENST00000392505.2_Missense_Mutation_p.L596P|OSBPL6_ENST00000359685.3_Missense_Mutation_p.L535P|OSBPL6_ENST00000409631.1_Missense_Mutation_p.L535P	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	571					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			AACATTAACCTGTGGAATATC	0.522																																					p.L596P		Atlas-SNP	.											.	OSBPL6	178	.	0			c.T1787C						.						89	92	91					2																	179247841		2203	4300	6503	SO:0001583	missense	114880	exon18			TTAACCTGTGGAA	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1712T>C	chr2.hg19:g.179247841T>C	ENSP00000190611:p.Leu571Pro	169.0	0.0		74.0	4.0	NM_001201480	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	hg19	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.837154	0.91117	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.75339	0.3836	H	0.98238	4.18	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.997;1.0;0.999	D;D;D;D;D	0.91635	0.997;0.993;0.989;0.999;0.991	D	0.85128	0.0973	10	0.87932	D	0	-9.8421	16.5885	0.84745	0.0:0.0:0.0:1.0	.	540;575;535;596;571	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3	.;.;.;.;OSBL6_HUMAN	P	596;535;540;571;535;575	ENSP00000376293:L596P;ENSP00000352713:L535P;ENSP00000387248:L540P;ENSP00000190611:L571P;ENSP00000386885:L535P;ENSP00000318723:L575P	ENSP00000190611:L571P	L	+	2	0	OSBPL6	178956087	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.317000	0.78254	0.460000	0.39030	CTG	.	.		0.522	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		C	179247841	T	C	179247841	3	2	113	1	0	0	0	0	1	0	0	0	11290	1580	55	2	1892	2	OSBPL6	2	179247841	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	937567	179247841	63951532	56	17933										
TTN	7273	hgsc.bcm.edu	37	chr2	179434805	179434805	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagacgcttatggcatcttgTccatctaatgccttctttat	6	11	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:179434805T>C	ENST00000591111.1	-	276	71355	c.71131A>G	c.(71131-71133)Aca>Gca	p.T23711A	TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T16287A|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T25352A|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T22784A|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T16479A|TTN_ENST00000359218.5_Missense_Mutation_p.T16412A|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23711	Fibronectin type-III 72. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGGCATCTTGTCCATCTAATG	0.428																																					p.T25352A		Atlas-SNP	.											TTN_ENST00000359218,right_upper_lobe,carcinoma,0,5	TTN	18412	.	0			c.A76054G						.						129	120	123					2																	179434805		1951	4146	6097	SO:0001583	missense	7273	exon326			ATCTTGTCCATCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.71131A>G	chr2.hg19:g.179434805T>C	ENSP00000465570:p.Thr23711Ala	107.0	0.0		71.0	3.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.53	1.665009	0.29604	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.87	3.41	0.39046	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.53738	0.1815	M	0.64170	1.965	0.49299	D	0.999773	P;P;P;P	0.38420	0.63;0.489;0.63;0.489	B;B;B;B	0.42495	0.389;0.389;0.389;0.273	T	0.54649	-0.8262	9	0.87932	D	0	.	11.1163	0.48262	0.247:0.0:0.0:0.7529	.	16287;16412;16479;23711	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	22784;16287;16479;16412;16285	ENSP00000343764:T22784A;ENSP00000434586:T16287A;ENSP00000340554:T16479A;ENSP00000352154:T16412A	ENSP00000340554:T16479A	T	-	1	0	TTN	179143051	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.119000	0.64679	0.430000	0.26230	-0.341000	0.08007	ACA	.	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179434805	T	C	179434805	3	2	113	1	0	0	0	0	1	0	0	0	16750	1667	58	2	32073	2	TTN	2	179434805	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	186964	179434805	63764568	57	17934										
TTN	7273	hgsc.bcm.edu	37	chr2	179640606	179640606	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttgaatttactgcgcagctcTtccgactcttcaggcacttt	7	12	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:179640606T>C	ENST00000591111.1	-	28	6209	c.5985A>G	c.(5983-5985)gaA>gaG	p.E1995E	TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000460472.2_Silent_p.E1949E|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Silent_p.E1995E|TTN_ENST00000342992.6_Silent_p.E1995E|TTN_ENST00000342175.6_Silent_p.E1949E|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000360870.5_Silent_p.E1995E|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000359218.5_Silent_p.E1949E			Q8WZ42	TITIN_HUMAN	titin	12808					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCGCAGCTCTTCCGACTCTT	0.443																																					p.E1995E		Atlas-SNP	.											.	TTN	18412	.	0			c.A5985G						.						114	121	118					2																	179640606		2203	4300	6503	SO:0001819	synonymous_variant	7273	exon28			CAGCTCTTCCGAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.5985A>G	chr2.hg19:g.179640606T>C		225.0	0.0		97.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179640606	T	C	179640606	2	2	113	1	0	0	0	0	0	0	0	1	16750	1606	56	2		2	TTN	2	179640606	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	205801	179640606	63558767	58	17935										
C2orf88	84281	hgsc.bcm.edu	37	chr2	191064868	191064868	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccatacattgagagtgagggGccttgaggctgtaggatgac	15	7	0	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:191064868G>A	ENST00000340623.4	+	2	693	c.282G>A	c.(280-282)ggG>ggA	p.G94G	C2orf88_ENST00000409870.1_Silent_p.G94G|C2orf88_ENST00000396974.2_Silent_p.G94G|C2orf88_ENST00000443551.2_Silent_p.G94G	NM_001042519.1|NM_001042520.1|NM_001042521.1|NM_032321.2	NP_001035984.1|NP_001035985.1|NP_001035986.1|NP_115697.2	Q9BSF0	SMAKA_HUMAN	chromosome 2 open reading frame 88	94						plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(1)	3						AGAGTGAGGGGCCTTGAGGCT	0.428																																					p.G94G		Atlas-SNP	.											.	C2orf88	7	.	0			c.G282A						.						132	129	130					2																	191064868		2027	4195	6222	SO:0001819	synonymous_variant	84281	exon2			TGAGGGGCCTTGA	BC005083	CCDS42792.1	2q32.2	2014-02-12	2009-04-08		ENSG00000187699	ENSG00000187699			28191	protein-coding gene	gene with protein product	"small membrane AKAP"	615117				23996002	Standard	NM_032321		Approved	MGC13057, smAKAP	uc002urt.3	Q9BSF0	OTTHUMG00000154361	ENST00000340623.4:c.282G>A	chr2.hg19:g.191064868G>A		233.0	0.0		135.0	23.0	NM_001042519	D3DPI3|P0C876|Q53TC7	Silent	SNP	ENST00000340623.4	hg19	CCDS42792.1																																																																																			.	.		0.428	C2orf88-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334954.1	NM_032321		A	191064868	G	A	191064868	2	1	113	1	0	0	0	0	0	0	0	1	2204	1190	42	3		3	C2orf88	2	191064868	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	11424262	191064868	52134505	59	17936										
HECW2	57520	hgsc.bcm.edu	37	chr2	197092980	197092980	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aggcccactgtaatccagccTgtaacaaaaatccacaaaaa	5	12	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:197092980T>C	ENST00000260983.3	-	22	3947		c.e22-2		HECW2_ENST00000409111.1_Splice_Site	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2						protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						TAATCCAGCCTGTAACAAAAA	0.363																																					.		Atlas-SNP	.											.	HECW2	239	.	0			c.3765-2A>G						.						51	53	52					2																	197092980		2202	4300	6502	SO:0001630	splice_region_variant	57520	exon23			CCAGCCTGTAACA	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.3765-2A>G	chr2.hg19:g.197092980T>C		148.0	0.0		87.0	4.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Splice_Site	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.026504	0.75390	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6649	0.77221	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HECW2	196801225	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	7.868000	0.87116	2.281000	0.76405	0.533000	0.62120	.	.	.		0.363	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760	Intron	C	197092980	T	C	197092980	5	2	113	1	0	0	0	0	0	0	1	0	7052	1594	55	2	987	2	HECW2	2	197092980	Splice_Site	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	6028112	197092980	46106393	60	17937										
CCDC150	284992	hgsc.bcm.edu	37	chr2	197539019	197539019	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agttgagctgcatgcttcagActgttactatggaaaaagcc	10	8	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:197539019A>G	ENST00000389175.4	+	10	1219	c.1084A>G	c.(1084-1086)Act>Gct	p.T362A	CCDC150_ENST00000472405.2_3'UTR|CCDC150_ENST00000272831.7_Missense_Mutation_p.T30A|CCDC150_ENST00000423093.2_Missense_Mutation_p.T30A	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	362										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						CATGCTTCAGACTGTTACTAT	0.408																																					p.T362A		Atlas-SNP	.											.	CCDC150	96	.	0			c.A1084G						.						91	90	90					2																	197539019		1899	4128	6027	SO:0001583	missense	284992	exon10			CTTCAGACTGTTA		CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.1084A>G	chr2.hg19:g.197539019A>G	ENSP00000373827:p.Thr362Ala	98.0	0.0		77.0	4.0	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Missense_Mutation	SNP	ENST00000389175.4	hg19	CCDS46478.1	.	.	.	.	.	.	.	.	.	.	A	1.409	-0.576000	0.03882	.	.	ENSG00000144395	ENST00000272831;ENST00000389175;ENST00000423093	T	0.28666	1.6	5.17	1.01	0.19927	.	0.349077	0.25112	N	0.033056	T	0.12518	0.0304	N	0.16903	0.455	0.20638	N	0.999876	B;B	0.09022	0.002;0.002	B;B	0.11329	0.001;0.006	T	0.28650	-1.0037	10	0.07813	T	0.8	0.0669	3.4833	0.07610	0.4741:0.0:0.3503:0.1756	.	30;362	B4DZ03;Q8NCX0	.;CC150_HUMAN	A	30;362;30	ENSP00000373827:T362A	ENSP00000272831:T30A	T	+	1	0	CCDC150	197247264	0.503000	0.26115	0.742000	0.31022	0.846000	0.48090	1.470000	0.35354	0.019000	0.15079	-0.353000	0.07706	ACT	.	.		0.408	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539		G	197539019	A	G	197539019	3	3	113	1	0	0	0	0	1	0	0	0	2787	275	10	2	1122	2	CCDC150	2	197539019	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	446039	197539019	45660354	61	17938										
GTF3C3	9330	hgsc.bcm.edu	37	chr2	197654717	197654717	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atgcgcagcaatcaactcaaActgcaatgatttttccatgt	6	10	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:197654717A>G	ENST00000263956.3	-	5	702	c.613T>C	c.(613-615)Ttt>Ctt	p.F205L	GTF3C3_ENST00000470386.1_5'UTR|GTF3C3_ENST00000409364.3_Missense_Mutation_p.F205L	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	205					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						ATCAACTCAAACTGCAATGAT	0.378																																					p.F205L		Atlas-SNP	.											.	GTF3C3	96	.	0			c.T613C						.						117	111	113					2																	197654717		2203	4300	6503	SO:0001583	missense	9330	exon5			ACTCAAACTGCAA	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.613T>C	chr2.hg19:g.197654717A>G	ENSP00000263956:p.Phe205Leu	156.0	0.0		84.0	4.0	NM_001206774	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	hg19	CCDS2316.1	.	.	.	.	.	.	.	.	.	.	A	33	5.277666	0.95459	.	.	ENSG00000119041	ENST00000263956;ENST00000409364	T;T	0.36157	1.27;1.27	5.66	5.66	0.87406	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.057710	0.64402	N	0.000001	T	0.47655	0.1457	L	0.42008	1.315	0.80722	D	1	P;D	0.67145	0.532;0.996	B;D	0.63192	0.348;0.912	T	0.27872	-1.0061	10	0.15066	T	0.55	-26.7547	15.8985	0.79353	1.0:0.0:0.0:0.0	.	205;205	Q9Y5Q9-2;Q9Y5Q9	.;TF3C3_HUMAN	L	205	ENSP00000263956:F205L;ENSP00000386465:F205L	ENSP00000263956:F205L	F	-	1	0	GTF3C3	197362962	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.202000	0.95026	2.169000	0.68431	0.374000	0.22700	TTT	.	.		0.378	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			G	197654717	A	G	197654717	3	3	113	1	0	0	0	0	1	0	0	0	6883	43	2	2	2103	2	GTF3C3	2	197654717	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	115698	197654717	45544656	62	17939										
PLCL1	5334	hgsc.bcm.edu	37	chr2	198948734	198948734	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttgatatttctgccataaaaGagatcagactggggaaaaac	9	6	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:198948734G>A	ENST00000428675.1	+	2	891	c.493G>A	c.(493-495)Gag>Aag	p.E165K	PLCL1_ENST00000437704.2_Missense_Mutation_p.E67K	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	165	Interaction with PPP1C.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.E67*(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	TGCCATAAAAGAGATCAGACT	0.453																																					p.E165K		Atlas-SNP	.											PLCL1_ENST00000428675,NS,carcinoma,0,3	PLCL1	358	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G493A						.						91	98	96					2																	198948734		2203	4300	6503	SO:0001583	missense	5334	exon2			ATAAAAGAGATCA	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.493G>A	chr2.hg19:g.198948734G>A	ENSP00000402861:p.Glu165Lys	124.0	0.0		69.0	3.0	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	hg19	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	G	35	5.585576	0.96578	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.65732	-0.17;-0.17	5.67	5.67	0.87782	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.64402	D	0.000001	T	0.79522	0.4460	M	0.80982	2.52	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.61722	0.893;0.893	T	0.79160	-0.1918	9	.	.	.	.	20.1421	0.98061	0.0:0.0:1.0:0.0	.	165;91	Q15111;B4DYZ4	PLCL1_HUMAN;.	K	165;67	ENSP00000402861:E165K;ENSP00000414138:E67K	.	E	+	1	0	PLCL1	198656979	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.800000	0.99124	2.836000	0.97738	0.655000	0.94253	GAG	.	.		0.453	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		A	198948734	G	A	198948734	3	1	113	1	0	0	0	0	1	0	0	0	12048	943	33	3	499	3	PLCL1	2	198948734	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	1294017	198948734	44250639	63	17940										
SPATS2L	26010	hgsc.bcm.edu	37	chr2	201334662	201334662	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgtcagcgagcgtaaatatgAcgaggagctcgggaaagctg	15	7	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:201334662A>G	ENST00000358677.5	+	11	1230	c.983A>G	c.(982-984)gAc>gGc	p.D328G	SPATS2L_ENST00000460095.1_3'UTR|SPATS2L_ENST00000451764.2_Missense_Mutation_p.D328G|SPATS2L_ENST00000409385.1_Missense_Mutation_p.D268G|SPATS2L_ENST00000409140.3_Missense_Mutation_p.D328G|SPATS2L_ENST00000409755.3_Missense_Mutation_p.D358G|SPATS2L_ENST00000409988.3_Missense_Mutation_p.D328G|SPATS2L_ENST00000409151.1_Missense_Mutation_p.D336G|SPATS2L_ENST00000360760.5_Missense_Mutation_p.D259G|SPATS2L_ENST00000409718.1_Missense_Mutation_p.D328G	NM_001282735.1|NM_001282743.1|NM_001282744.1|NM_015535.2	NP_001269664.1|NP_001269672.1|NP_001269673.1|NP_056350.2	Q9NUQ6	SPS2L_HUMAN	spermatogenesis associated, serine-rich 2-like	328						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	10						CGTAAATATGACGAGGAGCTC	0.498																																					p.D328G		Atlas-SNP	.											.	SPATS2L	88	.	0			c.A983G						.						59	57	58					2																	201334662		1892	4125	6017	SO:0001583	missense	26010	exon11			AATATGACGAGGA	AF193059	CCDS46483.1, CCDS46484.1, CCDS74621.1, CCDS74622.1	2q33.1	2009-06-12			ENSG00000196141	ENSG00000196141			24574	protein-coding gene	gene with protein product	"DNA polymerase transactivated protein 6"	613817				11230166	Standard	NM_001100422		Approved	DNAPTP6	uc002uvr.4	Q9NUQ6	OTTHUMG00000154589	ENST00000358677.5:c.983A>G	chr2.hg19:g.201334662A>G	ENSP00000351503:p.Asp328Gly	174.0	0.0		125.0	6.0	NM_001100423	A8K381|B4DRE6|B4DT67|B7WNZ7|Q53T22|Q8WV53|Q8WYG1|Q9NTW4	Missense_Mutation	SNP	ENST00000358677.5	hg19	CCDS46483.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.138924	0.77775	.	.	ENSG00000196141	ENST00000409718;ENST00000358677;ENST00000409988;ENST00000409385;ENST00000451764;ENST00000360760;ENST00000409140;ENST00000409397;ENST00000409755;ENST00000409151	.	.	.	4.96	4.96	0.65561	.	0.000000	0.64402	D	0.000003	T	0.75852	0.3906	M	0.64170	1.965	0.48040	D	0.999577	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.87578	0.997;0.998;0.997	T	0.78583	-0.2148	9	0.87932	D	0	-24.1067	13.6569	0.62344	1.0:0.0:0.0:0.0	.	358;259;328	B4DT67;Q9NUQ6-2;Q9NUQ6	.;.;SPS2L_HUMAN	G	328;328;328;268;328;259;328;259;358;336	.	ENSP00000351503:D328G	D	+	2	0	SPATS2L	201042907	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	7.160000	0.77495	2.218000	0.71995	0.533000	0.62120	GAC	.	.		0.498	SPATS2L-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336208.3	NM_015535		G	201334662	A	G	201334662	3	3	113	1	0	0	0	0	1	0	0	0	15035	275	10	2	1017	2	SPATS2L	2	201334662	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2385928	201334662	41864711	64	17941										
KCTD18	130535	hgsc.bcm.edu	37	chr2	201369657	201369657	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaaaggtatttaaatagacgTccatcacggtcaataacaca	6	8	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:201369657T>C	ENST00000359878.3	-	3	696	c.186A>G	c.(184-186)ggA>ggG	p.G62G	KCTD18_ENST00000468413.1_5'UTR|KCTD18_ENST00000409157.1_Silent_p.G62G	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	62	BTB.				protein homooligomerization (GO:0051260)					endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						TAAATAGACGTCCATCACGGT	0.393																																					p.G62G		Atlas-SNP	.											.	KCTD18	44	.	0			c.A186G						.						87	77	80					2																	201369657		2203	4300	6503	SO:0001819	synonymous_variant	130535	exon3			TAGACGTCCATCA	AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 18"				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.186A>G	chr2.hg19:g.201369657T>C		167.0	0.0		85.0	6.0	NM_152387	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Silent	SNP	ENST00000359878.3	hg19	CCDS2330.1																																																																																			.	.		0.393	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387		C	201369657	T	C	201369657	2	2	113	1	0	0	0	0	0	0	0	1	8114	1654	58	2		2	KCTD18	2	201369657	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	34995	201369657	41829716	65	17942										
ADAM23	8745	hgsc.bcm.edu	37	chr2	207414830	207414830	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttccgtagccatcacgtggTatatttgaagaaatgaaata	8	6	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:207414830T>C	ENST00000264377.3	+	9	1207	c.879T>C	c.(877-879)ggT>ggC	p.G293G	ADAM23_ENST00000374416.1_Silent_p.G293G|ADAM23_ENST00000374415.3_Silent_p.G293G	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	293					cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		CATCACGTGGTATATTTGAAG	0.308																																					p.G293G	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											.	ADAM23	239	.	0			c.T879C						.						83	83	83					2																	207414830		2202	4296	6498	SO:0001819	synonymous_variant	8745	exon9			ACGTGGTATATTT	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"ADAM metallopeptidase domain containing"	202	protein-coding gene	gene with protein product		603710	"a disintegrin and metalloproteinase domain 23"			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.879T>C	chr2.hg19:g.207414830T>C		160.0	0.0		92.0	4.0	NM_003812	A2RU59	Silent	SNP	ENST00000264377.3	hg19	CCDS2369.1																																																																																			.	.		0.308	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812		C	207414830	T	C	207414830	2	2	113	1	0	0	0	0	0	0	0	1	245	1625	57	2		2	ADAM23	2	207414830	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	6045173	207414830	35784543	66	17943										
MARCH4	57574	hgsc.bcm.edu	37	chr2	217124210	217124210	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cctgctcaggggcaggggtgCctgcggtctcctcttccgag	15	14	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:217124210C>T	ENST00000273067.4	-	4	2824	c.1058G>A	c.(1057-1059)gGc>gAc	p.G353D	AC012513.6_ENST00000417481.1_RNA	NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	353						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		GGCAGGGGTGCCTGCGGTCTC	0.632																																					p.G353D		Atlas-SNP	.											.	MARCH4	50	.	0			c.G1058A						.						52	53	53					2																	217124210		2202	4300	6502	SO:0001583	missense	57574	exon4			GGGGTGCCTGCGG	AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	29269	protein-coding gene	gene with protein product		608208	"membrane-associated ring finger (C3HC4) 4"			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.1058G>A	chr2.hg19:g.217124210C>T	ENSP00000273067:p.Gly353Asp	166.0	0.0		101.0	34.0	NM_020814	Q4KMN7|Q86WR8	Missense_Mutation	SNP	ENST00000273067.4	hg19	CCDS33376.1	.	.	.	.	.	.	.	.	.	.	C	6.190	0.403292	0.11754	.	.	ENSG00000144583	ENST00000273067	T	0.14893	2.47	5.62	2.81	0.32909	.	0.656708	0.14823	N	0.296336	T	0.11452	0.0279	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32903	-0.9889	10	0.25751	T	0.34	.	7.58	0.27959	0.0:0.5806:0.2718:0.1476	.	353	Q9P2E8	MARH4_HUMAN	D	353	ENSP00000273067:G353D	ENSP00000273067:G353D	G	-	2	0	MARCH4	216832455	0.989000	0.36119	0.024000	0.17045	0.091000	0.18340	1.148000	0.31614	0.305000	0.22832	0.561000	0.74099	GGC	.	.		0.632	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814		T	217124210	C	T	217124210	3	4	113	1	0	0	0	0	1	0	0	0	9312	739	26	3	178	3	MARCH4	2	217124210	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	9709380	217124210	26075163	67	17944										
DNER	92737	hgsc.bcm.edu	37	chr2	230272034	230272034	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gacagctgacgttagcgcagGgatccttgtacaattcacag	11	10	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:230272034G>T	ENST00000341772.4	-	10	1771	c.1637C>A	c.(1636-1638)cCc>cAc	p.P546H		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	546	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Follistatin-like.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		GTTAGCGCAGGGATCCTTGTA	0.537																																					p.P546H		Atlas-SNP	.											.	DNER	129	.	0			c.C1637A						.						122	105	111					2																	230272034		2203	4300	6503	SO:0001583	missense	92737	exon10			GCGCAGGGATCCT	AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.1637C>A	chr2.hg19:g.230272034G>T	ENSP00000345229:p.Pro546His	84.0	0.0		44.0	4.0	NM_139072	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Missense_Mutation	SNP	ENST00000341772.4	hg19	CCDS33390.1	.	.	.	.	.	.	.	.	.	.	G	18.66	3.672538	0.67928	.	.	ENSG00000187957	ENST00000341772;ENST00000543700	D	0.96136	-3.92	5.6	5.6	0.85130	Follistatin-like, N-terminal (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.96679	0.8916	L	0.43598	1.365	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96965	0.9704	10	0.59425	D	0.04	.	18.3815	0.90452	0.0:0.0:1.0:0.0	.	546	Q8NFT8	DNER_HUMAN	H	546;264	ENSP00000345229:P546H	ENSP00000345229:P546H	P	-	2	0	DNER	229980278	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.123000	0.77176	2.642000	0.89623	0.563000	0.77884	CCC	.	.		0.537	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072		T	230272034	G	T	230272034	3	4	113	1	0	0	0	0	1	0	0	0	4669	1232	43	3	592	3	DNER	2	230272034	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	13147824	230272034	12927339	68	17945										
CHRND	1144	hgsc.bcm.edu	37	chr2	233400022	233400022	+	Nonstop_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caggacaagcgcttcatctaGggtgggcctgttggggagcc	16	10	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:233400022G>T	ENST00000258385.3	+	12	1586	c.1554G>T	c.(1552-1554)taG>taT	p.*518Y	CHRND_ENST00000543200.1_Nonstop_Mutation_p.*503Y|CHRND_ENST00000457943.2_Nonstop_Mutation_p.*324Y	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)	0					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	GCTTCATCTAGGGTGGGCCTG	0.612																																					p.X518Y		Atlas-SNP	.											.	CHRND	67	.	0			c.G1554T						.						58	59	59					2																	233400022		2203	4300	6503	SO:0001578	stop_lost	1144	exon12			CATCTAGGGTGGG	X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1965	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, delta (muscle)"	100720	"cholinergic receptor, nicotinic, delta"	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.1554G>T	chr2.hg19:g.233400022G>T	ENSP00000258385:p.*518Tyrext*13	62.0	0.0		60.0	4.0	NM_000751	A8K661|B4DT92|Q52LH4	Missense_Mutation	SNP	ENST00000258385.3	hg19	CCDS2494.1	.	.	.	.	.	.	.	.	.	.	G	8.413	0.844661	0.16963	.	.	ENSG00000135902	ENST00000543200;ENST00000258385;ENST00000457943	.	.	.	4.97	4.09	0.47781	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.611	0.51059	0.083:0.0:0.917:0.0	.	.	.	.	Y	503;518;324	.	.	X	+	3	2	CHRND	233108266	1.000000	0.71417	0.128000	0.21923	0.182000	0.23217	3.220000	0.51207	1.091000	0.41335	0.655000	0.94253	TAG	.	.		0.612	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2			T	233400022	G	T	233400022	4	4	113	1	0	0	0	0	0	0	0	0	3396	995	35	3	1600	3	CHRND	2	233400022	Nonstop_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	3127988	233400022	9799351	69	17946										
HJURP	55355	hgsc.bcm.edu	37	chr2	234756059	234756059	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttactgctaaggcccaagcaActgactcttcctggtctgac	8	13	2	2	rs200818956	byFrequency	TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:234756059A>G	ENST00000411486.2	-	5	451	c.386T>C	c.(385-387)gTt>gCt	p.V129A	HJURP_ENST00000432087.1_Intron|HJURP_ENST00000434039.1_5'Flank|HJURP_ENST00000441687.1_Intron	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	129					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		GGCCCAAGCAACTGACTCTTC	0.507																																					p.V129A		Atlas-SNP	.											.	HJURP	72	.	0			c.T386C						.						119	101	107					2																	234756059		2203	4300	6503	SO:0001583	missense	55355	exon5			CAAGCAACTGACT		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.386T>C	chr2.hg19:g.234756059A>G	ENSP00000414109:p.Val129Ala	211.0	0.0		87.0	4.0	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	hg19	CCDS33406.1	.	.	.	.	.	.	.	.	.	.	A	11.19	1.564497	0.27915	.	.	ENSG00000123485	ENST00000411486;ENST00000454020	T;T	0.34859	3.14;1.34	3.05	-5.09	0.02920	.	.	.	.	.	T	0.20659	0.0497	L	0.44542	1.39	0.09310	N	1	B	0.15141	0.012	B	0.06405	0.002	T	0.41734	-0.9492	9	0.06365	T	0.9	1.8914	6.851	0.24014	0.2619:0.1633:0.5747:0.0	.	129	Q8NCD3	HJURP_HUMAN	A	129;88	ENSP00000414109:V129A;ENSP00000414051:V88A	ENSP00000414109:V129A	V	-	2	0	HJURP	234420798	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-0.421000	0.07053	-1.231000	0.02557	0.482000	0.46254	GTT	.	A|0.999;C|0.001		0.507	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410		G	234756059	A	G	234756059	3	3	113	1	0	0	0	0	1	0	0	0	7198	43	2	2	1880	2	HJURP	2	234756059	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1356037	234756059	8443314	70	17947										
HDLBP	3069	hgsc.bcm.edu	37	chr2	242194881	242194881	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctgtctgagggtgggatctCaacggaaactccagttctct	12	10	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr2:242194881C>T	ENST00000391975.1	-	8	1215	c.988G>A	c.(988-990)Gag>Aag	p.E330K	HDLBP_ENST00000427183.2_Intron|HDLBP_ENST00000310931.4_Missense_Mutation_p.E330K|HDLBP_ENST00000391976.2_Missense_Mutation_p.E330K	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	330	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		GGTGGGATCTCAACGGAAACT	0.478																																					p.E330K		Atlas-SNP	.											.	HDLBP	118	.	0			c.G988A						.						155	142	147					2																	242194881		2203	4300	6503	SO:0001583	missense	3069	exon8			GGATCTCAACGGA		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.988G>A	chr2.hg19:g.242194881C>T	ENSP00000375836:p.Glu330Lys	265.0	0.0		82.0	4.0	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	hg19	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650954	0.87958	.	.	ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931	T;T;T	0.27720	1.65;1.65;1.65	6.17	6.17	0.99709	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.63674	0.2531	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62895	-0.6757	10	0.51188	T	0.08	-36.6558	20.8794	0.99867	0.0:1.0:0.0:0.0	.	330;330	B2R5V9;Q00341	.;VIGLN_HUMAN	K	330	ENSP00000375836:E330K;ENSP00000375837:E330K;ENSP00000312042:E330K	ENSP00000312042:E330K	E	-	1	0	HDLBP	241843554	1.000000	0.71417	0.980000	0.43619	0.031000	0.12232	7.755000	0.85180	2.941000	0.99782	0.655000	0.94253	GAG	.	.		0.478	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		T	242194881	C	T	242194881	3	4	113	1	0	0	0	0	1	0	0	0	7034	835	29	3	2902	3	HDLBP	2	242194881	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	7438822	242194881	1004492	71	17948										
EDEM1	9695	hgsc.bcm.edu	37	chr3	5252876	5252876	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gatggagagcttctttctcaGtgagacctgtaaatatttgt	10	6	2	2	rs148682616		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:5252876G>C	ENST00000256497.4	+	10	1788	c.1655G>C	c.(1654-1656)aGt>aCt	p.S552T	EDEM1_ENST00000445686.1_Missense_Mutation_p.S357T	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	552					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		TTCTTTCTCAGTGAGACCTGT	0.448																																					p.S552T		Atlas-SNP	.											.	EDEM1	45	.	0			c.G1655C						.						111	103	106					3																	5252876		2203	4300	6503	SO:0001583	missense	9695	exon10			TTCTCAGTGAGAC	D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.1655G>C	chr3.hg19:g.5252876G>C	ENSP00000256497:p.Ser552Thr	151.0	0.0		73.0	31.0	NM_014674	A8K9C8|B4DXP3	Missense_Mutation	SNP	ENST00000256497.4	hg19	CCDS33686.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.777636	0.90195	.	.	ENSG00000134109	ENST00000256497;ENST00000445686	T;T	0.74002	-0.8;-0.8	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.90417	0.7000	H	0.94964	3.605	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.92807	0.6261	10	0.72032	D	0.01	-17.1796	19.1382	0.93436	0.0:0.0:1.0:0.0	.	552	Q92611	EDEM1_HUMAN	T	552;357	ENSP00000256497:S552T;ENSP00000394099:S357T	ENSP00000256497:S552T	S	+	2	0	EDEM1	5227876	1.000000	0.71417	0.978000	0.43139	0.796000	0.44982	7.451000	0.80668	2.505000	0.84491	0.655000	0.94253	AGT	.	G|1.000;A|0.000		0.448	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674		C	5252876	G	C	5252876	3	2	113	1	0	0	0	0	1	0	0	0	4913	1029	36	4	1693	4	EDEM1	3	5252876	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10		5252876	192769554	72	17949										
ATG7	10533	hgsc.bcm.edu	37	chr3	11354826	11354826	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggttttgctatcctgccctcTgtcttccagagagtttacct	8	12	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:11354826T>C	ENST00000354449.3	+	6	485	c.460T>C	c.(460-462)Tgt>Cgt	p.C154R	ATG7_ENST00000354956.5_Missense_Mutation_p.C154R|ATG7_ENST00000446450.2_Intron	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7	154					adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						TCCTGCCCTCTGTCTTCCAGA	0.353																																					p.C154R		Atlas-SNP	.											.	ATG7	56	.	0			c.T460C						.						130	122	125					3																	11354826		2203	4300	6503	SO:0001583	missense	10533	exon6			GCCCTCTGTCTTC	AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"Ubiquitin-like modifier activating enzymes"	16935	protein-coding gene	gene with protein product	"ubiquitin-activating enzyme E1-like protein"	608760	"APG7 autophagy 7-like (S. cerevisiae)", "ATG7 autophagy related 7 homolog (S. cerevisiae)"	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740	ENST00000354449.3:c.460T>C	chr3.hg19:g.11354826T>C	ENSP00000346437:p.Cys154Arg	123.0	0.0		93.0	4.0	NM_001136031	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Missense_Mutation	SNP	ENST00000354449.3	hg19	CCDS2605.1	.	.	.	.	.	.	.	.	.	.	T	14.11	2.437864	0.43326	.	.	ENSG00000197548	ENST00000451513;ENST00000354956;ENST00000354449	T;T;T	0.41400	1.0;1.0;1.0	6.03	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.38612	0.1047	M	0.68952	2.095	0.80722	D	1	P;P	0.45126	0.851;0.768	B;B	0.39840	0.311;0.165	T	0.18999	-1.0319	10	0.22706	T	0.39	-14.4518	9.9443	0.41600	0.0:0.0775:0.0:0.9225	.	154;154	O95352-2;O95352	.;ATG7_HUMAN	R	154	ENSP00000415223:C154R;ENSP00000347042:C154R;ENSP00000346437:C154R	ENSP00000346437:C154R	C	+	1	0	ATG7	11329826	1.000000	0.71417	0.999000	0.59377	0.775000	0.43874	6.578000	0.74032	1.104000	0.41587	-0.256000	0.11100	TGT	.	.		0.353	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395		C	11354826	T	C	11354826	3	2	113	1	0	0	0	0	1	0	0	0	1101	1580	55	2	478	2	ATG7	3	11354826	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	6101950	11354826	186667604	73	17950										
EFHB	151651	hgsc.bcm.edu	37	chr3	19921261	19921261	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttttcaaattcttcatcagaCagtttgacaccaatgttaca	4	9	4	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:19921261C>T	ENST00000295824.9	-	13	2525	c.2364G>A	c.(2362-2364)ctG>ctA	p.L788L	EFHB_ENST00000344838.4_Silent_p.L658L	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	788							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						CTTCATCAGACAGTTTGACAC	0.308																																					p.L788L		Atlas-SNP	.											.	EFHB	186	.	0			c.G2364A						.						158	148	152					3																	19921261		2203	4300	6503	SO:0001819	synonymous_variant	151651	exon13			ATCAGACAGTTTG	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"EF-hand domain containing"	26330	protein-coding gene	gene with protein product	"cilia and flagella associated protein 21"					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.2364G>A	chr3.hg19:g.19921261C>T		132.0	0.0		61.0	5.0	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Silent	SNP	ENST00000295824.9	hg19	CCDS33715.2																																																																																			.	.		0.308	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715		T	19921261	C	T	19921261	2	4	113	1	0	0	0	0	0	0	0	1	4947	465	17	3		3	EFHB	3	19921261	Silent	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	8566435	19921261	178101169	74	17951										
ZNF385D	79750	hgsc.bcm.edu	37	chr3	21606170	21606170	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tattacagctttctgaatcgGgtccatctgtaatgagaaaa	8	7	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:21606170G>A	ENST00000281523.2	-	3	690	c.172C>T	c.(172-174)Ccg>Tcg	p.P58S	ZNF385D_ENST00000494118.1_5'UTR|ZNF385D-AS1_ENST00000412369.1_RNA	NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	58						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.P58T(1)		NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						TTCTGAATCGGGTCCATCTGT	0.358																																					p.P58S		Atlas-SNP	.											ZNF385D,NS,carcinoma,0,1	ZNF385D	93	.	1	Substitution - Missense(1)	lung(1)	c.C172T						.						109	107	108					3																	21606170		2203	4300	6503	SO:0001583	missense	79750	exon3			GAATCGGGTCCAT	BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"zinc finger protein 659"	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.172C>T	chr3.hg19:g.21606170G>A	ENSP00000281523:p.Pro58Ser	82.0	0.0		43.0	4.0	NM_024697		Missense_Mutation	SNP	ENST00000281523.2	hg19	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.977372	0.92982	.	.	ENSG00000151789	ENST00000281523	T	0.41400	1.0	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.64951	0.2645	M	0.61703	1.905	0.52099	D	0.99994	D	0.89917	1.0	D	0.80764	0.994	T	0.63157	-0.6700	10	0.59425	D	0.04	-3.427	20.3632	0.98871	0.0:0.0:1.0:0.0	.	58	Q9H6B1	Z385D_HUMAN	S	58	ENSP00000281523:P58S	ENSP00000281523:P58S	P	-	1	0	ZNF385D	21581174	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.866000	0.99616	2.826000	0.97356	0.561000	0.74099	CCG	.	.		0.358	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		A	21606170	G	A	21606170	3	1	113	1	0	0	0	0	1	0	0	0	17893	1232	43	3	1039	3	ZNF385D	3	21606170	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	1684909	21606170	176416260	75	17952										
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37151023	37151023	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gaggaaaatacaaaccagacTggcacttctcagcagaccag	9	11	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:37151023T>C	ENST00000336686.4	-	11	684	c.604A>G	c.(604-606)Agt>Ggt	p.S202G	LRRFIP2_ENST00000421307.1_Missense_Mutation_p.S202G|LRRFIP2_ENST00000396428.2_Intron|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000354379.4_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	202	DVL3-binding.|Ser-rich.				Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						CAAACCAGACTGGCACTTCTC	0.428																																					p.S202G		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.A604G						.						125	120	121					3																	37151023		2203	4300	6503	SO:0001583	missense	9209	exon12			CCAGACTGGCACT	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.604A>G	chr3.hg19:g.37151023T>C	ENSP00000338727:p.Ser202Gly	139.0	0.0		90.0	4.0	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	hg19	CCDS2664.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.383358	0.61845	.	.	ENSG00000093167	ENST00000421307;ENST00000336686	T;T	0.48522	0.81;0.81	5.4	5.4	0.78164	.	0.093513	0.64402	D	0.000001	T	0.46073	0.1374	N	0.08118	0	0.40005	D	0.975219	D	0.58268	0.982	D	0.67548	0.952	T	0.47005	-0.9150	10	0.20046	T	0.44	-11.3299	15.2426	0.73482	0.0:0.0:0.0:1.0	.	202	Q9Y608	LRRF2_HUMAN	G	202	ENSP00000392217:S202G;ENSP00000338727:S202G	ENSP00000338727:S202G	S	-	1	0	LRRFIP2	37126027	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.294000	0.65687	2.274000	0.75844	0.533000	0.62120	AGT	.	.		0.428	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		C	37151023	T	C	37151023	3	2	113	1	0	0	0	0	1	0	0	0	9037	1580	55	2	1633	2	LRRFIP2	3	37151023	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	15544853	37151023	160871407	76	17953										
TGM4	7047	hgsc.bcm.edu	37	chr3	44952888	44952888	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcatctcctcactacagaccTctgaccatgggtgagtctgc	9	14	4	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:44952888T>C	ENST00000296125.4	+	13	1971	c.1903T>C	c.(1903-1905)Tct>Cct	p.S635P		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	635					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	ACTACAGACCTCTGACCATGG	0.448																																					p.S635P		Atlas-SNP	.											.	TGM4	82	.	0			c.T1903C						.						107	103	104					3																	44952888		2203	4300	6503	SO:0001583	missense	7047	exon13			CAGACCTCTGACC	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"Transglutaminases"	11780	protein-coding gene	gene with protein product		600585	"transglutaminase 4 (prostate)"			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.1903T>C	chr3.hg19:g.44952888T>C	ENSP00000296125:p.Ser635Pro	147.0	0.0		91.0	4.0	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	hg19	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	T	11.96	1.795320	0.31777	.	.	ENSG00000163810	ENST00000296125	T	0.70045	-0.45	2.72	-0.36	0.12568	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.384179	0.18202	U	0.148473	T	0.39064	0.1064	N	0.08118	0	0.09310	N	1	P	0.41524	0.753	B	0.36922	0.236	T	0.33523	-0.9865	10	0.46703	T	0.11	.	7.3662	0.26774	0.3471:0.0:0.0:0.6529	.	635	P49221	TGM4_HUMAN	P	635	ENSP00000296125:S635P	ENSP00000296125:S635P	S	+	1	0	TGM4	44927892	0.007000	0.16637	0.000000	0.03702	0.003000	0.03518	-0.100000	0.10990	-0.399000	0.07668	0.460000	0.39030	TCT	.	.		0.448	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		C	44952888	T	C	44952888	3	2	113	1	0	0	0	0	1	0	0	0	15847	1551	54	2	1953	2	TGM4	3	44952888	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	7801865	44952888	153069542	77	17954										
SETD2	29072	hgsc.bcm.edu	37	chr3	47155420	47155420	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctttcttttctgtgagtatgActtccacatctgcatgctgt	7	10	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:47155420A>G	ENST00000409792.3	-	5	4703	c.4661T>C	c.(4660-4662)gTc>gCc	p.V1554A		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1554	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.V1051G(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGTGAGTATGACTTCCACATC	0.403			"N, F, S, Mis"		clear cell renal carcinoma																																p.V1554A		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	SETD2_ENST00000409792,caecum,carcinoma,0,3	SETD2	721	.	1	Substitution - Missense(1)	kidney(1)	c.T4661C						.						139	140	139					3																	47155420		2203	4300	6503	SO:0001583	missense	29072	exon5			AGTATGACTTCCA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4661T>C	chr3.hg19:g.47155420A>G	ENSP00000386759:p.Val1554Ala	123.0	0.0		83.0	5.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	A	14.92	2.678586	0.47886	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	D	0.83837	-1.77	5.06	5.06	0.68205	SET domain (2);	0.000000	0.49916	D	0.000136	T	0.81922	0.4925	M	0.80847	2.515	0.80722	D	1	B;B	0.24675	0.109;0.109	B;B	0.21546	0.035;0.035	T	0.79867	-0.1622	10	0.45353	T	0.12	.	9.6237	0.39737	0.9207:0.0:0.0793:0.0	.	1554;1554	F2Z317;Q9BYW2	.;SETD2_HUMAN	A	1554	ENSP00000386759:V1554A	ENSP00000386759:V1554A	V	-	2	0	SETD2	47130424	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.142000	0.77339	2.036000	0.60181	0.477000	0.44152	GTC	.	.		0.403	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		G	47155420	A	G	47155420	3	3	113	1	0	0	0	0	1	0	0	0	14146	275	10	2	3101	2	SETD2	3	47155420	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2202532	47155420	150867010	78	17955										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48622492	48622492	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	taggccaggggctccaggggTcccaggattcccggcgcggc	17	14	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:48622492T>C	ENST00000328333.8	-	32	4059	c.3952A>G	c.(3952-3954)Acc>Gcc	p.T1318A	COL7A1_ENST00000454817.1_Missense_Mutation_p.T1318A	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1318	Interrupted collagenous region.|Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCTCCAGGGGTCCCAGGATTC	0.677																																					p.T1318A		Atlas-SNP	.											.	COL7A1	320	.	0			c.A3952G						.						31	37	35					3																	48622492		2202	4300	6502	SO:0001583	missense	1294	exon32			CAGGGGTCCCAGG	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.3952A>G	chr3.hg19:g.48622492T>C	ENSP00000332371:p.Thr1318Ala	185.0	0.0		119.0	8.0	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	hg19	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	T	9.997	1.232417	0.22626	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.93426	-3.22;-3.22	5.03	-3.56	0.04626	.	1.083700	0.07200	N	0.857311	T	0.78464	0.4287	N	0.03294	-0.36	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.69064	-0.5244	10	0.09843	T	0.71	.	4.86	0.13579	0.4991:0.2203:0.0:0.2806	.	1318	Q02388	CO7A1_HUMAN	A	1318	ENSP00000332371:T1318A;ENSP00000412569:T1318A	ENSP00000332371:T1318A	T	-	1	0	COL7A1	48597496	0.000000	0.05858	0.003000	0.11579	0.052000	0.14988	0.018000	0.13422	-0.360000	0.08138	0.533000	0.62120	ACC	.	.		0.677	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		C	48622492	T	C	48622492	3	2	113	1	0	0	0	0	1	0	0	0	3706	1667	58	2	5230	2	COL7A1	3	48622492	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1467072	48622492	149399938	79	17956										
FOXP1	27086	hgsc.bcm.edu	37	chr3	71026863	71026863	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttataaaattcttggttctgCgcaatatctgctgaataaga	7	6	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:71026863C>T	ENST00000318789.4	-	16	1884	c.1359G>A	c.(1357-1359)gcG>gcA	p.A453A	FOXP1_ENST00000491238.1_Silent_p.A455A|FOXP1_ENST00000498215.1_Silent_p.A453A|FOXP1_ENST00000493089.1_Silent_p.A452A|FOXP1_ENST00000475937.1_Silent_p.A453A|FOXP1_ENST00000468577.1_Silent_p.A453A|FOXP1_ENST00000484350.1_Silent_p.A377A	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	453					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		CTTGGTTCTGCGCAATATCTG	0.343			T	PAX5	ALL																																p.A455A		Atlas-SNP	.		Dom	yes		3	3p14.1	27086	forkhead box P1		L	.	FOXP1	104	.	0			c.G1365A						.						121	125	124					3																	71026863		2203	4300	6503	SO:0001819	synonymous_variant	27086	exon11			GTTCTGCGCAATA	AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"Forkhead boxes"	3823	protein-coding gene	gene with protein product	"fork head-related protein like B", "glutamine-rich factor 1", "PAX5/FOXP1 fusion protein"	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.1359G>A	chr3.hg19:g.71026863C>T		127.0	0.0		77.0	4.0	NM_001244815	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Silent	SNP	ENST00000318789.4	hg19	CCDS2914.1	.	.	.	.	.	.	.	.	.	.	C	5.336	0.247240	0.10130	.	.	ENSG00000114861	ENST00000318796	.	.	.	6.17	6.17	0.99709	.	0.142185	0.64402	D	0.000004	T	0.67767	0.2928	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69826	-0.5040	6	0.87932	D	0	.	10.6191	0.45470	0.0:0.7865:0.143:0.0705	.	.	.	.	T	353	.	ENSP00000319243:A353T	A	-	1	0	FOXP1	71109553	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.209000	0.32357	2.941000	0.99782	0.655000	0.94253	GCA	.	.		0.343	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682		T	71026863	C	T	71026863	2	4	113	1	0	0	0	0	0	0	0	1	6034	755	27	1		1	FOXP1	3	71026863	Silent	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	22404371	71026863	126995567	80	17957										
IMPG2	50939	hgsc.bcm.edu	37	chr3	100986353	100986353	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tagagaaagtgccaaaaagtAcctgtcattttccttggggg	11	7	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:100986353A>G	ENST00000193391.7	-	9	1096		c.e9+1			NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2						visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	GCCAAAAAGTACCTGTCATTT	0.353																																					.		Atlas-SNP	.											.	IMPG2	164	.	0			c.908+2T>C						.						67	67	67					3																	100986353		2203	4300	6503	SO:0001630	splice_region_variant	50939	exon10			AAAAGTACCTGTC	AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.908+1T>C	chr3.hg19:g.100986353A>G		145.0	0.0		80.0	4.0	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Splice_Site	SNP	ENST00000193391.7	hg19	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.310365	0.81358	.	.	ENSG00000081148	ENST00000193391	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9575	0.58438	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IMPG2	102469043	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.399000	0.44495	2.371000	0.80710	0.533000	0.62120	.	.	.		0.353	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3		Intron	G	100986353	A	G	100986353	5	3	113	1	0	0	0	0	0	0	1	0	7738	405	14	2	2859	2	IMPG2	3	100986353	Splice_Site	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	29959490	100986353	97036077	81	17958										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108367792	108367792	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtaaacaaaggaaaaagaagAagactaagaataaaaaggta	9	2	0	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:108367792A>G	ENST00000361582.3	+	17	2220	c.1990A>G	c.(1990-1992)Aag>Gag	p.K664E	DZIP3_ENST00000463306.1_Missense_Mutation_p.K664E	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	664	Poly-Lys.				protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						GAAAAAGAAGAAGACTAAGAA	0.239																																					p.K664E		Atlas-SNP	.											.	DZIP3	111	.	0			c.A1990G						.						29	28	28					3																	108367792		2058	4163	6221	SO:0001583	missense	9666	exon17			AAGAAGAAGACTA	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.1990A>G	chr3.hg19:g.108367792A>G	ENSP00000355028:p.Lys664Glu	132.0	0.0		95.0	4.0	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	hg19	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	a	13.95	2.388769	0.42308	.	.	ENSG00000198919	ENST00000361582;ENST00000463306	T;T	0.31247	1.5;1.5	3.93	3.93	0.45458	.	0.266695	0.26727	N	0.022819	T	0.21881	0.0527	L	0.40543	1.245	0.22096	N	0.999363	B;B	0.31318	0.319;0.155	B;B	0.24155	0.051;0.051	T	0.13899	-1.0492	10	0.41790	T	0.15	-4.5124	9.4659	0.38813	1.0:0.0:0.0:0.0	.	282;664	D3DN61;Q86Y13	.;DZIP3_HUMAN	E	664	ENSP00000355028:K664E;ENSP00000419981:K664E	ENSP00000355028:K664E	K	+	1	0	DZIP3	109850482	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.118000	0.41949	2.001000	0.58596	0.459000	0.35465	AAG	.	.		0.239	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		G	108367792	A	G	108367792	3	3	113	1	0	0	0	0	1	0	0	0	4867	247	9	2	2052	2	DZIP3	3	108367792	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	7381439	108367792	89654638	82	17959										
DPPA4	55211	hgsc.bcm.edu	37	chr3	109052833	109052833	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cttccctcgacttctctgtgGaggtccactggggaacagag	12	12	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:109052833G>T	ENST00000335658.6	-	2	116	c.62C>A	c.(61-63)tCc>tAc	p.S21Y	DPPA4_ENST00000478791.1_5'UTR	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	21					lung-associated mesenchyme development (GO:0060484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(17)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						CTTCTCTGTGGAGGTCCACTG	0.463																																					p.S21Y		Atlas-SNP	.											.	DPPA4	56	.	0			c.C62A						.						93	84	87					3																	109052833		2203	4300	6503	SO:0001583	missense	55211	exon2			TCTGTGGAGGTCC	AK001575	CCDS33814.1	3q13.13	2014-01-28			ENSG00000121570	ENSG00000121570			19200	protein-coding gene	gene with protein product		614125					Standard	NM_018189		Approved	FLJ10713	uc003dxq.4	Q7L190	OTTHUMG00000159222	ENST00000335658.6:c.62C>A	chr3.hg19:g.109052833G>T	ENSP00000335306:p.Ser21Tyr	142.0	0.0		94.0	4.0	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Missense_Mutation	SNP	ENST00000335658.6	hg19	CCDS33814.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.215112	0.39102	.	.	ENSG00000121570	ENST00000335658	T	0.25749	1.78	3.81	1.9	0.25705	.	2.779620	0.01301	N	0.010294	T	0.38825	0.1055	L	0.44542	1.39	0.09310	N	1	D;P;D	0.65815	0.995;0.492;0.978	P;B;P	0.59221	0.854;0.121;0.598	T	0.09907	-1.0653	9	.	.	.	-0.4121	6.1554	0.20334	0.0:0.2904:0.5215:0.1881	.	11;21;21	B7Z5Q7;B7Z595;Q7L190	.;.;DPPA4_HUMAN	Y	21	ENSP00000335306:S21Y	.	S	-	2	0	DPPA4	110535523	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	0.269000	0.18589	0.515000	0.28320	0.551000	0.68910	TCC	.	.		0.463	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189		T	109052833	G	T	109052833	3	4	113	1	0	0	0	0	1	0	0	0	4738	1174	41	3	876	3	DPPA4	3	109052833	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	685041	109052833	88969597	83	17960										
C3orf15	89876	hgsc.bcm.edu	37	chr3	119421983	119421983	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	catcgaggagccccaggcccAgccgcaggtgtctcaaactc	11	16	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:119421983A>G	ENST00000273390.5	+	1	115	c.38A>G	c.(37-39)cAg>cGg	p.Q13R	MAATS1_ENST00000463700.1_Missense_Mutation_p.Q13R	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	13						mitochondrion (GO:0005739)											CCCCAGGCCCAGCCGCAGGTG	0.642																																					p.Q13R		Atlas-SNP	.											.	.	.	.	0			c.A38G						.						33	36	35					3																	119421983		2202	4296	6498	SO:0001583	missense	89876	exon1			AGGCCCAGCCGCA	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"AMY-1-associating protein expressed in testis 1", "MYCBP-binding protein", "spermatogenesis associated 26"	609910	"chromosome 3 open reading frame 15", "MYCBP/AMY-1-associated, testis expressed 1"	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.38A>G	chr3.hg19:g.119421983A>G	ENSP00000273390:p.Gln13Arg	201.0	0.0		124.0	6.0	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	hg19	CCDS2994.1	.	.	.	.	.	.	.	.	.	.	A	9.225	1.034311	0.19590	.	.	ENSG00000183833	ENST00000383667;ENST00000273390;ENST00000463700	T;T	0.41758	2.01;0.99	3.8	1.33	0.21861	.	1.033970	0.07688	N	0.938177	T	0.26304	0.0642	N	0.22421	0.69	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.25257	-1.0137	10	0.23891	T	0.37	-14.938	5.4403	0.16504	0.7571:0.0:0.2429:0.0	.	13;13;13	Q4G0Y0;Q7Z4T9-7;Q7Z4T9-2	.;.;.	R	13	ENSP00000273390:Q13R;ENSP00000419489:Q13R	ENSP00000273390:Q13R	Q	+	2	0	C3orf15	120904673	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.087000	0.11215	0.176000	0.19873	0.460000	0.39030	CAG	.	.		0.642	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364		G	119421983	A	G	119421983	3	3	113	1	0	0	0	0	1	0	0	0	2211	188	7	2	40	2	C3orf15	3	119421983	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	10369150	119421983	78600447	84	17961										
PARP14	54625	hgsc.bcm.edu	37	chr3	122419251	122419251	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tggcaagaaatggaaagggcTcactcacaatttgcttaaga	10	7	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:122419251T>C	ENST00000474629.2	+	6	2116	c.1850T>C	c.(1849-1851)cTc>cCc	p.L617P		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	617					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TGGAAAGGGCTCACTCACAAT	0.393																																					p.L617P		Atlas-SNP	.											.	PARP14	242	.	0			c.T1850C						.						37	36	36					3																	122419251		1860	4100	5960	SO:0001583	missense	54625	exon6			AAGGGCTCACTCA	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1850T>C	chr3.hg19:g.122419251T>C	ENSP00000418194:p.Leu617Pro	108.0	0.0		58.0	4.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.811876	0.50527	.	.	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.12255	2.7	5.35	1.11	0.20524	.	0.541730	0.17633	N	0.167331	T	0.21347	0.0514	M	0.66939	2.045	0.23168	N	0.998187	P;P	0.50617	0.937;0.8	P;B	0.52267	0.694;0.347	T	0.07028	-1.0794	10	0.72032	D	0.01	.	6.3179	0.21200	0.3792:0.0:0.1224:0.4985	.	617;617	Q460N5-4;Q460N5	.;PAR14_HUMAN	P	617;536	ENSP00000418194:L617P	ENSP00000381228:L536P	L	+	2	0	PARP14	123901941	0.038000	0.19896	0.000000	0.03702	0.006000	0.05464	2.488000	0.45276	0.014000	0.14944	0.533000	0.62120	CTC	.	.		0.393	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		C	122419251	T	C	122419251	3	2	113	1	0	0	0	0	1	0	0	0	11467	1551	54	2	1872	2	PARP14	3	122419251	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2997268	122419251	75603179	85	17962										
HSPBAP1	79663	hgsc.bcm.edu	37	chr3	122459296	122459296	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agaaatgaatgtttgaggagTcgtagtagtatttgaggcaa	13	2	0	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:122459296T>G	ENST00000306103.2	-	8	1506	c.1363A>C	c.(1363-1365)Act>Cct	p.T455P	HSPBAP1_ENST00000383659.1_3'UTR	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	455						cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(114;0.0531)		GTTTGAGGAGTCGTAGTAGTA	0.398																																					p.T455P		Atlas-SNP	.											.	HSPBAP1	32	.	0			c.A1363C						.						209	189	196					3																	122459296		2203	4300	6503	SO:0001583	missense	79663	exon8			GAGGAGTCGTAGT	AF400663	CCDS3017.1	3q21.1	2008-07-18	2002-08-29		ENSG00000169087	ENSG00000169087			16389	protein-coding gene	gene with protein product		608263	"HSPB (heat shock 27kD) associated protein 1"			11978969	Standard	NM_024610		Approved	FLJ22623, PASS1	uc003efu.2	Q96EW2	OTTHUMG00000159550	ENST00000306103.2:c.1363A>C	chr3.hg19:g.122459296T>G	ENSP00000302562:p.Thr455Pro	448.0	0.0		281.0	16.0	NM_024610	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	Missense_Mutation	SNP	ENST00000306103.2	hg19	CCDS3017.1	.	.	.	.	.	.	.	.	.	.	C	9.069	0.996441	0.19043	.	.	ENSG00000169087	ENST00000306103	T	0.30981	1.51	5.65	1.49	0.22878	.	0.698441	0.13917	N	0.353847	T	0.12220	0.0297	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.01281	0.0	T	0.29579	-1.0007	10	0.19147	T	0.46	.	3.7375	0.08517	0.343:0.3436:0.0:0.3133	.	455	Q96EW2	HBAP1_HUMAN	P	455	ENSP00000302562:T455P	ENSP00000302562:T455P	T	-	1	0	HSPBAP1	123941986	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.066000	0.14489	0.168000	0.19655	-0.119000	0.15052	ACT	.	.		0.398	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610		G	122459296	T	G	122459296	3	3	113	1	0	0	0	0	1	0	0	0	7434	1667	58	5	107	5	HSPBAP1	3	122459296	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	40045	122459296	75563134	86	17963										
CCDC14	64770	hgsc.bcm.edu	37	chr3	123634213	123634213	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	catagtttcactcccttcatCagaatcctgttttgaaaggg	7	10	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:123634213C>T	ENST00000488653.2	-	13	2365	c.2275G>A	c.(2275-2277)Gat>Aat	p.D759N	CCDC14_ENST00000310351.4_Missense_Mutation_p.D599N|CCDC14_ENST00000485727.1_Missense_Mutation_p.D559N|CCDC14_ENST00000433542.2_Missense_Mutation_p.D718N|CCDC14_ENST00000483247.1_Intron|CCDC14_ENST00000489746.1_Missense_Mutation_p.D559N			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	759					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		CTCCCTTCATCAGAATCCTGT	0.398																																					p.D718N		Atlas-SNP	.											.	CCDC14	97	.	0			c.G2152A						.						118	121	120					3																	123634213		2203	4300	6503	SO:0001583	missense	64770	exon12			CTTCATCAGAATC	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.2275G>A	chr3.hg19:g.123634213C>T	ENSP00000420180:p.Asp759Asn	127.0	0.0		78.0	4.0	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Missense_Mutation	SNP	ENST00000488653.2	hg19		.	.	.	.	.	.	.	.	.	.	C	17.79	3.475338	0.63737	.	.	ENSG00000175455	ENST00000488653;ENST00000310351;ENST00000485727;ENST00000489746;ENST00000433542;ENST00000409697	T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63	5.23	5.23	0.72850	.	0.253594	0.33813	N	0.004522	T	0.53594	0.1806	L	0.50333	1.59	0.19775	N	0.999955	D;D;D	0.57571	0.98;0.98;0.963	P;P;P	0.53649	0.731;0.731;0.572	T	0.52245	-0.8601	10	0.72032	D	0.01	.	12.3288	0.55026	0.0:0.9232:0.0:0.0768	.	759;718;600	Q49A88;Q49A88-6;Q49A88-5	CCD14_HUMAN;.;.	N	759;599;559;559;718;740	ENSP00000420180:D759N;ENSP00000312031:D599N;ENSP00000418002:D559N;ENSP00000418403:D559N;ENSP00000395706:D718N;ENSP00000386866:D740N	ENSP00000312031:D599N	D	-	1	0	CCDC14	125116903	0.995000	0.38212	0.125000	0.21846	0.820000	0.46376	3.635000	0.54309	2.725000	0.93324	0.591000	0.81541	GAT	.	.		0.398	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757		T	123634213	C	T	123634213	3	4	113	1	0	0	0	0	1	0	0	0	2775	826	29	3	590	3	CCDC14	3	123634213	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	1174917	123634213	74388217	87	17964										
MUC13	56667	hgsc.bcm.edu	37	chr3	124646709	124646709	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgaagtagctgttgggaaagGtgtatttgctgtggtgctag	16	3	0	1	rs75727765		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:124646709G>A	ENST00000311075.3	-	2	219	c.181C>T	c.(181-183)Cct>Tct	p.P61S	MUC13_ENST00000497378.1_5'Flank	NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	61	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						GTTGGGAAAGGTGTATTTGCT	0.458																																					p.P61S		Atlas-SNP	.											.	MUC13	57	.	0			c.C181T						.						211	210	211					3																	124646709		2203	4300	6503	SO:0001583	missense	56667	exon2			GGAAAGGTGTATT	AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"Mucins"	7511	protein-coding gene	gene with protein product		612181	"down-regulated in colon cancer 1", "mucin 13, epithelial transmembrane"	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.181C>T	chr3.hg19:g.124646709G>A	ENSP00000312235:p.Pro61Ser	142.0	0.0		118.0	7.0	NM_033049	Q6UWD9|Q9NXT5	Missense_Mutation	SNP	ENST00000311075.3	hg19		.	.	.	.	.	.	.	.	.	.	g	2.803	-0.248730	0.05867	.	.	ENSG00000173702	ENST00000311075	T	0.13089	2.62	2.04	-4.08	0.03963	.	1.726750	0.03707	N	0.249513	T	0.05593	0.0147	N	0.08118	0	0.09310	N	1	B	0.32409	0.37	B	0.30646	0.118	T	0.25502	-1.0130	10	0.08837	T	0.75	-1.1529	6.1417	0.20263	0.0:0.1432:0.6122:0.2446	.	61	Q9H3R2	MUC13_HUMAN	S	61	ENSP00000312235:P61S	ENSP00000312235:P61S	P	-	1	0	MUC13	126129399	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.112000	0.10791	-1.159000	0.02807	-0.283000	0.09986	CCT	.	.		0.458	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049		A	124646709	G	A	124646709	3	1	113	1	0	0	0	0	1	0	0	0	9980	1261	44	3	1394	3	MUC13	3	124646709	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	1012496	124646709	73375721	88	17965										
C3orf72	401089	hgsc.bcm.edu	37	chr3	138668461	138668461	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccttcacatggctgtccggcAttcgaaggctcagaaaacag	10	12	2	1	rs141282655	byFrequency	TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:138668461A>T	ENST00000383165.3	+	2	331	c.200A>T	c.(199-201)cAt>cTt	p.H67L	FOXL2_ENST00000330315.3_5'Flank	NM_001040061.2	NP_001035150.1	Q6ZUU3	FOXNB_HUMAN		67								p.H67L(1)		large_intestine(1)|lung(3)	4						GCTGTCCGGCATTCGAAGGCT	0.572																																					p.H67L		Atlas-SNP	.											C3orf72,NS,carcinoma,0,2	C3orf72	13	.	1	Substitution - Missense(1)	lung(1)	c.A200T						.						68	70	70					3																	138668461		1945	4148	6093	SO:0001583	missense	401089	exon2			TCCGGCATTCGAA																												ENST00000383165.3:c.200A>T	chr3.hg19:g.138668461A>T	ENSP00000372651:p.His67Leu	42.0	0.0		21.0	2.0	NM_001040061	A6NGX0	Missense_Mutation	SNP	ENST00000383165.3	hg19	CCDS43155.1	.	.	.	.	.	.	.	.	.	.	A	8.507	0.865522	0.17250	.	.	ENSG00000206262	ENST00000383165	.	.	.	1.63	0.298	0.15766	.	.	.	.	.	T	0.10637	0.0260	N	0.14661	0.345	0.09310	N	1	P	0.50710	0.938	B	0.34931	0.192	T	0.18871	-1.0323	8	0.87932	D	0	.	4.518	0.11945	0.6589:0.3411:0.0:0.0	.	67	Q6ZUU3	CC072_HUMAN	L	67	.	ENSP00000372651:H67L	H	+	2	0	C3orf72	140151151	0.000000	0.05858	0.002000	0.10522	0.064000	0.16182	-0.312000	0.08113	0.065000	0.16485	0.454000	0.30748	CAT	.	.		0.572	C3orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357986.1			T	138668461	A	T	138668461	3	4	113	1	0	0	0	0	1	0	0	0	2246	217	8	4	206	4	C3orf72	3	138668461	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	14021752	138668461	59353969	89	17966										
KCNAB1	7881	hgsc.bcm.edu	37	chr3	155838405	155838405	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgaaagatctccacgatgcTggcagcccggacaggggcag	14	12	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:155838405T>C	ENST00000490337.1	+	1	69	c.5T>C	c.(4-6)cTg>cCg	p.L2P	KCNAB1_ENST00000389636.5_Missense_Mutation_p.L2P	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	2					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TCCACGATGCTGGCAGCCCGG	0.517																																					p.L2P		Atlas-SNP	.											.	KCNAB1	176	.	0			c.T5C						.						112	128	123					3																	155838405		2203	4300	6503	SO:0001583	missense	7881	exon1			CGATGCTGGCAGC	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.5T>C	chr3.hg19:g.155838405T>C	ENSP00000419952:p.Leu2Pro	104.0	0.0		63.0	4.0	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	hg19	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.007534	0.75046	.	.	ENSG00000169282	ENST00000490337;ENST00000389636	T;T	0.15139	2.91;2.45	5.33	5.33	0.75918	.	.	.	.	.	T	0.18882	0.0453	N	0.08118	0	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.56343	0.796;0.796	T	0.17776	-1.0358	9	0.87932	D	0	-17.1642	15.3008	0.73949	0.0:0.0:0.0:1.0	.	2;2	B7Z8E5;Q14722	.;KCAB1_HUMAN	P	2	ENSP00000419952:L2P;ENSP00000374287:L2P	ENSP00000374287:L2P	L	+	2	0	KCNAB1	157321099	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.273000	0.65564	2.000000	0.58554	0.455000	0.32223	CTG	.	.		0.517	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		C	155838405	T	C	155838405	3	2	113	1	0	0	0	0	1	0	0	0	8018	1580	55	2	7	2	KCNAB1	3	155838405	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	17169944	155838405	42184025	90	17967										
TNIK	23043	hgsc.bcm.edu	37	chr3	170784050	170784050	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tactccatccaaatgtcctgTttccactgaccggatctcaa	5	14	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:170784050T>C	ENST00000436636.2	-	32	4269	c.3925A>G	c.(3925-3927)Aca>Gca	p.T1309A	TNIK_ENST00000460047.1_Missense_Mutation_p.T1246A|TNIK_ENST00000488470.1_Missense_Mutation_p.T1254A|TNIK_ENST00000369326.5_Missense_Mutation_p.T1287A|TNIK_ENST00000470834.1_Missense_Mutation_p.T1272A|TNIK_ENST00000475336.1_Missense_Mutation_p.T1217A|TNIK_ENST00000464785.1_5'Flank|TNIK_ENST00000538048.1_Missense_Mutation_p.T1261A|TNIK_ENST00000357327.5_Missense_Mutation_p.T1280A|TNIK_ENST00000341852.6_Missense_Mutation_p.T1225A|TNIK_ENST00000284483.8_Missense_Mutation_p.T1301A	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	1309	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			AAATGTCCTGTTTCCACTGAC	0.378																																					p.T1309A		Atlas-SNP	.											.	TNIK	313	.	0			c.A3925G						.						123	118	120					3																	170784050		1879	4122	6001	SO:0001583	missense	23043	exon32			GTCCTGTTTCCAC	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.3925A>G	chr3.hg19:g.170784050T>C	ENSP00000399511:p.Thr1309Ala	136.0	0.0		94.0	4.0	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	hg19	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846585	0.71603	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	T;T;T;T;T;T;T;T;T;T	0.06218	3.33;3.33;3.33;3.33;3.33;3.33;3.33;3.33;3.33;3.33	5.87	5.87	0.94306	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.21801	0.0525	L	0.55103	1.725	0.80722	D	1	D;P;D;D;P;P;D;P	0.61697	0.974;0.76;0.99;0.974;0.871;0.76;0.99;0.951	D;B;D;D;P;B;D;P	0.72982	0.969;0.316;0.979;0.969;0.621;0.316;0.979;0.739	T	0.00068	-1.2139	10	0.87932	D	0	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	1217;1272;1246;1225;1301;1280;1254;1309	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	A	1309;1287;1261;1225;1301;1217;1280;1246;1254;1272	ENSP00000399511:T1309A;ENSP00000358332:T1287A;ENSP00000443278:T1261A;ENSP00000345352:T1225A;ENSP00000284483:T1301A;ENSP00000418156:T1217A;ENSP00000349880:T1280A;ENSP00000418916:T1246A;ENSP00000418378:T1254A;ENSP00000419990:T1272A	ENSP00000284483:T1301A	T	-	1	0	TNIK	172266744	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.371000	0.80710	0.533000	0.62120	ACA	.	.		0.378	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		C	170784050	T	C	170784050	3	2	113	1	0	0	0	0	1	0	0	0	16328	1725	60	2	165	2	TNIK	3	170784050	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	14945645	170784050	27238380	91	17968										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173997373	173997373	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagagttatttccttgcaatTtctccaaaaatgatgtgatg	7	7	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:173997373T>G	ENST00000457714.1	+	6	2011	c.1582T>G	c.(1582-1584)Ttc>Gtc	p.F528V	NLGN1_ENST00000545397.1_Missense_Mutation_p.F528V|NLGN1_ENST00000361589.4_Missense_Mutation_p.F528V|NLGN1_ENST00000401917.3_Missense_Mutation_p.F568V	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	545					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TCCTTGCAATTTCTCCAAAAA	0.423																																					p.F528V		Atlas-SNP	.											.	NLGN1	209	.	0			c.T1582G						.						55	53	54					3																	173997373		2203	4299	6502	SO:0001583	missense	22871	exon6			TGCAATTTCTCCA	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.1582T>G	chr3.hg19:g.173997373T>G	ENSP00000392500:p.Phe528Val	323.0	0.0		201.0	93.0	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	hg19	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.413882	0.83449	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000545397;ENST00000401917	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.74566	0.3733	L	0.61036	1.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.76063	-0.3096	10	0.66056	D	0.02	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	568;528	D2X2H5;Q8N2Q7-2	.;.	V	528;528;528;568	ENSP00000392500:F528V;ENSP00000354541:F528V;ENSP00000441108:F528V;ENSP00000385750:F568V	ENSP00000354541:F528V	F	+	1	0	NLGN1	175480067	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	TTC	.	.		0.423	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		G	173997373	T	G	173997373	3	3	113	1	0	0	0	0	1	0	0	0	10470	1841	64	5	1596	5	NLGN1	3	173997373	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	3213323	173997373	24025057	92	17969										
TBL1XR1	79718	hgsc.bcm.edu	37	chr3	176765128	176765128	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggatgaaatttcctttcttaTtccattttaatgcaaatata	4	6	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:176765128T>C	ENST00000430069.1	-	9	1083	c.824A>G	c.(823-825)aAt>aGt	p.N275S	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.N275S|TBL1XR1-AS1_ENST00000454723.2_RNA			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	275					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TCCTTTCTTATTCCATTTTAA	0.323																																					p.N275S		Atlas-SNP	.											.	TBL1XR1	87	.	0			c.A824G						.						31	30	30					3																	176765128		1817	4058	5875	SO:0001583	missense	79718	exon9			TTCTTATTCCATT	AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"WD repeat domain containing"	29529	protein-coding gene	gene with protein product		608628	"transducin (beta)-like 1X-linked receptor 1"			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.824A>G	chr3.hg19:g.176765128T>C	ENSP00000405574:p.Asn275Ser	226.0	0.0		106.0	5.0	NM_024665	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	hg19	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.356838	0.82243	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	T;T	0.54279	0.58;0.58	5.78	5.78	0.91487	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.095731	0.64402	D	0.000001	T	0.36991	0.0987	N	0.02275	-0.615	0.80722	D	1	D	0.55605	0.972	P	0.55303	0.773	T	0.40961	-0.9535	10	0.02654	T	1	-4.4403	15.282	0.73794	0.0:0.0:0.0:1.0	.	275	Q9BZK7	TBL1R_HUMAN	S	275;275;137	ENSP00000405574:N275S;ENSP00000413251:N275S	ENSP00000405574:N275S	N	-	2	0	TBL1XR1	178247822	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.040000	0.89188	2.206000	0.71126	0.533000	0.62120	AAT	.	.		0.323	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665		C	176765128	T	C	176765128	3	2	113	1	0	0	0	0	1	0	0	0	15655	1493	52	2	752	2	TBL1XR1	3	176765128	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2767755	176765128	21257302	93	17970										
KCNMB2	10242	hgsc.bcm.edu	37	chr3	178560484	178560484	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaaaaattttgaagaatccaTgtccctggtgaatgttgtca	8	6	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:178560484T>C	ENST00000432997.1	+	5	819	c.467T>C	c.(466-468)aTg>aCg	p.M156T	RP11-385J1.2_ENST00000425330.1_RNA|RP11-385J1.2_ENST00000451742.1_RNA|KCNMB2_ENST00000420517.2_Missense_Mutation_p.M156T|KCNMB2_ENST00000358316.3_Missense_Mutation_p.M156T|RP11-385J1.2_ENST00000432385.1_RNA|RP11-385J1.2_ENST00000437488.1_RNA|KCNMB2_ENST00000452583.1_Missense_Mutation_p.M156T	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	166					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	GAAGAATCCATGTCCCTGGTG	0.373																																					p.M156T		Atlas-SNP	.											.	KCNMB2	35	.	0			c.T467C						.						91	91	91					3																	178560484		2203	4300	6503	SO:0001583	missense	10242	exon6			AATCCATGTCCCT	AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584		"Potassium channels"	6286	protein-coding gene	gene with protein product		605214				10097176	Standard	NM_181361		Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.467T>C	chr3.hg19:g.178560484T>C	ENSP00000407592:p.Met156Thr	138.0	0.0		79.0	4.0	NM_005832	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000432997.1	hg19	CCDS3223.1	.	.	.	.	.	.	.	.	.	.	T	4.923	0.171559	0.09391	.	.	ENSG00000197584	ENST00000420517;ENST00000452583;ENST00000432997;ENST00000358316;ENST00000457763	T;T;T;T	0.08984	3.03;3.03;3.03;3.03	6.06	6.06	0.98353	.	0.186148	0.64402	D	0.000013	T	0.05364	0.0142	N	0.08118	0	0.41506	D	0.988319	B	0.06786	0.001	B	0.15484	0.013	T	0.45454	-0.9260	10	0.13108	T	0.6	-24.2237	16.6093	0.84858	0.0:0.0:0.0:1.0	.	156	Q9Y691	KCMB2_HUMAN	T	156;156;156;156;137	ENSP00000408252:M156T;ENSP00000397483:M156T;ENSP00000407592:M156T;ENSP00000351068:M156T	ENSP00000351068:M156T	M	+	2	0	KCNMB2	180043178	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.638000	0.46562	2.324000	0.78689	0.533000	0.62120	ATG	.	.		0.373	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348251.1	NM_181361		C	178560484	T	C	178560484	3	2	113	1	0	0	0	0	1	0	0	0	8084	1464	51	2	481	2	KCNMB2	3	178560484	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1795356	178560484	19461946	94	17971										
ABCC5	10057	hgsc.bcm.edu	37	chr3	183706403	183706403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctcgtgcttggacagagaccAcacgtcttccattgagagct	10	12	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:183706403A>G	ENST00000334444.6	-	4	640	c.400T>C	c.(400-402)Tgg>Cgg	p.W134R	ABCC5_ENST00000382494.2_Missense_Mutation_p.W134R|ABCC5_ENST00000427120.2_Missense_Mutation_p.W134R|ABCC5_ENST00000392579.2_Missense_Mutation_p.W134R|ABCC5_ENST00000265586.6_Missense_Mutation_p.W134R	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	134					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	GACAGAGACCACACGTCTTCC	0.572																																					p.W134R		Atlas-SNP	.											.	ABCC5	142	.	0			c.T400C						.						94	88	90					3																	183706403		2203	4300	6503	SO:0001583	missense	10057	exon4			GAGACCACACGTC	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.400T>C	chr3.hg19:g.183706403A>G	ENSP00000333926:p.Trp134Arg	143.0	0.0		79.0	4.0	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Missense_Mutation	SNP	ENST00000334444.6	hg19	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.434797	0.83885	.	.	ENSG00000114770	ENST00000334444;ENST00000382495;ENST00000265586;ENST00000427120;ENST00000392579;ENST00000382494;ENST00000437341	D;D;D;D;D;D	0.94457	-3.43;-3.43;-3.43;-3.43;-3.43;-3.43	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	D	0.97660	0.9233	M	0.88512	2.96	0.80722	D	1	D;D;D;D;B	0.89917	1.0;1.0;0.992;1.0;0.005	D;D;P;D;B	0.97110	0.999;0.999;0.887;1.0;0.014	D	0.98433	1.0583	10	0.87932	D	0	-10.0346	16.4943	0.84223	1.0:0.0:0.0:0.0	.	134;134;134;134;134	A5PKY6;Q29ZA9;Q86UX3;Q86W30;O15440	.;.;.;.;MRP5_HUMAN	R	134;70;134;134;134;134;134	ENSP00000333926:W134R;ENSP00000265586:W134R;ENSP00000404809:W134R;ENSP00000376358:W134R;ENSP00000371934:W134R;ENSP00000399726:W134R	ENSP00000265586:W134R	W	-	1	0	ABCC5	185189097	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.149000	0.77396	2.291000	0.77112	0.533000	0.62120	TGG	.	.		0.572	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		G	183706403	A	G	183706403	3	3	113	1	0	0	0	0	1	0	0	0	56	159	6	2	4061	2	ABCC5	3	183706403	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	5145919	183706403	14316027	95	17972										
LIPH	200879	hgsc.bcm.edu	37	chr3	185226629	185226629	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tggaagactgtttcaacgttTtccatcaggacaagatcata	8	8	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:185226629T>C	ENST00000296252.4	-	10	1446	c.1305A>G	c.(1303-1305)gaA>gaG	p.E435E	LIPH_ENST00000424591.2_Silent_p.E401E	NM_139248.2	NP_640341.1	Q8WWY8	LIPH_HUMAN	lipase, member H	435					lipid catabolic process (GO:0016042)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(2)	20	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			TTTCAACGTTTTCCATCAGGA	0.378																																					p.E435E		Atlas-SNP	.											.	LIPH	56	.	0			c.A1305G						.						76	72	73					3																	185226629		2203	4300	6503	SO:0001819	synonymous_variant	200879	exon10			AACGTTTTCCATC	AY093498	CCDS3272.1	3q27	2012-07-31			ENSG00000163898	ENSG00000163898			18483	protein-coding gene	gene with protein product		607365				12213196, 12063250	Standard	XM_006713529		Approved	mPA-PLA1, PLA1B, mPA-PLA1alpha, LPDLR	uc003fpm.3	Q8WWY8	OTTHUMG00000156657	ENST00000296252.4:c.1305A>G	chr3.hg19:g.185226629T>C		133.0	0.0		89.0	4.0	NM_139248	A2IBA7|Q8TEC7	Silent	SNP	ENST00000296252.4	hg19	CCDS3272.1																																																																																			.	.		0.378	LIPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345153.1			C	185226629	T	C	185226629	2	2	113	1	0	0	0	0	0	0	0	1	8833	1838	64	2		2	LIPH	3	185226629	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1520226	185226629	12795801	96	17973										
MASP1	5648	hgsc.bcm.edu	37	chr3	186938875	186938875	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtcactttcttcttcagcggGgcataagccttctggcaggt	11	11	5	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:186938875G>A	ENST00000337774.5	-	15	2246	c.1857C>T	c.(1855-1857)gcC>gcT	p.A619A		NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	619	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		TCTTCAGCGGGGCATAAGCCT	0.542																																					p.A619A		Atlas-SNP	.											.	MASP1	240	.	0			c.C1857T						.						147	112	124					3																	186938875		2203	4300	6503	SO:0001819	synonymous_variant	5648	exon15			CAGCGGGGCATAA	D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"Serine peptidases / Serine peptidases"	6901	protein-coding gene	gene with protein product		600521	"mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.1857C>T	chr3.hg19:g.186938875G>A		197.0	0.0		140.0	62.0	NM_001879	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Silent	SNP	ENST00000337774.5	hg19	CCDS33907.1																																																																																			.	.		0.542	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879		A	186938875	G	A	186938875	2	1	113	1	0	0	0	0	0	0	0	1	9331	1219	43	3		3	MASP1	3	186938875	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	1712246	186938875	11083555	97	17974										
PAK2	5062	hgsc.bcm.edu	37	chr3	196547362	196547362	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agcttatggccctaaagtcgAcatatggtctctgggtatca	10	9	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:196547362A>G	ENST00000327134.3	+	13	1596	c.1274A>G	c.(1273-1275)gAc>gGc	p.D425G		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	425	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		CCTAAAGTCGACATATGGTCT	0.498																																					p.D425G		Atlas-SNP	.											.	PAK2	113	.	0			c.A1274G						.						151	125	134					3																	196547362		2203	4300	6503	SO:0001583	missense	5062	exon13			AAGTCGACATATG	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"S6/H4 kinase"	605022	"p21 (CDKN1A)-activated kinase 2"			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.1274A>G	chr3.hg19:g.196547362A>G	ENSP00000314067:p.Asp425Gly	198.0	0.0		94.0	4.0	NM_002577	Q13154|Q6ISC3	Missense_Mutation	SNP	ENST00000327134.3	hg19	CCDS3321.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.2|24.2	4.499677|4.499677	0.85176|0.85176	.|.	.|.	ENSG00000180370|ENSG00000180370	ENST00000327134|ENST00000426668	T|.	0.52295|.	0.67|.	4.69|4.69	4.69|4.69	0.59074|0.59074	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.91226|0.91226	0.7235|0.7235	H|H	0.99712|0.99712	4.72|4.72	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.94889|0.94889	0.8046|0.8046	10|5	0.87932|.	D|.	0|.	.|.	14.6248|14.6248	0.68614|0.68614	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	425|.	Q13177|.	PAK2_HUMAN|.	G|A	425|168	ENSP00000314067:D425G|.	ENSP00000314067:D425G|.	D|T	+|+	2|1	0|0	PAK2|PAK2	198031759|198031759	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.988000|0.988000	0.76386|0.76386	8.709000|8.709000	0.91379|0.91379	2.097000|2.097000	0.63578|0.63578	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.		0.498	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577		G	196547362	A	G	196547362	3	3	113	1	0	0	0	0	1	0	0	0	11410	275	10	2	1320	2	PAK2	3	196547362	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	9608487	196547362	1475068	98	17975										
DLG1	1739	hgsc.bcm.edu	37	chr3	197023321	197023321	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttagttttgaacgatattccTccaaaaggtgcaatgctctc	7	9	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr3:197023321T>C	ENST00000419354.1	-	3	333	c.47A>G	c.(46-48)gAg>gGg	p.E16G	DLG1-AS1_ENST00000430666.1_RNA|DLG1_ENST00000448528.2_Missense_Mutation_p.E16G|MIR4797_ENST00000577559.1_RNA|DLG1_ENST00000450955.1_Missense_Mutation_p.E16G|DLG1_ENST00000314062.3_Missense_Mutation_p.E16G|DLG1_ENST00000346964.2_Missense_Mutation_p.E16G|DLG1_ENST00000485409.1_5'UTR|DLG1_ENST00000392382.2_Missense_Mutation_p.E16G|DLG1_ENST00000422288.1_Missense_Mutation_p.E16G|DLG1_ENST00000357674.4_Missense_Mutation_p.E16G|DLG1-AS1_ENST00000414529.1_RNA			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	16	L27. {ECO:0000255|PROSITE- ProRule:PRU00365}.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		ACGATATTCCTCCAAAAGGTG	0.368																																					p.E16G		Atlas-SNP	.											.	DLG1	120	.	0			c.A47G						.						145	145	145					3																	197023321		2203	4300	6503	SO:0001583	missense	1739	exon3			TATTCCTCCAAAA	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"discs large homolog 1", "presynaptic protein SAP97", "synapse-associated protein 97"	601014	"discs, large (Drosophila) homolog 1"			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.47A>G	chr3.hg19:g.197023321T>C	ENSP00000407531:p.Glu16Gly	154.0	0.0		82.0	4.0	NM_001204386	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	hg19	CCDS43194.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.979708	0.74360	.	.	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000422288;ENST00000448528;ENST00000392382;ENST00000450955;ENST00000456699;ENST00000392380;ENST00000419553;ENST00000436682;ENST00000412364;ENST00000434148	T;T;T;T;T;T;T;T;T;T;T	0.55413	2.12;2.13;2.14;2.14;2.14;2.14;2.16;2.13;0.52;0.52;0.52	5.09	5.09	0.68999	L27 (2);L27-1 (1);	0.148295	0.42172	D	0.000745	T	0.57257	0.2041	M	0.76574	2.34	0.58432	D	0.999999	B;B;B;P	0.42692	0.449;0.081;0.099;0.787	B;B;B;B	0.42959	0.205;0.094;0.152;0.403	T	0.65154	-0.6237	10	0.87932	D	0	.	13.4581	0.61210	0.0:0.0:0.0:1.0	.	16;16;16;16	Q12959-4;Q12959-3;Q12959;Q12959-2	.;.;DLG1_HUMAN;.	G	16	ENSP00000345731:E16G;ENSP00000350303:E16G;ENSP00000321087:E16G;ENSP00000407531:E16G;ENSP00000413238:E16G;ENSP00000391732:E16G;ENSP00000376187:E16G;ENSP00000411278:E16G;ENSP00000396474:E16G;ENSP00000376185:E16G;ENSP00000414189:E16G	ENSP00000321087:E16G	E	-	2	0	DLG1	198507718	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.818000	0.75257	2.213000	0.71641	0.528000	0.53228	GAG	.	.		0.368	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087		C	197023321	T	C	197023321	3	2	113	1	0	0	0	0	1	0	0	0	4556	1551	54	2	2867	2	DLG1	3	197023321	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	475959	197023321	999109	99	17976										
HTT	3064	hgsc.bcm.edu	37	chr4	3210595	3210595	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agtctcttcccacccgctggAcggggatgggcacgtgtcac	13	14	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:3210595A>G	ENST00000355072.5	+	46	6393	c.6248A>G	c.(6247-6249)gAc>gGc	p.D2083G		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2083					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CACCCGCTGGACGGGGATGGG	0.567																																					p.D2083G		Atlas-SNP	.											.	HTT	221	.	0			c.A6248G						.						63	63	63					4																	3210595		2025	4191	6216	SO:0001583	missense	3064	exon46			CGCTGGACGGGGA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.6248A>G	chr4.hg19:g.3210595A>G	ENSP00000347184:p.Asp2083Gly	114.0	0.0		73.0	4.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	A	18.94	3.729267	0.69074	.	.	ENSG00000197386	ENST00000355072	T	0.05717	3.4	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.23249	0.0562	M	0.70595	2.14	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	T	0.02917	-1.1094	10	0.19590	T	0.45	.	16.6288	0.85011	1.0:0.0:0.0:0.0	.	2083	P42858	HD_HUMAN	G	2083	ENSP00000347184:D2083G	ENSP00000347184:D2083G	D	+	2	0	HTT	3180393	1.000000	0.71417	0.999000	0.59377	0.768000	0.43524	8.570000	0.90748	2.326000	0.78906	0.533000	0.62120	GAC	.	.		0.567	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		G	3210595	A	G	3210595	3	3	113	1	0	0	0	0	1	0	0	0	7466	275	10	2	6430	2	HTT	4	3210595	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10		3210595	187943681	100	17977										
TBC1D14	57533	hgsc.bcm.edu	37	chr4	7006574	7006574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agaggcttttcttccagagcTctttgacatctgtcttgccc	8	12	4	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:7006574T>C	ENST00000409757.4	+	8	1398	c.1274T>C	c.(1273-1275)cTc>cCc	p.L425P	TBC1D14_ENST00000451522.2_Missense_Mutation_p.L145P|TBC1D14_ENST00000410031.1_Missense_Mutation_p.L197P|TBC1D14_ENST00000448507.1_Missense_Mutation_p.L425P|TBC1D14_ENST00000446947.2_Missense_Mutation_p.L38P	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	425	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						CTTCCAGAGCTCTTTGACATC	0.463																																					p.L425P		Atlas-SNP	.											.	TBC1D14	110	.	0			c.T1274C						.						105	104	104					4																	7006574		2203	4300	6503	SO:0001583	missense	57533	exon8			CAGAGCTCTTTGA	AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405			29246	protein-coding gene	gene with protein product		614855				10718198	Standard	NM_020773		Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.1274T>C	chr4.hg19:g.7006574T>C	ENSP00000386921:p.Leu425Pro	79.0	0.0		39.0	4.0	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	hg19	CCDS3394.2	.	.	.	.	.	.	.	.	.	.	T	24.7	4.563694	0.86335	.	.	ENSG00000132405	ENST00000448507;ENST00000409757;ENST00000410031;ENST00000451522;ENST00000439515;ENST00000446947	T;T;T;T;T;T	0.04317	3.65;3.65;3.65;3.65;3.65;3.65	5.27	5.27	0.74061	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.30230	0.0758	M	0.93507	3.425	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.987;0.992	T	0.33929	-0.9849	10	0.72032	D	0.01	-25.3524	14.5294	0.67915	0.0:0.0:0.0:1.0	.	38;145;425	F5GXK4;Q9P2M4-2;Q9P2M4	.;.;TBC14_HUMAN	P	425;425;197;145;44;38	ENSP00000404041:L425P;ENSP00000386921:L425P;ENSP00000386343:L197P;ENSP00000388886:L145P;ENSP00000389082:L44P;ENSP00000405875:L38P	ENSP00000386921:L425P	L	+	2	0	TBC1D14	7057475	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.393000	0.79851	2.198000	0.70561	0.533000	0.62120	CTC	.	.		0.463	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773		C	7006574	T	C	7006574	3	2	113	1	0	0	0	0	1	0	0	0	15618	1551	54	2	1307	2	TBC1D14	4	7006574	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	3795979	7006574	184147702	101	17978										
KLB	152831	hgsc.bcm.edu	37	chr4	39447995	39447995	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	acagttcagcgatcctcatcTgtacgtgtggaacgccactg	10	12	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:39447995T>C	ENST00000257408.4	+	4	1746	c.1649T>C	c.(1648-1650)cTg>cCg	p.L550P		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	550	Glycosyl hydrolase-1 2.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						GATCCTCATCTGTACGTGTGG	0.522																																					p.L550P		Atlas-SNP	.											.	KLB	95	.	0			c.T1649C						.						79	73	75					4																	39447995		2203	4300	6503	SO:0001583	missense	152831	exon4			CTCATCTGTACGT	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.1649T>C	chr4.hg19:g.39447995T>C	ENSP00000257408:p.Leu550Pro	29.0	0.0		43.0	4.0	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	hg19	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	T	19.94	3.920731	0.73213	.	.	ENSG00000134962	ENST00000257408	T	0.29917	1.55	5.77	5.77	0.91146	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.072978	0.56097	D	0.000033	T	0.42359	0.1199	N	0.21142	0.635	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71870	0.975;0.975	T	0.40136	-0.9579	10	0.62326	D	0.03	-14.1461	16.0874	0.81068	0.0:0.0:0.0:1.0	.	541;550	B7ZL50;Q86Z14	.;KLOTB_HUMAN	P	550	ENSP00000257408:L550P	ENSP00000257408:L550P	L	+	2	0	KLB	39124390	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	7.855000	0.86950	2.203000	0.70933	0.397000	0.26171	CTG	.	.		0.522	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		C	39447995	T	C	39447995	3	2	113	1	0	0	0	0	1	0	0	0	8341	1580	55	2	1663	2	KLB	4	39447995	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	32441421	39447995	151706281	102	17979										
RHOH	399	hgsc.bcm.edu	37	chr4	40245536	40245536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cgtcaaccaggccaggagacGaaacagaaggaggctcttct	12	11	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:40245536G>A	ENST00000381799.5	+	3	1254	c.530G>A	c.(529-531)cGa>cAa	p.R177Q	RHOH_ENST00000505618.1_Missense_Mutation_p.R177Q	NM_001278363.1|NM_001278365.1|NM_001278366.1|NM_001278367.1|NM_001278369.1|NM_004310.4	NP_001265292.1|NP_001265294.1|NP_001265295.1|NP_001265296.1|NP_001265298.1|NP_004301.1	Q15669	RHOH_HUMAN	ras homolog family member H	177					mast cell activation (GO:0045576)|negative regulation of catalytic activity (GO:0043086)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of phosphorylation (GO:0042326)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase inhibitor activity (GO:0005095)|kinase inhibitor activity (GO:0019210)|Rho GTPase binding (GO:0017048)	p.R177Q(1)		kidney(1)|large_intestine(3)|lung(7)|ovary(1)	12						GCCAGGAGACGAAACAGAAGG	0.527																																					p.R177Q		Atlas-SNP	.											RHOH,colon,carcinoma,0,1	RHOH	32	.	1	Substitution - Missense(1)	large_intestine(1)	c.G530A						.						32	33	33					4																	40245536		2203	4300	6503	SO:0001583	missense	399	exon3			GGAGACGAAACAG	Z35227	CCDS3458.1	4p13	2014-09-17	2012-02-27	2004-03-24	ENSG00000168421	ENSG00000168421			686	protein-coding gene	gene with protein product		602037	"ras homolog gene family, member H"	ARHH		7784061	Standard	NM_001278359		Approved	RhoH, TTF	uc003guz.2	Q15669	OTTHUMG00000099373	ENST00000381799.5:c.530G>A	chr4.hg19:g.40245536G>A	ENSP00000371219:p.Arg177Gln	216.0	0.0		105.0	10.0	NM_004310		Missense_Mutation	SNP	ENST00000381799.5	hg19	CCDS3458.1	.	.	.	.	.	.	.	.	.	.	g	6.416	0.444863	0.12164	.	.	ENSG00000168421	ENST00000505618;ENST00000381799	T;T	0.63580	-0.05;-0.05	6.03	4.3	0.51218	.	0.184661	0.35936	U	0.002886	T	0.41994	0.1183	N	0.12887	0.27	0.37252	D	0.906626	B	0.13145	0.007	B	0.01281	0.0	T	0.42344	-0.9457	10	0.41790	T	0.15	.	10.4219	0.44354	0.2106:0.0:0.7894:0.0	.	177	Q15669	RHOH_HUMAN	Q	177	ENSP00000425010:R177Q;ENSP00000371219:R177Q	ENSP00000371219:R177Q	R	+	2	0	RHOH	39921931	1.000000	0.71417	0.988000	0.46212	0.098000	0.18820	2.358000	0.44134	1.558000	0.49541	0.655000	0.94253	CGA	.	.		0.527	RHOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216820.3	NM_004310		A	40245536	G	A	40245536	3	1	113	1	0	0	0	0	1	0	0	0	13355	1058	37	1	532	1	RHOH	4	40245536	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	797541	40245536	150908740	103	17980										
REST	5978	hgsc.bcm.edu	37	chr4	57798184	57798184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caaaggaagccttggcagtcAaagcggctaagggagatttt	13	7	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:57798184A>G	ENST00000309042.7	+	4	3474	c.3160A>G	c.(3160-3162)Aaa>Gaa	p.K1054E		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	1054	Interaction with RCOR1.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CTTGGCAGTCAAAGCGGCTAA	0.433																																					p.K1054E		Atlas-SNP	.											.	REST	104	.	0			c.A3160G						.						79	76	77					4																	57798184		2203	4300	6503	SO:0001583	missense	5978	exon4			GCAGTCAAAGCGG	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.3160A>G	chr4.hg19:g.57798184A>G	ENSP00000311816:p.Lys1054Glu	189.0	0.0		101.0	5.0	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	hg19	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	A	10.87	1.473732	0.26423	.	.	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.33216	1.42	5.82	4.62	0.57501	.	0.000000	0.49305	D	0.000144	T	0.25158	0.0611	L	0.60455	1.87	0.09310	N	1	P;B	0.42518	0.782;0.251	B;B	0.37650	0.255;0.038	T	0.42749	-0.9433	10	0.72032	D	0.01	-27.0083	3.8101	0.08793	0.6679:0.1326:0.0718:0.1278	.	1031;1054	F8WAN5;Q13127	.;REST_HUMAN	E	1054;1031	ENSP00000311816:K1054E	ENSP00000311816:K1054E	K	+	1	0	REST	57492941	0.149000	0.22717	0.277000	0.24703	0.024000	0.10985	0.576000	0.23744	2.225000	0.72522	0.459000	0.35465	AAA	.	.		0.433	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		G	57798184	A	G	57798184	3	3	113	1	0	0	0	0	1	0	0	0	13249	131	5	2	3170	2	REST	4	57798184	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	17552648	57798184	133356092	104	17981										
RUFY3	22902	hgsc.bcm.edu	37	chr4	71668679	71668679	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cttctccattgtaggctgcaAccccaccctatggatgaaca	7	14	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:71668679A>C	ENST00000381006.3	+	16	2208	c.1629A>C	c.(1627-1629)caA>caC	p.Q543H	RUFY3_ENST00000512331.1_3'UTR|RUFY3_ENST00000502653.1_Missense_Mutation_p.Q490H	NM_001037442.2	NP_001032519.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	0					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			GTAGGCTGCAACCCCACCCTA	0.353																																					p.Q543H		Atlas-SNP	.											.	RUFY3	61	.	0			c.A1629C						.						95	85	88					4																	71668679		2203	4300	6503	SO:0001583	missense	22902	exon16			GCTGCAACCCCAC	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000381006.3:c.1629A>C	chr4.hg19:g.71668679A>C	ENSP00000370394:p.Gln543His	113.0	0.0		59.0	4.0	NM_001037442	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000381006.3	hg19	CCDS34001.1	.	.	.	.	.	.	.	.	.	.	A	9.058	0.993890	0.19043	.	.	ENSG00000018189	ENST00000381006;ENST00000502653	T;T	0.76316	-1.01;-1.01	4.72	3.87	0.44632	.	1.025600	0.07786	N	0.954219	T	0.72503	0.3468	.	.	.	0.80722	D	1	B	0.22541	0.071	B	0.27608	0.081	T	0.65121	-0.6245	9	0.62326	D	0.03	4.9739	7.9734	0.30140	0.1139:0.0:0.8861:0.0	.	543	Q7L099-3	.	H	543;490	ENSP00000370394:Q543H;ENSP00000425400:Q490H	ENSP00000370394:Q543H	Q	+	3	2	RUFY3	71887543	0.955000	0.32602	0.866000	0.34008	0.175000	0.22909	2.704000	0.47118	1.181000	0.42912	-0.242000	0.12053	CAA	.	.		0.353	RUFY3-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252162.1	NM_014961		C	71668679	A	C	71668679	3	2	113	1	0	0	0	0	1	0	0	0	13755	40	2	5	2134	5	RUFY3	4	71668679	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	13870495	71668679	119485597	105	17982										
ANTXR2	118429	hgsc.bcm.edu	37	chr4	80905088	80905088	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ataataggaagcatccacagTtggccactttttagtaggca	9	8	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:80905088T>C	ENST00000307333.7	-	14	1125	c.1123A>G	c.(1123-1125)Act>Gct	p.T375A	ANTXR2_ENST00000403729.2_Missense_Mutation_p.T375A|ANTXR2_ENST00000346652.6_Missense_Mutation_p.T272A|ANTXR2_ENST00000404191.1_Missense_Mutation_p.T298A	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2	375					reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.T375P(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						GCATCCACAGTTGGCCACTTT	0.348									Juvenile Hyaline Fibromatosis																												p.T375A		Atlas-SNP	.											ANTXR2_ENST00000403729,colon,carcinoma,0,1	ANTXR2	97	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1123G						.						79	74	75					4																	80905088		1808	4072	5880	SO:0001583	missense	118429	exon14	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	CCACAGTTGGCCA	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297			21732	protein-coding gene	gene with protein product	"capillary morphogenesis protein 2"	608041				11683410, 12700348	Standard	NM_058172		Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000307333.7:c.1123A>G	chr4.hg19:g.80905088T>C	ENSP00000306185:p.Thr375Ala	114.0	0.0		50.0	2.0	NM_001145794	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Missense_Mutation	SNP	ENST00000307333.7	hg19	CCDS47086.1	.	.	.	.	.	.	.	.	.	.	T	19.88	3.909381	0.72868	.	.	ENSG00000163297	ENST00000403729;ENST00000404191;ENST00000346652;ENST00000307333	T;T;T;T	0.52057	2.23;0.68;2.19;2.22	5.8	5.8	0.92144	Anthrax toxin receptor, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70902	0.3277	M	0.80746	2.51	0.80722	D	1	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.80764	0.994;0.916;0.961	T	0.75411	-0.3327	10	0.87932	D	0	-24.3475	16.1464	0.81575	0.0:0.0:0.0:1.0	.	272;375;375	P58335-2;P58335;P58335-4	.;ANTR2_HUMAN;.	A	375;298;272;375	ENSP00000385575:T375A;ENSP00000384028:T298A;ENSP00000314883:T272A;ENSP00000306185:T375A	ENSP00000306185:T375A	T	-	1	0	ANTXR2	81124112	1.000000	0.71417	0.966000	0.40874	0.553000	0.35397	7.648000	0.83479	2.220000	0.72140	0.383000	0.25322	ACT	.	.		0.348	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172		C	80905088	T	C	80905088	3	2	113	1	0	0	0	0	1	0	0	0	712	1725	60	2	401	2	ANTXR2	4	80905088	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	9236409	80905088	110249188	106	17983										
COPS4	51138	hgsc.bcm.edu	37	chr4	83996548	83996548	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtcaaacagcaccagaatggAcagcacaagccatggaagcc	10	12	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:83996548A>G	ENST00000264389.2	+	10	1321	c.1186A>G	c.(1186-1188)Aca>Gca	p.T396A	COPS4_ENST00000511653.1_3'UTR|COPS4_ENST00000503682.1_Missense_Mutation_p.T428A|COPS4_ENST00000509093.1_3'UTR	NM_016129.2	NP_057213.2	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4	396					cullin deneddylation (GO:0010388)|protein deneddylation (GO:0000338)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(2)	13		Hepatocellular(203;0.114)				ACCAGAATGGACAGCACAAGC	0.448																																					p.T396A		Atlas-SNP	.											.	COPS4	31	.	0			c.A1186G						.						111	113	112					4																	83996548		2203	4300	6503	SO:0001583	missense	51138	exon10			GAATGGACAGCAC	AF100757	CCDS3600.1, CCDS58909.1	4q21.22	2013-03-14	2013-03-14		ENSG00000138663	ENSG00000138663			16702	protein-coding gene	gene with protein product			"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 4", "COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)"			9707402	Standard	NM_016129		Approved	CSN4	uc003hoa.3	Q9BT78	OTTHUMG00000130298	ENST00000264389.2:c.1186A>G	chr4.hg19:g.83996548A>G	ENSP00000264389:p.Thr396Ala	149.0	0.0		92.0	4.0	NM_016129	B3KN88|B3KST5|Q561W7|Q9NW31|Q9Y677	Missense_Mutation	SNP	ENST00000264389.2	hg19	CCDS3600.1	.	.	.	.	.	.	.	.	.	.	A	9.432	1.085908	0.20390	.	.	ENSG00000138663	ENST00000264389;ENST00000503682	T;T	0.41065	1.01;1.07	6.08	6.08	0.98989	.	0.056317	0.64402	D	0.000001	T	0.15349	0.0370	N	0.00729	-1.24	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29336	-1.0015	10	0.07990	T	0.79	-19.3174	16.6512	0.85203	1.0:0.0:0.0:0.0	.	428;396	D6RFN0;Q9BT78	.;CSN4_HUMAN	A	396;428	ENSP00000264389:T396A;ENSP00000424791:T428A	ENSP00000264389:T396A	T	+	1	0	COPS4	84215572	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.872000	0.75536	2.333000	0.79357	0.482000	0.46254	ACA	.	.		0.448	COPS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252643.1			G	83996548	A	G	83996548	3	3	113	1	0	0	0	0	1	0	0	0	3737	275	10	2	1224	2	COPS4	4	83996548	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3091460	83996548	107157728	107	17984										
TBCK	93627	hgsc.bcm.edu	37	chr4	107154200	107154200	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagttcatcgtactgatgacAgcgaggaatatccacttcaa	8	10	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:107154200A>G	ENST00000273980.5	-	18	1981	c.1534T>C	c.(1534-1536)Tgt>Cgt	p.C512R	TBCK_ENST00000432496.2_Missense_Mutation_p.C512R|TBCK_ENST00000394708.2_Missense_Mutation_p.C512R|TBCK_ENST00000394706.3_Missense_Mutation_p.C473R|TBCK_ENST00000361687.4_Missense_Mutation_p.C449R					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TACTGATGACAGCGAGGAATA	0.353																																					p.C512R		Atlas-SNP	.											.	TBCK	89	.	0			c.T1534C						.						119	114	116					4																	107154200		2203	4300	6503	SO:0001583	missense	93627	exon17			GATGACAGCGAGG		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1534T>C	chr4.hg19:g.107154200A>G	ENSP00000273980:p.Cys512Arg	109.0	0.0		76.0	4.0	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	hg19	CCDS54788.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.499858	0.85176	.	.	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394706;ENST00000394708;ENST00000503516	T;T;T;T;T;T	0.11063	2.81;2.81;2.81;2.81;2.81;3.67	5.55	5.55	0.83447	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.42765	0.1217	M	0.91920	3.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.54616	-0.8267	10	0.87932	D	0	.	15.7093	0.77612	1.0:0.0:0.0:0.0	.	512;473;449	Q8TEA7;Q8TEA7-2;Q8TEA7-3	TBCK_HUMAN;.;.	R	512;512;449;473;512;42	ENSP00000273980:C512R;ENSP00000405847:C512R;ENSP00000355338:C449R;ENSP00000378196:C473R;ENSP00000378198:C512R;ENSP00000423834:C42R	ENSP00000273980:C512R	C	-	1	0	TBCK	107373649	1.000000	0.71417	0.994000	0.49952	0.956000	0.61745	9.141000	0.94612	2.111000	0.64477	0.533000	0.62120	TGT	.	.		0.353	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		G	107154200	A	G	107154200	3	3	113	1	0	0	0	0	1	0	0	0	15651	188	7	2	1187	2	TBCK	4	107154200	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	23157652	107154200	84000076	108	17985										
PRMT10	90826	hgsc.bcm.edu	37	chr4	148559822	148559822	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aggcttcacttgaagtatccAacctaatctcttcatcaagg	6	11	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:148559822A>G	ENST00000322396.6	-	12	2641	c.2399T>C	c.(2398-2400)tTg>tCg	p.L800S	TMEM184C_ENST00000508208.1_Intron|PRMT10_ENST00000541232.1_Missense_Mutation_p.L687S	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		800	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						TGAAGTATCCAACCTAATCTC	0.383																																					p.L800S		Atlas-SNP	.											.	PRMT10	68	.	0			c.T2399C						.						99	89	93					4																	148559822		2203	4300	6503	SO:0001583	missense	90826	exon12			GTATCCAACCTAA																												ENST00000322396.6:c.2399T>C	chr4.hg19:g.148559822A>G	ENSP00000314396:p.Leu800Ser	186.0	0.0		88.0	4.0	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	hg19	CCDS3771.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.534579	0.85812	.	.	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.29655	1.56;1.56	5.67	5.67	0.87782	.	0.143577	0.47852	D	0.000216	T	0.52306	0.1726	M	0.64997	1.995	0.49483	D	0.999791	D	0.69078	0.997	D	0.65773	0.938	T	0.55108	-0.8192	10	0.87932	D	0	-21.4202	15.9054	0.79423	1.0:0.0:0.0:0.0	.	800	Q6P2P2	ANM10_HUMAN	S	800;687	ENSP00000314396:L800S;ENSP00000439508:L687S	ENSP00000314396:L800S	L	-	2	0	PRMT10	148779272	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.639000	0.91023	2.157000	0.67596	0.533000	0.62120	TTG	.	.		0.383	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			G	148559822	A	G	148559822	3	3	113	1	0	0	0	0	1	0	0	0	12548	131	5	2	142	2	PRMT10	4	148559822	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	41405622	148559822	42594454	109	17986										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153268212	153268212	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtgttgctgaacatggtacaAgcccagtggtactacaaaaa	10	8	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:153268212A>G	ENST00000281708.4	-	4	1825	c.596T>C	c.(595-597)cTt>cCt	p.L199P	FBXW7_ENST00000603841.1_Missense_Mutation_p.L199P|FBXW7_ENST00000263981.5_Missense_Mutation_p.L119P|FBXW7_ENST00000296555.5_Missense_Mutation_p.L81P|FBXW7_ENST00000603548.1_Missense_Mutation_p.L199P|FBXW7_ENST00000393956.3_Missense_Mutation_p.L23P	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	199					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ACATGGTACAAGCCCAGTGGT	0.398			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																p.L199P		Atlas-SNP	.		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	.	FBXW7	2157	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.T596C						.						115	103	107					4																	153268212		2203	4300	6503	SO:0001583	missense	55294	exon4			GGTACAAGCCCAG	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.596T>C	chr4.hg19:g.153268212A>G	ENSP00000281708:p.Leu199Pro	179.0	0.0		95.0	4.0	NM_033632	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	hg19	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	A	14.74	2.625943	0.46840	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.61040	0.56;0.24;0.14;0.52	5.83	4.66	0.58398	.	0.322034	0.32041	N	0.006678	T	0.45577	0.1349	N	0.14661	0.345	0.80722	D	1	B;B;P;P	0.51537	0.0;0.001;0.856;0.946	B;B;P;P	0.46825	0.0;0.001;0.528;0.528	T	0.48559	-0.9025	10	0.56958	D	0.05	-12.3942	11.5742	0.50852	0.9306:0.0:0.0694:0.0	.	23;199;81;119	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	P	199;81;119;23	ENSP00000281708:L199P;ENSP00000296555:L81P;ENSP00000263981:L119P;ENSP00000377528:L23P	ENSP00000263981:L119P	L	-	2	0	FBXW7	153487662	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	1.044000	0.40200	0.460000	0.39030	CTT	.	.		0.398	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			G	153268212	A	G	153268212	3	3	113	1	0	0	0	0	1	0	0	0	5777	72	3	2	1563	2	FBXW7	4	153268212	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	4708390	153268212	37886064	110	17987										
TLR2	7097	hgsc.bcm.edu	37	chr4	154625449	154625449	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agacactggaaattttagatGttagcaacaacaatctcaat	6	7	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:154625449G>A	ENST00000260010.6	+	1	2798	c.1390G>A	c.(1390-1392)Gtt>Att	p.V464I		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	464					apoptotic process (GO:0006915)|cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to peptidoglycan (GO:0071224)|cellular response to triacyl bacterial lipopeptide (GO:0071727)|central nervous system myelin formation (GO:0032289)|chloramphenicol transport (GO:0042892)|defense response to Gram-positive bacterium (GO:0050830)|detection of diacyl bacterial lipopeptide (GO:0042496)|detection of triacyl bacterial lipopeptide (GO:0042495)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|induction by symbiont of defense-related host nitric oxide production (GO:0052063)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukotriene metabolic process (GO:0006691)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-17 production (GO:0032700)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of Wnt signaling pathway (GO:0030177)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to molecule of fungal origin (GO:0002238)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell body (GO:0044297)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopolysaccharide receptor activity (GO:0001875)|lipoteichoic acid binding (GO:0070891)|peptidoglycan binding (GO:0042834)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)|triacyl lipopeptide binding (GO:0042497)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	29	all_hematologic(180;0.093)	Renal(120;0.117)			OspA lipoprotein(DB00045)	AATTTTAGATGTTAGCAACAA	0.368																																					p.V464I		Atlas-SNP	.											.	TLR2	84	.	0			c.G1390A						.						96	98	97					4																	154625449		2203	4300	6503	SO:0001583	missense	7097	exon3			TTAGATGTTAGCA	U88878	CCDS3784.1	4q32	2008-02-05				ENSG00000137462		"CD molecules"	11848	protein-coding gene	gene with protein product		603028				9435236	Standard	XM_005263193		Approved	TIL4, CD282	uc003inq.3	O60603		ENST00000260010.6:c.1390G>A	chr4.hg19:g.154625449G>A	ENSP00000260010:p.Val464Ile	144.0	0.0		101.0	44.0	NM_003264	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	hg19	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	G	0.969	-0.700825	0.03279	.	.	ENSG00000137462	ENST00000260010	T	0.00816	5.66	5.42	-5.31	0.02730	.	0.347798	0.26927	N	0.021789	T	0.00784	0.0026	N	0.17838	0.53	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.40327	-0.9569	10	0.30078	T	0.28	.	16.5669	0.84601	0.1076:0.0701:0.8223:0.0	.	464	O60603	TLR2_HUMAN	I	464	ENSP00000260010:V464I	ENSP00000260010:V464I	V	+	1	0	TLR2	154844899	0.952000	0.32445	0.004000	0.12327	0.074000	0.17049	0.152000	0.16302	-1.581000	0.01642	-2.010000	0.00438	GTT	.	.		0.368	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1			A	154625449	G	A	154625449	3	1	113	1	0	0	0	0	1	0	0	0	15966	1377	48	3	1392	3	TLR2	4	154625449	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	1357237	154625449	36528827	111	17988										
MAP9	79884	hgsc.bcm.edu	37	chr4	156294381	156294381	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atccttattttgagattcagAgaaagattttacaacaatgt	6	5	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:156294381A>G	ENST00000311277.4	-	4	651	c.388T>C	c.(388-390)Tct>Cct	p.S130P	MAP9_ENST00000515654.1_Missense_Mutation_p.S130P|AC097467.2_ENST00000596165.1_RNA|MAP9_ENST00000379248.2_Missense_Mutation_p.S58P	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	130					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		TGAGATTCAGAGAAAGATTTT	0.338																																					p.S130P		Atlas-SNP	.											.	MAP9	79	.	0			c.T388C						.						87	88	87					4																	156294381		2203	4300	6503	SO:0001583	missense	79884	exon4			ATTCAGAGAAAGA	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"aster-associated protein"	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.388T>C	chr4.hg19:g.156294381A>G	ENSP00000310593:p.Ser130Pro	108.0	0.0		78.0	4.0	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	hg19	CCDS35493.1	.	.	.	.	.	.	.	.	.	.	A	10.15	1.271255	0.23221	.	.	ENSG00000164114	ENST00000311277;ENST00000515654;ENST00000433024;ENST00000393836;ENST00000379248	T;T;T;T	0.34667	2.1;2.08;1.35;1.36	5.84	-1.31	0.09230	.	0.727289	0.12968	N	0.424371	T	0.17619	0.0423	N	0.17674	0.51	0.09310	N	1	B;B;B;B	0.27559	0.002;0.181;0.004;0.004	B;B;B;B	0.26864	0.004;0.074;0.009;0.009	T	0.20505	-1.0273	10	0.23891	T	0.37	-0.8377	4.5813	0.12260	0.3867:0.0:0.4409:0.1724	.	130;58;130;130	B4DVG9;A8MSM7;B9EJB6;Q49MG5	.;.;.;MAP9_HUMAN	P	130;130;130;130;58	ENSP00000310593:S130P;ENSP00000427402:S130P;ENSP00000394048:S130P;ENSP00000368550:S58P	ENSP00000310593:S130P	S	-	1	0	MAP9	156513831	0.000000	0.05858	0.005000	0.12908	0.069000	0.16628	0.059000	0.14322	0.152000	0.19188	0.455000	0.32223	TCT	.	.		0.338	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580		G	156294381	A	G	156294381	3	3	113	1	0	0	0	0	1	0	0	0	9279	304	11	2	1599	2	MAP9	4	156294381	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1668932	156294381	34859895	112	17989										
ING2	3622	hgsc.bcm.edu	37	chr4	184426478	184426478	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cgctgccccacgacatgcagAggaacgtgtctgtgctgcga	13	13	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:184426478A>G	ENST00000302327.3	+	1	332	c.130A>G	c.(130-132)Agg>Ggg	p.R44G	RP11-367N14.2_ENST00000457303.3_RNA|ING2_ENST00000434682.2_5'Flank	NM_001564.2	NP_001555.1	Q9H160	ING2_HUMAN	inhibitor of growth family, member 2	44					chromatin modification (GO:0016568)|male germ-line stem cell asymmetric division (GO:0048133)|male meiosis I (GO:0007141)|negative regulation of cell proliferation (GO:0008285)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cellular senescence (GO:2000772)|regulation of growth (GO:0040008)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|seminiferous tubule development (GO:0072520)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleus (GO:0005634)|Sin3 complex (GO:0016580)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)	7		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|all_hematologic(60;0.0207)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		CGACATGCAGAGGAACGTGTC	0.682																																					p.R44G		Atlas-SNP	.											.	ING2	20	.	0			c.A130G						.						23	18	20					4																	184426478		2148	4238	6386	SO:0001583	missense	3622	exon1			ATGCAGAGGAACG	AB012853	CCDS3833.1	4q35.1	2013-01-28	2005-02-10	2005-02-11	ENSG00000168556	ENSG00000168556		"Zinc fingers, PHD-type"	6063	protein-coding gene	gene with protein product		604215	"inhibitor of growth family, member 1-like"	ING1L		10072587	Standard	XM_005262982		Approved	p33ING2	uc003ivs.1	Q9H160	OTTHUMG00000150502	ENST00000302327.3:c.130A>G	chr4.hg19:g.184426478A>G	ENSP00000307183:p.Arg44Gly	307.0	0.0		162.0	7.0	NM_001564	B6ZDS1|O95698	Missense_Mutation	SNP	ENST00000302327.3	hg19	CCDS3833.1	.	.	.	.	.	.	.	.	.	.	A	17.51	3.406629	0.62399	.	.	ENSG00000168556	ENST00000302327	.	.	.	4.29	3.11	0.35812	Inhibitor of growth protein, N-terminal (1);	0.054948	0.64402	D	0.000001	T	0.80253	0.4589	M	0.89715	3.055	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.83690	0.0176	9	0.87932	D	0	-18.3281	10.7999	0.46483	0.831:0.169:0.0:0.0	.	44	Q9H160	ING2_HUMAN	G	44	.	ENSP00000307183:R44G	R	+	1	2	ING2	184663472	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.604000	0.46274	1.798000	0.52647	0.459000	0.35465	AGG	.	.		0.682	ING2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318652.1	NM_001564		G	184426478	A	G	184426478	3	3	113	1	0	0	0	0	1	0	0	0	7745	295	11	2	132	2	ING2	4	184426478	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	28132097	184426478	6727798	113	17990										
SNX25	83891	hgsc.bcm.edu	37	chr4	186244833	186244833	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctacaaaatccaggaagatgTttatgagaccctaaaggata	8	7	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:186244833T>C	ENST00000504273.1	+	9	1430	c.1136T>C	c.(1135-1137)gTt>gCt	p.V379A	SNX25_ENST00000264694.8_Missense_Mutation_p.V379A|SNX25_ENST00000512853.1_3'UTR			Q9H3E2	SNX25_HUMAN	sorting nexin 25	379	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		CAGGAAGATGTTTATGAGACC	0.338																																					p.V379A		Atlas-SNP	.											.	SNX25	100	.	0			c.T1136C						.						74	75	75					4																	186244833		2203	4298	6501	SO:0001583	missense	83891	exon9			AAGATGTTTATGA	AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"Sorting nexins"	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.1136T>C	chr4.hg19:g.186244833T>C	ENSP00000426255:p.Val379Ala	200.0	0.0		98.0	4.0	NM_031953	Q3ZT30|Q8N6K3	Missense_Mutation	SNP	ENST00000504273.1	hg19	CCDS34116.1	.	.	.	.	.	.	.	.	.	.	.	23.0	4.366677	0.82463	.	.	ENSG00000109762	ENST00000504273;ENST00000264694	T;T	0.44881	0.91;0.91	5.81	5.81	0.92471	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.062970	0.64402	D	0.000006	T	0.47619	0.1455	M	0.68952	2.095	0.53005	D	0.999965	B;P	0.40000	0.39;0.698	B;B	0.41174	0.154;0.349	T	0.49437	-0.8940	10	0.49607	T	0.09	-14.9727	16.1616	0.81721	0.0:0.0:0.0:1.0	.	150;379	Q8N6K3;Q9H3E2	.;SNX25_HUMAN	A	379	ENSP00000426255:V379A;ENSP00000264694:V379A	ENSP00000264694:V379A	V	+	2	0	SNX25	186481827	1.000000	0.71417	0.982000	0.44146	0.919000	0.55068	7.403000	0.79983	2.221000	0.72209	0.454000	0.30748	GTT	.	.		0.338	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953		C	186244833	T	C	186244833	3	2	113	1	0	0	0	0	1	0	0	0	14911	1725	60	2	1166	2	SNX25	4	186244833	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1818355	186244833	4909443	114	17991										
FAT1	2195	hgsc.bcm.edu	37	chr4	187628064	187628064	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgagtttatccacatcgaagTttccttctccgtggtccaga	8	11	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr4:187628064T>C	ENST00000441802.2	-	2	3127	c.2918A>G	c.(2917-2919)aAc>aGc	p.N973S		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	973	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CACATCGAAGTTTCCTTCTCC	0.483										HNSCC(5;0.00058)																											p.N973S	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A2918G						.						165	160	161					4																	187628064		1934	4138	6072	SO:0001583	missense	2195	exon2			TCGAAGTTTCCTT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.2918A>G	chr4.hg19:g.187628064T>C	ENSP00000406229:p.Asn973Ser	204.0	0.0		97.0	4.0	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.560681	0.00136	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.51574	0.7	4.11	1.7	0.24286	Cadherin (4);Cadherin-like (1);	0.979756	0.08379	N	0.954783	T	0.21801	0.0525	N	0.03084	-0.415	0.09310	N	0.999999	B	0.11235	0.004	B	0.11329	0.006	T	0.25467	-1.0131	10	0.20046	T	0.44	.	5.122	0.14865	0.0:0.2579:0.1605:0.5816	.	973	Q14517	FAT1_HUMAN	S	973	ENSP00000406229:N973S	ENSP00000260147:N973S	N	-	2	0	FAT1	187865058	0.899000	0.30636	0.446000	0.26920	0.009000	0.06853	1.378000	0.34328	0.393000	0.25203	-0.415000	0.06103	AAC	.	.		0.483	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		C	187628064	T	C	187628064	3	2	113	1	0	0	0	0	1	0	0	0	5697	1725	60	2	10952	2	FAT1	4	187628064	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1383231	187628064	3526212	115	17992										
PAPD7	11044	hgsc.bcm.edu	37	chr5	6743905	6743905	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgaatgaagtttttacaggTggaattagctcatacagcct	9	7	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:6743905T>C	ENST00000230859.6	+	6	576	c.447T>C	c.(445-447)ggT>ggC	p.G149G		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	379					double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)			cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TTTTTACAGGTGGAATTAGCT	0.358																																					p.G149G	NSCLC(7;212 333 5667 23379 46547)	Atlas-SNP	.											.	PAPD7	69	.	0			c.T447C						.						155	160	158					5																	6743905		2203	4300	6503	SO:0001819	synonymous_variant	11044	exon6			TACAGGTGGAATT	AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"topoisomerase-related function protein 4-1", "polymerase (DNA-directed) sigma", "DNA polymerase kappa", "TUTase5"	605198	"polymerase (DNA directed) sigma"	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.447T>C	chr5.hg19:g.6743905T>C		147.0	0.0		87.0	4.0	NM_001171805	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Silent	SNP	ENST00000230859.6	hg19	CCDS3871.1																																																																																			.	.		0.358	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		C	6743905	T	C	6743905	2	2	113	1	0	0	0	0	0	0	0	1	11435	1683	59	2		2	PAPD7	5	6743905	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10		6743905	174171355	116	17993										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38337733	38337733	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcccatccttgggtacactgTgagtacacgggcatgggagt	13	10	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:38337733T>C	ENST00000354891.3	+	2	553		c.e2+2		EGFLAM_ENST00000322350.5_Splice_Site	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains						extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					GGGTACACTGTGAGTACACGG	0.488																																					.	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.207+2T>C						.						85	62	69					5																	38337733		2203	4299	6502	SO:0001630	splice_region_variant	133584	exon2			ACACTGTGAGTAC	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.207+2T>C	chr5.hg19:g.38337733T>C		128.0	0.0		57.0	26.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Splice_Site	SNP	ENST00000354891.3	hg19	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.174520	0.57692	.	.	ENSG00000164318	ENST00000354891;ENST00000322350	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9606	0.71153	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	EGFLAM	38373490	1.000000	0.71417	1.000000	0.80357	0.530000	0.34684	4.791000	0.62460	2.171000	0.68590	0.533000	0.62120	.	.	.		0.488	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	Intron	C	38337733	T	C	38337733	5	2	113	1	0	0	0	0	0	0	1	0	4968	1710	59	2	215	2	EGFLAM	5	38337733	Splice_Site	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	31593828	38337733	142577527	117	17994										
RPL37	6167	hgsc.bcm.edu	37	chr5	40834674	40834674	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggcacaacgtgtgcgtcttaTtgcgacgctttccaaacgat	10	11	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:40834674T>C	ENST00000274242.5	-	2	187	c.38A>G	c.(37-39)aAt>aGt	p.N13S	RPL37_ENST00000508493.1_Missense_Mutation_p.N13S|RPL37_ENST00000509877.1_Missense_Mutation_p.N13S|SNORD72_ENST00000390994.1_RNA|RPL37_ENST00000504562.1_5'UTR	NM_000997.4	NP_000988.1	P61927	RL37_HUMAN	ribosomal protein L37	13					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			lung(3)|ovary(1)	4		Breast(839;0.238)				GTGCGTCTTATTGCGACGCTT	0.507																																					p.N13S	Colon(188;1411 2035 4978 19588 31462)	Atlas-SNP	.											.	RPL37	7	.	0			c.A38G						.						64	61	62					5																	40834674		2203	4300	6503	SO:0001583	missense	6167	exon2			GTCTTATTGCGAC	L11567	CCDS3934.1	5p13.1	2013-09-23			ENSG00000145592	ENSG00000145592		"L ribosomal proteins"	10347	protein-coding gene	gene with protein product	"60S ribosomal protein L37a"	604181				7545944, 9582194	Standard	NM_000997		Approved	L37	uc003jme.1	P61927	OTTHUMG00000094774	ENST00000274242.5:c.38A>G	chr5.hg19:g.40834674T>C	ENSP00000274242:p.Asn13Ser	160.0	0.0		76.0	4.0	NM_000997	B2R4H2|P02403|Q6IBB4|Q99883	Missense_Mutation	SNP	ENST00000274242.5	hg19	CCDS3934.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.983776	0.74474	.	.	ENSG00000145592	ENST00000274242;ENST00000509877;ENST00000508493	T	0.44881	0.91	5.62	5.62	0.85841	Ribosomal protein L37e, conserved site (1);Ribosomal protein L37ae/L37e, N-terminal (1);Ribosomal protein, zinc-binding domain (1);	0.090386	0.85682	D	0.000000	T	0.40040	0.1101	.	.	.	0.80722	D	1	B	0.20671	0.047	B	0.24701	0.055	T	0.20739	-1.0266	9	0.51188	T	0.08	.	15.8181	0.78621	0.0:0.0:0.0:1.0	.	13	P61927	RL37_HUMAN	S	13	ENSP00000274242:N13S	ENSP00000274242:N13S	N	-	2	0	RPL37	40870431	1.000000	0.71417	0.998000	0.56505	0.942000	0.58702	8.012000	0.88631	2.142000	0.66516	0.460000	0.39030	AAT	.	.		0.507	RPL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000211583.2	NM_000997		C	40834674	T	C	40834674	3	2	113	1	0	0	0	0	1	0	0	0	13604	1493	52	2	267	2	RPL37	5	40834674	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2496941	40834674	140080586	118	17995										
ZNF131	7690	hgsc.bcm.edu	37	chr5	43161821	43161821	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccattttaaggagcacatgaAatcacactccactgagagtt	7	10	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:43161821A>G	ENST00000399534.1	+	5	886	c.842A>G	c.(841-843)aAa>aGa	p.K281R	ZNF131_ENST00000509931.1_Intron|ZNF131_ENST00000509156.1_Missense_Mutation_p.K281R|ZNF131_ENST00000509634.1_Missense_Mutation_p.K247R|ZNF131_ENST00000505606.2_Missense_Mutation_p.K247R|ZNF131_ENST00000306938.4_Missense_Mutation_p.K247R			P52739	ZN131_HUMAN	zinc finger protein 131	281					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	17						GAGCACATGAAATCACACTCC	0.378																																					p.K247R		Atlas-SNP	.											.	ZNF131	51	.	0			c.A740G						.						71	63	65					5																	43161821		1873	4116	5989	SO:0001583	missense	7690	exon6			ACATGAAATCACA	U09410	CCDS43313.1	5p12	2013-01-09	2006-06-13		ENSG00000172262	ENSG00000172262		"Zinc fingers, C2H2-type", "-", "BTB/POZ domain containing"	12915	protein-coding gene	gene with protein product	"zinc finger and BTB domain containing 35"	604073	"zinc finger protein 131 (clone pHZ-10)"				Standard	XM_005248359		Approved	ZBTB35, pHZ-10	uc003jnk.3	P52739	OTTHUMG00000162223	ENST00000399534.1:c.842A>G	chr5.hg19:g.43161821A>G	ENSP00000382450:p.Lys281Arg	183.0	0.0		100.0	4.0	NM_003432	B4DRL3|Q6PIF0	Missense_Mutation	SNP	ENST00000399534.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.59	2.878138	0.51801	.	.	ENSG00000172262	ENST00000515326;ENST00000509156;ENST00000306938;ENST00000399534;ENST00000505606;ENST00000509634	T;T;T;T;T;T	0.75050	-0.85;-0.9;2.64;-0.9;2.64;2.64	5.42	5.42	0.78866	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.70988	0.3287	N	0.12422	0.21	0.49687	D	0.999814	D;D	0.76494	0.999;0.996	D;D	0.81914	0.995;0.99	T	0.66630	-0.5875	10	0.02654	T	1	-21.327	15.4594	0.75342	1.0:0.0:0.0:0.0	.	281;247	P52739;P52739-2	ZN131_HUMAN;.	R	247;281;247;281;247;247	ENSP00000422079:K247R;ENSP00000426504:K281R;ENSP00000305804:K247R;ENSP00000382450:K281R;ENSP00000423945:K247R;ENSP00000421246:K247R	ENSP00000305804:K247R	K	+	2	0	ZNF131	43197578	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.906000	0.75719	2.058000	0.61347	0.528000	0.53228	AAA	.	.		0.378	ZNF131-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000367982.1	NM_003432		G	43161821	A	G	43161821	3	3	113	1	0	0	0	0	1	0	0	0	17736	14	1	2	758	2	ZNF131	5	43161821	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2327147	43161821	137753439	119	17996										
NNT	23530	hgsc.bcm.edu	37	chr5	43628311	43628311	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aatcaccctagagctgcagcTttggaacagttcaagtctct	8	11	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:43628311T>C	ENST00000264663.5	+	7	1007	c.786T>C	c.(784-786)gcT>gcC	p.A262A	NNT_ENST00000512996.2_Silent_p.A131A|NNT_ENST00000344920.4_Silent_p.A262A	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	262				A -> S (in Ref. 1; AAC51914). {ECO:0000305}.	cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					GAGCTGCAGCTTTGGAACAGT	0.413																																					p.A262A		Atlas-SNP	.											.	NNT	92	.	0			c.T786C						.						112	117	115					5																	43628311		2203	4300	6503	SO:0001819	synonymous_variant	23530	exon7			TGCAGCTTTGGAA	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.786T>C	chr5.hg19:g.43628311T>C		255.0	0.0		139.0	6.0	NM_182977	Q16796|Q2TB60|Q8N3V4	Silent	SNP	ENST00000264663.5	hg19	CCDS3949.1																																																																																			.	.		0.413	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		C	43628311	T	C	43628311	2	2	113	1	0	0	0	0	0	0	0	1	10519	1596	56	2		2	NNT	5	43628311	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	466490	43628311	137286949	120	17997										
GPX8	493869	hgsc.bcm.edu	37	chr5	54459895	54459895	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tattttagattcttcaaagaAggaaccaaggtggaattttt	8	4	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:54459895A>G	ENST00000503787.1	+	3	554	c.479A>G	c.(478-480)aAg>aGg	p.K160R	GPX8_ENST00000296734.6_Missense_Mutation_p.R73G|CDC20B_ENST00000296733.1_Intron|CDC20B_ENST00000322374.6_Intron|CDC20B_ENST00000381375.2_Intron|GPX8_ENST00000506123.1_3'UTR|CDC20B_ENST00000334206.5_Intron|GPX8_ENST00000515370.1_Missense_Mutation_p.K109R|CDC20B_ENST00000331730.3_Intron	NM_001008397.2	NP_001008398.2	Q8TED1	GPX8_HUMAN	glutathione peroxidase 8 (putative)	160					response to oxidative stress (GO:0006979)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	glutathione peroxidase activity (GO:0004602)|peroxidase activity (GO:0004601)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)	11					Glutathione(DB00143)	TCTTCAAAGAAGGAACCAAGG	0.368																																					p.K160R		Atlas-SNP	.											.	GPX8	20	.	0			c.A479G						.						58	62	61					5																	54459895		2203	4300	6503	SO:0001583	missense	493869	exon3			CAAAGAAGGAACC	BC029424	CCDS34156.1	5q11.2	2008-09-29				ENSG00000164294			33100	protein-coding gene	gene with protein product							Standard	NM_001008397		Approved	UNQ847, EPLA847	uc003jpq.2	Q8TED1		ENST00000503787.1:c.479A>G	chr5.hg19:g.54459895A>G	ENSP00000423822:p.Lys160Arg	87.0	0.0		52.0	4.0	NM_001008397		Missense_Mutation	SNP	ENST00000503787.1	hg19	CCDS34156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.58|15.58	2.875565|2.875565	0.51695|0.51695	.|.	.|.	ENSG00000164294|ENSG00000164294	ENST00000503787;ENST00000515370|ENST00000296734	T;T|.	0.03831|.	3.79;3.79|.	5.92|5.92	3.52|3.52	0.40303|0.40303	Thioredoxin-like fold (2);|.	0.126441|.	0.64402|.	N|.	0.000001|.	T|T	0.60457|0.60457	0.2270|0.2270	L|L	0.58583|0.58583	1.82|1.82	0.43172|0.43172	D|D	0.994973|0.994973	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.58493|0.58493	-0.7627|-0.7627	10|6	0.66056|0.54805	D|T	0.02|0.06	.|.	7.4915|7.4915	0.27464|0.27464	0.6612:0.2708:0.068:0.0|0.6612:0.2708:0.068:0.0	.|.	109;160|.	E7ETY7;Q8TED1|.	.;GPX8_HUMAN|.	R|G	160;109|73	ENSP00000423822:K160R;ENSP00000427466:K109R|.	ENSP00000423822:K160R|ENSP00000296734:R73G	K|R	+|+	2|1	0|2	GPX8|GPX8	54495652|54495652	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	4.537000|4.537000	0.60643|0.60643	0.476000|0.476000	0.27440|0.27440	0.528000|0.528000	0.53228|0.53228	AAG|AGG	.	.		0.368	GPX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369717.1	NM_001008397		G	54459895	A	G	54459895	3	3	113	1	0	0	0	0	1	0	0	0	6755	72	3	2	489	2	GPX8	5	54459895	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	10831584	54459895	126455365	121	17998										
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65321309	65321309	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttgtttcttccctcattaggTtcgttgaagaatataacaac	6	8	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:65321309T>C	ENST00000284037.5	+	11	1208	c.819T>C	c.(817-819)ggT>ggC	p.G273G	ERBB2IP_ENST00000380943.2_Splice_Site_p.G273G|ERBB2IP_ENST00000508515.1_Splice_Site_p.G273G|ERBB2IP_ENST00000380936.1_Splice_Site_p.G273G|ERBB2IP_ENST00000416865.2_Splice_Site_p.G273G|ERBB2IP_ENST00000380938.2_Splice_Site_p.G273G|ERBB2IP_ENST00000511297.1_Splice_Site_p.G273G|ERBB2IP_ENST00000506030.1_Splice_Site_p.G273G|ERBB2IP_ENST00000380935.1_Splice_Site_p.G273G|ERBB2IP_ENST00000380939.2_Splice_Site_p.G273G	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	273					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		CCTCATTAGGTTCGTTGAAGA	0.353																																					p.G273G		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.T819C						.						173	164	167					5																	65321309		2203	4299	6502	SO:0001630	splice_region_variant	55914	exon11			ATTAGGTTCGTTG		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"densin-180-like protein", "ERBB2-interacting protein"	606944	"erbb2-interacting protein"			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.818-1T>C	chr5.hg19:g.65321309T>C		78.0	0.0		56.0	4.0	NM_001253701	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Silent	SNP	ENST00000284037.5	hg19	CCDS58953.1																																																																																			.	.		0.353	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	Silent	C	65321309	T	C	65321309	5	2	113	1	0	0	0	0	0	0	1	0	5209	1739	60	2	853	2	ERBB2IP	5	65321309	Splice_Site	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	10861414	65321309	115593951	122	17999										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71492148	71492148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgatgcatacatcagggagaAgagggagtctgtggccagtg	16	6	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:71492148A>G	ENST00000296755.7	+	5	3264	c.2966A>G	c.(2965-2967)aAg>aGg	p.K989R		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	989					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ATCAGGGAGAAGAGGGAGTCT	0.562																																					p.K989R	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A2966G						.						75	75	75					5																	71492148		2203	4300	6503	SO:0001583	missense	4131	exon5			GGGAGAAGAGGGA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.2966A>G	chr5.hg19:g.71492148A>G	ENSP00000296755:p.Lys989Arg	222.0	0.0		123.0	5.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	15.06	2.722191	0.48728	.	.	ENSG00000131711	ENST00000296755	T	0.03920	3.76	6.08	6.08	0.98989	.	0.085246	0.51477	D	0.000099	T	0.03348	0.0097	N	0.08118	0	0.38208	D	0.940389	B;B	0.29188	0.236;0.236	B;B	0.24848	0.056;0.031	T	0.58059	-0.7703	10	0.22706	T	0.39	-25.627	16.3172	0.82932	1.0:0.0:0.0:0.0	.	863;989	A2BDK6;P46821	.;MAP1B_HUMAN	R	989	ENSP00000296755:K989R	ENSP00000296755:K989R	K	+	2	0	MAP1B	71527904	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	3.108000	0.50337	2.333000	0.79357	0.533000	0.62120	AAG	.	.		0.562	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		G	71492148	A	G	71492148	3	3	113	1	0	0	0	0	1	0	0	0	9237	72	3	2	2984	2	MAP1B	5	71492148	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	6170839	71492148	109423112	123	18000										
ZNF366	167465	hgsc.bcm.edu	37	chr5	71756449	71756449	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gggtatgcaggtggctgagcTgcttgaagagcttcccgcag	16	9	0	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:71756449T>C	ENST00000318442.5	-	2	1365	c.875A>G	c.(874-876)cAg>cGg	p.Q292R		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	292					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		GTGGCTGAGCTGCTTGAAGAG	0.622																																					p.Q292R		Atlas-SNP	.											.	ZNF366	108	.	0			c.A875G						.						112	99	103					5																	71756449		2203	4300	6503	SO:0001583	missense	167465	exon2			CTGAGCTGCTTGA	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"Zinc fingers, C2H2-type"	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.875A>G	chr5.hg19:g.71756449T>C	ENSP00000313158:p.Gln292Arg	146.0	0.0		98.0	4.0	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	hg19	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.278874	0.80692	.	.	ENSG00000178175	ENST00000318442	T	0.74632	-0.86	5.79	5.79	0.91817	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000008	T	0.71517	0.3349	N	0.11845	0.185	0.80722	D	1	D	0.63880	0.993	P	0.58620	0.842	T	0.72717	-0.4209	10	0.31617	T	0.26	-52.0909	16.1338	0.81465	0.0:0.0:0.0:1.0	.	292	Q8N895	ZN366_HUMAN	R	292	ENSP00000313158:Q292R	ENSP00000313158:Q292R	Q	-	2	0	ZNF366	71792205	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.216000	0.71823	0.459000	0.35465	CAG	.	.		0.622	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			C	71756449	T	C	71756449	3	2	113	1	0	0	0	0	1	0	0	0	17885	1580	55	2	1375	2	ZNF366	5	71756449	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	264301	71756449	109158811	124	18001										
ST8SIA4	7903	hgsc.bcm.edu	37	chr5	100222062	100222062	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctcaccttattacaaaattgTgactgtcaatctcctttcca	3	12	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:100222062T>C	ENST00000231461.5	-	3	798	c.488A>G	c.(487-489)cAc>cGc	p.H163R	ST8SIA4_ENST00000507360.2_5'UTR|ST8SIA4_ENST00000451528.2_Missense_Mutation_p.H163R	NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	163					axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		TACAAAATTGTGACTGTCAAT	0.353																																					p.H163R		Atlas-SNP	.											.	ST8SIA4	77	.	0			c.A488G						.						66	68	67					5																	100222062		2203	4300	6503	SO:0001583	missense	7903	exon3			AAATTGTGACTGT	L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532		"Sialyltransferases"	10871	protein-coding gene	gene with protein product	"ST8Sia IV"	602547	"sialyltransferase 8 (alpha-2, 8-polysialytransferase) D"	SIAT8D		7624364	Standard	NM_005668		Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.488A>G	chr5.hg19:g.100222062T>C	ENSP00000231461:p.His163Arg	132.0	0.0		95.0	4.0	NM_175052	A8KA07|G3V104|Q8N1F4|Q92693	Missense_Mutation	SNP	ENST00000231461.5	hg19	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.562779	0.86335	.	.	ENSG00000113532	ENST00000231461;ENST00000451528	T;T	0.35605	1.3;1.3	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.62011	0.2393	M	0.93594	3.435	0.80722	D	1	P	0.46706	0.883	P	0.52909	0.713	T	0.67409	-0.5678	10	0.25751	T	0.34	-3.8465	15.5406	0.76043	0.0:0.0:0.0:1.0	.	163	Q92187	SIA8D_HUMAN	R	163	ENSP00000231461:H163R;ENSP00000428914:H163R	ENSP00000231461:H163R	H	-	2	0	ST8SIA4	100249961	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.665000	0.83852	2.266000	0.75297	0.455000	0.32223	CAC	.	.		0.353	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668		C	100222062	T	C	100222062	3	2	113	1	0	0	0	0	1	0	0	0	15249	1696	59	2	607	2	ST8SIA4	5	100222062	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	28465613	100222062	80693198	125	18002										
FER	2241	hgsc.bcm.edu	37	chr5	108436123	108436123	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atttcctcacctttctgagaAggaagaaggatgaactaaaa	8	7	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:108436123A>G	ENST00000281092.4	+	17	2335	c.1951A>G	c.(1951-1953)Agg>Ggg	p.R651G	FER_ENST00000438717.2_Missense_Mutation_p.R476G	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	651	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		CTTTCTGAGAAGGAAGAAGGA	0.353																																					p.R651G	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.A1951G						.						69	75	73					5																	108436123		2202	4300	6502	SO:0001583	missense	2241	exon17			CTGAGAAGGAAGA	J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	3655	protein-coding gene	gene with protein product	"phosphoprotein NCP94", "protein phosphatase 1, regulatory subunit 74"	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.1951A>G	chr5.hg19:g.108436123A>G	ENSP00000281092:p.Arg651Gly	122.0	0.0		74.0	4.0	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	hg19	CCDS4098.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.671928	0.47781	.	.	ENSG00000151422	ENST00000281092;ENST00000438717	D;D	0.83335	-1.71;-1.71	5.35	5.35	0.76521	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.047719	0.85682	D	0.000000	T	0.75664	0.3880	L	0.31157	0.91	0.38468	D	0.947384	B	0.06786	0.001	B	0.11329	0.006	T	0.72462	-0.4286	10	0.38643	T	0.18	-13.2319	15.6245	0.76845	1.0:0.0:0.0:0.0	.	651	P16591	FER_HUMAN	G	651;476	ENSP00000281092:R651G;ENSP00000394297:R476G	ENSP00000281092:R651G	R	+	1	2	FER	108464022	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.768000	0.91737	2.161000	0.67846	0.374000	0.22700	AGG	.	.		0.353	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246		G	108436123	A	G	108436123	3	3	113	1	0	0	0	0	1	0	0	0	5821	63	3	2	2009	2	FER	5	108436123	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	8214061	108436123	72479137	126	18003										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112920155	112920155	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccaagtccttgtgctagtccTtctcctccatcctcaggaaa	6	15	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:112920155T>C	ENST00000161863.4	+	26	4017	c.3804T>C	c.(3802-3804)ccT>ccC	p.P1268P		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1268	Ser-rich.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GTGCTAGTCCTTCTCCTCCAT	0.393																																					p.P1268P		Atlas-SNP	.											.	YTHDC2	118	.	0			c.T3804C						.						142	125	131					5																	112920155		2202	4300	6502	SO:0001819	synonymous_variant	64848	exon26			TAGTCCTTCTCCT	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.3804T>C	chr5.hg19:g.112920155T>C		159.0	0.0		98.0	4.0	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	hg19	CCDS4113.1																																																																																			.	.		0.393	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		C	112920155	T	C	112920155	2	2	113	1	0	0	0	0	0	0	0	1	17512	1596	56	2		2	YTHDC2	5	112920155	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	4484032	112920155	67995105	127	18004										
PGGT1B	5229	hgsc.bcm.edu	37	chr5	114548112	114548112	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaatcagtcatgtggagataTgtacattctctgagcattgt	9	6	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:114548112T>C	ENST00000419445.1	-	9	1141	c.1121A>G	c.(1120-1122)cAt>cGt	p.H374R	PGGT1B_ENST00000379615.3_Missense_Mutation_p.H297R	NM_005023.3	NP_005014.2	P53609	PGTB1_HUMAN	protein geranylgeranyltransferase type I, beta subunit	374					negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|protein geranylgeranylation (GO:0018344)|response to cytokine (GO:0034097)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)	CAAX-protein geranylgeranyltransferase activity (GO:0004662)|protein geranylgeranyltransferase activity (GO:0004661)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)		TGTGGAGATATGTACATTCTC	0.423																																					p.H374R		Atlas-SNP	.											.	PGGT1B	26	.	0			c.A1121G						.						140	128	132					5																	114548112		2202	4300	6502	SO:0001583	missense	5229	exon9			GAGATATGTACAT		CCDS4116.1	5q23.1	2008-02-05			ENSG00000164219	ENSG00000164219			8895	protein-coding gene	gene with protein product		602031				8106351	Standard	NM_005023		Approved	GGTI, BGGI	uc003kqw.4	P53609	OTTHUMG00000128893	ENST00000419445.1:c.1121A>G	chr5.hg19:g.114548112T>C	ENSP00000404676:p.His374Arg	296.0	0.0		153.0	52.0	NM_005023	Q5MJP9	Missense_Mutation	SNP	ENST00000419445.1	hg19	CCDS4116.1	.	.	.	.	.	.	.	.	.	.	T	10.59	1.392167	0.25118	.	.	ENSG00000164219	ENST00000419445;ENST00000379615	T;T	0.42513	1.03;0.97	5.53	3.09	0.35607	.	0.341401	0.27117	N	0.020845	T	0.30324	0.0761	N	0.22421	0.69	0.09310	N	1	B;B	0.26258	0.145;0.02	B;B	0.28465	0.09;0.005	T	0.16928	-1.0386	10	0.41790	T	0.15	-3.1303	12.9202	0.58228	0.0:0.0:0.4221:0.5779	.	297;374	P53609-2;P53609	.;PGTB1_HUMAN	R	374;297	ENSP00000404676:H374R;ENSP00000368935:H297R	ENSP00000368935:H297R	H	-	2	0	PGGT1B	114576011	0.426000	0.25506	0.005000	0.12908	0.946000	0.59487	0.486000	0.22340	0.374000	0.24650	0.477000	0.44152	CAT	.	.		0.423	PGGT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250855.2	NM_005023		C	114548112	T	C	114548112	3	2	113	1	0	0	0	0	1	0	0	0	11798	1464	51	2	16	2	PGGT1B	5	114548112	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1627957	114548112	66367148	128	18005										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118469314	118469314	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	attcagcaggggaaacaaaaAccttctggcctcacccgttc	8	13	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:118469314A>G	ENST00000311085.8	+	12	1775	c.1695A>G	c.(1693-1695)aaA>aaG	p.K565K	DMXL1_ENST00000539542.1_Silent_p.K565K	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	565										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GGAAACAAAAACCTTCTGGCC	0.378																																					p.K565K		Atlas-SNP	.											.	DMXL1	268	.	0			c.A1695G						.																																			SO:0001819	synonymous_variant	1657	exon12			ACAAAAACCTTCT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.1695A>G	chr5.hg19:g.118469314A>G		179.0	0.0		103.0	5.0	NM_005509		Silent	SNP	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.		0.378	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		G	118469314	A	G	118469314	2	3	113	1	0	0	0	0	0	0	0	1	4596	40	2	2		2	DMXL1	5	118469314	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3921202	118469314	62445946	129	18006										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130834162	130834162	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcttaagctgtcgatcttaaAccattccaatagtttgatcc	5	10	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:130834162A>G	ENST00000509018.1	-	12	1598	c.1393T>C	c.(1393-1395)Ttt>Ctt	p.F465L	RAPGEF6_ENST00000307984.5_Missense_Mutation_p.F465L|RAPGEF6_ENST00000512052.1_Missense_Mutation_p.F180L|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.F465L|RAPGEF6_ENST00000510071.1_Missense_Mutation_p.F465L|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.F465L|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.F465L|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.F515L	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	465	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TCGATCTTAAACCATTCCAAT	0.318																																					p.F465L	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.T1393C						.						78	83	82					5																	130834162		2203	4300	6503	SO:0001583	missense	51735	exon12			TCTTAAACCATTC	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.1393T>C	chr5.hg19:g.130834162A>G	ENSP00000421684:p.Phe465Leu	119.0	0.0		87.0	4.0	NM_016340	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	A	16.60	3.169127	0.57584	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000512052;ENST00000308008;ENST00000510071;ENST00000514667	T;T;T;T;T;T;T;T	0.58506	0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33	5.46	4.28	0.50868	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.75004	0.3791	M	0.77616	2.38	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.97110	0.997;1.0;0.993;0.992;0.999;0.995;0.999	T	0.77378	-0.2610	10	0.87932	D	0	.	12.5614	0.56283	0.8607:0.1393:0.0:0.0	.	465;465;465;180;515;465;465	A3KN82;B7ZML2;Q8TEU7-2;D6RE77;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;.;.;RPGF6_HUMAN	L	465;465;465;465;465;180;465;465;515	ENSP00000421684:F465L;ENSP00000309298:F465L;ENSP00000426081:F465L;ENSP00000296859:F465L;ENSP00000426910:F180L;ENSP00000311419:F465L;ENSP00000425389:F465L;ENSP00000426948:F515L	ENSP00000426948:F515L	F	-	1	0	RAPGEF6;FNIP1	130862061	1.000000	0.71417	1.000000	0.80357	0.132000	0.20833	8.957000	0.93082	0.864000	0.35578	-0.313000	0.08912	TTT	.	.		0.318	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		G	130834162	A	G	130834162	3	3	113	1	0	0	0	0	1	0	0	0	13063	43	2	2	3966	2	RAPGEF6	5	130834162	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	12364848	130834162	50081098	130	18007										
FAM53C	51307	hgsc.bcm.edu	37	chr5	137682560	137682560	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agaggaggaggagggggctgTgcggtggggtcggcaggcgc	25	6	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:137682560T>C	ENST00000239906.5	+	5	1519	c.1091T>C	c.(1090-1092)gTg>gCg	p.V364A	RP11-256P1.1_ENST00000504539.1_RNA|FAM53C_ENST00000434981.2_Missense_Mutation_p.V364A|FAM53C_ENST00000513056.1_3'UTR	NM_016605.2	NP_057689.1	Q9NYF3	FA53C_HUMAN	family with sequence similarity 53, member C	364										breast(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GAGGGGGCTGTGCGGTGGGGT	0.607																																					p.V364A		Atlas-SNP	.											FAM53C,colon,carcinoma,-1,1	FAM53C	35	.	0			c.T1091C						.						37	45	42					5																	137682560		2203	4300	6503	SO:0001583	missense	51307	exon5			GGGCTGTGCGGTG	AF251040	CCDS4204.1	5q31	2008-02-05	2004-11-24	2004-11-26	ENSG00000120709	ENSG00000120709			1336	protein-coding gene	gene with protein product		609372	"chromosome 5 open reading frame 6"	C5orf6		11087669, 11161817	Standard	NM_001135647		Approved		uc003lcv.3	Q9NYF3	OTTHUMG00000129201	ENST00000239906.5:c.1091T>C	chr5.hg19:g.137682560T>C	ENSP00000239906:p.Val364Ala	106.0	0.0		72.0	3.0	NM_001135647	B2RDJ5|D3DQB9	Missense_Mutation	SNP	ENST00000239906.5	hg19	CCDS4204.1	.	.	.	.	.	.	.	.	.	.	T	13.37	2.217430	0.39201	.	.	ENSG00000120709	ENST00000434981;ENST00000239906	T;T	0.42513	0.97;0.97	5.72	3.21	0.36854	.	0.692831	0.13629	N	0.373862	T	0.22666	0.0547	N	0.22421	0.69	0.22412	N	0.999122	B	0.15930	0.015	B	0.11329	0.006	T	0.09487	-1.0672	10	0.20046	T	0.44	-0.0209	2.4711	0.04564	0.2145:0.0797:0.128:0.5777	.	364	Q9NYF3	FA53C_HUMAN	A	364	ENSP00000403705:V364A;ENSP00000239906:V364A	ENSP00000239906:V364A	V	+	2	0	FAM53C	137710459	0.998000	0.40836	1.000000	0.80357	0.988000	0.76386	1.951000	0.40333	2.171000	0.68590	0.533000	0.62120	GTG	.	.		0.607	FAM53C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251278.2	NM_016605		C	137682560	T	C	137682560	3	2	113	1	0	0	0	0	1	0	0	0	5589	1696	59	2	1105	2	FAM53C	5	137682560	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	6848398	137682560	43232700	131	18008										
PCDHB7	56129	hgsc.bcm.edu	37	chr5	140552784	140552784	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttccgtgctgaactatgggTcagagacatcaatgatcacg	10	9	3	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:140552784T>C	ENST00000231137.3	+	1	542	c.368T>C	c.(367-369)gTc>gCc	p.V123A		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	123	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAACTATGGGTCAGAGACATC	0.463																																					p.V123A		Atlas-SNP	.											PCDHB7,NS,carcinoma,0,1	PCDHB7	231	.	0			c.T368C						.						65	69	68					5																	140552784		2203	4300	6503	SO:0001583	missense	56129	exon1			TATGGGTCAGAGA	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.368T>C	chr5.hg19:g.140552784T>C	ENSP00000231137:p.Val123Ala	91.0	0.0		48.0	3.0	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	hg19	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	T	15.31	2.796977	0.50208	.	.	ENSG00000113212	ENST00000231137	T	0.63255	-0.03	4.61	4.61	0.57282	Cadherin conserved site (1);	.	.	.	.	T	0.78142	0.4237	H	0.97186	3.955	0.09310	N	1	D	0.54964	0.969	P	0.45881	0.496	T	0.76753	-0.2843	9	0.87932	D	0	.	13.9717	0.64245	0.0:0.0:0.0:1.0	.	123	Q9Y5E2	PCDB7_HUMAN	A	123	ENSP00000231137:V123A	ENSP00000231137:V123A	V	+	2	0	PCDHB7	140532968	0.982000	0.34865	0.864000	0.33941	0.224000	0.24922	7.958000	0.87877	1.823000	0.53134	0.533000	0.62120	GTC	.	.		0.463	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		C	140552784	T	C	140552784	3	2	113	1	0	0	0	0	1	0	0	0	11556	1667	58	2	370	2	PCDHB7	5	140552784	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2870224	140552784	40362476	132	18009										
PCDHGB6	56100	hgsc.bcm.edu	37	chr5	140790042	140790042	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttataatctgtgcattgcacAtacgggtacaaaagagttta	8	6	1	1	rs185995562		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:140790042A>G	ENST00000520790.1	+	1	2273	c.2273A>G	c.(2272-2274)cAt>cGt	p.H758R	PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA10_ENST00000398610.2_5'Flank|PCDHGA1_ENST00000517417.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	758					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCATTGCACATACGGGTACA	0.453																																					p.H758R		Atlas-SNP	.											.	PCDHGB6	120	.	0			c.A2273G						.						120	118	118					5																	140790042		1926	4147	6073	SO:0001583	missense	56100	exon1			TTGCACATACGGG	AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"Cadherins / Protocadherins : Clustered"	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.2273A>G	chr5.hg19:g.140790042A>G	ENSP00000428603:p.His758Arg	194.0	0.0		125.0	5.0	NM_032100	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	hg19	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	a	0.244	-1.011492	0.02095	.	.	ENSG00000253305	ENST00000520790	T	0.45276	0.9	5.39	5.39	0.77823	.	.	.	.	.	T	0.30634	0.0771	L	0.28274	0.84	0.09310	N	0.999999	B;B	0.11235	0.002;0.004	B;B	0.10450	0.002;0.005	T	0.13629	-1.0502	9	0.11485	T	0.65	.	14.3903	0.66973	1.0:0.0:0.0:0.0	.	758;758	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	R	758	ENSP00000428603:H758R	ENSP00000428603:H758R	H	+	2	0	PCDHGB6	140770226	0.010000	0.17322	0.028000	0.17463	0.016000	0.09150	1.872000	0.39549	2.038000	0.60285	0.460000	0.39030	CAT	.	A|1.000;T|0.000		0.453	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		G	140790042	A	G	140790042	3	3	113	1	0	0	0	0	1	0	0	0	11576	217	8	2	2275	2	PCDHGB6	5	140790042	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	237258	140790042	40125218	133	18010										
RBM27	54439	hgsc.bcm.edu	37	chr5	145613206	145613206	+	Silent	SNP	C	C	T													0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggcccgggcccaggtccaggCccaggcccgggcccaggtcc							TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:145613206C>T	ENST00000265271.5	+	7	1210	c.1044C>T	c.(1042-1044)ggC>ggT	p.G348G	RBM27_ENST00000506502.1_Silent_p.G348G	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	348	Pro-rich.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			caggtccaggcccaggcccgg	0.632																																					p.G348G		Atlas-SNP	.											.	RBM27	119	.	0			c.C1044T						.						41	43	42					5																	145613206		1568	3582	5150	SO:0001819	synonymous_variant	54439	exon7			TCCAGGCCCAGGC	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1044C>T	chr5.hg19:g.145613206C>T		156.0	0.0		68.0	17.0	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.		0.632	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		T	145613206	C	T	145613206	2	4	113	1	0	0	0	0	0	0	0	1	13142	726	26	3		3	RBM27	5	145613206	Silent	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	4823164	145613206	35302054	134	18011	81	2								
RBM27	54439	hgsc.bcm.edu	37	chr5	145613209	145613209	+	Silent	SNP	A	A	T													0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccgggcccaggtccaggcccAggcccgggcccaggtccagg							TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:145613209A>T	ENST00000265271.5	+	7	1213	c.1047A>T	c.(1045-1047)ccA>ccT	p.P349P	RBM27_ENST00000506502.1_Silent_p.P349P	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	349	Pro-rich.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			gtccaggcccaggcccgggcc	0.632																																					p.P349P		Atlas-SNP	.											RBM27,colon,carcinoma,0,1	RBM27	119	.	0			c.A1047T						.						38	40	40					5																	145613209		1568	3582	5150	SO:0001819	synonymous_variant	54439	exon7			AGGCCCAGGCCCG	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1047A>T	chr5.hg19:g.145613209A>T		162.0	0.0		71.0	16.0	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.		0.632	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		T	145613209	A	T	145613209	2	4	113	1	0	0	0	0	0	0	0	1	13142	175	7	4		4	RBM27	5	145613209	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3	145613209	35302051	135	18012	81	2								
HRH2	3274	hgsc.bcm.edu	37	chr5	175111079	175111079	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tggctgggctatgccaactcAgccctgaaccccatcctgta	9	15	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:175111079A>G	ENST00000231683.2	+	1	2616	c.843A>G	c.(841-843)tcA>tcG	p.S281S	HRH2_ENST00000377291.2_Silent_p.S281S	NM_022304.2	NP_071640.1	P25021	HRH2_HUMAN	histamine receptor H2	281					digestive tract development (GO:0048565)|epithelial cell morphogenesis (GO:0003382)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|gastrin-induced gastric acid secretion (GO:0001698)|gland development (GO:0048732)|histamine-induced gastric acid secretion (GO:0001697)|immune response (GO:0006955)|memory (GO:0007613)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(10)|ovary(1)	22	all_cancers(89;0.00805)|Renal(175;0.000269)|Lung NSC(126;0.00419)|all_lung(126;0.00711)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Colorectal(1;0.0154)|COAD - Colon adenocarcinoma(1;0.149)	Amitriptyline(DB00321)|Asenapine(DB06216)|Betazole(DB00272)|Cimetidine(DB00501)|Doxepin(DB01142)|Epinastine(DB00751)|Famotidine(DB00927)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Methantheline(DB00940)|Nizatidine(DB00585)|Olanzapine(DB00334)|Ranitidine(DB00863)|Roxatidine acetate(DB08806)|Tolazoline(DB00797)	ATGCCAACTCAGCCCTGAACC	0.562																																					p.S281S		Atlas-SNP	.											.	HRH2	108	.	0			c.A843G						.						124	96	106					5																	175111079		2203	4300	6503	SO:0001819	synonymous_variant	3274	exon2			CAACTCAGCCCTG		CCDS4395.1, CCDS47344.1	5q35	2012-08-08			ENSG00000113749	ENSG00000113749		"GPCR / Class A : Histamine receptors"	5183	protein-coding gene	gene with protein product		142703				1714721	Standard	NM_022304		Approved		uc003mdc.4	P25021	OTTHUMG00000130660	ENST00000231683.2:c.843A>G	chr5.hg19:g.175111079A>G		144.0	0.0		83.0	4.0	NM_001131055	B5BUP7|Q14464|Q7Z5R9	Silent	SNP	ENST00000231683.2	hg19	CCDS4395.1																																																																																			.	.		0.562	HRH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253151.1			G	175111079	A	G	175111079	2	3	113	1	0	0	0	0	0	0	0	1	7365	175	7	2		2	HRH2	5	175111079	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	29497870	175111079	5804181	136	18013										
RMND5B	64777	hgsc.bcm.edu	37	chr5	177570698	177570698	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gaatcgaatcctggaagcccTgcacgaacaagacctgggtc	11	12	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:177570698T>C	ENST00000515098.1	+	7	848	c.497T>C	c.(496-498)cTg>cCg	p.L166P	RMND5B_ENST00000542098.1_Missense_Mutation_p.L153P|RMND5B_ENST00000313386.4_Missense_Mutation_p.L166P			Q96G75	RMD5B_HUMAN	required for meiotic nuclear division 5 homolog B (S. cerevisiae)	166	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.									endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	17	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTGGAAGCCCTGCACGAACAA	0.542																																					p.L166P		Atlas-SNP	.											.	RMND5B	37	.	0			c.T497C						.						106	105	106					5																	177570698		2203	4300	6503	SO:0001583	missense	64777	exon6			AAGCCCTGCACGA	BC009911	CCDS4431.1, CCDS75382.1	5q35.3	2012-07-20			ENSG00000145916	ENSG00000145916			26181	protein-coding gene	gene with protein product	"GID complex subunit 2 homolog B"					12975309	Standard	NM_022762		Approved	FLJ22318, GID2, GID2B	uc003mim.3	Q96G75	OTTHUMG00000130897	ENST00000515098.1:c.497T>C	chr5.hg19:g.177570698T>C	ENSP00000420875:p.Leu166Pro	157.0	0.0		107.0	5.0	NM_022762	Q1HE27|Q6UVY7|Q9H6F6	Missense_Mutation	SNP	ENST00000515098.1	hg19	CCDS4431.1	.	.	.	.	.	.	.	.	.	.	T	18.66	3.671594	0.67928	.	.	ENSG00000145916	ENST00000313386;ENST00000515098;ENST00000542098	.	.	.	4.15	4.15	0.48705	CTLH, C-terminal LisH motif (2);	0.185437	0.35936	N	0.002894	T	0.81489	0.4833	M	0.92317	3.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.84479	0.0604	9	0.87932	D	0	-13.9828	9.5119	0.39082	0.0:0.0:0.0:1.0	.	153;153;166	B3KSG5;F5H6G4;Q96G75	.;.;RMD5B_HUMAN	P	166;166;153	.	ENSP00000320623:L166P	L	+	2	0	RMND5B	177503304	1.000000	0.71417	1.000000	0.80357	0.664000	0.39144	6.993000	0.76245	1.749000	0.51849	0.379000	0.24179	CTG	.	.		0.542	RMND5B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373542.1	NM_022762		C	177570698	T	C	177570698	3	2	113	1	0	0	0	0	1	0	0	0	13413	1580	55	2	511	2	RMND5B	5	177570698	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2459619	177570698	3344562	137	18014										
CANX	821	hgsc.bcm.edu	37	chr5	179155615	179155615	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gatgaaattttgaacagatcAccaagaaacagaaagccacg	8	8	1	5			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr5:179155615A>G	ENST00000247461.4	+	15	1949	c.1749A>G	c.(1747-1749)tcA>tcG	p.S583S	CANX_ENST00000504734.1_Silent_p.S583S|CANX_ENST00000415618.2_Silent_p.S618S|CANX_ENST00000452673.2_Silent_p.S583S|CANX_ENST00000512607.2_Silent_p.S475S	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin	583	Sufficient to mediate interaction with SGIP1. {ECO:0000250}.				aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	TGAACAGATCACCAAGAAACA	0.363																																					p.S583S		Atlas-SNP	.											.	CANX	47	.	0			c.A1749G						.						70	63	65					5																	179155615		2203	4300	6503	SO:0001819	synonymous_variant	821	exon15			CAGATCACCAAGA	L18887	CCDS4447.1	5q35	2008-07-18			ENSG00000127022	ENSG00000127022			1473	protein-coding gene	gene with protein product	"major histocompatibility complex class I antigen-binding protein p88"	114217				1326756, 8136357	Standard	NM_001746		Approved	CNX, IP90, P90	uc003mkl.3	P27824	OTTHUMG00000130910	ENST00000247461.4:c.1749A>G	chr5.hg19:g.179155615A>G		226.0	0.0		92.0	4.0	NM_001746	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Silent	SNP	ENST00000247461.4	hg19	CCDS4447.1																																																																																			.	.		0.363	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649		G	179155615	A	G	179155615	2	3	113	1	0	0	0	0	0	0	0	1	2620	146	6	2		2	CANX	5	179155615	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1584917	179155615	1759645	138	18015										
PAK1IP1	55003	hgsc.bcm.edu	37	chr6	10702604	10702604	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	attttggtttttccataggtAcaataacttgcctgaaattc	6	7	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:10702604A>G	ENST00000379568.3	+	3	541	c.250A>G	c.(250-252)Aca>Gca	p.T84A		NM_017906.2	NP_060376.2	Q9NWT1	PK1IP_HUMAN	PAK1 interacting protein 1	84					cell proliferation (GO:0008283)|negative regulation of signal transduction (GO:0009968)|palate development (GO:0060021)	nucleus (GO:0005634)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.117)				TTCCATAGGTACAATAACTTG	0.358																																					p.T84A		Atlas-SNP	.											.	PAK1IP1	30	.	0			c.A250G						.						58	57	57					6																	10702604		2203	4300	6503	SO:0001583	missense	55003	exon3			ATAGGTACAATAA	AF283303	CCDS34339.1	6p24.1	2013-05-21			ENSG00000111845	ENSG00000111845		"WD repeat domain containing"	20882	protein-coding gene	gene with protein product		607811				11371639	Standard	XM_005249204		Approved	FLJ20624, hPIP1, PIP1, bA421M1.5, MAK11, WDR84	uc003mzg.3	Q9NWT1	OTTHUMG00000014245	ENST00000379568.3:c.250A>G	chr6.hg19:g.10702604A>G	ENSP00000368887:p.Thr84Ala	97.0	0.0		76.0	17.0	NM_017906	Q5T4J2|Q96QJ8|Q96T87	Missense_Mutation	SNP	ENST00000379568.3	hg19	CCDS34339.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.246275	0.80024	.	.	ENSG00000111845	ENST00000379568	T	0.40756	1.02	5.91	5.91	0.95273	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.044405	0.85682	D	0.000000	T	0.23330	0.0564	L	0.31120	0.905	0.58432	D	0.999999	B	0.33171	0.4	B	0.41946	0.371	T	0.11867	-1.0570	10	0.22706	T	0.39	-0.2316	12.7401	0.57246	1.0:0.0:0.0:0.0	.	84	Q9NWT1	PK1IP_HUMAN	A	84	ENSP00000368887:T84A	ENSP00000368887:T84A	T	+	1	0	PAK1IP1	10810590	1.000000	0.71417	1.000000	0.80357	0.598000	0.36846	9.072000	0.93986	2.254000	0.74563	0.533000	0.62120	ACA	.	.		0.358	PAK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039835.1	NM_017906		G	10702604	A	G	10702604	3	3	113	1	0	0	0	0	1	0	0	0	11409	391	14	2	260	2	PAK1IP1	6	10702604	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10		10702604	160412463	139	18016										
CDKAL1	54901	hgsc.bcm.edu	37	chr6	21065331	21065331	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tctgtggttttcctggagaaAcagatcaggattttcaagaa	10	6	3	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:21065331A>G	ENST00000378610.1	+	10	1118	c.1108A>G	c.(1108-1110)Aca>Gca	p.T370A	CDKAL1_ENST00000378624.4_Missense_Mutation_p.T300A|CDKAL1_ENST00000274695.4_Missense_Mutation_p.T370A			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	370					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			TCCTGGAGAAACAGATCAGGA	0.353																																					p.T370A		Atlas-SNP	.											.	CDKAL1	55	.	0			c.A1108G						.						83	83	83					6																	21065331		2203	4300	6503	SO:0001583	missense	54901	exon12			GGAGAAACAGATC	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.1108A>G	chr6.hg19:g.21065331A>G	ENSP00000367873:p.Thr370Ala	146.0	0.0		125.0	5.0	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Missense_Mutation	SNP	ENST00000378610.1	hg19	CCDS4546.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.556035	0.86231	.	.	ENSG00000145996	ENST00000274695;ENST00000378624;ENST00000378610	T;T;T	0.36878	1.23;1.23;1.23	5.76	5.76	0.90799	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);Radical SAM (1);	0.000000	0.85682	D	0.000000	T	0.65565	0.2703	H	0.95504	3.68	0.80722	D	1	D;D	0.64830	0.994;0.99	D;D	0.66497	0.944;0.92	T	0.77520	-0.2557	10	0.87932	D	0	.	16.3634	0.83296	1.0:0.0:0.0:0.0	.	300;370	Q5VV42-2;Q5VV42	.;CDKAL_HUMAN	A	370;300;370	ENSP00000274695:T370A;ENSP00000367889:T300A;ENSP00000367873:T370A	ENSP00000274695:T370A	T	+	1	0	CDKAL1	21173310	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.910000	0.92685	2.324000	0.78689	0.533000	0.62120	ACA	.	.		0.353	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774		G	21065331	A	G	21065331	3	3	113	1	0	0	0	0	1	0	0	0	3154	43	2	2	1146	2	CDKAL1	6	21065331	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	10362727	21065331	150049736	140	18017										
GNL1	2794	hgsc.bcm.edu	37	chr6	30523924	30523924	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgacctctcttccgctcccgTttgtcctgcaactgcttctt	6	16	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:30523924T>C	ENST00000376621.3	-	1	1027	c.57A>G	c.(55-57)aaA>aaG	p.K19K	PRR3_ENST00000376557.3_5'Flank|PRR3_ENST00000376560.3_5'Flank	NM_005275.3	NP_005266.2	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	19					cellular response to DNA damage stimulus (GO:0006974)|GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)|signal transduction (GO:0007165)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			cervix(2)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						TCCGCTCCCGTTTGTCCTGCA	0.677																																					p.K19K		Atlas-SNP	.											.	GNL1	47	.	0			c.A57G						.						89	87	88					6																	30523924		1511	2709	4220	SO:0001819	synonymous_variant	2794	exon1			CTCCCGTTTGTCC		CCDS4680.1	6p21.3	2010-02-17			ENSG00000204590	ENSG00000204590			4413	protein-coding gene	gene with protein product		143024				8180467	Standard	NM_005275		Approved	HSR1	uc003nqh.3	P36915	OTTHUMG00000031137	ENST00000376621.3:c.57A>G	chr6.hg19:g.30523924T>C		111.0	0.0		89.0	4.0	NM_005275	B0S838|Q96CT5	Silent	SNP	ENST00000376621.3	hg19	CCDS4680.1																																																																																			.	.		0.677	GNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076241.2			C	30523924	T	C	30523924	2	2	113	1	0	0	0	0	0	0	0	1	6543	1722	60	2		2	GNL1	6	30523924	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	9458593	30523924	140591143	141	18018										
MDC1	9656	hgsc.bcm.edu	37	chr6	30680046	30680046	+	Frame_Shift_Del	DEL	C	C	-													0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccacaagcagctttgctggtCccccaactgctttcacatct							TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:30680046delC	ENST00000376406.3	-	5	2320	c.1673delG	c.(1672-1674)ggafs	p.G558fs	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Frame_Shift_Del_p.G558fs|MDC1_ENST00000494654.1_5'Flank	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	558	Required for nuclear localization (NLS1).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						CTTTGCTGGTCCCCCAACTGC	0.522								Other conserved DNA damage response genes																													p.G558fs		Atlas-Indel,Pindel	.											.	MDC1	218	.	0			c.1674delA						.						73	69	71					6																	30680046		1509	2709	4218	SO:0001589	frameshift_variant	9656	exon5			.	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.1673delG	chr6.hg19:g.30680046delC	ENSP00000365588:p.Gly558fs	245.0	0.0		214.0	41.0	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Frame_Shift_Del	DEL	ENST00000376406.3	hg19	CCDS34384.1																																																																																			.	.		0.522	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		-	30680046	C	-	30680046	7	5	113	1	0	1	0	1	0	0	0	0	9412	855	30	0	4640	0	MDC1	6	30680046	Frame_Shift_Del	DEL	C	TCGA-DD-A39Z-01A-11D-A20W-10	156122	30680046	140435021	142	18019										
FLOT1	10211	hgsc.bcm.edu	37	chr6	30707949	30707949	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tctgacctgaagctgataggCcaggtcagcctgtgctcggc	13	12	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:30707949C>A	ENST00000376389.3	-	8	929	c.709G>T	c.(709-711)Gcc>Tcc	p.A237S	FLOT1_ENST00000470643.1_5'UTR|XXbac-BPG252P9.10_ENST00000607333.1_RNA|FLOT1_ENST00000456573.2_Missense_Mutation_p.A189S	NM_005803.2	NP_005794.1	P41440	S19A1_HUMAN	flotillin 1	0					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	13					Methotrexate(DB00563)|Pralatrexate(DB06813)	AGCTGATAGGCCAGGTCAGCC	0.562																																					p.A237S		Atlas-SNP	.											.	FLOT1	28	.	0			c.G709T						.						94	71	79					6																	30707949		1511	2709	4220	SO:0001583	missense	10211	exon8			GATAGGCCAGGTC	AF089750	CCDS4688.1	6p21.3	2010-02-17			ENSG00000137312	ENSG00000137312			3757	protein-coding gene	gene with protein product		606998					Standard	XM_005248780		Approved		uc003nrm.3	O75955	OTTHUMG00000031151	ENST00000376389.3:c.709G>T	chr6.hg19:g.30707949C>A	ENSP00000365569:p.Ala237Ser	93.0	0.0		91.0	24.0	NM_005803	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000376389.3	hg19	CCDS4688.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.249218	0.59103	.	.	ENSG00000137312	ENST00000376389;ENST00000456573;ENST00000413165;ENST00000438162;ENST00000418160	D;T;D	0.96992	-3.79;1.3;-4.2	4.74	3.87	0.44632	.	0.058090	0.64402	D	0.000002	D	0.92586	0.7645	M	0.67625	2.065	0.51767	D	0.999934	B;B	0.32324	0.364;0.104	B;B	0.34489	0.184;0.117	D	0.92269	0.5823	10	0.56958	D	0.05	-16.5585	10.9434	0.47287	0.0:0.8114:0.1886:0.0	.	189;237	B4DVY7;O75955	.;FLOT1_HUMAN	S	237;189;174;237;142	ENSP00000365569:A237S;ENSP00000394375:A189S;ENSP00000400615:A237S	ENSP00000365569:A237S	A	-	1	0	FLOT1	30815928	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.160000	0.77495	1.212000	0.43366	0.609000	0.83330	GCC	.	.		0.562	FLOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076276.2			A	30707949	C	A	30707949	3	1	113	1	0	0	0	0	1	0	0	0	5944	739	26	3	598	3	FLOT1	6	30707949	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	27903	30707949	140407118	143	18020										
C6orf27	80737	hgsc.bcm.edu	37	chr6	31740763	31740763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaggcaccaggacatagtggAcaggctccatggggctgcct	14	11	0	0	rs377401343|rs149806946	byFrequency	TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:31740763A>G	ENST00000375688.4	-	7	1255	c.1055T>C	c.(1054-1056)gTc>gCc	p.V352A	VWA7_ENST00000447450.1_Missense_Mutation_p.V352A|VWA7_ENST00000375686.3_Missense_Mutation_p.V352A|VWA7_ENST00000467576.1_5'UTR			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	352	VWFA.					extracellular region (GO:0005576)											GACATAGTGGACAGGCTCCAT	0.577																																					p.V352A		Atlas-SNP	.											.,1	.	.	.	0			c.T1055C						.						46	41	43					6																	31740763		1510	2707	4217	SO:0001583	missense	80737	exon7			TAGTGGACAGGCT		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"chromosome 6 open reading frame 27"	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.1055T>C	chr6.hg19:g.31740763A>G	ENSP00000364840:p.Val352Ala	22.0	0.0		12.0	5.0	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	hg19	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	A	0	-2.652399	0.00109	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	D;D;D	0.97731	-4.51;-4.51;-4.51	5.74	-11.5	0.00074	von Willebrand factor, type A (1);	3.072470	0.00866	N	0.001976	T	0.81659	0.4869	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.71130	-0.4682	10	0.02654	T	1	0.7122	9.8299	0.40934	0.0705:0.2652:0.5324:0.1319	.	352	Q9Y334	G7C_HUMAN	A	352	ENSP00000364840:V352A;ENSP00000364838:V352A;ENSP00000390554:V352A	ENSP00000364838:V352A	V	-	2	0	C6orf27	31848742	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-4.526000	0.00220	-4.969000	0.00025	-0.385000	0.06624	GTC	.	.		0.577	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		G	31740763	A	G	31740763	3	3	113	1	0	0	0	0	1	0	0	0	2364	275	10	2	1663	2	C6orf27	6	31740763	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1032814	31740763	139374304	144	18021										
UHRF1BP1	54887	hgsc.bcm.edu	37	chr6	34831811	34831811	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caagacagatgagggggtggCagccccagtgagtggaggtg	19	7	0	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:34831811C>T	ENST00000192788.5	+	15	3419	c.3248C>T	c.(3247-3249)gCa>gTa	p.A1083V	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.A1083V	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	1083							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						GAGGGGGTGGCAGCCCCAGTG	0.473																																					p.A1083V		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C3248T						.						73	80	78					6																	34831811		1977	4130	6107	SO:0001583	missense	54887	exon15			GGGTGGCAGCCCC	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 107"	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.3248C>T	chr6.hg19:g.34831811C>T	ENSP00000192788:p.Ala1083Val	99.0	0.0		61.0	17.0	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	hg19	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	C	9.151	1.016206	0.19355	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.17528	2.27;2.27	6.04	0.942	0.19525	.	1.000120	0.08080	N	1.000000	T	0.01730	0.0055	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48019	-0.9071	10	0.14252	T	0.57	-1.4049	6.3567	0.21404	0.0:0.507:0.1343:0.3586	.	1083	Q6BDS2	URFB1_HUMAN	V	1083	ENSP00000192788:A1083V;ENSP00000400628:A1083V	ENSP00000192788:A1083V	A	+	2	0	UHRF1BP1	34939789	0.000000	0.05858	0.066000	0.19879	0.615000	0.37417	0.611000	0.24268	0.439000	0.26476	0.561000	0.74099	GCA	.	.		0.473	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		T	34831811	C	T	34831811	3	4	113	1	0	0	0	0	1	0	0	0	16983	710	25	3	3306	3	UHRF1BP1	6	34831811	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	3091048	34831811	136283256	145	18022										
MRPS10	55173	hgsc.bcm.edu	37	chr6	42185570	42185570	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cgccggcacacagcaccgaaCgctgtccgcgccgccatctt	10	19	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:42185570C>A	ENST00000053468.3	-	1	33	c.18G>T	c.(16-18)gcG>gcT	p.A6A		NM_018141.3	NP_060611.2	P82664	RT10_HUMAN	mitochondrial ribosomal protein S10	6						mitochondrion (GO:0005739)|ribosome (GO:0005840)				endometrium(1)|lung(1)	2	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00528)			CAGCACCGAACGCTGTCCGCG	0.597																																					p.A6A		Atlas-SNP	.											.	MRPS10	9	.	0			c.G18T						.						24	28	26					6																	42185570		2203	4300	6503	SO:0001819	synonymous_variant	55173	exon1			ACCGAACGCTGTC		CCDS4866.1	6p21.1	2012-09-13			ENSG00000048544	ENSG00000048544		"Mitochondrial ribosomal proteins / small subunits"	14502	protein-coding gene	gene with protein product		611976				11279123	Standard	NM_018141		Approved	FLJ10567	uc003osa.4	P82664	OTTHUMG00000014694	ENST00000053468.3:c.18G>T	chr6.hg19:g.42185570C>A		85.0	0.0		59.0	16.0	NM_018141	B2RE89|Q9H3E5|Q9NVR3	Silent	SNP	ENST00000053468.3	hg19	CCDS4866.1																																																																																			.	.		0.597	MRPS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040547.1			A	42185570	C	A	42185570	2	1	113	1	0	0	0	0	0	0	0	1	9830	523	19	1		1	MRPS10	6	42185570	Silent	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	7353759	42185570	128929497	146	18023										
CUL9	23113	hgsc.bcm.edu	37	chr6	43183025	43183025	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgccggggtcaggcagatgTccctttctgtggcagccaga	14	12	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:43183025T>C	ENST00000252050.4	+	30	5981	c.5897T>C	c.(5896-5898)gTc>gCc	p.V1966A	CUL9_ENST00000354495.3_Missense_Mutation_p.V1856A|CUL9_ENST00000372647.2_Missense_Mutation_p.V1938A|RP3-330M21.5_ENST00000500590.1_RNA	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1966					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CAGGCAGATGTCCCTTTCTGT	0.627																																					p.V1966A		Atlas-SNP	.											.	CUL9	248	.	0			c.T5897C						.						56	55	55					6																	43183025		2203	4300	6503	SO:0001583	missense	23113	exon30			CAGATGTCCCTTT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.5897T>C	chr6.hg19:g.43183025T>C	ENSP00000252050:p.Val1966Ala	80.0	0.0		66.0	4.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	T	17.33	3.361645	0.61403	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.74737	-0.87;-0.87;-0.75	5.65	5.65	0.86999	.	0.704021	0.13424	N	0.388888	T	0.56601	0.1996	L	0.44542	1.39	0.38148	D	0.938657	P;B;B	0.36837	0.571;0.034;0.034	B;B;B	0.33392	0.163;0.025;0.025	T	0.64076	-0.6492	10	0.59425	D	0.04	-6.9265	14.4426	0.67327	0.0:0.0:0.0:1.0	.	1856;1938;1966	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	A	1966;1856;1938	ENSP00000252050:V1966A;ENSP00000346490:V1856A;ENSP00000361730:V1938A	ENSP00000252050:V1966A	V	+	2	0	CUL9	43291003	1.000000	0.71417	0.942000	0.38095	0.723000	0.41478	5.684000	0.68197	2.140000	0.66376	0.459000	0.35465	GTC	.	.		0.627	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		C	43183025	T	C	43183025	3	2	113	1	0	0	0	0	1	0	0	0	4063	1667	58	2	6011	2	CUL9	6	43183025	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	997455	43183025	127932042	147	18024										
C6orf223	221416	hgsc.bcm.edu	37	chr6	43970788	43970788	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tacaggattgcaggggcacgGctaatgcgctctaattaccc	11	11	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:43970788G>T	ENST00000336600.5	+	4	674	c.654G>T	c.(652-654)cgG>cgT	p.R218R	RP5-1120P11.1_ENST00000607590.1_RNA|RP5-1120P11.1_ENST00000422059.1_RNA|C6orf223_ENST00000439969.2_3'UTR|C6orf223_ENST00000448947.2_3'UTR|C6orf223_ENST00000442114.2_Silent_p.R198R	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	218										central_nervous_system(1)|lung(2)|pancreas(1)|prostate(1)|urinary_tract(1)	6	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)			CAGGGGCACGGCTAATGCGCT	0.642																																					p.R218R		Atlas-SNP	.											.	C6orf223	14	.	0			c.G654T						.						27	34	31					6																	43970788		2202	4298	6500	SO:0001819	synonymous_variant	221416	exon4			GGCACGGCTAATG	BC032706	CCDS34459.1, CCDS55016.1	6p21.1	2012-09-05			ENSG00000181577	ENSG00000181577			28692	protein-coding gene	gene with protein product						12477932	Standard	NM_153246		Approved	MGC45491	uc003own.3	Q8N319	OTTHUMG00000014753	ENST00000336600.5:c.654G>T	chr6.hg19:g.43970788G>T		145.0	0.0		135.0	45.0	NM_153246	E9PB59|Q8N575	Silent	SNP	ENST00000336600.5	hg19	CCDS34459.1																																																																																			.	.		0.642	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246		T	43970788	G	T	43970788	2	4	113	1	0	0	0	0	0	0	0	1	2359	1190	42	3		3	C6orf223	6	43970788	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	787763	43970788	127144279	148	18025										
CAPN11	11131	hgsc.bcm.edu	37	chr6	44150883	44150883	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctgaacaacaaggtaatgcAggtcctggtggccaggtatg	14	8	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:44150883A>G	ENST00000398776.1	+	21	2083	c.2045A>G	c.(2044-2046)cAg>cGg	p.Q682R	CAPN11_ENST00000542245.1_Missense_Mutation_p.Q682R	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	682	Domain IV.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AAGGTAATGCAGGTCCTGGTG	0.527																																					p.Q682R		Atlas-SNP	.											.	CAPN11	66	.	0			c.A2045G						.						143	137	139					6																	44150883		2004	4185	6189	SO:0001583	missense	11131	exon21			TAATGCAGGTCCT	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.2045A>G	chr6.hg19:g.44150883A>G	ENSP00000381758:p.Gln682Arg	99.0	0.0		77.0	4.0	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	hg19	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.129688	0.56721	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	T;T	0.30981	1.51;1.51	5.38	4.18	0.49190	EF-hand-like domain (1);	0.175587	0.27797	N	0.017817	T	0.43344	0.1243	M	0.80422	2.495	0.25852	N	0.98393	D	0.61080	0.989	D	0.70227	0.968	T	0.25152	-1.0140	10	0.87932	D	0	.	10.9092	0.47099	0.9248:0.0:0.0751:0.0	.	682	Q9UMQ6	CAN11_HUMAN	R	682	ENSP00000381758:Q682R;ENSP00000441078:Q682R	ENSP00000381758:Q682R	Q	+	2	0	CAPN11	44258861	1.000000	0.71417	0.306000	0.25113	0.141000	0.21300	5.788000	0.69020	2.255000	0.74692	0.523000	0.50628	CAG	.	.		0.527	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			G	44150883	A	G	44150883	3	3	113	1	0	0	0	0	1	0	0	0	2626	188	7	2	2127	2	CAPN11	6	44150883	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	180095	44150883	126964184	149	18026										
PHIP	55023	hgsc.bcm.edu	37	chr6	79692705	79692705	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttaatctgtttttgcttctgTttttcagattcttcttcttc	4	8	6	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:79692705T>C	ENST00000275034.4	-	23	2834	c.2667A>G	c.(2665-2667)aaA>aaG	p.K889K	PHIP_ENST00000479165.1_5'Flank	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	889	Lys-rich.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		tttgcttctgtttttcagatt	0.333																																					p.K889K		Atlas-SNP	.											.	PHIP	177	.	0			c.A2667G						.																																			SO:0001819	synonymous_variant	55023	exon23			CTTCTGTTTTTCA	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2667A>G	chr6.hg19:g.79692705T>C		123.0	0.0		50.0	4.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	hg19	CCDS4987.1																																																																																			.	.		0.333	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			C	79692705	T	C	79692705	2	2	113	1	0	0	0	0	0	0	0	1	11851	1722	60	2		2	PHIP	6	79692705	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	35541822	79692705	91422362	150	18027										
RNGTT	8732	hgsc.bcm.edu	37	chr6	89322527	89322527	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttttcgcttctgtccttgagAagctgcagtacatctgtcga	9	10	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:89322527A>G	ENST00000369485.4	-	16	1891	c.1705T>C	c.(1705-1707)Tct>Cct	p.S569P	RNGTT_ENST00000265607.6_Missense_Mutation_p.S546P|RNGTT_ENST00000538899.1_Missense_Mutation_p.S486P	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	569	GTase.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA processing (GO:0006396)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|mRNA guanylyltransferase activity (GO:0004484)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA guanylyltransferase activity (GO:0008192)|triphosphatase activity (GO:0050355)			endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	21		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		TGTCCTTGAGAAGCTGCAGTA	0.512																																					p.S569P		Atlas-SNP	.											.	RNGTT	52	.	0			c.T1705C						.						231	176	194					6																	89322527		2203	4300	6503	SO:0001583	missense	8732	exon16			CTTGAGAAGCTGC	AF025654	CCDS5017.1	6q16	2011-06-09			ENSG00000111880	ENSG00000111880	2.7.7.50	"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	10073	protein-coding gene	gene with protein product		603512				9828141, 9512541	Standard	NM_001286428		Approved	HCE, HCE1, hCAP	uc003pmr.2	O60942	OTTHUMG00000015190	ENST00000369485.4:c.1705T>C	chr6.hg19:g.89322527A>G	ENSP00000358497:p.Ser569Pro	208.0	0.0		72.0	4.0	NM_003800	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	Missense_Mutation	SNP	ENST00000369485.4	hg19	CCDS5017.1	.	.	.	.	.	.	.	.	.	.	A	2.769	-0.256124	0.05829	.	.	ENSG00000111880	ENST00000369485;ENST00000265607;ENST00000538899;ENST00000536746	T;T;T	0.22945	1.93;1.93;1.93	5.84	3.35	0.38373	Nucleic acid-binding, OB-fold-like (1);	0.730694	0.14759	N	0.300081	T	0.04634	0.0126	N	0.19112	0.55	0.21652	N	0.9996	B;P;B	0.34977	0.0;0.478;0.347	B;B;B	0.31686	0.001;0.134;0.047	T	0.35101	-0.9802	10	0.25106	T	0.35	-2.9691	6.8469	0.23992	0.5041:0.1335:0.0:0.3624	.	486;546;569	B4DSJ8;O60942-2;O60942	.;.;MCE1_HUMAN	P	569;546;486;540	ENSP00000358497:S569P;ENSP00000265607:S546P;ENSP00000442609:S486P	ENSP00000265607:S546P	S	-	1	0	RNGTT	89379246	0.852000	0.29690	0.207000	0.23584	0.474000	0.32979	1.290000	0.33319	0.504000	0.28082	0.529000	0.55759	TCT	.	.		0.512	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041469.1			G	89322527	A	G	89322527	3	3	113	1	0	0	0	0	1	0	0	0	13518	246	9	2	92	2	RNGTT	6	89322527	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	9629822	89322527	81792540	151	18028										
GABRR2	2570	hgsc.bcm.edu	37	chr6	89977775	89977775	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggtctgggagtccaggggaaAgtggctgaagtccatgttgc	17	7	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:89977775A>G	ENST00000402938.3	-	5	686	c.553T>C	c.(553-555)Ttt>Ctt	p.F185L	GABRR2_ENST00000602808.1_5'Flank|GABRR2_ENST00000602399.1_Missense_Mutation_p.F210L	NM_002043.3	NP_002034.3	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 2	185					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(10)|prostate(2)|urinary_tract(1)	21		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	TCCAGGGGAAAGTGGCTGAAG	0.478																																					p.F185L		Atlas-SNP	.											.	GABRR2	41	.	0			c.T553C						.						115	95	102					6																	89977775		2203	4300	6503	SO:0001583	missense	2570	exon5			GGGGAAAGTGGCT		CCDS5020.2, CCDS5020.3	6q15	2012-06-22	2012-02-03		ENSG00000111886	ENSG00000111886		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4091	protein-coding gene	gene with protein product	"GABA(A) receptor, rho 2"	137162	"gamma-aminobutyric acid (GABA) receptor, rho 2"			1315307	Standard	NM_002043		Approved		uc003pnb.3	P28476	OTTHUMG00000015198	ENST00000402938.3:c.553T>C	chr6.hg19:g.89977775A>G	ENSP00000386029:p.Phe185Leu	293.0	0.0		89.0	4.0	NM_002043	A2BDE4|Q9H153	Missense_Mutation	SNP	ENST00000402938.3	hg19	CCDS5020.3	.	.	.	.	.	.	.	.	.	.	A	34	5.389607	0.95988	.	.	ENSG00000111886	ENST00000402938	.	.	.	5.91	5.91	0.95273	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.82167	0.4978	M	0.89715	3.055	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.85759	0.1348	8	.	.	.	.	16.3512	0.83208	1.0:0.0:0.0:0.0	.	210	P28476	GBRR2_HUMAN	L	210	.	.	F	-	1	0	GABRR2	90034494	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.252000	0.95491	2.266000	0.75297	0.533000	0.62120	TTT	.	.		0.478	GABRR2-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041482.3			G	89977775	A	G	89977775	3	3	113	1	0	0	0	0	1	0	0	0	6185	72	3	2	864	2	GABRR2	6	89977775	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	655248	89977775	81137292	152	18029										
ANKRD6	22881	hgsc.bcm.edu	37	chr6	90326289	90326289	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caattccaggctggagacacAgcacttcacgttgctgctgc	10	13	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:90326289A>G	ENST00000522441.1	+	8	1268	c.627A>G	c.(625-627)acA>acG	p.T209T	ANKRD6_ENST00000339746.4_Silent_p.T209T|ANKRD6_ENST00000520793.1_Silent_p.T176T|ANKRD6_ENST00000369408.5_Silent_p.T209T|ANKRD6_ENST00000485637.1_Silent_p.T209T|ANKRD6_ENST00000447838.2_Silent_p.T209T	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	209					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		CTGGAGACACAGCACTTCACG	0.488																																					p.T209T		Atlas-SNP	.											.	ANKRD6	51	.	0			c.A627G						.						134	132	133					6																	90326289		1992	4181	6173	SO:0001819	synonymous_variant	22881	exon8			AGACACAGCACTT	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"Ankyrin repeat domain containing"	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.627A>G	chr6.hg19:g.90326289A>G		287.0	0.0		100.0	4.0	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Silent	SNP	ENST00000522441.1	hg19	CCDS56441.1																																																																																			.	.		0.488	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1			G	90326289	A	G	90326289	2	3	113	1	0	0	0	0	0	0	0	1	685	175	7	2		2	ANKRD6	6	90326289	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	348514	90326289	80788778	153	18030										
FBXL4	26235	hgsc.bcm.edu	37	chr6	99374410	99374410	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagaacaagcgagaattctaAtgactgctccgggatgatag	11	8	1	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:99374410A>C	ENST00000369244.2	-	4	883	c.455T>G	c.(454-456)aTt>aGt	p.I152S	FBXL4_ENST00000229971.1_Missense_Mutation_p.I152S	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	152					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		GAGAATTCTAATGACTGCTCC	0.393																																					p.I152S		Atlas-SNP	.											.	FBXL4	54	.	0			c.T455G						.						93	88	90					6																	99374410		2203	4300	6503	SO:0001583	missense	26235	exon3			ATTCTAATGACTG	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"F-boxes / Leucine-rich repeats"	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.455T>G	chr6.hg19:g.99374410A>C	ENSP00000358247:p.Ile152Ser	187.0	0.0		63.0	45.0	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	hg19	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	A	16.13	3.035112	0.54896	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.14893	2.47;2.47	5.52	5.52	0.82312	.	0.050504	0.85682	D	0.000000	T	0.10423	0.0255	L	0.48642	1.525	0.53005	D	0.999967	B	0.32245	0.361	B	0.31686	0.134	T	0.02766	-1.1113	10	0.87932	D	0	.	15.9507	0.79835	1.0:0.0:0.0:0.0	.	152	Q9UKA2	FBXL4_HUMAN	S	152	ENSP00000358247:I152S;ENSP00000229971:I152S	ENSP00000229971:I152S	I	-	2	0	FBXL4	99481131	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	8.910000	0.92685	2.232000	0.73038	0.528000	0.53228	ATT	.	.		0.393	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			C	99374410	A	C	99374410	3	2	113	1	0	0	0	0	1	0	0	0	5729	101	4	5	1438	5	FBXL4	6	99374410	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	9048121	99374410	71740657	154	18031										
COQ3	51805	hgsc.bcm.edu	37	chr6	99823850	99823850	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agcagcactgtaaaaatgttTctagatcaatcacatgttct	6	8	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:99823850T>C	ENST00000254759.3	-	5	719	c.695A>G	c.(694-696)gAa>gGa	p.E232G	COQ3_ENST00000369240.1_Intron|COQ3_ENST00000479163.1_5'Flank|COQ3_ENST00000369242.1_Intron	NM_017421.3	NP_059117.3	Q9NZJ6	COQ3_HUMAN	coenzyme Q3 methyltransferase	232					glycerol metabolic process (GO:0006071)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0008425)|3-demethylubiquinone-9 3-O-methyltransferase activity (GO:0008689)|hexaprenyldihydroxybenzoate methyltransferase activity (GO:0004395)|O-methyltransferase activity (GO:0008171)			cervix(1)|lung(5)|upper_aerodigestive_tract(2)	8		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)		TAAAAATGTTTCTAGATCAAT	0.378																																					p.E232G		Atlas-SNP	.											.	COQ3	19	.	0			c.A695G						.						156	151	153					6																	99823850		2203	4300	6503	SO:0001583	missense	51805	exon5			AATGTTTCTAGAT	AF193016	CCDS5042.1	6q21	2013-05-01	2013-05-01		ENSG00000132423	ENSG00000132423	2.1.1.114		18175	protein-coding gene	gene with protein product	"polyprenyldihydroxybenzoate methyltransferase"	605196	"coenzyme Q3 homolog, methyltransferase (yeast)", "coenzyme Q3 homolog, methyltransferase (S. cerevisiae)"			10777520	Standard	NM_017421		Approved	bA9819.1	uc003ppk.3	Q9NZJ6	OTTHUMG00000015264	ENST00000254759.3:c.695A>G	chr6.hg19:g.99823850T>C	ENSP00000254759:p.Glu232Gly	164.0	0.0		63.0	4.0	NM_017421	B3KPX0|Q5T061|Q6P4F0|Q8IXG6|Q96BG1|Q9H0N1	Missense_Mutation	SNP	ENST00000254759.3	hg19	CCDS5042.1	.	.	.	.	.	.	.	.	.	.	T	17.06	3.293444	0.60086	.	.	ENSG00000132423	ENST00000254759	T	0.15487	2.42	5.49	5.49	0.81192	Methyltransferase type 11 (1);	0.152438	0.64402	D	0.000017	T	0.26011	0.0634	L	0.58969	1.84	0.80722	D	1	D	0.60160	0.987	D	0.64506	0.926	T	0.01048	-1.1469	10	0.38643	T	0.18	-8.7894	15.5817	0.76448	0.0:0.0:0.0:1.0	.	232	Q9NZJ6	COQ3_HUMAN	G	232	ENSP00000254759:E232G	ENSP00000254759:E232G	E	-	2	0	COQ3	99930571	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.606000	0.82863	2.090000	0.63153	0.459000	0.35465	GAA	.	.		0.378	COQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041602.1	NM_017421		C	99823850	T	C	99823850	3	2	113	1	0	0	0	0	1	0	0	0	3748	1783	62	2	426	2	COQ3	6	99823850	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	449440	99823850	71291217	155	18032										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101095214	101095214	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgtctcaaagggctagcccaAccccaaagcctcttgtcaat	7	14	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:101095214A>G	ENST00000369162.2	-	21	3710	c.3366T>C	c.(3364-3366)ggT>ggC	p.G1122G		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1122	SEC63 1.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GGCTAGCCCAACCCCAAAGCC	0.428																																					p.G1122G		Atlas-SNP	.											.	ASCC3	205	.	0			c.T3366C						.						115	113	114					6																	101095214		2203	4300	6503	SO:0001819	synonymous_variant	10973	exon21			AGCCCAACCCCAA	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.3366T>C	chr6.hg19:g.101095214A>G		168.0	0.0		67.0	4.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Silent	SNP	ENST00000369162.2	hg19	CCDS5046.1																																																																																			.	.		0.428	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		G	101095214	A	G	101095214	2	3	113	1	0	0	0	0	0	0	0	1	1033	30	2	2		2	ASCC3	6	101095214	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1271364	101095214	70019853	156	18033										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129621989	129621989	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	taaatgtgcacccaatacctGgggccacagcattaccactg	8	13	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:129621989G>A	ENST00000421865.2	+	22	3195	c.3146G>A	c.(3145-3147)tGg>tAg	p.W1049*		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1049	Laminin EGF-like 11. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CCCAATACCTGGGGCCACAGC	0.428																																					p.W1049X		Atlas-SNP	.											.	LAMA2	481	.	0			c.G3146A						.						126	126	126					6																	129621989		2203	4300	6503	SO:0001587	stop_gained	3908	exon22			ATACCTGGGGCCA	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.3146G>A	chr6.hg19:g.129621989G>A	ENSP00000400365:p.Trp1049*	182.0	0.0		87.0	4.0	NM_000426	Q14736|Q5VUM2|Q93022	Nonsense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	43	9.905006	0.99292	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.1725	0.93585	0.0:0.0:1.0:0.0	.	.	.	.	X	1049	.	ENSP00000346769:W1049X	W	+	2	0	LAMA2	129663682	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.471000	0.97696	2.515000	0.84797	0.585000	0.79938	TGG	.	.		0.428	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129621989	G	A	129621989	4	1	113	1	0	0	0	0	0	1	0	0	8615	1357	47	3	3232	3	LAMA2	6	129621989	Nonsense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	28526775	129621989	41493078	157	18034										
ZBTB2	57621	hgsc.bcm.edu	37	chr6	151686763	151686763	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caggagaatggatcgcccttCgtctagggcaaaaacatccg	11	11	1	1	rs529081721		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:151686763C>T	ENST00000325144.4	-	3	1578	c.1438G>A	c.(1438-1440)Gaa>Aaa	p.E480K		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	480					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		GATCGCCCTTCGTCTAGGGCA	0.473													C|||	1	0.000199681	0	0	5008	,	,		20129	0		0	False		,,,				2504	0.001				p.E480K		Atlas-SNP	.											.	ZBTB2	30	.	0			c.G1438A						.						149	139	142					6																	151686763		2203	4300	6503	SO:0001583	missense	57621	exon3			GCCCTTCGTCTAG	BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.1438G>A	chr6.hg19:g.151686763C>T	ENSP00000323183:p.Glu480Lys	242.0	0.0		92.0	5.0	NM_020861	A8K7C7|Q5SZ81|Q9P245	Missense_Mutation	SNP	ENST00000325144.4	hg19	CCDS5231.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.248474	0.59103	.	.	ENSG00000181472	ENST00000325144	T	0.04706	3.57	5.51	5.51	0.81932	.	0.212528	0.49305	D	0.000160	T	0.07369	0.0186	N	0.19112	0.55	0.58432	D	0.999999	D	0.76494	0.999	D	0.68621	0.959	T	0.47611	-0.9104	10	0.54805	T	0.06	-40.7497	19.4309	0.94765	0.0:1.0:0.0:0.0	.	480	Q8N680	ZBTB2_HUMAN	K	480	ENSP00000323183:E480K	ENSP00000323183:E480K	E	-	1	0	ZBTB2	151728456	0.999000	0.42202	0.866000	0.34008	0.890000	0.51754	4.144000	0.58057	2.595000	0.87683	0.563000	0.77884	GAA	.	.		0.473	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861		T	151686763	C	T	151686763	3	4	113	1	0	0	0	0	1	0	0	0	17543	893	31	1	110	1	ZBTB2	6	151686763	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	22064774	151686763	19428304	158	18035										
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	10	12	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000230354.6_Silent_p.Q60Q|TBP_ENST00000540980.1_Silent_p.Q40Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		91.0	0.0		42.0	5.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	113	1	0	0	0	0	0	0	0	1	15659	962	34	3		3	TBP	6	170871004	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	19184241	170871004	244063	159	18036										
SDK1	221935	hgsc.bcm.edu	37	chr7	4091349	4091349	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttccacggagtccaccatgGacacataacgaacctgaaga	8	12	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr7:4091349G>A	ENST00000404826.2	+	19	2937	c.2798G>A	c.(2797-2799)gGa>gAa	p.G933E	SDK1_ENST00000389531.3_Missense_Mutation_p.G933E	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	933	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GTCCACCATGGACACATAACG	0.577																																					p.G933E		Atlas-SNP	.											.	SDK1	361	.	0			c.G2798A						.						152	135	141					7																	4091349		2203	4300	6503	SO:0001583	missense	221935	exon19			ACCATGGACACAT	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.2798G>A	chr7.hg19:g.4091349G>A	ENSP00000385899:p.Gly933Glu	200.0	0.0		199.0	75.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.667580	0.47677	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.56941	0.43;0.43	5.62	5.62	0.85841	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.70876	0.3274	M	0.71296	2.17	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.71434	-0.4594	10	0.51188	T	0.08	.	14.519	0.67838	0.0:0.0:0.8536:0.1464	.	933;933	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	E	933	ENSP00000385899:G933E;ENSP00000374182:G933E	ENSP00000374182:G933E	G	+	2	0	SDK1	4057875	1.000000	0.71417	0.144000	0.22314	0.018000	0.09664	5.487000	0.66863	2.648000	0.89879	0.650000	0.86243	GGA	.	.		0.577	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		A	4091349	G	A	4091349	3	1	113	1	0	0	0	0	1	0	0	0	13983	1174	41	3	2872	3	SDK1	7	4091349	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10		4091349	155047314	160	18037										
RNF216	54476	hgsc.bcm.edu	37	chr7	5781438	5781438	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttgggtcgtgatctctgaggTttatttgtctaagaaaaaat	10	4	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr7:5781438T>C	ENST00000425013.2	-	4	426				RNF216_ENST00000389902.3_Silent_p.K70K	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216						apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		ATCTCTGAGGTTTATTTGTCT	0.388																																					p.K70K		Atlas-SNP	.											.	RNF216	71	.	0			c.A210G						.						65	66	66					7																	5781438		2191	4268	6459	SO:0001627	intron_variant	54476	exon4			CTGAGGTTTATTT	AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"RING-type (C3HC4) zinc fingers"	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.202-163A>G	chr7.hg19:g.5781438T>C		96.0	0.0		89.0	4.0	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Silent	SNP	ENST00000425013.2	hg19	CCDS34595.1																																																																																			.	.		0.388	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		C	5781438	T	C	5781438	1	2	113	0	1	0	0	0	0	0	0	0	13495	1722	60	2		2	RNF216	7	5781438	Intron	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1690089	5781438	153357225	161	18038										
GLCCI1	113263	hgsc.bcm.edu	37	chr7	8126065	8126065	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgatgacaccagcacagcggGctccatggaggcctctgtcc	12	14	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr7:8126065G>A	ENST00000223145.5	+	8	2098	c.1541G>A	c.(1540-1542)gGc>gAc	p.G514D		NM_138426.3	NP_612435.1	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	514						cytoplasm (GO:0005737)				endometrium(4)|large_intestine(4)|lung(13)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	25		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)		AGCACAGCGGGCTCCATGGAG	0.567																																					p.G514D		Atlas-SNP	.											.	GLCCI1	50	.	0			c.G1541A						.						144	163	157					7																	8126065		2203	4300	6503	SO:0001583	missense	113263	exon8			CAGCGGGCTCCAT	BC050291	CCDS34601.1	7p22.2	2008-08-18			ENSG00000106415	ENSG00000106415			18713	protein-coding gene	gene with protein product		614283					Standard	NM_138426		Approved	GIG18, FAM117C, TSSN1	uc003srk.4	Q86VQ1	OTTHUMG00000151984	ENST00000223145.5:c.1541G>A	chr7.hg19:g.8126065G>A	ENSP00000223145:p.Gly514Asp	132.0	0.0		161.0	7.0	NM_138426	A4D103|Q96FD0	Missense_Mutation	SNP	ENST00000223145.5	hg19	CCDS34601.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.859920	0.00552	.	.	ENSG00000106415	ENST00000223145	.	.	.	5.32	1.38	0.22167	.	0.718744	0.14391	N	0.322490	T	0.10508	0.0257	N	0.02011	-0.69	0.28412	N	0.918128	B	0.06786	0.001	B	0.09377	0.004	T	0.34279	-0.9835	9	0.06494	T	0.89	-24.0877	5.2103	0.15312	0.2283:0.3187:0.4531:0.0	.	514	Q86VQ1	GLCI1_HUMAN	D	514	.	ENSP00000223145:G514D	G	+	2	0	GLCCI1	8092590	0.998000	0.40836	0.006000	0.13384	0.477000	0.33069	2.109000	0.41863	0.431000	0.26258	-0.150000	0.13652	GGC	.	.		0.567	GLCCI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324672.1	NM_138426		A	8126065	G	A	8126065	3	1	113	1	0	0	0	0	1	0	0	0	6439	1203	42	3	1571	3	GLCCI1	7	8126065	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	2344627	8126065	151012598	162	18039										
SCIN	85477	hgsc.bcm.edu	37	chr7	12620702	12620702	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caggctggaggcgtggcatcTggattaaatcatgttcttac	12	8	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr7:12620702T>C	ENST00000297029.5	+	3	473	c.372T>C	c.(370-372)tcT>tcC	p.S124S		NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	124	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		GCGTGGCATCTGGATTAAATC	0.478																																					p.S124S		Atlas-SNP	.											.	SCIN	105	.	0			c.T372C						.						182	141	153					7																	12620702		692	1591	2283	SO:0001819	synonymous_variant	85477	exon3			GGCATCTGGATTA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.372T>C	chr7.hg19:g.12620702T>C		103.0	0.0		94.0	4.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Silent	SNP	ENST00000297029.5	hg19	CCDS47545.1																																																																																			.	.		0.478	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		C	12620702	T	C	12620702	2	2	113	1	0	0	0	0	0	0	0	1	13920	1567	55	2		2	SCIN	7	12620702	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	4494637	12620702	146517961	163	18040										
SNX13	23161	hgsc.bcm.edu	37	chr7	17933019	17933019	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	actgttctaggtacttctctGagtttgtttttccaaacagg	8	8	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr7:17933019G>A	ENST00000409389.1	-	3	336	c.164C>T	c.(163-165)tCa>tTa	p.S55L	SNX13_ENST00000409604.1_Missense_Mutation_p.S55L|SNX13_ENST00000428135.3_Missense_Mutation_p.S55L			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	55					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					GTACTTCTCTGAGTTTGTTTT	0.338																																					p.S55L		Atlas-SNP	.											.	SNX13	113	.	0			c.C164T						.						44	40	41					7																	17933019		1814	4067	5881	SO:0001583	missense	23161	exon3			TTCTCTGAGTTTG	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"Sorting nexins"	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.164C>T	chr7.hg19:g.17933019G>A	ENSP00000386705:p.Ser55Leu	229.0	0.0		199.0	41.0	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	hg19		.	.	.	.	.	.	.	.	.	.	G	28.8	4.949072	0.92660	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044;ENST00000409604	T;T	0.18810	2.19;2.46	5.71	5.71	0.89125	.	0.125660	0.56097	D	0.000026	T	0.36853	0.0982	L	0.34521	1.04	0.80722	D	1	D;P;P	0.63880	0.993;0.553;0.862	D;B;P	0.72338	0.977;0.142;0.607	T	0.01596	-1.1316	10	0.27785	T	0.31	-9.9993	19.4828	0.95017	0.0:0.0:1.0:0.0	.	55;55;55	Q9NSH0;B8ZZT9;Q9Y5W8-2	.;.;.	L	55;55;103;55	ENSP00000386705:S55L;ENSP00000398789:S55L	ENSP00000242044:S103L	S	-	2	0	SNX13	17899544	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.988000	0.93501	2.699000	0.92147	0.557000	0.71058	TCA	.	.		0.338	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132		A	17933019	G	A	17933019	3	1	113	1	0	0	0	0	1	0	0	0	14899	1294	45	3	2805	3	SNX13	7	17933019	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	5312317	17933019	141205644	164	18041										
SP4	6671	hgsc.bcm.edu	37	chr7	21469063	21469063	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cacaacagctagaactggtaAcaacgcaacttgctggaaac	8	11	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr7:21469063A>G	ENST00000222584.3	+	3	498	c.280A>G	c.(280-282)Aca>Gca	p.T94A		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	94					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						AGAACTGGTAACAACGCAACT	0.428																																					p.T94A		Atlas-SNP	.											.	SP4	91	.	0			c.A280G						.						103	89	94					7																	21469063		2203	4300	6503	SO:0001583	missense	6671	exon3			CTGGTAACAACGC		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.280A>G	chr7.hg19:g.21469063A>G	ENSP00000222584:p.Thr94Ala	105.0	0.0		104.0	5.0	NM_003112	O60402|Q32M52	Missense_Mutation	SNP	ENST00000222584.3	hg19	CCDS5373.1	.	.	.	.	.	.	.	.	.	.	A	7.458	0.644180	0.14451	.	.	ENSG00000105866	ENST00000222584	T	0.08370	3.1	4.46	4.46	0.54185	.	0.051668	0.85682	D	0.000000	T	0.05502	0.0145	N	0.16166	0.38	0.43179	D	0.994991	P	0.38504	0.634	B	0.35607	0.206	T	0.52328	-0.8590	10	0.25106	T	0.35	.	13.9273	0.63970	1.0:0.0:0.0:0.0	.	94	Q02446	SP4_HUMAN	A	94	ENSP00000222584:T94A	ENSP00000222584:T94A	T	+	1	0	SP4	21435588	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	6.380000	0.73158	1.873000	0.54277	0.533000	0.62120	ACA	.	.		0.428	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		G	21469063	A	G	21469063	3	3	113	1	0	0	0	0	1	0	0	0	14981	43	2	2	290	2	SP4	7	21469063	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3536044	21469063	137669600	165	18042										
STK31	56164	hgsc.bcm.edu	37	chr7	23802460	23802460	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgcccaaagaaatgaaatgcAgcagaagctgtacatgtcag	10	8	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr7:23802460A>G	ENST00000355870.3	+	11	1453	c.1334A>G	c.(1333-1335)cAg>cGg	p.Q445R	STK31_ENST00000433467.2_Missense_Mutation_p.Q445R|STK31_ENST00000405627.3_3'UTR|STK31_ENST00000428484.1_Missense_Mutation_p.Q422R|STK31_ENST00000354639.3_Missense_Mutation_p.Q422R	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	445						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						AATGAAATGCAGCAGAAGCTG	0.338																																					p.Q445R		Atlas-SNP	.											.	STK31	175	.	0			c.A1334G						.						99	100	100					7																	23802460		2203	4296	6499	SO:0001583	missense	56164	exon11			AAATGCAGCAGAA	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1334A>G	chr7.hg19:g.23802460A>G	ENSP00000348132:p.Gln445Arg	164.0	0.0		119.0	5.0	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	hg19	CCDS5386.1	.	.	.	.	.	.	.	.	.	.	A	8.705	0.910724	0.17833	.	.	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.13901	2.55;2.55;2.55;2.55	5.24	3.93	0.45458	.	0.289256	0.34906	N	0.003591	T	0.08670	0.0215	L	0.27053	0.805	0.34106	D	0.662474	B;B	0.12013	0.005;0.005	B;B	0.12156	0.007;0.007	T	0.16897	-1.0387	10	0.17369	T	0.5	-4.1223	8.8496	0.35192	0.8738:0.0:0.1262:0.0	.	445;445	B4DZ06;Q9BXU1	.;STK31_HUMAN	R	445;445;422;422	ENSP00000348132:Q445R;ENSP00000411852:Q445R;ENSP00000346660:Q422R;ENSP00000406146:Q422R	ENSP00000346660:Q422R	Q	+	2	0	STK31	23768985	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	2.819000	0.48049	2.110000	0.64415	0.477000	0.44152	CAG	.	.		0.338	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		G	23802460	A	G	23802460	3	3	113	1	0	0	0	0	1	0	0	0	15311	188	7	2	1376	2	STK31	7	23802460	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2333397	23802460	135336203	166	18043										
DNAJB9	4189	hgsc.bcm.edu	37	chr7	108212222	108212222	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caatctgcattttaatgataAcagaattaattctggcctca	5	8	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr7:108212222A>G	ENST00000249356.3	+	2	598	c.52A>G	c.(52-54)Aca>Gca	p.T18A	THAP5_ENST00000415914.3_5'Flank|THAP5_ENST00000493722.1_5'Flank|THAP5_ENST00000313516.5_5'Flank|DNAJB9_ENST00000465725.1_3'UTR|THAP5_ENST00000438865.1_5'Flank	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	18					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	misfolded protein binding (GO:0051787)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13						TTTAATGATAACAGAATTAAT	0.368																																					p.T18A		Atlas-SNP	.											.	DNAJB9	25	.	0			c.A52G						.						74	83	80					7																	108212222		2203	4300	6503	SO:0001583	missense	4189	exon2			ATGATAACAGAAT	AB026908	CCDS5752.1	7q31	2011-09-02			ENSG00000128590	ENSG00000128590		"Heat shock proteins / DNAJ (HSP40)"	6968	protein-coding gene	gene with protein product		602634		MDG1		9533036, 11147971	Standard	NM_012328		Approved		uc003vfn.3	Q9UBS3	OTTHUMG00000154866	ENST00000249356.3:c.52A>G	chr7.hg19:g.108212222A>G	ENSP00000249356:p.Thr18Ala	146.0	0.0		98.0	4.0	NM_012328		Missense_Mutation	SNP	ENST00000249356.3	hg19	CCDS5752.1	.	.	.	.	.	.	.	.	.	.	A	14.14	2.446014	0.43429	.	.	ENSG00000128590	ENST00000249356	T	0.60672	0.17	5.19	5.19	0.71726	Heat shock protein DnaJ, N-terminal (2);	0.183045	0.48286	D	0.000188	T	0.27169	0.0666	N	0.01729	-0.75	0.45607	D	0.998545	B	0.19706	0.038	B	0.16289	0.015	T	0.18178	-1.0345	9	.	.	.	.	9.6254	0.39748	0.8443:0.0:0.0:0.1557	.	18	Q9UBS3	DNJB9_HUMAN	A	18	ENSP00000249356:T18A	.	T	+	1	0	DNAJB9	107999458	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.518000	0.53451	1.946000	0.56461	0.460000	0.39030	ACA	.	.		0.368	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1			G	108212222	A	G	108212222	3	3	113	1	0	0	0	0	1	0	0	0	4629	43	2	2	54	2	DNAJB9	7	108212222	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	84409762	108212222	50926441	167	18044										
EXOC4	60412	hgsc.bcm.edu	37	chr7	133041177	133041177	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gggtatcctcattaagggctTggcgaaactgaagaagatcc	12	8	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr7:133041177T>C	ENST00000253861.4	+	6	886	c.857T>C	c.(856-858)tTg>tCg	p.L286S	EXOC4_ENST00000539845.1_Missense_Mutation_p.L185S|EXOC4_ENST00000393161.2_Missense_Mutation_p.L286S	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	286					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				ATTAAGGGCTTGGCGAAACTG	0.448																																					p.L286S		Atlas-SNP	.											.	EXOC4	118	.	0			c.T857C						.						86	82	83					7																	133041177		2203	4300	6503	SO:0001583	missense	60412	exon6			AGGGCTTGGCGAA	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"SEC8-like 1 (S. cerevisiae)"	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.857T>C	chr7.hg19:g.133041177T>C	ENSP00000253861:p.Leu286Ser	109.0	0.0		86.0	4.0	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	hg19	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.427511	0.83667	.	.	ENSG00000131558	ENST00000253861;ENST00000393161;ENST00000539845	.	.	.	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000001	T	0.80259	0.4590	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.997;0.996	T	0.82719	-0.0318	9	0.62326	D	0.03	.	15.9219	0.79583	0.0:0.0:0.0:1.0	.	286;286	Q96A65;Q8TAR2	EXOC4_HUMAN;.	S	286;286;185	.	ENSP00000253861:L286S	L	+	2	0	EXOC4	132691717	1.000000	0.71417	0.988000	0.46212	0.835000	0.47333	7.788000	0.85771	2.218000	0.71995	0.528000	0.53228	TTG	.	.		0.448	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		C	133041177	T	C	133041177	3	2	113	1	0	0	0	0	1	0	0	0	5308	1821	63	2	879	2	EXOC4	7	133041177	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	24828955	133041177	26097486	168	18045										
AGPAT5	55326	hgsc.bcm.edu	37	chr8	6614716	6614716	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	attttatgagtcaccagatcCagaaagaagaaaaagatttc	7	6	1	6			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:6614716C>A	ENST00000285518.6	+	8	1214	c.902C>A	c.(901-903)cCa>cAa	p.P301Q		NM_018361.3	NP_060831.2	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	301					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.P301L(1)	AGPAT5/MCPH1(2)	endometrium(2)|kidney(2)|large_intestine(4)|lung(3)	11			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		TCACCAGATCCAGAAAGAAGA	0.323																																					p.P301Q		Atlas-SNP	.											AGPAT5,NS,carcinoma,0,1	AGPAT5	31	.	1	Substitution - Missense(1)	kidney(1)	c.C902A						.						45	46	46					8																	6614716		2203	4300	6503	SO:0001583	missense	55326	exon8			CAGATCCAGAAAG	AF375789	CCDS34796.1	8p23.1	2013-02-05	2013-02-05		ENSG00000155189	ENSG00000155189	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20886	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, epsilon"	614796	"1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"				Standard	NM_018361		Approved	FLJ11210, LPAAT-e, LPAAT-epsilon	uc003wqo.3	Q9NUQ2	OTTHUMG00000163656	ENST00000285518.6:c.902C>A	chr8.hg19:g.6614716C>A	ENSP00000285518:p.Pro301Gln	108.0	0.0		48.0	2.0	NM_018361	Q8IZ47|Q9BQG4	Missense_Mutation	SNP	ENST00000285518.6	hg19	CCDS34796.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.8|20.8	4.043667|4.043667	0.75732|0.75732	.|.	.|.	ENSG00000155189|ENSG00000155189	ENST00000285518|ENST00000518327	T|.	0.63255|.	-0.03|.	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	0.346377|.	0.34725|.	N|.	0.003723|.	T|T	0.75803|0.75803	0.3899|0.3899	M|M	0.70595|0.70595	2.14|2.14	0.47994|0.47994	D|D	0.999562|0.999562	P|.	0.35745|.	0.518|.	B|.	0.33454|.	0.164|.	T|T	0.73167|0.73167	-0.4068|-0.4068	10|5	0.28530|.	T|.	0.3|.	-10.8366|-10.8366	18.073|18.073	0.89417|0.89417	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	301|.	Q9NUQ2|.	PLCE_HUMAN|.	Q|K	301|118	ENSP00000285518:P301Q|.	ENSP00000285518:P301Q|.	P|Q	+|+	2|1	0|0	AGPAT5|AGPAT5	6602124|6602124	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.436000|4.436000	0.59948|0.59948	2.873000|2.873000	0.98535|0.98535	0.561000|0.561000	0.74099|0.74099	CCA|CAG	.	.		0.323	AGPAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374684.1	NM_018361		A	6614716	C	A	6614716	3	1	113	1	0	0	0	0	1	0	0	0	390	594	21	3	932	3	AGPAT5	8	6614716	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10		6614716	139749306	169	18046										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10464506	10464506	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctcttgtaggtcataaccttCactggccccctgctctggag	9	14	4	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:10464506C>T	ENST00000382483.3	-	4	7325	c.7102G>A	c.(7102-7104)Gaa>Aaa	p.E2368K		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2448					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TCATAACCTTCACTGGCCCCC	0.557																																					p.E2368K		Atlas-SNP	.											.	RP1L1	453	.	0			c.G7102A						.						96	101	99					8																	10464506		1912	4113	6025	SO:0001583	missense	94137	exon4			AACCTTCACTGGC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.7102G>A	chr8.hg19:g.10464506C>T	ENSP00000371923:p.Glu2368Lys	96.0	0.0		32.0	25.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	9.958	1.221954	0.22457	.	.	ENSG00000183638	ENST00000382483	T	0.12879	2.64	4.29	-0.977	0.10282	.	.	.	.	.	T	0.04907	0.0132	N	0.04508	-0.205	0.09310	N	1	B	0.14805	0.011	B	0.11329	0.006	T	0.44772	-0.9306	9	0.17369	T	0.5	-0.015	5.0356	0.14432	0.1339:0.5556:0.0:0.3105	.	2368	A6NKC6	.	K	2368	ENSP00000371923:E2368K	ENSP00000371923:E2368K	E	-	1	0	RP1L1	10501916	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.058000	0.11750	-0.316000	0.08690	-1.093000	0.02169	GAA	.	.		0.557	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10464506	C	T	10464506	3	4	113	1	0	0	0	0	1	0	0	0	13548	835	29	3	104	3	RP1L1	8	10464506	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	3849790	10464506	135899516	170	18047										
MTMR7	9108	hgsc.bcm.edu	37	chr8	17218727	17218727	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagcacccagccttgctctcTttcttctttatccagcatgg	6	15	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:17218727T>C	ENST00000180173.5	-	4	401	c.367A>G	c.(367-369)Aga>Gga	p.R123G	MTMR7_ENST00000521857.1_Missense_Mutation_p.R123G	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	123					inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		CCTTGCTCTCTTTCTTCTTTA	0.423																																					p.R123G		Atlas-SNP	.											.	MTMR7	75	.	0			c.A367G						.						160	150	153					8																	17218727		2203	4300	6503	SO:0001583	missense	9108	exon4			GCTCTCTTTCTTC	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.367A>G	chr8.hg19:g.17218727T>C	ENSP00000180173:p.Arg123Gly	251.0	0.0		97.0	4.0	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	hg19	CCDS34851.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.758324	0.49468	.	.	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.92911	-3.13;-3.13	5.48	1.43	0.22495	.	0.048443	0.85682	D	0.000000	D	0.90198	0.6936	M	0.70595	2.14	0.80722	D	1	B	0.15930	0.015	B	0.20184	0.028	D	0.85015	0.0908	10	0.29301	T	0.29	.	14.6641	0.68893	0.0:0.0:0.5633:0.4367	.	123	Q9Y216	MTMR7_HUMAN	G	123	ENSP00000180173:R123G;ENSP00000429733:R123G	ENSP00000180173:R123G	R	-	1	2	MTMR7	17263098	0.999000	0.42202	0.997000	0.53966	0.985000	0.73830	0.393000	0.20817	0.440000	0.26502	0.533000	0.62120	AGA	.	.		0.423	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686		C	17218727	T	C	17218727	3	2	113	1	0	0	0	0	1	0	0	0	9957	1617	56	2	1659	2	MTMR7	8	17218727	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	6754221	17218727	129145295	171	18048										
GSR	2936	hgsc.bcm.edu	37	chr8	30537135	30537135	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	catcttcactgcaacagcaaAaccctgcagcatttcatcac	4	15	4	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:30537135A>G	ENST00000221130.5	-	13	1561	c.1471T>C	c.(1471-1473)Ttt>Ctt	p.F491L	GSR_ENST00000546342.1_Missense_Mutation_p.F462L|GSR_ENST00000414019.1_Missense_Mutation_p.F448L|GSR_ENST00000541648.1_Missense_Mutation_p.F438L|GSR_ENST00000537535.1_Missense_Mutation_p.F409L	NM_000637.3|NM_001195102.1|NM_001195103.1	NP_000628.2|NP_001182031.1|NP_001182032.1	P00390	GSHR_HUMAN	glutathione reductase	491					cell redox homeostasis (GO:0045454)|glutathione metabolic process (GO:0006749)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|glutathione-disulfide reductase activity (GO:0004362)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	23				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Flavin adenine dinucleotide(DB03147)|Glutathione(DB00143)	GCAACAGCAAAACCCTGCAGC	0.443																																					p.F491L		Atlas-SNP	.											.	GSR	53	.	0			c.T1471C						.						169	139	149					8																	30537135		2203	4300	6503	SO:0001583	missense	2936	exon13			CAGCAAAACCCTG		CCDS34877.1, CCDS56530.1, CCDS56531.1, CCDS56532.1	8p21.1	2012-10-02			ENSG00000104687	ENSG00000104687	1.8.1.7		4623	protein-coding gene	gene with protein product		138300					Standard	NM_000637		Approved		uc003xih.2	P00390	OTTHUMG00000163946	ENST00000221130.5:c.1471T>C	chr8.hg19:g.30537135A>G	ENSP00000221130:p.Phe491Leu	319.0	0.0		79.0	4.0	NM_000637	C8KIL8|C8KIL9|C8KIM0|D3DSV3|Q7Z5C9|Q9NP63	Missense_Mutation	SNP	ENST00000221130.5	hg19	CCDS34877.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.995070	0.93167	.	.	ENSG00000104687	ENST00000221130;ENST00000414019;ENST00000546342;ENST00000541648;ENST00000537535	D;D;D;D;D	0.91521	-2.86;-2.86;-2.86;-2.86;-2.86	5.34	5.34	0.76211	FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (2);	0.000000	0.85682	D	0.000000	D	0.94411	0.8202	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94458	0.7673	10	0.54805	T	0.06	-6.5594	13.5686	0.61832	1.0:0.0:0.0:0.0	.	491	P00390	GSHR_HUMAN	L	491;448;462;438;409	ENSP00000221130:F491L;ENSP00000390065:F448L;ENSP00000445516:F462L;ENSP00000444559:F438L;ENSP00000438845:F409L	ENSP00000221130:F491L	F	-	1	0	GSR	30656677	1.000000	0.71417	0.992000	0.48379	0.815000	0.46073	8.577000	0.90773	2.160000	0.67779	0.454000	0.30748	TTT	.	.		0.443	GSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376519.1			G	30537135	A	G	30537135	3	3	113	1	0	0	0	0	1	0	0	0	6837	14	1	2	101	2	GSR	8	30537135	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	13318408	30537135	115826887	172	18049										
GPR124	25960	hgsc.bcm.edu	37	chr8	37699046	37699046	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagcctccgccctgggcctcTtcgtcttcactcaccactgt	7	19	4	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:37699046T>C	ENST00000412232.2	+	19	3203	c.3190T>C	c.(3190-3192)Ttc>Ctc	p.F1064L	GPR124_ENST00000315215.7_Missense_Mutation_p.F847L	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	1064					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			CCTGGGCCTCTTCGTCTTCAC	0.741																																					p.F1064L		Atlas-SNP	.											.	GPR124	85	.	0			c.T3190C						.						20	23	22					8																	37699046		2202	4297	6499	SO:0001583	missense	25960	exon19			GGCCTCTTCGTCT	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.3190T>C	chr8.hg19:g.37699046T>C	ENSP00000406367:p.Phe1064Leu	138.0	0.0		49.0	4.0	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.03|19.03	3.747715|3.747715	0.69533|0.69533	.|.	.|.	ENSG00000020181|ENSG00000020181	ENST00000315215;ENST00000412232|ENST00000416514	T;T|.	0.60040|.	0.22;0.22|.	5.01|5.01	5.01|5.01	0.66863|0.66863	GPCR, family 2, secretin-like, conserved site (1);|.	0.114571|.	0.64402|.	D|.	0.000012|.	T|T	0.75148|0.75148	0.3810|0.3810	M|M	0.73598|0.73598	2.24|2.24	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.69078|.	0.997;0.997|.	P;D|.	0.75020|.	0.879;0.985|.	T|T	0.79065|0.79065	-0.1956|-0.1956	10|6	0.87932|0.87932	D|D	0|0	-30.5409|-30.5409	14.7311|14.7311	0.69383|0.69383	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	847;1064|.	Q96PE1-2;Q96PE1|.	.;GP124_HUMAN|.	L|P	847;1064|1056	ENSP00000323508:F847L;ENSP00000406367:F1064L|.	ENSP00000323508:F847L|ENSP00000405145:L1056P	F|L	+|+	1|2	0|0	GPR124|GPR124	37818204|37818204	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.025000|0.025000	0.11179|0.11179	7.764000|7.764000	0.85297|0.85297	1.882000|1.882000	0.54519|0.54519	0.528000|0.528000	0.53228|0.53228	TTC|CTT	.	.		0.741	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			C	37699046	T	C	37699046	3	2	113	1	0	0	0	0	1	0	0	0	6646	1609	56	2	3243	2	GPR124	8	37699046	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	7161911	37699046	108664976	173	18050										
CHRNA6	8973	hgsc.bcm.edu	37	chr8	42611479	42611479	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atgggatggtttctgtgatgAccagcaaaaacacagtcaga	11	7	2	3	rs373608967		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:42611479A>G	ENST00000276410.2	-	5	1218	c.863T>C	c.(862-864)gTc>gCc	p.V288A	CHRNA6_ENST00000530869.1_5'Flank|CHRNA6_ENST00000534622.1_Missense_Mutation_p.V273A	NM_004198.3	NP_004189.1	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6 (neuronal)	288					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|membrane depolarization (GO:0051899)|regulation of dopamine secretion (GO:0014059)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)			endometrium(2)|large_intestine(3)|liver(1)|lung(15)|ovary(1)	22	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)|Varenicline(DB01273)	TTCTGTGATGACCAGCAAAAA	0.473																																					p.V288A		Atlas-SNP	.											.	CHRNA6	60	.	0			c.T863C						.	A	ALA/VAL,ALA/VAL	1,4405	2.1+/-5.4	0,1,2202	99	84	90		818,863	6	1	8		90	0,8600		0,0,4300	no	missense,missense	CHRNA6	NM_001199279.1,NM_004198.3	64,64	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging,probably-damaging	273/480,288/495	42611479	1,13005	2203	4300	6503	SO:0001583	missense	8973	exon5			GTGATGACCAGCA	U62435	CCDS6135.1, CCDS56536.1	8p22	2012-02-11	2012-02-07					"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	15963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 6 (neuronal)"	606888	"cholinergic receptor, nicotinic, alpha polypeptide 6"			8906617	Standard	NM_004198		Approved		uc003xpj.3	Q15825		ENST00000276410.2:c.863T>C	chr8.hg19:g.42611479A>G	ENSP00000276410:p.Val288Ala	153.0	0.0		119.0	6.0	NM_004198	B2R8V4|B4DQH1	Missense_Mutation	SNP	ENST00000276410.2	hg19	CCDS6135.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.582810	0.86748	2.27E-4	0.0	ENSG00000147434	ENST00000276410;ENST00000534622	D;D	0.85702	-2.02;-2.02	5.97	5.97	0.96955	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.92561	0.7637	M	0.82056	2.57	0.80722	D	1	D;D	0.58620	0.983;0.965	D;D	0.72625	0.978;0.978	D	0.93358	0.6724	10	0.87932	D	0	.	16.4473	0.83942	1.0:0.0:0.0:0.0	.	273;288	B4DQH1;Q15825	.;ACHA6_HUMAN	A	288;273	ENSP00000276410:V288A;ENSP00000433871:V273A	ENSP00000276410:V288A	V	-	2	0	CHRNA6	42730636	1.000000	0.71417	0.983000	0.44433	0.989000	0.77384	9.253000	0.95501	2.281000	0.76405	0.533000	0.62120	GTC	.	.		0.473	CHRNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383156.1			G	42611479	A	G	42611479	3	3	113	1	0	0	0	0	1	0	0	0	3389	275	10	2	629	2	CHRNA6	8	42611479	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	4912433	42611479	103752543	174	18051										
RP1	6101	hgsc.bcm.edu	37	chr8	55542668	55542668	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	acaacttattaaataacagaTtccagggctcaagaacaaat	5	8	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:55542668T>A	ENST00000220676.1	+	4	6374	c.6226T>A	c.(6226-6228)Ttc>Atc	p.F2076I		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	2076					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AAATAACAGATTCCAGGGCTC	0.358																																					p.F2076I	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.T6226A						.						44	45	45					8																	55542668		2202	4297	6499	SO:0001583	missense	6101	exon4			AACAGATTCCAGG	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.6226T>A	chr8.hg19:g.55542668T>A	ENSP00000220676:p.Phe2076Ile	89.0	0.0		68.0	24.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.245740	0.39697	.	.	ENSG00000104237	ENST00000220676	T	0.24151	1.87	5.76	5.76	0.90799	.	0.236869	0.29668	N	0.011509	T	0.29491	0.0735	M	0.62723	1.935	0.09310	N	0.999999	P	0.35077	0.483	B	0.33392	0.163	T	0.32534	-0.9903	10	0.72032	D	0.01	.	14.6387	0.68708	0.0:0.0:0.0:1.0	.	2076	P56715	RP1_HUMAN	I	2076	ENSP00000220676:F2076I	ENSP00000220676:F2076I	F	+	1	0	RP1	55705221	0.574000	0.26684	0.362000	0.25862	0.126000	0.20510	2.402000	0.44521	2.201000	0.70794	0.533000	0.62120	TTC	.	.		0.358	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		A	55542668	T	A	55542668	3	1	113	1	0	0	0	0	1	0	0	0	13547	1493	52	4	6236	4	RP1	8	55542668	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	12931189	55542668	90821354	175	18052										
CHD7	55636	hgsc.bcm.edu	37	chr8	61757545	61757545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	taatcattacaaaggggatgAgaatatcaaaagcttcatct	7	6	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:61757545A>G	ENST00000423902.2	+	22	5452	c.4973A>G	c.(4972-4974)gAg>gGg	p.E1658G	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1658					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AAAGGGGATGAGAATATCAAA	0.488																																					p.E1658G		Atlas-SNP	.											.	CHD7	534	.	0			c.A4973G						.						143	142	142					8																	61757545		1971	4158	6129	SO:0001583	missense	55636	exon22			GGGATGAGAATAT	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.4973A>G	chr8.hg19:g.61757545A>G	ENSP00000392028:p.Glu1658Gly	147.0	0.0		100.0	4.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.759054	0.89843	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.89343	-2.5	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.92018	0.7471	M	0.86178	2.8	0.80722	D	1	B	0.24258	0.1	B	0.36845	0.234	D	0.91025	0.4860	10	0.87932	D	0	-27.3829	16.1412	0.81522	1.0:0.0:0.0:0.0	.	1658	Q9P2D1	CHD7_HUMAN	G	1658	ENSP00000392028:E1658G	ENSP00000307304:E1658G	E	+	2	0	CHD7	61920099	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.265000	0.75225	0.533000	0.62120	GAG	.	.		0.488	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		G	61757545	A	G	61757545	3	3	113	1	0	0	0	0	1	0	0	0	3332	304	11	2	5055	2	CHD7	8	61757545	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	6214877	61757545	84606477	176	18053										
PRDM14	63978	hgsc.bcm.edu	37	chr8	70970987	70970987	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atttcctatcgcccttgtccAcacagggggtgtacttgagg	11	11	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:70970987A>G	ENST00000276594.2	-	6	1475	c.1274T>C	c.(1273-1275)gTg>gCg	p.V425A		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	425					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			GCCCTTGTCCACACAGGGGGT	0.463																																					p.V425A	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											PRDM14,caecum,carcinoma,0,1	PRDM14	102	.	0			c.T1274C						.						111	101	104					8																	70970987		2203	4300	6503	SO:0001583	missense	63978	exon6			TTGTCCACACAGG	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1274T>C	chr8.hg19:g.70970987A>G	ENSP00000276594:p.Val425Ala	138.0	1.0		124.0	5.0	NM_024504	Q86UX9	Missense_Mutation	SNP	ENST00000276594.2	hg19	CCDS6206.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.883083	0.91740	.	.	ENSG00000147596	ENST00000276594	T	0.11712	2.75	5.73	5.73	0.89815	Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.30634	0.0771	L	0.58969	1.84	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.01228	-1.1412	10	0.87932	D	0	-26.0735	16.0233	0.80516	1.0:0.0:0.0:0.0	.	425	Q9GZV8	PRD14_HUMAN	A	425	ENSP00000276594:V425A	ENSP00000276594:V425A	V	-	2	0	PRDM14	71133541	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.785000	0.91822	2.186000	0.69663	0.533000	0.62120	GTG	.	.		0.463	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			G	70970987	A	G	70970987	3	3	113	1	0	0	0	0	1	0	0	0	12467	159	6	2	453	2	PRDM14	8	70970987	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	9213442	70970987	75393035	177	18054										
STMN2	11075	hgsc.bcm.edu	37	chr8	80553730	80553730	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agcttctccaaagaagaaagAcctgtccctggaggagatcc	10	11	1	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:80553730A>G	ENST00000220876.7	+	3	615	c.233A>G	c.(232-234)gAc>gGc	p.D78G	STMN2_ENST00000518491.1_Missense_Mutation_p.D67G|STMN2_ENST00000518111.1_Missense_Mutation_p.D78G	NM_001199214.1|NM_007029.3	NP_001186143.1|NP_008960.2	Q93045	STMN2_HUMAN	stathmin 2	78	Regulatory/phosphorylation domain. {ECO:0000255}.|SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				cellular response to nerve growth factor stimulus (GO:1990090)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|positive regulation of microtubule depolymerization (GO:0031117)|positive regulation of neuron projection development (GO:0010976)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)			AAGAAGAAAGACCTGTCCCTG	0.488																																					p.D78G		Atlas-SNP	.											.	STMN2	23	.	0			c.A233G						.						59	58	58					8																	80553730		1889	4125	6014	SO:0001583	missense	11075	exon3			AGAAAGACCTGTC		CCDS43748.1, CCDS56542.1	8q21.13	2014-04-01	2014-04-01	2001-07-13	ENSG00000104435	ENSG00000104435			10577	protein-coding gene	gene with protein product		600621	"stathmin-like 2"	SCGN10		8622778, 12140291	Standard	NM_007029		Approved	SCG10	uc022awk.1	Q93045	OTTHUMG00000164610	ENST00000220876.7:c.233A>G	chr8.hg19:g.80553730A>G	ENSP00000220876:p.Asp78Gly	149.0	0.0		111.0	5.0	NM_007029	A8K9M2|G3V110|O14952|Q6PK68	Missense_Mutation	SNP	ENST00000220876.7	hg19	CCDS43748.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.015897	0.75161	.	.	ENSG00000104435	ENST00000220876;ENST00000414622;ENST00000518111;ENST00000518491	.	.	.	5.68	4.5	0.54988	.	0.181657	0.64402	D	0.000020	T	0.76919	0.4055	M	0.78916	2.43	0.54753	D	0.999984	D;P	0.65815	0.995;0.902	D;P	0.66716	0.946;0.784	T	0.78219	-0.2289	9	0.59425	D	0.04	-16.4387	12.0053	0.53255	0.8702:0.0:0.0:0.1298	.	78;78	B7Z4K3;Q93045	.;STMN2_HUMAN	G	78;67;78;67	.	ENSP00000220876:D78G	D	+	2	0	STMN2	80716285	1.000000	0.71417	0.921000	0.36526	0.965000	0.64279	9.339000	0.96797	0.939000	0.37446	0.383000	0.25322	GAC	.	.		0.488	STMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379261.2	NM_007029		G	80553730	A	G	80553730	3	3	113	1	0	0	0	0	1	0	0	0	15324	275	10	2	243	2	STMN2	8	80553730	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	9582743	80553730	65810292	178	18055										
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126071720	126071720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgatcatttgatgaagaaacTttcgagtatcggcaagaaac	9	6	1	5			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:126071720T>C	ENST00000318410.7	-	13	1935	c.1586A>G	c.(1585-1587)aAg>aGg	p.K529R	KIAA0196_ENST00000517845.1_Missense_Mutation_p.K381R	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	529					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			ATGAAGAAACTTTCGAGTATC	0.383																																					p.K529R		Atlas-SNP	.											.	KIAA0196	90	.	0			c.A1586G						.						82	82	82					8																	126071720		2203	4300	6503	SO:0001583	missense	9897	exon13			AGAAACTTTCGAG		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.1586A>G	chr8.hg19:g.126071720T>C	ENSP00000318016:p.Lys529Arg	81.0	0.0		71.0	4.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	hg19	CCDS6355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.39|15.39	2.820659|2.820659	0.50633|0.50633	.|.	.|.	ENSG00000164961|ENSG00000164961	ENST00000318410;ENST00000517845|ENST00000523273	D;D|.	0.86230|.	-2.09;-2.09|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61862|0.61862	0.2381|0.2381	L|L	0.42245|0.42245	1.32|1.32	0.58432|0.58432	D|D	0.999996|0.999996	B;B|.	0.18610|.	0.002;0.029|.	B;B|.	0.19666|.	0.007;0.026|.	T|T	0.58086|0.58086	-0.7698|-0.7698	10|5	0.29301|.	T|.	0.29|.	-28.1368|-28.1368	16.2002|16.2002	0.82067|0.82067	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	381;529|.	E7EQI7;Q12768|.	.;STRUM_HUMAN|.	R|G	529;381|146	ENSP00000318016:K529R;ENSP00000429676:K381R|.	ENSP00000318016:K529R|.	K|S	-|-	2|1	0|0	KIAA0196|KIAA0196	126140902|126140902	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.981000|0.981000	0.71138|0.71138	2.771000|2.771000	0.47670|0.47670	2.285000|2.285000	0.76669|0.76669	0.528000|0.528000	0.53228|0.53228	AAG|AGT	.	.		0.383	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		C	126071720	T	C	126071720	3	2	113	1	0	0	0	0	1	0	0	0	8170	1609	56	2	1961	2	KIAA0196	8	126071720	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	45517990	126071720	20292302	179	18056										
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141381200	141381200	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cggccacgcgcttgaagaacGcagacttgcgatggaagccg	14	12	0	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:141381200G>A	ENST00000438773.2	-	8	1347	c.1214C>T	c.(1213-1215)gCg>gTg	p.A405V	TRAPPC9_ENST00000389328.4_Missense_Mutation_p.A503V|TRAPPC9_ENST00000389327.3_Missense_Mutation_p.A396V	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	405					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						CTTGAAGAACGCAGACTTGCG	0.582																																					p.A503V		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C1508T						.						59	58	58					8																	141381200		2203	4300	6503	SO:0001583	missense	83696	exon8			AAGAACGCAGACT	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.1214C>T	chr8.hg19:g.141381200G>A	ENSP00000405060:p.Ala405Val	93.0	0.0		65.0	21.0	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	hg19	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	G	36	5.641101	0.96693	.	.	ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773	.	.	.	5.65	5.65	0.86999	.	0.100710	0.64402	D	0.000002	T	0.78181	0.4243	M	0.73217	2.22	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;P;D	0.67103	0.941;0.903;0.949	T	0.79322	-0.1851	9	0.62326	D	0.03	.	17.9129	0.88939	0.0:0.0:1.0:0.0	.	405;396;503	Q96Q05;Q96Q05-3;Q96Q05-2	TPPC9_HUMAN;.;.	V	503;396;405	.	ENSP00000373978:A396V	A	-	2	0	TRAPPC9	141450382	1.000000	0.71417	0.892000	0.35008	0.903000	0.53119	9.330000	0.96422	2.663000	0.90544	0.455000	0.32223	GCG	.	.		0.582	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		A	141381200	G	A	141381200	3	1	113	1	0	0	0	0	1	0	0	0	16480	1087	38	1	2296	1	TRAPPC9	8	141381200	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	15309480	141381200	4982822	180	18057										
SCRIB	23513	hgsc.bcm.edu	37	chr8	144890960	144890960	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtgcgtgggggccattgtgcCagcccccgggagccacaggg	18	13	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:144890960C>T	ENST00000320476.3	-	15	1940	c.1934G>A	c.(1933-1935)tGg>tAg	p.W645*	SCRIB_ENST00000377533.3_Nonsense_Mutation_p.W564*|SCRIB_ENST00000356994.2_Nonsense_Mutation_p.W645*	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	645	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GCCATTGTGCCAGCCCCCGGG	0.667																																					p.W645X	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.G1934A						.						50	57	55					8																	144890960		2203	4300	6503	SO:0001587	stop_gained	23513	exon15			TTGTGCCAGCCCC	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.1934G>A	chr8.hg19:g.144890960C>T	ENSP00000322938:p.Trp645*	63.0	0.0		52.0	11.0	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Nonsense_Mutation	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	c	39	7.545454	0.98348	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	9.9332	0.41534	0.0:0.9046:0.0:0.0954	.	.	.	.	X	645;645;564;14	.	ENSP00000322938:W645X	W	-	2	0	SCRIB	144962948	1.000000	0.71417	0.999000	0.59377	0.420000	0.31355	2.760000	0.47581	2.153000	0.67306	0.401000	0.26515	TGG	.	.		0.667	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		T	144890960	C	T	144890960	4	4	113	1	0	0	0	0	0	1	0	0	13952	595	21	3	3125	3	SCRIB	8	144890960	Nonsense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	3509760	144890960	1473062	181	18058										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144944289	144944289	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtcaatgatccctcctgtggCcacttgagcctccaggaggc	11	14	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:144944289C>T	ENST00000525985.1	-	2	3204	c.3133G>A	c.(3133-3135)Gcc>Acc	p.A1045T				P58107	EPIPL_HUMAN	epiplakin 1	1045						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCTCCTGTGGCCACTTGAGCC	0.597																																					p.A1045T		Atlas-SNP	.											.	EPPK1	199	.	0			c.G3133A						.						30	34	33					8																	144944289		2098	4233	6331	SO:0001583	missense	83481	exon1			CTGTGGCCACTTG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.3133G>A	chr8.hg19:g.144944289C>T	ENSP00000436337:p.Ala1045Thr	170.0	0.0		154.0	52.0	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.90	3.501754	0.64298	.	.	ENSG00000227184	ENST00000525985	T	0.79454	-1.27	4.54	3.61	0.41365	.	.	.	.	.	T	0.81044	0.4741	L	0.50919	1.6	0.37637	D	0.921882	D	0.69078	0.997	D	0.64506	0.926	T	0.79115	-0.1936	9	0.23891	T	0.37	.	10.5803	0.45252	0.2398:0.7602:0.0:0.0	.	1045	E9PPU0	.	T	1045	ENSP00000436337:A1045T	ENSP00000436337:A1045T	A	-	1	0	EPPK1	145016277	1.000000	0.71417	1.000000	0.80357	0.336000	0.28762	3.864000	0.56024	1.005000	0.39183	0.563000	0.77884	GCC	.	.		0.597	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144944289	C	T	144944289	3	4	113	1	0	0	0	0	1	0	0	0	5192	739	26	3	4133	3	EPPK1	8	144944289	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	53329	144944289	1419733	182	18059										
CPSF1	29894	hgsc.bcm.edu	37	chr8	145619449	145619449	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccagggccctgcccacatacCcagaaaacccagctgggcat	9	17	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr8:145619449C>A	ENST00000349769.3	-	33	3905	c.3811G>T	c.(3811-3813)Gtg>Ttg	p.V1271L	MIR939_ENST00000401314.1_RNA|CPSF1_ENST00000531727.1_Intron	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	1271					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)	p.V1271L(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			GCCCACATACCCAGAAAACCC	0.672																																					p.V1271L	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											CPSF1,NS,carcinoma,0,1	CPSF1	92	.	1	Substitution - Missense(1)	lung(1)	c.G3811T						.						22	29	26					8																	145619449		2171	4258	6429	SO:0001630	splice_region_variant	29894	exon33			ACATACCCAGAAA	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.3811+1G>T	chr8.hg19:g.145619449C>A		272.0	0.0		167.0	47.0	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	hg19	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	16.92	3.255833	0.59321	.	.	ENSG00000071894	ENST00000349769	T	0.45276	0.9	5.06	5.06	0.68205	Cleavage/polyadenylation specificity factor, A subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.53433	0.1796	M	0.73372	2.23	0.80722	D	1	B	0.28055	0.199	B	0.42214	0.38	T	0.51076	-0.8751	9	.	.	.	-35.4922	16.2654	0.82577	0.0:1.0:0.0:0.0	.	1271	Q10570	CPSF1_HUMAN	L	1271	ENSP00000339353:V1271L	.	V	-	1	0	CPSF1	145590257	1.000000	0.71417	1.000000	0.80357	0.618000	0.37518	7.284000	0.78650	2.514000	0.84764	0.555000	0.69702	GTG	.	.		0.672	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	Missense_Mutation	A	145619449	C	A	145619449	5	1	113	1	0	0	0	0	0	0	1	0	3826	637	22	3	544	3	CPSF1	8	145619449	Splice_Site	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	675160	145619449	744573	183	18060										
C9orf46	55848	hgsc.bcm.edu	37	chr9	5361763	5361763	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaatagcaaacatacccagcTgttaaagagatggctgcaag	9	8	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:5361763T>C	ENST00000223864.2	-	4	428	c.207A>G	c.(205-207)acA>acG	p.T69T	PLGRKT_ENST00000482696.1_5'UTR	NM_018465.3	NP_060935.2	Q9HBL7	PLRKT_HUMAN	plasminogen receptor, C-terminal lysine transmembrane protein	69					chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of plasminogen activation (GO:0010756)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)											CATACCCAGCTGTTAAAGAGA	0.373																																					p.T69T		Atlas-SNP	.											.	.	.	.	0			c.A207G						.						81	81	81					9																	5361763		2203	4300	6503	SO:0001819	synonymous_variant	55848	exon4			CCCAGCTGTTAAA	AF225420	CCDS6463.1	9p24.1	2012-04-12	2012-04-12	2012-04-12	ENSG00000107020	ENSG00000107020			23633	protein-coding gene	gene with protein product	"uncharacterized hematopoietic stem/progenitor cells protein MDS030", "plasminogen receptor with a C-terminal lysine"		"chromosome 9 open reading frame 46"	C9orf46		12477932	Standard	NM_018465		Approved	MDS030, FLJ14688, AD025, Plg-RKT	uc003zjc.3	Q9HBL7	OTTHUMG00000019501	ENST00000223864.2:c.207A>G	chr9.hg19:g.5361763T>C		81.0	0.0		62.0	4.0	NM_018465	B2R6W0|Q9NZ44	Silent	SNP	ENST00000223864.2	hg19	CCDS6463.1																																																																																			.	.		0.373	PLGRKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051626.1	NM_018465		C	5361763	T	C	5361763	2	2	113	1	0	0	0	0	0	0	0	1	2486	1567	55	2		2	C9orf46	9	5361763	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10		5361763	135851668	184	18061										
ZDHHC21	340481	hgsc.bcm.edu	37	chr9	14639974	14639974	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcccataaaggctgctagtcTcattatggccaattcatgtc	8	11	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:14639974T>C	ENST00000380916.4	-	8	1007	c.541A>G	c.(541-543)Aga>Gga	p.R181G		NM_178566.4	NP_848661.1	Q8IVQ6	ZDH21_HUMAN	zinc finger, DHHC-type containing 21	181					hair follicle development (GO:0001942)|nitric oxide metabolic process (GO:0046209)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)|regulation of nitric-oxide synthase activity (GO:0050999)|sebaceous gland development (GO:0048733)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(2)|skin(1)	9				GBM - Glioblastoma multiforme(50;4.31e-06)		GCTGCTAGTCTCATTATGGCC	0.333																																					p.R181G		Atlas-SNP	.											.	ZDHHC21	22	.	0			c.A541G						.						92	96	94					9																	14639974		2203	4297	6500	SO:0001583	missense	340481	exon8			CTAGTCTCATTAT	AF161360	CCDS6475.1	9p22.3	2010-02-09			ENSG00000175893	ENSG00000175893		"Zinc fingers, DHHC-type"	20750	protein-coding gene	gene with protein product		614605				19956733	Standard	NM_178566		Approved	HSPC097, DNZ1	uc003zlg.2	Q8IVQ6	OTTHUMG00000019573	ENST00000380916.4:c.541A>G	chr9.hg19:g.14639974T>C	ENSP00000370303:p.Arg181Gly	76.0	0.0		61.0	7.0	NM_178566	A8KA95|D3DRI7|Q5VWG1	Missense_Mutation	SNP	ENST00000380916.4	hg19	CCDS6475.1	.	.	.	.	.	.	.	.	.	.	T	18.10	3.549267	0.65311	.	.	ENSG00000175893	ENST00000380916	T	0.23754	1.89	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.37128	0.0992	L	0.44542	1.39	0.54753	D	0.99998	D	0.53462	0.96	P	0.61328	0.887	T	0.05599	-1.0875	10	0.36615	T	0.2	-6.1186	11.0856	0.48084	0.0:0.0:0.155:0.845	.	181	Q8IVQ6	ZDH21_HUMAN	G	181	ENSP00000370303:R181G	ENSP00000370303:R181G	R	-	1	2	ZDHHC21	14629974	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.047000	0.41269	1.852000	0.53769	0.477000	0.44152	AGA	.	.		0.333	ZDHHC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051748.2	NM_178566		C	14639974	T	C	14639974	3	2	113	1	0	0	0	0	1	0	0	0	17627	1564	54	2	260	2	ZDHHC21	9	14639974	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	9278211	14639974	126573457	185	18062										
TMEM8B	51754	hgsc.bcm.edu	37	chr9	35853674	35853674	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttggcatatgctcattgcggGcagtgtgggcttcctgctgc	14	10	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:35853674G>T	ENST00000377991.4	+	14	2271	c.1256G>T	c.(1255-1257)gGc>gTc	p.G419V	TMEM8B_ENST00000377988.2_Missense_Mutation_p.G419V	NM_001042589.2	NP_001036054.1	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B	419					cell-matrix adhesion (GO:0007160)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle (GO:0007346)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	7						CTCATTGCGGGCAGTGTGGGC	0.587																																					p.G419V		Atlas-SNP	.											.	TMEM8B	53	.	0			c.G1256T						.						92	93	92					9																	35853674		1975	4142	6117	SO:0001583	missense	51754	exon13			TTGCGGGCAGTGT	BC043384	CCDS6595.1, CCDS43800.1	9p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000137103	ENSG00000137103			21427	protein-coding gene	gene with protein product	"nasopharyngeal carcinoma expressed 6"		"chromosome 9 open reading frame 127"	C9orf127		12918109, 8619474	Standard	NM_016446		Approved	NAG-5, NGX6	uc003zym.4	A6NDV4	OTTHUMG00000019885	ENST00000377991.4:c.1256G>T	chr9.hg19:g.35853674G>T	ENSP00000367230:p.Gly419Val	289.0	0.0		182.0	65.0	NM_001042590	B3KQF3|O75539|Q49AB1|Q4KMX5|Q5TCW5|Q9HBY2|Q9P0U7	Missense_Mutation	SNP	ENST00000377991.4	hg19	CCDS43800.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200632	0.79015	.	.	ENSG00000137103	ENST00000377991;ENST00000377988	T;T	0.41400	1.0;1.0	5.49	5.49	0.81192	.	.	.	.	.	T	0.59770	0.2218	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.51196	-0.8736	9	0.15066	T	0.55	.	17.9596	0.89081	0.0:0.0:1.0:0.0	.	419	A6NDV4	TMM8B_HUMAN	V	419	ENSP00000367230:G419V;ENSP00000367227:G419V	ENSP00000367227:G419V	G	+	2	0	TMEM8B	35843674	1.000000	0.71417	1.000000	0.80357	0.769000	0.43574	6.635000	0.74295	2.583000	0.87209	0.555000	0.69702	GGC	.	.		0.587	TMEM8B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052388.2	NM_016446		T	35853674	G	T	35853674	3	4	113	1	0	0	0	0	1	0	0	0	16230	1203	42	3	1484	3	TMEM8B	9	35853674	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	21213700	35853674	105359757	186	18063										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79322643	79322643	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gaaggctattttcagaccccTtaacgtcaagatttttggtt	8	8	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:79322643T>C	ENST00000376718.3	-	8	4670	c.4547A>G	c.(4546-4548)aAg>aGg	p.K1516R	PRUNE2_ENST00000428286.1_Missense_Mutation_p.K1157R	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1516					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TTCAGACCCCTTAACGTCAAG	0.443																																					p.K1516R		Atlas-SNP	.											PRUNE2_ENST00000376718,colon,carcinoma,0,1	PRUNE2	331	.	0			c.A4547G						.						54	50	51					9																	79322643		1568	3582	5150	SO:0001583	missense	158471	exon8			GACCCCTTAACGT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.4547A>G	chr9.hg19:g.79322643T>C	ENSP00000365908:p.Lys1516Arg	82.0	0.0		65.0	3.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	T	9.083	0.999880	0.19121	.	.	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.51325	0.72;0.71	5.61	3.21	0.36854	.	1.364110	0.04688	N	0.413663	T	0.45216	0.1331	L	0.50333	1.59	0.09310	N	1	B	0.15473	0.013	B	0.12156	0.007	T	0.35773	-0.9775	10	0.59425	D	0.04	-3.0491	7.2601	0.26199	0.0:0.0783:0.3563:0.5654	.	1516	Q8WUY3	PRUN2_HUMAN	R	1516;1157;1515	ENSP00000365908:K1516R;ENSP00000397425:K1157R	ENSP00000365908:K1516R	K	-	2	0	PRUNE2	78512463	0.002000	0.14202	0.000000	0.03702	0.027000	0.11550	1.113000	0.31184	0.471000	0.27319	0.533000	0.62120	AAG	.	.		0.443	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		C	79322643	T	C	79322643	3	2	113	1	0	0	0	0	1	0	0	0	12653	1609	56	2	4767	2	PRUNE2	9	79322643	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	43468969	79322643	61890788	187	18064										
UBQLN1	29979	hgsc.bcm.edu	37	chr9	86276838	86276838	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccagttgttgctgaaatctgActtctggattctgtagctat	9	8	3	2	rs79530639		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:86276838A>G	ENST00000376395.4	-	11	2157	c.1634T>C	c.(1633-1635)gTc>gCc	p.V545A	UBQLN1_ENST00000257468.7_Missense_Mutation_p.V517A	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	545					cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)			breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						CTGAAATCTGACTTCTGGATT	0.363																																					p.V545A	Melanoma(186;1284 2073 12755 14558 18426)	Atlas-SNP	.											.	UBQLN1	49	.	0			c.T1634C						.						126	123	124					9																	86276838		2203	4300	6503	SO:0001583	missense	29979	exon11			AATCTGACTTCTG	AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"Ubiquilin family"	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1634T>C	chr9.hg19:g.86276838A>G	ENSP00000365576:p.Val545Ala	140.0	0.0		103.0	5.0	NM_013438	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Missense_Mutation	SNP	ENST00000376395.4	hg19	CCDS6663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.61|16.61	3.172417|3.172417	0.57584|0.57584	.|.	.|.	ENSG00000135018|ENSG00000135018	ENST00000526134|ENST00000376395;ENST00000257468	.|T;T	.|0.40756	.|1.02;1.02	5.19|5.19	5.19|5.19	0.71726|0.71726	.|UBA-like (1);	.|0.000000	.|0.64402	.|D	.|0.000012	T|T	0.35128|0.35128	0.0921|0.0921	L|L	0.43152|0.43152	1.355|1.355	0.54753|0.54753	D|D	0.99998|0.99998	.|B;B	.|0.27679	.|0.041;0.185	.|B;B	.|0.23419	.|0.036;0.046	T|T	0.11891|0.11891	-1.0569|-1.0569	5|10	.|0.18710	.|T	.|0.47	.|.	15.4206|15.4206	0.75009|0.75009	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|517;545	.|Q9UMX0-2;Q9UMX0	.|.;UBQL1_HUMAN	P|A	152|545;517	.|ENSP00000365576:V545A;ENSP00000257468:V517A	.|ENSP00000257468:V517A	S|V	-|-	1|2	0|0	UBQLN1|UBQLN1	85466658|85466658	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.889000|8.889000	0.92470|0.92470	2.100000|2.100000	0.63781|0.63781	0.472000|0.472000	0.43445|0.43445	TCA|GTC	.	.		0.363	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438		G	86276838	A	G	86276838	3	3	113	1	0	0	0	0	1	0	0	0	16911	275	10	2	139	2	UBQLN1	9	86276838	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	6954195	86276838	54936593	188	18065										
NAA35	60560	hgsc.bcm.edu	37	chr9	88611410	88611410	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aataattaaaagggaagaaaTggtgaactattttgcaagat	9	2	0	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:88611410T>C	ENST00000361671.5	+	12	1107	c.974T>C	c.(973-975)aTg>aCg	p.M325T		NM_024635.3	NP_078911.3	Q5VZE5	NAA35_HUMAN	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	325					negative regulation of apoptotic process (GO:0043066)|smooth muscle cell proliferation (GO:0048659)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	25						AGGGAAGAAATGGTGAACTAT	0.343																																					p.M325T		Atlas-SNP	.											.	NAA35	50	.	0			c.T974C						.						62	66	65					9																	88611410		2203	4297	6500	SO:0001583	missense	60560	exon12			AAGAAATGGTGAA	AK025266	CCDS6673.1	9q22.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000135040	ENSG00000135040		"N(alpha)-acetyltransferase subunits"	24340	protein-coding gene	gene with protein product			"MAK10 homolog, amino-acid N-acetyltransferase subunit (S. cerevisiae)"	MAK10		14702039, 19660095	Standard	NM_024635		Approved	FLJ21613, FLJ22643, bA379P1.1	uc004aoi.4	Q5VZE5	OTTHUMG00000020131	ENST00000361671.5:c.974T>C	chr9.hg19:g.88611410T>C	ENSP00000354972:p.Met325Thr	166.0	0.0		90.0	4.0	NM_024635	Q5VZE6|Q9H631|Q9H703	Missense_Mutation	SNP	ENST00000361671.5	hg19	CCDS6673.1	.	.	.	.	.	.	.	.	.	.	T	9.477	1.097232	0.20552	.	.	ENSG00000135040	ENST00000361671	.	.	.	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.38612	0.1047	N	0.08118	0	0.80722	D	1	B	0.12630	0.006	B	0.04013	0.001	T	0.18871	-1.0323	9	0.33141	T	0.24	-14.6319	15.5547	0.76184	0.0:0.0:0.0:1.0	.	325	Q5VZE5	NAA35_HUMAN	T	325	.	ENSP00000354972:M325T	M	+	2	0	NAA35	87801230	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	7.816000	0.86201	2.144000	0.66660	0.460000	0.39030	ATG	.	.		0.343	NAA35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052906.1	NM_024635		C	88611410	T	C	88611410	3	2	113	1	0	0	0	0	1	0	0	0	10132	1464	51	2	1016	2	NAA35	9	88611410	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2334572	88611410	52602021	189	18066										
BICD2	23299	hgsc.bcm.edu	37	chr9	95481866	95481866	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccgccttttcccgctccatcTgcaaaggcacaggcagcagg	10	16	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:95481866T>C	ENST00000375512.3	-	5	1130		c.e5-2		BICD2_ENST00000356884.6_Splice_Site	NM_015250.3	NP_056065.1	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 (Drosophila)						cell death (GO:0008219)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase binding (GO:0017137)			cervix(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23						CCGCTCCATCTGCAAAGGCAC	0.617																																					.		Atlas-SNP	.											.	BICD2	68	.	0			c.1063-2A>G						.						17	17	17					9																	95481866		2202	4298	6500	SO:0001630	splice_region_variant	23299	exon6			TCCATCTGCAAAG	AB014599	CCDS6700.1, CCDS35064.1	9q22.32	2008-02-05			ENSG00000185963	ENSG00000185963			17208	protein-coding gene	gene with protein product		609797				9734811	Standard	NM_001003800		Approved	KIAA0699	uc004asp.1	Q8TD16	OTTHUMG00000021036	ENST00000375512.3:c.1063-2A>G	chr9.hg19:g.95481866T>C		91.0	0.0		56.0	4.0	NM_001003800	O75181|Q5TBQ2|Q5TBQ3|Q96LH2|Q9BT84|Q9H561	Splice_Site	SNP	ENST00000375512.3	hg19	CCDS6700.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.965675	0.74131	.	.	ENSG00000185963	ENST00000356884;ENST00000375512	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8505	0.57855	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	BICD2	94521687	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	7.933000	0.87642	1.987000	0.57996	0.459000	0.35465	.	.	.		0.617	BICD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055508.1	NM_015250	Intron	C	95481866	T	C	95481866	5	2	113	1	0	0	0	0	0	0	1	0	1429	1594	55	2	1528	2	BICD2	9	95481866	Splice_Site	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	6870456	95481866	45731565	190	18067										
ABCA1	19	hgsc.bcm.edu	37	chr9	107568697	107568697	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tccactcttcctcccctgccTggcagggcgtgtctctgcaa	9	17	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:107568697T>C	ENST00000374736.3	-	31	4683	c.4289A>G	c.(4288-4290)cAg>cGg	p.Q1430R		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1430					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CTCCCCTGCCTGGCAGGGCGT	0.557																																					p.Q1430R		Atlas-SNP	.											.	ABCA1	244	.	0			c.A4289G						.						95	74	81					9																	107568697		2203	4300	6503	SO:0001583	missense	19	exon31			CCTGCCTGGCAGG	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.4289A>G	chr9.hg19:g.107568697T>C	ENSP00000363868:p.Gln1430Arg	170.0	0.0		71.0	4.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	T	9.465	1.093997	0.20471	.	.	ENSG00000165029	ENST00000374736	D	0.94613	-3.47	5.75	-7.26	0.01466	.	1.041540	0.07498	N	0.906744	T	0.81273	0.4788	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.71364	-0.4615	10	0.16420	T	0.52	.	8.078	0.30729	0.2853:0.0:0.5128:0.2019	.	1430	O95477	ABCA1_HUMAN	R	1430	ENSP00000363868:Q1430R	ENSP00000363868:Q1430R	Q	-	2	0	ABCA1	106608518	0.001000	0.12720	0.146000	0.22360	0.064000	0.16182	0.562000	0.23531	-0.915000	0.03823	-0.445000	0.05633	CAG	.	.		0.557	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		C	107568697	T	C	107568697	3	2	113	1	0	0	0	0	1	0	0	0	28	1580	55	2	2576	2	ABCA1	9	107568697	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	12086831	107568697	33644734	191	18068										
ABCA1	19	hgsc.bcm.edu	37	chr9	107583711	107583711	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caggttctgccggatggtgcTcatctcagagcgaatgtctt	12	10	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:107583711T>C	ENST00000374736.3	-	20	3299	c.2905A>G	c.(2905-2907)Agc>Ggc	p.S969G		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	969	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CGGATGGTGCTCATCTCAGAG	0.527																																					p.S969G		Atlas-SNP	.											.	ABCA1	244	.	0			c.A2905G						.						81	65	70					9																	107583711		2203	4300	6503	SO:0001583	missense	19	exon20			TGGTGCTCATCTC	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.2905A>G	chr9.hg19:g.107583711T>C	ENSP00000363868:p.Ser969Gly	118.0	0.0		87.0	4.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.582464	0.65992	.	.	ENSG00000165029	ENST00000374736	D	0.93953	-3.32	5.7	5.7	0.88788	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.193654	0.64402	D	0.000004	D	0.89054	0.6606	N	0.21448	0.665	0.80722	D	1	B	0.14012	0.009	B	0.21360	0.034	D	0.85321	0.1084	10	0.59425	D	0.04	.	15.96	0.79923	0.0:0.0:0.0:1.0	.	969	O95477	ABCA1_HUMAN	G	969	ENSP00000363868:S969G	ENSP00000363868:S969G	S	-	1	0	ABCA1	106623532	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.289000	0.72696	2.165000	0.68154	0.460000	0.39030	AGC	.	.		0.527	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		C	107583711	T	C	107583711	3	2	113	1	0	0	0	0	1	0	0	0	28	1551	54	2	4004	2	ABCA1	9	107583711	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	15014	107583711	33629720	192	18069										
CTNNAL1	8727	hgsc.bcm.edu	37	chr9	111734974	111734974	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cctcaacaagctgctctttcTgttcagagagtttacaggca	8	11	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:111734974T>C	ENST00000325551.4	-	9	1414	c.1328A>G	c.(1327-1329)cAg>cGg	p.Q443R	CTNNAL1_ENST00000325580.6_Intron|CTNNAL1_ENST00000488130.1_5'UTR|CTNNAL1_ENST00000374595.4_Missense_Mutation_p.Q443R	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	443					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		CTGCTCTTTCTGTTCAGAGAG	0.343																																					p.Q443R		Atlas-SNP	.											.	CTNNAL1	51	.	0			c.A1328G						.						110	113	112					9																	111734974		2203	4300	6503	SO:0001583	missense	8727	exon9			TCTTTCTGTTCAG	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.1328A>G	chr9.hg19:g.111734974T>C	ENSP00000320434:p.Gln443Arg	108.0	0.0		75.0	4.0	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	hg19	CCDS6775.1	.	.	.	.	.	.	.	.	.	.	T	19.01	3.744326	0.69418	.	.	ENSG00000119326	ENST00000374595;ENST00000325551	T;T	0.36157	1.27;1.27	6.17	6.17	0.99709	.	0.049382	0.85682	D	0.000000	T	0.49098	0.1537	M	0.63428	1.95	0.80722	D	1	D;P;D	0.53619	0.961;0.778;0.961	P;P;P	0.54924	0.764;0.452;0.764	T	0.36841	-0.9731	10	0.22706	T	0.39	-11.7007	14.7743	0.69713	0.0:0.0:0.0:1.0	.	443;443;443	B2RBI4;Q9UBT7-2;Q9UBT7	.;.;CTNL1_HUMAN	R	443	ENSP00000363723:Q443R;ENSP00000320434:Q443R	ENSP00000320434:Q443R	Q	-	2	0	CTNNAL1	110774795	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.702000	0.68332	2.371000	0.80710	0.533000	0.62120	CAG	.	.		0.343	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		C	111734974	T	C	111734974	3	2	113	1	0	0	0	0	1	0	0	0	4017	1580	55	2	920	2	CTNNAL1	9	111734974	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	4151263	111734974	29478457	193	18070										
C9orf43	257169	hgsc.bcm.edu	37	chr9	116187645	116187645	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttacaggaaacagcagcagcGgcagcagcagcagcagcagc	13	12	0	0	rs527300639|rs371732185		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:116187645G>A	ENST00000288462.4	+	10	1333	c.887G>A	c.(886-888)cGg>cAg	p.R296Q	C9orf43_ENST00000374165.1_Missense_Mutation_p.R296Q	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	296	Gln-rich.									breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						cagcagcagcggcagcagcag	0.547																																					p.R296Q		Atlas-SNP	.											C9orf43,colon,carcinoma,0,1	C9orf43	49	.	0			c.G887A						.						62	64	63					9																	116187645		2203	4300	6503	SO:0001583	missense	257169	exon10			AGCAGCGGCAGCA	BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.887G>A	chr9.hg19:g.116187645G>A	ENSP00000288462:p.Arg296Gln	123.0	1.0		65.0	6.0	NM_152786		Missense_Mutation	SNP	ENST00000288462.4	hg19	CCDS6796.1	.	.	.	.	.	.	.	.	.	.	G	0.045	-1.269215	0.01421	.	.	ENSG00000157653	ENST00000374165;ENST00000288462	T;T	0.41758	0.99;0.99	2.74	-2.81	0.05805	.	3.844300	0.00357	N	0.000029	T	0.22936	0.0554	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.01281	0.0	T	0.14117	-1.0484	10	0.22109	T	0.4	.	8.4134	0.32657	0.3379:0.0:0.6621:0.0	.	296	Q8TAL5	CI043_HUMAN	Q	296	ENSP00000363280:R296Q;ENSP00000288462:R296Q	ENSP00000288462:R296Q	R	+	2	0	C9orf43	115227466	0.000000	0.05858	0.000000	0.03702	0.133000	0.20885	-0.501000	0.06398	-0.639000	0.05502	-0.379000	0.06801	CGG	.	.		0.547	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053739.1	NM_152786		A	116187645	G	A	116187645	3	1	113	1	0	0	0	0	1	0	0	0	2485	1116	39	1	921	1	C9orf43	9	116187645	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	4452671	116187645	25025786	194	18071										
PSMD5	5711	hgsc.bcm.edu	37	chr9	123589185	123589185	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	accatttctatacaggtggcTctaaaatgtcagaaggacaa	8	8	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:123589185T>C	ENST00000210313.3	-	6	746	c.672A>G	c.(670-672)agA>agG	p.R224R	PSMD5_ENST00000373904.5_Splice_Site_p.R181R|PSMD5-AS1_ENST00000589026.1_RNA	NM_001270427.1|NM_005047.3	NP_001257356.1|NP_005038.1	Q16401	PSMD5_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	224					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome regulatory particle assembly (GO:0070682)|protein folding (GO:0006457)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)				endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|prostate(1)	10						TACAGGTGGCTCTAAAATGTC	0.338																																					p.R224R		Atlas-SNP	.											.	PSMD5	34	.	0			c.A672G						.						84	84	84					9																	123589185		2203	4300	6503	SO:0001630	splice_region_variant	5711	exon6			GGTGGCTCTAAAA	AK001065	CCDS6824.1, CCDS59143.1	9q34.11	2008-02-05			ENSG00000095261	ENSG00000095261		"Proteasome (prosome, macropain) subunits"	9563	protein-coding gene	gene with protein product		604452				7559544	Standard	NM_005047		Approved	S5B, KIAA0072	uc004bko.4	Q16401	OTTHUMG00000020573	ENST00000210313.3:c.672-1A>G	chr9.hg19:g.123589185T>C		132.0	0.0		75.0	4.0	NM_005047	B4DZM8|Q15045|Q4VXG8	Silent	SNP	ENST00000210313.3	hg19	CCDS6824.1																																																																																			.	.		0.338	PSMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053825.2	NM_005047	Silent	C	123589185	T	C	123589185	5	2	113	1	0	0	0	0	0	0	1	0	12713	1565	54	2	862	2	PSMD5	9	123589185	Splice_Site	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	7401540	123589185	17624246	195	18072										
CEP110	11064	hgsc.bcm.edu	37	chr9	123857201	123857201	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gaaaaatgtgttaaacttgaAgtactgaatctcagctataa	7	5	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:123857201A>G	ENST00000373855.1	+	5	644	c.384A>G	c.(382-384)gaA>gaG	p.E128E	CNTRL_ENST00000373865.2_Silent_p.E128E|CNTRL_ENST00000238341.5_Silent_p.E128E			Q7Z7A1	CNTRL_HUMAN	centriolin	128					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						TTAAACTTGAAGTACTGAATC	0.294																																					p.E128E		Atlas-SNP	.											.	CNTRL	161	.	0			c.A384G						.						76	79	78					9																	123857201		2202	4296	6498	SO:0001819	synonymous_variant	11064	exon3			ACTTGAAGTACTG	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.384A>G	chr9.hg19:g.123857201A>G		102.0	0.0		54.0	4.0	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Silent	SNP	ENST00000373855.1	hg19	CCDS35118.1																																																																																			.	.		0.294	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123857201	A	G	123857201	2	3	113	1	0	0	0	0	0	0	0	1	3247	69	3	2		2	CEP110	9	123857201	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	268016	123857201	17356230	196	18073										
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139395092	139395092	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgttggcatctgcgctggccTccagcaggcgcttggcggca	15	13	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:139395092T>C	ENST00000277541.6	-	31	5921	c.5846A>G	c.(5845-5847)gAg>gGg	p.E1949G		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1949	HIF1AN-binding. {ECO:0000250}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGCGCTGGCCTCCAGCAGGCG	0.677			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.E1949G		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.A5846G						.						88	107	101					9																	139395092		2195	4299	6494	SO:0001583	missense	4851	exon31			CTGGCCTCCAGCA	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5846A>G	chr9.hg19:g.139395092T>C	ENSP00000277541:p.Glu1949Gly	201.0	0.0		117.0	5.0	NM_017617	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	hg19	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	T	32	5.185029	0.94885	.	.	ENSG00000148400	ENST00000277541	T	0.68765	-0.35	4.68	4.68	0.58851	Ankyrin repeat-containing domain (3);	0.051864	0.85682	D	0.000000	T	0.75443	0.3850	M	0.71871	2.18	0.80722	D	1	D	0.55800	0.973	P	0.54924	0.764	T	0.79553	-0.1756	10	0.87932	D	0	.	13.646	0.62281	0.0:0.0:0.0:1.0	.	1949	P46531	NOTC1_HUMAN	G	1949	ENSP00000277541:E1949G	ENSP00000277541:E1949G	E	-	2	0	NOTCH1	138514913	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.797000	0.85911	1.881000	0.54492	0.454000	0.30748	GAG	.	.		0.677	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		C	139395092	T	C	139395092	3	2	113	1	0	0	0	0	1	0	0	0	10556	1551	54	2	1837	2	NOTCH1	9	139395092	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	15537891	139395092	1818339	197	18074										
ABCA2	20	hgsc.bcm.edu	37	chr9	139913717	139913717	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atgttgagccagacctgggcAtagtgagtcacgttgcccac	12	11	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr9:139913717A>G	ENST00000371605.3	-	10	1611	c.1464T>C	c.(1462-1464)taT>taC	p.Y488Y	ABCA2_ENST00000492260.1_5'UTR|ABCA2_ENST00000341511.6_Silent_p.Y489Y|ABCA2_ENST00000265662.5_Silent_p.Y489Y			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	488					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		AGACCTGGGCATAGTGAGTCA	0.637																																					p.Y519Y		Atlas-SNP	.											.	ABCA2	113	.	0			c.T1557C						.						39	46	44					9																	139913717		2069	4201	6270	SO:0001819	synonymous_variant	20	exon11			CTGGGCATAGTGA	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.1464T>C	chr9.hg19:g.139913717A>G		159.0	0.0		84.0	4.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	hg19		.	.	.	.	.	.	.	.	.	.	a	10.84	1.464995	0.26335	.	.	ENSG00000107331	ENST00000470535	.	.	.	3.58	-2.81	0.05805	.	.	.	.	.	T	0.56093	0.1962	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54820	-0.8236	4	.	.	.	.	11.4306	0.50038	0.5697:0.0:0.4303:0.0	.	.	.	.	R	100	.	.	C	-	1	0	ABCA2	139033538	0.950000	0.32346	0.956000	0.39512	0.992000	0.81027	0.002000	0.13061	-0.412000	0.07519	0.398000	0.26397	TGC	.	.		0.637	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		G	139913717	A	G	139913717	2	3	113	1	0	0	0	0	0	0	0	1	32	224	8	2		2	ABCA2	9	139913717	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	518625	139913717	1299714	198	18075										
CUBN	8029	hgsc.bcm.edu	37	chr10	16970249	16970249	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tccagtagaccggatgggccCagggatctctctgccacaga	12	13	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr10:16970249C>T	ENST00000377833.4	-	41	6243	c.6178G>A	c.(6178-6180)Ggg>Agg	p.G2060R		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2060	CUB 14. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CGGATGGGCCCAGGGATCTCT	0.478																																					p.G2060R		Atlas-SNP	.											CUBN,NS,carcinoma,0,1	CUBN	515	.	0			c.G6178A						.						70	66	67					10																	16970249		2203	4300	6503	SO:0001583	missense	8029	exon41			TGGGCCCAGGGAT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.6178G>A	chr10.hg19:g.16970249C>T	ENSP00000367064:p.Gly2060Arg	124.0	0.0		75.0	3.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.903129	0.52333	.	.	ENSG00000107611	ENST00000377833	T	0.17528	2.27	5.7	4.8	0.61643	CUB (5);	0.158715	0.29737	N	0.011330	T	0.38134	0.1029	L	0.59912	1.85	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.14504	-1.0470	10	0.59425	D	0.04	.	14.7134	0.69249	0.0:0.9304:0.0:0.0696	.	2060	O60494	CUBN_HUMAN	R	2060	ENSP00000367064:G2060R	ENSP00000367064:G2060R	G	-	1	0	CUBN	17010255	0.998000	0.40836	0.351000	0.25721	0.011000	0.07611	5.390000	0.66261	1.427000	0.47276	-0.145000	0.13849	GGG	.	.		0.478	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	16970249	C	T	16970249	3	4	113	1	0	0	0	0	1	0	0	0	4053	594	21	3	4801	3	CUBN	10	16970249	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10		16970249	118564498	199	18076										
NEBL	10529	hgsc.bcm.edu	37	chr10	21134258	21134258	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtctaaatccagtgatgaccTtcctttaatctccttctcaa	4	12	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr10:21134258T>C	ENST00000377122.4	-	12	1552	c.1156A>G	c.(1156-1158)Agg>Ggg	p.R386G	NEBL_ENST00000377159.4_Intron|NEBL_ENST00000417816.2_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	386					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AGTGATGACCTTCCTTTAATC	0.323																																					p.R386G		Atlas-SNP	.											.	NEBL	199	.	0			c.A1156G						.						127	125	126					10																	21134258		2203	4300	6503	SO:0001583	missense	10529	exon12			ATGACCTTCCTTT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1156A>G	chr10.hg19:g.21134258T>C	ENSP00000366326:p.Arg386Gly	105.0	0.0		74.0	6.0	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	hg19	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	T	15.65	2.897608	0.52121	.	.	ENSG00000078114	ENST00000377122	T	0.04970	3.52	5.99	4.83	0.62350	.	0.341407	0.33772	N	0.004580	T	0.10035	0.0246	M	0.64997	1.995	0.80722	D	1	B	0.26081	0.141	B	0.33121	0.158	T	0.08310	-1.0728	10	0.27785	T	0.31	.	11.0863	0.48089	0.0:0.0:0.1552:0.8448	.	386	O76041	NEBL_HUMAN	G	386	ENSP00000366326:R386G	ENSP00000366326:R386G	R	-	1	2	NEBL	21174264	1.000000	0.71417	0.985000	0.45067	0.983000	0.72400	2.757000	0.47557	1.053000	0.40415	0.533000	0.62120	AGG	.	.		0.323	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		C	21134258	T	C	21134258	3	2	113	1	0	0	0	0	1	0	0	0	10312	1608	56	2	1956	2	NEBL	10	21134258	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	4164009	21134258	114400489	200	18077										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24834953	24834953	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaccctctcagcccccaaacAggaccacctgctcactctgc	5	20	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr10:24834953A>T	ENST00000376454.3	+	21	5562	c.5532A>T	c.(5530-5532)acA>acT	p.T1844T	KIAA1217_ENST00000376451.2_3'UTR|KIAA1217_ENST00000458595.1_Silent_p.T1250T|KIAA1217_ENST00000376452.3_Silent_p.T1275T|KIAA1217_ENST00000396445.1_3'UTR|KIAA1217_ENST00000376462.1_Silent_p.T1165T	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1844	Ser-rich. {ECO:0000255}.				embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						GCCCCCAAACAGGACCACCTG	0.493																																					p.T1844T		Atlas-SNP	.											.	KIAA1217	235	.	0			c.A5532T						.						192	199	197					10																	24834953		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon21			CCAAACAGGACCA	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.5532A>T	chr10.hg19:g.24834953A>T		346.0	0.0		196.0	73.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	hg19	CCDS31165.1																																																																																			.	.		0.493	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		T	24834953	A	T	24834953	2	4	113	1	0	0	0	0	0	0	0	1	8225	175	7	4		4	KIAA1217	10	24834953	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3700695	24834953	110699794	201	18078										
CDHR1	92211	hgsc.bcm.edu	37	chr10	85972881	85972881	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgcagaggaacccaacaaccTggtggactattccatcaccc	8	14	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr10:85972881T>C	ENST00000372117.3	+	16	1920	c.1817T>C	c.(1816-1818)cTg>cCg	p.L606P	CDHR1_ENST00000440770.2_Missense_Mutation_p.L310P|CDHR1_ENST00000332904.3_Missense_Mutation_p.L606P	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	606	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						CCCAACAACCTGGTGGACTAT	0.552																																					p.L606P		Atlas-SNP	.											.	CDHR1	122	.	0			c.T1817C						.						123	107	113					10																	85972881		2203	4300	6503	SO:0001583	missense	92211	exon16			ACAACCTGGTGGA	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1817T>C	chr10.hg19:g.85972881T>C	ENSP00000361189:p.Leu606Pro	143.0	0.0		114.0	5.0	NM_001171971	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	hg19	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.120240	0.77323	.	.	ENSG00000148600	ENST00000332904;ENST00000372117;ENST00000440770	T;T;T	0.52295	0.67;0.67;0.67	5.93	5.93	0.95920	Cadherin (4);Cadherin-like (1);	0.257738	0.38897	N	0.001533	T	0.63022	0.2476	M	0.63843	1.955	0.80722	D	1	D;D;D	0.69078	0.997;0.991;0.997	D;P;D	0.65773	0.93;0.861;0.938	T	0.59984	-0.7351	10	0.29301	T	0.29	-16.2473	14.3318	0.66561	0.0:0.0:0.0:1.0	.	310;606;606	E7EN47;Q96JP9-2;Q96JP9	.;.;CDHR1_HUMAN	P	606;606;310	ENSP00000331063:L606P;ENSP00000361189:L606P;ENSP00000415980:L310P	ENSP00000331063:L606P	L	+	2	0	CDHR1	85962861	1.000000	0.71417	0.998000	0.56505	0.794000	0.44872	7.580000	0.82523	2.271000	0.75665	0.533000	0.62120	CTG	.	.		0.552	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		C	85972881	T	C	85972881	3	2	113	1	0	0	0	0	1	0	0	0	3120	1580	55	2	1879	2	CDHR1	10	85972881	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	61137928	85972881	49561866	202	18079										
FAM190B	54462	hgsc.bcm.edu	37	chr10	86131960	86131960	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaccagaccatgaaacatgaTgctaaaatgagatacctgag	8	8	0	5			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr10:86131960T>C	ENST00000224756.8	+	2	1337	c.1152T>C	c.(1150-1152)gaT>gaC	p.D384D	CCSER2_ENST00000359979.4_Silent_p.D384D|CCSER2_ENST00000372088.2_Silent_p.D384D	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	384					microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)											TGAAACATGATGCTAAAATGA	0.353																																					p.D384D		Atlas-SNP	.											.	CCSER2	7	.	0			c.T1152C						.						104	100	101					10																	86131960		2203	4300	6503	SO:0001819	synonymous_variant	54462	exon2			ACATGATGCTAAA		CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771			29197	protein-coding gene	gene with protein product			"KIAA1128", "family with sequence similarity 190, member B"	KIAA1128, FAM190B		10574461	Standard	XM_005269905		Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.1152T>C	chr10.hg19:g.86131960T>C		118.0	0.0		98.0	4.0	NM_018999	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Silent	SNP	ENST00000224756.8	hg19	CCDS31235.1																																																																																			.	.		0.353	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999		C	86131960	T	C	86131960	2	2	113	1	0	0	0	0	0	0	0	1	5527	1461	51	2		2	FAM190B	10	86131960	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	159079	86131960	49402787	203	18080										
HELLS	3070	hgsc.bcm.edu	37	chr10	96354567	96354567	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cgatcagaaaattgtggaaaGagcagctgctaaaaggaaac	11	6	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr10:96354567G>A	ENST00000348459.5	+	19	2309	c.2204G>A	c.(2203-2205)aGa>aAa	p.R735K	HELLS_ENST00000371332.4_Missense_Mutation_p.R781K|HELLS_ENST00000394045.1_Missense_Mutation_p.R637K|RP11-119K6.6_ENST00000432120.1_RNA|HELLS_ENST00000394036.1_3'UTR|HELLS_ENST00000239026.6_3'UTR	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		ATTGTGGAAAGAGCAGCTGCT	0.368																																					p.R735K		Atlas-SNP	.											.	HELLS	63	.	0			c.G2204A						.						107	97	100					10																	96354567		2203	4300	6503	SO:0001583	missense	3070	exon19			TGGAAAGAGCAGC	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6", "proliferation-associated SNF2-like protein"	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.2204G>A	chr10.hg19:g.96354567G>A	ENSP00000239027:p.Arg735Lys	102.0	0.0		90.0	5.0	NM_018063		Missense_Mutation	SNP	ENST00000348459.5	hg19	CCDS7434.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.894364	0.91889	.	.	ENSG00000119969	ENST00000348459;ENST00000394045;ENST00000371332;ENST00000371327	D;D;D;D	0.95307	-3.67;-3.67;-3.67;-3.67	5.98	5.98	0.97165	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95822	0.8640	L	0.35793	1.09	0.80722	D	1	B;B;P;D;D	0.67145	0.289;0.415;0.712;0.996;0.996	B;B;B;D;P	0.76071	0.12;0.133;0.396;0.987;0.871	D	0.95501	0.8577	10	0.51188	T	0.08	-20.3011	19.4463	0.94849	0.0:0.0:1.0:0.0	.	719;706;605;637;735	Q9NRZ9-2;Q6I7N8;Q9NRZ9-6;Q9NRZ9-5;Q9NRZ9	.;.;.;.;HELLS_HUMAN	K	735;637;781;172	ENSP00000239027:R735K;ENSP00000377609:R637K;ENSP00000360383:R781K;ENSP00000360378:R172K	ENSP00000239027:R735K	R	+	2	0	HELLS	96344557	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.684000	0.74538	2.835000	0.97688	0.650000	0.86243	AGA	.	.		0.368	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		A	96354567	G	A	96354567	3	1	113	1	0	0	0	0	1	0	0	0	7055	942	33	3	2278	3	HELLS	10	96354567	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	10222607	96354567	39180180	204	18081										
SMNDC1	10285	hgsc.bcm.edu	37	chr10	112063340	112063340	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agctgctttgctaaatcctcTgacatctagggaaaataaaa	7	8	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr10:112063340T>C	ENST00000369603.5	-	2	209	c.6A>G	c.(4-6)tcA>tcG	p.S2S	SMNDC1_ENST00000471297.1_5'UTR|SMNDC1_ENST00000369592.1_Silent_p.S2S	NM_005871.3	NP_005862.1	O75940	SPF30_HUMAN	survival motor neuron domain containing 1	2					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	4		Breast(234;0.174)		Epithelial(162;6.86e-05)|all cancers(201;0.00149)|BRCA - Breast invasive adenocarcinoma(275;0.119)		CTAAATCCTCTGACATCTAGG	0.383																																					p.S2S		Atlas-SNP	.											.	SMNDC1	9	.	0			c.A6G						.						63	64	64					10																	112063340		2203	4300	6503	SO:0001819	synonymous_variant	10285	exon2			ATCCTCTGACATC	AF083385	CCDS7565.1	10q23	2013-01-23			ENSG00000119953	ENSG00000119953		"Tudor domain containing"	16900	protein-coding gene	gene with protein product	"splicing factor 30, survival of motor neuron-related", "tudor domain containing 16C"	603519				9731529, 9817934	Standard	NM_005871		Approved	SPF30, SMNR, TDRD16C	uc001kzc.4	O75940	OTTHUMG00000019036	ENST00000369603.5:c.6A>G	chr10.hg19:g.112063340T>C		85.0	0.0		69.0	4.0	NM_005871	B2RA27|D3DRB1|Q5T3K6	Silent	SNP	ENST00000369603.5	hg19	CCDS7565.1																																																																																			.	.		0.383	SMNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050325.2	NM_005871		C	112063340	T	C	112063340	2	2	113	1	0	0	0	0	0	0	0	1	14814	1567	55	2		2	SMNDC1	10	112063340	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	15708773	112063340	23471407	205	18082										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135012267	135012267	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcttggggcgtcagtgcagcGtgactcagcccagggccgcc	15	14	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr10:135012267G>A	ENST00000304613.3	+	14	2276	c.2255G>A	c.(2254-2256)cGt>cAt	p.R752H	KNDC1_ENST00000368572.2_Missense_Mutation_p.R752H|KNDC1_ENST00000368571.2_Missense_Mutation_p.R687H			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	752	Pro-rich.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TCAGTGCAGCGTGACTCAGCC	0.746																																					p.R752H		Atlas-SNP	.											.	KNDC1	155	.	0			c.G2255A						.						6	9	8					10																	135012267		2118	4187	6305	SO:0001583	missense	85442	exon14			TGCAGCGTGACTC	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.2255G>A	chr10.hg19:g.135012267G>A	ENSP00000304437:p.Arg752His	37.0	0.0		43.0	13.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.207072	0.39003	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.19532	2.66;2.66;2.14	3.11	-2.94	0.05581	.	15.918900	0.00639	U	0.000517	T	0.12689	0.0308	L	0.27053	0.805	0.09310	N	1	B;B;B	0.13145	0.007;0.006;0.003	B;B;B	0.06405	0.002;0.001;0.001	T	0.13845	-1.0494	10	0.14656	T	0.56	0.1441	4.1452	0.10212	0.3653:0.3857:0.2491:0.0	.	752;687;752	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	H	752;752;687	ENSP00000304437:R752H;ENSP00000357561:R752H;ENSP00000357560:R687H	ENSP00000304437:R752H	R	+	2	0	KNDC1	134862257	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.305000	0.08188	-0.654000	0.05394	0.306000	0.20318	CGT	.	.		0.746	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	135012267	G	A	135012267	3	1	113	1	0	0	0	0	1	0	0	0	8435	1145	40	1	2309	1	KNDC1	10	135012267	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	22948927	135012267	522480	206	18083										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1256342	1256342	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aggaaccggaggtgggagtgCagccaccggctctgcctggg	18	11	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:1256342C>T	ENST00000529681.1	+	22	2716	c.2658C>T	c.(2656-2658)tgC>tgT	p.C886C	MUC5B_ENST00000447027.1_Silent_p.C889C	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	886	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GGTGGGAGTGCAGCCACCGGC	0.652																																					p.C886C		Atlas-SNP	.											.	MUC5B	473	.	0			c.C2658T						.						41	49	47					11																	1256342		2099	4219	6318	SO:0001819	synonymous_variant	727897	exon22			GGAGTGCAGCCAC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.2658C>T	chr11.hg19:g.1256342C>T		137.0	0.0		100.0	48.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1256342	C	T	1256342	2	4	113	1	0	0	0	0	0	0	0	1	9988	718	25	3		3	MUC5B	11	1256342	Silent	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10		1256342	133750174	207	18084										
RRM1	6240	hgsc.bcm.edu	37	chr11	4142990	4142990	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcatgaaacgagtggagactAatcaggtgagagataggtac	13	5	2	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:4142990A>T	ENST00000300738.5	+	10	1237	c.1033A>T	c.(1033-1035)Aat>Tat	p.N345Y	RRM1_ENST00000534285.1_Missense_Mutation_p.N123Y|RRM1_ENST00000423050.2_Missense_Mutation_p.N248Y|RRM1_ENST00000537197.1_Missense_Mutation_p.N7Y|RRM1_ENST00000528470.1_3'UTR	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	345					cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	AGTGGAGACTAATCAGGTGAG	0.408																																					p.N345Y	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.A1033T						.						95	101	99					11																	4142990		2201	4298	6499	SO:0001583	missense	6240	exon10			GAGACTAATCAGG	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"ribonucleotide reductase M1 polypeptide"			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.1033A>T	chr11.hg19:g.4142990A>T	ENSP00000300738:p.Asn345Tyr	209.0	0.0		101.0	42.0	NM_001033	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	hg19	CCDS7750.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631683	0.87660	.	.	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	5.4	5.4	0.78164	Ribonucleoside-diphosphate reductase, alpha subunit (1);Ribonucleotide reductase large subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.74321	0.3701	H	0.97131	3.945	0.80722	D	1	D	0.69078	0.997	P	0.55545	0.778	D	0.84232	0.0467	10	0.87932	D	0	-21.6001	14.6003	0.68435	1.0:0.0:0.0:0.0	.	345	P23921	RIR1_HUMAN	Y	345;248;258;123;123;7	ENSP00000300738:N345Y;ENSP00000390539:N248Y;ENSP00000431464:N123Y;ENSP00000442148:N7Y	ENSP00000300738:N345Y	N	+	1	0	RRM1	4099566	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.962000	0.93254	2.030000	0.59900	0.528000	0.53228	AAT	.	.		0.408	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		T	4142990	A	T	4142990	3	4	113	1	0	0	0	0	1	0	0	0	13696	362	13	4	1071	4	RRM1	11	4142990	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2886648	4142990	130863526	208	18085										
UBQLN3	50613	hgsc.bcm.edu	37	chr11	5528949	5528949	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagctgcacctgaaagtgagCctcaggctgcagctgctggg	14	12	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:5528949C>G	ENST00000311659.4	-	2	1987	c.1840G>C	c.(1840-1842)Gct>Cct	p.A614P	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_5'Flank|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_5'Flank	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	614	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.									NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGAAAGTGAGCCTCAGGCTGC	0.562																																					p.A614P	Ovarian(72;684 1260 12332 41642 52180)	Atlas-SNP	.											.	UBQLN3	107	.	0			c.G1840C						.						59	64	62					11																	5528949		2201	4297	6498	SO:0001583	missense	50613	exon2			AGTGAGCCTCAGG	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"Ubiquilin family"	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.1840G>C	chr11.hg19:g.5528949C>G	ENSP00000347997:p.Ala614Pro	126.0	0.0		70.0	29.0	NM_017481	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	hg19	CCDS7758.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.964841	0.53507	.	.	ENSG00000175520	ENST00000311659	T	0.40476	1.03	5.14	-0.928	0.10448	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (1);UBA-like (1);	0.274307	0.25845	N	0.027932	T	0.31231	0.0790	L	0.50333	1.59	0.28172	N	0.928542	P	0.46395	0.877	B	0.38562	0.276	T	0.31223	-0.9951	10	0.72032	D	0.01	-1.2028	9.3221	0.37971	0.0:0.5256:0.0:0.4744	.	614	Q9H347	UBQL3_HUMAN	P	614	ENSP00000347997:A614P	ENSP00000347997:A614P	A	-	1	0	UBQLN3	5485525	0.990000	0.36364	0.683000	0.30040	0.969000	0.65631	1.652000	0.37313	-0.193000	0.10415	-0.136000	0.14681	GCT	.	.		0.562	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		G	5528949	C	G	5528949	3	3	113	1	0	0	0	0	1	0	0	0	16913	739	26	4	131	4	UBQLN3	11	5528949	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	1385959	5528949	129477567	209	18086										
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411941	6411942	+	Missense_Mutation	DNP	CG	CG	GC													0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttggatgggcctggtgctggCgctggcgctggcgctggcgc					rs550365194|rs550067660|rs71467507|rs78250081|rs558809956|rs3838786	byFrequency	TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:6411941_6411942CG>GC	ENST00000342245.4	+	1	281_282	c.113_114CG>GC	c.(112-114)gCG>gGC	p.A38G	SMPD1_ENST00000527275.1_Missense_Mutation_p.A38G|SMPD1_ENST00000299397.3_Missense_Mutation_p.A38G|SMPD1_ENST00000356761.2_Missense_Mutation_p.A38G|SMPD1_ENST00000533196.1_3'UTR	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	38					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	ctggtgctggcgctggcgctgg	0.708																																					p.A38G|p.A38A		Atlas-SNP	.											.	SMPD1	108	.	0			c.C113G|c.G114C						.																																			SO:0001583	missense	6609	exon1			TGCTGGCGCTGGC|GCTGGCGCTGGCG	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	Exception_encountered	chr11.hg19:g.6411941_6411942delinsGC	ENSP00000340409:p.Ala38Gly	0.0	0.0		19.0	7.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation|Silent	SNP	ENST00000342245.4	hg19	CCDS44531.1																																																																																			.	.		0.708	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		GC	6411942	CG	GC	6411941	3	3	113	1	0	0	0	0	1	0	0	0	14819	768	27	4	115	4	SMPD1	11	6411941	Missense_Mutation	DNP	CG	TCGA-DD-A39Z-01A-11D-A20W-10	882992	6411941	128594575	210	18087										
CYB5R2	51700	hgsc.bcm.edu	37	chr11	7687733	7687733	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gttgaactggtctgggtgagTcctggcaatttcttcaagct	12	8	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:7687733T>C	ENST00000533558.1	-	8	1163	c.607A>G	c.(607-609)Act>Gct	p.T203A	CYB5R2_ENST00000299497.9_Missense_Mutation_p.T203A|CYB5R2_ENST00000299498.6_Missense_Mutation_p.T203A|CYB5R2_ENST00000524790.1_Missense_Mutation_p.T203A|CYB5R2_ENST00000528585.1_Intron			Q6BCY4	NB5R2_HUMAN	cytochrome b5 reductase 2	203					oxidation-reduction process (GO:0055114)|sterol biosynthetic process (GO:0016126)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11				Epithelial(150;5.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TCTGGGTGAGTCCTGGCAATT	0.517											OREG0020724	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T203A		Atlas-SNP	.											.	CYB5R2	23	.	0			c.A607G						.						178	157	164					11																	7687733		2201	4296	6497	SO:0001583	missense	51700	exon8			GGTGAGTCCTGGC	AF169802	CCDS7780.1	11p15.4	2014-08-12			ENSG00000166394	ENSG00000166394	1.6.2.2		24376	protein-coding gene	gene with protein product		608342				10611283	Standard	XM_005252973		Approved		uc001mfm.3	Q6BCY4	OTTHUMG00000165665	ENST00000533558.1:c.607A>G	chr11.hg19:g.7687733T>C	ENSP00000437041:p.Thr203Ala	168.0	0.0	643	81.0	4.0	NM_016229	Q9BVA3|Q9UF68|Q9UHJ0	Missense_Mutation	SNP	ENST00000533558.1	hg19	CCDS7780.1	.	.	.	.	.	.	.	.	.	.	T	3.364	-0.129798	0.06753	.	.	ENSG00000166394	ENST00000524790;ENST00000299498;ENST00000533558;ENST00000299497	D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05	5.79	3.49	0.39957	Oxidoreductase FAD/NAD(P)-binding (1);	0.372921	0.32081	N	0.006610	T	0.60958	0.2309	N	0.01751	-0.74	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.50224	-0.8853	10	0.19590	T	0.45	-2.9356	6.7876	0.23682	0.0:0.0793:0.1546:0.7661	.	203	Q6BCY4	NB5R2_HUMAN	A	203	ENSP00000435916:T203A;ENSP00000299498:T203A;ENSP00000437041:T203A;ENSP00000299497:T203A	ENSP00000299497:T203A	T	-	1	0	CYB5R2	7644309	0.029000	0.19370	0.002000	0.10522	0.499000	0.33736	1.442000	0.35046	1.007000	0.39238	0.533000	0.62120	ACT	.	.		0.517	CYB5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385679.1	NM_016229		C	7687733	T	C	7687733	3	2	113	1	0	0	0	0	1	0	0	0	4129	1667	58	2	231	2	CYB5R2	11	7687733	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1275792	7687733	127318783	211	18088										
ZNF143	7702	hgsc.bcm.edu	37	chr11	9546829	9546829	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tggcagcattccatactgccTcatcagaaatggggcaccag	10	12	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:9546829T>C	ENST00000396602.2	+	15	1848	c.1729T>C	c.(1729-1731)Tca>Cca	p.S577P	ZNF143_ENST00000396604.1_Missense_Mutation_p.S576P|ZNF143_ENST00000530463.1_Missense_Mutation_p.S576P|ZNF143_ENST00000396597.3_Missense_Mutation_p.S546P|ZNF143_ENST00000299606.2_Missense_Mutation_p.S549P	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	577					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		CCATACTGCCTCATCAGAAAT	0.428																																					p.S577P		Atlas-SNP	.											.	ZNF143	38	.	0			c.T1729C						.						189	157	168					11																	9546829		2201	4294	6495	SO:0001583	missense	7702	exon15			ACTGCCTCATCAG	U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"Zinc fingers, C2H2-type"	12928	protein-coding gene	gene with protein product		603433	"zinc finger protein 143 (clone pHZ-1)"				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.1729T>C	chr11.hg19:g.9546829T>C	ENSP00000379847:p.Ser577Pro	155.0	0.0		83.0	5.0	NM_003442	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Missense_Mutation	SNP	ENST00000396602.2	hg19	CCDS7799.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.46|18.46	3.627818|3.627818	0.66901|0.66901	.|.	.|.	ENSG00000166478|ENSG00000166478	ENST00000447186|ENST00000396604;ENST00000396602;ENST00000530463;ENST00000396597;ENST00000299606	.|T;T;T;T;T	.|0.10573	.|2.86;2.87;2.86;2.88;2.89	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	.|0.095556	.|0.46442	.|D	.|0.000298	T|T	0.07863|0.07863	0.0197|0.0197	N|N	0.08118|0.08118	0|0	0.42671|0.42671	D|D	0.993519|0.993519	.|P;P;P	.|0.40476	.|0.718;0.596;0.596	.|B;B;B	.|0.43658	.|0.426;0.245;0.245	T|T	0.45644|0.45644	-0.9247|-0.9247	5|10	.|0.33940	.|T	.|0.23	.|.	11.8455|11.8455	0.52381|0.52381	0.0:0.0:0.146:0.854|0.0:0.0:0.146:0.854	.|.	.|546;576;577	.|P52747-2;E7ER34;P52747	.|.;.;ZN143_HUMAN	P|P	102|576;577;576;546;549	.|ENSP00000379849:S576P;ENSP00000379847:S577P;ENSP00000432154:S576P;ENSP00000379843:S546P;ENSP00000299606:S549P	.|ENSP00000299606:S549P	L|S	+|+	2|1	0|0	ZNF143|ZNF143	9503405|9503405	0.991000|0.991000	0.36638|0.36638	0.990000|0.990000	0.47175|0.47175	0.999000|0.999000	0.98932|0.98932	2.461000|2.461000	0.45040|0.45040	2.161000|2.161000	0.67846|0.67846	0.533000|0.533000	0.62120|0.62120	CTC|TCA	.	.		0.428	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442		C	9546829	T	C	9546829	3	2	113	1	0	0	0	0	1	0	0	0	17747	1551	54	2	1783	2	ZNF143	11	9546829	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1859096	9546829	125459687	212	18089										
MICAL2	9645	hgsc.bcm.edu	37	chr11	12183895	12183895	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccacctggaaagccaaagccCtgtggtacaaattggataag	10	10	0	0	rs368678535		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:12183895C>T	ENST00000256194.4	+	3	481	c.193C>T	c.(193-195)Ctg>Ttg	p.L65L	MICAL2_ENST00000379612.3_Silent_p.L65L|MICAL2_ENST00000527546.1_Silent_p.L65L|MICAL2_ENST00000342902.5_Silent_p.L65L|MICAL2_ENST00000537344.1_Silent_p.L65L	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	65	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		AGCCAAAGCCCTGTGGTACAA	0.493																																					p.L65L		Atlas-SNP	.											.	MICAL2	114	.	0			c.C193T						.						66	64	65					11																	12183895		2201	4294	6495	SO:0001819	synonymous_variant	9645	exon3			AAAGCCCTGTGGT	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.193C>T	chr11.hg19:g.12183895C>T		161.0	0.0		89.0	4.0	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	hg19	CCDS7809.1																																																																																			.	.		0.493	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		T	12183895	C	T	12183895	2	4	113	1	0	0	0	0	0	0	0	1	9579	680	24	3		3	MICAL2	11	12183895	Silent	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	2637066	12183895	122822621	213	18090										
TRAF6	7189	hgsc.bcm.edu	37	chr11	36520043	36520043	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gaaaagaactttaatacctcAagatgtctcagttccatctt	5	9	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:36520043A>G	ENST00000526995.1	-	3	690	c.444T>C	c.(442-444)ctT>ctC	p.L148L	TRAF6_ENST00000529150.1_5'Flank|TRAF6_ENST00000348124.5_Silent_p.L148L	NM_004620.3	NP_004611.1	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	148	Interaction with TAX1BP1.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of protein kinase activity (GO:0032147)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic signaling pathway (GO:0097190)|bone resorption (GO:0045453)|cell development (GO:0048468)|cellular response to lipopolysaccharide (GO:0071222)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein autoubiquitination (GO:0051865)|protein complex assembly (GO:0006461)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of immunoglobulin secretion (GO:0051023)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	histone deacetylase binding (GO:0042826)|ligase activity (GO:0016874)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)	27	all_lung(20;0.211)	all_hematologic(20;0.107)				TTAATACCTCAAGATGTCTCA	0.378																																					p.L148L		Atlas-SNP	.											.	TRAF6	56	.	0			c.T444C						.						105	101	102					11																	36520043		2202	4298	6500	SO:0001819	synonymous_variant	7189	exon3			TACCTCAAGATGT		CCDS7901.1	11p12	2013-01-09	2012-02-23		ENSG00000175104	ENSG00000175104		"RING-type (C3HC4) zinc fingers"	12036	protein-coding gene	gene with protein product		602355	"TNF receptor-associated factor 6"			8837778	Standard	NM_004620		Approved	RNF85	uc001mws.2	Q9Y4K3	OTTHUMG00000166391	ENST00000526995.1:c.444T>C	chr11.hg19:g.36520043A>G		125.0	0.0		88.0	4.0	NM_004620	A6NKI7|A8KAB3|D3DR16|Q8NEH5	Silent	SNP	ENST00000526995.1	hg19	CCDS7901.1																																																																																			.	.		0.378	TRAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389530.1	NM_145803		G	36520043	A	G	36520043	2	3	113	1	0	0	0	0	0	0	0	1	16460	117	5	2		2	TRAF6	11	36520043	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	24336148	36520043	98486473	214	18091										
PHF21A	51317	hgsc.bcm.edu	37	chr11	45991402	45991402	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggacgtggagtgagtctaggAggggggataaactgtggtac	19	4	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:45991402A>G	ENST00000418153.2	-	8	862	c.663T>C	c.(661-663)ccT>ccC	p.P221P	PHF21A_ENST00000323180.6_Silent_p.P222P|PHF21A_ENST00000257821.4_Silent_p.P222P			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	221					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						TGAGTCTAGGAGGGGGGATAA	0.438																																					p.P222P		Atlas-SNP	.											.	PHF21A	107	.	0			c.T666C						.						101	90	93					11																	45991402		2202	4299	6501	SO:0001819	synonymous_variant	51317	exon8			TCTAGGAGGGGGG	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.663T>C	chr11.hg19:g.45991402A>G		182.0	0.0		122.0	5.0	NM_016621	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Silent	SNP	ENST00000418153.2	hg19	CCDS44578.1																																																																																			.	.		0.438	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		G	45991402	A	G	45991402	2	3	113	1	0	0	0	0	0	0	0	1	11842	291	11	2		2	PHF21A	11	45991402	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	9471359	45991402	89015114	215	18092										
LRP4	4038	hgsc.bcm.edu	37	chr11	46890579	46890579	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	accacgatgatatccatgagTccttccacatttgccagcac	6	14	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:46890579T>C	ENST00000378623.1	-	32	5039	c.4797A>G	c.(4795-4797)ggA>ggG	p.G1599G	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1599					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		TATCCATGAGTCCTTCCACAT	0.542																																					p.G1599G		Atlas-SNP	.											.	LRP4	160	.	0			c.A4797G						.						265	217	233					11																	46890579		2201	4299	6500	SO:0001819	synonymous_variant	4038	exon32			CATGAGTCCTTCC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.4797A>G	chr11.hg19:g.46890579T>C		255.0	0.0		164.0	7.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	hg19	CCDS31478.1																																																																																			.	.		0.542	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		C	46890579	T	C	46890579	2	2	113	1	0	0	0	0	0	0	0	1	8968	1654	58	2		2	LRP4	11	46890579	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	899177	46890579	88115937	216	18093										
DDB2	1643	hgsc.bcm.edu	37	chr11	47238448	47238448	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgcacactctggattcttacCggatattacaaaaggctgcc	8	11	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:47238448C>T	ENST00000256996.4	+	3	499	c.304C>T	c.(304-306)Cgg>Tgg	p.R102W	DDB2_ENST00000378601.3_Missense_Mutation_p.R102W|DDB2_ENST00000378600.3_Missense_Mutation_p.R102W|DDB2_ENST00000378603.3_Intron	NM_000107.2	NP_000098.1	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2, 48kDa	102					DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|pyrimidine dimer repair (GO:0006290)|response to UV (GO:0009411)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(1)	17						GGATTCTTACCGGATATTACA	0.512			"Mis, N"			"skin basal cell, skin squamous cell, melanoma"		Direct reversal of damage;Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.R102W		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (E)	11	11p12	1643	damage-specific DNA binding protein 2		E	.	DDB2	31	.	0			c.C304T						.						50	51	51					11																	47238448		2201	4298	6499	SO:0001583	missense	1643	exon3	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TCTTACCGGATAT		CCDS7927.1, CCDS73284.1	11p12-p11	2014-09-17	2002-08-29			ENSG00000134574		"WD repeat domain containing"	2718	protein-coding gene	gene with protein product	"xeroderma pigmentosum group E protein", "UV-damaged DNA-binding protein 2", "DDB p48 subunit"	600811	"damage-specific DNA binding protein 2 (48kD)"			8407967, 8530102	Standard	NM_000107		Approved	DDBB, UV-DDB2, FLJ34321	uc001neb.2	Q92466		ENST00000256996.4:c.304C>T	chr11.hg19:g.47238448C>T	ENSP00000256996:p.Arg102Trp	121.0	0.0		78.0	4.0	NM_000107	B2R875|Q76E54|Q76E55|Q76E56|Q76E57	Missense_Mutation	SNP	ENST00000256996.4	hg19	CCDS7927.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.042384	0.75732	.	.	ENSG00000134574	ENST00000256996;ENST00000378600;ENST00000378601	T;T;T	0.73258	-0.73;-0.15;1.5	5.78	4.87	0.63330	.	0.370611	0.31709	N	0.007182	T	0.59252	0.2180	L	0.48642	1.525	0.37882	D	0.930413	B;B;B	0.29037	0.231;0.231;0.025	B;B;B	0.19666	0.026;0.026;0.001	T	0.63637	-0.6592	10	0.72032	D	0.01	-12.6168	6.7623	0.23548	0.1439:0.7092:0.0:0.1469	.	102;102;102	Q92466-3;Q92466-2;Q92466	.;.;DDB2_HUMAN	W	102	ENSP00000256996:R102W;ENSP00000367863:R102W;ENSP00000367864:R102W	ENSP00000256996:R102W	R	+	1	2	DDB2	47195024	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.854000	0.39368	1.450000	0.47717	0.655000	0.94253	CGG	.	.		0.512	DDB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000107		T	47238448	C	T	47238448	3	4	113	1	0	0	0	0	1	0	0	0	4326	643	23	1	314	1	DDB2	11	47238448	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	347869	47238448	87768068	217	18094										
PATL1	219988	hgsc.bcm.edu	37	chr11	59423450	59423450	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgtgctcctccaagaagctgTgctctctggagggggctgag	15	10	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:59423450T>C	ENST00000300146.9	-	7	876	c.792A>G	c.(790-792)gcA>gcG	p.A264A		NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	264	Involved in RNA-binding.|Involved in nuclear foci localization.|Pro-rich.|Region N; interaction with decapping machinery.				cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						CAAGAAGCTGTGCTCTCTGGA	0.428																																					p.A264A		Atlas-SNP	.											.	PATL1	92	.	0			c.A792G						.						13	14	14					11																	59423450		1835	4072	5907	SO:0001819	synonymous_variant	219988	exon7			AAGCTGTGCTCTC	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.792A>G	chr11.hg19:g.59423450T>C		189.0	0.0		116.0	5.0	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Silent	SNP	ENST00000300146.9	hg19	CCDS44613.1																																																																																			.	.		0.428	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716		C	59423450	T	C	59423450	2	2	113	1	0	0	0	0	0	0	0	1	11484	1683	59	2		2	PATL1	11	59423450	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	12185002	59423450	75583066	218	18095										
TMEM138	51524	hgsc.bcm.edu	37	chr11	61136089	61136089	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagcagtgttgtactgctacTtctataaacggacagccgta	9	10	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:61136089T>C	ENST00000278826.6	+	5	956	c.397T>C	c.(397-399)Ttc>Ctc	p.F133L	TMEM138_ENST00000381787.2_Missense_Mutation_p.F75L	NM_016464.4	NP_057548.1	Q9NPI0	TM138_HUMAN	transmembrane protein 138	133					cilium assembly (GO:0042384)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|vacuole (GO:0005773)				central_nervous_system(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5						GTACTGCTACTTCTATAAACG	0.517																																					p.F133L		Atlas-SNP	.											.	TMEM138	16	.	0			c.T397C						.						112	91	98					11																	61136089		2203	4299	6502	SO:0001583	missense	51524	exon5			TGCTACTTCTATA	AF151030	CCDS8005.1	11q12.2	2014-01-28			ENSG00000149483	ENSG00000149483			26944	protein-coding gene	gene with protein product		614459					Standard	NM_016464		Approved	HSPC196, JBTS16	uc001nrl.2	Q9NPI0	OTTHUMG00000168145	ENST00000278826.6:c.397T>C	chr11.hg19:g.61136089T>C	ENSP00000278826:p.Phe133Leu	184.0	0.0		96.0	4.0	NM_016464	A6NGA7|B4E044|Q5JPE1	Missense_Mutation	SNP	ENST00000278826.6	hg19	CCDS8005.1	.	.	.	.	.	.	.	.	.	.	T	13.37	2.218122	0.39201	.	.	ENSG00000149483	ENST00000278826;ENST00000381787	D;D	0.87887	-2.31;-2.31	5.82	5.82	0.92795	.	0.171309	0.53938	D	0.000048	T	0.79741	0.4498	N	0.21583	0.68	0.47374	D	0.999405	B	0.11235	0.004	B	0.11329	0.006	T	0.73886	-0.3841	10	0.21540	T	0.41	.	15.8512	0.78934	0.0:0.0:0.0:1.0	.	133	Q9NPI0	TM138_HUMAN	L	133;75	ENSP00000278826:F133L;ENSP00000371206:F75L	ENSP00000278826:F133L	F	+	1	0	TMEM138	60892665	1.000000	0.71417	1.000000	0.80357	0.549000	0.35272	4.555000	0.60767	2.225000	0.72522	0.459000	0.35465	TTC	.	.		0.517	TMEM138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398399.2	NM_016464		C	61136089	T	C	61136089	3	2	113	1	0	0	0	0	1	0	0	0	16068	1609	56	2	411	2	TMEM138	11	61136089	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1712639	61136089	73870427	219	18096										
BSCL2	26580	hgsc.bcm.edu	37	chr11	62458612	62458612	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgtctctttttcggatgttaAcctgtggaggaaaaactact	9	7	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:62458612A>G	ENST00000403550.1	-	8	1238	c.815T>C	c.(814-816)gTt>gCt	p.V272A	BSCL2_ENST00000278893.7_Splice_Site_p.L225L|BSCL2_ENST00000433053.1_Splice_Site_p.V336A|BSCL2_ENST00000421906.1_Splice_Site_p.V272A|BSCL2_ENST00000407022.3_Splice_Site_p.V272A|BSCL2_ENST00000360796.5_Splice_Site_p.V336A|BSCL2_ENST00000405837.1_Splice_Site_p.V336A|HNRNPUL2-BSCL2_ENST00000403734.2_3'UTR|LRRN4CL_ENST00000317449.4_5'Flank			Q96G97	BSCL2_HUMAN	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	272					cell death (GO:0008219)|fat cell differentiation (GO:0045444)|lipid catabolic process (GO:0016042)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of lipid catabolic process (GO:0050995)	integral component of endoplasmic reticulum membrane (GO:0030176)				endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	12						TCGGATGTTAACCTGTGGAGG	0.517																																					p.V336A		Atlas-SNP	.											.	BSCL2	35	.	0			c.T1007C						.						84	75	78					11																	62458612		2202	4299	6501	SO:0001630	splice_region_variant	26580	exon8			ATGTTAACCTGTG		CCDS8031.1, CCDS44627.1, CCDS55769.1	11q13	2014-09-17	2009-07-30		ENSG00000168000	ENSG00000168000			15832	protein-coding gene	gene with protein product		606158	"spastic paraplegia 17 (Silver syndrome)"	GNG3LG, SPG17		11479539, 14981520	Standard	NM_001122955		Approved		uc001nur.4	Q96G97	OTTHUMG00000150624	ENST00000403550.1:c.814-1T>C	chr11.hg19:g.62458612A>G		154.0	0.0		98.0	5.0	NM_001122955	G3XAE4|Q567S1|Q96SV1|Q9BSQ0	Missense_Mutation	SNP	ENST00000403550.1	hg19	CCDS8031.1	.	.	.	.	.	.	.	.	.	.	A	17.06	3.293725	0.60086	.	.	ENSG00000168000	ENST00000449636;ENST00000405837;ENST00000433053;ENST00000360796;ENST00000403550;ENST00000407022;ENST00000421906	D;D;D;D;D;D	0.89123	-2.42;-2.47;-2.47;-2.43;-2.43;-2.43	5.01	0.137	0.14787	.	0.188915	0.33875	U	0.004479	T	0.78470	0.4288	.	.	.	0.20196	N	0.999928	B;B;B	0.11235	0.002;0.004;0.002	B;B;B	0.11329	0.003;0.006;0.003	T	0.62426	-0.6857	9	0.27082	T	0.32	4.7959	7.1629	0.25675	0.6122:0.0:0.3878:0.0	.	272;336;272	Q53EN3;G3XAE4;Q96G97	.;.;BSCL2_HUMAN	A	21;336;336;336;272;272;272	ENSP00000385332:V336A;ENSP00000414002:V336A;ENSP00000354032:V336A;ENSP00000385561:V272A;ENSP00000384080:V272A;ENSP00000413209:V272A	ENSP00000354032:V336A	V	-	2	0	BSCL2	62215188	0.892000	0.30473	0.905000	0.35620	0.823000	0.46562	0.802000	0.27069	-0.005000	0.14395	0.402000	0.26972	GTT	.	.		0.517	BSCL2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319185.1	NM_032667	Missense_Mutation	G	62458612	A	G	62458612	5	3	113	1	0	0	0	0	0	0	1	0	1529	57	2	2	397	2	BSCL2	11	62458612	Splice_Site	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1322523	62458612	72547904	220	18097										
ZBTB3	79842	hgsc.bcm.edu	37	chr11	62521471	62521471	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggctccacgaagtagagatcTttttcgctcccaggccttgc	10	13	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:62521471T>C	ENST00000394807.3	-	1	189	c.64A>G	c.(64-66)Aga>Gga	p.R22G		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	22					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						AGTAGAGATCTTTTTCGCTCC	0.622																																					p.R22G		Atlas-SNP	.											.	ZBTB3	47	.	0			c.A64G						.						99	88	91					11																	62521471		2202	4299	6501	SO:0001583	missense	79842	exon1			GAGATCTTTTTCG	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.64A>G	chr11.hg19:g.62521471T>C	ENSP00000378286:p.Arg22Gly	145.0	0.0		89.0	4.0	NM_024784		Missense_Mutation	SNP	ENST00000394807.3	hg19	CCDS8034.1	.	.	.	.	.	.	.	.	.	.	T	7.517	0.655918	0.14580	.	.	ENSG00000185670	ENST00000394807	T	0.11712	2.75	5.65	4.49	0.54785	.	0.699662	0.12304	N	0.480815	T	0.07098	0.0180	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.22417	-1.0217	10	0.32370	T	0.25	.	10.1327	0.42689	0.0:0.0802:0.0:0.9198	.	22	Q9H5J0	ZBTB3_HUMAN	G	22	ENSP00000378286:R22G	ENSP00000378286:R22G	R	-	1	2	ZBTB3	62278047	0.007000	0.16637	0.349000	0.25694	0.005000	0.04900	0.819000	0.27308	2.371000	0.80710	0.533000	0.62120	AGA	.	.		0.622	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784		C	62521471	T	C	62521471	3	2	113	1	0	0	0	0	1	0	0	0	17549	1617	56	2	1668	2	ZBTB3	11	62521471	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	62859	62521471	72485045	221	18098										
STX5	6811	hgsc.bcm.edu	37	chr11	62592977	62592977	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tggctctcacgaaatcctggAgctgagcaatttgtttgttg	11	8	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:62592977A>G	ENST00000294179.3	-	6	611	c.458T>C	c.(457-459)cTc>cCc	p.L153P	STX5_ENST00000541317.1_Missense_Mutation_p.L57P|STX5_ENST00000394690.1_Missense_Mutation_p.L99P|STX5_ENST00000377897.4_Missense_Mutation_p.L153P	NM_001244666.1|NM_003164.4	NP_001231595.1|NP_003155.2	Q13190	STX5_HUMAN	syntaxin 5	153					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion with Golgi apparatus (GO:0048280)|vesicle targeting (GO:0006903)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|SNARE complex (GO:0031201)	protein N-terminus binding (GO:0047485)|SNAP receptor activity (GO:0005484)			breast(2)|endometrium(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	18						GAAATCCTGGAGCTGAGCAAT	0.517																																					p.L153P		Atlas-SNP	.											.	STX5	42	.	0			c.T458C						.						112	113	113					11																	62592977		2201	4299	6500	SO:0001583	missense	6811	exon6			TCCTGGAGCTGAG	U26648	CCDS8038.2, CCDS58140.1	11q12.3	2008-02-05	2006-04-25	2006-04-25	ENSG00000162236	ENSG00000162236			11440	protein-coding gene	gene with protein product		603189	"syntaxin 5A"	STX5A		9188044, 11959998	Standard	NM_003164		Approved	SED5	uc001nvh.3	Q13190	OTTHUMG00000143864	ENST00000294179.3:c.458T>C	chr11.hg19:g.62592977A>G	ENSP00000294179:p.Leu153Pro	182.0	0.0		118.0	5.0	NM_003164	B2R8T2|F8W8Q9|Q5U0D4|Q7Z3T6|Q9BUG1	Missense_Mutation	SNP	ENST00000294179.3	hg19	CCDS8038.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.181167|4.181167	0.78677|0.78677	.|.	.|.	ENSG00000162236|ENSG00000162236	ENST00000377897;ENST00000294179;ENST00000394690;ENST00000541317|ENST00000431400	T;T;T;T|.	0.25749|.	1.78;1.78;1.78;1.78|.	5.28|5.28	5.28|5.28	0.74379|0.74379	t-SNARE (1);Syntaxin, N-terminal (1);|.	0.062051|.	0.64402|.	D|.	0.000003|.	T|T	0.81894|0.81894	0.4919|0.4919	M|M	0.92169|0.92169	3.28|3.28	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.998;0.999|.	D|D	0.86173|0.86173	0.1601|0.1601	10|5	0.87932|.	D|.	0|.	-0.4057|-0.4057	13.2122|13.2122	0.59832|0.59832	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	153;153|.	F8W8Q9;Q13190|.	.;STX5_HUMAN|.	P|P	153;153;99;57|8	ENSP00000367129:L153P;ENSP00000294179:L153P;ENSP00000378182:L99P;ENSP00000441428:L57P|.	ENSP00000294179:L153P|.	L|S	-|-	2|1	0|0	STX5|STX5	62349553|62349553	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.955000|0.955000	0.61496|0.61496	8.718000|8.718000	0.91430|0.91430	2.227000|2.227000	0.72691|0.72691	0.460000|0.460000	0.39030|0.39030	CTC|TCC	.	.		0.517	STX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290113.1	NM_003164		G	62592977	A	G	62592977	3	3	113	1	0	0	0	0	1	0	0	0	15363	304	11	2	633	2	STX5	11	62592977	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	71506	62592977	72413539	222	18099										
WDR74	54663	hgsc.bcm.edu	37	chr11	62600449	62600449	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggctggtggacccaggccgcTtcttctttctccgtctcgtt	11	14	4	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:62600449T>C	ENST00000525239.1	-	12	1670	c.1133A>G	c.(1132-1134)aAg>aGg	p.K378R	STX5_ENST00000541317.1_5'Flank|WDR74_ENST00000525752.1_Missense_Mutation_p.K321R|RP11-727F15.9_ENST00000535817.1_RNA|WDR74_ENST00000540620.1_5'Flank|WDR74_ENST00000278856.4_Missense_Mutation_p.K378R|STX5_ENST00000394690.1_5'Flank|RP11-727F15.9_ENST00000535867.1_RNA|STX5_ENST00000377897.4_5'Flank|WDR74_ENST00000311713.7_Missense_Mutation_p.K359R|STX5_ENST00000294179.3_5'Flank|WDR74_ENST00000529106.1_Missense_Mutation_p.K378R			Q6RFH5	WDR74_HUMAN	WD repeat domain 74	378					blastocyst formation (GO:0001825)|RNA metabolic process (GO:0016070)	nucleolus (GO:0005730)|nucleus (GO:0005634)				kidney(2)|large_intestine(1)|liver(1)|lung(3)|ovary(1)	8						CCCAGGCCGCTTCTTCTTTCT	0.567																																					p.K378R		Atlas-SNP	.											WDR74_ENST00000525239,NS,carcinoma,0,2	WDR74	36	.	0			c.A1133G						.						53	58	57					11																	62600449		1861	4093	5954	SO:0001583	missense	54663	exon12			GGCCGCTTCTTCT		CCDS44630.1	11q12.3	2013-01-09				ENSG00000133316		"WD repeat domain containing"	25529	protein-coding gene	gene with protein product							Standard	NM_018093		Approved	FLJ10439	uc001nvm.2	Q6RFH5		ENST00000525239.1:c.1133A>G	chr11.hg19:g.62600449T>C	ENSP00000432119:p.Lys378Arg	79.0	0.0		49.0	2.0	NM_018093	A8K8G5|Q9BRC9|Q9H6X8|Q9NVY2	Missense_Mutation	SNP	ENST00000525239.1	hg19	CCDS44630.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.284|3.284	-0.146432|-0.146432	0.06627|0.06627	.|.	.|.	ENSG00000133316|ENSG00000133316	ENST00000311713;ENST00000529106;ENST00000525239;ENST00000278856;ENST00000525752|ENST00000536401	T|.	0.44881|.	0.91|.	4.27|4.27	3.14|3.14	0.36123|0.36123	.|.	0.603866|.	0.14738|.	N|.	0.301368|.	T|T	0.38453|0.38453	0.1041|0.1041	L|L	0.46157|0.46157	1.445|1.445	0.09310|0.09310	N|N	1|1	B;B;B|.	0.06786|.	0.0;0.0;0.001|.	B;B;B|.	0.09377|.	0.001;0.001;0.004|.	T|T	0.23940|0.23940	-1.0174|-1.0174	10|5	0.33940|.	T|.	0.23|.	-17.4921|-17.4921	6.3872|6.3872	0.21568|0.21568	0.0:0.1133:0.0:0.8867|0.0:0.1133:0.0:0.8867	.|.	321;378;359|.	E9PS41;Q6RFH5;Q6RFH5-2|.	.;WDR74_HUMAN;.|.	R|G	359;378;378;378;321|31	ENSP00000432113:K321R|.	ENSP00000278856:K378R|.	K|S	-|-	2|1	0|0	WDR74|WDR74	62357025|62357025	0.974000|0.974000	0.33945|0.33945	0.008000|0.008000	0.14137|0.14137	0.017000|0.017000	0.09413|0.09413	2.105000|2.105000	0.41825|0.41825	0.781000|0.781000	0.33589|0.33589	0.533000|0.533000	0.62120|0.62120	AAG|AGC	.	.		0.567	WDR74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395678.1	NM_018093		C	62600449	T	C	62600449	3	2	113	1	0	0	0	0	1	0	0	0	17339	1609	56	2	28	2	WDR74	11	62600449	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	7472	62600449	72406067	223	18100										
PYGM	5837	hgsc.bcm.edu	37	chr11	64527357	64527357	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttcttttctcttggtctgacAggggccgggacatggctgca	13	10	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:64527357A>G	ENST00000164139.3	-	1	412	c.14T>C	c.(13-15)cTg>cCg	p.L5P	PYGM_ENST00000377432.3_Missense_Mutation_p.L5P	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	5					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTGGTCTGACAGGGGCCGGGA	0.612																																					p.L5P		Atlas-SNP	.											.	PYGM	77	.	0			c.T14C	GRCh37	CD066398	PYGM	D		.						82	81	81					11																	64527357		2201	4297	6498	SO:0001583	missense	5837	exon1			TCTGACAGGGGCC		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.14T>C	chr11.hg19:g.64527357A>G	ENSP00000164139:p.Leu5Pro	127.0	0.0		81.0	4.0	NM_001164716	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	hg19	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	A	18.94	3.729408	0.69074	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.94537	-3.2;-3.45	5.41	5.41	0.78517	.	0.144353	0.32055	N	0.006651	D	0.95981	0.8691	M	0.67953	2.075	0.80722	D	1	D;B	0.69078	0.997;0.013	P;B	0.60789	0.879;0.021	D	0.96092	0.9062	10	0.62326	D	0.03	-17.9796	13.3929	0.60834	1.0:0.0:0.0:0.0	.	5;5	A6NDY6;P11217	.;PYGM_HUMAN	P	5	ENSP00000366650:L5P;ENSP00000164139:L5P	ENSP00000164139:L5P	L	-	2	0	PYGM	64283933	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	8.954000	0.93051	2.071000	0.62044	0.533000	0.62120	CTG	.	.		0.612	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		G	64527357	A	G	64527357	3	3	113	1	0	0	0	0	1	0	0	0	12877	188	7	2	2594	2	PYGM	11	64527357	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1926908	64527357	70479159	224	18101										
CAPN1	823	hgsc.bcm.edu	37	chr11	64977873	64977873	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctcggagcccgacctggcggTcgactttgacaatttcgttt	11	12	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:64977873T>C	ENST00000527323.1	+	19	2249	c.2009T>C	c.(2008-2010)gTc>gCc	p.V670A	CAPN1_ENST00000533129.1_Missense_Mutation_p.V670A|CAPN1_ENST00000524773.1_Missense_Mutation_p.V670A|CAPN1_ENST00000533820.1_Missense_Mutation_p.V670A|CAPN1_ENST00000279247.6_Missense_Mutation_p.V670A			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	670	Domain IV.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		GACCTGGCGGTCGACTTTGAC	0.587																																					p.V670A		Atlas-SNP	.											.	CAPN1	44	.	0			c.T2009C						.						55	58	57					11																	64977873		2010	4182	6192	SO:0001583	missense	823	exon20			TGGCGGTCGACTT	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"EF-hand domain containing"	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614	ENST00000527323.1:c.2009T>C	chr11.hg19:g.64977873T>C	ENSP00000431984:p.Val670Ala	142.0	0.0		75.0	5.0	NM_001198869	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	hg19	CCDS44644.1	.	.	.	.	.	.	.	.	.	.	T	18.19	3.569576	0.65765	.	.	ENSG00000014216	ENST00000533820;ENST00000533129;ENST00000524773;ENST00000279247;ENST00000259755;ENST00000527323	T;T;T;T;T	0.36699	1.24;1.24;1.24;1.24;1.24	4.21	4.21	0.49690	EF-hand-like domain (1);	0.067866	0.64402	D	0.000015	T	0.43299	0.1241	M	0.79805	2.47	0.58432	D	0.999999	P	0.35527	0.507	B	0.37888	0.26	T	0.51919	-0.8644	10	0.87932	D	0	.	11.5655	0.50802	0.0:0.0:0.0:1.0	.	670	P07384	CAN1_HUMAN	A	670;670;670;670;616;670	ENSP00000435272:V670A;ENSP00000431686:V670A;ENSP00000434176:V670A;ENSP00000279247:V670A;ENSP00000431984:V670A	ENSP00000259755:V616A	V	+	2	0	CAPN1	64734449	0.971000	0.33674	0.989000	0.46669	0.751000	0.42716	7.682000	0.84083	1.701000	0.51217	0.460000	0.39030	GTC	.	.		0.587	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1			C	64977873	T	C	64977873	3	2	113	1	0	0	0	0	1	0	0	0	2624	1667	58	2	2083	2	CAPN1	11	64977873	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	450516	64977873	70028643	225	18102										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65350029	65350029	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgctgggacagcacagtgtgAgggactggagacccaggaaa	16	8	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:65350029A>G	ENST00000309295.4	+	9	2151	c.1886A>G	c.(1885-1887)gAg>gGg	p.E629G		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	629	Glu-rich.					membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GCACAGTGTGAGGGACTGGAG	0.542																																					p.E629G		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.A1886G						.						59	65	63					11																	65350029		2008	4185	6193	SO:0001583	missense	254102	exon9			AGTGTGAGGGACT	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.1886A>G	chr11.hg19:g.65350029A>G	ENSP00000312671:p.Glu629Gly	138.0	0.0		76.0	4.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.771561	0.49680	.	.	ENSG00000173442	ENST00000309295	T	0.69175	-0.38	4.44	2.04	0.26737	.	.	.	.	.	T	0.53384	0.1793	L	0.36672	1.1	0.09310	N	0.999999	B	0.10296	0.003	B	0.08055	0.003	T	0.49753	-0.8906	9	0.87932	D	0	.	6.5881	0.22632	0.696:0.0:0.304:0.0	.	629	Q8N3D4	EH1L1_HUMAN	G	629	ENSP00000312671:E629G	ENSP00000312671:E629G	E	+	2	0	EHBP1L1	65106605	0.764000	0.28473	0.011000	0.14972	0.008000	0.06430	1.848000	0.39309	0.581000	0.29539	0.383000	0.25322	GAG	.	.		0.542	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		G	65350029	A	G	65350029	3	3	113	1	0	0	0	0	1	0	0	0	4978	304	11	2	1920	2	EHBP1L1	11	65350029	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	372156	65350029	69656487	226	18103										
MRPL48	51642	hgsc.bcm.edu	37	chr11	73536778	73536778	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	attctactaagtatcagtcgGccctacaagacaaagcccac	6	13	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:73536778G>A	ENST00000310614.7	+	4	794	c.138G>A	c.(136-138)cgG>cgA	p.R46R	MRPL48_ENST00000398483.3_5'UTR|MRPL48_ENST00000535529.1_Silent_p.R28R|MRPL48_ENST00000542303.1_Silent_p.R46R|MRPL48_ENST00000411840.2_5'UTR	NM_016055.5	NP_057139.1	Q96GC5	RM48_HUMAN	mitochondrial ribosomal protein L48	46						mitochondrial ribosome (GO:0005761)				kidney(1)	1						GTATCAGTCGGCCCTACAAGA	0.403																																					p.R46R		Atlas-SNP	.											.	MRPL48	16	.	0			c.G138A						.						43	43	43					11																	73536778		1848	4077	5925	SO:0001819	synonymous_variant	51642	exon4			CAGTCGGCCCTAC	AF151876	CCDS44676.1	11q13.4	2012-09-13			ENSG00000175581	ENSG00000175581		"Mitochondrial ribosomal proteins / large subunits"	16653	protein-coding gene	gene with protein product		611853				10810093	Standard	NM_016055		Approved	CGI-118	uc001ouh.4	Q96GC5	OTTHUMG00000168048	ENST00000310614.7:c.138G>A	chr11.hg19:g.73536778G>A		93.0	0.0		63.0	4.0	NM_016055	B4DN34|Q49AK7|Q4U2Q4|Q9P091|Q9Y5J0	Silent	SNP	ENST00000310614.7	hg19	CCDS44676.1																																																																																			.	.		0.403	MRPL48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397733.1	NM_016055		A	73536778	G	A	73536778	2	1	113	1	0	0	0	0	0	0	0	1	9821	1190	42	3		3	MRPL48	11	73536778	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	8186749	73536778	61469738	227	18104										
TMEM126A	84233	hgsc.bcm.edu	37	chr11	85367380	85367380	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcagctctgttaccacacaaAgggaacatcttaagttactg	7	10	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:85367380A>G	ENST00000304511.2	+	5	532	c.423A>G	c.(421-423)aaA>aaG	p.K141K	TMEM126A_ENST00000528105.1_Silent_p.K71K|TMEM126A_ENST00000532180.1_Silent_p.K71K	NM_032273.3	NP_115649.1	Q9H061	T126A_HUMAN	transmembrane protein 126A	141					optic nerve development (GO:0021554)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(2)|stomach(1)	7		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				TACCACACAAAGGGAACATCT	0.358																																					p.K141K		Atlas-SNP	.											.	TMEM126A	20	.	0			c.A423G						.						95	86	89					11																	85367380		2203	4298	6501	SO:0001819	synonymous_variant	84233	exon5			ACACAAAGGGAAC		CCDS8268.1, CCDS58165.1	11q14.1	2011-03-25			ENSG00000171202	ENSG00000171202			25382	protein-coding gene	gene with protein product		612988				11230166	Standard	NM_032273		Approved	DKFZp586C1924, OPA7	uc001par.3	Q9H061	OTTHUMG00000166975	ENST00000304511.2:c.423A>G	chr11.hg19:g.85367380A>G		161.0	0.0		83.0	4.0	NM_032273	B2R570|E9PI16	Silent	SNP	ENST00000304511.2	hg19	CCDS8268.1																																																																																			.	.		0.358	TMEM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392177.1	NM_032273		G	85367380	A	G	85367380	2	3	113	1	0	0	0	0	0	0	0	1	16053	69	3	2		2	TMEM126A	11	85367380	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	11830602	85367380	49639136	228	18105										
HYOU1	10525	hgsc.bcm.edu	37	chr11	118925746	118925746	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aattgagaaccatgcccaacActtcctcaggtgagaactgc	8	12	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr11:118925746A>G	ENST00000404233.3	-	6	570	c.446T>C	c.(445-447)gTg>gCg	p.V149A	HYOU1_ENST00000525859.1_Missense_Mutation_p.V149A|HYOU1_ENST00000529972.1_Missense_Mutation_p.V149A|HYOU1_ENST00000543287.1_Missense_Mutation_p.V62A	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	149					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		CATGCCCAACACTTCCTCAGG	0.532																																					p.V149A		Atlas-SNP	.											.	HYOU1	88	.	0			c.T446C						.						119	99	106					11																	118925746		2200	4295	6495	SO:0001583	missense	10525	exon6			CCCAACACTTCCT	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"Heat shock proteins / HSP70"	16931	protein-coding gene	gene with protein product	"glucose-regulated protein 170"	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.446T>C	chr11.hg19:g.118925746A>G	ENSP00000384144:p.Val149Ala	71.0	0.0		31.0	4.0	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	hg19	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.611289	0.87258	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000536103;ENST00000525859;ENST00000544701;ENST00000543287;ENST00000530473	T;T;T;T;T	0.01287	5.05;5.05;5.05;5.05;5.05	4.96	4.96	0.65561	.	0.122225	0.56097	D	0.000033	T	0.04048	0.0113	M	0.66378	2.025	0.44432	D	0.997352	P;P;P;P	0.43938	0.822;0.729;0.722;0.722	B;P;B;B	0.47603	0.42;0.551;0.42;0.42	T	0.33033	-0.9884	10	0.87932	D	0	-22.4032	13.3595	0.60648	1.0:0.0:0.0:0.0	.	140;193;149;149	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	A	149;140;149;149;149;192;62;149	ENSP00000384144:V149A;ENSP00000437313:V149A;ENSP00000433397:V149A;ENSP00000442727:V62A;ENSP00000431874:V149A	ENSP00000278752:V140A	V	-	2	0	HYOU1	118430956	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	6.467000	0.73547	2.074000	0.62210	0.459000	0.35465	GTG	.	.		0.532	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389		G	118925746	A	G	118925746	3	3	113	1	0	0	0	0	1	0	0	0	7479	159	6	2	2637	2	HYOU1	11	118925746	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	33558366	118925746	16080770	229	18106										
WNK1	65125	hgsc.bcm.edu	37	chr12	970296	970296	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agttggtacgggaggagcaaGaaaaaaaaaagcaggaagag	15	3	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:970296G>A	ENST00000315939.6	+	7	2381	c.1738G>A	c.(1738-1740)Gaa>Aaa	p.E580K	WNK1_ENST00000530271.2_Missense_Mutation_p.E580K|WNK1_ENST00000537687.1_Missense_Mutation_p.E580K|WNK1_ENST00000540360.1_3'UTR|WNK1_ENST00000340908.4_Missense_Mutation_p.E173K|WNK1_ENST00000535572.1_Missense_Mutation_p.E580K	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	580					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.?(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GGAGGAGCAAGAAAAAAAAAA	0.473																																					p.E580K	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											WNK1_ENST00000537687,rectum,carcinoma,-2,1	WNK1	403	.	1	Unknown(1)	skin(1)	c.G1738A						.						102	100	101					12																	970296		2203	4300	6503	SO:0001583	missense	65125	exon7			GAGCAAGAAAAAA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1738G>A	chr12.hg19:g.970296G>A	ENSP00000313059:p.Glu580Lys	88.0	2.0		56.0	3.0	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	hg19	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	35	5.473507	0.96274	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.16196	2.36;2.36;2.36;2.36;2.36	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000004	T	0.41259	0.1151	M	0.64567	1.98	0.51767	D	0.999937	D;D;P	0.65815	0.995;0.995;0.949	D;D;P	0.73380	0.98;0.98;0.815	T	0.02173	-1.1201	10	0.34782	T	0.22	-14.5807	19.774	0.96385	0.0:0.0:1.0:0.0	.	580;580;580	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	K	580;580;580;27;580;173	ENSP00000441972:E580K;ENSP00000313059:E580K;ENSP00000444465:E580K;ENSP00000433548:E580K;ENSP00000341292:E173K	ENSP00000252477:E27K	E	+	1	0	WNK1	840557	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.581000	0.82535	2.679000	0.91253	0.591000	0.81541	GAA	.	.		0.473	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	970296	G	A	970296	3	1	113	1	0	0	0	0	1	0	0	0	17392	943	33	3	1764	3	WNK1	12	970296	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10		970296	132881599	230	18107										
RAD51AP1	10635	hgsc.bcm.edu	37	chr12	4665649	4665649	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccttcagctgaaagcaagaaAcctaaatgggtcccaccagg	9	12	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:4665649A>G	ENST00000352618.4	+	8	902	c.852A>G	c.(850-852)aaA>aaG	p.K284K	RAD51AP1_ENST00000544927.1_Intron|RAD51AP1_ENST00000544931.1_Intron|RAD51AP1_ENST00000321524.7_Intron|RAD51AP1_ENST00000543041.1_Silent_p.K166K|RAD51AP1_ENST00000228843.9_Silent_p.K301K	NM_006479.4	NP_006470.1			RAD51 associated protein 1											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)			AAAGCAAGAAACCTAAATGGG	0.388																																					p.K301K		Atlas-SNP	.											.	RAD51AP1	30	.	0			c.A903G						.						80	78	79					12																	4665649		2203	4300	6503	SO:0001819	synonymous_variant	10635	exon9			CAAGAAACCTAAA	AF006259	CCDS8529.1, CCDS44805.1	12p13.2-p13.1	2004-09-16			ENSG00000111247	ENSG00000111247			16956	protein-coding gene	gene with protein product		603070				9396801	Standard	NM_001130862		Approved	PIR51	uc001qmw.3	Q96B01	OTTHUMG00000168125	ENST00000352618.4:c.852A>G	chr12.hg19:g.4665649A>G		106.0	0.0		62.0	4.0	NM_001130862		Silent	SNP	ENST00000352618.4	hg19	CCDS8529.1	.	.	.	.	.	.	.	.	.	.	A	7.453	0.643102	0.14451	.	.	ENSG00000111247	ENST00000536117	.	.	.	4.51	-0.502	0.12004	.	.	.	.	.	T	0.39963	0.1098	.	.	.	0.32907	D	0.513931	.	.	.	.	.	.	T	0.49643	-0.8918	4	.	.	.	-12.9997	7.4276	0.27109	0.5604:0.0:0.4396:0.0	.	.	.	.	A	253	.	.	T	+	1	0	RAD51AP1	4535910	0.940000	0.31905	0.520000	0.27837	0.886000	0.51366	-0.138000	0.10374	0.010000	0.14839	0.482000	0.46254	ACC	.	.		0.388	RAD51AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398293.1	NM_006479		G	4665649	A	G	4665649	2	3	113	1	0	0	0	0	0	0	0	1	13001	40	2	2		2	RAD51AP1	12	4665649	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3695353	4665649	129186246	231	18108										
PZP	5858	hgsc.bcm.edu	37	chr12	9345181	9345181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tatagtgtgccgtgatagtcTccgtgtggccacagggcagg	15	9	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:9345181T>C	ENST00000261336.2	-	12	1437	c.1409A>G	c.(1408-1410)gAg>gGg	p.E470G	PZP_ENST00000381997.2_Missense_Mutation_p.E339G	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	470					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CGTGATAGTCTCCGTGTGGCC	0.502																																					p.E470G	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A1409G						.						96	94	94					12																	9345181		2203	4300	6503	SO:0001583	missense	5858	exon12			ATAGTCTCCGTGT	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.1409A>G	chr12.hg19:g.9345181T>C	ENSP00000261336:p.Glu470Gly	181.0	0.0		134.0	6.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.558123	0.27827	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.62941	-0.01;-0.01	3.23	3.23	0.37069	Alpha-2-macroglobulin, N-terminal 2 (1);	0.493681	0.16547	U	0.209674	T	0.44286	0.1286	N	0.17474	0.49	0.09310	N	1	B;B	0.19073	0.033;0.022	B;B	0.24541	0.054;0.04	T	0.37056	-0.9722	10	0.48119	T	0.1	.	8.4735	0.32999	0.0:0.0:0.0:1.0	.	339;470	P20742-2;P20742	.;PZP_HUMAN	G	470;339	ENSP00000261336:E470G;ENSP00000371427:E339G	ENSP00000261336:E470G	E	-	2	0	PZP	9236448	0.000000	0.05858	0.004000	0.12327	0.058000	0.15608	0.112000	0.15479	1.448000	0.47680	0.260000	0.18958	GAG	.	.		0.502	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		C	9345181	T	C	9345181	3	2	113	1	0	0	0	0	1	0	0	0	12884	1551	54	2	3139	2	PZP	12	9345181	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	4679532	9345181	124506714	232	18109										
PLBD1	79887	hgsc.bcm.edu	37	chr12	14659104	14659104	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atagcatgttacctttgtgtCataacaacctccaggacttg	7	10	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:14659104C>T	ENST00000240617.5	-	10	2123	c.1471G>A	c.(1471-1473)Gac>Aac	p.D491N		NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	491					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						ACCTTTGTGTCATAACAACCT	0.458																																					p.D491N		Atlas-SNP	.											.	PLBD1	36	.	0			c.G1471A						.						123	107	113					12																	14659104		2203	4300	6503	SO:0001583	missense	79887	exon10			TTGTGTCATAACA	BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"PLB homolog 1 (Dictyostelium)"					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.1471G>A	chr12.hg19:g.14659104C>T	ENSP00000240617:p.Asp491Asn	160.0	0.0		77.0	5.0	NM_024829	A8K4E9|Q9BVV3|Q9H625	Missense_Mutation	SNP	ENST00000240617.5	hg19	CCDS31751.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.961166	0.92791	.	.	ENSG00000121316	ENST00000240617	T	0.21031	2.03	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.60353	0.2262	H	0.94462	3.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71279	-0.4640	10	0.87932	D	0	-31.7468	18.182	0.89781	0.0:1.0:0.0:0.0	.	491	Q6P4A8	PLBL1_HUMAN	N	491	ENSP00000240617:D491N	ENSP00000240617:D491N	D	-	1	0	PLBD1	14550371	1.000000	0.71417	1.000000	0.80357	0.542000	0.35054	7.425000	0.80255	2.793000	0.96121	0.655000	0.94253	GAC	.	.		0.458	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829		T	14659104	C	T	14659104	3	4	113	1	0	0	0	0	1	0	0	0	12034	826	29	3	198	3	PLBD1	12	14659104	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	5313923	14659104	119192791	233	18110										
CMAS	55907	hgsc.bcm.edu	37	chr12	22215331	22215331	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gttgtagatgaatggagaaaAgaaatgggcctgtgctggaa	15	3	0	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:22215331A>G	ENST00000229329.2	+	7	1207	c.1077A>G	c.(1075-1077)aaA>aaG	p.K359K		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	359					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						AATGGAGAAAAGAAATGGGCC	0.373																																					p.K359K		Atlas-SNP	.											.	CMAS	45	.	0			c.A1077G						.						152	170	164					12																	22215331		2203	4300	6503	SO:0001819	synonymous_variant	55907	exon7			GAGAAAAGAAATG	AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"CMP-Neu5Ac synthetase"	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.1077A>G	chr12.hg19:g.22215331A>G		255.0	0.0		141.0	6.0	NM_018686	Q96AX5|Q9NQZ0	Silent	SNP	ENST00000229329.2	hg19	CCDS8696.1																																																																																			.	.		0.373	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686		G	22215331	A	G	22215331	2	3	113	1	0	0	0	0	0	0	0	1	3577	69	3	2		2	CMAS	12	22215331	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	7556227	22215331	111636564	234	18111										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41318438	41318438	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atggtgcttctctgtgacccCccataccattttccaggtaa	7	13	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:41318438C>G	ENST00000551295.2	+	6	597	c.480C>G	c.(478-480)ccC>ccG	p.P160P	CNTN1_ENST00000360099.3_Silent_p.P160P|CNTN1_ENST00000347616.1_Silent_p.P160P|CNTN1_ENST00000547702.1_Silent_p.P160P|CNTN1_ENST00000547849.1_Silent_p.P160P|CNTN1_ENST00000348761.2_Silent_p.P149P	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	160	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TCTGTGACCCCCCATACCATT	0.378																																					p.P160P		Atlas-SNP	.											.	CNTN1	207	.	0			c.C480G						.						121	102	109					12																	41318438		2203	4300	6503	SO:0001819	synonymous_variant	1272	exon6			TGACCCCCCATAC	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.480C>G	chr12.hg19:g.41318438C>G		240.0	0.0		118.0	27.0	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Silent	SNP	ENST00000551295.2	hg19	CCDS8737.1																																																																																			.	.		0.378	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		G	41318438	C	G	41318438	2	3	113	1	0	0	0	0	0	0	0	1	3642	610	22	4		4	CNTN1	12	41318438	Silent	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	19103107	41318438	92533457	235	18112										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43856718	43856718	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cattccaggaccgcagtctgTtccatctgctggtggcacgt	11	13	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:43856718T>C	ENST00000389420.3	-	11	1593	c.1594A>G	c.(1594-1596)Aca>Gca	p.T532A	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.T532A	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	532	Disintegrin.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		CCGCAGTCTGTTCCATCTGCT	0.438																																					p.T532A		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A1594G						.						148	113	125					12																	43856718		2203	4300	6503	SO:0001583	missense	80070	exon11			AGTCTGTTCCATC	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1594A>G	chr12.hg19:g.43856718T>C	ENSP00000374071:p.Thr532Ala	145.0	0.0		82.0	4.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	21.2	4.111586	0.77210	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.70869	-0.34;-0.52	4.87	4.87	0.63330	.	0.000000	0.53938	D	0.000045	D	0.89451	0.6719	H	0.97564	4.03	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.93193	0.6585	10	0.87932	D	0	.	15.1967	0.73096	0.0:0.0:0.0:1.0	.	532	P59510	ATS20_HUMAN	A	532	ENSP00000374071:T532A;ENSP00000448341:T532A	ENSP00000374068:T532A	T	-	1	0	ADAMTS20	42142985	1.000000	0.71417	0.985000	0.45067	0.744000	0.42396	7.559000	0.82265	2.123000	0.65237	0.533000	0.62120	ACA	.	.		0.438	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		C	43856718	T	C	43856718	3	2	113	1	0	0	0	0	1	0	0	0	266	1725	60	2	4253	2	ADAMTS20	12	43856718	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2538280	43856718	89995177	236	18113										
PUS7L	83448	hgsc.bcm.edu	37	chr12	44148626	44148626	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cacttctctcttacatcacaGgcaaaattattcagtaactc	3	12	4	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:44148626G>A	ENST00000416848.2	-	2	911	c.423C>T	c.(421-423)gcC>gcT	p.A141A	PUS7L_ENST00000431332.3_Intron|PUS7L_ENST00000344862.5_Silent_p.A141A|PUS7L_ENST00000553166.1_Silent_p.A141A|PUS7L_ENST00000551923.1_Silent_p.A141A	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	141					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.A141A(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		TTACATCACAGGCAAAATTAT	0.368																																					p.A141A		Atlas-SNP	.											PUS7L,NS,carcinoma,0,1	PUS7L	73	.	1	Substitution - coding silent(1)	lung(1)	c.C423T						.						97	96	96					12																	44148626		2203	4299	6502	SO:0001819	synonymous_variant	83448	exon2			ATCACAGGCAAAA	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.423C>T	chr12.hg19:g.44148626G>A		119.0	0.0		75.0	25.0	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Silent	SNP	ENST00000416848.2	hg19	CCDS8743.1																																																																																			.	.		0.368	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		A	44148626	G	A	44148626	2	1	113	1	0	0	0	0	0	0	0	1	12849	987	35	3		3	PUS7L	12	44148626	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	291908	44148626	89703269	237	18114										
GPR84	53831	hgsc.bcm.edu	37	chr12	54757190	54757190	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agaggggagcaaagctggccAcgcccacaacccaggtgctc	13	14	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:54757190A>G	ENST00000551809.1	-	1	1081	c.446T>C	c.(445-447)gTg>gCg	p.V149A	GPR84_ENST00000267015.3_Missense_Mutation_p.V149A|RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	149						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						AAAGCTGGCCACGCCCACAAC	0.577																																					p.V149A		Atlas-SNP	.											.	GPR84	38	.	0			c.T446C						.						54	46	49					12																	54757190		2203	4300	6503	SO:0001583	missense	53831	exon2			CTGGCCACGCCCA	AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.446T>C	chr12.hg19:g.54757190A>G	ENSP00000450310:p.Val149Ala	83.0	0.0		50.0	24.0	NM_020370	B6V9G7	Missense_Mutation	SNP	ENST00000551809.1	hg19	CCDS8878.1	.	.	.	.	.	.	.	.	.	.	A	11.06	1.526378	0.27299	.	.	ENSG00000139572	ENST00000267015;ENST00000551809	T;T	0.37584	1.19;1.19	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	0.608353	0.13667	N	0.371156	T	0.26231	0.0640	N	0.25060	0.705	0.38787	D	0.954905	B	0.22541	0.071	B	0.25614	0.062	T	0.09357	-1.0678	10	0.16420	T	0.52	-2.519	12.9907	0.58616	1.0:0.0:0.0:0.0	.	149	Q9NQS5	GPR84_HUMAN	A	149	ENSP00000267015:V149A;ENSP00000450310:V149A	ENSP00000267015:V149A	V	-	2	0	GPR84	53043457	0.994000	0.37717	0.775000	0.31657	0.498000	0.33706	6.753000	0.74904	2.020000	0.59435	0.454000	0.30748	GTG	.	.		0.577	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			G	54757190	A	G	54757190	3	3	113	1	0	0	0	0	1	0	0	0	6722	159	6	2	748	2	GPR84	12	54757190	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	10608564	54757190	79094705	238	18115										
STAT6	6778	hgsc.bcm.edu	37	chr12	57498314	57498314	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agaagagcacagcgcacttcTcctctgtgacagactcagtg	10	12	3	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:57498314T>C	ENST00000300134.3	-	11	1470	c.1145A>G	c.(1144-1146)gAg>gGg	p.E382G	STAT6_ENST00000454075.3_Missense_Mutation_p.E382G|STAT6_ENST00000556155.1_Missense_Mutation_p.E382G|STAT6_ENST00000538913.2_Missense_Mutation_p.E272G|STAT6_ENST00000537215.2_Missense_Mutation_p.E272G|STAT6_ENST00000543873.2_Missense_Mutation_p.E382G	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	382					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						AGCGCACTTCTCCTCTGTGAC	0.612																																					p.E382G		Atlas-SNP	.											.	STAT6	69	.	0			c.A1145G						.						106	86	92					12																	57498314		2203	4300	6503	SO:0001583	missense	6778	exon11			CACTTCTCCTCTG	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"SH2 domain containing"	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.1145A>G	chr12.hg19:g.57498314T>C	ENSP00000300134:p.Glu382Gly	141.0	0.0		81.0	4.0	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	hg19	CCDS8931.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.814954	0.90790	.	.	ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516	D;D;D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24;-3.24;-3.24	4.44	4.44	0.53790	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.96222	0.8768	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.96482	0.9357	10	0.87932	D	0	-21.2024	11.7196	0.51675	0.0:0.0:0.0:1.0	.	382;382	A8K4S9;P42226	.;STAT6_HUMAN	G	382;272;272;382;382;272;382;272;382	ENSP00000300134:E382G;ENSP00000445409:E272G;ENSP00000438451:E382G;ENSP00000451742:E382G;ENSP00000444530:E272G;ENSP00000401486:E382G	ENSP00000300134:E382G	E	-	2	0	STAT6	55784581	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.848000	0.86902	1.863000	0.54032	0.533000	0.62120	GAG	.	.		0.612	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		C	57498314	T	C	57498314	3	2	113	1	0	0	0	0	1	0	0	0	15285	1551	54	2	1446	2	STAT6	12	57498314	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2741124	57498314	76353581	239	18116										
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72004493	72004493	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	acatctttccacagtgatgcAcaaagaggtaacttctgtaa	7	9	2	2	rs377232932		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:72004493A>G	ENST00000378743.3	-	34	6172	c.5814T>C	c.(5812-5814)tgT>tgC	p.C1938C		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1938					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ACAGTGATGCACAAAGAGGTA	0.343																																					p.C1938C		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.T5814C						.	A		0,3682		0,0,1841	79	72	74		5814	5.9	1	12		74	1,8171		0,1,4085	no	coding-synonymous	ZFC3H1	NM_144982.4		0,1,5926	GG,GA,AA		0.0122,0.0,0.0084		1938/1990	72004493	1,11853	1841	4086	5927	SO:0001819	synonymous_variant	196441	exon34			TGATGCACAAAGA	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.5814T>C	chr12.hg19:g.72004493A>G		97.0	0.0		80.0	4.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Silent	SNP	ENST00000378743.3	hg19	CCDS41813.1																																																																																			.	.		0.343	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		G	72004493	A	G	72004493	2	3	113	1	0	0	0	0	0	0	0	1	17648	157	6	2		2	ZFC3H1	12	72004493	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	14506179	72004493	61847402	240	18117										
PPP1R12A	4659	hgsc.bcm.edu	37	chr12	80226243	80226243	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctaagcatgatccgttcttcTtcctttcgagctgcttctat	6	12	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:80226243T>C	ENST00000450142.2	-	4	782	c.516A>G	c.(514-516)gaA>gaG	p.E172E	PPP1R12A_ENST00000550107.1_Silent_p.E172E|PPP1R12A_ENST00000261207.5_Silent_p.E172E|PPP1R12A_ENST00000546369.1_Silent_p.E85E|PPP1R12A_ENST00000437004.2_Silent_p.E172E	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	172					centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						TCCGTTCTTCTTCCTTTCGAG	0.373																																					p.E172E		Atlas-SNP	.											.	PPP1R12A	76	.	0			c.A516G						.						151	142	145					12																	80226243		1886	4112	5998	SO:0001819	synonymous_variant	4659	exon4			TTCTTCTTCCTTT	D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7618	protein-coding gene	gene with protein product	"myosin phosphatase-targeting subunit 1", "myosin binding subunit"	602021	"protein phosphatase 1, regulatory (inhibitor) subunit 12A"	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.516A>G	chr12.hg19:g.80226243T>C		133.0	0.0		91.0	4.0	NM_002480	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Silent	SNP	ENST00000450142.2	hg19	CCDS44947.1																																																																																			.	.		0.373	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		C	80226243	T	C	80226243	2	2	113	1	0	0	0	0	0	0	0	1	12366	1606	56	2		2	PPP1R12A	12	80226243	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	8221750	80226243	53625652	241	18118										
NR2C1	7181	hgsc.bcm.edu	37	chr12	95425194	95425194	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgctacattcatcacttgccAgcactgggcaagaccaagag	9	12	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:95425194A>G	ENST00000333003.5	-	11	1654	c.1324T>C	c.(1324-1326)Tgg>Cgg	p.W442R	NR2C1_ENST00000330677.7_Missense_Mutation_p.W442R|NR2C1_ENST00000393101.3_Missense_Mutation_p.W442R|NR2C1_ENST00000545833.1_Intron	NM_003297.3	NP_003288.2	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	442					gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	DNA binding (GO:0003677)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13						ATCACTTGCCAGCACTGGGCA	0.368																																					p.W442R		Atlas-SNP	.											.	NR2C1	56	.	0			c.T1324C						.						126	128	127					12																	95425194		2203	4300	6503	SO:0001583	missense	7181	exon11			CTTGCCAGCACTG	M29960	CCDS9051.1, CCDS41821.1, CCDS44953.1	12q22	2013-01-16				ENSG00000120798		"Nuclear hormone receptors"	7971	protein-coding gene	gene with protein product		601529		TR2		2597158	Standard	NM_001032287		Approved	TR2-11	uc001tdm.5	P13056	OTTHUMG00000170131	ENST00000333003.5:c.1324T>C	chr12.hg19:g.95425194A>G	ENSP00000333275:p.Trp442Arg	88.0	0.0		61.0	4.0	NM_001032287	A8K5K4|Q15625|Q15626	Missense_Mutation	SNP	ENST00000333003.5	hg19	CCDS9051.1	.	.	.	.	.	.	.	.	.	.	A	16.03	3.005809	0.54254	.	.	ENSG00000120798	ENST00000333003;ENST00000393101;ENST00000330677	D;D;D	0.96459	-4.02;-4.02;-4.02	5.53	5.53	0.82687	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.251067	0.43747	D	0.000526	D	0.88869	0.6554	N	0.02539	-0.55	0.39368	D	0.966038	P;B;B	0.37636	0.603;0.413;0.175	B;B;B	0.36845	0.234;0.097;0.163	D	0.89745	0.3936	10	0.23302	T	0.38	.	15.9481	0.79809	1.0:0.0:0.0:0.0	.	442;442;442	P13056-3;P13056-2;P13056	.;.;NR2C1_HUMAN	R	442	ENSP00000333275:W442R;ENSP00000376813:W442R;ENSP00000328843:W442R	ENSP00000328843:W442R	W	-	1	0	NR2C1	93949325	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	5.597000	0.67577	2.225000	0.72522	0.460000	0.39030	TGG	.	.		0.368	NR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407565.2	NM_003297		G	95425194	A	G	95425194	3	3	113	1	0	0	0	0	1	0	0	0	10631	188	7	2	581	2	NR2C1	12	95425194	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	15198951	95425194	38426701	242	18119										
NUP37	79023	hgsc.bcm.edu	37	chr12	102470582	102470582	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aacggtacattacctgaataAgcaggctcgatccatgtgaa	9	9	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:102470582A>G	ENST00000552283.1	-	8	905	c.766T>C	c.(766-768)Tta>Cta	p.L256L	RP11-554E23.4_ENST00000552707.1_RNA|NUP37_ENST00000251074.1_Silent_p.L256L|NUP37_ENST00000543021.1_5'Flank			Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	256					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(10)|ovary(1)	17						TACCTGAATAAGCAGGCTCGA	0.378																																					p.L256L		Atlas-SNP	.											.	NUP37	26	.	0			c.T766C						.						159	135	143					12																	102470582		2203	4300	6503	SO:0001819	synonymous_variant	79023	exon7			TGAATAAGCAGGC	AF514994	CCDS9089.1	12q23.2	2014-08-12			ENSG00000075188	ENSG00000075188		"WD repeat domain containing"	29929	protein-coding gene	gene with protein product		609264				12196509	Standard	NM_024057		Approved	MGC5585, FLJ22618	uc001tjc.3	Q8NFH4	OTTHUMG00000170478	ENST00000552283.1:c.766T>C	chr12.hg19:g.102470582A>G		143.0	0.0		76.0	4.0	NM_024057	Q9H644	Silent	SNP	ENST00000552283.1	hg19	CCDS9089.1																																																																																			.	.		0.378	NUP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409330.1	NM_024057		G	102470582	A	G	102470582	2	3	113	1	0	0	0	0	0	0	0	1	10773	69	3	2		2	NUP37	12	102470582	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	7045388	102470582	31381313	243	18120										
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105534132	105534132	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgattcagtttcacatataAcacagcaccttcaacatcag	4	12	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:105534132A>G	ENST00000332180.5	+	16	1600	c.1513A>G	c.(1513-1515)Aca>Gca	p.T505A		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						TTCACATATAACACAGCACCT	0.343																																					p.T505A		Atlas-SNP	.											.	KIAA1033	83	.	0			c.A1513G						.						185	177	180					12																	105534132		1912	4134	6046	SO:0001583	missense	23325	exon16			CATATAACACAGC	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.1513A>G	chr12.hg19:g.105534132A>G	ENSP00000328062:p.Thr505Ala	256.0	0.0		85.0	4.0	NM_015275		Missense_Mutation	SNP	ENST00000332180.5	hg19	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	A	13.27	2.185806	0.38609	.	.	ENSG00000136051	ENST00000332180	T	0.29917	1.55	5.84	5.84	0.93424	.	0.138898	0.64402	D	0.000004	T	0.27027	0.0662	L	0.53249	1.67	0.52501	D	0.999954	B;B	0.12630	0.006;0.006	B;B	0.10450	0.005;0.005	T	0.09143	-1.0688	10	0.07990	T	0.79	.	12.4697	0.55779	0.8749:0.0:0.0:0.1251	.	506;505	B7ZKT9;Q2M389	.;WASH7_HUMAN	A	505	ENSP00000328062:T505A	ENSP00000328062:T505A	T	+	1	0	KIAA1033	104058262	0.999000	0.42202	1.000000	0.80357	0.989000	0.77384	3.631000	0.54280	2.230000	0.72887	0.528000	0.53228	ACA	.	.		0.343	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		G	105534132	A	G	105534132	3	3	113	1	0	0	0	0	1	0	0	0	8215	43	2	2	1575	2	KIAA1033	12	105534132	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3063550	105534132	28317763	244	18121										
ACACB	32	hgsc.bcm.edu	37	chr12	109617834	109617834	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctgaatcctcgcttgcaggTggaacatccctgcacagaaa	10	12	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:109617834T>C	ENST00000338432.7	+	11	1879	c.1760T>C	c.(1759-1761)gTg>gCg	p.V587A	ACACB_ENST00000377854.5_Missense_Mutation_p.V587A|ACACB_ENST00000377848.3_Missense_Mutation_p.V587A|ACACB_ENST00000543080.1_3'UTR			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	587	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	CGCTTGCAGGTGGAACATCCC	0.557																																					p.V587A		Atlas-SNP	.											.	ACACB	330	.	0			c.T1760C						.						106	93	97					12																	109617834		2203	4300	6503	SO:0001583	missense	32	exon10			TGCAGGTGGAACA	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.1760T>C	chr12.hg19:g.109617834T>C	ENSP00000341044:p.Val587Ala	197.0	0.0		76.0	4.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.880874	0.91740	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	D;D;D	0.97598	-4.45;-4.45;-4.45	4.89	4.89	0.63831	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.000000	0.85682	D	0.000000	D	0.99171	0.9713	H	0.99104	4.43	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98671	1.0688	10	0.87932	D	0	.	14.4983	0.67704	0.0:0.0:0.0:1.0	.	587	O00763	ACACB_HUMAN	A	587	ENSP00000341044:V587A;ENSP00000367079:V587A;ENSP00000367085:V587A	ENSP00000341044:V587A	V	+	2	0	ACACB	108102217	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.929000	0.87595	1.835000	0.53391	0.533000	0.62120	GTG	.	.		0.557	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		C	109617834	T	C	109617834	3	2	113	1	0	0	0	0	1	0	0	0	107	1696	59	2	1798	2	ACACB	12	109617834	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	4083702	109617834	24234061	245	18122										
ATXN2	6311	hgsc.bcm.edu	37	chr12	111963044	111963044	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcattggctgtgagttcaccTgcatcccagggctccaggtc	11	13	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:111963044T>C	ENST00000377617.3	-	6	1289	c.1128A>G	c.(1126-1128)gcA>gcG	p.A376A	ATXN2_ENST00000608853.1_Silent_p.A216A|ATXN2_ENST00000389153.4_Silent_p.A111A|ATXN2_ENST00000542287.2_Silent_p.A111A|ATXN2_ENST00000535949.1_Silent_p.A87A|ATXN2_ENST00000550104.1_Silent_p.A376A|ATXN2_ENST00000549455.1_5'UTR	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	376					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						TGAGTTCACCTGCATCCCAGG	0.433																																					p.A376A		Atlas-SNP	.											.	ATXN2	99	.	0			c.A1128G						.						173	148	157					12																	111963044		2203	4300	6503	SO:0001819	synonymous_variant	6311	exon6			TTCACCTGCATCC	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.1128A>G	chr12.hg19:g.111963044T>C		138.0	0.0		54.0	4.0	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Silent	SNP	ENST00000377617.3	hg19	CCDS31902.1																																																																																			.	.		0.433	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		C	111963044	T	C	111963044	2	2	113	1	0	0	0	0	0	0	0	1	1211	1567	55	2		2	ATXN2	12	111963044	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2345210	111963044	21888851	246	18123										
SBNO1	55206	hgsc.bcm.edu	37	chr12	123793921	123793921	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cccaaatcttggtagcttccTcccatgacattcccctctct	4	17	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:123793921T>C	ENST00000602398.1	-	28	3693	c.3566A>G	c.(3565-3567)gAg>gGg	p.E1189G	SBNO1_ENST00000267176.4_Missense_Mutation_p.E1188G|SBNO1_ENST00000420886.2_Missense_Mutation_p.E1189G|SBNO1_ENST00000602750.1_Missense_Mutation_p.E1188G			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1189					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		GGTAGCTTCCTCCCATGACAT	0.388																																					p.E1189G		Atlas-SNP	.											.	SBNO1	138	.	0			c.A3566G						.						115	113	113					12																	123793921		2203	4300	6503	SO:0001583	missense	55206	exon27			GCTTCCTCCCATG	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.3566A>G	chr12.hg19:g.123793921T>C	ENSP00000473665:p.Glu1189Gly	181.0	0.0		91.0	5.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	hg19	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	T	17.59	3.426805	0.62733	.	.	ENSG00000139697	ENST00000420886;ENST00000267176	D;D	0.83673	-1.75;-1.75	5.2	4.06	0.47325	.	0.200475	0.42294	N	0.000721	T	0.81235	0.4780	M	0.82056	2.57	0.51012	D	0.999906	B;B;P	0.43431	0.039;0.066;0.807	B;B;B	0.37692	0.014;0.033;0.256	T	0.79052	-0.1961	10	0.39692	T	0.17	-11.4839	10.6188	0.45467	0.0:0.0756:0.0:0.9244	.	1189;1188;300	A3KN83;A3KN83-2;B3KUC1	SBNO1_HUMAN;.;.	G	1189;1188	ENSP00000387361:E1189G;ENSP00000267176:E1188G	ENSP00000267176:E1188G	E	-	2	0	SBNO1	122359874	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	8.013000	0.88655	0.825000	0.34637	0.383000	0.25322	GAG	.	.		0.388	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		C	123793921	T	C	123793921	3	2	113	1	0	0	0	0	1	0	0	0	13877	1551	54	2	635	2	SBNO1	12	123793921	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	11830877	123793921	10057974	247	18124										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124305128	124305128	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cggtgtatttatttactaggAgtagagcttttaggtgttta	11	3	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:124305128A>G	ENST00000409039.3	+	23	3673	c.3648A>G	c.(3646-3648)ggA>ggG	p.G1216G		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1216	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		ATTTACTAGGAGTAGAGCTTT	0.333																																					p.G1216G		Atlas-SNP	.											.	DNAH10	888	.	0			c.A3648G						.						65	67	66					12																	124305128		1826	4087	5913	SO:0001630	splice_region_variant	196385	exon23			ACTAGGAGTAGAG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.3647-1A>G	chr12.hg19:g.124305128A>G		155.0	0.0		63.0	4.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.333	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		Silent	G	124305128	A	G	124305128	5	3	113	1	0	0	0	0	0	0	1	0	4600	318	11	2	3738	2	DNAH10	12	124305128	Splice_Site	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	511207	124305128	9546767	248	18125										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	129694080	129694080	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cttgccttaatcacgtcttcAtcagacgatctacactccac	4	15	5	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr12:129694080A>G	ENST00000422113.2	-	5	1754	c.1428T>C	c.(1426-1428)gaT>gaC	p.D476D	RP11-669N7.3_ENST00000542578.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	476					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TCACGTCTTCATCAGACGATC	0.592																																					p.D476D		Atlas-SNP	.											.	TMEM132D	299	.	0			c.T1428C						.						106	86	93					12																	129694080		2203	4300	6503	SO:0001819	synonymous_variant	121256	exon5			GTCTTCATCAGAC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1428T>C	chr12.hg19:g.129694080A>G		230.0	0.0		73.0	4.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	hg19	CCDS9266.1																																																																																			.	.		0.592	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		G	129694080	A	G	129694080	2	3	113	1	0	0	0	0	0	0	0	1	16062	214	8	2		2	TMEM132D	12	129694080	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	5388952	129694080	4157815	249	18126										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24874603	24874603	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctcaaaaggcaggacatggAaagtcaaaaggtaagttatg	12	5	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr13:24874603A>G	ENST00000382095.4	+	11	2180	c.1773A>G	c.(1771-1773)ggA>ggG	p.G591G	SPATA13_ENST00000382108.3_Silent_p.G1216G|SPATA13_ENST00000399949.2_Silent_p.G513G|SPATA13_ENST00000409126.1_Silent_p.G451G|SPATA13_ENST00000343003.6_Silent_p.G535G|RP11-307N16.6_ENST00000382141.4_Silent_p.G1094G|SPATA13_ENST00000424834.2_Silent_p.G1216G	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	591	C-terminal tail.				cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		CAGGACATGGAAAGTCAAAAG	0.388																																					p.G1216G		Atlas-SNP	.											.	SPATA13	92	.	0			c.A3648G						.						87	79	82					13																	24874603		2203	4300	6503	SO:0001819	synonymous_variant	221178	exon12			ACATGGAAAGTCA	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.1773A>G	chr13.hg19:g.24874603A>G		161.0	0.0		98.0	4.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	hg19	CCDS9305.1	.	.	.	.	.	.	.	.	.	.	A	2.433	-0.330481	0.05314	.	.	ENSG00000182957	ENST00000424834	.	.	.	5.03	-9.43	0.00607	.	.	.	.	.	T	0.50309	0.1608	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61667	-0.7016	4	.	.	.	.	11.3878	0.49796	0.2594:0.2019:0.5388:0.0	.	.	.	.	E	1254	.	.	K	+	1	0	SPATA13	23772603	0.409000	0.25368	0.118000	0.21660	0.379000	0.30106	-0.268000	0.08607	-2.230000	0.00719	-1.119000	0.02030	AAA	.	.		0.388	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		G	24874603	A	G	24874603	2	3	113	1	0	0	0	0	0	0	0	1	15015	233	9	2		2	SPATA13	13	24874603	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10		24874603	90295275	250	18127										
ATP12A	479	hgsc.bcm.edu	37	chr13	25266933	25266933	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tctgtcttccagaccaagtcTttgaccaaagctctaggact	7	12	4	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr13:25266933T>C	ENST00000381946.3	+	10	1443	c.1276T>C	c.(1276-1278)Ttt>Ctt	p.F426L	ATP12A_ENST00000218548.6_Missense_Mutation_p.F432L			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	426					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		AGACCAAGTCTTTGACCAAAG	0.512																																					p.F432L	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.T1294C						.						214	212	213					13																	25266933		2203	4300	6503	SO:0001583	missense	479	exon10			CAAGTCTTTGACC	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1276T>C	chr13.hg19:g.25266933T>C	ENSP00000371372:p.Phe426Leu	152.0	0.0		98.0	4.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.281949	0.80692	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.95377	-3.69;-3.69	5.65	5.65	0.86999	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.95130	0.8422	N	0.20530	0.585	0.58432	D	0.999999	D;D	0.71674	0.998;0.998	D;D	0.87578	0.998;0.993	D	0.95044	0.8181	10	0.41790	T	0.15	.	13.8261	0.63351	0.0:0.0:0.0:1.0	.	432;426	P54707-2;P54707	.;AT12A_HUMAN	L	432;426	ENSP00000218548:F432L;ENSP00000371372:F426L	ENSP00000218548:F432L	F	+	1	0	ATP12A	24164933	1.000000	0.71417	0.929000	0.37066	0.467000	0.32768	7.479000	0.81095	2.154000	0.67381	0.533000	0.62120	TTT	.	.		0.512	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		C	25266933	T	C	25266933	3	2	113	1	0	0	0	0	1	0	0	0	1122	1609	56	2	1332	2	ATP12A	13	25266933	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	392330	25266933	89902945	251	18128										
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26114518	26114518	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atggggagacgaaccttaaaAtacgtcaggtaaagtcacct	10	8	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr13:26114518A>G	ENST00000381655.2	+	8	785	c.643A>G	c.(643-645)Ata>Gta	p.I215V	ATP8A2_ENST00000255283.8_Missense_Mutation_p.I175V	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	175					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		GAACCTTAAAATACGTCAGGT	0.388																																					p.I215V		Atlas-SNP	.											ATP8A2,colon,carcinoma,0,1	ATP8A2	181	.	0			c.A643G						.						120	111	114					13																	26114518		1872	4120	5992	SO:0001583	missense	51761	exon8			CTTAAAATACGTC	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.643A>G	chr13.hg19:g.26114518A>G	ENSP00000371070:p.Ile215Val	221.0	2.0		123.0	5.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	hg19	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.216889	0.79352	.	.	ENSG00000132932	ENST00000381655;ENST00000255283	T;T	0.73681	-0.77;-0.77	6.15	3.68	0.42216	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	T	0.77039	0.4072	L	0.46567	1.45	0.52501	D	0.999951	D;D;D	0.55385	0.971;0.97;0.971	P;P;P	0.59288	0.855;0.814;0.855	T	0.76982	-0.2757	10	0.59425	D	0.04	.	9.2631	0.37625	0.8124:0.1227:0.0648:0.0	.	175;175;175	B7Z880;Q9NTI2-3;Q9NTI2	.;.;AT8A2_HUMAN	V	215;175	ENSP00000371070:I215V;ENSP00000255283:I175V	ENSP00000255283:I175V	I	+	1	0	ATP8A2	25012518	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.013000	0.70776	1.121000	0.41925	0.523000	0.50628	ATA	.	.		0.388	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		G	26114518	A	G	26114518	3	3	113	1	0	0	0	0	1	0	0	0	1193	101	4	2	673	2	ATP8A2	13	26114518	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	847585	26114518	89055360	252	18129										
BRCA2	675	hgsc.bcm.edu	37	chr13	32911477	32911477	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tacatgaacaaatgggcaggActcttaggtccaatttcaaa	8	8	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr13:32911477A>G	ENST00000380152.3	+	11	3218	c.2985A>G	c.(2983-2985)ggA>ggG	p.G995G	BRCA2_ENST00000544455.1_Silent_p.G995G			P51587	BRCA2_HUMAN	breast cancer 2, early onset	995	Interaction with NPM1.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.G995G(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AATGGGCAGGACTCTTAGGTC	0.323			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.G995G	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	BRCA2_ENST00000544455,NS,carcinoma,0,2	BRCA2	812	.	2	Substitution - coding silent(2)	kidney(2)	c.A2985G						.						52	58	56					13																	32911477		2203	4294	6497	SO:0001819	synonymous_variant	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	GGCAGGACTCTTA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.2985A>G	chr13.hg19:g.32911477A>G		140.0	0.0		71.0	3.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	hg19	CCDS9344.1																																																																																			.	.		0.323	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32911477	A	G	32911477	2	3	113	1	0	0	0	0	0	0	0	1	1501	262	10	2		2	BRCA2	13	32911477	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	6796959	32911477	82258401	253	18130										
ERCC5	2073	hgsc.bcm.edu	37	chr13	103525646	103525646	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcggctggaacagaacgaagAcagatgaatctctgtttcct	10	9	1	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr13:103525646A>G	ENST00000355739.4	+	14	4340	c.2917A>G	c.(2917-2919)Aca>Gca	p.T973A	ERCC5_ENST00000375954.1_Missense_Mutation_p.T206A	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	973					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CAGAACGAAGACAGATGAATC	0.393			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.T1427A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"		E	.	.	.	.	0			c.A4279G						.						119	114	116					13																	103525646		2203	4300	6503	SO:0001583	missense	0	exon22	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ACGAAGACAGATG	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"Cockayne syndrome"	133530	"xeroderma pigmentosum, complementation group G", "excision repair cross-complementing rodent repair deficiency, complementation group 5"	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.2917A>G	chr13.hg19:g.103525646A>G	ENSP00000347978:p.Thr973Ala	130.0	0.0		94.0	4.0	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	hg19	CCDS32004.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.013286	0.93346	.	.	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000375955;ENST00000375954	T;T	0.79352	-1.26;-1.26	5.54	5.54	0.83059	-3&apos (1); exonuclease, C-terminal domain (1);5&apos (1);	0.000000	0.85682	D	0.000000	D	0.85089	0.5617	M	0.62209	1.925	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	D	0.83414	0.0029	10	0.29301	T	0.29	-18.1588	15.3376	0.74269	1.0:0.0:0.0:0.0	.	973	P28715	ERCC5_HUMAN	A	1398;973;805;206	ENSP00000347978:T973A;ENSP00000365121:T206A	ENSP00000347978:T973A	T	+	1	0	ERCC5	102323647	1.000000	0.71417	0.923000	0.36655	0.976000	0.68499	5.651000	0.67951	2.111000	0.64477	0.477000	0.44152	ACA	.	.		0.393	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			G	103525646	A	G	103525646	3	3	113	1	0	0	0	0	1	0	0	0	5218	275	10	2	2971	2	ERCC5	13	103525646	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	70614169	103525646	11644232	254	18131										
RNASE7	84659	hgsc.bcm.edu	37	chr14	21511444	21511444	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gaatggcgataaaaactgccAccagagccacggggccgtgt	13	11	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:21511444A>G	ENST00000298690.4	+	2	550	c.293A>G	c.(292-294)cAc>cGc	p.H98R	NDRG2_ENST00000403829.3_Intron	NM_032572.3	NP_115961	Q9H1E1	RNAS7_HUMAN	ribonuclease, RNase A family, 7	98					antibacterial humoral response (GO:0019731)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|membrane disruption in other organism (GO:0051673)|response to bacterium (GO:0009617)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|lipopolysaccharide binding (GO:0001530)|nucleic acid binding (GO:0003676)|peptidoglycan binding (GO:0042834)|ribonuclease activity (GO:0004540)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	6	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;3.42e-11)|Epithelial(56;5.57e-09)|all cancers(55;2.36e-08)	GBM - Glioblastoma multiforme(265;0.0191)		AAAAACTGCCACCAGAGCCAC	0.547																																					p.H98R		Atlas-SNP	.											.	RNASE7	18	.	0			c.A293G						.						101	99	100					14																	21511444		2203	4300	6503	SO:0001583	missense	84659	exon2			ACTGCCACCAGAG	AJ131212	CCDS41914.1	14q11.1	2013-02-15			ENSG00000165799	ENSG00000165799		"Ribonucleases, RNase A"	19278	protein-coding gene	gene with protein product		612484				12244054, 12527768	Standard	NM_032572		Approved		uc001vzk.4	Q9H1E1	OTTHUMG00000171358	ENST00000298690.4:c.293A>G	chr14.hg19:g.21511444A>G	ENSP00000298690:p.His98Arg	118.0	0.0		69.0	4.0	NM_032572	P80927|P83685|Q546N3	Missense_Mutation	SNP	ENST00000298690.4	hg19	CCDS41914.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.145191	0.57044	.	.	ENSG00000165799	ENST00000298690	T	0.15372	2.43	5.09	5.09	0.68999	Ribonuclease A, domain (4);	0.376195	0.23939	U	0.043076	T	0.37865	0.1019	M	0.66439	2.03	0.34757	D	0.732393	D	0.67145	0.996	D	0.72625	0.978	T	0.53599	-0.8416	10	0.87932	D	0	-38.3011	11.1778	0.48610	1.0:0.0:0.0:0.0	.	98	Q9H1E1	RNAS7_HUMAN	R	98	ENSP00000298690:H98R	ENSP00000298690:H98R	H	+	2	0	RNASE7	20581284	0.999000	0.42202	0.999000	0.59377	0.360000	0.29518	3.974000	0.56852	2.142000	0.66516	0.533000	0.62120	CAC	.	.		0.547	RNASE7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313936.1	NM_032572		G	21511444	A	G	21511444	3	3	113	1	0	0	0	0	1	0	0	0	13423	159	6	2	295	2	RNASE7	14	21511444	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10		21511444	85838096	255	18132										
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21544999	21544999	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagaggagctgcagtgggagTtaggaggtcacagggacccc	17	9	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:21544999T>C	ENST00000298694.4	+	8	2111	c.1984T>C	c.(1984-1986)Tta>Cta	p.L662L	ARHGEF40_ENST00000298693.3_Silent_p.L662L			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	662						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						GCAGTGGGAGTTAGGAGGTCA	0.567																																					p.L662L		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.T1984C						.						50	49	49					14																	21544999		2203	4300	6503	SO:0001819	synonymous_variant	55701	exon8			TGGGAGTTAGGAG		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"Rho guanine nucleotide exchange factors"	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.1984T>C	chr14.hg19:g.21544999T>C		168.0	0.0		89.0	4.0	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	hg19	CCDS32041.1																																																																																			.	.		0.567	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			C	21544999	T	C	21544999	2	2	113	1	0	0	0	0	0	0	0	1	5934	1722	60	2		2	FLJ10357	14	21544999	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	33555	21544999	85804541	256	18133										
SUPT16H	11198	hgsc.bcm.edu	37	chr14	21829290	21829311	+	Frame_Shift_Del	DEL	TAATAATTCGGAAAGCATTCTG	TAATAATTCGGAAAGCATTCTG	-													0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ataacgtttctgtacttcttTaataattcggaaagcattct							TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	TAATAATTCGGAAAGCATTCTG	TAATAATTCGGAAAGCATTCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:21829290_21829311delTAATAATTCGGAAAGCATTCTG	ENST00000216297.2	-	16	2193_2214	c.1855_1876delCAGAATGCTTTCCGAATTATTA	c.(1855-1878)cagaatgctttccgaattattaaafs	p.QNAFRIIK619fs		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	619					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		TGTACTTCTTTAATAATTCGGAAAGCATTCTGAAGGTTCAAG	0.396																																					p.619_626del		Pindel	.											.	SUPT16H	84	.	0			c.1856_1877del						.																																			SO:0001589	frameshift_variant	11198	exon16			.	AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 140 kDa subunit"	605012	"suppressor of Ty (S.cerevisiae) 16 homolog"			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.1855_1876delCAGAATGCTTTCCGAATTATTA	chr14.hg19:g.21829290_21829311delTAATAATTCGGAAAGCATTCTG	ENSP00000216297:p.Gln619fs	0.0	0.0		91.0	15.0	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Frame_Shift_Del	DEL	ENST00000216297.2	hg19	CCDS9569.1																																																																																			.	.		0.396	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2			-	21829311	TAATAATTCGGAAAGCATTCTG	-	21829290	7	5	113	1	0	1	0	1	0	0	0	0	15411	1763	61	0	1311	0	SUPT16H	14	21829290	Frame_Shift_Del	DEL	TAATAATTCGGAAAGCATTCTG	TCGA-DD-A39Z-01A-11D-A20W-10	284291	21829290	85520250	257	18134										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23551018	23551018	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tctcatcatcagagtcacctTtctcttcagaaattgaggag	7	10	6	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:23551018T>C	ENST00000262710.1	-	5	965	c.638A>G	c.(637-639)aAa>aGa	p.K213R	ACIN1_ENST00000605057.1_Missense_Mutation_p.K155R|ACIN1_ENST00000457657.1_Missense_Mutation_p.K173R|ACIN1_ENST00000555053.1_Missense_Mutation_p.K213R|ACIN1_ENST00000555352.1_5'Flank	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	213	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		AGAGTCACCTTTCTCTTCAGA	0.378																																					p.K213R		Atlas-SNP	.											.	ACIN1	147	.	0			c.A638G						.						223	203	210					14																	23551018		2203	4300	6503	SO:0001583	missense	22985	exon5			TCACCTTTCTCTT	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.638A>G	chr14.hg19:g.23551018T>C	ENSP00000262710:p.Lys213Arg	121.0	0.0		77.0	4.0	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	T	19.60	3.857153	0.71834	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.30182	2.38;1.54;2.38	5.93	5.93	0.95920	.	0.000000	0.42172	D	0.000751	T	0.41558	0.1164	L	0.36672	1.1	0.26012	N	0.981971	D;D	0.61697	0.99;0.982	D;D	0.72982	0.979;0.952	T	0.33828	-0.9853	10	0.41790	T	0.15	-16.835	8.8645	0.35278	0.0:0.0829:0.0:0.9171	.	213;213	G3V3M7;Q9UKV3	.;ACINU_HUMAN	R	213;173;213	ENSP00000262710:K213R;ENSP00000405677:K173R;ENSP00000451328:K213R	ENSP00000262710:K213R	K	-	2	0	ACIN1	22620858	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.631000	0.46502	2.265000	0.75225	0.533000	0.62120	AAA	.	.		0.378	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23551018	T	C	23551018	3	2	113	1	0	0	0	0	1	0	0	0	142	1841	64	2	3594	2	ACIN1	14	23551018	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1721728	23551018	83798522	258	18135										
FOXG1	2290	hgsc.bcm.edu	37	chr14	29237096	29237096	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccccgagaagcggctcacgcTcaacggcatctacgagttca	10	15	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:29237096T>C	ENST00000313071.4	+	1	810	c.611T>C	c.(610-612)cTc>cCc	p.L204P	RP11-966I7.1_ENST00000551395.1_RNA|RP11-966I7.1_ENST00000549487.1_RNA|RP11-966I7.1_ENST00000546560.1_RNA|FOXG1_ENST00000382535.3_Missense_Mutation_p.L204P	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	204					aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		CGGCTCACGCTCAACGGCATC	0.567																																					p.L204P		Atlas-SNP	.											.	FOXG1	92	.	0			c.T611C						.						52	51	51					14																	29237096		2203	4300	6503	SO:0001583	missense	2290	exon1			TCACGCTCAACGG		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.611T>C	chr14.hg19:g.29237096T>C	ENSP00000339004:p.Leu204Pro	175.0	0.0		120.0	5.0	NM_005249	A6NFY2|P55315|Q14488|Q86XT7	Missense_Mutation	SNP	ENST00000313071.4	hg19	CCDS9636.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.962050	0.74016	.	.	ENSG00000176165	ENST00000382535;ENST00000313071	D;D	0.97598	-4.45;-4.45	3.26	3.26	0.37387	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.64402	U	0.000002	D	0.98661	0.9551	H	0.94886	3.595	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99026	1.0819	10	0.87932	D	0	.	11.2949	0.49272	0.0:0.0:0.0:1.0	.	204	P55316	FOXG1_HUMAN	P	204	ENSP00000371975:L204P;ENSP00000339004:L204P	ENSP00000339004:L204P	L	+	2	0	FOXG1	28306847	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.895000	0.87343	1.121000	0.41925	0.254000	0.18369	CTC	.	.		0.567	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			C	29237096	T	C	29237096	3	2	113	1	0	0	0	0	1	0	0	0	6015	1551	54	2	613	2	FOXG1	14	29237096	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	5686078	29237096	78112444	259	18136										
SLC25A21	89874	hgsc.bcm.edu	37	chr14	37283153	37283153	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggaaaatcattcgaaagctgTctaccaagcttttataactg	7	8	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:37283153T>C	ENST00000331299.5	-	3	688	c.173A>G	c.(172-174)gAc>gGc	p.D58G	SLC25A21_ENST00000555449.1_Missense_Mutation_p.D58G|RP11-81F13.2_ENST00000557642.1_RNA	NM_030631.3	NP_085134.1	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial oxoadipate carrier), member 21	58					cellular nitrogen compound metabolic process (GO:0034641)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|pancreas(1)|prostate(1)|skin(1)	9	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		TCGAAAGCTGTCTACCAAGCT	0.318																																					p.D58G		Atlas-SNP	.											.	SLC25A21	24	.	0			c.A173G						.						77	77	77					14																	37283153		2202	4299	6501	SO:0001583	missense	89874	exon3			AAGCTGTCTACCA	AJ278148	CCDS9663.1, CCDS55913.1	14q13.3	2014-01-28	2012-03-29		ENSG00000183032	ENSG00000183032		"Solute carriers"	14411	protein-coding gene	gene with protein product		607571	"solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21"			11083877	Standard	NM_030631		Approved	ODC1, ODC	uc001wtz.2	Q9BQT8	OTTHUMG00000140250	ENST00000331299.5:c.173A>G	chr14.hg19:g.37283153T>C	ENSP00000329452:p.Asp58Gly	115.0	0.0		82.0	4.0	NM_030631	A8K0L0|G3V4L5|Q3MJ99	Missense_Mutation	SNP	ENST00000331299.5	hg19	CCDS9663.1	.	.	.	.	.	.	.	.	.	.	T	12.22	1.872262	0.33069	.	.	ENSG00000183032	ENST00000555449;ENST00000331299	T;T	0.79352	-1.26;-1.26	5.76	4.58	0.56647	Mitochondrial carrier domain (2);	0.097095	0.64402	N	0.000002	T	0.80874	0.4707	M	0.69248	2.105	0.54753	D	0.999986	B	0.29481	0.245	B	0.43575	0.424	T	0.79298	-0.1861	10	0.56958	D	0.05	-2.7184	10.2762	0.43512	0.0:0.0759:0.0:0.9241	.	58	Q9BQT8	ODC_HUMAN	G	58	ENSP00000451873:D58G;ENSP00000329452:D58G	ENSP00000329452:D58G	D	-	2	0	SLC25A21	36352904	1.000000	0.71417	1.000000	0.80357	0.282000	0.26991	3.501000	0.53325	1.068000	0.40764	0.533000	0.62120	GAC	.	.		0.318	SLC25A21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276732.2	NM_030631		C	37283153	T	C	37283153	3	2	113	1	0	0	0	0	1	0	0	0	14499	1667	58	2	763	2	SLC25A21	14	37283153	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	8046057	37283153	70066387	260	18137										
CDKN3	1033	hgsc.bcm.edu	37	chr14	54878223	54878223	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agaactaaagagctgtggtaTacaagacatatttgttttct	8	5	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:54878223T>C	ENST00000541304.1	+	5	255	c.215T>C	c.(214-216)aTa>aCa	p.I72T	CDKN3_ENST00000543789.2_Missense_Mutation_p.I72T|CDKN3_ENST00000458126.2_Missense_Mutation_p.I72T|CDKN3_ENST00000556102.2_Missense_Mutation_p.I72T|CDKN3_ENST00000556305.1_3'UTR|CDKN3_ENST00000395577.2_Missense_Mutation_p.I26T|CDKN3_ENST00000442975.2_Missense_Mutation_p.I32T|CDKN3_ENST00000335183.6_Missense_Mutation_p.I72T			Q00526	CDK3_HUMAN	cyclin-dependent kinase inhibitor 3	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|G0 to G1 transition (GO:0045023)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|stomach(1)	3						AGCTGTGGTATACAAGACATA	0.398																																					p.I72T	Pancreas(40;634 1012 9382 49950 52462)	Atlas-SNP	.											.	CDKN3	9	.	0			c.T215C						.						76	72	74					14																	54878223		2203	4300	6503	SO:0001583	missense	1033	exon5			GTGGTATACAAGA	U02681	CCDS9716.1, CCDS45109.1	14q22	2011-08-25	2008-08-01		ENSG00000100526	ENSG00000100526		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1791	protein-coding gene	gene with protein product	"kinase associated phosphatase", "cyclin-dependent kinase inhibitor", "CDK2-associated dual specificity phosphatase"	123832				8242750, 7698009	Standard	NM_005192		Approved	KAP, CDI1	uc001xap.3	Q16667	OTTHUMG00000140302	ENST00000541304.1:c.215T>C	chr14.hg19:g.54878223T>C	ENSP00000445572:p.Ile72Thr	84.0	0.0		42.0	27.0	NM_005192		Missense_Mutation	SNP	ENST00000541304.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.20	3.780740	0.70222	.	.	ENSG00000100526	ENST00000335183;ENST00000543789;ENST00000442975;ENST00000458126;ENST00000556102;ENST00000541304;ENST00000439312;ENST00000395577	T;T;T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54;0.54;0.54	5.67	4.53	0.55603	Cyclin-dependent kinase inhibitor 3, bac/eukaryotic (1);	0.158775	0.56097	D	0.000024	T	0.60104	0.2243	L	0.51422	1.61	0.41120	D	0.985802	B;P;P	0.44578	0.047;0.805;0.838	B;P;P	0.57679	0.213;0.732;0.825	T	0.60682	-0.7215	10	0.48119	T	0.1	-17.0445	9.7565	0.40506	0.0:0.077:0.0:0.923	.	32;72;72	Q16667-2;F8WDR6;Q16667	.;.;CDKN3_HUMAN	T	72;72;32;72;72;72;72;26	ENSP00000335357:I72T;ENSP00000440404:I72T;ENSP00000415333:I32T;ENSP00000396451:I72T;ENSP00000450711:I72T;ENSP00000445572:I72T;ENSP00000378944:I26T	ENSP00000335357:I72T	I	+	2	0	CDKN3	53947973	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.922000	0.40045	2.164000	0.68074	0.533000	0.62120	ATA	.	.		0.398	CDKN3-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000411158.1			C	54878223	T	C	54878223	3	2	113	1	0	0	0	0	1	0	0	0	3169	1406	49	2	233	2	CDKN3	14	54878223	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	17595070	54878223	52471317	261	18138										
SPTB	6710	hgsc.bcm.edu	37	chr14	65241871	65241871	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tctcatcggagatgacgtagAgctcctgctcgccaatccag	10	13	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:65241871A>G	ENST00000389721.5	-	22	4846	c.4814T>C	c.(4813-4815)cTc>cCc	p.L1605P	SPTB_ENST00000389722.3_Missense_Mutation_p.L1605P|SPTB_ENST00000389720.3_Missense_Mutation_p.L1605P|SPTB_ENST00000542895.1_Missense_Mutation_p.L1605P|SPTB_ENST00000556626.1_Missense_Mutation_p.L1605P	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1605					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GATGACGTAGAGCTCCTGCTC	0.632																																					p.L1605P		Atlas-SNP	.											.	SPTB	378	.	0			c.T4814C						.						138	108	118					14																	65241871		2203	4300	6503	SO:0001583	missense	6710	exon22			ACGTAGAGCTCCT		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4814T>C	chr14.hg19:g.65241871A>G	ENSP00000374371:p.Leu1605Pro	105.0	0.0		87.0	4.0	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	A	15.11	2.737202	0.49045	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000553938;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8	5.13	3.96	0.45880	.	0.132879	0.52532	D	0.000078	T	0.49253	0.1546	N	0.21617	0.685	0.80722	D	1	B;D;P	0.53462	0.031;0.96;0.721	B;P;B	0.60949	0.027;0.881;0.311	T	0.51340	-0.8718	10	0.87932	D	0	.	10.5594	0.45135	0.8549:0.0:0.0:0.1451	.	389;1605;1609	E7EV95;P11277;Q59FP5	.;SPTB1_HUMAN;.	P	1609;1605;389;270;1605;1605;1605;1605	ENSP00000374372:L1605P;ENSP00000451324:L270P;ENSP00000451752:L1605P;ENSP00000374371:L1605P;ENSP00000443882:L1605P;ENSP00000374370:L1605P	ENSP00000334218:L389P	L	-	2	0	SPTB	64311624	1.000000	0.71417	0.994000	0.49952	0.259000	0.26198	9.339000	0.96797	0.861000	0.35504	0.459000	0.35465	CTC	.	.		0.632	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			G	65241871	A	G	65241871	3	3	113	1	0	0	0	0	1	0	0	0	15133	304	11	2	2297	2	SPTB	14	65241871	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	10363648	65241871	42107669	262	18139										
MLH3	27030	hgsc.bcm.edu	37	chr14	75514922	75514922	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttctcattttctccagcttcTgatgctacaattgtctcttg	5	11	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:75514922T>C	ENST00000556740.1	-	1	1472	c.1437A>G	c.(1435-1437)tcA>tcG	p.S479S	MLH3_ENST00000238662.7_Silent_p.S479S|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000556257.1_Silent_p.S479S|MLH3_ENST00000355774.2_Silent_p.S479S|MLH3_ENST00000555671.1_5'Flank			Q9UHC1	MLH3_HUMAN	mutL homolog 3	479					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		CTCCAGCTTCTGATGCTACAA	0.378								Mismatch excision repair (MMR)																													p.S479S		Atlas-SNP	.											MLH3_ENST00000355774,right_upper_lobe,carcinoma,0,2	MLH3	200	.	0			c.A1437G						.						87	93	91					14																	75514922		2203	4299	6502	SO:0001819	synonymous_variant	27030	exon2			AGCTTCTGATGCT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.1437A>G	chr14.hg19:g.75514922T>C		130.0	0.0		81.0	4.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Silent	SNP	ENST00000556740.1	hg19	CCDS32123.1																																																																																			.	.		0.378	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		C	75514922	T	C	75514922	2	2	113	1	0	0	0	0	0	0	0	1	9627	1567	55	2		2	MLH3	14	75514922	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	10273051	75514922	31834618	263	18140										
SEL1L	6400	hgsc.bcm.edu	37	chr14	81956767	81956767	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cttaaagtagtggagagctgTctcattactctgaggtacaa	10	7	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:81956767T>C	ENST00000336735.4	-	13	1413	c.1297A>G	c.(1297-1299)Aca>Gca	p.T433A		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	433	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		TGGAGAGCTGTCTCATTACTC	0.363																																					p.T433A		Atlas-SNP	.											.	SEL1L	67	.	0			c.A1297G						.						139	121	127					14																	81956767		2203	4300	6503	SO:0001583	missense	6400	exon13			GAGCTGTCTCATT		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.1297A>G	chr14.hg19:g.81956767T>C	ENSP00000337053:p.Thr433Ala	137.0	0.0		94.0	4.0	NM_005065	Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	hg19	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.837866	0.91117	.	.	ENSG00000071537	ENST00000336735	T	0.50001	0.76	5.84	5.84	0.93424	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.52500	0.1738	L	0.52011	1.625	0.80722	D	1	P	0.46064	0.872	P	0.49561	0.615	T	0.44877	-0.9299	10	0.26408	T	0.33	.	16.2302	0.82332	0.0:0.0:0.0:1.0	.	433	Q9UBV2	SE1L1_HUMAN	A	433	ENSP00000337053:T433A	ENSP00000337053:T433A	T	-	1	0	SEL1L	81026520	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.236000	0.78154	2.228000	0.72767	0.533000	0.62120	ACA	.	.		0.363	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		C	81956767	T	C	81956767	3	2	113	1	0	0	0	0	1	0	0	0	14025	1667	58	2	1123	2	SEL1L	14	81956767	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	6441845	81956767	25392773	264	18141										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92474090	92474090	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gttcctttgcctccaaattaAgtcttaagtcatgtaattct	5	9	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:92474090A>G	ENST00000267622.4	-	10	1794	c.1421T>C	c.(1420-1422)cTt>cCt	p.L474P		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	474					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		CTCCAAATTAAGTCTTAAGTC	0.328			T	PDGFRB	AML																																p.L474P	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.T1421C						.						147	138	141					14																	92474090		2202	4300	6502	SO:0001583	missense	9321	exon10			AAATTAAGTCTTA	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.1421T>C	chr14.hg19:g.92474090A>G	ENSP00000267622:p.Leu474Pro	155.0	0.0		95.0	4.0	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	hg19	CCDS9899.1	.	.	.	.	.	.	.	.	.	.	A	11.43	1.637705	0.29157	.	.	ENSG00000100815	ENST00000267622;ENST00000542257	T	0.61040	0.14	6.04	-3.19	0.05171	.	1.823300	0.02222	N	0.064106	T	0.45438	0.1342	L	0.50333	1.59	0.09310	N	0.999999	P;P	0.41569	0.755;0.718	B;B	0.37888	0.26;0.251	T	0.39143	-0.9628	10	0.30854	T	0.27	.	2.5457	0.04736	0.2409:0.1922:0.07:0.4969	.	210;474	F5H1Z0;Q15643	.;TRIPB_HUMAN	P	474;210	ENSP00000267622:L474P	ENSP00000267622:L474P	L	-	2	0	TRIP11	91543843	0.037000	0.19845	0.861000	0.33841	0.982000	0.71751	0.476000	0.22180	-0.130000	0.11599	0.459000	0.35465	CTT	.	.		0.328	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			G	92474090	A	G	92474090	3	3	113	1	0	0	0	0	1	0	0	0	16570	72	3	2	4566	2	TRIP11	14	92474090	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	10517323	92474090	14875450	265	18142										
UBR7	55148	hgsc.bcm.edu	37	chr14	93678456	93678456	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcatttgcaagagaccttatCctgatcctgaagacgaggta	10	9	0	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:93678456C>T	ENST00000013070.6	+	4	660	c.424C>T	c.(424-426)Cct>Tct	p.P142S	RP11-371E8.4_ENST00000557574.1_Missense_Mutation_p.P161S|UBR7_ENST00000416753.1_Missense_Mutation_p.P66S|RP11-371E8.4_ENST00000557048.1_3'UTR	NM_175748.3	NP_786924.2	Q8N806	UBR7_HUMAN	ubiquitin protein ligase E3 component n-recognin 7 (putative)	142							ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(2)|lung(12)|urinary_tract(1)	19						GAGACCTTATCCTGATCCTGA	0.413																																					p.P142S		Atlas-SNP	.											UBR7,rectum,carcinoma,0,1	UBR7	36	.	0			c.C424T						.						77	73	74					14																	93678456		2203	4300	6503	SO:0001583	missense	55148	exon4			CCTTATCCTGATC	AK001345	CCDS9909.1	14q32.12	2008-06-23	2008-06-23	2008-06-23		ENSG00000012963		"Ubiquitin protein ligase E3 component n-recognins"	20344	protein-coding gene	gene with protein product		613816	"chromosome 14 open reading frame 130"	C14orf130		18162545	Standard	NM_175748		Approved		uc001ybm.4	Q8N806		ENST00000013070.6:c.424C>T	chr14.hg19:g.93678456C>T	ENSP00000013070:p.Pro142Ser	70.0	0.0		44.0	2.0	NM_175748	Q86U21|Q86UA9|Q96BY0|Q9NVV6	Missense_Mutation	SNP	ENST00000013070.6	hg19	CCDS9909.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.060317|5.060317	0.93846|0.93846	.|.	.|.	ENSG00000259066;ENSG00000012963;ENSG00000012963;ENSG00000012963|ENSG00000012963	ENST00000557574;ENST00000013070;ENST00000535646;ENST00000416753|ENST00000555113	T;T;T|.	0.76186|.	-1.0;0.1;0.1|.	5.89|5.89	5.89|5.89	0.94794|0.94794	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78142|0.78142	0.4237|0.4237	M|M	0.75777|0.75777	2.31|2.31	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.76075|0.76075	-0.3092|-0.3092	10|5	0.52906|.	T|.	0.07|.	-22.8126|-22.8126	20.2361|20.2361	0.98357|0.98357	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	66;142|.	E9PCJ7;Q8N806|.	.;UBR7_HUMAN|.	S|F	161;142;66;66|132	ENSP00000451369:P161S;ENSP00000013070:P142S;ENSP00000391706:P66S|.	ENSP00000013070:P142S|.	P|S	+|+	1|2	0|0	RP11-371E8.4;UBR7|UBR7	92748209|92748209	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.561000|7.561000	0.82288|0.82288	2.791000|2.791000	0.96007|0.96007	0.591000|0.591000	0.81541|0.81541	CCT|TCC	.	.		0.413	UBR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412693.1	NM_175748		T	93678456	C	T	93678456	3	4	113	1	0	0	0	0	1	0	0	0	16921	855	30	3	438	3	UBR7	14	93678456	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	1204366	93678456	13671084	266	18143										
BTBD7	55727	hgsc.bcm.edu	37	chr14	93709383	93709383	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtccttgagtgacagtgtggAcacacccaccgcgatgtctg	12	12	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:93709383A>G	ENST00000334746.5	-	11	2942	c.2635T>C	c.(2635-2637)Tcc>Ccc	p.S879P	BTBD7_ENST00000554565.1_Missense_Mutation_p.S528P|BTBD7_ENST00000393170.2_Missense_Mutation_p.S453P	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	879					multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		GACAGTGTGGACACACCCACC	0.522																																					p.S879P		Atlas-SNP	.											.	BTBD7	112	.	0			c.T2635C						.						136	123	128					14																	93709383		2203	4300	6503	SO:0001583	missense	55727	exon11			GTGTGGACACACC	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"BTB/POZ domain containing"	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.2635T>C	chr14.hg19:g.93709383A>G	ENSP00000335615:p.Ser879Pro	171.0	0.0		116.0	5.0	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	A	20.0	3.930422	0.73327	.	.	ENSG00000011114	ENST00000334746;ENST00000554565;ENST00000553975;ENST00000393170	T;T	0.59364	0.62;0.27	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.66257	0.2771	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.85130	0.997;0.997;0.986	T	0.70070	-0.4973	10	0.72032	D	0.01	.	16.3063	0.82849	1.0:0.0:0.0:0.0	.	453;528;879	E7ERI4;Q9P203-5;Q9P203	.;.;BTBD7_HUMAN	P	879;528;494;453	ENSP00000335615:S879P;ENSP00000451010:S528P	ENSP00000335615:S879P	S	-	1	0	BTBD7	92779136	1.000000	0.71417	0.985000	0.45067	0.975000	0.68041	6.831000	0.75324	2.259000	0.74868	0.529000	0.55759	TCC	.	.		0.522	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		G	93709383	A	G	93709383	3	3	113	1	0	0	0	0	1	0	0	0	1548	275	10	2	767	2	BTBD7	14	93709383	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	30927	93709383	13640157	267	18144										
IFI27	3429	hgsc.bcm.edu	37	chr14	94582130	94582130	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctcctcttccctgcagttgTggctgtgcccatggtgctca	11	14	2	0	rs3833507	byFrequency	TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:94582130T>C	ENST00000555744.1	+	4	313	c.125T>C	c.(124-126)gTg>gCg	p.V42A	IFI27_ENST00000557634.1_Missense_Mutation_p.V32A|IFI27_ENST00000298902.5_Missense_Mutation_p.V42A|IFI27_ENST00000557098.1_5'UTR|IFI27_ENST00000444961.1_Splice_Site_p.V45A|IFI27_ENST00000448882.1_Missense_Mutation_p.V45A			P40305	IFI27_HUMAN	interferon, alpha-inducible protein 27	42				V -> VAMA (in Ref. 1; CAA47739). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)		p.A43_V44insMAA(1)		breast(1)|lung(3)	4				Epithelial(152;0.112)|all cancers(159;0.187)|COAD - Colon adenocarcinoma(157;0.206)		CCTGCAGTTGTGGCTGTGCCC	0.627																																					p.V42A	GBM(128;797 1667 20895 29868 47129)	Atlas-SNP	.											IFI27,colon,carcinoma,0,16	IFI27	39	.	1	Insertion - In frame(1)	breast(1)	c.T125C						.						14	13	13					14																	94582130		2184	4278	6462	SO:0001583	missense	3429	exon4			CAGTTGTGGCTGT	X67325	CCDS32148.1	14q32.12	2012-10-02			ENSG00000165949	ENSG00000165949			5397	protein-coding gene	gene with protein product		600009				8358738	Standard	NM_005532		Approved	P27, FAM14D	uc021sba.1	P40305	OTTHUMG00000171303	ENST00000555744.1:c.125T>C	chr14.hg19:g.94582130T>C	ENSP00000451956:p.Val42Ala	48.0	0.0		27.0	2.0	NM_005532	Q53YA6|Q6IEC1|Q96BK3	Missense_Mutation	SNP	ENST00000555744.1	hg19	CCDS32148.1	.	.	.	.	.	.	.	.	.	.	T	0.082	-1.181118	0.01633	.	.	ENSG00000165949	ENST00000554448;ENST00000444961;ENST00000448882;ENST00000554800;ENST00000556544;ENST00000298902;ENST00000557634;ENST00000555744	T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;1.62	3.52	-1.47	0.08772	.	0.951477	0.08752	N	0.898966	T	0.09642	0.0237	N	0.02674	-0.535	0.09310	N	1	B	0.18166	0.026	B	0.19391	0.025	T	0.34925	-0.9809	10	0.02654	T	1	.	7.2043	0.25899	0.0:0.4761:0.0:0.5239	.	42	P40305	IFI27_HUMAN	A	42;45;45;42;42;42;32;42	ENSP00000451370:V42A;ENSP00000413536:V45A;ENSP00000410901:V45A;ENSP00000451875:V42A;ENSP00000298902:V42A;ENSP00000452560:V32A;ENSP00000451956:V42A	ENSP00000298902:V42A	V	+	2	0	IFI27	93651883	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.001000	0.13038	-0.296000	0.08947	-0.400000	0.06385	GTG	.	.		0.627	IFI27-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412889.1	NM_005532		C	94582130	T	C	94582130	3	2	113	1	0	0	0	0	1	0	0	0	7521	1710	59	2	135	2	IFI27	14	94582130	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	872747	94582130	12767410	268	18145										
SERPINA10	51156	hgsc.bcm.edu	37	chr14	94752493	94752493	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctgagagttcactaaggtcAgcaaagggtgagaagattct	13	6	3	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:94752493A>G	ENST00000393096.1	-	4	1560	c.1095T>C	c.(1093-1095)gcT>gcC	p.A365A	SERPINA10_ENST00000554173.1_Silent_p.A365A|SERPINA10_ENST00000554723.1_Silent_p.A405A|SERPINA10_ENST00000261994.4_Silent_p.A365A	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	365					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		CACTAAGGTCAGCAAAGGGTG	0.438																																					p.A365A		Atlas-SNP	.											.	SERPINA10	83	.	0			c.T1095C						.						124	110	115					14																	94752493		2203	4300	6503	SO:0001819	synonymous_variant	51156	exon4			AAGGTCAGCAAAG	AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"Serine (or cysteine) peptidase inhibitors"	15996	protein-coding gene	gene with protein product		605271	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.1095T>C	chr14.hg19:g.94752493A>G		171.0	0.0		89.0	4.0	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Silent	SNP	ENST00000393096.1	hg19	CCDS9923.1																																																																																			.	.		0.438	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186		G	94752493	A	G	94752493	2	3	113	1	0	0	0	0	0	0	0	1	14102	175	7	2		2	SERPINA10	14	94752493	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	170363	94752493	12597047	269	18146										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96798729	96798729	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttatgatgatcaaggaactCtccccaagtgggctgaagct	10	9	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:96798729C>A	ENST00000359933.4	-	10	2274	c.1381G>T	c.(1381-1383)Gag>Tag	p.E461*		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	461					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TCAAGGAACTCTCCCCAAGTG	0.348																																					p.E461X		Atlas-SNP	.											.	ATG2B	169	.	0			c.G1381T						.						118	111	113					14																	96798729		1830	4081	5911	SO:0001587	stop_gained	55102	exon10			GGAACTCTCCCCA	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.1381G>T	chr14.hg19:g.96798729C>A	ENSP00000353010:p.Glu461*	367.0	1.0		226.0	84.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Nonsense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	C	47	13.186436	0.99726	.	.	ENSG00000066739	ENST00000359933	.	.	.	5.55	5.55	0.83447	.	1.863070	0.05717	U	0.596957	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	13.2253	0.59911	0.0:0.9175:0.0:0.0825	.	.	.	.	X	461	.	ENSP00000353010:E461X	E	-	1	0	ATG2B	95868482	1.000000	0.71417	0.911000	0.35937	0.882000	0.50991	2.272000	0.43373	2.606000	0.88127	0.655000	0.94253	GAG	.	.		0.348	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		A	96798729	C	A	96798729	4	1	113	1	0	0	0	0	0	1	0	0	1094	922	32	3	4987	3	ATG2B	14	96798729	Nonsense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	2046236	96798729	10550811	270	18147										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96809538	96809538	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gagacactccagagagctgaAgtaacttgtgagcaaaagca	11	8	0	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:96809538A>G	ENST00000359933.4	-	5	1555	c.662T>C	c.(661-663)cTt>cCt	p.L221P		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	221					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AGAGAGCTGAAGTAACTTGTG	0.413																																					p.L221P		Atlas-SNP	.											.	ATG2B	169	.	0			c.T662C						.						106	102	104					14																	96809538		1897	4125	6022	SO:0001583	missense	55102	exon5			AGCTGAAGTAACT	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.662T>C	chr14.hg19:g.96809538A>G	ENSP00000353010:p.Leu221Pro	153.0	0.0		94.0	4.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	24.3	4.514933	0.85389	.	.	ENSG00000066739	ENST00000359933	T	0.15139	2.45	5.27	5.27	0.74061	.	0.198408	0.31636	U	0.007305	T	0.32882	0.0844	L	0.47190	1.495	0.80722	D	1	D	0.71674	0.998	P	0.62014	0.897	T	0.03795	-1.1003	10	0.72032	D	0.01	.	15.1796	0.72945	1.0:0.0:0.0:0.0	.	221	Q96BY7	ATG2B_HUMAN	P	221	ENSP00000353010:L221P	ENSP00000353010:L221P	L	-	2	0	ATG2B	95879291	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.730000	0.91510	1.995000	0.58328	0.482000	0.46254	CTT	.	.		0.413	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96809538	A	G	96809538	3	3	113	1	0	0	0	0	1	0	0	0	1094	72	3	2	5726	2	ATG2B	14	96809538	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	10809	96809538	10540002	271	18148										
PAPOLA	10914	hgsc.bcm.edu	37	chr14	97022280	97022280	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtaaattccagtgaaagctcAgggggtaaggagattgggtt	15	4	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:97022280A>G	ENST00000216277.8	+	18	1981	c.1761A>G	c.(1759-1761)tcA>tcG	p.S587S	PAPOLA_ENST00000392990.2_Silent_p.S587S	NM_032632.4	NP_116021.2	P51003	PAPOA_HUMAN	poly(A) polymerase alpha	587	Ser/Thr-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|RNA polyadenylation (GO:0043631)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		GTGAAAGCTCAGGGGGTAAGG	0.403																																					p.S587S	NSCLC(19;254 734 11908 35501 39234)	Atlas-SNP	.											.	PAPOLA	58	.	0			c.A1761G						.						78	79	79					14																	97022280		2203	4300	6503	SO:0001819	synonymous_variant	10914	exon18			AAGCTCAGGGGGT	X76770	CCDS9946.1, CCDS58334.1, CCDS58335.1	14q32.1-q32.2	2008-02-08				ENSG00000090060	2.7.7.19		14981	protein-coding gene	gene with protein product		605553				8302877, 10429366	Standard	NM_032632		Approved	PAP	uc001yfq.3	P51003		ENST00000216277.8:c.1761A>G	chr14.hg19:g.97022280A>G		177.0	0.0		113.0	5.0	NM_032632	Q86SX4|Q86TV0|Q8IYF5|Q9BVU2	Silent	SNP	ENST00000216277.8	hg19	CCDS9946.1	.	.	.	.	.	.	.	.	.	.	A	10.38	1.332840	0.24167	.	.	ENSG00000090060	ENST00000556459	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	T	0.73305	0.3570	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72221	-0.4356	4	.	.	.	.	16.4563	0.84015	1.0:0.0:0.0:0.0	.	.	.	.	R	88	.	.	Q	+	2	0	PAPOLA	96092033	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.361000	0.73070	2.343000	0.79666	0.533000	0.62120	CAG	.	.		0.403	PAPOLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413411.2			G	97022280	A	G	97022280	2	3	113	1	0	0	0	0	0	0	0	1	11438	175	7	2		2	PAPOLA	14	97022280	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	212742	97022280	10327260	272	18149										
CCNK	8812	hgsc.bcm.edu	37	chr14	99968554	99968554	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gttgaactagtctctgcaccAccttgtcactgcagtgggaa	10	11	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:99968554A>G	ENST00000389879.5	+	7	709	c.586A>G	c.(586-588)Acc>Gcc	p.T196A	CCNK_ENST00000555049.1_Missense_Mutation_p.T196A|CCNK_ENST00000557165.1_3'UTR	NM_001099402.1	NP_001092872.1	O75909	CCNK_HUMAN	cyclin K	196					cellular response to DNA damage stimulus (GO:0006974)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of cell cycle arrest (GO:0071157)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cyclin K-CDK12 complex (GO:0002944)|cyclin K-CDK13 complex (GO:0002945)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase binding (GO:0019901)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|endometrium(2)|lung(3)	6		all_cancers(154;0.224)|all_epithelial(191;0.0643)|Melanoma(154;0.0866)				TCTCTGCACCACCTTGTCACT	0.383																																					p.T196A		Atlas-SNP	.											.	CCNK	32	.	0			c.A586G						.						77	69	72					14																	99968554		1905	4111	6016	SO:0001583	missense	8812	exon7			TGCACCACCTTGT	AF060515	CCDS45160.1	14q32.2	2014-07-03			ENSG00000090061	ENSG00000090061			1596	protein-coding gene	gene with protein product		603544				9632813, 10574912	Standard	NM_001099402		Approved	CPR4	uc001ygi.4	O75909	OTTHUMG00000171495	ENST00000389879.5:c.586A>G	chr14.hg19:g.99968554A>G	ENSP00000374529:p.Thr196Ala	119.0	0.0		82.0	4.0	NM_001099402	Q59FT6|Q86U16|Q96B63|Q9NNY9	Missense_Mutation	SNP	ENST00000389879.5	hg19	CCDS45160.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.748000	0.89663	.	.	ENSG00000090061	ENST00000437596;ENST00000216279;ENST00000380246;ENST00000389879;ENST00000557441;ENST00000555049	T;T;T	0.44881	0.91;0.91;0.91	5.8	5.8	0.92144	Cyclin-like (2);	0.046992	0.85682	D	0.000000	T	0.65923	0.2738	M	0.80847	2.515	0.80722	D	1	D;D	0.71674	0.998;0.986	D;P	0.65987	0.94;0.852	T	0.70517	-0.4850	10	0.66056	D	0.02	-21.3293	16.1596	0.81693	1.0:0.0:0.0:0.0	.	196;196	O75909;O75909-2	CCNK_HUMAN;.	A	196;198;198;196;196;196	ENSP00000374529:T196A;ENSP00000450792:T196A;ENSP00000452307:T196A	ENSP00000216279:T198A	T	+	1	0	CCNK	99038307	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.307000	0.96226	2.216000	0.71823	0.533000	0.62120	ACC	.	.		0.383	CCNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413721.1			G	99968554	A	G	99968554	3	3	113	1	0	0	0	0	1	0	0	0	2932	159	6	2	608	2	CCNK	14	99968554	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2946274	99968554	7380986	273	18150										
WARS	7453	hgsc.bcm.edu	37	chr14	100808883	100808883	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agccgatcctgggggcgacgTcccttgtcattctaaagtaa	11	11	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:100808883T>C	ENST00000355338.2	-	9	1583	c.965A>G	c.(964-966)gAc>gGc	p.D322G	RP11-638I2.9_ENST00000556212.1_RNA|RP11-638I2.8_ENST00000557226.1_RNA|WARS_ENST00000344102.5_Missense_Mutation_p.D281G|WARS_ENST00000557135.1_Missense_Mutation_p.D322G|WARS_ENST00000392882.2_Missense_Mutation_p.D322G|WARS_ENST00000358655.4_Missense_Mutation_p.D281G|WARS_ENST00000556645.1_Missense_Mutation_p.D281G	NM_173701.1	NP_776049.1	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase	322					angiogenesis (GO:0001525)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|regulation of angiogenesis (GO:0045765)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)			breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	GGGGGCGACGTCCCTTGTCAT	0.587																																					p.D322G		Atlas-SNP	.											.	WARS	37	.	0			c.A965G						.						66	66	66					14																	100808883		2203	4300	6503	SO:0001583	missense	7453	exon9			GCGACGTCCCTTG	M61715	CCDS9960.1, CCDS9961.1	14q32.2	2014-03-19			ENSG00000140105	ENSG00000140105	6.1.1.2	"Aminoacyl tRNA synthetases / Class I"	12729	protein-coding gene	gene with protein product	"tryptophan tRNA ligase 1, cytoplasmic"	191050		IFI53		1537332, 1763065	Standard	NM_004184		Approved	IFP53	uc001yhl.1	P23381	OTTHUMG00000171572	ENST00000355338.2:c.965A>G	chr14.hg19:g.100808883T>C	ENSP00000347495:p.Asp322Gly	180.0	0.0		121.0	5.0	NM_004184	A6NGN1|A6NID3|P78535|Q502Y0|Q53XB6|Q9UDI5|Q9UDL3	Missense_Mutation	SNP	ENST00000355338.2	hg19	CCDS9960.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.5|28.5	4.926682|4.926682	0.92319|0.92319	.|.	.|.	ENSG00000140105|ENSG00000140105	ENST00000392882;ENST00000358655;ENST00000355338;ENST00000344102;ENST00000557135;ENST00000556645|ENST00000554601	T;T;T;T;T;T|.	0.56776|.	0.44;0.44;0.44;0.44;0.44;0.44|.	5.85|5.85	5.85|5.85	0.93711|0.93711	Rossmann-like alpha/beta/alpha sandwich fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.89188|0.89188	0.6644|0.6644	H|H	0.98507|0.98507	4.25|4.25	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.83275|.	0.996|.	D|D	0.93312|0.93312	0.6685|0.6685	10|5	0.87932|.	D|.	0|.	-2.3281|-2.3281	16.2303|16.2303	0.82332|0.82332	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	322|.	P23381|.	SYWC_HUMAN|.	G|A	322;281;322;281;322;281|75	ENSP00000376620:D322G;ENSP00000351481:D281G;ENSP00000347495:D322G;ENSP00000339485:D281G;ENSP00000451460:D322G;ENSP00000451887:D281G|.	ENSP00000339485:D281G|.	D|T	-|-	2|1	0|0	WARS|WARS	99878636|99878636	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.889000|0.889000	0.51656|0.51656	8.013000|8.013000	0.88655|0.88655	2.233000|2.233000	0.73108|0.73108	0.533000|0.533000	0.62120|0.62120	GAC|ACG	.	.		0.587	WARS-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414236.1	NM_004184		C	100808883	T	C	100808883	3	2	113	1	0	0	0	0	1	0	0	0	17264	1667	58	2	462	2	WARS	14	100808883	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	840329	100808883	6540657	274	18151										
RCOR1	23186	hgsc.bcm.edu	37	chr14	103148307	103148307	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	acccaatcaaaatctgtcagAagcaaagtgtaagtcttgga	8	8	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:103148307A>G	ENST00000570597.1	+	3	428	c.428A>G	c.(427-429)gAa>gGa	p.E143G	RCOR1_ENST00000262241.6_Missense_Mutation_p.E146G			Q9UKL0	RCOR1_HUMAN	REST corepressor 1	143	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interaction with HDAC1.				blood coagulation (GO:0007596)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	12						AATCTGTCAGAAGCAAAGTGT	0.373																																					p.E146G		Atlas-SNP	.											.	RCOR1	39	.	0			c.A437G						.						105	94	98					14																	103148307		2203	4300	6503	SO:0001583	missense	23186	exon3			TGTCAGAAGCAAA	AF155595	CCDS9974.1, CCDS9974.2	14q32.33	2004-04-16	2004-04-16	2004-04-16		ENSG00000089902			17441	protein-coding gene	gene with protein product		607675	"REST corepressor"	RCOR		10449787	Standard	NM_015156		Approved	COREST, KIAA0071	uc001ymb.4	Q9UKL0		ENST00000570597.1:c.428A>G	chr14.hg19:g.103148307A>G	ENSP00000459789:p.Glu143Gly	109.0	0.0		72.0	4.0	NM_015156	Q15044|Q6P2I9|Q86VG5	Missense_Mutation	SNP	ENST00000570597.1	hg19		.	.	.	.	.	.	.	.	.	.	A	22.2	4.261680	0.80358	.	.	ENSG00000089902	ENST00000262241	.	.	.	5.25	5.25	0.73442	ELM2 domain (2);	0.058965	0.64402	D	0.000004	T	0.70465	0.3227	L	0.50333	1.59	0.58432	D	0.999991	D	0.62365	0.991	D	0.76575	0.988	T	0.73594	-0.3933	9	0.87932	D	0	-23.7068	14.1505	0.65381	1.0:0.0:0.0:0.0	.	143	Q9UKL0	RCOR1_HUMAN	G	143	.	ENSP00000262241:E143G	E	+	2	0	RCOR1	102218060	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.041000	0.70988	1.985000	0.57927	0.533000	0.62120	GAA	.	.		0.373	RCOR1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015156		G	103148307	A	G	103148307	3	3	113	1	0	0	0	0	1	0	0	0	13197	246	9	2	438	2	RCOR1	14	103148307	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2339424	103148307	4201233	275	18152										
TDRD9	122402	hgsc.bcm.edu	37	chr14	104431724	104431724	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttatccatggggccacgggaAgcggtaaaagcactcagctc	12	11	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:104431724A>G	ENST00000409874.4	+	4	523	c.475A>G	c.(475-477)Agc>Ggc	p.S159G	TDRD9_ENST00000554571.1_3'UTR|TDRD9_ENST00000339063.5_Missense_Mutation_p.S159G	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	159	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				GGCCACGGGAAGCGGTAAAAG	0.478																																					p.S159G		Atlas-SNP	.											.	TDRD9	175	.	0			c.A475G						.						76	72	73					14																	104431724		692	1591	2283	SO:0001583	missense	122402	exon4			ACGGGAAGCGGTA	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.475A>G	chr14.hg19:g.104431724A>G	ENSP00000387303:p.Ser159Gly	126.0	0.0		90.0	4.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Missense_Mutation	SNP	ENST00000409874.4	hg19	CCDS9987.2	.	.	.	.	.	.	.	.	.	.	A	12.26	1.886119	0.33348	.	.	ENSG00000156414	ENST00000409874;ENST00000339063	T;T	0.05319	3.46;3.46	4.54	4.54	0.55810	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	.	.	.	.	T	0.35068	0.0919	H	0.95151	3.63	0.50632	D	0.999889	D	0.63046	0.992	D	0.70016	0.967	T	0.52808	-0.8526	9	0.66056	D	0.02	.	14.186	0.65605	1.0:0.0:0.0:0.0	.	159	Q8NDG6	TDRD9_HUMAN	G	159	ENSP00000387303:S159G;ENSP00000343545:S159G	ENSP00000343545:S159G	S	+	1	0	TDRD9	103501477	1.000000	0.71417	0.120000	0.21714	0.311000	0.27955	9.232000	0.95325	1.807000	0.52817	0.377000	0.23210	AGC	.	.		0.478	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		G	104431724	A	G	104431724	3	3	113	1	0	0	0	0	1	0	0	0	15751	72	3	2	489	2	TDRD9	14	104431724	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1283417	104431724	2917816	276	18153										
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105350781	105350781	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gacccccagctgaccaaggcAcggaaacaggaggaggacga	14	12	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr14:105350781A>G	ENST00000414716.3	+	9	1893	c.1665A>G	c.(1663-1665)gcA>gcG	p.A555A	CEP170B_ENST00000453495.1_Silent_p.A556A|CEP170B_ENST00000556508.1_Silent_p.A485A|CEP170B_ENST00000418279.1_Silent_p.A485A	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	555						cytoplasm (GO:0005737)|microtubule (GO:0005874)											TGACCAAGGCACGGAAACAGG	0.697																																					p.A555A		Atlas-SNP	.											.	.	.	.	0			c.A1665G						.						4	4	4					14																	105350781		1912	3898	5810	SO:0001819	synonymous_variant	283638	exon9			CAAGGCACGGAAA	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.1665A>G	chr14.hg19:g.105350781A>G		78.0	0.0		50.0	4.0	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	hg19	CCDS45175.1																																																																																			.	.		0.697	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		G	105350781	A	G	105350781	2	3	113	1	0	0	0	0	0	0	0	1	8175	146	6	2		2	KIAA0284	14	105350781	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	919057	105350781	1998759	277	18154										
TUBGCP5	114791	hgsc.bcm.edu	37	chr15	22869927	22869927	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtctgcaggtcagctttgtgAaagaagctatcatgaaggtg	13	6	3	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:22869927A>G	ENST00000283645.4	+	21	2981	c.2851A>G	c.(2851-2853)Aaa>Gaa	p.K951E	TUBGCP5_ENST00000453949.2_Missense_Mutation_p.K951E	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	951					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		CAGCTTTGTGAAAGAAGCTAT	0.443																																					p.K951E		Atlas-SNP	.											.	TUBGCP5	82	.	0			c.A2851G						.						215	156	176					15																	22869927		2203	4300	6503	SO:0001583	missense	114791	exon21			TTTGTGAAAGAAG	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"gamma-tubulin complex component GCP5"	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.2851A>G	chr15.hg19:g.22869927A>G	ENSP00000283645:p.Lys951Glu	153.0	0.0		121.0	5.0	NM_052903	E9PB12|Q6IQ52|Q96PY8	Missense_Mutation	SNP	ENST00000283645.4	hg19	CCDS10008.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.248217	0.80024	.	.	ENSG00000153575	ENST00000283645;ENST00000453949	T;T	0.23552	1.9;1.9	5.16	4.03	0.46877	.	0.000000	0.85682	D	0.000000	T	0.29126	0.0724	L	0.27053	0.805	0.58432	D	0.999999	D;D	0.63046	0.992;0.992	P;P	0.57425	0.82;0.82	T	0.01776	-1.1276	10	0.30854	T	0.27	-19.8559	11.3117	0.49368	0.9285:0.0:0.0715:0.0	.	951;951	Q96RT8;E9PB12	GCP5_HUMAN;.	E	951	ENSP00000283645:K951E;ENSP00000409217:K951E	ENSP00000283645:K951E	K	+	1	0	TUBGCP5	20421368	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.386000	0.90166	1.079000	0.41038	0.533000	0.62120	AAA	.	.		0.443	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903		G	22869927	A	G	22869927	3	3	113	1	0	0	0	0	1	0	0	0	16784	247	9	2	2933	2	TUBGCP5	15	22869927	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10		22869927	79661465	278	18155										
NDN	4692	hgsc.bcm.edu	37	chr15	23931977	23931977	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcaccacttcttgtagctgcCgatgacatctttcaccatgt	7	13	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:23931977C>T	ENST00000331837.4	-	1	473	c.388G>A	c.(388-390)Ggc>Agc	p.G130S		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	130	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.G130S(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		TTGTAGCTGCCGATGACATCT	0.582									Prader-Willi syndrome																												p.G130S		Atlas-SNP	.											NDN,NS,carcinoma,0,1	NDN	79	.	1	Substitution - Missense(1)	endometrium(1)	c.G388A						.						86	80	82					15																	23931977		2203	4300	6503	SO:0001583	missense	4692	exon1	Familial Cancer Database	Prader-Labhart-Willi syndrome	AGCTGCCGATGAC	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"Prader-Willi syndrome chromosome region"	602117	"necdin (mouse) homolog", "necdin homolog (mouse)"			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.388G>A	chr15.hg19:g.23931977C>T	ENSP00000332643:p.Gly130Ser	100.0	0.0		47.0	3.0	NM_002487	B2R6Z5	Missense_Mutation	SNP	ENST00000331837.4	hg19	CCDS10014.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.508486	0.64410	.	.	ENSG00000182636	ENST00000331837	T	0.04706	3.57	3.87	1.9	0.25705	.	0.203113	0.40064	N	0.001196	T	0.07503	0.0189	N	0.24115	0.695	0.27578	N	0.949674	D	0.76494	0.999	D	0.68039	0.955	T	0.12863	-1.0531	10	0.49607	T	0.09	.	4.5274	0.11988	0.0:0.6402:0.2343:0.1255	.	130	Q99608	NECD_HUMAN	S	130	ENSP00000332643:G130S	ENSP00000332643:G130S	G	-	1	0	NDN	21483070	1.000000	0.71417	0.986000	0.45419	0.996000	0.88848	1.271000	0.33098	0.891000	0.36235	0.561000	0.74099	GGC	.	.		0.582	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487		T	23931977	C	T	23931977	3	4	113	1	0	0	0	0	1	0	0	0	10256	652	23	1	581	1	NDN	15	23931977	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	1062050	23931977	78599415	279	18156										
RYR3	6263	hgsc.bcm.edu	37	chr15	33922201	33922201	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agttttcaaagctcccagaaActgagaagaactataacctg	7	9	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:33922201A>G	ENST00000389232.4	+	22	2810	c.2740A>G	c.(2740-2742)Act>Gct	p.T914A	RYR3_ENST00000415757.3_Missense_Mutation_p.T914A	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	914	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GCTCCCAGAAACTGAGAAGAA	0.338																																					p.T914A		Atlas-SNP	.											.	RYR3	760	.	0			c.A2740G						.						91	83	85					15																	33922201		1838	4094	5932	SO:0001583	missense	6263	exon22			CCAGAAACTGAGA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.2740A>G	chr15.hg19:g.33922201A>G	ENSP00000373884:p.Thr914Ala	125.0	0.0		81.0	4.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	A	11.98	1.801897	0.31869	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.91068	-2.78;-2.78	5.35	5.35	0.76521	Ryanodine receptor Ryr (1);	0.000000	0.85682	D	0.000000	D	0.89774	0.6812	N	0.16602	0.42	0.58432	D	0.999999	D;D	0.61697	0.99;0.977	D;P	0.72982	0.979;0.76	D	0.86331	0.1698	10	0.10902	T	0.67	.	15.503	0.75716	1.0:0.0:0.0:0.0	.	914;914	Q15413-2;Q15413	.;RYR3_HUMAN	A	914	ENSP00000373884:T914A;ENSP00000399610:T914A	ENSP00000354735:T914A	T	+	1	0	RYR3	31709493	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	6.858000	0.75461	2.236000	0.73375	0.528000	0.53228	ACT	.	.		0.338	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			G	33922201	A	G	33922201	3	3	113	1	0	0	0	0	1	0	0	0	13785	43	2	2	2826	2	RYR3	15	33922201	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	9990224	33922201	68609191	280	18157										
AQR	9716	hgsc.bcm.edu	37	chr15	35166047	35166047	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	acctgatagaagtaaggattAggttcagattctcccactcc	8	10	2	3	rs368882712		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:35166047A>G	ENST00000156471.5	-	30	3804	c.3579T>C	c.(3577-3579)ccT>ccC	p.P1193P		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1193					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		AGTAAGGATTAGGTTCAGATT	0.373																																					p.P1193P		Atlas-SNP	.											.	AQR	139	.	0			c.T3579C						.	A		0,3674		0,0,1837	85	85	85		3579	-3.1	1	15		85	1,8161		0,1,4080	no	coding-synonymous	AQR	NM_014691.2		0,1,5917	GG,GA,AA		0.0123,0.0,0.0084		1193/1486	35166047	1,11835	1837	4081	5918	SO:0001819	synonymous_variant	9716	exon30			AGGATTAGGTTCA	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.3579T>C	chr15.hg19:g.35166047A>G		122.0	0.0		83.0	4.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.		0.373	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		G	35166047	A	G	35166047	2	3	113	1	0	0	0	0	0	0	0	1	835	407	15	2		2	AQR	15	35166047	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1243846	35166047	67365345	281	18158										
AQR	9716	hgsc.bcm.edu	37	chr15	35167042	35167042	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atcataatccatcgttttagTcggctaaatccatcctgagg	7	10	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:35167042T>C	ENST00000156471.5	-	29	3486	c.3261A>G	c.(3259-3261)cgA>cgG	p.R1087R		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1087					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		ATCGTTTTAGTCGGCTAAATC	0.388																																					p.R1087R		Atlas-SNP	.											.	AQR	139	.	0			c.A3261G						.						117	109	111					15																	35167042		1862	4104	5966	SO:0001819	synonymous_variant	9716	exon29			TTTTAGTCGGCTA	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.3261A>G	chr15.hg19:g.35167042T>C		117.0	0.0		73.0	4.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.		0.388	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		C	35167042	T	C	35167042	2	2	113	1	0	0	0	0	0	0	0	1	835	1654	58	2		2	AQR	15	35167042	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	995	35167042	67364350	282	18159										
C15orf41	84529	hgsc.bcm.edu	37	chr15	36989565	36989565	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggtcctgctgagagacttgcTtctagagaaaaacctgtcct	10	10	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:36989565T>C	ENST00000566621.1	+	8	768	c.518T>C	c.(517-519)cTt>cCt	p.L173P	C15orf41_ENST00000569302.1_Missense_Mutation_p.L173P|C15orf41_ENST00000562877.1_Missense_Mutation_p.L75P|C15orf41_ENST00000437989.2_Missense_Mutation_p.L173P|C15orf41_ENST00000567389.1_Missense_Mutation_p.L75P|C15orf41_ENST00000565792.1_3'UTR|C15orf41_ENST00000338183.4_Missense_Mutation_p.L75P	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	173										kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		AGAGACTTGCTTCTAGAGAAA	0.413																																					p.L173P		Atlas-SNP	.											.	C15orf41	24	.	0			c.T518C						.						188	189	188					15																	36989565		1914	4139	6053	SO:0001583	missense	84529	exon8			ACTTGCTTCTAGA	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.518T>C	chr15.hg19:g.36989565T>C	ENSP00000455397:p.Leu173Pro	210.0	0.0		150.0	6.0	NM_001130010	B2RD87	Missense_Mutation	SNP	ENST00000566621.1	hg19	CCDS45215.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561220	0.65538	.	.	ENSG00000186073	ENST00000437989;ENST00000338183	T	0.62498	0.02	5.6	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.78123	0.4234	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.80037	-0.1550	10	0.87932	D	0	-11.632	11.6014	0.51006	0.0:0.07:0.0:0.93	.	173	Q9Y2V0	CO041_HUMAN	P	173;75	ENSP00000401362:L173P	ENSP00000342433:L75P	L	+	2	0	C15orf41	34776857	1.000000	0.71417	0.998000	0.56505	0.902000	0.53008	7.535000	0.82014	0.952000	0.37798	0.528000	0.53228	CTT	.	.		0.413	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499		C	36989565	T	C	36989565	3	2	113	1	0	0	0	0	1	0	0	0	1797	1609	56	2	548	2	C15orf41	15	36989565	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1822523	36989565	65541827	283	18160										
CHST14	113189	hgsc.bcm.edu	37	chr15	40764276	40764276	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtgtaccacctgtgccagccTtgtgccgtgcactatgactt	10	13	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:40764276T>C	ENST00000306243.5	+	1	1117	c.864T>C	c.(862-864)ccT>ccC	p.P288P	CHST14_ENST00000559991.1_Silent_p.P263P	NM_130468.3	NP_569735.1	Q8NCH0	CHSTE_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 14	288					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|dermatan sulfate proteoglycan metabolic process (GO:0050655)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)|phosphate ion binding (GO:0042301)			cervix(1)|large_intestine(1)|prostate(2)	4		all_cancers(109;2.34e-14)|all_epithelial(112;1.08e-11)|Lung NSC(122;2.95e-09)|all_lung(180;6.03e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;3e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0781)		TGTGCCAGCCTTGTGCCGTGC	0.572																																					p.P288P		Atlas-SNP	.											.	CHST14	19	.	0			c.T864C						.						122	122	122					15																	40764276		2203	4300	6503	SO:0001819	synonymous_variant	113189	exon1			CCAGCCTTGTGCC	AF401222	CCDS10059.1	15q15.1	2014-09-17	2007-03-27	2007-03-27	ENSG00000169105	ENSG00000169105		"Sulfotransferases, membrane-bound"	24464	protein-coding gene	gene with protein product		608429	"dermatan 4 sulfotransferase 1"	D4ST1		11470797	Standard	NM_130468		Approved	HD4ST, D4ST-1	uc001zlw.3	Q8NCH0	OTTHUMG00000129985	ENST00000306243.5:c.864T>C	chr15.hg19:g.40764276T>C		155.0	0.0		77.0	4.0	NM_130468	Q6PJ31|Q6UXA0|Q96P94	Silent	SNP	ENST00000306243.5	hg19	CCDS10059.1																																																																																			.	.		0.572	CHST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252251.1	NM_130468		C	40764276	T	C	40764276	2	2	113	1	0	0	0	0	0	0	0	1	3404	1596	56	2		2	CHST14	15	40764276	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	3774711	40764276	61767116	284	18161										
LTK	4058	hgsc.bcm.edu	37	chr15	41799394	41799394	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tggcaataatagggattgggGgctgtcctgatggcagaggt	17	5	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:41799394G>C	ENST00000263800.6	-	11	1536	c.1440C>G	c.(1438-1440)gcC>gcG	p.A480A	LTK_ENST00000355166.5_Silent_p.A419A|LTK_ENST00000561619.1_Silent_p.A178A|LTK_ENST00000453182.2_Intron	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	480					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		AGGGATTGGGGGCTGTCCTGA	0.612										TSP Lung(18;0.14)																											p.A480A		Atlas-SNP	.											.	LTK	117	.	0			c.C1440G						.						55	57	56					15																	41799394		2203	4300	6503	SO:0001819	synonymous_variant	4058	exon11			ATTGGGGGCTGTC	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.1440C>G	chr15.hg19:g.41799394G>C		117.0	0.0		77.0	35.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Silent	SNP	ENST00000263800.6	hg19	CCDS10077.1																																																																																			.	.		0.612	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			C	41799394	G	C	41799394	2	2	113	1	0	0	0	0	0	0	0	1	9089	1219	43	4		4	LTK	15	41799394	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	1035118	41799394	60731998	285	18162										
DUOX2	50506	hgsc.bcm.edu	37	chr15	45401796	45401796	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttcccagcagcagctcattcAcctcctgggtactgttcaga	8	14	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:45401796A>G	ENST00000603300.1	-	11	1362	c.1160T>C	c.(1159-1161)gTg>gCg	p.V387A	DUOX2_ENST00000389039.6_Missense_Mutation_p.V387A	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	387	Peroxidase-like; mediates peroxidase activity. {ECO:0000250}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CAGCTCATTCACCTCCTGGGT	0.522																																					p.V387A		Atlas-SNP	.											.	DUOX2	137	.	0			c.T1160C						.						103	95	98					15																	45401796		2198	4298	6496	SO:0001583	missense	50506	exon11			TCATTCACCTCCT	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"EF-hand domain containing"	13273	protein-coding gene	gene with protein product	"dual oxidase-like domains 2", "nicotinamide adenine dinucleotide phosphate oxidase", "flavoprotein NADPH oxidase", "NADPH thyroid oxidase 2", "NADH/NADPH thyroid oxidase p138-tox", "NADPH oxidase/peroxidase DUOX2"	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.1160T>C	chr15.hg19:g.45401796A>G	ENSP00000475084:p.Val387Ala	142.0	0.0		77.0	4.0	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	hg19	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.563590	0.86335	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.36	5.36	0.76844	.	0.264153	0.37012	N	0.002281	T	0.76285	0.3966	M	0.88377	2.95	0.58432	D	0.999999	P	0.40875	0.731	P	0.48738	0.588	T	0.81265	-0.1011	9	0.87932	D	0	-21.8641	14.5299	0.67917	1.0:0.0:0.0:0.0	.	387	Q9NRD8	DUOX2_HUMAN	A	387	.	ENSP00000373691:V387A	V	-	2	0	DUOX2	43189088	1.000000	0.71417	0.627000	0.29227	0.826000	0.46750	9.020000	0.93667	2.036000	0.60181	0.402000	0.26972	GTG	.	.		0.522	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		G	45401796	A	G	45401796	3	3	113	1	0	0	0	0	1	0	0	0	4803	159	6	2	3582	2	DUOX2	15	45401796	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3602402	45401796	57129596	286	18163										
CEP152	22995	hgsc.bcm.edu	37	chr15	49090248	49090248	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtctgtgagtaactgctgcaActgagtcaaaaggtctgcat	11	8	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:49090248A>G	ENST00000380950.2	-	3	275	c.88T>C	c.(88-90)Ttg>Ctg	p.L30L	CEP152_ENST00000399334.3_Splice_Site_p.L30L|CEP152_ENST00000325747.5_Splice_Site_p.L30L	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	30					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		AACTGCTGCAACTGAGTCAAA	0.493																																					p.L30L		Atlas-SNP	.											.	CEP152	145	.	0			c.T88C						.						67	69	68					15																	49090248		2046	4203	6249	SO:0001630	splice_region_variant	22995	exon3			GCTGCAACTGAGT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.88-1T>C	chr15.hg19:g.49090248A>G		97.0	0.0		55.0	4.0	NM_014985	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.		0.493	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	Silent	G	49090248	A	G	49090248	5	3	113	1	0	0	0	0	0	0	1	0	3250	57	2	2	4972	2	CEP152	15	49090248	Splice_Site	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3688452	49090248	53441144	287	18164										
SHC4	399694	hgsc.bcm.edu	37	chr15	49176517	49176517	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttatattcattcctgaaaaCtgaagattacttttgccaag	5	7	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:49176517C>A	ENST00000332408.4	-	4	1196	c.768G>T	c.(766-768)caG>caT	p.Q256H		NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	256	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		TTCCTGAAAACTGAAGATTAC	0.323																																					p.Q256H		Atlas-SNP	.											.	SHC4	70	.	0			c.G768T						.						111	109	110					15																	49176517		2196	4295	6491	SO:0001583	missense	399694	exon4			TGAAAACTGAAGA	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"SH2 domain containing"	16743	protein-coding gene	gene with protein product	"rai-like protein"						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.768G>T	chr15.hg19:g.49176517C>A	ENSP00000329668:p.Gln256His	117.0	0.0		67.0	6.0	NM_203349	Q6UXQ3|Q8IYW3	Missense_Mutation	SNP	ENST00000332408.4	hg19	CCDS10130.1	.	.	.	.	.	.	.	.	.	.	C	18.25	3.583076	0.65992	.	.	ENSG00000185634	ENST00000332408	T	0.20200	2.09	5.14	3.22	0.36961	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.64402	D	0.000002	T	0.29850	0.0746	M	0.68317	2.08	0.80722	D	1	P	0.38167	0.621	P	0.44897	0.463	T	0.12967	-1.0527	10	0.59425	D	0.04	-19.8923	11.744	0.51809	0.0:0.8525:0.0:0.1475	.	256	Q6S5L8	SHC4_HUMAN	H	256	ENSP00000329668:Q256H	ENSP00000329668:Q256H	Q	-	3	2	SHC4	46963809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.202000	0.51067	1.394000	0.46624	0.655000	0.94253	CAG	.	.		0.323	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349		A	49176517	C	A	49176517	3	1	113	1	0	0	0	0	1	0	0	0	14288	564	20	3	1160	3	SHC4	15	49176517	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	86269	49176517	53354875	288	18165										
AP4E1	23431	hgsc.bcm.edu	37	chr15	51289911	51289911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttttttggaagaaactactgAatacatacactcaaatgcta	5	7	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:51289911A>G	ENST00000261842.5	+	18	2841	c.2735A>G	c.(2734-2736)gAa>gGa	p.E912G	AP4E1_ENST00000560508.1_Missense_Mutation_p.E837G	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	912					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		GAAACTACTGAATACATACAC	0.348																																					p.E912G		Atlas-SNP	.											.	AP4E1	78	.	0			c.A2735G						.						66	68	67					15																	51289911		2196	4294	6490	SO:0001583	missense	23431	exon18			CTACTGAATACAT	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2735A>G	chr15.hg19:g.51289911A>G	ENSP00000261842:p.Glu912Gly	85.0	0.0		44.0	4.0	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	hg19	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	A	11.94	1.789433	0.31685	.	.	ENSG00000081014	ENST00000261842	T	0.19532	2.14	5.2	5.2	0.72013	Coatomer, beta subunit, C-terminal (1);	0.109704	0.64402	D	0.000008	T	0.20536	0.0494	L	0.43152	1.355	0.41394	D	0.987639	B	0.12013	0.005	B	0.10450	0.005	T	0.02444	-1.1158	10	0.41790	T	0.15	-16.8814	14.2599	0.66078	1.0:0.0:0.0:0.0	.	912	Q9UPM8	AP4E1_HUMAN	G	912	ENSP00000261842:E912G	ENSP00000261842:E912G	E	+	2	0	AP4E1	49077203	0.967000	0.33354	0.905000	0.35620	0.662000	0.39071	2.870000	0.48451	1.966000	0.57179	0.383000	0.25322	GAA	.	.		0.348	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			G	51289911	A	G	51289911	3	3	113	1	0	0	0	0	1	0	0	0	752	246	9	2	2805	2	AP4E1	15	51289911	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2113394	51289911	51241481	289	18166										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54825124	54825124	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttatttttagtttccaggtTataattgaagagtgtataaa	7	2	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:54825124T>A	ENST00000260323.11	+	25	5556	c.5556T>A	c.(5554-5556)gtT>gtA	p.V1852V	UNC13C_ENST00000545554.1_Silent_p.V1852V|UNC13C_ENST00000537900.1_Silent_p.V1850V	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1852					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GTTTCCAGGTTATAATTGAAG	0.323																																					p.V1852V		Atlas-SNP	.											.	UNC13C	674	.	0			c.T5556A						.						36	34	35					15																	54825124		1783	4049	5832	SO:0001819	synonymous_variant	440279	exon24			CCAGGTTATAATT	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5556T>A	chr15.hg19:g.54825124T>A		96.0	0.0		55.0	18.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.323	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54825124	T	A	54825124	2	1	113	1	0	0	0	0	0	0	0	1	17001	1741	61	4		4	UNC13C	15	54825124	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	3535213	54825124	47706268	290	18167										
ALDH1A2	8854	hgsc.bcm.edu	37	chr15	58306387	58306387	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agacataccttgtctgcttcTtgaacttcacacacctgttc	5	13	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:58306387T>C	ENST00000249750.4	-	2	977	c.210A>G	c.(208-210)caA>caG	p.Q70Q	ALDH1A2_ENST00000558231.1_Silent_p.Q41Q|ALDH1A2_ENST00000559517.1_5'Flank|ALDH1A2_ENST00000347587.3_Silent_p.Q70Q|ALDH1A2_ENST00000537372.1_Silent_p.Q49Q	NM_003888.3	NP_003879.2	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1 family, member A2	70					9-cis-retinoic acid biosynthetic process (GO:0042904)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|cardiac muscle tissue development (GO:0048738)|cellular response to retinoic acid (GO:0071300)|determination of bilateral symmetry (GO:0009855)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract development (GO:0048566)|embryonic forelimb morphogenesis (GO:0035115)|face development (GO:0060324)|heart morphogenesis (GO:0003007)|hindbrain development (GO:0030902)|kidney development (GO:0001822)|liver development (GO:0001889)|lung development (GO:0030324)|midgut development (GO:0007494)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|neural crest cell development (GO:0014032)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|proximal/distal pattern formation (GO:0009954)|regulation of endothelial cell proliferation (GO:0001936)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to vitamin A (GO:0033189)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)|retinoic acid receptor signaling pathway (GO:0048384)|retinol metabolic process (GO:0042572)|ureter maturation (GO:0035799)|vitamin A metabolic process (GO:0006776)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|retinal binding (GO:0016918)|retinal dehydrogenase activity (GO:0001758)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	Tretinoin(DB00755)|Vitamin A(DB00162)	TGTCTGCTTCTTGAACTTCAC	0.423																																					p.Q70Q		Atlas-SNP	.											.	ALDH1A2	69	.	0			c.A210G						.						111	106	108					15																	58306387		2192	4292	6484	SO:0001819	synonymous_variant	8854	exon2			TGCTTCTTGAACT	AB015228	CCDS10163.1, CCDS10164.1, CCDS45266.1, CCDS55968.1	15q21.2	2011-02-18			ENSG00000128918	ENSG00000128918		"Aldehyde dehydrogenases"	15472	protein-coding gene	gene with protein product	"retinaldehyde dehydrogenase 2"	603687				9819382	Standard	NM_003888		Approved	RALDH2	uc002aex.3	O94788	OTTHUMG00000132624	ENST00000249750.4:c.210A>G	chr15.hg19:g.58306387T>C		191.0	0.0		102.0	5.0	NM_003888	B3KY52|B4DZR2|F5H2Y9|H0YM00|Q2PJS6|Q8NHQ4|Q9UBR8|Q9UFY0	Silent	SNP	ENST00000249750.4	hg19	CCDS10163.1																																																																																			.	.		0.423	ALDH1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255869.1			C	58306387	T	C	58306387	2	2	113	1	0	0	0	0	0	0	0	1	491	1606	56	2		2	ALDH1A2	15	58306387	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	3481263	58306387	44225005	291	18168										
ADAM10	102	hgsc.bcm.edu	37	chr15	58919930	58919930	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttgtttctcttcttctcaagAacttggcttatatttctaat	4	8	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:58919930A>G	ENST00000260408.3	-	10	1772	c.1329T>C	c.(1327-1329)gtT>gtC	p.V443V	ADAM10_ENST00000402627.1_Intron|ADAM10_ENST00000396140.2_Silent_p.V142V|ADAM10_ENST00000561288.1_Intron	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	443	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		TCTTCTCAAGAACTTGGCTTA	0.308																																					p.V443V		Atlas-SNP	.											.	ADAM10	59	.	0			c.T1329C						.						141	138	139					15																	58919930		2191	4292	6483	SO:0001819	synonymous_variant	102	exon10			CTCAAGAACTTGG	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"ADAM metallopeptidase domain containing", "CD molecules"	188	protein-coding gene	gene with protein product		602192	"a disintegrin and metalloproteinase domain 10"			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.1329T>C	chr15.hg19:g.58919930A>G		118.0	0.0		90.0	4.0	NM_001110	B4DU28|Q10742|Q92650	Silent	SNP	ENST00000260408.3	hg19	CCDS10167.1																																																																																			.	.		0.308	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110		G	58919930	A	G	58919930	2	3	113	1	0	0	0	0	0	0	0	1	234	233	9	2		2	ADAM10	15	58919930	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	613543	58919930	43611462	292	18169										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62214150	62214150	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttaagatttccttacatcaAgccttaaattccattgtctc	3	10	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:62214150A>G	ENST00000261517.5	-	55	7131	c.7058T>C	c.(7057-7059)cTt>cCt	p.L2353P	VPS13C_ENST00000395896.4_Missense_Mutation_p.L2353P|VPS13C_ENST00000249837.3_Missense_Mutation_p.L2310P|VPS13C_ENST00000395898.3_Missense_Mutation_p.L2310P	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CCTTACATCAAGCCTTAAATT	0.373																																					p.L2353P		Atlas-SNP	.											.	VPS13C	506	.	0			c.T7058C						.						134	117	123					15																	62214150		2203	4300	6503	SO:0001583	missense	54832	exon55			ACATCAAGCCTTA	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.7058T>C	chr15.hg19:g.62214150A>G	ENSP00000261517:p.Leu2353Pro	141.0	0.0		96.0	4.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.005213	0.54254	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T;T	0.52983	2.41;2.41;2.41;0.64	5.67	5.67	0.87782	.	0.203719	0.43416	D	0.000565	T	0.65790	0.2725	M	0.76574	2.34	0.80722	D	1	D;D;B;D	0.58970	0.984;0.984;0.056;0.972	P;P;B;P	0.58873	0.847;0.847;0.097;0.707	T	0.70475	-0.4861	10	0.87932	D	0	.	15.9024	0.79392	1.0:0.0:0.0:0.0	.	2310;2353;2310;2353	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	P	2310;2353;2353;2353	ENSP00000249837:L2310P;ENSP00000261517:L2353P;ENSP00000379233:L2353P;ENSP00000379235:L2353P	ENSP00000249837:L2310P	L	-	2	0	VPS13C	60001442	1.000000	0.71417	0.447000	0.26932	0.209000	0.24338	8.543000	0.90651	2.146000	0.66826	0.533000	0.62120	CTT	.	.		0.373	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		G	62214150	A	G	62214150	3	3	113	1	0	0	0	0	1	0	0	0	17206	72	3	2	4355	2	VPS13C	15	62214150	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3294220	62214150	40317242	293	18170										
HERC1	8925	hgsc.bcm.edu	37	chr15	63966643	63966643	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atcagctaatcccaatgctcTctttatgggtgaccgcatga	8	11	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:63966643T>C	ENST00000443617.2	-	38	7831	c.7744A>G	c.(7744-7746)Aga>Gga	p.R2582G	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2582					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCCAATGCTCTCTTTATGGGT	0.483																																					p.R2582G		Atlas-SNP	.											.	HERC1	624	.	0			c.A7744G						.						65	63	64					15																	63966643		1978	4176	6154	SO:0001583	missense	8925	exon38			ATGCTCTCTTTAT	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.7744A>G	chr15.hg19:g.63966643T>C	ENSP00000390158:p.Arg2582Gly	200.0	0.0		84.0	4.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.664951	0.47572	.	.	ENSG00000103657	ENST00000443617	T	0.33216	1.42	5.87	3.46	0.39613	.	0.000000	0.85682	D	0.000000	T	0.25121	0.0610	L	0.29908	0.895	0.53688	D	0.999971	P	0.47762	0.9	B	0.42214	0.38	T	0.02294	-1.1181	10	0.87932	D	0	.	13.0115	0.58733	0.0:0.0:0.3996:0.6004	.	2582	Q15751	HERC1_HUMAN	G	2582	ENSP00000390158:R2582G	ENSP00000390158:R2582G	R	-	1	2	HERC1	61753696	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.705000	0.37867	0.426000	0.26116	0.528000	0.53228	AGA	.	.		0.483	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		C	63966643	T	C	63966643	3	2	113	1	0	0	0	0	1	0	0	0	7066	1559	54	2	7005	2	HERC1	15	63966643	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1752493	63966643	38564749	294	18171										
HERC1	8925	hgsc.bcm.edu	37	chr15	64039146	64039146	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttcatctgggacagttgagtCcatcagtctgaagagcaaat	10	8	4	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:64039146C>T	ENST00000443617.2	-	12	2578	c.2491G>A	c.(2491-2493)Gac>Aac	p.D831N		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	831					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						ACAGTTGAGTCCATCAGTCTG	0.448																																					p.D831N		Atlas-SNP	.											.	HERC1	624	.	0			c.G2491A						.						49	45	46					15																	64039146		1895	4064	5959	SO:0001583	missense	8925	exon12			TTGAGTCCATCAG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.2491G>A	chr15.hg19:g.64039146C>T	ENSP00000390158:p.Asp831Asn	141.0	0.0		98.0	4.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	35	5.565715	0.96540	.	.	ENSG00000103657	ENST00000443617	T	0.27557	1.66	5.35	5.35	0.76521	.	0.000000	0.85682	U	0.000000	T	0.53706	0.1813	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	T	0.55108	-0.8192	10	0.72032	D	0.01	.	19.0574	0.93070	0.0:1.0:0.0:0.0	.	831	Q15751	HERC1_HUMAN	N	831	ENSP00000390158:D831N	ENSP00000390158:D831N	D	-	1	0	HERC1	61826199	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.629000	0.83207	2.499000	0.84300	0.585000	0.79938	GAC	.	.		0.448	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	64039146	C	T	64039146	3	4	113	1	0	0	0	0	1	0	0	0	7066	855	30	3	12362	3	HERC1	15	64039146	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	72503	64039146	38492246	295	18172										
DENND4A	10260	hgsc.bcm.edu	37	chr15	65968921	65968921	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atctgttaaagaggtagattCagaatcctgggctcccactg	10	9	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:65968921C>G	ENST00000431932.2	-	23	4307	c.4099G>C	c.(4099-4101)Gaa>Caa	p.E1367Q	DENND4A_ENST00000443035.3_Missense_Mutation_p.E1410Q	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1367					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						GAGGTAGATTCAGAATCCTGG	0.393																																					p.E1410Q		Atlas-SNP	.											.	DENND4A	217	.	0			c.G4228C						.						80	75	77					15																	65968921		1851	4089	5940	SO:0001583	missense	10260	exon24			TAGATTCAGAATC	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.4099G>C	chr15.hg19:g.65968921C>G	ENSP00000396830:p.Glu1367Gln	181.0	0.0		120.0	5.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	hg19	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	C	14.12	2.440411	0.43326	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.05258	3.47;3.47	5.66	4.75	0.60458	.	1.745490	0.02428	N	0.083288	T	0.10035	0.0246	L	0.47716	1.5	0.47737	D	0.999507	B;B	0.32245	0.361;0.361	B;B	0.26864	0.074;0.074	T	0.33548	-0.9864	10	0.25751	T	0.34	.	14.6074	0.68489	0.0:0.93:0.0:0.07	.	1410;1367	E7EPL3;Q7Z401	.;MYCPP_HUMAN	Q	1410;1367	ENSP00000391167:E1410Q;ENSP00000396830:E1367Q	ENSP00000396830:E1367Q	E	-	1	0	DENND4A	63755975	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.997000	0.70646	1.412000	0.46977	0.655000	0.94253	GAA	.	.		0.393	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		G	65968921	C	G	65968921	3	3	113	1	0	0	0	0	1	0	0	0	4435	835	29	4	1532	4	DENND4A	15	65968921	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	1929775	65968921	36562471	296	18173										
NOX5	79400	hgsc.bcm.edu	37	chr15	69341315	69341315	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtaggtggactttatctggaTcaacagagaccagcggtctt	12	8	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:69341315T>C	ENST00000388866.3	+	14	1957	c.1916T>C	c.(1915-1917)aTc>aCc	p.I639T	NOX5_ENST00000448182.3_Missense_Mutation_p.I593T|NOX5_ENST00000455873.3_Missense_Mutation_p.I604T|NOX5_ENST00000530406.2_Missense_Mutation_p.I611T|NOX5_ENST00000260364.5_Missense_Mutation_p.I621T|NOX5_ENST00000525163.1_3'UTR	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	639					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						TTTATCTGGATCAACAGAGAC	0.552																																					p.I639T		Atlas-SNP	.											.	NOX5	60	.	0			c.T1916C						.						65	57	60					15																	69341315		2200	4298	6498	SO:0001583	missense	79400	exon14			TCTGGATCAACAG	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"EF-hand domain containing"	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.1916T>C	chr15.hg19:g.69341315T>C	ENSP00000373518:p.Ile639Thr	94.0	0.0		72.0	4.0	NM_024505	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Missense_Mutation	SNP	ENST00000388866.3	hg19	CCDS32276.2	.	.	.	.	.	.	.	.	.	.	T	15.64	2.893095	0.52121	.	.	ENSG00000255346	ENST00000455873;ENST00000448182;ENST00000388866;ENST00000530406	D;D;D	0.95588	-3.75;-3.75;-3.75	3.42	3.42	0.39159	Ferric reductase, NAD binding (1);	0.000000	0.85682	D	0.000000	D	0.96947	0.9003	M	0.76727	2.345	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.992;0.998;0.992	D	0.96683	0.9505	10	0.66056	D	0.02	-17.143	10.6958	0.45899	0.0:0.0:0.0:1.0	.	604;639;611	Q96PH1-6;Q96PH1;Q96PH1-3	.;NOX5_HUMAN;.	T	604;621;639;611	ENSP00000416828:I604T;ENSP00000373518:I639T;ENSP00000432440:I611T	ENSP00000373518:I639T	I	+	2	0	NOX5	67128369	1.000000	0.71417	0.995000	0.50966	0.554000	0.35429	5.155000	0.64900	1.209000	0.43321	0.164000	0.16699	ATC	.	.		0.552	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505		C	69341315	T	C	69341315	3	2	113	1	0	0	0	0	1	0	0	0	10568	1435	50	2	2003	2	NOX5	15	69341315	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	3372394	69341315	33190077	297	18174										
SGK269	79834	hgsc.bcm.edu	37	chr15	77473310	77473310	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agaccacagaattttcctcaTaaccattcaggatttcatca	4	11	4	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:77473310T>C	ENST00000560626.2	-	4	1434	c.959A>G	c.(958-960)tAt>tGt	p.Y320C	PEAK1_ENST00000312493.4_Missense_Mutation_p.Y320C|PEAK1_ENST00000558305.1_Missense_Mutation_p.Y320C			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	320					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ATTTTCCTCATAACCATTCAG	0.428																																					p.Y320C		Atlas-SNP	.											.	.	.	.	0			c.A959G						.						87	79	81					15																	77473310		1922	4130	6052	SO:0001583	missense	0	exon5			TCCTCATAACCAT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.959A>G	chr15.hg19:g.77473310T>C	ENSP00000452796:p.Tyr320Cys	155.0	0.0		89.0	4.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	T	13.27	2.187400	0.38609	.	.	ENSG00000173517	ENST00000312493	T	0.73789	-0.78	5.3	4.18	0.49190	.	0.000000	0.33382	U	0.004973	T	0.72985	0.3529	N	0.17082	0.46	0.43593	D	0.995949	D	0.89917	1.0	D	0.87578	0.998	T	0.71928	-0.4444	10	0.45353	T	0.12	-5.5403	8.1587	0.31185	0.0:0.1543:0.0:0.8457	.	320	Q9H792	PEAK1_HUMAN	C	320	ENSP00000309230:Y320C	ENSP00000309230:Y320C	Y	-	2	0	AC087465.1	75260365	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	5.028000	0.64115	0.861000	0.35504	0.455000	0.32223	TAT	.	.		0.428	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			C	77473310	T	C	77473310	3	2	113	1	0	0	0	0	1	0	0	0	14226	1406	49	2	4297	2	SGK269	15	77473310	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	8131995	77473310	25058082	298	18175										
SGK269	79834	hgsc.bcm.edu	37	chr15	77473962	77473962	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agctctgtttcggttccaccCtatgatgacaggtttgttct	9	10	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:77473962C>G	ENST00000560626.2	-	4	782	c.307G>C	c.(307-309)Ggg>Cgg	p.G103R	PEAK1_ENST00000312493.4_Missense_Mutation_p.G103R|PEAK1_ENST00000558305.1_Missense_Mutation_p.G103R			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	103					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CGGTTCCACCCTATGATGACA	0.423																																					p.G103R		Atlas-SNP	.											.	.	.	.	0			c.G307C						.						203	195	197					15																	77473962		1947	4138	6085	SO:0001583	missense	0	exon5			TCCACCCTATGAT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.307G>C	chr15.hg19:g.77473962C>G	ENSP00000452796:p.Gly103Arg	197.0	0.0		124.0	44.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	12.51	1.959287	0.34565	.	.	ENSG00000173517	ENST00000312493	T	0.68903	-0.36	5.76	4.66	0.58398	.	0.238594	0.17033	U	0.189628	T	0.49474	0.1559	N	0.19112	0.55	0.27427	N	0.954138	P	0.34780	0.468	B	0.27500	0.08	T	0.51718	-0.8670	10	0.49607	T	0.09	-8.351	13.9485	0.64101	0.0:0.9176:0.0:0.0824	.	103	Q9H792	PEAK1_HUMAN	R	103	ENSP00000309230:G103R	ENSP00000309230:G103R	G	-	1	0	AC087465.1	75261017	0.959000	0.32827	0.986000	0.45419	0.995000	0.86356	4.507000	0.60434	2.724000	0.93272	0.650000	0.86243	GGG	.	.		0.423	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			G	77473962	C	G	77473962	3	3	113	1	0	0	0	0	1	0	0	0	14226	681	24	4	4949	4	SGK269	15	77473962	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	652	77473962	25057430	299	18176										
SH2D7	646892	hgsc.bcm.edu	37	chr15	78393469	78393469	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagatggagaacagaacaggCctgatggcctggggcctgtc	15	10	0	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:78393469C>T	ENST00000328828.5	+	5	874	c.874C>T	c.(874-876)Cct>Tct	p.P292S	SH2D7_ENST00000409568.2_Missense_Mutation_p.P156S	NM_001101404.1	NP_001094874.1	A6NKC9	SH2D7_HUMAN	SH2 domain containing 7	292										endometrium(2)|kidney(2)|lung(3)	7						ACAGAACAGGCCTGATGGCCT	0.637																																					p.P292S		Atlas-SNP	.											.	SH2D7	26	.	0			c.C874T						.						22	25	24					15																	78393469		1891	4117	6008	SO:0001583	missense	646892	exon5			AACAGGCCTGATG		CCDS45315.1	15q25.1	2013-02-14			ENSG00000183476	ENSG00000183476		"SH2 domain containing"	34549	protein-coding gene	gene with protein product							Standard	NM_001101404		Approved	LOC646892	uc010blb.1	A6NKC9	OTTHUMG00000154271	ENST00000328828.5:c.874C>T	chr15.hg19:g.78393469C>T	ENSP00000327846:p.Pro292Ser	115.0	0.0		67.0	43.0	NM_001101404		Missense_Mutation	SNP	ENST00000328828.5	hg19	CCDS45315.1	.	.	.	.	.	.	.	.	.	.	C	8.777	0.927343	0.18056	.	.	ENSG00000183476	ENST00000409568;ENST00000328828	T;T	0.61742	0.08;0.24	3.75	-0.448	0.12230	.	0.716340	0.12608	N	0.454087	T	0.34861	0.0912	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.17198	-1.0377	10	0.46703	T	0.11	-1.4708	3.3582	0.07177	0.0:0.4337:0.2047:0.3615	.	292	A6NKC9	SH2D7_HUMAN	S	156;292	ENSP00000386676:P156S;ENSP00000327846:P292S	ENSP00000327846:P292S	P	+	1	0	SH2D7	76180524	0.011000	0.17503	0.006000	0.13384	0.014000	0.08584	0.724000	0.25954	0.028000	0.15324	-0.254000	0.11334	CCT	.	.		0.637	SH2D7-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000334660.2	NM_001101404		T	78393469	C	T	78393469	3	4	113	1	0	0	0	0	1	0	0	0	14254	739	26	3	892	3	SH2D7	15	78393469	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	919507	78393469	24137923	300	18177										
HDGFRP3	50810	hgsc.bcm.edu	37	chr15	83832756	83832756	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttttgctaacttacgtttcAtgggtgccaaaaaagaagat	8	6	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:83832756A>G	ENST00000299633.4	-	2	759	c.156T>C	c.(154-156)caT>caC	p.H52H		NM_016073.3	NP_057157.1	Q9Y3E1	HDGR3_HUMAN		52	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						CTTACGTTTCATGGGTGCCAA	0.388																																					p.H52H		Atlas-SNP	.											.	HDGFRP3	17	.	0			c.T156C						.						136	128	131					15																	83832756		2203	4300	6503	SO:0001819	synonymous_variant	0	exon2			CGTTTCATGGGTG																												ENST00000299633.4:c.156T>C	chr15.hg19:g.83832756A>G		101.0	0.0		85.0	4.0	NM_016073		Silent	SNP	ENST00000299633.4	hg19	CCDS32314.1																																																																																			.	.		0.388	HDGFRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419898.1			G	83832756	A	G	83832756	2	3	113	1	0	0	0	0	0	0	0	1	7030	214	8	2		2	HDGFRP3	15	83832756	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	5439287	83832756	18698636	301	18178										
POLG	5428	hgsc.bcm.edu	37	chr15	89864157	89864157	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttggcatgctcacggctgaTgcccacagtagtggctgtct	12	11	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:89864157T>C	ENST00000268124.5	-	18	3154	c.2821A>G	c.(2821-2823)Atc>Gtc	p.I941V	POLG_ENST00000442287.2_Missense_Mutation_p.I941V	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	941					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			TCACGGCTGATGCCCACAGTA	0.552								DNA polymerases (catalytic subunits)																													p.I941V	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.A2821G						.						115	92	100					15																	89864157		2200	4299	6499	SO:0001583	missense	5428	exon18			GGCTGATGCCCAC	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"DNA polymerases"	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.2821A>G	chr15.hg19:g.89864157T>C	ENSP00000268124:p.Ile941Val	136.0	0.0		50.0	4.0	NM_002693	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	hg19	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.359111	0.82353	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.96587	-4.06;-4.06	5.15	5.15	0.70609	DNA-directed DNA polymerase, family A, palm domain (2);	0.000000	0.85682	D	0.000000	D	0.97860	0.9297	M	0.79475	2.455	0.80722	D	1	D	0.63880	0.993	D	0.76071	0.987	D	0.98708	1.0703	10	0.72032	D	0.01	-21.6569	14.9635	0.71174	0.0:0.0:0.0:1.0	.	941	P54098	DPOG1_HUMAN	V	941	ENSP00000268124:I941V;ENSP00000399851:I941V	ENSP00000268124:I941V	I	-	1	0	POLG	87665161	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.698000	0.84413	1.944000	0.56390	0.482000	0.46254	ATC	.	.		0.552	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		C	89864157	T	C	89864157	3	2	113	1	0	0	0	0	1	0	0	0	12209	1464	51	2	922	2	POLG	15	89864157	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	6031401	89864157	12667235	302	18179										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94882652	94882652	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caaagccttgatcaaaagctAcgtgtgaaggtaatcacaga	9	8	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr15:94882652A>G	ENST00000357742.4	+	4	771	c.771A>G	c.(769-771)ctA>ctG	p.L257L	MCTP2_ENST00000543482.1_Silent_p.L257L|MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Silent_p.L257L	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	257	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			ATCAAAAGCTACGTGTGAAGG	0.373																																					p.L257L		Atlas-SNP	.											MCTP2,NS,carcinoma,0,1	MCTP2	122	.	0			c.A771G						.						99	100	100					15																	94882652		2197	4298	6495	SO:0001819	synonymous_variant	55784	exon4			AAAGCTACGTGTG	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.771A>G	chr15.hg19:g.94882652A>G		96.0	0.0		48.0	2.0	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	hg19	CCDS32338.1																																																																																			.	.		0.373	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		G	94882652	A	G	94882652	2	3	113	1	0	0	0	0	0	0	0	1	9410	378	14	2		2	MCTP2	15	94882652	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	5018495	94882652	7648740	303	18180										
AXIN1	8312	hgsc.bcm.edu	37	chr16	364598	364598	+	Frame_Shift_Del	DEL	C	C	-													0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctggacaggctctgctgctCgctgtcgttggcactggtgg					rs377639730		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:364598delC	ENST00000262320.3	-	3	1335	c.964delG	c.(964-966)gagfs	p.E322fs	AXIN1_ENST00000354866.3_Frame_Shift_Del_p.E322fs|AXIN1_ENST00000481769.1_5'UTR	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	322	Interaction with TP53. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)	p.E322fs*92(1)|p.E322K(1)		biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CTCTGCTGCTCGCTGTCGTTG	0.622																																					p.E322fs		Atlas-Indel,Pindel	.											.	AXIN1	290	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	biliary_tract(1)|liver(1)	c.965delA						.						78	61	67					16																	364598		2203	4300	6503	SO:0001589	frameshift_variant	8312	exon3			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.964delG	chr16.hg19:g.364598delC	ENSP00000262320:p.Glu322fs	112.0	0.0		37.0	25.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Del	DEL	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.622	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			-	364598	C	-	364598	7	5	113	1	0	1	0	1	0	0	0	0	1236	893	31	0	1660	0	AXIN1	16	364598	Frame_Shift_Del	DEL	C	TCGA-DD-A39Z-01A-11D-A20W-10		364598	89990155	304	18181										
DECR2	26063	hgsc.bcm.edu	37	chr16	457501	457501	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cgtccgagcgcccccagctgTcatggccgccgtggaccagg	14	17	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:457501T>C	ENST00000219481.5	+	4	416	c.278T>C	c.(277-279)gTc>gCc	p.V93A	DECR2_ENST00000424398.2_Missense_Mutation_p.V81A|DECR2_ENST00000397710.1_Missense_Mutation_p.V144A|DECR2_ENST00000461947.1_Intron	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	93					unsaturated fatty acid biosynthetic process (GO:0006636)	peroxisomal membrane (GO:0005778)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)	9		Hepatocellular(16;0.00015)				CCCCCAGCTGTCATGGCCGCC	0.612																																					p.V93A		Atlas-SNP	.											DECR2_ENST00000397710,NS,carcinoma,0,2	DECR2	47	.	0			c.T278C						.						79	79	79					16																	457501		2202	4300	6502	SO:0001583	missense	26063	exon4			CAGCTGTCATGGC	AJ293009	CCDS10409.1	16p13.3	2011-09-14			ENSG00000242612	ENSG00000242612	1.3.1.34	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	2754	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 17C, member 1"	615839				11514237, 19027726	Standard	NM_020664		Approved	PDCR, SDR17C1	uc002chb.3	Q9NUI1	OTTHUMG00000047846	ENST00000219481.5:c.278T>C	chr16.hg19:g.457501T>C	ENSP00000219481:p.Val93Ala	164.0	1.0		49.0	2.0	NM_020664	Q6ZRS7|Q96ET0	Missense_Mutation	SNP	ENST00000219481.5	hg19	CCDS10409.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.863054	0.51482	.	.	ENSG00000242612	ENST00000219481;ENST00000397710;ENST00000424398	T;T	0.53206	0.63;0.63	4.89	4.89	0.63831	NAD(P)-binding domain (1);	0.244793	0.47093	D	0.000243	T	0.45458	0.1343	L	0.52905	1.665	0.26923	N	0.966631	P	0.38020	0.615	B	0.39706	0.307	T	0.44421	-0.9329	10	0.40728	T	0.16	.	12.2476	0.54578	0.0:0.0:0.0:1.0	.	93	Q9NUI1	DECR2_HUMAN	A	93;144;81	ENSP00000219481:V93A;ENSP00000400374:V81A	ENSP00000219481:V93A	V	+	2	0	DECR2	397502	1.000000	0.71417	0.005000	0.12908	0.006000	0.05464	7.499000	0.81566	1.831000	0.53308	0.459000	0.35465	GTC	.	.		0.612	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664		C	457501	T	C	457501	3	2	113	1	0	0	0	0	1	0	0	0	4385	1667	58	2	292	2	DECR2	16	457501	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	92903	457501	89897252	305	18182										
TSC2	7249	hgsc.bcm.edu	37	chr16	2107122	2107122	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcagctgatgcggaacctccTtggcacccacctgggccaca	11	16	0	1	rs45517131|rs397515102		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:2107122T>G	ENST00000219476.3	+	9	1421	c.791T>G	c.(790-792)cTt>cGt	p.L264R	TSC2_ENST00000439673.2_Missense_Mutation_p.L227R|TSC2_ENST00000568454.1_Missense_Mutation_p.L275R|TSC2_ENST00000353929.4_Missense_Mutation_p.L264R|TSC2_ENST00000350773.4_Missense_Mutation_p.L264R|TSC2_ENST00000382538.6_Missense_Mutation_p.L215R|TSC2_ENST00000401874.2_Missense_Mutation_p.L264R	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	264	Required for interaction with TSC1.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CGGAACCTCCTTGGCACCCAC	0.672			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.L264R		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.T791G	GRCh37	CM090985	TSC2	M	rs45517131	.						40	28	32					16																	2107122		2080	4005	6085	SO:0001583	missense	7249	exon9	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	ACCTCCTTGGCAC	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.791T>G	chr16.hg19:g.2107122T>G	ENSP00000219476:p.Leu264Arg	251.0	0.0		92.0	5.0	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	.	22.1	4.243093	0.79912	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84;-1.84;-1.84	4.65	4.65	0.58169	Armadillo-type fold (1);Tuberin, N-terminal (1);	0.000000	0.64402	D	0.000002	D	0.92090	0.7493	M	0.81497	2.545	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.999;0.999	D;D;D;D;D;D	0.97110	1.0;0.996;0.999;0.999;1.0;0.998	D	0.93167	0.6563	10	0.72032	D	0.01	-13.3355	14.3569	0.66742	0.0:0.0:0.0:1.0	.	215;227;264;264;264;264	B4DIL8;P49815-6;P49815-4;P49815-3;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	R	264;264;264;227;215;264	ENSP00000219476:L264R;ENSP00000384468:L264R;ENSP00000248099:L264R;ENSP00000399232:L227R;ENSP00000371978:L215R;ENSP00000344383:L264R	ENSP00000219476:L264R	L	+	2	0	TSC2	2047123	1.000000	0.71417	0.994000	0.49952	0.931000	0.56810	7.730000	0.84881	1.857000	0.53885	0.459000	0.35465	CTT	.	.		0.672	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		G	2107122	T	G	2107122	3	3	113	1	0	0	0	0	1	0	0	0	16621	1609	56	5	821	5	TSC2	16	2107122	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1649621	2107122	88247631	306	18183										
C16orf68	79091	hgsc.bcm.edu	37	chr16	8735035	8735035	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	actggctgaaggacgacctcTgcacaggtgtgtgtttctct	12	10	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:8735035T>C	ENST00000381920.3	+	7	1078	c.820T>C	c.(820-822)Tgc>Cgc	p.C274R	METTL22_ENST00000561758.1_Missense_Mutation_p.C218R|METTL22_ENST00000568967.1_3'UTR	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	274						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			large_intestine(5)|lung(4)	9						GGACGACCTCTGCACAGGTGT	0.453																																					p.C274R		Atlas-SNP	.											.	METTL22	23	.	0			c.T820C						.						162	162	162					16																	8735035		1950	4142	6092	SO:0001583	missense	79091	exon7			GACCTCTGCACAG	AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"chromosome 16 open reading frame 68"	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.820T>C	chr16.hg19:g.8735035T>C	ENSP00000371345:p.Cys274Arg	238.0	0.0		60.0	4.0	NM_024109	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	hg19	CCDS10533.2	.	.	.	.	.	.	.	.	.	.	T	11.45	1.641694	0.29157	.	.	ENSG00000067365	ENST00000381920	T	0.39592	1.07	4.98	4.98	0.66077	.	0.122272	0.56097	D	0.000025	T	0.36413	0.0966	L	0.56124	1.755	0.80722	D	1	B;P	0.39551	0.267;0.678	B;B	0.38500	0.062;0.275	T	0.12656	-1.0539	10	0.13108	T	0.6	-16.8399	12.0339	0.53415	0.0:0.0:0.0:1.0	.	49;274	Q9BUU2-3;Q9BUU2	.;MET22_HUMAN	R	274	ENSP00000371345:C274R	ENSP00000371345:C274R	C	+	1	0	METTL22	8642536	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	3.670000	0.54569	1.880000	0.54463	0.459000	0.35465	TGC	.	.		0.453	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109		C	8735035	T	C	8735035	3	2	113	1	0	0	0	0	1	0	0	0	1829	1580	55	2	842	2	C16orf68	16	8735035	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	6627913	8735035	81619718	307	18184										
ACSM1	116285	hgsc.bcm.edu	37	chr16	20638583	20638583	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cttcatccatcttacctctgTccccagtgttgtagaagtcc	6	14	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:20638583T>C	ENST00000307493.4	-	10	1422	c.1355A>G	c.(1354-1356)gAc>gGc	p.D452G	ACSM1_ENST00000520010.1_Missense_Mutation_p.D452G|ACSM1_ENST00000219151.4_Missense_Mutation_p.D103G	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	452					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						CTTACCTCTGTCCCCAGTGTT	0.493																																					p.D452G		Atlas-SNP	.											.	ACSM1	118	.	0			c.A1355G						.						370	363	365					16																	20638583		2201	4300	6501	SO:0001583	missense	116285	exon10			CCTCTGTCCCCAG	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"Acyl-CoA synthetase family"	18049	protein-coding gene	gene with protein product		614357	"butyryl Coenzyme A synthetase 1"	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.1355A>G	chr16.hg19:g.20638583T>C	ENSP00000301956:p.Asp452Gly	204.0	0.0		63.0	4.0	NM_052956	Q08AH2|Q96A20	Missense_Mutation	SNP	ENST00000307493.4	hg19	CCDS10587.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	13.95|13.95	2.390732|2.390732	0.42410|0.42410	.|.	.|.	ENSG00000166743|ENSG00000166743	ENST00000307493;ENST00000219151;ENST00000520010|ENST00000524149	D;D;D|.	0.88046|.	-2.33;-2.33;-2.33|.	4.22|4.22	4.22|4.22	0.49857|0.49857	AMP-dependent synthetase/ligase (1);|.	0.000000|.	0.56097|.	D|.	0.000038|.	D|D	0.84229|0.84229	0.5426|0.5426	M|M	0.93854|0.93854	3.465|3.465	0.48632|0.48632	D|D	0.99968|0.99968	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.88282|0.88282	0.2937|0.2937	10|5	0.87932|.	D|.	0|.	.|.	12.7057|12.7057	0.57060|0.57060	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	452|.	Q08AH1|.	ACSM1_HUMAN|.	G|A	452;103;452|124	ENSP00000301956:D452G;ENSP00000219151:D103G;ENSP00000428047:D452G|.	ENSP00000219151:D103G|.	D|T	-|-	2|1	0|0	ACSM1|ACSM1	20546084|20546084	1.000000|1.000000	0.71417|0.71417	0.931000|0.931000	0.37212|0.37212	0.005000|0.005000	0.04900|0.04900	5.759000|5.759000	0.68785|0.68785	1.898000|1.898000	0.54952|0.54952	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.		0.493	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956		C	20638583	T	C	20638583	3	2	113	1	0	0	0	0	1	0	0	0	182	1667	58	2	394	2	ACSM1	16	20638583	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	11903548	20638583	69716170	308	18185										
USP31	57478	hgsc.bcm.edu	37	chr16	23093795	23093795	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agatgtataataagcacatcAggcagagtccagaggcttaa	10	7	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:23093795A>G	ENST00000219689.7	-	12	1913	c.1914T>C	c.(1912-1914)ccT>ccC	p.P638P		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	289	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		TAAGCACATCAGGCAGAGTCC	0.478																																					p.P638P		Atlas-SNP	.											.	USP31	122	.	0			c.T1914C						.						104	92	96					16																	23093795		2197	4300	6497	SO:0001819	synonymous_variant	57478	exon12			CACATCAGGCAGA	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.1914T>C	chr16.hg19:g.23093795A>G		186.0	0.0		69.0	4.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000219689.7	hg19	CCDS10607.1																																																																																			.	.		0.478	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		G	23093795	A	G	23093795	2	3	113	1	0	0	0	0	0	0	0	1	17077	175	7	2		2	USP31	16	23093795	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2455212	23093795	67260958	309	18186										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24834278	24834278	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aacctccctcacggaaatgcTctggtccgctacagttcaaa	7	14	3	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:24834278T>C	ENST00000395799.3	+	24	5586	c.5457T>C	c.(5455-5457)gcT>gcC	p.A1819A	TNRC6A_ENST00000315183.7_Silent_p.A1770A|TNRC6A_ENST00000432286.2_Silent_p.A297A	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1819	RRM.|Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ACGGAAATGCTCTGGTCCGCT	0.527																																					p.A1819A		Atlas-SNP	.											.	TNRC6A	171	.	0			c.T5457C						.						138	116	123					16																	24834278		2197	4300	6497	SO:0001819	synonymous_variant	27327	exon24			AAATGCTCTGGTC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.5457T>C	chr16.hg19:g.24834278T>C		181.0	0.0		67.0	4.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	t	11.23	1.577466	0.28180	.	.	ENSG00000090905	ENST00000450465	.	.	.	5.0	-3.21	0.05140	.	.	.	.	.	T	0.39682	0.1087	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34153	-0.9840	4	.	.	.	-6.313	2.6145	0.04900	0.2298:0.068:0.2108:0.4914	.	.	.	.	P	710	.	.	S	+	1	0	TNRC6A	24741779	0.558000	0.26554	0.955000	0.39395	0.996000	0.88848	0.181000	0.16880	-0.358000	0.08162	0.529000	0.55759	TCT	.	.		0.527	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		C	24834278	T	C	24834278	2	2	113	1	0	0	0	0	0	0	0	1	16355	1538	54	2		2	TNRC6A	16	24834278	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1740483	24834278	65520475	310	18187										
CORO1A	11151	hgsc.bcm.edu	37	chr16	30199817	30199817	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atggctacgtacccccaaagAgccgggagctgagggtcaac	13	12	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:30199817A>G	ENST00000219150.5	+	10	1506	c.1201A>G	c.(1201-1203)Agc>Ggc	p.S401G	CORO1A_ENST00000570045.1_Missense_Mutation_p.S401G|CORO1A_ENST00000565497.1_Intron	NM_001193333.2|NM_007074.3	NP_001180262.1|NP_009005.1	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	401					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|calcium ion transport (GO:0006816)|cell-substrate adhesion (GO:0031589)|cellular component movement (GO:0006928)|cellular response to interleukin-4 (GO:0071353)|homeostasis of number of cells within a tissue (GO:0048873)|innate immune response (GO:0045087)|leukocyte chemotaxis (GO:0030595)|negative regulation of actin nucleation (GO:0051126)|phagocytosis (GO:0006909)|phagolysosome assembly (GO:0001845)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of T cell proliferation (GO:0042102)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|T cell homeostasis (GO:0043029)|uropod organization (GO:0032796)	actin filament (GO:0005884)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|lamellipodium (GO:0030027)|membrane (GO:0016020)|phagocytic cup (GO:0001891)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|phosphatidylinositol 3-kinase binding (GO:0043548)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	9						ACCCCCAAAGAGCCGGGAGCT	0.701																																					p.S401G		Atlas-SNP	.											.	CORO1A	36	.	0			c.A1201G						.						21	25	23					16																	30199817		2196	4300	6496	SO:0001583	missense	11151	exon10			CCAAAGAGCCGGG	X89109	CCDS10673.1	16p11.2	2014-09-17	2001-11-28		ENSG00000102879	ENSG00000102879		"Coronins", "WD repeat domain containing"	2252	protein-coding gene	gene with protein product	"Clabp TACO"	605000	"coronin, actin-binding protein, 1A"			9778037	Standard	NM_007074		Approved	HCORO1, p57, coronin-1	uc002dww.3	P31146	OTTHUMG00000132148	ENST00000219150.5:c.1201A>G	chr16.hg19:g.30199817A>G	ENSP00000219150:p.Ser401Gly	224.0	0.0		89.0	4.0	NM_007074	B2RBL1|Q2YD73	Missense_Mutation	SNP	ENST00000219150.5	hg19	CCDS10673.1	.	.	.	.	.	.	.	.	.	.	.	14.37	2.516387	0.44763	.	.	ENSG00000102879	ENST00000219150	T	0.61627	0.09	4.96	4.96	0.65561	.	0.405411	0.25497	N	0.030262	T	0.54191	0.1843	M	0.62723	1.935	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.51301	-0.8723	10	0.29301	T	0.29	-3.8771	13.7669	0.63002	1.0:0.0:0.0:0.0	.	401	P31146	COR1A_HUMAN	G	401	ENSP00000219150:S401G	ENSP00000219150:S401G	S	+	1	0	CORO1A	30107318	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.084000	0.64462	2.082000	0.62665	0.459000	0.35465	AGC	.	.		0.701	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2	NM_007074		G	30199817	A	G	30199817	3	3	113	1	0	0	0	0	1	0	0	0	3755	304	11	2	1235	2	CORO1A	16	30199817	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	5365539	30199817	60154936	311	18188										
SIAH1	6477	hgsc.bcm.edu	37	chr16	48395979	48395979	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggaataaggcctaaactcacAgagctcttcatggtctgctt	9	10	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:48395979A>G	ENST00000380006.2	-	1	1814	c.361T>C	c.(361-363)Tgt>Cgt	p.C121R	SIAH1_ENST00000356721.3_Missense_Mutation_p.C152R|SIAH1_ENST00000394725.2_Missense_Mutation_p.C121R|SIAH1_ENST00000573005.1_5'Flank			Q8IUQ4	SIAH1_HUMAN	siah E3 ubiquitin protein ligase 1	121	SBD.				anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell cycle (GO:0007049)|nervous system development (GO:0007399)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein catabolic process (GO:0030163)|protein destabilization (GO:0031648)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	beta-catenin destruction complex (GO:0030877)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|stomach(1)	7		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)				CTAAACTCACAGAGCTCTTCA	0.468																																					p.C152R		Atlas-SNP	.											SIAH1_ENST00000356721,NS,malignant_melanoma,0,2	SIAH1	33	.	0			c.T454C						.						83	61	69					16																	48395979		2200	4300	6500	SO:0001583	missense	6477	exon2			ACTCACAGAGCTC	U76247	CCDS10735.1, CCDS32444.1	16q12.1	2013-06-03	2012-02-23		ENSG00000196470	ENSG00000196470			10857	protein-coding gene	gene with protein product		602212	"seven in absentia homolog 1 (Drosophila)"			9403064, 9334332	Standard	NM_001006610		Approved	hSIAH1	uc002efo.1	Q8IUQ4	OTTHUMG00000175417	ENST00000380006.2:c.361T>C	chr16.hg19:g.48395979A>G	ENSP00000369343:p.Cys121Arg	141.0	0.0		47.0	2.0	NM_001006610	A0FKF3|O43269|Q49A58|Q92880	Missense_Mutation	SNP	ENST00000380006.2	hg19	CCDS10735.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.453642	0.63290	.	.	ENSG00000196470	ENST00000356721;ENST00000394725;ENST00000380006	T;T	0.69926	-0.44;-0.44	5.2	5.2	0.72013	Seven-in-absentia protein, TRAF-like domain (1);TRAF-like (1);Seven In Absentia Homolog-type (1);Zinc finger, SIAH-type (1);	0.000000	0.85682	U	0.000000	D	0.87341	0.6153	H	0.96398	3.815	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91347	0.5101	10	0.72032	D	0.01	-7.0567	15.3506	0.74380	1.0:0.0:0.0:0.0	.	121;152	Q8IUQ4;Q8IUQ4-2	SIAH1_HUMAN;.	R	152;121;137	ENSP00000349156:C152R;ENSP00000378214:C121R	ENSP00000349156:C152R	C	-	1	0	SIAH1	46953480	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.094000	0.63399	0.533000	0.62120	TGT	.	.		0.468	SIAH1-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256842.12			G	48395979	A	G	48395979	3	3	113	1	0	0	0	0	1	0	0	0	14314	188	7	2	491	2	SIAH1	16	48395979	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	18196162	48395979	41958774	312	18189										
BRD7	29117	hgsc.bcm.edu	37	chr16	50367608	50367609	+	Splice_Site	DNP	CC	CC	AT													0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcaagcatatctttgtctttCctgaaaatatacattaatac							TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:50367608_50367609CC>AT	ENST00000394688.3	-	8	1047	c.888_888GG>AT	c.(886-888)aaGG>aaATg	p.K296K	BRD7_ENST00000394689.2_Splice_Site_p.K296K			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	296					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				CTTTGTCTTTCCTGAAAATATA	0.312																																					p.K296N|.		Atlas-SNP	.											.	BRD7	61	.	0			c.G888T|c.888-1G>A						.																																			SO:0001630	splice_region_variant	29117	exon8|exon9			GTCTTTCCTGAAA|TCTTTCCTGAAAA	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"bromodomain-containing 7"			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.888_888delinsAT	chr16.hg19:g.50367608_50367609delinsAT		131.0|129.0	0.0		50.0|49.0	35.0	NM_013263|NM_001173984	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation|Splice_Site	SNP	ENST00000394688.3	hg19	CCDS10742.1																																																																																			.	.		0.312	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263	Silent	AT	50367609	CC	AT	50367608	5	1	113	1	0	0	0	0	0	0	1	0	1507	869	30	3	1110	3	BRD7	16	50367608	Splice_Site	DNP	CC	TCGA-DD-A39Z-01A-11D-A20W-10	1971629	50367608	39987145	313	18190										
RBL2	5934	hgsc.bcm.edu	37	chr16	53496562	53496562	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaagactaggagacatggatTtatctgtgagtaaaataacc	9	5	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:53496562T>C	ENST00000262133.6	+	11	1692	c.1555T>C	c.(1555-1557)Tta>Cta	p.L519L	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Silent_p.L303L	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	519	Domain A.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						AGACATGGATTTATCTGTGAG	0.333																																					p.L519L		Atlas-SNP	.											.	RBL2	115	.	0			c.T1555C						.						57	60	59					16																	53496562		2198	4297	6495	SO:0001819	synonymous_variant	5934	exon11			ATGGATTTATCTG	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.1555T>C	chr16.hg19:g.53496562T>C		181.0	0.0		65.0	4.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Silent	SNP	ENST00000262133.6	hg19	CCDS10748.1																																																																																			.	.		0.333	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		C	53496562	T	C	53496562	2	2	113	1	0	0	0	0	0	0	0	1	13125	1838	64	2		2	RBL2	16	53496562	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	3128954	53496562	36858191	314	18191										
IRX5	10265	hgsc.bcm.edu	37	chr16	54966777	54966777	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cgacgaggacgagccccagaAgcccgaggacaagggcgacc	15	14	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:54966777A>G	ENST00000394636.4	+	2	954	c.617A>G	c.(616-618)aAg>aGg	p.K206R	IRX5_ENST00000558597.1_Missense_Mutation_p.K140R|IRX5_ENST00000560154.1_Intron|IRX5_ENST00000320990.5_Missense_Mutation_p.K206R|CTD-3032H12.2_ENST00000560487.1_lincRNA			P78411	IRX5_HUMAN	iroquois homeobox 5	206					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)			kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						GAGCCCCAGAAGCCCGAGGAC	0.597																																					p.K206R		Atlas-SNP	.											.	IRX5	41	.	0			c.A617G						.						70	87	81					16																	54966777		2198	4300	6498	SO:0001583	missense	10265	exon2			CCCAGAAGCCCGA	U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"Homeoboxes / TALE class"	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.617A>G	chr16.hg19:g.54966777A>G	ENSP00000378132:p.Lys206Arg	251.0	0.0		91.0	4.0	NM_001252197	H0YMS7|P78416|Q7Z2E1	Missense_Mutation	SNP	ENST00000394636.4	hg19	CCDS10751.1	.	.	.	.	.	.	.	.	.	.	A	18.96	3.733876	0.69189	.	.	ENSG00000176842	ENST00000394636;ENST00000320990	T;T	0.60424	0.29;0.19	4.14	4.14	0.48551	.	0.546743	0.18273	N	0.146243	T	0.63628	0.2527	L	0.56199	1.76	0.80722	D	1	D	0.61697	0.99	P	0.57101	0.813	T	0.59075	-0.7522	10	0.23302	T	0.38	-12.0352	12.2645	0.54670	1.0:0.0:0.0:0.0	.	206	P78411	IRX5_HUMAN	R	206	ENSP00000378132:K206R;ENSP00000316250:K206R	ENSP00000316250:K206R	K	+	2	0	IRX5	53524278	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.204000	0.77872	1.724000	0.51502	0.533000	0.62120	AAG	.	.		0.597	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256911.2			G	54966777	A	G	54966777	3	3	113	1	0	0	0	0	1	0	0	0	7856	72	3	2	623	2	IRX5	16	54966777	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1470215	54966777	35387976	315	18192										
TMED6	146456	hgsc.bcm.edu	37	chr16	69381728	69381728	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tatcattcagttgttttcttTccttctgtttgtgatcagtc	6	8	5	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:69381728T>C	ENST00000288025.3	-	3	507	c.452A>G	c.(451-453)gAa>gGa	p.E151G	RP11-343C2.7_ENST00000564737.1_Silent_p.G143G|RP11-343C2.9_ENST00000563634.1_Intron	NM_144676.3	NP_653277.2	Q8WW62	TMED6_HUMAN	transmembrane emp24 protein transport domain containing 6	151					transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	9						TTGTTTTCTTTCCTTCTGTTT	0.408																																					p.E151G		Atlas-SNP	.											.	TMED6	19	.	0			c.A452G						.						285	270	275					16																	69381728		2198	4300	6498	SO:0001583	missense	146456	exon3			TTTCTTTCCTTCT	BC020827	CCDS10878.1	16q22.1	2008-02-05			ENSG00000157315	ENSG00000157315			28331	protein-coding gene	gene with protein product						12477932	Standard	NM_144676		Approved	MGC23911	uc002exc.2	Q8WW62	OTTHUMG00000137571	ENST00000288025.3:c.452A>G	chr16.hg19:g.69381728T>C	ENSP00000288025:p.Glu151Gly	381.0	0.0		123.0	6.0	NM_144676	Q6UXN5	Missense_Mutation	SNP	ENST00000288025.3	hg19	CCDS10878.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.308662	0.81247	.	.	ENSG00000157315	ENST00000288025	T	0.18810	2.19	5.2	5.2	0.72013	GOLD (1);	0.623514	0.17351	N	0.177413	T	0.26882	0.0658	M	0.68952	2.095	0.46416	D	0.999031	B	0.11235	0.004	B	0.15052	0.012	T	0.02966	-1.1088	10	0.37606	T	0.19	-4.0412	15.354	0.74412	0.0:0.0:0.0:1.0	.	151	Q8WW62	TMED6_HUMAN	G	151	ENSP00000288025:E151G	ENSP00000288025:E151G	E	-	2	0	TMED6	67939229	1.000000	0.71417	0.952000	0.39060	0.942000	0.58702	4.156000	0.58138	2.090000	0.63153	0.533000	0.62120	GAA	.	.		0.408	TMED6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268951.1	NM_144676		C	69381728	T	C	69381728	3	2	113	1	0	0	0	0	1	0	0	0	16023	1783	62	2	278	2	TMED6	16	69381728	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	14414951	69381728	20973025	316	18193										
AP1G1	164	hgsc.bcm.edu	37	chr16	71779499	71779499	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	actttttccatgacaggcatTctctcaagtagggcagacct	8	11	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:71779499T>C	ENST00000299980.4	-	18	2190	c.1749A>G	c.(1747-1749)agA>agG	p.R583R	AP1G1_ENST00000569748.1_Silent_p.R583R|AP1G1_ENST00000393512.3_Silent_p.R586R|AP1G1_ENST00000423132.2_Silent_p.R586R|AP1G1_ENST00000564155.1_Silent_p.R8R|AP1G1_ENST00000433195.2_Silent_p.R606R	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	583					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				TGACAGGCATTCTCTCAAGTA	0.448																																					p.R586R		Atlas-SNP	.											.	AP1G1	83	.	0			c.A1758G						.						163	157	159					16																	71779499		2198	4300	6498	SO:0001819	synonymous_variant	164	exon19			AGGCATTCTCTCA	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.1749A>G	chr16.hg19:g.71779499T>C		195.0	0.0		79.0	4.0	NM_001030007	O75709|O75842|Q9UG09|Q9Y3U4	Silent	SNP	ENST00000299980.4	hg19	CCDS32480.1																																																																																			.	.		0.448	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			C	71779499	T	C	71779499	2	2	113	1	0	0	0	0	0	0	0	1	732	1780	62	2		2	AP1G1	16	71779499	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2397771	71779499	18575254	317	18194										
AP1G1	164	hgsc.bcm.edu	37	chr16	71798318	71798318	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttcataaagaatagcatttcCtacatttttactagtctcag	4	8	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr16:71798318C>A	ENST00000299980.4	-	9	1294	c.853G>T	c.(853-855)Gga>Tga	p.G285*	AP1G1_ENST00000569748.1_Nonsense_Mutation_p.G285*|AP1G1_ENST00000393512.3_Nonsense_Mutation_p.G288*|AP1G1_ENST00000423132.2_Nonsense_Mutation_p.G288*|AP1G1_ENST00000433195.2_Nonsense_Mutation_p.G308*	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	285					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				ATAGCATTTCCTACATTTTTA	0.363																																					p.G288X		Atlas-SNP	.											.	AP1G1	83	.	0			c.G862T						.						84	75	78					16																	71798318		2197	4300	6497	SO:0001587	stop_gained	164	exon10			CATTTCCTACATT	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.853G>T	chr16.hg19:g.71798318C>A	ENSP00000299980:p.Gly285*	255.0	0.0		85.0	65.0	NM_001030007	O75709|O75842|Q9UG09|Q9Y3U4	Nonsense_Mutation	SNP	ENST00000299980.4	hg19	CCDS32480.1	.	.	.	.	.	.	.	.	.	.	C	46	12.949327	0.99708	.	.	ENSG00000166747	ENST00000299980;ENST00000393512;ENST00000423132;ENST00000433195;ENST00000538574;ENST00000425422	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-12.4855	19.7714	0.96367	0.0:1.0:0.0:0.0	.	.	.	.	X	285;288;288;308;156;370	.	ENSP00000299980:G285X	G	-	1	0	AP1G1	70355819	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.666000	0.90696	0.655000	0.94253	GGA	.	.		0.363	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			A	71798318	C	A	71798318	4	1	113	1	0	0	0	0	0	1	0	0	732	690	24	3	1675	3	AP1G1	16	71798318	Nonsense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	18819	71798318	18556435	318	18195										
ARRB2	409	hgsc.bcm.edu	37	chr17	4624255	4624255	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	accaagctatgccacagatgAtgacattgtgtttgaggact	10	8	0	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:4624255A>G	ENST00000269260.2	+	15	1384	c.1151A>G	c.(1150-1152)gAt>gGt	p.D384G	ARRB2_ENST00000571206.1_Missense_Mutation_p.D192G|ARRB2_ENST00000574954.1_Missense_Mutation_p.D192G|ARRB2_ENST00000412477.3_Missense_Mutation_p.D405G|ARRB2_ENST00000346341.2_Missense_Mutation_p.D381G|ARRB2_ENST00000572457.1_Missense_Mutation_p.D192G|ARRB2_ENST00000381488.6_Missense_Mutation_p.D369G|ARRB2_ENST00000575877.1_3'UTR	NM_001257328.1|NM_001257330.1|NM_004313.3	NP_001244257.1|NP_001244259.1|NP_004304.1	P32121	ARRB2_HUMAN	arrestin, beta 2	384	Interaction with AP2B1.|Interaction with TRAF6.				adult walking behavior (GO:0007628)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell chemotaxis (GO:0060326)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|Notch signaling pathway (GO:0007219)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|receptor internalization (GO:0031623)|regulation of androgen receptor signaling pathway (GO:0060765)|transcription from RNA polymerase II promoter (GO:0006366)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	angiotensin receptor binding (GO:0031701)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|ubiquitin protein ligase binding (GO:0031625)			large_intestine(1)|liver(2)|lung(3)|prostate(1)	7						GCCACAGATGATGACATTGTG	0.567																																					p.D405G		Atlas-SNP	.											.	ARRB2	30	.	0			c.A1214G						.						192	149	164					17																	4624255		2203	4300	6503	SO:0001583	missense	409	exon15			CAGATGATGACAT		CCDS11050.1, CCDS11051.1, CCDS58504.1, CCDS58505.1, CCDS59276.1	17p13	2008-12-11			ENSG00000141480	ENSG00000141480			712	protein-coding gene	gene with protein product	"arrestin 3"	107941		ARR2		7695743	Standard	NM_001257329		Approved	BARR2, DKFZp686L0365	uc002fyl.3	P32121	OTTHUMG00000090759	ENST00000269260.2:c.1151A>G	chr17.hg19:g.4624255A>G	ENSP00000269260:p.Asp384Gly	197.0	0.0		97.0	4.0	NM_001257328	B4DLW0|B5B0C0|B7WPL3|D3DTK2|H0Y688|Q0Z8D3|Q2PP19|Q6ICT3|Q8N7Y2|Q9UEQ6	Missense_Mutation	SNP	ENST00000269260.2	hg19	CCDS11050.1	.	.	.	.	.	.	.	.	.	.	A	12.77	2.036839	0.35893	.	.	ENSG00000141480	ENST00000381488;ENST00000269260;ENST00000346341;ENST00000412477	T	0.20738	2.05	4.16	4.16	0.48862	Immunoglobulin E-set (1);Arrestin, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.24509	0.0594	L	0.52126	1.63	0.80722	D	1	B;P;P;B;B	0.39131	0.044;0.661;0.661;0.016;0.185	B;B;B;B;B	0.42798	0.048;0.398;0.398;0.024;0.109	T	0.03739	-1.1008	10	0.66056	D	0.02	-12.6481	11.4482	0.50136	1.0:0.0:0.0:0.0	.	405;381;396;369;384	B4DLW0;P32121-2;P32121-3;G5E980;P32121	.;.;.;.;ARRB2_HUMAN	G	396;384;369;385	ENSP00000269260:D384G	ENSP00000269260:D384G	D	+	2	0	ARRB2	4571004	1.000000	0.71417	0.504000	0.27639	0.438000	0.31896	6.685000	0.74543	1.885000	0.54596	0.450000	0.29827	GAT	.	.		0.567	ARRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439552.1	NM_004313		G	4624255	A	G	4624255	3	3	113	1	0	0	0	0	1	0	0	0	981	333	12	2	1209	2	ARRB2	17	4624255	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10		4624255	76570955	319	18196										
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6377793	6377793	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcctccgcatggccaggaccAggcccagtggcgagccgaag	14	15	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:6377793A>C	ENST00000262483.8	-	10	1304	c.1217T>G	c.(1216-1218)cTg>cGg	p.L406R	PITPNM3_ENST00000576664.1_5'Flank|PITPNM3_ENST00000421306.3_Missense_Mutation_p.L370R	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	406	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		GGCCAGGACCAGGCCCAGTGG	0.687																																					p.L406R		Atlas-SNP	.											.	PITPNM3	91	.	0			c.T1217G						.						40	35	37					17																	6377793		2203	4299	6502	SO:0001583	missense	83394	exon10			AGGACCAGGCCCA	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.1217T>G	chr17.hg19:g.6377793A>C	ENSP00000262483:p.Leu406Arg	201.0	0.0		115.0	5.0	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	hg19	CCDS11076.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.567773	0.86439	.	.	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.53857	0.61;0.6	5.13	5.13	0.70059	DDHD (2);	0.000000	0.64402	D	0.000001	T	0.74245	0.3691	M	0.84683	2.71	0.53005	D	0.999965	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.79077	-0.1951	10	0.87932	D	0	-18.6258	12.8851	0.58038	1.0:0.0:0.0:0.0	.	370;406	F8WEW5;Q9BZ71	.;PITM3_HUMAN	R	406;370	ENSP00000262483:L406R;ENSP00000407882:L370R	ENSP00000262483:L406R	L	-	2	0	PITPNM3	6318517	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.693000	0.91288	1.926000	0.55796	0.460000	0.39030	CTG	.	.		0.687	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		C	6377793	A	C	6377793	3	2	113	1	0	0	0	0	1	0	0	0	11961	188	7	5	1751	5	PITPNM3	17	6377793	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1753538	6377793	74817417	320	18197										
ASGR2	433	hgsc.bcm.edu	37	chr17	7011175	7011175	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgctttcaggtcctgctgcTgtttctccagcttggctcct	9	14	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:7011175T>C	ENST00000380952.2	-	5	668	c.404A>G	c.(403-405)cAg>cGg	p.Q135R	ASGR2_ENST00000254850.7_Missense_Mutation_p.Q111R|ASGR2_ENST00000446679.2_Missense_Mutation_p.Q116R|ASGR2_ENST00000355035.5_Missense_Mutation_p.Q135R	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	135					bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	GTCCTGCTGCTGTTTCTCCAG	0.602																																					p.Q135R		Atlas-SNP	.											.	ASGR2	38	.	0			c.A404G						.						277	169	206					17																	7011175		2203	4300	6503	SO:0001583	missense	433	exon5			TGCTGCTGTTTCT	M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"C-type lectin domain containing"	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.404A>G	chr17.hg19:g.7011175T>C	ENSP00000370339:p.Gln135Arg	195.0	0.0		120.0	6.0	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Missense_Mutation	SNP	ENST00000380952.2	hg19	CCDS32544.1	.	.	.	.	.	.	.	.	.	.	T	11.81	1.748814	0.30955	.	.	ENSG00000161944	ENST00000355035;ENST00000254850;ENST00000380952;ENST00000446679;ENST00000450034	T;T;T;T	0.16457	2.34;2.34;2.34;2.34	3.46	1.01	0.19927	Hepatic lectin, N-terminal (1);	0.700616	0.11929	N	0.515868	T	0.13756	0.0333	L	0.29908	0.895	0.09310	N	1	P;P;B;P;P;P	0.43352	0.704;0.617;0.203;0.589;0.766;0.804	B;B;B;B;B;P	0.47346	0.388;0.121;0.221;0.405;0.283;0.544	T	0.22103	-1.0226	10	0.15499	T	0.54	.	5.7864	0.18336	0.4399:0.0:0.0:0.5601	.	111;111;135;130;116;135	B4E1D2;P07307-3;P07307;Q7Z4G9;P07307-2;D3DTN0	.;.;ASGR2_HUMAN;.;.;.	R	135;111;135;116;111	ENSP00000347140:Q135R;ENSP00000254850:Q111R;ENSP00000370339:Q135R;ENSP00000405844:Q116R	ENSP00000254850:Q111R	Q	-	2	0	ASGR2	6951899	0.006000	0.16342	0.266000	0.24541	0.420000	0.31355	0.716000	0.25836	0.152000	0.19188	0.496000	0.49642	CAG	.	.		0.602	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914		C	7011175	T	C	7011175	3	2	113	1	0	0	0	0	1	0	0	0	1040	1580	55	2	551	2	ASGR2	17	7011175	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	633382	7011175	74184035	321	18198										
TMEM95	339168	hgsc.bcm.edu	37	chr17	7258602	7258602	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtcgcctcccagcccacgacTtgtcaggccgcctggctcgg	12	18	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:7258602T>C	ENST00000576060.1	+	1	106	c.79T>C	c.(79-81)Ttg>Ctg	p.L27L	TMEM95_ENST00000389982.4_Silent_p.L27L|RP11-542C16.1_ENST00000572417.1_RNA|TMEM95_ENST00000330767.4_Silent_p.L27L			Q3KNT9	TMM95_HUMAN	transmembrane protein 95	27						integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)	3		Prostate(122;0.173)				AGCCCACGACTTGTCAGGCCG	0.652																																					p.L27L		Atlas-SNP	.											.	TMEM95	11	.	0			c.T79C						.						30	32	32					17																	7258602		2203	4300	6503	SO:0001819	synonymous_variant	339168	exon1			CACGACTTGTCAG		CCDS32546.1	17p13.1	2005-12-15			ENSG00000182896	ENSG00000182896			27898	protein-coding gene	gene with protein product						12975309	Standard	NM_198154		Approved	MGC129793, UNQ9390	uc002ggf.1	Q3KNT9	OTTHUMG00000132899	ENST00000576060.1:c.79T>C	chr17.hg19:g.7258602T>C		123.0	0.0		68.0	5.0	NM_198154	B7WPI7|Q6UXT3|Q8IW68	Silent	SNP	ENST00000576060.1	hg19																																																																																				.	.		0.652	TMEM95-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440555.2	NM_198154		C	7258602	T	C	7258602	2	2	113	1	0	0	0	0	0	0	0	1	16238	1606	56	2		2	TMEM95	17	7258602	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	247427	7258602	73936608	322	18199										
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319654	21319654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttgagcccgtgctcttcgagGagaagaaccagtacaagatt	11	9	1	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:21319654G>A	ENST00000583088.1	+	3	1895	c.1000G>A	c.(1000-1002)Gag>Aag	p.E334K	KCNJ12_ENST00000331718.5_Missense_Mutation_p.E334K	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	334				Missing (in Ref. 2; AAC50615). {ECO:0000305}.	muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GCTCTTCGAGGAGAAGAACCA	0.577										Prostate(3;0.18)																											p.E334K		Atlas-SNP	.											.	.	.	.	0			c.G1000A						.						153	154	154					17																	21319654		2203	4300	6503	SO:0001583	missense	100134444	exon3			TTCGAGGAGAAGA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1000G>A	chr17.hg19:g.21319654G>A	ENSP00000463778:p.Glu334Lys	294.0	0.0		169.0	8.0	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	hg19	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.866216	0.71949	.	.	ENSG00000184185	ENST00000331718	D	0.91686	-2.89	5.76	5.76	0.90799	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.89884	0.6844	L	0.41632	1.29	0.80722	D	1	B	0.16603	0.018	B	0.17098	0.017	D	0.85181	0.1004	10	0.66056	D	0.02	.	19.9738	0.97296	0.0:0.0:1.0:0.0	.	334	Q14500	IRK12_HUMAN	K	334	ENSP00000328150:E334K	ENSP00000328150:E334K	E	+	1	0	KCNJ12	21260247	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.698000	0.98700	2.732000	0.93576	0.655000	0.94253	GAG	.	.		0.577	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21319654	G	A	21319654	3	1	113	1	0	0	0	0	1	0	0	0	8055	1175	41	3	1002	3	KCNJ12	17	21319654	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	14061052	21319654	59875556	323	18200										
NF1	4763	hgsc.bcm.edu	37	chr17	29559883	29559883	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aatgccaacgtagacagtggTctcatgcactccataggtga	10	10	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:29559883T>C	ENST00000358273.4	+	26	3863	c.3480T>C	c.(3478-3480)ggT>ggC	p.G1160G	NF1_ENST00000356175.3_Silent_p.G1160G	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1160					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TAGACAGTGGTCTCATGCACT	0.453			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.G1160G		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.T3480C						.						91	73	79					17																	29559883		2203	4300	6503	SO:0001819	synonymous_variant	4763	exon26	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CAGTGGTCTCATG		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.3480T>C	chr17.hg19:g.29559883T>C		120.0	0.0		71.0	4.0	NM_000267	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	hg19	CCDS42292.1																																																																																			.	.		0.453	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29559883	T	C	29559883	2	2	113	1	0	0	0	0	0	0	0	1	10365	1654	58	2		2	NF1	17	29559883	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	8240229	29559883	51635327	324	18201										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33495162	33495162	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcctgcagggcccctttgacCtgggcaaccagctgctggga	13	14	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:33495162C>G	ENST00000268876.5	+	10	1331	c.1234C>G	c.(1234-1236)Ctg>Gtg	p.L412V	RP11-799D4.3_ENST00000585646.1_RNA|UNC45B_ENST00000433649.1_Missense_Mutation_p.L412V|UNC45B_ENST00000591048.1_Missense_Mutation_p.L412V|UNC45B_ENST00000378449.1_Missense_Mutation_p.L412V|UNC45B_ENST00000394570.2_Missense_Mutation_p.L412V	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	412					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				CCCCTTTGACCTGGGCAACCA	0.577																																					p.L412V		Atlas-SNP	.											.	UNC45B	133	.	0			c.C1234G						.						99	81	87					17																	33495162		2203	4300	6503	SO:0001583	missense	146862	exon10			TTTGACCTGGGCA	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.1234C>G	chr17.hg19:g.33495162C>G	ENSP00000268876:p.Leu412Val	241.0	0.0		121.0	53.0	NM_001267052	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	hg19	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	C	1.551	-0.539168	0.04053	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T;T	0.38560	1.13;1.13;1.13;1.13	5.02	4.06	0.47325	Armadillo-like helical (1);Armadillo-type fold (1);	0.068819	0.64402	D	0.000019	T	0.18045	0.0433	N	0.05078	-0.115	0.27112	N	0.962358	B;B;B	0.23128	0.08;0.002;0.001	B;B;B	0.25140	0.058;0.01;0.012	T	0.25467	-1.0131	10	0.02654	T	1	-15.046	9.4724	0.38851	0.0:0.8216:0.0:0.1784	.	412;412;412	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	V	412	ENSP00000378071:L412V;ENSP00000268876:L412V;ENSP00000412840:L412V;ENSP00000367710:L412V	ENSP00000268876:L412V	L	+	1	2	UNC45B	30519275	0.987000	0.35691	1.000000	0.80357	0.994000	0.84299	0.642000	0.24735	1.484000	0.48361	-0.137000	0.14449	CTG	.	.		0.577	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		G	33495162	C	G	33495162	3	3	113	1	0	0	0	0	1	0	0	0	17004	680	24	4	1268	4	UNC45B	17	33495162	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	3935279	33495162	47700048	325	18202										
DNAJC7	7266	hgsc.bcm.edu	37	chr17	40128753	40128753	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgggtggttgcccttcattAgccaaattgaaaaaagaaat	9	7	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:40128753A>G	ENST00000457167.4	-	14	1719	c.1483T>C	c.(1483-1485)Taa>Caa	p.*495Q	CNP_ENST00000393892.3_3'UTR|DNAJC7_ENST00000316603.7_Nonstop_Mutation_p.*439Q|DNAJC7_ENST00000426588.3_Nonstop_Mutation_p.*439Q	NM_003315.3	NP_003306.3	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	0					chaperone cofactor-dependent protein refolding (GO:0070389)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)				GCCCTTCATTAGCCAAATTGA	0.433																																					p.X495Q	Colon(63;618 1117 8600 10857 19751)	Atlas-SNP	.											.	DNAJC7	51	.	0			c.T1483C						.						156	147	150					17																	40128753		1848	4093	5941	SO:0001578	stop_lost	7266	exon14			TTCATTAGCCAAA	U46571	CCDS45677.1, CCDS45678.1	17q11.2	2013-01-10				ENSG00000168259		"Heat shock proteins / DNAJ (HSP40)", "Tetratricopeptide (TTC) repeat domain containing"	12392	protein-coding gene	gene with protein product		601964		TTC2		8836031, 11147971	Standard	NR_029431		Approved	TPR2	uc002hyo.3	Q99615		ENST00000457167.4:c.1483T>C	chr17.hg19:g.40128753A>G	ENSP00000406463:p.*495Gluext*1	140.0	0.0		72.0	4.0	NM_003315	Q7Z784	Missense_Mutation	SNP	ENST00000457167.4	hg19	CCDS45677.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.673359	0.88445	.	.	ENSG00000168259	ENST00000457167;ENST00000426588;ENST00000316603	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.22858	N	0.998641	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3662	0.83325	1.0:0.0:0.0:0.0	.	.	.	.	Q	495;439;439	.	.	X	-	1	0	DNAJC7	37382279	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.935000	0.92923	2.274000	0.75844	0.533000	0.62120	TAA	.	.		0.433	DNAJC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453366.2			G	40128753	A	G	40128753	4	3	113	1	0	0	0	0	0	0	0	0	4656	433	15	2	5	2	DNAJC7	17	40128753	Nonstop_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	6633591	40128753	41066457	326	18203										
EZH1	2145	hgsc.bcm.edu	37	chr17	40857131	40857131	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cacagtattcagaaatgaatTcgttcttctgcacagactcc	6	11	3	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:40857131T>C	ENST00000428826.2	-	17	2031	c.1910A>G	c.(1909-1911)gAa>gGa	p.E637G	EZH1_ENST00000585893.1_Missense_Mutation_p.E597G|EZH1_ENST00000590783.1_5'UTR|EZH1_ENST00000415827.2_Missense_Mutation_p.E628G|EZH1_ENST00000590078.1_Missense_Mutation_p.E567G|EZH1_ENST00000592743.1_Missense_Mutation_p.E637G|EZH1_ENST00000435174.1_Missense_Mutation_p.E498G			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	637	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)			breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		AGAAATGAATTCGTTCTTCTG	0.527																																					p.E637G		Atlas-SNP	.											.	EZH1	62	.	0			c.A1910G						.						98	91	93					17																	40857131		2203	4300	6503	SO:0001583	missense	2145	exon17			ATGAATTCGTTCT		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.1910A>G	chr17.hg19:g.40857131T>C	ENSP00000404658:p.Glu637Gly	135.0	0.0		97.0	5.0	NM_001991	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Missense_Mutation	SNP	ENST00000428826.2	hg19	CCDS32659.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.936096	0.92458	.	.	ENSG00000108799	ENST00000264646;ENST00000428826;ENST00000415827;ENST00000435174	D;D	0.85702	-2.02;-2.02	5.41	5.41	0.78517	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.92760	0.7698	M	0.84846	2.72	0.80722	D	1	D;D;D;D;D	0.69078	0.995;0.996;0.989;0.989;0.997	D;D;D;D;D	0.73708	0.948;0.967;0.948;0.913;0.981	D	0.93869	0.7160	10	0.87932	D	0	.	15.5994	0.76613	0.0:0.0:0.0:1.0	.	498;597;643;567;637	Q92800-5;Q92800-3;Q92800-2;Q92800-4;Q92800	.;.;.;.;EZH1_HUMAN	G	640;637;597;498	ENSP00000404658:E637G;ENSP00000404071:E498G	ENSP00000264646:E640G	E	-	2	0	EZH1	38110657	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.864000	0.87037	2.261000	0.74972	0.460000	0.39030	GAA	.	.		0.527	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		C	40857131	T	C	40857131	3	2	113	1	0	0	0	0	1	0	0	0	5335	1783	62	2	353	2	EZH1	17	40857131	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	728378	40857131	40338079	327	18204										
FMNL1	752	hgsc.bcm.edu	37	chr17	43317843	43317843	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tccttccatctgggggacagAggcttcggctcaccgagagt	13	12	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:43317843A>G	ENST00000331495.3	+	12	1417	c.1081A>G	c.(1081-1083)Agg>Ggg	p.R361G	FMNL1_ENST00000587489.1_5'Flank|CTD-2020K17.3_ENST00000393507.2_RNA|FMNL1_ENST00000328118.3_Splice_Site_p.R361G|CTD-2020K17.3_ENST00000587534.1_RNA	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	361	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						TGGGGGACAGAGGCTTCGGCT	0.602																																					p.R361G	GBM(164;1247 1997 8702 11086 51972)	Atlas-SNP	.											.	FMNL1	78	.	0			c.A1081G						.						65	63	64					17																	43317843		2203	4300	6503	SO:0001630	splice_region_variant	752	exon12			GGACAGAGGCTTC	AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"formin-like"	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.1081-1A>G	chr17.hg19:g.43317843A>G		151.0	0.0		81.0	4.0	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Missense_Mutation	SNP	ENST00000331495.3	hg19	CCDS11497.1	.	.	.	.	.	.	.	.	.	.	A	11.44	1.640585	0.29157	.	.	ENSG00000184922	ENST00000328118;ENST00000331495;ENST00000539884	D;D	0.83673	-1.75;-1.75	3.87	2.75	0.32379	GTPase-binding/formin homology 3 (1);Diaphanous FH3 (1);Armadillo-type fold (1);	0.775970	0.12561	N	0.458141	T	0.76891	0.4051	L	0.52011	1.625	0.45962	D	0.998781	B	0.14012	0.009	B	0.22152	0.038	T	0.65936	-0.6047	9	.	.	.	.	8.3816	0.32474	0.8016:0.1984:0.0:0.0	.	361	O95466	FMNL_HUMAN	G	361;361;79	ENSP00000327442:R361G;ENSP00000329219:R361G	.	R	+	1	2	FMNL1	40673626	1.000000	0.71417	0.998000	0.56505	0.330000	0.28571	5.529000	0.67135	0.623000	0.30267	0.172000	0.16884	AGG	.	.		0.602	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892	Missense_Mutation	G	43317843	A	G	43317843	5	3	113	1	0	0	0	0	0	0	1	0	5959	318	11	2	1127	2	FMNL1	17	43317843	Splice_Site	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2460712	43317843	37877367	328	18205										
CDC27	996	hgsc.bcm.edu	37	chr17	45247316	45247316	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccaacaatgaaagagtaaagCaagctgaatcaccaaactca	6	10	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:45247316C>T	ENST00000066544.3	-	4	437	c.344G>A	c.(343-345)tGc>tAc	p.C115Y	CDC27_ENST00000446365.2_Missense_Mutation_p.C54Y|RP5-867C24.5_ENST00000572193.1_RNA|CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000531206.1_Missense_Mutation_p.C115Y|CDC27_ENST00000527547.1_Missense_Mutation_p.C115Y	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	115					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						AAGAGTAAAGCAAGCTGAATC	0.328																																					p.C115Y		Atlas-SNP	.											.	CDC27	337	.	0			c.G344A						.						85	87	86					17																	45247316		2203	4299	6502	SO:0001583	missense	996	exon4			GTAAAGCAAGCTG	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.344G>A	chr17.hg19:g.45247316C>T	ENSP00000066544:p.Cys115Tyr	84.0	0.0		60.0	4.0	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	hg19	CCDS11509.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.44|19.44	3.827908|3.827908	0.71143|0.71143	.|.	.|.	ENSG00000004897|ENSG00000004897	ENST00000533415|ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	.|T;T;T;T;T	.|0.73681	.|-0.77;-0.77;-0.77;-0.77;-0.77	5.35|5.35	4.36|4.36	0.52297|0.52297	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.|0.286342	.|0.39834	.|N	.|0.001241	T|T	0.80204|0.80204	0.4580|0.4580	L|L	0.49778|0.49778	1.585|1.585	0.58432|0.58432	D|D	0.999996|0.999996	.|D;D;D;D	.|0.65815	.|0.989;0.989;0.995;0.991	.|P;P;P;P	.|0.60345	.|0.832;0.814;0.861;0.873	T|T	0.82180|0.82180	-0.0585|-0.0585	6|10	0.66056|0.72032	D|D	0.02|0.01	-23.7538|-23.7538	13.94|13.94	0.64048|0.64048	0.0:0.8464:0.1536:0.0|0.0:0.8464:0.1536:0.0	.|.	.|54;115;115;115	.|B4DL80;G5EA36;G3V1C4;P30260	.|.;.;.;CDC27_HUMAN	T|Y	66|115;115;54;115;115	.|ENSP00000066544:C115Y;ENSP00000434614:C115Y;ENSP00000392802:C54Y;ENSP00000437339:C115Y;ENSP00000432105:C115Y	ENSP00000432211:A66T|ENSP00000066544:C115Y	A|C	-|-	1|2	0|0	CDC27|CDC27	42602315|42602315	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	4.960000|4.960000	0.63673|0.63673	1.350000|1.350000	0.45770|0.45770	0.655000|0.655000	0.94253|0.94253	GCT|TGC	.	.		0.328	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			T	45247316	C	T	45247316	3	4	113	1	0	0	0	0	1	0	0	0	3068	710	25	3	2212	3	CDC27	17	45247316	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	1929473	45247316	35947894	329	18206										
COL1A1	1277	hgsc.bcm.edu	37	chr17	48271982	48271982	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gggaaaccacggctaccaggTccaccctgcaggaggagagg	15	12	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:48271982T>C	ENST00000225964.5	-	22	1585	c.1467A>G	c.(1465-1467)ggA>ggG	p.G489G		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	489	Triple-helical region.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	GGCTACCAGGTCCACCCTGCA	0.662			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.G489G		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1	158	.	0			c.A1467G						.						34	35	34					17																	48271982		2177	4266	6443	SO:0001819	synonymous_variant	1277	exon22			ACCAGGTCCACCC	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.1467A>G	chr17.hg19:g.48271982T>C		108.0	0.0		47.0	4.0	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	hg19	CCDS11561.1																																																																																			.	.		0.662	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			C	48271982	T	C	48271982	2	2	113	1	0	0	0	0	0	0	0	1	3679	1654	58	2		2	COL1A1	17	48271982	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	3024666	48271982	32923228	330	18207										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901304	51901304	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccacctgctttgcctatgggCagacgggaagtgggaagacg	15	10	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:51901304C>T	ENST00000268919.4	+	1	1066	c.910C>T	c.(910-912)Cag>Tag	p.Q304*		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	304	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TGCCTATGGGCAGACGGGAAG	0.552																																					p.Q304X		Atlas-SNP	.											KIF2B,colon,carcinoma,0,1	KIF2B	254	.	0			c.C910T						.						93	84	87					17																	51901304		2203	4300	6503	SO:0001587	stop_gained	84643	exon1			TATGGGCAGACGG	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.910C>T	chr17.hg19:g.51901304C>T	ENSP00000268919:p.Gln304*	121.0	0.0		61.0	3.0	NM_032559	Q96MA2|Q9BXG6	Nonsense_Mutation	SNP	ENST00000268919.4	hg19	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	C	38	6.660945	0.97743	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	.	.	.	5.52	5.52	0.82312	.	0.000000	0.49305	D	0.000151	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.3543	0.90352	0.0:1.0:0.0:0.0	.	.	.	.	X	304;192	.	ENSP00000268919:Q304X	Q	+	1	0	KIF2B	49256303	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	7.776000	0.85560	2.739000	0.93911	0.655000	0.94253	CAG	.	.		0.552	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51901304	C	T	51901304	4	4	113	1	0	0	0	0	0	1	0	0	8307	711	25	3	912	3	KIF2B	17	51901304	Nonsense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	3629322	51901304	29293906	331	18208										
PRR11	55771	hgsc.bcm.edu	37	chr17	57262914	57262914	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaattatgcaagctccaggaAgcactgaaggttggtattgt	11	6	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:57262914A>G	ENST00000262293.4	+	4	705	c.393A>G	c.(391-393)gaA>gaG	p.E131E		NM_018304.3	NP_060774.2	Q96HE9	PRR11_HUMAN	proline rich 11	131						cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|pancreas(1)	16	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					AGCTCCAGGAAGCACTGAAGG	0.368																																					p.E131E		Atlas-SNP	.											.	PRR11	36	.	0			c.A393G						.						64	64	64					17																	57262914		2203	4300	6503	SO:0001819	synonymous_variant	55771	exon4			CCAGGAAGCACTG		CCDS11614.1	17q23.2	2005-12-13				ENSG00000068489			25619	protein-coding gene	gene with protein product		615920				11799066	Standard	NM_018304		Approved	FLJ11029	uc002ixf.2	Q96HE9		ENST00000262293.4:c.393A>G	chr17.hg19:g.57262914A>G		177.0	0.0		99.0	4.0	NM_018304	Q9NUZ7|Q9NXE9	Silent	SNP	ENST00000262293.4	hg19	CCDS11614.1																																																																																			.	.		0.368	PRR11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445949.1	NM_018304		G	57262914	A	G	57262914	2	3	113	1	0	0	0	0	0	0	0	1	12595	69	3	2		2	PRR11	17	57262914	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	5361610	57262914	23932296	332	18209										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67119418	67119418	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tggaattcaggagctactggTtcaaaataatcatcagaggg	11	6	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:67119418T>C	ENST00000284425.2	-	10	1572	c.1398A>G	c.(1396-1398)gaA>gaG	p.E466E		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	466					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					GAGCTACTGGTTCAAAATAAT	0.348																																					p.E466E		Atlas-SNP	.											.	ABCA6	210	.	0			c.A1398G						.						104	100	102					17																	67119418		2203	4300	6503	SO:0001819	synonymous_variant	23460	exon10			TACTGGTTCAAAA	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.1398A>G	chr17.hg19:g.67119418T>C		77.0	0.0		59.0	4.0	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	hg19	CCDS11683.1																																																																																			.	.		0.348	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		C	67119418	T	C	67119418	2	2	113	1	0	0	0	0	0	0	0	1	36	1722	60	2		2	ABCA6	17	67119418	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	9856504	67119418	14075792	333	18210										
ABCA10	10349	hgsc.bcm.edu	37	chr17	67189275	67189275	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caagatgtcagcctcatccaTgaattgggtactgaagagga	11	8	2	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:67189275T>C	ENST00000269081.4	-	16	2665	c.1756A>G	c.(1756-1758)Atg>Gtg	p.M586V	ABCA10_ENST00000416101.2_3'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	586	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					GCCTCATCCATGAATTGGGTA	0.418																																					p.M586V		Atlas-SNP	.											ABCA10,NS,carcinoma,0,1	ABCA10	209	.	0			c.A1756G						.						113	105	108					17																	67189275		2203	4300	6503	SO:0001583	missense	10349	exon16			CATCCATGAATTG	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.1756A>G	chr17.hg19:g.67189275T>C	ENSP00000269081:p.Met586Val	72.0	0.0		48.0	2.0	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	hg19	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	T	11.65	1.702727	0.30232	.	.	ENSG00000154263	ENST00000269081	T	0.39056	1.1	3.45	2.36	0.29203	ATPase, AAA+ type, core (1);ABC transporter-like (1);	.	.	.	.	T	0.33059	0.0850	L	0.41356	1.27	0.80722	D	1	P;P	0.36837	0.571;0.497	B;B	0.38378	0.272;0.188	T	0.08452	-1.0721	9	0.59425	D	0.04	.	7.7391	0.28831	0.0:0.1874:0.0:0.8126	.	586;586	E5RFN6;Q8WWZ4	.;ABCAA_HUMAN	V	586	ENSP00000269081:M586V	ENSP00000269081:M586V	M	-	1	0	ABCA10	64700870	1.000000	0.71417	0.686000	0.30086	0.796000	0.44982	3.675000	0.54605	0.413000	0.25759	0.460000	0.39030	ATG	.	.		0.418	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		C	67189275	T	C	67189275	3	2	113	1	0	0	0	0	1	0	0	0	29	1464	51	2	2975	2	ABCA10	17	67189275	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	69857	67189275	14005935	334	18211										
SDK2	54549	hgsc.bcm.edu	37	chr17	71346476	71346476	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctttcatccaagctcatcaTctcgctgtggcctagggctc	9	14	4	0	rs372386732		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:71346476T>C	ENST00000392650.3	-	43	5938	c.5938A>G	c.(5938-5940)Atg>Gtg	p.M1980V	SDK2_ENST00000410094.1_5'UTR|SDK2_ENST00000388726.3_Missense_Mutation_p.M1961V	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1980					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						AAGCTCATCATCTCGCTGTGG	0.567																																					p.M1980V		Atlas-SNP	.											.	SDK2	219	.	0			c.A5938G						.						102	80	88					17																	71346476		2203	4300	6503	SO:0001583	missense	54549	exon43			TCATCATCTCGCT	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.5938A>G	chr17.hg19:g.71346476T>C	ENSP00000376421:p.Met1980Val	154.0	0.0		90.0	4.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.533253	0.27387	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893;ENST00000410094	T;T;T	0.58506	0.33;0.34;1.56	5.53	5.53	0.82687	.	0.043708	0.85682	D	0.000000	T	0.50820	0.1638	L	0.44542	1.39	0.48901	D	0.999727	B;B	0.17465	0.004;0.022	B;B	0.16289	0.003;0.015	T	0.44034	-0.9354	10	0.33141	T	0.24	.	15.3336	0.74234	0.0:0.0:0.0:1.0	.	1980;1961	Q58EX2;Q58EX2-3	SDK2_HUMAN;.	V	1604;1980;1961;1137;1980;321	ENSP00000376421:M1980V;ENSP00000373378:M1961V;ENSP00000407098:M1137V	ENSP00000324967:M1980V	M	-	1	0	SDK2	68858071	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.748000	0.62148	2.103000	0.63969	0.528000	0.53228	ATG	.	.		0.567	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		C	71346476	T	C	71346476	3	2	113	1	0	0	0	0	1	0	0	0	13984	1435	50	2	592	2	SDK2	17	71346476	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	4157201	71346476	9848734	335	18212										
RAB37	326624	hgsc.bcm.edu	37	chr17	72741169	72741169	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gtacggtgttcccttcctggAgaccagcgccaagactggca	12	13	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr17:72741169A>G	ENST00000392613.5	+	8	568	c.512A>G	c.(511-513)gAg>gGg	p.E171G	RAB37_ENST00000392615.5_Missense_Mutation_p.E139G|RAB37_ENST00000392610.1_Missense_Mutation_p.E171G|RAB37_ENST00000528438.1_Missense_Mutation_p.E144G|RAB37_ENST00000340415.3_Missense_Mutation_p.E164G|RAB37_ENST00000392612.3_Missense_Mutation_p.E134G|RAB37_ENST00000392614.4_Missense_Mutation_p.E176G|RAB37_ENST00000402449.4_Missense_Mutation_p.E164G|MIR3615_ENST00000585285.1_RNA	NM_001006638.2	NP_001006639.1	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family	171					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|secretory granule (GO:0030141)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	12						CCCTTCCTGGAGACCAGCGCC	0.622											OREG0024716	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E176G		Atlas-SNP	.											.	RAB37	69	.	0			c.A527G						.						85	75	78					17																	72741169		2203	4300	6503	SO:0001583	missense	326624	exon8			TCCTGGAGACCAG	BC040547	CCDS11703.1, CCDS32722.1, CCDS54161.1, CCDS54162.1	17q25.2	2008-02-05			ENSG00000172794	ENSG00000172794		"RAB, member RAS oncogene"	30268	protein-coding gene	gene with protein product		609956				10722846	Standard	NM_175738		Approved		uc002jlk.3	Q96AX2	OTTHUMG00000134282	ENST00000392613.5:c.512A>G	chr17.hg19:g.72741169A>G	ENSP00000376389:p.Glu171Gly	171.0	0.0	1139	87.0	4.0	NM_001163989	A8MXF5|A8MYT0|Q8IWA7	Missense_Mutation	SNP	ENST00000392613.5	hg19	CCDS32722.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.987495	0.93106	.	.	ENSG00000172794	ENST00000340415;ENST00000402449;ENST00000469248;ENST00000528438;ENST00000392615;ENST00000392614;ENST00000392613;ENST00000392612;ENST00000392610	D;D;D;D;D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7	5.22	5.22	0.72569	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.94598	0.8259	H	0.98525	4.255	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D	0.87578	0.991;0.996;0.998;0.997;0.998;0.998	D	0.96486	0.9360	10	0.87932	D	0	.	14.3728	0.66852	1.0:0.0:0.0:0.0	.	134;139;176;164;171;164	A8MXF5;A8MZI4;A8MYT0;Q96AX2-2;Q96AX2;A8MSP2	.;.;.;.;RAB37_HUMAN;.	G	164;164;164;144;139;176;171;134;171	ENSP00000341354:E164G;ENSP00000383934:E164G;ENSP00000432086:E144G;ENSP00000376391:E139G;ENSP00000376390:E176G;ENSP00000376389:E171G;ENSP00000376388:E134G;ENSP00000376387:E171G	ENSP00000341354:E164G	E	+	2	0	RAB37	70252764	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.818000	0.75257	2.100000	0.63781	0.448000	0.29417	GAG	.	.		0.622	RAB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258872.2	NM_175738		G	72741169	A	G	72741169	3	3	113	1	0	0	0	0	1	0	0	0	12942	304	11	2	845	2	RAB37	17	72741169	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1394693	72741169	8454041	336	18213										
EMILIN2	84034	hgsc.bcm.edu	37	chr18	2890914	2890914	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tctggcatgaaggacatcaaGtctgaattggctgaagtcaa	11	7	4	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr18:2890914G>T	ENST00000254528.3	+	4	948	c.789G>T	c.(787-789)aaG>aaT	p.K263N		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	263					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		AGGACATCAAGTCTGAATTGG	0.498																																					p.K263N		Atlas-SNP	.											.	EMILIN2	97	.	0			c.G789T						.						47	50	49					18																	2890914		2203	4300	6503	SO:0001583	missense	84034	exon4			CATCAAGTCTGAA	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.789G>T	chr18.hg19:g.2890914G>T	ENSP00000254528:p.Lys263Asn	52.0	0.0		38.0	19.0	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	hg19	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.481739	0.44147	.	.	ENSG00000132205	ENST00000254528	T	0.36520	1.25	5.41	2.68	0.31781	.	0.372434	0.27715	N	0.018149	T	0.33118	0.0852	M	0.67953	2.075	0.32429	N	0.548359	P	0.40376	0.715	B	0.41723	0.365	T	0.36553	-0.9743	10	0.25106	T	0.35	-22.8633	5.1566	0.15038	0.348:0.0:0.5202:0.1318	.	263	Q9BXX0	EMIL2_HUMAN	N	263	ENSP00000254528:K263N	ENSP00000254528:K263N	K	+	3	2	EMILIN2	2880914	1.000000	0.71417	0.978000	0.43139	0.918000	0.54935	3.208000	0.51114	0.267000	0.21916	0.557000	0.71058	AAG	.	.		0.498	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2890914	G	T	2890914	3	4	113	1	0	0	0	0	1	0	0	0	5096	1020	36	3	803	3	EMILIN2	18	2890914	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10		2890914	75186334	337	18214										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7034666	7034666	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aatgacagaccctcagcctgTgtgcttaaagtgagtccgtt	10	10	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr18:7034666T>C	ENST00000389658.3	-	14	1956	c.1863A>G	c.(1861-1863)acA>acG	p.T621T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	621	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CCTCAGCCTGTGTGCTTAAAG	0.333																																					p.T621T		Atlas-SNP	.											.	LAMA1	458	.	0			c.A1863G						.						111	101	104					18																	7034666		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon14			AGCCTGTGTGCTT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.1863A>G	chr18.hg19:g.7034666T>C		110.0	0.0		86.0	5.0	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.333	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		C	7034666	T	C	7034666	2	2	113	1	0	0	0	0	0	0	0	1	8614	1683	59	2		2	LAMA1	18	7034666	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	4143752	7034666	71042582	338	18215										
SPIRE1	56907	hgsc.bcm.edu	37	chr18	12453068	12453068	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caattacaaaataccttaccTcttacagaactgacaggtat	4	10	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr18:12453068T>C	ENST00000409402.4	-	14	2113	c.1846A>G	c.(1846-1848)Agg>Ggg	p.R616G	SPIRE1_ENST00000453447.2_Splice_Site_p.R482G|SPIRE1_ENST00000410092.3_Splice_Site_p.R602G|SPIRE1_ENST00000309836.5_Splice_Site_p.R405G|SPIRE1_ENST00000383356.2_Splice_Site_p.S443G|SPIRE1_ENST00000464481.1_5'UTR	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1											breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						ATACCTTACCTCTTACAGAAC	0.313																																					p.R616G		Atlas-SNP	.											.	SPIRE1	120	.	0			c.A1846G						.						51	54	53					18																	12453068		2203	4300	6503	SO:0001630	splice_region_variant	56907	exon14			CTTACCTCTTACA	AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"spire homolog 1 (Drosophila)", "spire family actin nucleation factor 1"			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.1847+1A>G	chr18.hg19:g.12453068T>C		126.0	0.0		91.0	4.0	NM_001128626		Missense_Mutation	SNP	ENST00000409402.4	hg19	CCDS45829.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	34|34	5.301853|5.301853	0.95601|0.95601	.|.	.|.	ENSG00000134278|ENSG00000134278	ENST00000453447;ENST00000409402;ENST00000410092;ENST00000309836|ENST00000383356	T;T;T;T|T	0.77489|0.76448	-1.1;-1.1;-1.1;-1.1|-1.02	5.95|5.95	5.95|5.95	0.96441|0.96441	Zinc finger, FYVE/PHD-type (1);|.	0.085644|.	0.85682|.	D|.	0.000000|.	D|D	0.86611|0.86611	0.5974|0.5974	M|M	0.80332|0.80332	2.49|2.49	0.35873|0.35873	D|D	0.828374|0.828374	D;D;D|.	0.69078|.	0.969;0.992;0.997|.	P;P;D|.	0.76575|.	0.856;0.888;0.988|.	D|D	0.90193|0.90193	0.4251|0.4251	10|6	0.87932|.	D|.	0|.	-10.5008|-10.5008	16.4177|16.4177	0.83748|0.83748	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	602;405;616|.	Q08AE8-2;B4DWX0;Q08AE8|.	.;.;SPIR1_HUMAN|.	G|G	482;616;602;405|443	ENSP00000407050:R482G;ENSP00000387266:R616G;ENSP00000387226:R602G;ENSP00000309661:R405G|ENSP00000372847:S443G	ENSP00000309661:R405G|.	R|S	-|-	1|1	2|0	SPIRE1|SPIRE1	12443068|12443068	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	5.654000|5.654000	0.67974|0.67974	2.267000|2.267000	0.75376|0.75376	0.528000|0.528000	0.53228|0.53228	AGG|AGT	.	.		0.313	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818	Missense_Mutation	C	12453068	T	C	12453068	5	2	113	1	0	0	0	0	0	0	1	0	15086	1565	54	2	440	2	SPIRE1	18	12453068	Splice_Site	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	5418402	12453068	65624180	339	18216										
ANKRD30B	374860	hgsc.bcm.edu	37	chr18	14748609	14748609	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gacagtagggaagaagcccgTcaacctgaacaaaagagata	11	8	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr18:14748609T>C	ENST00000358984.4	+	1	371	c.191T>C	c.(190-192)gTc>gCc	p.V64A	ANKRD30B_ENST00000447268.2_Missense_Mutation_p.V64A|ANKRD30B_ENST00000579292.1_Intron	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	64										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						AAGAAGCCCGTCAACCTGAAC	0.582																																					p.V64A		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.T191C						.						47	44	45					18																	14748609		692	1591	2283	SO:0001583	missense	374860	exon1			AGCCCGTCAACCT	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"Ankyrin repeat domain containing"	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.191T>C	chr18.hg19:g.14748609T>C	ENSP00000351875:p.Val64Ala	135.0	0.0		77.0	4.0	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	hg19	CCDS54182.1	.	.	.	.	.	.	.	.	.	.	N	0.711	-0.787089	0.02907	.	.	ENSG00000180777	ENST00000358984;ENST00000447268	T;T	0.69175	-0.38;-0.38	0.14	0.14	0.14804	.	.	.	.	.	T	0.38904	0.1058	N	0.11313	0.125	0.09310	N	1	B	0.26445	0.149	B	0.19391	0.025	T	0.20042	-1.0287	8	0.15066	T	0.55	.	.	.	.	.	64	F8WAG3	.	A	64	ENSP00000351875:V64A;ENSP00000399031:V64A	ENSP00000351875:V64A	V	+	2	0	ANKRD30B	14738609	0.002000	0.14202	0.001000	0.08648	0.005000	0.04900	0.177000	0.16801	0.157000	0.19338	0.155000	0.16302	GTC	.	.		0.582	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029		C	14748609	T	C	14748609	3	2	113	1	0	0	0	0	1	0	0	0	659	1667	58	2	193	2	ANKRD30B	18	14748609	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	2295541	14748609	63328639	340	18217										
SYT4	6860	hgsc.bcm.edu	37	chr18	40853607	40853607	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tccttcagataattcaattcCcgagagaggaattagaactt	7	8	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr18:40853607C>A	ENST00000255224.3	-	2	1155	c.787G>T	c.(787-789)Gga>Tga	p.G263*	SYT4_ENST00000586678.1_Intron|SYT4_ENST00000590752.1_Nonsense_Mutation_p.G245*	NM_020783.3	NP_065834.1	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	263	Phospholipid binding. {ECO:0000305}.				exocytosis (GO:0006887)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of vesicle fusion (GO:0031339)|neurotransmitter secretion (GO:0007269)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44						AATTCAATTCCCGAGAGAGGA	0.328																																					p.G263X	NSCLC(85;81 1419 2855 22820 35912)	Atlas-SNP	.											.	SYT4	162	.	0			c.G787T						.						42	45	44					18																	40853607		2195	4293	6488	SO:0001587	stop_gained	6860	exon2			CAATTCCCGAGAG	BC036538	CCDS11922.1	18q12.3	2013-01-21			ENSG00000132872	ENSG00000132872		"Synaptotagmins"	11512	protein-coding gene	gene with protein product		600103				8058779	Standard	NM_020783		Approved	KIAA1342, HsT1192	uc002law.3	Q9H2B2	OTTHUMG00000132610	ENST00000255224.3:c.787G>T	chr18.hg19:g.40853607C>A	ENSP00000255224:p.Gly263*	217.0	0.0		131.0	57.0	NM_020783	B4DEU3|Q9P2K4	Nonsense_Mutation	SNP	ENST00000255224.3	hg19	CCDS11922.1	.	.	.	.	.	.	.	.	.	.	C	40	8.128881	0.98667	.	.	ENSG00000132872	ENST00000255224;ENST00000442661	.	.	.	5.72	5.72	0.89469	.	0.049066	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	20.2441	0.98394	0.0:1.0:0.0:0.0	.	.	.	.	X	263;68	.	ENSP00000255224:G263X	G	-	1	0	SYT4	39107605	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.729000	0.84864	2.865000	0.98341	0.655000	0.94253	GGA	.	.		0.328	SYT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255851.2	NM_020783		A	40853607	C	A	40853607	4	1	113	1	0	0	0	0	0	1	0	0	15491	632	22	3	502	3	SYT4	18	40853607	Nonsense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	26104998	40853607	37223641	341	18218										
DYM	54808	hgsc.bcm.edu	37	chr18	46906097	46906097	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aggaagaccttaattagtgcAccaagatttcctgttcgagg	10	8	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr18:46906097A>G	ENST00000269445.6	-	4	682	c.225T>C	c.(223-225)ggT>ggC	p.G75G	DYM_ENST00000442713.2_Intron|DYM_ENST00000578396.1_5'Flank	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	75					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						TAATTAGTGCACCAAGATTTC	0.313																																					p.G75G		Atlas-SNP	.											.	DYM	52	.	0			c.T225C						.						126	128	128					18																	46906097		2203	4299	6502	SO:0001819	synonymous_variant	54808	exon4			TAGTGCACCAAGA	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.225T>C	chr18.hg19:g.46906097A>G		116.0	0.0		96.0	4.0	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Silent	SNP	ENST00000269445.6	hg19	CCDS11937.1																																																																																			.	.		0.313	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		G	46906097	A	G	46906097	2	3	113	1	0	0	0	0	0	0	0	1	4842	146	6	2		2	DYM	18	46906097	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	6052490	46906097	31171151	342	18219										
ATP8B3	148229	hgsc.bcm.edu	37	chr19	1785272	1785272	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggtcgccacgcacagggcggTccagtacttgatgataagaa	13	10	0	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:1785272T>C	ENST00000310127.6	-	27	3656	c.3418A>G	c.(3418-3420)Acc>Gcc	p.T1140A	ATP8B3_ENST00000539485.1_Missense_Mutation_p.T1150A|ATP8B3_ENST00000525591.1_Missense_Mutation_p.T1103A	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1140					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACAGGGCGGTCCAGTACTTG	0.602																																					p.T1140A		Atlas-SNP	.											.	ATP8B3	108	.	0			c.A3418G						.						41	50	47					19																	1785272		2192	4289	6481	SO:0001583	missense	148229	exon27			GGGCGGTCCAGTA	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"ATPases / P-type"	13535	protein-coding gene	gene with protein product	"aminophospholipid translocase ATP8B3", "potential phospholipid-transporting ATPase IK"	605866	"ATPase, Class I, type 8B, member 3", "ATPase, class I, type 8B, member 3"			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.3418A>G	chr19.hg19:g.1785272T>C	ENSP00000311336:p.Thr1140Ala	130.0	0.0		63.0	5.0	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	hg19	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.094821	0.56075	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.62364	0.03;0.03;0.03	4.49	4.49	0.54785	.	0.055995	0.64402	D	0.000001	D	0.84844	0.5562	H	0.97540	4.025	0.40442	D	0.980054	D;D	0.76494	0.996;0.999	D;D	0.66847	0.928;0.947	D	0.90200	0.4256	10	0.87932	D	0	.	12.9712	0.58513	0.0:0.0:0.0:1.0	.	1140;1103	O60423;Q7Z485	AT8B3_HUMAN;.	A	1140;1150;1103	ENSP00000311336:T1140A;ENSP00000443574:T1150A;ENSP00000437115:T1103A	ENSP00000311336:T1140A	T	-	1	0	ATP8B3	1736272	1.000000	0.71417	0.979000	0.43373	0.103000	0.19146	6.508000	0.73721	1.660000	0.50760	0.533000	0.62120	ACC	.	.		0.602	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		C	1785272	T	C	1785272	3	2	113	1	0	0	0	0	1	0	0	0	1196	1667	58	2	496	2	ATP8B3	19	1785272	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10		1785272	57343711	343	18220										
REXO1	57455	hgsc.bcm.edu	37	chr19	1827477	1827477	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gccacaggagtggccgaagaTggcttcttcttggtcccttc	12	12	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:1827477T>C	ENST00000170168.4	-	2	1405	c.1311A>G	c.(1309-1311)ccA>ccG	p.P437P	CTB-31O20.4_ENST00000593201.1_RNA|REXO1_ENST00000587524.1_5'Flank|CTB-31O20.4_ENST00000587741.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	437						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGCCGAAGATGGCTTCTTCT	0.731																																					p.P437P		Atlas-SNP	.											.	REXO1	55	.	0			c.A1311G						.						15	16	16					19																	1827477		2150	4202	6352	SO:0001819	synonymous_variant	57455	exon2			CGAAGATGGCTTC	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"elongin A binding protein 1"	609614	"transcription elongation factor B polypeptide 3 binding protein 1"	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.1311A>G	chr19.hg19:g.1827477T>C		60.0	0.0		34.0	4.0	NM_020695	Q9ULT2	Silent	SNP	ENST00000170168.4	hg19	CCDS32866.1																																																																																			.	.		0.731	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		C	1827477	T	C	1827477	2	2	113	1	0	0	0	0	0	0	0	1	13256	1451	51	2		2	REXO1	19	1827477	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	42205	1827477	57301506	344	18221										
MUC16	94025	hgsc.bcm.edu	37	chr19	9087298	9087298	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgtatttctaatggcactgGtatctgcctctgactttgaa	8	9	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:9087298G>A	ENST00000397910.4	-	1	4720	c.4517C>T	c.(4516-4518)aCc>aTc	p.T1506I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1506	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AATGGCACTGGTATCTGCCTC	0.433																																					p.T1506I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C4517T						.						247	231	236					19																	9087298		1947	4130	6077	SO:0001583	missense	94025	exon1			GCACTGGTATCTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4517C>T	chr19.hg19:g.9087298G>A	ENSP00000381008:p.Thr1506Ile	153.0	0.0		66.0	28.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	8.063	0.768474	0.15983	.	.	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.01	1.01	0.19927	.	.	.	.	.	T	0.04003	0.0112	N	0.08118	0	.	.	.	D	0.69078	0.997	D	0.68483	0.958	T	0.43605	-0.9381	8	0.87932	D	0	.	5.3673	0.16121	0.0:0.0:1.0:0.0	.	1506	B5ME49	.	I	1506	ENSP00000381008:T1506I	ENSP00000381008:T1506I	T	-	2	0	MUC16	8948298	0.003000	0.15002	0.036000	0.18154	0.792000	0.44763	-0.342000	0.07801	0.850000	0.35239	0.313000	0.20887	ACC	.	.		0.433	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9087298	G	A	9087298	3	1	113	1	0	0	0	0	1	0	0	0	9982	1261	44	3	39342	3	MUC16	19	9087298	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	7259821	9087298	50041685	345	18222										
ICAM3	3385	hgsc.bcm.edu	37	chr19	10449552	10449552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aatcagtactgcagttcacaAacagggaccctccagcagag	9	12	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:10449552A>G	ENST00000160262.5	-	2	357	c.149T>C	c.(148-150)tTt>tCt	p.F50S	ICAM3_ENST00000589261.1_5'UTR	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	50	Ig-like C2-type 1.				extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			GCAGTTCACAAACAGGGACCC	0.572																																					p.F50S		Atlas-SNP	.											.	ICAM3	29	.	0			c.T149C						.						76	74	75					19																	10449552		2203	4300	6503	SO:0001583	missense	3385	exon2			TTCACAAACAGGG		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.149T>C	chr19.hg19:g.10449552A>G	ENSP00000160262:p.Phe50Ser	101.0	0.0		69.0	6.0	NM_002162	Q6PD68	Missense_Mutation	SNP	ENST00000160262.5	hg19	CCDS12235.1	.	.	.	.	.	.	.	.	.	.	A	8.188	0.795300	0.16327	.	.	ENSG00000076662	ENST00000160262	T	0.21191	2.02	5.66	2.47	0.30058	Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal (1);Intercellular adhesion molecule, N-terminal (1);Immunoglobulin-like fold (1);	1.072550	0.07277	N	0.870167	T	0.09949	0.0244	N	0.04959	-0.14	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.40961	-0.9535	10	0.15499	T	0.54	-0.1736	6.7699	0.23589	0.7189:0.0:0.2811:0.0	.	50	P32942	ICAM3_HUMAN	S	50	ENSP00000160262:F50S	ENSP00000160262:F50S	F	-	2	0	ICAM3	10310552	0.000000	0.05858	0.001000	0.08648	0.069000	0.16628	0.508000	0.22692	0.121000	0.18284	0.482000	0.46254	TTT	.	.		0.572	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1			G	10449552	A	G	10449552	3	3	113	1	0	0	0	0	1	0	0	0	7490	14	1	2	1518	2	ICAM3	19	10449552	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1362254	10449552	48679431	346	18223										
ZNF439	90594	hgsc.bcm.edu	37	chr19	11978999	11978999	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgccaagtcatttcaaagacAtgaaaaaactcacagtggag	8	8	3	2	rs147858709		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:11978999A>G	ENST00000304030.2	+	3	1315	c.1115A>G	c.(1114-1116)cAt>cGt	p.H372R	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Missense_Mutation_p.H236R	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	372					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H372L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						TTTCAAAGACATGAAAAAACT	0.393																																					p.H372R		Atlas-SNP	.											ZNF439,upper_leg,malignant_melanoma,0,1	ZNF439	67	.	1	Substitution - Missense(1)	skin(1)	c.A1115G						.						59	60	60					19																	11978999		2203	4300	6503	SO:0001583	missense	90594	exon3			AAAGACATGAAAA	AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"Zinc fingers, C2H2-type", "-"	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.1115A>G	chr19.hg19:g.11978999A>G	ENSP00000305077:p.His372Arg	65.0	0.0		46.0	3.0	NM_152262	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	hg19	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	a	13.75	2.330223	0.41297	.	.	ENSG00000171291	ENST00000455282;ENST00000304030	D;D	0.86865	-2.18;-2.18	0.575	0.575	0.17374	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94105	0.8110	H	0.96489	3.83	0.26735	N	0.970518	D	0.69078	0.997	D	0.68353	0.957	D	0.85113	0.0964	9	0.87932	D	0	.	6.7827	0.23654	1.0:0.0:0.0:0.0	.	372	Q8NDP4	ZN439_HUMAN	R	236;372	ENSP00000395632:H236R;ENSP00000305077:H372R	ENSP00000305077:H372R	H	+	2	0	ZNF439	11839999	0.409000	0.25368	0.009000	0.14445	0.049000	0.14656	4.046000	0.57376	0.485000	0.27652	0.163000	0.16589	CAT	.	.		0.393	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			G	11978999	A	G	11978999	3	3	113	1	0	0	0	0	1	0	0	0	17926	217	8	2	1125	2	ZNF439	19	11978999	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1529447	11978999	47149984	347	18224										
ZNF100	163227	hgsc.bcm.edu	37	chr19	21909685	21909685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttctctccagtatgaatcaTcttatgtgcagttagttgtg	8	7	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:21909685T>C	ENST00000358296.6	-	5	1627	c.1429A>G	c.(1429-1431)Atg>Gtg	p.M477V	ZNF100_ENST00000305570.6_Missense_Mutation_p.M413V	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	477					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						GTATGAATCATCTTATGTGCA	0.408																																					p.M477V		Atlas-SNP	.											ZNF100,NS,carcinoma,0,1	ZNF100	62	.	0			c.A1429G						.						63	68	66					19																	21909685		2200	4297	6497	SO:0001583	missense	163227	exon5			GAATCATCTTATG	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"Zinc fingers, C2H2-type", "-"	12880	protein-coding gene	gene with protein product		603982	"zinc finger protein 100 (Y1)"			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.1429A>G	chr19.hg19:g.21909685T>C	ENSP00000351042:p.Met477Val	44.0	1.0		20.0	2.0	NM_173531	Q7M4M0	Missense_Mutation	SNP	ENST00000358296.6	hg19	CCDS42538.1	.	.	.	.	.	.	.	.	.	.	.	0.046	-1.267526	0.01433	.	.	ENSG00000197020	ENST00000358296	T	0.17528	2.27	0.867	0.867	0.19085	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07548	0.0190	N	0.04090	-0.28	0.21445	N	0.99969	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.32771	-0.9894	9	0.51188	T	0.08	.	6.7014	0.23227	0.0:0.0:0.0:1.0	.	477;531	Q8IYN0;Q4G131	ZN100_HUMAN;.	V	477	ENSP00000351042:M477V	ENSP00000351042:M477V	M	-	1	0	ZNF100	21701525	0.000000	0.05858	0.308000	0.25141	0.309000	0.27889	-2.990000	0.00658	0.244000	0.21351	0.241000	0.17934	ATG	.	.		0.408	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531		C	21909685	T	C	21909685	3	2	113	1	0	0	0	0	1	0	0	0	17728	1435	50	2	203	2	ZNF100	19	21909685	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	9930686	21909685	37219298	348	18225										
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927409	23927409	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctggttgaaagctttgccacAttccttatattcattgagtt	7	8	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:23927409A>G	ENST00000402377.3	-	4	1084	c.943T>C	c.(943-945)Tgt>Cgt	p.C315R	ZNF681_ENST00000395385.3_Missense_Mutation_p.C246R	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				GCTTTGCCACATTCCTTATAT	0.373																																					p.C315R		Atlas-SNP	.											.	ZNF681	76	.	0			c.T943C						.						128	124	125					19																	23927409		2203	4300	6503	SO:0001583	missense	148213	exon4			TGCCACATTCCTT	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.943T>C	chr19.hg19:g.23927409A>G	ENSP00000384000:p.Cys315Arg	121.0	0.0		82.0	4.0	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	hg19	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	9.732	1.162483	0.21538	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.29655	1.56;1.56	1.64	1.64	0.23874	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41627	0.1167	M	0.91612	3.225	0.52099	D	0.999949	D	0.54964	0.969	P	0.44811	0.461	T	0.50939	-0.8768	9	0.87932	D	0	.	6.9185	0.24374	1.0:0.0:0.0:0.0	.	315	Q96N22	ZN681_HUMAN	R	315;246	ENSP00000384000:C315R;ENSP00000378783:C246R	ENSP00000378783:C246R	C	-	1	0	ZNF681	23719249	0.999000	0.42202	0.034000	0.17996	0.007000	0.05969	6.197000	0.72100	0.731000	0.32448	0.383000	0.25322	TGT	.	.		0.373	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		G	23927409	A	G	23927409	3	3	113	1	0	0	0	0	1	0	0	0	18103	217	8	2	998	2	ZNF681	19	23927409	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2017724	23927409	35201574	349	18226										
RYR1	6261	hgsc.bcm.edu	37	chr19	38979854	38979854	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cgatgaggatgtgaaacagaTcttgaagatgattgagcctg	13	5	1	7			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:38979854T>C	ENST00000359596.3	+	35	5585	c.5585T>C	c.(5584-5586)aTc>aCc	p.I1862T	RYR1_ENST00000355481.4_Missense_Mutation_p.I1862T|RYR1_ENST00000360985.3_Missense_Mutation_p.I1862T			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1862	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GTGAAACAGATCTTGAAGATG	0.532																																					p.I1862T		Atlas-SNP	.											.	RYR1	708	.	0			c.T5585C						.						129	108	115					19																	38979854		2203	4300	6503	SO:0001583	missense	6261	exon35			AACAGATCTTGAA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5585T>C	chr19.hg19:g.38979854T>C	ENSP00000352608:p.Ile1862Thr	134.0	0.0		75.0	4.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	t	14.52	2.560002	0.45590	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.74315	-0.83;-0.83;-0.83	4.06	4.06	0.47325	.	0.000000	0.64402	U	0.000004	D	0.82811	0.5118	M	0.71036	2.16	0.45554	D	0.998508	D;D	0.67145	0.996;0.983	D;D	0.63381	0.914;0.913	D	0.85204	0.1017	10	0.87932	D	0	.	12.8479	0.57839	0.0:0.0:0.0:1.0	.	1862;1862	P21817-2;P21817	.;RYR1_HUMAN	T	1862	ENSP00000352608:I1862T;ENSP00000347667:I1862T;ENSP00000354254:I1862T	ENSP00000347667:I1862T	I	+	2	0	RYR1	43671694	1.000000	0.71417	0.983000	0.44433	0.972000	0.66771	4.849000	0.62882	1.685000	0.51034	0.451000	0.29950	ATC	.	.		0.532	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			C	38979854	T	C	38979854	3	2	113	1	0	0	0	0	1	0	0	0	13783	1435	50	2	5723	2	RYR1	19	38979854	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	15052445	38979854	20149129	350	18227										
TMEM145	284339	hgsc.bcm.edu	37	chr19	42820704	42820704	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcattggcaacgagagtgtgAagatcttgggtgagaatgaa	15	4	1	5			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:42820704A>G	ENST00000301204.3	+	9	759	c.718A>G	c.(718-720)Aag>Gag	p.K240E	TMEM145_ENST00000598766.1_Missense_Mutation_p.K264E	NM_173633.2	NP_775904.2	Q8NBT3	TM145_HUMAN	transmembrane protein 145	240					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	27		Prostate(69;0.00682)				CGAGAGTGTGAAGATCTTGGG	0.582																																					p.K240E		Atlas-SNP	.											.	TMEM145	55	.	0			c.A718G						.						137	122	127					19																	42820704		2203	4300	6503	SO:0001583	missense	284339	exon9			AGTGTGAAGATCT	AK075286	CCDS12603.1	19q13.2	2008-02-05				ENSG00000167619			26912	protein-coding gene	gene with protein product							Standard	NM_173633		Approved	FLJ90805	uc002otk.1	Q8NBT3		ENST00000301204.3:c.718A>G	chr19.hg19:g.42820704A>G	ENSP00000301204:p.Lys240Glu	254.0	0.0		100.0	4.0	NM_173633		Missense_Mutation	SNP	ENST00000301204.3	hg19	CCDS12603.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.397848	0.62177	.	.	ENSG00000167619	ENST00000301204	T	0.44083	0.93	3.93	3.93	0.45458	Rhodopsin-like GPCR transmembrane domain (1);	0.133513	0.47093	D	0.000242	T	0.40473	0.1118	L	0.59436	1.845	0.52099	D	0.999945	P	0.51449	0.945	P	0.48488	0.579	T	0.39781	-0.9597	10	0.06099	T	0.92	-18.5071	11.0586	0.47933	1.0:0.0:0.0:0.0	.	240	Q8NBT3	TM145_HUMAN	E	240	ENSP00000301204:K240E	ENSP00000301204:K240E	K	+	1	0	TMEM145	47512544	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.525000	0.67110	1.568000	0.49683	0.374000	0.22700	AAG	.	.		0.582	TMEM145-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463737.1	NM_173633		G	42820704	A	G	42820704	3	3	113	1	0	0	0	0	1	0	0	0	16074	247	9	2	752	2	TMEM145	19	42820704	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3840850	42820704	16308279	351	18228										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42866592	42866592	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cccgaaggtgcttgcattggAcgcaatgggtcctgcacctc	12	13	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:42866592A>G	ENST00000251268.6	+	34	5901	c.5901A>G	c.(5899-5901)ggA>ggG	p.G1967G	MEGF8_ENST00000334370.4_Silent_p.G1900G	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1967	PSI 5.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CTTGCATTGGACGCAATGGGT	0.622																																					p.G1967G		Atlas-SNP	.											.	MEGF8	358	.	0			c.A5901G						.						131	110	118					19																	42866592		2203	4300	6503	SO:0001819	synonymous_variant	1954	exon34			CATTGGACGCAAT	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.5901A>G	chr19.hg19:g.42866592A>G		91.0	0.0		72.0	4.0	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	hg19																																																																																				.	.		0.622	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		G	42866592	A	G	42866592	2	3	113	1	0	0	0	0	0	0	0	1	9472	262	10	2		2	MEGF8	19	42866592	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	45888	42866592	16262391	352	18229										
PSG7	5676	hgsc.bcm.edu	37	chr19	43430131	43430131	+	RNA	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	acaagtagaggttttgtcctGaatggtaataggtgaatgaa	12	3	0	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:43430131G>T	ENST00000406070.2	-	0	1133				PSG7_ENST00000446844.3_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)						female pregnancy (GO:0007565)	extracellular region (GO:0005576)							Prostate(69;0.00682)				GTTTTGTCCTGAATGGTAATA	0.463																																					p.S224X		Atlas-SNP	.											.	.	.	.	0			c.C671A						.						147	157	154					19																	43430131		2201	4299	6500			5676	exon4			TGTCCTGAATGGT			19q13.2	2013-01-29	2010-02-26		ENSG00000221878	ENSG00000221878		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9524	protein-coding gene	gene with protein product		176396	"pregnancy specific beta-1-glycoprotein 7"				Standard	NM_002783		Approved		uc010xwl.2	Q13046	OTTHUMG00000151125		chr19.hg19:g.43430131G>T		171.0	0.0		90.0	43.0	NM_001206650	Q15232	Nonsense_Mutation	SNP	ENST00000406070.2	hg19																																																																																				.	.		0.463	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	NM_001206650		T	43430131	G	T	43430131	1	4	113	0	1	0	0	0	0	0	0	0	12672	1294	45	3		3	PSG7	19	43430131	RNA	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	563539	43430131	15698852	353	18230										
PVRL2	5819	hgsc.bcm.edu	37	chr19	45389426	45389426	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctctgggggcctcggagcacAgcccactcaagaccccctac	10	18	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:45389426A>G	ENST00000252483.5	+	8	1297	c.1297A>G	c.(1297-1299)Agc>Ggc	p.S433G	CTB-129P6.4_ENST00000585408.1_RNA	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	433					acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		CTCGGAGCACAGCCCACTCAA	0.637																																					p.S433G		Atlas-SNP	.											.	PVRL2	58	.	0			c.A1297G						.						40	42	42					19																	45389426		1888	4105	5993	SO:0001583	missense	5819	exon8			GAGCACAGCCCAC	X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.1297A>G	chr19.hg19:g.45389426A>G	ENSP00000252483:p.Ser433Gly	143.0	0.0		82.0	4.0	NM_001042724	A8K5L5|O75455|Q6IBI6|Q96J29	Missense_Mutation	SNP	ENST00000252483.5	hg19	CCDS42576.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.310333	0.40895	.	.	ENSG00000130202	ENST00000252483	D	0.83914	-1.78	5.23	4.15	0.48705	.	0.000000	0.64402	D	0.000009	T	0.68375	0.2994	L	0.27053	0.805	0.32084	N	0.592741	B	0.23377	0.084	B	0.21360	0.034	T	0.64015	-0.6506	10	0.14656	T	0.56	.	7.918	0.29829	0.8169:0.0:0.0:0.1831	.	433	Q92692	PVRL2_HUMAN	G	433	ENSP00000252483:S433G	ENSP00000252483:S433G	S	+	1	0	PVRL2	50081266	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.924000	0.40065	2.110000	0.64415	0.402000	0.26972	AGC	.	.		0.637	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856		G	45389426	A	G	45389426	3	3	113	1	0	0	0	0	1	0	0	0	12855	188	7	2	1729	2	PVRL2	19	45389426	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	1959295	45389426	13739557	354	18231										
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48908506	48908506	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcagctggcgtggccgtagtGgccagaggtgcccaggccct	17	13	0	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:48908506G>A	ENST00000263269.3	+	3	1069	c.981G>A	c.(979-981)gtG>gtA	p.V327V		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	327					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGGCCGTAGTGGCCAGAGGTG	0.701																																					p.V327V		Atlas-SNP	.											.	GRIN2D	76	.	0			c.G981A						.						15	18	17					19																	48908506		2184	4252	6436	SO:0001819	synonymous_variant	2906	exon3			CGTAGTGGCCAGA	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.981G>A	chr19.hg19:g.48908506G>A		35.0	0.0		14.0	5.0	NM_000836		Silent	SNP	ENST00000263269.3	hg19	CCDS12719.1																																																																																			.	.		0.701	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			A	48908506	G	A	48908506	2	1	113	1	0	0	0	0	0	0	0	1	6791	1335	47	3		3	GRIN2D	19	48908506	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	3519080	48908506	10220477	355	18232										
DKKL1	27120	hgsc.bcm.edu	37	chr19	49868005	49868005	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caaggcttcagccgacttttCctgaaagtaagcgatggcgg	12	10	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:49868005C>T	ENST00000221498.2	+	2	582	c.177C>T	c.(175-177)ttC>ttT	p.F59F	DKKL1_ENST00000594268.1_Intron|TEAD2_ENST00000601519.1_5'Flank|TEAD2_ENST00000311227.2_5'Flank|TEAD2_ENST00000593945.1_5'Flank|TEAD2_ENST00000539846.1_5'Flank	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	59					anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		GCCGACTTTTCCTGAAAGTAA	0.592																																					p.F59F		Atlas-SNP	.											.	DKKL1	23	.	0			c.C177T						.						49	49	49					19																	49868005		2202	4300	6502	SO:0001819	synonymous_variant	27120	exon2			ACTTTTCCTGAAA	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"cancer/testis antigen 34", "soggy"	605418	"dickkopf-like 1 (soggy)"			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.177C>T	chr19.hg19:g.49868005C>T		160.0	0.0		91.0	4.0	NM_014419		Silent	SNP	ENST00000221498.2	hg19	CCDS12762.1																																																																																			.	.		0.592	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419		T	49868005	C	T	49868005	2	4	113	1	0	0	0	0	0	0	0	1	4550	854	30	3		3	DKKL1	19	49868005	Silent	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	959499	49868005	9260978	356	18233										
NUP62	23636	hgsc.bcm.edu	37	chr19	50412103	50412103	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tggcggagctggcagccgccCctgcagctgcgccagggcca	16	16	0	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:50412103C>T	ENST00000596217.1	-	2	2849	c.962G>A	c.(961-963)gGg>gAg	p.G321E	NUP62_ENST00000600583.1_5'Flank|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000352066.3_Missense_Mutation_p.G321E|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000597029.1_Missense_Mutation_p.G321E|NUP62_ENST00000413454.1_Missense_Mutation_p.G321E|NUP62_ENST00000422090.2_Missense_Mutation_p.G321E|NUP62_ENST00000597723.1_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	321	Ala-rich.				carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GGCAGCCGCCCCTGCAGCTGC	0.637																																					p.G321E		Atlas-SNP	.											.	NUP62	50	.	0			c.G962A						.						32	38	36					19																	50412103		2181	4270	6451	SO:0001583	missense	23636	exon3			GCCGCCCCTGCAG	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"nuclear pore glycoprotein p62"	605815	"nucleoporin 62kD"			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.962G>A	chr19.hg19:g.50412103C>T	ENSP00000471191:p.Gly321Glu	95.0	0.0		39.0	13.0	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Missense_Mutation	SNP	ENST00000596217.1	hg19	CCDS12788.1	.	.	.	.	.	.	.	.	.	.	C	13.58	2.278653	0.40294	.	.	ENSG00000213024	ENST00000352066;ENST00000422090;ENST00000413454	T;T;T	0.37752	1.18;1.18;1.18	5.73	2.24	0.28232	Nucleoporin, NSP1-like, C-terminal (1);	0.373725	0.23930	U	0.043150	T	0.22003	0.0530	L	0.36672	1.1	0.09310	N	1	P	0.34934	0.476	B	0.33121	0.158	T	0.07790	-1.0754	9	.	.	.	-14.9936	4.2073	0.10495	0.1637:0.5934:0.1581:0.0848	.	321	P37198	NUP62_HUMAN	E	321	ENSP00000305503:G321E;ENSP00000407331:G321E;ENSP00000387991:G321E	.	G	-	2	0	NUP62	55103915	0.004000	0.15560	0.009000	0.14445	0.011000	0.07611	0.091000	0.15046	0.887000	0.36136	0.655000	0.94253	GGG	.	.		0.637	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		T	50412103	C	T	50412103	3	4	113	1	0	0	0	0	1	0	0	0	10777	623	22	3	610	3	NUP62	19	50412103	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	544098	50412103	8716880	357	18234										
MYH14	79784	hgsc.bcm.edu	37	chr19	50775221	50775221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atatgaggccacaatcgcagAcatggagggtgagctcccgc	13	11	0	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:50775221A>G	ENST00000596571.1	+	23	3164	c.3164A>G	c.(3163-3165)gAc>gGc	p.D1055G	MYH14_ENST00000440075.2_Missense_Mutation_p.D1096G|MYH14_ENST00000425460.1_Missense_Mutation_p.D1063G|MYH14_ENST00000262269.8_Missense_Mutation_p.D1096G|MYH14_ENST00000601313.1_Missense_Mutation_p.D1096G|MYH14_ENST00000376970.2_Missense_Mutation_p.D1088G|MYH14_ENST00000598205.1_Missense_Mutation_p.D1063G			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1055					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		ACAATCGCAGACATGGAGGGT	0.582																																					p.D1096G		Atlas-SNP	.											.	MYH14	261	.	0			c.A3287G						.						32	35	34					19																	50775221		2047	4183	6230	SO:0001583	missense	79784	exon26			TCGCAGACATGGA	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.3164A>G	chr19.hg19:g.50775221A>G	ENSP00000472819:p.Asp1055Gly	163.0	0.0		68.0	4.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.19|17.19	3.326243|3.326243	0.60743|0.60743	.|.	.|.	ENSG00000105357|ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000262269|ENST00000301415;ENST00000376965	D;D;D;D|.	0.86297|.	-2.1;-2.1;-2.1;-2.1|.	3.17|3.17	3.17|3.17	0.36434|0.36434	.|.	.|.	.|.	.|.	.|.	T|T	0.73628|0.73628	0.3611|0.3611	M|M	0.82056|0.82056	2.57|2.57	0.49582|0.49582	D|D	0.999808|0.999808	D;D;D|.	0.60575|.	0.976;0.98;0.988|.	P;P;P|.	0.59595|.	0.76;0.728;0.86|.	T|T	0.77109|0.77109	-0.2709|-0.2709	9|6	0.87932|0.87932	D|D	0|0	.|.	10.0621|10.0621	0.42282|0.42282	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1096;1055;1063|.	Q7Z406-2;Q7Z406;Q7Z406-6|.	.;MYH14_HUMAN;.|.	G|A	1096;1088;1063;1096|1055	ENSP00000406273:D1096G;ENSP00000366169:D1088G;ENSP00000407879:D1063G;ENSP00000262269:D1096G|.	ENSP00000262269:D1096G|ENSP00000301415:T1055A	D|T	+|+	2|1	0|0	MYH14|MYH14	55467033|55467033	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.640000|0.640000	0.38277|0.38277	8.595000|8.595000	0.90840|0.90840	1.684000|1.684000	0.51022|0.51022	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.		0.582	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		G	50775221	A	G	50775221	3	3	113	1	0	0	0	0	1	0	0	0	10042	275	10	2	3385	2	MYH14	19	50775221	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	363118	50775221	8353762	358	18235										
ETFB	2109	hgsc.bcm.edu	37	chr19	51857546	51857546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ccgtgaccacaccggtcctgTcaggcttcactcggatctgc	10	16	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:51857546T>C	ENST00000309244.4	-	2	165	c.74A>G	c.(73-75)gAc>gGc	p.D25G	CTD-2616J11.11_ENST00000600067.1_Nonstop_Mutation_p.*44W|CTD-2616J11.9_ENST00000600974.1_RNA|ETFB_ENST00000354232.4_Missense_Mutation_p.D116G	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide	25					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		ACCGGTCCTGTCAGGCTTCAC	0.627																																					p.D116G		Atlas-SNP	.											ETFB_ENST00000309244,NS,carcinoma,0,2	ETFB	46	.	0			c.A347G						.						90	72	78					19																	51857546		2203	4300	6503	SO:0001583	missense	2109	exon1			GTCCTGTCAGGCT	X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379			3482	protein-coding gene	gene with protein product		130410					Standard	NM_001014763		Approved		uc002pwg.3	P38117		ENST00000309244.4:c.74A>G	chr19.hg19:g.51857546T>C	ENSP00000311930:p.Asp25Gly	114.0	0.0		59.0	3.0	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	hg19	CCDS12828.1	.	.	.	.	.	.	.	.	.	.	t	15.75	2.925813	0.52759	.	.	ENSG00000105379	ENST00000309244;ENST00000354232	D;D	0.82893	-1.66;-1.66	5.22	5.22	0.72569	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.87597	0.6217	L	0.45581	1.43	0.80722	D	1	D;D	0.71674	0.965;0.998	P;D	0.79108	0.817;0.992	D	0.88588	0.3141	10	0.72032	D	0.01	.	13.0526	0.58962	0.0:0.0:0.0:1.0	.	25;116	P38117;P38117-2	ETFB_HUMAN;.	G	25;116	ENSP00000311930:D25G;ENSP00000346173:D116G	ENSP00000311930:D25G	D	-	2	0	ETFB	56549358	1.000000	0.71417	0.349000	0.25694	0.036000	0.12997	3.957000	0.56730	1.988000	0.58038	0.529000	0.55759	GAC	.	.		0.627	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1			C	51857546	T	C	51857546	3	2	113	1	0	0	0	0	1	0	0	0	5272	1667	58	2	713	2	ETFB	19	51857546	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1082325	51857546	7271437	359	18236										
NCR1	9437	hgsc.bcm.edu	37	chr19	55421416	55421416	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gccttgcacctgaagaccccAcctttcctggtgagtaactg	9	14	0	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:55421416A>G	ENST00000291890.4	+	5	711	c.673A>G	c.(673-675)Acc>Gcc	p.T225A	NCR1_ENST00000594765.1_Missense_Mutation_p.T225A|NCR1_ENST00000338835.5_Missense_Mutation_p.T225A|NCR1_ENST00000350790.5_Missense_Mutation_p.T130A|NCR1_ENST00000357397.5_Missense_Mutation_p.T118A|NCR1_ENST00000447255.1_Missense_Mutation_p.T225A|NCR1_ENST00000598576.1_Missense_Mutation_p.T213A	NM_004829.5	NP_004820.2	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	225					cellular defense response (GO:0006968)|intracellular signal transduction (GO:0035556)|natural killer cell activation (GO:0030101)|regulation of natural killer cell mediated cytotoxicity (GO:0042269)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|SWI/SNF complex (GO:0016514)	receptor signaling protein activity (GO:0005057)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(193;0.0449)		TGAAGACCCCACCTTTCCTGG	0.463																																					p.T225A		Atlas-SNP	.											.	NCR1	60	.	0			c.A673G						.						188	190	189					19																	55421416		2203	4300	6503	SO:0001583	missense	9437	exon5			GACCCCACCTTTC	AJ001383	CCDS12911.1, CCDS46181.1, CCDS46182.1, CCDS56103.1	19q13.42	2013-09-20	2002-11-13	2002-11-15	ENSG00000189430	ENSG00000189430		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6731	protein-coding gene	gene with protein product		604530	"lymphocyte antigen 94 (mouse) homolog (activating NK-receptor; NK-p46)"	LY94		9730896	Standard	NM_001145457		Approved	NK-p46, NKP46, CD335	uc002qib.2	O76036	OTTHUMG00000183212	ENST00000291890.4:c.673A>G	chr19.hg19:g.55421416A>G	ENSP00000291890:p.Thr225Ala	158.0	0.0		80.0	4.0	NM_001145458	B0V3L2|B0V3L3|B0V3L4|B0V3L5|B8JL03|O76016|O76017|O76018	Missense_Mutation	SNP	ENST00000291890.4	hg19	CCDS12911.1	.	.	.	.	.	.	.	.	.	.	A	6.689	0.495827	0.12762	.	.	ENSG00000189430	ENST00000291890;ENST00000447255;ENST00000338835;ENST00000350790;ENST00000357397	T;T;T;T;T	0.00543	6.98;7.02;7.07;6.93;6.68	3.19	0.932	0.19466	.	2.364040	0.01849	N	0.035808	T	0.00666	0.0022	L	0.52011	1.625	0.09310	N	1	B;B;B;B;B;B	0.15473	0.012;0.006;0.001;0.013;0.003;0.002	B;B;B;B;B;B	0.16289	0.015;0.002;0.003;0.01;0.009;0.004	T	0.50039	-0.8874	10	0.46703	T	0.11	.	3.6905	0.08344	0.6068:0.2642:0.129:0.0	.	118;130;225;130;225;225	O76036-5;B0V3L4;B0V3L5;B0V3L2;O76036-6;O76036	.;.;.;.;.;NCTR1_HUMAN	A	225;225;225;130;118	ENSP00000291890:T225A;ENSP00000404434:T225A;ENSP00000339515:T225A;ENSP00000344358:T130A;ENSP00000349972:T118A	ENSP00000291890:T225A	T	+	1	0	NCR1	60113228	0.002000	0.14202	0.004000	0.12327	0.384000	0.30261	0.650000	0.24858	0.118000	0.18165	0.472000	0.43445	ACC	.	.		0.463	NCR1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465680.1			G	55421416	A	G	55421416	3	3	113	1	0	0	0	0	1	0	0	0	10246	159	6	2	691	2	NCR1	19	55421416	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3563870	55421416	3707567	360	18237										
ZNF835	90485	hgsc.bcm.edu	37	chr19	57175497	57175497	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aggggtaaggccgctctccgGtgtgcgtgcgctggtgctgc	18	11	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:57175497G>T	ENST00000537055.2	-	2	1301	c.1070C>A	c.(1069-1071)aCc>aAc	p.T357N		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	357					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CCGCTCTCCGGTGTGCGTGCG	0.697																																					p.T357N		Atlas-SNP	.											.	ZNF835	106	.	0			c.C1070A						.						21	21	21					19																	57175497		2202	4293	6495	SO:0001583	missense	90485	exon2			TCTCCGGTGTGCG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.1070C>A	chr19.hg19:g.57175497G>T	ENSP00000444747:p.Thr357Asn	138.0	0.0		74.0	44.0	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	hg19	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158278	0.78114	.	.	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.26067	1.76	2.15	1.04	0.20106	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29423	0.0733	L	0.49126	1.545	0.22001	N	0.999428	B	0.32188	0.359	B	0.41236	0.351	T	0.35475	-0.9787	9	0.62326	D	0.03	.	9.8689	0.41162	0.0:0.2131:0.7869:0.0	.	379	Q9Y2P0	ZN835_HUMAN	N	379;357	ENSP00000444747:T357N	ENSP00000341756:T379N	T	-	2	0	ZNF835	61867309	0.902000	0.30710	0.011000	0.14972	0.924000	0.55760	1.556000	0.36288	0.430000	0.26230	0.561000	0.74099	ACC	.	.		0.697	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		T	57175497	G	T	57175497	3	4	113	1	0	0	0	0	1	0	0	0	18201	1261	44	3	545	3	ZNF835	19	57175497	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	1754081	57175497	1953486	361	18238										
PEG3	5178	hgsc.bcm.edu	37	chr19	57326944	57326944	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaatgtttgttcaccaaaagGcagagagtgaattacagagg	11	5	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:57326944G>T	ENST00000326441.9	-	10	3229	c.2866C>A	c.(2866-2868)Cct>Act	p.P956T	PEG3_ENST00000423103.2_Missense_Mutation_p.P956T|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.P830T|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.P832T|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000601070.1_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	956					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TCACCAAAAGGCAGAGAGTGA	0.473																																					p.P956T		Atlas-SNP	.											.	PEG3	414	.	0			c.C2866A						.						142	135	137					19																	57326944		2203	4300	6503	SO:0001583	missense	5178	exon9			CAAAAGGCAGAGA	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.2866C>A	chr19.hg19:g.57326944G>T	ENSP00000326581:p.Pro956Thr	283.0	0.0		119.0	43.0	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	hg19	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	G	0.175	-1.067845	0.01934	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02837	4.14;4.14	3.83	1.66	0.24008	.	1.031830	0.07707	N	0.941361	T	0.03783	0.0107	L	0.59436	1.845	.	.	.	B;B;B	0.31910	0.063;0.179;0.346	B;B;B	0.30943	0.026;0.052;0.122	T	0.40232	-0.9574	9	0.19147	T	0.46	-1.1974	6.4047	0.21658	0.1015:0.0:0.7156:0.1828	.	832;956;891	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	T	956	ENSP00000326581:P956T;ENSP00000403051:P956T	ENSP00000326581:P956T	P	-	1	0	ZIM2	62018756	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	0.044000	0.13992	0.591000	0.29711	0.655000	0.94253	CCT	.	.		0.473	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			T	57326944	G	T	57326944	3	4	113	1	0	0	0	0	1	0	0	0	11729	1203	42	3	1904	3	PEG3	19	57326944	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	151447	57326944	1802039	362	18239										
ZSCAN22	342945	hgsc.bcm.edu	37	chr19	58846297	58846297	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tccagccatgaccacattgcTcactctgaggctgcacgcct	8	16	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr19:58846297T>C	ENST00000329665.4	+	2	276	c.129T>C	c.(127-129)gcT>gcC	p.A43A		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	43					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|pancreas(1)|prostate(2)	16		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		ACCACATTGCTCACTCTGAGG	0.622																																					p.A43A		Atlas-SNP	.											.	ZSCAN22	47	.	0			c.T129C						.						87	77	80					19																	58846297		2203	4300	6503	SO:0001819	synonymous_variant	342945	exon2			CATTGCTCACTCT	M20675	CCDS12975.1	19q13.43	2013-01-08	2006-09-20	2006-09-20				"-", "Zinc fingers, C2H2-type"	4929	protein-coding gene	gene with protein product	"oncogene HKR2"	165260	"zinc finger protein 50", "GLI-Kruppel family member HKR2"	ZNF50, HKR2		2850480, 1505991	Standard	NM_181846		Approved		uc002qsc.2	P10073		ENST00000329665.4:c.129T>C	chr19.hg19:g.58846297T>C		131.0	0.0		93.0	4.0	NM_181846	Q15922|Q7Z3L8	Silent	SNP	ENST00000329665.4	hg19	CCDS12975.1																																																																																			.	.		0.622	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846		C	58846297	T	C	58846297	2	2	113	1	0	0	0	0	0	0	0	1	18249	1538	54	2		2	ZSCAN22	19	58846297	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1519353	58846297	282686	363	18240										
ZNF343	79175	hgsc.bcm.edu	37	chr20	2465247	2465247	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgttgactgaggaactgctgAcaggagaaggccagaaggca	15	7	0	5			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr20:2465247A>G	ENST00000278772.4	-	6	847	c.360T>C	c.(358-360)tgT>tgC	p.C120C	RP4-734P14.4_ENST00000461548.1_Intron	NM_001282495.1|NM_001282496.1|NM_024325.4	NP_001269424.1|NP_001269425.1|NP_077301.4	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	120	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|skin(4)|upper_aerodigestive_tract(1)	25						GGAACTGCTGACAGGAGAAGG	0.468																																					p.C120C		Atlas-SNP	.											.	ZNF343	47	.	0			c.T360C						.						90	93	92					20																	2465247		2203	4300	6503	SO:0001819	synonymous_variant	79175	exon6			CTGCTGACAGGAG	AK096911	CCDS13028.1, CCDS74692.1, CCDS74693.1, CCDS74694.1	20p13	2013-01-08			ENSG00000088876	ENSG00000088876		"Zinc fingers, C2H2-type", "-"	16017	protein-coding gene	gene with protein product							Standard	NM_001282498		Approved	MGC10715	uc002wge.1	Q6P1L6	OTTHUMG00000031701	ENST00000278772.4:c.360T>C	chr20.hg19:g.2465247A>G		101.0	0.0		81.0	4.0	NM_024325	Q5JXU8|Q5JXU9|Q8N8F2|Q96EX8|Q96NA5|Q9BQB0	Silent	SNP	ENST00000278772.4	hg19	CCDS13028.1																																																																																			.	.		0.468	ZNF343-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077617.1	NM_024325		G	2465247	A	G	2465247	2	3	113	1	0	0	0	0	0	0	0	1	17873	273	10	2		2	ZNF343	20	2465247	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10		2465247	60560273	364	18241										
TMC2	117532	hgsc.bcm.edu	37	chr20	2539363	2539363	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggagcggacagcagccccaaAgagggaaaaggagattccga	15	9	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr20:2539363A>G	ENST00000358864.1	+	3	359	c.344A>G	c.(343-345)aAg>aGg	p.K115R		NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	115	Arg/Asp/Glu/Lys-rich (highly charged).				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GCAGCCCCAAAGAGGGAAAAG	0.647																																					p.K115R		Atlas-SNP	.											.	TMC2	121	.	0			c.A344G						.						23	23	23					20																	2539363		2196	4298	6494	SO:0001583	missense	117532	exon3			CCCCAAAGAGGGA	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.344A>G	chr20.hg19:g.2539363A>G	ENSP00000351732:p.Lys115Arg	148.0	0.0		94.0	4.0	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	hg19	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	A	6.549	0.469630	0.12461	.	.	ENSG00000149488	ENST00000358864	T	0.51071	0.72	4.59	2.21	0.28008	.	0.584607	0.18463	N	0.140477	T	0.38904	0.1058	M	0.62723	1.935	0.25129	N	0.990581	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.28554	-1.0040	10	0.18710	T	0.47	-2.4822	7.0528	0.25083	0.805:0.0:0.195:0.0	.	115;115	Q8TDI7-3;Q8TDI7	.;TMC2_HUMAN	R	115	ENSP00000351732:K115R	ENSP00000351732:K115R	K	+	2	0	TMC2	2487363	0.935000	0.31712	0.502000	0.27614	0.039000	0.13416	1.787000	0.38704	0.297000	0.22615	0.454000	0.30748	AAG	.	.		0.647	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			G	2539363	A	G	2539363	3	3	113	1	0	0	0	0	1	0	0	0	16000	72	3	2	354	2	TMC2	20	2539363	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	74116	2539363	60486157	365	18242										
PTPRA	5786	hgsc.bcm.edu	37	chr20	3017865	3017865	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cctggagcgtgtgaaagcagAggggattttggatgtcttcc	15	7	1	2	rs35448106		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr20:3017865A>G	ENST00000216877.6	+	22	2637	c.2237A>G	c.(2236-2238)gAg>gGg	p.E746G	PTPRA_ENST00000318266.5_Missense_Mutation_p.E746G|PTPRA_ENST00000358719.4_Missense_Mutation_p.E611G|PTPRA_ENST00000356147.3_Missense_Mutation_p.E746G|PTPRA_ENST00000380393.3_Missense_Mutation_p.E755G|PTPRA_ENST00000425918.2_Missense_Mutation_p.E766G|PTPRA_ENST00000399903.2_Missense_Mutation_p.E755G	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	755	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GTGAAAGCAGAGGGGATTTTG	0.577																																					p.E755G		Atlas-SNP	.											.	PTPRA	75	.	0			c.A2264G						.						126	104	111					20																	3017865		2203	4300	6503	SO:0001583	missense	5786	exon27			AAGCAGAGGGGAT		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.2237A>G	chr20.hg19:g.3017865A>G	ENSP00000216877:p.Glu746Gly	171.0	0.0		87.0	5.0	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Missense_Mutation	SNP	ENST00000216877.6	hg19	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	A	33	5.282359	0.95489	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000542217;ENST00000425918;ENST00000318266;ENST00000356147	D;D;D;D;D;D;D	0.84660	-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88	5.65	5.65	0.86999	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	U	0.000000	D	0.92001	0.7466	M	0.76002	2.32	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.99	D	0.92917	0.6352	10	0.87932	D	0	.	15.8745	0.79151	1.0:0.0:0.0:0.0	.	766;755;746	B7Z2A4;P18433;P18433-4	.;PTPRA_HUMAN;.	G	755;746;755;611;365;766;746;746	ENSP00000369756:E755G;ENSP00000216877:E746G;ENSP00000382787:E755G;ENSP00000351559:E611G;ENSP00000393553:E766G;ENSP00000314568:E746G;ENSP00000348468:E746G	ENSP00000216877:E746G	E	+	2	0	PTPRA	2965865	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.271000	0.95698	2.153000	0.67306	0.528000	0.53228	GAG	.	.		0.577	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			G	3017865	A	G	3017865	3	3	113	1	0	0	0	0	1	0	0	0	12810	304	11	2	2342	2	PTPRA	20	3017865	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	478502	3017865	60007655	366	18243										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31024706	31024706	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agtcccctggaactggtgggTcacttggaagggatgccctt	14	10	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr20:31024706T>C	ENST00000375687.4	+	13	4615	c.4191T>C	c.(4189-4191)ggT>ggC	p.G1397G	ASXL1_ENST00000306058.5_Silent_p.G1392G	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1397					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						AACTGGTGGGTCACTTGGAAG	0.547			"F, N, Mis"		"MDS, CMML"																																p.G1397G		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.T4191C						.						99	104	102					20																	31024706		2203	4300	6503	SO:0001819	synonymous_variant	171023	exon12			GGTGGGTCACTTG	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.4191T>C	chr20.hg19:g.31024706T>C		138.0	0.0		58.0	5.0	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	hg19	CCDS13201.1																																																																																			.	.		0.547	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		C	31024706	T	C	31024706	2	2	113	1	0	0	0	0	0	0	0	1	1066	1654	58	2		2	ASXL1	20	31024706	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	28006841	31024706	32000814	367	18244										
E2F1	1869	hgsc.bcm.edu	37	chr20	32265257	32265257	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aagagtccacggcttggagcTgggtctcaggaggggctttg	17	8	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr20:32265257T>A	ENST00000343380.5	-	5	954	c.815A>T	c.(814-816)cAg>cTg	p.Q272L	NECAB3_ENST00000375238.4_5'Flank|RP1-63M2.5_ENST00000606866.1_RNA	NM_005225.2	NP_005216.1	Q01094	E2F1_HUMAN	E2F transcription factor 1	272	Dimerization. {ECO:0000255}.|Required for interaction with TRIM28.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|DNA damage checkpoint (GO:0000077)|forebrain development (GO:0030900)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|mRNA stabilization (GO:0048255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(2)|breast(1)|endometrium(3)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	16						GGCTTGGAGCTGGGTCTCAGG	0.612																																					p.Q272L		Atlas-SNP	.											.	E2F1	41	.	0			c.A815T						.						92	84	87					20																	32265257		2203	4300	6503	SO:0001583	missense	1869	exon5			TGGAGCTGGGTCT		CCDS13224.1	20q11	2008-05-14			ENSG00000101412	ENSG00000101412			3113	protein-coding gene	gene with protein product		189971		RBBP3		8964493	Standard	NM_005225		Approved	RBP3	uc002wzu.4	Q01094	OTTHUMG00000032265	ENST00000343380.5:c.815A>T	chr20.hg19:g.32265257T>A	ENSP00000345571:p.Gln272Leu	182.0	0.0		111.0	47.0	NM_005225	Q13143|Q92768	Missense_Mutation	SNP	ENST00000343380.5	hg19	CCDS13224.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.556112	0.45487	.	.	ENSG00000101412	ENST00000343380	D	0.85088	-1.94	5.02	3.92	0.45320	.	0.199142	0.45606	D	0.000347	T	0.77287	0.4108	L	0.50333	1.59	0.40587	D	0.981456	P	0.41345	0.746	B	0.30943	0.122	T	0.77885	-0.2421	10	0.72032	D	0.01	-9.7838	10.331	0.43823	0.0:0.0778:0.0:0.9222	.	272	Q01094	E2F1_HUMAN	L	272	ENSP00000345571:Q272L	ENSP00000345571:Q272L	Q	-	2	0	E2F1	31728918	1.000000	0.71417	0.988000	0.46212	0.969000	0.65631	3.976000	0.56867	0.946000	0.37632	0.379000	0.24179	CAG	.	.		0.612	E2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078731.2			A	32265257	T	A	32265257	3	1	113	1	0	0	0	0	1	0	0	0	4868	1580	55	4	510	4	E2F1	20	32265257	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1240551	32265257	30760263	368	18245										
LBP	3929	hgsc.bcm.edu	37	chr20	36974925	36974925	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cactgggaatctaggatgggGgccttggccagagccctgcc	15	12	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr20:36974925G>A	ENST00000217407.2	+	1	167	c.6G>A	c.(4-6)ggG>ggA	p.G2G		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	2					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				CTAGGATGGGGGCCTTGGCCA	0.642																																					p.G2G		Atlas-SNP	.											.	LBP	60	.	0			c.G6A						.						71	70	70					20																	36974925		2203	4300	6503	SO:0001819	synonymous_variant	3929	exon1			GATGGGGGCCTTG		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"BPI fold containing"	6517	protein-coding gene	gene with protein product	"BPI fold containing family D, member 2"	151990	"lipopolysaccharide-binding protein"			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.6G>A	chr20.hg19:g.36974925G>A		80.0	0.0		56.0	25.0	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Silent	SNP	ENST00000217407.2	hg19	CCDS13304.1																																																																																			.	.		0.642	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139		A	36974925	G	A	36974925	2	1	113	1	0	0	0	0	0	0	0	1	8660	1219	43	3		3	LBP	20	36974925	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	4709668	36974925	26050595	369	18246										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46275954	46275954	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggaggctttcatcttcagggAcaatcaccatcttttaactc	7	11	5	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr20:46275954A>G	ENST00000371998.3	+	18	3581	c.3390A>G	c.(3388-3390)ggA>ggG	p.G1130G	NCOA3_ENST00000341724.6_Silent_p.G1060G|NCOA3_ENST00000372004.3_Silent_p.G1130G|NCOA3_ENST00000371997.3_Silent_p.G1125G			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1130	Acetyltransferase.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						ATCTTCAGGGACAATCACCAT	0.483																																					p.G1130G		Atlas-SNP	.											.	NCOA3	156	.	0			c.A3390G						.						109	95	100					20																	46275954		2203	4300	6503	SO:0001819	synonymous_variant	8202	exon18			TCAGGGACAATCA	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3390A>G	chr20.hg19:g.46275954A>G		178.0	0.0		90.0	52.0	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.		0.483	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		G	46275954	A	G	46275954	2	3	113	1	0	0	0	0	0	0	0	1	10239	262	10	2		2	NCOA3	20	46275954	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	9301029	46275954	16749566	370	18247										
STAU1	6780	hgsc.bcm.edu	37	chr20	47740949	47740949	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ttttctttttgattctaggcTttactcgttcaactgcaggc	7	9	3	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr20:47740949T>C	ENST00000371856.2	-	7	1195	c.785A>G	c.(784-786)aAg>aGg	p.K262R	STAU1_ENST00000371792.1_Missense_Mutation_p.K181R|STAU1_ENST00000371802.1_Missense_Mutation_p.K187R|STAU1_ENST00000360426.4_Missense_Mutation_p.K181R|STAU1_ENST00000347458.5_Missense_Mutation_p.K181R|STAU1_ENST00000371828.3_Missense_Mutation_p.K187R|STAU1_ENST00000340954.7_Missense_Mutation_p.K181R	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	262					intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			GATTCTAGGCTTTACTCGTTC	0.423																																					p.K262R		Atlas-SNP	.											.	STAU1	54	.	0			c.A785G						.						211	235	227					20																	47740949		2203	4300	6503	SO:0001583	missense	6780	exon7			CTAGGCTTTACTC		CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 150"	601716	"staufen (Drosophila, RNA-binding protein)", "staufen, RNA binding protein (Drosophila)", "staufen, RNA binding protein, homolog 1 (Drosophila)"	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.785A>G	chr20.hg19:g.47740949T>C	ENSP00000360922:p.Lys262Arg	112.0	0.0		65.0	4.0	NM_017453	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Missense_Mutation	SNP	ENST00000371856.2	hg19	CCDS13414.1	.	.	.	.	.	.	.	.	.	.	T	11.44	1.639398	0.29157	.	.	ENSG00000124214	ENST00000371828;ENST00000340954;ENST00000371856;ENST00000360426;ENST00000347458;ENST00000371805;ENST00000371802;ENST00000371792;ENST00000437404	T;T;T;T;T;T;T;T	0.47528	1.37;1.38;1.38;1.38;1.38;1.37;1.4;0.84	5.33	4.22	0.49857	.	0.332870	0.35555	N	0.003134	T	0.38772	0.1053	L	0.49350	1.555	0.40451	D	0.980147	B;B	0.14012	0.009;0.0	B;B	0.15052	0.012;0.001	T	0.17471	-1.0368	10	0.18710	T	0.47	-8.297	9.9143	0.41425	0.0:0.0847:0.0:0.9153	.	262;187	O95793;Q5JW29	STAU1_HUMAN;.	R	187;181;262;181;181;181;187;181;187	ENSP00000360893:K187R;ENSP00000345425:K181R;ENSP00000360922:K262R;ENSP00000353604:K181R;ENSP00000323443:K181R;ENSP00000360867:K187R;ENSP00000360857:K181R;ENSP00000416779:K187R	ENSP00000345425:K181R	K	-	2	0	STAU1	47174356	1.000000	0.71417	0.994000	0.49952	0.814000	0.46013	2.733000	0.47360	0.854000	0.35336	0.528000	0.53228	AAG	.	.		0.423	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453		C	47740949	T	C	47740949	3	2	113	1	0	0	0	0	1	0	0	0	15287	1609	56	2	980	2	STAU1	20	47740949	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	1464995	47740949	15284571	371	18248										
DPM1	8813	hgsc.bcm.edu	37	chr20	49571794	49571794	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tccatctgggcttccatcatCtatgattataatttcatagt	5	9	4	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr20:49571794C>A	ENST00000371588.5	-	2	216	c.190G>T	c.(190-192)Gat>Tat	p.D64Y	DPM1_ENST00000371583.5_Missense_Mutation_p.D64Y|DPM1_ENST00000371582.4_Missense_Mutation_p.D64Y|DPM1_ENST00000466152.1_5'UTR	NM_003859.1	NP_003850.1	O60762	DPM1_HUMAN	dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit	64					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|dolichol metabolic process (GO:0019348)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose metabolic process (GO:0019673)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|protein mannosylation (GO:0035268)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked mannosylation (GO:0035269)	dolichol-phosphate-mannose synthase complex (GO:0033185)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nucleus (GO:0005634)	alcohol binding (GO:0043178)|dolichyl-phosphate beta-D-mannosyltransferase activity (GO:0004582)|dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannose binding (GO:0005537)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	7						CTTCCATCATCTATGATTATA	0.294																																					p.D64Y		Atlas-SNP	.											DPM1,right_upper_lobe,carcinoma,0,1	DPM1	24	.	0			c.G190T						.						106	95	99					20																	49571794		2203	4299	6502	SO:0001583	missense	8813	exon2			CATCATCTATGAT	AF007875	CCDS13434.1	20q13.1	2013-02-26			ENSG00000000419	ENSG00000000419	2.4.1.83	"Glycosyltransferase family 2 domain containing"	3005	protein-coding gene	gene with protein product	"DPM synthase complex, catalytic subunit"	603503				9223280, 9535917	Standard	NM_003859		Approved	MPDS, CDGIE	uc002xvw.1	O60762	OTTHUMG00000032742	ENST00000371588.5:c.190G>T	chr20.hg19:g.49571794C>A	ENSP00000360644:p.Asp64Tyr	94.0	0.0		44.0	2.0	NM_003859	O15157|Q6IB78|Q96HK0	Missense_Mutation	SNP	ENST00000371588.5	hg19	CCDS13434.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.1|26.1	4.707620|4.707620	0.89018|0.89018	.|.	.|.	ENSG00000000419|ENSG00000000419	ENST00000371588;ENST00000371582;ENST00000449701;ENST00000371583;ENST00000413082|ENST00000371584	T;T;T;T|.	0.75704|.	-0.96;-0.96;-0.96;-0.96|.	5.72|5.72	5.72|5.72	0.89469|0.89469	Glycosyl transferase, family 2 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.94434|0.94434	0.8209|0.8209	H|H	0.99989|0.99989	5.305|5.305	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.97292|0.97292	0.9925|0.9925	9|5	.|.	.|.	.|.	-17.3906|-17.3906	19.876|19.876	0.96870|0.96870	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	64|.	O60762|.	DPM1_HUMAN|.	Y|I	64|63	ENSP00000360644:D64Y;ENSP00000360638:D64Y;ENSP00000360639:D64Y;ENSP00000394921:D64Y|.	.|.	D|R	-|-	1|2	0|0	DPM1|DPM1	49005201|49005201	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.352000|7.352000	0.79404|0.79404	2.709000|2.709000	0.92574|0.92574	0.591000|0.591000	0.81541|0.81541	GAT|AGA	.	.		0.294	DPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079716.1	NM_003859		A	49571794	C	A	49571794	3	1	113	1	0	0	0	0	1	0	0	0	4726	913	32	3	624	3	DPM1	20	49571794	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	1830845	49571794	13453726	372	18249										
CHODL	140578	hgsc.bcm.edu	37	chr21	19632556	19632556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tgtagaaaagccttatcttaCaaatcaaccaggagacaccc	6	11	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr21:19632556C>T	ENST00000299295.2	+	4	978	c.587C>T	c.(586-588)aCa>aTa	p.T196I	CHODL_ENST00000543733.1_Missense_Mutation_p.T177I|CHODL_ENST00000338326.3_Missense_Mutation_p.T155I|CHODL_ENST00000400128.1_Missense_Mutation_p.T155I|CHODL_ENST00000400131.1_Missense_Mutation_p.T155I|CHODL_ENST00000400127.1_Missense_Mutation_p.T155I|CHODL_ENST00000400135.1_Missense_Mutation_p.T155I	NM_001204175.1|NM_024944.2	NP_001191104.1|NP_079220.2	Q9H9P2	CHODL_HUMAN	chondrolectin	196					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)			kidney(1)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_epithelial(11;0.21)		Epithelial(23;0.000191)|all cancers(11;0.000827)|LUSC - Lung squamous cell carcinoma(23;0.00646)|Lung(58;0.0129)|OV - Ovarian serous cystadenocarcinoma(11;0.017)|COAD - Colon adenocarcinoma(22;0.03)|Colorectal(24;0.0917)		CCTTATCTTACAAATCAACCA	0.328																																					p.T196I		Atlas-SNP	.											.	CHODL	54	.	0			c.C587T						.						102	102	102					21																	19632556		2203	4300	6503	SO:0001583	missense	140578	exon4			ATCTTACAAATCA	AF257472	CCDS13570.1, CCDS56208.1, CCDS56209.1, CCDS56210.1	21q11.2	2006-04-03	2002-07-04		ENSG00000154645	ENSG00000154645			17807	protein-coding gene	gene with protein product		607247	"chromosome 21 open reading frame 68"	C21orf68		12079284	Standard	NM_024944		Approved	FLJ12627, PRED12, MT75	uc021whs.1	Q9H9P2	OTTHUMG00000074519	ENST00000299295.2:c.587C>T	chr21.hg19:g.19632556C>T	ENSP00000299295:p.Thr196Ile	92.0	0.0		59.0	4.0	NM_024944	B2R9C0|B4DJB8|Q7Z798|Q7Z799|Q7Z7A0|Q9HCY3	Missense_Mutation	SNP	ENST00000299295.2	hg19	CCDS13570.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.855727	0.51376	.	.	ENSG00000154645	ENST00000400128;ENST00000400131;ENST00000400135;ENST00000400127;ENST00000299295;ENST00000338326;ENST00000543733	T;T;T;T;T;T;T	0.19806	2.19;2.12;2.12;2.19;2.17;2.12;2.17	5.41	5.41	0.78517	.	0.578427	0.19439	N	0.114234	T	0.26774	0.0655	L	0.51422	1.61	0.40735	D	0.98278	B;P;P	0.45126	0.294;0.845;0.851	B;B;B	0.43478	0.057;0.421;0.244	T	0.01720	-1.1288	9	.	.	.	-16.9145	18.1415	0.89641	0.0:1.0:0.0:0.0	.	196;177;155	Q9H9P2;B4DJB8;Q9H9P2-3	CHODL_HUMAN;.;.	I	155;155;155;155;196;155;177	ENSP00000382993:T155I;ENSP00000382996:T155I;ENSP00000383001:T155I;ENSP00000382992:T155I;ENSP00000299295:T196I;ENSP00000339975:T155I;ENSP00000443566:T177I	.	T	+	2	0	CHODL	18554427	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.679000	0.46909	2.700000	0.92200	0.650000	0.86243	ACA	.	.		0.328	CHODL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158232.1	NM_024944		T	19632556	C	T	19632556	3	4	113	1	0	0	0	0	1	0	0	0	3366	478	17	3	601	3	CHODL	21	19632556	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10		19632556	28497339	373	18250										
MORC3	23515	hgsc.bcm.edu	37	chr21	37747486	37747486	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aacgtaggacaactgctggcTatgattgtgcctgatcttga	11	8	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr21:37747486T>C	ENST00000400485.1	+	17	2788	c.2712T>C	c.(2710-2712)gcT>gcC	p.A904A	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	904					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						AACTGCTGGCTATGATTGTGC	0.363																																					p.A904A		Atlas-SNP	.											.	MORC3	78	.	0			c.T2712C						.						168	154	158					21																	37747486		1942	4143	6085	SO:0001819	synonymous_variant	23515	exon17			GCTGGCTATGATT	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"zinc finger, CW-type with coiled-coil domain 3", "zinc finger, CW type with coiled-coil domain 3"	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.2712T>C	chr21.hg19:g.37747486T>C		83.0	0.0		71.0	4.0	NM_015358	A8KA92|Q9UEZ2	Silent	SNP	ENST00000400485.1	hg19	CCDS42924.1																																																																																			.	.		0.363	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		C	37747486	T	C	37747486	2	2	113	1	0	0	0	0	0	0	0	1	9712	1509	53	2		2	MORC3	21	37747486	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	18114930	37747486	10382409	374	18251										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41455834	41455835	+	Splice_Site	DNP	CC	CC	GA													0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggacaatctatatcttattaCctctgatagagctgcccccg							TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr21:41455834_41455835CC>GA	ENST00000400454.1	-	24	4708_4709	c.4231_4232GG>TC	c.(4231-4233)GGa>TCa	p.G1411S		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1411	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TATCTTATTACCTCTGATAGAG	0.45																																					.|p.G1411X	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.4231+1G>C|c.G4231T						.																																			SO:0001630	splice_region_variant	1826	exon25|exon24			TTATTACCTCTGA|TATTACCTCTGAT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4231_4232delinsGA	chr21.hg19:g.41455834_41455835delinsGA		131.0|134.0	0.0		87.0|86.0	34.0|35.0	NM_001271534	O60468	Splice_Site|Nonsense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1																																																																																			.	.		0.45	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	Missense_Mutation	GA	41455835	CC	GA	41455834	5	3	113	1	0	0	0	0	0	0	1	0	4770	521	18	4	1846	4	DSCAM	21	41455834	Splice_Site	DNP	CC	TCGA-DD-A39Z-01A-11D-A20W-10	3708348	41455834	6674061	375	18252										
PKNOX1	5316	hgsc.bcm.edu	37	chr21	44424541	44424541	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cagctatcaagatgggcaacAggtgagcttgaacttgattc	11	8	1	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr21:44424541A>C	ENST00000291547.5	+	2	261	c.50A>C	c.(49-51)cAg>cCg	p.Q17P	PKNOX1_ENST00000432907.2_5'UTR	NM_004571.3	NP_004562.2	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	17					angiogenesis (GO:0001525)|camera-type eye development (GO:0043010)|erythrocyte differentiation (GO:0030218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|prostate(1)	22						GATGGGCAACAGGTGAGCTTG	0.383																																					p.Q17P		Atlas-SNP	.											.	PKNOX1	40	.	0			c.A50C						.						136	117	124					21																	44424541		2203	4300	6503	SO:0001630	splice_region_variant	5316	exon2			GGCAACAGGTGAG		CCDS13692.1, CCDS68211.1	21q22.3	2011-06-20			ENSG00000160199	ENSG00000160199		"Homeoboxes / TALE class"	9022	protein-coding gene	gene with protein product		602100				9479508	Standard	NM_001286258		Approved	PREP1	uc002zcq.1	P55347	OTTHUMG00000086833	ENST00000291547.5:c.51+1A>C	chr21.hg19:g.44424541A>C		117.0	0.0		85.0	4.0	NM_004571	O00528|Q8IWT7	Missense_Mutation	SNP	ENST00000291547.5	hg19	CCDS13692.1	.	.	.	.	.	.	.	.	.	.	A	11.21	1.570455	0.28003	.	.	ENSG00000160199	ENST00000291547	D	0.86230	-2.09	4.71	4.71	0.59529	.	0.151623	0.43416	D	0.000571	D	0.84032	0.5383	M	0.64997	1.995	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.80913	-0.1170	10	0.48119	T	0.1	10.0149	10.2713	0.43485	0.8351:0.1649:0.0:0.0	.	17;17;17	Q5DNB2;P55347;P55347-2	.;PKNX1_HUMAN;.	P	17	ENSP00000291547:Q17P	ENSP00000291547:Q17P	Q	+	2	0	PKNOX1	43297610	1.000000	0.71417	0.999000	0.59377	0.508000	0.34012	4.581000	0.60949	1.752000	0.51891	0.402000	0.26972	CAG	.	.		0.383	PKNOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195520.3		Missense_Mutation	C	44424541	A	C	44424541	5	2	113	1	0	0	0	0	0	0	1	0	11991	202	7	5	52	5	PKNOX1	21	44424541	Splice_Site	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2968707	44424541	3705354	376	18253										
C21orf58	54058	hgsc.bcm.edu	37	chr21	47731472	47731472	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctgaatgatggtggcaggagGctgggggacctaggaacagc	18	7	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr21:47731472G>A	ENST00000291691.7	-	6	1755	c.619C>T	c.(619-621)Cct>Tct	p.P207S	C21orf58_ENST00000472607.1_5'UTR|C21orf58_ENST00000397679.1_Missense_Mutation_p.P101S|C21orf58_ENST00000397680.1_Missense_Mutation_p.P101S|C21orf58_ENST00000397682.3_Missense_Mutation_p.P101S|C21orf58_ENST00000397683.1_Missense_Mutation_p.P101S	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	207										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		GTGGCAGGAGGCTGGGGGACC	0.532																																					p.P207S		Atlas-SNP	.											.	C21orf58	25	.	0			c.C619T						.						113	91	99					21																	47731472		2202	4299	6501	SO:0001583	missense	54058	exon6			CAGGAGGCTGGGG		CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.619C>T	chr21.hg19:g.47731472G>A	ENSP00000291691:p.Pro207Ser	147.0	0.0		86.0	4.0	NM_058180	B3KPI1	Missense_Mutation	SNP	ENST00000291691.7	hg19	CCDS13735.1	.	.	.	.	.	.	.	.	.	.	G	8.108	0.778264	0.16120	.	.	ENSG00000160298	ENST00000397683;ENST00000417060;ENST00000397682;ENST00000291691;ENST00000397679;ENST00000397680	T;T;T;T;T;T	0.42131	0.98;1.97;0.98;1.97;0.98;0.98	5.3	-2.89	0.05665	.	0.552015	0.16725	N	0.202113	T	0.15652	0.0377	N	0.17082	0.46	0.80722	D	1	P;B;B	0.37101	0.582;0.376;0.123	B;B;B	0.31686	0.134;0.084;0.057	T	0.20638	-1.0269	10	0.20519	T	0.43	-3.8222	2.0293	0.03526	0.152:0.3625:0.2385:0.247	.	207;101;207	P58505;Q8N7N9;P58505-2	CU058_HUMAN;.;.	S	101;169;101;207;101;101	ENSP00000380799:P101S;ENSP00000402356:P169S;ENSP00000380798:P101S;ENSP00000291691:P207S;ENSP00000380796:P101S;ENSP00000380797:P101S	ENSP00000291691:P207S	P	-	1	0	C21orf58	46555900	1.000000	0.71417	0.813000	0.32504	0.346000	0.29079	1.581000	0.36558	-1.028000	0.03321	-0.268000	0.10319	CCT	.	.		0.532	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180		A	47731472	G	A	47731472	3	1	113	1	0	0	0	0	1	0	0	0	2131	1203	42	3	361	3	C21orf58	21	47731472	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	3306931	47731472	398423	377	18254										
DIP2A	23181	hgsc.bcm.edu	37	chr21	47910539	47910539	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	acccatctctgcaagcagagAatagaattcctgggccctca	8	13	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr21:47910539A>G	ENST00000417564.2	+	3	211	c.190A>G	c.(190-192)Aat>Gat	p.N64D	DIP2A_ENST00000400274.1_Missense_Mutation_p.N64D|DIP2A_ENST00000466639.1_Missense_Mutation_p.N64D|DIP2A_ENST00000457905.3_Missense_Mutation_p.N64D|DIP2A_ENST00000427143.2_Intron|DIP2A_ENST00000435722.3_Missense_Mutation_p.N64D|DIP2A_ENST00000318711.7_Missense_Mutation_p.N64D			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	64	DMAP-interaction.				multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GCAAGCAGAGAATAGAATTCC	0.488																																					p.N64D		Atlas-SNP	.											.	DIP2A	332	.	0			c.A190G						.						34	37	36					21																	47910539		1905	4096	6001	SO:0001583	missense	23181	exon3			GCAGAGAATAGAA	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.190A>G	chr21.hg19:g.47910539A>G	ENSP00000392066:p.Asn64Asp	214.0	0.0		117.0	5.0	NM_206891	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	hg19	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	A	4.490	0.090818	0.08632	.	.	ENSG00000160305	ENST00000400274;ENST00000318711;ENST00000358985;ENST00000457905;ENST00000466639;ENST00000435722;ENST00000417564	T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85	5.14	2.73	0.32206	DMAP1-binding (1);	0.570024	0.16987	N	0.191452	T	0.38401	0.1039	L	0.43152	1.355	0.51233	D	0.99991	B;B;B;B;B	0.24317	0.0;0.066;0.002;0.101;0.057	B;B;B;B;B	0.25614	0.003;0.036;0.04;0.062;0.06	T	0.07731	-1.0757	10	0.22706	T	0.39	-0.002	11.2874	0.49230	0.6774:0.3226:0.0:0.0	.	64;64;64;64;64	E9PER1;Q14689-3;Q14689;Q14689-4;Q14689-2	.;.;DIP2A_HUMAN;.;.	D	64	ENSP00000383133:N64D;ENSP00000323633:N64D;ENSP00000393434:N64D;ENSP00000430249:N64D;ENSP00000415089:N64D;ENSP00000392066:N64D	ENSP00000323633:N64D	N	+	1	0	DIP2A	46734967	0.905000	0.30787	0.030000	0.17652	0.138000	0.21146	1.450000	0.35134	0.269000	0.21961	-0.429000	0.05907	AAT	.	.		0.488	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		G	47910539	A	G	47910539	3	3	113	1	0	0	0	0	1	0	0	0	4529	246	9	2	200	2	DIP2A	21	47910539	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	179067	47910539	219356	378	18255										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19263298	19263298	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tacatatgaacttgtcagatTccatggtcagtgtgctgaat	9	7	2	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr22:19263298T>C	ENST00000263200.10	-	2	170	c.98A>G	c.(97-99)gAa>gGa	p.E33G	CLTCL1_ENST00000353891.5_Missense_Mutation_p.E33G|CLTCL1_ENST00000427926.1_Missense_Mutation_p.E33G	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	33	Globular terminal domain.|WD40-like repeat 1.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					CTTGTCAGATTCCATGGTCAG	0.418			T	?	ALCL																																p.E33G		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.A98G						.						68	64	65					22																	19263298		1952	4142	6094	SO:0001583	missense	8218	exon2			TCAGATTCCATGG		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.98A>G	chr22.hg19:g.19263298T>C	ENSP00000445677:p.Glu33Gly	157.0	0.0		85.0	4.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.016323	0.75161	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926;ENST00000449918	T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38	4.2	2.04	0.26737	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.000000	0.85682	D	0.000000	T	0.80834	0.4699	M	0.92317	3.295	0.58432	D	0.999997	P;B	0.51933	0.949;0.373	P;P	0.61201	0.885;0.475	T	0.78404	-0.2217	10	0.59425	D	0.04	-13.1117	6.7597	0.23534	0.0:0.0814:0.153:0.7657	.	33;33	P53675-2;P53675	.;CLH2_HUMAN	G	33	ENSP00000439662:E33G;ENSP00000445677:E33G;ENSP00000441158:E33G;ENSP00000443264:E33G	ENSP00000445677:E33G	E	-	2	0	CLTCL1	17643298	1.000000	0.71417	0.986000	0.45419	0.950000	0.60333	4.284000	0.58983	0.183000	0.20059	0.528000	0.53228	GAA	.	.		0.418	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		C	19263298	T	C	19263298	3	2	113	1	0	0	0	0	1	0	0	0	3569	1783	62	2	4948	2	CLTCL1	22	19263298	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10		19263298	32041268	379	18256										
CHEK2	11200	hgsc.bcm.edu	37	chr22	29130547	29130547	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gctcagtgtcccagagctggAgtgagaggactggctggagt	17	8	1	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr22:29130547A>G	ENST00000405598.1	-	3	354	c.163T>C	c.(163-165)Tcc>Ccc	p.S55P	CHEK2_ENST00000544772.1_5'UTR|CHEK2_ENST00000402731.1_Missense_Mutation_p.S55P|CHEK2_ENST00000382565.1_Missense_Mutation_p.S55P|CHEK2_ENST00000382566.1_Missense_Mutation_p.S55P|CHEK2_ENST00000328354.6_Missense_Mutation_p.S55P|CHEK2_ENST00000348295.3_Missense_Mutation_p.S55P|CHEK2_ENST00000403642.1_Missense_Mutation_p.S55P|CHEK2_ENST00000382580.2_Missense_Mutation_p.S55P|CHEK2_ENST00000404276.1_Missense_Mutation_p.S55P|CHEK2_ENST00000382578.1_Missense_Mutation_p.S55P			O96017	CHK2_HUMAN	checkpoint kinase 2	55					cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAGAGCTGGAGTGAGAGGAC	0.562			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.S55P		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.T163C						.						131	122	125					22																	29130547		2203	4300	6503	SO:0001583	missense	11200	exon2			AGCTGGAGTGAGA	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"CHK2 (checkpoint, S.pombe) homolog", "CHK2 checkpoint homolog (S. pombe)"	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.163T>C	chr22.hg19:g.29130547A>G	ENSP00000386087:p.Ser55Pro	204.0	0.0		90.0	4.0	NM_145862	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	hg19	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.618529	0.87359	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000382565;ENST00000382563;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731;ENST00000447421;ENST00000439200;ENST00000398017	T;T;T;D;T;T;T;T;T;T;T;T;D	0.94931	0.51;-0.34;-0.67;-3.56;-0.47;-0.47;-0.47;2.21;-0.34;0.51;-0.09;2.21;-2.73	5.42	5.42	0.78866	.	0.093533	0.85682	D	0.000000	D	0.96204	0.8762	M	0.63843	1.955	0.44880	D	0.997895	D;D;D;D;D;D	0.76494	0.999;0.998;0.996;0.999;0.996;0.998	D;P;P;D;P;P	0.67548	0.952;0.905;0.806;0.952;0.806;0.905	D	0.95881	0.8899	10	0.45353	T	0.12	-7.3497	14.9384	0.70975	1.0:0.0:0.0:0.0	.	55;55;55;55;55;55	O96017-7;O96017-4;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	P	55;55;55;55;55;55;55;55;55;55;55;55;55;65	ENSP00000329012:S55P;ENSP00000372021:S55P;ENSP00000372006:S55P;ENSP00000372007:S55P;ENSP00000329178:S55P;ENSP00000385747:S55P;ENSP00000386087:S55P;ENSP00000372023:S55P;ENSP00000384919:S55P;ENSP00000384835:S55P;ENSP00000397478:S55P;ENSP00000408065:S55P;ENSP00000381099:S65P	ENSP00000329178:S55P	S	-	1	0	CHEK2	27460547	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.012000	0.70767	2.184000	0.69523	0.533000	0.62120	TCC	.	.		0.562	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		G	29130547	A	G	29130547	3	3	113	1	0	0	0	0	1	0	0	0	3337	304	11	2	1657	2	CHEK2	22	29130547	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	9867249	29130547	22174019	380	18257										
RHBDD3	25807	hgsc.bcm.edu	37	chr22	29656351	29656351	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aggacttggacagccatggtGcgctctggggttcctgggct	16	10	1	0	rs375477818		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr22:29656351G>T	ENST00000216085.7	-	6	1371	c.947C>A	c.(946-948)gCa>gAa	p.A316E	CTA-984G1.5_ENST00000433125.1_RNA	NM_012265.1	NP_036397.1	Q9Y3P4	RHBD3_HUMAN	rhomboid domain containing 3	316					liver development (GO:0001889)|MAPK cascade (GO:0000165)|negative regulation of natural killer cell activation (GO:0032815)|positive regulation of protein catabolic process (GO:0045732)|regulation of acute inflammatory response (GO:0002673)|regulation of protein secretion (GO:0050708)|response to xenobiotic stimulus (GO:0009410)	integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			lung(1)|ovary(1)	2						CAGCCATGGTGCGCTCTGGGG	0.667																																					p.A316E		Atlas-SNP	.											.	RHBDD3	17	.	0			c.C947A						.						24	23	23					22																	29656351		2200	4299	6499	SO:0001583	missense	25807	exon6			CATGGTGCGCTCT	AL050346	CCDS13850.1	22q12.2	2006-02-22	2006-02-22	2006-02-22	ENSG00000100263	ENSG00000100263			1308	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 3"	C22orf3		10591208, 15105437	Standard	NM_012265		Approved	PTAG	uc003aeq.1	Q9Y3P4	OTTHUMG00000151032	ENST00000216085.7:c.947C>A	chr22.hg19:g.29656351G>T	ENSP00000216085:p.Ala316Glu	171.0	0.0		84.0	4.0	NM_012265	Q6I9X3|Q9UGQ7	Missense_Mutation	SNP	ENST00000216085.7	hg19	CCDS13850.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.727020	0.00694	.	.	ENSG00000100263	ENST00000216085	T	0.21031	2.03	5.18	4.06	0.47325	UBA-like (1);	0.634631	0.14675	N	0.305127	T	0.07369	0.0186	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37478	-0.9704	10	0.10636	T	0.68	-1.3315	5.475	0.16690	0.0993:0.0:0.6482:0.2525	.	316	Q9Y3P4	RHBD3_HUMAN	E	316	ENSP00000216085:A316E	ENSP00000216085:A316E	A	-	2	0	RHBDD3	27986351	0.000000	0.05858	0.016000	0.15963	0.185000	0.23345	0.740000	0.26188	2.591000	0.87537	0.643000	0.83706	GCA	.	.		0.667	RHBDD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321085.1	NM_012265		T	29656351	G	T	29656351	3	4	113	1	0	0	0	0	1	0	0	0	13333	1319	46	3	221	3	RHBDD3	22	29656351	Missense_Mutation	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	525804	29656351	21648215	381	18258										
SEC14L4	284904	hgsc.bcm.edu	37	chr22	30890136	30890136	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tcatcccggtcatgggcttaCctcgaataacaattaaattc	6	11	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr22:30890136C>T	ENST00000255858.7	-	7	664		c.e7+1		RP4-539M6.14_ENST00000610156.1_RNA|RP4-539M6.14_ENST00000442126.1_RNA|SEC14L4_ENST00000392772.2_Splice_Site|SEC14L4_ENST00000540456.1_Splice_Site|SEC14L4_ENST00000381982.3_Splice_Site	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)							integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	CATGGGCTTACCTCGAATAAC	0.478																																					.		Atlas-SNP	.											.	SEC14L4	43	.	0			c.580+1G>A						.						91	91	91					22																	30890136		2203	4300	6503	SO:0001630	splice_region_variant	284904	exon8			GGCTTACCTCGAA	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.580+1G>A	chr22.hg19:g.30890136C>T		185.0	0.0		91.0	4.0	NM_174977	A5D6W7|A6NCV4	Splice_Site	SNP	ENST00000255858.7	hg19	CCDS13878.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.055302	0.55325	.	.	ENSG00000133488	ENST00000255858;ENST00000540456;ENST00000392772;ENST00000381982	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6154	0.84909	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEC14L4	29220136	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	6.007000	0.70731	2.593000	0.87608	0.591000	0.81541	.	.	.		0.478	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	Intron	T	30890136	C	T	30890136	5	4	113	1	0	0	0	0	0	0	1	0	13999	521	18	3	669	3	SEC14L4	22	30890136	Splice_Site	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	1233785	30890136	20414430	382	18259										
ELFN2	114794	hgsc.bcm.edu	37	chr22	37771035	37771035	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	aaggggttgccggccagctcAcacaccatcaggctggcgag	14	13	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr22:37771035A>G	ENST00000402918.2	-	3	1325	c.540T>C	c.(538-540)tgT>tgC	p.C180C	RP1-63G5.8_ENST00000609322.1_RNA|RP1-63G5.5_ENST00000430883.1_RNA|ELFN2_ENST00000435824.1_5'Flank	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	180					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					CGGCCAGCTCACACACCATCA	0.632																																					p.C180C		Atlas-SNP	.											.	ELFN2	89	.	0			c.T540C						.						42	45	44					22																	37771035		2203	4298	6501	SO:0001819	synonymous_variant	114794	exon3			CAGCTCACACACC	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing"	29396	protein-coding gene	gene with protein product			"leucine rich repeat containing 62", "extracellular leucine-rich repeat and fibronectin type III containing 2", "extracellular leucine-rich repeat and fibronectin type III domain containing 2", "protein phosphatase 1, regulatory subunit 29"	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.540T>C	chr22.hg19:g.37771035A>G		160.0	0.0		94.0	4.0	NM_052906	Q96PY3	Silent	SNP	ENST00000402918.2	hg19	CCDS33642.1																																																																																			.	.		0.632	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906		G	37771035	A	G	37771035	2	3	113	1	0	0	0	0	0	0	0	1	5060	157	6	2		2	ELFN2	22	37771035	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	6880899	37771035	13533531	383	18260										
TAB1	10454	hgsc.bcm.edu	37	chr22	39824030	39824030	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tctcttcctcccaaagctgcAggaggacgagtgtaccctgt	10	13	1	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr22:39824030A>G	ENST00000216160.6	+	10	1211	c.1149A>G	c.(1147-1149)gcA>gcG	p.A383A	TAB1_ENST00000331454.3_Silent_p.A383A	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	383					activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						CCAAAGCTGCAGGAGGACGAG	0.632																																					p.A383A		Atlas-SNP	.											.	TAB1	36	.	0			c.A1149G						.						97	81	86					22																	39824030		2203	4300	6503	SO:0001819	synonymous_variant	10454	exon10			AGCTGCAGGAGGA	U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"TAK1-binding protein 1", "mitogen-activated protein kinase kinase kinase 7 interacting protein 1"	602615	"mitogen-activated protein kinase kinase kinase 7 interacting protein 1"	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.1149A>G	chr22.hg19:g.39824030A>G		91.0	0.0		63.0	4.0	NM_153497	Q2PP09|Q8IZW2	Silent	SNP	ENST00000216160.6	hg19	CCDS13993.1																																																																																			.	.		0.632	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497		G	39824030	A	G	39824030	2	3	113	1	0	0	0	0	0	0	0	1	15510	175	7	2		2	TAB1	22	39824030	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	2052995	39824030	11480536	384	18261										
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50656199	50656199	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	agtagttgttgaagttgatgCgcagcagaaagtcctccagg	13	7	0	3	rs540957245		TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr22:50656199C>T	ENST00000248846.5	-	25	5530	c.5426G>A	c.(5425-5427)cGc>cAc	p.R1809H	TUBGCP6_ENST00000439308.2_3'UTR|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1809					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GAAGTTGATGCGCAGCAGAAA	0.597													C|||	1	0.000199681	0	0	5008	,	,		15018	0		0	False		,,,				2504	0.001				p.R1809H		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.G5426A						.						75	72	73					22																	50656199		2203	4300	6503	SO:0001583	missense	85378	exon25			TTGATGCGCAGCA	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.5426G>A	chr22.hg19:g.50656199C>T	ENSP00000248846:p.Arg1809His	176.0	0.0		61.0	4.0	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	hg19	CCDS14087.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.417971	0.83449	.	.	ENSG00000128159	ENST00000248846;ENST00000425018	T;T	0.29917	2.41;1.55	5.02	3.99	0.46301	.	0.000000	0.85682	D	0.000000	T	0.50633	0.1627	L	0.56769	1.78	0.80722	D	1	D;D;D	0.89917	0.978;1.0;1.0	B;D;D	0.91635	0.299;0.964;0.999	T	0.52689	-0.8542	10	0.66056	D	0.02	.	13.5312	0.61623	0.0:0.9235:0.0:0.0765	.	1801;1809;1792	B2RWN4;Q96RT7;Q96RT7-3	.;GCP6_HUMAN;.	H	1809;478	ENSP00000248846:R1809H;ENSP00000405979:R478H	ENSP00000248846:R1809H	R	-	2	0	TUBGCP6	48998326	1.000000	0.71417	1.000000	0.80357	0.498000	0.33706	5.831000	0.69330	1.094000	0.41399	0.555000	0.69702	CGC	.	.		0.597	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		T	50656199	C	T	50656199	3	4	113	1	0	0	0	0	1	0	0	0	16785	768	27	1	37	1	TUBGCP6	22	50656199	Missense_Mutation	SNP	C	TCGA-DD-A39Z-01A-11D-A20W-10	10832169	50656199	648367	385	18262										
SCO2	9997	hgsc.bcm.edu	37	chr22	50962276	50962276	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ggtggagccggtcagacccaAcagtcttgggtggaagtcct	15	10	2	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chr22:50962276A>G	ENST00000543927.1	-	2	771	c.565T>C	c.(565-567)Ttg>Ctg	p.L189L	CTA-384D8.36_ENST00000608319.1_RNA|SCO2_ENST00000535425.1_Silent_p.L189L|SCO2_ENST00000252785.3_Silent_p.L189L|SCO2_ENST00000395693.3_Silent_p.L189L	NM_001169109.1	NP_001162580.1	O43819	SCO2_HUMAN	SCO2 cytochrome c oxidase assembly protein	189	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|eye development (GO:0001654)|in utero embryonic development (GO:0001701)|muscle system process (GO:0003012)|oxidation-reduction process (GO:0055114)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			endometrium(1)|lung(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GTCAGACCCAACAGTCTTGGG	0.587																																					p.L189L		Atlas-SNP	.											.	SCO2	38	.	0			c.T565C						.						105	93	97					22																	50962276		2203	4300	6503	SO:0001819	synonymous_variant	9997	exon2			GACCCAACAGTCT	AL021683	CCDS14095.1	22q13.33	2014-01-30	2012-10-15		ENSG00000130489	ENSG00000130489		"Mitochondrial respiratory chain complex assembly factors"	10604	protein-coding gene	gene with protein product		604272	"SCO (cytochrome oxidase deficient, yeast) homolog 2", "SCO cytochrome oxidase deficient homolog 2 (yeast)", "myopia 6"	MYP6		10218584, 16091356, 23643385	Standard	NM_005138		Approved	SCO1L	uc003bma.3	O43819	OTTHUMG00000150251	ENST00000543927.1:c.565T>C	chr22.hg19:g.50962276A>G		180.0	0.0		93.0	4.0	NM_001169111	Q3T1B5|Q9UK87	Silent	SNP	ENST00000543927.1	hg19	CCDS14095.1																																																																																			.	.		0.587	SCO2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317091.1	NM_005138		G	50962276	A	G	50962276	2	3	113	1	0	0	0	0	0	0	0	1	13947	40	2	2		2	SCO2	22	50962276	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	306077	50962276	342290	386	18263										
ARSE	415	hgsc.bcm.edu	37	chrX	2876322	2876322	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	ctctgtcccttgcctcatggTgttgttgccatagcagccaa	9	13	2	0			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chrX:2876322T>C	ENST00000381134.3	-	3	244	c.178A>G	c.(178-180)Acc>Gcc	p.T60A	ARSE_ENST00000496095.1_5'Flank|ARSE_ENST00000545496.1_Missense_Mutation_p.T85A|ARSE_ENST00000540563.1_Intron	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	60					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGCCTCATGGTGTTGTTGCCA	0.522																																					p.T60A		Atlas-SNP	.											.	ARSE	43	.	0			c.A178G						.						104	77	86					X																	2876322		2203	4300	6503	SO:0001583	missense	415	exon3			TCATGGTGTTGTT	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"Arylsulfatase family"	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.178A>G	chrX.hg19:g.2876322T>C	ENSP00000370526:p.Thr60Ala	207.0	0.0		67.0	5.0	NM_000047	Q53FT2|Q53FU8	Missense_Mutation	SNP	ENST00000381134.3	hg19	CCDS14122.1	.	.	.	.	.	.	.	.	.	.	T	13.98	2.397915	0.42512	.	.	ENSG00000157399	ENST00000545496;ENST00000381134;ENST00000438544	D;D;D	0.98717	-5.09;-5.09;-5.09	3.62	3.62	0.41486	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.306749	0.34245	N	0.004127	D	0.97845	0.9292	M	0.75447	2.3	0.28704	N	0.903939	B;B	0.23377	0.084;0.003	B;B	0.34346	0.18;0.038	D	0.97024	0.9745	10	0.87932	D	0	.	11.761	0.51903	0.0:0.0:0.0:1.0	.	85;60	F5GYY5;P51690	.;ARSE_HUMAN	A	85;60;60	ENSP00000441417:T85A;ENSP00000370526:T60A;ENSP00000406528:T60A	ENSP00000370526:T60A	T	-	1	0	ARSE	2886322	1.000000	0.71417	0.002000	0.10522	0.003000	0.03518	3.702000	0.54800	1.277000	0.44412	0.486000	0.48141	ACC	.	.		0.522	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047		C	2876322	T	C	2876322	3	2	113	1	0	0	0	0	1	0	0	0	990	1696	59	2	1627	2	ARSE	23	2876322	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10		2876322	152394238	387	18264										
GPM6B	2824	hgsc.bcm.edu	37	chrX	13803853	13803853	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gcagaataaggccaccccggAgaagcagaggatggtggcca	15	10	0	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chrX:13803853A>G	ENST00000356942.5	-	2	577	c.136T>C	c.(136-138)Tcc>Ccc	p.S46P	GPM6B_ENST00000398361.3_5'UTR|GPM6B_ENST00000316715.4_Missense_Mutation_p.S86P|GPM6B_ENST00000355135.2_Missense_Mutation_p.S86P|GPM6B_ENST00000493677.1_Missense_Mutation_p.S60P|GPM6B_ENST00000454189.2_Missense_Mutation_p.S27P	NM_005278.3	NP_005269.1	Q13491	GPM6B_HUMAN	glycoprotein M6B	46					cell differentiation (GO:0030154)|extracellular matrix assembly (GO:0085029)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of serotonin uptake (GO:0051612)|nervous system development (GO:0007399)|ossification (GO:0001503)|positive regulation of bone mineralization (GO:0030501)|protein transport (GO:0015031)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of focal adhesion assembly (GO:0051893)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|ovary(1)|pancreas(1)	6						GCCACCCCGGAGAAGCAGAGG	0.572																																					p.S86P		Atlas-SNP	.											.	GPM6B	46	.	0			c.T256C						.						56	51	53					X																	13803853		2203	4300	6503	SO:0001583	missense	2824	exon3			CCCCGGAGAAGCA		CCDS14158.1, CCDS35206.1, CCDS35207.1, CCDS48084.1	Xp22.2	2010-08-03			ENSG00000046653	ENSG00000046653			4461	protein-coding gene	gene with protein product		300051				8661015	Standard	NM_001001995		Approved	M6B, MGC17150, MGC54284	uc004cvw.3	Q13491	OTTHUMG00000021162	ENST00000356942.5:c.136T>C	chrX.hg19:g.13803853A>G	ENSP00000349420:p.Ser46Pro	352.0	0.0		119.0	5.0	NM_001001995	O76077|Q86X43|Q8N956	Missense_Mutation	SNP	ENST00000356942.5	hg19	CCDS14158.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.882895	0.91740	.	.	ENSG00000046653	ENST00000316715;ENST00000454189;ENST00000493677;ENST00000355135;ENST00000356942;ENST00000475307	D;D;D;D;D;D	0.99252	-5.63;-5.63;-5.63;-5.63;-5.63;-5.63	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.99214	0.9727	M	0.71581	2.175	0.80722	D	1	D;D;D;D;D;D	0.69078	0.993;0.983;0.993;0.994;0.976;0.997	P;P;P;P;P;D	0.68483	0.828;0.736;0.876;0.878;0.828;0.958	D	0.99474	1.0946	10	0.46703	T	0.11	-1.6883	14.9261	0.70878	1.0:0.0:0.0:0.0	.	60;27;46;86;38;86	B7Z613;Q13491-2;Q13491;Q13491-3;Q59FD5;Q8N956	.;.;GPM6B_HUMAN;.;.;.	P	86;27;60;86;46;46	ENSP00000316861:S86P;ENSP00000389915:S27P;ENSP00000419904:S60P;ENSP00000347258:S86P;ENSP00000349420:S46P;ENSP00000418594:S46P	ENSP00000316861:S86P	S	-	1	0	GPM6B	13713774	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	7.007000	0.76335	1.907000	0.55213	0.486000	0.48141	TCC	.	.		0.572	GPM6B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055822.1	NM_001001995		G	13803853	A	G	13803853	3	3	113	1	0	0	0	0	1	0	0	0	6624	304	11	2	839	2	GPM6B	23	13803853	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	10927531	13803853	141466707	388	18265										
CXorf38	159013	hgsc.bcm.edu	37	chrX	40489973	40489973	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cttctgtaaggccatttctaAgatcctcattgtttctcaga	6	10	4	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chrX:40489973A>G	ENST00000327877.5	-	6	880	c.854T>C	c.(853-855)cTt>cCt	p.L285P	CXorf38_ENST00000378421.1_Missense_Mutation_p.L166P|CXorf38_ENST00000378426.1_Missense_Mutation_p.L166P|CXorf38_ENST00000440784.2_Missense_Mutation_p.L200P	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	285										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						GCCATTTCTAAGATCCTCATT	0.433																																					p.L285P		Atlas-SNP	.											.	CXorf38	29	.	0			c.T854C						.						157	123	134					X																	40489973		2203	4300	6503	SO:0001583	missense	159013	exon6			TTTCTAAGATCCT	AL832829	CCDS14253.1	Xp11	2008-02-05			ENSG00000185753	ENSG00000185753			28589	protein-coding gene	gene with protein product							Standard	NM_144970		Approved	MGC39350	uc004dew.3	Q8TB03	OTTHUMG00000024104	ENST00000327877.5:c.854T>C	chrX.hg19:g.40489973A>G	ENSP00000330488:p.Leu285Pro	199.0	0.0		67.0	4.0	NM_144970	B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	hg19	CCDS14253.1	.	.	.	.	.	.	.	.	.	.	a	20.5	3.999416	0.74818	.	.	ENSG00000185753	ENST00000378426;ENST00000327877;ENST00000378421;ENST00000440784	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000002	T	0.78698	0.4324	M	0.66939	2.045	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.68483	0.958;0.943	T	0.81046	-0.1110	10	0.87932	D	0	-20.1348	12.3606	0.55201	1.0:0.0:0.0:0.0	.	200;285	E7EN46;Q8TB03	.;CX038_HUMAN	P	166;285;166;200	ENSP00000367683:L166P;ENSP00000330488:L285P;ENSP00000367677:L166P;ENSP00000400019:L200P	ENSP00000330488:L285P	L	-	2	0	CXorf38	40374917	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	4.715000	0.61909	1.907000	0.55213	0.483000	0.47432	CTT	.	.		0.433	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3	NM_144970		G	40489973	A	G	40489973	3	3	113	1	0	0	0	0	1	0	0	0	4109	72	3	2	109	2	CXorf38	23	40489973	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	26686120	40489973	114780587	389	18266										
EFHC2	80258	hgsc.bcm.edu	37	chrX	44109537	44109537	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	caatagtatcatcacacaagAagtaatgcaggatgagttct	8	7	3	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chrX:44109537A>G	ENST00000420999.1	-	5	844	c.761T>C	c.(760-762)tTc>tCc	p.F254S		NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	254	DM10 2. {ECO:0000255|PROSITE- ProRule:PRU00665}.						calcium ion binding (GO:0005509)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						ATCACACAAGAAGTAATGCAG	0.448																																					p.F254S		Atlas-SNP	.											.	EFHC2	81	.	0			c.T761C						.						81	70	74					X																	44109537		1934	4125	6059	SO:0001583	missense	80258	exon5			CACAAGAAGTAAT	AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"EF-hand domain containing"	26233	protein-coding gene	gene with protein product		300817	"mental retardation, X-linked 74"	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.761T>C	chrX.hg19:g.44109537A>G	ENSP00000404232:p.Phe254Ser	184.0	0.0		60.0	4.0	NM_025184	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Missense_Mutation	SNP	ENST00000420999.1	hg19	CCDS55405.1	.	.	.	.	.	.	.	.	.	.	A	10.76	1.441764	0.25900	.	.	ENSG00000183690	ENST00000333807;ENST00000420999;ENST00000378056	T;T	0.59083	0.29;0.29	5.8	3.31	0.37934	Uncharacterised domain DM10 (2);	0.238136	0.41712	D	0.000838	T	0.78046	0.4222	M	0.91090	3.175	0.38279	D	0.942374	D	0.71674	0.998	D	0.70935	0.971	T	0.80973	-0.1143	10	0.87932	D	0	-14.1999	10.4636	0.44594	0.4759:0.0:0.0:0.5241	.	254	Q5JST6	EFHC2_HUMAN	S	254;282;58	ENSP00000333823:F254S;ENSP00000404232:F282S	ENSP00000333823:F254S	F	-	2	0	EFHC2	43994481	1.000000	0.71417	0.017000	0.16124	0.019000	0.09904	2.001000	0.40825	0.257000	0.21650	-0.367000	0.07326	TTC	.	.		0.448	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184		G	44109537	A	G	44109537	3	3	113	1	0	0	0	0	1	0	0	0	4949	246	9	2	1532	2	EFHC2	23	44109537	Missense_Mutation	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	3619564	44109537	111161023	390	18267										
ZNF81	347344	hgsc.bcm.edu	37	chrX	47775710	47775710	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	actggagagaaaccctatgtTtgtgctgattgtgggagggc	15	6	0	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chrX:47775710T>C	ENST00000376954.1	+	6	2033	c.1665T>C	c.(1663-1665)gtT>gtC	p.V555V	ZNF81_ENST00000338637.7_Silent_p.V555V			P51508	ZNF81_HUMAN	zinc finger protein 81	555					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(1)|lung(1)|skin(1)	4		all_lung(315;0.0973)				AACCCTATGTTTGTGCTGATT	0.423																																					p.V555V		Atlas-SNP	.											.	ZNF81	60	.	0			c.T1665C						.						55	54	54					X																	47775710		2148	4268	6416	SO:0001819	synonymous_variant	347344	exon5			CTATGTTTGTGCT	AK126949	CCDS43933.1	Xp11.23	2013-01-08	2006-05-12		ENSG00000197779	ENSG00000197779		"Zinc fingers, C2H2-type", "-"	13156	protein-coding gene	gene with protein product		314998	"zinc finger protein 81 (HFZ20)", "mental retardation, X-linked 45"	MRX45		8507979, 15121780	Standard	NM_007137		Approved	HFZ20	uc022bvq.1	P51508	OTTHUMG00000021462	ENST00000376954.1:c.1665T>C	chrX.hg19:g.47775710T>C		211.0	0.0		86.0	4.0	NM_007137	Q6RX22|Q96QH6	Silent	SNP	ENST00000376954.1	hg19	CCDS43933.1																																																																																			.	.		0.423	ZNF81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056455.2	NM_007137		C	47775710	T	C	47775710	2	2	113	1	0	0	0	0	0	0	0	1	18189	1828	64	2		2	ZNF81	23	47775710	Silent	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	3666173	47775710	107494850	391	18268										
NHSL2	340527	hgsc.bcm.edu	37	chrX	71358563	71358563	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	gacctacagaatcaaccttcTccacttcctggaagggagat	8	12	2	2			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chrX:71358563T>C	ENST00000373677.1	+	2	1329	c.67T>C	c.(67-69)Tcc>Ccc	p.S23P	NHSL2_ENST00000535692.1_Missense_Mutation_p.S23P|NHSL2_ENST00000540800.1_Missense_Mutation_p.S389P|NHSL2_ENST00000510661.1_Missense_Mutation_p.S158P			Q5HYW2	NHSL2_HUMAN	NHS-like 2	23										NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					ATCAACCTTCTCCACTTCCTG	0.507																																					p.S389P		Atlas-SNP	.											.	NHSL2	148	.	0			c.T1165C						.						98	73	81					X																	71358563		2203	4300	6503	SO:0001583	missense	340527	exon6			ACCTTCTCCACTT			Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.67T>C	chrX.hg19:g.71358563T>C	ENSP00000362781:p.Ser23Pro	318.0	0.0		107.0	5.0	NM_001013627	B2RN94	Missense_Mutation	SNP	ENST00000373677.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.55	2.865937	0.51588	.	.	ENSG00000204131	ENST00000540800;ENST00000373677;ENST00000510661;ENST00000535692	T;T;T;T	0.57436	1.01;0.47;0.4;0.47	5.88	5.88	0.94601	.	0.063088	0.64402	D	0.000004	T	0.67951	0.2948	L	0.56769	1.78	0.47778	D	0.999517	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.998	T	0.68693	-0.5341	10	0.48119	T	0.1	-12.7071	12.9953	0.58644	0.0:0.0:0.0:1.0	.	389;158;23	F5H593;D6RBM4;Q5HYW2	.;.;NHSL2_HUMAN	P	389;23;158;23	ENSP00000444617:S389P;ENSP00000362781:S23P;ENSP00000424079:S158P;ENSP00000444914:S23P	ENSP00000362781:S23P	S	+	1	0	NHSL2	71275288	1.000000	0.71417	0.970000	0.41538	0.934000	0.57294	3.477000	0.53151	1.977000	0.57605	0.441000	0.28932	TCC	.	.		0.507	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		C	71358563	T	C	71358563	3	2	113	1	0	0	0	0	1	0	0	0	10421	1551	54	2	1187	2	NHSL2	23	71358563	Missense_Mutation	SNP	T	TCGA-DD-A39Z-01A-11D-A20W-10	23582853	71358563	83911997	392	18269										
IL13RA1	3597	hgsc.bcm.edu	37	chrX	117874980	117874980	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	tttgtccttgatttgaacagAaactcagccacctgtgacaa	7	10	1	4			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chrX:117874980A>G	ENST00000371666.3	+	2	156	c.89A>G	c.(88-90)gAa>gGa	p.E30G	IL13RA1_ENST00000371642.1_Splice_Site_p.E30G|SNORA35_ENST00000458908.1_RNA	NM_001560.2	NP_001551.1	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1	30					cell surface receptor signaling pathway (GO:0007166)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin production (GO:0002639)	interleukin-13 receptor complex (GO:0005898)|plasma membrane (GO:0005886)	interleukin-13 receptor activity (GO:0016515)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)	12						ATTTGAACAGAAACTCAGCCA	0.383																																					p.E30G		Atlas-SNP	.											.	IL13RA1	41	.	0			c.A89G						.						99	96	97					X																	117874980		2203	4300	6503	SO:0001630	splice_region_variant	3597	exon2			GAACAGAAACTCA	U62858	CCDS14573.1	Xq24	2008-02-05			ENSG00000131724	ENSG00000131724		"Interleukins and interleukin receptors", "CD molecules"	5974	protein-coding gene	gene with protein product	"IL13 receptor alpha-1 chain", "CD213a1 antigen"	300119				8910586, 9013879	Standard	NM_001560		Approved	IL-13Ra, NR4, CD213a1	uc004eqs.3	P78552	OTTHUMG00000022258	ENST00000371666.3:c.89-1A>G	chrX.hg19:g.117874980A>G		129.0	0.0		37.0	4.0	NM_001560	O95646|Q5JSL4|Q99656|Q9UDY5	Missense_Mutation	SNP	ENST00000371666.3	hg19	CCDS14573.1	.	.	.	.	.	.	.	.	.	.	A	13.97	2.396737	0.42512	.	.	ENSG00000131724	ENST00000371666;ENST00000371642	D;D	0.93859	-2.81;-3.3	5.61	4.44	0.53790	.	0.647706	0.14237	N	0.332323	D	0.87241	0.6128	L	0.27053	0.805	0.80722	D	1	P;P;P	0.43094	0.792;0.792;0.799	B;B;B	0.40329	0.326;0.326;0.214	T	0.80928	-0.1163	9	.	.	.	.	7.2704	0.26254	0.899:0.0:0.101:0.0	.	30;30;30	Q5JSL4;P78552;Q9UDY5	.;I13R1_HUMAN;.	G	30	ENSP00000360730:E30G;ENSP00000360705:E30G	.	E	+	2	0	IL13RA1	117759008	0.996000	0.38824	0.991000	0.47740	0.732000	0.41865	1.529000	0.35996	0.752000	0.32923	0.486000	0.48141	GAA	.	.		0.383	IL13RA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058009.1	NM_001560	Missense_Mutation	G	117874980	A	G	117874980	5	3	113	1	0	0	0	0	0	0	1	0	7638	260	9	2	95	2	IL13RA1	23	117874980	Splice_Site	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	46516417	117874980	37395580	393	18270										
SLC25A5	292	hgsc.bcm.edu	37	chrX	118604919	118604919	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	cggaagattgctcgtgatgaAggaggcaaagcttttttcaa	12	6	1	3			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chrX:118604919A>G	ENST00000317881.8	+	4	911	c.795A>G	c.(793-795)gaA>gaG	p.E265E	SLC25A5-AS1_ENST00000446986.1_RNA	NM_001152.4	NP_001143.2	P05141	ADT2_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	265					adenine transport (GO:0015853)|chromosome segregation (GO:0007059)|energy reserve metabolic process (GO:0006112)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|MMXD complex (GO:0071817)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(2)	12					Clodronate(DB00720)	CTCGTGATGAAGGAGGCAAAG	0.458																																					p.E265E		Atlas-SNP	.											.	SLC25A5	33	.	0			c.A795G						.						107	81	90					X																	118604919		2203	4300	6503	SO:0001819	synonymous_variant	292	exon4			TGATGAAGGAGGC	BC068199	CCDS14578.1	Xq24	2013-08-09			ENSG00000005022	ENSG00000005022		"Solute carriers"	10991	protein-coding gene	gene with protein product		300150		ANT2		2168878, 2829183	Standard	NM_001152		Approved	T2, 2F1, T3	uc004erh.4	P05141	OTTHUMG00000022715	ENST00000317881.8:c.795A>G	chrX.hg19:g.118604919A>G		283.0	0.0		94.0	4.0	NM_001152	B2RCV1|O43350	Silent	SNP	ENST00000317881.8	hg19	CCDS14578.1																																																																																			.	.		0.458	SLC25A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058952.2	NM_001152		G	118604919	A	G	118604919	2	3	113	1	0	0	0	0	0	0	0	1	14527	69	3	2		2	SLC25A5	23	118604919	Silent	SNP	A	TCGA-DD-A39Z-01A-11D-A20W-10	729939	118604919	36665641	394	18271										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123654550	123654550	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0279187817258883	11	1	0.973070121040906	1.22076069730586	0.931088667436676	0.0183066361556064	0.284515636918383	0	atgtgtcagaaggatccgtaGcagggttttatacccagggg	14	7	1	1			TCGA-DD-A39Z-01A-11D-A20W-10	TCGA-DD-A39Z-11A-21D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5d662f8-35c9-4f38-9e23-10cd6e522078	7dbbd52e-3044-4bd2-8839-4471df1bd1dc	g.chrX:123654550G>A	ENST00000371130.3	-	18	3181	c.3118C>T	c.(3118-3120)Cta>Tta	p.L1040L	TENM1_ENST00000422452.2_Silent_p.L1040L	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1040					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AGGATCCGTAGCAGGGTTTTA	0.483																																					p.L1040L		Atlas-SNP	.											.	.	.	.	0			c.C3118T						.						86	78	81					X																	123654550		2203	4300	6503	SO:0001819	synonymous_variant	10178	exon18			TCCGTAGCAGGGT	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.3118C>T	chrX.hg19:g.123654550G>A		325.0	1.0		79.0	56.0	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	hg19	CCDS14609.1																																																																																			.	.		0.483	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123654550	G	A	123654550	2	1	113	1	0	0	0	0	0	0	0	1	10843	962	34	3		3	ODZ1	23	123654550	Silent	SNP	G	TCGA-DD-A39Z-01A-11D-A20W-10	5049631	123654550	31616010	395	18272										
AGRN	375790	hgsc.bcm.edu	37	chr1	987127	987127	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggctggtggagaagtcagcGggggacgtggataccttggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:987127delG	ENST00000379370.2	+	33	5633	c.5583delG	c.(5581-5583)gcgfs	p.A1861fs		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1865					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		AGAAGTCAGCGGGGGACGTGG	0.657																																					p.A1861fs		Atlas-INDEL	.											.	AGRN	110	.	0			c.5582delC						.						132	103	113					1																	987127		2203	4300	6503	SO:0001589	frameshift_variant	375790	exon33			.	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"Proteoglycans / Extracellular Matrix : Other"	329	protein-coding gene	gene with protein product	"agrin proteoglycan"	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.5583delG	chr1.hg19:g.987127delG	ENSP00000368678:p.Ala1861fs	232.0	0.0		152.0	12.0	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Frame_Shift_Del	DEL	ENST00000379370.2	hg19	CCDS30551.1																																																																																			.	.		0.657	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		-	987127	G	-	987127	7	5	114	1	0	1	0	1	0	0	0	0	397	1103	39	0	5713	0	AGRN	1	987127	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10		987127	248263494	1	18273										
ATAD3A	55210	hgsc.bcm.edu	37	chr1	1463179	1463179	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctgccagggcaggaggaacGggagcgcctggtgagaatgt					rs200868669		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:1463179delG	ENST00000378755.5	+	14	1680	c.1586delG	c.(1585-1587)cggfs	p.R529fs	ATAD3A_ENST00000378756.3_Frame_Shift_Del_p.R481fs|ATAD3A_ENST00000536055.1_Frame_Shift_Del_p.R402fs	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	529					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		CAGGAGGAACGGGAGCGCCTG	0.582																																					p.R529fs		Atlas-INDEL	.											.	ATAD3A	35	.	0			c.1585delC						.						110	114	112					1																	1463179		2203	4300	6503	SO:0001589	frameshift_variant	55210	exon14			.	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785		"ATPases / AAA-type"	25567	protein-coding gene	gene with protein product		612316				12477932	Standard	NM_018188		Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378755.5:c.1586delG	chr1.hg19:g.1463179delG	ENSP00000368030:p.Arg529fs	219.0	0.0		166.0	10.0	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Frame_Shift_Del	DEL	ENST00000378755.5	hg19	CCDS31.1																																																																																			.	.		0.582	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188		-	1463179	G	-	1463179	7	5	114	1	0	1	0	1	0	0	0	0	1073	1116	39	0	1640	0	ATAD3A	1	1463179	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	476052	1463179	247787442	2	18274										
CALML6	163688	hgsc.bcm.edu	37	chr1	1847882	1847882	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcgggtgtcccctgcagacAgagcgcctgtcggctgagca	15	13	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:1847882A>G	ENST00000307786.3	+	3	535	c.81A>G	c.(79-81)acA>acG	p.T27T	CALML6_ENST00000462293.1_Intron	NM_138705.2	NP_619650.2	Q8TD86	CALL6_HUMAN	calmodulin-like 6	27						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(1)|prostate(2)	7	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.94e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.83e-23)|GBM - Glioblastoma multiforme(42;3.23e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		CCCTGCAGACAGAGCGCCTGT	0.632																																					p.T27T		Atlas-SNP	.											.	CALML6	18	.	0			c.A81G						.						46	46	46					1																	1847882		2149	4247	6396	SO:0001819	synonymous_variant	163688	exon3			GCAGACAGAGCGC	AF490905	CCDS30566.1	1p36.33	2013-01-10			ENSG00000169885	ENSG00000169885		"EF-hand domain containing"	24193	protein-coding gene	gene with protein product		610171					Standard	NM_138705		Approved	CAGLP	uc001aih.1	Q8TD86	OTTHUMG00000000943	ENST00000307786.3:c.81A>G	chr1.hg19:g.1847882A>G		134.0	0.0		117.0	5.0	NM_138705	A2A2M3|Q6Q2C4	Silent	SNP	ENST00000307786.3	hg19	CCDS30566.1																																																																																			.	.		0.632	CALML6-004	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276929.1	NM_138705		G	1847882	A	G	1847882	2	3	114	1	0	0	0	0	0	0	0	1	2592	175	7	2		2	CALML6	1	1847882	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	384703	1847882	247402739	3	18275										
TNFRSF14	8764	hgsc.bcm.edu	37	chr1	2492097	2492097	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacaccctgtgtcagaactgCcccccggggaccttctctcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:2492097delC	ENST00000355716.4	+	5	794	c.495delC	c.(493-495)tgcfs	p.C165fs	TNFRSF14_ENST00000409119.1_Frame_Shift_Del_p.C165fs	NM_003820.2	NP_003811.2	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily, member 14	165					cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell migration (GO:2000406)|T cell costimulation (GO:0031295)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			kidney(1)	1	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;1.11e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000326)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.199)		GTCAGAACTGCCCCCCGGGGA	0.667			"Mis, N, F"		follicular lymphoma																																p.C165fs		Atlas-INDEL	.		Rec	yes		1	1p36.32	8764	"tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"		L	.	TNFRSF14	89	.	0			c.494delG						.						51	51	51					1																	2492097		2202	4300	6502	SO:0001589	frameshift_variant	8764	exon5			.	U70321	CCDS44046.1	1p36.32	2012-02-27	2011-08-11		ENSG00000157873	ENSG00000157873		"Tumor necrosis factor receptor superfamily", "CD molecules"	11912	protein-coding gene	gene with protein product	"herpesvirus entry mediator"	602746	"tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"			8898196, 9162061	Standard	XM_006711018		Approved	HVEM, ATAR, TR2, LIGHTR, HVEA, CD270	uc001ajt.1	Q92956	OTTHUMG00000000792	ENST00000355716.4:c.495delC	chr1.hg19:g.2492097delC	ENSP00000347948:p.Cys165fs	146.0	0.0		154.0	11.0	NM_003820	B3KW30|B9DI89|Q6IB95|Q8N634|Q8WXR1|Q96J31|Q9UM65	Frame_Shift_Del	DEL	ENST00000355716.4	hg19	CCDS44046.1																																																																																			.	.		0.667	TNFRSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002088.1			-	2492097	C	-	2492097	7	5	114	1	0	1	0	1	0	0	0	0	16304	747	26	0	513	0	TNFRSF14	1	2492097	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	644215	2492097	246758524	4	18276										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12439636	12439636	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aactgacctgtgggttacatGggttggtcgtccaggtcagt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:12439636delG	ENST00000358136.3	+	57	11306	c.11176delG	c.(11176-11178)gggfs	p.G3726fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.G3701fs|VPS13D_ENST00000496628.1_3'UTR	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TGGGTTACATGGGTTGGTCGT	0.478																																					p.H3725fs		Atlas-INDEL	.											.	VPS13D	316	.	0			c.11175delT						.						115	97	103					1																	12439636		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon57			.	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.11176delG	chr1.hg19:g.12439636delG	ENSP00000350854:p.Gly3726fs	133.0	0.0		155.0	10.0	NM_015378		Frame_Shift_Del	DEL	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.478	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		-	12439636	G	-	12439636	7	5	114	1	0	1	0	1	0	0	0	0	17207	1348	47	0	11398	0	VPS13D	1	12439636	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	9947539	12439636	236810985	5	18277										
EPHA2	1969	hgsc.bcm.edu	37	chr1	16475439	16475439	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctcagcctctcctcggtacAcccagttggtgcggagccag	12	15	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:16475439A>G	ENST00000358432.5	-	3	411	c.257T>C	c.(256-258)gTg>gCg	p.V86A	EPHA2_ENST00000461614.1_5'UTR	NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	86	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.|Mediates interaction with CLDN4.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	TCCTCGGTACACCCAGTTGGT	0.537																																					p.V86A		Atlas-SNP	.											.	EPHA2	102	.	0			c.T257C						.						113	95	101					1																	16475439		2203	4300	6503	SO:0001583	missense	1969	exon3			CGGTACACCCAGT	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3386	protein-coding gene	gene with protein product		176946	"EphA2"	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.257T>C	chr1.hg19:g.16475439A>G	ENSP00000351209:p.Val86Ala	105.0	0.0		121.0	5.0	NM_004431	B5A968|Q8N3Z2	Missense_Mutation	SNP	ENST00000358432.5	hg19	CCDS169.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.599982	0.87055	.	.	ENSG00000142627	ENST00000358432	T	0.11821	2.74	5.35	5.35	0.76521	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.155316	0.31438	N	0.007646	T	0.27169	0.0666	L	0.49126	1.545	0.50467	D	0.999875	P;B	0.52061	0.95;0.448	P;P	0.58172	0.834;0.511	T	0.00872	-1.1532	10	0.87932	D	0	.	13.2736	0.60175	1.0:0.0:0.0:0.0	.	86;86	B5A968;P29317	.;EPHA2_HUMAN	A	86	ENSP00000351209:V86A	ENSP00000351209:V86A	V	-	2	0	EPHA2	16348026	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.335000	0.96500	2.024000	0.59613	0.459000	0.35465	GTG	.	.		0.537	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431		G	16475439	A	G	16475439	3	3	114	1	0	0	0	0	1	0	0	0	5169	159	6	2	2733	2	EPHA2	1	16475439	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	4035803	16475439	232775182	6	18278										
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17312998	17312998	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgaagttgagggtgaccagaCccagcagcagcagcttgaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:17312998delC	ENST00000326735.8	-	28	3398	c.3365delG	c.(3364-3366)ggtfs	p.G1122fs	RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Intron|ATP13A2_ENST00000452699.1_Frame_Shift_Del_p.G1117fs			Q9NQ11	AT132_HUMAN	ATPase type 13A2	1122					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		GGTGACCAGACCCAGCAGCAG	0.677																																					p.G1122fs		Atlas-INDEL	.											.	ATP13A2	85	.	0			c.3366delT						.						48	53	51					1																	17312998		2203	4299	6502	SO:0001589	frameshift_variant	23400	exon28			.	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.3365delG	chr1.hg19:g.17312998delC	ENSP00000327214:p.Gly1122fs	165.0	0.0		170.0	11.0	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Frame_Shift_Del	DEL	ENST00000326735.8	hg19	CCDS175.1																																																																																			.	.		0.677	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		-	17312998	C	-	17312998	7	5	114	1	0	1	0	1	0	0	0	0	1124	507	18	0	421	0	ATP13A2	1	17312998	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	837559	17312998	231937623	7	18279										
HTR6	3362	hgsc.bcm.edu	37	chr1	19992674	19992674	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcgcatgacgcccctgcgtgCcctggccctagtcctgggcg					rs201579153		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:19992674delC	ENST00000289753.1	+	1	895	c.428delC	c.(427-429)gccfs	p.A143fs		NM_000871.1	NP_000862.1	P50406	5HT6R_HUMAN	5-hydroxytryptamine (serotonin) receptor 6, G protein-coupled	143					brain development (GO:0007420)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|long-term synaptic potentiation (GO:0060291)|negative regulation of acetylcholine secretion, neurotransmission (GO:0014058)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|synaptic transmission (GO:0007268)	cilium (GO:0005929)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)|serotonin receptor activity (GO:0004993)			endometrium(1)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.81e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00117)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Mianserin(DB06148)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Quetiapine(DB01224)|Sertindole(DB06144)|Ziprasidone(DB00246)	CCCCTGCGTGCCCTGGCCCTA	0.701																																					p.A143fs	Esophageal Squamous(168;1879 2619 6848 21062)	Atlas-INDEL	.											.	HTR6	38	.	0			c.427delG						.						47	42	43					1																	19992674		2203	4300	6503	SO:0001589	frameshift_variant	3362	exon1			.	L41147	CCDS197.1	1p36-p35	2012-08-08	2012-02-03		ENSG00000158748	ENSG00000158748		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5301	protein-coding gene	gene with protein product		601109	"5-hydroxytryptamine (serotonin) receptor 6"			8522988	Standard	NM_000871		Approved	5-HT6, 5-HT6R	uc001bcl.3	P50406	OTTHUMG00000002713	ENST00000289753.1:c.428delC	chr1.hg19:g.19992674delC	ENSP00000289753:p.Ala143fs	185.0	0.0		192.0	13.0	NM_000871	Q13640|Q5TGZ1	Frame_Shift_Del	DEL	ENST00000289753.1	hg19	CCDS197.1																																																																																			.	.		0.701	HTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007704.1	NM_000871		-	19992674	C	-	19992674	7	5	114	1	0	1	0	1	0	0	0	0	7460	739	26	0	430	0	HTR6	1	19992674	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2679676	19992674	229257947	8	18280										
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21181509	21181509	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctccaccactgctgccttttCcccagctgcctagctgtgct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:21181509delC	ENST00000264211.8	-	20	3421	c.3227delG	c.(3226-3228)ggafs	p.G1076fs	EIF4G3_ENST00000374935.3_Frame_Shift_Del_p.G796fs|EIF4G3_ENST00000374937.3_Frame_Shift_Del_p.G1082fs|EIF4G3_ENST00000400422.1_Frame_Shift_Del_p.G1076fs|EIF4G3_ENST00000602326.1_Frame_Shift_Del_p.G1082fs|EIF4G3_ENST00000536266.1_Frame_Shift_Del_p.G680fs|EIF4G3_ENST00000537738.1_Frame_Shift_Del_p.G566fs	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1076					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		GCTGCCTTTTCCCCAGCTGCC	0.458																																					p.G1112fs		Atlas-INDEL	.											.	EIF4G3	300	.	0			c.3336delA						.						233	195	208					1																	21181509		2203	4300	6503	SO:0001589	frameshift_variant	8672	exon24			.	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.3227delG	chr1.hg19:g.21181509delC	ENSP00000264211:p.Gly1076fs	90.0	0.0		103.0	10.0	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Frame_Shift_Del	DEL	ENST00000264211.8	hg19	CCDS214.1																																																																																			.	.		0.458	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		-	21181509	C	-	21181509	7	5	114	1	0	1	0	1	0	0	0	0	5040	855	30	0	1578	0	EIF4G3	1	21181509	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1188835	21181509	228069112	9	18281										
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21306905	21306905	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggttgaactggatattgttGggggggcccaacataaggag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:21306905delG	ENST00000264211.8	-	4	441	c.247delC	c.(247-249)caafs	p.Q84fs	EIF4G3_ENST00000356916.3_Frame_Shift_Del_p.Q95fs|EIF4G3_ENST00000374935.3_Frame_Shift_Del_p.Q84fs|EIF4G3_ENST00000374937.3_Frame_Shift_Del_p.Q91fs|EIF4G3_ENST00000400422.1_Frame_Shift_Del_p.Q84fs|EIF4G3_ENST00000602326.1_Frame_Shift_Del_p.Q91fs|EIF4G3_ENST00000374927.4_Frame_Shift_Del_p.Q84fs	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	84					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		GGATATTGTTGGGGGGGCCCA	0.443																																					p.Q94fs		Atlas-INDEL	.											.	EIF4G3	300	.	0			c.281delA						.						23	27	26					1																	21306905		2203	4300	6503	SO:0001589	frameshift_variant	8672	exon10			.	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.247delC	chr1.hg19:g.21306905delG	ENSP00000264211:p.Gln84fs	117.0	0.0		192.0	12.0	NM_001198803	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Frame_Shift_Del	DEL	ENST00000264211.8	hg19	CCDS214.1																																																																																			.	.		0.443	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		-	21306905	G	-	21306905	7	5	114	1	0	1	0	1	0	0	0	0	5040	1357	47	0	4622	0	EIF4G3	1	21306905	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	125396	21306905	227943716	10	18282										
KDM1A	23028	hgsc.bcm.edu	37	chr1	23376988	23376988	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accacaacagacccagaaggTttttcttttcattagaaacc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:23376988delT	ENST00000356634.3	+	3	775	c.626delT	c.(625-627)gttfs	p.V209fs	RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Frame_Shift_Del_p.V229fs|KDM1A_ENST00000542151.1_Frame_Shift_Del_p.V229fs	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	209	SWIRM. {ECO:0000255|PROSITE- ProRule:PRU00247}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						ACCCAGAAGGTTTTTCTTTTC	0.408																																					p.V229fs		Atlas-INDEL	.											.	KDM1A	49	.	0			c.685delG						.						120	116	118					1																	23376988		2203	4300	6503	SO:0001589	frameshift_variant	23028	exon4			.	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.626delT	chr1.hg19:g.23376988delT	ENSP00000349049:p.Val209fs	117.0	0.0		146.0	13.0	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Frame_Shift_Del	DEL	ENST00000356634.3	hg19	CCDS30627.1																																																																																			.	.		0.408	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		-	23376988	T	-	23376988	7	5	114	1	0	1	0	1	0	0	0	0	8131	1725	60	0	700	0	KDM1A	1	23376988	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2070083	23376988	225873633	11	18283										
MYOM3	127294	hgsc.bcm.edu	37	chr1	24394840	24394840	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accaggcccttctctcggtcAaaattgattttgcggttctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:24394840delA	ENST00000374434.3	-	26	3330	c.3168delT	c.(3166-3168)tttfs	p.F1056fs	MYOM3_ENST00000338909.5_5'Flank|MYOM3_ENST00000329601.7_Frame_Shift_Del_p.F1056fs|MYOM3_ENST00000330966.7_Frame_Shift_Del_p.F1057fs|RP11-293P20.4_ENST00000429191.1_RNA|RP11-293P20.2_ENST00000439239.2_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1056						M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		TCTCTCGGTCAAAATTGATTT	0.488																																					p.D1057fs		Atlas-INDEL	.											.	MYOM3	131	.	0			c.3169delG						.						210	203	205					1																	24394840		1902	4108	6010	SO:0001589	frameshift_variant	127294	exon26			.	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	26679	protein-coding gene	gene with protein product			"myomesin family, member 3"			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.3168delT	chr1.hg19:g.24394840delA	ENSP00000363557:p.Phe1056fs	147.0	0.0		165.0	10.0	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Frame_Shift_Del	DEL	ENST00000374434.3	hg19	CCDS41281.1																																																																																			.	.		0.488	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372		-	24394840	A	-	24394840	7	5	114	1	0	1	0	1	0	0	0	0	10102	127	5	0	1193	0	MYOM3	1	24394840	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1017852	24394840	224855781	12	18284										
SLC9A1	6548	hgsc.bcm.edu	37	chr1	27428223	27428223	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggcagaggctaccttctgcTccagctgccgggccttctgc	12	15	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:27428223T>C	ENST00000263980.3	-	10	2605	c.2030A>G	c.(2029-2031)gAg>gGg	p.E677G	SLC9A1_ENST00000545949.1_Missense_Mutation_p.E338G|SLC9A1_ENST00000490329.1_5'Flank	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	677					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	TACCTTCTGCTCCAGCTGCCG	0.602																																					p.E677G		Atlas-SNP	.											.	SLC9A1	68	.	0			c.A2030G						.						34	32	33					1																	27428223		2203	4299	6502	SO:0001583	missense	6548	exon10			TTCTGCTCCAGCT	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.2030A>G	chr1.hg19:g.27428223T>C	ENSP00000263980:p.Glu677Gly	73.0	0.0		120.0	6.0	NM_003047	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	ENST00000263980.3	hg19	CCDS295.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.897770	0.91962	.	.	ENSG00000090020	ENST00000263980;ENST00000374089;ENST00000545949;ENST00000447808	T;T	0.52983	0.64;0.64	4.97	4.97	0.65823	.	0.215214	0.47852	D	0.000217	T	0.48696	0.1514	M	0.70275	2.135	0.80722	D	1	B	0.18610	0.029	B	0.13407	0.009	T	0.48980	-0.8986	10	0.46703	T	0.11	.	14.4627	0.67462	0.0:0.0:0.0:1.0	.	677	P19634	SL9A1_HUMAN	G	677;181;338;98	ENSP00000263980:E677G;ENSP00000445520:E338G	ENSP00000263980:E677G	E	-	2	0	SLC9A1	27300810	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.737000	0.55060	2.082000	0.62665	0.459000	0.35465	GAG	.	.		0.602	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		C	27428223	T	C	27428223	3	2	114	1	0	0	0	0	1	0	0	0	14724	1551	54	2	429	2	SLC9A1	1	27428223	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3033383	27428223	221822398	13	18285										
AHDC1	27245	hgsc.bcm.edu	37	chr1	27876439	27876439	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccagtcacagcgtctacctCcccccggccccgtttgcgtg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:27876439delC	ENST00000247087.5	-	5	2784	c.2188delG	c.(2188-2190)gagfs	p.E730fs	AHDC1_ENST00000374011.2_Frame_Shift_Del_p.E730fs			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	730	Gly-rich.						DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GCGTCTACCTCCCCCCGGCCC	0.662																																					p.E730fs		Atlas-INDEL	.											.	AHDC1	98	.	0			c.2189delA						.						36	34	34					1																	27876439		2203	4300	6503	SO:0001589	frameshift_variant	27245	exon6			.	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.2188delG	chr1.hg19:g.27876439delC	ENSP00000247087:p.Glu730fs	238.0	0.0		249.0	18.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Frame_Shift_Del	DEL	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.		0.662	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			-	27876439	C	-	27876439	7	5	114	1	0	1	0	1	0	0	0	0	412	864	30	0	2627	0	AHDC1	1	27876439	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	448216	27876439	221374182	14	18286										
PHACTR4	65979	hgsc.bcm.edu	37	chr1	28818190	28818190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaggccaactgtcgctgaacTccttgccaggaagattctga	10	11	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:28818190T>C	ENST00000373839.3	+	12	2168	c.1907T>C	c.(1906-1908)cTc>cCc	p.L636P	PHACTR4_ENST00000373836.3_Missense_Mutation_p.L646P|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	636					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		GTCGCTGAACTCCTTGCCAGG	0.458																																					p.L646P		Atlas-SNP	.											.	PHACTR4	64	.	0			c.T1937C						.						87	92	90					1																	28818190		1965	4158	6123	SO:0001583	missense	65979	exon11			CTGAACTCCTTGC	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1907T>C	chr1.hg19:g.28818190T>C	ENSP00000362945:p.Leu636Pro	109.0	0.0		118.0	5.0	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	hg19	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.644786	0.87859	.	.	ENSG00000204138	ENST00000373839;ENST00000373836	T;T	0.57273	0.41;0.44	5.67	5.67	0.87782	.	0.066491	0.64402	D	0.000007	T	0.73289	0.3568	M	0.80183	2.485	0.80722	D	1	D;D	0.58268	0.982;0.979	D;D	0.69479	0.964;0.925	T	0.77523	-0.2556	10	0.87932	D	0	-4.5027	15.1316	0.72530	0.0:0.0:0.0:1.0	.	646;636	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	P	636;646	ENSP00000362945:L636P;ENSP00000362942:L646P	ENSP00000362942:L646P	L	+	2	0	PHACTR4	28690777	1.000000	0.71417	0.884000	0.34674	0.990000	0.78478	8.000000	0.88501	2.172000	0.68678	0.456000	0.33151	CTC	.	.		0.458	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		C	28818190	T	C	28818190	3	2	114	1	0	0	0	0	1	0	0	0	11821	1551	54	2	1999	2	PHACTR4	1	28818190	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	941751	28818190	220432431	15	18287										
PUM1	9698	hgsc.bcm.edu	37	chr1	31532353	31532353	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgagggtgatgtttcaggtGggggctgaaagagtcctgcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:31532353delG	ENST00000257075.5	-	2	154	c.61delC	c.(61-63)cacfs	p.H21fs	PUM1_ENST00000423018.2_Frame_Shift_Del_p.H21fs|PUM1_ENST00000373742.2_Frame_Shift_Del_p.H57fs|PUM1_ENST00000426105.2_Frame_Shift_Del_p.H21fs|PUM1_ENST00000373747.3_Frame_Shift_Del_p.H21fs|PUM1_ENST00000373741.4_Frame_Shift_Del_p.H57fs|PUM1_ENST00000440538.2_Frame_Shift_Del_p.H21fs|PUM1_ENST00000424085.2_Frame_Shift_Del_p.H21fs	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	21					membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TGTTTCAGGTGGGGGCTGAAA	0.473																																					p.H21fs		Atlas-INDEL	.											.	PUM1	107	.	0			c.62delA						.						95	98	97					1																	31532353		2203	4300	6503	SO:0001589	frameshift_variant	9698	exon2			.	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.61delC	chr1.hg19:g.31532353delG	ENSP00000257075:p.His21fs	97.0	0.0		129.0	11.0	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Frame_Shift_Del	DEL	ENST00000257075.5	hg19	CCDS338.1																																																																																			.	.		0.473	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			-	31532353	G	-	31532353	7	5	114	1	0	1	0	1	0	0	0	0	12840	1348	47	0	3589	0	PUM1	1	31532353	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2714163	31532353	217718268	16	18288										
BAI2	576	hgsc.bcm.edu	37	chr1	32207725	32207725	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atgtggcccaggctgggcccGccacgctgcacttccggctg	14	16	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:32207725G>A	ENST00000373658.3	-	8	1687	c.1346C>T	c.(1345-1347)gCg>gTg	p.A449V	BAI2_ENST00000398547.1_Missense_Mutation_p.A382V|BAI2_ENST00000398556.3_Missense_Mutation_p.A397V|BAI2_ENST00000373655.2_Missense_Mutation_p.A449V|BAI2_ENST00000527361.1_Missense_Mutation_p.A449V|BAI2_ENST00000257070.4_Missense_Mutation_p.A449V|BAI2_ENST00000398538.1_Missense_Mutation_p.A437V|BAI2_ENST00000440175.2_Missense_Mutation_p.A91V|BAI2_ENST00000398542.1_Missense_Mutation_p.A382V	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	449	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A449V(1)		breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GGCTGGGCCCGCCACGCTGCA	0.657																																					p.A449V		Atlas-SNP	.											BAI2,NS,carcinoma,0,1	BAI2	128	.	1	Substitution - Missense(1)	lung(1)	c.C1346T						.						30	35	33					1																	32207725		2201	4296	6497	SO:0001583	missense	576	exon8			GGGCCCGCCACGC	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.1346C>T	chr1.hg19:g.32207725G>A	ENSP00000362762:p.Ala449Val	88.0	0.0		139.0	61.0	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	hg19	CCDS346.2	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271041	0.59540	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538;ENST00000420125;ENST00000533175	T;T;T;T;T;T;T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62	4.1	3.17	0.36434	.	0.200067	0.24996	N	0.033949	T	0.38214	0.1032	N	0.17345	0.48	0.29032	N	0.885631	P;P;P;P;P;D;P	0.54964	0.89;0.936;0.936;0.709;0.89;0.969;0.89	P;B;B;B;B;P;P	0.48270	0.523;0.388;0.388;0.426;0.322;0.572;0.523	T	0.33369	-0.9871	10	0.54805	T	0.06	.	12.9627	0.58468	0.0:0.1647:0.8352:0.0	.	382;449;437;91;382;449;449	A2A3C3;O60241-4;O60241-3;B4DKC3;A2A3C1;O60241-2;O60241	.;.;.;.;.;.;BAI2_HUMAN	V	397;382;449;449;382;449;449;91;437;387;428	ENSP00000381564:A397V;ENSP00000381555:A382V;ENSP00000362762:A449V;ENSP00000362759:A449V;ENSP00000381550:A382V;ENSP00000257070:A449V;ENSP00000435397:A449V;ENSP00000391071:A91V;ENSP00000381548:A437V;ENSP00000410921:A387V;ENSP00000437219:A428V	ENSP00000257070:A449V	A	-	2	0	BAI2	31980312	1.000000	0.71417	0.918000	0.36340	0.806000	0.45545	9.594000	0.98254	1.049000	0.40321	0.561000	0.74099	GCG	.	.		0.657	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		A	32207725	G	A	32207725	3	1	114	1	0	0	0	0	1	0	0	0	1299	1087	38	1	3515	1	BAI2	1	32207725	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	675372	32207725	217042896	17	18289										
IQCC	55721	hgsc.bcm.edu	37	chr1	32671421	32671421	+	Intron	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagatgctaccacgttcagtCccctaactgcgcgccaacct					rs186875513		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:32671421delC	ENST00000291358.6	+	1	63				RP4-622L5.7_ENST00000421616.1_RNA|IQCC_ENST00000537469.1_Frame_Shift_Del_p.P47fs|RP4-622L5.7_ENST00000373604.4_RNA	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C											endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CACGTTCAGTCCCCTAACTGC	0.642																																					p.S46fs		Atlas-INDEL	.											.	IQCC	46	.	0			c.138delT						.						25	22	23					1																	32671421		692	1591	2283	SO:0001627	intron_variant	55721	exon1			.	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.42+97C>-	chr1.hg19:g.32671421delC		164.0	0.0		221.0	15.0	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Frame_Shift_Del	DEL	ENST00000291358.6	hg19	CCDS355.1																																																																																			.	.		0.642	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134		-	32671421	C	-	32671421	6	5	114	0	1	1	0	1	0	0	0	0	7813	855	30	0		0	IQCC	1	32671421	Intron	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	463696	32671421	216579200	18	18290										
IQCC	55721	hgsc.bcm.edu	37	chr1	32673443	32673443	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atcatctgggatggtaccttGggggggccagagcatagtgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:32673443delG	ENST00000291358.6	+	5	1182	c.1161delG	c.(1159-1161)ttgfs	p.L387fs	DCDC2B_ENST00000409358.1_5'Flank|RP4-622L5.7_ENST00000421616.1_RNA|IQCC_ENST00000537469.1_Frame_Shift_Del_p.L467fs|RP4-622L5.7_ENST00000373604.4_RNA	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	387										endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ATGGTACCTTGGGGGGGCCAG	0.552																																					p.L467fs		Atlas-INDEL	.											.,1	IQCC	46	.	0			c.1400delT						.						82	89	87					1																	32673443		2203	4300	6503	SO:0001589	frameshift_variant	55721	exon5			.	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.1161delG	chr1.hg19:g.32673443delG	ENSP00000291358:p.Leu387fs	135.0	0.0		187.0	13.0	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Frame_Shift_Del	DEL	ENST00000291358.6	hg19	CCDS355.1																																																																																			.	.		0.552	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134		-	32673443	G	-	32673443	7	5	114	1	0	1	0	1	0	0	0	0	7813	1339	47	0	1419	0	IQCC	1	32673443	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2022	32673443	216577178	19	18291										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34011768	34011768	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatcaaagctgtcccccaaaCggatgccatgagccgggatc	11	13	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:34011768C>T	ENST00000373381.4	-	57	9145	c.8969G>A	c.(8968-8970)cGt>cAt	p.R2990H		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2963	Sushi 22. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R2846H(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTCCCCCAAACGGATGCCATG	0.567																																					p.R2846H		Atlas-SNP	.											CSMD2,NS,carcinoma,0,2	CSMD2	946	.	1	Substitution - Missense(1)	prostate(1)	c.G8537A						.						59	53	55					1																	34011768		2203	4300	6503	SO:0001583	missense	114784	exon56			CCCAAACGGATGC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.8969G>A	chr1.hg19:g.34011768C>T	ENSP00000362479:p.Arg2990His	106.0	0.0		114.0	45.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	C	20.8	4.056281	0.76074	.	.	ENSG00000121904	ENST00000373381	T	0.64803	-0.12	4.97	4.97	0.65823	Complement control module (2);Sushi/SCR/CCP (3);	0.061352	0.64402	D	0.000003	T	0.67664	0.2917	M	0.69523	2.12	0.80722	D	1	P;B	0.46457	0.878;0.139	P;B	0.46339	0.513;0.072	T	0.68685	-0.5343	10	0.36615	T	0.2	.	17.4042	0.87469	0.0:1.0:0.0:0.0	.	2846;2990	Q7Z408;E7EUA6	CSMD2_HUMAN;.	H	2990	ENSP00000362479:R2990H	ENSP00000241312:R2846H	R	-	2	0	CSMD2	33784355	1.000000	0.71417	0.951000	0.38953	0.596000	0.36781	7.629000	0.83207	2.591000	0.87537	0.650000	0.86243	CGT	.	.		0.567	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34011768	C	T	34011768	3	4	114	1	0	0	0	0	1	0	0	0	3947	536	19	1	1982	1	CSMD2	1	34011768	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	1338325	34011768	215238853	20	18292										
EIF2C4	192670	hgsc.bcm.edu	37	chr1	36291638	36291638	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctaacagactcccagcgtgTcaaatttaccaaagaaatca	5	11	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:36291638T>C	ENST00000373210.3	+	6	982	c.737T>C	c.(736-738)gTc>gCc	p.V246A		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	246	PAZ. {ECO:0000255|HAMAP-Rule:MF_03033}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										TCCCAGCGTGTCAAATTTACC	0.453																																					p.V246A		Atlas-SNP	.											.	.	.	.	0			c.T737C						.						121	115	117					1																	36291638		2203	4300	6503	SO:0001583	missense	192670	exon6			AGCGTGTCAAATT	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"Argonaute/PIWI family"	18424	protein-coding gene	gene with protein product	"argonaute 4"	607356	"eukaryotic translation initiation factor 2C, 4"	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.737T>C	chr1.hg19:g.36291638T>C	ENSP00000362306:p.Val246Ala	93.0	0.0		118.0	5.0	NM_017629	A7MD27	Missense_Mutation	SNP	ENST00000373210.3	hg19	CCDS397.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.167221	0.78339	.	.	ENSG00000134698	ENST00000373210	T	0.12774	2.65	5.53	5.53	0.82687	Argonaute/Dicer protein, PAZ (4);	0.000000	0.85682	D	0.000000	T	0.27866	0.0686	M	0.76328	2.33	0.80722	D	1	B	0.18461	0.028	B	0.40329	0.326	T	0.07693	-1.0759	10	0.23302	T	0.38	-13.8332	15.6642	0.77213	0.0:0.0:0.0:1.0	.	246	Q9HCK5	AGO4_HUMAN	A	246	ENSP00000362306:V246A	ENSP00000362306:V246A	V	+	2	0	EIF2C4	36064225	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.098000	0.63641	0.455000	0.32223	GTC	.	.		0.453	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629		C	36291638	T	C	36291638	3	2	114	1	0	0	0	0	1	0	0	0	5010	1667	58	2	759	2	EIF2C4	1	36291638	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2279870	36291638	212958983	21	18293										
EPHA10	284656	hgsc.bcm.edu	37	chr1	38184055	38184055	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggggtccactcacacctgcaCcccctggccctgcagctgga					rs78757428	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:38184055delC	ENST00000373048.4	-	17	3015	c.3016delG	c.(3016-3018)gtgfs	p.V1006fs	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000540011.1_3'UTR|EPHA10_ENST00000330210.7_Frame_Shift_Del_p.V501fs|EPHA10_ENST00000427468.2_Frame_Shift_Del_p.V1006fs	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	1006					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)	p.V1007M(2)		NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CACACCTGCACCCCCTGGCCC	0.662																																					p.V1006fs		Atlas-INDEL	.											.	EPHA10	120	.	2	Substitution - Missense(2)	stomach(2)	c.3017delT						.						68	76	74					1																	38184055		2042	4175	6217	SO:0001589	frameshift_variant	284656	exon17			.	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.3016delG	chr1.hg19:g.38184055delC	ENSP00000362139:p.Val1006fs	169.0	0.0		230.0	15.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Frame_Shift_Del	DEL	ENST00000373048.4	hg19	CCDS41305.1																																																																																			.	.		0.662	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		-	38184055	C	-	38184055	7	5	114	1	0	1	0	1	0	0	0	0	5168	507	18	0	14	0	EPHA10	1	38184055	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1892417	38184055	211066566	22	18294										
EPHA10	284656	hgsc.bcm.edu	37	chr1	38185112	38185112	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggtagtcagggcacacttGgggggctctgggtcctgcac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:38185112delG	ENST00000373048.4	-	15	2729	c.2730delC	c.(2728-2730)cccfs	p.P910fs	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000540011.1_Intron|EPHA10_ENST00000330210.7_Frame_Shift_Del_p.P405fs|EPHA10_ENST00000427468.2_Frame_Shift_Del_p.P910fs	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	910					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGGCACACTTGGGGGGCTCTG	0.612																																					p.K911fs		Atlas-INDEL	.											.	EPHA10	120	.	0			c.2731delA						.						37	45	43					1																	38185112		2056	4173	6229	SO:0001589	frameshift_variant	284656	exon15			.	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2730delC	chr1.hg19:g.38185112delG	ENSP00000362139:p.Pro910fs	186.0	0.0		216.0	13.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Frame_Shift_Del	DEL	ENST00000373048.4	hg19	CCDS41305.1																																																																																			.	.		0.612	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		-	38185112	G	-	38185112	7	5	114	1	0	1	0	1	0	0	0	0	5168	1335	47	0	308	0	EPHA10	1	38185112	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1057	38185112	211065509	23	18295										
SF3A3	10946	hgsc.bcm.edu	37	chr1	38442595	38442595	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcatagatctgggcttctagAaaagcaatgtctttgttcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:38442595delA	ENST00000373019.4	-	12	1921	c.966delT	c.(964-966)tttfs	p.F322fs	SF3A3_ENST00000489537.1_5'Flank|SF3A3_ENST00000448721.2_Frame_Shift_Del_p.F269fs	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	322					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GGGCTTCTAGAAAAGCAATGT	0.403																																					p.L323X		Atlas-INDEL	.											.	SF3A3	37	.	0			c.967delC						.						142	144	143					1																	38442595		2201	4300	6501	SO:0001589	frameshift_variant	10946	exon12			.	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"splicing factor 3a, subunit 3, 60kD"			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.966delT	chr1.hg19:g.38442595delA	ENSP00000362110:p.Phe322fs	170.0	0.0		209.0	14.0	NM_006802	D3DPT5|Q15460|Q5VT87	Frame_Shift_Del	DEL	ENST00000373019.4	hg19	CCDS428.1																																																																																			.	.		0.403	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802		-	38442595	A	-	38442595	7	5	114	1	0	1	0	1	0	0	0	0	14163	243	9	0	563	0	SF3A3	1	38442595	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	257483	38442595	210808026	24	18296										
UTP11L	51118	hgsc.bcm.edu	37	chr1	38483393	38483393	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcttcggaagaaggctcttgAaaaaaatccagatgaattct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:38483393delA	ENST00000373014.4	+	3	240	c.179delA	c.(178-180)gaafs	p.E60fs	UTP11L_ENST00000488453.1_3'UTR|UTP11L_ENST00000537711.1_Frame_Shift_Del_p.E60fs	NM_016037.3	NP_057121.2	Q9Y3A2	UTP11_HUMAN	UTP11-like, U3 small nucleolar ribonucleoprotein (yeast)	60					nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleolus (GO:0005730)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				AAGGCTCTTGAAAAAAATCCA	0.378																																					p.E60fs		Atlas-INDEL	.											.	UTP11L	17	.	0			c.178delG						.						74	84	81					1																	38483393		2201	4300	6501	SO:0001589	frameshift_variant	51118	exon3			.	AF151852	CCDS429.1	1p34.3	2014-03-06	2014-03-06		ENSG00000183520	ENSG00000183520			24329	protein-coding gene	gene with protein product		609440				11860508, 10810093	Standard	NM_016037		Approved	CGI-94	uc001ccn.4	Q9Y3A2	OTTHUMG00000004435	ENST00000373014.4:c.179delA	chr1.hg19:g.38483393delA	ENSP00000362105:p.Glu60fs	136.0	0.0		188.0	15.0	NM_016037	A8K785|B4DJC6|D3DPT7|Q5VT93|Q9BS98|Q9NS31	Frame_Shift_Del	DEL	ENST00000373014.4	hg19	CCDS429.1																																																																																			.	.		0.378	UTP11L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012962.1	NM_016037		-	38483393	A	-	38483393	7	5	114	1	0	1	0	1	0	0	0	0	17109	246	9	0	189	0	UTP11L	1	38483393	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	40798	38483393	210767228	25	18297										
HEYL	26508	hgsc.bcm.edu	37	chr1	40105230	40105230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcccttacctcagctggcccTcttggcccacgtcgatgggt	11	16	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:40105230T>C	ENST00000372852.3	-	1	387	c.68A>G	c.(67-69)gAg>gGg	p.E23G		NM_014571.3	NP_055386	Q9NQ87	HEYL_HUMAN	hes-related family bHLH transcription factor with YRPW motif-like	23					atrioventricular valve morphogenesis (GO:0003181)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to BMP stimulus (GO:0071773)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|glomerulus development (GO:0032835)|mesenchymal cell development (GO:0014031)|negative regulation of androgen receptor activity (GO:2000824)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|pulmonary valve morphogenesis (GO:0003184)|skeletal muscle cell differentiation (GO:0035914)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-1 domain binding (GO:0050683)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	7	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.1e-18)|Epithelial(16;2.77e-17)|all cancers(16;5.64e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CAGCTGGCCCTCTTGGCCCAC	0.751																																					p.E23G		Atlas-SNP	.											.	HEYL	27	.	0			c.A68G						.						11	11	11					1																	40105230		2186	4285	6471	SO:0001583	missense	26508	exon1			TGGCCCTCTTGGC	BC006087	CCDS439.1	1p34.3	2013-10-17	2013-10-17		ENSG00000163909	ENSG00000163909		"Basic helix-loop-helix proteins"	4882	protein-coding gene	gene with protein product	"hairy/enhancer-of-split related with YRPW motif 3"	609034	"hairy/enhancer-of-split related with YRPW motif-like"			10415358, 10860664	Standard	NM_014571		Approved	bHLHb33, HEY3, HESR3	uc001cdp.3	Q9NQ87	OTTHUMG00000000458	ENST00000372852.3:c.68A>G	chr1.hg19:g.40105230T>C	ENSP00000361943:p.Glu23Gly	87.0	0.0		80.0	5.0	NM_014571	Q5TG99	Missense_Mutation	SNP	ENST00000372852.3	hg19	CCDS439.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.388348	0.42308	.	.	ENSG00000163909	ENST00000372852	T	0.63580	-0.05	3.68	3.68	0.42216	.	0.553967	0.19177	N	0.120783	T	0.57242	0.2040	L	0.57536	1.79	0.80722	D	1	B	0.20368	0.044	B	0.24848	0.056	T	0.61481	-0.7054	10	0.87932	D	0	-15.647	8.9953	0.36048	0.0:0.0:0.0:1.0	.	23	Q9NQ87	HEYL_HUMAN	G	23	ENSP00000361943:E23G	ENSP00000361943:E23G	E	-	2	0	HEYL	39877817	0.994000	0.37717	0.951000	0.38953	0.108000	0.19459	2.862000	0.48388	1.884000	0.54569	0.533000	0.62120	GAG	.	.		0.751	HEYL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001179.2	NM_014571		C	40105230	T	C	40105230	3	2	114	1	0	0	0	0	1	0	0	0	7089	1551	54	2	938	2	HEYL	1	40105230	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1621837	40105230	209145391	26	18298										
ZMPSTE24	10269	hgsc.bcm.edu	37	chr1	40751681	40751681	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggaagttgggacatacagtcAaaaatatcattattagccag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:40751681delA	ENST00000372759.3	+	8	1204	c.1039delA	c.(1039-1041)aaafs	p.K347fs		NM_005857.4	NP_005848.2	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	347					CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235)			endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	16	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			ACATACAGTCAAAAATATCAT	0.368																																					p.V346fs		Atlas-INDEL	.											ZMPSTE24,NS,carcinoma,0,1	ZMPSTE24	50	.	0			c.1038delC						.						105	104	104					1																	40751681		2203	4300	6503	SO:0001589	frameshift_variant	10269	exon8			.	Y13834	CCDS449.1	1p34	2014-09-17	2012-12-10		ENSG00000084073	ENSG00000084073	3.4.24.84		12877	protein-coding gene	gene with protein product	"Hutchinson-Gilford progeria syndrome", "CAAX prenyl protease 1 homolog"	606480	"zinc metalloproteinase (STE24 homolog, yeast)", "zinc metallopeptidase (STE24 homolog, yeast)", "zinc metallopeptidase STE24 homolog (S. cerevisiae)"			10373325, 9700155, 16671095	Standard	NM_005857		Approved	FACE-1, Ste24p, STE24, HGPS, PRO1	uc001cfg.4	O75844	OTTHUMG00000005762	ENST00000372759.3:c.1039delA	chr1.hg19:g.40751681delA	ENSP00000361845:p.Lys347fs	210.0	0.0		260.0	16.0	NM_005857	B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2	Frame_Shift_Del	DEL	ENST00000372759.3	hg19	CCDS449.1																																																																																			.	.		0.368	ZMPSTE24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015766.1			-	40751681	A	-	40751681	7	5	114	1	0	1	0	1	0	0	0	0	17713	131	5	0	1069	0	ZMPSTE24	1	40751681	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	646451	40751681	208498940	27	18299										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42050249	42050249	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggcttctgctgctggcccgTtttctcctgagagccttccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:42050249delT	ENST00000372583.1	-	4	1105	c.220delA	c.(220-222)acgfs	p.T74fs	HIVEP3_ENST00000429157.2_Frame_Shift_Del_p.T74fs|HIVEP3_ENST00000372584.1_Frame_Shift_Del_p.T74fs|HIVEP3_ENST00000247584.5_Frame_Shift_Del_p.T74fs	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	74					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TGCTGGCCCGTTTTCTCCTGA	0.632																																					p.T74fs		Atlas-INDEL	.											.	HIVEP3	235	.	0			c.221delC						.						90	106	100					1																	42050249		2203	4300	6503	SO:0001589	frameshift_variant	59269	exon4			.	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.220delA	chr1.hg19:g.42050249delT	ENSP00000361664:p.Thr74fs	126.0	0.0		179.0	12.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Frame_Shift_Del	DEL	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.		0.632	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		-	42050249	T	-	42050249	7	5	114	1	0	1	0	1	0	0	0	0	7197	1725	60	0	7024	0	HIVEP3	1	42050249	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1298568	42050249	207200372	28	18300										
MUTYH	4595	hgsc.bcm.edu	37	chr1	45797094	45797094	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attccgctgctcacttacctCcccaaggtgccggaggtgcg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:45797094delC	ENST00000372098.3	-	13	1445	c.1312delG	c.(1312-1314)gagfs	p.E438fs	MUTYH_ENST00000372100.5_Frame_Shift_Del_p.E424fs|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000355498.2_Frame_Shift_Del_p.E413fs|MUTYH_ENST00000372104.1_Frame_Shift_Del_p.E413fs|MUTYH_ENST00000456914.2_Frame_Shift_Del_p.E413fs|MUTYH_ENST00000488731.2_Frame_Shift_Del_p.E108fs|MUTYH_ENST00000354383.6_Frame_Shift_Del_p.E414fs|MUTYH_ENST00000450313.1_Frame_Shift_Del_p.E441fs|MUTYH_ENST00000372115.3_Frame_Shift_Del_p.E427fs|MUTYH_ENST00000528332.2_Frame_Shift_Del_p.E122fs|MUTYH_ENST00000372110.3_Frame_Shift_Del_p.E428fs|MUTYH_ENST00000529984.1_Frame_Shift_Del_p.E108fs|MUTYH_ENST00000448481.1_Frame_Shift_Del_p.E424fs|MUTYH_ENST00000528013.2_Frame_Shift_Del_p.E427fs			Q9UIF7	MUTYH_HUMAN	mutY homolog	438	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TCACTTACCTCCCCAAGGTGC	0.602			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.E441fs		Atlas-INDEL	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.1322delA						.						46	48	48					1																	45797094		2203	4300	6503	SO:0001589	frameshift_variant	4595	exon13	Familial Cancer Database	MAP, MYH-associated polyposis	.	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.1312delG	chr1.hg19:g.45797094delC	ENSP00000361170:p.Glu438fs	140.0	0.0		159.0	12.0	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Frame_Shift_Del	DEL	ENST00000372098.3	hg19	CCDS520.1																																																																																			.	.		0.602	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		-	45797094	C	-	45797094	7	5	114	1	0	1	0	1	0	0	0	0	10002	864	30	0	344	0	MUTYH	1	45797094	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3746845	45797094	203453527	29	18301										
TMEM69	51249	hgsc.bcm.edu	37	chr1	46158890	46158890	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgtagatactgaagtactcTttcccagtgggactaagaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:46158890delT	ENST00000372025.4	+	3	1214	c.57delT	c.(55-57)tctfs	p.S19fs	TMEM69_ENST00000496366.1_3'UTR|RP11-767N6.7_ENST00000430643.1_RNA	NM_016486.3	NP_057570.2	Q5SWH9	TMM69_HUMAN	transmembrane protein 69	19						integral component of membrane (GO:0016021)				kidney(3)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(166;0.155)					TGAAGTACTCTTTCCCAGTGG	0.358																																					p.S19fs		Atlas-INDEL	.											.	TMEM69	20	.	0			c.56delC						.						145	141	142					1																	46158890		1831	4082	5913	SO:0001589	frameshift_variant	51249	exon3			.	BC040289, BC013608	CCDS41325.1	1p34.1	2008-02-05	2005-08-17	2005-08-17	ENSG00000159596	ENSG00000159596			28035	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 154"	C1orf154			Standard	NM_016486		Approved	FLJ21029	uc001cor.1	Q5SWH9	OTTHUMG00000040993	ENST00000372025.4:c.57delT	chr1.hg19:g.46158890delT	ENSP00000361095:p.Ser19fs	136.0	0.0		165.0	10.0	NM_016486	Q3SWW5|Q7Z2G0|Q9P0P9	Frame_Shift_Del	DEL	ENST00000372025.4	hg19	CCDS41325.1																																																																																			.	.		0.358	TMEM69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098390.1	NM_016486		-	46158890	T	-	46158890	7	5	114	1	0	1	0	1	0	0	0	0	16213	1596	56	0	63	0	TMEM69	1	46158890	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	361796	46158890	203091731	30	18302										
DMBX1	127343	hgsc.bcm.edu	37	chr1	46976722	46976722	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggggaaggcaaggccgaggCccccactccagatacccagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:46976722delC	ENST00000360032.3	+	3	463	c.449delC	c.(448-450)gccfs	p.A150fs	DMBX1_ENST00000371956.4_Frame_Shift_Del_p.A155fs	NM_172225.1	NP_757379.1			diencephalon/mesencephalon homeobox 1											endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)					AAGGCCGAGGCCCCCACTCCA	0.647																																					p.A155fs		Atlas-INDEL	.											.	DMBX1	50	.	0			c.463delG						.						52	63	59					1																	46976722		2203	4300	6503	SO:0001589	frameshift_variant	127343	exon3			.	AB037699	CCDS536.1	1p34.1	2011-06-20	2004-03-29	2004-03-30	ENSG00000197587	ENSG00000197587		"Homeoboxes / PRD class"	19026	protein-coding gene	gene with protein product		607410	"orthodenticle homolog 3 (Drosophila)"	OTX3			Standard	NM_147192		Approved	PAXB	uc001cpx.3	Q8NFW5	OTTHUMG00000007982	ENST00000360032.3:c.449delC	chr1.hg19:g.46976722delC	ENSP00000353132:p.Ala150fs	165.0	0.0		198.0	14.0	NM_147192		Frame_Shift_Del	DEL	ENST00000360032.3	hg19	CCDS536.1																																																																																			.	.		0.647	DMBX1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021895.1			-	46976722	C	-	46976722	7	5	114	1	0	1	0	1	0	0	0	0	4580	739	26	0	474	0	DMBX1	1	46976722	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	817832	46976722	202273899	31	18303										
TMEM59	9528	hgsc.bcm.edu	37	chr1	54506473	54506473	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcactttctccatcttcaagAaaattcctgtgcgcttgtga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:54506473delA	ENST00000234831.5	-	6	912	c.663delT	c.(661-663)tttfs	p.F221fs	TMEM59_ENST00000371341.1_Frame_Shift_Del_p.F90fs|TMEM59_ENST00000371348.1_Frame_Shift_Del_p.F90fs|TMEM59_ENST00000371344.1_Frame_Shift_Del_p.F90fs	NM_004872.3	NP_004863.2	Q9BXS4	TMM59_HUMAN	transmembrane protein 59	221					autophagy (GO:0006914)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of protein glycosylation in Golgi (GO:0090285)|negative regulation of protein processing (GO:0010955)|positive regulation of autophagy (GO:0010508)	extracellular vesicular exosome (GO:0070062)|Golgi cis cisterna (GO:0000137)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			kidney(3)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7						CATCTTCAAGAAAATTCCTGT	0.343																																					p.L222fs		Atlas-INDEL	.											.	TMEM59	28	.	0			c.664delC						.						103	104	104					1																	54506473		2203	4300	6503	SO:0001589	frameshift_variant	9528	exon6			.	AF047439	CCDS586.1	1p32.3	2008-05-14	2005-07-22	2005-07-22	ENSG00000116209	ENSG00000116209			1239	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 8"	C1orf8		9653160	Standard	NM_004872		Approved	HSPC001	uc001cwp.3	Q9BXS4	OTTHUMG00000008437	ENST00000234831.5:c.663delT	chr1.hg19:g.54506473delA	ENSP00000234831:p.Phe221fs	186.0	0.0		190.0	13.0	NM_004872	B3KQL7|O75393|Q4VBP9|Q5T705|Q96KX7	Frame_Shift_Del	DEL	ENST00000234831.5	hg19	CCDS586.1																																																																																			.	.		0.343	TMEM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023254.2	NM_004872		-	54506473	A	-	54506473	7	5	114	1	0	1	0	1	0	0	0	0	16200	243	9	0	320	0	TMEM59	1	54506473	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	7529751	54506473	194744148	32	18304										
PCSK9	255738	hgsc.bcm.edu	37	chr1	55523861	55523861	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaacctggtggccgccctgCcccccagcacccatggggca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:55523861delC	ENST00000302118.5	+	8	1623	c.1333delC	c.(1333-1335)cccfs	p.P446fs	PCSK9_ENST00000543384.1_Intron|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	446					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						GGCCGCCCTGCCCCCCAGCAC	0.622																																					p.L444fs	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-INDEL	.											.	PCSK9	76	.	0			c.1332delG						.						33	34	34					1																	55523861		2203	4300	6503	SO:0001589	frameshift_variant	255738	exon8			.	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"hypercholesterolemia, autosomal dominant 3"	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1333delC	chr1.hg19:g.55523861delC	ENSP00000303208:p.Pro446fs	168.0	0.0		171.0	12.0	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Frame_Shift_Del	DEL	ENST00000302118.5	hg19	CCDS603.1																																																																																			.	.		0.622	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		-	55523861	C	-	55523861	7	5	114	1	0	1	0	1	0	0	0	0	11615	739	26	0	1363	0	PCSK9	1	55523861	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1017388	55523861	193726760	33	18305										
PPAP2B	8613	hgsc.bcm.edu	37	chr1	56990119	56990119	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gactggctgatggcacagccAaagaggaagcagcccacttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:56990119delA	ENST00000371250.3	-	3	956	c.405delT	c.(403-405)tttfs	p.F135fs		NM_003713.4	NP_003704.3	O14495	LPP3_HUMAN	phosphatidic acid phosphatase type 2B	135					Bergmann glial cell differentiation (GO:0060020)|blood vessel development (GO:0001568)|canonical Wnt signaling pathway involved in positive regulation of cell-cell adhesion (GO:0044329)|canonical Wnt signaling pathway involved in positive regulation of endothelial cell migration (GO:0044328)|canonical Wnt signaling pathway involved in positive regulation of wound healing (GO:0044330)|dephosphorylation (GO:0016311)|gastrulation with mouth forming second (GO:0001702)|germ cell migration (GO:0008354)|homotypic cell-cell adhesion (GO:0034109)|lipid metabolic process (GO:0006629)|negative regulation of protein phosphorylation (GO:0001933)|phospholipid metabolic process (GO:0006644)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of sphingolipid mediated signaling pathway (GO:1902068)|regulation of Wnt signaling pathway (GO:0030111)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)|sphingosine-1-phosphate phosphatase activity (GO:0042392)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						TGGCACAGCCAAAGAGGAAGC	0.532																																					p.G136fs		Atlas-INDEL	.											.	PPAP2B	30	.	0			c.406delG						.						91	96	94					1																	56990119		2203	4300	6503	SO:0001589	frameshift_variant	8613	exon3			.	AB000889	CCDS604.1	1p32.2	2009-05-27			ENSG00000162407	ENSG00000162407	3.1.3.4		9229	protein-coding gene	gene with protein product		607125				9305923	Standard	NM_003713		Approved	PAP-2b, LPP3	uc001cyj.2	O14495	OTTHUMG00000008160	ENST00000371250.3:c.405delT	chr1.hg19:g.56990119delA	ENSP00000360296:p.Phe135fs	109.0	0.0		151.0	10.0	NM_003713	B2R651|D3DQ52|Q5U0F7|Q96GW0|Q99782	Frame_Shift_Del	DEL	ENST00000371250.3	hg19	CCDS604.1																																																																																			.	.		0.532	PPAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022334.2	NM_003713		-	56990119	A	-	56990119	7	5	114	1	0	1	0	1	0	0	0	0	12300	127	5	0	546	0	PPAP2B	1	56990119	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1466258	56990119	192260502	34	18306										
INADL	10207	hgsc.bcm.edu	37	chr1	62550289	62550289	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggacgttcagggcttggtcTcagcattgtgggaggaaaag	17	6	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:62550289T>C	ENST00000371158.2	+	33	4460	c.4346T>C	c.(4345-4347)cTc>cCc	p.L1449P	INADL_ENST00000543708.1_Missense_Mutation_p.L233P|INADL_ENST00000545929.1_Missense_Mutation_p.L122P|INADL_ENST00000316485.6_Missense_Mutation_p.L1449P	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1449	PDZ 8. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GGGCTTGGTCTCAGCATTGTG	0.468																																					p.L1449P		Atlas-SNP	.											.	INADL	179	.	0			c.T4346C						.						102	101	101					1																	62550289		2203	4300	6503	SO:0001583	missense	10207	exon33			TTGGTCTCAGCAT	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4346T>C	chr1.hg19:g.62550289T>C	ENSP00000360200:p.Leu1449Pro	108.0	0.0		110.0	5.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	T	19.94	3.919454	0.73098	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000543708;ENST00000545929	T;T;T;T	0.31510	1.96;1.49;1.49;1.96	5.02	5.02	0.67125	PDZ/DHR/GLGF (4);	0.000000	0.56097	D	0.000022	T	0.65739	0.2720	M	0.93507	3.425	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.984	D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;1.0;0.952	T	0.76451	-0.2954	10	0.87932	D	0	.	15.0292	0.71694	0.0:0.0:0.0:1.0	.	122;233;908;1449;1449;1449	F5GY89;B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;.;INADL_HUMAN;.	P	1449;1449;1449;1449;233;122	ENSP00000360200:L1449P;ENSP00000326199:L1449P;ENSP00000445790:L233P;ENSP00000440094:L122P	ENSP00000326199:L1449P	L	+	2	0	INADL	62322877	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.588000	0.74076	2.005000	0.58758	0.533000	0.62120	CTC	.	.		0.468	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		C	62550289	T	C	62550289	3	2	114	1	0	0	0	0	1	0	0	0	7740	1551	54	2	4472	2	INADL	1	62550289	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	5560170	62550289	186700332	35	18307										
DOCK7	85440	hgsc.bcm.edu	37	chr1	63114152	63114152	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaaacttgttttggcaaaccTttttgcctttctttctgttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:63114152delT	ENST00000340370.5	-	5	470	c.453delA	c.(451-453)aaafs	p.K151fs	DOCK7_ENST00000404627.2_Frame_Shift_Del_p.K151fs|DOCK7_ENST00000251157.5_Frame_Shift_Del_p.K151fs	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	151					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TTGGCAAACCTTTTTGCCTTT	0.289																																					p.G152fs		Atlas-INDEL	.											.	DOCK7	184	.	0			c.454delG						.						40	33	35					1																	63114152		2196	4290	6486	SO:0001589	frameshift_variant	85440	exon5			.		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.453delA	chr1.hg19:g.63114152delT	ENSP00000340742:p.Lys151fs	145.0	0.0		160.0	10.0	NM_001272002	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Frame_Shift_Del	DEL	ENST00000340370.5	hg19	CCDS30734.1																																																																																			.	.		0.289	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		-	63114152	T	-	63114152	7	5	114	1	0	1	0	1	0	0	0	0	4694	1606	56	0	6056	0	DOCK7	1	63114152	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	563863	63114152	186136469	36	18308										
ATG4C	84938	hgsc.bcm.edu	37	chr1	63284957	63284957	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatatggaaagaagtctgggAaaaaagcaggagattggtat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:63284957delA	ENST00000317868.4	+	5	883	c.676delA	c.(676-678)aaafs	p.K227fs	ATG4C_ENST00000371120.3_Frame_Shift_Del_p.K227fs	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	227					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						GAAGTCTGGGAAAAAAGCAGG	0.368																																					p.G225fs		Atlas-INDEL	.											.	ATG4C	96	.	0			c.675delG						.						86	86	86					1																	63284957		2203	4300	6503	SO:0001589	frameshift_variant	84938	exon5			.	AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog C (S. cerevisiae)", "ATG4 autophagy related 4 homolog C (S. cerevisiae)"	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.676delA	chr1.hg19:g.63284957delA	ENSP00000322159:p.Lys227fs	157.0	0.0		177.0	11.0	NM_178221	A6NLR8|D3DQ58|Q96K04	Frame_Shift_Del	DEL	ENST00000317868.4	hg19	CCDS623.1																																																																																			.	.		0.368	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852		-	63284957	A	-	63284957	7	5	114	1	0	1	0	1	0	0	0	0	1098	247	9	0	690	0	ATG4C	1	63284957	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	170805	63284957	185965664	37	18309										
EFCAB7	84455	hgsc.bcm.edu	37	chr1	64034025	64034025	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tatgcagaaaaatgcaagccAaaaattaaagctgtccatat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:64034025delA	ENST00000371088.4	+	12	1788	c.1542delA	c.(1540-1542)ccafs	p.P514fs	EFCAB7_ENST00000461039.1_3'UTR	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	514							calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						AATGCAAGCCAAAAATTAAAG	0.348																																					p.P514fs		Atlas-INDEL	.											.	EFCAB7	45	.	0			c.1541delC						.						80	76	77					1																	64034025		2203	4300	6503	SO:0001589	frameshift_variant	84455	exon12			.	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"EF-hand domain containing"	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.1542delA	chr1.hg19:g.64034025delA	ENSP00000360129:p.Pro514fs	100.0	0.0		143.0	10.0	NM_032437	Q658P0|Q96B95|Q96JM6	Frame_Shift_Del	DEL	ENST00000371088.4	hg19	CCDS30737.1																																																																																			.	.		0.348	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437		-	64034025	A	-	64034025	7	5	114	1	0	1	0	1	0	0	0	0	4942	117	5	0	1584	0	EFCAB7	1	64034025	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	749068	64034025	185216596	38	18310										
LEPR	3953	hgsc.bcm.edu	37	chr1	66064394	66064394	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tagtagacagtatacttcctGggtcttcgtatgaggttcag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:66064394delG	ENST00000349533.6	+	8	1086	c.901delG	c.(901-903)gggfs	p.G301fs	LEPR_ENST00000371060.3_Frame_Shift_Del_p.G301fs|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371059.3_Frame_Shift_Del_p.G301fs|LEPR_ENST00000344610.8_Frame_Shift_Del_p.G301fs|LEPR_ENST00000371058.1_Frame_Shift_Del_p.G301fs	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TATACTTCCTGGGTCTTCGTA	0.453																																					p.P300fs		Atlas-INDEL	.											.	LEPR	284	.	0			c.900delT						.						113	109	110					1																	66064394		2203	4300	6503	SO:0001589	frameshift_variant	3953	exon8			.	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.901delG	chr1.hg19:g.66064394delG	ENSP00000330393:p.Gly301fs	179.0	0.0		205.0	15.0	NM_002303	Q6FHL5	Frame_Shift_Del	DEL	ENST00000349533.6	hg19	CCDS631.1																																																																																			.	.		0.453	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		-	66064394	G	-	66064394	7	5	114	1	0	1	0	1	0	0	0	0	8737	1348	47	0	923	0	LEPR	1	66064394	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2030369	66064394	183186227	39	18311										
LEPR	3953	hgsc.bcm.edu	37	chr1	66067119	66067119	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttctgacaagtgttgggtctAatgtttcttttcactgcatc	8	8	4	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:66067119A>C	ENST00000349533.6	+	9	1224	c.1039A>C	c.(1039-1041)Aat>Cat	p.N347H	LEPR_ENST00000371060.3_Missense_Mutation_p.N347H|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371059.3_Missense_Mutation_p.N347H|LEPR_ENST00000344610.8_Missense_Mutation_p.N347H|LEPR_ENST00000371058.1_Missense_Mutation_p.N347H	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TGTTGGGTCTAATGTTTCTTT	0.343																																					p.N347H		Atlas-SNP	.											.	LEPR	284	.	0			c.A1039C						.						123	118	120					1																	66067119		2203	4300	6503	SO:0001583	missense	3953	exon9			GGGTCTAATGTTT	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.1039A>C	chr1.hg19:g.66067119A>C	ENSP00000330393:p.Asn347His	66.0	0.0		79.0	28.0	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	hg19	CCDS631.1	.	.	.	.	.	.	.	.	.	.	A	16.20	3.056426	0.55325	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37	4.98	4.98	0.66077	Immunoglobulin-like (1);Immunoglobulin C2-set-like, ligand-binding (1);Immunoglobulin-like fold (1);	0.277175	0.45606	D	0.000356	D	0.86916	0.6048	M	0.73598	2.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.991	D	0.88639	0.3174	10	0.66056	D	0.02	-24.6842	14.8343	0.70172	1.0:0.0:0.0:0.0	.	347;347;347	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	H	347	ENSP00000340884:N347H;ENSP00000330393:N347H;ENSP00000360099:N347H;ENSP00000360098:N347H;ENSP00000360097:N347H	ENSP00000340884:N347H	N	+	1	0	LEPR	65839707	1.000000	0.71417	0.436000	0.26797	0.618000	0.37518	6.549000	0.73900	2.087000	0.62958	0.533000	0.62120	AAT	.	.		0.343	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		C	66067119	A	C	66067119	3	2	114	1	0	0	0	0	1	0	0	0	8737	362	13	5	1065	5	LEPR	1	66067119	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2725	66067119	183183502	40	18312										
RPE65	6121	hgsc.bcm.edu	37	chr1	68896995	68896995	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acaaagtgattcaagccaagTccatacgcatatgtgtaagg	9	8	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:68896995T>C	ENST00000262340.5	-	12	1361	c.1308A>G	c.(1306-1308)ggA>ggG	p.G436G		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	436			G -> V (in RP20). {ECO:0000269|PubMed:11095629}.		cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						TCAAGCCAAGTCCATACGCAT	0.353																																					p.G436G		Atlas-SNP	.											.	RPE65	87	.	0			c.A1308G						.						99	91	94					1																	68896995		2203	4300	6503	SO:0001819	synonymous_variant	6121	exon12			GCCAAGTCCATAC	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.1308A>G	chr1.hg19:g.68896995T>C		113.0	0.0		93.0	4.0	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	hg19	CCDS643.1																																																																																			.	.		0.353	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		C	68896995	T	C	68896995	2	2	114	1	0	0	0	0	0	0	0	1	13560	1654	58	2		2	RPE65	1	68896995	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2829876	68896995	180353626	41	18313										
LRRC40	55631	hgsc.bcm.edu	37	chr1	70618181	70618181	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatataaaggaaagtttattAaaactgagatcgacatcaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:70618181delA	ENST00000370952.3	-	12	1453	c.1374delT	c.(1372-1374)tttfs	p.F458fs		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	458						membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						AAAGTTTATTAAAACTGAGAT	0.303																																					p.N459fs		Atlas-INDEL	.											.	LRRC40	66	.	0			c.1375delA						.						75	74	75					1																	70618181		2203	4298	6501	SO:0001589	frameshift_variant	55631	exon12			.		CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1374delT	chr1.hg19:g.70618181delA	ENSP00000359990:p.Phe458fs	189.0	0.0		237.0	16.0	NM_017768	Q9BTR7|Q9NSK1|Q9NXC1	Frame_Shift_Del	DEL	ENST00000370952.3	hg19	CCDS646.1																																																																																			.	.		0.303	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		-	70618181	A	-	70618181	7	5	114	1	0	1	0	1	0	0	0	0	9007	359	13	0	450	0	LRRC40	1	70618181	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1721186	70618181	178632440	42	18314										
NEXN	91624	hgsc.bcm.edu	37	chr1	78408251	78408251	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catggttcaagaagcctcttAaaaacacatcagttgtagac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:78408251delA	ENST00000334785.7	+	13	1949	c.1765delA	c.(1765-1767)aaafs	p.K589fs	NEXN_ENST00000457030.1_Frame_Shift_Del_p.K575fs|NEXN_ENST00000480732.2_3'UTR|NEXN_ENST00000330010.8_Frame_Shift_Del_p.K525fs|FUBP1_ENST00000489495.1_5'Flank	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		GAAGCCTCTTAAAAACACATC	0.438																																					p.L588fs		Atlas-INDEL	.											.	NEXN	77	.	0			c.1764delT						.						100	98	99					1																	78408251		1893	4103	5996	SO:0001589	frameshift_variant	91624	exon13			.	AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"Immunoglobulin superfamily / I-set domain containing"	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.1765delA	chr1.hg19:g.78408251delA	ENSP00000333938:p.Lys589fs	120.0	0.0		138.0	10.0	NM_144573		Frame_Shift_Del	DEL	ENST00000334785.7	hg19	CCDS41351.1																																																																																			.	.		0.438	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573		-	78408251	A	-	78408251	7	5	114	1	0	1	0	1	0	0	0	0	10364	363	13	0	1811	0	NEXN	1	78408251	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	7790070	78408251	170842370	43	18315										
IFI44L	10964	hgsc.bcm.edu	37	chr1	79101136	79101136	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gactgtgcatggatgacattCcccacatcttaaaaggttgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:79101136delC	ENST00000370751.5	+	5	1017	c.838delC	c.(838-840)cccfs	p.P280fs	IFI44L_ENST00000342282.3_Frame_Shift_Del_p.P22fs|IFI44L_ENST00000476521.1_3'UTR	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	280					defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)				endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						GGATGACATTCCCCACATCTT	0.368																																					p.I279fs		Atlas-INDEL	.											.	IFI44L	93	.	0			c.837delT						.						145	143	144					1																	79101136		2203	4300	6503	SO:0001589	frameshift_variant	10964	exon5			.	AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"chromosome 1 open reading frame 29"	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.838delC	chr1.hg19:g.79101136delC	ENSP00000359787:p.Pro280fs	103.0	0.0		132.0	10.0	NM_006820	Q86TE1|Q96B64|Q99984	Frame_Shift_Del	DEL	ENST00000370751.5	hg19	CCDS687.2																																																																																			.	.		0.368	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820		-	79101136	C	-	79101136	7	5	114	1	0	1	0	1	0	0	0	0	7527	855	30	0	852	0	IFI44L	1	79101136	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	692885	79101136	170149485	44	18316										
IFI44	10561	hgsc.bcm.edu	37	chr1	79115893	79115893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caagaagtatggcagtgacaActcgtttgacatggttgcac	11	8	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:79115893A>G	ENST00000370747.4	+	2	98	c.13A>G	c.(13-15)Act>Gct	p.T5A	IFI44_ENST00000495254.1_Intron|IFI44_ENST00000545124.1_Intron	NM_006417.4	NP_006408.3	Q8TCB0	IFI44_HUMAN	interferon-induced protein 44	5					response to virus (GO:0009615)	cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21						GGCAGTGACAACTCGTTTGAC	0.358																																					p.T5A		Atlas-SNP	.											.	IFI44	55	.	0			c.A13G						.						91	85	87					1																	79115893		2203	4300	6503	SO:0001583	missense	10561	exon2			GTGACAACTCGTT	D28915	CCDS688.1	1p31.1	2013-03-14			ENSG00000137965	ENSG00000137965			16938	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 5"	610468				7925411	Standard	NM_006417		Approved	MTAP44, p44, TLDC5	uc001dip.4	Q8TCB0	OTTHUMG00000009723	ENST00000370747.4:c.13A>G	chr1.hg19:g.79115893A>G	ENSP00000359783:p.Thr5Ala	117.0	0.0		141.0	6.0	NM_006417	B7ZAG3|D3DQ80|Q14496	Missense_Mutation	SNP	ENST00000370747.4	hg19	CCDS688.1	.	.	.	.	.	.	.	.	.	.	A	8.520	0.868638	0.17322	.	.	ENSG00000137965	ENST00000370747	T	0.08896	3.04	3.3	2.17	0.27698	.	0.075957	0.53938	D	0.000047	T	0.09555	0.0235	M	0.64404	1.975	0.21105	N	0.999787	D;D	0.76494	0.999;0.999	D;D	0.75484	0.986;0.981	T	0.08351	-1.0726	10	0.46703	T	0.11	-10.591	5.2677	0.15607	0.8668:0.0:0.1332:0.0	.	5;5	B7ZB11;Q8TCB0	.;IFI44_HUMAN	A	5	ENSP00000359783:T5A	ENSP00000359783:T5A	T	+	1	0	IFI44	78888481	0.601000	0.26907	0.207000	0.23584	0.023000	0.10783	0.704000	0.25661	0.656000	0.30886	-0.467000	0.05162	ACT	.	.		0.358	IFI44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026825.1	NM_006417		G	79115893	A	G	79115893	3	3	114	1	0	0	0	0	1	0	0	0	7526	43	2	2	15	2	IFI44	1	79115893	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	14757	79115893	170134728	45	18317										
RPF1	80135	hgsc.bcm.edu	37	chr1	84945079	84945079	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggatggggcgacggaaaacGgggtccaacccccgaaagcg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:84945079delG	ENST00000370654.5	+	1	130	c.115delG	c.(115-117)gggfs	p.G39fs	RPF1_ENST00000370656.1_Frame_Shift_Del_p.G39fs	NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN	ribosome production factor 1 homolog (S. cerevisiae)	39					rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						GACGGAAAACGGGGTCCAACC	0.557																																					p.N38fs		Atlas-INDEL	.											.	RPF1	31	.	0			c.114delC						.						29	34	32					1																	84945079		2203	4300	6503	SO:0001589	frameshift_variant	80135	exon1			.	AF322053	CCDS695.1	1p22.3	2009-09-25	2009-09-25	2009-09-25	ENSG00000117133	ENSG00000117133			30350	protein-coding gene	gene with protein product	"RNA processing factor 1", "ribosome production factor 1"		"brix domain containing 5"	BXDC5		11864606	Standard	NM_025065		Approved		uc001djv.4	Q9H9Y2	OTTHUMG00000009857	ENST00000370654.5:c.115delG	chr1.hg19:g.84945079delG	ENSP00000359688:p.Gly39fs	136.0	0.0		155.0	10.0	NM_025065	Q5VSK7|Q6AHX1|Q8WXZ8	Frame_Shift_Del	DEL	ENST00000370654.5	hg19	CCDS695.1																																																																																			.	.		0.557	RPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027238.1	NM_025065		-	84945079	G	-	84945079	7	5	114	1	0	1	0	1	0	0	0	0	13561	1116	39	0	117	0	RPF1	1	84945079	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	5829186	84945079	164305542	46	18318										
PKN2	5586	hgsc.bcm.edu	37	chr1	89206728	89206728	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgctgttcaaaaattagacTtttcagatacaatggtgcag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:89206728delT	ENST00000370521.3	+	2	465	c.106delT	c.(106-108)tttfs	p.F36fs	PKN2_ENST00000370505.3_Intron|PKN2_ENST00000316005.7_Frame_Shift_Del_p.F36fs|PKN2_ENST00000370513.5_Frame_Shift_Del_p.F36fs	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	36					apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		AAAATTAGACTTTTCAGATAC	0.363																																					p.D35fs		Atlas-INDEL	.											.	PKN2	109	.	0			c.105delC						.						88	82	84					1																	89206728		1825	4091	5916	SO:0001589	frameshift_variant	5586	exon2			.	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"cardiolipin-activated protein kinase Pak2"	602549	"protein kinase C-like 2"	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.106delT	chr1.hg19:g.89206728delT	ENSP00000359552:p.Phe36fs	108.0	0.0		135.0	11.0	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Frame_Shift_Del	DEL	ENST00000370521.3	hg19	CCDS714.1																																																																																			.	.		0.363	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		-	89206728	T	-	89206728	7	5	114	1	0	1	0	1	0	0	0	0	11989	1609	56	0	112	0	PKN2	1	89206728	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	4261649	89206728	160043893	47	18319										
GBP5	115362	hgsc.bcm.edu	37	chr1	89729600	89729600	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atgcttccaggttccgtttaCaaatgtcattctgttttgca	7	9	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:89729600C>A	ENST00000370459.3	-	8	1308	c.1181G>T	c.(1180-1182)tGt>tTt	p.C394F	RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000471171.1_5'Flank|GBP5_ENST00000343435.5_Missense_Mutation_p.C394F			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	394						cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		GTTCCGTTTACAAATGTCATT	0.368																																					p.C394F		Atlas-SNP	.											.	GBP5	65	.	0			c.G1181T						.						136	141	139					1																	89729600		2203	4300	6503	SO:0001583	missense	115362	exon9			CGTTTACAAATGT	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.1181G>T	chr1.hg19:g.89729600C>A	ENSP00000359488:p.Cys394Phe	68.0	0.0		92.0	10.0	NM_052942	B2RCE1|Q86TM5	Missense_Mutation	SNP	ENST00000370459.3	hg19	CCDS722.1	.	.	.	.	.	.	.	.	.	.	C	8.934	0.964062	0.18583	.	.	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	T;T;T	0.54675	0.56;0.56;0.56	5.12	-1.2	0.09554	Guanylate-binding protein, C-terminal (3);	0.566743	0.20220	N	0.096703	T	0.18509	0.0444	L	0.46741	1.465	0.09310	N	1	B	0.18310	0.027	B	0.28385	0.089	T	0.24440	-1.0160	10	0.39692	T	0.17	0.5771	1.786	0.03041	0.1275:0.3928:0.1245:0.3552	.	394	Q96PP8	GBP5_HUMAN	F	394	ENSP00000340396:C394F;ENSP00000359488:C394F;ENSP00000403010:C394F	ENSP00000340396:C394F	C	-	2	0	GBP5	89502188	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.404000	0.07205	-0.262000	0.09392	-0.335000	0.08231	TGT	.	.		0.368	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942		A	89729600	C	A	89729600	3	1	114	1	0	0	0	0	1	0	0	0	6285	478	17	3	595	3	GBP5	1	89729600	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	522872	89729600	159521021	48	18320										
GBP6	163351	hgsc.bcm.edu	37	chr1	89847413	89847413	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atggcccagcgagtgaagctCcccacagacacgctccagga	11	15	0	2	rs373830740		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:89847413C>T	ENST00000370456.4	+	7	1125	c.1032C>T	c.(1030-1032)ctC>ctT	p.L344L	GBP6_ENST00000535065.1_Silent_p.L214L	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	344			L -> F (in dbSNP:rs4658360). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		GAGTGAAGCTCCCCACAGACA	0.572																																					p.L344L		Atlas-SNP	.											.	GBP6	87	.	0			c.C1032T						.						81	74	76					1																	89847413		2203	4300	6503	SO:0001819	synonymous_variant	163351	exon7			GAAGCTCCCCACA	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.1032C>T	chr1.hg19:g.89847413C>T		173.0	0.0		221.0	9.0	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Silent	SNP	ENST00000370456.4	hg19	CCDS723.1																																																																																			.	.		0.572	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460		T	89847413	C	T	89847413	2	4	114	1	0	0	0	0	0	0	0	1	6286	842	30	3		3	GBP6	1	89847413	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	117813	89847413	159403208	49	18321										
HFM1	164045	hgsc.bcm.edu	37	chr1	91844032	91844032	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcctagtcatgctatcccaTttttcctagagagaaaaaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:91844032delT	ENST00000370425.3	-	10	1262	c.1164delA	c.(1162-1164)aaafs	p.K388fs	HFM1_ENST00000370424.3_Frame_Shift_Del_p.K67fs|HFM1_ENST00000294696.5_De_novo_Start_OutOfFrame	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	388	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TGCTATCCCATTTTTCCTAGA	0.318																																					p.W389fs		Atlas-INDEL	.											.	HFM1	188	.	0			c.1165delT						.						88	85	86					1																	91844032		2203	4300	6503	SO:0001589	frameshift_variant	164045	exon10			.	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.1164delA	chr1.hg19:g.91844032delT	ENSP00000359454:p.Lys388fs	129.0	0.0		187.0	12.0	NM_001017975	B1B0B6|Q8N9Q0	Frame_Shift_Del	DEL	ENST00000370425.3	hg19	CCDS30769.2																																																																																			.	.		0.318	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		-	91844032	T	-	91844032	7	5	114	1	0	1	0	1	0	0	0	0	7092	1490	52	0	3263	0	HFM1	1	91844032	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1996619	91844032	157406589	50	18322										
BCAR3	8412	hgsc.bcm.edu	37	chr1	94140264	94140264	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgccgtggggatttggagtGggggagggtgcccatgtgac					rs141721897		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:94140264delG	ENST00000370244.1	-	4	511	c.223delC	c.(223-225)cacfs	p.H75fs	BCAR3_ENST00000370243.1_Frame_Shift_Del_p.H75fs|BCAR3_ENST00000260502.6_Frame_Shift_Del_p.H75fs	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	75					lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		GATTTGGAGTGGGGGAGGGTG	0.557																																					p.H75fs		Atlas-INDEL	.											.	BCAR3	62	.	0			c.224delA						.						68	63	65					1																	94140264		2203	4300	6503	SO:0001589	frameshift_variant	8412	exon2			.	U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"SH2 domain containing"	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.223delC	chr1.hg19:g.94140264delG	ENSP00000359264:p.His75fs	120.0	0.0		156.0	10.0	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Frame_Shift_Del	DEL	ENST00000370244.1	hg19	CCDS745.1																																																																																			.	.		0.557	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			-	94140264	G	-	94140264	7	5	114	1	0	1	0	1	0	0	0	0	1349	1348	47	0	2298	0	BCAR3	1	94140264	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2296232	94140264	155110357	51	18323										
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95356749	95356749	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catcagcaaaagatgcattcAaaatcttgtccaagaactca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:95356749delA	ENST00000271227.6	+	13	1648	c.1546delA	c.(1546-1548)aaafs	p.K516fs	SLC44A3_ENST00000529450.1_Frame_Shift_Del_p.K483fs|SLC44A3_ENST00000467909.1_Frame_Shift_Del_p.K468fs|SLC44A3_ENST00000532427.1_Frame_Shift_Del_p.K436fs|SLC44A3_ENST00000527077.1_Frame_Shift_Del_p.K448fs|SLC44A3_ENST00000446120.2_Frame_Shift_Del_p.K480fs|SLC44A3_ENST00000530397.1_3'UTR	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	516					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	AGATGCATTCAAAATCTTGTC	0.313																																					p.F515fs		Atlas-INDEL	.											.	SLC44A3	109	.	0			c.1545delC						.						102	111	108					1																	95356749		2203	4300	6503	SO:0001589	frameshift_variant	126969	exon13			.	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"Solute carriers"	28689	protein-coding gene	gene with protein product			"solute carrier family, member 3"			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.1546delA	chr1.hg19:g.95356749delA	ENSP00000271227:p.Lys516fs	150.0	0.0		189.0	12.0	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Frame_Shift_Del	DEL	ENST00000271227.6	hg19	CCDS44176.1																																																																																			.	.		0.313	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		-	95356749	A	-	95356749	7	5	114	1	0	1	0	1	0	0	0	0	14652	131	5	0	1596	0	SLC44A3	1	95356749	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1216485	95356749	153893872	52	18324										
HIAT1	64645	hgsc.bcm.edu	37	chr1	100542770	100542770	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattggaaataagaacaccaTtttactgggtctaggatttc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:100542770delT	ENST00000370152.3	+	9	1077	c.941delT	c.(940-942)attfs	p.I314fs	RP4-714D9.2_ENST00000432294.1_RNA	NM_033055.2	NP_149044.2	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	314					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|skin(1)	16		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		AAGAACACCATTTTACTGGGT	0.269																																					p.I314fs		Atlas-INDEL	.											.	HIAT1	46	.	0			c.940delA						.						95	99	98					1																	100542770		2203	4299	6502	SO:0001589	frameshift_variant	64645	exon9			.	AK096669	CCDS763.1	1p21.3	2008-02-05			ENSG00000156875	ENSG00000156875			23363	protein-coding gene	gene with protein product						9299464	Standard	NM_033055		Approved	DKFZP564L0864	uc001dst.3	Q96MC6	OTTHUMG00000010755	ENST00000370152.3:c.941delT	chr1.hg19:g.100542770delT	ENSP00000359171:p.Ile314fs	131.0	0.0		194.0	12.0	NM_033055	Q6P2N7|Q8N8K2|Q8NBV3|Q96NY0|Q9NT25	Frame_Shift_Del	DEL	ENST00000370152.3	hg19	CCDS763.1																																																																																			.	.		0.269	HIAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029657.1	NM_033055		-	100542770	T	-	100542770	7	5	114	1	0	1	0	1	0	0	0	0	7106	1493	52	0	975	0	HIAT1	1	100542770	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	5186021	100542770	148707851	53	18325										
CCDC76	54482	hgsc.bcm.edu	37	chr1	100613582	100613582	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttggccaaggaaggaaatgAaaaaaatgtcccagagaagt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:100613582delA	ENST00000370141.2	+	10	956	c.950delA	c.(949-951)gaafs	p.E317fs		NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)	317					tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										GAAGGAAATGAAAAAAATGTC	0.403																																					p.E317fs		Pindel	.											.	.	.	.	0			c.949delG						.						85	87	86					1																	100613582		2203	4300	6503	SO:0001589	frameshift_variant	54482	exon10			.	BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"coiled-coil domain containing 76"	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.950delA	chr1.hg19:g.100613582delA	ENSP00000359160:p.Glu317fs	183.0	0.0		201.0	10.0	NM_019083	Q5VVL0|Q9NW65	Frame_Shift_Del	DEL	ENST00000370141.2	hg19	CCDS765.1																																																																																			.	.		0.403	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083		-	100613582	A	-	100613582	7	5	114	1	0	1	0	1	0	0	0	0	2852	246	9	0	988	0	CCDC76	1	100613582	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	70812	100613582	148637039	54	18326										
PSRC1	84722	hgsc.bcm.edu	37	chr1	109824582	109824582	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taggctgagcctcacaccctGgggggcaggtgccactgcat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:109824582delG	ENST00000438534.2	-	4	316	c.178delC	c.(178-180)cagfs	p.Q60fs	PSRC1_ENST00000369909.2_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369904.3_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369903.2_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369907.3_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000409138.2_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000409267.1_Frame_Shift_Del_p.Q60fs	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	60					microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		CTCACACCCTGGGGGGCAGGT	0.622																																					p.Q60fs		Atlas-INDEL	.											.	PSRC1	12	.	0			c.179delA						.						16	15	16					1																	109824582		2188	4287	6475	SO:0001589	frameshift_variant	84722	exon4			.		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"differential display and activated by p53"	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.178delC	chr1.hg19:g.109824582delG	ENSP00000413591:p.Gln60fs	105.0	0.0		168.0	11.0	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Frame_Shift_Del	DEL	ENST00000438534.2	hg19																																																																																				.	.		0.622	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636		-	109824582	G	-	109824582	7	5	114	1	0	1	0	1	0	0	0	0	12731	1357	47	0	904	0	PSRC1	1	109824582	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	9211000	109824582	139426039	55	18327										
MYBPHL	343263	hgsc.bcm.edu	37	chr1	109837772	109837772	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtccacagatgcctcccctaGggggttcaccgccttgcagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:109837772delG	ENST00000357155.1	-	7	1064	c.1015delC	c.(1015-1017)ctafs	p.L339fs	MYBPHL_ENST00000477962.1_5'UTR	NM_001010985.2|NM_001265613.1	NP_001010985.2|NP_001252542.1	A2RUH7	MBPHL_HUMAN	myosin binding protein H-like	339	Ig-like C2-type 2.									central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(2)	14		all_lung(203;0.00519)|all_epithelial(167;0.00575)|Lung NSC(277;0.00822)		Colorectal(144;0.0306)|Lung(183;0.0681)|COAD - Colon adenocarcinoma(174;0.117)|Epithelial(280;0.197)|all cancers(265;0.225)		GCCTCCCCTAGGGGGTTCACC	0.577																																					p.L339fs		Atlas-INDEL	.											.	MYBPHL	28	.	0			c.1016delT						.						103	94	97					1																	109837772		2203	4300	6503	SO:0001589	frameshift_variant	343263	exon7			.	AK129834	CCDS30793.1	1p13	2013-02-11			ENSG00000221986	ENSG00000221986		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	30434	protein-coding gene	gene with protein product							Standard	NM_001010985		Approved		uc001dxk.1	A2RUH7	OTTHUMG00000012002	ENST00000357155.1:c.1015delC	chr1.hg19:g.109837772delG	ENSP00000349678:p.Leu339fs	184.0	0.0		205.0	15.0	NM_001010985	B7ZME5|Q5T2Z7	Frame_Shift_Del	DEL	ENST00000357155.1	hg19	CCDS30793.1																																																																																			.	.		0.577	MYBPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033197.1	NM_001010985		-	109837772	G	-	109837772	7	5	114	1	0	1	0	1	0	0	0	0	10024	991	35	0	57	0	MYBPHL	1	109837772	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	13190	109837772	139412849	56	18328										
DDX20	11218	hgsc.bcm.edu	37	chr1	112309341	112309341	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catagggaaatacgtctgagTttttctgatacctatcagga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:112309341delT	ENST00000369702.4	+	11	2915	c.2295delT	c.(2293-2295)agtfs	p.S765fs	DDX20_ENST00000475700.1_Frame_Shift_Del_p.S373fs	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	765					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACGTCTGAGTTTTTCTGATA	0.453																																					p.S765fs		Atlas-INDEL	.											.	DDX20	50	.	0			c.2294delG						.						107	105	106					1																	112309341		2203	4300	6503	SO:0001589	frameshift_variant	11218	exon11			.	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"DEAD-boxes"	2743	protein-coding gene	gene with protein product		606168	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2295delT	chr1.hg19:g.112309341delT	ENSP00000358716:p.Ser765fs	140.0	0.0		198.0	12.0	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Frame_Shift_Del	DEL	ENST00000369702.4	hg19	CCDS842.1																																																																																			.	.		0.453	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		-	112309341	T	-	112309341	7	5	114	1	0	1	0	1	0	0	0	0	4350	1722	60	0	2337	0	DDX20	1	112309341	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2471569	112309341	136941280	57	18329										
MAGI3	260425	hgsc.bcm.edu	37	chr1	114162410	114162410	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagtggaggaagccaaaaggAaaaagcagttaggacaggtt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:114162410delA	ENST00000307546.9	+	8	1204	c.1129delA	c.(1129-1131)aaafs	p.K378fs	MAGI3_ENST00000369617.4_Frame_Shift_Del_p.K403fs|MAGI3_ENST00000369611.4_Frame_Shift_Del_p.K378fs|MAGI3_ENST00000369615.1_Frame_Shift_Del_p.K378fs	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	403	Poly-Pro.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGCCAAAAGGAAAAAGCAGTT	0.338																																					p.R376fs		Atlas-INDEL	.											.	MAGI3	181	.	0			c.1128delG						.						99	107	104					1																	114162410		2203	4300	6503	SO:0001589	frameshift_variant	260425	exon8			.	AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.1129delA	chr1.hg19:g.114162410delA	ENSP00000304604:p.Lys378fs	184.0	0.0		213.0	14.0	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Frame_Shift_Del	DEL	ENST00000307546.9	hg19	CCDS44196.1																																																																																			.	.		0.338	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		-	114162410	A	-	114162410	7	5	114	1	0	1	0	1	0	0	0	0	9201	247	9	0	1159	0	MAGI3	1	114162410	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1853069	114162410	135088211	58	18330										
HIPK1	204851	hgsc.bcm.edu	37	chr1	114500897	114500897	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caacagacatttatagtatgTccacctgcgtttcaaagtaa	6	9	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:114500897T>C	ENST00000369558.1	+	8	2197	c.1965T>C	c.(1963-1965)tgT>tgC	p.C655C	HIPK1_ENST00000369559.4_Silent_p.C655C|HIPK1_ENST00000369554.2_Silent_p.C655C|HIPK1_ENST00000369553.1_Silent_p.C261C|HIPK1_ENST00000369561.4_Silent_p.C621C|HIPK1_ENST00000340480.4_Silent_p.C281C|HIPK1_ENST00000426820.2_Silent_p.C655C|HIPK1_ENST00000369555.2_Silent_p.C655C|HIPK1_ENST00000406344.1_Silent_p.C261C			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	655					anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTATAGTATGTCCACCTGCGT	0.458																																					p.C655C		Atlas-SNP	.											.	HIPK1	195	.	0			c.T1965C						.						77	73	75					1																	114500897		2203	4300	6503	SO:0001819	synonymous_variant	204851	exon8			AGTATGTCCACCT	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.1965T>C	chr1.hg19:g.114500897T>C		99.0	0.0		122.0	5.0	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Silent	SNP	ENST00000369558.1	hg19	CCDS867.1																																																																																			.	.		0.458	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		C	114500897	T	C	114500897	2	2	114	1	0	0	0	0	0	0	0	1	7125	1673	58	2		2	HIPK1	1	114500897	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	338487	114500897	134749724	59	18331										
PHGDH	26227	hgsc.bcm.edu	37	chr1	120266001	120266001	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttttctttgatctttagcaCccccaatgggaacagcctca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:120266001delC	ENST00000369409.4	+	3	429	c.293delC	c.(292-294)accfs	p.T98fs	PHGDH_ENST00000369407.3_Frame_Shift_Del_p.T64fs	NM_006623.3	NP_006614.2	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase	98					brain development (GO:0007420)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|G1 to G0 transition (GO:0070314)|gamma-aminobutyric acid metabolic process (GO:0009448)|glial cell development (GO:0021782)|glutamine metabolic process (GO:0006541)|glycine metabolic process (GO:0006544)|L-serine biosynthetic process (GO:0006564)|neural tube development (GO:0021915)|neuron projection development (GO:0031175)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|taurine metabolic process (GO:0019530)|threonine metabolic process (GO:0006566)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|phosphoglycerate dehydrogenase activity (GO:0004617)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	18	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)		ATCTTTAGCACCCCCAATGGG	0.527																																					p.T98fs		Atlas-INDEL	.											.	PHGDH	51	.	0			c.292delA						.						165	150	155					1																	120266001		2203	4300	6503	SO:0001589	frameshift_variant	26227	exon3			.	BC011262	CCDS904.1	1p12	2008-02-05			ENSG00000092621	ENSG00000092621	1.1.1.95		8923	protein-coding gene	gene with protein product		606879					Standard	NM_006623		Approved	SERA, PGDH, PDG	uc001ehz.3	O43175	OTTHUMG00000012100	ENST00000369409.4:c.293delC	chr1.hg19:g.120266001delC	ENSP00000358417:p.Thr98fs	209.0	0.0		239.0	16.0	NM_006623	B2RD08|Q5SZU3|Q9BQ01	Frame_Shift_Del	DEL	ENST00000369409.4	hg19	CCDS904.1																																																																																			.	.		0.527	PHGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033464.1	NM_006623		-	120266001	C	-	120266001	7	5	114	1	0	1	0	1	0	0	0	0	11850	507	18	0	303	0	PHGDH	1	120266001	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	5765104	120266001	128984620	60	18332										
NBPF16	284565	hgsc.bcm.edu	37	chr1	148744584	148744584	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctcaactctcattggctcatCctctcatgttgaatgggagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:148744584delC	ENST00000417839.1	+	6	921	c.731delC	c.(730-732)tccfs	p.S245fs		NM_001102663.1	NP_001096133	Q5SXJ2	NBPFG_HUMAN		245	NBPF 1. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4	all_hematologic(923;0.032)					ATTGGCTCATCCTCTCATGTT	0.443																																					p.S244fs		Atlas-INDEL	.											.	NBPF16	7	.	0			c.730delT						.						6	3	5					1																	148744584		630	176	806	SO:0001589	frameshift_variant	728936	exon6			.																												ENST00000417839.1:c.731delC	chr1.hg19:g.148744584delC	ENSP00000395369:p.Ser245fs	74.0	0.0		160.0	11.0	NM_001102663	A8MPT6	Frame_Shift_Del	DEL	ENST00000417839.1	hg19	CCDS41384.1																																																																																			.	.		0.443	NBPF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097693.1			-	148744584	C	-	148744584	7	5	114	1	0	1	0	1	0	0	0	0	10205	855	30	0	2822	0	NBPF16	1	148744584	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	28478583	148744584	100506037	61	18333										
ARNT	405	hgsc.bcm.edu	37	chr1	150789283	150789283	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctgaaattctctgccggccGgggggtaggagggaatgtgt					rs587670365		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:150789283delG	ENST00000358595.5	-	18	1983	c.1783delC	c.(1783-1785)cggfs	p.R595fs	ARNT_ENST00000505755.1_Frame_Shift_Del_p.R580fs|ARNT_ENST00000354396.2_Frame_Shift_Del_p.R595fs|ARNT_ENST00000515192.1_Frame_Shift_Del_p.R581fs	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	595					cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCTGCCGGCCGGGGGGTAGGA	0.527			T	ETV6	AML																																p.R595fs		Atlas-INDEL	.		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	.	ARNT	68	.	0			c.1784delG						.						83	83	83					1																	150789283		2203	4300	6503	SO:0001589	frameshift_variant	405	exon18			.	AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"Basic helix-loop-helix proteins"	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.1783delC	chr1.hg19:g.150789283delG	ENSP00000351407:p.Arg595fs	123.0	0.0		213.0	14.0	NM_001668	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Frame_Shift_Del	DEL	ENST00000358595.5	hg19	CCDS970.1																																																																																			.	.		0.527	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2			-	150789283	G	-	150789283	7	5	114	1	0	1	0	1	0	0	0	0	965	1115	39	0	606	0	ARNT	1	150789283	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2044699	150789283	98461338	62	18334										
SELENBP1	8991	hgsc.bcm.edu	37	chr1	151341939	151341939	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggcaatactggggagacttGgggtcaacatccacagtggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:151341939delG	ENST00000368868.5	-	3	244	c.153delC	c.(151-153)cccfs	p.P51fs	SELENBP1_ENST00000435071.1_5'UTR|SELENBP1_ENST00000473693.1_5'UTR|SELENBP1_ENST00000426705.2_Frame_Shift_Del_p.P93fs|SELENBP1_ENST00000447402.3_Frame_Shift_Del_p.P51fs	NM_003944.3	NP_003935.2	Q13228	SBP1_HUMAN	selenium binding protein 1	51					protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	selenium binding (GO:0008430)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|urinary_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GGGGAGACTTGGGGTCAACAT	0.607																																					p.K94fs		Atlas-INDEL	.											.	SELENBP1	44	.	0			c.280delA						.						43	39	40					1																	151341939		2203	4300	6503	SO:0001589	frameshift_variant	8991	exon3			.	U29091	CCDS995.1, CCDS58027.1, CCDS60266.1	1q21.3	2014-05-19			ENSG00000143416	ENSG00000143416			10719	protein-coding gene	gene with protein product		604188				9027582	Standard	NM_003944		Approved	hSP56, hSBP, LPSB	uc010pcy.3	Q13228	OTTHUMG00000012498	ENST00000368868.5:c.153delC	chr1.hg19:g.151341939delG	ENSP00000357861:p.Pro51fs	102.0	0.0		214.0	13.0	NM_001258289	A6NML9|A6PVW9|B2RDR3|B4DKP6|B4E1F3|Q49AQ8|Q96GX7	Frame_Shift_Del	DEL	ENST00000368868.5	hg19	CCDS995.1																																																																																			.	.		0.607	SELENBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034904.4			-	151341939	G	-	151341939	7	5	114	1	0	1	0	1	0	0	0	0	14029	1335	47	0	1305	0	SELENBP1	1	151341939	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	552656	151341939	97908682	63	18335										
SPRR1A	6698	hgsc.bcm.edu	37	chr1	152957833	152957833	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaaccaaggagccctgccacCccaaggtgcctgagccctgc	10	17	0	1	rs17882377	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:152957833C>A	ENST00000368762.1	+	1	127	c.127C>A	c.(127-129)Ccc>Acc	p.P43T	SPRR1A_ENST00000307122.2_Missense_Mutation_p.P43T			P35321	SPR1A_HUMAN	small proline-rich protein 1A	43	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.P43A(1)		breast(2)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)	7	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCCCTGCCACCCCAAGGTGCC	0.647																																					p.P43T		Atlas-SNP	.											SPRR1A,NS,carcinoma,0,1	SPRR1A	17	.	1	Substitution - Missense(1)	endometrium(1)	c.C127A						.						122	126	124					1																	152957833		2203	4300	6503	SO:0001583	missense	6698	exon2			TGCCACCCCAAGG	L05187	CCDS1032.1	1q21-q22	2008-02-05			ENSG00000169474	ENSG00000169474			11259	protein-coding gene	gene with protein product		182265				8325635	Standard	NM_005987		Approved		uc001faw.3	P35321	OTTHUMG00000014404	ENST00000368762.1:c.127C>A	chr1.hg19:g.152957833C>A	ENSP00000357751:p.Pro43Thr	182.0	0.0		363.0	0.0	NM_001199828	B1AN47|D3DV31|Q2M303|Q9UDG4	Missense_Mutation	SNP	ENST00000368762.1	hg19	CCDS1032.1	.	.	.	.	.	.	.	.	.	.	C	9.534	1.111525	0.20714	.	.	ENSG00000169474	ENST00000307122;ENST00000368762	T;T	0.10288	2.89;2.89	4.77	-1.11	0.09840	.	0.217028	0.23470	N	0.047830	T	0.01976	0.0062	.	.	.	0.25456	N	0.987967	B	0.34329	0.449	B	0.34873	0.191	T	0.43458	-0.9390	9	0.14252	T	0.57	5.8114	13.074	0.59077	0.6996:0.3004:0.0:0.0	.	43	P35321	SPR1A_HUMAN	T	43	ENSP00000307340:P43T;ENSP00000357751:P43T	ENSP00000307340:P43T	P	+	1	0	SPRR1A	151224457	0.574000	0.26684	0.960000	0.40013	0.738000	0.42128	-0.504000	0.06375	-0.541000	0.06257	-0.330000	0.08379	CCC	.	.		0.647	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987		A	152957833	C	A	152957833	3	1	114	1	0	0	0	0	1	0	0	0	15110	623	22	3	129	3	SPRR1A	1	152957833	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	1615894	152957833	96292788	64	18336										
NPR1	4881	hgsc.bcm.edu	37	chr1	153654991	153654991	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggtgtgacaggatacctgAaaattgatagcagtggcgat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:153654991delA	ENST00000368680.3	+	5	1661	c.1189delA	c.(1189-1191)aaafs	p.K397fs		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	397					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	AGGATACCTGAAAATTGATAG	0.483																																					p.L396fs	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-INDEL	.											.	NPR1	104	.	0			c.1188delG						.						124	103	110					1																	153654991		2203	4300	6503	SO:0001589	frameshift_variant	4881	exon5			.	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"guanylate cyclase A"	108960	"atrionatriuretic peptide receptor A", "natriuretic peptide receptor A"	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.1189delA	chr1.hg19:g.153654991delA	ENSP00000357669:p.Lys397fs	77.0	0.0		182.0	11.0	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Frame_Shift_Del	DEL	ENST00000368680.3	hg19	CCDS1051.1																																																																																			.	.		0.483	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		-	153654991	A	-	153654991	7	5	114	1	0	1	0	1	0	0	0	0	10603	247	9	0	1207	0	NPR1	1	153654991	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	697158	153654991	95595630	65	18337										
NUP210L	91181	hgsc.bcm.edu	37	chr1	154031143	154031143	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agatcatagacctccaaggtAaaaaatccaggatgtaatgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:154031143delA	ENST00000368559.3	-	21	2948	c.2877delT	c.(2875-2877)tttfs	p.F959fs	NUP210L_ENST00000368553.1_5'Flank|NUP210L_ENST00000271854.3_Frame_Shift_Del_p.F959fs	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	959					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CCTCCAAGGTAAAAAATCCAG	0.423																																					p.T960fs		Atlas-INDEL	.											.	NUP210L	181	.	0			c.2878delA						.						86	77	80					1																	154031143		1835	4094	5929	SO:0001589	frameshift_variant	91181	exon21			.	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2877delT	chr1.hg19:g.154031143delA	ENSP00000357547:p.Phe959fs	82.0	0.0		149.0	10.0	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Frame_Shift_Del	DEL	ENST00000368559.3	hg19	CCDS41399.1																																																																																			.	.		0.423	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		-	154031143	A	-	154031143	7	5	114	1	0	1	0	1	0	0	0	0	10770	359	13	0	2869	0	NUP210L	1	154031143	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	376152	154031143	95219478	66	18338										
ADAR	103	hgsc.bcm.edu	37	chr1	154561054	154561054	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acagatggaatgacacagtcTtttttatttggagcttttct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:154561054delT	ENST00000368474.4	-	10	3057	c.2858delA	c.(2857-2859)aagfs	p.K953fs	ADAR_ENST00000292205.5_Frame_Shift_Del_p.K996fs|ADAR_ENST00000368471.3_Frame_Shift_Del_p.K658fs	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	953	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		TGACACAGTCTTTTTTATTTG	0.443																																					p.K953fs		Atlas-INDEL	.											.	ADAR	113	.	0			c.2859delG						.						133	131	131					1																	154561054		2203	4300	6503	SO:0001589	frameshift_variant	103	exon10			.	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.2858delA	chr1.hg19:g.154561054delT	ENSP00000357459:p.Lys953fs	59.0	0.0		156.0	10.0	NM_001111	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Frame_Shift_Del	DEL	ENST00000368474.4	hg19	CCDS1071.1																																																																																			.	.		0.443	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		-	154561054	T	-	154561054	7	5	114	1	0	1	0	1	0	0	0	0	281	1609	56	0	846	0	ADAR	1	154561054	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	529911	154561054	94689567	67	18339										
DCST2	127579	hgsc.bcm.edu	37	chr1	155001838	155001838	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gttgaaggtctccagaatgtAaaaaaacttctcccattggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:155001838delA	ENST00000368424.3	-	8	1271	c.1213delT	c.(1213-1215)tacfs	p.Y405fs	DCST2_ENST00000295536.5_Frame_Shift_Del_p.Y405fs	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	405						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TCCAGAATGTAAAAAAACTTC	0.537																																					p.Y405fs		Atlas-INDEL	.											.	DCST2	80	.	0			c.1214delA						.						123	115	118					1																	155001838		2203	4300	6503	SO:0001589	frameshift_variant	127579	exon8			.	AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.1213delT	chr1.hg19:g.155001838delA	ENSP00000357409:p.Tyr405fs	93.0	0.0		209.0	13.0	NM_144622	Q2M2R2|Q8N810|Q96M03	Frame_Shift_Del	DEL	ENST00000368424.3	hg19	CCDS1082.2																																																																																			.	.		0.537	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622		-	155001838	A	-	155001838	7	5	114	1	0	1	0	1	0	0	0	0	4305	362	13	0	1140	0	DCST2	1	155001838	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	440784	155001838	94248783	68	18340										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155408163	155408163	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctctggtaatggcttctgcTtttttctggtctgttcttcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:155408163delT	ENST00000368346.3	-	5	6422	c.5783delA	c.(5782-5784)aagfs	p.K1928fs	ASH1L_ENST00000392403.3_Frame_Shift_Del_p.K1928fs			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1928					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TGGCTTCTGCTTTTTTCTGGT	0.368																																					p.K1928fs		Atlas-INDEL	.											.	ASH1L	279	.	0			c.5784delG						.						144	139	141					1																	155408163		2203	4300	6503	SO:0001589	frameshift_variant	55870	exon5			.	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.5783delA	chr1.hg19:g.155408163delT	ENSP00000357330:p.Lys1928fs	84.0	0.0		164.0	12.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Frame_Shift_Del	DEL	ENST00000368346.3	hg19																																																																																				.	.		0.368	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		-	155408163	T	-	155408163	7	5	114	1	0	1	0	1	0	0	0	0	1041	1609	56	0	3207	0	ASH1L	1	155408163	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	406325	155408163	93842458	69	18341										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155450361	155450361	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtcatgatctacaaatgaaGggggtccaatgtttttcata							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:155450361delG	ENST00000368346.3	-	3	2939	c.2300delC	c.(2299-2301)cctfs	p.P767fs	ASH1L_ENST00000392403.3_Frame_Shift_Del_p.P767fs			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	767					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TACAAATGAAGGGGGTCCAAT	0.383																																					p.P767fs		Atlas-INDEL	.											.	ASH1L	279	.	0			c.2301delT						.						134	137	136					1																	155450361		2203	4300	6503	SO:0001589	frameshift_variant	55870	exon3			.	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.2300delC	chr1.hg19:g.155450361delG	ENSP00000357330:p.Pro767fs	141.0	0.0		282.0	17.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Frame_Shift_Del	DEL	ENST00000368346.3	hg19																																																																																				.	.		0.383	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		-	155450361	G	-	155450361	7	5	114	1	0	1	0	1	0	0	0	0	1041	1000	35	0	6698	0	ASH1L	1	155450361	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	42198	155450361	93800260	70	18342										
SYT11	23208	hgsc.bcm.edu	37	chr1	155851197	155851197	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtggtggggaggctgatcctGggggcacacagtgtcacagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:155851197delG	ENST00000368324.4	+	4	1447	c.1194delG	c.(1192-1194)ctgfs	p.L398fs	SYT11_ENST00000539162.1_Frame_Shift_Del_p.L91fs	NM_152280.4	NP_689493.3	Q9BT88	SYT11_HUMAN	synaptotagmin XI	398					negative regulation of neurotransmitter secretion (GO:0046929)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(1)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;0.000162)			GGCTGATCCTGGGGGCACACA	0.587																																					p.L398fs		Atlas-INDEL	.											.	SYT11	55	.	0			c.1193delT						.						133	138	136					1																	155851197		2203	4300	6503	SO:0001589	frameshift_variant	23208	exon4			.	D38522	CCDS1122.1	1q22	2013-01-21			ENSG00000132718	ENSG00000132718		"Synaptotagmins"	19239	protein-coding gene	gene with protein product		608741				11543631	Standard	NM_152280		Approved	KIAA0080, MGC10881, MGC17226, DKFZp781D015	uc001fmg.3	Q9BT88	OTTHUMG00000014105	ENST00000368324.4:c.1194delG	chr1.hg19:g.155851197delG	ENSP00000357307:p.Leu398fs	132.0	0.0		258.0	17.0	NM_152280	Q14998|Q5W0D4|Q68CT5|Q8IXU3|Q96SU2	Frame_Shift_Del	DEL	ENST00000368324.4	hg19	CCDS1122.1																																																																																			.	.		0.587	SYT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039597.1	NM_152280		-	155851197	G	-	155851197	7	5	114	1	0	1	0	1	0	0	0	0	15482	1335	47	0	1208	0	SYT11	1	155851197	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	400836	155851197	93399424	71	18343										
SH2D2A	9047	hgsc.bcm.edu	37	chr1	156786488	156786488	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttggggacatatctgggccaGggggaactccatgagggcag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:156786488delG	ENST00000368199.3	-	1	166	c.13delC	c.(13-15)ctgfs	p.L5fs	NTRK1_ENST00000392302.2_Intron|SH2D2A_ENST00000495306.1_5'UTR|SH2D2A_ENST00000392306.2_Frame_Shift_Del_p.L5fs|SH2D2A_ENST00000368198.3_5'UTR	NM_001161443.1|NM_001161444.1|NM_003975.3	NP_001154915.1|NP_001154916.1|NP_003966.2	Q9NP31	SH22A_HUMAN	SH2 domain containing 2A	5					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|large_intestine(2)|lung(15)	18	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ATCTGGGCCAGGGGGAACTCC	0.582																																					p.L5fs		Atlas-INDEL	.											.	SH2D2A	78	.	0			c.14delT						.						90	85	87					1																	156786488		2203	4300	6503	SO:0001589	frameshift_variant	9047	exon1			.	AJ000553	CCDS1159.1, CCDS53380.1, CCDS53381.1	1q21	2013-02-14	2010-04-21		ENSG00000027869	ENSG00000027869		"SH2 domain containing"	10821	protein-coding gene	gene with protein product	"T lymphocyte specific adaptor protein", "T cell specific adapter protein TSAd", "T cell specific adpater protein TSAd"	604514	"SH2 domain protein 2A"			9468509	Standard	NM_003975		Approved	TSAd, F2771	uc009wsh.2	Q9NP31	OTTHUMG00000041305	ENST00000368199.3:c.13delC	chr1.hg19:g.156786488delG	ENSP00000357182:p.Leu5fs	83.0	0.0		156.0	10.0	NM_003975	O43817|Q5UBZ1|Q5VZS4|Q5VZS5|Q9UPA7	Frame_Shift_Del	DEL	ENST00000368199.3	hg19	CCDS1159.1																																																																																			.	.		0.582	SH2D2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098982.1	NM_003975		-	156786488	G	-	156786488	7	5	114	1	0	1	0	1	0	0	0	0	14247	991	35	0	1218	0	SH2D2A	1	156786488	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	935291	156786488	92464133	72	18344										
FCER1A	2205	hgsc.bcm.edu	37	chr1	159275825	159275825	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggtggtgatggagggccagCccctcttcctcaggtgccat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:159275825delC	ENST00000368115.1	+	5	478	c.379delC	c.(379-381)cccfs	p.P127fs	FCER1A_ENST00000368114.1_Frame_Shift_Del_p.P94fs	NM_002001.3	NP_001992.1	P12319	FCERA_HUMAN	Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide	127	Ig-like 2.				activation of JUN kinase activity (GO:0007257)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|leukotriene biosynthetic process (GO:0019370)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of type I hypersensitivity (GO:0001812)|serotonin secretion (GO:0001820)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	IgE receptor activity (GO:0019767)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(19)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_hematologic(112;0.0429)				Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043)	GGAGGGCCAGCCCCTCTTCCT	0.453																																					p.Q126fs		Atlas-INDEL	.											.	FCER1A	74	.	0			c.378delG						.						92	86	88					1																	159275825		2203	4300	6503	SO:0001589	frameshift_variant	2205	exon5			.	BC015195	CCDS1184.1	1q23	2013-01-11			ENSG00000179639	ENSG00000179639		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3609	protein-coding gene	gene with protein product		147140		FCE1A		8245459	Standard	NM_002001		Approved		uc001ftq.3	P12319	OTTHUMG00000037176	ENST00000368115.1:c.379delC	chr1.hg19:g.159275825delC	ENSP00000357097:p.Pro127fs	123.0	0.0		199.0	12.0	NM_002001		Frame_Shift_Del	DEL	ENST00000368115.1	hg19	CCDS1184.1																																																																																			.	.		0.453	FCER1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090328.2	NM_002001		-	159275825	C	-	159275825	7	5	114	1	0	1	0	1	0	0	0	0	5782	739	26	0	393	0	FCER1A	1	159275825	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2489337	159275825	89974796	73	18345										
OR10J5	127385	hgsc.bcm.edu	37	chr1	159505581	159505581	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggcacaatgaccagtgtgtAcaccgtctctgaactagcca	9	12	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:159505581A>T	ENST00000334857.2	-	1	261	c.217T>A	c.(217-219)Tac>Aac	p.Y73N		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	73						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					ACCAGTGTGTACACCGTCTCT	0.428																																					p.Y73N		Atlas-SNP	.											.	OR10J5	68	.	0			c.T217A						.						170	136	148					1																	159505581		2203	4300	6503	SO:0001583	missense	127385	exon1			GTGTGTACACCGT		CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"GPCR / Class A : Olfactory receptors"	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.217T>A	chr1.hg19:g.159505581A>T	ENSP00000334441:p.Tyr73Asn	116.0	0.0		202.0	43.0	NM_001004469	B9EH35|Q6IFH2	Missense_Mutation	SNP	ENST00000334857.2	hg19	CCDS30910.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.981560	0.34942	.	.	ENSG00000184155	ENST00000334857	T	0.00397	7.57	4.31	4.31	0.51392	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00784	0.0026	H	0.94345	3.525	0.35231	D	0.77694	D	0.89917	1.0	D	0.91635	0.999	T	0.22068	-1.0227	9	0.87932	D	0	.	11.7208	0.51680	1.0:0.0:0.0:0.0	.	73	Q8NHC4	O10J5_HUMAN	N	73	ENSP00000334441:Y73N	ENSP00000334441:Y73N	Y	-	1	0	OR10J5	157772205	0.030000	0.19436	0.510000	0.27712	0.058000	0.15608	2.989000	0.49393	1.923000	0.55706	0.377000	0.23210	TAC	.	.		0.428	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469		T	159505581	A	T	159505581	3	4	114	1	0	0	0	0	1	0	0	0	10921	391	14	4	714	4	OR10J5	1	159505581	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	229756	159505581	89745040	74	18346										
NCSTN	23385	hgsc.bcm.edu	37	chr1	160318871	160318871	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtattgactgatggccccaaCcccccttacatggttctgct					rs200450922		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:160318871delC	ENST00000294785.5	+	3	398	c.273delC	c.(271-273)aacfs	p.N91fs	NCSTN_ENST00000392212.4_Frame_Shift_Del_p.N71fs|NCSTN_ENST00000535857.1_Frame_Shift_Del_p.N91fs|NCSTN_ENST00000368063.1_Frame_Shift_Del_p.N71fs|NCSTN_ENST00000368065.4_5'Flank	NM_015331.2	NP_056146.1	Q92542	NICA_HUMAN	nicastrin	91					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2)	34	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ATGGCCCCAACCCCCCTTACA	0.478																																					p.N91fs		Atlas-INDEL	.											.	NCSTN	64	.	0			c.272delA						.																																			SO:0001589	frameshift_variant	23385	exon3			.	AF240468	CCDS1203.1	1q22-q23	2014-09-17			ENSG00000162736	ENSG00000162736			17091	protein-coding gene	gene with protein product		605254				9039502, 10993067	Standard	XM_005245053		Approved	KIAA0253, APH2	uc001fvx.3	Q92542	OTTHUMG00000033110	ENST00000294785.5:c.273delC	chr1.hg19:g.160318871delC	ENSP00000294785:p.Asn91fs	145.0	0.0		268.0	17.0	NM_015331	Q5T207|Q5T208|Q86VV5	Frame_Shift_Del	DEL	ENST00000294785.5	hg19	CCDS1203.1																																																																																			.	.		0.478	NCSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080622.1	NM_015331		-	160318871	C	-	160318871	7	5	114	1	0	1	0	1	0	0	0	0	10250	506	18	0	283	0	NCSTN	1	160318871	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	813290	160318871	88931750	75	18347										
PPOX	5498	hgsc.bcm.edu	37	chr1	161140731	161140731	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtatacactaggtcactggcAaaaactaggtaagttgggaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:161140731delA	ENST00000367999.4	+	12	1549	c.1283delA	c.(1282-1284)caafs	p.Q428fs	PPOX_ENST00000544598.1_Frame_Shift_Del_p.Q136fs|PPOX_ENST00000432542.2_Intron|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000352210.5_Frame_Shift_Del_p.Q428fs|B4GALT3_ENST00000470882.1_5'Flank	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	428					heme biosynthetic process (GO:0006783)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound biosynthetic process (GO:0006779)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of mitochondrial inner membrane (GO:0031304)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)	flavin adenine dinucleotide binding (GO:0050660)|oxygen-dependent protoporphyrinogen oxidase activity (GO:0004729)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			GGTCACTGGCAAAAACTAGGT	0.478																																					p.Q428fs		Atlas-INDEL	.											.	PPOX	34	.	0			c.1282delC						.						124	127	126					1																	161140731		2203	4300	6503	SO:0001589	frameshift_variant	5498	exon12			.	BC002357	CCDS1221.1	1q22	2008-02-05			ENSG00000143224	ENSG00000143224	1.3.3.4		9280	protein-coding gene	gene with protein product		600923	"variegate porphyria"	VP		8575762, 10457135	Standard	NM_000309		Approved	PPO	uc001fyg.2	P50336	OTTHUMG00000034342	ENST00000367999.4:c.1283delA	chr1.hg19:g.161140731delA	ENSP00000356978:p.Gln428fs	92.0	0.0		129.0	10.0	NM_001122764	D3DVG0|Q5VTW8	Frame_Shift_Del	DEL	ENST00000367999.4	hg19	CCDS1221.1																																																																																			.	.		0.478	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309		-	161140731	A	-	161140731	7	5	114	1	0	1	0	1	0	0	0	0	12360	130	5	0	1325	0	PPOX	1	161140731	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	821860	161140731	88109890	76	18348										
UHMK1	127933	hgsc.bcm.edu	37	chr1	162473569	162473569	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagttctgctattattgatcAcatatttgccagtaaagcag	7	8	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:162473569A>G	ENST00000489294.1	+	4	937	c.779A>G	c.(778-780)cAc>cGc	p.H260R	UHMK1_ENST00000538489.1_Missense_Mutation_p.H260R|UHMK1_ENST00000282169.8_3'UTR|UHMK1_ENST00000545294.1_Missense_Mutation_p.H186R	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	260	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)			endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			ATTATTGATCACATATTTGCC	0.363																																					p.H260R		Atlas-SNP	.											.	UHMK1	65	.	0			c.A779G						.						142	129	134					1																	162473569		2203	4300	6503	SO:0001583	missense	127933	exon4			TTGATCACATATT	BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332		"RNA binding motif (RRM) containing"	19683	protein-coding gene	gene with protein product		608849				12093740, 12782393	Standard	NM_175866		Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.779A>G	chr1.hg19:g.162473569A>G	ENSP00000420270:p.His260Arg	66.0	0.0		100.0	4.0	NM_175866	A8K8K4|G3V1M1|Q96C22	Missense_Mutation	SNP	ENST00000489294.1	hg19	CCDS1239.1	.	.	.	.	.	.	.	.	.	.	A	13.99	2.400809	0.42613	.	.	ENSG00000152332	ENST00000545294;ENST00000538489;ENST00000489294	T;T;T	0.63417	-0.04;-0.04;-0.04	6.07	6.07	0.98685	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.110634	0.64402	D	0.000006	T	0.16342	0.0393	N	0.03084	-0.415	.	.	.	B;B;B	0.12013	0.004;0.005;0.001	B;B;B	0.10450	0.003;0.005;0.003	T	0.12837	-1.0532	9	0.10377	T	0.69	-14.0615	9.109	0.36716	0.919:0.0:0.081:0.0	.	260;260;186	Q8TAS1-2;Q8TAS1;G3V1M1	.;UHMK1_HUMAN;.	R	186;260;260	ENSP00000441226:H186R;ENSP00000446416:H260R;ENSP00000420270:H260R	ENSP00000420270:H260R	H	+	2	0	UHMK1	160740193	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.453000	0.60061	2.326000	0.78906	0.533000	0.62120	CAC	.	.		0.363	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076788.1	NM_175866		G	162473569	A	G	162473569	3	3	114	1	0	0	0	0	1	0	0	0	16981	159	6	2	843	2	UHMK1	1	162473569	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1332838	162473569	86777052	77	18349										
ADCY10	55811	hgsc.bcm.edu	37	chr1	167806547	167806547	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgagttggacaagataagcTtttcttcagctagaaaataa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:167806547delT	ENST00000367851.4	-	22	3201	c.3017delA	c.(3016-3018)aagfs	p.K1006fs	ADCY10_ENST00000367848.1_Frame_Shift_Del_p.K914fs|ADCY10_ENST00000545172.1_Frame_Shift_Del_p.K853fs	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	1006					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						CAAGATAAGCTTTTCTTCAGC	0.378																																					p.K1006fs		Atlas-INDEL	.											.	ADCY10	175	.	0			c.3018delG						.						82	84	84					1																	167806547		2203	4300	6503	SO:0001589	frameshift_variant	55811	exon22			.	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.3017delA	chr1.hg19:g.167806547delT	ENSP00000356825:p.Lys1006fs	98.0	0.0		181.0	11.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Frame_Shift_Del	DEL	ENST00000367851.4	hg19	CCDS1265.1																																																																																			.	.		0.378	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		-	167806547	T	-	167806547	7	5	114	1	0	1	0	1	0	0	0	0	293	1609	56	0	1863	0	ADCY10	1	167806547	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	5332978	167806547	81444074	78	18350										
BLZF1	8548	hgsc.bcm.edu	37	chr1	169351458	169351458	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaatgttggcattaacaatcAaaaaaagattccatcaacag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:169351458delA	ENST00000367808.3	+	6	1379	c.956delA	c.(955-957)caafs	p.Q319fs	BLZF1_ENST00000329281.2_Frame_Shift_Del_p.Q319fs			Q9H2G9	GO45_HUMAN	basic leucine zipper nuclear factor 1	319					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|mitotic cell cycle (GO:0000278)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	14	all_hematologic(923;0.208)					ATTAACAATCAAAAAAAGATT	0.383																																					p.Q319fs		Atlas-INDEL	.											.,1	BLZF1	57	.	0			c.955delC						.						85	84	84					1																	169351458		2203	4300	6503	SO:0001589	frameshift_variant	8548	exon6			.	U79751	CCDS1278.1	1q24	2008-08-01	2008-08-01		ENSG00000117475	ENSG00000117475			1065	protein-coding gene	gene with protein product		608692				9129147	Standard	NM_003666		Approved	JEM-1	uc001gfy.3	Q9H2G9	OTTHUMG00000035453	ENST00000367808.3:c.956delA	chr1.hg19:g.169351458delA	ENSP00000356782:p.Gln319fs	65.0	0.0		170.0	12.0	NM_003666	O15298|Q5T531|Q5T533|Q9GZX4	Frame_Shift_Del	DEL	ENST00000367808.3	hg19	CCDS1278.1																																																																																			.	.		0.383	BLZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086109.1	NM_003666		-	169351458	A	-	169351458	7	5	114	1	0	1	0	1	0	0	0	0	1453	130	5	0	974	0	BLZF1	1	169351458	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1544911	169351458	79899163	79	18351										
SCYL3	57147	hgsc.bcm.edu	37	chr1	169839479	169839479	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catgtccatgacactctgggAgagttgtgaattctggagac	12	8	2	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:169839479A>G	ENST00000367770.1	-	5	589	c.542T>C	c.(541-543)cTc>cCc	p.L181P	SCYL3_ENST00000367772.4_Missense_Mutation_p.L181P|SCYL3_ENST00000367771.6_Missense_Mutation_p.L181P|SCYL3_ENST00000470238.1_5'UTR			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	181	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					ACACTCTGGGAGAGTTGTGAA	0.413																																					p.L181P		Atlas-SNP	.											.	SCYL3	116	.	0			c.T542C						.						82	82	82					1																	169839479		2203	4300	6503	SO:0001583	missense	57147	exon6			TCTGGGAGAGTTG	BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"ezrin-binding partner PACE-1"	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.542T>C	chr1.hg19:g.169839479A>G	ENSP00000356744:p.Leu181Pro	64.0	0.0		122.0	5.0	NM_020423	A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Missense_Mutation	SNP	ENST00000367770.1	hg19	CCDS1287.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.099246	0.76983	.	.	ENSG00000000457	ENST00000367772;ENST00000367771;ENST00000367770;ENST00000423670	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.064489	0.64402	D	0.000005	T	0.69433	0.3110	L	0.53729	1.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	T	0.73269	-0.4036	10	0.62326	D	0.03	-14.7759	15.1525	0.72713	1.0:0.0:0.0:0.0	.	181;181	Q8IZE3-2;Q8IZE3	.;PACE1_HUMAN	P	181	ENSP00000356746:L181P;ENSP00000356745:L181P;ENSP00000356744:L181P;ENSP00000407993:L181P	ENSP00000356744:L181P	L	-	2	0	SCYL3	168106103	1.000000	0.71417	0.657000	0.29651	0.987000	0.75469	8.491000	0.90468	2.113000	0.64589	0.455000	0.32223	CTC	.	.		0.413	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093		G	169839479	A	G	169839479	3	3	114	1	0	0	0	0	1	0	0	0	13964	304	11	2	1722	2	SCYL3	1	169839479	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	488021	169839479	79411142	80	18352										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171527040	171527040	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccaaatcctgccccacctgCcccagcccagactcaggcac					rs553054787		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:171527040delC	ENST00000338920.4	+	19	6020	c.5783delC	c.(5782-5784)gccfs	p.A1928fs	PRRC2C_ENST00000426496.2_Frame_Shift_Del_p.A1928fs|PRRC2C_ENST00000367742.3_Frame_Shift_Del_p.A1930fs|PRRC2C_ENST00000392078.3_Frame_Shift_Del_p.A1930fs	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1928	Ala-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										gccccacctgccccagcccAG	0.597																																					p.A1928fs		Atlas-INDEL	.											.	.	.	.	0			c.5782delG						.						73	62	66					1																	171527040		2177	4257	6434	SO:0001589	frameshift_variant	23215	exon19			.	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.5783delC	chr1.hg19:g.171527040delC	ENSP00000343629:p.Ala1928fs	186.0	0.0		279.0	19.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Frame_Shift_Del	DEL	ENST00000338920.4	hg19	CCDS1296.2																																																																																			.	.		0.597	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		-	171527040	C	-	171527040	7	5	114	1	0	1	0	1	0	0	0	0	1321	739	26	0	5853	0	BAT2L2	1	171527040	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1687561	171527040	77723581	81	18353										
DNM3	26052	hgsc.bcm.edu	37	chr1	172356459	172356459	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaccgtgtccactccggcaCcccctccagtggatgactcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:172356459delC	ENST00000355305.5	+	19	2420	c.2263delC	c.(2263-2265)cccfs	p.P757fs	DNM3_ENST00000358155.4_Frame_Shift_Del_p.P751fs|DNM3_ENST00000367731.1_Frame_Shift_Del_p.P747fs			Q9UQ16	DYN3_HUMAN	dynamin 3	757					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CACTCCGGCACCCCCTCCAGT	0.587																																					p.A748fs		Atlas-INDEL	.											.	DNM3	85	.	0			c.2244delA						.						28	31	30					1																	172356459		2053	4188	6241	SO:0001589	frameshift_variant	26052	exon19			.	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.2263delC	chr1.hg19:g.172356459delC	ENSP00000347457:p.Pro757fs	100.0	0.0		143.0	12.0	NM_015569	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Frame_Shift_Del	DEL	ENST00000355305.5	hg19																																																																																				.	.		0.587	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		-	172356459	C	-	172356459	7	5	114	1	0	1	0	1	0	0	0	0	4675	507	18	0	2319	0	DNM3	1	172356459	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	829419	172356459	76894162	82	18354										
SERPINC1	462	hgsc.bcm.edu	37	chr1	173876589	173876589	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtggggaaggtgtactcaccTcaagaaatgccttatggaat	12	7	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:173876589T>C	ENST00000367698.3	-	6	1335	c.1217A>G	c.(1216-1218)gAg>gGg	p.E406G		NM_000488.3	NP_000479.1	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C (antithrombin), member 1	406					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of inflammatory response (GO:0050728)|regulation of blood coagulation, intrinsic pathway (GO:2000266)|regulation of proteolysis (GO:0030162)|response to nutrient (GO:0007584)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1)	25					Ardeparin(DB00407)|Dalteparin(DB06779)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Nadroparin(DB08813)|Sulodexide(DB06271)|Tinzaparin(DB06822)	TGTACTCACCTCAAGAAATGC	0.478																																					p.E406G		Atlas-SNP	.											.	SERPINC1	57	.	0			c.A1217G						.						283	261	269					1																	173876589		2203	4300	6503	SO:0001630	splice_region_variant	462	exon6			CTCACCTCAAGAA	X68793	CCDS1313.1	1q25.1	2014-02-18	2005-08-18		ENSG00000117601	ENSG00000117601		"Serine (or cysteine) peptidase inhibitors"	775	protein-coding gene	gene with protein product	"antithrombin III", "signal peptide antithrombin part 1", "coding sequence signal peptide antithrombin part 1", "antithrombin (aa 375-432)"	107300	"serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1"	AT3		3979120, 24172014	Standard	NM_000488		Approved	ATIII, MGC22579	uc001gjt.3	P01008	OTTHUMG00000037276	ENST00000367698.3:c.1218+1A>G	chr1.hg19:g.173876589T>C		122.0	0.0		184.0	11.0	NM_000488	B2R6P0|P78439|P78447|Q13815|Q5TC78|Q7KZ43|Q7KZ97|Q9UC78	Missense_Mutation	SNP	ENST00000367698.3	hg19	CCDS1313.1	.	.	.	.	.	.	.	.	.	.	T	32	5.131952	0.94473	.	.	ENSG00000117601	ENST00000367698;ENST00000351522	D	0.86694	-2.16	5.98	5.98	0.97165	Serpin domain (3);	0.046461	0.85682	D	0.000000	D	0.92616	0.7654	M	0.90977	3.165	0.80722	D	1	D	0.60575	0.988	P	0.59825	0.864	D	0.92237	0.5797	10	0.34782	T	0.22	.	16.2018	0.82087	0.0:0.0:0.0:1.0	.	406	P01008	ANT3_HUMAN	G	406;201	ENSP00000356671:E406G	ENSP00000307953:E201G	E	-	2	0	SERPINC1	172143212	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	6.915000	0.75770	2.307000	0.77673	0.529000	0.55759	GAG	.	.		0.478	SERPINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090734.1	NM_000488	Missense_Mutation	C	173876589	T	C	173876589	5	2	114	1	0	0	0	0	0	0	1	0	14124	1565	54	2	185	2	SERPINC1	1	173876589	Splice_Site	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1520130	173876589	75374032	83	18355										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176708893	176708893	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtccgtggaagcaaccactcTcttggtgagtctgacaaata	10	10	2	2	rs371375924		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:176708893T>C	ENST00000367662.3	+	13	5094	c.3930T>C	c.(3928-3930)tcT>tcC	p.S1310S		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1310					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						GCAACCACTCTCTTGGTGAGT	0.473																																					p.S1310S		Atlas-SNP	.											.	PAPPA2	665	.	0			c.T3930C						.	T		0,3986		0,0,1993	60	59	60		3930	1.9	1	1		60	1,8325		0,1,4162	no	coding-synonymous	PAPPA2	NM_020318.2		0,1,6155	CC,CT,TT		0.012,0.0,0.0081		1310/1792	176708893	1,12311	1993	4163	6156	SO:0001819	synonymous_variant	60676	exon13			CCACTCTCTTGGT	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.3930T>C	chr1.hg19:g.176708893T>C		60.0	0.0		124.0	5.0	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.		0.473	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			C	176708893	T	C	176708893	2	2	114	1	0	0	0	0	0	0	0	1	11442	1538	54	2		2	PAPPA2	1	176708893	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2832304	176708893	72541728	84	18356										
SEC16B	89866	hgsc.bcm.edu	37	chr1	177901668	177901668	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccccagcgcccgcagctgctCccccgctggatgcggatcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:177901668delC	ENST00000308284.6	-	24	3058	c.2969delG	c.(2968-2970)ggafs	p.G990fs	SEC16B_ENST00000495165.1_5'UTR|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	990					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CGCAGCTGCTCCCCCGCTGGA	0.657																																					p.G990fs		Atlas-INDEL	.											.	SEC16B	92	.	0			c.2970delA						.						11	15	14					1																	177901668		2021	4112	6133	SO:0001589	frameshift_variant	89866	exon24			.	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"regucalcin gene promotor region related protein"	612855	"leucine zipper transcription regulator 2"	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2969delG	chr1.hg19:g.177901668delC	ENSP00000308339:p.Gly990fs	117.0	0.0		213.0	13.0	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Frame_Shift_Del	DEL	ENST00000308284.6	hg19	CCDS44281.1																																																																																			.	.		0.657	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		-	177901668	C	-	177901668	7	5	114	1	0	1	0	1	0	0	0	0	14002	855	30	0	225	0	SEC16B	1	177901668	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1192775	177901668	71348953	85	18357										
TOR1AIP1	26092	hgsc.bcm.edu	37	chr1	179887126	179887126	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attgtgaccatgaaaacgcgGccttcaaagatgtagcctta	9	9	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:179887126G>A	ENST00000606911.2	+	10	1695	c.1504G>A	c.(1504-1506)Gcc>Acc	p.A502T	TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.A518T|TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.A503T|TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.A381T			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	502	Interaction with TOR1A.				positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)	p.A502S(1)		breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						TGAAAACGCGGCCTTCAAAGA	0.423																																					p.A503T		Atlas-SNP	.											TOR1AIP1,leg,malignant_melanoma,0,1	TOR1AIP1	58	.	1	Substitution - Missense(1)	skin(1)	c.G1507A						.						94	96	95					1																	179887126		2203	4300	6503	SO:0001583	missense	26092	exon10			AACGCGGCCTTCA		CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"lamina associated polypeptide 1B"	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.1504G>A	chr1.hg19:g.179887126G>A	ENSP00000476687:p.Ala502Thr	150.0	1.0		237.0	0.0	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	hg19	CCDS1335.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.980768	0.92982	.	.	ENSG00000143337	ENST00000325993;ENST00000271583;ENST00000435319	T;T	0.35789	1.29;1.29	5.96	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.62938	0.2469	M	0.80616	2.505	0.58432	D	0.999995	D	0.89917	1.0	D	0.91635	0.999	T	0.67098	-0.5756	9	.	.	.	-8.2699	16.26	0.82535	0.0:0.0:0.8661:0.1339	.	502	Q5JTV8	TOIP1_HUMAN	T	297;518;502	ENSP00000271583:A518T;ENSP00000393292:A502T	.	A	+	1	0	TOR1AIP1	178153749	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	9.338000	0.96553	1.519000	0.48950	0.655000	0.94253	GCC	.	.		0.423	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602		A	179887126	G	A	179887126	3	1	114	1	0	0	0	0	1	0	0	0	16387	1203	42	3	1542	3	TOR1AIP1	1	179887126	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1985458	179887126	69363495	86	18358										
GLRX2	51022	hgsc.bcm.edu	37	chr1	193066820	193066820	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cattcatgtcatggaaaagcTtttttgccattgtacagtaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:193066820delT	ENST00000367439.3	-	3	302	c.254delA	c.(253-255)aagfs	p.K85fs	GLRX2_ENST00000367440.3_Frame_Shift_Del_p.K86fs|GLRX2_ENST00000472197.1_5'UTR	NM_197962.2	NP_932066.1	Q9NS18	GLRX2_HUMAN	glutaredoxin 2	85	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|DNA protection (GO:0042262)|glutathione metabolic process (GO:0006749)|protein folding (GO:0006457)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|response to hydrogen peroxide (GO:0042542)|response to organic substance (GO:0010033)|response to redox state (GO:0051775)|response to temperature stimulus (GO:0009266)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	2 iron, 2 sulfur cluster binding (GO:0051537)|arsenate reductase (glutaredoxin) activity (GO:0008794)|electron carrier activity (GO:0009055)|glutathione disulfide oxidoreductase activity (GO:0015038)|metal ion binding (GO:0046872)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|large_intestine(1)|lung(3)	5					Glutathione(DB00143)	ATGGAAAAGCTTTTTTGCCAT	0.333																																					p.K86fs		Atlas-INDEL	.											.	GLRX2	9	.	0			c.258delG						.						120	112	115					1																	193066820		2203	4300	6503	SO:0001589	frameshift_variant	51022	exon3			.	AF132495	CCDS1380.1, CCDS1381.1	1q31.2	2012-09-20			ENSG00000023572	ENSG00000023572			16065	protein-coding gene	gene with protein product	"bA101E13.1 (GRX2 glutaredoxin (thioltransferase) 2)"	606820				11297543	Standard	NM_016066		Approved	GRX2, bA101E13.1	uc001gsz.2	Q9NS18	OTTHUMG00000035677	ENST00000367439.3:c.254delA	chr1.hg19:g.193066820delT	ENSP00000356409:p.Lys85fs	113.0	0.0		187.0	12.0	NM_016066	Q3LR69|Q7L1N7|Q96JC0|Q9Y3D4	Frame_Shift_Del	DEL	ENST00000367439.3	hg19	CCDS1381.1																																																																																			.	.		0.333	GLRX2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086699.1	NM_016066		-	193066820	T	-	193066820	7	5	114	1	0	1	0	1	0	0	0	0	6468	1609	56	0	248	0	GLRX2	1	193066820	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	13179694	193066820	56183801	87	18359										
CFH	3075	hgsc.bcm.edu	37	chr1	196706674	196706674	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcatccaggtcttcacaagAaagttatgcacatgggacta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:196706674delA	ENST00000367429.4	+	17	2906	c.2666delA	c.(2665-2667)gaafs	p.E889fs		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	889	Sushi 15. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						TCTTCACAAGAAAGTTATGCA	0.358																																					p.E889fs		Atlas-INDEL	.											.	CFH	251	.	0			c.2665delG						.						77	73	74					1																	196706674		2203	4300	6503	SO:0001589	frameshift_variant	3075	exon17			.	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2666delA	chr1.hg19:g.196706674delA	ENSP00000356399:p.Glu889fs	104.0	0.0		171.0	11.0	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Frame_Shift_Del	DEL	ENST00000367429.4	hg19	CCDS1385.1																																																																																			.	.		0.358	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		-	196706674	A	-	196706674	7	5	114	1	0	1	0	1	0	0	0	0	3285	246	9	0	2750	0	CFH	1	196706674	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3639854	196706674	52543947	88	18360										
CFHR5	81494	hgsc.bcm.edu	37	chr1	196953169	196953169	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctggaaggtgatactgtacAaattatttgcaacacaggat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:196953169delA	ENST00000256785.4	+	3	441	c.332delA	c.(331-333)caafs	p.Q111fs	CFHR5_ENST00000367414.5_Frame_Shift_Del_p.Q135fs			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	111	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)				NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						GATACTGTACAAATTATTTGC	0.383																																					p.Q111fs		Atlas-INDEL	.											CFHR5,right_upper_lobe,carcinoma,0,1	CFHR5	150	.	0			c.331delC						.						110	98	102					1																	196953169		2203	4300	6503	SO:0001589	frameshift_variant	81494	exon3			.	AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"Complement system"	24668	protein-coding gene	gene with protein product	"factor H related protein 5"	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.332delA	chr1.hg19:g.196953169delA	ENSP00000256785:p.Gln111fs	103.0	0.0		194.0	12.0	NM_030787	Q2NKK2	Frame_Shift_Del	DEL	ENST00000256785.4	hg19	CCDS1387.1																																																																																			.	.		0.383	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787		-	196953169	A	-	196953169	7	5	114	1	0	1	0	1	0	0	0	0	3290	130	5	0	342	0	CFHR5	1	196953169	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	246495	196953169	52297452	89	18361										
PTPRC	5788	hgsc.bcm.edu	37	chr1	198678836	198678836	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtaatatgatatttgataatAaagaaattaaattagaaaac	5	1	0	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:198678836A>G	ENST00000367376.2	+	11	1219	c.1048A>G	c.(1048-1050)Aaa>Gaa	p.K350E	PTPRC_ENST00000352140.3_Missense_Mutation_p.K302E|PTPRC_ENST00000348564.6_Missense_Mutation_p.K191E|PTPRC_ENST00000442510.2_Missense_Mutation_p.K352E|PTPRC_ENST00000594404.1_Missense_Mutation_p.K189E	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	350					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						ATTTGATAATAAAGAAATTAA	0.254																																					p.K352E		Atlas-SNP	.											.	PTPRC	229	.	0			c.A1054G						.						29	35	33					1																	198678836		2139	4247	6386	SO:0001583	missense	5788	exon11			GATAATAAAGAAA	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1048A>G	chr1.hg19:g.198678836A>G	ENSP00000356346:p.Lys350Glu	86.0	0.0		186.0	129.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.078	-1.189267	0.01607	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.02579	4.24	4.21	-3.39	0.04868	.	2.390670	0.01835	N	0.034923	T	0.01387	0.0045	N	0.03324	-0.35	0.09310	N	1	B;B;B;B;B	0.06786	0.001;0.001;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.0;0.0;0.0	T	0.43605	-0.9381	10	0.08381	T	0.77	.	5.4709	0.16670	0.3809:0.2846:0.3344:0.0	.	286;286;191;302;350	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	E	352;286;302;302;236;350;284;189	ENSP00000193532:K302E	ENSP00000306782:K189E	K	+	1	0	PTPRC	196945459	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.531000	0.00220	-1.197000	0.02673	-1.431000	0.01090	AAA	.	.		0.254	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				G	198678836	A	G	198678836	3	3	114	1	0	0	0	0	1	0	0	0	12812	363	13	2	1097	2	PTPRC	1	198678836	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1725667	198678836	50571785	90	18362										
PPP1R12B	4660	hgsc.bcm.edu	37	chr1	202394742	202394742	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agaagagcagcagatgttgcAggatgcccgccagtggctca	14	10	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:202394742A>G	ENST00000608999.1	+	4	743	c.590A>G	c.(589-591)cAg>cGg	p.Q197R	PPP1R12B_ENST00000356764.2_Missense_Mutation_p.Q197R|PPP1R12B_ENST00000336894.4_Missense_Mutation_p.Q197R|PPP1R12B_ENST00000480184.1_Missense_Mutation_p.Q197R	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	197					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			CAGATGTTGCAGGATGCCCGC	0.512																																					p.Q197R		Atlas-SNP	.											.	PPP1R12B	100	.	0			c.A590G						.						180	198	192					1																	202394742		2203	4300	6503	SO:0001583	missense	4660	exon4			TGTTGCAGGATGC	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7619	protein-coding gene	gene with protein product	"myosin phosphatase regulatory subunit", "myosin phosphatase, target subunit 2"	603768	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.590A>G	chr1.hg19:g.202394742A>G	ENSP00000476755:p.Gln197Arg	93.0	0.0		164.0	8.0	NM_002481	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Missense_Mutation	SNP	ENST00000608999.1	hg19	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	A	5.524	0.281558	0.10458	.	.	ENSG00000077157	ENST00000406302;ENST00000336894;ENST00000480184;ENST00000356764	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.5	5.5	0.81552	Ankyrin repeat-containing domain (3);	0.000000	0.64402	D	0.000015	T	0.33469	0.0864	N	0.01493	-0.835	0.42160	D	0.99159	B;B;P;D	0.65815	0.001;0.112;0.532;0.995	B;B;B;D	0.78314	0.018;0.021;0.259;0.991	T	0.46076	-0.9217	10	0.02654	T	1	.	10.0332	0.42114	0.9246:0.0:0.0754:0.0	.	197;197;197;197	O60237-2;O60237;F8W8M3;Q2TAI8	.;MYPT2_HUMAN;.;.	R	197	ENSP00000384496:Q197R;ENSP00000337897:Q197R;ENSP00000417159:Q197R;ENSP00000349206:Q197R	ENSP00000337897:Q197R	Q	+	2	0	PPP1R12B	200661365	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.698000	0.54771	2.090000	0.63153	0.377000	0.23210	CAG	.	.		0.512	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105		G	202394742	A	G	202394742	3	3	114	1	0	0	0	0	1	0	0	0	12367	188	7	2	604	2	PPP1R12B	1	202394742	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3715906	202394742	46855879	91	18363										
ADORA1	134	hgsc.bcm.edu	37	chr1	203134406	203134406	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggtacaagatggtggtgaCcccccggagggcggcggtgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:203134406delC	ENST00000367236.4	+	3	1280	c.359delC	c.(358-360)accfs	p.T120fs	ADORA1_ENST00000472535.1_3'UTR|ADORA1_ENST00000337894.4_Frame_Shift_Del_p.T120fs|ADORA1_ENST00000309502.3_Frame_Shift_Del_p.T120fs|ADORA1_ENST00000367235.1_3'UTR	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	120					activation of MAPKK activity (GO:0000186)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cognition (GO:0050890)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood pressure (GO:0045776)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heart contraction (GO:0045822)|negative regulation of hormone secretion (GO:0046888)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of mucus secretion (GO:0070256)|negative regulation of neurotrophin production (GO:0032900)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of vasodilation (GO:0045908)|nervous system development (GO:0007399)|phagocytosis (GO:0006909)|positive regulation of blood pressure (GO:0045777)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of nucleoside transport (GO:0032244)|positive regulation of peptide secretion (GO:0002793)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of protein dephosphorylation (GO:0035307)|protein targeting to membrane (GO:0006612)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glomerular filtration (GO:0003093)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|relaxation of vascular smooth muscle (GO:0060087)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|temperature homeostasis (GO:0001659)	asymmetric synapse (GO:0032279)|axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled adenosine receptor activity (GO:0001609)|phospholipase C activity (GO:0004629)|purine nucleoside binding (GO:0001883)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(9)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25					Adenosine(DB00640)|Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Gabapentin(DB00996)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Theobromine(DB01412)|Theophylline(DB00277)	ATGGTGGTGACCCCCCGGAGG	0.652																																					p.T120fs		Atlas-INDEL	.											.	ADORA1	62	.	0			c.358delA						.						33	40	38					1																	203134406		2203	4300	6503	SO:0001589	frameshift_variant	134	exon3			.	BC026340	CCDS1434.1	1q32.1	2012-08-08			ENSG00000163485	ENSG00000163485		"GPCR / Class A : Adenosine receptors"	262	protein-coding gene	gene with protein product		102775				1662665, 2541503	Standard	NM_001048230		Approved	RDC7	uc001gzf.1	P30542	OTTHUMG00000042125	ENST00000367236.4:c.359delC	chr1.hg19:g.203134406delC	ENSP00000356205:p.Thr120fs	65.0	0.0		146.0	10.0	NM_001048230	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Frame_Shift_Del	DEL	ENST00000367236.4	hg19	CCDS1434.1																																																																																			.	.		0.652	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674		-	203134406	C	-	203134406	7	5	114	1	0	1	0	1	0	0	0	0	326	507	18	0	365	0	ADORA1	1	203134406	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	739664	203134406	46116215	92	18364										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204419065	204419065	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctctgaggagctccccggtGgggggatgggcagagcatag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:204419065delG	ENST00000367187.3	-	14	2703	c.2147delC	c.(2146-2148)ccafs	p.P717fs	PIK3C2B_ENST00000424712.2_Frame_Shift_Del_p.P717fs	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	717	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00041, ECO:0000255|PROSITE- ProRule:PRU00880}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			GCTCCCCGGTGGGGGGATGGG	0.617																																					p.P716fs		Atlas-INDEL	.											.	PIK3C2B	142	.	0			c.2148delA						.						25	28	27					1																	204419065		2203	4300	6503	SO:0001589	frameshift_variant	5287	exon14			.	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.2147delC	chr1.hg19:g.204419065delG	ENSP00000356155:p.Pro717fs	122.0	0.0		214.0	14.0	NM_002646	O95666|Q5SW99	Frame_Shift_Del	DEL	ENST00000367187.3	hg19	CCDS1446.1																																																																																			.	.		0.617	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		-	204419065	G	-	204419065	7	5	114	1	0	1	0	1	0	0	0	0	11919	1348	47	0	2841	0	PIK3C2B	1	204419065	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1284659	204419065	44831556	93	18365										
CD55	1604	hgsc.bcm.edu	37	chr1	207510725	207510725	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caagcattttcatgaaacaaCcccaaataaaggaagtggaa					rs150172588	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:207510725delC	ENST00000367064.3	+	8	1289	c.1031delC	c.(1030-1032)accfs	p.T344fs	CD55_ENST00000465534.1_3'UTR|CD55_ENST00000367065.5_Frame_Shift_Del_p.T344fs|CD55_ENST00000367062.4_Frame_Shift_Del_p.T344fs|CD55_ENST00000314754.8_Frame_Shift_Del_p.T344fs|CD55_ENST00000391921.4_Frame_Shift_Del_p.T280fs|CD55_ENST00000391920.4_Frame_Shift_Del_p.T344fs|CD55_ENST00000367067.4_3'UTR|CD55_ENST00000367063.2_Frame_Shift_Del_p.T344fs	NM_000574.3	NP_000565.1	P08174	DAF_HUMAN	CD55 molecule, decay accelerating factor for complement (Cromer blood group)	344	Ser/Thr-rich.				CD4-positive, alpha-beta T cell cytokine production (GO:0035743)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|maternal process involved in parturition (GO:0060137)|negative regulation of complement activation (GO:0045916)|positive regulation of CD4-positive, alpha-beta T cell activation (GO:2000516)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of complement activation (GO:0030449)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|respiratory burst (GO:0045730)|response to peptide hormone (GO:0043434)|response to virus (GO:0009615)|spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	enzyme inhibitor activity (GO:0004857)|lipid binding (GO:0008289)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16					Chloramphenicol(DB00446)	CATGAAACAACCCCAAATAAA	0.413																																					p.T344fs		Atlas-INDEL	.											.	CD55	55	.	0			c.1030delA						.						154	135	142					1																	207510725		2203	4300	6503	SO:0001589	frameshift_variant	1604	exon8			.	BC001288	CCDS31006.1, CCDS44307.1, CCDS73022.1	1q32	2014-09-17	2006-03-28	2006-02-23	ENSG00000196352	ENSG00000196352		"CD molecules", "Blood group antigens"	2665	protein-coding gene	gene with protein product		125240	"decay accelerating factor for complement (CD55, Cromer blood group system)"	DAF			Standard	XM_005273077		Approved	CR, TC, CROM	uc001hfr.4	P08174	OTTHUMG00000036255	ENST00000367064.3:c.1031delC	chr1.hg19:g.207510725delC	ENSP00000356031:p.Thr344fs	161.0	0.0		261.0	17.0	NM_001114752	B1AP14|D3DT83|D3DT84|E7ER69|P09679|P78361|Q14UF2|Q14UF3|Q14UF4|Q14UF5|Q14UF6	Frame_Shift_Del	DEL	ENST00000367064.3	hg19	CCDS31006.1																																																																																			.	.		0.413	CD55-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088208.2	NM_000574		-	207510725	C	-	207510725	7	5	114	1	0	1	0	1	0	0	0	0	3026	507	18	0	1061	0	CD55	1	207510725	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3091660	207510725	41739896	94	18366										
C1orf74	148304	hgsc.bcm.edu	37	chr1	209956336	209956336	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taaaagaatagagcaggattGggggttgacctagcaaccat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:209956336delG	ENST00000294811.1	-	2	900	c.644delC	c.(643-645)ccafs	p.P215fs		NM_152485.2	NP_689698.1	Q96LT6	CA074_HUMAN	chromosome 1 open reading frame 74	215										endometrium(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	15				OV - Ovarian serous cystadenocarcinoma(81;0.0328)		GAGCAGGATTGGGGGTTGACC	0.502																																					p.P215fs		Atlas-INDEL	.											.	C1orf74	30	.	0			c.645delA						.						85	94	91					1																	209956336		2203	4300	6503	SO:0001589	frameshift_variant	148304	exon2			.	AK057807	CCDS1491.1	1q32.2	2008-02-05			ENSG00000162757	ENSG00000162757			26319	protein-coding gene	gene with protein product						12477932	Standard	NM_152485		Approved	FLJ25078	uc001hhp.1	Q96LT6	OTTHUMG00000036483	ENST00000294811.1:c.644delC	chr1.hg19:g.209956336delG	ENSP00000294811:p.Pro215fs	101.0	0.0		175.0	11.0	NM_152485		Frame_Shift_Del	DEL	ENST00000294811.1	hg19	CCDS1491.1																																																																																			.	.		0.502	C1orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088745.1	NM_152485		-	209956336	G	-	209956336	7	5	114	1	0	1	0	1	0	0	0	0	2060	1348	47	0	169	0	C1orf74	1	209956336	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2445611	209956336	39294285	95	18367										
SYT14	255928	hgsc.bcm.edu	37	chr1	210329212	210329212	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agactatcagcagaagtgatAaaaggcagccacttcaaaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:210329212delA	ENST00000472886.1	+	7	1325	c.1311delA	c.(1309-1311)atafs	p.I437fs	SYT14_ENST00000534859.1_Frame_Shift_Del_p.I437fs|SYT14_ENST00000367015.1_Frame_Shift_Del_p.I399fs|SYT14_ENST00000399639.2_Frame_Shift_Del_p.I437fs|SYT14_ENST00000271745.7_3'UTR|SYT14_ENST00000537238.1_Frame_Shift_Del_p.I399fs|SYT14_ENST00000422431.1_Frame_Shift_Del_p.I482fs|SYT14_ENST00000367019.1_Frame_Shift_Del_p.I437fs			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	437	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)			endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		CAGAAGTGATAAAAGGCAGCC	0.393																																					p.I482fs		Atlas-INDEL	.											.	SYT14	89	.	0			c.1445delT						.						69	68	68					1																	210329212		2203	4300	6503	SO:0001589	frameshift_variant	255928	exon8			.	AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"Synaptotagmins"	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.1311delA	chr1.hg19:g.210329212delA	ENSP00000418901:p.Ile437fs	132.0	0.0		253.0	16.0	NM_001146264	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Frame_Shift_Del	DEL	ENST00000472886.1	hg19	CCDS31014.1																																																																																			.	.		0.393	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262		-	210329212	A	-	210329212	7	5	114	1	0	1	0	1	0	0	0	0	15485	352	13	0	1476	0	SYT14	1	210329212	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	372876	210329212	38921409	96	18368										
TRAF5	7188	hgsc.bcm.edu	37	chr1	211526743	211526743	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgccactcggtgcttcacaaCccccaccagacaggatgtgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:211526743delC	ENST00000261464.5	+	2	216	c.162delC	c.(160-162)aacfs	p.N54fs	TRAF5_ENST00000427925.2_Frame_Shift_Del_p.N54fs|TRAF5_ENST00000367004.3_Frame_Shift_Del_p.N54fs|TRAF5_ENST00000462410.1_3'UTR|TRAF5_ENST00000336184.2_Frame_Shift_Del_p.N54fs	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	54					apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		TGCTTCACAACCCCCACCAGA	0.572																																					p.N54fs		Atlas-INDEL	.											.	TRAF5	64	.	0			c.161delA						.																																			SO:0001589	frameshift_variant	7188	exon2			.	AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"RING-type (C3HC4) zinc fingers"	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	ENST00000261464.5:c.162delC	chr1.hg19:g.211526743delC	ENSP00000261464:p.Asn54fs	82.0	0.0		158.0	10.0	NM_001033910	B4DIS9|B4E0A2|Q6FHY1	Frame_Shift_Del	DEL	ENST00000261464.5	hg19	CCDS1497.1																																																																																			.	.		0.572	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619		-	211526743	C	-	211526743	7	5	114	1	0	1	0	1	0	0	0	0	16459	506	18	0	164	0	TRAF5	1	211526743	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1197531	211526743	37723878	97	18369										
DTL	51514	hgsc.bcm.edu	37	chr1	212238257	212238257	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atttccttggaatatctttcAgatgggttttataggcaagt	9	5	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:212238257A>G	ENST00000366991.4	+	7	840		c.e7-1		DTL_ENST00000542077.1_Splice_Site|DTL_ENST00000475419.1_Splice_Site	NM_016448.2	NP_057532.2	Q9NZJ0	DTL_HUMAN	denticleless E3 ubiquitin protein ligase homolog (Drosophila)						cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|chromosome (GO:0005694)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)		AATATCTTTCAGATGGGTTTT	0.343																																					.		Atlas-SNP	.											.	DTL	52	.	0			c.527-2A>G						.						93	95	95					1																	212238257		2203	4300	6503	SO:0001630	splice_region_variant	51514	exon7			TCTTTCAGATGGG	AF195765	CCDS1502.1, CCDS65778.1	1q32	2013-01-10	2012-02-23		ENSG00000143476	ENSG00000143476		"DDB1 and CUL4 associated factors", "WD repeat domain containing"	30288	protein-coding gene	gene with protein product	"RA regulated nuclear matrix associated protein", "DDB1 and CUL4 associated factor 2"	610617	"denticleless homolog (Drosophila)"			11278750	Standard	NM_001286229		Approved	RAMP, L2DTL, DCAF2	uc009xdc.3	Q9NZJ0	OTTHUMG00000037133	ENST00000366991.4:c.527-1A>G	chr1.hg19:g.212238257A>G		56.0	0.0		81.0	4.0	NM_016448	A8K8H8|D3DT98|Q5VT77|Q96SN0|Q9NW03|Q9NW34|Q9NWM5	Splice_Site	SNP	ENST00000366991.4	hg19	CCDS1502.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.302938	0.81136	.	.	ENSG00000143476	ENST00000366991;ENST00000542077	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8947	0.70636	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DTL	210304880	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.921000	0.87530	2.216000	0.71823	0.533000	0.62120	.	.	.		0.343	DTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090182.1	NM_016448	Intron	G	212238257	A	G	212238257	5	3	114	1	0	0	0	0	0	0	1	0	4789	202	7	2	551	2	DTL	1	212238257	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	711514	212238257	37012364	98	18370										
ATF3	467	hgsc.bcm.edu	37	chr1	212788594	212788594	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccctcggggtgtccatcacAaaagccgaggtgggttctat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:212788594delA	ENST00000341491.4	+	2	496	c.231delA	c.(229-231)acafs	p.T77fs	RN7SL512P_ENST00000578962.1_RNA|ATF3_ENST00000492118.1_Intron|ATF3_ENST00000366985.1_Frame_Shift_Del_p.T20fs|ATF3_ENST00000336937.4_Frame_Shift_Del_p.T48fs|ATF3_ENST00000366983.1_Frame_Shift_Del_p.T77fs|ATF3_ENST00000366987.2_Frame_Shift_Del_p.T77fs	NM_001040619.2|NM_001206488.2|NM_001674.3	NP_001035709.1|NP_001193417.2|NP_001665.1	P18847	ATF3_HUMAN	activating transcription factor 3	77					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gluconeogenesis (GO:0006094)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)	Pseudoephedrine(DB00852)	TGTCCATCACAAAAGCCGAGG	0.552																																					p.T77fs		Atlas-INDEL	.											.	ATF3	22	.	0			c.230delC						.						42	44	43					1																	212788594		2203	4300	6503	SO:0001589	frameshift_variant	467	exon2			.	L19871	CCDS1506.1, CCDS41464.1, CCDS55688.1, CCDS58059.1	1q32.3	2013-01-10			ENSG00000162772	ENSG00000162772		"basic leucine zipper proteins"	785	protein-coding gene	gene with protein product		603148				7515060	Standard	NM_001674		Approved		uc021pit.1	P18847	OTTHUMG00000036747	ENST00000341491.4:c.231delA	chr1.hg19:g.212788594delA	ENSP00000344352:p.Thr77fs	78.0	0.0		164.0	11.0	NM_001030287	Q5VTZ2|Q6ICQ9|Q7Z566|Q8WYM6	Frame_Shift_Del	DEL	ENST00000341491.4	hg19	CCDS1506.1																																																																																			.	.		0.552	ATF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089296.1	NM_001674		-	212788594	A	-	212788594	7	5	114	1	0	1	0	1	0	0	0	0	1081	117	5	0	233	0	ATF3	1	212788594	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	550337	212788594	36462027	99	18371										
VASH2	79805	hgsc.bcm.edu	37	chr1	213146180	213146180	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcaagattgggctgtacgtCccccatgagcctcatagctt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:213146180delC	ENST00000517399.1	+	5	756	c.756delC	c.(754-756)gtcfs	p.V252fs	VASH2_ENST00000366965.2_Frame_Shift_Del_p.V208fs|VASH2_ENST00000366966.2_Frame_Shift_Del_p.V187fs|VASH2_ENST00000366968.4_Frame_Shift_Del_p.V187fs|VASH2_ENST00000366967.2_Frame_Shift_Del_p.V148fs|VASH2_ENST00000366964.3_Frame_Shift_Del_p.V110fs|VASH2_ENST00000271776.4_3'UTR			Q86V25	VASH2_HUMAN	vasohibin 2	252					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)	cytoplasm (GO:0005737)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)		GGCTGTACGTCCCCCATGAGC	0.488																																					p.V208fs		Atlas-INDEL	.											.	VASH2	55	.	0			c.623delT						.						112	100	104					1																	213146180		2203	4300	6503	SO:0001589	frameshift_variant	79805	exon4			.	AK022567	CCDS1511.1, CCDS44315.1, CCDS44316.1, CCDS73026.1	1q23	2008-02-05			ENSG00000143494	ENSG00000143494			25723	protein-coding gene	gene with protein product		610471				16528006	Standard	XR_247041		Approved	FLJ12505	uc001hjw.3	Q86V25	OTTHUMG00000036925	ENST00000517399.1:c.756delC	chr1.hg19:g.213146180delC	ENSP00000428324:p.Val252fs	153.0	0.0		243.0	17.0	NM_024749	B4DYZ5|Q2VT46|Q5VTE7|Q5VTE9|Q7Z6E3|Q8IZ24|Q9H9W5	Frame_Shift_Del	DEL	ENST00000517399.1	hg19	CCDS1511.1																																																																																			.	.		0.488	VASH2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381686.1	NM_024749		-	213146180	C	-	213146180	7	5	114	1	0	1	0	1	0	0	0	0	17141	842	30	0	774	0	VASH2	1	213146180	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	357586	213146180	36104441	100	18372										
USH2A	7399	hgsc.bcm.edu	37	chr1	216062051	216062051	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaagccattggggtgggtaGggggttgccaagatataatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:216062051delG	ENST00000307340.3	-	41	8326	c.7940delC	c.(7939-7941)cctfs	p.P2647fs	USH2A_ENST00000366943.2_Frame_Shift_Del_p.P2647fs|RP5-1111A8.3_ENST00000414995.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2647	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GGGGTGGGTAGGGGGTTGCCA	0.507										HNSCC(13;0.011)																											p.P2647fs		Atlas-INDEL	.											.	USH2A	1168	.	0			c.7941delT						.						74	81	79					1																	216062051		2203	4300	6503	SO:0001589	frameshift_variant	7399	exon41			.	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7940delC	chr1.hg19:g.216062051delG	ENSP00000305941:p.Pro2647fs	99.0	0.0		171.0	11.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Frame_Shift_Del	DEL	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.507	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		-	216062051	G	-	216062051	7	5	114	1	0	1	0	1	0	0	0	0	17051	1000	35	0	7796	0	USH2A	1	216062051	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2915871	216062051	33188570	101	18373										
USH2A	7399	hgsc.bcm.edu	37	chr1	216592004	216592004	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acacaatctgcccatctactGtcttttctataacacacctt	2	14	4	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:216592004G>C	ENST00000307340.3	-	3	889	c.503C>G	c.(502-504)aCa>aGa	p.T168R	USH2A_ENST00000366943.2_Missense_Mutation_p.T168R|USH2A_ENST00000366942.3_Missense_Mutation_p.T168R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	168					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.T168I(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CCCATCTACTGTCTTTTCTAT	0.383										HNSCC(13;0.011)																											p.T168R		Atlas-SNP	.											USH2A,NS,carcinoma,0,1	USH2A	1168	.	1	Substitution - Missense(1)	lung(1)	c.C503G						.						117	109	112					1																	216592004		2203	4300	6503	SO:0001583	missense	7399	exon3			TCTACTGTCTTTT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.503C>G	chr1.hg19:g.216592004G>C	ENSP00000305941:p.Thr168Arg	133.0	0.0		214.0	0.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	10.07	1.249778	0.22880	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.72942	-0.7;-0.7;-0.7	5.62	2.77	0.32553	Concanavalin A-like lectin/glucanase (1);LamG-like jellyroll fold (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.177681	0.27043	U	0.021204	T	0.66257	0.2771	L	0.44542	1.39	0.09310	N	0.999999	B;P	0.46142	0.355;0.873	B;P	0.46629	0.205;0.522	T	0.59478	-0.7447	10	0.72032	D	0.01	.	10.4097	0.44285	0.2096:0.0:0.7904:0.0	.	168;168	O75445-2;O75445	.;USH2A_HUMAN	R	168	ENSP00000305941:T168R;ENSP00000355910:T168R;ENSP00000355909:T168R	ENSP00000305941:T168R	T	-	2	0	USH2A	214658627	0.985000	0.35326	0.012000	0.15200	0.439000	0.31926	2.441000	0.44864	0.328000	0.23435	0.655000	0.94253	ACA	.	.		0.383	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	216592004	G	C	216592004	3	2	114	1	0	0	0	0	1	0	0	0	17051	1377	48	4	15399	4	USH2A	1	216592004	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	529953	216592004	32658617	102	18374										
SUSD4	55061	hgsc.bcm.edu	37	chr1	223402546	223402546	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccttcagtcttacctgatttGatgcagtagacttgataaga	8	8	2	5			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:223402546G>T	ENST00000343846.3	-	5	1542	c.909C>A	c.(907-909)atC>atA	p.I303I	SUSD4_ENST00000484758.2_Silent_p.I234I|SUSD4_ENST00000494793.2_Silent_p.I303I|SUSD4_ENST00000366878.4_Silent_p.I303I|SUSD4_ENST00000454695.2_Silent_p.I143I|SUSD4_ENST00000478605.1_Intron			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	303	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		TACCTGATTTGATGCAGTAGA	0.498																																					p.I303I		Atlas-SNP	.											.	SUSD4	82	.	0			c.C909A						.						119	125	123					1																	223402546		2069	4219	6288	SO:0001819	synonymous_variant	55061	exon6			TGATTTGATGCAG	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.909C>A	chr1.hg19:g.223402546G>T		149.0	0.0		234.0	67.0	NM_017982	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Silent	SNP	ENST00000343846.3	hg19	CCDS41471.1																																																																																			.	.		0.498	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982		T	223402546	G	T	223402546	2	4	114	1	0	0	0	0	0	0	0	1	15425	1280	45	3		3	SUSD4	1	223402546	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	6810542	223402546	25848075	103	18375										
FBXO28	23219	hgsc.bcm.edu	37	chr1	224345442	224345442	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctaaacgtcttcggaatagAaagtaaattggaatgtggtt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:224345442delA	ENST00000366862.5	+	5	1144	c.1101delA	c.(1099-1101)agafs	p.R367fs	FBXO28_ENST00000424254.2_3'UTR	NM_015176.3	NP_055991.1	Q9NVF7	FBX28_HUMAN	F-box protein 28	367										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(2)|skin(1)	10	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		TTCGGAATAGAAAGTAAATTG	0.448																																					p.R367fs		Atlas-INDEL	.											.	FBXO28	34	.	0			c.1100delG						.						39	43	41					1																	224345442		2203	4300	6503	SO:0001589	frameshift_variant	23219	exon5			.	AK001628	CCDS1539.1, CCDS44320.1	1q42.12	2011-08-12			ENSG00000143756	ENSG00000143756		"F-boxes /  "other""	29046	protein-coding gene	gene with protein product	"centromere protein 30"	609100				9455484	Standard	NM_015176		Approved	FLJ10766, KIAA0483, Fbx28, CENP-30	uc001hoh.3	Q9NVF7	OTTHUMG00000037495	ENST00000366862.5:c.1101delA	chr1.hg19:g.224345442delA	ENSP00000355827:p.Arg367fs	47.0	0.0		124.0	10.0	NM_015176	E9PEM8|O75070	Frame_Shift_Del	DEL	ENST00000366862.5	hg19	CCDS1539.1																																																																																			.	.		0.448	FBXO28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091283.2	NM_015176		-	224345442	A	-	224345442	7	5	114	1	0	1	0	1	0	0	0	0	5746	243	9	0	1119	0	FBXO28	1	224345442	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	942896	224345442	24905179	104	18376										
LBR	3930	hgsc.bcm.edu	37	chr1	225607149	225607149	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctttcttgtgacaaactgaaTttttcctaaatgaaaaattt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:225607149delT	ENST00000338179.2	-	5	581	c.456delA	c.(454-456)aaafs	p.K152fs	LBR_ENST00000487054.1_5'Flank|LBR_ENST00000272163.4_Frame_Shift_Del_p.K152fs	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	152					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		ACAAACTGAATTTTTCCTAAA	0.303																																					p.F153fs		Atlas-INDEL	.											.	LBR	54	.	0			c.457delT						.						53	51	52					1																	225607149		2203	4300	6503	SO:0001589	frameshift_variant	3930	exon5			.	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"Tudor domain containing"	6518	protein-coding gene	gene with protein product	"tudor domain containing 18"	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.456delA	chr1.hg19:g.225607149delT	ENSP00000339883:p.Lys152fs	80.0	0.0		159.0	10.0	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Frame_Shift_Del	DEL	ENST00000338179.2	hg19	CCDS1545.1																																																																																			.	.		0.303	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		-	225607149	T	-	225607149	7	5	114	1	0	1	0	1	0	0	0	0	8661	1490	52	0	1431	0	LBR	1	225607149	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1261707	225607149	23643472	105	18377										
ITPKB	3707	hgsc.bcm.edu	37	chr1	226923526	226923526	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatcttggggtagcagctccGgacttgggagggcatcactg	16	9	2	0	rs149543375		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:226923526G>A	ENST00000272117.3	-	1	1633	c.1634C>T	c.(1633-1635)cCg>cTg	p.P545L	ITPKB_ENST00000366784.1_Missense_Mutation_p.P545L|ITPKB_ENST00000429204.1_Missense_Mutation_p.P545L			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	545					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				TAGCAGCTCCGGACTTGGGAG	0.597																																					p.P545L	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.C1634T						.	G	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	41	39	40		1634	-3.2	0	1	dbSNP_134	40	0,8600		0,0,4300	no	missense	ITPKB	NM_002221.3	98	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	545/947	226923526	1,13005	2203	4300	6503	SO:0001583	missense	3707	exon2			AGCTCCGGACTTG	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"inositol 1,4,5-trisphosphate 3-kinase B"			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1634C>T	chr1.hg19:g.226923526G>A	ENSP00000272117:p.Pro545Leu	72.0	0.0		132.0	46.0	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	hg19	CCDS1555.1	.	.	.	.	.	.	.	.	.	.	G	5.501	0.277439	0.10403	2.27E-4	0.0	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.21932	1.98;1.98;1.98	5.43	-3.18	0.05186	.	1.426790	0.04261	N	0.340381	T	0.11836	0.0288	N	0.19112	0.55	0.09310	N	1	B	0.15719	0.014	B	0.08055	0.003	T	0.33904	-0.9850	10	0.52906	T	0.07	1.5012	2.8086	0.05434	0.2829:0.2641:0.3599:0.0931	.	545	P27987	IP3KB_HUMAN	L	545	ENSP00000272117:P545L;ENSP00000411152:P545L;ENSP00000355748:P545L	ENSP00000272117:P545L	P	-	2	0	ITPKB	224990149	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.825000	0.04433	-0.164000	0.10927	-0.339000	0.08088	CCG	.	G|1.000;A|0.000		0.597	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		A	226923526	G	A	226923526	3	1	114	1	0	0	0	0	1	0	0	0	7927	1116	39	1	1234	1	ITPKB	1	226923526	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1316377	226923526	22327095	106	18378										
COG2	22796	hgsc.bcm.edu	37	chr1	230800279	230800279	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcggtcagttgagaaaattgAaaaaatcttaaactctcaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:230800279delA	ENST00000366669.4	+	5	546	c.431delA	c.(430-432)gaafs	p.E144fs	COG2_ENST00000535166.1_Frame_Shift_Del_p.E28fs|COG2_ENST00000534989.1_Frame_Shift_Del_p.E85fs|COG2_ENST00000366668.3_Frame_Shift_Del_p.E144fs	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	144					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GAGAAAATTGAAAAAATCTTA	0.269																																					p.E144fs		Atlas-INDEL	.											.	COG2	61	.	0			c.430delG						.						28	30	29					1																	230800279		2196	4274	6470	SO:0001589	frameshift_variant	22796	exon5			.	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"Components of oligomeric golgi complex"	6546	protein-coding gene	gene with protein product		606974	"low density lipoprotein receptor defect C complementing"	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.431delA	chr1.hg19:g.230800279delA	ENSP00000355629:p.Glu144fs	77.0	0.0		153.0	12.0	NM_007357	Q86U99	Frame_Shift_Del	DEL	ENST00000366669.4	hg19	CCDS1584.1																																																																																			.	.		0.269	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357		-	230800279	A	-	230800279	7	5	114	1	0	1	0	1	0	0	0	0	3660	246	9	0	449	0	COG2	1	230800279	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3876753	230800279	18450342	107	18379										
TTC13	79573	hgsc.bcm.edu	37	chr1	231044702	231044702	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acataccttccctttgggaaTttttcctgctacttcttttc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:231044702delT	ENST00000366661.4	-	21	2381	c.2374delA	c.(2374-2376)attfs	p.I792fs	TTC13_ENST00000414259.1_Frame_Shift_Del_p.I739fs|TTC13_ENST00000366662.4_Frame_Shift_Del_p.I738fs	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	792										central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		CCTTTGGGAATTTTTCCTGCT	0.393																																					p.I792fs		Atlas-INDEL	.											.	TTC13	74	.	0			c.2375delT						.						161	170	167					1																	231044702		2203	4300	6503	SO:0001589	frameshift_variant	79573	exon21			.		CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"Tetratricopeptide (TTC) repeat domain containing"	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.2374delA	chr1.hg19:g.231044702delT	ENSP00000355621:p.Ile792fs	145.0	0.0		214.0	13.0	NM_024525	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Frame_Shift_Del	DEL	ENST00000366661.4	hg19	CCDS1588.1																																																																																			.	.		0.393	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525		-	231044702	T	-	231044702	7	5	114	1	0	1	0	1	0	0	0	0	16695	1493	52	0	220	0	TTC13	1	231044702	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	244423	231044702	18205919	108	18380										
GNPAT	8443	hgsc.bcm.edu	37	chr1	231403484	231403484	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgtcactgaagttgcctacAaaatggagcttctgcaaatt					rs201138311		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:231403484delA	ENST00000366647.4	+	9	1283	c.1114delA	c.(1114-1116)aaafs	p.K372fs	GNPAT_ENST00000366646.3_Frame_Shift_Del_p.K311fs	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	372					cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				AGTTGCCTACAAAATGGAGCT	0.438																																					p.Y371X		Atlas-INDEL	.											.	GNPAT	73	.	0			c.1113delC						.						126	120	122					1																	231403484		2203	4300	6503	SO:0001589	frameshift_variant	8443	exon9			.	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.1114delA	chr1.hg19:g.231403484delA	ENSP00000355607:p.Lys372fs	73.0	0.0		146.0	10.0	NM_014236	B4DNM9|Q5TBH7|Q9BWC2	Frame_Shift_Del	DEL	ENST00000366647.4	hg19	CCDS1592.1																																																																																			.	.		0.438	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1			-	231403484	A	-	231403484	7	5	114	1	0	1	0	1	0	0	0	0	6549	131	5	0	1148	0	GNPAT	1	231403484	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	358782	231403484	17847137	109	18381										
EDARADD	128178	hgsc.bcm.edu	37	chr1	236577581	236577581	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagacaaatatcccattcaaGatacggaactccctaaaggt	6	11	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:236577581G>A	ENST00000334232.4	+	3	309	c.142G>A	c.(142-144)Gat>Aat	p.D48N	EDARADD_ENST00000359362.5_Missense_Mutation_p.D38N	NM_145861.2	NP_665860.2	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain	48					cell differentiation (GO:0030154)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|stomach(1)	12	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TCCCATTCAAGATACGGAACT	0.318																																					p.D48N		Atlas-SNP	.											.	EDARADD	31	.	0			c.G142A						.						100	103	102					1																	236577581		2203	4299	6502	SO:0001583	missense	128178	exon3			ATTCAAGATACGG	AY028914	CCDS1610.1, CCDS31065.1	1q42.3	2013-05-22			ENSG00000186197	ENSG00000186197			14341	protein-coding gene	gene with protein product		606603				11780064	Standard	NM_145861		Approved		uc001hxu.1	Q8WWZ3	OTTHUMG00000039954	ENST00000334232.4:c.142G>A	chr1.hg19:g.236577581G>A	ENSP00000335076:p.Asp48Asn	75.0	0.0		164.0	55.0	NM_145861	A2VCK5|A8K7B5|B1AL54|B9ZVW5|Q5VYJ7	Missense_Mutation	SNP	ENST00000334232.4	hg19	CCDS1610.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057813	0.76074	.	.	ENSG00000186197	ENST00000439430;ENST00000334232;ENST00000359362	T;T;D	0.83163	-0.04;-1.13;-1.69	4.72	4.72	0.59763	.	0.148151	0.28952	U	0.013607	D	0.89556	0.6749	M	0.71581	2.175	0.36604	D	0.874813	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	D	0.92304	0.5852	10	0.87932	D	0	.	13.0389	0.58887	0.0:0.0:1.0:0.0	.	38;48	A8K7B5;Q8WWZ3	.;EDAD_HUMAN	N	26;48;38	ENSP00000405815:D26N;ENSP00000335076:D48N;ENSP00000352320:D38N	ENSP00000335076:D48N	D	+	1	0	EDARADD	234644204	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	4.693000	0.61753	2.465000	0.83290	0.563000	0.77884	GAT	.	.		0.318	EDARADD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096368.1	NM_145861		A	236577581	G	A	236577581	3	1	114	1	0	0	0	0	1	0	0	0	4908	942	33	3	187	3	EDARADD	1	236577581	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	5174097	236577581	12673040	110	18382										
HEATR1	55127	hgsc.bcm.edu	37	chr1	236750749	236750749	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctttgaaagagattcagaagAtttgaaatcgtcacttctga	8	6	3	6			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:236750749A>T	ENST00000366582.3	-	14	1782	c.1668T>A	c.(1666-1668)aaT>aaA	p.N556K	HEATR1_ENST00000366581.2_Missense_Mutation_p.N556K	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	556					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GATTCAGAAGATTTGAAATCG	0.323																																					p.N556K		Atlas-SNP	.											.	HEATR1	197	.	0			c.T1668A						.						46	44	45					1																	236750749		2197	4289	6486	SO:0001583	missense	55127	exon14			CAGAAGATTTGAA	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.1668T>A	chr1.hg19:g.236750749A>T	ENSP00000355541:p.Asn556Lys	185.0	0.0		265.0	141.0	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	hg19	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	A	10.33	1.319392	0.23994	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.65732	-0.17;0.92	5.58	0.587	0.17439	Armadillo-like helical (1);Armadillo-type fold (1);	0.580156	0.19042	N	0.124248	T	0.47581	0.1453	L	0.47716	1.5	0.09310	N	0.999997	B	0.25169	0.119	B	0.28465	0.09	T	0.28202	-1.0051	10	0.19590	T	0.45	.	5.3855	0.16216	0.5651:0.1416:0.2933:0.0	.	556	Q9H583	HEAT1_HUMAN	K	556	ENSP00000355541:N556K;ENSP00000355540:N556K	ENSP00000355540:N556K	N	-	3	2	HEATR1	234817372	0.754000	0.28360	0.015000	0.15790	0.181000	0.23173	1.292000	0.33342	0.062000	0.16340	-0.313000	0.08912	AAT	.	.		0.323	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		T	236750749	A	T	236750749	3	4	114	1	0	0	0	0	1	0	0	0	7036	330	12	4	4894	4	HEATR1	1	236750749	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	173168	236750749	12499872	111	18383										
OPN3	23596	hgsc.bcm.edu	37	chr1	241757938	241757938	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgctggtaggtctttagcaGgcctctggcacctcagcagt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:241757938delG	ENST00000366554.2	-	4	1107	c.1001delC	c.(1000-1002)cctfs	p.P334fs	KMO_ENST00000366557.4_3'UTR|OPN3_ENST00000331838.5_Frame_Shift_Del_p.P255fs|KMO_ENST00000366559.4_3'UTR|OPN3_ENST00000469376.1_5'UTR	NM_014322.2	NP_055137.2	Q9H1Y3	OPN3_HUMAN	opsin 3	334					detection of light stimulus (GO:0009583)|detection of visible light (GO:0009584)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|large_intestine(5)|lung(5)	11	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			GTCTTTAGCAGGCCTCTGGCA	0.463																																					p.P334fs		Atlas-INDEL	.											.	OPN3	28	.	0			c.1002delT						.						103	105	105					1																	241757938		2203	4300	6503	SO:0001589	frameshift_variant	23596	exon4			.	AF140242	CCDS31072.1	1q43	2014-06-13	2008-04-16		ENSG00000054277	ENSG00000054277		"GPCR / Class A : Opsin receptors"	14007	protein-coding gene	gene with protein product	"panopsin", "protein phosphatase 1, regulatory subunit 116"	606695	"encephalopsin"	ECPN		10234000, 11401433	Standard	NM_014322		Approved	ERO, NMO-1, encephalopsin, PPP1R116	uc001hza.3	Q9H1Y3	OTTHUMG00000039691	ENST00000366554.2:c.1001delC	chr1.hg19:g.241757938delG	ENSP00000355512:p.Pro334fs	115.0	0.0		175.0	11.0	NM_014322	Q8IX08|Q9Y344	Frame_Shift_Del	DEL	ENST00000366554.2	hg19	CCDS31072.1																																																																																			.	.		0.463	OPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095713.1	NM_014322		-	241757938	G	-	241757938	7	5	114	1	0	1	0	1	0	0	0	0	10890	1000	35	0	211	0	OPN3	1	241757938	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	5007189	241757938	7492683	112	18384										
PXDN	7837	hgsc.bcm.edu	37	chr2	1670061	1670061	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcacgcatactctccgctgtCcccctgtacgacgttctgta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:1670061delC	ENST00000252804.4	-	10	1266	c.1216delG	c.(1216-1218)gacfs	p.D406fs	PXDN_ENST00000483018.1_5'UTR	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	406	Ig-like C2-type 2.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TCTCCGCTGTCCCCCTGTACG	0.582																																					p.D406fs		Atlas-INDEL	.											.	PXDN	255	.	0			c.1217delA						.						65	70	68					2																	1670061		2147	4254	6401	SO:0001589	frameshift_variant	7837	exon10			.	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1216delG	chr2.hg19:g.1670061delC	ENSP00000252804:p.Asp406fs	257.0	0.0		287.0	18.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Frame_Shift_Del	DEL	ENST00000252804.4	hg19	CCDS46221.1																																																																																			.	.		0.582	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		-	1670061	C	-	1670061	7	5	114	1	0	1	0	1	0	0	0	0	12862	855	30	0	3279	0	PXDN	2	1670061	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10		1670061	241529312	113	18385										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1795691	1795691	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tattttccagtagggctttaTtttctggactctgataacga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:1795691delT	ENST00000399161.2	-	25	4256	c.3509delA	c.(3508-3510)aatfs	p.N1170fs	MYT1L_ENST00000407844.1_Frame_Shift_Del_p.N168fs|MYT1L_ENST00000428368.2_Frame_Shift_Del_p.N1168fs	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1170					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TAGGGCTTTATTTTCTGGACT	0.378																																					p.N1168fs		Atlas-INDEL	.											.	MYT1L	241	.	0			c.3504delT						.						120	106	111					2																	1795691		1832	4081	5913	SO:0001589	frameshift_variant	23040	exon25			.	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.3509delA	chr2.hg19:g.1795691delT	ENSP00000382114:p.Asn1170fs	126.0	0.0		160.0	11.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Frame_Shift_Del	DEL	ENST00000399161.2	hg19																																																																																				.	.		0.378	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		-	1795691	T	-	1795691	7	5	114	1	0	1	0	1	0	0	0	0	10116	1493	52	0	55	0	MYT1L	2	1795691	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	125630	1795691	241403682	114	18386										
RNF144A	9781	hgsc.bcm.edu	37	chr2	7137130	7137130	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtcttgcaagctctgtcttGgggagtacccagtggagcag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:7137130delG	ENST00000320892.6	+	3	515	c.73delG	c.(73-75)gggfs	p.G25fs	RNF144A_ENST00000467276.1_Intron	NM_014746.3	NP_055561.2	P50876	R144A_HUMAN	ring finger protein 144A	25					protein ubiquitination (GO:0016567)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)	25	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		GCTCTGTCTTGGGGAGTACCC	0.507																																					p.L24fs		Atlas-INDEL	.											.	RNF144A	38	.	0			c.72delT						.						135	119	124					2																	7137130		2203	4300	6503	SO:0001589	frameshift_variant	9781	exon3			.	D79983	CCDS1657.1	2p25.2	2008-02-05	2007-08-20	2007-08-20	ENSG00000151692	ENSG00000151692		"RING-type (C3HC4) zinc fingers"	20457	protein-coding gene	gene with protein product			"ring finger protein 144"	RNF144		8724849, 10431818	Standard	NM_014746		Approved	UBCE7IP4, KIAA0161	uc002qys.3	P50876	OTTHUMG00000090353	ENST00000320892.6:c.73delG	chr2.hg19:g.7137130delG	ENSP00000321330:p.Gly25fs	143.0	0.0		187.0	12.0	NM_014746	D6W4Y6|Q585H5	Frame_Shift_Del	DEL	ENST00000320892.6	hg19	CCDS1657.1																																																																																			.	.		0.507	RNF144A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206725.2	NM_014746		-	7137130	G	-	7137130	7	5	114	1	0	1	0	1	0	0	0	0	13460	1348	47	0	75	0	RNF144A	2	7137130	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	5341439	7137130	236062243	115	18387										
IAH1	285148	hgsc.bcm.edu	37	chr2	9628363	9628363	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atctctggcctttgatagagAaaaaggtctcttctctacct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:9628363delA	ENST00000497473.1	+	6	689	c.652delA	c.(652-654)aaafs	p.K219fs	IAH1_ENST00000470914.1_Frame_Shift_Del_p.K106fs|IAH1_ENST00000545602.1_Frame_Shift_Del_p.K106fs|IAH1_ENST00000482918.1_Frame_Shift_Del_p.K106fs|IAH1_ENST00000489468.1_3'UTR	NM_001039613.1	NP_001034702.1	Q2TAA2	IAH1_HUMAN	isoamyl acetate-hydrolyzing esterase 1 homolog (S. cerevisiae)	219					lipid catabolic process (GO:0016042)	extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(1)|large_intestine(2)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTTGATAGAGAAAAAGGTCTC	0.433																																					p.E217fs		Atlas-INDEL	.											.	IAH1	12	.	0			c.651delG						.						146	132	136					2																	9628363		1867	4112	5979	SO:0001589	frameshift_variant	285148	exon6			.	BC111025	CCDS42651.1	2p25.1	2010-08-05			ENSG00000134330	ENSG00000134330			27696	protein-coding gene	gene with protein product						12477932	Standard	XR_426950		Approved		uc002qzr.3	Q2TAA2	OTTHUMG00000159076	ENST00000497473.1:c.652delA	chr2.hg19:g.9628363delA	ENSP00000417580:p.Lys219fs	152.0	0.0		159.0	10.0	NM_001039613	B4DMV3	Frame_Shift_Del	DEL	ENST00000497473.1	hg19	CCDS42651.1																																																																																			.	.		0.433	IAH1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353192.1	NM_001039613		-	9628363	A	-	9628363	7	5	114	1	0	1	0	1	0	0	0	0	7480	247	9	0	674	0	IAH1	2	9628363	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2491233	9628363	233571010	116	18388										
TAF1B	9014	hgsc.bcm.edu	37	chr2	10045015	10045015	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgactacgaggacatctacAaaaaaacagtagaagttgga	9	7	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:10045015A>T	ENST00000263663.5	+	9	1023	c.835A>T	c.(835-837)Aaa>Taa	p.K279*	TAF1B_ENST00000396242.3_Nonsense_Mutation_p.K24*	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	279	C-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGACATCTACAAAAAAACAGT	0.328																																					p.K279X		Atlas-SNP	.											TAF1B,NS,carcinoma,0,1	TAF1B	62	.	0			c.A835T						.						75	65	68					2																	10045015		2203	4300	6503	SO:0001587	stop_gained	9014	exon9			ATCTACAAAAAAA	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.835A>T	chr2.hg19:g.10045015A>T	ENSP00000263663:p.Lys279*	43.0	0.0		45.0	0.0	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Nonsense_Mutation	SNP	ENST00000263663.5	hg19	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648783	0.87958	.	.	ENSG00000115750	ENST00000263663;ENST00000396242	.	.	.	5.46	0.00658	0.14068	.	0.641420	0.17120	N	0.186264	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.238	2.8251	0.05483	0.6069:0.1237:0.1497:0.1198	.	.	.	.	X	279;24	.	.	K	+	1	0	TAF1B	9962466	0.964000	0.33143	0.630000	0.29268	0.414000	0.31173	0.565000	0.23578	0.355000	0.24131	0.383000	0.25322	AAA	.	.		0.328	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		T	10045015	A	T	10045015	4	4	114	1	0	0	0	0	0	1	0	0	15535	131	5	4	869	4	TAF1B	2	10045015	Nonsense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	416652	10045015	233154358	117	18389										
RAD51AP2	729475	hgsc.bcm.edu	37	chr2	17698475	17698475	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatttcctctatttcttctcAaaatatgtctaacgttacag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:17698475delA	ENST00000399080.2	-	1	1231	c.1208delT	c.(1207-1209)ttgfs	p.L403fs		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	403										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					ATTTCTTCTCAAAATATGTCT	0.318																																					p.L403fs		Atlas-INDEL	.											.	RAD51AP2	134	.	0			c.1209delG						.						51	50	50					2																	17698475		1803	4073	5876	SO:0001589	frameshift_variant	729475	exon1			.	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.1208delT	chr2.hg19:g.17698475delA	ENSP00000382030:p.Leu403fs	131.0	0.0		180.0	14.0	NM_001099218		Frame_Shift_Del	DEL	ENST00000399080.2	hg19	CCDS42656.1																																																																																			.	.		0.318	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		-	17698475	A	-	17698475	7	5	114	1	0	1	0	1	0	0	0	0	13002	131	5	0	2283	0	RAD51AP2	2	17698475	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	7653460	17698475	225500898	118	18390										
C2orf43	60526	hgsc.bcm.edu	37	chr2	20901391	20901391	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccacctccatcatttcttggCccccaaggtaggcagcatta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:20901391delC	ENST00000237822.3	-	6	804	c.725delG	c.(724-726)ggcfs	p.G242fs	C2orf43_ENST00000381090.3_Frame_Shift_Del_p.G242fs|C2orf43_ENST00000403006.2_Frame_Shift_Del_p.G112fs|C2orf43_ENST00000440866.2_Frame_Shift_Del_p.A164fs|C2orf43_ENST00000435420.2_Frame_Shift_Del_p.G194fs|C2orf43_ENST00000541941.1_Frame_Shift_Del_p.G112fs	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	242										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATTTCTTGGCCCCCAAGGTA	0.323																																					p.G242fs		Atlas-INDEL	.											.	C2orf43	28	.	0			c.726delC						.						240	234	236					2																	20901391		2203	4300	6503	SO:0001589	frameshift_variant	60526	exon6			.	AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961			26145	protein-coding gene	gene with protein product		613570				17135363, 24357060	Standard	NM_001282723		Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000237822.3:c.725delG	chr2.hg19:g.20901391delC	ENSP00000237822:p.Gly242fs	158.0	0.0		176.0	11.0	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Frame_Shift_Del	DEL	ENST00000237822.3	hg19	CCDS1702.1																																																																																			.	.		0.323	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925		-	20901391	C	-	20901391	7	5	114	1	0	1	0	1	0	0	0	0	2169	739	26	0	260	0	C2orf43	2	20901391	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3202916	20901391	222297982	119	18391										
APOB	338	hgsc.bcm.edu	37	chr2	21263838	21263838	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggctgcagcaaactcctcagAgttcttggttttcttcagca	9	11	4	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:21263838A>G	ENST00000233242.1	-	4	482	c.355T>C	c.(355-357)Tct>Cct	p.S119P	APOB_ENST00000399256.4_Missense_Mutation_p.S119P	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	119	Heparin-binding.|Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACTCCTCAGAGTTCTTGGTT	0.512																																					p.S119P		Atlas-SNP	.											.	APOB	761	.	0			c.T355C						.						112	88	96					2																	21263838		2203	4300	6503	SO:0001583	missense	338	exon4			CCTCAGAGTTCTT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.355T>C	chr2.hg19:g.21263838A>G	ENSP00000233242:p.Ser119Pro	109.0	0.0		139.0	6.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202606	0.79127	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.40476	1.03;1.03	4.9	4.9	0.64082	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.000000	0.56097	D	0.000028	T	0.64897	0.2640	M	0.78637	2.42	0.42803	D	0.993934	D	0.89917	1.0	D	0.91635	0.999	T	0.70428	-0.4874	10	0.72032	D	0.01	.	13.8314	0.63382	1.0:0.0:0.0:0.0	.	119	P04114	APOB_HUMAN	P	119	ENSP00000233242:S119P;ENSP00000382200:S119P	ENSP00000233242:S119P	S	-	1	0	APOB	21117343	1.000000	0.71417	0.998000	0.56505	0.937000	0.57800	2.630000	0.46494	1.974000	0.57490	0.533000	0.62120	TCT	.	.		0.512	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21263838	A	G	21263838	3	3	114	1	0	0	0	0	1	0	0	0	785	304	11	2	13440	2	APOB	2	21263838	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	362447	21263838	221935535	120	18392										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	24087705	24087705	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggctgaattttaaacttttcAaaaatttctggatataaaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:24087705delA	ENST00000238789.5	-	11	1621	c.1278delT	c.(1276-1278)tttfs	p.F426fs		NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	426						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAAACTTTTCAAAAATTTCTG	0.318																																					p.E427fs		Atlas-INDEL	.											.	ATAD2B	110	.	0			c.1279delG						.						37	35	36					2																	24087705		1796	4067	5863	SO:0001589	frameshift_variant	54454	exon11			.	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.1278delT	chr2.hg19:g.24087705delA	ENSP00000238789:p.Phe426fs	107.0	0.0		163.0	13.0	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Frame_Shift_Del	DEL	ENST00000238789.5	hg19	CCDS46227.1																																																																																			.	.		0.318	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		-	24087705	A	-	24087705	7	5	114	1	0	1	0	1	0	0	0	0	1072	127	5	0	3170	0	ATAD2B	2	24087705	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2823867	24087705	219111668	121	18393										
ITSN2	50618	hgsc.bcm.edu	37	chr2	24516590	24516590	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaactgcatgtttttaattcTttcatttaataattgcttct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:24516590delT	ENST00000355123.4	-	15	2133	c.1690delA	c.(1690-1692)agafs	p.R564fs	ITSN2_ENST00000361999.3_Frame_Shift_Del_p.R564fs|ITSN2_ENST00000406921.3_Frame_Shift_Del_p.R564fs	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	564					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTTTAATTCTTTCATTTAAT	0.294																																					p.R564fs		Atlas-INDEL	.											.	ITSN2	224	.	0			c.1691delG						.						112	113	113					2																	24516590		2202	4291	6493	SO:0001589	frameshift_variant	50618	exon15			.	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.1690delA	chr2.hg19:g.24516590delT	ENSP00000347244:p.Arg564fs	161.0	0.0		196.0	14.0	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Frame_Shift_Del	DEL	ENST00000355123.4	hg19	CCDS1710.2																																																																																			.	.		0.294	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		-	24516590	T	-	24516590	7	5	114	1	0	1	0	1	0	0	0	0	7936	1617	56	0	3558	0	ITSN2	2	24516590	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	428885	24516590	218682783	122	18394										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25505341	25505341	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggggctcctcggccctccttGggggtgcagcagccattttc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:25505341delG	ENST00000264709.3	-	4	754	c.417delC	c.(415-417)cccfs	p.P139fs	DNMT3A_ENST00000406659.3_Frame_Shift_Del_p.P139fs|DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.P139fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	139					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCCCTCCTTGGGGGTGCAGC	0.667			"Mis, F, N, S"		AML																																p.K140fs		Atlas-INDEL	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.418delA						.						20	23	22					2																	25505341		2202	4300	6502	SO:0001589	frameshift_variant	1788	exon4			.		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.417delC	chr2.hg19:g.25505341delG	ENSP00000264709:p.Pro139fs	121.0	0.0		158.0	12.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.		0.667	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		-	25505341	G	-	25505341	7	5	114	1	0	1	0	1	0	0	0	0	4678	1335	47	0	2534	0	DNMT3A	2	25505341	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	988751	25505341	217694032	123	18395										
HADHA	3030	hgsc.bcm.edu	37	chr2	26426951	26426951	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctttgaacacttgttgctgTcctcggtctagcgcagtgag	11	11	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:26426951T>C	ENST00000380649.3	-	12	1329	c.1200A>G	c.(1198-1200)ggA>ggG	p.G400G		NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	400					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTGTTGCTGTCCTCGGTCTA	0.498																																					p.G400G		Atlas-SNP	.											.	HADHA	87	.	0			c.A1200G						.						365	343	350					2																	26426951		2203	4300	6503	SO:0001819	synonymous_variant	3030	exon12			TTGCTGTCCTCGG	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.1200A>G	chr2.hg19:g.26426951T>C		112.0	0.0		163.0	7.0	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Silent	SNP	ENST00000380649.3	hg19	CCDS1721.1																																																																																			.	.		0.498	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		C	26426951	T	C	26426951	2	2	114	1	0	0	0	0	0	0	0	1	6952	1654	58	2		2	HADHA	2	26426951	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	921610	26426951	216772422	124	18396										
OTOF	9381	hgsc.bcm.edu	37	chr2	26724640	26724640	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acctggtaatccatgggccgCccagcacttggctccatctt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:26724640delC	ENST00000272371.2	-	8	873	c.747delG	c.(745-747)gggfs	p.G249fs	OTOF_ENST00000403946.3_Frame_Shift_Del_p.G249fs	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	249	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCATGGGCCGCCCAGCACTTG	0.537																																					p.R250fs	GBM(102;732 1451 20652 24062 31372)	Atlas-INDEL	.											.	OTOF	524	.	0			c.748delC						.						90	80	83					2																	26724640		2203	4300	6503	SO:0001589	frameshift_variant	9381	exon8			.	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.747delG	chr2.hg19:g.26724640delC	ENSP00000272371:p.Gly249fs	144.0	0.0		195.0	12.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Frame_Shift_Del	DEL	ENST00000272371.2	hg19	CCDS1725.1																																																																																			.	.		0.537	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			-	26724640	C	-	26724640	7	5	114	1	0	1	0	1	0	0	0	0	11312	726	26	0	5731	0	OTOF	2	26724640	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	297689	26724640	216474733	125	18397										
SUPT7L	9913	hgsc.bcm.edu	37	chr2	27883855	27883855	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caaagccttgccttaccgatAaaagtcactctctgggtcac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:27883855delA	ENST00000337768.5	-	3	984	c.415delT	c.(415-417)tatfs	p.Y139fs	SUPT7L_ENST00000404798.2_Intron|SLC4A1AP_ENST00000326019.6_5'Flank|SUPT7L_ENST00000405491.1_Frame_Shift_Del_p.Y137fs|SUPT7L_ENST00000406540.1_Frame_Shift_Del_p.Y137fs|SUPT7L_ENST00000464789.2_Frame_Shift_Del_p.Y137fs	NM_001282729.1|NM_014860.1	NP_001269658.1|NP_055675.1	O94864	ST65G_HUMAN	suppressor of Ty 7 (S. cerevisiae)-like	139					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|maintenance of protein location in nucleus (GO:0051457)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)					cctTACCGATAAAAGTCACTC	0.463																																					p.Y139fs		Atlas-INDEL	.											.	SUPT7L	36	.	0			c.416delA						.						75	75	75					2																	27883855		1978	4161	6139	SO:0001589	frameshift_variant	9913	exon3			.	AF197954	CCDS42667.1, CCDS62885.1, CCDS62886.1	2p23.3	2008-02-05			ENSG00000119760	ENSG00000119760			30632	protein-coding gene	gene with protein product		612762				9872452, 11564863	Standard	NM_001282732		Approved	STAF65, gamma, KIAA0764, SPT7L	uc002rli.1	O94864	OTTHUMG00000151947	ENST00000337768.5:c.415delT	chr2.hg19:g.27883855delA	ENSP00000336750:p.Tyr139fs	175.0	0.0		157.0	10.0	NM_014860	B4E3W3|Q6IB21|Q9H2T6	Frame_Shift_Del	DEL	ENST00000337768.5	hg19	CCDS42667.1																																																																																			.	.		0.463	SUPT7L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324568.1	NM_014860		-	27883855	A	-	27883855	7	5	114	1	0	1	0	1	0	0	0	0	15416	362	13	0	845	0	SUPT7L	2	27883855	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1159215	27883855	215315518	126	18398										
TRMT61B	55006	hgsc.bcm.edu	37	chr2	29087914	29087914	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaaaataagctcattccaccAgagcctgagccagcttccaa	6	13	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:29087914A>G	ENST00000306108.5	-	2	794	c.771T>C	c.(769-771)tcT>tcC	p.S257S		NM_017910.3	NP_060380.3	Q9BVS5	TR61B_HUMAN	tRNA methyltransferase 61 homolog B (S. cerevisiae)	257					mitochondrial tRNA methylation (GO:0070901)|protein homooligomerization (GO:0051260)	mitochondrion (GO:0005739)|tRNA (m1A) methyltransferase complex (GO:0031515)	tRNA (adenine-N1-)-methyltransferase activity (GO:0016429)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	13						TCATTCCACCAGAGCCTGAGC	0.373																																					p.S257S		Atlas-SNP	.											.	TRMT61B	28	.	0			c.T771C						.						70	63	65					2																	29087914		2203	4300	6503	SO:0001819	synonymous_variant	55006	exon2			TCCACCAGAGCCT	BC010365	CCDS1768.1	2p23.2	2009-01-09			ENSG00000171103	ENSG00000171103			26070	protein-coding gene	gene with protein product						11230166	Standard	NM_017910		Approved	FLJ20628	uc002rmm.3	Q9BVS5	OTTHUMG00000128433	ENST00000306108.5:c.771T>C	chr2.hg19:g.29087914A>G		86.0	0.0		88.0	4.0	NM_017910	Q9H0Q9|Q9NWS7	Silent	SNP	ENST00000306108.5	hg19	CCDS1768.1																																																																																			.	.		0.373	TRMT61B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250224.1	NM_017910		G	29087914	A	G	29087914	2	3	114	1	0	0	0	0	0	0	0	1	16585	175	7	2		2	TRMT61B	2	29087914	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1204059	29087914	214111459	127	18399										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29294038	29294038	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctggggctcacaggtgggctGgggggcgtctgcacagcaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:29294038delG	ENST00000331664.5	-	1	3089	c.3090delC	c.(3088-3090)cccfs	p.P1030fs		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1030	Pro-rich.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CAGGTGGGCTGGGGGGCGTCT	0.667																																					p.S1031fs		Atlas-INDEL	.											.	C2orf71	146	.	0			c.3091delA						.						29	35	33					2																	29294038		1942	4118	6060	SO:0001589	frameshift_variant	388939	exon1			.		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3090delC	chr2.hg19:g.29294038delG	ENSP00000332809:p.Pro1030fs	213.0	0.0		232.0	14.0	NM_001029883		Frame_Shift_Del	DEL	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.		0.667	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		-	29294038	G	-	29294038	7	5	114	1	0	1	0	1	0	0	0	0	2193	1335	47	0	784	0	C2orf71	2	29294038	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	206124	29294038	213905335	128	18400										
CLIP4	79745	hgsc.bcm.edu	37	chr2	29383293	29383293	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttagtggtaggacagagactGggcaccattaggttctttgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:29383293delG	ENST00000320081.5	+	12	1749	c.1494delG	c.(1492-1494)ctgfs	p.L498fs	CLIP4_ENST00000401617.2_Frame_Shift_Del_p.L391fs|CLIP4_ENST00000401605.1_Frame_Shift_Del_p.L498fs|CLIP4_ENST00000404424.1_Frame_Shift_Del_p.L498fs	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	498										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					GACAGAGACTGGGCACCATTA	0.423																																					p.L498fs		Atlas-INDEL	.											.	CLIP4	69	.	0			c.1493delT						.						121	113	116					2																	29383293		2203	4300	6503	SO:0001589	frameshift_variant	79745	exon12			.	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"Ankyrin repeat domain containing"	26108	protein-coding gene	gene with protein product			"restin-like 2"	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.1494delG	chr2.hg19:g.29383293delG	ENSP00000327009:p.Leu498fs	133.0	0.0		166.0	11.0	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Frame_Shift_Del	DEL	ENST00000320081.5	hg19	CCDS1770.1																																																																																			.	.		0.423	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		-	29383293	G	-	29383293	7	5	114	1	0	1	0	1	0	0	0	0	3537	1335	47	0	1536	0	CLIP4	2	29383293	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	89255	29383293	213816080	129	18401										
SLC30A6	55676	hgsc.bcm.edu	37	chr2	32417462	32417462	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acagtcttggcacagttgggAgctctctttatattaaaaga	9	7	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:32417462A>G	ENST00000282587.5	+	6	379	c.342A>G	c.(340-342)ggA>ggG	p.G114G	SLC30A6_ENST00000406369.1_Silent_p.G40G|SLC30A6_ENST00000435660.1_Silent_p.G114G|SLC30A6_ENST00000538303.1_Silent_p.G85G|SLC30A6_ENST00000357055.3_5'UTR|SLC30A6_ENST00000379343.2_Silent_p.G154G	NM_017964.3	NP_060434.2	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter), member 6	114					cellular protein metabolic process (GO:0044267)|Golgi to endosome transport (GO:0006895)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(4)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					CACAGTTGGGAGCTCTCTTTA	0.368																																					p.G154G		Atlas-SNP	.											.	SLC30A6	37	.	0			c.A462G						.						108	108	108					2																	32417462		2203	4300	6503	SO:0001819	synonymous_variant	55676	exon7			GTTGGGAGCTCTC	AK055663	CCDS1780.1, CCDS54341.1, CCDS54342.1, CCDS54343.1	2p22.3	2013-05-22			ENSG00000152683	ENSG00000152683		"Solute carriers"	19305	protein-coding gene	gene with protein product		611148					Standard	NM_017964		Approved	FLJ31101, ZNT6	uc002rof.2	Q6NXT4	OTTHUMG00000128456	ENST00000282587.5:c.342A>G	chr2.hg19:g.32417462A>G		95.0	0.0		93.0	4.0	NM_001193513	A5YM45|B7Z901|Q8N5C9|Q96NC3	Silent	SNP	ENST00000282587.5	hg19	CCDS1780.1																																																																																			.	.		0.368	SLC30A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250254.2			G	32417462	A	G	32417462	2	3	114	1	0	0	0	0	0	0	0	1	14574	291	11	2		2	SLC30A6	2	32417462	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3034169	32417462	210781911	130	18402										
NLRC4	58484	hgsc.bcm.edu	37	chr2	32449804	32449804	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaaattcaactgctggaagTttttcagagggttctttcca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:32449804delT	ENST00000404025.2	-	10	3301	c.2813delA	c.(2812-2814)aacfs	p.N938fs	NLRC4_ENST00000402280.1_Frame_Shift_Del_p.N938fs|NLRC4_ENST00000342905.6_Frame_Shift_Del_p.N273fs|NLRC4_ENST00000360906.5_Frame_Shift_Del_p.N938fs			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	938					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					CTGCTGGAAGTTTTTCAGAGG	0.348																																					p.N938fs		Atlas-INDEL	.											NLRC4_ENST00000404025,NS,carcinoma,0,1	NLRC4	165	.	0			c.2814delC						.						53	55	54					2																	32449804		2203	4300	6503	SO:0001589	frameshift_variant	58484	exon9			.	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.2813delA	chr2.hg19:g.32449804delT	ENSP00000385090:p.Asn938fs	77.0	0.0		102.0	11.0	NM_001199139	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Frame_Shift_Del	DEL	ENST00000404025.2	hg19	CCDS33174.1																																																																																			.	.		0.348	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		-	32449804	T	-	32449804	7	5	114	1	0	1	0	1	0	0	0	0	10478	1725	60	0	265	0	NLRC4	2	32449804	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	32342	32449804	210749569	131	18403										
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37455194	37455194	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccacttgcacaagaagagccTtttcttcctcaggcttgtta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:37455194delT	ENST00000234170.5	-	2	1287	c.1142delA	c.(1141-1143)aagfs	p.K381fs		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	381					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				AAGAAGAGCCTTTTCTTCCTC	0.418																																					p.K381fs		Atlas-INDEL	.											.	CEBPZ	68	.	0			c.1143delG						.						103	108	106					2																	37455194		2203	4300	6503	SO:0001589	frameshift_variant	10153	exon2			.	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1142delA	chr2.hg19:g.37455194delT	ENSP00000234170:p.Lys381fs	105.0	0.0		159.0	10.0	NM_005760	Q8NE75	Frame_Shift_Del	DEL	ENST00000234170.5	hg19	CCDS1787.1																																																																																			.	.		0.418	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		-	37455194	T	-	37455194	7	5	114	1	0	1	0	1	0	0	0	0	3206	1609	56	0	2082	0	CEBPZ	2	37455194	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	5005390	37455194	205744179	132	18404										
EML4	27436	hgsc.bcm.edu	37	chr2	42544610	42544610	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctcatgacaactttatttaCctctatgtagtctctgaaaa	4	9	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:42544610C>T	ENST00000318522.5	+	19	2362	c.2100C>T	c.(2098-2100)taC>taT	p.Y700Y	EML4_ENST00000453191.2_Intron|EML4_ENST00000402711.2_Silent_p.Y642Y|EML4_ENST00000401738.3_Silent_p.Y711Y	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	700					microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						ACTTTATTTACCTCTATGTAG	0.323			T	ALK	NSCLC																																p.Y700Y		Atlas-SNP	.		Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	.	EML4	92	.	0			c.C2100T						.						119	119	119					2																	42544610		2203	4298	6501	SO:0001819	synonymous_variant	27436	exon19			TATTTACCTCTAT	AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924		"WD repeat domain containing"	1316	protein-coding gene	gene with protein product		607442		C2orf2			Standard	NM_019063		Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.2100C>T	chr2.hg19:g.42544610C>T		88.0	0.0		98.0	4.0	NM_019063	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	Silent	SNP	ENST00000318522.5	hg19	CCDS1807.1																																																																																			.	.		0.323	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250463.3	NM_019063		T	42544610	C	T	42544610	2	4	114	1	0	0	0	0	0	0	0	1	5101	518	18	3		3	EML4	2	42544610	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	5089416	42544610	200654763	133	18405										
ABCG5	64240	hgsc.bcm.edu	37	chr2	44047175	44047175	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tagaaattcaccaattaagtGgggggccaagagagcagcag					rs199984328	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:44047175delG	ENST00000260645.1	-	11	1667	c.1528delC	c.(1528-1530)cacfs	p.H510fs	ABCG5_ENST00000543989.1_Frame_Shift_Del_p.H115fs|ABCG5_ENST00000405322.1_Frame_Shift_Del_p.H339fs	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	510	ABC transmembrane type-2.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	CCAATTAAGTGGGGGGCCAAG	0.463																																					p.H510fs		Atlas-INDEL	.											.	ABCG5	72	.	0			c.1529delA	GRCh37	CM074664	ABCG5	M		.						73	74	74					2																	44047175		2203	4300	6503	SO:0001589	frameshift_variant	64240	exon11			.	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"ATP binding cassette transporters / subfamily G"	13886	protein-coding gene	gene with protein product	"sterolin 1"	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.1528delC	chr2.hg19:g.44047175delG	ENSP00000260645:p.His510fs	148.0	0.0		150.0	10.0	NM_022436	Q2T9G2|Q96QZ2|Q96QZ3	Frame_Shift_Del	DEL	ENST00000260645.1	hg19	CCDS1814.1																																																																																			.	.		0.463	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436		-	44047175	G	-	44047175	7	5	114	1	0	1	0	1	0	0	0	0	71	1348	47	0	439	0	ABCG5	2	44047175	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1502565	44047175	199152198	134	18406										
SLC3A1	6519	hgsc.bcm.edu	37	chr2	44502687	44502687	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtgagacatggctgaagatAaaagcaagagagactccatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:44502687delA	ENST00000260649.6	+	1	89	c.13delA	c.(13-15)aaafs	p.K5fs	SLC3A1_ENST00000410056.3_Frame_Shift_Del_p.K5fs|SLC3A1_ENST00000409229.3_Frame_Shift_Del_p.K5fs|SLC3A1_ENST00000409387.1_Frame_Shift_Del_p.K5fs|SLC3A1_ENST00000409741.1_Frame_Shift_Del_p.K5fs	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	5					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	GGCTGAAGATAAAAGCAAGAG	0.488																																					p.D4fs		Atlas-INDEL	.											.	SLC3A1	62	.	0			c.12delT						.						58	57	58					2																	44502687		2203	4300	6503	SO:0001589	frameshift_variant	6519	exon1			.		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"Solute carriers"	11025	protein-coding gene	gene with protein product		104614	"solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.13delA	chr2.hg19:g.44502687delA	ENSP00000260649:p.Lys5fs	169.0	0.0		246.0	15.0	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Frame_Shift_Del	DEL	ENST00000260649.6	hg19	CCDS1819.1																																																																																			.	.		0.488	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341		-	44502687	A	-	44502687	7	5	114	1	0	1	0	1	0	0	0	0	14641	363	13	0	15	0	SLC3A1	2	44502687	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	455512	44502687	198696686	135	18407										
SRBD1	55133	hgsc.bcm.edu	37	chr2	45812867	45812867	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catcattaaagagacgaatgAtgttggcacaaacccaaggt	9	8	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:45812867A>G	ENST00000263736.4	-	5	757	c.695T>C	c.(694-696)aTc>aCc	p.I232T		NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	232					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			GAGACGAATGATGTTGGCACA	0.313																																					p.I232T		Atlas-SNP	.											.	SRBD1	107	.	0			c.T695C						.						104	109	108					2																	45812867		2203	4300	6503	SO:0001583	missense	55133	exon5			CGAATGATGTTGG	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.695T>C	chr2.hg19:g.45812867A>G	ENSP00000263736:p.Ile232Thr	58.0	0.0		75.0	4.0	NM_018079	Q53T56|Q96TA4|Q9NW11	Missense_Mutation	SNP	ENST00000263736.4	hg19	CCDS1823.1	.	.	.	.	.	.	.	.	.	.	A	9.156	1.017428	0.19355	.	.	ENSG00000068784	ENST00000263736	T	0.41400	1.0	5.04	2.69	0.31865	Tex-like protein, N-terminal (1);Tex-like protein, HTH domain (1);	0.156225	0.36972	N	0.002320	T	0.30479	0.0766	L	0.33792	1.035	0.80722	D	1	B	0.09022	0.002	B	0.15870	0.014	T	0.05616	-1.0874	10	0.24483	T	0.36	.	12.1881	0.54252	0.9233:0.0:0.0767:0.0	.	232	Q8N5C6	SRBD1_HUMAN	T	232	ENSP00000263736:I232T	ENSP00000263736:I232T	I	-	2	0	SRBD1	45666371	1.000000	0.71417	0.993000	0.49108	0.545000	0.35147	4.739000	0.62080	0.398000	0.25338	-1.438000	0.01074	ATC	.	.		0.313	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079		G	45812867	A	G	45812867	3	3	114	1	0	0	0	0	1	0	0	0	15148	333	12	2	2360	2	SRBD1	2	45812867	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1310180	45812867	197386506	136	18408										
MSH6	2956	hgsc.bcm.edu	37	chr2	48027194	48027194	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggtggttgtgtcttctaccTcaaaaaatgccttattgatc	8	8	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:48027194T>C	ENST00000234420.5	+	4	2224	c.2072T>C	c.(2071-2073)cTc>cCc	p.L691P	MSH6_ENST00000540021.1_Missense_Mutation_p.L561P|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_Missense_Mutation_p.L389P	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	691					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GTCTTCTACCTCAAAAAATGC	0.418			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.L691P		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T2072C						.						167	161	163					2																	48027194		2203	4300	6503	SO:0001583	missense	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TCTACCTCAAAAA	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.2072T>C	chr2.hg19:g.48027194T>C	ENSP00000234420:p.Leu691Pro	81.0	0.0		95.0	4.0	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	hg19	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	T	16.63	3.177804	0.57692	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000540021;ENST00000538136	D;D;D	0.90900	-2.75;-2.75;-2.75	5.01	5.01	0.66863	DNA mismatch repair protein MutS, connector (1);	0.000000	0.85682	D	0.000000	D	0.96414	0.8830	M	0.93808	3.46	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.97467	1.0038	10	0.87932	D	0	-10.0182	14.8876	0.70582	0.0:0.0:0.0:1.0	.	561;691;691	B4DF41;P52701;P52701-2	.;MSH6_HUMAN;.	P	691;689;561;389	ENSP00000234420:L691P;ENSP00000446475:L561P;ENSP00000438580:L389P	ENSP00000234420:L691P	L	+	2	0	MSH6	47880698	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.809000	0.86057	2.108000	0.64289	0.377000	0.23210	CTC	.	.		0.418	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		C	48027194	T	C	48027194	3	2	114	1	0	0	0	0	1	0	0	0	9883	1551	54	2	2086	2	MSH6	2	48027194	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2214327	48027194	195172179	137	18409										
PSME4	23198	hgsc.bcm.edu	37	chr2	54128608	54128608	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taagccctgaagaaacaatcGctggccacgtctgtacaata	8	11	1	2	rs369867748		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:54128608G>C	ENST00000404125.1	-	28	3219	c.3164C>G	c.(3163-3165)gCg>gGg	p.A1055G	PSME4_ENST00000421748.2_Missense_Mutation_p.A199G	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1055					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AGAAACAATCGCTGGCCACGT	0.443																																					p.A1055G		Atlas-SNP	.											.	PSME4	247	.	0			c.C3164G						.						143	136	138					2																	54128608		2203	4300	6503	SO:0001583	missense	23198	exon28			ACAATCGCTGGCC	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.3164C>G	chr2.hg19:g.54128608G>C	ENSP00000384211:p.Ala1055Gly	93.0	0.0		106.0	43.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	G	22.8	4.342604	0.82022	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.28069	1.63;1.69	5.6	5.6	0.85130	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	M	0.71581	2.175	0.80722	D	1	D;P;P	0.53151	0.958;0.783;0.93	P;P;P	0.54140	0.743;0.452;0.558	T	0.29212	-1.0019	10	0.21014	T	0.42	.	19.6148	0.95629	0.0:0.0:1.0:0.0	.	430;199;1055	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	G	199;1055	ENSP00000410830:A199G;ENSP00000384211:A1055G	ENSP00000384211:A1055G	A	-	2	0	PSME4	53982112	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.939000	0.87685	2.634000	0.89283	0.557000	0.71058	GCG	.	.		0.443	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		C	54128608	G	C	54128608	3	2	114	1	0	0	0	0	1	0	0	0	12721	1087	38	4	2443	4	PSME4	2	54128608	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	6101414	54128608	189070765	138	18410										
PSME4	23198	hgsc.bcm.edu	37	chr2	54133824	54133824	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acaaccctcaacagttagtgTccgtagctaagaaaacaatc	6	11	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:54133824T>C	ENST00000404125.1	-	26	2909	c.2854A>G	c.(2854-2856)Aca>Gca	p.T952A	PSME4_ENST00000421748.2_Missense_Mutation_p.T96A	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	952					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			ACAGTTAGTGTCCGTAGCTAA	0.308																																					p.T952A		Atlas-SNP	.											.	PSME4	247	.	0			c.A2854G						.						125	124	124					2																	54133824		2203	4300	6503	SO:0001583	missense	23198	exon26			TTAGTGTCCGTAG	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.2854A>G	chr2.hg19:g.54133824T>C	ENSP00000384211:p.Thr952Ala	91.0	0.0		95.0	4.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	13.84	2.357921	0.41801	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.10860	2.83;2.83	5.57	5.57	0.84162	Armadillo-type fold (1);	0.046373	0.85682	D	0.000000	T	0.08133	0.0203	L	0.29908	0.895	0.51482	D	0.999925	B;B;B	0.30824	0.296;0.205;0.196	B;B;B	0.26416	0.069;0.023;0.021	T	0.11372	-1.0590	10	0.07030	T	0.85	.	16.0388	0.80650	0.0:0.0:0.0:1.0	.	327;96;952	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	A	96;952	ENSP00000410830:T96A;ENSP00000384211:T952A	ENSP00000384211:T952A	T	-	1	0	PSME4	53987328	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.655000	0.83696	2.242000	0.73789	0.528000	0.53228	ACA	.	.		0.308	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		C	54133824	T	C	54133824	3	2	114	1	0	0	0	0	1	0	0	0	12721	1667	58	2	2761	2	PSME4	2	54133824	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	5216	54133824	189065549	139	18411										
SMEK2	57223	hgsc.bcm.edu	37	chr2	55791450	55791450	+	Splice_Site	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaattccgaattttaataccTtttttagtctccataaactt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:55791450delT	ENST00000345102.5	-	15	2560	c.2259delA	c.(2257-2259)aaa>aa	p.K753fs	SNORA12_ENST00000390873.1_RNA|SMEK2_ENST00000407823.3_Splice_Site_p.K721fs|SMEK2_ENST00000272313.5_Splice_Site_p.K668fs	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	753					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TTTTAATACCTTTTTTAGTCT	0.333																																					p.A754fs		Atlas-INDEL	.											.	SMEK2	86	.	0			c.2260delG						.						89	87	88					2																	55791450		2202	4298	6500	SO:0001630	splice_region_variant	57223	exon15			.	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.2260+1A>-	chr2.hg19:g.55791450delT		128.0	0.0		178.0	11.0	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Frame_Shift_Del	DEL	ENST00000345102.5	hg19	CCDS46289.1																																																																																			.	.		0.333	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463	Frame_Shift_Del	-	55791450	T	-	55791450	8	5	114	1	0	1	0	1	0	0	1	0	14809	1623	56	0	302	0	SMEK2	2	55791450	Splice_Site	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1657626	55791450	187407923	140	18412										
BCL11A	53335	hgsc.bcm.edu	37	chr2	60688969	60688969	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcggattgcagaggagggaGggggggcgtcgccaggaagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:60688969delG	ENST00000335712.6	-	4	1305	c.1078delC	c.(1078-1080)ctcfs	p.L360fs	BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000537768.1_Intron|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000356842.4_Frame_Shift_Del_p.L360fs|BCL11A_ENST00000538214.1_Frame_Shift_Del_p.L326fs|BCL11A_ENST00000358510.4_Frame_Shift_Del_p.L326fs	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	360	Pro-rich.				B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			AGAGGAGGGAGGGGGGGCGTC	0.632			T	IGH@	B-CLL																																p.L360fs		Atlas-INDEL	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.1079delT						.						39	48	44					2																	60688969		2198	4297	6495	SO:0001589	frameshift_variant	53335	exon4			.	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"Zinc fingers, C2H2-type"	13221	protein-coding gene	gene with protein product		606557	"ecotropic viral integration site 9"	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.1078delC	chr2.hg19:g.60688969delG	ENSP00000338774:p.Leu360fs	141.0	0.0		191.0	13.0	NM_022893	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Frame_Shift_Del	DEL	ENST00000335712.6	hg19	CCDS1862.1																																																																																			.	.		0.632	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		-	60688969	G	-	60688969	7	5	114	1	0	1	0	1	0	0	0	0	1363	1000	35	0	1539	0	BCL11A	2	60688969	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	4897519	60688969	182510404	141	18413										
REL	5966	hgsc.bcm.edu	37	chr2	61147771	61147771	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttggagaaggaagatacttcAaaaaaggtattttatttcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:61147771delA	ENST00000295025.8	+	10	1401	c.1081delA	c.(1081-1083)aaafs	p.K362fs	REL_ENST00000394479.3_Frame_Shift_Del_p.K330fs	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	362					cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			AAGATACTTCAAAAAAGGTAT	0.318			A		Hodgkin Lymphoma																																p.F360fs		Atlas-INDEL	.		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	REL	48	.	0			c.1080delC						.						34	38	37					2																	61147771		2202	4295	6497	SO:0001589	frameshift_variant	5966	exon10			.	M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.1081delA	chr2.hg19:g.61147771delA	ENSP00000295025:p.Lys362fs	153.0	0.0		213.0	13.0	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Frame_Shift_Del	DEL	ENST00000295025.8	hg19	CCDS1864.1																																																																																			.	.		0.318	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908		-	61147771	A	-	61147771	7	5	114	1	0	1	0	1	0	0	0	0	13230	131	5	0	1119	0	REL	2	61147771	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	458802	61147771	182051602	142	18414										
KIAA1841	84542	hgsc.bcm.edu	37	chr2	61304238	61304238	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacattttcaactggttgatAaaatacattaaaaggaacac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:61304238delA	ENST00000402291.1	+	6	856	c.615delA	c.(613-615)atafs	p.I205fs	KIAA1841_ENST00000356719.2_Frame_Shift_Del_p.I205fs|KIAA1841_ENST00000453873.1_Frame_Shift_Del_p.I205fs|KIAA1841_ENST00000295031.5_Frame_Shift_Del_p.I205fs|KIAA1841_ENST00000482513.1_3'UTR	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	205										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			ACTGGTTGATAAAATACATTA	0.358																																					p.I205fs		Atlas-INDEL	.											.	KIAA1841	95	.	0			c.614delT						.						90	94	93					2																	61304238		2203	4300	6503	SO:0001589	frameshift_variant	84542	exon6			.	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.615delA	chr2.hg19:g.61304238delA	ENSP00000385579:p.Ile205fs	145.0	0.0		183.0	11.0	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Frame_Shift_Del	DEL	ENST00000402291.1	hg19	CCDS46296.1																																																																																			.	.		0.358	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506		-	61304238	A	-	61304238	7	5	114	1	0	1	0	1	0	0	0	0	8270	352	13	0	629	0	KIAA1841	2	61304238	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	156467	61304238	181895135	143	18415										
USP34	9736	hgsc.bcm.edu	37	chr2	61507429	61507429	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aactaatttgcataacaaccAaaaatactctttacatcctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:61507429delA	ENST00000398571.2	-	39	5282	c.5206delT	c.(5206-5208)tggfs	p.W1736fs		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1736					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			CATAACAACCAAAAATACTCT	0.244																																					p.W1736fs		Atlas-INDEL	.											.	USP34	334	.	0			c.5207delG						.						55	55	55					2																	61507429		1793	4046	5839	SO:0001589	frameshift_variant	9736	exon39			.	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.5206delT	chr2.hg19:g.61507429delA	ENSP00000381577:p.Trp1736fs	176.0	0.0		195.0	13.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Frame_Shift_Del	DEL	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.		0.244	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			-	61507429	A	-	61507429	7	5	114	1	0	1	0	1	0	0	0	0	17080	130	5	0	5602	0	USP34	2	61507429	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	203191	61507429	181691944	144	18416										
FAM161A	84140	hgsc.bcm.edu	37	chr2	62067256	62067256	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttgactaaatcatggtaaaGggggagaaagacagatgcag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:62067256delG	ENST00000405894.3	-	3	984	c.883delC	c.(883-885)cttfs	p.L295fs	FAM161A_ENST00000404929.1_Frame_Shift_Del_p.L295fs	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	295					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TCATGGTAAAGGGGGAGAAAG	0.393																																					p.L295fs		Atlas-INDEL	.											.	FAM161A	200	.	0			c.884delT						.						169	153	158					2																	62067256		1850	4091	5941	SO:0001589	frameshift_variant	84140	exon3			.		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"retinitis pigmentosa 28 (autosomal recessive)"	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.883delC	chr2.hg19:g.62067256delG	ENSP00000385893:p.Leu295fs	155.0	0.0		156.0	11.0	NM_032180	B4DJV7|Q9H8R2	Frame_Shift_Del	DEL	ENST00000405894.3	hg19	CCDS42687.2																																																																																			.	.		0.393	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		-	62067256	G	-	62067256	7	5	114	1	0	1	0	1	0	0	0	0	5477	1000	35	0	1115	0	FAM161A	2	62067256	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	559827	62067256	181132117	145	18417										
EHBP1	23301	hgsc.bcm.edu	37	chr2	63176136	63176136	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagatccagaatctcctatcAaaaaaacaagtttatctcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:63176136delA	ENST00000263991.5	+	14	2742	c.2260delA	c.(2260-2262)aaafs	p.K755fs	EHBP1_ENST00000405015.3_Frame_Shift_Del_p.K720fs|EHBP1_ENST00000354487.3_Frame_Shift_Del_p.K720fs|EHBP1_ENST00000405289.1_Frame_Shift_Del_p.K720fs|EHBP1_ENST00000431489.1_Frame_Shift_Del_p.K720fs	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	755			K -> Q (in dbSNP:rs17432615).			cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			ATCTCCTATCAAAAAAACAAG	0.373																																					p.I753fs		Atlas-INDEL	.											.	EHBP1	127	.	0			c.2259delC						.						42	46	45					2																	63176136		2202	4299	6501	SO:0001589	frameshift_variant	23301	exon14			.	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.2260delA	chr2.hg19:g.63176136delA	ENSP00000263991:p.Lys755fs	163.0	0.0		177.0	12.0	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Frame_Shift_Del	DEL	ENST00000263991.5	hg19	CCDS1872.1																																																																																			.	.		0.373	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		-	63176136	A	-	63176136	7	5	114	1	0	1	0	1	0	0	0	0	4977	131	5	0	2310	0	EHBP1	2	63176136	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1108880	63176136	180023237	146	18418										
RAB1A	5861	hgsc.bcm.edu	37	chr2	65316146	65316146	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctaccaacaatttgttgacaTtttcactggcataacgatct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:65316146delT	ENST00000409784.3	-	5	537	c.347delA	c.(346-348)aatfs	p.N116fs	RAB1A_ENST00000409892.1_Frame_Shift_Del_p.N52fs|RAB1A_ENST00000409751.1_Frame_Shift_Del_p.N84fs|RAB1A_ENST00000494188.1_Intron|RAB1A_ENST00000260638.8_Intron|RAB1A_ENST00000356214.7_Frame_Shift_Del_p.N84fs|RAB1A_ENST00000398529.3_Intron	NM_004161.4	NP_004152.1	P62820	RAB1A_HUMAN	RAB1A, member RAS oncogene family	116					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cargo loading into COPII-coated vesicle (GO:0090110)|cell migration (GO:0016477)|defense response to bacterium (GO:0042742)|endocytosis (GO:0006897)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|growth hormone secretion (GO:0030252)|GTP catabolic process (GO:0006184)|interleukin-8 secretion (GO:0072606)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|positive regulation of glycoprotein metabolic process (GO:1903020)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle transport along microtubule (GO:0047496)|vesicle-mediated transport (GO:0016192)|virion assembly (GO:0019068)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|melanosome (GO:0042470)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|kidney(1)|lung(3)|prostate(1)	6						TTTGTTGACATTTTCACTGGC	0.333																																					p.N116fs		Atlas-INDEL	.											.	RAB1A	15	.	0			c.348delT						.						74	65	68					2																	65316146		1880	4104	5984	SO:0001589	frameshift_variant	5861	exon5			.	M28209	CCDS46305.1, CCDS46306.1	2p14	2008-02-05		2002-03-17	ENSG00000138069	ENSG00000138069		"RAB, member RAS oncogene"	9758	protein-coding gene	gene with protein product	"Rab GTPase YPT1 homolog (yeast)"	179508		RAB1		2501306	Standard	NM_004161		Approved	YPT1	uc002sdm.3	P62820	OTTHUMG00000152725	ENST00000409784.3:c.347delA	chr2.hg19:g.65316146delT	ENSP00000387286:p.Asn116fs	122.0	0.0		153.0	10.0	NM_004161	P11476|Q6FIE7|Q96N61|Q9Y3T2	Frame_Shift_Del	DEL	ENST00000409784.3	hg19	CCDS46306.1																																																																																			.	.		0.333	RAB1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327572.1	NM_004161		-	65316146	T	-	65316146	7	5	114	1	0	1	0	1	0	0	0	0	12920	1493	52	0	278	0	RAB1A	2	65316146	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2140010	65316146	177883227	147	18419										
C2orf42	54980	hgsc.bcm.edu	37	chr2	70402864	70402864	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggccacttttccttagattaCtgctcactgcatcttgaggc	8	12	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:70402864C>T	ENST00000264434.2	-	5	1359	c.980G>A	c.(979-981)aGt>aAt	p.S327N	C2orf42_ENST00000420306.1_Missense_Mutation_p.S327N	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	327										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						CCTTAGATTACTGCTCACTGC	0.408																																					p.S327N		Atlas-SNP	.											.	C2orf42	30	.	0			c.G980A						.						215	212	213					2																	70402864		2203	4300	6503	SO:0001583	missense	54980	exon5			AGATTACTGCTCA	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.980G>A	chr2.hg19:g.70402864C>T	ENSP00000264434:p.Ser327Asn	120.0	0.0		117.0	43.0	NM_017880	D6W5G3|Q9H629	Missense_Mutation	SNP	ENST00000264434.2	hg19	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.444671	0.43429	.	.	ENSG00000115998	ENST00000264434;ENST00000420306	D;D	0.93247	-3.19;-3.19	4.86	4.86	0.63082	.	0.448742	0.25596	N	0.029598	D	0.86793	0.6018	N	0.22421	0.69	0.26026	N	0.981805	B	0.33238	0.403	B	0.30029	0.11	T	0.78585	-0.2147	10	0.29301	T	0.29	-18.4621	13.335	0.60512	0.0:1.0:0.0:0.0	.	327	Q9NWW7	CB042_HUMAN	N	327	ENSP00000264434:S327N;ENSP00000404515:S327N	ENSP00000264434:S327N	S	-	2	0	C2orf42	70256368	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.937000	0.40193	2.516000	0.84829	0.491000	0.48974	AGT	.	.		0.408	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880		T	70402864	C	T	70402864	3	4	114	1	0	0	0	0	1	0	0	0	2168	565	20	3	768	3	C2orf42	2	70402864	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	5086718	70402864	172796509	148	18420										
SMYD5	10322	hgsc.bcm.edu	37	chr2	73452036	73452036	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcagagacctcctttccagAaaacaacttccttttgcatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:73452036delA	ENST00000389501.4	+	11	1028	c.983delA	c.(982-984)gaafs	p.E328fs		NM_006062.2	NP_006053.2	Q6GMV2	SMYD5_HUMAN	SMYD family member 5	328	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13						TCCTTTCCAGAAAACAACTTC	0.483																																					p.E328fs		Atlas-INDEL	.											.	SMYD5	58	.	0			c.982delG						.						125	107	113					2																	73452036		2203	4300	6503	SO:0001589	frameshift_variant	10322	exon11			.	U50383	CCDS33221.2	2p12	2007-02-09	2003-05-14	2003-05-16	ENSG00000135632	ENSG00000135632		"Zinc fingers, MYND-type"	16258	protein-coding gene	gene with protein product			"retinoic acid induced 15"	RAI15		8754834	Standard	NM_006062		Approved	RRG1, NN8-4AG, ZMYND23	uc002siw.2	Q6GMV2	OTTHUMG00000150482	ENST00000389501.4:c.983delA	chr2.hg19:g.73452036delA	ENSP00000374152:p.Glu328fs	131.0	0.0		133.0	11.0	NM_006062	D6W5H3|Q13558	Frame_Shift_Del	DEL	ENST00000389501.4	hg19	CCDS33221.2																																																																																			.	.		0.483	SMYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318301.1	NM_006062		-	73452036	A	-	73452036	7	5	114	1	0	1	0	1	0	0	0	0	14840	246	9	0	1025	0	SMYD5	2	73452036	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3049172	73452036	169747337	149	18421										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73653590	73653590	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctattttgtagagggcctgcAggggaaggttgagtctgacg	16	6	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:73653590A>G	ENST00000264448.6	+	6	1358	c.1247A>G	c.(1246-1248)cAg>cGg	p.Q416R	ALMS1_ENST00000377715.1_Missense_Mutation_p.Q416R|ALMS1_ENST00000409009.1_Missense_Mutation_p.Q374R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	416					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GAGGGCCTGCAGGGGAAGGTT	0.433																																					p.Q416R		Atlas-SNP	.											.	ALMS1	384	.	0			c.A1247G						.						236	225	229					2																	73653590		1938	4139	6077	SO:0001583	missense	7840	exon6			GCCTGCAGGGGAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.1247A>G	chr2.hg19:g.73653590A>G	ENSP00000264448:p.Gln416Arg	131.0	0.0		158.0	7.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.031238	0.35797	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.21191	2.9;2.9;2.02	5.2	4.02	0.46733	.	0.158118	0.30356	N	0.009813	T	0.30696	0.0773	L	0.36672	1.1	0.22701	N	0.998836	D;D	0.71674	0.998;0.998	D;D	0.66351	0.943;0.943	T	0.04413	-1.0953	10	0.87932	D	0	.	8.2798	0.31894	0.8238:0.0:0.0:0.1762	.	374;416	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	R	374;416;416	ENSP00000386627:Q374R;ENSP00000264448:Q416R;ENSP00000366944:Q416R	ENSP00000264448:Q416R	Q	+	2	0	ALMS1	73507098	0.956000	0.32656	1.000000	0.80357	0.547000	0.35210	1.156000	0.31712	1.074000	0.40909	0.533000	0.62120	CAG	.	.		0.433	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		G	73653590	A	G	73653590	3	3	114	1	0	0	0	0	1	0	0	0	535	188	7	2	1269	2	ALMS1	2	73653590	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	201554	73653590	169545783	150	18422										
POLR1A	25885	hgsc.bcm.edu	37	chr2	86297358	86297358	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcagtgtgggctgtcggttcAgtagcagaatgtccccattc	13	10	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:86297358A>G	ENST00000263857.6	-	13	2027	c.1649T>C	c.(1648-1650)cTg>cCg	p.L550P	POLR1A_ENST00000409681.1_Missense_Mutation_p.L550P			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	550					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						CTGTCGGTTCAGTAGCAGAAT	0.577																																					p.L550P		Atlas-SNP	.											.	POLR1A	137	.	0			c.T1649C						.						76	83	80					2																	86297358		2132	4228	6360	SO:0001583	missense	25885	exon13			CGGTTCAGTAGCA	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1649T>C	chr2.hg19:g.86297358A>G	ENSP00000263857:p.Leu550Pro	139.0	0.0		186.0	9.0	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.597932	0.66332	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.76316	-1.01;-1.01	5.3	5.3	0.74995	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91676	0.7369	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94197	0.7446	10	0.87932	D	0	-13.9506	14.9235	0.70859	1.0:0.0:0.0:0.0	.	550	O95602	RPA1_HUMAN	P	550	ENSP00000263857:L550P;ENSP00000386300:L550P	ENSP00000263857:L550P	L	-	2	0	POLR1A	86150869	1.000000	0.71417	0.980000	0.43619	0.986000	0.74619	8.935000	0.92923	2.007000	0.58848	0.533000	0.62120	CTG	.	.		0.577	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		G	86297358	A	G	86297358	3	3	114	1	0	0	0	0	1	0	0	0	12218	188	7	2	3601	2	POLR1A	2	86297358	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	12643768	86297358	156902015	151	18423										
RMND5A	64795	hgsc.bcm.edu	37	chr2	86992185	86992185	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccgggaaatgcttatagctcAaaacagctccttggaattta					rs201043371		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:86992185delA	ENST00000283632.4	+	5	1052	c.557delA	c.(556-558)caafs	p.Q186fs		NM_022780.3	NP_073617.1	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog A (S. cerevisiae)	186	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.									kidney(1)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	17						CTTATAGCTCAAAACAGCTCC	0.358																																					p.Q186fs		Atlas-INDEL	.											.	RMND5A	33	.	0			c.556delC						.						135	130	132					2																	86992185		2203	4300	6503	SO:0001589	frameshift_variant	64795	exon5			.	BC012165	CCDS1991.1	2p11.2	2012-07-20			ENSG00000153561	ENSG00000153561			25850	protein-coding gene	gene with protein product	"GID complex subunit 2 homolog A"					12477932	Standard	NM_022780		Approved	FLJ13910, RMD5, GID2, GID2A	uc002srs.4	Q9H871	OTTHUMG00000130262	ENST00000283632.4:c.557delA	chr2.hg19:g.86992185delA	ENSP00000283632:p.Gln186fs	173.0	0.0		214.0	13.0	NM_022780	D6W5M6|Q6NTF0|Q9H6W5|Q9H9H2	Frame_Shift_Del	DEL	ENST00000283632.4	hg19	CCDS1991.1																																																																																			.	.		0.358	RMND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252591.2	NM_022780		-	86992185	A	-	86992185	7	5	114	1	0	1	0	1	0	0	0	0	13412	130	5	0	575	0	RMND5A	2	86992185	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	694827	86992185	156207188	152	18424										
KRCC1	51315	hgsc.bcm.edu	37	chr2	88327573	88327573	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttagaccgctcctcctctgaTttttctctgccttcctctgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:88327573delT	ENST00000347055.3	-	4	903	c.510delA	c.(508-510)aaafs	p.K170fs		NM_016618.1	NP_057702.1	Q9NPI7	KRCC1_HUMAN	lysine-rich coiled-coil 1	170	Lys-rich.									cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	7						CCTCCTCTGATTTTTCTCTGC	0.428																																					p.S171fs		Atlas-INDEL	.											.	KRCC1	25	.	0			c.511delT						.						120	121	121					2																	88327573		2203	4300	6503	SO:0001589	frameshift_variant	51315	exon4			.	AF208845	CCDS2000.1	2p11.2	2008-02-05			ENSG00000172086	ENSG00000172086			28039	protein-coding gene	gene with protein product						12477932	Standard	XM_005264360		Approved	FLJ22333	uc002sso.1	Q9NPI7	OTTHUMG00000130315	ENST00000347055.3:c.510delA	chr2.hg19:g.88327573delT	ENSP00000340083:p.Lys170fs	238.0	0.0		354.0	24.0	NM_016618	Q3B7J7	Frame_Shift_Del	DEL	ENST00000347055.3	hg19	CCDS2000.1																																																																																			.	.		0.428	KRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252664.1	NM_016618		-	88327573	T	-	88327573	7	5	114	1	0	1	0	1	0	0	0	0	8450	1490	52	0	273	0	KRCC1	2	88327573	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1335388	88327573	154871800	153	18425										
ZAP70	7535	hgsc.bcm.edu	37	chr2	98351044	98351044	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacacgagcgtgtatgagagCccctacagcgacccagagga	13	12	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:98351044C>T	ENST00000264972.5	+	9	1166	c.951C>T	c.(949-951)agC>agT	p.S317S	ZAP70_ENST00000442208.1_Silent_p.S191S|ZAP70_ENST00000451498.2_Silent_p.S10S|ZAP70_ENST00000463643.1_3'UTR	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	317	Interdomain B.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						TGTATGAGAGCCCCTACAGCG	0.587																																					p.S317S		Atlas-SNP	.											.	ZAP70	77	.	0			c.C951T						.						116	101	106					2																	98351044		2203	4300	6503	SO:0001819	synonymous_variant	7535	exon9			TGAGAGCCCCTAC	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"SH2 domain containing"	12858	protein-coding gene	gene with protein product		176947	"zeta-chain (TCR) associated protein kinase (70 kD)"	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.951C>T	chr2.hg19:g.98351044C>T		80.0	0.0		99.0	4.0	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Silent	SNP	ENST00000264972.5	hg19	CCDS33254.1																																																																																			.	.		0.587	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1			T	98351044	C	T	98351044	2	4	114	1	0	0	0	0	0	0	0	1	17529	738	26	3		3	ZAP70	2	98351044	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	10023471	98351044	144848329	154	18426										
AFF3	3899	hgsc.bcm.edu	37	chr2	100170975	100170975	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggagaggggttgggagacatGggggatggggttccagtgct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:100170975delG	ENST00000409236.2	-	22	3469	c.3357delC	c.(3355-3357)cccfs	p.P1119fs	AFF3_ENST00000317233.4_Frame_Shift_Del_p.P1119fs|AFF3_ENST00000356421.2_Frame_Shift_Del_p.P1144fs|AFF3_ENST00000409579.1_Frame_Shift_Del_p.P1144fs			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	1119					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						TGGGAGACATGGGGGATGGGG	0.652																																					p.M1145fs		Atlas-INDEL	.											.	AFF3	164	.	0			c.3433delA						.						28	29	28					2																	100170975		2203	4299	6502	SO:0001589	frameshift_variant	3899	exon23			.	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.3357delC	chr2.hg19:g.100170975delG	ENSP00000387207:p.Pro1119fs	70.0	0.0		103.0	10.0	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Frame_Shift_Del	DEL	ENST00000409236.2	hg19	CCDS42723.1																																																																																			.	.		0.652	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		-	100170975	G	-	100170975	7	5	114	1	0	1	0	1	0	0	0	0	358	1335	47	0	331	0	AFF3	2	100170975	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1819931	100170975	143028398	155	18427										
IL1R2	7850	hgsc.bcm.edu	37	chr2	102636130	102636130	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttttggataaagacaatgagAaatttctaagtgtgaggggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:102636130delA	ENST00000332549.3	+	5	773	c.544delA	c.(544-546)aaafs	p.K182fs	IL1R2_ENST00000441002.1_Frame_Shift_Del_p.K182fs|IL1R2_ENST00000393414.2_Frame_Shift_Del_p.K182fs	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	182	Ig-like C2-type 2.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						AGACAATGAGAAATTTCTAAG	0.398																																					p.E181fs	Pancreas(106;189 1628 2302 5133 12295)	Atlas-INDEL	.											.	IL1R2	58	.	0			c.543delG						.						80	75	77					2																	102636130		2203	4300	6503	SO:0001589	frameshift_variant	7850	exon5			.	X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.544delA	chr2.hg19:g.102636130delA	ENSP00000330959:p.Lys182fs	129.0	0.0		178.0	11.0	NM_004633	D3DVJ5|Q6LCE6|Q9UE68	Frame_Shift_Del	DEL	ENST00000332549.3	hg19	CCDS2054.1																																																																																			.	.		0.398	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633		-	102636130	A	-	102636130	7	5	114	1	0	1	0	1	0	0	0	0	7668	247	9	0	558	0	IL1R2	2	102636130	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2465155	102636130	140563243	156	18428										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109392277	109392277	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccttctttctgtaaatctgaAgaacctgattctattaccaa	4	10	4	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:109392277A>G	ENST00000283195.6	+	24	8508	c.8382A>G	c.(8380-8382)gaA>gaG	p.E2794E		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2794					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GTAAATCTGAAGAACCTGATT	0.378																																					p.E2794E		Atlas-SNP	.											.	RANBP2	488	.	0			c.A8382G						.						161	160	160					2																	109392277		2203	4300	6503	SO:0001819	synonymous_variant	5903	exon24			ATCTGAAGAACCT	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.8382A>G	chr2.hg19:g.109392277A>G		83.0	0.0		96.0	4.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	hg19	CCDS2079.1																																																																																			.	.		0.378	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109392277	A	G	109392277	2	3	114	1	0	0	0	0	0	0	0	1	13043	69	3	2		2	RANBP2	2	109392277	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	6756147	109392277	133807096	157	18429										
CCDC138	165055	hgsc.bcm.edu	37	chr2	109492664	109492664	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattcaactctgttcaatctGggtttaacaaaatgtaactc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:109492664delG	ENST00000295124.4	+	15	2013	c.1953delG	c.(1951-1953)ctgfs	p.L651fs	CCDC138_ENST00000412964.2_3'UTR	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	651										endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						TGTTCAATCTGGGTTTAACAA	0.338																																					p.L651fs		Atlas-INDEL	.											.	CCDC138	49	.	0			c.1952delT						.						80	80	80					2																	109492664		2203	4300	6503	SO:0001589	frameshift_variant	165055	exon15			.	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.1953delG	chr2.hg19:g.109492664delG	ENSP00000295124:p.Leu651fs	157.0	0.0		199.0	12.0	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Frame_Shift_Del	DEL	ENST00000295124.4	hg19	CCDS2080.1																																																																																			.	.		0.338	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978		-	109492664	G	-	109492664	7	5	114	1	0	1	0	1	0	0	0	0	2774	1335	47	0	2011	0	CCDC138	2	109492664	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	100387	109492664	133706709	158	18430										
RGPD5	729540	hgsc.bcm.edu	37	chr2	111292773	111292773	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atcaaatctaaatagttttaCcccctgtgaatacagaactt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:111292773delC	ENST00000329516.3	-	20	3266	c.3190delG	c.(3190-3192)gtafs	p.V1064fs		NM_001123363.3	NP_001116835.1	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 6	1064	RanBD1 1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)											AATAGTTTTACCCCCTGTGAA	0.393																																					p.V1064fs		Atlas-INDEL	.											.	RGPD5	1	.	0			c.3191delT						.																																			SO:0001589	frameshift_variant	84220	exon20			.	AK056675	CCDS46388.1, CCDS42729.1	2q13	2013-01-10			ENSG00000183054	ENSG00000183054		"Tetratricopeptide (TTC) repeat domain containing"	32419	protein-coding gene	gene with protein product		612709				15710750, 15815621, 9480752	Standard	NM_001037866		Approved	RGP6	uc021vly.1	Q99666	OTTHUMG00000153196	ENST00000329516.3:c.3190delG	chr2.hg19:g.111292773delC	ENSP00000330842:p.Val1064fs	99.0	0.0		132.0	10.0	NM_005054	Q53QN2|Q53T03|Q59GM7|Q9H0B2	Frame_Shift_Del	DEL	ENST00000329516.3	hg19	CCDS46388.1																																																																																			.	.		0.393	RGPD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330029.5	NM_001123363		-	111292773	C	-	111292773	7	5	114	1	0	1	0	1	0	0	0	0	13304	507	18	0	7630	0	RGPD5	2	111292773	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1800109	111292773	131906600	159	18431										
TMEM87B	84910	hgsc.bcm.edu	37	chr2	112839016	112839016	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agaatccagttctggattgcAgctgttatttttttgggaat	10	5	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:112839016A>G	ENST00000283206.4	+	8	1128	c.759A>G	c.(757-759)gcA>gcG	p.A253A		NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	253						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						TCTGGATTGCAGCTGTTATTT	0.358																																					p.A253A		Atlas-SNP	.											.	TMEM87B	52	.	0			c.A759G						.						137	148	144					2																	112839016		2203	4300	6503	SO:0001819	synonymous_variant	84910	exon8			GATTGCAGCTGTT	AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.759A>G	chr2.hg19:g.112839016A>G		95.0	0.0		117.0	5.0	NM_032824	A8K2M9|Q1RLN2|Q53R54	Silent	SNP	ENST00000283206.4	hg19	CCDS33275.1																																																																																			.	.		0.358	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824		G	112839016	A	G	112839016	2	3	114	1	0	0	0	0	0	0	0	1	16226	175	7	2		2	TMEM87B	2	112839016	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1546243	112839016	130360357	160	18432										
CKAP2L	150468	hgsc.bcm.edu	37	chr2	113520086	113520086	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acagataaactcacttggtgTtttggctcttcagttttccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:113520086delT	ENST00000302450.6	-	2	176	c.98delA	c.(97-99)aacfs	p.N33fs	CKAP2L_ENST00000481732.1_5'UTR|CKAP2L_ENST00000541405.1_5'UTR	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	33						centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						TCACTTGGTGTTTTGGCTCTT	0.413																																					p.N33fs		Atlas-INDEL	.											.	CKAP2L	54	.	0			c.99delC						.						196	161	173					2																	113520086		2203	4300	6503	SO:0001589	frameshift_variant	150468	exon2			.	AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.98delA	chr2.hg19:g.113520086delT	ENSP00000305204:p.Asn33fs	83.0	0.0		156.0	10.0	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Frame_Shift_Del	DEL	ENST00000302450.6	hg19	CCDS2100.1																																																																																			.	.		0.413	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515		-	113520086	T	-	113520086	7	5	114	1	0	1	0	1	0	0	0	0	3445	1725	60	0	2171	0	CKAP2L	2	113520086	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	681070	113520086	129679287	161	18433										
DDX18	8886	hgsc.bcm.edu	37	chr2	118579744	118579744	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ataccccaggatttatgtatAaaaacctgcagtgtctggtt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:118579744delA	ENST00000263239.2	+	7	1101	c.973delA	c.(973-975)aaafs	p.K325fs	DDX18_ENST00000474694.1_3'UTR	NM_006773.3	NP_006764.3	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	325	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ATTTATGTATAAAAACCTGCA	0.348																																					p.Y324X		Atlas-INDEL	.											.	DDX18	79	.	0			c.972delT						.						129	125	126					2																	118579744		2203	4300	6503	SO:0001589	frameshift_variant	8886	exon7			.	X98743	CCDS2120.1	2q21.2	2008-02-05	2003-06-13		ENSG00000088205	ENSG00000088205		"DEAD-boxes"	2741	protein-coding gene	gene with protein product		606355	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-regulated)"			8861962	Standard	NM_006773		Approved	MrDb	uc002tlh.1	Q9NVP1	OTTHUMG00000058521	ENST00000263239.2:c.973delA	chr2.hg19:g.118579744delA	ENSP00000263239:p.Lys325fs	177.0	0.0		229.0	14.0	NM_006773	Q6GTZ9|Q6IAU4|Q92732|Q9BQB7	Frame_Shift_Del	DEL	ENST00000263239.2	hg19	CCDS2120.1																																																																																			.	.		0.348	DDX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129632.3	NM_006773		-	118579744	A	-	118579744	7	5	114	1	0	1	0	1	0	0	0	0	4347	363	13	0	999	0	DDX18	2	118579744	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	5059658	118579744	124619629	162	18434										
CCDC93	54520	hgsc.bcm.edu	37	chr2	118735578	118735578	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtttttcttaccttctccaTtttgctctggcggctaaatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:118735578delT	ENST00000376300.2	-	8	786	c.649delA	c.(649-651)atgfs	p.M217fs	CCDC93_ENST00000319432.5_Frame_Shift_Del_p.M216fs|CCDC93_ENST00000460781.1_5'UTR	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	217										breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						ACCTTCTCCATTTTGCTCTGG	0.398																																					p.M217fs		Atlas-INDEL	.											.	CCDC93	70	.	0			c.650delT						.						166	139	148					2																	118735578		2203	4300	6503	SO:0001589	frameshift_variant	54520	exon8			.	BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.649delA	chr2.hg19:g.118735578delT	ENSP00000365477:p.Met217fs	145.0	0.0		147.0	10.0	NM_019044	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Frame_Shift_Del	DEL	ENST00000376300.2	hg19	CCDS2121.2																																																																																			.	.		0.398	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044		-	118735578	T	-	118735578	7	5	114	1	0	1	0	1	0	0	0	0	2874	1493	52	0	1314	0	CCDC93	2	118735578	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	155834	118735578	124463795	163	18435										
SMPD4	55627	hgsc.bcm.edu	37	chr2	130910956	130910956	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgatgcagtcggggagttgcTtttttccattctcatcctgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:130910956delT	ENST00000409031.1	-	18	3226	c.2078delA	c.(2077-2079)aagfs	p.K693fs	SMPD4_ENST00000443958.2_Frame_Shift_Del_p.K357fs|SMPD4_ENST00000473720.1_5'Flank|SMPD4_ENST00000339679.7_Frame_Shift_Del_p.K551fs|SMPD4_ENST00000426662.2_Frame_Shift_Del_p.K329fs|SMPD4_ENST00000452225.2_Frame_Shift_Del_p.K434fs|SMPD4_ENST00000453750.1_Frame_Shift_Del_p.K442fs|SMPD4_ENST00000351288.6_Frame_Shift_Del_p.K664fs|SMPD4_ENST00000431183.2_Frame_Shift_Del_p.K591fs	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	654				L -> Q (in Ref. 2; BAA91567). {ECO:0000305}.	cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	GGGGAGTTGCTTTTTTCCATT	0.617																																					p.K693fs		Atlas-INDEL	.											.	SMPD4	67	.	0			c.2079delG						.						81	68	72					2																	130910956		2203	4300	6503	SO:0001589	frameshift_variant	55627	exon18			.	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.2078delA	chr2.hg19:g.130910956delT	ENSP00000386531:p.Lys693fs	156.0	0.0		194.0	12.0	NM_017951	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Frame_Shift_Del	DEL	ENST00000409031.1	hg19	CCDS42751.1																																																																																			.	.		0.617	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751		-	130910956	T	-	130910956	7	5	114	1	0	1	0	1	0	0	0	0	14822	1609	56	0	534	0	SMPD4	2	130910956	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	12175378	130910956	112288417	164	18436										
LCT	3938	hgsc.bcm.edu	37	chr2	136594658	136594658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggaccagcggtggaaatgaAatttctatcagactcccagt	10	9	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:136594658A>G	ENST00000264162.2	-	1	92	c.82T>C	c.(82-84)Ttc>Ctc	p.F28L		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	28					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GTGGAAATGAAATTTCTATCA	0.468																																					p.F28L		Atlas-SNP	.											.	LCT	309	.	0			c.T82C						.						51	52	52					2																	136594658		2203	4300	6503	SO:0001583	missense	3938	exon1			AAATGAAATTTCT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.82T>C	chr2.hg19:g.136594658A>G	ENSP00000264162:p.Phe28Leu	68.0	0.0		94.0	42.0	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	hg19	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	a	13.41	2.230199	0.39399	.	.	ENSG00000115850	ENST00000264162	T	0.31769	1.48	5.16	3.98	0.46160	Glycoside hydrolase, superfamily (1);	0.130956	0.51477	D	0.000090	T	0.20455	0.0492	L	0.36672	1.1	0.38355	D	0.944447	P	0.49090	0.919	B	0.37550	0.253	T	0.07214	-1.0784	10	0.18710	T	0.47	-21.1719	12.0775	0.53652	0.8559:0.1441:0.0:0.0	.	28	P09848	LPH_HUMAN	L	28	ENSP00000264162:F28L	ENSP00000264162:F28L	F	-	1	0	LCT	136311128	0.995000	0.38212	0.875000	0.34327	0.149000	0.21700	3.430000	0.52807	0.944000	0.37579	0.529000	0.55759	TTC	.	.		0.468	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		G	136594658	A	G	136594658	3	3	114	1	0	0	0	0	1	0	0	0	8702	14	1	2	5769	2	LCT	2	136594658	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	5683702	136594658	106604715	165	18437										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141739764	141739764	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catctgtctggtcaccacagTcgtcttccctgtcacacagc	7	16	5	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:141739764T>C	ENST00000389484.3	-	18	3823	c.2852A>G	c.(2851-2853)gAc>gGc	p.D951G		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	951	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GTCACCACAGTCGTCTTCCCT	0.448										TSP Lung(27;0.18)																											p.D951G	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A2852G						.						150	130	137					2																	141739764		2203	4300	6503	SO:0001583	missense	53353	exon18			CCACAGTCGTCTT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2852A>G	chr2.hg19:g.141739764T>C	ENSP00000374135:p.Asp951Gly	89.0	0.0		120.0	5.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.456410	0.84317	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.98947	-5.26;-5.26	5.43	5.43	0.79202	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	U	0.000000	D	0.99536	0.9834	H	0.98802	4.335	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.997	D	0.97791	1.0238	10	0.72032	D	0.01	.	15.4805	0.75521	0.0:0.0:0.0:1.0	.	134;951	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	G	951;889;96	ENSP00000374135:D951G;ENSP00000413239:D96G	ENSP00000374135:D951G	D	-	2	0	LRP1B	141456234	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	7.292000	0.78731	2.053000	0.61076	0.533000	0.62120	GAC	.	.		0.448	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141739764	T	C	141739764	3	2	114	1	0	0	0	0	1	0	0	0	8964	1667	58	2	11243	2	LRP1B	2	141739764	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	5145106	141739764	101459609	166	18438										
MBD5	55777	hgsc.bcm.edu	37	chr2	149243489	149243489	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccttgcccagctaacaataaCcccatggcttgtctgtttca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:149243489delC	ENST00000407073.1	+	11	4021	c.3024delC	c.(3022-3024)aacfs	p.N1008fs	MBD5_ENST00000404807.1_Frame_Shift_Del_p.N1241fs	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1008					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		CTAACAATAACCCCATGGCTT	0.443																																					p.N1008fs		Atlas-INDEL	.											.	MBD5	164	.	0			c.3023delA						.						107	113	111					2																	149243489		2203	4300	6503	SO:0001589	frameshift_variant	55777	exon11			.	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.3024delC	chr2.hg19:g.149243489delC	ENSP00000386049:p.Asn1008fs	155.0	0.0		204.0	13.0	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Frame_Shift_Del	DEL	ENST00000407073.1	hg19	CCDS33302.1																																																																																			.	.		0.443	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			-	149243489	C	-	149243489	7	5	114	1	0	1	0	1	0	0	0	0	9356	506	18	0	3046	0	MBD5	2	149243489	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	7503725	149243489	93955884	167	18439										
MBD5	55777	hgsc.bcm.edu	37	chr2	149247480	149247480	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagcaagttgccacacatccAaaaaacagtgggacggggag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:149247480delA	ENST00000407073.1	+	12	4577	c.3580delA	c.(3580-3582)aaafs	p.K1195fs	MBD5_ENST00000404807.1_Frame_Shift_Del_p.K1428fs	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1195					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		CCACACATCCAAAAAACAGTG	0.488																																					p.S1193fs		Atlas-INDEL	.											.,1	MBD5	164	.	0			c.3579delC						.						95	99	98					2																	149247480		2203	4300	6503	SO:0001589	frameshift_variant	55777	exon12			.	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.3580delA	chr2.hg19:g.149247480delA	ENSP00000386049:p.Lys1195fs	121.0	0.0		166.0	11.0	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Frame_Shift_Del	DEL	ENST00000407073.1	hg19	CCDS33302.1																																																																																			.	.		0.488	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			-	149247480	A	-	149247480	7	5	114	1	0	1	0	1	0	0	0	0	9356	131	5	0	3606	0	MBD5	2	149247480	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3991	149247480	93951893	168	18440										
ARL5A	26225	hgsc.bcm.edu	37	chr2	152668893	152668893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catgcgctaacattttatagAgttcttctctagttacagaa	6	8	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:152668893A>G	ENST00000295087.8	-	4	628	c.317T>C	c.(316-318)cTc>cCc	p.L106P	ARL5A_ENST00000428992.2_Missense_Mutation_p.L69P	NM_001037174.1|NM_012097.3	NP_001032251.1|NP_036229.1	Q9Y689	ARL5A_HUMAN	ADP-ribosylation factor-like 5A	106					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			breast(1)|large_intestine(2)|liver(1)|lung(2)	6				BRCA - Breast invasive adenocarcinoma(221;0.153)		CATTTTATAGAGTTCTTCTCT	0.318																																					p.L106P		Atlas-SNP	.											.	ARL5A	12	.	0			c.T317C						.						78	75	76					2																	152668893		2202	4296	6498	SO:0001583	missense	26225	exon4			TTATAGAGTTCTT	AF100740	CCDS2195.1, CCDS46425.1	2q23.3	2014-05-09	2005-11-03	2005-11-03	ENSG00000162980	ENSG00000162980		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	696	protein-coding gene	gene with protein product		608960	"ADP-ribosylation factor-like 5"	ARL5			Standard	NM_012097		Approved		uc002txx.1	Q9Y689	OTTHUMG00000131887	ENST00000295087.8:c.317T>C	chr2.hg19:g.152668893A>G	ENSP00000295087:p.Leu106Pro	84.0	0.0		143.0	6.0	NM_012097	Q580I5	Missense_Mutation	SNP	ENST00000295087.8	hg19	CCDS2195.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.376076	0.82682	.	.	ENSG00000162980	ENST00000295087;ENST00000452215;ENST00000428992	T;T	0.77098	-1.07;-1.07	5.01	5.01	0.66863	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.93575	0.7949	H	0.99770	4.765	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96305	0.9224	10	0.87932	D	0	-8.2811	14.7257	0.69343	1.0:0.0:0.0:0.0	.	106	Q9Y689	ARL5A_HUMAN	P	106;69;69	ENSP00000295087:L106P;ENSP00000415950:L69P	ENSP00000295087:L106P	L	-	2	0	ARL5A	152377139	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.339000	0.96797	1.886000	0.54624	0.377000	0.23210	CTC	.	.		0.318	ARL5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254837.1			G	152668893	A	G	152668893	3	3	114	1	0	0	0	0	1	0	0	0	939	304	11	2	234	2	ARL5A	2	152668893	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3421413	152668893	90530480	169	18441										
NR4A2	4929	hgsc.bcm.edu	37	chr2	157184439	157184439	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggcactgatcagactcaccGggggcgaagggggagagggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:157184439delG	ENST00000339562.4	-	5	1444	c.1082delC	c.(1081-1083)ccgfs	p.P361fs	NR4A2_ENST00000409108.2_Frame_Shift_Del_p.P361fs|NR4A2_ENST00000409572.1_Frame_Shift_Del_p.P361fs|NR4A2_ENST00000539077.1_Frame_Shift_Del_p.P372fs|NR4A2_ENST00000429376.1_Frame_Shift_Del_p.P298fs|NR4A2_ENST00000426264.1_Frame_Shift_Del_p.P298fs	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	361	Pro-rich.				adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						CAGACTCACCGGGGGCGAAGG	0.597																																					p.P361fs		Atlas-INDEL	.											.	NR4A2	82	.	0			c.1083delG						.						25	26	26					2																	157184439		2203	4298	6501	SO:0001589	frameshift_variant	4929	exon5			.	X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"Nuclear hormone receptors"	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.1082delC	chr2.hg19:g.157184439delG	ENSP00000344479:p.Pro361fs	138.0	0.0		200.0	12.0	NM_006186	Q16311|Q53RZ2|Q6NXU0	Frame_Shift_Del	DEL	ENST00000339562.4	hg19	CCDS2201.1																																																																																			.	.		0.597	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2			-	157184439	G	-	157184439	7	5	114	1	0	1	0	1	0	0	0	0	10642	1116	39	0	730	0	NR4A2	2	157184439	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	4515546	157184439	86014934	170	18442										
WDSUB1	151525	hgsc.bcm.edu	37	chr2	160092653	160092653	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcatgggacttgtacgtttcTttttgctgatccaattttcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:160092653delT	ENST00000409990.3	-	11	1578	c.1322delA	c.(1321-1323)aagfs	p.K442fs	WDSUB1_ENST00000359774.4_Frame_Shift_Del_p.K442fs|WDSUB1_ENST00000409124.1_Frame_Shift_Del_p.K395fs|WDSUB1_ENST00000358147.4_Frame_Shift_Del_p.K350fs|WDSUB1_ENST00000392796.3_Frame_Shift_Del_p.K442fs	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	442	U-box.						ubiquitin-protein transferase activity (GO:0004842)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|stomach(3)	16						TGTACGTTTCTTTTTGCTGAT	0.373																																					p.K441fs		Atlas-INDEL	.											.	WDSUB1	39	.	0			c.1323delG						.						112	101	104					2																	160092653		2203	4300	6503	SO:0001589	frameshift_variant	151525	exon11			.	AK093494	CCDS2208.1	2q24.2	2013-01-28	2006-02-17	2005-03-25	ENSG00000196151	ENSG00000196151		"WD repeat domain containing", "Sterile alpha motif (SAM) domain containing", "U-box domain containing"	26697	protein-coding gene	gene with protein product			"WD repeat and SAM domain containing 1", "WD repeat, SAM and U-box domain containing 1"	WDSAM1		12477932	Standard	NM_152528		Approved	UBOX6, FLJ36175	uc002ual.4	Q8N9V3	OTTHUMG00000132028	ENST00000409990.3:c.1322delA	chr2.hg19:g.160092653delT	ENSP00000387078:p.Lys442fs	110.0	0.0		148.0	11.0	NM_152528	Q53TI9|Q8N6N8	Frame_Shift_Del	DEL	ENST00000409990.3	hg19	CCDS2208.1																																																																																			.	.		0.373	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528		-	160092653	T	-	160092653	7	5	114	1	0	1	0	1	0	0	0	0	17356	1609	56	0	112	0	WDSUB1	2	160092653	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2908214	160092653	83106720	171	18443										
LY75	4065	hgsc.bcm.edu	37	chr2	160661583	160661583	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggaaagaaggaagcataatcTcatcttcattcactccttgt	7	9	4	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:160661583T>C	ENST00000263636.4	-	35	5168	c.5141A>G	c.(5140-5142)gAg>gGg	p.E1714G	LY75_ENST00000554112.1_Intron|LY75_ENST00000553424.1_Intron|LY75-CD302_ENST00000504764.1_Intron|LY75-CD302_ENST00000505052.1_Intron	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1714					endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		AAGCATAATCTCATCTTCATT	0.403																																					p.E1714G		Atlas-SNP	.											.	LY75	151	.	0			c.A5141G						.						80	76	77					2																	160661583		2203	4300	6503	SO:0001583	missense	4065	exon35			ATAATCTCATCTT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.5141A>G	chr2.hg19:g.160661583T>C	ENSP00000263636:p.Glu1714Gly	86.0	0.0		97.0	4.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.365558	0.82463	.	.	ENSG00000054219	ENST00000263636	T	0.11930	2.73	5.57	5.57	0.84162	.	1.577580	0.04385	N	0.361427	T	0.29716	0.0742	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.63488	0.915	T	0.00062	-1.2157	10	0.42905	T	0.14	.	13.2425	0.60006	0.0:0.0:0.0:1.0	.	1714	O60449	LY75_HUMAN	G	1714	ENSP00000263636:E1714G	ENSP00000263636:E1714G	E	-	2	0	LY75	160369829	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.502000	0.60400	2.128000	0.65567	0.533000	0.62120	GAG	.	.		0.403	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			C	160661583	T	C	160661583	3	2	114	1	0	0	0	0	1	0	0	0	9108	1551	54	2	31	2	LY75	2	160661583	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	568930	160661583	82537790	172	18444										
ITGB6	3694	hgsc.bcm.edu	37	chr2	160958277	160958277	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtggaaaggtctaccttttgTttttccctgtgtttataagt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:160958277delT	ENST00000283249.2	-	15	2574	c.2337delA	c.(2335-2337)aaafs	p.K779fs	ITGB6_ENST00000428609.2_Frame_Shift_Del_p.K737fs|ITGB6_ENST00000409872.1_Frame_Shift_Del_p.K779fs|ITGB6_ENST00000409967.2_Frame_Shift_Del_p.K672fs	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	779					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						CTACCTTTTGTTTTTCCCTGT	0.308																																					p.Q780fs		Atlas-INDEL	.											.	ITGB6	68	.	0			c.2338delC						.						170	166	167					2																	160958277		2202	4300	6502	SO:0001589	frameshift_variant	3694	exon15			.		CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"Integrins"	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.2337delA	chr2.hg19:g.160958277delT	ENSP00000283249:p.Lys779fs	135.0	0.0		162.0	11.0	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Frame_Shift_Del	DEL	ENST00000283249.2	hg19	CCDS2212.1																																																																																			.	.		0.308	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888		-	160958277	T	-	160958277	7	5	114	1	0	1	0	1	0	0	0	0	7908	1722	60	0	33	0	ITGB6	2	160958277	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	296694	160958277	82241096	173	18445										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166866301	166866301	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcctgagagatttgatggcTccaagttctgagtaacccaa	10	9	1	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:166866301T>C	ENST00000303395.4	-	20	3929	c.3930A>G	c.(3928-3930)ggA>ggG	p.G1310G	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Silent_p.G1299G|SCN1A_ENST00000409050.1_Silent_p.G1282G|SCN1A_ENST00000423058.2_Silent_p.G1310G			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1310					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATTTGATGGCTCCAAGTTCTG	0.378																																					p.G1310G		Atlas-SNP	.											.	SCN1A	641	.	0			c.A3930G						.						91	90	90					2																	166866301		2203	4300	6503	SO:0001819	synonymous_variant	6323	exon20			GATGGCTCCAAGT	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3930A>G	chr2.hg19:g.166866301T>C		61.0	0.0		96.0	4.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.378	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		C	166866301	T	C	166866301	2	2	114	1	0	0	0	0	0	0	0	1	13929	1538	54	2		2	SCN1A	2	166866301	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	5908024	166866301	76333072	174	18446										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166903448	166903448	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccaagaaaatgaccaatacAaaaaatatcatgtacgtttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:166903448delA	ENST00000303395.4	-	9	1208	c.1209delT	c.(1207-1209)tttfs	p.F403fs	AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000375405.3_Frame_Shift_Del_p.F403fs|SCN1A_ENST00000409050.1_Frame_Shift_Del_p.F403fs|SCN1A_ENST00000423058.2_Frame_Shift_Del_p.F403fs|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	403			F -> L (in EIEE6; dbSNP:rs121917966). {ECO:0000269|PubMed:16713920, ECO:0000269|PubMed:17347258}.		adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGACCAATACAAAAAATATCA	0.393																																					p.V404fs		Atlas-Indel,Pindel	.											.	SCN1A	641	.	0			c.1210delG						.						100	97	98					2																	166903448		2203	4300	6503	SO:0001589	frameshift_variant	6323	exon9			.	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1209delT	chr2.hg19:g.166903448delA	ENSP00000303540:p.Phe403fs	131.0	0.0		183.0	13.0	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Frame_Shift_Del	DEL	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.393	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		-	166903448	A	-	166903448	7	5	114	1	0	1	0	1	0	0	0	0	13929	127	5	0	4892	0	SCN1A	2	166903448	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	37147	166903448	76295925	175	18447										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167313428	167313428	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcttttccagtctgttgaaaTtttggttcaatcttcttaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:167313428delT	ENST00000409855.1	-	10	1368	c.1242delA	c.(1240-1242)aaafs	p.K414fs		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	414					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TCTGTTGAAATTTTGGTTCAA	0.313																																					p.F415fs		Atlas-INDEL	.											.	SCN7A	410	.	0			c.1243delT						.						56	52	53					2																	167313428		1794	4048	5842	SO:0001589	frameshift_variant	6332	exon10			.	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.1242delA	chr2.hg19:g.167313428delT	ENSP00000386796:p.Lys414fs	169.0	0.0		194.0	12.0	NM_002976		Frame_Shift_Del	DEL	ENST00000409855.1	hg19	CCDS46442.1																																																																																			.	.		0.313	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			-	167313428	T	-	167313428	7	5	114	1	0	1	0	1	0	0	0	0	13938	1490	52	0	3870	0	SCN7A	2	167313428	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	409980	167313428	75885945	176	18448										
ABCB11	8647	hgsc.bcm.edu	37	chr2	169874628	169874628	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tacttcgaagaattactgagTcagacatggtaattgcaacc	8	8	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:169874628T>C	ENST00000263817.6	-	2	132	c.8A>G	c.(7-9)gAc>gGc	p.D3G		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	3					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	AATTACTGAGTCAGACATGGT	0.348																																					p.D3G		Atlas-SNP	.											.	ABCB11	136	.	0			c.A8G						.						109	103	105					2																	169874628		1833	4087	5920	SO:0001583	missense	8647	exon2			ACTGAGTCAGACA	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"ATP binding cassette transporters / subfamily B"	42	protein-coding gene	gene with protein product	"ABC member 16, MDR/TAP subfamily"	603201	"progressive familial intrahepatic cholestasis 2", "bile salt export pump"	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.8A>G	chr2.hg19:g.169874628T>C	ENSP00000263817:p.Asp3Gly	50.0	0.0		82.0	4.0	NM_003742	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	hg19	CCDS46444.1	.	.	.	.	.	.	.	.	.	.	T	9.611	1.131152	0.21041	.	.	ENSG00000073734	ENST00000263817	D	0.86865	-2.18	5.86	5.86	0.93980	.	0.598116	0.18524	N	0.138690	T	0.75700	0.3885	N	0.08118	0	0.36440	D	0.865428	B	0.15141	0.012	B	0.09377	0.004	T	0.74019	-0.3799	10	0.33141	T	0.24	-8.9785	14.0078	0.64475	0.0:0.0:0.0:1.0	.	3	O95342	ABCBB_HUMAN	G	3	ENSP00000263817:D3G	ENSP00000263817:D3G	D	-	2	0	ABCB11	169582874	0.999000	0.42202	0.945000	0.38365	0.098000	0.18820	3.519000	0.53458	2.240000	0.73641	0.533000	0.62120	GAC	.	.		0.348	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742		C	169874628	T	C	169874628	3	2	114	1	0	0	0	0	1	0	0	0	42	1667	58	2	4065	2	ABCB11	2	169874628	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2561200	169874628	73324745	177	18449										
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170387133	170387133	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccagaatttccaaatgtcgTtttttcatagcagattttcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:170387133delT	ENST00000453153.2	-	14	2752	c.2406delA	c.(2404-2406)aaafs	p.K802fs	FASTKD1_ENST00000495505.1_5'UTR|FASTKD1_ENST00000453929.2_Frame_Shift_Del_p.K759fs	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	802	RAP. {ECO:0000255|PROSITE- ProRule:PRU00619}.				cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						CCAAATGTCGTTTTTTCATAG	0.338																																					p.R803fs		Atlas-INDEL	.											.	FASTKD1	86	.	0			c.2407delC						.						151	163	159					2																	170387133		2203	4300	6503	SO:0001589	frameshift_variant	79675	exon14			.	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.2406delA	chr2.hg19:g.170387133delT	ENSP00000400513:p.Lys802fs	230.0	0.0		285.0	20.0	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Frame_Shift_Del	DEL	ENST00000453153.2	hg19	CCDS33318.1																																																																																			.	.		0.338	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		-	170387133	T	-	170387133	7	5	114	1	0	1	0	1	0	0	0	0	5693	1722	60	0	145	0	FASTKD1	2	170387133	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	512505	170387133	72812240	178	18450										
WIPF1	7456	hgsc.bcm.edu	37	chr2	175436765	175436765	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgtcatccaaggccctgctGggggtaggcggcaggggagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:175436765delG	ENST00000392547.2	-	5	867	c.768delC	c.(766-768)cccfs	p.P256fs	WIPF1_ENST00000409891.1_Frame_Shift_Del_p.P256fs|AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000409415.3_Frame_Shift_Del_p.P256fs|WIPF1_ENST00000467149.1_5'Flank|WIPF1_ENST00000392546.2_Frame_Shift_Del_p.P256fs|WIPF1_ENST00000272746.5_Frame_Shift_Del_p.P256fs|AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000359761.3_Frame_Shift_Del_p.P256fs	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	256					actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)			NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						AGGCCCTGCTGGGGGTAGGCG	0.647																																					p.S257fs		Atlas-INDEL	.											.	WIPF1	88	.	0			c.769delA						.						16	18	17					2																	175436765		2199	4296	6495	SO:0001589	frameshift_variant	7456	exon5			.	AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"Wiskott-Aldrich syndrome protein interacting protein"	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.768delC	chr2.hg19:g.175436765delG	ENSP00000376330:p.Pro256fs	135.0	0.0		194.0	12.0	NM_003387	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Frame_Shift_Del	DEL	ENST00000392547.2	hg19	CCDS2260.1																																																																																			.	.		0.647	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387		-	175436765	G	-	175436765	7	5	114	1	0	1	0	1	0	0	0	0	17382	1335	47	0	759	0	WIPF1	2	175436765	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	5049632	175436765	67762608	179	18451										
DFNB59	494513	hgsc.bcm.edu	37	chr2	179325894	179325894	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctgtggaatggggaacttcAaaagggagacagtttatggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179325894delA	ENST00000409117.3	+	7	1308	c.952delA	c.(952-954)aaafs	p.K318fs	DFNB59_ENST00000375129.4_Frame_Shift_Del_p.K318fs	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	318					sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			GGGGAACTTCAAAAGGGAGAC	0.418																																					p.F317fs		Atlas-INDEL	.											.	DFNB59	37	.	0			c.951delC						.						176	164	168					2																	179325894		1869	4117	5986	SO:0001589	frameshift_variant	494513	exon7			.	BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311			29502	protein-coding gene	gene with protein product		610219				16804542	Standard	NM_001042702		Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.952delA	chr2.hg19:g.179325894delA	ENSP00000386647:p.Lys318fs	114.0	0.0		152.0	10.0	NM_001042702	A0PK14|B9EJE2	Frame_Shift_Del	DEL	ENST00000409117.3	hg19	CCDS42787.1																																																																																			.	.		0.418	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335160.1			-	179325894	A	-	179325894	7	5	114	1	0	1	0	1	0	0	0	0	4458	131	5	0	974	0	DFNB59	2	179325894	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3889129	179325894	63873479	180	18452										
TTN	7273	hgsc.bcm.edu	37	chr2	179483342	179483342	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaattgatgaatccttctgcTtttccatgtttgttctgaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179483342delT	ENST00000591111.1	-	201	42236	c.42012delA	c.(42010-42012)aaafs	p.K14004fs	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.K6705fs|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.K13077fs|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.K6772fs|TTN_ENST00000589042.1_Frame_Shift_Del_p.K15645fs|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.K6580fs|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14004	Ig-like 95.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATCCTTCTGCTTTTCCATGTT	0.363																																					p.A15646fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.46936delG						.						175	160	165					2																	179483342		1829	4074	5903	SO:0001589	frameshift_variant	7273	exon251			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.42012delA	chr2.hg19:g.179483342delT	ENSP00000465570:p.Lys14004fs	83.0	0.0		129.0	12.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179483342	T	-	179483342	7	5	114	1	0	1	0	1	0	0	0	0	16750	1606	56	0	61206	0	TTN	2	179483342	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	157448	179483342	63716031	181	18453										
TTN	7273	hgsc.bcm.edu	37	chr2	179560924	179560924	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagcttctttttctttctgaAcctctttctttctggttata	4	10	6	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179560924A>G	ENST00000591111.1	-	112	30148	c.29924T>C	c.(29923-29925)gTt>gCt	p.V9975A	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V9048A|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V10292A|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTTTCTGAACCTCTTTCTT	0.348																																					p.V10292A		Atlas-SNP	.											.	TTN	18412	.	0			c.T30875C						.						68	55	59					2																	179560924		1802	4045	5847	SO:0001583	missense	7273	exon114			TTCTGAACCTCTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.29924T>C	chr2.hg19:g.179560924A>G	ENSP00000465570:p.Val9975Ala	67.0	0.0		99.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.96	2.093867	0.36952	.	.	ENSG00000155657	ENST00000342992;ENST00000414766	T	0.65549	-0.16	5.28	5.28	0.74379	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.56016	0.1957	L	0.51422	1.61	0.80722	D	1	B;B	0.32507	0.021;0.373	B;B	0.31495	0.014;0.131	T	0.60840	-0.7183	9	0.87932	D	0	.	11.6393	0.51222	1.0:0.0:0.0:0.0	.	9975;9975	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	A	9048;170	ENSP00000343764:V9048A	ENSP00000343764:V9048A	V	-	2	0	TTN	179269169	1.000000	0.71417	1.000000	0.80357	0.368000	0.29767	4.525000	0.60559	2.004000	0.58718	0.528000	0.53228	GTT	.	.		0.348	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179560924	A	G	179560924	3	3	114	1	0	0	0	0	1	0	0	0	16750	43	2	2	73650	2	TTN	2	179560924	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	77582	179560924	63638449	182	18454										
TTN	7273	hgsc.bcm.edu	37	chr2	179579232	179579232	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcagcgccttcaatggtagTctgcagctgaacttctttac	8	11	4	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179579232T>C	ENST00000591111.1	-	89	25542	c.25318A>G	c.(25318-25320)Act>Gct	p.T8440A	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T7513A|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.T8757A|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12611	Ig-like 67.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAATGGTAGTCTGCAGCTGA	0.408																																					p.T8757A		Atlas-SNP	.											.	TTN	18412	.	0			c.A26269G						.						64	59	60					2																	179579232		1862	4102	5964	SO:0001583	missense	7273	exon91			TGGTAGTCTGCAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25318A>G	chr2.hg19:g.179579232T>C	ENSP00000465570:p.Thr8440Ala	98.0	0.0		93.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	7.880	0.729943	0.15507	.	.	ENSG00000155657	ENST00000342992	T	0.38401	1.14	5.96	-5.91	0.02269	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.10252	0.0251	N	0.00124	-2.055	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39035	-0.9633	9	0.87932	D	0	.	21.5632	0.99956	0.0:0.8617:0.0:0.1383	.	8440	Q8WZ42	TITIN_HUMAN	A	7513	ENSP00000343764:T7513A	ENSP00000343764:T7513A	T	-	1	0	TTN	179287477	0.017000	0.18338	0.076000	0.20297	0.005000	0.04900	-0.151000	0.10175	-1.020000	0.03354	-0.408000	0.06270	ACT	.	.		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179579232	T	C	179579232	3	2	114	1	0	0	0	0	1	0	0	0	16750	1667	58	2	78348	2	TTN	2	179579232	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	18308	179579232	63620141	183	18455										
TTN	7273	hgsc.bcm.edu	37	chr2	179614678	179614678	+	Intron	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gttcattagtaatatcagacAaaaatacaaatctgtgtttt					rs201544975		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179614678delA	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Frame_Shift_Del_p.L4150fs|TTN_ENST00000342992.6_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATATCAGACAAAAATACAAA	0.358																																					p.L4150fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.12450delG						.						77	82	80					2																	179614678		2203	4297	6500	SO:0001627	intron_variant	7273	exon46			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+3172T>-	chr2.hg19:g.179614678delA		196.0	0.0		220.0	14.0	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179614678	A	-	179614678	6	5	114	0	1	1	0	1	0	0	0	0	16750	131	5	0		0	TTN	2	179614678	Intron	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	35446	179614678	63584695	184	18456										
ZNF385B	151126	hgsc.bcm.edu	37	chr2	180634453	180634453	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttctttatccccttttcttcAaagccccgtagaaaatttgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:180634453delA	ENST00000410066.1	-	3	633	c.30delT	c.(28-30)tttfs	p.F10fs		NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	10	Required for induction of apoptosis.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			CCTTTTCTTCAAAGCCCCGTA	0.418																																					p.E11fs	Colon(155;204 2491 32774 51842)	Atlas-INDEL	.											.	ZNF385B	68	.	0			c.31delG						.						64	68	67					2																	180634453		2203	4300	6503	SO:0001589	frameshift_variant	151126	exon3			.	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.30delT	chr2.hg19:g.180634453delA	ENSP00000386845:p.Phe10fs	118.0	0.0		146.0	10.0	NM_152520	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Frame_Shift_Del	DEL	ENST00000410066.1	hg19	CCDS33339.1																																																																																			.	.		0.418	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		-	180634453	A	-	180634453	7	5	114	1	0	1	0	1	0	0	0	0	17892	127	5	0	1446	0	ZNF385B	2	180634453	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1019775	180634453	62564920	185	18457										
INPP1	3628	hgsc.bcm.edu	37	chr2	191233941	191233941	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtgtctatgacatacagacAggggttcccctgatgggagt	14	8	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:191233941A>G	ENST00000322522.4	+	5	1035	c.579A>G	c.(577-579)acA>acG	p.T193T	INPP1_ENST00000541441.1_Silent_p.T193T|INPP1_ENST00000392329.2_Silent_p.T193T	NM_002194.3	NP_002185.1	P49441	INPP_HUMAN	inositol polyphosphate-1-phosphatase	193					dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-1,3,4-trisphosphate 1-phosphatase activity (GO:0052829)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|metal ion binding (GO:0046872)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.000286)|Epithelial(96;0.0186)|all cancers(119;0.057)			ACATACAGACAGGGGTTCCCC	0.408																																					p.T193T	Melanoma(130;184 1743 2185 19805 38428)	Atlas-SNP	.											.	INPP1	29	.	0			c.A579G						.						129	127	127					2																	191233941		2203	4300	6503	SO:0001819	synonymous_variant	3628	exon5			ACAGACAGGGGTT		CCDS2305.1	2q32	2008-02-07			ENSG00000151689	ENSG00000151689	3.1.3.57		6071	protein-coding gene	gene with protein product		147263				8390685	Standard	NM_002194		Approved		uc010fsb.3	P49441	OTTHUMG00000132672	ENST00000322522.4:c.579A>G	chr2.hg19:g.191233941A>G		107.0	0.0		145.0	6.0	NM_002194		Silent	SNP	ENST00000322522.4	hg19	CCDS2305.1																																																																																			.	.		0.408	INPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255932.2			G	191233941	A	G	191233941	2	3	114	1	0	0	0	0	0	0	0	1	7760	175	7	2		2	INPP1	2	191233941	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	10599488	191233941	51965432	186	18458										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196673531	196673531	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttctgaggaagccatgtacAaaggttggcataaggattat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:196673531delA	ENST00000312428.6	-	53	10058	c.9958delT	c.(9958-9960)tgtfs	p.C3320fs		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3320					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AGCCATGTACAAAGGTTGGCA	0.423																																					p.C3320fs		Atlas-INDEL	.											.	DNAH7	512	.	0			c.9959delG						.						92	84	86					2																	196673531		1888	4124	6012	SO:0001589	frameshift_variant	56171	exon53			.	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.9958delT	chr2.hg19:g.196673531delA	ENSP00000311273:p.Cys3320fs	120.0	0.0		138.0	12.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Frame_Shift_Del	DEL	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.423	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		-	196673531	A	-	196673531	7	5	114	1	0	1	0	1	0	0	0	0	4608	130	5	0	2168	0	DNAH7	2	196673531	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	5439590	196673531	46525842	187	18459										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196799425	196799426	+	Frame_Shift_Del	DEL	CG	CG	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagttctacaacctctccttCgctgctcttcatgtgagtaa					rs372668189|rs199987634		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:196799425_196799426delCG	ENST00000312428.6	-	21	3460_3461	c.3360_3361delCG	c.(3358-3363)agcgaafs	p.SE1120fs		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1120	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						ACCTCTCCTTCGCTGCTCTTCA	0.401																																					p.1121_1121del		Atlas-Indel,Pindel	.											.	DNAH7	512	.	0			c.3361_3362del						.																																			SO:0001589	frameshift_variant	56171	exon21			.	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.3360_3361delCG	chr2.hg19:g.196799425_196799426delCG	ENSP00000311273:p.Ser1120fs	208.0	0.0		221.0	48.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Frame_Shift_Del	DEL	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.401	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		-	196799426	CG	-	196799425	7	5	114	1	0	1	0	1	0	0	0	0	4608	893	31	0	8893	0	DNAH7	2	196799425	Frame_Shift_Del	DEL	CG	TCGA-DD-A3A0-01A-11D-A20W-10	125894	196799425	46399948	188	18460										
PGAP1	80055	hgsc.bcm.edu	37	chr2	197737220	197737220	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ataatgccacatgggtattgTtttctggttgagcaatatgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:197737220delT	ENST00000354764.4	-	18	1787	c.1673delA	c.(1672-1674)aacfs	p.N559fs	PGAP1_ENST00000409475.1_Frame_Shift_Del_p.N559fs	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	559					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						ATGGGTATTGTTTTCTGGTTG	0.333																																					p.N558fs		Atlas-INDEL	.											.	PGAP1	84	.	0			c.1674delC						.						101	101	101					2																	197737220		2203	4300	6503	SO:0001589	frameshift_variant	80055	exon18			.		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.1673delA	chr2.hg19:g.197737220delT	ENSP00000346809:p.Asn559fs	138.0	0.0		171.0	11.0	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Frame_Shift_Del	DEL	ENST00000354764.4	hg19	CCDS2318.1																																																																																			.	.		0.333	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		-	197737220	T	-	197737220	7	5	114	1	0	1	0	1	0	0	0	0	11786	1725	60	0	1135	0	PGAP1	2	197737220	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	937795	197737220	45462153	189	18461										
PLCL1	5334	hgsc.bcm.edu	37	chr2	198950766	198950766	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catggagcacgtaaccctttTtgtccacatagcaataacta	6	11	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:198950766T>A	ENST00000428675.1	+	2	2923	c.2525T>A	c.(2524-2526)tTt>tAt	p.F842Y	PLCL1_ENST00000437704.2_Missense_Mutation_p.F744Y	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	842					gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	GTAACCCTTTTTGTCCACATA	0.458																																					p.F842Y		Atlas-SNP	.											.	PLCL1	358	.	0			c.T2525A						.						150	125	133					2																	198950766		2203	4300	6503	SO:0001583	missense	5334	exon2			CCCTTTTTGTCCA	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.2525T>A	chr2.hg19:g.198950766T>A	ENSP00000402861:p.Phe842Tyr	164.0	0.0		205.0	78.0	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	hg19	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	T	19.34	3.808520	0.70797	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.14640	2.49;2.49	5.41	5.41	0.78517	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000004	T	0.42630	0.1211	M	0.85945	2.785	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	T	0.43228	-0.9404	9	.	.	.	.	15.6048	0.76658	0.0:0.0:0.0:1.0	.	842;768	Q15111;B4DYZ4	PLCL1_HUMAN;.	Y	842;744	ENSP00000402861:F842Y;ENSP00000414138:F744Y	.	F	+	2	0	PLCL1	198659011	1.000000	0.71417	0.995000	0.50966	0.955000	0.61496	7.857000	0.86963	2.270000	0.75569	0.482000	0.46254	TTT	.	.		0.458	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		A	198950766	T	A	198950766	3	1	114	1	0	0	0	0	1	0	0	0	12048	1841	64	4	2531	4	PLCL1	2	198950766	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1213546	198950766	44248607	190	18462										
C2orf47	79568	hgsc.bcm.edu	37	chr2	200824539	200824539	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaccataaaaatgcccttgcTgctaacatagatgaaattgt	6	8	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:200824539T>C	ENST00000392290.1	+	3	781	c.585T>C	c.(583-585)gcT>gcC	p.A195A	C2orf47_ENST00000469156.1_3'UTR|C2orf47_ENST00000295079.2_Silent_p.A195A			Q8WWC4	CB047_HUMAN	chromosome 2 open reading frame 47	195						mitochondrion (GO:0005739)				cervix(1)|endometrium(2)|large_intestine(1)|lung(5)	9						ATGCCCTTGCTGCTAACATAG	0.358																																					p.A195A		Atlas-SNP	.											.	C2orf47	20	.	0			c.T585C						.						115	105	108					2																	200824539		2203	4298	6501	SO:0001819	synonymous_variant	79568	exon4			CCTTGCTGCTAAC	BC017959	CCDS2329.1	2q33.1	2011-03-08			ENSG00000162972	ENSG00000162972			26198	protein-coding gene	gene with protein product						12477932	Standard	NM_024520		Approved	DKFZp666A212, FLJ22555	uc002uvm.3	Q8WWC4	OTTHUMG00000132771	ENST00000392290.1:c.585T>C	chr2.hg19:g.200824539T>C		71.0	0.0		95.0	4.0	NM_024520	Q658V9|Q9H671	Silent	SNP	ENST00000392290.1	hg19	CCDS2329.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.327125	0.24080	.	.	ENSG00000162972	ENST00000435773	.	.	.	5.97	4.83	0.62350	.	.	.	.	.	T	0.54515	0.1863	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53781	-0.8390	4	.	.	.	-12.2038	5.6195	0.17450	0.2446:0.0741:0.0:0.6813	.	.	.	.	P	188	.	.	L	+	2	0	C2orf47	200532784	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.608000	0.36847	2.277000	0.76020	0.482000	0.46254	CTG	.	.		0.358	C2orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256146.1	NM_024520		C	200824539	T	C	200824539	2	2	114	1	0	0	0	0	0	0	0	1	2171	1567	55	2		2	C2orf47	2	200824539	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1873773	200824539	42374834	191	18463										
BMPR2	659	hgsc.bcm.edu	37	chr2	203407121	203407121	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tatgcaggttctcgtgtctaGggaaaaacagagacccaagt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:203407121delG	ENST00000374580.4	+	10	1903	c.1364delG	c.(1363-1365)aggfs	p.R455fs	BMPR2_ENST00000374574.2_Frame_Shift_Del_p.R455fs	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	455	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						CTCGTGTCTAGGGAAAAACAG	0.418																																					p.R455fs		Atlas-INDEL	.											.	BMPR2	142	.	0			c.1363delA						.						51	50	50					2																	203407121		2203	4300	6503	SO:0001589	frameshift_variant	659	exon10			.	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.1364delG	chr2.hg19:g.203407121delG	ENSP00000363708:p.Arg455fs	138.0	0.0		162.0	10.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Frame_Shift_Del	DEL	ENST00000374580.4	hg19	CCDS33361.1																																																																																			.	.		0.418	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204		-	203407121	G	-	203407121	7	5	114	1	0	1	0	1	0	0	0	0	1471	1000	35	0	1402	0	BMPR2	2	203407121	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2582582	203407121	39792252	192	18464										
RAPH1	65059	hgsc.bcm.edu	37	chr2	204305064	204305064	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctggagatccacttttgtcaGgggtaggagaagctgtgggt					rs137885175		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:204305064delG	ENST00000319170.5	-	14	3148	c.2849delC	c.(2848-2850)cctfs	p.P950fs	ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000457812.1_Intron|RAPH1_ENST00000374493.3_Frame_Shift_Del_p.P1002fs	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	950					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						ACTTTTGTCAggggtaggaga	0.592																																					p.P950fs		Atlas-INDEL	.											.	RAPH1	118	.	0			c.2850delT						.						62	62	62					2																	204305064		2203	4300	6503	SO:0001589	frameshift_variant	65059	exon14			.	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.2849delC	chr2.hg19:g.204305064delG	ENSP00000316543:p.Pro950fs	98.0	0.0		152.0	10.0	NM_213589	Q96Q37|Q9C0I2	Frame_Shift_Del	DEL	ENST00000319170.5	hg19	CCDS2359.1																																																																																			.	.		0.592	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		-	204305064	G	-	204305064	7	5	114	1	0	1	0	1	0	0	0	0	13065	1000	35	0	907	0	RAPH1	2	204305064	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	897943	204305064	38894309	193	18465										
INO80D	54891	hgsc.bcm.edu	37	chr2	206892990	206892990	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggcggcagaggtgcttataTttctgctgaaagtaagtgca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:206892990delT	ENST00000403263.1	-	6	1547	c.1143delA	c.(1141-1143)aaafs	p.K381fs	Y_RNA_ENST00000384656.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	381					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						GGTGCTTATATTTCTGCTGAA	0.498																																					p.Y382fs		Atlas-INDEL	.											.	INO80D	134	.	0			c.1144delT						.						73	71	72					2																	206892990		1891	4117	6008	SO:0001589	frameshift_variant	54891	exon6			.		CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"INO80 complex subunits"	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.1143delA	chr2.hg19:g.206892990delT	ENSP00000384198:p.Lys381fs	116.0	0.0		132.0	10.0	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Frame_Shift_Del	DEL	ENST00000403263.1	hg19	CCDS46500.1																																																																																			.	.		0.498	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759		-	206892990	T	-	206892990	7	5	114	1	0	1	0	1	0	0	0	0	7758	1490	52	0	1964	0	INO80D	2	206892990	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2587926	206892990	36306383	194	18466										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207162017	207162017	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgaccagacagagtagacgTcaaatatgtaccagtagttt	9	7	1	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:207162017T>C	ENST00000374423.3	+	4	494	c.108T>C	c.(106-108)cgT>cgC	p.R36R		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	36							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGAGTAGACGTCAAATATGTA	0.378																																					p.R36R		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T108C						.						128	118	121					2																	207162017		1875	4120	5995	SO:0001819	synonymous_variant	57683	exon4			TAGACGTCAAATA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.108T>C	chr2.hg19:g.207162017T>C		116.0	0.0		134.0	6.0	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	hg19	CCDS46501.1																																																																																			.	.		0.378	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		C	207162017	T	C	207162017	2	2	114	1	0	0	0	0	0	0	0	1	17614	1654	58	2		2	ZDBF2	2	207162017	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	269027	207162017	36037356	195	18467										
CPO	130749	hgsc.bcm.edu	37	chr2	207833909	207833909	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacctgtagatgcctcatcaGggtcttcaagagattgggcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:207833909delG	ENST00000272852.3	+	9	920	c.874delG	c.(874-876)gggfs	p.G292fs		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	292						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		TGCCTCATCAGGGTCTTCAAG	0.443																																					p.S291fs		Atlas-INDEL	.											.	CPO	42	.	0			c.873delA						.						121	122	121					2																	207833909		2203	4300	6503	SO:0001589	frameshift_variant	130749	exon9			.		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"metallocarboxypeptidase O", "metallocarboxypeptidase C"	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.874delG	chr2.hg19:g.207833909delG	ENSP00000272852:p.Gly292fs	119.0	0.0		148.0	10.0	NM_173077	Q2M277|Q7RTW7	Frame_Shift_Del	DEL	ENST00000272852.3	hg19	CCDS2372.1																																																																																			.	.		0.443	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077		-	207833909	G	-	207833909	7	5	114	1	0	1	0	1	0	0	0	0	3822	1000	35	0	908	0	CPO	2	207833909	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	671892	207833909	35365464	196	18468										
C2orf67	151050	hgsc.bcm.edu	37	chr2	210887743	210887743	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttccattccatctgactgcTtttttggatggtggccattc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:210887743delT	ENST00000281772.9	-	15	3157	c.2894delA	c.(2893-2895)aagfs	p.K965fs	KANSL1L_ENST00000418791.1_Frame_Shift_Del_p.K923fs	NM_152519.2	NP_689732.2	A0AUZ9	KAL1L_HUMAN	KAT8 regulatory NSL complex subunit 1-like	965						histone acetyltransferase complex (GO:0000123)											ATCTGACTGCTTTTTTGGATG	0.383																																					p.K965fs		Atlas-INDEL	.											.	.	.	.	0			c.2895delG						.						116	105	109					2																	210887743		2203	4300	6503	SO:0001589	frameshift_variant	151050	exon15			.	AK074441	CCDS33370.1	2q34	2012-02-20	2012-02-20	2012-02-20	ENSG00000144445	ENSG00000144445			26310	protein-coding gene	gene with protein product	"KIAA1267-like"	613833	"chromosome 2 open reading frame 67"	C2orf67		12477932	Standard	NM_152519		Approved	FLJ23861, FLJ32349, MSL1v2, KIAA1267L	uc002vds.3	A0AUZ9	OTTHUMG00000154697	ENST00000281772.9:c.2894delA	chr2.hg19:g.210887743delT	ENSP00000281772:p.Lys965fs	178.0	0.0		241.0	15.0	NM_152519	B7ZLN1|I6L9A8|Q53TV8|Q53TW3|Q6IS05|Q8TCI1|Q96MI0|Q9UFC3	Frame_Shift_Del	DEL	ENST00000281772.9	hg19	CCDS33370.1																																																																																			.	.		0.383	KANSL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336633.3	NM_152519		-	210887743	T	-	210887743	7	5	114	1	0	1	0	1	0	0	0	0	2188	1609	56	0	73	0	C2orf67	2	210887743	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3053834	210887743	32311630	197	18469										
C2orf67	151050	hgsc.bcm.edu	37	chr2	211018375	211018375	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgtacaccgtgcaaagccaTtttttgcatcatcccacaat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:211018375delT	ENST00000281772.9	-	2	1195	c.932delA	c.(931-933)aatfs	p.N311fs	KANSL1L_ENST00000452086.1_Frame_Shift_Del_p.N311fs|KANSL1L_ENST00000457374.1_Frame_Shift_Del_p.N311fs|KANSL1L_ENST00000429908.2_5'Flank|KANSL1L_ENST00000418791.1_Frame_Shift_Del_p.N311fs	NM_152519.2	NP_689732.2	A0AUZ9	KAL1L_HUMAN	KAT8 regulatory NSL complex subunit 1-like	311						histone acetyltransferase complex (GO:0000123)											TGCAAAGCCATTTTTTGCATC	0.408																																					p.N311fs		Atlas-INDEL	.											.	.	.	.	0			c.933delT						.						176	165	169					2																	211018375		2203	4300	6503	SO:0001589	frameshift_variant	151050	exon2			.	AK074441	CCDS33370.1	2q34	2012-02-20	2012-02-20	2012-02-20	ENSG00000144445	ENSG00000144445			26310	protein-coding gene	gene with protein product	"KIAA1267-like"	613833	"chromosome 2 open reading frame 67"	C2orf67		12477932	Standard	NM_152519		Approved	FLJ23861, FLJ32349, MSL1v2, KIAA1267L	uc002vds.3	A0AUZ9	OTTHUMG00000154697	ENST00000281772.9:c.932delA	chr2.hg19:g.211018375delT	ENSP00000281772:p.Asn311fs	205.0	0.0		257.0	16.0	NM_152519	B7ZLN1|I6L9A8|Q53TV8|Q53TW3|Q6IS05|Q8TCI1|Q96MI0|Q9UFC3	Frame_Shift_Del	DEL	ENST00000281772.9	hg19	CCDS33370.1																																																																																			.	.		0.408	KANSL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336633.3	NM_152519		-	211018375	T	-	211018375	7	5	114	1	0	1	0	1	0	0	0	0	2188	1493	52	0	2087	0	C2orf67	2	211018375	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	130632	211018375	32180998	198	18470										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212537944	212537944	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctcacactgggggtcacacTccacacagatggagccattc	9	14	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:212537944T>C	ENST00000342788.4	-	14	1971	c.1661A>G	c.(1660-1662)gAg>gGg	p.E554G	ERBB4_ENST00000436443.1_Missense_Mutation_p.E554G|ERBB4_ENST00000402597.1_Missense_Mutation_p.E554G	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	554	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GGGGTCACACTCCACACAGAT	0.468										TSP Lung(8;0.080)																											p.E554G		Atlas-SNP	.											.	ERBB4	480	.	0			c.A1661G						.						132	106	115					2																	212537944		2203	4300	6503	SO:0001583	missense	2066	exon14			TCACACTCCACAC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1661A>G	chr2.hg19:g.212537944T>C	ENSP00000342235:p.Glu554Gly	80.0	0.0		108.0	6.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.94|14.94	2.685276|2.685276	0.47991|0.47991	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597|ENST00000260943	T;T;T|.	0.46063|.	0.88;0.88;0.88|.	5.33|5.33	5.33|5.33	0.75918|0.75918	Growth factor, receptor (1);|.	0.092238|.	0.85682|.	D|.	0.000000|.	T|T	0.73544|0.73544	0.3600|0.3600	M|M	0.79926|0.79926	2.475|2.475	0.53005|0.53005	D|D	0.999965|0.999965	P;B;B;P;B|.	0.35872|.	0.525;0.377;0.11;0.525;0.391|.	B;B;B;B;B|.	0.34722|.	0.188;0.11;0.042;0.188;0.091|.	T|T	0.75368|0.75368	-0.3342|-0.3342	9|5	.|.	.|.	.|.	.|.	10.5161|10.5161	0.44889|0.44889	0.1446:0.0:0.0:0.8554|0.1446:0.0:0.0:0.8554	.|.	554;554;413;554;554|.	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303|.	.;.;.;.;ERBB4_HUMAN|.	G|G	554|554	ENSP00000342235:E554G;ENSP00000403204:E554G;ENSP00000385565:E554G|.	.|.	E|S	-|-	2|1	0|0	ERBB4|ERBB4	212246189|212246189	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.766000|5.766000	0.68843|0.68843	2.005000|2.005000	0.58758|0.58758	0.455000|0.455000	0.32223|0.32223	GAG|AGT	.	.		0.468	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		C	212537944	T	C	212537944	3	2	114	1	0	0	0	0	1	0	0	0	5211	1551	54	2	2325	2	ERBB4	2	212537944	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1519569	212537944	30661429	199	18471										
SMARCAL1	50485	hgsc.bcm.edu	37	chr2	217329366	217329366	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctcttcttcaacagaacagCtgaagctaaaatcccatctg	5	12	4	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:217329366C>T	ENST00000357276.4	+	13	2447	c.2117C>T	c.(2116-2118)gCt>gTt	p.A706V	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.A706V	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	706					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		AACAGAACAGCTGAAGCTAAA	0.383									Schimke Immuno-Osseous Dysplasia																												p.A706V		Atlas-SNP	.											.	SMARCAL1	93	.	0			c.C2117T						.						159	157	158					2																	217329366		2203	4300	6503	SO:0001583	missense	50485	exon13	Familial Cancer Database	SIOD	GAACAGCTGAAGC	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"HepA-related protein", "ATP-driven annealing helicase"	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.2117C>T	chr2.hg19:g.217329366C>T	ENSP00000349823:p.Ala706Val	70.0	0.0		91.0	4.0	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	hg19	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.724593	0.89298	.	.	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000392128	T;T;T	0.80123	-1.34;-1.34;-1.34	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.90143	0.6920	M	0.86343	2.81	0.58432	D	0.999996	P	0.51791	0.948	P	0.61132	0.884	D	0.91337	0.5094	10	0.72032	D	0.01	-14.0005	17.6906	0.88268	0.0:1.0:0.0:0.0	.	706	Q9NZC9	SMAL1_HUMAN	V	706;706;548	ENSP00000349823:A706V;ENSP00000350940:A706V;ENSP00000375974:A548V	ENSP00000349823:A706V	A	+	2	0	SMARCAL1	217037611	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.933000	0.70130	2.765000	0.95021	0.650000	0.86243	GCT	.	.		0.383	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			T	217329366	C	T	217329366	3	4	114	1	0	0	0	0	1	0	0	0	14788	797	28	3	2159	3	SMARCAL1	2	217329366	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	4791422	217329366	25870007	200	18472										
RUFY4	285180	hgsc.bcm.edu	37	chr2	218938584	218938584	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acccagggaaggagacccagAaaaaacaaagatgccccaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:218938584delA	ENST00000344321.7	+	8	1094	c.576delA	c.(574-576)agafs	p.R192fs	RUFY4_ENST00000441828.2_Frame_Shift_Del_p.K158fs|RUFY4_ENST00000374155.3_Frame_Shift_Del_p.R192fs|RUFY4_ENST00000463872.1_Intron	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	192							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGAGACCCAGAAAAAACAAAG	0.547											OREG0015195	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R192fs		Atlas-INDEL	.											.	RUFY4	59	.	0			c.575delG						.						85	97	93					2																	218938584		1970	4160	6130	SO:0001589	frameshift_variant	285180	exon8			.	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"Zinc fingers, FYVE domain containing"	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.576delA	chr2.hg19:g.218938584delA	ENSP00000345900:p.Arg192fs	131.0	0.0	2255	153.0	11.0	NM_198483	Q6ZR96	Frame_Shift_Del	DEL	ENST00000344321.7	hg19																																																																																				.	.		0.547	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483		-	218938584	A	-	218938584	7	5	114	1	0	1	0	1	0	0	0	0	13756	243	9	0	598	0	RUFY4	2	218938584	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1609218	218938584	24260789	201	18473										
USP37	57695	hgsc.bcm.edu	37	chr2	219353045	219353045	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accctaaagaaaagatcaagAgaatcttgaattgaacgagg	9	6	2	5			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:219353045A>G	ENST00000258399.3	-	15	1984	c.1572T>C	c.(1570-1572)tcT>tcC	p.S524S	USP37_ENST00000418019.1_Silent_p.S524S|USP37_ENST00000475553.1_5'Flank|USP37_ENST00000454775.1_Silent_p.S524S|USP37_ENST00000415516.1_Silent_p.S452S	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	524	USP.				G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		AAAGATCAAGAGAATCTTGAA	0.318																																					p.S524S		Atlas-SNP	.											.	USP37	76	.	0			c.T1572C						.						87	88	88					2																	219353045		2203	4300	6503	SO:0001819	synonymous_variant	57695	exon15			ATCAAGAGAATCT	AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"Ubiquitin-specific peptidases"	20063	protein-coding gene	gene with protein product			"ubiquitin specific protease 37"			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.1572T>C	chr2.hg19:g.219353045A>G		119.0	0.0		158.0	9.0	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Silent	SNP	ENST00000258399.3	hg19	CCDS2418.1																																																																																			.	.		0.318	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		G	219353045	A	G	219353045	2	3	114	1	0	0	0	0	0	0	0	1	17083	291	11	2		2	USP37	2	219353045	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	414461	219353045	23846328	202	18474										
PTPRN	5798	hgsc.bcm.edu	37	chr2	220159739	220159739	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcgtggaggccggtgtgcccTctgccggccagctgaggaag	18	12	1	1	rs376114976		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:220159739T>C	ENST00000295718.2	-	19	2873	c.2633A>G	c.(2632-2634)gAg>gGg	p.E878G	PTPRN_ENST00000409251.3_Missense_Mutation_p.E849G|MIR153-1_ENST00000384914.1_RNA|PTPRN_ENST00000497977.1_5'UTR|PTPRN_ENST00000423636.2_Missense_Mutation_p.E788G	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	878	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CGGTGTGCCCTCTGCCGGCCA	0.711																																					p.E878G		Atlas-SNP	.											.	PTPRN	138	.	0			c.A2633G						.	T	GLY/GLU,GLY/GLU,GLY/GLU	0,4398		0,0,2199	32	37	35		2633,2363,2546	5.2	1	2		35	1,8597		0,1,4298	no	missense,missense,missense	PTPRN	NM_002846.3,NM_001199764.1,NM_001199763.1	98,98,98	0,1,6497	CC,CT,TT		0.0116,0.0,0.0077	benign,benign,benign	878/980,788/890,849/951	220159739	1,12995	2199	4299	6498	SO:0001583	missense	5798	exon19			GTGCCCTCTGCCG		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.2633A>G	chr2.hg19:g.220159739T>C	ENSP00000295718:p.Glu878Gly	117.0	0.0		105.0	5.0	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	hg19	CCDS2440.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.63|18.63	3.664962|3.664962	0.67700|0.67700	0.0|0.0	1.16E-4|1.16E-4	ENSG00000054356|ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666|ENST00000443981	T;T;T|.	0.12672|.	2.66;2.66;2.66|.	5.18|5.18	5.18|5.18	0.71444|0.71444	Protein-tyrosine phosphatase, receptor/non-receptor type (4);|.	0.377447|.	0.28140|.	N|.	0.016448|.	T|T	0.41534|0.41534	0.1163|0.1163	N|N	0.11756|0.11756	0.17|0.17	0.54753|0.54753	D|D	0.99998|0.99998	D;B|.	0.76494|.	0.999;0.134|.	D;B|.	0.66979|.	0.948;0.039|.	T|T	0.32771|0.32771	-0.9894|-0.9894	10|5	0.51188|.	T|.	0.08|.	.|.	14.8751|14.8751	0.70488|0.70488	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	849;878|.	Q6NSL1;Q16849|.	.;PTPRN_HUMAN|.	G|G	849;878;849;788|81	ENSP00000386638:E849G;ENSP00000295718:E878G;ENSP00000444244:E788G|.	ENSP00000295718:E878G|.	E|R	-|-	2|1	0|2	PTPRN|PTPRN	219867983|219867983	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.031000|4.031000	0.57267|0.57267	2.172000|2.172000	0.68678|0.68678	0.519000|0.519000	0.50382|0.50382	GAG|AGG	.	.		0.711	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			C	220159739	T	C	220159739	3	2	114	1	0	0	0	0	1	0	0	0	12822	1551	54	2	326	2	PTPRN	2	220159739	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	806694	220159739	23039634	203	18475										
GMPPA	29926	hgsc.bcm.edu	37	chr2	220369963	220369963	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgccagggaggactcaccaGgcttgtggccaggggcaggt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:220369963delG	ENST00000358215.3	+	8	1003	c.634delG	c.(634-636)ggcfs	p.G212fs	GMPPA_ENST00000373917.3_Frame_Shift_Del_p.G212fs|GMPPA_ENST00000373908.1_Frame_Shift_Del_p.G212fs|GMPPA_ENST00000341142.3_Frame_Shift_Del_p.G212fs|GMPPA_ENST00000313597.5_Frame_Shift_Del_p.G212fs|AC053503.11_ENST00000429882.1_RNA	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	212					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		GGACTCACCAGGCTTGTGGCC	0.587																																					p.P211fs		Atlas-INDEL	.											.	GMPPA	50	.	0			c.633delA						.						66	66	66					2																	220369963		2203	4300	6503	SO:0001589	frameshift_variant	29926	exon8			.	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.634delG	chr2.hg19:g.220369963delG	ENSP00000350949:p.Gly212fs	144.0	0.0		165.0	11.0	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Frame_Shift_Del	DEL	ENST00000358215.3	hg19	CCDS2441.1																																																																																			.	.		0.587	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335		-	220369963	G	-	220369963	7	5	114	1	0	1	0	1	0	0	0	0	6502	1000	35	0	660	0	GMPPA	2	220369963	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	210224	220369963	22829410	204	18476										
SCG2	7857	hgsc.bcm.edu	37	chr2	224462280	224462280	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttggggtatcatcattcttcGggggccccacagggaacctt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:224462280delG	ENST00000305409.2	-	2	1953	c.1721delC	c.(1720-1722)ccgfs	p.P574fs		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.P574Q(1)		NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		ATCATTCTTCGGGGGCCCCAC	0.493																																					p.P574fs		Atlas-INDEL	.											.	SCG2	99	.	1	Substitution - Missense(1)	lung(1)	c.1722delG						.						84	85	85					2																	224462280		2203	4300	6503	SO:0001589	frameshift_variant	7857	exon2			.	M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"secretoneurin", "chromogranin C"	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.1721delC	chr2.hg19:g.224462280delG	ENSP00000304133:p.Pro574fs	187.0	0.0		249.0	15.0	NM_003469	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Frame_Shift_Del	DEL	ENST00000305409.2	hg19	CCDS2457.1																																																																																			.	.		0.493	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		-	224462280	G	-	224462280	7	5	114	1	0	1	0	1	0	0	0	0	13906	1116	39	0	136	0	SCG2	2	224462280	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	4092317	224462280	18737093	205	18477										
CUL3	8452	hgsc.bcm.edu	37	chr2	225368413	225368413	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcagagtcatcagaaacacTtttatttgtgagaagtctcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:225368413delT	ENST00000264414.4	-	9	1671	c.1333delA	c.(1333-1335)agtfs	p.S445fs	CUL3_ENST00000344951.4_Frame_Shift_Del_p.S379fs|CUL3_ENST00000409777.1_Frame_Shift_Del_p.S421fs|CUL3_ENST00000409096.1_Frame_Shift_Del_p.S421fs	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	445					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TCAGAAACACTTTTATTTGTG	0.313																																					p.S451fs		Atlas-INDEL	.											.	CUL3	96	.	0			c.1352delG						.						128	115	119					2																	225368413		2202	4299	6501	SO:0001589	frameshift_variant	8452	exon9			.	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.1333delA	chr2.hg19:g.225368413delT	ENSP00000264414:p.Ser445fs	128.0	0.0		154.0	10.0	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Frame_Shift_Del	DEL	ENST00000264414.4	hg19	CCDS2462.1																																																																																			.	.		0.313	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			-	225368413	T	-	225368413	7	5	114	1	0	1	0	1	0	0	0	0	4058	1609	56	0	1005	0	CUL3	2	225368413	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	906133	225368413	17830960	206	18478										
COL4A3	1285	hgsc.bcm.edu	37	chr2	228174007	228174007	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtcctcacggctggatttcTctctggaaaggattttcatt	9	9	4	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:228174007T>C	ENST00000396578.3	+	50	4890	c.4728T>C	c.(4726-4728)tcT>tcC	p.S1576S	AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000433324.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	1576	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		GCTGGATTTCTCTCTGGAAAG	0.448																																					p.S1576S		Atlas-SNP	.											.	COL4A3	293	.	0			c.T4728C						.						67	67	67					2																	228174007		1956	4153	6109	SO:0001819	synonymous_variant	1285	exon50			GATTTCTCTCTGG		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.4728T>C	chr2.hg19:g.228174007T>C		134.0	0.0		112.0	5.0	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	hg19	CCDS42829.1																																																																																			.	.		0.448	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		C	228174007	T	C	228174007	2	2	114	1	0	0	0	0	0	0	0	1	3693	1538	54	2		2	COL4A3	2	228174007	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2805594	228174007	15025366	207	18479										
AGFG1	3267	hgsc.bcm.edu	37	chr2	228389615	228389615	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattttgctaactttgcacaTttcaacagtcatgcaggtaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:228389615delT	ENST00000310078.8	+	5	938	c.678delT	c.(676-678)catfs	p.H226fs	AGFG1_ENST00000373671.3_Frame_Shift_Del_p.H226fs|AGFG1_ENST00000409171.1_Frame_Shift_Del_p.H226fs|AGFG1_ENST00000486932.1_3'UTR|AGFG1_ENST00000409315.1_Frame_Shift_Del_p.H226fs|AGFG1_ENST00000409979.2_Frame_Shift_Del_p.H226fs	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	226					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						ACTTTGCACATTTCAACAGTC	0.408																																					p.H226fs		Atlas-INDEL	.											.	AGFG1	80	.	0			c.677delA						.						143	129	134					2																	228389615		2203	4300	6503	SO:0001589	frameshift_variant	3267	exon5			.		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"ADP-ribosylation factor GTPase activating proteins"	5175	protein-coding gene	gene with protein product		600862	"HIV-1 Rev binding protein"	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.678delT	chr2.hg19:g.228389615delT	ENSP00000312059:p.His226fs	175.0	0.0		214.0	13.0	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Frame_Shift_Del	DEL	ENST00000310078.8	hg19	CCDS2467.1																																																																																			.	.		0.408	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		-	228389615	T	-	228389615	7	5	114	1	0	1	0	1	0	0	0	0	380	1490	52	0	696	0	AGFG1	2	228389615	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	215608	228389615	14809758	208	18480										
FBXO36	130888	hgsc.bcm.edu	37	chr2	230861591	230861591	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actatcatttcttatctggaTcttgaagatattgccaggct	7	8	4	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:230861591T>C	ENST00000283946.3	+	3	348	c.330T>C	c.(328-330)gaT>gaC	p.D110D	FBXO36_ENST00000373652.3_Silent_p.D79D|FBXO36_ENST00000409992.1_Silent_p.D90D	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	110	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.									endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTTATCTGGATCTTGAAGATA	0.348																																					p.D110D		Atlas-SNP	.											.	FBXO36	22	.	0			c.T330C						.						166	164	165					2																	230861591		2203	4300	6503	SO:0001819	synonymous_variant	130888	exon3			TCTGGATCTTGAA	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"F-boxes /  "other""	27020	protein-coding gene	gene with protein product		609105	"F-box only protein 36"			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.330T>C	chr2.hg19:g.230861591T>C		165.0	0.0		223.0	10.0	NM_174899	B3KVQ6|Q53TE6|Q8WWD4	Silent	SNP	ENST00000283946.3	hg19	CCDS2472.1																																																																																			.	.		0.348	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899		C	230861591	T	C	230861591	2	2	114	1	0	0	0	0	0	0	0	1	5753	1432	50	2		2	FBXO36	2	230861591	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2471976	230861591	12337782	209	18481										
SP100	6672	hgsc.bcm.edu	37	chr2	231339124	231339124	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctagataccatggatgttgAaaacaattctactttggaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:231339124delA	ENST00000264052.5	+	17	1917	c.1562delA	c.(1561-1563)gaafs	p.E521fs	SP100_ENST00000409112.1_Frame_Shift_Del_p.E521fs|SP100_ENST00000340126.4_Frame_Shift_Del_p.E521fs	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	521					cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		ATGGATGTTGAAAACAATTCT	0.284																																					p.E521fs		Atlas-INDEL	.											.	SP100	167	.	0			c.1561delG						.						62	66	65					2																	231339124		2203	4299	6502	SO:0001589	frameshift_variant	6672	exon17			.	AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"Zinc fingers, PHD-type"	11206	protein-coding gene	gene with protein product		604585	"nuclear antigen Sp100"			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.1562delA	chr2.hg19:g.231339124delA	ENSP00000264052:p.Glu521fs	166.0	0.0		229.0	18.0	NM_001206701	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Frame_Shift_Del	DEL	ENST00000264052.5	hg19	CCDS2477.1																																																																																			.	.		0.284	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113		-	231339124	A	-	231339124	7	5	114	1	0	1	0	1	0	0	0	0	14975	246	9	0	1628	0	SP100	2	231339124	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	477533	231339124	11860249	210	18482										
ARMC9	80210	hgsc.bcm.edu	37	chr2	232123766	232123766	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaaactgaagaaggatttgaTtttggggagtgaccgcttga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:232123766delT	ENST00000349938.4	+	11	1171	c.977delT	c.(976-978)attfs	p.I326fs	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	326						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		AAGGATTTGATTTTGGGGAGT	0.438																																					p.I326fs		Atlas-INDEL	.											.	ARMC9	129	.	0			c.976delA						.						144	134	138					2																	232123766		2203	4300	6503	SO:0001589	frameshift_variant	80210	exon11			.	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"Armadillo repeat containing"	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.977delT	chr2.hg19:g.232123766delT	ENSP00000258417:p.Ile326fs	157.0	0.0		185.0	13.0	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Frame_Shift_Del	DEL	ENST00000349938.4	hg19	CCDS2484.1																																																																																			.	.		0.438	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139		-	232123766	T	-	232123766	7	5	114	1	0	1	0	1	0	0	0	0	958	1493	52	0	1015	0	ARMC9	2	232123766	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	784642	232123766	11075607	211	18483										
C2orf57	165100	hgsc.bcm.edu	37	chr2	232457732	232457732	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggacagcccagcaggagagCcccaaggtcaggtcccactc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:232457732delC	ENST00000313965.2	+	1	158	c.70delC	c.(70-72)cccfs	p.P24fs		NM_152614.2	NP_689827.2	Q53QW1	CB057_HUMAN	chromosome 2 open reading frame 57	24										endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	19		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)		AGCAGGAGAGCCCCAAGGTCA	0.617																																					p.E23fs		Atlas-INDEL	.											C2orf57,NS,carcinoma,0,1	C2orf57	35	.	0			c.69delG						.						87	82	84					2																	232457732		2203	4300	6503	SO:0001589	frameshift_variant	165100	exon1			.	BC034405	CCDS2487.1	2q37.1	2008-02-05			ENSG00000177673	ENSG00000177673			28563	protein-coding gene	gene with protein product						12477932	Standard	NM_152614		Approved	MGC35154	uc002vrz.3	Q53QW1	OTTHUMG00000133226	ENST00000313965.2:c.70delC	chr2.hg19:g.232457732delC	ENSP00000315557:p.Pro24fs	117.0	0.0		159.0	10.0	NM_152614	Q8N4F2	Frame_Shift_Del	DEL	ENST00000313965.2	hg19	CCDS2487.1																																																																																			.	.		0.617	C2orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256962.1	NM_152614		-	232457732	C	-	232457732	7	5	114	1	0	1	0	1	0	0	0	0	2180	739	26	0	72	0	C2orf57	2	232457732	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	333966	232457732	10741641	212	18484										
DIS3L2	129563	hgsc.bcm.edu	37	chr2	233113947	233113947	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgggcctgtgctctatttacAggtggtccccatgcttccca	10	13	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:233113947A>G	ENST00000409307.1	+	11	1317		c.e11-1		DIS3L2_ENST00000273009.6_Splice_Site|DIS3L2_ENST00000325385.7_Splice_Site					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CTCTATTTACAGGTGGTCCCC	0.552																																					.		Atlas-SNP	.											.	DIS3L2	77	.	0			c.1318-2A>G						.						80	87	85					2																	233113947		2157	4260	6417	SO:0001630	splice_region_variant	129563	exon12			ATTTACAGGTGGT	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.1318-1A>G	chr2.hg19:g.233113947A>G		114.0	0.0		125.0	5.0	NM_152383		Splice_Site	SNP	ENST00000409307.1	hg19	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.216563	0.79352	.	.	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000431466;ENST00000409307;ENST00000424049	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1596	0.81693	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DIS3L2	232822191	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	8.670000	0.91168	2.216000	0.71823	0.533000	0.62120	.	.	.		0.552	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383	Intron	G	233113947	A	G	233113947	5	3	114	1	0	0	0	0	0	0	1	0	4539	202	7	2	1358	2	DIS3L2	2	233113947	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	656215	233113947	10085426	213	18485										
UGT1A5	54579	hgsc.bcm.edu	37	chr2	234622002	234622002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattatgaacaatatgtcttTgatcatacataggtcttgtg	7	5	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:234622002T>C	ENST00000373414.3	+	1	365	c.365T>C	c.(364-366)tTg>tCg	p.L122S	UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000608381.1_Missense_Mutation_p.L122S|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A10_ENST00000373445.1_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	122						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		AATATGTCTTTGATCATACAT	0.413																																					p.L122S		Atlas-SNP	.											.	UGT1A5	66	.	0			c.T365C						.						173	168	170					2																	234622002		2203	4300	6503	SO:0001583	missense	54579	exon1			TGTCTTTGATCAT	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"UDP glucuronosyltransferases"	12537	other	complex locus constituent		606430	"UDP glycosyltransferase 1 family, polypeptide A5"			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.365T>C	chr2.hg19:g.234622002T>C	ENSP00000362513:p.Leu122Ser	179.0	0.0		232.0	89.0	NM_019078	B8K294	Missense_Mutation	SNP	ENST00000373414.3	hg19	CCDS33404.1	.	.	.	.	.	.	.	.	.	.	T	5.192	0.221009	0.09863	.	.	ENSG00000240224	ENST00000373414	T	0.58797	0.31	4.69	-9.37	0.00626	.	3.783170	0.01269	N	0.009403	T	0.30103	0.0754	N	0.11284	0.12	0.09310	N	1	B;B	0.19583	0.037;0.037	B;B	0.19666	0.026;0.026	T	0.10382	-1.0632	10	0.26408	T	0.33	.	4.0361	0.09730	0.2323:0.4383:0.0787:0.2506	.	122;122	Q5DSZ9;P35504	.;UD15_HUMAN	S	122	ENSP00000362513:L122S	ENSP00000362513:L122S	L	+	2	0	UGT1A5	234286741	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.690000	0.05138	-1.286000	0.02384	-0.531000	0.04308	TTG	.	.		0.413	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078		C	234622002	T	C	234622002	3	2	114	1	0	0	0	0	1	0	0	0	16963	1821	63	2	367	2	UGT1A5	2	234622002	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1508055	234622002	8577371	214	18486										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234879010	234879010	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatttccattcggtgccacaCccccccgagctggtcctgta					rs201204922		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:234879010delC	ENST00000324695.4	+	17	2335	c.2295delC	c.(2293-2295)cacfs	p.H765fs	TRPM8_ENST00000433712.2_Intron	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	765					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	CGGTGCCACACCCCCCCGAGC	0.577																																					p.H765fs		Atlas-INDEL	.											.,2	TRPM8	146	.	0			c.2294delA						.						309	295	300					2																	234879010		2203	4300	6503	SO:0001589	frameshift_variant	79054	exon17			.	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.2295delC	chr2.hg19:g.234879010delC	ENSP00000323926:p.His765fs	189.0	0.0		242.0	15.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Frame_Shift_Del	DEL	ENST00000324695.4	hg19	CCDS33407.1																																																																																			.	.		0.577	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		-	234879010	C	-	234879010	7	5	114	1	0	1	0	1	0	0	0	0	16607	506	18	0	2357	0	TRPM8	2	234879010	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	257008	234879010	8320363	215	18487										
LRRFIP1	9208	hgsc.bcm.edu	37	chr2	238647924	238647924	+	Intron	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagctcccgcgcctcctccaGggccagctcggcccgggcca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:238647924delG	ENST00000392000.4	+	5	366				LRRFIP1_ENST00000289175.6_Intron|LRRFIP1_ENST00000308482.9_Frame_Shift_Del_p.R202fs|LRRFIP1_ENST00000244815.5_Intron	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1						innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		GCCTCCTCCAGGGCCAGCTCG	0.662																																					p.R202fs		Atlas-INDEL	.											.	LRRFIP1	171	.	0			c.604delA						.						8	10	9					2																	238647924		1546	3553	5099	SO:0001627	intron_variant	9208	exon11			.	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"GC-binding factor 2"	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.250-9083G>-	chr2.hg19:g.238647924delG		121.0	0.0		166.0	11.0	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Frame_Shift_Del	DEL	ENST00000392000.4	hg19	CCDS46552.1																																																																																			.	.		0.662	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		-	238647924	G	-	238647924	6	5	114	0	1	1	0	1	0	0	0	0	9036	1000	35	0		0	LRRFIP1	2	238647924	Intron	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	3768914	238647924	4551449	216	18488										
HDAC4	9759	hgsc.bcm.edu	37	chr2	240274391	240274391	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acctggatggctttgggagcTcattgctagcaatgtccact	11	10	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:240274391T>C	ENST00000345617.3	-	2	795	c.4A>G	c.(4-6)Agc>Ggc	p.S2G	MIR2467_ENST00000584559.1_RNA	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	2					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CTTTGGGAGCTCATTGCTAGC	0.493																																					p.S2G		Atlas-SNP	.											.	HDAC4	127	.	0			c.A4G						.						68	68	68					2																	240274391		2195	4274	6469	SO:0001583	missense	9759	exon2			GGGAGCTCATTGC	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.4A>G	chr2.hg19:g.240274391T>C	ENSP00000264606:p.Ser2Gly	88.0	0.0		110.0	5.0	NM_006037	Q9UND6	Missense_Mutation	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	T	9.445	1.088958	0.20390	.	.	ENSG00000068024	ENST00000345617;ENST00000544989	T	0.59364	0.27	3.73	3.73	0.42828	.	1.437920	0.05036	U	0.475568	T	0.31979	0.0814	N	0.02011	-0.69	0.80722	D	1	B	0.16603	0.018	B	0.15870	0.014	T	0.13229	-1.0517	9	.	.	.	.	9.4103	0.38487	0.0:0.0:0.0:1.0	.	2	P56524	HDAC4_HUMAN	G	2	ENSP00000264606:S2G	.	S	-	1	0	HDAC4	239939328	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	3.549000	0.53681	1.659000	0.50751	0.528000	0.53228	AGC	.	.		0.493	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		C	240274391	T	C	240274391	3	2	114	1	0	0	0	0	1	0	0	0	7018	1551	54	2	3354	2	HDAC4	2	240274391	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1626467	240274391	2924982	217	18489										
PPP1R7	5510	hgsc.bcm.edu	37	chr2	242089946	242089946	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcgcggggcagcaacagtcGcaggagatgatggagggtga	20	7	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:242089946G>A	ENST00000234038.6	+	1	510	c.36G>A	c.(34-36)tcG>tcA	p.S12S	PPP1R7_ENST00000401987.1_Silent_p.S12S|PASK_ENST00000234040.4_5'Flank|PPP1R7_ENST00000402734.1_Intron|PPP1R7_ENST00000406106.3_Silent_p.S12S|PASK_ENST00000358649.4_5'Flank|PASK_ENST00000405260.1_5'Flank|PASK_ENST00000403638.3_5'Flank|PPP1R7_ENST00000272983.8_Silent_p.S12S|PPP1R7_ENST00000407025.1_Silent_p.S12S|PPP1R7_ENST00000404405.3_Silent_p.S12S|PASK_ENST00000539818.1_5'Flank	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	12					positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		AGCAACAGTCGCAGGAGATGA	0.701																																					p.S12S	NSCLC(62;446 1299 5417 11238 27640)	Atlas-SNP	.											.	PPP1R7	35	.	0			c.G36A						.						15	19	18					2																	242089946		2187	4284	6471	SO:0001819	synonymous_variant	5510	exon1			ACAGTCGCAGGAG	AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9295	protein-coding gene	gene with protein product		602877	"protein phosphatase 1, regulatory (inhibitor) subunit 7"			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.36G>A	chr2.hg19:g.242089946G>A		93.0	0.0		78.0	4.0	NM_002712	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Silent	SNP	ENST00000234038.6	hg19	CCDS2546.1																																																																																			.	.		0.701	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712		A	242089946	G	A	242089946	2	1	114	1	0	0	0	0	0	0	0	1	12388	1074	38	1		1	PPP1R7	2	242089946	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1815555	242089946	1109427	218	18490										
HDLBP	3069	hgsc.bcm.edu	37	chr2	242194991	242194991	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgcaatggttgtagtcttcTttttctaaataagagcacca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:242194991delT	ENST00000391975.1	-	8	1105	c.878delA	c.(877-879)aagfs	p.K294fs	HDLBP_ENST00000427183.2_Intron|HDLBP_ENST00000310931.4_Frame_Shift_Del_p.K294fs|HDLBP_ENST00000391976.2_Frame_Shift_Del_p.K294fs	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	294	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		TGTAGTCTTCTTTTTCTAAAT	0.502																																					p.K293fs		Atlas-INDEL	.											.	HDLBP	118	.	0			c.879delG						.						105	97	99					2																	242194991		2203	4300	6503	SO:0001589	frameshift_variant	3069	exon8			.		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.878delA	chr2.hg19:g.242194991delT	ENSP00000375836:p.Lys294fs	115.0	0.0		207.0	13.0	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Frame_Shift_Del	DEL	ENST00000391975.1	hg19	CCDS2547.1																																																																																			.	.		0.502	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		-	242194991	T	-	242194991	7	5	114	1	0	1	0	1	0	0	0	0	7034	1609	56	0	3012	0	HDLBP	2	242194991	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	105045	242194991	1004382	219	18491										
SEPT2	4735	hgsc.bcm.edu	37	chr2	242275390	242275390	+	Splice_Site	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taagtttgtttcttttctagAaaaaattgaaagaactgtcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:242275390delA	ENST00000391973.2	+	5	746	c.218delA	c.(217-219)gaa>ga	p.E73fs	SEPT2_ENST00000391971.2_Splice_Site_p.E73fs|SEPT2_ENST00000360051.3_Splice_Site_p.E73fs|SEPT2_ENST00000402092.2_Splice_Site_p.E73fs|SEPT2_ENST00000407971.1_Splice_Site_p.E33fs|SEPT2_ENST00000401990.1_Splice_Site_p.E83fs	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	73	Septin-type G.				cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		TCTTTTCTAGAAAAAATTGAA	0.433																																					.		Atlas-INDEL	.											.	SEPT2	33	.	0			c.218-1A>-						.						66	69	68					2																	242275390		2203	4300	6503	SO:0001630	splice_region_variant	4735	exon5			.	D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"Septins"	7729	protein-coding gene	gene with protein product		601506	"neural precursor cell expressed, developmentally down-regulated 5"	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.218-1A>-	chr2.hg19:g.242275390delA		86.0	0.0		153.0	14.0	NM_006155	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Splice_Site	DEL	ENST00000391973.2	hg19	CCDS2548.1																																																																																			.	.		0.433	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155	Frame_Shift_Del	-	242275390	A	-	242275390	8	5	114	1	0	1	0	1	0	0	1	0	14079	260	9	0	232	0	SEPT2	2	242275390	Splice_Site	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	80399	242275390	923983	220	18492										
FARP2	9855	hgsc.bcm.edu	37	chr2	242373660	242373660	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttgtgtggagtatcacaccTtttttagacttttggaccaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:242373660delT	ENST00000264042.3	+	10	1125	c.955delT	c.(955-957)tttfs	p.F320fs	FARP2_ENST00000545004.1_Frame_Shift_Del_p.F320fs|FARP2_ENST00000373287.4_Frame_Shift_Del_p.F320fs	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	320	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GTATCACACCTTTTTTAGACT	0.453																																					p.T318fs		Atlas-INDEL	.											.	FARP2	92	.	0			c.954delC						.						140	144	142					2																	242373660		2203	4300	6503	SO:0001589	frameshift_variant	9855	exon10			.	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.955delT	chr2.hg19:g.242373660delT	ENSP00000264042:p.Phe320fs	119.0	0.0		170.0	12.0	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Frame_Shift_Del	DEL	ENST00000264042.3	hg19	CCDS33424.1																																																																																			.	.		0.453	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			-	242373660	T	-	242373660	7	5	114	1	0	1	0	1	0	0	0	0	5685	1609	56	0	989	0	FARP2	2	242373660	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	98270	242373660	825713	221	18493										
NEK10	152110	hgsc.bcm.edu	37	chr3	27332187	27332187	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcttatcctttccaaatgctGggttatgtaaattgacctct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:27332187delG	ENST00000429845.2	-	20	2026	c.1664delC	c.(1663-1665)ccafs	p.P555fs	NEK10_ENST00000341435.5_Frame_Shift_Del_p.P555fs|NEK10_ENST00000357467.2_Intron			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	555	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCCAAATGCTGGGTTATGTAA	0.328																																					p.P555fs		Atlas-INDEL	.											.	NEK10	271	.	0			c.1665delA						.						116	102	106					3																	27332187		1568	3582	5150	SO:0001589	frameshift_variant	152110	exon20			.	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)- related kinase 10"			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1664delC	chr3.hg19:g.27332187delG	ENSP00000395849:p.Pro555fs	89.0	0.0		141.0	11.0	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Frame_Shift_Del	DEL	ENST00000429845.2	hg19																																																																																				.	.		0.328	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534		-	27332187	G	-	27332187	7	5	114	1	0	1	0	1	0	0	0	0	10331	1348	47	0	498	0	NEK10	3	27332187	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10		27332187	170690243	222	18494										
STT3B	201595	hgsc.bcm.edu	37	chr3	31661295	31661295	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggcctttggttctgcatcAaaaatatcaacgatgaaaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:31661295delA	ENST00000295770.2	+	9	1509	c.1300delA	c.(1300-1302)aaafs	p.K434fs	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	434					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						GTTCTGCATCAAAAATATCAA	0.333																																					p.I433fs		Atlas-INDEL	.											.,1	STT3B	52	.	0			c.1299delC						.						159	139	146					3																	31661295		2203	4300	6503	SO:0001589	frameshift_variant	201595	exon9			.	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"source of immunodominant MHC associated peptides", "dolichyl-diphosphooligosaccharide protein glycotransferase"	608605	"STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.1300delA	chr3.hg19:g.31661295delA	ENSP00000295770:p.Lys434fs	129.0	0.0		159.0	10.0	NM_178862	Q96JZ4|Q96KY7	Frame_Shift_Del	DEL	ENST00000295770.2	hg19	CCDS2650.1																																																																																			.	.		0.333	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862		-	31661295	A	-	31661295	7	5	114	1	0	1	0	1	0	0	0	0	15349	131	5	0	1334	0	STT3B	3	31661295	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	4329108	31661295	166361135	223	18495										
DYNC1LI1	51143	hgsc.bcm.edu	37	chr3	32570036	32570036	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcctcctggagagccagtcTttttactcaacaaactgttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:32570036delT	ENST00000273130.4	-	12	1467	c.1364delA	c.(1363-1365)aagfs	p.K455fs	DYNC1LI1_ENST00000432458.2_Frame_Shift_Del_p.K339fs	NM_016141.3	NP_057225.2	Q9Y6G9	DC1L1_HUMAN	dynein, cytoplasmic 1, light intermediate chain 1	455					microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(1)|lung(3)|ovary(1)	7						AGAGCCAGTCTTTTTACTCAA	0.453																																					p.K455fs		Atlas-INDEL	.											.	DYNC1LI1	23	.	0			c.1365delG						.						66	68	68					3																	32570036		2203	4300	6503	SO:0001589	frameshift_variant	51143	exon12			.	AF078849	CCDS2654.1	3p23	2013-01-18	2005-11-25	2005-11-25	ENSG00000144635	ENSG00000144635		"Cytoplasmic dyneins"	18745	protein-coding gene	gene with protein product		615890	"dynein, cytoplasmic, light intermediate polypeptide 1"	DNCLI1		16260502	Standard	NM_016141		Approved		uc003cfb.4	Q9Y6G9	OTTHUMG00000130750	ENST00000273130.4:c.1364delA	chr3.hg19:g.32570036delT	ENSP00000273130:p.Lys455fs	101.0	0.0		116.0	10.0	NM_016141	A2RRG7|Q53HC8|Q53HK7	Frame_Shift_Del	DEL	ENST00000273130.4	hg19	CCDS2654.1																																																																																			.	.		0.453	DYNC1LI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253250.1	NM_016141		-	32570036	T	-	32570036	7	5	114	1	0	1	0	1	0	0	0	0	4846	1609	56	0	215	0	DYNC1LI1	3	32570036	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	908741	32570036	165452394	224	18496										
DYNC1LI1	51143	hgsc.bcm.edu	37	chr3	32611883	32611883	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agggagcttggagcgcgagcGggtggagacctcgctgagga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:32611883delG	ENST00000273130.4	-	2	278	c.175delC	c.(175-177)cgcfs	p.R59fs	DYNC1LI1_ENST00000432458.2_Frame_Shift_Del_p.R59fs	NM_016141.3	NP_057225.2	Q9Y6G9	DC1L1_HUMAN	dynein, cytoplasmic 1, light intermediate chain 1	59					microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(1)|lung(3)|ovary(1)	7						GAGCGCGAGCGGGTGGAGACC	0.731																																					p.R59fs		Atlas-INDEL	.											.	DYNC1LI1	23	.	0			c.176delG						.						23	23	23					3																	32611883		2195	4294	6489	SO:0001589	frameshift_variant	51143	exon2			.	AF078849	CCDS2654.1	3p23	2013-01-18	2005-11-25	2005-11-25	ENSG00000144635	ENSG00000144635		"Cytoplasmic dyneins"	18745	protein-coding gene	gene with protein product		615890	"dynein, cytoplasmic, light intermediate polypeptide 1"	DNCLI1		16260502	Standard	NM_016141		Approved		uc003cfb.4	Q9Y6G9	OTTHUMG00000130750	ENST00000273130.4:c.175delC	chr3.hg19:g.32611883delG	ENSP00000273130:p.Arg59fs	135.0	0.0		180.0	11.0	NM_016141	A2RRG7|Q53HC8|Q53HK7	Frame_Shift_Del	DEL	ENST00000273130.4	hg19	CCDS2654.1																																																																																			.	.		0.731	DYNC1LI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253250.1	NM_016141		-	32611883	G	-	32611883	7	5	114	1	0	1	0	1	0	0	0	0	4846	1116	39	0	1444	0	DYNC1LI1	3	32611883	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	41847	32611883	165410547	225	18497										
ITGA9	3680	hgsc.bcm.edu	37	chr3	37845344	37845344	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggccctgcacaatctggagCcccgtggctacgtcgtgggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:37845344delC	ENST00000264741.5	+	27	3176	c.2920delC	c.(2920-2922)cccfs	p.P974fs	AC093415.2_ENST00000438136.1_RNA|AC093415.2_ENST00000420870.1_RNA|AC093415.2_ENST00000450990.1_RNA|AC093415.2_ENST00000445429.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	974					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		CAATCTGGAGCCCCGTGGCTA	0.512																																					p.E973fs		Atlas-INDEL	.											.	ITGA9	98	.	0			c.2919delG						.						180	141	154					3																	37845344		2203	4300	6503	SO:0001589	frameshift_variant	3680	exon27			.	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2920delC	chr3.hg19:g.37845344delC	ENSP00000264741:p.Pro974fs	187.0	0.0		233.0	17.0	NM_002207	Q14638	Frame_Shift_Del	DEL	ENST00000264741.5	hg19	CCDS2669.1																																																																																			.	.		0.512	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		-	37845344	C	-	37845344	7	5	114	1	0	1	0	1	0	0	0	0	7892	739	26	0	3026	0	ITGA9	3	37845344	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	5233461	37845344	160177086	226	18498										
XYLB	9942	hgsc.bcm.edu	37	chr3	38417621	38417621	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctgcagctttaaaaatggcTccctcatgagagagaagatc	9	9	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:38417621T>C	ENST00000207870.3	+	13	1108	c.1018T>C	c.(1018-1020)Tcc>Ccc	p.S340P	XYLB_ENST00000542835.1_Missense_Mutation_p.S203P	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	340					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		TAAAAATGGCTCCCTCATGAG	0.532																																					p.S340P		Atlas-SNP	.											.	XYLB	50	.	0			c.T1018C						.						146	148	147					3																	38417621		2203	4300	6503	SO:0001583	missense	9942	exon13			AATGGCTCCCTCA	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"xylulokinase (H. influenzae) homolog"			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.1018T>C	chr3.hg19:g.38417621T>C	ENSP00000207870:p.Ser340Pro	129.0	0.0		128.0	8.0	NM_005108	B2RAW4|B4DDT2|B9EH64	Missense_Mutation	SNP	ENST00000207870.3	hg19	CCDS2678.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.191084	0.78902	.	.	ENSG00000093217	ENST00000207870;ENST00000542835	T;T	0.44482	0.92;0.92	4.91	4.91	0.64330	Carbohydrate kinase, FGGY, C-terminal (1);	0.060785	0.64402	D	0.000002	T	0.69993	0.3173	M	0.92169	3.28	0.47659	D	0.999488	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.992	T	0.76258	-0.3025	10	0.56958	D	0.05	.	11.2238	0.48871	0.0:0.0:0.0:1.0	.	203;340	B4DDT2;O75191	.;XYLB_HUMAN	P	340;203	ENSP00000207870:S340P;ENSP00000443659:S203P	ENSP00000207870:S340P	S	+	1	0	XYLB	38392625	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.606000	0.74159	1.966000	0.57179	0.379000	0.24179	TCC	.	.		0.532	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108		C	38417621	T	C	38417621	3	2	114	1	0	0	0	0	1	0	0	0	17477	1551	54	2	1068	2	XYLB	3	38417621	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	572277	38417621	159604809	227	18499										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38739704	38739704	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggggccctgtgttgaggatGgggctgaggaggccatccca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:38739704delG	ENST00000449082.2	-	27	5006	c.5007delC	c.(5005-5007)cccfs	p.P1669fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1669					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TGTTGAGGATGGGGCTGAGGA	0.597																																					p.I1670fs		Atlas-INDEL	.											.	SCN10A	359	.	0			c.5008delA						.						77	80	79					3																	38739704		2203	4300	6503	SO:0001589	frameshift_variant	6336	exon27			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.5007delC	chr3.hg19:g.38739704delG	ENSP00000390600:p.Pro1669fs	162.0	0.0		186.0	13.0	NM_006514	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.		0.597	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		-	38739704	G	-	38739704	7	5	114	1	0	1	0	1	0	0	0	0	13927	1335	47	0	867	0	SCN10A	3	38739704	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	322083	38739704	159282726	228	18500										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38793887	38793887	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggctttcgtggtctccaggAaagactccatcatctgtgac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:38793887delA	ENST00000449082.2	-	11	1577	c.1578delT	c.(1576-1578)tttfs	p.F526fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	526					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GGTCTCCAGGAAAGACTCCAT	0.607																																					p.P527fs		Atlas-INDEL	.											.	SCN10A	359	.	0			c.1579delC						.						52	57	55					3																	38793887		2203	4300	6503	SO:0001589	frameshift_variant	6336	exon11			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1578delT	chr3.hg19:g.38793887delA	ENSP00000390600:p.Phe526fs	121.0	0.0		151.0	10.0	NM_006514	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.		0.607	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		-	38793887	A	-	38793887	7	5	114	1	0	1	0	1	0	0	0	0	13927	243	9	0	4360	0	SCN10A	3	38793887	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	54183	38793887	159228543	229	18501										
VIPR1	7433	hgsc.bcm.edu	37	chr3	42576497	42576497	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggtccacactcctgctgatCcccctgtttggagtacacta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:42576497delC	ENST00000325123.4	+	11	1154	c.1041delC	c.(1039-1041)atcfs	p.I347fs	VIPR1-AS1_ENST00000602176.1_RNA|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1_ENST00000543411.1_Frame_Shift_Del_p.I299fs|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000610022.1_RNA|VIPR1-AS1_ENST00000593611.1_RNA|VIPR1_ENST00000433647.1_Frame_Shift_Del_p.I306fs|VIPR1-AS1_ENST00000608869.1_RNA|VIPR1-AS1_ENST00000593621.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|VIPR1_ENST00000438259.2_Frame_Shift_Del_p.I137fs	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	347					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		TCCTGCTGATCCCCCTGTTTG	0.527																																					p.I347fs		Atlas-INDEL	.											.	VIPR1	45	.	0			c.1040delT						.						169	136	147					3																	42576497		2203	4300	6503	SO:0001589	frameshift_variant	7433	exon11			.	AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12694	protein-coding gene	gene with protein product	"VIP and PACAP receptor 1"	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.1041delC	chr3.hg19:g.42576497delC	ENSP00000327246:p.Ile347fs	179.0	0.0		198.0	14.0	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Frame_Shift_Del	DEL	ENST00000325123.4	hg19	CCDS2698.1																																																																																			.	.		0.527	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624		-	42576497	C	-	42576497	7	5	114	1	0	1	0	1	0	0	0	0	17184	845	30	0	1083	0	VIPR1	3	42576497	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3782610	42576497	155445933	230	18502										
CCDC13	152206	hgsc.bcm.edu	37	chr3	42754657	42754657	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actgccctggcccctacctgTtttggtcctgggagctgctc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:42754657delT	ENST00000310232.6	-	14	1953	c.1870delA	c.(1870-1872)acafs	p.T624fs		NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	624										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						CCCCTACCTGTTTTGGTCCTG	0.617																																					p.T624fs		Atlas-INDEL	.											.	CCDC13	71	.	0			c.1871delC						.						97	89	92					3																	42754657		2203	4300	6503	SO:0001589	frameshift_variant	152206	exon14			.	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1870delA	chr3.hg19:g.42754657delT	ENSP00000309836:p.Thr624fs	124.0	0.0		170.0	11.0	NM_144719		Frame_Shift_Del	DEL	ENST00000310232.6	hg19	CCDS2705.1																																																																																			.	.		0.617	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		-	42754657	T	-	42754657	7	5	114	1	0	1	0	1	0	0	0	0	2767	1725	60	0	289	0	CCDC13	3	42754657	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	178160	42754657	155267773	231	18503										
ZNF167	55888	hgsc.bcm.edu	37	chr3	44606986	44606986	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tccctctctctaggtttcagCcccagcacagaaacaggaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:44606986delC	ENST00000273320.3	+	3	860	c.431delC	c.(430-432)gccfs	p.A144fs	RP11-944L7.4_ENST00000457331.1_RNA|ZKSCAN7_ENST00000426540.1_Frame_Shift_Del_p.A144fs|RP11-944L7.5_ENST00000419137.1_5'Flank|ZKSCAN7_ENST00000341840.3_Frame_Shift_Del_p.A144fs|ZKSCAN7_ENST00000431636.1_Frame_Shift_Del_p.A144fs	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	144					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TAGGTTTCAGCCCCAGCACAG	0.498																																					p.A144fs		Atlas-INDEL	.											.	.	.	.	0			c.430delG						.						142	140	141					3																	44606986		2203	4300	6503	SO:0001589	frameshift_variant	55888	exon3			.	L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"Zinc fingers, C2H2-type", "-", "-", "-"	12955	protein-coding gene	gene with protein product			"zinc finger protein 64", "zinc finger protein 448", "zinc finger protein 167"	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.431delC	chr3.hg19:g.44606986delC	ENSP00000273320:p.Ala144fs	123.0	0.0		164.0	11.0	NM_018651	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Frame_Shift_Del	DEL	ENST00000273320.3	hg19	CCDS2715.1																																																																																			.	.		0.498	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		-	44606986	C	-	44606986	7	5	114	1	0	1	0	1	0	0	0	0	17756	739	26	0	437	0	ZNF167	3	44606986	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1852329	44606986	153415444	232	18504										
KIF15	56992	hgsc.bcm.edu	37	chr3	44879844	44879844	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaggcctcaaaaaaacactcGgggctgctgcagtctgccca					rs369445825		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:44879844delG	ENST00000326047.4	+	27	3398	c.3249delG	c.(3247-3249)tcgfs	p.S1083fs	KIF15_ENST00000425755.1_Frame_Shift_Del_p.S718fs	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1083					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		AAAAACACTCGGGGCTGCTGC	0.517																																					p.S1083fs		Atlas-INDEL	.											KIF15,NS,carcinoma,0,1	KIF15	103	.	0			c.3248delC						.						52	56	54					3																	44879844		2203	4300	6503	SO:0001589	frameshift_variant	56992	exon27			.	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.3249delG	chr3.hg19:g.44879844delG	ENSP00000324020:p.Ser1083fs	153.0	0.0		159.0	10.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Frame_Shift_Del	DEL	ENST00000326047.4	hg19	CCDS33744.1																																																																																			.	.		0.517	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			-	44879844	G	-	44879844	7	5	114	1	0	1	0	1	0	0	0	0	8286	1103	39	0	3355	0	KIF15	3	44879844	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	272858	44879844	153142586	233	18505										
KIF15	56992	hgsc.bcm.edu	37	chr3	44882704	44882704	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taaatgaagacagagaagtcAaaaatgctgaaatcctcaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:44882704delA	ENST00000326047.4	+	29	3708	c.3559delA	c.(3559-3561)aaafs	p.K1187fs	KIF15_ENST00000425755.1_Frame_Shift_Del_p.K822fs	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1187					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		CAGAGAAGTCAAAAATGCTGA	0.368																																					p.V1186fs		Atlas-INDEL	.											.	KIF15	103	.	0			c.3558delC						.						61	66	64					3																	44882704		2203	4300	6503	SO:0001589	frameshift_variant	56992	exon29			.	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.3559delA	chr3.hg19:g.44882704delA	ENSP00000324020:p.Lys1187fs	94.0	0.0		127.0	11.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Frame_Shift_Del	DEL	ENST00000326047.4	hg19	CCDS33744.1																																																																																			.	.		0.368	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			-	44882704	A	-	44882704	7	5	114	1	0	1	0	1	0	0	0	0	8286	131	5	0	3673	0	KIF15	3	44882704	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2860	44882704	153139726	234	18506										
CCR5	1234	hgsc.bcm.edu	37	chr3	46415316	46415316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggagaagttcagaaactaccTcttagtcttcttccaaaagc	7	10	4	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:46415316T>C	ENST00000292303.4	+	2	1069	c.923T>C	c.(922-924)cTc>cCc	p.L308P	RP11-24F11.2_ENST00000451485.1_RNA|CCR5_ENST00000445772.1_Missense_Mutation_p.L308P|CCR5_ENST00000343801.4_Missense_Mutation_p.L308P	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	308					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	AGAAACTACCTCTTAGTCTTC	0.493																																					p.L308P		Atlas-SNP	.											.	CCR5	128	.	0			c.T923C						.						184	178	180					3																	46415316		2203	4296	6499	SO:0001583	missense	1234	exon3			ACTACCTCTTAGT		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1606	protein-coding gene	gene with protein product		601373	"chemokine (C-C motif) receptor 5"	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.923T>C	chr3.hg19:g.46415316T>C	ENSP00000292303:p.Leu308Pro	76.0	0.0		96.0	5.0	NM_000579	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Missense_Mutation	SNP	ENST00000292303.4	hg19	CCDS2739.1	.	.	.	.	.	.	.	.	.	.	T	16.33	3.092527	0.56075	.	.	ENSG00000160791	ENST00000343801;ENST00000400886;ENST00000292303;ENST00000445772	T;T;T	0.48522	0.81;0.81;0.81	5.69	5.69	0.88448	.	0.165190	0.25631	U	0.029349	T	0.72334	0.3447	M	0.93420	3.415	0.46774	D	0.999191	D	0.67145	0.996	P	0.61275	0.886	T	0.79581	-0.1744	10	0.87932	D	0	.	11.0514	0.47893	0.0:0.072:0.0:0.928	.	308	P51681	CCR5_HUMAN	P	308;288;308;308	ENSP00000343985:L308P;ENSP00000292303:L308P;ENSP00000404881:L308P	ENSP00000292303:L308P	L	+	2	0	CCR5	46390320	0.538000	0.26394	0.430000	0.26722	0.899000	0.52679	4.125000	0.57931	2.162000	0.67917	0.459000	0.35465	CTC	.	.		0.493	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579		C	46415316	T	C	46415316	3	2	114	1	0	0	0	0	1	0	0	0	2946	1551	54	2	925	2	CCR5	3	46415316	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1532612	46415316	151607114	235	18507										
SETD2	29072	hgsc.bcm.edu	37	chr3	47168143	47168143	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttaaattatacttacctcatTttcttcttctctatttccat	0	10	4	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:47168143T>C	ENST00000409792.3	-	2	124	c.82A>G	c.(82-84)Aat>Gat	p.N28D		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	28					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CTTACCTCATTTTCTTCTTCT	0.264			"N, F, S, Mis"		clear cell renal carcinoma																																p.N28D		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.A82G						.						122	103	108					3																	47168143		1475	3412	4887	SO:0001583	missense	29072	exon2			CCTCATTTTCTTC	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.82A>G	chr3.hg19:g.47168143T>C	ENSP00000386759:p.Asn28Asp	33.0	0.0		35.0	4.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	16.73	3.205346	0.58234	.	.	ENSG00000181555	ENST00000409792	D	0.88818	-2.43	4.46	4.46	0.54185	.	.	.	.	.	D	0.88584	0.6476	N	0.14661	0.345	0.24154	N	0.995682	D	0.63880	0.993	D	0.70935	0.971	T	0.80603	-0.1309	9	0.87932	D	0	.	11.5254	0.50576	0.0:0.0:0.0:1.0	.	28	Q9BYW2	SETD2_HUMAN	D	28	ENSP00000386759:N28D	ENSP00000386759:N28D	N	-	1	0	SETD2	47143147	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	4.399000	0.59703	1.996000	0.58369	0.402000	0.26972	AAT	.	.		0.264	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		C	47168143	T	C	47168143	3	2	114	1	0	0	0	0	1	0	0	0	14146	1841	64	2	7692	2	SETD2	3	47168143	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	752827	47168143	150854287	236	18508										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48610625	48610625	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accacaaggcctgaagggccGgggggtccaggaagtcccac					rs61729223	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:48610625delG	ENST00000328333.8	-	84	6803	c.6696delC	c.(6694-6696)cccfs	p.P2232fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.P2200fs	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2232	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTGAAGGGCCGGGGGGTCCAG	0.607																																					p.G2233fs		Atlas-INDEL	.											.	COL7A1	320	.	0			c.6697delG						.						52	53	53					3																	48610625		2203	4300	6503	SO:0001589	frameshift_variant	1294	exon84			.	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6696delC	chr3.hg19:g.48610625delG	ENSP00000332371:p.Pro2232fs	83.0	0.0		129.0	10.0	NM_000094	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.607	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		-	48610625	G	-	48610625	7	5	114	1	0	1	0	1	0	0	0	0	3706	1103	39	0	2278	0	COL7A1	3	48610625	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1442482	48610625	149411805	237	18509										
KLHDC8B	200942	hgsc.bcm.edu	37	chr3	49210244	49210244	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcctttgcttggcaagtgttCccccccatgcccacttgccg					rs201475255	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:49210244delC	ENST00000332780.2	+	2	251	c.42delC	c.(40-42)ttcfs	p.F14fs	KLHDC8B_ENST00000476495.2_3'UTR	NM_173546.2	NP_775817.1	Q8IXV7	KLD8B_HUMAN	kelch domain containing 8B	14						cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|stomach(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGCAAGTGTTCCCCCCCATGC	0.637																																					p.F14fs		Atlas-INDEL	.											.	KLHDC8B	28	.	0			c.41delT						.						54	52	53					3																	49210244		2203	4300	6503	SO:0001589	frameshift_variant	200942	exon2			.		CCDS2791.1	3p21.31	2008-02-05			ENSG00000185909	ENSG00000185909			28557	protein-coding gene	gene with protein product		613169					Standard	NM_173546		Approved	MGC35097	uc003cwh.3	Q8IXV7	OTTHUMG00000156814	ENST00000332780.2:c.42delC	chr3.hg19:g.49210244delC	ENSP00000327468:p.Phe14fs	128.0	0.0		145.0	10.0	NM_173546		Frame_Shift_Del	DEL	ENST00000332780.2	hg19	CCDS2791.1																																																																																			.	.		0.637	KLHDC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345974.1	NM_173546		-	49210244	C	-	49210244	7	5	114	1	0	1	0	1	0	0	0	0	8372	854	30	0	44	0	KLHDC8B	3	49210244	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	599619	49210244	148812186	238	18510										
MST1	327	hgsc.bcm.edu	37	chr3	49722912	49722912	+	IGR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaactcctaacctggggggTccaggattgatggcggctgg	15	11	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:49722912T>G	ENST00000296456.5	+	0	3220				MST1_ENST00000449682.2_Missense_Mutation_p.D472A|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000494828.2_5'Flank|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		ACCTGGGGGGTCCAGGATTGA	0.587																																					p.D472A		Atlas-SNP	.											.	MST1	84	.	0			c.A1415C						.						29	32	31					3																	49722912		2202	4299	6501	SO:0001628	intergenic_variant	4485	exon12			GGGGGGTCCAGGA	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		chr3.hg19:g.49722912T>G		304.0	0.0		488.0	30.0	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	T	11.73	1.724622	0.30593	.	.	ENSG00000173531	ENST00000449682	T	0.79454	-1.27	4.78	4.78	0.61160	.	0.707688	0.11995	N	0.509451	T	0.58278	0.2111	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.51293	-0.8724	10	0.16420	T	0.52	.	11.2685	0.49124	0.0:0.0:0.0:1.0	rs11393273	472	G3XAK1	.	A	472	ENSP00000414287:D472A	ENSP00000414287:D472A	D	-	2	0	MST1	49697916	1.000000	0.71417	0.990000	0.47175	0.783000	0.44284	4.165000	0.58196	2.087000	0.62958	0.533000	0.62120	GAC	.	.		0.587	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			G	49722912	T	G	49722912	1	3	114	0	1	0	0	0	0	0	0	0	9899	1667	58	5		5	MST1	3	49722912	IGR	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	512668	49722912	148299518	239	18511										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52712558	52712558	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agagctcacagagaagtctgCcctgttcatccttatagtct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:52712558delC	ENST00000296302.7	-	2	195	c.194delG	c.(193-195)ggcfs	p.G65fs	PBRM1_ENST00000410007.1_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.G65fs			Q86U86	PB1_HUMAN	polybromo 1	65	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.			G -> S (in Ref. 4; AAI15011). {ECO:0000305}.	chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GAGAAGTCTGCCCTGTTCATC	0.443			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.G65fs		Atlas-INDEL	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.195delC						.						139	127	131					3																	52712558		2203	4300	6503	SO:0001589	frameshift_variant	55193	exon3			.	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.194delG	chr3.hg19:g.52712558delC	ENSP00000296302:p.Gly65fs	130.0	0.0		149.0	10.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	hg19																																																																																				.	.		0.443	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		-	52712558	C	-	52712558	7	5	114	1	0	1	0	1	0	0	0	0	11500	739	26	0	4822	0	PBRM1	3	52712558	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2989646	52712558	145309872	240	18512										
NEK4	6787	hgsc.bcm.edu	37	chr3	52745814	52745814	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caaaaattcatgttttcttcAaaaaatttcaactggcgagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:52745814delA	ENST00000233027.5	-	16	2707	c.2505delT	c.(2503-2505)tttfs	p.F835fs	NEK4_ENST00000535191.1_Frame_Shift_Del_p.F746fs	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	835					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		TGTTTTCTTCAAAAAATTTCA	0.358																																					p.E836fs		Atlas-INDEL	.											.	NEK4	51	.	0			c.2506delG						.						140	163	155					3																	52745814		2202	4300	6502	SO:0001589	frameshift_variant	6787	exon16			.	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"serine/threonine protein kinase-2"	601959	"serine/threonine kinase 2", "NIMA (never in mitosis gene a)-related kinase 4"	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.2505delT	chr3.hg19:g.52745814delA	ENSP00000233027:p.Phe835fs	176.0	0.0		163.0	12.0	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Frame_Shift_Del	DEL	ENST00000233027.5	hg19	CCDS2863.1																																																																																			.	.		0.358	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157		-	52745814	A	-	52745814	7	5	114	1	0	1	0	1	0	0	0	0	10335	127	5	0	24	0	NEK4	3	52745814	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	33256	52745814	145276616	241	18513										
NEK4	6787	hgsc.bcm.edu	37	chr3	52775439	52775439	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaacttacccttccccgtaaTccccatctgacttatcagtt	4	15	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:52775439T>C	ENST00000233027.5	-	13	2283	c.2081A>G	c.(2080-2082)gAt>gGt	p.D694G	NEK4_ENST00000535191.1_Missense_Mutation_p.D605G|NEK4_ENST00000383721.4_Missense_Mutation_p.D648G	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	694					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		TTCCCCGTAATCCCCATCTGA	0.323																																					p.D694G		Atlas-SNP	.											.	NEK4	51	.	0			c.A2081G						.						126	119	122					3																	52775439		2203	4300	6503	SO:0001583	missense	6787	exon13			CCGTAATCCCCAT	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"serine/threonine protein kinase-2"	601959	"serine/threonine kinase 2", "NIMA (never in mitosis gene a)-related kinase 4"	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.2081A>G	chr3.hg19:g.52775439T>C	ENSP00000233027:p.Asp694Gly	71.0	0.0		91.0	4.0	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	hg19	CCDS2863.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.421719	0.43020	.	.	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;T;T	0.78924	2.32;2.32;-1.22;2.32	5.66	4.51	0.55191	.	0.143577	0.47093	N	0.000241	T	0.68063	0.2960	L	0.43152	1.355	0.49483	D	0.999793	B;B;B	0.33288	0.182;0.406;0.284	B;B;B	0.31191	0.085;0.125;0.085	T	0.66850	-0.5819	10	0.52906	T	0.07	.	9.417	0.38528	0.0:0.0819:0.0:0.9181	.	605;648;694	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	G	694;605;648;605	ENSP00000233027:D694G;ENSP00000437703:D605G;ENSP00000373227:D648G;ENSP00000419666:D605G	ENSP00000233027:D694G	D	-	2	0	NEK4	52750479	1.000000	0.71417	0.994000	0.49952	0.626000	0.37791	4.851000	0.62896	1.089000	0.41292	0.533000	0.62120	GAT	.	.		0.323	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157		C	52775439	T	C	52775439	3	2	114	1	0	0	0	0	1	0	0	0	10335	1435	50	2	460	2	NEK4	3	52775439	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	29625	52775439	145246991	242	18514										
RFT1	91869	hgsc.bcm.edu	37	chr3	53125923	53125923	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaggcttccctgaagtcatGtcattttgtcagtgcgtctg	10	11	4	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:53125923G>C	ENST00000296292.3	-	13	1683	c.1622C>G	c.(1621-1623)aCa>aGa	p.T541R	RP11-894J14.5_ENST00000607203.1_Intron|RFT1_ENST00000394738.3_Missense_Mutation_p.T502R	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	541					carbohydrate transport (GO:0008643)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		CTGAAGTCATGTCATTTTGTC	0.547																																					p.T541R		Atlas-SNP	.											RFT1,colon,carcinoma,0,1	RFT1	34	.	0			c.C1622G						.						119	99	106					3																	53125923		2203	4300	6503	SO:0001583	missense	91869	exon13			AGTCATGTCATTT	AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933			30220	protein-coding gene	gene with protein product	"congenital disorder of glycosylation 1N"	611908	"RFT1, requiring fifty three 1 homolog (S. cerevisiae)"			12477932	Standard	NM_052859		Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000296292.3:c.1622C>G	chr3.hg19:g.53125923G>C	ENSP00000296292:p.Thr541Arg	235.0	0.0		228.0	0.0	NM_052859	Q96J03	Missense_Mutation	SNP	ENST00000296292.3	hg19	CCDS2869.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981026	0.34942	.	.	ENSG00000163933	ENST00000296292;ENST00000394738	D;D	0.86164	-2.08;-1.89	5.55	1.74	0.24563	.	0.311043	0.39407	N	0.001378	T	0.81088	0.4750	L	0.53249	1.67	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.71715	-0.4509	10	0.72032	D	0.01	.	5.8914	0.18915	0.2386:0.1411:0.6203:0.0	.	502;541	B5MDE0;Q96AA3	.;RFT1_HUMAN	R	541;502	ENSP00000296292:T541R;ENSP00000378223:T502R	ENSP00000296292:T541R	T	-	2	0	RFT1	53100963	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.595000	0.24029	0.304000	0.22809	0.561000	0.74099	ACA	.	.		0.547	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859		C	53125923	G	C	53125923	3	2	114	1	0	0	0	0	1	0	0	0	13272	1377	48	4	7	4	RFT1	3	53125923	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	350484	53125923	144896507	243	18515										
ACTR8	93973	hgsc.bcm.edu	37	chr3	53902877	53902877	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcctttccatgcaatcagccGggggtccatgtcctacagaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:53902877delG	ENST00000335754.3	-	13	1844	c.1744delC	c.(1744-1746)cggfs	p.R582fs	ACTR8_ENST00000488802.1_5'UTR|ACTR8_ENST00000231909.7_Frame_Shift_Del_p.R287fs|ACTR8_ENST00000482349.1_Frame_Shift_Del_p.R471fs	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	582					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		GCAATCAGCCGGGGGTCCATG	0.478																																					p.R582fs		Atlas-INDEL	.											.	ACTR8	56	.	0			c.1745delG						.						70	65	67					3																	53902877		2203	4300	6503	SO:0001589	frameshift_variant	93973	exon13			.		CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"INO80 complex subunits"	14672	protein-coding gene	gene with protein product	"INO80 complex subunit N"		"ARP8 (actin-related protein 8, yeast) homolog"			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.1744delC	chr3.hg19:g.53902877delG	ENSP00000336842:p.Arg582fs	123.0	0.0		163.0	10.0	NM_022899	B3KSW7|Q8N566|Q9H663	Frame_Shift_Del	DEL	ENST00000335754.3	hg19	CCDS2875.1																																																																																			.	.		0.478	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899		-	53902877	G	-	53902877	7	5	114	1	0	1	0	1	0	0	0	0	217	1115	39	0	134	0	ACTR8	3	53902877	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	776954	53902877	144119553	244	18516										
CCDC66	285331	hgsc.bcm.edu	37	chr3	56651451	56651451	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atattccagcatcagaaaagTaccctaaacagcttcaaaag	5	10	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:56651451T>C	ENST00000394672.3	+	14	2225	c.2155T>C	c.(2155-2157)Tac>Cac	p.Y719H	CCDC66_ENST00000436465.2_Missense_Mutation_p.Y719H|CCDC66_ENST00000326595.7_Missense_Mutation_p.Y685H	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	719					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		ATCAGAAAAGTACCCTAAACA	0.353																																					p.Y719H		Atlas-SNP	.											.	CCDC66	145	.	0			c.T2155C						.						48	51	50					3																	56651451		2203	4299	6502	SO:0001583	missense	285331	exon14			GAAAAGTACCCTA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.2155T>C	chr3.hg19:g.56651451T>C	ENSP00000378167:p.Tyr719His	96.0	0.0		100.0	4.0	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	hg19	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.334206	0.81801	.	.	ENSG00000180376	ENST00000394672;ENST00000326595;ENST00000436465	T;T;T	0.36340	1.26;1.26;1.26	5.68	5.68	0.88126	.	0.000000	0.64402	D	0.000001	T	0.61590	0.2359	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65928	-0.6049	10	0.87932	D	0	-7.9358	15.9259	0.79615	0.0:0.0:0.0:1.0	.	719	A2RUB6	CCD66_HUMAN	H	719;685;719	ENSP00000378167:Y719H;ENSP00000326050:Y685H;ENSP00000404320:Y719H	ENSP00000326050:Y685H	Y	+	1	0	CCDC66	56626491	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.089000	0.71384	2.161000	0.67846	0.460000	0.39030	TAC	.	.		0.353	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		C	56651451	T	C	56651451	3	2	114	1	0	0	0	0	1	0	0	0	2840	1638	57	2	2209	2	CCDC66	3	56651451	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2748574	56651451	141370979	245	18517										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57357612	57357612	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctacaaactttttccctagTttgtcagttacatagtttgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:57357612delT	ENST00000351747.2	-	48	7590	c.7410delA	c.(7408-7410)aaafs	p.K2470fs	DNAH12_ENST00000344804.4_Frame_Shift_Del_p.K103fs	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	2470	AAA 4. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TTTTCCCTAGTTTGTCAGTTA	0.333																																					p.L2471X		Atlas-INDEL	.											.	DNAH12	182	.	0			c.7411delC						.						198	177	183					3																	57357612		692	1591	2283	SO:0001589	frameshift_variant	201625	exon48			.	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.7410delA	chr3.hg19:g.57357612delT	ENSP00000295937:p.Lys2470fs	119.0	0.0		161.0	10.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Frame_Shift_Del	DEL	ENST00000351747.2	hg19																																																																																				.	.		0.333	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		-	57357612	T	-	57357612	7	5	114	1	0	1	0	1	0	0	0	0	4602	1722	60	0	1916	0	DNAH12	3	57357612	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	706161	57357612	140664818	246	18518										
SLMAP	7871	hgsc.bcm.edu	37	chr3	57902753	57902753	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttcgggattcagctgatttAaaaactcttctcagtaaggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:57902753delA	ENST00000428312.1	+	20	2302	c.2208delA	c.(2206-2208)ttafs	p.L736fs	SLMAP_ENST00000295952.3_Frame_Shift_Del_p.L719fs|SLMAP_ENST00000495364.1_Frame_Shift_Del_p.L270fs|SLMAP_ENST00000442599.2_Frame_Shift_Del_p.L204fs|SLMAP_ENST00000449503.2_Frame_Shift_Del_p.L698fs|SLMAP_ENST00000295951.3_Frame_Shift_Del_p.L719fs|SLMAP_ENST00000494088.1_Frame_Shift_Del_p.L229fs|SLMAP_ENST00000416870.1_Frame_Shift_Del_p.L229fs			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	736					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)				endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		CAGCTGATTTAAAAACTCTTC	0.408																																					p.L719X		Atlas-INDEL	.											.	SLMAP	46	.	0			c.2156delT						.						92	89	90					3																	57902753		2203	4300	6503	SO:0001589	frameshift_variant	7871	exon19			.	AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"Sarcolemmal-associated protein"	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.2208delA	chr3.hg19:g.57902753delA	ENSP00000398661:p.Leu736fs	219.0	0.0		246.0	15.0	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Frame_Shift_Del	DEL	ENST00000428312.1	hg19																																																																																				.	.		0.408	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159		-	57902753	A	-	57902753	7	5	114	1	0	1	0	1	0	0	0	0	14764	359	13	0	2231	0	SLMAP	3	57902753	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	545141	57902753	140119677	247	18519										
UBA3	9039	hgsc.bcm.edu	37	chr3	69117114	69117114	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttaggaactctgtcatttagAaattctgcagcaacttcagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:69117114delA	ENST00000361055.4	-	6	447	c.393delT	c.(391-393)tttfs	p.F131fs	UBA3_ENST00000349511.4_Frame_Shift_Del_p.F117fs|UBA3_ENST00000540295.1_Intron|UBA3_ENST00000415609.2_Frame_Shift_Del_p.F90fs	NM_003968.3	NP_003959.3	Q8TBC4	UBA3_HUMAN	ubiquitin-like modifier activating enzyme 3	131					cellular protein modification process (GO:0006464)|endomitotic cell cycle (GO:0007113)|protein neddylation (GO:0045116)|proteolysis (GO:0006508)|regulation of cell cycle (GO:0051726)	cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|NEDD8 activating enzyme activity (GO:0019781)|protein heterodimerization activity (GO:0046982)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.98e-05)|Epithelial(33;0.000363)|LUSC - Lung squamous cell carcinoma(21;0.012)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.206)|Kidney(39;0.241)		TGTCATTTAGAAATTCTGCAG	0.269																																					p.L132X		Atlas-INDEL	.											.	UBA3	43	.	0			c.394delC						.						55	61	59					3																	69117114		2203	4297	6500	SO:0001589	frameshift_variant	9039	exon6			.	AB012190	CCDS2909.1, CCDS2910.1	3p14.1	2013-09-26	2007-11-30	2007-11-30	ENSG00000144744	ENSG00000144744		"Ubiquitin-like modifier activating enzymes"	12470	protein-coding gene	gene with protein product	"NEDD8-activating enzyme E1 catalytic subunit", "NEDD8-activating enzyme E1 subunit 2"	603172	"ubiquitin-activating enzyme E1C (homologous to yeast UBA3)", "ubiquitin-activating enzyme E1C (UBA3 homolog, yeast)"	UBE1C		9694792	Standard	NM_003968		Approved	hUba3, NAE2	uc003dno.3	Q8TBC4	OTTHUMG00000154325	ENST00000361055.4:c.393delT	chr3.hg19:g.69117114delA	ENSP00000354340:p.Phe131fs	167.0	0.0		208.0	13.0	NM_003968	A6NLB5|A8K027|O76088|Q9NTU3	Frame_Shift_Del	DEL	ENST00000361055.4	hg19	CCDS2909.1																																																																																			.	.		0.269	UBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334839.1	NM_198195		-	69117114	A	-	69117114	7	5	114	1	0	1	0	1	0	0	0	0	16844	243	9	0	1050	0	UBA3	3	69117114	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	11214361	69117114	128905316	248	18520										
CNTN3	5067	hgsc.bcm.edu	37	chr3	74413707	74413707	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagaatcagtcacacttaggTttgatattgtaagggcacca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:74413707delT	ENST00000263665.6	-	9	1151	c.1124delA	c.(1123-1125)aacfs	p.N375fs		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	375	Ig-like C2-type 4.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CACACTTAGGTTTGATATTGT	0.348																																					p.N375fs		Atlas-INDEL	.											CNTN3,NS,carcinoma,0,1	CNTN3	174	.	0			c.1125delC						.						204	184	191					3																	74413707		2203	4300	6503	SO:0001589	frameshift_variant	5067	exon9			.	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1124delA	chr3.hg19:g.74413707delT	ENSP00000263665:p.Asn375fs	130.0	0.0		179.0	12.0	NM_020872	B9EK50|Q9H039	Frame_Shift_Del	DEL	ENST00000263665.6	hg19	CCDS33790.1																																																																																			.	.		0.348	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		-	74413707	T	-	74413707	7	5	114	1	0	1	0	1	0	0	0	0	3644	1725	60	0	2018	0	CNTN3	3	74413707	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	5296593	74413707	123608723	249	18521										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89259454	89259454	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtctgtgagagtatacttcAaaaagtgcccatttacagtg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:89259454delA	ENST00000336596.2	+	3	823	c.598delA	c.(598-600)aaafs	p.K201fs	EPHA3_ENST00000494014.1_Frame_Shift_Del_p.K201fs|EPHA3_ENST00000452448.2_Frame_Shift_Del_p.K201fs	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	201	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		AGTATACTTCAAAAAGTGCCC	0.448										TSP Lung(6;0.00050)																											p.F199fs		Atlas-INDEL	.											.	EPHA3	501	.	0			c.597delC						.						144	132	136					3																	89259454		2203	4300	6503	SO:0001589	frameshift_variant	2042	exon3			.	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.598delA	chr3.hg19:g.89259454delA	ENSP00000337451:p.Lys201fs	202.0	0.0		283.0	17.0	NM_005233	Q9H2V3|Q9H2V4	Frame_Shift_Del	DEL	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.		0.448	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		-	89259454	A	-	89259454	7	5	114	1	0	1	0	1	0	0	0	0	5170	131	5	0	608	0	EPHA3	3	89259454	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	14845747	89259454	108762976	250	18522										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89521694	89521694	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgactggcttaatggtgtctGgacagcacactgcaaggaaa	12	8	1	1	rs150555764		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:89521694G>C	ENST00000336596.2	+	16	2996	c.2771G>C	c.(2770-2772)tGg>tCg	p.W924S	EPHA3_ENST00000494014.1_Intron	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	924	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.		W -> R (in dbSNP:rs35124509). {ECO:0000269|PubMed:1311845, ECO:0000269|PubMed:17344846}.		cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		AATGGTGTCTGGACAGCACAC	0.423										TSP Lung(6;0.00050)																											p.W924S		Atlas-SNP	.											EPHA3,NS,carcinoma,-1,1	EPHA3	501	.	0			c.G2771C						.						148	138	141					3																	89521694		2203	4300	6503	SO:0001583	missense	2042	exon16			GTGTCTGGACAGC	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2771G>C	chr3.hg19:g.89521694G>C	ENSP00000337451:p.Trp924Ser	144.0	0.0		206.0	0.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902669	0.52227	.	.	ENSG00000044524	ENST00000336596	D	0.83992	-1.79	5.73	5.73	0.89815	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.000000	0.85682	D	0.000000	T	0.61615	0.2361	N	0.02539	-0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60352	-0.7280	9	.	.	.	.	13.1385	0.59423	0.0728:0.0:0.9271:0.0	.	924	P29320	EPHA3_HUMAN	S	924	ENSP00000337451:W924S	.	W	+	2	0	EPHA3	89604384	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.370000	0.66144	2.700000	0.92200	0.655000	0.94253	TGG	.	G|1.000;A|0.000		0.423	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		C	89521694	G	C	89521694	3	2	114	1	0	0	0	0	1	0	0	0	5170	1357	47	4	2859	4	EPHA3	3	89521694	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	262240	89521694	108500736	251	18523										
COL8A1	1295	hgsc.bcm.edu	37	chr3	99513597	99513597	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcttccctgggccccagggCcccctgggaaagccaggggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:99513597delC	ENST00000261037.3	+	5	1232	c.852delC	c.(850-852)ggcfs	p.G284fs	COL8A1_ENST00000273342.4_Frame_Shift_Del_p.G284fs	NM_001850.4	NP_001841.2	P27658	CO8A1_HUMAN	collagen, type VIII, alpha 1	284	Triple-helical region (COL1).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen type VIII trimer (GO:0005591)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(15)|skin(5)|upper_aerodigestive_tract(1)	27						GGCCCCAGGGCCCCCTGGGAA	0.657																																					p.G284fs		Atlas-INDEL	.											.	COL8A1	68	.	0			c.851delG						.						18	25	22					3																	99513597		2174	4284	6458	SO:0001589	frameshift_variant	1295	exon5			.	AF170702	CCDS2934.1	3q11.1-q13.2	2013-01-16			ENSG00000144810	ENSG00000144810		"Collagens"	2215	protein-coding gene	gene with protein product		120251	"chromosome 3 open reading frame 7"	C3orf7		2029894	Standard	NM_001850		Approved	MGC9568	uc003dth.2	P27658	OTTHUMG00000148669	ENST00000261037.3:c.852delC	chr3.hg19:g.99513597delC	ENSP00000261037:p.Gly284fs	56.0	0.0		89.0	10.0	NM_001850	D3DN42|Q53XI6|Q96D07	Frame_Shift_Del	DEL	ENST00000261037.3	hg19	CCDS2934.1																																																																																			.	.		0.657	COL8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309001.1	NM_001850		-	99513597	C	-	99513597	7	5	114	1	0	1	0	1	0	0	0	0	3707	726	26	0	858	0	COL8A1	3	99513597	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	9991903	99513597	98508833	252	18524										
TBC1D23	55773	hgsc.bcm.edu	37	chr3	100002490	100002490	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggagaaggcagcagaattacTtttggatattgaatctgtaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:100002490delT	ENST00000394144.4	+	4	318	c.311delT	c.(310-312)cttfs	p.L105fs	TBC1D23_ENST00000344949.5_Frame_Shift_Del_p.L105fs|TBC1D23_ENST00000486274.1_3'UTR|TBC1D23_ENST00000475134.1_Intron	NM_001199198.2	NP_001186127.1	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23	105	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of interleukin-6 production (GO:0032755)|regulation of inflammatory response (GO:0050727)|regulation of tumor necrosis factor production (GO:0032680)		Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(10)|ovary(1)|prostate(2)|skin(2)	25						GCAGAATTACTTTTGGATATT	0.368																																					p.L104fs		Atlas-INDEL	.											.	TBC1D23	133	.	0			c.310delC						.						104	100	101					3																	100002490		2203	4300	6503	SO:0001589	frameshift_variant	55773	exon4			.	AK001908	CCDS2936.1, CCDS56265.1	3q12.2	2013-07-10			ENSG00000036054	ENSG00000036054			25622	protein-coding gene	gene with protein product						22312129	Standard	NM_001199198		Approved	FLJ11046	uc003dtt.4	Q9NUY8	OTTHUMG00000159067	ENST00000394144.4:c.311delT	chr3.hg19:g.100002490delT	ENSP00000377700:p.Leu105fs	122.0	0.0		139.0	11.0	NM_018309	B9A6M5|Q8TCN8|Q8WUB7|Q96D90|Q9NV75	Frame_Shift_Del	DEL	ENST00000394144.4	hg19	CCDS56265.1																																																																																			.	.		0.368	TBC1D23-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353150.1	NM_018309		-	100002490	T	-	100002490	7	5	114	1	0	1	0	1	0	0	0	0	15628	1609	56	0	325	0	TBC1D23	3	100002490	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	488893	100002490	98019940	253	18525										
ABI3BP	25890	hgsc.bcm.edu	37	chr3	100585744	100585744	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgttgtgggtcgtgctgagaTtttttcaacctctggtgttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:100585744delT	ENST00000284322.5	-	10	1097	c.988delA	c.(988-990)atcfs	p.I330fs	ABI3BP_ENST00000495063.1_Frame_Shift_Del_p.I330fs|ABI3BP_ENST00000471714.1_Frame_Shift_Del_p.I330fs	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	330					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						CGTGCTGAGATTTTTTCAACC	0.368																																					p.I330fs		Atlas-INDEL	.											.	ABI3BP	305	.	0			c.989delT						.						113	104	107					3																	100585744		1832	4086	5918	SO:0001589	frameshift_variant	25890	exon10			.	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"Fibronectin type III domain containing"	17265	protein-coding gene	gene with protein product	"target of Nesh-SH3"	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.988delA	chr3.hg19:g.100585744delT	ENSP00000284322:p.Ile330fs	136.0	0.0		147.0	11.0	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Frame_Shift_Del	DEL	ENST00000284322.5	hg19	CCDS46880.1																																																																																			.	.		0.368	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			-	100585744	T	-	100585744	7	5	114	1	0	1	0	1	0	0	0	0	91	1493	52	0	2343	0	ABI3BP	3	100585744	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	583254	100585744	97436686	254	18526										
SENP7	57337	hgsc.bcm.edu	37	chr3	101090875	101090875	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggctgagtatcagatattAaaagagaaatgccatcatcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:101090875delA	ENST00000394095.2	-	7	826	c.773delT	c.(772-774)ttafs	p.L258fs	SENP7_ENST00000314261.7_Frame_Shift_Del_p.L192fs|SENP7_ENST00000348610.3_Frame_Shift_Del_p.L225fs|SENP7_ENST00000394094.2_Frame_Shift_Del_p.L193fs|SENP7_ENST00000394091.1_Frame_Shift_Del_p.L94fs|SENP7_ENST00000358203.3_Frame_Shift_Del_p.L94fs	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	258						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						ATCAGATATTAAAAGAGAAAT	0.323																																					p.L258fs		Atlas-INDEL	.											.	SENP7	170	.	0			c.774delA						.						97	93	95					3																	101090875		2203	4300	6503	SO:0001589	frameshift_variant	57337	exon7			.		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.773delT	chr3.hg19:g.101090875delA	ENSP00000377655:p.Leu258fs	109.0	0.0		166.0	10.0	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Frame_Shift_Del	DEL	ENST00000394095.2	hg19	CCDS2941.2																																																																																			.	.		0.323	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		-	101090875	A	-	101090875	7	5	114	1	0	1	0	1	0	0	0	0	14066	372	13	0	2451	0	SENP7	3	101090875	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	505131	101090875	96931555	255	18527										
MYH15	22989	hgsc.bcm.edu	37	chr3	108205276	108205276	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctaacaagccttacttctgtGgccagcaattcttcagcatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:108205276delG	ENST00000273353.3	-	11	1085	c.1029delC	c.(1027-1029)gccfs	p.A343fs		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	343	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TTACTTCTGTGGCCAGCAATT	0.448																																					p.T344fs		Atlas-INDEL	.											.	MYH15	223	.	0			c.1030delA						.						88	84	85					3																	108205276		1893	4133	6026	SO:0001589	frameshift_variant	22989	exon11			.	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1029delC	chr3.hg19:g.108205276delG	ENSP00000273353:p.Ala343fs	162.0	0.0		159.0	10.0	NM_014981		Frame_Shift_Del	DEL	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.		0.448	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		-	108205276	G	-	108205276	7	5	114	1	0	1	0	1	0	0	0	0	10043	1335	47	0	4939	0	MYH15	3	108205276	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	7114401	108205276	89817154	256	18528										
PHLDB2	90102	hgsc.bcm.edu	37	chr3	111639163	111639163	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgctcttttggatggagaacAgaaatctgaaacaactgaac	9	7	2	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:111639163A>G	ENST00000431670.2	+	5	2309	c.1898A>G	c.(1897-1899)cAg>cGg	p.Q633R	PHLDB2_ENST00000412622.1_Missense_Mutation_p.Q633R|PHLDB2_ENST00000481953.1_Missense_Mutation_p.Q633R|PHLDB2_ENST00000393923.3_Missense_Mutation_p.Q660R|PHLDB2_ENST00000495180.1_Missense_Mutation_p.Q219R|PHLDB2_ENST00000393925.3_Missense_Mutation_p.Q633R	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	633						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						GATGGAGAACAGAAATCTGAA	0.403																																					p.Q660R		Atlas-SNP	.											.	PHLDB2	449	.	0			c.A1979G						.						131	136	135					3																	111639163		2203	4300	6503	SO:0001583	missense	90102	exon6			GAGAACAGAAATC		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"Pleckstrin homology (PH) domain containing"	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.1898A>G	chr3.hg19:g.111639163A>G	ENSP00000405405:p.Gln633Arg	81.0	0.0		108.0	5.0	NM_001134437	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Missense_Mutation	SNP	ENST00000431670.2	hg19	CCDS46886.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.192457	0.38707	.	.	ENSG00000144824	ENST00000359729;ENST00000393923;ENST00000431670;ENST00000412622;ENST00000498699;ENST00000393925;ENST00000481953;ENST00000495180	T;T;T;T;T;T;T	0.31510	1.49;1.53;1.49;1.51;1.53;1.49;1.63	5.13	5.13	0.70059	.	0.141393	0.47455	D	0.000223	T	0.34919	0.0914	N	0.20328	0.56	0.44995	D	0.998014	B;B;D;D	0.89917	0.041;0.112;1.0;1.0	B;B;D;D	0.70716	0.019;0.082;0.97;0.97	T	0.08249	-1.0731	10	0.12430	T	0.62	.	12.492	0.55905	1.0:0.0:0.0:0.0	.	219;633;633;660	E9PGF6;Q86SQ0;Q86SQ0-2;Q86SQ0-3	.;PHLB2_HUMAN;.;.	R	660;660;633;633;633;633;633;219	ENSP00000377500:Q660R;ENSP00000405405:Q633R;ENSP00000405292:Q633R;ENSP00000418296:Q633R;ENSP00000377502:Q633R;ENSP00000418319:Q633R;ENSP00000420303:Q219R	ENSP00000352764:Q660R	Q	+	2	0	PHLDB2	113121853	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.831000	0.86748	1.938000	0.56188	0.455000	0.32223	CAG	.	.		0.403	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		G	111639163	A	G	111639163	3	3	114	1	0	0	0	0	1	0	0	0	11861	188	7	2	1997	2	PHLDB2	3	111639163	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3433887	111639163	86383267	257	18529										
GCET2	257144	hgsc.bcm.edu	37	chr3	111842506	111842506	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgggtctctcagctttgcaGggaacattctcatagtactc	9	11	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:111842506G>A	ENST00000308910.4	-	6	517	c.333C>T	c.(331-333)ccC>ccT	p.P111P	GCSAM_ENST00000484193.1_Silent_p.P113P|C3orf52_ENST00000467942.2_Intron	NM_001190259.1|NM_001190260.1|NM_152785.4	NP_001177188.1|NP_001177189.1|NP_689998.1	Q8N6F7	GCSAM_HUMAN	germinal center-associated, signaling and motility	111					negative regulation of lymphocyte migration (GO:2000402)|regulation of B cell receptor signaling pathway (GO:0050855)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|myosin II binding (GO:0045159)|protein kinase binding (GO:0019901)										CAGCTTTGCAGGGAACATTCT	0.507																																					p.P113P		Atlas-SNP	.											.	.	.	.	0			c.C339T						.						117	110	112					3																	111842506		2203	4300	6503	SO:0001819	synonymous_variant	257144	exon6			TTTGCAGGGAACA	BC030506	CCDS2964.1, CCDS54621.1, CCDS54622.1	3q13.13	2012-09-03	2012-08-23	2012-08-23	ENSG00000174500	ENSG00000174500			20253	protein-coding gene	gene with protein product	"human germinal center-associated lymphoma"	607792	"germinal center expressed transcript 2"	GCET2			Standard	NM_152785		Approved	MGC40441, HGAL	uc021xcl.1	Q8N6F7	OTTHUMG00000159231	ENST00000308910.4:c.333C>T	chr3.hg19:g.111842506G>A		217.0	0.0		271.0	90.0	NM_001190259	C9JD17|C9JUG6	Silent	SNP	ENST00000308910.4	hg19	CCDS2964.1																																																																																			.	.		0.507	GCSAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353967.2	NM_152785		A	111842506	G	A	111842506	2	1	114	1	0	0	0	0	0	0	0	1	6296	987	35	3		3	GCET2	3	111842506	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	203343	111842506	86179924	258	18530										
CCDC52	152185	hgsc.bcm.edu	37	chr3	113188037	113188037	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttctgctgaatgtcagtccaCaacttactaattaactcaaa	4	10	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:113188037C>A	ENST00000295872.4	-	8	919	c.660G>T	c.(658-660)ttG>ttT	p.L220F		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	220					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						TGTCAGTCCACAACTTACTAA	0.353																																					p.L220F		Atlas-SNP	.											.	SPICE1	130	.	0			c.G660T						.						104	99	101					3																	113188037		2203	4300	6503	SO:0001583	missense	152185	exon8			AGTCCACAACTTA	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.660G>T	chr3.hg19:g.113188037C>A	ENSP00000295872:p.Leu220Phe	142.0	0.0		158.0	55.0	NM_144718	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	hg19	CCDS2973.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.22|15.22	2.769395|2.769395	0.49680|0.49680	.|.	.|.	ENSG00000163611|ENSG00000163611	ENST00000467618|ENST00000295872	.|T	.|0.34472	.|1.36	4.91|4.91	0.802|0.802	0.18686|0.18686	.|.	.|0.000000	.|0.49305	.|D	.|0.000155	T|T	0.50956|0.50956	0.1646|0.1646	M|M	0.70595|0.70595	2.14|2.14	0.33229|0.33229	D|D	0.555739|0.555739	.|D;D	.|0.89917	.|0.979;1.0	.|P;D	.|0.87578	.|0.858;0.998	T|T	0.58239|0.58239	-0.7671|-0.7671	5|10	.|0.54805	.|T	.|0.06	-8.0979|-8.0979	5.8902|5.8902	0.18909|0.18909	0.0:0.6236:0.1403:0.236|0.0:0.6236:0.1403:0.236	.|.	.|116;220	.|B3KX77;Q8N0Z3	.|.;SPICE_HUMAN	F|F	32|220	.|ENSP00000295872:L220F	.|ENSP00000295872:L220F	C|L	-|-	2|3	0|2	SPICE1|SPICE1	114670727|114670727	0.993000|0.993000	0.37304|0.37304	0.996000|0.996000	0.52242|0.52242	0.796000|0.796000	0.44982|0.44982	0.097000|0.097000	0.15168|0.15168	0.161000|0.161000	0.19458|0.19458	0.591000|0.591000	0.81541|0.81541	TGT|TTG	.	.		0.353	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		A	113188037	C	A	113188037	3	1	114	1	0	0	0	0	1	0	0	0	2824	477	17	3	1951	3	CCDC52	3	113188037	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	1345531	113188037	84834393	259	18531										
ATP6V1A	523	hgsc.bcm.edu	37	chr3	113514007	113514007	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgagcaggcagggtgaaatgTcttggaaatcctgaaagaga	14	6	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:113514007T>C	ENST00000273398.3	+	10	1290	c.1182T>C	c.(1180-1182)tgT>tgC	p.C394C	ATP6V1A_ENST00000538620.1_Silent_p.C361C	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	394					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	GGGTGAAATGTCTTGGAAATC	0.408																																					p.C394C		Atlas-SNP	.											.	ATP6V1A	71	.	0			c.T1182C						.						55	57	57					3																	113514007		2203	4300	6503	SO:0001819	synonymous_variant	523	exon10			GAAATGTCTTGGA	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"ATPases / V-type"	851	protein-coding gene	gene with protein product		607027	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.1182T>C	chr3.hg19:g.113514007T>C		75.0	0.0		90.0	4.0	NM_001690	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Silent	SNP	ENST00000273398.3	hg19	CCDS2976.1																																																																																			.	.		0.408	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		C	113514007	T	C	113514007	2	2	114	1	0	0	0	0	0	0	0	1	1177	1673	58	2		2	ATP6V1A	3	113514007	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	325970	113514007	84508423	260	18532										
GRAMD1C	54762	hgsc.bcm.edu	37	chr3	113595052	113595052	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tataaccttcatgaccaaggAaaaaactgctcgactcatcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:113595052delA	ENST00000358160.4	+	5	896	c.404delA	c.(403-405)gaafs	p.E135fs	GRAMD1C_ENST00000479212.1_3'UTR|GRAMD1C_ENST00000452134.2_5'UTR	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	135	GRAM.					integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						ATGACCAAGGAAAAAACTGCT	0.294																																					p.E135fs		Atlas-INDEL	.											.	GRAMD1C	71	.	0			c.403delG						.						101	107	105					3																	113595052		2203	4300	6503	SO:0001589	frameshift_variant	54762	exon5			.		CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.404delA	chr3.hg19:g.113595052delA	ENSP00000350881:p.Glu135fs	164.0	0.0		196.0	12.0	NM_017577	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Frame_Shift_Del	DEL	ENST00000358160.4	hg19	CCDS33826.1																																																																																			.	.		0.294	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577		-	113595052	A	-	113595052	7	5	114	1	0	1	0	1	0	0	0	0	6758	246	9	0	422	0	GRAMD1C	3	113595052	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	81045	113595052	84427378	261	18533										
POLQ	10721	hgsc.bcm.edu	37	chr3	121238748	121238748	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cactcctttcctgccagcacGgccaaccatctgcttataag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:121238748delG	ENST00000264233.5	-	9	1566	c.1438delC	c.(1438-1440)cgtfs	p.R480fs	POLQ_ENST00000488282.1_5'Flank	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	480	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTGCCAGCACGGCCAACCATC	0.428								DNA polymerases (catalytic subunits)																													p.R480fs	Pancreas(152;907 1925 26081 31236 36904)	Atlas-INDEL	.											.	POLQ	273	.	0			c.1439delG						.						156	165	162					3																	121238748		2203	4300	6503	SO:0001589	frameshift_variant	10721	exon9			.	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.1438delC	chr3.hg19:g.121238748delG	ENSP00000264233:p.Arg480fs	116.0	0.0		169.0	11.0	NM_199420	O95160|Q6VMB5	Frame_Shift_Del	DEL	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.428	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		-	121238748	G	-	121238748	7	5	114	1	0	1	0	1	0	0	0	0	12217	1116	39	0	6422	0	POLQ	3	121238748	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	7643696	121238748	76783682	262	18534										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121416461	121416461	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttgtcctgctgggctcatcTcatcataattttgtttaagg	8	8	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:121416461T>C	ENST00000340645.5	-	13	3019	c.2894A>G	c.(2893-2895)gAg>gGg	p.E965G	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E970G	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	965					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TGGGCTCATCTCATCATAATT	0.383																																					p.E970G		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A2909G						.						85	89	87					3																	121416461		2203	4300	6503	SO:0001583	missense	2804	exon13			CTCATCTCATCAT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.2894A>G	chr3.hg19:g.121416461T>C	ENSP00000341848:p.Glu965Gly	58.0	0.0		57.0	4.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.709|4.709	0.131878|0.131878	0.08981|0.08981	.|.	.|.	ENSG00000173230|ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235|ENST00000489400	T;T;T|.	0.26957|.	2.3;2.3;1.7|.	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	0.507164|.	0.19854|.	N|.	0.104568|.	T|T	0.54127|0.54127	0.1839|0.1839	L|L	0.56769|0.56769	1.78|1.78	0.22745|0.22745	N|N	0.998788|0.998788	P;B;D;D;P|.	0.89917|.	0.952;0.433;0.972;1.0;0.952|.	P;B;P;D;P|.	0.80764|.	0.461;0.084;0.691;0.994;0.599|.	T|T	0.49031|0.49031	-0.8981|-0.8981	10|5	0.38643|.	T|.	0.18|.	.|.	12.9343|12.9343	0.58305|0.58305	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	890;929;970;970;965|.	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789|.	.;.;.;.;GOGB1_HUMAN|.	G|G	965;970;929;777|836	ENSP00000341848:E965G;ENSP00000377275:E970G;ENSP00000418231:E929G|.	ENSP00000341848:E965G|.	E|R	-|-	2|1	0|2	GOLGB1|GOLGB1	122899151|122899151	0.958000|0.958000	0.32768|0.32768	0.778000|0.778000	0.31720|0.31720	0.182000|0.182000	0.23217|0.23217	3.169000|3.169000	0.50809|0.50809	2.152000|2.152000	0.67230|0.67230	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.383	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121416461	T	C	121416461	3	2	114	1	0	0	0	0	1	0	0	0	6573	1551	54	2	6925	2	GOLGB1	3	121416461	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	177713	121416461	76605969	263	18535										
ILDR1	286676	hgsc.bcm.edu	37	chr3	121712685	121712685	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caaatctgcctttgaggtcaGggggcagaggctgggccagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:121712685delG	ENST00000344209.5	-	7	1037	c.911delC	c.(910-912)cctfs	p.P304fs	ILDR1_ENST00000393631.1_Frame_Shift_Del_p.P215fs|ILDR1_ENST00000273691.3_Frame_Shift_Del_p.P260fs|ILDR1_ENST00000462014.1_Frame_Shift_Del_p.P272fs|ILDR1_ENST00000460554.1_5'UTR	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	304					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		TTTGAGGTCAGGGGGCAGAGG	0.582																																					p.P304fs		Atlas-INDEL	.											ILDR1_ENST00000344209,NS,carcinoma,0,2	ILDR1	120	.	0			c.912delT						.						80	76	77					3																	121712685		2203	4300	6503	SO:0001589	frameshift_variant	286676	exon7			.	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"deafness, autosomal recessive 42"	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.911delC	chr3.hg19:g.121712685delG	ENSP00000345667:p.Pro304fs	128.0	0.0		155.0	11.0	NM_001199799	Q6ZP61|Q7Z578	Frame_Shift_Del	DEL	ENST00000344209.5	hg19	CCDS56271.1																																																																																			.	.		0.582	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924		-	121712685	G	-	121712685	7	5	114	1	0	1	0	1	0	0	0	0	7718	1000	35	0	737	0	ILDR1	3	121712685	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	296224	121712685	76309745	264	18536										
DTX3L	151636	hgsc.bcm.edu	37	chr3	122284754	122284754	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcaccaaatacttgttgacgAaaaacctgtgcccattttcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:122284754delA	ENST00000296161.4	+	2	425	c.236delA	c.(235-237)gaafs	p.E79fs	PARP9_ENST00000360356.2_5'Flank|PARP9_ENST00000492382.1_5'Flank|DTX3L_ENST00000383661.3_Frame_Shift_Del_p.E79fs|PARP9_ENST00000462315.1_5'Flank|PARP9_ENST00000477522.2_5'Flank|PARP9_ENST00000471785.1_5'Flank	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	79					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		CTTGTTGACGAAAAACCTGTG	0.398																																					p.E79fs		Atlas-INDEL	.											DTX3L,colon,carcinoma,0,2	DTX3L	59	.	0			c.235delG						.						116	109	111					3																	122284754		2203	4300	6503	SO:0001589	frameshift_variant	151636	exon2			.		CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"RING-type (C3HC4) zinc fingers"	30323	protein-coding gene	gene with protein product	"rhysin 2"	613143	"deltex 3-like (Drosophila)"			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.236delA	chr3.hg19:g.122284754delA	ENSP00000296161:p.Glu79fs	135.0	0.0		149.0	13.0	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Frame_Shift_Del	DEL	ENST00000296161.4	hg19	CCDS3015.1																																																																																			.	.		0.398	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287		-	122284754	A	-	122284754	7	5	114	1	0	1	0	1	0	0	0	0	4798	246	9	0	242	0	DTX3L	3	122284754	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	572069	122284754	75737676	265	18537										
PARP14	54625	hgsc.bcm.edu	37	chr3	122399784	122399784	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagggctcctggggccccgaCcccccgaagaacttgaacac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:122399784delC	ENST00000474629.2	+	1	320	c.54delC	c.(52-54)gacfs	p.D18fs		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	18					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		GGGGCCCCGACCCCCCGAAGA	0.682																																					p.D18fs		Atlas-INDEL	.											.	PARP14	242	.	0			c.53delA						.						17	21	20					3																	122399784		1861	4092	5953	SO:0001589	frameshift_variant	54625	exon1			.	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.54delC	chr3.hg19:g.122399784delC	ENSP00000418194:p.Asp18fs	137.0	0.0		141.0	10.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Frame_Shift_Del	DEL	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.		0.682	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		-	122399784	C	-	122399784	7	5	114	1	0	1	0	1	0	0	0	0	11467	506	18	0	56	0	PARP14	3	122399784	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	115030	122399784	75622646	266	18538										
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122680077	122680077	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cggcccagggacgaggtggtGggcaacaggagacggactga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:122680077delG	ENST00000357599.3	-	2	420	c.34delC	c.(34-36)cacfs	p.H13fs	SEMA5B_ENST00000451055.2_Frame_Shift_Del_p.H67fs|SEMA5B_ENST00000195173.4_Frame_Shift_Del_p.H13fs|SEMA5B_ENST00000465147.1_Intron	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	13					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		ACGAGGTGGTGGGCAACAGGA	0.592																																					p.H66fs		Atlas-INDEL	.											.	SEMA5B	303	.	0			c.197delA						.						82	74	77					3																	122680077		2203	4300	6503	SO:0001589	frameshift_variant	54437	exon2			.	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.34delC	chr3.hg19:g.122680077delG	ENSP00000350215:p.His13fs	151.0	0.0		204.0	14.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Frame_Shift_Del	DEL	ENST00000357599.3	hg19	CCDS35491.1																																																																																			.	.		0.592	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		-	122680077	G	-	122680077	7	5	114	1	0	1	0	1	0	0	0	0	14053	1348	47	0	3509	0	SEMA5B	3	122680077	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	280293	122680077	75342353	267	18539										
ITGB5	3693	hgsc.bcm.edu	37	chr3	124578237	124578237	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcacctccacagccatttttGacaaggtttgccctcagatc	6	14	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:124578237G>A	ENST00000296181.4	-	3	509	c.213C>T	c.(211-213)gtC>gtT	p.V71V		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	71	PSI.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		AGCCATTTTTGACAAGGTTTG	0.592																																					p.V71V		Atlas-SNP	.											.	ITGB5	66	.	0			c.C213T						.						81	75	77					3																	124578237		2203	4300	6503	SO:0001819	synonymous_variant	3693	exon3			ATTTTTGACAAGG	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.213C>T	chr3.hg19:g.124578237G>A		165.0	0.0		226.0	87.0	NM_002213	B0LPF8|B2RD70	Silent	SNP	ENST00000296181.4	hg19	CCDS3030.1																																																																																			.	.		0.592	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		A	124578237	G	A	124578237	2	1	114	1	0	0	0	0	0	0	0	1	7907	1277	45	3		3	ITGB5	3	124578237	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1898160	124578237	73444193	268	18540										
ZNF148	7707	hgsc.bcm.edu	37	chr3	124952718	124952718	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgatggcacatctatttagTtttttgtcatgattttcatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:124952718delT	ENST00000360647.4	-	9	1337	c.852delA	c.(850-852)aaafs	p.K284fs	ZNF148_ENST00000485866.1_Frame_Shift_Del_p.K284fs|ZNF148_ENST00000497929.1_5'UTR|ZNF148_ENST00000492394.1_Frame_Shift_Del_p.K284fs|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000468369.1_Intron|ZNF148_ENST00000484491.1_Frame_Shift_Del_p.K284fs|SLC12A8_ENST00000423114.2_Intron	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	284					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						ATCTATTTAGTTTTTTGTCAT	0.383																																					p.L285X		Atlas-INDEL	.											.	ZNF148	84	.	0			c.853delC						.						86	86	86					3																	124952718		2203	4300	6503	SO:0001589	frameshift_variant	7707	exon9			.	U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"Zinc fingers, C2H2-type"	12933	protein-coding gene	gene with protein product		601897	"zinc finger protein 148 (pHZ-52)"			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.852delA	chr3.hg19:g.124952718delT	ENSP00000353863:p.Lys284fs	100.0	0.0		130.0	10.0	NM_021964	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Frame_Shift_Del	DEL	ENST00000360647.4	hg19	CCDS3031.1																																																																																			.	.		0.383	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964		-	124952718	T	-	124952718	7	5	114	1	0	1	0	1	0	0	0	0	17749	1722	60	0	1536	0	ZNF148	3	124952718	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	374481	124952718	73069712	269	18541										
ZNF148	7707	hgsc.bcm.edu	37	chr3	125007010	125007010	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctactggctctctgatttgTtttttgtctctcatcagttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:125007010delT	ENST00000360647.4	-	5	881	c.396delA	c.(394-396)aaafs	p.K132fs	ZNF148_ENST00000485866.1_Frame_Shift_Del_p.K132fs|ZNF148_ENST00000497929.1_5'UTR|ZNF148_ENST00000492394.1_Frame_Shift_Del_p.K132fs|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000468369.1_Intron|ZNF148_ENST00000484491.1_Frame_Shift_Del_p.K132fs	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	132					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						CTCTGATTTGTTTTTTGTCTC	0.343																																					p.Q133fs		Atlas-INDEL	.											ZNF148,NS,carcinoma,+1,1	ZNF148	84	.	0			c.397delC						.						202	174	183					3																	125007010		2203	4300	6503	SO:0001589	frameshift_variant	7707	exon5			.	U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"Zinc fingers, C2H2-type"	12933	protein-coding gene	gene with protein product		601897	"zinc finger protein 148 (pHZ-52)"			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.396delA	chr3.hg19:g.125007010delT	ENSP00000353863:p.Lys132fs	105.0	0.0		126.0	10.0	NM_021964	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Frame_Shift_Del	DEL	ENST00000360647.4	hg19	CCDS3031.1																																																																																			.	.		0.343	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964		-	125007010	T	-	125007010	7	5	114	1	0	1	0	1	0	0	0	0	17749	1722	60	0	2008	0	ZNF148	3	125007010	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	54292	125007010	73015420	270	18542										
RHO	6010	hgsc.bcm.edu	37	chr3	129251109	129251109	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctcaggtacatccccgagggCctgcagtgctcgtgtggaat	13	12	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:129251109C>T	ENST00000296271.3	+	3	640	c.546C>T	c.(544-546)ggC>ggT	p.G182G		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	182			G -> S (in RP4). {ECO:0000269|PubMed:1897520}.		G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)			breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	TCCCCGAGGGCCTGCAGTGCT	0.592																																					p.G182G	Esophageal Squamous(118;214 1623 30842 43234 46940)	Atlas-SNP	.											.	RHO	57	.	0			c.C546T						.						199	159	173					3																	129251109		2203	4300	6503	SO:0001819	synonymous_variant	6010	exon3			CGAGGGCCTGCAG	AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"GPCR / Class A : Opsin receptors"	10012	protein-coding gene	gene with protein product	"opsin 2, rod pigment"	180380	"retinitis pigmentosa 4, autosomal dominant"	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.546C>T	chr3.hg19:g.129251109C>T		172.0	0.0		203.0	92.0	NM_000539	Q16414|Q2M249	Silent	SNP	ENST00000296271.3	hg19	CCDS3063.1																																																																																			.	.		0.592	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539		T	129251109	C	T	129251109	2	4	114	1	0	0	0	0	0	0	0	1	13345	726	26	3		3	RHO	3	129251109	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	4244099	129251109	68771321	271	18543										
ASTE1	28990	hgsc.bcm.edu	37	chr3	130743653	130743653	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caaaacccagttttcaggtcAaaaatgcaaaagtcactatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:130743653delA	ENST00000264992.3	-	3	939	c.498delT	c.(496-498)tttfs	p.F166fs	NEK11_ENST00000507910.1_5'Flank|NEK11_ENST00000356918.4_5'Flank|ASTE1_ENST00000514044.1_Frame_Shift_Del_p.F166fs|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000429253.2_5'Flank|NEK11_ENST00000383366.4_5'Flank|NEK11_ENST00000412440.2_5'Flank|NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000511262.1_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	166					DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						TTTTCAGGTCAAAAATGCAAA	0.403																																					p.D167fs		Atlas-INDEL	.											.	ASTE1	67	.	0			c.499delG						.						64	63	63					3																	130743653		2203	4300	6503	SO:0001589	frameshift_variant	28990	exon3			.	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.498delT	chr3.hg19:g.130743653delA	ENSP00000264992:p.Phe166fs	121.0	0.0		172.0	11.0	NM_014065	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Frame_Shift_Del	DEL	ENST00000264992.3	hg19	CCDS3068.1																																																																																			.	.		0.403	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		-	130743653	A	-	130743653	7	5	114	1	0	1	0	1	0	0	0	0	1062	127	5	0	1557	0	ASTE1	3	130743653	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1492544	130743653	67278777	272	18544										
TMEM108	66000	hgsc.bcm.edu	37	chr3	133098904	133098904	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaagctccctgtccacagggCccgctccagcagccatggca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:133098904delC	ENST00000321871.6	+	4	559	c.349delC	c.(349-351)cccfs	p.P117fs	TMEM108_ENST00000508711.1_Intron|TMEM108_ENST00000515826.1_Frame_Shift_Del_p.P117fs|TMEM108_ENST00000393130.3_Frame_Shift_Del_p.P117fs	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	117	Pro-rich.					integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						GTCCACAGGGCCCGCTCCAGC	0.672																																					p.G116fs		Atlas-INDEL	.											.	TMEM108	67	.	0			c.348delG						.						47	41	43					3																	133098904		2201	4298	6499	SO:0001589	frameshift_variant	66000	exon4			.	AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"cancer/testis antigen 124"					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.349delC	chr3.hg19:g.133098904delC	ENSP00000324651:p.Pro117fs	153.0	0.0		181.0	11.0	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Frame_Shift_Del	DEL	ENST00000321871.6	hg19	CCDS33858.1																																																																																			.	.		0.672	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		-	133098904	C	-	133098904	7	5	114	1	0	1	0	1	0	0	0	0	16039	739	26	0	355	0	TMEM108	3	133098904	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2355251	133098904	64923526	273	18545										
TMEM108	66000	hgsc.bcm.edu	37	chr3	133099911	133099911	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aacatctcccatgtggccgaGggggacaaaccgcagcacag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:133099911delG	ENST00000321871.6	+	4	1566	c.1356delG	c.(1354-1356)gagfs	p.E452fs	TMEM108_ENST00000508711.1_Intron|TMEM108_ENST00000515826.1_Frame_Shift_Del_p.E452fs|TMEM108_ENST00000393130.3_Frame_Shift_Del_p.E452fs	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	452						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						ATGTGGCCGAGGGGGACAAAC	0.612																																					p.E452fs		Atlas-INDEL	.											.	TMEM108	67	.	0			c.1355delA						.						115	97	103					3																	133099911		2203	4300	6503	SO:0001589	frameshift_variant	66000	exon4			.	AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"cancer/testis antigen 124"					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.1356delG	chr3.hg19:g.133099911delG	ENSP00000324651:p.Glu452fs	210.0	0.0		226.0	14.0	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Frame_Shift_Del	DEL	ENST00000321871.6	hg19	CCDS33858.1																																																																																			.	.		0.612	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		-	133099911	G	-	133099911	7	5	114	1	0	1	0	1	0	0	0	0	16039	991	35	0	1362	0	TMEM108	3	133099911	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1007	133099911	64922519	274	18546										
BFSP2	8419	hgsc.bcm.edu	37	chr3	133119111	133119111	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggtctatgtaggaacagcaCccagtgggtgcataggtggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:133119111delC	ENST00000302334.2	+	1	273	c.184delC	c.(184-186)cccfs	p.P62fs		NM_003571.2	NP_003562.1	Q13515	BFSP2_HUMAN	beaded filament structural protein 2, phakinin	62	Head.				cell maturation (GO:0048469)|intermediate filament cytoskeleton organization (GO:0045104)|lens fiber cell development (GO:0070307)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|urinary_tract(1)	13						AGGAACAGCACCCAGTGGGTG	0.667																																					p.A61fs		Atlas-INDEL	.											.	BFSP2	48	.	0			c.183delA						.						46	51	49					3																	133119111		2203	4300	6503	SO:0001589	frameshift_variant	8419	exon1			.	U48224	CCDS33859.1	3q22.1	2013-01-16			ENSG00000170819	ENSG00000170819		"Intermediate filaments type VI, eye lens intermediate filaments"	1041	protein-coding gene	gene with protein product		603212					Standard	NM_003571		Approved	CP47, CP49, LIFL-L, phakinin	uc003epn.1	Q13515	OTTHUMG00000159719	ENST00000302334.2:c.184delC	chr3.hg19:g.133119111delC	ENSP00000304987:p.Pro62fs	188.0	0.0		153.0	11.0	NM_003571	Q14D32|Q9HBW5	Frame_Shift_Del	DEL	ENST00000302334.2	hg19	CCDS33859.1																																																																																			.	.		0.667	BFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357031.1			-	133119111	C	-	133119111	7	5	114	1	0	1	0	1	0	0	0	0	1416	507	18	0	186	0	BFSP2	3	133119111	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	19200	133119111	64903319	275	18547										
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135721003	135721003	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttggaaaaacataaaatagaTaatttttcttctgggacaga	7	4	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:135721003T>C	ENST00000264977.3	+	2	1280	c.663T>C	c.(661-663)gaT>gaC	p.D221D	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	221					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATAAAATAGATAATTTTTCTT	0.333																																					p.D221D		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T663C						.						43	48	46					3																	135721003		2184	4288	6472	SO:0001819	synonymous_variant	5523	exon2			AATAGATAATTTT	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.663T>C	chr3.hg19:g.135721003T>C		34.0	0.0		34.0	14.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	hg19	CCDS3087.1																																																																																			.	.		0.333	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		C	135721003	T	C	135721003	2	2	114	1	0	0	0	0	0	0	0	1	12400	1403	49	2		2	PPP2R3A	3	135721003	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2601892	135721003	62301427	276	18548										
DZIP1L	199221	hgsc.bcm.edu	37	chr3	137790628	137790628	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctgctcccgctggactctcAgcagggattccaggtgtctg	12	13	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:137790628A>G	ENST00000327532.2	-	12	1834	c.1472T>C	c.(1471-1473)cTg>cCg	p.L491P	DZIP1L_ENST00000488595.1_Intron|DZIP1L_ENST00000469243.1_Missense_Mutation_p.L491P	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	491					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						CTGGACTCTCAGCAGGGATTC	0.522																																					p.L491P		Atlas-SNP	.											.	DZIP1L	88	.	0			c.T1472C						.						48	51	50					3																	137790628		2203	4300	6503	SO:0001583	missense	199221	exon13			ACTCTCAGCAGGG	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"DAZ interacting protein 1-like"			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1472T>C	chr3.hg19:g.137790628A>G	ENSP00000332148:p.Leu491Pro	83.0	0.0		89.0	4.0	NM_001170538	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	hg19	CCDS3096.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.134802	0.37728	.	.	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.40756	1.14;1.02	4.86	4.86	0.63082	.	0.126271	0.34268	N	0.004102	T	0.61726	0.2370	M	0.71581	2.175	0.44816	D	0.997826	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.972	T	0.65664	-0.6113	10	0.72032	D	0.01	-14.5635	11.9778	0.53103	1.0:0.0:0.0:0.0	.	491;491	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	P	491	ENSP00000332148:L491P;ENSP00000419486:L491P	ENSP00000332148:L491P	L	-	2	0	DZIP1L	139273318	0.262000	0.24073	0.242000	0.24170	0.122000	0.20287	5.856000	0.69518	1.815000	0.52974	0.533000	0.62120	CTG	.	.		0.522	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		G	137790628	A	G	137790628	3	3	114	1	0	0	0	0	1	0	0	0	4866	188	7	2	860	2	DZIP1L	3	137790628	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2069625	137790628	60231802	277	18549										
ARMC8	25852	hgsc.bcm.edu	37	chr3	137982594	137982594	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctccagatcattgagactgAaaatatgatggaccgaattg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:137982594delA	ENST00000469044.1	+	13	1419	c.1148delA	c.(1147-1149)gaafs	p.E383fs	NME9_ENST00000536478.1_Intron|ARMC8_ENST00000491704.1_Frame_Shift_Del_p.E341fs|NME9_ENST00000341790.5_Intron|NME9_ENST00000317876.4_Intron|NME9_ENST00000484930.1_Intron|ARMC8_ENST00000485396.1_Frame_Shift_Del_p.E310fs|ARMC8_ENST00000461822.1_Frame_Shift_Del_p.E316fs|ARMC8_ENST00000393058.3_Frame_Shift_Del_p.E373fs|ARMC8_ENST00000538260.1_Frame_Shift_Del_p.E352fs|ARMC8_ENST00000481646.1_Frame_Shift_Del_p.E369fs|NME9_ENST00000383180.2_Intron	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	383										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						ATTGAGACTGAAAATATGATG	0.393																																					p.E369fs		Atlas-INDEL	.											.	ARMC8	79	.	0			c.1105delG						.						187	183	184					3																	137982594		1917	4132	6049	SO:0001589	frameshift_variant	25852	exon14			.		CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"Armadillo repeat containing"	24999	protein-coding gene	gene with protein product	"GID complex subunit 5, VID28 homolog (S. cerevisiae)"					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.1148delA	chr3.hg19:g.137982594delA	ENSP00000419413:p.Glu383fs	155.0	0.0		211.0	13.0	NM_015396	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Frame_Shift_Del	DEL	ENST00000469044.1	hg19																																																																																				.	.		0.393	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396		-	137982594	A	-	137982594	7	5	114	1	0	1	0	1	0	0	0	0	957	246	9	0	1222	0	ARMC8	3	137982594	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	191966	137982594	60039836	278	18550										
CEP70	80321	hgsc.bcm.edu	37	chr3	138227297	138227297	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atacctgaaagtatctctggTcaattagggcctgttgctga	10	8	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:138227297T>C	ENST00000264982.3	-	12	1300	c.1034A>G	c.(1033-1035)gAc>gGc	p.D345G	CEP70_ENST00000481834.1_Missense_Mutation_p.D345G|CEP70_ENST00000542237.1_Missense_Mutation_p.D325G|CEP70_ENST00000484888.1_Missense_Mutation_p.D345G|CEP70_ENST00000489254.1_Missense_Mutation_p.D193G	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	345					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						GTATCTCTGGTCAATTAGGGC	0.363																																					p.D345G		Atlas-SNP	.											.	CEP70	51	.	0			c.A1034G						.						210	221	217					3																	138227297		2203	4300	6503	SO:0001583	missense	80321	exon12			CTCTGGTCAATTA	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.1034A>G	chr3.hg19:g.138227297T>C	ENSP00000264982:p.Asp345Gly	191.0	0.0		256.0	11.0	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	hg19	CCDS3102.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.494594	0.26774	.	.	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000489254;ENST00000484888;ENST00000474781;ENST00000481834	T;T;T;T;T;T	0.45668	1.46;1.47;0.89;1.46;1.47;1.45	5.24	2.83	0.33086	.	0.530335	0.20801	N	0.085429	T	0.41073	0.1143	L	0.56769	1.78	0.22918	N	0.998561	B;P;P;P	0.49961	0.004;0.93;0.763;0.93	B;P;B;P	0.49829	0.006;0.623;0.382;0.623	T	0.18808	-1.0325	10	0.22109	T	0.4	-4.7183	5.1626	0.15070	0.0:0.0922:0.1824:0.7254	.	193;325;345;345	B7Z2D2;F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;.;CEP70_HUMAN	G	345;325;193;345;327;345	ENSP00000264982:D345G;ENSP00000444128:D325G;ENSP00000417821:D193G;ENSP00000419231:D345G;ENSP00000419833:D327G;ENSP00000417465:D345G	ENSP00000264982:D345G	D	-	2	0	CEP70	139709987	1.000000	0.71417	0.910000	0.35882	0.940000	0.58332	2.058000	0.41374	0.436000	0.26393	0.533000	0.62120	GAC	.	.		0.363	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491		C	138227297	T	C	138227297	3	2	114	1	0	0	0	0	1	0	0	0	3261	1667	58	2	787	2	CEP70	3	138227297	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	244703	138227297	59795133	279	18551										
PLOD2	5352	hgsc.bcm.edu	37	chr3	145806385	145806385	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atacttactttgttatgaatAaaaagtttaagtgcttcttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:145806385delA	ENST00000360060.3	-	9	1170	c.993delT	c.(991-993)tttfs	p.F331fs	RP11-274H2.2_ENST00000480247.1_RNA|PLOD2_ENST00000282903.5_Frame_Shift_Del_p.F331fs|PLOD2_ENST00000494950.1_Frame_Shift_Del_p.F276fs|PLOD2_ENST00000461497.1_5'Flank	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	331					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	TGTTATGAATAAAAAGTTTAA	0.284																																					p.I332fs		Atlas-INDEL	.											.	PLOD2	81	.	0			c.994delA						.						57	56	56					3																	145806385		2201	4296	6497	SO:0001589	frameshift_variant	5352	exon9			.	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"lysyl hydroxlase 2"	601865	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.993delT	chr3.hg19:g.145806385delA	ENSP00000353170:p.Phe331fs	110.0	0.0		162.0	12.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Frame_Shift_Del	DEL	ENST00000360060.3	hg19	CCDS3131.1																																																																																			.	.		0.284	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		-	145806385	A	-	145806385	7	5	114	1	0	1	0	1	0	0	0	0	12111	359	13	0	1331	0	PLOD2	3	145806385	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	7579088	145806385	52216045	280	18552										
PLSCR5	389158	hgsc.bcm.edu	37	chr3	146311885	146311885	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaattctttgtcccaagctgTttttaatctcatatttgttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:146311885delT	ENST00000443512.1	-	4	1278	c.275delA	c.(274-276)aacfs	p.N92fs	PLSCR5_ENST00000482567.1_Frame_Shift_Del_p.N80fs|PLSCR5_ENST00000492200.1_Frame_Shift_Del_p.N92fs	NM_001085420.1	NP_001078889.1	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	92										endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						TCCCAAGCTGTTTTTAATCTC	0.348																																					p.N92fs		Atlas-INDEL	.											.	PLSCR5	35	.	0			c.276delC						.						116	113	114					3																	146311885		1832	4087	5919	SO:0001589	frameshift_variant	389158	exon4			.	AY436642	CCDS46931.1	3q24	2004-06-28			ENSG00000231213	ENSG00000231213			19952	protein-coding gene	gene with protein product							Standard	NM_001085420		Approved		uc010hvc.3	A0PG75	OTTHUMG00000159437	ENST00000443512.1:c.275delA	chr3.hg19:g.146311885delT	ENSP00000390111:p.Asn92fs	111.0	0.0		138.0	10.0	NM_001085420	B2RXK5	Frame_Shift_Del	DEL	ENST00000443512.1	hg19	CCDS46931.1																																																																																			.	.		0.348	PLSCR5-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355365.1	XM_371670		-	146311885	T	-	146311885	7	5	114	1	0	1	0	1	0	0	0	0	12122	1725	60	0	556	0	PLSCR5	3	146311885	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	505500	146311885	51710545	281	18553										
AGTR1	185	hgsc.bcm.edu	37	chr3	148459417	148459417	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgatagggctgggcctgaccAaaaatatactgggtttcctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:148459417delA	ENST00000497524.1	+	2	986	c.595delA	c.(595-597)aaafs	p.K199fs	AGTR1_ENST00000418473.2_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000475347.1_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000542281.1_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000474935.1_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000404754.2_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000402260.1_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000349243.3_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000461609.1_Frame_Shift_Del_p.K199fs	NM_009585.3	NP_033611.1	P30556	AGTR1_HUMAN	angiotensin II receptor, type 1	199					angiotensin-activated signaling pathway (GO:0038166)|calcium-mediated signaling (GO:0019722)|cell chemotaxis (GO:0060326)|G-protein coupled receptor signaling pathway (GO:0007186)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|phospholipase C-activating angiotensin-activated signaling pathway (GO:0086097)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of phospholipase A2 activity (GO:0032430)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|renin-angiotensin regulation of aldosterone production (GO:0002018)|Rho protein signal transduction (GO:0007266)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin type I receptor activity (GO:0001596)|angiotensin type II receptor activity (GO:0004945)|bradykinin receptor binding (GO:0031711)|protein heterodimerization activity (GO:0046982)			breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30			LUSC - Lung squamous cell carcinoma(72;0.127)|Lung(72;0.152)		Azilsartan medoxomil(DB08822)|Candesartan(DB00796)|Eprosartan(DB00876)|Forasartan(DB01342)|Irbesartan(DB01029)|Losartan(DB00678)|Olmesartan(DB00275)|Saprisartan(DB01347)|Tasosartan(DB01349)|Telmisartan(DB00966)|Valsartan(DB00177)	GGGCCTGACCAAAAATATACT	0.378																																					p.T233fs		Atlas-INDEL	.											.	AGTR1	63	.	0			c.699delC						.						65	71	69					3																	148459417		2199	4299	6498	SO:0001589	frameshift_variant	185	exon4			.	M87290	CCDS3137.1	3q24	2012-08-08	2002-02-20		ENSG00000144891	ENSG00000144891		"GPCR / Class A : Angiotensin receptors"	336	protein-coding gene	gene with protein product		106165	"angiotensin receptor 1B"	AGTR1B		1550596	Standard	NM_009585		Approved	AT1, AT2R1, AGTR1A, AT2R1A, HAT1R, AG2S, AT2R1B, AT1B	uc003ewh.4	P30556	OTTHUMG00000159503	ENST00000497524.1:c.595delA	chr3.hg19:g.148459417delA	ENSP00000419422:p.Lys199fs	136.0	0.0		164.0	11.0	NM_031850	Q13725|Q8TBK4	Frame_Shift_Del	DEL	ENST00000497524.1	hg19	CCDS3137.1																																																																																			.	.		0.378	AGTR1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355807.1			-	148459417	A	-	148459417	7	5	114	1	0	1	0	1	0	0	0	0	401	131	5	0	597	0	AGTR1	3	148459417	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2147532	148459417	49563013	282	18554										
CPA3	1359	hgsc.bcm.edu	37	chr3	148599385	148599385	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttttacattcttcctgtgtTcaatgttgatggatatattt	6	5	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:148599385T>C	ENST00000296046.3	+	7	705	c.653T>C	c.(652-654)tTc>tCc	p.F218S	RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)	218					angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			CTTCCTGTGTTCAATGTTGAT	0.343																																					p.F218S		Atlas-SNP	.											.	CPA3	75	.	0			c.T653C						.						129	121	124					3																	148599385		2203	4300	6503	SO:0001583	missense	1359	exon7			CTGTGTTCAATGT		CCDS3138.1	3q24	2012-02-10			ENSG00000163751	ENSG00000163751	3.4.17.1		2298	protein-coding gene	gene with protein product	"mast cell carboxypeptidase A", "tissue carboxypeptidase A"	114851					Standard	NM_001870		Approved		uc003ewm.3	P15088	OTTHUMG00000159526	ENST00000296046.3:c.653T>C	chr3.hg19:g.148599385T>C	ENSP00000296046:p.Phe218Ser	72.0	0.0		96.0	4.0	NM_001870	Q96E94	Missense_Mutation	SNP	ENST00000296046.3	hg19	CCDS3138.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.601936	0.87055	.	.	ENSG00000163751	ENST00000296046	T	0.11277	2.79	5.06	5.06	0.68205	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.25121	0.0610	L	0.60957	1.885	0.54753	D	0.999987	P	0.50272	0.933	P	0.58077	0.832	T	0.00477	-1.1716	10	0.66056	D	0.02	.	13.9293	0.63983	0.0:0.0:0.0:1.0	.	218	P15088	CBPA3_HUMAN	S	218	ENSP00000296046:F218S	ENSP00000296046:F218S	F	+	2	0	CPA3	150082075	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.856000	0.62932	2.111000	0.64477	0.533000	0.62120	TTC	.	.		0.343	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	NM_001870		C	148599385	T	C	148599385	3	2	114	1	0	0	0	0	1	0	0	0	3793	1783	62	2	679	2	CPA3	3	148599385	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	139968	148599385	49423045	283	18555										
FAM194A	131831	hgsc.bcm.edu	37	chr3	150421477	150421477	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actcttcgctgaacgtctcaGgggcctccaactcctgctct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:150421477delG	ENST00000295910.6	-	1	261	c.209delC	c.(208-210)cctfs	p.P70fs	RP11-103G8.2_ENST00000471093.1_RNA|RP11-103G8.2_ENST00000475393.1_RNA|FAM194A_ENST00000491361.1_Intron	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						GAACGTCTCAGGGGCCTCCAA	0.622																																					p.P70fs		Atlas-INDEL	.											.	FAM194A	91	.	0			c.210delT						.						235	183	201					3																	150421477		2203	4300	6503	SO:0001589	frameshift_variant	131831	exon1			.																												ENST00000295910.6:c.209delC	chr3.hg19:g.150421477delG	ENSP00000295910:p.Pro70fs	175.0	0.0		183.0	11.0	NM_152394		Frame_Shift_Del	DEL	ENST00000295910.6	hg19	CCDS3151.2																																																																																			.	.		0.622	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			-	150421477	G	-	150421477	7	5	114	1	0	1	0	1	0	0	0	0	5531	1000	35	0	1838	0	FAM194A	3	150421477	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1822092	150421477	47600953	284	18556										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151176327	151176327	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaattgatgcgttccacattGggcgggatgctgtctgggat	14	7	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:151176327G>T	ENST00000282466.3	-	1	170	c.171C>A	c.(169-171)ccC>ccA	p.P57P		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	57					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GTTCCACATTGGGCGGGATGC	0.532																																					p.P57P		Atlas-SNP	.											.	IGSF10	279	.	0			c.C171A						.						120	98	106					3																	151176327		2203	4300	6503	SO:0001819	synonymous_variant	285313	exon1			CACATTGGGCGGG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.171C>A	chr3.hg19:g.151176327G>T		192.0	0.0		244.0	17.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	hg19	CCDS3160.1																																																																																			.	.		0.532	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		T	151176327	G	T	151176327	2	4	114	1	0	0	0	0	0	0	0	1	7606	1335	47	3		3	IGSF10	3	151176327	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	754850	151176327	46846103	285	18557										
SGEF	26084	hgsc.bcm.edu	37	chr3	153847453	153847453	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caaagaacagaagtcagatgAaaaaattgtgattcaccata							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:153847453delA	ENST00000356448.4	+	4	1498	c.1214delA	c.(1213-1215)gaafs	p.E405fs	ARHGEF26_ENST00000465093.1_Frame_Shift_Del_p.E405fs|ARHGEF26_ENST00000465817.1_Frame_Shift_Del_p.E405fs	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	405					endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						AAGTCAGATGAAAAAATTGTG	0.398																																					p.E405fs	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-INDEL	.											.	ARHGEF26	158	.	0			c.1213delG						.						100	93	95					3																	153847453		1855	4128	5983	SO:0001589	frameshift_variant	26084	exon4			.	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.1214delA	chr3.hg19:g.153847453delA	ENSP00000348828:p.Glu405fs	182.0	0.0		232.0	17.0	NM_015595	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Frame_Shift_Del	DEL	ENST00000356448.4	hg19	CCDS46938.1																																																																																			.	.		0.398	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		-	153847453	A	-	153847453	7	5	114	1	0	1	0	1	0	0	0	0	14220	246	9	0	1224	0	SGEF	3	153847453	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2671126	153847453	44174977	286	18558										
DHX36	170506	hgsc.bcm.edu	37	chr3	154010423	154010423	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgatattgttctgagtatcAaaatgcgtctcttttatttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:154010423delA	ENST00000496811.1	-	15	1811	c.1731delT	c.(1729-1731)tttfs	p.F577fs	DHX36_ENST00000308361.6_Frame_Shift_Del_p.F577fs|DHX36_ENST00000329463.5_Frame_Shift_Del_p.F563fs|DHX36_ENST00000544526.1_Frame_Shift_Del_p.F563fs	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	577	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TCTGAGTATCAAAATGCGTCT	0.378																																					p.D578fs		Atlas-INDEL	.											.	DHX36	98	.	0			c.1732delG						.						229	217	221					3																	154010423		2203	4300	6503	SO:0001589	frameshift_variant	170506	exon15			.	AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.1731delT	chr3.hg19:g.154010423delA	ENSP00000417078:p.Phe577fs	196.0	0.0		203.0	13.0	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Frame_Shift_Del	DEL	ENST00000496811.1	hg19	CCDS3171.1																																																																																			.	.		0.378	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		-	154010423	A	-	154010423	7	5	114	1	0	1	0	1	0	0	0	0	4511	127	5	0	1339	0	DHX36	3	154010423	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	162970	154010423	44012007	287	18559										
MME	4311	hgsc.bcm.edu	37	chr3	154802867	154802867	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatggtatttgcaagtcatcAgactgcataaaatcaggtaa	9	6	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:154802867A>G	ENST00000460393.1	+	3	300	c.180A>G	c.(178-180)tcA>tcG	p.S60S	MME_ENST00000493237.1_Silent_p.S60S|MME_ENST00000382989.3_Silent_p.S60S|MME_ENST00000360490.2_Silent_p.S60S|MME_ENST00000492661.1_Silent_p.S60S|MME_ENST00000462745.1_Silent_p.S60S	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	60					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	gcaagtcatcagactgcataa	0.239																																					p.S60S		Atlas-SNP	.											.	MME	133	.	0			c.A180G						.						36	38	38					3																	154802867		2182	4255	6437	SO:0001819	synonymous_variant	4311	exon3			GTCATCAGACTGC		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.180A>G	chr3.hg19:g.154802867A>G		177.0	0.0		196.0	8.0	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Silent	SNP	ENST00000460393.1	hg19	CCDS3172.1																																																																																			.	.		0.239	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		G	154802867	A	G	154802867	2	3	114	1	0	0	0	0	0	0	0	1	9654	175	7	2		2	MME	3	154802867	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	792444	154802867	43219563	288	18560										
KCNAB1	7881	hgsc.bcm.edu	37	chr3	155861084	155861084	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcagtgaccaagactcagccTcaggcggcctgcaaacctgt	11	14	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:155861084T>C	ENST00000490337.1	+	1	339				KCNAB1_ENST00000389636.5_Intron|KCNAB1_ENST00000471742.1_Silent_p.P39P	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1						learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			AGACTCAGCCTCAGGCGGCCT	0.527																																					p.P39P		Atlas-SNP	.											.	KCNAB1	176	.	0			c.T117C						.						58	57	57					3																	155861084		2203	4300	6503	SO:0001627	intron_variant	7881	exon1			TCAGCCTCAGGCG	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.275+22409T>C	chr3.hg19:g.155861084T>C		110.0	0.0		169.0	7.0	NM_003471	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Silent	SNP	ENST00000490337.1	hg19	CCDS3174.1																																																																																			.	.		0.527	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		C	155861084	T	C	155861084	1	2	114	0	1	0	0	0	0	0	0	0	8018	1538	54	2		2	KCNAB1	3	155861084	Intron	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1058217	155861084	42161346	289	18561										
SHOX2	6474	hgsc.bcm.edu	37	chr3	157820545	157820545	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcgggatagtgggtctcgtcAaaaagcctctccagctcatt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:157820545delA	ENST00000425436.3	-	2	502	c.477delT	c.(475-477)tttfs	p.F159fs	SHOX2_ENST00000483851.2_Frame_Shift_Del_p.F159fs|SHOX2_ENST00000554685.1_5'UTR|SHOX2_ENST00000389589.4_Frame_Shift_Del_p.F183fs|SHOX2_ENST00000441443.2_Frame_Shift_Del_p.F30fs|SHOX2_ENST00000490689.2_Frame_Shift_Del_p.F30fs	NM_001163678.1|NM_006884.3	NP_001157150.1|NP_006875.2	O60902	SHOX2_HUMAN	short stature homeobox 2	159					cardiac atrium morphogenesis (GO:0003209)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte development (GO:0002063)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|heart development (GO:0007507)|heart valve development (GO:0003170)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of axonogenesis (GO:0050772)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of chondrocyte differentiation (GO:0032330)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(10)|skin(3)|upper_aerodigestive_tract(1)	20			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)			GGGTCTCGTCAAAAAGCCTCT	0.582																																					p.D184fs		Atlas-INDEL	.											.	SHOX2	84	.	0			c.550delG						.						165	134	145					3																	157820545		2203	4300	6503	SO:0001589	frameshift_variant	6474	exon3			.	AJ002368	CCDS33884.1, CCDS43164.1, CCDS33884.2, CCDS54664.1	3q25.32	2011-06-20			ENSG00000168779	ENSG00000168779		"Homeoboxes / PRD class"	10854	protein-coding gene	gene with protein product		602504				9482898, 9466998	Standard	NM_006884		Approved	SHOT, OG12X, OG12	uc003fbs.3	O60902	OTTHUMG00000158755	ENST00000425436.3:c.477delT	chr3.hg19:g.157820545delA	ENSP00000398704:p.Phe159fs	212.0	0.0		230.0	14.0	NM_003030	O60465|O60467|O60903	Frame_Shift_Del	DEL	ENST00000425436.3	hg19	CCDS43164.1																																																																																			.	.		0.582	SHOX2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352057.2			-	157820545	A	-	157820545	7	5	114	1	0	1	0	1	0	0	0	0	14304	127	5	0	534	0	SHOX2	3	157820545	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1959461	157820545	40201885	290	18562										
LXN	56925	hgsc.bcm.edu	37	chr3	158387376	158387376	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gttgaagggtaaagtacttcAgctgtgcagttcaccttaac	10	8	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:158387376A>G	ENST00000264265.3	-	3	430	c.216T>C	c.(214-216)gcT>gcC	p.A72A	GFM1_ENST00000486715.1_Intron|GFM1_ENST00000478576.1_Intron|GFM1_ENST00000264263.5_Intron	NM_020169.3	NP_064554.3	Q9BS40	LXN_HUMAN	latexin	72	Cystatin-like fold 1. {ECO:0000250}.				detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|metalloendopeptidase inhibitor activity (GO:0008191)			breast(2)|endometrium(1)|kidney(2)	5			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			AAAGTACTTCAGCTGTGCAGT	0.348																																					p.A72A		Atlas-SNP	.											.	LXN	14	.	0			c.T216C						.						91	88	89					3																	158387376		2203	4300	6503	SO:0001819	synonymous_variant	56925	exon3			TACTTCAGCTGTG	AF087851	CCDS3183.1	3q25.32	2004-05-10			ENSG00000079257	ENSG00000079257			13347	protein-coding gene	gene with protein product		609305					Standard	NM_020169		Approved		uc003fch.3	Q9BS40	OTTHUMG00000158807	ENST00000264265.3:c.216T>C	chr3.hg19:g.158387376A>G		122.0	0.0		145.0	6.0	NM_020169	Q96PN2|Q9NQS6	Silent	SNP	ENST00000264265.3	hg19	CCDS3183.1	.	.	.	.	.	.	.	.	.	.	A	11.27	1.590659	0.28357	.	.	ENSG00000079257	ENST00000482640	.	.	.	5.14	-1.95	0.07548	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.0337	4.7898	0.13243	0.4195:0.0:0.1338:0.4467	.	.	.	.	R	3	.	.	X	-	1	0	LXN	159870070	0.360000	0.24964	0.999000	0.59377	0.989000	0.77384	-0.535000	0.06142	-0.001000	0.14495	0.477000	0.44152	TGA	.	.		0.348	LXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352284.1	NM_020169		G	158387376	A	G	158387376	2	3	114	1	0	0	0	0	0	0	0	1	9098	175	7	2		2	LXN	3	158387376	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	566831	158387376	39635054	291	18563										
OTOL1	131149	hgsc.bcm.edu	37	chr3	161221375	161221375	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcctcctcctaacatccccaTcaaatttgaaaagattctct	2	14	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:161221375T>C	ENST00000327928.4	+	4	1079	c.1079T>C	c.(1078-1080)aTc>aCc	p.I360T		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	360	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						AACATCCCCATCAAATTTGAA	0.463																																					p.I360T		Atlas-SNP	.											.	OTOL1	63	.	0			c.T1079C						.						55	50	51					3																	161221375		1869	4098	5967	SO:0001583	missense	131149	exon4			TCCCCATCAAATT		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"C1q and tumor necrosis factor related protein 15"		"otolin 1 homolog (zebrafish)"			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.1079T>C	chr3.hg19:g.161221375T>C	ENSP00000330808:p.Ile360Thr	64.0	0.0		121.0	5.0	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	hg19	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	T	11.19	1.564280	0.27915	.	.	ENSG00000182447	ENST00000327928	T	0.78595	-1.19	5.23	5.23	0.72850	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.049996	0.85682	D	0.000000	D	0.90031	0.6887	M	0.92970	3.365	0.40943	D	0.984485	D	0.65815	0.995	D	0.77557	0.99	D	0.91594	0.5289	10	0.44086	T	0.13	.	13.9732	0.64255	0.0:0.0:0.0:1.0	.	360	A6NHN0	OTOL1_HUMAN	T	360	ENSP00000330808:I360T	ENSP00000330808:I360T	I	+	2	0	OTOL1	162704069	1.000000	0.71417	0.120000	0.21714	0.048000	0.14542	7.748000	0.85085	1.966000	0.57179	0.455000	0.32223	ATC	.	.		0.463	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440		C	161221375	T	C	161221375	3	2	114	1	0	0	0	0	1	0	0	0	11313	1435	50	2	1093	2	OTOL1	3	161221375	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2833999	161221375	36801055	292	18564										
SI	6476	hgsc.bcm.edu	37	chr3	164735840	164735840	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taatagggatgaaatccataGgaattaagtttgtactgaaa	9	3	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:164735840G>A	ENST00000264382.3	-	29	3500	c.3438C>T	c.(3436-3438)tcC>tcT	p.S1146S		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1146	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	GAAATCCATAGGAATTAAGTT	0.299										HNSCC(35;0.089)																											p.S1146S		Atlas-SNP	.											.	SI	500	.	0			c.C3438T						.						86	86	86					3																	164735840		2203	4300	6503	SO:0001819	synonymous_variant	6476	exon29			TCCATAGGAATTA	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.3438C>T	chr3.hg19:g.164735840G>A		76.0	0.0		99.0	4.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	hg19	CCDS3196.1																																																																																			.	.		0.299	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		A	164735840	G	A	164735840	2	1	114	1	0	0	0	0	0	0	0	1	14312	987	35	3		3	SI	3	164735840	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	3514465	164735840	33286590	293	18565										
LRRC31	79782	hgsc.bcm.edu	37	chr3	169566057	169566057	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgaatacttccagagcagagAggtgaacagaggcttcagct	12	8	1	5			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:169566057A>G	ENST00000316428.5	-	8	1235	c.1178T>C	c.(1177-1179)cTc>cCc	p.L393P	LRRC31_ENST00000523069.1_Missense_Mutation_p.L393P|LRRC31_ENST00000264676.5_Missense_Mutation_p.L337P	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	393										cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			CAGAGCAGAGAGGTGAACAGA	0.413																																					p.L393P		Atlas-SNP	.											.	LRRC31	66	.	0			c.T1178C						.						65	62	63					3																	169566057		1936	4139	6075	SO:0001583	missense	79782	exon8			GCAGAGAGGTGAA	AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.1178T>C	chr3.hg19:g.169566057A>G	ENSP00000325978:p.Leu393Pro	72.0	0.0		100.0	5.0	NM_024727	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Missense_Mutation	SNP	ENST00000316428.5	hg19	CCDS43167.1	.	.	.	.	.	.	.	.	.	.	A	10.35	1.326882	0.24080	.	.	ENSG00000114248	ENST00000316428;ENST00000264676;ENST00000523069	T;T;T	0.57907	0.37;0.37;0.37	4.61	4.61	0.57282	.	0.000000	0.64402	D	0.000002	T	0.72342	0.3448	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.991	T	0.74420	-0.3671	10	0.41790	T	0.15	-1.7842	14.0296	0.64606	1.0:0.0:0.0:0.0	.	337;393	Q6UY01-2;Q6UY01	.;LRC31_HUMAN	P	393;337;393	ENSP00000325978:L393P;ENSP00000264676:L337P;ENSP00000429145:L393P	ENSP00000264676:L337P	L	-	2	0	LRRC31	171048751	1.000000	0.71417	0.052000	0.19188	0.010000	0.07245	5.814000	0.69208	1.707000	0.51288	0.533000	0.62120	CTC	.	.		0.413	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727		G	169566057	A	G	169566057	3	3	114	1	0	0	0	0	1	0	0	0	8995	304	11	2	488	2	LRRC31	3	169566057	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	4830217	169566057	28456373	294	18566										
NAALADL2	254827	hgsc.bcm.edu	37	chr3	175181236	175181236	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agacagtcacaaaattgaaaAcagttactaatgttgttgga	8	5	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:175181236A>G	ENST00000454872.1	+	7	1410	c.1282A>G	c.(1282-1284)Aca>Gca	p.T428A	NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	428						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		AAAATTGAAAACAGTTACTAA	0.284																																					p.T428A		Atlas-SNP	.											.	NAALADL2	86	.	0			c.A1282G						.						75	75	75					3																	175181236		1827	4079	5906	SO:0001583	missense	254827	exon7			TTGAAAACAGTTA		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"glutamate carboxypeptidase II-type non-peptidase homologue"	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.1282A>G	chr3.hg19:g.175181236A>G	ENSP00000404705:p.Thr428Ala	46.0	0.0		61.0	4.0	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	hg19	CCDS46960.1	.	.	.	.	.	.	.	.	.	.	A	2.054	-0.417083	0.04766	.	.	ENSG00000177694	ENST00000454872	T	0.44083	0.93	5.23	2.84	0.33178	.	0.222920	0.40064	N	0.001200	T	0.28267	0.0698	L	0.32530	0.975	0.20196	N	0.999926	B	0.13145	0.007	B	0.09377	0.004	T	0.15780	-1.0425	10	0.34782	T	0.22	-6.3495	7.6056	0.28100	0.7624:0.0:0.2375:0.0	.	428	Q58DX5	NADL2_HUMAN	A	428	ENSP00000404705:T428A	ENSP00000404705:T428A	T	+	1	0	NAALADL2	176663930	1.000000	0.71417	0.085000	0.20634	0.056000	0.15407	2.002000	0.40835	0.397000	0.25310	-0.371000	0.07208	ACA	.	.		0.284	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015		G	175181236	A	G	175181236	3	3	114	1	0	0	0	0	1	0	0	0	10139	43	2	2	1308	2	NAALADL2	3	175181236	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	5615179	175181236	22841194	295	18567										
USP13	8975	hgsc.bcm.edu	37	chr3	179501906	179501906	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagacctgggctacatgtacTtttaccgcaggataccaagc					rs34456126		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:179501906delT	ENST00000263966.3	+	21	3040	c.2569delT	c.(2569-2571)tttfs	p.F857fs	USP13_ENST00000496897.1_Frame_Shift_Del_p.F792fs	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	857	USP.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			CTACATGTACTTTTACCGCAG	0.378																																					p.Y856fs		Atlas-INDEL	.											.	USP13	117	.	0			c.2568delC						.						119	124	122					3																	179501906		2203	4300	6503	SO:0001589	frameshift_variant	8975	exon21			.	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"Ubiquitin-specific peptidases"	12611	protein-coding gene	gene with protein product		603591	"ubiquitin specific protease 13 (isopeptidase T-3)"			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.2569delT	chr3.hg19:g.179501906delT	ENSP00000263966:p.Phe857fs	179.0	0.0		166.0	10.0	NM_003940	A8K2S3|B4DYF3|D3DNS2|Q96B25	Frame_Shift_Del	DEL	ENST00000263966.3	hg19	CCDS3235.1																																																																																			.	.		0.378	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			-	179501906	T	-	179501906	7	5	114	1	0	1	0	1	0	0	0	0	17059	1609	56	0	2651	0	USP13	3	179501906	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	4320670	179501906	18520524	296	18568										
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184039824	184039824	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaaggaggagaggaactgctCcccccagagagtacccctat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:184039824delC	ENST00000346169.2	+	10	1723	c.1452delC	c.(1450-1452)ctcfs	p.L484fs	EIF4G1_ENST00000350481.5_Frame_Shift_Del_p.L320fs|EIF4G1_ENST00000392537.2_Frame_Shift_Del_p.L397fs|EIF4G1_ENST00000435046.2_Frame_Shift_Del_p.L288fs|EIF4G1_ENST00000411531.1_Frame_Shift_Del_p.L444fs|EIF4G1_ENST00000342981.4_Frame_Shift_Del_p.L484fs|EIF4G1_ENST00000382330.3_Frame_Shift_Del_p.L491fs|EIF4G1_ENST00000319274.6_Frame_Shift_Del_p.L484fs|EIF4G1_ENST00000352767.3_Frame_Shift_Del_p.L491fs|EIF4G1_ENST00000441154.1_Frame_Shift_Del_p.L320fs|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000434061.2_Frame_Shift_Del_p.L288fs|EIF4G1_ENST00000414031.1_Frame_Shift_Del_p.L444fs|EIF4G1_ENST00000427845.1_Frame_Shift_Del_p.L397fs|EIF4G1_ENST00000424196.1_Frame_Shift_Del_p.L491fs	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	484					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGGAACTGCTCCCCCCAGAGA	0.537																																					p.L491fs		Atlas-INDEL	.											.	EIF4G1	151	.	0			c.1472delT						.						63	64	64					3																	184039824		2203	4300	6503	SO:0001589	frameshift_variant	1981	exon10			.	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1452delC	chr3.hg19:g.184039824delC	ENSP00000316879:p.Leu484fs	177.0	0.0		224.0	16.0	NM_001194947	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Frame_Shift_Del	DEL	ENST00000346169.2	hg19	CCDS3259.1																																																																																			.	.		0.537	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		-	184039824	C	-	184039824	7	5	114	1	0	1	0	1	0	0	0	0	5038	842	30	0	1482	0	EIF4G1	3	184039824	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	4537918	184039824	13982606	297	18569										
HRG	3273	hgsc.bcm.edu	37	chr3	186390578	186390578	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgatcccatctgttctagagAggaggggaaggaactggtta	14	6	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:186390578A>G	ENST00000232003.4	+	5	641	c.561A>G	c.(559-561)agA>agG	p.R187R		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	187	Cystatin 2.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		TGTTCTAGAGAGGAGGGGAAG	0.413																																					p.R187R		Atlas-SNP	.											.	HRG	81	.	0			c.A561G						.						92	89	90					3																	186390578		2203	4300	6503	SO:0001819	synonymous_variant	3273	exon5			CTAGAGAGGAGGG		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.561A>G	chr3.hg19:g.186390578A>G		84.0	0.0		94.0	5.0	NM_000412	B9EK35|D3DNU7	Silent	SNP	ENST00000232003.4	hg19	CCDS3280.1																																																																																			.	.		0.413	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		G	186390578	A	G	186390578	2	3	114	1	0	0	0	0	0	0	0	1	7363	301	11	2		2	HRG	3	186390578	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2350754	186390578	11631852	298	18570										
HRG	3273	hgsc.bcm.edu	37	chr3	186392941	186392941	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccttggacttggaaagcccgAaaaaccttgtcataaactgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:186392941delA	ENST00000232003.4	+	6	783	c.703delA	c.(703-705)aaafs	p.K235fs		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	235	Cystatin 2.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		GGAAAGCCCGAAAAACCTTGT	0.443																																					p.P234fs		Atlas-INDEL	.											HRG,rectum,carcinoma,+1,1	HRG	81	.	0			c.702delG						.						229	233	232					3																	186392941		2203	4300	6503	SO:0001589	frameshift_variant	3273	exon6			.		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.703delA	chr3.hg19:g.186392941delA	ENSP00000232003:p.Lys235fs	164.0	0.0		249.0	17.0	NM_000412	B9EK35|D3DNU7	Frame_Shift_Del	DEL	ENST00000232003.4	hg19	CCDS3280.1																																																																																			.	.		0.443	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		-	186392941	A	-	186392941	7	5	114	1	0	1	0	1	0	0	0	0	7363	247	9	0	725	0	HRG	3	186392941	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2363	186392941	11629489	299	18571										
RFC4	5984	hgsc.bcm.edu	37	chr3	186507957	186507957	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttttctgtgataatagactTctgtttatcagataagttat	6	4	3	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:186507957T>A	ENST00000392481.2	-	10	1251	c.970A>T	c.(970-972)Aag>Tag	p.K324*	RFC4_ENST00000296273.2_Nonsense_Mutation_p.K324*|SNORA63_ENST00000363450.1_RNA|SNORA4_ENST00000584302.1_RNA|RFC4_ENST00000433496.1_Nonsense_Mutation_p.K297*	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	324					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		ATAATAGACTTCTGTTTATCA	0.338																																					p.K324X		Atlas-SNP	.											.	RFC4	54	.	0			c.A970T						.						106	103	104					3																	186507957		2203	4300	6503	SO:0001587	stop_gained	5984	exon10			TAGACTTCTGTTT		CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"ATPases / AAA-type"	9972	protein-coding gene	gene with protein product	"A1 37 kDa subunit", "activator 1 37 kDa subunit", "RFC 37 kDa subunit"	102577	"replication factor C (activator 1) 4 (37kD)"			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.970A>T	chr3.hg19:g.186507957T>A	ENSP00000376272:p.Lys324*	148.0	0.0		160.0	61.0	NM_181573	B4DM41|D3DNV2|Q6FHX7	Nonsense_Mutation	SNP	ENST00000392481.2	hg19	CCDS3283.1	.	.	.	.	.	.	.	.	.	.	T	38	6.877691	0.97904	.	.	ENSG00000163918	ENST00000433496;ENST00000392481;ENST00000296273;ENST00000417876	.	.	.	5.75	4.55	0.56014	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.566	0.45173	0.1436:0.0:0.0:0.8564	.	.	.	.	X	297;324;324;99	.	ENSP00000296273:K324X	K	-	1	0	RFC4	187990651	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.705000	0.68355	2.191000	0.70037	0.533000	0.62120	AAG	.	.		0.338	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916		A	186507957	T	A	186507957	4	1	114	1	0	0	0	0	0	1	0	0	13262	1792	62	4	129	4	RFC4	3	186507957	Nonsense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	115016	186507957	11514473	300	18572										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	193002803	193002803	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggccacagtgtggtggtctcAaaacttaaaattgaaccagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:193002803delA	ENST00000342358.4	-	27	3243	c.3126delT	c.(3124-3126)tttfs	p.F1042fs	ATP13A5_ENST00000495496.1_5'UTR	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	1042						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TGGTGGTCTCAAAACTTAAAA	0.388																																					p.E1043fs		Atlas-INDEL	.											.	ATP13A5	171	.	0			c.3127delG						.						123	128	127					3																	193002803		2203	4300	6503	SO:0001589	frameshift_variant	344905	exon27			.	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.3126delT	chr3.hg19:g.193002803delA	ENSP00000341942:p.Phe1042fs	153.0	0.0		190.0	12.0	NM_198505	Q6UWS4|Q6ZWL0	Frame_Shift_Del	DEL	ENST00000342358.4	hg19	CCDS33914.1																																																																																			.	.		0.388	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		-	193002803	A	-	193002803	7	5	114	1	0	1	0	1	0	0	0	0	1127	127	5	0	544	0	ATP13A5	3	193002803	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	6494846	193002803	5019627	301	18573										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	193029641	193029641	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgaaatgctgaaatatcacTtggtatgatttcccactcat	6	8	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:193029641T>C	ENST00000342358.4	-	20	2526	c.2409A>G	c.(2407-2409)caA>caG	p.Q803Q	ATP13A5_ENST00000495496.1_5'UTR|ATP13A5-AS1_ENST00000414634.1_RNA	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	803						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		GAAATATCACTTGGTATGATT	0.413																																					p.Q803Q		Atlas-SNP	.											.	ATP13A5	171	.	0			c.A2409G						.						128	116	120					3																	193029641		2203	4300	6503	SO:0001819	synonymous_variant	344905	exon20			TATCACTTGGTAT	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.2409A>G	chr3.hg19:g.193029641T>C		80.0	0.0		98.0	4.0	NM_198505	Q6UWS4|Q6ZWL0	Silent	SNP	ENST00000342358.4	hg19	CCDS33914.1																																																																																			.	.		0.413	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		C	193029641	T	C	193029641	2	2	114	1	0	0	0	0	0	0	0	1	1127	1606	56	2		2	ATP13A5	3	193029641	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	26838	193029641	4992789	302	18574										
HES1	3280	hgsc.bcm.edu	37	chr3	193854479	193854479	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagccagctgaaaacactgaTtttggatgctctgaagaaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:193854479delT	ENST00000232424.3	+	2	418	c.182delT	c.(181-183)attfs	p.I61fs		NM_005524.3	NP_005515.1	P30042	ES1_HUMAN	hes family bHLH transcription factor 1	0						mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6	all_cancers(143;7.3e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;3.65e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.48e-05)		AAAACACTGATTTTGGATGCT	0.388																																					p.I61fs		Atlas-INDEL	.											.	HES1	23	.	0			c.181delA						.						68	73	71					3																	193854479		2203	4300	6503	SO:0001589	frameshift_variant	3280	exon2			.	L19314	CCDS3305.1	3q28-q29	2013-10-17	2013-10-17	2003-01-10	ENSG00000114315	ENSG00000114315		"Basic helix-loop-helix proteins"	5192	protein-coding gene	gene with protein product		139605	"hairy homolog (Drosophila)", "hairy and enhancer of split 1, (Drosophila)"	HRY		8020957	Standard	NM_005524		Approved	FLJ20408, HES-1, Hes1, bHLHb39	uc003ftq.2	Q14469	OTTHUMG00000155984	ENST00000232424.3:c.182delT	chr3.hg19:g.193854479delT	ENSP00000232424:p.Ile61fs	155.0	0.0		220.0	14.0	NM_005524	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Frame_Shift_Del	DEL	ENST00000232424.3	hg19	CCDS3305.1																																																																																			.	.		0.388	HES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342632.1			-	193854479	T	-	193854479	7	5	114	1	0	1	0	1	0	0	0	0	7074	1493	52	0	188	0	HES1	3	193854479	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	824838	193854479	4167951	303	18575										
MUC4	4585	hgsc.bcm.edu	37	chr3	195498669	195498669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtctgactctgggaagatgaTctggccattgtctgtgaact	12	8	4	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:195498669T>C	ENST00000346145.4	-	4	427	c.388A>G	c.(388-390)Atc>Gtc	p.I130V	MUC4_ENST00000349607.4_Missense_Mutation_p.I79V|MUC4_ENST00000475231.1_Missense_Mutation_p.I4366V|MUC4_ENST00000463781.3_Missense_Mutation_p.I4366V	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1123					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGAAGATGATCTGGCCATTG	0.567																																					p.I4366V		Atlas-SNP	.											.	MUC4	1505	.	0			c.A13096G						.						162	144	150					3																	195498669		2203	4300	6503	SO:0001583	missense	4585	exon5			AGATGATCTGGCC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.388A>G	chr3.hg19:g.195498669T>C	ENSP00000304207:p.Ile130Val	77.0	0.0		87.0	5.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	hg19	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	.	11.15	1.552544	0.27739	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.57752	0.38;0.73;0.54;0.43	5.5	5.5	0.81552	.	0.000000	0.53938	D	0.000050	T	0.67487	0.2898	M	0.70595	2.14	0.26241	N	0.978876	D;P;P;P	0.53885	0.963;0.816;0.745;0.745	P;B;B;B	0.62089	0.898;0.288;0.27;0.27	T	0.62072	-0.6931	10	0.33141	T	0.24	-30.229	13.4362	0.61086	0.0:0.0:0.0:1.0	.	4238;1123;79;130	E7ESK3;Q99102;Q99102-12;Q99102-13	.;MUC4_HUMAN;.;.	V	79;130;4366;4366;1092	ENSP00000338109:I79V;ENSP00000304207:I130V;ENSP00000417498:I4366V;ENSP00000420243:I4366V	ENSP00000304207:I130V	I	-	1	0	MUC4	196984303	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	2.739000	0.47409	2.122000	0.65172	0.458000	0.33432	ATC	.	.		0.567	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		C	195498669	T	C	195498669	3	2	114	1	0	0	0	0	1	0	0	0	9987	1435	50	2	3226	2	MUC4	3	195498669	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1644190	195498669	2523761	304	18576										
SENP5	205564	hgsc.bcm.edu	37	chr3	196626588	196626588	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagtttggttccactcagtgAaaaagaagtccttggaagat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:196626588delA	ENST00000323460.5	+	3	1814	c.1565delA	c.(1564-1566)gaafs	p.E522fs	SENP5_ENST00000419026.1_Frame_Shift_Del_p.E12fs|SENP5_ENST00000445299.2_Frame_Shift_Del_p.E522fs	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	522					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		CCACTCAGTGAAAAAGAAGTC	0.303																																					p.E522fs	Ovarian(47;891 1095 11174 13858 51271)	Atlas-INDEL	.											.	SENP5	68	.	0			c.1564delG						.						91	99	96					3																	196626588		2202	4298	6500	SO:0001589	frameshift_variant	205564	exon3			.	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"SUMO1/sentrin specific protease 5"			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1565delA	chr3.hg19:g.196626588delA	ENSP00000327197:p.Glu522fs	190.0	0.0		175.0	11.0	NM_152699	B4DY82|Q96SA5	Frame_Shift_Del	DEL	ENST00000323460.5	hg19	CCDS3322.1																																																																																			.	.		0.303	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699		-	196626588	A	-	196626588	7	5	114	1	0	1	0	1	0	0	0	0	14064	246	9	0	1571	0	SENP5	3	196626588	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1127919	196626588	1395842	305	18577										
LETM1	3954	hgsc.bcm.edu	37	chr4	1818594	1818594	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctttagattcttccacgtaCttttcttcaccagtctttga					rs9328763	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:1818594delC	ENST00000302787.2	-	12	2087	c.1791delG	c.(1789-1791)aagfs	p.K597fs		NM_012318.2	NP_036450.1	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane protein 1	597					cristae formation (GO:0042407)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(2)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	13			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)			CTTCCACGTACTTTTCTTCAC	0.418																																					p.Y598fs		Atlas-INDEL	.											.	LETM1	48	.	0			c.1792delT						.						137	122	127					4																	1818594		2203	4300	6503	SO:0001589	frameshift_variant	3954	exon12			.	AF061025	CCDS3355.1	4p16.3	2013-01-10			ENSG00000168924	ENSG00000168924		"EF-hand domain containing"	6556	protein-coding gene	gene with protein product	"Mdm38 homolog (yeast)"	604407				10486213	Standard	NM_012318		Approved		uc003gdv.3	O95202	OTTHUMG00000121149	ENST00000302787.2:c.1791delG	chr4.hg19:g.1818594delC	ENSP00000305653:p.Lys597fs	258.0	0.0		316.0	20.0	NM_012318	B4DED2|Q9UF65	Frame_Shift_Del	DEL	ENST00000302787.2	hg19	CCDS3355.1																																																																																			.	.		0.418	LETM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241634.1			-	1818594	C	-	1818594	7	5	114	1	0	1	0	1	0	0	0	0	8743	564	20	0	440	0	LETM1	4	1818594	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10		1818594	189335682	306	18578										
WHSC1	7468	hgsc.bcm.edu	37	chr4	1957786	1957786	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgaagcacgagattggagaaTtccctgtgtttttctttggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:1957786delT	ENST00000382895.3	+	17	3183	c.2752delT	c.(2752-2754)ttcfs	p.F918fs	WHSC1_ENST00000382892.2_Frame_Shift_Del_p.F918fs|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000382891.5_Frame_Shift_Del_p.F918fs|WHSC1_ENST00000382888.3_Frame_Shift_Del_p.F266fs|WHSC1_ENST00000508803.1_Frame_Shift_Del_p.F918fs	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	918	PWWP 2. {ECO:0000255|PROSITE- ProRule:PRU00162}.				anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		GATTGGAGAATTCCCTGTGTT	0.473			T	IGH@	MM																																p.E917fs		Atlas-INDEL	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.2751delA						.						148	175	166					4																	1957786		2203	4300	6503	SO:0001589	frameshift_variant	7468	exon15			.	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"Zinc fingers, PHD-type"	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.2752delT	chr4.hg19:g.1957786delT	ENSP00000372351:p.Phe918fs	129.0	0.0		169.0	11.0	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Frame_Shift_Del	DEL	ENST00000382895.3	hg19	CCDS33940.1																																																																																			.	.		0.473	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		-	1957786	T	-	1957786	7	5	114	1	0	1	0	1	0	0	0	0	17377	1493	52	0	2882	0	WHSC1	4	1957786	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	139192	1957786	189196490	307	18579										
TNIP2	79155	hgsc.bcm.edu	37	chr4	2749657	2749657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttttcttctagtcgctcagTcagcctctcaatttcctaag	5	12	5	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:2749657T>C	ENST00000315423.7	-	2	378	c.292A>G	c.(292-294)Act>Gct	p.T98A	TNIP2_ENST00000510267.1_5'UTR|TNIP2_ENST00000505186.1_5'Flank|TNIP2_ENST00000503235.1_Missense_Mutation_p.T98A	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AGTCGCTCAGTCAGCCTCTCA	0.473																																					p.T98A		Atlas-SNP	.											.	TNIP2	28	.	0			c.A292G						.						31	33	32					4																	2749657		2203	4300	6503	SO:0001583	missense	79155	exon2			GCTCAGTCAGCCT	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.292A>G	chr4.hg19:g.2749657T>C	ENSP00000321203:p.Thr98Ala	69.0	0.0		95.0	4.0	NM_024309		Missense_Mutation	SNP	ENST00000315423.7	hg19	CCDS3362.1	.	.	.	.	.	.	.	.	.	.	t	10.11	1.260152	0.23051	.	.	ENSG00000168884	ENST00000315423;ENST00000503235	T;T	0.23348	1.91;1.91	3.62	0.807	0.18714	.	0.834029	0.10437	N	0.674834	T	0.17746	0.0426	L	0.43152	1.355	0.09310	N	0.999998	B;B	0.22003	0.048;0.063	B;B	0.22386	0.036;0.039	T	0.36866	-0.9730	10	0.15952	T	0.53	-6.1241	4.5043	0.11879	0.3937:0.0:0.1454:0.4608	.	98;98	D6RGJ2;Q8NFZ5	.;TNIP2_HUMAN	A	98	ENSP00000321203:T98A;ENSP00000426314:T98A	ENSP00000321203:T98A	T	-	1	0	TNIP2	2719455	0.938000	0.31826	0.000000	0.03702	0.956000	0.61745	2.576000	0.46033	0.053000	0.16036	0.449000	0.29647	ACT	.	.		0.473	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309		C	2749657	T	C	2749657	3	2	114	1	0	0	0	0	1	0	0	0	16330	1667	58	2	1017	2	TNIP2	4	2749657	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	791871	2749657	188404619	308	18580										
STK32B	55351	hgsc.bcm.edu	37	chr4	5053615	5053615	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcgggaaccactcccacaagCcccccgtgtttgacgagaat					rs142664782		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:5053615delC	ENST00000282908.5	+	1	447	c.25delC	c.(25-27)cccfs	p.P10fs		NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						CTCCCACAAGCCCCCCGTGTT	0.657																																					p.K8fs		Atlas-INDEL	.											.	STK32B	87	.	0			c.24delG						.						61	57	58					4																	5053615		2198	4295	6493	SO:0001589	frameshift_variant	55351	exon1			.	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.25delC	chr4.hg19:g.5053615delC	ENSP00000282908:p.Pro10fs	145.0	0.0		166.0	14.0	NM_018401		Frame_Shift_Del	DEL	ENST00000282908.5	hg19	CCDS3380.1																																																																																			.	.		0.657	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		-	5053615	C	-	5053615	7	5	114	1	0	1	0	1	0	0	0	0	15313	739	26	0	27	0	STK32B	4	5053615	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2303958	5053615	186100661	309	18581										
EVC2	132884	hgsc.bcm.edu	37	chr4	5664909	5664909	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttggtcgttaagggaaaggTcctcattcacgccatcagct	10	10	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:5664909T>C	ENST00000344408.5	-	9	1123	c.1070A>G	c.(1069-1071)gAc>gGc	p.D357G	EVC2_ENST00000310917.2_Missense_Mutation_p.D277G|EVC2_ENST00000344938.1_Missense_Mutation_p.D357G	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	357					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						AAGGGAAAGGTCCTCATTCAC	0.458																																					p.D357G		Atlas-SNP	.											.	EVC2	202	.	0			c.A1070G						.						142	136	138					4																	5664909		2203	4300	6503	SO:0001583	missense	132884	exon9			GAAAGGTCCTCAT	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1070A>G	chr4.hg19:g.5664909T>C	ENSP00000342144:p.Asp357Gly	84.0	0.0		87.0	4.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	T	17.76	3.468891	0.63625	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.79247	-1.25;-1.25;-1.25	5.27	4.09	0.47781	.	0.406333	0.24818	N	0.035349	D	0.83298	0.5224	M	0.62723	1.935	0.32763	N	0.504886	D	0.76494	0.999	D	0.72982	0.979	D	0.85700	0.1312	10	0.72032	D	0.01	-21.1828	7.2396	0.26090	0.0:0.0986:0.0:0.9014	.	357	Q86UK5	LBN_HUMAN	G	357;277;357	ENSP00000339954:D357G;ENSP00000311683:D277G;ENSP00000342144:D357G	ENSP00000311683:D277G	D	-	2	0	EVC2	5715810	0.997000	0.39634	0.753000	0.31225	0.787000	0.44495	2.373000	0.44266	2.103000	0.63969	0.533000	0.62120	GAC	.	.		0.458	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		C	5664909	T	C	5664909	3	2	114	1	0	0	0	0	1	0	0	0	5288	1667	58	2	2912	2	EVC2	4	5664909	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	611294	5664909	185489367	310	18582										
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8230126	8230126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctgggccagcaaaggaaccAggcagtggggctggccaact	15	12	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:8230126A>G	ENST00000245105.3	+	12	2772	c.2705A>G	c.(2704-2706)cAg>cGg	p.Q902R	SH3TC1_ENST00000539824.1_Missense_Mutation_p.Q826R	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	902										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						CAAAGGAACCAGGCAGTGGGG	0.701																																					p.Q902R	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.A2705G						.						36	43	41					4																	8230126		2202	4297	6499	SO:0001583	missense	54436	exon12			GGAACCAGGCAGT	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"Tetratricopeptide (TTC) repeat domain containing"	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.2705A>G	chr4.hg19:g.8230126A>G	ENSP00000245105:p.Gln902Arg	86.0	0.0		75.0	5.0	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	hg19	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	A	13.10	2.136918	0.37728	.	.	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.62788	-0.0;-0.0	4.63	4.63	0.57726	Tetratricopeptide-like helical (1);	0.212960	0.42682	D	0.000673	T	0.68485	0.3006	M	0.78049	2.395	0.31092	N	0.710711	P	0.43287	0.802	P	0.45343	0.477	T	0.76239	-0.3032	10	0.66056	D	0.02	-29.9447	14.0349	0.64638	1.0:0.0:0.0:0.0	.	902	Q8TE82	S3TC1_HUMAN	R	640;902;826;731	ENSP00000245105:Q902R;ENSP00000441045:Q826R	ENSP00000245105:Q902R	Q	+	2	0	SH3TC1	8281026	1.000000	0.71417	0.996000	0.52242	0.235000	0.25334	3.114000	0.50383	1.716000	0.51395	0.459000	0.35465	CAG	.	.		0.701	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		G	8230126	A	G	8230126	3	3	114	1	0	0	0	0	1	0	0	0	14276	188	7	2	2747	2	SH3TC1	4	8230126	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2565217	8230126	182924150	311	18583										
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8230236	8230236	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgttctcgaggctgccccttGgggagtgtggccgggacttc	16	11	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:8230236G>C	ENST00000245105.3	+	12	2882	c.2815G>C	c.(2815-2817)Ggg>Cgg	p.G939R	SH3TC1_ENST00000539824.1_Missense_Mutation_p.G863R	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	939										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GCTGCCCCTTGGGGAGTGTGG	0.706																																					p.G939R	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.G2815C						.						20	23	22					4																	8230236		2197	4294	6491	SO:0001583	missense	54436	exon12			CCCCTTGGGGAGT	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"Tetratricopeptide (TTC) repeat domain containing"	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.2815G>C	chr4.hg19:g.8230236G>C	ENSP00000245105:p.Gly939Arg	164.0	0.0		141.0	6.0	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	hg19	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.658883	0.00772	.	.	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.67865	-0.29;-0.29	4.06	-3.09	0.05331	Tetratricopeptide-like helical (1);	1.841800	0.02336	N	0.074412	T	0.41050	0.1142	N	0.12746	0.255	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.14868	-1.0457	10	0.11794	T	0.64	-9.1413	1.8813	0.03228	0.4062:0.2187:0.2643:0.1108	.	939	Q8TE82	S3TC1_HUMAN	R	677;939;863;768	ENSP00000245105:G939R;ENSP00000441045:G863R	ENSP00000245105:G939R	G	+	1	0	SH3TC1	8281136	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.576000	0.05854	-0.557000	0.06126	-1.459000	0.01027	GGG	.	.		0.706	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		C	8230236	G	C	8230236	3	2	114	1	0	0	0	0	1	0	0	0	14276	1348	47	4	2857	4	SH3TC1	4	8230236	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	110	8230236	182924040	312	18584										
DEFB131	644414	hgsc.bcm.edu	37	chr4	9446272	9446272	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attcaaccatgagggtcttgTtttttgtctttggagtcctt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:9446272delT	ENST00000334879.1	+	1	13	c.13delT	c.(13-15)tttfs	p.F6fs		NM_001040448.2|NM_001242853.1	NP_001035538.2|NP_001229782.1	P59861	DB131_HUMAN	defensin, beta 131	6					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				lung(2)	2						GAGGGTCTTGTTTTTTGTCTT	0.368																																					p.L4fs		Atlas-INDEL	.											.,1	DEFB131	12	.	0			c.12delG						.						166	131	142					4																	9446272		1841	4085	5926	SO:0001589	frameshift_variant	644414	exon1			.	AF529414	CCDS43213.1	4p16.1	2010-03-30			ENSG00000186146	ENSG00000186146		"Defensins, beta"	18108	protein-coding gene	gene with protein product						11854508, 16033865, 12600824	Standard	NM_001040448		Approved	DEFB-31	uc011bwt.2	P59861	OTTHUMG00000160187	ENST00000334879.1:c.13delT	chr4.hg19:g.9446272delT	ENSP00000335538:p.Phe6fs	208.0	0.0		213.0	14.0	NM_001040448		Frame_Shift_Del	DEL	ENST00000334879.1	hg19	CCDS43213.1																																																																																			.	.		0.368	DEFB131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359607.1	NM_001040448		-	9446272	T	-	9446272	7	5	114	1	0	1	0	1	0	0	0	0	4418	1725	60	0	15	0	DEFB131	4	9446272	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1216036	9446272	181708004	313	18585										
ZNF518B	85460	hgsc.bcm.edu	37	chr4	10445202	10445202	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttagttgccttgcaacctgAaaaattgaaggatccttgag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:10445202delA	ENST00000326756.3	-	3	3189	c.2751delT	c.(2749-2751)tttfs	p.F917fs		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	917					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						TTGCAACCTGAAAAATTGAAG	0.413																																					p.Q918fs		Atlas-INDEL	.											.	ZNF518B	116	.	0			c.2752delC						.						102	102	102					4																	10445202		2203	4300	6503	SO:0001589	frameshift_variant	85460	exon3			.	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.2751delT	chr4.hg19:g.10445202delA	ENSP00000317614:p.Phe917fs	141.0	0.0		158.0	10.0	NM_053042	Q96LN8	Frame_Shift_Del	DEL	ENST00000326756.3	hg19	CCDS33960.1																																																																																			.	.		0.413	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		-	10445202	A	-	10445202	7	5	114	1	0	1	0	1	0	0	0	0	17978	243	9	0	477	0	ZNF518B	4	10445202	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	998930	10445202	180709074	314	18586										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13582665	13582665	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgacaatgccagtatctgtTttggagtcgtcttctaaaaa	9	7	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:13582665T>C	ENST00000040738.5	-	21	8817	c.8682A>G	c.(8680-8682)aaA>aaG	p.K2894K		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2894						nucleus (GO:0005634)	DNA binding (GO:0003677)										CAGTATCTGTTTTGGAGTCGT	0.308																																					p.K2894K		Atlas-SNP	.											.	.	.	.	0			c.A8682G						.						80	78	78					4																	13582665		2201	4295	6496	SO:0001819	synonymous_variant	259282	exon21			ATCTGTTTTGGAG	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.8682A>G	chr4.hg19:g.13582665T>C		78.0	0.0		83.0	4.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Silent	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	1.524	-0.546022	0.04024	.	.	ENSG00000038219	ENST00000507943	T	0.52526	0.66	5.52	3.03	0.35002	.	0.000000	0.64402	D	0.000014	T	0.50803	0.1637	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45644	-0.9247	7	0.54805	T	0.06	-9.1104	5.7277	0.18022	0.1489:0.0797:0.0:0.7714	.	.	.	.	R	3	ENSP00000425492:K3R	ENSP00000425492:K3R	K	-	2	0	BOD1L	13191763	0.980000	0.34600	0.993000	0.49108	0.150000	0.21749	1.134000	0.31442	0.368000	0.24481	-0.336000	0.08194	AAA	.	.		0.308	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		C	13582665	T	C	13582665	2	2	114	1	0	0	0	0	0	0	0	1	1483	1838	64	2		2	BOD1L	4	13582665	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3137463	13582665	177571611	315	18587										
DCAF16	54876	hgsc.bcm.edu	37	chr4	17805674	17805674	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcagaggaatcccactcttCcccagaactctcatttaggt					rs372001633		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:17805674delC	ENST00000382247.1	-	3	1151	c.91delG	c.(91-93)gaafs	p.E32fs	DCAF16_ENST00000536863.1_Frame_Shift_Del_p.E32fs|DCAF16_ENST00000507768.1_5'Flank	NM_017741.3	NP_060211.3	Q9NXF7	DCA16_HUMAN	DDB1 and CUL4 associated factor 16	32					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				cervix(1)|endometrium(1)|lung(2)|ovary(1)	5						TCCCACTCTTCCCCAGAACTC	0.428																																					p.E31fs		Atlas-INDEL	.											.	DCAF16	19	.	0			c.92delA						.						67	71	70					4																	17805674		2203	4300	6503	SO:0001589	frameshift_variant	54876	exon3			.	AK000287	CCDS3423.1	4p15.32	2009-07-17	2009-07-17	2009-07-17	ENSG00000163257	ENSG00000163257		"DDB1 and CUL4 associated factors"	25987	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 30"	C4orf30		12477932	Standard	XM_005248169		Approved	FLJ20280	uc003gpn.3	Q9NXF7	OTTHUMG00000128536	ENST00000382247.1:c.91delG	chr4.hg19:g.17805674delC	ENSP00000371682:p.Glu32fs	105.0	0.0		146.0	10.0	NM_017741	B3KPB7	Frame_Shift_Del	DEL	ENST00000382247.1	hg19	CCDS3423.1																																																																																			.	.		0.428	DCAF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250371.1	NM_017741		-	17805674	C	-	17805674	7	5	114	1	0	1	0	1	0	0	0	0	4270	864	30	0	563	0	DCAF16	4	17805674	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	4223009	17805674	173348602	316	18588										
PI4K2B	55300	hgsc.bcm.edu	37	chr4	25254053	25254053	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaatttttccagaaagaatcTctcaaggttcaagtggaagt	9	6	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:25254053T>C	ENST00000264864.6	+	2	568	c.379T>C	c.(379-381)Tct>Cct	p.S127P	PI4K2B_ENST00000512921.1_Missense_Mutation_p.S31P	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	127					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				AGAAAGAATCTCTCAAGGTTC	0.363																																					p.S127P		Atlas-SNP	.											.	PI4K2B	42	.	0			c.T379C						.						110	117	115					4																	25254053		2203	4300	6503	SO:0001583	missense	55300	exon2			AGAATCTCTCAAG	AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.379T>C	chr4.hg19:g.25254053T>C	ENSP00000264864:p.Ser127Pro	86.0	0.0		113.0	6.0	NM_018323	Q9NUW2	Missense_Mutation	SNP	ENST00000264864.6	hg19	CCDS3433.1	.	.	.	.	.	.	.	.	.	.	T	14.37	2.516251	0.44763	.	.	ENSG00000038210	ENST00000512921;ENST00000264864;ENST00000537420	T	0.48201	0.82	5.43	2.93	0.34026	.	0.102171	0.64402	D	0.000001	T	0.37652	0.1011	L	0.50333	1.59	0.51767	D	0.999938	B	0.10296	0.003	B	0.13407	0.009	T	0.11767	-1.0574	10	0.31617	T	0.26	-4.7481	7.2615	0.26205	0.1296:0.0708:0.0:0.7997	.	127	Q8TCG2	P4K2B_HUMAN	P	31;127;96	ENSP00000264864:S127P	ENSP00000264864:S127P	S	+	1	0	PI4K2B	24863151	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	4.184000	0.58323	0.345000	0.23873	0.383000	0.25322	TCT	.	.		0.363	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323		C	25254053	T	C	25254053	3	2	114	1	0	0	0	0	1	0	0	0	11881	1551	54	2	385	2	PI4K2B	4	25254053	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	7448379	25254053	165900223	317	18589										
TBC1D1	23216	hgsc.bcm.edu	37	chr4	38097556	38097556	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atggtctattccagcctctgAaaatgatttgctgaacaagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:38097556delA	ENST00000261439.4	+	14	2598	c.2243delA	c.(2242-2244)gaafs	p.E748fs	TBC1D1_ENST00000508802.1_Frame_Shift_Del_p.E842fs	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	748					membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						CCAGCCTCTGAAAATGATTTG	0.433																																					p.E842fs		Atlas-INDEL	.											.	TBC1D1	94	.	0			c.2524delG						.						91	94	93					4																	38097556		2203	4300	6503	SO:0001589	frameshift_variant	23216	exon16			.	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.2243delA	chr4.hg19:g.38097556delA	ENSP00000261439:p.Glu748fs	88.0	0.0		102.0	10.0	NM_001253912	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Frame_Shift_Del	DEL	ENST00000261439.4	hg19	CCDS33972.1																																																																																			.	.		0.433	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173		-	38097556	A	-	38097556	7	5	114	1	0	1	0	1	0	0	0	0	15612	246	9	0	2293	0	TBC1D1	4	38097556	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	12843503	38097556	153056720	318	18590										
UGDH	7358	hgsc.bcm.edu	37	chr4	39515764	39515764	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tattggtagaaaaaaaaagaTtttttcctcgacaggattct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:39515764delT	ENST00000316423.6	-	3	545	c.203delA	c.(202-204)aatfs	p.N68fs	UGDH_ENST00000501493.2_Frame_Shift_Del_p.N68fs|UGDH_ENST00000515398.1_5'UTR|UGDH_ENST00000507089.1_5'UTR|UGDH_ENST00000506179.1_Frame_Shift_Del_p.N68fs	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	68					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)			breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						AAAAAAAAGATTTTTTCCTCG	0.308																																					p.N68fs		Atlas-INDEL	.											.	UGDH	52	.	0			c.204delT						.						63	75	71					4																	39515764		2201	4289	6490	SO:0001589	frameshift_variant	7358	exon3			.	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"UDP-glucose dehydrogenase"			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.203delA	chr4.hg19:g.39515764delT	ENSP00000319501:p.Asn68fs	134.0	0.0		155.0	10.0	NM_001184700	B3KUU2|B4DN25|O60589	Frame_Shift_Del	DEL	ENST00000316423.6	hg19	CCDS3455.1																																																																																			.	.		0.308	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359		-	39515764	T	-	39515764	7	5	114	1	0	1	0	1	0	0	0	0	16955	1493	52	0	1321	0	UGDH	4	39515764	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1418208	39515764	151638512	319	18591										
N4BP2	55728	hgsc.bcm.edu	37	chr4	40121838	40121838	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acaaaagtgaaaacgagcaaAtagaaatggtggctgtaaaa	10	4	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:40121838A>G	ENST00000261435.6	+	9	2523	c.2107A>G	c.(2107-2109)Ata>Gta	p.I703V		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	703					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						AAACGAGCAAATAGAAATGGT	0.368																																					p.I703V		Atlas-SNP	.											.	N4BP2	166	.	0			c.A2107G						.						91	98	96					4																	40121838		2203	4300	6503	SO:0001583	missense	55728	exon9			GAGCAAATAGAAA	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.2107A>G	chr4.hg19:g.40121838A>G	ENSP00000261435:p.Ile703Val	48.0	0.0		50.0	4.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0|0	-2.687186|-2.687186	0.00100|0.00100	.|.	.|.	ENSG00000078177|ENSG00000078177	ENST00000261435;ENST00000381804|ENST00000513269	T|.	0.15603|.	2.41|.	5.19|5.19	2.35|2.35	0.29111|0.29111	.|.	1.190420|.	0.06024|.	N|.	0.651874|.	T|T	0.06962|0.06962	0.0177|0.0177	N|N	0.00436|0.00436	-1.5|-1.5	0.09310|0.09310	N|N	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.36040|0.36040	-0.9764|-0.9764	10|5	0.02654|.	T|.	1|.	-1.4195|-1.4195	3.628|3.628	0.08120|0.08120	0.0837:0.1441:0.4759:0.2963|0.0837:0.1441:0.4759:0.2963	.|.	703;703|.	Q86UW6-2;Q86UW6|.	.;N4BP2_HUMAN|.	V|S	703;623|349	ENSP00000261435:I703V|.	ENSP00000261435:I703V|.	I|N	+|+	1|2	0|0	N4BP2|N4BP2	39798233|39798233	0.000000|0.000000	0.05858|0.05858	0.126000|0.126000	0.21872|0.21872	0.037000|0.037000	0.13140|0.13140	0.156000|0.156000	0.16382|0.16382	0.151000|0.151000	0.19162|0.19162	-0.375000|-0.375000	0.07067|0.07067	ATA|AAT	.	.		0.368	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		G	40121838	A	G	40121838	3	3	114	1	0	0	0	0	1	0	0	0	10119	101	4	2	2133	2	N4BP2	4	40121838	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	606074	40121838	151032438	320	18592										
CWH43	80157	hgsc.bcm.edu	37	chr4	49063874	49063874	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattatgaaaacaaccatcaTtttcatatgaatactcccaa	2	9	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:49063874T>A	ENST00000226432.4	+	16	2250	c.2067T>A	c.(2065-2067)caT>caA	p.H689Q	CWH43_ENST00000513409.1_Missense_Mutation_p.H662Q	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	689			H -> N (in dbSNP:rs1051447). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						ACAACCATCATTTTCATATGA	0.249																																					p.H689Q		Atlas-SNP	.											.	CWH43	101	.	0			c.T2067A						.						28	26	27					4																	49063874		2183	4238	6421	SO:0001583	missense	80157	exon16			CCATCATTTTCAT		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.2067T>A	chr4.hg19:g.49063874T>A	ENSP00000226432:p.His689Gln	92.0	0.0		157.0	7.0	NM_025087	B2RPD7	Missense_Mutation	SNP	ENST00000226432.4	hg19	CCDS3486.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.112985	0.37242	.	.	ENSG00000109182	ENST00000226432;ENST00000513409	T;T	0.41758	1.58;0.99	4.59	2.18	0.27775	.	0.209202	0.34025	N	0.004323	T	0.40909	0.1136	L	0.43152	1.355	0.36487	D	0.868185	D	0.56746	0.977	P	0.53593	0.73	T	0.41610	-0.9499	9	.	.	.	.	6.0925	0.20003	0.0:0.2:0.0:0.8	.	689	Q9H720	PG2IP_HUMAN	Q	689;662	ENSP00000226432:H689Q;ENSP00000422802:H662Q	.	H	+	3	2	CWH43	48758631	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.024000	0.30077	0.520000	0.28426	-0.379000	0.06801	CAT	.	.		0.249	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		A	49063874	T	A	49063874	3	1	114	1	0	0	0	0	1	0	0	0	4075	1490	52	4	2129	4	CWH43	4	49063874	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	8942036	49063874	142090402	321	18593										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55146491	55146491	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgtttttacagctatgttaTtttatcttttgaaaacaatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:55146491delT	ENST00000257290.5	+	16	2496	c.2165delT	c.(2164-2166)attfs	p.I722fs	FIP1L1_ENST00000507166.1_Frame_Shift_Del_p.I482fs	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	722	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	AGCTATGTTATTTTATCTTTT	0.393			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.I722fs	Pancreas(151;208 1913 7310 23853 37092)	Atlas-INDEL	.		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	.	PDGFRA	1583	.	0			c.2164delA						.						114	111	112					4																	55146491		2203	4300	6503	SO:0001589	frameshift_variant	5156	exon16	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	.	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.2165delT	chr4.hg19:g.55146491delT	ENSP00000257290:p.Ile722fs	174.0	0.0		185.0	12.0	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Frame_Shift_Del	DEL	ENST00000257290.5	hg19	CCDS3495.1																																																																																			.	.		0.393	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		-	55146491	T	-	55146491	7	5	114	1	0	1	0	1	0	0	0	0	11670	1493	52	0	2223	0	PDGFRA	4	55146491	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	6082617	55146491	136007785	322	18594										
PPAT	5471	hgsc.bcm.edu	37	chr4	57272752	57272752	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caacaacgaagggctgacaaTtttctagttcacattttcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:57272752delT	ENST00000264220.2	-	3	448	c.311delA	c.(310-312)aatfs	p.N104fs	PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	104	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	GGGCTGACAATTTTCTAGTTC	0.383																																					p.N104fs		Atlas-INDEL	.											.	PPAT	41	.	0			c.312delT						.						149	123	132					4																	57272752		2203	4300	6503	SO:0001589	frameshift_variant	5471	exon3			.		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.311delA	chr4.hg19:g.57272752delT	ENSP00000264220:p.Asn104fs	136.0	0.0		164.0	12.0	NM_002703		Frame_Shift_Del	DEL	ENST00000264220.2	hg19	CCDS3505.1																																																																																			.	.		0.383	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		-	57272752	T	-	57272752	7	5	114	1	0	1	0	1	0	0	0	0	12311	1493	52	0	1278	0	PPAT	4	57272752	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2126261	57272752	133881524	323	18595										
REST	5978	hgsc.bcm.edu	37	chr4	57798156	57798156	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gttccacaagaatctagcagAaaaaatgcaaaggaagcctt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:57798156delA	ENST00000309042.7	+	4	3446	c.3132delA	c.(3130-3132)agafs	p.R1044fs		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	1044	Interaction with RCOR1.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					AATCTAGCAGAAAAAATGCAA	0.448																																					p.R1044fs		Atlas-INDEL	.											REST,right_lower_lobe,carcinoma,0,1	REST	104	.	0			c.3131delG						.						71	67	68					4																	57798156		2203	4300	6503	SO:0001589	frameshift_variant	5978	exon4			.	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.3132delA	chr4.hg19:g.57798156delA	ENSP00000311816:p.Arg1044fs	145.0	0.0		166.0	10.0	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Frame_Shift_Del	DEL	ENST00000309042.7	hg19	CCDS3509.1																																																																																			.	.		0.448	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		-	57798156	A	-	57798156	7	5	114	1	0	1	0	1	0	0	0	0	13249	243	9	0	3142	0	REST	4	57798156	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	525404	57798156	133356120	324	18596										
TMPRSS11D	9407	hgsc.bcm.edu	37	chr4	68725283	68725283	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctggtacttaccaaaagctAaaaagtaaacaagtagagct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:68725283delA	ENST00000283916.6	-	2	220	c.122delT	c.(121-123)ttafs	p.L41fs	UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11D_ENST00000545541.1_Intron|TMPRSS11D_ENST00000509584.1_Intron	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	41					proteolysis (GO:0006508)|respiratory gaseous exchange (GO:0007585)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						ACCAAAAGCTAAAAAGTAAAC	0.353																																					p.L41fs		Atlas-INDEL	.											.	TMPRSS11D	68	.	0			c.123delA						.						86	85	85					4																	68725283		2203	4300	6503	SO:0001589	frameshift_variant	9407	exon2			.	AB002134	CCDS3518.1	4q13.2	2010-04-13			ENSG00000153802	ENSG00000153802		"Serine peptidases / Transmembrane"	24059	protein-coding gene	gene with protein product	"airway trypsin like protease"	605369				9565616, 9070615	Standard	XM_005265710		Approved		uc003hdq.3	O60235	OTTHUMG00000129300	ENST00000283916.6:c.122delT	chr4.hg19:g.68725283delA	ENSP00000283916:p.Leu41fs	112.0	0.0		144.0	10.0	NM_004262	Q08AF6	Frame_Shift_Del	DEL	ENST00000283916.6	hg19	CCDS3518.1																																																																																			.	.		0.353	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3	NM_004262		-	68725283	A	-	68725283	7	5	114	1	0	1	0	1	0	0	0	0	16256	372	13	0	1170	0	TMPRSS11D	4	68725283	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	10927127	68725283	122428993	325	18597										
TMPRSS11B	132724	hgsc.bcm.edu	37	chr4	69100333	69100333	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actgcacatttgaaccattgGcattaggcctagaaacaaca	7	10	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:69100333G>A	ENST00000332644.5	-	5	478	c.317C>T	c.(316-318)gCc>gTc	p.A106V		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	106	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						TGAACCATTGGCATTAGGCCT	0.338																																					p.A106V		Atlas-SNP	.											.	TMPRSS11B	66	.	0			c.C317T						.						82	76	78					4																	69100333		2203	4300	6503	SO:0001583	missense	132724	exon5			CCATTGGCATTAG	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"Serine peptidases / Transmembrane"	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.317C>T	chr4.hg19:g.69100333G>A	ENSP00000330475:p.Ala106Val	112.0	0.0		134.0	6.0	NM_182502	A8K4D9	Missense_Mutation	SNP	ENST00000332644.5	hg19	CCDS3521.1	.	.	.	.	.	.	.	.	.	.	G	9.583	1.124050	0.20959	.	.	ENSG00000185873	ENST00000332644	T	0.33654	1.4	5.02	-0.132	0.13489	SEA (2);	1.431730	0.04911	N	0.453172	T	0.17789	0.0427	N	0.08118	0	0.09310	N	1	B	0.24483	0.104	B	0.25614	0.062	T	0.16867	-1.0388	10	0.33141	T	0.24	.	2.0873	0.03649	0.1695:0.2848:0.3995:0.1462	.	106	Q86T26	TM11B_HUMAN	V	106	ENSP00000330475:A106V	ENSP00000330475:A106V	A	-	2	0	TMPRSS11B	68782928	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.709000	0.05030	-0.303000	0.08856	0.655000	0.94253	GCC	.	.		0.338	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502		A	69100333	G	A	69100333	3	1	114	1	0	0	0	0	1	0	0	0	16255	1203	42	3	957	3	TMPRSS11B	4	69100333	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	375050	69100333	122053943	326	18598										
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72363374	72363374	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acacctcttccatggctctgAaaaaattcaaaactagtcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:72363374delA	ENST00000264485.5	+	16	2248	c.2131delA	c.(2131-2133)aaafs	p.K712fs	SLC4A4_ENST00000425175.1_Frame_Shift_Del_p.K712fs|SLC4A4_ENST00000340595.3_Frame_Shift_Del_p.K668fs|SLC4A4_ENST00000351898.6_Frame_Shift_Del_p.K712fs	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	712					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	CATGGCTCTGAAAAAATTCAA	0.363																																					p.L710fs		Atlas-INDEL	.											SLC4A4_ENST00000425175,caecum,carcinoma,0,2	SLC4A4	269	.	0			c.2130delG						.						113	117	115					4																	72363374		2203	4300	6503	SO:0001589	frameshift_variant	8671	exon16			.	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.2131delA	chr4.hg19:g.72363374delA	ENSP00000264485:p.Lys712fs	101.0	0.0		132.0	11.0	NM_001134742	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Frame_Shift_Del	DEL	ENST00000264485.5	hg19	CCDS43236.1																																																																																			.	.		0.363	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		-	72363374	A	-	72363374	7	5	114	1	0	1	0	1	0	0	0	0	14671	247	9	0	2310	0	SLC4A4	4	72363374	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3263041	72363374	118790902	327	18599										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	73985933	73985933	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctttatctgctgctatggttAaagctgtatctcttgaggag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:73985933delA	ENST00000358602.4	-	21	4087	c.3971delT	c.(3970-3972)ttafs	p.L1324fs	ANKRD17_ENST00000509867.2_Frame_Shift_Del_p.L1211fs|ANKRD17_ENST00000330838.6_Frame_Shift_Del_p.L1073fs|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1324					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGCTATGGTTAAAGCTGTATC	0.448																																					p.L1324fs		Atlas-INDEL	.											.	ANKRD17	214	.	0			c.3972delA						.						169	153	159					4																	73985933		2203	4300	6503	SO:0001589	frameshift_variant	26057	exon21			.	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.3971delT	chr4.hg19:g.73985933delA	ENSP00000351416:p.Leu1324fs	145.0	0.0		162.0	10.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Frame_Shift_Del	DEL	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.448	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		-	73985933	A	-	73985933	7	5	114	1	0	1	0	1	0	0	0	0	646	372	13	0	3896	0	ANKRD17	4	73985933	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1622559	73985933	117168343	328	18600										
CDKL2	8999	hgsc.bcm.edu	37	chr4	76523281	76523281	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgtaccacaagtgtttttcTttcttcaactaaggaatcat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:76523281delT	ENST00000429927.2	-	8	1703	c.1000delA	c.(1000-1002)agafs	p.R334fs	CDKL2_ENST00000307465.4_Frame_Shift_Del_p.R334fs	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	334					sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			AGTGTTTTTCTTTCTTCAACT	0.244																																					p.R334fs		Atlas-INDEL	.											CDKL2,NS,carcinoma,0,1	CDKL2	58	.	0			c.1001delG						.						37	37	37					4																	76523281		2201	4276	6477	SO:0001589	frameshift_variant	8999	exon8			.	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"Cyclin-dependent kinases"	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.1000delA	chr4.hg19:g.76523281delT	ENSP00000412365:p.Arg334fs	118.0	0.0		173.0	11.0	NM_003948	B2R695	Frame_Shift_Del	DEL	ENST00000429927.2	hg19	CCDS3570.1																																																																																			.	.		0.244	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		-	76523281	T	-	76523281	7	5	114	1	0	1	0	1	0	0	0	0	3156	1617	56	0	497	0	CDKL2	4	76523281	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2537348	76523281	114630995	329	18601										
ART3	419	hgsc.bcm.edu	37	chr4	77003227	77003227	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atatatttccgaagctcaagAgcaaactcccttttaccatc	4	12	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:77003227A>G	ENST00000355810.4	+	3	439	c.320A>G	c.(319-321)gAg>gGg	p.E107G	ART3_ENST00000513494.1_3'UTR|ART3_ENST00000349321.3_Missense_Mutation_p.E107G|ART3_ENST00000341029.5_Missense_Mutation_p.E107G	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	107					protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|stomach(1)	16			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GAAGCTCAAGAGCAAACTCCC	0.423																																					p.E107G		Atlas-SNP	.											.	ART3	34	.	0			c.A320G						.						75	75	75					4																	77003227		2203	4300	6503	SO:0001583	missense	419	exon3			CTCAAGAGCAAAC	X95827	CCDS3575.1, CCDS47079.1, CCDS47080.1	4q21.1	2008-05-15			ENSG00000156219	ENSG00000156219			725	protein-coding gene	gene with protein product		603086				9119374	Standard	NM_001130017		Approved		uc003hjo.3	Q13508	OTTHUMG00000130110	ENST00000355810.4:c.320A>G	chr4.hg19:g.77003227A>G	ENSP00000348064:p.Glu107Gly	52.0	0.0		78.0	4.0	NM_001130017	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Missense_Mutation	SNP	ENST00000355810.4	hg19	CCDS47079.1	.	.	.	.	.	.	.	.	.	.	A	11.88	1.769559	0.31320	.	.	ENSG00000156219	ENST00000513353;ENST00000341029;ENST00000513122;ENST00000504914;ENST00000355810;ENST00000349321;ENST00000510423	T;T;T;T;T;T;T	0.49720	0.77;3.18;2.69;1.45;3.18;3.18;2.46	6.04	3.32	0.38043	.	0.762936	0.12436	N	0.469141	T	0.43787	0.1263	M	0.63428	1.95	0.09310	N	0.999997	B;B;B;B;B;B;B	0.30914	0.016;0.039;0.3;0.004;0.131;0.052;0.002	B;B;B;B;B;B;B	0.27262	0.03;0.065;0.065;0.01;0.078;0.033;0.009	T	0.38824	-0.9643	10	0.56958	D	0.05	-20.0283	9.4093	0.38482	0.8323:0.0:0.1677:0.0	.	77;107;107;107;107;107;107	D6RBN3;E7ESB3;B4DHX3;E7ER42;Q13508;Q13508-3;Q13508-2	.;.;.;.;NAR3_HUMAN;.;.	G	107	ENSP00000421345:E107G;ENSP00000343843:E107G;ENSP00000422287:E107G;ENSP00000421431:E107G;ENSP00000348064:E107G;ENSP00000304313:E107G;ENSP00000425327:E107G	ENSP00000343843:E107G	E	+	2	0	ART3	77222251	0.656000	0.27385	0.696000	0.30242	0.576000	0.36127	0.833000	0.27504	1.103000	0.41568	0.460000	0.39030	GAG	.	.		0.423	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179		G	77003227	A	G	77003227	3	3	114	1	0	0	0	0	1	0	0	0	998	304	11	2	326	2	ART3	4	77003227	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	479946	77003227	114151049	330	18602										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79239975	79239975	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catttgcagcctgtcactccTcctgcctggcttgtatgggt	10	13	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:79239975T>C	ENST00000325942.6	+	18	2412	c.1972T>C	c.(1972-1974)Tcc>Ccc	p.S658P	FRAS1_ENST00000264899.6_Missense_Mutation_p.S658P|FRAS1_ENST00000264895.6_Missense_Mutation_p.S658P	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	658					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CTGTCACTCCTCCTGCCTGGC	0.458																																					p.S658P		Atlas-SNP	.											.	FRAS1	779	.	0			c.T1972C						.						92	87	89					4																	79239975		1942	4140	6082	SO:0001583	missense	80144	exon18			CACTCCTCCTGCC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1972T>C	chr4.hg19:g.79239975T>C	ENSP00000326330:p.Ser658Pro	97.0	0.0		126.0	6.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.73|13.73	2.325055|2.325055	0.41197|0.41197	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000508900|ENST00000325942;ENST00000264895;ENST00000264899	.|T;T;T	.|0.76578	.|-1.03;-1.03;-1.03	5.93|5.93	4.73|4.73	0.59995|0.59995	.|Growth factor, receptor (1);	.|0.121046	.|0.56097	.|D	.|0.000023	D|D	0.87172|0.87172	0.6111|0.6111	M|M	0.82716|0.82716	2.605|2.605	0.53005|0.53005	D|D	0.999969|0.999969	.|D;D;D;D	.|0.67145	.|0.996;0.996;0.992;0.977	.|D;D;D;P	.|0.68039	.|0.955;0.955;0.921;0.905	D|D	0.88003|0.88003	0.2757|0.2757	5|10	.|0.87932	.|D	.|0	.|.	11.4759|11.4759	0.50297|0.50297	0.135:0.0:0.0:0.8649|0.135:0.0:0.0:0.8649	.|.	.|658;658;658;658	.|E9PHH6;Q86XX4;E7EWM9;A2RRR8	.|.;FRAS1_HUMAN;.;.	P|P	500|658	.|ENSP00000326330:S658P;ENSP00000264895:S658P;ENSP00000264899:S658P	.|ENSP00000264895:S658P	L|S	+|+	2|1	0|0	FRAS1|FRAS1	79458999|79458999	0.993000|0.993000	0.37304|0.37304	0.706000|0.706000	0.30403|0.30403	0.023000|0.023000	0.10783|0.10783	3.321000|3.321000	0.51999|0.51999	1.027000|1.027000	0.39758|0.39758	0.533000|0.533000	0.62120|0.62120	CTC|TCC	.	.		0.458	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			C	79239975	T	C	79239975	3	2	114	1	0	0	0	0	1	0	0	0	6050	1551	54	2	2042	2	FRAS1	4	79239975	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2236748	79239975	111914301	331	18603										
HNRPDL	9987	hgsc.bcm.edu	37	chr4	83348625	83348625	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggtatctgctttctaacaaTttttttactggctcttcatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:83348625delT	ENST00000295470.5	-	4	1042	c.867delA	c.(865-867)aaafs	p.K289fs	HNRNPDL_ENST00000349655.4_Frame_Shift_Del_p.K170fs|HNRNPDL_ENST00000514511.1_5'UTR|HNRNPDL_ENST00000502762.1_Frame_Shift_Del_p.K289fs|HNRNPDL_ENST00000602300.1_Frame_Shift_Del_p.K170fs	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	289	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										TTTCTAACAATTTTTTTACTG	0.289																																					p.L290fs		Atlas-INDEL	.											.	HNRPDL	35	.	0			c.868delT						.						74	75	75					4																	83348625		2202	4299	6501	SO:0001589	frameshift_variant	9987	exon4			.	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"RNA binding motif (RRM) containing"	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.867delA	chr4.hg19:g.83348625delT	ENSP00000295470:p.Lys289fs	121.0	0.0		183.0	12.0	NM_031372	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Frame_Shift_Del	DEL	ENST00000295470.5	hg19	CCDS3593.1																																																																																			.	.		0.289	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463		-	83348625	T	-	83348625	7	5	114	1	0	1	0	1	0	0	0	0	7285	1490	52	0	411	0	HNRPDL	4	83348625	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	4108650	83348625	107805651	332	18604										
ENOPH1	9987	hgsc.bcm.edu	37	chr4	83352029	83352029	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtcaccgtgatcctgttagAtatcgaaggtaccacaaccc	8	12	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:83352029A>G	ENST00000295470.5	-	0	0				HNRNPDL_ENST00000349655.4_5'Flank|HNRNPDL_ENST00000514511.1_5'Flank|ENOPH1_ENST00000509635.1_5'UTR|HNRNPDL_ENST00000502762.1_5'Flank|ENOPH1_ENST00000273920.3_Missense_Mutation_p.D16G|HNRNPDL_ENST00000602300.1_5'Flank	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like						regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										ATCCTGTTAGATATCGAAGGT	0.542																																					p.D16G		Atlas-SNP	.											.	ENOPH1	26	.	0			c.A47G						.						90	77	82					4																	83352029		2203	4300	6503	SO:0001631	upstream_gene_variant	58478	exon1			TGTTAGATATCGA	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"RNA binding motif (RRM) containing"	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299		chr4.hg19:g.83352029A>G	Exception_encountered	73.0	0.0		85.0	4.0	NM_021204	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Missense_Mutation	SNP	ENST00000295470.5	hg19	CCDS3593.1	.	.	.	.	.	.	.	.	.	.	a	28.3	4.906413	0.92107	.	.	ENSG00000145293	ENST00000273920;ENST00000456931	T	0.54866	0.55	5.57	5.57	0.84162	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);2,3-diketo-5-methylthio-1-phosphopentane phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.80586	0.4651	H	0.96208	3.785	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.86855	0.2026	10	0.87932	D	0	-19.5014	14.5624	0.68151	1.0:0.0:0.0:0.0	.	16	Q9UHY7	ENOPH_HUMAN	G	16	ENSP00000273920:D16G	ENSP00000273920:D16G	D	+	2	0	ENOPH1	83571053	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	4.754000	0.62191	2.110000	0.64415	0.459000	0.35465	GAT	.	.		0.542	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463		G	83352029	A	G	83352029	1	3	114	0	1	0	0	0	0	0	0	0	5126	333	12	2		2	ENOPH1	4	83352029	5'Flank	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3404	83352029	107802247	333	18605										
SEC31A	22872	hgsc.bcm.edu	37	chr4	83763594	83763594	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgaggtcgatacattgctgaCccccctgttccgaagggata							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:83763594delC	ENST00000395310.2	-	22	2849	c.2667delG	c.(2665-2667)gggfs	p.G889fs	SEC31A_ENST00000348405.4_Frame_Shift_Del_p.G850fs|SEC31A_ENST00000500777.2_Intron|SEC31A_ENST00000509142.1_Intron|SEC31A_ENST00000432794.1_Frame_Shift_Del_p.G889fs|SEC31A_ENST00000448323.1_Frame_Shift_Del_p.G889fs|SEC31A_ENST00000264405.5_Frame_Shift_Del_p.G653fs|SEC31A_ENST00000508502.1_Frame_Shift_Del_p.G889fs|SEC31A_ENST00000513858.1_Intron|SEC31A_ENST00000326950.5_Frame_Shift_Del_p.G850fs|SEC31A_ENST00000443462.2_Frame_Shift_Del_p.G884fs|SEC31A_ENST00000355196.2_Frame_Shift_Del_p.G889fs|SEC31A_ENST00000505984.1_Frame_Shift_Del_p.G850fs|SEC31A_ENST00000505472.1_Frame_Shift_Del_p.G920fs|SEC31A_ENST00000311785.7_Intron	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	889	Interaction with PDCD6.|Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				ACATTGCTGACCCCCCTGTTC	0.458																																					p.S890fs		Atlas-INDEL	.											.	SEC31A	227	.	0			c.2668delT						.						43	36	38					4																	83763594		2203	4300	6503	SO:0001589	frameshift_variant	22872	exon22			.	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.2667delG	chr4.hg19:g.83763594delC	ENSP00000378721:p.Gly889fs	127.0	0.0		151.0	12.0	NM_001077207	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Frame_Shift_Del	DEL	ENST00000395310.2	hg19	CCDS3596.1																																																																																			.	.		0.458	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		-	83763594	C	-	83763594	7	5	114	1	0	1	0	1	0	0	0	0	14013	494	18	0	1019	0	SEC31A	4	83763594	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	411565	83763594	107390682	334	18606										
AGPAT9	84803	hgsc.bcm.edu	37	chr4	84465717	84465717	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatacgaattgaaaaaggaaCcccaaaggagtcgattctta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:84465717delC	ENST00000395226.2	+	3	388	c.170delC	c.(169-171)accfs	p.T57fs	AGPAT9_ENST00000264409.4_Frame_Shift_Del_p.T57fs	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	57					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				GAAAAAGGAACCCCAAAGGAG	0.348																																					p.T57fs		Atlas-INDEL	.											.	AGPAT9	41	.	0			c.169delA						.						195	211	205					4																	84465717		2203	4300	6503	SO:0001589	frameshift_variant	84803	exon2			.	AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	28157	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, theta"	610958	"1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.170delC	chr4.hg19:g.84465717delC	ENSP00000378651:p.Thr57fs	117.0	0.0		166.0	11.0	NM_032717	Q68CJ4|Q6GPI6|Q96NA3	Frame_Shift_Del	DEL	ENST00000395226.2	hg19	CCDS3606.1																																																																																			.	.		0.348	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717		-	84465717	C	-	84465717	7	5	114	1	0	1	0	1	0	0	0	0	392	507	18	0	176	0	AGPAT9	4	84465717	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	702123	84465717	106688559	335	18607										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87556466	87556466	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtggaccacttcaggaggaAgaaatatgggctgtattaaa	13	5	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:87556466A>G	ENST00000411767.2	+	2	120	c.57A>G	c.(55-57)gaA>gaG	p.E19E	PTPN13_ENST00000511467.1_Silent_p.E19E|PTPN13_ENST00000316707.6_Silent_p.E19E|PTPN13_ENST00000436978.1_Silent_p.E19E|PTPN13_ENST00000427191.2_Silent_p.E19E|PTPN13_ENST00000502971.1_Silent_p.E19E			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	19	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TTCAGGAGGAAGAAATATGGG	0.453																																					p.E19E		Atlas-SNP	.											.	PTPN13	203	.	0			c.A57G						.						62	63	63					4																	87556466		1923	4129	6052	SO:0001819	synonymous_variant	5783	exon2			GGAGGAAGAAATA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.57A>G	chr4.hg19:g.87556466A>G		97.0	0.0		85.0	38.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	hg19	CCDS47094.1																																																																																			.	.		0.453	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			G	87556466	A	G	87556466	2	3	114	1	0	0	0	0	0	0	0	1	12795	69	3	2		2	PTPN13	4	87556466	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3090749	87556466	103597810	336	18608										
HERC6	55008	hgsc.bcm.edu	37	chr4	89326115	89326115	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagaaaaatggatagcagtgAaaagaagaagtactgaacat					rs369850043		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:89326115delA	ENST00000264346.7	+	9	1239	c.1180delA	c.(1180-1182)aaafs	p.K394fs	HERC6_ENST00000380265.5_Frame_Shift_Del_p.K394fs	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	394					hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		GATAGCAGTGAAAAGAAGAAG	0.433																																					p.V393fs		Atlas-INDEL	.											.	HERC6	104	.	0			c.1179delG						.						139	131	133					4																	89326115		1845	4104	5949	SO:0001589	frameshift_variant	55008	exon9			.	AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"hect domain and RLD 6"				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.1180delA	chr4.hg19:g.89326115delA	ENSP00000264346:p.Lys394fs	129.0	0.0		166.0	10.0	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Frame_Shift_Del	DEL	ENST00000264346.7	hg19	CCDS47098.1																																																																																			.	.		0.433	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2			-	89326115	A	-	89326115	7	5	114	1	0	1	0	1	0	0	0	0	7071	247	9	0	1011	0	HERC6	4	89326115	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1769649	89326115	101828161	337	18609										
HERC5	51191	hgsc.bcm.edu	37	chr4	89407334	89407334	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaactcttgcaccgtctcaaTttttttgtagaagtatgcag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:89407334delT	ENST00000264350.3	+	14	1959	c.1806delT	c.(1804-1806)aatfs	p.N602fs	HERC5_ENST00000508159.1_Frame_Shift_Del_p.N240fs	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	602					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		ACCGTCTCAATTTTTTTGTAG	0.348																																					p.N602fs	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-INDEL	.											.	HERC5	114	.	0			c.1805delA						.						129	132	131					4																	89407334		2203	4300	6503	SO:0001589	frameshift_variant	51191	exon14			.	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"hect domain and RLD 5"			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1806delT	chr4.hg19:g.89407334delT	ENSP00000264350:p.Asn602fs	130.0	0.0		163.0	15.0	NM_016323	B2RTQ1|Q69G20	Frame_Shift_Del	DEL	ENST00000264350.3	hg19	CCDS3630.1																																																																																			.	.		0.348	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		-	89407334	T	-	89407334	7	5	114	1	0	1	0	1	0	0	0	0	7070	1490	52	0	1860	0	HERC5	4	89407334	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	81219	89407334	101746942	338	18610										
NHEDC1	150159	hgsc.bcm.edu	37	chr4	103911043	103911043	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtggttttatttcttctgtaTctgataagacagttttagtt	8	4	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:103911043T>C	ENST00000296422.7	-	3	266	c.125A>G	c.(124-126)gAt>gGt	p.D42G	SLC9B1_ENST00000394789.3_Missense_Mutation_p.D42G	NM_139173.3	NP_631912	Q4ZJI4	SL9B1_HUMAN	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	42					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TTCTTCTGTATCTGATAAGAC	0.308																																					p.D42G		Atlas-SNP	.											.	.	.	.	0			c.A125G						.						170	151	157					4																	103911043		2201	4293	6494	SO:0001583	missense	150159	exon3			TCTGTATCTGATA	AF447585	CCDS34041.1, CCDS47119.1	4q24	2013-05-22	2012-03-22	2011-07-26	ENSG00000164037	ENSG00000164037		"Solute carriers"	24244	protein-coding gene	gene with protein product		611527	"Na+/H+ exchanger domain containing 1", "solute carrier family 9, subfamily B (cation proton antiporter 2), member 1"	NHEDC1		16850186	Standard	NM_139173		Approved	NHA1	uc003hww.3	Q4ZJI4	OTTHUMG00000161114	ENST00000296422.7:c.125A>G	chr4.hg19:g.103911043T>C	ENSP00000296422:p.Asp42Gly	91.0	0.0		92.0	4.0	NM_001100874	A1KXV1|B9EH04|C9JBP7|Q49A30|Q8NCV2|Q8WVZ0	Missense_Mutation	SNP	ENST00000296422.7	hg19	CCDS34041.1	.	.	.	.	.	.	.	.	.	.	T	7.782	0.709690	0.15239	.	.	ENSG00000164037	ENST00000394789;ENST00000296422;ENST00000514340;ENST00000452285;ENST00000510559	T;T;T;T	0.55234	2.21;2.23;1.87;0.53	3.74	2.55	0.30701	.	22.639300	0.00166	N	0.000001	T	0.37625	0.1010	N	0.19112	0.55	0.09310	N	1	B;B	0.19073	0.033;0.001	B;B	0.12156	0.007;0.003	T	0.18777	-1.0326	10	0.17832	T	0.49	-3.1	5.7884	0.18347	0.0:0.1197:0.0:0.8803	.	42;42	Q4ZJI4;Q4ZJI4-3	SL9B1_HUMAN;.	G	42	ENSP00000378269:D42G;ENSP00000296422:D42G;ENSP00000426056:D42G;ENSP00000426325:D42G	ENSP00000296422:D42G	D	-	2	0	SLC9B1	104130492	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.673000	0.25203	0.805000	0.34159	0.377000	0.23210	GAT	.	.		0.308	SLC9B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363841.1	NM_139173		C	103911043	T	C	103911043	3	2	114	1	0	0	0	0	1	0	0	0	10409	1435	50	2	1562	2	NHEDC1	4	103911043	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	14503709	103911043	87243233	339	18611										
RRH	10692	hgsc.bcm.edu	37	chr4	110754368	110754368	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaggaacttcggacacccacAaatgcaattattattaacct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:110754368delA	ENST00000317735.4	+	2	214	c.180delA	c.(178-180)acafs	p.T60fs		NM_006583.2	NP_006574.1	O14718	OPSX_HUMAN	retinal pigment epithelium-derived rhodopsin homolog	60					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	12		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)		GGACACCCACAAATGCAATTA	0.393																																					p.T60fs		Atlas-INDEL	.											.	RRH	24	.	0			c.179delC						.						99	95	97					4																	110754368		2203	4300	6503	SO:0001589	frameshift_variant	10692	exon2			.	AF012270	CCDS3687.1	4q25	2012-08-08			ENSG00000180245	ENSG00000180245		"GPCR / Class A : Opsin receptors"	10450	protein-coding gene	gene with protein product	"peropsin"	605224				9275222	Standard	NM_006583		Approved	peropsin	uc003hzv.3	O14718	OTTHUMG00000132045	ENST00000317735.4:c.180delA	chr4.hg19:g.110754368delA	ENSP00000314992:p.Thr60fs	190.0	0.0		154.0	10.0	NM_006583	A1A4V2|Q7RTS4	Frame_Shift_Del	DEL	ENST00000317735.4	hg19	CCDS3687.1																																																																																			.	.		0.393	RRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255066.1	NM_006583		-	110754368	A	-	110754368	7	5	114	1	0	1	0	1	0	0	0	0	13695	117	5	0	186	0	RRH	4	110754368	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	6843325	110754368	80399908	340	18612										
ENPEP	2028	hgsc.bcm.edu	37	chr4	111409837	111409837	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actttcaaatatgccagtggCggtaagtattttttaaatgt	8	5	1	0	rs373049379		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:111409837C>T	ENST00000265162.5	+	2	1127	c.785C>T	c.(784-786)gCg>gTg	p.A262V		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	262					angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1)	54		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)		ATGCCAGTGGCGGTAAGTATT	0.358																																					p.A262V		Atlas-SNP	.											ENPEP,NS,carcinoma,0,2	ENPEP	149	.	0			c.C785T						.	C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	93	92	92		785	-1.1	1	4		92	0,8600		0,0,4300	no	missense-near-splice	ENPEP	NM_001977.3	64	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	262/958	111409837	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	2028	exon2			CAGTGGCGGTAAG	L12468	CCDS3691.1	4q25	2008-02-05			ENSG00000138792	ENSG00000138792	3.4.11.7	"CD molecules"	3355	protein-coding gene	gene with protein product		138297				9268642	Standard	NM_001977		Approved	gp160, CD249	uc003iab.4	Q07075	OTTHUMG00000132546	ENST00000265162.5:c.786+1C>T	chr4.hg19:g.111409837C>T		57.0	0.0		32.0	19.0	NM_001977	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	hg19	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.588973	0.46110	2.27E-4	0.0	ENSG00000138792	ENST00000265162	T	0.02579	4.24	4.61	-1.13	0.09775	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.425182	0.24999	N	0.033928	T	0.01454	0.0047	N	0.05574	-0.02	0.31035	N	0.716968	P	0.47350	0.894	B	0.40165	0.321	T	0.52102	-0.8620	10	0.28530	T	0.3	.	8.6135	0.33817	0.463:0.4203:0.0:0.1166	.	262	Q07075	AMPE_HUMAN	V	262	ENSP00000265162:A262V	ENSP00000265162:A262V	A	+	2	0	ENPEP	111629286	0.616000	0.27035	0.991000	0.47740	0.798000	0.45092	1.105000	0.31086	-0.498000	0.06632	-0.251000	0.11542	GCG	.	.		0.358	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2		Missense_Mutation	T	111409837	C	T	111409837	5	4	114	1	0	0	0	0	0	0	1	0	5130	782	27	1	791	1	ENPEP	4	111409837	Splice_Site	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	655469	111409837	79744439	341	18613										
ARSJ	79642	hgsc.bcm.edu	37	chr4	114899693	114899693	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagcttgtcaagagtaggtgTtttaatctcagatccgtggt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:114899693delT	ENST00000315366.7	-	1	1164	c.298delA	c.(298-300)acafs	p.T100fs	ARSJ_ENST00000541197.1_Frame_Shift_Del_p.T100fs|ARSJ_ENST00000503013.2_5'UTR	NM_024590.3	NP_078866.3	Q5FYB0	ARSJ_HUMAN	arylsulfatase family, member J	100					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	21		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)		AGAGTAGGTGTTTTAATCTCA	0.473																																					p.T100fs		Atlas-INDEL	.											.	ARSJ	55	.	0			c.299delC						.						98	97	97					4																	114899693		1926	4127	6053	SO:0001589	frameshift_variant	79642	exon1			.		CCDS43264.1	4q26	2013-02-14	2006-03-07		ENSG00000180801	ENSG00000180801		"Arylsulfatase family"	26286	protein-coding gene	gene with protein product		610010	"arylsulfatase J"			12975309, 16174644	Standard	NM_024590		Approved	FLJ23548	uc003ibq.1	Q5FYB0	OTTHUMG00000161067	ENST00000315366.7:c.298delA	chr4.hg19:g.114899693delT	ENSP00000320219:p.Thr100fs	175.0	0.0		154.0	10.0	NM_024590	A2RUG0|B7ZM45|Q1HA39|Q5FWE4|Q6UWT9	Frame_Shift_Del	DEL	ENST00000315366.7	hg19	CCDS43264.1																																																																																			.	.		0.473	ARSJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363650.1	NM_024590		-	114899693	T	-	114899693	7	5	114	1	0	1	0	1	0	0	0	0	995	1725	60	0	1509	0	ARSJ	4	114899693	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3489856	114899693	76254583	342	18614										
CCNA2	890	hgsc.bcm.edu	37	chr4	122742218	122742218	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcttttcatcttctaatatAattgacatgtccatagtatg	6	7	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:122742218A>C	ENST00000274026.5	-	3	789	c.486T>G	c.(484-486)atT>atG	p.I162M		NM_001237.3	NP_001228	P20248	CCNA2_HUMAN	cyclin A2	162					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|organ regeneration (GO:0031100)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|response to estradiol (GO:0032355)|response to glucagon (GO:0033762)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	12						CTTCTAATATAATTGACATGT	0.343																																					p.I162M		Atlas-SNP	.											CCNA2,colon,carcinoma,0,1	CCNA2	30	.	0			c.T486G						.						196	187	190					4																	122742218		2203	4299	6502	SO:0001583	missense	890	exon3			TAATATAATTGAC		CCDS3723.1	4q27	2012-07-12			ENSG00000145386	ENSG00000145386			1578	protein-coding gene	gene with protein product		123835		CCNA, CCN1		1675006	Standard	NM_001237		Approved		uc003iec.4	P20248	OTTHUMG00000133072	ENST00000274026.5:c.486T>G	chr4.hg19:g.122742218A>C	ENSP00000274026:p.Ile162Met	157.0	0.0		120.0	0.0	NM_001237	A8K7B6|Q2M3U6|Q4W5P4|Q6LER8	Missense_Mutation	SNP	ENST00000274026.5	hg19	CCDS3723.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.121146	0.37436	.	.	ENSG00000145386	ENST00000274026	T	0.15256	2.44	5.86	3.55	0.40652	.	0.665471	0.12795	U	0.438573	T	0.14787	0.0357	L	0.58101	1.795	0.32550	N	0.532438	B	0.12630	0.006	B	0.12156	0.007	T	0.18429	-1.0337	10	0.33940	T	0.23	.	1.6245	0.02720	0.5393:0.1859:0.0894:0.1854	.	162	P20248	CCNA2_HUMAN	M	162	ENSP00000274026:I162M	ENSP00000274026:I162M	I	-	3	3	CCNA2	122961668	0.997000	0.39634	0.569000	0.28460	0.977000	0.68977	1.504000	0.35726	1.038000	0.40049	0.482000	0.46254	ATT	.	.		0.343	CCNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256712.2	NM_001237		C	122742218	A	C	122742218	3	2	114	1	0	0	0	0	1	0	0	0	2912	358	13	5	836	5	CCNA2	4	122742218	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	7842525	122742218	68412058	343	18615										
INTU	27152	hgsc.bcm.edu	37	chr4	128635178	128635178	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttaaagaacatggtgtgttgTttgaatgttcacctggaaac	10	5	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:128635178T>C	ENST00000335251.6	+	15	2750	c.2647T>C	c.(2647-2649)Ttt>Ctt	p.F883L		NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	883					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						TGGTGTGTTGTTTGAATGTTC	0.363																																					p.F883L		Atlas-SNP	.											.	INTU	92	.	0			c.T2647C						.						142	142	142					4																	128635178		2203	4300	6503	SO:0001583	missense	27152	exon15			GTGTTGTTTGAAT	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.2647T>C	chr4.hg19:g.128635178T>C	ENSP00000334003:p.Phe883Leu	82.0	0.0		65.0	4.0	NM_015693	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	hg19	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.832049	0.91036	.	.	ENSG00000164066	ENST00000335251	.	.	.	4.2	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.76912	0.4054	M	0.71206	2.165	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80241	-0.1464	9	0.87932	D	0	-19.9757	13.455	0.61193	0.0:0.0:0.0:1.0	.	883	Q9ULD6	PDZD6_HUMAN	L	883	.	ENSP00000334003:F883L	F	+	1	0	INTU	128854628	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.142000	0.77339	1.751000	0.51876	0.528000	0.53228	TTT	.	.		0.363	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		C	128635178	T	C	128635178	3	2	114	1	0	0	0	0	1	0	0	0	7795	1725	60	2	2705	2	INTU	4	128635178	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	5892960	128635178	62519098	344	18616										
CLGN	1047	hgsc.bcm.edu	37	chr4	141320135	141320135	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaccacatcctctaggaggcTtcctttgtttacaactgttt	6	11	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:141320135T>C	ENST00000325617.5	-	8	1194	c.754A>G	c.(754-756)Agc>Ggc	p.S252G	CLGN_ENST00000537281.1_Missense_Mutation_p.S252G|CLGN_ENST00000414773.1_Missense_Mutation_p.S252G	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	252					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					TCTAGGAGGCTTCCTTTGTTT	0.358																																					p.S252G		Atlas-SNP	.											.	CLGN	76	.	0			c.A754G						.						128	122	124					4																	141320135		2203	4300	6503	SO:0001583	missense	1047	exon9			GGAGGCTTCCTTT	D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.754A>G	chr4.hg19:g.141320135T>C	ENSP00000326699:p.Ser252Gly	143.0	0.0		80.0	4.0	NM_001130675	B3KS90|B4DXV8|D3DNY8	Missense_Mutation	SNP	ENST00000325617.5	hg19	CCDS3751.1	.	.	.	.	.	.	.	.	.	.	T	18.43	3.622996	0.66901	.	.	ENSG00000153132	ENST00000325617;ENST00000414773;ENST00000537281;ENST00000545667	T;T;T	0.53206	0.63;0.63;0.63	5.74	5.74	0.90152	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.110160	0.85682	D	0.000000	T	0.56790	0.2009	M	0.83852	2.665	0.52099	D	0.999942	B	0.17667	0.023	B	0.26310	0.068	T	0.59005	-0.7535	10	0.87932	D	0	-3.9327	16.0359	0.80628	0.0:0.0:0.0:1.0	.	252	O14967	CLGN_HUMAN	G	252;252;252;169	ENSP00000326699:S252G;ENSP00000392782:S252G;ENSP00000439381:S252G	ENSP00000326699:S252G	S	-	1	0	CLGN	141539585	1.000000	0.71417	0.977000	0.42913	0.783000	0.44284	7.997000	0.88414	2.187000	0.69744	0.519000	0.50382	AGC	.	.		0.358	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362		C	141320135	T	C	141320135	3	2	114	1	0	0	0	0	1	0	0	0	3526	1609	56	2	1110	2	CLGN	4	141320135	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	12684957	141320135	49834141	345	18617										
ZNF330	27309	hgsc.bcm.edu	37	chr4	142154925	142154925	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagagggagatggagcttctGggtatgatgcttattggaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:142154925delG	ENST00000262990.4	+	10	973	c.745delG	c.(745-747)gggfs	p.G249fs	ZNF330_ENST00000421169.2_Frame_Shift_Del_p.G189fs	NM_014487.4	NP_055302.1	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330	249						chromosome, centromeric region (GO:0000775)|midbody (GO:0030496)|nucleolus (GO:0005730)	metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	14	all_hematologic(180;0.162)					TGGAGCTTCTGGGTATGATGC	0.453																																					p.S248fs		Atlas-INDEL	.											.	ZNF330	31	.	0			c.744delT						.						131	120	123					4																	142154925		2203	4300	6503	SO:0001589	frameshift_variant	27309	exon10			.	AJ006591	CCDS3754.1	4q31.21	2008-05-15			ENSG00000109445	ENSG00000109445		"Zinc fingers, C2H2-type"	15462	protein-coding gene	gene with protein product		609550				11528117, 10593942	Standard	NM_001292002		Approved	NOA36, HSA6591	uc003iiq.4	Q9Y3S2	OTTHUMG00000133413	ENST00000262990.4:c.745delG	chr4.hg19:g.142154925delG	ENSP00000262990:p.Gly249fs	199.0	0.0		161.0	12.0	NM_014487	B2RDA3	Frame_Shift_Del	DEL	ENST00000262990.4	hg19	CCDS3754.1																																																																																			.	.		0.453	ZNF330-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257271.2	NM_014487		-	142154925	G	-	142154925	7	5	114	1	0	1	0	1	0	0	0	0	17863	1348	47	0	779	0	ZNF330	4	142154925	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	834790	142154925	48999351	346	18618										
USP38	84640	hgsc.bcm.edu	37	chr4	144109051	144109051	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcttcagatgattacagttcTcatcaggagccttactacgg	8	10	4	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:144109051T>C	ENST00000307017.4	+	2	1261	c.755T>C	c.(754-756)cTc>cCc	p.L252P	USP38_ENST00000510377.1_Missense_Mutation_p.L252P	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	252					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					ATTACAGTTCTCATCAGGAGC	0.383																																					p.L252P		Atlas-SNP	.											.	USP38	92	.	0			c.T755C						.						103	98	100					4																	144109051		2203	4300	6503	SO:0001583	missense	84640	exon2			CAGTTCTCATCAG	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.755T>C	chr4.hg19:g.144109051T>C	ENSP00000303434:p.Leu252Pro	100.0	0.0		87.0	4.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.597610	0.87055	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	T;T	0.76186	-0.96;-1.0	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000001	T	0.81269	0.4787	L	0.44542	1.39	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.71184	0.931;0.972	T	0.83119	-0.0119	10	0.66056	D	0.02	-11.0503	15.0837	0.72133	0.0:0.0:0.0:1.0	.	252;252	Q8NB14;Q3ZCV1	UBP38_HUMAN;.	P	252	ENSP00000427647:L252P;ENSP00000303434:L252P	ENSP00000303434:L252P	L	+	2	0	USP38	144328501	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	1.972000	0.57404	0.383000	0.25322	CTC	.	.		0.383	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		C	144109051	T	C	144109051	3	2	114	1	0	0	0	0	1	0	0	0	17084	1551	54	2	761	2	USP38	4	144109051	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1954126	144109051	47045225	347	18619										
GAB1	2549	hgsc.bcm.edu	37	chr4	144361320	144361320	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaatcccaattcaccaccacGacaacattccagcagtttta	4	14	1	0	rs369383480		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:144361320G>A	ENST00000262994.4	+	6	1672	c.1370G>A	c.(1369-1371)cGa>cAa	p.R457Q	GAB1_ENST00000262995.4_Missense_Mutation_p.R457Q|GAB1_ENST00000505913.1_Missense_Mutation_p.R354Q	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	457	Pro-rich.				activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					TCACCACCACGACAACATTCC	0.383																																					p.R457Q		Atlas-SNP	.											.	GAB1	80	.	0			c.G1370A						.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	138	131	134		1370,1370	5.9	0.9	4		134	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GAB1	NM_002039.3,NM_207123.2	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	457/695,457/725	144361320	1,13005	2203	4300	6503	SO:0001583	missense	2549	exon6			CACCACGACAACA	U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"Pleckstrin homology (PH) domain containing"	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.1370G>A	chr4.hg19:g.144361320G>A	ENSP00000262994:p.Arg457Gln	195.0	0.0		159.0	7.0	NM_207123	A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	ENST00000262994.4	hg19	CCDS3759.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.742467	0.69418	0.0	1.16E-4	ENSG00000109458	ENST00000262995;ENST00000262994;ENST00000505913	T;T;T	0.18338	2.69;2.71;2.22	5.91	5.91	0.95273	.	0.063133	0.64402	D	0.000003	T	0.28101	0.0693	L	0.43152	1.355	0.44048	D	0.996782	P;D	0.63880	0.913;0.993	B;P	0.55303	0.357;0.773	T	0.01010	-1.1482	10	0.12766	T	0.61	-2.8214	20.3011	0.98612	0.0:0.0:1.0:0.0	.	457;457	Q13480;Q13480-2	GAB1_HUMAN;.	Q	457;457;354	ENSP00000262995:R457Q;ENSP00000262994:R457Q;ENSP00000424554:R354Q	ENSP00000262994:R457Q	R	+	2	0	GAB1	144580770	1.000000	0.71417	0.906000	0.35671	0.989000	0.77384	7.353000	0.79414	2.804000	0.96469	0.650000	0.86243	CGA	.	.		0.383	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039		A	144361320	G	A	144361320	3	1	114	1	0	0	0	0	1	0	0	0	6156	1058	37	1	1392	1	GAB1	4	144361320	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	252269	144361320	46792956	348	18620										
SMARCA5	8467	hgsc.bcm.edu	37	chr4	144442631	144442631	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttattaaagcagacagaacTttttgcacatttcattcaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:144442631delT	ENST00000283131.3	+	3	764	c.302delT	c.(301-303)cttfs	p.L101fs		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	101					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					CAGACAGAACTTTTTGCACAT	0.353																																					p.L101fs		Atlas-INDEL	.											.	SMARCA5	73	.	0			c.301delC						.						60	64	63					4																	144442631		2203	4300	6503	SO:0001589	frameshift_variant	8467	exon3			.	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.302delT	chr4.hg19:g.144442631delT	ENSP00000283131:p.Leu101fs	125.0	0.0		106.0	12.0	NM_003601		Frame_Shift_Del	DEL	ENST00000283131.3	hg19	CCDS3761.1																																																																																			.	.		0.353	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			-	144442631	T	-	144442631	7	5	114	1	0	1	0	1	0	0	0	0	14786	1609	56	0	312	0	SMARCA5	4	144442631	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	81311	144442631	46711645	349	18621										
PRMT10	90826	hgsc.bcm.edu	37	chr4	148559833	148559833	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaagtatccaacctaatctcTtcatcaaggtacatatgata	5	9	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:148559833T>C	ENST00000322396.6	-	12	2630	c.2388A>G	c.(2386-2388)gaA>gaG	p.E796E	PRMT10_ENST00000541232.1_Silent_p.E683E|TMEM184C_ENST00000508208.1_Intron	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		796	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						ACCTAATCTCTTCATCAAGGT	0.373																																					p.E796E		Atlas-SNP	.											.	PRMT10	68	.	0			c.A2388G						.						89	81	84					4																	148559833		2203	4300	6503	SO:0001819	synonymous_variant	90826	exon12			AATCTCTTCATCA																												ENST00000322396.6:c.2388A>G	chr4.hg19:g.148559833T>C		115.0	0.0		86.0	4.0	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Silent	SNP	ENST00000322396.6	hg19	CCDS3771.1																																																																																			.	.		0.373	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			C	148559833	T	C	148559833	2	2	114	1	0	0	0	0	0	0	0	1	12548	1606	56	2		2	PRMT10	4	148559833	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4117202	148559833	42594443	350	18622										
LRBA	987	hgsc.bcm.edu	37	chr4	151773390	151773390	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcagtaacaggttttccttCttgaaatattaatttgtcat	5	6	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:151773390C>T	ENST00000357115.3	-	23	3715	c.3472G>A	c.(3472-3474)Gaa>Aaa	p.E1158K	LRBA_ENST00000535741.1_Missense_Mutation_p.E1158K|LRBA_ENST00000510413.1_Missense_Mutation_p.E1158K|LRBA_ENST00000507224.1_Missense_Mutation_p.E1158K	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1158						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					GGTTTTCCTTCTTGAAATATT	0.393																																					p.E1158K		Atlas-SNP	.											.	LRBA	253	.	0			c.G3472A						.						72	73	73					4																	151773390		2203	4300	6503	SO:0001583	missense	987	exon23			TTCCTTCTTGAAA	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.3472G>A	chr4.hg19:g.151773390C>T	ENSP00000349629:p.Glu1158Lys	112.0	0.0		93.0	4.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	C	8.123	0.781444	0.16120	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.55760	0.92;1.07;0.92;0.5	5.45	4.6	0.57074	.	0.846744	0.10452	N	0.673006	T	0.39200	0.1069	N	0.24115	0.695	0.18873	N	0.999988	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.06110	-1.0845	10	0.13470	T	0.59	.	14.4517	0.67389	0.0:0.9282:0.0:0.0718	.	1158;1158	P50851;P50851-2	LRBA_HUMAN;.	K	1158	ENSP00000446299:E1158K;ENSP00000421552:E1158K;ENSP00000349629:E1158K;ENSP00000422180:E1158K	ENSP00000349629:E1158K	E	-	1	0	LRBA	151992840	0.918000	0.31147	0.523000	0.27875	0.018000	0.09664	1.324000	0.33712	2.941000	0.99782	0.655000	0.94253	GAA	.	.		0.393	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151773390	C	T	151773390	3	4	114	1	0	0	0	0	1	0	0	0	8940	922	32	3	5263	3	LRBA	4	151773390	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	3213557	151773390	39380886	351	18623										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158238831	158238831	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttattaccattggaaaacatGttaaagggtaccactacatc	6	8	0	0	rs199950609		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:158238831G>C	ENST00000264426.9	+	5	967	c.688G>C	c.(688-690)Gtt>Ctt	p.V230L	GRIA2_ENST00000507898.1_Missense_Mutation_p.V183L|GRIA2_ENST00000449365.1_Missense_Mutation_p.V183L|GRIA2_ENST00000393815.2_Missense_Mutation_p.V183L|GRIA2_ENST00000296526.7_Missense_Mutation_p.V230L	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	230					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TGGAAAACATGTTAAAGGGTA	0.229																																					p.V230L		Atlas-SNP	.											GRIA2_ENST00000264426,NS,carcinoma,0,2	GRIA2	358	.	0			c.G688C						.						37	39	38					4																	158238831		2195	4288	6483	SO:0001583	missense	2891	exon5			AAACATGTTAAAG		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.688G>C	chr4.hg19:g.158238831G>C	ENSP00000264426:p.Val230Leu	121.0	0.0		111.0	0.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.038022	0.75617	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365;ENST00000503437	T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98	5.17	5.17	0.71159	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.27419	0.0673	N	0.24115	0.695	0.80722	D	1	P;B;B	0.37955	0.612;0.001;0.351	P;B;B	0.48425	0.577;0.005;0.373	T	0.05971	-1.0853	10	0.59425	D	0.04	.	19.041	0.92999	0.0:0.0:1.0:0.0	.	230;230;183	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	L	183;183;230;230;183;103	ENSP00000426845:V183L;ENSP00000377403:V183L;ENSP00000296526:V230L;ENSP00000264426:V230L;ENSP00000389837:V183L	ENSP00000264426:V230L	V	+	1	0	GRIA2	158458281	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.466000	0.80914	2.547000	0.85894	0.563000	0.77884	GTT	.	G|0.999;A|0.001		0.229	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			C	158238831	G	C	158238831	3	2	114	1	0	0	0	0	1	0	0	0	6777	1377	48	4	706	4	GRIA2	4	158238831	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	6465441	158238831	32915445	352	18624										
RAPGEF2	9693	hgsc.bcm.edu	37	chr4	160273871	160273871	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccagtggtactgtggataaTttttcagattctggtcacag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:160273871delT	ENST00000264431.4	+	21	3836	c.3417delT	c.(3415-3417)aatfs	p.N1139fs		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1139	Ser-rich.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		CTGTGGATAATTTTTCAGATT	0.423																																					p.N1139fs		Atlas-INDEL	.											.	RAPGEF2	171	.	0			c.3416delA						.						109	102	104					4																	160273871		1884	4107	5991	SO:0001589	frameshift_variant	9693	exon21			.	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.3417delT	chr4.hg19:g.160273871delT	ENSP00000264431:p.Asn1139fs	218.0	0.0		179.0	12.0	NM_014247	D3DP27	Frame_Shift_Del	DEL	ENST00000264431.4	hg19	CCDS43277.1																																																																																			.	.		0.423	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		-	160273871	T	-	160273871	7	5	114	1	0	1	0	1	0	0	0	0	13059	1490	52	0	3499	0	RAPGEF2	4	160273871	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2035040	160273871	30880405	353	18625										
NAF1	92345	hgsc.bcm.edu	37	chr4	164085383	164085383	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acttacattaagaagtaattCatcttttgttttaagaggaa	6	4	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:164085383C>G	ENST00000274054.2	-	2	719	c.526G>C	c.(526-528)Gaa>Caa	p.E176Q	NAF1_ENST00000422287.2_Missense_Mutation_p.E176Q	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	176					pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				AGAAGTAATTCATCTTTTGTT	0.308																																					p.E176Q		Atlas-SNP	.											.	NAF1	69	.	0			c.G526C						.						29	31	30					4																	164085383		2200	4299	6499	SO:0001583	missense	92345	exon2			GTAATTCATCTTT		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"nuclear assembly factor 1 homolog (S. cerevisiae)"			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.526G>C	chr4.hg19:g.164085383C>G	ENSP00000274054:p.Glu176Gln	128.0	0.0		117.0	11.0	NM_138386	D3DP28|E9PAZ2	Missense_Mutation	SNP	ENST00000274054.2	hg19	CCDS3803.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.943608	0.73672	.	.	ENSG00000145414	ENST00000422287;ENST00000274054	T;T	0.54279	0.78;0.58	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.71576	0.3356	M	0.74881	2.28	0.51012	D	0.999908	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	T	0.74682	-0.3583	10	0.87932	D	0	-27.7111	14.4072	0.67090	0.0:1.0:0.0:0.0	.	176;176	E9PAZ2;Q96HR8	.;NAF1_HUMAN	Q	176	ENSP00000408963:E176Q;ENSP00000274054:E176Q	ENSP00000274054:E176Q	E	-	1	0	NAF1	164304833	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.939000	0.56591	2.678000	0.91216	0.591000	0.81541	GAA	.	.		0.308	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386		G	164085383	C	G	164085383	3	3	114	1	0	0	0	0	1	0	0	0	10149	835	29	4	1127	4	NAF1	4	164085383	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	3811512	164085383	27068893	354	18626										
WDR17	116966	hgsc.bcm.edu	37	chr4	177052791	177052791	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctttaacacagaatcaagcaTtttctcttcctcctggtcat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:177052791delT	ENST00000280190.4	+	8	1228	c.1072delT	c.(1072-1074)tttfs	p.F358fs	WDR17_ENST00000393643.2_Frame_Shift_Del_p.F334fs|WDR17_ENST00000507824.2_Frame_Shift_Del_p.F341fs|WDR17_ENST00000508596.1_Frame_Shift_Del_p.F334fs			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	358										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		GAATCAAGCATTTTCTCTTCC	0.403																																					p.A357fs		Atlas-INDEL	.											.	WDR17	198	.	0			c.1071delA						.						289	279	282					4																	177052791		2203	4300	6503	SO:0001589	frameshift_variant	116966	exon8			.	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.1072delT	chr4.hg19:g.177052791delT	ENSP00000280190:p.Phe358fs	223.0	0.0		173.0	12.0	NM_170710	E7EQX0|Q0QD35	Frame_Shift_Del	DEL	ENST00000280190.4	hg19	CCDS3825.1																																																																																			.	.		0.403	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			-	177052791	T	-	177052791	7	5	114	1	0	1	0	1	0	0	0	0	17292	1493	52	0	1098	0	WDR17	4	177052791	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	12967408	177052791	14101485	355	18627										
C4orf41	60684	hgsc.bcm.edu	37	chr4	184596365	184596365	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tagctttcttcagtgagttgAaacaagatacacaaaatgcg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:184596365delA	ENST00000334690.6	+	7	911	c.709delA	c.(709-711)aaafs	p.K237fs	TRAPPC11_ENST00000357207.4_Frame_Shift_Del_p.K237fs|TRAPPC11_ENST00000511409.1_3'UTR|RNU6-335P_ENST00000364563.1_RNA	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	237					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											CAGTGAGTTGAAACAAGATAC	0.264																																					p.L236fs		Atlas-INDEL	.											.	.	.	.	0			c.708delG						.						47	50	49					4																	184596365		2199	4288	6487	SO:0001589	frameshift_variant	60684	exon7			.		CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"Trafficking protein particle complex"	25751	protein-coding gene	gene with protein product	"gryzun homolog (Drosophila)", "foie gras homolog (zebrafish)"	614138	"chromosome 4 open reading frame 41"	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.709delA	chr4.hg19:g.184596365delA	ENSP00000335371:p.Lys237fs	155.0	0.0		131.0	11.0	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Frame_Shift_Del	DEL	ENST00000334690.6	hg19	CCDS34112.1																																																																																			.	.		0.264	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942		-	184596365	A	-	184596365	7	5	114	1	0	1	0	1	0	0	0	0	2272	247	9	0	731	0	C4orf41	4	184596365	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	7543574	184596365	6557911	356	18628										
NSUN2	54888	hgsc.bcm.edu	37	chr5	6607400	6607400	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caccagttcctgtgaatgacGgactttccagcttagaggga	11	10	0	3	rs374268482		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:6607400G>T	ENST00000264670.6	-	13	1732	c.1421C>A	c.(1420-1422)cCg>cAg	p.P474Q	NSUN2_ENST00000539938.1_Missense_Mutation_p.P238Q|NSUN2_ENST00000506139.1_Missense_Mutation_p.P439Q	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	474					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)	p.P474Q(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						TGTGAATGACGGACTTTCCAG	0.478																																					p.P474Q		Atlas-SNP	.											NSUN2,colon,carcinoma,0,1	NSUN2	82	.	1	Substitution - Missense(1)	lung(1)	c.C1421A						.						252	238	242					5																	6607400		2203	4300	6503	SO:0001583	missense	54888	exon13			AATGACGGACTTT	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"NOP2/Sun domain containing"	25994	protein-coding gene	gene with protein product	"tRNA methyltransferase 4 homolog (S. cerevisiae)", "Myc-induced SUN-domain-containing protein"	610916	"NOL1/NOP2/Sun domain family, member 2", "NOP2/Sun domain family, member 2", "mental retardation, non-syndromic, autosomal recessive, 5"	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.1421C>A	chr5.hg19:g.6607400G>T	ENSP00000264670:p.Pro474Gln	386.0	0.0		466.0	0.0	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	hg19	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	G	8.838	0.941559	0.18281	.	.	ENSG00000037474	ENST00000264670;ENST00000539938;ENST00000506139	T;T;T	0.54479	1.31;0.57;1.31	5.61	1.85	0.25348	.	0.693519	0.14807	N	0.297283	T	0.27967	0.0689	N	0.10874	0.06	0.09310	N	1	B;B	0.14438	0.01;0.002	B;B	0.10450	0.005;0.002	T	0.20075	-1.0286	10	0.13853	T	0.58	-21.3728	7.9826	0.30192	0.0:0.0786:0.465:0.4564	.	439;474	B4DQW2;Q08J23	.;NSUN2_HUMAN	Q	474;238;439	ENSP00000264670:P474Q;ENSP00000444338:P238Q;ENSP00000420957:P439Q	ENSP00000264670:P474Q	P	-	2	0	NSUN2	6660400	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.243000	0.18106	0.459000	0.27016	-0.274000	0.10170	CCG	.	.		0.478	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		T	6607400	G	T	6607400	3	4	114	1	0	0	0	0	1	0	0	0	10687	1116	39	1	910	1	NSUN2	5	6607400	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10		6607400	174307860	357	18629										
MTRR	4552	hgsc.bcm.edu	37	chr5	7900115	7900115	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgaaaaactagaagcaatgAaaaccctggccactttaaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:7900115delA	ENST00000264668.2	+	15	2152	c.2122delA	c.(2122-2124)aaafs	p.K708fs	MTRR_ENST00000440940.2_Frame_Shift_Del_p.K681fs	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	708					cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	AGAAGCAATGAAAACCCTGGC	0.353																																					p.M707fs		Atlas-INDEL	.											.	MTRR	74	.	0			c.2121delG						.						89	93	92					5																	7900115		2203	4300	6503	SO:0001589	frameshift_variant	4552	exon15			.	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.2122delA	chr5.hg19:g.7900115delA	ENSP00000264668:p.Lys708fs	150.0	0.0		132.0	10.0	NM_024010	O60471|Q32MA9|Q7Z4M8	Frame_Shift_Del	DEL	ENST00000264668.2	hg19	CCDS3874.1																																																																																			.	.		0.353	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			-	7900115	A	-	7900115	7	5	114	1	0	1	0	1	0	0	0	0	9970	247	9	0	2180	0	MTRR	5	7900115	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1292715	7900115	173015145	358	18630										
MYO10	4651	hgsc.bcm.edu	37	chr5	16763789	16763789	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atattctagttgttctaaagAaaaaatatgcttgttgaagt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:16763789delA	ENST00000513610.1	-	13	1856	c.1402delT	c.(1402-1404)tctfs	p.S468fs		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	468	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						TGTTCTAAAGAAAAAATATGC	0.323																																					p.S468fs		Atlas-INDEL	.											.	MYO10	198	.	0			c.1403delC						.						64	60	61					5																	16763789		1802	4068	5870	SO:0001589	frameshift_variant	4651	exon13			.	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.1402delT	chr5.hg19:g.16763789delA	ENSP00000421280:p.Ser468fs	211.0	0.0		232.0	14.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Frame_Shift_Del	DEL	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.323	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		-	16763789	A	-	16763789	7	5	114	1	0	1	0	1	0	0	0	0	10071	246	9	0	4890	0	MYO10	5	16763789	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	8863674	16763789	164151471	359	18631										
CDH10	1008	hgsc.bcm.edu	37	chr5	24488013	24488013	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cattaatgaaatcccggacgTccgtgttatctggagctgta	10	9	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:24488013T>C	ENST00000264463.4	-	12	2633	c.2126A>G	c.(2125-2127)gAc>gGc	p.D709G	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	709					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		ATCCCGGACGTCCGTGTTATC	0.468										HNSCC(23;0.051)																											p.D709G		Atlas-SNP	.											.	CDH10	391	.	0			c.A2126G						.						83	89	87					5																	24488013		2203	4300	6503	SO:0001583	missense	1008	exon12			CGGACGTCCGTGT	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.2126A>G	chr5.hg19:g.24488013T>C	ENSP00000264463:p.Asp709Gly	115.0	0.0		119.0	7.0	NM_006727	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	hg19	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.988638	0.74589	.	.	ENSG00000040731	ENST00000264463	T	0.79247	-1.25	5.41	5.41	0.78517	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.81283	0.4790	M	0.81682	2.555	0.54753	D	0.999983	P	0.38617	0.64	B	0.41764	0.366	T	0.83225	-0.0066	10	0.54805	T	0.06	.	14.6395	0.68714	0.0:0.0:0.0:1.0	.	709	Q9Y6N8	CAD10_HUMAN	G	709	ENSP00000264463:D709G	ENSP00000264463:D709G	D	-	2	0	CDH10	24523770	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	6.177000	0.71961	2.058000	0.61347	0.533000	0.62120	GAC	.	.		0.468	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		C	24488013	T	C	24488013	3	2	114	1	0	0	0	0	1	0	0	0	3098	1667	58	2	244	2	CDH10	5	24488013	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	7724224	24488013	156427247	360	18632										
C5orf33	133686	hgsc.bcm.edu	37	chr5	36226660	36226660	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctagacgaacctcaattcccTcattcctaggataaaaaagg	6	11	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:36226660T>C	ENST00000381937.4	-	3	394	c.395A>G	c.(394-396)gAg>gGg	p.E132G	NADK2_ENST00000282512.3_5'UTR|NADK2_ENST00000506945.1_5'UTR|NADK2_ENST00000514504.1_Missense_Mutation_p.E132G|NADK2_ENST00000397338.1_5'UTR	NM_001085411.1	NP_001078880.1	Q4G0N4	NAKD2_HUMAN	NAD kinase 2, mitochondrial	132					NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|NAD+ kinase activity (GO:0003951)|protein homodimerization activity (GO:0042803)										CTCAATTCCCTCATTCCTAGG	0.368																																					p.E132G		Atlas-SNP	.											.	NADKD1	47	.	0			c.A395G						.						132	120	124					5																	36226660		1853	4088	5941	SO:0001583	missense	133686	exon3			ATTCCCTCATTCC	BC062567	CCDS3917.1, CCDS47197.1, CCDS75235.1	5p13.2	2013-04-30	2013-04-30	2013-04-30	ENSG00000152620	ENSG00000152620			26404	protein-coding gene	gene with protein product	"mitochondrial NAD kinase"	615787	"chromosome 5 open reading frame 33", "NAD kinase domain containing 1"	C5orf33, NADKD1		23616928	Standard	NM_001085411		Approved	FLJ30596, MNADK	uc003jkf.4	Q4G0N4	OTTHUMG00000131105	ENST00000381937.4:c.395A>G	chr5.hg19:g.36226660T>C	ENSP00000371362:p.Glu132Gly	50.0	0.0		69.0	4.0	NM_001085411	B5MC93|Q6UTX5|Q96NM0	Missense_Mutation	SNP	ENST00000381937.4	hg19	CCDS47197.1	.	.	.	.	.	.	.	.	.	.	T	14.12	2.440998	0.43326	.	.	ENSG00000152620	ENST00000381937;ENST00000514504	T;T	0.42513	0.97;0.97	5.96	5.96	0.96718	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	.	.	.	.	T	0.29355	0.0731	N	0.05124	-0.11	0.48901	D	0.999721	P	0.43826	0.818	P	0.45449	0.481	T	0.15723	-1.0427	9	0.26408	T	0.33	.	15.4164	0.74974	0.0:0.0:0.0:1.0	.	132	Q4G0N4	NAKD1_HUMAN	G	132	ENSP00000371362:E132G;ENSP00000421029:E132G	ENSP00000371362:E132G	E	-	2	0	NADKD1	36262417	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	4.223000	0.58587	2.270000	0.75569	0.533000	0.62120	GAG	.	.		0.368	NADK2-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367541.1	NM_153013		C	36226660	T	C	36226660	3	2	114	1	0	0	0	0	1	0	0	0	2294	1551	54	2	973	2	C5orf33	5	36226660	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	11738647	36226660	144688600	361	18633										
NIPBL	25836	hgsc.bcm.edu	37	chr5	36975946	36975946	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacctcgagatgttccaccaGatatcttgctagattctcca	6	13	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:36975946G>A	ENST00000282516.8	+	9	1436	c.937G>A	c.(937-939)Gat>Aat	p.D313N	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Missense_Mutation_p.D313N	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	313					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TGTTCCACCAGATATCTTGCT	0.383																																					p.D313N		Atlas-SNP	.											.	NIPBL	513	.	0			c.G937A						.						104	108	107					5																	36975946		2203	4300	6503	SO:0001583	missense	25836	exon9			CCACCAGATATCT	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.937G>A	chr5.hg19:g.36975946G>A	ENSP00000282516:p.Asp313Asn	82.0	0.0		93.0	4.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	hg19	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.047233	0.75846	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.96265	-3.94;-3.96	5.14	5.14	0.70334	.	0.141527	0.46758	D	0.000269	D	0.95730	0.8611	L	0.29908	0.895	0.38104	D	0.937345	D;D	0.64830	0.99;0.994	P;P	0.54759	0.58;0.76	D	0.97291	0.9924	10	0.66056	D	0.02	.	18.5966	0.91231	0.0:0.0:1.0:0.0	.	313;313	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	N	313	ENSP00000282516:D313N;ENSP00000406266:D313N	ENSP00000282516:D313N	D	+	1	0	NIPBL	37011703	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.703000	0.91344	2.390000	0.81377	0.467000	0.42956	GAT	.	.		0.383	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		A	36975946	G	A	36975946	3	1	114	1	0	0	0	0	1	0	0	0	10437	942	33	3	967	3	NIPBL	5	36975946	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	749286	36975946	143939314	362	18634										
NUP155	9631	hgsc.bcm.edu	37	chr5	37309279	37309279	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaggtccacttgattgctaaTtttttgatattcctttaatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:37309279delT	ENST00000231498.3	-	24	2922	c.2719delA	c.(2719-2721)attfs	p.I907fs	NUP155_ENST00000513532.1_Frame_Shift_Del_p.I843fs|NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000381843.2_Frame_Shift_Del_p.I848fs	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	907					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGATTGCTAATTTTTTGATAT	0.343																																					p.I907fs		Atlas-INDEL	.											.	NUP155	116	.	0			c.2720delT						.						159	152	154					5																	37309279		2203	4300	6503	SO:0001589	frameshift_variant	9631	exon24			.	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.2719delA	chr5.hg19:g.37309279delT	ENSP00000231498:p.Ile907fs	166.0	0.0		150.0	11.0	NM_153485	Q9UBE9|Q9UFL5	Frame_Shift_Del	DEL	ENST00000231498.3	hg19	CCDS3921.1																																																																																			.	.		0.343	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		-	37309279	T	-	37309279	7	5	114	1	0	1	0	1	0	0	0	0	10765	1493	52	0	1504	0	NUP155	5	37309279	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	333333	37309279	143605981	363	18635										
DAB2	1601	hgsc.bcm.edu	37	chr5	39377005	39377005	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcactggagatgtccttgggAgggccagctctgggaggtgg	18	8	2	1	rs538907566		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:39377005A>G	ENST00000320816.6	-	12	2351	c.1884T>C	c.(1882-1884)ccT>ccC	p.P628P	DAB2_ENST00000339788.6_Silent_p.P410P|DAB2_ENST00000545653.1_Silent_p.P607P|DAB2_ENST00000509337.1_Silent_p.P607P	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	628	Sufficient for interaction with GRB2. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			TGTCCTTGGGAGGGCCAGCTC	0.527											OREG0016586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1	0.000199681	8e-04	0	5008	,	,		19965	0		0	False		,,,				2504	0				p.P628P		Atlas-SNP	.											DAB2,lower_third,carcinoma,0,1	DAB2	124	.	0			c.T1884C						.						76	90	85					5																	39377005		2203	4300	6503	SO:0001819	synonymous_variant	1601	exon12			CTTGGGAGGGCCA	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1884T>C	chr5.hg19:g.39377005A>G		98.0	0.0	885	143.0	6.0	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	hg19	CCDS34149.1																																																																																			.	.		0.527	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		G	39377005	A	G	39377005	2	3	114	1	0	0	0	0	0	0	0	1	4220	291	11	2		2	DAB2	5	39377005	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2067726	39377005	141538255	364	18636										
FBXO4	26272	hgsc.bcm.edu	37	chr5	41927229	41927229	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atccaattctgtggagatacTttttgttgagggatcttcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:41927229delT	ENST00000281623.3	+	2	360	c.304delT	c.(304-306)tttfs	p.F102fs	FBXO4_ENST00000296812.2_Frame_Shift_Del_p.F102fs|FBXO4_ENST00000509134.1_Frame_Shift_Del_p.F102fs	NM_012176.2	NP_036308.1	Q9UKT5	FBX4_HUMAN	F-box protein 4	102	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|telomere maintenance (GO:0000723)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(11)|prostate(1)|stomach(1)|urinary_tract(2)	27		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				GTGGAGATACTTTTTGTTGAG	0.378																																					p.Y101fs		Atlas-INDEL	.											.	FBXO4	42	.	0			c.303delC						.						183	180	181					5																	41927229		2203	4300	6503	SO:0001589	frameshift_variant	26272	exon2			.	AF129534	CCDS3938.1, CCDS3939.1, CCDS75238.1	5p12	2008-02-05	2004-06-15		ENSG00000151876	ENSG00000151876		"F-boxes /  "other""	13583	protein-coding gene	gene with protein product		609090	"F-box only protein 4"			10531035, 10531037	Standard	NM_033484		Approved	FBX4	uc003jmq.3	Q9UKT5	OTTHUMG00000094799	ENST00000281623.3:c.304delT	chr5.hg19:g.41927229delT	ENSP00000281623:p.Phe102fs	134.0	0.0		192.0	12.0	NM_033484	Q68CU8|Q86VT8|Q9UK98	Frame_Shift_Del	DEL	ENST00000281623.3	hg19	CCDS3938.1																																																																																			.	.		0.378	FBXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211614.1			-	41927229	T	-	41927229	7	5	114	1	0	1	0	1	0	0	0	0	5756	1609	56	0	310	0	FBXO4	5	41927229	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2550224	41927229	138988031	365	18637										
MGC42105	167359	hgsc.bcm.edu	37	chr5	43245927	43245927	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctggtgaacccccactatgCccggtgggatcggcgcgaca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:43245927delC	ENST00000512796.1	+	2	1549	c.50delC	c.(49-51)gccfs	p.A17fs	NIM1_ENST00000326035.2_Frame_Shift_Del_p.A17fs			Q8IY84	NIM1_HUMAN		17					protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)										CCCCACTATGCCCGGTGGGAT	0.607																																					p.A17fs		Atlas-INDEL	.											.	.	.	.	0			c.49delG						.						123	117	119					5																	43245927		2203	4300	6503	SO:0001589	frameshift_variant	0	exon2			.																												ENST00000512796.1:c.50delC	chr5.hg19:g.43245927delC	ENSP00000420849:p.Ala17fs	170.0	0.0		170.0	11.0	NM_153361	B3KVM1	Frame_Shift_Del	DEL	ENST00000512796.1	hg19	CCDS3943.1																																																																																			.	.		0.607	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1			-	43245927	C	-	43245927	7	5	114	1	0	1	0	1	0	0	0	0	9561	739	26	0	52	0	MGC42105	5	43245927	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1318698	43245927	137669333	366	18638										
HCN1	348980	hgsc.bcm.edu	37	chr5	45262631	45262631	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgacaggatggctgatggctGgggggtctgtgtgctgggac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:45262631delG	ENST00000303230.4	-	8	2122	c.2065delC	c.(2065-2067)cagfs	p.Q689fs		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	689					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						GCTGATGGCTGGGGGGTCTGT	0.637																																					p.Q689fs		Atlas-INDEL	.											.	HCN1	298	.	0			c.2066delA						.						82	82	82					5																	45262631		2203	4300	6503	SO:0001589	frameshift_variant	348980	exon8			.	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.2065delC	chr5.hg19:g.45262631delG	ENSP00000307342:p.Gln689fs	158.0	0.0		182.0	11.0	NM_021072		Frame_Shift_Del	DEL	ENST00000303230.4	hg19	CCDS3952.1																																																																																			.	.		0.637	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		-	45262631	G	-	45262631	7	5	114	1	0	1	0	1	0	0	0	0	7005	1357	47	0	611	0	HCN1	5	45262631	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2016704	45262631	135652629	367	18639										
SLC38A9	153129	hgsc.bcm.edu	37	chr5	54952575	54952575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tattggtactcagtatagtgTctgtgtcattaatgtgatga	10	4	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:54952575T>C	ENST00000396865.2	-	9	1316	c.725A>G	c.(724-726)gAc>gGc	p.D242G	SLC38A9_ENST00000515629.1_Missense_Mutation_p.D179G|SLC38A9_ENST00000539768.1_Missense_Mutation_p.D242G|SLC38A9_ENST00000512595.1_Missense_Mutation_p.D215G|SLC38A9_ENST00000416547.2_Missense_Mutation_p.D118G|SLC38A9_ENST00000318672.3_Missense_Mutation_p.D242G	NM_173514.3	NP_775785.2	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	242					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				CAGTATAGTGTCTGTGTCATT	0.313																																					p.D242G		Atlas-SNP	.											.	SLC38A9	50	.	0			c.A725G						.						105	102	103					5																	54952575		2201	4298	6499	SO:0001583	missense	153129	exon9			ATAGTGTCTGTGT		CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058		"Solute carriers"	26907	protein-coding gene	gene with protein product							Standard	NM_173514		Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000396865.2:c.725A>G	chr5.hg19:g.54952575T>C	ENSP00000380074:p.Asp242Gly	87.0	0.0		88.0	4.0	NM_173514	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	Missense_Mutation	SNP	ENST00000396865.2	hg19	CCDS3968.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.520895	0.44866	.	.	ENSG00000177058	ENST00000396865;ENST00000318672;ENST00000539768;ENST00000515629;ENST00000416547;ENST00000512595;ENST00000512208	T;T;T;T;T;T;T	0.48836	1.87;1.87;0.84;1.9;1.91;1.4;0.8	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	T	0.47040	0.1424	M	0.65975	2.015	0.80722	D	1	B;B	0.29162	0.003;0.235	B;B	0.29524	0.016;0.103	T	0.39272	-0.9622	10	0.19590	T	0.45	-17.3328	14.7662	0.69640	0.0:0.0:0.0:1.0	.	215;242	B3KXV1;Q8NBW4	.;S38A9_HUMAN	G	242;242;242;179;118;215;179	ENSP00000380074:D242G;ENSP00000316596:D242G;ENSP00000437771:D242G;ENSP00000420934:D179G;ENSP00000397429:D118G;ENSP00000427335:D215G;ENSP00000426413:D179G	ENSP00000316596:D242G	D	-	2	0	SLC38A9	54988332	1.000000	0.71417	0.939000	0.37840	0.912000	0.54170	5.082000	0.64450	2.301000	0.77427	0.523000	0.50628	GAC	.	.		0.313	SLC38A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253912.2	NM_173514		C	54952575	T	C	54952575	3	2	114	1	0	0	0	0	1	0	0	0	14626	1667	58	2	992	2	SLC38A9	5	54952575	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	9689944	54952575	125962685	368	18640										
PLK2	10769	hgsc.bcm.edu	37	chr5	57753128	57753128	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatgaggacggcattgtataCcttgcttcccttatgcacct	8	11	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:57753128C>T	ENST00000274289.3	-	7	1188	c.888G>A	c.(886-888)agG>agA	p.R296R	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	296	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		GCATTGTATACCTTGCTTCCC	0.433																																					p.R296R		Atlas-SNP	.											.	PLK2	71	.	0			c.G888A						.						82	79	80					5																	57753128		2203	4300	6503	SO:0001819	synonymous_variant	10769	exon7			TGTATACCTTGCT		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"serum-inducible kinase"	607023	"polo-like kinase 2 (Drosophila)"				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.888G>A	chr5.hg19:g.57753128C>T		32.0	0.0		56.0	4.0	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	hg19	CCDS3974.1																																																																																			.	.		0.433	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		T	57753128	C	T	57753128	2	4	114	1	0	0	0	0	0	0	0	1	12105	506	18	3		3	PLK2	5	57753128	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	2800553	57753128	123162132	369	18641										
KIF2A	3796	hgsc.bcm.edu	37	chr5	61643927	61643927	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgaccttgttcctgatgaagAaattgaacccagtccagaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:61643927delA	ENST00000401507.3	+	3	523	c.212delA	c.(211-213)gaafs	p.E71fs	KIF2A_ENST00000506857.1_Frame_Shift_Del_p.E44fs|KIF2A_ENST00000407818.3_Frame_Shift_Del_p.E71fs|KIF2A_ENST00000381103.2_Frame_Shift_Del_p.E51fs|KIF2A_ENST00000509663.2_Intron	NM_001243953.1|NM_004520.4	NP_001230882.1|NP_004511.2	O00139	KIF2A_HUMAN	kinesin heavy chain member 2A	71	Globular. {ECO:0000255}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|nervous system development (GO:0007399)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	15		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		CCTGATGAAGAAATTGAACCC	0.403																																					p.E71fs		Atlas-INDEL	.											.	KIF2A	69	.	0			c.211delG						.						139	137	138					5																	61643927		2203	4300	6503	SO:0001589	frameshift_variant	3796	exon3			.	BC031828	CCDS3980.2, CCDS47216.1, CCDS58949.1	5q12-q13	2008-02-05	2006-09-26	2006-09-26	ENSG00000068796	ENSG00000068796		"Kinesins"	6318	protein-coding gene	gene with protein product		602591	"kinesin heavy chain member 2"	KIF2		9177777	Standard	NM_001098511		Approved	HK2	uc003jsz.4	O00139	OTTHUMG00000097755	ENST00000401507.3:c.212delA	chr5.hg19:g.61643927delA	ENSP00000385622:p.Glu71fs	123.0	0.0		170.0	11.0	NM_001243953	A5YM42|A5YM54|B4DY54|D3DW97|E9PB70|Q7Z5I3|Q8N5Q7	Frame_Shift_Del	DEL	ENST00000401507.3	hg19	CCDS3980.2																																																																																			.	.		0.403	KIF2A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317989.1	NM_004520		-	61643927	A	-	61643927	7	5	114	1	0	1	0	1	0	0	0	0	8306	246	9	0	222	0	KIF2A	5	61643927	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3890799	61643927	119271333	370	18642										
SFRS12IP1	285672	hgsc.bcm.edu	37	chr5	64050152	64050152	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaatacttacggtagccacaTtttttacagcctgctctgac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:64050152delT	ENST00000513458.4	-	2	218	c.51delA	c.(49-51)aaafs	p.K17fs	SREK1IP1_ENST00000506252.1_5'UTR	NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	17					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						GGTAGCCACATTTTTTACAGC	0.353																																					p.C18fs		Atlas-INDEL	.											.	SREK1IP1	28	.	0			c.52delT						.						93	86	89					5																	64050152		2203	4300	6503	SO:0001589	frameshift_variant	285672	exon2			.	AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006			26716	protein-coding gene	gene with protein product	"p18 splicing regulatory protein"		"SFRS12-interacting protein 1"	SFRS12IP1		15456940	Standard	NM_173829		Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.51delA	chr5.hg19:g.64050152delT	ENSP00000427401:p.Lys17fs	175.0	0.0		243.0	17.0	NM_173829	Q32NC8	Frame_Shift_Del	DEL	ENST00000513458.4	hg19	CCDS34171.1																																																																																			.	.		0.353	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829		-	64050152	T	-	64050152	7	5	114	1	0	1	0	1	0	0	0	0	14183	1490	52	0	432	0	SFRS12IP1	5	64050152	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2406225	64050152	116865108	371	18643										
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67575562	67575565	+	Splice_Site	DEL	GTTT	GTTT	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatgatttctttagctccagGtttgttttttctcttctggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	GTTT	GTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:67575562_67575565delGTTT	ENST00000521381.1	+	5	1250		c.e5+1		PIK3R1_ENST00000396611.1_Splice_Site|PIK3R1_ENST00000274335.5_Splice_Site|PIK3R1_ENST00000521657.1_Splice_Site	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TTAGCTCCAGGTTTGTTTTTTCTC	0.397			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.212_212del		Atlas-Indel,Pindel	.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1	869	.	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	c.634_634del						.																																			SO:0001630	splice_region_variant	5295	exon5			.	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.634+1GTTT>-	chr5.hg19:g.67575566_67575569delGTTT		127.0	0.0		159.0	34.0	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Frame_Shift_Del	DEL	ENST00000521381.1	hg19	CCDS3993.1																																																																																			.	.		0.397	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	Intron	-	67575565	GTTT	-	67575562	8	5	114	1	0	1	0	1	0	0	1	0	11927	1275	44	0	649	0	PIK3R1	5	67575562	Splice_Site	DEL	GTTT	TCGA-DD-A3A0-01A-11D-A20W-10	3525410	67575562	113339698	372	18644										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71494401	71494401	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttctgctcataccccttctcAgatcgcttctcctctccaag	4	17	5	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:71494401A>G	ENST00000296755.7	+	5	5517	c.5219A>G	c.(5218-5220)cAg>cGg	p.Q1740R		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1740					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ACCCCTTCTCAGATCGCTTCT	0.493																																					p.Q1740R	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A5219G						.						153	160	158					5																	71494401		2203	4300	6503	SO:0001583	missense	4131	exon5			CTTCTCAGATCGC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.5219A>G	chr5.hg19:g.71494401A>G	ENSP00000296755:p.Gln1740Arg	75.0	0.0		126.0	6.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	13.76	2.334459	0.41297	.	.	ENSG00000131711	ENST00000296755	T	0.03801	3.8	5.0	5.0	0.66597	.	0.000000	0.64402	D	0.000012	T	0.06005	0.0156	L	0.29908	0.895	0.54753	D	0.999989	P;P	0.47106	0.89;0.791	P;B	0.45232	0.474;0.272	T	0.35001	-0.9806	10	0.59425	D	0.04	-18.8371	11.6428	0.51244	0.8516:0.1484:0.0:0.0	.	1614;1740	A2BDK6;P46821	.;MAP1B_HUMAN	R	1740	ENSP00000296755:Q1740R	ENSP00000296755:Q1740R	Q	+	2	0	MAP1B	71530157	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.877000	0.75562	2.015000	0.59207	0.368000	0.22195	CAG	.	.		0.493	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		G	71494401	A	G	71494401	3	3	114	1	0	0	0	0	1	0	0	0	9237	188	7	2	5237	2	MAP1B	5	71494401	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3918839	71494401	109420859	373	18645										
ZNF366	167465	hgsc.bcm.edu	37	chr5	71739993	71739993	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtggctgccctgggcactctCcccgtctgactggaacaccg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:71739993delC	ENST00000318442.5	-	5	2315	c.1825delG	c.(1825-1827)gagfs	p.E609fs	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	609	Interaction with CTBP1.|Interaction with NRIP1.				negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TGGGCACTCTCCCCGTCTGAC	0.657																																					p.E609fs		Atlas-INDEL	.											.	ZNF366	108	.	0			c.1826delA						.						59	70	66					5																	71739993		2203	4299	6502	SO:0001589	frameshift_variant	167465	exon5			.	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"Zinc fingers, C2H2-type"	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.1825delG	chr5.hg19:g.71739993delC	ENSP00000313158:p.Glu609fs	122.0	0.0		141.0	10.0	NM_152625	Q5HYI9|Q7RTV4	Frame_Shift_Del	DEL	ENST00000318442.5	hg19	CCDS4015.1																																																																																			.	.		0.657	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			-	71739993	C	-	71739993	7	5	114	1	0	1	0	1	0	0	0	0	17885	864	30	0	413	0	ZNF366	5	71739993	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	245592	71739993	109175267	374	18646										
TMEM171	134285	hgsc.bcm.edu	37	chr5	72424240	72424240	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actcggtaataatatttccaCcccctccaccaccttacttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:72424240delC	ENST00000454765.2	+	3	1137	c.664delC	c.(664-666)cccfs	p.P226fs	TMEM171_ENST00000287773.5_Frame_Shift_Del_p.P226fs			Q8WVE6	TM171_HUMAN	transmembrane protein 171	226						integral component of membrane (GO:0016021)				endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|stomach(1)	15		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.87e-54)|Lung(70;0.115)		AATATTTCCACCCCCTCCACC	0.403																																					p.P221fs	NSCLC(112;638 2280 27369 30736)	Atlas-INDEL	.											.	TMEM171	41	.	0			c.663delA						.		,	11,4255		5,1,2127	209	211	210		,	-7	0.6	5		210	38,8214		18,2,4106	no	frameshift,frameshift	TMEM171	NM_173490.6,NM_001161342.1	,	23,3,6233	A1A1,A1R,RR		0.4605,0.2579,0.3914	,	,	72424240	49,12469	2203	4300	6503	SO:0001589	frameshift_variant	134285	exon3			.	BC018083	CCDS4017.1, CCDS54869.1	5q13.2	2008-02-05			ENSG00000157111	ENSG00000157111			27031	protein-coding gene	gene with protein product						12477932	Standard	NM_173490		Approved	PRP2	uc003kcm.2	Q8WVE6	OTTHUMG00000131269	ENST00000454765.2:c.664delC	chr5.hg19:g.72424240delC	ENSP00000415030:p.Pro226fs	196.0	0.0		220.0	15.0	NM_001161342	Q8N0S1|Q8TDT7	Frame_Shift_Del	DEL	ENST00000454765.2	hg19	CCDS4017.1																																																																																			.	.		0.403	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490		-	72424240	C	-	72424240	7	5	114	1	0	1	0	1	0	0	0	0	16103	507	18	0	670	0	TMEM171	5	72424240	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	684247	72424240	108491020	375	18647										
UTP15	84135	hgsc.bcm.edu	37	chr5	72864105	72864105	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgcagtttcaaaagtagacTtttctcctcagcctccatat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:72864105delT	ENST00000296792.4	+	3	391	c.136delT	c.(136-138)tttfs	p.F46fs	UTP15_ENST00000508491.1_Intron|ANKRA2_ENST00000296785.3_5'Flank|UTP15_ENST00000543251.1_5'UTR	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	46					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		AAAAGTAGACTTTTCTCCTCA	0.308																																					p.D45fs		Atlas-INDEL	.											.	UTP15	30	.	0			c.135delC						.						75	80	79					5																	72864105		2203	4299	6502	SO:0001589	frameshift_variant	84135	exon3			.	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"WD repeat domain containing"	25758	protein-coding gene	gene with protein product			"UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.136delT	chr5.hg19:g.72864105delT	ENSP00000296792:p.Phe46fs	171.0	0.0		249.0	17.0	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Frame_Shift_Del	DEL	ENST00000296792.4	hg19	CCDS34186.1																																																																																			.	.		0.308	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175		-	72864105	T	-	72864105	7	5	114	1	0	1	0	1	0	0	0	0	17112	1609	56	0	142	0	UTP15	5	72864105	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	439865	72864105	108051155	376	18648										
UTP15	84135	hgsc.bcm.edu	37	chr5	72874641	72874641	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tatgacagggatctgaaacaTtttcggatctctaaggcact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:72874641delT	ENST00000296792.4	+	10	1365	c.1110delT	c.(1108-1110)catfs	p.H370fs	UTP15_ENST00000508491.1_Frame_Shift_Del_p.H351fs|UTP15_ENST00000543251.1_Frame_Shift_Del_p.H180fs	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	370					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		ATCTGAAACATTTTCGGATCT	0.358																																					p.H370fs		Atlas-INDEL	.											.	UTP15	30	.	0			c.1109delA						.						120	123	122					5																	72874641		2203	4300	6503	SO:0001589	frameshift_variant	84135	exon10			.	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"WD repeat domain containing"	25758	protein-coding gene	gene with protein product			"UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.1110delT	chr5.hg19:g.72874641delT	ENSP00000296792:p.His370fs	128.0	0.0		147.0	10.0	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Frame_Shift_Del	DEL	ENST00000296792.4	hg19	CCDS34186.1																																																																																			.	.		0.358	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175		-	72874641	T	-	72874641	7	5	114	1	0	1	0	1	0	0	0	0	17112	1490	52	0	1144	0	UTP15	5	72874641	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	10536	72874641	108040619	377	18649										
DMGDH	29958	hgsc.bcm.edu	37	chr5	78324266	78324266	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaatcttaccagtataagaTatcctaatagcagtgacagg	7	9	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:78324266T>C	ENST00000255189.3	-	12	2050	c.2022A>G	c.(2020-2022)atA>atG	p.I674M	DMGDH_ENST00000380311.4_Missense_Mutation_p.I473M|DMGDH_ENST00000540686.1_Missense_Mutation_p.I294M	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	674					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		CAGTATAAGATATCCTAATAG	0.313																																					p.I674M		Atlas-SNP	.											DMGDH,NS,carcinoma,0,1	DMGDH	88	.	0			c.A2022G						.						51	53	52					5																	78324266		2203	4300	6503	SO:0001583	missense	29958	exon12			ATAAGATATCCTA	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.2022A>G	chr5.hg19:g.78324266T>C	ENSP00000255189:p.Ile674Met	57.0	0.0		66.0	3.0	NM_013391	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	hg19	CCDS4044.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.057417	0.36277	.	.	ENSG00000132837	ENST00000255189;ENST00000523732;ENST00000380311;ENST00000540686;ENST00000539598	T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87	5.81	1.95	0.26073	Glycine cleavage T-protein, N-terminal (1);	0.042826	0.85682	D	0.000000	T	0.68714	0.3031	L	0.48877	1.53	0.41589	D	0.988787	P;P;B;B	0.42735	0.788;0.753;0.164;0.198	P;B;B;B	0.45167	0.472;0.281;0.138;0.217	T	0.64918	-0.6294	10	0.52906	T	0.07	.	8.8284	0.35069	0.1183:0.0:0.4305:0.4511	.	294;473;524;674	B4E1J9;F8W6P8;F5H1C7;Q9UI17	.;.;.;M2GD_HUMAN	M	674;513;473;294;524	ENSP00000255189:I674M;ENSP00000430972:I513M;ENSP00000369667:I473M;ENSP00000439478:I294M	ENSP00000255189:I674M	I	-	3	3	DMGDH	78360022	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.772000	0.38552	0.092000	0.17331	0.533000	0.62120	ATA	.	.		0.313	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391		C	78324266	T	C	78324266	3	2	114	1	0	0	0	0	1	0	0	0	4583	1396	49	2	598	2	DMGDH	5	78324266	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	5449625	78324266	102590994	378	18650										
RASGRF2	5924	hgsc.bcm.edu	37	chr5	80475996	80475996	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtttctttttctcctaaggcTttaacaacaccgagagaaca	6	10	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:80475996T>C	ENST00000265080.4	+	18	2756	c.2689T>C	c.(2689-2691)Ttt>Ctt	p.F897L		NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	897					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		CTCCTAAGGCTTTAACAACAC	0.438																																					p.F897L		Atlas-SNP	.											.	RASGRF2	165	.	0			c.T2689C						.						174	169	171					5																	80475996		2203	4300	6503	SO:0001583	missense	5924	exon18			TAAGGCTTTAACA	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.2689T>C	chr5.hg19:g.80475996T>C	ENSP00000265080:p.Phe897Leu	89.0	0.0		89.0	4.0	NM_006909	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	hg19	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.006545	0.74932	.	.	ENSG00000113319	ENST00000265080	T	0.27890	1.64	5.93	5.93	0.95920	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (1);	0.099192	0.64402	D	0.000001	T	0.48447	0.1500	M	0.62016	1.91	0.58432	D	0.999998	D	0.69078	0.997	D	0.70716	0.97	T	0.41466	-0.9507	10	0.08179	T	0.78	.	15.3582	0.74443	0.0:0.0:0.0:1.0	.	897	O14827	RGRF2_HUMAN	L	897	ENSP00000265080:F897L	ENSP00000265080:F897L	F	+	1	0	RASGRF2	80511752	1.000000	0.71417	0.961000	0.40146	0.282000	0.26991	7.338000	0.79269	2.270000	0.75569	0.460000	0.39030	TTT	.	.		0.438	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		C	80475996	T	C	80475996	3	2	114	1	0	0	0	0	1	0	0	0	13088	1609	56	2	2759	2	RASGRF2	5	80475996	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2151730	80475996	100439264	379	18651										
CKMT2	1160	hgsc.bcm.edu	37	chr5	80552810	80552810	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccgtgactggccagatgccaGgggaatctggtatggatgca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:80552810delG	ENST00000424301.2	+	7	984	c.746delG	c.(745-747)aggfs	p.R249fs	CKMT2-AS1_ENST00000501927.2_RNA|CKMT2_ENST00000437669.1_Frame_Shift_Del_p.R249fs|CKMT2-AS1_ENST00000500148.2_RNA|CKMT2_ENST00000254035.4_Frame_Shift_Del_p.R249fs|CKMT2-AS1_ENST00000512287.1_RNA|CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000505295.1_RNA|CKMT2-AS1_ENST00000502041.2_RNA	NM_001825.2	NP_001816.2	P17540	KCRS_HUMAN	creatine kinase, mitochondrial 2 (sarcomeric)	249	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(4)|urinary_tract(1)	17		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	CCAGATGCCAGGGGAATCTGG	0.468																																					p.R249fs		Atlas-INDEL	.											.	CKMT2	44	.	0			c.745delA						.						112	105	108					5																	80552810		2203	4300	6503	SO:0001589	frameshift_variant	1160	exon7			.		CCDS4053.1	5q14.1	2013-09-20			ENSG00000131730	ENSG00000131730	2.7.3.2		1996	protein-coding gene	gene with protein product		123295				2324105	Standard	NM_001825		Approved	SMTCK	uc003khd.4	P17540	OTTHUMG00000119013	ENST00000424301.2:c.746delG	chr5.hg19:g.80552810delG	ENSP00000404203:p.Arg249fs	185.0	0.0		206.0	15.0	NM_001825	Q6ICS8|Q8N1E1	Frame_Shift_Del	DEL	ENST00000424301.2	hg19	CCDS4053.1																																																																																			.	.		0.468	CKMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369600.1	NM_001825		-	80552810	G	-	80552810	7	5	114	1	0	1	0	1	0	0	0	0	3453	1000	35	0	764	0	CKMT2	5	80552810	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	76814	80552810	100362450	380	18652										
ANKRD32	84250	hgsc.bcm.edu	37	chr5	93989080	93989080	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caagaaaggcgttgaacatgAaaaaataaaaagtaccttaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:93989080delA	ENST00000265140.5	+	8	1405	c.986delA	c.(985-987)gaafs	p.E329fs		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	329						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		GTTGAACATGAAAAAATAAAA	0.308																																					p.E329fs		Atlas-INDEL	.											.	ANKRD32	117	.	0			c.985delG						.						149	132	137					5																	93989080		692	1591	2283	SO:0001589	frameshift_variant	84250	exon8			.	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"Ankyrin repeat domain containing"	25408	protein-coding gene	gene with protein product			"BRCT domain containing 1"	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.986delA	chr5.hg19:g.93989080delA	ENSP00000265140:p.Glu329fs	133.0	0.0		213.0	16.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Frame_Shift_Del	DEL	ENST00000265140.5	hg19	CCDS4071.2																																																																																			.	.		0.308	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290		-	93989080	A	-	93989080	7	5	114	1	0	1	0	1	0	0	0	0	660	246	9	0	1012	0	ANKRD32	5	93989080	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	13436270	93989080	86926180	381	18653										
ANKRD32	84250	hgsc.bcm.edu	37	chr5	94030556	94030556	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcccagtgcttttacaacagAggaatgctaagggagaattg	12	7	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:94030556A>G	ENST00000265140.5	+	21	3135	c.2716A>G	c.(2716-2718)Agg>Ggg	p.R906G	ANKRD32_ENST00000493934.1_Intron	NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	906						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		TTTACAACAGAGGAATGCTAA	0.368																																					p.R906G		Atlas-SNP	.											.	ANKRD32	117	.	0			c.A2716G						.						88	88	88					5																	94030556		2203	4298	6501	SO:0001583	missense	84250	exon21			CAACAGAGGAATG	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"Ankyrin repeat domain containing"	25408	protein-coding gene	gene with protein product			"BRCT domain containing 1"	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.2716A>G	chr5.hg19:g.94030556A>G	ENSP00000265140:p.Arg906Gly	114.0	0.0		97.0	5.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Missense_Mutation	SNP	ENST00000265140.5	hg19	CCDS4071.2	.	.	.	.	.	.	.	.	.	.	A	20.7	4.032548	0.75504	.	.	ENSG00000133302	ENST00000265140	T	0.71934	-0.61	5.62	5.62	0.85841	Ankyrin repeat-containing domain (3);	0.225578	0.46758	D	0.000278	T	0.81384	0.4811	M	0.74647	2.275	0.37407	D	0.913074	D	0.57257	0.979	P	0.57846	0.828	D	0.86007	0.1498	10	0.66056	D	0.02	.	15.823	0.78673	1.0:0.0:0.0:0.0	.	906	Q9BQI6	ANR32_HUMAN	G	906	ENSP00000265140:R906G	ENSP00000265140:R906G	R	+	1	2	ANKRD32	94056312	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	6.352000	0.73027	2.149000	0.67028	0.477000	0.44152	AGG	.	.		0.368	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290		G	94030556	A	G	94030556	3	3	114	1	0	0	0	0	1	0	0	0	660	295	11	2	2794	2	ANKRD32	5	94030556	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	41476	94030556	86884704	382	18654										
ELL2	22936	hgsc.bcm.edu	37	chr5	95226880	95226880	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taaatcttctagctacagtcTccatcctggcatgcaaagct	6	12	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:95226880T>C	ENST00000237853.4	-	10	2037	c.1688A>G	c.(1687-1689)gAg>gGg	p.E563G	ELL2_ENST00000431061.2_Missense_Mutation_p.E313G	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	563					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		AGCTACAGTCTCCATCCTGGC	0.408																																					p.E563G		Atlas-SNP	.											.	ELL2	63	.	0			c.A1688G						.						189	181	183					5																	95226880		2203	4298	6501	SO:0001583	missense	22936	exon10			ACAGTCTCCATCC	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1688A>G	chr5.hg19:g.95226880T>C	ENSP00000237853:p.Glu563Gly	143.0	0.0		149.0	7.0	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	hg19	CCDS4080.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.7|28.7	4.939091|4.939091	0.92526|0.92526	.|.	.|.	ENSG00000118985|ENSG00000118985	ENST00000237853;ENST00000431061|ENST00000508757	T;T|.	0.22743|.	1.94;1.94|.	6.16|6.16	6.16|6.16	0.99307|0.99307	Occludin/RNA polymerase II elongation factor, ELL domain (1);|.	0.087556|.	0.85682|.	D|.	0.000000|.	T|T	0.56848|0.56848	0.2013|0.2013	L|L	0.28458|0.28458	0.855|0.855	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.81914|.	0.995|.	T|T	0.52548|0.52548	-0.8561|-0.8561	10|5	0.48119|.	T|.	0.1|.	0.4799|0.4799	16.4675|16.4675	0.84087|0.84087	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	563|.	O00472|.	ELL2_HUMAN|.	G|G	563;313|81	ENSP00000237853:E563G;ENSP00000399704:E313G|.	ENSP00000237853:E563G|.	E|R	-|-	2|1	0|2	ELL2|ELL2	95252636|95252636	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.977000|7.977000	0.88081|0.88081	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	GAG|AGA	.	.		0.408	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		C	95226880	T	C	95226880	3	2	114	1	0	0	0	0	1	0	0	0	5065	1551	54	2	246	2	ELL2	5	95226880	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1196324	95226880	85688380	383	18655										
ERAP1	51752	hgsc.bcm.edu	37	chr5	96130756	96130756	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatctctaccttgtttgggtAggggatacggtatgctgaaa	12	6	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:96130756A>G	ENST00000443439.2	-	5	974	c.908T>C	c.(907-909)cTa>cCa	p.L303P	ERAP1_ENST00000296754.3_Missense_Mutation_p.L303P	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	303					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TTGTTTGGGTAGGGGATACGG	0.393																																					p.L303P		Atlas-SNP	.											.	ERAP1	59	.	0			c.T908C						.						76	72	73					5																	96130756		2203	4300	6503	SO:0001583	missense	51752	exon5			TTGGGTAGGGGAT	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.908T>C	chr5.hg19:g.96130756A>G	ENSP00000406304:p.Leu303Pro	77.0	0.0		116.0	5.0	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	hg19	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.294803	0.81025	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.04406	3.63;3.63	5.91	5.91	0.95273	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.64402	D	0.000001	T	0.38639	0.1048	H	0.98682	4.3	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.62234	-0.6897	10	0.87932	D	0	.	15.9979	0.80265	1.0:0.0:0.0:0.0	.	303;303;303	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	P	303	ENSP00000296754:L303P;ENSP00000406304:L303P	ENSP00000296754:L303P	L	-	2	0	ERAP1	96156512	1.000000	0.71417	0.999000	0.59377	0.891000	0.51852	8.760000	0.91671	2.252000	0.74401	0.528000	0.53228	CTA	.	.		0.393	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		G	96130756	A	G	96130756	3	3	114	1	0	0	0	0	1	0	0	0	5205	420	15	2	2010	2	ERAP1	5	96130756	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	903876	96130756	84784504	384	18656										
CHD1	1105	hgsc.bcm.edu	37	chr5	98207855	98207855	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattggaatcatcttctttgCcccagtctatatcaaaatga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:98207855delC	ENST00000284049.3	-	27	3910	c.3761delG	c.(3760-3762)ggcfs	p.G1254fs	CHD1_ENST00000511067.1_5'Flank	NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1254					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	ATCTTCTTTGCCCCAGTCTAT	0.368																																					p.G1254fs		Atlas-INDEL	.											.	CHD1	137	.	0			c.3762delC						.						109	108	109					5																	98207855		2203	4300	6503	SO:0001589	frameshift_variant	1105	exon27			.	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.3761delG	chr5.hg19:g.98207855delC	ENSP00000284049:p.Gly1254fs	128.0	0.0		181.0	11.0	NM_001270	Q17RZ3	Frame_Shift_Del	DEL	ENST00000284049.3	hg19	CCDS34204.1																																																																																			.	.		0.368	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		-	98207855	C	-	98207855	7	5	114	1	0	1	0	1	0	0	0	0	3325	739	26	0	1407	0	CHD1	5	98207855	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2077099	98207855	82707405	385	18657										
EPB41L4A	64097	hgsc.bcm.edu	37	chr5	111545590	111545590	+	Splice_Site	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcagttaacttcactgaccTttttactggtgaaggtgcaa					rs34402942		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:111545590delT	ENST00000261486.5	-	13	1453	c.1177delA	c.(1177-1179)agc>gc	p.S393fs	EPB41L4A_ENST00000507810.1_5'UTR|CTC-459M5.2_ENST00000506875.1_RNA|CTC-459M5.2_ENST00000505825.1_RNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	393						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TTCACTGACCTTTTTACTGGT	0.313																																					p.S393fs		Atlas-INDEL	.											.	EPB41L4A	130	.	0			c.1178delG						.						191	175	180					5																	111545590		1819	4083	5902	SO:0001630	splice_region_variant	64097	exon13			.	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1178+1A>-	chr5.hg19:g.111545590delT		89.0	0.0		152.0	10.0	NM_022140	A4FUI6	Frame_Shift_Del	DEL	ENST00000261486.5	hg19	CCDS43350.1																																																																																			.	.		0.313	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		Frame_Shift_Del	-	111545590	T	-	111545590	8	5	114	1	0	1	0	1	0	0	1	0	5157	1623	56	0	927	0	EPB41L4A	5	111545590	Splice_Site	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	13337735	111545590	69369670	386	18658										
APC	324	hgsc.bcm.edu	37	chr5	112164604	112164604	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcgagcagatgtaaatagtAaaaagacgttgcgagaagtt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:112164604delA	ENST00000457016.1	+	14	2058	c.1678delA	c.(1678-1680)aaafs	p.K561fs	APC_ENST00000508376.2_Frame_Shift_Del_p.K561fs|APC_ENST00000257430.4_Frame_Shift_Del_p.K561fs|CTC-554D6.1_ENST00000520401.1_Frame_Shift_Del_p.V55fs			P25054	APC_HUMAN	adenomatous polyposis coli	561	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGTAAATAGTAAAAAGACGTT	0.303		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.S559fs	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-INDEL	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	1	Unknown(1)	skin(1)	c.1677delT						.						124	134	131					5																	112164604		2202	4300	6502	SO:0001589	frameshift_variant	324	exon15	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	.	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1678delA	chr5.hg19:g.112164604delA	ENSP00000413133:p.Lys561fs	203.0	0.0		239.0	16.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.303	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112164604	A	-	112164604	7	5	114	1	0	1	0	1	0	0	0	0	763	363	13	0	1728	0	APC	5	112164604	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	619014	112164604	68750656	387	18659										
APC	324	hgsc.bcm.edu	37	chr5	112176345	112176345	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcacagtcaggtgaatttgAaaaacgagataccattccta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:112176345delA	ENST00000457016.1	+	16	5434	c.5054delA	c.(5053-5055)gaafs	p.E1685fs	APC_ENST00000508376.2_Frame_Shift_Del_p.E1685fs|APC_ENST00000257430.4_Frame_Shift_Del_p.E1685fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1685	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GGTGAATTTGAAAAACGAGAT	0.438		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.E1685fs	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-INDEL	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.5053delG						.						58	58	58					5																	112176345		2202	4300	6502	SO:0001589	frameshift_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	.	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5054delA	chr5.hg19:g.112176345delA	ENSP00000413133:p.Glu1685fs	104.0	0.0		114.0	11.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112176345	A	-	112176345	7	5	114	1	0	1	0	1	0	0	0	0	763	246	9	0	5112	0	APC	5	112176345	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	11741	112176345	68738915	388	18660										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112917159	112917159	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacagaagtggcatagcttaTttttacgccgaatgagagct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:112917159delT	ENST00000161863.4	+	25	3613	c.3400delT	c.(3400-3402)tttfs	p.F1134fs		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1134					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GCATAGCTTATTTTTACGCCG	0.388																																					p.L1133fs		Atlas-INDEL	.											.	YTHDC2	118	.	0			c.3399delA						.						110	104	106					5																	112917159		2202	4300	6502	SO:0001589	frameshift_variant	64848	exon25			.	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.3400delT	chr5.hg19:g.112917159delT	ENSP00000161863:p.Phe1134fs	178.0	0.0		246.0	15.0	NM_022828	B2RP66	Frame_Shift_Del	DEL	ENST00000161863.4	hg19	CCDS4113.1																																																																																			.	.		0.388	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		-	112917159	T	-	112917159	7	5	114	1	0	1	0	1	0	0	0	0	17512	1493	52	0	3498	0	YTHDC2	5	112917159	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	740814	112917159	67998101	389	18661										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112926912	112926912	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcagcatagtttacttggtaTtttctgttcaaggatctgga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:112926912delT	ENST00000161863.4	+	27	4213	c.4000delT	c.(4000-4002)tttfs	p.F1334fs		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1334	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		TTACTTGGTATTTTCTGTTCA	0.393																																					p.V1333fs		Atlas-INDEL	.											.	YTHDC2	118	.	0			c.3999delA						.						145	147	146					5																	112926912		2202	4300	6502	SO:0001589	frameshift_variant	64848	exon27			.	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.4000delT	chr5.hg19:g.112926912delT	ENSP00000161863:p.Phe1334fs	127.0	0.0		162.0	11.0	NM_022828	B2RP66	Frame_Shift_Del	DEL	ENST00000161863.4	hg19	CCDS4113.1																																																																																			.	.		0.393	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		-	112926912	T	-	112926912	7	5	114	1	0	1	0	1	0	0	0	0	17512	1493	52	0	4106	0	YTHDC2	5	112926912	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	9753	112926912	67988348	390	18662										
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115824677	115824677	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcaatggcaaggaagtcagTcactgtggctgagtatagtt	13	6	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:115824677T>C	ENST00000343348.6	-	8	1349	c.562A>G	c.(562-564)Act>Gct	p.T188A	SEMA6A_ENST00000257414.8_Missense_Mutation_p.T188A|SEMA6A_ENST00000503962.1_5'UTR|CTB-118N6.3_ENST00000514214.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000510263.1_Missense_Mutation_p.T188A|CTB-118N6.3_ENST00000510682.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	188	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		AGGAAGTCAGTCACTGTGGCT	0.473																																					p.T188A		Atlas-SNP	.											.	SEMA6A	93	.	0			c.A562G						.						43	40	41					5																	115824677		1955	4163	6118	SO:0001583	missense	57556	exon8			AGTCAGTCACTGT	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"Semaphorins"	10738	protein-coding gene	gene with protein product	"sema VIa"	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.562A>G	chr5.hg19:g.115824677T>C	ENSP00000345512:p.Thr188Ala	89.0	0.0		111.0	5.0	NM_020796	Q9P2H9	Missense_Mutation	SNP	ENST00000343348.6	hg19	CCDS47256.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.914488	0.33815	.	.	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000510263	T;T;T	0.09630	2.96;2.96;2.96	5.58	5.58	0.84498	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.17577	0.0422	N	0.25957	0.775	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.998	T	0.02639	-1.1130	10	0.02654	T	1	.	15.4142	0.74952	0.0:0.0:0.0:1.0	.	188;188	Q9H2E6;Q9H2E6-2	SEM6A_HUMAN;.	A	188	ENSP00000345512:T188A;ENSP00000257414:T188A;ENSP00000424388:T188A	ENSP00000257414:T188A	T	-	1	0	SEMA6A	115852576	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	6.276000	0.72601	2.130000	0.65690	0.528000	0.53228	ACT	.	.		0.473	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796		C	115824677	T	C	115824677	3	2	114	1	0	0	0	0	1	0	0	0	14054	1667	58	2	2578	2	SEMA6A	5	115824677	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2897765	115824677	65090583	391	18663										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118450216	118450216	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattttcaccagatggagaaTtttttgccactgctgggaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:118450216delT	ENST00000311085.8	+	6	624	c.544delT	c.(544-546)tttfs	p.F183fs	DMXL1_ENST00000539542.1_Frame_Shift_Del_p.F183fs	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	183										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AGATGGAGAATTTTTTGCCAC	0.299																																					p.E181fs		Atlas-INDEL	.											.	DMXL1	268	.	0			c.543delA						.						53	55	54					5																	118450216		2197	4293	6490	SO:0001589	frameshift_variant	1657	exon6			.	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.544delT	chr5.hg19:g.118450216delT	ENSP00000309690:p.Phe183fs	220.0	0.0		275.0	17.0	NM_005509		Frame_Shift_Del	DEL	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.		0.299	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		-	118450216	T	-	118450216	7	5	114	1	0	1	0	1	0	0	0	0	4596	1493	52	0	566	0	DMXL1	5	118450216	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2625539	118450216	62465044	392	18664										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118483090	118483090	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtaccagcaggttgactctgTtttcagaaatggtttatagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:118483090delT	ENST00000311085.8	+	17	2916	c.2836delT	c.(2836-2838)tttfs	p.F946fs	DMXL1_ENST00000539542.1_Frame_Shift_Del_p.F946fs	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	946										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GTTGACTCTGTTTTCAGAAAT	0.368																																					p.L945fs		Atlas-INDEL	.											.	DMXL1	268	.	0			c.2835delG						.						61	64	63					5																	118483090		2202	4300	6502	SO:0001589	frameshift_variant	1657	exon17			.	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.2836delT	chr5.hg19:g.118483090delT	ENSP00000309690:p.Phe946fs	167.0	0.0		216.0	14.0	NM_005509		Frame_Shift_Del	DEL	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.		0.368	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		-	118483090	T	-	118483090	7	5	114	1	0	1	0	1	0	0	0	0	4596	1725	60	0	2902	0	DMXL1	5	118483090	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	32874	118483090	62432170	393	18665										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118569090	118569090	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttgaatggggccattctcaAcaaataacctgttttcgatc	7	9	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:118569090A>G	ENST00000311085.8	+	38	8411	c.8331A>G	c.(8329-8331)caA>caG	p.Q2777Q	DMXL1_ENST00000539542.1_Silent_p.Q2798Q|DMXL1_ENST00000505312.1_3'UTR	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2777										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GCCATTCTCAACAAATAACCT	0.343																																					p.Q2777Q		Atlas-SNP	.											.	DMXL1	268	.	0			c.A8331G						.						116	110	112					5																	118569090		2202	4300	6502	SO:0001819	synonymous_variant	1657	exon38			TTCTCAACAAATA	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.8331A>G	chr5.hg19:g.118569090A>G		115.0	0.0		122.0	6.0	NM_005509		Silent	SNP	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.		0.343	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		G	118569090	A	G	118569090	2	3	114	1	0	0	0	0	0	0	0	1	4596	40	2	2		2	DMXL1	5	118569090	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	86000	118569090	62346170	394	18666										
FAM170A	340069	hgsc.bcm.edu	37	chr5	118969957	118969957	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggttgtgagggtaggtactCccccctctgatgtgtccacc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:118969957delC	ENST00000515256.1	+	3	686	c.514delC	c.(514-516)cccfs	p.P173fs				A1A519	F170A_HUMAN	family with sequence similarity 170, member A	173			P -> S (in dbSNP:rs328694).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	24						GGTAGGTACTCCCCCCTCTGA	0.537																																					p.T171fs		Atlas-INDEL	.											.	FAM170A	47	.	0			c.513delT						.						92	96	95					5																	118969957		1992	4181	6173	SO:0001589	frameshift_variant	340069	exon3			.	AF427126	CCDS43353.1, CCDS54889.1	5q23.1	2008-06-12			ENSG00000164334	ENSG00000164334			27963	protein-coding gene	gene with protein product						12477932	Standard	NM_182761		Approved		uc003ksn.3	A1A519	OTTHUMG00000162946	ENST00000515256.1:c.514delC	chr5.hg19:g.118969957delC	ENSP00000422684:p.Pro173fs	132.0	0.0		145.0	10.0	NM_182761	Q66LM8|Q7Z4V2|Q8IW94	Frame_Shift_Del	DEL	ENST00000515256.1	hg19																																																																																				.	.		0.537	FAM170A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371126.1	NM_182761		-	118969957	C	-	118969957	7	5	114	1	0	1	0	1	0	0	0	0	5494	855	30	0	524	0	FAM170A	5	118969957	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	400867	118969957	61945303	395	18667										
SNX24	28966	hgsc.bcm.edu	37	chr5	122272475	122272475	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggaagaaaacattttgttgAaaagagatacagcgaatttc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:122272475delA	ENST00000261369.4	+	2	292	c.107delA	c.(106-108)gaafs	p.E36fs	SNX24_ENST00000511211.1_3'UTR|SNX24_ENST00000513881.1_Frame_Shift_Del_p.E36fs|SNX24_ENST00000506996.1_Frame_Shift_Del_p.E36fs|SNX24_ENST00000395451.4_Frame_Shift_Del_p.E69fs	NM_014035.2	NP_054754.1	Q9Y343	SNX24_HUMAN	sorting nexin 24	36	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			lung(5)	5		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)		CATTTTGTTGAAAAGAGATAC	0.294																																					p.E36fs		Atlas-INDEL	.											.	SNX24	14	.	0			c.106delG						.						129	117	121					5																	122272475		2203	4299	6502	SO:0001589	frameshift_variant	28966	exon2			.	AF139461	CCDS4132.1	5q23.2	2008-03-11	2007-08-15		ENSG00000064652	ENSG00000064652		"Sorting nexins"	21533	protein-coding gene	gene with protein product						12461558	Standard	NM_014035		Approved	SBBI31	uc011cwo.2	Q9Y343	OTTHUMG00000128913	ENST00000261369.4:c.107delA	chr5.hg19:g.122272475delA	ENSP00000261369:p.Glu36fs	142.0	0.0		180.0	13.0	NM_014035	Q6UY33	Frame_Shift_Del	DEL	ENST00000261369.4	hg19	CCDS4132.1																																																																																			.	.		0.294	SNX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250885.2	NM_014035		-	122272475	A	-	122272475	7	5	114	1	0	1	0	1	0	0	0	0	14910	246	9	0	113	0	SNX24	5	122272475	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3302518	122272475	58642785	396	18668										
SLC12A2	6558	hgsc.bcm.edu	37	chr5	127514330	127514330	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagctagtacacagtttcagAaaaaacaaggaaagaatact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:127514330delA	ENST00000262461.2	+	22	3238	c.3049delA	c.(3049-3051)aaafs	p.K1018fs	SLC12A2_ENST00000343225.4_Frame_Shift_Del_p.K1002fs|SLC12A2_ENST00000507791.1_3'UTR	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	1018					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	ACAGTTTCAGAAAAAACAAGG	0.313																																					p.Q1016fs		Atlas-INDEL	.											SLC12A2,NS,carcinoma,0,1	SLC12A2	119	.	0			c.3048delG						.						82	86	84					5																	127514330		2203	4300	6503	SO:0001589	frameshift_variant	6558	exon22			.		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.3049delA	chr5.hg19:g.127514330delA	ENSP00000262461:p.Lys1018fs	158.0	0.0		212.0	13.0	NM_001046	Q8N713|Q8WWH7	Frame_Shift_Del	DEL	ENST00000262461.2	hg19	CCDS4144.1																																																																																			.	.		0.313	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		-	127514330	A	-	127514330	7	5	114	1	0	1	0	1	0	0	0	0	14398	247	9	0	3135	0	SLC12A2	5	127514330	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	5241855	127514330	53400930	397	18669										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130769319	130769319	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atggctggagtcagacaagtTgtcagatttagctgatggaa	13	5	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:130769319T>C	ENST00000509018.1	-	25	3983	c.3778A>G	c.(3778-3780)Aac>Gac	p.N1260D	RAPGEF6_ENST00000296859.6_Missense_Mutation_p.N1268D|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.N1268D|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.N1310D|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.N1273D	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1260	Ser-rich.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TCAGACAAGTTGTCAGATTTA	0.443																																					p.N1273D	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.A3817G						.						98	91	93					5																	130769319		2203	4300	6503	SO:0001583	missense	51735	exon27			ACAAGTTGTCAGA	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3778A>G	chr5.hg19:g.130769319T>C	ENSP00000421684:p.Asn1260Asp	79.0	0.0		92.0	4.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	T	31	5.083514	0.94050	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000514667	T;T;T;T;T	0.31247	1.62;1.5;1.5;1.62;1.72	5.83	5.83	0.93111	.	0.094015	0.85682	D	0.000000	T	0.50633	0.1627	M	0.69823	2.125	0.80722	D	1	P;P;P;D;P	0.54772	0.945;0.945;0.945;0.968;0.945	P;P;P;P;P	0.56960	0.65;0.549;0.549;0.81;0.549	T	0.51787	-0.8661	10	0.54805	T	0.06	.	16.2141	0.82191	0.0:0.0:0.0:1.0	.	1268;1268;1310;1273;1260	A3KN82;B7ZML2;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;RPGF6_HUMAN	D	1260;1273;1268;1268;1273;1310	ENSP00000421684:N1260D;ENSP00000309298:N1273D;ENSP00000426081:N1268D;ENSP00000296859:N1268D;ENSP00000426948:N1310D	ENSP00000426948:N1310D	N	-	1	0	RAPGEF6;FNIP1	130797218	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.364000	0.66110	2.224000	0.72417	0.528000	0.53228	AAC	.	.		0.443	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		C	130769319	T	C	130769319	3	2	114	1	0	0	0	0	1	0	0	0	13063	1812	63	2	1043	2	RAPGEF6	5	130769319	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3254989	130769319	50145941	398	18670										
SEPT8	23176	hgsc.bcm.edu	37	chr5	132096620	132096620	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctcctccagttcccggcgcTtttcctccaccttgcgcttc	6	20	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:132096620T>C	ENST00000378719.2	-	9	1397	c.1160A>G	c.(1159-1161)aAg>aGg	p.K387R	SEPT8_ENST00000378706.1_Missense_Mutation_p.K387R|SEPT8_ENST00000378701.1_Missense_Mutation_p.K385R|SEPT8_ENST00000378721.4_Missense_Mutation_p.K385R|SEPT8_ENST00000296873.7_Missense_Mutation_p.K387R|SEPT8_ENST00000458488.2_Missense_Mutation_p.K387R|SEPT8_ENST00000378699.2_Missense_Mutation_p.K327R|SEPT8_ENST00000481030.1_5'Flank|SEPT8_ENST00000448933.1_Missense_Mutation_p.K327R	NM_001098811.1	NP_001092281.1	Q92599	SEPT8_HUMAN	septin 8	387					cell cycle (GO:0007049)	septin complex (GO:0031105)	GTP binding (GO:0005525)		SEPT8/AFF4(2)	kidney(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTCCCGGCGCTTTTCCTCCAC	0.637																																					p.K387R		Atlas-SNP	.											.	SEPT8	28	.	0			c.A1160G						.						102	109	107					5																	132096620		2044	4171	6215	SO:0001583	missense	23176	exon9			CGGCGCTTTTCCT	AF179995	CCDS43358.1, CCDS43359.1, CCDS43360.1, CCDS47262.1, CCDS75298.1	5q31	2013-01-21			ENSG00000164402	ENSG00000164402		"Septins"	16511	protein-coding gene	gene with protein product		608418				9039502, 9149945	Standard	NM_001098812		Approved	KIAA0202, SEP2	uc003kxr.2	Q92599	OTTHUMG00000059735	ENST00000378719.2:c.1160A>G	chr5.hg19:g.132096620T>C	ENSP00000367991:p.Lys387Arg	73.0	0.0		78.0	4.0	NM_015146	A6NC65|A6NKP6|F6W7K9|Q8IX36|Q8IX37|Q9BVB3	Missense_Mutation	SNP	ENST00000378719.2	hg19	CCDS43358.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.627307	0.66901	.	.	ENSG00000164402	ENST00000378719;ENST00000378721;ENST00000296873;ENST00000448933;ENST00000378706;ENST00000378699;ENST00000378701;ENST00000458488	D;D;D;D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86	5.7	5.7	0.88788	.	0.170387	0.49916	D	0.000121	D	0.85323	0.5670	L	0.46157	1.445	0.54753	D	0.999986	P;P;B;P	0.51791	0.908;0.948;0.037;0.948	B;P;B;P	0.48952	0.419;0.516;0.104;0.596	D	0.85481	0.1179	10	0.44086	T	0.13	.	15.9745	0.80049	0.0:0.0:0.0:1.0	.	385;385;387;387	B7ZVZ1;A6NFQ9;F6W7K9;Q92599	.;.;.;SEPT8_HUMAN	R	387;385;387;327;387;327;385;387	ENSP00000367991:K387R;ENSP00000367993:K385R;ENSP00000296873:K387R;ENSP00000399840:K327R;ENSP00000367978:K387R;ENSP00000367971:K327R;ENSP00000367973:K385R;ENSP00000394766:K387R	ENSP00000296873:K387R	K	-	2	0	SEPT8	132124519	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	6.289000	0.72696	2.168000	0.68352	0.533000	0.62120	AAG	.	.		0.637	SEPT8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132827.2	XM_034872		C	132096620	T	C	132096620	3	2	114	1	0	0	0	0	1	0	0	0	14085	1609	56	2	354	2	SEPT8	5	132096620	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1327301	132096620	48818640	399	18671										
FSTL4	23105	hgsc.bcm.edu	37	chr5	132553042	132553042	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actggcagggctgggttgcaTttttttctctttgaggacag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:132553042delT	ENST00000265342.7	-	13	1736	c.1487delA	c.(1486-1488)aatfs	p.N496fs	CTB-49A3.2_ENST00000502776.1_RNA|CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	496						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTGGGTTGCATTTTTTTCTCT	0.493																																					p.N496fs		Atlas-INDEL	.											.	FSTL4	74	.	0			c.1488delT						.						87	85	86					5																	132553042		2203	4300	6503	SO:0001589	frameshift_variant	23105	exon13			.	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.1487delA	chr5.hg19:g.132553042delT	ENSP00000265342:p.Asn496fs	150.0	0.0		167.0	11.0	NM_015082	Q8TBU0|Q9UPU1	Frame_Shift_Del	DEL	ENST00000265342.7	hg19	CCDS34238.1																																																																																			.	.		0.493	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786		-	132553042	T	-	132553042	7	5	114	1	0	1	0	1	0	0	0	0	6087	1493	52	0	1057	0	FSTL4	5	132553042	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	456422	132553042	48362218	400	18672										
DDX46	9879	hgsc.bcm.edu	37	chr5	134109494	134109494	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggaaaacataggagaactgAaaaaggaaatcgaagagatg					rs35026423		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:134109494delA	ENST00000354283.4	+	5	691	c.556delA	c.(556-558)aaafs	p.K187fs	DDX46_ENST00000452510.2_Frame_Shift_Del_p.K187fs			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	187					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGGAGAACTGAAAAAGGAAAT	0.373																																					p.L185fs	Colon(13;391 453 4901 21675 24897)	Atlas-INDEL	.											.	DDX46	77	.	0			c.555delG						.						131	131	131					5																	134109494		2203	4300	6503	SO:0001589	frameshift_variant	9879	exon5			.		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.556delA	chr5.hg19:g.134109494delA	ENSP00000346236:p.Lys187fs	118.0	0.0		172.0	12.0	NM_014829	O94894|Q96EI0|Q9Y658	Frame_Shift_Del	DEL	ENST00000354283.4	hg19	CCDS34240.1																																																																																			.	.		0.373	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		-	134109494	A	-	134109494	7	5	114	1	0	1	0	1	0	0	0	0	4366	247	9	0	574	0	DDX46	5	134109494	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1556452	134109494	46805766	401	18673										
TIFAB	140947	hgsc.bcm.edu	37	chr5	134785335	134785335	+	5'Flank	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaccctgttgacggtgctcaGggggacctgctccaggtacc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:134785335delG	ENST00000503143.2	-	0	0				TIFAB_ENST00000537858.1_Frame_Shift_Del_p.L99fs|CTB-138E5.1_ENST00000510230.1_RNA	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN								nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACGGTGCTCAGGGGGACCTGC	0.592																																					p.L99fs		Atlas-INDEL	.											.	TIFAB	23	.	0			c.296delT						.						100	104	103					5																	134785335		2114	4228	6342	SO:0001631	upstream_gene_variant	497189	exon2			.																													chr5.hg19:g.134785335delG	Exception_encountered	129.0	0.0		168.0	11.0	NM_001099221		Frame_Shift_Del	DEL	ENST00000503143.2	hg19	CCDS4186.1																																																																																			.	.		0.592	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1			-	134785335	G	-	134785335	6	5	114	0	1	1	0	1	0	0	0	0	15910	991	35	0		0	TIFAB	5	134785335	5'Flank	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	675841	134785335	46129925	402	18674										
CDC23	8697	hgsc.bcm.edu	37	chr5	137537124	137537124	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcctcatttttcacttgtccTttttccagggggcctaggaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:137537124delT	ENST00000394886.2	-	5	459	c.429delA	c.(427-429)aaafs	p.K143fs		NM_004661.3	NP_004652.2	Q9UJX2	CDC23_HUMAN	cell division cycle 23	143					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of exit from mitosis (GO:0007096)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(6)|prostate(2)|skin(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCACTTGTCCTTTTTCCAGGG	0.373																																					p.G144fs		Atlas-INDEL	.											.	CDC23	46	.	0			c.430delG						.						77	76	77					5																	137537124		2203	4300	6503	SO:0001589	frameshift_variant	8697	exon5			.	AF053977	CCDS4200.2	5q31	2013-01-17	2013-01-17		ENSG00000094880	ENSG00000094880		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1724	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 8"	603462	"CDC23 (cell division cycle 23, yeast, homolog)", "cell division cycle 23 homolog (S. cerevisiae)"			9790767	Standard	NM_004661		Approved	APC8, ANAPC8, CUT23	uc003lcl.3	Q9UJX2	OTTHUMG00000129198	ENST00000394886.2:c.429delA	chr5.hg19:g.137537124delT	ENSP00000378350:p.Lys143fs	108.0	0.0		147.0	10.0	NM_004661	A8K6E5|B4E3A2|B7WP05|D3DQB7|O75433|Q53FN2|Q9BS73	Frame_Shift_Del	DEL	ENST00000394886.2	hg19	CCDS4200.2																																																																																			.	.		0.373	CDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251275.2			-	137537124	T	-	137537124	7	5	114	1	0	1	0	1	0	0	0	0	3063	1606	56	0	1412	0	CDC23	5	137537124	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2751789	137537124	43378136	403	18675										
SIL1	64374	hgsc.bcm.edu	37	chr5	138286953	138286953	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agggtcctcaggacctgcagCcccccgagcttcaggaactg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:138286953delC	ENST00000394817.2	-	9	1075	c.936delG	c.(934-936)gggfs	p.G312fs	SIL1_ENST00000515008.1_5'UTR|SIL1_ENST00000265195.5_Frame_Shift_Del_p.G312fs|SIL1_ENST00000509534.1_Frame_Shift_Del_p.G319fs	NM_022464.4	NP_071909.1	Q9H173	SIL1_HUMAN	SIL1 nucleotide exchange factor	312					intracellular protein transport (GO:0006886)|protein folding (GO:0006457)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GGACCTGCAGCCCCCCGAGCT	0.657									Marinesco-Sjgren syndrome																												p.L313fs		Atlas-INDEL	.											.	SIL1	31	.	0			c.937delC						.						26	24	25					5																	138286953		2202	4297	6499	SO:0001589	frameshift_variant	64374	exon9	Familial Cancer Database	Marinesco-Sjogren syndrome	.	AK075177	CCDS4209.1	5q31	2013-08-21	2013-08-21		ENSG00000120725	ENSG00000120725			24624	protein-coding gene	gene with protein product		608005	"Marinesco-Sjogren syndrome", "SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae)"	MSS		11101517, 12356756, 16282977	Standard	XM_006714671		Approved	BAP, ULG5	uc003ldp.3	Q9H173	OTTHUMG00000129226	ENST00000394817.2:c.936delG	chr5.hg19:g.138286953delC	ENSP00000378294:p.Gly312fs	144.0	0.0		183.0	11.0	NM_022464	D3DQC2|Q8N2L3	Frame_Shift_Del	DEL	ENST00000394817.2	hg19	CCDS4209.1																																																																																			.	.		0.657	SIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251319.1	NM_022464		-	138286953	C	-	138286953	7	5	114	1	0	1	0	1	0	0	0	0	14336	726	26	0	457	0	SIL1	5	138286953	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	749829	138286953	42628307	404	18676										
TMEM173	340061	hgsc.bcm.edu	37	chr5	138857961	138857961	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtttatccaggaagcgaatgTtggggtcagccatactcagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:138857961delT	ENST00000330794.4	-	6	986	c.653delA	c.(652-654)aacfs	p.N218fs	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	218	c-di-GMP-binding domain (CBD).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GAAGCGAATGTTGGGGTCAGC	0.542																																					p.N218fs		Atlas-Indel,Pindel	.											.	TMEM173	19	.	0			c.654delC						.						137	123	128					5																	138857961		2203	4300	6503	SO:0001589	frameshift_variant	340061	exon6			.		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.653delA	chr5.hg19:g.138857961delT	ENSP00000331288:p.Asn218fs	170.0	0.0		151.0	43.0	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Frame_Shift_Del	DEL	ENST00000330794.4	hg19	CCDS4215.1																																																																																			.	.		0.542	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282		-	138857961	T	-	138857961	7	5	114	1	0	1	0	1	0	0	0	0	16104	1725	60	0	498	0	TMEM173	5	138857961	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	571008	138857961	42057299	405	18677										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140214086	140214086	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actcggtccccgaggaggctAaacatggcaacttcgtgggc					rs532311058		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:140214086delA	ENST00000525929.1	+	1	118	c.118delA	c.(118-120)aaafs	p.K40fs	PCDHA7_ENST00000378125.3_Frame_Shift_Del_p.K40fs|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	40	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGAGGAGGCTAAACATGGCAA	0.622																																					p.A39fs	NSCLC(160;258 2013 5070 22440 28951)	Atlas-INDEL	.											.	PCDHA7	367	.	0			c.117delT						.						58	71	66					5																	140214086		2203	4300	6503	SO:0001589	frameshift_variant	56141	exon1			.	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.118delA	chr5.hg19:g.140214086delA	ENSP00000436426:p.Lys40fs	155.0	0.0		182.0	11.0	NM_031852	O75282	Frame_Shift_Del	DEL	ENST00000525929.1	hg19	CCDS54918.1																																																																																			.	.		0.622	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		-	140214086	A	-	140214086	7	5	114	1	0	1	0	1	0	0	0	0	11538	363	13	0	120	0	PCDHA7	5	140214086	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1356125	140214086	40701174	406	18678										
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140515047	140515047	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgctagcaaaaacgccacagAaaaggcaagttatgtttctt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:140515047delA	ENST00000231134.5	+	1	248	c.31delA	c.(31-33)aaafs	p.K11fs		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	11					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AACGCCACAGAAAAGGCAAGT	0.448																																					p.Q10fs		Atlas-INDEL	.											.	PCDHB5	184	.	0			c.30delG						.						97	86	90					5																	140515047		2203	4300	6503	SO:0001589	frameshift_variant	26167	exon1			.	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.31delA	chr5.hg19:g.140515047delA	ENSP00000231134:p.Lys11fs	200.0	0.0		229.0	14.0	NM_015669	Q549F4|Q9UFU9	Frame_Shift_Del	DEL	ENST00000231134.5	hg19	CCDS4247.1																																																																																			.	.		0.448	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		-	140515047	A	-	140515047	7	5	114	1	0	1	0	1	0	0	0	0	11554	247	9	0	33	0	PCDHB5	5	140515047	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	300961	140515047	40400213	407	18679										
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140588664	140588664	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtgagtgagctgtcttcgcGgggggctcgggtggtttcta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:140588664delG	ENST00000239450.2	+	1	374	c.185delG	c.(184-186)cggfs	p.R62fs	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	62	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGTCTTCGCGGGGGGCTCGG	0.512																																					p.R62fs		Atlas-INDEL	.											PCDHB12,caecum,carcinoma,0,2	PCDHB12	179	.	0			c.184delC						.						83	94	90					5																	140588664		2203	4300	6503	SO:0001589	frameshift_variant	56124	exon1			.	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.185delG	chr5.hg19:g.140588664delG	ENSP00000239450:p.Arg62fs	115.0	0.0		162.0	11.0	NM_018932	B4DDU1	Frame_Shift_Del	DEL	ENST00000239450.2	hg19	CCDS4254.1																																																																																			.	.		0.512	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		-	140588664	G	-	140588664	7	5	114	1	0	1	0	1	0	0	0	0	11546	1116	39	0	187	0	PCDHB12	5	140588664	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	73617	140588664	40326596	408	18680										
JAKMIP2	9832	hgsc.bcm.edu	37	chr5	147021317	147021317	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctttcttctacggatgagcTtttctcggtcctggaaaaca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:147021317delT	ENST00000265272.5	-	8	1702	c.1235delA	c.(1234-1236)aagfs	p.K412fs	JAKMIP2_ENST00000333010.6_Frame_Shift_Del_p.K370fs|JAKMIP2_ENST00000507386.1_Frame_Shift_Del_p.K412fs	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	412						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGATGAGCTTTTCTCGGTC	0.378																																					p.K412fs		Atlas-INDEL	.											.	JAKMIP2	154	.	0			c.1236delG						.						166	158	161					5																	147021317		2203	4300	6503	SO:0001589	frameshift_variant	9832	exon8			.	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.1235delA	chr5.hg19:g.147021317delT	ENSP00000265272:p.Lys412fs	148.0	0.0		175.0	12.0	NM_001270934	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Frame_Shift_Del	DEL	ENST00000265272.5	hg19	CCDS4285.1																																																																																			.	.		0.378	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790		-	147021317	T	-	147021317	7	5	114	1	0	1	0	1	0	0	0	0	7950	1609	56	0	1253	0	JAKMIP2	5	147021317	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	6432653	147021317	33893943	409	18681										
SPINK6	404203	hgsc.bcm.edu	37	chr5	147593496	147593496	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gactgtggtgagttccaggaCcccaaggtctactgcactcg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:147593496delC	ENST00000325630.2	+	3	361	c.105delC	c.(103-105)gacfs	p.D35fs		NM_001195290.1|NM_205841.3	NP_001182219.1|NP_995313.2	Q6UWN8	ISK6_HUMAN	serine peptidase inhibitor, Kazal type 6	35	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTTCCAGGACCCCAAGGTCT	0.468																																					p.D35fs		Atlas-INDEL	.											.	SPINK6	8	.	0			c.104delA						.						136	110	119					5																	147593496		2203	4300	6503	SO:0001589	frameshift_variant	404203	exon3			.	AY358716	CCDS34268.1	5q32	2011-08-31	2005-08-17		ENSG00000178172	ENSG00000178172		"Serine peptidase inhibitors, Kazal type"	29486	protein-coding gene	gene with protein product	"protease inhibitor H"	615868	"serine protease inhibitor, Kazal type 6"			15060002	Standard	NM_205841		Approved	MGC21394, UNQ844, BUSI2	uc021yff.1	Q6UWN8	OTTHUMG00000163425	ENST00000325630.2:c.105delC	chr5.hg19:g.147593496delC	ENSP00000324870:p.Asp35fs	149.0	0.0		159.0	10.0	NM_205841	E0X656|Q8N5P0	Frame_Shift_Del	DEL	ENST00000325630.2	hg19	CCDS34268.1																																																																																			.	.		0.468	SPINK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373332.1	NM_205841		-	147593496	C	-	147593496	7	5	114	1	0	1	0	1	0	0	0	0	15078	506	18	0	115	0	SPINK6	5	147593496	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	572179	147593496	33321764	410	18682	82	2								
SPINK6	404203	hgsc.bcm.edu	37	chr5	147593498	147593498	+	Missense_Mutation	SNP	C	C	A													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgtggtgagttccaggaccCcaaggtctactgcactcggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:147593498C>A	ENST00000325630.2	+	3	363	c.107C>A	c.(106-108)cCc>cAc	p.P36H		NM_001195290.1|NM_205841.3	NP_001182219.1|NP_995313.2	Q6UWN8	ISK6_HUMAN	serine peptidase inhibitor, Kazal type 6	36	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.		P -> T (in dbSNP:rs12186491). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20667819}.			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCAGGACCCCAAGGTCTAC	0.458																																					p.P36H		Atlas-SNP	.											.	SPINK6	8	.	0			c.C107A						.						134	110	118					5																	147593498		2203	4300	6503	SO:0001583	missense	404203	exon3			AGGACCCCAAGGT	AY358716	CCDS34268.1	5q32	2011-08-31	2005-08-17		ENSG00000178172	ENSG00000178172		"Serine peptidase inhibitors, Kazal type"	29486	protein-coding gene	gene with protein product	"protease inhibitor H"	615868	"serine protease inhibitor, Kazal type 6"			15060002	Standard	NM_205841		Approved	MGC21394, UNQ844, BUSI2	uc021yff.1	Q6UWN8	OTTHUMG00000163425	ENST00000325630.2:c.107C>A	chr5.hg19:g.147593498C>A	ENSP00000324870:p.Pro36His	145.0	0.0		153.0	7.0	NM_205841	E0X656|Q8N5P0	Missense_Mutation	SNP	ENST00000325630.2	hg19	CCDS34268.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.164563	0.38217	.	.	ENSG00000178172	ENST00000514389;ENST00000325630	T;T	0.79554	-1.28;-0.88	5.75	5.75	0.90469	Proteinase inhibitor I1, Kazal (2);	0.000000	0.64402	D	0.000004	D	0.89581	0.6756	.	.	.	0.39180	D	0.962751	D	0.89917	1.0	D	0.91635	0.999	D	0.90728	0.4640	9	0.72032	D	0.01	-9.9478	15.8177	0.78615	0.0:1.0:0.0:0.0	.	36	Q6UWN8	ISK6_HUMAN	H	36	ENSP00000421119:P36H;ENSP00000324870:P36H	ENSP00000324870:P36H	P	+	2	0	SPINK6	147573691	0.065000	0.20965	1.000000	0.80357	0.407000	0.30961	1.151000	0.31651	2.885000	0.99019	0.655000	0.94253	CCC	.	.		0.458	SPINK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373332.1	NM_205841		A	147593498	C	A	147593498	3	1	114	1	0	0	0	0	1	0	0	0	15078	623	22	3	117	3	SPINK6	5	147593498	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	2	147593498	33321762	411	18683	82	2								
SLC6A7	6534	hgsc.bcm.edu	37	chr5	149583547	149583547	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cggcccaagaaggcggtgttCtcagggctcatctgcgtggc	15	12	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:149583547C>A	ENST00000230671.2	+	10	1649	c.1278C>A	c.(1276-1278)ttC>ttA	p.F426L	SLC6A7_ENST00000524041.1_Missense_Mutation_p.F426L	NM_014228.3	NP_055043.2	Q99884	SC6A7_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 7	426					proline transport (GO:0015824)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	AGGCGGTGTTCTCAGGGCTCA	0.587																																					p.F426L		Atlas-SNP	.											.	SLC6A7	52	.	0			c.C1278A						.						98	68	78					5																	149583547		2203	4300	6503	SO:0001583	missense	6534	exon10			GGTGTTCTCAGGG	S80071	CCDS4305.1	5q32	2013-07-19	2013-07-19		ENSG00000011083	ENSG00000011083		"Solute carriers"	11054	protein-coding gene	gene with protein product	"brain-specific L-proline transporter", "sodium-dependent proline transporter"	606205	"solute carrier family 6 (neurotransmitter transporter, L-proline), member 7"			7651355	Standard	NM_014228		Approved	PROT	uc003lrr.3	Q99884	OTTHUMG00000130046	ENST00000230671.2:c.1278C>A	chr5.hg19:g.149583547C>A	ENSP00000230671:p.Phe426Leu	205.0	0.0		236.0	73.0	NM_014228	Q0VG81|Q52LU6	Missense_Mutation	SNP	ENST00000230671.2	hg19	CCDS4305.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.814341	0.32053	.	.	ENSG00000011083	ENST00000230671;ENST00000524041	T;T	0.73575	-0.76;-0.76	5.04	4.17	0.49024	.	0.000000	0.85682	D	0.000000	T	0.59362	0.2188	N	0.13327	0.33	0.58432	D	0.999999	B	0.24317	0.101	B	0.32533	0.147	T	0.55101	-0.8193	10	0.21540	T	0.41	.	12.8423	0.57811	0.0:0.9212:0.0:0.0788	.	426	Q99884	SC6A7_HUMAN	L	426	ENSP00000230671:F426L;ENSP00000428200:F426L	ENSP00000230671:F426L	F	+	3	2	SLC6A7	149563740	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	2.656000	0.46716	2.323000	0.78572	0.561000	0.74099	TTC	.	.		0.587	SLC6A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252325.1	NM_014228		A	149583547	C	A	149583547	3	1	114	1	0	0	0	0	1	0	0	0	14704	912	32	3	1316	3	SLC6A7	5	149583547	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	1990049	149583547	31331713	412	18684										
CD74	972	hgsc.bcm.edu	37	chr5	149792276	149792276	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcatccatgactggcttctGatcttcccgacagctcctgc	8	15	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:149792276G>A	ENST00000009530.7	-	1	38	c.37C>T	c.(37-39)Cag>Tag	p.Q13*	CD74_ENST00000353334.6_Nonsense_Mutation_p.Q13*|CD74_ENST00000377795.3_Nonsense_Mutation_p.Q13*|CD74_ENST00000524315.1_Nonsense_Mutation_p.Q13*			P04233	HG2A_HUMAN	CD74 molecule, major histocompatibility complex, class II invariant chain	13					activation of MAPK activity (GO:0000187)|antigen processing and presentation of endogenous antigen (GO:0019883)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|chaperone mediated protein folding requiring cofactor (GO:0051085)|defense response (GO:0006952)|immunoglobulin mediated immune response (GO:0016064)|intracellular protein transport (GO:0006886)|macrophage migration inhibitory factor signaling pathway (GO:0035691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of peptide secretion (GO:0002792)|negative regulation of T cell differentiation (GO:0045581)|negative thymic T cell selection (GO:0045060)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type 2 immune response (GO:0002830)|positive thymic T cell selection (GO:0045059)|prostaglandin biosynthetic process (GO:0001516)|protein complex assembly (GO:0006461)|regulation of macrophage activation (GO:0043030)|signal transduction (GO:0007165)|T cell selection (GO:0045058)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|macrophage migration inhibitory factor receptor complex (GO:0035692)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|NOS2-CD74 complex (GO:0035693)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)|vacuole (GO:0005773)	beta-amyloid binding (GO:0001540)|cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|macrophage migration inhibitory factor binding (GO:0035718)|MHC class II protein binding (GO:0042289)|MHC class II protein binding, via antigen binding groove (GO:0042658)|MHC class II protein complex binding (GO:0023026)|protein binding involved in protein folding (GO:0044183)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACTGGCTTCTGATCTTCCCGA	0.607			T	ROS1	NSCLC																																p.Q13X		Atlas-SNP	.		Dom	yes		5	5q32	972	"CD74 molecule, major histocompatibility complex, class II invariant chain"		E	.	CD74	35	.	0			c.C37T						.						150	152	152					5																	149792276		2203	4300	6503	SO:0001587	stop_gained	972	exon1			GCTTCTGATCTTC		CCDS34276.1, CCDS47308.1, CCDS47309.1	5q32	2012-09-20	2006-03-28		ENSG00000019582	ENSG00000019582		"CD molecules"	1697	protein-coding gene	gene with protein product	"HLA-DR-gamma", "Ia-associated invariant chain", "gamma chain of class II antigens", "MHC HLA-DR gamma chain"	142790	"CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)"	DHLAG		6324166, 3001652	Standard	NM_004355		Approved		uc003lsc.3	P04233	OTTHUMG00000163559	ENST00000009530.7:c.37C>T	chr5.hg19:g.149792276G>A	ENSP00000009530:p.Gln13*	105.0	0.0		122.0	5.0	NM_001025159	A8K7R1|B4DNE8|D3DQG3|D3DQG4|Q14597|Q29832|Q5U0J8|Q8SNA0|Q8WLP6	Nonsense_Mutation	SNP	ENST00000009530.7	hg19	CCDS47309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.42|17.42	3.385145|3.385145	0.61956|0.61956	.|.	.|.	ENSG00000019582|ENSG00000019582	ENST00000377795;ENST00000353334;ENST00000524315;ENST00000009530|ENST00000518797	.|.	.|.	.|.	5.13|5.13	3.33|3.33	0.38152|0.38152	.|.	1.222100|.	0.05855|.	N|.	0.621922|.	.|T	.|0.43322	.|0.1242	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.51348	.|-0.8717	.|3	0.49607|.	T|.	0.09|.	-3.3246|-3.3246	7.3893|7.3893	0.26901|0.26901	0.2051:0.0:0.7949:0.0|0.2051:0.0:0.7949:0.0	.|.	.|.	.|.	.|.	X|L	13|7	.|.	ENSP00000009530:Q13X|.	Q|S	-|-	1|2	0|0	CD74|CD74	149772469|149772469	0.992000|0.992000	0.36948|0.36948	0.652000|0.652000	0.29579|0.29579	0.099000|0.099000	0.18886|0.18886	2.272000|2.272000	0.43373|0.43373	0.538000|0.538000	0.28769|0.28769	0.591000|0.591000	0.81541|0.81541	CAG|TCA	.	.		0.607	CD74-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374178.1	NM_004355		A	149792276	G	A	149792276	4	1	114	1	0	0	0	0	0	1	0	0	3037	1299	45	3	889	3	CD74	5	149792276	Nonsense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	208729	149792276	31122984	413	18685										
MFAP3	4238	hgsc.bcm.edu	37	chr5	153432802	153432802	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttgagattgcaaaacgtatCcccatcattacctcagccaa					rs142736423		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:153432802delC	ENST00000436816.1	+	3	837	c.618delC	c.(616-618)atcfs	p.I206fs	MFAP3_ENST00000322602.5_Frame_Shift_Del_p.I206fs|MFAP3_ENST00000439768.2_Frame_Shift_Del_p.I60fs	NM_001242336.1|NM_005927.4	NP_001229265.1|NP_005918.1	P55082	MFAP3_HUMAN	microfibrillar-associated protein 3	206					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)	7	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		CAAAACGTATCCCCATCATTA	0.448																																					p.I206fs		Atlas-INDEL	.											.	MFAP3	20	.	0			c.617delT						.						81	82	82					5																	153432802		2203	4300	6503	SO:0001589	frameshift_variant	4238	exon3			.		CCDS4324.1, CCDS47319.1	5q32-q33.2	2013-01-11			ENSG00000037749	ENSG00000037749		"Immunoglobulin superfamily / I-set domain containing"	7034	protein-coding gene	gene with protein product		600491				7782085	Standard	NM_005927		Approved		uc010jib.2	P55082	OTTHUMG00000130149	ENST00000436816.1:c.618delC	chr5.hg19:g.153432802delC	ENSP00000409933:p.Ile206fs	119.0	0.0		136.0	10.0	NM_005927	B2RDK0|B4DKA1|Q9NXA7	Frame_Shift_Del	DEL	ENST00000436816.1	hg19	CCDS4324.1																																																																																			.	.		0.448	MFAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252457.2	NM_005927		-	153432802	C	-	153432802	7	5	114	1	0	1	0	1	0	0	0	0	9524	845	30	0	624	0	MFAP3	5	153432802	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3640526	153432802	27482458	414	18686										
RNF145	153830	hgsc.bcm.edu	37	chr5	158585835	158585835	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctggagtatgctcctggcctGggggttcagtaccttcctga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:158585835delG	ENST00000424310.2	-	11	2194	c.1835delC	c.(1834-1836)ccafs	p.P612fs	RNF145_ENST00000518284.1_5'UTR|RNF145_ENST00000519865.1_Frame_Shift_Del_p.P612fs|RNF145_ENST00000274542.2_Frame_Shift_Del_p.P640fs|RNF145_ENST00000520638.1_Frame_Shift_Del_p.P626fs|RNF145_ENST00000521606.2_Frame_Shift_Del_p.P629fs|RNF145_ENST00000518802.1_Frame_Shift_Del_p.P642fs	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	612						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTCCTGGCCTGGGGGTTCAGT	0.512																																					p.P642fs		Atlas-INDEL	.											.	RNF145	110	.	0			c.1926delA						.						93	86	88					5																	158585835		2203	4300	6503	SO:0001589	frameshift_variant	153830	exon11			.	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"RING-type (C3HC4) zinc fingers"	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.1835delC	chr5.hg19:g.158585835delG	ENSP00000409064:p.Pro612fs	168.0	0.0		210.0	15.0	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Frame_Shift_Del	DEL	ENST00000424310.2	hg19	CCDS56390.1																																																																																			.	.		0.512	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		-	158585835	G	-	158585835	7	5	114	1	0	1	0	1	0	0	0	0	13462	1348	47	0	160	0	RNF145	5	158585835	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	5153033	158585835	22329425	415	18687										
TTC1	7265	hgsc.bcm.edu	37	chr5	159476629	159476629	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agactataaatctatattagAaaaagatccatcaatacatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:159476629delA	ENST00000231238.5	+	6	760	c.650delA	c.(649-651)gaafs	p.E217fs	TTC1_ENST00000520274.1_3'UTR|TTC1_ENST00000522793.1_Frame_Shift_Del_p.E217fs	NM_001282500.1|NM_003314.1	NP_001269429.1|NP_003305.1	Q99614	TTC1_HUMAN	tetratricopeptide repeat domain 1	217					protein folding (GO:0006457)	peroxisomal membrane (GO:0005778)	unfolded protein binding (GO:0051082)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|prostate(1)|skin(1)	12	Renal(175;0.00196)	all_hematologic(541;0.00014)|Breast(839;0.0101)|all_neural(177;0.0281)|Medulloblastoma(196;0.0425)|Lung NSC(249;0.119)|all_lung(500;0.163)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Epithelial(171;8.37e-05)|all cancers(165;0.000694)|OV - Ovarian serous cystadenocarcinoma(192;0.0402)		TCTATATTAGAAAAAGATCCA	0.358																																					p.E217fs		Atlas-INDEL	.											.	TTC1	26	.	0			c.649delG						.						51	54	53					5																	159476629		2203	4300	6503	SO:0001589	frameshift_variant	7265	exon6			.	U46570	CCDS4348.1	5q32-q33.2	2013-01-10			ENSG00000113312	ENSG00000113312		"Tetratricopeptide (TTC) repeat domain containing"	12391	protein-coding gene	gene with protein product		601963				8836031	Standard	NM_003314		Approved	TPR1	uc003lxu.3	Q99614	OTTHUMG00000130326	ENST00000231238.5:c.650delA	chr5.hg19:g.159476629delA	ENSP00000231238:p.Glu217fs	96.0	0.0		139.0	12.0	NM_003314	B2RCT2|D3DQJ8|Q9BVT3	Frame_Shift_Del	DEL	ENST00000231238.5	hg19	CCDS4348.1																																																																																			.	.		0.358	TTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252675.3	NM_003314		-	159476629	A	-	159476629	7	5	114	1	0	1	0	1	0	0	0	0	16693	246	9	0	668	0	TTC1	5	159476629	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	890794	159476629	21438631	416	18688										
PTTG1	9232	hgsc.bcm.edu	37	chr5	159854837	159854837	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaaaagctgtttcagctgggCcccccttcacctgtgaagat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:159854837delC	ENST00000393964.1	+	4	889	c.486delC	c.(484-486)ggcfs	p.G162fs	PTTG1_ENST00000520452.1_Frame_Shift_Del_p.G162fs|PTTG1_ENST00000519287.1_3'UTR|PTTG1_ENST00000352433.5_Frame_Shift_Del_p.G162fs	NM_001282382.1	NP_001269311.1	O95997	PTTG1_HUMAN	pituitary tumor-transforming 1	162					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|DNA repair (GO:0006281)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of endopeptidase activity (GO:0010951)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(1)|lung(4)	6	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.00219)|Epithelial(171;0.00348)|all cancers(165;0.0104)		TTCAGCTGGGCCCCCCTTCAC	0.527																																					p.G162fs		Atlas-INDEL	.											.	PTTG1	15	.	0			c.485delG						.						80	75	77					5																	159854837		2203	4300	6503	SO:0001589	frameshift_variant	9232	exon5			.	AF062649	CCDS4353.1	5q35.1	2014-08-04			ENSG00000164611	ENSG00000164611			9690	protein-coding gene	gene with protein product	"ESP1-associated protein 1", "tumor-transforming protein 1"	604147		TUTR1		9811450, 9892021	Standard	NM_004219		Approved	PTTG, HPTTG, EAP1, securin	uc003lyj.3	O95997	OTTHUMG00000130328	ENST00000393964.1:c.486delC	chr5.hg19:g.159854837delC	ENSP00000377536:p.Gly162fs	131.0	0.0		164.0	10.0	NM_004219		Frame_Shift_Del	DEL	ENST00000393964.1	hg19	CCDS4353.1																																																																																			.	.		0.527	PTTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252677.1	NM_004219		-	159854837	C	-	159854837	7	5	114	1	0	1	0	1	0	0	0	0	12834	726	26	0	500	0	PTTG1	5	159854837	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	378208	159854837	21060423	417	18689										
HMMR	3161	hgsc.bcm.edu	37	chr5	162891750	162891750	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atctaaacaaaatcttaatgTtgacaaagatactaccttgc	4	8	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:162891750T>C	ENST00000358715.3	+	3	203	c.167T>C	c.(166-168)gTt>gCt	p.V56A	HMMR_ENST00000353866.3_Missense_Mutation_p.V56A|HMMR_ENST00000393915.4_Missense_Mutation_p.V56A|HMMR_ENST00000432118.2_Intron			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	56					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	AATCTTAATGTTGACAAAGAT	0.343																																					p.V56A		Atlas-SNP	.											.	HMMR	64	.	0			c.T167C						.						122	121	121					5																	162891750		2203	4300	6503	SO:0001583	missense	3161	exon3			TTAATGTTGACAA	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"CD molecules"	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.167T>C	chr5.hg19:g.162891750T>C	ENSP00000351554:p.Val56Ala	65.0	0.0		73.0	4.0	NM_012485	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	hg19	CCDS4362.1	.	.	.	.	.	.	.	.	.	.	T	1.522	-0.546775	0.04024	.	.	ENSG00000072571	ENST00000353866;ENST00000434157;ENST00000393915;ENST00000426586;ENST00000358715	T;T;T	0.08282	3.11;3.19;3.19	4.85	0.829	0.18847	.	1.167870	0.05896	N	0.629184	T	0.03695	0.0105	N	0.08118	0	0.09310	N	1	B;B;B	0.23249	0.018;0.082;0.082	B;B;B	0.25140	0.031;0.058;0.058	T	0.38134	-0.9675	10	0.02654	T	1	-1.1384	5.0531	0.14518	0.177:0.0:0.3658:0.4572	.	56;56;56	O75330-3;O75330-2;O75330	.;.;HMMR_HUMAN	A	56	ENSP00000185942:V56A;ENSP00000377492:V56A;ENSP00000351554:V56A	ENSP00000185942:V56A	V	+	2	0	HMMR	162824328	0.367000	0.25023	0.427000	0.26684	0.038000	0.13279	0.419000	0.21247	0.771000	0.33359	0.460000	0.39030	GTT	.	.		0.343	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484		C	162891750	T	C	162891750	3	2	114	1	0	0	0	0	1	0	0	0	7251	1725	60	2	177	2	HMMR	5	162891750	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3036913	162891750	18023510	418	18690										
RARS	5917	hgsc.bcm.edu	37	chr5	167937675	167937675	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atccatggacaagttgaaggAaaaagaaagagacaaggtaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:167937675delA	ENST00000231572.3	+	12	1490	c.1436delA	c.(1435-1437)gaafs	p.E479fs	RARS_ENST00000538719.1_Frame_Shift_Del_p.E273fs	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	479					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		AAGTTGAAGGAAAAAGAAAGA	0.363																																					p.E479fs		Atlas-INDEL	.											.	RARS	58	.	0			c.1435delG						.						66	66	66					5																	167937675		2203	4300	6503	SO:0001589	frameshift_variant	5917	exon12			.	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	9870	protein-coding gene	gene with protein product	"arginine tRNA ligase 1, cytoplasmic"	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1436delA	chr5.hg19:g.167937675delA	ENSP00000231572:p.Glu479fs	144.0	0.0		149.0	10.0	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Frame_Shift_Del	DEL	ENST00000231572.3	hg19	CCDS4367.1																																																																																			.	.		0.363	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887		-	167937675	A	-	167937675	7	5	114	1	0	1	0	1	0	0	0	0	13073	246	9	0	1482	0	RARS	5	167937675	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	5045925	167937675	12977585	419	18691										
FOXI1	2299	hgsc.bcm.edu	37	chr5	169533034	169533034	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tccccagcatcggccaggagCcccccgagatgaacctctac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:169533034delC	ENST00000306268.6	+	1	134	c.73delC	c.(73-75)cccfs	p.P26fs	FOXI1_ENST00000449804.2_Frame_Shift_Del_p.P26fs			Q12951	FOXI1_HUMAN	forkhead box I1	26	Pro-rich.				embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGGCCAGGAGCCCCCCGAGAT	0.697									Pendred syndrome																												p.E24fs		Atlas-INDEL	.											.	FOXI1	70	.	0			c.72delG						.						24	28	26					5																	169533034		2203	4298	6501	SO:0001589	frameshift_variant	2299	exon1	Familial Cancer Database	Goiter-Deafness syndrome	.	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.73delC	chr5.hg19:g.169533034delC	ENSP00000304286:p.Pro26fs	296.0	0.0		294.0	18.0	NM_012188	Q14518|Q66SR7|Q8N6L8	Frame_Shift_Del	DEL	ENST00000306268.6	hg19	CCDS4372.1																																																																																			.	.		0.697	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		-	169533034	C	-	169533034	7	5	114	1	0	1	0	1	0	0	0	0	6017	739	26	0	75	0	FOXI1	5	169533034	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1595359	169533034	11382226	420	18692										
C5orf41	153222	hgsc.bcm.edu	37	chr5	172537584	172537584	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagacctgactccaaatcctAaaaaactcctccagataggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:172537584delA	ENST00000296953.2	+	6	1796	c.1477delA	c.(1477-1479)aaafs	p.K494fs	CREBRF_ENST00000540014.1_Frame_Shift_Del_p.K496fs	NM_153607.2	NP_705835.2	Q8IUR6	CRERF_HUMAN	CREB3 regulatory factor	494					negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular transport (GO:0032388)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein transport (GO:0051222)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TCCAAATCCTAAAAAACTCCT	0.403																																					p.P492fs		Atlas-INDEL	.											.	.	.	.	0			c.1476delT						.						80	81	81					5																	172537584		2203	4300	6503	SO:0001589	frameshift_variant	153222	exon6			.	AY139008	CCDS34293.1, CCDS54948.1	5q35.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164463	ENSG00000164463			24050	protein-coding gene	gene with protein product	"luman/CREB3 recruitment factor"		"chromosome 5 open reading frame 41"	C5orf41		18391022	Standard	NM_153607		Approved	LRF	uc003mch.3	Q8IUR6	OTTHUMG00000163322	ENST00000296953.2:c.1477delA	chr5.hg19:g.172537584delA	ENSP00000296953:p.Lys494fs	143.0	0.0		161.0	10.0	NM_153607	B3DFH2|B3KW49|D3DQM2|F5GXN3|Q5HYG4|Q5HYK0|Q86YR3|Q8IZG1	Frame_Shift_Del	DEL	ENST00000296953.2	hg19	CCDS34293.1																																																																																			.	.		0.403	CREBRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372667.1	NM_153607		-	172537584	A	-	172537584	7	5	114	1	0	1	0	1	0	0	0	0	2302	363	13	0	1527	0	C5orf41	5	172537584	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3004550	172537584	8377676	421	18693										
STC2	8614	hgsc.bcm.edu	37	chr5	172744893	172744893	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagactgttcgtcttcccacTcgctgcttccggaaggtccc	9	16	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:172744893T>C	ENST00000265087.4	-	4	2175	c.866A>G	c.(865-867)gAg>gGg	p.E289G	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	289					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GTCTTCCCACTCGCTGCTTCC	0.577																																					p.E289G		Atlas-SNP	.											.	STC2	59	.	0			c.A866G						.						83	87	86					5																	172744893		2203	4300	6503	SO:0001583	missense	8614	exon4			TCCCACTCGCTGC	AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.866A>G	chr5.hg19:g.172744893T>C	ENSP00000265087:p.Glu289Gly	80.0	0.0		81.0	4.0	NM_003714		Missense_Mutation	SNP	ENST00000265087.4	hg19	CCDS4388.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.982278	0.53827	.	.	ENSG00000113739	ENST00000265087	.	.	.	4.78	4.78	0.61160	.	0.167000	0.52532	D	0.000068	T	0.36991	0.0987	N	0.24115	0.695	0.43263	D	0.995204	P	0.35433	0.501	B	0.27608	0.081	T	0.39542	-0.9609	9	0.56958	D	0.05	-29.9991	14.5043	0.67743	0.0:0.0:0.0:1.0	.	289	O76061	STC2_HUMAN	G	289	.	ENSP00000265087:E289G	E	-	2	0	STC2	172677499	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	3.650000	0.54424	2.008000	0.58898	0.528000	0.53228	GAG	.	.		0.577	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	NM_003714		C	172744893	T	C	172744893	3	2	114	1	0	0	0	0	1	0	0	0	15291	1551	54	2	46	2	STC2	5	172744893	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	207309	172744893	8170367	422	18694										
CPEB4	80315	hgsc.bcm.edu	37	chr5	173317577	173317577	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggcgaataatcttaacaaaCccccctctccgtggagcagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:173317577delC	ENST00000265085.5	+	1	2295	c.841delC	c.(841-843)cccfs	p.P282fs	CPEB4_ENST00000520867.1_Frame_Shift_Del_p.P282fs|CPEB4_ENST00000519835.1_Frame_Shift_Del_p.P282fs|CPEB4_ENST00000522336.1_5'Flank|CPEB4_ENST00000334035.5_Frame_Shift_Del_p.P282fs|CPEB4_ENST00000517880.1_5'Flank	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	282					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TCTTAACAAACCCCCCTCTCC	0.577																																					p.K280fs		Atlas-INDEL	.											.	CPEB4	54	.	0			c.840delA						.						185	198	194					5																	173317577		2203	4300	6503	SO:0001589	frameshift_variant	80315	exon1			.	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.841delC	chr5.hg19:g.173317577delC	ENSP00000265085:p.Pro282fs	92.0	0.0		140.0	11.0	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Frame_Shift_Del	DEL	ENST00000265085.5	hg19	CCDS4390.1																																																																																			.	.		0.577	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		-	173317577	C	-	173317577	7	5	114	1	0	1	0	1	0	0	0	0	3805	507	18	0	843	0	CPEB4	5	173317577	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	572684	173317577	7597683	423	18695										
NOP16	51491	hgsc.bcm.edu	37	chr5	175812233	175812233	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccgctcaccttatagtcctCcccgtggttctctaccatgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:175812233delC	ENST00000389158.5	-	4	817	c.382delG	c.(382-384)gagfs	p.E128fs	NOP16_ENST00000507413.1_Intron|NOP16_ENST00000509257.1_Frame_Shift_Del_p.E128fs|NOP16_ENST00000510123.1_Frame_Shift_Del_p.E128fs			Q9Y3C1	NOP16_HUMAN	NOP16 nucleolar protein	128						intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|lung(4)|ovary(1)	8						TTATAGTCCTCCCCGTGGTTC	0.567																																					p.E128fs		Atlas-INDEL	.											.	NOP16	26	.	0			c.383delA						.						103	104	104					5																	175812233		1905	4116	6021	SO:0001589	frameshift_variant	51491	exon4			.		CCDS43403.1, CCDS58991.1	5q35.2	2012-12-10	2012-12-10		ENSG00000048162	ENSG00000048162			26934	protein-coding gene	gene with protein product	"hypothetical protein HSPC111", "HBV pre-S2 trans-regulated protein 3"	612861	"nucleolar protein 16 homolog (yeast)", "NOP16 nucleolar protein homolog (yeast)"			10810093, 11042152	Standard	NM_001291308		Approved	HSPC111, HSPC185, LOC51491	uc003mee.4	Q9Y3C1	OTTHUMG00000163186	ENST00000389158.5:c.382delG	chr5.hg19:g.175812233delC	ENSP00000373810:p.Glu128fs	101.0	0.0		136.0	11.0	NM_016391	B4DV13|D6RGD3|Q05D05|Q6IAI6|Q8IXL5	Frame_Shift_Del	DEL	ENST00000389158.5	hg19	CCDS43403.1																																																																																			.	.		0.567	NOP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371963.1	NM_016391		-	175812233	C	-	175812233	7	5	114	1	0	1	0	1	0	0	0	0	10546	864	30	0	161	0	NOP16	5	175812233	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2494656	175812233	5103027	424	18696										
RNF44	22838	hgsc.bcm.edu	37	chr5	175956599	175956599	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctatgtctgctttggtgagaCcccggggcttggcatctccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:175956599delC	ENST00000274811.4	-	9	1585	c.1061delG	c.(1060-1062)ggtfs	p.G354fs	RNF44_ENST00000537487.1_Frame_Shift_Del_p.G273fs|RNF44_ENST00000509404.1_5'Flank	NM_014901.4	NP_055716.1	Q7L0R7	RNF44_HUMAN	ring finger protein 44	354							zinc ion binding (GO:0008270)			endometrium(2)|lung(3)|prostate(1)|skin(1)|stomach(1)	8	all_cancers(89;0.0029)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTTGGTGAGACCCCGGGGCTT	0.667																																					p.G354fs		Atlas-INDEL	.											.	RNF44	33	.	0			c.1062delT						.						68	63	65					5																	175956599		2203	4300	6503	SO:0001589	frameshift_variant	22838	exon9			.	AB029023	CCDS4404.1	5q35.3	2013-01-09			ENSG00000146083	ENSG00000146083		"RING-type (C3HC4) zinc fingers"	19180	protein-coding gene	gene with protein product						10470851	Standard	NM_014901		Approved	KIAA1100	uc003mek.1	Q7L0R7	OTTHUMG00000130664	ENST00000274811.4:c.1061delG	chr5.hg19:g.175956599delC	ENSP00000274811:p.Gly354fs	164.0	0.0		181.0	11.0	NM_014901	B4DYE0|Q8ND05|Q9UPQ2	Frame_Shift_Del	DEL	ENST00000274811.4	hg19	CCDS4404.1																																																																																			.	.		0.667	RNF44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253156.2			-	175956599	C	-	175956599	7	5	114	1	0	1	0	1	0	0	0	0	13511	507	18	0	249	0	RNF44	5	175956599	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	144366	175956599	4958661	425	18697										
PDLIM7	9260	hgsc.bcm.edu	37	chr5	176910650	176910650	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgggcagaaggggctcacaCatgagagaaggcatggctct	16	8	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:176910650C>G	ENST00000355841.2	-	13	1435	c.1369G>C	c.(1369-1371)Gtg>Ctg	p.V457L	PDLIM7_ENST00000359895.2_Missense_Mutation_p.V423L|PDLIM7_ENST00000505746.1_5'Flank|PDLIM7_ENST00000356618.4_3'UTR	NM_005451.3	NP_005442.2	Q9NR12	PDLI7_HUMAN	PDZ and LIM domain 7 (enigma)	457	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|receptor-mediated endocytosis (GO:0006898)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ruffle (GO:0001726)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGGGCTCACACATGAGAGAAG	0.582																																					p.V457L		Atlas-SNP	.											.	PDLIM7	32	.	0			c.G1369C						.						71	68	69					5																	176910650		2203	4300	6503	SO:0001583	missense	9260	exon13			CTCACACATGAGA	BC001093	CCDS4422.1, CCDS4423.1, CCDS4424.1	5q35.3	2008-02-05			ENSG00000196923	ENSG00000196923			22958	protein-coding gene	gene with protein product		605903				11874232	Standard	NM_005451		Approved	ENIGMA	uc003mhc.1	Q9NR12	OTTHUMG00000130853	ENST00000355841.2:c.1369G>C	chr5.hg19:g.176910650C>G	ENSP00000348099:p.Val457Leu	206.0	0.0		277.0	106.0	NM_005451	Q14250|Q5XG82|Q6NVZ5|Q96C91|Q9BXB8|Q9BXB9	Missense_Mutation	SNP	ENST00000355841.2	hg19	CCDS4422.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.007169	0.93287	.	.	ENSG00000196923	ENST00000359895;ENST00000355841	T;T	0.49720	0.88;0.77	5.53	5.53	0.82687	Zinc finger, LIM-type (1);	0.000000	0.47455	D	0.000239	T	0.52108	0.1714	N	0.08118	0	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.63225	-0.6685	10	0.66056	D	0.02	.	19.128	0.93393	0.0:1.0:0.0:0.0	.	457;423	Q9NR12;Q9NR12-2	PDLI7_HUMAN;.	L	423;457	ENSP00000352964:V423L;ENSP00000348099:V457L	ENSP00000348099:V457L	V	-	1	0	PDLIM7	176843256	0.999000	0.42202	0.977000	0.42913	0.833000	0.47200	5.471000	0.66762	2.625000	0.88918	0.650000	0.86243	GTG	.	.		0.582	PDLIM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253423.1	NM_005451		G	176910650	C	G	176910650	3	3	114	1	0	0	0	0	1	0	0	0	11693	478	17	4	8	4	PDLIM7	5	176910650	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	954051	176910650	4004610	426	18698										
ZNF354A	6940	hgsc.bcm.edu	37	chr5	178139937	178139937	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcatgaattttttgatgtatAaaaaggcctgaccttcggct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:178139937delA	ENST00000335815.2	-	5	1139	c.942delT	c.(940-942)tttfs	p.F314fs		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	314					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		TTTGATGTATAAAAAGGCCTG	0.393																																					p.I315fs		Atlas-INDEL	.											.	ZNF354A	74	.	0			c.943delA						.						54	57	56					5																	178139937		2202	4300	6502	SO:0001589	frameshift_variant	6940	exon5			.	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"Zinc fingers, C2H2-type", "-"	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.942delT	chr5.hg19:g.178139937delA	ENSP00000337122:p.Phe314fs	104.0	0.0		158.0	12.0	NM_005649	Q9UNJ8	Frame_Shift_Del	DEL	ENST00000335815.2	hg19	CCDS4438.1																																																																																			.	.		0.393	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649		-	178139937	A	-	178139937	7	5	114	1	0	1	0	1	0	0	0	0	17879	359	13	0	879	0	ZNF354A	5	178139937	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1229287	178139937	2775323	427	18699										
ZNF354B	117608	hgsc.bcm.edu	37	chr5	178311121	178311121	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttaaatgtaatacatgtggAaaaacttttagacaaagctc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:178311121delA	ENST00000322434.3	+	5	1894	c.1668delA	c.(1666-1668)ggafs	p.G556fs	RNU1-39P_ENST00000383897.1_RNA|ZNF354B_ENST00000522714.1_3'UTR	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	556					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATACATGTGGAAAAACTTTTA	0.368																																					p.G556fs		Atlas-Indel,Pindel	.											.	ZNF354B	67	.	0			c.1667delG						.						66	63	64					5																	178311121		2203	4300	6503	SO:0001589	frameshift_variant	117608	exon5			.	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"Zinc fingers, C2H2-type", "-"	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.1668delA	chr5.hg19:g.178311121delA	ENSP00000327143:p.Gly556fs	107.0	0.0		127.0	31.0	NM_058230	A8K0V2|Q5U5Z4	Frame_Shift_Del	DEL	ENST00000322434.3	hg19	CCDS4439.1																																																																																			.	.		0.368	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230		-	178311121	A	-	178311121	7	5	114	1	0	1	0	1	0	0	0	0	17880	233	9	0	1682	0	ZNF354B	5	178311121	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	171184	178311121	2604139	428	18700										
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178507066	178507066	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacttacccagtatcagagaTtttttaaaggagataaagcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:178507066delT	ENST00000315475.6	+	5	1939	c.1633delT	c.(1633-1635)tttfs	p.F546fs		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	546			F -> L (in dbSNP:rs1445846).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		GTATCAGAGATTTTTTAAAGG	0.373																																					p.R544fs		Atlas-INDEL	.											.	ZNF354C	77	.	0			c.1632delA						.						59	65	63					5																	178507066		2201	4297	6498	SO:0001589	frameshift_variant	30832	exon5			.		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"Zinc fingers, C2H2-type", "-"	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.1633delT	chr5.hg19:g.178507066delT	ENSP00000324064:p.Phe546fs	139.0	0.0		183.0	12.0	NM_014594	Q6P4P9|Q8NFX1	Frame_Shift_Del	DEL	ENST00000315475.6	hg19	CCDS4443.1																																																																																			.	.		0.373	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			-	178507066	T	-	178507066	7	5	114	1	0	1	0	1	0	0	0	0	17881	1493	52	0	1647	0	ZNF354C	5	178507066	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	195945	178507066	2408194	429	18701										
GFPT2	9945	hgsc.bcm.edu	37	chr5	179762947	179762947	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccacttttaagtccatgctgTcttgttctaaatgaaaggaa	7	8	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:179762947T>C	ENST00000253778.8	-	4	390	c.221A>G	c.(220-222)gAc>gGc	p.D74G		NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	74	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	GTCCATGCTGTCTTGTTCTAA	0.537																																					p.D74G		Atlas-SNP	.											.	GFPT2	74	.	0			c.A221G						.						147	167	161					5																	179762947		2027	4189	6216	SO:0001583	missense	9945	exon4			ATGCTGTCTTGTT	AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"glutamine: fructose-6-phosphate aminotransferase 2"	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.221A>G	chr5.hg19:g.179762947T>C	ENSP00000253778:p.Asp74Gly	131.0	0.0		174.0	7.0	NM_005110	Q53XM2|Q9BWS4	Missense_Mutation	SNP	ENST00000253778.8	hg19	CCDS43411.1	.	.	.	.	.	.	.	.	.	.	T	12.56	1.975261	0.34848	.	.	ENSG00000131459	ENST00000253778	T	0.76578	-1.03	5.21	5.21	0.72293	Glutamine amidotransferase, type II (1);	0.096682	0.64402	D	0.000001	T	0.68044	0.2958	N	0.25647	0.755	0.80722	D	1	B	0.19935	0.04	B	0.29440	0.102	T	0.62627	-0.6814	9	.	.	.	-31.9146	14.7751	0.69726	0.0:0.0:0.0:1.0	.	74	O94808	GFPT2_HUMAN	G	74	ENSP00000253778:D74G	.	D	-	2	0	GFPT2	179695553	1.000000	0.71417	1.000000	0.80357	0.314000	0.28054	6.032000	0.70918	1.965000	0.57142	0.533000	0.62120	GAC	.	.		0.537	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110		C	179762947	T	C	179762947	3	2	114	1	0	0	0	0	1	0	0	0	6354	1667	58	2	1891	2	GFPT2	5	179762947	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1255881	179762947	1152313	430	18702										
EXOC2	55770	hgsc.bcm.edu	37	chr6	556010	556010	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgtgttttaggttgttggaAgacctgtaaggaagaatttt	12	3	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:556010A>G	ENST00000230449.4	-	19	2071	c.1936T>C	c.(1936-1938)Ttc>Ctc	p.F646L	EXOC2_ENST00000448181.3_Missense_Mutation_p.F241L	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	646					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GGTTGTTGGAAGACCTGTAAG	0.348																																					p.F646L		Atlas-SNP	.											.	EXOC2	81	.	0			c.T1936C						.						130	123	125					6																	556010		2203	4300	6503	SO:0001583	missense	55770	exon19			GTTGGAAGACCTG	AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"SEC5-like 1 (S. cerevisiae)"	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.1936T>C	chr6.hg19:g.556010A>G	ENSP00000230449:p.Phe646Leu	94.0	0.0		115.0	5.0	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Missense_Mutation	SNP	ENST00000230449.4	hg19	CCDS34327.1	.	.	.	.	.	.	.	.	.	.	A	13.20	2.165846	0.38217	.	.	ENSG00000112685	ENST00000230449;ENST00000448181	T;T	0.21191	2.02;2.02	5.6	5.6	0.85130	.	0.194343	0.51477	D	0.000084	T	0.09291	0.0229	L	0.47190	1.495	0.58432	D	0.999995	B	0.15141	0.012	B	0.12156	0.007	T	0.09574	-1.0668	10	0.14656	T	0.56	-0.0157	14.6565	0.68835	1.0:0.0:0.0:0.0	.	646	Q96KP1	EXOC2_HUMAN	L	646;241	ENSP00000230449:F646L;ENSP00000398113:F241L	ENSP00000230449:F646L	F	-	1	0	EXOC2	501010	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	5.571000	0.67404	2.248000	0.74166	0.460000	0.39030	TTC	.	.		0.348	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303		G	556010	A	G	556010	3	3	114	1	0	0	0	0	1	0	0	0	5304	72	3	2	878	2	EXOC2	6	556010	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10		556010	170559057	431	18703										
RIPK1	8737	hgsc.bcm.edu	37	chr6	3077159	3077159	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttgggaaggtgtctctgtgTttccacagaacccagggact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:3077159delT	ENST00000259808.4	+	2	400	c.102delT	c.(100-102)tgtfs	p.C34fs	RIPK1_ENST00000479389.1_Intron|RIPK1_ENST00000380409.2_Frame_Shift_Del_p.C34fs|RIPK1_ENST00000541791.1_Frame_Shift_Del_p.C34fs			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	34	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				TGTCTCTGTGTTTCCACAGAA	0.507																																					p.C34fs		Atlas-INDEL	.											.	RIPK1	56	.	0			c.101delG						.						81	74	76					6																	3077159		2203	4300	6503	SO:0001589	frameshift_variant	8737	exon1			.	U25994	CCDS4482.1	6p25.2	2008-02-05			ENSG00000137275	ENSG00000137275			10019	protein-coding gene	gene with protein product		603453				7538908, 8612133	Standard	XM_005249458		Approved	RIP	uc003mux.3	Q13546	OTTHUMG00000014134	ENST00000259808.4:c.102delT	chr6.hg19:g.3077159delT	ENSP00000259808:p.Cys34fs	129.0	0.0		181.0	11.0	NM_003804	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	Frame_Shift_Del	DEL	ENST00000259808.4	hg19	CCDS4482.1																																																																																			.	.		0.507	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039659.2	NM_003804		-	3077159	T	-	3077159	7	5	114	1	0	1	0	1	0	0	0	0	13395	1731	60	0	104	0	RIPK1	6	3077159	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2521149	3077159	168037908	432	18704										
PHACTR1	221692	hgsc.bcm.edu	37	chr6	13206215	13206215	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcccagcaccaccacactgTcctgccctcccagatccagc	7	21	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:13206215T>C	ENST00000379350.1	+	7	962	c.833T>C	c.(832-834)gTc>gCc	p.V278A	PHACTR1_ENST00000332995.7_Missense_Mutation_p.V278A|PHACTR1_ENST00000457702.2_Missense_Mutation_p.V133A|PHACTR1_ENST00000379345.2_Intron			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	278					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			CACCACACTGTCCTGCCCTCC	0.667																																					p.V278A		Atlas-SNP	.											.	PHACTR1	94	.	0			c.T833C						.						44	54	51					6																	13206215		2136	4229	6365	SO:0001583	missense	221692	exon8			ACACTGTCCTGCC	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"Phosphatase and actin regulators"	20990	protein-coding gene	gene with protein product		608723	"RPEL repeat containing 1"	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379350.1:c.833T>C	chr6.hg19:g.13206215T>C	ENSP00000368655:p.Val278Ala	99.0	0.0		126.0	6.0	NM_030948	A8K1V2|Q3MJ93|Q5JSJ2	Missense_Mutation	SNP	ENST00000379350.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.0|22.0	4.229746|4.229746	0.79688|0.79688	.|.	.|.	ENSG00000112137|ENSG00000112137	ENST00000415087|ENST00000379350;ENST00000332995;ENST00000432934;ENST00000457702	.|T;T;T	.|0.32272	.|1.46;1.48;1.52	5.12|5.12	5.12|5.12	0.69794|0.69794	.|.	.|0.279063	.|0.35378	.|N	.|0.003248	T|T	0.21631|0.21631	0.0521|0.0521	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|D;P;P	.|0.56287	.|0.975;0.779;0.859	.|D;B;B	.|0.67103	.|0.949;0.204;0.351	T|T	0.04191|0.04191	-1.0970|-1.0970	5|10	.|0.08381	.|T	.|0.77	-16.2317|-16.2317	14.251|14.251	0.66019|0.66019	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|347;278;278	.|E7ESR5;Q9C0D0;Q9C0D0-2	.|.;PHAR1_HUMAN;.	P|A	113|278;278;347;133	.|ENSP00000368655:V278A;ENSP00000329880:V278A;ENSP00000397669:V133A	.|ENSP00000329880:V278A	S|V	+|+	1|2	0|0	PHACTR1|PHACTR1	13314194|13314194	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.962000|0.962000	0.63368|0.63368	4.110000|4.110000	0.57831|0.57831	2.143000|2.143000	0.66587|0.66587	0.459000|0.459000	0.35465|0.35465	TCC|GTC	.	.		0.667	PHACTR1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039876.1	XM_166420		C	13206215	T	C	13206215	3	2	114	1	0	0	0	0	1	0	0	0	11818	1667	58	2	855	2	PHACTR1	6	13206215	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	10129056	13206215	157908852	433	18705										
CAP2	10486	hgsc.bcm.edu	37	chr6	17543332	17543332	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctggtgtttgacaatgtggtGggcattgtggaagtgatcaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:17543332delG	ENST00000229922.2	+	11	1699	c.1167delG	c.(1165-1167)gtgfs	p.V389fs	CAP2_ENST00000489374.1_Frame_Shift_Del_p.V277fs|CAP2_ENST00000465994.1_Frame_Shift_Del_p.V325fs|CAP2_ENST00000378990.2_Frame_Shift_Del_p.V363fs|CAP2_ENST00000493172.1_Frame_Shift_Del_p.V129fs	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	389	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			ACAATGTGGTGGGCATTGTGG	0.433																																					p.V389fs		Atlas-INDEL	.											.	CAP2	61	.	0			c.1166delT						.						167	165	166					6																	17543332		2203	4300	6503	SO:0001589	frameshift_variant	10486	exon11			.	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.1167delG	chr6.hg19:g.17543332delG	ENSP00000229922:p.Val389fs	138.0	0.0		173.0	12.0	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Frame_Shift_Del	DEL	ENST00000229922.2	hg19	CCDS4539.1																																																																																			.	.		0.433	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2			-	17543332	G	-	17543332	7	5	114	1	0	1	0	1	0	0	0	0	2622	1335	47	0	1205	0	CAP2	6	17543332	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	4337117	17543332	153571735	434	18706										
KIF13A	63971	hgsc.bcm.edu	37	chr6	17852235	17852235	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaccatctacatatggtcccAaaactttatgttctcgaact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:17852235delA	ENST00000259711.6	-	7	638	c.533delT	c.(532-534)ttgfs	p.L178fs	KIF13A_ENST00000378843.2_Frame_Shift_Del_p.L178fs|KIF13A_ENST00000378826.2_Frame_Shift_Del_p.L178fs|KIF13A_ENST00000378816.5_Frame_Shift_Del_p.L178fs|KIF13A_ENST00000378814.5_Frame_Shift_Del_p.L178fs	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	178	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			ATATGGTCCCAAAACTTTATG	0.353																																					p.L178fs		Atlas-INDEL	.											.	KIF13A	276	.	0			c.534delG						.						51	48	49					6																	17852235		1819	4075	5894	SO:0001589	frameshift_variant	63971	exon7			.	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.533delT	chr6.hg19:g.17852235delA	ENSP00000259711:p.Leu178fs	128.0	0.0		184.0	16.0	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Frame_Shift_Del	DEL	ENST00000259711.6	hg19	CCDS47381.1																																																																																			.	.		0.353	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			-	17852235	A	-	17852235	7	5	114	1	0	1	0	1	0	0	0	0	8283	131	5	0	5041	0	KIF13A	6	17852235	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	308903	17852235	153262832	435	18707										
KDM1B	221656	hgsc.bcm.edu	37	chr6	18197380	18197380	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaagtggagagaatactgtaTtttatgaccagaaaaggtct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:18197380delT	ENST00000297792.5	+	9	843	c.666delT	c.(664-666)tatfs	p.Y222fs	KDM1B_ENST00000397244.1_Frame_Shift_Del_p.Y222fs|KDM1B_ENST00000546309.2_Intron|KDM1B_ENST00000388870.2_Frame_Shift_Del_p.Y354fs			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	354					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						GAATACTGTATTTTATGACCA	0.463																																					p.Y222fs		Atlas-INDEL	.											.	KDM1B	58	.	0			c.665delA						.						126	112	116					6																	18197380		2203	4300	6503	SO:0001589	frameshift_variant	221656	exon9			.	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"Chromatin-modifying enzymes / K-demethylases"	21577	protein-coding gene	gene with protein product		613081	"amine oxidase, flavin containing 1", "chromosome 6 open reading frame 193", "amine oxidase (flavin containing) domain 1"	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.666delT	chr6.hg19:g.18197380delT	ENSP00000297792:p.Tyr222fs	196.0	0.0		159.0	10.0	NM_153042	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Frame_Shift_Del	DEL	ENST00000297792.5	hg19	CCDS34343.1																																																																																			.	.		0.463	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042		-	18197380	T	-	18197380	7	5	114	1	0	1	0	1	0	0	0	0	8132	1500	52	0	692	0	KDM1B	6	18197380	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	345145	18197380	152917687	436	18708										
CDKAL1	54901	hgsc.bcm.edu	37	chr6	21108646	21108646	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcacagaaaaagcaaaggacAaaagatctttctcgggtgtt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:21108646delA	ENST00000378610.1	+	11	1261	c.1251delA	c.(1249-1251)acafs	p.T417fs	CDKAL1_ENST00000378624.4_Intron|CDKAL1_ENST00000274695.4_Frame_Shift_Del_p.T417fs			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	417					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			AGCAAAGGACAAAAGATCTTT	0.294																																					p.T417fs		Atlas-INDEL	.											.	CDKAL1	55	.	0			c.1250delC						.						56	56	56					6																	21108646		2203	4291	6494	SO:0001589	frameshift_variant	54901	exon13			.	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.1251delA	chr6.hg19:g.21108646delA	ENSP00000367873:p.Thr417fs	106.0	0.0		139.0	11.0	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Frame_Shift_Del	DEL	ENST00000378610.1	hg19	CCDS4546.1																																																																																			.	.		0.294	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774		-	21108646	A	-	21108646	7	5	114	1	0	1	0	1	0	0	0	0	3154	117	5	0	1293	0	CDKAL1	6	21108646	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2911266	21108646	150006421	437	18709										
DDR1	780	hgsc.bcm.edu	37	chr6	30865154	30865154	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcagcttctccttgttctccAggaatgatttcctgaaagag	8	10	3	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:30865154A>G	ENST00000324771.8	+	17	2545		c.e17-1		DDR1_ENST00000446312.1_Splice_Site|DDR1_ENST00000361741.4_Splice_Site|DDR1_ENST00000418800.2_Splice_Site|DDR1_ENST00000452441.1_Splice_Site|DDR1_ENST00000513240.1_Missense_Mutation_p.R672G|DDR1_ENST00000376575.3_Missense_Mutation_p.R672G|DDR1_ENST00000454612.2_Splice_Site|DDR1_ENST00000508312.1_Splice_Site|DDR1_ENST00000376569.3_Splice_Site|DDR1_ENST00000376570.4_Splice_Site|DDR1_ENST00000376568.3_Splice_Site|DDR1_ENST00000376567.2_Splice_Site			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1						branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CTTGTTCTCCAGGAATGATTT	0.617																																					p.R672G		Atlas-SNP	.											.	DDR1	213	.	0			c.A2014G						.						56	55	55					6																	30865154		2203	4300	6503	SO:0001630	splice_region_variant	780	exon14			TTCTCCAGGAATG	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"CD molecules"	2730	protein-coding gene	gene with protein product		600408	"discoidin domain receptor family, member 1"	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1998-1A>G	chr6.hg19:g.30865154A>G		57.0	0.0		79.0	4.0	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	hg19	CCDS34385.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	19.18|19.18|19.18	3.778524|3.778524|3.778524	0.70107|0.70107|0.70107	.|.|.	.|.|.	ENSG00000204580|ENSG00000204580|ENSG00000204580	ENST00000324771;ENST00000418800;ENST00000454612;ENST00000376569;ENST00000376570;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000376567;ENST00000417521;ENST00000361741;ENST00000484556|ENST00000514434|ENST00000376575;ENST00000513240	.|.|D;D	.|.|0.83250	.|.|-1.7;-1.7	5.39|5.39|5.39	5.39|5.39|5.39	0.77823|0.77823|0.77823	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|D|D	.|0.88310|0.88310	.|0.6402|0.6402	M|M|M	0.75884|0.75884|0.75884	2.315|2.315|2.315	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D	.|.|0.89917	.|.|1.0	.|.|D	.|.|0.80764	.|.|0.994	.|D|D	.|0.90136|0.90136	.|0.4210|0.4210	.|5|9	.|.|0.87932	.|.|D	.|.|0	.|.|.	13.3551|13.3551|13.3551	0.60623|0.60623|0.60623	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|.|672	.|.|Q08345-5	.|.|.	.|R|G	-1|163|672	.|.|ENSP00000365759:R672G;ENSP00000427552:R672G	.|.|ENSP00000365759:R672G	.|Q|R	+|+|+	.|2|1	.|0|2	DDR1|DDR1|DDR1	30973133|30973133|30973133	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.898000|0.898000|0.898000	0.52572|0.52572|0.52572	9.178000|9.178000|9.178000	0.94855|0.94855|0.94855	2.043000|2.043000|2.043000	0.60533|0.60533|0.60533	0.379000|0.379000|0.379000	0.24179|0.24179|0.24179	.|CAG|AGG	.	.		0.617	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	Intron	G	30865154	A	G	30865154	5	3	114	1	0	0	0	0	0	0	1	0	4338	202	7	2	2068	2	DDR1	6	30865154	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	9756508	30865154	140249913	438	18710										
ZBTB12	221527	hgsc.bcm.edu	37	chr6	31868583	31868583	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggggtagaggaggtgggggtGggggcttcggggctggcttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:31868583delG	ENST00000375527.2	-	2	675	c.500delC	c.(499-501)ccafs	p.P171fs	C2_ENST00000452323.2_5'Flank|C2_ENST00000469372.1_Intron	NM_181842.2	NP_862825.1	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	171	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(5)|prostate(1)|skin(1)	10						AGGTGGGGGTGGGGGCTTCGG	0.617																																					p.P167fs		Atlas-INDEL	.											.	ZBTB12	25	.	0			c.501delA						.						22	27	25					6																	31868583		2203	4296	6499	SO:0001589	frameshift_variant	221527	exon2			.	BC043609	CCDS4727.1	6p21.31	2013-01-08	2004-04-15	2004-04-16	ENSG00000204366	ENSG00000204366		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	19066	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 46"	C6orf46		9545376	Standard	NM_181842		Approved	G10, NG35, D6S59E	uc003nyd.1	Q9Y330	OTTHUMG00000031169	ENST00000375527.2:c.500delC	chr6.hg19:g.31868583delG	ENSP00000364677:p.Pro171fs	59.0	0.0		164.0	12.0	NM_181842	B0UY00|Q5JQ98	Frame_Shift_Del	DEL	ENST00000375527.2	hg19	CCDS4727.1																																																																																			.	.		0.617	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842		-	31868583	G	-	31868583	7	5	114	1	0	1	0	1	0	0	0	0	17540	1348	47	0	883	0	ZBTB12	6	31868583	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1003429	31868583	139246484	439	18711										
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31929439	31929439	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttctatcgcctcattccccAgccagccttccaggtacttt	5	16	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:31929439A>T	ENST00000375394.2	+	9	1018	c.905A>T	c.(904-906)cAg>cTg	p.Q302L	NELFE_ENST00000375425.5_5'Flank|SKIV2L_ENST00000544581.1_Missense_Mutation_p.Q109L|NELFE_ENST00000375429.3_5'Flank|NELFE_ENST00000444811.2_5'Flank	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	302					ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						CTCATTCCCCAGCCAGCCTTC	0.602																																					p.Q302L		Atlas-SNP	.											.	SKIV2L	97	.	0			c.A905T						.						115	102	107					6																	31929439		1511	2709	4220	SO:0001583	missense	6499	exon9			TTCCCCAGCCAGC		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.905A>T	chr6.hg19:g.31929439A>T	ENSP00000364543:p.Gln302Leu	58.0	0.0		117.0	36.0	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	A	19.74	3.884208	0.72410	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.49432	0.92;0.78	5.58	5.58	0.84498	.	0.203542	0.45126	D	0.000396	T	0.25606	0.0623	L	0.37561	1.115	0.43430	D	0.995596	B	0.17667	0.023	B	0.12837	0.008	T	0.08126	-1.0737	10	0.44086	T	0.13	-14.2619	14.7342	0.69404	1.0:0.0:0.0:0.0	.	302	Q15477	SKIV2_HUMAN	L	302;144;109	ENSP00000364543:Q302L;ENSP00000442645:Q109L	ENSP00000364543:Q302L	Q	+	2	0	SKIV2L	32037418	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.509000	0.81698	2.131000	0.65755	0.533000	0.62120	CAG	.	.		0.602	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			T	31929439	A	T	31929439	3	4	114	1	0	0	0	0	1	0	0	0	14374	188	7	4	939	4	SKIV2L	6	31929439	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	60856	31929439	139185628	440	18712										
TNXB	7148	hgsc.bcm.edu	37	chr6	32062950	32062950	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaagagatgcatcctcatgCcctcaatggttggcacctct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:32062950delC	ENST00000479795.1	-	4	2401	c.2261delG	c.(2260-2262)ggcfs	p.G754fs	TNXB_ENST00000375247.2_Frame_Shift_Del_p.G754fs|TNXB_ENST00000375244.3_Frame_Shift_Del_p.G754fs			P22105	TENX_HUMAN	tenascin XB	1345					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CATCCTCATGCCCTCAATGGT	0.567																																					p.G754fs		Atlas-INDEL	.											.	TNXB	553	.	0			c.2262delC						.						140	132	134					6																	32062950		692	1591	2283	SO:0001589	frameshift_variant	7148	exon4			.	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.2261delG	chr6.hg19:g.32062950delC	ENSP00000418248:p.Gly754fs	118.0	0.0		157.0	10.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Frame_Shift_Del	DEL	ENST00000479795.1	hg19																																																																																				.	.		0.567	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	NM_019105		-	32062950	C	-	32062950	7	5	114	1	0	1	0	1	0	0	0	0	16361	739	26	0	12616	0	TNXB	6	32062950	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	133511	32062950	139052117	441	18713										
BTNL2	56244	hgsc.bcm.edu	37	chr6	32370747	32370747	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccgaccccttctcctcagtgAggacggggttgtggaccaag	13	13	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:32370747A>G	ENST00000374993.1	-	3	673	c.674T>C	c.(673-675)cTc>cCc	p.L225P	BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000374995.3_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000454136.3_Missense_Mutation_p.L225P|BTNL2_ENST00000544175.1_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	225	Ig-like V-type 2.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CTCCTCAGTGAGGACGGGGTT	0.592																																					p.L225P		Atlas-SNP	.											.	BTNL2	50	.	0			c.T674C						.						70	59	63					6																	32370747		1511	2708	4219	SO:0001583	missense	56244	exon3			TCAGTGAGGACGG	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.674T>C	chr6.hg19:g.32370747A>G	ENSP00000364132:p.Leu225Pro	173.0	0.0		193.0	8.0	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.89	2.671742	0.47781	.	.	ENSG00000204290	ENST00000468270;ENST00000374993	T	0.17854	2.25	4.49	3.34	0.38264	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.160951	0.29916	N	0.010867	T	0.33440	0.0863	M	0.93462	3.42	0.19775	N	0.99996	D	0.89917	1.0	D	0.97110	1.0	T	0.28554	-1.0040	10	0.87932	D	0	.	6.5935	0.22659	0.8925:0.0:0.1075:0.0	.	225	Q9UIR0	BTNL2_HUMAN	P	225	ENSP00000364132:L225P	ENSP00000364132:L225P	L	-	2	0	BTNL2	32478725	0.083000	0.21467	0.008000	0.14137	0.084000	0.17831	3.018000	0.49625	0.911000	0.36747	0.509000	0.49947	CTC	.	.		0.592	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602		G	32370747	A	G	32370747	3	3	114	1	0	0	0	0	1	0	0	0	1567	304	11	2	709	2	BTNL2	6	32370747	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	307797	32370747	138744320	442	18714										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33152022	33152022	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtaatcgtagggcccttcaGgggggtctgtgccaccctcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:33152022delG	ENST00000341947.2	-	8	1246	c.1019delC	c.(1018-1020)cctfs	p.P340fs	COL11A2_ENST00000361917.1_Intron|COL11A2_ENST00000374712.1_Intron|COL11A2_ENST00000374708.4_Intron|COL11A2_ENST00000374714.1_Frame_Shift_Del_p.P314fs|COL11A2_ENST00000374713.1_Frame_Shift_Del_p.P293fs|COL11A2_ENST00000357486.1_Frame_Shift_Del_p.P319fs|COL11A2_ENST00000395197.1_Intron	NM_080680.2	NP_542411.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	340	Nonhelical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						GGGCCCTTCAGGGGGGTCTGT	0.617																																					p.P340fs	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.1020delT						.						63	65	64					6																	33152022		2203	4300	6503	SO:0001589	frameshift_variant	1302	exon8			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000341947.2:c.1019delC	chr6.hg19:g.33152022delG	ENSP00000339915:p.Pro340fs	72.0	0.0		102.0	11.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Del	DEL	ENST00000341947.2	hg19																																																																																				.	.		0.617	COL11A2-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				-	33152022	G	-	33152022	7	5	114	1	0	1	0	1	0	0	0	0	3670	1000	35	0	4427	0	COL11A2	6	33152022	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	781275	33152022	137963045	443	18715										
RXRB	6257	hgsc.bcm.edu	37	chr6	33166144	33166144	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagccccagggccacctggaGggggtggacagtgcaggccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:33166144delG	ENST00000374680.3	-	3	792	c.581delC	c.(580-582)cctfs	p.P195fs	RXRB_ENST00000374685.4_Frame_Shift_Del_p.P195fs|RXRB_ENST00000413614.2_Frame_Shift_Del_p.P99fs|SLC39A7_ENST00000374675.3_5'Flank|RNY4P10_ENST00000365571.1_RNA|RXRB_ENST00000544186.1_Intron|SLC39A7_ENST00000374677.3_5'Flank	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	195	Modulating. {ECO:0000250}.|Pro-rich.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	GCCACCTGGAGGGGGTGGACA	0.612																																					p.P194fs		Atlas-INDEL	.											.	RXRB	34	.	0			c.582delT						.						108	129	122					6																	33166144		1508	2707	4215	SO:0001589	frameshift_variant	6257	exon3			.	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"Nuclear hormone receptors"	10478	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 2"	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.581delC	chr6.hg19:g.33166144delG	ENSP00000363812:p.Pro195fs	101.0	0.0		137.0	11.0	NM_021976	P28703|Q59G65|Q5JP92|Q5STQ1	Frame_Shift_Del	DEL	ENST00000374680.3	hg19	CCDS4768.1																																																																																			.	.		0.612	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		-	33166144	G	-	33166144	7	5	114	1	0	1	0	1	0	0	0	0	13779	1000	35	0	1052	0	RXRB	6	33166144	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	14122	33166144	137948923	444	18716										
B3GALT4	8705	hgsc.bcm.edu	37	chr6	33245843	33245843	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgagcaggaaggaggccaggTtttgcacagcgaggaagtgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:33245843delT	ENST00000451237.1	+	1	927	c.647delT	c.(646-648)gttfs	p.V216fs		NM_003782.3	NP_003773.1	O96024	B3GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	216					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ganglioside galactosyltransferase activity (GO:0047915)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|urinary_tract(2)	13						GGAGGCCAGGTTTTGCACAGC	0.637																																					p.V216fs		Atlas-INDEL	.											.	B3GALT4	30	.	0			c.646delG						.						71	72	72					6																	33245843		2203	4300	6503	SO:0001589	frameshift_variant	8705	exon1			.	Y15061	CCDS34425.1	6p21.3	2013-02-19			ENSG00000235863	ENSG00000235863		"Beta 3-glycosyltransferases"	919	protein-coding gene	gene with protein product		603095				9582303	Standard	NM_003782		Approved	beta3Gal-T4, GalT4	uc003odr.3	O96024	OTTHUMG00000031100	ENST00000451237.1:c.647delT	chr6.hg19:g.33245843delT	ENSP00000390784:p.Val216fs	135.0	0.0		154.0	10.0	NM_003782		Frame_Shift_Del	DEL	ENST00000451237.1	hg19	CCDS34425.1																																																																																			.	.		0.637	B3GALT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076162.2			-	33245843	T	-	33245843	7	5	114	1	0	1	0	1	0	0	0	0	1249	1725	60	0	649	0	B3GALT4	6	33245843	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	79699	33245843	137869224	445	18717										
WDR46	9277	hgsc.bcm.edu	37	chr6	33247088	33247088	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtccagggcagatggccgggCccccgtgggcttggccttcg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:33247088delC	ENST00000374617.4	-	15	2154	c.1798delG	c.(1798-1800)gccfs	p.A600fs	B3GALT4_ENST00000606990.1_Intron	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	600							poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						GATGGCCGGGCCCCCGTGGGC	0.617																																					p.A600fs		Atlas-INDEL	.											.	WDR46	43	.	0			c.1799delC						.						88	96	93					6																	33247088		2203	4300	6503	SO:0001589	frameshift_variant	9277	exon15			.	Z97184	CCDS4772.1	6p21.3	2013-01-09	2005-05-31	2005-05-31	ENSG00000227057	ENSG00000227057		"WD repeat domain containing"	13923	protein-coding gene	gene with protein product		611440	"chromosome 6 open reading frame 11"	C6orf11		9545376, 9521053	Standard	NM_005452		Approved	BING4, UTP7	uc003ods.3	O15213	OTTHUMG00000031192	ENST00000374617.4:c.1798delG	chr6.hg19:g.33247088delC	ENSP00000363746:p.Ala600fs	139.0	0.0		159.0	10.0	NM_005452	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Frame_Shift_Del	DEL	ENST00000374617.4	hg19	CCDS4772.1																																																																																			.	.		0.617	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452		-	33247088	C	-	33247088	7	5	114	1	0	1	0	1	0	0	0	0	17314	739	26	0	38	0	WDR46	6	33247088	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1245	33247088	137867979	446	18718										
C6orf1	221491	hgsc.bcm.edu	37	chr6	34214570	34214570	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggctctgaagggtggggcaaGggggtcaggtcacgtcttga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:34214570delG	ENST00000476320.1	-	5	883	c.201delC	c.(199-201)cccfs	p.P67fs	C6orf1_ENST00000413013.2_Frame_Shift_Del_p.P47fs|C6orf1_ENST00000481533.1_Frame_Shift_Del_p.P67fs|C6orf1_ENST00000468145.1_Frame_Shift_Del_p.P67fs|C6orf1_ENST00000335352.3_Frame_Shift_Del_p.P47fs|C6orf1_ENST00000394990.4_Frame_Shift_Del_p.P67fs	NM_001008703.1	NP_001008703.1	Q86T20	CF001_HUMAN	chromosome 6 open reading frame 1	67						extracellular region (GO:0005576)				endometrium(1)|prostate(1)	2		Ovarian(999;0.0228)		BRCA - Breast invasive adenocarcinoma(397;1.11e-10)		GGTGGGGCAAGGGGGTCAGGT	0.652											OREG0017364	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L68fs		Atlas-INDEL	.											.	C6orf1	6	.	0			c.202delT						.						36	36	36					6																	34214570		2202	4300	6502	SO:0001589	frameshift_variant	221491	exon5			.	AY062936	CCDS4790.1, CCDS75433.1	6p21.3	2011-12-12			ENSG00000186577	ENSG00000186577			1340	protein-coding gene	gene with protein product		611419				10036196	Standard	NM_178508		Approved	LBH, MGC57858	uc003ojh.3	Q86T20	OTTHUMG00000159754	ENST00000476320.1:c.201delC	chr6.hg19:g.34214570delG	ENSP00000417604:p.Pro67fs	116.0	0.0	846	153.0	10.0	NM_001008704	A8K299	Frame_Shift_Del	DEL	ENST00000476320.1	hg19	CCDS4790.1																																																																																			.	.		0.652	C6orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357175.1	NM_178508		-	34214570	G	-	34214570	7	5	114	1	0	1	0	1	0	0	0	0	2318	987	35	0	282	0	C6orf1	6	34214570	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	967482	34214570	136900497	447	18719										
FKBP5	2289	hgsc.bcm.edu	37	chr6	35587912	35587912	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atcacacacatacttgcctcAaaaaagagagttgcattcga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:35587912delA	ENST00000539068.1	-	4	592	c.390delT	c.(388-390)tttfs	p.F130fs	FKBP5_ENST00000357266.4_Frame_Shift_Del_p.F130fs|FKBP5_ENST00000536438.1_Frame_Shift_Del_p.F130fs|FKBP5_ENST00000542713.1_Frame_Shift_Del_p.F130fs|FKBP5_ENST00000540787.1_Intron	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	130	PPIase FKBP-type 1. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						TACTTGCCTCAAAAAAGAGAG	0.443																																					p.E131fs		Atlas-INDEL	.											FKBP5_ENST00000542713,NS,carcinoma,0,2	FKBP5	64	.	0			c.391delG						.						130	112	118					6																	35587912		2203	4300	6503	SO:0001589	frameshift_variant	2289	exon5			.	U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060		"Tetratricopeptide (TTC) repeat domain containing"	3721	protein-coding gene	gene with protein product		602623	"FK506-binding protein 5"			9001212	Standard	NM_004117		Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.390delT	chr6.hg19:g.35587912delA	ENSP00000441205:p.Phe130fs	105.0	0.0		139.0	11.0	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Frame_Shift_Del	DEL	ENST00000539068.1	hg19	CCDS4808.1																																																																																			.	.		0.443	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2			-	35587912	A	-	35587912	7	5	114	1	0	1	0	1	0	0	0	0	5919	127	5	0	1073	0	FKBP5	6	35587912	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1373342	35587912	135527155	448	18720										
MAPK14	1432	hgsc.bcm.edu	37	chr6	36063826	36063826	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggggctgagcttttgaagAaaatctcctcagagtctgtg					rs150174370		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:36063826delA	ENST00000229794.4	+	9	1133	c.745delA	c.(745-747)aaafs	p.K249fs	MAPK14_ENST00000310795.4_Frame_Shift_Del_p.K249fs|MAPK14_ENST00000229795.3_Intron|MAPK14_ENST00000468133.1_Frame_Shift_Del_p.K172fs	NM_139012.2|NM_139014.2	NP_620581.1|NP_620583.1	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cartilage condensation (GO:0001502)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to ionizing radiation (GO:0071479)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chemotaxis (GO:0006935)|chondrocyte differentiation (GO:0002062)|DNA damage checkpoint (GO:0000077)|fatty acid oxidation (GO:0019395)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoclast differentiation (GO:0030316)|p38MAPK cascade (GO:0038066)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to muramyl dipeptide (GO:0032495)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|signal transduction in response to DNA damage (GO:0042770)|skeletal muscle tissue development (GO:0007519)|stress-activated MAPK cascade (GO:0051403)|stress-induced premature senescence (GO:0090400)|striated muscle cell differentiation (GO:0051146)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|MAP kinase kinase activity (GO:0004708)|NFAT protein binding (GO:0051525)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|stomach(1)	16						GCTTTTGAAGAAAATCTCCTC	0.438																																					p.K248fs	Pancreas(20;8 363 26997 32430 36377 43317 49243 50560 51947)|Colon(176;951 1093 20177 30266 32328 34418 35271 44052 51610)	Atlas-INDEL	.											MAPK14_ENST00000229794,NS,carcinoma,0,1	MAPK14	75	.	0			c.744delG						.						116	114	115					6																	36063826		2203	4300	6503	SO:0001589	frameshift_variant	1432	exon9			.	L35263	CCDS4815.1, CCDS4816.1, CCDS4817.1	6p21.3-p21.2	2011-06-09			ENSG00000112062	ENSG00000112062		"Mitogen-activated protein kinase cascade / Kinases"	6876	protein-coding gene	gene with protein product	"p38 MAP kinase"	600289		CSPB1, CSBP1, CSBP2		7997261	Standard	NM_139012		Approved	PRKM14, p38, Mxi2, PRKM15	uc003olq.3	Q16539	OTTHUMG00000159806	ENST00000229794.4:c.745delA	chr6.hg19:g.36063826delA	ENSP00000229794:p.Lys249fs	118.0	0.0		118.0	10.0	NM_139014	A6ZJ92|A8K6P4|B0LPH0|B5TY32|O60776|Q13083|Q14084|Q8TDX0	Frame_Shift_Del	DEL	ENST00000229794.4	hg19	CCDS4816.1																																																																																			.	.		0.438	MAPK14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357450.1	NM_001315		-	36063826	A	-	36063826	7	5	114	1	0	1	0	1	0	0	0	0	9285	247	9	0	779	0	MAPK14	6	36063826	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	475914	36063826	135051241	449	18721										
BRPF3	27154	hgsc.bcm.edu	37	chr6	36179276	36179276	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagctgccagcagggccccaGggggatgcagctgtgctgga					rs79041393		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:36179276delG	ENST00000357641.6	+	7	2674	c.2421delG	c.(2419-2421)cagfs	p.Q807fs	BRPF3_ENST00000534400.1_Frame_Shift_Del_p.Q807fs|BRPF3_ENST00000339717.7_Intron|BRPF3_ENST00000543502.1_Intron|BRPF3_ENST00000534694.1_Intron|BRPF3_ENST00000443324.2_Intron	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	807					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						CAGGGCCCCAGGGGGATGCAG	0.607																																					p.Q807fs		Atlas-INDEL	.											.	BRPF3	93	.	0			c.2420delA						.						15	14	14					6																	36179276		2187	4287	6474	SO:0001589	frameshift_variant	27154	exon7			.	AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.2421delG	chr6.hg19:g.36179276delG	ENSP00000350267:p.Gln807fs	141.0	0.0		140.0	10.0	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Frame_Shift_Del	DEL	ENST00000357641.6	hg19	CCDS34437.1																																																																																			.	.		0.607	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695		-	36179276	G	-	36179276	7	5	114	1	0	1	0	1	0	0	0	0	1523	991	35	0	2443	0	BRPF3	6	36179276	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	115450	36179276	134935791	450	18722										
PPIL1	51645	hgsc.bcm.edu	37	chr6	36823778	36823778	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggctgccattggtatctggCcccgcattggccattgcgag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:36823778delC	ENST00000373699.5	-	4	563	c.312delG	c.(310-312)gggfs	p.G104fs	PPIL1_ENST00000483552.1_5'UTR	NM_016059.4	NP_057143.1	Q9Y3C6	PPIL1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 1	104	Cyclosporin A binding.|PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			lung(1)|ovary(1)	2						TGGTATCTGGCCCCGCATTGG	0.547																																					p.P105fs		Atlas-INDEL	.											PPIL1,caecum,carcinoma,0,1	PPIL1	6	.	0			c.313delC						.						50	48	49					6																	36823778		2203	4300	6503	SO:0001589	frameshift_variant	51645	exon4			.	AF090992	CCDS4826.1	6p21.1	2008-08-29			ENSG00000137168	ENSG00000137168			9260	protein-coding gene	gene with protein product		601301				10072585, 8978786	Standard	NM_016059		Approved	CYPL1	uc003omu.2	Q9Y3C6	OTTHUMG00000014612	ENST00000373699.5:c.312delG	chr6.hg19:g.36823778delC	ENSP00000362803:p.Gly104fs	132.0	0.0		161.0	11.0	NM_016059	O15001|Q5TDC9	Frame_Shift_Del	DEL	ENST00000373699.5	hg19	CCDS4826.1																																																																																			.	.		0.547	PPIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040382.1			-	36823778	C	-	36823778	7	5	114	1	0	1	0	1	0	0	0	0	12338	726	26	0	192	0	PPIL1	6	36823778	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	644502	36823778	134291289	451	18723										
C6orf89	221477	hgsc.bcm.edu	37	chr6	36870160	36870160	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgccaagaagtacatgtcagAaaataagggagttcctctgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:36870160delA	ENST00000480824.2	+	4	647	c.353delA	c.(352-354)gaafs	p.E118fs	C6orf89_ENST00000373685.1_Frame_Shift_Del_p.E118fs|C6orf89_ENST00000359359.2_Frame_Shift_Del_p.E12fs|C6orf89_ENST00000355190.3_Frame_Shift_Del_p.E125fs|C6orf89_ENST00000510325.2_Frame_Shift_Del_p.E12fs			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89	118					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						TACATGTCAGAAAATAAGGGA	0.438																																					p.E125fs		Atlas-INDEL	.											.	C6orf89	39	.	0			c.373delG						.						117	111	113					6																	36870160		2203	4300	6503	SO:0001589	frameshift_variant	221477	exon3			.	AK058086	CCDS4827.1, CCDS69100.1, CCDS75444.1	6p21.31	2013-03-14			ENSG00000198663	ENSG00000198663			21114	protein-coding gene	gene with protein product	"bombesin receptor activated protein"					21857995, 23460338	Standard	NM_152734		Approved	FLJ25357, BRAP	uc003omw.3	Q6UWU4	OTTHUMG00000014613	ENST00000480824.2:c.353delA	chr6.hg19:g.36870160delA	ENSP00000475947:p.Glu118fs	135.0	0.0		155.0	10.0	NM_152734	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Frame_Shift_Del	DEL	ENST00000480824.2	hg19																																																																																				.	.		0.438	C6orf89-004	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000040387.2	NM_152734		-	36870160	A	-	36870160	7	5	114	1	0	1	0	1	0	0	0	0	2375	246	9	0	384	0	C6orf89	6	36870160	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	46382	36870160	134244907	452	18724										
RNF8	9025	hgsc.bcm.edu	37	chr6	37344709	37344709	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgtgtcttgcaggaagagaAggagaagatgcaagcacaga	15	5	1	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:37344709A>G	ENST00000373479.4	+	6	1329	c.1136A>G	c.(1135-1137)aAg>aGg	p.K379R	RNF8_ENST00000469731.1_Missense_Mutation_p.K379R	NM_003958.3|NM_183078.2	NP_003949.1|NP_898901.1	O76064	RNF8_HUMAN	ring finger protein 8, E3 ubiquitin protein ligase	379					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|histone exchange (GO:0043486)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A ubiquitination (GO:0033522)|histone H2B ubiquitination (GO:0033523)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|mitotic nuclear division (GO:0007067)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|response to ionizing radiation (GO:0010212)|spermatid development (GO:0007286)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome, telomeric region (GO:0000781)|nucleolus (GO:0005730)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	13						CAGGAAGAGAAGGAGAAGATG	0.403																																					p.K379R		Atlas-SNP	.											.	RNF8	78	.	0			c.A1136G						.						136	124	128					6																	37344709		2203	4300	6503	SO:0001583	missense	9025	exon6			AAGAGAAGGAGAA	AB012770	CCDS4833.1, CCDS4834.1	6p21.3	2013-01-09	2012-02-23		ENSG00000112130	ENSG00000112130		"RING-type (C3HC4) zinc fingers"	10071	protein-coding gene	gene with protein product		611685	"ring finger protein (C3HC4 type) 8", "ring finger protein 8"			9734811, 9852682	Standard	NM_003958		Approved	KIAA0646	uc003onq.4	O76064	OTTHUMG00000014620	ENST00000373479.4:c.1136A>G	chr6.hg19:g.37344709A>G	ENSP00000362578:p.Lys379Arg	63.0	0.0		90.0	5.0	NM_003958	A6NN24|A8MYC0|B4DPG0|Q53H16|Q5NKW5	Missense_Mutation	SNP	ENST00000373479.4	hg19	CCDS4834.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.689319	0.88735	.	.	ENSG00000112130	ENST00000373479;ENST00000469731	D;T	0.84660	-1.88;-0.4	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.89223	0.6654	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.90435	0.4427	10	0.62326	D	0.03	.	14.8201	0.70065	1.0:0.0:0.0:0.0	.	379	O76064	RNF8_HUMAN	R	379	ENSP00000362578:K379R;ENSP00000418879:K379R	ENSP00000362578:K379R	K	+	2	0	RNF8	37452687	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.962000	0.93254	2.093000	0.63338	0.533000	0.62120	AAG	.	.		0.403	RNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040403.2			G	37344709	A	G	37344709	3	3	114	1	0	0	0	0	1	0	0	0	13515	72	3	2	1158	2	RNF8	6	37344709	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	474549	37344709	133770358	453	18725										
MDGA1	266727	hgsc.bcm.edu	37	chr6	37631783	37631783	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttacaaggcactgcagcatgAgggtgtccccctcccggatg	12	13	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:37631783A>G	ENST00000434837.3	-	2	1345	c.167T>C	c.(166-168)cTc>cCc	p.L56P	MDGA1_ENST00000505425.1_Missense_Mutation_p.L56P|MDGA1_ENST00000297153.7_Missense_Mutation_p.L56P	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	56	Ig-like 1.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						CTGCAGCATGAGGGTGTCCCC	0.637																																					p.L56P		Atlas-SNP	.											.	MDGA1	104	.	0			c.T167C						.						77	79	79					6																	37631783		2119	4230	6349	SO:0001583	missense	266727	exon2			AGCATGAGGGTGT	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.167T>C	chr6.hg19:g.37631783A>G	ENSP00000402584:p.Leu56Pro	148.0	0.0		175.0	7.0	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	hg19	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.722819	0.89298	.	.	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425	T;T;T	0.52983	0.64;0.64;0.64	5.25	5.25	0.73442	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.40818	N	0.001019	T	0.65354	0.2683	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.72846	-0.4169	10	0.72032	D	0.01	.	14.3559	0.66738	1.0:0.0:0.0:0.0	.	56	Q8NFP4	MDGA1_HUMAN	P	56	ENSP00000402584:L56P;ENSP00000297153:L56P;ENSP00000422042:L56P	ENSP00000297153:L56P	L	-	2	0	MDGA1	37739761	1.000000	0.71417	0.968000	0.41197	0.985000	0.73830	9.339000	0.96797	1.994000	0.58287	0.533000	0.62120	CTC	.	.		0.637	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			G	37631783	A	G	37631783	3	3	114	1	0	0	0	0	1	0	0	0	9415	304	11	2	2764	2	MDGA1	6	37631783	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	287074	37631783	133483284	454	18726										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42232472	42232472	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgggggaggccctcattccCccgtgggaccgcatgtggcc	15	14	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:42232472C>T	ENST00000372922.4	-	7	2167	c.1605G>A	c.(1603-1605)ggG>ggA	p.G535G	TRERF1_ENST00000372917.4_Silent_p.G535G|TRERF1_ENST00000340840.2_Silent_p.G535G|TRERF1_ENST00000354325.2_Silent_p.G535G|TRERF1_ENST00000541110.1_Silent_p.G535G	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	535	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CCCTCATTCCCCCGTGGGACC	0.567																																					p.G535G		Atlas-SNP	.											.	TRERF1	124	.	0			c.G1605A						.						96	85	89					6																	42232472		2203	4300	6503	SO:0001819	synonymous_variant	55809	exon7			CATTCCCCCGTGG	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1605G>A	chr6.hg19:g.42232472C>T		98.0	0.0		121.0	5.0	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	hg19	CCDS4867.1																																																																																			.	.		0.567	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		T	42232472	C	T	42232472	2	4	114	1	0	0	0	0	0	0	0	1	16490	610	22	3		3	TRERF1	6	42232472	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	4600689	42232472	128882595	455	18727										
UBR2	23304	hgsc.bcm.edu	37	chr6	42637938	42637938	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaggatcctcgtgttcccatAatgtgttggggtagctgcgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:42637938delA	ENST00000372899.1	+	35	4248	c.3990delA	c.(3988-3990)atafs	p.I1330fs	UBR2_ENST00000372883.3_3'UTR|UBR2_ENST00000372901.1_Frame_Shift_Del_p.I1330fs	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1330					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			GTGTTCCCATAATGTGTTGGG	0.418																																					p.I1330fs		Atlas-INDEL	.											.	UBR2	134	.	0			c.3989delT						.						147	124	132					6																	42637938		2203	4300	6503	SO:0001589	frameshift_variant	23304	exon35			.	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.3990delA	chr6.hg19:g.42637938delA	ENSP00000361990:p.Ile1330fs	136.0	0.0		155.0	10.0	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Frame_Shift_Del	DEL	ENST00000372899.1	hg19	CCDS4870.1																																																																																			.	.		0.418	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		-	42637938	A	-	42637938	7	5	114	1	0	1	0	1	0	0	0	0	16917	352	13	0	4274	0	UBR2	6	42637938	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	405466	42637938	128477129	456	18728										
PPP2R5D	5528	hgsc.bcm.edu	37	chr6	42975751	42975751	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcatcgcatctatggcaagTttttggggctccgggcttat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:42975751delT	ENST00000485511.1	+	7	984	c.805delT	c.(805-807)tttfs	p.F269fs	PPP2R5D_ENST00000461010.1_Frame_Shift_Del_p.F163fs|PPP2R5D_ENST00000472118.1_Frame_Shift_Del_p.F261fs|PPP2R5D_ENST00000394110.3_Frame_Shift_Del_p.F237fs	NM_001270476.1|NM_006245.3	NP_001257405.1|NP_006236.1	Q14738	2A5D_HUMAN	protein phosphatase 2, regulatory subunit B', delta	269					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of catalytic activity (GO:0050790)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	25			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CTATGGCAAGTTTTTGGGGCT	0.527																																					p.K268fs	Melanoma(63;587 1613 29742 31770)	Atlas-INDEL	.											.	PPP2R5D	47	.	0			c.804delG						.						111	107	109					6																	42975751		2203	4300	6503	SO:0001589	frameshift_variant	5528	exon7			.	L76702	CCDS4878.1, CCDS43464.1, CCDS55002.1	6p21.1	2010-06-18	2010-04-14		ENSG00000112640	ENSG00000112640		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9312	protein-coding gene	gene with protein product		601646	"protein phosphatase 2, regulatory subunit B (B56), delta isoform", "protein phosphatase 2, regulatory subunit B', delta isoform"			7592815	Standard	NM_006245		Approved	B56D	uc003oth.4	Q14738	OTTHUMG00000014716	ENST00000485511.1:c.805delT	chr6.hg19:g.42975751delT	ENSP00000417963:p.Phe269fs	140.0	0.0		190.0	12.0	NM_006245	A8K3I9|B5BUA6|O00494|O00696|Q15171|Q5TC39	Frame_Shift_Del	DEL	ENST00000485511.1	hg19	CCDS4878.1																																																																																			.	.		0.527	PPP2R5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040573.3	NM_006245		-	42975751	T	-	42975751	7	5	114	1	0	1	0	1	0	0	0	0	12407	1725	60	0	831	0	PPP2R5D	6	42975751	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	337813	42975751	128139316	457	18729										
PTK7	5754	hgsc.bcm.edu	37	chr6	43100230	43100230	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggagcgtgtgacctgccttCcccccaagggtctgccagag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:43100230delC	ENST00000230419.4	+	7	1254	c.1033delC	c.(1033-1035)cccfs	p.P346fs	PTK7_ENST00000471863.1_Frame_Shift_Del_p.P346fs|PTK7_ENST00000352931.2_Frame_Shift_Del_p.P346fs|PTK7_ENST00000349241.2_Frame_Shift_Del_p.P346fs|PTK7_ENST00000345201.2_Frame_Shift_Del_p.P346fs|PTK7_ENST00000481273.1_Frame_Shift_Del_p.P354fs	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	346	Ig-like C2-type 4.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			GACCTGCCTTCCCCCCAAGGG	0.617																																					p.L352fs		Atlas-INDEL	.											.	PTK7	101	.	0			c.1056delT						.						61	63	62					6																	43100230		2203	4300	6503	SO:0001589	frameshift_variant	5754	exon7			.	AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.1033delC	chr6.hg19:g.43100230delC	ENSP00000230419:p.Pro346fs	155.0	0.0		166.0	15.0	NM_001270398	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Frame_Shift_Del	DEL	ENST00000230419.4	hg19	CCDS4884.1																																																																																			.	.		0.617	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2			-	43100230	C	-	43100230	7	5	114	1	0	1	0	1	0	0	0	0	12778	855	30	0	1059	0	PTK7	6	43100230	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	124479	43100230	128014837	458	18730										
ABCC10	89845	hgsc.bcm.edu	37	chr6	43413441	43413441	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgcccttcatcctcaacatCctcctggccaacgcggcagg	8	18	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:43413441C>A	ENST00000372530.4	+	15	3350	c.3135C>A	c.(3133-3135)atC>atA	p.I1045I	ABCC10_ENST00000244533.3_Silent_p.I1017I	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	1045	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	TCCTCAACATCCTCCTGGCCA	0.627																																					p.I1045I		Atlas-SNP	.											.	ABCC10	118	.	0			c.C3135A						.						64	56	58					6																	43413441		2203	4300	6503	SO:0001819	synonymous_variant	89845	exon15			CAACATCCTCCTG	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.3135C>A	chr6.hg19:g.43413441C>A		258.0	0.0		251.0	102.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	hg19	CCDS56430.1																																																																																			.	.		0.627	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		A	43413441	C	A	43413441	2	1	114	1	0	0	0	0	0	0	0	1	50	845	30	3		3	ABCC10	6	43413441	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	313211	43413441	127701626	459	18731										
TJAP1	93643	hgsc.bcm.edu	37	chr6	43473140	43473140	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctagctctgccagctctgaAgaggacctgctggtcagctg	13	12	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:43473140A>G	ENST00000372445.5	+	11	1597	c.1221A>G	c.(1219-1221)gaA>gaG	p.E407E	TJAP1_ENST00000438588.2_Silent_p.E407E|TJAP1_ENST00000259751.1_Silent_p.E397E|TJAP1_ENST00000372444.2_Silent_p.E397E|TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000436109.2_Silent_p.E397E|TJAP1_ENST00000372452.1_Silent_p.E397E|TJAP1_ENST00000372449.1_Silent_p.E407E	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	407					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CCAGCTCTGAAGAGGACCTGC	0.667																																					p.E407E		Atlas-SNP	.											.	TJAP1	35	.	0			c.A1221G						.						38	39	39					6																	43473140		2203	4300	6503	SO:0001819	synonymous_variant	93643	exon11			CTCTGAAGAGGAC	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.1221A>G	chr6.hg19:g.43473140A>G		55.0	0.0		79.0	4.0	NM_001146016	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Silent	SNP	ENST00000372445.5	hg19	CCDS55004.1																																																																																			.	.		0.667	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		G	43473140	A	G	43473140	2	3	114	1	0	0	0	0	0	0	0	1	15943	69	3	2		2	TJAP1	6	43473140	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	59699	43473140	127641927	460	18732										
MUT	4594	hgsc.bcm.edu	37	chr6	49416619	49416619	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agctttggccattccacccaTttcttcaatttcattaatga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:49416619delT	ENST00000274813.3	-	7	1481	c.1354delA	c.(1354-1356)atgfs	p.M452fs		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	452					cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATTCCACCCATTTCTTCAATT	0.318																																					p.M452fs		Atlas-INDEL	.											.	MUT	70	.	0			c.1355delT						.						121	122	122					6																	49416619		2203	4300	6503	SO:0001589	frameshift_variant	4594	exon7			.		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"methylmalonyl Coenzyme A mutase"			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1354delA	chr6.hg19:g.49416619delT	ENSP00000274813:p.Met452fs	116.0	0.0		162.0	11.0	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Frame_Shift_Del	DEL	ENST00000274813.3	hg19	CCDS4924.1																																																																																			.	.		0.318	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1			-	49416619	T	-	49416619	7	5	114	1	0	1	0	1	0	0	0	0	10000	1493	52	0	926	0	MUT	6	49416619	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	5943479	49416619	121698448	461	18733										
CRISP2	7180	hgsc.bcm.edu	37	chr6	49660494	49660494	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcactaggtaaatcagtaaaTtttgttctcacataggcaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:49660494delT	ENST00000339139.4	-	10	960	c.724delA	c.(724-726)attfs	p.I242fs		NM_001142407.2|NM_001142408.2|NM_001142417.2|NM_001142435.2|NM_001261822.1|NM_003296.3	NP_001135879.1|NP_001135880.1|NP_001135889.1|NP_001135907.1|NP_001248751.1|NP_003287.1	P16562	CRIS2_HUMAN	cysteine-rich secretory protein 2	242					single organismal cell-cell adhesion (GO:0016337)	extracellular space (GO:0005615)				kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	19	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			AATCAGTAAATTTTGTTCTCA	0.398																																					p.I242fs		Atlas-INDEL	.											.	CRISP2	53	.	0			c.725delT						.						167	146	153					6																	49660494		2203	4300	6503	SO:0001589	frameshift_variant	7180	exon10			.	X95239	CCDS4928.1	6p12.3	2009-03-12	2003-09-03	2003-09-05	ENSG00000124490	ENSG00000124490			12024	protein-coding gene	gene with protein product	"cancer/testis antigen 36"	187430	"testis specific protein 1 (probe H4-1 p3-1)"	GAPDL5, TPX1		2613236, 8665901	Standard	NM_003296		Approved	CRISP-2, CT36	uc003ozo.3	P16562	OTTHUMG00000014822	ENST00000339139.4:c.724delA	chr6.hg19:g.49660494delT	ENSP00000339155:p.Ile242fs	97.0	0.0		136.0	10.0	NM_001142408	A8K8M0|Q53FF2|Q5U8Z9|Q7Z7B2	Frame_Shift_Del	DEL	ENST00000339139.4	hg19	CCDS4928.1																																																																																			.	.		0.398	CRISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040870.2	NM_003296		-	49660494	T	-	49660494	7	5	114	1	0	1	0	1	0	0	0	0	3882	1493	52	0	11	0	CRISP2	6	49660494	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	243875	49660494	121454573	462	18734										
MCM3	4172	hgsc.bcm.edu	37	chr6	52147525	52147525	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagtccgcggggagacgtgcTtggagccaaagctgccttcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:52147525delT	ENST00000229854.7	-	3	402	c.326delA	c.(325-327)aagfs	p.K109fs	MCM3_ENST00000596288.1_Frame_Shift_Del_p.K154fs|MCM3_ENST00000419835.2_Frame_Shift_Del_p.K63fs			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	109					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					GGAGACGTGCTTGGAGCCAAA	0.532																																					p.K154fs		Atlas-INDEL	.											.	MCM3	63	.	0			c.462delG						.						97	97	97					6																	52147525		2203	4300	6503	SO:0001589	frameshift_variant	4172	exon3			.	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"minichromosome maintenance deficient (S. cerevisiae) 3", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.326delA	chr6.hg19:g.52147525delT	ENSP00000229854:p.Lys109fs	132.0	0.0		162.0	10.0	NM_002388	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Frame_Shift_Del	DEL	ENST00000229854.7	hg19																																																																																				.	.		0.532	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1			-	52147525	T	-	52147525	7	5	114	1	0	1	0	1	0	0	0	0	9396	1609	56	0	2160	0	MCM3	6	52147525	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2487031	52147525	118967542	463	18735										
EFHC1	114327	hgsc.bcm.edu	37	chr6	52343943	52343943	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcgcaattctggtatcattGggggcaagtaccttggcagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:52343943delG	ENST00000371068.5	+	8	1490	c.1387delG	c.(1387-1389)gggfs	p.G464fs	EFHC1_ENST00000538167.1_Frame_Shift_Del_p.G445fs|EFHC1_ENST00000433625.2_Frame_Shift_Del_p.G373fs	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	464	DM10 3. {ECO:0000255|PROSITE- ProRule:PRU00665}.					axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					TGGTATCATTGGGGGCAAGTA	0.458																																					p.I462fs		Atlas-INDEL	.											.	EFHC1	68	.	0			c.1386delT						.						159	146	150					6																	52343943		2203	4300	6503	SO:0001589	frameshift_variant	114327	exon8			.	AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"EF-hand domain containing"	16406	protein-coding gene	gene with protein product	"myoclonin-1"	608815	"epilepsy, juvenile myoclonic 1"	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.1387delG	chr6.hg19:g.52343943delG	ENSP00000360107:p.Gly464fs	131.0	0.0		151.0	12.0	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Frame_Shift_Del	DEL	ENST00000371068.5	hg19	CCDS4942.1																																																																																			.	.		0.458	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		-	52343943	G	-	52343943	7	5	114	1	0	1	0	1	0	0	0	0	4948	1348	47	0	1427	0	EFHC1	6	52343943	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	196418	52343943	118771124	464	18736										
DST	667	hgsc.bcm.edu	37	chr6	56336022	56336022	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgattcatccatcgcatgtaTtttttgcgccagatatcaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:56336022delT	ENST00000361203.3	-	90	21250	c.21243delA	c.(21241-21243)aaafs	p.K7081fs	DST_ENST00000370754.5_Frame_Shift_Del_p.K7370fs|DST_ENST00000446842.2_Frame_Shift_Del_p.K6866fs|DST_ENST00000312431.6_3'UTR|DST_ENST00000370769.4_Frame_Shift_Del_p.K7192fs|DST_ENST00000370788.2_Frame_Shift_Del_p.K4995fs|DST_ENST00000421834.2_Frame_Shift_Del_p.K5077fs|DST_ENST00000244364.6_Frame_Shift_Del_p.K4778fs			Q03001	DYST_HUMAN	dystonin	7190					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ATCGCATGTATTTTTTGCGCC	0.358																																					p.Y4779fs		Atlas-INDEL	.											.	DST	1427	.	0			c.14335delT						.						59	54	55					6																	56336022		1870	4146	6016	SO:0001589	frameshift_variant	667	exon76			.	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.21243delA	chr6.hg19:g.56336022delT	ENSP00000354508:p.Lys7081fs	142.0	0.0		158.0	11.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Frame_Shift_Del	DEL	ENST00000361203.3	hg19																																																																																				.	.		0.358	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		-	56336022	T	-	56336022	7	5	114	1	0	1	0	1	0	0	0	0	4785	1490	52	0	1217	0	DST	6	56336022	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3992079	56336022	114779045	465	18737										
PHF3	23469	hgsc.bcm.edu	37	chr6	64395267	64395267	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cataggccagtcaaagtcagAaaaaaacaaattgataagga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:64395267delA	ENST00000262043.3	+	4	1984	c.1644delA	c.(1642-1644)agafs	p.R548fs	PHF3_ENST00000509330.1_Frame_Shift_Del_p.R548fs|PHF3_ENST00000393387.1_Frame_Shift_Del_p.R548fs			Q92576	PHF3_HUMAN	PHD finger protein 3	548					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			TCAAAGTCAGAAAAAAACAAA	0.333																																					p.R548fs	GBM(135;136 1820 29512 34071 46235)	Atlas-INDEL	.											.	PHF3	191	.	0			c.1643delG						.						51	54	53					6																	64395267		2203	4298	6501	SO:0001589	frameshift_variant	23469	exon3			.	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.1644delA	chr6.hg19:g.64395267delA	ENSP00000262043:p.Arg548fs	162.0	0.0		182.0	11.0	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Frame_Shift_Del	DEL	ENST00000262043.3	hg19	CCDS4966.1																																																																																			.	.		0.333	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			-	64395267	A	-	64395267	7	5	114	1	0	1	0	1	0	0	0	0	11845	243	9	0	1654	0	PHF3	6	64395267	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	8059245	64395267	106719800	466	18738										
EYS	346007	hgsc.bcm.edu	37	chr6	66204564	66204564	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaacaatcttacctgtaaatGgtgggtgacagacacattca	8	8	2	2	rs367977860	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:66204564G>A	ENST00000370621.3	-	4	1266	c.740C>T	c.(739-741)cCa>cTa	p.P247L	EYS_ENST00000370618.3_Missense_Mutation_p.P247L|EYS_ENST00000393380.2_Missense_Mutation_p.P247L|EYS_ENST00000342421.5_Missense_Mutation_p.P247L|EYS_ENST00000503581.1_Missense_Mutation_p.P247L|EYS_ENST00000370616.2_Missense_Mutation_p.P247L			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	247	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						ACCTGTAAATGGTGGGTGACA	0.284													G|||	3	0.000599042	0.0023	0	5008	,	,		16336	0		0	False		,,,				2504	0				p.P247L		Atlas-SNP	.											.	EYS	527	.	0			c.C740T						.	G	LEU/PRO,LEU/PRO,LEU/PRO	4,4388		0,4,2192	14	14	14		740,740,740	-4.2	0	6		14	0,8560		0,0,4280	no	missense,missense,missense	EYS	NM_001142800.1,NM_001142801.1,NM_198283.1	98,98,98	0,4,6472	AA,AG,GG		0.0,0.0911,0.0309	possibly-damaging,possibly-damaging,possibly-damaging	247/3145,247/620,247/595	66204564	4,12948	2196	4280	6476	SO:0001583	missense	346007	exon4			GTAAATGGTGGGT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.740C>T	chr6.hg19:g.66204564G>A	ENSP00000359655:p.Pro247Leu	62.0	0.0		73.0	4.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	G	14.46	2.540902	0.45280	9.11E-4	0.0	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	D;D;D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08;-3.08;-3.08	4.72	-4.15	0.03881	.	.	.	.	.	T	0.75810	0.3900	N	0.08118	0	0.09310	N	1	P;P;P	0.44139	0.557;0.793;0.827	B;B;P	0.47827	0.085;0.422;0.558	T	0.70839	-0.4763	9	0.87932	D	0	.	9.0906	0.36607	0.089:0.0:0.1952:0.7158	.	247;247;247	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	L	247	ENSP00000424243:P247L;ENSP00000359655:P247L;ENSP00000359650:P247L;ENSP00000377042:P247L;ENSP00000341818:P247L;ENSP00000359652:P247L	ENSP00000341818:P247L	P	-	2	0	EYS	66261285	0.289000	0.24334	0.004000	0.12327	0.896000	0.52359	0.673000	0.25203	-0.453000	0.07076	0.591000	0.81541	CCA	.	.		0.284	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	66204564	G	A	66204564	3	1	114	1	0	0	0	0	1	0	0	0	5334	1348	47	3	8816	3	EYS	6	66204564	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1809297	66204564	104910503	467	18739										
KCNQ5	56479	hgsc.bcm.edu	37	chr6	73787512	73787512	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcacagcttggtacataggaTttttggttcttattttttcg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:73787512delT	ENST00000370398.1	+	5	929	c.820delT	c.(820-822)tttfs	p.F274fs	KCNQ5_ENST00000355635.3_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000370392.1_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000355194.4_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000402622.2_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000342056.2_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000403813.2_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000414165.2_Frame_Shift_Del_p.F274fs	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	274					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	GTACATAGGATTTTTGGTTCT	0.353																																					p.G273fs	GBM(142;1375 1859 14391 23261 44706)	Atlas-INDEL	.											.	KCNQ5	153	.	0			c.819delA						.						137	116	123					6																	73787512		2203	4300	6503	SO:0001589	frameshift_variant	56479	exon5			.	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.820delT	chr6.hg19:g.73787512delT	ENSP00000359425:p.Phe274fs	107.0	0.0		140.0	11.0	NM_001160132	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Frame_Shift_Del	DEL	ENST00000370398.1	hg19	CCDS4976.1																																																																																			.	.		0.353	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		-	73787512	T	-	73787512	7	5	114	1	0	1	0	1	0	0	0	0	8095	1493	52	0	838	0	KCNQ5	6	73787512	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	7582948	73787512	97327555	468	18740										
DDX43	55510	hgsc.bcm.edu	37	chr6	74125911	74125911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaagggaaatggaaagaaaaAtggaaagacctcaaggaagg	13	3	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:74125911A>G	ENST00000370336.4	+	16	2067	c.1909A>G	c.(1909-1911)Atg>Gtg	p.M637V	MB21D1_ENST00000370318.1_Intron	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	637					ATP catabolic process (GO:0006200)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						GGAAAGAAAAATGGAAAGACC	0.378																																					p.M637V		Atlas-SNP	.											.	DDX43	69	.	0			c.A1909G						.						112	111	112					6																	74125911		2203	4300	6503	SO:0001583	missense	55510	exon16			AGAAAAATGGAAA		CCDS4977.1	6q13	2014-01-21			ENSG00000080007	ENSG00000080007		"DEAD-boxes"	18677	protein-coding gene	gene with protein product	"cancer/testis antigen 13"	606286				10919659	Standard	NM_018665		Approved	HAGE, DKFZp434H2114, CT13	uc003pgw.3	Q9NXZ2	OTTHUMG00000015033	ENST00000370336.4:c.1909A>G	chr6.hg19:g.74125911A>G	ENSP00000359361:p.Met637Val	57.0	0.0		71.0	4.0	NM_018665	B4E0C8|Q6NXR1	Missense_Mutation	SNP	ENST00000370336.4	hg19	CCDS4977.1	.	.	.	.	.	.	.	.	.	.	A	6.548	0.469322	0.12461	.	.	ENSG00000080007	ENST00000370336	T	0.14266	2.52	5.26	-0.547	0.11836	.	0.548016	0.18229	N	0.147631	T	0.02119	0.0066	L	0.36672	1.1	0.23581	N	0.997368	B	0.15719	0.014	B	0.12837	0.008	T	0.45175	-0.9279	10	0.16896	T	0.51	-8.7957	2.6132	0.04897	0.3832:0.0897:0.0848:0.4424	.	637	Q9NXZ2	DDX43_HUMAN	V	637	ENSP00000359361:M637V	ENSP00000359361:M637V	M	+	1	0	DDX43	74182632	0.000000	0.05858	0.995000	0.50966	0.973000	0.67179	-0.607000	0.05648	0.085000	0.17107	0.482000	0.46254	ATG	.	.		0.378	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665		G	74125911	A	G	74125911	3	3	114	1	0	0	0	0	1	0	0	0	4365	101	4	2	1971	2	DDX43	6	74125911	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	338399	74125911	96989156	469	18741										
C6orf150	115004	hgsc.bcm.edu	37	chr6	74161746	74161746	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgggatcccgacttcctggcGgggccgaactttcccgcctt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:74161746delG	ENST00000370315.3	-	1	253	c.159delC	c.(157-159)cccfs	p.P53fs	MB21D1_ENST00000370318.1_Frame_Shift_Del_p.P53fs	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	53					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						ACTTCCTGGCGGGGCCGAACT	0.716																																					p.A54fs		Atlas-INDEL	.											.	MB21D1	33	.	0			c.160delG						.						4	5	5					6																	74161746		1997	3978	5975	SO:0001589	frameshift_variant	115004	exon1			.	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"chromosome 6 open reading frame 150"	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.159delC	chr6.hg19:g.74161746delG	ENSP00000359339:p.Pro53fs	145.0	0.0		179.0	12.0	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Frame_Shift_Del	DEL	ENST00000370315.3	hg19	CCDS4978.1																																																																																			.	.		0.716	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441		-	74161746	G	-	74161746	7	5	114	1	0	1	0	1	0	0	0	0	2339	1103	39	0	1429	0	C6orf150	6	74161746	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	35835	74161746	96953321	470	18742										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76124421	76124421	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtttgactctacctgcaactCcccttccattatactgagta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:76124421delC	ENST00000237172.7	-	2	598	c.268delG	c.(268-270)gagfs	p.E90fs	FILIP1_ENST00000393004.2_Frame_Shift_Del_p.E90fs	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	90				ELSKEDLIQLLSIMEGE -> AQYAIYIVSRLILLHFL (in Ref. 2; BAA86589). {ECO:0000305}.						breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						ACCTGCAACTCCCCTTCCATT	0.383																																					p.E90fs		Atlas-INDEL	.											.	FILIP1	173	.	0			c.269delA						.						175	168	171					6																	76124421		2203	4300	6503	SO:0001589	frameshift_variant	27145	exon2			.	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.268delG	chr6.hg19:g.76124421delC	ENSP00000237172:p.Glu90fs	112.0	0.0		143.0	10.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Frame_Shift_Del	DEL	ENST00000237172.7	hg19	CCDS4984.1																																																																																			.	.		0.383	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		-	76124421	C	-	76124421	7	5	114	1	0	1	0	1	0	0	0	0	5902	864	30	0	3393	0	FILIP1	6	76124421	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1962675	76124421	94990646	471	18743										
MYO6	4646	hgsc.bcm.edu	37	chr6	76558143	76558143	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttagaatgtgcacggctatgAaaaaaattggtttggatgat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:76558143delA	ENST00000369977.3	+	11	1112	c.973delA	c.(973-975)aaafs	p.K326fs	MYO6_ENST00000369981.3_Frame_Shift_Del_p.K326fs|MYO6_ENST00000369985.4_Frame_Shift_Del_p.K326fs|MYO6_ENST00000369975.1_Frame_Shift_Del_p.K326fs	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	326	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		CACGGCTATGAAAAAAATTGG	0.413																																					p.M324fs		Atlas-INDEL	.											.	MYO6	124	.	0			c.972delG						.						140	141	141					6																	76558143		2203	4300	6503	SO:0001589	frameshift_variant	4646	exon11			.	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.973delA	chr6.hg19:g.76558143delA	ENSP00000358994:p.Lys326fs	141.0	0.0		178.0	11.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Frame_Shift_Del	DEL	ENST00000369977.3	hg19	CCDS34487.1																																																																																			.	.		0.413	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		-	76558143	A	-	76558143	7	5	114	1	0	1	0	1	0	0	0	0	10090	247	9	0	1011	0	MYO6	6	76558143	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	433722	76558143	94556924	472	18744										
TTK	7272	hgsc.bcm.edu	37	chr6	80721476	80721476	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaccacaagatgcagaaatAggttaccggaattcattgag	9	9	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:80721476A>G	ENST00000369798.2	+	7	870	c.759A>G	c.(757-759)atA>atG	p.I253M	TTK_ENST00000230510.3_Missense_Mutation_p.I253M|TTK_ENST00000509894.1_Missense_Mutation_p.I253M	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	253					chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		ATGCAGAAATAGGTTACCGGA	0.333																																					p.I253M		Atlas-SNP	.											.	TTK	199	.	0			c.A759G						.						59	54	56					6																	80721476		2201	4298	6499	SO:0001583	missense	7272	exon7			AGAAATAGGTTAC		CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"cancer/testis antigen 96", "monopolar spindle 1 kinase"	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.759A>G	chr6.hg19:g.80721476A>G	ENSP00000358813:p.Ile253Met	104.0	0.0		125.0	5.0	NM_003318	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	hg19	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	A	11.38	1.622276	0.28889	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798	D;D;D	0.88509	-2.39;-2.39;-2.39	5.36	1.1	0.20463	.	0.389746	0.30820	N	0.008803	T	0.63367	0.2505	L	0.34521	1.04	0.20975	N	0.999816	B;B	0.15141	0.01;0.012	B;B	0.08055	0.002;0.003	T	0.55121	-0.8190	10	0.33940	T	0.23	.	3.5593	0.07875	0.5676:0.1947:0.2377:0.0	.	253;253	P33981;A8K8U5	TTK_HUMAN;.	M	253	ENSP00000422936:I253M;ENSP00000230510:I253M;ENSP00000358813:I253M	ENSP00000230510:I253M	I	+	3	3	TTK	80778195	0.005000	0.15991	0.693000	0.30195	0.812000	0.45895	-0.045000	0.12003	0.374000	0.24650	0.533000	0.62120	ATA	.	.		0.333	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2			G	80721476	A	G	80721476	3	3	114	1	0	0	0	0	1	0	0	0	16735	410	15	2	781	2	TTK	6	80721476	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	4163333	80721476	90393591	473	18745										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84368767	84368767	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctgtagtattggcatactcTttagcagcttttcgggagcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:84368767delT	ENST00000439399.2	-	6	813	c.497delA	c.(496-498)aagfs	p.K166fs	SNAP91_ENST00000195649.6_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000437520.1_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000428679.2_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000369694.2_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000521743.1_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000520213.1_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000521485.1_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000520302.1_Frame_Shift_Del_p.K166fs	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	166					clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		TGGCATACTCTTTAGCAGCTT	0.353																																					p.K166fs		Atlas-INDEL	.											.	SNAP91	199	.	0			c.498delG						.						116	112	114					6																	84368767		1877	4099	5976	SO:0001589	frameshift_variant	9892	exon6			.	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.497delA	chr6.hg19:g.84368767delT	ENSP00000400459:p.Lys166fs	118.0	0.0		129.0	10.0	NM_001242794	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Frame_Shift_Del	DEL	ENST00000439399.2	hg19	CCDS47455.1																																																																																			.	.		0.353	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			-	84368767	T	-	84368767	7	5	114	1	0	1	0	1	0	0	0	0	14848	1609	56	0	2318	0	SNAP91	6	84368767	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3647291	84368767	86746300	474	18746										
RARS2	57038	hgsc.bcm.edu	37	chr6	88279277	88279277	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagatattgatgtgatcaagTtttctggtggaagattcaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:88279277delT	ENST00000369536.5	-	2	113	c.68delA	c.(67-69)aacfs	p.N23fs		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	23					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		TGTGATCAAGTTTTCTGGTGG	0.323																																					p.N23fs		Atlas-INDEL	.											.	RARS2	61	.	0			c.69delC						.						113	116	115					6																	88279277		2203	4300	6503	SO:0001589	frameshift_variant	57038	exon2			.	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	21406	protein-coding gene	gene with protein product	"arginine tRNA ligase 2, mitochondrial (putative)"	611524	"arginyl-tRNA synthetase-like"	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.68delA	chr6.hg19:g.88279277delT	ENSP00000358549:p.Asn23fs	139.0	0.0		161.0	10.0	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Frame_Shift_Del	DEL	ENST00000369536.5	hg19	CCDS5011.1																																																																																			.	.		0.323	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		-	88279277	T	-	88279277	7	5	114	1	0	1	0	1	0	0	0	0	13074	1725	60	0	1744	0	RARS2	6	88279277	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3910510	88279277	82835790	475	18747										
PM20D2	135293	hgsc.bcm.edu	37	chr6	89864571	89864571	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagaacttcaagttttgaccAaaaaggcagaagattgcttc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:89864571delA	ENST00000275072.4	+	4	957	c.862delA	c.(862-864)aaafs	p.K289fs		NM_001010853.1	NP_001010853.1	Q8IYS1	P20D2_HUMAN	peptidase M20 domain containing 2	289						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|skin(1)	12		all_cancers(76;9.47e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00813)		AGTTTTGACCAAAAAGGCAGA	0.358																																					p.T287fs		Atlas-INDEL	.											.	PM20D2	30	.	0			c.861delC						.						88	93	91					6																	89864571		2203	4300	6503	SO:0001589	frameshift_variant	135293	exon4			.	BC035036	CCDS34499.1	6q15	2014-07-14	2007-11-14	2007-11-14	ENSG00000146281	ENSG00000146281			21408	protein-coding gene	gene with protein product	"&#946;-alanyl-lysine dipeptidase"	615913	"aminoacylase 1-like 2"	ACY1L2		24891507	Standard	NM_001010853		Approved	bA63L7.3	uc003pmz.4	Q8IYS1	OTTHUMG00000015193	ENST00000275072.4:c.862delA	chr6.hg19:g.89864571delA	ENSP00000275072:p.Lys289fs	178.0	0.0		213.0	13.0	NM_001010853	B4DYJ2|Q5T7J9|Q6MZV2|Q86XD9	Frame_Shift_Del	DEL	ENST00000275072.4	hg19	CCDS34499.1																																																																																			.	.		0.358	PM20D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041477.1	NM_001010853		-	89864571	A	-	89864571	7	5	114	1	0	1	0	1	0	0	0	0	12138	131	5	0	876	0	PM20D2	6	89864571	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1585294	89864571	81250496	476	18748										
MDN1	23195	hgsc.bcm.edu	37	chr6	90382309	90382309	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggtcagtgttctcctctgcTttttcattctttctttcttc					rs201481158		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:90382309delT	ENST00000369393.3	-	81	13702	c.13587delA	c.(13585-13587)aaafs	p.K4529fs	MDN1_ENST00000468568.1_5'Flank|MDN1_ENST00000428876.1_Frame_Shift_Del_p.K4529fs|RP1-122O8.7_ENST00000438877.1_RNA			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4529					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCTCCTCTGCTTTTTCATTCT	0.393																																					p.A4530fs		Atlas-INDEL	.											.	MDN1	478	.	0			c.13588delG						.						108	112	110					6																	90382309		2203	4300	6503	SO:0001589	frameshift_variant	23195	exon81			.	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.13587delA	chr6.hg19:g.90382309delT	ENSP00000358400:p.Lys4529fs	95.0	0.0		164.0	11.0	NM_014611	O15019|Q5T794	Frame_Shift_Del	DEL	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.393	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			-	90382309	T	-	90382309	7	5	114	1	0	1	0	1	0	0	0	0	9424	1606	56	0	3291	0	MDN1	6	90382309	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	517738	90382309	80732758	477	18749										
EPHA7	2045	hgsc.bcm.edu	37	chr6	94120235	94120235	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttacgttcacaagtgtctccTttttgctggtagcctgcttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:94120235delT	ENST00000369303.4	-	3	1000	c.816delA	c.(814-816)aaafs	p.K272fs	EPHA7_ENST00000369297.1_Frame_Shift_Del_p.K272fs	NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	272	Cys-rich.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		AAGTGTCTCCTTTTTGCTGGT	0.393																																					p.G273fs		Atlas-INDEL	.											.	EPHA7	251	.	0			c.817delG						.						120	125	123					6																	94120235		2203	4300	6503	SO:0001589	frameshift_variant	2045	exon3			.	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.816delA	chr6.hg19:g.94120235delT	ENSP00000358309:p.Lys272fs	142.0	0.0		166.0	13.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Frame_Shift_Del	DEL	ENST00000369303.4	hg19	CCDS5031.1																																																																																			.	.		0.393	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			-	94120235	T	-	94120235	7	5	114	1	0	1	0	1	0	0	0	0	5174	1606	56	0	2240	0	EPHA7	6	94120235	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3737926	94120235	76994832	478	18750										
GPR63	81491	hgsc.bcm.edu	37	chr6	97246738	97246738	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcagactcatgagacccagTttgctggcctggctgaggca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:97246738delT	ENST00000229955.3	-	2	1215	c.870delA	c.(868-870)aaafs	p.K290fs	GPR63_ENST00000417980.1_Frame_Shift_Del_p.K290fs	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		TGAGACCCAGTTTGCTGGCCT	0.463																																					p.L291fs		Atlas-INDEL	.											.	GPR63	60	.	0			c.871delC						.						89	85	86					6																	97246738		2203	4300	6503	SO:0001589	frameshift_variant	81491	exon2			.	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.870delA	chr6.hg19:g.97246738delT	ENSP00000229955:p.Lys290fs	102.0	0.0		124.0	10.0	NM_030784	Q9UJH3	Frame_Shift_Del	DEL	ENST00000229955.3	hg19	CCDS5036.1																																																																																			.	.		0.463	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			-	97246738	T	-	97246738	7	5	114	1	0	1	0	1	0	0	0	0	6712	1722	60	0	393	0	GPR63	6	97246738	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3126503	97246738	73868329	479	18751										
NDUFAF4	29078	hgsc.bcm.edu	37	chr6	97338980	97338980	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggaaatttctgtgattttctTcattttgatcgtattgcttt	7	5	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:97338980T>C	ENST00000316149.7	-	3	607	c.528A>G	c.(526-528)tgA>tgG	p.*176W	NDUFAF4_ENST00000489477.1_5'Flank	NM_014165.3	NP_054884.1	Q9P032	NDUF4_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 4	0					mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)				large_intestine(5)|lung(3)|ovary(1)|skin(1)	10						GTGATTTTCTTCATTTTGATC	0.299																																					p.X176W		Atlas-SNP	.											.	NDUFAF4	16	.	0			c.A528G						.						64	61	62					6																	97338980		2202	4297	6499	SO:0001578	stop_lost	29078	exon3			TTTTCTTCATTTT	AF161474	CCDS5037.1	6q16.3	2012-10-12	2012-05-08	2009-03-18	ENSG00000123545	ENSG00000123545		"Mitochondrial respiratory chain complex assembly factors"	21034	protein-coding gene	gene with protein product		611776	"chromosome 6 open reading frame 66", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4"	C6orf66		11042152, 18179882	Standard	NM_014165		Approved	HSPC125, bA22L21.1, My013, HRPAP20	uc003pow.3	Q9P032	OTTHUMG00000015246	ENST00000316149.7:c.528A>G	chr6.hg19:g.97338980T>C	ENSP00000358272:p.*176Cysext*28	47.0	0.0		87.0	4.0	NM_014165	B2R4J5	Missense_Mutation	SNP	ENST00000316149.7	hg19	CCDS5037.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.141894	0.37825	.	.	ENSG00000123545	ENST00000316149	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0252	0.42068	0.1504:0.0:0.0:0.8496	.	.	.	.	W	176	.	.	X	-	3	0	NDUFAF4	97445701	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	5.084000	0.64462	1.870000	0.54199	0.533000	0.62120	TGA	.	.		0.299	NDUFAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041567.1	NM_014165		C	97338980	T	C	97338980	4	2	114	1	0	0	0	0	0	0	0	0	10286	1796	62	2	3	2	NDUFAF4	6	97338980	Nonstop_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	92242	97338980	73776087	480	18752										
MCHR2	84539	hgsc.bcm.edu	37	chr6	100395834	100395834	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatatagatgtcagggactgTttttttcctggatctgaaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:100395834delT	ENST00000281806.2	-	3	510	c.196delA	c.(196-198)acafs	p.T66fs	MCHR2_ENST00000369212.2_Frame_Shift_Del_p.T66fs	NM_001040179.1	NP_001035269.1	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	39		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		TCAGGGACTGTTTTTTTCCTG	0.413																																					p.T66fs		Atlas-INDEL	.											.	MCHR2	97	.	0			c.197delC						.						57	60	59					6																	100395834		2203	4300	6503	SO:0001589	frameshift_variant	84539	exon3			.	AF347063	CCDS5044.1	6q16	2012-08-08	2006-02-15	2006-02-15	ENSG00000152034	ENSG00000152034		"GPCR / Class A : MCH receptors"	20867	protein-coding gene	gene with protein product		606111	"G protein-coupled receptor 145"	GPR145		11355873, 11274220	Standard	NM_032503		Approved	SLT, MCH2, MCH2R	uc003pqi.1	Q969V1	OTTHUMG00000015270	ENST00000281806.2:c.196delA	chr6.hg19:g.100395834delT	ENSP00000281806:p.Thr66fs	149.0	0.0		184.0	13.0	NM_001040179	B3KVW4|E1P5D7|Q5VTV7|Q6Q377|Q9BXA8	Frame_Shift_Del	DEL	ENST00000281806.2	hg19	CCDS5044.1																																																																																			.	.		0.413	MCHR2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041620.2	NM_032503		-	100395834	T	-	100395834	7	5	114	1	0	1	0	1	0	0	0	0	9392	1725	60	0	842	0	MCHR2	6	100395834	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3056854	100395834	70719233	481	18753										
PRDM1	639	hgsc.bcm.edu	37	chr6	106536122	106536122	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtgaggtttcagggattggCagaggggaccaaggggacca	18	6	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:106536122C>T	ENST00000369096.4	+	2	323	c.89C>T	c.(88-90)gCa>gTa	p.A30V	PRDM1_ENST00000369091.2_5'UTR	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	30					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CAGGGATTGGCAGAGGGGACC	0.517			"D, N, Mis, F, S"		DLBCL																																p.A30V		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.	PRDM1	195	.	0			c.C89T						.						93	82	86					6																	106536122		2203	4300	6503	SO:0001583	missense	639	exon2			GATTGGCAGAGGG		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"Zinc fingers, C2H2-type"	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.89C>T	chr6.hg19:g.106536122C>T	ENSP00000358092:p.Ala30Val	130.0	0.0		172.0	59.0	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	hg19	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	C	6.475	0.455764	0.12283	.	.	ENSG00000057657	ENST00000369096	T	0.07021	3.23	5.68	3.66	0.41972	.	.	.	.	.	T	0.00998	0.0033	N	0.02011	-0.69	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.42292	-0.9460	9	0.31617	T	0.26	-1.9257	4.8248	0.13410	0.0:0.5646:0.1843:0.251	.	30	O75626	PRDM1_HUMAN	V	30	ENSP00000358092:A30V	ENSP00000358092:A30V	A	+	2	0	PRDM1	106642815	0.749000	0.28305	0.999000	0.59377	0.644000	0.38419	0.020000	0.13466	1.402000	0.46780	0.655000	0.94253	GCA	.	.		0.517	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			T	106536122	C	T	106536122	3	4	114	1	0	0	0	0	1	0	0	0	12462	710	25	3	95	3	PRDM1	6	106536122	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	6140288	106536122	64578945	482	18754										
PRDM1	639	hgsc.bcm.edu	37	chr6	106553019	106553019	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acgtacatcactcgctccccCattccatcctccaccactcc	2	22	1	0	rs542551556		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:106553019C>T	ENST00000369096.4	+	5	1218	c.984C>T	c.(982-984)ccC>ccT	p.P328P	PRDM1_ENST00000369089.3_Silent_p.P194P|PRDM1_ENST00000369091.2_Silent_p.P292P	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	328					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CTCGCTCCCCCATTCCATCCT	0.607			"D, N, Mis, F, S"		DLBCL																																p.P328P		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.	PRDM1	195	.	0			c.C984T						.						76	70	72					6																	106553019		2203	4300	6503	SO:0001819	synonymous_variant	639	exon5			CTCCCCCATTCCA		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"Zinc fingers, C2H2-type"	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.984C>T	chr6.hg19:g.106553019C>T		26.0	0.0		44.0	18.0	NM_001198	B2REA6|E1P5E0|Q86WM7	Silent	SNP	ENST00000369096.4	hg19	CCDS5054.2																																																																																			.	.		0.607	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			T	106553019	C	T	106553019	2	4	114	1	0	0	0	0	0	0	0	1	12462	581	21	3		3	PRDM1	6	106553019	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	16897	106553019	64562048	483	18755										
AIM1	202	hgsc.bcm.edu	37	chr6	106967727	106967727	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cactgtctgcacccgctcctGgggatgttcccaaagacaca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:106967727delG	ENST00000369066.3	+	2	1907	c.1420delG	c.(1420-1422)gggfs	p.G474fs		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		ACCCGCTCCTGGGGATGTTCC	0.488																																					p.P473fs		Atlas-INDEL	.											.	AIM1	161	.	0			c.1419delT						.						93	97	95					6																	106967727		2203	4300	6503	SO:0001589	frameshift_variant	202	exon2			.	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1420delG	chr6.hg19:g.106967727delG	ENSP00000358062:p.Gly474fs	134.0	0.0		183.0	11.0	NM_001624	Q6P2P0|Q9BTM3	Frame_Shift_Del	DEL	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.		0.488	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			-	106967727	G	-	106967727	7	5	114	1	0	1	0	1	0	0	0	0	430	1348	47	0	1426	0	AIM1	6	106967727	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	414708	106967727	64147340	484	18756										
C6orf203	51250	hgsc.bcm.edu	37	chr6	107372314	107372314	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggagaggataaagaagcaggAacagagacagttatgcggat	15	4	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:107372314A>G	ENST00000405204.2	+	4	1204	c.597A>G	c.(595-597)ggA>ggG	p.G199G	C6orf203_ENST00000311381.5_Silent_p.G199G|C6orf203_ENST00000443043.1_Silent_p.G204G	NM_001142468.1	NP_001135940.1	Q9P0P8	CF203_HUMAN	chromosome 6 open reading frame 203	199						mitochondrion (GO:0005739)				large_intestine(4)|lung(2)|prostate(1)|urinary_tract(1)	8	Breast(9;0.00124)|all_epithelial(6;0.0729)	all_cancers(87;0.00461)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|Colorectal(196;0.171)|all_epithelial(87;0.23)	BRCA - Breast invasive adenocarcinoma(8;0.000395)|all cancers(7;0.00065)|Epithelial(6;0.000834)|OV - Ovarian serous cystadenocarcinoma(5;0.244)	BRCA - Breast invasive adenocarcinoma(108;0.117)		AAGAAGCAGGAACAGAGACAG	0.393																																					p.G204G		Atlas-SNP	.											.	C6orf203	26	.	0			c.A612G						.						109	114	112					6																	107372314		2203	4300	6503	SO:0001819	synonymous_variant	51250	exon5			AGCAGGAACAGAG	AF151064	CCDS5058.1	6q21	2012-02-22			ENSG00000130349	ENSG00000130349			17971	protein-coding gene	gene with protein product						11042152, 11707072	Standard	XM_005267008		Approved	HSPC230, PRED31	uc003prq.3	Q9P0P8	OTTHUMG00000015307	ENST00000405204.2:c.597A>G	chr6.hg19:g.107372314A>G		64.0	0.0		93.0	4.0	NM_001142470	B3KRG9	Silent	SNP	ENST00000405204.2	hg19	CCDS5058.1																																																																																			.	.		0.393	C6orf203-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041684.1	NM_016487		G	107372314	A	G	107372314	2	3	114	1	0	0	0	0	0	0	0	1	2354	233	9	2		2	C6orf203	6	107372314	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	404587	107372314	63742753	485	18757										
OSTM1	28962	hgsc.bcm.edu	37	chr6	108370618	108370618	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tccatagttttcgagtgatgTtcatctggaacaagagcaaa	9	7	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:108370618T>C	ENST00000193322.3	-	5	873	c.788A>G	c.(787-789)aAc>aGc	p.N263S		NM_014028.3	NP_054747.2	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1	263					ion transmembrane transport (GO:0034220)|osteoclast differentiation (GO:0030316)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)		TCGAGTGATGTTCATCTGGAA	0.333																																					p.N263S	Melanoma(162;1427 1909 3096 17430 21396)	Atlas-SNP	.											.	OSTM1	22	.	0			c.A788G						.						120	114	116					6																	108370618		2203	4300	6503	SO:0001583	missense	28962	exon5			GTGATGTTCATCT	AF533891	CCDS5062.1	6q21	2014-06-17			ENSG00000081087	ENSG00000081087			21652	protein-coding gene	gene with protein product	"CLCN7 accessory beta subunit"	607649				12627228, 21527911	Standard	NM_014028		Approved	HSPC019, GL	uc003psd.3	Q86WC4	OTTHUMG00000015317	ENST00000193322.3:c.788A>G	chr6.hg19:g.108370618T>C	ENSP00000193322:p.Asn263Ser	82.0	0.0		100.0	4.0	NM_014028	E1P5E3|Q5R391|Q6PCA7|Q7RTW6|Q8NC29|Q8TC82|Q9Y2S9	Missense_Mutation	SNP	ENST00000193322.3	hg19	CCDS5062.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.211517	0.79240	.	.	ENSG00000081087	ENST00000193322;ENST00000440575	T	0.79141	-1.24	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.87285	0.6139	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89687	0.3895	10	0.87932	D	0	-8.0917	15.6053	0.76664	0.0:0.0:0.0:1.0	.	263	Q86WC4	OSTM1_HUMAN	S	263;116	ENSP00000193322:N263S	ENSP00000193322:N263S	N	-	2	0	OSTM1	108477311	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	7.694000	0.84235	2.095000	0.63458	0.482000	0.46254	AAC	.	.		0.333	OSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041709.3	NM_014028		C	108370618	T	C	108370618	3	2	114	1	0	0	0	0	1	0	0	0	11307	1725	60	2	224	2	OSTM1	6	108370618	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	998304	108370618	62744449	486	18758										
LACE1	246269	hgsc.bcm.edu	37	chr6	108668193	108668193	+	Splice_Site	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atttgttcttaatttgcagcTtttttcaaggagcaaacctc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:108668193delT	ENST00000368977.4	+	3	551	c.365delT	c.(364-366)ctt>ct	p.L122fs		NM_145315.3	NP_660358.2	Q8WV93	LACE1_HUMAN	lactation elevated 1	122						mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.S124fs*55(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)		AATTTGCAGCTTTTTTCAAGG	0.343																																					p.L122fs		Atlas-INDEL	.											.,1	LACE1	30	.	1	Insertion - Frameshift(1)	upper_aerodigestive_tract(1)	c.364delC						.						103	105	104					6																	108668193		2203	4300	6503	SO:0001630	splice_region_variant	246269	exon3			.	AF520418	CCDS5067.1	6q22.1	2006-11-10			ENSG00000135537	ENSG00000135537			16411	protein-coding gene	gene with protein product	"ATPase family gene 1 homolog (S. cerevisiae)"					12079282	Standard	XM_005266885		Approved	AFG1	uc003psj.3	Q8WV93	OTTHUMG00000015324	ENST00000368977.4:c.364-1T>-	chr6.hg19:g.108668193delT		124.0	0.0		142.0	10.0	NM_145315	Q8N6A3	Frame_Shift_Del	DEL	ENST00000368977.4	hg19	CCDS5067.1																																																																																			.	.		0.343	LACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041719.4	NM_145315	Frame_Shift_Del	-	108668193	T	-	108668193	8	5	114	1	0	1	0	1	0	0	1	0	8604	1623	56	0	375	0	LACE1	6	108668193	Splice_Site	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	297575	108668193	62446874	487	18759										
MICAL1	64780	hgsc.bcm.edu	37	chr6	109773524	109773524	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actgatctccggcacctgtgTctcctccacggtgcgtccat	9	16	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:109773524T>C	ENST00000358807.3	-	6	1068	c.757A>G	c.(757-759)Aca>Gca	p.T253A	MICAL1_ENST00000368952.4_Missense_Mutation_p.T272A|MICAL1_ENST00000483856.1_5'UTR|MICAL1_ENST00000358577.3_Missense_Mutation_p.T253A	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	253	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		GGCACCTGTGTCTCCTCCACG	0.537																																					p.T253A		Atlas-SNP	.											.	MICAL1	79	.	0			c.A757G						.						124	121	122					6																	109773524		2203	4300	6503	SO:0001583	missense	64780	exon6			CCTGTGTCTCCTC	AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"NEDD9 interacting protein with calponin homology and LIM domains"	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.757A>G	chr6.hg19:g.109773524T>C	ENSP00000351664:p.Thr253Ala	80.0	0.0		128.0	6.0	NM_001159291	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Missense_Mutation	SNP	ENST00000358807.3	hg19	CCDS5076.1	.	.	.	.	.	.	.	.	.	.	T	7.749	0.703019	0.15172	.	.	ENSG00000135596	ENST00000358807;ENST00000368952;ENST00000358577	T;T;T	0.05382	3.45;3.45;3.45	5.63	5.63	0.86233	.	0.122445	0.56097	D	0.000034	T	0.00784	0.0026	N	0.04805	-0.155	0.27264	N	0.958543	B;B;B	0.21688	0.006;0.059;0.035	B;B;B	0.20955	0.006;0.032;0.014	T	0.46925	-0.9156	10	0.02654	T	1	.	8.3661	0.32387	0.0:0.0873:0.0:0.9127	.	272;253;253	B7Z3R5;Q8TDZ2-2;Q8TDZ2	.;.;MICA1_HUMAN	A	253;272;253	ENSP00000351664:T253A;ENSP00000357948:T272A;ENSP00000351385:T253A	ENSP00000351385:T253A	T	-	1	0	MICAL1	109880217	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	4.959000	0.63666	2.140000	0.66376	0.448000	0.29417	ACA	.	.		0.537	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765		C	109773524	T	C	109773524	3	2	114	1	0	0	0	0	1	0	0	0	9578	1667	58	2	2526	2	MICAL1	6	109773524	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1105331	109773524	61341543	488	18760										
KIAA1919	91749	hgsc.bcm.edu	37	chr6	111587466	111587466	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caacgcccttctttgtctccTttttctgttcttcttttttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:111587466delT	ENST00000368847.4	+	4	1054	c.701delT	c.(700-702)cttfs	p.L234fs		NM_153369.2	NP_699200.2	Q5TF39	NAGT1_HUMAN	KIAA1919	234					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			large_intestine(3)|lung(2)|ovary(4)|skin(3)	12		all_cancers(87;2.35e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.055)|all cancers(137;0.0871)|Epithelial(106;0.0884)		CTTTGTCTCCTTTTTCTGTTC	0.378																																					p.L234fs		Atlas-INDEL	.											.	KIAA1919	54	.	0			c.700delC						.						109	99	102					6																	111587466		2203	4300	6503	SO:0001589	frameshift_variant	91749	exon4			.	BC036115	CCDS5090.1	6q22	2013-10-02			ENSG00000173214	ENSG00000173214			21053	protein-coding gene	gene with protein product							Standard	NM_153369		Approved	MGC33953, MFSD4B	uc003puv.4	Q5TF39	OTTHUMG00000015372	ENST00000368847.4:c.701delT	chr6.hg19:g.111587466delT	ENSP00000357840:p.Leu234fs	129.0	0.0		176.0	11.0	NM_153369	A8K9M0|Q8IYB6|Q96PW9|Q9P0D6	Frame_Shift_Del	DEL	ENST00000368847.4	hg19	CCDS5090.1																																																																																			.	.		0.378	KIAA1919-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041827.1	NM_153369		-	111587466	T	-	111587466	7	5	114	1	0	1	0	1	0	0	0	0	8271	1609	56	0	715	0	KIAA1919	6	111587466	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1813942	111587466	59527601	489	18761										
LAMA4	3910	hgsc.bcm.edu	37	chr6	112450166	112450166	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcttggataaattttttccTtttttatggaggagaaacaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:112450166delT	ENST00000230538.7	-	31	4642	c.4245delA	c.(4243-4245)aaafs	p.K1415fs	LAMA4_ENST00000389463.4_Frame_Shift_Del_p.K1408fs|LAMA4_ENST00000424408.2_Frame_Shift_Del_p.K1408fs|LAMA4_ENST00000522006.1_Frame_Shift_Del_p.K1408fs	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1415					blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		AATTTTTTCCTTTTTTATGGA	0.373																																					p.G1416fs		Atlas-INDEL	.											.	LAMA4	227	.	0			c.4246delG						.						113	111	111					6																	112450166		2203	4300	6503	SO:0001589	frameshift_variant	3910	exon31			.		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.4245delA	chr6.hg19:g.112450166delT	ENSP00000230538:p.Lys1415fs	129.0	0.0		158.0	11.0	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Frame_Shift_Del	DEL	ENST00000230538.7	hg19	CCDS43491.1																																																																																			.	.		0.373	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		-	112450166	T	-	112450166	7	5	114	1	0	1	0	1	0	0	0	0	8617	1606	56	0	1262	0	LAMA4	6	112450166	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	862700	112450166	58664901	490	18762										
ROS1	6098	hgsc.bcm.edu	37	chr6	117683915	117683915	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatttcaaattttgttaacaCcccattttcatgcttaggtt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:117683915delC	ENST00000368508.3	-	21	3430	c.3232delG	c.(3232-3234)gtgfs	p.V1078fs	ROS1_ENST00000368507.3_Frame_Shift_Del_p.V1073fs|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1078	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TTTGTTAACACCCCATTTTCA	0.348			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.V1078fs		Atlas-INDEL	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.3233delT						.						117	123	121					6																	117683915		2203	4300	6503	SO:0001589	frameshift_variant	6098	exon21			.	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.3232delG	chr6.hg19:g.117683915delC	ENSP00000357494:p.Val1078fs	131.0	0.0		165.0	10.0	NM_002944	Q15368|Q5TDB5	Frame_Shift_Del	DEL	ENST00000368508.3	hg19	CCDS5116.1																																																																																			.	.		0.348	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			-	117683915	C	-	117683915	7	5	114	1	0	1	0	1	0	0	0	0	13546	507	18	0	3903	0	ROS1	6	117683915	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	5233749	117683915	53431152	491	18763										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121624805	121624805	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccttggtatcaactaatgcAaaaaagtagatcggatccaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:121624805delA	ENST00000398212.2	-	9	1087	c.1038delT	c.(1036-1038)tttfs	p.F346fs	TBC1D32_ENST00000275159.6_Frame_Shift_Del_p.F346fs	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	346					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										CAACTAATGCAAAAAAGTAGA	0.313																																					p.A347fs		Atlas-INDEL	.											.	C6orf170	146	.	0			c.1039delG						.						94	85	88					6																	121624805		1806	4073	5879	SO:0001589	frameshift_variant	221322	exon9			.	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1038delT	chr6.hg19:g.121624805delA	ENSP00000381270:p.Phe346fs	112.0	0.0		131.0	10.0	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Frame_Shift_Del	DEL	ENST00000398212.2	hg19	CCDS43501.1																																																																																			.	.		0.313	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		-	121624805	A	-	121624805	7	5	114	1	0	1	0	1	0	0	0	0	2346	127	5	0	2831	0	C6orf170	6	121624805	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3940890	121624805	49490262	492	18764										
HDDC2	51020	hgsc.bcm.edu	37	chr6	125621689	125621689	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tccagctcagcttaccggtcTttgttaagacggtcatcttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:125621689delT	ENST00000398153.2	-	2	243	c.201delA	c.(199-201)aaafs	p.K67fs	HDDC2_ENST00000368377.4_Frame_Shift_Del_p.K67fs|HDDC2_ENST00000608284.1_Frame_Shift_Del_p.K67fs|HDDC2_ENST00000608295.1_Frame_Shift_Del_p.K67fs	NM_016063.2	NP_057147.2	Q7Z4H3	HDDC2_HUMAN	HD domain containing 2	67	HD.					extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(4)	6			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0186)		CTTACCGGTCTTTGTTAAGAC	0.483																																					p.D68fs		Atlas-INDEL	.											.	HDDC2	21	.	0			c.202delG						.						91	97	95					6																	125621689		1980	4165	6145	SO:0001589	frameshift_variant	51020	exon2			.	AF151888	CCDS43503.1	6q13-q24.3	2008-02-05	2005-08-22	2005-08-22	ENSG00000111906	ENSG00000111906			21078	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 74"	C6orf74		10810093	Standard	NM_016063		Approved	CGI-130, dJ167O5.2	uc003qaa.1	Q7Z4H3	OTTHUMG00000015506	ENST00000398153.2:c.201delA	chr6.hg19:g.125621689delT	ENSP00000381220:p.Lys67fs	154.0	0.0		178.0	11.0	NM_016063	Q5TDQ4|Q6NZ49|Q9BTT2|Q9BV31|Q9Y3D1	Frame_Shift_Del	DEL	ENST00000398153.2	hg19	CCDS43503.1																																																																																			.	.		0.483	HDDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472493.1	NM_016063		-	125621689	T	-	125621689	7	5	114	1	0	1	0	1	0	0	0	0	7025	1606	56	0	433	0	HDDC2	6	125621689	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3996884	125621689	45493378	493	18765										
MED23	9439	hgsc.bcm.edu	37	chr6	131931307	131931307	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcccccatcgtcaaacttcTcctcggtctcagatcgctcc	5	18	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:131931307T>C	ENST00000368068.3	-	11	1135	c.956A>G	c.(955-957)gAg>gGg	p.E319G	MED23_ENST00000368053.4_Missense_Mutation_p.E325G|MED23_ENST00000539158.1_Missense_Mutation_p.E319G|MED23_ENST00000368060.3_Missense_Mutation_p.E319G|MED23_ENST00000368058.1_Missense_Mutation_p.E325G|MED23_ENST00000354577.4_Missense_Mutation_p.E325G|MED23_ENST00000403834.3_Missense_Mutation_p.E325G|MED23_ENST00000540546.1_Missense_Mutation_p.E325G|MED23_ENST00000545957.1_Missense_Mutation_p.E8G	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	319					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		GTCAAACTTCTCCTCGGTCTC	0.493																																					p.E325G		Atlas-SNP	.											.	MED23	112	.	0			c.A974G						.						115	108	110					6																	131931307		2203	4300	6503	SO:0001583	missense	9439	exon12			AACTTCTCCTCGG	AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.956A>G	chr6.hg19:g.131931307T>C	ENSP00000357047:p.Glu319Gly	44.0	0.0		78.0	4.0	NM_015979	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Missense_Mutation	SNP	ENST00000368068.3	hg19	CCDS5147.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.545336	0.65198	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000545957;ENST00000368053;ENST00000540546;ENST00000539158	T;T;T;T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	5.76	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.74084	0.3670	L	0.39898	1.24	0.80722	D	1	P;B;D;D	0.63046	0.625;0.435;0.992;0.99	B;B;D;P	0.63113	0.265;0.179;0.911;0.856	T	0.72487	-0.4278	10	0.29301	T	0.29	-0.0437	12.3052	0.54898	0.1264:0.0:0.0:0.8736	.	8;325;319;325	B4E3G4;Q9ULK4-2;Q9ULK4;Q9ULK4-3	.;.;MED23_HUMAN;.	G	325;319;325;319;325;8;325;325;319	ENSP00000346588:E325G;ENSP00000357047:E319G;ENSP00000384536:E325G;ENSP00000357039:E319G;ENSP00000357037:E325G;ENSP00000439977:E8G;ENSP00000357032:E325G;ENSP00000437818:E325G;ENSP00000445072:E319G	ENSP00000346588:E325G	E	-	2	0	MED23	131973000	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.281000	0.72632	2.204000	0.70986	0.482000	0.46254	GAG	.	.		0.493	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			C	131931307	T	C	131931307	3	2	114	1	0	0	0	0	1	0	0	0	9450	1551	54	2	3233	2	MED23	6	131931307	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	6309618	131931307	39183760	494	18766										
HBS1L	10767	hgsc.bcm.edu	37	chr6	135358603	135358603	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattatcaacagtcatatttTccaacgagctagttaagtac	5	8	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:135358603T>C	ENST00000367837.5	-	4	637				HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.E331G|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000415177.2_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		AGTCATATTTTCCAACGAGCT	0.289																																					p.E331G		Atlas-SNP	.											.	HBS1L	75	.	0			c.A992G						.						32	26	28					6																	135358603		692	1590	2282	SO:0001627	intron_variant	10767	exon5			ATATTTTCCAACG	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"eRF3 family member"	612450	"HBS1 (S. cerevisiae)-like", "HBS1-like (S. cerevisiae)"			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2107A>G	chr6.hg19:g.135358603T>C		106.0	0.0		137.0	6.0	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	hg19	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	T	13.07	2.128182	0.37533	.	.	ENSG00000112339	ENST00000367822	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	T	0.31104	0.0786	.	.	.	0.80722	D	1	B	0.27559	0.181	B	0.30646	0.118	T	0.42599	-0.9442	7	0.54805	T	0.06	.	4.8834	0.13690	0.0:0.1141:0.1863:0.6996	.	331	Q9Y450-2	.	G	331	.	ENSP00000356796:E331G	E	-	2	0	HBS1L	135400296	1.000000	0.71417	0.998000	0.56505	0.510000	0.34073	2.111000	0.41883	2.194000	0.70268	0.533000	0.62120	GAA	.	.		0.289	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			C	135358603	T	C	135358603	1	2	114	0	1	0	0	0	0	0	0	0	6996	1783	62	2		2	HBS1L	6	135358603	Intron	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3427296	135358603	35756464	495	18767										
MYB	4602	hgsc.bcm.edu	37	chr6	135507076	135507076	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgaggatgatgaggactttgAgatgtgtgaccatgactatg	14	5	0	5			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:135507076A>G	ENST00000367814.4	+	2	245	c.59A>G	c.(58-60)gAg>gGg	p.E20G	MYB_ENST00000525369.1_Missense_Mutation_p.E20G|MYB_ENST00000527615.1_Missense_Mutation_p.E20G|MYB_ENST00000533624.1_Missense_Mutation_p.E20G|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000442647.2_Missense_Mutation_p.E20G|MYB_ENST00000534044.1_Missense_Mutation_p.E20G|MYB_ENST00000534121.1_Missense_Mutation_p.E20G|MYB_ENST00000341911.5_Missense_Mutation_p.E20G|MYB_ENST00000420123.2_Missense_Mutation_p.E20G|MYB_ENST00000316528.8_Missense_Mutation_p.E20G|MYB_ENST00000528774.1_Missense_Mutation_p.E20G	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	20					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		GAGGACTTTGAGATGTGTGAC	0.448			T	NFIB	adenoid cystic carcinoma																																p.E20G		Atlas-SNP	.		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	MYB	137	.	0			c.A59G						.						179	163	168					6																	135507076		2203	4300	6503	SO:0001583	missense	4602	exon2			ACTTTGAGATGTG		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.59A>G	chr6.hg19:g.135507076A>G	ENSP00000356788:p.Glu20Gly	80.0	0.0		90.0	4.0	NM_001161660	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	hg19	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	A	19.25	3.792115	0.70452	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000420123;ENST00000525369;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000533624	T;T;T;T;T;T;T;T;T;T	0.34859	2.57;2.09;2.09;2.1;1.34;1.84;2.56;2.55;1.76;2.17	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.37679	0.1012	M	0.63428	1.95	0.80722	D	1	P;B;P;P;P;D;P;P;P	0.55172	0.682;0.181;0.493;0.653;0.754;0.97;0.73;0.474;0.605	B;B;B;B;B;P;B;B;B	0.51193	0.172;0.054;0.116;0.219;0.306;0.662;0.318;0.097;0.108	T	0.39210	-0.9625	10	0.87932	D	0	-15.4352	15.2562	0.73588	1.0:0.0:0.0:0.0	.	20;20;20;20;20;20;20;20;20	E9PI07;E9PLZ5;P10242-2;E9PNL6;E9PRS2;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;.;MYB_HUMAN;.	G	20	ENSP00000339992:E20G;ENSP00000410825:E20G;ENSP00000326328:E20G;ENSP00000356788:E20G;ENSP00000433227:E20G;ENSP00000435938:E20G;ENSP00000434723:E20G;ENSP00000432851:E20G;ENSP00000435055:E20G;ENSP00000436605:E20G	ENSP00000237302:E20G	E	+	2	0	MYB	135548769	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.071000	0.62044	0.460000	0.39030	GAG	.	.		0.448	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4			G	135507076	A	G	135507076	3	3	114	1	0	0	0	0	1	0	0	0	10016	304	11	2	65	2	MYB	6	135507076	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	148473	135507076	35607991	496	18768										
MAP3K5	4217	hgsc.bcm.edu	37	chr6	136935403	136935403	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtttatgcaatgctatttcTtcatgcaggggctgagagta	11	6	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:136935403T>C	ENST00000359015.4	-	16	2532	c.2172A>G	c.(2170-2172)gaA>gaG	p.E724E	MAP3K5_ENST00000355845.4_5'UTR	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	724	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		ATGCTATTTCTTCATGCAGGG	0.353																																					p.E724E		Atlas-SNP	.											.	MAP3K5	136	.	0			c.A2172G						.						171	166	168					6																	136935403		2203	4300	6503	SO:0001819	synonymous_variant	4217	exon16			TATTTCTTCATGC	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6857	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 1"	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.2172A>G	chr6.hg19:g.136935403T>C		57.0	0.0		76.0	4.0	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	hg19	CCDS5179.1																																																																																			.	.		0.353	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1			C	136935403	T	C	136935403	2	2	114	1	0	0	0	0	0	0	0	1	9262	1606	56	2		2	MAP3K5	6	136935403	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1428327	136935403	34179664	497	18769										
SLC35D3	340146	hgsc.bcm.edu	37	chr6	137243900	137243900	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggtcttcaagcgctgcctgCccctggtcaccatgctcatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:137243900delC	ENST00000331858.4	+	1	499	c.334delC	c.(334-336)cccfs	p.P112fs		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	112					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		GCGCTGCCTGCCCCTGGTCAC	0.711																																					p.L111fs		Atlas-INDEL	.											.	SLC35D3	33	.	0			c.333delG						.						12	13	13					6																	137243900		2178	4274	6452	SO:0001589	frameshift_variant	340146	exon1			.		CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"Solute carriers"	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.334delC	chr6.hg19:g.137243900delC	ENSP00000333591:p.Pro112fs	252.0	0.0		218.0	19.0	NM_001008783	B4DI58|Q5QNZ6|Q6NX71	Frame_Shift_Del	DEL	ENST00000331858.4	hg19	CCDS34544.1																																																																																			.	.		0.711	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017		-	137243900	C	-	137243900	7	5	114	1	0	1	0	1	0	0	0	0	14598	739	26	0	336	0	SLC35D3	6	137243900	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	308497	137243900	33871167	498	18770										
ECT2L	345930	hgsc.bcm.edu	37	chr6	139197610	139197610	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtttccattcaatcttcaggAaagaaatgttgtagaagaca	8	6	3	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:139197610A>G	ENST00000423192.1	+	13	1741	c.1580A>G	c.(1579-1581)gAa>gGa	p.E527G	RP3-509I19.6_ENST00000572284.1_RNA|ECT2L_ENST00000541398.1_Splice_Site_p.E458G|ECT2L_ENST00000367682.2_Splice_Site_p.E527G			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	527			E -> K (in dbSNP:rs1529151).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						AATCTTCAGGAAAGAAATGTT	0.413			"N, Splice, Mis"		ETP ALL																																p.E527G		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A1580G						.						64	61	62					6																	139197610		1859	4099	5958	SO:0001630	splice_region_variant	345930	exon13			TTCAGGAAAGAAA		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.1579-1A>G	chr6.hg19:g.139197610A>G		64.0	0.0		72.0	4.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	hg19	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	A	11.84	1.758092	0.31137	.	.	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	T;T;T	0.77098	0.06;0.06;-1.07	5.25	-0.205	0.13196	Dbl homology (DH) domain (1);	0.000000	0.41712	U	0.000821	T	0.48857	0.1523	L	0.60455	1.87	0.25093	N	0.990847	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.46048	-0.9219	10	0.44086	T	0.13	22.768	4.6103	0.12399	0.5108:0.3155:0.1737:0.0	.	458;527	F5H7S9;Q008S8	.;ECT2L_HUMAN	G	527;527;458	ENSP00000387388:E527G;ENSP00000356655:E527G;ENSP00000442307:E458G	ENSP00000356655:E527G	E	+	2	0	ECT2L	139239303	0.997000	0.39634	0.063000	0.19743	0.092000	0.18411	1.273000	0.33121	0.022000	0.15160	0.528000	0.53228	GAA	.	.		0.413	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	Missense_Mutation	G	139197610	A	G	139197610	5	3	114	1	0	0	0	0	0	0	1	0	4904	260	9	2	1626	2	ECT2L	6	139197610	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1953710	139197610	31917457	499	18771										
STXBP5	134957	hgsc.bcm.edu	37	chr6	147631274	147631274	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tatgatactgtaggaagaagAccttgcttaacagtgatgca	10	6	0	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:147631274A>G	ENST00000321680.6	+	10	972	c.972A>G	c.(970-972)agA>agG	p.R324R	STXBP5_ENST00000179882.6_5'UTR|STXBP5_ENST00000367481.3_Silent_p.R324R|STXBP5_ENST00000367480.3_Silent_p.R324R	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	324					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TAGGAAGAAGACCTTGCTTAA	0.348																																					p.R324R		Atlas-SNP	.											.	STXBP5	163	.	0			c.A972G						.						132	137	136					6																	147631274		2203	4300	6503	SO:0001819	synonymous_variant	134957	exon10			AAGAAGACCTTGC	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.972A>G	chr6.hg19:g.147631274A>G		81.0	0.0		70.0	4.0	NM_139244	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Silent	SNP	ENST00000321680.6	hg19	CCDS47499.1																																																																																			.	.		0.348	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			G	147631274	A	G	147631274	2	3	114	1	0	0	0	0	0	0	0	1	15371	272	10	2		2	STXBP5	6	147631274	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	8433664	147631274	23483793	500	18772										
UST	10090	hgsc.bcm.edu	37	chr6	149340329	149340329	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtgctccaaccccaggttaTtttacatcattccgtacttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:149340329delT	ENST00000367463.4	+	6	839	c.736delT	c.(736-738)tttfs	p.F246fs		NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	246					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		CCCCAGGTTATTTTACATCAT	0.463																																					p.L245fs		Atlas-INDEL	.											.	UST	42	.	0			c.735delA						.						179	169	172					6																	149340329		2203	4300	6503	SO:0001589	frameshift_variant	10090	exon6			.	AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"Sulfotransferases, membrane-bound"	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.736delT	chr6.hg19:g.149340329delT	ENSP00000356433:p.Phe246fs	125.0	0.0		174.0	11.0	NM_005715	B2RCX6	Frame_Shift_Del	DEL	ENST00000367463.4	hg19	CCDS5213.1																																																																																			.	.		0.463	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715		-	149340329	T	-	149340329	7	5	114	1	0	1	0	1	0	0	0	0	17108	1493	52	0	758	0	UST	6	149340329	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1709055	149340329	21774738	501	18773										
LATS1	9113	hgsc.bcm.edu	37	chr6	149997708	149997708	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tacctgttcgtagcaacactTcaggtgcaatataattggga	9	8	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:149997708T>C	ENST00000543571.1	-	6	3306	c.2759A>G	c.(2758-2760)gAa>gGa	p.E920G	LATS1_ENST00000253339.5_Missense_Mutation_p.E920G|LATS1_ENST00000542747.1_5'UTR	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TAGCAACACTTCAGGTGCAAT	0.448																																					p.E920G		Atlas-SNP	.											.	LATS1	241	.	0			c.A2759G						.						65	65	65					6																	149997708		2203	4300	6503	SO:0001583	missense	9113	exon6			AACACTTCAGGTG	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2759A>G	chr6.hg19:g.149997708T>C	ENSP00000437550:p.Glu920Gly	63.0	0.0		81.0	4.0	NM_004690		Missense_Mutation	SNP	ENST00000543571.1	hg19	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.799498	0.90538	.	.	ENSG00000131023	ENST00000543571;ENST00000253339	T;T	0.38887	1.11;1.11	5.81	5.81	0.92471	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000011	T	0.70011	0.3175	H	0.94886	3.595	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80058	-0.1541	9	.	.	.	.	16.1708	0.81812	0.0:0.0:0.0:1.0	.	920	O95835	LATS1_HUMAN	G	920	ENSP00000437550:E920G;ENSP00000253339:E920G	.	E	-	2	0	LATS1	150039401	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.698000	0.84413	2.225000	0.72522	0.533000	0.62120	GAA	.	.		0.448	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		C	149997708	T	C	149997708	3	2	114	1	0	0	0	0	1	0	0	0	8655	1783	62	2	645	2	LATS1	6	149997708	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	657379	149997708	21117359	502	18774										
MTRF1L	54516	hgsc.bcm.edu	37	chr6	153315778	153315778	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtgcctataggcttctgaaCccccaatgctggcagatgca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:153315778delC	ENST00000367233.5	-	4	556	c.557delG	c.(556-558)ggtfs	p.G186fs	MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367230.1_Frame_Shift_Del_p.G150fs|MTRF1L_ENST00000367231.5_Frame_Shift_Del_p.G186fs	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	186						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		GGCTTCTGAACCCCCAATGCT	0.413																																					p.G186fs		Atlas-INDEL	.											.	MTRF1L	21	.	0			c.558delT						.						92	91	91					6																	153315778		2203	4300	6503	SO:0001589	frameshift_variant	54516	exon4			.	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.557delG	chr6.hg19:g.153315778delC	ENSP00000356202:p.Gly186fs	123.0	0.0		121.0	10.0	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Frame_Shift_Del	DEL	ENST00000367233.5	hg19	CCDS5243.1																																																																																			.	.		0.413	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041		-	153315778	C	-	153315778	7	5	114	1	0	1	0	1	0	0	0	0	9969	507	18	0	601	0	MTRF1L	6	153315778	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3318070	153315778	17799289	503	18775										
T	6862	hgsc.bcm.edu	37	chr6	166579270	166579270	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggtgatcatgcgctgtggaCccccaactctcactatgtgg					rs2305089	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:166579270delC	ENST00000296946.2	-	4	998	c.530delG	c.(529-531)ggtfs	p.G177fs	T_ENST00000366871.3_Frame_Shift_Del_p.G177fs	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	177			G -> D (in dbSNP:rs2305089). {ECO:0000269|PubMed:15489334}.		anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		GCGCTGTGGACCCCCAACTCT	0.537									Chordoma, Familial Clustering of																												p.G177fs		Atlas-INDEL	.											.	T	77	.	0			c.531delT						.						325	283	297					6																	166579270		2203	4300	6503	SO:0001589	frameshift_variant	6862	exon4	Familial Cancer Database		.	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"T-boxes"	11515	protein-coding gene	gene with protein product		601397	"T brachyury (mouse) homolog"			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.530delG	chr6.hg19:g.166579270delC	ENSP00000296946:p.Gly177fs	192.0	0.0		154.0	10.0	NM_001270484	E7ERD6|Q4KMP4	Frame_Shift_Del	DEL	ENST00000296946.2	hg19	CCDS5290.1																																																																																			.	.		0.537	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181		-	166579270	C	-	166579270	7	5	114	1	0	1	0	1	0	0	0	0	15503	507	18	0	801	0	T	6	166579270	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	13263492	166579270	4535797	504	18776										
GPR31	2853	hgsc.bcm.edu	37	chr6	167571153	167571153	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acagcaggtcagccagggccAggttgagcaggtagacagcg	16	10	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:167571153A>G	ENST00000366834.1	-	1	664	c.167T>C	c.(166-168)cTg>cCg	p.L56P		NM_005299.2	NP_005290.2	O00270	GPR31_HUMAN	G protein-coupled receptor 31	56					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(4)|large_intestine(4)|lung(7)|prostate(1)	17		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)		AGCCAGGGCCAGGTTGAGCAG	0.667																																					p.L56P		Atlas-SNP	.											.	GPR31	44	.	0			c.T167C						.						55	42	47					6																	167571153		2201	4300	6501	SO:0001583	missense	2853	exon1			AGGGCCAGGTTGA	U65402	CCDS5299.1	6q27	2012-08-21				ENSG00000120436		"GPCR / Class A : Orphans"	4486	protein-coding gene	gene with protein product	"hydroxyeicosatetraenoic (HETE) acid receptor 1", "12-(S)-HETE acid receptor"	602043				9205127, 21712392	Standard	NM_005299		Approved	HETER1, 12-HETER	uc011egq.2	O00270		ENST00000366834.1:c.167T>C	chr6.hg19:g.167571153A>G	ENSP00000355799:p.Leu56Pro	196.0	0.0		151.0	7.0	NM_005299	B0M0K2|Q4VBL3|Q9NQ20	Missense_Mutation	SNP	ENST00000366834.1	hg19	CCDS5299.1	.	.	.	.	.	.	.	.	.	.	A	14.37	2.516398	0.44763	.	.	ENSG00000120436	ENST00000366834	D	0.91521	-2.86	3.54	3.54	0.40534	GPCR, rhodopsin-like superfamily (1);	0.000000	0.30109	N	0.010393	D	0.95335	0.8486	M	0.93594	3.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95783	0.8818	10	0.87932	D	0	-15.3335	11.0872	0.48093	1.0:0.0:0.0:0.0	.	56	O00270	GPR31_HUMAN	P	56	ENSP00000355799:L56P	ENSP00000355799:L56P	L	-	2	0	GPR31	167491143	1.000000	0.71417	0.934000	0.37439	0.082000	0.17680	7.874000	0.87199	1.473000	0.48159	0.260000	0.18958	CTG	.	.		0.667	GPR31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043111.1	NM_005299		G	167571153	A	G	167571153	3	3	114	1	0	0	0	0	1	0	0	0	6695	188	7	2	795	2	GPR31	6	167571153	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	991883	167571153	3543914	505	18777										
ADAP1	11033	hgsc.bcm.edu	37	chr7	939058	939058	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccacagctcctccttaccaGggggtctttgaagtacatga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:939058delG	ENST00000265846.5	-	9	1084	c.865delC	c.(865-867)ctgfs	p.L289fs	ADAP1_ENST00000539900.1_Frame_Shift_Del_p.L300fs|ADAP1_ENST00000449296.2_Frame_Shift_Del_p.L217fs	NM_001284308.1|NM_001284309.1|NM_001284311.1|NM_006869.2	NP_001271237.1|NP_001271238.1|NP_001271240.1|NP_006860	O75689	ADAP1_HUMAN	ArfGAP with dual PH domains 1	289	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell surface receptor signaling pathway (GO:0007166)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF GTPase activity (GO:0032312)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	6						CTCCTTACCAGGGGGTCTTTG	0.657																																					p.L289fs		Atlas-INDEL	.											.	ADAP1	23	.	0			c.866delT						.						58	49	52					7																	939058		2203	4300	6503	SO:0001589	frameshift_variant	11033	exon9			.	AJ006422	CCDS5318.1, CCDS64576.1, CCDS64577.1, CCDS75558.1	7p22.3	2013-01-10	2008-09-22	2008-09-22	ENSG00000105963	ENSG00000105963		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16486	protein-coding gene	gene with protein product		608114	"centaurin, alpha 1"	CENTA1		10333475	Standard	NM_006869		Approved	GCS1L	uc003sjo.4	O75689	OTTHUMG00000023380	ENST00000265846.5:c.865delC	chr7.hg19:g.939058delG	ENSP00000265846:p.Leu289fs	202.0	0.0		254.0	16.0	NM_006869	A4D2Q2|B3KRZ4|B4DVA6|F6XZ68|H7C2Q4	Frame_Shift_Del	DEL	ENST00000265846.5	hg19	CCDS5318.1																																																																																			.	.		0.657	ADAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059701.2	NM_006869		-	939058	G	-	939058	7	5	114	1	0	1	0	1	0	0	0	0	279	991	35	0	271	0	ADAP1	7	939058	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10		939058	158199605	506	18778										
FTSJ2	8379	hgsc.bcm.edu	37	chr7	2274931	2274931	+	5'Flank	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggttttacaaaggaatgtCcccccaggttgcaggatgtc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:2274931delC	ENST00000406869.1	-	0	0				FTSJ2_ENST00000242257.8_Frame_Shift_Del_p.G189fs|MAD1L1_ENST00000399654.2_5'Flank|MAD1L1_ENST00000402746.1_5'Flank|FTSJ2_ENST00000486040.1_5'UTR|FTSJ2_ENST00000407040.1_Frame_Shift_Del_p.G95fs|MAD1L1_ENST00000265854.7_5'Flank|FTSJ2_ENST00000440306.2_3'UTR			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)						mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		AAAGGAATGTCCCCCCAGGTT	0.547																																					p.T190fs		Atlas-INDEL	.											.	FTSJ2	22	.	0			c.568delA						.						87	80	82					7																	2274931		2203	4300	6503	SO:0001631	upstream_gene_variant	29960	exon3			.	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493		chr7.hg19:g.2274931delC	Exception_encountered	154.0	0.0		179.0	17.0	NM_013393	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Frame_Shift_Del	DEL	ENST00000406869.1	hg19	CCDS43539.1																																																																																			.	.		0.547	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		-	2274931	C	-	2274931	6	5	114	0	1	1	0	1	0	0	0	0	6096	842	30	0		0	FTSJ2	7	2274931	5'Flank	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1335873	2274931	156863732	507	18779										
FOXK1	221937	hgsc.bcm.edu	37	chr7	4798978	4798978	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccagccagtgatcatggccgTgcctccccgaccgtccagcc	10	19	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:4798978T>C	ENST00000328914.4	+	7	1448	c.1448T>C	c.(1447-1449)gTg>gCg	p.V483A	FOXK1_ENST00000446823.1_Missense_Mutation_p.V320A	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		ATCATGGCCGTGCCTCCCCGA	0.736																																					p.V483A		Atlas-SNP	.											.	FOXK1	64	.	0			c.T1448C						.						19	20	20					7																	4798978		2194	4295	6489	SO:0001583	missense	221937	exon7			TGGCCGTGCCTCC	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.1448T>C	chr7.hg19:g.4798978T>C	ENSP00000328720:p.Val483Ala	68.0	0.0		30.0	4.0	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	hg19	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.461008	0.43736	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.96011	-3.45;-3.88	5.34	5.34	0.76211	.	0.126422	0.53938	D	0.000044	D	0.92397	0.7587	L	0.42245	1.32	0.47659	D	0.999486	B;B	0.27625	0.057;0.183	B;B	0.26416	0.01;0.069	D	0.90058	0.4154	10	0.25751	T	0.34	.	14.7896	0.69830	0.0:0.0:0.0:1.0	.	483;320	P85037;P85037-2	FOXK1_HUMAN;.	A	320;239;483;366	ENSP00000394442:V320A;ENSP00000328720:V483A	ENSP00000328720:V483A	V	+	2	0	FOXK1	4765504	1.000000	0.71417	0.948000	0.38648	0.442000	0.32017	5.699000	0.68310	2.153000	0.67306	0.482000	0.46254	GTG	.	.		0.736	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			C	4798978	T	C	4798978	3	2	114	1	0	0	0	0	1	0	0	0	6022	1696	59	2	1474	2	FOXK1	7	4798978	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2524047	4798978	154339685	508	18780										
RADIL	55698	hgsc.bcm.edu	37	chr7	4841575	4841575	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccagggtccctgggagccaGggggcagctcggggcctcca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:4841575delG	ENST00000399583.3	-	12	2738	c.2551delC	c.(2551-2553)ctgfs	p.L851fs	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Frame_Shift_Del_p.L611fs	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	851	Pro-rich.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CTGGGAGCCAGGGGGCAGCTC	0.697																																					p.L851fs		Atlas-INDEL	.											.	RADIL	110	.	0			c.2552delT						.						6	7	6					7																	4841575		1508	3379	4887	SO:0001589	frameshift_variant	55698	exon12			.	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2551delC	chr7.hg19:g.4841575delG	ENSP00000382492:p.Leu851fs	87.0	0.0		128.0	10.0	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Frame_Shift_Del	DEL	ENST00000399583.3	hg19	CCDS43544.1																																																																																			.	.		0.697	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		-	4841575	G	-	4841575	7	5	114	1	0	1	0	1	0	0	0	0	13012	991	35	0	692	0	RADIL	7	4841575	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	42597	4841575	154297088	509	18781										
RBAK	57786	hgsc.bcm.edu	37	chr7	5104405	5104405	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtgtgggaaattcttttctCgggtgtcatacctcactata	9	8	4	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:5104405C>T	ENST00000353796.3	+	6	1642	c.1318C>T	c.(1318-1320)Cgg>Tgg	p.R440W	RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK-RBAKDN_ENST00000407184.1_Intron|RBAK_ENST00000396912.1_Missense_Mutation_p.R440W	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	440	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		ATTCTTTTCTCGGGTGTCATA	0.398																																					p.R440W		Atlas-SNP	.											RBAK_ENST00000396912,NS,malignant_melanoma,0,2	RBAK	82	.	0			c.C1318T						.						52	51	51					7																	5104405		2202	4299	6501	SO:0001583	missense	57786	exon6			TTTTCTCGGGTGT	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"Zinc fingers, C2H2-type", "-"	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.1318C>T	chr7.hg19:g.5104405C>T	ENSP00000275423:p.Arg440Trp	61.0	0.0		72.0	3.0	NM_001204456	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Missense_Mutation	SNP	ENST00000353796.3	hg19	CCDS5337.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.015536	0.54468	.	.	ENSG00000146587	ENST00000353796;ENST00000396912	T;T	0.16073	2.37;2.37	3.76	1.82	0.25136	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44902	D	0.000410	T	0.36166	0.0957	M	0.72353	2.195	0.32329	N	0.561318	D	0.89917	1.0	D	0.87578	0.998	T	0.48175	-0.9058	8	.	.	.	.	10.1859	0.42998	0.3584:0.6416:0.0:0.0	.	440	Q9NYW8	RBAK_HUMAN	W	440	ENSP00000275423:R440W;ENSP00000380120:R440W	.	R	+	1	2	RBAK	5070931	0.000000	0.05858	0.817000	0.32601	0.984000	0.73092	0.185000	0.16958	0.490000	0.27771	0.555000	0.69702	CGG	.	.		0.398	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163		T	5104405	C	T	5104405	3	4	114	1	0	0	0	0	1	0	0	0	13115	875	31	1	1332	1	RBAK	7	5104405	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	262830	5104405	154034258	510	18782										
FBXL18	80028	hgsc.bcm.edu	37	chr7	5540757	5540757	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggtggcgcaggttgcagcaGgacgccaccagagtctccag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:5540757delG	ENST00000382368.3	-	3	1266	c.1143delC	c.(1141-1143)tccfs	p.S381fs	FBXL18_ENST00000453700.3_Frame_Shift_Del_p.S381fs	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	381									FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		GGTTGCAGCAGGACGCCACCA	0.692																																					p.C382fs		Atlas-INDEL	.											.	FBXL18	99	.	0			c.1144delT						.						18	26	23					7																	5540757		2170	4266	6436	SO:0001589	frameshift_variant	80028	exon3			.	AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"F-boxes / Leucine-rich repeats"	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.1143delC	chr7.hg19:g.5540757delG	ENSP00000371805:p.Ser381fs	170.0	0.0		153.0	10.0	NM_024963	Q9BR90|Q9BTC7|Q9HAK7	Frame_Shift_Del	DEL	ENST00000382368.3	hg19	CCDS43546.1																																																																																			.	.		0.692	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963		-	5540757	G	-	5540757	7	5	114	1	0	1	0	1	0	0	0	0	5722	987	35	0	1025	0	FBXL18	7	5540757	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	436352	5540757	153597906	511	18783										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7555463	7555463	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accttgtcacccttgtacccAggaattccctaatttaaaaa	4	12	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:7555463A>G	ENST00000399429.3	-	8	1004	c.864T>C	c.(862-864)ccT>ccC	p.P288P		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	288					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCTTGTACCCAGGAATTCCCT	0.284																																					p.P288P		Atlas-SNP	.											.	COL28A1	113	.	0			c.T864C						.						77	73	74					7																	7555463		1791	4051	5842	SO:0001819	synonymous_variant	340267	exon8			GTACCCAGGAATT	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.864T>C	chr7.hg19:g.7555463A>G		84.0	0.0		94.0	4.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.284	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		G	7555463	A	G	7555463	2	3	114	1	0	0	0	0	0	0	0	1	3688	175	7	2		2	COL28A1	7	7555463	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2014706	7555463	151583200	512	18784										
MGC87042	256227	hgsc.bcm.edu	37	chr7	22533027	22533027	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taaattgcatgcagtacagcAaaaaacaaactgagaagccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:22533027delA	ENST00000406890.2	-	3	550	c.456delT	c.(454-456)tttfs	p.F152fs	STEAP1B_ENST00000404369.4_Frame_Shift_Del_p.F171fs	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	152						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						GCAGTACAGCAAAAAACAAAC	0.388																																					p.A172fs		Atlas-INDEL	.											.	STEAP1B	22	.	0			c.514delG						.						204	166	178					7																	22533027		692	1591	2283	SO:0001589	frameshift_variant	256227	exon3			.		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.456delT	chr7.hg19:g.22533027delA	ENSP00000385239:p.Phe152fs	177.0	0.0		225.0	17.0	NM_001164460	B5MCI2	Frame_Shift_Del	DEL	ENST00000406890.2	hg19	CCDS55094.1																																																																																			.	.		0.388	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2			-	22533027	A	-	22533027	7	5	114	1	0	1	0	1	0	0	0	0	9563	127	5	0	564	0	MGC87042	7	22533027	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	14977564	22533027	136605636	513	18785										
OSBPL3	26031	hgsc.bcm.edu	37	chr7	24911688	24911688	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttccaccacttcccagctgtCctgttccaacaaaagagttc	5	15	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:24911688C>T	ENST00000313367.2	-	3	548	c.97G>A	c.(97-99)Gac>Aac	p.D33N	OSBPL3_ENST00000396431.1_Splice_Site_p.D33N|OSBPL3_ENST00000353930.1_Splice_Site_p.D33N|OSBPL3_ENST00000352860.1_Splice_Site_p.D33N|OSBPL3_ENST00000431825.2_Splice_Site_p.D33N|OSBPL3_ENST00000409069.1_Splice_Site_p.D33N|OSBPL3_ENST00000396429.1_Splice_Site_p.D33N	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	33					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						TCCCAGCTGTCCTGTTCCAAC	0.413																																					p.D33N		Atlas-SNP	.											.	OSBPL3	100	.	0			c.G97A						.						86	80	82					7																	24911688		2203	4300	6503	SO:0001630	splice_region_variant	26031	exon3			AGCTGTCCTGTTC	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.97-1G>A	chr7.hg19:g.24911688C>T		90.0	0.0		114.0	46.0	NM_145321	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	hg19	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	C	34	5.328783	0.95733	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069;ENST00000415162;ENST00000441059;ENST00000415952	T;T;T;T;T;T;T;T;T;T	0.30714	2.76;2.76;2.76;2.76;2.76;2.76;2.76;2.76;2.76;1.52	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.57213	0.2038	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.48779	-0.9005	10	0.42905	T	0.14	-2.2432	20.5407	0.99260	0.0:1.0:0.0:0.0	.	33;33;33;33	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	N	33	ENSP00000315410:D33N;ENSP00000315331:D33N;ENSP00000315277:D33N;ENSP00000389779:D33N;ENSP00000379708:D33N;ENSP00000379706:D33N;ENSP00000386953:D33N;ENSP00000407829:D33N;ENSP00000403374:D33N;ENSP00000411249:D33N	ENSP00000315410:D33N	D	-	1	0	OSBPL3	24878213	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.380000	0.79704	2.865000	0.98341	0.655000	0.94253	GAC	.	.		0.413	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		Missense_Mutation	T	24911688	C	T	24911688	5	4	114	1	0	0	0	0	0	0	1	0	11288	869	30	3	2650	3	OSBPL3	7	24911688	Splice_Site	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	2378661	24911688	134226975	514	18786										
SKAP2	8935	hgsc.bcm.edu	37	chr7	26765146	26765146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atcatcatataattctcctcTctcatcataatcctcaggaa	2	12	7	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:26765146T>C	ENST00000345317.2	-	9	1010	c.697A>G	c.(697-699)Aga>Gga	p.R233G	SKAP2_ENST00000539623.1_Missense_Mutation_p.R61G|SKAP2_ENST00000489977.1_5'UTR	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	233					B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						AATTCTCCTCTCTCATCATAA	0.299																																					p.R233G		Atlas-SNP	.											.	SKAP2	40	.	0			c.A697G						.						119	118	118					7																	26765146		2203	4300	6503	SO:0001583	missense	8935	exon9			CTCCTCTCTCATC		CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"Pleckstrin homology (PH) domain containing"	15687	protein-coding gene	gene with protein product		605215	"src family associated phosphoprotein 2"	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.697A>G	chr7.hg19:g.26765146T>C	ENSP00000005587:p.Arg233Gly	68.0	0.0		91.0	4.0	NM_003930	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Missense_Mutation	SNP	ENST00000345317.2	hg19	CCDS5400.1	.	.	.	.	.	.	.	.	.	.	T	8.498	0.863483	0.17250	.	.	ENSG00000005020	ENST00000345317;ENST00000539623;ENST00000535331	T;T	0.31247	2.04;1.5	5.86	4.71	0.59529	.	0.533626	0.23314	N	0.049527	T	0.17450	0.0419	N	0.19112	0.55	0.30063	N	0.810719	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.16305	-1.0407	10	0.20519	T	0.43	-8.7302	7.4719	0.27353	0.0:0.1655:0.0:0.8345	.	218;233	B7Z5N4;O75563	.;SKAP2_HUMAN	G	233;61;218	ENSP00000005587:R233G;ENSP00000443593:R61G	ENSP00000005587:R233G	R	-	1	2	SKAP2	26731671	0.978000	0.34361	1.000000	0.80357	0.990000	0.78478	0.179000	0.16840	1.047000	0.40274	0.533000	0.62120	AGA	.	.		0.299	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214128.1			C	26765146	T	C	26765146	3	2	114	1	0	0	0	0	1	0	0	0	14371	1559	54	2	398	2	SKAP2	7	26765146	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1853458	26765146	132373517	515	18787										
JAZF1	221895	hgsc.bcm.edu	37	chr7	28220144	28220144	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggggaagtggagtccgcagCccccgaatcggcaggtattg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:28220144delC	ENST00000283928.5	-	1	218	c.53delG	c.(52-54)ggcfs	p.G18fs	JAZF1-AS1_ENST00000436758.1_RNA|JAZF1-AS1_ENST00000455963.1_RNA	NM_175061.3	NP_778231.2	Q86VZ6	JAZF1_HUMAN	JAZF zinc finger 1	18					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)		JAZF1/SUZ12(133)	endometrium(1)|large_intestine(1)|lung(4)	6						GAGTCCGCAGCCCCCGAATCG	0.682			T	SUZ12	endometrial stromal tumours																																p.G18fs		Atlas-INDEL	.		Dom	yes		7	7p15.2-p15.1	221895	juxtaposed with another zinc finger gene 1		M	.	JAZF1	13	.	0			c.54delC						.						41	41	41					7																	28220144		2203	4300	6503	SO:0001589	frameshift_variant	221895	exon1			.	BC047229	CCDS5416.1	7p15.2-p15.1	2010-04-14			ENSG00000153814	ENSG00000153814		"Zinc fingers, C2H2-type"	28917	protein-coding gene	gene with protein product		606246				8401585	Standard	XM_006715656		Approved	TIP27, DKFZp761K2222, ZNF802	uc003szn.3	Q86VZ6	OTTHUMG00000128545	ENST00000283928.5:c.53delG	chr7.hg19:g.28220144delC	ENSP00000283928:p.Gly18fs	113.0	0.0		187.0	12.0	NM_175061	A4D195|Q8N3L7	Frame_Shift_Del	DEL	ENST00000283928.5	hg19	CCDS5416.1																																																																																			.	.		0.682	JAZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250382.2	NM_175061		-	28220144	C	-	28220144	7	5	114	1	0	1	0	1	0	0	0	0	7955	739	26	0	698	0	JAZF1	7	28220144	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1454998	28220144	130918519	516	18788										
ANLN	54443	hgsc.bcm.edu	37	chr7	36445866	36445866	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcccctcccagacctctgctTtcaaatgcctcggcaactcc	5	19	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:36445866T>G	ENST00000265748.2	+	4	785	c.564T>G	c.(562-564)ctT>ctG	p.L188L	ANLN_ENST00000396068.2_Silent_p.L188L	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	188	Nuclear localization.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						GACCTCTGCTTTCAAATGCCT	0.473																																					p.L188L		Atlas-SNP	.											.	ANLN	101	.	0			c.T564G						.						75	76	76					7																	36445866		2203	4300	6503	SO:0001819	synonymous_variant	54443	exon4			TCTGCTTTCAAAT	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.564T>G	chr7.hg19:g.36445866T>G		117.0	0.0		133.0	44.0	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Silent	SNP	ENST00000265748.2	hg19	CCDS5447.1																																																																																			.	.		0.473	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		G	36445866	T	G	36445866	2	3	114	1	0	0	0	0	0	0	0	1	694	1828	64	5		5	ANLN	7	36445866	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	8225722	36445866	122692797	517	18789										
GLI3	2737	hgsc.bcm.edu	37	chr7	42006102	42006102	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcggcggctgctcaggtaggCcgagctgatggtgctggcgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:42006102delC	ENST00000395925.3	-	15	2653	c.2569delG	c.(2569-2571)gccfs	p.A857fs	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	857					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CTCAGGTAGGCCGAGCTGATG	0.662									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.A857fs		Atlas-INDEL	.											.	GLI3	312	.	0			c.2570delC						.						34	35	35					7																	42006102		2202	4300	6502	SO:0001589	frameshift_variant	2737	exon15	Familial Cancer Database	;	.		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.2569delG	chr7.hg19:g.42006102delC	ENSP00000379258:p.Ala857fs	145.0	0.0		154.0	10.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Frame_Shift_Del	DEL	ENST00000395925.3	hg19	CCDS5465.1																																																																																			.	.		0.662	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		-	42006102	C	-	42006102	7	5	114	1	0	1	0	1	0	0	0	0	6447	739	26	0	2177	0	GLI3	7	42006102	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	5560236	42006102	117132561	518	18790										
GLI3	2737	hgsc.bcm.edu	37	chr7	42012094	42012094	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atctctcgggggtggcggccGaggatggatgtcccctcgct	16	12	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:42012094G>T	ENST00000395925.3	-	13	2029	c.1945C>A	c.(1945-1947)Cgg>Agg	p.R649R	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	649					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GGTGGCGGCCGAGGATGGATG	0.612									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.R649R		Atlas-SNP	.											.	GLI3	312	.	0			c.C1945A						.						86	88	88					7																	42012094		2203	4300	6503	SO:0001819	synonymous_variant	2737	exon13	Familial Cancer Database	;	GCGGCCGAGGATG		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.1945C>A	chr7.hg19:g.42012094G>T		129.0	0.0		190.0	79.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	hg19	CCDS5465.1																																																																																			.	.		0.612	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42012094	G	T	42012094	2	4	114	1	0	0	0	0	0	0	0	1	6447	1057	37	1		1	GLI3	7	42012094	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	5992	42012094	117126569	519	18791										
YKT6	10652	hgsc.bcm.edu	37	chr7	44247796	44247796	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agatgagaccaaaatcattcTggtaagcaggaagatggaga	12	5	2	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:44247796T>C	ENST00000223369.2	+	5	545	c.458T>C	c.(457-459)cTg>cCg	p.L153P	YKT6_ENST00000496112.1_Splice_Site_p.L153P|YKT6_ENST00000447123.1_3'UTR	NM_006555.3	NP_006546.1	O15498	YKT6_HUMAN	YKT6 v-SNARE homolog (S. cerevisiae)	153	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				ER to Golgi vesicle-mediated transport (GO:0006888)|metabolic process (GO:0008152)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle docking involved in exocytosis (GO:0006904)|vesicle targeting (GO:0006903)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|SNARE complex (GO:0031201)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7						AAAATCATTCTGGTAAGCAGG	0.468																																					p.L153P		Atlas-SNP	.											.	YKT6	12	.	0			c.T458C						.						72	62	65					7																	44247796		2203	4300	6503	SO:0001630	splice_region_variant	10652	exon5			TCATTCTGGTAAG	BC007319	CCDS5482.1	7p13	2006-07-07			ENSG00000106636	ENSG00000106636			16959	protein-coding gene	gene with protein product	"R-SNARE"	606209				15479160, 15544955	Standard	NM_006555		Approved		uc003tkm.3	O15498	OTTHUMG00000129089	ENST00000223369.2:c.459+1T>C	chr7.hg19:g.44247796T>C		61.0	0.0		92.0	4.0	NM_006555	B4DR94|Q53F01|Q6FGU9|Q6IB15	Missense_Mutation	SNP	ENST00000223369.2	hg19	CCDS5482.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.679652	0.88542	.	.	ENSG00000106636	ENST00000496112;ENST00000223369	T	0.48201	0.82	5.88	5.88	0.94601	Synaptobrevin (2);	0.000000	0.85682	D	0.000000	T	0.77232	0.4100	H	0.95365	3.66	0.80722	D	1	D;D	0.63880	0.993;0.99	P;D	0.67382	0.878;0.951	D	0.84440	0.0582	10	0.87932	D	0	-6.8608	15.2725	0.73717	0.0:0.0:0.0:1.0	.	153;153	B4DR94;O15498	.;YKT6_HUMAN	P	153	ENSP00000223369:L153P	ENSP00000223369:L153P	L	+	2	0	YKT6	44214321	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.190000	0.77755	2.241000	0.73720	0.528000	0.53228	CTG	.	.		0.468	YKT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251125.2	NM_006555	Missense_Mutation	C	44247796	T	C	44247796	5	2	114	1	0	0	0	0	0	0	1	0	17500	1594	55	2	476	2	YKT6	7	44247796	Splice_Site	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2235702	44247796	114890867	520	18792										
TNS3	64759	hgsc.bcm.edu	37	chr7	47333390	47333390	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccttcggggtacactcgatcAaaaagtgccggacgagttca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:47333390delA	ENST00000398879.1	-	25	4079	c.3713delT	c.(3712-3714)ttgfs	p.L1238fs	TNS3_ENST00000311160.9_Frame_Shift_Del_p.L1238fs|TNS3_ENST00000355730.3_Frame_Shift_Del_p.L998fs			Q68CZ2	TENS3_HUMAN	tensin 3	1238	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						ACACTCGATCAAAAAGTGCCG	0.438																																					p.L1238fs		Atlas-INDEL	.											.	TNS3	140	.	0			c.3714delG						.						93	90	91					7																	47333390		1902	4114	6016	SO:0001589	frameshift_variant	64759	exon25			.	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.3713delT	chr7.hg19:g.47333390delA	ENSP00000381854:p.Leu1238fs	92.0	0.0		108.0	10.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Frame_Shift_Del	DEL	ENST00000398879.1	hg19	CCDS5506.2																																																																																			.	.		0.438	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		-	47333390	A	-	47333390	7	5	114	1	0	1	0	1	0	0	0	0	16359	131	5	0	652	0	TNS3	7	47333390	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3085594	47333390	111805273	521	18793										
COBL	23242	hgsc.bcm.edu	37	chr7	51287562	51287562	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgacccgagggccccatcgtGggggggcttctggtcactgt					rs368613191		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:51287562delG	ENST00000265136.7	-	2	286	c.121delC	c.(121-123)cacfs	p.H41fs	COBL_ENST00000395540.2_Frame_Shift_Del_p.H41fs|COBL_ENST00000441453.1_Frame_Shift_Del_p.H41fs|COBL_ENST00000395542.2_Frame_Shift_Del_p.H41fs	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	41					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					GCCCCATCGTGGGGGGGCTTC	0.602																																					p.H41fs	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-INDEL	.											.,1	COBL	167	.	0			c.122delA						.						40	42	42					7																	51287562		2203	4300	6503	SO:0001589	frameshift_variant	23242	exon2			.	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.121delC	chr7.hg19:g.51287562delG	ENSP00000265136:p.His41fs	146.0	0.0		169.0	16.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Frame_Shift_Del	DEL	ENST00000265136.7	hg19	CCDS34637.1																																																																																			.	.		0.602	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		-	51287562	G	-	51287562	7	5	114	1	0	1	0	1	0	0	0	0	3655	1348	47	0	3712	0	COBL	7	51287562	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	3954172	51287562	107851101	522	18794										
SUMF2	25870	hgsc.bcm.edu	37	chr7	56136261	56136261	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagacagcagagatggtgacGggcctgtgcgggaggcgaca	18	9	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:56136261G>A	ENST00000413756.1	+	2	177	c.154G>A	c.(154-156)Ggg>Agg	p.G52R	SUMF2_ENST00000275607.9_Intron|SUMF2_ENST00000342190.6_Missense_Mutation_p.G71R|SUMF2_ENST00000437307.2_Missense_Mutation_p.G52R|SUMF2_ENST00000395435.2_Missense_Mutation_p.G71R|SUMF2_ENST00000434526.2_Missense_Mutation_p.G71R|SUMF2_ENST00000395436.2_Missense_Mutation_p.G71R			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	52					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			AGATGGTGACGGGCCTGTGCG	0.493																																					p.G71R		Atlas-SNP	.											SUMF2_ENST00000342190,NS,carcinoma,0,4	SUMF2	56	.	0			c.G211A						.						69	62	64					7																	56136261		2203	4300	6503	SO:0001583	missense	25870	exon2			GGTGACGGGCCTG	AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103			20415	protein-coding gene	gene with protein product		607940				12757706	Standard	NM_015411		Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.154G>A	chr7.hg19:g.56136261G>A	ENSP00000406445:p.Gly52Arg	96.0	0.0		128.0	0.0	NM_015411	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Missense_Mutation	SNP	ENST00000413756.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.99	2.102779	0.37145	.	.	ENSG00000129103	ENST00000395436;ENST00000434526;ENST00000395435;ENST00000413952;ENST00000342190;ENST00000437307;ENST00000413756;ENST00000451338	D;D;D;D;D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38;-3.38;-3.38;-3.38;-3.38	5.01	4.13	0.48395	C-type lectin fold (1);Formylglycine-generating sulphatase enzyme domain (2);	0.276505	0.41712	D	0.000834	D	0.93331	0.7874	L	0.31845	0.965	0.80722	D	1	P;D;D;D;D;D	0.89917	0.868;0.999;0.966;0.999;1.0;1.0	P;P;B;P;D;D	0.72075	0.483;0.887;0.308;0.87;0.96;0.976	D	0.92822	0.6273	10	0.66056	D	0.02	-15.0969	8.9043	0.35515	0.1732:0.0:0.8268:0.0	.	52;71;71;52;71;71	Q8NBJ7-5;A8MXB9;E7EMF9;Q8NBJ7;F8WA42;C9JL30	.;.;.;SUMF2_HUMAN;.;.	R	71;71;71;71;71;52;52;49	ENSP00000378824:G71R;ENSP00000400922:G71R;ENSP00000378823:G71R;ENSP00000414434:G71R;ENSP00000341938:G71R;ENSP00000415989:G52R;ENSP00000406445:G52R;ENSP00000410796:G49R	ENSP00000341938:G71R	G	+	1	0	SUMF2	56103755	1.000000	0.71417	1.000000	0.80357	0.238000	0.25445	2.971000	0.49248	1.248000	0.43934	0.484000	0.47621	GGG	.	.		0.493	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411		A	56136261	G	A	56136261	3	1	114	1	0	0	0	0	1	0	0	0	15401	1116	39	1	217	1	SUMF2	7	56136261	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	4848699	56136261	103002402	523	18795										
ZNF273	10793	hgsc.bcm.edu	37	chr7	64388426	64388426	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tacaaatgtaagacatgtggAaaagcctttaaccagttctc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:64388426delA	ENST00000476120.1	+	4	791	c.720delA	c.(718-720)ggafs	p.G240fs	ZNF273_ENST00000319636.5_Frame_Shift_Del_p.G175fs|ZNF273_ENST00000527278.1_3'UTR	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	240					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AGACATGTGGAAAAGCCTTTA	0.343																																					p.G240fs	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-INDEL	.											.	ZNF273	45	.	0			c.719delG						.						66	72	70					7																	64388426		2203	4297	6500	SO:0001589	frameshift_variant	10793	exon4			.	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"Zinc fingers, C2H2-type", "-"	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.720delA	chr7.hg19:g.64388426delA	ENSP00000418719:p.Gly240fs	73.0	0.0		183.0	11.0	NM_021148	B3KQZ5|Q6P3V4	Frame_Shift_Del	DEL	ENST00000476120.1	hg19	CCDS5528.2																																																																																			.	.		0.343	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1			-	64388426	A	-	64388426	7	5	114	1	0	1	0	1	0	0	0	0	17823	233	9	0	734	0	ZNF273	7	64388426	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	8252165	64388426	94750237	524	18796										
ZNF92	168374	hgsc.bcm.edu	37	chr7	64863524	64863524	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtaaatagaaataagataaGacatactggaaagaaacctt	7	4	0	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:64863524G>A	ENST00000328747.7	+	4	696	c.497G>A	c.(496-498)aGa>aAa	p.R166K	ZNF92_ENST00000431504.1_Missense_Mutation_p.R90K|ZNF92_ENST00000357512.2_Missense_Mutation_p.R134K|ZNF92_ENST00000450302.2_Missense_Mutation_p.R97K	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	166					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				AATAAGATAAGACATACTGGA	0.299																																					p.R166K		Atlas-SNP	.											.	ZNF92	68	.	0			c.G497A						.						34	37	36					7																	64863524		2203	4293	6496	SO:0001583	missense	168374	exon4			AGATAAGACATAC	M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"Zinc fingers, C2H2-type", "-"	13168	protein-coding gene	gene with protein product		603974	"zinc finger protein 92 (HTF12)"			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.497G>A	chr7.hg19:g.64863524G>A	ENSP00000332595:p.Arg166Lys	37.0	0.0		91.0	4.0	NM_152626	A6NNF9|Q8N492|Q8NB35	Missense_Mutation	SNP	ENST00000328747.7	hg19	CCDS34646.1	.	.	.	.	.	.	.	.	.	.	G	0.028	-1.352673	0.01256	.	.	ENSG00000146757	ENST00000328747;ENST00000431504;ENST00000357512;ENST00000450302	T;T;T;T	0.27890	2.47;1.64;1.64;1.64	0.427	-0.854	0.10705	.	.	.	.	.	T	0.20820	0.0501	L	0.59967	1.855	0.19575	N	0.999961	P;B	0.35411	0.5;0.075	B;B	0.35312	0.2;0.081	T	0.29640	-1.0005	9	0.05620	T	0.96	.	4.3647	0.11218	0.0:0.0:0.3617:0.6382	.	134;166	Q03936-3;Q03936	.;ZNF92_HUMAN	K	166;90;134;97	ENSP00000332595:R166K;ENSP00000400495:R90K;ENSP00000350113:R134K;ENSP00000396126:R97K	ENSP00000332595:R166K	R	+	2	0	ZNF92	64500959	0.000000	0.05858	0.024000	0.17045	0.023000	0.10783	-0.162000	0.10012	-0.514000	0.06488	-0.518000	0.04402	AGA	.	.		0.299	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626		A	64863524	G	A	64863524	3	1	114	1	0	0	0	0	1	0	0	0	18216	942	33	3	511	3	ZNF92	7	64863524	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	475098	64863524	94275139	525	18797										
LIMK1	3984	hgsc.bcm.edu	37	chr7	73523283	73523283	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaacgtgctcaagttcatcGgggtgctctacaaggacaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:73523283delG	ENST00000336180.2	+	10	1252	c.1201delG	c.(1201-1203)gggfs	p.G401fs	LIMK1_ENST00000538333.3_Frame_Shift_Del_p.G367fs|LIMK1_ENST00000418310.1_Frame_Shift_Del_p.G431fs	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	401	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	CAAGTTCATCGGGGTGCTCTA	0.602																																					p.I400fs		Atlas-INDEL	.											.	LIMK1	55	.	0			c.1200delC						.						123	95	104					7																	73523283		2203	4300	6503	SO:0001589	frameshift_variant	3984	exon10			.	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.1201delG	chr7.hg19:g.73523283delG	ENSP00000336740:p.Gly401fs	85.0	0.0		211.0	14.0	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Frame_Shift_Del	DEL	ENST00000336180.2	hg19	CCDS5563.1																																																																																			.	.		0.602	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		-	73523283	G	-	73523283	7	5	114	1	0	1	0	1	0	0	0	0	8810	1116	39	0	1239	0	LIMK1	7	73523283	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	8659759	73523283	85615380	526	18798										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81662161	81662161	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atctcctgggctctctcttcTcctccatccgtgaatagcat	6	15	4	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:81662161T>C	ENST00000356253.5	-	12	1350	c.1095A>G	c.(1093-1095)ggA>ggG	p.G365G	CACNA2D1_ENST00000356860.3_Silent_p.G365G|MIR1255B1_ENST00000439234.1_RNA|CACNA2D1_ENST00000464354.1_5'UTR			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	365	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CTCTCTCTTCTCCTCCATCCG	0.279																																					p.G365G		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A1095G						.						76	77	76					7																	81662161		2203	4297	6500	SO:0001819	synonymous_variant	781	exon12			CTCTTCTCCTCCA	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.1095A>G	chr7.hg19:g.81662161T>C		37.0	0.0		91.0	5.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	hg19																																																																																				.	.		0.279	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				C	81662161	T	C	81662161	2	2	114	1	0	0	0	0	0	0	0	1	2550	1538	54	2		2	CACNA2D1	7	81662161	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	8138878	81662161	77476502	527	18799										
DMTF1	9988	hgsc.bcm.edu	37	chr7	86813845	86813845	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acgagtcggtacccgctcagAaaagcaatgtcgttctaaat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:86813845delA	ENST00000394703.5	+	13	1516	c.953delA	c.(952-954)gaafs	p.E318fs	DMTF1_ENST00000414194.2_Frame_Shift_Del_p.E52fs|DMTF1_ENST00000432937.2_Frame_Shift_Del_p.E230fs|DMTF1_ENST00000331242.7_Frame_Shift_Del_p.E318fs|DMTF1_ENST00000413276.2_Frame_Shift_Del_p.E318fs	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	318	HTH myb-type. {ECO:0000255|PROSITE- ProRule:PRU00625}.|Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					ACCCGCTCAGAAAAGCAATGT	0.488																																					p.E318fs		Atlas-INDEL	.											.	DMTF1	48	.	0			c.952delG						.						121	98	106					7																	86813845		2203	4300	6503	SO:0001589	frameshift_variant	9988	exon11			.	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.953delA	chr7.hg19:g.86813845delA	ENSP00000378193:p.Glu318fs	74.0	0.0		193.0	12.0	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Frame_Shift_Del	DEL	ENST00000394703.5	hg19	CCDS5601.1																																																																																			.	.		0.488	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145		-	86813845	A	-	86813845	7	5	114	1	0	1	0	1	0	0	0	0	4594	246	9	0	987	0	DMTF1	7	86813845	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	5151684	86813845	72324818	528	18800										
CROT	54677	hgsc.bcm.edu	37	chr7	86988625	86988625	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caccagaaattgcttgaaagAgcaaaaggaaaaagaaattg	9	5	0	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:86988625A>G	ENST00000331536.3	+	4	404	c.219A>G	c.(217-219)agA>agG	p.R73R	CROT_ENST00000419147.2_Silent_p.R101R|CROT_ENST00000412227.2_Silent_p.R73R|CROT_ENST00000442291.1_Silent_p.R73R	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	73					carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	TGCTTGAAAGAGCAAAAGGAA	0.249																																					p.R101R		Atlas-SNP	.											.	CROT	81	.	0			c.A303G						.						61	71	68					7																	86988625		2203	4289	6492	SO:0001819	synonymous_variant	54677	exon5			TGAAAGAGCAAAA		CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.219A>G	chr7.hg19:g.86988625A>G		68.0	0.0		141.0	6.0	NM_001143935	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Silent	SNP	ENST00000331536.3	hg19	CCDS5604.1																																																																																			.	.		0.249	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		G	86988625	A	G	86988625	2	3	114	1	0	0	0	0	0	0	0	1	3896	301	11	2		2	CROT	7	86988625	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	174780	86988625	72150038	529	18801										
CASD1	64921	hgsc.bcm.edu	37	chr7	94166946	94166946	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttttttacataattcatcgtAatgctcatcggaagaataag	6	6	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:94166946A>G	ENST00000297273.4	+	9	1293	c.1006A>G	c.(1006-1008)Aat>Gat	p.N336D		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	336						integral component of membrane (GO:0016021)				NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			AATTCATCGTAATGCTCATCG	0.343																																					p.N336D		Atlas-SNP	.											.	CASD1	70	.	0			c.A1006G						.						99	106	104					7																	94166946		2203	4300	6503	SO:0001583	missense	64921	exon9			CATCGTAATGCTC	AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 12"	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1006A>G	chr7.hg19:g.94166946A>G	ENSP00000297273:p.Asn336Asp	104.0	0.0		228.0	47.0	NM_022900	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Missense_Mutation	SNP	ENST00000297273.4	hg19	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	A	11.12	1.544602	0.27563	.	.	ENSG00000127995	ENST00000297273	T	0.41400	1.0	5.27	4.08	0.47627	.	0.135452	0.64402	D	0.000003	T	0.25901	0.0631	N	0.08118	0	0.38203	D	0.940245	P;P	0.38711	0.643;0.643	B;B	0.40506	0.331;0.331	T	0.21965	-1.0230	10	0.35671	T	0.21	.	12.8372	0.57780	0.8208:0.1792:0.0:0.0	.	336;336	Q8WZ77;Q96PB1	.;CASD1_HUMAN	D	336	ENSP00000297273:N336D	ENSP00000297273:N336D	N	+	1	0	CASD1	94004882	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.296000	0.65698	2.124000	0.65301	0.482000	0.46254	AAT	.	.		0.343	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900		G	94166946	A	G	94166946	3	3	114	1	0	0	0	0	1	0	0	0	2666	362	13	2	1040	2	CASD1	7	94166946	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	7178321	94166946	64971717	530	18802										
PEG10	23089	hgsc.bcm.edu	37	chr7	94293774	94293774	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctctactgtggaacaggaggTcactacgctgacaattgtcc	10	11	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:94293774T>C	ENST00000482108.1	+	2	1385	c.906T>C	c.(904-906)ggT>ggC	p.G302G	PEG10_ENST00000488574.1_Silent_p.G302G	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	302					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GAACAGGAGGTCACTACGCTG	0.597																																					p.G378G		Atlas-SNP	.											.	PEG10	36	.	0			c.T1134C						.						22	28	26					7																	94293774		1976	4156	6132	SO:0001819	synonymous_variant	23089	exon2			AGGAGGTCACTAC	AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.906T>C	chr7.hg19:g.94293774T>C		96.0	0.0		180.0	9.0	NM_001172438	Q96A68|Q9UPV1	Silent	SNP	ENST00000482108.1	hg19	CCDS55126.1																																																																																			.	.		0.597	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340751.1	NM_015068		C	94293774	T	C	94293774	2	2	114	1	0	0	0	0	0	0	0	1	11728	1667	58	2		2	PEG10	7	94293774	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	126828	94293774	64844889	531	18803										
SLC25A13	10165	hgsc.bcm.edu	37	chr7	95906607	95906607	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtatcgagtgacaaagtcaTtgggggacatgaaaaattca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:95906607delT	ENST00000265631.5	-	3	249	c.113delA	c.(112-114)aatfs	p.N38fs	SLC25A13_ENST00000542654.1_De_novo_Start_OutOfFrame|SLC25A13_ENST00000416240.2_Frame_Shift_Del_p.N38fs			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	38					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	GACAAAGTCATTGGGGGACAT	0.343																																					p.N38fs		Atlas-INDEL	.											.	SLC25A13	131	.	0			c.114delT						.						53	50	51					7																	95906607		2202	4299	6501	SO:0001589	frameshift_variant	10165	exon3			.	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"Solute carriers", "EF-hand domain containing"	10983	protein-coding gene	gene with protein product	"mitochondrial aspartate glutamate carrier 2"	603859	"solute carrier family 25, member 13 (citrin)"	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.113delA	chr7.hg19:g.95906607delT	ENSP00000265631:p.Asn38fs	76.0	0.0		151.0	10.0	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Frame_Shift_Del	DEL	ENST00000265631.5	hg19	CCDS5645.1																																																																																			.	.		0.343	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		-	95906607	T	-	95906607	7	5	114	1	0	1	0	1	0	0	0	0	14490	1493	52	0	1981	0	SLC25A13	7	95906607	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1612833	95906607	63232056	532	18804										
TMEM130	222865	hgsc.bcm.edu	37	chr7	98452869	98452869	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggagctcacttacctccccAggaagttcaaggtcacggtc	10	13	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:98452869A>G	ENST00000416379.2	-	5	801	c.797T>C	c.(796-798)cTg>cCg	p.L266P	TMEM130_ENST00000546258.1_Missense_Mutation_p.L247P|TMEM130_ENST00000339375.4_Missense_Mutation_p.L266P|TMEM130_ENST00000450876.1_Missense_Mutation_p.L182P|TMEM130_ENST00000345589.4_Missense_Mutation_p.L164P			Q8N3G9	TM130_HUMAN	transmembrane protein 130	266						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	25	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TTACCTCCCCAGGAAGTTCAA	0.582																																					p.L266P		Atlas-SNP	.											.	TMEM130	54	.	0			c.T797C						.						114	101	105					7																	98452869		2203	4300	6503	SO:0001583	missense	222865	exon5			CTCCCCAGGAAGT		CCDS5658.1, CCDS47649.1, CCDS47650.1	7q22.1	2006-03-09			ENSG00000166448	ENSG00000166448			25429	protein-coding gene	gene with protein product						12975309	Standard	NM_152913		Approved	DKFZp761L1417, FLJ42643	uc003upo.3	Q8N3G9	OTTHUMG00000154419	ENST00000416379.2:c.797T>C	chr7.hg19:g.98452869A>G	ENSP00000413163:p.Leu266Pro	89.0	0.0		167.0	7.0	NM_152913	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Missense_Mutation	SNP	ENST00000416379.2	hg19	CCDS47650.1	.	.	.	.	.	.	.	.	.	.	A	11.74	1.729952	0.30684	.	.	ENSG00000166448	ENST00000416379;ENST00000339375;ENST00000450876;ENST00000345589;ENST00000546258	T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93	4.01	2.87	0.33458	.	0.934094	0.08847	N	0.884975	T	0.38188	0.1031	L	0.51422	1.61	0.42957	D	0.99439	D;D;D;D	0.69078	0.99;0.99;0.997;0.994	D;D;D;P	0.66979	0.912;0.912;0.948;0.827	T	0.31861	-0.9928	10	0.27785	T	0.31	-12.6495	5.5051	0.16850	0.8757:0.0:0.1243:0.0	.	266;247;266;164	Q8N3G9-2;B7Z2F1;Q8N3G9;Q8N3G9-3	.;.;TM130_HUMAN;.	P	266;266;182;164;247	ENSP00000413163:L266P;ENSP00000341256:L266P;ENSP00000390200:L182P;ENSP00000330262:L164P;ENSP00000445869:L247P	ENSP00000341256:L266P	L	-	2	0	TMEM130	98290805	1.000000	0.71417	0.999000	0.59377	0.203000	0.24098	2.441000	0.44864	1.797000	0.52628	0.455000	0.32223	CTG	.	.		0.582	TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913		G	98452869	A	G	98452869	3	3	114	1	0	0	0	0	1	0	0	0	16058	188	7	2	526	2	TMEM130	7	98452869	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2546262	98452869	60685794	533	18805										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98574152	98574152	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctgtgcagcggcagtcaccAggtgcagcgggactgccagc	15	13	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:98574152A>G	ENST00000359863.4	+	54	8194	c.7985A>G	c.(7984-7986)cAg>cGg	p.Q2662R	TRRAP_ENST00000355540.3_Missense_Mutation_p.Q2644R|TRRAP_ENST00000446306.3_Missense_Mutation_p.Q2644R	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2662					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GGCAGTCACCAGGTGCAGCGG	0.567																																					p.Q2662R		Atlas-SNP	.											.	TRRAP	863	.	0			c.A7985G						.						63	60	61					7																	98574152		2203	4300	6503	SO:0001583	missense	8295	exon54			GTCACCAGGTGCA	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.7985A>G	chr7.hg19:g.98574152A>G	ENSP00000352925:p.Gln2662Arg	19.0	0.0		84.0	4.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.0|22.0	4.225129|4.225129	0.79576|0.79576	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306|ENST00000456197	T;T|.	0.64438|.	-0.1;-0.1|.	6.06|6.06	6.06|6.06	0.98353|0.98353	Armadillo-like helical (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58337|0.58337	0.2115|0.2115	L|L	0.31926|0.31926	0.97|0.97	0.80722|0.80722	D|D	1|1	B;B;B|.	0.31910|.	0.295;0.207;0.346|.	B;B;B|.	0.31495|.	0.131;0.093;0.093|.	T|T	0.53913|0.53913	-0.8371|-0.8371	10|5	0.15952|.	T|.	0.53|.	.|.	16.6093|16.6093	0.84858|0.84858	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	2644;2383;2662|.	Q9Y4A5-2;Q59FH1;Q9Y4A5|.	.;.;TRRAP_HUMAN|.	R|G	2662;2644;2643|2384	ENSP00000352925:Q2662R;ENSP00000347733:Q2644R|.	ENSP00000347733:Q2644R|.	Q|R	+|+	2|1	0|2	TRRAP|TRRAP	98412088|98412088	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.917000|0.917000	0.54804|0.54804	9.040000|9.040000	0.93783|0.93783	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	CAG|AGG	.	.		0.567	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		G	98574152	A	G	98574152	3	3	114	1	0	0	0	0	1	0	0	0	16616	188	7	2	8137	2	TRRAP	7	98574152	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	121283	98574152	60564511	534	18806										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98575870	98575870	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaaaggcaatggataaagccAaaaaagaacatgagaggagt					rs56341061		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:98575870delA	ENST00000359863.4	+	56	8610	c.8401delA	c.(8401-8403)aaafs	p.K2802fs	TRRAP_ENST00000355540.3_Frame_Shift_Del_p.K2784fs|TRRAP_ENST00000446306.3_Frame_Shift_Del_p.K2784fs	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2802	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GGATAAAGCCAAAAAAGAACA	0.388																																					p.A2800fs		Atlas-INDEL	.											.	TRRAP	863	.	0			c.8400delC						.						142	139	140					7																	98575870		2203	4300	6503	SO:0001589	frameshift_variant	8295	exon56			.	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.8401delA	chr7.hg19:g.98575870delA	ENSP00000352925:p.Lys2802fs	127.0	0.0		258.0	17.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Frame_Shift_Del	DEL	ENST00000359863.4	hg19	CCDS59066.1																																																																																			.	.		0.388	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		-	98575870	A	-	98575870	7	5	114	1	0	1	0	1	0	0	0	0	16616	131	5	0	8561	0	TRRAP	7	98575870	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1718	98575870	60562793	535	18807										
AP4M1	9179	hgsc.bcm.edu	37	chr7	99701731	99701731	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcagagccaaaagaatgaagTttttttggatgtggtcgaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:99701731delT	ENST00000359593.4	+	7	718	c.560delT	c.(559-561)gttfs	p.V187fs	AP4M1_ENST00000421755.1_Frame_Shift_Del_p.V187fs|AP4M1_ENST00000422582.1_Frame_Shift_Del_p.V59fs|MCM7_ENST00000343023.6_5'Flank|MCM7_ENST00000303887.5_5'Flank|AP4M1_ENST00000429084.1_Frame_Shift_Del_p.V194fs	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	187	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AAGAATGAAGTTTTTTTGGAT	0.438																																					p.V187fs	Pancreas(174;1182 2812 29595 49511)	Atlas-INDEL	.											.	AP4M1	39	.	0			c.559delG						.						123	109	113					7																	99701731		2203	4300	6503	SO:0001589	frameshift_variant	9179	exon7			.	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"mu-adaptin-related protein-2", "mu subunit of AP-4", "AP-4 adapter complex mu subunit", "adaptor-related protein complex AP-4 mu4 subunit"	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.560delT	chr7.hg19:g.99701731delT	ENSP00000352603:p.Val187fs	81.0	0.0		171.0	11.0	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Frame_Shift_Del	DEL	ENST00000359593.4	hg19	CCDS5685.1																																																																																			.	.		0.438	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722		-	99701731	T	-	99701731	7	5	114	1	0	1	0	1	0	0	0	0	753	1725	60	0	586	0	AP4M1	7	99701731	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1125861	99701731	59436932	536	18808										
ZCWPW1	55063	hgsc.bcm.edu	37	chr7	99998706	99998706	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgctgcagctccccgctctgCcccagctctctcccaacatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:99998706delC	ENST00000398027.2	-	18	2125	c.1878delG	c.(1876-1878)gggfs	p.G626fs	ZCWPW1_ENST00000324725.6_Frame_Shift_Del_p.G455fs|ZCWPW1_ENST00000490721.1_Frame_Shift_Del_p.G455fs|ZCWPW1_ENST00000360951.4_3'UTR	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	626							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CCCCGCTCTGCCCCAGCTCTC	0.607																																					p.Q627fs		Atlas-INDEL	.											.	ZCWPW1	41	.	0			c.1879delC						.						48	52	51					7																	99998706		2054	4204	6258	SO:0001589	frameshift_variant	55063	exon18			.	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"zinc finger, CW-type with PWWP domain 1"			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.1878delG	chr7.hg19:g.99998706delC	ENSP00000381109:p.Gly626fs	95.0	0.0		207.0	13.0	NM_017984	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Frame_Shift_Del	DEL	ENST00000398027.2	hg19	CCDS43623.1																																																																																			.	.		0.607	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984		-	99998706	C	-	99998706	7	5	114	1	0	1	0	1	0	0	0	0	17612	726	26	0	72	0	ZCWPW1	7	99998706	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	296975	99998706	59139957	537	18809										
SRRT	51593	hgsc.bcm.edu	37	chr7	100485681	100485681	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtactccccccaggtttgaCcccaggactcccctacccac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:100485681delC	ENST00000347433.4	+	18	2503	c.2345delC	c.(2344-2346)accfs	p.T782fs	SRRT_ENST00000432932.1_Frame_Shift_Del_p.T777fs|SRRT_ENST00000457580.2_Frame_Shift_Del_p.T778fs|SRRT_ENST00000388793.4_Frame_Shift_Del_p.T781fs			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	782	Pro-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CCAGGTTTGACCCCAGGACTC	0.617																																					p.T782fs		Atlas-INDEL	.											.	SRRT	108	.	0			c.2344delA						.						47	52	50					7																	100485681		2203	4300	6503	SO:0001589	frameshift_variant	51593	exon18			.		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2345delC	chr7.hg19:g.100485681delC	ENSP00000314491:p.Thr782fs	137.0	0.0		165.0	10.0	NM_015908	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Frame_Shift_Del	DEL	ENST00000347433.4	hg19	CCDS34709.1																																																																																			.	.		0.617	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		-	100485681	C	-	100485681	7	5	114	1	0	1	0	1	0	0	0	0	15187	507	18	0	2411	0	SRRT	7	100485681	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	486975	100485681	58652982	538	18810										
UFSP1	402682	hgsc.bcm.edu	37	chr7	100486590	100486590	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccagcagcctgtagttcactGgggctttttggagtgcccca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:100486590delG	ENST00000388761.2	-	1	749	c.303delC	c.(301-303)cccfs	p.P101fs		NM_001015072.3	NP_001015072.2	Q6NVU6	UFSP1_HUMAN	UFM1-specific peptidase 1 (non-functional)	101						extracellular vesicular exosome (GO:0070062)	thiolester hydrolase activity (GO:0016790)|UFM1 hydrolase activity (GO:0071567)			lung(1)|stomach(1)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)					GTAGTTCACTGGGGCTTTTTG	0.587																																					p.S102fs		Atlas-INDEL	.											.	UFSP1	8	.	0			c.304delA						.						88	92	91					7																	100486590		2203	4300	6503	SO:0001589	frameshift_variant	402682	exon1			.	AF312032	CCDS34710.1	7q22.1	2008-03-25			ENSG00000176125	ENSG00000176125			33821	protein-coding gene	gene with protein product		611481				17182609, 18321862	Standard	NM_001015072		Approved	UFSP	uc003uxc.4	Q6NVU6	OTTHUMG00000159662	ENST00000388761.2:c.303delC	chr7.hg19:g.100486590delG	ENSP00000373413:p.Pro101fs	131.0	0.0		171.0	11.0	NM_001015072	A4D2E4|A8K8V2|B6ZDG6|Q9BXP6	Frame_Shift_Del	DEL	ENST00000388761.2	hg19	CCDS34710.1																																																																																			.	.		0.587	UFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356751.1	NM_001015072		-	100486590	G	-	100486590	7	5	114	1	0	1	0	1	0	0	0	0	16952	1335	47	0	129	0	UFSP1	7	100486590	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	909	100486590	58652073	539	18811										
DNAJC2	27000	hgsc.bcm.edu	37	chr7	102953447	102953447	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccaggcaccgcttctgctaTtttttcccatctttcaggtg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:102953447delT	ENST00000379263.3	-	16	1988	c.1738delA	c.(1738-1740)atafs	p.I580fs	PMPCB_ENST00000249269.4_3'UTR|PMPCB_ENST00000420236.2_Intron|DNAJC2_ENST00000249270.7_Frame_Shift_Del_p.I527fs	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	580	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)			endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						GCTTCTGCTATTTTTTCCCAT	0.398																																					p.I580fs		Atlas-INDEL	.											.	DNAJC2	46	.	0			c.1739delT						.						267	247	253					7																	102953447		1852	4090	5942	SO:0001589	frameshift_variant	27000	exon16			.	X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"Heat shock proteins / DNAJ (HSP40)"	13192	protein-coding gene	gene with protein product		605502	"zuotin related factor 1"	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.1738delA	chr7.hg19:g.102953447delT	ENSP00000368565:p.Ile580fs	152.0	0.0		176.0	12.0	NM_014377	A4VCI0|Q9BVX1	Frame_Shift_Del	DEL	ENST00000379263.3	hg19	CCDS43628.1																																																																																			.	.		0.398	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1			-	102953447	T	-	102953447	7	5	114	1	0	1	0	1	0	0	0	0	4641	1493	52	0	135	0	DNAJC2	7	102953447	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2466857	102953447	56185216	540	18812										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107866100	107866100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ataactcaccaccataaaacTcagtgtcactcaaattagca	3	12	4	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:107866100T>C	ENST00000425651.2	-	7	766	c.767A>G	c.(766-768)gAg>gGg	p.E256G	NRCAM_ENST00000379022.4_Missense_Mutation_p.E256G|NRCAM_ENST00000351718.4_Missense_Mutation_p.E250G|NRCAM_ENST00000379028.3_Missense_Mutation_p.E256G|NRCAM_ENST00000379024.4_Intron|NRCAM_ENST00000413765.2_Intron	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	256					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						ACCATAAAACTCAGTGTCACT	0.353																																					p.E256G		Atlas-SNP	.											.	NRCAM	267	.	0			c.A767G						.						208	205	206					7																	107866100		2203	4300	6503	SO:0001583	missense	4897	exon7			TAAAACTCAGTGT		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.767A>G	chr7.hg19:g.107866100T>C	ENSP00000401244:p.Glu256Gly	60.0	0.0		84.0	4.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.531062	0.64972	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000537765;ENST00000351718;ENST00000425651;ENST00000379022;ENST00000445979;ENST00000417701	T;T;T;T;T	0.69435	0.3;0.27;0.3;0.31;-0.4	5.86	5.86	0.93980	.	0.049690	0.85682	D	0.000000	T	0.49949	0.1587	N	0.08118	0	0.43403	D	0.995536	B;B;B	0.13145	0.007;0.002;0.001	B;B;B	0.14578	0.011;0.002;0.003	T	0.47749	-0.9093	10	0.56958	D	0.05	.	16.5602	0.84551	0.0:0.0:0.0:1.0	.	256;250;256	Q92823-5;Q92823-4;Q92823	.;.;NRCAM_HUMAN	G	256;256;256;250;256;256;250;250	ENSP00000368314:E256G;ENSP00000325269:E250G;ENSP00000401244:E256G;ENSP00000368308:E256G;ENSP00000390421:E250G	ENSP00000325269:E250G	E	-	2	0	NRCAM	107653336	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.636000	0.83301	2.367000	0.80283	0.528000	0.53228	GAG	.	.		0.353	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		C	107866100	T	C	107866100	3	2	114	1	0	0	0	0	1	0	0	0	10653	1551	54	2	3273	2	NRCAM	7	107866100	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4912653	107866100	51272563	541	18813										
C7orf66	154907	hgsc.bcm.edu	37	chr7	108524086	108524086	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatttcccatttcctttggaAaagattttgcataactgatt	5	7	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:108524086A>G	ENST00000379007.2	-	2	380	c.326T>C	c.(325-327)tTt>tCt	p.F109S		NM_001024607.1	NP_001019778.1	A4D0T2	CG066_HUMAN	chromosome 7 open reading frame 66	109						integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	15						TTCCTTTGGAAAAGATTTTGC	0.323																																					p.F109S		Atlas-SNP	.											.	C7orf66	29	.	0			c.T326C						.						115	108	110					7																	108524086		2203	4300	6503	SO:0001583	missense	154907	exon2			TTTGGAAAAGATT	AF103078	CCDS34735.1	7q31.1	2009-03-06			ENSG00000205174	ENSG00000205174			33712	protein-coding gene	gene with protein product							Standard	NM_001024607		Approved		uc003vfo.3	A4D0T2	OTTHUMG00000154867	ENST00000379007.2:c.326T>C	chr7.hg19:g.108524086A>G	ENSP00000368292:p.Phe109Ser	88.0	0.0		89.0	4.0	NM_001024607		Missense_Mutation	SNP	ENST00000379007.2	hg19	CCDS34735.1	.	.	.	.	.	.	.	.	.	.	a	8.917	0.960139	0.18507	.	.	ENSG00000205174	ENST00000379007	.	.	.	3.62	-0.0197	0.13958	.	.	.	.	.	T	0.14442	0.0349	N	0.08118	0	0.09310	N	1	B	0.24963	0.115	B	0.21546	0.035	T	0.26467	-1.0102	7	.	.	.	.	3.2723	0.06886	0.5156:0.2404:0.244:0.0	.	109	A4D0T2	CG066_HUMAN	S	109	.	.	F	-	2	0	C7orf66	108311322	0.099000	0.21834	0.000000	0.03702	0.030000	0.12068	0.899000	0.28417	-0.009000	0.14296	0.451000	0.29950	TTT	.	.		0.323	C7orf66-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337420.1	NM_001024607		G	108524086	A	G	108524086	3	3	114	1	0	0	0	0	1	0	0	0	2414	14	1	2	25	2	C7orf66	7	108524086	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	657986	108524086	50614577	542	18814										
LRRN3	54674	hgsc.bcm.edu	37	chr7	110764583	110764583	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatcttactcatctgaatccAtcaactgagtataaaatttg	4	8	4	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:110764583A>G	ENST00000422987.3	+	2	2586	c.1755A>G	c.(1753-1755)ccA>ccG	p.P585P	IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000489381.1_Intron|LRRN3_ENST00000451085.1_Silent_p.P585P|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|LRRN3_ENST00000308478.5_Silent_p.P585P|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000331762.3_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	585	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		ATCTGAATCCATCAACTGAGT	0.358																																					p.P585P		Atlas-SNP	.											.	LRRN3	132	.	0			c.A1755G						.						50	47	48					7																	110764583		2203	4300	6503	SO:0001819	synonymous_variant	54674	exon2			GAATCCATCAACT	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17200	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 5"					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1755A>G	chr7.hg19:g.110764583A>G		73.0	0.0		65.0	4.0	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	hg19	CCDS5754.1																																																																																			.	.		0.358	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		G	110764583	A	G	110764583	2	3	114	1	0	0	0	0	0	0	0	1	9045	204	8	2		2	LRRN3	7	110764583	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2240497	110764583	48374080	543	18815										
ST7	7982	hgsc.bcm.edu	37	chr7	116771958	116771958	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtaatgcagaaagcctggagAgagagaaacccccaagctag	12	9	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:116771958A>G	ENST00000393446.2	+	6	888	c.585A>G	c.(583-585)agA>agG	p.R195R	ST7-AS2_ENST00000442719.1_RNA|ST7-AS2_ENST00000434993.1_RNA|ST7_ENST00000422922.1_Silent_p.R149R|ST7_ENST00000393444.3_Silent_p.R152R|ST7_ENST00000323984.3_Silent_p.R195R|ST7_ENST00000393449.1_Silent_p.R195R|ST7_ENST00000393451.3_Silent_p.R195R|ST7_ENST00000265437.5_Silent_p.R195R|ST7-AS2_ENST00000432541.1_RNA|ST7_ENST00000432298.1_Silent_p.R149R|ST7_ENST00000487459.1_3'UTR|ST7_ENST00000393443.1_Silent_p.R145R|ST7_ENST00000393447.4_Silent_p.R152R|ST7_ENST00000465133.1_Silent_p.R152R			Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		AAGCCTGGAGAGAGAGAAACC	0.388																																					p.R195R		Atlas-SNP	.											.	ST7	64	.	0			c.A585G						.						73	80	77					7																	116771958		2203	4300	6503	SO:0001819	synonymous_variant	7982	exon6			CTGGAGAGAGAGA	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000393446.2:c.585A>G	chr7.hg19:g.116771958A>G		45.0	0.0		61.0	5.0	NM_018412	A8K137|B4DRQ2	Silent	SNP	ENST00000393446.2	hg19																																																																																				.	.		0.388	ST7-013	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000319687.1	NM_021908		G	116771958	A	G	116771958	2	3	114	1	0	0	0	0	0	0	0	1	15244	301	11	2		2	ST7	7	116771958	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	6007375	116771958	42366705	544	18816										
ANKRD7	56311	hgsc.bcm.edu	37	chr7	117876139	117876139	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccgttattaacaataatccAaaaatggtaaaatttcttct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:117876139delA	ENST00000265224.4	+	4	668	c.513delA	c.(511-513)ccafs	p.P171fs	ANKRD7_ENST00000357099.4_Frame_Shift_Del_p.P191fs|ANKRD7_ENST00000433239.1_Frame_Shift_Del_p.P118fs|ANKRD7_ENST00000477532.1_3'UTR|ANKRD7_ENST00000417525.1_Frame_Shift_Del_p.P118fs	NM_019644.3	NP_062618.2	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	171					male gonad development (GO:0008584)	nucleus (GO:0005634)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)	29						ACAATAATCCAAAAATGGTAA	0.274																																					p.P171fs		Atlas-INDEL	.											.	ANKRD7	44	.	0			c.512delC						.						77	79	79					7																	117876139		1797	4070	5867	SO:0001589	frameshift_variant	56311	exon4			.	D78334	CCDS43638.1	7q31	2013-01-10			ENSG00000106013	ENSG00000106013		"Ankyrin repeat domain containing"	18588	protein-coding gene	gene with protein product	"testis-specific ankyrin motif containing protein"	610731				8812458	Standard	NM_019644		Approved	TSA806	uc003vji.3	Q92527	OTTHUMG00000156960	ENST00000265224.4:c.513delA	chr7.hg19:g.117876139delA	ENSP00000265224:p.Pro171fs	110.0	0.0		159.0	11.0	NM_019644	B4DYF5|Q96QN1|Q9UDM3	Frame_Shift_Del	DEL	ENST00000265224.4	hg19	CCDS43638.1																																																																																			.	.		0.274	ANKRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346826.1	NM_001077708		-	117876139	A	-	117876139	7	5	114	1	0	1	0	1	0	0	0	0	686	117	5	0	527	0	ANKRD7	7	117876139	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1104181	117876139	41262524	545	18817										
ZNF800	168850	hgsc.bcm.edu	37	chr7	127026148	127026148	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcaattatttgttgaataccAgatttggatgtctgtagtgg	10	4	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:127026148A>G	ENST00000393313.1	-	3	714	c.123T>C	c.(121-123)tcT>tcC	p.S41S	ZNF800_ENST00000265827.3_Silent_p.S41S|ZNF800_ENST00000393312.1_Silent_p.S41S			Q2TB10	ZN800_HUMAN	zinc finger protein 800	41					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						GTTGAATACCAGATTTGGATG	0.373																																					p.S41S		Atlas-SNP	.											.	ZNF800	78	.	0			c.T123C						.						113	107	109					7																	127026148		2203	4300	6503	SO:0001819	synonymous_variant	168850	exon3			AATACCAGATTTG	AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"Zinc fingers, C2H2-type"	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.123T>C	chr7.hg19:g.127026148A>G		83.0	0.0		91.0	4.0	NM_176814	Q9HBN0	Silent	SNP	ENST00000393313.1	hg19	CCDS5795.1																																																																																			.	.		0.373	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814		G	127026148	A	G	127026148	2	3	114	1	0	0	0	0	0	0	0	1	18184	175	7	2		2	ZNF800	7	127026148	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	9150009	127026148	32112515	546	18818										
CPA4	51200	hgsc.bcm.edu	37	chr7	129944394	129944394	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaagattggacattcgtttgAaaaccggccgatgtatgtac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:129944394delA	ENST00000222482.4	+	5	489	c.461delA	c.(460-462)gaafs	p.E154fs	CPA4_ENST00000493259.1_Frame_Shift_Del_p.E50fs|CPA4_ENST00000445470.2_Frame_Shift_Del_p.E121fs	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	154					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					CATTCGTTTGAAAACCGGCCG	0.522																																					p.E154fs		Atlas-INDEL	.											.	CPA4	47	.	0			c.460delG						.						159	142	148					7																	129944394		2203	4300	6503	SO:0001589	frameshift_variant	51200	exon5			.	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"carboxypeptidase A3"	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.461delA	chr7.hg19:g.129944394delA	ENSP00000222482:p.Glu154fs	169.0	0.0		188.0	12.0	NM_016352	B7Z576|Q86UY9	Frame_Shift_Del	DEL	ENST00000222482.4	hg19	CCDS5818.1																																																																																			.	.		0.522	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352		-	129944394	A	-	129944394	7	5	114	1	0	1	0	1	0	0	0	0	3794	246	9	0	479	0	CPA4	7	129944394	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2918246	129944394	29194269	547	18819										
NUP205	23165	hgsc.bcm.edu	37	chr7	135311045	135311045	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cattagagctgctaagatcaGgggtgattgtgagactagct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:135311045delG	ENST00000285968.6	+	33	4755	c.4729delG	c.(4729-4731)gggfs	p.G1577fs		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1577					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.V1578fs*1(1)		breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						GCTAAGATCAGGGGTGATTGT	0.448																																					p.S1576fs		Atlas-INDEL	.											.	NUP205	198	.	1	Deletion - Frameshift(1)	lung(1)	c.4728delA						.						124	114	117					7																	135311045		2203	4300	6503	SO:0001589	frameshift_variant	23165	exon33			.	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.4729delG	chr7.hg19:g.135311045delG	ENSP00000285968:p.Gly1577fs	91.0	0.0		129.0	10.0	NM_015135	A6H8X3|Q86YC1	Frame_Shift_Del	DEL	ENST00000285968.6	hg19	CCDS34759.1																																																																																			.	.		0.448	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			-	135311045	G	-	135311045	7	5	114	1	0	1	0	1	0	0	0	0	10768	1000	35	0	4859	0	NUP205	7	135311045	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	5366651	135311045	23827618	548	18820										
SVOPL	136306	hgsc.bcm.edu	37	chr7	138312173	138312173	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaaggctcagccgtcttcccAggaaattgatgcccagtata	9	11	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:138312173A>G	ENST00000419765.3	-	11	1136	c.1103T>C	c.(1102-1104)cTg>cCg	p.L368P	SVOPL_ENST00000421622.1_Missense_Mutation_p.L248P|SVOPL_ENST00000288513.5_Missense_Mutation_p.L216P|SVOPL_ENST00000463557.1_5'UTR|SVOPL_ENST00000436657.1_Missense_Mutation_p.L216P|SNORA40_ENST00000516379.1_RNA	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	368						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						CCGTCTTCCCAGGAAATTGAT	0.408																																					p.L368P		Atlas-SNP	.											.	SVOPL	111	.	0			c.T1103C						.						97	90	92					7																	138312173		2203	4300	6503	SO:0001583	missense	136306	exon11			CTTCCCAGGAAAT	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"SV2 related protein homolog (rat)-like"				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.1103T>C	chr7.hg19:g.138312173A>G	ENSP00000405482:p.Leu368Pro	59.0	0.0		90.0	4.0	NM_001139456		Missense_Mutation	SNP	ENST00000419765.3	hg19	CCDS47721.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.978296	0.74360	.	.	ENSG00000157703	ENST00000288513;ENST00000421622;ENST00000436657;ENST00000419765	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	5.81	5.81	0.92471	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.187326	0.48286	D	0.000192	D	0.85792	0.5779	M	0.76170	2.325	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.73380	0.979;0.98	D	0.87434	0.2390	10	0.87932	D	0	-16.9639	16.1708	0.81812	1.0:0.0:0.0:0.0	.	368;216	Q8N434;Q8N434-2	SVOPL_HUMAN;.	P	216;248;216;368	ENSP00000288513:L216P;ENSP00000412830:L248P;ENSP00000417018:L216P;ENSP00000405482:L368P	ENSP00000288513:L216P	L	-	2	0	SVOPL	137962713	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	6.414000	0.73318	2.225000	0.72522	0.533000	0.62120	CTG	.	.		0.408	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959		G	138312173	A	G	138312173	3	3	114	1	0	0	0	0	1	0	0	0	15439	188	7	2	395	2	SVOPL	7	138312173	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3001128	138312173	20826490	549	18821										
TMEM139	135932	hgsc.bcm.edu	37	chr7	142983605	142983605	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccaagagttggaccaaccaCccccctacagcactgttgtg					rs200902226		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:142983605delC	ENST00000359333.3	+	3	847	c.334delC	c.(334-336)cccfs	p.P113fs	TMEM139_ENST00000409102.1_Frame_Shift_Del_p.P113fs|AC073342.12_ENST00000446192.1_RNA|AC073342.12_ENST00000427392.1_RNA|TMEM139_ENST00000409541.1_Frame_Shift_Del_p.P113fs|TMEM139_ENST00000410004.1_Frame_Shift_Del_p.P113fs|CASP2_ENST00000310447.5_5'Flank|CASP2_ENST00000392925.2_5'Flank|TMEM139_ENST00000409244.1_Frame_Shift_Del_p.P113fs|TMEM139_ENST00000471161.1_3'UTR	NM_001242775.2|NM_001282876.1|NM_001282877.1	NP_001229704.1|NP_001269805.1|NP_001269806.1	Q8IV31	TM139_HUMAN	transmembrane protein 139	113						integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|ovary(1)|prostate(1)	7	Melanoma(164;0.059)					GGACCAACCACCCCCCTACAG	0.577																																					p.P111fs		Atlas-INDEL	.											.	TMEM139	18	.	0			c.333delA						.		,,,,,	0,4264		0,0,2132	74	78	77		,,,,,	-0.1	1	7	dbSNP_126	77	1,8253		0,1,4126	no	frameshift,utr-5,utr-5,frameshift,frameshift,frameshift	TMEM139	NM_153345.2,NM_001242777.1,NM_001242776.1,NM_001242775.1,NM_001242774.1,NM_001242773.1	,,,,,	0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080	,,,,,	,,,,,	142983605	1,12517	2203	4300	6503	SO:0001589	frameshift_variant	135932	exon4			.	AK075067	CCDS5878.1	7q34	2006-03-17			ENSG00000178826	ENSG00000178826			22058	protein-coding gene	gene with protein product							Standard	NM_153345		Approved	FLJ90586	uc003wck.4	Q8IV31	OTTHUMG00000152652	ENST00000359333.3:c.334delC	chr7.hg19:g.142983605delC	ENSP00000352284:p.Pro113fs	101.0	0.0		163.0	11.0	NM_001242773	B2RCL5|D3DXD4|Q6ZME2|Q8NC22|Q96AU8	Frame_Shift_Del	DEL	ENST00000359333.3	hg19	CCDS5878.1																																																																																			.	.		0.577	TMEM139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327145.1	NM_153345		-	142983605	C	-	142983605	7	5	114	1	0	1	0	1	0	0	0	0	16069	507	18	0	340	0	TMEM139	7	142983605	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	4671432	142983605	16155058	550	18822										
EPHA1	2041	hgsc.bcm.edu	37	chr7	143088824	143088824	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actcagagacggttcgatatGggatcccatctgagccactc	10	12	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:143088824G>C	ENST00000275815.3	-	17	2827	c.2741C>G	c.(2740-2742)cCa>cGa	p.P914R	EPHA1_ENST00000458129.1_5'Flank	NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	914	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				GGTTCGATATGGGATCCCATC	0.582																																					p.P914R		Atlas-SNP	.											EPHA1_ENST00000275815,NS,carcinoma,0,2	EPHA1	193	.	0			c.C2741G						.						81	63	69					7																	143088824		2203	4300	6503	SO:0001583	missense	2041	exon17			CGATATGGGATCC	M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.2741C>G	chr7.hg19:g.143088824G>C	ENSP00000275815:p.Pro914Arg	64.0	0.0		131.0	0.0	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	hg19	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.941320	0.34283	.	.	ENSG00000146904	ENST00000275815	T	0.47528	0.84	4.67	3.77	0.43336	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.109437	0.41194	N	0.000925	T	0.44030	0.1274	L	0.43757	1.38	0.44643	D	0.99762	B	0.18610	0.029	B	0.26202	0.067	T	0.46679	-0.9174	10	0.72032	D	0.01	.	15.2057	0.73177	0.0:0.1413:0.8587:0.0	.	914	P21709	EPHA1_HUMAN	R	914	ENSP00000275815:P914R	ENSP00000275815:P914R	P	-	2	0	EPHA1	142798946	1.000000	0.71417	0.953000	0.39169	0.006000	0.05464	3.709000	0.54853	1.304000	0.44892	-0.305000	0.09177	CCA	.	.		0.582	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			C	143088824	G	C	143088824	3	2	114	1	0	0	0	0	1	0	0	0	5167	1348	47	4	197	4	EPHA1	7	143088824	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	105219	143088824	16049839	551	18823										
ARHGEF35	445328	hgsc.bcm.edu	37	chr7	143884040	143884040	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tatcaaagtactgatagaagTttttccttgtcaggtgactc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:143884040delT	ENST00000378115.2	-	2	1566	c.1437delA	c.(1435-1437)aaafs	p.K479fs	ARHGEF35_ENST00000543357.1_Frame_Shift_Del_p.K479fs	NM_001003702.2	NP_001003702.2	A5YM69	ARG35_HUMAN	Rho guanine nucleotide exchange factor (GEF) 35	479										kidney(1)|large_intestine(1)|lung(3)|stomach(1)	6						CTGATAGAAGTTTTTCCTTGT	0.408																																					p.L480fs		Atlas-INDEL	.											.	ARHGEF35	11	.	0			c.1438delC						.						19	19	19					7																	143884040		2128	4129	6257	SO:0001589	frameshift_variant	445328	exon2			.	AK125680	CCDS34770.1	7q35	2012-07-24	2010-04-13	2010-04-13	ENSG00000213214	ENSG00000213214		"Rho guanine nucleotide exchange factors"	33846	protein-coding gene	gene with protein product			"Rho guanine nucleotide exchange factor (GEF) 5-like"	ARHGEF5L			Standard	NM_001003702		Approved	FLJ43692, CTAGE4	uc003wdz.2	A5YM69	OTTHUMG00000158010	ENST00000378115.2:c.1437delA	chr7.hg19:g.143884040delT	ENSP00000367355:p.Lys479fs	103.0	0.0		201.0	14.0	NM_001003702	Q6ZUI2	Frame_Shift_Del	DEL	ENST00000378115.2	hg19	CCDS34770.1																																																																																			.	.		0.408	ARHGEF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349997.1	NM_001003702		-	143884040	T	-	143884040	7	5	114	1	0	1	0	1	0	0	0	0	905	1722	60	0	21	0	ARHGEF35	7	143884040	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	795216	143884040	15254623	552	18824										
EZH2	2146	hgsc.bcm.edu	37	chr7	148515025	148515025	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttctttatcattgttctctCcccccgtttcagtccctgct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:148515025delC	ENST00000460911.1	-	10	1257	c.1169delG	c.(1168-1170)ggafs	p.G390fs	EZH2_ENST00000350995.2_Frame_Shift_Del_p.G351fs|EZH2_ENST00000476773.1_Frame_Shift_Del_p.G381fs|EZH2_ENST00000478654.1_Frame_Shift_Del_p.G381fs|EZH2_ENST00000541220.1_Frame_Shift_Del_p.G381fs|EZH2_ENST00000320356.2_Frame_Shift_Del_p.G395fs|EZH2_ENST00000483967.1_Frame_Shift_Del_p.G381fs			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	390	Interaction with CDYL.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			ATTGTTCTCTCCCCCCGTTTC	0.458			Mis		DLBCL																																p.G395fs		Atlas-INDEL	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	.	EZH2	823	.	0			c.1185delA						.						240	186	204					7																	148515025		2203	4300	6503	SO:0001589	frameshift_variant	2146	exon10			.		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"Chromatin-modifying enzymes / K-methyltransferases"	3527	protein-coding gene	gene with protein product		601573	"enhancer of zeste (Drosophila) homolog 2", "enhancer of zeste homolog 2 (Drosophila)"			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.1169delG	chr7.hg19:g.148515025delC	ENSP00000419711:p.Gly390fs	190.0	0.0		336.0	23.0	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Frame_Shift_Del	DEL	ENST00000460911.1	hg19	CCDS56516.1																																																																																			.	.		0.458	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		-	148515025	C	-	148515025	7	5	114	1	0	1	0	1	0	0	0	0	5336	855	30	0	1115	0	EZH2	7	148515025	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	4630985	148515025	10623638	553	18825										
GIMAP2	26157	hgsc.bcm.edu	37	chr7	150390266	150390266	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcacagcatgtgcaatttgTtttgttgcttactctttagt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:150390266delT	ENST00000223293.5	+	3	986	c.892delT	c.(892-894)tttfs	p.F298fs		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	298						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(8)|skin(2)|urinary_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTGCAATTTGTTTTGTTGCTT	0.313																																					p.L297fs		Atlas-INDEL	.											.	GIMAP2	39	.	0			c.891delG						.						112	103	106					7																	150390266		2203	4299	6502	SO:0001589	frameshift_variant	26157	exon3			.	AL110151	CCDS5905.1	7q36.1	2014-04-04			ENSG00000106560	ENSG00000106560		"GTPases, IMAP"	21789	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 12"	608085				15474311	Standard	NM_015660		Approved	DKFZp586D0824, HIMAP2, IMAP2, IAN12	uc003who.3	Q9UG22	OTTHUMG00000157488	ENST00000223293.5:c.892delT	chr7.hg19:g.150390266delT	ENSP00000223293:p.Phe298fs	79.0	0.0		155.0	10.0	NM_015660	Q96L25	Frame_Shift_Del	DEL	ENST00000223293.5	hg19	CCDS5905.1																																																																																			.	.		0.313	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660		-	150390266	T	-	150390266	7	5	114	1	0	1	0	1	0	0	0	0	6388	1725	60	0	898	0	GIMAP2	7	150390266	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1875241	150390266	8748397	554	18826										
NOS3	4846	hgsc.bcm.edu	37	chr7	150693569	150693569	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagggccggccctcccccggCcccccggcccctgagcagct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:150693569delC	ENST00000484524.1	+	3	348	c.348delC	c.(346-348)ggcfs	p.G116fs	NOS3_ENST00000461406.1_Intron|NOS3_ENST00000297494.3_Frame_Shift_Del_p.G116fs|NOS3_ENST00000467517.1_Frame_Shift_Del_p.G116fs	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		cctcccccggccccccggccc	0.652																																					p.G116fs		Atlas-INDEL	.											.	NOS3	131	.	0			c.347delG						.						11	13	12					7																	150693569		2159	4269	6428	SO:0001589	frameshift_variant	4846	exon3			.		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.348delC	chr7.hg19:g.150693569delC	ENSP00000420215:p.Gly116fs	148.0	0.0		257.0	17.0	NM_001160111	Q495E5	Frame_Shift_Del	DEL	ENST00000484524.1	hg19	CCDS55182.1																																																																																			.	.		0.652	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		-	150693569	C	-	150693569	7	5	114	1	0	1	0	1	0	0	0	0	10553	726	26	0	358	0	NOS3	7	150693569	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	303303	150693569	8445094	555	18827										
NUB1	51667	hgsc.bcm.edu	37	chr7	151052912	151052912	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaagcgatggtgcttgaactAaaacaatctgaagaggacgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:151052912delA	ENST00000355851.4	+	6	551	c.474delA	c.(472-474)ctafs	p.L158fs	NUB1_ENST00000413040.2_Frame_Shift_Del_p.L182fs|NUB1_ENST00000568733.1_Frame_Shift_Del_p.L182fs|NUB1_ENST00000566856.1_Frame_Shift_Del_p.L158fs|NUB1_ENST00000477666.1_3'UTR	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	158					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		TGCTTGAACTAAAACAATCTG	0.398																																					p.L182fs		Atlas-INDEL	.											.	NUB1	31	.	0			c.545delT						.						56	50	52					7																	151052912		1853	4109	5962	SO:0001589	frameshift_variant	51667	exon6			.	AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"NEDD8 ultimate buster-1"	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.474delA	chr7.hg19:g.151052912delA	ENSP00000348110:p.Leu158fs	113.0	0.0		176.0	11.0	NM_016118	O95422|Q75MR9|Q8IX22|Q9BXR2	Frame_Shift_Del	DEL	ENST00000355851.4	hg19																																																																																				.	.		0.398	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118		-	151052912	A	-	151052912	7	5	114	1	0	1	0	1	0	0	0	0	10723	349	13	0	492	0	NUB1	7	151052912	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	359343	151052912	8085751	556	18828										
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157926551	157926551	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggctccgaatgcggctgctgCcccagcagatctttggaata							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:157926551delC	ENST00000389418.4	-	9	1383	c.1374delG	c.(1372-1374)gggfs	p.G458fs	PTPRN2_ENST00000404321.2_Frame_Shift_Del_p.G481fs|PTPRN2_ENST00000409483.1_Frame_Shift_Del_p.G420fs|PTPRN2_ENST00000389416.4_Frame_Shift_Del_p.G441fs|PTPRN2_ENST00000389413.3_Frame_Shift_Del_p.G458fs	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	458					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCGGCTGCTGCCCCAGCAGAT	0.617																																					p.Q459fs		Atlas-INDEL	.											.	PTPRN2	243	.	0			c.1375delC						.						51	57	55					7																	157926551		2203	4300	6503	SO:0001589	frameshift_variant	5799	exon9			.	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.1374delG	chr7.hg19:g.157926551delC	ENSP00000374069:p.Gly458fs	97.0	0.0		128.0	10.0	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Frame_Shift_Del	DEL	ENST00000389418.4	hg19	CCDS5947.1																																																																																			.	.		0.617	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			-	157926551	C	-	157926551	7	5	114	1	0	1	0	1	0	0	0	0	12823	726	26	0	1733	0	PTPRN2	7	157926551	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	6873639	157926551	1212112	557	18829										
VIPR2	7434	hgsc.bcm.edu	37	chr7	158902515	158902515	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacagtacctgctttgctgtAaaaattgctgaagacttttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:158902515delA	ENST00000262178.2	-	3	432	c.247delT	c.(247-249)tacfs	p.Y83fs	VIPR2_ENST00000402066.1_Frame_Shift_Del_p.Y224fs	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	83					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		GCTTTGCTGTAAAAATTGCTG	0.547																																					p.Y83fs	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-INDEL	.											.	VIPR2	53	.	0			c.248delA						.						110	97	101					7																	158902515		2203	4300	6503	SO:0001589	frameshift_variant	7434	exon3			.	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12695	protein-coding gene	gene with protein product	"VIP and PACAP receptor 2"	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.247delT	chr7.hg19:g.158902515delA	ENSP00000262178:p.Tyr83fs	75.0	0.0		145.0	11.0	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Frame_Shift_Del	DEL	ENST00000262178.2	hg19	CCDS5950.1																																																																																			.	.		0.547	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382		-	158902515	A	-	158902515	7	5	114	1	0	1	0	1	0	0	0	0	17185	362	13	0	1113	0	VIPR2	7	158902515	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	975964	158902515	236148	558	18830										
C8orf42	157695	hgsc.bcm.edu	37	chr8	442414	442414	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccccctcactccgcctcctcCgggctatctgtcaggtggcc	9	20	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:442414C>T	ENST00000324079.6	-	3	783	c.543G>A	c.(541-543)ccG>ccA	p.P181P	TDRP_ENST00000427263.2_Intron|TDRP_ENST00000523656.1_Intron|TDRP_ENST00000524229.1_5'Flank			Q86YL5	TDRP_HUMAN	testis development related protein	181					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCGCCTCCTCCGGGCTATCTG	0.607																																					p.P181P		Atlas-SNP	.											C8orf42,caecum,carcinoma,0,1	C8orf42	23	.	0			c.G543A						.						10	11	11					8																	442414		2056	4204	6260	SO:0001819	synonymous_variant	157695	exon4			CTCCTCCGGGCTA	AY194292	CCDS47759.1, CCDS59090.1	8p23.3	2013-06-03	2013-06-03	2013-06-03	ENSG00000180190	ENSG00000180190			26951	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 42"	C8orf42		20170638	Standard	NM_175075		Approved	INM01, TDRP1, TDRP2		Q86YL5	OTTHUMG00000163593	ENST00000324079.6:c.543G>A	chr8.hg19:g.442414C>T		60.0	0.0		49.0	2.0	NM_175075	B6VF03|B9EG53	Silent	SNP	ENST00000324079.6	hg19	CCDS47759.1																																																																																			.	.		0.607	TDRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374442.1	NM_175075		T	442414	C	T	442414	2	4	114	1	0	0	0	0	0	0	0	1	2430	639	23	1		1	C8orf42	8	442414	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10		442414	145921608	559	18831										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2820095	2820095	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actggaagaagacttcggacTtataggtgaaacttttccca	9	8	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:2820095T>A	ENST00000520002.1	-	62	10079	c.9524A>T	c.(9523-9525)aAg>aTg	p.K3175M	CSMD1_ENST00000537824.1_Missense_Mutation_p.K3174M|CSMD1_ENST00000602723.1_Missense_Mutation_p.K2998M|CSMD1_ENST00000400186.3_Missense_Mutation_p.K2998M|CSMD1_ENST00000542608.1_Missense_Mutation_p.K2997M|CSMD1_ENST00000602557.1_Missense_Mutation_p.K3175M			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3175	Sushi 26. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GACTTCGGACTTATAGGTGAA	0.522																																					p.K3174M		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A9521T						.						57	56	56					8																	2820095		1897	4120	6017	SO:0001583	missense	64478	exon61			TCGGACTTATAGG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9524A>T	chr8.hg19:g.2820095T>A	ENSP00000430733:p.Lys3175Met	91.0	0.0		71.0	42.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.95|11.95	1.791085|1.791085	0.31685|0.31685	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	T;T;T;T|.	0.66280|.	-0.2;-0.2;-0.2;-0.2|.	5.6|5.6	0.158|0.158	0.14942|0.14942	Complement control module (2);Sushi/SCR/CCP (3);|.	0.208600|.	0.38436|.	N|.	0.001684|.	T|.	0.52581|.	0.1743|.	M|M	0.73217|0.73217	2.22|2.22	0.09310|0.09310	N|N	1|1	P;P;P|.	0.50617|.	0.912;0.779;0.937|.	P;P;P|.	0.57371|.	0.65;0.608;0.819|.	T|.	0.48210|.	-0.9055|.	10|.	0.54805|.	T|.	0.06|.	.|.	9.5169|9.5169	0.39111|0.39111	0.0:0.4619:0.0:0.5381|0.0:0.4619:0.0:0.5381	.|.	3175;3175;2997|.	E5RIG2;Q96PZ7;F5H2I8|.	.;CSMD1_HUMAN;.|.	M|Y	2998;3175;3036;3174;2997|2591	ENSP00000383047:K2998M;ENSP00000430733:K3175M;ENSP00000441462:K3174M;ENSP00000446243:K2997M|.	ENSP00000320445:K3036M|.	K|X	-|-	2|3	0|2	CSMD1|CSMD1	2807502|2807502	0.005000|0.005000	0.15991|0.15991	0.006000|0.006000	0.13384|0.13384	0.123000|0.123000	0.20343|0.20343	0.317000|0.317000	0.19487|0.19487	0.101000|0.101000	0.17610|0.17610	0.533000|0.533000	0.62120|0.62120	AAG|TAA	.	.		0.522	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2820095	T	A	2820095	3	1	114	1	0	0	0	0	1	0	0	0	3946	1609	56	4	1213	4	CSMD1	8	2820095	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2377681	2820095	143543927	560	18832										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3216715	3216715	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cactccacacacggcggcccCcacccaggcaggtaagcttg	10	18	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:3216715C>T	ENST00000520002.1	-	22	3821	c.3266G>A	c.(3265-3267)gGg>gAg	p.G1089E	CSMD1_ENST00000539096.1_Missense_Mutation_p.G1088E|CSMD1_ENST00000537824.1_Missense_Mutation_p.G1088E|CSMD1_ENST00000602723.1_Missense_Mutation_p.G1089E|CSMD1_ENST00000400186.3_Missense_Mutation_p.G1089E|CSMD1_ENST00000542608.1_Missense_Mutation_p.G1088E|CSMD1_ENST00000602557.1_Missense_Mutation_p.G1089E			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1089	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.G817E(1)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ACGGCGGCCCCCACCCAGGCA	0.552																																					p.G1088E		Atlas-SNP	.											CSMD1_ENST00000537824,right_lower_lobe,carcinoma,-1,1	CSMD1	1469	.	1	Substitution - Missense(1)	ovary(1)	c.G3263A						.						68	73	72					8																	3216715		2203	4300	6503	SO:0001583	missense	64478	exon21			CGGCCCCCACCCA			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3266G>A	chr8.hg19:g.3216715C>T	ENSP00000430733:p.Gly1089Glu	90.0	1.0		74.0	3.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	32|32	5.145942|5.145942	0.94603|0.94603	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096|ENST00000335551	T;T;T;T;T|.	0.23950|.	1.88;1.88;1.88;1.88;1.88|.	5.34|5.34	5.34|5.34	0.76211|0.76211	Complement control module (2);Sushi/SCR/CCP (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.77003|.	0.4067|.	M|M	0.75085|0.75085	2.285|2.285	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	T|.	0.76599|.	-0.2900|.	10|.	0.52906|.	T|.	0.07|.	.|.	19.067|19.067	0.93116|0.93116	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1089;1089;1089|.	E5RIG2;Q96PZ7;Q96PZ7-4|.	.;CSMD1_HUMAN;.|.	E|X	1089;1089;951;1088;1088;1088|568	ENSP00000383047:G1089E;ENSP00000430733:G1089E;ENSP00000441462:G1088E;ENSP00000446243:G1088E;ENSP00000441675:G1088E|.	ENSP00000320445:G951E|.	G|W	-|-	2|3	0|0	CSMD1|CSMD1	3204122|3204122	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	7.612000|7.612000	0.82975|0.82975	2.489000|2.489000	0.83994|0.83994	0.550000|0.550000	0.68814|0.68814	GGG|TGG	.	.		0.552	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3216715	C	T	3216715	3	4	114	1	0	0	0	0	1	0	0	0	3946	623	22	3	7631	3	CSMD1	8	3216715	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	396620	3216715	143147307	561	18833										
ANGPT2	285	hgsc.bcm.edu	37	chr8	6389963	6389963	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgtactgcattctgctgtaTctctaccatttctttcttca	4	12	5	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:6389963T>C	ENST00000325203.5	-	2	808	c.334A>G	c.(334-336)Ata>Gta	p.I112V	ANGPT2_ENST00000338312.6_Intron|ANGPT2_ENST00000415216.1_Missense_Mutation_p.I112V|ANGPT2_ENST00000523120.1_Missense_Mutation_p.I112V|MCPH1_ENST00000344683.5_Intron			O15123	ANGP2_HUMAN	angiopoietin 2	112					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		TTCTGCTGTATCTCTACCATT	0.418																																					p.I112V		Atlas-SNP	.											.	ANGPT2	126	.	0			c.A334G						.						234	207	216					8																	6389963		2203	4300	6503	SO:0001583	missense	285	exon2			GCTGTATCTCTAC	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"Fibrinogen C domain containing"	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.334A>G	chr8.hg19:g.6389963T>C	ENSP00000314897:p.Ile112Val	203.0	0.0		121.0	5.0	NM_001118887	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Missense_Mutation	SNP	ENST00000325203.5	hg19	CCDS5958.1	.	.	.	.	.	.	.	.	.	.	T	2.619	-0.289104	0.05605	.	.	ENSG00000091879	ENST00000325203;ENST00000415216;ENST00000523120	D;D;D	0.82984	-1.67;-1.67;-1.67	5.27	1.39	0.22231	.	0.575243	0.20952	N	0.082728	T	0.72953	0.3525	L	0.45228	1.405	0.37254	D	0.906672	B;B;B	0.24823	0.003;0.112;0.001	B;B;B	0.28232	0.01;0.087;0.004	T	0.61123	-0.7126	10	0.23302	T	0.38	.	6.5889	0.22636	0.0:0.0796:0.2949:0.6255	.	112;112;112	E7EVQ3;O15123-3;O15123	.;.;ANGP2_HUMAN	V	112	ENSP00000314897:I112V;ENSP00000400782:I112V;ENSP00000428023:I112V	ENSP00000314897:I112V	I	-	1	0	ANGPT2	6377371	1.000000	0.71417	0.145000	0.22337	0.044000	0.14063	2.000000	0.40816	0.057000	0.16193	0.533000	0.62120	ATA	.	.		0.418	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147		C	6389963	T	C	6389963	3	2	114	1	0	0	0	0	1	0	0	0	611	1435	50	2	1188	2	ANGPT2	8	6389963	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3173248	6389963	139974059	562	18834										
ERI1	90459	hgsc.bcm.edu	37	chr8	8875834	8875834	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tagacagagctgataccttcCctcaggtactaaaaaaagta	7	9	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:8875834C>T	ENST00000523898.1	+	6	1289	c.610C>T	c.(610-612)Cct>Tct	p.P204S	ERI1_ENST00000250263.7_Missense_Mutation_p.P204S|ERI1_ENST00000520332.1_3'UTR|ERI1_ENST00000519292.1_Missense_Mutation_p.P204S			Q8IV48	ERI1_HUMAN	exoribonuclease 1	204	Exonuclease.				gene silencing by RNA (GO:0031047)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|rRNA 3'-end processing (GO:0031125)	cytoplasm (GO:0005737)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|histone pre-mRNA stem-loop binding (GO:0071207)|metal ion binding (GO:0046872)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11						TGATACCTTCCCTCAGGTACT	0.358																																					p.P204S		Atlas-SNP	.											.	ERI1	20	.	0			c.C610T						.						58	59	59					8																	8875834		2203	4300	6503	SO:0001583	missense	90459	exon5			ACCTTCCCTCAGG	BC035279	CCDS5972.1	8p23.1	2008-12-16	2008-12-16	2008-12-16	ENSG00000104626	ENSG00000104626		"Enhanced RNAi three prime mRNA exonucleases"	23994	protein-coding gene	gene with protein product	"exoribonuclease 1", "enhanced RNAi three prime mRNA exonuclease homolog 1 (C.elegans)"	608739	"three prime histone mRNA exonuclease 1"	THEX1		14536070	Standard	NM_153332		Approved	3'HEXO	uc003wsk.2	Q8IV48	OTTHUMG00000129328	ENST00000523898.1:c.610C>T	chr8.hg19:g.8875834C>T	ENSP00000429615:p.Pro204Ser	114.0	0.0		66.0	4.0	NM_153332	A8K4U7|Q9NSX3	Missense_Mutation	SNP	ENST00000523898.1	hg19	CCDS5972.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.907533	0.92107	.	.	ENSG00000104626	ENST00000523898;ENST00000250263;ENST00000519292	T;T;T	0.21543	2.0;2.0;2.0	5.97	5.97	0.96955	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.046969	0.85682	D	0.000000	T	0.33381	0.0861	M	0.63428	1.95	0.80722	D	1	P	0.39883	0.693	P	0.44623	0.455	T	0.00783	-1.1568	10	0.38643	T	0.18	-15.1539	19.4222	0.94726	0.0:1.0:0.0:0.0	.	204	Q8IV48	ERI1_HUMAN	S	204	ENSP00000429615:P204S;ENSP00000250263:P204S;ENSP00000430190:P204S	ENSP00000250263:P204S	P	+	1	0	ERI1	8913244	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.361000	0.66092	2.838000	0.97847	0.561000	0.74099	CCT	.	.		0.358	ERI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251471.2	NM_153332		T	8875834	C	T	8875834	3	4	114	1	0	0	0	0	1	0	0	0	5229	623	22	3	628	3	ERI1	8	8875834	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	2485871	8875834	137488188	563	18835										
MTMR7	9108	hgsc.bcm.edu	37	chr8	17159699	17159699	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agttcttcctctagctgctgAgtttcttccttcactgccat	6	13	4	1	rs373353287		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:17159699A>G	ENST00000180173.5	-	13	1618	c.1584T>C	c.(1582-1584)acT>acC	p.T528T	MTMR7_ENST00000398099.3_Silent_p.T119T|MTMR7_ENST00000521857.1_Silent_p.T528T	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	528					inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		CTAGCTGCTGAGTTTCTTCCT	0.433																																					p.T528T		Atlas-SNP	.											.	MTMR7	75	.	0			c.T1584C						.	A		2,4404	4.2+/-10.8	0,2,2201	176	161	166		1584	-7.5	0.1	8		166	0,8600		0,0,4300	no	coding-synonymous	MTMR7	NM_004686.4		0,2,6501	GG,GA,AA		0.0,0.0454,0.0154		528/661	17159699	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9108	exon13			CTGCTGAGTTTCT	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1584T>C	chr8.hg19:g.17159699A>G		130.0	0.0		86.0	4.0	NM_004686	A1L4K9|B4DG87|Q68DX4	Silent	SNP	ENST00000180173.5	hg19	CCDS34851.1																																																																																			.	.		0.433	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686		G	17159699	A	G	17159699	2	3	114	1	0	0	0	0	0	0	0	1	9957	291	11	2		2	MTMR7	8	17159699	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	8283865	17159699	129204323	564	18836										
INTS10	55174	hgsc.bcm.edu	37	chr8	19694579	19694579	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttagatgacatgtgaaaaagTccttgatttgatgtgctaca	9	5	0	5			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:19694579T>C	ENST00000397977.3	+	13	1945	c.1547T>C	c.(1546-1548)gTc>gCc	p.V516A		NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	516					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	20				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		TGTGAAAAAGTCCTTGATTTG	0.383																																					p.V516A		Atlas-SNP	.											.	INTS10	46	.	0			c.T1547C						.						105	100	102					8																	19694579		1857	4102	5959	SO:0001583	missense	55174	exon13			AAAAAGTCCTTGA	AK001431	CCDS6011.2	8p21.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000104613	ENSG00000104613			25548	protein-coding gene	gene with protein product		611353	"chromosome 8 open reading frame 35"	C8orf35		16239144	Standard	XM_005273558		Approved	FLJ10569, INT10	uc003wzj.3	Q9NVR2	OTTHUMG00000131065	ENST00000397977.3:c.1547T>C	chr8.hg19:g.19694579T>C	ENSP00000381064:p.Val516Ala	153.0	0.0		96.0	4.0	NM_018142	Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Missense_Mutation	SNP	ENST00000397977.3	hg19	CCDS6011.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.71|14.71	2.616541|2.616541	0.46736|0.46736	.|.	.|.	ENSG00000104613|ENSG00000104613	ENST00000520670|ENST00000397977	.|.	.|.	.|.	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	.|0.186912	.|0.46758	.|D	.|0.000268	T|T	0.40932|0.40932	0.1137|0.1137	N|N	0.14661|0.14661	0.345|0.345	0.42019|0.42019	D|D	0.990975|0.990975	.|B	.|0.16396	.|0.017	.|B	.|0.21360	.|0.034	T|T	0.28713|0.28713	-1.0035|-1.0035	5|9	.|0.20519	.|T	.|0.43	-11.9322|-11.9322	14.5209|14.5209	0.67849|0.67849	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|516	.|Q9NVR2	.|INT10_HUMAN	P|A	6|516	.|.	.|ENSP00000381064:V516A	S|V	+|+	1|2	0|0	INTS10|INTS10	19738859|19738859	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.945000|0.945000	0.59286|0.59286	7.070000|7.070000	0.76763|0.76763	2.108000|2.108000	0.64289|0.64289	0.533000|0.533000	0.62120|0.62120	TCC|GTC	.	.		0.383	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253724.2	NM_018142		C	19694579	T	C	19694579	3	2	114	1	0	0	0	0	1	0	0	0	7785	1667	58	2	1597	2	INTS10	8	19694579	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2534880	19694579	126669443	565	18837										
SLC39A14	23516	hgsc.bcm.edu	37	chr8	22273673	22273673	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggcctggatgatcactctgAgcgacggcctccataatttc	10	12	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:22273673A>G	ENST00000381237.1	+	7	1146	c.1027A>G	c.(1027-1029)Agc>Ggc	p.S343G	SLC39A14_ENST00000289952.5_Missense_Mutation_p.S343G|SLC39A14_ENST00000359741.5_Missense_Mutation_p.S343G|SLC39A14_ENST00000240095.6_Missense_Mutation_p.S343G	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	343					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		GATCACTCTGAGCGACGGCCT	0.552																																					p.S343G		Atlas-SNP	.											.	SLC39A14	59	.	0			c.A1027G						.						101	92	95					8																	22273673		2203	4300	6503	SO:0001583	missense	23516	exon7			ACTCTGAGCGACG	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"Solute carriers"	20858	protein-coding gene	gene with protein product		608736	"solute carrier family 39 (metal ion transporter), member 14"			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.1027A>G	chr8.hg19:g.22273673A>G	ENSP00000370635:p.Ser343Gly	174.0	0.0		143.0	6.0	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Missense_Mutation	SNP	ENST00000381237.1	hg19	CCDS47823.1	.	.	.	.	.	.	.	.	.	.	A	15.11	2.737514	0.49045	.	.	ENSG00000104635	ENST00000359741;ENST00000240095;ENST00000381237;ENST00000289952;ENST00000517370	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	5.99	5.99	0.97316	.	0.073878	0.85682	D	0.000000	T	0.15998	0.0385	N	0.02315	-0.6	0.80722	D	1	B;B;B	0.24576	0.106;0.034;0.034	B;B;B	0.28139	0.086;0.085;0.085	T	0.16158	-1.0412	10	0.02654	T	1	-36.6727	15.4768	0.75489	1.0:0.0:0.0:0.0	.	343;343;343	Q15043-2;Q15043;B6EU88	.;S39AE_HUMAN;.	G	343;343;343;343;166	ENSP00000352779:S343G;ENSP00000240095:S343G;ENSP00000370635:S343G;ENSP00000289952:S343G;ENSP00000427981:S166G	ENSP00000240095:S343G	S	+	1	0	SLC39A14	22329618	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	9.182000	0.94881	2.291000	0.77112	0.533000	0.62120	AGC	.	.		0.552	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677		G	22273673	A	G	22273673	3	3	114	1	0	0	0	0	1	0	0	0	14632	304	11	2	1223	2	SLC39A14	8	22273673	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2579094	22273673	124090349	566	18838										
DOCK5	80005	hgsc.bcm.edu	37	chr8	25136115	25136115	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accgtgattcctggcgagctCcccctggtgcaggagctcac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:25136115delC	ENST00000276440.7	+	5	299	c.255delC	c.(253-255)ctcfs	p.L85fs	DOCK5_ENST00000481100.1_Frame_Shift_Del_p.L85fs	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	85					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CTGGCGAGCTCCCCCTGGTGC	0.552																																					p.L85fs	Pancreas(145;34 1887 3271 10937 30165)	Atlas-INDEL	.											.	DOCK5	167	.	0			c.254delT						.						137	112	121					8																	25136115		2203	4300	6503	SO:0001589	frameshift_variant	80005	exon5			.		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.255delC	chr8.hg19:g.25136115delC	ENSP00000276440:p.Leu85fs	215.0	0.0		198.0	12.0	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Frame_Shift_Del	DEL	ENST00000276440.7	hg19	CCDS6047.1																																																																																			.	.		0.552	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		-	25136115	C	-	25136115	7	5	114	1	0	1	0	1	0	0	0	0	4692	842	30	0	273	0	DOCK5	8	25136115	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2862442	25136115	121227907	567	18839										
ESCO2	157570	hgsc.bcm.edu	37	chr8	27634369	27634369	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgtggagaaggaaaataatTgtcattcagctgaaaataat	9	3	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:27634369T>C	ENST00000305188.8	+	3	782	c.544T>C	c.(544-546)Tgt>Cgt	p.C182R	ESCO2_ENST00000523910.1_3'UTR|ESCO2_ENST00000397418.2_5'UTR	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	182					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		GGAAAATAATTGTCATTCAGC	0.373									SC Phocomelia syndrome																												p.C182R		Atlas-SNP	.											.	ESCO2	50	.	0			c.T544C						.						55	58	57					8																	27634369		2203	4300	6503	SO:0001583	missense	157570	exon3	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	AATAATTGTCATT	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"Roberts syndrome", "establishment of cohesion 1 homolog 2 (S. cerevisiae)"	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.544T>C	chr8.hg19:g.27634369T>C	ENSP00000306999:p.Cys182Arg	50.0	0.0		54.0	4.0	NM_001017420	B3KW59|Q49AP4	Missense_Mutation	SNP	ENST00000305188.8	hg19	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	T	1.802	-0.476850	0.04414	.	.	ENSG00000171320	ENST00000523566;ENST00000305188	T;T	0.64085	0.83;-0.08	5.93	1.81	0.25067	.	1.026470	0.07659	N	0.933369	T	0.63402	0.2508	L	0.56769	1.78	0.09310	N	0.999996	D;P	0.53151	0.958;0.744	P;B	0.51866	0.682;0.154	T	0.48917	-0.8992	10	0.25751	T	0.34	-0.2848	5.0166	0.14339	0.3938:0.0:0.1481:0.4581	.	182;182	E5RFE4;Q56NI9	.;ESCO2_HUMAN	R	182	ENSP00000428435:C182R;ENSP00000306999:C182R	ENSP00000306999:C182R	C	+	1	0	ESCO2	27690288	0.000000	0.05858	0.084000	0.20598	0.068000	0.16541	0.417000	0.21214	0.435000	0.26365	0.482000	0.46254	TGT	.	.		0.373	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420		C	27634369	T	C	27634369	3	2	114	1	0	0	0	0	1	0	0	0	5251	1812	63	2	550	2	ESCO2	8	27634369	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2498254	27634369	118729653	568	18840										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36793121	36793121	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccttcagcactgcttgttatAaaaggaatgaagagttctca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:36793121delA	ENST00000399881.3	+	27	3170	c.3133delA	c.(3133-3135)aaafs	p.K1045fs		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	1045					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TGCTTGTTATAAAAGGAATGA	0.418																																					p.Y1044X		Atlas-INDEL	.											.	KCNU1	359	.	0			c.3132delT						.						122	117	119					8																	36793121		1893	4115	6008	SO:0001589	frameshift_variant	157855	exon27			.	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.3133delA	chr8.hg19:g.36793121delA	ENSP00000382770:p.Lys1045fs	132.0	0.0		180.0	15.0	NM_001031836		Frame_Shift_Del	DEL	ENST00000399881.3	hg19	CCDS55220.1																																																																																			.	.		0.418	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		-	36793121	A	-	36793121	7	5	114	1	0	1	0	1	0	0	0	0	8102	363	13	0	3239	0	KCNU1	8	36793121	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	9158752	36793121	109570901	569	18841										
PROSC	11212	hgsc.bcm.edu	37	chr8	37633463	37633463	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtccctccgggaggagctgTgtaaaaagctgaacatccct	11	11	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:37633463T>C	ENST00000328195.3	+	7	692	c.625T>C	c.(625-627)Tgt>Cgt	p.C209R		NM_007198.3	NP_009129.1	O94903	PROSC_HUMAN	proline synthetase co-transcribed homolog (bacterial)	209					alpha-amino acid metabolic process (GO:1901605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)	pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)	7		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)		L-Proline(DB00172)	GGAGGAGCTGTGTAAAAAGCT	0.522																																					p.C209R		Atlas-SNP	.											.	PROSC	20	.	0			c.T625C						.						208	202	204					8																	37633463		2203	4300	6503	SO:0001583	missense	11212	exon7			GAGCTGTGTAAAA	AB018566	CCDS6096.1	8p11.2	2008-01-07	2001-12-04		ENSG00000147471	ENSG00000147471			9457	protein-coding gene	gene with protein product		604436	"proline synthetase co-transcribed (bacterial homolog)"				Standard	NM_007198		Approved		uc003xkh.3	O94903	OTTHUMG00000164024	ENST00000328195.3:c.625T>C	chr8.hg19:g.37633463T>C	ENSP00000333551:p.Cys209Arg	51.0	0.0		84.0	4.0	NM_007198	Q6FI94	Missense_Mutation	SNP	ENST00000328195.3	hg19	CCDS6096.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.630660	0.46944	.	.	ENSG00000147471	ENST00000328195	T	0.39787	1.06	6.07	6.07	0.98685	Alanine racemase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.37598	0.1009	L	0.31065	0.9	0.80722	D	1	B	0.23058	0.079	B	0.29077	0.098	T	0.17018	-1.0383	10	0.59425	D	0.04	.	16.2903	0.82747	0.0:0.0:0.0:1.0	.	209	O94903	PROSC_HUMAN	R	209	ENSP00000333551:C209R	ENSP00000333551:C209R	C	+	1	0	PROSC	37752621	1.000000	0.71417	0.998000	0.56505	0.222000	0.24845	7.761000	0.85260	2.326000	0.78906	0.533000	0.62120	TGT	.	.		0.522	PROSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376796.1	NM_007198		C	37633463	T	C	37633463	3	2	114	1	0	0	0	0	1	0	0	0	12571	1696	59	2	651	2	PROSC	8	37633463	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	840342	37633463	108730559	570	18842										
WHSC1L1	54904	hgsc.bcm.edu	37	chr8	38205330	38205330	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttttccagaatttcatgtggTcttgtgtttggaatttctga	9	5	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:38205330T>C	ENST00000317025.8	-	2	877	c.360A>G	c.(358-360)agA>agG	p.R120R	WHSC1L1_ENST00000527502.1_Silent_p.R120R|WHSC1L1_ENST00000433384.2_Silent_p.R120R|WHSC1L1_ENST00000316985.3_Silent_p.R120R	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	120					histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			TTTCATGTGGTCTTGTGTTTG	0.433			T	NUP98	AML																																p.R120R		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.A360G						.						115	116	116					8																	38205330		2203	4300	6503	SO:0001819	synonymous_variant	54904	exon2			ATGTGGTCTTGTG	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.360A>G	chr8.hg19:g.38205330T>C		76.0	0.0		75.0	4.0	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Silent	SNP	ENST00000317025.8	hg19	CCDS43729.1																																																																																			.	.		0.433	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		C	38205330	T	C	38205330	2	2	114	1	0	0	0	0	0	0	0	1	17378	1664	58	2		2	WHSC1L1	8	38205330	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	571867	38205330	108158692	571	18843										
IKBKB	3551	hgsc.bcm.edu	37	chr8	42176819	42176819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tccgaaacaacagctgcctcTccaaaatgaagaattccatg	6	12	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:42176819T>C	ENST00000520810.1	+	14	1582	c.1396T>C	c.(1396-1398)Tcc>Ccc	p.S466P	IKBKB_ENST00000416505.2_Missense_Mutation_p.S407P|IKBKB_ENST00000379708.3_Missense_Mutation_p.S243P|IKBKB_ENST00000522785.1_3'UTR|IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000520835.1_Missense_Mutation_p.S464P	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	466	Leucine-zipper.				B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CAGCTGCCTCTCCAAAATGAA	0.468											OREG0018747	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S466P		Atlas-SNP	.											.	IKBKB	88	.	0			c.T1396C						.						90	88	88					8																	42176819		2203	4300	6503	SO:0001583	missense	3551	exon14			TGCCTCTCCAAAA	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.1396T>C	chr8.hg19:g.42176819T>C	ENSP00000430684:p.Ser466Pro	72.0	0.0	906	87.0	4.0	NM_001556	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	hg19	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.396695	0.83120	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	T;T;T;T	0.75821	-0.89;-0.97;-0.78;2.84	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.80308	0.4599	L	0.34521	1.04	0.58432	D	0.999991	D;D;D;D;D	0.76494	0.999;0.997;0.999;0.979;0.994	D;D;D;P;P	0.83275	0.996;0.921;0.994;0.756;0.885	T	0.79964	-0.1581	10	0.41790	T	0.15	-25.3868	16.0684	0.80907	0.0:0.0:0.0:1.0	.	407;464;243;417;466	B4E0U4;O14920-2;B3KRB7;Q59GL9;O14920	.;.;.;.;IKKB_HUMAN	P	466;407;464;243	ENSP00000430684:S466P;ENSP00000404920:S407P;ENSP00000430868:S464P;ENSP00000369030:S243P	ENSP00000369030:S243P	S	+	1	0	IKBKB	42295976	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	3.218000	0.51192	2.272000	0.75746	0.460000	0.39030	TCC	.	.		0.468	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			C	42176819	T	C	42176819	3	2	114	1	0	0	0	0	1	0	0	0	7620	1551	54	2	1446	2	IKBKB	8	42176819	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3971489	42176819	104187203	572	18844										
NSMAF	8439	hgsc.bcm.edu	37	chr8	59522272	59522272	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctttgcattccatgtgcagcTtttcagaaatgttttggaac	8	8	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:59522272T>C	ENST00000038176.3	-	10	790	c.578A>G	c.(577-579)aAg>aGg	p.K193R	NSMAF_ENST00000519858.1_5'UTR|NSMAF_ENST00000427130.2_Missense_Mutation_p.K224R	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	193	GRAM.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				CATGTGCAGCTTTTCAGAAAT	0.413																																					p.K224R		Atlas-SNP	.											.	NSMAF	156	.	0			c.A671G						.						85	80	81					8																	59522272		2203	4300	6503	SO:0001583	missense	8439	exon10			TGCAGCTTTTCAG	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.578A>G	chr8.hg19:g.59522272T>C	ENSP00000038176:p.Lys193Arg	62.0	0.0		85.0	4.0	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	hg19	CCDS6173.1	.	.	.	.	.	.	.	.	.	.	T	5.841	0.339458	0.11069	.	.	ENSG00000035681	ENST00000038176;ENST00000427130	D;D	0.87179	-2.22;-2.22	5.31	1.51	0.23008	GRAM (2);PH-BEACH domain (1);	0.412070	0.28877	N	0.013843	T	0.67183	0.2866	N	0.10809	0.05	0.23391	N	0.997774	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.09377	0.004;0.002;0.003	T	0.49021	-0.8982	9	.	.	.	.	2.267	0.04081	0.2007:0.079:0.1876:0.5326	.	224;193;193	Q92636-2;A8K9G4;Q92636	.;.;FAN_HUMAN	R	193;224	ENSP00000038176:K193R;ENSP00000411012:K224R	.	K	-	2	0	NSMAF	59684826	0.331000	0.24713	1.000000	0.80357	0.152000	0.21847	0.164000	0.16542	0.951000	0.37770	-0.280000	0.10049	AAG	.	.		0.413	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		C	59522272	T	C	59522272	3	2	114	1	0	0	0	0	1	0	0	0	10683	1609	56	2	2263	2	NSMAF	8	59522272	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	17345453	59522272	86841750	573	18845										
ADHFE1	137872	hgsc.bcm.edu	37	chr8	67359569	67359569	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gactatgaacacttgaaagtAaaaattggtaagaaccatac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:67359569delA	ENST00000396623.3	+	7	652	c.621delA	c.(619-621)gtafs	p.V207fs	ADHFE1_ENST00000379385.4_Frame_Shift_Del_p.V207fs|ADHFE1_ENST00000415254.1_Frame_Shift_Del_p.V159fs|ADHFE1_ENST00000496501.1_3'UTR	NM_144650.2	NP_653251.2	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	207					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|molecular hydrogen transport (GO:0015993)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacid-oxoacid transhydrogenase activity (GO:0047988)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	29		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			ACTTGAAAGTAAAAATTGGTA	0.318																																					p.V207fs		Atlas-INDEL	.											.	ADHFE1	83	.	0			c.620delT						.						62	67	65					8																	67359569		2203	4300	6503	SO:0001589	frameshift_variant	137872	exon7			.	AK056992	CCDS6190.2	8q12.3	2013-05-21			ENSG00000147576	ENSG00000147576	1.1.99.24	"Alcohol dehydrogenases"	16354	protein-coding gene	gene with protein product	"hydroxyacid-oxoacid transhydrogenase"	611083				12592711	Standard	NM_144650		Approved	ADHFe1, FLJ32430	uc003xwb.4	Q8IWW8	OTTHUMG00000150215	ENST00000396623.3:c.621delA	chr8.hg19:g.67359569delA	ENSP00000379865:p.Val207fs	138.0	0.0		151.0	10.0	NM_144650	B4DTJ8|Q49A19|Q68CI7|Q6P2B6|Q96MF9	Frame_Shift_Del	DEL	ENST00000396623.3	hg19	CCDS6190.2																																																																																			.	.		0.318	ADHFE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316867.3	NM_144650		-	67359569	A	-	67359569	7	5	114	1	0	1	0	1	0	0	0	0	314	349	13	0	647	0	ADHFE1	8	67359569	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	7837297	67359569	79004453	574	18846										
SULF1	23213	hgsc.bcm.edu	37	chr8	70550813	70550813	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acagttaatgagacgcataaTtttcttttctgtgagtttgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:70550813delT	ENST00000260128.4	+	20	3078	c.2361delT	c.(2359-2361)aatfs	p.N787fs	SULF1_ENST00000458141.2_Frame_Shift_Del_p.N787fs|SULF1_ENST00000419716.3_Frame_Shift_Del_p.N787fs|SULF1_ENST00000402687.4_Frame_Shift_Del_p.N787fs|SULF1_ENST00000521946.1_3'UTR	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	787					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			AGACGCATAATTTTCTTTTCT	0.353																																					p.N787fs		Atlas-INDEL	.											.	SULF1	153	.	0			c.2360delA						.						152	142	145					8																	70550813		2203	4300	6503	SO:0001589	frameshift_variant	23213	exon20			.	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2361delT	chr8.hg19:g.70550813delT	ENSP00000260128:p.Asn787fs	120.0	0.0		177.0	11.0	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Frame_Shift_Del	DEL	ENST00000260128.4	hg19	CCDS6204.1																																																																																			.	.		0.353	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		-	70550813	T	-	70550813	7	5	114	1	0	1	0	1	0	0	0	0	15385	1490	52	0	2423	0	SULF1	8	70550813	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3191244	70550813	75813209	575	18847										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73480531	73480531	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acttgctggagaaacctaacTcatcagtggctgcaaaggta	10	9	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:73480531T>C	ENST00000523207.1	+	2	1150	c.562T>C	c.(562-564)Tca>Cca	p.S188P		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	188					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GAAACCTAACTCATCAGTGGC	0.438																																					p.S188P		Atlas-SNP	.											.	KCNB2	228	.	0			c.T562C						.						69	73	72					8																	73480531		2200	4298	6498	SO:0001583	missense	9312	exon2			CCTAACTCATCAG	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.562T>C	chr8.hg19:g.73480531T>C	ENSP00000430846:p.Ser188Pro	48.0	0.0		74.0	5.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.149108	0.78001	.	.	ENSG00000182674	ENST00000523207	D	0.98135	-4.74	5.77	5.77	0.91146	.	0.485631	0.15369	U	0.265950	D	0.98985	0.9654	H	0.95260	3.645	0.58432	D	0.999998	D	0.53462	0.96	P	0.58266	0.836	D	0.99869	1.1093	10	0.72032	D	0.01	.	16.068	0.80903	0.0:0.0:0.0:1.0	.	188	Q92953	KCNB2_HUMAN	P	188	ENSP00000430846:S188P	ENSP00000430846:S188P	S	+	1	0	KCNB2	73643085	1.000000	0.71417	0.991000	0.47740	0.926000	0.56050	7.997000	0.88414	2.326000	0.78906	0.533000	0.62120	TCA	.	.		0.438	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		C	73480531	T	C	73480531	3	2	114	1	0	0	0	0	1	0	0	0	8022	1551	54	2	564	2	KCNB2	8	73480531	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2929718	73480531	72883491	576	18848										
CRISPLD1	83690	hgsc.bcm.edu	37	chr8	75932282	75932282	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acaactgtggaacagctctgTccatttcataagcctgcttc	7	12	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:75932282T>C	ENST00000262207.4	+	12	1680	c.1212T>C	c.(1210-1212)tgT>tgC	p.C404C	CRISPLD1_ENST00000523524.1_Silent_p.C216C|CRISPLD1_ENST00000517786.1_Silent_p.C218C	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	404	LCCL 2. {ECO:0000255|PROSITE- ProRule:PRU00123}.				face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			AACAGCTCTGTCCATTTCATA	0.413																																					p.C404C		Atlas-SNP	.											.	CRISPLD1	94	.	0			c.T1212C						.						134	121	126					8																	75932282		2203	4300	6503	SO:0001819	synonymous_variant	83690	exon12			GCTCTGTCCATTT	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.1212T>C	chr8.hg19:g.75932282T>C		157.0	0.0		248.0	11.0	NM_031461	B2RA60|B7Z929	Silent	SNP	ENST00000262207.4	hg19	CCDS6219.1																																																																																			.	.		0.413	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		C	75932282	T	C	75932282	2	2	114	1	0	0	0	0	0	0	0	1	3884	1673	58	2		2	CRISPLD1	8	75932282	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2451751	75932282	70431740	577	18849										
RALYL	138046	hgsc.bcm.edu	37	chr8	85097244	85097244	+	Intron	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctcttcgcaatgagtaaacGacgcagtaggtcctacccag	9	13	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:85097244G>C	ENST00000521268.1	+	1	1082				RALYL_ENST00000522455.1_Intron|RALYL_ENST00000521695.1_Intron|RALYL_ENST00000517638.1_Missense_Mutation_p.R4P|RALYL_ENST00000518566.1_Intron	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like								nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						ATGAGTAAACGACGCAGTAGG	0.532																																					p.R4P		Atlas-SNP	.											.	RALYL	123	.	0			c.G11C						.						101	108	106					8																	85097244		2104	4233	6337	SO:0001627	intron_variant	138046	exon1			GTAAACGACGCAG		CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"RNA binding motif (RRM) containing"	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.-24+585G>C	chr8.hg19:g.85097244G>C		160.0	0.0		174.0	7.0	NM_001100391	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Missense_Mutation	SNP	ENST00000521268.1	hg19	CCDS55253.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.397600	0.25205	.	.	ENSG00000184672	ENST00000517638	T	0.10960	2.82	5.2	1.45	0.22620	.	.	.	.	.	T	0.06188	0.0160	N	0.14661	0.345	0.80722	D	1	B	0.23490	0.086	B	0.24269	0.052	T	0.30001	-0.9993	9	0.87932	D	0	.	6.0671	0.19870	0.6026:0.3142:0.0832:0.0	.	4	G3V129	.	P	4	ENSP00000430128:R4P	ENSP00000430128:R4P	R	+	2	0	RALYL	85259799	0.358000	0.24947	0.013000	0.15412	0.927000	0.56198	0.153000	0.16323	0.087000	0.17167	-0.471000	0.05019	CGA	.	.		0.532	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1			C	85097244	G	C	85097244	1	2	114	0	1	0	0	0	0	0	0	0	13035	1058	37	4		4	RALYL	8	85097244	Intron	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	9164962	85097244	61266778	578	18850										
WWP1	11059	hgsc.bcm.edu	37	chr8	87410810	87410810	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgttgttcagtagaaatacAggaaaatggtgatgccttac	10	5	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:87410810A>G	ENST00000517970.1	+	7	789	c.482A>G	c.(481-483)cAg>cGg	p.Q161R	WWP1_ENST00000341922.2_Intron|WWP1_ENST00000349423.2_Intron|WWP1_ENST00000265428.4_Missense_Mutation_p.Q161R	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	161					central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						GTAGAAATACAGGAAAATGGT	0.328																																					p.Q161R		Atlas-SNP	.											.	WWP1	97	.	0			c.A482G						.						99	100	100					8																	87410810		2203	4300	6503	SO:0001583	missense	11059	exon7			AAATACAGGAAAA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.482A>G	chr8.hg19:g.87410810A>G	ENSP00000427793:p.Gln161Arg	132.0	0.0		146.0	6.0	NM_007013	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	hg19	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.129496	0.37630	.	.	ENSG00000123124	ENST00000517970;ENST00000265428	T;T	0.45276	0.9;0.9	5.41	4.24	0.50183	.	0.493228	0.21765	N	0.069451	T	0.35038	0.0918	L	0.53249	1.67	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.10268	-1.0637	10	0.15952	T	0.53	.	10.2698	0.43477	0.9172:0.0:0.0828:0.0	.	161	Q9H0M0	WWP1_HUMAN	R	161	ENSP00000427793:Q161R;ENSP00000265428:Q161R	ENSP00000265428:Q161R	Q	+	2	0	WWP1	87479926	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.030000	0.64128	0.987000	0.38709	0.477000	0.44152	CAG	.	.		0.328	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		G	87410810	A	G	87410810	3	3	114	1	0	0	0	0	1	0	0	0	17430	188	7	2	500	2	WWP1	8	87410810	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2313566	87410810	58953212	579	18851										
WWP1	11059	hgsc.bcm.edu	37	chr8	87454970	87454970	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaccattaatccagaccatcTttcatacttctgtttcattg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:87454970delT	ENST00000517970.1	+	18	2268	c.1961delT	c.(1960-1962)cttfs	p.L654fs	WWP1_ENST00000341922.2_Frame_Shift_Del_p.L524fs|WWP1_ENST00000349423.2_Frame_Shift_Del_p.L436fs|WWP1_ENST00000265428.4_Frame_Shift_Del_p.L654fs	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	654	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						CCAGACCATCTTTCATACTTC	0.338																																					p.L654fs		Atlas-INDEL	.											.	WWP1	97	.	0			c.1960delC						.						128	118	121					8																	87454970		2203	4300	6503	SO:0001589	frameshift_variant	11059	exon18			.	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1961delT	chr8.hg19:g.87454970delT	ENSP00000427793:p.Leu654fs	143.0	0.0		165.0	12.0	NM_007013	O00307|Q5YLC1|Q96BP4	Frame_Shift_Del	DEL	ENST00000517970.1	hg19	CCDS6242.1																																																																																			.	.		0.338	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		-	87454970	T	-	87454970	7	5	114	1	0	1	0	1	0	0	0	0	17430	1609	56	0	2023	0	WWP1	8	87454970	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	44160	87454970	58909052	580	18852										
PDP1	54704	hgsc.bcm.edu	37	chr8	94934597	94934597	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagtgccagaatttgacggcAaaaatgtcagttctatcctt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:94934597delA	ENST00000297598.4	+	2	579	c.310delA	c.(310-312)aaafs	p.K104fs	PDP1_ENST00000517764.1_Frame_Shift_Del_p.K104fs|PDP1_ENST00000396200.3_Frame_Shift_Del_p.K129fs|PDP1_ENST00000520728.1_Frame_Shift_Del_p.K104fs	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	104					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						ATTTGACGGCAAAAATGTCAG	0.448																																					p.G128fs		Atlas-INDEL	.											.	PDP1	97	.	0			c.384delC						.						108	111	110					8																	94934597		2203	4300	6503	SO:0001589	frameshift_variant	54704	exon3			.	AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9279	protein-coding gene	gene with protein product		605993	"protein phosphatase 2C, magnesium-dependent, catalytic subunit"	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.310delA	chr8.hg19:g.94934597delA	ENSP00000297598:p.Lys104fs	144.0	0.0		200.0	13.0	NM_001161780	B3KX71|J3KPU0|Q5U5K1	Frame_Shift_Del	DEL	ENST00000297598.4	hg19	CCDS6259.1																																																																																			.	.		0.448	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		-	94934597	A	-	94934597	7	5	114	1	0	1	0	1	0	0	0	0	11694	131	5	0	493	0	PDP1	8	94934597	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	7479627	94934597	51429425	581	18853										
TSPYL5	85453	hgsc.bcm.edu	37	chr8	98289664	98289664	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccacgccggtttccaacgcGgggggcatttttcggccttc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:98289664delG	ENST00000322128.3	-	1	512	c.409delC	c.(409-411)cgcfs	p.R137fs		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	137					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					TTTCCAACGCGGGGGGCATTT	0.677																																					p.R137fs		Atlas-INDEL	.											.	TSPYL5	48	.	0			c.410delG						.						20	24	23					8																	98289664		2196	4292	6488	SO:0001589	frameshift_variant	85453	exon1			.	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.409delC	chr8.hg19:g.98289664delG	ENSP00000322802:p.Arg137fs	178.0	0.0		187.0	13.0	NM_033512	B3KRF0|Q9C0B3	Frame_Shift_Del	DEL	ENST00000322128.3	hg19	CCDS34927.1																																																																																			.	.		0.677	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512		-	98289664	G	-	98289664	7	5	114	1	0	1	0	1	0	0	0	0	16677	1116	39	0	848	0	TSPYL5	8	98289664	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	3355067	98289664	48074358	582	18854										
STK3	6788	hgsc.bcm.edu	37	chr8	99608284	99608284	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaaagttgtgttgcagtagcTctctgctcaggattcttcac	9	9	4	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:99608284T>C	ENST00000419617.2	-	7	938	c.798A>G	c.(796-798)agA>agG	p.R266R	STK3_ENST00000521768.1_5'UTR|STK3_ENST00000523601.1_Silent_p.R294R	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	266	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		TTGCAGTAGCTCTCTGCTCAG	0.428																																					p.R294R		Atlas-SNP	.											.	STK3	47	.	0			c.A882G						.						71	69	70					8																	99608284		1895	4105	6000	SO:0001819	synonymous_variant	6788	exon9			AGTAGCTCTCTGC	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"serine/threonine kinase 3 (Ste20, yeast homolog)"			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.798A>G	chr8.hg19:g.99608284T>C		182.0	0.0		247.0	10.0	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Silent	SNP	ENST00000419617.2	hg19	CCDS47900.1																																																																																			.	.		0.428	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281		C	99608284	T	C	99608284	2	2	114	1	0	0	0	0	0	0	0	1	15310	1548	54	2		2	STK3	8	99608284	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1318620	99608284	46755738	583	18855										
STK3	6788	hgsc.bcm.edu	37	chr8	99718796	99718796	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacacagttatagcctatttCttgaatcacctcaggagcca	6	12	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:99718796C>T	ENST00000419617.2	-	6	723	c.583G>A	c.(583-585)Gaa>Aaa	p.E195K	STK3_ENST00000523601.1_Missense_Mutation_p.E223K	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	195	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		TAGCCTATTTCTTGAATCACC	0.403																																					p.E223K		Atlas-SNP	.											STK3,NS,carcinoma,0,2	STK3	47	.	0			c.G667A						.						142	142	142					8																	99718796		2035	4217	6252	SO:0001583	missense	6788	exon8			CTATTTCTTGAAT	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"serine/threonine kinase 3 (Ste20, yeast homolog)"			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.583G>A	chr8.hg19:g.99718796C>T	ENSP00000390500:p.Glu195Lys	80.0	0.0		110.0	5.0	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Missense_Mutation	SNP	ENST00000419617.2	hg19	CCDS47900.1	.	.	.	.	.	.	.	.	.	.	C	35	5.439199	0.96168	.	.	ENSG00000104375	ENST00000419617;ENST00000523601	T;T	0.13420	2.59;2.59	4.78	4.78	0.61160	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.20495	0.0493	N	0.11201	0.11	0.80722	D	1	P;D	0.76494	0.69;0.999	P;D	0.69479	0.479;0.964	T	0.29610	-1.0006	10	0.87932	D	0	.	17.3864	0.87417	0.0:1.0:0.0:0.0	.	195;223	Q13188;B3KYA7	STK3_HUMAN;.	K	195;223	ENSP00000390500:E195K;ENSP00000429744:E223K	ENSP00000390500:E195K	E	-	1	0	STK3	99787972	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.794000	0.85869	2.196000	0.70406	0.467000	0.42956	GAA	.	.		0.403	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281		T	99718796	C	T	99718796	3	4	114	1	0	0	0	0	1	0	0	0	15310	922	32	3	916	3	STK3	8	99718796	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	110512	99718796	46645226	584	18856										
FZD6	8323	hgsc.bcm.edu	37	chr8	104330820	104330820	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcttgatgtctttaatagcaTtttcttcctctcgcaaatct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:104330820delT	ENST00000358755.4	+	3	497	c.180delT	c.(178-180)catfs	p.H60fs	FZD6_ENST00000522566.1_Frame_Shift_Del_p.H60fs|FZD6_ENST00000540287.1_Intron|FZD6_ENST00000523739.1_Frame_Shift_Del_p.H28fs	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	60	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			TTTAATAGCATTTTCTTCCTC	0.299																																					p.H60fs		Atlas-INDEL	.											.	FZD6	61	.	0			c.179delA						.						70	70	70					8																	104330820		2203	4300	6503	SO:0001589	frameshift_variant	8323	exon3			.	AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"GPCR / Class F : Frizzled receptors"	4044	protein-coding gene	gene with protein product		603409	"frizzled (Drosophila) homolog 6", "frizzled homolog 6 (Drosophila)", "frizzled 6, seven transmembrane spanning receptor", "frizzled family receptor 6"			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.180delT	chr8.hg19:g.104330820delT	ENSP00000351605:p.His60fs	87.0	0.0		125.0	11.0	NM_003506	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Frame_Shift_Del	DEL	ENST00000358755.4	hg19	CCDS6298.1																																																																																			.	.		0.299	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506		-	104330820	T	-	104330820	7	5	114	1	0	1	0	1	0	0	0	0	6142	1490	52	0	186	0	FZD6	8	104330820	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	4612024	104330820	42033202	585	18857										
ANGPT1	284	hgsc.bcm.edu	37	chr8	108348381	108348381	+	5'UTR	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aataaagcaatcctcacctgTttttttcatggatcttcaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:108348381delT	ENST00000520734.1	-	0	257				ANGPT1_ENST00000520052.1_5'UTR			Q15389	ANGP1_HUMAN	angiopoietin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			TCCTCACCTGTTTTTTTCATG	0.368																																					p.N191fs		Atlas-INDEL	.											.	ANGPT1	111	.	0			c.573delC						.						135	123	127					8																	108348381		2203	4300	6503	SO:0001623	5_prime_UTR_variant	284	exon3			.	D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"Fibrinogen C domain containing"	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.-29A>-	chr8.hg19:g.108348381delT		107.0	0.0		175.0	12.0	NM_001199859	Q5HYA0	Frame_Shift_Del	DEL	ENST00000520734.1	hg19																																																																																				.	.		0.368	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290		-	108348381	T	-	108348381	6	5	114	0	1	1	0	1	0	0	0	0	610	1725	60	0		0	ANGPT1	8	108348381	5'UTR	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	4017561	108348381	38015641	586	18858										
UTP23	84294	hgsc.bcm.edu	37	chr8	117783923	117783923	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtagaagaaaaaagcgcaagAaaataagtggtcccaatcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:117783923delA	ENST00000309822.2	+	3	693	c.592delA	c.(592-594)aaafs	p.K198fs	UTP23_ENST00000517820.1_Intron|UTP23_ENST00000357148.3_Intron|UTP23_ENST00000520733.1_Intron	NM_032334.2	NP_115710.2	Q9BRU9	UTP23_HUMAN	UTP23, small subunit (SSU) processome component, homolog (yeast)	198					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	12						AAAGCGCAAGAAAATAAGTGG	0.363																																					p.K197fs		Atlas-INDEL	.											.	UTP23	38	.	0			c.591delG						.						55	57	56					8																	117783923		2203	4300	6503	SO:0001589	frameshift_variant	84294	exon3			.		CCDS6320.1	8q24.11	2008-06-12	2008-06-12	2008-06-12		ENSG00000147679			28224	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 53"	C8orf53		16769905	Standard	NM_032334		Approved	MGC14595	uc003yoc.3	Q9BRU9		ENST00000309822.2:c.592delA	chr8.hg19:g.117783923delA	ENSP00000308332:p.Lys198fs	129.0	0.0		151.0	10.0	NM_032334	B2RE25|Q96NJ8	Frame_Shift_Del	DEL	ENST00000309822.2	hg19	CCDS6320.1																																																																																			.	.		0.363	UTP23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381173.1	NM_032334		-	117783923	A	-	117783923	7	5	114	1	0	1	0	1	0	0	0	0	17115	247	9	0	602	0	UTP23	8	117783923	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	9435542	117783923	28580099	587	18859										
TNFRSF11B	4982	hgsc.bcm.edu	37	chr8	119945174	119945174	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcacattgacacgtaccagcTtgcaccactccaaatccagg	7	15	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:119945174T>C	ENST00000297350.4	-	2	774	c.396A>G	c.(394-396)caA>caG	p.Q132Q		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	132					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			ACGTACCAGCTTGCACCACTC	0.463																																					p.Q132Q		Atlas-SNP	.											.	TNFRSF11B	87	.	0			c.A396G						.						47	48	48					8																	119945174		2203	4300	6503	SO:0001819	synonymous_variant	4982	exon2			ACCAGCTTGCACC	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"Tumor necrosis factor receptor superfamily"	11909	protein-coding gene	gene with protein product		602643	"osteoprotegerin"	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.396A>G	chr8.hg19:g.119945174T>C		78.0	0.0		90.0	4.0	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Silent	SNP	ENST00000297350.4	hg19	CCDS6326.1																																																																																			.	.		0.463	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1			C	119945174	T	C	119945174	2	2	114	1	0	0	0	0	0	0	0	1	16300	1606	56	2		2	TNFRSF11B	8	119945174	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2161251	119945174	26418848	588	18860										
SNTB1	6641	hgsc.bcm.edu	37	chr8	121823695	121823695	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgggcatcttgttctccttgCcccccttgatgctgatcccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:121823695delC	ENST00000395601.3	-	2	803	c.389delG	c.(388-390)ggcfs	p.G130fs	RP11-713M15.2_ENST00000605955.1_RNA|SNTB1_ENST00000519177.1_5'UTR|SNTB1_ENST00000517992.1_Frame_Shift_Del_p.G130fs	NM_021021.3	NP_066301.1	Q13884	SNTB1_HUMAN	syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)	130	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|protein complex (GO:0043234)|synapse (GO:0045202)				NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(6)	24	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			GTTCTCCTTGCCCCCCTTGAT	0.637																																					p.G130fs		Atlas-INDEL	.											.	SNTB1	54	.	0			c.390delC						.						59	60	60					8																	121823695		2203	4300	6503	SO:0001589	frameshift_variant	6641	exon1			.	AF028828	CCDS6334.1	8q23-q24	2013-01-10	2002-08-29		ENSG00000172164	ENSG00000172164		"Pleckstrin homology (PH) domain containing"	11168	protein-coding gene	gene with protein product	"tax interaction protein 43"	600026	"syntrophin, beta 1 (dystrophin-associated protein A1, 59kD, basic component 1)"	SNT2B1		8183929, 9482110	Standard	NM_021021		Approved	59-DAP, A1B, BSYN2, TIP-43, SNT2	uc010mdg.3	Q13884	OTTHUMG00000165041	ENST00000395601.3:c.389delG	chr8.hg19:g.121823695delC	ENSP00000378965:p.Gly130fs	166.0	0.0		243.0	15.0	NM_021021	A8K9E0|O14912|Q4KMG8	Frame_Shift_Del	DEL	ENST00000395601.3	hg19	CCDS6334.1																																																																																			.	.		0.637	SNTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381535.1	NM_021021		-	121823695	C	-	121823695	7	5	114	1	0	1	0	1	0	0	0	0	14887	739	26	0	1255	0	SNTB1	8	121823695	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1878521	121823695	24540327	589	18861										
ANXA13	312	hgsc.bcm.edu	37	chr8	124748069	124748069	+	Intron	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gactgtcgagggttgggagtCccctttaggcaactgttgac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:124748069delC	ENST00000419625.1	-	1	88				ANXA13_ENST00000262219.6_Frame_Shift_Del_p.D22fs	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13						cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			GGTTGGGAGTCCCCTTTAGGC	0.512																																					p.D22fs		Atlas-INDEL	.											.	ANXA13	38	.	0			c.65delA						.						140	140	140					8																	124748069		2203	4300	6503	SO:0001627	intron_variant	312	exon2			.	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"Annexins"	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.15+1490G>-	chr8.hg19:g.124748069delC		147.0	0.0		142.0	11.0	NM_001003954	Q9BQR5	Frame_Shift_Del	DEL	ENST00000419625.1	hg19	CCDS47917.1																																																																																			.	.		0.512	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306		-	124748069	C	-	124748069	6	5	114	0	1	1	0	1	0	0	0	0	717	855	30	0		0	ANXA13	8	124748069	Intron	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2924374	124748069	21615953	590	18862										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125029888	125029888	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcctttatctctgaagcagAaaaaaagcccaagatgttga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:125029888delA	ENST00000522917.1	+	16	2149	c.1943delA	c.(1942-1944)gaafs	p.E648fs	FER1L6-AS1_ENST00000518567.1_RNA|FER1L6_ENST00000399018.1_Frame_Shift_Del_p.E648fs	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	648						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TCTGAAGCAGAAAAAAAGCCC	0.343																																					p.E648fs		Atlas-INDEL	.											.	FER1L6	268	.	0			c.1942delG						.						87	84	85					8																	125029888		1808	4068	5876	SO:0001589	frameshift_variant	654463	exon16			.	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.1943delA	chr8.hg19:g.125029888delA	ENSP00000428280:p.Glu648fs	104.0	0.0		101.0	11.0	NM_001039112		Frame_Shift_Del	DEL	ENST00000522917.1	hg19	CCDS43767.1																																																																																			.	.		0.343	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		-	125029888	A	-	125029888	7	5	114	1	0	1	0	1	0	0	0	0	5823	246	9	0	2001	0	FER1L6	8	125029888	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	281819	125029888	21334134	591	18863										
MTSS1	9788	hgsc.bcm.edu	37	chr8	125569986	125569986	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggtgtaataatgagcgtagTctggaaggtggacagaggtg	17	3	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:125569986T>C	ENST00000518547.1	-	11	1639	c.1166A>G	c.(1165-1167)gAc>gGc	p.D389G	MTSS1_ENST00000354184.4_Intron|MTSS1_ENST00000524090.1_Missense_Mutation_p.D279G|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000325064.5_Missense_Mutation_p.D393G|MTSS1_ENST00000431961.2_Intron|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000378017.3_Intron|MTSS1_ENST00000395508.2_Missense_Mutation_p.D163G	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	389					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ATGAGCGTAGTCTGGAAGGTG	0.602																																					p.D389G	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.A1166G						.						115	84	94					8																	125569986		2203	4300	6503	SO:0001583	missense	9788	exon11			GCGTAGTCTGGAA	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1166A>G	chr8.hg19:g.125569986T>C	ENSP00000429064:p.Asp389Gly	120.0	0.0		142.0	7.0	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Missense_Mutation	SNP	ENST00000518547.1	hg19	CCDS6353.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.670812	0.47781	.	.	ENSG00000170873	ENST00000518547;ENST00000395508;ENST00000325064;ENST00000524090;ENST00000522118	T;T;T;T;T	0.54071	1.4;1.34;1.4;1.38;0.59	5.14	5.14	0.70334	.	0.175996	0.52532	D	0.000074	T	0.33673	0.0871	N	0.22421	0.69	0.54753	D	0.999987	P;B;B	0.43094	0.799;0.028;0.295	B;B;B	0.30179	0.112;0.015;0.055	T	0.19128	-1.0315	10	0.30854	T	0.27	-22.2155	14.9595	0.71144	0.0:0.0:0.0:1.0	.	279;163;389	E7EWW5;B7Z3B6;O43312	.;.;MTSS1_HUMAN	G	389;163;393;279;189	ENSP00000429064:D389G;ENSP00000378884:D163G;ENSP00000322804:D393G;ENSP00000428319:D279G;ENSP00000428145:D189G	ENSP00000322804:D393G	D	-	2	0	MTSS1	125639167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.771000	0.68881	1.931000	0.55961	0.459000	0.35465	GAC	.	.		0.602	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		C	125569986	T	C	125569986	3	2	114	1	0	0	0	0	1	0	0	0	9971	1667	58	2	1117	2	MTSS1	8	125569986	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	540098	125569986	20794036	592	18864										
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126052109	126052109	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aataatttaattcattggcaAtctgttgtctcagaatctgc	6	7	4	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:126052109A>G	ENST00000318410.7	-	24	3231	c.2882T>C	c.(2881-2883)aTt>aCt	p.I961T	KIAA0196_ENST00000517845.1_Missense_Mutation_p.I813T|KIAA0196-AS1_ENST00000519140.1_RNA	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	961					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TTCATTGGCAATCTGTTGTCT	0.428																																					p.I961T		Atlas-SNP	.											.	KIAA0196	90	.	0			c.T2882C						.						76	70	72					8																	126052109		2203	4300	6503	SO:0001583	missense	9897	exon24			TTGGCAATCTGTT		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.2882T>C	chr8.hg19:g.126052109A>G	ENSP00000318016:p.Ile961Thr	63.0	0.0		81.0	4.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	hg19	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.497961	0.85069	.	.	ENSG00000164961	ENST00000318410;ENST00000517845	D;D	0.91351	-2.83;-2.83	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.95834	0.8644	M	0.86651	2.83	0.80722	D	1	D;P	0.89917	1.0;0.901	D;P	0.83275	0.996;0.559	D	0.96516	0.9382	10	0.87932	D	0	-21.0437	15.7714	0.78173	1.0:0.0:0.0:0.0	.	813;961	E7EQI7;Q12768	.;STRUM_HUMAN	T	961;813	ENSP00000318016:I961T;ENSP00000429676:I813T	ENSP00000318016:I961T	I	-	2	0	KIAA0196	126121291	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.299000	0.96137	2.127000	0.65507	0.459000	0.35465	ATT	.	.		0.428	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		G	126052109	A	G	126052109	3	3	114	1	0	0	0	0	1	0	0	0	8170	101	4	2	621	2	KIAA0196	8	126052109	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	482123	126052109	20311913	593	18865										
PTK2	5747	hgsc.bcm.edu	37	chr8	141675017	141675017	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggggaagattgtgccctaccTctcggtgggtgctggctggt	17	9	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:141675017T>C	ENST00000522684.1	-	31	3174	c.2945A>G	c.(2944-2946)gAg>gGg	p.E982G	PTK2_ENST00000517712.1_Splice_Site_p.E45G|PTK2_ENST00000430260.2_Splice_Site_p.E292G|PTK2_ENST00000340930.3_Splice_Site_p.E995G|PTK2_ENST00000517887.1_Splice_Site_p.E1026G|PTK2_ENST00000522950.1_5'Flank|PTK2_ENST00000521059.1_Splice_Site_p.E982G|PTK2_ENST00000538769.1_Splice_Site_p.E650G|PTK2_ENST00000535192.1_Splice_Site_p.E936G|PTK2_ENST00000519419.1_Splice_Site_p.E1026G|PTK2_ENST00000519465.1_Splice_Site_p.E610G|PTK2_ENST00000395218.2_Splice_Site_p.E995G	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	982	Interaction with ARHGEF28. {ECO:0000250}.|Interaction with TGFB1I1.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			GTGCCCTACCTCTCGGTGGGT	0.577																																					p.E1004G		Atlas-SNP	.											.	PTK2	311	.	0			c.A3011G						.						132	86	101					8																	141675017		2203	4300	6503	SO:0001630	splice_region_variant	5747	exon31			CCTACCTCTCGGT	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9611	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 71"	600758	"PTK2 protein tyrosine kinase 2"			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.2946+1A>G	chr8.hg19:g.141675017T>C		89.0	0.0		123.0	6.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.111148	0.77210	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000517712;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986	T;T;T;T;T;T;T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19	5.77	5.77	0.91146	Focal adhesion kinase, targeting (FAT) domain (3);	0.000000	0.85682	D	0.000000	T	0.48978	0.1530	M	0.67397	2.05	0.80722	D	1	B;B;P;B;B;B;B;P;B;B	0.41008	0.154;0.017;0.735;0.129;0.302;0.104;0.307;0.529;0.325;0.07	B;B;P;B;B;B;B;B;B;B	0.47402	0.229;0.107;0.546;0.161;0.333;0.121;0.398;0.331;0.269;0.133	T	0.51148	-0.8742	10	0.66056	D	0.02	.	15.7592	0.78063	0.0:0.0:0.0:1.0	.	995;680;905;982;1004;936;937;809;650;610	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	G	982;936;610;1026;982;937;995;906;680;45;654;995;650;1026;292;683	ENSP00000429911:E982G;ENSP00000438009:E936G;ENSP00000429170:E610G;ENSP00000429082:E1026G;ENSP00000429474:E982G;ENSP00000378644:E995G;ENSP00000430916:E45G;ENSP00000428492:E654G;ENSP00000341189:E995G;ENSP00000445742:E650G;ENSP00000429129:E1026G;ENSP00000403416:E292G;ENSP00000430603:E683G	ENSP00000341189:E995G	E	-	2	0	PTK2	141744199	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.687000	0.84139	2.216000	0.71823	0.528000	0.53228	GAG	.	.		0.577	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	Missense_Mutation	C	141675017	T	C	141675017	5	2	114	1	0	0	0	0	0	0	1	0	12775	1565	54	2	221	2	PTK2	8	141675017	Splice_Site	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	15622908	141675017	4689005	594	18866										
C8orf73	642475	hgsc.bcm.edu	37	chr8	144654667	144654667	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgccagcttcagggacggtgGccccacgtccaggctctgcc	13	16	2	0	rs368816807		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:144654667G>A	ENST00000398882.3	-	1	474	c.218C>T	c.(217-219)gCc>gTc	p.A73V	NAPRT1_ENST00000460623.1_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA|MROH6_ENST00000533679.1_5'Flank	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	73																	AGGGACGGTGGCCCCACGTCC	0.682																																					p.A73V		Atlas-SNP	.											.	.	.	.	0			c.C218T						.		VAL/ALA	0,3968		0,0,1984	15	20	19		218	1.4	0	8		19	1,8303		0,1,4151	no	missense	C8orf73	NM_001100878.1	64	0,1,6135	AA,AG,GG		0.012,0.0,0.0081	benign	73/720	144654667	1,12271	1984	4152	6136	SO:0001583	missense	642475	exon1			ACGGTGGCCCCAC	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"maestro heat-like repeat containing"	27814	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 73"	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.218C>T	chr8.hg19:g.144654667G>A	ENSP00000381857:p.Ala73Val	62.0	0.0		93.0	16.0	NM_001100878	A8MWB1	Missense_Mutation	SNP	ENST00000398882.3	hg19	CCDS47928.1	.	.	.	.	.	.	.	.	.	.	g	12.09	1.835002	0.32421	0.0	1.2E-4	ENSG00000204839	ENST00000398882;ENST00000529971	T;T	0.24151	4.3;1.87	3.8	1.37	0.22104	.	.	.	.	.	T	0.12050	0.0293	N	0.14661	0.345	0.19775	N	0.999953	B;B	0.19331	0.035;0.002	B;B	0.14023	0.01;0.003	T	0.32587	-0.9901	9	0.23302	T	0.38	-2.2287	4.1419	0.10198	0.1943:0.2146:0.5911:0.0	.	73;73	E9PPP7;A6NGR9	.;CH073_HUMAN	V	73	ENSP00000381857:A73V;ENSP00000436959:A73V	ENSP00000381857:A73V	A	-	2	0	C8orf73	144725810	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.207000	0.09384	0.133000	0.18654	0.558000	0.71614	GCC	.	.		0.682	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		A	144654667	G	A	144654667	3	1	114	1	0	0	0	0	1	0	0	0	2437	1203	42	3	1997	3	C8orf73	8	144654667	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	2979650	144654667	1709355	595	18867										
ERMP1	79956	hgsc.bcm.edu	37	chr9	5805053	5805053	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggacgagagaatcattgtacAgccagccaaaatggatgcca	11	9	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:5805053A>G	ENST00000339450.5	-	10	1977	c.1888T>C	c.(1888-1890)Tgt>Cgt	p.C630R	ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000381506.3_Intron|ERMP1_ENST00000543230.1_Missense_Mutation_p.C208R	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	630						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		ATCATTGTACAGCCAGCCAAA	0.378																																					p.C630R		Atlas-SNP	.											.	ERMP1	63	.	0			c.T1888C						.						83	76	78					9																	5805053		2203	4300	6503	SO:0001583	missense	79956	exon10			TTGTACAGCCAGC	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"Felix-ina"	611156	"KIAA1815"	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.1888T>C	chr9.hg19:g.5805053A>G	ENSP00000340427:p.Cys630Arg	105.0	0.0		77.0	4.0	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	hg19	CCDS34983.1	.	.	.	.	.	.	.	.	.	.	A	11.93	1.785491	0.31593	.	.	ENSG00000099219	ENST00000339450;ENST00000543230	T;T	0.23147	1.92;1.92	5.7	5.7	0.88788	.	0.145914	0.64402	D	0.000007	T	0.18964	0.0455	L	0.43152	1.355	0.80722	D	1	P	0.46952	0.887	B	0.35931	0.214	T	0.04165	-1.0972	10	0.25106	T	0.35	-21.0705	11.7192	0.51672	0.8603:0.0:0.0:0.1397	.	630	Q7Z2K6	ERMP1_HUMAN	R	630;208	ENSP00000340427:C630R;ENSP00000439368:C208R	ENSP00000340427:C630R	C	-	1	0	ERMP1	5795053	0.975000	0.34042	0.180000	0.23079	0.807000	0.45602	4.165000	0.58196	2.170000	0.68504	0.482000	0.46254	TGT	.	.		0.378	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896		G	5805053	A	G	5805053	3	3	114	1	0	0	0	0	1	0	0	0	5238	188	7	2	850	2	ERMP1	9	5805053	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10		5805053	135408378	596	18868										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13168371	13168371	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caaatgatacttactttatgTcagggccaatgagagaatgt	9	6	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:13168371T>C	ENST00000319217.7	-	22	3495	c.3248A>G	c.(3247-3249)gAc>gGc	p.D1083G	MPDZ_ENST00000381022.2_Missense_Mutation_p.D1083G|MPDZ_ENST00000546205.1_Missense_Mutation_p.D1083G|MPDZ_ENST00000538841.1_5'Flank|MPDZ_ENST00000381015.4_Missense_Mutation_p.D1083G|MPDZ_ENST00000541718.1_Missense_Mutation_p.D1083G|MPDZ_ENST00000536827.1_Missense_Mutation_p.D1083G|MPDZ_ENST00000447879.1_Missense_Mutation_p.D1083G	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1083	PDZ 6. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TTACTTTATGTCAGGGCCAAT	0.388																																					p.D1083G		Atlas-SNP	.											.	MPDZ	324	.	0			c.A3248G						.						173	165	168					9																	13168371		1880	4122	6002	SO:0001583	missense	8777	exon22			TTTATGTCAGGGC	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.3248A>G	chr9.hg19:g.13168371T>C	ENSP00000320006:p.Asp1083Gly	95.0	0.0		84.0	5.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	T	21.1	4.101891	0.76983	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000545857;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13;1.13;1.13;1.13	5.23	4.1	0.47936	.	0.000000	0.45867	D	0.000322	T	0.55386	0.1917	L	0.61218	1.895	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	P;D;D	0.70227	0.848;0.968;0.928	T	0.51348	-0.8717	10	0.17832	T	0.49	.	10.9259	0.47191	0.0:0.0737:0.0:0.9263	.	1083;1083;1083	B7ZMI4;O75970-3;O75970-2	.;.;.	G	1083;1083;1083;89;1083;1083;1083;1033;1083	ENSP00000320006:D1083G;ENSP00000439807:D1083G;ENSP00000370410:D1083G;ENSP00000444230:D89G;ENSP00000444151:D1083G;ENSP00000415208:D1083G;ENSP00000370403:D1083G;ENSP00000446358:D1083G	ENSP00000320006:D1083G	D	-	2	0	MPDZ	13158371	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	7.655000	0.83696	0.936000	0.37367	0.460000	0.39030	GAC	.	.		0.388	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		C	13168371	T	C	13168371	3	2	114	1	0	0	0	0	1	0	0	0	9731	1667	58	2	2977	2	MPDZ	9	13168371	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	7363318	13168371	128045060	597	18869										
FREM1	158326	hgsc.bcm.edu	37	chr9	14737508	14737508	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttccaagcttggagcgttgAgagggccctcttctcccatt	10	12	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:14737508A>G	ENST00000380880.3	-	37	7209	c.6426T>C	c.(6424-6426)tcT>tcC	p.S2142S	FREM1_ENST00000422223.2_Silent_p.S2142S|FREM1_ENST00000380881.4_Silent_p.S2143S|FREM1_ENST00000380894.1_Silent_p.S678S			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	2142	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TGGAGCGTTGAGAGGGCCCTC	0.478																																					p.S2142S		Atlas-SNP	.											.	FREM1	261	.	0			c.T6426C						.						66	65	65					9																	14737508		1907	4127	6034	SO:0001819	synonymous_variant	158326	exon38			GCGTTGAGAGGGC	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.6426T>C	chr9.hg19:g.14737508A>G		133.0	0.0		93.0	4.0	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	hg19	CCDS47952.1																																																																																			.	.		0.478	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		G	14737508	A	G	14737508	2	3	114	1	0	0	0	0	0	0	0	1	6052	291	11	2		2	FREM1	9	14737508	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1569137	14737508	126475923	598	18870										
HAUS6	54801	hgsc.bcm.edu	37	chr9	19094365	19094365	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttttcggaattcagtgtcacTtttttggtcaaatgggggcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:19094365delT	ENST00000380502.3	-	3	720	c.253delA	c.(253-255)agtfs	p.S85fs	HAUS6_ENST00000380496.1_5'Flank	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	85					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TCAGTGTCACTTTTTTGGTCA	0.318																																					p.S85fs		Atlas-INDEL	.											.	HAUS6	66	.	0			c.254delG						.						42	44	43					9																	19094365		2203	4299	6502	SO:0001589	frameshift_variant	54801	exon3			.	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"HAUS augmin-like complex subunits"	25948	protein-coding gene	gene with protein product		613433	"family with sequence similarity 29, member A"	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.253delA	chr9.hg19:g.19094365delT	ENSP00000369871:p.Ser85fs	279.0	0.0		211.0	13.0	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Frame_Shift_Del	DEL	ENST00000380502.3	hg19	CCDS6489.1																																																																																			.	.		0.318	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645		-	19094365	T	-	19094365	7	5	114	1	0	1	0	1	0	0	0	0	6979	1609	56	0	2674	0	HAUS6	9	19094365	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	4356857	19094365	122119066	599	18871										
PLIN2	123	hgsc.bcm.edu	37	chr9	19123604	19123604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aataggcagtctctcctcaaTcctgtctagccccttacagg	7	14	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:19123604T>C	ENST00000276914.2	-	4	447	c.268A>G	c.(268-270)Att>Gtt	p.I90V	PLIN2_ENST00000411567.1_Missense_Mutation_p.I90V|PLIN2_ENST00000380464.3_Missense_Mutation_p.I90V|PLIN2_ENST00000380465.3_Missense_Mutation_p.I90V	NM_001122.3	NP_001113.2	Q99541	PLIN2_HUMAN	perilipin 2	90					cellular lipid metabolic process (GO:0044255)|lipid storage (GO:0019915)|long-chain fatty acid transport (GO:0015909)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	19						CTCTCCTCAATCCTGTCTAGC	0.413																																					p.I90V		Atlas-SNP	.											.	PLIN2	41	.	0			c.A268G						.						123	96	105					9																	19123604		2203	4300	6503	SO:0001583	missense	123	exon4			CCTCAATCCTGTC	X97324	CCDS6490.1	9p22.1	2009-08-12	2009-08-12	2009-08-12	ENSG00000147872	ENSG00000147872		"Perilipins"	248	protein-coding gene	gene with protein product	"adipophilin"	103195	"adipose differentiation-related protein"	ADFP		9003395, 19638644	Standard	NM_001122		Approved	ADRP	uc003zno.3	Q99541	OTTHUMG00000019624	ENST00000276914.2:c.268A>G	chr9.hg19:g.19123604T>C	ENSP00000276914:p.Ile90Val	130.0	0.0		96.0	4.0	NM_001122	Q9BSC3	Missense_Mutation	SNP	ENST00000276914.2	hg19	CCDS6490.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.222425	0.39300	.	.	ENSG00000147872	ENST00000411567;ENST00000276914;ENST00000434144;ENST00000380465;ENST00000380464	T;T;T;T;T	0.05717	3.4;3.4;3.4;3.4;3.4	5.94	4.8	0.61643	.	0.092733	0.64402	N	0.000001	T	0.06872	0.0175	L	0.47016	1.485	0.37812	D	0.928078	B;B	0.12630	0.006;0.005	B;B	0.21708	0.01;0.036	T	0.24440	-1.0160	10	0.15066	T	0.55	.	10.0527	0.42225	0.0:0.1355:0.0:0.8645	.	90;90	E9PG83;Q99541	.;PLIN2_HUMAN	V	90	ENSP00000415270:I90V;ENSP00000276914:I90V;ENSP00000403421:I90V;ENSP00000369832:I90V;ENSP00000369831:I90V	ENSP00000276914:I90V	I	-	1	0	PLIN2	19113604	1.000000	0.71417	0.999000	0.59377	0.837000	0.47467	3.724000	0.54962	1.054000	0.40438	0.482000	0.46254	ATT	.	.		0.413	PLIN2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051835.1	NM_001122		C	19123604	T	C	19123604	3	2	114	1	0	0	0	0	1	0	0	0	12099	1435	50	2	1065	2	PLIN2	9	19123604	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	29239	19123604	122089827	600	18872										
IFNA2	3440	hgsc.bcm.edu	37	chr9	21385289	21385289	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcagcttgacttgcagctgaGcaccaggagggccaccagta	13	12	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:21385289G>A	ENST00000380206.2	-	1	107	c.40C>T	c.(40-42)Ctc>Ttc	p.L14F		NM_000605.3	NP_000596.2	P01563	IFNA2_HUMAN	interferon, alpha 2	14					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of gene expression (GO:0010629)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	type I interferon receptor binding (GO:0005132)			breast(2)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	13				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		TTGCAGCTGAGCACCAGGAGG	0.537																																					p.L14F		Atlas-SNP	.											.	IFNA2	32	.	0			c.C40T						.						109	96	100					9																	21385289		2203	4300	6503	SO:0001583	missense	3440	exon1			AGCTGAGCACCAG		CCDS6506.1	9p22	2010-08-24			ENSG00000188379	ENSG00000188379		"Interferons"	5423	protein-coding gene	gene with protein product	"alpha-2a interferon", "interferon alpha 2b", "interferon alpha A"	147562				1385305	Standard	NM_000605		Approved	IFNA, IFN-alphaA	uc003zpb.3	P01563	OTTHUMG00000019674	ENST00000380206.2:c.40C>T	chr9.hg19:g.21385289G>A	ENSP00000369554:p.Leu14Phe	133.0	0.0		118.0	67.0	NM_000605	H2DF54|H2DF55|P01564|Q14606|Q6DJX8|Q96KI6	Missense_Mutation	SNP	ENST00000380206.2	hg19	CCDS6506.1	.	.	.	.	.	.	.	.	.	.	G	7.915	0.737272	0.15574	.	.	ENSG00000188379	ENST00000380206	T	0.03689	3.84	3.24	1.17	0.20885	.	0.094776	0.44688	D	0.000430	T	0.09423	0.0232	M	0.86097	2.795	0.09310	N	1	D	0.54047	0.964	P	0.50314	0.637	T	0.11036	-1.0604	10	0.52906	T	0.07	.	5.3592	0.16077	0.0:0.1916:0.3847:0.4236	.	14	Q6DJX8	.	F	14	ENSP00000369554:L14F	ENSP00000369554:L14F	L	-	1	0	IFNA2	21375289	0.004000	0.15560	0.002000	0.10522	0.013000	0.08279	0.405000	0.21015	0.052000	0.16007	0.484000	0.47621	CTC	.	.		0.537	IFNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051903.1	NM_000605		A	21385289	G	A	21385289	3	1	114	1	0	0	0	0	1	0	0	0	7546	971	34	3	530	3	IFNA2	9	21385289	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	2261685	21385289	119828142	601	18873										
TEK	7010	hgsc.bcm.edu	37	chr9	27157926	27157926	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcattgcctctgggtggcgCccccatgagcccatcaccat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:27157926delC	ENST00000380036.4	+	2	592	c.150delC	c.(148-150)cgcfs	p.R50fs	TEK_ENST00000519097.1_Intron|TEK_ENST00000406359.4_Frame_Shift_Del_p.R50fs	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	50	Ig-like C2-type 1.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CTGGGTGGCGCCCCCATGAGC	0.502																																					p.R50fs		Atlas-INDEL	.											TEK_ENST00000380036,caecum,carcinoma,0,1	TEK	250	.	0			c.149delG						.						145	128	134					9																	27157926		2203	4300	6503	SO:0001589	frameshift_variant	7010	exon2			.	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.150delC	chr9.hg19:g.27157926delC	ENSP00000369375:p.Arg50fs	184.0	0.0		133.0	10.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Frame_Shift_Del	DEL	ENST00000380036.4	hg19	CCDS6519.1																																																																																			.	.		0.502	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			-	27157926	C	-	27157926	7	5	114	1	0	1	0	1	0	0	0	0	15766	726	26	0	156	0	TEK	9	27157926	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	5772637	27157926	114055505	602	18874										
TEK	7010	hgsc.bcm.edu	37	chr9	27169566	27169566	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccccaggatgctggagtgtaCtcggccaggtatataggagg	15	9	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:27169566C>T	ENST00000380036.4	+	4	1009	c.567C>T	c.(565-567)taC>taT	p.Y189Y	TEK_ENST00000519097.1_Silent_p.Y85Y|TEK_ENST00000406359.4_Silent_p.Y189Y	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	189					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CTGGAGTGTACTCGGCCAGGT	0.512																																					p.Y189Y		Atlas-SNP	.											.	TEK	250	.	0			c.C567T						.						147	138	141					9																	27169566		2203	4300	6503	SO:0001819	synonymous_variant	7010	exon4			AGTGTACTCGGCC	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.567C>T	chr9.hg19:g.27169566C>T		94.0	0.0		77.0	4.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	hg19	CCDS6519.1																																																																																			.	.		0.512	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			T	27169566	C	T	27169566	2	4	114	1	0	0	0	0	0	0	0	1	15766	576	20	3		3	TEK	9	27169566	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	11640	27169566	114043865	603	18875										
LINGO2	158038	hgsc.bcm.edu	37	chr9	27950495	27950495	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actgaggtccaagattttggTttcgatgggaatgccctctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:27950495delT	ENST00000379992.2	-	6	624	c.175delA	c.(175-177)accfs	p.T59fs	LINGO2_ENST00000308675.3_Frame_Shift_Del_p.T59fs	NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	59						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		AAGATTTTGGTTTCGATGGGA	0.478																																					p.T59fs		Atlas-INDEL	.											.	LINGO2	244	.	0			c.176delC						.						180	183	182					9																	27950495		2203	4300	6503	SO:0001589	frameshift_variant	158038	exon7			.	AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482		"Immunoglobulin superfamily / I-set domain containing"	21207	protein-coding gene	gene with protein product		609793	"leucine rich repeat neuronal 6C"	LRRN6C		14686891	Standard	NM_152570		Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.175delA	chr9.hg19:g.27950495delT	ENSP00000369328:p.Thr59fs	352.0	0.0		232.0	15.0	NM_152570	A8K4K7|B2RPM5|Q6ZMD0	Frame_Shift_Del	DEL	ENST00000379992.2	hg19	CCDS6524.1																																																																																			.	.		0.478	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051978.2	NM_152570		-	27950495	T	-	27950495	7	5	114	1	0	1	0	1	0	0	0	0	8824	1725	60	0	1649	0	LINGO2	9	27950495	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	780929	27950495	113262936	604	18876										
DNAJA1	3301	hgsc.bcm.edu	37	chr9	33037024	33037024	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtttttaggtcagattgtcAagcatggagatatcaagtgt	11	4	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:33037024A>G	ENST00000330899.4	+	8	1069	c.886A>G	c.(886-888)Aag>Gag	p.K296E	DNAJA1_ENST00000495015.1_3'UTR|DNAJA1_ENST00000544625.1_Missense_Mutation_p.K139E	NM_001539.2	NP_001530.1	P31689	DNJA1_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 1	296					androgen receptor signaling pathway (GO:0030521)|DNA damage response, detection of DNA damage (GO:0042769)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of apoptotic process (GO:0043065)|protein folding (GO:0006457)|protein localization to mitochondrion (GO:0070585)|regulation of protein transport (GO:0051223)|response to heat (GO:0009408)|response to unfolded protein (GO:0006986)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasmic side of endoplasmic reticulum membrane (GO:0098554)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|G-protein coupled receptor binding (GO:0001664)|Hsp70 protein binding (GO:0030544)|low-density lipoprotein particle receptor binding (GO:0050750)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			large_intestine(2)|ovary(1)|skin(3)	6			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.102)		TCAGATTGTCAAGCATGGAGA	0.383																																					p.K296E		Atlas-SNP	.											.	DNAJA1	26	.	0			c.A886G						.						136	122	127					9																	33037024		2203	4300	6503	SO:0001583	missense	3301	exon8			ATTGTCAAGCATG	L08069	CCDS6533.1	9p13.3	2011-09-02			ENSG00000086061	ENSG00000086061		"Heat shock proteins / DNAJ (HSP40)"	5229	protein-coding gene	gene with protein product	"neural precursor cell expressed, developmentally down-regulated 7"	602837		HSJ2		8334160, 11147971	Standard	NM_001539		Approved	HSPF4, hdj-2, dj-2, NEDD7	uc003zsd.1	P31689	OTTHUMG00000019760	ENST00000330899.4:c.886A>G	chr9.hg19:g.33037024A>G	ENSP00000369127:p.Lys296Glu	51.0	0.0		82.0	4.0	NM_001539	Q5T7Q0|Q86TL9	Missense_Mutation	SNP	ENST00000330899.4	hg19	CCDS6533.1	.	.	.	.	.	.	.	.	.	.	A	17.15	3.316808	0.60524	.	.	ENSG00000086061	ENST00000330899;ENST00000539152;ENST00000544625	T;T	0.48522	0.81;0.81	5.33	5.33	0.75918	Chaperone DnaJ, C-terminal (1);HSP40/DnaJ peptide-binding (1);	0.000000	0.85682	D	0.000000	T	0.53818	0.1820	M	0.74389	2.26	0.80722	D	1	B;B	0.29481	0.118;0.245	B;B	0.37346	0.108;0.247	T	0.54774	-0.8243	10	0.40728	T	0.16	-19.7625	13.5499	0.61726	1.0:0.0:0.0:0.0	.	296;296	Q86TL9;P31689	.;DNJA1_HUMAN	E	296;139;139	ENSP00000369127:K296E;ENSP00000439010:K139E	ENSP00000369127:K296E	K	+	1	0	DNAJA1	33027024	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.465000	0.80898	2.157000	0.67596	0.482000	0.46254	AAG	.	.		0.383	DNAJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052031.1			G	33037024	A	G	33037024	3	3	114	1	0	0	0	0	1	0	0	0	4613	131	5	2	912	2	DNAJA1	9	33037024	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	5086529	33037024	108176407	605	18877										
ARID3C	138715	hgsc.bcm.edu	37	chr9	34625744	34625744	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catcatgccactcacccctcTtttgcatgaagctaaacagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:34625744delT	ENST00000378909.2	-	2	478	c.386delA	c.(385-387)aagfs	p.K129fs		NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	129	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		CTCACCCCTCTTTTGCATGAA	0.547																																					p.K129fs		Atlas-INDEL	.											.	ARID3C	33	.	0			c.387delG						.						196	157	170					9																	34625744		2203	4300	6503	SO:0001589	frameshift_variant	138715	exon2			.		CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"-"	21209	protein-coding gene	gene with protein product			"AT rich interactive domain 3C (BRIGHT- like)"				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.386delA	chr9.hg19:g.34625744delT	ENSP00000368189:p.Lys129fs	144.0	0.0		163.0	10.0	NM_001017363		Frame_Shift_Del	DEL	ENST00000378909.2	hg19	CCDS35006.1																																																																																			.	.		0.547	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061		-	34625744	T	-	34625744	7	5	114	1	0	1	0	1	0	0	0	0	918	1609	56	0	875	0	ARID3C	9	34625744	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1588720	34625744	106587687	606	18878										
TESK1	7016	hgsc.bcm.edu	37	chr9	35607647	35607647	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatggctccagaggtgttacGgggtgagctgtatgatgaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:35607647delG	ENST00000336395.5	+	6	939	c.689delG	c.(688-690)cggfs	p.R230fs	CD72_ENST00000490239.1_5'Flank|MIR4667_ENST00000578933.1_RNA|TESK1_ENST00000498522.1_3'UTR	NM_006285.2	NP_006276.2	Q15569	TESK1_HUMAN	testis-specific kinase 1	230	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell junction assembly (GO:0034329)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	27			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GAGGTGTTACGGGGTGAGCTG	0.582																																					p.R230fs		Atlas-INDEL	.											.	TESK1	46	.	0			c.688delC						.						99	94	96					9																	35607647		2203	4300	6503	SO:0001589	frameshift_variant	7016	exon6			.	D50863	CCDS6580.1	9p13	2010-04-27			ENSG00000107140	ENSG00000107140	2.7.12.1		11731	protein-coding gene	gene with protein product	"testis-specific kinase-1", "testis specific kinase-1"	601782				8537404	Standard	NM_006285		Approved		uc003zxa.3	Q15569	OTTHUMG00000019863	ENST00000336395.5:c.689delG	chr9.hg19:g.35607647delG	ENSP00000338127:p.Arg230fs	125.0	0.0		119.0	11.0	NM_006285	Q8IXZ8	Frame_Shift_Del	DEL	ENST00000336395.5	hg19	CCDS6580.1																																																																																			.	.		0.582	TESK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052314.1	NM_006285		-	35607647	G	-	35607647	7	5	114	1	0	1	0	1	0	0	0	0	15782	1116	39	0	711	0	TESK1	9	35607647	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	981903	35607647	105605784	607	18879										
C9orf128	392307	hgsc.bcm.edu	37	chr9	35825746	35825746	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggtagacctccttgtccatGggacctcattggaagaagac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:35825746delG	ENST00000423537.2	-	2	682	c.413delC	c.(412-414)ccafs	p.P138fs	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	138										endometrium(2)|kidney(1)|lung(4)	7						CCTTGTCCATGGGACCTCATT	0.498											OREG0019180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P138fs		Atlas-INDEL	.											.	FAM221B	38	.	0			c.414delA						.						206	195	198					9																	35825746		1905	4140	6045	SO:0001589	frameshift_variant	392307	exon2			.	BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 128"	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.413delC	chr9.hg19:g.35825746delG	ENSP00000415299:p.Pro138fs	109.0	0.0	858	140.0	11.0	NM_001012446	Q5TCW2	Frame_Shift_Del	DEL	ENST00000423537.2	hg19	CCDS43799.2																																																																																			.	.		0.498	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1	NM_001012446		-	35825746	G	-	35825746	7	5	114	1	0	1	0	1	0	0	0	0	2457	1348	47	0	819	0	C9orf128	9	35825746	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	218099	35825746	105387685	608	18880										
FAM75A1	642265	hgsc.bcm.edu	37	chr9	39890582	39890582	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accagtcactgctgagagccAaaaaacagtgaaaaacagat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:39890582delA	ENST00000456183.2	+	4	3598	c.3569delA	c.(3568-3570)caafs	p.Q1190fs		NM_001040065.1	NP_001035154.1	Q5RGS2	S31A2_HUMAN	SPATA31 subfamily A, member 2	1190					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GCTGAGAGCCAAAAAACAGTG	0.438																																					p.Q1190fs		Atlas-INDEL	.											.,1	.	.	.	0			c.3568delC						.						1	1	1					9																	39890582		1	3	4	SO:0001589	frameshift_variant	647060	exon4			.			9p13.1	2012-10-15	2012-10-12	2012-10-12	ENSG00000204848				32002	protein-coding gene	gene with protein product			"family with sequence similarity 75, member A2"	FAM75A2		20850414	Standard			Approved	OTTHUMG00000013563	uc004abm.3	Q5RGS2	OTTHUMG00000013563	ENST00000456183.2:c.3569delA	chr9.hg19:g.39890582delA	ENSP00000406957:p.Gln1190fs	153.0	0.0		187.0	14.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000456183.2	hg19	CCDS43809.1																																																																																			.	.		0.438	SPATA31A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037739.1	NM_001040065		-	39890582	A	-	39890582	7	5	114	1	0	1	0	1	0	0	0	0	5627	130	5	0	7643	0	FAM75A1	9	39890582	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	4064836	39890582	101322849	609	18881										
TMEM2	23670	hgsc.bcm.edu	37	chr9	74327107	74327107	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctatctggagttggcacataTtttttgaaagtgctccttgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:74327107delT	ENST00000377044.4	-	16	3200	c.2661delA	c.(2659-2661)aaafs	p.K887fs	TMEM2_ENST00000377066.5_Frame_Shift_Del_p.K824fs	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	887					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		TTGGCACATATTTTTTGAAAG	0.418																																					p.Y888fs		Atlas-INDEL	.											.	TMEM2	112	.	0			c.2662delT						.						136	125	129					9																	74327107		2203	4300	6503	SO:0001589	frameshift_variant	23670	exon16			.		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.2661delA	chr9.hg19:g.74327107delT	ENSP00000366243:p.Lys887fs	185.0	0.0		197.0	12.0	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Frame_Shift_Del	DEL	ENST00000377044.4	hg19	CCDS6638.1																																																																																			.	.		0.418	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		-	74327107	T	-	74327107	7	5	114	1	0	1	0	1	0	0	0	0	16136	1490	52	0	1526	0	TMEM2	9	74327107	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	34436525	74327107	66886324	610	18882										
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88204546	88204546	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcacataacacatctttccgAaaatagatttgctgaggatt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:88204546delA	ENST00000357081.3	-	20	2763	c.2619delT	c.(2617-2619)tttfs	p.F873fs	AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000432218.1_Intron|AGTPBP1_ENST00000376109.3_Frame_Shift_Del_p.F885fs|AGTPBP1_ENST00000376083.3_Frame_Shift_Del_p.F833fs			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	873					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						CATCTTTCCGAAAATAGATTT	0.343																																					p.R834fs		Atlas-INDEL	.											AGTPBP1,NS,carcinoma,0,1	AGTPBP1	128	.	0			c.2500delC						.						98	94	95					9																	88204546		2203	4299	6502	SO:0001589	frameshift_variant	23287	exon20			.	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.2619delT	chr9.hg19:g.88204546delA	ENSP00000349592:p.Phe873fs	93.0	0.0		142.0	10.0	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Frame_Shift_Del	DEL	ENST00000357081.3	hg19																																																																																				.	.		0.343	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		-	88204546	A	-	88204546	7	5	114	1	0	1	0	1	0	0	0	0	400	243	9	0	1089	0	AGTPBP1	9	88204546	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	13877439	88204546	53008885	611	18883										
OMD	4958	hgsc.bcm.edu	37	chr9	95179318	95179318	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agcatttgtctgcagtttggAgatttcattgtaaccaagaa	9	6	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:95179318A>G	ENST00000375550.4	-	2	798	c.523T>C	c.(523-525)Tcc>Ccc	p.S175P	CENPP_ENST00000375587.3_Intron	NM_005014.2	NP_005005.1	Q99983	OMD_HUMAN	osteomodulin	175					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|skin(2)	16						TGCAGTTTGGAGATTTCATTG	0.338			T	USP6	aneurysmal bone cysts																																p.S175P		Atlas-SNP	.		Dom	yes		9	9q22.31	4958	osteomodulin		M	.	OMD	42	.	0			c.T523C						.						107	106	106					9																	95179318		2203	4300	6503	SO:0001583	missense	4958	exon2			GTTTGGAGATTTC	AB000114	CCDS6696.1	9q22.31	2008-02-05			ENSG00000127083	ENSG00000127083		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8134	protein-coding gene	gene with protein product	"osteoadherin proteoglycan"						Standard	NM_005014		Approved	osteoadherin, SLRR2C	uc004asd.4	Q99983	OTTHUMG00000020225	ENST00000375550.4:c.523T>C	chr9.hg19:g.95179318A>G	ENSP00000364700:p.Ser175Pro	109.0	0.0		142.0	6.0	NM_005014	Q5TBF4	Missense_Mutation	SNP	ENST00000375550.4	hg19	CCDS6696.1	.	.	.	.	.	.	.	.	.	.	a	18.99	3.739644	0.69304	.	.	ENSG00000127083	ENST00000375550	T	0.05447	3.44	5.41	5.41	0.78517	.	0.080378	0.50627	D	0.000107	T	0.20780	0.0500	M	0.73753	2.245	0.46678	D	0.99915	D	0.76494	0.999	P	0.61477	0.889	T	0.00259	-1.1870	10	0.72032	D	0.01	-6.1556	11.7062	0.51599	0.8524:0.1476:0.0:0.0	.	175	Q99983	OMD_HUMAN	P	175	ENSP00000364700:S175P	ENSP00000364700:S175P	S	-	1	0	OMD	94219139	1.000000	0.71417	0.984000	0.44739	0.960000	0.62799	4.708000	0.61859	2.178000	0.69098	0.477000	0.44152	TCC	.	.		0.338	OMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053090.1	NM_005014		G	95179318	A	G	95179318	3	3	114	1	0	0	0	0	1	0	0	0	10874	304	11	2	750	2	OMD	9	95179318	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	6974772	95179318	46034113	612	18884										
SLC35D2	11046	hgsc.bcm.edu	37	chr9	99099002	99099002	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tatctatggtttcttaccccAaaaaacaggaaagaagaaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:99099002delA	ENST00000253270.7	-	9	811	c.749delT	c.(748-750)ttgfs	p.L250fs	SLC35D2_ENST00000375259.4_Intron	NM_007001.2	NP_008932.2	Q76EJ3	S35D2_HUMAN	solute carrier family 35 (UDP-GlcNAc/UDP-glucose transporter), member D2	250					carbohydrate derivative transport (GO:1901264)|carbohydrate metabolic process (GO:0005975)|carbohydrate transport (GO:0008643)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)			endometrium(3)|large_intestine(3)|lung(4)|skin(2)	12		Acute lymphoblastic leukemia(62;0.0167)				TTCTTACCCCAAAAAACAGGA	0.328																																					p.L250fs		Atlas-INDEL	.											.	SLC35D2	20	.	0			c.750delG						.						55	49	51					9																	99099002		2192	4297	6489	SO:0001589	frameshift_variant	11046	exon9			.	AB122077	CCDS6717.1, CCDS69625.1	9q22.33	2013-07-17	2013-07-17		ENSG00000130958	ENSG00000130958		"Solute carriers"	20799	protein-coding gene	gene with protein product		609182	"solute carrier family 35, member D2"			15607426	Standard	NM_007001		Approved	UGTrel8, SQV7L	uc004awc.3	Q76EJ3	OTTHUMG00000020293	ENST00000253270.7:c.749delT	chr9.hg19:g.99099002delA	ENSP00000253270:p.Leu250fs	115.0	0.0		149.0	10.0	NM_007001	O95454|Q498C1|Q75W21|Q7Z5X5	Frame_Shift_Del	DEL	ENST00000253270.7	hg19	CCDS6717.1																																																																																			.	.		0.328	SLC35D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053261.1			-	99099002	A	-	99099002	7	5	114	1	0	1	0	1	0	0	0	0	14597	131	5	0	280	0	SLC35D2	9	99099002	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3919684	99099002	42114429	613	18885										
NCBP1	4686	hgsc.bcm.edu	37	chr9	100429054	100429054	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atttctttaagattgtttgtTtgggaaattttgcactctac	7	5	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:100429054T>C	ENST00000375147.3	+	20	2167	c.1911T>C	c.(1909-1911)gtT>gtC	p.V637V		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	637					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				GATTGTTTGTTTGGGAAATTT	0.338																																					p.V637V	Ovarian(36;879 898 2893 44212 50307)	Atlas-SNP	.											.	NCBP1	64	.	0			c.T1911C						.						87	86	87					9																	100429054		2203	4300	6503	SO:0001819	synonymous_variant	4686	exon20			GTTTGTTTGGGAA	BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.1911T>C	chr9.hg19:g.100429054T>C		70.0	0.0		83.0	4.0	NM_002486	B2R718|Q59G76|Q5T1V0|Q5T7X2	Silent	SNP	ENST00000375147.3	hg19	CCDS6728.1																																																																																			.	.		0.338	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		C	100429054	T	C	100429054	2	2	114	1	0	0	0	0	0	0	0	1	10220	1828	64	2		2	NCBP1	9	100429054	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1330052	100429054	40784377	614	18886										
CORO2A	7464	hgsc.bcm.edu	37	chr9	100889088	100889088	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagctcagagccaggcctaaGggacaccaggattgggtctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:100889088delG	ENST00000343933.5	-	11	1446	c.1189delC	c.(1189-1191)cttfs	p.L397fs	CORO2A_ENST00000375077.4_Frame_Shift_Del_p.L397fs	NM_003389.3	NP_003380.3	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	397					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	actin cytoskeleton (GO:0015629)|transcriptional repressor complex (GO:0017053)	actin filament binding (GO:0051015)			endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|skin(4)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				CCAGGCCTAAGGGACACCAGG	0.602																																					p.L397fs		Atlas-INDEL	.											.	CORO2A	54	.	0			c.1190delT						.						72	74	73					9																	100889088		2203	4300	6503	SO:0001589	frameshift_variant	7464	exon11			.	U57057	CCDS6735.1	9q22.3	2013-01-10	2001-11-28		ENSG00000106789	ENSG00000106789		"Coronins", "WD repeat domain containing"	2255	protein-coding gene	gene with protein product	"coronin 2A", "coronin-like protein B", "WD protein IR10", "WD-repeat protein 2"	602159	"coronin, actin-binding protein, 2A"			8985118	Standard	NM_052820		Approved	IR10, WDR2	uc004aym.3	Q92828	OTTHUMG00000020340	ENST00000343933.5:c.1189delC	chr9.hg19:g.100889088delG	ENSP00000343746:p.Leu397fs	80.0	0.0		120.0	10.0	NM_003389	Q5TBR5|Q92829|Q9BWS5	Frame_Shift_Del	DEL	ENST00000343933.5	hg19	CCDS6735.1																																																																																			.	.		0.602	CORO2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053357.1	NM_003389		-	100889088	G	-	100889088	7	5	114	1	0	1	0	1	0	0	0	0	3758	1000	35	0	396	0	CORO2A	9	100889088	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	460034	100889088	40324343	615	18887										
COL15A1	1306	hgsc.bcm.edu	37	chr9	101829178	101829178	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttcagctgcatttggctgcTctgaacatgccattttctgg	9	10	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:101829178T>C	ENST00000375001.3	+	40	4089	c.3666T>C	c.(3664-3666)gcT>gcC	p.A1222A		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	1222	Nonhelical region 10 (NC10).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				ATTTGGCTGCTCTGAACATGC	0.478																																					p.A1222A		Atlas-SNP	.											.	COL15A1	211	.	0			c.T3666C						.						116	107	110					9																	101829178		2203	4300	6503	SO:0001819	synonymous_variant	1306	exon40			GGCTGCTCTGAAC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.3666T>C	chr9.hg19:g.101829178T>C		80.0	0.0		102.0	5.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	hg19	CCDS35081.1																																																																																			.	.		0.478	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		C	101829178	T	C	101829178	2	2	114	1	0	0	0	0	0	0	0	1	3674	1538	54	2		2	COL15A1	9	101829178	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	940090	101829178	39384253	616	18888										
ABCA1	19	hgsc.bcm.edu	37	chr9	107581925	107581925	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgggagtaagggtccacaccAgctgtgggttcatccagaat	13	10	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:107581925A>G	ENST00000374736.3	-	22	3577	c.3183T>C	c.(3181-3183)gcT>gcC	p.A1061A		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1061	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	GGTCCACACCAGCTGTGGGTT	0.488																																					p.A1061A		Atlas-SNP	.											.	ABCA1	244	.	0			c.T3183C						.						111	114	113					9																	107581925		2203	4300	6503	SO:0001819	synonymous_variant	19	exon22			CACACCAGCTGTG	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.3183T>C	chr9.hg19:g.107581925A>G		147.0	0.0		132.0	6.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	hg19	CCDS6762.1																																																																																			.	.		0.488	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		G	107581925	A	G	107581925	2	3	114	1	0	0	0	0	0	0	0	1	28	175	7	2		2	ABCA1	9	107581925	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	5752747	107581925	33631506	617	18889										
PTGR1	22949	hgsc.bcm.edu	37	chr9	114355220	114355220	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattacttggccacttgctgCcccatcattgtatcaccttc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:114355220delC	ENST00000407693.2	-	4	457	c.195delG	c.(193-195)gggfs	p.G65fs	PTGR1_ENST00000238248.3_5'UTR|PTGR1_ENST00000309195.5_Frame_Shift_Del_p.G65fs|PTGR1_ENST00000538962.1_Frame_Shift_Del_p.G65fs	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	65					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						CCACTTGCTGCCCCATCATTG	0.368																																					p.Q66fs	Ovarian(200;132 2151 7551 19220 46064)	Atlas-INDEL	.											.	PTGR1	23	.	0			c.196delC						.						109	99	102					9																	114355220		2203	4300	6503	SO:0001589	frameshift_variant	22949	exon4			.	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.195delG	chr9.hg19:g.114355220delC	ENSP00000385763:p.Gly65fs	134.0	0.0		208.0	15.0	NM_001146108	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Frame_Shift_Del	DEL	ENST00000407693.2	hg19	CCDS6779.1																																																																																			.	.		0.368	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			-	114355220	C	-	114355220	7	5	114	1	0	1	0	1	0	0	0	0	12766	726	26	0	853	0	PTGR1	9	114355220	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	6773295	114355220	26858211	618	18890										
FKBP15	23307	hgsc.bcm.edu	37	chr9	115931867	115931867	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctcaggtggaattgaagtcGggggccctagaactctgtgg					rs370970009		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:115931867delG	ENST00000238256.3	-	26	3239	c.3122delC	c.(3121-3123)ccgfs	p.P1041fs		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1041					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						AATTGAAGTCGGGGGCCCTAG	0.557																																					p.P1041fs		Atlas-INDEL	.											.	FKBP15	128	.	0			c.3123delG						.						84	88	87					9																	115931867		1901	4126	6027	SO:0001589	frameshift_variant	23307	exon26			.	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23397	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 76", "WASP and FKBP-like protein"		"KIAA0674"	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.3122delC	chr9.hg19:g.115931867delG	ENSP00000238256:p.Pro1041fs	146.0	0.0		202.0	13.0	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Frame_Shift_Del	DEL	ENST00000238256.3	hg19	CCDS48007.1																																																																																			.	.		0.557	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258		-	115931867	G	-	115931867	7	5	114	1	0	1	0	1	0	0	0	0	5913	1116	39	0	549	0	FKBP15	9	115931867	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1576647	115931867	25281564	619	18891										
RGS3	5998	hgsc.bcm.edu	37	chr9	116359110	116359110	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgcagagcgtcacgcggggCtgcttcgacctggcacagaa	14	13	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:116359110C>T	ENST00000374140.2	+	26	3683	c.3474C>T	c.(3472-3474)ggC>ggT	p.G1158G	RGS3_ENST00000462403.1_Silent_p.G271G|RGS3_ENST00000350696.5_Silent_p.G1158G|RGS3_ENST00000343817.5_Silent_p.G877G|RGS3_ENST00000374134.3_Silent_p.G479G|RGS3_ENST00000342620.5_Silent_p.G128G|RGS3_ENST00000394646.3_Silent_p.G551G|RGS3_ENST00000462143.1_Silent_p.G479G	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	1158	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						TCACGCGGGGCTGCTTCGACC	0.602																																					p.G1158G		Atlas-SNP	.											.	RGS3	251	.	0			c.C3474T						.						142	111	121					9																	116359110		2203	4300	6503	SO:0001819	synonymous_variant	5998	exon26			GCGGGGCTGCTTC	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"Regulators of G-protein signaling"	9999	protein-coding gene	gene with protein product		602189	"regulator of G-protein signalling 3"			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3474C>T	chr9.hg19:g.116359110C>T		111.0	0.0		144.0	6.0	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Silent	SNP	ENST00000374140.2	hg19	CCDS43869.1																																																																																			.	.		0.602	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		T	116359110	C	T	116359110	2	4	114	1	0	0	0	0	0	0	0	1	13321	784	28	3		3	RGS3	9	116359110	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	427243	116359110	24854321	620	18892										
COL27A1	85301	hgsc.bcm.edu	37	chr9	117052561	117052561	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggagacagggcctcgagggcAtcgctggaccagatgggctt	17	10	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:117052561A>T	ENST00000356083.3	+	47	4709	c.4318A>T	c.(4318-4320)Atc>Ttc	p.I1440F		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1440	Collagen-like 13.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						CCTCGAGGGCATCGCTGGACC	0.647																																					p.I1440F		Atlas-SNP	.											.	COL27A1	200	.	0			c.A4318T						.						29	23	25					9																	117052561		2191	4287	6478	SO:0001583	missense	85301	exon47			GAGGGCATCGCTG	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4318A>T	chr9.hg19:g.117052561A>T	ENSP00000348385:p.Ile1440Phe	186.0	0.0		211.0	27.0	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	A	8.277	0.814710	0.16607	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.96136	-3.92	5.32	-5.66	0.02451	.	.	.	.	.	D	0.88581	0.6475	L	0.35414	1.06	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.76252	-0.3027	9	0.54805	T	0.06	.	2.8828	0.05653	0.5308:0.1868:0.1822:0.1003	.	1440	Q8IZC6	CORA1_HUMAN	F	1440	ENSP00000348385:I1440F	ENSP00000348385:I1440F	I	+	1	0	COL27A1	116092382	0.000000	0.05858	0.000000	0.03702	0.978000	0.69477	0.013000	0.13310	-0.840000	0.04206	0.402000	0.26972	ATC	.	.		0.647	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		T	117052561	A	T	117052561	3	4	114	1	0	0	0	0	1	0	0	0	3687	217	8	4	4504	4	COL27A1	9	117052561	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	693451	117052561	24160870	621	18893										
CEP110	11064	hgsc.bcm.edu	37	chr9	123857214	123857214	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aacttgaagtactgaatctcAgctataatctaatagggaag	8	6	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:123857214A>G	ENST00000373855.1	+	5	657	c.397A>G	c.(397-399)Agc>Ggc	p.S133G	CNTRL_ENST00000238341.5_Missense_Mutation_p.S133G|CNTRL_ENST00000373865.2_Missense_Mutation_p.S133G			Q7Z7A1	CNTRL_HUMAN	centriolin	133					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						ACTGAATCTCAGCTATAATCT	0.284																																					p.S133G		Atlas-SNP	.											.	CNTRL	161	.	0			c.A397G						.						75	78	77					9																	123857214		2202	4298	6500	SO:0001583	missense	11064	exon3			AATCTCAGCTATA	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.397A>G	chr9.hg19:g.123857214A>G	ENSP00000362962:p.Ser133Gly	80.0	0.0		86.0	4.0	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	18.99	3.740140	0.69304	.	.	ENSG00000119397	ENST00000373865;ENST00000373855;ENST00000238341;ENST00000454238	T;T	0.54675	0.56;0.56	5.57	5.57	0.84162	.	.	.	.	.	T	0.66781	0.2824	L	0.56280	1.765	0.41027	D	0.985122	D	0.69078	0.997	D	0.70716	0.97	T	0.66284	-0.5962	9	0.39692	T	0.17	.	14.9182	0.70815	1.0:0.0:0.0:0.0	.	133	Q7Z7A1	CNTRL_HUMAN	G	133	ENSP00000362962:S133G;ENSP00000238341:S133G	ENSP00000238341:S133G	S	+	1	0	CNTRL	122897035	1.000000	0.71417	1.000000	0.80357	0.720000	0.41350	7.343000	0.79319	2.123000	0.65237	0.533000	0.62120	AGC	.	.		0.284	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123857214	A	G	123857214	3	3	114	1	0	0	0	0	1	0	0	0	3247	188	7	2	407	2	CEP110	9	123857214	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	6804653	123857214	17356217	622	18894										
LHX2	9355	hgsc.bcm.edu	37	chr9	126774713	126774713	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caagagcgaggctcccgccaTcagctccgccatcgaccgcg	11	18	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:126774713T>C	ENST00000373615.4	+	1	825	c.86T>C	c.(85-87)aTc>aCc	p.I29T	RP11-85O21.4_ENST00000421041.1_RNA	NM_004789.3	NP_004780.3	P50458	LHX2_HUMAN	LIM homeobox 2	29					axon extension (GO:0048675)|axon guidance (GO:0007411)|cerebral cortex development (GO:0021987)|dorsal/ventral pattern formation (GO:0009953)|mesoderm development (GO:0007498)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural tube closure (GO:0001843)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|retina development in camera-type eye (GO:0060041)|telencephalon regionalization (GO:0021978)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)	10						GCTCCCGCCATCAGCTCCGCC	0.726																																					p.I29T		Atlas-SNP	.											.	LHX2	30	.	0			c.T86C						.						6	8	7					9																	126774713		2081	4114	6195	SO:0001583	missense	9355	exon1			CCGCCATCAGCTC	U11701	CCDS6853.1	9q33.3	2011-06-20			ENSG00000106689	ENSG00000106689		"Homeoboxes / LIM class"	6594	protein-coding gene	gene with protein product		603759				8649822, 10051612	Standard	NM_004789		Approved	LH-2, hLhx2	uc004boe.1	P50458	OTTHUMG00000020647	ENST00000373615.4:c.86T>C	chr9.hg19:g.126774713T>C	ENSP00000362717:p.Ile29Thr	41.0	0.0		45.0	4.0	NM_004789	O95860|Q52M57|Q8N1Z3	Missense_Mutation	SNP	ENST00000373615.4	hg19	CCDS6853.1	.	.	.	.	.	.	.	.	.	.	t	14.81	2.645110	0.47258	.	.	ENSG00000106689	ENST00000373615	D	0.83335	-1.71	5.07	3.93	0.45458	.	0.000000	0.85682	D	0.000000	T	0.69682	0.3138	L	0.27053	0.805	0.41898	D	0.990408	P;B	0.36789	0.57;0.421	B;B	0.32465	0.146;0.027	T	0.65417	-0.6173	10	0.33141	T	0.24	.	9.9851	0.41837	0.0:0.0806:0.0:0.9194	.	29;29	B3KNJ5;P50458	.;LHX2_HUMAN	T	29	ENSP00000362717:I29T	ENSP00000362717:I29T	I	+	2	0	LHX2	125814534	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.874000	0.69652	0.778000	0.33520	0.414000	0.27820	ATC	.	.		0.726	LHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054010.2			C	126774713	T	C	126774713	3	2	114	1	0	0	0	0	1	0	0	0	8780	1435	50	2	88	2	LHX2	9	126774713	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2917499	126774713	14438718	623	18895										
GARNL3	84253	hgsc.bcm.edu	37	chr9	130087373	130087373	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctggttcttgaagaacaagAggtgagtaattctatggaga	13	4	2	5			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:130087373A>G	ENST00000373387.4	+	7	945	c.593A>G	c.(592-594)gAg>gGg	p.E198G	GARNL3_ENST00000435213.2_Splice_Site_p.E176G|GARNL3_ENST00000314904.5_Splice_Site_p.E198G	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	198	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						GAAGAACAAGAGGTGAGTAAT	0.373																																					p.E198G		Atlas-SNP	.											.	GARNL3	83	.	0			c.A593G						.						119	105	110					9																	130087373		2203	4300	6503	SO:0001630	splice_region_variant	84253	exon7			AACAAGAGGTGAG	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.594+1A>G	chr9.hg19:g.130087373A>G		74.0	0.0		96.0	4.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	hg19	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	A	20.2	3.955707	0.73902	.	.	ENSG00000136895	ENST00000439286;ENST00000373399;ENST00000435213;ENST00000314904;ENST00000373387	D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28	5.91	5.91	0.95273	Rap/ran-GAP (1);	0.192085	0.53938	D	0.000052	D	0.94689	0.8287	L	0.44542	1.39	0.58432	D	0.999992	D;D	0.76494	0.998;0.999	D;D	0.69654	0.965;0.931	D	0.94073	0.7337	9	.	.	.	.	15.1723	0.72884	1.0:0.0:0.0:0.0	.	198;176	Q5VVW2;B7Z3Q6	GARL3_HUMAN;.	G	221;221;176;198;198	ENSP00000400579:E221G;ENSP00000396205:E176G;ENSP00000313970:E198G;ENSP00000362485:E198G	.	E	+	2	0	GARNL3	129127194	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.078000	0.76821	2.254000	0.74563	0.533000	0.62120	GAG	.	.		0.373	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293	Missense_Mutation	G	130087373	A	G	130087373	5	3	114	1	0	0	0	0	0	0	1	0	6249	318	11	2	619	2	GARNL3	9	130087373	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3312660	130087373	11126058	624	18896										
GARNL3	84253	hgsc.bcm.edu	37	chr9	130107748	130107748	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggcagcttcagggatctgtAaaaaagaggtgagttcatga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:130107748delA	ENST00000373387.4	+	16	1775	c.1423delA	c.(1423-1425)aaafs	p.K476fs	GARNL3_ENST00000435213.2_Frame_Shift_Del_p.K454fs|GARNL3_ENST00000314904.5_Frame_Shift_Del_p.K476fs	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	476					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						AGGGATCTGTAAAAAAGAGGT	0.363																																					p.C474X		Atlas-INDEL	.											.	GARNL3	83	.	0			c.1422delT						.						95	94	94					9																	130107748		2203	4300	6503	SO:0001589	frameshift_variant	84253	exon16			.	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.1423delA	chr9.hg19:g.130107748delA	ENSP00000362485:p.Lys476fs	140.0	0.0		162.0	13.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Frame_Shift_Del	DEL	ENST00000373387.4	hg19	CCDS6869.2																																																																																			.	.		0.363	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		-	130107748	A	-	130107748	7	5	114	1	0	1	0	1	0	0	0	0	6249	363	13	0	1485	0	GARNL3	9	130107748	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	20375	130107748	11105683	625	18897										
GARNL3	84253	hgsc.bcm.edu	37	chr9	130116628	130116628	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctctgcaaaagggccttgaGgggaagcaggctgggaagag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:130116628delG	ENST00000373387.4	+	19	2050	c.1698delG	c.(1696-1698)gagfs	p.E566fs	GARNL3_ENST00000435213.2_Frame_Shift_Del_p.E544fs|GARNL3_ENST00000314904.5_Frame_Shift_Del_p.E566fs	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	566	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						AGGGCCTTGAGGGGAAGCAGG	0.438																																					p.E566fs		Atlas-INDEL	.											.	GARNL3	83	.	0			c.1697delA						.						75	77	77					9																	130116628		2203	4300	6503	SO:0001589	frameshift_variant	84253	exon19			.	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.1698delG	chr9.hg19:g.130116628delG	ENSP00000362485:p.Glu566fs	126.0	0.0		155.0	10.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Frame_Shift_Del	DEL	ENST00000373387.4	hg19	CCDS6869.2																																																																																			.	.		0.438	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		-	130116628	G	-	130116628	7	5	114	1	0	1	0	1	0	0	0	0	6249	991	35	0	1772	0	GARNL3	9	130116628	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	8880	130116628	11096803	626	18898										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131374459	131374459	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcggaaaagagccagaaactGaaagaagccaacaagcagca	11	9	0	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:131374459G>C	ENST00000372731.4	+	38	5072	c.4962G>C	c.(4960-4962)ctG>ctC	p.L1654L	SPTAN1_ENST00000372739.3_Silent_p.L1659L|SPTAN1_ENST00000358161.5_Silent_p.L1659L	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1654					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GCCAGAAACTGAAAGAAGCCA	0.522																																					p.L1659L	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.G4977C						.						125	124	125					9																	131374459		2203	4300	6503	SO:0001819	synonymous_variant	6709	exon39			GAAACTGAAAGAA	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4962G>C	chr9.hg19:g.131374459G>C		123.0	0.0		196.0	85.0	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	hg19	CCDS6905.1																																																																																			.	.		0.522	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		C	131374459	G	C	131374459	2	2	114	1	0	0	0	0	0	0	0	1	15132	1277	45	4		4	SPTAN1	9	131374459	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1257831	131374459	9838972	627	18899										
NUP214	8021	hgsc.bcm.edu	37	chr9	134073130	134073130	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttttggcagtctgccagtcAccagtgcaggatcctctggg	12	11	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:134073130A>G	ENST00000359428.5	+	29	4393	c.4249A>G	c.(4249-4251)Acc>Gcc	p.T1417A	NUP214_ENST00000483497.2_Missense_Mutation_p.T243A|NUP214_ENST00000451030.1_Missense_Mutation_p.T1418A|NUP214_ENST00000465486.2_3'UTR|NUP214_ENST00000411637.2_Missense_Mutation_p.T1407A			P35658	NU214_HUMAN	nucleoporin 214kDa	1417	11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TCTGCCAGTCACCAGTGCAGG	0.537			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.T1417A	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.A4249G						.						84	82	83					9																	134073130		2203	4300	6503	SO:0001583	missense	8021	exon29			CCAGTCACCAGTG	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4249A>G	chr9.hg19:g.134073130A>G	ENSP00000352400:p.Thr1417Ala	87.0	0.0		89.0	4.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.441630	0.43326	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497;ENST00000531600;ENST00000541688	T;T;T;T;T	0.56103	1.32;1.33;1.41;0.82;0.48	5.58	-6.7	0.01766	.	0.329934	0.21905	N	0.067390	T	0.18467	0.0443	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.23377	0.084;0.021;0.084;0.001;0.0	B;B;B;B;B	0.18561	0.022;0.022;0.022;0.004;0.003	T	0.06552	-1.0820	10	0.31617	T	0.26	-1.6062	0.5819	0.00713	0.2944:0.2331:0.267:0.2056	.	243;846;1011;1407;1417	B7ZAV2;F5H131;Q5JUP9;P35658-4;P35658	.;.;.;.;NU214_HUMAN	A	1417;1407;1418;1396;1011;846;243;194;194	ENSP00000352400:T1417A;ENSP00000396576:T1407A;ENSP00000405014:T1418A;ENSP00000436793:T243A;ENSP00000435364:T194A	ENSP00000352400:T1417A	T	+	1	0	NUP214	133062951	0.000000	0.05858	0.000000	0.03702	0.550000	0.35303	-0.408000	0.07169	-1.319000	0.02286	0.402000	0.26972	ACC	.	.		0.537	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		G	134073130	A	G	134073130	3	3	114	1	0	0	0	0	1	0	0	0	10771	159	6	2	4363	2	NUP214	9	134073130	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2698671	134073130	7140301	628	18900										
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134514137	134514137	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accagcgaatgaggttggcgAggctttggtacactcggcta	14	9	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:134514137A>G	ENST00000372189.3	-	5	608	c.485T>C	c.(484-486)cTc>cCc	p.L162P	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.L180P|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.L179P|RAPGEF1_ENST00000481260.1_5'UTR	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	162					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		GAGGTTGGCGAGGCTTTGGTA	0.498																																					p.L180P		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.T539C						.						75	75	75					9																	134514137		2047	4202	6249	SO:0001583	missense	2889	exon5			TTGGCGAGGCTTT	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.485T>C	chr9.hg19:g.134514137A>G	ENSP00000361263:p.Leu162Pro	142.0	0.0		199.0	8.0	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	hg19	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.662359	0.88251	.	.	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000357686;ENST00000438647;ENST00000427994	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.64483	0.2602	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.68055	-0.5510	10	0.87932	D	0	.	15.263	0.73640	1.0:0.0:0.0:0.0	.	179;162;180	Q68DL3;Q13905;Q13905-3	.;RPGF1_HUMAN;.	P	162;179;56;162;180;142;88;179;141;180	ENSP00000361269:L179P;ENSP00000361263:L162P;ENSP00000361264:L180P;ENSP00000410640:L141P;ENSP00000402174:L180P	ENSP00000266110:L162P	L	-	2	0	RAPGEF1	133503958	1.000000	0.71417	0.977000	0.42913	0.986000	0.74619	8.661000	0.91125	2.206000	0.71126	0.455000	0.32223	CTC	.	.		0.498	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		G	134514137	A	G	134514137	3	3	114	1	0	0	0	0	1	0	0	0	13058	304	11	2	2828	2	RAPGEF1	9	134514137	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	441007	134514137	6699294	629	18901										
SETX	23064	hgsc.bcm.edu	37	chr9	135173586	135173586	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agacatggctttcaacttccTttgtgtagttaccagagaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:135173586delT	ENST00000224140.5	-	13	5844	c.5662delA	c.(5662-5664)aggfs	p.R1888fs	SETX_ENST00000393220.1_Frame_Shift_Del_p.R1888fs|SETX_ENST00000372169.2_Frame_Shift_Del_p.R1888fs	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1888					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TTCAACTTCCTTTGTGTAGTT	0.413																																					p.R1888fs		Atlas-INDEL	.											.	SETX	234	.	0			c.5663delG						.						135	125	128					9																	135173586		2203	4300	6503	SO:0001589	frameshift_variant	23064	exon13			.	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.5662delA	chr9.hg19:g.135173586delT	ENSP00000224140:p.Arg1888fs	155.0	0.0		174.0	11.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Frame_Shift_Del	DEL	ENST00000224140.5	hg19	CCDS6947.1																																																																																			.	.		0.413	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		-	135173586	T	-	135173586	7	5	114	1	0	1	0	1	0	0	0	0	14156	1608	56	0	2427	0	SETX	9	135173586	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	659449	135173586	6039845	630	18902										
SARDH	1757	hgsc.bcm.edu	37	chr9	136559454	136559454	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagtcaggtcactctcggtgCccccacggtggttgagcatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:136559454delC	ENST00000371872.4	-	15	2104	c.1847delG	c.(1846-1848)ggcfs	p.G616fs	SARDH_ENST00000371868.1_Frame_Shift_Del_p.G44fs|SARDH_ENST00000439388.1_Frame_Shift_Del_p.G616fs|SARDH_ENST00000422262.2_Frame_Shift_Del_p.G448fs	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	616					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		ACTCTCGGTGCCCCCACGGTG	0.677																																					p.G616fs		Atlas-INDEL	.											.	SARDH	112	.	0			c.1848delC						.						41	33	36					9																	136559454		1923	3716	5639	SO:0001589	frameshift_variant	1757	exon15			.		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1847delG	chr9.hg19:g.136559454delC	ENSP00000360938:p.Gly616fs	225.0	0.0		273.0	17.0	NM_001134707	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Frame_Shift_Del	DEL	ENST00000371872.4	hg19	CCDS6978.1																																																																																			.	.		0.677	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			-	136559454	C	-	136559454	7	5	114	1	0	1	0	1	0	0	0	0	13856	739	26	0	937	0	SARDH	9	136559454	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1385868	136559454	4653977	631	18903										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137726974	137726974	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagctacgacaaggccctccGcttcctgggctccaacgacg	10	17	0	0	rs150608071		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:137726974G>A	ENST00000371817.3	+	65	5708	c.5294G>A	c.(5293-5295)cGc>cAc	p.R1765H		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1765	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AAGGCCCTCCGCTTCCTGGGC	0.657													G|||	1	0.000199681	0	0	5008	,	,		16790	0		0.001	False		,,,				2504	0				p.R1765H		Atlas-SNP	.											.	COL5A1	323	.	0			c.G5294A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	89	70	76		5294	5	1	9	dbSNP_134	76	0,8600		0,0,4300	no	missense	COL5A1	NM_000093.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1765/1839	137726974	1,13005	2203	4300	6503	SO:0001583	missense	1289	exon65			CCCTCCGCTTCCT	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.5294G>A	chr9.hg19:g.137726974G>A	ENSP00000360882:p.Arg1765His	122.0	0.0		129.0	53.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.612809	0.87258	2.27E-4	0.0	ENSG00000130635	ENST00000371817;ENST00000355306	T	0.74632	-0.86	5.03	5.03	0.67393	Fibrillar collagen, C-terminal (4);	0.000000	0.64402	U	0.000002	T	0.82263	0.4999	L	0.41961	1.31	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82165	-0.0592	10	0.44086	T	0.13	.	18.3643	0.90385	0.0:0.0:1.0:0.0	.	1765	P20908	CO5A1_HUMAN	H	1765;302	ENSP00000360882:R1765H	ENSP00000347458:R302H	R	+	2	0	COL5A1	136866795	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.659000	0.98597	2.340000	0.79590	0.561000	0.74099	CGC	.	G|1.000;A|0.000		0.657	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137726974	G	A	137726974	3	1	114	1	0	0	0	0	1	0	0	0	3698	1087	38	1	5552	1	COL5A1	9	137726974	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1167520	137726974	3486457	632	18904										
SOHLH1	402381	hgsc.bcm.edu	37	chr9	138586277	138586277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcagcaggaaggacgtcccaTcgtccacatcagaccccaac	8	16	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:138586277T>C	ENST00000298466.5	-	7	962	c.902A>G	c.(901-903)gAt>gGt	p.D301G	SOHLH1_ENST00000425225.1_Missense_Mutation_p.D301G	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1	301					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(5)|prostate(1)	12		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		GGACGTCCCATCGTCCACATC	0.627																																					p.D301G		Atlas-SNP	.											.	SOHLH1	70	.	0			c.A902G						.						80	67	71					9																	138586277		2202	4300	6502	SO:0001583	missense	402381	exon7			GTCCCATCGTCCA	BC031861	CCDS35174.1, CCDS48054.1	9q34.3	2013-05-21	2006-03-16	2006-03-16	ENSG00000165643	ENSG00000165643		"Basic helix-loop-helix proteins"	27845	protein-coding gene	gene with protein product	"spermatogenesis associated 27"	610224	"chromosome 9 open reading frame 157"	C9orf157		12477932	Standard	NM_001012415		Approved	NOHLH, TEB2, bA100C15.3, bHLHe80, SPATA27	uc010nbe.3	Q5JUK2	OTTHUMG00000020915	ENST00000298466.5:c.902A>G	chr9.hg19:g.138586277T>C	ENSP00000298466:p.Asp301Gly	40.0	0.0		68.0	4.0	NM_001012415	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Missense_Mutation	SNP	ENST00000298466.5	hg19	CCDS35174.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.007886	0.54361	.	.	ENSG00000165643	ENST00000298466;ENST00000425225	T;T	0.39229	1.25;1.09	4.08	2.93	0.34026	.	0.244290	0.21097	N	0.080233	T	0.33585	0.0868	L	0.52573	1.65	0.19775	N	0.999957	B;B	0.27013	0.166;0.104	B;B	0.24974	0.057;0.026	T	0.32981	-0.9886	10	0.87932	D	0	-12.8959	6.1542	0.20328	0.0:0.1175:0.0:0.8825	.	301;301	Q5JUK2-2;Q5JUK2	.;SOLH1_HUMAN	G	301	ENSP00000298466:D301G;ENSP00000404438:D301G	ENSP00000298466:D301G	D	-	2	0	SOHLH1	137726098	0.005000	0.15991	0.021000	0.16686	0.011000	0.07611	0.507000	0.22675	0.739000	0.32628	0.444000	0.29173	GAT	.	.		0.627	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		C	138586277	T	C	138586277	3	2	114	1	0	0	0	0	1	0	0	0	14938	1435	50	2	310	2	SOHLH1	9	138586277	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	859303	138586277	2627154	633	18905										
UBAC1	10422	hgsc.bcm.edu	37	chr9	138845578	138845578	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaagtggtgatggagcacgcTtttttatcaataataggaca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:138845578delT	ENST00000371756.3	-	3	498	c.281delA	c.(280-282)aagfs	p.K94fs		NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	94	Ubiquitin-like.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		TGGAGCACGCTTTTTTATCAA	0.408																																					p.K94fs	NSCLC(78;973 1398 27381 29552 42415)	Atlas-INDEL	.											.	UBAC1	40	.	0			c.282delG						.						85	79	81					9																	138845578		2203	4300	6503	SO:0001589	frameshift_variant	10422	exon3			.	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"ubiquitin associated domain containing 1"	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.281delA	chr9.hg19:g.138845578delT	ENSP00000360821:p.Lys94fs	116.0	0.0		120.0	10.0	NM_016172	O75500|Q9UMW7	Frame_Shift_Del	DEL	ENST00000371756.3	hg19	CCDS35177.1																																																																																			.	.		0.408	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172		-	138845578	T	-	138845578	7	5	114	1	0	1	0	1	0	0	0	0	16849	1609	56	0	968	0	UBAC1	9	138845578	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	259301	138845578	2367853	634	18906										
CARD9	64170	hgsc.bcm.edu	37	chr9	139266450	139266450	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggtaaggtgtgatgcgtgaGgggtcgatgaccgaggtgag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:139266450delG	ENST00000371732.5	-	2	246	c.81delC	c.(79-81)cccfs	p.P27fs	CARD9_ENST00000315908.7_Frame_Shift_Del_p.P27fs|CARD9_ENST00000371734.3_Frame_Shift_Del_p.P27fs	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	27	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)	p.P27P(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		TGATGCGTGAGGGGTCGATGA	0.622																																					p.S28fs		Atlas-INDEL	.											.	CARD9	47	.	1	Substitution - coding silent(1)	kidney(1)	c.82delT						.						155	118	130					9																	139266450		2203	4300	6503	SO:0001589	frameshift_variant	64170	exon2			.	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.81delC	chr9.hg19:g.139266450delG	ENSP00000360797:p.Pro27fs	146.0	0.0		174.0	11.0	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Frame_Shift_Del	DEL	ENST00000371732.5	hg19	CCDS6997.1																																																																																			.	.		0.622	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813		-	139266450	G	-	139266450	7	5	114	1	0	1	0	1	0	0	0	0	2654	987	35	0	1630	0	CARD9	9	139266450	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	420872	139266450	1946981	635	18907										
SDCCAG3	10807	hgsc.bcm.edu	37	chr9	139303504	139303504	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctgcttagaacatttccccTttccatagccaaaatctgca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:139303504delT	ENST00000357365.3	-	3	365	c.236delA	c.(235-237)aagfs	p.K79fs	PMPCA_ENST00000371720.1_5'Flank|SDCCAG3_ENST00000298537.7_Intron|SDCCAG3_ENST00000371725.3_Intron|PMPCA_ENST00000371717.3_5'Flank|PMPCA_ENST00000399219.3_5'Flank	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	79						cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		ACATTTCCCCTTTCCATAGCC	0.453																																					p.K79fs		Atlas-INDEL	.											.	SDCCAG3	41	.	0			c.237delG						.						133	139	137					9																	139303504		1938	4146	6084	SO:0001589	frameshift_variant	10807	exon3			.	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.236delA	chr9.hg19:g.139303504delT	ENSP00000349929:p.Lys79fs	127.0	0.0		151.0	10.0	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Frame_Shift_Del	DEL	ENST00000357365.3	hg19	CCDS43904.1																																																																																			.	.		0.453	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643		-	139303504	T	-	139303504	7	5	114	1	0	1	0	1	0	0	0	0	13973	1609	56	0	1103	0	SDCCAG3	9	139303504	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	37054	139303504	1909927	636	18908										
LCN15	389812	hgsc.bcm.edu	37	chr9	139656669	139656669	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcagcatgaccatcatgtccTtggggagccccagggtcggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:139656669delT	ENST00000316144.5	-	5	515	c.491delA	c.(490-492)aagfs	p.K164fs	LCN15_ENST00000482511.1_5'UTR	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15	164			K -> E (in dbSNP:rs2297722).		lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						CATCATGTCCTTGGGGAGCCC	0.647																																					p.K164fs		Atlas-INDEL	.											.	LCN15	11	.	0			c.492delG						.						18	19	19					9																	139656669		2190	4295	6485	SO:0001589	frameshift_variant	389812	exon5			.		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"Lipocalins"	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943	ENST00000316144.5:c.491delA	chr9.hg19:g.139656669delT	ENSP00000313833:p.Lys164fs	167.0	0.0		226.0	14.0	NM_203347		Frame_Shift_Del	DEL	ENST00000316144.5	hg19	CCDS7006.1																																																																																			.	.		0.647	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347		-	139656669	T	-	139656669	7	5	114	1	0	1	0	1	0	0	0	0	8692	1609	56	0	71	0	LCN15	9	139656669	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	353165	139656669	1556762	637	18909										
MAMDC4	158056	hgsc.bcm.edu	37	chr9	139753286	139753286	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctccgcttctggtaccacatGggttttcctgagcacttctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:139753286delG	ENST00000317446.2	+	23	2987	c.2937delG	c.(2935-2937)atgfs	p.M979fs	MAMDC4_ENST00000485732.1_3'UTR|MAMDC4_ENST00000445819.1_Frame_Shift_Del_p.M1058fs	NM_206920.2	NP_996803.2			MAM domain containing 4											breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	19	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		GGTACCACATGGGTTTTCCTG	0.706																																					p.M979fs		Atlas-INDEL	.											.	MAMDC4	117	.	0			c.2936delT						.						17	20	19					9																	139753286		2190	4295	6485	SO:0001589	frameshift_variant	158056	exon23			.	AL834531	CCDS7010.1	9q34.3	2013-10-21			ENSG00000177943	ENSG00000177943			24083	protein-coding gene	gene with protein product	"apical early endosomal glycoprotein precursor", "endotubin"					7829488	Standard	NM_206920		Approved	AEGP, DKFZp434M1411	uc004cjs.3	Q6UXC1	OTTHUMG00000020951	ENST00000317446.2:c.2937delG	chr9.hg19:g.139753286delG	ENSP00000319388:p.Met979fs	112.0	0.0		110.0	10.0	NM_206920		Frame_Shift_Del	DEL	ENST00000317446.2	hg19	CCDS7010.1																																																																																			.	.		0.706	MAMDC4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254642.3	NM_206920		-	139753286	G	-	139753286	7	5	114	1	0	1	0	1	0	0	0	0	9213	1348	47	0	3027	0	MAMDC4	9	139753286	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	96617	139753286	1460145	638	18910										
TPRN	286262	hgsc.bcm.edu	37	chr9	140087119	140087119	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctcaaatgtggtctgcaggcTtttgtcgttgaaggagatct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:140087119delT	ENST00000409012.4	-	2	1836	c.1750delA	c.(1750-1752)agcfs	p.S584fs	TPRN_ENST00000541945.1_5'UTR|TPRN_ENST00000321773.2_Frame_Shift_Del_p.S523fs	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	584					sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						GTCTGCAGGCTTTTGTCGTTG	0.587																																					p.S584fs		Atlas-INDEL	.											.	TPRN	28	.	0			c.1751delG						.						98	91	94					9																	140087119		2203	4300	6503	SO:0001589	frameshift_variant	286262	exon2			.	AK074735	CCDS56594.1	9q34.3	2011-01-06	2010-03-24	2010-03-24	ENSG00000176058	ENSG00000176058			26894	protein-coding gene	gene with protein product		613354	"chromosome 9 open reading frame 75", "deafness, autosomal recessive 79"	C9orf75, DFNB79		20170898, 20170899	Standard	NM_001128228		Approved	FLJ90254	uc004clu.3	Q4KMQ1	OTTHUMG00000020984	ENST00000409012.4:c.1750delA	chr9.hg19:g.140087119delT	ENSP00000387100:p.Ser584fs	122.0	0.0		164.0	12.0	NM_001128228	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Frame_Shift_Del	DEL	ENST00000409012.4	hg19	CCDS56594.1																																																																																			.	.		0.587	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691		-	140087119	T	-	140087119	7	5	114	1	0	1	0	1	0	0	0	0	16436	1609	56	0	477	0	TPRN	9	140087119	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	333833	140087119	1126312	639	18911										
EXD3	54932	hgsc.bcm.edu	37	chr9	140268006	140268006	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catgtccagaagcccggccaGggggtcgtccaaggcagcaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:140268006delG	ENST00000340951.4	-	4	361	c.166delC	c.(166-168)ctgfs	p.L56fs	EXD3_ENST00000342129.4_5'UTR|EXD3_ENST00000479452.1_Frame_Shift_Del_p.L56fs|EXD3_ENST00000475006.1_5'UTR	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0	Pro-rich.									NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						AGCCCGGCCAGGGGGTCGTCC	0.662																																					p.L56fs		Atlas-INDEL	.											.	EXD3	86	.	0			c.167delT						.						7	9	8					9																	140268006		1855	4043	5898	SO:0001589	frameshift_variant	54932	exon4			.		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.166delC	chr9.hg19:g.140268006delG	ENSP00000340474:p.Leu56fs	151.0	0.0		183.0	11.0	NM_017820	Q6P1M1|Q8IXT8	Frame_Shift_Del	DEL	ENST00000340951.4	hg19	CCDS48066.1																																																																																			.	.		0.662	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820		-	140268006	G	-	140268006	7	5	114	1	0	1	0	1	0	0	0	0	5301	991	35	0	2540	0	EXD3	9	140268006	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	180887	140268006	945425	640	18912										
PNPLA7	375775	hgsc.bcm.edu	37	chr9	140356679	140356679	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agggtgctgtagctgtcgatGggggggcgcaggtactcgca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:140356679delG	ENST00000277531.4	-	30	3708	c.3522delC	c.(3520-3522)cccfs	p.P1174fs	NSMF_ENST00000392812.4_5'Flank|NSMF_ENST00000265663.7_5'Flank|NSMF_ENST00000371473.3_5'Flank|PNPLA7_ENST00000371457.1_Frame_Shift_Del_p.P780fs|NSMF_ENST00000371475.3_5'Flank|PNPLA7_ENST00000406427.1_Frame_Shift_Del_p.P1199fs|NSMF_ENST00000371474.3_5'Flank|PNPLA7_ENST00000492278.1_5'UTR|NSMF_ENST00000371472.2_5'Flank|NSMF_ENST00000437259.1_5'Flank	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1174					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		AGCTGTCGATGGGGGGGCGCA	0.652																																					p.I1200fs		Atlas-INDEL	.											.	PNPLA7	124	.	0			c.3598delA						.						46	43	44					9																	140356679		2203	4298	6501	SO:0001589	frameshift_variant	375775	exon31			.	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"Patatin-like phospholipase domain containing"	24768	protein-coding gene	gene with protein product		612122	"chromosome 9 open reading frame 111"	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.3522delC	chr9.hg19:g.140356679delG	ENSP00000277531:p.Pro1174fs	165.0	0.0		166.0	10.0	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Frame_Shift_Del	DEL	ENST00000277531.4	hg19	CCDS7045.1																																																																																			.	.		0.652	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286		-	140356679	G	-	140356679	7	5	114	1	0	1	0	1	0	0	0	0	12179	1335	47	0	451	0	PNPLA7	9	140356679	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	88673	140356679	856752	641	18913										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7605064	7605064	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcagagctccctggacattCcccggccaagtgtccatccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:7605064delC	ENST00000256861.6	-	14	2889	c.2811delG	c.(2809-2811)gggfs	p.G937fs	ITIH5_ENST00000397146.2_Intron|ITIH5_ENST00000446830.2_Frame_Shift_Del_p.G718fs|ITIH5_ENST00000298441.6_Frame_Shift_Del_p.G723fs	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	0					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CCTGGACATTCCCCGGCCAAG	0.542																																					p.G937fs		Atlas-INDEL	.											.	ITIH5	343	.	0			c.2811delA						.						188	180	183					10																	7605064		2203	4300	6503	SO:0001589	frameshift_variant	80760	exon15			.			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.2811delG	chr10.hg19:g.7605064delC	ENSP00000256861:p.Gly937fs	172.0	0.0		172.0	11.0	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Frame_Shift_Del	DEL	ENST00000256861.6	hg19																																																																																				.	.		0.542	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		-	7605064	C	-	7605064	7	5	114	1	0	1	0	1	0	0	0	0	7916	842	30	0	63	0	ITIH5	10	7605064	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10		7605064	127929683	642	18914										
ITIH2	3698	hgsc.bcm.edu	37	chr10	7751097	7751097	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaacaattccccgcagcctcAgaatgtcgtgtttgatgttc	9	11	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:7751097A>G	ENST00000358415.4	+	4	471	c.305A>G	c.(304-306)cAg>cGg	p.Q102R	ITIH2_ENST00000480387.1_Intron|ITIH2_ENST00000379587.4_Missense_Mutation_p.Q91R	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	102	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CCGCAGCCTCAGAATGTCGTG	0.443																																					p.Q102R		Atlas-SNP	.											.	ITIH2	144	.	0			c.A305G						.						137	129	131					10																	7751097		2203	4300	6503	SO:0001583	missense	3698	exon4			AGCCTCAGAATGT	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.305A>G	chr10.hg19:g.7751097A>G	ENSP00000351190:p.Gln102Arg	117.0	0.0		153.0	7.0	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	hg19	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	A	15.21	2.766878	0.49574	.	.	ENSG00000151655	ENST00000358415;ENST00000429820;ENST00000379587	T;T;T	0.23754	1.89;1.89;1.89	5.79	4.65	0.58169	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.054507	0.85682	N	0.000000	T	0.26304	0.0642	L	0.50993	1.605	0.58432	D	0.999998	B	0.20988	0.05	B	0.31686	0.134	T	0.03761	-1.1006	10	0.22706	T	0.39	-13.5033	11.7175	0.51661	0.931:0.0:0.069:0.0	.	102	P19823	ITIH2_HUMAN	R	102;77;91	ENSP00000351190:Q102R;ENSP00000388826:Q77R;ENSP00000368906:Q91R	ENSP00000351190:Q102R	Q	+	2	0	ITIH2	7791103	1.000000	0.71417	0.852000	0.33557	0.799000	0.45148	7.163000	0.77524	1.021000	0.39600	0.477000	0.44152	CAG	.	.		0.443	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		G	7751097	A	G	7751097	3	3	114	1	0	0	0	0	1	0	0	0	7913	188	7	2	319	2	ITIH2	10	7751097	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	146033	7751097	127783650	643	18915										
USP6NL	9712	hgsc.bcm.edu	37	chr10	11505825	11505825	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggaagctgccccaagggctTctttggatattcatcctctt	9	11	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:11505825T>C	ENST00000609104.1	-	15	1496	c.1102A>G	c.(1102-1104)Aag>Gag	p.K368E	USP6NL_ENST00000277575.5_Missense_Mutation_p.K385E|USP6NL_ENST00000379237.2_Missense_Mutation_p.K391E	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	368					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						CCCAAGGGCTTCTTTGGATAT	0.507																																					p.K385E		Atlas-SNP	.											.	USP6NL	57	.	0			c.A1153G						.						20	24	23					10																	11505825		1883	4089	5972	SO:0001583	missense	9712	exon14			AGGGCTTCTTTGG	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"related to the N terminus of tre"	605405	"USP6NL intronic transcript 1 (non-protein coding)"	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.1102A>G	chr10.hg19:g.11505825T>C	ENSP00000476462:p.Lys368Glu	64.0	0.0		82.0	4.0	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	hg19	CCDS53492.1	.	.	.	.	.	.	.	.	.	.	T	18.13	3.554638	0.65425	.	.	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.05081	3.5;3.51	5.53	5.53	0.82687	.	0.146826	0.64402	D	0.000012	T	0.23806	0.0576	M	0.75447	2.3	0.58432	D	0.999999	D;D	0.61697	0.983;0.99	P;D	0.66084	0.874;0.941	T	0.00478	-1.1715	10	0.45353	T	0.12	.	15.6709	0.77274	0.0:0.0:0.0:1.0	.	368;385	Q92738;Q92738-2	US6NL_HUMAN;.	E	368;385;368	ENSP00000277575:K385E;ENSP00000368539:K368E	ENSP00000277575:K385E	K	-	1	0	USP6NL	11545831	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	5.754000	0.68743	2.099000	0.63709	0.482000	0.46254	AAG	.	.		0.507	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688		C	11505825	T	C	11505825	3	2	114	1	0	0	0	0	1	0	0	0	17102	1792	62	2	1388	2	USP6NL	10	11505825	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3754728	11505825	124028922	644	18916										
DHTKD1	55526	hgsc.bcm.edu	37	chr10	12154919	12154919	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atgtgtgacagtgcggaagaGggggtggacggagacactgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:12154919delG	ENST00000263035.4	+	13	2237	c.2175delG	c.(2173-2175)gagfs	p.E725fs		NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	725					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			GTGCGGAAGAGGGGGTGGACG	0.493																																					p.E725fs		Atlas-INDEL	.											.	DHTKD1	104	.	0			c.2174delA						.						162	142	149					10																	12154919		2203	4300	6503	SO:0001589	frameshift_variant	55526	exon13			.	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2175delG	chr10.hg19:g.12154919delG	ENSP00000263035:p.Glu725fs	111.0	0.0		154.0	12.0	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Frame_Shift_Del	DEL	ENST00000263035.4	hg19	CCDS7087.1																																																																																			.	.		0.493	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		-	12154919	G	-	12154919	7	5	114	1	0	1	0	1	0	0	0	0	4502	991	35	0	2225	0	DHTKD1	10	12154919	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	649094	12154919	123379828	645	18917										
PHYH	5264	hgsc.bcm.edu	37	chr10	13336580	13336580	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttcacctcctttctgcagaTtttttcaaactcattcctag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:13336580delT	ENST00000263038.4	-	4	320	c.262delA	c.(262-264)atcfs	p.I88fs	PHYH_ENST00000396920.3_Frame_Shift_Del_p.I69fs|PHYH_ENST00000396913.2_5'UTR	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	88					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|isoprenoid metabolic process (GO:0006720)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|electron carrier activity (GO:0009055)|L-ascorbic acid binding (GO:0031418)|metal ion binding (GO:0046872)|phytanoyl-CoA dioxygenase activity (GO:0048244)			NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	TTTCTGCAGATTTTTTCAAAC	0.433																																					p.I88fs		Atlas-INDEL	.											.	PHYH	50	.	0			c.263delT						.						112	103	106					10																	13336580		2203	4300	6503	SO:0001589	frameshift_variant	5264	exon4			.		CCDS7097.1, CCDS41489.1	10p13	2010-04-27	2006-01-09		ENSG00000107537	ENSG00000107537	1.14.11.18		8940	protein-coding gene	gene with protein product	"Refsum disease", "phytanoyl-CoA dioxygenase"	602026	"phytanoyl-CoA hydroxylase (Refsum disease)", "phytanoyl-CoA hydroxylase"			9326939	Standard	XM_005252469		Approved	PAHX, RD, PHYH1	uc001imf.3	O14832	OTTHUMG00000017693	ENST00000263038.4:c.262delA	chr10.hg19:g.13336580delT	ENSP00000263038:p.Ile88fs	157.0	0.0		166.0	10.0	NM_006214	A8MTS8|B1ALH5	Frame_Shift_Del	DEL	ENST00000263038.4	hg19	CCDS7097.1																																																																																			.	.		0.433	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2			-	13336580	T	-	13336580	7	5	114	1	0	1	0	1	0	0	0	0	11873	1493	52	0	778	0	PHYH	10	13336580	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1181661	13336580	122198167	646	18918										
CUBN	8029	hgsc.bcm.edu	37	chr10	17113457	17113457	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtttcacagtgggcagaacTtccaatttcaaagacagtga	9	8	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:17113457T>C	ENST00000377833.4	-	19	2658	c.2593A>G	c.(2593-2595)Agt>Ggt	p.S865G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	865	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGGGCAGAACTTCCAATTTCA	0.383																																					p.S865G		Atlas-SNP	.											.	CUBN	515	.	0			c.A2593G						.						85	83	84					10																	17113457		2203	4300	6503	SO:0001583	missense	8029	exon19			CAGAACTTCCAAT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2593A>G	chr10.hg19:g.17113457T>C	ENSP00000367064:p.Ser865Gly	77.0	0.0		122.0	5.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	8.706	0.910891	0.17833	.	.	ENSG00000107611	ENST00000377833	T	0.18338	2.22	5.47	-1.12	0.09808	CUB (5);	0.458452	0.18463	N	0.140464	T	0.04724	0.0128	N	0.04245	-0.25	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.40308	-0.9570	10	0.02654	T	1	.	5.2611	0.15573	0.0:0.2753:0.262:0.4627	.	865	O60494	CUBN_HUMAN	G	865	ENSP00000367064:S865G	ENSP00000367064:S865G	S	-	1	0	CUBN	17153463	0.000000	0.05858	0.211000	0.23655	0.894000	0.52154	0.479000	0.22228	-0.189000	0.10482	0.411000	0.27672	AGT	.	.		0.383	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	17113457	T	C	17113457	3	2	114	1	0	0	0	0	1	0	0	0	4053	1609	56	2	8474	2	CUBN	10	17113457	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3776877	17113457	118421290	647	18919										
NEBL	10529	hgsc.bcm.edu	37	chr10	21134239	21134239	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtaaaaattctggagtcttgTctaaatccagtgatgacctt	8	7	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:21134239T>C	ENST00000377122.4	-	12	1571	c.1175A>G	c.(1174-1176)gAc>gGc	p.D392G	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	392					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TGGAGTCTTGTCTAAATCCAG	0.308																																					p.D392G		Atlas-SNP	.											.	NEBL	199	.	0			c.A1175G						.						132	131	131					10																	21134239		2203	4300	6503	SO:0001583	missense	10529	exon12			GTCTTGTCTAAAT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1175A>G	chr10.hg19:g.21134239T>C	ENSP00000366326:p.Asp392Gly	47.0	0.0		80.0	5.0	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	hg19	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.651277	0.88056	.	.	ENSG00000078114	ENST00000377122	T	0.06218	3.33	5.99	5.99	0.97316	.	0.050585	0.85682	D	0.000000	T	0.18800	0.0451	L	0.57536	1.79	0.80722	D	1	D	0.62365	0.991	D	0.63703	0.917	T	0.00785	-1.1567	10	0.32370	T	0.25	.	14.0175	0.64533	0.0:0.0:0.0:1.0	.	392	O76041	NEBL_HUMAN	G	392	ENSP00000366326:D392G	ENSP00000366326:D392G	D	-	2	0	NEBL	21174245	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.303000	0.65738	2.291000	0.77112	0.533000	0.62120	GAC	.	.		0.308	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		C	21134239	T	C	21134239	3	2	114	1	0	0	0	0	1	0	0	0	10312	1667	58	2	1937	2	NEBL	10	21134239	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4020782	21134239	114400508	648	18920										
BMI1	648	hgsc.bcm.edu	37	chr10	22618212	22618212	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaagatcagtcaccagagagAtggactgacaaatgctggag	13	7	2	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:22618212A>G	ENST00000376663.3	+	10	1227	c.722A>G	c.(721-723)gAt>gGt	p.D241G	COMMD3-BMI1_ENST00000602390.1_Missense_Mutation_p.D384G	NM_005180.8	NP_005171.4	P35226	BMI1_HUMAN	BMI1 proto-oncogene, polycomb ring finger	241					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|regulation of gene expression (GO:0010468)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|ubiquitin ligase complex (GO:0000151)	RING-like zinc finger domain binding (GO:0071535)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|urinary_tract(1)	12						CACCAGAGAGATGGACTGACA	0.438																																					p.D384G		Atlas-SNP	.											.	.	.	.	0			c.A1151G						.						64	61	62					10																	22618212		2203	4300	6503	SO:0001583	missense	0	exon14			AGAGAGATGGACT	BC011652	CCDS7138.1	10p13	2014-06-26	2014-06-26	2006-04-26	ENSG00000168283	ENSG00000168283		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	1066	protein-coding gene	gene with protein product		164831	"polycomb group ring finger 4", "B lymphoma Mo-MLV insertion region 1 homolog (mouse)"	PCGF4		8268912	Standard	NM_005180		Approved	RNF51		P35226	OTTHUMG00000017807	ENST00000376663.3:c.722A>G	chr10.hg19:g.22618212A>G	ENSP00000365851:p.Asp241Gly	61.0	0.0		66.0	4.0	NM_001204062	Q16030|Q5T8Z3|Q96F37	Missense_Mutation	SNP	ENST00000376663.3	hg19	CCDS7138.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.195977	0.38806	.	.	ENSG00000168283	ENST00000376691;ENST00000376663;ENST00000443519	T;T	0.47869	1.44;0.83	5.68	5.68	0.88126	.	0.211158	0.52532	D	0.000079	T	0.24160	0.0585	N	0.02011	-0.69	0.52099	D	0.999949	B;B	0.22080	0.003;0.064	B;B	0.20767	0.004;0.031	T	0.12372	-1.0550	10	0.30854	T	0.27	-16.8412	14.7675	0.69651	1.0:0.0:0.0:0.0	.	241;241	Q5U0M5;P35226	.;BMI1_HUMAN	G	153;241;146	ENSP00000365851:D241G;ENSP00000390768:D146G	ENSP00000365851:D241G	D	+	2	0	BMI1	22658218	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.908000	0.75730	2.169000	0.68431	0.528000	0.53228	GAT	.	.		0.438	BMI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047176.1	NM_005180		G	22618212	A	G	22618212	3	3	114	1	0	0	0	0	1	0	0	0	1455	333	12	2	756	2	BMI1	10	22618212	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1483973	22618212	112916535	649	18921										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26359089	26359089	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aactgccagtcctcctcacaTttttgcaatggctgacttag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:26359089delT	ENST00000265944.5	+	13	1386	c.1220delT	c.(1219-1221)attfs	p.I407fs	MYO3A_ENST00000543632.1_Frame_Shift_Del_p.I407fs	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	407	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CCTCCTCACATTTTTGCAATG	0.318																																					p.I407fs		Atlas-INDEL	.											.	MYO3A	371	.	0			c.1219delA						.						69	70	70					10																	26359089		2202	4300	6502	SO:0001589	frameshift_variant	53904	exon13			.	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1220delT	chr10.hg19:g.26359089delT	ENSP00000265944:p.Ile407fs	149.0	0.0		174.0	11.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Frame_Shift_Del	DEL	ENST00000265944.5	hg19	CCDS7148.1																																																																																			.	.		0.318	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		-	26359089	T	-	26359089	7	5	114	1	0	1	0	1	0	0	0	0	10085	1493	52	0	1262	0	MYO3A	10	26359089	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3740877	26359089	109175658	650	18922										
YME1L1	10730	hgsc.bcm.edu	37	chr10	27408356	27408356	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaaaagccaacagtacctcgAgctataatttctggatcaac	7	10	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:27408356A>G	ENST00000326799.3	-	15	1753	c.1605T>C	c.(1603-1605)gcT>gcC	p.A535A	YME1L1_ENST00000376016.3_Silent_p.A478A|YME1L1_ENST00000375972.3_Silent_p.A445A	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	535					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						CAGTACCTCGAGCTATAATTT	0.403																																					p.A535A		Atlas-SNP	.											.	YME1L1	71	.	0			c.T1605C						.						73	72	72					10																	27408356		2203	4300	6503	SO:0001819	synonymous_variant	10730	exon15			ACCTCGAGCTATA	AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"ATPases / AAA-type"	12843	protein-coding gene	gene with protein product		607472	"YME1 (S.cerevisiae)-like 1", "YME1-like 1 (S. cerevisiae)"			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.1605T>C	chr10.hg19:g.27408356A>G		43.0	0.0		65.0	4.0	NM_139312	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Silent	SNP	ENST00000326799.3	hg19	CCDS7152.1																																																																																			.	.		0.403	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312		G	27408356	A	G	27408356	2	3	114	1	0	0	0	0	0	0	0	1	17502	291	11	2		2	YME1L1	10	27408356	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1049267	27408356	108126391	651	18923										
SVIL	6840	hgsc.bcm.edu	37	chr10	29822101	29822101	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggaggtttggggacattctGggtggctgatgctacccagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:29822101delG	ENST00000355867.4	-	8	1947	c.1195delC	c.(1195-1197)cagfs	p.Q399fs	SVIL_ENST00000375398.2_Frame_Shift_Del_p.Q399fs|SVIL_ENST00000375400.3_Intron	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	399					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GGGACATTCTGGGTGGCTGAT	0.537																																					p.Q399fs		Atlas-INDEL	.											.	SVIL	226	.	0			c.1196delA						.						81	67	72					10																	29822101		2203	4300	6503	SO:0001589	frameshift_variant	6840	exon8			.	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1195delC	chr10.hg19:g.29822101delG	ENSP00000348128:p.Gln399fs	168.0	0.0		197.0	13.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Frame_Shift_Del	DEL	ENST00000355867.4	hg19	CCDS7164.1																																																																																			.	.		0.537	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			-	29822101	G	-	29822101	7	5	114	1	0	1	0	1	0	0	0	0	15436	1357	47	0	5573	0	SVIL	10	29822101	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2413745	29822101	105712646	652	18924										
KIF5B	3799	hgsc.bcm.edu	37	chr10	32320045	32320045	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagcaattcatattccttagTtttgtcttcaacttcctgag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:32320045delT	ENST00000302418.4	-	14	1994	c.1537delA	c.(1537-1539)actfs	p.T513fs		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	513					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)		KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				TATTCCTTAGTTTTGTCTTCA	0.318			T	"RET, ALK"	NSCLC																																p.T513fs		Atlas-INDEL	.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	KIF5B	81	.	0			c.1538delC						.						104	102	103					10																	32320045		2203	4300	6503	SO:0001589	frameshift_variant	3799	exon14			.	X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.1537delA	chr10.hg19:g.32320045delT	ENSP00000307078:p.Thr513fs	121.0	0.0		145.0	11.0	NM_004521	A0AVB2|Q5VZ85	Frame_Shift_Del	DEL	ENST00000302418.4	hg19	CCDS7171.1																																																																																			.	.		0.318	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		-	32320045	T	-	32320045	7	5	114	1	0	1	0	1	0	0	0	0	8315	1725	60	0	1402	0	KIF5B	10	32320045	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2497944	32320045	103214702	653	18925										
FZD8	8325	hgsc.bcm.edu	37	chr10	35929138	35929138	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accagatggagctggccatgCcgaagaagtagaccagcaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:35929138delC	ENST00000374694.1	-	1	1224	c.1220delG	c.(1219-1221)ggcfs	p.G407fs	MIR4683_ENST00000579659.1_RNA	NM_031866.2	NP_114072.1	Q9H461	FZD8_HUMAN	frizzled class receptor 8	407					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	11						GCTGGCCATGCCGAAGAAGTA	0.642																																					p.G407fs		Atlas-INDEL	.											.	FZD8	41	.	0			c.1221delC						.						57	56	57					10																	35929138		2203	4300	6503	SO:0001589	frameshift_variant	8325	exon1			.	AB043703	CCDS7192.1	10p11.2	2014-01-29	2014-01-29		ENSG00000177283	ENSG00000177283		"GPCR / Class F : Frizzled receptors"	4046	protein-coding gene	gene with protein product		606146	"frizzled (Drosophila) homolog 8", "frizzled homolog 8 (Drosophila)", "frizzled 8, seven transmembrane spanning receptor", "frizzled family receptor 8"			11295046	Standard	NM_031866		Approved		uc001iyz.1	Q9H461	OTTHUMG00000017956	ENST00000374694.1:c.1220delG	chr10.hg19:g.35929138delC	ENSP00000363826:p.Gly407fs	61.0	0.0		117.0	10.0	NM_031866		Frame_Shift_Del	DEL	ENST00000374694.1	hg19	CCDS7192.1																																																																																			.	.		0.642	FZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047575.2	NM_031866		-	35929138	C	-	35929138	7	5	114	1	0	1	0	1	0	0	0	0	6144	739	26	0	868	0	FZD8	10	35929138	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3609093	35929138	99605609	654	18926										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37505286	37505286	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaaatcacagttagagaaccAaaaagttaaatgggaacaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:37505286delA	ENST00000602533.1	+	32	2978	c.2879delA	c.(2878-2880)caafs	p.Q960fs	ANKRD30A_ENST00000361713.1_Frame_Shift_Del_p.Q960fs|ANKRD30A_ENST00000374660.1_Frame_Shift_Del_p.Q1079fs			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1016					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						TTAGAGAACCAAAAAGTTAAA	0.313																																					p.Q960fs		Atlas-INDEL	.											.	ANKRD30A	448	.	0			c.2878delC						.						75	76	76					10																	37505286		1831	4079	5910	SO:0001589	frameshift_variant	91074	exon32			.	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.2879delA	chr10.hg19:g.37505286delA	ENSP00000473551:p.Gln960fs	277.0	0.0		363.0	25.0	NM_052997	Q5W025	Frame_Shift_Del	DEL	ENST00000602533.1	hg19																																																																																				.	.		0.313	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		-	37505286	A	-	37505286	7	5	114	1	0	1	0	1	0	0	0	0	658	130	5	0	3005	0	ANKRD30A	10	37505286	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1576148	37505286	98029461	655	18927										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37508625	37508625	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattatttcaactacaaagcAaaaatatgtggcttcaacag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:37508625delA	ENST00000602533.1	+	34	3916	c.3817delA	c.(3817-3819)aaafs	p.K1273fs	ANKRD30A_ENST00000361713.1_Frame_Shift_Del_p.K1273fs|ANKRD30A_ENST00000374660.1_Frame_Shift_Del_p.K1392fs			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1329					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						ACTACAAAGCAAAAATATGTG	0.343																																					p.S1272fs		Atlas-INDEL	.											.	ANKRD30A	448	.	0			c.3816delC						.						53	48	50					10																	37508625		1854	4093	5947	SO:0001589	frameshift_variant	91074	exon34			.	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.3817delA	chr10.hg19:g.37508625delA	ENSP00000473551:p.Lys1273fs	135.0	0.0		199.0	12.0	NM_052997	Q5W025	Frame_Shift_Del	DEL	ENST00000602533.1	hg19																																																																																				.	.		0.343	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		-	37508625	A	-	37508625	7	5	114	1	0	1	0	1	0	0	0	0	658	131	5	0	3951	0	ANKRD30A	10	37508625	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3339	37508625	98026122	656	18928										
ZNF248	57209	hgsc.bcm.edu	37	chr10	38121237	38121237	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cattgtaatcataagactttCcccccatgtgtactatttga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:38121237delC	ENST00000395867.3	-	6	1596	c.1046delG	c.(1045-1047)ggafs	p.G349fs	AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000494133.1_Intron|ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000357328.4_Frame_Shift_Del_p.G349fs	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	349					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						ATAAGACTTTCCCCCCATGTG	0.398																																					p.G349fs		Atlas-INDEL	.											.	ZNF248	61	.	0			c.1047delA						.						107	103	104					10																	38121237		2203	4299	6502	SO:0001589	frameshift_variant	57209	exon6			.	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"Zinc fingers, C2H2-type", "-"	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.1046delG	chr10.hg19:g.38121237delC	ENSP00000379208:p.Gly349fs	172.0	0.0		243.0	15.0	NM_021045	Q8NDV8|Q9UMP3	Frame_Shift_Del	DEL	ENST00000395867.3	hg19	CCDS7194.1																																																																																			.	.		0.398	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		-	38121237	C	-	38121237	7	5	114	1	0	1	0	1	0	0	0	0	17808	855	30	0	697	0	ZNF248	10	38121237	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	612612	38121237	97413510	657	18929										
RUFY2	55680	hgsc.bcm.edu	37	chr10	70139221	70139221	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggctgcagtaattttattggTtttttcttctagtcgggcaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:70139221delT	ENST00000602465.1	-	12	1265	c.1165delA	c.(1165-1167)accfs	p.T389fs	RUFY2_ENST00000472394.2_5'Flank|RUFY2_ENST00000454950.2_Frame_Shift_Del_p.T331fs|RUFY2_ENST00000265865.3_5'Flank|RUFY2_ENST00000399200.2_Frame_Shift_Del_p.T355fs|RUFY2_ENST00000388768.2_Frame_Shift_Del_p.T424fs			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	438						nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						ATTTTATTGGTTTTTTCTTCT	0.333																																					p.T424fs		Atlas-INDEL	.											.	RUFY2	58	.	0			c.1271delC						.						117	118	118					10																	70139221		1826	4078	5904	SO:0001589	frameshift_variant	55680	exon12			.	AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130		"Zinc fingers, FYVE domain containing"	19761	protein-coding gene	gene with protein product		610328				11877430	Standard	NM_001042417		Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.1165delA	chr10.hg19:g.70139221delT	ENSP00000473462:p.Thr389fs	125.0	0.0		151.0	11.0	NM_017987	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Frame_Shift_Del	DEL	ENST00000602465.1	hg19																																																																																				.	.		0.333	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987		-	70139221	T	-	70139221	7	5	114	1	0	1	0	1	0	0	0	0	13754	1725	60	0	796	0	RUFY2	10	70139221	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	32017984	70139221	65395526	658	18930										
TSPAN15	23555	hgsc.bcm.edu	37	chr10	71211441	71211441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttatcatctattccaccgtgTtctgggtgagtgaccccagt	9	11	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:71211441T>C	ENST00000373290.2	+	1	213	c.91T>C	c.(91-93)Ttc>Ctc	p.F31L		NM_012339.3	NP_036471.1	O95858	TSN15_HUMAN	tetraspanin 15	31					establishment of protein localization to plasma membrane (GO:0090002)|protein maturation (GO:0051604)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	9						TTCCACCGTGTTCTGGGTGAG	0.657																																					p.F31L		Atlas-SNP	.											.	TSPAN15	22	.	0			c.T91C						.						32	30	31					10																	71211441		2193	4280	6473	SO:0001583	missense	23555	exon1			ACCGTGTTCTGGG	AY358934	CCDS7294.1	10q22.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000099282	ENSG00000099282		"Tetraspanins"	23298	protein-coding gene	gene with protein product		613140	"transmembrane 4 superfamily member 15"	TM4SF15		11739647, 10719184	Standard	NM_012339		Approved	NET-7	uc001jpo.1	O95858	OTTHUMG00000018381	ENST00000373290.2:c.91T>C	chr10.hg19:g.71211441T>C	ENSP00000362387:p.Phe31Leu	64.0	0.0		90.0	4.0	NM_012339	Q6UW79	Missense_Mutation	SNP	ENST00000373290.2	hg19	CCDS7294.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.187200	0.78789	.	.	ENSG00000099282	ENST00000373290	T	0.80909	-1.43	5.65	5.65	0.86999	.	0.235800	0.44688	D	0.000436	D	0.83672	0.5305	M	0.68728	2.09	0.80722	D	1	P	0.44659	0.84	P	0.48952	0.596	D	0.85404	0.1133	10	0.66056	D	0.02	-46.3035	13.6952	0.62575	0.0:0.0:0.0:1.0	.	31	O95858	TSN15_HUMAN	L	31	ENSP00000362387:F31L	ENSP00000362387:F31L	F	+	1	0	TSPAN15	70881447	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	4.201000	0.58439	2.284000	0.76573	0.533000	0.62120	TTC	.	.		0.657	TSPAN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048444.1	NM_012339		C	71211441	T	C	71211441	3	2	114	1	0	0	0	0	1	0	0	0	16654	1725	60	2	93	2	TSPAN15	10	71211441	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1072220	71211441	64323306	659	18931										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72496514	72496514	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctgcaagaccaagaaggggCccccgctggatgggactgag					rs553557226		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:72496514delC	ENST00000373207.1	+	10	1564	c.1564delC	c.(1564-1566)cccfs	p.P523fs	ADAMTS14_ENST00000373208.1_Frame_Shift_Del_p.P526fs	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	523	Disintegrin.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CAAGAAGGGGCCCCCGCTGGA	0.617																																					p.G524fs		Atlas-INDEL	.											.	ADAMTS14	148	.	0			c.1572delG						.						81	73	76					10																	72496514		2203	4300	6503	SO:0001589	frameshift_variant	140766	exon10			.	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1564delC	chr10.hg19:g.72496514delC	ENSP00000362303:p.Pro523fs	152.0	0.0		147.0	10.0	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Frame_Shift_Del	DEL	ENST00000373207.1	hg19	CCDS7306.1																																																																																			.	.		0.617	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		-	72496514	C	-	72496514	7	5	114	1	0	1	0	1	0	0	0	0	259	739	26	0	1611	0	ADAMTS14	10	72496514	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1285073	72496514	63038233	660	18932										
CDH23	64072	hgsc.bcm.edu	37	chr10	73326586	73326586	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcgtcctctactccttccagCccccctcccaattcttcgcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:73326586delC	ENST00000224721.6	+	6	537	c.532delC	c.(532-534)cccfs	p.P179fs	CDH23_ENST00000398809.4_Frame_Shift_Del_p.P174fs|CDH23_ENST00000461841.3_Frame_Shift_Del_p.P219fs|CDH23_ENST00000398842.3_Frame_Shift_Del_p.P174fs|CDH23_ENST00000299366.7_Frame_Shift_Del_p.P219fs	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	174	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CTCCTTCCAGCCCCCCTCCCA	0.612																																					p.Q172fs		Atlas-INDEL	.											.	CDH23	365	.	0			c.516delG						.						47	51	49					10																	73326586		2028	4188	6216	SO:0001589	frameshift_variant	64072	exon7			.	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.532delC	chr10.hg19:g.73326586delC	ENSP00000224721:p.Pro179fs	128.0	0.0		120.0	10.0	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Frame_Shift_Del	DEL	ENST00000224721.6	hg19																																																																																				.	.		0.612	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		-	73326586	C	-	73326586	7	5	114	1	0	1	0	1	0	0	0	0	3110	739	26	0	539	0	CDH23	10	73326586	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	830072	73326586	62208161	661	18933										
PPP3CB	5532	hgsc.bcm.edu	37	chr10	75230481	75230481	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atctaagtaattaggtgccgAaaaaattgttattaatgaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:75230481delA	ENST00000360663.5	-	8	1057	c.946delT	c.(946-948)tcgfs	p.S316fs	PPP3CB_ENST00000342558.3_Frame_Shift_Del_p.S316fs|PPP3CB_ENST00000394829.2_Frame_Shift_Del_p.S316fs|PPP3CB_ENST00000394822.2_Frame_Shift_Del_p.S334fs|PPP3CB_ENST00000545874.1_Frame_Shift_Del_p.S230fs|PPP3CB_ENST00000394828.2_Frame_Shift_Del_p.S316fs|PPP3CB_ENST00000495897.1_5'UTR			P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta isozyme	316					axon extension (GO:0048675)|calcium ion-dependent exocytosis (GO:0017156)|cellular response to drug (GO:0035690)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|learning (GO:0007612)|locomotion involved in locomotory behavior (GO:0031987)|memory (GO:0007613)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of transcription, DNA-templated (GO:0045893)|protein dephosphorylation (GO:0006470)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)|social behavior (GO:0035176)|T cell activation (GO:0042110)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein phosphatase 2B binding (GO:0030346)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(7)|skin(1)|urinary_tract(1)	22	Prostate(51;0.0119)					TTAGGTGCCGAAAAAATTGTT	0.264																																					p.S316fs		Atlas-INDEL	.											PPP3CB,caecum,carcinoma,0,1	PPP3CB	68	.	0			c.947delC						.						79	79	79					10																	75230481		2202	4298	6500	SO:0001589	frameshift_variant	5532	exon8			.	M29551	CCDS7328.1, CCDS44436.1, CCDS44437.1	10q22.2	2010-03-17	2010-03-05		ENSG00000107758	ENSG00000107758	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9315	protein-coding gene	gene with protein product	"calcineurin A beta", "protein phosphatase 2B, catalytic subunit, beta isoform"	114106	"protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform (calcineurin A beta)", "protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform"	CALNB		1659808, 2558868	Standard	XM_005269944		Approved	CALNA2, CNA2, PP2Bbeta	uc001juf.3	P16298	OTTHUMG00000018472	ENST00000360663.5:c.946delT	chr10.hg19:g.75230481delA	ENSP00000353881:p.Ser316fs	127.0	0.0		165.0	10.0	NM_001142354	P16299|Q5F2F9|Q8N1F0|Q8N3W4	Frame_Shift_Del	DEL	ENST00000360663.5	hg19	CCDS7328.1																																																																																			.	.		0.264	PPP3CB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048669.1	NM_021132		-	75230481	A	-	75230481	7	5	114	1	0	1	0	1	0	0	0	0	12410	246	9	0	659	0	PPP3CB	10	75230481	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1903895	75230481	60304266	662	18934										
PLAU	414236	hgsc.bcm.edu	37	chr10	75673438	75673438	+	Intron	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggccatctacaggaggcaccGggggggctctgtcacctacg					rs549461157	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:75673438delG	ENST00000409178.1	-	3	268				PLAU_ENST00000446342.1_Frame_Shift_Del_p.R184fs|PLAU_ENST00000372762.4_Frame_Shift_Del_p.R165fs|C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000494287.1_3'UTR|PLAU_ENST00000372764.3_Frame_Shift_Del_p.R201fs	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55											endometrium(1)	1	Prostate(51;0.0112)					AGGAGGCACCGGGGGGGCTCT	0.587																																					p.R201fs		Atlas-INDEL	.											.,1	PLAU	47	.	0			c.601delC						.		,,	17,4245		5,7,2119					,,	2	0.9			66	27,8227		11,5,4111	no	frameshift,frameshift,intron	PLAU,C10orf55	NM_002658.3,NM_001145031.1,NM_001001791.2	,,	16,12,6230	A1A1,A1R,RR		0.3271,0.3989,0.3516	,,	,,		44,12472				SO:0001627	intron_variant	5328	exon7			.		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.73-605C>-	chr10.hg19:g.75673438delG		189.0	0.0		264.0	16.0	NM_002658	Q3KRG4|Q8NAK4	Frame_Shift_Del	DEL	ENST00000409178.1	hg19	CCDS53541.1																																																																																			.	.		0.587	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791		-	75673438	G	-	75673438	6	5	114	0	1	1	0	1	0	0	0	0	12031	1116	39	0		0	PLAU	10	75673438	Intron	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	442957	75673438	59861309	663	18935										
ZCCHC24	219654	hgsc.bcm.edu	37	chr10	81154153	81154153	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtactcgccgaagcagcgcTttttgccctggtatggagtc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:81154153delT	ENST00000372336.3	-	3	677	c.491delA	c.(490-492)aagfs	p.K164fs	ZCCHC24_ENST00000372333.3_Frame_Shift_Del_p.K104fs|RP11-342M3.5_ENST00000438554.2_RNA	NM_153367.3	NP_699198.2	Q8N2G6	ZCH24_HUMAN	zinc finger, CCHC domain containing 24	164							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)	9						GAAGCAGCGCTTTTTGCCCTG	0.577																																					p.K164fs		Atlas-INDEL	.											.	ZCCHC24	22	.	0			c.492delG						.						138	111	120					10																	81154153		2203	4300	6503	SO:0001589	frameshift_variant	219654	exon3			.	AK075279	CCDS7359.1	10q22.3	2014-02-20	2008-06-23	2008-06-23	ENSG00000165424	ENSG00000165424		"Zinc fingers, CCHC domain containing"	26911	protein-coding gene	gene with protein product	"zinc finger, 3CxxC-type 8"		"chromosome 10 open reading frame 56"	C10orf56		12477932	Standard	NM_153367		Approved	FLJ90798, Z3CXXC8	uc010qlr.2	Q8N2G6	OTTHUMG00000018561	ENST00000372336.3:c.491delA	chr10.hg19:g.81154153delT	ENSP00000361411:p.Lys164fs	196.0	0.0		166.0	11.0	NM_153367	Q5U5T9|Q8TAG0	Frame_Shift_Del	DEL	ENST00000372336.3	hg19	CCDS7359.1																																																																																			.	.		0.577	ZCCHC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048947.1	NM_153367		-	81154153	T	-	81154153	7	5	114	1	0	1	0	1	0	0	0	0	17603	1609	56	0	242	0	ZCCHC24	10	81154153	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	5480715	81154153	54380594	664	18936										
NRG3	10718	hgsc.bcm.edu	37	chr10	84711320	84711320	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctgtgcagcattctacttcAaaagcaagtaagactatttc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:84711320delA	ENST00000404547.1	+	5	1150	c.1150delA	c.(1150-1152)aaafs	p.K384fs	NRG3_ENST00000404576.2_Frame_Shift_Del_p.K188fs|NRG3_ENST00000545131.1_Frame_Shift_Del_p.K34fs|NRG3_ENST00000372142.2_Frame_Shift_Del_p.K163fs|NRG3_ENST00000537893.1_Frame_Shift_Del_p.K34fs|NRG3_ENST00000556918.1_Frame_Shift_Del_p.K214fs|NRG3_ENST00000372141.2_Frame_Shift_Del_p.K384fs			P56975	NRG3_HUMAN	neuregulin 3	384					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		ATTCTACTTCAAAAGCAAGTA	0.398																																					p.F383fs		Atlas-INDEL	.											.	NRG3	301	.	0			c.1149delC						.						195	179	184					10																	84711320		2203	4300	6503	SO:0001589	frameshift_variant	10718	exon5			.	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1150delA	chr10.hg19:g.84711320delA	ENSP00000384796:p.Lys384fs	232.0	0.0		212.0	13.0	NM_001010848	A4D7U1|Q0PEH2|Q5VYH3	Frame_Shift_Del	DEL	ENST00000404547.1	hg19	CCDS31233.1																																																																																			.	.		0.398	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		-	84711320	A	-	84711320	7	5	114	1	0	1	0	1	0	0	0	0	10658	131	5	0	1336	0	NRG3	10	84711320	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3557167	84711320	50823427	665	18937										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88232474	88232474	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatggtggtgcaggagccttAaaaactccatcatctttttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:88232474delA	ENST00000298767.5	-	6	2260	c.1788delT	c.(1786-1788)tttfs	p.F596fs	WAPAL_ENST00000263070.7_5'Flank	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	596	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						CAGGAGCCTTAAAAACTCCAT	0.348																																					p.K597fs		Atlas-INDEL	.											.	WAPAL	81	.	0			c.1789delA						.						123	110	114					10																	88232474		2203	4300	6503	SO:0001589	frameshift_variant	23063	exon6			.	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.1788delT	chr10.hg19:g.88232474delA	ENSP00000298767:p.Phe596fs	141.0	0.0		130.0	12.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Frame_Shift_Del	DEL	ENST00000298767.5	hg19	CCDS7375.1																																																																																			.	.		0.348	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		-	88232474	A	-	88232474	7	5	114	1	0	1	0	1	0	0	0	0	17263	359	13	0	1840	0	WAPAL	10	88232474	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3521154	88232474	47302273	666	18938										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717725	89717725	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctcagccgttacctgtgtgTggtgatatcaaagtagagtt	11	8	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:89717725T>A	ENST00000371953.3	+	7	2107	c.750T>A	c.(748-750)tgT>tgA	p.C250*	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	250	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.C250fs*2(5)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.C250*(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TACCTGTGTGTGGTGATATCA	0.403		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.C250X		Atlas-SNP	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,NS,carcinoma,0,5	PTEN	3652	.	54	Whole gene deletion(37)|Deletion - Frameshift(14)|Substitution - Nonsense(1)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|endometrium(3)|breast(3)|ovary(3)|vulva(2)|urinary_tract(2)|large_intestine(1)|soft_tissue(1)	c.T750A						.						126	110	116					10																	89717725		2203	4300	6503	SO:0001587	stop_gained	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	TGTGTGTGGTGAT	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.750T>A	chr10.hg19:g.89717725T>A	ENSP00000361021:p.Cys250*	124.0	0.0		74.0	50.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Nonsense_Mutation	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	48	14.739521	0.99808	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.15	4.02	0.46733	.	0.127565	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.1324	7.3482	0.26676	0.0:0.2568:0.0:0.7432	.	.	.	.	X	250	.	.	C	+	3	2	PTEN	89707705	0.990000	0.36364	1.000000	0.80357	0.991000	0.79684	0.211000	0.17474	0.801000	0.34066	0.477000	0.44152	TGT	.	.		0.403	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89717725	T	A	89717725	4	1	114	1	0	0	0	0	0	1	0	0	12750	1702	59	4	776	4	PTEN	10	89717725	Nonsense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1485251	89717725	45817022	667	18939										
CPEB3	22849	hgsc.bcm.edu	37	chr10	93904731	93904731	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tatcaggaggaagtcctccaAcaaacacctttctagagtag	8	10	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:93904731A>G	ENST00000265997.4	-	5	1506	c.1334T>C	c.(1333-1335)gTt>gCt	p.V445A	CPEB3_ENST00000412050.4_Missense_Mutation_p.V431A	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	445	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				AAGTCCTCCAACAAACACCTT	0.438																																					p.V445A		Atlas-SNP	.											.	CPEB3	43	.	0			c.T1334C						.						147	131	136					10																	93904731		2203	4300	6503	SO:0001583	missense	22849	exon5			CCTCCAACAAACA	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.1334T>C	chr10.hg19:g.93904731A>G	ENSP00000265997:p.Val445Ala	70.0	0.0		72.0	4.0	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	hg19	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.956130	0.92726	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.36157	1.27;1.27	5.8	5.8	0.92144	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.056550	0.64402	D	0.000001	T	0.70245	0.3202	M	0.93763	3.455	0.80722	D	1	P;D;D	0.61697	0.524;0.979;0.99	P;D;D	0.81914	0.799;0.995;0.994	T	0.79097	-0.1943	10	0.87932	D	0	-8.262	16.1639	0.81739	1.0:0.0:0.0:0.0	.	445;431;431	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	A	431;431;445	ENSP00000398310:V431A;ENSP00000265997:V445A	ENSP00000265997:V445A	V	-	2	0	CPEB3	93894711	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.211000	0.95120	2.219000	0.72066	0.533000	0.62120	GTT	.	.		0.438	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		G	93904731	A	G	93904731	3	3	114	1	0	0	0	0	1	0	0	0	3804	43	2	2	786	2	CPEB3	10	93904731	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	4187006	93904731	41630016	668	18940										
EXOC6	54536	hgsc.bcm.edu	37	chr10	94688164	94688164	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caagcaagactggtattgcaAccccagtcgaatatggtaag	10	9	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:94688164A>G	ENST00000260762.6	+	9	971	c.957A>G	c.(955-957)caA>caG	p.Q319Q	EXOC6_ENST00000443748.2_Silent_p.Q296Q|EXOC6_ENST00000371552.4_Silent_p.Q314Q|EXOC6_ENST00000371547.4_Silent_p.Q335Q	NM_019053.4	NP_061926.3	Q8TAG9	EXOC6_HUMAN	exocyst complex component 6	319					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	26		Colorectal(252;0.123)				TGGTATTGCAACCCCAGTCGA	0.333																																					p.Q319Q		Atlas-SNP	.											.	EXOC6	147	.	0			c.A957G						.						106	110	109					10																	94688164		2203	4300	6503	SO:0001819	synonymous_variant	54536	exon9			ATTGCAACCCCAG	BC028395	CCDS7424.2, CCDS31247.1	10q23.33	2013-01-22	2006-11-07	2006-11-07	ENSG00000138190	ENSG00000138190			23196	protein-coding gene	gene with protein product		609672	"SEC15-like 1 (S. cerevisiae)"	SEC15L1		8889548	Standard	NM_001013848		Approved	SEC15L, FLJ1125, DKFZp761I2124, MGC33397, Sec15p, EXOC6A	uc001kig.3	Q8TAG9	OTTHUMG00000018767	ENST00000260762.6:c.957A>G	chr10.hg19:g.94688164A>G		81.0	0.0		60.0	4.0	NM_019053	E9PHI3|Q5VXH8|Q9NZ24	Silent	SNP	ENST00000260762.6	hg19	CCDS7424.2																																																																																			.	.		0.333	EXOC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049410.2	NM_019053		G	94688164	A	G	94688164	2	3	114	1	0	0	0	0	0	0	0	1	5310	40	2	2		2	EXOC6	10	94688164	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	783433	94688164	40846583	669	18941										
TLL2	7093	hgsc.bcm.edu	37	chr10	98170214	98170214	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaagtttcccgttgtgtcctGcagggtctccccacacgctg	10	14	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:98170214G>T	ENST00000357947.3	-	9	1291	c.1066C>A	c.(1066-1068)Cag>Aag	p.Q356K	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	356	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		GTTGTGTCCTGCAGGGTCTCC	0.577																																					p.Q356K		Atlas-SNP	.											.	TLL2	122	.	0			c.C1066A						.						86	74	78					10																	98170214		2203	4300	6503	SO:0001583	missense	7093	exon9			TGTCCTGCAGGGT	AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.1066C>A	chr10.hg19:g.98170214G>T	ENSP00000350630:p.Gln356Lys	102.0	0.0		59.0	40.0	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	hg19	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	G	32	5.133537	0.94517	.	.	ENSG00000095587	ENST00000357947	T	0.34472	1.36	5.64	5.64	0.86602	CUB (5);	0.000000	0.43416	D	0.000567	T	0.55641	0.1933	L	0.53729	1.69	0.80722	D	1	D	0.60160	0.987	D	0.70016	0.967	T	0.38845	-0.9642	10	0.27785	T	0.31	.	19.0544	0.93058	0.0:0.0:1.0:0.0	.	356	Q9Y6L7	TLL2_HUMAN	K	356	ENSP00000350630:Q356K	ENSP00000350630:Q356K	Q	-	1	0	TLL2	98160204	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.736000	0.98828	2.826000	0.97356	0.561000	0.74099	CAG	.	.		0.577	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			T	98170214	G	T	98170214	3	4	114	1	0	0	0	0	1	0	0	0	15961	1328	46	3	2033	3	TLL2	10	98170214	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	3482050	98170214	37364533	670	18942										
MORN4	118812	hgsc.bcm.edu	37	chr10	99376156	99376156	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttccatgagaaccatcagggAaagtcagcaggcctttgagg	12	9	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:99376156A>G	ENST00000307450.6	-	5	468	c.305T>C	c.(304-306)tTc>tCc	p.F102S	PI4K2A_ENST00000370649.3_Intron|MORN4_ENST00000335628.3_Missense_Mutation_p.F160S|PI4K2A_ENST00000555577.1_Intron|MORN4_ENST00000478953.1_Silent_p.F65F	NM_001098831.1|NM_178832.3	NP_001092301.1|NP_849154.1	Q8NDC4	MORN4_HUMAN	MORN repeat containing 4	102										large_intestine(1)|lung(1)|stomach(2)	4						ACCATCAGGGAAAGTCAGCAG	0.493																																					p.F102S		Atlas-SNP	.											.	MORN4	24	.	0			c.T305C						.						44	43	44					10																	99376156		2203	4300	6503	SO:0001583	missense	118812	exon5			TCAGGGAAAGTCA	AJ431726	CCDS7468.1	10q24.2	2008-06-23	2008-06-23	2008-06-23	ENSG00000171160	ENSG00000171160			24001	protein-coding gene	gene with protein product	"44050 protein"		"chromosome 10 open reading frame 83"	C10orf83		12477932	Standard	NM_178832		Approved	bA548K23.4, FLJ25925	uc001koe.3	Q8NDC4	OTTHUMG00000018861	ENST00000307450.6:c.305T>C	chr10.hg19:g.99376156A>G	ENSP00000307636:p.Phe102Ser	79.0	0.0		53.0	4.0	NM_001098831	Q86Y54	Missense_Mutation	SNP	ENST00000307450.6	hg19	CCDS7468.1	.	.	.	.	.	.	.	.	.	.	A	19.99	3.928027	0.73327	.	.	ENSG00000171160	ENST00000307450;ENST00000515674;ENST00000335628	T;T	0.58652	0.32;0.32	5.03	5.03	0.67393	.	0.099330	0.64402	D	0.000001	T	0.70343	0.3213	M	0.65320	2	0.80722	D	1	D;D	0.89917	1.0;0.96	D;P	0.74674	0.984;0.657	T	0.73036	-0.4109	10	0.72032	D	0.01	-6.224	10.2083	0.43126	0.8519:0.0:0.0:0.1481	.	160;102	Q8NDC4-2;Q8NDC4	.;MORN4_HUMAN	S	102;102;160	ENSP00000307636:F102S;ENSP00000335498:F160S	ENSP00000307636:F102S	F	-	2	0	MORN4	99366146	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.106000	0.77039	2.119000	0.64992	0.459000	0.35465	TTC	.	.		0.493	MORN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049730.1	NM_178832		G	99376156	A	G	99376156	3	3	114	1	0	0	0	0	1	0	0	0	9719	246	9	2	139	2	MORN4	10	99376156	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1205942	99376156	36158591	671	18943										
GOLGA7B	401647	hgsc.bcm.edu	37	chr10	99619216	99619216	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgcccgcacgtctcctcaggTccacaatctgcaggagctcc	9	18	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:99619216T>C	ENST00000370602.1	+	2	79	c.14T>C	c.(13-15)gTc>gCc	p.V5A		NM_001010917.2	NP_001010917.1	Q2TAP0	GOG7B_HUMAN	golgin A7 family, member B	5						Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|prostate(1)	5						TCTCCTCAGGTCCACAATCTG	0.557																																					p.V5A		Atlas-SNP	.											.	GOLGA7B	11	.	0			c.T14C						.						59	51	54					10																	99619216		2203	4300	6503	SO:0001630	splice_region_variant	401647	exon2			CTCAGGTCCACAA	BC008047	CCDS31265.1	10q24.2	2011-10-25	2010-02-12	2008-10-03	ENSG00000155265	ENSG00000155265			31668	protein-coding gene	gene with protein product		614189	"chromosome 10 open reading frame 133", "chromosome 10 open reading frame 132", "golgi autoantigen, golgin subfamily a, 7B"	C10orf133, C10orf132			Standard	NM_001010917		Approved	bA459F3.4, bA451M19.3	uc001kos.3	Q2TAP0	OTTHUMG00000018869	ENST00000370602.1:c.13-1T>C	chr10.hg19:g.99619216T>C		77.0	0.0		69.0	4.0	NM_001010917	Q5T4F5	Missense_Mutation	SNP	ENST00000370602.1	hg19	CCDS31265.1	.	.	.	.	.	.	.	.	.	.	T	12.37	1.918922	0.33908	.	.	ENSG00000155265	ENST00000370602	.	.	.	4.71	3.56	0.40772	.	0.068494	0.64402	D	0.000014	T	0.30386	0.0763	N	0.08118	0	0.37472	D	0.91565	B	0.18461	0.028	B	0.09377	0.004	T	0.20773	-1.0265	9	0.30854	T	0.27	-47.6928	12.2438	0.54558	0.0:0.0:0.1511:0.8489	.	5	Q2TAP0	GOG7B_HUMAN	A	5	.	ENSP00000359634:V5A	V	+	2	0	GOLGA7B	99609206	0.998000	0.40836	1.000000	0.80357	0.910000	0.53928	2.951000	0.49089	1.994000	0.58287	0.454000	0.30748	GTC	.	.		0.557	GOLGA7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049752.1	NM_001010917	Missense_Mutation	C	99619216	T	C	99619216	5	2	114	1	0	0	0	0	0	0	1	0	6570	1681	58	2	20	2	GOLGA7B	10	99619216	Splice_Site	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	243060	99619216	35915531	672	18944										
PYROXD2	84795	hgsc.bcm.edu	37	chr10	100152700	100152700	+	Splice_Site	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggtagaggggccgttcaccTtttcagtgaagatgcttgct					rs554216343		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:100152700delT	ENST00000370575.4	-	9	974	c.926delA	c.(925-927)aag>ag	p.K309fs	MIR1287_ENST00000408492.1_RNA|PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	309							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						GCCGTTCACCTTTTCAGTGAA	0.542																																					p.K309fs		Atlas-INDEL	.											.	PYROXD2	43	.	0			c.927delG						.						96	84	88					10																	100152700		2203	4300	6503	SO:0001630	splice_region_variant	84795	exon9			.	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 33"	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.927+1A>-	chr10.hg19:g.100152700delT		218.0	0.0		156.0	10.0	NM_032709	D3DR61|Q5TAA9|Q9BRQ1	Frame_Shift_Del	DEL	ENST00000370575.4	hg19	CCDS7474.1																																																																																			.	.		0.542	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709	Frame_Shift_Del	-	100152700	T	-	100152700	8	5	114	1	0	1	0	1	0	0	1	0	12882	1623	56	0	851	0	PYROXD2	10	100152700	Splice_Site	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	533484	100152700	35382047	673	18945										
GBF1	8729	hgsc.bcm.edu	37	chr10	104128552	104128552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgatgtgtttgacaatctcaTcatctctctatgcaaattca	5	10	5	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:104128552T>C	ENST00000369983.3	+	23	3193	c.2933T>C	c.(2932-2934)aTc>aCc	p.I978T		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	978					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GACAATCTCATCATCTCTCTA	0.512																																					p.I979T		Atlas-SNP	.											.	GBF1	142	.	0			c.T2936C						.						162	144	150					10																	104128552		2203	4300	6503	SO:0001583	missense	8729	exon23			ATCTCATCATCTC	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.2933T>C	chr10.hg19:g.104128552T>C	ENSP00000359000:p.Ile978Thr	153.0	0.0		80.0	4.0	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.429649	0.83776	.	.	ENSG00000107862	ENST00000369983	T	0.70045	-0.45	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	D	0.83686	0.5308	M	0.84433	2.695	0.80722	D	1	P;D;D	0.69078	0.911;0.997;0.993	P;P;D	0.72338	0.505;0.88;0.977	D	0.86256	0.1652	10	0.87932	D	0	-17.7878	16.5763	0.84648	0.0:0.0:0.0:1.0	.	978;978;978	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	T	978	ENSP00000359000:I978T	ENSP00000359000:I978T	I	+	2	0	GBF1	104118542	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.317000	0.78254	0.459000	0.35465	ATC	.	.		0.512	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			C	104128552	T	C	104128552	3	2	114	1	0	0	0	0	1	0	0	0	6279	1435	50	2	3019	2	GBF1	10	104128552	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3975852	104128552	31406195	674	18946										
SFXN2	118980	hgsc.bcm.edu	37	chr10	104486829	104486829	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cggccttccaccccgacactGgggagaagatgaatgtcatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:104486829delG	ENST00000369893.5	+	3	414	c.247delG	c.(247-249)gggfs	p.G83fs	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	83					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		CCCCGACACTGGGGAGAAGAT	0.602																																					p.T82fs		Atlas-INDEL	.											.	SFXN2	40	.	0			c.246delT						.						84	74	77					10																	104486829		2203	4300	6503	SO:0001589	frameshift_variant	118980	exon3			.	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"Sideroflexins"	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.247delG	chr10.hg19:g.104486829delG	ENSP00000358909:p.Gly83fs	210.0	0.0		161.0	11.0	NM_178858	Q5JSM6	Frame_Shift_Del	DEL	ENST00000369893.5	hg19	CCDS7539.1																																																																																			.	.		0.602	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359		-	104486829	G	-	104486829	7	5	114	1	0	1	0	1	0	0	0	0	14210	1348	47	0	253	0	SFXN2	10	104486829	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	358277	104486829	31047918	675	18947										
NT5C2	22978	hgsc.bcm.edu	37	chr10	104849568	104849568	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtgccgcttgtagtcagtgTctttgaaatccactgatgtg	12	8	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:104849568T>C	ENST00000404739.3	-	17	1570	c.1547A>G	c.(1546-1548)gAc>gGc	p.D516G	NT5C2_ENST00000369857.4_5'UTR|CNNM2_ENST00000369878.4_3'UTR|NT5C2_ENST00000343289.5_Missense_Mutation_p.D516G|NT5C2_ENST00000423468.2_Missense_Mutation_p.D487G			P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	516					cell death (GO:0008219)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|nucleobase-containing small molecule metabolic process (GO:0055086)|phosphorylation (GO:0016310)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleoside phosphotransferase activity (GO:0050146)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|urinary_tract(1)	16		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	GTAGTCAGTGTCTTTGAAATC	0.507																																					p.D516G		Atlas-SNP	.											.	NT5C2	41	.	0			c.A1547G						.						149	124	132					10																	104849568		2203	4300	6503	SO:0001583	missense	22978	exon19			TCAGTGTCTTTGA	D38524	CCDS7544.1	10q24.32	2014-03-03	2002-04-18	2002-04-19	ENSG00000076685	ENSG00000076685			8022	protein-coding gene	gene with protein product	"purine 5' nucleotidase"	600417	"5'-nucleotidase (purine), cytosolic type B"	NT5B		7999131, 24482476	Standard	NM_012229		Approved	PNT5, GMP, cN-II, SPG65	uc001kwq.3	P49902	OTTHUMG00000018981	ENST00000404739.3:c.1547A>G	chr10.hg19:g.104849568T>C	ENSP00000383960:p.Asp516Gly	185.0	0.0		134.0	6.0	NM_012229	B7Z382|D3DR91|Q5JUV5	Missense_Mutation	SNP	ENST00000404739.3	hg19	CCDS7544.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.551289	0.45383	.	.	ENSG00000076685	ENST00000343289;ENST00000404739;ENST00000423468	T;T;T	0.25085	2.14;2.14;1.82	5.96	5.96	0.96718	.	0.092833	0.64402	D	0.000001	T	0.16428	0.0395	N	0.14661	0.345	0.58432	D	0.999999	B;B;B	0.30482	0.099;0.281;0.18	B;B;B	0.27170	0.016;0.077;0.047	T	0.11299	-1.0593	10	0.19147	T	0.46	-20.79	16.4484	0.83959	0.0:0.0:0.0:1.0	.	487;363;516	B7Z382;B3KXN5;P49902	.;.;5NTC_HUMAN	G	516;516;487	ENSP00000339479:D516G;ENSP00000383960:D516G;ENSP00000392236:D487G	ENSP00000339479:D516G	D	-	2	0	NT5C2	104839558	1.000000	0.71417	0.982000	0.44146	0.501000	0.33797	4.972000	0.63756	2.285000	0.76669	0.533000	0.62120	GAC	.	.		0.507	NT5C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050121.1	NM_012229		C	104849568	T	C	104849568	3	2	114	1	0	0	0	0	1	0	0	0	10696	1667	58	2	142	2	NT5C2	10	104849568	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	362739	104849568	30685179	676	18948										
C10orf79	80217	hgsc.bcm.edu	37	chr10	105921776	105921776	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctcccatcatgtccatcagAgctcggagtcttgtactggc	9	14	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:105921776A>G	ENST00000357060.3	-	26	3472	c.3357T>C	c.(3355-3357)gcT>gcC	p.A1119A	WDR96_ENST00000428666.1_Silent_p.A1120A	NM_025145.5	NP_079421.5														NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TGTCCATCAGAGCTCGGAGTC	0.483																																					p.A1119A		Atlas-SNP	.											.	WDR96	183	.	0			c.T3357C						.						240	245	243					10																	105921776		2203	4300	6503	SO:0001819	synonymous_variant	80217	exon26			CATCAGAGCTCGG																												ENST00000357060.3:c.3357T>C	chr10.hg19:g.105921776A>G		114.0	0.0		95.0	4.0	NM_025145		Silent	SNP	ENST00000357060.3	hg19	CCDS31281.1	.	.	.	.	.	.	.	.	.	.	A	3.651	-0.071434	0.07228	.	.	ENSG00000197748	ENST00000434629	.	.	.	5.73	1.34	0.21922	.	.	.	.	.	T	0.52256	0.1723	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43766	-0.9371	4	.	.	.	.	5.9649	0.19320	0.2974:0.0:0.5652:0.1374	.	.	.	.	P	480	.	.	L	-	2	0	WDR96	105911766	0.991000	0.36638	1.000000	0.80357	0.248000	0.25809	0.054000	0.14205	0.756000	0.33013	-0.261000	0.10672	CTC	.	.		0.483	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	105921776	A	G	105921776	2	3	114	1	0	0	0	0	0	0	0	1	1620	291	11	2		2	C10orf79	10	105921776	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1072208	105921776	29612971	677	18949										
ADD3	120	hgsc.bcm.edu	37	chr10	111883900	111883900	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacgatacagtgccactctcTcctctcaaatacatggcaca	6	14	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:111883900T>C	ENST00000356080.4	+	10	1636	c.1269T>C	c.(1267-1269)tcT>tcC	p.S423S	ADD3_ENST00000277900.8_Silent_p.S423S|ADD3_ENST00000360162.3_Silent_p.S423S	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	423						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		TGCCACTCTCTCCTCTCAAAT	0.468																																					p.S423S		Atlas-SNP	.											.	ADD3	89	.	0			c.T1269C						.						132	109	117					10																	111883900		2203	4300	6503	SO:0001819	synonymous_variant	120	exon10			ACTCTCTCCTCTC	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.1269T>C	chr10.hg19:g.111883900T>C		125.0	0.0		100.0	4.0	NM_001121	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Silent	SNP	ENST00000356080.4	hg19	CCDS7561.1																																																																																			.	.		0.468	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903		C	111883900	T	C	111883900	2	2	114	1	0	0	0	0	0	0	0	1	306	1538	54	2		2	ADD3	10	111883900	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	5962124	111883900	23650847	678	18950										
SHOC2	8036	hgsc.bcm.edu	37	chr10	112769581	112769581	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctacttactcaccttcctgaAgaaattggtatgaaccctgt	6	11	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:112769581A>G	ENST00000369452.4	+	8	1878	c.1533A>G	c.(1531-1533)gaA>gaG	p.E511E	SHOC2_ENST00000265277.5_Silent_p.E465E|SHOC2_ENST00000489390.1_3'UTR	NM_007373.3	NP_031399.2	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog (C. elegans)	511					fibroblast growth factor receptor signaling pathway (GO:0008543)|positive regulation of Ras protein signal transduction (GO:0046579)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase binding (GO:0019903)|protein phosphatase regulator activity (GO:0019888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(2)	17				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		ACCTTCCTGAAGAAATTGGTA	0.393																																					p.E511E		Atlas-SNP	.											.	SHOC2	49	.	0			c.A1533G						.						98	86	90					10																	112769581		2203	4300	6503	SO:0001819	synonymous_variant	8036	exon8			TCCTGAAGAAATT	AB020669	CCDS7568.1, CCDS58095.1	10q25	2014-09-17	2001-11-28		ENSG00000108061	ENSG00000108061			15454	protein-coding gene	gene with protein product		602775	"soc-2 (suppressor of clear, C.elegans) homolog"			9618511, 9674433, 10783161	Standard	NM_007373		Approved	KIAA0862, SOC2, SUR-8, SOC-2, SUR8	uc001kzl.4	Q9UQ13	OTTHUMG00000019047	ENST00000369452.4:c.1533A>G	chr10.hg19:g.112769581A>G		127.0	0.0		96.0	4.0	NM_007373	A8K9W8|B3KR23|O76063|Q5VZS8|Q5VZS9	Silent	SNP	ENST00000369452.4	hg19	CCDS7568.1																																																																																			.	.		0.393	SHOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050355.1	NM_007373		G	112769581	A	G	112769581	2	3	114	1	0	0	0	0	0	0	0	1	14302	69	3	2		2	SHOC2	10	112769581	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	885681	112769581	22765166	679	18951										
PNLIPRP3	119548	hgsc.bcm.edu	37	chr10	118196248	118196248	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaagtttgctatgaaaggttAgggtgtttcaaagatggttt	13	2	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:118196248A>G	ENST00000369230.3	+	2	221	c.75A>G	c.(73-75)ttA>ttG	p.L25L		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	25					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		ATGAAAGGTTAGGGTGTTTCA	0.443																																					p.L25L		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.A75G						.						148	140	143					10																	118196248		2203	4300	6503	SO:0001819	synonymous_variant	119548	exon2			AAGGTTAGGGTGT	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.75A>G	chr10.hg19:g.118196248A>G		88.0	0.0		94.0	4.0	NM_001011709		Silent	SNP	ENST00000369230.3	hg19	CCDS31292.1																																																																																			.	.		0.443	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		G	118196248	A	G	118196248	2	3	114	1	0	0	0	0	0	0	0	1	12161	417	15	2		2	PNLIPRP3	10	118196248	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	5426667	118196248	17338499	680	18952										
SLC18A2	6571	hgsc.bcm.edu	37	chr10	119026263	119026263	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcgttgccttcttgccagcTagtatctcttatctcattgg	9	11	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:119026263T>C	ENST00000298472.5	+	11	1154	c.1011T>C	c.(1009-1011)gcT>gcC	p.A337A	SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	337					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	TCTTGCCAGCTAGTATCTCTT	0.353																																					p.A337A		Atlas-SNP	.											.	SLC18A2	58	.	0			c.T1011C						.						167	165	166					10																	119026263		2203	4300	6503	SO:0001819	synonymous_variant	6571	exon11			GCCAGCTAGTATC	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"Solute carriers"	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.1011T>C	chr10.hg19:g.119026263T>C		139.0	0.0		85.0	4.0	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Silent	SNP	ENST00000298472.5	hg19	CCDS7599.1																																																																																			.	.		0.353	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054		C	119026263	T	C	119026263	2	2	114	1	0	0	0	0	0	0	0	1	14441	1509	53	2		2	SLC18A2	10	119026263	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	830015	119026263	16508484	681	18953										
EIF3A	8661	hgsc.bcm.edu	37	chr10	120828985	120828985	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctcatcttgtgtgagattcTttctcatttctctagagaga	7	8	5	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:120828985T>C	ENST00000369144.3	-	6	1050	c.923A>G	c.(922-924)aAg>aGg	p.K308R	EIF3A_ENST00000541549.1_Missense_Mutation_p.K274R	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A	0					mature ribosome assembly (GO:0042256)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal subunit export from nucleus (GO:0000054)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lamin filament (GO:0005638)|nucleus (GO:0005634)	ribosomal large subunit binding (GO:0043023)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)			endometrium(8)|kidney(4)|large_intestine(14)|lung(22)|prostate(1)|skin(4)|urinary_tract(3)	56		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		TGTGAGATTCTTTCTCATTTC	0.318																																					p.K308R		Atlas-SNP	.											.	EIF3A	142	.	0			c.A923G						.						98	90	93					10																	120828985		2203	4300	6503	SO:0001583	missense	8661	exon6			AGATTCTTTCTCA	U78311	CCDS7608.1	10q26.11	2007-08-03	2007-07-27	2007-07-27	ENSG00000107581	ENSG00000107581			3271	protein-coding gene	gene with protein product		602039	"eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa"	EIF3, EIF3S10		9054404, 8590280	Standard	NM_003750		Approved	eIF3-theta, eIF3-p170, KIAA0139, eIF3a, TIF32	uc001ldu.3	Q14152	OTTHUMG00000019144	ENST00000369144.3:c.923A>G	chr10.hg19:g.120828985T>C	ENSP00000358140:p.Lys308Arg	93.0	0.0		68.0	4.0	NM_003750	B7ZBG9|Q6IBN8|Q96TD5	Missense_Mutation	SNP	ENST00000369144.3	hg19	CCDS7608.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.000719	0.74818	.	.	ENSG00000107581	ENST00000369144;ENST00000541549	T;T	0.46063	0.88;0.88	5.87	5.87	0.94306	.	0.000000	0.41097	D	0.000944	T	0.61274	0.2334	L	0.60904	1.88	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	T	0.60063	-0.7336	10	0.46703	T	0.11	-34.5111	16.5764	0.84681	0.0:0.0:0.0:1.0	.	308	Q14152	EIF3A_HUMAN	R	308;274	ENSP00000358140:K308R;ENSP00000438178:K274R	ENSP00000358140:K308R	K	-	2	0	EIF3A	120818975	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.965000	0.87945	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.318	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750		C	120828985	T	C	120828985	3	2	114	1	0	0	0	0	1	0	0	0	5014	1609	56	2	3293	2	EIF3A	10	120828985	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1802722	120828985	14705762	682	18954										
DOCK1	1793	hgsc.bcm.edu	37	chr10	129242484	129242484	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtccccctcgtcaccgtcctCccagcaaacaccccctccag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:129242484delC	ENST00000280333.6	+	50	5400	c.5291delC	c.(5290-5292)tccfs	p.S1764fs		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1764					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TCACCGTCCTCCCAGCAAACA	0.572																																					p.S1764fs		Atlas-INDEL	.											.	DOCK1	188	.	0			c.5290delT						.						87	101	96					10																	129242484		2089	4209	6298	SO:0001589	frameshift_variant	1793	exon50			.	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.5291delC	chr10.hg19:g.129242484delC	ENSP00000280333:p.Ser1764fs	99.0	0.0		139.0	10.0	NM_001380	A9Z1Z5	Frame_Shift_Del	DEL	ENST00000280333.6	hg19																																																																																				.	.		0.572	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		-	129242484	C	-	129242484	7	5	114	1	0	1	0	1	0	0	0	0	4686	855	30	0	5489	0	DOCK1	10	129242484	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	8413499	129242484	6292263	683	18955										
KNDC1	85442	hgsc.bcm.edu	37	chr10	134980888	134980888	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agggccggtcttggcaggagAacgtgtctctggctgacatc	15	10	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:134980888A>G	ENST00000304613.3	+	2	127	c.106A>G	c.(106-108)Aac>Gac	p.N36D	KNDC1_ENST00000368571.2_5'UTR|KNDC1_ENST00000368572.2_Missense_Mutation_p.N36D|KNDC1_ENST00000530127.1_3'UTR			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	36					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TTGGCAGGAGAACGTGTCTCT	0.701																																					p.N36D		Atlas-SNP	.											.	KNDC1	155	.	0			c.A106G						.						17	16	17					10																	134980888		2195	4284	6479	SO:0001583	missense	85442	exon2			CAGGAGAACGTGT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.106A>G	chr10.hg19:g.134980888A>G	ENSP00000304437:p.Asn36Asp	103.0	0.0		125.0	5.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	.	13.91	2.377048	0.42105	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.74106	-0.81;-0.81	3.98	3.98	0.46160	.	0.000000	0.53938	D	0.000049	D	0.83362	0.5238	M	0.70595	2.14	0.45216	D	0.998225	D	0.89917	1.0	D	0.80764	0.994	D	0.84529	0.0632	10	0.62326	D	0.03	-15.0533	11.1105	0.48230	1.0:0.0:0.0:0.0	.	36	Q76NI1	VKIND_HUMAN	D	36	ENSP00000304437:N36D;ENSP00000357561:N36D	ENSP00000304437:N36D	N	+	1	0	KNDC1	134830878	1.000000	0.71417	0.995000	0.50966	0.176000	0.22953	8.734000	0.91543	1.583000	0.49898	0.172000	0.16884	AAC	.	.		0.701	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		G	134980888	A	G	134980888	3	3	114	1	0	0	0	0	1	0	0	0	8435	246	9	2	112	2	KNDC1	10	134980888	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	5738404	134980888	553859	684	18956										
KNDC1	85442	hgsc.bcm.edu	37	chr10	134999520	134999520	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggagagacctgccccaggaaAcgctgggcccaggaggccgc	16	14	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:134999520A>G	ENST00000304613.3	+	6	689	c.668A>G	c.(667-669)aAc>aGc	p.N223S	KNDC1_ENST00000368571.2_Missense_Mutation_p.N158S|KNDC1_ENST00000368572.2_Missense_Mutation_p.N223S			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	223					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GCCCCAGGAAACGCTGGGCCC	0.716																																					p.N223S		Atlas-SNP	.											.	KNDC1	155	.	0			c.A668G						.						8	10	9					10																	134999520		2123	4205	6328	SO:0001583	missense	85442	exon6			CAGGAAACGCTGG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.668A>G	chr10.hg19:g.134999520A>G	ENSP00000304437:p.Asn223Ser	117.0	0.0		92.0	5.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	A	0.091	-1.167444	0.01660	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.15603	2.91;2.91;2.41	4.05	-1.53	0.08611	.	1.239190	0.05937	N	0.636354	T	0.07143	0.0181	N	0.04880	-0.145	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.37220	-0.9715	10	0.23891	T	0.37	.	3.9334	0.09296	0.3551:0.3607:0.2842:0.0	.	158;223	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	S	223;223;158	ENSP00000304437:N223S;ENSP00000357561:N223S;ENSP00000357560:N158S	ENSP00000304437:N223S	N	+	2	0	KNDC1	134849510	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.328000	0.19681	-0.161000	0.10983	-0.401000	0.06369	AAC	.	.		0.716	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		G	134999520	A	G	134999520	3	3	114	1	0	0	0	0	1	0	0	0	8435	43	2	2	690	2	KNDC1	10	134999520	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	18632	134999520	535227	685	18957										
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	376081	376081	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccccaccccccaggtgtaccTgtccttcgtttatcccaacg	6	19	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:376081T>C	ENST00000329962.6	+	12	1103	c.1103T>C	c.(1102-1104)cTg>cCg	p.L368P		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	368					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGGTGTACCTGTCCTTCGTT	0.672																																					p.L368P		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.T1103C						.						27	28	27					11																	376081		2197	4290	6487	SO:0001583	missense	338707	exon12			TGTACCTGTCCTT	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"Beta 4-glycosyltransferases"	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.1103T>C	chr11.hg19:g.376081T>C	ENSP00000328277:p.Leu368Pro	55.0	0.0		62.0	4.0	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	hg19	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	t	17.34	3.363741	0.61513	.	.	ENSG00000182272	ENST00000329962	T	0.73152	-0.72	2.83	2.83	0.33086	.	0.286546	0.27636	N	0.018484	T	0.80166	0.4573	M	0.62723	1.935	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.82078	-0.0635	10	0.87932	D	0	-10.2847	11.839	0.52342	0.0:0.0:0.0:1.0	.	368	Q76KP1	B4GN4_HUMAN	P	368	ENSP00000328277:L368P	ENSP00000328277:L368P	L	+	2	0	B4GALNT4	366081	1.000000	0.71417	1.000000	0.80357	0.566000	0.35808	5.765000	0.68834	1.533000	0.49186	0.358000	0.22013	CTG	.	.		0.672	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		C	376081	T	C	376081	3	2	114	1	0	0	0	0	1	0	0	0	1269	1580	55	2	1149	2	B4GALNT4	11	376081	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10		376081	134630435	686	18958										
LRDD	79751	hgsc.bcm.edu	37	chr11	799358	799358	+	5'Flank	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccgaggagccaggcagagcGgggtccttgggggccaagcc					rs11820580	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:799358delG	ENST00000320230.5	-	0	0				PIDD_ENST00000411829.2_Frame_Shift_Del_p.P877fs|PIDD_ENST00000347755.5_Frame_Shift_Del_p.P894fs|SLC25A22_ENST00000531214.1_5'Flank	NM_001191061.1|NM_024698.5	NP_001177990.1|NP_078974.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22						L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGGCAGAGCGGGGTCCTTGG	0.672																																					p.A895fs	Colon(93;848 1468 3270 23355 49636)	Atlas-INDEL	.											.	PIDD	76	.	0			c.2683delG						.						44	48	47					11																	799358		2202	4295	6497	SO:0001631	upstream_gene_variant	55367	exon16			.	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"Solute carriers"	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310		chr11.hg19:g.799358delG	Exception_encountered	204.0	0.0		208.0	13.0	NM_145886	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Frame_Shift_Del	DEL	ENST00000320230.5	hg19	CCDS7715.1																																																																																			.	.		0.672	SLC25A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257107.2			-	799358	G	-	799358	6	5	114	0	1	1	0	1	0	0	0	0	8945	1103	39	0		0	LRDD	11	799358	5'Flank	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	423277	799358	134207158	687	18959										
KRTAP5-2	440021	hgsc.bcm.edu	37	chr11	1619161	1619161	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agcagccacaagaaccacagCcccccttggaacccccacag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:1619161delC	ENST00000412090.1	-	1	363	c.320delG	c.(319-321)ggcfs	p.G107fs	KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	107	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				large_intestine(1)|lung(2)|skin(1)	4		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AGAACCACAGCCCCCCTTGGA	0.657																																					p.G107fs		Atlas-INDEL	.											.	KRTAP5-2	38	.	0			c.321delC						.						85	110	101					11																	1619161		2201	4299	6500	SO:0001589	frameshift_variant	440021	exon1			.	AB126071	CCDS31331.1	11p15.5	2008-02-05				ENSG00000205867		"Keratin associated proteins"	23597	protein-coding gene	gene with protein product						15144888	Standard	NM_001004325		Approved	KRTAP5.2, KRTAP5-8	uc001ltv.3	Q701N4		ENST00000412090.1:c.320delG	chr11.hg19:g.1619161delC	ENSP00000400041:p.Gly107fs	180.0	0.0		238.0	15.0	NM_001004325	A9JTZ1	Frame_Shift_Del	DEL	ENST00000412090.1	hg19	CCDS31331.1																																																																																			.	.		0.657	KRTAP5-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384775.1	NM_001004325		-	1619161	C	-	1619161	7	5	114	1	0	1	0	1	0	0	0	0	8570	739	26	0	217	0	KRTAP5-2	11	1619161	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	819803	1619161	133387355	688	18960										
ZNF195	7748	hgsc.bcm.edu	37	chr11	3380971	3380971	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttatgtttagtaaggtctgAgaaccacttgaagatgctgt	10	6	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:3380971A>G	ENST00000399602.4	-	6	1393	c.1267T>C	c.(1267-1269)Tca>Cca	p.S423P	ZNF195_ENST00000005082.9_Missense_Mutation_p.S400P|ZNF195_ENST00000526601.1_Missense_Mutation_p.S404P|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000429541.2_Missense_Mutation_p.S355P|ZNF195_ENST00000343338.7_Missense_Mutation_p.S355P|ZNF195_ENST00000354599.6_Missense_Mutation_p.S351P	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	423					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		GTAAGGTCTGAGAACCACTTG	0.423																																					p.S423P		Atlas-SNP	.											.	ZNF195	77	.	0			c.T1267C						.						112	117	115					11																	3380971		2140	4270	6410	SO:0001583	missense	7748	exon6			GGTCTGAGAACCA		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"Zinc fingers, C2H2-type", "-"	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.1267T>C	chr11.hg19:g.3380971A>G	ENSP00000382511:p.Ser423Pro	59.0	0.0		68.0	4.0	NM_001130520	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Missense_Mutation	SNP	ENST00000399602.4	hg19	CCDS44522.1	.	.	.	.	.	.	.	.	.	.	a	12.51	1.960294	0.34565	.	.	ENSG00000005801	ENST00000354599;ENST00000399602;ENST00000343338;ENST00000429541;ENST00000005082;ENST00000526601	T;T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15;3.15	1.27	1.27	0.21489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24275	0.0588	M	0.82323	2.585	0.09310	N	1	P;D;D;D;D;D	0.65815	0.782;0.992;0.981;0.995;0.967;0.995	P;P;D;P;D;P	0.68621	0.838;0.588;0.959;0.766;0.91;0.766	T	0.06427	-1.0827	9	0.87932	D	0	.	4.0656	0.09859	0.6251:0.3749:0.0:0.0	.	404;282;400;355;423;351	O14628-6;Q59EZ7;O14628-5;O14628-7;O14628;O14628-4	.;.;.;.;ZN195_HUMAN;.	P	351;423;355;355;400;404	ENSP00000346613:S351P;ENSP00000382511:S423P;ENSP00000344483:S355P;ENSP00000387998:S355P;ENSP00000005082:S400P;ENSP00000435828:S404P	ENSP00000005082:S400P	S	-	1	0	ZNF195	3337547	0.000000	0.05858	0.002000	0.10522	0.199000	0.23934	-0.161000	0.10026	0.535000	0.28714	0.254000	0.18369	TCA	.	.		0.423	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2			G	3380971	A	G	3380971	3	3	114	1	0	0	0	0	1	0	0	0	17773	304	11	2	626	2	ZNF195	11	3380971	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1761810	3380971	131625545	689	18961										
ZNF195	7748	hgsc.bcm.edu	37	chr11	3392251	3392251	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctcttcacattccagggctcTtttcgttgctccaggcaggt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:3392251delT	ENST00000399602.4	-	3	306	c.180delA	c.(178-180)aaafs	p.K60fs	ZNF195_ENST00000005082.9_Frame_Shift_Del_p.K60fs|ZNF195_ENST00000527386.1_5'UTR|ZNF195_ENST00000526601.1_Frame_Shift_Del_p.K64fs|ZNF195_ENST00000438262.2_Frame_Shift_Del_p.K64fs|ZNF195_ENST00000528796.1_Frame_Shift_Del_p.K60fs|ZNF195_ENST00000429541.2_Frame_Shift_Del_p.K64fs|ZNF195_ENST00000343338.7_Frame_Shift_Del_p.K64fs|ZNF195_ENST00000354599.6_Frame_Shift_Del_p.K60fs|AC123788.1_ENST00000581561.1_RNA	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	60	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		TCCAGGGCTCTTTTCGTTGCT	0.498																																					p.E65fs		Atlas-INDEL	.											.	ZNF195	77	.	0			c.193delG						.						159	163	162					11																	3392251		2170	4280	6450	SO:0001589	frameshift_variant	7748	exon4			.		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"Zinc fingers, C2H2-type", "-"	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.180delA	chr11.hg19:g.3392251delT	ENSP00000382511:p.Lys60fs	88.0	0.0		125.0	10.0	NM_001256824	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Frame_Shift_Del	DEL	ENST00000399602.4	hg19	CCDS44522.1																																																																																			.	.		0.498	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2			-	3392251	T	-	3392251	7	5	114	1	0	1	0	1	0	0	0	0	17773	1606	56	0	1725	0	ZNF195	11	3392251	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	11280	3392251	131614265	690	18962										
RRM1	6240	hgsc.bcm.edu	37	chr11	4127278	4127278	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttggttttatttttgtaggcTcagatcaccatgaaagtaat	8	5	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:4127278T>C	ENST00000300738.5	+	3	315	c.111T>C	c.(109-111)gcT>gcC	p.A37A	RRM1_ENST00000423050.2_Intron	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	37	ATP-cone. {ECO:0000255|PROSITE- ProRule:PRU00492}.				cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	TTTTGTAGGCTCAGATCACCA	0.413																																					p.A37A	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.T111C						.						75	68	71					11																	4127278		2201	4298	6499	SO:0001819	synonymous_variant	6240	exon3			GTAGGCTCAGATC	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"ribonucleotide reductase M1 polypeptide"			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.111T>C	chr11.hg19:g.4127278T>C		68.0	0.0		82.0	5.0	NM_001033	Q9UNN2	Silent	SNP	ENST00000300738.5	hg19	CCDS7750.1																																																																																			.	.		0.413	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		C	4127278	T	C	4127278	2	2	114	1	0	0	0	0	0	0	0	1	13696	1538	54	2		2	RRM1	11	4127278	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	735027	4127278	130879238	691	18963										
UBQLN3	50613	hgsc.bcm.edu	37	chr11	5529234	5529234	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccgcagggcttgcagggcacGggggtttgccatggctgcct					rs141131818	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:5529234delG	ENST00000311659.4	-	2	1702	c.1555delC	c.(1555-1557)cgtfs	p.R519fs	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_5'Flank|HBG2_ENST00000380252.1_5'Flank|AC104389.28_ENST00000415970.1_RNA	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	519										NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCAGGGCACGGGGGTTTGCC	0.577																																					p.R519fs	Ovarian(72;684 1260 12332 41642 52180)	Atlas-INDEL	.											.	UBQLN3	107	.	0			c.1556delG						.						54	55	55					11																	5529234		2201	4297	6498	SO:0001589	frameshift_variant	50613	exon2			.	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"Ubiquilin family"	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.1555delC	chr11.hg19:g.5529234delG	ENSP00000347997:p.Arg519fs	128.0	0.0		180.0	11.0	NM_017481	Q9NRE0	Frame_Shift_Del	DEL	ENST00000311659.4	hg19	CCDS7758.1																																																																																			.	.		0.577	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		-	5529234	G	-	5529234	7	5	114	1	0	1	0	1	0	0	0	0	16913	1116	39	0	416	0	UBQLN3	11	5529234	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1401956	5529234	129477282	692	18964										
OR56B1	387748	hgsc.bcm.edu	37	chr11	5758619	5758619	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatgtgttgcacaacatcatCcccccttccctcaaccctac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:5758619delC	ENST00000317121.3	+	1	939	c.873delC	c.(871-873)atcfs	p.I291fs	TRIM5_ENST00000380027.1_Intron	NM_001005180.2	NP_001005180.1	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B, member 1	291						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.086)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.184)		ACAACATCATCCCCCCTTCCC	0.403																																					p.I291fs		Atlas-INDEL	.											.	OR56B1	38	.	0			c.872delT						.						290	270	277					11																	5758619		2201	4297	6498	SO:0001589	frameshift_variant	387748	exon1			.	BK004386	CCDS31395.1	11p15.4	2012-08-09		2004-03-10	ENSG00000181023	ENSG00000181023		"GPCR / Class A : Olfactory receptors"	15245	protein-coding gene	gene with protein product				OR56B1P			Standard	NM_001005180		Approved		uc001mbt.2	Q8NGI3	OTTHUMG00000066891	ENST00000317121.3:c.873delC	chr11.hg19:g.5758619delC	ENSP00000322939:p.Ile291fs	120.0	0.0		146.0	10.0	NM_001005180	B2RNY6|B3KV42|Q6IF76	Frame_Shift_Del	DEL	ENST00000317121.3	hg19	CCDS31395.1																																																																																			.	.		0.403	OR56B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143354.1	NM_001005180		-	5758619	C	-	5758619	7	5	114	1	0	1	0	1	0	0	0	0	11146	845	30	0	875	0	OR56B1	11	5758619	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	229385	5758619	129247897	693	18965										
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411941	6411941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttggatgggcctggtgctggCgctggcgctggcgctggcgc	20	11	0	0	rs550365194|rs550067660|rs71467507|rs78250081|rs558809956|rs3838786	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:6411941C>T	ENST00000342245.4	+	1	281	c.113C>T	c.(112-114)gCg>gTg	p.A38V	SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000356761.2_Missense_Mutation_p.A38V|SMPD1_ENST00000299397.3_Missense_Mutation_p.A38V|SMPD1_ENST00000527275.1_Missense_Mutation_p.A38V	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	38					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	ctggtgctggcgctggcgctg	0.711																																					p.A38V		Atlas-SNP	.											.	SMPD1	108	.	0			c.C113T						.						11	14	13					11																	6411941		2185	4258	6443	SO:0001583	missense	6609	exon1			TGCTGGCGCTGGC	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.113C>T	chr11.hg19:g.6411941C>T	ENSP00000340409:p.Ala38Val	13.0	0.0		20.0	5.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	hg19	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.234305	0.39498	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.09723	2.95;2.95;2.95;2.95	4.54	-1.08	0.09936	.	.	.	.	.	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B;B	0.15473	0.002;0.013	B;B	0.10450	0.002;0.005	T	0.47275	-0.9130	9	0.12103	T	0.63	.	6.8659	0.24093	0.0:0.5614:0.262:0.1766	.	38;38	E9PKS3;G3XAB5	.;.	V	38	ENSP00000299397:A38V;ENSP00000349203:A38V;ENSP00000340409:A38V;ENSP00000435350:A38V	ENSP00000299397:A38V	A	+	2	0	SMPD1	6368517	0.000000	0.05858	0.130000	0.21974	0.033000	0.12548	-2.110000	0.01334	-0.479000	0.06813	-1.305000	0.01319	GCG	.	.		0.711	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		T	6411941	C	T	6411941	3	4	114	1	0	0	0	0	1	0	0	0	14819	768	27	1	115	1	SMPD1	11	6411941	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	653322	6411941	128594575	694	18966										
OR6A2	8590	hgsc.bcm.edu	37	chr11	6816516	6816516	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgcacacacagccggccacTgacaatgactgggtagtgga	12	12	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:6816516T>C	ENST00000332601.3	-	1	612	c.424A>G	c.(424-426)Agt>Ggt	p.S142G		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	142					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AGCCGGCCACTGACAATGACT	0.517																																					p.S142G		Atlas-SNP	.											.	OR6A2	68	.	0			c.A424G						.						62	62	62					11																	6816516		2201	4296	6497	SO:0001583	missense	8590	exon1			GGCCACTGACAAT	AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"GPCR / Class A : Olfactory receptors"	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.424A>G	chr11.hg19:g.6816516T>C	ENSP00000330384:p.Ser142Gly	66.0	0.0		78.0	4.0	NM_003696	Q3MJC7|Q6IF35|Q9H206	Missense_Mutation	SNP	ENST00000332601.3	hg19	CCDS7772.1	.	.	.	.	.	.	.	.	.	.	T	11.30	1.597517	0.28445	.	.	ENSG00000184933	ENST00000332601	T	0.01998	4.51	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.278035	0.31145	N	0.008167	T	0.03871	0.0109	L	0.59912	1.85	0.36081	D	0.842809	B	0.10296	0.003	B	0.09377	0.004	T	0.19451	-1.0305	10	0.52906	T	0.07	.	13.1051	0.59244	0.0:0.0:0.0:1.0	.	142	O95222	OR6A2_HUMAN	G	142	ENSP00000330384:S142G	ENSP00000330384:S142G	S	-	1	0	OR6A2	6773092	0.762000	0.28451	0.345000	0.25642	0.081000	0.17604	0.895000	0.28363	2.264000	0.75181	0.533000	0.62120	AGT	.	.		0.517	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696		C	6816516	T	C	6816516	3	2	114	1	0	0	0	0	1	0	0	0	11195	1580	55	2	563	2	OR6A2	11	6816516	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	404575	6816516	128190000	695	18967										
NLRP14	338323	hgsc.bcm.edu	37	chr11	7092523	7092523	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taatgaagaagatgtgtcttGgtggtggtgtttctgatttg	14	2	2	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:7092523G>T	ENST00000299481.4	+	12	3612	c.3266G>T	c.(3265-3267)tGg>tTg	p.W1089L		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	1089					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GATGTGTCTTGGTGGTGGTGT	0.368																																					p.W1089L		Atlas-SNP	.											.	NLRP14	187	.	0			c.G3266T						.						121	115	117					11																	7092523		2201	4296	6497	SO:0001583	missense	338323	exon12			TGTCTTGGTGGTG	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.3266G>T	chr11.hg19:g.7092523G>T	ENSP00000299481:p.Trp1089Leu	52.0	0.0		74.0	22.0	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	hg19	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974465	0.53720	.	.	ENSG00000158077	ENST00000299481	T	0.70045	-0.45	4.17	3.26	0.37387	.	0.000000	0.41712	D	0.000823	T	0.72374	0.3452	L	0.46157	1.445	0.32892	D	0.511986	D	0.89917	1.0	D	0.80764	0.994	T	0.77175	-0.2684	10	0.66056	D	0.02	.	7.8046	0.29195	0.1123:0.0:0.8877:0.0	.	1089	Q86W24	NAL14_HUMAN	L	1089	ENSP00000299481:W1089L	ENSP00000299481:W1089L	W	+	2	0	NLRP14	7049099	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	1.000000	0.29770	1.354000	0.45846	0.655000	0.94253	TGG	.	.		0.368	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		T	7092523	G	T	7092523	3	4	114	1	0	0	0	0	1	0	0	0	10485	1357	47	3	3308	3	NLRP14	11	7092523	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	276007	7092523	127913993	696	18968										
OVCH2	341277	hgsc.bcm.edu	37	chr11	7721868	7721868	+	RNA	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggatgtgttcgtggatccaGggaagcactttactaatgtc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:7721868delG	ENST00000534193.2	-	0	902				OVCH2_ENST00000454689.1_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		CGTGGATCCAGGGAAGCACTT	0.507																																					p.W293fs		Atlas-INDEL	.											.	OVCH2	47	.	0			c.877delT						.						100	94	96					11																	7721868		1982	4166	6148			341277	exon7			.	BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"ovochymase 2"			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		chr11.hg19:g.7721868delG		184.0	0.0		208.0	13.0	NM_198185		Frame_Shift_Del	DEL	ENST00000534193.2	hg19																																																																																				.	.		0.507	OVCH2-001	KNOWN	non_canonical_polymorphism|not_organism_supported|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000383929.7	NM_198185		-	7721868	G	-	7721868	6	5	114	0	1	1	0	1	0	0	0	0	11333	987	35	0		0	OVCH2	11	7721868	RNA	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	629345	7721868	127284648	697	18969										
TUB	7275	hgsc.bcm.edu	37	chr11	8117161	8117161	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggggagacggcagctggtGggggcgaacggcccagcggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:8117161delG	ENST00000299506.2	+	5	663	c.514delG	c.(514-516)gggfs	p.G173fs	TUB_ENST00000534099.1_Frame_Shift_Del_p.G179fs|TUB_ENST00000305253.4_Frame_Shift_Del_p.G228fs	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	173					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		GGCAGCTGGTGGGGGCGAACG	0.642																																					p.G226fs		Atlas-INDEL	.											.	TUB	71	.	0			c.678delT						.						22	24	23					11																	8117161		2197	4292	6489	SO:0001589	frameshift_variant	7275	exon6			.	U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"tubby (mouse) homolog", "tubby homolog (mouse)"			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.514delG	chr11.hg19:g.8117161delG	ENSP00000299506:p.Gly173fs	174.0	0.0		216.0	13.0	NM_003320	D3DQU4|O00293|Q6B007	Frame_Shift_Del	DEL	ENST00000299506.2	hg19	CCDS7787.1																																																																																			.	.		0.642	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320		-	8117161	G	-	8117161	7	5	114	1	0	1	0	1	0	0	0	0	16757	1348	47	0	743	0	TUB	11	8117161	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	395293	8117161	126889355	698	18970										
USP47	55031	hgsc.bcm.edu	37	chr11	11977603	11977603	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agcaaagaaatgaactgatgAaaaaagaaagcagtcgactc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:11977603delA	ENST00000399455.2	+	29	4129	c.4009delA	c.(4009-4011)aaafs	p.K1338fs	USP47_ENST00000539466.1_Frame_Shift_Del_p.K120fs|USP47_ENST00000339865.5_Frame_Shift_Del_p.K1250fs|USP47_ENST00000527733.1_Frame_Shift_Del_p.K1318fs|USP47_ENST00000305481.6_3'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1338					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		TGAACTGATGAAAAAAGAAAG	0.358																																					p.M1248fs		Atlas-INDEL	.											.	USP47	91	.	0			c.3744delG						.						106	105	106					11																	11977603		1831	4077	5908	SO:0001589	frameshift_variant	55031	exon27			.	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.4009delA	chr11.hg19:g.11977603delA	ENSP00000382382:p.Lys1338fs	137.0	0.0		150.0	11.0	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Frame_Shift_Del	DEL	ENST00000399455.2	hg19																																																																																				.	.		0.358	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		-	11977603	A	-	11977603	7	5	114	1	0	1	0	1	0	0	0	0	17093	247	9	0	3851	0	USP47	11	11977603	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3860442	11977603	123028913	699	18971										
PARVA	55742	hgsc.bcm.edu	37	chr11	12499491	12499491	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggacaagtcctgcagaagcTtttcggtaggagagttgagt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:12499491delT	ENST00000550549.1	+	4	444	c.395delT	c.(394-396)cttfs	p.L132fs	PARVA_ENST00000334956.8_Frame_Shift_Del_p.L172fs|PARVA_ENST00000539723.1_Frame_Shift_Del_p.L132fs|PARVA_ENST00000538608.1_Frame_Shift_Del_p.L79fs			Q9NVD7	PARVA_HUMAN	parvin, alpha	132	CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|actin-mediated cell contraction (GO:0070252)|cell junction assembly (GO:0034329)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|heterotypic cell-cell adhesion (GO:0034113)|outflow tract septum morphogenesis (GO:0003148)|regulation of cell shape (GO:0008360)|smooth muscle cell chemotaxis (GO:0071670)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)	11				Epithelial(150;0.00624)		CTGCAGAAGCTTTTCGGTAGG	0.403																																					p.L172fs		Atlas-INDEL	.											.	PARVA	27	.	0			c.514delC						.						175	171	173					11																	12499491		1926	4126	6052	SO:0001589	frameshift_variant	55742	exon4			.	AF237771	CCDS44541.1, CCDS44541.2	11p15.3	2014-06-13	2005-05-26		ENSG00000197702	ENSG00000197702		"Parvins"	14652	protein-coding gene	gene with protein product		608120	"matrix-remodelling associated 2"	MXRA2		11171322	Standard	NM_018222		Approved	FLJ12254, FLJ10793	uc001mki.4	Q9NVD7	OTTHUMG00000165778	ENST00000550549.1:c.395delT	chr11.hg19:g.12499491delT	ENSP00000447198:p.Leu132fs	133.0	0.0		173.0	11.0	NM_018222	Q96C85|Q9HA48	Frame_Shift_Del	DEL	ENST00000550549.1	hg19																																																																																				.	.		0.403	PARVA-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018222		-	12499491	T	-	12499491	7	5	114	1	0	1	0	1	0	0	0	0	11477	1609	56	0	409	0	PARVA	11	12499491	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	521888	12499491	122507025	700	18972										
PLEKHA7	144100	hgsc.bcm.edu	37	chr11	16816462	16816462	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agatgaacatctcacccggaTtttttactgactccactaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:16816462delT	ENST00000355661.3	-	18	2523	c.2513delA	c.(2512-2514)aatfs	p.N838fs	PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000448080.2_Frame_Shift_Del_p.N838fs|PLEKHA7_ENST00000531066.1_Frame_Shift_Del_p.N838fs			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	838					epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)	p.N838fs*61(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						CTCACCCGGATTTTTTACTGA	0.498																																					p.N838fs		Atlas-INDEL	.											.	PLEKHA7	120	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2514delT						.						154	151	152					11																	16816462		2200	4294	6494	SO:0001589	frameshift_variant	144100	exon18			.	BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"Pleckstrin homology (PH) domain containing"	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.2513delA	chr11.hg19:g.16816462delT	ENSP00000347883:p.Asn838fs	121.0	0.0		140.0	10.0	NM_175058	B4DK33|B4DWC3|Q86VZ7	Frame_Shift_Del	DEL	ENST00000355661.3	hg19	CCDS31434.1																																																																																			.	.		0.498	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058		-	16816462	T	-	16816462	7	5	114	1	0	1	0	1	0	0	0	0	12070	1493	52	0	876	0	PLEKHA7	11	16816462	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	4316971	16816462	118190054	701	18973										
NUCB2	4925	hgsc.bcm.edu	37	chr11	17332420	17332420	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agactcgtcatgaagaatttAaaaaatatgaaatgatgaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:17332420delA	ENST00000529010.1	+	7	751	c.532delA	c.(532-534)aaafs	p.K179fs	NUCB2_ENST00000458064.2_Frame_Shift_Del_p.K179fs|NUCB2_ENST00000323688.6_Frame_Shift_Del_p.K179fs	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	179						cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						TGAAGAATTTAAAAAATATGA	0.279																																					p.F177fs		Atlas-INDEL	.											.	NUCB2	31	.	0			c.531delT						.						67	67	67					11																	17332420		1800	4032	5832	SO:0001589	frameshift_variant	4925	exon7			.	AF052642	CCDS41623.1	11p15.1	2013-01-10						"EF-hand domain containing"	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		ENST00000529010.1:c.532delA	chr11.hg19:g.17332420delA	ENSP00000436455:p.Lys179fs	130.0	0.0		157.0	11.0	NM_005013	A8K642|D3DQX5|Q8NFT5	Frame_Shift_Del	DEL	ENST00000529010.1	hg19	CCDS41623.1																																																																																			.	.		0.279	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013		-	17332420	A	-	17332420	7	5	114	1	0	1	0	1	0	0	0	0	10728	363	13	0	550	0	NUCB2	11	17332420	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	515958	17332420	117674096	702	18974										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17449417	17449417	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtggactgggccatacctcGggggatacgaatggtgatgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:17449417delG	ENST00000389817.3	-	15	2181	c.2113delC	c.(2113-2115)cgafs	p.R705fs	ABCC8_ENST00000302539.4_Frame_Shift_Del_p.R705fs|ABCC8_ENST00000528202.1_5'Flank			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	705	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	GCCATACCTCGGGGGATACGA	0.537																																					p.R705fs		Atlas-INDEL	.											.	ABCC8	170	.	0			c.2114delG						.						138	112	121					11																	17449417		2200	4293	6493	SO:0001589	frameshift_variant	6833	exon15			.	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.2113delC	chr11.hg19:g.17449417delG	ENSP00000374467:p.Arg705fs	176.0	0.0		210.0	13.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Frame_Shift_Del	DEL	ENST00000389817.3	hg19	CCDS31437.1																																																																																			.	.		0.537	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		-	17449417	G	-	17449417	7	5	114	1	0	1	0	1	0	0	0	0	58	1124	39	0	2732	0	ABCC8	11	17449417	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	116997	17449417	117557099	703	18975										
IGSF22	283284	hgsc.bcm.edu	37	chr11	18741308	18741308	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctttgagcttcctgagcagCccccgaaagtcggtgaaacc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:18741308delC	ENST00000513874.1	-	7	790	c.651delG	c.(649-651)gggfs	p.G217fs	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	217	Lys-rich.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TCCTGAGCAGCCCCCGAAAGT	0.522																																					p.L218fs		Atlas-INDEL	.											.	IGSF22	211	.	0			c.652delC						.						150	151	151					11																	18741308		1889	4112	6001	SO:0001589	frameshift_variant	283284	exon7			.	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.651delG	chr11.hg19:g.18741308delC	ENSP00000421191:p.Gly217fs	141.0	0.0		191.0	13.0	NM_173588	A6NNA0|D6RGV7	Frame_Shift_Del	DEL	ENST00000513874.1	hg19	CCDS41625.2																																																																																			.	.		0.522	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		-	18741308	C	-	18741308	7	5	114	1	0	1	0	1	0	0	0	0	7609	726	26	0	3397	0	IGSF22	11	18741308	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1291891	18741308	116265208	704	18976										
CCDC73	493860	hgsc.bcm.edu	37	chr11	32663555	32663555	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctagtgctttttcatgctcaTtttgaagattaagaaacttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:32663555delT	ENST00000335185.5	-	13	1056	c.1013delA	c.(1012-1014)aatfs	p.N338fs	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	338										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TTCATGCTCATTTTGAAGATT	0.249																																					p.T338fs		Atlas-INDEL	.											.	CCDC73	136	.	0			c.1014delT						.						77	69	71					11																	32663555		1785	4050	5835	SO:0001589	frameshift_variant	493860	exon13			.	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.1013delA	chr11.hg19:g.32663555delT	ENSP00000335325:p.Asn338fs	172.0	0.0		161.0	10.0	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Frame_Shift_Del	DEL	ENST00000335185.5	hg19	CCDS41630.1																																																																																			.	.		0.249	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		-	32663555	T	-	32663555	7	5	114	1	0	1	0	1	0	0	0	0	2848	1493	52	0	2250	0	CCDC73	11	32663555	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	13922247	32663555	102342961	705	18977										
CCDC73	493860	hgsc.bcm.edu	37	chr11	32722338	32722338	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttaaaaaaattataaataccTtttcttcttccagggcacac	3	9	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:32722338T>C	ENST00000335185.5	-	5	357	c.314A>G	c.(313-315)aAg>aGg	p.K105R	CCDC73_ENST00000534415.1_5'UTR|CCDC73_ENST00000531481.1_Splice_Site_p.K105R	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	105										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					tataaataCCTTTTCTTCTTC	0.259																																					p.C105C		Atlas-SNP	.											.	CCDC73	136	.	0			c.G314G						.						15	13	14					11																	32722338		900	2018	2918	SO:0001630	splice_region_variant	493860	exon5			AATACCTTTTCTT	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.315+1A>G	chr11.hg19:g.32722338T>C		62.0	0.0		82.0	4.0	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Silent	SNP	ENST00000335185.5	hg19	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.129783	0.77549	.	.	ENSG00000186714	ENST00000335185;ENST00000531481	.	.	.	4.72	4.72	0.59763	.	.	.	.	.	T	0.67776	0.2929	L	0.56769	1.78	0.33360	D	0.572167	D;D;D	0.89917	0.974;0.998;1.0	D;D;D	0.87578	0.969;0.994;0.998	T	0.75806	-0.3188	8	0.48119	T	0.1	.	13.4851	0.61359	0.0:0.0:0.0:1.0	.	105;105;105	A6H8Y7;Q6ZRK6-2;Q6ZRK6	.;.;CCD73_HUMAN	R	105	.	ENSP00000335325:K105R	K	-	2	0	CCDC73	32678914	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.185000	0.50934	1.899000	0.54978	0.459000	0.35465	AAG	.	.		0.259	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	Missense_Mutation	C	32722338	T	C	32722338	5	2	114	1	0	0	0	0	0	0	1	0	2848	1623	56	2	2981	2	CCDC73	11	32722338	Splice_Site	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	58783	32722338	102284178	706	18978										
DEPDC7	91614	hgsc.bcm.edu	37	chr11	33050250	33050250	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aacagcaagaggctgtacctAaaattcctcaacctaagagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:33050250delA	ENST00000241051.3	+	4	786	c.694delA	c.(694-696)aaafs	p.K232fs	DEPDC7_ENST00000311388.3_Frame_Shift_Del_p.K223fs	NM_001077242.1	NP_001070710.1	Q96QD5	DEPD7_HUMAN	DEP domain containing 7	232					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17						GGCTGTACCTAAAATTCCTCA	0.428																																					p.P231fs		Atlas-INDEL	.											.	DEPDC7	94	.	0			c.693delT						.						106	101	103					11																	33050250		1922	4140	6062	SO:0001589	frameshift_variant	91614	exon4			.		CCDS41632.1, CCDS41633.1	11p13	2006-03-24			ENSG00000121690	ENSG00000121690			29899	protein-coding gene	gene with protein product		612294				10568747	Standard	NM_001077242		Approved		uc001mub.3	Q96QD5	OTTHUMG00000166242	ENST00000241051.3:c.694delA	chr11.hg19:g.33050250delA	ENSP00000241051:p.Lys232fs	132.0	0.0		166.0	10.0	NM_001077242	G5E941|Q8N602|Q8NCU9|Q9UGK5	Frame_Shift_Del	DEL	ENST00000241051.3	hg19	CCDS41632.1																																																																																			.	.		0.428	DEPDC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388655.1	NM_139160		-	33050250	A	-	33050250	7	5	114	1	0	1	0	1	0	0	0	0	4446	363	13	0	758	0	DEPDC7	11	33050250	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	327912	33050250	101956266	707	18979										
NAT10	55226	hgsc.bcm.edu	37	chr11	34158558	34158558	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctggatttgttcctgtttaTctgagacagaccccggtgag	12	9	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:34158558T>C	ENST00000257829.3	+	21	2402	c.2196T>C	c.(2194-2196)taT>taC	p.Y732Y	NAT10_ENST00000531159.2_Silent_p.Y660Y|NAT10_ENST00000527971.1_Intron	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	732	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.|Required for localization to the nucleolus and midbody.					membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				TTCCTGTTTATCTGAGACAGA	0.512																																					p.Y732Y		Atlas-SNP	.											.	NAT10	78	.	0			c.T2196C						.						128	116	120					11																	34158558		2202	4298	6500	SO:0001819	synonymous_variant	55226	exon21			TGTTTATCTGAGA	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.2196T>C	chr11.hg19:g.34158558T>C		95.0	0.0		122.0	6.0	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Silent	SNP	ENST00000257829.3	hg19	CCDS7889.1																																																																																			.	.		0.512	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		C	34158558	T	C	34158558	2	2	114	1	0	0	0	0	0	0	0	1	10183	1442	50	2		2	NAT10	11	34158558	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1108308	34158558	100847958	708	18980										
CAT	847	hgsc.bcm.edu	37	chr11	34470817	34470817	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttacagtagggccccgtgggCcccttcttgttcaggatgtg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:34470817delC	ENST00000241052.4	+	2	234	c.145delC	c.(145-147)cccfs	p.P49fs		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	49					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	GCCCCGTGGGCCCCTTCTTGT	0.468																																					p.G48fs		Atlas-INDEL	.											.	CAT	42	.	0			c.144delG						.						95	96	95					11																	34470817		2202	4298	6500	SO:0001589	frameshift_variant	847	exon2			.	AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.145delC	chr11.hg19:g.34470817delC	ENSP00000241052:p.Pro49fs	106.0	0.0		164.0	10.0	NM_001752	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Frame_Shift_Del	DEL	ENST00000241052.4	hg19	CCDS7891.1																																																																																			.	.		0.468	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752		-	34470817	C	-	34470817	7	5	114	1	0	1	0	1	0	0	0	0	2688	739	26	0	151	0	CAT	11	34470817	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	312259	34470817	100535699	709	18981										
PDHX	8050	hgsc.bcm.edu	37	chr11	34953022	34953022	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaaacattgtgaaatggctgAaaaaggaaggtgaggaggta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:34953022delA	ENST00000227868.4	+	2	316	c.232delA	c.(232-234)aaafs	p.K79fs	PDHX_ENST00000430469.2_Frame_Shift_Del_p.K79fs|PDHX_ENST00000448838.3_Frame_Shift_Del_p.K64fs			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	79	Lipoyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.				cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			GAAATGGCTGAAAAAGGAAGG	0.363																																					p.L77fs		Atlas-INDEL	.											.	PDHX	40	.	0			c.231delG						.						113	107	109					11																	34953022		2202	4298	6500	SO:0001589	frameshift_variant	8050	exon2			.	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.232delA	chr11.hg19:g.34953022delA	ENSP00000227868:p.Lys79fs	184.0	0.0		211.0	14.0	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Frame_Shift_Del	DEL	ENST00000227868.4	hg19	CCDS7896.1																																																																																			.	.		0.363	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477		-	34953022	A	-	34953022	7	5	114	1	0	1	0	1	0	0	0	0	11676	247	9	0	357	0	PDHX	11	34953022	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	482205	34953022	100053494	710	18982										
PDHX	8050	hgsc.bcm.edu	37	chr11	35016619	35016619	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcagcgccagctcataacagTcacaatgtcaagtgacagtc	9	12	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:35016619T>C	ENST00000227868.4	+	11	1490	c.1406T>C	c.(1405-1407)gTc>gCc	p.V469A	PDHX_ENST00000430469.2_Missense_Mutation_p.V242A|PDHX_ENST00000477173.3_Intron|PDHX_ENST00000448838.3_Missense_Mutation_p.V454A			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	469					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			CTCATAACAGTCACAATGTCA	0.493																																					p.V469A		Atlas-SNP	.											.	PDHX	40	.	0			c.T1406C						.						126	117	120					11																	35016619		2202	4298	6500	SO:0001583	missense	8050	exon11			TAACAGTCACAAT	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.1406T>C	chr11.hg19:g.35016619T>C	ENSP00000227868:p.Val469Ala	84.0	0.0		98.0	4.0	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	hg19	CCDS7896.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.51|16.51	3.144021|3.144021	0.57044|0.57044	.|.	.|.	ENSG00000110435|ENSG00000110435	ENST00000526309|ENST00000448838;ENST00000227868;ENST00000430469	.|T;T;T	.|0.50001	.|0.76;0.76;0.76	6.04|6.04	6.04|6.04	0.98038|0.98038	.|2-oxoacid dehydrogenase acyltransferase, catalytic domain (1);Chloramphenicol acetyltransferase-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.66848|0.66848	0.2831|0.2831	M|M	0.69248|0.69248	2.105|2.105	0.80722|0.80722	D|D	1|1	.|D;D;P	.|0.76494	.|0.999;0.977;0.756	.|D;D;P	.|0.80764	.|0.994;0.934;0.456	T|T	0.65915|0.65915	-0.6052|-0.6052	5|10	.|0.41790	.|T	.|0.15	-22.7959|-22.7959	15.7697|15.7697	0.78157|0.78157	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|242;454;469	.|E9PBP7;E9PB14;O00330	.|.;.;ODPX_HUMAN	P|A	157|454;469;242	.|ENSP00000389404:V454A;ENSP00000227868:V469A;ENSP00000415695:V242A	.|ENSP00000227868:V469A	S|V	+|+	1|2	0|0	PDHX|PDHX	34973195|34973195	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.698000|0.698000	0.40448|0.40448	7.647000|7.647000	0.83462|0.83462	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	TCA|GTC	.	.		0.493	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477		C	35016619	T	C	35016619	3	2	114	1	0	0	0	0	1	0	0	0	11676	1667	58	2	1567	2	PDHX	11	35016619	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	63597	35016619	99989897	711	18983										
CD82	3732	hgsc.bcm.edu	37	chr11	44639810	44639810	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccctgttcctgcgaagtcaaGggggaagaggacaacagcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:44639810delG	ENST00000227155.4	+	8	785	c.537delG	c.(535-537)aagfs	p.K179fs	CD82_ENST00000530931.1_3'UTR|CD82_ENST00000342935.3_Frame_Shift_Del_p.K154fs	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	179						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						GCGAAGTCAAGGGGGAAGAGG	0.597																																					p.K179fs		Atlas-INDEL	.											.	CD82	27	.	0			c.536delA						.						68	60	63					11																	44639810		2203	4299	6502	SO:0001589	frameshift_variant	3732	exon8			.	U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"CD molecules", "Tetraspanins"	6210	protein-coding gene	gene with protein product	"suppression of tumorigenicity 6", "R2 leukocyte antigen"	600623	"kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))", "CD82 antigen"	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.537delG	chr11.hg19:g.44639810delG	ENSP00000227155:p.Lys179fs	129.0	0.0		163.0	10.0	NM_002231	D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Frame_Shift_Del	DEL	ENST00000227155.4	hg19	CCDS7909.1																																																																																			.	.		0.597	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1			-	44639810	G	-	44639810	7	5	114	1	0	1	0	1	0	0	0	0	3042	991	35	0	559	0	CD82	11	44639810	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	9623191	44639810	90366706	712	18984										
TSPAN18	90139	hgsc.bcm.edu	37	chr11	44931375	44931375	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcctacatcctcctggccatGgggggcctgctctttctgct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:44931375delG	ENST00000520358.2	+	5	598	c.183delG	c.(181-183)atgfs	p.M61fs	TSPAN18_ENST00000340160.3_Frame_Shift_Del_p.M61fs			Q96SJ8	TSN18_HUMAN	tetraspanin 18	61						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						TCCTGGCCATGGGGGGCCTGC	0.647																																					p.M61fs		Atlas-INDEL	.											.	TSPAN18	38	.	0			c.182delT						.						48	52	51					11																	44931375		2203	4299	6502	SO:0001589	frameshift_variant	90139	exon4			.	AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"Tetraspanins"	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.183delG	chr11.hg19:g.44931375delG	ENSP00000429993:p.Met61fs	110.0	0.0		149.0	11.0	NM_130783	Q6UY44|Q8NBI9	Frame_Shift_Del	DEL	ENST00000520358.2	hg19	CCDS7910.1																																																																																			.	.		0.647	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783		-	44931375	G	-	44931375	7	5	114	1	0	1	0	1	0	0	0	0	16657	1348	47	0	189	0	TSPAN18	11	44931375	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	291565	44931375	90075141	713	18985										
PHF21A	51317	hgsc.bcm.edu	37	chr11	45957241	45957241	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctagttgttctcgttcttgTtttaaatctgaactccattt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:45957241delT	ENST00000418153.2	-	17	1930	c.1731delA	c.(1729-1731)aaafs	p.K577fs	PHF21A_ENST00000323180.6_Frame_Shift_Del_p.K531fs|PHF21A_ENST00000257821.4_Frame_Shift_Del_p.K578fs|PHF21A_ENST00000527753.1_5'Flank			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	577	Required for transcriptional repression.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						CTCGTTCTTGTTTTAAATCTG	0.328																																					p.Q578fs		Atlas-INDEL	.											.	PHF21A	107	.	0			c.1732delC						.						344	287	307					11																	45957241		2202	4298	6500	SO:0001589	frameshift_variant	51317	exon17			.	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.1731delA	chr11.hg19:g.45957241delT	ENSP00000398824:p.Lys577fs	161.0	0.0		145.0	10.0	NM_001101802	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Frame_Shift_Del	DEL	ENST00000418153.2	hg19	CCDS44578.1																																																																																			.	.		0.328	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		-	45957241	T	-	45957241	7	5	114	1	0	1	0	1	0	0	0	0	11842	1722	60	0	319	0	PHF21A	11	45957241	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1025866	45957241	89049275	714	18986										
MDK	4192	hgsc.bcm.edu	37	chr11	46404272	46404272	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccgcgtcaccaagccctgcaCccccaagaccaaagcaaagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:46404272delC	ENST00000405308.2	+	4	809	c.380delC	c.(379-381)accfs	p.T127fs	MDK_ENST00000407067.1_Frame_Shift_Del_p.T127fs|MDK_ENST00000395565.1_Frame_Shift_Del_p.T127fs|MDK_ENST00000395566.4_Frame_Shift_Del_p.T127fs|MDK_ENST00000533283.1_3'UTR|MDK_ENST00000395569.4_Frame_Shift_Del_p.T71fs|MDK_ENST00000359803.3_Frame_Shift_Del_p.T127fs	NM_001270550.1	NP_001257479.1	P21741	MK_HUMAN	midkine (neurite growth-promoting factor 2)	127					adrenal gland development (GO:0030325)|behavioral fear response (GO:0001662)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cerebellar granular layer development (GO:0021681)|cerebral cortex development (GO:0021987)|defecation (GO:0030421)|dentate gyrus development (GO:0021542)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of cell division (GO:0051781)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of behavior (GO:0050795)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to wounding (GO:0009611)|short-term memory (GO:0007614)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			lung(1)	1				GBM - Glioblastoma multiforme(35;0.0252)|Lung(87;0.14)		AAGCCCTGCACCCCCAAGACC	0.657																																					p.T127fs		Atlas-INDEL	.											.	MDK	4	.	0			c.379delA						.						49	37	41					11																	46404272		2200	4298	6498	SO:0001589	frameshift_variant	4192	exon4			.		CCDS7919.1, CCDS59226.1	11p11.2	2008-07-18			ENSG00000110492	ENSG00000110492			6972	protein-coding gene	gene with protein product		162096		NEGF2		8406506	Standard	NM_002391		Approved	MK, FLJ27379	uc001nco.4	P21741	OTTHUMG00000150315	ENST00000405308.2:c.380delC	chr11.hg19:g.46404272delC	ENSP00000385451:p.Thr127fs	252.0	0.0		289.0	19.0	NM_001012333	Q2LEK4|Q9UCC7	Frame_Shift_Del	DEL	ENST00000405308.2	hg19	CCDS7919.1																																																																																			.	.		0.657	MDK-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317546.2	NM_001012334		-	46404272	C	-	46404272	7	5	114	1	0	1	0	1	0	0	0	0	9420	507	18	0	390	0	MDK	11	46404272	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	447031	46404272	88602244	715	18987										
LRP4	4038	hgsc.bcm.edu	37	chr11	46903431	46903431	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gttcaatcttggggctcgcaCcccagtcagtccaatacatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:46903431delC	ENST00000378623.1	-	20	2878	c.2636delG	c.(2635-2637)ggtfs	p.G879fs		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	879					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GGGGCTCGCACCCCAGTCAGT	0.493																																					p.G879fs		Atlas-INDEL	.											.	LRP4	160	.	0			c.2637delT						.						69	63	65					11																	46903431		2201	4299	6500	SO:0001589	frameshift_variant	4038	exon20			.	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.2636delG	chr11.hg19:g.46903431delC	ENSP00000367888:p.Gly879fs	129.0	0.0		157.0	10.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Frame_Shift_Del	DEL	ENST00000378623.1	hg19	CCDS31478.1																																																																																			.	.		0.493	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		-	46903431	C	-	46903431	7	5	114	1	0	1	0	1	0	0	0	0	8968	507	18	0	3157	0	LRP4	11	46903431	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	499159	46903431	88103085	716	18988										
NR1H3	10062	hgsc.bcm.edu	37	chr11	47283563	47283563	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ataaccgggaagactttgccAaagcaggtgagaactgagat					rs191811598		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:47283563delA	ENST00000467728.1	+	6	2220	c.982delA	c.(982-984)aaafs	p.K328fs	NR1H3_ENST00000405576.1_Frame_Shift_Del_p.K223fs|NR1H3_ENST00000527949.1_Frame_Shift_Del_p.K177fs|NR1H3_ENST00000529540.1_3'UTR|NR1H3_ENST00000405853.3_Frame_Shift_Del_p.K268fs|NR1H3_ENST00000481889.2_Frame_Shift_Del_p.K347fs|NR1H3_ENST00000407404.1_Frame_Shift_Del_p.K268fs|NR1H3_ENST00000395397.3_Frame_Shift_Del_p.K283fs|NR1H3_ENST00000441012.2_Frame_Shift_Del_p.K328fs			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	328	Ligand-binding. {ECO:0000255}.				apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						AGACTTTGCCAAAGCAGGTGA	0.468																																					p.A333fs		Atlas-INDEL	.											.	NR1H3	52	.	0			c.999delC						.						110	106	107					11																	47283563		2201	4298	6499	SO:0001589	frameshift_variant	10062	exon7			.	U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434		"Nuclear hormone receptors"	7966	protein-coding gene	gene with protein product	"liver X receptor-alpha"	602423				8621574, 7744246	Standard	NM_005693		Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.982delA	chr11.hg19:g.47283563delA	ENSP00000420656:p.Lys328fs	95.0	0.0		162.0	10.0	NM_001251934	A8K3J9|D3DQR1|Q8IW13|Q96H87	Frame_Shift_Del	DEL	ENST00000467728.1	hg19	CCDS7929.1																																																																																			.	.		0.468	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319214.3			-	47283563	A	-	47283563	7	5	114	1	0	1	0	1	0	0	0	0	10627	131	5	0	1004	0	NR1H3	11	47283563	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	380132	47283563	87722953	717	18989										
SLC43A1	8501	hgsc.bcm.edu	37	chr11	57259093	57259093	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaccttttgttgctgttcaTttgtctctgtgggtagggaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:57259093delT	ENST00000278426.3	-	10	1380	c.1025delA	c.(1024-1026)aatfs	p.N342fs	SLC43A1_ENST00000533515.1_5'UTR|SLC43A1_ENST00000528450.1_Frame_Shift_Del_p.N342fs	NM_003627.5	NP_003618.1			solute carrier family 43 (amino acid system L transporter), member 1											breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19						TTGCTGTTCATTTGTCTCTGT	0.637											OREG0020651	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N342fs		Atlas-INDEL	.											.	SLC43A1	48	.	0			c.1026delT						.						135	117	123					11																	57259093		2201	4296	6497	SO:0001589	frameshift_variant	8501	exon10			.	AF045584	CCDS7958.1	11q12.1	2013-07-17	2013-07-17	2003-09-12	ENSG00000149150	ENSG00000149150		"Solute carriers"	9225	protein-coding gene	gene with protein product		603733	"prostate cancer overexpressed gene 1"	POV1		9255310, 9722952	Standard	NM_003627		Approved	R00504, PB39	uc001nkk.3	O75387	OTTHUMG00000167030	ENST00000278426.3:c.1025delA	chr11.hg19:g.57259093delT	ENSP00000278426:p.Asn342fs	130.0	0.0	1021	161.0	10.0	NM_001198810		Frame_Shift_Del	DEL	ENST00000278426.3	hg19	CCDS7958.1																																																																																			.	.		0.637	SLC43A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392541.1	NM_003627		-	57259093	T	-	57259093	7	5	114	1	0	1	0	1	0	0	0	0	14647	1493	52	0	678	0	SLC43A1	11	57259093	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	9975530	57259093	77747423	718	18990										
MRPL16	54948	hgsc.bcm.edu	37	chr11	59575183	59575183	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattcactcaccaagattgcAaaattgccttctgtaaactc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:59575183delA	ENST00000300151.4	-	3	474	c.261delT	c.(259-261)tttfs	p.F87fs		NM_017840.3	NP_060310.1	Q9NX20	RM16_HUMAN	mitochondrial ribosomal protein L16	87					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|liver(1)|lung(8)	11						CCAAGATTGCAAAATTGCCTT	0.418																																					p.A88fs		Atlas-INDEL	.											.	MRPL16	25	.	0			c.262delG						.						269	282	278					11																	59575183		2201	4295	6496	SO:0001589	frameshift_variant	54948	exon3			.	AF183428	CCDS7976.1	11q12.1	2012-09-13			ENSG00000166902	ENSG00000166902		"Mitochondrial ribosomal proteins / large subunits"	14476	protein-coding gene	gene with protein product		611829					Standard	NM_017840		Approved	FLJ20484, PNAS-111	uc001noh.2	Q9NX20	OTTHUMG00000167410	ENST00000300151.4:c.261delT	chr11.hg19:g.59575183delA	ENSP00000300151:p.Phe87fs	170.0	0.0		216.0	13.0	NM_017840	Q9BYD0|Q9HB70	Frame_Shift_Del	DEL	ENST00000300151.4	hg19	CCDS7976.1																																																																																			.	.		0.418	MRPL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394521.1	NM_017840		-	59575183	A	-	59575183	7	5	114	1	0	1	0	1	0	0	0	0	9790	127	5	0	502	0	MRPL16	11	59575183	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2316090	59575183	75431333	719	18991										
EML3	256364	hgsc.bcm.edu	37	chr11	62379012	62379012	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taccagttccatctcctgctCctgcacccgaagccgctggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:62379012delC	ENST00000394773.2	-	2	386	c.79delG	c.(79-81)gagfs	p.E27fs	ROM1_ENST00000278833.3_5'Flank|EML3_ENST00000278845.4_Frame_Shift_Del_p.E27fs|ROM1_ENST00000534093.1_5'Flank|EML3_ENST00000494176.2_5'UTR|EML3_ENST00000529309.1_Frame_Shift_Del_p.E27fs|EML3_ENST00000531557.1_5'Flank	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	27						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						ATCTCCTGCTCCTGCACCCGA	0.642																																					p.E27fs		Atlas-INDEL	.											.	EML3	61	.	0			c.80delA						.						27	29	28					11																	62379012		2202	4299	6501	SO:0001589	frameshift_variant	256364	exon2			.	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"WD repeat domain containing"	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.79delG	chr11.hg19:g.62379012delC	ENSP00000378254:p.Glu27fs	119.0	0.0		256.0	17.0	NM_153265	Q6ZQW7|Q8NA55	Frame_Shift_Del	DEL	ENST00000394773.2	hg19	CCDS8023.2																																																																																			.	.		0.642	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265		-	62379012	C	-	62379012	7	5	114	1	0	1	0	1	0	0	0	0	5100	864	30	0	2695	0	EML3	11	62379012	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2803829	62379012	72627504	720	18992										
C11orf84	144097	hgsc.bcm.edu	37	chr11	63586119	63586119	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaccaaaaacctggaccctgAcccaggtgaaggggaggccc	13	13	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:63586119A>G	ENST00000294244.4	+	4	1027	c.728A>G	c.(727-729)gAc>gGc	p.D243G		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	243	Pro-rich.									endometrium(3)|kidney(1)|lung(3)|skin(1)	8						CTGGACCCTGACCCAGGTGAA	0.617																																					p.D243G		Atlas-SNP	.											.	C11orf84	33	.	0			c.A728G						.						41	48	45					11																	63586119		2201	4298	6499	SO:0001583	missense	144097	exon4			ACCCTGACCCAGG	BC007540	CCDS31594.1	11q13.1	2014-02-10			ENSG00000168005	ENSG00000168005			25115	protein-coding gene	gene with protein product						12477932	Standard	NM_138471		Approved		uc001nxt.3	Q9BUA3	OTTHUMG00000167746	ENST00000294244.4:c.728A>G	chr11.hg19:g.63586119A>G	ENSP00000294244:p.Asp243Gly	34.0	0.0		73.0	5.0	NM_138471	Q68CV7|Q6PHS2|Q96IH0	Missense_Mutation	SNP	ENST00000294244.4	hg19	CCDS31594.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.583846	0.28268	.	.	ENSG00000168005	ENST00000294244;ENST00000540893	T	0.50001	0.76	5.59	1.8	0.24995	.	0.534807	0.17920	N	0.157523	T	0.35364	0.0929	L	0.51422	1.61	0.25275	N	0.98948	B	0.06786	0.001	B	0.09377	0.004	T	0.35176	-0.9799	10	0.87932	D	0	-11.1871	2.6359	0.04957	0.5927:0.0:0.2125:0.1948	.	243	Q9BUA3	CK084_HUMAN	G	243;18	ENSP00000294244:D243G	ENSP00000294244:D243G	D	+	2	0	C11orf84	63342695	0.986000	0.35501	0.935000	0.37517	0.832000	0.47134	1.276000	0.33156	0.963000	0.38082	0.533000	0.62120	GAC	.	.		0.617	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471		G	63586119	A	G	63586119	3	3	114	1	0	0	0	0	1	0	0	0	1669	275	10	2	742	2	C11orf84	11	63586119	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1207107	63586119	71420397	721	18993										
RCOR2	283248	hgsc.bcm.edu	37	chr11	63679557	63679557	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcaaaggtggcctcagcagcGggggtggctgggacagcgag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:63679557delG	ENST00000301459.4	-	12	1739	c.1352delC	c.(1351-1353)ccgfs	p.P451fs	RCOR2_ENST00000473926.2_5'UTR	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	451	Pro-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						CCTCAGCAGCGGGGGTGGCTG	0.706																																					p.P451fs		Atlas-INDEL	.											.	RCOR2	43	.	0			c.1353delG						.						4	5	5					11																	63679557		1770	3514	5284	SO:0001589	frameshift_variant	283248	exon12			.	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.1352delC	chr11.hg19:g.63679557delG	ENSP00000301459:p.Pro451fs	142.0	0.0		153.0	10.0	NM_173587	Q96FP3	Frame_Shift_Del	DEL	ENST00000301459.4	hg19	CCDS8052.1																																																																																			.	.		0.706	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		-	63679557	G	-	63679557	7	5	114	1	0	1	0	1	0	0	0	0	13198	1116	39	0	223	0	RCOR2	11	63679557	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	93438	63679557	71326959	722	18994										
RCOR2	283248	hgsc.bcm.edu	37	chr11	63681765	63681765	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atctgcaggatcgggctctcCctcactcacgcctcctcgac	8	18	4	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:63681765C>T	ENST00000301459.4	-	7	1030	c.643G>A	c.(643-645)Gga>Aga	p.G215R	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	215					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						TCGGGCTCTCCCTCACTCACG	0.632																																					p.G215R		Atlas-SNP	.											RCOR2,colon,carcinoma,0,1	RCOR2	43	.	0			c.G643A						.						65	54	58					11																	63681765		2201	4297	6498	SO:0001583	missense	283248	exon7			GCTCTCCCTCACT	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.643G>A	chr11.hg19:g.63681765C>T	ENSP00000301459:p.Gly215Arg	121.0	0.0		221.0	64.0	NM_173587	Q96FP3	Missense_Mutation	SNP	ENST00000301459.4	hg19	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.260926	0.39995	.	.	ENSG00000167771	ENST00000301459	T	0.28895	1.59	4.73	4.73	0.59995	.	0.465811	0.21906	N	0.067380	T	0.16769	0.0403	N	0.14661	0.345	0.30039	N	0.812813	B	0.02656	0.0	B	0.04013	0.001	T	0.10291	-1.0636	10	0.16896	T	0.51	.	10.5414	0.45035	0.0:0.9086:0.0:0.0914	.	215	Q8IZ40	RCOR2_HUMAN	R	215	ENSP00000301459:G215R	ENSP00000301459:G215R	G	-	1	0	RCOR2	63438341	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	4.124000	0.57924	2.333000	0.79357	0.561000	0.74099	GGA	.	.		0.632	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		T	63681765	C	T	63681765	3	4	114	1	0	0	0	0	1	0	0	0	13198	632	22	3	952	3	RCOR2	11	63681765	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	2208	63681765	71324751	723	18995										
MACROD1	28992	hgsc.bcm.edu	37	chr11	63767024	63767024	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aacacgccggtggagatgcaGgggaacgcctgggcggggag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:63767024delG	ENST00000255681.6	-	7	861	c.795delC	c.(793-795)cccfs	p.P265fs	OTUB1_ENST00000535715.1_Intron	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1	265	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						TGGAGATGCAGGGGAACGCCT	0.716																																					p.C266fs		Atlas-INDEL	.											.	MACROD1	17	.	0			c.796delT						.						13	15	14					11																	63767024		2189	4284	6473	SO:0001589	frameshift_variant	28992	exon7			.	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.795delC	chr11.hg19:g.63767024delG	ENSP00000255681:p.Pro265fs	92.0	0.0		154.0	11.0	NM_014067	Q9UH96	Frame_Shift_Del	DEL	ENST00000255681.6	hg19	CCDS8056.1																																																																																			.	.		0.716	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		-	63767024	G	-	63767024	7	5	114	1	0	1	0	1	0	0	0	0	9154	987	35	0	198	0	MACROD1	11	63767024	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	85259	63767024	71239492	724	18996										
PLCB3	5331	hgsc.bcm.edu	37	chr11	64031017	64031017	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgcattgcagcctttgaggaGgggggtaaattcgtagggca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:64031017delG	ENST00000540288.1	+	20	2506	c.2403delG	c.(2401-2403)gagfs	p.E801fs	PLCB3_ENST00000279230.6_Frame_Shift_Del_p.E801fs|PLCB3_ENST00000325234.5_Frame_Shift_Del_p.E734fs	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	801	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						CCTTTGAGGAGGGGGGTAAAT	0.657																																					p.E801fs		Atlas-INDEL	.											.	PLCB3	103	.	0			c.2402delA						.																																			SO:0001589	frameshift_variant	5331	exon20			.	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.2403delG	chr11.hg19:g.64031017delG	ENSP00000443631:p.Glu801fs	79.0	0.0		169.0	11.0	NM_000932	A5PKZ6|G5E960|Q8N1A4	Frame_Shift_Del	DEL	ENST00000540288.1	hg19	CCDS8064.1																																																																																			.	.		0.657	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1			-	64031017	G	-	64031017	7	5	114	1	0	1	0	1	0	0	0	0	12038	991	35	0	2481	0	PLCB3	11	64031017	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	263993	64031017	70975499	725	18997										
NRXN2	9379	hgsc.bcm.edu	37	chr11	64375286	64375286	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taaaagtcctcgtcgtccgtGggggggaggctggagtcaaa					rs369377520		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:64375286delG	ENST00000377551.1	-	22	4732	c.4521delC	c.(4519-4521)cccfs	p.P1507fs	NRXN2_ENST00000409571.1_Frame_Shift_Del_p.P1500fs|NRXN2_ENST00000377559.3_Frame_Shift_Del_p.P1437fs|NRXN2_ENST00000301894.2_Frame_Shift_Del_p.P461fs|NRXN2_ENST00000265459.6_Frame_Shift_Del_p.P1507fs			Q9P2S2	NRX2A_HUMAN	neurexin 2	1507					adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)	p.T1508fs*82(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						CGTCGTCCGTGGGGGGGAGGC	0.697																																					p.T1508fs		Atlas-INDEL	.											.,3	NRXN2	247	.	1	Insertion - Frameshift(1)	ovary(1)	c.4522delA						.						37	33	34					11																	64375286		2190	4293	6483	SO:0001589	frameshift_variant	9379	exon23			.		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"neurexin II"	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.4521delC	chr11.hg19:g.64375286delG	ENSP00000366774:p.Pro1507fs	102.0	0.0		145.0	12.0	NM_015080	A7E2C1|Q9Y2D6	Frame_Shift_Del	DEL	ENST00000377551.1	hg19	CCDS8077.1																																																																																			.	.		0.697	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		-	64375286	G	-	64375286	7	5	114	1	0	1	0	1	0	0	0	0	10675	1335	47	0	621	0	NRXN2	11	64375286	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	344269	64375286	70631230	726	18998										
PYGM	5837	hgsc.bcm.edu	37	chr11	64521090	64521090	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgttgatgcgcttcactgcgCcctcctccaccagcgacatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:64521090delC	ENST00000164139.3	-	11	1702	c.1304delG	c.(1303-1305)ggcfs	p.G435fs	PYGM_ENST00000377432.3_Frame_Shift_Del_p.G347fs|PYGM_ENST00000462303.1_5'Flank	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	435					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTTCACTGCGCCCTCCTCCAC	0.662																																					p.G435fs		Atlas-INDEL	.											.	PYGM	77	.	0			c.1305delC						.						45	31	35					11																	64521090		2199	4295	6494	SO:0001589	frameshift_variant	5837	exon11			.		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.1304delG	chr11.hg19:g.64521090delC	ENSP00000164139:p.Gly435fs	116.0	0.0		150.0	10.0	NM_005609	A0AVK1|A6NDY6	Frame_Shift_Del	DEL	ENST00000164139.3	hg19	CCDS8079.1																																																																																			.	.		0.662	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		-	64521090	C	-	64521090	7	5	114	1	0	1	0	1	0	0	0	0	12877	739	26	0	1264	0	PYGM	11	64521090	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	145804	64521090	70485426	727	18999										
SF1	7536	hgsc.bcm.edu	37	chr11	64540917	64540917	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaacctgtcctcagggttaGgggggatgcccaggtctcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:64540917delG	ENST00000377390.3	-	3	558	c.221delC	c.(220-222)cctfs	p.P74fs	SF1_ENST00000377387.1_Frame_Shift_Del_p.P199fs|SF1_ENST00000433274.2_Frame_Shift_Del_p.P48fs|SF1_ENST00000227503.9_Frame_Shift_Del_p.P74fs|SF1_ENST00000334944.5_Frame_Shift_Del_p.P74fs|SF1_ENST00000422298.2_Intron|SF1_ENST00000377394.3_Frame_Shift_Del_p.P74fs	NM_004630.3	NP_004621.2	Q15637	SF01_HUMAN	splicing factor 1	74					Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of steroid biosynthetic process (GO:0050810)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribosome (GO:0005840)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.P74fs*63(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	31						CTCAGGGTTAGGGGGGATGCC	0.453																																					p.P199fs		Atlas-INDEL	.											.	SF1	124	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.597delT						.						80	69	73					11																	64540917		2201	4297	6498	SO:0001589	frameshift_variant	7536	exon3			.	D26120	CCDS8080.1, CCDS8081.1, CCDS31599.1, CCDS44642.1, CCDS44642.2, CCDS53660.1, CCDS53661.1	11q13	2014-09-17	2001-12-19	2002-01-11	ENSG00000168066	ENSG00000168066		"Zinc fingers, CCHC domain containing"	12950	protein-coding gene	gene with protein product		601516	"zinc finger protein 162"	ZNF162		7912130, 9573336	Standard	NM_201997		Approved	ZFM1, ZCCHC25	uc001oaz.2	Q15637	OTTHUMG00000066833	ENST00000377390.3:c.221delC	chr11.hg19:g.64540917delG	ENSP00000366607:p.Pro74fs	93.0	0.0		166.0	10.0	NM_001178030	B7Z1Q1|C9JJE2|Q14818|Q14819|Q15913|Q8IY00|Q92744|Q92745|Q969H7|Q9BW01|Q9UEI0	Frame_Shift_Del	DEL	ENST00000377390.3	hg19	CCDS31599.1																																																																																			.	.		0.453	SF1-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143242.1	NM_004630		-	64540917	G	-	64540917	7	5	114	1	0	1	0	1	0	0	0	0	14160	1000	35	0	1880	0	SF1	11	64540917	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	19827	64540917	70465599	728	19000										
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64598997	64598997	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgaggatggcagcgcagagcGtgtgaggcagcagcggcagc	19	10	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:64598997G>A	ENST00000342711.5	-	28	3283	c.3284C>T	c.(3283-3285)aCg>aTg	p.T1095M	CDC42BPG_ENST00000491280.1_5'UTR	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						AGCGCAGAGCGTGTGAGGCAG	0.657											OREG0004016	type=REGULATORY REGION|Gene=CDC42BPG|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T1095M		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.C3284T						.						50	48	49					11																	64598997		2195	4290	6485	SO:0001583	missense	55561	exon28			CAGAGCGTGTGAG	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"Pleckstrin homology (PH) domain containing"	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.3284C>T	chr11.hg19:g.64598997G>A	ENSP00000345133:p.Thr1095Met	180.0	0.0	1077	240.0	30.0	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	hg19	CCDS31601.1	.	.	.	.	.	.	.	.	.	.	G	12.62	1.991419	0.35131	.	.	ENSG00000171219	ENST00000342711	T	0.68765	-0.35	4.33	4.33	0.51752	Citron-like (1);	0.500739	0.16910	N	0.194528	T	0.60907	0.2305	L	0.39147	1.195	0.28328	N	0.921926	D	0.59767	0.986	B	0.43809	0.432	T	0.62201	-0.6904	10	0.66056	D	0.02	.	14.7225	0.69317	0.0:0.0:1.0:0.0	.	1095	Q6DT37	MRCKG_HUMAN	M	1095	ENSP00000345133:T1095M	ENSP00000345133:T1095M	T	-	2	0	CDC42BPG	64355573	0.898000	0.30612	0.439000	0.26833	0.277000	0.26821	5.264000	0.65513	2.416000	0.81992	0.467000	0.42956	ACG	.	.		0.657	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		A	64598997	G	A	64598997	3	1	114	1	0	0	0	0	1	0	0	0	3076	1145	40	1	1411	1	CDC42BPG	11	64598997	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	58080	64598997	70407519	729	19001										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65351025	65351025	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaggaagcagagatgaaggTtttagagtctccagagaaca					rs559675386		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:65351025delT	ENST00000309295.4	+	9	3147	c.2882delT	c.(2881-2883)gttfs	p.V961fs		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	961						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GAGATGAAGGTTTTAGAGTCT	0.552																																					p.V961fs		Atlas-INDEL	.											.	EHBP1L1	64	.	0			c.2881delG						.						23	24	24					11																	65351025		1832	4082	5914	SO:0001589	frameshift_variant	254102	exon9			.	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.2882delT	chr11.hg19:g.65351025delT	ENSP00000312671:p.Val961fs	115.0	0.0		190.0	13.0	NM_001099409	Q8TB89|Q9H7M7	Frame_Shift_Del	DEL	ENST00000309295.4	hg19	CCDS44649.1																																																																																			.	.		0.552	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		-	65351025	T	-	65351025	7	5	114	1	0	1	0	1	0	0	0	0	4978	1725	60	0	2916	0	EHBP1L1	11	65351025	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	752028	65351025	69655491	730	19002										
DRAP1	10589	hgsc.bcm.edu	37	chr11	65688853	65688853	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctctgcctttgcccccagcgCccccgggcccctcagcacct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:65688853delC	ENST00000312515.2	+	7	810	c.565delC	c.(565-567)cccfs	p.P190fs	C11orf68_ENST00000438576.2_5'Flank|DRAP1_ENST00000532933.1_Frame_Shift_Del_p.P170fs|DRAP1_ENST00000376991.2_Frame_Shift_Del_p.P197fs|C11orf68_ENST00000449692.3_5'Flank|DRAP1_ENST00000527119.1_Frame_Shift_Del_p.P146fs	NM_006442.3	NP_006433.2	Q14919	NC2A_HUMAN	DR1-associated protein 1 (negative cofactor 2 alpha)	190	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	5				READ - Rectum adenocarcinoma(159;0.166)		GCCCCCAGCGCCCCCGGGCCC	0.627																																					p.A188fs		Atlas-INDEL	.											.	DRAP1	18	.	0			c.564delG						.						72	81	78					11																	65688853		2201	4296	6497	SO:0001589	frameshift_variant	10589	exon7			.	U41843	CCDS8123.1	11q13	2010-09-29			ENSG00000175550	ENSG00000175550			3019	protein-coding gene	gene with protein product	"negative cofactor 2 alpha", "DR1-associated corepressor"	602289				8608938	Standard	NM_006442		Approved	NC2-alpha	uc001ogj.2	Q14919	OTTHUMG00000166723	ENST00000312515.2:c.565delC	chr11.hg19:g.65688853delC	ENSP00000307850:p.Pro190fs	218.0	0.0		378.0	23.0	NM_006442	Q13448	Frame_Shift_Del	DEL	ENST00000312515.2	hg19	CCDS8123.1																																																																																			.	.		0.627	DRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391197.2	NM_006442		-	65688853	C	-	65688853	7	5	114	1	0	1	0	1	0	0	0	0	4757	739	26	0	591	0	DRAP1	11	65688853	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	337828	65688853	69317663	731	19003										
CST6	1474	hgsc.bcm.edu	37	chr11	65779730	65779730	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catctactacttccgagacaCgcacatcatcaaggcgcaga	7	14	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:65779730C>T	ENST00000312134.2	+	1	419	c.215C>T	c.(214-216)aCg>aTg	p.T72M		NM_001323.3	NP_001314.1	Q15828	CYTM_HUMAN	cystatin E/M	72					anatomical structure morphogenesis (GO:0009653)|epidermis development (GO:0008544)|negative regulation of endopeptidase activity (GO:0010951)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			large_intestine(1)|lung(1)|ovary(1)	3						TTCCGAGACACGCACATCATC	0.697																																					p.T72M		Atlas-SNP	.											.	CST6	14	.	0			c.C215T						.						14	13	14					11																	65779730		2072	4116	6188	SO:0001583	missense	1474	exon1			GAGACACGCACAT	U62800	CCDS8126.1	11q13	2005-09-29			ENSG00000175315	ENSG00000175315			2478	protein-coding gene	gene with protein product		601891				9154125, 9099741	Standard	NM_001323		Approved		uc001ogr.3	Q15828	OTTHUMG00000166750	ENST00000312134.2:c.215C>T	chr11.hg19:g.65779730C>T	ENSP00000311313:p.Thr72Met	60.0	0.0		94.0	4.0	NM_001323	Q540N7	Missense_Mutation	SNP	ENST00000312134.2	hg19	CCDS8126.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.357715	0.24598	.	.	ENSG00000175315	ENST00000312134	T	0.26373	1.74	5.11	-0.399	0.12415	Proteinase inhibitor I25, cystatin (2);	0.448476	0.23450	N	0.048046	T	0.16642	0.0400	L	0.46157	1.445	0.09310	N	1	B	0.34226	0.443	B	0.31946	0.138	T	0.10314	-1.0635	10	0.42905	T	0.14	-18.5484	4.3212	0.11018	0.0:0.4217:0.1806:0.3977	.	72	Q15828	CYTM_HUMAN	M	72	ENSP00000311313:T72M	ENSP00000311313:T72M	T	+	2	0	CST6	65536306	0.296000	0.24398	0.102000	0.21198	0.005000	0.04900	0.598000	0.24074	0.197000	0.20387	-0.768000	0.03414	ACG	.	.		0.697	CST6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391348.1	NM_001323		T	65779730	C	T	65779730	3	4	114	1	0	0	0	0	1	0	0	0	3978	536	19	1	217	1	CST6	11	65779730	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	90877	65779730	69226786	732	19004										
RIN1	9610	hgsc.bcm.edu	37	chr11	66101126	66101126	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actcgtcggcacccgcgcccTcccctgtggggacatggtga	13	16	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:66101126T>C	ENST00000311320.4	-	8	1721	c.1595A>G	c.(1594-1596)gAg>gGg	p.E532G	RIN1_ENST00000530056.1_Missense_Mutation_p.E366G|RIN1_ENST00000424433.2_Missense_Mutation_p.E427G|RIN1_ENST00000524804.1_5'Flank|RP11-867G23.12_ENST00000526655.1_RNA	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	532	Ras and 14-3-3 protein binding region.|VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						ACCCGCGCCCTCCCCTGTGGG	0.612																																					p.E532G		Atlas-SNP	.											.	RIN1	64	.	0			c.A1595G						.						36	39	38					11																	66101126		2200	4295	6495	SO:0001583	missense	9610	exon8			GCGCCCTCCCCTG	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.1595A>G	chr11.hg19:g.66101126T>C	ENSP00000310406:p.Glu532Gly	172.0	0.0		221.0	9.0	NM_004292	O15010|Q00427|Q96CC8	Missense_Mutation	SNP	ENST00000311320.4	hg19	CCDS31614.1	.	.	.	.	.	.	.	.	.	.	T	12.20	1.865936	0.32977	.	.	ENSG00000174791	ENST00000311320;ENST00000424433;ENST00000530056	T;T;T	0.32023	1.47;1.47;1.47	4.49	4.49	0.54785	Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2);	0.255042	0.37437	N	0.002095	T	0.40862	0.1134	L	0.41573	1.285	0.37105	D	0.900093	B;D;B	0.64830	0.025;0.994;0.071	B;P;B	0.62298	0.089;0.9;0.18	T	0.45366	-0.9266	10	0.52906	T	0.07	-20.8263	10.7295	0.46087	0.0:0.0:0.0:1.0	.	366;163;532	E9PNR2;B4DW96;Q13671	.;.;RIN1_HUMAN	G	532;427;366	ENSP00000310406:E532G;ENSP00000400560:E427G;ENSP00000432798:E366G	ENSP00000310406:E532G	E	-	2	0	RIN1	65857702	0.752000	0.28338	0.935000	0.37517	0.194000	0.23727	3.079000	0.50104	1.967000	0.57214	0.379000	0.24179	GAG	.	.		0.612	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292		C	66101126	T	C	66101126	3	2	114	1	0	0	0	0	1	0	0	0	13386	1551	54	2	768	2	RIN1	11	66101126	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	321396	66101126	68905390	733	19005										
PELI3	246330	hgsc.bcm.edu	37	chr11	66243164	66243164	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccggcggggctgctgcgggcTcccacactgaagcaactgga	15	14	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:66243164T>C	ENST00000320740.7	+	8	1096	c.936T>C	c.(934-936)gcT>gcC	p.A312A	PELI3_ENST00000531856.1_Intron|CTD-3074O7.5_ENST00000533502.1_RNA|PELI3_ENST00000349459.6_Silent_p.A288A|CTD-3074O7.5_ENST00000527274.2_RNA|CTD-3074O7.5_ENST00000525142.1_RNA|CTD-3074O7.5_ENST00000527092.1_RNA|CTD-3074O7.5_ENST00000602951.1_RNA	NM_001243136.1|NM_145065.2	NP_001230065.1|NP_659502.2	Q8N2H9	PELI3_HUMAN	pellino E3 ubiquitin protein ligase family member 3	312					defense response to Gram-negative bacterium (GO:0050829)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Toll signaling pathway (GO:0045751)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon production (GO:0032480)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|protein K63-linked ubiquitination (GO:0070534)|regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070428)|Toll signaling pathway (GO:0008063)	cytosol (GO:0005829)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	15						TGCTGCGGGCTCCCACACTGA	0.692																																					p.A312A		Atlas-SNP	.											.	PELI3	36	.	0			c.T936C						.						22	24	23					11																	66243164		2164	4233	6397	SO:0001819	synonymous_variant	246330	exon8			GCGGGCTCCCACA	AL834395	CCDS31615.1, CCDS41675.1, CCDS73328.1	11q13.2	2012-02-23	2012-02-23		ENSG00000174516	ENSG00000174516		"Pellino homologs"	30010	protein-coding gene	gene with protein product		609827	"pellino homolog 3 (Drosophila)"			12874243, 15917247	Standard	NM_145065		Approved	MGC35521	uc001oic.4	Q8N2H9	OTTHUMG00000167109	ENST00000320740.7:c.936T>C	chr11.hg19:g.66243164T>C		127.0	0.0		216.0	10.0	NM_145065	Q8N3E1|Q8N9Q6|Q8TAW7|Q8TED5	Silent	SNP	ENST00000320740.7	hg19	CCDS31615.1																																																																																			.	.		0.692	PELI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393226.1	NM_145065		C	66243164	T	C	66243164	2	2	114	1	0	0	0	0	0	0	0	1	11732	1538	54	2		2	PELI3	11	66243164	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	142038	66243164	68763352	734	19006										
RAD9A	5883	hgsc.bcm.edu	37	chr11	67164988	67164988	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctgtacgctccccccagggCcccagccctgtgctggcgga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:67164988delC	ENST00000307980.2	+	11	1227	c.1134delC	c.(1132-1134)ggcfs	p.G378fs	PPP1CA_ENST00000532446.1_5'Flank|RNU6-1238P_ENST00000517215.1_RNA|RAD9A_ENST00000535644.1_3'UTR	NM_001243224.1|NM_004584.2	NP_001230153.1|NP_004575.1	Q99638	RAD9A_HUMAN	RAD9 homolog A (S. pombe)	378	Sufficient for interaction with ABL1.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|intra-S DNA damage checkpoint (GO:0031573)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|enzyme binding (GO:0019899)|exodeoxyribonuclease III activity (GO:0008853)|histone deacetylase binding (GO:0042826)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			lung(7)|upper_aerodigestive_tract(1)	8			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			CCCCCCAGGGCCCCAGCCCTG	0.607								Other conserved DNA damage response genes																													p.G378fs		Atlas-INDEL	.											.	RAD9A	15	.	0			c.1133delG						.						61	50	54					11																	67164988		2200	4295	6495	SO:0001589	frameshift_variant	5883	exon11			.	U53174	CCDS8159.1	11q13.1-q13.2	2008-02-05	2003-07-21	2003-07-23	ENSG00000172613	ENSG00000172613			9827	protein-coding gene	gene with protein product		603761	"RAD9 (S. pombe) homolog"	RAD9		8943031	Standard	NM_004584		Approved		uc001okr.3	Q99638	OTTHUMG00000167670	ENST00000307980.2:c.1134delC	chr11.hg19:g.67164988delC	ENSP00000311360:p.Gly378fs	146.0	0.0		257.0	16.0	NM_004584	B2RCZ8|Q6FI29|Q96C41	Frame_Shift_Del	DEL	ENST00000307980.2	hg19	CCDS8159.1																																																																																			.	.		0.607	RAD9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395481.2	NM_004584		-	67164988	C	-	67164988	7	5	114	1	0	1	0	1	0	0	0	0	13010	726	26	0	1176	0	RAD9A	11	67164988	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	921824	67164988	67841528	735	19007										
RPS6KB2	6199	hgsc.bcm.edu	37	chr11	67200629	67200629	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctggtgcgcagtggccacaAccgggctgtggactggtgga	17	10	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:67200629A>G	ENST00000312629.5	+	9	785	c.740A>G	c.(739-741)aAc>aGc	p.N247S	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	247	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			AGTGGCCACAACCGGGCTGTG	0.692																																					p.N247S		Atlas-SNP	.											.	RPS6KB2	92	.	0			c.A740G						.						13	16	15					11																	67200629		1966	4125	6091	SO:0001583	missense	6199	exon9			GCCACAACCGGGC	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"ribosomal protein S6 kinase, 70kD, polypeptide 2"			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.740A>G	chr11.hg19:g.67200629A>G	ENSP00000308413:p.Asn247Ser	60.0	0.0		87.0	24.0	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	hg19	CCDS41677.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.049764	0.55218	.	.	ENSG00000175634	ENST00000312629	T	0.21932	1.98	4.88	3.73	0.42828	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.058351	0.64402	D	0.000004	T	0.15825	0.0381	N	0.02315	-0.6	0.80722	D	1	P;D	0.56035	0.637;0.974	B;P	0.60012	0.414;0.867	T	0.17531	-1.0366	10	0.17369	T	0.5	.	11.5682	0.50818	0.8502:0.1498:0.0:0.0	.	247;247	Q9BRS0;Q9UBS0	.;KS6B2_HUMAN	S	247	ENSP00000308413:N247S	ENSP00000308413:N247S	N	+	2	0	RPS6KB2	66957205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.465000	0.90383	0.861000	0.35504	0.459000	0.35465	AAC	.	.		0.692	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952		G	67200629	A	G	67200629	3	3	114	1	0	0	0	0	1	0	0	0	13672	43	2	2	774	2	RPS6KB2	11	67200629	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	35641	67200629	67805887	736	19008										
PITPNM1	9600	hgsc.bcm.edu	37	chr11	67261213	67261213	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtcgctgcccatgatggagAcgctggcggtgaaggagccg	18	10	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:67261213A>G	ENST00000534749.1	-	20	3292	c.3104T>C	c.(3103-3105)gTc>gCc	p.V1035A	PITPNM1_ENST00000526450.1_5'UTR|PITPNM1_ENST00000436757.2_Missense_Mutation_p.V1034A|PITPNM1_ENST00000356404.3_Missense_Mutation_p.V1035A			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	1035					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						CATGATGGAGACGCTGGCGGT	0.667																																					p.V1035A	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.T3104C						.						26	23	24					11																	67261213		2092	4115	6207	SO:0001583	missense	9600	exon21			ATGGAGACGCTGG	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"PYK2 N-terminal domain-interacting receptor 2", "retinal degeneration B alpha 1"	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.3104T>C	chr11.hg19:g.67261213A>G	ENSP00000437286:p.Val1035Ala	114.0	0.0		193.0	10.0	NM_004910	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Missense_Mutation	SNP	ENST00000534749.1	hg19	CCDS31620.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.022898	0.93462	.	.	ENSG00000110697	ENST00000534749;ENST00000436757;ENST00000356404	T;T;T	0.78246	-1.16;-1.16;-1.16	4.2	4.2	0.49525	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.000000	0.44097	D	0.000486	D	0.88351	0.6413	M	0.87180	2.865	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.993;0.994	D	0.90043	0.4143	10	0.72032	D	0.01	-42.8079	12.4022	0.55420	1.0:0.0:0.0:0.0	.	1034;1035	O00562-2;O00562	.;PITM1_HUMAN	A	1035;1034;1035	ENSP00000437286:V1035A;ENSP00000398787:V1034A;ENSP00000348772:V1035A	ENSP00000348772:V1035A	V	-	2	0	PITPNM1	67017789	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.283000	0.95860	1.673000	0.50895	0.402000	0.26972	GTC	.	.		0.667	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		G	67261213	A	G	67261213	3	3	114	1	0	0	0	0	1	0	0	0	11959	275	10	2	646	2	PITPNM1	11	67261213	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	60584	67261213	67745303	737	19009										
ANO1	55107	hgsc.bcm.edu	37	chr11	70017033	70017033	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accctgtttgtcgcctccttCcccctggccccactgtttgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:70017033delC	ENST00000355303.5	+	22	2543	c.2238delC	c.(2236-2238)ttcfs	p.F746fs	ANO1_ENST00000398543.2_Frame_Shift_Del_p.F600fs|ANO1_ENST00000530676.1_Frame_Shift_Del_p.F600fs|ANO1_ENST00000531349.1_Frame_Shift_Del_p.F455fs|ANO1_ENST00000538023.1_Frame_Shift_Del_p.F746fs|ANO1_ENST00000525494.1_3'UTR	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	746					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	TCGCCTCCTTCCCCCTGGCCC	0.587																																					p.F746fs		Atlas-INDEL	.											.	ANO1	156	.	0			c.2237delT						.						64	72	70					11																	70017033		2117	4227	6344	SO:0001589	frameshift_variant	55107	exon22			.	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	21625	protein-coding gene	gene with protein product		610108	"oral cancer overexpressed 2", "transmembrane protein 16A"	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.2238delC	chr11.hg19:g.70017033delC	ENSP00000347454:p.Phe746fs	135.0	0.0		244.0	15.0	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Frame_Shift_Del	DEL	ENST00000355303.5	hg19	CCDS44663.1																																																																																			.	.		0.587	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043		-	70017033	C	-	70017033	7	5	114	1	0	1	0	1	0	0	0	0	695	854	30	0	2324	0	ANO1	11	70017033	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2755820	70017033	64989483	738	19010										
PHOX2A	401	hgsc.bcm.edu	37	chr11	71950817	71950817	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagagattggtcttcagggcGgggccgggcttccggtgaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:71950817delG	ENST00000298231.5	-	3	1002	c.831delC	c.(829-831)cccfs	p.P277fs	PHOX2A_ENST00000544057.1_5'Flank	NM_005169.3	NP_005160.2	O14813	PHX2A_HUMAN	paired-like homeobox 2a	277					dopaminergic neuron differentiation (GO:0071542)|locus ceruleus development (GO:0021703)|midbrain development (GO:0030901)|noradrenergic neuron differentiation (GO:0003357)|oculomotor nerve formation (GO:0021623)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of respiratory gaseous exchange (GO:0043576)|somatic motor neuron differentiation (GO:0021523)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)|trochlear nerve formation (GO:0021642)	nuclear chromatin (GO:0000790)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)	5						TCTTCAGGGCGGGGCCGGGCT	0.697																																					p.A278fs		Atlas-INDEL	.											.	PHOX2A	14	.	0			c.832delG						.						5	7	6					11																	71950817		1982	3943	5925	SO:0001589	frameshift_variant	401	exon3			.	AF022722	CCDS8214.1	11q13.4	2014-09-04	2007-07-12	2003-02-14	ENSG00000165462	ENSG00000165462		"Homeoboxes / PRD class"	691	protein-coding gene	gene with protein product		602753	"aristaless (Drosophila) homeobox, aristaless homeobox (Drosophila), fibrosis of extraocular muscles, congenital, 2, autosomal recessive", "paired-like (aristaless) homeobox 2a"	ARIX, FEOM2		8661014, 11600883	Standard	NM_005169		Approved	PMX2A, CFEOM2	uc001osh.4	O14813	OTTHUMG00000167899	ENST00000298231.5:c.831delC	chr11.hg19:g.71950817delG	ENSP00000298231:p.Pro277fs	108.0	0.0		181.0	14.0	NM_005169	A8K3N0|Q8IVZ2	Frame_Shift_Del	DEL	ENST00000298231.5	hg19	CCDS8214.1																																																																																			.	.		0.697	PHOX2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396885.1	NM_005169		-	71950817	G	-	71950817	7	5	114	1	0	1	0	1	0	0	0	0	11867	1103	39	0	27	0	PHOX2A	11	71950817	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1933784	71950817	63055699	739	19011										
RAB6A	5870	hgsc.bcm.edu	37	chr11	73431914	73431914	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcgatcctccaagtacatagTttttgataaaaagtcaatgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:73431914delT	ENST00000336083.3	-	3	615	c.160delA	c.(160-162)actfs	p.T54fs	RP11-456I15.2_ENST00000538624.1_RNA|RAB6A_ENST00000310653.6_Frame_Shift_Del_p.T54fs|RAB6A_ENST00000541588.1_Frame_Shift_Del_p.T54fs|RAB6A_ENST00000536566.1_Frame_Shift_Del_p.T21fs	NM_198896.1	NP_942599.1	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	54					antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						AAGTACATAGTTTTTGATAAA	0.328																																					p.T54fs		Atlas-INDEL	.											.	RAB6A	17	.	0			c.161delC						.						115	112	113					11																	73431914		2199	4293	6492	SO:0001589	frameshift_variant	5870	exon3			.	AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582		"RAB, member RAS oncogene"	9786	protein-coding gene	gene with protein product		179513		RAB6			Standard	NM_001243718		Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000336083.3:c.160delA	chr11.hg19:g.73431914delT	ENSP00000336850:p.Thr54fs	74.0	0.0		160.0	12.0	NM_002869	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	Frame_Shift_Del	DEL	ENST00000336083.3	hg19	CCDS8224.1																																																																																			.	.		0.328	RAB6A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259241.2			-	73431914	T	-	73431914	7	5	114	1	0	1	0	1	0	0	0	0	12966	1725	60	0	600	0	RAB6A	11	73431914	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1481097	73431914	61574602	740	19012										
C11orf30	56946	hgsc.bcm.edu	37	chr11	76162945	76162945	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atcagtgcacttcgggcacaGggggatctcaccaaggaaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:76162945delG	ENST00000529032.1	+	2	114	c.114delG	c.(112-114)cagfs	p.Q38fs	C11orf30_ENST00000533988.1_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000334736.3_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000524490.1_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000343878.3_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000533248.1_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000525919.1_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000524767.1_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000525959.1_3'UTR|C11orf30_ENST00000525038.1_Frame_Shift_Del_p.Q38fs			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	38	ENT. {ECO:0000255|PROSITE- ProRule:PRU00476}.|Interaction with BRCA2.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						TTCGGGCACAGGGGGATCTCA	0.333																																					p.Q38fs		Atlas-INDEL	.											.	C11orf30	123	.	0			c.113delA						.						38	39	39					11																	76162945		2200	4292	6492	SO:0001589	frameshift_variant	56946	exon3			.	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.114delG	chr11.hg19:g.76162945delG	ENSP00000432327:p.Gln38fs	88.0	0.0		173.0	12.0	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Frame_Shift_Del	DEL	ENST00000529032.1	hg19	CCDS8244.1																																																																																			.	.		0.333	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193		-	76162945	G	-	76162945	7	5	114	1	0	1	0	1	0	0	0	0	1638	991	35	0	120	0	C11orf30	11	76162945	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	2731031	76162945	58843571	741	19013										
ALG8	79053	hgsc.bcm.edu	37	chr11	77812229	77812229	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtttccatccaattaaaaagAggtttttcttttctgaagga	7	6	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:77812229A>G	ENST00000299626.5	-	13	1433	c.1362T>C	c.(1360-1362)ccT>ccC	p.P454P	ALG8_ENST00000532552.2_5'UTR|ALG8_ENST00000376156.3_3'UTR	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	454					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)			NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			AATTAAAAAGAGGTTTTTCTT	0.423																																					p.P454P		Atlas-SNP	.											.	ALG8	54	.	0			c.T1362C						.						40	43	42					11																	77812229		2200	4292	6492	SO:0001819	synonymous_variant	79053	exon13			AAAAAGAGGTTTT	AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"	608103	"asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)", "asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.1362T>C	chr11.hg19:g.77812229A>G		58.0	0.0		94.0	5.0	NM_024079	A6NDW6|O60860	Silent	SNP	ENST00000299626.5	hg19	CCDS8258.1	.	.	.	.	.	.	.	.	.	.	A	10.64	1.406086	0.25378	.	.	ENSG00000159063	ENST00000530608;ENST00000532306	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	T	0.61540	0.2355	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60172	-0.7315	4	.	.	.	-2.0507	10.9174	0.47144	0.843:0.157:0.0:0.0	.	.	.	.	P	156;241	.	.	L	-	2	0	ALG8	77489877	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.577000	0.36515	2.131000	0.65755	0.460000	0.39030	CTC	.	.		0.423	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079		G	77812229	A	G	77812229	2	3	114	1	0	0	0	0	0	0	0	1	523	291	11	2		2	ALG8	11	77812229	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1649284	77812229	57194287	742	19014										
USP35	57558	hgsc.bcm.edu	37	chr11	77920940	77920940	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggaggaaaggatagagagggAggaagaagggaaggaggaga	22	0	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:77920940A>G	ENST00000529308.1	+	10	2300	c.2039A>G	c.(2038-2040)gAg>gGg	p.E680G	USP35_ENST00000530267.1_Missense_Mutation_p.E248G|USP35_ENST00000530535.1_3'UTR|USP35_ENST00000526425.1_Missense_Mutation_p.E411G|USP35_ENST00000441408.2_Missense_Mutation_p.E266G	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	680	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			ATAgagagggaggaagaaggg	0.582																																					p.E680G		Atlas-SNP	.											.	USP35	179	.	0			c.A2039G						.						61	79	73					11																	77920940		2017	4176	6193	SO:0001583	missense	57558	exon10			AGAGGGAGGAAGA	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"Ubiquitin-specific peptidases"	20061	protein-coding gene	gene with protein product			"ubiquitin specific protease 35"			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.2039A>G	chr11.hg19:g.77920940A>G	ENSP00000431876:p.Glu680Gly	109.0	0.0		188.0	9.0	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	hg19	CCDS41693.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.133231	0.37630	.	.	ENSG00000118369	ENST00000530267;ENST00000529308;ENST00000441408;ENST00000526425	T;T;T;T	0.10382	3.15;3.2;3.2;2.88	5.11	3.99	0.46301	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.601320	0.04148	N	0.320886	T	0.08802	0.0218	N	0.22421	0.69	0.09310	N	1	B;P	0.37914	0.322;0.611	B;B	0.34824	0.142;0.19	T	0.31998	-0.9923	10	0.30854	T	0.27	-0.8059	7.2851	0.26333	0.9025:0.0:0.0975:0.0	.	680;266	Q9P2H5;E7EWV7	UBP35_HUMAN;.	G	248;680;266;411	ENSP00000435468:E248G;ENSP00000431876:E680G;ENSP00000400825:E266G;ENSP00000434942:E411G	ENSP00000400825:E266G	E	+	2	0	USP35	77598588	0.690000	0.27699	0.005000	0.12908	0.002000	0.02628	1.423000	0.34837	0.978000	0.38470	0.496000	0.49642	GAG	.	.		0.582	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527		G	77920940	A	G	77920940	3	3	114	1	0	0	0	0	1	0	0	0	17081	304	11	2	2073	2	USP35	11	77920940	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	108711	77920940	57085576	743	19015										
ANKRD42	338699	hgsc.bcm.edu	37	chr11	82938845	82938845	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgatttggggatgcttaagAaattagtggaagatggagta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:82938845delA	ENST00000393392.2	+	7	922	c.760delA	c.(760-762)aaafs	p.K254fs	ANKRD42_ENST00000533342.1_Frame_Shift_Del_p.K282fs|ANKRD42_ENST00000260047.6_Frame_Shift_Del_p.K281fs|ANKRD42_ENST00000531895.1_Frame_Shift_Del_p.K282fs	NM_182603.2	NP_872409.2	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42	254					positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						GATGCTTAAGAAATTAGTGGA	0.358																																					p.K253fs		Atlas-INDEL	.											ANKRD42,NS,carcinoma,0,1	ANKRD42	38	.	0			c.759delG						.						142	132	135					11																	82938845		2203	4300	6503	SO:0001589	frameshift_variant	338699	exon7			.	AK095193	CCDS8265.1, CCDS73355.1, CCDS73356.1	11q14.1	2014-06-12			ENSG00000137494	ENSG00000137494		"Ankyrin repeat domain containing"	26752	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 79"						Standard	XM_005273971		Approved	FLJ37874, SARP, PPP1R79	uc001ozz.1	Q8N9B4	OTTHUMG00000167075	ENST00000393392.2:c.760delA	chr11.hg19:g.82938845delA	ENSP00000377051:p.Lys254fs	64.0	0.0		153.0	11.0	NM_182603	Q49A49	Frame_Shift_Del	DEL	ENST00000393392.2	hg19	CCDS8265.1																																																																																			.	.		0.358	ANKRD42-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000392934.1	NM_182603		-	82938845	A	-	82938845	7	5	114	1	0	1	0	1	0	0	0	0	670	247	9	0	786	0	ANKRD42	11	82938845	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	5017905	82938845	52067671	744	19016										
C11orf73	51501	hgsc.bcm.edu	37	chr11	86056631	86056631	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgttttcttttctaggtatgAaaactttcaaagacgactag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:86056631delA	ENST00000278483.3	+	5	771	c.545delA	c.(544-546)gaafs	p.E182fs	C11orf73_ENST00000533986.1_3'UTR|C11orf73_ENST00000530208.1_3'UTR	NM_016401.3	NP_057485.2	Q53FT3	HIKES_HUMAN	chromosome 11 open reading frame 73	182					cellular response to heat (GO:0034605)|Golgi organization (GO:0007030)|lung development (GO:0030324)|protein import into nucleus (GO:0006606)|protein transport (GO:0015031)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	Hsp70 protein binding (GO:0030544)|protein transporter activity (GO:0008565)			kidney(1)|large_intestine(1)|urinary_tract(1)	3		Acute lymphoblastic leukemia(157;1.17e-07)|all_hematologic(158;0.000556)				TCTAGGTATGAAAACTTTCAA	0.269																																					p.E182fs		Atlas-INDEL	.											.	C11orf73	9	.	0			c.544delG						.						44	49	47					11																	86056631		2194	4269	6463	SO:0001589	frameshift_variant	51501	exon5			.	BC015991	CCDS8275.1	11q14.2	2013-03-12			ENSG00000149196	ENSG00000149196			26938	protein-coding gene	gene with protein product		614908				11042152, 22541429	Standard	NM_016401		Approved	HSPC138, HSPC179, Hikeshi, OPI10	uc001pbu.3	Q53FT3	OTTHUMG00000167212	ENST00000278483.3:c.545delA	chr11.hg19:g.86056631delA	ENSP00000278483:p.Glu182fs	58.0	0.0		125.0	10.0	NM_016401	Q8WVE8|Q9NVQ2|Q9NZZ1|Q9P022|Q9P0N1	Frame_Shift_Del	DEL	ENST00000278483.3	hg19	CCDS8275.1																																																																																			.	.		0.269	C11orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393747.1	NM_016401		-	86056631	A	-	86056631	7	5	114	1	0	1	0	1	0	0	0	0	1663	246	9	0	563	0	C11orf73	11	86056631	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3117786	86056631	48949885	745	19017										
TMEM135	65084	hgsc.bcm.edu	37	chr11	87020678	87020678	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aataaagaaaacttccagctTggagcttttcttggctcttt	7	8	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:87020678T>C	ENST00000305494.5	+	10	939	c.900T>C	c.(898-900)ctT>ctC	p.L300L	TMEM135_ENST00000532959.1_Silent_p.L171L|TMEM135_ENST00000340353.7_Silent_p.L278L|TMEM135_ENST00000535167.1_Silent_p.L161L	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	300					peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ACTTCCAGCTTGGAGCTTTTC	0.383																																					p.L300L		Atlas-SNP	.											.	TMEM135	40	.	0			c.T900C						.						78	86	83					11																	87020678		2201	4299	6500	SO:0001819	synonymous_variant	65084	exon10			CCAGCTTGGAGCT	BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.900T>C	chr11.hg19:g.87020678T>C		55.0	0.0		105.0	5.0	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Silent	SNP	ENST00000305494.5	hg19	CCDS8280.1																																																																																			.	.		0.383	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918		C	87020678	T	C	87020678	2	2	114	1	0	0	0	0	0	0	0	1	16066	1799	63	2		2	TMEM135	11	87020678	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	964047	87020678	47985838	746	19018										
TYR	7299	hgsc.bcm.edu	37	chr11	89028385	89028385	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctggtcatggctccttgggGcggcgatggtaggggccgtc	18	10	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:89028385G>C	ENST00000263321.5	+	5	1943	c.1441G>C	c.(1441-1443)Gcg>Ccg	p.A481P		NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	481					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	GCTCCTTGGGGCGGCGATGGT	0.512																																					p.A481P		Atlas-SNP	.											.	TYR	130	.	0			c.G1441C						.						63	64	64					11																	89028385		2201	4299	6500	SO:0001583	missense	7299	exon5			CTTGGGGCGGCGA	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"oculocutaneous albinism IA"	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.1441G>C	chr11.hg19:g.89028385G>C	ENSP00000263321:p.Ala481Pro	238.0	0.0		384.0	25.0	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	hg19	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278972	0.59758	.	.	ENSG00000077498	ENST00000263321	D	0.99304	-5.72	5.02	5.02	0.67125	.	0.111169	0.64402	D	0.000011	D	0.99345	0.9770	M	0.79258	2.445	0.58432	D	0.999999	D	0.76494	0.999	D	0.83275	0.996	D	0.99184	1.0868	9	.	.	.	.	17.4703	0.87645	0.0:0.0:1.0:0.0	.	481	P14679	TYRO_HUMAN	P	481	ENSP00000263321:A481P	.	A	+	1	0	TYR	88668033	1.000000	0.71417	0.929000	0.37066	0.176000	0.22953	6.287000	0.72671	2.488000	0.83962	0.455000	0.32223	GCG	.	.		0.512	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		C	89028385	G	C	89028385	3	2	114	1	0	0	0	0	1	0	0	0	16828	1203	42	4	1459	4	TYR	11	89028385	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	2007707	89028385	45978131	747	19019										
NAALAD2	10003	hgsc.bcm.edu	37	chr11	89911108	89911108	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aattttatgaccccacatttAaaaaacaactttctgtggct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:89911108delA	ENST00000534061.1	+	16	1911	c.1681delA	c.(1681-1683)aaafs	p.K562fs	NAALAD2_ENST00000375944.3_Intron|NAALAD2_ENST00000321955.4_Frame_Shift_Del_p.K529fs	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	562	NAALADase.				neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CCCCACATTTAAAAAACAACT	0.338																																					p.F560fs		Atlas-INDEL	.											.	NAALAD2	113	.	0			c.1680delT						.						66	73	71					11																	89911108		2201	4295	6496	SO:0001589	frameshift_variant	10003	exon16			.	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1681delA	chr11.hg19:g.89911108delA	ENSP00000432481:p.Lys562fs	162.0	0.0		243.0	18.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Frame_Shift_Del	DEL	ENST00000534061.1	hg19	CCDS8288.1																																																																																			.	.		0.338	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		-	89911108	A	-	89911108	7	5	114	1	0	1	0	1	0	0	0	0	10137	363	13	0	1743	0	NAALAD2	11	89911108	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	882723	89911108	45095408	748	19020										
CNTN5	53942	hgsc.bcm.edu	37	chr11	99715962	99715962	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaccaacactgtggggagtaTtcttagtagagaagctacac	10	8	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:99715962T>C	ENST00000524871.1	+	6	835	c.545T>C	c.(544-546)aTt>aCt	p.I182T	CNTN5_ENST00000528682.1_Missense_Mutation_p.I182T|CNTN5_ENST00000418526.2_Missense_Mutation_p.I108T|CNTN5_ENST00000279463.3_Missense_Mutation_p.I182T|CNTN5_ENST00000527185.1_Missense_Mutation_p.I182T	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	182	Ig-like C2-type 1.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		GTGGGGAGTATTCTTAGTAGA	0.343																																					p.I182T		Atlas-SNP	.											.	CNTN5	324	.	0			c.T545C						.						141	132	135					11																	99715962		1828	4097	5925	SO:0001583	missense	53942	exon5			GGAGTATTCTTAG	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.545T>C	chr11.hg19:g.99715962T>C	ENSP00000435637:p.Ile182Thr	51.0	0.0		86.0	4.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	T	16.99	3.273069	0.59649	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19	5.8	5.8	0.92144	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.232270	0.43260	D	0.000584	T	0.68063	0.2960	L	0.46819	1.47	0.58432	D	0.999993	P;P;P	0.49447	0.924;0.697;0.924	P;B;P	0.53185	0.72;0.42;0.635	T	0.70791	-0.4776	10	0.66056	D	0.02	.	15.3151	0.74069	0.0:0.0:0.0:1.0	.	182;108;182	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	T	182;182;182;108;182	ENSP00000433575:I182T;ENSP00000436185:I182T;ENSP00000435637:I182T;ENSP00000393229:I108T;ENSP00000279463:I182T	ENSP00000279463:I182T	I	+	2	0	CNTN5	99221172	1.000000	0.71417	1.000000	0.80357	0.447000	0.32167	5.896000	0.69822	2.216000	0.71823	0.528000	0.53228	ATT	.	.		0.343	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		C	99715962	T	C	99715962	3	2	114	1	0	0	0	0	1	0	0	0	3646	1493	52	2	559	2	CNTN5	11	99715962	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	9804854	99715962	35290554	749	19021										
TRPC6	7225	hgsc.bcm.edu	37	chr11	101454149	101454149	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtccatgagcagatagtccTggctctcgttgcgccgcgca	12	13	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:101454149T>C	ENST00000344327.3	-	1	510	c.86A>G	c.(85-87)cAg>cGg	p.Q29R	TRPC6_ENST00000348423.4_Missense_Mutation_p.Q29R|TRPC6_ENST00000360497.4_Missense_Mutation_p.Q29R|RP11-748H22.1_ENST00000527374.1_RNA|TRPC6_ENST00000532133.1_Missense_Mutation_p.Q29R|TRPC6_ENST00000526713.1_Intron	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	29					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		CAGATAGTCCTGGCTCTCGTT	0.711																																					p.Q29R	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											.	TRPC6	132	.	0			c.A86G						.						14	15	15					11																	101454149		2193	4279	6472	SO:0001583	missense	7225	exon1			TAGTCCTGGCTCT	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.86A>G	chr11.hg19:g.101454149T>C	ENSP00000340913:p.Gln29Arg	42.0	0.0		67.0	4.0	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	hg19	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	T	9.153	1.016658	0.19355	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.78481	-1.0;-1.08;-0.92;-1.18	5.02	2.7	0.31948	.	0.705449	0.12815	N	0.436907	T	0.59514	0.2199	N	0.14661	0.345	0.25956	N	0.982688	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.49437	-0.8940	10	0.46703	T	0.11	-2.4914	6.4429	0.21859	0.0:0.1975:0.0:0.8025	.	29;29;29	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	R	29	ENSP00000340913:Q29R;ENSP00000435574:Q29R;ENSP00000343672:Q29R;ENSP00000353687:Q29R	ENSP00000340913:Q29R	Q	-	2	0	TRPC6	100959359	0.997000	0.39634	0.999000	0.59377	0.993000	0.82548	0.380000	0.20602	0.272000	0.22027	0.459000	0.35465	CAG	.	.		0.711	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		C	101454149	T	C	101454149	3	2	114	1	0	0	0	0	1	0	0	0	16598	1580	55	2	2761	2	TRPC6	11	101454149	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1738187	101454149	33552367	750	19022										
BIRC2	329	hgsc.bcm.edu	37	chr11	102239232	102239232	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acttcttaatgctgaagatgAaaaaagagaagaggagaagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:102239232delA	ENST00000227758.2	+	6	2718	c.1319delA	c.(1318-1320)gaafs	p.E440fs	BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000530675.1_Frame_Shift_Del_p.E391fs|BIRC2_ENST00000532672.1_Frame_Shift_Del_p.E419fs	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	440					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		GCTGAAGATGAAAAAAGAGAA	0.388																																					p.E440fs		Atlas-INDEL	.											.	BIRC2	51	.	0			c.1318delG						.						117	122	120					11																	102239232		2203	4299	6502	SO:0001589	frameshift_variant	329	exon6			.	L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	590	protein-coding gene	gene with protein product	"NFR2-TRAF signalling complex protein", "apoptosis inhibitor 1"	601712	"baculoviral IAP repeat-containing 2"	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.1319delA	chr11.hg19:g.102239232delA	ENSP00000227758:p.Glu440fs	97.0	0.0		150.0	10.0	NM_001256163	B4E026|Q16516|Q4TTG0	Frame_Shift_Del	DEL	ENST00000227758.2	hg19	CCDS8316.1																																																																																			.	.		0.388	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166		-	102239232	A	-	102239232	7	5	114	1	0	1	0	1	0	0	0	0	1435	246	9	0	1337	0	BIRC2	11	102239232	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	785083	102239232	32767284	751	19023										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103158325	103158325	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccatggctctttttgcatgtAaaactctgggtaagtgtgat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:103158325delA	ENST00000375735.2	+	75	11230	c.11086delA	c.(11086-11088)aaafs	p.K3696fs	DYNC2H1_ENST00000398093.3_Frame_Shift_Del_p.K3703fs|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3696	AAA 6. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TTTTGCATGTAAAACTCTGGG	0.333																																					p.C3702X		Atlas-INDEL	.											.	DYNC2H1	246	.	0			c.11106delT						.						90	87	88					11																	103158325		1848	4091	5939	SO:0001589	frameshift_variant	79659	exon76			.	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.11086delA	chr11.hg19:g.103158325delA	ENSP00000364887:p.Lys3696fs	185.0	0.0		230.0	15.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Frame_Shift_Del	DEL	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.333	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		-	103158325	A	-	103158325	7	5	114	1	0	1	0	1	0	0	0	0	4848	363	13	0	11409	0	DYNC2H1	11	103158325	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	919093	103158325	31848191	752	19024										
PTS	5805	hgsc.bcm.edu	37	chr11	112101391	112101391	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttatgaatctggctgatctcAaaaaatatatggaggtaatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:112101391delA	ENST00000280362.3	+	4	308	c.229delA	c.(229-231)aaafs	p.K78fs	PTS_ENST00000524931.1_Frame_Shift_Del_p.K10fs|PTS_ENST00000525803.1_Intron	NM_000317.2	NP_000308.1	Q03393	PTPS_HUMAN	6-pyruvoyltetrahydropterin synthase	78					cellular amino acid metabolic process (GO:0006520)|central nervous system development (GO:0007417)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	6-pyruvoyltetrahydropterin synthase activity (GO:0003874)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|large_intestine(1)	2		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)		GGCTGATCTCAAAAAATATAT	0.408																																					p.L76fs		Atlas-INDEL	.											.	PTS	7	.	0			c.228delC						.						180	183	182					11																	112101391		2201	4297	6498	SO:0001589	frameshift_variant	5805	exon4			.	U63382	CCDS8359.1	11q22.3	2014-04-01				ENSG00000150787	4.2.3.12		9689	protein-coding gene	gene with protein product		612719				8188266	Standard	NM_000317		Approved	PTPS	uc001pnj.4	Q03393		ENST00000280362.3:c.229delA	chr11.hg19:g.112101391delA	ENSP00000280362:p.Lys78fs	82.0	0.0		136.0	10.0	NM_000317	B0YJ87|Q8WVG8	Frame_Shift_Del	DEL	ENST00000280362.3	hg19	CCDS8359.1																																																																																			.	.		0.408	PTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393541.1	NM_000317		-	112101391	A	-	112101391	7	5	114	1	0	1	0	1	0	0	0	0	12833	131	5	0	243	0	PTS	11	112101391	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	8943066	112101391	22905125	753	19025										
FAM55D	54827	hgsc.bcm.edu	37	chr11	114450944	114450944	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcctctcaggcattccttcaTtttgactgtagccaaactac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:114450944delT	ENST00000375478.3	-	5	1189	c.1009delA	c.(1009-1011)atgfs	p.M337fs	NXPE4_ENST00000424261.2_Frame_Shift_Del_p.M53fs	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	337						extracellular vesicular exosome (GO:0070062)											CATTCCTTCATTTTGACTGTA	0.448																																					p.M337fs		Atlas-INDEL	.											.	.	.	.	0			c.1010delT						.						193	182	186					11																	114450944		1879	4127	6006	SO:0001589	frameshift_variant	54827	exon5			.	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 33", "family with sequence similarity 55, member D"	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1009delA	chr11.hg19:g.114450944delT	ENSP00000364627:p.Met337fs	254.0	0.0		293.0	18.0	NM_001077639	Q6QDB4|Q9NXP5	Frame_Shift_Del	DEL	ENST00000375478.3	hg19	CCDS41718.1																																																																																			.	.		0.448	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678		-	114450944	T	-	114450944	7	5	114	1	0	1	0	1	0	0	0	0	5595	1493	52	0	633	0	FAM55D	11	114450944	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2349553	114450944	20555572	754	19026										
ABCG4	64137	hgsc.bcm.edu	37	chr11	119028987	119028987	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacctttgccaccagcacccTcacacagttctgcatcctct	4	19	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:119028987T>C	ENST00000449422.2	+	10	1300	c.1112T>C	c.(1111-1113)cTc>cCc	p.L371P	AP002956.1_ENST00000599663.1_5'Flank|ABCG4_ENST00000531739.1_Missense_Mutation_p.L371P|ABCG4_ENST00000307417.3_Missense_Mutation_p.L371P	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	371					cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		ACCAGCACCCTCACACAGTTC	0.577																																					p.L371P		Atlas-SNP	.											.	ABCG4	77	.	0			c.T1112C						.						294	275	281					11																	119028987		2200	4295	6495	SO:0001583	missense	64137	exon10			GCACCCTCACACA	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"ATP binding cassette transporters / subfamily G"	13884	protein-coding gene	gene with protein product	"putative ABC transporter", "ATP-binding cassette, subfamily G, member 4"	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1112T>C	chr11.hg19:g.119028987T>C	ENSP00000406874:p.Leu371Pro	117.0	0.0		174.0	7.0	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.073509	0.76415	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739;ENST00000534402	D;D;D;T	0.88046	-2.33;-2.33;-2.33;0.24	5.46	5.46	0.80206	.	0.178675	0.49916	D	0.000136	D	0.85660	0.5748	L	0.59436	1.845	0.80722	D	1	B	0.29085	0.232	B	0.36608	0.229	T	0.83001	-0.0177	10	0.37606	T	0.19	-20.679	10.7027	0.45937	0.0:0.0767:0.0:0.9233	.	371	Q9H172	ABCG4_HUMAN	P	371;371;371;49	ENSP00000304111:L371P;ENSP00000406874:L371P;ENSP00000434318:L371P;ENSP00000434571:L49P	ENSP00000304111:L371P	L	+	2	0	ABCG4	118534197	0.917000	0.31117	0.998000	0.56505	0.912000	0.54170	4.894000	0.63206	2.055000	0.61198	0.455000	0.32223	CTC	.	.		0.577	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		C	119028987	T	C	119028987	3	2	114	1	0	0	0	0	1	0	0	0	70	1551	54	2	1146	2	ABCG4	11	119028987	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4578043	119028987	15977529	755	19027										
OAF	220323	hgsc.bcm.edu	37	chr11	120097608	120097608	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcgctgtcaacttcagccaGggggccctgctgagccccca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:120097608delG	ENST00000328965.4	+	3	963	c.450delG	c.(448-450)cagfs	p.Q150fs	OAF_ENST00000531220.1_Frame_Shift_Del_p.Q34fs	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	150						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(5)	6		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		ACTTCAGCCAGGGGGCCCTGC	0.627																																					p.Q150fs		Atlas-INDEL	.											.	OAF	12	.	0			c.449delA						.						67	60	62					11																	120097608		2203	4300	6503	SO:0001589	frameshift_variant	220323	exon3			.	BC047726	CCDS8430.1	11q23.3	2010-11-23			ENSG00000184232	ENSG00000184232			28752	protein-coding gene	gene with protein product						12477932	Standard	NM_178507		Approved	MGC52117	uc001pxb.3	Q86UD1	OTTHUMG00000166139	ENST00000328965.4:c.450delG	chr11.hg19:g.120097608delG	ENSP00000332613:p.Gln150fs	75.0	0.0		146.0	11.0	NM_178507		Frame_Shift_Del	DEL	ENST00000328965.4	hg19	CCDS8430.1																																																																																			.	.		0.627	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507		-	120097608	G	-	120097608	7	5	114	1	0	1	0	1	0	0	0	0	10807	991	35	0	460	0	OAF	11	120097608	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1068621	120097608	14908908	756	19028										
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120346091	120346091	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agacattcttgtattgttacAaaagcaggatgatagactgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:120346091delA	ENST00000397843.2	+	33	3318	c.3152delA	c.(3151-3153)caafs	p.Q1051fs	ARHGEF12_ENST00000356641.3_Frame_Shift_Del_p.Q1032fs|ARHGEF12_ENST00000532993.1_Frame_Shift_Del_p.Q948fs	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	1051	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		GTATTGTTACAAAAGCAGGAT	0.368			T	MLL	AML																																p.Q1051fs		Atlas-INDEL	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.3151delC						.						180	163	169					11																	120346091		1917	4122	6039	SO:0001589	frameshift_variant	23365	exon33			.	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.3152delA	chr11.hg19:g.120346091delA	ENSP00000380942:p.Gln1051fs	126.0	0.0		228.0	14.0	NM_015313	O15086|Q6P526	Frame_Shift_Del	DEL	ENST00000397843.2	hg19	CCDS41727.1																																																																																			.	.		0.368	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		-	120346091	A	-	120346091	7	5	114	1	0	1	0	1	0	0	0	0	897	130	5	0	3282	0	ARHGEF12	11	120346091	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	248483	120346091	14660425	757	19029										
VWA5A	4013	hgsc.bcm.edu	37	chr11	123994945	123994945	+	Splice_Site	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attttctttctttgtatagcTttttgtctttacagatggag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:123994945delT	ENST00000456829.2	+	11	1417	c.1166delT	c.(1165-1167)ctt>ct	p.L389fs	VWA5A_ENST00000361352.5_Splice_Site_p.L389fs|VWA5A_ENST00000392748.1_Splice_Site_p.L389fs|VWA5A_ENST00000392744.4_Splice_Site_p.L405fs|VWA5A_ENST00000360334.4_Intron|VWA5A_ENST00000449321.1_Splice_Site_p.L389fs	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	389	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.									autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						TTTGTATAGCTTTTTGTCTTT	0.348																																					p.L389fs		Atlas-INDEL	.											.	VWA5A	102	.	0			c.1165delC						.						96	90	92					11																	123994945		2201	4299	6500	SO:0001630	splice_region_variant	4013	exon10			.	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"loss of heterozygosity, 11, chromosomal region 2, gene A"	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.1165-1T>-	chr11.hg19:g.123994945delT		121.0	0.0		230.0	14.0	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Frame_Shift_Del	DEL	ENST00000456829.2	hg19	CCDS8444.1																																																																																			.	.		0.348	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	Frame_Shift_Del	-	123994945	T	-	123994945	8	5	114	1	0	1	0	1	0	0	1	0	17257	1623	56	0	1200	0	VWA5A	11	123994945	Splice_Site	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3648854	123994945	11011571	758	19030										
OR8A1	390275	hgsc.bcm.edu	37	chr11	124440280	124440280	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggtgaactttgtgtcagagAaaaacatcatctcctacgca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:124440280delA	ENST00000284287.3	+	1	388	c.316delA	c.(316-318)aaafs	p.K106fs		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	106					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		TGTGTCAGAGAAAAACATCAT	0.478																																					p.E105fs		Atlas-INDEL	.											.	OR8A1	61	.	0			c.315delG						.						182	163	170					11																	124440280		2201	4299	6500	SO:0001589	frameshift_variant	390275	exon1			.	BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"GPCR / Class A : Olfactory receptors"	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.316delA	chr11.hg19:g.124440280delA	ENSP00000284287:p.Lys106fs	123.0	0.0		190.0	13.0	NM_001005194	Q6IEW7|Q96RC6	Frame_Shift_Del	DEL	ENST00000284287.3	hg19	CCDS31712.1																																																																																			.	.		0.478	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194		-	124440280	A	-	124440280	7	5	114	1	0	1	0	1	0	0	0	0	11234	247	9	0	318	0	OR8A1	11	124440280	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	445335	124440280	10566236	759	19031										
EI24	9538	hgsc.bcm.edu	37	chr11	125452299	125452299	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atcagcgccaatgaagcaaaGaccctggcaaagcatagtaa	9	10	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:125452299G>A	ENST00000343678.4	+	9	973	c.731G>A	c.(730-732)aGa>aAa	p.R244K	STT3A-AS1_ENST00000532714.1_RNA|STT3A-AS1_ENST00000530526.1_RNA|EI24_ENST00000530985.1_3'UTR|EI24_ENST00000278903.6_Splice_Site_p.K281K	NM_001007277.1	NP_001007278.1	O14681	EI24_HUMAN	etoposide induced 2.4	0					apoptotic process (GO:0006915)|autophagy (GO:0006914)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of cell growth (GO:0030308)|neuromuscular process controlling balance (GO:0050885)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|response to drug (GO:0042493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(1)|lung(9)|ovary(1)	11	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)		ATGAAGCAAAGACCCTGGCAA	0.358																																					p.R244K		Atlas-SNP	.											EI24_ENST00000278903,caecum,carcinoma,0,2	EI24	33	.	0			c.G731A						.						32	32	32					11																	125452299		1819	4073	5892	SO:0001583	missense	9538	exon9			AGCAAAGACCCTG	AF010313	CCDS73410.1	11q24.2	2012-11-19	2012-11-16		ENSG00000149547	ENSG00000149547			13276	protein-coding gene	gene with protein product	"ectopic P-granules autophagy protein 4 homolog (C. elegans)"	605170	"etoposide induced 2.4 mRNA"			10594026, 9305847	Standard	NM_001290135		Approved	PIG8, TP53I8, EPG4	uc001qcb.3	O14681	OTTHUMG00000165851	ENST00000343678.4:c.731G>A	chr11.hg19:g.125452299G>A	ENSP00000364081:p.Arg244Lys	36.0	1.0		35.0	4.0	NM_001007277	A8K7D6|B4DKL6|Q9BUQ1	Missense_Mutation	SNP	ENST00000343678.4	hg19		.	.	.	.	.	.	.	.	.	.	G	19.25	3.791980	0.70452	.	.	ENSG00000149547	ENST00000343678	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	T	0.28167	0.0695	.	.	.	0.22226	N	0.999272	B	0.06786	0.001	B	0.04013	0.001	T	0.09596	-1.0667	6	.	.	.	.	11.4257	0.50009	0.0837:0.0:0.9163:0.0	.	244	A6NES3	.	K	244	.	.	R	+	2	0	EI24	124957509	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.959000	0.70339	2.534000	0.85438	0.557000	0.71058	AGA	.	.		0.358	EI24-202	KNOWN	basic	protein_coding	protein_coding		NM_004879		A	125452299	G	A	125452299	3	1	114	1	0	0	0	0	1	0	0	0	4987	942	33	3	877	3	EI24	11	125452299	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1012019	125452299	9554217	760	19032										
CHEK1	1111	hgsc.bcm.edu	37	chr11	125505404	125505404	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaacatacctcaacccttggAaaaaaatcgattctgctcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:125505404delA	ENST00000534070.1	+	7	949	c.694delA	c.(694-696)aaafs	p.K233fs	CHEK1_ENST00000532449.1_3'UTR|CHEK1_ENST00000438015.1_Frame_Shift_Del_p.K233fs|CHEK1_ENST00000544373.1_Frame_Shift_Del_p.K233fs|CHEK1_ENST00000524737.1_Frame_Shift_Del_p.K233fs|CHEK1_ENST00000278916.3_Frame_Shift_Del_p.K233fs|CHEK1_ENST00000427383.2_Frame_Shift_Del_p.K249fs|CHEK1_ENST00000428830.2_Frame_Shift_Del_p.K233fs	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	233	Interaction with CLSPN. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		CAACCCTTGGAAAAAAATCGA	0.383								Other conserved DNA damage response genes																													p.W231X		Atlas-INDEL	.											.,1	CHEK1	44	.	0			c.693delG						.						86	93	90					11																	125505404		2201	4299	6500	SO:0001589	frameshift_variant	1111	exon7			.	AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"CHK1 (checkpoint, S.pombe) homolog", "CHK1 checkpoint homolog (S. pombe)"			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.694delA	chr11.hg19:g.125505404delA	ENSP00000435371:p.Lys233fs	99.0	0.0		129.0	10.0	NM_001114122	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Frame_Shift_Del	DEL	ENST00000534070.1	hg19	CCDS8459.1																																																																																			.	.		0.383	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274		-	125505404	A	-	125505404	7	5	114	1	0	1	0	1	0	0	0	0	3336	247	9	0	716	0	CHEK1	11	125505404	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	53105	125505404	9501112	761	19033										
ADAMTS8	11095	hgsc.bcm.edu	37	chr11	130297563	130297563	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccgcttggtcctactcgtggCccccaggggcggtggcggct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:130297563delC	ENST00000257359.6	-	1	1325	c.619delG	c.(619-621)gccfs	p.A207fs		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	207					negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		CTACTCGTGGCCCCCAGGGGC	0.667																																					p.A207fs		Atlas-INDEL	.											.	ADAMTS8	172	.	0			c.620delC						.						20	30	27					11																	130297563		2179	4267	6446	SO:0001589	frameshift_variant	11095	exon1			.	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"ADAM metallopeptidases with thrombospondin type 1 motif"	224	protein-coding gene	gene with protein product		605175	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.619delG	chr11.hg19:g.130297563delC	ENSP00000257359:p.Ala207fs	83.0	0.0		166.0	10.0	NM_007037	Q9NZS0	Frame_Shift_Del	DEL	ENST00000257359.6	hg19	CCDS41732.1																																																																																			.	.		0.667	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037		-	130297563	C	-	130297563	7	5	114	1	0	1	0	1	0	0	0	0	272	739	26	0	2086	0	ADAMTS8	11	130297563	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	4792159	130297563	4708953	762	19034										
GLB1L3	112937	hgsc.bcm.edu	37	chr11	134152001	134152001	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctgcagtgagatggacctcGggggcttgcccaggtaagcg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:134152001delG	ENST00000431683.2	+	5	514	c.514delG	c.(514-516)gggfs	p.G173fs	GLB1L3_ENST00000389887.5_Frame_Shift_Del_p.G173fs	NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	173					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		GATGGACCTCGGGGGCTTGCC	0.537																																					p.L171fs		Atlas-INDEL	.											.	GLB1L3	102	.	0			c.513delC						.						40	39	39					11																	134152001		2200	4297	6497	SO:0001589	frameshift_variant	112937	exon5			.		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.514delG	chr11.hg19:g.134152001delG	ENSP00000396615:p.Gly173fs	142.0	0.0		202.0	14.0	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Frame_Shift_Del	DEL	ENST00000431683.2	hg19	CCDS44780.1																																																																																			.	.		0.537	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416		-	134152001	G	-	134152001	7	5	114	1	0	1	0	1	0	0	0	0	6438	1116	39	0	532	0	GLB1L3	11	134152001	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	3854438	134152001	854515	763	19035										
WNT5B	81029	hgsc.bcm.edu	37	chr12	1741875	1741875	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagatgtttatcatcggtgcCcagcccgtgtgcagtcagct	12	11	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:1741875C>G	ENST00000397196.2	+	3	364	c.132C>G	c.(130-132)gcC>gcG	p.A44A	WNT5B_ENST00000537031.1_Silent_p.A44A|WNT5B_ENST00000310594.3_Silent_p.A44A|WNT5B_ENST00000542408.1_Silent_p.A44A	NM_032642.2	NP_116031.1	Q9H1J7	WNT5B_HUMAN	wingless-type MMTV integration site family, member 5B	44					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fat cell differentiation (GO:0045444)|lens fiber cell development (GO:0070307)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor binding (GO:0005102)			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)			TCATCGGTGCCCAGCCCGTGT	0.562																																					p.A44A		Atlas-SNP	.											.	WNT5B	27	.	0			c.C132G						.						107	111	110					12																	1741875		2203	4300	6503	SO:0001819	synonymous_variant	81029	exon3			CGGTGCCCAGCCC	AB060966	CCDS8510.1	12p13.3	2008-07-07			ENSG00000111186	ENSG00000111186		"Wingless-type MMTV integration sites"	16265	protein-coding gene	gene with protein product		606361				11445850	Standard	NM_030775		Approved		uc001qjk.3	Q9H1J7	OTTHUMG00000090375	ENST00000397196.2:c.132C>G	chr12.hg19:g.1741875C>G		129.0	0.0		147.0	61.0	NM_032642	A8K315|D3DUP9|Q96S49|Q9BV04	Silent	SNP	ENST00000397196.2	hg19	CCDS8510.1																																																																																			.	.		0.562	WNT5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206747.2			G	1741875	C	G	1741875	2	3	114	1	0	0	0	0	0	0	0	1	17407	610	22	4		4	WNT5B	12	1741875	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10		1741875	132110020	764	19036										
FKBP4	2288	hgsc.bcm.edu	37	chr12	2907011	2907011	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggcagtcctccaaagattCcccccaatgccacgcttgta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:2907011delC	ENST00000001008.4	+	3	554	c.367delC	c.(367-369)cccfs	p.P124fs	RP4-816N1.6_ENST00000547834.1_RNA|RP4-816N1.7_ENST00000547042.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	124	PPIase FKBP-type 1. {ECO:0000255|PROSITE- ProRule:PRU00277}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			TCCAAAGATTCCCCCCAATGC	0.552																																					p.I122fs		Atlas-INDEL	.											.	FKBP4	29	.	0			c.366delT						.						161	136	145					12																	2907011		2203	4300	6503	SO:0001589	frameshift_variant	2288	exon3			.	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.367delC	chr12.hg19:g.2907011delC	ENSP00000001008:p.Pro124fs	154.0	0.0		154.0	11.0	NM_002014	D3DUQ1|Q9UCP1|Q9UCV7	Frame_Shift_Del	DEL	ENST00000001008.4	hg19	CCDS8512.1																																																																																			.	.		0.552	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			-	2907011	C	-	2907011	7	5	114	1	0	1	0	1	0	0	0	0	5918	855	30	0	377	0	FKBP4	12	2907011	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1165136	2907011	130944884	765	19037										
DYRK4	8798	hgsc.bcm.edu	37	chr12	4700393	4700393	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agaaatacctttccaccctaGcattaaaacccaggatccca	4	14	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:4700393G>C	ENST00000540757.2	+	3	207	c.47G>C	c.(46-48)aGc>aCc	p.S16T	DYRK4_ENST00000543431.1_Missense_Mutation_p.S16T|DYRK4_ENST00000010132.5_Missense_Mutation_p.S16T	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	16						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			TTCCACCCTAGCATTAAAACC	0.498																																					p.S16T		Atlas-SNP	.											.	DYRK4	75	.	0			c.G47C						.						89	80	83					12																	4700393		2203	4300	6503	SO:0001583	missense	8798	exon3			ACCCTAGCATTAA	Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.47G>C	chr12.hg19:g.4700393G>C	ENSP00000441755:p.Ser16Thr	170.0	0.0		197.0	66.0	NM_003845	A8K8F7|Q8NEF2|Q92631	Missense_Mutation	SNP	ENST00000540757.2	hg19	CCDS8530.1	.	.	.	.	.	.	.	.	.	.	G	10.21	1.288611	0.23478	.	.	ENSG00000010219	ENST00000542744;ENST00000540757;ENST00000010132;ENST00000543431	T;T;T;T	0.64438	-0.1;-0.03;-0.03;-0.03	4.34	0.201	0.15186	.	1.896970	0.02033	N	0.048652	T	0.52629	0.1746	L	0.44542	1.39	0.09310	N	1	B;B;B	0.28636	0.218;0.11;0.139	B;B;B	0.25291	0.059;0.059;0.027	T	0.24584	-1.0156	10	0.35671	T	0.21	.	5.3065	0.15807	0.2707:0.16:0.5693:0.0	.	131;16;16	F5H6L9;Q9NR20-2;Q9NR20	.;.;DYRK4_HUMAN	T	131;16;16;16	ENSP00000437534:S131T;ENSP00000441755:S16T;ENSP00000010132:S16T;ENSP00000439697:S16T	ENSP00000010132:S16T	S	+	2	0	DYRK4	4570654	0.003000	0.15002	0.000000	0.03702	0.293000	0.27360	0.383000	0.20651	-0.074000	0.12820	-0.430000	0.05897	AGC	.	.		0.498	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398780.2			C	4700393	G	C	4700393	3	2	114	1	0	0	0	0	1	0	0	0	4860	971	34	4	49	4	DYRK4	12	4700393	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1793382	4700393	129151502	766	19038										
ANO2	57101	hgsc.bcm.edu	37	chr12	5721863	5721863	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgttctggatcaactgcttCcccaacatgatgatgctgag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:5721863delC	ENST00000356134.5	-	21	2120	c.2049delG	c.(2047-2049)gggfs	p.G683fs	ANO2_ENST00000546188.1_Frame_Shift_Del_p.G683fs|ANO2_ENST00000327087.8_Frame_Shift_Del_p.G682fs	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	687					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						TCAACTGCTTCCCCAACATGA	0.507																																					p.K683fs		Atlas-INDEL	.											.	ANO2	309	.	0			c.2047delA						.						76	77	77					12																	5721863		1942	4156	6098	SO:0001589	frameshift_variant	57101	exon20			.	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	1183	protein-coding gene	gene with protein product	"transmembrane protein 16B (eight membrane-spanning domains)"	610109	"chromosome 12 open reading frame 3", "transmembrane protein 16B", "anoctamin 2"	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.2049delG	chr12.hg19:g.5721863delC	ENSP00000348453:p.Gly683fs	114.0	0.0		161.0	11.0	NM_020373	C4N787|Q9H847	Frame_Shift_Del	DEL	ENST00000356134.5	hg19																																																																																				.	.		0.507	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		-	5721863	C	-	5721863	7	5	114	1	0	1	0	1	0	0	0	0	697	842	30	0	978	0	ANO2	12	5721863	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1021470	5721863	128130032	767	19039										
NOP2	4839	hgsc.bcm.edu	37	chr12	6672806	6672806	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccatctccccagcagggggcAgcacaaatggttcctcatcc	9	16	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:6672806A>G	ENST00000322166.5	-	7	783	c.662T>C	c.(661-663)cTg>cCg	p.L221P	NOP2_ENST00000541778.1_Missense_Mutation_p.L217P|NOP2_ENST00000545200.1_Missense_Mutation_p.L217P|NOP2_ENST00000399466.2_Missense_Mutation_p.L217P|NOP2_ENST00000537442.1_Missense_Mutation_p.L221P|NOP2_ENST00000382421.3_Missense_Mutation_p.L254P|NOP2_ENST00000542015.1_Intron	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	221					positive regulation of cell proliferation (GO:0008284)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	19						AGCAGGGGGCAGCACAAATGG	0.562											OREG0021630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L254P		Atlas-SNP	.											.	NOP2	44	.	0			c.T761C						.						47	49	49					12																	6672806		1974	4146	6120	SO:0001583	missense	4839	exon8			GGGGGCAGCACAA		CCDS44811.1, CCDS58202.1, CCDS58203.1, CCDS58204.1	12p13	2012-12-10	2012-12-10	2008-10-13	ENSG00000111641	ENSG00000111641		"NOP2/Sun domain containing"	7867	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 1"	164031	"nucleolar protein 1 (120kD)", "nucleolar protein 1, 120kDa", "nucleolar protein 2 homolog (yeast)", "NOP2 nucleolar protein homolog (yeast)"	NOL1		8088812	Standard	NM_006170		Approved	NOP120, NSUN1, p120	uc021qtz.2	P46087	OTTHUMG00000169163	ENST00000322166.5:c.662T>C	chr12.hg19:g.6672806A>G	ENSP00000313272:p.Leu221Pro	96.0	0.0	635	95.0	4.0	NM_001258309	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Missense_Mutation	SNP	ENST00000322166.5	hg19	CCDS58203.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.951896	0.73787	.	.	ENSG00000111641	ENST00000537442;ENST00000382421;ENST00000545200;ENST00000399466;ENST00000322166;ENST00000541778;ENST00000542944;ENST00000542867	T;T;T;T;T;T;T;T	0.71103	1.92;1.7;2.08;1.9;1.92;1.9;0.39;-0.54	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000004	D	0.83050	0.5170	M	0.93197	3.39	0.80722	D	1	P;P	0.39576	0.63;0.679	B;P	0.46825	0.328;0.528	D	0.86931	0.2073	10	0.87932	D	0	-15.4916	14.2848	0.66240	1.0:0.0:0.0:0.0	.	254;217	Q3KQS4;P46087-2	.;.	P	221;254;217;217;221;217;97;217	ENSP00000444437:L221P;ENSP00000371858:L254P;ENSP00000439422:L217P;ENSP00000382392:L217P;ENSP00000313272:L221P;ENSP00000443150:L217P;ENSP00000440754:L97P;ENSP00000443035:L217P	ENSP00000313272:L221P	L	-	2	0	NOP2	6543067	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	6.076000	0.71267	2.063000	0.61619	0.460000	0.39030	CTG	.	.		0.562	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170		G	6672806	A	G	6672806	3	3	114	1	0	0	0	0	1	0	0	0	10547	188	7	2	1816	2	NOP2	12	6672806	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	950943	6672806	127179089	768	19040										
LPAR5	57121	hgsc.bcm.edu	37	chr12	6729711	6729711	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgacgaggttagccagcaggAggcgcacggtcttccgccgc	15	13	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:6729711A>G	ENST00000329858.4	-	2	1460	c.704T>C	c.(703-705)cTc>cCc	p.L235P	LPAR5_ENST00000431922.1_Missense_Mutation_p.L235P|LPAR5_ENST00000540335.1_5'UTR	NM_020400.5	NP_065133.1	Q9H1C0	LPAR5_HUMAN	lysophosphatidic acid receptor 5	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7						AGCCAGCAGGAGGCGCACGGT	0.701																																					p.L235P	NSCLC(74;891 2312 37538)	Atlas-SNP	.											.	LPAR5	30	.	0			c.T704C						.						10	6	8					12																	6729711		2113	4105	6218	SO:0001583	missense	57121	exon2			AGCAGGAGGCGCA	AJ272207	CCDS8553.1	12p13.31	2012-08-08	2008-04-11	2008-04-11		ENSG00000184574		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	13307	protein-coding gene	gene with protein product		606926	"G protein-coupled receptor 92"	GPR93, GPR92		11062477, 11574155, 16774927, 16651401	Standard	NM_020400		Approved	KPG_010, LPA5	uc009zer.2	Q9H1C0		ENST00000329858.4:c.704T>C	chr12.hg19:g.6729711A>G	ENSP00000327875:p.Leu235Pro	42.0	0.0		30.0	4.0	NM_001142961		Missense_Mutation	SNP	ENST00000329858.4	hg19	CCDS8553.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.152688	0.78001	.	.	ENSG00000184574	ENST00000329858;ENST00000431922;ENST00000435659	T;T	0.40225	1.04;1.04	4.93	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000039	T	0.70124	0.3188	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.77869	-0.2427	10	0.87932	D	0	.	14.7338	0.69402	1.0:0.0:0.0:0.0	.	235	Q9H1C0	LPAR5_HUMAN	P	235	ENSP00000327875:L235P;ENSP00000393098:L235P	ENSP00000327875:L235P	L	-	2	0	LPAR5	6599972	0.998000	0.40836	1.000000	0.80357	0.988000	0.76386	4.770000	0.62309	2.077000	0.62373	0.459000	0.35465	CTC	.	.		0.701	LPAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400699.1	NM_020400		G	6729711	A	G	6729711	3	3	114	1	0	0	0	0	1	0	0	0	8917	304	11	2	418	2	LPAR5	12	6729711	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	56905	6729711	127122184	769	19041										
ATN1	1822	hgsc.bcm.edu	37	chr12	7050600	7050600	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcagcagctcatcagctgcAggccatgcacgcacagtcag	11	14	4	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:7050600A>G	ENST00000356654.4	+	9	3659	c.3422A>G	c.(3421-3423)cAg>cGg	p.Q1141R	RNU7-1_ENST00000458811.1_RNA|C12orf57_ENST00000229281.5_5'Flank|C12orf57_ENST00000544681.1_5'Flank|C12orf57_ENST00000540506.2_5'Flank|U47924.31_ENST00000607421.1_RNA|C12orf57_ENST00000537087.1_5'Flank|ATN1_ENST00000396684.2_Missense_Mutation_p.Q1141R	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	1141					cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						CATCAGCTGCAGGCCATGCAC	0.652																																					p.Q1141R		Atlas-SNP	.											.	ATN1	95	.	0			c.A3422G						.						62	63	62					12																	7050600		2202	4298	6500	SO:0001583	missense	1822	exon9			AGCTGCAGGCCAT	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"dentatorubral-pallidoluysian atrophy (atrophin-1)"	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.3422A>G	chr12.hg19:g.7050600A>G	ENSP00000349076:p.Gln1141Arg	78.0	0.0		81.0	4.0	NM_001007026	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	hg19	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631954	0.87660	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325;ENST00000229279	T;T;T	0.70399	-0.48;-0.48;-0.48	4.32	4.32	0.51571	.	0.000000	0.32401	U	0.006153	T	0.81182	0.4769	M	0.62723	1.935	0.80722	D	1	D	0.57571	0.98	D	0.75020	0.985	D	0.83576	0.0115	10	0.87932	D	0	.	13.987	0.64341	1.0:0.0:0.0:0.0	.	1141	P54259	ATN1_HUMAN	R	1141;1141;1141;726	ENSP00000349076:Q1141R;ENSP00000379915:Q1141R;ENSP00000441744:Q1141R	ENSP00000229279:Q726R	Q	+	2	0	ATN1	6920861	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.139000	0.94554	1.961000	0.56991	0.533000	0.62120	CAG	.	.		0.652	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		G	7050600	A	G	7050600	3	3	114	1	0	0	0	0	1	0	0	0	1111	188	7	2	3452	2	ATN1	12	7050600	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	320889	7050600	126801295	770	19042										
CLSTN3	9746	hgsc.bcm.edu	37	chr12	7295529	7295529	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtttcagcgtgcgctcaggTcgcctggagagccgcgaggt	17	11	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:7295529T>C	ENST00000266546.6	+	11	2055	c.1605T>C	c.(1603-1605)ggT>ggC	p.G535G	CLSTN3_ENST00000537408.1_Silent_p.G547G	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	535					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						TGCGCTCAGGTCGCCTGGAGA	0.587																																					p.G535G		Atlas-SNP	.											.	CLSTN3	84	.	0			c.T1605C						.						116	89	98					12																	7295529		2203	4300	6503	SO:0001819	synonymous_variant	9746	exon11			CTCAGGTCGCCTG	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1605T>C	chr12.hg19:g.7295529T>C		183.0	0.0		233.0	11.0	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Silent	SNP	ENST00000266546.6	hg19	CCDS8575.1																																																																																			.	.		0.587	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		C	7295529	T	C	7295529	2	2	114	1	0	0	0	0	0	0	0	1	3565	1654	58	2		2	CLSTN3	12	7295529	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	244929	7295529	126556366	771	19043										
KLRK1	22914	hgsc.bcm.edu	37	chr12	10539504	10539504	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atggaacataggacttaccaTtttctctacatttgcttttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:10539504delT	ENST00000240618.6	-	3	286	c.146delA	c.(145-147)aatfs	p.N49fs	KLRK1_ENST00000540818.1_Frame_Shift_Del_p.N49fs|KLRC4-KLRK1_ENST00000539300.1_3'UTR|RP11-277P12.20_ENST00000500682.1_RNA	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	49					cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						GGACTTACCATTTTCTCTACA	0.323																																					p.N49fs		Atlas-INDEL	.											.	.	.	.	0			c.147delT						.						193	172	179					12																	10539504		2203	4298	6501	SO:0001589	frameshift_variant	0	exon8			.	AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"Killer cell lectin-like receptors", "CD molecules"	18788	protein-coding gene	gene with protein product		611817	"DNA segment on chromosome 12 (unique) 2489 expressed sequence"	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.146delA	chr12.hg19:g.10539504delT	ENSP00000240618:p.Asn49fs	121.0	0.0		183.0	11.0	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Frame_Shift_Del	DEL	ENST00000240618.6	hg19	CCDS8623.1																																																																																			.	.		0.323	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		-	10539504	T	-	10539504	7	5	114	1	0	1	0	1	0	0	0	0	8432	1493	52	0	528	0	KLRK1	12	10539504	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3243975	10539504	123312391	772	19044										
TAS2R13	50838	hgsc.bcm.edu	37	chr12	11061232	11061232	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttgtatggaccttggtcctGgggtctctgtgtcctttgta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:11061232delG	ENST00000390677.2	-	1	929	c.666delC	c.(664-666)cccfs	p.P222fs	PRR4_ENST00000536668.1_Intron	NM_023920.2	NP_076409.1	Q9NYV9	T2R13_HUMAN	taste receptor, type 2, member 13	222					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						CCTTGGTCCTGGGGTCTCTGT	0.393																																					p.R223fs		Atlas-INDEL	.											.	TAS2R13	29	.	0			c.667delA						.						98	99	99					12																	11061232		2203	4300	6503	SO:0001589	frameshift_variant	50838	exon1			.	AF227137	CCDS8635.1	12p13	2012-08-22			ENSG00000212128	ENSG00000212128		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14919	protein-coding gene	gene with protein product		604792				10761934, 10766242	Standard	NM_023920		Approved	T2R13, TRB3	uc001qzg.1	Q9NYV9		ENST00000390677.2:c.666delC	chr12.hg19:g.11061232delG	ENSP00000375095:p.Pro222fs	171.0	0.0		216.0	14.0	NM_023920	Q4G0I5|Q502V8|Q645X2	Frame_Shift_Del	DEL	ENST00000390677.2	hg19	CCDS8635.1																																																																																			.	.		0.393	TAS2R13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400229.1			-	11061232	G	-	11061232	7	5	114	1	0	1	0	1	0	0	0	0	15582	1335	47	0	249	0	TAS2R13	12	11061232	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	521728	11061232	122790663	773	19045										
LRP6	4040	hgsc.bcm.edu	37	chr12	12300340	12300340	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attcgccggagatctgaatcAgcccaaaagagcttgcccag	10	12	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:12300340A>G	ENST00000261349.4	-	15	3433	c.3357T>C	c.(3355-3357)gcT>gcC	p.A1119A	LRP6_ENST00000543091.1_Silent_p.A1119A	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1119	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				GATCTGAATCAGCCCAAAAGA	0.418																																					p.A1119A		Atlas-SNP	.											.	LRP6	170	.	0			c.T3357C						.						100	101	101					12																	12300340		2203	4300	6503	SO:0001819	synonymous_variant	4040	exon15			TGAATCAGCCCAA	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.3357T>C	chr12.hg19:g.12300340A>G		92.0	0.0		117.0	5.0	NM_002336	Q17RZ2	Silent	SNP	ENST00000261349.4	hg19	CCDS8647.1																																																																																			.	.		0.418	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			G	12300340	A	G	12300340	2	3	114	1	0	0	0	0	0	0	0	1	8971	175	7	2		2	LRP6	12	12300340	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1239108	12300340	121551555	774	19046										
CDKN1B	1027	hgsc.bcm.edu	37	chr12	12871837	12871837	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccaaatgccggttctgtggAgcagacgcccaagaagcctg	12	13	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:12871837A>G	ENST00000228872.4	+	2	1270	c.554A>G	c.(553-555)gAg>gGg	p.E185G	CDKN1B_ENST00000477087.1_3'UTR|CDKN1B_ENST00000396340.1_Intron	NM_004064.3	NP_004055.1	P46527	CDN1B_HUMAN	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	185					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|cellular response to antibiotic (GO:0071236)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular component movement (GO:0051271)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of kinase activity (GO:0033673)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|potassium ion transport (GO:0006813)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein phosphatase binding (GO:0019903)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)			breast(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(5)	13		Prostate(47;0.0322)|all_epithelial(100;0.159)		BRCA - Breast invasive adenocarcinoma(232;0.0336)		GGTTCTGTGGAGCAGACGCCC	0.498																																					p.E185G		Atlas-SNP	.											.	CDKN1B	48	.	0			c.A554G						.						78	86	83					12																	12871837		2203	4300	6503	SO:0001583	missense	1027	exon2			CTGTGGAGCAGAC	AF480891	CCDS8653.1	12p13.1-p12	2008-08-04			ENSG00000111276	ENSG00000111276			1785	protein-coding gene	gene with protein product		600778				8033212	Standard	NM_004064		Approved	KIP1, P27KIP1	uc001rat.2	P46527	OTTHUMG00000149914	ENST00000228872.4:c.554A>G	chr12.hg19:g.12871837A>G	ENSP00000228872:p.Glu185Gly	62.0	0.0		71.0	4.0	NM_004064	Q16307|Q5U0H2|Q9BUS6	Missense_Mutation	SNP	ENST00000228872.4	hg19	CCDS8653.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.826681	0.90955	.	.	ENSG00000111276	ENST00000228872;ENST00000535674;ENST00000442489	T;T	0.59772	0.24;0.24	5.37	5.37	0.77165	.	.	.	.	.	T	0.73651	0.3614	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.76675	-0.2872	9	0.72032	D	0.01	.	13.9531	0.64131	1.0:0.0:0.0:0.0	.	185	P46527	CDN1B_HUMAN	G	185;134;91	ENSP00000228872:E185G;ENSP00000407597:E91G	ENSP00000228872:E185G	E	+	2	0	CDKN1B	12763104	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.539000	0.73856	2.024000	0.59613	0.533000	0.62120	GAG	.	.		0.498	CDKN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313878.2	NM_004064		G	12871837	A	G	12871837	3	3	114	1	0	0	0	0	1	0	0	0	3161	304	11	2	560	2	CDKN1B	12	12871837	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	571497	12871837	120980058	775	19047										
HEBP1	50865	hgsc.bcm.edu	37	chr12	13142225	13142225	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actcacccttgtcattggtgCcccccgcatactttgcgacc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:13142225delC	ENST00000014930.4	-	2	361	c.203delG	c.(202-204)ggcfs	p.G68fs	HEBP1_ENST00000536942.1_Frame_Shift_Del_p.G68fs	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	68					circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		GTCATTGGTGCCCCCCGCATA	0.552																																					p.G68fs		Atlas-INDEL	.											.	HEBP1	16	.	0			c.204delC						.						239	174	196					12																	13142225		2203	4300	6503	SO:0001589	frameshift_variant	50865	exon2			.	AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"Endogenous ligands"	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771	ENST00000014930.4:c.203delG	chr12.hg19:g.13142225delC	ENSP00000014930:p.Gly68fs	199.0	0.0		275.0	17.0	NM_015987	A8K1G2|Q9Y5Z5	Frame_Shift_Del	DEL	ENST00000014930.4	hg19	CCDS31749.1																																																																																			.	.		0.552	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1			-	13142225	C	-	13142225	7	5	114	1	0	1	0	1	0	0	0	0	7045	739	26	0	378	0	HEBP1	12	13142225	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	270388	13142225	120709670	776	19048										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19475253	19475253	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttataacctaggccaagttaAgccgattatgtgaacaagat	8	7	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:19475253A>G	ENST00000299275.6	+	14	1924	c.1918A>G	c.(1918-1920)Agc>Ggc	p.S640G	PLEKHA5_ENST00000538714.1_Missense_Mutation_p.S698G|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.S559G|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.S398G|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.S571G|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.S743G|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.S698G|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.S640G|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.S640G	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	640					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					GGCCAAGTTAAGCCGATTATG	0.343																																					p.S743G	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A2227G						.						93	92	92					12																	19475253		2203	4300	6503	SO:0001583	missense	54477	exon19			AAGTTAAGCCGAT	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.1918A>G	chr12.hg19:g.19475253A>G	ENSP00000299275:p.Ser640Gly	18.0	0.0		53.0	4.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	12.17	1.858438	0.32791	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T	0.39787	1.07;1.06;1.07;1.06;1.07;1.07;1.06;1.06;1.06;1.06	4.76	4.76	0.60689	.	0.042036	0.85682	D	0.000000	T	0.50377	0.1612	L	0.42245	1.32	0.39951	D	0.974546	D;P;B;D;B;P;B	0.76494	0.999;0.49;0.357;0.997;0.038;0.497;0.127	D;B;B;D;B;B;B	0.87578	0.998;0.217;0.108;0.91;0.028;0.108;0.147	T	0.45687	-0.9244	10	0.06757	T	0.87	-14.9551	12.9989	0.58664	1.0:0.0:0.0:0.0	.	640;559;571;743;743;640;698	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;PKHA5_HUMAN;.	G	640;698;640;744;743;640;398;698;571;559;532	ENSP00000325155:S640G;ENSP00000347560:S698G;ENSP00000352104:S640G;ENSP00000404296:S743G;ENSP00000299275:S640G;ENSP00000440611:S398G;ENSP00000439673:S698G;ENSP00000400411:S571G;ENSP00000439837:S559G;ENSP00000440371:S532G	ENSP00000299275:S640G	S	+	1	0	PLEKHA5	19366520	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	8.091000	0.89528	1.992000	0.58205	0.455000	0.32223	AGC	.	.		0.343	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		G	19475253	A	G	19475253	3	3	114	1	0	0	0	0	1	0	0	0	12068	72	3	2	2097	2	PLEKHA5	12	19475253	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	6333028	19475253	114376642	777	19049										
GYS2	2998	hgsc.bcm.edu	37	chr12	21692268	21692268	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcaggtgtctggcatgctggTaatactattgatagaaagcc	11	7	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:21692268T>C	ENST00000261195.2	-	15	2068	c.1814A>G	c.(1813-1815)tAc>tGc	p.Y605C		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	605					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GGCATGCTGGTAATACTATTG	0.333																																					p.Y605C	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											.	GYS2	110	.	0			c.A1814G						.						146	153	151					12																	21692268		2203	4300	6503	SO:0001583	missense	2998	exon15			TGCTGGTAATACT		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1814A>G	chr12.hg19:g.21692268T>C	ENSP00000261195:p.Tyr605Cys	101.0	0.0		89.0	4.0	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	hg19	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.990812	0.74589	.	.	ENSG00000111713	ENST00000261195	T	0.73575	-0.76	5.3	5.3	0.74995	.	0.064498	0.64402	D	0.000004	D	0.86318	0.5904	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88259	0.2922	10	0.87932	D	0	-16.451	14.569	0.68200	0.0:0.0:0.0:1.0	.	605	P54840	GYS2_HUMAN	C	605	ENSP00000261195:Y605C	ENSP00000261195:Y605C	Y	-	2	0	GYS2	21583535	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.002000	0.76304	2.218000	0.71995	0.528000	0.53228	TAC	.	.		0.333	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		C	21692268	T	C	21692268	3	2	114	1	0	0	0	0	1	0	0	0	6922	1638	57	2	305	2	GYS2	12	21692268	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2217015	21692268	112159627	778	19050										
ABCC9	10060	hgsc.bcm.edu	37	chr12	21960279	21960279	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagcttagataatgcactcaCtgtggccatgtcaatggaag	10	8	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:21960279C>T	ENST00000261201.4	-	36	4449		c.e36+1		ABCC9_ENST00000345162.2_Splice_Site|ABCC9_ENST00000261200.4_Splice_Site	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9						defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	AATGCACTCACTGTGGCCATG	0.403																																					.		Atlas-SNP	.											.	ABCC9	411	.	0			c.4449+1G>A						.						163	154	157					12																	21960279		2203	4300	6503	SO:0001630	splice_region_variant	10060	exon37			CACTCACTGTGGC	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.4449+1G>A	chr12.hg19:g.21960279C>T		96.0	0.0		97.0	5.0	NM_020297	O60707	Splice_Site	SNP	ENST00000261201.4	hg19	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.826729	0.90955	.	.	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	.	.	.	5.15	5.15	0.70609	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8248	0.92114	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCC9	21851546	1.000000	0.71417	0.997000	0.53966	0.981000	0.71138	7.534000	0.82004	2.654000	0.90174	0.655000	0.94253	.	.	.		0.403	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691	Intron	T	21960279	C	T	21960279	5	4	114	1	0	0	0	0	0	0	1	0	59	579	20	3	353	3	ABCC9	12	21960279	Splice_Site	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	268011	21960279	111891616	779	19051										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22666279	22666279	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttaaaagagctttaaagggCcccccttcttttccagcact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:22666279delC	ENST00000333957.4	-	9	1242	c.987delG	c.(985-987)gggfs	p.G329fs	C2CD5_ENST00000536386.1_Frame_Shift_Del_p.G320fs|C2CD5_ENST00000544930.1_Frame_Shift_Del_p.G122fs|C2CD5_ENST00000446597.1_Frame_Shift_Del_p.G329fs|C2CD5_ENST00000396028.2_Frame_Shift_Del_p.G320fs|C2CD5_ENST00000542676.1_Frame_Shift_Del_p.G329fs|C2CD5_ENST00000545552.1_Frame_Shift_Del_p.G320fs	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	329					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CTTTAAAGGGCCCCCCTTCTT	0.363																																					p.P330fs		Atlas-INDEL	.											.	.	.	.	0			c.988delC						.						144	133	137					12																	22666279		2203	4300	6503	SO:0001589	frameshift_variant	9847	exon9			.	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.987delG	chr12.hg19:g.22666279delC	ENSP00000334229:p.Gly329fs	115.0	0.0		142.0	10.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Frame_Shift_Del	DEL	ENST00000333957.4	hg19	CCDS31758.1																																																																																			.	.		0.363	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		-	22666279	C	-	22666279	7	5	114	1	0	1	0	1	0	0	0	0	8191	726	26	0	2083	0	KIAA0528	12	22666279	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	706000	22666279	111185616	780	19052										
C12orf11	55726	hgsc.bcm.edu	37	chr12	27067353	27067353	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acacttaccgcttgcatgttAaaaatggtggtttgtgaaat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:27067353delA	ENST00000261191.7	-	12	1943	c.1407delT	c.(1405-1407)tttfs	p.F469fs	ASUN_ENST00000539625.1_Frame_Shift_Del_p.F368fs	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	469					centrosome localization (GO:0051642)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|protein localization to nuclear envelope (GO:0090435)|regulation of fertilization (GO:0080154)|regulation of mitotic cell cycle (GO:0007346)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CTTGCATGTTAAAAATGGTGG	0.323																																					p.N470fs		Atlas-INDEL	.											.	.	.	.	0			c.1408delA						.						140	140	140					12																	27067353		2203	4300	6503	SO:0001589	frameshift_variant	55726	exon12			.	AK001222	CCDS8708.1	12p12.3	2013-05-08	2013-05-08	2011-12-09	ENSG00000064102	ENSG00000064102			20174	protein-coding gene	gene with protein product	"spermatogenesis associated 30"	615079	"chromosome 12 open reading frame 11", "asunder, spermatogenesis regulator homolog (Drosphila)"	C12orf11		12414650, 19357193, 23097494	Standard	NM_018164		Approved	FLJ10637, NET48, Mat89Bb, SPATA30	uc001rhk.4	Q9NVM9	OTTHUMG00000169193	ENST00000261191.7:c.1407delT	chr12.hg19:g.27067353delA	ENSP00000261191:p.Phe469fs	131.0	0.0		173.0	12.0	NM_018164	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Frame_Shift_Del	DEL	ENST00000261191.7	hg19	CCDS8708.1																																																																																			.	.		0.323	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164		-	27067353	A	-	27067353	7	5	114	1	0	1	0	1	0	0	0	0	1677	359	13	0	737	0	C12orf11	12	27067353	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	4401074	27067353	106784542	781	19053										
OVCH1	341350	hgsc.bcm.edu	37	chr12	29630051	29630051	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctacctttataatgtgcttcTctggagcacaaatgaaccaa	6	10	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:29630051T>C	ENST00000318184.5	-	12	1360	c.1361A>G	c.(1360-1362)gAg>gGg	p.E454G	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	454	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AATGTGCTTCTCTGGAGCACA	0.393																																					p.E454G		Atlas-SNP	.											.	OVCH1	195	.	0			c.A1361G						.						80	79	79					12																	29630051		1888	4110	5998	SO:0001583	missense	341350	exon12			TGCTTCTCTGGAG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1361A>G	chr12.hg19:g.29630051T>C	ENSP00000326708:p.Glu454Gly	86.0	0.0		89.0	4.0	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	hg19		.	.	.	.	.	.	.	.	.	.	T	6.608	0.480572	0.12581	.	.	ENSG00000187950	ENST00000318184	T	0.58210	0.35	2.73	-2.36	0.06663	CUB (5);	.	.	.	.	T	0.37625	0.1010	L	0.39467	1.215	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.25641	-1.0126	9	0.42905	T	0.14	.	5.716	0.17960	0.0:0.4222:0.1557:0.4222	.	454	Q7RTY7	OVCH1_HUMAN	G	454	ENSP00000326708:E454G	ENSP00000326708:E454G	E	-	2	0	OVCH1	29521318	0.022000	0.18835	0.000000	0.03702	0.001000	0.01503	-0.258000	0.08733	-0.581000	0.05937	-0.304000	0.09214	GAG	.	.		0.393	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		C	29630051	T	C	29630051	3	2	114	1	0	0	0	0	1	0	0	0	11332	1551	54	2	2111	2	OVCH1	12	29630051	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2562698	29630051	104221844	782	19054										
TMTC1	83857	hgsc.bcm.edu	37	chr12	29904627	29904627	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggaccacacagctcgtggggAcactgggaatccactgctct	12	13	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:29904627A>G	ENST00000539277.1	-	5	968	c.910T>C	c.(910-912)Tcc>Ccc	p.S304P	TMTC1_ENST00000381224.2_Missense_Mutation_p.S196P|TMTC1_ENST00000256062.5_Missense_Mutation_p.S196P|TMTC1_ENST00000552618.1_Missense_Mutation_p.S304P|TMTC1_ENST00000551659.1_Missense_Mutation_p.S304P	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	304						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					gctcgtggggACACTGGGAAT	0.582																																					p.S304P		Atlas-SNP	.											.	TMTC1	147	.	0			c.T910C						.						112	100	104					12																	29904627		2203	4300	6503	SO:0001583	missense	83857	exon5			GTGGGGACACTGG		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.910T>C	chr12.hg19:g.29904627A>G	ENSP00000442046:p.Ser304Pro	91.0	0.0		103.0	5.0	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	hg19	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	A	3.009	-0.204394	0.06180	.	.	ENSG00000133687	ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277;ENST00000381224	T;T;T;T;T	0.69175	-0.36;-0.14;-0.38;-0.22;1.43	4.51	1.99	0.26369	.	0.628295	0.16615	N	0.206723	T	0.30510	0.0767	N	0.02120	-0.675	0.09310	N	1	B;B	0.14438	0.01;0.002	B;B	0.11329	0.006;0.002	T	0.13980	-1.0489	9	.	.	.	-4.486	1.8015	0.03072	0.5629:0.175:0.0938:0.1683	.	196;304	Q8IUR5-3;Q8IUR5	.;TMTC1_HUMAN	P	196;304;304;304;196	ENSP00000256062:S196P;ENSP00000448112:S304P;ENSP00000449043:S304P;ENSP00000442046:S304P;ENSP00000370622:S196P	.	S	-	1	0	TMTC1	29795894	0.961000	0.32948	0.032000	0.17829	0.406000	0.30931	1.745000	0.38278	0.278000	0.22164	-0.341000	0.08007	TCC	.	.		0.582	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		G	29904627	A	G	29904627	3	3	114	1	0	0	0	0	1	0	0	0	16275	275	10	2	1794	2	TMTC1	12	29904627	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	274576	29904627	103947268	783	19055										
DENND5B	160518	hgsc.bcm.edu	37	chr12	31632582	31632582	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggtaaacacctgcaccaggTtctctaatcccaggagctca	8	13	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:31632582T>C	ENST00000389082.5	-	3	1109	c.845A>G	c.(844-846)aAc>aGc	p.N282S	DENND5B_ENST00000354285.4_Missense_Mutation_p.N304S|DENND5B_ENST00000536562.1_Missense_Mutation_p.N317S|DENND5B_ENST00000306833.6_Missense_Mutation_p.N317S|DENND5B_ENST00000545147.1_Intron	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	282	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CTGCACCAGGTTCTCTAATCC	0.473																																					p.N282S		Atlas-SNP	.											.	DENND5B	114	.	0			c.A845G						.						21	20	20					12																	31632582		1824	4078	5902	SO:0001583	missense	160518	exon3			ACCAGGTTCTCTA	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.845A>G	chr12.hg19:g.31632582T>C	ENSP00000373734:p.Asn282Ser	76.0	0.0		95.0	4.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	hg19	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.898681	0.52227	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285;ENST00000546299	T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58	4.56	4.56	0.56223	DENN (3);	0.000000	0.85682	D	0.000000	T	0.30978	0.0782	M	0.64676	1.99	0.80722	D	1	P;P;D;P;P	0.54397	0.843;0.929;0.966;0.763;0.925	P;P;D;P;P	0.63033	0.53;0.674;0.91;0.657;0.792	T	0.01791	-1.1273	10	0.39692	T	0.17	-29.5519	14.1051	0.65083	0.0:0.0:0.0:1.0	.	317;204;304;282;317	Q6ZUT9-2;Q6ZUT9-3;Q6ZUT9-4;Q6ZUT9;G3V1S3	.;.;.;DEN5B_HUMAN;.	S	282;317;317;304;234	ENSP00000373734:N282S;ENSP00000306482:N317S;ENSP00000444889:N317S;ENSP00000346238:N304S;ENSP00000442938:N234S	ENSP00000306482:N317S	N	-	2	0	DENND5B	31523849	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.663000	0.83820	1.924000	0.55735	0.533000	0.62120	AAC	.	.		0.473	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		C	31632582	T	C	31632582	3	2	114	1	0	0	0	0	1	0	0	0	4439	1725	60	2	3055	2	DENND5B	12	31632582	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1727955	31632582	102219313	784	19056										
ALG10B	144245	hgsc.bcm.edu	37	chr12	38714025	38714025	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcagtatttccaacactttaTttttttaacttcctttatta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:38714025delT	ENST00000308742.4	+	3	748	c.432delT	c.(430-432)tatfs	p.Y144fs	AC117372.1_ENST00000401168.2_RNA|ALG10B_ENST00000551464.1_Intron	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	144					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				CAACACTTTATTTTTTTAACT	0.318																																					p.Y144fs		Atlas-INDEL	.											.	ALG10B	58	.	0			c.431delA						.						68	74	72					12																	38714025		2203	4295	6498	SO:0001589	frameshift_variant	144245	exon3			.	AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"		"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.432delT	chr12.hg19:g.38714025delT	ENSP00000310120:p.Tyr144fs	317.0	0.0		405.0	25.0	NM_001013620	B2RPF4	Frame_Shift_Del	DEL	ENST00000308742.4	hg19	CCDS31772.1																																																																																			.	.		0.318	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620		-	38714025	T	-	38714025	7	5	114	1	0	1	0	1	0	0	0	0	512	1500	52	0	442	0	ALG10B	12	38714025	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	7081443	38714025	95137870	785	19057										
KIF21A	55605	hgsc.bcm.edu	37	chr12	39688246	39688246	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttaattactggcaatatcttCccccagatctcctgtgtcag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:39688246delC	ENST00000361418.5	-	38	5020	c.5005delG	c.(5005-5007)gaafs	p.E1669fs	KIF21A_ENST00000361961.3_Frame_Shift_Del_p.E1656fs|KIF21A_ENST00000544797.2_Frame_Shift_Del_p.E1632fs|KIF21A_ENST00000541463.2_Frame_Shift_Del_p.E1616fs|KIF21A_ENST00000395670.3_Frame_Shift_Del_p.E1670fs			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1669					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				GCAATATCTTCCCCCAGATCT	0.363																																					p.E1669fs		Atlas-INDEL	.											.	KIF21A	238	.	0			c.5006delA						.						123	113	116					12																	39688246		2203	4300	6503	SO:0001589	frameshift_variant	55605	exon38			.	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.5005delG	chr12.hg19:g.39688246delC	ENSP00000354878:p.Glu1669fs	199.0	0.0		193.0	13.0	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Frame_Shift_Del	DEL	ENST00000361418.5	hg19	CCDS53776.1																																																																																			.	.		0.363	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		-	39688246	C	-	39688246	7	5	114	1	0	1	0	1	0	0	0	0	8297	864	30	0	23	0	KIF21A	12	39688246	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	974221	39688246	94163649	786	19058										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43822261	43822261	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttcaggatcacagtaattcTcatcaattggctgatggtag	9	8	4	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:43822261T>C	ENST00000389420.3	-	26	3727	c.3728A>G	c.(3727-3729)gAg>gGg	p.E1243G	ADAMTS20_ENST00000395541.2_Missense_Mutation_p.E361G|ADAMTS20_ENST00000553158.1_Missense_Mutation_p.E1243G	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1243	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ACAGTAATTCTCATCAATTGG	0.463																																					p.E1243G		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A3728G						.						60	62	61					12																	43822261		2203	4300	6503	SO:0001583	missense	80070	exon26			TAATTCTCATCAA	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.3728A>G	chr12.hg19:g.43822261T>C	ENSP00000374071:p.Glu1243Gly	153.0	0.0		162.0	7.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	16.44	3.123471	0.56613	.	.	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	5.35	5.35	0.76521	.	0.000000	0.51477	D	0.000094	T	0.58264	0.2110	L	0.31664	0.95	0.44110	D	0.99688	B;D	0.63046	0.107;0.992	B;D	0.63192	0.199;0.912	T	0.53927	-0.8369	10	0.27082	T	0.32	.	16.0388	0.80650	0.0:0.0:0.0:1.0	.	1243;361	P59510;E9PBD5	ATS20_HUMAN;.	G	1243;373;361;1243;1243	ENSP00000374071:E1243G;ENSP00000447427:E373G;ENSP00000378911:E361G;ENSP00000448341:E1243G	ENSP00000374068:E1243G	E	-	2	0	ADAMTS20	42108528	1.000000	0.71417	0.999000	0.59377	0.934000	0.57294	3.106000	0.50322	2.330000	0.79161	0.477000	0.44152	GAG	.	.		0.463	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		C	43822261	T	C	43822261	3	2	114	1	0	0	0	0	1	0	0	0	266	1551	54	2	2059	2	ADAMTS20	12	43822261	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4134015	43822261	90029634	787	19059										
ANO6	196527	hgsc.bcm.edu	37	chr12	45771870	45771870	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgacagttttggaaccctggTctttgcagtatttatgggag	12	7	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:45771870T>C	ENST00000320560.8	+	10	1341	c.1139T>C	c.(1138-1140)gTc>gCc	p.V380A	ANO6_ENST00000435642.1_Missense_Mutation_p.V380A|ANO6_ENST00000441606.2_Missense_Mutation_p.V362A|ANO6_ENST00000423947.3_Missense_Mutation_p.V401A|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000425752.2_Missense_Mutation_p.V380A	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	380					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						GGAACCCTGGTCTTTGCAGTA	0.313																																					p.V401A		Atlas-SNP	.											.	ANO6	163	.	0			c.T1202C						.						176	178	177					12																	45771870		2203	4300	6503	SO:0001583	missense	196527	exon11			CCCTGGTCTTTGC	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.1139T>C	chr12.hg19:g.45771870T>C	ENSP00000320087:p.Val380Ala	80.0	0.0		94.0	5.0	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.122971	0.56613	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.23	5.23	0.72850	.	0.339267	0.30989	N	0.008469	T	0.58906	0.2155	L	0.48174	1.505	0.38052	D	0.935795	B;B;B;B	0.23591	0.01;0.002;0.088;0.013	B;B;B;B	0.30495	0.038;0.012;0.116;0.05	T	0.61729	-0.7003	10	0.49607	T	0.09	.	14.3961	0.67013	0.0:0.0:0.0:1.0	.	362;401;380;380	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	A	380;401;380;380;362	ENSP00000391417:V380A;ENSP00000409126:V401A;ENSP00000413840:V380A;ENSP00000320087:V380A;ENSP00000413137:V362A	ENSP00000320087:V380A	V	+	2	0	ANO6	44058137	1.000000	0.71417	0.757000	0.31301	0.925000	0.55904	5.103000	0.64578	2.279000	0.76181	0.533000	0.62120	GTC	.	.		0.313	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743		C	45771870	T	C	45771870	3	2	114	1	0	0	0	0	1	0	0	0	701	1667	58	2	1197	2	ANO6	12	45771870	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1949609	45771870	88080025	788	19060										
ARID2	196528	hgsc.bcm.edu	37	chr12	46243493	46243493	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agatgtactatcagcagcaaCcagtttctacttctgttgtt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:46243493delC	ENST00000334344.6	+	14	2018	c.1846delC	c.(1846-1848)ccafs	p.P616fs	ARID2_ENST00000422737.1_Frame_Shift_Del_p.P467fs|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000444670.1_Frame_Shift_Del_p.P226fs	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	616					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCAGCAGCAACCAGTTTCTAC	0.413			"N, S, F"		hepatocellular carcinoma																																p.Q615fs		Atlas-INDEL	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.1845delA						.						326	304	311					12																	46243493		2203	4300	6503	SO:0001589	frameshift_variant	196528	exon14			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1846delC	chr12.hg19:g.46243493delC	ENSP00000335044:p.Pro616fs	175.0	0.0		180.0	11.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.413	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		-	46243493	C	-	46243493	7	5	114	1	0	1	0	1	0	0	0	0	915	507	18	0	1900	0	ARID2	12	46243493	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	471623	46243493	87608402	789	19061										
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46328022	46328022	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagaagaaaacatattggagAaaaaatttctgaagcactga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:46328022delA	ENST00000369367.3	-	8	802	c.569delT	c.(568-570)ttcfs	p.F190fs	SCAF11_ENST00000549162.1_5'UTR|SCAF11_ENST00000419565.2_Frame_Shift_Del_p.F190fs	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	190					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						CATATTGGAGAAAAAATTTCT	0.303																																					p.F190fs		Atlas-INDEL	.											.	SCAF11	145	.	0			c.570delC						.						47	45	46					12																	46328022		1790	4055	5845	SO:0001589	frameshift_variant	9169	exon8			.	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"RING-type (C3HC4) zinc fingers"	10784	protein-coding gene	gene with protein product		603668	"splicing factor, arginine/serine-rich 2, interacting protein", "serine/arginine-rich splicing factor 2, interacting protein"	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.569delT	chr12.hg19:g.46328022delA	ENSP00000358374:p.Phe190fs	118.0	0.0		171.0	11.0	NM_004719	A6NEU9|A6NLW5|Q8IW59	Frame_Shift_Del	DEL	ENST00000369367.3	hg19	CCDS8748.2																																																																																			.	.		0.303	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		-	46328022	A	-	46328022	7	5	114	1	0	1	0	1	0	0	0	0	14192	246	9	0	3854	0	SFRS2IP	12	46328022	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	84529	46328022	87523873	790	19062										
AMIGO2	91523	hgsc.bcm.edu	37	chr12	47471280	47471280	+	5'Flank	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actgaatctgagtcagatttCcccctcgtggactttaggat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:47471280delC	ENST00000546455.1	+	0	0				AMIGO2_ENST00000550413.1_Frame_Shift_Del_p.G502fs|AMIGO2_ENST00000429635.1_Frame_Shift_Del_p.G502fs|AMIGO2_ENST00000266581.4_Frame_Shift_Del_p.G502fs|AMIGO2_ENST00000321382.3_Frame_Shift_Del_p.G502fs			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)										AGTCAGATTTCCCCCTCGTGG	0.463																																					p.K503fs		Atlas-INDEL	.											.	AMIGO2	50	.	0			c.1507delA						.						70	67	68					12																	47471280		2203	4300	6503	SO:0001631	upstream_gene_variant	347902	exon2			.	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617		chr12.hg19:g.47471280delC	Exception_encountered	133.0	0.0		173.0	11.0	NM_181847	Q96B20	Frame_Shift_Del	DEL	ENST00000546455.1	hg19	CCDS8752.1																																																																																			.	.		0.463	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		-	47471280	C	-	47471280	6	5	114	0	1	1	0	1	0	0	0	0	576	842	30	0		0	AMIGO2	12	47471280	5'Flank	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1143258	47471280	86380615	791	19063										
FAM113B	91523	hgsc.bcm.edu	37	chr12	47630043	47630043	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccccagtggtacataggggTtttggcaggtatcgtccccg					rs202147059		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:47630043delT	ENST00000546455.1	+	4	1928	c.1197delT	c.(1195-1197)ggtfs	p.G399fs	PCED1B_ENST00000432328.1_Frame_Shift_Del_p.G399fs|RP11-493L12.3_ENST00000547748.1_RNA			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	399	Pro-rich.						hydrolase activity (GO:0016787)										TACATAGGGGTTTTGGCAGGT	0.582																																					p.G399fs		Atlas-INDEL	.											.	.	.	.	0			c.1196delG						.																																			SO:0001589	frameshift_variant	91523	exon2			.	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.1197delT	chr12.hg19:g.47630043delT	ENSP00000446688:p.Gly399fs	127.0	0.0		186.0	12.0	NM_138371	Q96B20	Frame_Shift_Del	DEL	ENST00000546455.1	hg19	CCDS8752.1																																																																																			.	.		0.582	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		-	47630043	T	-	47630043	7	5	114	1	0	1	0	1	0	0	0	0	5407	1712	60	0	1199	0	FAM113B	12	47630043	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	158763	47630043	86221852	792	19064										
RAPGEF3	10411	hgsc.bcm.edu	37	chr12	48134787	48134787	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggtccagcccctcagcagAgcccacagtgggccccagct	11	18	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:48134787A>G	ENST00000449771.2	-	20	2048	c.1960T>C	c.(1960-1962)Tct>Cct	p.S654P	RAPGEF3_ENST00000548919.1_Missense_Mutation_p.S563P|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.S654P|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.S612P|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.S612P|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.S612P			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	654					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		CCCTCAGCAGAGCCCACAGTG	0.652																																					p.S654P		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.T1960C						.						22	21	21					12																	48134787		2203	4300	6503	SO:0001583	missense	10411	exon20			CAGCAGAGCCCAC	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"exchange protein directly activated by cAMP 1"	606057	"RAP guanine-nucleotide-exchange factor (GEF) 3"			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1960T>C	chr12.hg19:g.48134787A>G	ENSP00000395708:p.Ser654Pro	192.0	0.0		198.0	9.0	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	hg19	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.730539	0.48939	.	.	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919	T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58	3.87	3.87	0.44632	Ras guanine nucleotide exchange factor, domain (1);	0.165039	0.39544	N	0.001338	T	0.34542	0.0901	N	0.24115	0.695	0.41254	D	0.986732	D	0.76494	0.999	D	0.66351	0.943	T	0.13926	-1.0491	10	0.54805	T	0.06	.	7.6408	0.28292	0.8108:0.0:0.0:0.1892	.	654	O95398	RPGF3_HUMAN	P	612;654;301;612;612;612;654;617;563	ENSP00000384521:S612P;ENSP00000395708:S654P;ENSP00000448619:S612P;ENSP00000171000:S612P;ENSP00000373864:S654P;ENSP00000448480:S563P	ENSP00000171000:S612P	S	-	1	0	RAPGEF3	46421054	0.127000	0.22367	0.999000	0.59377	0.991000	0.79684	0.373000	0.20484	1.552000	0.49463	0.379000	0.24179	TCT	.	.		0.652	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		G	48134787	A	G	48134787	3	3	114	1	0	0	0	0	1	0	0	0	13060	304	11	2	847	2	RAPGEF3	12	48134787	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	504744	48134787	85717108	793	19065										
SPATS2	65244	hgsc.bcm.edu	37	chr12	49878388	49878388	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcagattcatcaggattcaTttttgatttgcagtccaata					rs141171093	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:49878388delT	ENST00000553127.1	+	5	554	c.41delT	c.(40-42)attfs	p.I14fs	SPATS2_ENST00000552918.1_Frame_Shift_Del_p.I14fs|SPATS2_ENST00000321898.6_Frame_Shift_Del_p.I14fs			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	14						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						TCAGGATTCATTTTTGATTTG	0.388																																					p.I14fs		Atlas-INDEL	.											.	SPATS2	43	.	0			c.40delA						.						109	98	102					12																	49878388		2203	4300	6503	SO:0001589	frameshift_variant	65244	exon4			.	AK023179	CCDS31794.1	12q13.12	2009-06-12							18650	protein-coding gene	gene with protein product		611667				11944913, 17989879	Standard	NM_023071		Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000553127.1:c.41delT	chr12.hg19:g.49878388delT	ENSP00000448228:p.Ile14fs	151.0	0.0		165.0	14.0	NM_023071	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	Frame_Shift_Del	DEL	ENST00000553127.1	hg19	CCDS31794.1																																																																																			.	.		0.388	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404023.1	NM_023071		-	49878388	T	-	49878388	7	5	114	1	0	1	0	1	0	0	0	0	15034	1493	52	0	47	0	SPATS2	12	49878388	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1743601	49878388	83973507	794	19066										
RACGAP1	29127	hgsc.bcm.edu	37	chr12	50399098	50399098	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgagaaaagccagagctgaTttttgctcctcgcttagttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:50399098delT	ENST00000427314.2	-	6	589	c.366delA	c.(364-366)aaafs	p.K122fs	RACGAP1_ENST00000454520.2_Frame_Shift_Del_p.K122fs|RACGAP1_ENST00000434422.1_Frame_Shift_Del_p.K122fs|RACGAP1_ENST00000551016.1_Frame_Shift_Del_p.K122fs|RACGAP1_ENST00000312377.5_Frame_Shift_Del_p.K122fs|RACGAP1_ENST00000547061.1_5'Flank|RACGAP1_ENST00000547905.1_Frame_Shift_Del_p.K122fs	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						CCAGAGCTGATTTTTGCTCCT	0.458																																					p.S123fs		Atlas-INDEL	.											.	RACGAP1	36	.	0			c.367delT						.						136	118	124					12																	50399098		2203	4300	6503	SO:0001589	frameshift_variant	29127	exon6			.		CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000427314.2:c.366delA	chr12.hg19:g.50399098delT	ENSP00000404190:p.Lys122fs	143.0	0.0		144.0	10.0	NM_013277		Frame_Shift_Del	DEL	ENST00000427314.2	hg19	CCDS8795.1																																																																																			.	.		0.458	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277		-	50399098	T	-	50399098	7	5	114	1	0	1	0	1	0	0	0	0	12992	1490	52	0	1588	0	RACGAP1	12	50399098	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	520710	50399098	83452797	795	19067										
DIP2B	57609	hgsc.bcm.edu	37	chr12	51077012	51077012	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtgattccagtgcctatagAggtacctcttaccagaaagg	10	9	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:51077012A>G	ENST00000301180.5	+	10	1332	c.1298A>G	c.(1297-1299)gAg>gGg	p.E433G		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	433						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						GTGCCTATAGAGGTACCTCTT	0.438																																					p.E433G		Atlas-SNP	.											.	DIP2B	167	.	0			c.A1298G						.						150	140	144					12																	51077012		2203	4300	6503	SO:0001583	missense	57609	exon10			CTATAGAGGTACC	AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.1298A>G	chr12.hg19:g.51077012A>G	ENSP00000301180:p.Glu433Gly	53.0	0.0		82.0	4.0	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.559283	0.86335	.	.	ENSG00000066084	ENST00000301180	T	0.10477	2.87	4.98	4.98	0.66077	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.34048	0.0884	M	0.83953	2.67	0.80722	D	1	D	0.63046	0.992	D	0.66979	0.948	T	0.10382	-1.0632	10	0.38643	T	0.18	-20.033	14.8272	0.70122	1.0:0.0:0.0:0.0	.	433	Q9P265	DIP2B_HUMAN	G	433	ENSP00000301180:E433G	ENSP00000301180:E433G	E	+	2	0	DIP2B	49363279	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.107000	0.94261	2.091000	0.63221	0.533000	0.62120	GAG	.	.		0.438	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		G	51077012	A	G	51077012	3	3	114	1	0	0	0	0	1	0	0	0	4530	304	11	2	1336	2	DIP2B	12	51077012	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	677914	51077012	82774883	796	19068										
SLC11A2	4891	hgsc.bcm.edu	37	chr12	51386667	51386667	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agccaggatccccactgcccAaatgtagagtgcagcaggcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:51386667delA	ENST00000262051.7	-	12	1210	c.1123delT	c.(1123-1125)tggfs	p.W375fs	SLC11A2_ENST00000546743.1_Frame_Shift_Del_p.W296fs|SLC11A2_ENST00000545993.2_Frame_Shift_Del_p.W371fs|SLC11A2_ENST00000394904.3_Frame_Shift_Del_p.W404fs|SLC11A2_ENST00000541174.2_Frame_Shift_Del_p.W375fs|SLC11A2_ENST00000547688.1_Frame_Shift_Del_p.W404fs|SLC11A2_ENST00000547198.1_Frame_Shift_Del_p.W375fs|SLC11A2_ENST00000262052.5_Frame_Shift_Del_p.W375fs	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	375					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						CCCACTGCCCAAATGTAGAGT	0.512																																					p.W404fs		Atlas-INDEL	.											.	SLC11A2	51	.	0			c.1211delG						.						130	111	117					12																	51386667		2203	4300	6503	SO:0001589	frameshift_variant	4891	exon12			.	AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"Solute carriers"	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.1123delT	chr12.hg19:g.51386667delA	ENSP00000262051:p.Trp375fs	110.0	0.0		152.0	10.0	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Frame_Shift_Del	DEL	ENST00000262051.7	hg19	CCDS53792.1																																																																																			.	.		0.512	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1			-	51386667	A	-	51386667	7	5	114	1	0	1	0	1	0	0	0	0	14396	130	5	0	664	0	SLC11A2	12	51386667	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	309655	51386667	82465228	797	19069										
TFCP2	7024	hgsc.bcm.edu	37	chr12	51510142	51510142	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcggttccacctccagcccTctagctgctgatgctcagtg	10	15	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:51510142T>C	ENST00000257915.5	-	4	871	c.413A>G	c.(412-414)gAg>gGg	p.E138G	TFCP2_ENST00000307660.4_Missense_Mutation_p.E138G|TFCP2_ENST00000549867.1_Missense_Mutation_p.E138G|TFCP2_ENST00000548115.1_Missense_Mutation_p.E138G	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	138	DNA-binding.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						CCTCCAGCCCTCTAGCTGCTG	0.448																																					p.E138G		Atlas-SNP	.											.	TFCP2	49	.	0			c.A413G						.						116	103	108					12																	51510142		2203	4300	6503	SO:0001583	missense	7024	exon4			CAGCCCTCTAGCT	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.413A>G	chr12.hg19:g.51510142T>C	ENSP00000257915:p.Glu138Gly	166.0	0.0		200.0	10.0	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	hg19	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.557249	0.45590	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000549867;ENST00000548115;ENST00000548108	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	4.86	3.69	0.42338	CP2 transcription factor (1);	0.108853	0.64402	D	0.000010	T	0.33702	0.0872	M	0.75264	2.295	0.58432	D	0.99999	P;B;P;B	0.45768	0.557;0.094;0.866;0.039	B;B;P;B	0.49421	0.234;0.126;0.61;0.067	T	0.15263	-1.0443	10	0.72032	D	0.01	-19.9447	11.1675	0.48552	0.0:0.0:0.1546:0.8454	.	138;138;138;138	Q12800-2;F8VX55;Q12800;Q12800-4	.;.;TFCP2_HUMAN;.	G	138;138;138;138;40	ENSP00000257915:E138G;ENSP00000304411:E138G;ENSP00000449742:E138G;ENSP00000447991:E138G;ENSP00000449280:E40G	ENSP00000257915:E138G	E	-	2	0	TFCP2	49796409	1.000000	0.71417	1.000000	0.80357	0.061000	0.15899	7.772000	0.85439	0.982000	0.38575	-0.316000	0.08728	GAG	.	.		0.448	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653		C	51510142	T	C	51510142	3	2	114	1	0	0	0	0	1	0	0	0	15810	1551	54	2	1143	2	TFCP2	12	51510142	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	123475	51510142	82341753	798	19070										
ACVR1B	91	hgsc.bcm.edu	37	chr12	52385707	52385707	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccctctgacccttccattgAggaaatgcgaaaggttgtat	10	10	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:52385707A>G	ENST00000257963.4	+	8	1399	c.1322A>G	c.(1321-1323)gAg>gGg	p.E441G	ACVR1B_ENST00000426655.2_Missense_Mutation_p.E441G|ACVR1B_ENST00000541224.1_Missense_Mutation_p.E482G|ACVR1B_ENST00000542485.1_Missense_Mutation_p.E389G|ACVR1B_ENST00000563121.1_3'UTR	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	441	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	CCTTCCATTGAGGAAATGCGA	0.483																																					p.E482G		Atlas-SNP	.											.	ACVR1B	167	.	0			c.A1445G						.						181	161	168					12																	52385707		2203	4300	6503	SO:0001583	missense	91	exon9			CCATTGAGGAAAT		CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.1322A>G	chr12.hg19:g.52385707A>G	ENSP00000257963:p.Glu441Gly	140.0	0.0		150.0	6.0	NM_020328	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Missense_Mutation	SNP	ENST00000257963.4	hg19	CCDS8816.1	.	.	.	.	.	.	.	.	.	.	A	19.27	3.794416	0.70452	.	.	ENSG00000135503	ENST00000257963;ENST00000541224;ENST00000426655;ENST00000542485	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	4.05	4.05	0.47172	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.051797	0.85682	D	0.000000	T	0.66117	0.2757	L	0.52126	1.63	0.80722	D	1	B;B;B	0.32071	0.242;0.215;0.355	B;B;B	0.39904	0.222;0.313;0.218	T	0.71374	-0.4612	10	0.87932	D	0	.	14.0635	0.64815	1.0:0.0:0.0:0.0	.	482;441;441	P36896-4;P36896;P36896-2	.;ACV1B_HUMAN;.	G	441;482;441;389	ENSP00000257963:E441G;ENSP00000442656:E482G;ENSP00000390477:E441G;ENSP00000442885:E389G	ENSP00000257963:E441G	E	+	2	0	ACVR1B	50671974	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.044000	0.93805	2.059000	0.61396	0.379000	0.24179	GAG	.	.		0.483	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328		G	52385707	A	G	52385707	3	3	114	1	0	0	0	0	1	0	0	0	221	304	11	2	1479	2	ACVR1B	12	52385707	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	875565	52385707	81466188	799	19071										
KRT1	3848	hgsc.bcm.edu	37	chr12	53069297	53069297	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccgccacctccagaaccatAgctaccacctccggagccat	7	19	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:53069297A>G	ENST00000252244.3	-	9	1673	c.1615T>C	c.(1615-1617)Tat>Cat	p.Y539H		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	539	Gly/Ser-rich.|Tail.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)	p.Y539N(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						ccagaaccatagctaccacct	0.677																																					p.Y539H		Atlas-SNP	.											KRT1,NS,carcinoma,0,1	KRT1	110	.	1	Substitution - Missense(1)	lung(1)	c.T1615C						.						16	17	17					12																	53069297		2201	4299	6500	SO:0001583	missense	3848	exon9			AACCATAGCTACC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1615T>C	chr12.hg19:g.53069297A>G	ENSP00000252244:p.Tyr539His	43.0	0.0		56.0	3.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	hg19	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	A	9.015	0.983400	0.18889	.	.	ENSG00000167768	ENST00000252244	T	0.77877	-1.13	3.52	0.923	0.19413	.	.	.	.	.	T	0.51958	0.1705	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.33394	-0.9870	9	0.15952	T	0.53	.	4.9696	0.14108	0.5319:0.359:0.1091:0.0	.	539	P04264	K2C1_HUMAN	H	539	ENSP00000252244:Y539H	ENSP00000252244:Y539H	Y	-	1	0	KRT1	51355564	0.013000	0.17824	0.007000	0.13788	0.191000	0.23601	0.921000	0.28718	0.316000	0.23135	0.374000	0.22700	TAT	.	.		0.677	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		G	53069297	A	G	53069297	3	3	114	1	0	0	0	0	1	0	0	0	8456	420	15	2	323	2	KRT1	12	53069297	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	683590	53069297	80782598	800	19072										
ITGA5	3678	hgsc.bcm.edu	37	chr12	54797420	54797420	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggccataccctgaggtagaTcttcatctctctgcaatcct	8	13	4	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:54797420T>C	ENST00000293379.4	-	17	2026	c.1765A>G	c.(1765-1767)Atc>Gtc	p.I589V	RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	589					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						CTGAGGTAGATCTTCATCTCT	0.622																																					p.I589V		Atlas-SNP	.											.	ITGA5	99	.	0			c.A1765G						.						71	71	71					12																	54797420		2203	4300	6503	SO:0001583	missense	3678	exon17			GGTAGATCTTCAT		CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"CD molecules", "Integrins"	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.1765A>G	chr12.hg19:g.54797420T>C	ENSP00000293379:p.Ile589Val	71.0	0.0		111.0	5.0	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	hg19	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	T	2.663	-0.279223	0.05642	.	.	ENSG00000161638	ENST00000293379	T	0.39592	1.07	5.05	0.0378	0.14198	Integrin alpha-2 (1);	0.149585	0.64402	N	0.000017	T	0.16642	0.0400	N	0.05414	-0.055	0.44030	D	0.996753	B	0.16166	0.016	B	0.21708	0.036	T	0.27088	-1.0084	10	0.05525	T	0.97	.	8.28	0.31896	0.0:0.3406:0.0:0.6594	.	589	P08648	ITA5_HUMAN	V	589	ENSP00000293379:I589V	ENSP00000293379:I589V	I	-	1	0	ITGA5	53083687	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	1.424000	0.34848	0.053000	0.16036	-0.379000	0.06801	ATC	.	.		0.622	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			C	54797420	T	C	54797420	3	2	114	1	0	0	0	0	1	0	0	0	7888	1435	50	2	1440	2	ITGA5	12	54797420	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1728123	54797420	79054475	801	19073										
PDE1B	5153	hgsc.bcm.edu	37	chr12	54968906	54968906	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacaagcccaaggccctgtcTctactgctccatgctgctga	9	15	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:54968906T>C	ENST00000243052.3	+	11	1525	c.1089T>C	c.(1087-1089)tcT>tcC	p.S363S	PDE1B_ENST00000538346.1_Silent_p.S322S|PDE1B_ENST00000550620.1_Silent_p.S343S|PDE1B_ENST00000394277.3_3'UTR	NM_000924.3	NP_000915.1	Q01064	PDE1B_HUMAN	phosphodiesterase 1B, calmodulin-dependent	363	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|monocyte differentiation (GO:0030224)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of dopamine metabolic process (GO:0042053)|regulation of neurotransmitter levels (GO:0001505)|response to amphetamine (GO:0001975)|serotonin metabolic process (GO:0042428)|signal transduction (GO:0007165)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(4)	31					Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	AGGCCCTGTCTCTACTGCTCC	0.542																																					p.S363S		Atlas-SNP	.											.	PDE1B	76	.	0			c.T1089C						.						130	117	121					12																	54968906		2203	4300	6503	SO:0001819	synonymous_variant	5153	exon11			CCTGTCTCTACTG	U56976	CCDS8882.1, CCDS53800.1, CCDS73477.1	12q13	2008-03-18				ENSG00000123360	3.1.4.17	"Phosphodiesterases"	8775	protein-coding gene	gene with protein product		171891		PDES1B		8855339, 9419816	Standard	NM_000924		Approved		uc001sgd.2	Q01064	OTTHUMG00000169844	ENST00000243052.3:c.1089T>C	chr12.hg19:g.54968906T>C		89.0	0.0		95.0	4.0	NM_000924	Q92825|Q96KP3	Silent	SNP	ENST00000243052.3	hg19	CCDS8882.1																																																																																			.	.		0.542	PDE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406203.1			C	54968906	T	C	54968906	2	2	114	1	0	0	0	0	0	0	0	1	11643	1538	54	2		2	PDE1B	12	54968906	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	171486	54968906	78882989	802	19074										
OR6C70	390327	hgsc.bcm.edu	37	chr12	55863303	55863303	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggattactaaaaacaatgtgAcaataagtgtcatcacagct	7	7	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:55863303A>G	ENST00000327335.4	-	1	619	c.620T>C	c.(619-621)gTc>gCc	p.V207A	RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_001005499.1	NP_001005499.1	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C, member 70	207						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	18						AAACAATGTGACAATAAGTGT	0.358																																					p.V207A		Atlas-SNP	.											.	OR6C70	35	.	0			c.T620C						.						118	123	121					12																	55863303		2203	4300	6503	SO:0001583	missense	390327	exon1			AATGTGACAATAA		CCDS31825.1	12q13.2	2013-09-23			ENSG00000184954	ENSG00000184954		"GPCR / Class A : Olfactory receptors"	31299	protein-coding gene	gene with protein product							Standard	NM_001005499		Approved		uc010spn.2	A6NIJ9	OTTHUMG00000171127	ENST00000327335.4:c.620T>C	chr12.hg19:g.55863303A>G	ENSP00000329153:p.Val207Ala	66.0	0.0		100.0	6.0	NM_001005499		Missense_Mutation	SNP	ENST00000327335.4	hg19	CCDS31825.1	.	.	.	.	.	.	.	.	.	.	A	8.759	0.923233	0.18056	.	.	ENSG00000184954	ENST00000327335	T	0.39229	1.09	4.13	1.73	0.24493	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	D	0.000303	T	0.44307	0.1287	L	0.45581	1.43	0.09310	N	1	D	0.55385	0.971	P	0.60068	0.868	T	0.32161	-0.9917	10	0.72032	D	0.01	.	1.6624	0.02795	0.5567:0.1394:0.1685:0.1354	.	207	A6NIJ9	O6C70_HUMAN	A	207	ENSP00000329153:V207A	ENSP00000329153:V207A	V	-	2	0	OR6C70	54149570	0.000000	0.05858	0.026000	0.17262	0.003000	0.03518	0.258000	0.18387	0.255000	0.21593	-0.253000	0.11424	GTC	.	.		0.358	OR6C70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411820.1			G	55863303	A	G	55863303	3	3	114	1	0	0	0	0	1	0	0	0	11206	275	10	2	320	2	OR6C70	12	55863303	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	894397	55863303	77988592	803	19075										
PA2G4	5036	hgsc.bcm.edu	37	chr12	56498590	56498590	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcgtgaccaagtataagatGgggggcgacatcgccaacag					rs144476801		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:56498590delG	ENST00000303305.6	+	1	488	c.69delG	c.(67-69)atgfs	p.M23fs	PA2G4_ENST00000552766.1_Frame_Shift_Del_p.M23fs|RP11-603J24.9_ENST00000548861.1_Intron|RP11-603J24.17_ENST00000548595.1_RNA	NM_006191.2	NP_006182.2	Q9UQ80	PA2G4_HUMAN	proliferation-associated 2G4, 38kDa	23	Necessary for nucleolar localization.				cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of translation (GO:0006417)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(18;0.0739)			AGTATAAGATGGGGGGCGACA	0.607																																					p.M23fs		Atlas-INDEL	.											.	PA2G4	24	.	0			c.68delT						.						108	99	102					12																	56498590		2203	4300	6503	SO:0001589	frameshift_variant	5036	exon1			.	U59435, BC007561	CCDS8902.1	12q13.2	2008-09-05	2002-08-29		ENSG00000170515	ENSG00000170515			8550	protein-coding gene	gene with protein product		602145	"proliferation-associated 2G4, 38kD"			9345902	Standard	NM_006191		Approved		uc001sjm.3	Q9UQ80	OTTHUMG00000170173	ENST00000303305.6:c.69delG	chr12.hg19:g.56498590delG	ENSP00000302886:p.Met23fs	166.0	0.0		164.0	11.0	NM_006191	O43846|Q9UM59	Frame_Shift_Del	DEL	ENST00000303305.6	hg19	CCDS8902.1																																																																																			.	.		0.607	PA2G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407767.1	NM_006191		-	56498590	G	-	56498590	7	5	114	1	0	1	0	1	0	0	0	0	11370	1348	47	0	71	0	PA2G4	12	56498590	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	635287	56498590	77353305	804	19076										
ESYT1	23344	hgsc.bcm.edu	37	chr12	56525317	56525317	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attggggaccttcccttcgtGggggctgtgtcaatgttctt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:56525317delG	ENST00000394048.5	+	6	1035	c.771delG	c.(769-771)gtgfs	p.V257fs	ESYT1_ENST00000267113.4_Frame_Shift_Del_p.V257fs|RP11-603J24.5_ENST00000550947.1_RNA|ESYT1_ENST00000541590.1_Frame_Shift_Del_p.V257fs|RP11-603J24.5_ENST00000549438.1_RNA	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	257	Glycerophospholipid-binding barrel-like domain. {ECO:0000250}.				lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						TTCCCTTCGTGGGGGCTGTGT	0.537																																					p.V257fs		Atlas-INDEL	.											.	ESYT1	84	.	0			c.770delT						.						160	164	162					12																	56525317		2203	4300	6503	SO:0001589	frameshift_variant	23344	exon6			.	AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"Synaptotagmins"	29534	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member A"	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.771delG	chr12.hg19:g.56525317delG	ENSP00000377612:p.Val257fs	168.0	0.0		193.0	12.0	NM_015292	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Frame_Shift_Del	DEL	ENST00000394048.5	hg19	CCDS8904.1																																																																																			.	.		0.537	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292		-	56525317	G	-	56525317	7	5	114	1	0	1	0	1	0	0	0	0	5266	1335	47	0	793	0	ESYT1	12	56525317	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	26727	56525317	77326578	805	19077										
GLS2	27165	hgsc.bcm.edu	37	chr12	56867277	56867277	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctggtccccctatggctgttCcccagcttgtccaatggggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:56867277delC	ENST00000311966.4	-	13	1604	c.1326delG	c.(1324-1326)gggfs	p.G442fs	GLS2_ENST00000476991.1_5'Flank	NM_013267.2	NP_037399.2	Q9UI32	GLSL_HUMAN	glutaminase 2 (liver, mitochondrial)	442					cellular amino acid biosynthetic process (GO:0008652)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate secretion (GO:0014047)|glutamine metabolic process (GO:0006541)|neurotransmitter secretion (GO:0007269)|reactive oxygen species metabolic process (GO:0072593)|regulation of apoptotic process (GO:0042981)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13					L-Glutamine(DB00130)	TATGGCTGTTCCCCAGCTTGT	0.483																																					p.N443fs		Atlas-INDEL	.											.	GLS2	42	.	0			c.1327delA						.						81	77	78					12																	56867277		2203	4300	6503	SO:0001589	frameshift_variant	27165	exon13			.		CCDS8921.1, CCDS73482.1	12q13	2013-01-10			ENSG00000135423	ENSG00000135423		"Ankyrin repeat domain containing"	29570	protein-coding gene	gene with protein product		606365				11130979, 10620514	Standard	NM_013267		Approved	GA, GLS, LGA, hLGA	uc001slj.3	Q9UI32	OTTHUMG00000140379	ENST00000311966.4:c.1326delG	chr12.hg19:g.56867277delC	ENSP00000310447:p.Gly442fs	70.0	0.0		115.0	10.0	NM_013267	B7Z8Q9|Q8IX91|Q9NYY2|Q9UI31	Frame_Shift_Del	DEL	ENST00000311966.4	hg19	CCDS8921.1																																																																																			.	.		0.483	GLS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277113.1	NM_013267		-	56867277	C	-	56867277	7	5	114	1	0	1	0	1	0	0	0	0	6472	842	30	0	506	0	GLS2	12	56867277	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	341960	56867277	76984618	806	19078										
TAC3	6866	hgsc.bcm.edu	37	chr12	57406176	57406176	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccttaccctattctgctctcGggggatacttgaggatgcca					rs368243990		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:57406176delG	ENST00000458521.2	-	6	512	c.353delC	c.(352-354)ccgfs	p.P118fs	TAC3_ENST00000441881.1_Frame_Shift_Del_p.P100fs|TAC3_ENST00000415231.1_Frame_Shift_Del_p.P118fs	NM_013251.3	NP_037383.1	Q9UHF0	TKNK_HUMAN	tachykinin 3	118					female pregnancy (GO:0007565)|neuropeptide signaling pathway (GO:0007218)|tachykinin receptor signaling pathway (GO:0007217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						TTCTGCTCTCGGGGGATACTT	0.527																																					p.P118fs		Atlas-INDEL	.											.	TAC3	11	.	0			c.354delG						.						73	66	68					12																	57406176		2203	4300	6503	SO:0001589	frameshift_variant	6866	exon6			.	AF186112	CCDS8928.1, CCDS53803.1	12q13-q21	2013-02-26	2008-07-31		ENSG00000166863	ENSG00000166863		"Endogenous ligands"	11521	protein-coding gene	gene with protein product	"preprotachykinin-B"	162330	"neuromedin K", "neurokinin beta"	NKNB		3479225, 10866201	Standard	NM_013251		Approved	ZNEUROK1, NKB	uc001smp.3	Q9UHF0	OTTHUMG00000156958	ENST00000458521.2:c.353delC	chr12.hg19:g.57406176delG	ENSP00000404056:p.Pro118fs	104.0	0.0		146.0	10.0	NM_013251	Q6IAG2|Q71BC6|Q71BC9	Frame_Shift_Del	DEL	ENST00000458521.2	hg19	CCDS8928.1																																																																																			.	.		0.527	TAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346793.1	NM_001006667		-	57406176	G	-	57406176	7	5	114	1	0	1	0	1	0	0	0	0	15514	1116	39	0	16	0	TAC3	12	57406176	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	538899	57406176	76445719	807	19079										
STAT6	6778	hgsc.bcm.edu	37	chr12	57499025	57499025	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagcggaggcttggctggggCccccaggaacctcaagccca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:57499025delC	ENST00000300134.3	-	9	1235	c.910delG	c.(910-912)gccfs	p.A304fs	STAT6_ENST00000538913.2_Frame_Shift_Del_p.A194fs|STAT6_ENST00000537215.2_Frame_Shift_Del_p.A194fs|STAT6_ENST00000454075.3_Frame_Shift_Del_p.A304fs|STAT6_ENST00000543873.2_Frame_Shift_Del_p.A304fs|STAT6_ENST00000556155.1_Frame_Shift_Del_p.A304fs	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	304					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.A304T(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						TTGGCTGGGGCCCCCAGGAAC	0.632																																					p.A304fs		Atlas-INDEL	.											.	STAT6	69	.	1	Substitution - Missense(1)	large_intestine(1)	c.911delC						.						39	43	42					12																	57499025		2203	4300	6503	SO:0001589	frameshift_variant	6778	exon9			.	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"SH2 domain containing"	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.910delG	chr12.hg19:g.57499025delC	ENSP00000300134:p.Ala304fs	98.0	0.0		133.0	10.0	NM_003153	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Frame_Shift_Del	DEL	ENST00000300134.3	hg19	CCDS8931.1																																																																																			.	.		0.632	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		-	57499025	C	-	57499025	7	5	114	1	0	1	0	1	0	0	0	0	15285	739	26	0	1689	0	STAT6	12	57499025	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	92849	57499025	76352870	808	19080										
GLI1	2735	hgsc.bcm.edu	37	chr12	57857530	57857530	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctatggcgagccctgctgtcTccggcccctccccagtcagg	11	18	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:57857530T>C	ENST00000228682.2	+	2	147	c.56T>C	c.(55-57)cTc>cCc	p.L19P	GLI1_ENST00000543426.1_Intron|GLI1_ENST00000546141.1_Missense_Mutation_p.L19P	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	19	SNAG domain. {ECO:0000250}.				cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			CCCTGCTGTCTCCGGCCCCTC	0.592																																					p.L19P	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.T56C						.						78	70	73					12																	57857530		2203	4300	6503	SO:0001583	missense	2735	exon2			GCTGTCTCCGGCC		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.56T>C	chr12.hg19:g.57857530T>C	ENSP00000228682:p.Leu19Pro	48.0	0.0		53.0	4.0	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	hg19	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	T	18.76	3.693279	0.68386	.	.	ENSG00000111087	ENST00000228682;ENST00000546141;ENST00000528432;ENST00000528467	T;T;T	0.18016	2.24;2.33;2.33	4.42	4.42	0.53409	.	0.470469	0.17701	N	0.164920	T	0.21347	0.0514	N	0.17082	0.46	0.80722	D	1	D	0.63880	0.993	P	0.59595	0.86	T	0.02844	-1.1103	10	0.56958	D	0.05	.	11.572	0.50839	0.0:0.0:0.0:1.0	.	19	P08151	GLI1_HUMAN	P	19	ENSP00000228682:L19P;ENSP00000441006:L19P;ENSP00000434408:L19P	ENSP00000228682:L19P	L	+	2	0	GLI1	56143797	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.974000	0.56852	1.983000	0.57843	0.528000	0.53228	CTC	.	.		0.592	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		C	57857530	T	C	57857530	3	2	114	1	0	0	0	0	1	0	0	0	6445	1551	54	2	58	2	GLI1	12	57857530	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	358505	57857530	75994365	809	19081										
OSBPL8	114882	hgsc.bcm.edu	37	chr12	76749732	76749732	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggaaaatgatgaagtagtcTttttgttgcagaaaataatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:76749732delT	ENST00000261183.3	-	24	3086	c.2607delA	c.(2605-2607)aaafs	p.K869fs	OSBPL8_ENST00000393250.4_Frame_Shift_Del_p.K827fs|OSBPL8_ENST00000393249.2_Frame_Shift_Del_p.K827fs	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	869					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						TGAAGTAGTCTTTTTGTTGCA	0.323																																					p.D870fs		Atlas-INDEL	.											.	OSBPL8	86	.	0			c.2608delG						.						89	91	90					12																	76749732		2203	4300	6503	SO:0001589	frameshift_variant	114882	exon24			.	AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.2607delA	chr12.hg19:g.76749732delT	ENSP00000261183:p.Lys869fs	119.0	0.0		147.0	12.0	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Frame_Shift_Del	DEL	ENST00000261183.3	hg19	CCDS31862.1																																																																																			.	.		0.323	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841		-	76749732	T	-	76749732	7	5	114	1	0	1	0	1	0	0	0	0	11292	1606	56	0	66	0	OSBPL8	12	76749732	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	18892202	76749732	57102163	810	19082										
OSBPL8	114882	hgsc.bcm.edu	37	chr12	76780366	76780366	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caaacattattacctttggcTttttatagaatcctgacaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:76780366delT	ENST00000261183.3	-	13	1906	c.1427delA	c.(1426-1428)aagfs	p.K476fs	OSBPL8_ENST00000393250.4_Frame_Shift_Del_p.K434fs|OSBPL8_ENST00000393249.2_Frame_Shift_Del_p.K434fs	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	476					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						TACCTTTGGCTTTTTATAGAA	0.279																																					p.K476fs		Atlas-INDEL	.											.	OSBPL8	86	.	0			c.1428delG						.						55	62	59					12																	76780366		2200	4278	6478	SO:0001589	frameshift_variant	114882	exon13			.	AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.1427delA	chr12.hg19:g.76780366delT	ENSP00000261183:p.Lys476fs	143.0	0.0		229.0	16.0	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Frame_Shift_Del	DEL	ENST00000261183.3	hg19	CCDS31862.1																																																																																			.	.		0.279	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841		-	76780366	T	-	76780366	7	5	114	1	0	1	0	1	0	0	0	0	11292	1609	56	0	1290	0	OSBPL8	12	76780366	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	30634	76780366	57071529	811	19083										
CCDC59	29080	hgsc.bcm.edu	37	chr12	82746994	82746994	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cattcaagtttggttggcccTttttagtctttttgttcagt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:82746994delT	ENST00000256151.7	-	4	1073	c.662delA	c.(661-663)aagfs	p.K221fs	CCDC59_ENST00000548126.1_5'UTR	NM_014167.4	NP_054886.2	Q9P031	TAP26_HUMAN	coiled-coil domain containing 59	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)	5						TGGTTGGCCCTTTTTAGTCTT	0.343																																					p.K221fs		Atlas-INDEL	.											.	CCDC59	17	.	0			c.663delG						.						162	150	154					12																	82746994		2203	4298	6501	SO:0001589	frameshift_variant	29080	exon4			.	AF213377	CCDS9023.1	12q21.31	2007-10-17				ENSG00000133773			25005	protein-coding gene	gene with protein product						16630564, 12882447	Standard	NM_014167		Approved	HSPC128, TAP26, BR22	uc001szp.4	Q9P031		ENST00000256151.7:c.662delA	chr12.hg19:g.82746994delT	ENSP00000256151:p.Lys221fs	163.0	0.0		190.0	12.0	NM_014167	Q9H2V5|Q9NW62	Frame_Shift_Del	DEL	ENST00000256151.7	hg19	CCDS9023.1																																																																																			.	.		0.343	CCDC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408186.1	NM_014167		-	82746994	T	-	82746994	7	5	114	1	0	1	0	1	0	0	0	0	2831	1609	56	0	67	0	CCDC59	12	82746994	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	5966628	82746994	51104901	812	19084										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85279291	85279291	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagactgagaaaaataaaacAaactccagccaatgatgacg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:85279291delA	ENST00000266682.5	-	4	1038	c.497delT	c.(496-498)ttgfs	p.L166fs	SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000552192.1_Frame_Shift_Del_p.L59fs|SLC6A15_ENST00000450363.3_Frame_Shift_Del_p.L166fs	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	166					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						AAAATAAAACAAACTCCAGCC	0.373																																					p.L166fs		Atlas-INDEL	.											.	SLC6A15	159	.	0			c.498delG						.						97	95	96					12																	85279291		2203	4300	6503	SO:0001589	frameshift_variant	55117	exon4			.	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.497delT	chr12.hg19:g.85279291delA	ENSP00000266682:p.Leu166fs	145.0	0.0		155.0	10.0	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Frame_Shift_Del	DEL	ENST00000266682.5	hg19	CCDS9026.1																																																																																			.	.		0.373	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		-	85279291	A	-	85279291	7	5	114	1	0	1	0	1	0	0	0	0	14693	131	5	0	1845	0	SLC6A15	12	85279291	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2532297	85279291	48572604	813	19085										
CEP290	80184	hgsc.bcm.edu	37	chr12	88454605	88454606	+	Splice_Site	DNP	AC	AC	TA													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgatcacattaaaaaaaattAccttcaatttttcattttcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:88454605_88454606AC>TA	ENST00000552810.1	-	47	6866		c.e47+1		CEP290_ENST00000397838.3_Splice_Site|CEP290_ENST00000309041.7_Splice_Site|CEP290_ENST00000547691.2_Splice_Site	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						AAAAAAAATTACCTTCAATTTT	0.262																																					.		Atlas-SNP	.											.	CEP290	195	.	0			c.6522+2T>A|c.6522+1G>T						.																																			SO:0001630	splice_region_variant	80184	exon48			AAAATTACCTTCA|AAATTACCTTCAA	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.6523_6523delinsTA	chr12.hg19:g.88454605_88454606delinsTA		84.0|86.0	0.0		80.0|82.0	7.0|5.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Splice_Site	SNP	ENST00000552810.1	hg19	CCDS55858.1																																																																																			.	.		0.262	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	Intron	TA	88454606	AC	TA	88454605	5	4	114	1	0	0	0	0	0	0	1	0	3255	405	14	4	947	4	CEP290	12	88454605	Splice_Site	DNP	AC	TCGA-DD-A3A0-01A-11D-A20W-10	3175314	88454605	45397290	814	19086										
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94642030	94642030	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atgacaacttcaacatttccAaaaaagacattgaaattact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:94642030delA	ENST00000258526.4	+	14	2869	c.2620delA	c.(2620-2622)aaafs	p.K875fs		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	875					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CAACATTTCCAAAAAAGACAT	0.338																																					p.S873fs		Atlas-INDEL	.											.	PLXNC1	135	.	0			c.2619delC						.						35	37	37					12																	94642030		2203	4300	6503	SO:0001589	frameshift_variant	10154	exon14			.	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.2620delA	chr12.hg19:g.94642030delA	ENSP00000258526:p.Lys875fs	131.0	0.0		148.0	10.0	NM_005761	Q59H25	Frame_Shift_Del	DEL	ENST00000258526.4	hg19	CCDS9049.1																																																																																			.	.		0.338	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			-	94642030	A	-	94642030	7	5	114	1	0	1	0	1	0	0	0	0	12135	131	5	0	2674	0	PLXNC1	12	94642030	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	6187425	94642030	39209865	815	19087										
CCDC41	51134	hgsc.bcm.edu	37	chr12	94769731	94769731	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attaaaaaggtattttgttcActgcttgattgtagctcttt	7	5	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:94769731A>G	ENST00000397809.5	-	8	1413	c.864T>C	c.(862-864)agT>agC	p.S288S	CCDC41_ENST00000397807.2_Silent_p.S255S|CCDC41_ENST00000549352.1_5'UTR|CCDC41_ENST00000547575.1_Silent_p.S288S|CCDC41_ENST00000339839.5_Silent_p.S288S	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		280					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						TATTTTGTTCACTGCTTGATT	0.284																																					p.S288S		Atlas-SNP	.											.	CCDC41	59	.	0			c.T864C						.						79	77	77					12																	94769731		1807	4068	5875	SO:0001819	synonymous_variant	51134	exon8			TTGTTCACTGCTT																												ENST00000397809.5:c.864T>C	chr12.hg19:g.94769731A>G		71.0	0.0		69.0	4.0	NM_016122	A4FVB1|Q08AP1	Silent	SNP	ENST00000397809.5	hg19	CCDS41820.1																																																																																			.	.		0.284	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3			G	94769731	A	G	94769731	2	3	114	1	0	0	0	0	0	0	0	1	2815	156	6	2		2	CCDC41	12	94769731	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	127701	94769731	39082164	816	19088										
FGD6	55785	hgsc.bcm.edu	37	chr12	95501402	95501402	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atcagaattccttctttgagAaaaacctgattcacccaaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:95501402delA	ENST00000343958.4	-	12	3493	c.3270delT	c.(3268-3270)tttfs	p.F1090fs	FGD6_ENST00000549499.1_Frame_Shift_Del_p.F1090fs|FGD6_ENST00000546711.1_Frame_Shift_Del_p.F1090fs	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1090	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						CTTCTTTGAGAAAAACCTGAT	0.398																																					p.L1091fs		Atlas-INDEL	.											.	FGD6	127	.	0			c.3271delC						.						127	117	121					12																	95501402		2203	4300	6503	SO:0001589	frameshift_variant	55785	exon12			.	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.3270delT	chr12.hg19:g.95501402delA	ENSP00000344446:p.Phe1090fs	109.0	0.0		126.0	13.0	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Frame_Shift_Del	DEL	ENST00000343958.4	hg19	CCDS31878.1																																																																																			.	.		0.398	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		-	95501402	A	-	95501402	7	5	114	1	0	1	0	1	0	0	0	0	5845	243	9	0	1062	0	FGD6	12	95501402	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	731671	95501402	38350493	817	19089										
CCDC38	120935	hgsc.bcm.edu	37	chr12	96292465	96292465	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgttccctcattgctatgtcTttttcaaactttttgattgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:96292465delT	ENST00000344280.3	-	6	971	c.414delA	c.(412-414)aaafs	p.K138fs	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	138										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTGCTATGTCTTTTTCAAACT	0.373																																					p.D139fs		Atlas-INDEL	.											.	CCDC38	45	.	0			c.415delG						.						158	142	148					12																	96292465		2203	4300	6503	SO:0001589	frameshift_variant	120935	exon6			.	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.414delA	chr12.hg19:g.96292465delT	ENSP00000345470:p.Lys138fs	285.0	0.0		313.0	19.0	NM_182496	Q8N835	Frame_Shift_Del	DEL	ENST00000344280.3	hg19	CCDS9056.1																																																																																			.	.		0.373	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496		-	96292465	T	-	96292465	7	5	114	1	0	1	0	1	0	0	0	0	2812	1606	56	0	1321	0	CCDC38	12	96292465	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	791063	96292465	37559430	818	19090										
NEDD1	121441	hgsc.bcm.edu	37	chr12	97328852	97328852	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgggatgtaaatagtcagagTccataccataactttgacag	9	7	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:97328852T>C	ENST00000266742.4	+	7	927	c.588T>C	c.(586-588)agT>agC	p.S196S	NEDD1_ENST00000411739.2_Silent_p.S107S|NEDD1_ENST00000557644.1_Silent_p.S203S|NEDD1_ENST00000555114.1_3'UTR|NEDD1_ENST00000429527.2_Silent_p.S196S|NEDD1_ENST00000457368.2_Silent_p.S107S	NM_152905.3	NP_690869.1	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally down-regulated 1	196					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	apical part of cell (GO:0045177)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|pericentriolar material (GO:0000242)|spindle pole (GO:0000922)				breast(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)	22						ATAGTCAGAGTCCATACCATA	0.408																																					p.S203S		Atlas-SNP	.											.	NEDD1	47	.	0			c.T609C						.						223	210	215					12																	97328852		2203	4300	6503	SO:0001819	synonymous_variant	121441	exon6			TCAGAGTCCATAC		CCDS9063.1, CCDS44955.1, CCDS44956.1	12q23.1	2013-01-10			ENSG00000139350	ENSG00000139350		"WD repeat domain containing"	7723	protein-coding gene	gene with protein product		600372					Standard	NM_001135175		Approved	GCP-WD, TUBGCP7	uc001tev.4	Q8NHV4	OTTHUMG00000170604	ENST00000266742.4:c.588T>C	chr12.hg19:g.97328852T>C		192.0	0.0		203.0	9.0	NM_001135175	B0AZN0|B4E145|G3V3F1|Q8NA30	Silent	SNP	ENST00000266742.4	hg19	CCDS9063.1																																																																																			.	.		0.408	NEDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409792.1			C	97328852	T	C	97328852	2	2	114	1	0	0	0	0	0	0	0	1	10318	1664	58	2		2	NEDD1	12	97328852	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1036387	97328852	36523043	819	19091										
APAF1	317	hgsc.bcm.edu	37	chr12	99060128	99060128	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tacagagaagaattgcagccAgcttcaggtacttgcatctt	9	9	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:99060128A>G	ENST00000551964.1	+	9	2091	c.1355A>G	c.(1354-1356)cAg>cGg	p.Q452R	APAF1_ENST00000359972.2_Missense_Mutation_p.Q441R|APAF1_ENST00000547045.1_Missense_Mutation_p.Q452R|APAF1_ENST00000550527.1_Missense_Mutation_p.Q441R|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000549007.1_Missense_Mutation_p.Q452R|APAF1_ENST00000357310.1_Missense_Mutation_p.Q452R|APAF1_ENST00000339433.3_Missense_Mutation_p.Q452R|APAF1_ENST00000552268.1_Intron	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	452					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	AATTGCAGCCAGCTTCAGGTA	0.289																																					p.Q452R		Atlas-SNP	.											.	APAF1	111	.	0			c.A1355G						.						89	95	93					12																	99060128		2203	4300	6503	SO:0001583	missense	317	exon9			GCAGCCAGCTTCA	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.1355A>G	chr12.hg19:g.99060128A>G	ENSP00000448165:p.Gln452Arg	75.0	0.0		99.0	4.0	NM_181868	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.624000	0.66901	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.59906	0.24;0.35;0.32;0.43;0.23;0.32;0.43	5.77	4.62	0.57501	.	0.052584	0.85682	D	0.000000	T	0.65760	0.2722	L	0.50333	1.59	0.80722	D	1	B;B;B;P	0.51653	0.078;0.01;0.023;0.947	B;B;B;D	0.65323	0.142;0.04;0.027;0.934	T	0.63422	-0.6641	10	0.40728	T	0.16	-21.8531	8.8201	0.35020	0.8556:0.0:0.1444:0.0	.	452;441;452;441	O14727-4;O14727-3;O14727;O14727-2	.;.;APAF_HUMAN;.	R	452;441;452;452;441;452;452	ENSP00000448165:Q452R;ENSP00000353059:Q441R;ENSP00000349862:Q452R;ENSP00000341830:Q452R;ENSP00000448449:Q441R;ENSP00000449791:Q452R;ENSP00000448161:Q452R	ENSP00000341830:Q452R	Q	+	2	0	APAF1	97584259	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	4.832000	0.62759	1.012000	0.39366	0.477000	0.44152	CAG	.	.		0.289	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		G	99060128	A	G	99060128	3	3	114	1	0	0	0	0	1	0	0	0	755	188	7	2	1385	2	APAF1	12	99060128	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1731276	99060128	34791767	820	19092										
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99129364	99129364	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttttctgagtgcctcctcagTgtgtctctctgatggttcct	9	11	4	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:99129364T>C	ENST00000547776.2	-	26	3720	c.3721A>G	c.(3721-3723)Act>Gct	p.T1241A	ANKS1B_ENST00000547010.1_Missense_Mutation_p.T757A|ANKS1B_ENST00000549558.2_Missense_Mutation_p.T407A|ANKS1B_ENST00000341752.7_Missense_Mutation_p.T247A|ANKS1B_ENST00000329257.7_Missense_Mutation_p.T1241A	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	1241						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GCCTCCTCAGTGTGTCTCTCT	0.353																																					p.T1241A		Atlas-SNP	.											.	ANKS1B	180	.	0			c.A3721G						.						117	112	113					12																	99129364		1841	4094	5935	SO:0001583	missense	56899	exon26			CCTCAGTGTGTCT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.3721A>G	chr12.hg19:g.99129364T>C	ENSP00000449629:p.Thr1241Ala	64.0	0.0		67.0	4.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	T	12.63	1.994346	0.35226	.	.	ENSG00000185046	ENST00000341752;ENST00000549558;ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702	T;T;T;T;T	0.64260	-0.09;-0.08;1.1;0.28;1.1	2.95	2.95	0.34219	.	1.415530	0.05657	U	0.586107	T	0.60560	0.2278	N	0.08118	0	0.22213	N	0.999284	P;P;P	0.52842	0.874;0.956;0.917	P;D;P	0.65010	0.641;0.931;0.878	T	0.56878	-0.7906	10	0.66056	D	0.02	0.4115	7.7143	0.28696	0.0:0.0:0.0:1.0	.	757;1241;407	Q7Z6G8-6;Q7Z6G8;Q7Z6G8-7	.;ANS1B_HUMAN;.	A	247;407;1241;757;1241;756	ENSP00000345510:T247A;ENSP00000448993:T407A;ENSP00000449629:T1241A;ENSP00000448512:T757A;ENSP00000331381:T1241A	ENSP00000331381:T1241A	T	-	1	0	ANKS1B	97653495	0.001000	0.12720	0.004000	0.12327	0.908000	0.53690	0.330000	0.19715	1.587000	0.49959	0.379000	0.24179	ACT	.	.		0.353	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		C	99129364	T	C	99129364	3	2	114	1	0	0	0	0	1	0	0	0	689	1696	59	2	29	2	ANKS1B	12	99129364	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	69236	99129364	34722531	821	19093										
ANKS1B	56899	hgsc.bcm.edu	37	chr12	100166806	100166806	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtcttcaaacgaataatccTtttcttgacagagttttatt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:100166806delT	ENST00000547776.2	-	8	1021	c.1022delA	c.(1021-1023)aagfs	p.K341fs	ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000329257.7_Frame_Shift_Del_p.K341fs	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	341						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		CGAATAATCCTTTTCTTGACA	0.353																																					p.K341fs		Atlas-INDEL	.											.	ANKS1B	180	.	0			c.1023delG						.						130	122	125					12																	100166806		1823	4078	5901	SO:0001589	frameshift_variant	56899	exon8			.	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1022delA	chr12.hg19:g.100166806delT	ENSP00000449629:p.Lys341fs	212.0	0.0		234.0	15.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Frame_Shift_Del	DEL	ENST00000547776.2	hg19	CCDS55872.1																																																																																			.	.		0.353	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		-	100166806	T	-	100166806	7	5	114	1	0	1	0	1	0	0	0	0	689	1609	56	0	3088	0	ANKS1B	12	100166806	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1037442	100166806	33685089	822	19094										
ANKS1B	56899	hgsc.bcm.edu	37	chr12	100173672	100173672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtaagagtgttgcaatctggAgagatttctgagatggatgt	14	3	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:100173672A>G	ENST00000547776.2	-	6	823	c.824T>C	c.(823-825)cTc>cCc	p.L275P	ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000329257.7_Missense_Mutation_p.L275P	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	275						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TGCAATCTGGAGAGATTTCTG	0.343																																					p.L275P		Atlas-SNP	.											.	ANKS1B	180	.	0			c.T824C						.						156	153	154					12																	100173672		1829	4091	5920	SO:0001583	missense	56899	exon6			ATCTGGAGAGATT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.824T>C	chr12.hg19:g.100173672A>G	ENSP00000449629:p.Leu275Pro	133.0	0.0		167.0	7.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.328604	0.60743	.	.	ENSG00000185046	ENST00000547776;ENST00000329257	T;T	0.46819	0.86;0.86	5.95	5.95	0.96441	Ankyrin repeat-containing domain (2);	0.084158	0.52532	D	0.000068	T	0.54481	0.1861	L	0.47716	1.5	0.80722	D	1	D	0.53745	0.962	P	0.54590	0.756	T	0.51601	-0.8685	9	.	.	.	-7.7214	13.9333	0.64010	1.0:0.0:0.0:0.0	.	275	Q7Z6G8	ANS1B_HUMAN	P	275	ENSP00000449629:L275P;ENSP00000331381:L275P	.	L	-	2	0	ANKS1B	98697803	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.946000	0.56644	2.280000	0.76307	0.460000	0.39030	CTC	.	.		0.343	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		G	100173672	A	G	100173672	3	3	114	1	0	0	0	0	1	0	0	0	689	304	11	2	3294	2	ANKS1B	12	100173672	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	6866	100173672	33678223	823	19095										
ACTR6	64431	hgsc.bcm.edu	37	chr12	100599500	100599500	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagacaagtttgggattaccTttttggaaaagaaatgtatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:100599500delT	ENST00000188312.2	+	3	998	c.233delT	c.(232-234)cttfs	p.L78fs	ACTR6_ENST00000550813.1_3'UTR|ACTR6_ENST00000551617.1_5'UTR|ACTR6_ENST00000546902.1_5'UTR|ACTR6_ENST00000552376.1_Frame_Shift_Del_p.L78fs	NM_022496.4	NP_071941.1	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog (yeast)	78						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14						TGGGATTACCTTTTTGGAAAA	0.234																																					p.L78fs		Atlas-INDEL	.											.	ACTR6	29	.	0			c.232delC						.						57	62	60					12																	100599500		2198	4270	6468	SO:0001589	frameshift_variant	64431	exon3			.	AF212251	CCDS9074.1	12q23.1	2012-07-09			ENSG00000075089	ENSG00000075089			24025	protein-coding gene	gene with protein product						11368909	Standard	NM_022496		Approved	ARP6, FLJ13433	uc001thb.2	Q9GZN1	OTTHUMG00000170245	ENST00000188312.2:c.233delT	chr12.hg19:g.100599500delT	ENSP00000188312:p.Leu78fs	110.0	0.0		175.0	13.0	NM_022496	B3KW37|B4DLG9|Q53GH2|Q9BY39|Q9H8H6	Frame_Shift_Del	DEL	ENST00000188312.2	hg19	CCDS9074.1																																																																																			.	.		0.234	ACTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408159.1	NM_022496		-	100599500	T	-	100599500	7	5	114	1	0	1	0	1	0	0	0	0	216	1609	56	0	243	0	ACTR6	12	100599500	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	425828	100599500	33252395	824	19096										
GAS2L3	283431	hgsc.bcm.edu	37	chr12	101017470	101017470	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acaaaaaattttagcatttcAaaaaggagtttctaatgaaa					rs201339445		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:101017470delA	ENST00000539410.1	+	9	1273	c.887delA	c.(886-888)caafs	p.Q296fs	GAS2L3_ENST00000266754.5_Frame_Shift_Del_p.Q296fs|GAS2L3_ENST00000537247.1_Frame_Shift_Del_p.Q192fs|GAS2L3_ENST00000547754.1_Frame_Shift_Del_p.Q296fs			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	296					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						TTAGCATTTCAAAAAGGAGTT	0.388																																					p.Q296fs		Atlas-INDEL	.											.	GAS2L3	76	.	0			c.886delC						.						67	70	69					12																	101017470		2203	4299	6502	SO:0001589	frameshift_variant	283431	exon10			.	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.887delA	chr12.hg19:g.101017470delA	ENSP00000439672:p.Gln296fs	149.0	0.0		183.0	11.0	NM_174942	B2RCN2	Frame_Shift_Del	DEL	ENST00000539410.1	hg19	CCDS9079.1																																																																																			.	.		0.388	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942		-	101017470	A	-	101017470	7	5	114	1	0	1	0	1	0	0	0	0	6256	130	5	0	917	0	GAS2L3	12	101017470	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	417970	101017470	32834425	825	19097										
CHPT1	56994	hgsc.bcm.edu	37	chr12	102107976	102107976	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caaactcttgttcccctttaGgggagctctttgaccatggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:102107976delG	ENST00000229266.3	+	2	617	c.382delG	c.(382-384)gggfs	p.G128fs	CHPT1_ENST00000550385.1_3'UTR|CHPT1_ENST00000549872.1_Frame_Shift_Del_p.G128fs	NM_020244.2	NP_064629.2	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	128					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	diacylglycerol binding (GO:0019992)|diacylglycerol cholinephosphotransferase activity (GO:0004142)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						TTCCCCTTTAGGGGAGCTCTT	0.383																																					p.L127fs		Atlas-INDEL	.											.	CHPT1	27	.	0			c.381delA						.						134	143	140					12																	102107976		2203	4300	6503	SO:0001589	frameshift_variant	56994	exon2			.		CCDS9086.1	12q	2010-07-08				ENSG00000111666	2.7.8.2		17852	protein-coding gene	gene with protein product	"phosphatidylcholine synthesizing enzyme"					10893425	Standard	NM_020244		Approved	CPT1	uc001tin.3	Q8WUD6		ENST00000229266.3:c.382delG	chr12.hg19:g.102107976delG	ENSP00000229266:p.Gly128fs	125.0	0.0		175.0	11.0	NM_020244	B3KQM2|Q7Z7H0|Q7Z7H1|Q7Z7H2|Q8IWQ4|Q8IWQ5|Q8WYI4|Q9NRQ6|Q9NRQ7|Q9Y6M6	Frame_Shift_Del	DEL	ENST00000229266.3	hg19	CCDS9086.1																																																																																			.	.		0.383	CHPT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409173.1	NM_020244		-	102107976	G	-	102107976	7	5	114	1	0	1	0	1	0	0	0	0	3372	1000	35	0	388	0	CHPT1	12	102107976	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1090506	102107976	31743919	826	19098										
GNPTAB	79158	hgsc.bcm.edu	37	chr12	102155033	102155033	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attcagtggctgcactgcacTcatgagataataaaaataag	8	7	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:102155033T>C	ENST00000299314.7	-	15	3269	c.3007A>G	c.(3007-3009)Agt>Ggt	p.S1003G		NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	1003					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						TGCACTGCACTCATGAGATAA	0.413																																					p.S1003G		Atlas-SNP	.											.	GNPTAB	120	.	0			c.A3007G						.						96	94	95					12																	102155033		2203	4300	6503	SO:0001583	missense	79158	exon15			CTGCACTCATGAG	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"EF-hand domain containing"	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.3007A>G	chr12.hg19:g.102155033T>C	ENSP00000299314:p.Ser1003Gly	67.0	0.0		94.0	4.0	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Missense_Mutation	SNP	ENST00000299314.7	hg19	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.240692	0.58995	.	.	ENSG00000111670	ENST00000299314	D	0.92099	-2.97	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.94341	0.8181	L	0.55017	1.72	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	D	0.92377	0.5910	10	0.18276	T	0.48	-26.3129	16.255	0.82510	0.0:0.0:0.0:1.0	.	1003	Q3T906	GNPTA_HUMAN	G	1003	ENSP00000299314:S1003G	ENSP00000299314:S1003G	S	-	1	0	GNPTAB	100679164	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.240000	0.73641	0.533000	0.62120	AGT	.	.		0.413	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			C	102155033	T	C	102155033	3	2	114	1	0	0	0	0	1	0	0	0	6553	1551	54	2	791	2	GNPTAB	12	102155033	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	47057	102155033	31696862	827	19099										
NT5DC3	51559	hgsc.bcm.edu	37	chr12	104208851	104208851	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggctcatttcattgtttgagAaaatggcatctggattcaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:104208851delA	ENST00000392876.3	-	2	297	c.257delT	c.(256-258)ttcfs	p.F86fs		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	86						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						ATTGTTTGAGAAAATGGCATC	0.333																																					p.F86fs		Atlas-INDEL	.											.	NT5DC3	113	.	0			c.258delC						.						85	79	81					12																	104208851		2203	4300	6503	SO:0001589	frameshift_variant	51559	exon2			.	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.257delT	chr12.hg19:g.104208851delA	ENSP00000376615:p.Phe86fs	136.0	0.0		148.0	12.0	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Frame_Shift_Del	DEL	ENST00000392876.3	hg19	CCDS41824.1																																																																																			.	.		0.333	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575		-	104208851	A	-	104208851	7	5	114	1	0	1	0	1	0	0	0	0	10701	246	9	0	1441	0	NT5DC3	12	104208851	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2053818	104208851	29643044	828	19100										
HSP90B1	7184	hgsc.bcm.edu	37	chr12	104340586	104340586	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agatgaagatgataaaacagTtttggatcttgctgtggttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:104340586delT	ENST00000299767.5	+	16	2311	c.2129delT	c.(2128-2130)gttfs	p.V710fs		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	710					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	GATAAAACAGTTTTGGATCTT	0.353																																					p.V710fs		Atlas-INDEL	.											.	HSP90B1	72	.	0			c.2128delG						.						74	72	73					12																	104340586		2203	4300	6503	SO:0001589	frameshift_variant	7184	exon16			.	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.2129delT	chr12.hg19:g.104340586delT	ENSP00000299767:p.Val710fs	123.0	0.0		189.0	13.0	NM_003299	Q96A97	Frame_Shift_Del	DEL	ENST00000299767.5	hg19	CCDS9094.1																																																																																			.	.		0.353	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		-	104340586	T	-	104340586	7	5	114	1	0	1	0	1	0	0	0	0	7412	1725	60	0	2191	0	HSP90B1	12	104340586	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	131735	104340586	29511309	829	19101										
TDG	6996	hgsc.bcm.edu	37	chr12	104370720	104370720	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcccttcagcaagctcaagcTttttatacgtttccatttca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:104370720delT	ENST00000392872.3	+	2	282	c.48delT	c.(46-48)gctfs	p.A16fs	TDG_ENST00000544861.1_Intron|TDG_ENST00000266775.9_Frame_Shift_Del_p.A12fs	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	16					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		AAGCTCAAGCTTTTTATACGT	0.388								Base excision repair (BER), DNA glycosylases																													p.A16fs		Atlas-INDEL	.											.	TDG	43	.	0			c.47delC						.						53	51	52					12																	104370720		2203	4300	6503	SO:0001589	frameshift_variant	6996	exon2			.	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"G/T mismatch-specific thymine DNA glycosylase"	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.48delT	chr12.hg19:g.104370720delT	ENSP00000376611:p.Ala16fs	160.0	0.0		195.0	12.0	NM_003211	Q8IUZ6|Q8IZM3	Frame_Shift_Del	DEL	ENST00000392872.3	hg19	CCDS9095.1																																																																																			.	.		0.388	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2			-	104370720	T	-	104370720	7	5	114	1	0	1	0	1	0	0	0	0	15740	1596	56	0	54	0	TDG	12	104370720	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	30134	104370720	29481175	830	19102										
HCFC2	29915	hgsc.bcm.edu	37	chr12	104490206	104490206	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacatgctacagcaacgccgTtttctgtaagtacatgacct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:104490206delT	ENST00000229330.4	+	12	1839	c.1735delT	c.(1735-1737)tttfs	p.F579fs	HCFC2_ENST00000550335.1_3'UTR	NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	579					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						AGCAACGCCGTTTTCTGTAAG	0.343																																					p.P578fs	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-INDEL	.											.	HCFC2	94	.	0			c.1734delG						.						121	120	120					12																	104490206		2203	4300	6503	SO:0001589	frameshift_variant	29915	exon12			.	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1735delT	chr12.hg19:g.104490206delT	ENSP00000229330:p.Phe579fs	173.0	0.0		155.0	10.0	NM_013320	B2R8Q5|C0H5X3	Frame_Shift_Del	DEL	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.343	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		-	104490206	T	-	104490206	7	5	114	1	0	1	0	1	0	0	0	0	7002	1725	60	0	1781	0	HCFC2	12	104490206	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	119486	104490206	29361689	831	19103										
HCFC2	29915	hgsc.bcm.edu	37	chr12	104495863	104495863	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgggataggtcctttcagcAaaatcagtgaatttaaaact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:104495863delA	ENST00000229330.4	+	14	2100	c.1996delA	c.(1996-1998)aaafs	p.K666fs	HCFC2_ENST00000550335.1_3'UTR	NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	666	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						TCCTTTCAGCAAAATCAGTGA	0.428																																					p.S665fs	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-INDEL	.											.	HCFC2	94	.	0			c.1995delC						.						161	152	155					12																	104495863		2203	4300	6503	SO:0001589	frameshift_variant	29915	exon14			.	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1996delA	chr12.hg19:g.104495863delA	ENSP00000229330:p.Lys666fs	162.0	0.0		164.0	11.0	NM_013320	B2R8Q5|C0H5X3	Frame_Shift_Del	DEL	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.428	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		-	104495863	A	-	104495863	7	5	114	1	0	1	0	1	0	0	0	0	7002	131	5	0	2050	0	HCFC2	12	104495863	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	5657	104495863	29356032	832	19104										
FOXN4	121643	hgsc.bcm.edu	37	chr12	109725737	109725737	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcaggccagatgagggctggCcccccacggggaactggctc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:109725737delC	ENST00000299162.5	-	5	484	c.380delG	c.(379-381)ggcfs	p.G127fs	FOXN4_ENST00000355216.1_Intron	NM_213596.2	NP_998761.2	Q96NZ1	FOXN4_HUMAN	forkhead box N4	127	Pro-rich.				amacrine cell differentiation (GO:0035881)|atrioventricular canal development (GO:0036302)|heart looping (GO:0001947)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of heart contraction (GO:0008016)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(9)|ovary(2)	16						TGAGGGCTGGCCCCCCACGGG	0.677																																					p.G127fs		Atlas-INDEL	.											.	FOXN4	74	.	0			c.381delC						.						12	19	17					12																	109725737		690	1590	2280	SO:0001589	frameshift_variant	121643	exon5			.	AF425596	CCDS9126.2	12q24.12	2008-02-05			ENSG00000139445	ENSG00000139445		"Forkhead boxes"	21399	protein-coding gene	gene with protein product		609429					Standard	NM_213596		Approved		uc001toe.4	Q96NZ1	OTTHUMG00000152868	ENST00000299162.5:c.380delG	chr12.hg19:g.109725737delC	ENSP00000299162:p.Gly127fs	139.0	0.0		182.0	11.0	NM_213596	Q6ZMR4|Q96NZ0	Frame_Shift_Del	DEL	ENST00000299162.5	hg19	CCDS9126.2																																																																																			.	.		0.677	FOXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328306.1	XM_062735		-	109725737	C	-	109725737	7	5	114	1	0	1	0	1	0	0	0	0	6030	739	26	0	1197	0	FOXN4	12	109725737	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	5229874	109725737	24126158	833	19105										
NAA25	80018	hgsc.bcm.edu	37	chr12	112479858	112479858	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttaccttttaactggtctaGtaaagacttaaaactatttt	4	7	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:112479858G>C	ENST00000261745.4	-	20	2673	c.2425C>G	c.(2425-2427)Cta>Gta	p.L809V		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	809						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						AACTGGTCTAGTAAAGACTTA	0.318																																					p.L809V		Atlas-SNP	.											.	NAA25	105	.	0			c.C2425G						.						86	80	82					12																	112479858		2188	4297	6485	SO:0001583	missense	80018	exon20			GGTCTAGTAAAGA	AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"N(alpha)-acetyltransferase subunits"	25783	protein-coding gene	gene with protein product		612755	"chromosome 12 open reading frame 30"	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.2425C>G	chr12.hg19:g.112479858G>C	ENSP00000261745:p.Leu809Val	17.0	0.0		25.0	6.0	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	hg19	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	G	9.682	1.149581	0.21288	.	.	ENSG00000111300	ENST00000261745;ENST00000550701	T	0.26223	1.75	5.9	2.78	0.32641	.	0.157403	0.44902	D	0.000416	T	0.11707	0.0285	N	0.17082	0.46	0.29966	N	0.818958	B	0.06786	0.001	B	0.08055	0.003	T	0.15378	-1.0439	10	0.25106	T	0.35	-6.2634	2.4052	0.04411	0.2487:0.1231:0.5018:0.1265	.	809	Q14CX7	NAA25_HUMAN	V	809;15	ENSP00000261745:L809V	ENSP00000261745:L809V	L	-	1	2	NAA25	110964241	0.996000	0.38824	1.000000	0.80357	0.844000	0.47949	0.198000	0.17217	0.265000	0.21872	0.655000	0.94253	CTA	.	.		0.318	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		C	112479858	G	C	112479858	3	2	114	1	0	0	0	0	1	0	0	0	10130	1020	36	4	513	4	NAA25	12	112479858	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	2754121	112479858	21372037	834	19106										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112703054	112703054	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgattaagatacaggattcTcgtacaacaatcttcagaat	7	7	3	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:112703054T>C	ENST00000430131.2	-	15	2393	c.1248A>G	c.(1246-1248)cgA>cgG	p.R416R	HECTD4_ENST00000377560.5_Silent_p.R666R|HECTD4_ENST00000550722.1_Silent_p.R704R|RN7SKP71_ENST00000364558.1_RNA			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	416					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TACAGGATTCTCGTACAACAA	0.299																																					p.R704R		Atlas-SNP	.											.	.	.	.	0			c.A2112G						.						100	106	104					12																	112703054		2203	4299	6502	SO:0001819	synonymous_variant	283450	exon16			GGATTCTCGTACA	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.1248A>G	chr12.hg19:g.112703054T>C		74.0	0.0		92.0	4.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19																																																																																				.	.		0.299	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		C	112703054	T	C	112703054	2	2	114	1	0	0	0	0	0	0	0	1	1698	1538	54	2		2	C12orf51	12	112703054	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	223196	112703054	21148841	835	19107										
OAS3	4940	hgsc.bcm.edu	37	chr12	113402157	113402157	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccgttgataccatctgttcaTttttgaaggaaaactgcttc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:113402157delT	ENST00000228928.7	+	11	2526	c.2347delT	c.(2347-2349)tttfs	p.F783fs	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	783	OAS domain 3.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						CATCTGTTCATTTTTGAAGGA	0.512																																					p.S782fs		Atlas-INDEL	.											.	OAS3	63	.	0			c.2346delA						.						49	50	50					12																	113402157		1875	4106	5981	SO:0001589	frameshift_variant	4940	exon11			.	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"2'-5'-oligoadenylate synthetase 3 (100 kD)"			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.2347delT	chr12.hg19:g.113402157delT	ENSP00000228928:p.Phe783fs	172.0	0.0		180.0	12.0	NM_006187	Q2HJ14|Q9H3P5	Frame_Shift_Del	DEL	ENST00000228928.7	hg19	CCDS44981.1																																																																																			.	.		0.512	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1			-	113402157	T	-	113402157	7	5	114	1	0	1	0	1	0	0	0	0	10810	1493	52	0	2389	0	OAS3	12	113402157	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	699103	113402157	20449738	836	19108										
TPCN1	53373	hgsc.bcm.edu	37	chr12	113704017	113704017	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aacgacaagttcttcacccaCcccaaggatgccaaggcgct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:113704017delC	ENST00000335509.6	+	4	584	c.270delC	c.(268-270)cacfs	p.H90fs	TPCN1_ENST00000392569.4_Frame_Shift_Del_p.H22fs|TPCN1_ENST00000541517.1_Frame_Shift_Del_p.H162fs|TPCN1_ENST00000550785.1_Frame_Shift_Del_p.H162fs	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	90					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						TCTTCACCCACCCCAAGGATG	0.587																																					p.H162fs		Atlas-INDEL	.											.	TPCN1	109	.	0			c.485delA						.						202	177	186					12																	113704017		2203	4300	6503	SO:0001589	frameshift_variant	53373	exon5			.	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"Voltage-gated ion channels / Two-pore channels"	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.270delC	chr12.hg19:g.113704017delC	ENSP00000335300:p.His90fs	179.0	0.0		149.0	10.0	NM_001143819	A7E258|Q86XS9|Q8NC20	Frame_Shift_Del	DEL	ENST00000335509.6	hg19	CCDS31908.1																																																																																			.	.		0.587	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		-	113704017	C	-	113704017	7	5	114	1	0	1	0	1	0	0	0	0	16410	506	18	0	500	0	TPCN1	12	113704017	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	301860	113704017	20147878	837	19109										
TBX3	6926	hgsc.bcm.edu	37	chr12	115112498	115112498	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgctcagcagcgaaaaggtgAgccttgaccgcggggctgcc	15	13	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:115112498A>G	ENST00000257566.3	-	7	1631	c.1242T>C	c.(1240-1242)gcT>gcC	p.A414A	TBX3_ENST00000349155.2_Silent_p.A394A	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	414					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		CGAAAAGGTGAGCCTTGACCG	0.697																																					p.A414A		Atlas-SNP	.											.	TBX3	106	.	0			c.T1242C						.						16	18	17					12																	115112498		2197	4292	6489	SO:0001819	synonymous_variant	6926	exon7			AAGGTGAGCCTTG	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.1242T>C	chr12.hg19:g.115112498A>G		89.0	0.0		67.0	4.0	NM_016569	Q8TB20|Q9UKF8	Silent	SNP	ENST00000257566.3	hg19	CCDS9176.1																																																																																			.	.		0.697	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		G	115112498	A	G	115112498	2	3	114	1	0	0	0	0	0	0	0	1	15674	291	11	2		2	TBX3	12	115112498	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1408481	115112498	18739397	838	19110										
SPPL3	121665	hgsc.bcm.edu	37	chr12	121222293	121222293	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttacctgctgtacatattgtAaaaactacttgaactgagtc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:121222293delA	ENST00000353487.2	-	4	797	c.294delT	c.(292-294)tttfs	p.F98fs		NM_139015.4	NP_620584.2	Q8TCT6	SPPL3_HUMAN	signal peptide peptidase like 3	99						Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|rough endoplasmic reticulum (GO:0005791)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|protein homodimerization activity (GO:0042803)					all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TACATATTGTAAAAACTACTT	0.323																																					p.T99fs		Atlas-INDEL	.											.	.	.	.	0			c.295delA						.						69	68	68					12																	121222293		2203	4300	6503	SO:0001589	frameshift_variant	121665	exon4			.		CCDS9208.1	12q24.31	2012-02-21			ENSG00000157837	ENSG00000157837			30424	protein-coding gene	gene with protein product	"intramembrane protease 2", "presenilin-like protein 4"	608240				12139484	Standard	NM_139015		Approved	IMP2, PSL4, MGC90402, MGC126674, MGC126676, DKFZP586C1324	uc001tzd.3	Q8TCT6	OTTHUMG00000169232	ENST00000353487.2:c.294delT	chr12.hg19:g.121222293delA	ENSP00000288680:p.Phe98fs	106.0	0.0		165.0	12.0	NM_139015	Q3MJ04|Q8TAU4|Q96DD9	Frame_Shift_Del	DEL	ENST00000353487.2	hg19	CCDS9208.1																																																																																			.	.		0.323	SPPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402980.2	NM_139015		-	121222293	A	-	121222293	7	5	114	1	0	1	0	1	0	0	0	0	15105	359	13	0	892	0	SPPL3	12	121222293	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	6109795	121222293	12629602	839	19111										
KDM2B	84678	hgsc.bcm.edu	37	chr12	121880092	121880092	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaggggtagcgagtcaggcGgggggctgatggggggtggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:121880092delG	ENST00000377071.4	-	19	3224	c.3152delC	c.(3151-3153)ccgfs	p.P1052fs	KDM2B_ENST00000542973.1_Frame_Shift_Del_p.P420fs|KDM2B_ENST00000377069.4_Frame_Shift_Del_p.P983fs|KDM2B_ENST00000536437.1_Intron	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1052	Pro-rich.				embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						CGAGTCAGGCGGGGGGCTGAT	0.672																																					p.P1051fs		Atlas-INDEL	.											.	KDM2B	218	.	0			c.3153delG						.						14	16	16					12																	121880092		1912	4085	5997	SO:0001589	frameshift_variant	84678	exon19			.	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3152delC	chr12.hg19:g.121880092delG	ENSP00000366271:p.Pro1052fs	157.0	0.0		205.0	21.0	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Frame_Shift_Del	DEL	ENST00000377071.4	hg19	CCDS41850.1																																																																																			.	.		0.672	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		-	121880092	G	-	121880092	7	5	114	1	0	1	0	1	0	0	0	0	8134	1116	39	0	930	0	KDM2B	12	121880092	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	657799	121880092	11971803	840	19112										
ORAI1	84876	hgsc.bcm.edu	37	chr12	122064777	122064777	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggagcccccgggggccccgCcaccgccaccgccgccgtcc	14	23	0	0	rs141919534|rs531278468		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:122064777C>G	ENST00000330079.7	+	1	323	c.130C>G	c.(130-132)Cca>Gca	p.P44A		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	0	Pro-rich.				blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)	p.P43_P44delPP(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		gggggccccgccaccgccacc	0.751																																					p.P44A		Atlas-SNP	.											.	ORAI1	66	.	1	Deletion - In frame(1)	breast(1)	c.C130G						.						2	2	2					12																	122064777		1171	2472	3643	SO:0001583	missense	84876	exon1			GCCCCGCCACCGC	AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"ORAI calcium release-activated calcium modulators"	25896	protein-coding gene	gene with protein product	"calcium release-activated calcium modulator 1"	610277	"transmembrane protein 142A"	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.130C>G	chr12.hg19:g.122064777C>G	ENSP00000328216:p.Pro44Ala	6.0	0.0		13.0	5.0	NM_032790	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	Missense_Mutation	SNP	ENST00000330079.7	hg19	CCDS41851.1	.	.	.	.	.	.	.	.	.	.	C	0.076	-1.193262	0.01607	.	.	ENSG00000182500	ENST00000330079	D	0.87334	-2.24	3.79	0.849	0.18972	.	1.175890	0.06482	N	0.732998	T	0.79246	0.4413	.	.	.	0.36521	D	0.870159	.	.	.	.	.	.	T	0.63932	-0.6525	7	0.11794	T	0.64	-18.2923	7.7875	0.29101	0.0:0.7001:0.0:0.2999	.	.	.	.	A	44	ENSP00000328216:P44A	ENSP00000328216:P44A	P	+	1	0	ORAI1	120549160	.	.	0.663000	0.29738	0.096000	0.18686	.	.	0.049000	0.15920	0.195000	0.17529	CCA	.	.		0.751	ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790		G	122064777	C	G	122064777	3	3	114	1	0	0	0	0	1	0	0	0	11266	739	26	4	132	4	ORAI1	12	122064777	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	184685	122064777	11787118	841	19113										
ABCB9	23457	hgsc.bcm.edu	37	chr12	123416813	123416813	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggggggttccgcaccagagCccgggccatggccacccgct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:123416813delC	ENST00000542678.1	-	11	4804	c.1966delG	c.(1966-1968)gctfs	p.A656fs	ABCB9_ENST00000346530.5_Frame_Shift_Del_p.A613fs|ABCB9_ENST00000442028.2_Frame_Shift_Del_p.A656fs|ABCB9_ENST00000280560.8_Frame_Shift_Del_p.A656fs|ABCB9_ENST00000344275.7_Frame_Shift_Del_p.A656fs|ABCB9_ENST00000540285.1_Frame_Shift_Del_p.A593fs|ABCB9_ENST00000442833.2_Frame_Shift_Del_p.A656fs|ABCB9_ENST00000392439.3_Frame_Shift_Del_p.A656fs			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	656	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		CGCACCAGAGCCCGGGCCATG	0.617																																					p.A656fs	Ovarian(49;786 1333 9175 38236)	Atlas-INDEL	.											.	ABCB9	50	.	0			c.1967delC						.						25	24	24					12																	123416813		2105	4156	6261	SO:0001589	frameshift_variant	23457	exon11			.	U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"ATP binding cassette transporters / subfamily B"	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.1966delG	chr12.hg19:g.123416813delC	ENSP00000440288:p.Ala656fs	120.0	0.0		141.0	10.0	NM_019625	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Frame_Shift_Del	DEL	ENST00000542678.1	hg19	CCDS9241.1																																																																																			.	.		0.617	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		-	123416813	C	-	123416813	7	5	114	1	0	1	0	1	0	0	0	0	48	739	26	0	342	0	ABCB9	12	123416813	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1352036	123416813	10435082	842	19114										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124323027	124323027	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgggtgagaccttaaaagacCccgtgatcaagaggtgctgt	13	8	1	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:124323027C>A	ENST00000409039.3	+	28	4598	c.4573C>A	c.(4573-4575)Ccc>Acc	p.P1525T		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1525	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CTTAAAAGACCCCGTGATCAA	0.552																																					p.P1525T		Atlas-SNP	.											.	DNAH10	888	.	0			c.C4573A						.						41	43	42					12																	124323027		2010	4167	6177	SO:0001583	missense	196385	exon28			AAAGACCCCGTGA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.4573C>A	chr12.hg19:g.124323027C>A	ENSP00000386770:p.Pro1525Thr	72.0	0.0		50.0	19.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	14.86	2.662236	0.47572	.	.	ENSG00000197653	ENST00000409039	T	0.62498	0.02	5.57	5.57	0.84162	Dynein heavy chain, domain-2 (1);	0.248516	0.33272	U	0.005089	T	0.66674	0.2813	L	0.60067	1.865	0.80722	D	1	P	0.42456	0.78	P	0.45232	0.474	T	0.65117	-0.6246	10	0.37606	T	0.19	.	19.554	0.95333	0.0:1.0:0.0:0.0	.	1525	Q8IVF4	DYH10_HUMAN	T	1525	ENSP00000386770:P1525T	ENSP00000386770:P1525T	P	+	1	0	DNAH10	122888980	1.000000	0.71417	0.997000	0.53966	0.240000	0.25518	7.584000	0.82572	2.632000	0.89209	0.650000	0.86243	CCC	.	.		0.552	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124323027	C	A	124323027	3	1	114	1	0	0	0	0	1	0	0	0	4600	623	22	3	4683	3	DNAH10	12	124323027	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	906214	124323027	9528868	843	19115										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124354958	124354958	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcattttgataacaaacggaAtcaatgggtcccatggagta	9	7	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:124354958A>G	ENST00000409039.3	+	43	7236	c.7211A>G	c.(7210-7212)aAt>aGt	p.N2404S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2404					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AACAAACGGAATCAATGGGTC	0.398																																					p.N2404S		Atlas-SNP	.											.	DNAH10	888	.	0			c.A7211G						.						98	93	95					12																	124354958		1875	4113	5988	SO:0001583	missense	196385	exon43			AACGGAATCAATG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.7211A>G	chr12.hg19:g.124354958A>G	ENSP00000386770:p.Asn2404Ser	78.0	0.0		65.0	4.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	7.640	0.680644	0.14907	.	.	ENSG00000197653	ENST00000409039	T	0.21031	2.03	5.21	1.52	0.23074	.	0.665037	0.13286	N	0.399382	T	0.16981	0.0408	L	0.47716	1.5	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.31308	-0.9948	10	0.20519	T	0.43	.	9.1845	0.37163	0.7913:0.0:0.2087:0.0	.	2404	Q8IVF4	DYH10_HUMAN	S	2404	ENSP00000386770:N2404S	ENSP00000386770:N2404S	N	+	2	0	DNAH10	122920911	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	5.213000	0.65230	0.018000	0.15052	-0.290000	0.09829	AAT	.	.		0.398	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			G	124354958	A	G	124354958	3	3	114	1	0	0	0	0	1	0	0	0	4600	101	4	2	7381	2	DNAH10	12	124354958	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	31931	124354958	9496937	844	19116										
CHFR	55743	hgsc.bcm.edu	37	chr12	133418144	133418144	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagggcctctggatgcttagTttttgaaccttgtctgttca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:133418144delT	ENST00000432561.2	-	18	2064	c.1991delA	c.(1990-1992)aacfs	p.N664fs	CHFR_ENST00000537522.1_Frame_Shift_Del_p.N286fs|CHFR_ENST00000266880.7_Frame_Shift_Del_p.N663fs|CHFR_ENST00000443047.2_Frame_Shift_Del_p.N572fs|CHFR_ENST00000450056.2_Frame_Shift_Del_p.N652fs|CHFR_ENST00000541341.1_Frame_Shift_Del_p.N91fs|CHFR_ENST00000315585.7_Frame_Shift_Del_p.N623fs|CHFR_ENST00000541837.2_5'UTR			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	664					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		GGATGCTTAGTTTTTGAACCT	0.433																																					p.N664fs		Atlas-INDEL	.											.	CHFR	83	.	0			c.1992delC						.						137	136	136					12																	133418144		2203	4300	6503	SO:0001589	frameshift_variant	55743	exon18			.	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"RING-type (C3HC4) zinc fingers"	20455	protein-coding gene	gene with protein product		605209	"checkpoint with forkhead and ring finger domains"			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.1991delA	chr12.hg19:g.133418144delT	ENSP00000392395:p.Asn664fs	160.0	0.0		123.0	10.0	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Frame_Shift_Del	DEL	ENST00000432561.2	hg19	CCDS53849.1																																																																																			.	.		0.433	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2			-	133418144	T	-	133418144	7	5	114	1	0	1	0	1	0	0	0	0	3339	1725	60	0	7	0	CHFR	12	133418144	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	9063186	133418144	433751	845	19117										
SACS	26278	hgsc.bcm.edu	37	chr13	23907453	23907453	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggattatcaataaactttccAgtttttcaaaaagttgttcc	5	7	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:23907453A>G	ENST00000382292.3	-	9	10835	c.10562T>C	c.(10561-10563)cTg>cCg	p.L3521P	SACS_ENST00000382298.3_Missense_Mutation_p.L3521P|SACS_ENST00000402364.1_Missense_Mutation_p.L2771P			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3521					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TAAACTTTCCAGTTTTTCAAA	0.328																																					p.L3521P		Atlas-SNP	.											.	SACS	871	.	0			c.T10562C						.						38	39	38					13																	23907453		2202	4293	6495	SO:0001583	missense	26278	exon10			CTTTCCAGTTTTT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.10562T>C	chr13.hg19:g.23907453A>G	ENSP00000371729:p.Leu3521Pro	125.0	0.0		87.0	4.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	A	18.73	3.685799	0.68157	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.93659	-3.07;-3.26;-3.07	6.04	6.04	0.98038	.	0.000000	0.64402	D	0.000002	D	0.94538	0.8241	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95406	0.8494	10	0.87932	D	0	.	16.5763	0.84648	1.0:0.0:0.0:0.0	.	3521	Q9NZJ4	SACS_HUMAN	P	3521;2771;3521	ENSP00000371729:L3521P;ENSP00000385844:L2771P;ENSP00000371735:L3521P	ENSP00000371729:L3521P	L	-	2	0	SACS	22805453	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	9.339000	0.96797	2.317000	0.78254	0.459000	0.35465	CTG	.	.		0.328	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23907453	A	G	23907453	3	3	114	1	0	0	0	0	1	0	0	0	13819	188	7	2	3181	2	SACS	13	23907453	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10		23907453	91262425	846	19118										
ATP12A	479	hgsc.bcm.edu	37	chr13	25280558	25280558	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gattgtctttgcccggacatCcccccagcagaagctgatca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:25280558delC	ENST00000381946.3	+	15	2293	c.2126delC	c.(2125-2127)tccfs	p.S709fs	RNY1P7_ENST00000384743.1_RNA|ATP12A_ENST00000218548.6_Frame_Shift_Del_p.S715fs			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	709					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		GCCCGGACATCCCCCCAGCAG	0.567																																					p.S715fs	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-INDEL	.											.	ATP12A	172	.	0			c.2143delT						.						114	87	96					13																	25280558		2203	4300	6503	SO:0001589	frameshift_variant	479	exon15			.	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2126delC	chr13.hg19:g.25280558delC	ENSP00000371372:p.Ser709fs	222.0	0.0		190.0	12.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Frame_Shift_Del	DEL	ENST00000381946.3	hg19	CCDS31948.1																																																																																			.	.		0.567	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		-	25280558	C	-	25280558	7	5	114	1	0	1	0	1	0	0	0	0	1122	855	30	0	2202	0	ATP12A	13	25280558	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1373105	25280558	89889320	847	19119										
PABPC3	5042	hgsc.bcm.edu	37	chr13	25670906	25670906	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggagctagggcaaaagagttCcccaatgtttacatcaagaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:25670906delC	ENST00000281589.3	+	1	607	c.570delC	c.(568-570)ttcfs	p.F190fs		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	190					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		CAAAAGAGTTCCCCAATGTTT	0.423																																					p.F190fs		Atlas-INDEL	.											.	PABPC3	129	.	0			c.569delT						.						100	93	95					13																	25670906		2203	4300	6503	SO:0001589	frameshift_variant	5042	exon1			.	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.570delC	chr13.hg19:g.25670906delC	ENSP00000281589:p.Phe190fs	164.0	0.0		110.0	10.0	NM_030979	Q8NHV0|Q9H086	Frame_Shift_Del	DEL	ENST00000281589.3	hg19	CCDS9311.1																																																																																			.	.		0.423	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		-	25670906	C	-	25670906	7	5	114	1	0	1	0	1	0	0	0	0	11374	854	30	0	572	0	PABPC3	13	25670906	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	390348	25670906	89498972	848	19120										
USP12	219333	hgsc.bcm.edu	37	chr13	27664255	27664255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgatgtattttgttccacgTcaacagaaaggtctaaaaaa	7	6	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:27664255T>C	ENST00000282344.6	-	5	870	c.614A>G	c.(613-615)gAc>gGc	p.D205G		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	205	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		TTGTTCCACGTCAACAGAAAG	0.269																																					p.D205G	Ovarian(37;808 911 7590 44442 44991)	Atlas-SNP	.											.	USP12	35	.	0			c.A614G						.						83	77	79					13																	27664255		2203	4295	6498	SO:0001583	missense	219333	exon5			TCCACGTCAACAG	AL049221	CCDS31952.1	13q12.13	2010-05-12	2005-08-08	2003-10-08	ENSG00000152484	ENSG00000152484		"Ubiquitin-specific peptidases"	20485	protein-coding gene	gene with protein product			"ubiquitin specific protease 12 like 1", "ubiquitin specific protease 12"	USP12L1		12838346	Standard	NM_182488		Approved		uc001uqy.3	O75317	OTTHUMG00000016626	ENST00000282344.6:c.614A>G	chr13.hg19:g.27664255T>C	ENSP00000282344:p.Asp205Gly	130.0	0.0		118.0	5.0	NM_182488	A8K0X0|Q5VZV3|Q8TC49	Missense_Mutation	SNP	ENST00000282344.6	hg19	CCDS31952.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.451886	0.84209	.	.	ENSG00000152484	ENST00000282344	T	0.06608	3.28	5.17	5.17	0.71159	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.40469	U	0.001091	T	0.29556	0.0737	M	0.89030	3	0.80722	D	1	D	0.59767	0.986	D	0.65573	0.936	T	0.16748	-1.0392	10	0.87932	D	0	-18.9994	15.3074	0.74004	0.0:0.0:0.0:1.0	.	205	O75317	UBP12_HUMAN	G	205	ENSP00000282344:D205G	ENSP00000282344:D205G	D	-	2	0	USP12	26562255	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.076000	0.71267	2.087000	0.62958	0.533000	0.62120	GAC	.	.		0.269	USP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044264.1	NM_182488		C	27664255	T	C	27664255	3	2	114	1	0	0	0	0	1	0	0	0	17058	1667	58	2	518	2	USP12	13	27664255	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1993349	27664255	87505623	849	19121										
USP12	219333	hgsc.bcm.edu	37	chr13	27679961	27679961	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctatggaagagatctgctaAgcatgtaagaaggctctcct	11	8	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:27679961A>G	ENST00000282344.6	-	3	506	c.250T>C	c.(250-252)Tta>Cta	p.L84L		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	84	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		AGATCTGCTAAGCATGTAAGA	0.388																																					p.L84L	Ovarian(37;808 911 7590 44442 44991)	Atlas-SNP	.											.	USP12	35	.	0			c.T250C						.						100	100	100					13																	27679961		2203	4298	6501	SO:0001819	synonymous_variant	219333	exon3			CTGCTAAGCATGT	AL049221	CCDS31952.1	13q12.13	2010-05-12	2005-08-08	2003-10-08	ENSG00000152484	ENSG00000152484		"Ubiquitin-specific peptidases"	20485	protein-coding gene	gene with protein product			"ubiquitin specific protease 12 like 1", "ubiquitin specific protease 12"	USP12L1		12838346	Standard	NM_182488		Approved		uc001uqy.3	O75317	OTTHUMG00000016626	ENST00000282344.6:c.250T>C	chr13.hg19:g.27679961A>G		60.0	0.0		54.0	4.0	NM_182488	A8K0X0|Q5VZV3|Q8TC49	Silent	SNP	ENST00000282344.6	hg19	CCDS31952.1																																																																																			.	.		0.388	USP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044264.1	NM_182488		G	27679961	A	G	27679961	2	3	114	1	0	0	0	0	0	0	0	1	17058	69	3	2		2	USP12	13	27679961	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	15706	27679961	87489917	850	19122										
PAN3	255967	hgsc.bcm.edu	37	chr13	28854573	28854573	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgttgactgaccaaaacagGatgcgaagtgtaaatgacat	10	6	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:28854573G>C	ENST00000380958.3	+	16	2366	c.2214G>C	c.(2212-2214)agG>agC	p.R738S	PAN3_ENST00000282391.5_Missense_Mutation_p.R426S|PAN3_ENST00000399613.1_Missense_Mutation_p.R538S	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit											endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		ACCAAAACAGGATGCGAAGTG	0.378																																					p.R738S		Atlas-SNP	.											.	PAN3	123	.	0			c.G2214C						.						142	125	131					13																	28854573		2203	4300	6503	SO:0001583	missense	255967	exon16			AAACAGGATGCGA	AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.2214G>C	chr13.hg19:g.28854573G>C	ENSP00000370345:p.Arg738Ser	75.0	0.0		73.0	48.0	NM_175854		Missense_Mutation	SNP	ENST00000380958.3	hg19	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	G	19.44	3.827725	0.71143	.	.	ENSG00000152520	ENST00000380958;ENST00000399613;ENST00000282391	T;T;T	0.41758	0.99;0.99;0.99	5.74	2.98	0.34508	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.57315	0.2045	M	0.71206	2.165	0.80722	D	1	D;D;D	0.71674	0.998;0.982;0.998	D;P;D	0.70487	0.969;0.873;0.937	T	0.51980	-0.8636	10	0.27785	T	0.31	-12.9652	10.1084	0.42548	0.2872:0.0:0.7128:0.0	.	738;426;684	Q58A45;Q58A45-2;Q58A45-3	PAN3_HUMAN;.;.	S	738;538;426	ENSP00000370345:R738S;ENSP00000382522:R538S;ENSP00000282391:R426S	ENSP00000282391:R426S	R	+	3	2	PAN3	27752573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.656000	0.24948	0.402000	0.25451	0.561000	0.74099	AGG	.	.		0.378	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854		C	28854573	G	C	28854573	3	2	114	1	0	0	0	0	1	0	0	0	11424	1165	41	4	2276	4	PAN3	13	28854573	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1174612	28854573	86315305	851	19123										
TRPC4	7223	hgsc.bcm.edu	37	chr13	38211176	38211176	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtcctccaccaccaccttcTctgacttgaatggacacact	5	16	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:38211176T>C	ENST00000379705.3	-	11	3655	c.2798A>G	c.(2797-2799)gAg>gGg	p.E933G	TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000338947.5_Missense_Mutation_p.E760G|TRPC4_ENST00000379679.1_Missense_Mutation_p.E760G|TRPC4_ENST00000358477.2_Missense_Mutation_p.E849G|TRPC4_ENST00000379673.2_Missense_Mutation_p.E784G|TRPC4_ENST00000355779.2_Missense_Mutation_p.E792G|TRPC4_ENST00000447043.1_Missense_Mutation_p.E792G|TRPC4_ENST00000379681.3_Missense_Mutation_p.E938G			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	933	Binds to ITPR1, ITPR2 and ITPR3.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CACCACCTTCTCTGACTTGAA	0.453																																					p.E938G		Atlas-SNP	.											.	TRPC4	389	.	0			c.A2813G						.						166	138	147					13																	38211176		2203	4300	6503	SO:0001583	missense	7223	exon11			ACCTTCTCTGACT	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2798A>G	chr13.hg19:g.38211176T>C	ENSP00000369027:p.Glu933Gly	183.0	0.0		125.0	5.0	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	hg19	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	T	14.92	2.679250	0.47886	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	T;T;T;T;T;T;T;T	0.75050	-0.39;-0.4;-0.21;-0.21;-0.64;-0.56;-0.9;-0.64	5.72	5.72	0.89469	.	0.279855	0.31335	N	0.007826	T	0.74642	0.3743	N	0.19112	0.55	0.80722	D	1	B;B;P;B;B;B	0.51933	0.058;0.042;0.949;0.039;0.223;0.079	B;B;P;B;B;B	0.58721	0.037;0.036;0.844;0.034;0.142;0.025	T	0.78486	-0.2185	10	0.72032	D	0.01	-18.7257	14.8693	0.70444	0.0:0.0:0.0:1.0	.	792;784;938;760;849;933	Q9UBN4-3;Q9UBN4-4;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;.;TRPC4_HUMAN	G	933;938;760;760;792;849;784;792	ENSP00000369027:E933G;ENSP00000369003:E938G;ENSP00000342580:E760G;ENSP00000369001:E760G;ENSP00000348025:E792G;ENSP00000351264:E849G;ENSP00000368995:E784G;ENSP00000414316:E792G	ENSP00000342580:E760G	E	-	2	0	TRPC4	37109176	1.000000	0.71417	0.998000	0.56505	0.763000	0.43281	2.632000	0.46511	2.311000	0.77944	0.533000	0.62120	GAG	.	.		0.453	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		C	38211176	T	C	38211176	3	2	114	1	0	0	0	0	1	0	0	0	16595	1551	54	2	139	2	TRPC4	13	38211176	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	9356603	38211176	76958702	852	19124										
ALG11	440138	hgsc.bcm.edu	37	chr13	52602568	52602568	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taactggctttctggctgagAgtgaagaagactatgctgaa	12	6	1	5			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:52602568A>G	ENST00000521508.1	+	4	1326	c.1321A>G	c.(1321-1323)Agt>Ggt	p.S441G	ALG11_ENST00000519151.1_3'UTR|UTP14C_ENST00000521776.2_5'UTR|ALG11_ENST00000523764.1_3'UTR	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	441					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0004377)			endometrium(1)|large_intestine(6)|lung(4)|ovary(2)	13		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.44e-08)		TCTGGCTGAGAGTGAAGAAGA	0.453																																					p.S441G		Atlas-SNP	.											.	ALG11	39	.	0			c.A1321G						.						124	111	116					13																	52602568		2203	4300	6503	SO:0001583	missense	440138	exon4			GCTGAGAGTGAAG	AK025456	CCDS31977.1	13q14.3	2013-02-22	2013-02-22		ENSG00000253710	ENSG00000253710	2.4.1.131	"Glycosyltransferase group 1 domain containing"	32456	protein-coding gene	gene with protein product	"GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"	613666	"asparagine-linked glycosylation 11 homolog (S. cerevisiae, alpha-1,2-mannosyltransferase)", "asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)"			20080937	Standard	NM_001004127		Approved	KIAA0266		Q2TAA5	OTTHUMG00000016959	ENST00000521508.1:c.1321A>G	chr13.hg19:g.52602568A>G	ENSP00000430236:p.Ser441Gly	115.0	0.0		99.0	4.0	NM_001004127	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Missense_Mutation	SNP	ENST00000521508.1	hg19	CCDS31977.1	.	.	.	.	.	.	.	.	.	.	A	12.45	1.942875	0.34283	.	.	ENSG00000253710	ENST00000521508	T	0.80653	-1.4	5.82	5.82	0.92795	Glycosyl transferase, family 1 (1);	0.344698	0.33110	U	0.005274	T	0.75613	0.3873	L	0.50333	1.59	0.29812	N	0.831557	B	0.06786	0.001	B	0.12156	0.007	T	0.70938	-0.4736	10	0.45353	T	0.12	.	12.0169	0.53319	0.9312:0.0:0.0688:0.0	.	441	Q2TAA5	ALG11_HUMAN	G	441	ENSP00000430236:S441G	ENSP00000430236:S441G	S	+	1	0	ALG11	51500569	0.005000	0.15991	0.935000	0.37517	0.881000	0.50899	1.821000	0.39041	2.225000	0.72522	0.460000	0.39030	AGT	.	.		0.453	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127		G	52602568	A	G	52602568	3	3	114	1	0	0	0	0	1	0	0	0	513	304	11	2	1335	2	ALG11	13	52602568	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	14391392	52602568	62567310	853	19125										
NEK3	4752	hgsc.bcm.edu	37	chr13	52707932	52707932	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtttcttcagacagggggccTttcaagaacccttctgaacc	9	12	4	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:52707932T>C	ENST00000400357.2	-	13	2571	c.1278A>G	c.(1276-1278)aaA>aaG	p.K426K	NEK3_ENST00000339406.3_Silent_p.K443K|NEK3_ENST00000378101.2_Silent_p.K443K|NEK3_ENST00000452082.2_Silent_p.K447K			P51956	NEK3_HUMAN	NIMA-related kinase 3	443					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		ACAGGGGGCCTTTCAAGAACC	0.413																																					p.K443K		Atlas-SNP	.											.	NEK3	41	.	0			c.A1329G						.						39	37	38					13																	52707932		1868	4110	5978	SO:0001819	synonymous_variant	4752	exon15			GGGGCCTTTCAAG	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"serine/threonine-protein kinase NEK3", "phosphorylase B kinase kinase", "glycogen synthase A kinase", "hydroxyalkyl-protein kinase"	604044	"NIMA (never in mitosis gene a)-related kinase 3"			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.1278A>G	chr13.hg19:g.52707932T>C		84.0	0.0		60.0	4.0	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Silent	SNP	ENST00000400357.2	hg19	CCDS53871.1																																																																																			.	.		0.413	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3			C	52707932	T	C	52707932	2	2	114	1	0	0	0	0	0	0	0	1	10334	1606	56	2		2	NEK3	13	52707932	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	105364	52707932	62461946	854	19126										
PCDH8	5100	hgsc.bcm.edu	37	chr13	53418699	53418699	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacatgcagcatgggattacAcattttcattggctcccttc	8	11	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:53418699A>G	ENST00000377942.3	-	3	3412	c.3209T>C	c.(3208-3210)gTg>gCg	p.V1070A	PCDH8_ENST00000338862.4_Missense_Mutation_p.V973A	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	1070					cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		ATGGGATTACACATTTTCATT	0.502																																					p.V1070A	GBM(36;25 841 9273 49207)	Atlas-SNP	.											.	PCDH8	95	.	0			c.T3209C						.						52	56	55					13																	53418699		2203	4300	6503	SO:0001583	missense	5100	exon3			GATTACACATTTT	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"Cadherins / Protocadherins : Non-clustered"	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.3209T>C	chr13.hg19:g.53418699A>G	ENSP00000367177:p.Val1070Ala	123.0	0.0		95.0	4.0	NM_002590	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	hg19	CCDS9438.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.043593	0.36085	.	.	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.56444	0.55;0.46	6.07	6.07	0.98685	.	0.000000	0.39834	N	0.001257	T	0.23210	0.0561	N	0.02011	-0.69	0.25048	N	0.991151	B;B	0.09022	0.001;0.002	B;B	0.10450	0.005;0.002	T	0.04255	-1.0965	10	0.87932	D	0	.	2.867	0.05604	0.6247:0.1518:0.0785:0.145	.	973;1070	O95206-2;O95206	.;PCDH8_HUMAN	A	1070;973;596;913	ENSP00000367177:V1070A;ENSP00000341350:V973A	ENSP00000341350:V973A	V	-	2	0	PCDH8	52316700	0.653000	0.27358	1.000000	0.80357	0.988000	0.76386	0.862000	0.27899	2.326000	0.78906	0.533000	0.62120	GTG	.	.		0.502	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590		G	53418699	A	G	53418699	3	3	114	1	0	0	0	0	1	0	0	0	11526	159	6	2	7	2	PCDH8	13	53418699	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	710767	53418699	61751179	855	19127										
DIS3	22894	hgsc.bcm.edu	37	chr13	73342977	73342977	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctagtttattcagtccacggAgactagtggtaatatcatca	8	8	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:73342977A>G	ENST00000377767.4	-	14	1929	c.1829T>C	c.(1828-1830)cTc>cCc	p.L610P	DIS3_ENST00000545453.1_Missense_Mutation_p.L448P|DIS3_ENST00000377780.4_Missense_Mutation_p.L580P	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	610					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		CAGTCCACGGAGACTAGTGGT	0.299										Multiple Myeloma(4;0.011)																											p.L610P		Atlas-SNP	.											.	DIS3	103	.	0			c.T1829C						.						84	86	85					13																	73342977		2201	4298	6499	SO:0001583	missense	22894	exon14			CCACGGAGACTAG	AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"exosome component 11"	607533	"KIAA1008", "DIS3 mitotic control homolog (S. cerevisiae)"	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.1829T>C	chr13.hg19:g.73342977A>G	ENSP00000366997:p.Leu610Pro	214.0	0.0		170.0	7.0	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	hg19	CCDS9447.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.641932	0.87859	.	.	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.63580	-0.05;-0.05;-0.05	5.87	5.87	0.94306	Ribonuclease II/R (2);	0.114481	0.64402	D	0.000016	D	0.87981	0.6315	H	0.98786	4.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.92806	0.6260	10	0.87932	D	0	.	16.2806	0.82678	1.0:0.0:0.0:0.0	.	580;610	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	P	610;580;448	ENSP00000366997:L610P;ENSP00000367011:L580P;ENSP00000440058:L448P	ENSP00000366997:L610P	L	-	2	0	DIS3	72240978	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.169000	0.94788	2.248000	0.74166	0.533000	0.62120	CTC	.	.		0.299	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953		G	73342977	A	G	73342977	3	3	114	1	0	0	0	0	1	0	0	0	4537	304	11	2	1079	2	DIS3	13	73342977	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	19924278	73342977	41826901	856	19128										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77798633	77798633	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcccatgctgcccataaccAaatgtatagacatctccatt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:77798633delA	ENST00000544440.2	-	20	2795	c.2778delT	c.(2776-2778)tttfs	p.F926fs	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Frame_Shift_Del_p.F926fs|MYCBP2_ENST00000407578.2_Frame_Shift_Del_p.F964fs					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		GCCCATAACCAAATGTATAGA	0.353																																					p.G965fs		Atlas-INDEL	.											.	MYCBP2	1029	.	0			c.2893delG						.						117	111	113					13																	77798633		2203	4300	6503	SO:0001589	frameshift_variant	23077	exon20			.	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.2778delT	chr13.hg19:g.77798633delA	ENSP00000444596:p.Phe926fs	218.0	0.0		157.0	11.0	NM_015057		Frame_Shift_Del	DEL	ENST00000544440.2	hg19																																																																																				.	.		0.353	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		-	77798633	A	-	77798633	7	5	114	1	0	1	0	1	0	0	0	0	10027	127	5	0	11400	0	MYCBP2	13	77798633	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	4455656	77798633	37371245	857	19129										
GPC5	2262	hgsc.bcm.edu	37	chr13	92345489	92345489	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agaaaattacaccagtatacTtttttgcagtacctacagga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:92345489delT	ENST00000377067.3	+	3	746	c.374delT	c.(373-375)cttfs	p.L125fs		NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	125					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				ACCAGTATACTTTTTTGCAGT	0.413																																					p.L125fs		Atlas-INDEL	.											.	GPC5	140	.	0			c.373delC						.						89	94	92					13																	92345489		2203	4300	6503	SO:0001589	frameshift_variant	2262	exon3			.	AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"Proteoglycans / Cell Surface : Glypicans"	4453	protein-coding gene	gene with protein product	"glypican proteoglycan 5"	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.374delT	chr13.hg19:g.92345489delT	ENSP00000366267:p.Leu125fs	162.0	0.0		166.0	10.0	NM_004466	B2R726|O60436|Q9BX27	Frame_Shift_Del	DEL	ENST00000377067.3	hg19	CCDS9468.1																																																																																			.	.		0.413	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466		-	92345489	T	-	92345489	7	5	114	1	0	1	0	1	0	0	0	0	6609	1609	56	0	384	0	GPC5	13	92345489	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	14546856	92345489	22824389	858	19130										
GPC5	2262	hgsc.bcm.edu	37	chr13	92345688	92345688	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacagttccctggaatactcAgaatgcatccggatggctcg	11	11	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:92345688A>G	ENST00000377067.3	+	3	945	c.573A>G	c.(571-573)tcA>tcG	p.S191S		NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	191					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				TGGAATACTCAGAATGCATCC	0.483																																					p.S191S		Atlas-SNP	.											.	GPC5	140	.	0			c.A573G						.						99	97	98					13																	92345688		2203	4300	6503	SO:0001819	synonymous_variant	2262	exon3			ATACTCAGAATGC	AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"Proteoglycans / Cell Surface : Glypicans"	4453	protein-coding gene	gene with protein product	"glypican proteoglycan 5"	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.573A>G	chr13.hg19:g.92345688A>G		85.0	0.0		74.0	5.0	NM_004466	B2R726|O60436|Q9BX27	Silent	SNP	ENST00000377067.3	hg19	CCDS9468.1																																																																																			.	.		0.483	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466		G	92345688	A	G	92345688	2	3	114	1	0	0	0	0	0	0	0	1	6609	175	7	2		2	GPC5	13	92345688	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	199	92345688	22824190	859	19131										
GPC5	2262	hgsc.bcm.edu	37	chr13	92797194	92797194	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgatgatgaagatggttgcGggggatcaggaagtggagaa					rs368333375		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:92797194delG	ENST00000377067.3	+	7	1885	c.1513delG	c.(1513-1515)gggfs	p.G506fs		NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	506					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				AGATGGTTGCGGGGGATCAGG	0.438																																					p.C504fs		Atlas-INDEL	.											GPC5,NS,carcinoma,0,1	GPC5	140	.	0			c.1512delC						.						164	140	148					13																	92797194		2203	4300	6503	SO:0001589	frameshift_variant	2262	exon7			.	AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"Proteoglycans / Cell Surface : Glypicans"	4453	protein-coding gene	gene with protein product	"glypican proteoglycan 5"	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.1513delG	chr13.hg19:g.92797194delG	ENSP00000366267:p.Gly506fs	169.0	0.0		160.0	10.0	NM_004466	B2R726|O60436|Q9BX27	Frame_Shift_Del	DEL	ENST00000377067.3	hg19	CCDS9468.1																																																																																			.	.		0.438	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466		-	92797194	G	-	92797194	7	5	114	1	0	1	0	1	0	0	0	0	6609	1116	39	0	1539	0	GPC5	13	92797194	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	451506	92797194	22372684	860	19132										
TM9SF2	9375	hgsc.bcm.edu	37	chr13	100191778	100191778	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aacaaggcttctggggagatAaaaattgcctatacttactc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:100191778delA	ENST00000376387.4	+	7	985	c.795delA	c.(793-795)atafs	p.I265fs		NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	265					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					CTGGGGAGATAAAAATTGCCT	0.373																																					p.I265fs		Atlas-INDEL	.											.	TM9SF2	52	.	0			c.794delT						.						122	131	128					13																	100191778		2203	4300	6503	SO:0001589	frameshift_variant	9375	exon7			.	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.795delA	chr13.hg19:g.100191778delA	ENSP00000365567:p.Ile265fs	152.0	0.0		131.0	12.0	NM_004800	A8K399|Q2TAY5	Frame_Shift_Del	DEL	ENST00000376387.4	hg19	CCDS9493.1																																																																																			.	.		0.373	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3			-	100191778	A	-	100191778	7	5	114	1	0	1	0	1	0	0	0	0	15993	352	13	0	821	0	TM9SF2	13	100191778	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	7394584	100191778	14978100	861	19133										
TPP2	7174	hgsc.bcm.edu	37	chr13	103268804	103268804	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtggcccttgcagaagcctGtagaaaacaggaagaatttg	12	7	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:103268804G>T	ENST00000376065.4	+	4	485	c.449G>T	c.(448-450)tGt>tTt	p.C150F	TPP2_ENST00000376052.3_Missense_Mutation_p.C150F	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	150	Peptidase S8.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)			breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GCAGAAGCCTGTAGAAAACAG	0.408																																					p.C150F		Atlas-SNP	.											.	TPP2	124	.	0			c.G449T						.						94	102	100					13																	103268804		2203	4300	6503	SO:0001583	missense	7174	exon4			AAGCCTGTAGAAA	M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.449G>T	chr13.hg19:g.103268804G>T	ENSP00000365233:p.Cys150Phe	58.0	0.0		73.0	38.0	NM_003291	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	hg19	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.841963	0.51057	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.64	5.64	0.86602	Peptidase S8/S53, subtilisin/kexin/sedolisin (2);	0.102040	0.64402	D	0.000001	T	0.48223	0.1488	L	0.29908	0.895	0.49389	D	0.999781	P	0.39601	0.68	B	0.36378	0.223	T	0.40961	-0.9535	9	0.30078	T	0.28	.	20.0769	0.97748	0.0:0.0:1.0:0.0	.	150	P29144	TPP2_HUMAN	F	150	.	ENSP00000365220:C150F	C	+	2	0	TPP2	102066805	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.172000	0.71932	2.820000	0.97059	0.650000	0.86243	TGT	.	.		0.408	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			T	103268804	G	T	103268804	3	4	114	1	0	0	0	0	1	0	0	0	16427	1377	48	3	463	3	TPP2	13	103268804	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	3077026	103268804	11901074	862	19134										
ARHGEF7	8874	hgsc.bcm.edu	37	chr13	111919988	111919988	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acgtattgtgccaatcacccTtctgcagtgaatgtcctcac	7	13	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:111919988T>C	ENST00000375741.2	+	10	1357	c.1107T>C	c.(1105-1107)ccT>ccC	p.P369P	ARHGEF7_ENST00000375739.2_Silent_p.P319P|ARHGEF7_ENST00000370623.3_Silent_p.P276P|ARHGEF7_ENST00000478679.1_Silent_p.P113P|ARHGEF7_ENST00000375723.1_Silent_p.P191P|ARHGEF7_ENST00000218789.5_Silent_p.P191P|ARHGEF7_ENST00000426073.2_Silent_p.P191P|ARHGEF7_ENST00000483189.1_3'UTR|ARHGEF7_ENST00000544132.1_Missense_Mutation_p.F72L|ARHGEF7_ENST00000375737.5_Silent_p.P266P|ARHGEF7_ENST00000375736.4_Silent_p.P191P|ARHGEF7_ENST00000317133.5_Silent_p.P348P	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	369	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CCAATCACCCTTCTGCAGTGA	0.517																																					p.P369P		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.T1107C						.						181	130	147					13																	111919988		2203	4300	6503	SO:0001819	synonymous_variant	8874	exon10			TCACCCTTCTGCA	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.1107T>C	chr13.hg19:g.111919988T>C		90.0	0.0		96.0	4.0	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Silent	SNP	ENST00000375741.2	hg19	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	T	14.09	2.432566	0.43224	.	.	ENSG00000102606	ENST00000544132	.	.	.	4.29	-7.74	0.01241	.	.	.	.	.	T	0.09468	0.0233	.	.	.	0.23309	N	0.997931	.	.	.	.	.	.	T	0.32771	-0.9894	5	0.02654	T	1	.	5.4464	0.16537	0.2787:0.0:0.3891:0.3322	.	.	.	.	L	72	.	ENSP00000445384:F72L	F	+	1	0	ARHGEF7	110717989	0.000000	0.05858	0.952000	0.39060	0.885000	0.51271	-2.928000	0.00690	-1.052000	0.03222	-1.304000	0.01323	TTC	.	.		0.517	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511		C	111919988	T	C	111919988	2	2	114	1	0	0	0	0	0	0	0	1	911	1596	56	2		2	ARHGEF7	13	111919988	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	8651184	111919988	3249890	863	19135										
TUBGCP3	10426	hgsc.bcm.edu	37	chr13	113170854	113170854	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctccagaggaagttaaatacTcttaggtagtggctcataca	9	8	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:113170854T>C	ENST00000261965.3	-	17	2172	c.1986A>G	c.(1984-1986)agA>agG	p.R662R	TUBGCP3_ENST00000375669.3_Silent_p.R662R	NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	662					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					AGTTAAATACTCTTAGGTAGT	0.463																																					p.R662R		Atlas-SNP	.											.	TUBGCP3	74	.	0			c.A1986G						.						119	100	107					13																	113170854		2203	4300	6503	SO:0001819	synonymous_variant	10426	exon17			AAATACTCTTAGG	AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"spindle pole body protein"					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.1986A>G	chr13.hg19:g.113170854T>C		87.0	0.0		95.0	4.0	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Silent	SNP	ENST00000261965.3	hg19	CCDS9525.1																																																																																			.	.		0.463	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322		C	113170854	T	C	113170854	2	2	114	1	0	0	0	0	0	0	0	1	16782	1548	54	2		2	TUBGCP3	13	113170854	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1250866	113170854	1999024	864	19136										
OR4K17	390436	hgsc.bcm.edu	37	chr14	20586015	20586015	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtactgttggtctccatggcTtttgacagatatgtggccat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:20586015delT	ENST00000315543.4	+	1	450	c.450delT	c.(448-450)gctfs	p.A150fs		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		TCTCCATGGCTTTTGACAGAT	0.433																																					p.A150fs		Atlas-INDEL	.											.	OR4K17	58	.	0			c.449delC						.						167	144	152					14																	20586015		2203	4300	6503	SO:0001589	frameshift_variant	390436	exon1			.		CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"GPCR / Class A : Olfactory receptors"	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.450delT	chr14.hg19:g.20586015delT	ENSP00000319197:p.Ala150fs	146.0	0.0		176.0	11.0	NM_001004715	Q6IF12	Frame_Shift_Del	DEL	ENST00000315543.4	hg19	CCDS32030.1																																																																																			.	.		0.433	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1			-	20586015	T	-	20586015	7	5	114	1	0	1	0	1	0	0	0	0	11080	1596	56	0	452	0	OR4K17	14	20586015	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10		20586015	86763525	865	19137										
TEP1	7011	hgsc.bcm.edu	37	chr14	20846338	20846338	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagccggcccacagccacaaCccccccaggcacattgaagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:20846338delC	ENST00000262715.5	-	39	5606	c.5566delG	c.(5566-5568)gttfs	p.V1857fs	TEP1_ENST00000556935.1_Frame_Shift_Del_p.V1749fs|TEP1_ENST00000545983.1_Frame_Shift_Del_p.V195fs	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1857					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		ACAGCCACAACCCCCCCAGGC	0.627																																					p.V1856fs		Atlas-INDEL	.											.	TEP1	224	.	0			c.5567delT						.						63	70	68					14																	20846338		2203	4300	6503	SO:0001589	frameshift_variant	7011	exon39			.		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5566delG	chr14.hg19:g.20846338delC	ENSP00000262715:p.Val1857fs	154.0	0.0		174.0	13.0	NM_007110	A0AUV9	Frame_Shift_Del	DEL	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	.		0.627	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		-	20846338	C	-	20846338	7	5	114	1	0	1	0	1	0	0	0	0	15774	507	18	0	2385	0	TEP1	14	20846338	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	260323	20846338	86503202	866	19138										
JPH4	84502	hgsc.bcm.edu	37	chr14	24040276	24040276	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcctgctggggccctcagcGggggcaggggctcttcatcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:24040276delG	ENST00000397118.3	-	6	2566	c.1664delC	c.(1663-1665)ccgfs	p.P555fs	RP11-66N24.3_ENST00000555968.1_RNA|JPH4_ENST00000544177.1_Frame_Shift_Del_p.P220fs|JPH4_ENST00000356300.4_Frame_Shift_Del_p.P555fs|AP1G2_ENST00000308724.5_5'Flank	NM_032452.2	NP_115828.2	Q96JJ6	JPH4_HUMAN	junctophilin 4	555					calcium ion transport into cytosol (GO:0060402)|learning (GO:0007612)|neuromuscular process controlling balance (GO:0050885)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic plasticity (GO:0048167)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)				endometrium(1)|large_intestine(2)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		GGCCCTCAGCGGGGGCAGGGG	0.677																																					p.P555fs		Atlas-INDEL	.											.	JPH4	64	.	0			c.1665delG						.						52	57	56					14																	24040276		2203	4300	6503	SO:0001589	frameshift_variant	84502	exon5			.	AB058734	CCDS9603.1	14q11	2004-05-28	2004-05-28	2004-05-28	ENSG00000092051	ENSG00000092051			20156	protein-coding gene	gene with protein product			"junctophilin like 1"	JPHL1		11347906	Standard	NM_032452		Approved	KIAA1831	uc001wkr.2	Q96JJ6	OTTHUMG00000028769	ENST00000397118.3:c.1664delC	chr14.hg19:g.24040276delG	ENSP00000380307:p.Pro555fs	127.0	0.0		167.0	11.0	NM_001146028	D3DS53|Q8ND44|Q96DQ0	Frame_Shift_Del	DEL	ENST00000397118.3	hg19	CCDS9603.1																																																																																			.	.		0.677	JPH4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413853.1	NM_032452		-	24040276	G	-	24040276	7	5	114	1	0	1	0	1	0	0	0	0	7972	1116	39	0	230	0	JPH4	14	24040276	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	3193938	24040276	83309264	867	19139										
RIPK3	11035	hgsc.bcm.edu	37	chr14	24807655	24807655	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgtcactggctgtggaggccTtccggtttacgttaacaaac	11	11	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:24807655T>C	ENST00000216274.5	-	4	808	c.590A>G	c.(589-591)aAg>aGg	p.K197R	RP11-934B9.3_ENST00000555591.1_5'Flank|RIPK3_ENST00000554338.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	197	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		TGTGGAGGCCTTCCGGTTTAC	0.587																																					p.K197R	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.A590G						.						129	136	133					14																	24807655		2203	4300	6503	SO:0001583	missense	11035	exon4			GAGGCCTTCCGGT	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.590A>G	chr14.hg19:g.24807655T>C	ENSP00000216274:p.Lys197Arg	47.0	0.0		72.0	4.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	hg19	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.652481	0.29336	.	.	ENSG00000129465	ENST00000216274	T	0.66280	-0.2	4.51	-0.947	0.10382	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.573247	0.15817	N	0.243178	T	0.51719	0.1691	N	0.11000	0.08	0.09310	N	1	D	0.57899	0.981	D	0.66602	0.945	T	0.50355	-0.8838	10	0.16420	T	0.52	-17.8474	7.8234	0.29300	0.0:0.4955:0.0:0.5045	.	197	Q9Y572	RIPK3_HUMAN	R	197	ENSP00000216274:K197R	ENSP00000216274:K197R	K	-	2	0	RIPK3	23877495	0.000000	0.05858	0.001000	0.08648	0.206000	0.24218	-0.205000	0.09411	-0.036000	0.13669	0.459000	0.35465	AAG	.	.		0.587	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		C	24807655	T	C	24807655	3	2	114	1	0	0	0	0	1	0	0	0	13397	1609	56	2	994	2	RIPK3	14	24807655	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	767379	24807655	82541885	868	19140										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31576779	31576779	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agaaatattcttacgtgacgAgattcatcatctggaaaatt	7	6	4	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:31576779A>G	ENST00000399332.1	-	37	7100	c.6612T>C	c.(6610-6612)tcT>tcC	p.S2204S	HECTD1_ENST00000553700.1_Silent_p.S2204S	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2204	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTACGTGACGAGATTCATCAT	0.398																																					p.S2204S		Atlas-SNP	.											.	HECTD1	159	.	0			c.T6612C						.						77	71	73					14																	31576779		1874	4116	5990	SO:0001819	synonymous_variant	25831	exon37			GTGACGAGATTCA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.6612T>C	chr14.hg19:g.31576779A>G		55.0	0.0		54.0	4.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	A	5.588	0.293241	0.10567	.	.	ENSG00000092148	ENST00000554882	.	.	.	5.55	3.16	0.36331	.	.	.	.	.	T	0.45438	0.1342	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31971	-0.9924	4	.	.	.	-11.5924	2.1063	0.03692	0.5933:0.134:0.1439:0.1288	.	.	.	.	P	570	.	.	L	-	2	0	HECTD1	30646530	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.764000	0.26532	0.381000	0.24851	-1.506000	0.00953	CTC	.	.		0.398	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			G	31576779	A	G	31576779	2	3	114	1	0	0	0	0	0	0	0	1	7048	291	11	2		2	HECTD1	14	31576779	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	6769124	31576779	75772761	869	19141										
NUBPL	80224	hgsc.bcm.edu	37	chr14	32142559	32142559	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agaggattttttttttttccAggcaacctaatgaggcctct	8	8	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:32142559A>C	ENST00000281081.7	+	5	427		c.e5-1		NUBPL_ENST00000536705.1_Splice_Site	NM_001201573.1|NM_001201574.1|NM_025152.2	NP_001188502.1|NP_001188503.1|NP_079428.2	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like						mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrion morphogenesis (GO:0070584)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)|prostate(1)|skin(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		TTTTTTTTCCAGGCAACCTAA	0.244																																					.		Atlas-SNP	.											.	NUBPL	21	.	0			c.383-2A>C						.						33	32	32					14																	32142559		1786	4058	5844	SO:0001630	splice_region_variant	80224	exon5			TTTTCCAGGCAAC	AK022722	CCDS41940.1	14q12	2012-10-12	2005-01-07	2005-01-07	ENSG00000151413	ENSG00000151413		"Mitochondrial respiratory chain complex assembly factors"	20278	protein-coding gene	gene with protein product	"iron-sulfur protein required for NADH dehydrogenase"	613621	"chromosome 14 open reading frame 127"	C14orf127			Standard	NM_025152		Approved	FLJ12660, IND1, huInd1	uc001wrk.4	Q8TB37	OTTHUMG00000170521	ENST00000281081.7:c.383-1A>C	chr14.hg19:g.32142559A>C		51.0	0.0		60.0	4.0	NM_025152	B4DHZ1|Q86TZ4|Q9H9M2	Splice_Site	SNP	ENST00000281081.7	hg19	CCDS41940.1	.	.	.	.	.	.	.	.	.	.	A	14.46	2.543163	0.45280	.	.	ENSG00000151413	ENST00000281081;ENST00000551314;ENST00000536705	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3964	0.60856	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NUBPL	31212310	1.000000	0.71417	0.964000	0.40570	0.465000	0.32709	7.779000	0.85648	2.097000	0.63578	0.455000	0.32223	.	.	.		0.244	NUBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409519.1	NM_025152	Intron	C	32142559	A	C	32142559	5	2	114	1	0	0	0	0	0	0	1	0	10726	202	7	5	399	5	NUBPL	14	32142559	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	565780	32142559	75206981	870	19142										
PAX9	5083	hgsc.bcm.edu	37	chr14	37132384	37132384	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctacaagcagagagaccccgGcatcttcgcctgggagatcc	11	14	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:37132384G>A	ENST00000361487.6	+	2	512	c.287G>A	c.(286-288)gGc>gAc	p.G96D	PAX9_ENST00000554201.1_5'UTR|PAX9_ENST00000402703.2_Missense_Mutation_p.G96D			P55771	PAX9_HUMAN	paired box 9	96	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				cellular response to growth factor stimulus (GO:0071363)|endoderm development (GO:0007492)|face morphogenesis (GO:0060325)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|regulation of odontogenesis (GO:0042481)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(3)	12	Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.218)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.00998)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0181)		AGAGACCCCGGCATCTTCGCC	0.647																																					p.G96D		Atlas-SNP	.											.	PAX9	34	.	0			c.G287A						.						64	67	66					14																	37132384		2203	4300	6503	SO:0001583	missense	5083	exon3			ACCCCGGCATCTT	AJ238381	CCDS9662.1	14q13.3	2007-07-12	2007-07-12		ENSG00000198807	ENSG00000198807		"Paired boxes"	8623	protein-coding gene	gene with protein product		167416	"paired box gene 9"			7981748	Standard	NM_006194		Approved		uc001wty.4	P55771	OTTHUMG00000140251	ENST00000361487.6:c.287G>A	chr14.hg19:g.37132384G>A	ENSP00000355245:p.Gly96Asp	112.0	0.0		184.0	11.0	NM_006194	Q99582|Q9UQR4	Missense_Mutation	SNP	ENST00000361487.6	hg19	CCDS9662.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.961383	0.92791	.	.	ENSG00000198807	ENST00000402703;ENST00000361487	D;D	0.99245	-5.62;-5.62	5.21	5.21	0.72293	Paired box protein, N-terminal (3);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99387	0.9784	M	0.79343	2.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99177	1.0866	10	0.87932	D	0	.	18.742	0.91777	0.0:0.0:1.0:0.0	.	96	P55771	PAX9_HUMAN	D	96	ENSP00000384817:G96D;ENSP00000355245:G96D	ENSP00000355245:G96D	G	+	2	0	PAX9	36202135	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.440000	0.82611	0.561000	0.74099	GGC	.	.		0.647	PAX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276733.2			A	37132384	G	A	37132384	3	1	114	1	0	0	0	0	1	0	0	0	11495	1203	42	3	293	3	PAX9	14	37132384	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	4989825	37132384	70217156	871	19143										
PNN	5411	hgsc.bcm.edu	37	chr14	39648419	39648419	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taaacagacagaactgcggcTtttggaacagaaagttgagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:39648419delT	ENST00000216832.4	+	7	690	c.623delT	c.(622-624)cttfs	p.L209fs	PNN_ENST00000557680.1_3'UTR|PNN_ENST00000553331.1_3'UTR	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	209	Glu-rich.|Necessary for interaction with RNPS1.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		GAACTGCGGCTTTTGGAACAG	0.418																																					p.L208fs		Atlas-INDEL	.											.	PNN	67	.	0			c.622delC						.						127	131	130					14																	39648419		2203	4300	6503	SO:0001589	frameshift_variant	5411	exon7			.	U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.623delT	chr14.hg19:g.39648419delT	ENSP00000216832:p.Leu209fs	106.0	0.0		145.0	11.0	NM_002687	B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	Frame_Shift_Del	DEL	ENST00000216832.4	hg19	CCDS9671.1																																																																																			.	.		0.418	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687		-	39648419	T	-	39648419	7	5	114	1	0	1	0	1	0	0	0	0	12169	1609	56	0	649	0	PNN	14	39648419	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2516035	39648419	67701121	872	19144										
FANCM	57697	hgsc.bcm.edu	37	chr14	45654537	45654537	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagattcctcattacttgacTttttaaatgatgaaactcaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:45654537delT	ENST00000267430.5	+	18	4718	c.4633delT	c.(4633-4635)tttfs	p.F1545fs	FANCM_ENST00000555013.1_3'UTR|FANCM_ENST00000542564.2_Frame_Shift_Del_p.F1519fs	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1545					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						ATTACTTGACTTTTTAAATGA	0.269								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.D1544fs		Atlas-INDEL	.											.	FANCM	225	.	0			c.4632delC						.						62	63	63					14																	45654537		2203	4292	6495	SO:0001589	frameshift_variant	57697	exon18	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.4633delT	chr14.hg19:g.45654537delT	ENSP00000267430:p.Phe1545fs	153.0	0.0		188.0	13.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Frame_Shift_Del	DEL	ENST00000267430.5	hg19	CCDS32070.1																																																																																			.	.		0.269	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		-	45654537	T	-	45654537	7	5	114	1	0	1	0	1	0	0	0	0	5679	1609	56	0	4703	0	FANCM	14	45654537	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	6006118	45654537	61695003	873	19145										
SAMD4A	23034	hgsc.bcm.edu	37	chr14	55231225	55231225	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaggaaaatataagttcctaTttacagctcatagacaagtg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:55231225delT	ENST00000554335.1	+	8	2226	c.1563delT	c.(1561-1563)tatfs	p.Y521fs	SAMD4A_ENST00000357634.3_Frame_Shift_Del_p.Y520fs|SAMD4A_ENST00000251091.5_Frame_Shift_Del_p.Y433fs|SAMD4A_ENST00000555192.1_Frame_Shift_Del_p.Y112fs|SAMD4A_ENST00000392067.3_Frame_Shift_Del_p.Y521fs			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	521					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						TAAGTTCCTATTTACAGCTCA	0.343																																					p.Y521fs		Atlas-INDEL	.											.	SAMD4A	68	.	0			c.1562delA						.						151	159	156					14																	55231225		2203	4300	6503	SO:0001589	frameshift_variant	23034	exon7			.	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"Sterile alpha motif (SAM) domain containing"	23023	protein-coding gene	gene with protein product	"smaug homolog (Drosophila)"	610747	"sterile alpha motif domain containing 4"	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1563delT	chr14.hg19:g.55231225delT	ENSP00000452535:p.Tyr521fs	81.0	0.0		121.0	10.0	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Frame_Shift_Del	DEL	ENST00000554335.1	hg19	CCDS32084.2																																																																																			.	.		0.343	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		-	55231225	T	-	55231225	7	5	114	1	0	1	0	1	0	0	0	0	13836	1500	52	0	1586	0	SAMD4A	14	55231225	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	9576688	55231225	52118315	874	19146										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64494280	64494280	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agattaatgctcatagaactAaagaagaaacaggaagcagg	10	5	1	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:64494280A>T	ENST00000344113.4	+	43	6695	c.6483A>T	c.(6481-6483)ctA>ctT	p.L2161L	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.L2161L|SYNE2_ENST00000358025.3_Silent_p.L2161L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2161					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TCATAGAACTAAAGAAGAAAC	0.343																																					p.L2161L		Atlas-SNP	.											.	SYNE2	577	.	0			c.A6483T						.						90	84	86					14																	64494280		1809	4077	5886	SO:0001819	synonymous_variant	23224	exon43			AGAACTAAAGAAG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.6483A>T	chr14.hg19:g.64494280A>T		125.0	0.0		145.0	6.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.343	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64494280	A	T	64494280	2	4	114	1	0	0	0	0	0	0	0	1	15461	349	13	4		4	SYNE2	14	64494280	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	9263055	64494280	42855260	875	19147										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64518666	64518666	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tccaggctaccaagcatggaTtttctgttttaaaggggcaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:64518666delT	ENST00000344113.4	+	48	8247	c.8035delT	c.(8035-8037)tttfs	p.F2679fs	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Frame_Shift_Del_p.F2712fs|SYNE2_ENST00000358025.3_Frame_Shift_Del_p.F2679fs	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2679					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		CAAGCATGGATTTTCTGTTTT	0.433																																					p.G2678fs		Atlas-INDEL	.											.	SYNE2	577	.	0			c.8034delA						.						91	91	91					14																	64518666		1907	4118	6025	SO:0001589	frameshift_variant	23224	exon48			.	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.8035delT	chr14.hg19:g.64518666delT	ENSP00000341781:p.Phe2679fs	153.0	0.0		186.0	12.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Frame_Shift_Del	DEL	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.433	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		-	64518666	T	-	64518666	7	5	114	1	0	1	0	1	0	0	0	0	15461	1493	52	0	8221	0	SYNE2	14	64518666	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	24386	64518666	42830874	876	19148										
ACTN1	87	hgsc.bcm.edu	37	chr14	69345708	69345708	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catgcaggaggcgagtacctGggggtcgttgccaatatcat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:69345708delG	ENST00000193403.6	-	19	2742	c.2359delC	c.(2359-2361)cagfs	p.Q787fs	ACTN1_ENST00000376839.3_Intron|ACTN1_ENST00000538545.2_Intron|ACTN1_ENST00000394419.4_Frame_Shift_Del_p.Q787fs|ACTN1_ENST00000438964.2_Intron	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	787	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GCGAGTACCTGGGGGTCGTTG	0.582																																					p.Q787fs		Atlas-INDEL	.											.	ACTN1	77	.	0			c.2360delA						.						198	197	197					14																	69345708		2203	4300	6503	SO:0001589	frameshift_variant	87	exon19			.	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"EF-hand domain containing"	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.2359delC	chr14.hg19:g.69345708delG	ENSP00000193403:p.Gln787fs	147.0	0.0		176.0	11.0	NM_001102	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Frame_Shift_Del	DEL	ENST00000193403.6	hg19	CCDS9792.1																																																																																			.	.		0.582	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		-	69345708	G	-	69345708	7	5	114	1	0	1	0	1	0	0	0	0	204	1357	47	0	401	0	ACTN1	14	69345708	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	4827042	69345708	38003832	877	19149										
PCNX	22990	hgsc.bcm.edu	37	chr14	71522272	71522272	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttggcttcccagcttgatagAaatccaggtaatagctctat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:71522272delA	ENST00000304743.2	+	25	5075	c.4629delA	c.(4627-4629)agafs	p.R1543fs	PCNX_ENST00000439984.3_Frame_Shift_Del_p.R1432fs|PCNX_ENST00000238570.5_Frame_Shift_Del_p.R1543fs	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1543						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		AGCTTGATAGAAATCCAGGTA	0.308																																					p.R1543fs		Atlas-INDEL	.											.	PCNX	198	.	0			c.4628delG						.						109	117	114					14																	71522272		2203	4300	6503	SO:0001589	frameshift_variant	22990	exon25			.	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4629delA	chr14.hg19:g.71522272delA	ENSP00000304192:p.Arg1543fs	171.0	0.0		192.0	12.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Frame_Shift_Del	DEL	ENST00000304743.2	hg19	CCDS9806.1																																																																																			.	.		0.308	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		-	71522272	A	-	71522272	7	5	114	1	0	1	0	1	0	0	0	0	11600	243	9	0	4727	0	PCNX	14	71522272	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2176564	71522272	35827268	878	19150										
RGS6	9628	hgsc.bcm.edu	37	chr14	72985093	72985093	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tccaagatcttaagaaacaaCccctacaggatgtggccaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:72985093delC	ENST00000553530.1	+	15	1333	c.1126delC	c.(1126-1128)cccfs	p.P376fs	RGS6_ENST00000553525.1_Frame_Shift_Del_p.P376fs|RGS6_ENST00000554782.1_Frame_Shift_Del_p.P237fs|RGS6_ENST00000407322.4_Frame_Shift_Del_p.P376fs|RGS6_ENST00000404301.2_Frame_Shift_Del_p.P376fs|RGS6_ENST00000406236.4_Frame_Shift_Del_p.P376fs|RGS6_ENST00000402788.2_Frame_Shift_Del_p.P376fs|RGS6_ENST00000556437.1_Frame_Shift_Del_p.P376fs|RGS6_ENST00000555571.1_Frame_Shift_Del_p.P376fs|RGS6_ENST00000434263.2_Frame_Shift_Del_p.P307fs|RGS6_ENST00000355512.6_Frame_Shift_Del_p.P376fs|RGS6_ENST00000343854.6_Frame_Shift_Del_p.P339fs	NM_001204417.1|NM_001204418.1|NM_001204420.1|NM_001204421.1|NM_001204422.1|NM_004296.5	NP_001191346.1|NP_001191347.1|NP_001191349.1|NP_001191350.1|NP_001191351.1|NP_004287.3	P49758	RGS6_HUMAN	regulator of G-protein signaling 6	376	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neuron differentiation (GO:0045666)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		TAAGAAACAACCCCTACAGGA	0.522																																					p.Q375fs	Ovarian(143;1926 2468 21071 48641)	Atlas-INDEL	.											.	RGS6	92	.	0			c.1125delA						.						74	74	74					14																	72985093		2203	4300	6503	SO:0001589	frameshift_variant	9628	exon15			.	AF073920	CCDS9808.1, CCDS55924.1, CCDS73655.1	14q24.3	2008-07-28	2007-08-14			ENSG00000182732		"Regulators of G-protein signaling"	10002	protein-coding gene	gene with protein product		603894	"regulator of G-protein signalling 6"			10083744, 14734556	Standard	NM_004296		Approved		uc010ttn.2	P49758		ENST00000553530.1:c.1126delC	chr14.hg19:g.72985093delC	ENSP00000452331:p.Pro376fs	110.0	0.0		171.0	14.0	NM_001204424	C9JE95|F8W7W5|O75576|O75577|Q7Z4K3|Q7Z4K4|Q7Z4K5|Q7Z4K6|Q8TE13|Q8TE14|Q8TE15|Q8TE16|Q8TE17|Q8TE18|Q8TE19|Q8TE20|Q8TE21|Q8TE22|Q9UDS8|Q9UDT0|Q9Y245|Q9Y647	Frame_Shift_Del	DEL	ENST00000553530.1	hg19	CCDS9808.1																																																																																			.	.		0.522	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2			-	72985093	C	-	72985093	7	5	114	1	0	1	0	1	0	0	0	0	13324	507	18	0	1180	0	RGS6	14	72985093	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1462821	72985093	34364447	879	19151										
NUMB	8650	hgsc.bcm.edu	37	chr14	73753987	73753987	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgcgctctaaacaggctgcAaaagcacagcctactgcatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:73753987delA	ENST00000355058.3	-	9	764	c.486delT	c.(484-486)tttfs	p.F162fs	NUMB_ENST00000555238.1_Frame_Shift_Del_p.F162fs|NUMB_ENST00000555738.2_Frame_Shift_Del_p.F151fs|NUMB_ENST00000560335.1_Frame_Shift_Del_p.F162fs|NUMB_ENST00000554546.1_Frame_Shift_Del_p.F151fs|NUMB_ENST00000554521.2_Frame_Shift_Del_p.F151fs|NUMB_ENST00000559312.1_Frame_Shift_Del_p.F162fs|NUMB_ENST00000356296.4_Frame_Shift_Del_p.F162fs|NUMB_ENST00000535282.1_Frame_Shift_Del_p.F151fs|NUMB_ENST00000555394.1_Frame_Shift_Del_p.F162fs|NUMB_ENST00000359560.3_Frame_Shift_Del_p.F151fs|NUMB_ENST00000557597.1_Frame_Shift_Del_p.F151fs|NUMB_ENST00000544991.3_Frame_Shift_Del_p.F162fs|NUMB_ENST00000454166.4_Frame_Shift_Del_p.F162fs|NUMB_ENST00000556772.1_Frame_Shift_Del_p.F18fs			P49757	NUMB_HUMAN	numb homolog (Drosophila)	162	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		AACAGGCTGCAAAAGCACAGC	0.423																																					p.A163fs		Atlas-INDEL	.											.	NUMB	56	.	0			c.487delG						.						83	71	75					14																	73753987		2203	4300	6503	SO:0001589	frameshift_variant	8650	exon9			.	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"numb (Drosophila) homolog", "chromosome 14 open reading frame 41"	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.486delT	chr14.hg19:g.73753987delA	ENSP00000347169:p.Phe162fs	147.0	0.0		164.0	10.0	NM_001005744	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Frame_Shift_Del	DEL	ENST00000355058.3	hg19	CCDS32116.1																																																																																			.	.		0.423	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1			-	73753987	A	-	73753987	7	5	114	1	0	1	0	1	0	0	0	0	10760	127	5	0	1489	0	NUMB	14	73753987	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	768894	73753987	33595553	880	19152										
ENTPD5	957	hgsc.bcm.edu	37	chr14	74443074	74443074	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtggaggctccccctaggtCcaaggtccccacagtctcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:74443074delC	ENST00000334696.6	-	9	914	c.595delG	c.(595-597)gacfs	p.D199fs	ENTPD5_ENST00000557325.1_Frame_Shift_Del_p.D199fs	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	199					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		CCCCCTAGGTCCAAGGTCCCC	0.537																																					p.D199fs		Atlas-INDEL	.											.	ENTPD5	26	.	0			c.596delA						.						103	88	93					14																	74443074		2203	4300	6503	SO:0001589	frameshift_variant	957	exon9			.	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"proto-oncogene CPH"	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.595delG	chr14.hg19:g.74443074delC	ENSP00000335246:p.Asp199fs	109.0	0.0		147.0	10.0	NM_001249	A1L4C5|Q96RX0	Frame_Shift_Del	DEL	ENST00000334696.6	hg19	CCDS9825.1																																																																																			.	.		0.537	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249		-	74443074	C	-	74443074	7	5	114	1	0	1	0	1	0	0	0	0	5144	855	30	0	723	0	ENTPD5	14	74443074	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	689087	74443074	32906466	881	19153										
ENTPD5	957	hgsc.bcm.edu	37	chr14	74453565	74453565	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtcctggcttcacagaatcAaaaacttccccttctagaat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:74453565delA	ENST00000334696.6	-	5	568	c.249delT	c.(247-249)tttfs	p.F83fs	ENTPD5_ENST00000557325.1_Frame_Shift_Del_p.F83fs|ENTPD5_ENST00000554664.1_5'Flank|ENTPD5_ENST00000556242.1_3'UTR	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	83					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		TCACAGAATCAAAAACTTCCC	0.403																																					p.D84fs		Atlas-INDEL	.											.,1	ENTPD5	26	.	0			c.250delG						.						113	105	108					14																	74453565		2203	4300	6503	SO:0001589	frameshift_variant	957	exon5			.	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"proto-oncogene CPH"	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.249delT	chr14.hg19:g.74453565delA	ENSP00000335246:p.Phe83fs	162.0	0.0		201.0	13.0	NM_001249	A1L4C5|Q96RX0	Frame_Shift_Del	DEL	ENST00000334696.6	hg19	CCDS9825.1																																																																																			.	.		0.403	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249		-	74453565	A	-	74453565	7	5	114	1	0	1	0	1	0	0	0	0	5144	127	5	0	1085	0	ENTPD5	14	74453565	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	10491	74453565	32895975	882	19154										
YLPM1	56252	hgsc.bcm.edu	37	chr14	75264632	75264632	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtaaccagcagaagaattttAaaatgcaatcagctgcattt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:75264632delA	ENST00000325680.7	+	5	2756	c.2632delA	c.(2632-2634)aaafs	p.K878fs	YLPM1_ENST00000238571.3_Frame_Shift_Del_p.K683fs|YLPM1_ENST00000552421.1_Intron	NM_019589.2	NP_062535.2	P49750	YLPM1_HUMAN	YLP motif containing 1	683	Arg-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		GAAGAATTTTAAAATGCAATC	0.438																																					p.F877fs		Atlas-INDEL	.											.	YLPM1	298	.	0			c.2631delT						.						63	61	62					14																	75264632		1891	4114	6005	SO:0001589	frameshift_variant	56252	exon5			.	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000325680.7:c.2632delA	chr14.hg19:g.75264632delA	ENSP00000324463:p.Lys878fs	146.0	0.0		194.0	12.0	NM_019589	P49752|Q96I64|Q9P1V7	Frame_Shift_Del	DEL	ENST00000325680.7	hg19	CCDS45135.1																																																																																			.	.		0.438	YLPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404451.1	NM_019589		-	75264632	A	-	75264632	7	5	114	1	0	1	0	1	0	0	0	0	17501	363	13	0	2650	0	YLPM1	14	75264632	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	811067	75264632	32084908	883	19155										
GSTZ1	2954	hgsc.bcm.edu	37	chr14	77797449	77797449	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccccctaccctaccatcagcTccatcaacaagaggctgctg	6	18	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:77797449T>C	ENST00000556627.1	+	8	612	c.481T>C	c.(481-483)Tcc>Ccc	p.S161P	GSTZ1_ENST00000557053.1_Missense_Mutation_p.S91P|GSTZ1_ENST00000393734.1_Missense_Mutation_p.S133P|GSTZ1_ENST00000216465.5_Missense_Mutation_p.S188P|GSTZ1_ENST00000557639.1_Missense_Mutation_p.S133P|GSTZ1_ENST00000361389.4_Missense_Mutation_p.S133P|GSTZ1_ENST00000553586.1_Missense_Mutation_p.S189P|GSTZ1_ENST00000554279.1_Missense_Mutation_p.S174P|GSTZ1_ENST00000349555.3_Missense_Mutation_p.S146P			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	188	GST C-terminal.				cellular nitrogen compound metabolic process (GO:0034641)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|L-phenylalanine catabolic process (GO:0006559)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|maleylacetoacetate isomerase activity (GO:0016034)|protein homodimerization activity (GO:0042803)			lung(2)|prostate(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	TACCATCAGCTCCATCAACAA	0.562																																					p.S188P		Atlas-SNP	.											.	GSTZ1	35	.	0			c.T562C						.						104	91	95					14																	77797449		2203	4300	6503	SO:0001583	missense	2954	exon9			ATCAGCTCCATCA	U86529	CCDS9858.1, CCDS9859.1, CCDS9860.1	14q24.3	2012-06-22	2012-06-22		ENSG00000100577	ENSG00000100577	5.2.1.2, 2.5.1.18	"Glutathione S-transferases / Soluble"	4643	protein-coding gene	gene with protein product	"maleylacetoacetate isomerase"	603758	"glutathione transferase zeta 1"			9396740, 9417084	Standard	NM_001513		Approved	GSTZ1-1, MAAI, MAI	uc001xtj.3	O43708	OTTHUMG00000171551	ENST00000556627.1:c.481T>C	chr14.hg19:g.77797449T>C	ENSP00000450487:p.Ser161Pro	114.0	0.0		136.0	6.0	NM_145870	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	hg19		.	.	.	.	.	.	.	.	.	.	T	8.678	0.904372	0.17760	.	.	ENSG00000100577	ENST00000216465;ENST00000361389;ENST00000554279;ENST00000557639;ENST00000349555;ENST00000556627;ENST00000557053;ENST00000393734;ENST00000553586	T;T;T;T;T;T;T;T;T	0.02158	4.42;4.42;4.42;4.42;4.42;4.42;4.42;4.42;4.42	5.48	4.59	0.56863	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.291066	0.40818	N	0.001010	T	0.03564	0.0102	L	0.42245	1.32	0.09310	N	0.999997	B;B	0.22909	0.072;0.077	B;B	0.32864	0.154;0.087	T	0.30504	-0.9976	10	0.87932	D	0	-2.6754	10.7717	0.46327	0.0:0.908:0.0:0.092	.	146;188	A6NED0;O43708	.;MAAI_HUMAN	P	188;133;174;133;146;161;91;133;189	ENSP00000216465:S188P;ENSP00000354959:S133P;ENSP00000452498:S174P;ENSP00000451927:S133P;ENSP00000314404:S146P;ENSP00000450487:S161P;ENSP00000451150:S91P;ENSP00000377335:S133P;ENSP00000451976:S189P	ENSP00000216465:S188P	S	+	1	0	GSTZ1	76867202	0.682000	0.27624	0.714000	0.30535	0.004000	0.04260	1.159000	0.31749	1.282000	0.44496	-0.468000	0.05107	TCC	.	.		0.562	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870		C	77797449	T	C	77797449	3	2	114	1	0	0	0	0	1	0	0	0	6857	1551	54	2	596	2	GSTZ1	14	77797449	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2532817	77797449	29552091	884	19156										
AHSA1	10598	hgsc.bcm.edu	37	chr14	77929054	77929054	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taatgaaggaagaaggggtgAaacttctaagagaagcaatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:77929054delA	ENST00000216479.3	+	4	584	c.424delA	c.(424-426)aaafs	p.K142fs	AHSA1_ENST00000535854.2_Frame_Shift_Del_p.K142fs|AHSA1_ENST00000555457.1_Intron	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	142					positive regulation of ATPase activity (GO:0032781)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		AGAAGGGGTGAAACTTCTAAG	0.438																																					p.V141fs		Atlas-INDEL	.											.	AHSA1	24	.	0			c.423delG						.						125	117	120					14																	77929054		2203	4300	6503	SO:0001589	frameshift_variant	10598	exon4			.	AJ243310	CCDS9863.1	14q	2008-02-05	2003-04-04	2003-04-11		ENSG00000100591			1189	protein-coding gene	gene with protein product		608466	"chromosome 14 open reading frame 3"	C14orf3			Standard	NM_012111		Approved	p38	uc001xtw.3	O95433		ENST00000216479.3:c.424delA	chr14.hg19:g.77929054delA	ENSP00000216479:p.Lys142fs	120.0	0.0		157.0	10.0	NM_012111	B2R9L2|B4DUR9|Q96IL6|Q9P060	Frame_Shift_Del	DEL	ENST00000216479.3	hg19	CCDS9863.1																																																																																			.	.		0.438	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111		-	77929054	A	-	77929054	7	5	114	1	0	1	0	1	0	0	0	0	418	247	9	0	438	0	AHSA1	14	77929054	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	131605	77929054	29420486	885	19157										
TSHR	7253	hgsc.bcm.edu	37	chr14	81610522	81610522	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acgccaggctcaggcataccGggggcagagggttcctccaa					rs368452281		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:81610522delG	ENST00000541158.2	+	11	2442	c.2120delG	c.(2119-2121)cggfs	p.R707fs	RP11-114N19.3_ENST00000557775.1_RNA|TSHR_ENST00000298171.2_Frame_Shift_Del_p.R707fs			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	707					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)			breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	CAGGCATACCGGGGGCAGAGG	0.488			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																														p.R707fs		Atlas-INDEL	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	TSHR,NS,carcinoma,0,1	TSHR	462	.	0			c.2119delC						.						114	109	111					14																	81610522		2203	4300	6503	SO:0001589	frameshift_variant	7253	exon10			.	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"GPCR / Class A : Gonadotropin and TSH receptors"	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.2120delG	chr14.hg19:g.81610522delG	ENSP00000441235:p.Arg707fs	152.0	0.0		200.0	13.0	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Frame_Shift_Del	DEL	ENST00000541158.2	hg19	CCDS9872.1																																																																																			.	.		0.488	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		-	81610522	G	-	81610522	7	5	114	1	0	1	0	1	0	0	0	0	16637	1116	39	0	2295	0	TSHR	14	81610522	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	3681468	81610522	25739018	886	19158										
SPATA7	55812	hgsc.bcm.edu	37	chr14	88883150	88883150	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgcaatgcgagccaattatAaaaataattccaagtcactt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:88883150delA	ENST00000393545.4	+	5	623	c.334delA	c.(334-336)aaafs	p.K112fs	SPATA7_ENST00000356583.5_Frame_Shift_Del_p.K80fs|SPATA7_ENST00000556553.1_Frame_Shift_Del_p.K80fs|SPATA7_ENST00000045347.7_Frame_Shift_Del_p.K112fs	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	112					response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						AGCCAATTATAAAAATAATTC	0.289																																					p.Y111X		Atlas-INDEL	.											.	SPATA7	58	.	0			c.333delT						.						46	50	49					14																	88883150		2199	4294	6493	SO:0001589	frameshift_variant	55812	exon5			.	AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"Leber congenital amaurosis 3"	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.334delA	chr14.hg19:g.88883150delA	ENSP00000377176:p.Lys112fs	174.0	0.0		163.0	10.0	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Frame_Shift_Del	DEL	ENST00000393545.4	hg19	CCDS9883.1																																																																																			.	.		0.289	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1			-	88883150	A	-	88883150	7	5	114	1	0	1	0	1	0	0	0	0	15029	363	13	0	352	0	SPATA7	14	88883150	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	7272628	88883150	18466390	887	19159										
EML5	161436	hgsc.bcm.edu	37	chr14	89087164	89087164	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttttagagaactcactagtAaaatgataaattctccattt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:89087164delA	ENST00000380664.5	-	37	5284	c.5285delT	c.(5284-5286)ttafs	p.L1763fs	EML5_ENST00000352093.5_Frame_Shift_Del_p.L1725fs|EML5_ENST00000554922.1_Frame_Shift_Del_p.L1771fs|EML5_ENST00000553320.1_5'Flank			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1763						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						ACTCACTAGTAAAATGATAAA	0.378																																					p.L1770fs		Atlas-INDEL	.											.	EML5	141	.	0			c.5310delA						.						103	93	96					14																	89087164		1859	4114	5973	SO:0001589	frameshift_variant	161436	exon38			.	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.5285delT	chr14.hg19:g.89087164delA	ENSP00000370039:p.Leu1763fs	171.0	0.0		201.0	14.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Frame_Shift_Del	DEL	ENST00000380664.5	hg19	CCDS45148.1																																																																																			.	.		0.378	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			-	89087164	A	-	89087164	7	5	114	1	0	1	0	1	0	0	0	0	5102	372	13	0	648	0	EML5	14	89087164	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	204014	89087164	18262376	888	19160										
EML5	161436	hgsc.bcm.edu	37	chr14	89206909	89206909	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcagagcatttccacataaaCtccagaactaaaaggtatat	5	9	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:89206909C>T	ENST00000380664.5	-	5	532	c.533G>A	c.(532-534)aGt>aAt	p.S178N	EML5_ENST00000352093.5_Missense_Mutation_p.S178N|EML5_ENST00000554922.1_Missense_Mutation_p.S178N			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	178						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						TCCACATAAACTCCAGAACTA	0.363																																					p.S178N		Atlas-SNP	.											.	EML5	141	.	0			c.G533A						.						108	102	103					14																	89206909		1830	4082	5912	SO:0001583	missense	161436	exon5			CATAAACTCCAGA	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.533G>A	chr14.hg19:g.89206909C>T	ENSP00000370039:p.Ser178Asn	116.0	0.0		121.0	6.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.105746	0.37145	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.01258	5.09;5.09;5.09	5.05	4.15	0.48705	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.051418	0.85682	D	0.000000	T	0.01523	0.0049	L	0.41236	1.265	0.45867	D	0.998724	B	0.16396	0.017	B	0.16722	0.016	T	0.55879	-0.8071	10	0.13853	T	0.58	-12.4644	10.3523	0.43943	0.0:0.8476:0.0:0.1524	.	178	Q05BV3	EMAL5_HUMAN	N	178	ENSP00000451998:S178N;ENSP00000298315:S178N;ENSP00000370039:S178N	ENSP00000298315:S178N	S	-	2	0	EML5	88276662	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.172000	0.31908	2.331000	0.79229	0.467000	0.42956	AGT	.	.		0.363	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89206909	C	T	89206909	3	4	114	1	0	0	0	0	1	0	0	0	5102	565	20	3	5556	3	EML5	14	89206909	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	119745	89206909	18142631	889	19161										
TDP1	55775	hgsc.bcm.edu	37	chr14	90446955	90446955	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctccaacctcatccatgctgActggcaccagaaaactcaag	6	15	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:90446955A>G	ENST00000335725.4	+	8	1113	c.863A>G	c.(862-864)gAc>gGc	p.D288G	TDP1_ENST00000357382.3_Missense_Mutation_p.D49G|TDP1_ENST00000555880.1_Missense_Mutation_p.D288G|TDP1_ENST00000393454.2_Missense_Mutation_p.D288G|TDP1_ENST00000393452.3_Missense_Mutation_p.D288G	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	288					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		ATCCATGCTGACTGGCACCAG	0.453								Repair of DNA-protein crosslinks																													p.D288G		Atlas-SNP	.											.	TDP1	47	.	0			c.A863G						.						99	90	93					14																	90446955		2203	4300	6503	SO:0001583	missense	55775	exon8			ATGCTGACTGGCA	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.863A>G	chr14.hg19:g.90446955A>G	ENSP00000337353:p.Asp288Gly	70.0	0.0		88.0	4.0	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	hg19	CCDS9888.1	.	.	.	.	.	.	.	.	.	.	A	17.72	3.458048	0.63401	.	.	ENSG00000042088	ENST00000393452;ENST00000393454;ENST00000553617;ENST00000335725;ENST00000357382;ENST00000555880	T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.85548	0.5722	H	0.95187	3.635	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.89724	0.3921	10	0.87932	D	0	-11.2052	16.2903	0.82747	1.0:0.0:0.0:0.0	.	288;288;49;288	G3V2F4;E7EPD8;Q86TV8;Q9NUW8	.;.;.;TYDP1_HUMAN	G	288;288;189;288;49;288	ENSP00000377098:D288G;ENSP00000377099:D288G;ENSP00000450708:D189G;ENSP00000337353:D288G;ENSP00000349952:D49G;ENSP00000450628:D288G	ENSP00000337353:D288G	D	+	2	0	TDP1	89516708	1.000000	0.71417	0.998000	0.56505	0.410000	0.31052	8.727000	0.91480	2.326000	0.78906	0.533000	0.62120	GAC	.	.		0.453	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		G	90446955	A	G	90446955	3	3	114	1	0	0	0	0	1	0	0	0	15743	275	10	2	885	2	TDP1	14	90446955	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1240046	90446955	16902585	890	19162										
RIN3	79890	hgsc.bcm.edu	37	chr14	93022212	93022212	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccggggcatcagcatcctggAgaagctcatcaaaacatgcc	10	13	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:93022212A>G	ENST00000216487.7	+	2	320	c.161A>G	c.(160-162)gAg>gGg	p.E54G		NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	54					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				AGCATCCTGGAGAAGCTCATC	0.622																																					p.E54G		Atlas-SNP	.											.	RIN3	81	.	0			c.A161G						.						59	57	58					14																	93022212		2203	4300	6503	SO:0001583	missense	79890	exon2			TCCTGGAGAAGCT	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.161A>G	chr14.hg19:g.93022212A>G	ENSP00000216487:p.Glu54Gly	81.0	0.0		88.0	4.0	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	hg19	CCDS32144.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.295482	0.60086	.	.	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.10288	2.89	5.51	5.51	0.81932	.	0.064919	0.64402	D	0.000019	T	0.33614	0.0869	M	0.78456	2.415	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.08391	-1.0724	10	0.87932	D	0	-29.4605	13.1403	0.59430	1.0:0.0:0.0:0.0	.	54	Q8TB24	RIN3_HUMAN	G	54	ENSP00000216487:E54G	ENSP00000216487:E54G	E	+	2	0	RIN3	92091965	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	6.035000	0.70940	2.079000	0.62486	0.533000	0.62120	GAG	.	.		0.622	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			G	93022212	A	G	93022212	3	3	114	1	0	0	0	0	1	0	0	0	13388	304	11	2	167	2	RIN3	14	93022212	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2575257	93022212	14327328	891	19163										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94100954	94100954	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctggagcatcagtctagcgCcccccataacatcagcaact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:94100954delC	ENST00000393151.2	+	32	5804	c.5804delC	c.(5803-5805)gccfs	p.A1935fs	UNC79_ENST00000553484.1_Frame_Shift_Del_p.A1957fs|UNC79_ENST00000256339.4_Frame_Shift_Del_p.A1758fs|UNC79_ENST00000555664.1_Intron			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1935					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CAGTCTAGCGCCCCCCATAAC	0.498																																					p.A1758fs		Atlas-INDEL	.											.	UNC79	366	.	0			c.5272delG						.						115	112	113					14																	94100954		2203	4300	6503	SO:0001589	frameshift_variant	57578	exon32			.	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.5804delC	chr14.hg19:g.94100954delC	ENSP00000376858:p.Ala1935fs	196.0	0.0		207.0	15.0	NM_020818	B5MDL6|Q6ZUT7	Frame_Shift_Del	DEL	ENST00000393151.2	hg19																																																																																				.	.		0.498	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		-	94100954	C	-	94100954	7	5	114	1	0	1	0	1	0	0	0	0	8239	739	26	0	5387	0	KIAA1409	14	94100954	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1078742	94100954	13248586	892	19164										
SERPINA9	327657	hgsc.bcm.edu	37	chr14	94933604	94933604	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcagctctgtatccaccccAaaagcgaactgctctttctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:94933604delA	ENST00000380365.3	-	3	822	c.744delT	c.(742-744)tttfs	p.F248fs	SERPINA9_ENST00000546329.1_Frame_Shift_Del_p.F230fs|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000448305.2_Frame_Shift_Del_p.F168fs|SERPINA9_ENST00000298845.7_Frame_Shift_Del_p.F166fs|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000424550.2_Frame_Shift_Del_p.F117fs|SERPINA9_ENST00000337425.5_Frame_Shift_Del_p.F266fs			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	248					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TATCCACCCCAAAAGCGAACT	0.517																																					p.G267fs		Atlas-INDEL	.											.	SERPINA9	105	.	0			c.799delG						.						70	69	69					14																	94933604		2010	4184	6194	SO:0001589	frameshift_variant	327657	exon3			.	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"Serine (or cysteine) peptidase inhibitors"	15995	protein-coding gene	gene with protein product		615677	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.744delT	chr14.hg19:g.94933604delA	ENSP00000369723:p.Phe248fs	114.0	0.0		165.0	13.0	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Frame_Shift_Del	DEL	ENST00000380365.3	hg19																																																																																				.	.		0.517	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739		-	94933604	A	-	94933604	7	5	114	1	0	1	0	1	0	0	0	0	14110	127	5	0	521	0	SERPINA9	14	94933604	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	832650	94933604	12415936	893	19165										
DICER1	23405	hgsc.bcm.edu	37	chr14	95562262	95562262	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcttttcaaaattttcaaaCcccgatataaggtgattcag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:95562262delC	ENST00000526495.1	-	25	5286	c.4995delG	c.(4993-4995)gggfs	p.G1665fs	DICER1_ENST00000343455.3_Frame_Shift_Del_p.G1665fs|DICER1_ENST00000541352.1_Frame_Shift_Del_p.G1665fs|DICER1_ENST00000556045.1_Frame_Shift_Del_p.G563fs|DICER1_ENST00000527414.1_Frame_Shift_Del_p.G1665fs|DICER1_ENST00000393063.1_Frame_Shift_Del_p.G1665fs			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1665					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		AATTTTCAAACCCCGATATAA	0.368			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.F1666fs		Atlas-INDEL	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.4996delT						.						106	108	107					14																	95562262		2203	4300	6503	SO:0001589	frameshift_variant	23405	exon23	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	.	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.4995delG	chr14.hg19:g.95562262delC	ENSP00000437256:p.Gly1665fs	139.0	0.0		166.0	11.0	NM_001271282	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Frame_Shift_Del	DEL	ENST00000526495.1	hg19	CCDS9931.1																																																																																			.	.		0.368	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			-	95562262	C	-	95562262	7	5	114	1	0	1	0	1	0	0	0	0	4523	494	18	0	793	0	DICER1	14	95562262	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	628658	95562262	11787278	894	19166										
AK7	122481	hgsc.bcm.edu	37	chr14	96916175	96916175	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctggccctgggaaaatccagAaaatacccagagaaaatgca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:96916175delA	ENST00000267584.4	+	9	951	c.907delA	c.(907-909)aaafs	p.K303fs		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	303					axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GAAAATCCAGAAAATACCCAG	0.323																																					p.Q302fs		Atlas-INDEL	.											.	AK7	69	.	0			c.906delG						.						52	55	54					14																	96916175		2203	4300	6503	SO:0001589	frameshift_variant	122481	exon9			.	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.907delA	chr14.hg19:g.96916175delA	ENSP00000267584:p.Lys303fs	92.0	0.0		157.0	13.0	NM_152327	Q8IYP6	Frame_Shift_Del	DEL	ENST00000267584.4	hg19	CCDS9945.1																																																																																			.	.		0.323	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			-	96916175	A	-	96916175	7	5	114	1	0	1	0	1	0	0	0	0	444	247	9	0	941	0	AK7	14	96916175	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1353913	96916175	10433365	895	19167										
AK7	122481	hgsc.bcm.edu	37	chr14	96937927	96937927	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaaagacctatgatcaagcAaaagacctgttcaatcgtaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:96937927delA	ENST00000267584.4	+	13	1514	c.1470delA	c.(1468-1470)gcafs	p.A490fs		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	490	Adenylate kinase.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		ATGATCAAGCAAAAGACCTGT	0.303																																					p.A490fs		Atlas-INDEL	.											.	AK7	69	.	0			c.1469delC						.						90	86	87					14																	96937927		2203	4300	6503	SO:0001589	frameshift_variant	122481	exon13			.	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1470delA	chr14.hg19:g.96937927delA	ENSP00000267584:p.Ala490fs	107.0	0.0		162.0	13.0	NM_152327	Q8IYP6	Frame_Shift_Del	DEL	ENST00000267584.4	hg19	CCDS9945.1																																																																																			.	.		0.303	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			-	96937927	A	-	96937927	7	5	114	1	0	1	0	1	0	0	0	0	444	117	5	0	1520	0	AK7	14	96937927	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	21752	96937927	10411613	896	19168										
AMN	81693	hgsc.bcm.edu	37	chr14	103390126	103390126	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caactggagccagaaccggaCcccgtgcgccggcggcgccg					rs119478058		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:103390126delC	ENST00000299155.5	+	2	155	c.122delC	c.(121-123)accfs	p.T41fs		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	41			T -> I (in RH-MGA1; dbSNP:rs28939377). {ECO:0000269|PubMed:12590260}.		cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|excretion (GO:0007588)|Golgi to plasma membrane protein transport (GO:0043001)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAGAACCGGACCCCGTGCGCC	0.706																																					p.T41fs		Atlas-INDEL	.											.	AMN	13	.	0			c.121delA	GRCh37	CM030407	AMN	M	rs119478058	.						29	36	34					14																	103390126		2203	4298	6501	SO:0001589	frameshift_variant	81693	exon2			.	AF328788	CCDS9977.1	14q32.32	2014-09-17	2012-12-07		ENSG00000166126	ENSG00000166126			14604	protein-coding gene	gene with protein product		605799	"amnionless homolog (mouse)"			11279523	Standard	NM_030943		Approved	amnionless	uc001ymg.4	Q9BXJ7		ENST00000299155.5:c.122delC	chr14.hg19:g.103390126delC	ENSP00000299155:p.Thr41fs	104.0	0.0		150.0	11.0	NM_030943	Q6UX83	Frame_Shift_Del	DEL	ENST00000299155.5	hg19	CCDS9977.1																																																																																			.	.		0.706	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1			-	103390126	C	-	103390126	7	5	114	1	0	1	0	1	0	0	0	0	580	507	18	0	128	0	AMN	14	103390126	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	6452199	103390126	3959414	897	19169										
KLC1	3831	hgsc.bcm.edu	37	chr14	104143836	104143836	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctgcagaaacgttagaagaAgctgctatgaggtctcgtaa	12	7	1	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:104143836A>G	ENST00000348520.6	+	12	1783	c.1464A>G	c.(1462-1464)gaA>gaG	p.E488E	KLC1_ENST00000557575.1_Silent_p.E488E|KLC1_ENST00000347839.6_Silent_p.E488E|KLC1_ENST00000554280.1_Silent_p.E488E|KLC1_ENST00000334553.6_Silent_p.E488E|KLC1_ENST00000389744.4_Silent_p.E488E|KLC1_ENST00000246489.7_Silent_p.E488E|KLC1_ENST00000452929.2_Silent_p.E488E|KLC1_ENST00000445352.4_Silent_p.E486E|KLC1_ENST00000553286.1_Silent_p.E488E|RP11-73M18.2_ENST00000472726.2_Silent_p.E660E|KLC1_ENST00000557450.1_Silent_p.E488E|KLC1_ENST00000555836.1_Silent_p.E488E|KLC1_ENST00000380038.3_Silent_p.E488E	NM_182923.3	NP_891553.2	Q07866	KLC1_HUMAN	kinesin light chain 1	488					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|stress granule disassembly (GO:0035617)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|growth cone (GO:0030426)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)|motor activity (GO:0003774)		KLC1/ALK(2)	NS(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	12		Melanoma(154;0.155)|all_epithelial(191;0.19)				CGTTAGAAGAAGCTGCTATGA	0.403																																					p.E488E		Atlas-SNP	.											.	KLC1	54	.	0			c.A1464G						.						144	138	140					14																	104143836		2203	4300	6503	SO:0001819	synonymous_variant	3831	exon12			AGAAGAAGCTGCT	AF267530	CCDS32165.1, CCDS41996.1, CCDS45168.1	14q32.3	2013-01-10	2007-03-09	2007-03-09	ENSG00000126214	ENSG00000126214		"Tetratricopeptide (TTC) repeat domain containing"	6387	protein-coding gene	gene with protein product		600025	"kinesin 2 60/70kDa", "kinesin 2"	KNS2		8274221, 11106729	Standard	NM_005552		Approved	KNS2A, KLC, hKLC1S, hKLC1N, hKLC1P, hKLC1G, hKLC1R, hKLC1J, hKLC1B	uc010tyf.2	Q07866	OTTHUMG00000169227	ENST00000348520.6:c.1464A>G	chr14.hg19:g.104143836A>G		43.0	0.0		82.0	4.0	NM_182923	A6NF62|F8VTM4|Q7RTM2|Q7RTM3|Q7RTM5|Q7RTP9|Q7RTQ3|Q7RTQ5|Q7RTQ6|Q86SF5|Q86TF5|Q86V74|Q86V75|Q86V76|Q86V77|Q86V78|Q86V79|Q96H62	Silent	SNP	ENST00000348520.6	hg19	CCDS41996.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.267|9.267	1.044712|1.044712	0.19748|0.19748	.|.	.|.	ENSG00000126214|ENSG00000126214	ENST00000553325;ENST00000553436;ENST00000555856|ENST00000537046	.|.	.|.	.|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|.	.|.	.|.	.|.	T|T	0.62865|0.62865	0.2463|0.2463	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.62020|0.62020	-0.6942|-0.6942	4|4	.|.	.|.	.|.	-16.5552|-16.5552	10.6404|10.6404	0.45590|0.45590	0.9191:0.0:0.0809:0.0|0.9191:0.0:0.0809:0.0	.|.	.|.	.|.	.|.	R|G	68;64;62|94	.|.	.|.	K|S	+|+	2|1	0|0	KLC1|KLC1	103213589|103213589	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.887000|0.887000	0.51463|0.51463	1.691000|1.691000	0.37721|0.37721	2.234000|2.234000	0.73211|0.73211	0.533000|0.533000	0.62120|0.62120	AAG|AGC	.	.		0.403	KLC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402947.2	NM_005552		G	104143836	A	G	104143836	2	3	114	1	0	0	0	0	0	0	0	1	8342	69	3	2		2	KLC1	14	104143836	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	753710	104143836	3205704	898	19170										
INF2	64423	hgsc.bcm.edu	37	chr14	105174185	105174185	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctactgccctgcacctgcagCccccccgtggcgggaggcat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:105174185delC	ENST00000392634.4	+	8	1693	c.1581delC	c.(1579-1581)agcfs	p.S527fs	INF2_ENST00000330634.7_Frame_Shift_Del_p.S527fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	527					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.V530fs*50(1)		large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		GCACCTGCAGCCCCCCCGTGG	0.716																																					p.S527fs		Atlas-Indel,Pindel	.											.,1	INF2	148	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1580delG						.						14	16	15					14																	105174185		1937	4086	6023	SO:0001589	frameshift_variant	64423	exon8			.	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"inverted formin 2"	610982	"chromosome 14 open reading frame 151", "chromosome 14 open reading frame 173"	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.1581delC	chr14.hg19:g.105174185delC	ENSP00000376410:p.Ser527fs	128.0	0.0		144.0	13.0	NM_001031714	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Frame_Shift_Del	DEL	ENST00000392634.4	hg19	CCDS9989.2																																																																																			.	.		0.716	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		-	105174185	C	-	105174185	7	5	114	1	0	1	0	1	0	0	0	0	7743	738	26	0	1611	0	INF2	14	105174185	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1030349	105174185	2175355	899	19171										
AKT1	207	hgsc.bcm.edu	37	chr14	105240253	105240253	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagccccagcccctacctcgCccccgttggcgtactccatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:105240253delC	ENST00000554581.1	-	7	2178	c.698delG	c.(697-699)ggcfs	p.G233fs	AKT1_ENST00000544168.1_Frame_Shift_Del_p.G171fs|AKT1_ENST00000554585.1_5'Flank|AKT1_ENST00000554192.1_5'Flank|AKT1_ENST00000349310.3_Frame_Shift_Del_p.G233fs|AKT1_ENST00000555458.1_5'Flank|AKT1_ENST00000402615.2_Frame_Shift_Del_p.G233fs|AKT1_ENST00000554848.1_Frame_Shift_Del_p.G233fs|AKT1_ENST00000407796.2_Frame_Shift_Del_p.G233fs|AKT1_ENST00000555528.1_Frame_Shift_Del_p.G233fs			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	233	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	CCCTACCTCGCCCCCGTTGGC	0.677		1	Mis		"breast, colorectal, ovarian, NSCLC"																																p.G233fs		Atlas-INDEL	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.699delC						.						32	29	30					14																	105240253		2202	4299	6501	SO:0001589	frameshift_variant	207	exon9			.	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"Pleckstrin homology (PH) domain containing"	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.698delG	chr14.hg19:g.105240253delC	ENSP00000451828:p.Gly233fs	168.0	0.0		173.0	11.0	NM_001014432	B2RAM5|B7Z5R1|Q9BWB6	Frame_Shift_Del	DEL	ENST00000554581.1	hg19	CCDS9994.1																																																																																			.	.		0.677	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163		-	105240253	C	-	105240253	7	5	114	1	0	1	0	1	0	0	0	0	478	739	26	0	772	0	AKT1	14	105240253	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	66068	105240253	2109287	900	19172										
AKT1	207	hgsc.bcm.edu	37	chr14	105246536	105246536	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaggaagtagcgtggccgccAggtcttgatgtactccccta	13	11	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:105246536A>G	ENST00000554581.1	-	2	1544	c.64T>C	c.(64-66)Tgg>Cgg	p.W22R	AKT1_ENST00000544168.1_5'Flank|AKT1_ENST00000349310.3_Missense_Mutation_p.W22R|AKT1_ENST00000402615.2_Missense_Mutation_p.W22R|AKT1_ENST00000554848.1_Missense_Mutation_p.W22R|AKT1_ENST00000407796.2_Missense_Mutation_p.W22R|AKT1_ENST00000555528.1_Missense_Mutation_p.W22R			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	22	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	CGTGGCCGCCAGGTCTTGATG	0.607		1	Mis		"breast, colorectal, ovarian, NSCLC"																																p.W22R		Atlas-SNP	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.T64C						.						138	100	113					14																	105246536		2203	4300	6503	SO:0001583	missense	207	exon3			GCCGCCAGGTCTT	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"Pleckstrin homology (PH) domain containing"	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.64T>C	chr14.hg19:g.105246536A>G	ENSP00000451828:p.Trp22Arg	127.0	0.0		153.0	7.0	NM_005163	B2RAM5|B7Z5R1|Q9BWB6	Missense_Mutation	SNP	ENST00000554581.1	hg19	CCDS9994.1	.	.	.	.	.	.	.	.	.	.	A	17.17	3.321365	0.60634	.	.	ENSG00000142208	ENST00000554581;ENST00000407796;ENST00000349310;ENST00000402615;ENST00000555528;ENST00000554848;ENST00000555926	T;T;T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26;-1.26;-1.26	4.61	4.61	0.57282	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.90300	0.6966	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92522	0.6026	10	0.87932	D	0	.	12.969	0.58501	1.0:0.0:0.0:0.0	.	22	P31749	AKT1_HUMAN	R	22	ENSP00000451828:W22R;ENSP00000384293:W22R;ENSP00000270202:W22R;ENSP00000385326:W22R;ENSP00000450688:W22R;ENSP00000451166:W22R;ENSP00000451824:W22R	ENSP00000270202:W22R	W	-	1	0	AKT1	104317581	0.997000	0.39634	0.989000	0.46669	0.289000	0.27227	4.804000	0.62554	1.939000	0.56221	0.379000	0.24179	TGG	.	.		0.607	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163		G	105246536	A	G	105246536	3	3	114	1	0	0	0	0	1	0	0	0	478	188	7	2	1426	2	AKT1	14	105246536	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	6283	105246536	2103004	901	19173										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105412200	105412200	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggacctccagttgggcagaGgggggctcaatgctgatgtc					rs55752740		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:105412200delG	ENST00000333244.5	-	7	9707	c.9588delC	c.(9586-9588)cccfs	p.P3196fs	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3196						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GTTGGGCAGAGGGGGGCTCAA	0.632																																					p.S3197fs		Pindel	.											.	AHNAK2	719	.	0			c.9589delT						.						113	77	89					14																	105412200		1948	3947	5895	SO:0001589	frameshift_variant	113146	exon7			.	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.9588delC	chr14.hg19:g.105412200delG	ENSP00000353114:p.Pro3196fs	166.0	0.0		254.0	11.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Del	DEL	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		-	105412200	G	-	105412200	7	5	114	1	0	1	0	1	0	0	0	0	415	987	35	0	7803	0	AHNAK2	14	105412200	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	165664	105412200	1937340	902	19174										
BRF1	2972	hgsc.bcm.edu	37	chr14	105676904	105676904	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacttcagtagccgtcgtccTcatcgccatcacagccatag	7	16	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:105676904T>C	ENST00000546474.1	-	18	16977	c.2018A>G	c.(2017-2019)gAg>gGg	p.E673G	BRF1_ENST00000379932.4_Intron|BRF1_ENST00000327359.3_Missense_Mutation_p.E558G|BRF1_ENST00000551787.1_Intron|BRF1_ENST00000379937.2_Missense_Mutation_p.E646G|BRF1_ENST00000392557.4_Missense_Mutation_p.E469G|BRF1_ENST00000440513.3_Missense_Mutation_p.E580G|BRF1_ENST00000446501.2_Missense_Mutation_p.E435G|BRF1_ENST00000547530.1_Missense_Mutation_p.E199G	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	673					gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		GCCGTCGTCCTCATCGCCATC	0.642																																					p.E673G		Atlas-SNP	.											.	BRF1	102	.	0			c.A2018G						.						86	68	74					14																	105676904		2202	4300	6502	SO:0001583	missense	2972	exon18			TCGTCCTCATCGC	U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"General transcription factors"	11551	protein-coding gene	gene with protein product		604902	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2", "BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.2018A>G	chr14.hg19:g.105676904T>C	ENSP00000448323:p.Glu673Gly	87.0	0.0		108.0	5.0	NM_001519	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Missense_Mutation	SNP	ENST00000546474.1	hg19	CCDS10001.1	.	.	.	.	.	.	.	.	.	.	T	9.470	1.095404	0.20471	.	.	ENSG00000185024	ENST00000392557;ENST00000379937;ENST00000546474;ENST00000547530;ENST00000446501;ENST00000327359;ENST00000440513	.	.	.	3.22	3.22	0.36961	.	0.302288	0.29152	N	0.012999	T	0.45256	0.1333	L	0.50333	1.59	0.58432	D	0.999998	B;B;B	0.34290	0.241;0.447;0.319	B;B;B	0.26969	0.075;0.075;0.034	T	0.52503	-0.8567	9	0.72032	D	0.01	.	8.2057	0.31454	0.0:0.0:0.0:1.0	.	580;646;673	F5H5Z7;Q92994-5;Q92994	.;.;TF3B_HUMAN	G	469;646;673;199;435;558;580	.	ENSP00000329029:E558G	E	-	2	0	BRF1	104747949	0.198000	0.23374	0.023000	0.16930	0.005000	0.04900	2.325000	0.43840	1.709000	0.51313	0.460000	0.39030	GAG	.	.		0.642	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519		C	105676904	T	C	105676904	3	2	114	1	0	0	0	0	1	0	0	0	1512	1551	54	2	19	2	BRF1	14	105676904	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	264704	105676904	1672636	903	19175										
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32929175	32929176	+	Frame_Shift_Del	DEL	AT	AT	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtccccaaaggataaactaaAtaataaattaaaagagaatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:32929175_32929176delAT	ENST00000361627.3	+	12	2923_2924	c.2201_2202delAT	c.(2200-2202)aatfs	p.N735fs	ARHGAP11A_ENST00000543522.1_Frame_Shift_Del_p.N546fs|ARHGAP11A_ENST00000565905.1_Frame_Shift_Del_p.N546fs	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	735					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		GATAAACTAAATAATAAATTAA	0.356																																					p.734_734del	Colon(45;757 1134 30003 36652)	Atlas-INDEL	.											.	ARHGAP11A	84	.	0			c.2200_2201del						.																																			SO:0001589	frameshift_variant	9824	exon12			.	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.2201_2202delAT	chr15.hg19:g.32929175_32929176delAT	ENSP00000355090:p.Asn735fs	47.0	0.0		63.0	11.0	NM_014783	B4DZN9|Q6PI96|Q9Y3S6	Frame_Shift_Del	DEL	ENST00000361627.3	hg19	CCDS10028.1																																																																																			.	.		0.356	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		-	32929176	AT	-	32929175	7	5	114	1	0	1	0	1	0	0	0	0	863	101	4	0	2270	0	ARHGAP11A	15	32929175	Frame_Shift_Del	DEL	AT	TCGA-DD-A3A0-01A-11D-A20W-10		32929175	69602217	904	19176										
SCG5	6447	hgsc.bcm.edu	37	chr15	32936003	32936003	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggccatgaatcttgtgggCccccagagcattgaaggtat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:32936003delC	ENST00000300175.4	+	2	320	c.210delC	c.(208-210)ggcfs	p.G70fs	SCG5_ENST00000413748.2_Frame_Shift_Del_p.G70fs|SCG5_ENST00000497208.1_Frame_Shift_Del_p.G70fs|SCG5_ENST00000494364.1_Frame_Shift_Del_p.G70fs	NM_001144757.1	NP_001138229.1	P05408	7B2_HUMAN	secretogranin V (7B2 protein)	70					intracellular protein transport (GO:0006886)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|regulation of hormone secretion (GO:0046883)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	enzyme inhibitor activity (GO:0004857)|GTP binding (GO:0005525)|unfolded protein binding (GO:0051082)			lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	6		all_lung(180;7.32e-08)		all cancers(64;6.48e-17)|Epithelial(43;1.23e-11)|GBM - Glioblastoma multiforme(186;1.39e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0212)		ATCTTGTGGGCCCCCAGAGCA	0.443																																					p.G70fs		Atlas-INDEL	.											.	SCG5	13	.	0			c.209delG						.						36	35	35					15																	32936003		1862	4105	5967	SO:0001589	frameshift_variant	6447	exon2			.	Y00757	CCDS45207.1, CCDS45208.1	15q13-q14	2006-03-20	2006-03-20	2006-03-20	ENSG00000166922	ENSG00000166922			10816	protein-coding gene	gene with protein product	"prohormone convertase chaperone"	173120	"secretory granule, neuroendocrine protein 1 (7B2 protein)"	SGNE1		8162254, 12646671	Standard	NM_003020		Approved	7B2, SgV	uc001zha.2	P05408	OTTHUMG00000159447	ENST00000300175.4:c.210delC	chr15.hg19:g.32936003delC	ENSP00000300175:p.Gly70fs	141.0	0.0		152.0	11.0	NM_003020	P01164|Q6FHD0|Q9BS38	Frame_Shift_Del	DEL	ENST00000300175.4	hg19	CCDS45207.1																																																																																			.	.		0.443	SCG5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355438.1	NM_003020		-	32936003	C	-	32936003	7	5	114	1	0	1	0	1	0	0	0	0	13908	726	26	0	212	0	SCG5	15	32936003	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	6828	32936003	69595389	905	19177										
RYR3	6263	hgsc.bcm.edu	37	chr15	34018695	34018695	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcatccccttgaaactgcccTccctcaacaaaggtaagggg	9	14	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:34018695T>C	ENST00000389232.4	+	46	7091	c.7021T>C	c.(7021-7023)Tcc>Ccc	p.S2341P	RYR3_ENST00000415757.3_Missense_Mutation_p.S2341P	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2341	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GAAACTGCCCTCCCTCAACAA	0.622																																					p.S2341P		Atlas-SNP	.											.	RYR3	760	.	0			c.T7021C						.						40	42	41					15																	34018695		2020	4161	6181	SO:0001583	missense	6263	exon46			CTGCCCTCCCTCA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.7021T>C	chr15.hg19:g.34018695T>C	ENSP00000373884:p.Ser2341Pro	79.0	0.0		108.0	6.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.775373	0.31411	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.96554	-4.05;-4.05	4.96	2.42	0.29668	.	0.487971	0.21537	N	0.072951	D	0.90417	0.7000	L	0.27053	0.805	0.09310	N	1	B;B	0.34329	0.256;0.449	B;B	0.33254	0.039;0.16	D	0.83890	0.0284	10	0.45353	T	0.12	.	5.3348	0.15951	0.4277:0.0:0.1303:0.442	.	2341;2341	Q15413-2;Q15413	.;RYR3_HUMAN	P	2341	ENSP00000373884:S2341P;ENSP00000399610:S2341P	ENSP00000354735:S2341P	S	+	1	0	RYR3	31805987	0.861000	0.29849	0.943000	0.38184	0.931000	0.56810	1.927000	0.40094	0.991000	0.38814	0.445000	0.29226	TCC	.	.		0.622	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			C	34018695	T	C	34018695	3	2	114	1	0	0	0	0	1	0	0	0	13785	1551	54	2	7203	2	RYR3	15	34018695	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1082692	34018695	68512697	906	19178										
C15orf29	79768	hgsc.bcm.edu	37	chr15	34455865	34455865	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccgttttttaacattgtgggTttctgatgccataatctctt	7	8	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:34455865T>C	ENST00000256544.3	-	2	155	c.13A>G	c.(13-15)Acc>Gcc	p.T5A		NM_024713.2	NP_078989.1	Q9H079	KTBL1_HUMAN	katanin p80 subunit B-like 1	5						nucleolus (GO:0005730)											ACATTGTGGGTTTCTGATGCC	0.279																																					p.T5A		Atlas-SNP	.											.	.	.	.	0			c.A13G						.						56	58	57					15																	34455865		2201	4289	6490	SO:0001583	missense	79768	exon2			TGTGGGTTTCTGA	AL136908	CCDS10034.1	15q13.2	2012-09-27	2012-09-27	2012-09-27	ENSG00000134152	ENSG00000134152			26199	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 29"	C15orf29		11230166	Standard	NM_024713		Approved	FLJ22557	uc001zhp.3	Q9H079	OTTHUMG00000129368	ENST00000256544.3:c.13A>G	chr15.hg19:g.34455865T>C	ENSP00000256544:p.Thr5Ala	61.0	0.0		82.0	4.0	NM_024713	A8KAF6|Q2TAC0|Q9H670	Missense_Mutation	SNP	ENST00000256544.3	hg19	CCDS10034.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.555506	0.27739	.	.	ENSG00000134152	ENST00000256544	.	.	.	4.49	2.17	0.27698	.	0.419216	0.26567	N	0.023648	T	0.13157	0.0319	N	0.08118	0	0.26407	N	0.976323	B	0.02656	0.0	B	0.01281	0.0	T	0.28138	-1.0053	9	0.06625	T	0.88	.	5.0984	0.14747	0.0:0.4575:0.0:0.5425	.	5	Q9H079	CO029_HUMAN	A	5	.	ENSP00000256544:T5A	T	-	1	0	C15orf29	32243157	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.365000	0.44196	0.849000	0.35215	0.455000	0.32223	ACC	.	.		0.279	KATNBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251520.1	NM_024713		C	34455865	T	C	34455865	3	2	114	1	0	0	0	0	1	0	0	0	1791	1725	60	2	937	2	C15orf29	15	34455865	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	437170	34455865	68075527	907	19179										
AQR	9716	hgsc.bcm.edu	37	chr15	35182501	35182501	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atcaatgtctaatgccatgaTtttctcaaacaactggttta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:35182501delT	ENST00000156471.5	-	24	2821	c.2596delA	c.(2596-2598)atcfs	p.I866fs		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	866					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		AATGCCATGATTTTCTCAAAC	0.428																																					p.I866fs		Atlas-INDEL	.											.	AQR	139	.	0			c.2597delT						.						164	155	158					15																	35182501		1902	4136	6038	SO:0001589	frameshift_variant	9716	exon24			.	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.2596delA	chr15.hg19:g.35182501delT	ENSP00000156471:p.Ile866fs	145.0	0.0		152.0	10.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Frame_Shift_Del	DEL	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.		0.428	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		-	35182501	T	-	35182501	7	5	114	1	0	1	0	1	0	0	0	0	835	1493	52	0	1909	0	AQR	15	35182501	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	726636	35182501	67348891	908	19180										
FSIP1	161835	hgsc.bcm.edu	37	chr15	40031895	40031895	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctcttaataaaatcctggtTgtgtttacccctgagctcaa	6	10	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:40031895T>C	ENST00000350221.3	-	7	960	c.751A>G	c.(751-753)Aac>Gac	p.N251D	FSIP1_ENST00000559692.1_5'UTR	NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	251										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		AAATCCTGGTTGTGTTTACCC	0.338																																					p.N251D		Atlas-SNP	.											.	FSIP1	53	.	0			c.A751G						.						102	98	99					15																	40031895		2202	4296	6498	SO:0001583	missense	161835	exon7			CCTGGTTGTGTTT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.751A>G	chr15.hg19:g.40031895T>C	ENSP00000280236:p.Asn251Asp	119.0	0.0		118.0	5.0	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	hg19	CCDS10050.1	.	.	.	.	.	.	.	.	.	.	T	16.73	3.204411	0.58234	.	.	ENSG00000150667	ENST00000350221	T	0.23147	1.92	5.77	4.66	0.58398	.	0.308416	0.31020	N	0.008407	T	0.19406	0.0466	L	0.29908	0.895	0.20703	N	0.999862	P	0.46142	0.873	B	0.44044	0.439	T	0.09840	-1.0656	9	.	.	.	-8.0796	7.7222	0.28740	0.0:0.0911:0.0:0.9089	.	251	Q8NA03	FSIP1_HUMAN	D	251	ENSP00000280236:N251D	.	N	-	1	0	FSIP1	37819187	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.499000	0.45372	2.199000	0.70637	0.533000	0.62120	AAC	.	.		0.338	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		C	40031895	T	C	40031895	3	2	114	1	0	0	0	0	1	0	0	0	6082	1812	63	2	1018	2	FSIP1	15	40031895	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4849394	40031895	62499497	909	19181										
CASC5	57082	hgsc.bcm.edu	37	chr15	40914323	40914323	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaattaccaaaagtcgtaatGaaccatttcagcgatcagac	6	9	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:40914323G>A	ENST00000346991.5	+	11	2329	c.1939G>A	c.(1939-1941)Gaa>Aaa	p.E647K	CASC5_ENST00000399668.2_Missense_Mutation_p.E621K|CASC5_ENST00000527044.1_3'UTR			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	647	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		AAGTCGTAATGAACCATTTCA	0.398																																					p.E647K		Atlas-SNP	.											.	CASC5	269	.	0			c.G1939A						.						69	66	67					15																	40914323		1885	4110	5995	SO:0001583	missense	57082	exon11			CGTAATGAACCAT	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1939G>A	chr15.hg19:g.40914323G>A	ENSP00000335463:p.Glu647Lys	95.0	0.0		97.0	4.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	hg19	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	G	3.393	-0.123936	0.06795	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.16597	2.33;2.33	3.92	1.67	0.24075	.	1.360810	0.05590	N	0.574557	T	0.15739	0.0379	L	0.44542	1.39	0.09310	N	1	B;B;B	0.10296	0.002;0.002;0.003	B;B;B	0.12156	0.007;0.007;0.003	T	0.36114	-0.9761	10	0.25751	T	0.34	.	7.0409	0.25019	0.4947:0.0:0.5053:0.0	.	621;647;621	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	K	647;621;621	ENSP00000335463:E647K;ENSP00000382576:E621K	ENSP00000260369:E621K	E	+	1	0	CASC5	38701615	0.003000	0.15002	0.002000	0.10522	0.018000	0.09664	0.856000	0.27818	0.123000	0.18342	0.557000	0.71058	GAA	.	.		0.398	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		A	40914323	G	A	40914323	3	1	114	1	0	0	0	0	1	0	0	0	2665	1291	45	3	1977	3	CASC5	15	40914323	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	882428	40914323	61617069	910	19182										
RPAP1	26015	hgsc.bcm.edu	37	chr15	41826958	41826958	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcctgcaggatctcctcaggAgccatggcctgcagtcttgc	11	14	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:41826958A>G	ENST00000304330.4	-	6	833	c.717T>C	c.(715-717)gcT>gcC	p.A239A	RPAP1_ENST00000568413.1_5'Flank|RPAP1_ENST00000561603.1_Silent_p.A239A	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	239						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TCTCCTCAGGAGCCATGGCCT	0.562																																					p.A239A		Atlas-SNP	.											.	RPAP1	111	.	0			c.T717C						.						112	89	97					15																	41826958		2203	4300	6503	SO:0001819	synonymous_variant	26015	exon6			CTCAGGAGCCATG	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.717T>C	chr15.hg19:g.41826958A>G		98.0	0.0		122.0	6.0	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	ENST00000304330.4	hg19	CCDS10079.1																																																																																			.	.		0.562	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		G	41826958	A	G	41826958	2	3	114	1	0	0	0	0	0	0	0	1	13556	291	11	2		2	RPAP1	15	41826958	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	912635	41826958	60704434	911	19183										
MGA	23269	hgsc.bcm.edu	37	chr15	41961559	41961559	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acctcatgttttggggagggTtttcattcatccagaatctc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:41961559delT	ENST00000570161.1	+	1	467	c.467delT	c.(466-468)gttfs	p.V156fs	MGA_ENST00000545763.1_Frame_Shift_Del_p.V156fs|MGA_ENST00000219905.7_Frame_Shift_Del_p.V156fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.V156fs|MGA_ENST00000566586.1_Frame_Shift_Del_p.V156fs|MGA_ENST00000568630.1_Intron			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTGGGGAGGGTTTTCATTCAT	0.423																																					p.V156fs		Atlas-INDEL	.											.	MGA	264	.	0			c.466delG						.						279	277	278					15																	41961559		1897	4101	5998	SO:0001589	frameshift_variant	23269	exon2			.	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.467delT	chr15.hg19:g.41961559delT	ENSP00000457035:p.Val156fs	171.0	0.0		203.0	15.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.423	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		-	41961559	T	-	41961559	7	5	114	1	0	1	0	1	0	0	0	0	9549	1725	60	0	469	0	MGA	15	41961559	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	134601	41961559	60569833	912	19184										
MGA	23269	hgsc.bcm.edu	37	chr15	42057143	42057143	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accttgtgatgactccgcaaGggcaattgctcaccctaaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:42057143delG	ENST00000570161.1	+	22	7804	c.7804delG	c.(7804-7806)gggfs	p.G2602fs	MGA_ENST00000545763.1_Frame_Shift_Del_p.G2393fs|MGA_ENST00000219905.7_Frame_Shift_Del_p.G2602fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.G2563fs|MGA_ENST00000566586.1_Frame_Shift_Del_p.G2393fs			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GACTCCGCAAGGGCAATTGCT	0.443																																					p.Q2601fs		Atlas-INDEL	.											.	MGA	264	.	0			c.7803delA						.						126	129	128					15																	42057143		2024	4188	6212	SO:0001589	frameshift_variant	23269	exon23			.	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7804delG	chr15.hg19:g.42057143delG	ENSP00000457035:p.Gly2602fs	146.0	0.0		194.0	12.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.443	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		-	42057143	G	-	42057143	7	5	114	1	0	1	0	1	0	0	0	0	9549	1000	35	0	7890	0	MGA	15	42057143	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	95584	42057143	60474249	913	19185										
TMEM87A	25963	hgsc.bcm.edu	37	chr15	42512286	42512286	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttctttcagcataggctccTtttgttcatcctcctcctct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:42512286delT	ENST00000389834.4	-	16	1715	c.1451delA	c.(1450-1452)aagfs	p.K484fs	RP11-546B15.1_ENST00000563846.1_RNA|TMEM87A_ENST00000448392.1_Frame_Shift_Del_p.K423fs	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	484						integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		CATAGGCTCCTTTTGTTCATC	0.308																																					p.K484fs		Atlas-INDEL	.											.	TMEM87A	56	.	0			c.1452delG						.						110	119	116					15																	42512286		2203	4299	6502	SO:0001589	frameshift_variant	25963	exon16			.	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.1451delA	chr15.hg19:g.42512286delT	ENSP00000374484:p.Lys484fs	141.0	0.0		198.0	12.0	NM_015497	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Frame_Shift_Del	DEL	ENST00000389834.4	hg19	CCDS32205.1																																																																																			.	.		0.308	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497		-	42512286	T	-	42512286	7	5	114	1	0	1	0	1	0	0	0	0	16225	1609	56	0	236	0	TMEM87A	15	42512286	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	455143	42512286	60019106	914	19186										
CAPN3	825	hgsc.bcm.edu	37	chr15	42698130	42698130	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttttcttatgcagaaaaagAaaaaaaccaaggtaggtgtg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:42698130delA	ENST00000397163.3	+	15	2008	c.1789delA	c.(1789-1791)aaafs	p.K598fs	CAPN3_ENST00000356316.3_Intron|CAPN3_ENST00000397200.4_Frame_Shift_Del_p.K86fs|CAPN3_ENST00000318023.7_Intron|CAPN3_ENST00000349748.3_Intron|CAPN3_ENST00000569136.1_5'UTR|CAPN3_ENST00000561817.1_Intron|CAPN3_ENST00000357568.3_Intron|CAPN3_ENST00000337571.4_Intron|CAPN3_ENST00000397204.4_5'UTR|RP11-164J13.1_ENST00000495723.1_RNA	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	598	Linker.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		GCAGAAAAAGAAAAAAACCAA	0.418																																					p.K596fs		Atlas-INDEL	.											.,1	CAPN3	172	.	0			c.1788delG						.						176	189	185					15																	42698130		1919	4131	6050	SO:0001589	frameshift_variant	825	exon15			.	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"EF-hand domain containing"	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.1789delA	chr15.hg19:g.42698130delA	ENSP00000380349:p.Lys598fs	110.0	0.0		156.0	11.0	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Frame_Shift_Del	DEL	ENST00000397163.3	hg19	CCDS45245.1																																																																																			.	.		0.418	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1			-	42698130	A	-	42698130	7	5	114	1	0	1	0	1	0	0	0	0	2630	247	9	0	1899	0	CAPN3	15	42698130	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	185844	42698130	59833262	915	19187										
ZFP106	64397	hgsc.bcm.edu	37	chr15	42742679	42742679	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aactcaattttcaaagacccTttttcagattcttctacatt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:42742679delT	ENST00000263805.4	-	2	2048	c.1722delA	c.(1720-1722)aaafs	p.K574fs	ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	574					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TCAAAGACCCTTTTTCAGATT	0.388																																					p.G575fs		Atlas-INDEL	.											.	ZFP106	117	.	0			c.1723delG						.						115	114	114					15																	42742679		2203	4299	6502	SO:0001589	frameshift_variant	64397	exon2			.	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"Zinc fingers, C2H2-type"	12886	protein-coding gene	gene with protein product	"SH3-domain binding protein 3"		"zinc finger protein 106 homolog (mouse)"	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.1722delA	chr15.hg19:g.42742679delT	ENSP00000263805:p.Lys574fs	128.0	0.0		155.0	10.0	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Frame_Shift_Del	DEL	ENST00000263805.4	hg19	CCDS32208.1																																																																																			.	.		0.388	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		-	42742679	T	-	42742679	7	5	114	1	0	1	0	1	0	0	0	0	17652	1606	56	0	4001	0	ZFP106	15	42742679	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	44549	42742679	59788713	916	19188										
CCNDBP1	23582	hgsc.bcm.edu	37	chr15	43483239	43483239	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcacatgaagaaatggagcAggtgaggggacctccatcat	13	8	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:43483239A>G	ENST00000300213.4	+	7	820	c.578A>G	c.(577-579)cAg>cGg	p.Q193R	CCNDBP1_ENST00000356633.5_Splice_Site_p.Q32R|EPB42_ENST00000563128.1_Intron	NM_012142.4	NP_036274.3	O95273	CCDB1_HUMAN	cyclin D-type binding-protein 1	193	Interaction with TCF3.|Required for interaction with CCND1.				cell cycle (GO:0007049)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	13		all_cancers(109;3.31e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.42e-07)		GAAATGGAGCAGGTGAGGGGA	0.413																																					p.Q193R		Atlas-SNP	.											.	CCNDBP1	22	.	0			c.A578G						.						108	104	106					15																	43483239		2203	4299	6502	SO:0001630	splice_region_variant	23582	exon7			TGGAGCAGGTGAG	AF082569	CCDS10092.1	15q14-q15	2008-07-18			ENSG00000166946	ENSG00000166946			1587	protein-coding gene	gene with protein product	"D-type cyclin-interacting protein 1", "MAID protein", "HHM Protein", "grap2 cyclin interacting protein"	607089				10801854	Standard	NM_012142		Approved	DIP1, GCIP	uc001zqv.3	O95273	OTTHUMG00000130703	ENST00000300213.4:c.579+1A>G	chr15.hg19:g.43483239A>G		104.0	0.0		93.0	7.0	NM_012142	A8K3Q0|A8K3U2|Q6ZQN9|Q7Z519|Q8NBS7|Q8NBY2|Q9NS19|Q9NYH3|Q9UHX9	Missense_Mutation	SNP	ENST00000300213.4	hg19	CCDS10092.1	.	.	.	.	.	.	.	.	.	.	A	7.678	0.688454	0.14973	.	.	ENSG00000166946	ENST00000300213;ENST00000356633;ENST00000444658	T;T	0.47869	0.83;0.83	5.11	-4.54	0.03452	.	0.683858	0.14983	N	0.287154	T	0.30916	0.0780	L	0.31664	0.95	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.003;0.005;0.004	T	0.02789	-1.1110	10	0.36615	T	0.2	-12.4265	12.3289	0.55028	0.7871:0.0:0.2129:0.0	.	193;193;65	O95273-2;O95273;O95273-4	.;CCDB1_HUMAN;.	R	193;32;65	ENSP00000300213:Q193R;ENSP00000349047:Q32R	ENSP00000300213:Q193R	Q	+	2	0	CCNDBP1	41270531	0.978000	0.34361	0.880000	0.34516	0.180000	0.23129	0.129000	0.15830	-0.801000	0.04427	-1.179000	0.01719	CAG	.	.		0.413	CCNDBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253203.1	NM_012142	Missense_Mutation	G	43483239	A	G	43483239	5	3	114	1	0	0	0	0	0	0	1	0	2921	202	7	2	604	2	CCNDBP1	15	43483239	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	740560	43483239	59048153	917	19189										
TUBGCP4	27229	hgsc.bcm.edu	37	chr15	43675520	43675520	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaatcctggccgtttgtcatGgggtcatgtataaacagctc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:43675520delG	ENST00000260383.7	+	7	795	c.541delG	c.(541-543)gggfs	p.G181fs	TUBGCP4_ENST00000399460.3_Frame_Shift_Del_p.G45fs|TUBGCP4_ENST00000564079.1_Frame_Shift_Del_p.G181fs			Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	181					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|spindle pole (GO:0000922)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(4)|prostate(2)|upper_aerodigestive_tract(2)	21		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		CGTTTGTCATGGGGTCATGTA	0.453																																					p.H180fs		Atlas-INDEL	.											.	TUBGCP4	48	.	0			c.540delT						.						83	79	81					15																	43675520		1884	4131	6015	SO:0001589	frameshift_variant	27229	exon7			.	AJ249677	CCDS42030.1, CCDS66745.1	15q15.3	2014-08-12			ENSG00000137822	ENSG00000137822			16691	protein-coding gene	gene with protein product		609610				10562286	Standard	NM_001286414		Approved	76P, FLJ14797	uc001zrn.3	Q9UGJ1	OTTHUMG00000176647	ENST00000260383.7:c.541delG	chr15.hg19:g.43675520delG	ENSP00000260383:p.Gly181fs	159.0	0.0		150.0	10.0	NM_014444	B3KNK6|Q969X3|Q9NVF0	Frame_Shift_Del	DEL	ENST00000260383.7	hg19																																																																																				.	.		0.453	TUBGCP4-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000432970.1	NM_014444		-	43675520	G	-	43675520	7	5	114	1	0	1	0	1	0	0	0	0	16783	1348	47	0	567	0	TUBGCP4	15	43675520	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	192281	43675520	58855872	918	19190										
MAP1A	4130	hgsc.bcm.edu	37	chr15	43816721	43816721	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcatcagtccccagtggaagAaaagtctgagccccaagact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:43816721delA	ENST00000300231.5	+	4	3500	c.3050delA	c.(3049-3051)gaafs	p.E1017fs	MAP1A_ENST00000399453.1_Frame_Shift_Del_p.E1017fs|MAP1A_ENST00000382031.1_Frame_Shift_Del_p.E1255fs			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1017					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	CCAGTGGAAGAAAAGTCTGAG	0.562																																					p.E1017fs		Atlas-INDEL	.											.	MAP1A	189	.	0			c.3049delG						.						61	64	63					15																	43816721		1995	4159	6154	SO:0001589	frameshift_variant	4130	exon4			.	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.3050delA	chr15.hg19:g.43816721delA	ENSP00000300231:p.Glu1017fs	108.0	0.0		123.0	10.0	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Frame_Shift_Del	DEL	ENST00000300231.5	hg19	CCDS42031.1																																																																																			.	.		0.562	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		-	43816721	A	-	43816721	7	5	114	1	0	1	0	1	0	0	0	0	9236	246	9	0	3052	0	MAP1A	15	43816721	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	141201	43816721	58714671	919	19191										
SPATA5L1	79029	hgsc.bcm.edu	37	chr15	45707941	45707941	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tagatggtgttggacttaagAcaatagagagaagaggaagt	14	2	0	5			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:45707941A>G	ENST00000305560.6	+	5	1900	c.1801A>G	c.(1801-1803)Aca>Gca	p.T601A	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.T601A	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	601						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		TGGACTTAAGACAATAGAGAG	0.403																																					p.T601A		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.A1801G						.						56	54	55					15																	45707941		2198	4298	6496	SO:0001583	missense	79029	exon5			CTTAAGACAATAG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"ATPases / AAA-type"	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.1801A>G	chr15.hg19:g.45707941A>G	ENSP00000305494:p.Thr601Ala	64.0	0.0		79.0	4.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	hg19	CCDS10123.1	.	.	.	.	.	.	.	.	.	.	A	13.06	2.124180	0.37533	.	.	ENSG00000171763	ENST00000305560	D	0.94046	-3.34	5.54	4.39	0.52855	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.183872	0.47093	D	0.000255	D	0.86822	0.6025	N	0.25485	0.75	0.27516	N	0.951533	B	0.27791	0.189	B	0.27380	0.079	T	0.79259	-0.1877	10	0.51188	T	0.08	-19.2834	7.1502	0.25606	0.7725:0.1496:0.0779:0.0	.	601	Q9BVQ7	SPA5L_HUMAN	A	601	ENSP00000305494:T601A	ENSP00000305494:T601A	T	+	1	0	SPATA5L1	43495233	0.993000	0.37304	0.996000	0.52242	0.997000	0.91878	1.565000	0.36386	0.999000	0.39023	0.533000	0.62120	ACA	.	.		0.403	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		G	45707941	A	G	45707941	3	3	114	1	0	0	0	0	1	0	0	0	15027	275	10	2	1819	2	SPATA5L1	15	45707941	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1891220	45707941	56823451	920	19192										
HDC	3067	hgsc.bcm.edu	37	chr15	50534669	50534669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggcagtggcttctgagcacTcactggcacactgttgcaac	12	12	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:50534669T>C	ENST00000267845.3	-	12	2179	c.1777A>G	c.(1777-1779)Agt>Ggt	p.S593G	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Missense_Mutation_p.S560G	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		TTCTGAGCACTCACTGGCACA	0.527																																					p.S593G	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.A1777G						.						155	170	165					15																	50534669		2196	4295	6491	SO:0001583	missense	3067	exon12			GAGCACTCACTGG		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1777A>G	chr15.hg19:g.50534669T>C	ENSP00000267845:p.Ser593Gly	101.0	0.0		104.0	6.0	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	hg19	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	T	8.433	0.849030	0.17034	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.09255	3.08;3.0	5.48	-1.75	0.08031	.	0.332817	0.26086	N	0.026433	T	0.04227	0.0117	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27971	-1.0058	10	0.49607	T	0.09	-1.7839	0.9748	0.01423	0.1419:0.2124:0.2895:0.3562	.	560;593	B7ZM01;P19113	.;DCHS_HUMAN	G	593;560	ENSP00000267845:S593G;ENSP00000440252:S560G	ENSP00000267845:S593G	S	-	1	0	HDC	48321961	0.000000	0.05858	0.034000	0.17996	0.592000	0.36648	0.348000	0.20031	0.022000	0.15160	0.460000	0.39030	AGT	.	.		0.527	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			C	50534669	T	C	50534669	3	2	114	1	0	0	0	0	1	0	0	0	7024	1551	54	2	215	2	HDC	15	50534669	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4826728	50534669	51996723	921	19193										
HDC	3067	hgsc.bcm.edu	37	chr15	50549687	50549687	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgctctggaagtcccagcaTttttgccaaccagtccatga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:50549687delT	ENST00000267845.3	-	4	778	c.376delA	c.(376-378)atgfs	p.M126fs	HDC_ENST00000543581.1_Frame_Shift_Del_p.M126fs	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		AGTCCCAGCATTTTTGCCAAC	0.577																																					p.M126fs	GBM(95;1627 1936 6910 9570)	Atlas-INDEL	.											HDC,NS,carcinoma,0,1	HDC	86	.	0			c.377delT						.						139	117	124					15																	50549687		2196	4295	6491	SO:0001589	frameshift_variant	3067	exon4			.		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.376delA	chr15.hg19:g.50549687delT	ENSP00000267845:p.Met126fs	108.0	0.0		164.0	16.0	NM_002112		Frame_Shift_Del	DEL	ENST00000267845.3	hg19	CCDS10134.1																																																																																			.	.		0.577	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			-	50549687	T	-	50549687	7	5	114	1	0	1	0	1	0	0	0	0	7024	1493	52	0	1648	0	HDC	15	50549687	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	15018	50549687	51981705	922	19194										
AP4E1	23431	hgsc.bcm.edu	37	chr15	51285814	51285814	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtctaggatcagaaagtacaAtcaacctggtaagtaatcgg	10	7	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:51285814A>G	ENST00000261842.5	+	17	2444	c.2338A>G	c.(2338-2340)Atc>Gtc	p.I780V	AP4E1_ENST00000560508.1_Missense_Mutation_p.I705V	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	780					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		AGAAAGTACAATCAACCTGGT	0.373																																					p.I780V		Atlas-SNP	.											.	AP4E1	78	.	0			c.A2338G						.						114	111	112					15																	51285814		2196	4294	6490	SO:0001583	missense	23431	exon17			AGTACAATCAACC	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2338A>G	chr15.hg19:g.51285814A>G	ENSP00000261842:p.Ile780Val	75.0	0.0		84.0	4.0	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	hg19	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	A	0.006	-2.102690	0.00356	.	.	ENSG00000081014	ENST00000261842	T	0.14266	2.52	5.37	-8.36	0.00980	.	0.468479	0.23003	N	0.053058	T	0.03695	0.0105	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23048	-1.0199	10	0.02654	T	1	-0.0055	18.3925	0.90487	0.258:0.0:0.742:0.0	.	780	Q9UPM8	AP4E1_HUMAN	V	780	ENSP00000261842:I780V	ENSP00000261842:I780V	I	+	1	0	AP4E1	49073106	0.002000	0.14202	0.011000	0.14972	0.077000	0.17291	-0.267000	0.08619	-1.562000	0.01682	-1.389000	0.01157	ATC	.	.		0.373	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			G	51285814	A	G	51285814	3	3	114	1	0	0	0	0	1	0	0	0	752	101	4	2	2404	2	AP4E1	15	51285814	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	736127	51285814	51245578	923	19195										
WDR72	256764	hgsc.bcm.edu	37	chr15	54004983	54004983	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taataccttccaacatttagAaaataccaccaatagaagtc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:54004983delA	ENST00000396328.1	-	7	936	c.697delT	c.(697-699)tctfs	p.S233fs	WDR72_ENST00000557913.1_Frame_Shift_Del_p.S232fs|WDR72_ENST00000559418.1_Frame_Shift_Del_p.S233fs|WDR72_ENST00000360509.5_Frame_Shift_Del_p.S233fs	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	233										NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		CAACATTTAGAAAATACCACC	0.289																																					p.S233fs		Atlas-INDEL	.											.	WDR72	177	.	0			c.698delC						.						53	56	55					15																	54004983		2191	4293	6484	SO:0001589	frameshift_variant	256764	exon7			.	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"WD repeat domain containing"	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.697delT	chr15.hg19:g.54004983delA	ENSP00000379619:p.Ser233fs	203.0	0.0		229.0	14.0	NM_182758	Q7Z3I3|Q8N8X2	Frame_Shift_Del	DEL	ENST00000396328.1	hg19	CCDS10151.1																																																																																			.	.		0.289	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		-	54004983	A	-	54004983	7	5	114	1	0	1	0	1	0	0	0	0	17337	246	9	0	2667	0	WDR72	15	54004983	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2719169	54004983	48526409	924	19196										
MNS1	55329	hgsc.bcm.edu	37	chr15	56723587	56723587	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttactttagggagatagcctAgtaagtttgtagcatgctct	10	6	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:56723587A>G	ENST00000260453.3	-	9	1543	c.1379T>C	c.(1378-1380)cTa>cCa	p.L460P	MNS1_ENST00000566386.1_5'UTR|TEX9_ENST00000352903.2_Intron|TEX9_ENST00000537232.1_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	460					cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		GAGATAGCCTAGTAAGTTTGT	0.363																																					p.L460P		Atlas-SNP	.											.	MNS1	39	.	0			c.T1379C						.						120	114	116					15																	56723587		2192	4292	6484	SO:0001583	missense	55329	exon9			TAGCCTAGTAAGT	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"spermatogenesis associated 40"	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.1379T>C	chr15.hg19:g.56723587A>G	ENSP00000260453:p.Leu460Pro	162.0	0.0		204.0	9.0	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	hg19	CCDS10158.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.199532	0.79015	.	.	ENSG00000138587	ENST00000260453	T	0.15372	2.43	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.47154	0.1430	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.50320	-0.8842	10	0.72032	D	0.01	-8.5883	15.9872	0.80168	1.0:0.0:0.0:0.0	.	460	Q8NEH6	MNS1_HUMAN	P	460	ENSP00000260453:L460P	ENSP00000260453:L460P	L	-	2	0	MNS1	54510879	1.000000	0.71417	0.923000	0.36655	0.979000	0.70002	7.991000	0.88244	2.367000	0.80283	0.528000	0.53228	CTA	.	.		0.363	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365		G	56723587	A	G	56723587	3	3	114	1	0	0	0	0	1	0	0	0	9686	420	15	2	116	2	MNS1	15	56723587	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2718604	56723587	45807805	925	19197										
CGNL1	84952	hgsc.bcm.edu	37	chr15	57743740	57743740	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcaaagatctattggaacagAaaagcaagttgaccatagaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:57743740delA	ENST00000281282.5	+	5	1924	c.1846delA	c.(1846-1848)aaafs	p.K616fs		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	616						myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		ATTGGAACAGAAAAGCAAGTT	0.328																																					p.Q615fs		Atlas-INDEL	.											.	CGNL1	125	.	0			c.1845delG						.						88	94	92					15																	57743740		2192	4292	6484	SO:0001589	frameshift_variant	84952	exon6			.	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.1846delA	chr15.hg19:g.57743740delA	ENSP00000281282:p.Lys616fs	154.0	0.0		179.0	11.0	NM_001252335	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Frame_Shift_Del	DEL	ENST00000281282.5	hg19	CCDS10161.1																																																																																			.	.		0.328	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		-	57743740	A	-	57743740	7	5	114	1	0	1	0	1	0	0	0	0	3306	247	9	0	1860	0	CGNL1	15	57743740	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1020153	57743740	44787652	926	19198										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62283910	62283910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttcgtcctttttcttagacTctttcttaccccacaaccca	2	16	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:62283910T>C	ENST00000261517.5	-	17	1518	c.1445A>G	c.(1444-1446)gAg>gGg	p.E482G	VPS13C_ENST00000249837.3_Missense_Mutation_p.E439G|VPS13C_ENST00000395898.3_Missense_Mutation_p.E439G|VPS13C_ENST00000395896.4_Missense_Mutation_p.E482G	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TTTCTTAGACTCTTTCTTACC	0.368																																					p.E482G		Atlas-SNP	.											.	VPS13C	506	.	0			c.A1445G						.						165	173	170					15																	62283910		2203	4300	6503	SO:0001583	missense	54832	exon17			TTAGACTCTTTCT	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.1445A>G	chr15.hg19:g.62283910T>C	ENSP00000261517:p.Glu482Gly	143.0	0.0		147.0	6.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	13.99	2.402608	0.42613	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.47177	0.85;0.85;1.02	5.78	5.78	0.91487	.	0.178046	0.48767	D	0.000180	T	0.44286	0.1286	L	0.43923	1.385	0.46564	D	0.999105	B;B;B;B	0.18166	0.011;0.026;0.011;0.015	B;B;B;B	0.22880	0.025;0.042;0.004;0.017	T	0.29150	-1.0021	10	0.46703	T	0.11	.	16.1103	0.81259	0.0:0.0:0.0:1.0	.	439;482;439;482	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	G	439;482;482;482	ENSP00000249837:E439G;ENSP00000261517:E482G;ENSP00000379233:E482G	ENSP00000249837:E439G	E	-	2	0	VPS13C	60071202	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.206000	0.58473	2.207000	0.71202	0.482000	0.46254	GAG	.	.		0.368	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		C	62283910	T	C	62283910	3	2	114	1	0	0	0	0	1	0	0	0	17206	1551	54	2	10120	2	VPS13C	15	62283910	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4540170	62283910	40247482	927	19199										
MTFMT	123263	hgsc.bcm.edu	37	chr15	65295429	65295429	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcattgttgcatagcaacagTttttttctgcttcttctttg					rs368759868		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:65295429delT	ENST00000220058.4	-	9	1154	c.1141delA	c.(1141-1143)actfs	p.T381fs		NM_139242.3	NP_640335.2	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase	381						mitochondrion (GO:0005739)	methionyl-tRNA formyltransferase activity (GO:0004479)			endometrium(1)|large_intestine(3)|lung(3)|ovary(3)	10					Tetrahydrofolic acid(DB00116)	ATAGCAACAGTTTTTTTCTGC	0.343																																					p.T381fs		Atlas-INDEL	.											.	MTFMT	28	.	0			c.1142delC						.						114	102	106					15																	65295429		1828	4086	5914	SO:0001589	frameshift_variant	123263	exon9			.	AK055688	CCDS45280.1	15q22.31	2006-11-29		2005-08-09		ENSG00000103707			29666	protein-coding gene	gene with protein product		611766				9614118	Standard	NM_139242		Approved	FMT1	uc002aof.4	Q96DP5		ENST00000220058.4:c.1141delA	chr15.hg19:g.65295429delT	ENSP00000220058:p.Thr381fs	76.0	0.0		115.0	10.0	NM_139242	B7Z734	Frame_Shift_Del	DEL	ENST00000220058.4	hg19	CCDS45280.1																																																																																			.	.		0.343	MTFMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418155.1	NM_139242		-	65295429	T	-	65295429	7	5	114	1	0	1	0	1	0	0	0	0	9933	1725	60	0	32	0	MTFMT	15	65295429	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3011519	65295429	37235963	928	19200										
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65676554	65676554	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agctcacaccctcccaactcCctgtccagccaggctgcccc	6	22	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:65676554C>A	ENST00000352385.2	-	20	3755	c.3546G>T	c.(3544-3546)agG>agT	p.R1182S	IGDCC4_ENST00000558048.1_5'UTR	NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	1182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						CTCCCAACTCCCTGTCCAGCC	0.657																																					p.R1182S		Atlas-SNP	.											.	IGDCC4	95	.	0			c.G3546T						.						23	27	25					15																	65676554		2201	4299	6500	SO:0001583	missense	57722	exon20			CAACTCCCTGTCC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.3546G>T	chr15.hg19:g.65676554C>A	ENSP00000319623:p.Arg1182Ser	143.0	0.0		178.0	62.0	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	C	7.389	0.630391	0.14322	.	.	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.60672	0.17	5.02	1.62	0.23740	.	0.845108	0.10220	N	0.700982	T	0.42899	0.1223	L	0.29908	0.895	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.31696	-0.9934	10	0.40728	T	0.16	-3.6858	7.4997	0.27511	0.0:0.6794:0.0:0.3206	.	1182	Q8TDY8	IGDC4_HUMAN	S	1182;911	ENSP00000319623:R1182S	ENSP00000319623:R1182S	R	-	3	2	IGDCC4	63463607	0.012000	0.17670	0.637000	0.29366	0.105000	0.19272	0.430000	0.21428	0.545000	0.28902	0.555000	0.69702	AGG	.	.		0.657	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		A	65676554	C	A	65676554	3	1	114	1	0	0	0	0	1	0	0	0	7578	622	22	3	210	3	IGDCC4	15	65676554	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	381125	65676554	36854838	929	19201										
TLE3	7090	hgsc.bcm.edu	37	chr15	70358457	70358457	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cggagctgctccctgtcactGgggggattcctggaggctgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:70358457delG	ENST00000558939.1	-	7	1850	c.473delC	c.(472-474)ccafs	p.P158fs	TLE3_ENST00000559191.1_Intron|TLE3_ENST00000442299.2_Frame_Shift_Del_p.P158fs|TLE3_ENST00000440567.3_Frame_Shift_Del_p.P151fs|TLE3_ENST00000557907.1_Frame_Shift_Del_p.P158fs|TLE3_ENST00000451782.2_Frame_Shift_Del_p.P158fs|TLE3_ENST00000558379.1_Frame_Shift_Del_p.P158fs|TLE3_ENST00000317509.8_Frame_Shift_Del_p.P158fs|TLE3_ENST00000560589.1_Frame_Shift_Del_p.P102fs|TLE3_ENST00000558201.1_Frame_Shift_Del_p.P164fs|TLE3_ENST00000559048.1_Frame_Shift_Del_p.P163fs|TLE3_ENST00000557997.1_Frame_Shift_Del_p.P158fs|TLE3_ENST00000560939.1_Frame_Shift_Del_p.P163fs|TLE3_ENST00000559929.1_Frame_Shift_Del_p.P168fs|TLE3_ENST00000539550.1_Frame_Shift_Del_p.P102fs	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	158	Gly/Pro-rich.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CCCTGTCACTGGGGGGATTCC	0.667																																					p.P158fs		Atlas-INDEL	.											.	TLE3	104	.	0			c.474delA						.						22	25	24					15																	70358457		1948	4153	6101	SO:0001589	frameshift_variant	7090	exon7			.	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"WD repeat domain containing"	11839	protein-coding gene	gene with protein product		600190	"transducin-like enhancer of split 3, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.473delC	chr15.hg19:g.70358457delG	ENSP00000452871:p.Pro158fs	161.0	0.0		226.0	14.0	NM_001105192	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Frame_Shift_Del	DEL	ENST00000558939.1	hg19	CCDS45293.1																																																																																			.	.		0.667	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078		-	70358457	G	-	70358457	7	5	114	1	0	1	0	1	0	0	0	0	15955	1348	47	0	1901	0	TLE3	15	70358457	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	4681903	70358457	32172935	930	19202										
UACA	55075	hgsc.bcm.edu	37	chr15	70959454	70959454	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgttttggctttcttcttccTtttctctcaagctggctttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:70959454delT	ENST00000322954.6	-	16	3754	c.3569delA	c.(3568-3570)aagfs	p.K1190fs	UACA_ENST00000560441.1_Frame_Shift_Del_p.K1175fs|UACA_ENST00000379983.2_Frame_Shift_Del_p.K1177fs|UACA_ENST00000539319.1_Frame_Shift_Del_p.K1081fs	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1190					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TTCTTCTTCCTTTTCTCTCAA	0.373																																					p.K1190fs		Atlas-INDEL	.											.	UACA	235	.	0			c.3570delG						.						147	141	143					15																	70959454		2199	4297	6496	SO:0001589	frameshift_variant	55075	exon16			.	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.3569delA	chr15.hg19:g.70959454delT	ENSP00000314556:p.Lys1190fs	136.0	0.0		156.0	10.0	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Frame_Shift_Del	DEL	ENST00000322954.6	hg19	CCDS10235.1																																																																																			.	.		0.373	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			-	70959454	T	-	70959454	7	5	114	1	0	1	0	1	0	0	0	0	16839	1609	56	0	697	0	UACA	15	70959454	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	600997	70959454	31571938	931	19203										
LRRC49	54839	hgsc.bcm.edu	37	chr15	71188254	71188254	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttttacaacatgaccttgaaAgaaactactcaagtaggcaa	6	8	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:71188254A>G	ENST00000260382.5	+	3	432	c.172A>G	c.(172-174)Aga>Gga	p.R58G	LRRC49_ENST00000544974.2_Missense_Mutation_p.R48G|LRRC49_ENST00000436542.2_3'UTR|LRRC49_ENST00000443425.2_5'UTR|LRRC49_ENST00000560691.1_5'UTR|LRRC49_ENST00000560369.1_Missense_Mutation_p.R63G	NM_001199017.1|NM_017691.3	NP_001185946.1|NP_060161.2	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49	58						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						TGACCTTGAAAGAAACTACTC	0.308																																					p.R63G		Atlas-SNP	.											.	LRRC49	73	.	0			c.A187G						.						78	76	77					15																	71188254		2199	4297	6496	SO:0001583	missense	54839	exon3			CTTGAAAGAAACT		CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1	15q23	2005-08-09				ENSG00000137821			25965	protein-coding gene	gene with protein product						12477932	Standard	NM_001199017		Approved	FLJ20156	uc010ukf.2	Q8IUZ0		ENST00000260382.5:c.172A>G	chr15.hg19:g.71188254A>G	ENSP00000260382:p.Arg58Gly	59.0	0.0		90.0	4.0	NM_001199017	B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6	Missense_Mutation	SNP	ENST00000260382.5	hg19	CCDS32282.1	.	.	.	.	.	.	.	.	.	.	A	16.48	3.136024	0.56936	.	.	ENSG00000137821	ENST00000544974;ENST00000260382	T;T	0.36157	1.27;1.28	5.37	5.37	0.77165	.	0.077557	0.52532	D	0.000065	T	0.25082	0.0609	N	0.14661	0.345	0.80722	D	1	B;B;B	0.22211	0.039;0.039;0.066	B;B;B	0.24394	0.016;0.016;0.053	T	0.06881	-1.0802	10	0.59425	D	0.04	-19.6097	13.6216	0.62140	1.0:0.0:0.0:0.0	.	63;58;48	B7Z366;Q8IUZ0;F5H1J4	.;LRC49_HUMAN;.	G	48;58	ENSP00000439600:R48G;ENSP00000260382:R58G	ENSP00000260382:R58G	R	+	1	2	LRRC49	68975308	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.831000	0.69330	2.155000	0.67459	0.460000	0.39030	AGA	.	.		0.308	LRRC49-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417209.3	NM_017691		G	71188254	A	G	71188254	3	3	114	1	0	0	0	0	1	0	0	0	9015	64	3	2	182	2	LRRC49	15	71188254	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	228800	71188254	31343138	932	19204										
STOML1	9399	hgsc.bcm.edu	37	chr15	74284520	74284520	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctcgactgctggaagcggtcAaaatcacccaggggcagcgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:74284520delA	ENST00000316900.5	-	1	169	c.45delT	c.(43-45)tttfs	p.F15fs	PML_ENST00000395135.3_5'Flank|STOML1_ENST00000316911.6_Frame_Shift_Del_p.F15fs|PML_ENST00000563500.1_5'Flank|STOML1_ENST00000564777.1_Frame_Shift_Del_p.F15fs|PML_ENST00000268058.3_5'Flank|PML_ENST00000565898.1_5'Flank|STOML1_ENST00000359750.4_Frame_Shift_Del_p.F15fs|STOML1_ENST00000561656.1_Intron|PML_ENST00000435786.2_5'Flank|PML_ENST00000436891.3_5'Flank|PML_ENST00000395132.2_5'Flank|PML_ENST00000564428.1_5'Flank|PML_ENST00000569965.1_5'Flank|PML_ENST00000354026.6_5'Flank|STOML1_ENST00000541638.1_5'UTR|PML_ENST00000268059.6_5'Flank|PML_ENST00000567543.1_5'Flank|PML_ENST00000359928.4_5'Flank|PML_ENST00000569477.1_5'Flank	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	15						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						GGAAGCGGTCAAAATCACCCA	0.711																																					p.D16fs		Atlas-INDEL	.											.	STOML1	22	.	0			c.46delG						.						22	27	25					15																	74284520		2191	4290	6481	SO:0001589	frameshift_variant	9399	exon1			.	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"stomatin-like 1", "stomatin (EBP72)-like 1"	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.45delT	chr15.hg19:g.74284520delA	ENSP00000319323:p.Phe15fs	188.0	0.0		155.0	11.0	NM_004809	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Frame_Shift_Del	DEL	ENST00000316900.5	hg19	CCDS10254.1																																																																																			.	.		0.711	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809		-	74284520	A	-	74284520	7	5	114	1	0	1	0	1	0	0	0	0	15328	127	5	0	1179	0	STOML1	15	74284520	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3096266	74284520	28246872	933	19205										
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84539614	84539614	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagctttaacagccccggcgTctttctcgtagaaaacacaa	7	13	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:84539614T>C	ENST00000286744.5	+	9	1087	c.863T>C	c.(862-864)gTc>gCc	p.V288A	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.V288A	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	288						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AGCCCCGGCGTCTTTCTCGTA	0.378																																					p.V288A		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.T863C						.						61	67	65					15																	84539614		2203	4300	6503	SO:0001583	missense	57188	exon9			CCGGCGTCTTTCT	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.863T>C	chr15.hg19:g.84539614T>C	ENSP00000286744:p.Val288Ala	40.0	0.0		31.0	6.0	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	hg19	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	T	5.437	0.265673	0.10294	.	.	ENSG00000156218	ENST00000286744	T	0.62498	0.02	4.69	2.32	0.28847	.	1.314130	0.05205	N	0.505614	T	0.49115	0.1538	L	0.28458	0.855	0.09310	N	1	B;B	0.24483	0.032;0.104	B;B	0.28991	0.097;0.058	T	0.31223	-0.9951	10	0.09590	T	0.72	.	7.0714	0.25181	0.0:0.2726:0.0:0.7274	.	288;288	P82987-2;P82987	.;ATL3_HUMAN	A	288	ENSP00000286744:V288A	ENSP00000286744:V288A	V	+	2	0	ADAMTSL3	82330618	0.712000	0.27916	0.007000	0.13788	0.039000	0.13416	0.777000	0.26718	0.171000	0.19730	0.379000	0.24179	GTC	.	.		0.378	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		C	84539614	T	C	84539614	3	2	114	1	0	0	0	0	1	0	0	0	276	1667	58	2	893	2	ADAMTSL3	15	84539614	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	10255094	84539614	17991778	934	19206										
ALPK3	57538	hgsc.bcm.edu	37	chr15	85400767	85400767	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaccatggccaccagcagtgAgggggcctgcgcccaggtac	14	14	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:85400767A>G	ENST00000258888.5	+	6	3571	c.3404A>G	c.(3403-3405)gAg>gGg	p.E1135G		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1135					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			ACCAGCAGTGAGGGGGCCTGC	0.627																																					p.E1135G		Atlas-SNP	.											.	ALPK3	289	.	0			c.A3404G						.						36	42	40					15																	85400767		2201	4299	6500	SO:0001583	missense	57538	exon6			GCAGTGAGGGGGC	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.3404A>G	chr15.hg19:g.85400767A>G	ENSP00000258888:p.Glu1135Gly	96.0	0.0		97.0	4.0	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	hg19	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.418055	0.25552	.	.	ENSG00000136383	ENST00000258888	T	0.61742	0.08	5.17	2.21	0.28008	.	1.559240	0.03447	N	0.210078	T	0.49321	0.1550	L	0.32530	0.975	0.27262	N	0.958594	B	0.27351	0.176	B	0.30251	0.113	T	0.44298	-0.9337	10	0.54805	T	0.06	-27.3278	6.3279	0.21255	0.7036:0.0:0.2964:0.0	.	1135	Q96L96	ALPK3_HUMAN	G	1135	ENSP00000258888:E1135G	ENSP00000258888:E1135G	E	+	2	0	ALPK3	83201771	0.090000	0.21635	0.977000	0.42913	0.199000	0.23934	0.625000	0.24477	0.687000	0.31509	0.460000	0.39030	GAG	.	.		0.627	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		G	85400767	A	G	85400767	3	3	114	1	0	0	0	0	1	0	0	0	546	304	11	2	3426	2	ALPK3	15	85400767	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	861153	85400767	17130625	935	19207										
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85431063	85431063	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccaagggtctggagaacatGggggctgatttcttggaaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:85431063delG	ENST00000286749.3	+	2	162	c.72delG	c.(70-72)atgfs	p.M24fs	SLC28A1_ENST00000338602.2_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000538177.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000394573.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000537703.1_5'UTR|SLC28A1_ENST00000537624.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000537216.1_Frame_Shift_Del_p.M24fs			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	24					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TGGAGAACATGGGGGCTGATT	0.567																																					p.M24fs		Atlas-INDEL	.											.	SLC28A1	118	.	0			c.71delT						.						172	155	161					15																	85431063		2203	4299	6502	SO:0001589	frameshift_variant	9154	exon3			.	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"Solute carriers"	11001	protein-coding gene	gene with protein product		606207	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.72delG	chr15.hg19:g.85431063delG	ENSP00000286749:p.Met24fs	161.0	0.0		190.0	12.0	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Frame_Shift_Del	DEL	ENST00000286749.3	hg19	CCDS10334.1																																																																																			.	.		0.567	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			-	85431063	G	-	85431063	7	5	114	1	0	1	0	1	0	0	0	0	14546	1348	47	0	74	0	SLC28A1	15	85431063	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	30296	85431063	17100329	936	19208										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86207943	86207943	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtgtcactttcagaagaggAtctggagtcagaccagagag	14	7	4	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:86207943A>G	ENST00000394518.2	+	13	5044	c.4949A>G	c.(4948-4950)gAt>gGt	p.D1650G	AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000361243.2_Missense_Mutation_p.D1654G|RP11-815J21.4_ENST00000558980.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1650					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						TCAGAAGAGGATCTGGAGTCA	0.403																																					p.D1654G	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.A4961G						.						101	92	95					15																	86207943		2202	4299	6501	SO:0001583	missense	11214	exon13			AAGAGGATCTGGA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.4949A>G	chr15.hg19:g.86207943A>G	ENSP00000378026:p.Asp1650Gly	81.0	0.0		94.0	4.0	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.629807	0.46944	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000452008	T;T	0.13420	2.62;2.59	5.64	5.64	0.86602	.	.	.	.	.	T	0.27866	0.0686	L	0.60455	1.87	0.80722	D	1	D;P;D	0.55385	0.971;0.952;0.971	P;P;P	0.55749	0.783;0.612;0.783	T	0.00756	-1.1579	9	0.66056	D	0.02	.	14.1079	0.65104	1.0:0.0:0.0:0.0	.	1632;1650;1654	Q12802-4;Q12802;Q12802-2	.;AKP13_HUMAN;.	G	1654;1650;1653;1631;272	ENSP00000354718:D1654G;ENSP00000378026:D1650G	ENSP00000354718:D1654G	D	+	2	0	AKAP13	84008947	1.000000	0.71417	0.964000	0.40570	0.144000	0.21451	5.933000	0.70130	2.275000	0.75901	0.528000	0.53228	GAT	.	.		0.403	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		G	86207943	A	G	86207943	3	3	114	1	0	0	0	0	1	0	0	0	449	333	12	2	5065	2	AKAP13	15	86207943	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	776880	86207943	16323449	937	19209										
ACAN	176	hgsc.bcm.edu	37	chr15	89398305	89398305	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attcccctccaaggagccatCcccctcagaggaaccatcag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:89398305delC	ENST00000561243.1	+	11	2489	c.2489delC	c.(2488-2490)tccfs	p.S830fs	ACAN_ENST00000559004.1_Frame_Shift_Del_p.S830fs|ACAN_ENST00000352105.7_Frame_Shift_Del_p.S830fs|ACAN_ENST00000439576.2_Frame_Shift_Del_p.S830fs			P16112	PGCA_HUMAN	aggrecan	829	12 X 6 AA approximate tandem repeats of E-[GVE]-P-[SFY]-[APT]-[TSP].|KS.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			AAGGAGCCATCCCCCTCAGAG	0.632																																					p.S830fs		Atlas-INDEL	.											.	ACAN	220	.	0			c.2488delT						.						32	37	35					15																	89398305		1967	4151	6118	SO:0001589	frameshift_variant	176	exon12			.	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.2489delC	chr15.hg19:g.89398305delC	ENSP00000453342:p.Ser830fs	129.0	0.0		184.0	12.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Frame_Shift_Del	DEL	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.632	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		-	89398305	C	-	89398305	7	5	114	1	0	1	0	1	0	0	0	0	117	855	30	0	2531	0	ACAN	15	89398305	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3190362	89398305	13133087	938	19210										
POLG	5428	hgsc.bcm.edu	37	chr15	89860003	89860003	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tatggtccaggctggcttcgTttttccaaggagcctttggt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:89860003delT	ENST00000268124.5	-	23	4032	c.3699delA	c.(3697-3699)aaafs	p.K1233fs	FANCI_ENST00000300027.8_3'UTR|POLG_ENST00000442287.2_Frame_Shift_Del_p.K1233fs|FANCI_ENST00000310775.7_3'UTR	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	1233					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			GCTGGCTTCGTTTTTCCAAGG	0.507								DNA polymerases (catalytic subunits)																													p.R1234fs	Colon(73;648 1203 11348 18386 27782)	Atlas-INDEL	.											.	POLG	75	.	0			c.3700delC						.						105	98	100					15																	89860003		2200	4299	6499	SO:0001589	frameshift_variant	5428	exon23			.	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"DNA polymerases"	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.3699delA	chr15.hg19:g.89860003delT	ENSP00000268124:p.Lys1233fs	192.0	0.0		168.0	11.0	NM_001126131	Q8NFM2|Q92515	Frame_Shift_Del	DEL	ENST00000268124.5	hg19	CCDS10350.1																																																																																			.	.		0.507	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		-	89860003	T	-	89860003	7	5	114	1	0	1	0	1	0	0	0	0	12209	1722	60	0	24	0	POLG	15	89860003	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	461698	89860003	12671389	939	19211										
UNC45A	55898	hgsc.bcm.edu	37	chr15	91488144	91488144	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgaaaaagattttggaagtGgggggctctctacaggaccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:91488144delG	ENST00000418476.2	+	9	1090	c.1050delG	c.(1048-1050)gtgfs	p.V350fs	UNC45A_ENST00000394275.2_Frame_Shift_Del_p.V335fs	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	350					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TTTTGGAAGTGGGGGGCTCTC	0.507																																					p.V350fs		Atlas-INDEL	.											.	UNC45A	57	.	0			c.1049delT						.																																			SO:0001589	frameshift_variant	55898	exon9			.		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"smooth muscle cell associated protein-1"	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.1050delG	chr15.hg19:g.91488144delG	ENSP00000407487:p.Val350fs	142.0	0.0		178.0	11.0	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Frame_Shift_Del	DEL	ENST00000418476.2	hg19	CCDS10367.1																																																																																			.	.		0.507	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671		-	91488144	G	-	91488144	7	5	114	1	0	1	0	1	0	0	0	0	17003	1335	47	0	1084	0	UNC45A	15	91488144	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1628141	91488144	11043248	940	19212										
RCCD1	91433	hgsc.bcm.edu	37	chr15	91500927	91500927	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcatggctgaggtggccgcGgggggctggcattctgtgtg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:91500927delG	ENST00000394258.2	+	4	853	c.651delG	c.(649-651)gcgfs	p.A217fs	RCCD1_ENST00000556774.1_Intron|RCCD1_ENST00000555155.1_Frame_Shift_Del_p.A217fs|RCCD1_ENST00000556618.1_Frame_Shift_Del_p.A217fs|AC068831.6_ENST00000553321.1_RNA	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	217						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			AGGTGGCCGCGGGGGGCTGGC	0.597																																					p.A217fs		Atlas-INDEL	.											.	RCCD1	9	.	0			c.650delC						.						109	107	108					15																	91500927		2198	4298	6496	SO:0001589	frameshift_variant	91433	exon4			.		CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.651delG	chr15.hg19:g.91500927delG	ENSP00000377801:p.Ala217fs	153.0	0.0		226.0	16.0	NM_001017919	B2RTP9|Q29RX6	Frame_Shift_Del	DEL	ENST00000394258.2	hg19	CCDS32333.1																																																																																			.	.		0.597	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544		-	91500927	G	-	91500927	7	5	114	1	0	1	0	1	0	0	0	0	13190	1103	39	0	661	0	RCCD1	15	91500927	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	12783	91500927	11030465	941	19213										
CHD2	1106	hgsc.bcm.edu	37	chr15	93547897	93547897	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaatcaaagcgatctcagggTcctgtccatattacagcagg	9	10	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:93547897T>C	ENST00000394196.4	+	34	5397	c.4329T>C	c.(4327-4329)ggT>ggC	p.G1443G	CHD2_ENST00000557381.1_Silent_p.G1443G	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1443					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GATCTCAGGGTCCTGTCCATA	0.433																																					p.G1443G		Atlas-SNP	.											.	CHD2	280	.	0			c.T4329C						.						173	156	162					15																	93547897		2197	4298	6495	SO:0001819	synonymous_variant	1106	exon34			TCAGGGTCCTGTC	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4329T>C	chr15.hg19:g.93547897T>C		100.0	0.0		104.0	5.0	NM_001271	C6G482|Q96IP5	Silent	SNP	ENST00000394196.4	hg19	CCDS10374.2																																																																																			.	.		0.433	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		C	93547897	T	C	93547897	2	2	114	1	0	0	0	0	0	0	0	1	3327	1654	58	2		2	CHD2	15	93547897	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2046970	93547897	8983495	942	19214										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99434602	99434602	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgcaccgagaacaatgagtGctgccaccccgagtgcctgg	13	13	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:99434602G>A	ENST00000268035.6	+	3	1300	c.689G>A	c.(688-690)tGc>tAc	p.C230Y	RP11-654A16.1_ENST00000558736.1_RNA|IGF1R_ENST00000560432.1_3'UTR|IGF1R_ENST00000558762.1_Missense_Mutation_p.C230Y	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	230					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	AACAATGAGTGCTGCCACCCC	0.652																																					p.C230Y		Atlas-SNP	.											.	IGF1R	147	.	0			c.G689A						.						50	41	44					15																	99434602		2197	4297	6494	SO:0001583	missense	3480	exon3			ATGAGTGCTGCCA	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.689G>A	chr15.hg19:g.99434602G>A	ENSP00000268035:p.Cys230Tyr	50.0	0.0		93.0	4.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.544444	0.86022	.	.	ENSG00000140443	ENST00000268035	D	0.89485	-2.52	5.12	5.12	0.69794	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.000000	0.64402	D	0.000004	D	0.95981	0.8691	M	0.92833	3.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.96814	0.9599	10	0.87932	D	0	.	18.9213	0.92526	0.0:0.0:1.0:0.0	.	230;230	C9J5X1;P08069	.;IGF1R_HUMAN	Y	230	ENSP00000268035:C230Y	ENSP00000268035:C230Y	C	+	2	0	IGF1R	97252125	1.000000	0.71417	1.000000	0.80357	0.673000	0.39480	9.768000	0.98965	2.549000	0.85964	0.561000	0.74099	TGC	.	.		0.652	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99434602	G	A	99434602	3	1	114	1	0	0	0	0	1	0	0	0	7580	1319	46	3	699	3	IGF1R	15	99434602	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	5886705	99434602	3096790	943	19215										
RGS11	8786	hgsc.bcm.edu	37	chr16	323531	323531	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcacgcaatgaccagcctgtCccccttgctgcgctgcttgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:323531delC	ENST00000397770.3	-	8	549	c.532delG	c.(532-534)gacfs	p.D178fs	RGS11_ENST00000359740.5_Frame_Shift_Del_p.D167fs|RGS11_ENST00000316163.5_Frame_Shift_Del_p.D157fs|RGS11_ENST00000397768.3_Frame_Shift_Del_p.D178fs			O94810	RGS11_HUMAN	regulator of G-protein signaling 11	178					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)	8		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				ACCAGCCTGTCCCCCTTGCTG	0.711																																					p.D178fs		Atlas-INDEL	.											.	RGS11	29	.	0			c.533delA						.						27	24	25					16																	323531		2156	4260	6416	SO:0001589	frameshift_variant	8786	exon8			.	AF035153	CCDS10403.1, CCDS42088.1, CCDS66884.1	16p13.3	2008-07-28	2007-08-14		ENSG00000076344	ENSG00000076344		"Regulators of G-protein signaling"	9993	protein-coding gene	gene with protein product		603895	"regulator of G-protein signalling 11"			9789084	Standard	NM_001286486		Approved		uc002cgj.1	O94810	OTTHUMG00000064893	ENST00000397770.3:c.532delG	chr16.hg19:g.323531delC	ENSP00000380876:p.Asp178fs	201.0	0.0		197.0	13.0	NM_183337	O75883|Q4TT71|Q4TT72	Frame_Shift_Del	DEL	ENST00000397770.3	hg19	CCDS42088.1																																																																																			.	.		0.711	RGS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139325.2			-	323531	C	-	323531	7	5	114	1	0	1	0	1	0	0	0	0	13309	855	30	0	911	0	RGS11	16	323531	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10		323531	90031222	944	19216										
RAB11FIP3	9727	hgsc.bcm.edu	37	chr16	538888	538888	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtctgtcatcacggtgatcGggggcgaggagcactttgag					rs139898544	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:538888delG	ENST00000262305.4	+	5	1541	c.1153delG	c.(1153-1155)gggfs	p.G386fs	RAB11FIP3_ENST00000450428.1_Frame_Shift_Del_p.G90fs|RAB11FIP3_ENST00000457159.1_Frame_Shift_Del_p.G386fs	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	386					cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.G385R(1)		breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				CACGGTGATCGGGGGCGAGGA	0.602																																					p.I384fs	Melanoma(160;2366 2595 4474 8099)	Atlas-INDEL	.											.	RAB11FIP3	31	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.1152delC						.						89	77	81					16																	538888		2202	4300	6502	SO:0001589	frameshift_variant	9727	exon5			.	AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"EF-hand domain containing"	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.1153delG	chr16.hg19:g.538888delG	ENSP00000262305:p.Gly386fs	117.0	0.0		140.0	12.0	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Frame_Shift_Del	DEL	ENST00000262305.4	hg19	CCDS32351.1																																																																																			.	.		0.602	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700		-	538888	G	-	538888	7	5	114	1	0	1	0	1	0	0	0	0	12910	1116	39	0	1190	0	RAB11FIP3	16	538888	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	215357	538888	89815865	945	19217										
HAGHL	84264	hgsc.bcm.edu	37	chr16	777988	777988	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctggagatcgtgggccgggaGggggtgtctctgaccgctgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:777988delG	ENST00000341413.4	+	3	410	c.129delG	c.(127-129)gagfs	p.E43fs	NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000564537.1_Frame_Shift_Del_p.E43fs|HAGHL_ENST00000561546.1_Frame_Shift_Del_p.E43fs|HAGHL_ENST00000564545.1_Intron|HAGHL_ENST00000549114.1_Frame_Shift_Del_p.E43fs|HAGHL_ENST00000389703.3_Frame_Shift_Del_p.E43fs|CCDC78_ENST00000293889.6_5'Flank			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	43							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				TGGGCCGGGAGGGGGTGTCTC	0.687																																					p.E43fs	Pancreas(46;538 1326 12403 32360)	Atlas-INDEL	.											.	HAGHL	18	.	0			c.128delA						.						26	32	30					16																	777988		2191	4290	6481	SO:0001589	frameshift_variant	84264	exon2			.	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"hydroxyacyl glutathione hydrolase-like"			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.129delG	chr16.hg19:g.777988delG	ENSP00000341952:p.Glu43fs	217.0	0.0		246.0	15.0	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Frame_Shift_Del	DEL	ENST00000341413.4	hg19																																																																																				.	.		0.687	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304		-	777988	G	-	777988	7	5	114	1	0	1	0	1	0	0	0	0	6955	991	35	0	135	0	HAGHL	16	777988	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	239100	777988	89576765	946	19218										
C16orf42	84572	hgsc.bcm.edu	37	chr16	1400082	1400082	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctcctcctcctgggggctcTccttggcattggccaagaac	10	15	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:1400082T>C	ENST00000204679.4	+	0	0				TSR3_ENST00000007390.2_Missense_Mutation_p.E227G	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit						carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				CTGGGGGCTCTCCTTGGCATT	0.662																																					p.E227G		Atlas-SNP	.											.	.	.	.	0			c.A680G						.						27	30	29					16																	1400082		2194	4298	6492	SO:0001631	upstream_gene_variant	115939	exon4			GGGCTCTCCTTGG	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"GlcNAc-phosphotransferase gamma-subunit"	607838	"N-acetylglucosamine-1-phosphotransferase, gamma subunit", "chromosome 16 open reading frame 27"	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835		chr16.hg19:g.1400082T>C	Exception_encountered	70.0	0.0		129.0	6.0	NM_001001410	B2R556|Q6XYD7|Q96L13	Missense_Mutation	SNP	ENST00000204679.4	hg19	CCDS10436.1	.	.	.	.	.	.	.	.	.	.	T	10.86	1.469735	0.26423	.	.	ENSG00000007520	ENST00000007390	.	.	.	5.22	5.22	0.72569	.	0.665917	0.14028	N	0.346356	T	0.41604	0.1166	M	0.72894	2.215	0.09310	N	0.999991	P	0.41313	0.745	B	0.33454	0.164	T	0.46133	-0.9213	9	0.56958	D	0.05	-7.1259	13.0485	0.58942	0.0:0.0:0.0:1.0	.	227	Q9UJK0	TSR3_HUMAN	G	227	.	ENSP00000007390:E227G	E	-	2	0	C16orf42	1340083	0.031000	0.19500	0.089000	0.20774	0.143000	0.21401	2.197000	0.42696	1.969000	0.57287	0.459000	0.35465	GAG	.	.		0.662	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520		C	1400082	T	C	1400082	1	2	114	0	1	0	0	0	0	0	0	0	1815	1551	54	2		2	C16orf42	16	1400082	5'Flank	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	622094	1400082	88954671	947	19219										
UNKL	64718	hgsc.bcm.edu	37	chr16	1449385	1449385	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcaggctcacctgtactggaAccgccgggggttgcgccgcc	15	15	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:1449385A>G	ENST00000389221.4	-	5	723	c.724T>C	c.(724-726)Ttc>Ctc	p.F242L	UNKL_ENST00000503648.1_5'Flank|UNKL_ENST00000301712.5_Missense_Mutation_p.F242L|UNKL_ENST00000397462.1_Missense_Mutation_p.F345L|UNKL_ENST00000508903.2_Missense_Mutation_p.F242L	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	242					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Hepatocellular(780;0.0893)				CTGTACTGGAACCGCCGGGGG	0.697																																					p.F242L		Atlas-SNP	.											.	UNKL	46	.	0			c.T724C						.						24	23	23					16																	1449385		2193	4299	6492	SO:0001583	missense	64718	exon5			ACTGGAACCGCCG	BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145		"Zinc fingers, CCCH-type domain containing"	14184	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 28", "unkempt homolog (Drosophila)-like"	C16orf28		20148946	Standard	NM_001193389		Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000389221.4:c.724T>C	chr16.hg19:g.1449385A>G	ENSP00000373873:p.Phe242Leu	75.0	0.0		91.0	4.0	NM_001193388	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Missense_Mutation	SNP	ENST00000389221.4	hg19	CCDS53981.1	.	.	.	.	.	.	.	.	.	.	A	19.49	3.838298	0.71373	.	.	ENSG00000059145	ENST00000389221;ENST00000508903;ENST00000397462;ENST00000301712	T	0.64991	-0.13	4.22	4.22	0.49857	.	0.000000	0.85682	D	0.000000	T	0.78091	0.4229	M	0.83953	2.67	0.58432	D	0.999993	D	0.61697	0.99	D	0.72982	0.979	T	0.79553	-0.1756	10	0.46703	T	0.11	.	11.5623	0.50785	1.0:0.0:0.0:0.0	.	242	Q9H9P5-5	.	L	242;242;345;242	ENSP00000373873:F242L	ENSP00000301712:F242L	F	-	1	0	UNKL	1389386	1.000000	0.71417	0.943000	0.38184	0.508000	0.34012	1.849000	0.39318	1.684000	0.51022	0.459000	0.35465	TTC	.	.		0.697	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125		G	1449385	A	G	1449385	3	3	114	1	0	0	0	0	1	0	0	0	17016	43	2	2	832	2	UNKL	16	1449385	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	49303	1449385	88905368	948	19220										
CRAMP1L	57585	hgsc.bcm.edu	37	chr16	1719148	1719148	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccagtgactccaccgactccTcgctcagcagcctgtttggt	9	16	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:1719148T>C	ENST00000397412.3	+	19	3580	c.3481T>C	c.(3481-3483)Tcg>Ccg	p.S1161P	LA16c-431H6.6_ENST00000454337.1_3'UTR|CRAMP1L_ENST00000293925.5_Missense_Mutation_p.S1161P|CRAMP1L_ENST00000436138.3_Missense_Mutation_p.S1158P|CRAMP1L_ENST00000262317.4_Missense_Mutation_p.S536P			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	1161	Ser-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						CACCGACTCCTCGCTCAGCAG	0.632																																					p.S1161P		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.T3481C						.						37	44	41					16																	1719148		1993	4153	6146	SO:0001583	missense	57585	exon18			GACTCCTCGCTCA	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"Crm (Cramped Drosophila)-like"				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.3481T>C	chr16.hg19:g.1719148T>C	ENSP00000380559:p.Ser1161Pro	90.0	0.0		79.0	4.0	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Missense_Mutation	SNP	ENST00000397412.3	hg19	CCDS10440.2	.	.	.	.	.	.	.	.	.	.	T	14.61	2.585914	0.46110	.	.	ENSG00000007545	ENST00000397412;ENST00000293925;ENST00000436138;ENST00000262317	.	.	.	5.73	5.73	0.89815	.	0.065225	0.64402	D	0.000006	T	0.66752	0.2821	L	0.34521	1.04	0.42796	D	0.993916	D	0.76494	0.999	D	0.69479	0.964	T	0.70766	-0.4783	9	0.87932	D	0	-17.7105	16.0225	0.80509	0.0:0.0:0.0:1.0	.	1161	Q96RY5	CRML_HUMAN	P	1161;1161;1158;536	.	ENSP00000262317:S536P	S	+	1	0	CRAMP1L	1659149	1.000000	0.71417	0.680000	0.29994	0.902000	0.53008	6.060000	0.71141	2.198000	0.70561	0.533000	0.62120	TCG	.	.		0.632	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4			C	1719148	T	C	1719148	3	2	114	1	0	0	0	0	1	0	0	0	3848	1551	54	2	3551	2	CRAMP1L	16	1719148	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	269763	1719148	88635605	949	19221										
ZNF598	90850	hgsc.bcm.edu	37	chr16	2048327	2048327	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgctggcatcgccatgcgcgAgcacctgctggcaggtgggg	17	12	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:2048327A>G	ENST00000563630.1	-	12	2698	c.2456T>C	c.(2455-2457)cTc>cCc	p.L819P	ZNF598_ENST00000431526.1_Missense_Mutation_p.L874P|AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000562103.1_Missense_Mutation_p.L819P			Q86UK7	ZN598_HUMAN	zinc finger protein 598	874							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCCATGCGCGAGCACCTGCTG	0.667																																					p.L874P		Atlas-SNP	.											.	ZNF598	55	.	0			c.T2621C						.						62	73	69					16																	2048327		2096	4207	6303	SO:0001583	missense	90850	exon14			TGCGCGAGCACCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.2456T>C	chr16.hg19:g.2048327A>G	ENSP00000455882:p.Leu819Pro	96.0	0.0		75.0	4.0	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	hg19		.	.	.	.	.	.	.	.	.	.	.	15.30	2.793668	0.50102	.	.	ENSG00000167962	ENST00000431526	T	0.29142	1.58	4.42	4.42	0.53409	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.58538	0.2129	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.66256	-0.5969	10	0.87932	D	0	-22.7937	13.0182	0.58771	1.0:0.0:0.0:0.0	.	874;866	Q86UK7;Q86UK7-2	ZN598_HUMAN;.	P	874	ENSP00000411409:L874P	ENSP00000411409:L874P	L	-	2	0	ZNF598	1988328	1.000000	0.71417	0.865000	0.33974	0.379000	0.30106	8.455000	0.90355	1.858000	0.53909	0.460000	0.39030	CTC	.	.		0.667	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167		G	2048327	A	G	2048327	3	3	114	1	0	0	0	0	1	0	0	0	18043	304	11	2	97	2	ZNF598	16	2048327	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	329179	2048327	88306426	950	19222										
CASKIN1	57524	hgsc.bcm.edu	37	chr16	2239271	2239271	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaactcgcaggccaggtccaGgggcgtcttccccgagttgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:2239271delG	ENST00000343516.6	-	5	546	c.454delC	c.(454-456)ctgfs	p.L152fs		NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	152					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|liver(1)|lung(7)|ovary(4)|prostate(5)|skin(3)	28						GCCAGGTCCAGGGGCGTCTTC	0.667																																					p.L152fs		Atlas-INDEL	.											.	CASKIN1	130	.	0			c.455delT						.						40	51	47					16																	2239271		2077	4196	6273	SO:0001589	frameshift_variant	57524	exon5			.	AF451977	CCDS42103.1	16p13.3	2013-01-10				ENSG00000167971		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20879	protein-coding gene	gene with protein product		612184				12040031	Standard	NM_020764		Approved	KIAA1306, ANKS5A	uc010bsg.1	Q8WXD9		ENST00000343516.6:c.454delC	chr16.hg19:g.2239271delG	ENSP00000345436:p.Leu152fs	98.0	0.0		165.0	11.0	NM_020764	Q9P2P0	Frame_Shift_Del	DEL	ENST00000343516.6	hg19	CCDS42103.1																																																																																			.	.		0.667	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764		-	2239271	G	-	2239271	7	5	114	1	0	1	0	1	0	0	0	0	2668	991	35	0	3905	0	CASKIN1	16	2239271	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	190944	2239271	88115482	951	19223										
RNPS1	10921	hgsc.bcm.edu	37	chr16	2314622	2314622	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgactcctagcaagctcttcTttttcactcctgataaatcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:2314622delT	ENST00000565678.1	-	2	568	c.23delA	c.(22-24)aagfs	p.K9fs	RNPS1_ENST00000397086.2_Frame_Shift_Del_p.K9fs|RNPS1_ENST00000301730.8_Frame_Shift_Del_p.K9fs|RNPS1_ENST00000566397.1_5'Flank|RNPS1_ENST00000566458.1_Intron|RNPS1_ENST00000568631.1_Frame_Shift_Del_p.K9fs|RNPS1_ENST00000561718.1_Intron|RNPS1_ENST00000569598.2_Frame_Shift_Del_p.K9fs|RNPS1_ENST00000567147.1_Intron|RNPS1_ENST00000320225.5_Frame_Shift_Del_p.K9fs			Q15287	RNPS1_HUMAN	RNA binding protein S1, serine-rich domain	9	Lys-rich.|Necessary for interaction with SRP54, nuclear localization and exon-skipping.|Necessary for interaction with the cleaved p110 isoform of CDC2L1.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)|urinary_tract(1)	9						CAAGCTCTTCTTTTTCACTCC	0.413																																					p.K8fs		Atlas-INDEL	.											.	RNPS1	18	.	0			c.24delG						.						118	114	116					16																	2314622		2198	4300	6498	SO:0001589	frameshift_variant	10921	exon2			.	AF015608	CCDS10465.1, CCDS66907.1, CCDS73811.1	16p13.3	2013-02-12	2001-11-28		ENSG00000205937	ENSG00000205937		"RNA binding motif (RRM) containing"	10080	protein-coding gene	gene with protein product		606447	"RNA-binding protein S1, serine-rich domain"			9580558, 8543184	Standard	XM_005255048		Approved		uc002cpu.3	Q15287	OTTHUMG00000128828	ENST00000565678.1:c.23delA	chr16.hg19:g.2314622delT	ENSP00000457723:p.Lys9fs	90.0	0.0		126.0	11.0	NM_006711	A8K1P0|B4DDU8|B4DZU7|B7ZA17|O75308|Q32P25|Q8WY42|Q9NYG3	Frame_Shift_Del	DEL	ENST00000565678.1	hg19	CCDS10465.1																																																																																			.	.		0.413	RNPS1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435415.1	NM_080594		-	2314622	T	-	2314622	7	5	114	1	0	1	0	1	0	0	0	0	13526	1609	56	0	922	0	RNPS1	16	2314622	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	75351	2314622	88040131	952	19224										
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3085376	3085376	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgggctcctcaggccctgggCcccctcccaggaatgagtcc	12	18	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:3085376C>A	ENST00000572449.1	-	2	184	c.122G>T	c.(121-123)gGc>gTc	p.G41V	CCDC64B_ENST00000573514.1_5'Flank|CCDC64B_ENST00000389347.4_Missense_Mutation_p.G41V|RP11-473M20.5_ENST00000382225.3_RNA			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	41										breast(1)|endometrium(2)|large_intestine(1)	4						AGGCCCTGGGCCCCCTCCCAG	0.677																																					p.G41V		Atlas-SNP	.											.	CCDC64B	19	.	0			c.G122T						.						10	13	12					16																	3085376		1877	4093	5970	SO:0001583	missense	146439	exon1			CCTGGGCCCCCTC	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.122G>T	chr16.hg19:g.3085376C>A	ENSP00000459043:p.Gly41Val	97.0	0.0		134.0	7.0	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	c	14.32	2.500813	0.44455	.	.	ENSG00000162069	ENST00000389347	T	0.28255	1.62	4.35	4.35	0.52113	.	0.401453	0.20157	U	0.098038	T	0.43166	0.1235	L	0.46157	1.445	0.58432	D	0.999996	D	0.89917	1.0	D	0.79784	0.993	T	0.10154	-1.0642	10	0.29301	T	0.29	-32.6859	8.9083	0.35537	0.0:0.8944:0.0:0.1056	.	41	A1A5D9	BICR2_HUMAN	V	41	ENSP00000373998:G41V	ENSP00000373998:G41V	G	-	2	0	CCDC64B	3025377	0.989000	0.36119	1.000000	0.80357	0.946000	0.59487	0.942000	0.29017	2.361000	0.80049	0.457000	0.33378	GGC	.	.		0.677	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1			A	3085376	C	A	3085376	3	1	114	1	0	0	0	0	1	0	0	0	2838	739	26	3	1440	3	CCDC64B	16	3085376	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	770754	3085376	87269377	953	19225										
GLIS2	84662	hgsc.bcm.edu	37	chr16	4385330	4385330	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aacgagaagccacaccgctgTccgacctgcagcaagagctt	10	14	0	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:4385330T>C	ENST00000262366.3	+	7	1532	c.711T>C	c.(709-711)tgT>tgC	p.C237C	GLIS2_ENST00000433375.1_Silent_p.C237C|PAM16_ENST00000577031.1_Intron|RP11-295D4.1_ENST00000574705.1_RNA			Q9BZE0	GLIS2_HUMAN	GLIS family zinc finger 2	237					cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(4)|endometrium(1)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	11						CACACCGCTGTCCGACCTGCA	0.642																																					p.C237C		Atlas-SNP	.											.	GLIS2	29	.	0			c.T711C						.						88	88	88					16																	4385330		2196	4300	6496	SO:0001819	synonymous_variant	84662	exon5			CCGCTGTCCGACC	AF325914	CCDS10511.1	16p13.3	2013-01-08			ENSG00000126603	ENSG00000126603		"Zinc fingers, C2H2-type"	29450	protein-coding gene	gene with protein product	"nephrocystin-7"	608539				11741991, 14500813, 17618285	Standard	NM_032575		Approved	NPHP7	uc002cwc.1	Q9BZE0	OTTHUMG00000129467	ENST00000262366.3:c.711T>C	chr16.hg19:g.4385330T>C		153.0	0.0		162.0	7.0	NM_032575	B3KX84	Silent	SNP	ENST00000262366.3	hg19	CCDS10511.1																																																																																			.	.		0.642	GLIS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251630.1	NM_032575		C	4385330	T	C	4385330	2	2	114	1	0	0	0	0	0	0	0	1	6454	1673	58	2		2	GLIS2	16	4385330	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1299954	4385330	85969423	954	19226										
VASN	114990	hgsc.bcm.edu	37	chr16	4432163	4432163	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggggacacggcaccacctgGcgtgcttgtgccccgaaggc	15	14	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:4432163G>A	ENST00000304735.3	+	2	1440	c.1285G>A	c.(1285-1287)Gcg>Acg	p.A429T	CORO7_ENST00000539968.1_Intron|CORO7_ENST00000423908.2_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000574025.1_Intron|CORO7_ENST00000251166.4_Intron|CORO7_ENST00000537233.2_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	429	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						GCACCACCTGGCGTGCTTGTG	0.692																																					p.A429T		Atlas-SNP	.											.	VASN	21	.	0			c.G1285A						.						17	16	16					16																	4432163		2168	4272	6440	SO:0001583	missense	114990	exon2			CACCTGGCGTGCT	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"slit-like 2 (Drosophila)"	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.1285G>A	chr16.hg19:g.4432163G>A	ENSP00000306864:p.Ala429Thr	124.0	0.0		80.0	4.0	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Missense_Mutation	SNP	ENST00000304735.3	hg19	CCDS10514.1	.	.	.	.	.	.	.	.	.	.	G	2.558	-0.302473	0.05495	.	.	ENSG00000168140	ENST00000304735	D	0.91521	-2.86	5.63	3.66	0.41972	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.761271	0.12153	N	0.494708	T	0.71443	0.3340	N	0.01277	-0.915	0.20638	N	0.999877	B	0.17038	0.02	B	0.14023	0.01	T	0.60667	-0.7218	10	0.13853	T	0.58	-11.1698	6.1836	0.20486	0.0742:0.1337:0.6538:0.1383	.	429	Q6EMK4	VASN_HUMAN	T	429	ENSP00000306864:A429T	ENSP00000306864:A429T	A	+	1	0	VASN	4372164	0.712000	0.27916	0.771000	0.31576	0.131000	0.20780	1.754000	0.38369	0.734000	0.32515	0.650000	0.86243	GCG	.	.		0.692	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440		A	4432163	G	A	4432163	3	1	114	1	0	0	0	0	1	0	0	0	17142	1203	42	3	1287	3	VASN	16	4432163	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	46833	4432163	85922590	955	19227										
A2BP1	54715	hgsc.bcm.edu	37	chr16	7680656	7680656	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggatcttccatgtacagtgCccccagttcacttgtatata							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:7680656delC	ENST00000550418.1	+	11	1716	c.728delC	c.(727-729)gccfs	p.A243fs	RBFOX1_ENST00000552089.1_Frame_Shift_Del_p.A260fs|RBFOX1_ENST00000311745.5_Frame_Shift_Del_p.A263fs|RBFOX1_ENST00000422070.4_Frame_Shift_Del_p.A286fs|RBFOX1_ENST00000436368.2_Frame_Shift_Del_p.A263fs|RBFOX1_ENST00000547338.1_Frame_Shift_Del_p.A243fs|RBFOX1_ENST00000535565.2_Frame_Shift_Del_p.A200fs|RBFOX1_ENST00000355637.4_Frame_Shift_Del_p.A263fs|RBFOX1_ENST00000553186.1_Intron|RBFOX1_ENST00000340209.4_Frame_Shift_Del_p.A248fs|RBFOX1_ENST00000547372.1_Frame_Shift_Del_p.A286fs	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	243					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						ATGTACAGTGCCCCCAGTTCA	0.483																																					p.A263fs	Ovarian(157;934 2567 15163 39509)	Atlas-INDEL	.											RBFOX1_ENST00000550418,colon,carcinoma,0,3	RBFOX1	341	.	0			c.787delG						.						195	157	170					16																	7680656		2197	4300	6497	SO:0001589	frameshift_variant	54715	exon8			.	AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"RNA binding motif (RRM) containing"	18222	protein-coding gene	gene with protein product	"ataxin 2-binding protein 1", "hexaribonucleotide binding protein 1"	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.728delC	chr16.hg19:g.7680656delC	ENSP00000450031:p.Ala243fs	154.0	0.0		213.0	15.0	NM_145891	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Frame_Shift_Del	DEL	ENST00000550418.1	hg19	CCDS55983.1																																																																																			.	.		0.483	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		-	7680656	C	-	7680656	7	5	114	1	0	1	0	1	0	0	0	0	3	739	26	0	849	0	A2BP1	16	7680656	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3248493	7680656	82674097	956	19228										
ABCC6	368	hgsc.bcm.edu	37	chr16	16292011	16292011	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catcacccaccgcactggccTttctggagccgctggacaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:16292011delT	ENST00000205557.7	-	10	1234	c.1205delA	c.(1204-1206)aagfs	p.K402fs	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	402	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CGCACTGGCCTTTCTGGAGCC	0.652																																					p.K402fs		Atlas-INDEL	.											.	ABCC6	110	.	0			c.1206delG						.						37	28	31					16																	16292011		2196	4300	6496	SO:0001589	frameshift_variant	368	exon10			.	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.1205delA	chr16.hg19:g.16292011delT	ENSP00000205557:p.Lys402fs	149.0	0.0		155.0	12.0	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Frame_Shift_Del	DEL	ENST00000205557.7	hg19	CCDS10568.1																																																																																			.	.		0.652	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			-	16292011	T	-	16292011	7	5	114	1	0	1	0	1	0	0	0	0	57	1609	56	0	3394	0	ABCC6	16	16292011	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	8611355	16292011	74062742	957	19229										
SMG1	23049	hgsc.bcm.edu	37	chr16	18865999	18865999	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgctgtataaagcaatttggTtttttcaatatcaagttcgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:18865999delT	ENST00000446231.2	-	30	4874	c.4462delA	c.(4462-4464)accfs	p.T1488fs	SMG1_ENST00000389467.3_Frame_Shift_Del_p.T1488fs			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1488	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						AGCAATTTGGTTTTTTCAATA	0.318																																					p.T1488fs		Atlas-INDEL	.											SMG1,colon,carcinoma,0,1	SMG1	401	.	0			c.4463delC						.						64	58	60					16																	18865999		1808	4072	5880	SO:0001589	frameshift_variant	23049	exon30			.	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.4462delA	chr16.hg19:g.18865999delT	ENSP00000402515:p.Thr1488fs	158.0	0.0		196.0	13.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Frame_Shift_Del	DEL	ENST00000446231.2	hg19	CCDS45430.1																																																																																			.	.		0.318	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		-	18865999	T	-	18865999	7	5	114	1	0	1	0	1	0	0	0	0	14810	1725	60	0	6659	0	SMG1	16	18865999	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2573988	18865999	71488754	958	19230										
CDR2	1039	hgsc.bcm.edu	37	chr16	22376296	22376296	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctccaactctgtgttccgaTccagtaatgtcttcccaagc	6	15	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:22376296T>C	ENST00000268383.2	-	2	426	c.119A>G	c.(118-120)gAt>gGt	p.D40G	RP11-21M24.3_ENST00000566764.1_RNA|CDR2_ENST00000569045.1_5'UTR	NM_001802.1	NP_001793.1	Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa	40						cytoplasm (GO:0005737)				endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		TGTGTTCCGATCCAGTAATGT	0.393																																					p.D40G		Atlas-SNP	.											.	CDR2	34	.	0			c.A119G						.						148	120	129					16																	22376296		2197	4300	6497	SO:0001583	missense	1039	exon2			TTCCGATCCAGTA	M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"Yo paraneoplastic antigen"	117340	"cerebellar degeneration-related protein (62kD)"			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850		ENST00000268383.2:c.119A>G	chr16.hg19:g.22376296T>C	ENSP00000268383:p.Asp40Gly	138.0	0.0		137.0	6.0	NM_001802	A8K8A8|Q13977	Missense_Mutation	SNP	ENST00000268383.2	hg19	CCDS32404.1	.	.	.	.	.	.	.	.	.	.	T	32	5.170362	0.94768	.	.	ENSG00000140743	ENST00000268383	T	0.30448	1.53	5.91	5.91	0.95273	.	0.047350	0.85682	D	0.000000	T	0.52645	0.1747	M	0.64997	1.995	0.80722	D	1	D	0.71674	0.998	D	0.65684	0.937	T	0.54268	-0.8319	10	0.72032	D	0.01	-21.8145	16.3426	0.83092	0.0:0.0:0.0:1.0	.	40	Q01850	CDR2_HUMAN	G	40	ENSP00000268383:D40G	ENSP00000268383:D40G	D	-	2	0	CDR2	22283797	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.390000	0.79816	2.263000	0.75096	0.379000	0.24179	GAT	.	.		0.393	CDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430081.1			C	22376296	T	C	22376296	3	2	114	1	0	0	0	0	1	0	0	0	3174	1435	50	2	1261	2	CDR2	16	22376296	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3510297	22376296	67978457	959	19231										
IL21R	50615	hgsc.bcm.edu	37	chr16	27441412	27441412	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catgccgcgtggctgggccgCccccttgctcctgctgctgc					rs559469718		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:27441412delC	ENST00000337929.3	+	2	493	c.20delC	c.(19-21)gccfs	p.A7fs	IL21R_ENST00000395755.1_Frame_Shift_Del_p.A7fs|IL21R_ENST00000395754.4_Frame_Shift_Del_p.A7fs|IL21R_ENST00000564089.1_Frame_Shift_Del_p.A7fs	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	7					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						GGCTGGGCCGCCCCCTTGCTC	0.721			T	BCL6	NHL																																p.A29fs		Atlas-INDEL	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.85delG						.						19	20	20					16																	27441412		2194	4295	6489	SO:0001589	frameshift_variant	50615	exon3			.	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.20delC	chr16.hg19:g.27441412delC	ENSP00000338010:p.Ala7fs	144.0	0.0		135.0	10.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Frame_Shift_Del	DEL	ENST00000337929.3	hg19	CCDS10630.1																																																																																			.	.		0.721	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		-	27441412	C	-	27441412	7	5	114	1	0	1	0	1	0	0	0	0	7680	739	26	0	22	0	IL21R	16	27441412	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	5065116	27441412	62913341	960	19232										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27503691	27503691	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgaggcagacgcactgcaggTcaaaccagtagttttccaca	10	11	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:27503691T>C	ENST00000356183.4	-	19	3134	c.3119A>G	c.(3118-3120)gAc>gGc	p.D1040G	GTF3C1_ENST00000561623.1_Missense_Mutation_p.D1040G	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1040					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						GCACTGCAGGTCAAACCAGTA	0.562																																					p.D1040G		Atlas-SNP	.											.	GTF3C1	210	.	0			c.A3119G						.						71	73	72					16																	27503691		2197	4300	6497	SO:0001583	missense	2975	exon19			TGCAGGTCAAACC	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.3119A>G	chr16.hg19:g.27503691T>C	ENSP00000348510:p.Asp1040Gly	115.0	0.0		170.0	8.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.039968	0.93630	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.27402	1.67	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.57799	0.2078	M	0.79475	2.455	0.53688	D	0.999974	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.60439	-0.7263	10	0.52906	T	0.07	-26.005	15.8433	0.78868	0.0:0.0:0.0:1.0	.	1040;1040	Q12789;Q12789-3	TF3C1_HUMAN;.	G	1040;1038	ENSP00000348510:D1040G	ENSP00000348510:D1040G	D	-	2	0	GTF3C1	27411192	1.000000	0.71417	0.978000	0.43139	0.974000	0.67602	7.698000	0.84413	2.217000	0.71921	0.533000	0.62120	GAC	.	.		0.562	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		C	27503691	T	C	27503691	3	2	114	1	0	0	0	0	1	0	0	0	6881	1667	58	2	3286	2	GTF3C1	16	27503691	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	62279	27503691	62851062	961	19233										
SETD1A	9739	hgsc.bcm.edu	37	chr16	30990582	30990582	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttctcccatccccctcctgCccccacccaagaaacgccgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:30990582delC	ENST00000262519.8	+	14	4161	c.3475delC	c.(3475-3477)cccfs	p.P1161fs		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	1161	Pro-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CCCCCTCCTGCCCCCACCCAA	0.701																																					p.L1158fs		Atlas-INDEL	.											.	SETD1A	143	.	0			c.3474delG						.						15	19	17					16																	30990582		2155	4223	6378	SO:0001589	frameshift_variant	9739	exon14			.	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.3475delC	chr16.hg19:g.30990582delC	ENSP00000262519:p.Pro1161fs	212.0	0.0		246.0	18.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Frame_Shift_Del	DEL	ENST00000262519.8	hg19	CCDS32435.1																																																																																			.	.		0.701	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		-	30990582	C	-	30990582	7	5	114	1	0	1	0	1	0	0	0	0	14145	739	26	0	3525	0	SETD1A	16	30990582	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3486891	30990582	59364171	962	19234										
ZNF646	9726	hgsc.bcm.edu	37	chr16	31089058	31089058	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tataagtgcagtgagtgtggTcgtgcttaccgccaccgggg	15	9	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:31089058T>C	ENST00000394979.2	+	1	1836	c.1413T>C	c.(1411-1413)ggT>ggC	p.G471G	ZNF646_ENST00000300850.5_Silent_p.G471G			O15015	ZN646_HUMAN	zinc finger protein 646	471					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						GTGAGTGTGGTCGTGCTTACC	0.617																																					p.G471G		Atlas-SNP	.											ZNF646,NS,carcinoma,0,1	ZNF646	133	.	0			c.T1413C						.						81	84	83					16																	31089058		2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			GTGTGGTCGTGCT	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.1413T>C	chr16.hg19:g.31089058T>C		94.0	0.0		109.0	5.0	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	hg19																																																																																				.	.		0.617	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		C	31089058	T	C	31089058	2	2	114	1	0	0	0	0	0	0	0	1	18077	1654	58	2		2	ZNF646	16	31089058	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	98476	31089058	59265695	963	19235										
PRSS36	146547	hgsc.bcm.edu	37	chr16	31152016	31152016	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atacctggtggccctgtgggAgggagctggcccctgcccgg	17	13	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:31152016A>G	ENST00000268281.4	-	13	2022	c.1964T>C	c.(1963-1965)cTc>cCc	p.L655P	PRSS36_ENST00000569305.1_Missense_Mutation_p.L650P|PRSS36_ENST00000418068.2_Missense_Mutation_p.L655P	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	655	Peptidase S1 3. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						GCCCTGTGGGAGGGAGCTGGC	0.642																																					p.L655P		Atlas-SNP	.											.	PRSS36	50	.	0			c.T1964C						.						40	43	42					16																	31152016		2197	4300	6497	SO:0001583	missense	146547	exon13			TGTGGGAGGGAGC	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"Serine peptidases / Serine peptidases"	26906	protein-coding gene	gene with protein product	"polyserase 2"	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.1964T>C	chr16.hg19:g.31152016A>G	ENSP00000268281:p.Leu655Pro	133.0	0.0		194.0	9.0	NM_001258291	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	hg19	CCDS32436.1	.	.	.	.	.	.	.	.	.	.	a	15.56	2.869255	0.51588	.	.	ENSG00000178226	ENST00000268281;ENST00000418068	D;D	0.90324	-2.46;-2.65	4.15	1.84	0.25277	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.85579	0.5729	N	0.22421	0.69	0.51012	D	0.999906	P;D;D	0.57257	0.948;0.979;0.979	P;P;P	0.55303	0.601;0.773;0.773	T	0.80074	-0.1534	9	0.32370	T	0.25	.	2.9529	0.05867	0.6671:0.0:0.1168:0.2161	.	655;650;655	E7EX56;B7ZMK8;Q5K4E3	.;.;POLS2_HUMAN	P	655	ENSP00000268281:L655P;ENSP00000407160:L655P	ENSP00000268281:L655P	L	-	2	0	PRSS36	31059517	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.410000	0.34691	0.697000	0.31718	0.449000	0.29647	CTC	.	.		0.642	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502		G	31152016	A	G	31152016	3	3	114	1	0	0	0	0	1	0	0	0	12637	304	11	2	615	2	PRSS36	16	31152016	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	62958	31152016	59202737	964	19236										
ITGAM	3684	hgsc.bcm.edu	37	chr16	31308914	31308914	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgacctggtcctcatcggggCcccccattactacgagcaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:31308914delC	ENST00000287497.8	+	13	1511	c.1436delC	c.(1435-1437)gccfs	p.A479fs	ITGAM_ENST00000544665.3_Frame_Shift_Del_p.A479fs			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	479					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						CTCATCGGGGCCCCCCATTAC	0.677																																					p.A479fs		Atlas-INDEL	.											.	ITGAM	137	.	0			c.1435delG						.						67	75	72					16																	31308914		2193	4295	6488	SO:0001589	frameshift_variant	3684	exon13			.	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.1436delC	chr16.hg19:g.31308914delC	ENSP00000287497:p.Ala479fs	149.0	0.0		208.0	13.0	NM_000632	Q4VAK0|Q4VAK1|Q4VAK2	Frame_Shift_Del	DEL	ENST00000287497.8	hg19	CCDS45470.1																																																																																			.	.		0.677	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		-	31308914	C	-	31308914	7	5	114	1	0	1	0	1	0	0	0	0	7896	739	26	0	1486	0	ITGAM	16	31308914	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	156898	31308914	59045839	965	19237										
ITFG1	81533	hgsc.bcm.edu	37	chr16	47347686	47347686	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agatggtactcttttggcaaTttttatcttcacagcctggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:47347686delT	ENST00000320640.6	-	9	1079	c.851delA	c.(850-852)aatfs	p.N284fs	Y_RNA_ENST00000410835.1_RNA|RP11-474B12.1_ENST00000564739.1_RNA|ITFG1_ENST00000544001.2_Frame_Shift_Del_p.N171fs|ITFG1_ENST00000568047.1_5'Flank	NM_030790.3	NP_110417.2	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	284						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	19		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				CTTTTGGCAATTTTTATCTTC	0.338																																					p.N284fs		Atlas-INDEL	.											.	ITFG1	49	.	0			c.852delT						.						114	101	106					16																	47347686		2202	4300	6502	SO:0001589	frameshift_variant	81533	exon9			.	AF503339	CCDS10728.1	16q12.1	2008-02-05			ENSG00000129636	ENSG00000129636			30697	protein-coding gene	gene with protein product	"T cell immunomodulatory protein"	611803				12598909	Standard	NM_030790		Approved	CDA08, TIP	uc002eet.3	Q8TB96	OTTHUMG00000133103	ENST00000320640.6:c.851delA	chr16.hg19:g.47347686delT	ENSP00000319918:p.Asn284fs	93.0	0.0		146.0	10.0	NM_030790	Q96SR4|Q9BRE2|Q9H2V9	Frame_Shift_Del	DEL	ENST00000320640.6	hg19	CCDS10728.1																																																																																			.	.		0.338	ITFG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256768.3	NM_030790		-	47347686	T	-	47347686	7	5	114	1	0	1	0	1	0	0	0	0	7878	1493	52	0	1027	0	ITFG1	16	47347686	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	16038772	47347686	43007067	966	19238										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48596002	48596002	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtgtgagtgtcaaaagttcTtttttcaaggaagtgggcaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:48596002delT	ENST00000262384.3	-	2	788	c.552delA	c.(550-552)aaafs	p.K184fs	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	184					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				TCAAAAGTTCTTTTTTCAAGG	0.368																																					p.E185fs		Atlas-INDEL	.											.	N4BP1	121	.	0			c.553delG						.						98	87	91					16																	48596002		1851	4094	5945	SO:0001589	frameshift_variant	9683	exon2			.	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.552delA	chr16.hg19:g.48596002delT	ENSP00000262384:p.Lys184fs	121.0	0.0		128.0	11.0	NM_153029	A7MD49|Q2YDX1	Frame_Shift_Del	DEL	ENST00000262384.3	hg19	CCDS45479.1																																																																																			.	.		0.368	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		-	48596002	T	-	48596002	7	5	114	1	0	1	0	1	0	0	0	0	10118	1606	56	0	2162	0	N4BP1	16	48596002	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1248316	48596002	41758751	967	19239										
HEATR3	55027	hgsc.bcm.edu	37	chr16	50106592	50106592	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgttaaagtatttaagtaggTttcctaccaatgttgacctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:50106592delT	ENST00000299192.7	+	5	780	c.589delT	c.(589-591)tttfs	p.F197fs	HEATR3_ENST00000285767.4_Frame_Shift_Del_p.F111fs	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	197				F -> L (in Ref. 1; AAP97710). {ECO:0000305}.						cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TTTAAGTAGGTTTCCTACCAA	0.343																																					p.R196fs		Atlas-INDEL	.											.	HEATR3	59	.	0			c.588delG						.						193	180	184					16																	50106592		2198	4300	6498	SO:0001589	frameshift_variant	55027	exon5			.	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.589delT	chr16.hg19:g.50106592delT	ENSP00000299192:p.Phe197fs	157.0	0.0		153.0	11.0	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Frame_Shift_Del	DEL	ENST00000299192.7	hg19	CCDS10739.1																																																																																			.	.		0.343	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		-	50106592	T	-	50106592	7	5	114	1	0	1	0	1	0	0	0	0	7038	1725	60	0	607	0	HEATR3	16	50106592	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1510590	50106592	40248161	968	19240										
CYLD	1540	hgsc.bcm.edu	37	chr16	50785567	50785567	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtgtaccaagggaaacagcTttttcagtgtgatgaagatt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:50785567delT	ENST00000427738.3	+	3	762	c.557delT	c.(556-558)cttfs	p.L186fs	CYLD_ENST00000569418.1_Frame_Shift_Del_p.L186fs|CYLD_ENST00000540145.1_Frame_Shift_Del_p.L186fs|CYLD_ENST00000398568.2_Frame_Shift_Del_p.L186fs|CYLD_ENST00000311559.9_Frame_Shift_Del_p.L186fs|CYLD_ENST00000566206.1_Frame_Shift_Del_p.L186fs|CYLD_ENST00000564326.1_Frame_Shift_Del_p.L186fs|CYLD_ENST00000568704.2_Frame_Shift_Del_p.L186fs			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	186	CAP-Gly 1. {ECO:0000255|PROSITE- ProRule:PRU00045}.|Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				GGGAAACAGCTTTTTCAGTGT	0.428			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.L186fs		Atlas-INDEL	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.556delC						.						215	204	208					16																	50785567		1990	4169	6159	SO:0001589	frameshift_variant	1540	exon4	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.557delT	chr16.hg19:g.50785567delT	ENSP00000392025:p.Leu186fs	116.0	0.0		142.0	10.0	NM_001042355	O94934|Q7L3N6|Q96EH0|Q9NZX9	Frame_Shift_Del	DEL	ENST00000427738.3	hg19	CCDS45482.1																																																																																			.	.		0.428	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			-	50785567	T	-	50785567	7	5	114	1	0	1	0	1	0	0	0	0	4145	1609	56	0	563	0	CYLD	16	50785567	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	678975	50785567	39569186	969	19241										
CETP	1071	hgsc.bcm.edu	37	chr16	57005938	57005938	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatggagacattggggtggaCatttccctgacaggtgatcc	14	8	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:57005938C>T	ENST00000566128.1	+	8	765	c.498C>T	c.(496-498)gaC>gaT	p.D166D	CETP_ENST00000200676.3_Silent_p.D231D|CETP_ENST00000379780.2_Silent_p.D231D|CETP_ENST00000569082.1_3'UTR					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						TTGGGGTGGACATTTCCCTGA	0.597																																					p.D231D		Atlas-SNP	.											.	CETP	50	.	0			c.C693T						.						113	92	99					16																	57005938		2198	4300	6498	SO:0001819	synonymous_variant	1071	exon8			GGTGGACATTTCC	M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"BPI fold containing"	1869	protein-coding gene	gene with protein product	"BPI fold containing family F"	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.498C>T	chr16.hg19:g.57005938C>T		131.0	0.0		122.0	35.0	NM_000078		Silent	SNP	ENST00000566128.1	hg19																																																																																				.	.		0.597	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078		T	57005938	C	T	57005938	2	4	114	1	0	0	0	0	0	0	0	1	3279	477	17	3		3	CETP	16	57005938	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	6220371	57005938	33348815	970	19242										
NLRC5	84166	hgsc.bcm.edu	37	chr16	57063748	57063748	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtggaggttctccctcacctAccacggctccggaagcttga	11	14	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:57063748A>G	ENST00000262510.6	+	9	2532	c.2307A>G	c.(2305-2307)ctA>ctG	p.L769L	NLRC5_ENST00000436936.1_Silent_p.L769L|NLRC5_ENST00000308149.7_Silent_p.L769L|NLRC5_ENST00000539144.1_Silent_p.L769L	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	769					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				TCCCTCACCTACCACGGCTCC	0.572																																					p.L769L		Atlas-SNP	.											.	NLRC5	186	.	0			c.A2307G						.						103	81	88					16																	57063748		2198	4300	6498	SO:0001819	synonymous_variant	84166	exon8			TCACCTACCACGG	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2307A>G	chr16.hg19:g.57063748A>G		106.0	0.0		100.0	4.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	hg19	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	A	11.11	1.541858	0.27563	.	.	ENSG00000140853	ENST00000538805	.	.	.	5.12	1.99	0.26369	.	.	.	.	.	T	0.24661	0.0598	.	.	.	0.20638	N	0.999874	.	.	.	.	.	.	T	0.22382	-1.0218	4	.	.	.	.	4.0495	0.09788	0.2043:0.0:0.594:0.2017	.	.	.	.	A	522	.	.	T	+	1	0	NLRC5	55621249	0.072000	0.21174	0.102000	0.21198	0.708000	0.40852	0.449000	0.21744	0.137000	0.18759	-0.468000	0.05107	ACC	.	.		0.572	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		G	57063748	A	G	57063748	2	3	114	1	0	0	0	0	0	0	0	1	10479	378	14	2		2	NLRC5	16	57063748	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	57810	57063748	33291005	971	19243										
ARL2BP	23568	hgsc.bcm.edu	37	chr16	57282542	57282542	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taaactcatctacacacctaTttttaatgaatacgtaagta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:57282542delT	ENST00000219204.3	+	3	464	c.194delT	c.(193-195)attfs	p.I65fs	RP11-407G23.4_ENST00000562409.1_RNA|ARL2BP_ENST00000562023.1_Intron|RP11-407G23.3_ENST00000564376.1_RNA	NM_012106.3	NP_036238.1	Q9Y2Y0	AR2BP_HUMAN	ADP-ribosylation factor-like 2 binding protein	65					maintenance of protein location in nucleus (GO:0051457)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of catalytic activity (GO:0050790)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	centrosome (GO:0005813)|cilium (GO:0005929)|midbody (GO:0030496)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	small GTPase regulator activity (GO:0005083)|transcription coactivator activity (GO:0003713)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|urinary_tract(1)	12						TACACACCTATTTTTAATGAA	0.338																																					p.I65fs		Atlas-INDEL	.											.	ARL2BP	20	.	0			c.193delA						.						78	79	79					16																	57282542		2198	4300	6498	SO:0001589	frameshift_variant	23568	exon3			.	AF126062	CCDS10776.1	16q13	2014-01-30			ENSG00000102931	ENSG00000102931			17146	protein-coding gene	gene with protein product	"binder of Arl2"	615407	"retinitis pigmentosa 66 (autosomal recessive)"	RP66		10488091, 18981177, 23849777	Standard	NM_012106		Approved	BART1, BART	uc002elf.1	Q9Y2Y0	OTTHUMG00000133459	ENST00000219204.3:c.194delT	chr16.hg19:g.57282542delT	ENSP00000219204:p.Ile65fs	105.0	0.0		163.0	10.0	NM_012106	B3KQJ5|Q504R0	Frame_Shift_Del	DEL	ENST00000219204.3	hg19	CCDS10776.1																																																																																			.	.		0.338	ARL2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257334.2	NM_012106		-	57282542	T	-	57282542	7	5	114	1	0	1	0	1	0	0	0	0	934	1493	52	0	204	0	ARL2BP	16	57282542	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	218794	57282542	33072211	972	19244										
GPR114	221188	hgsc.bcm.edu	37	chr16	57597883	57597883	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctacttctccaacacccacTttttcaaggtcagtgtgatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:57597883delT	ENST00000340339.4	+	5	944	c.421delT	c.(421-423)tttfs	p.F142fs	GPR114_ENST00000349457.3_Frame_Shift_Del_p.F142fs|GPR114_ENST00000394361.4_3'UTR	NM_153837.1	NP_722579.1	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	142					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(5)|ovary(2)|stomach(1)|urinary_tract(1)	23						CAACACCCACTTTTTCAAGGT	0.637																																					p.H140fs		Atlas-INDEL	.											.	GPR114	52	.	0			c.420delC						.						74	76	76					16																	57597883		2198	4300	6498	SO:0001589	frameshift_variant	221188	exon5			.	AY140956	CCDS10785.1	16q13	2014-08-08			ENSG00000159618	ENSG00000159618		"-", "GPCR / Class B : Orphans"	19010	protein-coding gene	gene with protein product						12435584	Standard	NM_153837		Approved	PGR27	uc002ely.3	Q8IZF4	OTTHUMG00000133461	ENST00000340339.4:c.421delT	chr16.hg19:g.57597883delT	ENSP00000342981:p.Phe142fs	130.0	0.0		173.0	13.0	NM_153837	B3KXZ5|Q6ZMH7|Q6ZML4|Q86SL8|Q8IZ14	Frame_Shift_Del	DEL	ENST00000340339.4	hg19	CCDS10785.1																																																																																			.	.		0.637	GPR114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257336.3	NM_153837		-	57597883	T	-	57597883	7	5	114	1	0	1	0	1	0	0	0	0	6639	1609	56	0	435	0	GPR114	16	57597883	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	315341	57597883	32756870	973	19245										
PLEKHG4	25894	hgsc.bcm.edu	37	chr16	67316441	67316441	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggctgacgagctatatgaccGggtggatggattgctgcacc					rs143955884	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:67316441delG	ENST00000360461.5	+	9	3824	c.1289delG	c.(1288-1290)cggfs	p.R430fs	PLEKHG4_ENST00000427155.2_Frame_Shift_Del_p.R430fs|PLEKHG4_ENST00000379344.3_Frame_Shift_Del_p.R430fs|PLEKHG4_ENST00000450733.1_Frame_Shift_Del_p.R349fs	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	430							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CTATATGACCGGGTGGATGGA	0.582																																					p.R430fs		Atlas-INDEL	.											PLEKHG4,NS,carcinoma,0,1	PLEKHG4	94	.	0			c.1288delC						.						102	87	92					16																	67316441		2198	4300	6498	SO:0001589	frameshift_variant	25894	exon10			.	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24501	protein-coding gene	gene with protein product	"puratrophin-1"	609526	"spinocerebellar ataxia 4"	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.1289delG	chr16.hg19:g.67316441delG	ENSP00000353646:p.Arg430fs	110.0	0.0		156.0	10.0	NM_001129729	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Frame_Shift_Del	DEL	ENST00000360461.5	hg19	CCDS32466.1																																																																																			.	.		0.582	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432		-	67316441	G	-	67316441	7	5	114	1	0	1	0	1	0	0	0	0	12080	1116	39	0	1323	0	PLEKHG4	16	67316441	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	9718558	67316441	23038312	974	19246										
LRRC36	55282	hgsc.bcm.edu	37	chr16	67360810	67360810	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaggaaggcattcgccgcctGggggcgctgacgctggagca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:67360810delG	ENST00000329956.6	+	1	64	c.45delG	c.(43-45)ctgfs	p.L15fs	LRRC36_ENST00000563303.1_Intron|KCTD19_ENST00000304372.5_5'Flank	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36	15										endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	24		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		TTCGCCGCCTGGGGGCGCTGA	0.692											OREG0023877	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L15fs		Atlas-INDEL	.											.	LRRC36	68	.	0			c.44delT						.						13	16	15					16																	67360810		2181	4277	6458	SO:0001589	frameshift_variant	55282	exon1			.	BC026156	CCDS32467.1, CCDS58474.1	16q22.1	2008-02-05				ENSG00000159708			25615	protein-coding gene	gene with protein product						12477932	Standard	NM_001161575		Approved	FLJ11004	uc002esv.3	Q1X8D7		ENST00000329956.6:c.45delG	chr16.hg19:g.67360810delG	ENSP00000329943:p.Leu15fs	96.0	0.0	1098	109.0	11.0	NM_018296	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Frame_Shift_Del	DEL	ENST00000329956.6	hg19	CCDS32467.1																																																																																			.	.		0.692	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296		-	67360810	G	-	67360810	7	5	114	1	0	1	0	1	0	0	0	0	8999	1335	47	0	47	0	LRRC36	16	67360810	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	44369	67360810	22993943	975	19247										
RLTPR	146206	hgsc.bcm.edu	37	chr16	67688777	67688777	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taggcgtcagccgaggcagcGggggtgccgaaggcaagagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:67688777delG	ENST00000334583.6	+	32	4007	c.3679delG	c.(3679-3681)gggfs	p.G1228fs	RLTPR_ENST00000545661.1_Frame_Shift_Del_p.G1192fs	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	1228					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		CCGAGGCAGCGGGGGTGCCGA	0.587																																					p.S1226fs		Atlas-INDEL	.											.	RLTPR	124	.	0			c.3678delC						.						42	51	48					16																	67688777		2167	4263	6430	SO:0001589	frameshift_variant	146206	exon32			.	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.3679delG	chr16.hg19:g.67688777delG	ENSP00000334958:p.Gly1228fs	121.0	0.0		141.0	13.0	NM_001013838	B8X2Z3	Frame_Shift_Del	DEL	ENST00000334583.6	hg19	CCDS45513.1																																																																																			.	.		0.587	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		-	67688777	G	-	67688777	7	5	114	1	0	1	0	1	0	0	0	0	13409	1116	39	0	3805	0	RLTPR	16	67688777	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	327967	67688777	22665976	976	19248										
CTRL	1506	hgsc.bcm.edu	37	chr16	67963841	67963841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agggcctgtggtgagctcagTtgtaggctatgacctggttg	16	7	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:67963841T>C	ENST00000574481.1	-	7	1352	c.791A>G	c.(790-792)aAc>aGc	p.N264S	CTRL_ENST00000576408.1_5'Flank	NM_001907.2	NP_001898.1	P40313	CTRL_HUMAN	chymotrypsin-like	264					digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|urinary_tract(1)	4		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		GTGAGCTCAGTTGTAGGCTAT	0.527																																					p.N264S		Atlas-SNP	.											.	CTRL	11	.	0			c.A791G						.						144	133	137					16																	67963841		2198	4300	6498	SO:0001583	missense	1506	exon7			GCTCAGTTGTAGG		CCDS10852.1	16q22.1	2008-02-05			ENSG00000141086	ENSG00000141086			2524	protein-coding gene	gene with protein product		118888				8268911	Standard	NM_001907		Approved		uc002euw.3	P40313	OTTHUMG00000137552	ENST00000574481.1:c.791A>G	chr16.hg19:g.67963841T>C	ENSP00000458537:p.Asn264Ser	92.0	0.0		97.0	4.0	NM_001907		Missense_Mutation	SNP	ENST00000574481.1	hg19	CCDS10852.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.054839	0.75960	.	.	ENSG00000141086	ENST00000319955	.	.	.	5.55	3.31	0.37934	Peptidase cysteine/serine, trypsin-like (1);	0.815645	0.10574	U	0.658757	T	0.66944	0.2841	L	0.39633	1.23	0.44352	D	0.997249	D	0.71674	0.998	D	0.77557	0.99	T	0.59506	-0.7442	9	0.87932	D	0	.	9.505	0.39042	0.0:0.1453:0.0:0.8547	.	264	P40313	CTRL_HUMAN	S	264	.	ENSP00000322629:N264S	N	-	2	0	CTRL	66521342	1.000000	0.71417	0.269000	0.24586	0.928000	0.56348	4.465000	0.60141	0.405000	0.25532	0.402000	0.26972	AAC	.	.		0.527	CTRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268886.3			C	67963841	T	C	67963841	3	2	114	1	0	0	0	0	1	0	0	0	4030	1725	60	2	7	2	CTRL	16	67963841	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	275064	67963841	22390912	977	19249										
SLC12A4	6560	hgsc.bcm.edu	37	chr16	67985797	67985797	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgttgagcatgaagtaggggTcacaggagtcggtcgtaagg	17	5	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:67985797T>C	ENST00000316341.3	-	8	1201	c.1061A>G	c.(1060-1062)gAc>gGc	p.D354G	SLC12A4_ENST00000576616.1_Missense_Mutation_p.D354G|SLC12A4_ENST00000541864.2_Missense_Mutation_p.D323G|SLC12A4_ENST00000422611.2_Missense_Mutation_p.D356G|SLC12A4_ENST00000572010.1_5'Flank|SLC12A4_ENST00000572037.1_Missense_Mutation_p.D306G|SLC12A4_ENST00000338335.3_Missense_Mutation_p.D354G|SLC12A4_ENST00000537830.2_Missense_Mutation_p.D348G	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	354					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	GAAGTAGGGGTCACAGGAGTC	0.587																																					p.D356G		Atlas-SNP	.											.	SLC12A4	81	.	0			c.A1067G						.						120	76	91					16																	67985797		2198	4300	6498	SO:0001583	missense	6560	exon7			TAGGGGTCACAGG		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.1061A>G	chr16.hg19:g.67985797T>C	ENSP00000318557:p.Asp354Gly	136.0	0.0		167.0	7.0	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	hg19	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.259565	0.80246	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.82079	0.4959	M	0.89785	3.06	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.991;0.999;0.985;0.974;0.991	D;P;D;P;P;P	0.87578	0.979;0.792;0.998;0.844;0.743;0.792	D	0.84609	0.0677	10	0.44086	T	0.13	.	14.9987	0.71455	0.0:0.0:0.0:1.0	.	356;354;323;348;354;354	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	G	356;323;348;354;354	ENSP00000395983:D356G;ENSP00000438334:D323G;ENSP00000445962:D348G;ENSP00000343374:D354G;ENSP00000318557:D354G	ENSP00000318557:D354G	D	-	2	0	SLC12A4	66543298	1.000000	0.71417	0.998000	0.56505	0.899000	0.52679	7.997000	0.88414	2.022000	0.59522	0.383000	0.25322	GAC	.	.		0.587	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		C	67985797	T	C	67985797	3	2	114	1	0	0	0	0	1	0	0	0	14400	1667	58	2	2264	2	SLC12A4	16	67985797	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	21956	67985797	22368956	978	19250										
SNTB2	6645	hgsc.bcm.edu	37	chr16	69333538	69333538	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaggcttactattcactatgAaaatgggttcaccatctcaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:69333538delA	ENST00000336278.4	+	6	1429	c.1391delA	c.(1390-1392)gaafs	p.E464fs	RP11-343C2.11_ENST00000570054.2_5'Flank	NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)	464						cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|microtubule (GO:0005874)|protein complex (GO:0043234)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		ATTCACTATGAAAATGGGTTC	0.428																																					p.E464fs	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-INDEL	.											.	SNTB2	22	.	0			c.1390delG						.						110	99	103					16																	69333538		2198	4300	6498	SO:0001589	frameshift_variant	6645	exon6			.	U40572	CCDS10873.1	16q22.1	2008-05-14	2002-08-29		ENSG00000168807	ENSG00000168807			11169	protein-coding gene	gene with protein product		600027	"syntrophin, beta 2 (dystrophin-associated protein A1, 59kD, basic component 2)"	SNT2B2, SNTL, D16S2531E		8576247, 8183929	Standard	NM_006750		Approved	EST25263, SNT3	uc002ewu.3	Q13425	OTTHUMG00000137567	ENST00000336278.4:c.1391delA	chr16.hg19:g.69333538delA	ENSP00000338191:p.Glu464fs	108.0	0.0		148.0	14.0	NM_006750	Q9BY09	Frame_Shift_Del	DEL	ENST00000336278.4	hg19	CCDS10873.1																																																																																			.	.		0.428	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1			-	69333538	A	-	69333538	7	5	114	1	0	1	0	1	0	0	0	0	14888	246	9	0	1413	0	SNTB2	16	69333538	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1347741	69333538	21021215	979	19251										
NFAT5	10725	hgsc.bcm.edu	37	chr16	69727260	69727260	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acacagtagcccaagaagcaTtttttgcagcaccgaactca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:69727260delT	ENST00000354436.2	+	12	3796	c.3478delT	c.(3478-3480)tttfs	p.F1161fs	NFAT5_ENST00000393742.2_Frame_Shift_Del_p.F1085fs|NFAT5_ENST00000349945.1_Frame_Shift_Del_p.F1085fs|NFAT5_ENST00000432919.1_Frame_Shift_Del_p.F1179fs|NFAT5_ENST00000566899.1_Frame_Shift_Del_p.F1085fs|NFAT5_ENST00000567239.1_Frame_Shift_Del_p.F1178fs	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	1161					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						CCAAGAAGCATTTTTTGCAGC	0.438																																					p.A1177fs		Atlas-INDEL	.											.	NFAT5	184	.	0			c.3531delA						.						140	132	134					16																	69727260		2198	4300	6498	SO:0001589	frameshift_variant	10725	exon13			.	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.3478delT	chr16.hg19:g.69727260delT	ENSP00000346420:p.Phe1161fs	112.0	0.0		206.0	15.0	NM_138713	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Frame_Shift_Del	DEL	ENST00000354436.2	hg19	CCDS10881.1																																																																																			.	.		0.438	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		-	69727260	T	-	69727260	7	5	114	1	0	1	0	1	0	0	0	0	10369	1493	52	0	3582	0	NFAT5	16	69727260	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	393722	69727260	20627493	980	19252										
NOB1	28987	hgsc.bcm.edu	37	chr16	69788569	69788569	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacagcgagccgcctgcgtgTggccttgtcccgaatctcag	13	14	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:69788569T>C	ENST00000268802.5	-	2	153	c.124A>G	c.(124-126)Aca>Gca	p.T42A		NM_014062.1	NP_054781.1	Q9ULX3	NOB1_HUMAN	NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)	42	PINc.				visual perception (GO:0007601)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CGCCTGCGTGTGGCCTTGTCC	0.627																																					p.T42A		Atlas-SNP	.											.	NOB1	24	.	0			c.A124G						.						73	65	67					16																	69788569		2198	4300	6498	SO:0001583	missense	28987	exon2			TGCGTGTGGCCTT	AB026125	CCDS10884.1	16q22.1	2008-02-05	2006-04-20	2006-04-20	ENSG00000141101	ENSG00000141101			29540	protein-coding gene	gene with protein product	"nin one binding protein"	613586	"PSMD8 binding protein 1"	PSMD8BP1		16172919	Standard	NM_014062		Approved	NOB1P, ART-4, MST158	uc002exs.4	Q9ULX3	OTTHUMG00000137576	ENST00000268802.5:c.124A>G	chr16.hg19:g.69788569T>C	ENSP00000268802:p.Thr42Ala	63.0	0.0		104.0	5.0	NM_014062	Q7L6B7|Q7M4M4|Q7Z4B5|Q9NWB0	Missense_Mutation	SNP	ENST00000268802.5	hg19	CCDS10884.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.016757	0.93404	.	.	ENSG00000141101	ENST00000268802	T	0.28454	1.61	4.45	4.45	0.53987	Nucleotide binding protein, PINc (1);	1.464880	0.04777	N	0.429098	T	0.24967	0.0606	N	0.19112	0.55	0.58432	D	0.999998	B	0.11235	0.004	B	0.13407	0.009	T	0.01549	-1.1327	9	.	.	.	.	13.1095	0.59265	0.0:0.0:0.0:1.0	.	42	Q9ULX3	NOB1_HUMAN	A	42	ENSP00000268802:T42A	.	T	-	1	0	NOB1	68346070	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.049000	0.64244	1.998000	0.58463	0.482000	0.46254	ACA	.	.		0.627	NOB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268958.2	NM_014062		C	69788569	T	C	69788569	3	2	114	1	0	0	0	0	1	0	0	0	10520	1696	59	2	1146	2	NOB1	16	69788569	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	61309	69788569	20566184	981	19253										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72829897	72829897	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttggaggttccggcgaaggGggccgggagtcaatcttgag	18	7	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:72829897G>C	ENST00000268489.5	-	9	7356	c.6684C>G	c.(6682-6684)ccC>ccG	p.P2228P	ZFHX3_ENST00000397992.5_Silent_p.P1314P	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2228					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CCGGCGAAGGGGGCCGGGAGT	0.527																																					p.P2228P		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C6684G						.						106	105	105					16																	72829897		2198	4300	6498	SO:0001819	synonymous_variant	463	exon9			CGAAGGGGGCCGG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.6684C>G	chr16.hg19:g.72829897G>C		143.0	0.0		173.0	68.0	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.527	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		C	72829897	G	C	72829897	2	2	114	1	0	0	0	0	0	0	0	1	17649	1219	43	4		4	ZFHX3	16	72829897	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	3041328	72829897	17524856	982	19254										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72993684	72993684	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctccacgtcactctcctcgtCcccctcctcaccggtgtcgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:72993684delC	ENST00000268489.5	-	2	1033	c.361delG	c.(361-363)gacfs	p.D121fs	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	121					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CTCTCCTCGTCCCCCTCCTCA	0.687																																					p.D121fs		Atlas-INDEL	.											.	ZFHX3	404	.	0			c.362delA						.						31	32	32					16																	72993684		2198	4300	6498	SO:0001589	frameshift_variant	463	exon2			.	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.361delG	chr16.hg19:g.72993684delC	ENSP00000268489:p.Asp121fs	166.0	0.0		179.0	14.0	NM_006885	D3DWS8|O15101|Q13719	Frame_Shift_Del	DEL	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.687	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		-	72993684	C	-	72993684	7	5	114	1	0	1	0	1	0	0	0	0	17649	855	30	0	10786	0	ZFHX3	16	72993684	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	163787	72993684	17361069	983	19255										
MLKL	197259	hgsc.bcm.edu	37	chr16	74725195	74725195	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcaatgctgccagcctggagTtttttgaatacttttatggc					rs56247416	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:74725195delT	ENST00000308807.7	-	4	1165	c.702delA	c.(700-702)aaafs	p.K234fs	MLKL_ENST00000306247.7_Intron	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						CAGCCTGGAGTTTTTTGAATA	0.438																																					p.L235fs		Atlas-INDEL	.											.	MLKL	51	.	0			c.703delC						.						255	264	261					16																	74725195		2198	4300	6498	SO:0001589	frameshift_variant	197259	exon4			.	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000308807.7:c.702delA	chr16.hg19:g.74725195delT	ENSP00000308351:p.Lys234fs	139.0	0.0		161.0	12.0	NM_152649		Frame_Shift_Del	DEL	ENST00000308807.7	hg19	CCDS32487.1																																																																																			.	.		0.438	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	NM_152649		-	74725195	T	-	74725195	7	5	114	1	0	1	0	1	0	0	0	0	9628	1722	60	0	776	0	MLKL	16	74725195	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1731511	74725195	15629558	984	19256										
PLCG2	5336	hgsc.bcm.edu	37	chr16	81939079	81939079	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaggacgaacacaagcaacaGggggagctgtacatgtggga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:81939079delG	ENST00000359376.3	+	15	1648	c.1434delG	c.(1432-1434)cagfs	p.Q478fs		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	478					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						ACAAGCAACAGGGGGAGCTGT	0.577																																					p.Q478fs		Atlas-INDEL	.											.	PLCG2	276	.	0			c.1433delA						.						71	77	75					16																	81939079		2041	4196	6237	SO:0001589	frameshift_variant	5336	exon15			.		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1434delG	chr16.hg19:g.81939079delG	ENSP00000352336:p.Gln478fs	172.0	0.0		235.0	16.0	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Frame_Shift_Del	DEL	ENST00000359376.3	hg19	CCDS42204.1																																																																																			.	.		0.577	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			-	81939079	G	-	81939079	7	5	114	1	0	1	0	1	0	0	0	0	12045	991	35	0	1488	0	PLCG2	16	81939079	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	7213884	81939079	8415674	985	19257										
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88691079	88691079	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accaaaaccactgctcctgtCcccgagcccaccaagccagg					rs540178633		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:88691079delC	ENST00000301011.5	+	12	2168	c.1968delC	c.(1966-1968)gtcfs	p.V656fs	ZC3H18_ENST00000452588.2_Frame_Shift_Del_p.V680fs	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	656	Ser-rich.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CTGCTCCTGTCCCCGAGCCCA	0.692																																					p.V656fs	Ovarian(121;375 2276 20373 38669)	Atlas-INDEL	.											.	ZC3H18	90	.	0			c.1967delT						.						46	65	59					16																	88691079		2198	4300	6498	SO:0001589	frameshift_variant	124245	exon12			.	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.1968delC	chr16.hg19:g.88691079delC	ENSP00000301011:p.Val656fs	123.0	0.0		209.0	14.0	NM_144604	Q96DG4|Q96MP7	Frame_Shift_Del	DEL	ENST00000301011.5	hg19	CCDS10967.1																																																																																			.	.		0.692	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		-	88691079	C	-	88691079	7	5	114	1	0	1	0	1	0	0	0	0	17583	842	30	0	2010	0	ZC3H18	16	88691079	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	6752000	88691079	1663674	986	19258										
CTU2	9780	hgsc.bcm.edu	37	chr16	88780815	88780815	+	IGR	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtgagaagctggtgaagggCccccgggatggccctgctgc					rs573239956		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:88780815delC	ENST00000301015.9	-	0	8072				MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000453996.2_Frame_Shift_Del_p.G374fs|CTU2_ENST00000567949.1_Frame_Shift_Del_p.G445fs|CTU2_ENST00000378384.3_Frame_Shift_Del_p.G287fs|CTU2_ENST00000312060.5_Frame_Shift_Del_p.G374fs	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						TGGTGAAGGGCCCCCGGGATG	0.662																																					p.G374fs		Atlas-INDEL	.											.	CTU2	66	.	0			c.1121delG						.						64	80	75					16																	88780815		2193	4293	6486	SO:0001628	intergenic_variant	348180	exon11			.	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"family with sequence similarity 38, member A"	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776		chr16.hg19:g.88780815delC		162.0	0.0		192.0	12.0	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Frame_Shift_Del	DEL	ENST00000301015.9	hg19	CCDS54058.1																																																																																			.	.		0.662	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745		-	88780815	C	-	88780815	6	5	114	0	1	1	0	1	0	0	0	0	4050	726	26	0		0	CTU2	16	88780815	IGR	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	89736	88780815	1573938	987	19259										
ZNF778	197320	hgsc.bcm.edu	37	chr16	89294115	89294115	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catgtaaggactcacactggAgagaaaccatatgaatgtaa	9	7	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:89294115A>G	ENST00000433976.2	+	6	1667	c.1335A>G	c.(1333-1335)ggA>ggG	p.G445G	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Silent_p.G403G	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	445					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		CTCACACTGGAGAGAAACCAT	0.488																																					p.G473G		Atlas-SNP	.											.	ZNF778	67	.	0			c.A1419G						.						89	93	91					16																	89294115		2194	4299	6493	SO:0001819	synonymous_variant	197320	exon7			CACTGGAGAGAAA	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"Zinc fingers, C2H2-type", "-"	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.1335A>G	chr16.hg19:g.89294115A>G		53.0	0.0		59.0	5.0	NM_001201407	Q08AG0	Silent	SNP	ENST00000433976.2	hg19	CCDS45550.1																																																																																			.	.		0.488	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		G	89294115	A	G	89294115	2	3	114	1	0	0	0	0	0	0	0	1	18166	291	11	2		2	ZNF778	16	89294115	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	513300	89294115	1060638	988	19260										
TCF25	22980	hgsc.bcm.edu	37	chr16	89972662	89972662	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgccatgtgatcctctctgaGatcaaggaagccgtcgctgc	11	13	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:89972662G>A	ENST00000263346.8	+	15	1745	c.1689G>A	c.(1687-1689)gaG>gaA	p.E563E	RP11-566K11.7_ENST00000570217.1_RNA|TCF25_ENST00000263347.7_Silent_p.E328E	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	563					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		TCCTCTCTGAGATCAAGGAAG	0.597																																					p.E563E		Atlas-SNP	.											.	TCF25	61	.	0			c.G1689A						.						57	49	52					16																	89972662		2197	4300	6497	SO:0001819	synonymous_variant	22980	exon15			CTCTGAGATCAAG	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.1689G>A	chr16.hg19:g.89972662G>A		103.0	0.0		92.0	4.0	NM_014972	Q2MK75|Q9UPV3	Silent	SNP	ENST00000263346.8	hg19	CCDS10987.1																																																																																			.	.		0.597	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972		A	89972662	G	A	89972662	2	1	114	1	0	0	0	0	0	0	0	1	15708	933	33	3		3	TCF25	16	89972662	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	678547	89972662	382091	989	19261										
MYO1C	4641	hgsc.bcm.edu	37	chr17	1383903	1383903	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcttgtcgttgatggaggagActttggcacactggccctgg	14	9	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:1383903A>G	ENST00000575158.1	-	7	895	c.719T>C	c.(718-720)gTc>gCc	p.V240A	MYO1C_ENST00000361007.2_Missense_Mutation_p.V240A|MYO1C_ENST00000545534.2_Missense_Mutation_p.V251A|MYO1C_ENST00000359786.5_Missense_Mutation_p.V275A|MYO1C_ENST00000438665.2_Missense_Mutation_p.V256A|MYO1C_ENST00000573198.1_5'UTR			Q12965	MYO1E_HUMAN	myosin IC	246	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)	p.Q236fs*17(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GATGGAGGAGACTTTGGCACA	0.602																																					p.V275A		Atlas-SNP	.											.,1	MYO1C	57	.	1	Deletion - Frameshift(1)	liver(1)	c.T824C						.						121	109	113					17																	1383903		2203	4300	6503	SO:0001583	missense	4641	exon7			GAGGAGACTTTGG	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"Myosins / Myosin superfamily : Class I"	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.719T>C	chr17.hg19:g.1383903A>G	ENSP00000459174:p.Val240Ala	93.0	0.0		79.0	4.0	NM_001080779	Q14778	Missense_Mutation	SNP	ENST00000575158.1	hg19	CCDS11003.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.799959	0.70567	.	.	ENSG00000197879	ENST00000359786;ENST00000438665;ENST00000535856;ENST00000361007;ENST00000545534;ENST00000535421	D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74	5.66	5.66	0.87406	Myosin head, motor domain (2);	0.115086	0.64402	D	0.000016	D	0.90779	0.7105	M	0.70275	2.135	0.80722	D	1	B;B;B	0.18610	0.013;0.029;0.01	B;B;B	0.29077	0.068;0.098;0.041	D	0.88515	0.3092	10	0.66056	D	0.02	.	15.0719	0.72042	1.0:0.0:0.0:0.0	.	251;275;256	B7Z3E5;O00159;O00159-3	.;MYO1C_HUMAN;.	A	275;256;256;240;251;240	ENSP00000352834:V275A;ENSP00000412197:V256A;ENSP00000354283:V240A;ENSP00000437685:V251A	ENSP00000352834:V275A	V	-	2	0	MYO1C	1330653	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.161000	0.67846	0.418000	0.28097	GTC	.	.		0.602	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2			G	1383903	A	G	1383903	3	3	114	1	0	0	0	0	1	0	0	0	10079	275	10	2	2471	2	MYO1C	17	1383903	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10		1383903	79811307	990	19262										
SERPINF1	5176	hgsc.bcm.edu	37	chr17	1680585	1680585	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctttgagtggaacgaggatGgggcgggaaccacccccagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:1680585delG	ENST00000254722.4	+	8	1265	c.1102delG	c.(1102-1104)gggfs	p.G368fs		NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	368					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						GAACGAGGATGGGGCGGGAAC	0.567																																					p.D367fs		Atlas-INDEL	.											.	SERPINF1	31	.	0			c.1101delT						.						125	125	125					17																	1680585		2203	4300	6503	SO:0001589	frameshift_variant	5176	exon8			.	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"Serine (or cysteine) peptidase inhibitors"	8824	protein-coding gene	gene with protein product	"pigment epithelium-derived factor", "proliferation-inducing protein 35"	172860	"serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.1102delG	chr17.hg19:g.1680585delG	ENSP00000254722:p.Gly368fs	239.0	0.0		163.0	10.0	NM_002615	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Frame_Shift_Del	DEL	ENST00000254722.4	hg19	CCDS11012.1																																																																																			.	.		0.567	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615		-	1680585	G	-	1680585	7	5	114	1	0	1	0	1	0	0	0	0	14129	1348	47	0	1128	0	SERPINF1	17	1680585	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	296682	1680585	79514625	991	19263										
TSR1	55720	hgsc.bcm.edu	37	chr17	2228075	2228075	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctctcttgatgaccattctgTctggatctactgacataaga	7	10	4	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:2228075T>C	ENST00000301364.5	-	13	3148	c.2069A>G	c.(2068-2070)gAc>gGc	p.D690G	SRR_ENST00000344595.5_3'UTR	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	690					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						GACCATTCTGTCTGGATCTAC	0.403																																					p.D690G		Atlas-SNP	.											.	TSR1	57	.	0			c.A2069G						.						98	96	97					17																	2228075		2203	4300	6503	SO:0001583	missense	55720	exon13			ATTCTGTCTGGAT	AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"TSR1, 20S rRNA accumulation, homolog (yeast)"			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.2069A>G	chr17.hg19:g.2228075T>C	ENSP00000301364:p.Asp690Gly	124.0	0.0		138.0	6.0	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	hg19	CCDS32525.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.014693	0.54468	.	.	ENSG00000167721	ENST00000301364	T	0.19105	2.17	5.28	5.28	0.74379	Ribosome biogenesis protein BMS1/TSR1, C-terminal (1);	0.256103	0.46145	D	0.000311	T	0.49201	0.1543	M	0.86178	2.8	0.53688	D	0.999978	D	0.71674	0.998	D	0.74348	0.983	T	0.54715	-0.8252	10	0.54805	T	0.06	-8.3068	12.94	0.58337	0.0:0.0:0.0:1.0	.	690	Q2NL82	TSR1_HUMAN	G	690	ENSP00000301364:D690G	ENSP00000301364:D690G	D	-	2	0	TSR1	2174825	1.000000	0.71417	1.000000	0.80357	0.656000	0.38851	4.719000	0.61937	2.003000	0.58678	0.402000	0.26972	GAC	.	.		0.403	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128		C	2228075	T	C	2228075	3	2	114	1	0	0	0	0	1	0	0	0	16679	1667	58	2	357	2	TSR1	17	2228075	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	547490	2228075	78967135	992	19264										
PAFAH1B1	5048	hgsc.bcm.edu	37	chr17	2569341	2569341	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agataaaaagtatgctggtcTtttggaaaaaaaatggacat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:2569341delT	ENST00000397195.5	+	4	600	c.149delT	c.(148-150)cttfs	p.L51fs	PAFAH1B1_ENST00000572915.2_Intron	NM_000430.3	NP_000421.1			platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)											endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|skin(1)	11						TATGCTGGTCTTTTGGAAAAA	0.244																																					p.L50fs		Atlas-INDEL	.											.	PAFAH1B1	26	.	0			c.148delC						.						13	14	13					17																	2569341		2093	4168	6261	SO:0001589	frameshift_variant	5048	exon4			.	L25107	CCDS32528.1	17p13.3	2014-04-04	2010-02-10		ENSG00000007168	ENSG00000007168		"WD repeat domain containing"	8574	protein-coding gene	gene with protein product	"lissencephaly-1"	601545	"platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)", "Miller-Dieker syndrome chromosome region", "platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa", "platelet-activating factor acetylhydrolase, isoform Ib, subunit 1 (45kDa)"	MDCR, MDS		8355785, 9063735	Standard	NM_000430		Approved	LIS1, PAFAH	uc002fuw.4	P43034	OTTHUMG00000177574	ENST00000397195.5:c.149delT	chr17.hg19:g.2569341delT	ENSP00000380378:p.Leu51fs	123.0	0.0		112.0	12.0	NM_000430		Frame_Shift_Del	DEL	ENST00000397195.5	hg19	CCDS32528.1																																																																																			.	.		0.244	PAFAH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437797.2	NM_000430		-	2569341	T	-	2569341	7	5	114	1	0	1	0	1	0	0	0	0	11393	1609	56	0	159	0	PAFAH1B1	17	2569341	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	341266	2569341	78625869	993	19265										
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2604059	2604059	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atggcatgctccgcctggggGgctgtccagctgtacacctg	14	13	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:2604059G>A	ENST00000570628.2	-	8	1077	c.972C>T	c.(970-972)gcC>gcT	p.A324A	CLUH_ENST00000435359.1_Silent_p.A324A|CLUH_ENST00000538975.1_Silent_p.A324A			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	324					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											CCGCCTGGGGGGCTGTCCAGC	0.657																																					p.A324A		Atlas-SNP	.											.	.	.	.	0			c.C972T						.						40	46	44					17																	2604059		2161	4252	6413	SO:0001819	synonymous_variant	23277	exon8			CTGGGGGGCTGTC	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"KIAA0664"	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.972C>T	chr17.hg19:g.2604059G>A		65.0	0.0		71.0	4.0	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	hg19	CCDS45572.1																																																																																			.	.		0.657	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		A	2604059	G	A	2604059	2	1	114	1	0	0	0	0	0	0	0	1	8198	1219	43	3		3	KIAA0664	17	2604059	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	34718	2604059	78591151	994	19266										
SPATA22	84690	hgsc.bcm.edu	37	chr17	3352342	3352342	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccgaactcactggacaagaaTtttttccatcatttgccact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:3352342delT	ENST00000573128.1	-	6	914	c.431delA	c.(430-432)aatfs	p.N144fs	SPATA22_ENST00000541913.1_Frame_Shift_Del_p.N128fs|SPATA22_ENST00000268981.5_Frame_Shift_Del_p.N144fs|SPATA22_ENST00000355380.4_Frame_Shift_Del_p.N101fs|SPATA22_ENST00000575375.1_Frame_Shift_Del_p.N144fs|SPATA22_ENST00000572969.1_Frame_Shift_Del_p.N144fs|SPATA22_ENST00000397168.3_Frame_Shift_Del_p.N144fs			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	144					fertilization (GO:0009566)|gamete generation (GO:0007276)|meiotic DNA repair synthesis (GO:0000711)|regulation of meiotic cell cycle (GO:0051445)|reproductive system development (GO:0061458)|synapsis (GO:0007129)	chromosome (GO:0005694)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)	19						TGGACAAGAATTTTTTCCATC	0.358																																					p.N144fs		Atlas-INDEL	.											.	SPATA22	49	.	0			c.432delT						.						197	189	192					17																	3352342		2203	4300	6503	SO:0001589	frameshift_variant	84690	exon6			.	AY035868	CCDS11027.1, CCDS54066.1, CCDS54067.1	17p13.3	2005-12-19							30705	protein-coding gene	gene with protein product						12477932	Standard	NM_001170696		Approved	NYD-SP20	uc002fvn.3	Q8NHS9		ENST00000573128.1:c.431delA	chr17.hg19:g.3352342delT	ENSP00000459580:p.Asn144fs	158.0	0.0		138.0	11.0	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Frame_Shift_Del	DEL	ENST00000573128.1	hg19	CCDS11027.1																																																																																			.	.		0.358	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598		-	3352342	T	-	3352342	7	5	114	1	0	1	0	1	0	0	0	0	15023	1493	52	0	676	0	SPATA22	17	3352342	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	748283	3352342	77842868	995	19267										
ATP2A3	489	hgsc.bcm.edu	37	chr17	3854948	3854948	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctccacgaaggcggtcgtgGtctcctcgccctcctcgaac	11	17	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:3854948G>C	ENST00000352011.3	-	4	305	c.251C>G	c.(250-252)aCc>aGc	p.T84S	ATP2A3_ENST00000359983.3_Missense_Mutation_p.T84S|ATP2A3_ENST00000397035.3_Missense_Mutation_p.T84S|ATP2A3_ENST00000397043.3_Missense_Mutation_p.T84S|ATP2A3_ENST00000397041.3_Missense_Mutation_p.T84S|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000309890.7_Missense_Mutation_p.T84S			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	84					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		GGCGGTCGTGGTCTCCTCGCC	0.662																																					p.T84S	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.C251G						.						40	28	32					17																	3854948		2202	4300	6502	SO:0001583	missense	489	exon4			GTCGTGGTCTCCT		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"ATPases / P-type"	813	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 3", "calcium pump 3"	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.251C>G	chr17.hg19:g.3854948G>C	ENSP00000301387:p.Thr84Ser	222.0	0.0		167.0	103.0	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Missense_Mutation	SNP	ENST00000352011.3	hg19	CCDS11041.1	.	.	.	.	.	.	.	.	.	.	G	8.608	0.888349	0.17540	.	.	ENSG00000074370	ENST00000397043;ENST00000352011;ENST00000359983;ENST00000397041;ENST00000397045;ENST00000309890;ENST00000397035	D;D;D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31;-2.31;-2.31	3.83	3.83	0.44106	ATPase, P-type,  transmembrane domain (1);	0.181563	0.32819	N	0.005615	T	0.77130	0.4085	N	0.19112	0.55	0.44523	D	0.997474	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001	T	0.72020	-0.4416	10	0.28530	T	0.3	.	12.8645	0.57932	0.0:0.1647:0.8353:0.0	.	84;84;84;84;84;84	Q93084-4;Q93084-2;Q93084;Q93084-6;G3XAE1;Q93084-3	.;.;AT2A3_HUMAN;.;.;.	S	84	ENSP00000380236:T84S;ENSP00000301387:T84S;ENSP00000353072:T84S;ENSP00000380234:T84S;ENSP00000312577:T84S;ENSP00000380229:T84S	ENSP00000312577:T84S	T	-	2	0	ATP2A3	3801697	1.000000	0.71417	0.992000	0.48379	0.977000	0.68977	5.506000	0.66993	2.125000	0.65367	0.514000	0.50259	ACC	.	.		0.662	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953		C	3854948	G	C	3854948	3	2	114	1	0	0	0	0	1	0	0	0	1138	1261	44	4	3031	4	ATP2A3	17	3854948	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	502606	3854948	77340262	996	19268										
ANKFY1	51479	hgsc.bcm.edu	37	chr17	4076695	4076695	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtgcactctgtcaggagaaCccggatgttgttgagccggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:4076695delC	ENST00000341657.4	-	21	3003	c.2968delG	c.(2968-2970)gttfs	p.V990fs	CYB5D2_ENST00000573984.1_Intron|ANKFY1_ENST00000574367.1_Frame_Shift_Del_p.V991fs|ANKFY1_ENST00000570535.1_Frame_Shift_Del_p.V1032fs	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	990					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GTCAGGAGAACCCGGATGTTG	0.582																																					p.V1032fs		Atlas-INDEL	.											.	ANKFY1	81	.	0			c.3095delT						.						69	78	75					17																	4076695		1981	4155	6136	SO:0001589	frameshift_variant	51479	exon21			.	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"Zinc fingers, FYVE domain containing", "BTB/POZ domain containing", "Ankyrin repeat domain containing"	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.2968delG	chr17.hg19:g.4076695delC	ENSP00000343362:p.Val990fs	150.0	0.0		151.0	11.0	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Frame_Shift_Del	DEL	ENST00000341657.4	hg19																																																																																				.	.		0.582	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		-	4076695	C	-	4076695	7	5	114	1	0	1	0	1	0	0	0	0	626	507	18	0	561	0	ANKFY1	17	4076695	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	221747	4076695	77118515	997	19269										
DHX33	56919	hgsc.bcm.edu	37	chr17	5353579	5353579	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attgagcagggtcatgtgatCcccctcgctggatatgaact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:5353579delC	ENST00000225296.3	-	10	1872	c.1672delG	c.(1672-1674)gatfs	p.D558fs	DHX33_ENST00000433302.3_Frame_Shift_Del_p.D334fs	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	558					positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GTCATGTGATCCCCCTCGCTG	0.542																																					p.D558fs		Atlas-INDEL	.											.	DHX33	41	.	0			c.1673delA						.						151	152	152					17																	5353579		2203	4300	6503	SO:0001589	frameshift_variant	56919	exon10			.	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"DEAH-boxes"	16718	protein-coding gene	gene with protein product		614405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.1672delG	chr17.hg19:g.5353579delC	ENSP00000225296:p.Asp558fs	173.0	0.0		147.0	11.0	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Frame_Shift_Del	DEL	ENST00000225296.3	hg19	CCDS11072.1																																																																																			.	.		0.542	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162		-	5353579	C	-	5353579	7	5	114	1	0	1	0	1	0	0	0	0	4508	855	30	0	463	0	DHX33	17	5353579	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1276884	5353579	75841631	998	19270										
DVL2	1856	hgsc.bcm.edu	37	chr17	7132947	7132947	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctgcttccttcgccgccggTggcgcttaaggaggcgggag	16	12	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:7132947T>C	ENST00000005340.5	-	6	989	c.707A>G	c.(706-708)cAc>cGc	p.H236R	DVL2_ENST00000574642.1_5'UTR|DVL2_ENST00000575458.1_Missense_Mutation_p.H230R	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	236	Poly-Arg.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						TCGCCGCCGGTGGCGCTTAAG	0.632																																					p.H236R		Atlas-SNP	.											.	DVL2	49	.	0			c.A707G						.						52	60	58					17																	7132947		2203	4300	6503	SO:0001583	missense	1856	exon6			CGCCGGTGGCGCT	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"Dishevelled homologs"	3086	protein-coding gene	gene with protein product		602151	"dishevelled 2 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 2 (Drosophila)"			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.707A>G	chr17.hg19:g.7132947T>C	ENSP00000005340:p.His236Arg	89.0	0.0		81.0	4.0	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	hg19	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	T	9.563	1.119064	0.20877	.	.	ENSG00000004975	ENST00000005340	T	0.04194	3.68	5.0	5.0	0.66597	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.08670	0.0215	N	0.16368	0.405	0.58432	D	0.999999	D;B;B	0.57899	0.981;0.112;0.112	D;B;B	0.69824	0.966;0.023;0.074	T	0.51834	-0.8655	10	0.14656	T	0.56	-18.0085	12.6392	0.56700	0.0:0.0:0.0:1.0	.	143;230;236	B4DM44;B4DLQ0;O14641	.;.;DVL2_HUMAN	R	236	ENSP00000005340:H236R	ENSP00000005340:H236R	H	-	2	0	DVL2	7073671	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	7.514000	0.81750	1.890000	0.54733	0.334000	0.21626	CAC	.	.		0.632	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422		C	7132947	T	C	7132947	3	2	114	1	0	0	0	0	1	0	0	0	4838	1696	59	2	1543	2	DVL2	17	7132947	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1779368	7132947	74062263	999	19271										
SPEM1	374768	hgsc.bcm.edu	37	chr17	7324238	7324238	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tactcagaaagcagacccagCcccctaagaagcagagttct					rs377239691		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:7324238delC	ENST00000323675.3	+	3	269	c.244delC	c.(244-246)cccfs	p.P83fs	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	83					sperm individualization (GO:0007291)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	12		Prostate(122;0.173)				GCAGACCCAGCCCCCTAAGAA	0.597																																					p.Q81fs		Atlas-INDEL	.											.	SPEM1	41	.	0			c.243delG						.						121	129	126					17																	7324238		2045	4185	6230	SO:0001589	frameshift_variant	374768	exon3			.	AK097400	CCDS42254.1	17p13.1	2011-12-12	2008-02-04	2008-02-04	ENSG00000181323	ENSG00000181323			32429	protein-coding gene	gene with protein product		615116	"chromosome 17 open reading frame 83"	C17orf83		17426145, 20558241, 21184802	Standard	NM_199339		Approved	FLJ40081	uc002ggv.3	Q8N4L4		ENST00000323675.3:c.244delC	chr17.hg19:g.7324238delC	ENSP00000315554:p.Pro83fs	165.0	0.0		119.0	11.0	NM_199339		Frame_Shift_Del	DEL	ENST00000323675.3	hg19	CCDS42254.1																																																																																			.	.		0.597	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339		-	7324238	C	-	7324238	7	5	114	1	0	1	0	1	0	0	0	0	15052	739	26	0	254	0	SPEM1	17	7324238	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	191291	7324238	73870972	1000	19272										
TP53	7157	hgsc.bcm.edu	37	chr17	7577557	7577557	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccggttcatgccgcccatgcAggaactgttacacatgtagt	10	12	1	0	rs397516437		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:7577557A>T	ENST00000269305.4	-	7	913	c.724T>A	c.(724-726)Tgc>Agc	p.C242S	TP53_ENST00000420246.2_Missense_Mutation_p.C242S|TP53_ENST00000359597.4_Missense_Mutation_p.C242S|TP53_ENST00000413465.2_Missense_Mutation_p.C242S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.C242S|TP53_ENST00000455263.2_Missense_Mutation_p.C242S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	242	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:16959974}.|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C242R(12)|p.C242S(10)|p.0?(8)|p.?(5)|p.N239_C242delNSSC(3)|p.C242G(2)|p.S241del(2)|p.N239_C242>S(1)|p.S241_C242insX(1)|p.C238fs*21(1)|p.C242fs*20(1)|p.C242fs*23(1)|p.C242fs*5(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCGCCCATGCAGGAACTGTTA	0.577		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.C242S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,caecum,carcinoma,0,1	TP53	33396	.	55	Substitution - Missense(24)|Deletion - In frame(10)|Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Complex - deletion inframe(1)	breast(8)|large_intestine(7)|biliary_tract(5)|upper_aerodigestive_tract(4)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|liver(3)|ovary(3)|pancreas(3)|prostate(3)|stomach(2)|oesophagus(2)|lung(2)|urinary_tract(1)	c.T724A						.						138	106	117					17																	7577557		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CCATGCAGGAACT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.724T>A	chr17.hg19:g.7577557A>T	ENSP00000269305:p.Cys242Ser	224.0	0.0		129.0	81.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.639501	0.87760	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99914	-7.98;-7.98;-7.98;-7.98;-7.98;-7.98;-7.98;-7.98	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99924	0.9965	M	0.92784	3.345	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;0.999	D	0.95737	0.8780	10	0.87932	D	0	-27.558	12.3101	0.54924	1.0:0.0:0.0:0.0	.	242;242;149;242;242;242	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	S	242;242;242;242;242;242;231;149;110;149	ENSP00000410739:C242S;ENSP00000352610:C242S;ENSP00000269305:C242S;ENSP00000398846:C242S;ENSP00000391127:C242S;ENSP00000391478:C242S;ENSP00000425104:C110S;ENSP00000423862:C149S	ENSP00000269305:C242S	C	-	1	0	TP53	7518282	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.087000	0.94110	2.074000	0.62210	0.379000	0.24179	TGC	.	.		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577557	A	T	7577557	3	4	114	1	0	0	0	0	1	0	0	0	16396	188	7	4	566	4	TP53	17	7577557	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	253319	7577557	73617653	1001	19273										
CHD3	1107	hgsc.bcm.edu	37	chr17	7809999	7809999	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacccgcattggagtcatgtCtctcgtcaaaaagaaggtat	10	9	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:7809999C>A	ENST00000330494.7	+	29	4637	c.4487C>A	c.(4486-4488)tCt>tAt	p.S1496Y	SCARNA21_ENST00000517026.1_RNA|CHD3_ENST00000358181.4_Missense_Mutation_p.S1496Y|CHD3_ENST00000380358.4_Missense_Mutation_p.S1555Y	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1496					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				GGAGTCATGTCTCTCGTCAAA	0.557																																					p.S1555Y		Atlas-SNP	.											.	CHD3	169	.	0			c.C4664A						.						99	95	96					17																	7809999		2203	4300	6503	SO:0001583	missense	1107	exon29			TCATGTCTCTCGT	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.4487C>A	chr17.hg19:g.7809999C>A	ENSP00000332628:p.Ser1496Tyr	105.0	0.0		78.0	48.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.041720	0.55003	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	D;D;D	0.91631	-2.88;-2.82;-2.81	4.69	4.69	0.59074	Domain of unknown function DUF1086 (1);	0.000000	0.44688	D	0.000435	D	0.95971	0.8688	M	0.78637	2.42	0.80722	D	1	D;D;D;D	0.76494	0.998;0.997;0.997;0.999	D;D;D;D	0.87578	0.998;0.994;0.996;0.998	D	0.96542	0.9401	10	0.87932	D	0	-14.2861	17.8077	0.88606	0.0:1.0:0.0:0.0	.	72;1496;1496;1555	B3KWV4;Q12873-2;Q12873;E9PG89	.;.;CHD3_HUMAN;.	Y	1555;1496;1496	ENSP00000369716:S1555Y;ENSP00000350907:S1496Y;ENSP00000332628:S1496Y	ENSP00000332628:S1496Y	S	+	2	0	CHD3	7750724	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.452000	0.66638	2.429000	0.82318	0.313000	0.20887	TCT	.	.		0.557	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		A	7809999	C	A	7809999	3	1	114	1	0	0	0	0	1	0	0	0	3328	913	32	3	4882	3	CHD3	17	7809999	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	232442	7809999	73385211	1002	19274										
PFAS	5198	hgsc.bcm.edu	37	chr17	8172524	8172524	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atttgatactctgaccacctCcccctggctccagctcttta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:8172524delC	ENST00000314666.6	+	28	4092	c.3959delC	c.(3958-3960)tccfs	p.S1320fs	PFAS_ENST00000545834.1_Frame_Shift_Del_p.S896fs	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1320					'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)	p.S1320F(1)		central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	CTGACCACCTCCCCCTGGCTC	0.622																																					p.S1320fs		Atlas-INDEL	.											.	PFAS	91	.	1	Substitution - Missense(1)	large_intestine(1)	c.3958delT						.						41	41	41					17																	8172524		2203	4300	6503	SO:0001589	frameshift_variant	5198	exon28			.	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"FGAR amidotransferase"	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.3959delC	chr17.hg19:g.8172524delC	ENSP00000313490:p.Ser1320fs	144.0	0.0		114.0	11.0	NM_012393	A6H8V8	Frame_Shift_Del	DEL	ENST00000314666.6	hg19	CCDS11136.1																																																																																			.	.		0.622	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2			-	8172524	C	-	8172524	7	5	114	1	0	1	0	1	0	0	0	0	11763	855	30	0	4065	0	PFAS	17	8172524	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	362525	8172524	73022686	1003	19275										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11686973	11686973	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actgttccaggtatgatcggAgcaagctgtccctaaaggag	12	9	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:11686973A>G	ENST00000262442.4	+	40	7797	c.7729A>G	c.(7729-7731)Agc>Ggc	p.S2577G	DNAH9_ENST00000454412.2_Missense_Mutation_p.S2577G	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2577	AAA 3. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GTATGATCGGAGCAAGCTGTC	0.522																																					p.S2577G		Atlas-SNP	.											.	DNAH9	695	.	0			c.A7729G						.						101	74	83					17																	11686973		2203	4300	6503	SO:0001583	missense	1770	exon40			GATCGGAGCAAGC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.7729A>G	chr17.hg19:g.11686973A>G	ENSP00000262442:p.Ser2577Gly	84.0	0.0		109.0	5.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	11.37	1.619839	0.28801	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.33865	1.39;1.39	5.37	4.26	0.50523	ATPase, AAA+ type, core (1);	0.200961	0.40302	N	0.001126	T	0.16300	0.0392	N	0.05031	-0.125	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.18808	-1.0325	10	0.23891	T	0.37	.	6.9322	0.24447	0.7731:0.1518:0.0751:0.0	.	2577	Q9NYC9	DYH9_HUMAN	G	2577;2577;1159	ENSP00000262442:S2577G;ENSP00000414874:S2577G	ENSP00000262442:S2577G	S	+	1	0	DNAH9	11627698	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	2.208000	0.42797	0.846000	0.35142	0.523000	0.50628	AGC	.	.		0.522	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		G	11686973	A	G	11686973	3	3	114	1	0	0	0	0	1	0	0	0	4610	304	11	2	7887	2	DNAH9	17	11686973	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3514449	11686973	69508237	1004	19276										
ZNF286A	57335	hgsc.bcm.edu	37	chr17	15619756	15619756	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agcagagaacttataaagagAaaaaacctcataaatgtaat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:15619756delA	ENST00000464847.2	+	5	1271	c.718delA	c.(718-720)aaafs	p.K241fs	ZNF286A_ENST00000593105.1_Frame_Shift_Del_p.K231fs|ZNF286A_ENST00000583566.1_Frame_Shift_Del_p.K241fs|ZNF286A_ENST00000395894.2_3'UTR|ZNF286A_ENST00000472486.1_3'UTR|ZNF286A_ENST00000421016.1_Frame_Shift_Del_p.K241fs|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000413242.2_Frame_Shift_Del_p.K241fs			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	241					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		TTATAAAGAGAAAAAACCTCA	0.368																																					p.E239fs		Atlas-INDEL	.											ZNF286A,NS,carcinoma,0,1	ZNF286A	58	.	0			c.717delG						.						28	28	28					17																	15619756		2199	4291	6490	SO:0001589	frameshift_variant	57335	exon6			.	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"Zinc fingers, C2H2-type", "-"	13501	protein-coding gene	gene with protein product			"zinc finger protein 286"	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.718delA	chr17.hg19:g.15619756delA	ENSP00000464218:p.Lys241fs	177.0	0.0		228.0	14.0	NM_020652	B4DKF9|Q96JF3	Frame_Shift_Del	DEL	ENST00000464847.2	hg19	CCDS11172.1																																																																																			.	.		0.368	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		-	15619756	A	-	15619756	7	5	114	1	0	1	0	1	0	0	0	0	17838	247	9	0	736	0	ZNF286A	17	15619756	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3932783	15619756	65575454	1005	19277										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18051452	18051452	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgggggctgcccgcaccttaCccccgacccagctcgagtgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:18051452delC	ENST00000205890.5	+	31	6957	c.6619delC	c.(6619-6621)cccfs	p.P2208fs	snoU13_ENST00000459354.1_RNA	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2208	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CCGCACCTTACCCCCGACCCA	0.647																																					p.L2206fs		Atlas-INDEL	.											.	MYO15A	268	.	0			c.6618delA						.						38	42	41					17																	18051452		2028	4177	6205	SO:0001589	frameshift_variant	51168	exon30			.	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.6619delC	chr17.hg19:g.18051452delC	ENSP00000205890:p.Pro2208fs	148.0	0.0		202.0	13.0	NM_016239	B4DFC7	Frame_Shift_Del	DEL	ENST00000205890.5	hg19	CCDS42271.1																																																																																			.	.		0.647	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		-	18051452	C	-	18051452	7	5	114	1	0	1	0	1	0	0	0	0	10072	507	18	0	6733	0	MYO15A	17	18051452	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2431696	18051452	63143758	1006	19278										
TOP3A	7156	hgsc.bcm.edu	37	chr17	18217965	18217965	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgatccccttggccgcgtcgTttttttcggccacacagagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:18217965delT	ENST00000321105.5	-	1	342	c.128delA	c.(127-129)aacfs	p.N43fs	SMCR8_ENST00000406438.3_5'Flank|TOP3A_ENST00000582230.1_5'UTR|TOP3A_ENST00000542570.1_5'UTR	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	43	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						GGCCGCGTCGTTTTTTTCGGC	0.652																																					p.N43fs		Atlas-INDEL	.											.	TOP3A	85	.	0			c.129delC						.						53	42	46					17																	18217965		2203	4300	6503	SO:0001589	frameshift_variant	7156	exon1			.	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 7"	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.128delA	chr17.hg19:g.18217965delT	ENSP00000321636:p.Asn43fs	151.0	0.0		216.0	15.0	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Frame_Shift_Del	DEL	ENST00000321105.5	hg19	CCDS11194.1																																																																																			.	.		0.652	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			-	18217965	T	-	18217965	7	5	114	1	0	1	0	1	0	0	0	0	16382	1725	60	0	2953	0	TOP3A	17	18217965	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	166513	18217965	62977245	1007	19279										
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319360	21319360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcgcgcagctcatcaagccgCgggtcaccgaggagggcgag	17	13	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:21319360C>T	ENST00000583088.1	+	3	1601	c.706C>T	c.(706-708)Cgg>Tgg	p.R236W	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R236W	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	236					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CATCAAGCCGCGGGTCACCGA	0.637										Prostate(3;0.18)																											p.R236W		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	.	0			c.C706T						.						94	72	80					17																	21319360		2203	4300	6503	SO:0001583	missense	100134444	exon3			AAGCCGCGGGTCA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.706C>T	chr17.hg19:g.21319360C>T	ENSP00000463778:p.Arg236Trp	190.0	1.0		236.0	23.0	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	hg19	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.407256	0.62399	.	.	ENSG00000184185	ENST00000331718	D	0.94497	-3.44	5.32	-8.56	0.00904	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.97284	0.9112	M	0.93898	3.47	0.38797	D	0.955108	D	0.89917	1.0	D	0.75484	0.986	D	0.95584	0.8649	10	0.87932	D	0	.	20.5697	0.99360	0.7808:0.2191:0.0:0.0	.	236	Q14500	IRK12_HUMAN	W	236	ENSP00000328150:R236W	ENSP00000328150:R236W	R	+	1	2	KCNJ12	21259953	0.001000	0.12720	0.203000	0.23512	0.944000	0.59088	-0.033000	0.12246	-0.938000	0.03714	-0.274000	0.10170	CGG	.	.		0.637	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		T	21319360	C	T	21319360	3	4	114	1	0	0	0	0	1	0	0	0	8055	759	27	1	708	1	KCNJ12	17	21319360	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	3101395	21319360	59875850	1008	19280										
NEK8	284086	hgsc.bcm.edu	37	chr17	27064915	27064915	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctggggtggtgggctgggcaCccccctgcggctgccaatgc					rs371295223		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:27064915delC	ENST00000268766.6	+	7	1002	c.968delC	c.(967-969)accfs	p.T323fs	AC010761.6_ENST00000584779.1_RNA	NM_178170.2	NP_835464.1	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	323					organ morphogenesis (GO:0009887)|regulation of hippo signaling (GO:0035330)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|primary cilium (GO:0072372)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Lung NSC(42;0.0158)					GGGCTGGGCACCCCCCTGCGG	0.667																																					p.T323fs	NSCLC(6;19 293 14866 25253 49845)	Atlas-INDEL	.											.	NEK8	76	.	0			c.967delA						.						43	49	47					17																	27064915		2203	4298	6501	SO:0001589	frameshift_variant	284086	exon7			.	AY267371	CCDS32597.1	17q11.1	2012-11-15	2012-11-15			ENSG00000160602			13387	protein-coding gene	gene with protein product		609799	"NIMA (never in mitosis gene a)- related kinase 8"			18199800	Standard	NM_178170		Approved	NPHP9	uc002hcp.3	Q86SG6		ENST00000268766.6:c.968delC	chr17.hg19:g.27064915delC	ENSP00000268766:p.Thr323fs	80.0	0.0		116.0	10.0	NM_178170	A6NIC5|Q14CL7|Q2M1S6|Q8NDH1	Frame_Shift_Del	DEL	ENST00000268766.6	hg19	CCDS32597.1																																																																																			.	.		0.667	NEK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446467.2			-	27064915	C	-	27064915	7	5	114	1	0	1	0	1	0	0	0	0	10339	507	18	0	994	0	NEK8	17	27064915	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	5745555	27064915	54130295	1009	19281										
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28407894	28407894	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggttcattcctggctctgccTcttcaagatgcatatatgag	9	10	4	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:28407894T>C	ENST00000394835.3	+	17	3513	c.3321T>C	c.(3319-3321)ccT>ccC	p.P1107P	EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000320856.5_Silent_p.P983P	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1107							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TGGCTCTGCCTCTTCAAGATG	0.433																																					p.P1107P		Atlas-SNP	.											.	EFCAB5	122	.	0			c.T3321C						.						96	93	94					17																	28407894		1883	4112	5995	SO:0001819	synonymous_variant	374786	exon17			TCTGCCTCTTCAA	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.3321T>C	chr17.hg19:g.28407894T>C		101.0	0.0		144.0	6.0	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	hg19	CCDS11254.2																																																																																			.	.		0.433	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		C	28407894	T	C	28407894	2	2	114	1	0	0	0	0	0	0	0	1	4940	1538	54	2		2	EFCAB5	17	28407894	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1342979	28407894	52787316	1010	19282										
GOSR1	9527	hgsc.bcm.edu	37	chr17	28849276	28849276	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taaagatttcccaaagatcgTtttcctgctgtaaacagcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:28849276delT	ENST00000225724.5	+	9	705	c.633delT	c.(631-633)cgtfs	p.R211fs	GOSR1_ENST00000581721.1_Frame_Shift_Del_p.R197fs|GOSR1_ENST00000451249.2_Frame_Shift_Del_p.R209fs|GOSR1_ENST00000467337.2_Frame_Shift_Del_p.R146fs	NM_001007024.1|NM_001007025.1|NM_004871.2	NP_001007025.1|NP_001007026.1|NP_004862.1	O95249	GOSR1_HUMAN	golgi SNAP receptor complex member 1	211					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			endometrium(2)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	12						CCAAAGATCGTTTTCCTGCTG	0.463																																					p.R211fs		Atlas-INDEL	.											.	GOSR1	25	.	0			c.632delG						.						281	311	300					17																	28849276		2203	4300	6503	SO:0001589	frameshift_variant	9527	exon9			.	AF047438	CCDS11258.1, CCDS45643.1, CCDS45644.1	17q11	2011-04-15			ENSG00000108587	ENSG00000108587			4430	protein-coding gene	gene with protein product	"golgi integral membrane protein 2"	604026				8638159, 9653160, 15004235	Standard	XM_005258072		Approved	GOS28, P28, GS28, GOS-28, GOLIM2	uc002hfe.3	O95249	OTTHUMG00000132796	ENST00000225724.5:c.633delT	chr17.hg19:g.28849276delT	ENSP00000225724:p.Arg211fs	147.0	0.0		177.0	12.0	NM_004871	J3KST5|O75392	Frame_Shift_Del	DEL	ENST00000225724.5	hg19	CCDS11258.1																																																																																			.	.		0.463	GOSR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256208.2			-	28849276	T	-	28849276	7	5	114	1	0	1	0	1	0	0	0	0	6585	1712	60	0	667	0	GOSR1	17	28849276	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	441382	28849276	52345934	1011	19283										
MYO1D	4642	hgsc.bcm.edu	37	chr17	30965824	30965824	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cggtcagtgacaaaaattgcTctgtcttccaccttactaaa	6	11	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:30965824T>C	ENST00000318217.5	-	20	2929	c.2625A>G	c.(2623-2625)agA>agG	p.R875R	RP11-220C2.1_ENST00000582272.1_RNA|MYO1D_ENST00000579584.1_Silent_p.R875R|MYO1D_ENST00000394649.4_Silent_p.R787R	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	875	Myosin tail. {ECO:0000255}.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			CAAAAATTGCTCTGTCTTCCA	0.383																																					p.R875R		Atlas-SNP	.											.	MYO1D	93	.	0			c.A2625G						.						180	167	171					17																	30965824		2203	4300	6503	SO:0001819	synonymous_variant	4642	exon20			AATTGCTCTGTCT	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"Myosins / Myosin superfamily : Class I"	7598	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 108"	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.2625A>G	chr17.hg19:g.30965824T>C		164.0	0.0		184.0	8.0	NM_015194	A6H8V3|Q8NHP9	Silent	SNP	ENST00000318217.5	hg19	CCDS32615.1																																																																																			.	.		0.383	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			C	30965824	T	C	30965824	2	2	114	1	0	0	0	0	0	0	0	1	10080	1548	54	2		2	MYO1D	17	30965824	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2116548	30965824	50229386	1012	19284										
LIG3	3980	hgsc.bcm.edu	37	chr17	33323630	33323630	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgctaatgtctgcctgtttgTttttgattgtatctacttta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:33323630delT	ENST00000378526.4	+	11	1914	c.1781delT	c.(1780-1782)gttfs	p.V594fs	LIG3_ENST00000262327.5_Frame_Shift_Del_p.V594fs	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	594					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	TGCCTGTTTGTTTTTGATTGT	0.403								Other BER factors																													p.V594fs		Atlas-INDEL	.											.	LIG3	164	.	0			c.1780delG						.						232	197	209					17																	33323630		2203	4300	6503	SO:0001589	frameshift_variant	3980	exon11			.		CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"ligase II, DNA, ATP-dependent"	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.1781delT	chr17.hg19:g.33323630delT	ENSP00000367787:p.Val594fs	127.0	0.0		167.0	11.0	NM_013975	Q16714|Q6NVK3	Frame_Shift_Del	DEL	ENST00000378526.4	hg19	CCDS11284.2																																																																																			.	.		0.403	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975		-	33323630	T	-	33323630	7	5	114	1	0	1	0	1	0	0	0	0	8791	1725	60	0	1819	0	LIG3	17	33323630	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2357806	33323630	47871580	1013	19285										
RAD51L3	5892	hgsc.bcm.edu	37	chr17	33434027	33434027	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgttcctcctcatcctgggTtttagcctgaagcagctgga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:33434027delT	ENST00000345365.6	-	5	715	c.460delA	c.(460-462)accfs	p.T154fs	RAD51D_ENST00000460118.2_Frame_Shift_Del_p.T35fs|RAD51D_ENST00000590380.1_5'UTR|RAD51L3-RFFL_ENST00000593039.1_Intron|RAD51D_ENST00000335858.7_Intron|RAD51D_ENST00000394589.4_Frame_Shift_Del_p.T154fs|RAD51D_ENST00000360276.3_Intron|RAD51D_ENST00000590016.1_Frame_Shift_Del_p.T174fs	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D	154					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|reciprocal meiotic recombination (GO:0007131)|strand invasion (GO:0042148)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|gamma-tubulin binding (GO:0043015)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						TCATCCTGGGTTTTAGCCTGA	0.507								Direct reversal of damage																													p.T174fs		Atlas-INDEL	.											.	RAD51D	53	.	0			c.521delC						.						103	89	94					17																	33434027		2203	4300	6503	SO:0001589	frameshift_variant	5892	exon5			.	AF034956	CCDS11287.1, CCDS11288.1, CCDS45646.1	17q11	2014-09-17	2013-07-02	2011-07-01	ENSG00000185379	ENSG00000185379			9823	protein-coding gene	gene with protein product	"recombination repair protein", "DNA repair protein RAD51 homolog 4"	602954	"RAD51 (S. cerevisiae)-like 3", "RAD51-like 3 (S. cerevisiae)", "RAD51 homolog D (S. cerevisiae)"	RAD51L3		9570954	Standard	NM_001142571		Approved	R51H3, Trad, HsTRAD	uc010ctj.2	O75771	OTTHUMG00000132930	ENST00000345365.6:c.460delA	chr17.hg19:g.33434027delT	ENSP00000338790:p.Thr154fs	103.0	0.0		122.0	10.0	NM_001142571	B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Frame_Shift_Del	DEL	ENST00000345365.6	hg19	CCDS11287.1																																																																																			.	.		0.507	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878		-	33434027	T	-	33434027	7	5	114	1	0	1	0	1	0	0	0	0	13005	1725	60	0	550	0	RAD51L3	17	33434027	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	110397	33434027	47761183	1014	19286										
SLFN12L	100506736	hgsc.bcm.edu	37	chr17	33806378	33806378	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggcagtttcccaatggaaTtttttgttacttcttctaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:33806378delT	ENST00000260908.7	-	2	968	c.851delA	c.(850-852)aatfs	p.N284fs	SLFN12L_ENST00000449046.1_Frame_Shift_Del_p.N315fs|SLFN12L_ENST00000361112.4_Frame_Shift_Del_p.N313fs|RP11-686D22.9_ENST00000587076.1_RNA	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	284						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						CCCAATGGAATTTTTTGTTAC	0.353																																					p.N284fs		Atlas-INDEL	.											.	SLFN12L	140	.	0			c.852delT						.						126	104	110					17																	33806378		692	1591	2283	SO:0001589	frameshift_variant	100506736	exon2			.	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.851delA	chr17.hg19:g.33806378delT	ENSP00000437635:p.Asn284fs	121.0	0.0		189.0	12.0	NM_001195790	F5H6G3	Frame_Shift_Del	DEL	ENST00000260908.7	hg19	CCDS56026.1																																																																																			.	.		0.353	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206		-	33806378	T	-	33806378	7	5	114	1	0	1	0	1	0	0	0	0	14750	1493	52	0	927	0	SLFN12L	17	33806378	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	372351	33806378	47388832	1015	19287										
HNF1B	6928	hgsc.bcm.edu	37	chr17	36104535	36104535	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctcgctctgcgcctacctgAgcatccggtccacctccgcc	8	21	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:36104535A>G	ENST00000225893.4	-	1	702	c.341T>C	c.(340-342)cTc>cCc	p.L114P	HNF1B_ENST00000561193.1_Missense_Mutation_p.L114P|HNF1B_ENST00000560016.1_Missense_Mutation_p.L114P|RP11-115K3.1_ENST00000558143.1_RNA|HNF1B_ENST00000427275.2_Missense_Mutation_p.L114P	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	114					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			CGCCTACCTGAGCATCCGGTC	0.706																																					p.L114P	Colon(71;102 1179 9001 27917 43397)	Atlas-SNP	.											.	HNF1B	61	.	0			c.T341C						.						35	39	38					17																	36104535		2203	4298	6501	SO:0001583	missense	6928	exon1			TACCTGAGCATCC	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"Homeoboxes / HNF class"	11630	protein-coding gene	gene with protein product		189907	"transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.341T>C	chr17.hg19:g.36104535A>G	ENSP00000225893:p.Leu114Pro	47.0	0.0		61.0	4.0	NM_001165923	B4DKM3|E0YMJ9	Missense_Mutation	SNP	ENST00000225893.4	hg19	CCDS11324.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.181257	0.57800	.	.	ENSG00000108753	ENST00000225893;ENST00000427275;ENST00000544593;ENST00000539087	D;D	0.99474	-5.97;-5.97	5.24	5.24	0.73138	Hepatocyte nuclear factor 1, N-terminal (1);Lambda repressor-like, DNA-binding (2);	0.199993	0.44483	D	0.000453	D	0.99039	0.9671	M	0.78049	2.395	0.80722	D	1	B;B	0.21381	0.055;0.001	B;B	0.36989	0.238;0.014	D	0.99529	1.0960	10	0.87932	D	0	.	14.4703	0.67512	1.0:0.0:0.0:0.0	.	114;114	E0YMJ6;P35680	.;HNF1B_HUMAN	P	114;114;114;2	ENSP00000225893:L114P;ENSP00000412212:L114P	ENSP00000225893:L114P	L	-	2	0	HNF1B	33178648	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.816000	0.91979	2.203000	0.70933	0.459000	0.35465	CTC	.	.		0.706	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458		G	36104535	A	G	36104535	3	3	114	1	0	0	0	0	1	0	0	0	7261	304	11	2	1368	2	HNF1B	17	36104535	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2298157	36104535	45090675	1016	19288										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37868282	37868282	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacagcggtgtgagaagtgcAgcaagccctgtgcccgaggt	15	11	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:37868282A>G	ENST00000269571.5	+	8	1162	c.1003A>G	c.(1003-1005)Agc>Ggc	p.S335G	ERBB2_ENST00000541774.1_Missense_Mutation_p.S320G|ERBB2_ENST00000578199.1_Missense_Mutation_p.S305G|ERBB2_ENST00000584450.1_Missense_Mutation_p.S335G|ERBB2_ENST00000445658.2_Missense_Mutation_p.S59G|ERBB2_ENST00000584601.1_Missense_Mutation_p.S305G|ERBB2_ENST00000406381.2_Missense_Mutation_p.S305G|ERBB2_ENST00000540147.1_Missense_Mutation_p.S305G|ERBB2_ENST00000540042.1_Missense_Mutation_p.S305G			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	335					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	TGAGAAGTGCAGCAAGCCCTG	0.627		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.S335G		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	.	ERBB2	429	.	0			c.A1003G						.						131	101	111					17																	37868282		2203	4300	6503	SO:0001583	missense	2064	exon8			AAGTGCAGCAAGC	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1003A>G	chr17.hg19:g.37868282A>G	ENSP00000269571:p.Ser335Gly	92.0	0.0		89.0	4.0	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	hg19	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	A	13.26	2.183264	0.38511	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147;ENST00000540042	T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	5.83	5.83	0.93111	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	.	.	.	.	T	0.44808	0.1311	L	0.31526	0.94	0.33907	D	0.639189	B;P;P;P;B	0.38729	0.37;0.644;0.644;0.559;0.089	B;B;B;B;B	0.34652	0.055;0.098;0.09;0.187;0.021	T	0.54556	-0.8276	9	0.14252	T	0.57	.	9.6526	0.39906	0.9214:0.0:0.0786:0.0	.	59;305;320;335;335	B4DTR1;F5H1T4;P04626-4;P04626;Q9UK79	.;.;.;ERBB2_HUMAN;.	G	305;320;59;335;305;305	ENSP00000385185:S305G;ENSP00000446466:S320G;ENSP00000404047:S59G;ENSP00000269571:S335G;ENSP00000443562:S305G;ENSP00000446382:S305G	ENSP00000269571:S335G	S	+	1	0	ERBB2	35121808	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.657000	0.54474	2.232000	0.73038	0.402000	0.26972	AGC	.	.		0.627	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			G	37868282	A	G	37868282	3	3	114	1	0	0	0	0	1	0	0	0	5208	188	7	2	1033	2	ERBB2	17	37868282	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1763747	37868282	43326928	1017	19289										
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40635054	40635054	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttcgatgttcttatattccAggttccgagcctcactctat	6	12	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:40635054A>G	ENST00000343619.4	+	9	839		c.e9-1		ATP6V0A1_ENST00000264649.6_Splice_Site|ATP6V0A1_ENST00000585525.1_Splice_Site|ATP6V0A1_ENST00000546249.1_Splice_Site|ATP6V0A1_ENST00000537728.1_Splice_Site|ATP6V0A1_ENST00000544137.1_Intron|ATP6V0A1_ENST00000393829.2_Splice_Site	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1						ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		CTTATATTCCAGGTTCCGAGC	0.408																																					.		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.717-2A>G						.						69	68	68					17																	40635054		2203	4300	6503	SO:0001630	splice_region_variant	535	exon9			TATTCCAGGTTCC	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"ATPases / V-type"	865	protein-coding gene	gene with protein product		192130	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 1", "ATPase, H+ transporting, lysosomal V0 subunit A1"	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.717-1A>G	chr17.hg19:g.40635054A>G		67.0	0.0		80.0	4.0	NM_001130021	B7Z3B7|Q8N5G7|Q9NSX0	Splice_Site	SNP	ENST00000343619.4	hg19	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.465243	0.84425	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0812	0.81005	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP6V0A1	37888580	1.000000	0.71417	0.993000	0.49108	0.865000	0.49528	9.339000	0.96797	2.196000	0.70406	0.460000	0.39030	.	.	.		0.408	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020	Intron	G	40635054	A	G	40635054	5	3	114	1	0	0	0	0	0	0	1	0	1168	202	7	2	766	2	ATP6V0A1	17	40635054	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2766772	40635054	40560156	1018	19290										
ADAM11	4185	hgsc.bcm.edu	37	chr17	42854589	42854589	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtggaggggacggagcgtggGagctgtgggcgcaagggatc	23	6	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:42854589G>C	ENST00000200557.6	+	21	1906	c.1737G>C	c.(1735-1737)ggG>ggC	p.G579G	ADAM11_ENST00000535346.1_Silent_p.G379G	NM_002390.4	NP_002381.2	O75078	ADA11_HUMAN	ADAM metallopeptidase domain 11	579	Cys-rich.				integrin-mediated signaling pathway (GO:0007229)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Prostate(33;0.0959)				CGGAGCGTGGGAGCTGTGGGC	0.627																																					p.G579G		Atlas-SNP	.											.	ADAM11	118	.	0			c.G1737C						.						54	54	54					17																	42854589		2203	4300	6503	SO:0001819	synonymous_variant	4185	exon21			GCGTGGGAGCTGT	D17390	CCDS11486.1	17q21.3	2014-08-12	2005-08-18		ENSG00000073670			"ADAM metallopeptidase domain containing"	189	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, cysteine-rich protein"	155120	"a disintegrin and metalloproteinase domain 11"	MDC		8252040	Standard	XM_005257373		Approved		uc002ihh.3	O75078	OTTHUMG00000179038	ENST00000200557.6:c.1737G>C	chr17.hg19:g.42854589G>C		68.0	0.0		69.0	19.0	NM_002390	Q14808|Q14809|Q14810	Silent	SNP	ENST00000200557.6	hg19	CCDS11486.1																																																																																			.	.		0.627	ADAM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444531.1	NM_002390		C	42854589	G	C	42854589	2	2	114	1	0	0	0	0	0	0	0	1	235	1161	41	4		4	ADAM11	17	42854589	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	2219535	42854589	38340621	1019	19291										
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44109416	44109416	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aaggctgcgtcccttacctgTtcatccagccccagctctgg	9	16	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:44109416T>C	ENST00000262419.6	-	14	3557	c.3087A>G	c.(3085-3087)gaA>gaG	p.E1029E	KANSL1_ENST00000432791.1_Silent_p.E1029E|KANSL1_ENST00000393476.3_Silent_p.E323E|KANSL1_ENST00000574590.1_Silent_p.E1029E|KANSL1_ENST00000572904.1_Silent_p.E1029E|KANSL1_ENST00000575318.1_Silent_p.E965E	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	1029	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CCCTTACCTGTTCATCCAGCC	0.617																																					p.E1029E		Atlas-SNP	.											.	.	.	.	0			c.A3087G						.						56	49	52					17																	44109416		2203	4300	6503	SO:0001819	synonymous_variant	284058	exon14			TACCTGTTCATCC	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"centromere protein 36"	612452	"KIAA1267"	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.3087A>G	chr17.hg19:g.44109416T>C		82.0	0.0		79.0	4.0	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	hg19	CCDS11503.1																																																																																			.	.		0.617	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		C	44109416	T	C	44109416	2	2	114	1	0	0	0	0	0	0	0	1	8228	1722	60	2		2	KIAA1267	17	44109416	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1254827	44109416	37085794	1020	19292										
SP2	6668	hgsc.bcm.edu	37	chr17	45994350	45994350	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tccagcaggtccaggtggtgCcccccaaggccgagcagcag					rs142857959		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:45994350delC	ENST00000376741.4	+	3	1050	c.913delC	c.(913-915)cccfs	p.P306fs	AC003665.1_ENST00000585280.1_RNA|AC003665.1_ENST00000451140.2_RNA|AC003665.1_ENST00000433001.1_RNA|AC003665.1_ENST00000411573.2_RNA	NM_003110.5	NP_003101.3	Q02086	SP2_HUMAN	Sp2 transcription factor	306					cardiovascular system development (GO:0072358)|embryonic organ development (GO:0048568)|fibroblast proliferation (GO:0048144)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	13						CCAGGTGGTGCCCCCCAAGGC	0.652																																					p.V304fs		Atlas-INDEL	.											.	SP2	38	.	0			c.912delG						.						43	47	46					17																	45994350		2203	4300	6503	SO:0001589	frameshift_variant	6668	exon3			.		CCDS11521.2	17q21.3-q22	2013-01-08			ENSG00000167182	ENSG00000167182		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11207	protein-coding gene	gene with protein product		601801				1341900, 9730617	Standard	NM_003110		Approved	KIAA0048	uc002imk.3	Q02086	OTTHUMG00000150196	ENST00000376741.4:c.913delC	chr17.hg19:g.45994350delC	ENSP00000365931:p.Pro306fs	124.0	0.0		166.0	10.0	NM_003110	A6NK74	Frame_Shift_Del	DEL	ENST00000376741.4	hg19	CCDS11521.2																																																																																			.	.		0.652	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110		-	45994350	C	-	45994350	7	5	114	1	0	1	0	1	0	0	0	0	14979	739	26	0	923	0	SP2	17	45994350	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1884934	45994350	35200860	1021	19293										
PHB	5245	hgsc.bcm.edu	37	chr17	47486764	47486764	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atagtcctctccgatgctggTgaagatgcgaggaagctggc	14	9	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:47486764T>C	ENST00000300408.3	-	4	394	c.322A>G	c.(322-324)Acc>Gcc	p.T108A	RP11-81K2.1_ENST00000576461.1_Intron|PHB_ENST00000508009.1_5'UTR|PHB_ENST00000511832.1_Missense_Mutation_p.T108A	NM_001281496.1|NM_001281715.1|NM_002634.2	NP_001268425.1|NP_001268644.1|NP_002625.1	P35232	PHB_HUMAN	prohibitin	108					cellular response to interleukin-6 (GO:0071354)|DNA replication (GO:0006260)|histone deacetylation (GO:0016575)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone receptor signaling pathway (GO:0050847)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|transcription regulatory region DNA binding (GO:0044212)			endometrium(4)|large_intestine(2)|lung(4)	10	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)			CCGATGCTGGTGAAGATGCGA	0.537																																					p.T108A		Atlas-SNP	.											.	PHB	25	.	0			c.A322G						.						89	84	85					17																	47486764		2203	4300	6503	SO:0001583	missense	5245	exon4			TGCTGGTGAAGAT		CCDS11548.1, CCDS62244.1	17q21	2010-11-25			ENSG00000167085	ENSG00000167085			8912	protein-coding gene	gene with protein product		176705				10376528, 8244394	Standard	NM_001281496		Approved	PHB1	uc002iox.1	P35232	OTTHUMG00000134271	ENST00000300408.3:c.322A>G	chr17.hg19:g.47486764T>C	ENSP00000300408:p.Thr108Ala	60.0	0.0		97.0	5.0	NM_002634	B4DY47|Q4VBQ0	Missense_Mutation	SNP	ENST00000300408.3	hg19	CCDS11548.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.225023	0.58668	.	.	ENSG00000167085	ENST00000300408;ENST00000511832;ENST00000419140;ENST00000504124;ENST00000512041;ENST00000446735;ENST00000434917	D;D;D;D;D;D;D	0.93906	-3.31;-3.31;-3.31;-3.31;-3.31;-3.31;-3.31	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	D	0.90208	0.6939	L	0.40543	1.245	0.80722	D	1	B	0.18013	0.025	B	0.23852	0.049	D	0.87407	0.2373	10	0.51188	T	0.08	.	14.2643	0.66107	0.0:0.0:0.0:1.0	.	108	P35232	PHB_HUMAN	A	108	ENSP00000300408:T108A;ENSP00000425035:T108A;ENSP00000393320:T108A;ENSP00000426433:T108A;ENSP00000422182:T108A;ENSP00000407828:T108A;ENSP00000410680:T108A	ENSP00000300408:T108A	T	-	1	0	PHB	44841763	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.966000	0.87956	1.856000	0.53863	0.379000	0.24179	ACC	.	.		0.537	PHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258826.1	NM_002634		C	47486764	T	C	47486764	3	2	114	1	0	0	0	0	1	0	0	0	11823	1696	59	2	512	2	PHB	17	47486764	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1492414	47486764	33708446	1022	19294										
PHB	5245	hgsc.bcm.edu	37	chr17	47489105	47489105	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtcaaagataattggtttcTgtacccacgggatgagaaaa	10	6	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:47489105T>C	ENST00000300408.3	-	3	257	c.185A>G	c.(184-186)cAg>cGg	p.Q62R	RP11-81K2.1_ENST00000576461.1_Intron|PHB_ENST00000508009.1_Intron|PHB_ENST00000511832.1_Missense_Mutation_p.Q62R	NM_001281496.1|NM_001281715.1|NM_002634.2	NP_001268425.1|NP_001268644.1|NP_002625.1	P35232	PHB_HUMAN	prohibitin	62					cellular response to interleukin-6 (GO:0071354)|DNA replication (GO:0006260)|histone deacetylation (GO:0016575)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone receptor signaling pathway (GO:0050847)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|transcription regulatory region DNA binding (GO:0044212)			endometrium(4)|large_intestine(2)|lung(4)	10	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)			AATTGGTTTCTGTACCCACGG	0.502																																					p.Q62R		Atlas-SNP	.											.	PHB	25	.	0			c.A185G						.						98	70	79					17																	47489105		2203	4300	6503	SO:0001583	missense	5245	exon3			GGTTTCTGTACCC		CCDS11548.1, CCDS62244.1	17q21	2010-11-25			ENSG00000167085	ENSG00000167085			8912	protein-coding gene	gene with protein product		176705				10376528, 8244394	Standard	NM_001281496		Approved	PHB1	uc002iox.1	P35232	OTTHUMG00000134271	ENST00000300408.3:c.185A>G	chr17.hg19:g.47489105T>C	ENSP00000300408:p.Gln62Arg	84.0	0.0		89.0	26.0	NM_002634	B4DY47|Q4VBQ0	Missense_Mutation	SNP	ENST00000300408.3	hg19	CCDS11548.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.378621	0.82682	.	.	ENSG00000167085	ENST00000300408;ENST00000511832;ENST00000419140;ENST00000504124;ENST00000512041;ENST00000446735;ENST00000434917	D;D;D;D;D;D;D	0.94376	-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.41	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.94938	0.8363	M	0.87547	2.89	0.80722	D	1	P	0.40909	0.732	B	0.44163	0.443	D	0.95543	0.8614	10	0.87932	D	0	.	15.3327	0.74226	0.0:0.0:0.0:1.0	.	62	P35232	PHB_HUMAN	R	62	ENSP00000300408:Q62R;ENSP00000425035:Q62R;ENSP00000393320:Q62R;ENSP00000426433:Q62R;ENSP00000422182:Q62R;ENSP00000407828:Q62R;ENSP00000410680:Q62R	ENSP00000300408:Q62R	Q	-	2	0	PHB	44844104	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.988000	0.88194	2.095000	0.63458	0.460000	0.39030	CAG	.	.		0.502	PHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258826.1	NM_002634		C	47489105	T	C	47489105	3	2	114	1	0	0	0	0	1	0	0	0	11823	1580	55	2	653	2	PHB	17	47489105	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2341	47489105	33706105	1023	19295										
XYLT2	64132	hgsc.bcm.edu	37	chr17	48435819	48435819	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggccctggactgttcgactCcttcagttctgggaaccgct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:48435819delC	ENST00000017003.2	+	10	2242	c.2193delC	c.(2191-2193)ctcfs	p.L732fs	XYLT2_ENST00000507602.1_Intron	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	732					chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					CTGTTCGACTCCTTCAGTTCT	0.572																																					p.L731fs		Atlas-INDEL	.											.	XYLT2	51	.	0			c.2192delT						.						47	47	47					17																	48435819		2203	4300	6503	SO:0001589	frameshift_variant	64132	exon10			.	AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"protein xylosyltransferase 2"	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.2193delC	chr17.hg19:g.48435819delC	ENSP00000017003:p.Leu732fs	139.0	0.0		151.0	10.0	NM_022167	Q6UY41|Q86V00	Frame_Shift_Del	DEL	ENST00000017003.2	hg19	CCDS11563.1																																																																																			.	.		0.572	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167		-	48435819	C	-	48435819	7	5	114	1	0	1	0	1	0	0	0	0	17479	842	30	0	2231	0	XYLT2	17	48435819	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	946714	48435819	32759391	1024	19296										
ACSF2	80221	hgsc.bcm.edu	37	chr17	48541615	48541615	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccctgcacctccagagttgaTccgagccatcatcaacaaga	7	15	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:48541615T>C	ENST00000300441.4	+	10	1279	c.1175T>C	c.(1174-1176)aTc>aCc	p.I392T	ACSF2_ENST00000427954.2_Missense_Mutation_p.I417T|ACSF2_ENST00000541920.1_Missense_Mutation_p.I232T|ACSF2_ENST00000502667.1_Missense_Mutation_p.I379T|ACSF2_ENST00000504392.1_Missense_Mutation_p.I349T	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	392					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CCAGAGTTGATCCGAGCCATC	0.577																																					p.I392T		Atlas-SNP	.											.	ACSF2	46	.	0			c.T1175C						.						138	126	130					17																	48541615		2203	4300	6503	SO:0001583	missense	80221	exon10			AGTTGATCCGAGC	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1175T>C	chr17.hg19:g.48541615T>C	ENSP00000300441:p.Ile392Thr	93.0	0.0		131.0	6.0	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	T	19.93	3.917982	0.73098	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.34	4.34	0.51931	AMP-dependent synthetase/ligase (1);	0.396338	0.26359	N	0.024827	T	0.50154	0.1599	M	0.64676	1.99	0.49130	D	0.99975	P;P;P;P	0.37688	0.605;0.605;0.605;0.605	P;B;P;P	0.45712	0.491;0.388;0.491;0.491	T	0.57093	-0.7870	10	0.87932	D	0	-15.4607	14.0101	0.64490	0.0:0.0:0.0:1.0	.	379;417;349;392	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	T	392;232;349;417;379	ENSP00000300441:I392T;ENSP00000437987:I232T;ENSP00000425964:I349T;ENSP00000401831:I417T;ENSP00000421884:I379T	ENSP00000300441:I392T	I	+	2	0	ACSF2	45896614	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	6.350000	0.73017	1.961000	0.56991	0.459000	0.35465	ATC	.	.		0.577	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149		C	48541615	T	C	48541615	3	2	114	1	0	0	0	0	1	0	0	0	175	1435	50	2	1213	2	ACSF2	17	48541615	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	105796	48541615	32653595	1025	19297										
MYCBPAP	84073	hgsc.bcm.edu	37	chr17	48598485	48598485	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgctaggattaccagcccagAgggacgcttcataccgctac	10	13	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:48598485A>G	ENST00000323776.5	+	8	1222	c.1060A>G	c.(1060-1062)Agg>Ggg	p.R354G	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.R317G	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			ACCAGCCCAGAGGGACGCTTC	0.557																																					p.R354G		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.A1060G						.						76	58	64					17																	48598485		2203	4300	6503	SO:0001583	missense	84073	exon8			GCCCAGAGGGACG	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.1060A>G	chr17.hg19:g.48598485A>G	ENSP00000323184:p.Arg354Gly	51.0	0.0		57.0	4.0	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	hg19	CCDS32680.2	.	.	.	.	.	.	.	.	.	.	A	12.38	1.919821	0.33908	.	.	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.42513	0.97;0.97	5.47	0.295	0.15752	.	0.663614	0.14290	N	0.328982	T	0.23054	0.0557	L	0.27053	0.805	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.09377	0.004;0.004	T	0.15723	-1.0427	10	0.46703	T	0.11	-11.5632	1.3763	0.02221	0.4384:0.2735:0.1554:0.1327	.	317;354	Q8TBZ2;B4DZQ1	MYBPP_HUMAN;.	G	354;317	ENSP00000323184:R354G;ENSP00000397209:R317G	ENSP00000323184:R354G	R	+	1	2	MYCBPAP	45953484	0.273000	0.24181	0.025000	0.17156	0.387000	0.30353	0.679000	0.25291	0.034000	0.15491	0.454000	0.30748	AGG	.	.		0.557	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133		G	48598485	A	G	48598485	3	3	114	1	0	0	0	0	1	0	0	0	10028	295	11	2	1090	2	MYCBPAP	17	48598485	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	56870	48598485	32596725	1026	19298										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48704048	48704048	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagcatggctgcctcgccctCcccaaagaaagatgtgctga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:48704048delC	ENST00000359106.5	+	38	7070	c.7070delC	c.(7069-7071)tccfs	p.S2357fs	CACNA1G_ENST00000514717.1_Frame_Shift_Del_p.S2207fs|CACNA1G_ENST00000507510.2_Frame_Shift_Del_p.S2312fs|CACNA1G_ENST00000512389.1_Frame_Shift_Del_p.S2253fs|CACNA1G_ENST00000513964.1_Frame_Shift_Del_p.S2219fs|CACNA1G_ENST00000510115.1_Frame_Shift_Del_p.S2278fs|CACNA1G_ENST00000503485.1_Frame_Shift_Del_p.S2230fs|CACNA1G_ENST00000515765.1_Frame_Shift_Del_p.S2301fs|CACNA1G_ENST00000429973.2_Frame_Shift_Del_p.S2246fs|CACNA1G_ENST00000502264.1_Frame_Shift_Del_p.S2286fs|CACNA1G_ENST00000510366.1_Frame_Shift_Del_p.S2212fs|CACNA1G_ENST00000515165.1_Frame_Shift_Del_p.S2264fs|CACNA1G_ENST00000360761.4_Frame_Shift_Del_p.S2241fs|CACNA1G_ENST00000352832.5_Frame_Shift_Del_p.S2230fs|CACNA1G_ENST00000507336.1_Frame_Shift_Del_p.S2346fs|CACNA1G_ENST00000514181.1_Frame_Shift_Del_p.S2239fs|CACNA1G_ENST00000514079.1_Frame_Shift_Del_p.S2271fs|CACNA1G_ENST00000507609.1_Frame_Shift_Del_p.S2257fs|CACNA1G_ENST00000505165.1_Frame_Shift_Del_p.S2185fs|CACNA1G_ENST00000358244.5_Frame_Shift_Del_p.S2151fs|CACNA1G_ENST00000513689.2_Frame_Shift_Del_p.S2267fs|CACNA1G_ENST00000507896.1_Frame_Shift_Del_p.S2174fs|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000442258.2_Frame_Shift_Del_p.S2223fs|CACNA1G_ENST00000354983.4_Frame_Shift_Del_p.S2323fs|CACNA1G_ENST00000515411.1_Frame_Shift_Del_p.S2294fs	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2357					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GCCTCGCCCTCCCCAAAGAAA	0.632											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S2357fs		Atlas-INDEL	.											.	CACNA1G	659	.	0			c.7069delT						.						57	63	61					17																	48704048		1984	4143	6127	SO:0001589	frameshift_variant	8913	exon38			.	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.7070delC	chr17.hg19:g.48704048delC	ENSP00000352011:p.Ser2357fs	151.0	0.0	956	156.0	12.0	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Frame_Shift_Del	DEL	ENST00000359106.5	hg19	CCDS45730.1																																																																																			.	.		0.632	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		-	48704048	C	-	48704048	7	5	114	1	0	1	0	1	0	0	0	0	2546	855	30	0	7487	0	CACNA1G	17	48704048	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	105563	48704048	32491162	1027	19299										
ANKFN1	162282	hgsc.bcm.edu	37	chr17	54428175	54428175	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atgcaaaatttacatctctgTcagtcaaaaaaacatagtgc	5	8	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:54428175T>C	ENST00000318698.2	+	4	281	c.246T>C	c.(244-246)tgT>tgC	p.C82C	ANKFN1_ENST00000566473.2_Silent_p.C82C	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	82										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						TACATCTCTGTCAGTCAAAAA	0.413																																					p.C82C		Atlas-SNP	.											.	ANKFN1	115	.	0			c.T246C						.						110	109	109					17																	54428175		2203	4300	6503	SO:0001819	synonymous_variant	162282	exon4			TCTCTGTCAGTCA	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.246T>C	chr17.hg19:g.54428175T>C		102.0	0.0		106.0	5.0	NM_153228		Silent	SNP	ENST00000318698.2	hg19	CCDS32686.1																																																																																			.	.		0.413	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		C	54428175	T	C	54428175	2	2	114	1	0	0	0	0	0	0	0	1	625	1673	58	2		2	ANKFN1	17	54428175	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	5724127	54428175	26767035	1028	19300										
DGKE	8526	hgsc.bcm.edu	37	chr17	54926133	54926133	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctatccaatacattgggttGgggtacaggttatgctggag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:54926133delG	ENST00000284061.3	+	6	1145	c.965delG	c.(964-966)tggfs	p.W322fs		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	322	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					ACATTGGGTTGGGGTACAGGT	0.413																																					p.W322fs		Atlas-INDEL	.											.	DGKE	47	.	0			c.964delT						.						137	132	133					17																	54926133		2203	4300	6503	SO:0001589	frameshift_variant	8526	exon6			.	U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"diacylglycerol kinase, epsilon (64kD)"			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.965delG	chr17.hg19:g.54926133delG	ENSP00000284061:p.Trp322fs	158.0	0.0		193.0	12.0	NM_003647	Q8TBM4|Q9UKQ3	Frame_Shift_Del	DEL	ENST00000284061.3	hg19	CCDS11590.1																																																																																			.	.		0.413	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647		-	54926133	G	-	54926133	7	5	114	1	0	1	0	1	0	0	0	0	4470	1357	47	0	983	0	DGKE	17	54926133	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	497958	54926133	26269077	1029	19301										
OR4D2	124538	hgsc.bcm.edu	37	chr17	56247313	56247313	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcttaccagggctgcatgggTcagatcttcttcttccactt	8	12	5	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:56247313T>C	ENST00000545221.1	+	1	297	c.297T>C	c.(295-297)ggT>ggC	p.G99G		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						GCTGCATGGGTCAGATCTTCT	0.527																																					p.G99G		Atlas-SNP	.											.	OR4D2	48	.	0			c.T297C						.						109	99	102					17																	56247313		2203	4300	6503	SO:0001819	synonymous_variant	124538	exon1			CATGGGTCAGATC		CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"GPCR / Class A : Olfactory receptors"	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.297T>C	chr17.hg19:g.56247313T>C		46.0	0.0		100.0	4.0	NM_001004707	Q6IFN8|Q96R75	Silent	SNP	ENST00000545221.1	hg19	CCDS32688.1																																																																																			.	.		0.527	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1			C	56247313	T	C	56247313	2	2	114	1	0	0	0	0	0	0	0	1	11065	1654	58	2		2	OR4D2	17	56247313	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1321180	56247313	24947897	1030	19302										
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56393388	56393388	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccactacattcctaccttcAaaaaagccatcctcatccat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:56393388delA	ENST00000343736.4	-	16	2257	c.2094delT	c.(2092-2094)tttfs	p.F698fs	BZRAP1_ENST00000355701.3_Frame_Shift_Del_p.F698fs|BZRAP1_ENST00000268893.6_Frame_Shift_Del_p.F638fs			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	698	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCCTACCTTCAAAAAAGCCAT	0.502																																					p.E699fs		Pindel	.											.	BZRAP1	287	.	0			c.2095delG						.						194	158	170					17																	56393388		2203	4300	6503	SO:0001589	frameshift_variant	9256	exon16			.	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.2094delT	chr17.hg19:g.56393388delA	ENSP00000345824:p.Phe698fs	202.0	0.0		232.0	11.0	NM_004758	O75111|Q8N5W3	Frame_Shift_Del	DEL	ENST00000343736.4	hg19	CCDS11605.1																																																																																			.	.		0.502	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		-	56393388	A	-	56393388	7	5	114	1	0	1	0	1	0	0	0	0	1579	127	5	0	3543	0	BZRAP1	17	56393388	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	146075	56393388	24801822	1031	19303										
INTS2	57508	hgsc.bcm.edu	37	chr17	59946495	59946495	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgagaaagcaactggatagcAaatatctgcaatacaaaatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:59946495delA	ENST00000444766.3	-	23	3243	c.3168delT	c.(3166-3168)tttfs	p.F1056fs	INTS2_ENST00000251334.6_Frame_Shift_Del_p.F1048fs	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	1056					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						ACTGGATAGCAAATATCTGCA	0.323																																					p.A1057fs		Atlas-INDEL	.											.	INTS2	89	.	0			c.3169delG						.						92	84	87					17																	59946495		1838	4080	5918	SO:0001589	frameshift_variant	57508	exon23			.	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.3168delT	chr17.hg19:g.59946495delA	ENSP00000414237:p.Phe1056fs	133.0	0.0		160.0	10.0	NM_020748	Q9ULD3	Frame_Shift_Del	DEL	ENST00000444766.3	hg19	CCDS45750.1																																																																																			.	.		0.323	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		-	59946495	A	-	59946495	7	5	114	1	0	1	0	1	0	0	0	0	7787	127	5	0	458	0	INTS2	17	59946495	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3553107	59946495	21248715	1032	19304										
MED13	9969	hgsc.bcm.edu	37	chr17	60028243	60028243	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catgctgaccagaaccagtcAggtaatggacctgctttggc	11	11	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:60028243A>G	ENST00000397786.2	-	28	6310	c.6234T>C	c.(6232-6234)ccT>ccC	p.P2078P		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	2078					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AGAACCAGTCAGGTAATGGAC	0.428																																					p.P2078P		Atlas-SNP	.											.	MED13	181	.	0			c.T6234C						.						155	141	146					17																	60028243		1943	4166	6109	SO:0001819	synonymous_variant	9969	exon28			CCAGTCAGGTAAT	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.6234T>C	chr17.hg19:g.60028243A>G		66.0	0.0		84.0	4.0	NM_005121	B2RU05|O60334	Silent	SNP	ENST00000397786.2	hg19	CCDS42366.1																																																																																			.	.		0.428	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		G	60028243	A	G	60028243	2	3	114	1	0	0	0	0	0	0	0	1	9439	175	7	2		2	MED13	17	60028243	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	81748	60028243	21166967	1033	19305										
PSMD12	5718	hgsc.bcm.edu	37	chr17	65340878	65340878	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgcatcaactccattgtggtAaaaagctttaaaagatccct					rs142928637		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:65340878delA	ENST00000356126.3	-	9	1034	c.927delT	c.(925-927)tttfs	p.F309fs	PSMD12_ENST00000357146.4_Frame_Shift_Del_p.F289fs	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	309	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					CCATTGTGGTAAAAAGCTTTA	0.323																																					p.T310fs		Atlas-INDEL	.											.	PSMD12	32	.	0			c.928delA						.						53	52	52					17																	65340878		2203	4300	6503	SO:0001589	frameshift_variant	5718	exon9			.	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.927delT	chr17.hg19:g.65340878delA	ENSP00000348442:p.Phe309fs	215.0	0.0		258.0	16.0	NM_002816	A6NP15|Q53HA2|Q6P053	Frame_Shift_Del	DEL	ENST00000356126.3	hg19	CCDS11669.1																																																																																			.	.		0.323	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		-	65340878	A	-	65340878	7	5	114	1	0	1	0	1	0	0	0	0	12707	359	13	0	455	0	PSMD12	17	65340878	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	5312635	65340878	15854332	1034	19306										
KPNA2	3838	hgsc.bcm.edu	37	chr17	66038453	66038453	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtgaacaagctgtctgggcTctaggaaacattgcaggtac	12	8	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:66038453T>C	ENST00000537025.2	+	5	1175	c.555T>C	c.(553-555)gcT>gcC	p.A185A	KPNA2_ENST00000330459.3_Silent_p.A185A			P52292	IMA1_HUMAN	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	185	NLS binding site (major). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|DNA metabolic process (GO:0006259)|NLS-bearing protein import into nucleus (GO:0006607)|regulation of DNA recombination (GO:0000018)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|kidney(2)|lung(9)|prostate(1)|urinary_tract(2)	22	all_cancers(12;1.18e-09)		BRCA - Breast invasive adenocarcinoma(8;1.03e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			CTGTCTGGGCTCTAGGAAACA	0.433																																					p.A185A		Atlas-SNP	.											.	KPNA2	55	.	0			c.T555C						.						269	273	271					17																	66038453		2203	4296	6499	SO:0001819	synonymous_variant	3838	exon5			CTGGGCTCTAGGA	U09559	CCDS32713.1	17q24.2	2013-02-14						"Importins", "Armadillo repeat containing"	6395	protein-coding gene	gene with protein product		600685		RCH1		8016130, 7754385	Standard	NM_002266		Approved	SRP1alpha, IPOA1, QIP2	uc002jgk.3	P52292		ENST00000537025.2:c.555T>C	chr17.hg19:g.66038453T>C		62.0	0.0		71.0	4.0	NM_002266	B9EJD6|Q53YE3|Q9BRU5	Silent	SNP	ENST00000537025.2	hg19	CCDS32713.1																																																																																			.	.		0.433	KPNA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448111.1	NM_002266		C	66038453	T	C	66038453	2	2	114	1	0	0	0	0	0	0	0	1	8439	1538	54	2		2	KPNA2	17	66038453	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	697575	66038453	15156757	1035	19307										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67092459	67092459	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatatcatatatatgaagaaGacaagagaagctgcataacc	8	6	1	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:67092459G>A	ENST00000284425.2	-	25	3504	c.3330C>T	c.(3328-3330)gtC>gtT	p.V1110V	ABCA6_ENST00000446604.2_5'UTR	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1110					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					ATATGAAGAAGACAAGAGAAG	0.274																																					p.V1110V		Atlas-SNP	.											.	ABCA6	210	.	0			c.C3330T						.						23	27	26					17																	67092459		2180	4237	6417	SO:0001819	synonymous_variant	23460	exon25			GAAGAAGACAAGA	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.3330C>T	chr17.hg19:g.67092459G>A		64.0	0.0		104.0	5.0	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	hg19	CCDS11683.1																																																																																			.	.		0.274	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		A	67092459	G	A	67092459	2	1	114	1	0	0	0	0	0	0	0	1	36	929	33	3		3	ABCA6	17	67092459	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1054006	67092459	14102751	1036	19308										
CDC42EP4	23580	hgsc.bcm.edu	37	chr17	71281984	71281984	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccatgatgctgaggacgtcaCccagcatggagggccccagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:71281984delC	ENST00000335793.3	-	2	1050	c.656delG	c.(655-657)ggtfs	p.G219fs	CDC42EP4_ENST00000439510.2_Frame_Shift_Del_p.G149fs|CDC42EP4_ENST00000581014.1_Intron			Q9H3Q1	BORG4_HUMAN	CDC42 effector protein (Rho GTPase binding) 4	219					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	GTP-Rho binding (GO:0017049)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(7)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)			GAGGACGTCACCCAGCATGGA	0.632																																					p.G219fs		Atlas-INDEL	.											.	CDC42EP4	19	.	0			c.657delT						.						81	72	75					17																	71281984		2203	4300	6503	SO:0001589	frameshift_variant	23580	exon2			.	AB042237	CCDS11695.1	17q24-q25	2008-07-18				ENSG00000179604			17147	protein-coding gene	gene with protein product	"Cdc42 effector protein 4", "binder of Rho GTPases 4"	605468				11035016, 10490598	Standard	NM_012121		Approved	CEP4, KAIA1777, BORG4, MGC3740, MGC17125	uc002jjo.3	Q9H3Q1		ENST00000335793.3:c.656delG	chr17.hg19:g.71281984delC	ENSP00000338258:p.Gly219fs	177.0	0.0		173.0	11.0	NM_012121	B3KUS7|O95828|Q96FT3	Frame_Shift_Del	DEL	ENST00000335793.3	hg19	CCDS11695.1																																																																																			.	.		0.632	CDC42EP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441898.1	NM_012121		-	71281984	C	-	71281984	7	5	114	1	0	1	0	1	0	0	0	0	3080	507	18	0	418	0	CDC42EP4	17	71281984	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	4189525	71281984	9913226	1037	19309										
KIF19	124602	hgsc.bcm.edu	37	chr17	72338849	72338849	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccactgtctttgcctatggCcccacaggtaaggggaatgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:72338849delC	ENST00000389916.4	+	4	450	c.312delC	c.(310-312)ggcfs	p.G104fs		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	104	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						TTGCCTATGGCCCCACAGGTA	0.587																																					p.G104fs		Atlas-INDEL	.											.	KIF19	102	.	0			c.311delG						.						137	105	116					17																	72338849		2203	4300	6503	SO:0001589	frameshift_variant	124602	exon4			.	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.312delC	chr17.hg19:g.72338849delC	ENSP00000374566:p.Gly104fs	132.0	0.0		163.0	10.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Frame_Shift_Del	DEL	ENST00000389916.4	hg19	CCDS32718.2																																																																																			.	.		0.587	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		-	72338849	C	-	72338849	7	5	114	1	0	1	0	1	0	0	0	0	8291	726	26	0	326	0	KIF19	17	72338849	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1056865	72338849	8856361	1038	19310										
KIF19	124602	hgsc.bcm.edu	37	chr17	72350520	72350520	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actacagcatgctgccagtgAggacaacctgtccagcagca	10	13	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:72350520A>G	ENST00000389916.4	+	18	2666	c.2528A>G	c.(2527-2529)gAg>gGg	p.E843G	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	843					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GCTGCCAGTGAGGACAACCTG	0.697																																					p.E843G		Atlas-SNP	.											.	KIF19	102	.	0			c.A2528G						.						11	14	13					17																	72350520		1946	4108	6054	SO:0001583	missense	124602	exon18			CCAGTGAGGACAA	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2528A>G	chr17.hg19:g.72350520A>G	ENSP00000374566:p.Glu843Gly	94.0	0.0		60.0	5.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	A	19.92	3.915684	0.73098	.	.	ENSG00000196169	ENST00000389916	T	0.74632	-0.86	5.06	5.06	0.68205	.	.	.	.	.	T	0.67239	0.2872	L	0.54323	1.7	0.37026	D	0.896437	P	0.39665	0.682	B	0.32980	0.156	T	0.72239	-0.4351	9	0.32370	T	0.25	.	14.5258	0.67887	1.0:0.0:0.0:0.0	.	843	Q2TAC6	KIF19_HUMAN	G	843	ENSP00000374566:E843G	ENSP00000374566:E843G	E	+	2	0	KIF19	69862115	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.488000	0.66869	1.915000	0.55452	0.454000	0.30748	GAG	.	.		0.697	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		G	72350520	A	G	72350520	3	3	114	1	0	0	0	0	1	0	0	0	8291	304	11	2	2598	2	KIF19	17	72350520	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	11671	72350520	8844690	1039	19311										
C17orf77	146723	hgsc.bcm.edu	37	chr17	72588775	72588775	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagaccacagtgcacaggacTcacacccagccttgctggag	10	14	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:72588775T>C	ENST00000392620.1	+	3	952	c.590T>C	c.(589-591)cTc>cCc	p.L197P	C17orf77_ENST00000328023.2_Missense_Mutation_p.L197P|CD300LD_ENST00000375352.1_5'Flank	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	197						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						TGCACAGGACTCACACCCAGC	0.602																																					p.L197P		Atlas-SNP	.											.	C17orf77	31	.	0			c.T590C						.						89	85	87					17																	72588775		2203	4300	6503	SO:0001583	missense	146723	exon3			CAGGACTCACACC		CCDS32721.1	17q25.1	2006-01-16			ENSG00000182352	ENSG00000182352			26480	protein-coding gene	gene with protein product							Standard	NM_152460		Approved	FLJ31882	uc002jla.1	Q96MU5	OTTHUMG00000067611	ENST00000392620.1:c.590T>C	chr17.hg19:g.72588775T>C	ENSP00000376396:p.Leu197Pro	103.0	0.0		124.0	6.0	NM_152460		Missense_Mutation	SNP	ENST00000392620.1	hg19	CCDS32721.1	.	.	.	.	.	.	.	.	.	.	T	3.951	-0.012295	0.07727	.	.	ENSG00000182352	ENST00000392620;ENST00000328023	T;T	0.57907	0.37;0.37	2.38	2.38	0.29361	.	.	.	.	.	T	0.47192	0.1432	N	0.08118	0	0.09310	N	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.27502	-1.0072	8	.	.	.	.	6.6738	0.23083	0.0:0.0:0.0:1.0	.	197	Q96MU5	CQ077_HUMAN	P	197	ENSP00000376396:L197P;ENSP00000329353:L197P	.	L	+	2	0	C17orf77	70100370	0.001000	0.12720	0.011000	0.14972	0.027000	0.11550	0.157000	0.16402	1.342000	0.45619	0.418000	0.28097	CTC	.	.		0.602	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460		C	72588775	T	C	72588775	3	2	114	1	0	0	0	0	1	0	0	0	1884	1551	54	2	592	2	C17orf77	17	72588775	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	238255	72588775	8606435	1040	19312										
SLC16A5	9121	hgsc.bcm.edu	37	chr17	73094135	73094135	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggctgtcttctcccacagggCccctgtgcagcatcctggtg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:73094135delC	ENST00000450736.2	+	3	617	c.202delC	c.(202-204)cccfs	p.P68fs	SLC16A5_ENST00000538213.2_Frame_Shift_Del_p.P108fs|SLC16A5_ENST00000580123.1_Frame_Shift_Del_p.P68fs|SLC16A5_ENST00000329783.4_Frame_Shift_Del_p.P68fs|SLC16A5_ENST00000585293.1_3'UTR			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	68					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	TCCCACAGGGCCCCTGTGCAG	0.652																																					p.G67fs		Atlas-INDEL	.											.	SLC16A5	80	.	0			c.201delG						.						50	50	50					17																	73094135		2203	4300	6503	SO:0001589	frameshift_variant	9121	exon4			.	U59299	CCDS11713.1	17q25.1	2013-07-18	2013-07-18		ENSG00000170190	ENSG00000170190		"Solute carriers"	10926	protein-coding gene	gene with protein product		603879	"solute carrier family 16 (monocarboxylic acid transporters), member 5", "solute carrier family 16, member 5 (monocarboxylic acid transporter 6)"			9425115	Standard	NM_004695		Approved	MCT5, MCT6	uc002jmr.4	O15375	OTTHUMG00000179277	ENST00000450736.2:c.202delC	chr17.hg19:g.73094135delC	ENSP00000390564:p.Pro68fs	147.0	0.0		225.0	15.0	NM_001271765	B4E288	Frame_Shift_Del	DEL	ENST00000450736.2	hg19	CCDS11713.1																																																																																			.	.		0.652	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695		-	73094135	C	-	73094135	7	5	114	1	0	1	0	1	0	0	0	0	14426	739	26	0	208	0	SLC16A5	17	73094135	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	505360	73094135	8101075	1041	19313										
UNK	85451	hgsc.bcm.edu	37	chr17	73808634	73808634	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcgagccatgccatgatagAaaagatcctcagcgaggagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:73808634delA	ENST00000589666.1	+	4	700	c.590delA	c.(589-591)gaafs	p.E197fs	UNK_ENST00000293218.3_Frame_Shift_Del_p.E273fs	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	197							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCCATGATAGAAAAGATCCTC	0.617																																					p.E197fs		Atlas-INDEL	.											.	UNK	87	.	0			c.589delG						.						40	46	44					17																	73808634		2054	4201	6255	SO:0001589	frameshift_variant	85451	exon4			.	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"Zinc fingers, CCCH-type domain containing"	29369	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 5", "zinc finger CCCH-type containing 5", "unkempt homolog (Drosophila)"	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.590delA	chr17.hg19:g.73808634delA	ENSP00000464893:p.Glu197fs	84.0	0.0		155.0	11.0	NM_001080419		Frame_Shift_Del	DEL	ENST00000589666.1	hg19	CCDS45778.2																																																																																			.	.		0.617	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		-	73808634	A	-	73808634	7	5	114	1	0	1	0	1	0	0	0	0	17015	246	9	0	836	0	UNK	17	73808634	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	714499	73808634	7386576	1042	19314										
EXOC7	23265	hgsc.bcm.edu	37	chr17	74099763	74099763	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcgagcggatgcctcctgtGggggaatcatcgctctgaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:74099763delG	ENST00000335146.7	-	1	64	c.11delC	c.(10-12)ccafs	p.P4fs	EXOC7_ENST00000467929.2_5'Flank|EXOC7_ENST00000405575.4_Frame_Shift_Del_p.P4fs|EXOC7_ENST00000332065.5_Frame_Shift_Del_p.P4fs|EXOC7_ENST00000607838.1_Frame_Shift_Del_p.P4fs|EXOC7_ENST00000589210.1_Frame_Shift_Del_p.P4fs|EXOC7_ENST00000406660.3_Frame_Shift_Del_p.P4fs|EXOC7_ENST00000411744.2_Frame_Shift_Del_p.P4fs			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	4					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			TGCCTCCTGTGGGGGAATCAT	0.682																																					p.P4fs		Atlas-INDEL	.											.	EXOC7	47	.	0			c.12delA						.						30	31	31					17																	74099763		2203	4300	6503	SO:0001589	frameshift_variant	23265	exon1			.	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.11delC	chr17.hg19:g.74099763delG	ENSP00000334100:p.Pro4fs	104.0	0.0		170.0	12.0	NM_001145298	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Frame_Shift_Del	DEL	ENST00000335146.7	hg19	CCDS45782.1																																																																																			.	.		0.682	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		-	74099763	G	-	74099763	7	5	114	1	0	1	0	1	0	0	0	0	5312	1348	47	0	2276	0	EXOC7	17	74099763	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	291129	74099763	7095447	1043	19315										
SPHK1	8877	hgsc.bcm.edu	37	chr17	74383312	74383312	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctggcactgctgcactcgcAcctgggcagtgagatgtttg	13	12	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:74383312A>G	ENST00000545180.1	+	8	1609	c.800A>G	c.(799-801)cAc>cGc	p.H267R	SPHK1_ENST00000590959.1_Missense_Mutation_p.H281R|SPHK1_ENST00000323374.4_Missense_Mutation_p.H353R|SPHK1_ENST00000392496.3_Missense_Mutation_p.H267R|SPHK1_ENST00000592299.1_Missense_Mutation_p.H267R			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	267					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	CTGCACTCGCACCTGGGCAGT	0.617																																					p.H353R	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.A1058G						.						62	46	51					17																	74383312		2203	4300	6503	SO:0001583	missense	8877	exon6			ACTCGCACCTGGG	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.800A>G	chr17.hg19:g.74383312A>G	ENSP00000440970:p.His267Arg	62.0	0.0		132.0	6.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	hg19	CCDS45785.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.751995	0.89753	.	.	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.13196	2.61;2.61;2.61	5.08	5.08	0.68730	.	0.048515	0.85682	D	0.000000	T	0.43255	0.1239	M	0.89968	3.075	0.80722	D	1	D;D;D	0.89917	0.999;0.997;1.0	D;D;D	0.77557	0.988;0.947;0.99	T	0.49153	-0.8969	10	0.27785	T	0.31	-16.2198	14.8579	0.70355	1.0:0.0:0.0:0.0	.	353;281;267	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	R	267;353;267;266	ENSP00000440970:H267R;ENSP00000313681:H353R;ENSP00000376285:H267R	ENSP00000313681:H353R	H	+	2	0	SPHK1	71894907	1.000000	0.71417	0.968000	0.41197	0.881000	0.50899	6.951000	0.75983	1.901000	0.55032	0.460000	0.39030	CAC	.	.		0.617	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		G	74383312	A	G	74383312	3	3	114	1	0	0	0	0	1	0	0	0	15061	159	6	2	1122	2	SPHK1	17	74383312	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	283549	74383312	6811898	1044	19316										
SEC14L1	6397	hgsc.bcm.edu	37	chr17	75192380	75192380	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcgccagtggctccaggagaCccacaagggcaaagtgagtg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:75192380delC	ENST00000413679.2	+	8	1109	c.806delC	c.(805-807)accfs	p.T269fs	SEC14L1_ENST00000443798.4_Frame_Shift_Del_p.T269fs|SEC14L1_ENST00000436233.4_Frame_Shift_Del_p.T269fs|SEC14L1_ENST00000585618.1_Frame_Shift_Del_p.T269fs|SEC14L1_ENST00000431431.2_Frame_Shift_Del_p.T235fs|SEC14L1_ENST00000430767.4_Frame_Shift_Del_p.T269fs|SEC14L1_ENST00000392476.2_Frame_Shift_Del_p.T269fs|SEC14L1_ENST00000591437.1_Frame_Shift_Del_p.T235fs	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	269					transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						CTCCAGGAGACCCACAAGGGC	0.522																																					p.T269fs		Atlas-INDEL	.											.	SEC14L1	81	.	0			c.805delA						.						56	52	53					17																	75192380		2203	4300	6503	SO:0001589	frameshift_variant	6397	exon10			.	D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"SEC14 (S. cerevisiae)-like 1"	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.806delC	chr17.hg19:g.75192380delC	ENSP00000394716:p.Thr269fs	101.0	0.0		179.0	11.0	NM_001204408	A8K4E8|B4DDI5|D5G3K1|Q99780	Frame_Shift_Del	DEL	ENST00000413679.2	hg19	CCDS11752.1																																																																																			.	.		0.522	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003		-	75192380	C	-	75192380	7	5	114	1	0	1	0	1	0	0	0	0	13996	507	18	0	828	0	SEC14L1	17	75192380	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	809068	75192380	6002830	1045	19317										
TK1	7083	hgsc.bcm.edu	37	chr17	76170874	76170874	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcattgcagaatctgctgtGgggcaaagagcttcctggca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:76170874delG	ENST00000301634.7	-	7	909	c.671delC	c.(670-672)ccafs	p.P224fs	TK1_ENST00000588734.1_Frame_Shift_Del_p.P257fs|TK1_ENST00000405273.1_Frame_Shift_Del_p.P224fs|TK1_ENST00000590862.1_Intron	NM_003258.4	NP_003249.3	P04183	KITH_HUMAN	thymidine kinase 1, soluble	224					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|digestive tract development (GO:0048565)|DNA replication (GO:0006260)|fetal process involved in parturition (GO:0060138)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to copper ion (GO:0046688)|response to cortisol (GO:0051414)|response to nutrient levels (GO:0031667)|response to toxic substance (GO:0009636)|skeletal muscle cell proliferation (GO:0014856)|small molecule metabolic process (GO:0044281)|thymidine metabolic process (GO:0046104)	cytosol (GO:0005829)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|nucleoside kinase activity (GO:0019206)|thymidine kinase activity (GO:0004797)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|urinary_tract(2)	4			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.0804)|Lung(188;0.23)		Trifluridine(DB00432)|Zidovudine(DB00495)	AATCTGCTGTGGGGCAAAGAG	0.652																																					p.P224fs		Atlas-INDEL	.											.	TK1	23	.	0			c.672delA						.						41	38	39					17																	76170874		2202	4300	6502	SO:0001589	frameshift_variant	7083	exon7			.		CCDS11754.1	17q23.2-q25.3	2012-10-02			ENSG00000167900	ENSG00000167900	2.7.1.21		11830	protein-coding gene	gene with protein product		188300					Standard	NM_003258		Approved		uc002juw.2	P04183	OTTHUMG00000150674	ENST00000301634.7:c.671delC	chr17.hg19:g.76170874delG	ENSP00000301634:p.Pro224fs	116.0	0.0		173.0	11.0	NM_003258	B2RC58|Q969V0|Q9UMG9	Frame_Shift_Del	DEL	ENST00000301634.7	hg19	CCDS11754.1																																																																																			.	.		0.652	TK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319577.1	NM_003258		-	76170874	G	-	76170874	7	5	114	1	0	1	0	1	0	0	0	0	15947	1348	47	0	37	0	TK1	17	76170874	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	978494	76170874	5024336	1046	19318										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76482378	76482378	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tacagctcgtacagctccctGggggagtcggggggcacggt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:76482378delG	ENST00000585328.1	-	45	7138	c.7014delC	c.(7012-7014)cccfs	p.P2338fs	DNAH17_ENST00000389840.5_Frame_Shift_Del_p.P2329fs|RP11-559N14.5_ENST00000588565.1_RNA|DNAH17_ENST00000586052.1_5'UTR|RP11-559N14.5_ENST00000585969.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2329					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			ACAGCTCCCTGGGGGAGTCGG	0.627																																					p.R2344fs		Atlas-INDEL	.											.	DNAH17	347	.	0			c.7030delA						.						46	52	50					17																	76482378		2078	4197	6275	SO:0001589	frameshift_variant	8632	exon45			.	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.7014delC	chr17.hg19:g.76482378delG	ENSP00000465516:p.Pro2338fs	84.0	0.0		181.0	11.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Frame_Shift_Del	DEL	ENST00000585328.1	hg19																																																																																				.	.		0.627	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		-	76482378	G	-	76482378	7	5	114	1	0	1	0	1	0	0	0	0	4603	1335	47	0	6507	0	DNAH17	17	76482378	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	311504	76482378	4712832	1047	19319										
RNF213	57674	hgsc.bcm.edu	37	chr17	78261894	78261894	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcaggcccaggctttgggagAggcaggagtggccacaggaa	18	9	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:78261894A>G	ENST00000582970.1	+	4	685	c.542A>G	c.(541-543)gAg>gGg	p.E181G	RNF213_ENST00000508628.2_Missense_Mutation_p.E230G|RNF213_ENST00000319921.4_Missense_Mutation_p.E181G|RNF213_ENST00000456466.1_Missense_Mutation_p.E181G	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	181					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCTTTGGGAGAGGCAGGAGTG	0.687																																					p.E181G		Atlas-SNP	.											.	RNF213	766	.	0			c.A542G						.						19	19	19					17																	78261894		2196	4294	6490	SO:0001583	missense	57674	exon4			TGGGAGAGGCAGG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.542A>G	chr17.hg19:g.78261894A>G	ENSP00000464087:p.Glu181Gly	69.0	0.0		104.0	5.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	A	8.037	0.763092	0.15914	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.46819	0.86;0.86	3.78	-6.45	0.01914	.	10.914700	0.00166	N	0.000000	T	0.22437	0.0541	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.07770	-1.0755	10	0.38643	T	0.18	3.1023	2.1781	0.03867	0.5159:0.1395:0.2038:0.1408	.	181	Q9HCF4-2	.	G	181;230;181;181	ENSP00000392123:E181G;ENSP00000324392:E181G	ENSP00000324392:E181G	E	+	2	0	RNF213	75876489	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.297000	0.08276	-1.150000	0.02840	-0.366000	0.07423	GAG	.	.		0.687	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78261894	A	G	78261894	3	3	114	1	0	0	0	0	1	0	0	0	13492	304	11	2	703	2	RNF213	17	78261894	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1779516	78261894	2933316	1048	19320										
HGS	9146	hgsc.bcm.edu	37	chr17	79660963	79660963	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgccctcggcctcctcagcgCcccccgccagcagcctgtac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:79660963delC	ENST00000329138.4	+	11	1039	c.904delC	c.(904-906)cccfs	p.P303fs		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	303	Interaction with SNX1. {ECO:0000250}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CTCCTCAGCGCCCCCCGCCAG	0.652																																					p.A301fs		Atlas-INDEL	.											.	HGS	54	.	0			c.903delG						.						31	35	34					17																	79660963		2203	4300	6503	SO:0001589	frameshift_variant	9146	exon11			.	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"Zinc fingers, FYVE domain containing"	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.904delC	chr17.hg19:g.79660963delC	ENSP00000331201:p.Pro303fs	117.0	0.0		158.0	10.0	NM_004712	Q9NR36	Frame_Shift_Del	DEL	ENST00000329138.4	hg19	CCDS11784.1																																																																																			.	.		0.652	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712		-	79660963	C	-	79660963	7	5	114	1	0	1	0	1	0	0	0	0	7096	739	26	0	946	0	HGS	17	79660963	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1399069	79660963	1534247	1049	19321										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3129514	3129514	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acacatctggagacactcctCcccctacagttgccagacaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:3129514delC	ENST00000356443.4	-	18	2843	c.2510delG	c.(2509-2511)ggafs	p.G838fs	MYOM1_ENST00000582016.1_5'UTR|MYOM1_ENST00000261606.7_Intron|MYOM1_ENST00000400569.3_Frame_Shift_Del_p.G838fs	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	838					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AGACACTCCTCCCCCTACAGT	0.547											OREG0024838	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G837fs		Atlas-INDEL	.											.	MYOM1	192	.	0			c.2511delA						.						52	54	53					18																	3129514		1998	4178	6176	SO:0001589	frameshift_variant	8736	exon18			.	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2510delG	chr18.hg19:g.3129514delC	ENSP00000348821:p.Gly838fs	182.0	0.0	608	233.0	15.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Frame_Shift_Del	DEL	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.547	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		-	3129514	C	-	3129514	7	5	114	1	0	1	0	1	0	0	0	0	10100	855	30	0	2631	0	MYOM1	18	3129514	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10		3129514	74947734	1050	19322										
PTPRM	5797	hgsc.bcm.edu	37	chr18	8085685	8085685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcagatcacctacaaagcagTcagttcctttgacccagaaa	7	12	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:8085685T>C	ENST00000332175.8	+	10	2605	c.1568T>C	c.(1567-1569)gTc>gCc	p.V523A	PTPRM_ENST00000400060.4_Missense_Mutation_p.V523A|PTPRM_ENST00000400053.4_Missense_Mutation_p.V461A|PTPRM_ENST00000444013.1_Missense_Mutation_p.V310A|PTPRM_ENST00000578571.1_3'UTR|PTPRM_ENST00000580170.1_Missense_Mutation_p.V523A	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	523	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				TACAAAGCAGTCAGTTCCTTT	0.388																																					p.V523A		Atlas-SNP	.											.	PTPRM	185	.	0			c.T1568C						.						80	78	79					18																	8085685		2203	4299	6502	SO:0001583	missense	5797	exon10			AAGCAGTCAGTTC	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.1568T>C	chr18.hg19:g.8085685T>C	ENSP00000331418:p.Val523Ala	106.0	0.0		147.0	6.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.326764	0.81690	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.87	5.87	0.94306	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.060088	0.64402	D	0.000003	T	0.56978	0.2022	L	0.42632	1.34	0.58432	D	0.999993	P;P;P	0.40875	0.731;0.507;0.507	P;B;B	0.48552	0.581;0.435;0.435	T	0.55805	-0.8083	10	0.44086	T	0.13	.	16.2806	0.82678	0.0:0.0:0.0:1.0	.	310;523;523	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	A	523;523;461;310	ENSP00000331418:V523A;ENSP00000382933:V523A;ENSP00000382927:V461A;ENSP00000387608:V310A	ENSP00000331418:V523A	V	+	2	0	PTPRM	8075685	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.991000	0.88244	2.248000	0.74166	0.533000	0.62120	GTC	.	.		0.388	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			C	8085685	T	C	8085685	3	2	114	1	0	0	0	0	1	0	0	0	12821	1667	58	2	1606	2	PTPRM	18	8085685	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4956171	8085685	69991563	1051	19323										
CEP76	79959	hgsc.bcm.edu	37	chr18	12678387	12678387	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gttcgatatgggtacagtggTttgggctgttcagcaactgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:12678387delT	ENST00000262127.2	-	10	1569	c.1344delA	c.(1342-1344)aaafs	p.K448fs	CEP76_ENST00000423709.2_Frame_Shift_Del_p.K373fs|PSMG2_ENST00000585331.2_Intron|PSMG2_ENST00000589405.1_Intron	NM_024899.2	NP_079175.2	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	448					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GGTACAGTGGTTTGGGCTGTT	0.348																																					p.P449fs		Atlas-INDEL	.											.	CEP76	45	.	0			c.1345delC						.						122	118	120					18																	12678387		2203	4300	6503	SO:0001589	frameshift_variant	79959	exon10			.	BC026307	CCDS11861.1, CCDS62390.1	18p11.21	2014-02-20	2005-12-01	2005-12-01	ENSG00000101624	ENSG00000101624			25727	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 9"	C18orf9		14654843	Standard	NM_024899		Approved	HsT1705, FLJ12542	uc002kri.4	Q8TAP6	OTTHUMG00000131701	ENST00000262127.2:c.1344delA	chr18.hg19:g.12678387delT	ENSP00000262127:p.Lys448fs	134.0	0.0		154.0	10.0	NM_024899	B0YJB2|B4DXG5|B4DZW1|Q658N5|Q9H9U7	Frame_Shift_Del	DEL	ENST00000262127.2	hg19	CCDS11861.1																																																																																			.	.		0.348	CEP76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254611.1	NM_024899		-	12678387	T	-	12678387	7	5	114	1	0	1	0	1	0	0	0	0	3263	1722	60	0	647	0	CEP76	18	12678387	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	4592702	12678387	65398861	1052	19324										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21399914	21399914	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttggatttgatccgctggcaTttcctgagtttagctggaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:21399914delT	ENST00000313654.9	+	19	2498	c.2257delT	c.(2257-2259)tttfs	p.F753fs	LAMA3_ENST00000399516.3_Frame_Shift_Del_p.F753fs	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	753					cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TCCGCTGGCATTTCCTGAGTT	0.473																																					p.A752fs		Atlas-INDEL	.											.	LAMA3	397	.	0			c.2256delA						.						119	117	118					18																	21399914		1954	4136	6090	SO:0001589	frameshift_variant	3909	exon19			.	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.2257delT	chr18.hg19:g.21399914delT	ENSP00000324532:p.Phe753fs	199.0	0.0		312.0	20.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Del	DEL	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.		0.473	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		-	21399914	T	-	21399914	7	5	114	1	0	1	0	1	0	0	0	0	8616	1493	52	0	2331	0	LAMA3	18	21399914	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	8721527	21399914	56677334	1053	19325										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21425024	21425024	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atgactaccaaatacttcacAaaaaatccatggacaagtca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:21425024delA	ENST00000313654.9	+	30	3896	c.3655delA	c.(3655-3657)aaafs	p.K1220fs	LAMA3_ENST00000399516.3_Frame_Shift_Del_p.K1220fs	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1220	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					AATACTTCACAAAAAATCCAT	0.413																																					p.H1218fs		Atlas-INDEL	.											.	LAMA3	397	.	0			c.3654delC						.						141	132	135					18																	21425024		1886	4123	6009	SO:0001589	frameshift_variant	3909	exon30			.	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3655delA	chr18.hg19:g.21425024delA	ENSP00000324532:p.Lys1220fs	126.0	0.0		166.0	10.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Del	DEL	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.		0.413	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		-	21425024	A	-	21425024	7	5	114	1	0	1	0	1	0	0	0	0	8616	131	5	0	3773	0	LAMA3	18	21425024	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	25110	21425024	56652224	1054	19326										
DSC3	1825	hgsc.bcm.edu	37	chr18	28604328	28604328	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacttaccaggtctactactTtccaaaacttcaaaattata	3	10	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:28604328T>C	ENST00000360428.4	-	6	842	c.762A>G	c.(760-762)gaA>gaG	p.E254E	DSC3_ENST00000434452.1_Silent_p.E254E	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	254	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			GTCTACTACTTTCCAAAACTT	0.358																																					p.E254E		Atlas-SNP	.											.	DSC3	225	.	0			c.A762G						.						61	66	64					18																	28604328		2203	4299	6502	SO:0001819	synonymous_variant	1825	exon6			ACTACTTTCCAAA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"Cadherins / Major cadherins"	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.762A>G	chr18.hg19:g.28604328T>C		40.0	0.0		53.0	5.0	NM_024423	A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	hg19	CCDS32810.1																																																																																			.	.		0.358	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		C	28604328	T	C	28604328	2	2	114	1	0	0	0	0	0	0	0	1	4769	1838	64	2		2	DSC3	18	28604328	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	7179304	28604328	49472920	1055	19327										
DSG3	1830	hgsc.bcm.edu	37	chr18	29054359	29054359	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgaattttctggactcctacTtttctcaggtaatttggtga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:29054359delT	ENST00000257189.4	+	15	2460	c.2377delT	c.(2377-2379)tttfs	p.F793fs		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	793					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GGACTCCTACTTTTCTCAGGT	0.373																																					p.Y792fs		Atlas-INDEL	.											.	DSG3	172	.	0			c.2376delC						.						129	135	133					18																	29054359		2203	4300	6503	SO:0001589	frameshift_variant	1830	exon15			.	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2377delT	chr18.hg19:g.29054359delT	ENSP00000257189:p.Phe793fs	134.0	0.0		142.0	10.0	NM_001944	A8K2V2	Frame_Shift_Del	DEL	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.373	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		-	29054359	T	-	29054359	7	5	114	1	0	1	0	1	0	0	0	0	4780	1609	56	0	2435	0	DSG3	18	29054359	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	450031	29054359	49022889	1056	19328										
DSG3	1830	hgsc.bcm.edu	37	chr18	29055783	29055783	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actcacttggacccaaatttAaaaaacttgcagagataagc					rs552614590		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:29055783delA	ENST00000257189.4	+	16	2643	c.2560delA	c.(2560-2562)aaafs	p.K855fs		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	855					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACCCAAATTTAAAAAACTTGC	0.488																																					p.F853fs		Atlas-INDEL	.											.	DSG3	172	.	0			c.2559delT						.						98	98	98					18																	29055783		2203	4300	6503	SO:0001589	frameshift_variant	1830	exon16			.	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2560delA	chr18.hg19:g.29055783delA	ENSP00000257189:p.Lys855fs	165.0	0.0		192.0	12.0	NM_001944	A8K2V2	Frame_Shift_Del	DEL	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.488	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		-	29055783	A	-	29055783	7	5	114	1	0	1	0	1	0	0	0	0	4780	363	13	0	2622	0	DSG3	18	29055783	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1424	29055783	49021465	1057	19329										
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29432603	29432603	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttaaagcaaaactttccctTctccctactggcaagtttgg	6	12	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:29432603T>C	ENST00000283351.4	-	23	3792	c.3457A>G	c.(3457-3459)Aag>Gag	p.K1153E	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.K1099E	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	1153					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AACTTTCCCTTCTCCCTACTG	0.313																																					p.K1153E		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.A3457G						.						163	179	173					18																	29432603		2203	4300	6503	SO:0001583	missense	22878	exon23			TTCCCTTCTCCCT	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.3457A>G	chr18.hg19:g.29432603T>C	ENSP00000283351:p.Lys1153Glu	68.0	0.0		69.0	4.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	hg19	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.175307	0.38413	.	.	ENSG00000153339	ENST00000283351	T	0.19105	2.17	5.78	5.78	0.91487	.	0.137195	0.64402	D	0.000006	T	0.18130	0.0435	L	0.40543	1.245	0.80722	D	1	B	0.22276	0.067	B	0.27380	0.079	T	0.03969	-1.0988	10	0.02654	T	1	.	16.092	0.81098	0.0:0.0:0.0:1.0	.	1153	Q9Y2L5	TPPC8_HUMAN	E	1153	ENSP00000283351:K1153E	ENSP00000283351:K1153E	K	-	1	0	TRAPPC8	27686601	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.370000	0.52372	2.202000	0.70862	0.477000	0.44152	AAG	.	.		0.313	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		C	29432603	T	C	29432603	3	2	114	1	0	0	0	0	1	0	0	0	8213	1792	62	2	878	2	KIAA1012	18	29432603	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	376820	29432603	48644645	1058	19330										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34335198	34335198	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agagtatcgcacaaccagggAaagggttttgcagcagaaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:34335198delA	ENST00000359247.4	+	21	3773	c.3773delA	c.(3772-3774)gaafs	p.E1258fs	FHOD3_ENST00000591635.1_Frame_Shift_Del_p.E471fs|FHOD3_ENST00000445677.1_Frame_Shift_Del_p.E1237fs|FHOD3_ENST00000590592.1_Frame_Shift_Del_p.E1450fs|FHOD3_ENST00000257209.4_Frame_Shift_Del_p.E1275fs|FHOD3_ENST00000592128.1_Frame_Shift_Del_p.E254fs	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1258	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				ACAACCAGGGAAAGGGTTTTG	0.443																																					p.E1275fs		Atlas-INDEL	.											.	FHOD3	210	.	0			c.3823delG						.						102	83	89					18																	34335198		2203	4300	6503	SO:0001589	frameshift_variant	80206	exon22			.	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.3773delA	chr18.hg19:g.34335198delA	ENSP00000352186:p.Glu1258fs	133.0	0.0		154.0	10.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Frame_Shift_Del	DEL	ENST00000359247.4	hg19																																																																																				.	.		0.443	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		-	34335198	A	-	34335198	7	5	114	1	0	1	0	1	0	0	0	0	5891	246	9	0	3910	0	FHOD3	18	34335198	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	4902595	34335198	43742050	1059	19331										
PIK3C3	5289	hgsc.bcm.edu	37	chr18	39593452	39593452	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtccaggctctcaaatatgAaaattttgatgatataaaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:39593452delA	ENST00000262039.4	+	11	1303	c.1217delA	c.(1216-1218)gaafs	p.E406fs	PIK3C3_ENST00000398870.3_Frame_Shift_Del_p.E343fs	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	406	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						CTCAAATATGAAAATTTTGAT	0.308										TSP Lung(28;0.18)																											p.E406fs	NSCLC(37;552 1060 2683 16430 37914)	Atlas-INDEL	.											.	PIK3C3	138	.	0			c.1216delG						.						79	86	84					18																	39593452		2203	4298	6501	SO:0001589	frameshift_variant	5289	exon11			.	Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"phosphoinositide-3-kinase, class 3"			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.1217delA	chr18.hg19:g.39593452delA	ENSP00000262039:p.Glu406fs	215.0	0.0		256.0	16.0	NM_002647	Q15134	Frame_Shift_Del	DEL	ENST00000262039.4	hg19	CCDS11920.1																																																																																			.	.		0.308	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647		-	39593452	A	-	39593452	7	5	114	1	0	1	0	1	0	0	0	0	11921	246	9	0	1259	0	PIK3C3	18	39593452	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	5258254	39593452	38483796	1060	19332										
SLC14A1	6563	hgsc.bcm.edu	37	chr18	43329808	43329808	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgttcctcatcatgaccacAaaaaattccaacatctacaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:43329808delA	ENST00000321925.4	+	10	1294	c.1062delA	c.(1060-1062)acafs	p.T354fs	RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000402943.2_Frame_Shift_Del_p.T249fs|SLC14A1_ENST00000589700.1_3'UTR|SLC14A1_ENST00000591541.1_Frame_Shift_Del_p.T58fs|SLC14A1_ENST00000502059.2_Frame_Shift_Del_p.T246fs|SLC14A1_ENST00000436407.3_Frame_Shift_Del_p.T410fs|SLC14A1_ENST00000415427.3_Frame_Shift_Del_p.T410fs|SLC14A1_ENST00000535474.1_Frame_Shift_Del_p.T222fs|SLC14A1_ENST00000586142.1_Frame_Shift_Del_p.T354fs	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	354					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						TCATGACCACAAAAAATTCCA	0.468																																					p.T410fs		Atlas-INDEL	.											.	SLC14A1	84	.	0			c.1229delC						.						145	134	138					18																	43329808		2203	4300	6503	SO:0001589	frameshift_variant	6563	exon9			.	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"Blood group antigens", "Solute carriers"	10918	protein-coding gene	gene with protein product		613868	"Kidd blood group", "solute carrier family 14 (urea transporter), member 1"	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.1062delA	chr18.hg19:g.43329808delA	ENSP00000318546:p.Thr354fs	198.0	0.0		248.0	15.0	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Frame_Shift_Del	DEL	ENST00000321925.4	hg19	CCDS11925.1																																																																																			.	.		0.468	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865		-	43329808	A	-	43329808	7	5	114	1	0	1	0	1	0	0	0	0	14411	117	5	0	1264	0	SLC14A1	18	43329808	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	3736356	43329808	34747440	1061	19333										
ATP5A1	498	hgsc.bcm.edu	37	chr18	43666170	43666170	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggtcagaaccgaactgggcAaaagcagcaacctcacgata							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:43666170delA	ENST00000398752.6	-	10	1459	c.1338delT	c.(1336-1338)tttfs	p.F446fs	ATP5A1_ENST00000590665.1_Frame_Shift_Del_p.F424fs|ATP5A1_ENST00000593152.2_Frame_Shift_Del_p.F396fs|ATP5A1_ENST00000282050.2_Frame_Shift_Del_p.F446fs	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	446					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						CGAACTGGGCAAAAGCAGCAA	0.473																																					p.A447fs		Atlas-INDEL	.											.	ATP5A1	52	.	0			c.1339delG						.						94	87	89					18																	43666170		2203	4300	6503	SO:0001589	frameshift_variant	498	exon10			.	D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.1338delT	chr18.hg19:g.43666170delA	ENSP00000381736:p.Phe446fs	141.0	0.0		209.0	13.0	NM_004046	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Frame_Shift_Del	DEL	ENST00000398752.6	hg19	CCDS11927.1																																																																																			.	.		0.473	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046		-	43666170	A	-	43666170	7	5	114	1	0	1	0	1	0	0	0	0	1147	127	5	0	335	0	ATP5A1	18	43666170	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	336362	43666170	34411078	1062	19334										
PIAS2	9063	hgsc.bcm.edu	37	chr18	44444168	44444168	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acttgttgaggtgtcaaagcAaaaataaaaaacttctcttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:44444168delA	ENST00000585916.1	-	3	542	c.543delT	c.(541-543)tttfs	p.F181fs	PIAS2_ENST00000545673.1_5'UTR|PIAS2_ENST00000324794.7_Frame_Shift_Del_p.F181fs	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	181	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						GTGTCAAAGCAAAAATAAAAA	0.313																																					p.A182fs		Atlas-INDEL	.											.	PIAS2	85	.	0			c.544delG						.						53	58	56					18																	44444168		2202	4300	6502	SO:0001589	frameshift_variant	9063	exon3			.	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"Zinc fingers, MIZ-type"	17311	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 4"	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.543delT	chr18.hg19:g.44444168delA	ENSP00000465676:p.Phe181fs	102.0	0.0		146.0	10.0	NM_173206	O75927|Q96BT5|Q96KE3	Frame_Shift_Del	DEL	ENST00000585916.1	hg19	CCDS32824.1																																																																																			.	.		0.313	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671		-	44444168	A	-	44444168	7	5	114	1	0	1	0	1	0	0	0	0	11885	127	5	0	1445	0	PIAS2	18	44444168	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	777998	44444168	33633080	1063	19335										
MBD1	4152	hgsc.bcm.edu	37	chr18	47801526	47801526	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgggctctggggactgtgaTgggggtggtggaggcagtgg	24	4	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:47801526T>C	ENST00000591416.1	-	9	1313	c.882A>G	c.(880-882)ccA>ccG	p.P294P	MBD1_ENST00000588937.1_Silent_p.P294P|MBD1_ENST00000269468.5_Silent_p.P294P|MBD1_ENST00000353909.3_Silent_p.P245P|MBD1_ENST00000591535.1_Silent_p.P294P|MBD1_ENST00000339998.6_Silent_p.P294P|MBD1_ENST00000457839.2_Silent_p.P319P|MBD1_ENST00000424334.2_Silent_p.P345P|MBD1_ENST00000349085.2_Silent_p.P294P|MBD1_ENST00000398493.1_Silent_p.P294P|MBD1_ENST00000587605.1_Silent_p.P294P|MBD1_ENST00000269471.5_Silent_p.P294P|MBD1_ENST00000585595.1_Silent_p.P319P|MBD1_ENST00000590208.1_Silent_p.P294P|MBD1_ENST00000347968.3_Silent_p.P294P|MBD1_ENST00000585672.1_Silent_p.P245P|MBD1_ENST00000398488.1_Silent_p.P294P|MBD1_ENST00000382948.5_Silent_p.P294P|MBD1_ENST00000398495.2_Silent_p.P319P|MBD1_ENST00000436910.1_Silent_p.P294P			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	294	Pro-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						GGGACTGTGATGGGGGTGGTG	0.657																																					p.P319P		Atlas-SNP	.											.	MBD1	228	.	0			c.A957G						.						36	44	41					18																	47801526		2203	4300	6503	SO:0001819	synonymous_variant	4152	exon10			CTGTGATGGGGGT	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.882A>G	chr18.hg19:g.47801526T>C		85.0	0.0		95.0	36.0	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Silent	SNP	ENST00000591416.1	hg19	CCDS11943.1																																																																																			.	.		0.657	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846		C	47801526	T	C	47801526	2	2	114	1	0	0	0	0	0	0	0	1	9351	1451	51	2		2	MBD1	18	47801526	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	3357358	47801526	30275722	1064	19336										
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56018257	56018257	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagaattcacttggatggccGaacgttttatattgatcata	8	6	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:56018257G>A	ENST00000400345.3	+	18	1971	c.1688G>A	c.(1687-1689)cGa>cAa	p.R563Q	NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000357895.5_Missense_Mutation_p.R555Q|NEDD4L_ENST00000456173.2_Missense_Mutation_p.R422Q|NEDD4L_ENST00000256830.9_Missense_Mutation_p.R459Q|NEDD4L_ENST00000256832.7_Missense_Mutation_p.R422Q|NEDD4L_ENST00000456986.1_Missense_Mutation_p.R442Q|NEDD4L_ENST00000382850.4_Missense_Mutation_p.R543Q|NEDD4L_ENST00000431212.2_Missense_Mutation_p.R442Q|NEDD4L_ENST00000356462.6_Missense_Mutation_p.R499Q|NEDD4L_ENST00000586263.1_Missense_Mutation_p.R535Q|NEDD4L_ENST00000435432.2_Missense_Mutation_p.R422Q	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	563	WW 4. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						TTGGATGGCCGAACGTTTTAT	0.423																																					p.R563Q		Atlas-SNP	.											.	NEDD4L	126	.	0			c.G1688A						.						104	92	96					18																	56018257		1859	4086	5945	SO:0001583	missense	23327	exon18			ATGGCCGAACGTT	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1688G>A	chr18.hg19:g.56018257G>A	ENSP00000383199:p.Arg563Gln	60.0	0.0		96.0	7.0	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	hg19	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	G	36	5.924514	0.97110	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	D;D;D;D;D;D;D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19;-2.19;-2.19;-2.19;-2.19;-2.19;-2.19	5.57	5.57	0.84162	WW/Rsp5/WWP (6);	0.000000	0.85682	D	0.000000	D	0.93374	0.7887	M	0.76574	2.34	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.997;0.996;0.996;0.998;0.998;1.0;0.996	D;P;P;D;D;D;P	0.72338	0.95;0.634;0.634;0.97;0.915;0.977;0.634	D	0.93251	0.6635	10	0.56958	D	0.05	.	19.5497	0.95312	0.0:0.0:1.0:0.0	.	459;535;555;422;499;563;543	Q96PU5-3;Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;.;.;NED4L_HUMAN;.	Q	563;543;499;459;422;442;555;422;422;442	ENSP00000383199:R563Q;ENSP00000372301:R543Q;ENSP00000348847:R499Q;ENSP00000256830:R459Q;ENSP00000256832:R422Q;ENSP00000411947:R442Q;ENSP00000350569:R555Q;ENSP00000393395:R422Q;ENSP00000405440:R422Q;ENSP00000389406:R442Q	ENSP00000256830:R459Q	R	+	2	0	NEDD4L	54169237	1.000000	0.71417	0.989000	0.46669	0.985000	0.73830	9.120000	0.94369	2.602000	0.87976	0.655000	0.94253	CGA	.	.		0.423	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			A	56018257	G	A	56018257	3	1	114	1	0	0	0	0	1	0	0	0	10320	1058	37	1	1786	1	NEDD4L	18	56018257	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	8216731	56018257	22058991	1065	19337										
CDH20	28316	hgsc.bcm.edu	37	chr18	59195338	59195338	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgtggaagacgtggacgagCcccctgtgtttgaacctggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:59195338delC	ENST00000262717.4	+	7	1554	c.1156delC	c.(1156-1158)cccfs	p.P387fs	CDH20_ENST00000538374.1_Frame_Shift_Del_p.P387fs|CDH20_ENST00000536675.2_Frame_Shift_Del_p.P387fs			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	387	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				CGTGGACGAGCCCCCTGTGTT	0.517																																					p.E385fs		Atlas-INDEL	.											.	CDH20	117	.	0			c.1155delG						.						158	152	154					18																	59195338		2203	4300	6503	SO:0001589	frameshift_variant	28316	exon6			.	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1156delC	chr18.hg19:g.59195338delC	ENSP00000262717:p.Pro387fs	227.0	0.0		281.0	17.0	NM_031891	Q495S3	Frame_Shift_Del	DEL	ENST00000262717.4	hg19	CCDS11977.1																																																																																			.	.		0.517	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		-	59195338	C	-	59195338	7	5	114	1	0	1	0	1	0	0	0	0	3108	739	26	0	1178	0	CDH20	18	59195338	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3177081	59195338	18881910	1066	19338										
PIGN	23556	hgsc.bcm.edu	37	chr18	59752471	59752471	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaagctatatttccagttccAaaaaatgctgtcactaagaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:59752471delA	ENST00000357637.5	-	26	2812	c.2397delT	c.(2395-2397)tttfs	p.F799fs	PIGN_ENST00000400334.3_Frame_Shift_Del_p.F799fs	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	799					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				TTCCAGTTCCAAAAAATGCTG	0.303																																					p.G800fs		Atlas-INDEL	.											.	PIGN	62	.	0			c.2398delG						.						31	28	29					18																	59752471		1717	3847	5564	SO:0001589	frameshift_variant	23556	exon26			.	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.2397delT	chr18.hg19:g.59752471delA	ENSP00000350263:p.Phe799fs	154.0	0.0		190.0	12.0	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Frame_Shift_Del	DEL	ENST00000357637.5	hg19	CCDS45879.1																																																																																			.	.		0.303	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		-	59752471	A	-	59752471	7	5	114	1	0	1	0	1	0	0	0	0	11902	127	5	0	422	0	PIGN	18	59752471	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	557133	59752471	18324777	1067	19339										
VPS4B	9525	hgsc.bcm.edu	37	chr18	61067829	61067829	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagatcagaggaagatattgAaaaaaatgttgagttgttgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:61067829delA	ENST00000238497.5	-	6	795	c.592delT	c.(592-594)tcafs	p.S198fs	VPS4B_ENST00000591383.1_5'UTR	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	198					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						GAAGATATTGAAAAAAATGTT	0.373																																					p.S198X		Atlas-INDEL	.											.	VPS4B	33	.	0			c.593delC						.						115	115	115					18																	61067829		2203	4300	6503	SO:0001589	frameshift_variant	9525	exon6			.	AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"ATPases / AAA-type"	10895	protein-coding gene	gene with protein product		609983	"suppressor of K+ transport defect 1", "vacuolar protein sorting 4B (yeast)"	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.592delT	chr18.hg19:g.61067829delA	ENSP00000238497:p.Ser198fs	151.0	0.0		150.0	10.0	NM_004869	Q69HW4|Q9GZS7	Frame_Shift_Del	DEL	ENST00000238497.5	hg19	CCDS11983.1																																																																																			.	.		0.373	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869		-	61067829	A	-	61067829	7	5	114	1	0	1	0	1	0	0	0	0	17228	246	9	0	766	0	VPS4B	18	61067829	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1315358	61067829	17009419	1068	19340										
TMX3	54495	hgsc.bcm.edu	37	chr18	66377317	66377317	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagaaccaatgcttttcatcTcaagaccaacttcattccaa	4	12	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:66377317T>C	ENST00000299608.2	-	4	522	c.206A>G	c.(205-207)gAg>gGg	p.E69G	TMX3_ENST00000562706.1_Missense_Mutation_p.E69G|TMX3_ENST00000443099.2_Missense_Mutation_p.E69G	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	69	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						GCTTTTCATCTCAAGACCAAC	0.353																																					p.E69G		Atlas-SNP	.											.	TMX3	44	.	0			c.A206G						.						110	100	103					18																	66377317		2203	4300	6503	SO:0001583	missense	54495	exon4			TTCATCTCAAGAC	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"Protein disulfide isomerases"	24718	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 13"		"thioredoxin domain containing 10"	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.206A>G	chr18.hg19:g.66377317T>C	ENSP00000299608:p.Glu69Gly	83.0	0.0		114.0	5.0	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	hg19	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.269900	0.80469	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	T;T;T	0.03860	3.78;3.78;3.78	5.57	5.57	0.84162	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.20901	0.0503	M	0.78285	2.405	0.80722	D	1	D;D;D	0.76494	0.999;0.983;0.999	D;P;D	0.75020	0.96;0.858;0.985	T	0.00593	-1.1654	10	0.38643	T	0.18	.	14.5486	0.68050	0.0:0.0:0.0:1.0	.	69;69;69	B4DIE3;Q96JJ7-2;Q96JJ7	.;.;TMX3_HUMAN	G	69	ENSP00000299608:E69G;ENSP00000444954:E69G;ENSP00000402605:E69G	ENSP00000299608:E69G	E	-	2	0	TMX3	64528297	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.193000	0.72075	2.116000	0.64780	0.460000	0.39030	GAG	.	.		0.353	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022		C	66377317	T	C	66377317	3	2	114	1	0	0	0	0	1	0	0	0	16283	1551	54	2	1210	2	TMX3	18	66377317	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	5309488	66377317	11699931	1069	19341										
RTTN	25914	hgsc.bcm.edu	37	chr18	67801730	67801730	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttctaaaaacggaaacaggcAaactgaagaccgatggcaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:67801730delA	ENST00000255674.6	-	23	3219	c.2933delT	c.(2932-2934)ttgfs	p.L978fs	RTTN_ENST00000437017.1_Frame_Shift_Del_p.L978fs|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	978					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				GGAAACAGGCAAACTGAAGAC	0.323																																					p.L978fs		Atlas-INDEL	.											.	RTTN	184	.	0			c.2934delG						.						81	74	76					18																	67801730		1827	4073	5900	SO:0001589	frameshift_variant	25914	exon23			.	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.2933delT	chr18.hg19:g.67801730delA	ENSP00000255674:p.Leu978fs	119.0	0.0		142.0	10.0	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Frame_Shift_Del	DEL	ENST00000255674.6	hg19	CCDS42443.1																																																																																			.	.		0.323	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		-	67801730	A	-	67801730	7	5	114	1	0	1	0	1	0	0	0	0	13752	131	5	0	3855	0	RTTN	18	67801730	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1424413	67801730	10275518	1070	19342										
ZNF516	9658	hgsc.bcm.edu	37	chr18	74153203	74153203	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgggtacacttgctcacctGgtgcaggttcaggggcgccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:74153203delG	ENST00000443185.2	-	3	2125	c.1808delC	c.(1807-1809)ccafs	p.P603fs	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	603					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		TTGCTCACCTGGTGCAGGTTC	0.647																																					p.P603fs		Atlas-INDEL	.											.	ZNF516	102	.	0			c.1809delA						.						8	10	9					18																	74153203		1957	4040	5997	SO:0001589	frameshift_variant	9658	exon3			.	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"Zinc fingers, C2H2-type"	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.1808delC	chr18.hg19:g.74153203delG	ENSP00000394757:p.Pro603fs	106.0	0.0		134.0	10.0	NM_014643		Frame_Shift_Del	DEL	ENST00000443185.2	hg19																																																																																				.	.		0.647	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		-	74153203	G	-	74153203	7	5	114	1	0	1	0	1	0	0	0	0	17975	1348	47	0	1704	0	ZNF516	18	74153203	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	6351473	74153203	3924045	1071	19343										
NFATC1	4772	hgsc.bcm.edu	37	chr18	77227633	77227633	+	Intron	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aacatgagcgcgtggggtgcTttttctaaagacgcagaaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:77227633delT	ENST00000427363.2	+	8	2092				NFATC1_ENST00000586434.1_Intron|NFATC1_ENST00000253506.5_Intron|NFATC1_ENST00000591814.1_Frame_Shift_Del_p.F716fs|NFATC1_ENST00000587635.1_3'UTR|NFATC1_ENST00000329101.4_Intron|NFATC1_ENST00000318065.5_Intron|NFATC1_ENST00000545796.1_Intron|NFATC1_ENST00000397790.2_Intron|NFATC1_ENST00000592223.1_Frame_Shift_Del_p.F703fs|NFATC1_ENST00000542384.1_Intron			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1						calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	CGTGGGGTGCTTTTTCTAAAG	0.537																																					p.C714fs	GBM(151;1210 2593 28719 45011)	Atlas-INDEL	.											.	NFATC1	105	.	0			c.2142delC						.						69	60	63					18																	77227633		2202	4300	6502	SO:0001627	intron_variant	4772	exon8			.	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"Nuclear factor of activated T-cells"	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.2092+51T>-	chr18.hg19:g.77227633delT		76.0	0.0		149.0	10.0	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Frame_Shift_Del	DEL	ENST00000427363.2	hg19																																																																																				.	.		0.537	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390		-	77227633	T	-	77227633	6	5	114	0	1	1	0	1	0	0	0	0	10370	1609	56	0		0	NFATC1	18	77227633	Intron	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3074430	77227633	849615	1072	19344										
GZMM	3004	hgsc.bcm.edu	37	chr19	549133	549133	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttctggaacggcagcctctCccccagcatggtctgcctgg					rs373974834		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:549133delC	ENST00000264553.3	+	4	598	c.560delC	c.(559-561)tccfs	p.S187fs		NM_001258351.1|NM_005317.3	NP_001245280.1|NP_005308	P51124	GRAM_HUMAN	granzyme M (lymphocyte met-ase 1)	187	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|large_intestine(1)|prostate(1)	3		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCAGCCTCTCCCCCAGCATG	0.706																																					p.S187fs		Atlas-INDEL	.											.	GZMM	11	.	0			c.559delT						.						12	9	10					19																	549133		2157	4212	6369	SO:0001589	frameshift_variant	3004	exon4			.		CCDS12031.1, CCDS74240.1	19p13.3	2008-07-16				ENSG00000197540			4712	protein-coding gene	gene with protein product	"lymphocyte met-ase 1"	600311				8119738	Standard	NM_005317		Approved	MET1, LMET1	uc002low.2	P51124		ENST00000264553.3:c.560delC	chr19.hg19:g.549133delC	ENSP00000264553:p.Ser187fs	137.0	0.0		154.0	10.0	NM_005317		Frame_Shift_Del	DEL	ENST00000264553.3	hg19	CCDS12031.1																																																																																			.	.		0.706	GZMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451895.2	NM_005317		-	549133	C	-	549133	7	5	114	1	0	1	0	1	0	0	0	0	6928	855	30	0	574	0	GZMM	19	549133	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10		549133	58579850	1073	19345										
GAMT	2593	hgsc.bcm.edu	37	chr19	1398959	1398959	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtacttggacttcatcagctCcccccaggaggtgaggttgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:1398959delC	ENST00000252288.2	-	5	592	c.526delG	c.(526-528)gagfs	p.E176fs	GAMT_ENST00000447102.3_Frame_Shift_Del_p.E176fs|AC005329.7_ENST00000501448.1_RNA	NM_000156.5	NP_000147.1	Q14353	GAMT_HUMAN	guanidinoacetate N-methyltransferase	176	RMT2. {ECO:0000255|PROSITE- ProRule:PRU00892}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|organ morphogenesis (GO:0009887)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	guanidinoacetate N-methyltransferase activity (GO:0030731)|methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(3)|kidney(1)|upper_aerodigestive_tract(1)	6		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Lung NSC(49;0.000195)|Breast(49;0.000231)|all_lung(49;0.000247)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Creatine(DB00148)|Guanidine(DB00536)	TTCATCAGCTCCCCCCAGGAG	0.602																																					p.E176fs	Colon(167;1531 1939 13427 28842 31956)	Atlas-INDEL	.											.	GAMT	39	.	0			c.527delA						.						82	66	71					19																	1398959		2203	4300	6503	SO:0001589	frameshift_variant	2593	exon5			.	Z49878	CCDS12064.1, CCDS45897.1	19p13.3	2008-02-05							4136	protein-coding gene	gene with protein product		601240				9570966, 8547310	Standard	NM_000156		Approved	PIG2, TP53I2	uc002lsk.4	Q14353		ENST00000252288.2:c.526delG	chr19.hg19:g.1398959delC	ENSP00000252288:p.Glu176fs	197.0	0.0		285.0	20.0	NM_138924	A8K0A0|Q53Y34|Q8WVJ1	Frame_Shift_Del	DEL	ENST00000252288.2	hg19	CCDS12064.1																																																																																			.	.		0.602	GAMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449739.1	NM_138924		-	1398959	C	-	1398959	7	5	114	1	0	1	0	1	0	0	0	0	6239	864	30	0	432	0	GAMT	19	1398959	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	849826	1398959	57730024	1074	19346										
LMNB2	84823	hgsc.bcm.edu	37	chr19	2432473	2432473	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaacttgtaggcgatctcctCcccctccaagacctgcctct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:2432473delC	ENST00000582871.1	-	9	1557	c.1471delG	c.(1471-1473)gagfs	p.E492fs	LMNB2_ENST00000325327.3_Frame_Shift_Del_p.E512fs|LMNB2_ENST00000475819.1_5'Flank	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	492	LTD.|Tail.					lamin filament (GO:0005638)|nuclear inner membrane (GO:0005637)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGATCTCCTCCCCCTCCAAG	0.632																																					p.E511fs		Atlas-INDEL	.											.	LMNB2	40	.	0			c.1532delA						.						309	228	255					19																	2432473		2203	4300	6503	SO:0001589	frameshift_variant	84823	exon9			.	M94362	CCDS12090.1, CCDS12090.2	19p13.3	2013-01-16			ENSG00000176619	ENSG00000176619		"Intermediate filaments type V, lamins"	6638	protein-coding gene	gene with protein product		150341		LMN2		1630457	Standard	NM_032737		Approved		uc002lvy.4	Q03252	OTTHUMG00000150626	ENST00000582871.1:c.1471delG	chr19.hg19:g.2432473delC	ENSP00000462730:p.Glu492fs	124.0	0.0		165.0	10.0	NM_032737	O75292|Q14734|Q96DF6	Frame_Shift_Del	DEL	ENST00000582871.1	hg19																																																																																				.	.		0.632	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737		-	2432473	C	-	2432473	7	5	114	1	0	1	0	1	0	0	0	0	8859	864	30	0	347	0	LMNB2	19	2432473	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1033514	2432473	56696510	1075	19347										
CELF5	60680	hgsc.bcm.edu	37	chr19	3290263	3290263	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aacctgtttatctaccacctCccccaggagtttggagacac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:3290263delC	ENST00000292672.2	+	11	1258	c.1221delC	c.(1219-1221)ctcfs	p.L407fs	CELF5_ENST00000541430.2_Intron	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	407	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						TCTACCACCTCCCCCAGGAGT	0.572																																					p.L407fs		Atlas-INDEL	.											.	CELF5	32	.	0			c.1220delT						.						88	77	81					19																	3290263		2203	4300	6503	SO:0001589	frameshift_variant	60680	exon11			.	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"RNA binding motif (RRM) containing"	14058	protein-coding gene	gene with protein product		612680	"Bruno (Drosophila) -like 5, RNA binding protein", "bruno-like 5, RNA binding protein (Drosophila)"	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.1221delC	chr19.hg19:g.3290263delC	ENSP00000292672:p.Leu407fs	268.0	0.0		315.0	19.0	NM_021938	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Frame_Shift_Del	DEL	ENST00000292672.2	hg19	CCDS12106.1																																																																																			.	.		0.572	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938		-	3290263	C	-	3290263	7	5	114	1	0	1	0	1	0	0	0	0	3221	842	30	0	1263	0	CELF5	19	3290263	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	857790	3290263	55838720	1076	19348										
PTPRS	5802	hgsc.bcm.edu	37	chr19	5258114	5258114	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atttgccctggtcggtttccTcactgctttcaatctgcagg	9	12	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:5258114T>C	ENST00000587303.1	-	7	719	c.620A>G	c.(619-621)gAg>gGg	p.E207G	PTPRS_ENST00000357368.4_Missense_Mutation_p.E207G|PTPRS_ENST00000588012.1_Missense_Mutation_p.E198G|PTPRS_ENST00000592099.1_Missense_Mutation_p.E198G|PTPRS_ENST00000372412.4_Missense_Mutation_p.E208G|PTPRS_ENST00000353284.2_Missense_Mutation_p.E198G|PTPRS_ENST00000348075.2_Missense_Mutation_p.E198G|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Missense_Mutation_p.E207G			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	207	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GTCGGTTTCCTCACTGCTTTC	0.597																																					p.E207G		Atlas-SNP	.											.	PTPRS	169	.	0			c.A620G						.						116	111	113					19																	5258114		2203	4300	6503	SO:0001583	missense	5802	exon8			GTTTCCTCACTGC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.620A>G	chr19.hg19:g.5258114T>C	ENSP00000467537:p.Glu207Gly	149.0	0.0		137.0	6.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	hg19	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.303899	0.81136	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37	3.75	3.75	0.43078	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	U	0.000006	T	0.72036	0.3411	L	0.35249	1.045	0.33769	D	0.622812	P;D;P;D;D;P	0.89917	0.911;1.0;0.845;0.994;1.0;0.936	B;D;B;P;D;P	0.97110	0.357;0.999;0.264;0.798;1.0;0.462	T	0.80111	-0.1519	10	0.62326	D	0.03	.	12.6585	0.56801	0.0:0.0:0.0:1.0	.	207;198;198;198;207;224	F8W800;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;PTPRS_HUMAN;.	G	224;208;207;207;207;207;198;207;198;198	ENSP00000361489:E208G;ENSP00000349932:E207G;ENSP00000262963:E207G;ENSP00000269907:E198G;ENSP00000327313:E198G	ENSP00000262963:E207G	E	-	2	0	PTPRS	5209114	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.753000	0.85153	1.589000	0.49982	0.454000	0.30748	GAG	.	.		0.597	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			C	5258114	T	C	5258114	3	2	114	1	0	0	0	0	1	0	0	0	12826	1551	54	2	5350	2	PTPRS	19	5258114	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1967851	5258114	53870869	1077	19349										
ACSBG2	81616	hgsc.bcm.edu	37	chr19	6183239	6183239	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tatgggttgagtgagagctcGggaccccacacgatatccaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:6183239delG	ENST00000586696.1	+	10	1554	c.1278delG	c.(1276-1278)tcgfs	p.S426fs	ACSBG2_ENST00000252669.5_Frame_Shift_Del_p.S426fs|ACSBG2_ENST00000588304.1_Frame_Shift_Del_p.S376fs|ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000591403.1_Frame_Shift_Del_p.S426fs|ACSBG2_ENST00000588485.1_Frame_Shift_Del_p.S239fs			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	426					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTGAGAGCTCGGGACCCCACA	0.547																																					p.S426fs		Atlas-INDEL	.											.	ACSBG2	83	.	0			c.1277delC						.						68	70	69					19																	6183239		2203	4300	6503	SO:0001589	frameshift_variant	81616	exon10			.		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1278delG	chr19.hg19:g.6183239delG	ENSP00000465589:p.Ser426fs	138.0	0.0		170.0	11.0	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Frame_Shift_Del	DEL	ENST00000586696.1	hg19	CCDS12159.1																																																																																			.	.		0.547	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		-	6183239	G	-	6183239	7	5	114	1	0	1	0	1	0	0	0	0	174	1103	39	0	1312	0	ACSBG2	19	6183239	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	925125	6183239	52945744	1078	19350										
KHSRP	8570	hgsc.bcm.edu	37	chr19	6415893	6415893	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggggtgggtactggtgaggaGggggccccccggcactgcag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:6415893delG	ENST00000398148.3	-	16	1705	c.1613delC	c.(1612-1614)cctfs	p.P539fs	MIR3940_ENST00000579148.1_RNA	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	539	Ala/Gly/Pro-rich.				gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						CTGGTGAGGAGGGGGCCCCCC	0.662																																					p.P538fs	Colon(55;593 1006 2067 9135 22980)	Atlas-INDEL	.											.	KHSRP	51	.	0			c.1614delT						.						6	8	7					19																	6415893		1850	4037	5887	SO:0001589	frameshift_variant	8570	exon16			.	U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247			6316	protein-coding gene	gene with protein product	"FUSE binding protein 2"	603445				9136930, 8940189	Standard	NM_003685		Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945		ENST00000398148.3:c.1613delC	chr19.hg19:g.6415893delG	ENSP00000381216:p.Pro539fs	154.0	0.0		193.0	12.0	NM_003685	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Frame_Shift_Del	DEL	ENST00000398148.3	hg19	CCDS45936.1																																																																																			.	.		0.662	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1			-	6415893	G	-	6415893	7	5	114	1	0	1	0	1	0	0	0	0	8160	1000	35	0	542	0	KHSRP	19	6415893	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	232654	6415893	52713090	1079	19351										
TRIP10	9322	hgsc.bcm.edu	37	chr19	6750606	6750606	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttcgaggaggaacccacatCccccataggtcactgtgtgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:6750606delC	ENST00000313244.9	+	14	1654	c.1619delC	c.(1618-1620)tccfs	p.S540fs	CTD-3128G10.6_ENST00000594056.1_RNA|TRIP10_ENST00000600428.1_Frame_Shift_Del_p.S376fs|TRIP10_ENST00000596758.1_Frame_Shift_Del_p.S484fs|TRIP10_ENST00000313285.8_Frame_Shift_Del_p.S484fs			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	540	Interaction with DNM1 and WASL.|Interaction with DNM2 and WASL. {ECO:0000250}.|Interaction with PDE6G. {ECO:0000250}.|Required for interaction with FASLG and localization to lysosomes.|Required for podosome formation.|SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						GAACCCACATCCCCCATAGGT	0.547																																					p.S484fs		Atlas-INDEL	.											.	TRIP10	104	.	0			c.1450delT						.																																			SO:0001589	frameshift_variant	9322	exon13			.	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"Cdc42-interacting protein"	604504	"salt tolerator"	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.1619delC	chr19.hg19:g.6750606delC	ENSP00000320117:p.Ser540fs	189.0	0.0		216.0	15.0	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Frame_Shift_Del	DEL	ENST00000313244.9	hg19																																																																																				.	.		0.547	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2			-	6750606	C	-	6750606	7	5	114	1	0	1	0	1	0	0	0	0	16569	855	30	0	1501	0	TRIP10	19	6750606	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	334713	6750606	52378377	1080	19352										
TRIP10	9322	hgsc.bcm.edu	37	chr19	6751209	6751209	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcccacctcctacctccgagTcacgctcaattgaaccctgc	6	19	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:6751209T>C	ENST00000313244.9	+	15	1828	c.1793T>C	c.(1792-1794)gTc>gCc	p.V598A	CTD-3128G10.6_ENST00000594056.1_RNA|TRIP10_ENST00000600428.1_Missense_Mutation_p.V434A|TRIP10_ENST00000596758.1_Missense_Mutation_p.S552P|TRIP10_ENST00000313285.8_Missense_Mutation_p.V542A			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	598	Interaction with ARHGAP17, DAAM1, DIAPH1 and DIAPH2.|Interaction with DNM1 and WASL.|Interaction with PDE6G. {ECO:0000250}.|Interaction with WAS.|Required for interaction with FASLG and localization to lysosomes.|Required for podosome formation.|SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						TACCTCCGAGTCACGCTCAAT	0.612																																					p.V542A		Atlas-SNP	.											.	TRIP10	104	.	0			c.T1625C						.						60	67	65					19																	6751209		2203	4300	6503	SO:0001583	missense	9322	exon14			TCCGAGTCACGCT	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"Cdc42-interacting protein"	604504	"salt tolerator"	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.1793T>C	chr19.hg19:g.6751209T>C	ENSP00000320117:p.Val598Ala	110.0	0.0		134.0	6.0	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Missense_Mutation	SNP	ENST00000313244.9	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.82|17.82	3.484267|3.484267	0.63962|0.63962	.|.	.|.	ENSG00000125733|ENSG00000125733	ENST00000420690|ENST00000313285;ENST00000313244	.|T;T	.|0.18174	.|2.23;3.08	4.84|4.84	4.84|4.84	0.62591|0.62591	.|Src homology-3 domain (3);	.|0.220353	.|0.37530	.|N	.|0.002051	T|T	0.29061|0.29061	0.0722|0.0722	L|L	0.37850|0.37850	1.14|1.14	0.45946|0.45946	D|D	0.998773|0.998773	D|P;P	0.64830|0.49447	0.994|0.924;0.89	P|P;P	0.59889|0.62298	0.865|0.9;0.496	T|T	0.01661|0.01661	-1.1301|-1.1301	8|10	0.87932|0.72032	D|D	0|0.01	-28.6222|-28.6222	12.6835|12.6835	0.56934|0.56934	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	552|598;542	G5E9U1|Q15642;Q15642-2	.|CIP4_HUMAN;.	P|A	552|542;598	.|ENSP00000320493:V542A;ENSP00000320117:V598A	ENSP00000415493:S552P|ENSP00000320117:V598A	S|V	+|+	1|2	0|0	TRIP10|TRIP10	6702209|6702209	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.148000|0.148000	0.21650|0.21650	5.542000|5.542000	0.67218|0.67218	2.163000|2.163000	0.67991|0.67991	0.254000|0.254000	0.18369|0.18369	TCA|GTC	.	.		0.612	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2			C	6751209	T	C	6751209	3	2	114	1	0	0	0	0	1	0	0	0	16569	1667	58	2	1679	2	TRIP10	19	6751209	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	603	6751209	52377774	1081	19353										
INSR	3643	hgsc.bcm.edu	37	chr19	7152932	7152932	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accaggtcctcgagggcagcTtcagccctggagaaagaaac	12	12	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:7152932T>C	ENST00000302850.5	-	10	2178	c.2036A>G	c.(2035-2037)aAg>aGg	p.K679R	INSR_ENST00000341500.5_Missense_Mutation_p.K679R	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	679	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""Insulin(DB00071)|""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	CGAGGGCAGCTTCAGCCCTGG	0.542																																					p.K679R		Atlas-SNP	.											.	INSR	265	.	0			c.A2036G						.						63	58	60					19																	7152932		2203	4300	6503	SO:0001583	missense	3643	exon10			GGCAGCTTCAGCC	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"CD molecules", "Fibronectin type III domain containing"	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.2036A>G	chr19.hg19:g.7152932T>C	ENSP00000303830:p.Lys679Arg	58.0	0.0		67.0	4.0	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	hg19	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	t	13.44	2.237562	0.39598	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	T;T	0.75367	-0.93;-0.93	5.55	5.55	0.83447	Fibronectin, type III (3);	0.000000	0.47852	U	0.000209	T	0.67970	0.2950	L	0.46947	1.48	0.58432	D	0.999995	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.0	T	0.63571	-0.6607	10	0.36615	T	0.2	.	13.6724	0.62434	0.0:0.0:0.0:1.0	.	670;679;679	Q86WY9;P06213-2;P06213	.;.;INSR_HUMAN	R	679	ENSP00000303830:K679R;ENSP00000342838:K679R	ENSP00000303830:K679R	K	-	2	0	INSR	7103932	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	7.477000	0.81069	2.121000	0.65114	0.487000	0.48397	AAG	.	.		0.542	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			C	7152932	T	C	7152932	3	2	114	1	0	0	0	0	1	0	0	0	7782	1609	56	2	2164	2	INSR	19	7152932	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	401723	7152932	51976051	1082	19354										
KIAA1543	57662	hgsc.bcm.edu	37	chr19	7672746	7672746	+	Intron	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgaaggagtcggggagcaaaCcccccatggtaatgtatccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:7672746delC	ENST00000160298.4	+	5	722				CAMSAP3_ENST00000446248.2_Frame_Shift_Del_p.P233fs	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3						epithelial cell-cell adhesion (GO:0090136)|microtubule anchoring (GO:0034453)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of organelle organization (GO:0033043)|zonula adherens maintenance (GO:0045218)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)|zonula adherens (GO:0005915)	microtubule minus-end binding (GO:0051011)			cervix(1)|endometrium(7)|kidney(3)|lung(6)|urinary_tract(2)	19						GGGGAGCAAACCCCCCATGGT	0.657																																					p.K231fs		Atlas-INDEL	.											.	CAMSAP3	131	.	0			c.693delA						.						23	26	25					19																	7672746		1919	4116	6035	SO:0001627	intron_variant	57662	exon6			.	AB040976	CCDS42489.1, CCDS45947.1	19p13.3-p13.2	2014-06-12	2011-08-18	2011-08-18		ENSG00000076826			29307	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 80"	612685	"KIAA1543"	KIAA1543		11318610, 10819331, 19041755, 19508979	Standard	NM_001080429		Approved	Nezha, PPP1R80	uc002mgu.4	Q9P1Y5		ENST00000160298.4:c.622-266C>-	chr19.hg19:g.7672746delC		253.0	0.0		306.0	19.0	NM_001080429	Q8NDF1	Frame_Shift_Del	DEL	ENST00000160298.4	hg19	CCDS42489.1																																																																																			.	.		0.657	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362		-	7672746	C	-	7672746	6	5	114	0	1	1	0	1	0	0	0	0	8252	507	18	0		0	KIAA1543	19	7672746	Intron	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	519814	7672746	51456237	1083	19355										
MUC16	94025	hgsc.bcm.edu	37	chr19	9066715	9066715	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cattggagctgtggccttggTtttttctgagtcagctagga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:9066715delT	ENST00000397910.4	-	3	20934	c.20731delA	c.(20731-20733)accfs	p.T6911fs		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6913	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGCCTTGGTTTTTTCTGAG	0.473																																					p.T6911fs		Atlas-INDEL	.											.	MUC16	4315	.	0			c.20732delC						.						296	280	285					19																	9066715		2106	4215	6321	SO:0001589	frameshift_variant	94025	exon3			.	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20731delA	chr19.hg19:g.9066715delT	ENSP00000381008:p.Thr6911fs	164.0	0.0		196.0	13.0	NM_024690	Q6ZQW5|Q96RK2	Frame_Shift_Del	DEL	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		-	9066715	T	-	9066715	7	5	114	1	0	1	0	1	0	0	0	0	9982	1725	60	0	23120	0	MUC16	19	9066715	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1393969	9066715	50062268	1084	19356										
MUC16	94025	hgsc.bcm.edu	37	chr19	9089471	9089471	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgcatttctgactctttcagGacttgttgctgcattgctta	8	9	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:9089471G>C	ENST00000397910.4	-	1	2547	c.2344C>G	c.(2344-2346)Cct>Gct	p.P782A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	782	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ACTCTTTCAGGACTTGTTGCT	0.507																																					p.P782A		Atlas-SNP	.											.	MUC16	4315	.	0			c.C2344G						.						232	224	227					19																	9089471		2020	4191	6211	SO:0001583	missense	94025	exon1			TTTCAGGACTTGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.2344C>G	chr19.hg19:g.9089471G>C	ENSP00000381008:p.Pro782Ala	111.0	0.0		158.0	66.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	0.547	-0.851007	0.02651	.	.	ENSG00000181143	ENST00000397910	T	0.03094	4.05	1.56	-3.12	0.05282	.	.	.	.	.	T	0.01661	0.0053	N	0.03608	-0.345	.	.	.	B	0.15473	0.013	B	0.09377	0.004	T	0.44421	-0.9329	8	0.87932	D	0	.	4.2204	0.10554	0.0:0.2703:0.4022:0.3275	.	782	B5ME49	.	A	782	ENSP00000381008:P782A	ENSP00000381008:P782A	P	-	1	0	MUC16	8950471	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-2.843000	0.00736	-1.645000	0.01515	0.205000	0.17691	CCT	.	.		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9089471	G	C	9089471	3	2	114	1	0	0	0	0	1	0	0	0	9982	1174	41	4	41515	4	MUC16	19	9089471	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	22756	9089471	50039512	1085	19357										
ZNF562	54811	hgsc.bcm.edu	37	chr19	9767254	9767254	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagtgaatatttgattcttcAaaaaaccctgctgaagtgat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:9767254delA	ENST00000448622.1	-	5	479	c.317delT	c.(316-318)ttgfs	p.L106fs	ZNF562_ENST00000453372.2_Frame_Shift_Del_p.L106fs|ZNF562_ENST00000453792.2_Frame_Shift_Del_p.L37fs|ZNF562_ENST00000590155.1_Frame_Shift_Del_p.L106fs|ZNF562_ENST00000587392.1_Intron|ZNF562_ENST00000537617.1_5'UTR|ZNF562_ENST00000293648.4_Frame_Shift_Del_p.L34fs|ZNF562_ENST00000541032.1_Frame_Shift_Del_p.L69fs	NM_001130031.1|NM_001130032.1	NP_001123503.1|NP_001123504.1	Q6V9R5	ZN562_HUMAN	zinc finger protein 562	106	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	17						TTGATTCTTCAAAAAACCCTG	0.373																																					p.L106fs		Atlas-INDEL	.											.	ZNF562	72	.	0			c.318delG						.						145	142	143					19																	9767254		2203	4300	6503	SO:0001589	frameshift_variant	54811	exon5			.	AK000086	CCDS12217.1, CCDS45956.1, CCDS74280.1	19p13.2	2013-09-20			ENSG00000171466	ENSG00000171466		"Zinc fingers, C2H2-type", "-"	25950	protein-coding gene	gene with protein product							Standard	NM_001130031		Approved	FLJ20079	uc010xks.2	Q6V9R5	OTTHUMG00000180205	ENST00000448622.1:c.317delT	chr19.hg19:g.9767254delA	ENSP00000411784:p.Leu106fs	168.0	0.0		228.0	14.0	NM_001130032	Q32MN2|Q9NXS5	Frame_Shift_Del	DEL	ENST00000448622.1	hg19	CCDS45956.1																																																																																			.	.		0.373	ZNF562-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450239.1	NM_017656		-	9767254	A	-	9767254	7	5	114	1	0	1	0	1	0	0	0	0	18008	131	5	0	971	0	ZNF562	19	9767254	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	677783	9767254	49361729	1086	19358										
FBXL12	54850	hgsc.bcm.edu	37	chr19	9922291	9922291	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caacagagcaggggacaactGgggggcctgggagccagaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:9922291delG	ENST00000247977.4	-	3	503	c.262delC	c.(262-264)cagfs	p.Q88fs	FBXL12_ENST00000586469.1_Frame_Shift_Del_p.P63fs|FBXL12_ENST00000592067.1_3'UTR|FBXL12_ENST00000586651.1_3'UTR|FBXL12_ENST00000589626.1_3'UTR|FBXL12_ENST00000591009.1_Frame_Shift_Del_p.Q35fs|FBXL12_ENST00000585379.1_Frame_Shift_Del_p.Q35fs|FBXL12_ENST00000588922.1_3'UTR	NM_017703.1	NP_060173.1	Q9NXK8	FXL12_HUMAN	F-box and leucine-rich repeat protein 12	88					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)		p.Q88fs*7(1)		endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(2)	10						GGGGACAACTGGGGGGCCTGG	0.632																																					p.Q88fs		Atlas-INDEL	.											.	FBXL12	17	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.263delA						.						42	48	46					19																	9922291		2202	4295	6497	SO:0001589	frameshift_variant	54850	exon3			.	AK000195	CCDS12218.1	19p13.2	2011-06-09				ENSG00000127452		"F-boxes / Leucine-rich repeats"	13611	protein-coding gene	gene with protein product		609079				10531037	Standard	XM_005259964		Approved	FLJ20188, Fbl12	uc002mme.3	Q9NXK8		ENST00000247977.4:c.262delC	chr19.hg19:g.9922291delG	ENSP00000247977:p.Gln88fs	120.0	0.0		175.0	11.0	NM_017703	B3KSJ8|Q9H5K4	Frame_Shift_Del	DEL	ENST00000247977.4	hg19	CCDS12218.1																																																																																			.	.		0.632	FBXL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450265.1	NM_017703		-	9922291	G	-	9922291	7	5	114	1	0	1	0	1	0	0	0	0	5716	1357	47	0	722	0	FBXL12	19	9922291	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	155037	9922291	49206692	1087	19359										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11099991	11099991	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgctccttgtctctgctcccAggctgcaggctcgcatcgca	10	16	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:11099991A>G	ENST00000429416.3	+	8	1399		c.e8-1		SMARCA4_ENST00000541122.2_Splice_Site|SMARCA4_ENST00000444061.3_Splice_Site|SMARCA4_ENST00000344626.4_Splice_Site|SMARCA4_ENST00000589677.1_Splice_Site|SMARCA4_ENST00000358026.2_Splice_Site|SMARCA4_ENST00000590574.1_Splice_Site|SMARCA4_ENST00000413806.3_Splice_Site|SMARCA4_ENST00000450717.3_Splice_Site	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4						aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CTCTGCTCCCAGGCTGCAGGC	0.607			"F, N, Mis"		NSCLC																																.		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.1119-2A>G						.						82	85	84					19																	11099991		2203	4300	6503	SO:0001630	splice_region_variant	6597	exon7			GCTCCCAGGCTGC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.1119-1A>G	chr19.hg19:g.11099991A>G		103.0	0.0		123.0	5.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Splice_Site	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.009744	0.75046	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	.	.	.	4.42	4.42	0.53409	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8048	0.57607	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMARCA4	10960991	1.000000	0.71417	0.989000	0.46669	0.910000	0.53928	7.271000	0.78506	1.871000	0.54225	0.379000	0.24179	.	.	.		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	Intron	G	11099991	A	G	11099991	5	3	114	1	0	0	0	0	0	0	1	0	14785	202	7	2	1139	2	SMARCA4	19	11099991	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1177700	11099991	48028992	1088	19360										
RGL3	57139	hgsc.bcm.edu	37	chr19	11526663	11526663	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctctcgctcagcctcctccAaaaaatcttccagaagcttc					rs151155820	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:11526663delA	ENST00000380456.3	-	5	650	c.587delT	c.(586-588)ttgfs	p.L196fs	RGL3_ENST00000393423.3_Frame_Shift_Del_p.L196fs	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	196	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						AGCCTCCTCCAAAAAATCTTC	0.582																																					p.L196fs	GBM(174;751 2067 17998 27979 33959)	Atlas-INDEL	.											.	RGL3	100	.	0			c.588delG						.						130	145	140					19																	11526663		2203	4300	6503	SO:0001589	frameshift_variant	57139	exon5			.	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.587delT	chr19.hg19:g.11526663delA	ENSP00000369823:p.Leu196fs	118.0	0.0		155.0	11.0	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Frame_Shift_Del	DEL	ENST00000380456.3	hg19	CCDS32910.1																																																																																			.	.		0.582	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867		-	11526663	A	-	11526663	7	5	114	1	0	1	0	1	0	0	0	0	13293	131	5	0	1623	0	RGL3	19	11526663	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	426672	11526663	47602320	1089	19361										
ZNF44	51710	hgsc.bcm.edu	37	chr19	12383437	12383437	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcatgtcttagaaggaaagAgggccaaaagaatgctttcc	10	7	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:12383437A>G	ENST00000356109.5	-	5	1895	c.1777T>C	c.(1777-1779)Tct>Cct	p.S593P	ZNF44_ENST00000355684.5_Missense_Mutation_p.S545P	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	593					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		AGAAGGAAAGAGGGCCAAAAG	0.428																																					p.S593P		Atlas-SNP	.											.	ZNF44	55	.	0			c.T1777C						.						51	56	54					19																	12383437		2196	4300	6496	SO:0001583	missense	51710	exon5			GGAAAGAGGGCCA	X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"Zinc fingers, C2H2-type", "-"	13110	protein-coding gene	gene with protein product		194542	"zinc finger protein 58", "zinc finger protein 44 (KOX 7)", "zinc finger protein 55"	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.1777T>C	chr19.hg19:g.12383437A>G	ENSP00000348419:p.Ser593Pro	59.0	0.0		76.0	4.0	NM_001164276	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Missense_Mutation	SNP	ENST00000356109.5	hg19	CCDS54223.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.664520	0.47572	.	.	ENSG00000197857	ENST00000393337;ENST00000356109;ENST00000457673;ENST00000355684	T;T;T	0.18810	2.19;2.2;2.2	1.1	-0.0512	0.13827	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27629	0.0679	M	0.76838	2.35	.	.	.	P;P	0.52577	0.954;0.893	P;P	0.47470	0.548;0.544	T	0.34601	-0.9822	8	0.66056	D	0.02	.	5.2493	0.15514	0.6907:0.0:0.0:0.3093	.	593;545	P15621;F8W7T7	ZNF44_HUMAN;.	P	593;593;545;545	ENSP00000377008:S593P;ENSP00000348419:S593P;ENSP00000347910:S545P	ENSP00000347910:S545P	S	-	1	0	ZNF44	12244437	0.000000	0.05858	0.000000	0.03702	0.876000	0.50452	-3.128000	0.00592	-0.064000	0.13043	0.254000	0.18369	TCT	.	.		0.428	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264		G	12383437	A	G	12383437	3	3	114	1	0	0	0	0	1	0	0	0	17927	304	11	2	218	2	ZNF44	19	12383437	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	856774	12383437	46745546	1090	19362										
ZNF443	10224	hgsc.bcm.edu	37	chr19	12541062	12541062	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgggttctctccagtgtgagTttttttccagtgagtctttt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:12541062delT	ENST00000301547.5	-	4	2121	c.1924delA	c.(1924-1926)actfs	p.T642fs	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	642					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						CCAGTGTGAGTTTTTTTCCAG	0.398																																					p.T642fs		Pindel	.											.	ZNF443	63	.	0			c.1925delC						.						105	108	107					19																	12541062		2203	4300	6503	SO:0001589	frameshift_variant	10224	exon4			.	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"Zinc fingers, C2H2-type", "-"	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1924delA	chr19.hg19:g.12541062delT	ENSP00000301547:p.Thr642fs	219.0	0.0		277.0	14.0	NM_005815		Frame_Shift_Del	DEL	ENST00000301547.5	hg19	CCDS32918.1																																																																																			.	.		0.398	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		-	12541062	T	-	12541062	7	5	114	1	0	1	0	1	0	0	0	0	17931	1725	60	0	95	0	ZNF443	19	12541062	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	157625	12541062	46587921	1091	19363										
MAN2B1	4125	hgsc.bcm.edu	37	chr19	12760238	12760238	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttccaggtgggtcgataatCccgcctggggttgggggtga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:12760238delC	ENST00000456935.2	-	19	2312	c.2272delG	c.(2272-2274)gatfs	p.D758fs	CTD-2192J16.22_ENST00000597692.1_5'Flank|MAN2B1_ENST00000221363.4_Frame_Shift_Del_p.D757fs	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	758					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGTCGATAATCCCGCCTGGGG	0.522																																					p.D758fs		Atlas-INDEL	.											.	MAN2B1	91	.	0			c.2273delA						.						53	42	46					19																	12760238		2203	4300	6503	SO:0001589	frameshift_variant	4125	exon19			.		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.2272delG	chr19.hg19:g.12760238delC	ENSP00000395473:p.Asp758fs	152.0	0.0		216.0	18.0	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Frame_Shift_Del	DEL	ENST00000456935.2	hg19	CCDS32919.1																																																																																			.	.		0.522	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1			-	12760238	C	-	12760238	7	5	114	1	0	1	0	1	0	0	0	0	9225	855	30	0	787	0	MAN2B1	19	12760238	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	219176	12760238	46368745	1092	19364										
TNPO2	30000	hgsc.bcm.edu	37	chr19	12825735	12825735	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aacgttctcatcatggtcctGggtcctctgcagcatgtact							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:12825735delG	ENST00000592287.1	-	9	898	c.790delC	c.(790-792)cagfs	p.Q264fs	TNPO2_ENST00000425528.1_Frame_Shift_Del_p.Q264fs|TNPO2_ENST00000356861.5_Frame_Shift_Del_p.Q264fs|TNPO2_ENST00000589956.1_Intron|TNPO2_ENST00000588216.1_Frame_Shift_Del_p.Q264fs|TNPO2_ENST00000441499.1_Frame_Shift_Del_p.Q264fs|TNPO2_ENST00000450764.2_Frame_Shift_Del_p.Q264fs	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	264					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TCATGGTCCTGGGTCCTCTGC	0.662																																					p.Q264fs		Atlas-INDEL	.											.	TNPO2	108	.	0			c.791delA						.						115	121	119					19																	12825735		2121	4228	6349	SO:0001589	frameshift_variant	30000	exon9			.	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"Importins"	19998	protein-coding gene	gene with protein product	"importin 3", "karyopherin beta 2b"	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.790delC	chr19.hg19:g.12825735delG	ENSP00000468434:p.Gln264fs	152.0	0.0		148.0	10.0	NM_013433	O14655|Q6IN77	Frame_Shift_Del	DEL	ENST00000592287.1	hg19	CCDS45991.1																																																																																			.	.		0.662	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433		-	12825735	G	-	12825735	7	5	114	1	0	1	0	1	0	0	0	0	16351	1357	47	0	1967	0	TNPO2	19	12825735	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	65497	12825735	46303248	1093	19365										
FARSA	2193	hgsc.bcm.edu	37	chr19	13033615	13033615	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctcggcatccaggcggcacaGgggactgtcatacaccatct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:13033615delG	ENST00000314606.4	-	13	1492	c.1474delC	c.(1474-1476)ctgfs	p.L492fs	FARSA_ENST00000423140.2_Frame_Shift_Del_p.L461fs|MIR5695_ENST00000579717.1_RNA|FARSA_ENST00000588025.1_Frame_Shift_Del_p.L532fs	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	492					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	AGGCGGCACAGGGGACTGTCA	0.612																																					p.L492fs		Atlas-INDEL	.											.	FARSA	46	.	0			c.1475delT						.						150	124	133					19																	13033615		2203	4300	6503	SO:0001589	frameshift_variant	2193	exon13			.	U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	3592	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 1, alpha, cytoplasmic"	602918	"phenylalanine-tRNA synthetase-like", "phenylalanyl-tRNA synthetase-like, alpha subunit"	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.1474delC	chr19.hg19:g.13033615delG	ENSP00000320309:p.Leu492fs	113.0	0.0		169.0	11.0	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Frame_Shift_Del	DEL	ENST00000314606.4	hg19	CCDS12287.1																																																																																			.	.		0.612	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461		-	13033615	G	-	13033615	7	5	114	1	0	1	0	1	0	0	0	0	5687	991	35	0	56	0	FARSA	19	13033615	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	207880	13033615	46095368	1094	19366										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13394203	13394203	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggatgtaatggcacaggcGgcgaaggctgttggagacag	17	7	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:13394203G>A	ENST00000360228.5	-	22	3699	c.3700C>T	c.(3700-3702)Cgc>Tgc	p.R1234C	CACNA1A_ENST00000573710.2_Missense_Mutation_p.R1235C	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1235					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGCACAGGCGGCGAAGGCTG	0.547																																					p.R1235C		Atlas-SNP	.											.	CACNA1A	715	.	0			c.C3703T						.						77	84	81					19																	13394203		2165	4263	6428	SO:0001583	missense	773	exon22			ACAGGCGGCGAAG	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3700C>T	chr19.hg19:g.13394203G>A	ENSP00000353362:p.Arg1234Cys	179.0	0.0		236.0	76.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816993	0.50633	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	T	0.42513	0.97	4.92	3.83	0.44106	.	0.063724	0.56097	D	0.000035	T	0.45296	0.1335	L	0.46670	1.46	0.53688	D	0.999979	D;D;D	0.76494	0.959;0.988;0.999	B;P;P	0.50490	0.241;0.576;0.642	T	0.51108	-0.8747	10	0.87932	D	0	.	13.4591	0.61217	0.0:0.0:0.8427:0.1573	.	1235;1238;1234	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	C	1234;1238;1235;1235	ENSP00000353362:R1234C	ENSP00000317661:R1235C	R	-	1	0	CACNA1A	13255203	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.503000	0.53340	2.301000	0.77427	0.561000	0.74099	CGC	.	.		0.547	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13394203	G	A	13394203	3	1	114	1	0	0	0	0	1	0	0	0	2540	1116	39	1	4026	1	CACNA1A	19	13394203	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	360588	13394203	45734780	1095	19367										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14023137	14023137	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcatccccctaccgccaggTcccttgccgatggaggccat	11	17	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:14023137T>C	ENST00000318003.7	+	3	439	c.198T>C	c.(196-198)ggT>ggC	p.G66G	CC2D1A_ENST00000589606.1_Splice_Site_p.G66G	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	66					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			TACCGCCAGGTCCCTTGCCGA	0.612																																					p.G66G		Atlas-SNP	.											.	CC2D1A	67	.	0			c.T198C						.						39	45	43					19																	14023137		2111	4215	6326	SO:0001630	splice_region_variant	54862	exon3			GCCAGGTCCCTTG	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.197-1T>C	chr19.hg19:g.14023137T>C		62.0	0.0		81.0	4.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Silent	SNP	ENST00000318003.7	hg19	CCDS42512.1																																																																																			.	.		0.612	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	Silent	C	14023137	T	C	14023137	5	2	114	1	0	0	0	0	0	0	1	0	2728	1681	58	2	208	2	CC2D1A	19	14023137	Splice_Site	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	628934	14023137	45105846	1096	19368										
CD97	976	hgsc.bcm.edu	37	chr19	14508727	14508727	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctttctccacctggaccccgCcccctggagtccacagccag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:14508727delC	ENST00000242786.5	+	8	879	c.799delC	c.(799-801)cccfs	p.P268fs	CD97_ENST00000357355.3_Frame_Shift_Del_p.P219fs|CD97_ENST00000358600.3_Frame_Shift_Del_p.P175fs	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	268					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTGGACCCCGCCCCCTGGAGT	0.607																																					p.P266fs		Atlas-INDEL	.											.	CD97	86	.	0			c.798delG						.						6	9	8					19																	14508727		1874	3927	5801	SO:0001589	frameshift_variant	976	exon8			.		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.799delC	chr19.hg19:g.14508727delC	ENSP00000242786:p.Pro268fs	149.0	0.0		197.0	13.0	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Frame_Shift_Del	DEL	ENST00000242786.5	hg19	CCDS32929.1																																																																																			.	.		0.607	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		-	14508727	C	-	14508727	7	5	114	1	0	1	0	1	0	0	0	0	3051	739	26	0	829	0	CD97	19	14508727	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	485590	14508727	44620256	1097	19369										
PKN1	5585	hgsc.bcm.edu	37	chr19	14561143	14561143	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctcacagggagtcctgacctGggggctgtggagctgcgcat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:14561143delG	ENST00000242783.6	+	5	789	c.624delG	c.(622-624)ctgfs	p.L208fs	PKN1_ENST00000342216.4_Frame_Shift_Del_p.L214fs	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	208					activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						GTCCTGACCTGGGGGCTGTGG	0.647																																					p.L214fs	NSCLC(185;2539 2965 10733 52867)	Atlas-INDEL	.											.	PKN1	99	.	0			c.641delT						.						17	20	19					19																	14561143		2134	4222	6356	SO:0001589	frameshift_variant	5585	exon5			.	S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"protein kinase C-like 1"	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.624delG	chr19.hg19:g.14561143delG	ENSP00000242783:p.Leu208fs	219.0	0.0		227.0	16.0	NM_213560	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Frame_Shift_Del	DEL	ENST00000242783.6	hg19	CCDS42513.1																																																																																			.	.		0.647	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560		-	14561143	G	-	14561143	7	5	114	1	0	1	0	1	0	0	0	0	11988	1335	47	0	685	0	PKN1	19	14561143	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	52416	14561143	44567840	1098	19370										
OR7C2	26658	hgsc.bcm.edu	37	chr19	15052711	15052711	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cactacacggtcatcatgaaCccccggctctgtggactgct					rs201572109		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:15052711delC	ENST00000248072.3	+	1	411	c.411delC	c.(409-411)aacfs	p.N137fs		NM_012377.1	NP_036509.1	O60412	OR7C2_HUMAN	olfactory receptor, family 7, subfamily C, member 2	137						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(8)|ovary(2)|skin(2)	15	Ovarian(108;0.203)					TCATCATGAACCCCCGGCTCT	0.542																																					p.N137fs		Atlas-INDEL	.											.	OR7C2	50	.	0			c.410delA						.						134	129	131					19																	15052711		2203	4300	6503	SO:0001589	frameshift_variant	26658	exon1			.	U86255	CCDS12320.1	19p13.1	2012-08-09				ENSG00000127529		"GPCR / Class A : Olfactory receptors"	8374	protein-coding gene	gene with protein product				OR7C3			Standard	NM_012377		Approved	OR19-18	uc010xoc.2	O60412		ENST00000248072.3:c.411delC	chr19.hg19:g.15052711delC	ENSP00000248072:p.Asn137fs	190.0	0.0		202.0	14.0	NM_012377	O43881|Q6IFP9	Frame_Shift_Del	DEL	ENST00000248072.3	hg19	CCDS12320.1																																																																																			.	.		0.542	OR7C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466281.1			-	15052711	C	-	15052711	7	5	114	1	0	1	0	1	0	0	0	0	11227	506	18	0	413	0	OR7C2	19	15052711	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	491568	15052711	44076272	1099	19371										
OR10H2	26538	hgsc.bcm.edu	37	chr19	15838973	15838973	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atgtacctgttcacgctgctGggcaacctgctcatcatggc	10	13	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:15838973G>A	ENST00000305899.3	+	1	140	c.120G>A	c.(118-120)ctG>ctA	p.L40L		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	40			L -> Q (in dbSNP:rs4569397).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L40L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					TCACGCTGCTGGGCAACCTGC	0.582																																					p.L40L		Atlas-SNP	.											OR10H2,NS,carcinoma,0,1	OR10H2	59	.	1	Substitution - coding silent(1)	lung(1)	c.G120A						.						227	188	201					19																	15838973		2203	4298	6501	SO:0001819	synonymous_variant	26538	exon1			GCTGCTGGGCAAC	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"GPCR / Class A : Olfactory receptors"	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.120G>A	chr19.hg19:g.15838973G>A		277.0	0.0		363.0	0.0	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	hg19	CCDS12333.1																																																																																			.	.		0.582	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1			A	15838973	G	A	15838973	2	1	114	1	0	0	0	0	0	0	0	1	10915	1335	47	3		3	OR10H2	19	15838973	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	786262	15838973	43290010	1100	19372										
EPS15L1	58513	hgsc.bcm.edu	37	chr19	16524615	16524615	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggttttctgtctgattgccTcttccttttctcgaatgtct	7	10	5	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:16524615T>C	ENST00000248070.6	-	13	1374	c.1235A>G	c.(1234-1236)gAg>gGg	p.E412G	EPS15L1_ENST00000597937.1_Missense_Mutation_p.E412G|EPS15L1_ENST00000455140.2_Missense_Mutation_p.E412G|EPS15L1_ENST00000535753.2_Missense_Mutation_p.E412G|EPS15L1_ENST00000594975.1_Missense_Mutation_p.E412G|EPS15L1_ENST00000602009.1_Missense_Mutation_p.E258G	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	412					endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						TCTGATTGCCTCTTCCTTTTC	0.403																																					p.E412G		Atlas-SNP	.											.	EPS15L1	81	.	0			c.A1235G						.						245	198	214					19																	16524615		2203	4300	6503	SO:0001583	missense	58513	exon13			ATTGCCTCTTCCT	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.1235A>G	chr19.hg19:g.16524615T>C	ENSP00000248070:p.Glu412Gly	214.0	0.0		212.0	9.0	NM_021235	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	SNP	ENST00000248070.6	hg19	CCDS32944.1	.	.	.	.	.	.	.	.	.	.	T	13.11	2.138822	0.37728	.	.	ENSG00000127527	ENST00000455140;ENST00000248070;ENST00000535753	T;D;D	0.83335	1.47;-1.71;-1.71	4.62	3.6	0.41247	.	0.058511	0.64402	D	0.000003	T	0.72914	0.3520	L	0.31926	0.97	0.58432	D	0.999994	B;B;B;B;B;B	0.14438	0.006;0.003;0.01;0.01;0.001;0.001	B;B;B;B;B;B	0.15870	0.014;0.009;0.008;0.01;0.004;0.009	T	0.65026	-0.6268	10	0.36615	T	0.2	.	9.7855	0.40673	0.0:0.0824:0.0:0.9176	.	412;412;411;412;412;412	A8K5P4;A5PL29;A5PKY0;A2RRF3;Q9UBC2;G3V0H2	.;.;.;.;EP15R_HUMAN;.	G	412	ENSP00000393313:E412G;ENSP00000248070:E412G;ENSP00000440103:E412G	ENSP00000248070:E412G	E	-	2	0	EPS15L1	16385615	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	4.099000	0.57755	0.736000	0.32559	-0.378000	0.06908	GAG	.	.		0.403	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		C	16524615	T	C	16524615	3	2	114	1	0	0	0	0	1	0	0	0	5195	1551	54	2	1403	2	EPS15L1	19	16524615	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	685642	16524615	42604368	1101	19373										
MAP1S	55201	hgsc.bcm.edu	37	chr19	17836717	17836717	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgccccaccttcggtgactGggctcagctggcacccgctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:17836717delG	ENST00000324096.4	+	5	675	c.524delG	c.(523-525)tggfs	p.W175fs	MAP1S_ENST00000597681.1_Intron|MAP1S_ENST00000544059.2_Frame_Shift_Del_p.W149fs|CTD-3149D2.4_ENST00000595363.1_RNA	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	175	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						TTCGGTGACTGGGCTCAGCTG	0.687																																					p.W175fs		Atlas-INDEL	.											.	MAP1S	74	.	0			c.523delT						.						32	32	32					19																	17836717		2201	4297	6498	SO:0001589	frameshift_variant	55201	exon5			.	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.524delG	chr19.hg19:g.17836717delG	ENSP00000325313:p.Trp175fs	208.0	0.0		171.0	12.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Frame_Shift_Del	DEL	ENST00000324096.4	hg19	CCDS32954.1																																																																																			.	.		0.687	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		-	17836717	G	-	17836717	7	5	114	1	0	1	0	1	0	0	0	0	9243	1357	47	0	542	0	MAP1S	19	17836717	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1312102	17836717	41292266	1102	19374										
FCHO1	23149	hgsc.bcm.edu	37	chr19	17897403	17897403	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaacctggaggagaagcggcTcacttggaggcttccagatg	15	9	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:17897403T>C	ENST00000596536.1	+	27	2730	c.2447T>C	c.(2446-2448)cTc>cCc	p.L816P	FCHO1_ENST00000389133.4_Missense_Mutation_p.L816P|FCHO1_ENST00000595033.1_Missense_Mutation_p.L766P|FCHO1_ENST00000594202.1_Missense_Mutation_p.L816P|FCHO1_ENST00000252771.7_Missense_Mutation_p.L816P|FCHO1_ENST00000597512.1_Missense_Mutation_p.L823P|FCHO1_ENST00000596951.1_Missense_Mutation_p.L816P|FCHO1_ENST00000600676.1_Missense_Mutation_p.L816P|FCHO1_ENST00000539407.1_Missense_Mutation_p.L816P	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	816	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.|Mediates interaction with AGFG1, CALM, DAB2, EPS15, EPS15R, ITSN1 and clathrin.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						GAGAAGCGGCTCACTTGGAGG	0.597																																					p.L816P		Atlas-SNP	.											.	FCHO1	69	.	0			c.T2447C						.						56	59	58					19																	17897403		2203	4300	6503	SO:0001583	missense	23149	exon26			AGCGGCTCACTTG	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.2447T>C	chr19.hg19:g.17897403T>C	ENSP00000470731:p.Leu816Pro	49.0	0.0		89.0	4.0	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	hg19	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.564618	0.45694	.	.	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.48836	0.8;0.8;0.8	3.83	3.83	0.44106	Muniscin C-terminal mu homology domain (1);	0.470872	0.18121	N	0.151039	T	0.53206	0.1782	L	0.42245	1.32	0.80722	D	1	D;D	0.56287	0.975;0.969	P;P	0.59761	0.814;0.863	T	0.51694	-0.8673	10	0.49607	T	0.09	-9.159	9.1655	0.37050	0.0:0.0:0.0:1.0	.	816;816	O14526;O14526-2	FCHO1_HUMAN;.	P	816	ENSP00000252771:L816P;ENSP00000373785:L816P;ENSP00000437978:L816P	ENSP00000252771:L816P	L	+	2	0	FCHO1	17758403	0.998000	0.40836	0.615000	0.29064	0.324000	0.28378	5.524000	0.67105	1.761000	0.52028	0.402000	0.26972	CTC	.	.		0.597	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122		C	17897403	T	C	17897403	3	2	114	1	0	0	0	0	1	0	0	0	5795	1551	54	2	2541	2	FCHO1	19	17897403	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	60686	17897403	41231580	1103	19375										
SFRS14	10147	hgsc.bcm.edu	37	chr19	19136181	19136181	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tatttctatcccaaatcttgAaaaaacatcagacttatcta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:19136181delA	ENST00000601879.1	-	3	1273	c.976delT	c.(976-978)tcafs	p.S326fs	SUGP2_ENST00000456085.2_Frame_Shift_Del_p.S95fs|SUGP2_ENST00000452918.2_Frame_Shift_Del_p.S326fs|SUGP2_ENST00000600377.1_Frame_Shift_Del_p.S340fs|SUGP2_ENST00000598202.1_5'Flank|SUGP2_ENST00000337018.6_Frame_Shift_Del_p.S326fs			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	326					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CCAAATCTTGAAAAAACATCA	0.393																																					p.S326X		Atlas-INDEL	.											.	SUGP2	107	.	0			c.977delC						.						71	77	75					19																	19136181		2203	4300	6503	SO:0001589	frameshift_variant	10147	exon3			.	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.976delT	chr19.hg19:g.19136181delA	ENSP00000472286:p.Ser326fs	102.0	0.0		159.0	10.0	NM_014884	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Frame_Shift_Del	DEL	ENST00000601879.1	hg19	CCDS12392.1																																																																																			.	.		0.393	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		-	19136181	A	-	19136181	7	5	114	1	0	1	0	1	0	0	0	0	14185	246	9	0	2304	0	SFRS14	19	19136181	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1238778	19136181	39992802	1104	19376										
GATAD2A	54815	hgsc.bcm.edu	37	chr19	19609429	19609429	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcgagatccccccacccaagCccccagccccagagatgaac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:19609429delC	ENST00000360315.3	+	8	1414	c.1102delC	c.(1102-1104)cccfs	p.P369fs	GATAD2A_ENST00000404158.1_Frame_Shift_Del_p.P369fs|GATAD2A_ENST00000358713.3_Frame_Shift_Del_p.P369fs|GATAD2A_ENST00000537887.1_5'UTR|GATAD2A_ENST00000429563.2_Frame_Shift_Del_p.P196fs|GATAD2A_ENST00000252577.5_Frame_Shift_Del_p.P369fs	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	369	CR2; histone tail-binding.				anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						CCCACCCAAGCCCCCAGCCCC	0.637																																					p.K367fs		Atlas-INDEL	.											.	GATAD2A	81	.	0			c.1101delG						.						38	39	39					19																	19609429		2203	4300	6503	SO:0001589	frameshift_variant	54815	exon8			.	AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"GATA zinc finger domain containing"	29989	protein-coding gene	gene with protein product	"p66 alpha"	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.1102delC	chr19.hg19:g.19609429delC	ENSP00000353463:p.Pro369fs	210.0	0.0		279.0	17.0	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Frame_Shift_Del	DEL	ENST00000360315.3	hg19	CCDS12402.2																																																																																			.	.		0.637	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660		-	19609429	C	-	19609429	7	5	114	1	0	1	0	1	0	0	0	0	6268	739	26	0	1128	0	GATAD2A	19	19609429	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	473248	19609429	39519554	1105	19377										
YJEFN3	374887	hgsc.bcm.edu	37	chr19	19645920	19645920	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccggagcagaacggggcagtGgggctggtctgtgcccggca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:19645920delG	ENST00000514277.4	+	4	434	c.396delG	c.(394-396)gtgfs	p.V132fs	CTC-260F20.3_ENST00000555938.1_Frame_Shift_Del_p.V131fs|YJEFN3_ENST00000436027.5_Frame_Shift_Del_p.V82fs|YJEFN3_ENST00000608404.1_Frame_Shift_Del_p.V131fs	NM_198537.3	NP_940939.2	A6XGL0	YJEN3_HUMAN	YjeF N-terminal domain containing 3	132	YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.									NS(1)|breast(1)|lung(3)	5						ACGGGGCAGTGGGGCTGGTCT	0.627																																					p.V132fs		Atlas-INDEL	.											.	YJEFN3	10	.	0			c.395delT						.						72	91	85					19																	19645920		2111	4223	6334	SO:0001589	frameshift_variant	374887	exon4			.		CCDS42530.1, CCDS54236.1	19p13.11	2014-09-11			ENSG00000250067	ENSG00000250067			24785	protein-coding gene	gene with protein product						17533573	Standard	NM_198537		Approved	hYjeF_N3-19p13.11, FLJ44968	uc002nmt.2	A6XGL0	OTTHUMG00000162251	ENST00000514277.4:c.396delG	chr19.hg19:g.19645920delG	ENSP00000426964:p.Val132fs	102.0	0.0		146.0	13.0	NM_198537	A6XGK9|Q4G1C0	Frame_Shift_Del	DEL	ENST00000514277.4	hg19	CCDS42530.1																																																																																			.	.		0.627	YJEFN3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368157.5	NM_198537		-	19645920	G	-	19645920	7	5	114	1	0	1	0	1	0	0	0	0	17499	1335	47	0	410	0	YJEFN3	19	19645920	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	36491	19645920	39483063	1106	19378										
ZNF493	284443	hgsc.bcm.edu	37	chr19	21588652	21588652	+	Intron	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacacagtacggtagtcaaaCccccaggtaggtgagagtga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:21588652delC	ENST00000355504.4	+	1	135				ZNF493_ENST00000594390.1_Frame_Shift_Del_p.P84fs|ZNF493_ENST00000596302.1_Frame_Shift_Del_p.P85fs|ZNF493_ENST00000392288.2_Frame_Shift_Del_p.P84fs|CTD-2561J22.3_ENST00000600810.1_Frame_Shift_Del_p.P65fs|ZNF493_ENST00000339914.6_Frame_Shift_Del_p.P85fs	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						GGTAGTCAAACCCCCAGGTAG	0.418																																					p.K83fs		Atlas-INDEL	.											.	ZNF493	178	.	0			c.249delA						.						78	81	80					19																	21588652		2203	4300	6503	SO:0001627	intron_variant	284443	exon3			.	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.-132+8583C>-	chr19.hg19:g.21588652delC		74.0	0.0		103.0	11.0	NM_145326	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Frame_Shift_Del	DEL	ENST00000355504.4	hg19	CCDS12412.1																																																																																			.	.		0.418	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		-	21588652	C	-	21588652	6	5	114	0	1	1	0	1	0	0	0	0	17959	507	18	0		0	ZNF493	19	21588652	Intron	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1942732	21588652	37540331	1107	19379										
ZNF675	171392	hgsc.bcm.edu	37	chr19	23837367	23837367	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tataacctcccttgtgcaacTtacattcatccacactttta	2	13	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:23837367T>C	ENST00000359788.4	-	4	536	c.368A>G	c.(367-369)aAg>aGg	p.K123R	ZNF675_ENST00000600313.1_Intron|ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	123					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				CTTGTGCAACTTACATTCATC	0.294																																					p.K123R		Atlas-SNP	.											.	ZNF675	88	.	0			c.A368G						.						83	81	82					19																	23837367		2203	4298	6501	SO:0001583	missense	171392	exon4			TGCAACTTACATT		CCDS32981.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	30768	protein-coding gene	gene with protein product	"TRAF6 inhibitory zinc finger"					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.368A>G	chr19.hg19:g.23837367T>C	ENSP00000352836:p.Lys123Arg	102.0	0.0		123.0	5.0	NM_138330	Q8N211	Missense_Mutation	SNP	ENST00000359788.4	hg19	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	7.721	0.697156	0.15106	.	.	ENSG00000197372	ENST00000359788	T	0.07114	3.22	1.13	1.13	0.20643	.	.	.	.	.	T	0.12433	0.0302	M	0.84156	2.68	0.09310	N	1	B	0.23937	0.094	B	0.25614	0.062	T	0.20638	-1.0269	9	0.41790	T	0.15	.	6.0138	0.19589	0.0:0.0:0.0:1.0	.	123	Q8TD23	ZN675_HUMAN	R	123	ENSP00000352836:K123R	ENSP00000352836:K123R	K	-	2	0	ZNF675	23629207	0.001000	0.12720	0.002000	0.10522	0.021000	0.10359	0.295000	0.19065	0.469000	0.27268	0.254000	0.18369	AAG	.	.		0.294	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330		C	23837367	T	C	23837367	3	2	114	1	0	0	0	0	1	0	0	0	18097	1609	56	2	1342	2	ZNF675	19	23837367	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2248715	23837367	35291616	1108	19380										
KIAA0355	9710	hgsc.bcm.edu	37	chr19	34832365	34832365	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	catacagatccagctgcaaaGggagatctgtgattttggca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:34832365delG	ENST00000299505.6	+	10	2399	c.1526delG	c.(1525-1527)aggfs	p.R509fs		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	509										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					CAGCTGCAAAGGGAGATCTGT	0.393																																					p.R509fs		Atlas-INDEL	.											.	KIAA0355	105	.	0			c.1525delA						.						73	75	74					19																	34832365		2203	4300	6503	SO:0001589	frameshift_variant	9710	exon10			.		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.1526delG	chr19.hg19:g.34832365delG	ENSP00000299505:p.Arg509fs	160.0	0.0		200.0	12.0	NM_014686	Q2M3W4	Frame_Shift_Del	DEL	ENST00000299505.6	hg19	CCDS12436.1																																																																																			.	.		0.393	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686		-	34832365	G	-	34832365	7	5	114	1	0	1	0	1	0	0	0	0	8179	1000	35	0	1560	0	KIAA0355	19	34832365	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	10994998	34832365	24296618	1109	19381										
C19orf55	148137	hgsc.bcm.edu	37	chr19	36252918	36252918	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcctatcccctgatgttcacAggtatataaacaggttccgc	7	12	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:36252918A>G	ENST00000544099.1	+	4	374		c.e4-1		C19orf55_ENST00000396908.4_Splice_Site|C19orf55_ENST00000537459.1_Splice_Site|C19orf55_ENST00000536950.1_Splice_Site|C19orf55_ENST00000421853.2_Splice_Site			Q2NL68	PRSR3_HUMAN												cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGATGTTCACAGGTATATAAA	0.527																																					.		Atlas-SNP	.											.	C19orf55	39	.	0			c.312-2A>G						.						31	31	31					19																	36252918		1911	4145	6056	SO:0001630	splice_region_variant	148137	exon4			GTTCACAGGTATA																												ENST00000544099.1:c.312-1A>G	chr19.hg19:g.36252918A>G		70.0	0.0		79.0	5.0	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Splice_Site	SNP	ENST00000544099.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.71	2.913051	0.52439	.	.	ENSG00000167595	ENST00000444637;ENST00000396908;ENST00000301165;ENST00000537459;ENST00000545674	.	.	.	4.78	4.78	0.61160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8688	0.46870	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C19orf55	40944758	0.995000	0.38212	0.989000	0.46669	0.725000	0.41563	4.251000	0.58778	2.124000	0.65301	0.528000	0.53228	.	.	.		0.527	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2		Intron	G	36252918	A	G	36252918	5	3	114	1	0	0	0	0	0	0	1	0	1939	202	7	2	324	2	C19orf55	19	36252918	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1420553	36252918	22876065	1110	19382										
C19orf55	148137	hgsc.bcm.edu	37	chr19	36258938	36258938	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcggaggccctgcttgcccaGggccgccctgctgctgcagg	15	16	0	0	rs398034467|rs5827939		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:36258938G>A	ENST00000396908.4	+	9	1264	c.1191G>A	c.(1189-1191)caG>caA	p.Q397Q	AC002398.13_ENST00000589397.1_RNA|C19orf55_ENST00000544099.1_Silent_p.Q397Q	NM_001039887.2	NP_001034976.2	Q2NL68	PRSR3_HUMAN		398										cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGCTTGCCCAGGGCCGCCCTG	0.731																																					.		Atlas-SNP	.											.,11	C19orf55	39	.	0			c.1190+1G>A						.						1	1	1					19																	36258938		567	1236	1803	SO:0001630	splice_region_variant	148137	exon9			TGCCCAGGGCCGC																												ENST00000396908.4:c.1191+1G>A	chr19.hg19:g.36258938G>A		16.0	0.0		26.0	4.0	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Splice_Site	SNP	ENST00000396908.4	hg19																																																																																				.	.		0.731	C19orf55-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			Silent	A	36258938	G	A	36258938	5	1	114	1	0	0	0	0	0	0	1	0	1939	991	35	3	1225	3	C19orf55	19	36258938	Splice_Site	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	6020	36258938	22870045	1111	19383										
ZNF607	84775	hgsc.bcm.edu	37	chr19	38190282	38190282	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgttacattcaaagggcttCtcaccagtgtgaatactctg	8	9	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:38190282C>T	ENST00000355202.4	-	5	1345	c.750G>A	c.(748-750)gaG>gaA	p.E250E	CTD-2528L19.4_ENST00000586606.2_Intron|ZNF607_ENST00000395835.3_Silent_p.E249E	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	250					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			CAAAGGGCTTCTCACCAGTGT	0.423																																					p.E250E		Atlas-SNP	.											.	ZNF607	82	.	0			c.G750A						.						51	52	52					19																	38190282		2203	4300	6503	SO:0001819	synonymous_variant	84775	exon5			GGGCTTCTCACCA	AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.750G>A	chr19.hg19:g.38190282C>T		83.0	0.0		116.0	5.0	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Silent	SNP	ENST00000355202.4	hg19	CCDS33006.1																																																																																			.	.		0.423	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		T	38190282	C	T	38190282	2	4	114	1	0	0	0	0	0	0	0	1	18048	912	32	3		3	ZNF607	19	38190282	Silent	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	1931344	38190282	20938701	1112	19384										
RYR1	6261	hgsc.bcm.edu	37	chr19	39025415	39025415	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcaagcacggctgcacacccGgggggcggccgagatggtgc					rs193922839		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:39025415delG	ENST00000359596.3	+	79	11315	c.11315delG	c.(11314-11316)cggfs	p.R3772fs	RYR1_ENST00000355481.4_Frame_Shift_Del_p.R3767fs|RYR1_ENST00000360985.3_Frame_Shift_Del_p.R3772fs|AC067969.2_ENST00000595853.1_RNA			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3772			R -> Q (in CCD; autosomal recessive form). {ECO:0000269|PubMed:18253926}.|R -> W (in MHS1). {ECO:0000269|PubMed:19191329}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTGCACACCCGGGGGGCGGCC	0.587																																					p.R3772fs		Atlas-INDEL	.											.,1	RYR1	708	.	0			c.11314delC	GRCh37	CM073325	RYR1	M		.						41	40	40					19																	39025415		2203	4300	6503	SO:0001589	frameshift_variant	6261	exon79			.	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.11315delG	chr19.hg19:g.39025415delG	ENSP00000352608:p.Arg3772fs	132.0	0.0		194.0	12.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Frame_Shift_Del	DEL	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.587	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			-	39025415	G	-	39025415	7	5	114	1	0	1	0	1	0	0	0	0	13783	1116	39	0	11629	0	RYR1	19	39025415	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	835133	39025415	20103568	1113	19385										
LGALS4	3960	hgsc.bcm.edu	37	chr19	39294528	39294528	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagggtaaggtggcatcatcGggggtccctgtgggcacaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:39294528delG	ENST00000307751.4	-	5	959	c.482delC	c.(481-483)ccgfs	p.P161fs	LGALS4_ENST00000597803.1_5'Flank	NM_006149.3	NP_006140.1	P56470	LEG4_HUMAN	lectin, galactoside-binding, soluble, 4	161					cell adhesion (GO:0007155)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17	all_cancers(60;1.02e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			TGGCATCATCGGGGGTCCCTG	0.582																																					p.P161fs		Atlas-INDEL	.											.	LGALS4	39	.	0			c.483delG						.						46	47	47					19																	39294528		2203	4300	6503	SO:0001589	frameshift_variant	3960	exon5			.		CCDS12521.1	19q13.2	2014-03-19	2008-07-25		ENSG00000171747	ENSG00000171747		"Lectins, galactoside-binding"	6565	protein-coding gene	gene with protein product	"galectin 4"	602518				8063692	Standard	NM_006149		Approved	GAL4	uc002ojg.3	P56470	OTTHUMG00000182608	ENST00000307751.4:c.482delC	chr19.hg19:g.39294528delG	ENSP00000302100:p.Pro161fs	93.0	0.0		129.0	10.0	NM_006149		Frame_Shift_Del	DEL	ENST00000307751.4	hg19	CCDS12521.1																																																																																			.	.		0.582	LGALS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462641.1	NM_006149		-	39294528	G	-	39294528	7	5	114	1	0	1	0	1	0	0	0	0	8754	1116	39	0	513	0	LGALS4	19	39294528	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	269113	39294528	19834455	1114	19386										
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39329068	39329068	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tctcctcggtcacctccagcGgggcgttgaagaagtgcagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:39329068delG	ENST00000221419.5	-	10	1892	c.1526delC	c.(1525-1527)ccgfs	p.P509fs	HNRNPL_ENST00000600873.1_Frame_Shift_Del_p.P376fs|AC104534.3_ENST00000594769.1_Frame_Shift_Del_p.R126fs	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	509	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			CACCTCCAGCGGGGCGTTGAA	0.597																																					p.P509fs		Atlas-INDEL	.											.	HNRNPL	67	.	0			c.1527delG						.						67	58	61					19																	39329068		2203	4300	6503	SO:0001589	frameshift_variant	3191	exon10			.	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1526delC	chr19.hg19:g.39329068delG	ENSP00000221419:p.Pro509fs	139.0	0.0		150.0	10.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Frame_Shift_Del	DEL	ENST00000221419.5	hg19	CCDS33015.1																																																																																			.	.		0.597	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			-	39329068	G	-	39329068	7	5	114	1	0	1	0	1	0	0	0	0	7279	1116	39	0	259	0	HNRNPL	19	39329068	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	34540	39329068	19799915	1115	19387										
RINL	126432	hgsc.bcm.edu	37	chr19	39359906	39359906	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctgggctctgggatgatccTttctgtgcagcgtccgcctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:39359906delT	ENST00000591812.1	-	11	1705	c.1619delA	c.(1618-1620)aagfs	p.K540fs	RINL_ENST00000340740.3_Frame_Shift_Del_p.K426fs|CTC-360G5.6_ENST00000593830.1_RNA|RINL_ENST00000598904.1_Frame_Shift_Del_p.K426fs|RINL_ENST00000602238.1_5'Flank			Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like	540					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|ruffle (GO:0001726)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|urinary_tract(2)	17						GGGATGATCCTTTCTGTGCAG	0.677																																					p.K540fs		Atlas-INDEL	.											.	RINL	32	.	0			c.1620delG						.						84	83	84					19																	39359906		2203	4300	6503	SO:0001589	frameshift_variant	126432	exon11			.	AK127808	CCDS12522.1, CCDS59386.1	19q13.2	2010-07-13			ENSG00000187994	ENSG00000187994			24795	protein-coding gene	gene with protein product							Standard	NM_001195833		Approved	FLJ45909	uc010xuo.2	Q6ZS11		ENST00000591812.1:c.1619delA	chr19.hg19:g.39359906delT	ENSP00000467107:p.Lys540fs	157.0	0.0		156.0	10.0	NM_001195833	B4DPG5	Frame_Shift_Del	DEL	ENST00000591812.1	hg19	CCDS59386.1																																																																																			.	.		0.677	RINL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460433.1	NM_198445		-	39359906	T	-	39359906	7	5	114	1	0	1	0	1	0	0	0	0	13390	1609	56	0	89	0	RINL	19	39359906	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	30838	39359906	19769077	1116	19388										
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39955533	39955533	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacgtgaagcaggccattgaGggggtgggcaacctgcggct					rs2304217	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:39955533delG	ENST00000599117.1	+	12	1087	c.720delG	c.(718-720)gagfs	p.E240fs	SUPT5H_ENST00000402194.2_Frame_Shift_Del_p.E236fs|SUPT5H_ENST00000359191.6_Frame_Shift_Del_p.E236fs|SUPT5H_ENST00000432763.2_Frame_Shift_Del_p.E240fs|SUPT5H_ENST00000598725.1_Frame_Shift_Del_p.E240fs			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	240	Interaction with SUPT4H1.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGGCCATTGAGGGGGTGGGCA	0.577																																					p.E240fs		Atlas-INDEL	.											.	SUPT5H	119	.	0			c.719delA						.						97	83	88					19																	39955533		2203	4300	6503	SO:0001589	frameshift_variant	6829	exon10			.	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"suppressor of Ty (S.cerevisiae) 5 homolog"			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.720delG	chr19.hg19:g.39955533delG	ENSP00000470252:p.Glu240fs	141.0	0.0		194.0	12.0	NM_003169	O43279|Q59G52|Q99639	Frame_Shift_Del	DEL	ENST00000599117.1	hg19	CCDS12536.1																																																																																			.	.		0.577	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		-	39955533	G	-	39955533	7	5	114	1	0	1	0	1	0	0	0	0	15414	991	35	0	758	0	SUPT5H	19	39955533	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	595627	39955533	19173450	1117	19389										
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40589113	40589113	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccactcctcctgagagaagTcaatggccacatccctgaat	7	15	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:40589113T>C	ENST00000595687.2	-	4	250	c.41A>G	c.(40-42)gAc>gGc	p.D14G	ZNF780A_ENST00000455521.1_Missense_Mutation_p.D14G|ZNF780A_ENST00000450241.2_5'UTR|ZNF780A_ENST00000414720.2_Missense_Mutation_p.D30G|ZNF780A_ENST00000594395.1_Missense_Mutation_p.D14G|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000340963.5_Missense_Mutation_p.D14G	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	14	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTGAGAGAAGTCAATGGCCAC	0.468																																					p.D30G		Atlas-SNP	.											.	ZNF780A	156	.	0			c.A89G						.						96	81	85					19																	40589113		692	1590	2282	SO:0001583	missense	284323	exon5			GAGAAGTCAATGG	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"Zinc fingers, C2H2-type", "-"	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.41A>G	chr19.hg19:g.40589113T>C	ENSP00000472189:p.Asp14Gly	104.0	0.0		135.0	7.0	NM_001142579	E9PB48|Q6ZN87	Missense_Mutation	SNP	ENST00000595687.2	hg19	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	T	14.85	2.657103	0.47467	.	.	ENSG00000197782	ENST00000443072;ENST00000450241;ENST00000414720;ENST00000455521;ENST00000340963	T;T;T	0.02140	4.43;4.43;4.43	1.65	0.207	0.15214	Krueppel-associated box (4);	.	.	.	.	T	0.04543	0.0124	M	0.83852	2.665	0.25125	N	0.990619	P;B;B	0.36909	0.573;0.245;0.096	B;B;B	0.38842	0.283;0.096;0.211	T	0.22138	-1.0225	9	0.62326	D	0.03	.	4.6707	0.12687	0.0:0.2454:0.0:0.7546	.	14;14;30	E9PB48;O75290;O75290-2	.;Z780A_HUMAN;.	G	14;14;30;14;14	ENSP00000416294:D30G;ENSP00000400997:D14G;ENSP00000341507:D14G	ENSP00000341507:D14G	D	-	2	0	ZNF780A	45280953	0.390000	0.25213	0.355000	0.25773	0.905000	0.53344	1.816000	0.38992	-0.205000	0.10219	0.254000	0.18369	GAC	.	.		0.468	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		C	40589113	T	C	40589113	3	2	114	1	0	0	0	0	1	0	0	0	18167	1667	58	2	2026	2	ZNF780A	19	40589113	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	633580	40589113	18539870	1118	19390										
ADCK4	79934	hgsc.bcm.edu	37	chr19	41220518	41220518	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caccggtcccccgaagtaggCcccccaccttcagccacatt					rs113871093	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:41220518delC	ENST00000324464.3	-	2	321	c.20delG	c.(19-21)ggcfs	p.G7fs	ADCK4_ENST00000243583.6_Frame_Shift_Del_p.G7fs|ITPKC_ENST00000263370.2_5'Flank|ADCK4_ENST00000450541.1_Frame_Shift_Del_p.G7fs	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	7						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)	p.G7fs*69(2)		NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CCGAAGTAGGCCCCCCACCTT	0.642																																					p.G7fs		Atlas-INDEL	.											.	ADCK4	92	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.21delC						.						34	39	37					19																	41220518		2203	4300	6503	SO:0001589	frameshift_variant	79934	exon2			.	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.20delG	chr19.hg19:g.41220518delC	ENSP00000315118:p.Gly7fs	155.0	0.0		169.0	12.0	NM_001142555	Q8TAJ1|Q9HA52	Frame_Shift_Del	DEL	ENST00000324464.3	hg19	CCDS12562.1																																																																																			.	.		0.642	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876		-	41220518	C	-	41220518	7	5	114	1	0	1	0	1	0	0	0	0	290	739	26	0	1670	0	ADCK4	19	41220518	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	631405	41220518	17908465	1119	19391										
EGLN2	112398	hgsc.bcm.edu	37	chr19	41306911	41306911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcaagagaaccaggaggcagAgcgggagggtggcatgagct	19	7	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:41306911A>G	ENST00000593726.1	+	1	1462	c.434A>G	c.(433-435)gAg>gGg	p.E145G	EGLN2_ENST00000406058.2_Missense_Mutation_p.E145G|EGLN2_ENST00000594140.1_5'Flank|EGLN2_ENST00000303961.4_Missense_Mutation_p.E145G|CTC-490E21.12_ENST00000601627.1_5'Flank|RAB4B-EGLN2_ENST00000594136.1_3'UTR			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	145					cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	CAGGAGGCAGAGCGGGAGGGT	0.692																																					p.E145G		Atlas-SNP	.											.	EGLN2	31	.	0			c.A434G						.						29	25	26					19																	41306911		2200	4297	6497	SO:0001583	missense	112398	exon2			AGGCAGAGCGGGA	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"HIF prolyl hydroxylase 1"	606424	"EGL nine (C.elegans) homolog 2", "egl nine homolog 2 (C. elegans)"				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.434A>G	chr19.hg19:g.41306911A>G	ENSP00000469686:p.Glu145Gly	179.0	0.0		203.0	11.0	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Missense_Mutation	SNP	ENST00000593726.1	hg19	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.323522	0.24080	.	.	ENSG00000171570	ENST00000303961;ENST00000406058	T;T	0.27256	1.68;1.68	4.16	3.13	0.36017	.	0.358142	0.19945	N	0.102543	T	0.12305	0.0299	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22906	-1.0203	10	0.30854	T	0.27	-11.7353	9.2935	0.37802	0.8386:0.0:0.0:0.1614	.	145	Q96KS0	EGLN2_HUMAN	G	145	ENSP00000307080:E145G;ENSP00000385253:E145G	ENSP00000307080:E145G	E	+	2	0	EGLN2	45998751	0.997000	0.39634	0.005000	0.12908	0.529000	0.34654	4.294000	0.59043	0.740000	0.32651	0.482000	0.46254	GAG	.	.		0.692	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1			G	41306911	A	G	41306911	3	3	114	1	0	0	0	0	1	0	0	0	4971	304	11	2	436	2	EGLN2	19	41306911	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	86393	41306911	17822072	1120	19392										
CYP2B6	1555	hgsc.bcm.edu	37	chr19	41510031	41510031	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaggccttctctggccggggAaaaatcgccatggtcgaccc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:41510031delA	ENST00000324071.4	+	2	304	c.297delA	c.(295-297)ggafs	p.G99fs	CYP2B6_ENST00000593831.1_Frame_Shift_Del_p.G23fs|CYP2B6_ENST00000598834.1_3'UTR|CYP2B6_ENST00000330446.5_Frame_Shift_Del_p.G59fs	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	99			G -> E (in allele CYP2B6*12; dbSNP:rs36060847). {ECO:0000269|PubMed:15190123}.		cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	CTGGCCGGGGAAAAATCGCCA	0.622																																					p.G99fs		Atlas-INDEL	.											CYP2B6,NS,malignant_melanoma,0,1	CYP2B6	79	.	0			c.296delG						.						78	79	79					19																	41510031		2203	4300	6503	SO:0001589	frameshift_variant	1555	exon2			.	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"Cytochrome P450s"	2615	protein-coding gene	gene with protein product		123930	"cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6", "cytochrome P450, family 2, subfamily B", "cytochrome P450, subfamily IIB (phenobarbital-inducible)"	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.297delA	chr19.hg19:g.41510031delA	ENSP00000324648:p.Gly99fs	120.0	0.0		147.0	10.0	NM_000767	B4DWP3|Q2V565|Q9UK46	Frame_Shift_Del	DEL	ENST00000324071.4	hg19	CCDS12570.1																																																																																			.	.		0.622	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767		-	41510031	A	-	41510031	7	5	114	1	0	1	0	1	0	0	0	0	4166	233	9	0	303	0	CYP2B6	19	41510031	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	203120	41510031	17618952	1121	19393										
AXL	558	hgsc.bcm.edu	37	chr19	41725374	41725374	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgcggctgggcgtgcatggCccccaggggtgagtgatggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:41725374delC	ENST00000301178.4	+	1	267	c.77delC	c.(76-78)gccfs	p.A26fs	CTD-2195B23.3_ENST00000598541.1_RNA|AXL_ENST00000359092.3_Frame_Shift_Del_p.A26fs	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	26	Interaction with GAS6.				apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						GCGTGCATGGCCCCCAGGGGT	0.701																																					p.A26fs		Atlas-INDEL	.											.	AXL	126	.	0			c.76delG						.						12	16	14					19																	41725374		2192	4287	6479	SO:0001589	frameshift_variant	558	exon1			.	M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	2.7.10.1	"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	905	protein-coding gene	gene with protein product		109135				1656220	Standard	NM_021913		Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.77delC	chr19.hg19:g.41725374delC	ENSP00000301178:p.Ala26fs	279.0	0.0		222.0	14.0	NM_021913	Q8N5L2|Q9UD27	Frame_Shift_Del	DEL	ENST00000301178.4	hg19	CCDS12575.1																																																																																			.	.		0.701	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2			-	41725374	C	-	41725374	7	5	114	1	0	1	0	1	0	0	0	0	1238	739	26	0	79	0	AXL	19	41725374	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	215343	41725374	17403609	1122	19394										
CXCL17	284340	hgsc.bcm.edu	37	chr19	42937936	42937936	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgaattactgacctttgcacTcacattcttggccgccttcc	6	14	2	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:42937936T>C	ENST00000601181.1	-	2	367	c.152A>G	c.(151-153)gAg>gGg	p.E51G	LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000593740.2_RNA	NM_198477.1	NP_940879.1	Q6UXB2	VCC1_HUMAN	chemokine (C-X-C motif) ligand 17	51					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)	extracellular region (GO:0005576)				large_intestine(2)|skin(1)	3		Prostate(69;0.00899)				ACCTTTGCACTCACATTCTTG	0.567											OREG0025504	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E51G		Atlas-SNP	.											.	CXCL17	8	.	0			c.A152G						.						179	148	158					19																	42937936		2203	4300	6503	SO:0001583	missense	284340	exon2			TTGCACTCACATT		CCDS12608.1	19q13.2	2007-10-15				ENSG00000189377			19232	protein-coding gene	gene with protein product		611387				17201934	Standard	NM_198477		Approved	Dcip1, UNQ473, DMC, VCC1	uc002otu.3	Q6UXB2		ENST00000601181.1:c.152A>G	chr19.hg19:g.42937936T>C	ENSP00000472467:p.Glu51Gly	99.0	0.0	912	111.0	5.0	NM_198477	A8KAC0	Missense_Mutation	SNP	ENST00000601181.1	hg19	CCDS12608.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.875696	0.72180	.	.	ENSG00000189377	ENST00000341918	.	.	.	4.7	3.61	0.41365	.	0.150264	0.31092	N	0.008275	T	0.33876	0.0878	L	0.29908	0.895	0.31048	N	0.715566	P	0.51351	0.944	P	0.47645	0.553	T	0.38950	-0.9637	9	0.72032	D	0.01	-12.1552	7.1759	0.25744	0.1986:0.0:0.0:0.8014	.	51	Q6UXB2	VCC1_HUMAN	G	51	.	ENSP00000345317:E51G	E	-	2	0	CXCL17	47629776	0.981000	0.34729	1.000000	0.80357	0.995000	0.86356	1.821000	0.39041	2.106000	0.64143	0.443000	0.29094	GAG	.	.		0.567	CXCL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463872.1			C	42937936	T	C	42937936	3	2	114	1	0	0	0	0	1	0	0	0	4086	1551	54	2	219	2	CXCL17	19	42937936	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1212562	42937936	16191047	1123	19395										
ZNF284	342909	hgsc.bcm.edu	37	chr19	44590888	44590888	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagggccattcacatcagagAgcctatagagaagaagaact	10	9	2	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:44590888A>G	ENST00000421176.3	+	5	1473	c.1257A>G	c.(1255-1257)agA>agG	p.R419R	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	419					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				CACATCAGAGAGCCTATAGAG	0.438																																					p.R419R		Atlas-SNP	.											.	ZNF284	38	.	0			c.A1257G						.						135	142	140					19																	44590888		2136	4263	6399	SO:0001819	synonymous_variant	342909	exon5			TCAGAGAGCCTAT	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"Zinc fingers, C2H2-type", "-"	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.1257A>G	chr19.hg19:g.44590888A>G		119.0	0.0		117.0	6.0	NM_001037813	Q86WM1	Silent	SNP	ENST00000421176.3	hg19	CCDS46099.1																																																																																			.	.		0.438	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813		G	44590888	A	G	44590888	2	3	114	1	0	0	0	0	0	0	0	1	17836	301	11	2		2	ZNF284	19	44590888	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1652952	44590888	14538095	1124	19396										
PVRL2	5819	hgsc.bcm.edu	37	chr19	45375206	45375206	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caaagagggccgcccacctgCccggatctcctggctctcat	10	17	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:45375206C>T	ENST00000252483.5	+	3	575	c.575C>T	c.(574-576)gCc>gTc	p.A192V	PVRL2_ENST00000252485.4_Missense_Mutation_p.A192V	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	192	Ig-like C2-type 1.				acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		CGCCCACCTGCCCGGATCTCC	0.622																																					p.A192V		Atlas-SNP	.											.	PVRL2	58	.	0			c.C575T						.						38	37	37					19																	45375206		2203	4300	6503	SO:0001583	missense	5819	exon3			CACCTGCCCGGAT	X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.575C>T	chr19.hg19:g.45375206C>T	ENSP00000252483:p.Ala192Val	102.0	0.0		112.0	15.0	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Missense_Mutation	SNP	ENST00000252483.5	hg19	CCDS42576.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737142	0.69304	.	.	ENSG00000130202	ENST00000252483;ENST00000252485	T;T	0.76709	-1.04;-1.04	4.25	4.25	0.50352	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000077	D	0.89687	0.6787	M	0.92923	3.36	0.42513	D	0.992971	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.993	D	0.91776	0.5431	10	0.87932	D	0	.	12.0078	0.53270	0.0:1.0:0.0:0.0	.	192;192	Q92692;Q92692-2	PVRL2_HUMAN;.	V	192	ENSP00000252483:A192V;ENSP00000252485:A192V	ENSP00000252483:A192V	A	+	2	0	PVRL2	50067046	0.937000	0.31787	0.990000	0.47175	0.576000	0.36127	3.927000	0.56499	2.190000	0.69967	0.561000	0.74099	GCC	.	.		0.622	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856		T	45375206	C	T	45375206	3	4	114	1	0	0	0	0	1	0	0	0	12855	739	26	3	585	3	PVRL2	19	45375206	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	784318	45375206	13753777	1125	19397										
CKM	1158	hgsc.bcm.edu	37	chr19	45811713	45811713	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggaaaacctccttcatgttgCcccccttctccatggagatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:45811713delC	ENST00000221476.3	-	6	905	c.731delG	c.(730-732)ggcfs	p.G244fs		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	244	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.N245fs*17(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	CTTCATGTTGCCCCCCTTCTC	0.577																																					p.G244fs		Atlas-INDEL	.											.,1	CKM	40	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.732delC						.						119	96	104					19																	45811713		2203	4300	6503	SO:0001589	frameshift_variant	1158	exon6			.	M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.731delG	chr19.hg19:g.45811713delC	ENSP00000221476:p.Gly244fs	104.0	0.0		162.0	12.0	NM_001824	Q96QL9	Frame_Shift_Del	DEL	ENST00000221476.3	hg19	CCDS12659.1																																																																																			.	.		0.577	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1			-	45811713	C	-	45811713	7	5	114	1	0	1	0	1	0	0	0	0	3450	739	26	0	426	0	CKM	19	45811713	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	436507	45811713	13317270	1126	19398										
ERCC1	2067	hgsc.bcm.edu	37	chr19	45916842	45916842	+	Intron	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgtgtctggtctttggttcTtttttcaccttaaaactttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:45916842delT	ENST00000300853.3	-	9	1435				ERCC1_ENST00000591636.1_Intron|ERCC1_ENST00000013807.5_Frame_Shift_Del_p.K312fs|ERCC1_ENST00000588738.1_Intron|ERCC1_ENST00000589165.1_Intron|ERCC1_ENST00000423698.2_Intron|ERCC1_ENST00000340192.7_Intron	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1						cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		tcTTTGGTTCTTTTTTCACCT	0.512								Nucleotide excision repair (NER)																													p.E313fs		Atlas-INDEL	.											.	ERCC1	46	.	0			c.937delG						.						122	127	125					19																	45916842		2203	4300	6503	SO:0001627	intron_variant	2067	exon8			.		CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.843+92A>-	chr19.hg19:g.45916842delT		132.0	0.0		166.0	10.0	NM_202001	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Frame_Shift_Del	DEL	ENST00000300853.3	hg19	CCDS12662.1																																																																																			.	.		0.512	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983		-	45916842	T	-	45916842	6	5	114	0	1	1	0	1	0	0	0	0	5214	1606	56	0		0	ERCC1	19	45916842	Intron	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	105129	45916842	13212141	1127	19399										
DMPK	1760	hgsc.bcm.edu	37	chr19	46283130	46283130	+	Intron	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcaccacgatgggctccgctGggggggtggtgggggaaaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:46283130delG	ENST00000291270.4	-	2	286				DMPK_ENST00000343373.4_Frame_Shift_Del_p.P63fs|DMPK_ENST00000458663.2_Intron|AC011530.4_ENST00000593999.1_Intron|DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000354227.5_Intron|DMPK_ENST00000447742.2_Intron|DMPK_ENST00000600757.1_Frame_Shift_Del_p.P63fs	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase						cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		GGGCTCCGCTGGGGGGGTGGT	0.617																																					p.P63fs	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-INDEL	.											.	DMPK	74	.	0			c.189delA						.						37	40	39					19																	46283130		2203	4300	6503	SO:0001627	intron_variant	1760	exon1			.	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"dystrophia myotonica 1", "DM protein kinase", "myotonin protein kinase A", "myotonic dystrophy associated protein kinase", "thymopoietin homolog"	605377	"dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.161-3C>-	chr19.hg19:g.46283130delG		70.0	0.0		107.0	10.0	NM_001081563	E5KR08|Q16205|Q6P5Z6	Frame_Shift_Del	DEL	ENST00000291270.4	hg19	CCDS12674.1																																																																																			.	.		0.617	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409		-	46283130	G	-	46283130	6	5	114	0	1	1	0	1	0	0	0	0	4586	1348	47	0		0	DMPK	19	46283130	Intron	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	366288	46283130	12845853	1128	19400										
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305864	48305864	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcctgaaattgggcctgggAttggggctgggatcgggctt	19	7	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:48305864A>G	ENST00000322175.3	-	2	559	c.404T>C	c.(403-405)aTc>aCc	p.I135T	TPRX1_ENST00000535759.1_Missense_Mutation_p.I232T|TPRX1_ENST00000543508.1_Missense_Mutation_p.I135T	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	135	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		tgggcctgggattggggctgg	0.642																																					p.I135T	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.T404C						.						19	17	18					19																	48305864		2047	4026	6073	SO:0001583	missense	284355	exon2			CCTGGGATTGGGG		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"Homeoboxes / PRD class"	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.404T>C	chr19.hg19:g.48305864A>G	ENSP00000323455:p.Ile135Thr	108.0	0.0		136.0	6.0	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	hg19	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.719608	0.00092	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.40476	1.03;1.03;1.03	0.383	-0.766	0.11020	.	.	.	.	.	T	0.16385	0.0394	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.08055	0.003	T	0.24728	-1.0152	8	0.11794	T	0.64	.	.	.	.	.	135	Q8N7U7	TPRX1_HUMAN	T	135;232;135	ENSP00000323455:I135T;ENSP00000438832:I232T;ENSP00000438712:I135T	ENSP00000323455:I135T	I	-	2	0	TPRX1	52997676	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-1.564000	0.02152	-0.783000	0.04534	-0.834000	0.03071	ATC	.	.		0.642	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		G	48305864	A	G	48305864	3	3	114	1	0	0	0	0	1	0	0	0	16437	333	12	2	835	2	TPRX1	19	48305864	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2022734	48305864	10823119	1129	19401										
LIG1	3978	hgsc.bcm.edu	37	chr19	48665558	48665558	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctctgctgctattggatgccTccttctcaggcttctttgct	8	13	3	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:48665558T>C	ENST00000263274.7	-	3	487	c.68A>G	c.(67-69)gAg>gGg	p.E23G	LIG1_ENST00000427526.2_Intron|LIG1_ENST00000536218.1_Missense_Mutation_p.E23G|LIG1_ENST00000599165.1_5'UTR	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	23					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	ATTGGATGCCTCCTTCTCAGG	0.458								Nucleotide excision repair (NER)																													p.E23G		Atlas-SNP	.											.	LIG1	151	.	0			c.A68G						.						193	186	188					19																	48665558		2203	4300	6503	SO:0001583	missense	3978	exon3			GATGCCTCCTTCT		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.68A>G	chr19.hg19:g.48665558T>C	ENSP00000263274:p.Glu23Gly	90.0	0.0		102.0	5.0	NM_000234	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	hg19	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.220080	0.58560	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000536218;ENST00000542460	T;T;T	0.56611	0.49;0.45;1.89	4.23	3.1	0.35709	.	0.610961	0.15354	N	0.266809	T	0.40694	0.1127	L	0.60455	1.87	0.27667	N	0.946872	B;B	0.34290	0.447;0.201	B;B	0.26969	0.075;0.039	T	0.21177	-1.0253	10	0.24483	T	0.36	-21.4369	7.1349	0.25523	0.0:0.0:0.2299:0.7701	.	23;23	F5GZ28;P18858	.;DNLI1_HUMAN	G	23;55;23;23	ENSP00000263274:E23G;ENSP00000441531:E23G;ENSP00000445928:E23G	ENSP00000263274:E23G	E	-	2	0	LIG1	53357370	0.953000	0.32496	0.893000	0.35052	0.961000	0.63080	1.800000	0.38833	1.850000	0.53721	0.533000	0.62120	GAG	.	.		0.458	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		C	48665558	T	C	48665558	3	2	114	1	0	0	0	0	1	0	0	0	8790	1551	54	2	2795	2	LIG1	19	48665558	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	359694	48665558	10463425	1130	19402										
TULP2	7288	hgsc.bcm.edu	37	chr19	49400644	49400644	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctcatagcagcgagctcatgCcccaggatgctgagagagac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:49400644delC	ENST00000221399.3	-	3	186	c.42delG	c.(40-42)gggfs	p.G14fs	NUCB1_ENST00000405315.4_5'Flank|NUCB1_ENST00000407032.1_5'Flank	NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	14					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		CGAGCTCATGCCCCAGGATGC	0.597																																					p.H15fs		Atlas-INDEL	.											.	TULP2	60	.	0			c.43delC						.						134	94	107					19																	49400644		2203	4300	6503	SO:0001589	frameshift_variant	7288	exon3			.	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"cancer/testis antigen 65"	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.42delG	chr19.hg19:g.49400644delC	ENSP00000221399:p.Gly14fs	124.0	0.0		153.0	10.0	NM_003323	Q8TC50	Frame_Shift_Del	DEL	ENST00000221399.3	hg19	CCDS12739.1																																																																																			.	.		0.597	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323		-	49400644	C	-	49400644	7	5	114	1	0	1	0	1	0	0	0	0	16789	726	26	0	1564	0	TULP2	19	49400644	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	735086	49400644	9728339	1131	19403										
SCAF1	58506	hgsc.bcm.edu	37	chr19	50148321	50148321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtctcgagggaagacagaggAgtcgggggaggatcggggcg	22	6	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:50148321A>G	ENST00000360565.3	+	2	162	c.38A>G	c.(37-39)gAg>gGg	p.E13G		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	13					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		AAGACAGAGGAGTCGGGGGAG	0.612																																					p.E13G		Atlas-SNP	.											.	SCAF1	78	.	0			c.A38G						.						49	45	46					19																	50148321		2203	4300	6503	SO:0001583	missense	58506	exon2			CAGAGGAGTCGGG	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.38A>G	chr19.hg19:g.50148321A>G	ENSP00000353769:p.Glu13Gly	60.0	0.0		85.0	6.0	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	hg19	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	8.230	0.804409	0.16467	.	.	ENSG00000126461	ENST00000360565;ENST00000447618	T	0.50548	0.74	4.16	4.16	0.48862	.	0.000000	0.33023	U	0.005369	T	0.50154	0.1599	N	0.19112	0.55	0.29291	N	0.869341	D	0.76494	0.999	D	0.75484	0.986	T	0.47394	-0.9121	10	0.87932	D	0	-25.6664	9.5033	0.39031	1.0:0.0:0.0:0.0	.	13	Q9H7N4	SFR19_HUMAN	G	13	ENSP00000353769:E13G	ENSP00000353769:E13G	E	+	2	0	SCAF1	54840133	1.000000	0.71417	1.000000	0.80357	0.276000	0.26787	2.853000	0.48317	1.743000	0.51761	0.254000	0.18369	GAG	.	.		0.612	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		G	50148321	A	G	50148321	3	3	114	1	0	0	0	0	1	0	0	0	13883	304	11	2	40	2	SCAF1	19	50148321	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	747677	50148321	8980662	1132	19404										
SCAF1	58506	hgsc.bcm.edu	37	chr19	50156035	50156035	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtcatccaagaaggcccggCcccccaaggagtcggcgcct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:50156035delC	ENST00000360565.3	+	7	2513	c.2389delC	c.(2389-2391)cccfs	p.P798fs		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	798	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		GAAGGCCCGGCCCCCCAAGGA	0.667																																					p.R796fs		Atlas-INDEL	.											.	SCAF1	78	.	0			c.2388delG						.						37	47	44					19																	50156035		2199	4300	6499	SO:0001589	frameshift_variant	58506	exon7			.	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.2389delC	chr19.hg19:g.50156035delC	ENSP00000353769:p.Pro798fs	113.0	0.0		159.0	13.0	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Frame_Shift_Del	DEL	ENST00000360565.3	hg19	CCDS33074.1																																																																																			.	.		0.667	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		-	50156035	C	-	50156035	7	5	114	1	0	1	0	1	0	0	0	0	13883	739	26	0	2411	0	SCAF1	19	50156035	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	7714	50156035	8972948	1133	19405										
TBC1D17	79735	hgsc.bcm.edu	37	chr19	50386052	50386052	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcctcggccaaccgtggagcGgggccctccagttacagagg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:50386052delG	ENST00000221543.5	+	8	1129	c.830delG	c.(829-831)cggfs	p.R277fs	TBC1D17_ENST00000535102.2_Frame_Shift_Del_p.R244fs	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	277	Required for interaction with OPTN.				autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		ACCGTGGAGCGGGGCCCTCCA	0.682																																					p.R277fs		Atlas-INDEL	.											.	TBC1D17	39	.	0			c.829delC						.						19	22	21					19																	50386052		2201	4296	6497	SO:0001589	frameshift_variant	79735	exon8			.	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.830delG	chr19.hg19:g.50386052delG	ENSP00000221543:p.Arg277fs	143.0	0.0		181.0	11.0	NM_024682	B4DT12|B9A6L8|F5H1W7	Frame_Shift_Del	DEL	ENST00000221543.5	hg19	CCDS12785.1																																																																																			.	.		0.682	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682		-	50386052	G	-	50386052	7	5	114	1	0	1	0	1	0	0	0	0	15621	1116	39	0	860	0	TBC1D17	19	50386052	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	230017	50386052	8742931	1134	19406										
NAPSA	9476	hgsc.bcm.edu	37	chr19	50868809	50868809	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	accataccggatcagtgtggCcccggaaggctccacattca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:50868809delC	ENST00000253719.2	-	1	278	c.70delG	c.(70-72)gccfs	p.A24fs	NR1H2_ENST00000600978.1_Intron|CTB-191K22.6_ENST00000597049.1_RNA|NR1H2_ENST00000542413.1_Intron	NM_004851.1	NP_004842.1	O96009	NAPSA_HUMAN	napsin A aspartic peptidase	24					membrane protein proteolysis (GO:0033619)|proteolysis (GO:0006508)|surfactant homeostasis (GO:0043129)	alveolar lamellar body (GO:0097208)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)|peptidase activity (GO:0008233)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		ATCAGTGTGGCCCCGGAAGGC	0.592																																					p.A24fs		Atlas-INDEL	.											.	NAPSA	38	.	0			c.71delC						.						67	60	62					19																	50868809		2203	4300	6503	SO:0001589	frameshift_variant	9476	exon1			.	AF090386	CCDS12794.1	19q13.33	2011-08-25				ENSG00000131400			13395	protein-coding gene	gene with protein product	"kidney-derived aspartic protease-like protein"	605631					Standard	NM_004851		Approved	NAP1, NAPA, Kdap, KAP	uc002prx.3	O96009		ENST00000253719.2:c.70delG	chr19.hg19:g.50868809delC	ENSP00000253719:p.Ala24fs	71.0	0.0		170.0	13.0	NM_004851	Q8WWD9	Frame_Shift_Del	DEL	ENST00000253719.2	hg19	CCDS12794.1																																																																																			.	.		0.592	NAPSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464714.1	NM_004851		-	50868809	C	-	50868809	7	5	114	1	0	1	0	1	0	0	0	0	10175	739	26	0	1228	0	NAPSA	19	50868809	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	482757	50868809	8260174	1135	19407										
SYT3	84258	hgsc.bcm.edu	37	chr19	51133356	51133356	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggtaagggcagggcaggtggCcgctcctcactgctggggtc					rs10407511	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:51133356delC	ENST00000338916.4	-	3	1380	c.747delG	c.(745-747)cggfs	p.R249fs	SYT3_ENST00000600079.1_Frame_Shift_Del_p.R249fs|SYT3_ENST00000544769.1_Frame_Shift_Del_p.R249fs|SYT3_ENST00000593901.1_Frame_Shift_Del_p.R249fs	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	249					calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		GGGCAGGTGGCCGCTCCTCAC	0.657																																					p.P250fs		Atlas-INDEL	.											.	SYT3	85	.	0			c.748delC						.						32	32	32					19																	51133356		2203	4300	6503	SO:0001589	frameshift_variant	84258	exon3			.	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.747delG	chr19.hg19:g.51133356delC	ENSP00000340914:p.Arg249fs	106.0	0.0		145.0	10.0	NM_032298	Q8N5Z1|Q8N640	Frame_Shift_Del	DEL	ENST00000338916.4	hg19	CCDS12798.1																																																																																			.	.		0.657	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		-	51133356	C	-	51133356	7	5	114	1	0	1	0	1	0	0	0	0	15490	726	26	0	1049	0	SYT3	19	51133356	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	264547	51133356	7995627	1136	19408										
KLK6	5653	hgsc.bcm.edu	37	chr19	51470427	51470427	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttacagtgtagactcacggTtttttgcagtgggcagctgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:51470427delT	ENST00000376851.3	-	3	634	c.195delA	c.(193-195)aaafs	p.K65fs	KLK6_ENST00000376853.4_Frame_Shift_Del_p.K65fs|KLK6_ENST00000310157.2_Frame_Shift_Del_p.K65fs|CTB-147C22.9_ENST00000594512.1_RNA|KLK6_ENST00000424910.2_Intron|KLK6_ENST00000594641.1_Frame_Shift_Del_p.K65fs|KLK6_ENST00000391808.1_5'UTR	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	65	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		AGACTCACGGTTTTTTGCAGT	0.557																																					p.P66fs		Atlas-INDEL	.											.	KLK6	35	.	0			c.196delC						.						102	92	95					19																	51470427		2203	4300	6503	SO:0001589	frameshift_variant	5653	exon3			.	U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"Kallikreins", "Serine peptidases / Serine peptidases"	6367	protein-coding gene	gene with protein product		602652	"protease, serine, 18", "kallikrein 6 (neurosin, zyme)"	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.195delA	chr19.hg19:g.51470427delT	ENSP00000366047:p.Lys65fs	104.0	0.0		190.0	13.0	NM_001012964	A6NJA1|A8MW09|Q6H301	Frame_Shift_Del	DEL	ENST00000376851.3	hg19	CCDS12811.1																																																																																			.	.		0.557	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774		-	51470427	T	-	51470427	7	5	114	1	0	1	0	1	0	0	0	0	8417	1722	60	0	555	0	KLK6	19	51470427	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	337071	51470427	7658556	1137	19409										
CEACAM18	729767	hgsc.bcm.edu	37	chr19	51981947	51981947	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tggaggagggtcttcctcatGggtaagagatgctggatgct	16	6	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:51981947G>C	ENST00000396477.4	+	1	72	c.51G>C	c.(49-51)atG>atC	p.M17I	CEACAM18_ENST00000451626.1_Splice_Site_p.M78I	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	17										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TCTTCCTCATGGGTAAGAGAT	0.632																																					p.M78I		Atlas-SNP	.											CEACAM18_ENST00000451626,NS,chondrosarcoma,0,1	CEACAM18	96	.	0			c.G234C						.						25	27	26					19																	51981947		1952	4167	6119	SO:0001630	splice_region_variant	729767	exon2			CCTCATGGGTAAG			19q13.41	2013-01-29				ENSG00000213822		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.52+1G>C	chr19.hg19:g.51981947G>C		40.0	0.0		72.0	0.0	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	hg19		.	.	.	.	.	.	.	.	.	.	.	8.544	0.873956	0.17395	.	.	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.04758	3.56	2.8	0.459	0.16678	.	.	.	.	.	T	0.02455	0.0075	N	0.08118	0	0.18873	N	0.999987	B	0.10296	0.003	B	0.01281	0.0	T	0.44128	-0.9348	9	0.66056	D	0.02	.	2.992	0.05986	0.1641:0.0:0.5758:0.2601	.	78	A8MTB9	CEA18_HUMAN	I	78;17;17	ENSP00000402203:M78I	ENSP00000379738:M17I	M	+	3	0	CEACAM18	56673759	0.305000	0.24481	0.417000	0.26559	0.127000	0.20565	-0.370000	0.07523	0.200000	0.20447	0.655000	0.94253	ATG	.	.		0.632	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		Missense_Mutation	C	51981947	G	C	51981947	5	2	114	1	0	0	0	0	0	0	1	0	3191	1362	47	4	240	4	CEACAM18	19	51981947	Splice_Site	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	511520	51981947	7147036	1138	19410										
ZNF813	126017	hgsc.bcm.edu	37	chr19	53995078	53995078	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgtaatgaatgtggcaaggTttttaatcgaaaaacacacc					rs111582892	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:53995078delT	ENST00000396403.4	+	4	1720	c.1592delT	c.(1591-1593)gttfs	p.V531fs	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	531					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		TGTGGCAAGGTTTTTAATCGA	0.363																																					p.V531fs		Atlas-INDEL	.											.	ZNF813	81	.	0			c.1591delG						.						50	54	52					19																	53995078		2198	4295	6493	SO:0001589	frameshift_variant	126017	exon4			.	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"Zinc fingers, C2H2-type", "-"	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.1592delT	chr19.hg19:g.53995078delT	ENSP00000379684:p.Val531fs	108.0	0.0		164.0	11.0	NM_001004301		Frame_Shift_Del	DEL	ENST00000396403.4	hg19	CCDS46172.1																																																																																			.	.		0.363	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301		-	53995078	T	-	53995078	7	5	114	1	0	1	0	1	0	0	0	0	18190	1725	60	0	1602	0	ZNF813	19	53995078	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2013131	53995078	5133905	1139	19411										
KIR2DL3	3804	hgsc.bcm.edu	37	chr19	55263169	55263169	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcctcttcatcctcctcctcTtctttctccttcatcgctgg	3	18	6	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:55263169T>C	ENST00000342376.3	+	6	815	c.784T>C	c.(784-786)Ttc>Ctc	p.F262L	KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR2DL3_ENST00000434419.2_Intron	NM_015868.2	NP_056952.2	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	262					immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		cctcctcctcttctttctcct	0.512																																					p.F262L		Atlas-SNP	.											.	KIR2DL3	68	.	0			c.T784C						.						137	112	121					19																	55263169		1408	2560	3968	SO:0001583	missense	3804	exon6			CTCCTCTTCTTTC	L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6331	protein-coding gene	gene with protein product		604938				7749980, 8662091	Standard	XM_006725426		Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000342376.3:c.784T>C	chr19.hg19:g.55263169T>C	ENSP00000342215:p.Phe262Leu	48.0	0.0		116.0	5.0	NM_015868	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	Missense_Mutation	SNP	ENST00000342376.3	hg19	CCDS33107.1	.	.	.	.	.	.	.	.	.	.	T	8.827	0.939009	0.18281	.	.	ENSG00000243772	ENST00000342376	T	0.00455	7.31	0.635	0.635	0.17723	.	.	.	.	.	T	0.00384	0.0012	N	0.25094	0.71	0.09310	N	0.999999	B;P;B;B	0.46395	0.0;0.877;0.001;0.001	B;P;B;B	0.51866	0.001;0.682;0.005;0.005	T	0.57248	-0.7844	8	0.62326	D	0.03	.	.	.	.	.	262;164;262;262	E3NZD7;P43628-2;P43628;E3NZD8	.;.;KI2L3_HUMAN;.	L	262	ENSP00000342215:F262L	ENSP00000342215:F262L	F	+	1	0	KIR2DL3	59954981	0.007000	0.16637	0.061000	0.19648	0.079000	0.17450	-0.023000	0.12456	0.516000	0.28340	0.248000	0.18094	TTC	.	.		0.512	KIR2DL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141150.1			C	55263169	T	C	55263169	3	2	114	1	0	0	0	0	1	0	0	0	8326	1609	56	2	806	2	KIR2DL3	19	55263169	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1268091	55263169	3865814	1140	19412										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55508725	55508725	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctccgttcagttgtgaagacCtctgctctgccctcagctgc	9	15	4	2	rs61735074	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:55508725C>A	ENST00000543010.1	+	12	3063	c.2920C>A	c.(2920-2922)Ctc>Atc	p.L974I	NLRP2_ENST00000339757.7_Missense_Mutation_p.L952I|NLRP2_ENST00000263437.6_Missense_Mutation_p.L971I|NLRP2_ENST00000448584.2_Missense_Mutation_p.L974I|NLRP2_ENST00000537859.1_Missense_Mutation_p.L952I|NLRP2_ENST00000538819.1_Missense_Mutation_p.L950I|NLRP2_ENST00000427260.2_Missense_Mutation_p.L951I|NLRP2_ENST00000391721.4_Missense_Mutation_p.L950I	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	974					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TTGTGAAGACCTCTGCTCTGC	0.542																																					p.L974I		Atlas-SNP	.											.	NLRP2	161	.	0			c.C2920A						.						187	157	167					19																	55508725		2203	4300	6503	SO:0001583	missense	55655	exon12			GAAGACCTCTGCT	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.2920C>A	chr19.hg19:g.55508725C>A	ENSP00000445135:p.Leu974Ile	232.0	0.0		316.0	156.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	C	13.36	2.214248	0.39102	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0	3.2	0.921	0.19403	.	.	.	.	.	T	0.70745	0.3259	M	0.65320	2	0.09310	N	1	D;D;D;D;D	0.71674	0.998;0.994;0.994;0.994;0.99	D;D;D;D;D	0.70935	0.971;0.971;0.917;0.971;0.936	T	0.57142	-0.7862	9	0.59425	D	0.04	.	5.7987	0.18401	0.0:0.7173:0.0:0.2827	.	951;952;971;950;974	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	I	974;950;952;974;952;951;950;971	ENSP00000445135:L974I;ENSP00000375601:L950I;ENSP00000344074:L952I;ENSP00000409370:L974I;ENSP00000440601:L952I;ENSP00000402474:L951I;ENSP00000441133:L950I;ENSP00000263437:L971I	ENSP00000263437:L971I	L	+	1	0	NLRP2	60200537	0.195000	0.23338	0.014000	0.15608	0.031000	0.12232	1.773000	0.38563	0.153000	0.19213	0.561000	0.74099	CTC	.	C|0.981;G|0.019		0.542	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		A	55508725	C	A	55508725	3	1	114	1	0	0	0	0	1	0	0	0	10486	681	24	3	2962	3	NLRP2	19	55508725	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	245556	55508725	3620258	1141	19413										
ZNF805	390980	hgsc.bcm.edu	37	chr19	57766049	57766049	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcgtacataccaaagagaaaCcccacaagtgtcttcactgt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:57766049delC	ENST00000414468.2	+	4	1862	c.1862delC	c.(1861-1863)accfs	p.T621fs	ZNF805_ENST00000535550.1_Frame_Shift_Del_p.T488fs|ZNF805_ENST00000354309.4_Frame_Shift_Del_p.T488fs	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	621					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(3)|lung(1)|stomach(1)	9						CAAAGAGAAACCCCACAAGTG	0.393																																					p.T621fs		Atlas-INDEL	.											.	ZNF805	30	.	0			c.1861delA						.						37	33	34					19																	57766049		692	1591	2283	SO:0001589	frameshift_variant	390980	exon4			.	AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"Zinc fingers, C2H2-type", "-"	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.1862delC	chr19.hg19:g.57766049delC	ENSP00000412999:p.Thr621fs	129.0	0.0		205.0	13.0	NM_001023563	B4DNM5	Frame_Shift_Del	DEL	ENST00000414468.2	hg19	CCDS46207.1																																																																																			.	.		0.393	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1	NM_001023563		-	57766049	C	-	57766049	7	5	114	1	0	1	0	1	0	0	0	0	18187	507	18	0	1876	0	ZNF805	19	57766049	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2257324	57766049	1362934	1142	19414										
ZNF17	7565	hgsc.bcm.edu	37	chr19	57932806	57932806	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atgtggaagagtctttaaccAaaattctcatctcattcagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:57932806delA	ENST00000601808.1	+	3	2159	c.1946delA	c.(1945-1947)caafs	p.Q649fs	ZNF17_ENST00000307658.7_Frame_Shift_Del_p.Q651fs|AC004076.7_ENST00000597410.1_Intron	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	649					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		GTCTTTAACCAAAATTCTCAT	0.388																																					p.Q649fs	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-INDEL	.											.	ZNF17	49	.	0			c.1945delC						.						50	53	52					19																	57932806		2119	4282	6401	SO:0001589	frameshift_variant	7565	exon3			.	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"Zinc fingers, C2H2-type", "-"	12958	protein-coding gene	gene with protein product			"zinc finger protein 17 (HPF3, KOX 10)"			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.1946delA	chr19.hg19:g.57932806delA	ENSP00000471905:p.Gln649fs	120.0	0.0		177.0	11.0	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Frame_Shift_Del	DEL	ENST00000601808.1	hg19	CCDS42636.1																																																																																			.	.		0.388	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959		-	57932806	A	-	57932806	7	5	114	1	0	1	0	1	0	0	0	0	17758	130	5	0	1956	0	ZNF17	19	57932806	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	166757	57932806	1196177	1143	19415										
ZNF8	7554	hgsc.bcm.edu	37	chr19	58806805	58806805	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctggctttgtttgacatccAaaaaatcatgcaagagaaaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:58806805delA	ENST00000196548.5	+	4	1762	c.1631delA	c.(1630-1632)caafs	p.Q544fs	ZNF8_ENST00000608843.1_Frame_Shift_Del_p.Q544fs|AC010642.1_ENST00000591325.1_3'UTR			P17098	ZNF8_HUMAN	zinc finger protein 8	544					BMP signaling pathway (GO:0030509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	19		all_cancers(17;6.46e-05)|Lung NSC(17;0.0233)|all_neural(62;0.0381)|all_epithelial(17;0.0427)|all_lung(17;0.057)|Ovarian(87;0.17)|Colorectal(82;0.227)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.00619)		TTTGACATCCAAAAAATCATG	0.507																																					p.Q544fs		Atlas-INDEL	.											.	ZNF8	60	.	0			c.1630delC						.						43	46	45					19																	58806805		2201	4298	6499	SO:0001589	frameshift_variant	7554	exon4			.	M29581	CCDS12974.1	19q13.43	2013-01-08	2006-05-09					"Zinc fingers, C2H2-type", "-"	13154	protein-coding gene	gene with protein product		194532	"zinc finger protein 8 (clone HF.18)"			2106481	Standard	NM_021089		Approved	HF.18, Zfp128	uc002qry.1	P17098		ENST00000196548.5:c.1631delA	chr19.hg19:g.58806805delA	ENSP00000196548:p.Gln544fs	90.0	0.0		117.0	10.0	NM_021089	Q6PI99	Frame_Shift_Del	DEL	ENST00000196548.5	hg19	CCDS12974.1																																																																																			.	.		0.507	ZNF8-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000459135.1	NM_021089		-	58806805	A	-	58806805	7	5	114	1	0	1	0	1	0	0	0	0	18182	130	5	0	1645	0	ZNF8	19	58806805	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	873999	58806805	322178	1144	19416										
ZNF324B	388569	hgsc.bcm.edu	37	chr19	58967548	58967548	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcagccagggctcctcgctcTttttgcaccagcgcgtgcac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:58967548delT	ENST00000336614.4	+	4	1344	c.1237delT	c.(1237-1239)tttfs	p.F413fs	ZNF324B_ENST00000391696.1_Frame_Shift_Del_p.F403fs|ZNF324B_ENST00000545523.1_Frame_Shift_Del_p.F413fs	NM_207395.2	NP_997278.2	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CTCCTCGCTCTTTTTGCACCA	0.657																																					p.L412fs		Atlas-INDEL	.											.	ZNF324B	58	.	0			c.1236delC						.						49	51	50					19																	58967548		2203	4300	6503	SO:0001589	frameshift_variant	388569	exon4			.	AK127750	CCDS33138.1	19q13.43	2013-01-08				ENSG00000249471		"Zinc fingers, C2H2-type", "-"	33107	protein-coding gene	gene with protein product							Standard	NM_207395		Approved	FLJ45850	uc002qsv.1	Q6AW86		ENST00000336614.4:c.1237delT	chr19.hg19:g.58967548delT	ENSP00000337473:p.Phe413fs	139.0	0.0		226.0	14.0	NM_207395	B2RTZ6|Q6ZMX8|Q6ZS42	Frame_Shift_Del	DEL	ENST00000336614.4	hg19	CCDS33138.1																																																																																			.	.		0.657	ZNF324B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467038.1	NM_207395		-	58967548	T	-	58967548	7	5	114	1	0	1	0	1	0	0	0	0	17860	1609	56	0	1247	0	ZNF324B	19	58967548	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	160743	58967548	161435	1145	19417										
ZNF446	55663	hgsc.bcm.edu	37	chr19	58989035	58989035	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtcctgaagcaggaggtgcTccctgcagcccagaagacag	13	12	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:58989035T>C	ENST00000594369.1	+	3	755	c.374T>C	c.(373-375)cTc>cCc	p.L125P	ZNF446_ENST00000335841.4_Missense_Mutation_p.L125P|CTD-2619J13.23_ENST00000598051.1_RNA|ZNF446_ENST00000596341.1_Missense_Mutation_p.L125P	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	125					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CAGGAGGTGCTCCCTGCAGCC	0.602																																					p.L125P		Atlas-SNP	.											.	ZNF446	22	.	0			c.T374C						.						55	59	58					19																	58989035		2203	4300	6503	SO:0001583	missense	55663	exon3			AGGTGCTCCCTGC		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"Zinc fingers, C2H2-type", "-", "-", "-"	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.374T>C	chr19.hg19:g.58989035T>C	ENSP00000472802:p.Leu125Pro	106.0	0.0		135.0	6.0	NM_017908		Missense_Mutation	SNP	ENST00000594369.1	hg19	CCDS12982.1	.	.	.	.	.	.	.	.	.	.	T	4.962	0.178769	0.09443	.	.	ENSG00000083838	ENST00000335841;ENST00000540481;ENST00000539679	T	0.06768	3.26	4.35	3.33	0.38152	Transcription regulator SCAN (1);	0.000000	0.32952	N	0.005441	T	0.06416	0.0165	L	0.27053	0.805	0.26798	N	0.969264	B;B;B	0.27450	0.174;0.041;0.179	B;B;B	0.29267	0.1;0.018;0.046	T	0.25572	-1.0128	10	0.66056	D	0.02	-24.4462	7.0245	0.24932	0.0:0.1093:0.0:0.8907	.	125;125;125	F5H201;Q96AF5;Q9NWS9	.;.;ZN446_HUMAN	P	125	ENSP00000336565:L125P	ENSP00000336565:L125P	L	+	2	0	ZNF446	63680847	0.000000	0.05858	0.519000	0.27824	0.073000	0.16967	0.154000	0.16343	0.782000	0.33613	0.402000	0.26972	CTC	.	.		0.602	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908		C	58989035	T	C	58989035	3	2	114	1	0	0	0	0	1	0	0	0	17934	1551	54	2	380	2	ZNF446	19	58989035	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	21487	58989035	139948	1146	19418										
PDYN	5173	hgsc.bcm.edu	37	chr20	1961108	1961108	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacgaatgcgccgcaagaagCccccatagcgtttgtacagg					rs141379855		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:1961108delC	ENST00000217305.2	-	4	851	c.626delG	c.(625-627)ggcfs	p.G209fs	RP4-684O24.5_ENST00000446562.1_RNA|PDYN_ENST00000540134.1_Frame_Shift_Del_p.G209fs|PDYN_ENST00000539905.1_Frame_Shift_Del_p.G209fs	NM_001190892.1|NM_001190898.2|NM_024411.4	NP_001177821.1|NP_001177827.1|NP_077722.1	P01213	PDYN_HUMAN	prodynorphin	209					cell death (GO:0008219)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CCGCAAGAAGCCCCCATAGCG	0.597																																					p.G209fs		Atlas-INDEL	.											.	PDYN	74	.	0			c.627delC						.						104	115	111					20																	1961108		2203	4300	6503	SO:0001589	frameshift_variant	5173	exon4			.		CCDS13023.1	20p13	2014-09-17			ENSG00000101327	ENSG00000101327		"Endogenous ligands"	8820	protein-coding gene	gene with protein product	"preproenkephalin B", "rimorphin", "beta-neoendorphin", "dynorphin", "leu-enkephalin", "leumorphin", "neoendorphin-dynorphin-enkephalin prepropeptide"	131340	"spinocerebellar ataxia 23"	SCA23		21035104	Standard	NM_001190892		Approved	PENKB, ADCA	uc021vzs.1	P01213	OTTHUMG00000031683	ENST00000217305.2:c.626delG	chr20.hg19:g.1961108delC	ENSP00000217305:p.Gly209fs	189.0	0.0		219.0	16.0	NM_001190898	A8K0Q3	Frame_Shift_Del	DEL	ENST00000217305.2	hg19	CCDS13023.1																																																																																			.	.		0.597	PDYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077569.2			-	1961108	C	-	1961108	7	5	114	1	0	1	0	1	0	0	0	0	11708	739	26	0	142	0	PDYN	20	1961108	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10		1961108	61064412	1147	19419										
NOP56	10528	hgsc.bcm.edu	37	chr20	2634016	2634016	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctcatcccaggttgccttggAaaatgccaacgccgtgtctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:2634016delA	ENST00000329276.5	+	3	701	c.185delA	c.(184-186)gaafs	p.E62fs	SNORD110_ENST00000408189.1_RNA|SNORD86_ENST00000391196.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORA51_ENST00000606420.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	62					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						GTTGCCTTGGAAAATGCCAAC	0.547																																					p.E62fs		Atlas-INDEL	.											.	NOP56	73	.	0			c.184delG						.						208	179	189					20																	2634016		2203	4300	6503	SO:0001589	frameshift_variant	10528	exon3			.	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"spinocerebellar ataxia 36"	614154	"nucleolar protein 5A (56kD with KKE/D repeat)", "nucleolar protein 5A (56kDa with KKE/D repeat)", "NOP56 ribonucleoprotein homolog (yeast)"	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.185delA	chr20.hg19:g.2634016delA	ENSP00000370589:p.Glu62fs	201.0	0.0		250.0	16.0	NM_006392	Q2M3T6|Q9NQ05	Frame_Shift_Del	DEL	ENST00000329276.5	hg19	CCDS13030.1																																																																																			.	.		0.547	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392		-	2634016	A	-	2634016	7	5	114	1	0	1	0	1	0	0	0	0	10548	246	9	0	195	0	NOP56	20	2634016	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	672908	2634016	60391504	1148	19420										
C20orf194	25943	hgsc.bcm.edu	37	chr20	3285095	3285095	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taaaacacctaccccatcatAgaaggaaatggaattcatgt	6	9	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:3285095A>G	ENST00000252032.9	-	21	1841	c.1774T>C	c.(1774-1776)Tat>Cat	p.Y592H	C20orf194_ENST00000498079.1_5'UTR|C20orf194_ENST00000453730.2_Missense_Mutation_p.Y330H	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	592										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						ACCCCATCATAGAAGGAAATG	0.413																																					p.Y592H		Atlas-SNP	.											.	C20orf194	83	.	0			c.T1774C						.						105	100	102					20																	3285095		1892	4112	6004	SO:0001583	missense	25943	exon21			CATCATAGAAGGA	AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.1774T>C	chr20.hg19:g.3285095A>G	ENSP00000252032:p.Tyr592His	69.0	0.0		98.0	4.0	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	hg19	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.190935	0.78789	.	.	ENSG00000088854	ENST00000252032;ENST00000453730	T;T	0.42900	1.81;0.96	5.83	5.83	0.93111	.	0.063315	0.64402	D	0.000004	T	0.62792	0.2457	M	0.72894	2.215	0.51482	D	0.99992	D;D	0.76494	0.999;0.999	D;D	0.71656	0.961;0.974	T	0.66578	-0.5888	10	0.87932	D	0	.	13.7216	0.62730	1.0:0.0:0.0:0.0	.	331;592	Q0IIP3;Q5TEA3	.;CT194_HUMAN	H	592;330	ENSP00000252032:Y592H;ENSP00000407229:Y330H	ENSP00000252032:Y592H	Y	-	1	0	C20orf194	3233095	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.441000	0.66569	2.223000	0.72356	0.402000	0.26972	TAT	.	.		0.413	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984		G	3285095	A	G	3285095	3	3	114	1	0	0	0	0	1	0	0	0	2101	420	15	2	1827	2	C20orf194	20	3285095	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	651079	3285095	59740425	1149	19421										
ADAM33	80332	hgsc.bcm.edu	37	chr20	3650236	3650236	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctgtggggcccaactccatGgggtgaacgccgcccagggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:3650236delG	ENST00000356518.2	-	20	2530	c.2289delC	c.(2287-2289)cccfs	p.P763fs	ADAM33_ENST00000350009.2_Frame_Shift_Del_p.P737fs|ADAM33_ENST00000466620.1_5'UTR|ADAM33_ENST00000379861.4_Frame_Shift_Del_p.P763fs	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	763					proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|skin(3)	29						CCAACTCCATGGGGTGAACGC	0.647																																					p.M764fs		Atlas-INDEL	.											.	ADAM33	76	.	0			c.2290delA						.						21	21	21					20																	3650236		2202	4296	6498	SO:0001589	frameshift_variant	80332	exon20			.	AL117415, AB055891	CCDS13058.1, CCDS63219.1	20p13	2010-04-06	2005-08-18		ENSG00000149451	ENSG00000149451		"ADAM metallopeptidase domain containing"	15478	protein-coding gene	gene with protein product		607114	"a disintegrin and metalloproteinase domain 33", "chromosome 20 open reading frame 153"	C20orf153		11814695	Standard	XM_005260843		Approved	DKFZp434K0521, dJ964F7.1	uc002wit.3	Q9BZ11	OTTHUMG00000031758	ENST00000356518.2:c.2289delC	chr20.hg19:g.3650236delG	ENSP00000348912:p.Pro763fs	120.0	0.0		161.0	10.0	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Frame_Shift_Del	DEL	ENST00000356518.2	hg19	CCDS13058.1																																																																																			.	.		0.647	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220		-	3650236	G	-	3650236	7	5	114	1	0	1	0	1	0	0	0	0	250	1335	47	0	164	0	ADAM33	20	3650236	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	365141	3650236	59375284	1150	19422										
RASSF2	9770	hgsc.bcm.edu	37	chr20	4776514	4776514	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaggaggaggatggagggggTcgaatgcgttcgttgtcatc	19	5	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:4776514T>C	ENST00000379400.3	-	5	429	c.234A>G	c.(232-234)cgA>cgG	p.R78R	RASSF2_ENST00000379376.2_Silent_p.R78R|RASSF2_ENST00000478553.1_5'Flank	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	78					bone remodeling (GO:0046849)|cell cycle (GO:0007049)|epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade (GO:0038168)|homeostasis of number of cells (GO:0048872)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|ossification (GO:0001503)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|pancreas(2)|prostate(2)|skin(2)	34						ATGGAGGGGGTCGAATGCGTT	0.617																																					p.R78R	Melanoma(158;1891 3343 50738)	Atlas-SNP	.											.	RASSF2	75	.	0			c.A234G						.						138	128	131					20																	4776514		2203	4300	6503	SO:0001819	synonymous_variant	9770	exon5			AGGGGGTCGAATG	D79990	CCDS13083.1	20p13	2011-08-12	2008-02-22		ENSG00000101265	ENSG00000101265			9883	protein-coding gene	gene with protein product	"centromere protein 34"	609492				8724849, 15806169	Standard	NM_014737		Approved	KIAA0168, CENP-34	uc002wld.3	P50749	OTTHUMG00000031790	ENST00000379400.3:c.234A>G	chr20.hg19:g.4776514T>C		73.0	0.0		121.0	5.0	NM_014737	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Silent	SNP	ENST00000379400.3	hg19	CCDS13083.1																																																																																			.	.		0.617	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737		C	4776514	T	C	4776514	2	2	114	1	0	0	0	0	0	0	0	1	13101	1654	58	2		2	RASSF2	20	4776514	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1126278	4776514	58249006	1151	19423										
GPCPD1	56261	hgsc.bcm.edu	37	chr20	5550794	5550794	+	Splice_Site	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgaagaaatttcaacgtaccTttttcatagtcaaacaacag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:5550794delT	ENST00000379019.4	-	12	1360	c.1148delA	c.(1147-1149)aag>ag	p.K384fs	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	384	GP-PDE.				glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						TCAACGTACCTTTTTCATAGT	0.303																																					p.K383fs		Atlas-INDEL	.											.	GPCPD1	52	.	0			c.1149delG						.						78	75	76					20																	5550794		2203	4300	6503	SO:0001630	splice_region_variant	56261	exon12			.		CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.1149+1A>-	chr20.hg19:g.5550794delT		128.0	0.0		280.0	17.0	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Frame_Shift_Del	DEL	ENST00000379019.4	hg19	CCDS13090.1																																																																																			.	.		0.303	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593	Frame_Shift_Del	-	5550794	T	-	5550794	8	5	114	1	0	1	0	1	0	0	1	0	6611	1623	56	0	906	0	GPCPD1	20	5550794	Splice_Site	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	774280	5550794	57474726	1152	19424										
GPCPD1	56261	hgsc.bcm.edu	37	chr20	5560674	5560674	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctaaatctagatttttttaaTtttttcttggttattgacac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:5560674delT	ENST00000379019.4	-	7	665	c.453delA	c.(451-453)aaafs	p.K151fs	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	151					glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						ATTTTTTTAATTTTTTCTTGG	0.338																																					p.L152X		Atlas-INDEL	.											.	GPCPD1	52	.	0			c.454delT						.						53	55	54					20																	5560674		2203	4296	6499	SO:0001589	frameshift_variant	56261	exon7			.		CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.453delA	chr20.hg19:g.5560674delT	ENSP00000368305:p.Lys151fs	104.0	0.0		202.0	13.0	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Frame_Shift_Del	DEL	ENST00000379019.4	hg19	CCDS13090.1																																																																																			.	.		0.338	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593		-	5560674	T	-	5560674	7	5	114	1	0	1	0	1	0	0	0	0	6611	1490	52	0	1621	0	GPCPD1	20	5560674	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	9880	5560674	57464846	1153	19425										
PLCB1	23236	hgsc.bcm.edu	37	chr20	8130989	8130989	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgaggactgaccctcagggaTttttcttttactggacagat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:8130989delT	ENST00000338037.6	+	2	175	c.148delT	c.(148-150)tttfs	p.F52fs	PLCB1_ENST00000378641.3_Frame_Shift_Del_p.F52fs|PLCB1_ENST00000378637.2_Frame_Shift_Del_p.F52fs	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	52					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)	p.F50I(1)		NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						CCCTCAGGGATTTTTCTTTTA	0.308																																					p.L49fs		Atlas-INDEL	.											.	PLCB1	394	.	1	Substitution - Missense(1)	skin(1)	c.147delG						.						78	78	78					20																	8130989		2203	4292	6495	SO:0001589	frameshift_variant	23236	exon2			.	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.148delT	chr20.hg19:g.8130989delT	ENSP00000338185:p.Phe52fs	124.0	0.0		181.0	11.0	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Frame_Shift_Del	DEL	ENST00000338037.6	hg19	CCDS13102.1																																																																																			.	.		0.308	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			-	8130989	T	-	8130989	7	5	114	1	0	1	0	1	0	0	0	0	12036	1493	52	0	154	0	PLCB1	20	8130989	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2570315	8130989	54894531	1154	19426										
ANKRD5	63926	hgsc.bcm.edu	37	chr20	10032309	10032309	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gttcatctatcttattttacAgagctaacgttaatgcaaca	5	8	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:10032309A>G	ENST00000378380.3	+	7	1972		c.e7-1		SNAP25-AS1_ENST00000421143.2_RNA|ANKEF1_ENST00000378392.1_Splice_Site|ANKEF1_ENST00000488991.1_Splice_Site|SNAP25-AS1_ENST00000603542.1_RNA	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1								calcium ion binding (GO:0005509)										CTTATTTTACAGAGCTAACGT	0.358																																					.		Atlas-SNP	.											.	.	.	.	0			c.1644-2A>G						.						69	66	67					20																	10032309		2203	4300	6503	SO:0001630	splice_region_variant	63926	exon8			TTTTACAGAGCTA	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.1644-1A>G	chr20.hg19:g.10032309A>G		87.0	0.0		98.0	6.0	NM_022096	B3KUQ0|Q9H6Y9	Splice_Site	SNP	ENST00000378380.3	hg19	CCDS13108.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.550589	0.27739	.	.	ENSG00000132623	ENST00000378392;ENST00000378380	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3035	0.82836	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ANKRD5	9980309	1.000000	0.71417	0.907000	0.35723	0.004000	0.04260	8.242000	0.89818	2.299000	0.77371	0.528000	0.53228	.	.	.		0.358	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096	Intron	G	10032309	A	G	10032309	5	3	114	1	0	0	0	0	0	0	1	0	676	202	7	2	1664	2	ANKRD5	20	10032309	Splice_Site	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1901320	10032309	52993211	1155	19427										
ESF1	51575	hgsc.bcm.edu	37	chr20	13695562	13695562	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcttgcttgaaactgctctgTtttggtttttatagatttaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:13695562delT	ENST00000202816.1	-	14	2622	c.2515delA	c.(2515-2517)acafs	p.T839fs		NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	839	Lys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						AACTGCTCTGTTTTGGTTTTT	0.294																																					p.T839fs		Atlas-INDEL	.											.	ESF1	77	.	0			c.2516delC						.						105	99	101					20																	13695562		2203	4300	6503	SO:0001589	frameshift_variant	51575	exon14			.		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 6"	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.2515delA	chr20.hg19:g.13695562delT	ENSP00000202816:p.Thr839fs	96.0	0.0		149.0	10.0	NM_001276380	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Frame_Shift_Del	DEL	ENST00000202816.1	hg19	CCDS13117.1																																																																																			.	.		0.294	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649		-	13695562	T	-	13695562	7	5	114	1	0	1	0	1	0	0	0	0	5253	1725	60	0	44	0	ESF1	20	13695562	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3663253	13695562	49329958	1156	19428										
MACROD2	140733	hgsc.bcm.edu	37	chr20	13976431	13976431	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtaccccagcaacaagaagAaaaaggtgtggagagaggag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:13976431delA	ENST00000310348.4	+	1	22	c.22delA	c.(22-24)aaafs	p.K9fs	MACROD2_ENST00000217246.4_Frame_Shift_Del_p.K9fs|SEL1L2_ENST00000486903.1_5'Flank			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	9	Poly-Lys.				brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				CAACAAGAAGAAAAAGGTGTG	0.637																																					p.K7fs		Atlas-INDEL	.											.	MACROD2	34	.	0			c.21delG						.						45	38	40					20																	13976431		2203	4300	6503	SO:0001589	frameshift_variant	140733	exon1			.	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"chromosome 20 open reading frame 133"	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.22delA	chr20.hg19:g.13976431delA	ENSP00000309809:p.Lys9fs	130.0	0.0		160.0	10.0	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Frame_Shift_Del	DEL	ENST00000310348.4	hg19	CCDS13120.2																																																																																			.	.		0.637	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676		-	13976431	A	-	13976431	7	5	114	1	0	1	0	1	0	0	0	0	9155	247	9	0	24	0	MACROD2	20	13976431	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	280869	13976431	49049089	1157	19429										
PCSK2	5126	hgsc.bcm.edu	37	chr20	17208071	17208071	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcttgtggagttgcataaaGggggagaggacaaagctcgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:17208071delG	ENST00000262545.2	+	1	436	c.121delG	c.(121-123)gggfs	p.G42fs	PCSK2_ENST00000377899.1_Frame_Shift_Del_p.G23fs|PCSK2_ENST00000536609.1_Frame_Shift_Del_p.G42fs	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	42					cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""Insulin(DB00071)|Insulin Regular(DB00030)"	GTTGCATAAAGGGGGAGAGGA	0.532																																					p.K40fs		Atlas-INDEL	.											.	PCSK2	112	.	0			c.120delA						.						81	72	75					20																	17208071		2203	4300	6503	SO:0001589	frameshift_variant	5126	exon1			.	AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"neuroendocrine convertase 2", "KEX2-like endoprotease 2"	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.121delG	chr20.hg19:g.17208071delG	ENSP00000262545:p.Gly42fs	186.0	0.0		205.0	14.0	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Frame_Shift_Del	DEL	ENST00000262545.2	hg19	CCDS13125.1																																																																																			.	.		0.532	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		-	17208071	G	-	17208071	7	5	114	1	0	1	0	1	0	0	0	0	11610	1000	35	0	123	0	PCSK2	20	17208071	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	3231640	17208071	45817449	1158	19430										
ZNF133	7692	hgsc.bcm.edu	37	chr20	18296753	18296753	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggtgtgtgggcacagcttcAgccagaattcaaccctcatc	11	12	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:18296753A>G	ENST00000316358.4	+	4	1355	c.1258A>G	c.(1258-1260)Agc>Ggc	p.S420G	ZNF133_ENST00000377671.3_Missense_Mutation_p.S419G|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000401790.1_Missense_Mutation_p.S420G|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000538547.1_Missense_Mutation_p.S325G|ZNF133_ENST00000535822.1_Missense_Mutation_p.S325G|ZNF133_ENST00000402618.2_Missense_Mutation_p.S357G|ZNF133_ENST00000396026.3_Missense_Mutation_p.S423G	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	420					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						GCACAGCTTCAGCCAGAATTC	0.567																																					p.S419G		Atlas-SNP	.											.	ZNF133	63	.	0			c.A1255G						.						84	89	87					20																	18296753		2203	4300	6503	SO:0001583	missense	7692	exon4			AGCTTCAGCCAGA	AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"Zinc fingers, C2H2-type", "-"	12917	protein-coding gene	gene with protein product		604075	"zinc finger protein 150 (pHZ-66)", "zinc finger protein 133 (clone pHZ-13)"	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.1258A>G	chr20.hg19:g.18296753A>G	ENSP00000346090:p.Ser420Gly	70.0	0.0		81.0	4.0	NM_001083330	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Missense_Mutation	SNP	ENST00000316358.4	hg19		.	.	.	.	.	.	.	.	.	.	A	16.70	3.195857	0.58126	.	.	ENSG00000125846	ENST00000377671;ENST00000396026;ENST00000402618;ENST00000401790;ENST00000538547;ENST00000535822;ENST00000316358	T;T;T;T;T;T;T	0.19250	2.16;2.16;3.17;2.16;3.17;3.17;2.16	4.45	3.33	0.38152	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000013	T	0.30417	0.0764	L	0.31476	0.935	0.28358	N	0.920574	D;D;D;P	0.76494	0.999;0.995;0.999;0.925	D;D;D;B	0.72075	0.955;0.924;0.976;0.434	T	0.04128	-1.0975	10	0.66056	D	0.02	-32.8372	10.0274	0.42079	0.831:0.169:0.0:0.0	.	357;423;420;419	B4DIB8;B4DHU7;P52736;P52736-2	.;.;ZN133_HUMAN;.	G	419;423;357;420;325;325;420	ENSP00000366899:S419G;ENSP00000400897:S423G;ENSP00000385279:S357G;ENSP00000383945:S420G;ENSP00000442978:S325G;ENSP00000439427:S325G;ENSP00000346090:S420G	ENSP00000346090:S420G	S	+	1	0	ZNF133	18244753	0.000000	0.05858	0.994000	0.49952	0.975000	0.68041	0.823000	0.27366	1.004000	0.39156	0.459000	0.35465	AGC	.	.		0.567	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434		G	18296753	A	G	18296753	3	3	114	1	0	0	0	0	1	0	0	0	17738	188	7	2	1265	2	ZNF133	20	18296753	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1088682	18296753	44728767	1159	19431										
RALGAPA2	57186	hgsc.bcm.edu	37	chr20	20493319	20493319	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctcttgagcattttggcgcAaaatgacctcaatgatttcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:20493319delA	ENST00000202677.7	-	32	4701	c.4694delT	c.(4693-4695)ttgfs	p.L1565fs		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1565					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						ATTTTGGCGCAAAATGACCTC	0.473																																					p.L1565fs		Atlas-INDEL	.											.	RALGAPA2	274	.	0			c.4695delG						.						135	126	129					20																	20493319		1925	4143	6068	SO:0001589	frameshift_variant	57186	exon32			.	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.4694delT	chr20.hg19:g.20493319delA	ENSP00000202677:p.Leu1565fs	148.0	0.0		187.0	13.0	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Frame_Shift_Del	DEL	ENST00000202677.7	hg19	CCDS46584.1																																																																																			.	.		0.473	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		-	20493319	A	-	20493319	7	5	114	1	0	1	0	1	0	0	0	0	13029	131	5	0	959	0	RALGAPA2	20	20493319	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	2196566	20493319	42532201	1160	19432										
NAPB	63908	hgsc.bcm.edu	37	chr20	23383704	23383704	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagcctcttctattcttgtgTttcctctgagaaaaagttaa	6	8	4	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:23383704T>C	ENST00000377026.4	-	2	189	c.104A>G	c.(103-105)aAc>aGc	p.N35S	NAPB_ENST00000472855.1_5'UTR|NAPB_ENST00000432543.2_Missense_Mutation_p.N35S|NAPB_ENST00000398425.3_5'UTR	NM_001283018.1|NM_001283020.1|NM_022080.2	NP_001269947.1|NP_001269949.1|NP_071363.1	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, beta	35					intracellular protein transport (GO:0006886)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	extracellular vesicular exosome (GO:0070062)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					TATTCTTGTGTTTCCTCTGAG	0.323																																					p.N35S		Atlas-SNP	.											.	NAPB	22	.	0			c.A104G						.						80	75	77					20																	23383704		2201	4300	6501	SO:0001583	missense	63908	exon2			CTTGTGTTTCCTC	AK022817	CCDS13152.1, CCDS63241.1, CCDS63242.1, CCDS74710.1	20p12.3-p11.21	2008-08-01			ENSG00000125814	ENSG00000125814			15751	protein-coding gene	gene with protein product		611270				8455721	Standard	NM_022080		Approved	SNAP-BETA, SNAPB	uc002wta.3	Q9H115	OTTHUMG00000032062	ENST00000377026.4:c.104A>G	chr20.hg19:g.23383704T>C	ENSP00000366225:p.Asn35Ser	68.0	0.0		92.0	4.0	NM_022080	B4DK44|Q4G0M0|Q4G187|Q5JXF9|Q8N3C4	Missense_Mutation	SNP	ENST00000377026.4	hg19	CCDS13152.1	.	.	.	.	.	.	.	.	.	.	T	3.726	-0.056567	0.07362	.	.	ENSG00000125814	ENST00000377026;ENST00000432543	T;T	0.74842	1.68;-0.88	5.95	5.95	0.96441	Tetratricopeptide-like helical (1);	0.343450	0.33591	N	0.004749	T	0.38480	0.1042	N	0.00315	-1.66	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.002	T	0.55354	-0.8154	10	0.02654	T	1	0.4372	15.5971	0.76595	0.0:0.0:0.0:1.0	.	35;35;35	B4DK44;B4DIV0;Q9H115	.;.;SNAB_HUMAN	S	35	ENSP00000366225:N35S;ENSP00000413600:N35S	ENSP00000366225:N35S	N	-	2	0	NAPB	23331704	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.146000	0.50631	2.279000	0.76181	0.533000	0.62120	AAC	.	.		0.323	NAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078317.2	NM_022080		C	23383704	T	C	23383704	3	2	114	1	0	0	0	0	1	0	0	0	10171	1725	60	2	832	2	NAPB	20	23383704	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2890385	23383704	39641816	1161	19433										
ENTPD6	955	hgsc.bcm.edu	37	chr20	25187773	25187773	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atccaaccacgggagcctgcGggtggcgaaggtggcatacc					rs369864358		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:25187773delG	ENST00000376652.4	+	3	279	c.116delG	c.(115-117)cggfs	p.R39fs	ENTPD6_ENST00000433259.2_Frame_Shift_Del_p.R39fs|ENTPD6_ENST00000354989.5_Frame_Shift_Del_p.R22fs|ENTPD6_ENST00000360031.2_Frame_Shift_Del_p.R38fs			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	39					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						GGGAGCCTGCGGGTGGCGAAG	0.607																																					p.R39fs		Atlas-INDEL	.											.	ENTPD6	57	.	0			c.115delC						.						55	56	56					20																	25187773		2203	4300	6503	SO:0001589	frameshift_variant	955	exon3			.	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"interleukin 6 signal transducer-2"	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.116delG	chr20.hg19:g.25187773delG	ENSP00000365840:p.Arg39fs	100.0	0.0		129.0	10.0	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Frame_Shift_Del	DEL	ENST00000376652.4	hg19	CCDS13170.1																																																																																			.	.		0.607	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2			-	25187773	G	-	25187773	7	5	114	1	0	1	0	1	0	0	0	0	5145	1116	39	0	129	0	ENTPD6	20	25187773	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1804069	25187773	37837747	1162	19434										
C20orf185	359710	hgsc.bcm.edu	37	chr20	31656746	31656746	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtgctgttctatgtccctaaGgggacccctgaatccctctt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:31656746delG	ENST00000375494.3	+	10	1116	c.1116delG	c.(1114-1116)aagfs	p.K372fs		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	372					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										ATGTCCCTAAGGGGACCCCTG	0.592																																					p.K372fs		Atlas-INDEL	.											.	.	.	.	0			c.1115delA						.						101	79	86					20																	31656746		2203	4300	6503	SO:0001589	frameshift_variant	359710	exon10			.	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"BPI fold containing"	16178	protein-coding gene	gene with protein product		615717	"chromosome 20 open reading frame 185"	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1116delG	chr20.hg19:g.31656746delG	ENSP00000364643:p.Lys372fs	150.0	0.0		155.0	11.0	NM_182658	Q5TDX7	Frame_Shift_Del	DEL	ENST00000375494.3	hg19	CCDS13212.1																																																																																			.	.		0.592	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		-	31656746	G	-	31656746	7	5	114	1	0	1	0	1	0	0	0	0	2099	991	35	0	1154	0	C20orf185	20	31656746	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	6468973	31656746	31368774	1163	19435										
CBFA2T2	9139	hgsc.bcm.edu	37	chr20	32207380	32207380	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tccaagaagccacaaactttCcccttcgtccttttgtgatt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:32207380delC	ENST00000346541.3	+	5	1042	c.505delC	c.(505-507)cccfs	p.P169fs	CBFA2T2_ENST00000359606.3_Frame_Shift_Del_p.P179fs|CBFA2T2_ENST00000375279.2_Frame_Shift_Del_p.P169fs|CBFA2T2_ENST00000492345.1_Frame_Shift_Del_p.P140fs|CBFA2T2_ENST00000342704.6_Frame_Shift_Del_p.P160fs|CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000344201.3_Frame_Shift_Del_p.P140fs|CBFA2T2_ENST00000397800.1_Frame_Shift_Del_p.P140fs|CBFA2T2_ENST00000397798.2_Frame_Shift_Del_p.P140fs	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	169	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						CACAAACTTTCCCCTTCGTCC	0.348																																					p.F168fs	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-INDEL	.											.	CBFA2T2	93	.	0			c.504delT						.						88	90	90					20																	32207380		2203	4300	6503	SO:0001589	frameshift_variant	9139	exon5			.	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"Zinc fingers, MYND-type"	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.505delC	chr20.hg19:g.32207380delC	ENSP00000262653:p.Pro169fs	95.0	0.0		143.0	10.0	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Frame_Shift_Del	DEL	ENST00000346541.3	hg19	CCDS13221.1																																																																																			.	.		0.348	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		-	32207380	C	-	32207380	7	5	114	1	0	1	0	1	0	0	0	0	2699	855	30	0	557	0	CBFA2T2	20	32207380	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	550634	32207380	30818140	1164	19436										
CBFA2T2	9139	hgsc.bcm.edu	37	chr20	32212691	32212691	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgtgcccctcatgaatcccGggggccaattccatcctacc	8	17	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:32212691G>T	ENST00000346541.3	+	7	1378	c.841G>T	c.(841-843)Ggg>Tgg	p.G281W	CBFA2T2_ENST00000359606.3_Missense_Mutation_p.G291W|CBFA2T2_ENST00000375279.2_Missense_Mutation_p.G281W|CBFA2T2_ENST00000492345.1_Missense_Mutation_p.G252W|CBFA2T2_ENST00000342704.6_Missense_Mutation_p.G272W|CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000397800.1_Missense_Mutation_p.G252W	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	281					epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						CATGAATCCCGGGGGCCAATT	0.532																																					p.G281W	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-SNP	.											.	CBFA2T2	93	.	0			c.G841T						.						122	100	108					20																	32212691		2203	4300	6503	SO:0001583	missense	9139	exon7			AATCCCGGGGGCC	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"Zinc fingers, MYND-type"	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.841G>T	chr20.hg19:g.32212691G>T	ENSP00000262653:p.Gly281Trp	106.0	0.0		151.0	7.0	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Missense_Mutation	SNP	ENST00000346541.3	hg19	CCDS13221.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.760539	0.31137	.	.	ENSG00000078699	ENST00000397803;ENST00000375279;ENST00000342704;ENST00000346541;ENST00000397800;ENST00000359606	T;T;T;T;T	0.45276	0.9;0.91;0.9;0.91;1.49	5.5	4.55	0.56014	.	0.231387	0.38492	N	0.001668	T	0.42743	0.1216	N	0.22421	0.69	0.19300	N	0.999975	D;D	0.61080	0.989;0.989	P;P	0.57960	0.823;0.83	T	0.26087	-1.0113	10	0.66056	D	0.02	-5.192	10.1107	0.42561	0.2103:0.0:0.7897:0.0	.	281;272	O43439;F8W6D7	MTG8R_HUMAN;.	W	55;281;272;281;252;291	ENSP00000364428:G281W;ENSP00000345810:G272W;ENSP00000262653:G281W;ENSP00000380902:G252W;ENSP00000352622:G291W	ENSP00000345810:G272W	G	+	1	0	CBFA2T2	31676352	0.228000	0.23718	0.470000	0.27216	0.003000	0.03518	2.130000	0.42064	1.471000	0.48121	0.650000	0.86243	GGG	.	.		0.532	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		T	32212691	G	T	32212691	3	4	114	1	0	0	0	0	1	0	0	0	2699	1116	39	1	901	1	CBFA2T2	20	32212691	Missense_Mutation	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	5311	32212691	30812829	1165	19437										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33329681	33329681	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatccgaaggctgcccatccTttttggactgatcttcaggg					rs148955887		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:33329681delT	ENST00000374796.2	-	12	6949	c.4379delA	c.(4378-4380)aagfs	p.K1460fs	NCOA6_ENST00000359003.2_Frame_Shift_Del_p.K1460fs			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1460					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						CTGCCCATCCTTTTTGGACTG	0.448																																					p.K1460fs		Atlas-INDEL	.											.	NCOA6	219	.	0			c.4380delG						.						104	96	99					20																	33329681		2203	4300	6503	SO:0001589	frameshift_variant	23054	exon11			.	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.4379delA	chr20.hg19:g.33329681delT	ENSP00000363929:p.Lys1460fs	166.0	0.0		197.0	12.0	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Frame_Shift_Del	DEL	ENST00000374796.2	hg19	CCDS13241.1																																																																																			.	.		0.448	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		-	33329681	T	-	33329681	7	5	114	1	0	1	0	1	0	0	0	0	10242	1609	56	0	1832	0	NCOA6	20	33329681	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1116990	33329681	29695839	1166	19438										
GSS	2937	hgsc.bcm.edu	37	chr20	33530430	33530430	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	attcaggcccaggaacacagTctgtggggaaaactgaaggc	13	9	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:33530430T>C	ENST00000216951.2	-	5	450	c.352A>G	c.(352-354)Act>Gct	p.T118A	GSS_ENST00000451957.2_Intron|GSS_ENST00000541098.1_5'UTR	NM_000178.2	NP_000169.1	P48637	GSHB_HUMAN	glutathione synthetase	118					aging (GO:0007568)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|nervous system development (GO:0007399)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to nutrient levels (GO:0031667)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|glutathione binding (GO:0043295)|glutathione synthase activity (GO:0004363)|glycine binding (GO:0016594)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(18;0.035)		Acetylcysteine(DB06151)|Glutathione(DB00143)|Glycine(DB00145)|L-Cysteine(DB00151)	AGGAACACAGTCTGTGGGGAA	0.542																																					p.T118A		Atlas-SNP	.											.	GSS	33	.	0			c.A352G						.						90	85	87					20																	33530430		2203	4300	6503	SO:0001630	splice_region_variant	2937	exon5			ACACAGTCTGTGG		CCDS13245.1	20q11.2	1996-06-18			ENSG00000100983	ENSG00000100983	6.3.2.3		4624	protein-coding gene	gene with protein product		601002				8825653	Standard	NM_000178		Approved		uc002xbg.3	P48637	OTTHUMG00000032315	ENST00000216951.2:c.352-1A>G	chr20.hg19:g.33530430T>C		79.0	0.0		116.0	5.0	NM_000178	B2R697|B6F210|E1P5P9|Q4TTD9	Missense_Mutation	SNP	ENST00000216951.2	hg19	CCDS13245.1	.	.	.	.	.	.	.	.	.	.	T	5.497	0.276732	0.10403	.	.	ENSG00000100983	ENST00000216951	D	0.90444	-2.67	5.77	5.77	0.91146	Glutathione synthase, N-terminal, eukaryotic (1);	0.592570	0.18646	N	0.135159	T	0.82061	0.4955	L	0.33339	1.005	0.80722	D	1	B	0.13145	0.007	B	0.12837	0.008	T	0.72523	-0.4267	10	0.08837	T	0.75	-17.5509	6.3195	0.21208	0.1417:0.0748:0.0:0.7836	.	118	P48637	GSHB_HUMAN	A	118	ENSP00000216951:T118A	ENSP00000216951:T118A	T	-	1	0	GSS	32994091	1.000000	0.71417	0.998000	0.56505	0.926000	0.56050	0.614000	0.24314	2.199000	0.70637	0.533000	0.62120	ACT	.	.		0.542	GSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078821.2		Missense_Mutation	C	33530430	T	C	33530430	5	2	114	1	0	0	0	0	0	0	1	0	6838	1681	58	2	1108	2	GSS	20	33530430	Splice_Site	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	200749	33530430	29495090	1167	19439										
NDRG3	57446	hgsc.bcm.edu	37	chr20	35310974	35310974	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aactccaattccaatgatgcTtttcaggctgtgaatgggac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:35310974delT	ENST00000349004.1	-	7	472	c.391delA	c.(391-393)agcfs	p.S131fs	NDRG3_ENST00000373773.3_Frame_Shift_Del_p.S36fs|NDRG3_ENST00000540765.1_Frame_Shift_Del_p.S27fs|NDRG3_ENST00000373803.2_Frame_Shift_Del_p.S131fs|NDRG3_ENST00000359675.2_Frame_Shift_Del_p.S119fs	NM_032013.3	NP_114402.1	Q9UGV2	NDRG3_HUMAN	NDRG family member 3	131					cell differentiation (GO:0030154)|negative regulation of cell growth (GO:0030308)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Myeloproliferative disorder(115;0.00878)				CCAATGATGCTTTTCAGGCTG	0.453																																					p.S131fs		Atlas-INDEL	.											.	NDRG3	32	.	0			c.392delG						.						171	135	147					20																	35310974		2203	4300	6503	SO:0001589	frameshift_variant	57446	exon7			.	AL031662	CCDS13284.1, CCDS13285.1	20q11.21-q11.23	2008-07-28			ENSG00000101079	ENSG00000101079			14462	protein-coding gene	gene with protein product		605273				10831399, 17998568	Standard	NM_032013		Approved		uc002xfw.3	Q9UGV2	OTTHUMG00000032398	ENST00000349004.1:c.391delA	chr20.hg19:g.35310974delT	ENSP00000345292:p.Ser131fs	135.0	0.0		211.0	16.0	NM_032013	A2A2S8|E1P5U7|E1P5U8|Q5TH32|Q96PL8|Q96SM2|Q9BXY7|Q9H3N7|Q9H411|Q9H8J6	Frame_Shift_Del	DEL	ENST00000349004.1	hg19	CCDS13285.1																																																																																			.	.		0.453	NDRG3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079053.2			-	35310974	T	-	35310974	7	5	114	1	0	1	0	1	0	0	0	0	10262	1609	56	0	776	0	NDRG3	20	35310974	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1780544	35310974	27714546	1168	19440										
RPRD1B	58490	hgsc.bcm.edu	37	chr20	36676769	36676769	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gagaggcagatgaaggctgtAaaaaacctttagaaagattg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:36676769delA	ENST00000373433.4	+	3	703	c.301delA	c.(301-303)aaafs	p.K102fs		NM_021215.3	NP_067038.1	Q9NQG5	RPR1B_HUMAN	regulation of nuclear pre-mRNA domain containing 1B	102	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.				dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle process (GO:0010564)|transcription, DNA-templated (GO:0006351)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)	12						TGAAGGCTGTAAAAAACCTTT	0.388																																					p.C100X		Atlas-INDEL	.											.	RPRD1B	25	.	0			c.300delT						.						96	82	87					20																	36676769		2203	4300	6503	SO:0001589	frameshift_variant	58490	exon3			.	AL109823	CCDS13301.1	20q11.21-q12	2012-02-09	2008-08-15	2008-07-28	ENSG00000101413	ENSG00000101413			16209	protein-coding gene	gene with protein product		614694	"chromosome 20 open reading frame 77"	C20orf77		22231121	Standard	NM_021215		Approved	dJ1057B20.2, DKFZp434P0735, CREPT, FLJ44520, NET60	uc002xho.4	Q9NQG5	OTTHUMG00000032434	ENST00000373433.4:c.301delA	chr20.hg19:g.36676769delA	ENSP00000362532:p.Lys102fs	157.0	0.0		155.0	12.0	NM_021215	Q1WDE7|Q6PKF4	Frame_Shift_Del	DEL	ENST00000373433.4	hg19	CCDS13301.1																																																																																			.	.		0.388	RPRD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079142.2	NM_021215		-	36676769	A	-	36676769	7	5	114	1	0	1	0	1	0	0	0	0	13631	363	13	0	311	0	RPRD1B	20	36676769	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1365795	36676769	26348751	1169	19441										
LPIN3	64900	hgsc.bcm.edu	37	chr20	39977799	39977799	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctactcggatggcgagtggCccccccaggccaggtaagag					rs559175371	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:39977799delC	ENST00000373257.3	+	5	716	c.625delC	c.(625-627)cccfs	p.P210fs		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	210					fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				TGGCGAGTGGCCCCCCCAGGC	0.537													CCCCCCC|CCCCCCC|CCCCCC|deletion	3	0.000599042	0	0	5008	,	,		17869	0		0.003	False		,,,				2504	0				p.W208fs		Atlas-INDEL	.											.	LPIN3	69	.	0			c.624delG						.			6,0,4258		0,0,6,0,0,2126	70	71	71			-1.4	0	20		72	6,2,8246		0,0,6,0,2,4119	no	codingComplex	LPIN3	NM_022896.1		0,0,12,0,2,6245	A1A1,A1A2,A1R,A2A2,A2R,RR		0.0969,0.1407,0.1118			39977799	12,2,12504	2203	4300	6503	SO:0001589	frameshift_variant	64900	exon5			.	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"lipin 3-like"	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.625delC	chr20.hg19:g.39977799delC	ENSP00000362354:p.Pro210fs	130.0	0.0		158.0	10.0	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Frame_Shift_Del	DEL	ENST00000373257.3	hg19	CCDS33469.1																																																																																			.	.		0.537	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896		-	39977799	C	-	39977799	7	5	114	1	0	1	0	1	0	0	0	0	8929	739	26	0	639	0	LPIN3	20	39977799	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3301030	39977799	23047721	1170	19442										
PTPRT	11122	hgsc.bcm.edu	37	chr20	41306553	41306553	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaggccctggcggtcccgtaCccccctcacctggtcgtgtg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:41306553delC	ENST00000373187.1	-	7	1105	c.1106delG	c.(1105-1107)ggtfs	p.G369fs	PTPRT_ENST00000373190.1_Frame_Shift_Del_p.G369fs|PTPRT_ENST00000373193.3_Frame_Shift_Del_p.G369fs|PTPRT_ENST00000373184.1_Frame_Shift_Del_p.G369fs|PTPRT_ENST00000356100.2_Frame_Shift_Del_p.G369fs|PTPRT_ENST00000373201.1_Frame_Shift_Del_p.G369fs|PTPRT_ENST00000373198.4_Frame_Shift_Del_p.G369fs			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	369	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CGGTCCCGTACCCCCCTCACC	0.547																																					p.G369fs		Atlas-INDEL	.											.	PTPRT	372	.	0			c.1107delT						.						96	96	96					20																	41306553		1937	4139	6076	SO:0001589	frameshift_variant	11122	exon7			.	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1106delG	chr20.hg19:g.41306553delC	ENSP00000362283:p.Gly369fs	125.0	0.0		177.0	12.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Frame_Shift_Del	DEL	ENST00000373187.1	hg19	CCDS42874.1																																																																																			.	.		0.547	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			-	41306553	C	-	41306553	7	5	114	1	0	1	0	1	0	0	0	0	12827	507	18	0	3380	0	PTPRT	20	41306553	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1328754	41306553	21718967	1171	19443										
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42162009	42162009	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cccagcagcccctacatccaCccagtgggctggtgccagaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:42162009delC	ENST00000427442.2	+	13	1557	c.1398delC	c.(1396-1398)cacfs	p.H466fs	L3MBTL1_ENST00000418998.1_Frame_Shift_Del_p.H466fs|L3MBTL1_ENST00000444063.1_Frame_Shift_Del_p.H398fs|L3MBTL1_ENST00000373135.3_Frame_Shift_Del_p.H398fs|L3MBTL1_ENST00000373134.1_Frame_Shift_Del_p.H398fs			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	398					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						CCTACATCCACCCAGTGGGCT	0.582																																					p.H466fs		Atlas-INDEL	.											.	L3MBTL1	105	.	0			c.1397delA						.						76	73	74					20																	42162009		2203	4300	6503	SO:0001589	frameshift_variant	26013	exon13			.	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.1398delC	chr20.hg19:g.42162009delC	ENSP00000402107:p.His466fs	97.0	0.0		148.0	10.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Frame_Shift_Del	DEL	ENST00000427442.2	hg19	CCDS46602.2																																																																																			.	.		0.582	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		-	42162009	C	-	42162009	7	5	114	1	0	1	0	1	0	0	0	0	8600	506	18	0	1232	0	L3MBTL	20	42162009	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	855456	42162009	20863511	1172	19444										
WFDC3	140686	hgsc.bcm.edu	37	chr20	44416474	44416474	+	Splice_Site	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtggggacagcgtttcttaCccagcttctgtttagagatt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:44416474delC	ENST00000243938.4	-	4	442		c.e4+1		WFDC3_ENST00000372630.2_Intron|WFDC3_ENST00000481847.1_Splice_Site|WFDC3_ENST00000372632.2_Intron	NM_080614.1	NP_542181.1	Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3							extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				GCGTTTCTTACCCAGCTTCTG	0.433																																					.		Atlas-INDEL	.											.	WFDC3	18	.	0			c.358+2G>-						.						173	134	147					20																	44416474		2203	4300	6503	SO:0001630	splice_region_variant	140686	exon5			.	AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116		"WAP four-disulfide core domain containing"	15957	protein-coding gene	gene with protein product						12206714, 10680116	Standard	NM_080614		Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000243938.4:c.358+1G>-	chr20.hg19:g.44416474delC		197.0	0.0		217.0	14.0	NM_080614	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	Splice_Site	DEL	ENST00000243938.4	hg19	CCDS33478.1																																																																																			.	.		0.433	WFDC3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316858.1		Intron	-	44416474	C	-	44416474	8	5	114	1	0	1	0	1	0	0	1	0	17368	521	18	0	352	0	WFDC3	20	44416474	Splice_Site	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	2254465	44416474	18609046	1173	19445										
CDH22	64405	hgsc.bcm.edu	37	chr20	44839091	44839091	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gtcggtcacggccacgcgcaCgatcgcctggtcgcggaacg	15	15	1	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:44839091C>T	ENST00000372262.3	-	6	1541	c.1141G>A	c.(1141-1143)Gtg>Atg	p.V381M	CDH22_ENST00000537909.1_Missense_Mutation_p.V381M|CDH22_ENST00000474438.1_5'UTR	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	381	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				GCCACGCGCACGATCGCCTGG	0.711																																					p.V381M		Atlas-SNP	.											.	CDH22	112	.	0			c.G1141A						.						20	19	19					20																	44839091		2198	4294	6492	SO:0001583	missense	64405	exon7			CGCGCACGATCGC	AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"Cadherins / Major cadherins"	13251	protein-coding gene	gene with protein product		609920	"cadherin-like 22"	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.1141G>A	chr20.hg19:g.44839091C>T	ENSP00000361336:p.Val381Met	89.0	0.0		128.0	58.0	NM_021248	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	hg19	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.721056	0.89205	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.55588	0.51;0.51	4.17	4.17	0.49024	Cadherin (3);Cadherin-like (1);	0.072247	0.56097	D	0.000034	T	0.75788	0.3897	H	0.96142	3.775	0.58432	D	0.999992	D	0.76494	0.999	P	0.60415	0.874	T	0.81920	-0.0712	10	0.87932	D	0	.	9.4414	0.38670	0.0:0.9025:0.0:0.0975	.	381	Q9UJ99	CAD22_HUMAN	M	381	ENSP00000361336:V381M;ENSP00000437790:V381M	ENSP00000361336:V381M	V	-	1	0	CDH22	44272498	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.776000	0.62354	2.171000	0.68590	0.555000	0.69702	GTG	.	.		0.711	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		T	44839091	C	T	44839091	3	4	114	1	0	0	0	0	1	0	0	0	3109	536	19	1	1369	1	CDH22	20	44839091	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	422617	44839091	18186429	1174	19446										
PREX1	57580	hgsc.bcm.edu	37	chr20	47256419	47256419	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccacggattgtacactcttcTttctgtttaaactctggggc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:47256419delT	ENST00000371941.3	-	30	3811	c.3789delA	c.(3787-3789)aaafs	p.K1263fs	PREX1_ENST00000496915.1_5'Flank|PREX1_ENST00000396220.1_Frame_Shift_Del_p.K1263fs	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1263					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TACACTCTTCTTTCTGTTTAA	0.552																																					p.E1264fs		Atlas-INDEL	.											.	PREX1	441	.	0			c.3790delG						.						124	125	125					20																	47256419		2203	4300	6503	SO:0001589	frameshift_variant	57580	exon30			.	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3789delA	chr20.hg19:g.47256419delT	ENSP00000361009:p.Lys1263fs	131.0	0.0		183.0	11.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Frame_Shift_Del	DEL	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.		0.552	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		-	47256419	T	-	47256419	7	5	114	1	0	1	0	1	0	0	0	0	12488	1606	56	0	1234	0	PREX1	20	47256419	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2417328	47256419	15769101	1175	19447										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50307291	50307291	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cacttactcgggtaaaagttCccacgaagttgtgaatgtca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:50307291delC	ENST00000338821.5	-	8	974	c.710delG	c.(709-711)ggafs	p.G237fs	ATP9A_ENST00000311637.5_Intron|ATP9A_ENST00000402822.1_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	237					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GGTAAAAGTTCCCACGAAGTT	0.458																																					p.G237fs		Atlas-INDEL	.											.	ATP9A	135	.	0			c.711delA						.						203	181	189					20																	50307291		2203	4300	6503	SO:0001589	frameshift_variant	10079	exon8			.	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.710delG	chr20.hg19:g.50307291delC	ENSP00000342481:p.Gly237fs	120.0	0.0		156.0	11.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Frame_Shift_Del	DEL	ENST00000338821.5	hg19	CCDS33489.1																																																																																			.	.		0.458	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		-	50307291	C	-	50307291	7	5	114	1	0	1	0	1	0	0	0	0	1198	855	30	0	2517	0	ATP9A	20	50307291	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	3050872	50307291	12718229	1176	19448										
ZFP64	55734	hgsc.bcm.edu	37	chr20	50713933	50713933	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cgtgtggattctgagatggcGgtccaagtctttcatgccat							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:50713933delG	ENST00000361387.2	-	7	1015	c.955delC	c.(955-957)cgcfs	p.R319fs	ZFP64_ENST00000371523.4_Frame_Shift_Del_p.R100fs|ZFP64_ENST00000371518.2_Frame_Shift_Del_p.R319fs|ZFP64_ENST00000477786.1_5'UTR	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	276					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CTGAGATGGCGGTCCAAGTCT	0.408																																					p.R319fs		Atlas-INDEL	.											.	ZFP64	240	.	0			c.956delG						.						267	266	267					20																	50713933		2203	4300	6503	SO:0001589	frameshift_variant	55734	exon7			.	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000361387.2:c.955delC	chr20.hg19:g.50713933delG	ENSP00000355179:p.Arg319fs	131.0	0.0		179.0	11.0	NM_199427	Q9NTS7|Q9NVH4	Frame_Shift_Del	DEL	ENST00000361387.2	hg19	CCDS13439.1																																																																																			.	.		0.408	ZFP64-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079743.2	NM_018197		-	50713933	G	-	50713933	7	5	114	1	0	1	0	1	0	0	0	0	17667	1116	39	0	994	0	ZFP64	20	50713933	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	406642	50713933	12311587	1177	19449										
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51872669	51872669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatctctaagtttacgggacTctcaatgaccactatcagtc	6	11	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:51872669T>C	ENST00000371497.5	+	2	3559	c.2672T>C	c.(2671-2673)cTc>cCc	p.L891P	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.L888P|TSHZ2_ENST00000603338.2_Missense_Mutation_p.L888P	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	891					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			TTTACGGGACTCTCAATGACC	0.512																																					p.L891P		Atlas-SNP	.											.	TSHZ2	209	.	0			c.T2672C						.						84	81	82					20																	51872669		2203	4300	6503	SO:0001583	missense	128553	exon2			CGGGACTCTCAAT	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2672T>C	chr20.hg19:g.51872669T>C	ENSP00000360552:p.Leu891Pro	92.0	0.0		98.0	4.0	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.995405	0.54147	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.32753	1.46;1.44	5.67	5.67	0.87782	Homeobox (1);Homeodomain-like (1);	0.060169	0.64402	D	0.000004	T	0.50137	0.1598	L	0.47190	1.495	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.51140	-0.8743	10	0.87932	D	0	-1.7421	15.9017	0.79384	0.0:0.0:0.0:1.0	.	891	Q9NRE2	TSH2_HUMAN	P	891;888;417	ENSP00000360552:L891P;ENSP00000333114:L888P	ENSP00000333114:L888P	L	+	2	0	TSHZ2	51306076	1.000000	0.71417	0.344000	0.25628	0.568000	0.35870	7.693000	0.84214	2.152000	0.67230	0.450000	0.29827	CTC	.	.		0.512	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		C	51872669	T	C	51872669	3	2	114	1	0	0	0	0	1	0	0	0	16639	1551	54	2	2678	2	TSHZ2	20	51872669	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1158736	51872669	11152851	1178	19450										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52193705	52193705	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gatttttaccatcgttcttgActtcagcagcaacatcggtt	7	10	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:52193705A>G	ENST00000371471.2	-	4	2023	c.1598T>C	c.(1597-1599)gTc>gCc	p.V533A	ZNF217_ENST00000302342.3_Missense_Mutation_p.V533A|RP4-724E16.2_ENST00000424252.1_RNA			O75362	ZN217_HUMAN	zinc finger protein 217	533					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			ATCGTTCTTGACTTCAGCAGC	0.398																																					p.V533A		Atlas-SNP	.											.	ZNF217	227	.	0			c.T1598C						.						113	107	109					20																	52193705		2203	4300	6503	SO:0001583	missense	7764	exon3			TTCTTGACTTCAG	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1598T>C	chr20.hg19:g.52193705A>G	ENSP00000360526:p.Val533Ala	75.0	0.0		93.0	4.0	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	hg19	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	A	4.692	0.128602	0.08981	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.09163	3.01;3.01	5.69	-5.58	0.02512	.	1.338680	0.04850	N	0.442196	T	0.07863	0.0197	L	0.33485	1.01	0.09310	N	0.999999	B	0.02656	0.0	B	0.06405	0.002	T	0.39078	-0.9631	10	0.28530	T	0.3	-7.4465	8.1405	0.31080	0.5039:0.1812:0.3149:0.0	.	533	O75362	ZN217_HUMAN	A	533	ENSP00000360526:V533A;ENSP00000304308:V533A	ENSP00000304308:V533A	V	-	2	0	ZNF217	51627112	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-2.380000	0.01066	-0.943000	0.03691	-0.810000	0.03169	GTC	.	.		0.398	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		G	52193705	A	G	52193705	3	3	114	1	0	0	0	0	1	0	0	0	17787	275	10	2	1556	2	ZNF217	20	52193705	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	321036	52193705	10831815	1179	19451										
OSBPL2	9885	hgsc.bcm.edu	37	chr20	60861769	60861769	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccccccaactctgcccaggTctgtgtccctccatggcctg	9	19	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:60861769T>C	ENST00000313733.3	+	11	1327		c.e11+2		OSBPL2_ENST00000358053.2_Splice_Site|OSBPL2_ENST00000439951.2_Splice_Site	NM_144498.1	NP_653081.1	Q9H1P3	OSBL2_HUMAN	oxysterol binding protein-like 2						lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			TCTGCCCAGGTCTGTGTCCCT	0.662																																					.		Atlas-SNP	.											.	OSBPL2	51	.	0			c.1125+2T>C						.						61	54	57					20																	60861769		2203	4300	6503	SO:0001630	splice_region_variant	9885	exon11			CCCAGGTCTGTGT	AB018315	CCDS13494.1, CCDS13495.1, CCDS63323.1	20q13.3	2008-08-01	2001-11-28		ENSG00000130703	ENSG00000130703		"Oxysterol binding proteins"	15761	protein-coding gene	gene with protein product		606731	"oxysterol-binding protein-like 2"			10588946, 11861666	Standard	NM_144498		Approved	KIAA0772, ORP-2	uc002yck.1	Q9H1P3	OTTHUMG00000032909	ENST00000313733.3:c.1125+2T>C	chr20.hg19:g.60861769T>C		58.0	0.0		76.0	4.0	NM_144498	A8K736|Q6IBT0|Q9BZB1|Q9Y4B8	Splice_Site	SNP	ENST00000313733.3	hg19	CCDS13495.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.203267	0.79127	.	.	ENSG00000130703	ENST00000358053;ENST00000313733;ENST00000439951	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6244	0.56622	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	OSBPL2	60295164	1.000000	0.71417	0.968000	0.41197	0.893000	0.52053	7.945000	0.87732	1.812000	0.52913	0.533000	0.62120	.	.	.		0.662	OSBPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080021.1	NM_014835	Intron	C	60861769	T	C	60861769	5	2	114	1	0	0	0	0	0	0	1	0	11287	1681	58	2	1165	2	OSBPL2	20	60861769	Splice_Site	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	8668064	60861769	2163751	1180	19452										
ADRM1	11047	hgsc.bcm.edu	37	chr20	60882434	60882434	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgcccctcgcaggtgggctGggggccctgactggacctgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:60882434delG	ENST00000253003.2	+	6	595	c.549delG	c.(547-549)ctgfs	p.L183fs	LAMA5_ENST00000492698.1_5'Flank|RP11-157P1.4_ENST00000414042.1_RNA	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	183	Gly-rich.				positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			CAGGTGGGCTGGGGGCCCTGA	0.667																																					p.L183fs		Atlas-INDEL	.											.	ADRM1	28	.	0			c.548delT						.						29	30	30					20																	60882434		2197	4297	6494	SO:0001589	frameshift_variant	11047	exon6			.	D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.549delG	chr20.hg19:g.60882434delG	ENSP00000253003:p.Leu183fs	115.0	0.0		159.0	10.0	NM_175573	A0PKB1|Q96FJ7|Q9H1P2	Frame_Shift_Del	DEL	ENST00000253003.2	hg19	CCDS13496.1																																																																																			.	.		0.667	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1			-	60882434	G	-	60882434	7	5	114	1	0	1	0	1	0	0	0	0	345	1335	47	0	567	0	ADRM1	20	60882434	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	20665	60882434	2143086	1181	19453										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60928262	60928262	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagcacccagaggtccggccGgggtgagttggcaaacttga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:60928262delG	ENST00000252999.3	-	3	562	c.496delC	c.(496-498)cggfs	p.R166fs	RP11-157P1.5_ENST00000487421.1_RNA|RP11-157P1.5_ENST00000456721.2_RNA|LAMA5_ENST00000370692.3_Frame_Shift_Del_p.R166fs|RP11-157P1.5_ENST00000477848.1_RNA|LAMA5_ENST00000370677.3_Frame_Shift_Del_p.R166fs|RP11-157P1.5_ENST00000478167.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	166	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGGTCCGGCCGGGGTGAGTTG	0.672																																					p.R166fs		Atlas-INDEL	.											.	LAMA5	268	.	0			c.497delG						.						41	38	39					20																	60928262		2182	4282	6464	SO:0001589	frameshift_variant	3911	exon3			.	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.496delC	chr20.hg19:g.60928262delG	ENSP00000252999:p.Arg166fs	137.0	0.0		178.0	11.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Frame_Shift_Del	DEL	ENST00000252999.3	hg19	CCDS33502.1																																																																																			.	.		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		-	60928262	G	-	60928262	7	5	114	1	0	1	0	1	0	0	0	0	8618	1115	39	0	10903	0	LAMA5	20	60928262	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	45828	60928262	2097258	1182	19454										
COL9A3	1299	hgsc.bcm.edu	37	chr20	61458146	61458146	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttgggttccgagggccgcctGggatcccaggagcgcctggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:61458146delG	ENST00000343916.3	+	15	769	c.766delG	c.(766-768)gggfs	p.G256fs		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	256	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					AGGGCCGCCTGGGATCCCAGG	0.667																																					p.P255fs		Atlas-INDEL	.											.	COL9A3	70	.	0			c.765delT						.						36	35	35					20																	61458146		2200	4298	6498	SO:0001589	frameshift_variant	1299	exon15			.	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2219	protein-coding gene	gene with protein product	"collagen type IX proteoglycan"	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.766delG	chr20.hg19:g.61458146delG	ENSP00000341640:p.Gly256fs	85.0	0.0		134.0	10.0	NM_001853	Q13681|Q9H4G9|Q9UPE2	Frame_Shift_Del	DEL	ENST00000343916.3	hg19	CCDS13505.1																																																																																			.	.		0.667	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853		-	61458146	G	-	61458146	7	5	114	1	0	1	0	1	0	0	0	0	3711	1348	47	0	824	0	COL9A3	20	61458146	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	529884	61458146	1567374	1183	19455										
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62059777	62059777	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcagctccagctggttcagcGgggggataagtctggggcaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:62059777delG	ENST00000359125.2	-	10	1334	c.1160delC	c.(1159-1161)ccgfs	p.P387fs	KCNQ2_ENST00000370224.1_Frame_Shift_Del_p.P377fs|KCNQ2_ENST00000357249.2_Frame_Shift_Del_p.P387fs|KCNQ2_ENST00000360480.3_Frame_Shift_Del_p.P377fs|KCNQ2_ENST00000359689.1_Frame_Shift_Del_p.P387fs|KCNQ2_ENST00000344462.4_Frame_Shift_Del_p.P387fs|KCNQ2_ENST00000354587.3_Frame_Shift_Del_p.P377fs	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	387					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CTGGTTCAGCGGGGGGATAAG	0.627																																					p.P387fs		Atlas-INDEL	.											KCNQ2,rectum,carcinoma,0,1	KCNQ2	201	.	0			c.1161delG						.						31	30	30					20																	62059777		2200	4297	6497	SO:0001589	frameshift_variant	3785	exon10			.	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1160delC	chr20.hg19:g.62059777delG	ENSP00000352035:p.Pro387fs	143.0	0.0		195.0	13.0	NM_172106	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Frame_Shift_Del	DEL	ENST00000359125.2	hg19	CCDS13520.1																																																																																			.	.		0.627	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		-	62059777	G	-	62059777	7	5	114	1	0	1	0	1	0	0	0	0	8092	1116	39	0	1490	0	KCNQ2	20	62059777	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	601631	62059777	965743	1184	19456										
PRIC285	85441	hgsc.bcm.edu	37	chr20	62193204	62193204	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	acatccaccgacttgttggaGgggccgcagtacaagatgca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:62193204delG	ENST00000467148.1	-	11	6732	c.6663delC	c.(6661-6663)cccfs	p.P2221fs	HELZ2_ENST00000427522.2_Frame_Shift_Del_p.P1652fs	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2221	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										ACTTGTTGGAGGGGCCGCAGT	0.667																																					p.S2222fs		Atlas-INDEL	.											.	.	.	.	0			c.6664delT						.						8	10	9					20																	62193204		2149	4237	6386	SO:0001589	frameshift_variant	85441	exon12			.	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.6663delC	chr20.hg19:g.62193204delG	ENSP00000417401:p.Pro2221fs	109.0	0.0		139.0	11.0	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Frame_Shift_Del	DEL	ENST00000467148.1	hg19	CCDS33508.1																																																																																			.	.		0.667	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		-	62193204	G	-	62193204	7	5	114	1	0	1	0	1	0	0	0	0	12497	987	35	0	1322	0	PRIC285	20	62193204	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	133427	62193204	832316	1185	19457										
PRPF6	57473	hgsc.bcm.edu	37	chr20	62614445	62614445	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gacattgggcccgcccgtgaTgcaaatgaccctgtggatga	13	11	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:62614445T>C	ENST00000450537.1	-	2	56				PRPF6_ENST00000535781.1_Silent_p.D39D|ZNF512B_ENST00000217130.3_Intron			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CCGCCCGTGATGCAAATGACC	0.577																																					p.D39D		Atlas-SNP	.											.	PRPF6	88	.	0			c.T117C						.						83	69	74					20																	62614445		2203	4300	6503	SO:0001627	intron_variant	24148	exon2			CCGTGATGCAAAT	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.5-15137A>G	chr20.hg19:g.62614445T>C		89.0	0.0		117.0	5.0	NM_012469	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	.		0.577	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		C	62614445	T	C	62614445	1	2	114	0	1	0	0	0	0	0	0	0	12586	1461	51	2		2	PRPF6	20	62614445	Intron	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	421241	62614445	411075	1186	19458										
APP	351	hgsc.bcm.edu	37	chr21	27354754	27354754	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggtgtctcgagatacttgTcaacggcatcaggggtactg	13	9	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:27354754T>C	ENST00000346798.3	-	9	1160	c.1127A>G	c.(1126-1128)gAc>gGc	p.D376G	APP_ENST00000359726.3_Missense_Mutation_p.D320G|APP_ENST00000357903.3_Missense_Mutation_p.D357G|APP_ENST00000440126.3_Missense_Mutation_p.D352G|APP_ENST00000439274.2_Missense_Mutation_p.D320G|APP_ENST00000348990.5_Missense_Mutation_p.D301G|APP_ENST00000358918.3_Missense_Mutation_p.D376G|APP_ENST00000448388.2_Missense_Mutation_p.D266G|APP_ENST00000354192.3_Missense_Mutation_p.D245G	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	376					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				GAGATACTTGTCAACGGCATC	0.468																																					p.D376G		Atlas-SNP	.											APP,NS,carcinoma,0,1	APP	90	.	0			c.A1127G						.						91	81	85					21																	27354754		2203	4300	6503	SO:0001583	missense	351	exon9			TACTTGTCAACGG	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1127A>G	chr21.hg19:g.27354754T>C	ENSP00000284981:p.Asp376Gly	91.0	0.0		94.0	4.0	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	hg19	CCDS13576.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.2|25.2	4.608698|4.608698	0.87258|0.87258	.|.	.|.	ENSG00000142192|ENSG00000142192	ENST00000346798;ENST00000354192;ENST00000348990;ENST00000357903;ENST00000358918;ENST00000359726;ENST00000448388;ENST00000440126;ENST00000439274|ENST00000448850;ENST00000415997	T;T;T;T;T;T;T;T;T|.	0.72051|.	-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62|.	5.45|5.45	5.45|5.45	0.79879|0.79879	Amyloidogenic glycoprotein, E2 domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.79644|.	0.4481|.	M|M	0.86343|0.86343	2.81|2.81	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.76494|.	0.999;0.998;0.993;0.999;0.991;0.991;0.995|.	D;D;D;D;D;D;D|.	0.76071|.	0.965;0.965;0.987;0.941;0.977;0.977;0.924|.	T|.	0.82438|.	-0.0457|.	10|.	0.87932|.	D|.	0|.	-28.6988|-28.6988	15.3372|15.3372	0.74266|0.74266	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	266;320;352;245;301;357;376|.	E9PEV0;E9PG40;B4DII8;P05067-10;P05067-4;P05067-8;P05067|.	.;.;.;.;.;.;A4_HUMAN|.	G|W	376;245;301;357;376;320;266;352;320|278;110	ENSP00000284981:D376G;ENSP00000346129:D245G;ENSP00000345463:D301G;ENSP00000350578:D357G;ENSP00000351796:D376G;ENSP00000352760:D320G;ENSP00000388538:D266G;ENSP00000387483:D352G;ENSP00000398879:D320G|.	ENSP00000284981:D376G|.	D|X	-|-	2|3	0|0	APP|APP	26276625|26276625	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.937000|0.937000	0.57800|0.57800	5.760000|5.760000	0.68793|0.68793	2.288000|2.288000	0.76882|0.76882	0.533000|0.533000	0.62120|0.62120	GAC|TGA	.	.		0.468	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		C	27354754	T	C	27354754	3	2	114	1	0	0	0	0	1	0	0	0	815	1667	58	2	1225	2	APP	21	27354754	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10		27354754	20775141	1187	19459										
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28210011	28210011	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggacagacacttcaagcttcTttttttgtaacccttcccac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:28210011delT	ENST00000284984.3	-	9	3245	c.2791delA	c.(2791-2793)agafs	p.R931fs		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	931	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		TTCAAGCTTCTTTTTTTGTAA	0.493																																					p.R931fs		Atlas-INDEL	.											.	ADAMTS1	131	.	0			c.2792delG						.						116	122	120					21																	28210011		2203	4300	6503	SO:0001589	frameshift_variant	9510	exon9			.	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.2791delA	chr21.hg19:g.28210011delT	ENSP00000284984:p.Arg931fs	257.0	0.0		204.0	14.0	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Frame_Shift_Del	DEL	ENST00000284984.3	hg19	CCDS33524.1																																																																																			.	.		0.493	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			-	28210011	T	-	28210011	7	5	114	1	0	1	0	1	0	0	0	0	255	1617	56	0	116	0	ADAMTS1	21	28210011	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	855257	28210011	19919884	1188	19460										
CLDN8	9073	hgsc.bcm.edu	37	chr21	31587622	31587622	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttctttccggtgtgataacTtttttgggttgtgcgatggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:31587622delT	ENST00000399899.1	-	1	769	c.622delA	c.(622-624)agtfs	p.S208fs	CLDN8_ENST00000286809.1_Frame_Shift_Del_p.S208fs	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	208					calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						GTGTGATAACTTTTTTGGGTT	0.423																																					p.S208fs		Atlas-INDEL	.											.	CLDN8	40	.	0			c.623delG						.						152	138	142					21																	31587622		2203	4300	6503	SO:0001589	frameshift_variant	9073	exon1			.	AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284		"Claudins"	2050	protein-coding gene	gene with protein product		611231				9892664	Standard	NM_199328		Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.622delA	chr21.hg19:g.31587622delT	ENSP00000382783:p.Ser208fs	207.0	0.0		182.0	12.0	NM_199328	D3DSE3|Q53EX7	Frame_Shift_Del	DEL	ENST00000399899.1	hg19	CCDS13587.1																																																																																			.	.		0.423	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	NM_199328		-	31587622	T	-	31587622	7	5	114	1	0	1	0	1	0	0	0	0	3493	1609	56	0	59	0	CLDN8	21	31587622	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	3377611	31587622	16542273	1189	19461										
TTC3	7267	hgsc.bcm.edu	37	chr21	38494152	38494152	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgtgatgctctttctatgctGggggaatatgactgggccct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:38494152delG	ENST00000399017.2	+	12	3683	c.936delG	c.(934-936)ctgfs	p.L312fs	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Frame_Shift_Del_p.L312fs|TTC3_ENST00000540756.1_Frame_Shift_Del_p.L2fs|TTC3_ENST00000355666.1_Frame_Shift_Del_p.L312fs	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	312					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TTTCTATGCTGGGGGAATATG	0.353																																					p.L312fs	Ovarian(38;194 1649 35661)	Atlas-INDEL	.											.	TTC3	182	.	0			c.935delT						.						59	60	60					21																	38494152		2203	4300	6503	SO:0001589	frameshift_variant	7267	exon12			.	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.936delG	chr21.hg19:g.38494152delG	ENSP00000381981:p.Leu312fs	204.0	0.0		187.0	12.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Frame_Shift_Del	DEL	ENST00000399017.2	hg19	CCDS13651.1																																																																																			.	.		0.353	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			-	38494152	G	-	38494152	7	5	114	1	0	1	0	1	0	0	0	0	16712	1335	47	0	978	0	TTC3	21	38494152	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	6906530	38494152	9635743	1190	19462										
IGSF5	150084	hgsc.bcm.edu	37	chr21	41151128	41151128	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actagcaggcaccatgcttcTgacgccgacgtgtactctta	9	13	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:41151128T>C	ENST00000380588.4	+	5	933	c.830T>C	c.(829-831)cTg>cCg	p.L277P	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	277					single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				ACCATGCTTCTGACGCCGACG	0.478																																					p.L277P		Atlas-SNP	.											.	IGSF5	62	.	0			c.T830C						.						116	107	110					21																	41151128		2203	4300	6503	SO:0001583	missense	150084	exon5			TGCTTCTGACGCC		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5952	protein-coding gene	gene with protein product	"junctional adhesion molecule 4"	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.830T>C	chr21.hg19:g.41151128T>C	ENSP00000369962:p.Leu277Pro	103.0	0.0		94.0	4.0	NM_001080444		Missense_Mutation	SNP	ENST00000380588.4	hg19	CCDS33562.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.598544	0.46318	.	.	ENSG00000183067	ENST00000380588	T	0.10099	2.91	4.24	3.09	0.35607	.	0.398152	0.26038	N	0.026714	T	0.15696	0.0378	L	0.27053	0.805	0.45962	D	0.998788	D	0.69078	0.997	D	0.65573	0.936	T	0.02444	-1.1158	10	0.87932	D	0	-1.6326	6.6193	0.22794	0.0:0.1056:0.0:0.8944	.	277	Q9NSI5	IGSF5_HUMAN	P	277	ENSP00000369962:L277P	ENSP00000369962:L277P	L	+	2	0	IGSF5	40072998	0.960000	0.32886	0.282000	0.24776	0.019000	0.09904	0.317000	0.19487	0.967000	0.38186	0.533000	0.62120	CTG	.	.		0.478	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1			C	41151128	T	C	41151128	3	2	114	1	0	0	0	0	1	0	0	0	7611	1580	55	2	848	2	IGSF5	21	41151128	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2656976	41151128	6978767	1191	19463										
C2CD2	25966	hgsc.bcm.edu	37	chr21	43362260	43362260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggctcctgggctcaccttcTcctccgccgacctgagcacg	11	18	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:43362260T>C	ENST00000380486.3	-	2	615	c.374A>G	c.(373-375)gAg>gGg	p.E125G		NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	125						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						GCTCACCTTCTCCTCCGCCGA	0.597																																					p.E125G		Atlas-SNP	.											.	C2CD2	47	.	0			c.A374G						.						10	12	11					21																	43362260		1678	3353	5031	SO:0001583	missense	25966	exon2			ACCTTCTCCTCCG	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"TMEM24-like"		"chromosome 21 open reading frame 25"	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.374A>G	chr21.hg19:g.43362260T>C	ENSP00000369853:p.Glu125Gly	161.0	0.0		111.0	6.0	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	hg19	CCDS42933.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.513290	0.64522	.	.	ENSG00000157617	ENST00000380486	T	0.25414	1.8	4.57	4.57	0.56435	.	0.247937	0.43579	D	0.000557	T	0.39627	0.1085	M	0.69823	2.125	0.38930	D	0.957913	D	0.60575	0.988	P	0.54815	0.761	T	0.33777	-0.9855	10	0.44086	T	0.13	-48.8196	10.6194	0.45470	0.0:0.0:0.0:1.0	.	125	Q9Y426	CU025_HUMAN	G	125	ENSP00000369853:E125G	ENSP00000369853:E125G	E	-	2	0	C2CD2	42235329	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	2.926000	0.48892	2.279000	0.76181	0.533000	0.62120	GAG	.	.		0.597	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500		C	43362260	T	C	43362260	3	2	114	1	0	0	0	0	1	0	0	0	2154	1551	54	2	1768	2	C2CD2	21	43362260	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2211132	43362260	4767635	1192	19464										
WDR4	10785	hgsc.bcm.edu	37	chr21	44282502	44282502	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagcggtcatcaggactcacAgcctgcatcaccaggggcca	11	14	4	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:44282502A>G	ENST00000398208.2	-	5	515	c.456T>C	c.(454-456)gcT>gcC	p.A152A	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Silent_p.A152A	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4											haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		CAGGACTCACAGCCTGCATCA	0.607																																					p.A152A		Atlas-SNP	.											.	WDR4	35	.	0			c.T456C						.						26	24	24					21																	44282502		2203	4300	6503	SO:0001819	synonymous_variant	10785	exon5			ACTCACAGCCTGC	AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"WD repeat domain containing"	12756	protein-coding gene	gene with protein product	"TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.456T>C	chr21.hg19:g.44282502A>G		41.0	0.0		43.0	4.0	NM_018669		Silent	SNP	ENST00000398208.2	hg19	CCDS13691.1																																																																																			.	.		0.607	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1			G	44282502	A	G	44282502	2	3	114	1	0	0	0	0	0	0	0	1	17308	175	7	2		2	WDR4	21	44282502	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	920242	44282502	3847393	1193	19465										
NDUFV3	4731	hgsc.bcm.edu	37	chr21	44323563	44323563	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctcgtcaggtgggtcggaaAgtgacgtcgccttcgtcttc	14	11	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:44323563A>G	ENST00000340344.4	+	3	235				NDUFV3_ENST00000354250.2_Silent_p.K147K|NDUFV3_ENST00000460259.1_3'UTR	NM_001001503.1	NP_001001503.1	P56181	NDUV3_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	10				STAD - Stomach adenocarcinoma(101;0.0606)		TGGGTCGGAAAGTGACGTCGC	0.473																																					p.K147K		Atlas-SNP	.											.	NDUFV3	23	.	0			c.A441G						.						118	122	120					21																	44323563		2203	4300	6503	SO:0001627	intron_variant	4731	exon3			TCGGAAAGTGACG		CCDS33572.1, CCDS33573.1	21q22.3	2011-07-04	2002-08-29		ENSG00000160194	ENSG00000160194	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7719	protein-coding gene	gene with protein product	"complex I 10kDa subunit"	602184	"NADH dehydrogenase (ubiquinone) flavoprotein 3 (10kD)"			9344673	Standard	NM_021075		Approved	CI-10k	uc002zcm.3	P56181	OTTHUMG00000086823	ENST00000340344.4:c.170-5411A>G	chr21.hg19:g.44323563A>G		109.0	0.0		91.0	4.0	NM_021075	A8K0M1|J3KNX7|Q6FGD3|Q8WU60|Q9HCR5	Silent	SNP	ENST00000340344.4	hg19	CCDS33573.1																																																																																			.	.		0.473	NDUFV3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195448.2			G	44323563	A	G	44323563	1	3	114	0	1	0	0	0	0	0	0	0	10310	69	3	2		2	NDUFV3	21	44323563	Intron	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	41061	44323563	3806332	1194	19466										
AIRE	326	hgsc.bcm.edu	37	chr21	45707420	45707420	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gctctcaactgaaggccaagCcccccaagaagccggagagc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:45707420delC	ENST00000291582.5	+	4	611	c.484delC	c.(484-486)cccfs	p.P163fs		NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	163					humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		GAAGGCCAAGCCCCCCAAGAA	0.716									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy																												p.K161fs		Atlas-INDEL	.											.	AIRE	61	.	0			c.483delG						.																																			SO:0001589	frameshift_variant	326	exon4	Familial Cancer Database	APECED	.	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"Zinc fingers, PHD-type"	360	protein-coding gene	gene with protein product	"autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"	607358	"autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.484delC	chr21.hg19:g.45707420delC	ENSP00000291582:p.Pro163fs	347.0	0.0		263.0	17.0	NM_000383	B2RP50|O43922|O43932|O75745	Frame_Shift_Del	DEL	ENST00000291582.5	hg19	CCDS13706.1																																																																																			.	.		0.716	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2			-	45707420	C	-	45707420	7	5	114	1	0	1	0	1	0	0	0	0	437	739	26	0	498	0	AIRE	21	45707420	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1383857	45707420	2422475	1195	19467										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46899863	46899863	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggactccaggggacgtaggTcccaagggcgacaaggtgag	18	9	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:46899863T>C	ENST00000359759.4	+	9	2562	c.2541T>C	c.(2539-2541)ggT>ggC	p.G847G	COL18A1_ENST00000355480.5_Silent_p.G612G|COL18A1_ENST00000400337.2_Silent_p.G432G			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	847	Triple-helical region 2 (COL2).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GGGACGTAGGTCCCAAGGGCG	0.672																																					p.G612G		Atlas-SNP	.											.	COL18A1	129	.	0			c.T1836C						.						65	79	74					21																	46899863		2008	4167	6175	SO:0001819	synonymous_variant	80781	exon9			CGTAGGTCCCAAG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2541T>C	chr21.hg19:g.46899863T>C		67.0	0.0		60.0	4.0	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	hg19																																																																																				.	.		0.672	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			C	46899863	T	C	46899863	2	2	114	1	0	0	0	0	0	0	0	1	3677	1654	58	2		2	COL18A1	21	46899863	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1192443	46899863	1230032	1196	19468										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47685325	47685325	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggcgccacagacggggtcagTgccaggacaggaggcagagg	19	10	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:47685325T>C	ENST00000397708.1	-	13	3398	c.3144A>G	c.(3142-3144)gcA>gcG	p.A1048A	MCM3AP_ENST00000291688.1_Silent_p.A1048A			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1048					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					ACGGGGTCAGTGCCAGGACAG	0.647																																					p.A1048A		Atlas-SNP	.											.	MCM3AP	146	.	0			c.A3144G						.						73	69	71					21																	47685325		2203	4300	6503	SO:0001819	synonymous_variant	8888	exon12			GGTCAGTGCCAGG	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.3144A>G	chr21.hg19:g.47685325T>C		78.0	0.0		66.0	4.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	hg19	CCDS13734.1																																																																																			.	.		0.647	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		C	47685325	T	C	47685325	2	2	114	1	0	0	0	0	0	0	0	1	9397	1683	59	2		2	MCM3AP	21	47685325	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	785462	47685325	444570	1197	19469										
TUBA8	51807	hgsc.bcm.edu	37	chr22	18609172	18609172	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgattttccacagttttggtGggggcactggctccggcttc					rs377420893		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:18609172delG	ENST00000330423.3	+	4	500	c.427delG	c.(427-429)gggfs	p.G144fs	TUBA8_ENST00000316027.6_Frame_Shift_Del_p.G78fs	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	144					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	14						CAGTTTTGGTGGGGGCACTGG	0.532																																					p.G142fs		Atlas-INDEL	.											.	TUBA8	36	.	0			c.426delT						.						95	100	98					22																	18609172		2203	4300	6503	SO:0001589	frameshift_variant	51807	exon4			.	AJ245922	CCDS13751.1, CCDS54495.1	22q11	2005-06-11			ENSG00000183785	ENSG00000183785		"Tubulins"	12410	protein-coding gene	gene with protein product		605742		TUBAL2		10772959, 10591208	Standard	NM_001193414		Approved		uc002znv.2	Q9NY65	OTTHUMG00000150097	ENST00000330423.3:c.427delG	chr22.hg19:g.18609172delG	ENSP00000333326:p.Gly144fs	134.0	0.0		169.0	11.0	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Frame_Shift_Del	DEL	ENST00000330423.3	hg19	CCDS13751.1																																																																																			.	.		0.532	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943		-	18609172	G	-	18609172	7	5	114	1	0	1	0	1	0	0	0	0	16765	1348	47	0	441	0	TUBA8	22	18609172	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10		18609172	32695394	1198	19470										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19217362	19217362	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tagcctacaagtcactgaccTggggtgcatgaacaaggttc	11	10	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:19217362T>C	ENST00000263200.10	-	11	1853	c.1781A>G	c.(1780-1782)cAg>cGg	p.Q594R	CLTCL1_ENST00000353891.5_Splice_Site_p.Q594R|CLTCL1_ENST00000427926.1_Splice_Site_p.Q594R	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	594	Distal segment.|Heavy chain arm.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GTCACTGACCTGGGGTGCATG	0.537			T	?	ALCL																																p.Q594R		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.A1781G						.						40	40	40					22																	19217362		1993	4180	6173	SO:0001630	splice_region_variant	8218	exon11			CTGACCTGGGGTG		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.1782+1A>G	chr22.hg19:g.19217362T>C		66.0	0.0		93.0	4.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.987145	0.74589	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.21543	2.0;2.0;2.0	4.28	4.28	0.50868	Armadillo-type fold (1);	0.072576	0.56097	D	0.000025	T	0.48607	0.1509	M	0.83603	2.65	0.58432	D	0.999998	D;D	0.64830	0.993;0.994	D;D	0.87578	0.968;0.998	T	0.53528	-0.8426	10	0.49607	T	0.09	-15.6511	13.7083	0.62653	0.0:0.0:0.0:1.0	.	594;594	P53675-2;P53675	.;CLH2_HUMAN	R	594	ENSP00000439662:Q594R;ENSP00000445677:Q594R;ENSP00000441158:Q594R	ENSP00000445677:Q594R	Q	-	2	0	CLTCL1	17597362	1.000000	0.71417	1.000000	0.80357	0.465000	0.32709	7.261000	0.78400	1.696000	0.51158	0.528000	0.53228	CAG	.	.		0.537	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	Missense_Mutation	C	19217362	T	C	19217362	5	2	114	1	0	0	0	0	0	0	1	0	3569	1594	55	2	3229	2	CLTCL1	22	19217362	Splice_Site	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	608190	19217362	32087204	1199	19471										
HIRA	7290	hgsc.bcm.edu	37	chr22	19346949	19346949	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcaggcggctcagcttcacgCcccccaccactgtcacttca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:19346949delC	ENST00000263208.5	-	18	2400	c.2144delG	c.(2143-2145)ggcfs	p.G715fs	HIRA_ENST00000340170.4_Intron|HIRA_ENST00000541063.1_Frame_Shift_Del_p.G671fs|HIRA_ENST00000546308.1_Frame_Shift_Del_p.G671fs	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	715	Interaction with CCNA1.|Interaction with PAX3. {ECO:0000250}.|Interaction with histone H2B.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					CAGCTTCACGCCCCCCACCAC	0.597																																					p.G715fs		Atlas-INDEL	.											.	HIRA	100	.	0			c.2145delC						.						146	121	129					22																	19346949		2203	4300	6503	SO:0001589	frameshift_variant	7290	exon18			.	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"WD repeat domain containing"	4916	protein-coding gene	gene with protein product	"DiGeorge critical region gene 1"	600237	"HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)", "HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.2144delG	chr22.hg19:g.19346949delC	ENSP00000263208:p.Gly715fs	112.0	0.0		154.0	10.0	NM_003325	Q05BU9|Q8IXN2	Frame_Shift_Del	DEL	ENST00000263208.5	hg19	CCDS13759.1																																																																																			.	.		0.597	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		-	19346949	C	-	19346949	7	5	114	1	0	1	0	1	0	0	0	0	7129	739	26	0	941	0	HIRA	22	19346949	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	129587	19346949	31957617	1200	19472										
ARVCF	421	hgsc.bcm.edu	37	chr22	19959474	19959474	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccgtggcctccgctccctccGgtccaccgtggagtatccgt	11	18	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:19959474G>T	ENST00000263207.3	-	18	3007	c.2716C>A	c.(2716-2718)Cgg>Agg	p.R906R	ARVCF_ENST00000344269.3_Silent_p.R843R|ARVCF_ENST00000401994.1_Silent_p.R843R|ARVCF_ENST00000406259.1_Silent_p.R900R|ARVCF_ENST00000406522.1_Silent_p.R837R	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	906			R -> Q (in dbSNP:rs165815). {ECO:0000269|PubMed:19690332}.		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CGCTCCCTCCGGTCCACCGTG	0.637																																					p.R906R		Atlas-SNP	.											.	ARVCF	54	.	0			c.C2716A						.						65	63	64					22																	19959474		2203	4300	6503	SO:0001819	synonymous_variant	421	exon18			CCCTCCGGTCCAC		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"Armadillo repeat containing"	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.2716C>A	chr22.hg19:g.19959474G>T		47.0	0.0		88.0	6.0	NM_001670	B7WNV2	Silent	SNP	ENST00000263207.3	hg19	CCDS13771.1																																																																																			.	.		0.637	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		T	19959474	G	T	19959474	2	4	114	1	0	0	0	0	0	0	0	1	1003	1115	39	1		1	ARVCF	22	19959474	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	612525	19959474	31345092	1201	19473										
AIFM3	150209	hgsc.bcm.edu	37	chr22	21328152	21328152	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cactacggcgcacccctggtGaaaggtgagctgtcaggtgg	15	11	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:21328152G>T	ENST00000399167.2	+	4	591	c.351G>T	c.(349-351)gtG>gtT	p.V117V	AIFM3_ENST00000405089.1_Silent_p.V123V|AIFM3_ENST00000440238.2_Silent_p.V117V|AIFM3_ENST00000335375.5_Intron|AIFM3_ENST00000333607.6_Silent_p.V117V|AIFM3_ENST00000399163.2_Silent_p.V117V	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	117	Rieske. {ECO:0000255|PROSITE- ProRule:PRU00628}.				cell redox homeostasis (GO:0045454)|execution phase of apoptosis (GO:0097194)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	21	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			CACCCCTGGTGAAAGGTGAGC	0.617																																					p.V123V		Atlas-SNP	.											.	AIFM3	49	.	0			c.G369T						.						35	30	32					22																	21328152		2187	4291	6478	SO:0001819	synonymous_variant	150209	exon4			CCTGGTGAAAGGT	AK094844	CCDS13786.1, CCDS33605.1, CCDS54503.1	22q11.21	2007-05-03			ENSG00000183773	ENSG00000183773			26398	protein-coding gene	gene with protein product						15764604	Standard	NM_144704		Approved	AIFL, FLJ30473		Q96NN9	OTTHUMG00000150804	ENST00000399167.2:c.351G>T	chr22.hg19:g.21328152G>T		63.0	0.0		113.0	34.0	NM_001146288	B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Silent	SNP	ENST00000399167.2	hg19	CCDS13786.1																																																																																			.	.		0.617	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704		T	21328152	G	T	21328152	2	4	114	1	0	0	0	0	0	0	0	1	428	1277	45	3		3	AIFM3	22	21328152	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	1368678	21328152	29976414	1202	19474										
PPM1F	9647	hgsc.bcm.edu	37	chr22	22277539	22277539	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgcctcctcccttctgcctGggggtccccttctccctggt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:22277539delG	ENST00000263212.5	-	8	1396	c.1291delC	c.(1291-1293)cagfs	p.Q431fs	PPM1F_ENST00000407142.1_Frame_Shift_Del_p.Q263fs|PPM1F_ENST00000538191.1_Frame_Shift_Del_p.Q327fs	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	431					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		CCTTCTGCCTGGGGGTCCCCT	0.662																																					p.Q431fs		Atlas-INDEL	.											.	PPM1F	34	.	0			c.1292delA						.						53	62	59					22																	22277539		2203	4300	6503	SO:0001589	frameshift_variant	9647	exon8			.	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19388	protein-coding gene	gene with protein product	"partner of PIX 2", "Ca(2+)/calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1F (PP2C domain containing)"			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.1291delC	chr22.hg19:g.22277539delG	ENSP00000263212:p.Gln431fs	128.0	0.0		182.0	11.0	NM_014634	A8K6G3|B7Z2C3|Q96PM2	Frame_Shift_Del	DEL	ENST00000263212.5	hg19	CCDS13796.1																																																																																			.	.		0.662	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634		-	22277539	G	-	22277539	7	5	114	1	0	1	0	1	0	0	0	0	12351	1357	47	0	77	0	PPM1F	22	22277539	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	949387	22277539	29027027	1203	19475										
TOP3B	8940	hgsc.bcm.edu	37	chr22	22318323	22318323	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcctctgtggcagacttcatGggggtgatggggggatggtc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:22318323delG	ENST00000398793.2	-	11	1610	c.1176delC	c.(1174-1176)cccfs	p.P392fs	TOP3B_ENST00000357179.5_Frame_Shift_Del_p.P392fs|TOP3B_ENST00000413067.2_Frame_Shift_Del_p.P121fs	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	392					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		CAGACTTCATGGGGGTGATGG	0.607																																					p.M393X		Atlas-INDEL	.											.	TOP3B	107	.	0			c.1177delA						.						80	76	77					22																	22318323		2203	4300	6503	SO:0001589	frameshift_variant	8940	exon11			.	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.1176delC	chr22.hg19:g.22318323delG	ENSP00000381773:p.Pro392fs	103.0	0.0		139.0	10.0	NM_003935	A0M8Q3|Q9BUP5	Frame_Shift_Del	DEL	ENST00000398793.2	hg19	CCDS13797.1																																																																																			.	.		0.607	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935		-	22318323	G	-	22318323	7	5	114	1	0	1	0	1	0	0	0	0	16383	1335	47	0	1444	0	TOP3B	22	22318323	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	40784	22318323	28986243	1204	19476										
ZNF280B	140883	hgsc.bcm.edu	37	chr22	22842944	22842944	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agactcaaaatgtctgttttTgccaattcattttccctatc	4	10	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:22842944T>A	ENST00000406426.1	-	4	1522	c.780A>T	c.(778-780)gcA>gcT	p.A260A	ZNF280B_ENST00000360412.2_Silent_p.A260A			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TGTCTGTTTTTGCCAATTCAT	0.363																																					p.A260A		Atlas-SNP	.											.	ZNF280B	67	.	0			c.A780T						.						106	100	102					22																	22842944		2203	4300	6503	SO:0001819	synonymous_variant	140883	exon4			TGTTTTTGCCAAT	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"zinc finger protein 279", "suppressor of hairy wing homolog 2 (Drosophila)"	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.780A>T	chr22.hg19:g.22842944T>A		81.0	0.0		100.0	17.0	NM_080764		Silent	SNP	ENST00000406426.1	hg19	CCDS13799.1																																																																																			.	.		0.363	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764		A	22842944	T	A	22842944	2	1	114	1	0	0	0	0	0	0	0	1	17830	1799	63	4		4	ZNF280B	22	22842944	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	524621	22842944	28461622	1205	19477										
CYTSA	23384	hgsc.bcm.edu	37	chr22	24726381	24726381	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaaactcacaaaagaattggAggaaataaagtcacgcaagt	9	6	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:24726381A>G	ENST00000314328.9	+	8	2663	c.2378A>G	c.(2377-2379)gAg>gGg	p.E793G	SPECC1L_ENST00000541492.1_Missense_Mutation_p.E793G|SPECC1L_ENST00000437398.1_Missense_Mutation_p.E793G|SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.E793G	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	793					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						AAAGAATTGGAGGAAATAAAG	0.378																																					p.E793G		Atlas-SNP	.											.	SPECC1L	85	.	0			c.A2378G						.						87	91	90					22																	24726381		2203	4300	6503	SO:0001583	missense	23384	exon7			AATTGGAGGAAAT	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"cytokinesis and spindle organization A", "cytospin A"	614140	"SPECC1-like"			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.2378A>G	chr22.hg19:g.24726381A>G	ENSP00000325785:p.Glu793Gly	67.0	0.0		82.0	4.0	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	hg19	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.829453	0.71258	.	.	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000314328;ENST00000541492	T;T;T	0.46451	0.87;0.87;0.87	5.94	5.94	0.96194	.	0.097898	0.64402	D	0.000002	T	0.38054	0.1026	L	0.33753	1.03	0.80722	D	1	B;P	0.46987	0.124;0.888	B;P	0.44561	0.031;0.453	T	0.09907	-1.0653	9	.	.	.	-30.0623	15.5759	0.76387	1.0:0.0:0.0:0.0	.	793;793	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	G	821;793;793;793	ENSP00000393363:E793G;ENSP00000325785:E793G;ENSP00000439633:E793G	.	E	+	2	0	SPECC1L	23056381	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.000000	0.93564	2.272000	0.75746	0.459000	0.35465	GAG	.	.		0.378	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		G	24726381	A	G	24726381	3	3	114	1	0	0	0	0	1	0	0	0	4211	304	11	2	2400	2	CYTSA	22	24726381	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1883437	24726381	26578185	1206	19478										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26164836	26164836	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccaaatccctgggagaaagtGgggaggtttcctgggaagaa					rs369889484		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:26164836delG	ENST00000407587.2	+	4	1122	c.953delG	c.(952-954)tggfs	p.W318fs	MYO18B_ENST00000335473.7_Frame_Shift_Del_p.W318fs|MYO18B_ENST00000536101.1_Frame_Shift_Del_p.W318fs			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	318						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GGGAGAAAGTGGGGAGGTTTC	0.537																																					p.W318fs		Atlas-INDEL	.											.	MYO18B	322	.	0			c.952delT						.						29	30	30					22																	26164836		1949	4146	6095	SO:0001589	frameshift_variant	84700	exon4			.	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.953delG	chr22.hg19:g.26164836delG	ENSP00000386096:p.Trp318fs	99.0	0.0		127.0	11.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Frame_Shift_Del	DEL	ENST00000407587.2	hg19																																																																																				.	.		0.537	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		-	26164836	G	-	26164836	7	5	114	1	0	1	0	1	0	0	0	0	10075	1357	47	0	963	0	MYO18B	22	26164836	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1438455	26164836	25139730	1207	19479										
TFIP11	24144	hgsc.bcm.edu	37	chr22	26902743	26902743	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcctgcaatagagactaccgTttttagcttccttggtccaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:26902743delT	ENST00000407690.1	-	5	644	c.361delA	c.(361-363)acgfs	p.T121fs	TFIP11_ENST00000496523.1_5'Flank|TFIP11_ENST00000407148.1_Frame_Shift_Del_p.T121fs|TFIP11_ENST00000407431.1_Frame_Shift_Del_p.T121fs|TFIP11_ENST00000405938.1_Frame_Shift_Del_p.T121fs	NM_012143.2	NP_036275.1	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	121					biomineral tissue development (GO:0031214)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|spliceosomal complex disassembly (GO:0000390)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	DNA binding (GO:0003677)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25						GAGACTACCGTTTTTAGCTTC	0.463																																					p.T121fs		Atlas-INDEL	.											.	TFIP11	72	.	0			c.362delC						.						115	107	110					22																	26902743		2203	4300	6503	SO:0001589	frameshift_variant	24144	exon6			.	AL050258	CCDS13838.1	22q12.1	2013-01-28			ENSG00000100109	ENSG00000100109		"G patch domain containing"	17165	protein-coding gene	gene with protein product		612747				10806191, 11230166	Standard	NM_012143		Approved	TIP39, DKFZP434B194, Spp382	uc003acs.2	Q9UBB9	OTTHUMG00000150883	ENST00000407690.1:c.361delA	chr22.hg19:g.26902743delT	ENSP00000384421:p.Thr121fs	103.0	0.0		140.0	10.0	NM_001008697	O95908|Q20WL0|Q5H8V8|Q9UGV7|Q9Y2Q8	Frame_Shift_Del	DEL	ENST00000407690.1	hg19	CCDS13838.1																																																																																			.	.		0.463	TFIP11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320750.1	NM_001008697		-	26902743	T	-	26902743	7	5	114	1	0	1	0	1	0	0	0	0	15822	1725	60	0	2196	0	TFIP11	22	26902743	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	737907	26902743	24401823	1208	19480										
CHEK2	11200	hgsc.bcm.edu	37	chr22	29099532	29099532	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatcttctgcatcaaaaaagTttttaatcttgatgatgcaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:29099532delT	ENST00000405598.1	-	9	1060	c.869delA	c.(868-870)aacfs	p.N290fs	CHEK2_ENST00000402731.1_Frame_Shift_Del_p.N290fs|CHEK2_ENST00000403642.1_Frame_Shift_Del_p.N199fs|CHEK2_ENST00000544772.1_Frame_Shift_Del_p.N69fs|CHEK2_ENST00000328354.6_Frame_Shift_Del_p.N290fs|CHEK2_ENST00000382578.1_Frame_Shift_Del_p.N199fs|CHEK2_ENST00000382580.2_Frame_Shift_Del_p.N333fs|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000404276.1_Frame_Shift_Del_p.N290fs|CHEK2_ENST00000464581.1_5'UTR|CHEK2_ENST00000382566.1_Intron|CHEK2_ENST00000348295.3_Frame_Shift_Del_p.N290fs			O96017	CHK2_HUMAN	checkpoint kinase 2	290	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						ATCAAAAAAGTTTTTAATCTT	0.333			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.N333fs		Atlas-INDEL	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.999delC						.						16	18	17					22																	29099532		2197	4295	6492	SO:0001589	frameshift_variant	11200	exon9			.	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"CHK2 (checkpoint, S.pombe) homolog", "CHK2 checkpoint homolog (S. pombe)"	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.869delA	chr22.hg19:g.29099532delT	ENSP00000386087:p.Asn290fs	84.0	0.0		131.0	10.0	NM_001005735	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Frame_Shift_Del	DEL	ENST00000405598.1	hg19	CCDS13843.1																																																																																			.	.		0.333	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		-	29099532	T	-	29099532	7	5	114	1	0	1	0	1	0	0	0	0	3337	1725	60	0	794	0	CHEK2	22	29099532	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	2196789	29099532	22205034	1209	19481										
MTMR3	8897	hgsc.bcm.edu	37	chr22	30387534	30387534	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcagtgtcaagagtggctgaAgagactgaacaacgcaatcc	12	9	1	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:30387534A>G	ENST00000401950.2	+	7	677	c.335A>G	c.(334-336)aAg>aGg	p.K112R	MTMR3_ENST00000415511.1_3'UTR|MTMR3_ENST00000323630.5_5'UTR|MTMR3_ENST00000351488.3_Missense_Mutation_p.K112R|MTMR3_ENST00000333027.3_Missense_Mutation_p.K112R|MTMR3_ENST00000406629.1_Missense_Mutation_p.K112R	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	112					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			GAGTGGCTGAAGAGACTGAAC	0.413																																					p.K112R		Atlas-SNP	.											.	MTMR3	106	.	0			c.A335G						.						119	103	108					22																	30387534		2203	4300	6503	SO:0001583	missense	8897	exon7			GGCTGAAGAGACT	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.335A>G	chr22.hg19:g.30387534A>G	ENSP00000384651:p.Lys112Arg	68.0	0.0		79.0	5.0	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	hg19	CCDS13870.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.040850	0.35989	.	.	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000445401;ENST00000351488;ENST00000406629	D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.76630	0.4014	L	0.32530	0.975	0.80722	D	1	P;B;P	0.40302	0.712;0.125;0.712	B;B;B	0.38683	0.279;0.05;0.279	T	0.77270	-0.2650	10	0.40728	T	0.16	.	15.3779	0.74625	1.0:0.0:0.0:0.0	.	112;112;112	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	R	112	ENSP00000384651:K112R;ENSP00000331649:K112R;ENSP00000409063:K112R;ENSP00000307271:K112R;ENSP00000384077:K112R	ENSP00000331649:K112R	K	+	2	0	MTMR3	28717534	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.225000	0.72522	0.533000	0.62120	AAG	.	.		0.413	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		G	30387534	A	G	30387534	3	3	114	1	0	0	0	0	1	0	0	0	9954	72	3	2	353	2	MTMR3	22	30387534	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1288002	30387534	20917032	1210	19482										
SEC14L4	284904	hgsc.bcm.edu	37	chr22	30887947	30887947	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agtagctcttgggcacctcaCccccatagttgatctgtggg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:30887947delC	ENST00000255858.7	-	10	868	c.785delG	c.(784-786)ggtfs	p.G262fs	SEC14L4_ENST00000381982.3_Frame_Shift_Del_p.G262fs|RP4-539M6.14_ENST00000610156.1_RNA|SEC14L4_ENST00000392772.2_Frame_Shift_Del_p.G208fs|RP4-539M6.14_ENST00000442126.1_RNA|SEC14L4_ENST00000540456.1_Frame_Shift_Del_p.G247fs	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	262	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	GGGCACCTCACCCCCATAGTT	0.617																																					p.G262fs		Atlas-INDEL	.											.	SEC14L4	43	.	0			c.786delT						.						64	57	59					22																	30887947		2203	4300	6503	SO:0001589	frameshift_variant	284904	exon10			.	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.785delG	chr22.hg19:g.30887947delC	ENSP00000255858:p.Gly262fs	118.0	0.0		158.0	10.0	NM_001161368	A5D6W7|A6NCV4	Frame_Shift_Del	DEL	ENST00000255858.7	hg19	CCDS13878.1																																																																																			.	.		0.617	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977		-	30887947	C	-	30887947	7	5	114	1	0	1	0	1	0	0	0	0	13999	507	18	0	453	0	SEC14L4	22	30887947	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	500413	30887947	20416619	1211	19483										
MORC2	22880	hgsc.bcm.edu	37	chr22	31334114	31334114	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atcagtcggctacagttgtaGatgaacatgccatccagatc	9	10	1	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:31334114G>A	ENST00000397641.3	-	13	1560	c.1152C>T	c.(1150-1152)atC>atT	p.I384I	MORC2_ENST00000215862.4_Silent_p.I322I|MORC2_ENST00000469915.1_Intron			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	384						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						TACAGTTGTAGATGAACATGC	0.443																																					p.I322I		Atlas-SNP	.											.	MORC2	78	.	0			c.C966T						.						123	98	107					22																	31334114		2203	4300	6503	SO:0001819	synonymous_variant	22880	exon14			GTTGTAGATGAAC	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1152C>T	chr22.hg19:g.31334114G>A		137.0	0.0		155.0	7.0	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Silent	SNP	ENST00000397641.3	hg19																																																																																				.	.		0.443	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		A	31334114	G	A	31334114	2	1	114	1	0	0	0	0	0	0	0	1	9711	932	33	3		3	MORC2	22	31334114	Silent	SNP	G	TCGA-DD-A3A0-01A-11D-A20W-10	446167	31334114	19970452	1212	19484										
PATZ1	23598	hgsc.bcm.edu	37	chr22	31723029	31723029	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccaagggcagggcccaggtCccccagggggcccccgagag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:31723029delC	ENST00000266269.5	-	5	2541	c.1912delG	c.(1912-1914)gacfs	p.D638fs	PATZ1_ENST00000405309.3_3'UTR|PATZ1_ENST00000351933.4_Frame_Shift_Del_p.D592fs|RP3-400N23.6_ENST00000440456.1_RNA	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	638					male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)		EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						GGGCCCAGGTCCCCCAGGGGG	0.567																																					p.D638fs		Atlas-INDEL	.											.	PATZ1	24	.	0			c.1913delA						.						72	79	77					22																	31723029		2203	4300	6503	SO:0001589	frameshift_variant	23598	exon5			.	AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13071	protein-coding gene	gene with protein product		605165	"zinc finger protein 278"	ZNF278		10591208, 18241078, 18401526	Standard	NM_014323		Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.1912delG	chr22.hg19:g.31723029delC	ENSP00000266269:p.Asp638fs	126.0	0.0		183.0	13.0	NM_014323	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Frame_Shift_Del	DEL	ENST00000266269.5	hg19	CCDS13894.1																																																																																			.	.		0.567	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052		-	31723029	C	-	31723029	7	5	114	1	0	1	0	1	0	0	0	0	11485	855	30	0	155	0	PATZ1	22	31723029	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	388915	31723029	19581537	1213	19485										
C22orf28	51493	hgsc.bcm.edu	37	chr22	32789991	32789991	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcactggctgtccagtgagcTgaggatgcacataaatcaaa	11	9	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:32789991T>C	ENST00000216038.5	-	10	1278		c.e10-2		RTCB_ENST00000451746.2_Intron	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		TCCAGTGAGCTGAGGATGCAC	0.403																																					.		Atlas-SNP	.											.	C22orf28	43	.	0			c.1180-2A>G						.						111	98	102					22																	32789991		2203	4300	6503	SO:0001630	splice_region_variant	51493	exon11			GTGAGCTGAGGAT	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"focal adhesion-associated protein"	613901	"chromosome 22 open reading frame 28"	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.1180-2A>G	chr22.hg19:g.32789991T>C		56.0	0.0		75.0	4.0	NM_014306		Splice_Site	SNP	ENST00000216038.5	hg19	CCDS13905.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.082258	0.76528	.	.	ENSG00000100220	ENST00000216038	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6325	0.68666	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	C22orf28	31119991	1.000000	0.71417	0.999000	0.59377	0.956000	0.61745	7.885000	0.87282	1.851000	0.53745	0.482000	0.46254	.	.	.		0.403	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306	Intron	C	32789991	T	C	32789991	5	2	114	1	0	0	0	0	0	0	1	0	2142	1594	55	2	351	2	C22orf28	22	32789991	Splice_Site	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1066962	32789991	18514575	1214	19486										
BPIL2	254240	hgsc.bcm.edu	37	chr22	32811918	32811918	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttacctcaagaacttcaataTctgaattgacgaataagaat	5	7	3	4			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:32811918T>C	ENST00000397452.1	-	15	1495	c.1385A>G	c.(1384-1386)gAt>gGt	p.D462G	BPIFC_ENST00000534972.1_Missense_Mutation_p.D186G|BPIFC_ENST00000300399.3_Missense_Mutation_p.D462G|BPIFC_ENST00000432451.2_Missense_Mutation_p.D219G			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	462						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										AACTTCAATATCTGAATTGAC	0.363																																					p.D462G		Atlas-SNP	.											.	.	.	.	0			c.A1385G						.						87	87	87					22																	32811918		2203	4300	6503	SO:0001583	missense	254240	exon14			TCAATATCTGAAT	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.1385A>G	chr22.hg19:g.32811918T>C	ENSP00000380594:p.Asp462Gly	68.0	0.0		99.0	4.0	NM_174932	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	hg19	CCDS13906.1	.	.	.	.	.	.	.	.	.	.	T	15.53	2.860192	0.51482	.	.	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000534972;ENST00000432451	T;T;T;T	0.08634	3.07;3.07;3.07;3.07	5.5	5.5	0.81552	.	0.649988	0.17083	N	0.187690	T	0.14527	0.0351	M	0.62016	1.91	0.35916	D	0.831468	B;B	0.34103	0.437;0.379	B;B	0.40864	0.342;0.272	T	0.09707	-1.0662	10	0.37606	T	0.19	-8.6693	12.2787	0.54751	0.0:0.0:0.0:1.0	.	219;462	A2RRF1;Q8NFQ6	.;BPIFC_HUMAN	G	462;462;186;219	ENSP00000380594:D462G;ENSP00000300399:D462G;ENSP00000439123:D186G;ENSP00000408920:D219G	ENSP00000300399:D462G	D	-	2	0	BPIFC	31141918	0.010000	0.17322	0.987000	0.45799	0.942000	0.58702	1.682000	0.37628	2.212000	0.71576	0.528000	0.53228	GAT	.	.		0.363	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		C	32811918	T	C	32811918	3	2	114	1	0	0	0	0	1	0	0	0	1494	1435	50	2	146	2	BPIL2	22	32811918	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	21927	32811918	18492648	1215	19487										
SSTR3	6753	hgsc.bcm.edu	37	chr22	37602587	37602587	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcctggctttccccaggcccTacaggtagctgatgcgcatc	10	15	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:37602587T>C	ENST00000328544.3	-	2	1789	c.1256A>G	c.(1255-1257)tAg>tGg	p.*419W	SSTR3_ENST00000402501.1_Nonstop_Mutation_p.*419W	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	0					cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	CCCCAGGCCCTACAGGTAGCT	0.637																																					p.X419W		Atlas-SNP	.											.	SSTR3	42	.	0			c.A1256G						.						42	47	46					22																	37602587		2202	4298	6500	SO:0001578	stop_lost	6753	exon2			AGGCCCTACAGGT		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"GPCR / Class A : Somatostatin receptors"	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.1256A>G	chr22.hg19:g.37602587T>C	ENSP00000330138:p.*419Serext*19	58.0	0.0		60.0	5.0	NM_001051	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	hg19	CCDS13944.1	.	.	.	.	.	.	.	.	.	.	T	8.854	0.945208	0.18356	.	.	ENSG00000183473	ENST00000328544;ENST00000402501	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7675	0.28988	0.0:0.1619:0.0:0.8381	rs11406761;rs58031140	.	.	.	W	419	.	.	X	-	2	0	SSTR3	35932533	1.000000	0.71417	0.982000	0.44146	0.186000	0.23388	4.076000	0.57591	2.053000	0.61076	0.402000	0.26972	TAG	.	.		0.637	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1			C	37602587	T	C	37602587	4	2	114	1	0	0	0	0	0	0	0	0	15214	1535	53	2	4	2	SSTR3	22	37602587	Nonstop_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4790669	37602587	13701979	1216	19488										
CYTH4	27128	hgsc.bcm.edu	37	chr22	37707049	37707049	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggggccgcgtgaagacgtggAaacggcgctggttcatcctg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:37707049delA	ENST00000248901.6	+	10	1016	c.829delA	c.(829-831)aaafs	p.K277fs		NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	277	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						GAAGACGTGGAAACGGCGCTG	0.637																																					p.W276X		Atlas-INDEL	.											.	CYTH4	51	.	0			c.828delG						.						169	137	148					22																	37707049		2203	4300	6503	SO:0001589	frameshift_variant	27128	exon10			.	AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"Pleckstrin homology (PH) domain containing"	9505	protein-coding gene	gene with protein product		606514	"pleckstrin homology, Sec7 and coiled/coil domains 4", "pleckstrin homology, Sec7 and coiled-coil domains 4"	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.829delA	chr22.hg19:g.37707049delA	ENSP00000248901:p.Lys277fs	140.0	0.0		178.0	13.0	NM_013385	Q5R3F9|Q9UGT6	Frame_Shift_Del	DEL	ENST00000248901.6	hg19	CCDS13946.1																																																																																			.	.		0.637	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1			-	37707049	A	-	37707049	7	5	114	1	0	1	0	1	0	0	0	0	4208	247	9	0	867	0	CYTH4	22	37707049	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	104462	37707049	13597517	1217	19489										
CYTH4	27128	hgsc.bcm.edu	37	chr22	37709517	37709517	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tccccttctacgacctggtcTctactcggaagaagaagatt	8	12	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:37709517T>C	ENST00000248901.6	+	13	1337	c.1150T>C	c.(1150-1152)Tct>Cct	p.S384P		NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	384					positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						CGACCTGGTCTCTACTCGGAA	0.587																																					p.S384P		Atlas-SNP	.											.	CYTH4	51	.	0			c.T1150C						.						158	132	141					22																	37709517		2203	4300	6503	SO:0001583	missense	27128	exon13			CTGGTCTCTACTC	AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"Pleckstrin homology (PH) domain containing"	9505	protein-coding gene	gene with protein product		606514	"pleckstrin homology, Sec7 and coiled/coil domains 4", "pleckstrin homology, Sec7 and coiled-coil domains 4"	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.1150T>C	chr22.hg19:g.37709517T>C	ENSP00000248901:p.Ser384Pro	129.0	0.0		146.0	6.0	NM_013385	Q5R3F9|Q9UGT6	Missense_Mutation	SNP	ENST00000248901.6	hg19	CCDS13946.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.94|15.94	2.981290|2.981290	0.53827|0.53827	.|.	.|.	ENSG00000100055|ENSG00000100055	ENST00000446506|ENST00000248901;ENST00000404204	.|T	.|0.07216	.|3.21	4.86|4.86	4.86|4.86	0.63082|0.63082	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.14743|0.14743	0.0356|0.0356	M|M	0.70275|0.70275	2.135|2.135	0.51233|0.51233	D|D	0.999912|0.999912	.|P	.|0.36647	.|0.563	.|B	.|0.42555	.|0.391	T|T	0.00899|0.00899	-1.1522|-1.1522	5|10	.|0.59425	.|D	.|0.04	.|.	9.6363|9.6363	0.39809|0.39809	0.0:0.0:0.2993:0.7007|0.0:0.0:0.2993:0.7007	.|.	.|384	.|Q9UIA0	.|CYH4_HUMAN	P|P	136|384;43	.|ENSP00000248901:S384P	.|ENSP00000248901:S384P	L|S	+|+	2|1	0|0	CYTH4|CYTH4	36039463|36039463	0.336000|0.336000	0.24757|0.24757	1.000000|1.000000	0.80357|0.80357	0.957000|0.957000	0.61999|0.61999	0.512000|0.512000	0.22755|0.22755	1.950000|1.950000	0.56595|0.56595	0.402000|0.402000	0.26972|0.26972	CTC|TCT	.	.		0.587	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1			C	37709517	T	C	37709517	3	2	114	1	0	0	0	0	1	0	0	0	4208	1551	54	2	1200	2	CYTH4	22	37709517	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2468	37709517	13595049	1218	19490										
MICALL1	85377	hgsc.bcm.edu	37	chr22	38321985	38321985	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gcacccctggtacggcatcaCccctaccagcagccccaaga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:38321985delC	ENST00000215957.6	+	8	1526	c.1400delC	c.(1399-1401)accfs	p.T467fs		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	467	Pro-rich.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					TACGGCATCACCCCTACCAGC	0.682																																					p.T467fs		Atlas-INDEL	.											.	MICALL1	53	.	0			c.1399delA						.						31	37	35					22																	38321985		2202	4299	6501	SO:0001589	frameshift_variant	85377	exon8			.	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"molecule interacting with Rab13"					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.1400delC	chr22.hg19:g.38321985delC	ENSP00000215957:p.Thr467fs	212.0	0.0		237.0	16.0	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Frame_Shift_Del	DEL	ENST00000215957.6	hg19	CCDS13961.1																																																																																			.	.		0.682	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		-	38321985	C	-	38321985	7	5	114	1	0	1	0	1	0	0	0	0	9582	507	18	0	1430	0	MICALL1	22	38321985	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	612468	38321985	12982581	1219	19491										
RANGAP1	5905	hgsc.bcm.edu	37	chr22	41645369	41645369	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agcagcaggggtgcaagggcCttggggaaatagtcctgctg	17	8	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:41645369C>A	ENST00000455915.2	-	14	3128	c.1659G>T	c.(1657-1659)aaG>aaT	p.K553N	RANGAP1_ENST00000356244.3_Missense_Mutation_p.K553N|RANGAP1_ENST00000407260.4_Missense_Mutation_p.K498N|RANGAP1_ENST00000405486.1_Missense_Mutation_p.K553N			P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	553					mitotic cell cycle (GO:0000278)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear pore (GO:0005643)|perinuclear region of cytoplasm (GO:0048471)	Ran GTPase activator activity (GO:0005098)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTGCAAGGGCCTTGGGGAAAT	0.602																																					p.K553N		Atlas-SNP	.											.	RANGAP1	47	.	0			c.G1659T						.						72	60	64					22																	41645369		2203	4300	6503	SO:0001583	missense	5905	exon15			AAGGGCCTTGGGG	X82260	CCDS14012.1	22q13	2013-01-17			ENSG00000100401	ENSG00000100401			9854	protein-coding gene	gene with protein product		602362	"segregation distorter homolog (Drosophila)"	SD		7878053	Standard	NM_002883		Approved	Fug1, KIAA1835	uc003azu.3	P46060	OTTHUMG00000150940	ENST00000455915.2:c.1659G>T	chr22.hg19:g.41645369C>A	ENSP00000401470:p.Lys553Asn	91.0	0.0		99.0	17.0	NM_002883	Q96JJ2	Missense_Mutation	SNP	ENST00000455915.2	hg19	CCDS14012.1	.	.	.	.	.	.	.	.	.	.	C	19.57	3.852060	0.71719	.	.	ENSG00000100401	ENST00000405486;ENST00000356244;ENST00000405383;ENST00000455915;ENST00000407260	T;T;T;T	0.47528	0.84;0.84;0.84;1.3	5.4	5.4	0.78164	Ran-GTPase activating protein 1, C-terminal (3);	0.147294	0.64402	D	0.000013	T	0.61135	0.2323	M	0.72894	2.215	0.47584	D	0.999464	D;P	0.67145	0.996;0.928	D;P	0.63597	0.916;0.74	T	0.59241	-0.7491	10	0.30854	T	0.27	-33.7749	9.5133	0.39091	0.0:0.8375:0.0:0.1625	.	498;553	F8W7I9;P46060	.;RAGP1_HUMAN	N	553;553;553;553;498	ENSP00000385866:K553N;ENSP00000348577:K553N;ENSP00000401470:K553N;ENSP00000385354:K498N	ENSP00000348577:K553N	K	-	3	2	RANGAP1	39975315	0.956000	0.32656	1.000000	0.80357	0.858000	0.48976	1.094000	0.30951	2.515000	0.84797	0.467000	0.42956	AAG	.	.		0.602	RANGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320606.1	NM_002883		A	41645369	C	A	41645369	3	1	114	1	0	0	0	0	1	0	0	0	13048	680	24	3	112	3	RANGAP1	22	41645369	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	3323384	41645369	9659197	1220	19492										
POLDIP3	84271	hgsc.bcm.edu	37	chr22	42991558	42991558	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttacaacaatgtcctcctcAgtgactcgagggtgcagatt	9	11	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:42991558A>G	ENST00000252115.5	-	6	980	c.876T>C	c.(874-876)acT>acC	p.T292T	POLDIP3_ENST00000491021.1_5'UTR|POLDIP3_ENST00000348657.2_Silent_p.T263T|POLDIP3_ENST00000451060.2_Silent_p.T136T|POLDIP3_ENST00000339677.6_Intron	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	292	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						TGTCCTCCTCAGTGACTCGAG	0.478																																					p.T292T	Ovarian(52;967 1128 5875 19997 42537)	Atlas-SNP	.											.	POLDIP3	58	.	0			c.T876C						.						179	140	154					22																	42991558		2203	4300	6503	SO:0001819	synonymous_variant	84271	exon6			CTCCTCAGTGACT		CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"RNA binding motif (RRM) containing"	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.876T>C	chr22.hg19:g.42991558A>G		146.0	0.0		170.0	7.0	NM_032311	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Silent	SNP	ENST00000252115.5	hg19	CCDS14038.1																																																																																			.	.		0.478	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311		G	42991558	A	G	42991558	2	3	114	1	0	0	0	0	0	0	0	1	12204	175	7	2		2	POLDIP3	22	42991558	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1346189	42991558	8313008	1221	19493										
PARVG	64098	hgsc.bcm.edu	37	chr22	44587943	44587943	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcttagagcaccaaaagtggTctgaagtcagagaagttggt	12	6	3	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:44587943T>C	ENST00000444313.3	+	8	1003	c.519T>C	c.(517-519)ggT>ggC	p.G173G	PARVG_ENST00000415224.1_Silent_p.G173G|PARVG_ENST00000422871.1_Silent_p.G173G	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	173					actin cytoskeleton reorganization (GO:0031532)|cell-matrix adhesion (GO:0007160)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)	17		Ovarian(80;0.024)|all_neural(38;0.0299)				CCAAAAGTGGTCTGAAGTCAG	0.512																																					p.G173G		Atlas-SNP	.											PARVG,NS,carcinoma,0,1	PARVG	41	.	0			c.T519C						.						63	68	66					22																	44587943		2203	4300	6503	SO:0001819	synonymous_variant	64098	exon8			AAGTGGTCTGAAG	AF237772	CCDS14057.1	22q13.31	2013-01-24			ENSG00000138964	ENSG00000138964		"Parvins"	14654	protein-coding gene	gene with protein product		608122				11171322	Standard	NM_022141		Approved		uc003bep.4	Q9HBI0	OTTHUMG00000150473	ENST00000444313.3:c.519T>C	chr22.hg19:g.44587943T>C		53.0	0.0		82.0	4.0	NM_001137606	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Silent	SNP	ENST00000444313.3	hg19	CCDS14057.1																																																																																			.	.		0.512	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141		C	44587943	T	C	44587943	2	2	114	1	0	0	0	0	0	0	0	1	11479	1654	58	2		2	PARVG	22	44587943	Silent	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	1596385	44587943	6716623	1222	19494										
SMC1B	27127	hgsc.bcm.edu	37	chr22	45789663	45789663	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ttcagacattcttgattttgTtttttcaatttcatccacta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:45789663delT	ENST00000357450.4	-	9	1395	c.1396delA	c.(1396-1398)acafs	p.T466fs	SMC1B_ENST00000404354.3_Frame_Shift_Del_p.T466fs	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	466					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CTTGATTTTGTTTTTTCAATT	0.323																																					p.T466fs		Atlas-INDEL	.											.	SMC1B	215	.	0			c.1397delC						.						83	73	76					22																	45789663		1817	4074	5891	SO:0001589	frameshift_variant	27127	exon9			.	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.1396delA	chr22.hg19:g.45789663delT	ENSP00000350036:p.Thr466fs	122.0	0.0		183.0	14.0	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Frame_Shift_Del	DEL	ENST00000357450.4	hg19	CCDS43027.1																																																																																			.	.		0.323	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		-	45789663	T	-	45789663	7	5	114	1	0	1	0	1	0	0	0	0	14797	1725	60	0	2379	0	SMC1B	22	45789663	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1201720	45789663	5514903	1223	19495										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46777807	46777807	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccccagggtgcggtaaatgaTgaccagagcgacggcgaact	14	11	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:46777807T>C	ENST00000262738.3	-	21	7023	c.7024A>G	c.(7024-7026)Atc>Gtc	p.I2342V		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2342					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CGGTAAATGATGACCAGAGCG	0.726																																					p.I2342V		Atlas-SNP	.											.	CELSR1	242	.	0			c.A7024G						.						17	19	19					22																	46777807		2183	4283	6466	SO:0001583	missense	9620	exon21			AAATGATGACCAG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.7024A>G	chr22.hg19:g.46777807T>C	ENSP00000262738:p.Ile2342Val	80.0	0.0		88.0	4.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	T	5.349	0.249717	0.10130	.	.	ENSG00000075275	ENST00000262738	T	0.07216	3.21	4.89	-9.78	0.00496	Domain of unknown function DUF3497 (1);	0.465341	0.17759	N	0.162948	T	0.04815	0.0130	L	0.39898	1.24	0.31121	N	0.708885	B;B	0.31893	0.345;0.041	B;B	0.33392	0.163;0.097	T	0.16689	-1.0394	10	0.15952	T	0.53	.	9.9564	0.41668	0.0:0.4477:0.2836:0.2686	.	663;2342	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	V	2342	ENSP00000262738:I2342V	ENSP00000262738:I2342V	I	-	1	0	CELSR1	45156471	0.927000	0.31430	0.003000	0.11579	0.013000	0.08279	-0.011000	0.12721	-2.205000	0.00742	-0.388000	0.06559	ATC	.	.		0.726	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		C	46777807	T	C	46777807	3	2	114	1	0	0	0	0	1	0	0	0	3223	1464	51	2	2080	2	CELSR1	22	46777807	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	988144	46777807	4526759	1224	19496										
BRD1	23774	hgsc.bcm.edu	37	chr22	50187702	50187703	+	Missense_Mutation	DNP	CC	CC	AA													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttcctcgcccgcctccggcCccagcgcagctccgtcctct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:50187702_50187703CC>AA	ENST00000216267.8	-	6	2824_2825	c.2338_2339GG>TT	c.(2338-2340)GGg>TTg	p.G780L	BRD1_ENST00000342989.5_Missense_Mutation_p.G375L|BRD1_ENST00000404034.1_Missense_Mutation_p.G780L|BRD1_ENST00000457780.2_Missense_Mutation_p.G780L|BRD1_ENST00000404760.1_Missense_Mutation_p.G780L|BRD1_ENST00000542442.1_Missense_Mutation_p.G468L	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	780					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.G780V(1)|p.G375V(1)		endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		CGCCTCCGGCCCCAGCGCAGCT	0.663																																					p.G780V|p.G780W		Atlas-SNP	.											BRD1_ENST00000342989,NS,carcinoma,0,2|.	BRD1	144	.	2	Substitution - Missense(2)	kidney(2)	c.G2339T|c.G2338T						.																																			SO:0001583	missense	23774	exon6			TCCGGCCCCAGCG|CCGGCCCCAGCGC	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"BR140-like"	604589	"bromodomain-containing 1"			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2338_2339delinsAA	chr22.hg19:g.50187702_50187703delinsAA	ENSP00000216267:p.Gly780Leu	67.0	0.0		58.0|57.0	43.0|42.0	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	hg19	CCDS14080.1																																																																																			.	.		0.663	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		AA	50187703	CC	AA	50187702	3	1	114	1	0	0	0	0	1	0	0	0	1503	623	22	3	865	3	BRD1	22	50187702	Missense_Mutation	DNP	CC	TCGA-DD-A3A0-01A-11D-A20W-10	3409895	50187702	1116864	1225	19497										
TRABD	80305	hgsc.bcm.edu	37	chr22	50632890	50632890	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gggagcagggtgtacgtggtGgggacagcccacttcagcga							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:50632890delG	ENST00000303434.4	+	4	353	c.234delG	c.(232-234)gtgfs	p.V78fs	TRABD_ENST00000395827.1_Frame_Shift_Del_p.V78fs|RP3-402G11.25_ENST00000607943.1_RNA|TRABD_ENST00000380909.4_Frame_Shift_Del_p.V78fs|TRABD_ENST00000395829.1_Frame_Shift_Del_p.V78fs	NM_025204.2	NP_079480.2	Q9H4I3	TRABD_HUMAN	TraB domain containing	78										breast(1)|central_nervous_system(1)|large_intestine(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	7		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)		TGTACGTGGTGGGGACAGCCC	0.652																																					p.V78fs		Atlas-INDEL	.											.	TRABD	21	.	0			c.233delT						.						51	49	50					22																	50632890		2199	4295	6494	SO:0001589	frameshift_variant	80305	exon4			.	AL449244	CCDS14086.1	22q13.33	2006-07-06			ENSG00000170638	ENSG00000170638			28805	protein-coding gene	gene with protein product						12477932	Standard	NM_025204		Approved	PP2447	uc003bjs.1	Q9H4I3	OTTHUMG00000044644	ENST00000303434.4:c.234delG	chr22.hg19:g.50632890delG	ENSP00000305664:p.Val78fs	184.0	0.0		161.0	10.0	NM_025204	Q19CC5|Q96ED8|Q9H7N1|Q9UGX6|Q9UGX7	Frame_Shift_Del	DEL	ENST00000303434.4	hg19	CCDS14086.1																																																																																			.	.		0.652	TRABD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316987.1	NM_025204		-	50632890	G	-	50632890	7	5	114	1	0	1	0	1	0	0	0	0	16450	1335	47	0	244	0	TRABD	22	50632890	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	445188	50632890	671676	1226	19498										
MAPK12	6300	hgsc.bcm.edu	37	chr22	50695539	50695539	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccttcagcatctggtacacgAggaactggatccggtcctcg	11	13	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:50695539A>G	ENST00000215659.8	-	4	713	c.398T>C	c.(397-399)cTc>cCc	p.L133P	MAPK12_ENST00000497036.1_5'UTR|MAPK12_ENST00000395780.1_Missense_Mutation_p.L53P	NM_002969.3	NP_002960.2	P53778	MK12_HUMAN	mitogen-activated protein kinase 12	133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle arrest (GO:0007050)|DNA damage induced protein phosphorylation (GO:0006975)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of peptidase activity (GO:0010952)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTGGTACACGAGGAACTGGAT	0.662																																					p.L133P		Atlas-SNP	.											.	MAPK12	43	.	0			c.T398C						.						84	72	76					22																	50695539		2203	4300	6503	SO:0001583	missense	6300	exon4			TACACGAGGAACT	U66243	CCDS14089.1	22q13.3	2012-05-08			ENSG00000188130	ENSG00000188130	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6874	protein-coding gene	gene with protein product		602399		SAPK3		9169156	Standard	NM_002969		Approved	ERK6, PRKM12, p38gamma, SAPK-3	uc003bkm.1	P53778	OTTHUMG00000030145	ENST00000215659.8:c.398T>C	chr22.hg19:g.50695539A>G	ENSP00000215659:p.Leu133Pro	98.0	0.0		71.0	4.0	NM_002969	Q14260|Q6IC53|Q99588|Q99672	Missense_Mutation	SNP	ENST00000215659.8	hg19	CCDS14089.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.269694	0.80469	.	.	ENSG00000188130	ENST00000438835;ENST00000395780;ENST00000215659	T;T	0.15487	2.42;2.42	4.71	4.71	0.59529	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.25543	U	0.029959	T	0.46658	0.1404	M	0.87971	2.92	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.55036	-0.8203	10	0.87932	D	0	-20.3739	13.3024	0.60332	1.0:0.0:0.0:0.0	.	53;133;133	B5MDL5;P53778;F6TXG5	.;MK12_HUMAN;.	P	133;53;133	ENSP00000379126:L53P;ENSP00000215659:L133P	ENSP00000215659:L133P	L	-	2	0	MAPK12	49037666	1.000000	0.71417	0.888000	0.34837	0.817000	0.46193	5.780000	0.68956	1.988000	0.58038	0.402000	0.26972	CTC	.	.		0.662	MAPK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074999.2	NM_002969		G	50695539	A	G	50695539	3	3	114	1	0	0	0	0	1	0	0	0	9283	304	11	2	741	2	MAPK12	22	50695539	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	62649	50695539	609027	1227	19499										
MAPK11	5600	hgsc.bcm.edu	37	chr22	50704089	50704089	+	Splice_Site	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggactggatatatgtccgggCctgggggcacacaagaacac							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:50704089delC	ENST00000330651.6	-	10	863	c.763delG	c.(763-765)gcc>cc	p.A255fs	MAPK11_ENST00000495277.1_5'Flank	NM_002751.5	NP_002742.3	Q15759	MK11_HUMAN	mitogen-activated protein kinase 11	255	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|lung(4)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Regorafenib(DB08896)	TATGTCCGGGCCTGGGGGCAC	0.632																																					p.A255fs	GBM(9;634 739 50668)	Atlas-INDEL	.											.	MAPK11	23	.	0			c.764delC						.						27	31	30					22																	50704089		2203	4299	6502	SO:0001630	splice_region_variant	5600	exon10			.	Y14440	CCDS14090.1	22q13.33	2011-06-09			ENSG00000185386	ENSG00000185386	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6873	protein-coding gene	gene with protein product		602898		PRKM11		9218798	Standard	NM_002751		Approved	p38-2, p38Beta, SAPK2	uc003bkr.3	Q15759	OTTHUMG00000150226	ENST00000330651.6:c.763-1G>-	chr22.hg19:g.50704089delC		135.0	0.0		148.0	10.0	NM_002751	A8K730|B0LPG1|B7Z630|E7ETQ1|L7RT27|O00284|O15472|Q2XNF2	Frame_Shift_Del	DEL	ENST00000330651.6	hg19	CCDS14090.1																																																																																			.	.		0.632	MAPK11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316900.1		Frame_Shift_Del	-	50704089	C	-	50704089	8	5	114	1	0	1	0	1	0	0	1	0	9282	753	26	0	343	0	MAPK11	22	50704089	Splice_Site	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	8550	50704089	600477	1228	19500										
MIOX	55586	hgsc.bcm.edu	37	chr22	50928027	50928027	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gccgcgactaccagcagctgTgcagccagcaggacctggcc	13	16	0	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:50928027T>A	ENST00000216075.6	+	9	777	c.703T>A	c.(703-705)Tgc>Agc	p.C235S	MIOX_ENST00000395732.3_Missense_Mutation_p.C235S|MIOX_ENST00000395733.3_Intron	NM_017584.5	NP_060054.4	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	235					inositol catabolic process (GO:0019310)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)	aldo-keto reductase (NADP) activity (GO:0004033)|ferric iron binding (GO:0008199)|inositol oxygenase activity (GO:0050113)|NADP binding (GO:0050661)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	13		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCAGCAGCTGTGCAGCCAGCA	0.657																																					p.C235S		Atlas-SNP	.											MIOX,colon,carcinoma,0,1	MIOX	21	.	0			c.T703A						.						23	24	24					22																	50928027		2196	4292	6488	SO:0001583	missense	55586	exon9			CAGCTGTGCAGCC	AF197129	CCDS14092.1	22q13.3	2008-06-11	2005-06-15	2005-06-15	ENSG00000100253	ENSG00000100253			14522	protein-coding gene	gene with protein product	"kidney-specific protein 32"	606774	"aldehyde reductase (aldose reductase) like 6"	ALDRL6		10944187, 11716759	Standard	NM_017584		Approved		uc003bll.1	Q9UGB7	OTTHUMG00000150207	ENST00000216075.6:c.703T>A	chr22.hg19:g.50928027T>A	ENSP00000216075:p.Cys235Ser	124.0	0.0		128.0	0.0	NM_017584	Q05DJ6|Q5S8C9|Q9BZZ1|Q9UHB8	Missense_Mutation	SNP	ENST00000216075.6	hg19	CCDS14092.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.477193	0.84640	.	.	ENSG00000100253	ENST00000216075;ENST00000395732;ENST00000451761	.	.	.	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.73094	0.3543	M	0.63843	1.955	0.80722	D	1	P;P	0.45283	0.855;0.674	P;P	0.60473	0.875;0.8	T	0.70699	-0.4800	9	0.30078	T	0.28	2.714	13.0331	0.58854	0.0:0.0:0.0:1.0	.	235;235	A6PVH2;Q9UGB7	.;MIOX_HUMAN	S	235;235;215	.	ENSP00000216075:C235S	C	+	1	0	MIOX	49274893	1.000000	0.71417	0.999000	0.59377	0.938000	0.57974	7.608000	0.82898	1.953000	0.56701	0.533000	0.62120	TGC	.	.		0.657	MIOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316835.1	NM_017584		A	50928027	T	A	50928027	3	1	114	1	0	0	0	0	1	0	0	0	9599	1696	59	4	737	4	MIOX	22	50928027	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	223938	50928027	376539	1229	19501										
SHROOM2	357	hgsc.bcm.edu	37	chrX	9900715	9900715	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggacaccccgaaggccactgTctgtgagcgtggaagccagc	14	13	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:9900715T>C	ENST00000380913.3	+	6	3482	c.3392T>C	c.(3391-3393)gTc>gCc	p.V1131A	SHROOM2_ENST00000493668.1_3'UTR|SHROOM2_ENST00000418909.2_5'UTR	NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	1131					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				AAGGCCACTGTCTGTGAGCGT	0.662																																					p.V1131A		Atlas-SNP	.											.	SHROOM2	139	.	0			c.T3392C						.						62	52	56					X																	9900715		2203	4300	6503	SO:0001583	missense	357	exon6			CCACTGTCTGTGA	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"apical protein, Xenopus laevis-like", "apical protein-like (Xenopus laevis)"	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.3392T>C	chrX.hg19:g.9900715T>C	ENSP00000370299:p.Val1131Ala	70.0	0.0		88.0	4.0	NM_001649	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	hg19	CCDS14135.1	.	.	.	.	.	.	.	.	.	.	T	1.909	-0.451286	0.04572	.	.	ENSG00000146950	ENST00000380913	T	0.14391	2.51	3.15	1.25	0.21368	.	.	.	.	.	T	0.05135	0.0137	N	0.08118	0	0.34014	D	0.651804	B	0.02656	0.0	B	0.01281	0.0	T	0.44937	-0.9295	9	0.05833	T	0.94	.	7.3423	0.26644	0.0:0.7319:0.1661:0.102	.	1131	Q13796	SHRM2_HUMAN	A	1131	ENSP00000370299:V1131A	ENSP00000370299:V1131A	V	+	2	0	SHROOM2	9860715	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	1.717000	0.37991	-0.156000	0.11079	-0.188000	0.12872	GTC	.	.		0.662	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649		C	9900715	T	C	9900715	3	2	114	1	0	0	0	0	1	0	0	0	14309	1667	58	2	3414	2	SHROOM2	23	9900715	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10		9900715	145369845	1230	19502										
PIGA	5277	hgsc.bcm.edu	37	chrX	15339659	15339659	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cagatatctcattattctcaCcccctcttttactgtgagaa							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:15339659delC	ENST00000333590.4	-	6	1508	c.1424delG	c.(1423-1425)ggtfs	p.G475fs	PIGA_ENST00000482148.1_5'UTR|PIGA_ENST00000428964.1_Frame_Shift_Del_p.G160fs|PIGA_ENST00000542278.1_Frame_Shift_Del_p.G241fs	NM_002641.3	NP_002632.1	P37287	PIGA_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class A	475					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|positive regulation of metabolic process (GO:0009893)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)|UDP-glycosyltransferase activity (GO:0008194)			endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Hepatocellular(33;0.183)					ATTATTCTCACCCCCTCTTTT	0.383																																					p.G475fs		Atlas-INDEL	.											.	PIGA	34	.	0			c.1425delT						.						90	91	91					X																	15339659		2203	4300	6503	SO:0001589	frameshift_variant	5277	exon6			.	BC038236	CCDS14165.1, CCDS48086.1, CCDS48086.2	Xp22.1	2014-09-17	2008-07-31		ENSG00000165195	ENSG00000165195	2.4.1.198	"Glycosyltransferase group 1 domain containing", "Phosphatidylinositol glycan anchor biosynthesis"	8957	protein-coding gene	gene with protein product	"paroxysmal nocturnal hemoglobinuria", "phosphatidylinositol N-acetylglucosaminyltransferase"	311770	"phosphatidylinositol glycan, class A (paroxysmal nocturnal hemoglobinuria)"			8500164	Standard	NM_002641		Approved	GPI3	uc004cwr.3	P37287	OTTHUMG00000021174	ENST00000333590.4:c.1424delG	chrX.hg19:g.15339659delC	ENSP00000369820:p.Gly475fs	138.0	0.0		176.0	12.0	NM_002641	B4E0V2|Q16025|Q16250	Frame_Shift_Del	DEL	ENST00000333590.4	hg19	CCDS14165.1																																																																																			.	.		0.383	PIGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055854.1	NM_002641		-	15339659	C	-	15339659	7	5	114	1	0	1	0	1	0	0	0	0	11893	507	18	0	34	0	PIGA	23	15339659	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	5438944	15339659	139930901	1231	19503										
CDKL5	6792	hgsc.bcm.edu	37	chrX	18593549	18593549	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caagcaggaaaacattgtggAgttgaaggaagcatttcgtc	12	6	0	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:18593549A>G	ENST00000379989.3	+	6	506	c.221A>G	c.(220-222)gAg>gGg	p.E74G	CDKL5_ENST00000379996.3_Missense_Mutation_p.E74G	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	74	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					AACATTGTGGAGTTGAAGGAA	0.393																																					p.E74G		Atlas-SNP	.											.	CDKL5	124	.	0			c.A221G						.						182	167	172					X																	18593549		2203	4300	6503	SO:0001583	missense	6792	exon5			TTGTGGAGTTGAA	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"Cyclin-dependent kinases"	11411	protein-coding gene	gene with protein product		300203	"serine/threonine kinase 9"	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.221A>G	chrX.hg19:g.18593549A>G	ENSP00000369325:p.Glu74Gly	105.0	0.0		97.0	5.0	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	hg19	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.986496	0.74589	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.42513	0.97;0.97	5.69	5.69	0.88448	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.53351	0.1791	L	0.31845	0.965	0.53005	D	0.999966	D	0.71674	0.998	D	0.71870	0.975	T	0.55811	-0.8082	10	0.59425	D	0.04	-21.4508	14.8699	0.70448	1.0:0.0:0.0:0.0	.	74	O76039	CDKL5_HUMAN	G	74	ENSP00000369332:E74G;ENSP00000369325:E74G	ENSP00000369325:E74G	E	+	2	0	CDKL5	18503470	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.339000	0.96797	1.893000	0.54813	0.486000	0.48141	GAG	.	.		0.393	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159		G	18593549	A	G	18593549	3	3	114	1	0	0	0	0	1	0	0	0	3159	304	11	2	235	2	CDKL5	23	18593549	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	3253890	18593549	136677011	1232	19504										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23411677	23411677	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctccaaggtgaagttcatcgTcttcaatccgtcctttgtat	7	11	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:23411677T>C	ENST00000379361.4	+	3	2902	c.2042T>C	c.(2041-2043)gTc>gCc	p.V681A		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	681					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						AAGTTCATCGTCTTCAATCCG	0.483																																					p.V681A		Atlas-SNP	.											.	PTCHD1	213	.	0			c.T2042C						.						91	82	85					X																	23411677		2203	4300	6503	SO:0001583	missense	139411	exon3			TCATCGTCTTCAA	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.2042T>C	chrX.hg19:g.23411677T>C	ENSP00000368666:p.Val681Ala	74.0	0.0		113.0	5.0	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	hg19	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	T	14.08	2.429925	0.43122	.	.	ENSG00000165186	ENST00000379361	D	0.88509	-2.39	5.34	5.34	0.76211	.	0.059808	0.64402	D	0.000002	D	0.84606	0.5509	L	0.34521	1.04	0.41461	D	0.988041	B	0.23937	0.094	B	0.32149	0.141	T	0.80369	-0.1411	10	0.25106	T	0.35	.	14.3778	0.66889	0.0:0.0:0.0:1.0	.	681	Q96NR3	PTHD1_HUMAN	A	681	ENSP00000368666:V681A	ENSP00000368666:V681A	V	+	2	0	PTCHD1	23321598	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	7.694000	0.84235	1.775000	0.52247	0.430000	0.28490	GTC	.	.		0.483	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		C	23411677	T	C	23411677	3	2	114	1	0	0	0	0	1	0	0	0	12744	1667	58	2	2052	2	PTCHD1	23	23411677	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4818128	23411677	131858883	1233	19505										
POLA1	5422	hgsc.bcm.edu	37	chrX	24741325	24741325	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aatcagccgagacccatgtgAgctgttgtgtcatggtgaaa	12	8	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:24741325A>G	ENST00000379059.3	+	11	1138	c.1123A>G	c.(1123-1125)Agc>Ggc	p.S375G	POLA1_ENST00000379068.3_Missense_Mutation_p.S381G	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	375					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	GACCCATGTGAGCTGTTGTGT	0.383																																					p.S375G		Atlas-SNP	.											.	POLA1	117	.	0			c.A1123G						.						224	205	211					X																	24741325		2203	4300	6503	SO:0001583	missense	5422	exon11			CATGTGAGCTGTT		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1123A>G	chrX.hg19:g.24741325A>G	ENSP00000368349:p.Ser375Gly	139.0	0.0		178.0	8.0	NM_016937	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	hg19	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	A	18.52	3.641159	0.67244	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.12672	2.66;2.66	5.25	5.25	0.73442	DNA-directed DNA polymerase, family B, exonuclease domain (1);	0.040115	0.85682	D	0.000000	T	0.51991	0.1707	H	0.96861	3.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.69281	-0.5186	10	0.87932	D	0	-9.3184	14.239	0.65945	1.0:0.0:0.0:0.0	.	381;375	A6NMQ1;P09884	.;DPOLA_HUMAN	G	381;375	ENSP00000368358:S381G;ENSP00000368349:S375G	ENSP00000368349:S375G	S	+	1	0	POLA1	24651246	1.000000	0.71417	1.000000	0.80357	0.369000	0.29798	8.673000	0.91186	1.939000	0.56221	0.486000	0.48141	AGC	.	.		0.383	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		G	24741325	A	G	24741325	3	3	114	1	0	0	0	0	1	0	0	0	12196	304	11	2	1165	2	POLA1	23	24741325	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1329648	24741325	130529235	1234	19506										
POLA1	5422	hgsc.bcm.edu	37	chrX	24844595	24844595	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctatgcgcctgagcagctgCagaaacaggataatctaacc	9	12	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:24844595C>T	ENST00000379059.3	+	32	3610	c.3595C>T	c.(3595-3597)Cag>Tag	p.Q1199*	POLA1_ENST00000379068.3_Nonsense_Mutation_p.Q1205*	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	1199					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	TGAGCAGCTGCAGAAACAGGA	0.468																																					p.Q1199X		Atlas-SNP	.											.	POLA1	117	.	0			c.C3595T						.						114	74	87					X																	24844595		2203	4300	6503	SO:0001587	stop_gained	5422	exon32			CAGCTGCAGAAAC		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.3595C>T	chrX.hg19:g.24844595C>T	ENSP00000368349:p.Gln1199*	77.0	0.0		73.0	4.0	NM_016937	Q86UQ7	Nonsense_Mutation	SNP	ENST00000379059.3	hg19	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	C	42	9.569633	0.99207	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	.	.	.	5.69	4.8	0.61643	.	0.111512	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.9983	14.2989	0.66334	0.3139:0.6861:0.0:0.0	.	.	.	.	X	1205;1199	.	ENSP00000368349:Q1199X	Q	+	1	0	POLA1	24754516	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.980000	0.49321	2.407000	0.81776	0.529000	0.55759	CAG	.	.		0.468	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		T	24844595	C	T	24844595	4	4	114	1	0	0	0	0	0	1	0	0	12196	711	25	3	3721	3	POLA1	23	24844595	Nonsense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	103270	24844595	130425965	1235	19507										
XK	7504	hgsc.bcm.edu	37	chrX	37553772	37553772	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctacagctgtacataagtgTcatgcagcaggacgtcactg	10	11	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:37553772T>C	ENST00000378616.3	+	2	682	c.479T>C	c.(478-480)gTc>gCc	p.V160A	TM4SF2_ENST00000465127.1_Intron	NM_021083.2	NP_066569.1	P51811	XK_HUMAN	X-linked Kx blood group	160					amino acid transport (GO:0006865)|transport (GO:0006810)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		all_lung(315;0.175)				TACATAAGTGTCATGCAGCAG	0.483																																					p.V160A		Atlas-SNP	.											.	XK	48	.	0			c.T479C						.						68	50	56					X																	37553772		2200	4296	6496	SO:0001583	missense	7504	exon2			TAAGTGTCATGCA	Z32684	CCDS14241.1	Xp21.1	2014-07-19	2014-06-18		ENSG00000047597	ENSG00000047597		"Blood group antigens"	12811	protein-coding gene	gene with protein product	"Kx antigen", "McLeod syndrome"	314850	"Kell blood group precursor (McLeod phenotype)", "XK, Kell blood group complex subunit (McLeod syndrome)", "neuroacanthocytosis", "neurocanthocytosis"	NA, NAC		8004674, 11761473	Standard	NM_021083		Approved	XKR1, Kx, X1k	uc004ddq.3	P51811	OTTHUMG00000033171	ENST00000378616.3:c.479T>C	chrX.hg19:g.37553772T>C	ENSP00000367879:p.Val160Ala	100.0	0.0		115.0	5.0	NM_021083	Q4TTN6|Q8IUK6|Q9UC77	Missense_Mutation	SNP	ENST00000378616.3	hg19	CCDS14241.1	.	.	.	.	.	.	.	.	.	.	T	11.49	1.653096	0.29425	.	.	ENSG00000047597	ENST00000378616	T	0.66995	-0.24	6.04	3.72	0.42706	.	0.565552	0.19027	N	0.124642	T	0.64382	0.2593	M	0.72894	2.215	0.34753	D	0.73195	B	0.12013	0.005	B	0.20955	0.032	T	0.63902	-0.6532	10	0.31617	T	0.26	-3.2206	11.3662	0.49673	0.0:0.0841:0.0:0.9159	.	160	P51811	XK_HUMAN	A	160	ENSP00000367879:V160A	ENSP00000367879:V160A	V	+	2	0	XK	37438711	0.835000	0.29415	0.001000	0.08648	0.370000	0.29829	4.857000	0.62939	0.384000	0.24942	0.417000	0.27973	GTC	.	.		0.483	XK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080875.1	NM_021083		C	37553772	T	C	37553772	3	2	114	1	0	0	0	0	1	0	0	0	17446	1667	58	2	485	2	XK	23	37553772	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	12709177	37553772	117716788	1236	19508										
RPGR	6103	hgsc.bcm.edu	37	chrX	38146456	38146456	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cctcttgctcctctattccaTttccttttgaatcctctgct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:38146456delT	ENST00000339363.3	-	14	2578	c.2411delA	c.(2410-2412)aatfs	p.N804fs	RPGR_ENST00000378505.2_Frame_Shift_Del_p.N599fs|RPGR_ENST00000338898.3_3'UTR|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Frame_Shift_Del_p.N599fs|RPGR_ENST00000309513.3_Frame_Shift_Del_p.N537fs|RPGR_ENST00000318842.7_Frame_Shift_Del_p.N599fs			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	804	Glu-rich.				cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						ctctattccatttccttttga	0.413																																					p.N599fs		Atlas-INDEL	.											.	RPGR	175	.	0			c.1797delT						.						79	58	65					X																	38146456		2202	4300	6502	SO:0001589	frameshift_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"retinitis pigmentosa 15", "cone dystrophy 1 (X-linked)"	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2411delA	chrX.hg19:g.38146456delT	ENSP00000343671:p.Asn804fs	116.0	0.0		181.0	11.0	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Frame_Shift_Del	DEL	ENST00000339363.3	hg19																																																																																				.	.		0.413	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		-	38146456	T	-	38146456	7	5	114	1	0	1	0	1	0	0	0	0	13563	1493	52	0	2225	0	RPGR	23	38146456	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	592684	38146456	117124104	1237	19509										
ZNF41	7592	hgsc.bcm.edu	37	chrX	47307869	47307869	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tacataaggtttctctcccgTgtggattctctgatgcatcc	8	11	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:47307869T>C	ENST00000377065.4	-	5	1939	c.1300A>G	c.(1300-1302)Acg>Gcg	p.T434A	ZNF41_ENST00000397050.2_Missense_Mutation_p.T444A|ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000313116.7_Missense_Mutation_p.T434A	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	476					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				TTCTCTCCCGTGTGGATTCTC	0.433																																					p.T434A		Atlas-SNP	.											.	ZNF41	71	.	0			c.A1300G						.						114	105	108					X																	47307869		2203	4300	6503	SO:0001583	missense	7592	exon5			CTCCCGTGTGGAT	X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"Zinc fingers, C2H2-type", "-"	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.1300A>G	chrX.hg19:g.47307869T>C	ENSP00000366265:p.Thr434Ala	54.0	0.0		63.0	4.0	NM_007130	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	hg19	CCDS14279.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561575	0.65538	.	.	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050	T;T;T	0.26518	1.73;1.73;1.73	3.58	3.58	0.41010	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36338	N	0.002655	T	0.24661	0.0598	N	0.03948	-0.315	0.32078	N	0.593589	D;D;D;D;D	0.63880	0.992;0.992;0.984;0.992;0.993	D;D;D;D;D	0.76575	0.979;0.979;0.967;0.979;0.988	T	0.30090	-0.9990	10	0.87932	D	0	.	9.74	0.40413	0.0:0.0:0.0:1.0	.	434;436;444;468;476	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	A	434;434;444	ENSP00000315173:T434A;ENSP00000366265:T434A;ENSP00000380243:T444A	ENSP00000315173:T434A	T	-	1	0	ZNF41	47192813	1.000000	0.71417	0.998000	0.56505	0.962000	0.63368	5.119000	0.64679	1.655000	0.50712	0.486000	0.48141	ACG	.	.		0.433	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380		C	47307869	T	C	47307869	3	2	114	1	0	0	0	0	1	0	0	0	17904	1696	59	2	1043	2	ZNF41	23	47307869	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	9161413	47307869	107962691	1238	19510										
GPKOW	27238	hgsc.bcm.edu	37	chrX	48970804	48970804	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gactcacccttccagtctgtGggcccagcaccaccatcaca							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:48970804delG	ENST00000156109.5	-	10	1361	c.1283delC	c.(1282-1284)ccafs	p.P428fs		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	428	KOW 2.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						TCCAGTCTGTGGGCCCAGCAC	0.592																																					p.P428fs		Atlas-INDEL	.											.	GPKOW	38	.	0			c.1284delA						.						142	92	109					X																	48970804		2203	4300	6503	SO:0001589	frameshift_variant	27238	exon10			.	U66359	CCDS35251.1	Xp11.23	2013-01-28			ENSG00000068394	ENSG00000068394		"G patch domain containing"	30677	protein-coding gene	gene with protein product	"G patch domain containing 5"					21880142, 22365833	Standard	NM_015698		Approved	T54, GPATC5, GPATCH5, Spp2	uc004dmr.3	Q92917	OTTHUMG00000021511	ENST00000156109.5:c.1283delC	chrX.hg19:g.48970804delG	ENSP00000156109:p.Pro428fs	103.0	0.0		156.0	10.0	NM_015698	Q59EK5|Q9BQA8	Frame_Shift_Del	DEL	ENST00000156109.5	hg19	CCDS35251.1																																																																																			.	.		0.592	GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698		-	48970804	G	-	48970804	7	5	114	1	0	1	0	1	0	0	0	0	6621	1348	47	0	155	0	GPKOW	23	48970804	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1662935	48970804	106299756	1239	19511										
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53264288	53264288	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gttggagacgggcctctggcTcttgtactcctctggcggcg	15	12	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:53264288T>C	ENST00000375368.5	-	14	3750	c.3550A>G	c.(3550-3552)Agc>Ggc	p.S1184G	IQSEC2_ENST00000396435.3_Missense_Mutation_p.S1194G|IQSEC2_ENST00000375365.2_3'UTR			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1184	Pro-rich.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						GGCCTCTGGCTCTTGTACTCC	0.652																																					p.S1194G		Atlas-SNP	.											.	IQSEC2	195	.	0			c.A3580G						.						32	31	31					X																	53264288		692	1591	2283	SO:0001583	missense	23096	exon15			TCTGGCTCTTGTA	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.3550A>G	chrX.hg19:g.53264288T>C	ENSP00000364517:p.Ser1184Gly	47.0	0.0		68.0	4.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	T	1.025	-0.683714	0.03353	.	.	ENSG00000124313	ENST00000396435;ENST00000375368	T;T	0.43294	0.95;0.95	2.06	2.06	0.26882	.	0.114198	0.64402	N	0.000015	T	0.15782	0.0380	N	0.03608	-0.345	0.22521	N	0.999021	B	0.16396	0.017	B	0.16289	0.015	T	0.08371	-1.0725	10	0.48119	T	0.1	.	2.4407	0.04493	0.0:0.181:0.2965:0.5225	.	1194	Q5JU85-2	.	G	1194;1184	ENSP00000379712:S1194G;ENSP00000364517:S1184G	ENSP00000364517:S1184G	S	-	1	0	IQSEC2	53281013	1.000000	0.71417	0.998000	0.56505	0.207000	0.24258	1.070000	0.30653	1.069000	0.40788	0.235000	0.17854	AGC	.	.		0.652	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		C	53264288	T	C	53264288	3	2	114	1	0	0	0	0	1	0	0	0	7827	1551	54	2	890	2	IQSEC2	23	53264288	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	4293484	53264288	102006272	1240	19512										
WNK3	65267	hgsc.bcm.edu	37	chrX	54263832	54263832	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taagaaaacgaagtttttggAttttgtgtggcaggttctat	11	3	1	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:54263832A>G	ENST00000375159.2	-	19	4166	c.4167T>C	c.(4165-4167)aaT>aaC	p.N1389N	WNK3_ENST00000375169.3_Silent_p.N1342N|WNK3_ENST00000354646.2_Silent_p.N1389N			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1389					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AAGTTTTTGGATTTTGTGTGG	0.358																																					p.N1389N		Atlas-SNP	.											.	WNK3	218	.	0			c.T4167C						.						95	88	90					X																	54263832		2203	4300	6503	SO:0001819	synonymous_variant	65267	exon20			TTTTGGATTTTGT	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.4167T>C	chrX.hg19:g.54263832A>G		49.0	0.0		41.0	4.0	NM_020922	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Silent	SNP	ENST00000375159.2	hg19	CCDS14357.1																																																																																			.	.		0.358	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		G	54263832	A	G	54263832	2	3	114	1	0	0	0	0	0	0	0	1	17394	330	12	2		2	WNK3	23	54263832	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	999544	54263832	101006728	1241	19513										
USP51	158880	hgsc.bcm.edu	37	chrX	55514365	55514365	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggctcctgttcctttgtctcAcaggttgattgcttgtcttc	9	11	2	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:55514365A>G	ENST00000500968.3	-	2	1090	c.1008T>C	c.(1006-1008)tgT>tgC	p.C336C	USP51_ENST00000586165.1_5'UTR	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	336					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						CCTTTGTCTCACAGGTTGATT	0.373																																					p.C336C		Atlas-SNP	.											.	USP51	71	.	0			c.T1008C						.						100	98	99					X																	55514365		2203	4300	6503	SO:0001819	synonymous_variant	158880	exon2			TGTCTCACAGGTT	BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"Ubiquitin-specific peptidases"	23086	protein-coding gene	gene with protein product			"ubiquitin specific protease 51"			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.1008T>C	chrX.hg19:g.55514365A>G		98.0	0.0		114.0	5.0	NM_201286	Q8IWJ8	Silent	SNP	ENST00000500968.3	hg19	CCDS14370.1																																																																																			.	.		0.373	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286		G	55514365	A	G	55514365	2	3	114	1	0	0	0	0	0	0	0	1	17098	157	6	2		2	USP51	23	55514365	Silent	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1250533	55514365	99756195	1242	19514										
ABCB7	22	hgsc.bcm.edu	37	chrX	74282215	74282215	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttcatcatagagtatgactGgggggtccttcaaaatggct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:74282215delG	ENST00000373394.3	-	14	1890	c.1883delC	c.(1882-1884)ccafs	p.P628fs	ABCB7_ENST00000339447.4_Frame_Shift_Del_p.P588fs|ABCB7_ENST00000253577.3_Frame_Shift_Del_p.P629fs|ABCB7_ENST00000534570.1_5'Flank			O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 7	628	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)			breast(1)|endometrium(5)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)	20						GAGTATGACTGGGGGGTCCTT	0.348																																					p.P629fs		Atlas-Indel,Pindel	.											.	ABCB7	69	.	0			c.1887delA						.						101	90	94					X																	74282215		2203	4300	6503	SO:0001589	frameshift_variant	22	exon14			.	AF038950	CCDS14428.1, CCDS65290.1, CCDS65291.1, CCDS75994.1	Xq13.3	2012-03-14			ENSG00000131269	ENSG00000131269		"ATP binding cassette transporters / subfamily B"	48	protein-coding gene	gene with protein product		300135		ABC7		9143506	Standard	NM_004299		Approved	EST140535, Atm1p, ASAT	uc004ebz.4	O75027	OTTHUMG00000021862	ENST00000373394.3:c.1883delC	chrX.hg19:g.74282215delG	ENSP00000362492:p.Pro628fs	126.0	0.0		166.0	13.0	NM_004299	G3XAC4|O75345|Q5VWY7|Q5VWY8|Q9BRE1|Q9UND1|Q9UP01	Frame_Shift_Del	DEL	ENST00000373394.3	hg19																																																																																				.	.		0.348	ABCB7-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000057274.1	NM_004299		-	74282215	G	-	74282215	7	5	114	1	0	1	0	1	0	0	0	0	46	1348	47	0	387	0	ABCB7	23	74282215	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	18767850	74282215	80988345	1243	19515										
MAGEE1	57692	hgsc.bcm.edu	37	chrX	75650522	75650522	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaggtttccagctattcctcAaaatatgccccacattcatg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:75650522delA	ENST00000361470.2	+	1	2477	c.2199delA	c.(2197-2199)tcafs	p.S733fs		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	733						dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						GCTATTCCTCAAAATATGCCC	0.493																																					p.S733X		Atlas-INDEL	.											.	MAGEE1	236	.	0			c.2198delC						.						73	59	64					X																	75650522		2203	4300	6503	SO:0001589	frameshift_variant	57692	exon1			.	AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.2199delA	chrX.hg19:g.75650522delA	ENSP00000354912:p.Ser733fs	124.0	0.0		164.0	10.0	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Frame_Shift_Del	DEL	ENST00000361470.2	hg19	CCDS14433.1																																																																																			.	.		0.493	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		-	75650522	A	-	75650522	7	5	114	1	0	1	0	1	0	0	0	0	9194	117	5	0	2201	0	MAGEE1	23	75650522	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	1368307	75650522	79620038	1244	19516										
GPR174	84636	hgsc.bcm.edu	37	chrX	78427231	78427231	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	caggggtattcctaatttgcTttgcaccttatcatttcagt	7	9	2	0			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:78427231T>C	ENST00000276077.1	+	1	763	c.727T>C	c.(727-729)Ttt>Ctt	p.F243L		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						CCTAATTTGCTTTGCACCTTA	0.383										HNSCC(63;0.18)																											p.F243L		Atlas-SNP	.											.	GPR174	79	.	0			c.T727C						.						108	99	102					X																	78427231		2203	4300	6503	SO:0001583	missense	84636	exon1			ATTTGCTTTGCAC	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.727T>C	chrX.hg19:g.78427231T>C	ENSP00000276077:p.Phe243Leu	101.0	0.0		86.0	4.0	NM_032553	Q2M3F7	Missense_Mutation	SNP	ENST00000276077.1	hg19	CCDS14443.1	.	.	.	.	.	.	.	.	.	.	t	20.7	4.040197	0.75732	.	.	ENSG00000147138	ENST00000276077	T	0.72615	-0.67	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.84320	0.5446	M	0.83223	2.63	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	D	0.86664	0.1906	10	0.87932	D	0	.	12.8586	0.57901	0.0:0.0:0.0:1.0	.	243	Q9BXC1	GP174_HUMAN	L	243	ENSP00000276077:F243L	ENSP00000276077:F243L	F	+	1	0	GPR174	78313887	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.802000	0.85969	1.716000	0.51395	0.397000	0.26171	TTT	.	.		0.383	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		C	78427231	T	C	78427231	3	2	114	1	0	0	0	0	1	0	0	0	6680	1609	56	2	729	2	GPR174	23	78427231	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2776709	78427231	76843329	1245	19517										
BRWD3	254065	hgsc.bcm.edu	37	chrX	79938011	79938011	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctgctgctgcttcttagacgTtttctgtaccgtggccttct							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:79938011delT	ENST00000373275.4	-	38	4566	c.4350delA	c.(4348-4350)aaafs	p.K1450fs	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1450					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						TTCTTAGACGTTTTCTGTACC	0.368																																					p.R1451fs		Atlas-INDEL	.											.	BRWD3	251	.	0			c.4351delC						.						304	238	261					X																	79938011		2203	4300	6503	SO:0001589	frameshift_variant	254065	exon38			.		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.4350delA	chrX.hg19:g.79938011delT	ENSP00000362372:p.Lys1450fs	163.0	0.0		149.0	10.0	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Frame_Shift_Del	DEL	ENST00000373275.4	hg19	CCDS14447.1																																																																																			.	.		0.368	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		-	79938011	T	-	79938011	7	5	114	1	0	1	0	1	0	0	0	0	1528	1722	60	0	1074	0	BRWD3	23	79938011	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1510780	79938011	75332549	1246	19518										
CHM	1121	hgsc.bcm.edu	37	chrX	85282510	85282510	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cttacgaatcaacatgcagaActctccggccacttcttgaa	6	13	3	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:85282510A>G	ENST00000357749.2	-	2	130	c.101T>C	c.(100-102)gTt>gCt	p.V34A	CHM_ENST00000358786.4_Missense_Mutation_p.V34A|CHM_ENST00000537751.1_Intron|CHM_ENST00000467744.2_5'UTR	NM_000390.2	NP_000381.1	P24386	RAE1_HUMAN	choroideremia (Rab escort protein 1)	34					blood vessel development (GO:0001568)|protein geranylgeranylation (GO:0018344)|protein targeting to membrane (GO:0006612)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytosol (GO:0005829)|Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|prostate(1)	20		all_lung(315;5.41e-06)				AACATGCAGAACTCTCCGGCC	0.328																																					p.V34A		Atlas-SNP	.											.	CHM	57	.	0			c.T101C						.						66	58	61					X																	85282510		2203	4300	6503	SO:0001583	missense	1121	exon2			TGCAGAACTCTCC	X78121	CCDS14454.1, CCDS48139.1	Xq21.1-q21.3	2014-09-17			ENSG00000188419	ENSG00000188419			1940	protein-coding gene	gene with protein product		300390		TCD, DXS540		1373238	Standard	XM_006724615		Approved	REP-1	uc004eet.3	P24386	OTTHUMG00000021937	ENST00000357749.2:c.101T>C	chrX.hg19:g.85282510A>G	ENSP00000350386:p.Val34Ala	92.0	0.0		124.0	5.0	NM_001145414	A1L4D2|O43732	Missense_Mutation	SNP	ENST00000357749.2	hg19	CCDS14454.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.038231	0.75617	.	.	ENSG00000188419	ENST00000357749;ENST00000358786	T;T	0.81078	-1.45;-1.45	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.89955	0.6865	M	0.90650	3.135	0.80722	D	1	P;P	0.43973	0.823;0.656	P;P	0.56474	0.799;0.749	D	0.91743	0.5406	10	0.87932	D	0	-11.761	14.2794	0.66200	1.0:0.0:0.0:0.0	.	34;34	A1L4D2;P24386	.;RAE1_HUMAN	A	34	ENSP00000350386:V34A;ENSP00000362228:V34A	ENSP00000350386:V34A	V	-	2	0	CHM	85169166	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	6.769000	0.74985	1.750000	0.51863	0.356000	0.21956	GTT	.	.		0.328	CHM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057396.3	NM_000390		G	85282510	A	G	85282510	3	3	114	1	0	0	0	0	1	0	0	0	3352	43	2	2	1939	2	CHM	23	85282510	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	5344499	85282510	69988050	1247	19519										
TAF7L	54457	hgsc.bcm.edu	37	chrX	100524209	100524209	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tcagaaaacgctgcaactgtTcctgtagggaaatgagctgt	11	8	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:100524209T>C	ENST00000372907.3	-	13	1372	c.1361A>G	c.(1360-1362)gAa>gGa	p.E454G	TAF7L_ENST00000372905.2_Missense_Mutation_p.E294G|TAF7L_ENST00000324762.6_Missense_Mutation_p.E294G|TAF7L_ENST00000356784.1_Missense_Mutation_p.E368G	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	454					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						CTGCAACTGTTCCTGTAGGGA	0.433																																					p.E454G	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.A1361G						.						169	151	157					X																	100524209		2203	4300	6503	SO:0001583	missense	54457	exon13			AACTGTTCCTGTA	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"cancer/testis antigen 40"	300314	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.1361A>G	chrX.hg19:g.100524209T>C	ENSP00000361998:p.Glu454Gly	70.0	0.0		100.0	4.0	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	hg19	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.547717	0.45383	.	.	ENSG00000102387	ENST00000372907;ENST00000372905;ENST00000324762;ENST00000356784	T;T;T;T	0.29142	2.11;1.58;1.58;1.63	4.48	4.48	0.54585	.	0.687962	0.12318	N	0.479575	T	0.45637	0.1352	M	0.75615	2.305	0.22240	N	0.999268	D;P	0.54207	0.965;0.944	P;P	0.51016	0.656;0.526	T	0.36915	-0.9728	10	0.66056	D	0.02	-2.3587	11.4937	0.50396	0.0:0.0:0.0:1.0	.	454;294	Q5H9L4;Q5H9L4-3	TAF7L_HUMAN;.	G	454;294;294;368	ENSP00000361998:E454G;ENSP00000361996:E294G;ENSP00000320283:E294G;ENSP00000349235:E368G	ENSP00000320283:E294G	E	-	2	0	TAF7L	100410865	0.996000	0.38824	0.002000	0.10522	0.057000	0.15508	3.401000	0.52601	1.566000	0.49654	0.417000	0.27973	GAA	.	.		0.433	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2			C	100524209	T	C	100524209	3	2	114	1	0	0	0	0	1	0	0	0	15548	1783	62	2	31	2	TAF7L	23	100524209	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	15241699	100524209	54746351	1248	19520										
TCEAL6	158931	hgsc.bcm.edu	37	chrX	101395774	101395774	+	Missense_Mutation	SNP	T	T	C													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	actcccctgacaccccgttgTccccttgggcgaatggatcc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:101395774T>C	ENST00000372774.3	-	3	779	c.530A>G	c.(529-531)gAc>gGc	p.D177G	TCEAL6_ENST00000372773.1_Missense_Mutation_p.D177G	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						CACCCCGTTGTCCCCTTGGGC	0.507																																					p.D177G		Atlas-SNP	.											.	TCEAL6	27	.	0			c.A530G						.						19	18	19					X																	101395774		2197	4274	6471	SO:0001583	missense	158931	exon3			CCGTTGTCCCCTT	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.530A>G	chrX.hg19:g.101395774T>C	ENSP00000361860:p.Asp177Gly	62.0	0.0		163.0	11.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.	.	.	.	.	.	.	.	.	.	A	0.755	-0.771235	0.02951	.	.	ENSG00000204071	ENST00000372774;ENST00000372773	T;T	0.23147	1.92;1.92	2.82	-3.23	0.05109	.	0.272209	0.20313	N	0.094788	T	0.11836	0.0288	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08186	-1.0734	10	0.48119	T	0.1	.	3.3698	0.07216	0.1211:0.4969:0.222:0.1599	.	177	Q6IPX3-2	.	G	177	ENSP00000361860:D177G;ENSP00000361859:D177G	ENSP00000361859:D177G	D	-	2	0	TCEAL6	101282430	0.001000	0.12720	0.010000	0.14722	0.828000	0.46876	-1.039000	0.03550	-1.000000	0.03438	-0.742000	0.03525	GAC	.	.		0.507	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938		C	101395774	T	C	101395774	3	2	114	1	0	0	0	0	1	0	0	0	15690	1667	58	2	25	2	TCEAL6	23	101395774	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	871565	101395774	53874786	1249	19521	83	2								
TCEAL6	158931	hgsc.bcm.edu	37	chrX	101395778	101395778	+	Missense_Mutation	SNP	C	C	T													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccctgacaccccgttgtcccCttgggcgaatggatcctgta							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:101395778C>T	ENST00000372774.3	-	3	775	c.526G>A	c.(526-528)Ggg>Agg	p.G176R	TCEAL6_ENST00000372773.1_Missense_Mutation_p.G176R	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						CCGTTGTCCCCTTGGGCGAAT	0.502																																					p.G176R		Atlas-SNP	.											.	TCEAL6	27	.	0			c.G526A						.						13	13	13					X																	101395778		2197	4251	6448	SO:0001583	missense	158931	exon3			TGTCCCCTTGGGC	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.526G>A	chrX.hg19:g.101395778C>T	ENSP00000361860:p.Gly176Arg	60.0	0.0		155.0	17.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.605|9.605	1.129729|1.129729	0.21041|0.21041	.|.	.|.	ENSG00000204071|ENSG00000204071	ENST00000372774;ENST00000372773|ENST00000536102	T;T|.	0.40225|.	1.04;1.04|.	2.82|2.82	2.82|2.82	0.32997|0.32997	.|.	0.000000|.	0.39341|.	N|.	0.001392|.	T|T	0.27832|0.27832	0.0685|0.0685	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	D|.	0.57257|.	0.979|.	P|.	0.56563|.	0.801|.	T|T	0.22243|0.22243	-1.0222|-1.0222	10|6	0.54805|0.06365	T|T	0.06|0.9	.|.	8.3639|8.3639	0.32374|0.32374	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	176|.	Q6IPX3-2|.	.|.	R|K	176|175	ENSP00000361860:G176R;ENSP00000361859:G176R|.	ENSP00000361859:G176R|ENSP00000437364:R175K	G|R	-|-	1|2	0|0	TCEAL6|TCEAL6	101282434|101282434	0.007000|0.007000	0.16637|0.16637	0.089000|0.089000	0.20774|0.20774	0.743000|0.743000	0.42351|0.42351	1.059000|1.059000	0.30517|0.30517	1.692000|1.692000	0.51112|0.51112	0.468000|0.468000	0.43344|0.43344	GGG|AGG	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938		T	101395778	C	T	101395778	3	4	114	1	0	0	0	0	1	0	0	0	15690	681	24	3	29	3	TCEAL6	23	101395778	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	4	101395778	53874782	1250	19522	83	2								
CLDN2	9075	hgsc.bcm.edu	37	chrX	106171549	106171549	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ccatgctgctccccagctggAaaacaagttcttatgtcggt							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:106171549delA	ENST00000541806.1	+	2	610	c.91delA	c.(91-93)aaafs	p.K31fs	CLDN2_ENST00000540876.1_Frame_Shift_Del_p.K31fs|CLDN2_ENST00000336803.1_Frame_Shift_Del_p.K31fs	NM_001171092.1	NP_001164563.1	P57739	CLD2_HUMAN	claudin 2	31					calcium-independent cell-cell adhesion (GO:0016338)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						CCCCAGCTGGAAAACAAGTTC	0.567																																					p.W30X		Atlas-INDEL	.											.	CLDN2	22	.	0			c.90delG						.						91	78	82					X																	106171549		2203	4300	6503	SO:0001589	frameshift_variant	9075	exon2			.	AK075405	CCDS14524.1	Xq22.3-q23	2008-05-14			ENSG00000165376	ENSG00000165376		"Claudins"	2041	protein-coding gene	gene with protein product		300520				9892664	Standard	NM_020384		Approved		uc022ccc.1	P57739	OTTHUMG00000022154	ENST00000541806.1:c.91delA	chrX.hg19:g.106171549delA	ENSP00000441283:p.Lys31fs	93.0	0.0		116.0	10.0	NM_001171092	B2R6B9	Frame_Shift_Del	DEL	ENST00000541806.1	hg19	CCDS14524.1																																																																																			.	.		0.567	CLDN2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057815.1			-	106171549	A	-	106171549	7	5	114	1	0	1	0	1	0	0	0	0	3483	247	9	0	93	0	CLDN2	23	106171549	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	4775771	106171549	49099011	1251	19523										
TEX13B	56156	hgsc.bcm.edu	37	chrX	107224619	107224619	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agcccctgcaagacctctgcGggggcaggccctgcctctgc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:107224619delG	ENST00000302917.1	-	3	722	c.630delC	c.(628-630)cccfs	p.P210fs		NM_031273.2	NP_112563.1	Q9BXU2	TX13B_HUMAN	testis expressed 13B	210								p.P210P(1)		breast(1)|endometrium(5)|large_intestine(4)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28						AGACCTCTGCGGGGGCAGGCC	0.612																																					p.A211fs		Atlas-INDEL	.											.	TEX13B	40	.	1	Substitution - coding silent(1)	lung(1)	c.631delG						.						99	110	106					X																	107224619		2200	4299	6499	SO:0001589	frameshift_variant	56156	exon3			.	AF285598	CCDS14534.1	Xq23	2008-02-05	2007-03-13		ENSG00000170925	ENSG00000170925			11736	protein-coding gene	gene with protein product		300313	"testis expressed sequence 13B"			11279525	Standard	NM_031273		Approved	TSGA5, TGC3B	uc004enn.1	Q9BXU2	OTTHUMG00000022174	ENST00000302917.1:c.630delC	chrX.hg19:g.107224619delG	ENSP00000303777:p.Pro210fs	134.0	0.0		170.0	11.0	NM_031273	Q5JYF6	Frame_Shift_Del	DEL	ENST00000302917.1	hg19	CCDS14534.1																																																																																			.	.		0.612	TEX13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057857.1			-	107224619	G	-	107224619	7	5	114	1	0	1	0	1	0	0	0	0	15792	1103	39	0	312	0	TEX13B	23	107224619	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	1053070	107224619	48045941	1252	19524										
COL4A6	1288	hgsc.bcm.edu	37	chrX	107448673	107448673	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tttaaaagctgtttaccttgActcctttctctccttgaaaa	4	10	1	2			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:107448673A>G	ENST00000372216.4	-	11	786	c.686T>C	c.(685-687)gTc>gCc	p.V229A	COL4A6_ENST00000334504.7_Missense_Mutation_p.V228A|COL4A6_ENST00000538570.1_Missense_Mutation_p.V228A|COL4A6_ENST00000394872.2_Intron|COL4A6_ENST00000545689.1_Missense_Mutation_p.V228A	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	229	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						GTTTACCTTGACTCCTTTCTC	0.393									Alport syndrome with Diffuse Leiomyomatosis																												p.V229A	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.T686C						.						165	165	165					X																	107448673		2203	4300	6503	SO:0001583	missense	1288	exon11	Familial Cancer Database		ACCTTGACTCCTT	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.686T>C	chrX.hg19:g.107448673A>G	ENSP00000361290:p.Val229Ala	59.0	0.0		99.0	5.0	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	hg19	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.462002	0.26248	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55	4.97	-1.77	0.07982	.	.	.	.	.	T	0.82268	0.5000	N	0.05534	-0.03	0.26412	N	0.97625	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.004;0.004;0.002;0.004	T	0.70554	-0.4840	9	0.10902	T	0.67	.	4.0947	0.09985	0.4061:0.0:0.4004:0.1935	.	228;228;229;228	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	A	229;228;228;228;228	ENSP00000361290:V229A;ENSP00000334733:V228A;ENSP00000443707:V228A;ENSP00000445236:V228A	ENSP00000334733:V228A	V	-	2	0	COL4A6	107335329	0.885000	0.30320	0.989000	0.46669	0.933000	0.57130	-0.249000	0.08842	-0.297000	0.08934	-0.360000	0.07572	GTC	.	.		0.393	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			G	107448673	A	G	107448673	3	3	114	1	0	0	0	0	1	0	0	0	3697	275	10	2	4529	2	COL4A6	23	107448673	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	224054	107448673	47821887	1253	19525										
ATP1B4	23439	hgsc.bcm.edu	37	chrX	119509268	119509268	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aggaaatgaatgtagattgtCccccggggcagtacttcatc							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:119509268delC	ENST00000218008.3	+	5	661	c.604delC	c.(604-606)cccfs	p.P203fs	ATP1B4_ENST00000361319.3_Frame_Shift_Del_p.P199fs|ATP1B4_ENST00000539306.1_Frame_Shift_Del_p.P160fs	NM_001142447.2	NP_001135919.1	Q9UN42	AT1B4_HUMAN	ATPase, Na+/K+ transporting, beta 4 polypeptide	203					monovalent inorganic cation transport (GO:0015672)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|nuclear inner membrane (GO:0005637)|sodium:potassium-exchanging ATPase complex (GO:0005890)	monovalent inorganic cation transmembrane transporter activity (GO:0015077)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	33						TGTAGATTGTCCCCCGGGGCA	0.483																																					p.C201fs		Atlas-INDEL	.											.	ATP1B4	61	.	0			c.603delT						.						121	111	114					X																	119509268		2203	4300	6503	SO:0001589	frameshift_variant	23439	exon5			.	AF158383	CCDS14598.1, CCDS48158.1	Xq24	2012-10-22	2010-04-20		ENSG00000101892	ENSG00000101892		"ATPases / P-type"	808	protein-coding gene	gene with protein product	"Na,K-ATPase beta m-subunit"		"ATPase, (Na+)/K+ transporting, beta 4 polypeptide"			10456317, 17592128	Standard	NM_012069		Approved		uc004esr.3	Q9UN42	OTTHUMG00000022299	ENST00000218008.3:c.604delC	chrX.hg19:g.119509268delC	ENSP00000218008:p.Pro203fs	138.0	0.0		170.0	13.0	NM_001142447	Q17RR0|Q9UN41	Frame_Shift_Del	DEL	ENST00000218008.3	hg19	CCDS48158.1																																																																																			.	.		0.483	ATP1B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058095.1	NM_001142447		-	119509268	C	-	119509268	7	5	114	1	0	1	0	1	0	0	0	0	1135	855	30	0	622	0	ATP1B4	23	119509268	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	12060595	119509268	35761292	1254	19526										
GRIA3	2892	hgsc.bcm.edu	37	chrX	122528855	122528855	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tactggaaagagtcatgcatGggggagccaacattacaggt					rs191962905		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:122528855delG	ENST00000371251.1	+	6	839	c.787delG	c.(787-789)gggfs	p.G264fs	GRIA3_ENST00000371256.5_Frame_Shift_Del_p.G264fs|GRIA3_ENST00000541091.1_Frame_Shift_Del_p.G248fs|GRIA3_ENST00000264357.5_Frame_Shift_Del_p.G264fs|GRIA3_ENST00000542149.1_Frame_Shift_Del_p.G264fs			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	264					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	AGTCATGCATGGGGGAGCCAA	0.428																																					p.H262fs		Atlas-INDEL	.											.	GRIA3	386	.	0			c.786delT						.						113	102	106					X																	122528855		2203	4300	6503	SO:0001589	frameshift_variant	2892	exon6			.	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.787delG	chrX.hg19:g.122528855delG	ENSP00000360297:p.Gly264fs	155.0	0.0		200.0	12.0	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Frame_Shift_Del	DEL	ENST00000371251.1	hg19	CCDS14604.1																																																																																			.	.		0.428	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		-	122528855	G	-	122528855	7	5	114	1	0	1	0	1	0	0	0	0	6778	1348	47	0	809	0	GRIA3	23	122528855	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	3019587	122528855	32741705	1255	19527										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128649751	128649751	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	atctgataatctctcagtggCccccctttcacatctggtga					rs139862410	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:128649751delC	ENST00000371122.4	-	5	672	c.543delG	c.(541-543)gggfs	p.G181fs	SMARCA1_ENST00000371121.3_Frame_Shift_Del_p.G181fs|SMARCA1_ENST00000478420.1_5'UTR|SMARCA1_ENST00000371123.1_Frame_Shift_Del_p.G181fs	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	181					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						CTCTCAGTGGCCCCCCTTTCA	0.348																																					p.P182fs		Atlas-INDEL	.											.	SMARCA1	126	.	0			c.544delC						.						70	66	67					X																	128649751		2203	4300	6503	SO:0001589	frameshift_variant	6594	exon5			.	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.543delG	chrX.hg19:g.128649751delC	ENSP00000360163:p.Gly181fs	153.0	0.0		212.0	13.0	NM_139035	Q5JV41|Q5JV42	Frame_Shift_Del	DEL	ENST00000371122.4	hg19	CCDS14612.1																																																																																			.	.		0.348	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		-	128649751	C	-	128649751	7	5	114	1	0	1	0	1	0	0	0	0	14783	726	26	0	2701	0	SMARCA1	23	128649751	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	6120896	128649751	26620809	1256	19528										
IGSF1	3547	hgsc.bcm.edu	37	chrX	130417076	130417076	+	Frame_Shift_Del	DEL	T	T	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggaagaagaaatttgcctcaTtttttattgtcttcttgtgg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:130417076delT	ENST00000361420.3	-	6	909	c.830delA	c.(829-831)aatfs	p.N277fs	IGSF1_ENST00000370904.1_Frame_Shift_Del_p.N268fs|IGSF1_ENST00000370903.3_Frame_Shift_Del_p.N277fs|IGSF1_ENST00000370910.1_Frame_Shift_Del_p.N268fs			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	277	Ig-like C2-type 3.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						ATTTGCCTCATTTTTTATTGT	0.398																																					p.N277fs		Atlas-INDEL	.											.	IGSF1	231	.	0			c.831delT						.						113	97	103					X																	130417076		2203	4300	6503	SO:0001589	frameshift_variant	3547	exon6			.	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.830delA	chrX.hg19:g.130417076delT	ENSP00000355010:p.Asn277fs	226.0	0.0		249.0	16.0	NM_001555	B5MEG2|H9KV64|O15070|Q9NTC8	Frame_Shift_Del	DEL	ENST00000361420.3	hg19	CCDS14629.1																																																																																			.	.		0.398	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			-	130417076	T	-	130417076	7	5	114	1	0	1	0	1	0	0	0	0	7605	1493	52	0	3255	0	IGSF1	23	130417076	Frame_Shift_Del	DEL	T	TCGA-DD-A3A0-01A-11D-A20W-10	1767325	130417076	24853484	1257	19529										
GPC4	2239	hgsc.bcm.edu	37	chrX	132438856	132438856	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	aagggaggaccagaatttctTggcctgtttcagtttctcct	10	9	3	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:132438856T>C	ENST00000370828.3	-	7	1713	c.1189A>G	c.(1189-1191)Aag>Gag	p.K397E	GPC4_ENST00000535467.1_Missense_Mutation_p.K327E	NM_001448.2	NP_001439.2	O75487	GPC4_HUMAN	glypican 4	397					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					CAGAATTTCTTGGCCTGTTTC	0.423																																					p.K397E		Atlas-SNP	.											.	GPC4	58	.	0			c.A1189G						.						217	176	190					X																	132438856		2203	4300	6503	SO:0001583	missense	2239	exon7			ATTTCTTGGCCTG	AF030186	CCDS14637.1	Xq26.1	2008-02-05			ENSG00000076716	ENSG00000076716		"Proteoglycans / Cell Surface : Glypicans"	4452	protein-coding gene	gene with protein product	"glypican proteoglycan 4"	300168				9787072	Standard	NM_001448		Approved	K-glypican	uc004exc.1	O75487	OTTHUMG00000022434	ENST00000370828.3:c.1189A>G	chrX.hg19:g.132438856T>C	ENSP00000359864:p.Lys397Glu	76.0	0.0		84.0	4.0	NM_001448	B2R6J7|B4E2C0|Q6ZMA6|Q96L43|Q9NU08|Q9UJN1|Q9UPD9	Missense_Mutation	SNP	ENST00000370828.3	hg19	CCDS14637.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.065833	0.76187	.	.	ENSG00000076716	ENST00000370828;ENST00000536418;ENST00000535467	T;T	0.53640	0.61;0.61	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.55497	0.1924	M	0.82716	2.605	0.80722	D	1	B	0.25521	0.128	B	0.31869	0.137	T	0.59847	-0.7377	10	0.72032	D	0.01	-13.423	13.1714	0.59599	0.0:0.0:0.0:1.0	.	397	O75487	GPC4_HUMAN	E	397;391;327	ENSP00000359864:K397E;ENSP00000444959:K327E	ENSP00000359864:K397E	K	-	1	0	GPC4	132266522	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.635000	0.83286	1.702000	0.51228	0.481000	0.45027	AAG	.	.		0.423	GPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058338.1	NM_001448		C	132438856	T	C	132438856	3	2	114	1	0	0	0	0	1	0	0	0	6608	1821	63	2	493	2	GPC4	23	132438856	Missense_Mutation	SNP	T	TCGA-DD-A3A0-01A-11D-A20W-10	2021780	132438856	22831704	1258	19530										
ZNF449	203523	hgsc.bcm.edu	37	chrX	134481371	134481371	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	cactgatagaagacttacagAgagaacttgagataccagag	10	7	0	7			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:134481371A>G	ENST00000339249.4	+	2	468	c.328A>G	c.(328-330)Aga>Gga	p.R110G	ZNF449_ENST00000370760.3_Missense_Mutation_p.R110G|ZNF449_ENST00000370761.3_Missense_Mutation_p.R110G	NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	110	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					AGACTTACAGAGAGAACTTGA	0.473																																					p.R110G		Atlas-SNP	.											.	ZNF449	68	.	0			c.A328G						.						67	59	61					X																	134481371		2203	4300	6503	SO:0001583	missense	203523	exon2			TTACAGAGAGAAC	AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"-", "Zinc fingers, C2H2-type"	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.328A>G	chrX.hg19:g.134481371A>G	ENSP00000339585:p.Arg110Gly	60.0	0.0		76.0	4.0	NM_152695	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Missense_Mutation	SNP	ENST00000339249.4	hg19	CCDS14649.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.045253	0.36085	.	.	ENSG00000173275	ENST00000370761;ENST00000339249;ENST00000370760	T;T;T	0.04706	3.57;3.57;3.57	4.6	3.4	0.38934	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.000000	0.47455	D	0.000229	T	0.09379	0.0231	N	0.21545	0.675	0.31957	N	0.608961	D;D;B	0.76494	0.999;0.999;0.001	D;D;B	0.85130	0.997;0.996;0.008	T	0.05649	-1.0872	10	0.87932	D	0	.	7.2429	0.26106	0.7767:0.2233:0.0:0.0	.	110;110;110	Q6P9G9;Q6P9G9-2;Q6P9G9-3	ZN449_HUMAN;.;.	G	110	ENSP00000359797:R110G;ENSP00000339585:R110G;ENSP00000359796:R110G	ENSP00000339585:R110G	R	+	1	2	ZNF449	134309037	0.954000	0.32549	1.000000	0.80357	0.981000	0.71138	0.498000	0.22530	0.835000	0.34877	0.481000	0.45027	AGA	.	.		0.473	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695		G	134481371	A	G	134481371	3	3	114	1	0	0	0	0	1	0	0	0	17935	296	11	2	330	2	ZNF449	23	134481371	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	2042515	134481371	20789189	1259	19531										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135314194	135314194	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	gaatacttccacattcacctGggggggtgcatccacacttg							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:135314194delG	ENST00000316077.9	-	8	1142	c.922delC	c.(922-924)cagfs	p.Q308fs	MAP7D3_ENST00000370663.5_Frame_Shift_Del_p.Q290fs|MAP7D3_ENST00000370661.1_Frame_Shift_Del_p.Q273fs	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	308					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					ACATTCACCTGGGGGGGTGCA	0.532																																					p.Q308fs		Atlas-INDEL	.											.	MAP7D3	102	.	0			c.923delA						.						179	175	176					X																	135314194		2042	4171	6213	SO:0001589	frameshift_variant	79649	exon8			.	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.922delC	chrX.hg19:g.135314194delG	ENSP00000318086:p.Gln308fs	130.0	0.0		135.0	11.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Frame_Shift_Del	DEL	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.532	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			-	135314194	G	-	135314194	7	5	114	1	0	1	0	1	0	0	0	0	9278	1357	47	0	1752	0	MAP7D3	23	135314194	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	832823	135314194	19956366	1260	19532										
CXorf40A	91966	hgsc.bcm.edu	37	chrX	148627384	148627384	+	Frame_Shift_Del	DEL	A	A	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	tgactcctgctcagattcagAccttgctcaggaaaggggaa					rs145921071		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:148627384delA	ENST00000441248.1	+	3	1795	c.208delA	c.(208-210)accfs	p.T70fs	CXorf40A_ENST00000423540.2_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000393985.3_Frame_Shift_Del_p.T70fs|RP5-937E21.8_ENST00000431993.1_RNA|CXorf40A_ENST00000450602.2_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000514208.1_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000359293.5_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000423421.1_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000434353.2_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000422892.2_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000428236.1_Frame_Shift_Del_p.T8fs			Q8TE69	CX04A_HUMAN	chromosome X open reading frame 40A	70				T -> A (in Ref. 2; AAL71889, 3; BAF84588/ BAH13262 and 5; AAH65539/AAI04931/ AAI04933/AAI43661/AAI43662/AAI43663). {ECO:0000305}.						breast(1)|endometrium(3)|large_intestine(1)|lung(2)	7	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					TCAGATTCAGACCTTGCTCAG	0.567																																					p.Q69fs		Atlas-INDEL	.											.	CXorf40A	15	.	0			c.207delG						.						38	5	16					X																	148627384		2088	3933	6021	SO:0001589	frameshift_variant	91966	exon4			.	AF011889	CCDS14687.1, CCDS55522.1	Xq28	2010-03-16	2005-09-13	2005-09-13	ENSG00000197620	ENSG00000197620			28089	protein-coding gene	gene with protein product	"endothelial-overexpressed lipopolysaccharide-associated factor 1"		"chromosome X open reading frame 40"	CXorf40		8717057, 9147653, 16383041	Standard	XM_005278212		Approved	EOLA1	uc004fdg.3	Q8TE69	OTTHUMG00000022622	ENST00000441248.1:c.208delA	chrX.hg19:g.148627384delA	ENSP00000423099:p.Thr70fs	163.0	0.0		201.0	16.0	NM_178124	A8K784|B7Z6H6|B7ZL96|D6RA72|E7ENU3|Q2M3E9	Frame_Shift_Del	DEL	ENST00000441248.1	hg19	CCDS14687.1																																																																																			.	.		0.567	CXorf40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058699.3	NM_178124		-	148627384	A	-	148627384	7	5	114	1	0	1	0	1	0	0	0	0	4110	275	10	0	210	0	CXorf40A	23	148627384	Frame_Shift_Del	DEL	A	TCGA-DD-A3A0-01A-11D-A20W-10	13313190	148627384	6643176	1261	19533										
HMGB3	3149	hgsc.bcm.edu	37	chrX	150155773	150155773	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agctgaaggagaagtatgagAaggtaaggtggggctggaag	19	2	0	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:150155773A>G	ENST00000325307.7	+	4	559	c.463A>G	c.(463-465)Aag>Gag	p.K155E	HMGB3_ENST00000448905.2_Missense_Mutation_p.K155E	NM_005342.2	NP_005333.2	O15347	HMGB3_HUMAN	high mobility group box 3	155					DNA recombination (GO:0006310)|multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(2)|lung(2)|skin(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					GAAGTATGAGAAGGTAAGGTG	0.493																																					p.K155E		Atlas-SNP	.											.	HMGB3	27	.	0			c.A463G						.						50	46	48					X																	150155773		2203	4300	6503	SO:0001583	missense	3149	exon4			TATGAGAAGGTAA	AF274572	CCDS35428.1	Xq28	2011-07-01	2011-04-05	2002-08-16	ENSG00000029993	ENSG00000029993		"High-mobility group / Canonical"	5004	protein-coding gene	gene with protein product	"non-histone chromosomal protein"	300193	"high-mobility group (nonhistone chromosomal) protein 4", "high-mobility group box 3"	HMG4		9598312	Standard	XM_005274665		Approved	HMG2A, MGC90319	uc004fep.3	O15347	OTTHUMG00000024162	ENST00000325307.7:c.463A>G	chrX.hg19:g.150155773A>G	ENSP00000359393:p.Lys155Glu	54.0	0.0		83.0	4.0	NM_005342	O95556|Q6NS40	Missense_Mutation	SNP	ENST00000325307.7	hg19	CCDS35428.1	.	.	.	.	.	.	.	.	.	.	a	29.6	5.018090	0.93404	.	.	ENSG00000029993	ENST00000419110;ENST00000325307;ENST00000455596;ENST00000448905	D;D;D;D	0.98150	-4.75;-4.75;-4.75;-4.75	5.05	5.05	0.67936	High mobility group, HMG1/HMG2, subgroup (1);High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	D	0.98065	0.9362	M	0.73753	2.245	0.58432	D	0.999993	P	0.49961	0.93	P	0.58820	0.846	D	0.97957	1.0335	10	0.44086	T	0.13	.	13.0733	0.59074	1.0:0.0:0.0:0.0	.	155	O15347	HMGB3_HUMAN	E	155	ENSP00000410354:K155E;ENSP00000359393:K155E;ENSP00000405601:K155E;ENSP00000442758:K155E	ENSP00000359393:K155E	K	+	1	0	HMGB3	149906431	1.000000	0.71417	0.998000	0.56505	0.952000	0.60782	5.753000	0.68736	1.678000	0.50952	0.430000	0.28490	AAG	.	.		0.493	HMGB3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060867.1	NM_005342		G	150155773	A	G	150155773	3	3	114	1	0	0	0	0	1	0	0	0	7236	247	9	2	473	2	HMGB3	23	150155773	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	1528389	150155773	5114787	1262	19534										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151820189	151820189	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	agcctaggcgacacaggagaCcccgaagagtcattgcccgc					rs76177030		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:151820189delC	ENST00000370306.2	+	8	1122	c.1102delC	c.(1102-1104)cccfs	p.P368fs		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	368					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ACACAGGAGACCCCGAAGAGT	0.517																																					p.R367fs		Atlas-INDEL	.											.	GABRQ	131	.	0			c.1101delA						.						128	107	114					X																	151820189		2203	4300	6503	SO:0001589	frameshift_variant	55879	exon8			.	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1102delC	chrX.hg19:g.151820189delC	ENSP00000359329:p.Pro368fs	78.0	0.0		105.0	11.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Frame_Shift_Del	DEL	ENST00000370306.2	hg19	CCDS14707.1																																																																																			.	.		0.517	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		-	151820189	C	-	151820189	7	5	114	1	0	1	0	1	0	0	0	0	6183	507	18	0	1132	0	GABRQ	23	151820189	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1664416	151820189	3450371	1263	19535										
PNMA5	114824	hgsc.bcm.edu	37	chrX	152159005	152159005	+	Frame_Shift_Del	DEL	G	G	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	taagcctccctgtatggtctGggggctgctgtcgctaaaag							TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:152159005delG	ENST00000439251.1	-	2	1576	c.1138delC	c.(1138-1140)cagfs	p.Q380fs	PNMA5_ENST00000361887.5_Frame_Shift_Del_p.Q380fs|PNMA5_ENST00000535214.1_Frame_Shift_Del_p.Q380fs|PNMA5_ENST00000452693.1_Frame_Shift_Del_p.Q380fs	NM_001103150.1	NP_001096620.1	Q96PV4	PNMA5_HUMAN	paraneoplastic Ma antigen family member 5	380					positive regulation of apoptotic process (GO:0043065)					breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					TGTATGGTCTGGGGGCTGCTG	0.607																																					p.Q380fs		Atlas-INDEL	.											.	PNMA5	63	.	0			c.1139delA						.						88	78	81					X																	152159005		2203	4300	6503	SO:0001589	frameshift_variant	114824	exon2			.	AB067521	CCDS14718.1	Xq28	2012-02-09	2012-02-09		ENSG00000198883	ENSG00000198883		"Paraneoplastic Ma antigens"	18743	protein-coding gene	gene with protein product	"paraneoplastic antigen family 5"	300916	"paraneoplastic antigen like 5"			16214224	Standard	NM_052926		Approved	KIAA1934	uc004fgy.4	Q96PV4	OTTHUMG00000024184	ENST00000439251.1:c.1138delC	chrX.hg19:g.152159005delG	ENSP00000388850:p.Gln380fs	93.0	0.0		144.0	10.0	NM_001103150	B4DI72|B7Z9Y9|Q495L5|Q8NET3	Frame_Shift_Del	DEL	ENST00000439251.1	hg19	CCDS14718.1																																																																																			.	.		0.607	PNMA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060925.1	NM_052926		-	152159005	G	-	152159005	7	5	114	1	0	1	0	1	0	0	0	0	12165	1357	47	0	212	0	PNMA5	23	152159005	Frame_Shift_Del	DEL	G	TCGA-DD-A3A0-01A-11D-A20W-10	338816	152159005	3111555	1264	19536										
IRAK1	3654	hgsc.bcm.edu	37	chrX	153278528	153278528	+	Frame_Shift_Del	DEL	C	C	-													0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ggccgggatcctgggccactCccccagctcgattctcctgc					rs192366956		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:153278528delC	ENST00000369980.3	-	12	2063	c.1896delG	c.(1894-1896)gggfs	p.G632fs	IRAK1_ENST00000477274.1_Intron|IRAK1_ENST00000393687.2_Frame_Shift_Del_p.G602fs|IRAK1_ENST00000429936.2_Frame_Shift_Del_p.G628fs|IRAK1_ENST00000369974.2_Frame_Shift_Del_p.G553fs|IRAK1_ENST00000393682.1_Frame_Shift_Del_p.G613fs	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	632					activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTGGGCCACTCCCCCAGCTCG	0.667																																					p.S633fs		Atlas-INDEL	.											.	IRAK1	107	.	0			c.1897delA						.						14	16	15					X																	153278528		2184	4254	6438	SO:0001589	frameshift_variant	3654	exon12			.	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.1896delG	chrX.hg19:g.153278528delC	ENSP00000358997:p.Gly632fs	85.0	0.0		123.0	10.0	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Frame_Shift_Del	DEL	ENST00000369980.3	hg19	CCDS14740.1																																																																																			.	.		0.667	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3			-	153278528	C	-	153278528	7	5	114	1	0	1	0	1	0	0	0	0	7830	842	30	0	254	0	IRAK1	23	153278528	Frame_Shift_Del	DEL	C	TCGA-DD-A3A0-01A-11D-A20W-10	1119523	153278528	1992032	1265	19537										
F8	2157	hgsc.bcm.edu	37	chrX	154088732	154088732	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctttgccattctgaaaaaagAgagtccactgatggccatct	8	10	2	3			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:154088732A>G	ENST00000360256.4	-	25	7075	c.6875T>C	c.(6874-6876)cTc>cCc	p.L2292P	F8_ENST00000330287.6_Missense_Mutation_p.L157P	NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	2292	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CTGAAAAAAGAGAGTCCACTG	0.408																																					p.L2292P		Atlas-SNP	.											.	F8	646	.	0			c.T6875C						.						129	124	126					X																	154088732		2203	4300	6503	SO:0001583	missense	2157	exon25			AAAAAGAGAGTCC	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.6875T>C	chrX.hg19:g.154088732A>G	ENSP00000353393:p.Leu2292Pro	72.0	0.0		77.0	4.0	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	hg19	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	a	8.464	0.856006	0.17106	.	.	ENSG00000185010	ENST00000330287;ENST00000360256	D;D	0.98207	-4.79;-4.79	5.47	-1.42	0.08913	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.789610	0.12244	N	0.486278	D	0.90442	0.7007	N	0.02973	-0.45	0.23101	N	0.998298	B;B	0.13594	0.008;0.001	B;B	0.13407	0.009;0.002	D	0.84433	0.0578	10	0.22109	T	0.4	0.0413	4.7331	0.12975	0.5281:0.0:0.3332:0.1387	.	2292;157	P00451;Q14286	FA8_HUMAN;.	P	157;2292	ENSP00000327895:L157P;ENSP00000353393:L2292P	ENSP00000327895:L157P	L	-	2	0	F8	153741926	0.182000	0.23173	0.024000	0.17045	0.952000	0.60782	0.513000	0.22770	-0.684000	0.05183	0.441000	0.28932	CTC	.	.		0.408	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			G	154088732	A	G	154088732	3	3	114	1	0	0	0	0	1	0	0	0	5352	304	11	2	188	2	F8	23	154088732	Missense_Mutation	SNP	A	TCGA-DD-A3A0-01A-11D-A20W-10	810204	154088732	1181828	1266	19538										
F8	2157	hgsc.bcm.edu	37	chrX	154157276	154157276	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0126482213438735	16	1	1.1663882344542	0.57656691134952	1.36602006688963	0.000244361757153748	0.0130209907740497	0	ctcttgggatttccactcttCttttggtatctgagtaccat	7	10	4	1			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:154157276C>T	ENST00000360256.4	-	14	4989	c.4789G>A	c.(4789-4791)Gaa>Aaa	p.E1597K		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1597	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TTCCACTCTTCTTTTGGTATC	0.423																																					p.E1597K		Atlas-SNP	.											.	F8	646	.	0			c.G4789A	GRCh37	CI080940	F8	I		.						171	170	170					X																	154157276		2203	4300	6503	SO:0001583	missense	2157	exon14			ACTCTTCTTTTGG	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.4789G>A	chrX.hg19:g.154157276C>T	ENSP00000353393:p.Glu1597Lys	116.0	0.0		136.0	7.0	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	hg19	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	c	7.861	0.726083	0.15439	.	.	ENSG00000185010	ENST00000360256	D	0.99176	-5.52	5.38	2.68	0.31781	.	0.532899	0.21047	N	0.081071	D	0.96506	0.8860	L	0.43701	1.375	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	D	0.90812	0.4702	10	0.29301	T	0.29	-2.2032	7.2414	0.26098	0.0:0.7141:0.0:0.2859	.	1597	P00451	FA8_HUMAN	K	1597	ENSP00000353393:E1597K	ENSP00000353393:E1597K	E	-	1	0	F8	153810470	0.721000	0.28007	0.003000	0.11579	0.373000	0.29922	0.485000	0.22324	0.149000	0.19098	-0.250000	0.11733	GAA	.	.		0.423	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			T	154157276	C	T	154157276	3	4	114	1	0	0	0	0	1	0	0	0	5352	922	32	3	2346	3	F8	23	154157276	Missense_Mutation	SNP	C	TCGA-DD-A3A0-01A-11D-A20W-10	68544	154157276	1113284	1267	19539										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7797597	7797597	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcagctctccagaaatacccAagggagtcactgttattgca	8	11	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:7797597A>G	ENST00000303635.7	+	15	3832	c.3625A>G	c.(3625-3627)Aag>Gag	p.K1209E	CAMTA1_ENST00000439411.2_Missense_Mutation_p.K1209E	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1209					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		AGAAATACCCAAGGGAGTCAC	0.527			T	WWTR1	epitheliod hemangioendothelioma																																p.K1209E		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.A3625G						.						38	38	38					1																	7797597		2203	4300	6503	SO:0001583	missense	23261	exon15			ATACCCAAGGGAG	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3625A>G	chr1.hg19:g.7797597A>G	ENSP00000306522:p.Lys1209Glu	113.0	0.0		86.0	4.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	hg19	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.528854	0.64860	.	.	ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646	T;T	0.22134	1.97;1.98	5.91	5.91	0.95273	.	0.103364	0.64402	D	0.000003	T	0.25791	0.0628	L	0.55481	1.735	0.48341	D	0.999631	D;D;P;P	0.56521	0.962;0.976;0.919;0.877	P;P;B;B	0.47603	0.5;0.551;0.3;0.251	T	0.05289	-1.0894	10	0.07813	T	0.8	-14.3216	16.3483	0.83171	1.0:0.0:0.0:0.0	.	1209;296;165;1209	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1	.;.;.;CMTA1_HUMAN	E	1209;1209;296;165	ENSP00000306522:K1209E;ENSP00000402561:K1209E	ENSP00000306522:K1209E	K	+	1	0	CAMTA1	7720184	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.514000	0.90545	2.254000	0.74563	0.533000	0.62120	AAG	.	.		0.527	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		G	7797597	A	G	7797597	3	3	115	1	0	0	0	0	1	0	0	0	2615	131	5	2	3683	2	CAMTA1	1	7797597	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10		7797597	241453024	1	19540										
UBE4B	10277	hgsc.bcm.edu	37	chr1	10179596	10179596	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cagccagccagcagtcagccAgcttctgagcaacatccgct	9	16	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:10179596A>G	ENST00000253251.8	+	8	1816	c.977A>G	c.(976-978)cAg>cGg	p.Q326R	UBE4B_ENST00000475795.1_3'UTR|UBE4B_ENST00000343090.6_Missense_Mutation_p.Q455R|UBE4B_ENST00000377157.3_Missense_Mutation_p.Q210R					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GCAGTCAGCCAGCTTCTGAGC	0.463																																					p.Q455R		Atlas-SNP	.											.	UBE4B	233	.	0			c.A1364G						.						124	103	110					1																	10179596		2203	4300	6503	SO:0001583	missense	10277	exon9			TCAGCCAGCTTCT	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.977A>G	chr1.hg19:g.10179596A>G	ENSP00000253251:p.Gln326Arg	91.0	0.0		74.0	4.0	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	A	17.04	3.287488	0.59976	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.46819	0.86;0.86;0.86	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.59945	0.2231	L	0.51422	1.61	0.80722	D	1	P;P	0.48294	0.537;0.908	B;P	0.61397	0.102;0.888	T	0.53315	-0.8456	10	0.22706	T	0.39	-22.1223	16.0786	0.80985	1.0:0.0:0.0:0.0	.	455;326	O95155;O95155-2	UBE4B_HUMAN;.	R	326;210;455	ENSP00000253251:Q326R;ENSP00000366362:Q210R;ENSP00000343001:Q455R	ENSP00000253251:Q326R	Q	+	2	0	UBE4B	10102183	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.866000	0.92307	2.254000	0.74563	0.460000	0.39030	CAG	.	.		0.463	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		G	10179596	A	G	10179596	3	3	115	1	0	0	0	0	1	0	0	0	16898	188	7	2	1398	2	UBE4B	1	10179596	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2381999	10179596	239071025	2	19541										
MTOR	2475	hgsc.bcm.edu	37	chr1	11301615	11301615	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtttctgacacccaccttagTcccactgccagcatgggctc	8	16	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:11301615T>C	ENST00000361445.4	-	10	1612	c.1536A>G	c.(1534-1536)ggA>ggG	p.G512G		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	512	Interaction with NBN.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CCCACCTTAGTCCCACTGCCA	0.552											OREG0013097	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G512G		Atlas-SNP	.											.	MTOR	327	.	0			c.A1536G						.						61	54	57					1																	11301615		2203	4300	6503	SO:0001819	synonymous_variant	2475	exon10			CCTTAGTCCCACT	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.1536A>G	chr1.hg19:g.11301615T>C		170.0	0.0	671	133.0	7.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	hg19	CCDS127.1																																																																																			.	.		0.552	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		C	11301615	T	C	11301615	2	2	115	1	0	0	0	0	0	0	0	1	9963	1654	58	2		2	MTOR	1	11301615	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1122019	11301615	237949006	3	19542										
PADI1	29943	hgsc.bcm.edu	37	chr1	17550123	17550123	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctatgttctgcaggtgagggTctcctactttggggagcagg	15	8	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:17550123T>C	ENST00000375471.4	+	3	373	c.281T>C	c.(280-282)gTc>gCc	p.V94A		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	94					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	CAGGTGAGGGTCTCCTACTTT	0.587																																					p.V94A	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.T281C						.						118	95	103					1																	17550123		2203	4300	6503	SO:0001583	missense	29943	exon3			TGAGGGTCTCCTA	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"Peptidyl arginine deiminases"	18367	protein-coding gene	gene with protein product	"peptidylarginine deiminase type I", "protein-arginine deiminase type-1", "hPAD-colony 10"	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.281T>C	chr1.hg19:g.17550123T>C	ENSP00000364620:p.Val94Ala	82.0	0.0		67.0	4.0	NM_013358	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	hg19	CCDS178.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.420046	0.62622	.	.	ENSG00000142623	ENST00000375471	T	0.12465	2.68	3.71	3.71	0.42584	Cupredoxin (1);Protein-arginine deiminase (PAD) N-terminal (1);	0.196908	0.33040	N	0.005350	T	0.22126	0.0533	M	0.63843	1.955	0.80722	D	1	P	0.45634	0.863	P	0.49252	0.604	T	0.01496	-1.1340	10	0.87932	D	0	-21.5259	10.6528	0.45657	0.0:0.0:0.0:1.0	.	94	Q9ULC6	PADI1_HUMAN	A	94	ENSP00000364620:V94A	ENSP00000364620:V94A	V	+	2	0	PADI1	17422710	1.000000	0.71417	0.958000	0.39756	0.025000	0.11179	4.472000	0.60189	1.464000	0.47987	0.454000	0.30748	GTC	.	.		0.587	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		C	17550123	T	C	17550123	3	2	115	1	0	0	0	0	1	0	0	0	11386	1667	58	2	291	2	PADI1	1	17550123	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	6248508	17550123	231700498	4	19543										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22180832	22180832	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggagccgcagacgggagccgTgcacctgggccaggaggagc	19	12	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:22180832T>C	ENST00000374695.3	-	50	6372	c.6293A>G	c.(6292-6294)cAc>cGc	p.H2098R	HSPG2_ENST00000430507.1_Missense_Mutation_p.H48R	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2098	Ig-like C2-type 6.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	ACGGGAGCCGTGCACCTGGGC	0.597																																					p.H2098R		Atlas-SNP	.											.	HSPG2	311	.	0			c.A6293G						.						16	14	14					1																	22180832		2191	4283	6474	SO:0001583	missense	3339	exon50			GAGCCGTGCACCT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6293A>G	chr1.hg19:g.22180832T>C	ENSP00000363827:p.His2098Arg	67.0	0.0		62.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.888674	0.33348	.	.	ENSG00000142798	ENST00000374695;ENST00000430507	T;T	0.65732	-0.17;-0.17	5.56	4.44	0.53790	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.182328	0.26156	N	0.026013	T	0.41488	0.1161	N	0.16130	0.375	0.20563	N	0.999884	B;B	0.06786	0.001;0.001	B;B	0.13407	0.005;0.009	T	0.20438	-1.0275	10	0.19590	T	0.45	.	9.6938	0.40145	0.0:0.0824:0.0:0.9176	.	38;2098	Q59EG0;P98160	.;PGBM_HUMAN	R	2098;48	ENSP00000363827:H2098R;ENSP00000416385:H48R	ENSP00000363827:H2098R	H	-	2	0	HSPG2	22053419	0.788000	0.28762	0.589000	0.28718	0.729000	0.41735	1.141000	0.31528	0.950000	0.37743	0.533000	0.62120	CAC	.	.		0.597	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		C	22180832	T	C	22180832	3	2	115	1	0	0	0	0	1	0	0	0	7439	1696	59	2	7074	2	HSPG2	1	22180832	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4630709	22180832	227069789	5	19544										
LUZP1	7798	hgsc.bcm.edu	37	chr1	23420185	23420185	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctctcacttacaaagctcagAgttaatgatttcagcttttc	5	10	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:23420185A>G	ENST00000302291.4	-	4	1371	c.570T>C	c.(568-570)acT>acC	p.T190T	LUZP1_ENST00000374623.3_Silent_p.T190T|LUZP1_ENST00000314174.5_Silent_p.T190T|LUZP1_ENST00000418342.1_Silent_p.T190T			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	190					artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		CAAAGCTCAGAGTTAATGATT	0.353																																					p.T190T		Atlas-SNP	.											.	LUZP1	83	.	0			c.T570C						.						73	73	73					1																	23420185		2203	4300	6503	SO:0001819	synonymous_variant	7798	exon4			GCTCAGAGTTAAT	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.570T>C	chr1.hg19:g.23420185A>G		99.0	0.0		74.0	4.0	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Silent	SNP	ENST00000302291.4	hg19	CCDS30628.1																																																																																			.	.		0.353	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631		G	23420185	A	G	23420185	2	3	115	1	0	0	0	0	0	0	0	1	9095	291	11	2		2	LUZP1	1	23420185	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1239353	23420185	225830436	6	19545										
PAQR7	164091	hgsc.bcm.edu	37	chr1	26189417	26189417	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gccagtgcgtgtgcagaggcTcatagatgggccgtcgggcc	17	11	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:26189417T>G	ENST00000374296.3	-	2	1580	c.914A>C	c.(913-915)gAg>gCg	p.E305A	RP1-125I3.2_ENST00000455431.1_RNA	NM_178422.5	NP_848509.1	Q86WK9	MPRA_HUMAN	progestin and adipoQ receptor family member VII	305					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)			breast(3)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.16e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000724)|BRCA - Breast invasive adenocarcinoma(304;0.000965)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0136)|READ - Rectum adenocarcinoma(331;0.0649)		GTGCAGAGGCTCATAGATGGG	0.602																																					p.E305A	Esophageal Squamous(111;1206 1556 18433 19151 38418)	Atlas-SNP	.											.	PAQR7	23	.	0			c.A914C						.						68	68	68					1																	26189417		2203	4300	6503	SO:0001583	missense	164091	exon2			AGAGGCTCATAGA		CCDS267.1	1p35.3	2012-08-10			ENSG00000182749	ENSG00000182749			23146	protein-coding gene	gene with protein product	"membrane progestin receptor alpha"	607779					Standard	NM_178422		Approved	mSR, MPRA	uc001bkx.3	Q86WK9	OTTHUMG00000007373	ENST00000374296.3:c.914A>C	chr1.hg19:g.26189417T>G	ENSP00000363414:p.Glu305Ala	304.0	0.0		246.0	150.0	NM_178422	A2A2D3|Q5XKF9|Q86VE4	Missense_Mutation	SNP	ENST00000374296.3	hg19	CCDS267.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.618986	0.46736	.	.	ENSG00000182749	ENST00000374296	T	0.23147	1.92	5.07	5.07	0.68467	.	0.216294	0.38111	N	0.001807	T	0.18341	0.0440	L	0.36672	1.1	0.45648	D	0.998571	B	0.28055	0.199	B	0.28991	0.097	T	0.06023	-1.0850	10	0.12766	T	0.61	-11.1793	9.474	0.38860	0.0:0.0:0.2321:0.7678	.	305	Q86WK9	MPRA_HUMAN	A	305	ENSP00000363414:E305A	ENSP00000363414:E305A	E	-	2	0	PAQR7	26062004	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.476000	0.60216	2.117000	0.64856	0.460000	0.39030	GAG	.	.		0.602	PAQR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019312.1	NM_178422		G	26189417	T	G	26189417	3	3	115	1	0	0	0	0	1	0	0	0	11449	1551	54	5	130	5	PAQR7	1	26189417	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2769232	26189417	223061204	7	19546										
SLC9A1	6548	hgsc.bcm.edu	37	chr1	27480593	27480593	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcttcatgccatgatcagtgAcggaatgattaacagggcgg	13	8	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:27480593A>G	ENST00000263980.3	-	1	808	c.233T>C	c.(232-234)gTc>gCc	p.V78A	SLC9A1_ENST00000374086.3_Missense_Mutation_p.V78A|SLC9A1_ENST00000545949.1_5'UTR	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	78					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	ATGATCAGTGACGGAATGATT	0.592																																					p.V78A		Atlas-SNP	.											.	SLC9A1	68	.	0			c.T233C						.						109	109	109					1																	27480593		2203	4300	6503	SO:0001583	missense	6548	exon1			TCAGTGACGGAAT	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.233T>C	chr1.hg19:g.27480593A>G	ENSP00000263980:p.Val78Ala	104.0	0.0		71.0	4.0	NM_003047	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	ENST00000263980.3	hg19	CCDS295.1	.	.	.	.	.	.	.	.	.	.	A	3.331	-0.136598	0.06711	.	.	ENSG00000090020	ENST00000263980;ENST00000374086;ENST00000374084	T;T	0.63255	0.99;-0.03	4.68	0.914	0.19360	.	2.503810	0.01272	N	0.009470	T	0.33760	0.0874	N	0.03608	-0.345	0.19945	N	0.999945	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44003	-0.9356	10	0.05833	T	0.94	.	4.5126	0.11919	0.4806:0.1772:0.0:0.3422	.	78;78	P19634-2;P19634	.;SL9A1_HUMAN	A	78	ENSP00000263980:V78A;ENSP00000363199:V78A	ENSP00000263980:V78A	V	-	2	0	SLC9A1	27353180	0.000000	0.05858	0.006000	0.13384	0.970000	0.65996	-0.056000	0.11787	0.800000	0.34041	0.533000	0.62120	GTC	.	.		0.592	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		G	27480593	A	G	27480593	3	3	115	1	0	0	0	0	1	0	0	0	14724	275	10	2	2262	2	SLC9A1	1	27480593	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1291176	27480593	221770028	8	19547										
KIAA1522	57648	hgsc.bcm.edu	37	chr1	33235850	33235850	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cctgtcgaagttgattccacAtgctgtgctgccgcctacag	10	13	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:33235850A>G	ENST00000373480.1	+	6	996	c.893A>G	c.(892-894)cAt>cGt	p.H298R	KIAA1522_ENST00000401073.2_Missense_Mutation_p.H357R|KIAA1522_ENST00000373481.3_Missense_Mutation_p.H309R|KIAA1522_ENST00000294521.3_Intron	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	298										breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				TTGATTCCACATGCTGTGCTG	0.667																																					p.H357R		Atlas-SNP	.											.	KIAA1522	68	.	0			c.A1070G						.						45	47	46					1																	33235850		2064	4191	6255	SO:0001583	missense	57648	exon6			TTCCACATGCTGT	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.893A>G	chr1.hg19:g.33235850A>G	ENSP00000362579:p.His298Arg	109.0	0.0		97.0	4.0	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	hg19	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.028773	0.54790	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.28069	1.63;1.63;1.63	4.39	4.39	0.52855	.	0.088890	0.45361	D	0.000365	T	0.22781	0.0550	L	0.36672	1.1	0.40453	D	0.980162	B;B;P	0.41265	0.231;0.231;0.744	B;B;B	0.32864	0.109;0.109;0.154	T	0.11470	-1.0586	10	0.59425	D	0.04	-9.7024	13.9093	0.63857	1.0:0.0:0.0:0.0	.	309;298;357	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	R	357;309;298	ENSP00000383851:H357R;ENSP00000362580:H309R;ENSP00000362579:H298R	ENSP00000362579:H298R	H	+	2	0	KIAA1522	33008437	1.000000	0.71417	0.885000	0.34714	0.984000	0.73092	8.804000	0.91921	1.742000	0.51746	0.402000	0.26972	CAT	.	.		0.667	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			G	33235850	A	G	33235850	3	3	115	1	0	0	0	0	1	0	0	0	8247	217	8	2	1092	2	KIAA1522	1	33235850	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5755257	33235850	216014771	9	19548										
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35477608	35477608	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgacatgaaacctggacaccTtggtgacaaaaaattaaaaa	7	7	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:35477608T>C	ENST00000357182.4	-	8	1174		c.e8-2		ZMYM6_ENST00000373340.2_Splice_Site|ZMYM6_ENST00000487874.1_Splice_Site|ZMYM6_ENST00000493328.1_Splice_Site	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6						cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				CCTGGACACCTTGGTGACAAA	0.323																																					.		Atlas-SNP	.											.	ZMYM6	110	.	0			c.947-2A>G						.						93	87	89					1																	35477608		2203	4300	6503	SO:0001630	splice_region_variant	9204	exon9			GACACCTTGGTGA	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"Zinc fingers, MYM type", "Zinc fingers, BED-type"	13050	protein-coding gene	gene with protein product	"zinc finger, BED-type containing 7"	613567	"zinc finger protein 258", "zinc finger, MYM-type containing 6"	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.947-2A>G	chr1.hg19:g.35477608T>C		71.0	0.0		74.0	4.0	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Splice_Site	SNP	ENST00000357182.4	hg19	CCDS387.2	.	.	.	.	.	.	.	.	.	.	T	15.93	2.976898	0.53720	.	.	ENSG00000163867	ENST00000373340;ENST00000357182	.	.	.	5.13	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8892	0.46986	0.0:0.0733:0.0:0.9267	.	.	.	.	.	-1	.	.	.	-	.	.	ZMYM6	35250195	1.000000	0.71417	0.994000	0.49952	0.906000	0.53458	5.224000	0.65288	1.091000	0.41335	0.528000	0.53228	.	.	.		0.323	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167	Intron	C	35477608	T	C	35477608	5	2	115	1	0	0	0	0	0	0	1	0	17719	1623	56	2	3068	2	ZMYM6	1	35477608	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2241758	35477608	213773013	10	19549										
EIF2C4	192670	hgsc.bcm.edu	37	chr1	36298069	36298069	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agccacacccaaccagggtgTctgggacatgcgaggaaagc	13	12	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:36298069T>C	ENST00000373210.3	+	11	1522	c.1277T>C	c.(1276-1278)gTc>gCc	p.V426A		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	426					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										AACCAGGGTGTCTGGGACATG	0.363																																					p.V426A		Atlas-SNP	.											.	.	.	.	0			c.T1277C						.						96	96	96					1																	36298069		2203	4300	6503	SO:0001583	missense	192670	exon11			AGGGTGTCTGGGA	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"Argonaute/PIWI family"	18424	protein-coding gene	gene with protein product	"argonaute 4"	607356	"eukaryotic translation initiation factor 2C, 4"	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.1277T>C	chr1.hg19:g.36298069T>C	ENSP00000362306:p.Val426Ala	48.0	0.0		86.0	4.0	NM_017629	A7MD27	Missense_Mutation	SNP	ENST00000373210.3	hg19	CCDS397.1	.	.	.	.	.	.	.	.	.	.	T	11.52	1.663613	0.29515	.	.	ENSG00000134698	ENST00000373210	T	0.05447	3.44	5.27	5.27	0.74061	.	0.114509	0.64402	D	0.000014	T	0.07954	0.0199	L	0.55990	1.75	0.58432	D	0.999991	B	0.06786	0.001	B	0.10450	0.005	T	0.13764	-1.0497	10	0.08381	T	0.77	-7.7221	15.2499	0.73536	0.0:0.0:0.0:1.0	.	426	Q9HCK5	AGO4_HUMAN	A	426	ENSP00000362306:V426A	ENSP00000362306:V426A	V	+	2	0	EIF2C4	36070656	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.012000	0.59069	0.529000	0.55759	GTC	.	.		0.363	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629		C	36298069	T	C	36298069	3	2	115	1	0	0	0	0	1	0	0	0	5010	1667	58	2	1319	2	EIF2C4	1	36298069	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	820461	36298069	212952552	11	19550										
MTF1	4520	hgsc.bcm.edu	37	chr1	38281195	38281195	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	catgcctcttcttgtttgatGatgatcacaggaacactgag	9	9	3	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:38281195G>A	ENST00000373036.4	-	11	2015	c.1875C>T	c.(1873-1875)atC>atT	p.I625I		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	625					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CTTGTTTGATGATGATCACAG	0.577																																					p.I625I		Atlas-SNP	.											.	MTF1	67	.	0			c.C1875T						.						62	61	61					1																	38281195		2203	4300	6503	SO:0001819	synonymous_variant	4520	exon11			TTTGATGATGATC	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1875C>T	chr1.hg19:g.38281195G>A		173.0	0.0		235.0	113.0	NM_005955	B2RAK6|Q96CB1	Silent	SNP	ENST00000373036.4	hg19	CCDS30676.1																																																																																			.	.		0.577	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955		A	38281195	G	A	38281195	2	1	115	1	0	0	0	0	0	0	0	1	9931	1280	45	3		3	MTF1	1	38281195	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	1983126	38281195	210969426	12	19551										
TIE1	7075	hgsc.bcm.edu	37	chr1	43782874	43782874	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtctcatcctgtgaagggcgAggagaccatcctgcagttca	12	11	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:43782874A>G	ENST00000372476.3	+	15	2493	c.2414A>G	c.(2413-2415)gAg>gGg	p.E805G	TIE1_ENST00000433781.2_Missense_Mutation_p.E450G|TIE1_ENST00000473014.1_3'UTR	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	805					angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GTGAAGGGCGAGGAGACCATC	0.607																																					p.E805G		Atlas-SNP	.											.	TIE1	132	.	0			c.A2414G						.						61	58	59					1																	43782874		2203	4300	6503	SO:0001583	missense	7075	exon15			AGGGCGAGGAGAC	BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11809	protein-coding gene	gene with protein product		600222	"tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.2414A>G	chr1.hg19:g.43782874A>G	ENSP00000361554:p.Glu805Gly	95.0	0.0		140.0	7.0	NM_005424	B5A949|B5A950	Missense_Mutation	SNP	ENST00000372476.3	hg19	CCDS482.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.759175	0.89843	.	.	ENSG00000066056	ENST00000372476;ENST00000372475;ENST00000536913;ENST00000433781	T;T	0.77877	-1.1;-1.13	5.24	5.24	0.73138	.	0.000000	0.38436	N	0.001688	D	0.82719	0.5098	L	0.49126	1.545	0.80722	D	1	D;B;D	0.65815	0.986;0.217;0.995	P;B;P	0.59703	0.722;0.022;0.862	D	0.83661	0.0161	10	0.51188	T	0.08	.	15.1435	0.72630	1.0:0.0:0.0:0.0	.	760;450;805	B4DTW8;B4DKW0;P35590	.;.;TIE1_HUMAN	G	805;208;88;450	ENSP00000361554:E805G;ENSP00000411728:E450G	ENSP00000361553:E208G	E	+	2	0	TIE1	43555461	1.000000	0.71417	0.990000	0.47175	0.979000	0.70002	8.962000	0.93254	1.983000	0.57843	0.528000	0.53228	GAG	.	.		0.607	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424		G	43782874	A	G	43782874	3	3	115	1	0	0	0	0	1	0	0	0	15908	304	11	2	2472	2	TIE1	1	43782874	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5501679	43782874	205467747	13	19552										
GPBP1L1	60313	hgsc.bcm.edu	37	chr1	46120863	46120863	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaagttggacatggctcaccTcctgcagttcgtaggggacc	12	11	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:46120863T>C	ENST00000290795.3	-	4	1410	c.189A>G	c.(187-189)ggA>ggG	p.G63G	GPBP1L1_ENST00000355105.3_Splice_Site_p.G63G			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	63					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					ATGGCTCACCTCCTGCAGTTC	0.448																																					p.G63G		Atlas-SNP	.											.	GPBP1L1	43	.	0			c.A189G						.						96	99	98					1																	46120863		2203	4300	6503	SO:0001630	splice_region_variant	60313	exon5			CTCACCTCCTGCA		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.190+1A>G	chr1.hg19:g.46120863T>C		103.0	0.0		122.0	5.0	NM_021639	D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	hg19	CCDS528.1																																																																																			.	.		0.448	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639	Silent	C	46120863	T	C	46120863	5	2	115	1	0	0	0	0	0	0	1	0	6604	1565	54	2	1271	2	GPBP1L1	1	46120863	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2337989	46120863	203129758	14	19553										
MAST2	23139	hgsc.bcm.edu	37	chr1	46501154	46501154	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caggccccaacctaggtcagTctggagccacagaccccatc	9	17	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:46501154T>C	ENST00000361297.2	+	29	5096	c.4813T>C	c.(4813-4815)Tct>Cct	p.S1605P	MAST2_ENST00000372009.2_Missense_Mutation_p.S1415P	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CCTAGGTCAGTCTGGAGCCAC	0.617																																					p.S1605P		Atlas-SNP	.											.	MAST2	136	.	0			c.T4813C						.						27	30	29					1																	46501154		2012	4153	6165	SO:0001583	missense	23139	exon29			GGTCAGTCTGGAG	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.4813T>C	chr1.hg19:g.46501154T>C	ENSP00000354671:p.Ser1605Pro	89.0	0.0		174.0	7.0	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	hg19	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	t	6.142	0.394495	0.11638	.	.	ENSG00000086015	ENST00000361297;ENST00000372009;ENST00000456625	T;T	0.65549	-0.07;-0.16	5.18	0.0341	0.14182	.	2.498500	0.01356	N	0.012075	T	0.42040	0.1185	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21861	-1.0233	10	0.33141	T	0.24	-0.7147	2.0349	0.03538	0.1133:0.1694:0.2054:0.5119	.	1415;1605	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	P	1605;1415;292	ENSP00000354671:S1605P;ENSP00000361079:S1415P	ENSP00000354671:S1605P	S	+	1	0	MAST2	46273741	0.000000	0.05858	0.848000	0.33437	0.100000	0.18952	0.314000	0.19432	0.415000	0.25817	0.454000	0.30748	TCT	.	.		0.617	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		C	46501154	T	C	46501154	3	2	115	1	0	0	0	0	1	0	0	0	9334	1667	58	2	4927	2	MAST2	1	46501154	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	380291	46501154	202749467	15	19554										
LRP8	7804	hgsc.bcm.edu	37	chr1	53716471	53716471	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgtcaaaattcatgcttttgGtgttcttccgcttccagttt	7	9	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:53716471G>T	ENST00000306052.6	-	17	2668	c.2567C>A	c.(2566-2568)aCc>aAc	p.T856N	LRP8_ENST00000354412.3_Missense_Mutation_p.T652N|LRP8_ENST00000371454.2_Missense_Mutation_p.T856N|LRP8_ENST00000465675.1_Missense_Mutation_p.T409N|LRP8_ENST00000347547.2_Missense_Mutation_p.T686N	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	856					ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						CATGCTTTTGGTGTTCTTCCG	0.493																																					p.T856N		Atlas-SNP	.											.	LRP8	58	.	0			c.C2567A						.						302	255	271					1																	53716471		2203	4300	6503	SO:0001583	missense	7804	exon17			CTTTTGGTGTTCT	D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"Low density lipoprotein receptors"	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.2567C>A	chr1.hg19:g.53716471G>T	ENSP00000303634:p.Thr856Asn	199.0	0.0		206.0	111.0	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	hg19	CCDS578.1	.	.	.	.	.	.	.	.	.	.	G	33	5.285224	0.95517	.	.	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000465675;ENST00000354412;ENST00000347547	T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91	5.42	5.42	0.78866	.	.	.	.	.	T	0.53238	0.1784	M	0.72353	2.195	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.996;0.998;0.999	D;D;D;D;D;D	0.91635	0.979;0.999;0.996;0.99;0.954;0.979	T	0.54873	-0.8228	9	0.66056	D	0.02	.	19.2098	0.93749	0.0:0.0:1.0:0.0	.	409;652;686;856;856;409	B3KU40;Q14114-2;Q14114-4;Q14114-3;Q14114;E9PP15	.;.;.;.;LRP8_HUMAN;.	N	856;856;409;652;686	ENSP00000303634:T856N;ENSP00000360509:T856N;ENSP00000437009:T409N;ENSP00000346391:T652N;ENSP00000334522:T686N	ENSP00000303634:T856N	T	-	2	0	LRP8	53489059	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.855000	0.99526	2.528000	0.85240	0.563000	0.77884	ACC	.	.		0.493	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		T	53716471	G	T	53716471	3	4	115	1	0	0	0	0	1	0	0	0	8972	1261	44	3	336	3	LRP8	1	53716471	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	7215317	53716471	195534150	16	19555										
INADL	10207	hgsc.bcm.edu	37	chr1	62456035	62456035	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tattggagatgaactcttagAggtgagaagcatgtgttttt	12	3	1	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:62456035A>G	ENST00000371158.2	+	28	3980	c.3866A>G	c.(3865-3867)gAg>gGg	p.E1289G	INADL_ENST00000545929.1_5'UTR|INADL_ENST00000543708.1_Splice_Site_p.E73G|INADL_ENST00000316485.6_Splice_Site_p.E1289G	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1289	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GAACTCTTAGAGGTGAGAAGC	0.433																																					p.E1289G		Atlas-SNP	.											.	INADL	179	.	0			c.A3866G						.						63	61	61					1																	62456035		2203	4300	6503	SO:0001630	splice_region_variant	10207	exon28			TCTTAGAGGTGAG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.3867+1A>G	chr1.hg19:g.62456035A>G		89.0	0.0		120.0	5.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	26.5	4.740262	0.89573	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000307297;ENST00000543708	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.73	5.73	0.89815	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000001	T	0.62122	0.2402	M	0.87617	2.895	0.80722	D	1	D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.996;1.0;0.999;1.0;0.999	T	0.69202	-0.5207	10	0.72032	D	0.01	.	16.0234	0.80516	1.0:0.0:0.0:0.0	.	73;748;1289;1289;1289	B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;INADL_HUMAN;.	G	1289;1289;1289;1289;73;73	ENSP00000360200:E1289G;ENSP00000326199:E1289G;ENSP00000307496:E73G;ENSP00000445790:E73G	ENSP00000307496:E73G	E	+	2	0	INADL	62228623	1.000000	0.71417	1.000000	0.80357	0.697000	0.40408	9.225000	0.95219	2.172000	0.68678	0.533000	0.62120	GAG	.	.		0.433	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	Missense_Mutation	G	62456035	A	G	62456035	5	3	115	1	0	0	0	0	0	0	1	0	7740	318	11	2	3972	2	INADL	1	62456035	Splice_Site	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	8739564	62456035	186794586	17	19556										
SLC35D1	23169	hgsc.bcm.edu	37	chr1	67518481	67518481	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggtacatttctgtcaaggtcAggaaacttgactactctgag	10	8	4	2	rs371868604		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:67518481A>G	ENST00000235345.5	-	3	382	c.297T>C	c.(295-297)ccT>ccC	p.P99P	SLC35D1_ENST00000506472.2_Silent_p.P20P	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	99					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						TGTCAAGGTCAGGAAACTTGA	0.393																																					p.P99P		Atlas-SNP	.											.	SLC35D1	22	.	0			c.T297C						.	A		1,4405	2.1+/-5.4	0,1,2202	115	114	114		297	2.9	1	1		114	0,8600		0,0,4300	no	coding-synonymous	SLC35D1	NM_015139.2		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		99/356	67518481	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23169	exon3			AAGGTCAGGAAAC	AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"Solute carriers"	20800	protein-coding gene	gene with protein product		610804	"solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.297T>C	chr1.hg19:g.67518481A>G		68.0	0.0		124.0	5.0	NM_015139	A8K185|B7Z3X2|Q52LU5|Q92548	Silent	SNP	ENST00000235345.5	hg19	CCDS636.1																																																																																			.	.		0.393	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139		G	67518481	A	G	67518481	2	3	115	1	0	0	0	0	0	0	0	1	14596	175	7	2		2	SLC35D1	1	67518481	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5062446	67518481	181732140	18	19557										
DNTTIP2	30836	hgsc.bcm.edu	37	chr1	94341250	94341250	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttagggttctcttgttagacTgtagtttatctgcattaaaa	8	5	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:94341250T>C	ENST00000436063.2	-	3	1814	c.1757A>G	c.(1756-1758)cAg>cGg	p.Q586R	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	586	TdBR region; mediates interaction with DNTT.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		CTTGTTAGACTGTAGTTTATC	0.363																																					p.Q586R		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.A1757G						.						239	206	216					1																	94341250		1838	4081	5919	SO:0001583	missense	30836	exon3			TTAGACTGTAGTT	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"acidic 82 kDa protein mRNA"	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.1757A>G	chr1.hg19:g.94341250T>C	ENSP00000411010:p.Gln586Arg	90.0	0.0		108.0	5.0	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	hg19	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	T	15.53	2.862276	0.51482	.	.	ENSG00000067334	ENST00000436063	T	0.14516	2.5	5.93	4.74	0.60224	.	0.343382	0.27986	N	0.017043	T	0.06645	0.0170	M	0.62723	1.935	0.09310	N	1	B	0.19935	0.04	B	0.16289	0.015	T	0.09952	-1.0651	10	0.31617	T	0.26	.	12.0766	0.53647	0.1288:0.0:0.0:0.8712	.	586	Q5QJE6	TDIF2_HUMAN	R	586	ENSP00000411010:Q586R	ENSP00000411010:Q586R	Q	-	2	0	DNTTIP2	94113838	0.999000	0.42202	0.233000	0.24025	0.959000	0.62525	3.577000	0.53885	2.263000	0.75096	0.533000	0.62120	CAG	.	.		0.363	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		C	94341250	T	C	94341250	3	2	115	1	0	0	0	0	1	0	0	0	4684	1580	55	2	533	2	DNTTIP2	1	94341250	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	26822769	94341250	154909371	19	19558										
SASS6	163786	hgsc.bcm.edu	37	chr1	100571335	100571335	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aatcttaccacattcaggttAggagaaattccacttctgat	6	9	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:100571335A>G	ENST00000287482.5	-	13	1673	c.1533T>C	c.(1531-1533)ccT>ccC	p.P511P	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_Silent_p.P344P	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	511					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		CATTCAGGTTAGGAGAAATTC	0.368																																					p.P511P		Atlas-SNP	.											.	SASS6	61	.	0			c.T1533C						.						161	145	150					1																	100571335		2203	4300	6503	SO:0001819	synonymous_variant	163786	exon13			CAGGTTAGGAGAA	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.1533T>C	chr1.hg19:g.100571335A>G		128.0	0.0		141.0	6.0	NM_194292	D3DT55|Q8N3K0	Silent	SNP	ENST00000287482.5	hg19	CCDS764.1																																																																																			.	.		0.368	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292		G	100571335	A	G	100571335	2	3	115	1	0	0	0	0	0	0	0	1	13865	407	15	2		2	SASS6	1	100571335	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6230085	100571335	148679286	20	19559										
KCNA3	3738	hgsc.bcm.edu	37	chr1	111216834	111216834	+	Frame_Shift_Del	DEL	C	C	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctcccgcaggaagccctcgtCctcgcggaacttctccatgg							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:111216834delC	ENST00000369769.2	-	1	821	c.598delG	c.(598-600)gacfs	p.D200fs		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	200					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	AAGCCCTCGTCCTCGCGGAAC	0.692																																					p.D200fs		Atlas-Indel,Pindel	.											.	KCNA3	91	.	0			c.599delA						.						43	49	47					1																	111216834		2203	4300	6503	SO:0001589	frameshift_variant	3738	exon1			.	L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.598delG	chr1.hg19:g.111216834delC	ENSP00000358784:p.Asp200fs	69.0	0.0		109.0	55.0	NM_002232	Q5VWN2	Frame_Shift_Del	DEL	ENST00000369769.2	hg19	CCDS828.2																																																																																			.	.		0.692	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		-	111216834	C	-	111216834	7	5	115	1	0	1	0	1	0	0	0	0	8013	855	30	0	1133	0	KCNA3	1	111216834	Frame_Shift_Del	DEL	C	TCGA-DD-A3A1-01A-11D-A20W-10	10645499	111216834	138033787	21	19560										
TRIM33	51592	hgsc.bcm.edu	37	chr1	114973529	114973530	+	Frame_Shift_Ins	INS	-	-	CAAC													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gttagtctcatttacttcttINSttatcctgaataagagaaat							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:114973529_114973530insCAAC	ENST00000358465.2	-	6	1128_1129	c.1045_1046insGTTG	c.(1045-1047)aaafs	p.K349fs	TRIM33_ENST00000369543.2_Frame_Shift_Ins_p.K349fs|TRIM33_ENST00000450349.2_5'UTR	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	349	Necessary for oligomerization.				gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATTTACTTCTTTTATCCTGAAT	0.337			T	RET	papillary thyroid																																p.K349_E350delinsSX		Atlas-INDEL	.		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	.	TRIM33	115	.	0			c.1046_1047insGTTG						.																																			SO:0001589	frameshift_variant	51592	exon6			.	AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.1045_1046insGTTG	chr1.hg19:g.114973529_114973530insCAAC	ENSP00000351250:p.Lys349fs	172.0	0.0		148.0	11.0	NM_033020	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Frame_Shift_Ins	INS	ENST00000358465.2	hg19	CCDS872.1																																																																																			.	.		0.337	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		CAAC	114973530	-	CAAC	114973529	7	5	115	1	0	1	1	0	0	0	0	0	16522	1841	64	0	2397	0	TRIM33	1	114973529	Frame_Shift_Ins	INS	-	TCGA-DD-A3A1-01A-11D-A20W-10	3756695	114973529	134277092	22	19561										
ITGA10	8515	hgsc.bcm.edu	37	chr1	145534216	145534216	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggctgtgggggcgcctctggAagatgggcaccagggagcac	19	10	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:145534216A>G	ENST00000369304.3	+	14	1896	c.1721A>G	c.(1720-1722)gAa>gGa	p.E574G	ITGA10_ENST00000539363.1_Missense_Mutation_p.E431G|ITGA10_ENST00000538811.1_Missense_Mutation_p.E443G	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	574					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GCGCCTCTGGAAGATGGGCAC	0.587																																					p.E574G		Atlas-SNP	.											.	ITGA10	131	.	0			c.A1721G						.						109	114	113					1																	145534216		2203	4300	6503	SO:0001583	missense	8515	exon14			CTCTGGAAGATGG	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.1721A>G	chr1.hg19:g.145534216A>G	ENSP00000358310:p.Glu574Gly	154.0	0.0		191.0	50.0	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.175848	0.78564	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.60797	0.16;0.16;0.16	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000001	T	0.67961	0.2949	M	0.70275	2.135	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.85130	0.997;0.997;0.995;0.994	T	0.73398	-0.3995	10	0.87932	D	0	.	12.9882	0.58604	1.0:0.0:0.0:0.0	.	540;443;431;574	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	G	574;540;431;443	ENSP00000358310:E574G;ENSP00000439894:E431G;ENSP00000440011:E443G	ENSP00000358310:E574G	E	+	2	0	ITGA10	144245573	1.000000	0.71417	1.000000	0.80357	0.647000	0.38526	8.959000	0.93110	2.014000	0.59158	0.533000	0.62120	GAA	.	.		0.587	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		G	145534216	A	G	145534216	3	3	115	1	0	0	0	0	1	0	0	0	7882	246	9	2	1775	2	ITGA10	1	145534216	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	30560687	145534216	103716405	23	19562										
HRNR	388697	hgsc.bcm.edu	37	chr1	152189562	152189562	+	Frame_Shift_Del	DEL	T	T	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acctaagccagaagagtgacTggagccagactcatatgggc					rs144150413		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:152189562delT	ENST00000368801.2	-	3	4618	c.4543delA	c.(4543-4545)agtfs	p.S1515fs	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1515					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAAGAGTGACTGGAGCCAGAC	0.577																																					p.S1515fs		Atlas-INDEL	.											.	HRNR	403	.	0			c.4544delG						.																																			SO:0001589	frameshift_variant	388697	exon3			.	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.4543delA	chr1.hg19:g.152189562delT	ENSP00000357791:p.Ser1515fs	6.0	1.0		15.0	13.0	NM_001009931	Q5DT20|Q5U1F4	Frame_Shift_Del	DEL	ENST00000368801.2	hg19	CCDS30859.1																																																																																			.	.		0.577	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		-	152189562	T	-	152189562	7	5	115	1	0	1	0	1	0	0	0	0	7368	1580	55	0	4013	0	HRNR	1	152189562	Frame_Shift_Del	DEL	T	TCGA-DD-A3A1-01A-11D-A20W-10	6655346	152189562	97061059	24	19563										
FLG	2312	hgsc.bcm.edu	37	chr1	152277969	152277969	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaccctgagtgtccagagctAtctaccgaatgctcgtggtg	12	11	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:152277969A>C	ENST00000368799.1	-	3	9428	c.9393T>G	c.(9391-9393)gaT>gaG	p.D3131E	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3131	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTCCAGAGCTATCTACCGAAT	0.587									Ichthyosis																												p.D3131E		Atlas-SNP	.											.	FLG	900	.	0			c.T9393G						.						69	92	84					1																	152277969		2197	4272	6469	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGAGCTATCTACC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9393T>G	chr1.hg19:g.152277969A>C	ENSP00000357789:p.Asp3131Glu	341.0	0.0		441.0	111.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	A	9.659	1.143502	0.21205	.	.	ENSG00000143631	ENST00000368799	T	0.04234	3.67	2.49	0.55	0.17219	.	.	.	.	.	T	0.04227	0.0117	M	0.79475	2.455	0.09310	N	1	D	0.71674	0.998	D	0.64144	0.922	T	0.20009	-1.0288	9	0.06099	T	0.92	.	4.881	0.13679	0.3146:0.0:0.6854:0.0	.	3131	P20930	FILA_HUMAN	E	3131	ENSP00000357789:D3131E	ENSP00000357789:D3131E	D	-	3	2	FLG	150544593	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.963000	0.03837	0.138000	0.18790	-0.429000	0.05907	GAT	.	.		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152277969	A	C	152277969	3	2	115	1	0	0	0	0	1	0	0	0	5930	446	16	5	2796	5	FLG	1	152277969	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	88407	152277969	96972652	25	19564										
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156496391	156496391	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atactggagctgcaggagatCctaggagggaagaggcaggg	18	6	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:156496391C>A	ENST00000361170.2	-	38	4793	c.4783G>T	c.(4783-4785)Gat>Tat	p.D1595Y	snoU13_ENST00000458777.1_RNA	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1595					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGCAGGAGATCCTAGGAGGGA	0.498																																					p.D1595Y		Atlas-SNP	.											IQGAP3,NS,carcinoma,0,2	IQGAP3	146	.	0			c.G4783T						.						71	64	66					1																	156496391		2203	4300	6503	SO:0001630	splice_region_variant	128239	exon38			GGAGATCCTAGGA	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.4783-1G>T	chr1.hg19:g.156496391C>A		69.0	0.0		78.0	21.0	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	hg19	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.572555	0.86542	.	.	ENSG00000183856	ENST00000361170	T	0.06849	3.25	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.30262	0.0759	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.34229	-0.9837	10	0.87932	D	0	-29.8599	16.507	0.84274	0.0:1.0:0.0:0.0	.	1595	Q86VI3	IQGA3_HUMAN	Y	1595	ENSP00000354451:D1595Y	ENSP00000354451:D1595Y	D	-	1	0	IQGAP3	154763015	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.584000	0.82572	2.475000	0.83589	0.561000	0.74099	GAT	.	.		0.498	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	Missense_Mutation	A	156496391	C	A	156496391	5	1	115	1	0	0	0	0	0	0	1	0	7825	869	30	3	116	3	IQGAP3	1	156496391	Splice_Site	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	4218422	156496391	92754230	26	19565										
ETV3	2117	hgsc.bcm.edu	37	chr1	157095521	157095521	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttctgatggccaatccctccTccaccaatggcattcctgga	7	15	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:157095521T>C	ENST00000368192.4	-	5	715	c.651A>G	c.(649-651)ggA>ggG	p.G217G		NM_001145312.1	NP_001138784.1	P41162	ETV3_HUMAN	ets variant 3	217					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	9	Hepatocellular(266;0.158)	Prostate(1639;0.174)				CAATCCCTCCTCCACCAATGG	0.567																																					p.G217G		Atlas-SNP	.											.	ETV3	50	.	0			c.A651G						.						86	82	83					1																	157095521		692	1591	2283	SO:0001819	synonymous_variant	2117	exon5			CCCTCCTCCACCA	BC022868	CCDS1164.1, CCDS44250.1	1q21-q23	2008-09-12	2008-09-12		ENSG00000117036	ENSG00000117036			3492	protein-coding gene	gene with protein product		164873	"ets variant gene 3, ETS family transcriptional repressor", "ets variant gene 3"			8020980	Standard	NM_005240		Approved	PE-1	uc001fqr.2	P41162	OTTHUMG00000034298	ENST00000368192.4:c.651A>G	chr1.hg19:g.157095521T>C		84.0	0.0		144.0	6.0	NM_001145312	B4E3M7|Q8TAC8|Q9BX30	Silent	SNP	ENST00000368192.4	hg19	CCDS44250.1																																																																																			.	.		0.567	ETV3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082843.2	NM_005240		C	157095521	T	C	157095521	2	2	115	1	0	0	0	0	0	0	0	1	5281	1538	54	2		2	ETV3	1	157095521	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	599130	157095521	92155100	27	19566										
PYHIN1	149628	hgsc.bcm.edu	37	chr1	158908887	158908887	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tagaaaagaaaaaaaccatcTgaagaagagactggaaccaa	8	6	1	5			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:158908887T>A	ENST00000368140.1	+	4	674	c.429T>A	c.(427-429)tcT>tcA	p.S143S	PYHIN1_ENST00000368138.3_Silent_p.S134S|PYHIN1_ENST00000392252.3_Silent_p.S134S|PYHIN1_ENST00000368135.4_Silent_p.S143S|PYHIN1_ENST00000392254.2_Silent_p.S143S	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	143					cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					AAAAACCATCTGAAGAAGAGA	0.413																																					p.S143S		Atlas-SNP	.											.	PYHIN1	208	.	0			c.T429A						.						53	53	53					1																	158908887		2203	4300	6503	SO:0001819	synonymous_variant	149628	exon4			ACCATCTGAAGAA	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.429T>A	chr1.hg19:g.158908887T>A		130.0	0.0		149.0	50.0	NM_152501	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Silent	SNP	ENST00000368140.1	hg19	CCDS1178.1																																																																																			.	.		0.413	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		A	158908887	T	A	158908887	2	1	115	1	0	0	0	0	0	0	0	1	12880	1567	55	4		4	PYHIN1	1	158908887	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1813366	158908887	90341734	28	19567										
KLHL20	27252	hgsc.bcm.edu	37	chr1	173754356	173754356	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtggcgtaggagttattaaaAtgacacattgtgaatcccat	10	6	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:173754356A>G	ENST00000209884.4	+	12	1937	c.1801A>G	c.(1801-1803)Atg>Gtg	p.M601V	KLHL20_ENST00000546011.1_Missense_Mutation_p.M412V	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	601					cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)			breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						AGTTATTAAAATGACACATTG	0.403																																					p.M601V	GBM(159;862 2695 6559 23041)	Atlas-SNP	.											.	KLHL20	54	.	0			c.A1801G						.						111	111	111					1																	173754356		2203	4300	6503	SO:0001583	missense	27252	exon12			ATTAAAATGACAC	AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"Kelch-like", "BTB/POZ domain containing"	25056	protein-coding gene	gene with protein product			"kelch-like 20 (Drosophila)"			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.1801A>G	chr1.hg19:g.173754356A>G	ENSP00000209884:p.Met601Val	81.0	0.0		81.0	4.0	NM_014458	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Missense_Mutation	SNP	ENST00000209884.4	hg19	CCDS1310.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.840786	0.51057	.	.	ENSG00000076321	ENST00000546011;ENST00000209884	T;T	0.68331	-0.04;-0.32	6.06	6.06	0.98353	.	.	.	.	.	T	0.34454	0.0898	N	0.14661	0.345	0.80722	D	1	B;B	0.24317	0.101;0.05	B;B	0.18871	0.023;0.013	T	0.27400	-1.0075	9	0.26408	T	0.33	.	15.6071	0.76682	1.0:0.0:0.0:0.0	.	412;601	B4DUR0;Q9Y2M5	.;KLH20_HUMAN	V	412;601	ENSP00000443121:M412V;ENSP00000209884:M601V	ENSP00000209884:M601V	M	+	1	0	KLHL20	172020979	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.128000	0.94424	2.323000	0.78572	0.528000	0.53228	ATG	.	.		0.403	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458		G	173754356	A	G	173754356	3	3	115	1	0	0	0	0	1	0	0	0	8384	101	4	2	1843	2	KLHL20	1	173754356	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	14845469	173754356	75496265	29	19568										
TOR1AIP1	26092	hgsc.bcm.edu	37	chr1	179887172	179887172	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gactgtcttattggaggaagAgacacttggaacaagtctag	12	6	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:179887172A>G	ENST00000606911.2	+	10	1741	c.1550A>G	c.(1549-1551)gAg>gGg	p.E517G	TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.E518G|TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.E533G|TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.E396G			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	517	Interaction with TOR1A.				positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						TTGGAGGAAGAGACACTTGGA	0.403																																					p.E518G		Atlas-SNP	.											.	TOR1AIP1	58	.	0			c.A1553G						.						89	89	89					1																	179887172		2203	4300	6503	SO:0001583	missense	26092	exon10			AGGAAGAGACACT		CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"lamina associated polypeptide 1B"	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.1550A>G	chr1.hg19:g.179887172A>G	ENSP00000476687:p.Glu517Gly	141.0	0.0		196.0	8.0	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	hg19	CCDS1335.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.12|15.12	2.739708|2.739708	0.49045|0.49045	.|.	.|.	ENSG00000143337|ENSG00000143337	ENST00000325993;ENST00000271583;ENST00000435319|ENST00000447964	T;T|.	0.27402|.	1.67;1.67|.	5.96|5.96	4.81|4.81	0.61882|0.61882	.|.	0.697515|.	0.15176|.	N|.	0.276378|.	T|T	0.45458|0.45458	0.1343|0.1343	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	1|1	P|.	0.44521|.	0.837|.	B|.	0.43990|.	0.438|.	T|T	0.30966|0.30966	-0.9960|-0.9960	9|5	.|.	.|.	.|.	-1.6777|-1.6777	11.7058|11.7058	0.51597|0.51597	0.7189:0.2811:0.0:0.0|0.7189:0.2811:0.0:0.0	.|.	517|.	Q5JTV8|.	TOIP1_HUMAN|.	G|G	312;533;517|252	ENSP00000271583:E533G;ENSP00000393292:E517G|.	.|.	E|R	+|+	2|1	0|2	TOR1AIP1|TOR1AIP1	178153795|178153795	1.000000|1.000000	0.71417|0.71417	0.450000|0.450000	0.26969|0.26969	0.967000|0.967000	0.64934|0.64934	5.142000|5.142000	0.64820|0.64820	1.033000|1.033000	0.39918|0.39918	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.403	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602		G	179887172	A	G	179887172	3	3	115	1	0	0	0	0	1	0	0	0	16387	304	11	2	1588	2	TOR1AIP1	1	179887172	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6132816	179887172	69363449	30	19569										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183095398	183095398	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tggacctgaaggctgcaaacGtaaggggtgttggtggcata	16	6	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:183095398G>T	ENST00000258341.4	+	16	3201		c.e16+1		LAMC1_ENST00000466964.1_Splice_Site	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GGCTGCAAACGTAAGGGGTGT	0.532																																					.		Atlas-SNP	.											.	LAMC1	176	.	0			c.2944+1G>T						.						86	77	80					1																	183095398		2203	4300	6503	SO:0001630	splice_region_variant	3915	exon16			GCAAACGTAAGGG	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.2944+1G>T	chr1.hg19:g.183095398G>T		140.0	0.0		284.0	140.0	NM_002293	Q5VYE7	Splice_Site	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.814480	0.90790	.	.	ENSG00000135862	ENST00000258341	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6934	0.96010	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LAMC1	181362021	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.135000	0.94478	2.651000	0.90000	0.655000	0.94253	.	.	.		0.532	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	Intron	T	183095398	G	T	183095398	5	4	115	1	0	0	0	0	0	0	1	0	8623	1159	40	1	3007	1	LAMC1	1	183095398	Splice_Site	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	3208226	183095398	66155223	31	19570										
PPP1R15B	84919	hgsc.bcm.edu	37	chr1	204378837	204378837	+	Frame_Shift_Del	DEL	G	G	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaggagccttaaaatttaaaGggttgtaggggtcatcagaa							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:204378837delG	ENST00000367188.4	-	1	2082	c.1703delC	c.(1702-1704)cctfs	p.P568fs	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	568					ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			AAAATTTAAAGGGTTGTAGGG	0.443																																					p.P568fs		Atlas-INDEL	.											.	PPP1R15B	67	.	0			c.1704delT						.						66	67	67					1																	204378837		2203	4300	6503	SO:0001589	frameshift_variant	84919	exon1			.	AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14951	protein-coding gene	gene with protein product		613257	"protein phosphatase 1, regulatory (inhibitor) subunit 15B"			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.1703delC	chr1.hg19:g.204378837delG	ENSP00000356156:p.Pro568fs	115.0	0.0		163.0	10.0	NM_032833	Q53GQ4|Q658M2|Q6P156|Q96SN1	Frame_Shift_Del	DEL	ENST00000367188.4	hg19	CCDS1445.1																																																																																			.	.		0.443	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833		-	204378837	G	-	204378837	7	5	115	1	0	1	0	1	0	0	0	0	12376	1000	35	0	446	0	PPP1R15B	1	204378837	Frame_Shift_Del	DEL	G	TCGA-DD-A3A1-01A-11D-A20W-10	21283439	204378837	44871784	32	19571										
NFASC	23114	hgsc.bcm.edu	37	chr1	204955096	204955096	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtgggtgtctcagaagagacAgcaagccagcttccctggtg	14	10	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:204955096A>G	ENST00000404076.1	+	21	3004	c.2582A>G	c.(2581-2583)cAg>cGg	p.Q861R	NFASC_ENST00000338515.6_Missense_Mutation_p.Q882R|NFASC_ENST00000539706.1_Missense_Mutation_p.Q878R|NFASC_ENST00000404907.1_Missense_Mutation_p.Q878R|NFASC_ENST00000513543.1_Missense_Mutation_p.Q878R|NFASC_ENST00000367172.4_Missense_Mutation_p.Q882R|NFASC_ENST00000367171.4_Missense_Mutation_p.Q867R|NFASC_ENST00000367170.4_Missense_Mutation_p.Q882R|NFASC_ENST00000401399.1_Intron|NFASC_ENST00000339876.6_Intron|NFASC_ENST00000338586.6_Missense_Mutation_p.Q882R|NFASC_ENST00000367169.4_Intron|NFASC_ENST00000360049.4_Missense_Mutation_p.Q878R			O94856	NFASC_HUMAN	neurofascin	882	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CAGAAGAGACAGCAAGCCAGC	0.602																																					p.Q893R		Atlas-SNP	.											.	NFASC	396	.	0			c.A2678G						.						64	52	56					1																	204955096		2203	4300	6503	SO:0001583	missense	23114	exon21			AGAGACAGCAAGC	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000404076.1:c.2582A>G	chr1.hg19:g.204955096A>G	ENSP00000385676:p.Gln861Arg	106.0	0.0		183.0	8.0	NM_001160331	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000404076.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.64	2.595708	0.46318	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000404076;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38	5.66	5.66	0.87406	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.48767	D	0.000176	T	0.46268	0.1384	L	0.42245	1.32	0.80722	D	1	B;B;B;B;B	0.30973	0.302;0.148;0.051;0.018;0.257	B;B;B;B;B	0.33799	0.115;0.17;0.062;0.032;0.062	T	0.35919	-0.9769	10	0.13470	T	0.59	.	15.5631	0.76266	1.0:0.0:0.0:0.0	.	882;893;878;867;878	O94856;O94856-11;O94856-8;F8W791;O94856-3	NFASC_HUMAN;.;.;.;.	R	882;867;882;882;882;893;878;878;861;878;878;869	ENSP00000356140:Q882R;ENSP00000356139:Q867R;ENSP00000356138:Q882R;ENSP00000342128:Q882R;ENSP00000343509:Q882R;ENSP00000438614:Q878R;ENSP00000353154:Q878R;ENSP00000385676:Q861R;ENSP00000384061:Q878R;ENSP00000425908:Q878R;ENSP00000415031:Q869R	ENSP00000295776:Q893R	Q	+	2	0	NFASC	203221719	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.991000	0.56973	2.153000	0.67306	0.460000	0.39030	CAG	.	.		0.602	NFASC-012	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000131243.1	NM_001005388		G	204955096	A	G	204955096	3	3	115	1	0	0	0	0	1	0	0	0	10368	188	7	2	2811	2	NFASC	1	204955096	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	576259	204955096	44295525	33	19572										
CNTN2	6900	hgsc.bcm.edu	37	chr1	205031113	205031113	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcgctggctgcggaacggggAgcctctggcctcccaggtag	17	13	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:205031113A>G	ENST00000331830.4	+	9	1378	c.1094A>G	c.(1093-1095)gAg>gGg	p.E365G	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	365	Ig-like C2-type 4.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CGGAACGGGGAGCCTCTGGCC	0.652											OREG0014144	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E365G	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.A1094G						.						16	18	17					1																	205031113		2202	4297	6499	SO:0001583	missense	6900	exon9			ACGGGGAGCCTCT	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.1094A>G	chr1.hg19:g.205031113A>G	ENSP00000330633:p.Glu365Gly	85.0	0.0	2149	145.0	6.0	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	hg19	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.566387	0.45694	.	.	ENSG00000184144	ENST00000331830	T	0.69040	-0.37	4.94	4.94	0.65067	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.379896	0.22016	N	0.065790	T	0.54679	0.1873	L	0.33137	0.985	0.36963	D	0.893448	B;B;B	0.20052	0.034;0.034;0.041	B;B;B	0.25506	0.061;0.061;0.061	T	0.57556	-0.7791	10	0.37606	T	0.19	.	9.6646	0.39977	0.9158:0.0:0.0842:0.0	.	365;365;256	A1L3A3;Q02246;Q68DA2	.;CNTN2_HUMAN;.	G	365	ENSP00000330633:E365G	ENSP00000330633:E365G	E	+	2	0	CNTN2	203297736	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.753000	0.62183	1.850000	0.53721	0.455000	0.32223	GAG	.	.		0.652	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		G	205031113	A	G	205031113	3	3	115	1	0	0	0	0	1	0	0	0	3643	304	11	2	1124	2	CNTN2	1	205031113	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	76017	205031113	44219508	34	19573										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208270080	208270080	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcagatatttcttaccttgaTccagcgggatgacagggaca	11	9	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:208270080T>C	ENST00000367033.3	-	7	2637	c.1880A>G	c.(1879-1881)gAt>gGt	p.D627G		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	627					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CTTACCTTGATCCAGCGGGAT	0.547																																					p.D627G		Atlas-SNP	.											.	PLXNA2	178	.	0			c.A1880G						.						78	76	77					1																	208270080		2203	4300	6503	SO:0001583	missense	5362	exon7			CCTTGATCCAGCG	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.1880A>G	chr1.hg19:g.208270080T>C	ENSP00000356000:p.Asp627Gly	70.0	0.0		123.0	5.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	T	5.882	0.346811	0.11126	.	.	ENSG00000076356	ENST00000367033	T	0.00801	5.68	4.92	4.92	0.64577	.	0.100091	0.64402	D	0.000002	T	0.00552	0.0018	N	0.04373	-0.215	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47861	-0.9084	10	0.02654	T	1	.	10.833	0.46671	0.0:0.0:0.1581:0.8419	.	627	O75051	PLXA2_HUMAN	G	627	ENSP00000356000:D627G	ENSP00000356000:D627G	D	-	2	0	PLXNA2	206336703	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.250000	0.58772	2.072000	0.62099	0.533000	0.62120	GAT	.	.		0.547	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		C	208270080	T	C	208270080	3	2	115	1	0	0	0	0	1	0	0	0	12129	1435	50	2	3908	2	PLXNA2	1	208270080	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3238967	208270080	40980541	35	19574										
INTS7	25896	hgsc.bcm.edu	37	chr1	212141249	212141249	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttcctcaaagttgctgagtcAgcatcaaaagatgcctggta	9	9	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:212141249A>G	ENST00000366994.3	-	15	2189	c.2085T>C	c.(2083-2085)gcT>gcC	p.A695A	INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000366992.3_Silent_p.A695A|INTS7_ENST00000366993.3_Silent_p.A695A|INTS7_ENST00000440600.2_Silent_p.A646A	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	695					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		TTGCTGAGTCAGCATCAAAAG	0.368																																					p.A695A		Atlas-SNP	.											.	INTS7	68	.	0			c.T2085C						.						112	115	114					1																	212141249		2203	4300	6503	SO:0001819	synonymous_variant	25896	exon15			TGAGTCAGCATCA	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.2085T>C	chr1.hg19:g.212141249A>G		45.0	0.0		69.0	4.0	NM_015434	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Silent	SNP	ENST00000366994.3	hg19	CCDS1501.1																																																																																			.	.		0.368	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434		G	212141249	A	G	212141249	2	3	115	1	0	0	0	0	0	0	0	1	7792	175	7	2		2	INTS7	1	212141249	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3871169	212141249	37109372	36	19575										
RYR2	6262	hgsc.bcm.edu	37	chr1	237823324	237823324	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atggagaaatatattcagacTcttctaaggttcagccatta	7	7	4	2	rs547987180	byFrequency	TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:237823324T>C	ENST00000366574.2	+	55	8565	c.8248T>C	c.(8248-8250)Tct>Cct	p.S2750P	RYR2_ENST00000542537.1_Missense_Mutation_p.S2734P|RYR2_ENST00000360064.6_Missense_Mutation_p.S2748P	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2750	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATATTCAGACTCTTCTAAGGT	0.274																																					p.S2750P		Atlas-SNP	.											.	RYR2	1273	.	0			c.T8248C						.						60	57	58					1																	237823324		1803	4058	5861	SO:0001583	missense	6262	exon55			TCAGACTCTTCTA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.8248T>C	chr1.hg19:g.237823324T>C	ENSP00000355533:p.Ser2750Pro	90.0	0.0		114.0	6.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.977311	0.53720	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.91792	-2.91;-2.91;-2.91	5.63	5.63	0.86233	Ryanodine receptor Ryr (1);	0.207429	0.33199	N	0.005176	D	0.90184	0.6932	L	0.38175	1.15	0.33503	D	0.590166	P	0.48407	0.91	P	0.47827	0.558	D	0.92876	0.6319	10	0.41790	T	0.15	.	14.4208	0.67183	0.0:0.0:0.0:1.0	.	2750	Q92736	RYR2_HUMAN	P	2750;2748;2734	ENSP00000355533:S2750P;ENSP00000353174:S2748P;ENSP00000443798:S2734P	ENSP00000353174:S2748P	S	+	1	0	RYR2	235889947	0.106000	0.21978	1.000000	0.80357	0.990000	0.78478	0.785000	0.26830	2.142000	0.66516	0.383000	0.25322	TCT	.	.		0.274	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237823324	T	C	237823324	3	2	115	1	0	0	0	0	1	0	0	0	13784	1551	54	2	8466	2	RYR2	1	237823324	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	25682075	237823324	11427297	37	19576										
RGS7	6000	hgsc.bcm.edu	37	chr1	240978079	240978079	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtatttgccaatattttatcTgaaaagagggttagagaagg	11	3	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr1:240978079T>C	ENST00000407727.1	-	11	783		c.e11-2		RGS7_ENST00000446183.2_Splice_Site|RGS7_ENST00000366564.1_Splice_Site|RGS7_ENST00000366565.1_Splice_Site|RGS7_ENST00000331110.7_Splice_Site|RGS7_ENST00000366563.1_Splice_Site|RGS7_ENST00000366562.4_Splice_Site|RGS7_ENST00000348120.2_Splice_Site|RGS7_ENST00000401882.1_Splice_Site			P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			ATATTTTATCTGAAAAGAGGG	0.323																																					.		Atlas-SNP	.											.	RGS7	308	.	0			c.784-2A>G						.						98	105	102					1																	240978079		2203	4296	6499	SO:0001630	splice_region_variant	6000	exon13			TTTATCTGAAAAG	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"Regulators of G-protein signaling"	10003	protein-coding gene	gene with protein product		602517	"regulator of G-protein signalling 7"			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.784-2A>G	chr1.hg19:g.240978079T>C		47.0	0.0		85.0	24.0	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Splice_Site	SNP	ENST00000407727.1	hg19		.	.	.	.	.	.	.	.	.	.	T	24.5	4.535076	0.85812	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000440928;ENST00000348120;ENST00000446183;ENST00000366562;ENST00000407727;ENST00000401882	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7905	0.78357	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RGS7	239044702	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.825000	0.86693	2.324000	0.78689	0.533000	0.62120	.	.	.		0.323	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924	Intron	C	240978079	T	C	240978079	5	2	115	1	0	0	0	0	0	0	1	0	13325	1594	55	2	709	2	RGS7	1	240978079	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3154755	240978079	8272542	38	19577										
TAF1B	9014	hgsc.bcm.edu	37	chr2	10045015	10045015	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgactacgaggacatctacAaaaaaacagtagaagttgga	9	7	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:10045015A>T	ENST00000263663.5	+	9	1023	c.835A>T	c.(835-837)Aaa>Taa	p.K279*	TAF1B_ENST00000396242.3_Nonsense_Mutation_p.K24*	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	279	C-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGACATCTACAAAAAAACAGT	0.328																																					p.K279X		Atlas-SNP	.											TAF1B,NS,carcinoma,0,1	TAF1B	62	.	0			c.A835T						.						75	65	68					2																	10045015		2203	4300	6503	SO:0001587	stop_gained	9014	exon9			ATCTACAAAAAAA	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.835A>T	chr2.hg19:g.10045015A>T	ENSP00000263663:p.Lys279*	58.0	0.0		45.0	0.0	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Nonsense_Mutation	SNP	ENST00000263663.5	hg19	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648783	0.87958	.	.	ENSG00000115750	ENST00000263663;ENST00000396242	.	.	.	5.46	0.00658	0.14068	.	0.641420	0.17120	N	0.186264	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.238	2.8251	0.05483	0.6069:0.1237:0.1497:0.1198	.	.	.	.	X	279;24	.	.	K	+	1	0	TAF1B	9962466	0.964000	0.33143	0.630000	0.29268	0.414000	0.31173	0.565000	0.23578	0.355000	0.24131	0.383000	0.25322	AAA	.	.		0.328	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		T	10045015	A	T	10045015	4	4	115	1	0	0	0	0	0	1	0	0	15535	131	5	4	869	4	TAF1B	2	10045015	Nonsense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10		10045015	233154358	39	19578										
SMC6	79677	hgsc.bcm.edu	37	chr2	17898050	17898050	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgtccttttctatggcttgcTgaaactgttcgatctcttga	8	9	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:17898050T>C	ENST00000448223.2	-	14	1573	c.1304A>G	c.(1303-1305)cAg>cGg	p.Q435R	SMC6_ENST00000402989.1_Missense_Mutation_p.Q435R|SMC6_ENST00000351948.4_Missense_Mutation_p.Q435R|SMC6_ENST00000381272.4_Missense_Mutation_p.Q461R	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	435					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TATGGCTTGCTGAAACTGTTC	0.308																																					p.Q435R		Atlas-SNP	.											.	SMC6	102	.	0			c.A1304G						.						152	145	147					2																	17898050		2203	4300	6503	SO:0001583	missense	79677	exon14			GCTTGCTGAAACT	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.1304A>G	chr2.hg19:g.17898050T>C	ENSP00000404092:p.Gln435Arg	190.0	0.0		142.0	6.0	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.055288	0.36277	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.73	5.79	4.62	0.57501	RecF/RecN/SMC (1);	0.264860	0.44285	D	0.000465	T	0.27419	0.0673	L	0.59436	1.845	0.39951	D	0.974539	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.13407	0.004;0.005;0.009	T	0.09058	-1.0692	10	0.15066	T	0.55	.	9.7857	0.40675	0.0:0.1389:0.0:0.8611	.	461;461;435	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	R	435;435;461;435;461	ENSP00000404092:Q435R;ENSP00000323439:Q435R;ENSP00000370672:Q461R;ENSP00000384539:Q435R;ENSP00000408644:Q461R	ENSP00000323439:Q435R	Q	-	2	0	SMC6	17761531	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.261000	0.43276	1.012000	0.39366	0.459000	0.35465	CAG	.	.		0.308	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		C	17898050	T	C	17898050	3	2	115	1	0	0	0	0	1	0	0	0	14802	1580	55	2	2031	2	SMC6	2	17898050	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	7853035	17898050	225301323	40	19579										
PLB1	151056	hgsc.bcm.edu	37	chr2	28855824	28855824	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gttgcagagaggggacactgAcctcaccttcttctccgagg	12	12	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:28855824A>G	ENST00000327757.5	+	56	4060	c.4016A>G	c.(4015-4017)gAc>gGc	p.D1339G	PLB1_ENST00000541605.1_Missense_Mutation_p.D304G|AC074011.2_ENST00000431376.1_RNA|PLB1_ENST00000422425.2_Missense_Mutation_p.D1328G	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1339	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					GGGGACACTGACCTCACCTTC	0.592																																					p.D1339G		Atlas-SNP	.											.	PLB1	255	.	0			c.A4016G						.						158	149	152					2																	28855824		2203	4300	6503	SO:0001583	missense	151056	exon56			ACACTGACCTCAC		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.4016A>G	chr2.hg19:g.28855824A>G	ENSP00000330442:p.Asp1339Gly	125.0	0.0		141.0	7.0	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	hg19	CCDS33168.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	19.91|19.91|19.91	3.914979|3.914979|3.914979	0.72983|0.72983|0.72983	.|.|.	.|.|.	ENSG00000163803|ENSG00000163803|ENSG00000163803	ENST00000327757;ENST00000422425;ENST00000541605|ENST00000404858|ENST00000436775	T;T;T|.|.	0.14516|.|.	2.5;2.5;2.5|.|.	5.77|5.77|5.77	5.77|5.77|5.77	0.91146|0.91146|0.91146	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	D|D|.	0.85414|0.85414|.	0.5691|0.5691|.	H|H|H	0.94183|0.94183|0.94183	3.505|3.505|3.505	0.53688|0.53688|0.53688	D|D|D	0.999973|0.999973|0.999973	D;D|.|.	0.76494|.|.	0.997;0.999|.|.	D;D|.|.	0.69142|.|.	0.962;0.958|.|.	D|D|.	0.89040|0.89040|.	0.3448|0.3448|.	10|5|.	0.54805|.|.	T|.|.	0.06|.|.	-43.4542|-43.4542|-43.4542	12.4895|12.4895|12.4895	0.55891|0.55891|0.55891	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	1328;1339|.|.	Q6P1J6-3;Q6P1J6|.|.	.;PLB1_HUMAN|.|.	G|A|W	1339;1328;304|1327|66	ENSP00000330442:D1339G;ENSP00000416440:D1328G;ENSP00000437426:D304G|.|.	ENSP00000330442:D1339G|.|.	D|T|X	+|+|+	2|1|3	0|0|0	PLB1|PLB1|PLB1	28709328|28709328|28709328	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.984000|0.984000|0.984000	0.44739|0.44739|0.44739	0.845000|0.845000|0.845000	0.48019|0.48019|0.48019	4.827000|4.827000|4.827000	0.62723|0.62723|0.62723	2.215000|2.215000|2.215000	0.71742|0.71742|0.71742	0.459000|0.459000|0.459000	0.35465|0.35465|0.35465	GAC|ACC|TGA	.	.		0.592	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			G	28855824	A	G	28855824	3	3	115	1	0	0	0	0	1	0	0	0	12033	275	10	2	4271	2	PLB1	2	28855824	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	10957774	28855824	214343549	41	19580										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32640568	32640568	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atctttgtatagactcaataActccttgtgctgacggaatt	7	8	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:32640568A>G	ENST00000421745.2	+	10	2343	c.2209A>G	c.(2209-2211)Act>Gct	p.T737A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	737					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AGACTCAATAACTCCTTGTGC	0.438																																					p.T737A	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A2209G						.						51	50	50					2																	32640568		2203	4300	6503	SO:0001583	missense	57448	exon10			TCAATAACTCCTT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.2209A>G	chr2.hg19:g.32640568A>G	ENSP00000393596:p.Thr737Ala	96.0	0.0		99.0	4.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	13.84	2.356660	0.41801	.	.	ENSG00000115760	ENST00000421745	T	0.74632	-0.86	5.46	5.46	0.80206	.	0.057803	0.64402	D	0.000002	T	0.61825	0.2378	N	0.19112	0.55	0.51482	D	0.999926	B	0.29766	0.256	B	0.29077	0.098	T	0.60444	-0.7262	10	0.33141	T	0.24	.	15.825	0.78698	1.0:0.0:0.0:0.0	.	737	Q9NR09	BIRC6_HUMAN	A	737	ENSP00000393596:T737A	ENSP00000393596:T737A	T	+	1	0	BIRC6	32494072	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.998000	0.93550	2.198000	0.70561	0.528000	0.53228	ACT	.	.		0.438	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		G	32640568	A	G	32640568	3	3	115	1	0	0	0	0	1	0	0	0	1438	43	2	2	2247	2	BIRC6	2	32640568	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3784744	32640568	210558805	42	19581										
MSH6	2956	hgsc.bcm.edu	37	chr2	48010412	48010412	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgtacagcttcttccccaagTctccggcgctgagtgatgcc	10	14	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:48010412T>C	ENST00000234420.5	+	1	192	c.40T>C	c.(40-42)Tct>Cct	p.S14P	MSH6_ENST00000540021.1_Missense_Mutation_p.S14P|MSH6_ENST00000538136.1_5'Flank|RNU6-688P_ENST00000516063.1_RNA	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	14					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTTCCCCAAGTCTCCGGCGCT	0.672			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.S14P		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T40C						.						33	31	32					2																	48010412		2194	4286	6480	SO:0001583	missense	2956	exon1	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CCCAAGTCTCCGG	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.40T>C	chr2.hg19:g.48010412T>C	ENSP00000234420:p.Ser14Pro	83.0	0.0		93.0	4.0	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	hg19	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	T	17.24	3.338799	0.60963	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000446255;ENST00000540021	D;D	0.87103	-2.04;-2.21	4.64	0.545	0.17190	.	0.280963	0.34676	N	0.003776	T	0.75744	0.3891	L	0.29908	0.895	0.80722	D	1	P;B;P	0.39883	0.567;0.38;0.693	B;B;B	0.38194	0.137;0.07;0.267	T	0.70510	-0.4852	10	0.66056	D	0.02	-10.0552	4.9778	0.14149	0.2736:0.0:0.2141:0.5123	.	14;14;14	B4DF41;P52701;P52701-2	.;MSH6_HUMAN;.	P	14	ENSP00000234420:S14P;ENSP00000446475:S14P	ENSP00000234420:S14P	S	+	1	0	MSH6	47863916	0.975000	0.34042	0.999000	0.59377	0.887000	0.51463	0.482000	0.22276	0.575000	0.29434	0.260000	0.18958	TCT	.	.		0.672	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		C	48010412	T	C	48010412	3	2	115	1	0	0	0	0	1	0	0	0	9883	1667	58	2	42	2	MSH6	2	48010412	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	15369844	48010412	195188961	43	19582										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54850714	54850714	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	catgccccgggaggggaagcTcatctctgacatcaacaagg	12	12	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:54850714T>G	ENST00000356805.4	+	10	1444	c.1163T>G	c.(1162-1164)cTc>cGc	p.L388R	SPTBN1_ENST00000333896.5_Missense_Mutation_p.L375R	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	388					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GAGGGGAAGCTCATCTCTGAC	0.522																																					p.L388R		Atlas-SNP	.											.	SPTBN1	378	.	0			c.T1163G						.						87	83	85					2																	54850714		2203	4300	6503	SO:0001583	missense	6711	exon10			GGAAGCTCATCTC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.1163T>G	chr2.hg19:g.54850714T>G	ENSP00000349259:p.Leu388Arg	137.0	0.0		126.0	56.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.788548	0.90367	.	.	ENSG00000115306	ENST00000356805;ENST00000389980;ENST00000333896	T;T;T	0.40225	1.04;1.04;1.04	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.66470	0.2792	M	0.88310	2.945	0.80722	D	1	P;P	0.49253	0.721;0.921	B;P	0.56960	0.414;0.81	T	0.72626	-0.4236	10	0.56958	D	0.05	.	16.0044	0.80349	0.0:0.0:0.0:1.0	.	375;388	Q01082-3;Q01082	.;SPTB2_HUMAN	R	388;388;375	ENSP00000349259:L388R;ENSP00000374630:L388R;ENSP00000334156:L375R	ENSP00000334156:L375R	L	+	2	0	SPTBN1	54704218	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.250000	0.72435	2.191000	0.70037	0.528000	0.53228	CTC	.	.		0.522	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			G	54850714	T	G	54850714	3	3	115	1	0	0	0	0	1	0	0	0	15134	1551	54	5	1310	5	SPTBN1	2	54850714	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	6840302	54850714	188348659	44	19583										
EFEMP1	2202	hgsc.bcm.edu	37	chr2	56149567	56149567	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agcatagttaggaaaagggcTttcaacattgtgaatctcaa	9	6	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:56149567T>C	ENST00000394555.2	-	2	444	c.9A>G	c.(7-9)aaA>aaG	p.K3K	EFEMP1_ENST00000355426.3_Silent_p.K3K|EFEMP1_ENST00000424836.2_5'UTR|EFEMP1_ENST00000394554.1_Silent_p.K3K|EFEMP1_ENST00000497698.1_5'UTR	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	3					epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GGAAAAGGGCTTTCAACATTG	0.428																																					p.K3K	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.A9G						.						144	135	138					2																	56149567		2203	4300	6503	SO:0001819	synonymous_variant	2202	exon2			AAGGGCTTTCAAC	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"Fibulins"	3218	protein-coding gene	gene with protein product	"fibulin 3"	601548	"fibrillin-like", "EGF-containing fibulin-like extracellular matrix protein 1"	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.9A>G	chr2.hg19:g.56149567T>C		91.0	0.0		124.0	5.0	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Silent	SNP	ENST00000394555.2	hg19	CCDS1857.1																																																																																			.	.		0.428	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2			C	56149567	T	C	56149567	2	2	115	1	0	0	0	0	0	0	0	1	4943	1606	56	2		2	EFEMP1	2	56149567	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1298853	56149567	187049806	45	19584										
EHBP1	23301	hgsc.bcm.edu	37	chr2	63086343	63086343	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctttttggatgaagcagaaaAggacttggccaccgtgaatt	11	7	0	3	rs145562120	byFrequency	TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:63086343A>G	ENST00000263991.5	+	9	1261	c.779A>G	c.(778-780)aAg>aGg	p.K260R	EHBP1_ENST00000354487.3_Missense_Mutation_p.K225R|EHBP1_ENST00000405289.1_Missense_Mutation_p.K225R|EHBP1_ENST00000431489.1_Missense_Mutation_p.K225R|AC007098.1_ENST00000452397.1_RNA|EHBP1_ENST00000405015.3_Missense_Mutation_p.K225R	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	260						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			GAAGCAGAAAAGGACTTGGCC	0.363																																					p.K260R		Atlas-SNP	.											.	EHBP1	127	.	0			c.A779G						.						121	119	120					2																	63086343		2203	4300	6503	SO:0001583	missense	23301	exon9			CAGAAAAGGACTT	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.779A>G	chr2.hg19:g.63086343A>G	ENSP00000263991:p.Lys260Arg	99.0	0.0		89.0	4.0	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	hg19	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	A	9.631	1.136458	0.21123	.	.	ENSG00000115504	ENST00000405015;ENST00000405482;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T;T	0.73363	-0.71;0.96;-0.71;-0.74;-0.71;-0.71	4.88	4.88	0.63580	.	0.312268	0.32314	N	0.006264	T	0.55862	0.1947	N	0.16478	0.41	0.33647	D	0.607964	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.09377	0.004;0.001;0.002	T	0.60016	-0.7345	10	0.27082	T	0.32	.	9.1039	0.36685	0.9173:0.0:0.0827:0.0	.	225;225;260	Q8NDI1-2;Q8NDI1-3;Q8NDI1	.;.;EHBP1_HUMAN	R	225;225;225;260;225;225	ENSP00000384143:K225R;ENSP00000384829:K225R;ENSP00000403783:K225R;ENSP00000263991:K260R;ENSP00000346482:K225R;ENSP00000385524:K225R	ENSP00000263991:K260R	K	+	2	0	EHBP1	62939847	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.393000	0.59665	1.835000	0.53391	0.482000	0.46254	AAG	.	A|1.000;C|0.000		0.363	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		G	63086343	A	G	63086343	3	3	115	1	0	0	0	0	1	0	0	0	4977	72	3	2	809	2	EHBP1	2	63086343	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6936776	63086343	180113030	46	19585										
ETAA1	54465	hgsc.bcm.edu	37	chr2	67632364	67632364	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atgtctgataccaaaattacAcagggtgtggagaaaaagaa	10	5	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:67632364A>G	ENST00000272342.5	+	5	2680	c.2550A>G	c.(2548-2550)acA>acG	p.T850T	ETAA1_ENST00000462772.1_3'UTR	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	850						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						CCAAAATTACACAGGGTGTGG	0.338																																					p.T850T		Atlas-SNP	.											.	ETAA1	88	.	0			c.A2550G						.						38	39	39					2																	67632364		2199	4292	6491	SO:0001819	synonymous_variant	54465	exon5			AATTACACAGGGT	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"Ewing's tumor-associated antigen 1"			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.2550A>G	chr2.hg19:g.67632364A>G		125.0	0.0		132.0	7.0	NM_019002	Q05BT7|Q53SC4	Silent	SNP	ENST00000272342.5	hg19	CCDS1882.1																																																																																			.	.		0.338	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		G	67632364	A	G	67632364	2	3	115	1	0	0	0	0	0	0	0	1	5269	146	6	2		2	ETAA1	2	67632364	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	4546021	67632364	175567009	47	19586										
NAGK	55577	hgsc.bcm.edu	37	chr2	71297898	71297898	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggacagacaagtgtgtggagAggatcaatgagatggtgaac	16	4	1	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:71297898A>G	ENST00000244204.6	+	3	204	c.142A>G	c.(142-144)Agg>Ggg	p.R48G	NAGK_ENST00000455662.2_Missense_Mutation_p.R94G|NAGK_ENST00000428360.2_3'UTR|NAGK_ENST00000418807.3_5'UTR|NAGK_ENST00000443938.2_Missense_Mutation_p.R48G|NAGK_ENST00000443872.2_Intron|RP11-467P9.1_ENST00000608897.1_lincRNA			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	48					carbohydrate phosphorylation (GO:0046835)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|N-acetylglucosamine kinase activity (GO:0045127)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|urinary_tract(1)	18					N-Acetyl-D-glucosamine(DB00141)	GTGTGTGGAGAGGATCAATGA	0.557											OREG0014689	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R94G		Atlas-SNP	.											.	NAGK	34	.	0			c.A280G						.						149	138	142					2																	71297898		2203	4300	6503	SO:0001583	missense	55577	exon3			GTGGAGAGGATCA	AJ242910	CCDS33220.1, CCDS33220.2	2p24.3-p24.1	2008-02-05			ENSG00000124357	ENSG00000124357	2.7.1.59		17174	protein-coding gene	gene with protein product		606828				10824116	Standard	NM_017567		Approved	GNK	uc002shp.4	Q9UJ70	OTTHUMG00000153239	ENST00000244204.6:c.142A>G	chr2.hg19:g.71297898A>G	ENSP00000244204:p.Arg48Gly	100.0	0.0	1128	107.0	5.0	NM_017567	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Missense_Mutation	SNP	ENST00000244204.6	hg19		.	.	.	.	.	.	.	.	.	.	A	13.81	2.348708	0.41599	.	.	ENSG00000124357	ENST00000244204;ENST00000455662	T;T	0.30981	1.51;1.51	4.95	3.78	0.43462	ATPase, BadF/BadG/BcrA/BcrD type (1);	0.345509	0.32134	N	0.006538	T	0.19248	0.0462	L	0.37561	1.115	0.45378	D	0.998367	B	0.24882	0.113	B	0.20767	0.031	T	0.07328	-1.0778	10	0.21014	T	0.42	-34.1254	4.9744	0.14133	0.7183:0.1888:0.0929:0.0	.	48	Q9UJ70	NAGK_HUMAN	G	48;94	ENSP00000244204:R48G;ENSP00000389087:R94G	ENSP00000244204:R48G	R	+	1	2	NAGK	71151406	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.321000	0.33678	0.890000	0.36211	-0.461000	0.05368	AGG	.	.		0.557	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1			G	71297898	A	G	71297898	3	3	115	1	0	0	0	0	1	0	0	0	10151	295	11	2	290	2	NAGK	2	71297898	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3665534	71297898	171901475	48	19587										
DYSF	8291	hgsc.bcm.edu	37	chr2	71908171	71908171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggagattgtagcagagagtgAgcatgaggagcggcctgctg	18	6	0	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:71908171A>G	ENST00000258104.3	+	53	6264	c.5987A>G	c.(5986-5988)gAg>gGg	p.E1996G	DYSF_ENST00000409366.1_Missense_Mutation_p.E2018G|DYSF_ENST00000410041.1_Missense_Mutation_p.E2014G|DYSF_ENST00000410020.3_Missense_Mutation_p.E2035G|DYSF_ENST00000394120.2_Missense_Mutation_p.E1997G|DYSF_ENST00000429174.2_Missense_Mutation_p.E2017G|DYSF_ENST00000409651.1_Missense_Mutation_p.E2028G|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000413539.2_Missense_Mutation_p.E2027G|DYSF_ENST00000409762.1_Missense_Mutation_p.E2013G|DYSF_ENST00000409744.1_Missense_Mutation_p.E2004G|DYSF_ENST00000409582.3_Missense_Mutation_p.E2034G	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1996					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GCAGAGAGTGAGCATGAGGAG	0.612																																					p.E2035G		Atlas-SNP	.											DYSF_ENST00000410020,colon,carcinoma,0,2	DYSF	536	.	0			c.A6104G						.						62	58	60					2																	71908171		2203	4300	6503	SO:0001583	missense	8291	exon54			AGAGTGAGCATGA	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.5987A>G	chr2.hg19:g.71908171A>G	ENSP00000258104:p.Glu1996Gly	70.0	0.0		92.0	4.0	NM_001130987	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.026828	0.93518	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.86865	-2.18;-2.17;-2.17;-2.16;-2.17;-2.18;-2.17;-2.16;-2.16;-2.17;-2.17	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.94673	0.8282	M	0.91612	3.225	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.993;1.0;1.0;1.0;0.999;0.999;0.999;0.999;1.0;1.0;0.999;1.0;0.999;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.964;0.999;0.999;0.999;0.999;0.982;0.991;0.982;0.995;0.999;0.991;0.998;0.999;0.999;0.998	D	0.95565	0.8633	10	0.87932	D	0	-36.0147	14.3168	0.66457	1.0:0.0:0.0:0.0	.	760;2028;2035;2018;1983;2014;2004;2013;2003;2027;2034;2017;1982;1997;1996	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	G	2027;2013;2034;2017;1996;2028;1997;2004;2018;2035;2014	ENSP00000407046:E2027G;ENSP00000387137:E2013G;ENSP00000386547:E2034G;ENSP00000398305:E2017G;ENSP00000258104:E1996G;ENSP00000386683:E2028G;ENSP00000377678:E1997G;ENSP00000386285:E2004G;ENSP00000386512:E2018G;ENSP00000386881:E2035G;ENSP00000386617:E2014G	ENSP00000258104:E1996G	E	+	2	0	DYSF	71761679	1.000000	0.71417	0.995000	0.50966	0.976000	0.68499	9.253000	0.95501	2.263000	0.75096	0.533000	0.62120	GAG	.	.		0.612	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		G	71908171	A	G	71908171	3	3	115	1	0	0	0	0	1	0	0	0	4861	304	11	2	6456	2	DYSF	2	71908171	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	610273	71908171	171291202	49	19588										
DCTN1	1639	hgsc.bcm.edu	37	chr2	74600056	74600056	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caggggcctgttttctcaccTtgggtcgccgagttgtggtc	14	11	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:74600056T>C	ENST00000361874.3	-	7	769	c.452A>G	c.(451-453)aAg>aGg	p.K151R	DCTN1_ENST00000409567.3_Intron|DCTN1_ENST00000394003.3_Splice_Site_p.K144R|DCTN1_ENST00000407639.2_Splice_Site_p.K17R|DCTN1_ENST00000409868.1_Splice_Site_p.K134R|DCTN1_ENST00000409438.1_Splice_Site_p.K17R|DCTN1_ENST00000409240.1_Intron	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	151					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						TTTTCTCACCTTGGGTCGCCG	0.517																																					p.K151R		Atlas-SNP	.											.	DCTN1	110	.	0			c.A452G						.						103	90	94					2																	74600056		2203	4300	6503	SO:0001630	splice_region_variant	1639	exon7			CTCACCTTGGGTC		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"p150 glued homolog (Drosophila)"	601143	"dynactin 1 (p150, Glued (Drosophila) homolog)"			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.453+1A>G	chr2.hg19:g.74600056T>C		97.0	0.0		90.0	4.0	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	hg19	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.821546	0.32237	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000407639;ENST00000409438;ENST00000409868;ENST00000458655	T;T;T;T;T;T	0.74632	-0.64;-0.86;-0.72;-0.72;-0.83;-0.57	5.07	5.07	0.68467	.	.	.	.	.	T	0.72598	0.3480	N	0.14661	0.345	0.53005	D	0.999969	P;B;D;D	0.56035	0.956;0.037;0.974;0.974	P;B;D;D	0.67725	0.899;0.005;0.953;0.953	T	0.68903	-0.5286	9	0.17369	T	0.5	.	14.2566	0.66055	0.0:0.0:0.0:1.0	.	151;144;17;17	Q14203;A8MY36;Q14203-2;G5E9H4	DCTN1_HUMAN;.;.;.	R	151;144;17;17;134;158	ENSP00000354791:K151R;ENSP00000377571:K144R;ENSP00000384844:K17R;ENSP00000387270:K17R;ENSP00000387327:K134R;ENSP00000414315:K158R	ENSP00000354791:K151R	K	-	2	0	DCTN1	74453564	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.069000	0.71209	2.261000	0.74972	0.459000	0.35465	AAG	.	.		0.517	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	Missense_Mutation	C	74600056	T	C	74600056	5	2	115	1	0	0	0	0	0	0	1	0	4308	1623	56	2	3488	2	DCTN1	2	74600056	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2691885	74600056	168599317	50	19589										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84822906	84822906	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atacaaggtggaaaaaatgaAagaaaaggtaaggttggtag	13	1	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:84822906A>G	ENST00000237449.6	+	17	2869	c.2861A>G	c.(2860-2862)aAa>aGa	p.K954R	DNAH6_ENST00000389394.3_Missense_Mutation_p.K954R|DNAH6_ENST00000398278.2_Missense_Mutation_p.K954R			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	954	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GAAAAAATGAAAGAAAAGGTA	0.368																																					p.K954R		Atlas-SNP	.											.	DNAH6	194	.	0			c.A2861G						.						100	94	96					2																	84822906		692	1591	2283	SO:0001583	missense	1768	exon18			AAATGAAAGAAAA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.2861A>G	chr2.hg19:g.84822906A>G	ENSP00000237449:p.Lys954Arg	33.0	0.0		27.0	4.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	10.63	1.404845	0.25378	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.64260	-0.09;-0.09;-0.09	5.82	4.68	0.58851	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.40595	0.1123	N	0.10760	0.04	0.32173	N	0.581378	B	0.16603	0.018	B	0.20184	0.028	T	0.44787	-0.9305	9	0.24483	T	0.36	.	10.425	0.44373	0.9227:0.0:0.0773:0.0	.	954	Q9C0G6	DYH6_HUMAN	R	954	ENSP00000374045:K954R;ENSP00000381326:K954R;ENSP00000237449:K954R	ENSP00000237449:K954R	K	+	2	0	DNAH6	84676417	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	2.301000	0.43628	2.215000	0.71742	0.528000	0.53228	AAA	.	.		0.368	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84822906	A	G	84822906	3	3	115	1	0	0	0	0	1	0	0	0	4607	14	1	2	2927	2	DNAH6	2	84822906	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	10222850	84822906	158376467	51	19590										
PCDP1	200373	hgsc.bcm.edu	37	chr2	120366133	120366133	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aacttaaaaaagagcttactGaagagtggcaaaaagcatgt	9	5	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:120366133G>A	ENST00000413369.3	+	12	1276	c.1189G>A	c.(1189-1191)Gaa>Aaa	p.E397K	PCDP1_ENST00000602047.1_Missense_Mutation_p.E111K|PCDP1_ENST00000597189.1_Intron	NM_001271049.1	NP_001257978																Colorectal(110;0.196)					AGAGCTTACTGAAGAGTGGCA	0.363																																					p.E397K		Atlas-SNP	.											.	.	.	.	0			c.G1189A						.						141	153	149					2																	120366133		2203	4300	6503	SO:0001583	missense	0	exon12			CTTACTGAAGAGT																												ENST00000413369.3:c.1189G>A	chr2.hg19:g.120366133G>A	ENSP00000393222:p.Glu397Lys	84.0	0.0		100.0	4.0	NM_001271049		Missense_Mutation	SNP	ENST00000413369.3	hg19	CCDS33282.2	.	.	.	.	.	.	.	.	.	.	G	11.07	1.530334	0.27387	.	.	ENSG00000163075	ENST00000295220;ENST00000413369	T	0.27104	1.69	4.65	3.76	0.43208	.	0.093605	0.46442	D	0.000282	T	0.15609	0.0376	N	0.16368	0.405	0.38273	D	0.942199	B;B	0.34200	0.441;0.254	B;B	0.33846	0.171;0.055	T	0.10200	-1.0640	10	0.62326	D	0.03	-21.1996	10.2713	0.43485	0.0979:0.0:0.902:0.0	.	241;397	Q4G0U5-3;Q4G0U5	.;PCDP1_HUMAN	K	111;397	ENSP00000393222:E397K	ENSP00000295220:E111K	E	+	1	0	AC069154.2	120082603	1.000000	0.71417	0.473000	0.27253	0.012000	0.07955	3.786000	0.55431	2.558000	0.86282	0.655000	0.94253	GAA	.	.		0.363	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1			A	120366133	G	A	120366133	3	1	115	1	0	0	0	0	1	0	0	0	11581	1291	45	3	345	3	PCDP1	2	120366133	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	35543227	120366133	122833240	52	19591										
MAP3K2	10746	hgsc.bcm.edu	37	chr2	128075251	128075251	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaagtgttttttcctggggaTccctcaaacagccataatac	7	10	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:128075251T>C	ENST00000409947.1	-	14	1562	c.1280A>G	c.(1279-1281)gAt>gGt	p.D427G	RNU6-1147P_ENST00000363380.1_RNA|MAP3K2_ENST00000344908.5_Missense_Mutation_p.D427G			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	427	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	TTCCTGGGGATCCCTCAAACA	0.328																																					p.D427G		Atlas-SNP	.											.	MAP3K2	78	.	0			c.A1280G						.						51	48	49					2																	128075251		1821	4079	5900	SO:0001583	missense	10746	exon13			TGGGGATCCCTCA	AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6854	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 2"	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.1280A>G	chr2.hg19:g.128075251T>C	ENSP00000387246:p.Asp427Gly	73.0	0.0		60.0	4.0	NM_006609	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Missense_Mutation	SNP	ENST00000409947.1	hg19	CCDS46404.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.816622	0.90790	.	.	ENSG00000169967	ENST00000409947;ENST00000344908	T;T	0.67345	-0.26;-0.26	5.94	5.94	0.96194	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.041858	0.85682	D	0.000000	T	0.70962	0.3284	L	0.60067	1.865	0.80722	D	1	P	0.37423	0.594	B	0.44224	0.444	T	0.73503	-0.3962	10	0.72032	D	0.01	.	16.3891	0.83525	0.0:0.0:0.0:1.0	.	427	Q9Y2U5	M3K2_HUMAN	G	427	ENSP00000387246:D427G;ENSP00000343463:D427G	ENSP00000343463:D427G	D	-	2	0	MAP3K2	127791721	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.953000	0.87836	2.276000	0.75962	0.397000	0.26171	GAT	.	.		0.328	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609		C	128075251	T	C	128075251	3	2	115	1	0	0	0	0	1	0	0	0	9259	1435	50	2	595	2	MAP3K2	2	128075251	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	7709118	128075251	115124122	53	19592										
GPR17	2840	hgsc.bcm.edu	37	chr2	128408877	128408877	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agctgtaccgggagaaggccTcccaccatgccctggtgtcc	12	15	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:128408877T>C	ENST00000272644.3	+	3	726	c.652T>C	c.(652-654)Tcc>Ccc	p.S218P	GPR17_ENST00000486700.1_3'UTR|LIMS2_ENST00000409254.1_5'Flank|GPR17_ENST00000544369.1_Missense_Mutation_p.S218P|LIMS2_ENST00000410011.1_Intron|LIMS2_ENST00000409455.1_Intron|GPR17_ENST00000393018.3_Missense_Mutation_p.S218P|LIMS2_ENST00000545738.2_Intron|LIMS2_ENST00000409808.2_Intron|LIMS2_ENST00000355119.4_Intron|LIMS2_ENST00000324938.5_Intron	NM_001161416.1|NM_001161417.1|NM_005291.2	NP_001154888.1|NP_001154889.1|NP_005282.1	Q13304	GPR17_HUMAN	G protein-coupled receptor 17	218					chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)|urinary_tract(1)	19	Colorectal(110;0.1)	Ovarian(717;0.15)		BRCA - Breast invasive adenocarcinoma(221;0.0677)		GGAGAAGGCCTCCCACCATGC	0.662																																					p.S218P		Atlas-SNP	.											.	GPR17	56	.	0			c.T652C						.						115	104	108					2																	128408877		2203	4300	6503	SO:0001583	missense	2840	exon3			AAGGCCTCCCACC		CCDS2148.1	2q21	2014-01-30			ENSG00000144230	ENSG00000144230		"GPCR / Class A : Orphans"	4471	protein-coding gene	gene with protein product		603071				8558062	Standard	NM_001161415		Approved		uc002tpc.3	Q13304	OTTHUMG00000131533	ENST00000272644.3:c.652T>C	chr2.hg19:g.128408877T>C	ENSP00000272644:p.Ser218Pro	77.0	0.0		112.0	5.0	NM_005291	A8K9L0|B2R9X0|Q8N5S7|Q9UDZ6|Q9UE21	Missense_Mutation	SNP	ENST00000272644.3	hg19	CCDS2148.1	.	.	.	.	.	.	.	.	.	.	t	18.51	3.639747	0.67244	.	.	ENSG00000144230	ENST00000544369;ENST00000272644;ENST00000393018	T;T;T	0.37752	1.18;1.18;1.18	5.21	5.21	0.72293	GPCR, rhodopsin-like superfamily (1);	0.105408	0.56097	D	0.000032	T	0.47469	0.1447	L	0.37750	1.13	0.80722	D	1	D	0.69078	0.997	D	0.67548	0.952	T	0.31641	-0.9936	10	0.27082	T	0.32	.	15.0785	0.72096	0.0:0.0:0.0:1.0	.	218	Q13304	GPR17_HUMAN	P	218	ENSP00000442982:S218P;ENSP00000272644:S218P;ENSP00000376741:S218P	ENSP00000272644:S218P	S	+	1	0	GPR17	128125347	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	8.012000	0.88631	1.971000	0.57363	0.379000	0.24179	TCC	.	.		0.662	GPR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254390.1			C	128408877	T	C	128408877	3	2	115	1	0	0	0	0	1	0	0	0	6675	1551	54	2	658	2	GPR17	2	128408877	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	333626	128408877	114790496	54	19593										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141457981	141457981	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acgtggattctcatatggccTtattggggaatttaaattgg	11	5	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:141457981T>C	ENST00000389484.3	-	41	7608	c.6637A>G	c.(6637-6639)Agg>Ggg	p.R2213G		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2213					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCATATGGCCTTATTGGGGAA	0.348										TSP Lung(27;0.18)																											p.R2213G	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A6637G						.						123	131	129					2																	141457981		2203	4300	6503	SO:0001583	missense	53353	exon41			ATGGCCTTATTGG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.6637A>G	chr2.hg19:g.141457981T>C	ENSP00000374135:p.Arg2213Gly	119.0	0.0		93.0	5.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.598198	0.46318	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91351	-2.83	4.47	1.77	0.24775	Six-bladed beta-propeller, TolB-like (1);	0.079529	0.51477	U	0.000087	D	0.84678	0.5525	L	0.43152	1.355	0.27563	N	0.950117	B	0.19583	0.037	B	0.16722	0.016	T	0.70579	-0.4833	10	0.20046	T	0.44	.	12.3099	0.54922	0.0:0.0:0.5484:0.4516	.	2213	Q9NZR2	LRP1B_HUMAN	G	2213;2151	ENSP00000374135:R2213G	ENSP00000374135:R2213G	R	-	1	2	LRP1B	141174451	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.516000	0.35856	0.639000	0.30564	0.477000	0.44152	AGG	.	.		0.348	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141457981	T	C	141457981	3	2	115	1	0	0	0	0	1	0	0	0	8964	1608	56	2	7366	2	LRP1B	2	141457981	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	13049104	141457981	101741392	55	19594										
SLC4A10	57282	hgsc.bcm.edu	37	chr2	162821621	162821621	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgttcacgaagcgggaactcAgctggttggatgatttgatg	14	6	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:162821621A>G	ENST00000446997.1	+	23	3190	c.3097A>G	c.(3097-3099)Agc>Ggc	p.S1033G	SLC4A10_ENST00000421911.1_Missense_Mutation_p.S1033G|SLC4A10_ENST00000415876.2_Missense_Mutation_p.S1003G|SLC4A10_ENST00000272716.5_Missense_Mutation_p.S1003G|SLC4A10_ENST00000375514.5_Missense_Mutation_p.S1014G	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	1033				S -> C (in Ref. 1; BAB18301). {ECO:0000305}.	bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	GCGGGAACTCAGCTGGTTGGA	0.338																																					p.S1033G		Atlas-SNP	.											.	SLC4A10	309	.	0			c.A3097G						.						86	80	82					2																	162821621		1816	4090	5906	SO:0001583	missense	57282	exon23			GAACTCAGCTGGT		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.3097A>G	chr2.hg19:g.162821621A>G	ENSP00000393066:p.Ser1033Gly	86.0	0.0		88.0	4.0	NM_001178015	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	hg19	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.143451	0.77888	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.85106	0.5621	M	0.90369	3.11	0.80722	D	1	D;D;B	0.89917	1.0;1.0;0.438	D;D;B	0.91635	0.999;0.999;0.302	D	0.87276	0.2289	10	0.52906	T	0.07	.	16.3839	0.83495	1.0:0.0:0.0:0.0	.	1014;1003;1033	F8W675;Q6U841-2;Q6U841	.;.;S4A10_HUMAN	G	1014;1003;1003;1002;1033;1033;1032	ENSP00000364664:S1014G;ENSP00000395797:S1003G;ENSP00000272716:S1003G;ENSP00000393066:S1033G;ENSP00000404486:S1033G	ENSP00000272716:S1003G	S	+	1	0	SLC4A10	162529867	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	2.258000	0.74832	0.533000	0.62120	AGC	.	.		0.338	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		G	162821621	A	G	162821621	3	3	115	1	0	0	0	0	1	0	0	0	14666	188	7	2	3272	2	SLC4A10	2	162821621	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	21363640	162821621	80377752	56	19595										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168104144	168104144	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tagagatgaatatatgagcaGacaattaacttcaactgtgt	8	5	1	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:168104144G>A	ENST00000409195.1	+	9	6331	c.6242G>A	c.(6241-6243)aGa>aAa	p.R2081K	XIRP2_ENST00000409273.1_Missense_Mutation_p.R1859K|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R2081K|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1906					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TATATGAGCAGACAATTAACT	0.373																																					p.R2081K		Atlas-SNP	.											.	XIRP2	914	.	0			c.G6242A						.						63	57	59					2																	168104144		1910	4135	6045	SO:0001583	missense	129446	exon9			TGAGCAGACAATT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6242G>A	chr2.hg19:g.168104144G>A	ENSP00000386840:p.Arg2081Lys	155.0	0.0		158.0	71.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	5.477	0.273026	0.10349	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.20332	2.08;2.08;2.08	5.92	0.254	0.15557	.	0.894418	0.09823	N	0.751235	T	0.08935	0.0221	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.0;0.001;0.001	T	0.37079	-0.9721	10	0.06099	T	0.92	-0.3941	9.7961	0.40735	0.5242:0.0:0.4758:0.0	.	1906;1906;1859	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	K	2081;2081;1859	ENSP00000386840:R2081K;ENSP00000295237:R2081K;ENSP00000387255:R1859K	ENSP00000295237:R2081K	R	+	2	0	XIRP2	167812390	0.002000	0.14202	0.004000	0.12327	0.180000	0.23129	0.460000	0.21924	-0.010000	0.14271	0.650000	0.86243	AGA	.	.		0.373	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168104144	G	A	168104144	3	1	115	1	0	0	0	0	1	0	0	0	17445	942	33	3	6272	3	XIRP2	2	168104144	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	5282523	168104144	75095229	57	19596										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179197376	179197376	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttttgatttcagattcagaaAggaaaggtccatgggagcat	11	5	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:179197376A>G	ENST00000190611.4	+	7	757	c.381A>G	c.(379-381)aaA>aaG	p.K127K	OSBPL6_ENST00000359685.3_Silent_p.K127K|OSBPL6_ENST00000392505.2_Silent_p.K127K|OSBPL6_ENST00000357080.4_Silent_p.K127K|OSBPL6_ENST00000409045.3_Silent_p.K127K|OSBPL6_ENST00000477097.1_3'UTR|OSBPL6_ENST00000315022.2_Silent_p.K106K|OSBPL6_ENST00000409631.1_Silent_p.K127K	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	127	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			AGATTCAGAAAGGAAAGGTCC	0.353																																					p.K127K		Atlas-SNP	.											.	OSBPL6	178	.	0			c.A381G						.						96	101	99					2																	179197376		2203	4300	6503	SO:0001819	synonymous_variant	114880	exon7			TCAGAAAGGAAAG	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.381A>G	chr2.hg19:g.179197376A>G		108.0	0.0		113.0	5.0	NM_001201482	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Silent	SNP	ENST00000190611.4	hg19	CCDS2277.1																																																																																			.	.		0.353	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		G	179197376	A	G	179197376	2	3	115	1	0	0	0	0	0	0	0	1	11290	69	3	2		2	OSBPL6	2	179197376	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	11093232	179197376	64001997	58	19597										
PRKRA	8575	hgsc.bcm.edu	37	chr2	179300978	179300978	+	Frame_Shift_Del	DEL	G	G	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aggcttcttttcagtaagttGatcttttcaccaggagaatt							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:179300978delG	ENST00000325748.4	-	7	878	c.678delC	c.(676-678)atcfs	p.I226fs	PRKRA_ENST00000487082.1_Frame_Shift_Del_p.I201fs|PRKRA_ENST00000432031.2_Frame_Shift_Del_p.I215fs|PRKRA_ENST00000438687.3_Frame_Shift_Del_p.I113fs|AC009948.5_ENST00000436616.2_RNA|AC009948.5_ENST00000454488.1_RNA|AC009948.5_ENST00000453026.2_RNA	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	226	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			TCAGTAAGTTGATCTTTTCAC	0.358																																					p.N227fs	Melanoma(200;68 3001 23825 48764)	Atlas-INDEL	.											.	PRKRA	56	.	0			c.679delA						.						158	180	173					2																	179300978		2203	4300	6503	SO:0001589	frameshift_variant	8575	exon7			.	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"protein activator of the interferon-induced protein kinase"	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.678delC	chr2.hg19:g.179300978delG	ENSP00000318176:p.Ile226fs	149.0	0.0		130.0	17.0	NM_003690	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Frame_Shift_Del	DEL	ENST00000325748.4	hg19	CCDS2279.1																																																																																			.	.		0.358	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690		-	179300978	G	-	179300978	7	5	115	1	0	1	0	1	0	0	0	0	12536	1280	45	0	271	0	PRKRA	2	179300978	Frame_Shift_Del	DEL	G	TCGA-DD-A3A1-01A-11D-A20W-10	103602	179300978	63898395	59	19598										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185800820	185800820	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tagagtcctcagctgcagccTtctctgaatacagtgatgat	9	10	2	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:185800820T>C	ENST00000302277.6	+	4	1291	c.697T>C	c.(697-699)Ttc>Ctc	p.F233L		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	233							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						AGCTGCAGCCTTCTCTGAATA	0.453																																					p.F233L		Atlas-SNP	.											.	ZNF804A	322	.	0			c.T697C						.						78	77	77					2																	185800820		2203	4299	6502	SO:0001583	missense	91752	exon4			GCAGCCTTCTCTG	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.697T>C	chr2.hg19:g.185800820T>C	ENSP00000303252:p.Phe233Leu	115.0	0.0		120.0	5.0	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.505633	0.85282	.	.	ENSG00000170396	ENST00000302277	T	0.40756	1.02	5.22	5.22	0.72569	.	0.000000	0.56097	D	0.000026	T	0.65417	0.2689	M	0.78456	2.415	0.50632	D	0.999881	D	0.89917	1.0	D	0.83275	0.996	T	0.70513	-0.4851	10	0.87932	D	0	-14.2051	14.2738	0.66167	0.0:0.0:0.0:1.0	.	233	Q7Z570	Z804A_HUMAN	L	233	ENSP00000303252:F233L	ENSP00000303252:F233L	F	+	1	0	ZNF804A	185509065	1.000000	0.71417	0.994000	0.49952	0.820000	0.46376	7.404000	0.79996	1.964000	0.57103	0.482000	0.46254	TTC	.	.		0.453	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		C	185800820	T	C	185800820	3	2	115	1	0	0	0	0	1	0	0	0	18185	1609	56	2	711	2	ZNF804A	2	185800820	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	6499842	185800820	57398553	60	19599										
TFPI	7035	hgsc.bcm.edu	37	chr2	188348910	188348910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agttattcacagcattgagcTgggttccataattatccacc	7	10	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:188348910T>C	ENST00000233156.3	-	6	863	c.569A>G	c.(568-570)cAg>cGg	p.Q190R	TFPI_ENST00000409676.1_Missense_Mutation_p.Q190R|AC007319.1_ENST00000453517.1_RNA|TFPI_ENST00000392365.1_Missense_Mutation_p.Q190R|AC007319.1_ENST00000412276.1_RNA|TFPI_ENST00000339091.4_Missense_Mutation_p.Q190R	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)	190					blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	AGCATTGAGCTGGGTTCCATA	0.383																																					p.Q190R		Atlas-SNP	.											.	TFPI	66	.	0			c.A569G						.						104	105	105					2																	188348910		2203	4300	6503	SO:0001583	missense	7035	exon6			TTGAGCTGGGTTC		CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"extrinsic pathway inhibitor"	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.569A>G	chr2.hg19:g.188348910T>C	ENSP00000233156:p.Gln190Arg	81.0	0.0		91.0	4.0	NM_001032281	O95103|Q53TS4	Missense_Mutation	SNP	ENST00000233156.3	hg19	CCDS2294.1	.	.	.	.	.	.	.	.	.	.	T	9.193	1.026632	0.19512	.	.	ENSG00000003436	ENST00000392365;ENST00000233156;ENST00000426055;ENST00000435414;ENST00000409676;ENST00000339091	T;T;T;T;T;T	0.63744	0.54;0.54;0.37;-0.06;-0.04;-0.04	5.3	1.16	0.20824	.	1.375500	0.04633	N	0.403955	T	0.53546	0.1803	L	0.54323	1.7	0.09310	N	1	P;B	0.35363	0.497;0.113	B;B	0.28465	0.09;0.033	T	0.31806	-0.9930	10	0.12766	T	0.61	.	10.8865	0.46971	0.0:0.0:0.459:0.541	.	190;190	P10646-2;P10646	.;TFPI1_HUMAN	R	190;190;190;177;190;190	ENSP00000376172:Q190R;ENSP00000233156:Q190R;ENSP00000397248:Q190R;ENSP00000409177:Q177R;ENSP00000386344:Q190R;ENSP00000342306:Q190R	ENSP00000233156:Q190R	Q	-	2	0	TFPI	188057155	0.000000	0.05858	0.002000	0.10522	0.062000	0.15995	-1.460000	0.02368	0.375000	0.24679	0.533000	0.62120	CAG	.	.		0.383	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287		C	188348910	T	C	188348910	3	2	115	1	0	0	0	0	1	0	0	0	15823	1580	55	2	489	2	TFPI	2	188348910	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2548090	188348910	54850463	61	19600										
GTF3C3	9330	hgsc.bcm.edu	37	chr2	197664287	197664287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccgttcgaactcctcaaaggAgattttcccttccaagtagt	7	12	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:197664287A>G	ENST00000263956.3	-	1	138	c.49T>C	c.(49-51)Tcc>Ccc	p.S17P	GTF3C3_ENST00000409364.3_Missense_Mutation_p.S17P	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	17					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TCCTCAAAGGAGATTTTCCCT	0.532																																					p.S17P		Atlas-SNP	.											.	GTF3C3	96	.	0			c.T49C						.						121	130	127					2																	197664287		2203	4300	6503	SO:0001583	missense	9330	exon1			CAAAGGAGATTTT	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.49T>C	chr2.hg19:g.197664287A>G	ENSP00000263956:p.Ser17Pro	94.0	0.0		100.0	4.0	NM_001206774	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	hg19	CCDS2316.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.789042	0.49997	.	.	ENSG00000119041	ENST00000263956;ENST00000409364	T;T	0.53857	0.64;0.6	5.36	5.36	0.76844	.	0.064358	0.64402	D	0.000005	T	0.62024	0.2394	L	0.36672	1.1	0.50632	D	0.999885	D;P	0.76494	0.999;0.928	D;B	0.64776	0.929;0.382	T	0.65290	-0.6204	10	0.72032	D	0.01	-11.5443	15.1834	0.72978	1.0:0.0:0.0:0.0	.	17;17	Q9Y5Q9-2;Q9Y5Q9	.;TF3C3_HUMAN	P	17	ENSP00000263956:S17P;ENSP00000386465:S17P	ENSP00000263956:S17P	S	-	1	0	GTF3C3	197372532	0.999000	0.42202	1.000000	0.80357	0.963000	0.63663	3.361000	0.52306	2.250000	0.74265	0.477000	0.44152	TCC	.	.		0.532	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			G	197664287	A	G	197664287	3	3	115	1	0	0	0	0	1	0	0	0	6883	304	11	2	2683	2	GTF3C3	2	197664287	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	9315377	197664287	45535086	62	19601										
MPP4	58538	hgsc.bcm.edu	37	chr2	202514868	202514868	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acgcccattcatttcgtaacTctttttagtacgagtagtgt	7	9	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:202514868T>C	ENST00000409474.3	-	19	1609	c.1402A>G	c.(1402-1404)Agt>Ggt	p.S468G	MPP4_ENST00000428900.2_Missense_Mutation_p.S444G|MPP4_ENST00000447335.2_Missense_Mutation_p.S461G|MPP4_ENST00000315506.7_Missense_Mutation_p.S424G|MPP4_ENST00000359962.5_Missense_Mutation_p.S468G|MPP4_ENST00000409143.1_Missense_Mutation_p.S410G|MPP4_ENST00000396886.3_Missense_Mutation_p.S393G	NM_033066.2	NP_149055	Q96JB8	MPP4_HUMAN	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	468	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				protein localization to synapse (GO:0035418)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|presynaptic membrane (GO:0042734)				kidney(1)|lung(11)	12						ATTTCGTAACTCTTTTTAGTA	0.348																																					p.S468G		Atlas-SNP	.											.	MPP4	93	.	0			c.A1402G						.						104	91	95					2																	202514868		1848	4087	5935	SO:0001583	missense	58538	exon19			CGTAACTCTTTTT	AF316032	CCDS46491.1	2q33.2	2008-05-15			ENSG00000082126	ENSG00000082126			13680	protein-coding gene	gene with protein product		606575		DLG6		11414766	Standard	NM_033066		Approved		uc002uyk.4	Q96JB8	OTTHUMG00000154525	ENST00000409474.3:c.1402A>G	chr2.hg19:g.202514868T>C	ENSP00000387278:p.Ser468Gly	77.0	0.0		93.0	4.0	NM_033066	C9IZK4|Q53TT3|Q6ZNH6|Q96Q43|Q96Q44	Missense_Mutation	SNP	ENST00000409474.3	hg19	CCDS46491.1	.	.	.	.	.	.	.	.	.	.	T	13.77	2.337673	0.41398	.	.	ENSG00000082126	ENST00000409474;ENST00000315506;ENST00000396886;ENST00000359962;ENST00000315549;ENST00000374605;ENST00000428900;ENST00000409143;ENST00000447335	T;T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3;2.3	5.51	4.32	0.51571	Guanylate kinase/L-type calcium channel (1);Guanylate kinase, conserved site (1);Guanylate kinase (2);	0.203963	0.52532	D	0.000079	T	0.13329	0.0323	N	0.25789	0.76	0.35709	D	0.816254	B;B;B;B;B;B;B;B	0.17667	0.019;0.012;0.023;0.023;0.019;0.013;0.023;0.019	B;B;B;B;B;B;B;B	0.23275	0.023;0.034;0.039;0.039;0.023;0.039;0.039;0.045	T	0.09773	-1.0659	10	0.52906	T	0.07	.	11.8224	0.52247	0.0:0.0696:0.0:0.9304	.	410;393;444;437;424;461;468;433	F6Q0Y6;B4DUF3;E7ET46;B7ZM19;Q96JB8-2;E7EUL8;Q96JB8;Q96JB8-4	.;.;.;.;.;.;MPP4_HUMAN;.	G	468;424;393;468;433;397;444;410;461	ENSP00000387278:S468G;ENSP00000319363:S424G;ENSP00000353047:S468G;ENSP00000416781:S444G;ENSP00000387293:S410G;ENSP00000406160:S461G	ENSP00000319363:S424G	S	-	1	0	MPP4	202223113	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	2.486000	0.45259	2.317000	0.78254	0.459000	0.35465	AGT	.	.		0.348	MPP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335748.2			C	202514868	T	C	202514868	3	2	115	1	0	0	0	0	1	0	0	0	9745	1551	54	2	527	2	MPP4	2	202514868	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4850581	202514868	40684505	63	19602										
CPS1	1373	hgsc.bcm.edu	37	chr2	211523326	211523326	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tatgctttttaattcaggtgAaggatgctacccggaagatt	10	6	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:211523326A>G	ENST00000233072.5	+	31	3866	c.3670A>G	c.(3670-3672)Aag>Gag	p.K1224E	CPS1_ENST00000451903.2_Missense_Mutation_p.K773E|CPS1_ENST00000430249.2_Missense_Mutation_p.K1230E	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1224	ATP-grasp 2.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	AATTCAGGTGAAGGATGCTAC	0.368																																					p.K1230E		Atlas-SNP	.											.	CPS1	485	.	0			c.A3688G						.						112	104	107					2																	211523326		2203	4300	6503	SO:0001583	missense	1373	exon32			CAGGTGAAGGATG	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3670A>G	chr2.hg19:g.211523326A>G	ENSP00000233072:p.Lys1224Glu	61.0	0.0		91.0	4.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.519772	0.44866	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.97161	-4.27;-4.27;-4.27	5.29	5.29	0.74685	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.000000	0.85682	D	0.000000	D	0.94988	0.8378	L	0.39085	1.19	0.53005	D	0.999962	P;P	0.41673	0.759;0.759	B;B	0.43990	0.438;0.438	D	0.94030	0.7300	10	0.25751	T	0.34	-11.1284	15.2413	0.73471	1.0:0.0:0.0:0.0	.	1234;1224	Q59HF8;P31327	.;CPSM_HUMAN	E	1230;1232;1224;773	ENSP00000402608:K1230E;ENSP00000233072:K1224E;ENSP00000406136:K773E	ENSP00000233072:K1224E	K	+	1	0	CPS1	211231571	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	8.625000	0.90965	2.001000	0.58596	0.460000	0.39030	AAG	.	.		0.368	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			G	211523326	A	G	211523326	3	3	115	1	0	0	0	0	1	0	0	0	3825	247	9	2	3814	2	CPS1	2	211523326	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	9008458	211523326	31676047	64	19603										
SLC23A3	151295	hgsc.bcm.edu	37	chr2	220028989	220028989	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gggatggtggtgaggagctgAgccaacctgggggagagtcc	20	7	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:220028989A>G	ENST00000409878.3	-	9	1271	c.1239T>C	c.(1237-1239)gcT>gcC	p.A413A	SLC23A3_ENST00000396775.3_3'UTR|SLC23A3_ENST00000455516.2_Silent_p.A421A|SLC23A3_ENST00000295738.7_Silent_p.A296A	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	413					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGAGGAGCTGAGCCAACCTGG	0.542																																					p.A421A		Atlas-SNP	.											.	SLC23A3	60	.	0			c.T1263C						.						38	40	39					2																	220028989		2068	4211	6279	SO:0001819	synonymous_variant	151295	exon9			GAGCTGAGCCAAC	BC030243	CCDS42819.1, CCDS46517.1, CCDS46518.1	2q35	2013-07-18	2013-07-18		ENSG00000213901	ENSG00000213901		"Solute carriers"	20601	protein-coding gene	gene with protein product							Standard	NM_144712		Approved	SVCT3, FLJ31168, Yspl1	uc010zkr.2	Q6PIS1	OTTHUMG00000154616	ENST00000409878.3:c.1239T>C	chr2.hg19:g.220028989A>G		117.0	0.0		118.0	5.0	NM_001144890	B7Z512|Q2PYN6|Q96NA6	Silent	SNP	ENST00000409878.3	hg19	CCDS46518.1																																																																																			.	.		0.542	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2	NM_144712		G	220028989	A	G	220028989	2	3	115	1	0	0	0	0	0	0	0	1	14479	291	11	2		2	SLC23A3	2	220028989	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	8505663	220028989	23170384	65	19604										
TUBA4A	7277	hgsc.bcm.edu	37	chr2	220115976	220115976	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctccatcaggagtgaggtgaAgccagagccagtgcccccac	12	14	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr2:220115976A>G	ENST00000248437.4	-	4	618	c.445T>C	c.(445-447)Ttc>Ctc	p.F149L	TUBA4A_ENST00000498660.1_5'UTR|TUBA4A_ENST00000392088.2_Missense_Mutation_p.F134L|TUBA4B_ENST00000490341.1_RNA	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	149					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	AGTGAGGTGAAGCCAGAGCCA	0.542																																					p.F149L		Atlas-SNP	.											.	TUBA4A	96	.	0			c.T445C						.						46	51	50					2																	220115976		2202	4300	6502	SO:0001583	missense	7277	exon4			AGGTGAAGCCAGA	AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"Tubulins"	12407	protein-coding gene	gene with protein product		191110	"tubulin, alpha 1 (testis specific)", "tubulin, alpha 1"	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.445T>C	chr2.hg19:g.220115976A>G	ENSP00000248437:p.Phe149Leu	82.0	0.0		82.0	4.0	NM_006000	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	hg19	CCDS2438.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.044376	0.55110	.	.	ENSG00000127824	ENST00000248437;ENST00000392088;ENST00000427737;ENST00000456818;ENST00000447205	T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08	5.06	5.06	0.68205	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	T	0.54870	0.1885	N	0.13140	0.3	0.80722	D	1	B	0.34313	0.448	P	0.44394	0.448	T	0.59521	-0.7439	10	0.46703	T	0.11	.	14.9694	0.71220	1.0:0.0:0.0:0.0	.	149	P68366	TBA4A_HUMAN	L	149;134;134;172;134	ENSP00000248437:F149L;ENSP00000375938:F134L;ENSP00000408194:F134L;ENSP00000416992:F172L;ENSP00000396061:F134L	ENSP00000248437:F149L	F	-	1	0	TUBA4A	219824220	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.928000	0.92853	2.131000	0.65755	0.533000	0.62120	TTC	.	.		0.542	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000		G	220115976	A	G	220115976	3	3	115	1	0	0	0	0	1	0	0	0	16764	72	3	2	905	2	TUBA4A	2	220115976	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	86987	220115976	23083397	66	19605										
GRM7	2917	hgsc.bcm.edu	37	chr3	7494418	7494418	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaggatctctgtgctgactaCcggggtgtctgcccagagat	13	10	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:7494418C>T	ENST00000357716.4	+	6	1573	c.1299C>T	c.(1297-1299)taC>taT	p.Y433Y	GRM7_ENST00000486284.1_Silent_p.Y433Y|GRM7_ENST00000389336.4_Silent_p.Y433Y|GRM7_ENST00000403881.1_Silent_p.Y433Y|GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000402647.2_Silent_p.Y433Y	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	433			Y -> F (in dbSNP:rs2229902). {ECO:0000269|PubMed:11163549}.		adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						GTGCTGACTACCGGGGTGTCT	0.483																																					p.Y433Y		Atlas-SNP	.											GRM7,NS,carcinoma,0,1	GRM7	223	.	0			c.C1299T						.						86	73	78					3																	7494418		2203	4300	6503	SO:0001819	synonymous_variant	2917	exon6			TGACTACCGGGGT	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1299C>T	chr3.hg19:g.7494418C>T		114.0	0.0		109.0	0.0	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	hg19	CCDS43042.1																																																																																			.	.		0.483	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		T	7494418	C	T	7494418	2	4	115	1	0	0	0	0	0	0	0	1	6811	518	18	3		3	GRM7	3	7494418	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10		7494418	190528012	67	19606										
IL17RC	84818	hgsc.bcm.edu	37	chr3	9972089	9972089	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cctttggcttggcagagggcAgctcgccttggagagtactt	14	10	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:9972089A>G	ENST00000295981.3	+	15	1715	c.1497A>G	c.(1495-1497)gcA>gcG	p.A499A	IL17RC_ENST00000498214.1_Intron|IL17RC_ENST00000403601.3_Silent_p.A428A|IL17RC_ENST00000383812.4_Silent_p.A413A|IL17RC_ENST00000455057.1_Silent_p.A396A|IL17RC_ENST00000416074.2_Silent_p.A267A|IL17RC_ENST00000413608.1_Silent_p.A428A	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	499					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGCAGAGGGCAGCTCGCCTTG	0.587																																					p.A499A		Atlas-SNP	.											.	IL17RC	55	.	0			c.A1497G						.						56	54	55					3																	9972089		2203	4300	6503	SO:0001819	synonymous_variant	84818	exon15			GAGGGCAGCTCGC	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"Interleukins and interleukin receptors"	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.1497A>G	chr3.hg19:g.9972089A>G		153.0	0.0		159.0	7.0	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	hg19	CCDS2590.1																																																																																			.	.		0.587	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		G	9972089	A	G	9972089	2	3	115	1	0	0	0	0	0	0	0	1	7650	175	7	2		2	IL17RC	3	9972089	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2477671	9972089	188050341	68	19607										
CAND2	23066	hgsc.bcm.edu	37	chr3	12875342	12875342	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agtggctgccctgctgaccaTccccgaggtggggaaaagcc	14	13	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:12875342T>C	ENST00000456430.2	+	15	3613	c.3572T>C	c.(3571-3573)aTc>aCc	p.I1191T	RP11-767C1.2_ENST00000606447.1_RNA|CAND2_ENST00000295989.5_Missense_Mutation_p.I1074T	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	1191					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CTGCTGACCATCCCCGAGGTG	0.517																																					p.I1191T	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.T3572C						.						91	95	94					3																	12875342		1978	4181	6159	SO:0001583	missense	23066	exon15			TGACCATCCCCGA		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.3572T>C	chr3.hg19:g.12875342T>C	ENSP00000387641:p.Ile1191Thr	124.0	0.0		140.0	7.0	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.053793	0.55218	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.67171	-0.25;-0.25	4.84	3.65	0.41850	TATA-binding protein interacting (TIP20) (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.136423	0.48767	D	0.000176	T	0.75191	0.3816	M	0.83953	2.67	0.80722	D	1	P;B	0.41188	0.741;0.137	P;B	0.51550	0.673;0.109	T	0.73649	-0.3916	10	0.42905	T	0.14	-19.4285	8.7859	0.34821	0.175:0.0:0.0:0.825	.	1191;1074	O75155;O75155-2	CAND2_HUMAN;.	T	1074;1191	ENSP00000295989:I1074T;ENSP00000387641:I1191T	ENSP00000295989:I1074T	I	+	2	0	CAND2	12850342	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.056000	0.71111	0.828000	0.34709	0.482000	0.46254	ATC	.	.		0.517	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		C	12875342	T	C	12875342	3	2	115	1	0	0	0	0	1	0	0	0	2618	1435	50	2	3630	2	CAND2	3	12875342	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2903253	12875342	185147088	69	19608										
HACL1	26061	hgsc.bcm.edu	37	chr3	15613278	15613278	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tatcaagttcctctaaaagcTtaaaaaaaaaaaaacacaca	2	8	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:15613278T>C	ENST00000321169.5	-	12	1361		c.e12-2		HACL1_ENST00000457447.2_Intron|HACL1_ENST00000451445.2_Splice_Site|HACL1_ENST00000456194.2_Splice_Site|HACL1_ENST00000435217.2_Splice_Site	NM_012260.2	NP_036392.2	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1						cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)			NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						CTCTAAAAGCTTAAAAAAAAA	0.323																																					.		Atlas-SNP	.											.,1	HACL1	33	.	0			c.994-2A>G						.						77	75	76					3																	15613278		2203	4300	6503	SO:0001630	splice_region_variant	26061	exon13			AAAAGCTTAAAAA	AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	"2-hydroxyphytanoyl-CoA lyase"	HPCL		10468558, 15644336	Standard	NM_001284416		Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000321169.5:c.994-2A>G	chr3.hg19:g.15613278T>C		31.0	0.0		39.0	3.0	NM_012260	B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	Splice_Site	SNP	ENST00000321169.5	hg19	CCDS2627.1	.	.	.	.	.	.	.	.	.	.	T	12.26	1.885022	0.33255	.	.	ENSG00000131373	ENST00000321169;ENST00000435217;ENST00000451445;ENST00000456194	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0137	0.71567	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HACL1	15588282	1.000000	0.71417	0.997000	0.53966	0.137000	0.21094	6.518000	0.73764	1.994000	0.58287	0.529000	0.55759	.	.	.		0.323	HACL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252104.3	NM_012260	Intron	C	15613278	T	C	15613278	5	2	115	1	0	0	0	0	0	0	1	0	6950	1623	56	2	768	2	HACL1	3	15613278	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2737936	15613278	182409152	70	19609										
OSBPL10	114884	hgsc.bcm.edu	37	chr3	31712394	31712394	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttcctccgagctccacccacGggatggtgagaatggaccgg	13	13	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:31712394G>T	ENST00000396556.2	-	9	1930	c.1808C>A	c.(1807-1809)cCg>cAg	p.P603Q	OSBPL10_ENST00000438237.2_Missense_Mutation_p.P539Q	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	603					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)	p.P603L(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		CTCCACCCACGGGATGGTGAG	0.567																																					p.P603Q		Atlas-SNP	.											OSBPL10_ENST00000396556,extremity,malignant_melanoma,0,6	OSBPL10	160	.	2	Substitution - Missense(2)	skin(2)	c.C1808A						.						131	115	120					3																	31712394		2203	4300	6503	SO:0001583	missense	114884	exon9			ACCCACGGGATGG	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.1808C>A	chr3.hg19:g.31712394G>T	ENSP00000379804:p.Pro603Gln	175.0	0.0		176.0	0.0	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	hg19	CCDS2651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.72|17.72	3.458058|3.458058	0.63401|0.63401	.|.	.|.	ENSG00000144645|ENSG00000144645	ENST00000396556;ENST00000438237|ENST00000429492	T;T|.	0.32753|.	1.44;1.44|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87565|0.87565	0.6209|0.6209	H|H	0.95004|0.95004	3.61|3.61	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	D|D	0.90774|0.90774	0.4674|0.4674	10|5	0.72032|.	D|.	0.01|.	-18.8515|-18.8515	19.3207|19.3207	0.94237|0.94237	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	539;603;371|.	B4E212;Q9BXB5;Q59ED9|.	.;OSB10_HUMAN;.|.	Q|S	603;539|372	ENSP00000379804:P603Q;ENSP00000406124:P539Q|.	ENSP00000379804:P603Q|.	P|R	-|-	2|1	0|0	OSBPL10|OSBPL10	31687398|31687398	1.000000|1.000000	0.71417|0.71417	0.841000|0.841000	0.33234|0.33234	0.009000|0.009000	0.06853|0.06853	9.869000|9.869000	0.99810|0.99810	2.550000|2.550000	0.86006|0.86006	0.557000|0.557000	0.71058|0.71058	CCG|CGT	.	.		0.567	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			T	31712394	G	T	31712394	3	4	115	1	0	0	0	0	1	0	0	0	11284	1116	39	1	502	1	OSBPL10	3	31712394	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	16099116	31712394	166310036	71	19610										
MAP4	4134	hgsc.bcm.edu	37	chr3	47960309	47960309	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaccacccctgaggtacaacAgctgtgttgcagggagacat	12	11	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:47960309A>G	ENST00000360240.6	-	6	1070	c.552T>C	c.(550-552)gcT>gcC	p.A184A	MAP4_ENST00000395734.3_Silent_p.A184A|MAP4_ENST00000383737.4_Silent_p.A184A|MAP4_ENST00000426837.2_Silent_p.A201A	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	184					cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	GAGGTACAACAGCTGTGTTGC	0.418																																					p.A184A		Atlas-SNP	.											.	MAP4	176	.	0			c.T552C						.						87	81	83					3																	47960309		2203	4300	6503	SO:0001819	synonymous_variant	4134	exon6			TACAACAGCTGTG		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.552T>C	chr3.hg19:g.47960309A>G		90.0	0.0		107.0	5.0	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Silent	SNP	ENST00000360240.6	hg19	CCDS33750.1	.	.	.	.	.	.	.	.	.	.	A	2.665	-0.278962	0.05642	.	.	ENSG00000047849	ENST00000423088	.	.	.	4.51	2.06	0.26882	.	.	.	.	.	T	0.24470	0.0593	.	.	.	0.26100	N	0.980838	.	.	.	.	.	.	T	0.21381	-1.0247	4	.	.	.	0.1461	3.8037	0.08768	0.7111:0.0:0.1016:0.1873	.	.	.	.	P	153	.	.	L	-	2	0	MAP4	47935313	0.090000	0.21635	0.122000	0.21767	0.369000	0.29798	1.613000	0.36900	0.325000	0.23359	0.459000	0.35465	CTG	.	.		0.418	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375		G	47960309	A	G	47960309	2	3	115	1	0	0	0	0	0	0	0	1	9267	175	7	2		2	MAP4	3	47960309	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	16247915	47960309	150062121	72	19611										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48628195	48628195	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agctaagcccagcctgaacgTcatccaagtcgaatgctgtc	9	13	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:48628195T>C	ENST00000328333.8	-	13	1798	c.1691A>G	c.(1690-1692)gAc>gGc	p.D564G	COL7A1_ENST00000454817.1_Missense_Mutation_p.D564G	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	564	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region (NC1).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AGCCTGAACGTCATCCAAGTC	0.607																																					p.D564G		Atlas-SNP	.											.	COL7A1	320	.	0			c.A1691G						.						145	109	121					3																	48628195		2203	4300	6503	SO:0001583	missense	1294	exon13			TGAACGTCATCCA	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.1691A>G	chr3.hg19:g.48628195T>C	ENSP00000332371:p.Asp564Gly	108.0	0.0		124.0	5.0	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	hg19	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	T	11.33	1.606260	0.28623	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	T;T	0.53423	0.62;0.62	5.01	3.87	0.44632	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.269957	0.25789	N	0.028282	T	0.37999	0.1024	N	0.20685	0.6	0.35462	D	0.796603	P	0.50819	0.939	P	0.53360	0.724	T	0.27673	-1.0067	10	0.09084	T	0.74	.	9.6616	0.39958	0.0:0.0838:0.0:0.9162	.	564	Q02388	CO7A1_HUMAN	G	564	ENSP00000332371:D564G;ENSP00000412569:D564G	ENSP00000332371:D564G	D	-	2	0	COL7A1	48603199	1.000000	0.71417	0.930000	0.37139	0.631000	0.37964	3.234000	0.51320	2.249000	0.74217	0.528000	0.53228	GAC	.	.		0.607	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		C	48628195	T	C	48628195	3	2	115	1	0	0	0	0	1	0	0	0	3706	1667	58	2	7567	2	COL7A1	3	48628195	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	667886	48628195	149394235	73	19612										
DCP1A	55802	hgsc.bcm.edu	37	chr3	53326495	53326495	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggtaagctggggggaacctgTgcagtaggagcttcagctgg	18	7	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:53326495T>A	ENST00000607628.1	-	7	1096	c.987A>T	c.(985-987)gcA>gcT	p.A329A	DCP1A_ENST00000294241.6_Silent_p.A329A|DCP1A_ENST00000480258.1_5'UTR|Y_RNA_ENST00000384175.1_RNA|DCP1A_ENST00000606822.1_Silent_p.A291A	NM_018403.5	NP_060873.4	Q9NPI6	DCP1A_HUMAN	decapping mRNA 1A	329					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)		GGGGAACCTGTGCAGTAGGAG	0.562																																					p.A329A		Atlas-SNP	.											.	DCP1A	30	.	0			c.A987T						.						67	74	72					3																	53326495		2142	4253	6395	SO:0001819	synonymous_variant	55802	exon7			AACCTGTGCAGTA	AJ275986	CCDS74946.1	3p21.1	2013-05-02	2013-05-02		ENSG00000162290	ENSG00000272886			18714	protein-coding gene	gene with protein product		607010	"DCP1 decapping enzyme homolog A (S. cerevisiae)"				Standard	XM_005278360		Approved	HSA275986, SMIF, SMAD4IP1	uc021wzi.1	Q9NPI6	OTTHUMG00000158193	ENST00000607628.1:c.987A>T	chr3.hg19:g.53326495T>A		464.0	0.0		431.0	164.0	NM_018403	B4DHN9|U3KQM8	Silent	SNP	ENST00000607628.1	hg19																																																																																				.	.		0.562	DCP1A-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018403		A	53326495	T	A	53326495	2	1	115	1	0	0	0	0	0	0	0	1	4300	1683	59	4		4	DCP1A	3	53326495	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4698300	53326495	144695935	74	19613										
IL17RB	55540	hgsc.bcm.edu	37	chr3	53899048	53899048	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acagtgtgtgcgatggtaccTgtggcaagagcgagggcagt	17	7	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:53899048T>C	ENST00000288167.3	+	11	1231	c.1222T>C	c.(1222-1224)Tgt>Cgt	p.C408R		NM_018725.3	NP_061195.2	Q9NRM6	I17RB_HUMAN	interleukin 17 receptor B	408	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|regulation of cell growth (GO:0001558)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		CGATGGTACCTGTGGCAAGAG	0.507																																					p.C408R		Atlas-SNP	.											.	IL17RB	27	.	0			c.T1222C						.						82	74	77					3																	53899048		2203	4300	6503	SO:0001583	missense	55540	exon11			GGTACCTGTGGCA	AF212365	CCDS2874.1	3p21.1	2008-02-05		2003-07-09	ENSG00000056736	ENSG00000056736		"Interleukins and interleukin receptors"	18015	protein-coding gene	gene with protein product		605458	"interleukin 17B receptor"	IL17BR		10749887, 10815801	Standard	NM_018725		Approved	IL17RH1, EVI27, CRL4	uc003dha.3	Q9NRM6	OTTHUMG00000158280	ENST00000288167.3:c.1222T>C	chr3.hg19:g.53899048T>C	ENSP00000288167:p.Cys408Arg	121.0	0.0		114.0	5.0	NM_018725	Q9BPZ0|Q9NRL4|Q9NRM5	Missense_Mutation	SNP	ENST00000288167.3	hg19	CCDS2874.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.721627	0.48728	.	.	ENSG00000056736	ENST00000288167	T	0.28895	1.59	5.65	5.65	0.86999	SEFIR (1);	0.150888	0.45867	D	0.000329	T	0.50034	0.1592	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44697	-0.9311	10	0.13470	T	0.59	-14.1381	13.4094	0.60933	0.0:0.0:0.0:1.0	.	408	Q9NRM6	I17RB_HUMAN	R	408	ENSP00000288167:C408R	ENSP00000288167:C408R	C	+	1	0	IL17RB	53874088	0.999000	0.42202	0.944000	0.38274	0.186000	0.23388	5.102000	0.64572	2.150000	0.67090	0.528000	0.53228	TGT	.	.		0.507	IL17RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350563.1	NM_172234		C	53899048	T	C	53899048	3	2	115	1	0	0	0	0	1	0	0	0	7649	1580	55	2	1264	2	IL17RB	3	53899048	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	572553	53899048	144123382	75	19614										
FILIP1L	11259	hgsc.bcm.edu	37	chr3	99567249	99567249	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gttaattaagccttgagttcGgttatcctgcagtggtgctg	12	7	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:99567249G>A	ENST00000354552.3	-	5	3741	c.3271C>T	c.(3271-3273)Cga>Tga	p.R1091*	CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000487087.1_Nonsense_Mutation_p.R667*|FILIP1L_ENST00000476723.1_Intron|CMSS1_ENST00000421999.2_Intron|FILIP1L_ENST00000471562.1_Nonsense_Mutation_p.R851*|FILIP1L_ENST00000331335.5_Nonsense_Mutation_p.R1091*|FILIP1L_ENST00000383694.2_Nonsense_Mutation_p.R851*	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	1091						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R1091R(2)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						CCTTGAGTTCGGTTATCCTGC	0.463																																					p.R1091X		Atlas-SNP	.											FILIP1L_ENST00000354552,NS,lymphoid_neoplasm,0,2	FILIP1L	154	.	2	Substitution - coding silent(2)	lung(2)	c.C3271T						.						275	277	276					3																	99567249		2029	4191	6220	SO:0001587	stop_gained	11259	exon5			GAGTTCGGTTATC		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"downregulated in ovarian cancer 1", "GPBP-interacting protein of 130 kDa"	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.3271C>T	chr3.hg19:g.99567249G>A	ENSP00000346560:p.Arg1091*	553.0	0.0		502.0	27.0	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Nonsense_Mutation	SNP	ENST00000354552.3	hg19	CCDS43117.1	.	.	.	.	.	.	.	.	.	.	G	35	5.566464	0.96540	.	.	ENSG00000168386	ENST00000477258;ENST00000354552;ENST00000487087;ENST00000471562;ENST00000331335;ENST00000383694;ENST00000441620	.	.	.	5.79	3.94	0.45596	.	0.000000	0.43110	D	0.000602	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.9685	13.9686	0.64225	0.0:0.0:0.4159:0.5841	.	.	.	.	X	70;1091;667;851;1091;851;837	.	ENSP00000327880:R1091X	R	-	1	2	FILIP1L	101049939	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.592000	0.36676	0.741000	0.32674	0.655000	0.94253	CGA	.	.		0.463	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890		A	99567249	G	A	99567249	4	1	115	1	0	0	0	0	0	1	0	0	5903	1124	39	1	165	1	FILIP1L	3	99567249	Nonsense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	45668201	99567249	98455181	76	19615										
ABI3BP	25890	hgsc.bcm.edu	37	chr3	100569517	100569517	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acattacccagtgttgccctTggctgttcaagagttctaga	9	10	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:100569517T>C	ENST00000284322.5	-	14	1396	c.1287A>G	c.(1285-1287)ccA>ccG	p.P429P	ABI3BP_ENST00000495063.1_Silent_p.P478P|ABI3BP_ENST00000471714.1_Silent_p.P478P	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	429	Pro-rich.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						GTGTTGCCCTTGGCTGTTCAA	0.333																																					p.P429P		Atlas-SNP	.											.	ABI3BP	305	.	0			c.A1287G						.						124	121	122					3																	100569517		1805	4070	5875	SO:0001819	synonymous_variant	25890	exon14			TGCCCTTGGCTGT	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"Fibronectin type III domain containing"	17265	protein-coding gene	gene with protein product	"target of Nesh-SH3"	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.1287A>G	chr3.hg19:g.100569517T>C		88.0	0.0		77.0	5.0	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Silent	SNP	ENST00000284322.5	hg19	CCDS46880.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.226|9.226	1.034565|1.034565	0.19590|0.19590	.|.	.|.	ENSG00000154175|ENSG00000154175	ENST00000459682|ENST00000533855	.|.	.|.	.|.	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	.|.	.|.	.|.	.|.	T|T	0.71643|0.71643	0.3364|0.3364	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.70443|0.70443	-0.4870|-0.4870	4|4	.|.	.|.	.|.	-17.0179|-17.0179	15.1469|15.1469	0.72662|0.72662	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	E|R	55|107	.|.	.|.	K|Q	-|-	1|2	0|0	ABI3BP|ABI3BP	102052207|102052207	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.846000|4.846000	0.62860|0.62860	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	AAG|CAA	.	.		0.333	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			C	100569517	T	C	100569517	2	2	115	1	0	0	0	0	0	0	0	1	91	1799	63	2		2	ABI3BP	3	100569517	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1002268	100569517	97452913	77	19616										
TAGLN3	29114	hgsc.bcm.edu	37	chr3	111718279	111718279	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctttccagagatggctaacAggggcccgagctatggctta	12	10	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:111718279A>G	ENST00000393917.2	+	2	562	c.10A>G	c.(10-12)Agg>Ggg	p.R4G	TAGLN3_ENST00000486460.1_5'Flank|TAGLN3_ENST00000273368.4_Missense_Mutation_p.R4G|TAGLN3_ENST00000455401.2_Missense_Mutation_p.R4G|TAGLN3_ENST00000478951.1_Missense_Mutation_p.R4G	NM_013259.2	NP_037391.2	Q9UI15	TAGL3_HUMAN	transgelin 3	4					central nervous system development (GO:0007417)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				endometrium(2)|lung(5)|urinary_tract(1)	8						GATGGCTAACAGGGGCCCGAG	0.582																																					p.R4G		Atlas-SNP	.											.	TAGLN3	44	.	0			c.A10G						.						47	46	46					3																	111718279		2203	4300	6503	SO:0001583	missense	29114	exon2			GCTAACAGGGGCC	AF303058	CCDS33816.1	3q13.2	2008-02-05			ENSG00000144834	ENSG00000144834			29868	protein-coding gene	gene with protein product		607953				8015377, 11238712	Standard	NM_013259		Approved	NP25, NP22	uc003dyo.3	Q9UI15	OTTHUMG00000159281	ENST00000393917.2:c.10A>G	chr3.hg19:g.111718279A>G	ENSP00000377494:p.Arg4Gly	95.0	0.0		117.0	5.0	NM_001008272	D3DN64|Q96A74	Missense_Mutation	SNP	ENST00000393917.2	hg19	CCDS33816.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.709334	0.89018	.	.	ENSG00000144834	ENST00000478951;ENST00000393917;ENST00000273368;ENST00000540095;ENST00000455401;ENST00000494932	T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44	5.38	-7.72	0.01250	.	0.000000	0.85682	D	0.000000	T	0.66771	0.2823	M	0.77616	2.38	0.50632	D	0.999886	D	0.62365	0.991	D	0.63703	0.917	T	0.77305	-0.2637	10	0.87932	D	0	-4.411	20.4015	0.98996	0.251:0.749:0.0:0.0	.	4	Q9UI15	TAGL3_HUMAN	G	4	ENSP00000419105:R4G;ENSP00000377494:R4G;ENSP00000273368:R4G;ENSP00000391160:R4G;ENSP00000420675:R4G	ENSP00000273368:R4G	R	+	1	2	TAGLN3	113200969	0.301000	0.24444	0.959000	0.39883	0.998000	0.95712	-0.209000	0.09358	-1.107000	0.03004	0.533000	0.62120	AGG	.	.		0.582	TAGLN3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354331.1	NM_013259		G	111718279	A	G	111718279	3	3	115	1	0	0	0	0	1	0	0	0	15555	179	7	2	12	2	TAGLN3	3	111718279	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	11148762	111718279	86304151	78	19617										
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113723571	113723571	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggagtcacttctgccttcagTcccaggggaagcaacaggtg	13	11	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:113723571T>C	ENST00000295878.3	-	11	2037	c.1891A>G	c.(1891-1893)Act>Gct	p.T631A	KIAA1407_ENST00000545063.1_Missense_Mutation_p.T462A	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	631										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						CTGCCTTCAGTCCCAGGGGAA	0.448																																					p.T631A		Atlas-SNP	.											.	KIAA1407	80	.	0			c.A1891G						.						141	138	139					3																	113723571		2203	4300	6503	SO:0001583	missense	57577	exon11			CTTCAGTCCCAGG	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.1891A>G	chr3.hg19:g.113723571T>C	ENSP00000295878:p.Thr631Ala	73.0	0.0		95.0	4.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	T	4.651	0.121024	0.08881	.	.	ENSG00000163617	ENST00000295878;ENST00000545063	T;T	0.42513	1.57;0.97	5.39	0.056	0.14317	.	0.648857	0.16203	N	0.224840	T	0.16514	0.0397	N	0.08118	0	0.09310	N	1	B;B	0.10296	0.003;0.0	B;B	0.09377	0.004;0.002	T	0.15578	-1.0432	10	0.20519	T	0.43	.	2.9719	0.05925	0.3225:0.1756:0.0:0.5019	.	507;631	B4DIZ9;Q8NCU4	.;K1407_HUMAN	A	631;462	ENSP00000295878:T631A;ENSP00000446381:T462A	ENSP00000295878:T631A	T	-	1	0	KIAA1407	115206261	0.005000	0.15991	0.035000	0.18076	0.842000	0.47809	0.356000	0.20181	-0.121000	0.11787	-0.280000	0.10049	ACT	.	.		0.448	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		C	113723571	T	C	113723571	3	2	115	1	0	0	0	0	1	0	0	0	8238	1667	58	2	947	2	KIAA1407	3	113723571	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2005292	113723571	84298859	79	19618										
ZNF80	7634	hgsc.bcm.edu	37	chr3	113955213	113955213	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tttctctccagtgtgactccTtgtatgtcgagtgagggaat	11	8	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:113955213T>C	ENST00000482457.2	-	1	1212	c.709A>G	c.(709-711)Agg>Ggg	p.R237G	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	237					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				GTGTGACTCCTTGTATGTCGA	0.463																																					p.R237G	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.A709G						.						104	104	104					3																	113955213		2203	4300	6503	SO:0001583	missense	7634	exon1			GACTCCTTGTATG	X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"Zinc fingers, C2H2-type"	13155	protein-coding gene	gene with protein product		194553	"zinc finger protein 80 (pT17)"			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.709A>G	chr3.hg19:g.113955213T>C	ENSP00000417192:p.Arg237Gly	106.0	0.0		97.0	4.0	NM_007136	Q6NSW4|Q6NT14	Missense_Mutation	SNP	ENST00000482457.2	hg19	CCDS2979.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.059753	0.36373	.	.	ENSG00000174255	ENST00000482457	T	0.24723	1.84	2.79	-2.76	0.05896	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32852	0.0843	M	0.85099	2.735	0.09310	N	1	B	0.33073	0.396	B	0.40477	0.33	T	0.44190	-0.9344	9	0.62326	D	0.03	.	4.2459	0.10672	0.0:0.2185:0.3359:0.4456	.	237	P51504	ZNF80_HUMAN	G	237	ENSP00000417192:R237G	ENSP00000309812:R237G	R	-	1	2	ZNF80	115437903	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-0.492000	0.06467	-0.632000	0.05553	0.459000	0.35465	AGG	.	.		0.463	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136		C	113955213	T	C	113955213	3	2	115	1	0	0	0	0	1	0	0	0	18183	1608	56	2	116	2	ZNF80	3	113955213	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	231642	113955213	84067217	80	19619										
KTELC1	56983	hgsc.bcm.edu	37	chr3	119187934	119187934	+	Frame_Shift_Del	DEL	G	G	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttcctcctgccctcagcgcaGggccgccagaaggagtcagg							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:119187934delG	ENST00000295588.4	+	1	150	c.66delG	c.(64-66)cagfs	p.Q22fs		NM_152305.2	NP_689518.1	Q8NBL1	PGLT1_HUMAN	protein O-glucosyltransferase 1	22					cardiovascular system development (GO:0072358)|Notch signaling pathway (GO:0007219)|protein O-linked glycosylation (GO:0006493)|regulation of Notch signaling pathway (GO:0008593)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	glucosyltransferase activity (GO:0046527)|protein xylosyltransferase activity (GO:0030158)|UDP-glucosyltransferase activity (GO:0035251)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(1)	16						CCTCAGCGCAGGGCCGCCAGA	0.731																																					p.Q22fs		Atlas-INDEL	.											.	POGLUT1	32	.	0			c.65delA						.						35	30	32					3																	119187934		2202	4296	6498	SO:0001589	frameshift_variant	56983	exon1			.	BC030614	CCDS2988.1	3q13.33	2010-09-29	2010-09-29	2010-09-29	ENSG00000163389	ENSG00000163389			22954	protein-coding gene	gene with protein product	"KDELC family like 1"	615618	"chromosome 3 open reading frame 9", "KTEL (Lys-Tyr-Glu-Leu) containing 1"	C3orf9, KTELC1		16524674	Standard	NM_152305		Approved	MDS010, MGC32995, 9630046K23Rik, MDSRP, hCLP46, KDELCL1, Rumi	uc003ecm.3	Q8NBL1	OTTHUMG00000159379	ENST00000295588.4:c.66delG	chr3.hg19:g.119187934delG	ENSP00000295588:p.Gln22fs	108.0	0.0		178.0	11.0	NM_152305	B2RD13|Q53GJ4|Q8N2T1	Frame_Shift_Del	DEL	ENST00000295588.4	hg19	CCDS2988.1																																																																																			.	.		0.731	POGLUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355034.2	NM_152305		-	119187934	G	-	119187934	7	5	115	1	0	1	0	1	0	0	0	0	8592	991	35	0	68	0	KTELC1	3	119187934	Frame_Shift_Del	DEL	G	TCGA-DD-A3A1-01A-11D-A20W-10	5232721	119187934	78834496	81	19620										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	120976155	120976155	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgttgctagtgaaggagtaAcaaaggacagtattccatgc	11	7	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:120976155A>G	ENST00000273666.6	+	17	2078	c.1807A>G	c.(1807-1809)Aca>Gca	p.T603A	STXBP5L_ENST00000497029.1_Missense_Mutation_p.T603A|STXBP5L_ENST00000471454.1_Missense_Mutation_p.T603A|STXBP5L_ENST00000472879.1_Missense_Mutation_p.T603A|STXBP5L_ENST00000492541.1_Missense_Mutation_p.T603A	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	603					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		TGAAGGAGTAACAAAGGACAG	0.383																																					p.T603A		Atlas-SNP	.											.	STXBP5L	159	.	0			c.A1807G						.						101	96	98					3																	120976155		1838	4084	5922	SO:0001583	missense	9515	exon17			GGAGTAACAAAGG	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.1807A>G	chr3.hg19:g.120976155A>G	ENSP00000273666:p.Thr603Ala	94.0	0.0		91.0	4.0	NM_014980	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	hg19	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	A	4.717	0.133386	0.09032	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.34859	2.01;2.0;1.79;1.34;1.82;1.97	5.33	4.16	0.48862	WD40 repeat-like-containing domain (1);	0.607810	0.18179	N	0.149203	T	0.21590	0.0520	L	0.34521	1.04	0.24318	N	0.995055	B;B	0.06786	0.001;0.001	B;B	0.04013	0.0;0.001	T	0.29088	-1.0023	10	0.08599	T	0.76	-23.8525	5.7046	0.17901	0.7101:0.1424:0.1475:0.0	.	603;603	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	A	603	ENSP00000273666:T603A;ENSP00000420019:T603A;ENSP00000419627:T603A;ENSP00000420287:T603A;ENSP00000420666:T603A;ENSP00000420167:T603A	ENSP00000273666:T603A	T	+	1	0	STXBP5L	122458845	0.999000	0.42202	0.998000	0.56505	0.995000	0.86356	2.673000	0.46858	0.950000	0.37743	0.377000	0.23210	ACA	.	.		0.383	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			G	120976155	A	G	120976155	3	3	115	1	0	0	0	0	1	0	0	0	15372	43	2	2	1869	2	STXBP5L	3	120976155	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1788221	120976155	77046275	82	19621										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121413392	121413392	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtattttctccaaatattccTttcgtatttctgattccacc	3	11	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:121413392T>C	ENST00000340645.5	-	13	6088	c.5963A>G	c.(5962-5964)aAg>aGg	p.K1988R	GOLGB1_ENST00000393667.3_Missense_Mutation_p.K1993R	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1988					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.K1988R(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CAAATATTCCTTTCGTATTTC	0.353																																					p.K1993R		Atlas-SNP	.											GOLGB1,NS,carcinoma,0,1	GOLGB1	319	.	1	Substitution - Missense(1)	lung(1)	c.A5978G						.						166	176	173					3																	121413392		2203	4300	6503	SO:0001583	missense	2804	exon13			TATTCCTTTCGTA	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.5963A>G	chr3.hg19:g.121413392T>C	ENSP00000341848:p.Lys1988Arg	88.0	0.0		68.0	3.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.103219	0.37145	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.15139	2.45;2.52	5.2	5.2	0.72013	.	0.000000	0.56097	D	0.000030	T	0.30166	0.0756	L	0.43757	1.38	0.36538	D	0.871104	D;D;P;P	0.71674	0.998;0.998;0.884;0.907	D;D;P;B	0.80764	0.994;0.994;0.509;0.364	T	0.14868	-1.0457	10	0.15952	T	0.53	.	13.0579	0.58990	0.0:0.0:0.0:1.0	.	1913;1993;1993;1988	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	R	1988;1993	ENSP00000341848:K1988R;ENSP00000377275:K1993R	ENSP00000341848:K1988R	K	-	2	0	GOLGB1	122896082	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.450000	0.44943	2.171000	0.68590	0.528000	0.53228	AAG	.	.		0.353	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121413392	T	C	121413392	3	2	115	1	0	0	0	0	1	0	0	0	6573	1609	56	2	3856	2	GOLGB1	3	121413392	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	437237	121413392	76609038	83	19622										
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122642473	122642473	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agattctgtacctggaaattGgggatggggttggctatggg	17	4	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:122642473G>A	ENST00000357599.3	-	10	1649	c.1263C>T	c.(1261-1263)ccC>ccT	p.P421P	SEMA5B_ENST00000195173.4_Silent_p.P421P|SEMA5B_ENST00000451055.2_Silent_p.P475P	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	421	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		CCTGGAAATTGGGGATGGGGT	0.552																																					p.P475P		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C1425T						.						89	88	88					3																	122642473		2203	4300	6503	SO:0001819	synonymous_variant	54437	exon10			GAAATTGGGGATG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.1263C>T	chr3.hg19:g.122642473G>A		82.0	0.0		93.0	5.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	hg19	CCDS35491.1																																																																																			.	.		0.552	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		A	122642473	G	A	122642473	2	1	115	1	0	0	0	0	0	0	0	1	14053	1335	47	3		3	SEMA5B	3	122642473	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	1229081	122642473	75379957	84	19623										
ZNF148	7707	hgsc.bcm.edu	37	chr3	124996586	124996586	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcaccagtatgaatcttctcAtgtctctgaagcaggtactt	7	10	4	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:124996586A>G	ENST00000360647.4	-	7	1136	c.651T>C	c.(649-651)caT>caC	p.H217H	ZNF148_ENST00000497929.1_5'UTR|SLC12A8_ENST00000423114.2_Missense_Mutation_p.M41T|ZNF148_ENST00000485866.1_Silent_p.H217H|ZNF148_ENST00000544464.1_Silent_p.H12H|ZNF148_ENST00000484491.1_Silent_p.H217H|ZNF148_ENST00000468369.1_Silent_p.H25H|ZNF148_ENST00000492394.1_Silent_p.H217H	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	217					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						GAATCTTCTCATGTCTCTGAA	0.343																																					p.H217H		Atlas-SNP	.											.	ZNF148	84	.	0			c.T651C						.						112	102	105					3																	124996586		2203	4299	6502	SO:0001819	synonymous_variant	7707	exon7			CTTCTCATGTCTC	U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"Zinc fingers, C2H2-type"	12933	protein-coding gene	gene with protein product		601897	"zinc finger protein 148 (pHZ-52)"			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.651T>C	chr3.hg19:g.124996586A>G		106.0	0.0		96.0	4.0	NM_021964	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Silent	SNP	ENST00000360647.4	hg19	CCDS3031.1	.	.	.	.	.	.	.	.	.	.	A	11.47	1.649150	0.29336	.	.	ENSG00000221955	ENST00000423114	D	0.87256	-2.23	5.04	-1.2	0.09554	.	.	.	.	.	T	0.74884	0.3775	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.56655	-0.7943	8	0.14252	T	0.57	-13.9577	10.1612	0.42853	0.5436:0.0:0.4564:0.0	.	41	A0AV02-2	.	T	41	ENSP00000404243:M41T	ENSP00000404243:M41T	M	-	2	0	SLC12A8	126479276	0.998000	0.40836	0.992000	0.48379	0.997000	0.91878	0.774000	0.26675	-0.360000	0.08138	0.459000	0.35465	ATG	.	.		0.343	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964		G	124996586	A	G	124996586	2	3	115	1	0	0	0	0	0	0	0	1	17749	214	8	2		2	ZNF148	3	124996586	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2354113	124996586	73025844	85	19624										
DNAJB8	165721	hgsc.bcm.edu	37	chr3	128181700	128181700	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgccgagaaggcccccctcAggccatggccccggccacca	11	20	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:128181700A>G	ENST00000469083.1	-	2	2946	c.389T>C	c.(388-390)cTg>cCg	p.L130P	DNAJB8-AS1_ENST00000471626.1_RNA|DNAJB8_ENST00000319153.3_Missense_Mutation_p.L130P			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	130					chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		GGCCCCCCTCAGGCCATGGCC	0.602																																					p.L130P		Atlas-SNP	.											.	DNAJB8	34	.	0			c.T389C						.						37	42	40					3																	128181700		2203	4300	6503	SO:0001583	missense	165721	exon3			CCCCTCAGGCCAT		CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"Heat shock proteins / DNAJ (HSP40)"	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.389T>C	chr3.hg19:g.128181700A>G	ENSP00000417418:p.Leu130Pro	70.0	0.0		86.0	4.0	NM_153330	B3KWV7	Missense_Mutation	SNP	ENST00000469083.1	hg19	CCDS3048.1	.	.	.	.	.	.	.	.	.	.	A	0.569	-0.842153	0.02671	.	.	ENSG00000179407	ENST00000469083;ENST00000319153	T;T	0.73897	-0.79;-0.79	4.75	4.75	0.60458	.	1.463120	0.04448	N	0.372090	T	0.66982	0.2845	L	0.33485	1.01	0.22034	N	0.999403	P	0.50943	0.94	B	0.41571	0.36	T	0.55585	-0.8118	10	0.31617	T	0.26	.	9.4475	0.38706	0.7577:0.2423:0.0:0.0	.	130	Q8NHS0	DNJB8_HUMAN	P	130	ENSP00000417418:L130P;ENSP00000316053:L130P	ENSP00000316053:L130P	L	-	2	0	DNAJB8	129664390	0.006000	0.16342	0.059000	0.19551	0.057000	0.15508	1.522000	0.35921	1.772000	0.52199	0.459000	0.35465	CTG	.	.		0.602	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330		G	128181700	A	G	128181700	3	3	115	1	0	0	0	0	1	0	0	0	4628	188	7	2	313	2	DNAJB8	3	128181700	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3185114	128181700	69840730	86	19625										
RPN1	6184	hgsc.bcm.edu	37	chr3	128356928	128356928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gatcaagagcaactgggagcTtgactgtgaagaatctccca	11	9	2	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:128356928T>C	ENST00000296255.3	-	3	395	c.347A>G	c.(346-348)aAg>aGg	p.K116R	RPN1_ENST00000497289.1_5'UTR	NM_002950.3	NP_002941.1	P04843	RPN1_HUMAN	ribophorin I	116					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|stomach(2)	13				GBM - Glioblastoma multiforme(114;0.189)		AACTGGGAGCTTGACTGTGAA	0.453			T	EVI1	AML																																p.K116R		Atlas-SNP	.		Dom	yes		3	3q21.3-q25.2	6184	ribophorin I		L	.	RPN1	39	.	0			c.A347G						.						78	71	73					3																	128356928		2203	4300	6503	SO:0001583	missense	6184	exon3			GGGAGCTTGACTG		CCDS3051.1	3q21.3	2013-03-06			ENSG00000163902	ENSG00000163902			10381	protein-coding gene	gene with protein product	"oligosaccharyltransferase 1 homolog (S. cerevisiae)", "oligosaccharyltransferase complex subunit (non-catalytic)"	180470					Standard	NM_002950		Approved	OST1	uc003ekr.1	P04843	OTTHUMG00000159691	ENST00000296255.3:c.347A>G	chr3.hg19:g.128356928T>C	ENSP00000296255:p.Lys116Arg	102.0	0.0		97.0	4.0	NM_002950	B2R5Z0|D3DNB6|Q68DT1	Missense_Mutation	SNP	ENST00000296255.3	hg19	CCDS3051.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.890737	0.33348	.	.	ENSG00000163902	ENST00000296255;ENST00000545956	.	.	.	5.68	1.99	0.26369	.	0.165039	0.56097	N	0.000039	T	0.36936	0.0985	N	0.20685	0.6	0.80722	D	1	B	0.09022	0.002	B	0.11329	0.006	T	0.06679	-1.0813	9	0.21540	T	0.41	-10.8861	8.7744	0.34753	0.0:0.2751:0.0:0.7249	.	116	P04843	RPN1_HUMAN	R	116;90	.	ENSP00000296255:K116R	K	-	2	0	RPN1	129839618	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	1.543000	0.36147	0.102000	0.17638	-1.205000	0.01647	AAG	.	.		0.453	RPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356934.2	NM_002950		C	128356928	T	C	128356928	3	2	115	1	0	0	0	0	1	0	0	0	13622	1609	56	2	1508	2	RPN1	3	128356928	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	175228	128356928	69665502	87	19626										
SR140	23350	hgsc.bcm.edu	37	chr3	142733211	142733211	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaaaatgagtacagctaagcGaactttaagtaaaaaggaac	8	5	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:142733211G>A	ENST00000473835.2	+	4	371	c.281G>A	c.(280-282)cGa>cAa	p.R94Q	U2SURP_ENST00000397933.2_5'UTR|U2SURP_ENST00000493598.2_Missense_Mutation_p.R94Q	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	94					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R94Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						ACAGCTAAGCGAACTTTAAGT	0.294																																					p.R94Q		Atlas-SNP	.											U2SURP,rectum,carcinoma,0,1	U2SURP	66	.	1	Substitution - Missense(1)	large_intestine(1)	c.G281A						.						53	49	51					3																	142733211		1811	4074	5885	SO:0001583	missense	23350	exon4			CTAAGCGAACTTT	BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"RNA binding motif (RRM) containing"	30855	protein-coding gene	gene with protein product	"functional spliceosome-associated protein a", "Ser/Arg-rich domain protein, 140 kDa", "U2 associated SR140 protein"					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.281G>A	chr3.hg19:g.142733211G>A	ENSP00000418563:p.Arg94Gln	190.0	1.0		173.0	7.0	NM_001080415	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Missense_Mutation	SNP	ENST00000473835.2	hg19	CCDS46928.1	.	.	.	.	.	.	.	.	.	.	G	36	5.670812	0.96754	.	.	ENSG00000163714	ENST00000473835;ENST00000493782;ENST00000319822;ENST00000493598;ENST00000465175	T;T	0.11495	2.77;2.79	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.35038	0.0918	M	0.78456	2.415	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;D;P	0.64776	0.929;0.913;0.806	T	0.01961	-1.1239	10	0.48119	T	0.1	-8.5639	19.7727	0.96373	0.0:0.0:1.0:0.0	.	94;94;94	B4DK81;O15042-2;O15042	.;.;SR140_HUMAN	Q	94;94;94;94;64	ENSP00000418563:R94Q;ENSP00000422011:R94Q	ENSP00000322376:R94Q	R	+	2	0	U2SURP	144215901	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.301000	0.96167	2.758000	0.94735	0.563000	0.77884	CGA	.	.		0.294	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415		A	142733211	G	A	142733211	3	1	115	1	0	0	0	0	1	0	0	0	15146	1058	37	1	295	1	SR140	3	142733211	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	14376283	142733211	55289219	88	19627										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaaacaaatgaatgatgcacAtcatggtggctggacaacaa	10	7	1	2	rs121913279		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.H1047R	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,adenocarcinoma,0,2044	PIK3CA	8460	.	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)	c.A3140G						.						99	89	92					3																	178952085		1912	4130	6042	SO:0001583	missense	5290	exon21			ATGCACATCATGG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	chr3.hg19:g.178952085A>G	ENSP00000263967:p.His1047Arg	122.0	0.0		126.0	47.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	.	.		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952085	A	G	178952085	3	3	115	1	0	0	0	0	1	0	0	0	11922	217	8	2	3218	2	PIK3CA	3	178952085	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	36218874	178952085	19070345	89	19628										
DNAJC19	131118	hgsc.bcm.edu	37	chr3	180702431	180702431	+	Frame_Shift_Del	DEL	T	T	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttcatcatacatttacttcaTtttttagcttgaccttctag							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:180702431delT	ENST00000382564.2	-	6	518	c.348delA	c.(346-348)aaafs	p.K116fs	DNAJC19_ENST00000491873.1_Frame_Shift_Del_p.K91fs|DNAJC19_ENST00000479269.1_Frame_Shift_Del_p.K91fs|DNAJC19_ENST00000486355.1_3'UTR	NM_145261.3	NP_660304.1	Q96DA6	TIM14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 19	116	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				cellular protein metabolic process (GO:0044267)|genitalia development (GO:0048806)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				large_intestine(2)|lung(1)	3	all_cancers(143;3.12e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-36)|OV - Ovarian serous cystadenocarcinoma(80;1.55e-22)			ATTTACTTCATTTTTTAGCTT	0.274																																					p.X117E		Pindel	.											.	DNAJC19	4	.	0			c.349delT						.						53	50	51					3																	180702431		2200	4289	6489	SO:0001589	frameshift_variant	131118	exon6			.		CCDS33895.1, CCDS54684.1	3q26.33	2014-09-17			ENSG00000205981	ENSG00000205981		"Heat shock proteins / DNAJ (HSP40)"	30528	protein-coding gene	gene with protein product		608977				19564938	Standard	NM_145261		Approved	TIMM14, Tim14, Pam18	uc003fkt.3	Q96DA6	OTTHUMG00000158180	ENST00000382564.2:c.348delA	chr3.hg19:g.180702431delT	ENSP00000372005:p.Lys116fs	291.0	0.0		241.0	10.0	NM_145261	B2R4B1|C9JBV1	Frame_Shift_Del	DEL	ENST00000382564.2	hg19	CCDS33895.1																																																																																			.	.		0.274	DNAJC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350336.1	NM_145261		-	180702431	T	-	180702431	7	5	115	1	0	1	0	1	0	0	0	0	4640	1490	52	0	6	0	DNAJC19	3	180702431	Frame_Shift_Del	DEL	T	TCGA-DD-A3A1-01A-11D-A20W-10	1750346	180702431	17319999	90	19629										
IGF2BP2	10644	hgsc.bcm.edu	37	chr3	185410534	185410534	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtgacgttgacaacggcggtTtctgtgtctgtgttgactag	14	7	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:185410534T>C	ENST00000382199.2	-	5	452	c.357A>G	c.(355-357)gaA>gaG	p.E119E	IGF2BP2_ENST00000457616.2_Silent_p.E125E|IGF2BP2_ENST00000421047.2_Silent_p.E62E|IGF2BP2_ENST00000346192.3_Silent_p.E119E	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	119	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			CAACGGCGGTTTCTGTGTCTG	0.358																																					p.E119E		Atlas-SNP	.											.	IGF2BP2	69	.	0			c.A357G						.						127	122	124					3																	185410534		2203	4300	6503	SO:0001819	synonymous_variant	10644	exon5			GGCGGTTTCTGTG	BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792		"RNA binding motif (RRM) containing"	28867	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 2"	608289				10190901, 9891060	Standard	NM_001007225		Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.357A>G	chr3.hg19:g.185410534T>C		115.0	0.0		113.0	5.0	NM_001007225	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Silent	SNP	ENST00000382199.2	hg19	CCDS3273.2																																																																																			.	.		0.358	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548		C	185410534	T	C	185410534	2	2	115	1	0	0	0	0	0	0	0	1	7583	1838	64	2		2	IGF2BP2	3	185410534	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4708103	185410534	12611896	91	19630										
CLDN16	10686	hgsc.bcm.edu	37	chr3	190106065	190106065	+	Frame_Shift_Del	DEL	G	G	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgacacccgccacttaagtGgggccagggctggtgtctgc							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr3:190106065delG	ENST00000264734.2	+	1	405	c.157delG	c.(157-159)gggfs	p.G53fs	CLDN16_ENST00000456423.1_Frame_Shift_Del_p.G53fs|CLDN16_ENST00000468220.1_Intron	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	53					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		CCACTTAAGTGGGGCCAGGGC	0.502																																					p.S52fs		Pindel	.											.	CLDN16	59	.	0			c.156delT						.						146	129	135					3																	190106065		2203	4300	6503	SO:0001589	frameshift_variant	10686	exon1			.	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"Claudins"	2037	protein-coding gene	gene with protein product	"paracellin-1", "hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.157delG	chr3.hg19:g.190106065delG	ENSP00000264734:p.Gly53fs	204.0	0.0		211.0	10.0	NM_006580		Frame_Shift_Del	DEL	ENST00000264734.2	hg19	CCDS3296.1																																																																																			.	.		0.502	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580		-	190106065	G	-	190106065	7	5	115	1	0	1	0	1	0	0	0	0	3479	1348	47	0	159	0	CLDN16	3	190106065	Frame_Shift_Del	DEL	G	TCGA-DD-A3A1-01A-11D-A20W-10	4695531	190106065	7916365	92	19631										
TNIP2	79155	hgsc.bcm.edu	37	chr4	2746449	2746449	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gttccagcatctgcacccgcTccaacgcagcatcccgggcc	9	19	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:2746449T>C	ENST00000315423.7	-	4	967	c.881A>G	c.(880-882)gAg>gGg	p.E294G	TNIP2_ENST00000503235.1_Intron|TNIP2_ENST00000505186.1_5'UTR|TNIP2_ENST00000510267.1_Missense_Mutation_p.E187G	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTGCACCCGCTCCAACGCAGC	0.612																																					p.E294G		Atlas-SNP	.											.	TNIP2	28	.	0			c.A881G						.						38	43	42					4																	2746449		2203	4300	6503	SO:0001583	missense	79155	exon4			ACCCGCTCCAACG	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.881A>G	chr4.hg19:g.2746449T>C	ENSP00000321203:p.Glu294Gly	39.0	0.0		60.0	4.0	NM_024309		Missense_Mutation	SNP	ENST00000315423.7	hg19	CCDS3362.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.226462	0.79576	.	.	ENSG00000168884	ENST00000510267;ENST00000315423	T;T	0.48836	0.8;0.8	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.71904	0.3395	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.76173	-0.3056	10	0.56958	D	0.05	-41.3956	15.089	0.72177	0.0:0.0:0.0:1.0	.	294	Q8NFZ5	TNIP2_HUMAN	G	187;294	ENSP00000427613:E187G;ENSP00000321203:E294G	ENSP00000321203:E294G	E	-	2	0	TNIP2	2716247	1.000000	0.71417	1.000000	0.80357	0.420000	0.31355	7.206000	0.77891	2.159000	0.67721	0.454000	0.30748	GAG	.	.		0.612	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309		C	2746449	T	C	2746449	3	2	115	1	0	0	0	0	1	0	0	0	16330	1551	54	2	420	2	TNIP2	4	2746449	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10		2746449	188407827	93	19632										
SORCS2	57537	hgsc.bcm.edu	37	chr4	7730078	7730078	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttctctgcgtctttccagaTcaatttcaagtcatgcctct	5	13	6	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:7730078T>C	ENST00000507866.2	+	22	2980	c.2871T>C	c.(2869-2871)gaT>gaC	p.D957D	SORCS2_ENST00000329016.9_Splice_Site_p.D785D	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	957					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						TCTTTCCAGATCAATTTCAAG	0.607																																					p.D957D		Atlas-SNP	.											.	SORCS2	98	.	0			c.T2871C						.						59	63	62					4																	7730078		1966	4142	6108	SO:0001630	splice_region_variant	57537	exon22			TCCAGATCAATTT	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2870-1T>C	chr4.hg19:g.7730078T>C		92.0	0.0		107.0	5.0	NM_020777	Q9P2L7	Silent	SNP	ENST00000507866.2	hg19	CCDS47008.1																																																																																			.	.		0.607	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	Silent	C	7730078	T	C	7730078	5	2	115	1	0	0	0	0	0	0	1	0	14946	1449	50	2	2957	2	SORCS2	4	7730078	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4983629	7730078	183424198	94	19633										
NCAPG	64151	hgsc.bcm.edu	37	chr4	17839331	17839331	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cctgcatcttctcctttagcTgaaattgatatcacaaatgt	5	10	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:17839331T>C	ENST00000251496.2	+	16	2549	c.2373T>C	c.(2371-2373)gcT>gcC	p.A791A		NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	791					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		CTCCTTTAGCTGAAATTGATA	0.408																																					p.A791A		Atlas-SNP	.											.	NCAPG	76	.	0			c.T2373C						.						164	161	162					4																	17839331		2203	4300	6503	SO:0001819	synonymous_variant	64151	exon16			TTTAGCTGAAATT	AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"chromosome condensation protein G"	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.2373T>C	chr4.hg19:g.17839331T>C		68.0	0.0		80.0	4.0	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Silent	SNP	ENST00000251496.2	hg19	CCDS3424.1																																																																																			.	.		0.408	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346		C	17839331	T	C	17839331	2	2	115	1	0	0	0	0	0	0	0	1	10216	1567	55	2		2	NCAPG	4	17839331	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	10109253	17839331	173314945	95	19634										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20547710	20547710	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggaactctccaactacaaacAtttaacacttatgtgagtaa	5	9	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:20547710A>G	ENST00000504154.1	+	22	2585	c.2333A>G	c.(2332-2334)cAt>cGt	p.H778R	SLIT2_ENST00000509394.2_3'UTR|SLIT2_ENST00000503823.1_Missense_Mutation_p.H770R|SLIT2_ENST00000503837.1_Missense_Mutation_p.H774R|SLIT2_ENST00000273739.5_Missense_Mutation_p.H782R	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	778					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						AACTACAAACATTTAACACTT	0.363																																					p.H778R		Atlas-SNP	.											.	SLIT2	290	.	0			c.A2333G						.						111	103	106					4																	20547710		2203	4300	6503	SO:0001583	missense	9353	exon22			ACAAACATTTAAC	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.2333A>G	chr4.hg19:g.20547710A>G	ENSP00000422591:p.His778Arg	85.0	0.0		95.0	4.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	A	19.63	3.862963	0.71949	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	5.47	5.47	0.80525	.	0.043065	0.85682	D	0.000000	T	0.10423	0.0255	N	0.02120	-0.675	0.80722	D	1	B;B	0.33280	0.405;0.18	B;B	0.26094	0.039;0.066	T	0.28870	-1.0030	10	0.26408	T	0.33	.	15.8443	0.78876	1.0:0.0:0.0:0.0	.	770;778	O94813-3;O94813	.;SLIT2_HUMAN	R	770;778;782;774;774	ENSP00000427548:H770R;ENSP00000422591:H778R;ENSP00000273739:H782R;ENSP00000422261:H774R	ENSP00000273739:H782R	H	+	2	0	SLIT2	20156808	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.204000	0.77872	2.194000	0.70268	0.528000	0.53228	CAT	.	.		0.363	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			G	20547710	A	G	20547710	3	3	115	1	0	0	0	0	1	0	0	0	14755	217	8	2	2419	2	SLIT2	4	20547710	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2708379	20547710	170606566	96	19635										
GPR125	166647	hgsc.bcm.edu	37	chr4	22425934	22425934	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cacaggacacgttcatcagcCaacatgatgttacttgcaat	7	11	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:22425934C>T	ENST00000334304.5	-	11	1754	c.1485G>A	c.(1483-1485)ttG>ttA	p.L495L	GPR125_ENST00000502482.1_Silent_p.L495L|GPR125_ENST00000282943.5_5'UTR|GPR125_ENST00000508133.1_Silent_p.L269L	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	495					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				GTTCATCAGCCAACATGATGT	0.483																																					p.L495L		Atlas-SNP	.											.	GPR125	118	.	0			c.G1485A						.						136	119	125					4																	22425934		2203	4300	6503	SO:0001819	synonymous_variant	166647	exon11			ATCAGCCAACATG	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.1485G>A	chr4.hg19:g.22425934C>T		239.0	0.0		213.0	88.0	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Silent	SNP	ENST00000334304.5	hg19	CCDS33964.1																																																																																			.	.		0.483	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			T	22425934	C	T	22425934	2	4	115	1	0	0	0	0	0	0	0	1	6647	593	21	3		3	GPR125	4	22425934	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	1878224	22425934	168728342	97	19636										
GPR125	166647	hgsc.bcm.edu	37	chr4	22439915	22439915	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgtttaccaccctctctggaGgacagtactgtgcagaactc	9	12	1	1	rs147843055		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:22439915G>C	ENST00000334304.5	-	8	1318	c.1049C>G	c.(1048-1050)cCt>cGt	p.P350R	GPR125_ENST00000502482.1_Missense_Mutation_p.P350R|GPR125_ENST00000282943.5_5'UTR|GPR125_ENST00000508133.1_Missense_Mutation_p.P124R	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	350					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				CCTCTCTGGAGGACAGTACTG	0.448																																					p.P350R		Atlas-SNP	.											GPR125,colon,carcinoma,0,2	GPR125	118	.	0			c.C1049G						.						164	144	150					4																	22439915		2203	4300	6503	SO:0001583	missense	166647	exon8			TCTGGAGGACAGT	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.1049C>G	chr4.hg19:g.22439915G>C	ENSP00000334952:p.Pro350Arg	252.0	0.0		221.0	0.0	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	hg19	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.150664	0.78001	.	.	ENSG00000152990	ENST00000334304;ENST00000508133;ENST00000502482;ENST00000514129	T;T;T	0.55413	0.52;0.52;0.52	5.6	5.6	0.85130	GPCR, family 2, extracellular hormone receptor domain (1);	0.054916	0.85682	D	0.000000	T	0.72415	0.3457	M	0.69823	2.125	0.54753	D	0.999983	D;D;D;P	0.65815	0.995;0.983;0.962;0.912	D;P;P;P	0.65443	0.935;0.905;0.605;0.611	T	0.74680	-0.3584	10	0.87932	D	0	-24.3783	19.618	0.95643	0.0:0.0:1.0:0.0	.	225;350;124;350	Q8IWK6-3;Q8IWK6-2;Q8IWK6-4;Q8IWK6	.;.;.;GP125_HUMAN	R	350;124;350;86	ENSP00000334952:P350R;ENSP00000422606:P124R;ENSP00000421006:P350R	ENSP00000334952:P350R	P	-	2	0	GPR125	22049013	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	4.196000	0.58407	2.635000	0.89317	0.650000	0.86243	CCT	.	.		0.448	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			C	22439915	G	C	22439915	3	2	115	1	0	0	0	0	1	0	0	0	6647	1000	35	4	2964	4	GPR125	4	22439915	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	13981	22439915	168714361	98	19637										
PI4K2B	55300	hgsc.bcm.edu	37	chr4	25256736	25256736	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agaagagccttatggtcaacTcaatccaaaatggaccaaat	7	9	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:25256736T>C	ENST00000264864.6	+	3	662	c.473T>C	c.(472-474)cTc>cCc	p.L158P	PI4K2B_ENST00000512921.1_Missense_Mutation_p.L62P	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	158	PI3K/PI4K.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.L158P(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				TATGGTCAACTCAATCCAAAA	0.393																																					p.L158P		Atlas-SNP	.											PI4K2B,NS,carcinoma,0,1	PI4K2B	42	.	1	Substitution - Missense(1)	kidney(1)	c.T473C						.						53	51	52					4																	25256736		2203	4300	6503	SO:0001583	missense	55300	exon3			GTCAACTCAATCC	AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.473T>C	chr4.hg19:g.25256736T>C	ENSP00000264864:p.Leu158Pro	71.0	1.0		94.0	4.0	NM_018323	Q9NUW2	Missense_Mutation	SNP	ENST00000264864.6	hg19	CCDS3433.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.646763	0.87958	.	.	ENSG00000038210	ENST00000512921;ENST00000264864;ENST00000537420	T	0.53640	0.61	6.17	6.17	0.99709	Phosphatidylinositol 3-/4-kinase, catalytic (1);	0.000000	0.85682	D	0.000000	T	0.76343	0.3974	M	0.93016	3.37	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80158	-0.1499	10	0.44086	T	0.13	-12.1399	16.8222	0.85835	0.0:0.0:0.0:1.0	.	158	Q8TCG2	P4K2B_HUMAN	P	62;158;127	ENSP00000264864:L158P	ENSP00000264864:L158P	L	+	2	0	PI4K2B	24865834	1.000000	0.71417	0.987000	0.45799	0.961000	0.63080	7.997000	0.88414	2.371000	0.80710	0.533000	0.62120	CTC	.	.		0.393	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323		C	25256736	T	C	25256736	3	2	115	1	0	0	0	0	1	0	0	0	11881	1551	54	2	483	2	PI4K2B	4	25256736	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2816821	25256736	165897540	99	19638										
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54256722	54256722	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggagtagaccttgatgcaccTggaagcattaatggagttcc	12	8	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:54256722T>C	ENST00000337488.6	+	7	626	c.432T>C	c.(430-432)ccT>ccC	p.P144P	FIP1L1_ENST00000306932.6_Silent_p.P129P|FIP1L1_ENST00000358575.5_Silent_p.P129P|FIP1L1_ENST00000507922.1_Silent_p.P129P|FIP1L1_ENST00000507166.1_Silent_p.P144P	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	144	Necessary for stimulating PAPOLA activity.|Sufficient for interaction with CPSF4.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TTGATGCACCTGGAAGCATTA	0.363			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.P144P		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.T432C						.						114	114	114					4																	54256722		2203	4300	6503	SO:0001819	synonymous_variant	81608	exon7			TGCACCTGGAAGC	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.432T>C	chr4.hg19:g.54256722T>C		101.0	0.0		88.0	4.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Silent	SNP	ENST00000337488.6	hg19	CCDS3491.1																																																																																			.	.		0.363	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		C	54256722	T	C	54256722	2	2	115	1	0	0	0	0	0	0	0	1	5904	1567	55	2		2	FIP1L1	4	54256722	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	28999986	54256722	136897554	100	19639										
KIT	3815	hgsc.bcm.edu	37	chr4	55565812	55565812	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctagccttcaaagctgtgccTgttgtgtctgtgtccaaagc	10	11	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:55565812T>C	ENST00000288135.5	+	4	733	c.636T>C	c.(634-636)ccT>ccC	p.P212P		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	212	Ig-like C2-type 3.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AAGCTGTGCCTGTTGTGTCTG	0.388		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.P212P		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT	7396	.	0			c.T636C						.						132	115	121					4																	55565812		2203	4300	6503	SO:0001819	synonymous_variant	3815	exon4	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	TGTGCCTGTTGTG	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.636T>C	chr4.hg19:g.55565812T>C		83.0	0.0		104.0	5.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	hg19	CCDS3496.1																																																																																			.	.		0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			C	55565812	T	C	55565812	2	2	115	1	0	0	0	0	0	0	0	1	8338	1567	55	2		2	KIT	4	55565812	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1309090	55565812	135588464	101	19640										
ALB	213	hgsc.bcm.edu	37	chr4	74277806	74277806	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	accaaagtccacacggaatgCtgccatggagatctgcttga	10	11	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:74277806C>T	ENST00000503124.1	+	5	564	c.357C>T	c.(355-357)tgC>tgT	p.C119C	ALB_ENST00000295897.4_Silent_p.C269C|ALB_ENST00000509063.1_Silent_p.C269C|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000415165.2_Silent_p.C77C|ALB_ENST00000401494.3_Silent_p.C154C			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACACGGAATGCTGCCATGGAG	0.458																																					p.C269C		Atlas-SNP	.											.	ALB	132	.	0			c.C807T						.						214	191	199					4																	74277806		2203	4300	6503	SO:0001819	synonymous_variant	213	exon7			GGAATGCTGCCAT	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.357C>T	chr4.hg19:g.74277806C>T		109.0	0.0		123.0	5.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000503124.1	hg19																																																																																				.	.		0.458	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		T	74277806	C	T	74277806	2	4	115	1	0	0	0	0	0	0	0	1	486	805	28	3		3	ALB	4	74277806	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	18711994	74277806	116876470	102	19641										
MTHFD2L	441024	hgsc.bcm.edu	37	chr4	75147266	75147266	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gttggagatgtggacttcgaAggtaataaaccaatatcttt	10	5	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:75147266A>G	ENST00000395759.2	+	7	957	c.930A>G	c.(928-930)gaA>gaG	p.E310E	MTHFD2L_ENST00000325278.6_Splice_Site_p.E252E	NM_001144978.1	NP_001138450.1	Q9H903	MTD2L_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	310					folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|tetrahydrofolate interconversion (GO:0035999)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NAD+) activity (GO:0004487)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)			central_nervous_system(1)|endometrium(1)|lung(4)|ovary(2)	8			all cancers(17;0.0101)|Lung(101;0.196)			TGGACTTCGAAGGTAATAAAC	0.333																																					p.E310E		Atlas-SNP	.											.	MTHFD2L	41	.	0			c.A930G						.						94	94	94					4																	75147266		2203	4300	6503	SO:0001630	splice_region_variant	441024	exon7			CTTCGAAGGTAAT	BC065771	CCDS47075.1	4q13.3	2011-08-03			ENSG00000163738	ENSG00000163738			31865	protein-coding gene	gene with protein product		614047				21163947	Standard	NM_001144978		Approved	MGC72244	uc011cbk.2	Q9H903	OTTHUMG00000157135	ENST00000395759.2:c.931+1A>G	chr4.hg19:g.75147266A>G		72.0	0.0		84.0	4.0	NM_001144978	Q6P079|Q8N560	Silent	SNP	ENST00000395759.2	hg19	CCDS47075.1																																																																																			.	.		0.333	MTHFD2L-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004346	Silent	G	75147266	A	G	75147266	5	3	115	1	0	0	0	0	0	0	1	0	9939	86	3	2	956	2	MTHFD2L	4	75147266	Splice_Site	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	869460	75147266	116007010	103	19642										
CNOT6L	246175	hgsc.bcm.edu	37	chr4	78697513	78697513	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	taaattctgcgaggatctggAggatcatatttttcctttgg	10	6	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:78697513A>G	ENST00000504123.1	-	2	169	c.39T>C	c.(37-39)ccT>ccC	p.P13P	CNOT6L_ENST00000264903.4_Silent_p.P13P|CNOT6L_ENST00000506166.1_5'UTR			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	13	Required for interaction with CNOT1, CNOT3 and CNOT7.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						GAGGATCTGGAGGATCATATT	0.358																																					p.P13P		Atlas-SNP	.											.	CNOT6L	57	.	0			c.T39C						.						84	76	78					4																	78697513		1816	4084	5900	SO:0001819	synonymous_variant	246175	exon2			ATCTGGAGGATCA	AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.39T>C	chr4.hg19:g.78697513A>G		97.0	0.0		125.0	5.0	NM_144571	Q9UF92	Silent	SNP	ENST00000504123.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.07	1.250433	0.22880	.	.	ENSG00000138767	ENST00000515506	.	.	.	5.72	3.23	0.37069	.	.	.	.	.	T	0.56790	0.2009	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51942	-0.8641	4	.	.	.	-5.2525	8.0722	0.30695	0.8128:0.0:0.0667:0.1205	.	.	.	.	P	42	.	.	S	-	1	0	CNOT6L	78916537	0.991000	0.36638	1.000000	0.80357	0.998000	0.95712	0.471000	0.22100	0.974000	0.38366	0.455000	0.32223	TCC	.	.		0.358	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1			G	78697513	A	G	78697513	2	3	115	1	0	0	0	0	0	0	0	1	3625	291	11	2		2	CNOT6L	4	78697513	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3550247	78697513	112456763	104	19643										
HNRNPD	3184	hgsc.bcm.edu	37	chr4	83280683	83280683	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaaaccccttgatcgccctgTgataggatctaacttcagag	8	11	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:83280683T>C	ENST00000313899.7	-	3	677	c.400A>G	c.(400-402)Aca>Gca	p.T134A	HNRNPD_ENST00000353341.4_Missense_Mutation_p.T134A|HNRNPD_ENST00000543098.1_Missense_Mutation_p.T82A|HNRNPD_ENST00000508119.1_5'Flank|HNRNPD_ENST00000541060.1_Intron|HNRNPD_ENST00000352301.4_Missense_Mutation_p.T115A	NM_031370.2	NP_112738.1	Q14103	HNRPD_HUMAN	heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)	134	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				circadian regulation of translation (GO:0097167)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|regulation of circadian rhythm (GO:0042752)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	7						GATCGCCCTGTGATAGGATCT	0.388																																					p.T134A		Atlas-SNP	.											.	HNRNPD	23	.	0			c.A400G						.						115	111	112					4																	83280683		2203	4300	6503	SO:0001583	missense	3184	exon3			GCCCTGTGATAGG	AF026126	CCDS3590.1, CCDS3591.1, CCDS3592.1	4q21	2013-02-12	2002-08-29	2008-04-18	ENSG00000138668	ENSG00000138668		"RNA binding motif (RRM) containing"	5036	protein-coding gene	gene with protein product		601324	"heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA-binding protein 1, 37kD)"	AUF1, HNRPD		9615222	Standard	NM_001003810		Approved		uc003hmm.1	Q14103	OTTHUMG00000130290	ENST00000313899.7:c.400A>G	chr4.hg19:g.83280683T>C	ENSP00000313199:p.Thr134Ala	110.0	0.0		100.0	4.0	NM_031370	A8K9J2|P07029|Q01858|Q14100|Q14101|Q14102|Q4W5A1|Q9UCE8|Q9UCE9	Missense_Mutation	SNP	ENST00000313899.7	hg19	CCDS3592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.7|27.7	4.859151|4.859151	0.91433|0.91433	.|.	.|.	ENSG00000138668|ENSG00000138668	ENST00000514671|ENST00000313899;ENST00000353341;ENST00000352301;ENST00000543098;ENST00000307213;ENST00000509263;ENST00000507010;ENST00000515432;ENST00000503822;ENST00000509107	.|T;T;T;T;T;T;T;T;T	.|0.79554	.|1.97;1.97;1.97;1.97;1.97;1.97;1.97;1.97;-1.28	5.86|5.86	5.86|5.86	0.93980|0.93980	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.90266|0.90266	0.6956|0.6956	M|M	0.82433|0.82433	2.59|2.59	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.987;0.999;0.993;0.995	.|D;D;D;D	.|0.72075	.|0.944;0.976;0.925;0.968	D|D	0.91532|0.91532	0.5243|0.5243	5|10	.|0.87932	.|D	.|0	.|.	16.5602|16.5602	0.84551|0.84551	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|115;134;115;134	.|Q14103-4;Q14103-3;Q14103-2;Q14103	.|.;.;.;HNRPD_HUMAN	R|A	37|134;134;115;82;109;67;134;36;115;88	.|ENSP00000313199:T134A;ENSP00000313327:T134A;ENSP00000305860:T115A;ENSP00000439380:T82A;ENSP00000420926:T67A;ENSP00000421952:T134A;ENSP00000426666:T36A;ENSP00000422615:T115A;ENSP00000425439:T88A	.|ENSP00000307544:T109A	H|T	-|-	2|1	0|0	HNRNPD|HNRNPD	83499707|83499707	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.606000|7.606000	0.82863|0.82863	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	CAC|ACA	.	.		0.388	HNRNPD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252630.2	NM_031370		C	83280683	T	C	83280683	3	2	115	1	0	0	0	0	1	0	0	0	7273	1696	59	2	691	2	HNRNPD	4	83280683	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4583170	83280683	107873593	105	19644										
FAM13A	10144	hgsc.bcm.edu	37	chr4	89652508	89652508	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtctgaaaaagttgtcttcaAaatcccgaagtttctttcga	7	8	4	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:89652508A>C	ENST00000264344.5	-	23	3122	c.2915T>G	c.(2914-2916)tTt>tGt	p.F972C	FAM13A-AS1_ENST00000500765.1_RNA|FAM13A-AS1_ENST00000511543.1_RNA|FAM13A_ENST00000513837.1_Missense_Mutation_p.F618C|FAM13A_ENST00000508369.1_Missense_Mutation_p.F646C|FAM13A_ENST00000511976.1_Missense_Mutation_p.F558C|FAM13A_ENST00000395002.2_Missense_Mutation_p.F618C|FAM13A_ENST00000503556.1_Missense_Mutation_p.F632C	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	972					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						GTTGTCTTCAAAATCCCGAAG	0.483																																					p.F972C		Atlas-SNP	.											.	FAM13A	181	.	0			c.T2915G						.						54	58	57					4																	89652508		2203	4300	6503	SO:0001583	missense	10144	exon23			TCTTCAAAATCCC	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.2915T>G	chr4.hg19:g.89652508A>C	ENSP00000264344:p.Phe972Cys	39.0	0.0		25.0	8.0	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	hg19	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.640699	0.87859	.	.	ENSG00000138640	ENST00000395002;ENST00000264344;ENST00000503556;ENST00000511976;ENST00000508369;ENST00000513837	T;T;T;T;T;T	0.63417	-0.04;0.96;0.27;0.41;0.26;0.27	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.80829	0.4698	M	0.83012	2.62	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.998;0.997;0.999;0.999;0.999	D	0.83885	0.0281	10	0.87932	D	0	.	15.7623	0.78096	1.0:0.0:0.0:0.0	.	618;558;972;618;632;646	O94988-6;E9PGM7;O94988;O94988-3;O94988-5;O94988-1	.;.;FA13A_HUMAN;.;.;.	C	618;972;632;558;646;618	ENSP00000378450:F618C;ENSP00000264344:F972C;ENSP00000427189:F632C;ENSP00000421914:F558C;ENSP00000421562:F646C;ENSP00000423252:F618C	ENSP00000264344:F972C	F	-	2	0	FAM13A	89871531	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.469000	0.73555	2.311000	0.77944	0.533000	0.62120	TTT	.	.		0.483	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			C	89652508	A	C	89652508	3	2	115	1	0	0	0	0	1	0	0	0	5457	14	1	5	164	5	FAM13A	4	89652508	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6371825	89652508	101501768	106	19645										
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90170622	90170622	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttcaggtccacctacaggagAggatgagtgactgaccaccc	11	12	1	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:90170622A>G	ENST00000609438.1	-	2	1158	c.640T>C	c.(640-642)Tct>Cct	p.S214P	GPRIN3_ENST00000333209.4_Missense_Mutation_p.S214P	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	214										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CCTACAGGAGAGGATGAGTGA	0.507																																					p.S214P		Atlas-SNP	.											.	GPRIN3	90	.	0			c.T640C						.						63	61	62					4																	90170622		2203	4300	6503	SO:0001583	missense	285513	exon2			CAGGAGAGGATGA	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.640T>C	chr4.hg19:g.90170622A>G	ENSP00000476603:p.Ser214Pro	73.0	0.0		78.0	5.0	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	hg19	CCDS34030.1	.	.	.	.	.	.	.	.	.	.	A	9.662	1.144353	0.21205	.	.	ENSG00000185477	ENST00000333209	T	0.10099	2.91	5.15	-4.64	0.03349	.	0.538685	0.14052	N	0.344654	T	0.04407	0.0121	N	0.24115	0.695	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.36432	-0.9748	10	0.25751	T	0.34	-0.1805	0.8212	0.01111	0.3496:0.1066:0.2706:0.2732	.	214	Q6ZVF9	GRIN3_HUMAN	P	214	ENSP00000328672:S214P	ENSP00000328672:S214P	S	-	1	0	GPRIN3	90389645	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.693000	0.05121	-0.565000	0.06061	0.528000	0.53228	TCT	.	.		0.507	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		G	90170622	A	G	90170622	3	3	115	1	0	0	0	0	1	0	0	0	6740	304	11	2	1694	2	GPRIN3	4	90170622	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	518114	90170622	100983654	107	19646										
RAP1GDS1	5910	hgsc.bcm.edu	37	chr4	99342470	99342470	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cgtttggtggaatggtgtgaAgccaaagatcatgctggtgt	15	5	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:99342470A>G	ENST00000408927.3	+	12	1478	c.1365A>G	c.(1363-1365)gaA>gaG	p.E455E	RAP1GDS1_ENST00000380158.4_Silent_p.E407E|RAP1GDS1_ENST00000339360.5_Silent_p.E456E|RAP1GDS1_ENST00000408900.3_Silent_p.E406E|RAP1GDS1_ENST00000453712.2_Silent_p.E455E|RAP1GDS1_ENST00000264572.7_Silent_p.E364E	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	455					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		AATGGTGTGAAGCCAAAGATC	0.438			T	NUP98	T-ALL																																p.E456E		Atlas-SNP	.		Dom	yes		4	4q21-q25	5910	"RAP1, GTP-GDP dissociation stimulator 1"		L	.	RAP1GDS1	61	.	0			c.A1368G						.						123	124	123					4																	99342470		1996	4177	6173	SO:0001819	synonymous_variant	5910	exon12			GTGTGAAGCCAAA		CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"Armadillo repeat containing"	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	ENST00000408927.3:c.1365A>G	chr4.hg19:g.99342470A>G		104.0	0.0		96.0	4.0	NM_001100426	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Silent	SNP	ENST00000408927.3	hg19	CCDS43253.1																																																																																			.	.		0.438	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363273.2	NM_001100426		G	99342470	A	G	99342470	2	3	115	1	0	0	0	0	0	0	0	1	13054	69	3	2		2	RAP1GDS1	4	99342470	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	9171848	99342470	91811806	108	19647										
PPP3CA	5530	hgsc.bcm.edu	37	chr4	101953446	101953446	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctttgcagggtttgcttcccTccagaaagtactccgctggg	11	12	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:101953446T>C	ENST00000394854.3	-	12	2000	c.1317A>G	c.(1315-1317)ggA>ggG	p.G439G	PPP3CA_ENST00000323055.6_Silent_p.G397G|PPP3CA_ENST00000507176.1_Silent_p.G341G|PPP3CA_ENST00000523694.2_Silent_p.G372G|PPP3CA_ENST00000512215.1_Silent_p.G207G|PPP3CA_ENST00000394853.4_Silent_p.G439G	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	439					calcineurin-NFAT signaling cascade (GO:0033173)|calcium ion transport (GO:0006816)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|multicellular organismal response to stress (GO:0033555)|negative regulation of insulin secretion (GO:0046676)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|protein import into nucleus (GO:0006606)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic transmission (GO:0050804)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|skeletal muscle fiber development (GO:0048741)|T cell activation (GO:0042110)|transition between fast and slow fiber (GO:0014883)	calcineurin complex (GO:0005955)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		TTTGCTTCCCTCCAGAAAGTA	0.542																																					p.G439G		Atlas-SNP	.											.	PPP3CA	51	.	0			c.A1317G						.						87	63	71					4																	101953446		2203	4300	6503	SO:0001819	synonymous_variant	5530	exon12			CTTCCCTCCAGAA		CCDS34037.1, CCDS47113.1, CCDS47114.1	4q24	2010-03-17	2010-03-05		ENSG00000138814	ENSG00000138814	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9314	protein-coding gene	gene with protein product	"calcineurin A alpha", "protein phosphatase 2B, catalytic subunit, alpha isoform"	114105	"protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)", "protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform"	CALN, CALNA		2848250, 1659808	Standard	NM_000944		Approved	CNA1, PPP2B	uc011cen.1	Q08209	OTTHUMG00000133839	ENST00000394854.3:c.1317A>G	chr4.hg19:g.101953446T>C		113.0	0.0		172.0	7.0	NM_000944	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Silent	SNP	ENST00000394854.3	hg19	CCDS34037.1																																																																																			.	.		0.542	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944		C	101953446	T	C	101953446	2	2	115	1	0	0	0	0	0	0	0	1	12409	1538	54	2		2	PPP3CA	4	101953446	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2610976	101953446	89200830	109	19648										
BANK1	55024	hgsc.bcm.edu	37	chr4	102751252	102751252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctttgctttgtggagtgaagAgttcagatcagctctatgaa	11	6	3	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:102751252A>G	ENST00000322953.4	+	2	632	c.358A>G	c.(358-360)Agt>Ggt	p.S120G	BANK1_ENST00000444316.2_Missense_Mutation_p.S90G|BANK1_ENST00000428908.1_Intron|BANK1_ENST00000508653.1_Intron|BANK1_ENST00000504592.1_Missense_Mutation_p.S105G	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	120	Interaction with ITPR2.				B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		TGGAGTGAAGAGTTCAGATCA	0.378																																					p.S120G		Atlas-SNP	.											.	BANK1	95	.	0			c.A358G						.						69	74	72					4																	102751252		2203	4300	6503	SO:0001583	missense	55024	exon2			GTGAAGAGTTCAG	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.358A>G	chr4.hg19:g.102751252A>G	ENSP00000320509:p.Ser120Gly	92.0	0.0		81.0	4.0	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	hg19	CCDS34038.1	.	.	.	.	.	.	.	.	.	.	A	5.909	0.351884	0.11182	.	.	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000444316	T;T;T	0.09445	2.98;2.98;2.98	5.18	3.98	0.46160	.	0.156955	0.38005	N	0.001850	T	0.13628	0.0330	L	0.44542	1.39	0.50813	D	0.999892	P;P	0.49559	0.925;0.925	P;P	0.47162	0.54;0.54	T	0.01621	-1.1310	10	0.45353	T	0.12	.	11.441	0.50096	0.8487:0.1513:0.0:0.0	.	120;105	Q8NDB2;Q8NDB2-2	BANK1_HUMAN;.	G	105;120;90	ENSP00000421443:S105G;ENSP00000320509:S120G;ENSP00000388817:S90G	ENSP00000320509:S120G	S	+	1	0	BANK1	102970275	1.000000	0.71417	0.004000	0.12327	0.006000	0.05464	6.428000	0.73383	0.791000	0.33826	-0.321000	0.08615	AGT	.	.		0.378	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		G	102751252	A	G	102751252	3	3	115	1	0	0	0	0	1	0	0	0	1309	304	11	2	364	2	BANK1	4	102751252	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	797806	102751252	88403024	110	19649										
COL25A1	84570	hgsc.bcm.edu	37	chr4	109895542	109895542	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccctaggtccctgatcacctTgttctccctgtagaatagaa	7	13	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:109895542T>C	ENST00000399132.1	-	8	1003	c.473A>G	c.(472-474)cAa>cGa	p.Q158R	COL25A1_ENST00000399126.1_Missense_Mutation_p.Q158R|COL25A1_ENST00000399127.1_Missense_Mutation_p.Q158R	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1									p.Q158L(2)		NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		CTGATCACCTTGTTCTCCCTG	0.373																																					p.Q158R		Atlas-SNP	.											COL25A1_ENST00000399126,NS,carcinoma,0,2	COL25A1	178	.	2	Substitution - Missense(2)	lung(2)	c.A473G						.						125	117	120					4																	109895542		1865	4095	5960	SO:0001583	missense	84570	exon7			TCACCTTGTTCTC	AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"Collagens"	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.473A>G	chr4.hg19:g.109895542T>C	ENSP00000382083:p.Gln158Arg	109.0	0.0		68.0	3.0	NM_198721		Missense_Mutation	SNP	ENST00000399132.1	hg19	CCDS43258.1	.	.	.	.	.	.	.	.	.	.	T	13.57	2.276237	0.40294	.	.	ENSG00000188517	ENST00000399132;ENST00000333642;ENST00000401873;ENST00000399127;ENST00000399126;ENST00000443653	D;T;D	0.95035	-3.59;0.88;-3.59	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.92724	0.7687	N	0.04787	-0.16	0.36613	D	0.875305	D;D	0.59357	0.981;0.985	D;D	0.74023	0.969;0.982	D	0.93430	0.6784	9	.	.	.	-7.2521	14.7834	0.69784	0.0:0.0:0.0:1.0	.	158;158	Q9BXS0-2;Q9BXS0	.;COPA1_HUMAN	R	158;160;154;158;158;160	ENSP00000382083:Q158R;ENSP00000382078:Q158R;ENSP00000382077:Q158R	.	Q	-	2	0	COL25A1	110114991	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.896000	0.63222	2.231000	0.72958	0.455000	0.32223	CAA	.	.		0.373	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518		C	109895542	T	C	109895542	3	2	115	1	0	0	0	0	1	0	0	0	3686	1812	63	2	1699	2	COL25A1	4	109895542	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	7144290	109895542	81258734	111	19650										
CASP6	839	hgsc.bcm.edu	37	chr4	110617568	110617568	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gatagcaaaactacctacccTcatgaattttgagcagtagt	7	9	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:110617568T>C	ENST00000265164.2	-	4	382	c.305A>G	c.(304-306)gAg>gGg	p.E102G	CASP6_ENST00000352981.3_Intron|CASP6_ENST00000510324.1_5'Flank|CASP6_ENST00000505486.1_Intron	NM_001226.3	NP_001217.2	P55212	CASP6_HUMAN	caspase 6, apoptosis-related cysteine peptidase	102					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|epithelial cell differentiation (GO:0030855)|proteolysis (GO:0006508)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)		CTACCTACCCTCATGAATTTT	0.333																																					p.E102G		Atlas-SNP	.											.	CASP6	25	.	0			c.A305G						.						92	86	88					4																	110617568		2201	4300	6501	SO:0001583	missense	839	exon4			CTACCCTCATGAA	U20536	CCDS3684.1, CCDS3685.1	4q25	2008-02-05	2005-08-17		ENSG00000138794	ENSG00000138794		"Caspases"	1507	protein-coding gene	gene with protein product		601532	"caspase 6, apoptosis-related cysteine protease"			8780721, 7796396	Standard	XM_005263271		Approved	MCH2	uc003hzn.1	P55212	OTTHUMG00000131914	ENST00000265164.2:c.305A>G	chr4.hg19:g.110617568T>C	ENSP00000265164:p.Glu102Gly	65.0	0.0		54.0	4.0	NM_001226	Q9BQE7	Missense_Mutation	SNP	ENST00000265164.2	hg19	CCDS3684.1	.	.	.	.	.	.	.	.	.	.	T	15.74	2.922484	0.52653	.	.	ENSG00000138794	ENST00000265164;ENST00000503684	T;T	0.23348	1.91;1.91	5.68	1.6	0.23607	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.438446	0.27168	N	0.020618	T	0.34193	0.0889	M	0.83953	2.67	0.58432	D	0.999993	P	0.37688	0.605	B	0.42738	0.396	T	0.23762	-1.0179	10	0.54805	T	0.06	.	8.1826	0.31319	0.121:0.0:0.2505:0.6285	.	102	P55212	CASP6_HUMAN	G	102;84	ENSP00000265164:E102G;ENSP00000427669:E84G	ENSP00000265164:E102G	E	-	2	0	CASP6	110837017	0.995000	0.38212	0.999000	0.59377	0.965000	0.64279	2.798000	0.47884	0.947000	0.37659	0.528000	0.53228	GAG	.	.		0.333	CASP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254866.1	NM_001226		C	110617568	T	C	110617568	3	2	115	1	0	0	0	0	1	0	0	0	2677	1551	54	2	592	2	CASP6	4	110617568	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	722026	110617568	80536708	112	19651										
NDST4	64579	hgsc.bcm.edu	37	chr4	115858629	115858629	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgagtgatgtggggccacagCatagcccatgttgattggta	14	7	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:115858629C>A	ENST00000264363.2	-	5	1930	c.1252G>T	c.(1252-1254)Gct>Tct	p.A418S		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	418	Heparan sulfate N-deacetylase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		GGGGCCACAGCATAGCCCATG	0.453																																					p.A418S		Atlas-SNP	.											.	NDST4	193	.	0			c.G1252T						.						121	104	110					4																	115858629		2203	4300	6503	SO:0001583	missense	64579	exon5			CCACAGCATAGCC	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.1252G>T	chr4.hg19:g.115858629C>A	ENSP00000264363:p.Ala418Ser	254.0	0.0		267.0	96.0	NM_022569	Q2KHM8	Missense_Mutation	SNP	ENST00000264363.2	hg19	CCDS3706.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.766399	0.69878	.	.	ENSG00000138653	ENST00000264363	T	0.42513	0.97	5.47	5.47	0.80525	.	0.094770	0.64402	D	0.000001	T	0.50446	0.1616	M	0.63208	1.945	0.80722	D	1	P	0.42556	0.783	P	0.46585	0.521	T	0.34925	-0.9809	10	0.20519	T	0.43	.	19.6922	0.96007	0.0:1.0:0.0:0.0	.	418	Q9H3R1	NDST4_HUMAN	S	418	ENSP00000264363:A418S	ENSP00000264363:A418S	A	-	1	0	NDST4	116078078	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	7.740000	0.84986	2.704000	0.92352	0.655000	0.94253	GCT	.	.		0.453	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		A	115858629	C	A	115858629	3	1	115	1	0	0	0	0	1	0	0	0	10267	710	25	3	1406	3	NDST4	4	115858629	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	5241061	115858629	75295647	113	19652										
LARP1B	55132	hgsc.bcm.edu	37	chr4	129028308	129028308	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	taataggcactgaaggatagCacagaagtagaaattgtgga	12	4	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:129028308C>A	ENST00000326639.6	+	9	1039	c.828C>A	c.(826-828)agC>agA	p.S276R	LARP1B_ENST00000441387.1_Missense_Mutation_p.S276R|LARP1B_ENST00000394288.3_Missense_Mutation_p.S276R|LARP1B_ENST00000427266.1_Missense_Mutation_p.S276R|LARP1B_ENST00000354456.3_5'UTR|LARP1B_ENST00000432347.2_Missense_Mutation_p.S276R|LARP1B_ENST00000512292.1_Missense_Mutation_p.S276R|LARP1B_ENST00000264584.5_Missense_Mutation_p.S229R	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	276	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						TGAAGGATAGCACAGAAGTAG	0.383																																					p.S276R		Atlas-SNP	.											.	LARP1B	120	.	0			c.C828A						.						58	62	60					4																	129028308		2203	4300	6503	SO:0001583	missense	55132	exon9			GGATAGCACAGAA		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.828C>A	chr4.hg19:g.129028308C>A	ENSP00000321997:p.Ser276Arg	123.0	0.0		111.0	47.0	NM_032239	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Missense_Mutation	SNP	ENST00000326639.6	hg19	CCDS3738.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.10|16.10	3.027507|3.027507	0.54683|0.54683	.|.	.|.	ENSG00000138709|ENSG00000138709	ENST00000507377|ENST00000326639;ENST00000512292;ENST00000508819;ENST00000394288;ENST00000432347;ENST00000264584;ENST00000441387;ENST00000427266	.|T;T;T;T;T;T;T;T	.|0.58358	.|0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34	5.38|5.38	3.51|3.51	0.40186|0.40186	.|Winged helix-turn-helix transcription repressor DNA-binding (1);RNA-binding protein Lupus La (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.80177|0.80177	0.4575|0.4575	H|H	0.99117|0.99117	4.435|4.435	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|1.0;0.999;0.998;0.998	T|T	0.80665|0.80665	-0.1281|-0.1281	5|10	.|0.87932	.|D	.|0	.|.	4.4731|4.4731	0.11722|0.11722	0.0:0.6006:0.0:0.3994|0.0:0.6006:0.0:0.3994	.|.	.|276;276;276;276	.|Q659C4;G3XAJ5;Q659C4-3;G3V0E9	.|LAR1B_HUMAN;.;.;.	N|R	245|276;276;229;276;276;229;276;276	.|ENSP00000321997:S276R;ENSP00000422850:S276R;ENSP00000427281:S229R;ENSP00000377829:S276R;ENSP00000390395:S276R;ENSP00000264584:S229R;ENSP00000396521:S276R;ENSP00000403586:S276R	.|ENSP00000264584:S229R	H|S	+|+	1|3	0|2	LARP1B|LARP1B	129247758|129247758	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	0.813000|0.813000	0.27225|0.27225	1.500000|1.500000	0.48636|0.48636	0.655000|0.655000	0.94253|0.94253	CAC|AGC	.	.		0.383	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		A	129028308	C	A	129028308	3	1	115	1	0	0	0	0	1	0	0	0	8638	709	25	3	854	3	LARP1B	4	129028308	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	13169679	129028308	62125968	114	19653										
TLL1	7092	hgsc.bcm.edu	37	chr4	167020635	167020635	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atgtggagctctttgatggtCttgattcaacagctgtgggg	14	6	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr4:167020635C>G	ENST00000061240.2	+	20	3510	c.2863C>G	c.(2863-2865)Ctt>Gtt	p.L955V	TLL1_ENST00000507499.1_Missense_Mutation_p.L978V	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	955	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		CTTTGATGGTCTTGATTCAAC	0.448																																					p.L955V		Atlas-SNP	.											.	TLL1	194	.	0			c.C2863G						.						199	203	202					4																	167020635		2203	4300	6503	SO:0001583	missense	7092	exon20			GATGGTCTTGATT	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2863C>G	chr4.hg19:g.167020635C>G	ENSP00000061240:p.Leu955Val	266.0	0.0		290.0	104.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	hg19	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	C	2.910	-0.225583	0.06022	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	T;T	0.18174	2.23;2.23	5.54	4.7	0.59300	CUB (5);	0.145379	0.47093	U	0.000248	T	0.11367	0.0277	N	0.16602	0.42	0.80722	D	1	B;B	0.24317	0.101;0.081	B;B	0.31442	0.13;0.089	T	0.17899	-1.0354	10	0.17369	T	0.5	.	10.7403	0.46149	0.0:0.8542:0.0:0.1458	.	978;955	E9PD25;O43897	.;TLL1_HUMAN	V	955;978	ENSP00000061240:L955V;ENSP00000426082:L978V	ENSP00000061240:L955V	L	+	1	0	TLL1	167240085	0.021000	0.18746	0.123000	0.21794	0.006000	0.05464	1.892000	0.39748	1.342000	0.45619	-0.244000	0.11960	CTT	.	.		0.448	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			G	167020635	C	G	167020635	3	3	115	1	0	0	0	0	1	0	0	0	15960	913	32	4	2941	4	TLL1	4	167020635	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	37992327	167020635	24133641	115	19654										
MED10	84246	hgsc.bcm.edu	37	chr5	6374436	6374436	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgacactccttagagtcttaCcttcatggtgtcgatcttgc	8	11	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:6374436C>T	ENST00000255764.3	-	3	420		c.e3+1			NM_032286.2	NP_115662.2	Q9BTT4	MED10_HUMAN	mediator complex subunit 10						gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	RNA polymerase II transcription cofactor activity (GO:0001104)			kidney(1)|large_intestine(1)|ovary(1)|prostate(1)|urinary_tract(1)	5						TAGAGTCTTACCTTCATGGTG	0.418																																					.		Atlas-SNP	.											.	MED10	7	.	0			c.309+1G>A						.						170	164	166					5																	6374436		2203	4300	6503	SO:0001630	splice_region_variant	84246	exon4			GTCTTACCTTCAT		CCDS34134.1	5p15.31	2008-02-05	2007-07-30		ENSG00000133398	ENSG00000133398			28760	protein-coding gene	gene with protein product	"NUT2 homolog (S. cerevisiae)"	612382	"mediator of RNA polymerase II transcription, subunit 10 homolog (NUT2, S. cerevisiae)"			15657623, 15175163	Standard	NM_032286		Approved	TRG20, L6, MGC5309, NUT2	uc003jdo.3	Q9BTT4	OTTHUMG00000161682	ENST00000255764.3:c.309+1G>A	chr5.hg19:g.6374436C>T		186.0	0.0		264.0	58.0	NM_032286	C6G491	Splice_Site	SNP	ENST00000255764.3	hg19	CCDS34134.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.358031	0.82243	.	.	ENSG00000133398	ENST00000255764	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7542	0.91826	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MED10	6427436	1.000000	0.71417	0.998000	0.56505	0.914000	0.54420	7.149000	0.77396	2.735000	0.93741	0.655000	0.94253	.	.	.		0.418	MED10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365714.1	NM_032286	Intron	T	6374436	C	T	6374436	5	4	115	1	0	0	0	0	0	0	1	0	9435	521	18	3	105	3	MED10	5	6374436	Splice_Site	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10		6374436	174540824	116	19655										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32090198	32090198	+	Frame_Shift_Del	DEL	C	C	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggaggaccatctctacttcaCcccaaggccagcgaccagga							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:32090198delC	ENST00000438447.1	+	20	7032	c.6644delC	c.(6643-6645)accfs	p.T2215fs	PDZD2_ENST00000282493.3_Frame_Shift_Del_p.T2215fs			O15018	PDZD2_HUMAN	PDZ domain containing 2	2215					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CTCTACTTCACCCCAAGGCCA	0.617																																					p.T2215fs		Atlas-INDEL	.											.	PDZD2	306	.	0			c.6643delA						.						141	155	150					5																	32090198		2203	4300	6503	SO:0001589	frameshift_variant	23037	exon19			.	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.6644delC	chr5.hg19:g.32090198delC	ENSP00000402033:p.Thr2215fs	91.0	0.0		166.0	10.0	NM_178140	Q9BXD4	Frame_Shift_Del	DEL	ENST00000438447.1	hg19	CCDS34137.1																																																																																			.	.		0.617	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			-	32090198	C	-	32090198	7	5	115	1	0	1	0	1	0	0	0	0	11710	507	18	0	6718	0	PDZD2	5	32090198	Frame_Shift_Del	DEL	C	TCGA-DD-A3A1-01A-11D-A20W-10	25715762	32090198	148825062	117	19656										
IL7R	3575	hgsc.bcm.edu	37	chr5	35867499	35867499	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aattcttactgattggaaagAgcaatatatgtgtgaaggtt	10	3	1	3	rs199742437		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:35867499A>G	ENST00000303115.3	+	3	442	c.313A>G	c.(313-315)Agc>Ggc	p.S105G	IL7R_ENST00000343305.4_Missense_Mutation_p.S105G|IL7R_ENST00000511031.1_3'UTR|IL7R_ENST00000511982.1_Missense_Mutation_p.S105G|IL7R_ENST00000506850.1_Missense_Mutation_p.S105G	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	105					B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			GATTGGAAAGAGCAATATATG	0.373			"Mis, O"		"ALL, ETP ALL"		Severe combined immune deficiency																														p.S105G		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	.	IL7R	200	.	0			c.A313G						.						94	96	95					5																	35867499		2203	4300	6503	SO:0001583	missense	3575	exon3			GGAAAGAGCAATA	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.313A>G	chr5.hg19:g.35867499A>G	ENSP00000306157:p.Ser105Gly	70.0	0.0		100.0	26.0	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	hg19	CCDS3911.1	.	.	.	.	.	.	.	.	.	.	A	9.228	1.035063	0.19590	.	.	ENSG00000168685	ENST00000303115;ENST00000343305;ENST00000506850;ENST00000511982	T;T;T;T	0.76709	-1.04;-1.04;-1.04;1.39	5.7	3.18	0.36537	.	0.418548	0.28192	N	0.016249	T	0.73916	0.3648	M	0.62723	1.935	0.09310	N	1	B;D	0.71674	0.135;0.998	B;P	0.50162	0.027;0.633	T	0.62718	-0.6795	10	0.23302	T	0.38	-4.551	3.9495	0.09363	0.6719:0.0:0.1001:0.228	.	105;105	D6RGV2;P16871	.;IL7RA_HUMAN	G	105	ENSP00000306157:S105G;ENSP00000345819:S105G;ENSP00000421207:S105G;ENSP00000425309:S105G	ENSP00000306157:S105G	S	+	1	0	IL7R	35903256	0.306000	0.24490	0.073000	0.20177	0.009000	0.06853	1.654000	0.37334	0.983000	0.38602	0.528000	0.53228	AGC	.	.		0.373	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2			G	35867499	A	G	35867499	3	3	115	1	0	0	0	0	1	0	0	0	7714	304	11	2	323	2	IL7R	5	35867499	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3777301	35867499	145047761	118	19657										
PLCXD3	345557	hgsc.bcm.edu	37	chr5	41382499	41382499	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctggccagtaaaattcattgTctgagtggctaaccatttcc	8	10	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:41382499T>C	ENST00000377801.3	-	2	315	c.241A>G	c.(241-243)Aca>Gca	p.T81A	PLCXD3_ENST00000328457.3_Missense_Mutation_p.T81A			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	81	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						AAATTCATTGTCTGAGTGGCT	0.458																																					p.T81A		Atlas-SNP	.											.	PLCXD3	86	.	0			c.A241G						.						59	64	62					5																	41382499		2203	4300	6503	SO:0001583	missense	345557	exon2			TCATTGTCTGAGT		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.241A>G	chr5.hg19:g.41382499T>C	ENSP00000367032:p.Thr81Ala	70.0	0.0		121.0	5.0	NM_001005473	A6NL04	Missense_Mutation	SNP	ENST00000377801.3	hg19	CCDS34150.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.513612	0.64522	.	.	ENSG00000182836	ENST00000377801;ENST00000328457	T;T	0.62364	0.03;0.03	6.07	6.07	0.98685	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (2);	0.044920	0.85682	D	0.000000	T	0.65048	0.2654	N	0.16602	0.42	0.80722	D	1	D	0.57257	0.979	D	0.71414	0.973	T	0.62364	-0.6870	10	0.20519	T	0.43	-10.3218	16.6407	0.85098	0.0:0.0:0.0:1.0	.	81	Q63HM9	PLCX3_HUMAN	A	81	ENSP00000367032:T81A;ENSP00000333751:T81A	ENSP00000333751:T81A	T	-	1	0	PLCXD3	41418256	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	7.665000	0.83852	2.326000	0.78906	0.533000	0.62120	ACA	.	.		0.458	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875		C	41382499	T	C	41382499	3	2	115	1	0	0	0	0	1	0	0	0	12052	1667	58	2	732	2	PLCXD3	5	41382499	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	5515000	41382499	139532761	119	19658										
GHR	2690	hgsc.bcm.edu	37	chr5	42713594	42713594	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgggctaacagtgatgctatTtgtattcttattttctaaac	7	6	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:42713594T>C	ENST00000230882.4	+	8	1038	c.848T>C	c.(847-849)tTt>tCt	p.F283S	GHR_ENST00000537449.1_Missense_Mutation_p.F96S|GHR_ENST00000357703.3_Missense_Mutation_p.F261S	NM_000163.4|NM_001242399.2|NM_001242400.2|NM_001242401.3|NM_001242402.2|NM_001242403.2|NM_001242404.2|NM_001242405.2|NM_001242406.2	NP_000154.1|NP_001229328.1|NP_001229329.1|NP_001229330.1|NP_001229331.1|NP_001229332.1|NP_001229333.1|NP_001229334.1|NP_001229335.1	P10912	GHR_HUMAN	growth hormone receptor	283					2-oxoglutarate metabolic process (GO:0006103)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPK activity (GO:0000187)|allantoin metabolic process (GO:0000255)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|endocytosis (GO:0006897)|fatty acid metabolic process (GO:0006631)|growth hormone receptor signaling pathway (GO:0060396)|insulin-like growth factor receptor signaling pathway (GO:0048009)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|multicellular organismal metabolic process (GO:0044236)|oxaloacetate metabolic process (GO:0006107)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|receptor internalization (GO:0031623)|regulation of multicellular organism growth (GO:0040014)|response to cycloheximide (GO:0046898)|response to estradiol (GO:0032355)|succinate metabolic process (GO:0006105)|taurine metabolic process (GO:0019530)|valine metabolic process (GO:0006573)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|growth hormone receptor complex (GO:0070195)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine receptor activity (GO:0004896)|growth factor binding (GO:0019838)|peptide hormone binding (GO:0017046)|proline-rich region binding (GO:0070064)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			NS(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	GTGATGCTATTTGTATTCTTA	0.313																																					p.F290S		Atlas-SNP	.											.	GHR	94	.	0			c.T869C						.						177	179	178					5																	42713594		2202	4296	6498	SO:0001583	missense	2690	exon8			TGCTATTTGTATT		CCDS3940.1, CCDS56364.1, CCDS75239.1, CCDS75240.1	5p14-p12	2013-03-25			ENSG00000112964	ENSG00000112964		"Fibronectin type III domain containing"	4263	protein-coding gene	gene with protein product	"growth hormone binding protein"	600946					Standard	NM_001242460		Approved	GHBP	uc003jmt.3	P10912	OTTHUMG00000094791	ENST00000230882.4:c.848T>C	chr5.hg19:g.42713594T>C	ENSP00000230882:p.Phe283Ser	56.0	0.0		88.0	4.0	NM_001242399	Q9HCX2	Missense_Mutation	SNP	ENST00000230882.4	hg19	CCDS3940.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.059811	0.36373	.	.	ENSG00000112964	ENST00000230882;ENST00000357703;ENST00000356276;ENST00000537449	D;D;T	0.84873	-1.91;-1.77;-0.76	5.42	5.42	0.78866	.	0.167630	0.51477	D	0.000089	T	0.82084	0.4960	L	0.46741	1.465	0.32131	N	0.586786	D	0.54397	0.966	P	0.46479	0.518	D	0.85324	0.1086	10	0.49607	T	0.09	-11.7242	9.3428	0.38089	0.0:0.0803:0.0:0.9197	.	283	P10912	GHR_HUMAN	S	283;261;283;96	ENSP00000230882:F283S;ENSP00000350335:F261S;ENSP00000442206:F96S	ENSP00000230882:F283S	F	+	2	0	GHR	42749351	1.000000	0.71417	0.999000	0.59377	0.510000	0.34073	3.865000	0.56033	2.059000	0.61396	0.477000	0.44152	TTT	.	.		0.313	GHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211605.2	NM_000163		C	42713594	T	C	42713594	3	2	115	1	0	0	0	0	1	0	0	0	6379	1841	64	2	874	2	GHR	5	42713594	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1331095	42713594	138201666	120	19659										
CCDC125	202243	hgsc.bcm.edu	37	chr5	68578778	68578778	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttttctttattctcgtttgaAgcagtgtctttgtcttccaa	6	8	4	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:68578778A>G	ENST00000396496.2	-	12	1421	c.1314T>C	c.(1312-1314)gcT>gcC	p.A438A	CCDC125_ENST00000383374.2_3'UTR|CCDC125_ENST00000511257.1_Silent_p.A313A|CCDC125_ENST00000460090.1_5'UTR|CCDC125_ENST00000396499.1_Silent_p.A438A			Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	438						cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|urinary_tract(1)	19		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)		TCTCGTTTGAAGCAGTGTCTT	0.383																																					p.A438A		Atlas-SNP	.											.	CCDC125	41	.	0			c.T1314C						.						103	101	102					5																	68578778		2203	4300	6503	SO:0001819	synonymous_variant	202243	exon11			GTTTGAAGCAGTG	AB024691	CCDS4000.1, CCDS75255.1	5q13.2	2008-02-05			ENSG00000183323	ENSG00000183323			28924	protein-coding gene	gene with protein product		613781					Standard	XM_005248461		Approved	KENAE	uc003jvv.1	Q86Z20	OTTHUMG00000131259	ENST00000396496.2:c.1314T>C	chr5.hg19:g.68578778A>G		91.0	0.0		117.0	6.0	NM_176816	Q86Z19	Silent	SNP	ENST00000396496.2	hg19	CCDS4000.1																																																																																			.	.		0.383	CCDC125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254027.4	NM_176816		G	68578778	A	G	68578778	2	3	115	1	0	0	0	0	0	0	0	1	2763	59	3	2		2	CCDC125	5	68578778	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	25865184	68578778	112336482	121	19660										
DDX46	9879	hgsc.bcm.edu	37	chr5	134121198	134121198	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaactggctttacagattacTaaagagtgtaagaagttttc	9	5	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:134121198T>A	ENST00000354283.4	+	11	1521	c.1386T>A	c.(1384-1386)acT>acA	p.T462T	DDX46_ENST00000452510.2_Silent_p.T462T|DDX46_ENST00000509178.1_3'UTR			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	462	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.			TKECKKFS -> PKGVRSF (in Ref. 1; AAD43033). {ECO:0000305}.	mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TACAGATTACTAAAGAGTGTA	0.393																																					p.T462T	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.T1386A						.						154	155	155					5																	134121198		2203	4300	6503	SO:0001819	synonymous_variant	9879	exon11			GATTACTAAAGAG		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.1386T>A	chr5.hg19:g.134121198T>A		156.0	0.0		167.0	34.0	NM_014829	O94894|Q96EI0|Q9Y658	Silent	SNP	ENST00000354283.4	hg19	CCDS34240.1																																																																																			.	.		0.393	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		A	134121198	T	A	134121198	2	1	115	1	0	0	0	0	0	0	0	1	4366	1509	53	4		4	DDX46	5	134121198	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	65542420	134121198	46794062	122	19661										
PKD2L2	27039	hgsc.bcm.edu	37	chr5	137257346	137257346	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tttgcacaatttcgaattgtTcttggagattttaattttgc	7	5	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:137257346T>C	ENST00000508883.1	+	9	1376	c.1350T>C	c.(1348-1350)gtT>gtC	p.V450V	PKD2L2_ENST00000290431.5_Silent_p.V450V|PKD2L2_ENST00000502810.1_Silent_p.V428V|PKD2L2_ENST00000350250.4_Silent_p.V416V|PKD2L2_ENST00000508638.1_Intron			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	450					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTCGAATTGTTCTTGGAGATT	0.338																																					p.V450V		Atlas-SNP	.											.	PKD2L2	68	.	0			c.T1350C						.						138	125	129					5																	137257346		1798	4069	5867	SO:0001819	synonymous_variant	27039	exon9			AATTGTTCTTGGA	AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"Voltage-gated ion channels / Transient receptor potential cation channels"	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.1350T>C	chr5.hg19:g.137257346T>C		114.0	0.0		121.0	5.0	NM_014386	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Silent	SNP	ENST00000508883.1	hg19																																																																																				.	.		0.338	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		C	137257346	T	C	137257346	2	2	115	1	0	0	0	0	0	0	0	1	11977	1770	62	2		2	PKD2L2	5	137257346	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3136148	137257346	43657914	123	19662										
KDM3B	51780	hgsc.bcm.edu	37	chr5	137727543	137727543	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcccattgagatgccaactcTctcctctagccccacagagg	8	16	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:137727543T>C	ENST00000314358.5	+	8	2422	c.2222T>C	c.(2221-2223)cTc>cCc	p.L741P	KDM3B_ENST00000394866.1_Missense_Mutation_p.L397P|KDM3B_ENST00000542866.1_Intron	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	741	Ser-rich.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						ATGCCAACTCTCTCCTCTAGC	0.607																																					p.L741P		Atlas-SNP	.											.	KDM3B	177	.	0			c.T2222C						.						79	91	87					5																	137727543		2202	4300	6502	SO:0001583	missense	51780	exon8			CAACTCTCTCCTC	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.2222T>C	chr5.hg19:g.137727543T>C	ENSP00000326563:p.Leu741Pro	52.0	0.0		89.0	4.0	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	T	15.74	2.923032	0.52653	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866	T;T	0.77489	-0.53;-1.1	5.25	5.25	0.73442	.	0.376195	0.27122	N	0.020823	T	0.79811	0.4510	N	0.24115	0.695	0.80722	D	1	D;D	0.69078	0.997;0.995	D;P	0.65010	0.931;0.854	T	0.82141	-0.0604	10	0.56958	D	0.05	-24.5692	15.4446	0.75220	0.0:0.0:0.0:1.0	.	397;741	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	P	741;531;397	ENSP00000326563:L741P;ENSP00000378335:L397P	ENSP00000326563:L741P	L	+	2	0	KDM3B	137755442	0.478000	0.25917	1.000000	0.80357	0.998000	0.95712	2.591000	0.46163	2.111000	0.64477	0.533000	0.62120	CTC	.	.		0.607	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		C	137727543	T	C	137727543	3	2	115	1	0	0	0	0	1	0	0	0	8136	1551	54	2	2252	2	KDM3B	5	137727543	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	470197	137727543	43187717	124	19663										
SIL1	64374	hgsc.bcm.edu	37	chr5	138362514	138362514	+	Frame_Shift_Del	DEL	A	A	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tggacataatattcaagatcAaagagcgcagcaatcttctc							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:138362514delA	ENST00000394817.2	-	6	760	c.621delT	c.(619-621)tttfs	p.F207fs	CTB-46B19.2_ENST00000512875.2_RNA|SIL1_ENST00000509534.1_Frame_Shift_Del_p.F214fs|SIL1_ENST00000265195.5_Frame_Shift_Del_p.F207fs	NM_022464.4	NP_071909.1	Q9H173	SIL1_HUMAN	SIL1 nucleotide exchange factor	207	Interaction with HSPA5 and localization to the endoplasmic reticulum. {ECO:0000250}.				intracellular protein transport (GO:0006886)|protein folding (GO:0006457)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ATTCAAGATCAAAGAGCGCAG	0.408									Marinesco-Sjgren syndrome																												p.D208fs		Atlas-INDEL	.											.	SIL1	31	.	0			c.622delG						.						117	109	112					5																	138362514		2203	4300	6503	SO:0001589	frameshift_variant	64374	exon7	Familial Cancer Database	Marinesco-Sjogren syndrome	.	AK075177	CCDS4209.1	5q31	2013-08-21	2013-08-21		ENSG00000120725	ENSG00000120725			24624	protein-coding gene	gene with protein product		608005	"Marinesco-Sjogren syndrome", "SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae)"	MSS		11101517, 12356756, 16282977	Standard	XM_006714671		Approved	BAP, ULG5	uc003ldp.3	Q9H173	OTTHUMG00000129226	ENST00000394817.2:c.621delT	chr5.hg19:g.138362514delA	ENSP00000378294:p.Phe207fs	108.0	0.0		194.0	13.0	NM_001037633	D3DQC2|Q8N2L3	Frame_Shift_Del	DEL	ENST00000394817.2	hg19	CCDS4209.1																																																																																			.	.		0.408	SIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251319.1	NM_022464		-	138362514	A	-	138362514	7	5	115	1	0	1	0	1	0	0	0	0	14336	127	5	0	784	0	SIL1	5	138362514	Frame_Shift_Del	DEL	A	TCGA-DD-A3A1-01A-11D-A20W-10	634971	138362514	42552746	125	19664										
ANKHD1-EIF4EBP3	8637	hgsc.bcm.edu	37	chr5	139928556	139928556	+	Frame_Shift_Del	DEL	C	C	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	actcacccattgcccggacaCccccctgctgcctccctcag							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:139928556delC	ENST00000310331.2	+	2	241	c.169delC	c.(169-171)cccfs	p.P58fs	ANKHD1-EIF4EBP3_ENST00000532219.1_Frame_Shift_Del_p.T2582fs|SRA1_ENST00000520427.1_5'Flank|ANKHD1_ENST00000297183.6_Frame_Shift_Del_p.T2582fs	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3	58					negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCCCGGACACCCCCCTGCTG	0.582																																					p.T2582fs		Pindel	.											.	ANKHD1-EIF4EBP3	179	.	0			c.7744delA						.						43	43	43					5																	139928556		2203	4300	6503	SO:0001589	frameshift_variant	404734	exon35			.	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498	ENST00000310331.2:c.169delC	chr5.hg19:g.139928556delC	ENSP00000308472:p.Pro58fs	146.0	0.0		238.0	10.0	NM_020690		Frame_Shift_Del	DEL	ENST00000310331.2	hg19	CCDS4226.1																																																																																			.	.		0.582	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732		-	139928556	C	-	139928556	7	5	115	1	0	1	0	1	0	0	0	0	629	507	18	0	7883	0	ANKHD1-EIF4EBP3	5	139928556	Frame_Shift_Del	DEL	C	TCGA-DD-A3A1-01A-11D-A20W-10	1566042	139928556	40986704	126	19665										
PCDHB15	56121	hgsc.bcm.edu	37	chr5	140627100	140627100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aggacaatggcgagcctccgCgctcggccaccgccacgctg	13	17	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:140627100C>T	ENST00000231173.3	+	1	1954	c.1954C>T	c.(1954-1956)Cgc>Tgc	p.R652C		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	652	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGAGCCTCCGCGCTCGGCCAC	0.706																																					p.R652C		Atlas-SNP	.											.	PCDHB15	138	.	0			c.C1954T						.						33	36	35					5																	140627100		2168	4243	6411	SO:0001583	missense	56121	exon1			CCTCCGCGCTCGG	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1954C>T	chr5.hg19:g.140627100C>T	ENSP00000231173:p.Arg652Cys	65.0	0.0		95.0	4.0	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	hg19	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	C	11.29	1.595627	0.28445	.	.	ENSG00000113248	ENST00000231173	T	0.55234	0.53	4.36	3.46	0.39613	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.56761	0.2007	M	0.82323	2.585	0.41476	D	0.988137	B	0.19200	0.034	B	0.19148	0.024	T	0.60667	-0.7218	9	0.62326	D	0.03	.	13.426	0.61026	0.1586:0.8414:0.0:0.0	.	652	Q9Y5E8	PCDBF_HUMAN	C	652	ENSP00000231173:R652C	ENSP00000231173:R652C	R	+	1	0	PCDHB15	140607284	0.019000	0.18553	0.902000	0.35471	0.192000	0.23643	2.843000	0.48238	0.951000	0.37770	0.549000	0.68633	CGC	.	.		0.706	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		T	140627100	C	T	140627100	3	4	115	1	0	0	0	0	1	0	0	0	11549	768	27	1	1956	1	PCDHB15	5	140627100	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	698544	140627100	40288160	127	19666										
G3BP1	10146	hgsc.bcm.edu	37	chr5	151179526	151179526	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcaaagagtgcgagaacaacGaataaatattcctccccaaa	6	10	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:151179526G>A	ENST00000394123.3	+	9	1065	c.920G>A	c.(919-921)cGa>cAa	p.R307Q	G3BP1_ENST00000356245.3_Missense_Mutation_p.R307Q|G3BP1_ENST00000543466.1_Missense_Mutation_p.R125Q			Q13283	G3BP1_HUMAN	GTPase activating protein (SH3 domain) binding protein 1	307					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Ras protein signal transduction (GO:0007265)|transport (GO:0006810)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)	p.R307Q(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|skin(3)|urinary_tract(2)	29		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			CGAGAACAACGAATAAATATT	0.463																																					p.R307Q		Atlas-SNP	.											G3BP1,rectum,carcinoma,0,1	G3BP1	53	.	1	Substitution - Missense(1)	large_intestine(1)	c.G920A						.						38	40	39					5																	151179526		2203	4300	6503	SO:0001583	missense	10146	exon9			AACAACGAATAAA	BC006997	CCDS4319.1	5q33.1	2013-02-12	2006-11-01		ENSG00000145907	ENSG00000145907		"RNA binding motif (RRM) containing"	30292	protein-coding gene	gene with protein product	"Ras-GTPase-activating protein SH3-domain-binding protein"	608431				8649363, 9889278	Standard	NM_005754		Approved	HDH-VIII, G3BP	uc003lum.3	Q13283	OTTHUMG00000130123	ENST00000394123.3:c.920G>A	chr5.hg19:g.151179526G>A	ENSP00000377681:p.Arg307Gln	105.0	1.0		158.0	9.0	NM_005754	Q5HYE9	Missense_Mutation	SNP	ENST00000394123.3	hg19	CCDS4319.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390704	0.62066	.	.	ENSG00000145907	ENST00000394123;ENST00000543466;ENST00000356245;ENST00000274596	T;T;T	0.73681	-0.66;-0.77;-0.66	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.70727	0.3257	M	0.80183	2.485	0.58432	D	0.999999	P	0.37997	0.614	B	0.24394	0.053	T	0.72424	-0.4298	10	0.13108	T	0.6	-18.7807	18.4052	0.90533	0.0:0.0:1.0:0.0	.	307	Q13283	G3BP1_HUMAN	Q	307;125;307;149	ENSP00000377681:R307Q;ENSP00000445035:R125Q;ENSP00000348578:R307Q	ENSP00000274596:R149Q	R	+	2	0	G3BP1	151159719	1.000000	0.71417	0.978000	0.43139	0.965000	0.64279	6.851000	0.75425	2.415000	0.81967	0.650000	0.86243	CGA	.	.		0.463	G3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252431.1	NM_005754		A	151179526	G	A	151179526	3	1	115	1	0	0	0	0	1	0	0	0	6149	1058	37	1	950	1	G3BP1	5	151179526	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	10552426	151179526	29735734	128	19667										
GABRB2	2561	hgsc.bcm.edu	37	chr5	160763717	160763717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aagttcaattttcgttactcCtgttactgcattatcatcgc	5	10	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:160763717C>T	ENST00000393959.1	-	6	600	c.601G>A	c.(601-603)Gga>Aga	p.G201R	GABRB2_ENST00000517901.1_Missense_Mutation_p.G138R|GABRB2_ENST00000353437.6_Missense_Mutation_p.G201R|GABRB2_ENST00000520240.1_Missense_Mutation_p.G201R|GABRB2_ENST00000274547.2_Missense_Mutation_p.G201R|GABRB2_ENST00000517547.1_Missense_Mutation_p.G41R			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	201					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTCGTTACTCCTGTTACTGCA	0.373																																					p.G201R		Atlas-SNP	.											.	GABRB2	161	.	0			c.G601A						.						134	132	133					5																	160763717		2203	4300	6503	SO:0001583	missense	2561	exon7			TTACTCCTGTTAC		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.601G>A	chr5.hg19:g.160763717C>T	ENSP00000377531:p.Gly201Arg	70.0	0.0		78.0	4.0	NM_021911	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Missense_Mutation	SNP	ENST00000393959.1	hg19	CCDS4355.1	.	.	.	.	.	.	.	.	.	.	C	34	5.294104	0.95546	.	.	ENSG00000145864	ENST00000393959;ENST00000274547;ENST00000353437;ENST00000520240;ENST00000517901;ENST00000517547	T;T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18;-1.18	5.56	5.56	0.83823	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.86952	0.6057	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;1.0	D;D;D;D	0.97110	1.0;0.993;0.995;0.997	D	0.83514	0.0082	10	0.25106	T	0.35	.	19.5644	0.95388	0.0:1.0:0.0:0.0	.	41;138;201;201	B7Z279;E7EV50;P47870;P47870-1	.;.;GBRB2_HUMAN;.	R	201;201;201;201;138;41	ENSP00000377531:G201R;ENSP00000274547:G201R;ENSP00000274546:G201R;ENSP00000429320:G201R;ENSP00000430532:G138R;ENSP00000429750:G41R	ENSP00000274547:G201R	G	-	1	0	GABRB2	160696295	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.639000	0.83342	2.617000	0.88574	0.655000	0.94253	GGA	.	.		0.373	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1			T	160763717	C	T	160763717	3	4	115	1	0	0	0	0	1	0	0	0	6175	690	24	3	957	3	GABRB2	5	160763717	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	9584191	160763717	20151543	129	19668										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167675302	167675302	+	Frame_Shift_Del	DEL	C	C	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaacgtgggcaaggagccggCcccctttaacctgtatatgt							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:167675302delC	ENST00000518659.1	+	27	7397	c.7358delC	c.(7357-7359)gccfs	p.A2453fs	TENM2_ENST00000545108.1_Frame_Shift_Del_p.A2452fs|TENM2_ENST00000520394.1_Frame_Shift_Del_p.A2214fs|TENM2_ENST00000519204.1_Frame_Shift_Del_p.A2332fs|TENM2_ENST00000403607.2_Frame_Shift_Del_p.A2277fs	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2453					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										AAGGAGCCGGCCCCCTTTAAC	0.512																																					p.A2444fs		Atlas-INDEL	.											.	.	.	.	0			c.7330delG						.						60	61	61					5																	167675302		1939	4140	6079	SO:0001589	frameshift_variant	57451	exon27			.	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.7358delC	chr5.hg19:g.167675302delC	ENSP00000429430:p.Ala2453fs	82.0	0.0		121.0	10.0	NM_001122679	Q9ULU2	Frame_Shift_Del	DEL	ENST00000518659.1	hg19																																																																																				.	.		0.512	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		-	167675302	C	-	167675302	7	5	115	1	0	1	0	1	0	0	0	0	10844	739	26	0	7437	0	ODZ2	5	167675302	Frame_Shift_Del	DEL	C	TCGA-DD-A3A1-01A-11D-A20W-10	6911585	167675302	13239958	130	19669										
STC2	8614	hgsc.bcm.edu	37	chr5	172752906	172752906	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tccagcgttgtgcagaaaagTcatgcaaatcccatgtaagc	9	10	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:172752906T>C	ENST00000265087.4	-	2	1568	c.259A>G	c.(259-261)Act>Gct	p.T87A	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	87					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TGCAGAAAAGTCATGCAAATC	0.463																																					p.T87A		Atlas-SNP	.											.	STC2	59	.	0			c.A259G						.						271	295	287					5																	172752906		2203	4300	6503	SO:0001583	missense	8614	exon2			GAAAAGTCATGCA	AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.259A>G	chr5.hg19:g.172752906T>C	ENSP00000265087:p.Thr87Ala	73.0	0.0		131.0	6.0	NM_003714		Missense_Mutation	SNP	ENST00000265087.4	hg19	CCDS4388.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	31|31	5.069789|5.069789	0.93950|0.93950	.|.	.|.	ENSG00000113739|ENSG00000113739	ENST00000520648|ENST00000265087;ENST00000518455	.|.	.|.	.|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	.|0.047193	.|0.85682	.|D	.|0.000000	T|T	0.73628|0.73628	0.3611|0.3611	L|L	0.48642|0.48642	1.525|1.525	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.79108	.|0.992	T|T	0.74372|0.74372	-0.3687|-0.3687	5|9	.|0.49607	.|T	.|0.09	-11.5548|-11.5548	15.7961|15.7961	0.78412|0.78412	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|87	.|O76061	.|STC2_HUMAN	G|A	40|87;2	.|.	.|ENSP00000265087:T87A	D|T	-|-	2|1	0|0	STC2|STC2	172685512|172685512	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.698000|7.698000	0.84413|0.84413	2.131000|2.131000	0.65755|0.65755	0.533000|0.533000	0.62120|0.62120	GAC|ACT	.	.		0.463	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	NM_003714		C	172752906	T	C	172752906	3	2	115	1	0	0	0	0	1	0	0	0	15291	1667	58	2	661	2	STC2	5	172752906	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	5077604	172752906	8162354	131	19670										
CANX	821	hgsc.bcm.edu	37	chr5	179133285	179133285	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tacaaagctccagttccaacAggggaagtatattttgctga	9	8	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:179133285A>G	ENST00000247461.4	+	3	398	c.198A>G	c.(196-198)acA>acG	p.T66T	CANX_ENST00000452673.2_Silent_p.T66T|CANX_ENST00000512607.2_5'UTR|CANX_ENST00000504734.1_Silent_p.T66T|CANX_ENST00000415618.2_Silent_p.T101T	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin	66					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	CAGTTCCAACAGGGGAAGTAT	0.333																																					p.T66T		Atlas-SNP	.											.	CANX	47	.	0			c.A198G						.						82	85	84					5																	179133285		2203	4300	6503	SO:0001819	synonymous_variant	821	exon3			TCCAACAGGGGAA	L18887	CCDS4447.1	5q35	2008-07-18			ENSG00000127022	ENSG00000127022			1473	protein-coding gene	gene with protein product	"major histocompatibility complex class I antigen-binding protein p88"	114217				1326756, 8136357	Standard	NM_001746		Approved	CNX, IP90, P90	uc003mkl.3	P27824	OTTHUMG00000130910	ENST00000247461.4:c.198A>G	chr5.hg19:g.179133285A>G		60.0	0.0		64.0	4.0	NM_001746	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Silent	SNP	ENST00000247461.4	hg19	CCDS4447.1	.	.	.	.	.	.	.	.	.	.	A	10.05	1.242880	0.22796	.	.	ENSG00000127022	ENST00000510810	.	.	.	5.38	1.68	0.24146	.	.	.	.	.	T	0.51176	0.1659	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35276	-0.9795	4	.	.	.	-8.1475	4.6583	0.12630	0.6287:0.0:0.2316:0.1397	.	.	.	.	R	35	.	.	Q	+	2	0	CANX	179065891	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.924000	0.28777	0.116000	0.18110	0.459000	0.35465	CAG	.	.		0.333	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649		G	179133285	A	G	179133285	2	3	115	1	0	0	0	0	0	0	0	1	2620	175	7	2		2	CANX	5	179133285	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6380379	179133285	1781975	132	19671										
MAML1	9794	hgsc.bcm.edu	37	chr5	179193646	179193646	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgatggcttatcttccccaGcagctgtcccatataagtca	7	13	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr5:179193646G>T	ENST00000292599.3	+	2	1898	c.1635G>T	c.(1633-1635)caG>caT	p.Q545H	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATCTTCCCCAGCAGCTGTCCC	0.537																																					p.Q545H		Atlas-SNP	.											.	MAML1	118	.	0			c.G1635T						.						63	64	64					5																	179193646		2203	4300	6503	SO:0001583	missense	9794	exon2			TCCCCAGCAGCTG	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1635G>T	chr5.hg19:g.179193646G>T	ENSP00000292599:p.Gln545His	76.0	0.0		83.0	4.0	NM_014757		Missense_Mutation	SNP	ENST00000292599.3	hg19	CCDS34315.1	.	.	.	.	.	.	.	.	.	.	G	15.11	2.737205	0.49045	.	.	ENSG00000161021	ENST00000292599;ENST00000376951	T	0.30448	1.53	5.15	4.28	0.50868	.	0.000000	0.64402	D	0.000002	T	0.56673	0.2001	M	0.81942	2.565	0.58432	D	0.999991	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.994	T	0.61917	-0.6964	10	0.62326	D	0.03	-13.7616	13.2773	0.60194	0.0769:0.0:0.9231:0.0	.	582;545	Q59GH4;Q92585	.;MAML1_HUMAN	H	545;582	ENSP00000292599:Q545H	ENSP00000292599:Q545H	Q	+	3	2	MAML1	179126252	0.998000	0.40836	1.000000	0.80357	0.652000	0.38707	0.397000	0.20883	1.157000	0.42530	0.563000	0.77884	CAG	.	.		0.537	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		T	179193646	G	T	179193646	3	4	115	1	0	0	0	0	1	0	0	0	9214	962	34	3	1641	3	MAML1	5	179193646	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	60361	179193646	1721614	133	19672										
FAM8A1	51439	hgsc.bcm.edu	37	chr6	17601073	17601073	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcccagcctactgcagccccCagccctccccgcagagcttc	7	22	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:17601073C>T	ENST00000259963.3	+	1	488	c.433C>T	c.(433-435)Cag>Tag	p.Q145*		NM_016255.2	NP_057339.1	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	145						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(3)	6	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			CTGCAGCCCCCAGCCCTCCCC	0.701																																					p.Q145X		Atlas-SNP	.											.	FAM8A1	26	.	0			c.C433T						.						11	14	13					6																	17601073		2082	4090	6172	SO:0001587	stop_gained	51439	exon1			AGCCCCCAGCCCT	AF097027	CCDS4540.1	6p23	2010-11-22			ENSG00000137414	ENSG00000137414			16372	protein-coding gene	gene with protein product						11707071	Standard	NM_016255		Approved	AHCP	uc003ncc.3	Q9UBU6	OTTHUMG00000014309	ENST00000259963.3:c.433C>T	chr6.hg19:g.17601073C>T	ENSP00000259963:p.Gln145*	44.0	0.0		70.0	28.0	NM_016255	B2R725	Nonsense_Mutation	SNP	ENST00000259963.3	hg19	CCDS4540.1	.	.	.	.	.	.	.	.	.	.	C	36	5.712685	0.96830	.	.	ENSG00000137414	ENST00000259963	.	.	.	4.11	4.11	0.48088	.	0.585175	0.13297	N	0.398547	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	-1.2679	14.4741	0.67535	0.0:1.0:0.0:0.0	.	.	.	.	X	145	.	ENSP00000259963:Q145X	Q	+	1	0	FAM8A1	17709052	0.003000	0.15002	0.862000	0.33874	0.716000	0.41182	1.327000	0.33746	1.986000	0.57962	0.484000	0.47621	CAG	.	.		0.701	FAM8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039950.1			T	17601073	C	T	17601073	4	4	115	1	0	0	0	0	0	1	0	0	5657	595	21	3	435	3	FAM8A1	6	17601073	Nonsense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10		17601073	153513994	134	19673										
KDM1B	221656	hgsc.bcm.edu	37	chr6	18166515	18166515	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cagccataaggatggatatgAcaaatatactacatggaaaa	8	6	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:18166515A>G	ENST00000297792.5	+	6	500	c.323A>G	c.(322-324)gAc>gGc	p.D108G	KDM1B_ENST00000397244.1_Missense_Mutation_p.D108G|KDM1B_ENST00000546309.2_Intron|KDM1B_ENST00000388870.2_Missense_Mutation_p.D108G			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	108					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						GATGGATATGACAAATATACT	0.373																																					p.D108G		Atlas-SNP	.											.	KDM1B	58	.	0			c.A323G						.						70	69	69					6																	18166515		2203	4300	6503	SO:0001583	missense	221656	exon6			GATATGACAAATA	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"Chromatin-modifying enzymes / K-demethylases"	21577	protein-coding gene	gene with protein product		613081	"amine oxidase, flavin containing 1", "chromosome 6 open reading frame 193", "amine oxidase (flavin containing) domain 1"	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.323A>G	chr6.hg19:g.18166515A>G	ENSP00000297792:p.Asp108Gly	87.0	0.0		87.0	5.0	NM_153042	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Missense_Mutation	SNP	ENST00000297792.5	hg19	CCDS34343.1	.	.	.	.	.	.	.	.	.	.	A	18.52	3.642100	0.67244	.	.	ENSG00000165097	ENST00000388870;ENST00000397244;ENST00000297792;ENST00000388869	T;T;T	0.34667	1.42;1.35;1.35	5.66	5.66	0.87406	.	0.464102	0.26258	N	0.025403	T	0.23532	0.0569	L	0.50333	1.59	0.80722	D	1	B	0.31383	0.321	B	0.29353	0.101	T	0.10965	-1.0607	10	0.87932	D	0	-6.3985	16.2026	0.82095	1.0:0.0:0.0:0.0	.	108	A2A2C6	.	G	108	ENSP00000373522:D108G;ENSP00000380419:D108G;ENSP00000297792:D108G	ENSP00000297792:D108G	D	+	2	0	KDM1B	18274494	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.524000	0.90579	2.285000	0.76669	0.533000	0.62120	GAC	.	.		0.373	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042		G	18166515	A	G	18166515	3	3	115	1	0	0	0	0	1	0	0	0	8132	275	10	2	337	2	KDM1B	6	18166515	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	565442	18166515	152948552	135	19674										
ZNF322A	79692	hgsc.bcm.edu	37	chr6	26638586	26638586	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tttataaggtttctccccagTatgggttctctcacacataa	6	10	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:26638586T>C	ENST00000415922.2	-	4	841	c.196A>G	c.(196-198)Act>Gct	p.T66A	RP11-457M11.2_ENST00000456172.1_RNA|ZNF322_ENST00000461899.1_5'Flank|ZNF322_ENST00000471278.1_Missense_Mutation_p.T66A	NM_024639.4	NP_078915.2	Q6U7Q0	ZN322_HUMAN	zinc finger protein 322	66					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TTCTCCCCAGTATGGGTTCTC	0.383																																					p.T66A		Atlas-SNP	.											.	.	.	.	0			c.A196G						.						157	143	148					6																	26638586		2202	4298	6500	SO:0001583	missense	79692	exon5			CCCCAGTATGGGT	AY376736	CCDS4617.1	6p22.1	2013-01-08	2011-07-29	2011-07-29	ENSG00000181315	ENSG00000181315		"Zinc fingers, C2H2-type"	23640	protein-coding gene	gene with protein product		610847	"zinc finger protein 489", "HLA complex group 12", "zinc finger protein 322A"	ZNF489, ZNF388, HCG12, ZNF322A		15555580	Standard	NM_024639		Approved	bA457M11.3, bA457M11.2	uc021yny.1	Q6U7Q0	OTTHUMG00000014460	ENST00000415922.2:c.196A>G	chr6.hg19:g.26638586T>C	ENSP00000418897:p.Thr66Ala	390.0	0.0		397.0	92.0	NM_001242797	A8K1X3|Q0VDH6|Q6B0G2|Q86W72|Q9H5I9	Missense_Mutation	SNP	ENST00000415922.2	hg19	CCDS4617.1	.	.	.	.	.	.	.	.	.	.	t	10.88	1.476530	0.26511	.	.	ENSG00000181315	ENST00000415922;ENST00000471278	T;T	0.26518	1.73;1.73	4.75	0.888	0.19206	.	0.150080	0.31279	N	0.007940	T	0.06416	0.0165	L	0.38692	1.165	0.31393	N	0.67759	B	0.02656	0.0	B	0.08055	0.003	T	0.16247	-1.0409	10	0.87932	D	0	-5.0444	4.1573	0.10266	0.1514:0.1746:0.0:0.674	.	66	Q6U7Q0	ZN322_HUMAN	A	66	ENSP00000418897:T66A;ENSP00000419728:T66A	ENSP00000418897:T66A	T	-	1	0	ZNF322	26746565	0.003000	0.15002	0.193000	0.23327	0.885000	0.51271	0.400000	0.20932	0.068000	0.16574	0.533000	0.62120	ACT	.	.		0.383	ZNF322-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040126.2	NM_024639		C	26638586	T	C	26638586	3	2	115	1	0	0	0	0	1	0	0	0	17856	1638	57	2	1016	2	ZNF322A	6	26638586	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	8472071	26638586	144476481	136	19675										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32188846	32188846	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cagcccctaggagggcagggTcctgcccgcagctcacaacg	13	16	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:32188846T>C	ENST00000375023.3	-	4	846	c.708A>G	c.(706-708)ggA>ggG	p.G236G		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	236	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GAGGGCAGGGTCCTGCCCGCA	0.642																																					p.G236G		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A708G						.						63	53	57					6																	32188846		1511	2709	4220	SO:0001819	synonymous_variant	4855	exon4			GCAGGGTCCTGCC		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.708A>G	chr6.hg19:g.32188846T>C		76.0	0.0		92.0	4.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	hg19	CCDS34420.1																																																																																			.	.		0.642	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			C	32188846	T	C	32188846	2	2	115	1	0	0	0	0	0	0	0	1	10560	1654	58	2		2	NOTCH4	6	32188846	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	5550260	32188846	138926221	137	19676										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33141808	33141808	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cgtggggccccgttctccccGaggccctgacttccccgaca	11	19	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:33141808G>T	ENST00000374708.4	-	31	2509	c.2251C>A	c.(2251-2253)Cgg>Agg	p.R751R	COL11A2_ENST00000374713.1_Silent_p.R790R|COL11A2_ENST00000374712.1_Silent_p.R756R|COL11A2_ENST00000357486.1_Silent_p.R816R|COL11A2_ENST00000341947.2_Silent_p.R837R|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000361917.1_Silent_p.R730R|COL11A2_ENST00000374714.1_Silent_p.R811R|COL11A2_ENST00000395197.1_Silent_p.R777R	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	837	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CGTTCTCCCCGAGGCCCTGAC	0.612																																					p.R837R	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.C2509A						.						55	56	56					6																	33141808		1511	2709	4220	SO:0001819	synonymous_variant	1302	exon33			CTCCCCGAGGCCC	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.2251C>A	chr6.hg19:g.33141808G>T		158.0	0.0		187.0	67.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.612	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			T	33141808	G	T	33141808	2	4	115	1	0	0	0	0	0	0	0	1	3670	1057	37	1		1	COL11A2	6	33141808	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	952962	33141808	137973259	138	19677										
C6orf89	221477	hgsc.bcm.edu	37	chr6	36882066	36882066	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccttcctctctcagactttgAcccctggtggacaaacgact	7	15	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:36882066A>G	ENST00000480824.2	+	5	704	c.410A>G	c.(409-411)gAc>gGc	p.D137G	C6orf89_ENST00000373685.1_Missense_Mutation_p.D137G|C6orf89_ENST00000510325.2_Missense_Mutation_p.D31G|C6orf89_ENST00000359359.2_Missense_Mutation_p.D31G|C6orf89_ENST00000355190.3_Missense_Mutation_p.D144G			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89	137					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						TCAGACTTTGACCCCTGGTGG	0.483																																					p.D144G		Atlas-SNP	.											.	C6orf89	39	.	0			c.A431G						.						54	57	56					6																	36882066		2203	4300	6503	SO:0001583	missense	221477	exon4			ACTTTGACCCCTG	AK058086	CCDS4827.1, CCDS69100.1, CCDS75444.1	6p21.31	2013-03-14			ENSG00000198663	ENSG00000198663			21114	protein-coding gene	gene with protein product	"bombesin receptor activated protein"					21857995, 23460338	Standard	NM_152734		Approved	FLJ25357, BRAP	uc003omw.3	Q6UWU4	OTTHUMG00000014613	ENST00000480824.2:c.410A>G	chr6.hg19:g.36882066A>G	ENSP00000475947:p.Asp137Gly	80.0	0.0		88.0	4.0	NM_152734	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000480824.2	hg19		.	.	.	.	.	.	.	.	.	.	A	15.50	2.853219	0.51270	.	.	ENSG00000198663	ENST00000359359;ENST00000510325;ENST00000355190;ENST00000373685;ENST00000416621;ENST00000540072	T;T	0.26660	1.72;1.72	5.44	4.3	0.51218	.	0.284847	0.34133	N	0.004239	T	0.14056	0.0340	L	0.56769	1.78	0.28353	N	0.920801	P;P	0.51933	0.867;0.949	B;P	0.49085	0.288;0.6	T	0.06516	-1.0822	10	0.15952	T	0.53	-15.1665	7.2552	0.26173	0.9032:0.0:0.0968:0.0	.	137;144	Q6UWU4;Q6UWU4-2	CF089_HUMAN;.	G	31;31;144;137;144;143	ENSP00000347322:D144G;ENSP00000362789:D137G	ENSP00000347322:D144G	D	+	2	0	C6orf89	36990044	0.939000	0.31865	0.998000	0.56505	0.404000	0.30871	3.036000	0.49767	2.066000	0.61787	0.533000	0.62120	GAC	.	.		0.483	C6orf89-004	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000040387.2	NM_152734		G	36882066	A	G	36882066	3	3	115	1	0	0	0	0	1	0	0	0	2375	275	10	2	445	2	C6orf89	6	36882066	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3740258	36882066	134233001	139	19678										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38874140	38874140	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgacagtgaaataaaagatgAggcatttctagaatacctta	8	5	1	5			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:38874140A>G	ENST00000359357.3	+	61	8908	c.8654A>G	c.(8653-8655)gAg>gGg	p.E2885G	DNAH8_ENST00000441566.1_Missense_Mutation_p.E2849G|DNAH8_ENST00000449981.2_Missense_Mutation_p.E3102G			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2885	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ATAAAAGATGAGGCATTTCTA	0.333																																					p.E3102G		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A9305G						.						55	54	54					6																	38874140		2203	4300	6503	SO:0001583	missense	1769	exon63			AAGATGAGGCATT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.8654A>G	chr6.hg19:g.38874140A>G	ENSP00000352312:p.Glu2885Gly	169.0	0.0		147.0	6.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	A	28.3	4.907281	0.92107	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.56275	0.47;0.47;0.47	5.72	5.72	0.89469	Dynein heavy chain, P-loop containing D4 domain (1);	0.051449	0.85682	D	0.000000	T	0.81588	0.4854	H	0.98802	4.335	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.89439	0.3722	10	0.87932	D	0	.	16.0204	0.80478	1.0:0.0:0.0:0.0	.	2885	Q96JB1	DYH8_HUMAN	G	3090;3090;2885;2849	ENSP00000333363:E3090G;ENSP00000352312:E2885G;ENSP00000402294:E2849G	ENSP00000333363:E3090G	E	+	2	0	DNAH8	38982118	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.253000	0.95501	2.174000	0.68829	0.533000	0.62120	GAG	.	.		0.333	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38874140	A	G	38874140	3	3	115	1	0	0	0	0	1	0	0	0	4609	304	11	2	8888	2	DNAH8	6	38874140	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1992074	38874140	132240927	140	19679										
TDRD6	221400	hgsc.bcm.edu	37	chr6	46661339	46661339	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	attactaccacatgctaatgAaacaaaggagatactagaac	6	8	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:46661339A>G	ENST00000316081.6	+	1	5474	c.5474A>G	c.(5473-5475)gAa>gGa	p.E1825G	TDRD6_ENST00000544460.1_Missense_Mutation_p.E1825G	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1825					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			CATGCTAATGAAACAAAGGAG	0.368																																					p.E1825G		Atlas-SNP	.											TDRD6,NS,carcinoma,+1,1	TDRD6	205	.	0			c.A5474G						.						77	81	80					6																	46661339		2203	4300	6503	SO:0001583	missense	221400	exon1			CTAATGAAACAAA	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.5474A>G	chr6.hg19:g.46661339A>G	ENSP00000346065:p.Glu1825Gly	34.0	0.0		41.0	2.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	hg19	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	A	15.53	2.861586	0.51482	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.15718	2.4;2.4	5.68	5.68	0.88126	.	0.441828	0.22978	N	0.053350	T	0.12732	0.0309	L	0.56769	1.78	0.09310	N	1	D;P	0.53462	0.96;0.933	P;B	0.50537	0.643;0.441	T	0.21895	-1.0232	10	0.72032	D	0.01	0.3847	6.3877	0.21569	0.7836:0.0:0.0759:0.1406	.	1825;1825	F5H5M3;O60522	.;TDRD6_HUMAN	G	1825	ENSP00000443299:E1825G;ENSP00000346065:E1825G	ENSP00000346065:E1825G	E	+	2	0	TDRD6	46769298	0.056000	0.20664	0.061000	0.19648	0.165000	0.22458	3.088000	0.50175	2.156000	0.67533	0.460000	0.39030	GAA	.	.		0.368	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		G	46661339	A	G	46661339	3	3	115	1	0	0	0	0	1	0	0	0	15749	246	9	2	5476	2	TDRD6	6	46661339	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	7787199	46661339	124453728	141	19680										
BAI3	577	hgsc.bcm.edu	37	chr6	70065719	70065719	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atttattgttacagacagacTttgaaaaggatgtagacatt	8	4	0	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:70065719T>C	ENST00000370598.1	+	28	4383	c.3562T>C	c.(3562-3564)Ttt>Ctt	p.F1188L	BAI3_ENST00000238918.8_Missense_Mutation_p.F394L|BAI3_ENST00000546190.1_Missense_Mutation_p.F152L	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1188					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				ACAGACAGACTTTGAAAAGGA	0.289																																					p.F1188L		Atlas-SNP	.											.	BAI3	451	.	0			c.T3562C						.						115	126	122					6																	70065719		2203	4297	6500	SO:0001583	missense	577	exon28			ACAGACTTTGAAA	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.3562T>C	chr6.hg19:g.70065719T>C	ENSP00000359630:p.Phe1188Leu	74.0	0.0		60.0	4.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	T	33	5.255188	0.95336	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.58940	1.76;2.44;0.3	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.70011	0.3175	M	0.70595	2.14	0.58432	D	0.999999	P;D	0.69078	0.924;0.997	P;D	0.75020	0.878;0.985	T	0.74103	-0.3773	10	0.72032	D	0.01	.	16.3426	0.83092	0.0:0.0:0.0:1.0	.	394;1188	B7Z356;O60242	.;BAI3_HUMAN	L	1188;394;152	ENSP00000359630:F1188L;ENSP00000238918:F394L;ENSP00000441821:F152L	ENSP00000238918:F394L	F	+	1	0	BAI3	70122440	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.304000	0.78882	2.317000	0.78254	0.460000	0.39030	TTT	.	.		0.289	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			C	70065719	T	C	70065719	3	2	115	1	0	0	0	0	1	0	0	0	1300	1609	56	2	3664	2	BAI3	6	70065719	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	23404380	70065719	101049348	142	19681										
GABRR1	2569	hgsc.bcm.edu	37	chr6	89890138	89890138	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agatgtccacggccttgatgTaggagacgcgcggcatggag	16	9	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:89890138T>C	ENST00000454853.2	-	9	1129	c.1019A>G	c.(1018-1020)tAc>tGc	p.Y340C	GABRR1_ENST00000435811.1_Missense_Mutation_p.Y323C|GABRR1_ENST00000369451.3_Missense_Mutation_p.Y253C	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	340					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	GGCCTTGATGTAGGAGACGCG	0.542																																					p.Y340C		Atlas-SNP	.											.	GABRR1	63	.	0			c.A1019G						.						161	128	139					6																	89890138		2203	4300	6503	SO:0001583	missense	2569	exon9			TTGATGTAGGAGA		CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4090	protein-coding gene	gene with protein product	"GABA(A) receptor, rho 1"	137161	"gamma-aminobutyric acid (GABA) receptor, rho 1"			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.1019A>G	chr6.hg19:g.89890138T>C	ENSP00000412673:p.Tyr340Cys	106.0	0.0		93.0	4.0	NM_002042	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Missense_Mutation	SNP	ENST00000454853.2	hg19	CCDS5019.2	.	.	.	.	.	.	.	.	.	.	T	24.9	4.576836	0.86645	.	.	ENSG00000146276	ENST00000454853;ENST00000435811;ENST00000369451;ENST00000436331	D;D;D	0.87334	-2.24;-2.24;-2.24	5.25	5.25	0.73442	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.94185	0.8134	M	0.92459	3.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.95593	0.8656	9	.	.	.	-15.644	15.1818	0.72965	0.0:0.0:0.0:1.0	.	323;340	P24046-2;P24046	.;GBRR1_HUMAN	C	340;323;253;253	ENSP00000412673:Y340C;ENSP00000394687:Y323C;ENSP00000358463:Y253C	.	Y	-	2	0	GABRR1	89946857	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	8.040000	0.89188	1.972000	0.57404	0.455000	0.32223	TAC	.	.		0.542	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2			C	89890138	T	C	89890138	3	2	115	1	0	0	0	0	1	0	0	0	6184	1638	57	2	428	2	GABRR1	6	89890138	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	19824419	89890138	81224929	143	19682										
MDN1	23195	hgsc.bcm.edu	37	chr6	90513153	90513153	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tttaatggcttcggcattccTttccagcaaatccaaaagga	7	10	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:90513153T>C	ENST00000369393.3	-	2	338	c.223A>G	c.(223-225)Agg>Ggg	p.R75G	MDN1_ENST00000428876.1_Missense_Mutation_p.R75G			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	75					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCGGCATTCCTTTCCAGCAAA	0.488																																					p.R75G		Atlas-SNP	.											.	MDN1	478	.	0			c.A223G						.						196	172	180					6																	90513153		2203	4300	6503	SO:0001583	missense	23195	exon2			CATTCCTTTCCAG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.223A>G	chr6.hg19:g.90513153T>C	ENSP00000358400:p.Arg75Gly	100.0	0.0		58.0	4.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.723436	0.48728	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.28895	1.59;1.59;1.59	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.44008	0.1273	M	0.72894	2.215	0.44966	D	0.997988	D;D	0.89917	1.0;0.995	D;P	0.87578	0.998;0.791	T	0.47674	-0.9099	10	0.66056	D	0.02	.	11.8462	0.52385	0.0:0.0:0.1458:0.8542	.	75;75	Q6ZVV6;Q9NU22	.;MDN1_HUMAN	G	75	ENSP00000358400:R75G;ENSP00000413970:R75G;ENSP00000409664:R75G	ENSP00000358400:R75G	R	-	1	2	MDN1	90569874	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	3.125000	0.50469	1.917000	0.55516	0.254000	0.18369	AGG	.	.		0.488	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90513153	T	C	90513153	3	2	115	1	0	0	0	0	1	0	0	0	9424	1608	56	2	16971	2	MDN1	6	90513153	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	623015	90513153	80601914	144	19683										
OSTM1	28962	hgsc.bcm.edu	37	chr6	108375753	108375753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tagattaaggaaatatactgTgctgtttgataattcttcac	7	5	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:108375753T>C	ENST00000193322.3	-	3	641	c.556A>G	c.(556-558)Aca>Gca	p.T186A		NM_014028.3	NP_054747.2	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1	186					ion transmembrane transport (GO:0034220)|osteoclast differentiation (GO:0030316)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)		p.T186S(1)		central_nervous_system(2)|endometrium(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)		AAATATACTGTGCTGTTTGAT	0.264																																					p.T186A	Melanoma(162;1427 1909 3096 17430 21396)	Atlas-SNP	.											OSTM1,NS,carcinoma,0,1	OSTM1	22	.	1	Substitution - Missense(1)	lung(1)	c.A556G						.						100	105	103					6																	108375753		2202	4296	6498	SO:0001583	missense	28962	exon3			ATACTGTGCTGTT	AF533891	CCDS5062.1	6q21	2014-06-17			ENSG00000081087	ENSG00000081087			21652	protein-coding gene	gene with protein product	"CLCN7 accessory beta subunit"	607649				12627228, 21527911	Standard	NM_014028		Approved	HSPC019, GL	uc003psd.3	Q86WC4	OTTHUMG00000015317	ENST00000193322.3:c.556A>G	chr6.hg19:g.108375753T>C	ENSP00000193322:p.Thr186Ala	49.0	0.0		30.0	2.0	NM_014028	E1P5E3|Q5R391|Q6PCA7|Q7RTW6|Q8NC29|Q8TC82|Q9Y2S9	Missense_Mutation	SNP	ENST00000193322.3	hg19	CCDS5062.1	.	.	.	.	.	.	.	.	.	.	T	19.51	3.841793	0.71488	.	.	ENSG00000081087	ENST00000193322;ENST00000440575	T	0.55930	0.49	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.68714	0.3031	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74993	-0.3474	10	0.72032	D	0.01	-9.3235	14.1596	0.65438	0.0:0.0:0.0:1.0	.	186	Q86WC4	OSTM1_HUMAN	A	186;39	ENSP00000193322:T186A	ENSP00000193322:T186A	T	-	1	0	OSTM1	108482446	1.000000	0.71417	0.991000	0.47740	0.732000	0.41865	5.580000	0.67464	2.094000	0.63399	0.533000	0.62120	ACA	.	.		0.264	OSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041709.3	NM_014028		C	108375753	T	C	108375753	3	2	115	1	0	0	0	0	1	0	0	0	11307	1696	59	2	464	2	OSTM1	6	108375753	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	17862600	108375753	62739314	145	19684										
TSPYL4	23270	hgsc.bcm.edu	37	chr6	116574326	116574326	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgtttaagctcctccacctcCaaattgatcatgtacctcag	5	13	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:116574326C>T	ENST00000420283.1	-	1	935	c.846G>A	c.(844-846)ttG>ttA	p.L282L	RP3-486I3.7_ENST00000448740.2_lincRNA|DSE_ENST00000540275.1_5'Flank	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	282					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(2)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.045)|OV - Ovarian serous cystadenocarcinoma(136;0.0666)|GBM - Glioblastoma multiforme(226;0.095)|Epithelial(106;0.125)		CCTCCACCTCCAAATTGATCA	0.488																																					p.L282L		Atlas-SNP	.											.	TSPYL4	18	.	0			c.G846A						.						62	63	63					6																	116574326		1972	4179	6151	SO:0001819	synonymous_variant	23270	exon1			CACCTCCAAATTG		CCDS5106.1	6q22.1	2010-05-12			ENSG00000187189	ENSG00000187189			21559	protein-coding gene	gene with protein product							Standard	NM_021648		Approved	dJ486I3.2, KIAA0721	uc003pwn.3	Q9UJ04	OTTHUMG00000015429	ENST00000420283.1:c.846G>A	chr6.hg19:g.116574326C>T		112.0	0.0		69.0	4.0	NM_021648	B4DYQ2|O94828|Q96GW8	Silent	SNP	ENST00000420283.1	hg19	CCDS5106.1																																																																																			.	.		0.488	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2			T	116574326	C	T	116574326	2	4	115	1	0	0	0	0	0	0	0	1	16676	593	21	3		3	TSPYL4	6	116574326	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	8198573	116574326	54540741	146	19685										
RFX6	222546	hgsc.bcm.edu	37	chr6	117198525	117198525	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gggatccaggaagactgctgTgtgcagctcctgggcaaggg	17	9	0	1	rs368582780		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:117198525T>C	ENST00000332958.2	+	1	103	c.87T>C	c.(85-87)tgT>tgC	p.C29C		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	29					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AAGACTGCTGTGTGCAGCTCC	0.677																																					p.C29C		Atlas-SNP	.											.	RFX6	141	.	0			c.T87C						.	T		0,4406		0,0,2203	20	23	22		87	-10.2	0	6		22	1,8599		0,1,4299	no	coding-synonymous	RFX6	NM_173560.3		0,1,6502	CC,CT,TT		0.0116,0.0,0.0077		29/929	117198525	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	222546	exon1			CTGCTGTGTGCAG	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.87T>C	chr6.hg19:g.117198525T>C		91.0	0.0		91.0	5.0	NM_173560	Q5T6B3	Silent	SNP	ENST00000332958.2	hg19	CCDS5113.1																																																																																			.	.		0.677	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		C	117198525	T	C	117198525	2	2	115	1	0	0	0	0	0	0	0	1	13282	1702	59	2		2	RFX6	6	117198525	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	624199	117198525	53916542	147	19686										
NCOA7	135112	hgsc.bcm.edu	37	chr6	126203615	126203615	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttgaaacccattgaaagagTcttatcgtctacttctgaag	7	9	3	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:126203615T>C	ENST00000368357.3	+	8	969	c.617T>C	c.(616-618)gTc>gCc	p.V206A	NCOA7_ENST00000229634.9_Missense_Mutation_p.V102A|NCOA7_ENST00000392477.2_Missense_Mutation_p.V206A	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	206					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		ATTGAAAGAGTCTTATCGTCT	0.338																																					p.V206A		Atlas-SNP	.											.	NCOA7	92	.	0			c.T617C						.						57	55	55					6																	126203615		2203	4300	6503	SO:0001583	missense	135112	exon8			AAAGAGTCTTATC	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 4"	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.617T>C	chr6.hg19:g.126203615T>C	ENSP00000357341:p.Val206Ala	57.0	0.0		50.0	5.0	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	hg19	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.480371	0.84747	.	.	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000413085	T;T;T;T	0.37752	2.42;2.42;2.42;1.18	5.63	5.63	0.86233	.	0.280930	0.34628	N	0.003811	T	0.49762	0.1576	M	0.61703	1.905	0.51482	D	0.999924	D;D;D;D	0.89917	1.0;0.998;0.993;0.995	D;D;P;D	0.87578	0.998;0.913;0.826;0.914	T	0.49790	-0.8902	10	0.49607	T	0.09	-0.3706	16.1251	0.81386	0.0:0.0:0.0:1.0	.	206;206;206;206	B3KXK4;Q8NI08-2;Q8NI08-4;Q8NI08	.;.;.;NCOA7_HUMAN	A	206;206;102;15	ENSP00000357341:V206A;ENSP00000376269:V206A;ENSP00000229634:V102A;ENSP00000389186:V15A	ENSP00000229634:V102A	V	+	2	0	NCOA7	126245308	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.999000	0.57031	2.261000	0.74972	0.528000	0.53228	GTC	.	.		0.338	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748		C	126203615	T	C	126203615	3	2	115	1	0	0	0	0	1	0	0	0	10243	1667	58	2	639	2	NCOA7	6	126203615	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	9005090	126203615	44911452	148	19687										
MAP3K5	4217	hgsc.bcm.edu	37	chr6	136878915	136878915	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtcaagtctgtttgtttcgaAagtcaatgatagccttccac	8	9	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:136878915A>G	ENST00000359015.4	-	30	4466	c.4106T>C	c.(4105-4107)tTt>tCt	p.F1369S	MAP3K5_ENST00000355845.4_Missense_Mutation_p.F616S	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	1369					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		TTTGTTTCGAAAGTCAATGAT	0.408																																					p.F1369S		Atlas-SNP	.											.	MAP3K5	136	.	0			c.T4106C						.						141	123	129					6																	136878915		2203	4300	6503	SO:0001583	missense	4217	exon30			TTTCGAAAGTCAA	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6857	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 1"	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.4106T>C	chr6.hg19:g.136878915A>G	ENSP00000351908:p.Phe1369Ser	93.0	0.0		71.0	4.0	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Missense_Mutation	SNP	ENST00000359015.4	hg19	CCDS5179.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.469096	0.43839	.	.	ENSG00000197442	ENST00000359015;ENST00000355845	D;D	0.87809	-2.3;-2.3	5.46	2.89	0.33648	Sterile alpha motif/pointed domain (1);	0.246535	0.42548	D	0.000683	T	0.66307	0.2776	L	0.36672	1.1	0.31781	N	0.630875	B	0.28128	0.201	B	0.24155	0.051	T	0.56854	-0.7910	10	0.33141	T	0.24	.	9.7268	0.40337	0.6042:0.0:0.0:0.3957	.	1369	Q99683	M3K5_HUMAN	S	1369;616	ENSP00000351908:F1369S;ENSP00000348104:F616S	ENSP00000348104:F616S	F	-	2	0	MAP3K5	136920608	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	1.594000	0.36697	0.885000	0.36088	0.533000	0.62120	TTT	.	.		0.408	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1			G	136878915	A	G	136878915	3	3	115	1	0	0	0	0	1	0	0	0	9262	14	1	2	22	2	MAP3K5	6	136878915	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	10675300	136878915	34236152	149	19688										
RAB32	10981	hgsc.bcm.edu	37	chr6	146875606	146875606	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttacaggataacataaacatAgaggaagctgcccggttcct	9	9	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:146875606A>G	ENST00000367495.3	+	3	722	c.543A>G	c.(541-543)atA>atG	p.I181M		NM_006834.3	NP_006825.1	Q13637	RAB32_HUMAN	RAB32, member RAS oncogene family	181	PKA-RII subunit binding domain.				antigen processing and presentation (GO:0019882)|endosome to melanosome transport (GO:0035646)|GTP catabolic process (GO:0006184)|melanosome organization (GO:0032438)|phagosome maturation (GO:0090382)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	early endosome (GO:0005769)|melanosome (GO:0042470)|membrane (GO:0016020)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)	AP-1 adaptor complex binding (GO:0035650)|AP-3 adaptor complex binding (GO:0035651)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	8		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.68e-09)|GBM - Glioblastoma multiforme(68;0.00608)		ACATAAACATAGAGGAAGCTG	0.363																																					p.I181M		Atlas-SNP	.											.	RAB32	16	.	0			c.A543G						.						77	78	78					6																	146875606		2203	4300	6503	SO:0001583	missense	10981	exon3			AAACATAGAGGAA	U71127	CCDS5210.1	6q24.2	2010-08-20			ENSG00000118508	ENSG00000118508		"RAB, member RAS oncogene", "A-kinase anchor proteins"	9772	protein-coding gene	gene with protein product		612906					Standard	NM_006834		Approved		uc003qln.1	Q13637	OTTHUMG00000015755	ENST00000367495.3:c.543A>G	chr6.hg19:g.146875606A>G	ENSP00000356465:p.Ile181Met	86.0	0.0		62.0	37.0	NM_006834		Missense_Mutation	SNP	ENST00000367495.3	hg19	CCDS5210.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.499544	0.64298	.	.	ENSG00000118508	ENST00000367495	T	0.78924	-1.22	5.8	-3.7	0.04437	Small GTP-binding protein domain (1);	0.044767	0.85682	D	0.000000	D	0.84656	0.5520	H	0.95187	3.635	0.53005	D	0.999965	D	0.67145	0.996	D	0.71414	0.973	D	0.84060	0.0374	10	0.87932	D	0	-20.0784	7.5792	0.27955	0.2846:0.3199:0.0:0.3955	.	181	Q13637	RAB32_HUMAN	M	181	ENSP00000356465:I181M	ENSP00000356465:I181M	I	+	3	3	RAB32	146917299	0.771000	0.28555	0.979000	0.43373	0.719000	0.41307	-0.036000	0.12185	-0.467000	0.06932	0.533000	0.62120	ATA	.	.		0.363	RAB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042579.1	NM_006834		G	146875606	A	G	146875606	3	3	115	1	0	0	0	0	1	0	0	0	12936	410	15	2	553	2	RAB32	6	146875606	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	9996691	146875606	24239461	150	19689										
NUP43	348995	hgsc.bcm.edu	37	chr6	150059861	150059861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aattgaatttacagtaagaaTctcaggagttcgaagaaagg	10	4	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:150059861T>C	ENST00000340413.2	-	5	632	c.556A>G	c.(556-558)Att>Gtt	p.I186V	NUP43_ENST00000367403.3_Intron|NUP43_ENST00000367404.4_Intron|NUP43_ENST00000460354.2_Missense_Mutation_p.I186V	NM_198887.1	NP_942590.1	Q8NFH3	NUP43_HUMAN	nucleoporin 43kDa	186					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				breast(1)|large_intestine(2)|lung(8)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;4.71e-13)|GBM - Glioblastoma multiforme(68;0.101)		ACAGTAAGAATCTCAGGAGTT	0.338																																					p.I186V		Atlas-SNP	.											.	NUP43	32	.	0			c.A556G						.						121	116	118					6																	150059861		2203	4299	6502	SO:0001583	missense	348995	exon5			TAAGAATCTCAGG	AF514997	CCDS5218.1	6q25.1	2013-01-10			ENSG00000120253	ENSG00000120253		"WD repeat domain containing"	21182	protein-coding gene	gene with protein product		608141				12196509	Standard	XM_005266961		Approved	bA350J20.1, FLJ13287	uc003qmz.3	Q8NFH3	OTTHUMG00000015795	ENST00000340413.2:c.556A>G	chr6.hg19:g.150059861T>C	ENSP00000342262:p.Ile186Val	72.0	0.0		58.0	4.0	NM_198887	B4E2F0|Q9H8S0	Missense_Mutation	SNP	ENST00000340413.2	hg19	CCDS5218.1	.	.	.	.	.	.	.	.	.	.	T	11.86	1.764785	0.31228	.	.	ENSG00000120253	ENST00000340413;ENST00000460354	T;T	0.64085	-0.08;-0.08	5.53	5.53	0.82687	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.094377	0.64402	D	0.000001	T	0.31888	0.0811	L	0.31420	0.93	0.80722	D	1	B	0.26512	0.151	B	0.21708	0.036	T	0.25187	-1.0139	10	0.12103	T	0.63	-21.8061	15.6916	0.77457	0.0:0.0:0.0:1.0	.	186	Q8NFH3	NUP43_HUMAN	V	186	ENSP00000342262:I186V;ENSP00000432401:I186V	ENSP00000342262:I186V	I	-	1	0	NUP43	150101554	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	4.089000	0.57685	2.120000	0.65058	0.372000	0.22366	ATT	.	.		0.338	NUP43-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396947.1	NM_198887		C	150059861	T	C	150059861	3	2	115	1	0	0	0	0	1	0	0	0	10774	1435	50	2	602	2	NUP43	6	150059861	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3184255	150059861	21055206	151	19690										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151144808	151144808	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agaaacagcacaagacatccAaaaggtaagctctatctcat	6	10	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:151144808A>G	ENST00000358517.2	+	14	1677	c.1466A>G	c.(1465-1467)cAa>cGa	p.Q489R	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.Q489R			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	489							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		CAAGACATCCAAAAGGTAAGC	0.358																																					p.Q489R		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.A1466G						.						95	92	93					6																	151144808		2203	4299	6502	SO:0001583	missense	57480	exon15			ACATCCAAAAGGT	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.1466A>G	chr6.hg19:g.151144808A>G	ENSP00000351318:p.Gln489Arg	54.0	0.0		31.0	16.0	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	hg19	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	A	11.76	1.735276	0.30774	.	.	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	T;T	0.60171	0.21;0.21	5.42	2.99	0.34606	.	0.357494	0.32719	N	0.005727	T	0.30386	0.0763	L	0.51422	1.61	0.42169	D	0.991637	B;B;B	0.12013	0.0;0.005;0.005	B;B;B	0.09377	0.001;0.004;0.004	T	0.17349	-1.0372	10	0.54805	T	0.06	.	7.198	0.25864	0.779:0.146:0.0751:0.0	.	296;489;489	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	R	489	ENSP00000356297:Q489R;ENSP00000351318:Q489R	ENSP00000351318:Q489R	Q	+	2	0	PLEKHG1	151186501	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	1.643000	0.37217	0.420000	0.25954	-0.274000	0.10170	CAA	.	.		0.358	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			G	151144808	A	G	151144808	3	3	115	1	0	0	0	0	1	0	0	0	12077	130	5	2	1516	2	PLEKHG1	6	151144808	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1084947	151144808	19970259	152	19691										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151152053	151152053	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acagagacctccagctctggTcacaggattgtcaggcgggc	13	12	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:151152053T>C	ENST00000358517.2	+	15	2017	c.1806T>C	c.(1804-1806)ggT>ggC	p.G602G	PLEKHG1_ENST00000367328.1_Silent_p.G602G			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	602							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		CCAGCTCTGGTCACAGGATTG	0.537																																					p.G602G		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.T1806C						.						69	68	68					6																	151152053		2203	4300	6503	SO:0001819	synonymous_variant	57480	exon16			CTCTGGTCACAGG	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.1806T>C	chr6.hg19:g.151152053T>C		76.0	0.0		55.0	4.0	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	hg19	CCDS34552.1																																																																																			.	.		0.537	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			C	151152053	T	C	151152053	2	2	115	1	0	0	0	0	0	0	0	1	12077	1654	58	2		2	PLEKHG1	6	151152053	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	7245	151152053	19963014	153	19692										
LPA	4018	hgsc.bcm.edu	37	chr6	161016501	161016501	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tactcccacctgacactgggAtccatggtgtaacaccaagg	9	13	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:161016501A>G	ENST00000316300.5	-	21	3398	c.3354T>C	c.(3352-3354)gaT>gaC	p.D1118D	LPA_ENST00000447678.1_Silent_p.D1118D			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3626	Kringle 10. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TGACACTGGGATCCATGGTGT	0.517																																					p.D1118D		Atlas-SNP	.											.	LPA	237	.	0			c.T3354C						.						110	110	110					6																	161016501		2130	4263	6393	SO:0001819	synonymous_variant	4018	exon22			ACTGGGATCCATG	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.3354T>C	chr6.hg19:g.161016501A>G		151.0	0.0		86.0	4.0	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	hg19	CCDS43523.1																																																																																			.	.		0.517	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		G	161016501	A	G	161016501	2	3	115	1	0	0	0	0	0	0	0	1	8912	330	12	2		2	LPA	6	161016501	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	9864448	161016501	10098566	154	19693										
SMOC2	64094	hgsc.bcm.edu	37	chr6	168944304	168944304	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctccttattttcctcttttaGgttccgtaaatgaaaagtta	5	8	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr6:168944304G>T	ENST00000356284.2	+	5	683		c.e5-1		SMOC2_ENST00000354536.5_Splice_Site	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2						extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		TCCTCTTTTAGGTTCCGTAAA	0.328																																					.		Atlas-SNP	.											SMOC2,NS,carcinoma,0,1	SMOC2	57	.	0			c.464-1G>T						.						96	94	95					6																	168944304		2203	4300	6503	SO:0001630	splice_region_variant	64094	exon5			CTTTTAGGTTCCG	AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"EF-hand domain containing"	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.464-1G>T	chr6.hg19:g.168944304G>T		61.0	0.0		28.0	2.0	NM_022138	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Splice_Site	SNP	ENST00000356284.2	hg19	CCDS55076.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274547	0.23307	.	.	ENSG00000112562	ENST00000356284;ENST00000354536;ENST00000366793	.	.	.	4.69	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8554	0.70332	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMOC2	168687153	1.000000	0.71417	0.976000	0.42696	0.075000	0.17131	5.201000	0.65163	2.157000	0.67596	0.650000	0.86243	.	.	.		0.328	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043201.1		Intron	T	168944304	G	T	168944304	5	4	115	1	0	0	0	0	0	0	1	0	14817	1014	35	3	481	3	SMOC2	6	168944304	Splice_Site	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	7927803	168944304	2170763	155	19694										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11446083	11446083	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aatgttccttgttctggtccCttctccacactgggcctcct	7	15	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:11446083C>G	ENST00000423059.4	-	22	4332	c.4081G>C	c.(4081-4083)Ggg>Cgg	p.G1361R	AC004160.4_ENST00000425837.1_RNA|AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1361	TSP type-1 14. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		GTTCTGGTCCCTTCTCCACAC	0.418										HNSCC(18;0.044)																											p.G1361R		Atlas-SNP	.											.	THSD7A	219	.	0			c.G4081C						.						60	59	59					7																	11446083		1909	4125	6034	SO:0001583	missense	221981	exon21			TGGTCCCTTCTCC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.4081G>C	chr7.hg19:g.11446083C>G	ENSP00000406482:p.Gly1361Arg	193.0	0.0		242.0	84.0	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	hg19	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.712990	0.89112	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	D	0.83673	-1.75	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.92198	0.7526	M	0.80422	2.495	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91831	0.5475	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1361	Q9UPZ6	THS7A_HUMAN	R	1361	ENSP00000406482:G1361R	ENSP00000262042:G1361R	G	-	1	0	THSD7A	11412608	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.790000	0.85794	2.941000	0.99782	0.655000	0.94253	GGG	.	.		0.418	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		G	11446083	C	G	11446083	3	3	115	1	0	0	0	0	1	0	0	0	15894	681	24	4	920	4	THSD7A	7	11446083	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10		11446083	147692580	156	19695										
HIBADH	11112	hgsc.bcm.edu	37	chr7	27672029	27672029	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agcattgtaataattctgtcAgctttttcagcaacatctgc	6	9	4	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:27672029A>G	ENST00000265395.2	-	3	494	c.288T>C	c.(286-288)gcT>gcC	p.A96A		NM_152740.3	NP_689953.1	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase	96					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	3-hydroxyisobutyrate dehydrogenase activity (GO:0008442)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(4)|kidney(2)|lung(3)|ovary(2)|prostate(1)	12			GBM - Glioblastoma multiforme(3;0.0368)			TAATTCTGTCAGCTTTTTCAG	0.353																																					p.A96A		Atlas-SNP	.											.	HIBADH	28	.	0			c.T288C						.						134	129	131					7																	27672029		2203	4300	6503	SO:0001819	synonymous_variant	11112	exon3			TCTGTCAGCTTTT	AF529362	CCDS5414.1	7p15	2009-06-12			ENSG00000106049	ENSG00000106049	1.1.1.31		4907	protein-coding gene	gene with protein product		608475					Standard	NM_152740		Approved	NS5ATP1	uc003szf.3	P31937	OTTHUMG00000097035	ENST00000265395.2:c.288T>C	chr7.hg19:g.27672029A>G		69.0	0.0		82.0	4.0	NM_152740	Q546Z2|Q9UDN3	Silent	SNP	ENST00000265395.2	hg19	CCDS5414.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.535153	0.27475	.	.	ENSG00000106049	ENST00000425715	.	.	.	5.8	-6.09	0.02145	.	.	.	.	.	T	0.37293	0.0998	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45175	-0.9279	4	.	.	.	-21.1549	3.1029	0.06331	0.385:0.1537:0.0601:0.4012	.	.	.	.	P	39	.	.	L	-	2	0	HIBADH	27638554	0.589000	0.26807	0.991000	0.47740	0.998000	0.95712	-0.196000	0.09532	-0.446000	0.07149	0.528000	0.53228	CTG	.	.		0.353	HIBADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214132.1	NM_152740		G	27672029	A	G	27672029	2	3	115	1	0	0	0	0	0	0	0	1	7108	175	7	2		2	HIBADH	7	27672029	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	16225946	27672029	131466634	157	19696										
AMPH	273	hgsc.bcm.edu	37	chr7	38431545	38431545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctccttgggctctgcacctAtagttatttcgttttctcct	6	12	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:38431545A>G	ENST00000356264.2	-	19	1897	c.1682T>C	c.(1681-1683)aTa>aCa	p.I561T	AMPH_ENST00000428293.2_Missense_Mutation_p.I519T|AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000325590.5_Missense_Mutation_p.I519T	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	561					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						CTCTGCACCTATAGTTATTTC	0.587																																					p.I561T		Atlas-SNP	.											.	AMPH	157	.	0			c.T1682C						.						71	68	69					7																	38431545		2203	4300	6503	SO:0001583	missense	273	exon19			GCACCTATAGTTA		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1682T>C	chr7.hg19:g.38431545A>G	ENSP00000348602:p.Ile561Thr	107.0	0.0		106.0	5.0	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	hg19	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	A	11.82	1.751719	0.31046	.	.	ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242	T;T;T	0.60171	0.25;0.24;0.21	5.24	-4.31	0.03698	.	2.013320	0.02734	N	0.115458	T	0.31888	0.0811	N	0.08118	0	0.09310	N	1	B;B;B	0.13145	0.0;0.0;0.007	B;B;B	0.11329	0.002;0.002;0.006	T	0.20605	-1.0270	10	0.10902	T	0.67	6.6467	7.0376	0.25002	0.4722:0.0:0.4127:0.1151	.	519;561;449	P49418-2;P49418;Q8NFL4	.;AMPH_HUMAN;.	T	519;561;519;463	ENSP00000317441:I519T;ENSP00000348602:I561T;ENSP00000390734:I519T	ENSP00000317441:I519T	I	-	2	0	AMPH	38398070	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	0.178000	0.16820	-0.877000	0.04012	-0.326000	0.08463	ATA	.	.		0.587	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		G	38431545	A	G	38431545	3	3	115	1	0	0	0	0	1	0	0	0	588	449	16	2	417	2	AMPH	7	38431545	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	10759516	38431545	120707118	158	19697										
POLM	27434	hgsc.bcm.edu	37	chr7	44119318	44119318	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgccttcaaagcctgctgccTcggccagtatctccagagcc	9	16	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:44119318T>C	ENST00000242248.5	-	4	595	c.494A>G	c.(493-495)gAg>gGg	p.E165G	POLM_ENST00000492971.1_5'Flank|POLM_ENST00000335195.6_Missense_Mutation_p.E165G|POLM_ENST00000395831.3_Missense_Mutation_p.E165G	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	165					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(3)|skin(2)	22						GCCTGCTGCCTCGGCCAGTAT	0.647								DNA polymerases (catalytic subunits)																													p.E165G		Atlas-SNP	.											POLM,NS,carcinoma,0,1	POLM	50	.	0			c.A494G						.						37	41	40					7																	44119318		2203	4299	6502	SO:0001583	missense	27434	exon4			GCTGCCTCGGCCA	AF176097	CCDS34625.1, CCDS64635.1, CCDS64636.1	7p13	2012-05-18			ENSG00000122678	ENSG00000122678		"DNA polymerases"	9185	protein-coding gene	gene with protein product	"Pol iota"	606344				10982892	Standard	XM_005249708		Approved	Tdt-N	uc003tjt.3	Q9NP87	OTTHUMG00000155353	ENST00000242248.5:c.494A>G	chr7.hg19:g.44119318T>C	ENSP00000242248:p.Glu165Gly	47.0	0.0		68.0	3.0	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Missense_Mutation	SNP	ENST00000242248.5	hg19	CCDS34625.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.932015	0.73442	.	.	ENSG00000122678	ENST00000335195;ENST00000242248;ENST00000395831;ENST00000414235	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.75	5.75	0.90469	DNA-directed DNA polymerase X (1);DNA-directed DNA polymerase, family X, beta-like, N-terminal (2);	0.154038	0.56097	D	0.000024	T	0.70020	0.3176	M	0.84326	2.69	0.46823	D	0.99921	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;1.0;0.999	D;D;D;D;D;D	0.91635	0.943;0.967;0.943;0.999;0.964;0.947	T	0.74674	-0.3586	10	0.72032	D	0.01	-36.2438	12.4405	0.55621	0.0:0.0:0.0:1.0	.	132;165;165;165;165;165	B4DG75;Q6PIY2;Q9H980;Q86WQ9;Q6P5X8;Q9NP87	.;.;.;.;.;DPOLM_HUMAN	G	165;165;165;132	ENSP00000335141:E165G;ENSP00000242248:E165G;ENSP00000379174:E165G;ENSP00000390899:E132G	ENSP00000242248:E165G	E	-	2	0	POLM	44085843	1.000000	0.71417	0.949000	0.38748	0.402000	0.30811	5.621000	0.67743	2.200000	0.70718	0.533000	0.62120	GAG	.	.		0.647	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284		C	44119318	T	C	44119318	3	2	115	1	0	0	0	0	1	0	0	0	12215	1551	54	2	1022	2	POLM	7	44119318	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	5687773	44119318	115019345	159	19698										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48318670	48318670	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcatactctcatatatgaacCaatctaaggacttttctgat	5	9	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:48318670C>A	ENST00000435803.1	+	18	7903	c.7879C>A	c.(7879-7881)Caa>Aaa	p.Q2627K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2627					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATATATGAACCAATCTAAGGA	0.333																																					p.Q2627K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C7879A						.						42	41	41					7																	48318670		1808	4066	5874	SO:0001583	missense	154664	exon18			ATGAACCAATCTA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.7879C>A	chr7.hg19:g.48318670C>A	ENSP00000411096:p.Gln2627Lys	63.0	0.0		54.0	20.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	2.973	-0.211932	0.06140	.	.	ENSG00000179869	ENST00000435803	T	0.56611	0.45	4.93	2.15	0.27550	.	0.632381	0.13900	N	0.354941	T	0.33294	0.0858	N	0.20986	0.625	0.09310	N	0.999998	B	0.06786	0.001	B	0.06405	0.002	T	0.20505	-1.0273	10	0.46703	T	0.11	.	3.8515	0.08957	0.1687:0.5792:0.1627:0.0894	.	2627	Q86UQ4	ABCAD_HUMAN	K	2627	ENSP00000411096:Q2627K	ENSP00000411096:Q2627K	Q	+	1	0	ABCA13	48289216	0.002000	0.14202	0.008000	0.14137	0.006000	0.05464	-0.167000	0.09940	0.163000	0.19507	-0.776000	0.03382	CAA	.	.		0.333	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48318670	C	A	48318670	3	1	115	1	0	0	0	0	1	0	0	0	31	595	21	3	7778	3	ABCA13	7	48318670	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	4199352	48318670	110819993	160	19699										
ZNF679	168417	hgsc.bcm.edu	37	chr7	63727165	63727165	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	accctacaaatgtgaagaatGtgacaaagcttttaagtggt	9	6	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:63727165G>A	ENST00000421025.1	+	5	1423	c.1154G>A	c.(1153-1155)tGt>tAt	p.C385Y	ZNF679_ENST00000255746.4_Missense_Mutation_p.C385Y	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						TGTGAAGAATGTGACAAAGCT	0.383																																					p.C385Y		Atlas-SNP	.											.	ZNF679	80	.	0			c.G1154A						.						41	40	41					7																	63727165		692	1591	2283	SO:0001583	missense	168417	exon5			AAGAATGTGACAA	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"Zinc fingers, C2H2-type", "-"	28650	protein-coding gene	gene with protein product	"hypothetical protein MGC42415"					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.1154G>A	chr7.hg19:g.63727165G>A	ENSP00000416809:p.Cys385Tyr	38.0	0.0		40.0	4.0	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	hg19	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	G	13.25	2.181612	0.38511	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	D;D	0.85861	-2.04;-2.04	0.819	0.819	0.18785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93025	0.7780	H	0.95151	3.63	0.36675	D	0.878734	D	0.76494	0.999	D	0.83275	0.996	D	0.91639	0.5325	9	0.87932	D	0	.	6.9957	0.24780	0.0:0.0:1.0:0.0	.	385	Q8IYX0	ZN679_HUMAN	Y	385	ENSP00000416809:C385Y;ENSP00000255746:C385Y	ENSP00000255746:C385Y	C	+	2	0	ZNF679	63364600	1.000000	0.71417	0.751000	0.31187	0.752000	0.42762	6.652000	0.74377	0.191000	0.20236	0.194000	0.17425	TGT	.	.		0.383	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		A	63727165	G	A	63727165	3	1	115	1	0	0	0	0	1	0	0	0	18101	1377	48	3	1168	3	ZNF679	7	63727165	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	15408495	63727165	95411498	161	19700										
HIP1	3092	hgsc.bcm.edu	37	chr7	75174427	75174427	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cccacagccttggaggctgaGataagtccttctgtccatcg	10	13	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:75174427G>C	ENST00000336926.6	-	26	2645	c.2619C>G	c.(2617-2619)atC>atG	p.I873M	HIP1_ENST00000434438.2_Missense_Mutation_p.I822M	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	873	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.|Important for actin binding. {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						TGGAGGCTGAGATAAGTCCTT	0.473			T	PDGFRB	CMML																																p.I873M		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.C2619G						.						126	128	128					7																	75174427		2203	4300	6503	SO:0001583	missense	3092	exon26			GGCTGAGATAAGT	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.2619C>G	chr7.hg19:g.75174427G>C	ENSP00000336747:p.Ile873Met	78.0	0.0		60.0	24.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	hg19	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	g	18.44	3.623706	0.66901	.	.	ENSG00000127946	ENST00000336926;ENST00000434438	T;T	0.62788	0.0;0.0	5.6	1.69	0.24217	I/LWEQ (4);	0.000000	0.85682	D	0.000000	T	0.80742	0.4681	H	0.94771	3.58	0.43771	D	0.99629	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	T	0.77474	-0.2574	10	0.87932	D	0	-29.4678	5.955	0.19269	0.2214:0.0:0.6411:0.1375	.	822;873	E7ES17;O00291	.;HIP1_HUMAN	M	873;822	ENSP00000336747:I873M;ENSP00000410300:I822M	ENSP00000336747:I873M	I	-	3	3	HIP1	75012363	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	1.353000	0.34045	0.032000	0.15435	0.655000	0.94253	ATC	.	.		0.473	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		C	75174427	G	C	75174427	3	2	115	1	0	0	0	0	1	0	0	0	7123	932	33	4	518	4	HIP1	7	75174427	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	11447262	75174427	83964236	162	19701										
CCDC146	57639	hgsc.bcm.edu	37	chr7	76866342	76866342	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccttgctgcatgacgccgtgAtgaggtatgcaatttaccaa	10	10	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:76866342A>G	ENST00000285871.4	+	3	362	c.235A>G	c.(235-237)Atg>Gtg	p.M79V	CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	79										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				TGACGCCGTGATGAGGTATGC	0.418																																					p.M79V		Atlas-SNP	.											.	CCDC146	87	.	0			c.A235G						.						174	129	144					7																	76866342		2203	4300	6503	SO:0001583	missense	57639	exon3			GCCGTGATGAGGT	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.235A>G	chr7.hg19:g.76866342A>G	ENSP00000285871:p.Met79Val	102.0	0.0		98.0	4.0	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	hg19	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	A	4.999	0.185457	0.09495	.	.	ENSG00000135205	ENST00000415750;ENST00000285871	D;D	0.83506	-1.73;-1.73	5.55	-2.84	0.05751	.	0.776569	0.11905	N	0.518229	T	0.47600	0.1454	N	0.00538	-1.39	0.23791	N	0.996834	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.48736	-0.9009	10	0.19590	T	0.45	0.0885	6.0693	0.19881	0.5474:0.0:0.3389:0.1137	.	79;79	Q8IYE0;C9JRR4	CC146_HUMAN;.	V	79	ENSP00000388649:M79V;ENSP00000285871:M79V	ENSP00000285871:M79V	M	+	1	0	AC007000.1	76704278	1.000000	0.71417	0.012000	0.15200	0.839000	0.47603	1.536000	0.36072	-0.667000	0.05303	0.477000	0.44152	ATG	.	.		0.418	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		G	76866342	A	G	76866342	3	3	115	1	0	0	0	0	1	0	0	0	2782	333	12	2	241	2	CCDC146	7	76866342	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1691915	76866342	82272321	163	19702										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77551975	77551975	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ataacaaatgtctctgatgaAgtctccagtgaggaaggtcc	10	8	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:77551975A>G	ENST00000248550.7	+	10	1075	c.999A>G	c.(997-999)gaA>gaG	p.E333E	PHTF2_ENST00000416283.2_Silent_p.E299E|PHTF2_ENST00000454592.1_3'UTR|PHTF2_ENST00000424760.1_Silent_p.E295E|PHTF2_ENST00000275575.7_Silent_p.E295E|PHTF2_ENST00000422959.2_Silent_p.E299E|PHTF2_ENST00000307305.8_Silent_p.E295E|PHTF2_ENST00000415251.2_Silent_p.E295E|PHTF2_ENST00000450574.1_Silent_p.E299E			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	333					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						TCTCTGATGAAGTCTCCAGTG	0.393																																					p.E299E		Atlas-SNP	.											.	PHTF2	104	.	0			c.A897G						.						66	63	64					7																	77551975		1856	4090	5946	SO:0001819	synonymous_variant	57157	exon9			TGATGAAGTCTCC	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.999A>G	chr7.hg19:g.77551975A>G		92.0	0.0		90.0	4.0	NM_001127359	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Silent	SNP	ENST00000248550.7	hg19																																																																																				.	.		0.393	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		G	77551975	A	G	77551975	2	3	115	1	0	0	0	0	0	0	0	1	11872	69	3	2		2	PHTF2	7	77551975	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	685633	77551975	81586688	164	19703										
PEX1	5189	hgsc.bcm.edu	37	chr7	92123943	92123943	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cagggctttgcagcctgtgcTctgggaaaaacaaacaacat	10	10	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:92123943T>C	ENST00000248633.4	-	18	2879	c.2784A>G	c.(2782-2784)agA>agG	p.R928R	PEX1_ENST00000438045.1_Splice_Site_p.R606R|PEX1_ENST00000428214.1_Splice_Site_p.R871R	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	928					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			CAGCCTGTGCTCTGGGAAAAA	0.353																																					p.R928R		Atlas-SNP	.											.	PEX1	102	.	0			c.A2784G						.						50	52	51					7																	92123943		2203	4300	6503	SO:0001630	splice_region_variant	5189	exon18			CTGTGCTCTGGGA	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.2784-1A>G	chr7.hg19:g.92123943T>C		84.0	0.0		83.0	4.0	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	hg19	CCDS5627.1																																																																																			.	.		0.353	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466	Silent	C	92123943	T	C	92123943	5	2	115	1	0	0	0	0	0	0	1	0	11744	1565	54	2	1095	2	PEX1	7	92123943	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	14571968	92123943	67014720	165	19704										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94056343	94056343	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caccatggtgatcaaggtgcTcctggctccgtgggtcctgc	13	13	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:94056343T>C	ENST00000297268.6	+	47	3600	c.3129T>C	c.(3127-3129)gcT>gcC	p.A1043A		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1043					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	ATCAAGGTGCTCCTGGCTCCG	0.463										HNSCC(75;0.22)																											p.A1043A		Atlas-SNP	.											.	COL1A2	240	.	0			c.T3129C						.						93	82	86					7																	94056343		2203	4300	6503	SO:0001819	synonymous_variant	1278	exon47			AGGTGCTCCTGGC	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3129T>C	chr7.hg19:g.94056343T>C		88.0	0.0		91.0	5.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	hg19	CCDS34682.1																																																																																			.	.		0.463	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		C	94056343	T	C	94056343	2	2	115	1	0	0	0	0	0	0	0	1	3680	1538	54	2		2	COL1A2	7	94056343	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1932400	94056343	65082320	166	19705										
CASD1	64921	hgsc.bcm.edu	37	chr7	94164818	94164818	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tggatggcttacatcttcctGaatcgagcagagaaactgtg	11	8	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:94164818G>C	ENST00000297273.4	+	8	1113	c.826G>C	c.(826-828)Gaa>Caa	p.E276Q		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	276						integral component of membrane (GO:0016021)				NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			ACATCTTCCTGAATCGAGCAG	0.323																																					p.E276Q		Atlas-SNP	.											.	CASD1	70	.	0			c.G826C						.						85	83	83					7																	94164818		2203	4300	6503	SO:0001583	missense	64921	exon8			CTTCCTGAATCGA	AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 12"	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.826G>C	chr7.hg19:g.94164818G>C	ENSP00000297273:p.Glu276Gln	190.0	0.0		192.0	77.0	NM_022900	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Missense_Mutation	SNP	ENST00000297273.4	hg19	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057289	0.76074	.	.	ENSG00000127995	ENST00000297273	T	0.17370	2.28	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.21509	0.0518	N	0.19112	0.55	0.80722	D	1	D;D	0.61080	0.989;0.989	P;P	0.55785	0.784;0.784	T	0.04103	-1.0977	10	0.16896	T	0.51	.	19.0801	0.93178	0.0:0.0:1.0:0.0	.	276;276	Q8WZ77;Q96PB1	.;CASD1_HUMAN	Q	276	ENSP00000297273:E276Q	ENSP00000297273:E276Q	E	+	1	0	CASD1	94002754	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.391000	0.97249	2.593000	0.87608	0.591000	0.81541	GAA	.	.		0.323	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900		C	94164818	G	C	94164818	3	2	115	1	0	0	0	0	1	0	0	0	2666	1291	45	4	856	4	CASD1	7	94164818	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	108475	94164818	64973845	167	19706										
ZNF394	84124	hgsc.bcm.edu	37	chr7	99091412	99091412	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agagcgctgtttgaagctctTctcgcattcttcacacttat	7	11	4	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:99091412T>C	ENST00000337673.6	-	3	1629	c.1426A>G	c.(1426-1428)Aag>Gag	p.K476E	ZNF394_ENST00000394177.3_5'Flank|ZNF394_ENST00000426306.2_3'UTR|ZNF789_ENST00000493485.1_Intron|ZNF789_ENST00000494186.1_Intron	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	476					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					TTGAAGCTCTTCTCGCATTCT	0.453																																					p.K476E	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											.	ZNF394	48	.	0			c.A1426G						.						120	116	117					7																	99091412		2203	4300	6503	SO:0001583	missense	84124	exon3			AGCTCTTCTCGCA	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"Zinc fingers, C2H2-type", "-", "-", "-"	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.1426A>G	chr7.hg19:g.99091412T>C	ENSP00000337363:p.Lys476Glu	187.0	0.0		219.0	68.0	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Missense_Mutation	SNP	ENST00000337673.6	hg19	CCDS5666.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.028863	0.75504	.	.	ENSG00000160908	ENST00000337673	T	0.07567	3.18	3.58	3.58	0.41010	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.51477	D	0.000085	T	0.26340	0.0643	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.01371	-1.1372	10	0.54805	T	0.06	.	10.7684	0.46308	0.0:0.0:0.0:1.0	.	476	Q53GI3	ZN394_HUMAN	E	476	ENSP00000337363:K476E	ENSP00000337363:K476E	K	-	1	0	ZNF394	98929348	0.916000	0.31088	0.963000	0.40424	0.817000	0.46193	3.134000	0.50538	1.858000	0.53909	0.533000	0.62120	AAG	.	.		0.453	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164		C	99091412	T	C	99091412	3	2	115	1	0	0	0	0	1	0	0	0	17895	1792	62	2	263	2	ZNF394	7	99091412	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4926594	99091412	60047251	168	19707										
TRIM4	89122	hgsc.bcm.edu	37	chr7	99500933	99500933	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aatagttcacatcctggatcTcactcctaagaaggtagaga	8	9	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:99500933T>C	ENST00000355947.2	-	6	956	c.827A>G	c.(826-828)gAg>gGg	p.E276G	TRIM4_ENST00000354241.5_Missense_Mutation_p.E250G|TRIM4_ENST00000349062.2_Missense_Mutation_p.E250G	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	276					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				ATCCTGGATCTCACTCCTAAG	0.473																																					p.E276G		Atlas-SNP	.											.	TRIM4	33	.	0			c.A827G						.						105	99	101					7																	99500933		2203	4300	6503	SO:0001583	missense	89122	exon6			TGGATCTCACTCC	AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16275	protein-coding gene	gene with protein product	"tripartite motif protein TRIM4", "tripartite motif protein 4"		"tripartite motif-containing 4"			11331580	Standard	NM_033017		Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.827A>G	chr7.hg19:g.99500933T>C	ENSP00000348216:p.Glu276Gly	89.0	0.0		85.0	4.0	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Missense_Mutation	SNP	ENST00000355947.2	hg19	CCDS5679.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.515|7.515	0.655393|0.655393	0.14580|0.14580	.|.	.|.	ENSG00000146833|ENSG00000146833	ENST00000355947;ENST00000349062;ENST00000542799;ENST00000354241|ENST00000447480	T;T;T|.	0.05855|.	3.38;3.38;3.38|.	2.16|2.16	0.984|0.984	0.19773|0.19773	.|.	.|.	.|.	.|.	.|.	T|.	0.44159|.	0.1280|.	M|M	0.71871|0.71871	2.18|2.18	0.18873|0.18873	N|N	0.999984|0.999984	P;P;P|.	0.46987|.	0.591;0.827;0.888|.	B;B;B|.	0.43889|.	0.399;0.424;0.435|.	T|.	0.38222|.	-0.9671|.	9|.	0.62326|.	D|.	0.03|.	.|.	3.9474|3.9474	0.09353|0.09353	0.0:0.1841:0.0:0.8159|0.0:0.1841:0.0:0.8159	.|.	250;250;276|.	Q9C037-3;Q9C037-2;Q9C037|.	.;.;TRIM4_HUMAN|.	G|W	276;250;106;250|151	ENSP00000348216:E276G;ENSP00000275736:E250G;ENSP00000346186:E250G|.	ENSP00000275736:E250G|.	E|X	-|-	2|3	0|0	TRIM4|TRIM4	99338869|99338869	0.965000|0.965000	0.33210|0.33210	0.463000|0.463000	0.27130|0.27130	0.079000|0.079000	0.17450|0.17450	2.157000|2.157000	0.42320|0.42320	0.291000|0.291000	0.22468|0.22468	-0.263000|-0.263000	0.10527|0.10527	GAG|TGA	.	.		0.473	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017		C	99500933	T	C	99500933	3	2	115	1	0	0	0	0	1	0	0	0	16529	1551	54	2	683	2	TRIM4	7	99500933	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	409521	99500933	59637730	169	19708										
TAF6	6878	hgsc.bcm.edu	37	chr7	99711537	99711537	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agtcaatgtcactggtggtgAgcttctgccgcttccccatg	11	12	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:99711537A>G	ENST00000344095.4	-	3	722	c.197T>C	c.(196-198)cTc>cCc	p.L66P	RP11-506M12.1_ENST00000494221.1_RNA|TAF6_ENST00000437822.2_Missense_Mutation_p.L103P|TAF6_ENST00000452041.1_Missense_Mutation_p.L66P|TAF6_ENST00000453269.2_Missense_Mutation_p.L66P|TAF6_ENST00000497233.1_5'Flank|TAF6_ENST00000418432.2_Missense_Mutation_p.L9P|TAF6_ENST00000472509.1_Missense_Mutation_p.L123P	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	66					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACTGGTGGTGAGCTTCTGCCG	0.577																																					p.L103P		Atlas-SNP	.											.	TAF6	55	.	0			c.T308C						.						125	108	114					7																	99711537		2203	4300	6503	SO:0001583	missense	6878	exon3			GTGGTGAGCTTCT		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD", "transcription initiation factor TFIID 70 kD subunit"	602955	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.197T>C	chr7.hg19:g.99711537A>G	ENSP00000344537:p.Leu66Pro	152.0	0.0		147.0	6.0	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	hg19	CCDS5686.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.512368	0.85389	.	.	ENSG00000106290	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822;ENST00000493322;ENST00000440225;ENST00000452438;ENST00000523306;ENST00000449571;ENST00000520135;ENST00000451699;ENST00000417349	T;T;T;T;T;T;T;T;T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29	5.63	5.63	0.86233	Histone-fold (2);TATA box binding protein associated factor (TAF) (2);	0.000000	0.85682	D	0.000000	D	0.84460	0.5477	M	0.89968	3.075	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.998;0.996;0.998;0.998;0.986;0.99	D	0.87673	0.2542	10	0.87932	D	0	-23.7828	13.785	0.63104	1.0:0.0:0.0:0.0	.	103;66;56;66;66;9	B4DT11;P49848-2;A4D299;P49848;C9JTY6;B3KUR4	.;.;.;TAF6_HUMAN;.;.	P	66;123;66;66;9;103;66;66;66;56;66;56;66;66	ENSP00000389575:L66P;ENSP00000419760:L123P;ENSP00000416396:L66P;ENSP00000344537:L66P;ENSP00000399982:L103P;ENSP00000419555:L66P;ENSP00000410012:L66P;ENSP00000412346:L66P;ENSP00000428639:L56P;ENSP00000390073:L66P;ENSP00000428071:L56P;ENSP00000406315:L66P;ENSP00000390220:L66P	ENSP00000344537:L66P	L	-	2	0	TAF6	99549473	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.451000	0.90343	2.139000	0.66308	0.459000	0.35465	CTC	.	.		0.577	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		G	99711537	A	G	99711537	3	3	115	1	0	0	0	0	1	0	0	0	15545	304	11	2	1888	2	TAF6	7	99711537	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	210604	99711537	59427126	170	19709										
STAG3	10734	hgsc.bcm.edu	37	chr7	99808723	99808723	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cgcccacgcccaccctcaccTccacagctgtgaagagcagg	9	19	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:99808723T>C	ENST00000426455.1	+	30	3735	c.3328T>C	c.(3328-3330)Tcc>Ccc	p.S1110P	STAG3_ENST00000317296.5_Missense_Mutation_p.S1110P|STAG3_ENST00000394018.2_Missense_Mutation_p.S1052P|GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA|STAG3_ENST00000440830.1_3'UTR	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	1110					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CACCCTCACCTCCACAGCTGT	0.602																																					p.S1110P		Atlas-SNP	.											.	STAG3	121	.	0			c.T3328C						.						60	63	62					7																	99808723		2203	4300	6503	SO:0001583	missense	10734	exon30			CTCACCTCCACAG	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.3328T>C	chr7.hg19:g.99808723T>C	ENSP00000400359:p.Ser1110Pro	86.0	0.0		113.0	7.0	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	hg19	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	t	18.27	3.587288	0.66105	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000339784;ENST00000379577;ENST00000317296;ENST00000412190	T;T;T;T	0.35973	1.28;1.28;1.28;1.28	5.41	5.41	0.78517	.	0.000000	0.47093	D	0.000241	T	0.56645	0.1999	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	0.989;0.999;1.0	P;D;D	0.80764	0.837;0.994;0.963	T	0.60459	-0.7259	10	0.87932	D	0	-13.0087	11.841	0.52355	0.0:0.0:0.0:1.0	.	1052;1110;1110	B4DZ10;D6W5U7;Q9UJ98	.;.;STAG3_HUMAN	P	1110;1052;773;130;1110;68	ENSP00000400359:S1110P;ENSP00000377586:S1052P;ENSP00000319318:S1110P;ENSP00000395039:S68P	ENSP00000319318:S1110P	S	+	1	0	STAG3	99646659	1.000000	0.71417	0.899000	0.35326	0.309000	0.27889	4.506000	0.60428	2.056000	0.61249	0.459000	0.35465	TCC	.	.		0.602	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		C	99808723	T	C	99808723	3	2	115	1	0	0	0	0	1	0	0	0	15259	1551	54	2	3442	2	STAG3	7	99808723	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	97186	99808723	59329940	171	19710										
MUC17	140453	hgsc.bcm.edu	37	chr7	100680430	100680430	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agttcatctcctacaactgcTgacggtagcagcatgccaac	8	13	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:100680430T>C	ENST00000306151.4	+	3	5797	c.5733T>C	c.(5731-5733)gcT>gcC	p.A1911A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1911	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CTACAACTGCTGACGGTAGCA	0.502																																					p.A1911A		Atlas-SNP	.											.	MUC17	804	.	0			c.T5733C						.						248	252	251					7																	100680430		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTGCTGACGGT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5733T>C	chr7.hg19:g.100680430T>C		130.0	0.0		97.0	4.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100680430	T	C	100680430	2	2	115	1	0	0	0	0	0	0	0	1	9983	1567	55	2		2	MUC17	7	100680430	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	871707	100680430	58458233	172	19711										
CUX1	1523	hgsc.bcm.edu	37	chr7	101840321	101840321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gccagtcagaaagtgctgggAgcgtctccgagggcgaggag	18	9	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:101840321A>G	ENST00000292535.7	+	15	1668	c.1630A>G	c.(1630-1632)Agc>Ggc	p.S544G	SNORA48_ENST00000517015.1_RNA|CUX1_ENST00000550008.2_Missense_Mutation_p.S544G|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000556210.1_Missense_Mutation_p.S442G|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Missense_Mutation_p.S442G|CUX1_ENST00000360264.3_Missense_Mutation_p.S555G|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000549414.2_Missense_Mutation_p.S544G|CUX1_ENST00000437600.4_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	544					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						AAGTGCTGGGAGCGTCTCCGA	0.512																																					p.S555G		Atlas-SNP	.											.	CUX1	253	.	0			c.A1663G						.						94	98	97					7																	101840321		2203	4300	6503	SO:0001583	missense	1523	exon15			GCTGGGAGCGTCT	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1630A>G	chr7.hg19:g.101840321A>G	ENSP00000292535:p.Ser544Gly	50.0	0.0		80.0	4.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.914871	0.52546	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.61627	0.11;0.09;0.09;0.1;0.11;0.11	5.71	3.33	0.38152	Homeodomain protein CUT (1);Lambda repressor-like, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.38427	0.1040	N	0.24115	0.695	0.80722	D	1	B;B	0.12013	0.005;0.004	B;B	0.16722	0.016;0.009	T	0.09530	-1.0670	10	0.29301	T	0.29	-6.7211	6.5345	0.22346	0.7314:0.1321:0.1365:0.0	.	544;555	P39880;P39880-3	CUX1_HUMAN;.	G	555;544;544;544;442;442	ENSP00000353401:S555G;ENSP00000292535:S544G;ENSP00000446630:S544G;ENSP00000447373:S544G;ENSP00000450125:S442G;ENSP00000451558:S442G	ENSP00000292535:S544G	S	+	1	0	CUX1	101627041	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	5.058000	0.64300	0.434000	0.26340	0.459000	0.35465	AGC	.	.		0.512	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		G	101840321	A	G	101840321	3	3	115	1	0	0	0	0	1	0	0	0	4066	304	11	2	1755	2	CUX1	7	101840321	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1159891	101840321	57298342	173	19712										
DNAJC2	27000	hgsc.bcm.edu	37	chr7	102957429	102957429	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cgagcctcagcttcctctttCtcttttctgatttgctcatt	5	13	5	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:102957429C>T	ENST00000379263.3	-	13	1525	c.1275G>A	c.(1273-1275)gaG>gaA	p.E425E	PMPCB_ENST00000420236.2_Intron|DNAJC2_ENST00000249270.7_Silent_p.E372E	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	425					'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)			endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						CTTCCTCTTTCTCTTTTCTGA	0.393																																					p.E425E		Atlas-SNP	.											.	DNAJC2	46	.	0			c.G1275A						.						127	117	120					7																	102957429		1860	4098	5958	SO:0001819	synonymous_variant	27000	exon13			CTCTTTCTCTTTT	X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"Heat shock proteins / DNAJ (HSP40)"	13192	protein-coding gene	gene with protein product		605502	"zuotin related factor 1"	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.1275G>A	chr7.hg19:g.102957429C>T		280.0	1.0		232.0	89.0	NM_014377	A4VCI0|Q9BVX1	Silent	SNP	ENST00000379263.3	hg19	CCDS43628.1																																																																																			.	.		0.393	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1			T	102957429	C	T	102957429	2	4	115	1	0	0	0	0	0	0	0	1	4641	912	32	3		3	DNAJC2	7	102957429	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	1117108	102957429	56181234	174	19713										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128445476	128445476	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agtatgacgtcagcagagtcTcagacttcagaaatggattt	10	7	3	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:128445476T>C	ENST00000297788.4	+	6	1213	c.846T>C	c.(844-846)tcT>tcC	p.S282S	CCDC136_ENST00000464832.1_Silent_p.S332S|CCDC136_ENST00000487361.1_Silent_p.S282S|CCDC136_ENST00000378685.4_Silent_p.S320S	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	282	Glu-rich.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CAGCAGAGTCTCAGACTTCAG	0.493																																					p.S320S		Atlas-SNP	.											.	CCDC136	170	.	0			c.T960C						.						82	85	84					7																	128445476		2006	4185	6191	SO:0001819	synonymous_variant	64753	exon7			AGAGTCTCAGACT		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.846T>C	chr7.hg19:g.128445476T>C		70.0	0.0		86.0	4.0	NM_001201372	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Silent	SNP	ENST00000297788.4	hg19	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	T	7.414	0.635312	0.14322	.	.	ENSG00000128596	ENST00000494552	.	.	.	5.65	-0.905	0.10527	.	.	.	.	.	T	0.50017	0.1591	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38023	-0.9680	4	.	.	.	-3.3201	4.9651	0.14087	0.0:0.344:0.1606:0.4954	.	.	.	.	P	159	.	.	L	+	2	0	CCDC136	128232712	1.000000	0.71417	0.996000	0.52242	0.572000	0.35998	0.524000	0.22940	-0.144000	0.11314	-0.274000	0.10170	CTC	.	.		0.493	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		C	128445476	T	C	128445476	2	2	115	1	0	0	0	0	0	0	0	1	2772	1538	54	2		2	CCDC136	7	128445476	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	25488047	128445476	30693187	175	19714										
CPA5	93979	hgsc.bcm.edu	37	chr7	130007288	130007288	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtcggagccggaggtggctgCcatagtgaacttcatcacag	14	10	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:130007288C>T	ENST00000485477.1	+	10	2043	c.914C>T	c.(913-915)gCc>gTc	p.A305V	CPA5_ENST00000355388.3_Missense_Mutation_p.A305V|CPA5_ENST00000461828.1_Missense_Mutation_p.A305V|CPA5_ENST00000466363.2_Missense_Mutation_p.A305V|CPA5_ENST00000474905.1_Missense_Mutation_p.A305V|CPA5_ENST00000431780.2_Missense_Mutation_p.A305V|CPA5_ENST00000393213.3_Missense_Mutation_p.A305V			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	305						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					GAGGTGGCTGCCATAGTGAAC	0.522																																					p.A305V		Atlas-SNP	.											.	CPA5	61	.	0			c.C914T						.						96	91	93					7																	130007288		2203	4300	6503	SO:0001583	missense	93979	exon11			TGGCTGCCATAGT	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.914C>T	chr7.hg19:g.130007288C>T	ENSP00000420237:p.Ala305Val	269.0	0.0		299.0	91.0	NM_080385	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	hg19	CCDS5819.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344562	0.61073	.	.	ENSG00000158525	ENST00000355388;ENST00000461828;ENST00000466363;ENST00000485477;ENST00000431780;ENST00000474905;ENST00000393213	T;T;T;T;T;T;T	0.16743	2.32;2.32;2.32;2.32;2.32;2.32;2.32	5.87	5.87	0.94306	Peptidase M14, carboxypeptidase A (2);	0.099447	0.44688	D	0.000433	T	0.36880	0.0983	M	0.68728	2.09	0.20307	N	0.999917	D;P	0.54964	0.969;0.873	P;P	0.56216	0.794;0.791	T	0.10337	-1.0634	9	.	.	.	.	19.2073	0.93736	0.0:1.0:0.0:0.0	.	305;305	G3V0G8;Q8WXQ8	.;CBPA5_HUMAN	V	305	ENSP00000347549:A305V;ENSP00000418183:A305V;ENSP00000419025:A305V;ENSP00000420237:A305V;ENSP00000393045:A305V;ENSP00000417314:A305V;ENSP00000376907:A305V	.	A	+	2	0	CPA5	129794524	0.974000	0.33945	0.983000	0.44433	0.003000	0.03518	4.787000	0.62432	2.780000	0.95670	0.655000	0.94253	GCC	.	.		0.522	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441		T	130007288	C	T	130007288	3	4	115	1	0	0	0	0	1	0	0	0	3795	739	26	3	948	3	CPA5	7	130007288	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	1561812	130007288	29131375	176	19715										
WDR91	29062	hgsc.bcm.edu	37	chr7	134870994	134870994	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agtccatggcagtgctccagTccacggtgaccacaggggct	13	13	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:134870994T>C	ENST00000354475.4	-	15	2184	c.2153A>G	c.(2152-2154)gAc>gGc	p.D718G	WDR91_ENST00000344400.5_3'UTR|WDR91_ENST00000423565.1_Missense_Mutation_p.D683G	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	718										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						AGTGCTCCAGTCCACGGTGAC	0.607																																					p.D718G		Atlas-SNP	.											.	WDR91	82	.	0			c.A2153G						.						91	75	81					7																	134870994		2203	4300	6503	SO:0001583	missense	29062	exon15			CTCCAGTCCACGG	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.2153A>G	chr7.hg19:g.134870994T>C	ENSP00000346466:p.Asp718Gly	98.0	0.0		117.0	5.0	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	hg19	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.811966	0.70797	.	.	ENSG00000105875	ENST00000354475;ENST00000423565	T;T	0.61510	0.1;0.1	5.54	4.37	0.52481	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.043871	0.85682	D	0.000000	T	0.57184	0.2036	M	0.65975	2.015	0.80722	D	1	P	0.36110	0.537	B	0.40410	0.328	T	0.51411	-0.8709	10	0.18710	T	0.47	-30.8023	12.7783	0.57461	0.0:0.0:0.1369:0.863	.	718	A4D1P6	WDR91_HUMAN	G	718;683	ENSP00000346466:D718G;ENSP00000392555:D683G	ENSP00000346466:D718G	D	-	2	0	WDR91	134521534	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.294000	0.72738	0.912000	0.36772	0.533000	0.62120	GAC	.	.		0.607	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		C	134870994	T	C	134870994	3	2	115	1	0	0	0	0	1	0	0	0	17353	1667	58	2	94	2	WDR91	7	134870994	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4863706	134870994	24267669	177	19716										
CREB3L2	64764	hgsc.bcm.edu	37	chr7	137586166	137586166	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctcagttgaacaagactccActctacaaaggagggagaaa	9	9	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:137586166A>G	ENST00000330387.6	-	8	1328	c.977T>C	c.(976-978)gTg>gCg	p.V326A	CREB3L2_ENST00000456390.1_Missense_Mutation_p.V326A	NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	326	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)		FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						ACAAGACTCCACTCTACAAAG	0.453			T	FUS	fibromyxoid sarcoma																																p.V326A		Atlas-SNP	.		Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	.	CREB3L2	62	.	0			c.T977C						.						72	67	69					7																	137586166		2203	4300	6503	SO:0001583	missense	64764	exon8			GACTCCACTCTAC	AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158		"basic leucine zipper proteins"	23720	protein-coding gene	gene with protein product		608834					Standard	NM_194071		Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.977T>C	chr7.hg19:g.137586166A>G	ENSP00000329140:p.Val326Ala	77.0	0.0		89.0	5.0	NM_194071	Q6P454|Q6ZMR6	Missense_Mutation	SNP	ENST00000330387.6	hg19	CCDS34760.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.427123	0.83667	.	.	ENSG00000182158	ENST00000330387;ENST00000456390	T;T	0.60171	0.21;0.21	5.46	5.46	0.80206	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.000000	0.85682	D	0.000000	T	0.72061	0.3414	M	0.69248	2.105	0.80722	D	1	P;P	0.52463	0.953;0.935	P;P	0.61003	0.867;0.882	T	0.75127	-0.3427	10	0.66056	D	0.02	0.5739	15.5429	0.76070	1.0:0.0:0.0:0.0	.	326;326	Q70SY1-2;Q70SY1	.;CR3L2_HUMAN	A	326	ENSP00000329140:V326A;ENSP00000403550:V326A	ENSP00000329140:V326A	V	-	2	0	CREB3L2	137236706	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	7.826000	0.86716	2.077000	0.62373	0.528000	0.53228	GTG	.	.		0.453	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341462.1	NM_194071		G	137586166	A	G	137586166	3	3	115	1	0	0	0	0	1	0	0	0	3859	159	6	2	605	2	CREB3L2	7	137586166	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2715172	137586166	21552497	178	19717										
UBN2	254048	hgsc.bcm.edu	37	chr7	138944069	138944069	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aagcggaagcggaaagaggaAggggaaaaggagaagaagcc	18	4	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:138944069A>G	ENST00000473989.3	+	5	858	c.858A>G	c.(856-858)gaA>gaG	p.E286E	UBN2_ENST00000288561.8_Silent_p.E203E	NM_173569.3	NP_775840.3	Q6ZU65	UBN2_HUMAN	ubinuclein 2	286	Lys-rich.					extracellular space (GO:0005615)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	42						GGAAAGAGGAAGGGGAAAAGG	0.398																																					p.E286E		Atlas-SNP	.											.	UBN2	90	.	0			c.A858G						.						137	143	141					7																	138944069		1840	4089	5929	SO:0001819	synonymous_variant	254048	exon5			AGAGGAAGGGGAA	AK098644	CCDS43655.1, CCDS43655.2	7q34	2008-12-08			ENSG00000157741	ENSG00000157741			21931	protein-coding gene	gene with protein product		613841				19029251	Standard	NM_173569		Approved	FLJ25778, KIAA2030	uc011kqr.2	Q6ZU65	OTTHUMG00000157623	ENST00000473989.3:c.858A>G	chr7.hg19:g.138944069A>G		100.0	0.0		86.0	5.0	NM_173569	A4D1S2|Q2YDY4|Q6P1K0|Q86XN9|Q8N7D1	Silent	SNP	ENST00000473989.3	hg19	CCDS43655.2	.	.	.	.	.	.	.	.	.	.	A	10.22	1.290846	0.23564	.	.	ENSG00000157741	ENST00000483726	.	.	.	5.34	1.57	0.23409	.	.	.	.	.	T	0.46112	0.1376	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24941	-1.0146	4	.	.	.	-9.0277	3.8046	0.08771	0.6043:0.0:0.2474:0.1483	.	.	.	.	R	55	.	.	K	+	2	0	UBN2	138594609	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	0.340000	0.19892	0.177000	0.19895	0.528000	0.53228	AAG	.	.		0.398	UBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349272.3	NM_173569		G	138944069	A	G	138944069	2	3	115	1	0	0	0	0	0	0	0	1	16908	69	3	2		2	UBN2	7	138944069	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1357903	138944069	20194594	179	19718										
GIMAP4	55303	hgsc.bcm.edu	37	chr7	150269812	150269812	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtggtgagggagaacaaggaAggctgctacactaataggat	15	5	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:150269812A>G	ENST00000255945.2	+	3	829	c.654A>G	c.(652-654)gaA>gaG	p.E218E	GIMAP4_ENST00000461940.1_Silent_p.E232E|GIMAP4_ENST00000494750.1_3'UTR	NM_018326.2	NP_060796.1	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	218	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGAACAAGGAAGGCTGCTACA	0.552																																					p.E218E		Atlas-SNP	.											.	GIMAP4	61	.	0			c.A654G						.						97	92	94					7																	150269812		2203	4300	6503	SO:0001819	synonymous_variant	55303	exon3			CAAGGAAGGCTGC	AK001972	CCDS5904.1	7q36.1	2014-04-04			ENSG00000133574	ENSG00000133574		"GTPases, IMAP"	21872	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 1"	608087				15474311, 18701445	Standard	NM_018326		Approved	HIMAP4, FLJ11110, IMAP4, IAN1	uc003whl.3	Q9NUV9	OTTHUMG00000157475	ENST00000255945.2:c.654A>G	chr7.hg19:g.150269812A>G		90.0	0.0		134.0	7.0	NM_018326		Silent	SNP	ENST00000255945.2	hg19	CCDS5904.1																																																																																			.	.		0.552	GIMAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348927.1	NM_018326		G	150269812	A	G	150269812	2	3	115	1	0	0	0	0	0	0	0	1	6389	69	3	2		2	GIMAP4	7	150269812	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	11325743	150269812	8868851	180	19719										
NOS3	4846	hgsc.bcm.edu	37	chr7	150704003	150704003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	taagatccgcttcaacagcaTctcctgctcagacccactgg	7	15	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:150704003T>C	ENST00000297494.3	+	16	2204	c.1847T>C	c.(1846-1848)aTc>aCc	p.I616T	NOS3_ENST00000461406.1_Missense_Mutation_p.I410T	NM_000603.4	NP_000594.2	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTCAACAGCATCTCCTGCTCA	0.607																																					p.I616T		Atlas-SNP	.											.	NOS3	131	.	0			c.T1847C						.						107	99	102					7																	150704003		2203	4300	6503	SO:0001583	missense	4846	exon16			ACAGCATCTCCTG		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000297494.3:c.1847T>C	chr7.hg19:g.150704003T>C	ENSP00000297494:p.Ile616Thr	189.0	0.0		207.0	9.0	NM_000603	Q495E5	Missense_Mutation	SNP	ENST00000297494.3	hg19	CCDS5912.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.945880	0.53079	.	.	ENSG00000164867	ENST00000297494;ENST00000461406	T;T	0.58358	0.34;0.34	5.14	5.14	0.70334	Flavodoxin/nitric oxide synthase (2);	0.116551	0.35903	N	0.002904	T	0.42200	0.1192	L	0.29908	0.895	0.80722	D	1	B;B	0.19331	0.011;0.035	B;B	0.25987	0.063;0.065	T	0.27123	-1.0083	10	0.29301	T	0.29	-10.0815	13.2187	0.59875	0.0:0.0:0.0:1.0	.	410;616	E7ESA7;P29474	.;NOS3_HUMAN	T	616;410	ENSP00000297494:I616T;ENSP00000417143:I410T	ENSP00000297494:I616T	I	+	2	0	NOS3	150334936	1.000000	0.71417	0.978000	0.43139	0.980000	0.70556	7.001000	0.76297	2.066000	0.61787	0.491000	0.48974	ATC	.	.		0.607	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603		C	150704003	T	C	150704003	3	2	115	1	0	0	0	0	1	0	0	0	10553	1435	50	2	2187	2	NOS3	7	150704003	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	434191	150704003	8434660	181	19720										
CHPF2	54480	hgsc.bcm.edu	37	chr7	150935431	150935431	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcccggggggctcctataggGgggagatttgaccggcaggc	18	10	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:150935431G>C	ENST00000035307.2	+	4	3496	c.1983G>C	c.(1981-1983)ggG>ggC	p.G661G	MIR671_ENST00000390183.1_RNA|RP4-548D19.3_ENST00000607902.1_RNA|CHPF2_ENST00000495645.1_Silent_p.G653G	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	661					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						CTCCTATAGGGGGGAGATTTG	0.701																																					p.G661G		Atlas-SNP	.											.	CHPF2	52	.	0			c.G1983C						.						9	13	11					7																	150935431		2184	4268	6452	SO:0001819	synonymous_variant	54480	exon4			TATAGGGGGGAGA	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.1983G>C	chr7.hg19:g.150935431G>C		71.0	0.0		88.0	4.0	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Silent	SNP	ENST00000035307.2	hg19	CCDS34779.1																																																																																			.	.		0.701	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015		C	150935431	G	C	150935431	2	2	115	1	0	0	0	0	0	0	0	1	3371	1219	43	4		4	CHPF2	7	150935431	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	231428	150935431	8203232	182	19721										
SMARCD3	6604	hgsc.bcm.edu	37	chr7	150939255	150939255	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gttgtcagggccataaagatCtttgtccagctcgatgacca	10	10	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:150939255C>T	ENST00000262188.8	-	6	1053	c.643G>A	c.(643-645)Gat>Aat	p.D215N	SMARCD3_ENST00000477169.1_5'UTR|RP4-548D19.3_ENST00000607902.1_RNA|SMARCD3_ENST00000392811.2_Missense_Mutation_p.D202N|SMARCD3_ENST00000356800.2_Missense_Mutation_p.D202N	NM_001003801.1	NP_001003801.1	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	215					cardiac right ventricle formation (GO:0003219)|cellular lipid metabolic process (GO:0044255)|chromatin remodeling (GO:0006338)|muscle cell differentiation (GO:0042692)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein binding (GO:0043393)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|secondary heart field specification (GO:0003139)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|receptor binding (GO:0005102)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCATAAAGATCTTTGTCCAGC	0.542																																					p.D215N		Atlas-SNP	.											.	SMARCD3	92	.	0			c.G643A						.						103	108	106					7																	150939255		2203	4300	6503	SO:0001583	missense	6604	exon6			AAAGATCTTTGTC	U66619	CCDS5924.1, CCDS34780.1	7q35-q36	2008-07-18			ENSG00000082014	ENSG00000082014			11108	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60C", "Swp73-like protein", "SWI/SNF complex 60 kDa subunit C", "60kDa BRG-1/Brm associated factor subunit c"	601737				8804307, 9693044	Standard	NM_001003801		Approved	BAF60C, Rsc6p, CRACD3	uc003wjs.3	Q6STE5	OTTHUMG00000157431	ENST00000262188.8:c.643G>A	chr7.hg19:g.150939255C>T	ENSP00000262188:p.Asp215Asn	99.0	0.0		124.0	5.0	NM_001003801	D3DX10|Q2YD86|Q75MJ2|Q75MR8|Q92926|Q9BUH1	Missense_Mutation	SNP	ENST00000262188.8	hg19	CCDS34780.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.453643	0.84209	.	.	ENSG00000082014	ENST00000262188;ENST00000392811;ENST00000356800;ENST00000347683	T;T;T	0.50001	0.76;0.76;0.76	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.59824	0.2222	L	0.39898	1.24	0.80722	D	1	D;D;D;B	0.67145	0.993;0.972;0.996;0.049	D;P;D;B	0.74674	0.984;0.83;0.981;0.065	T	0.58008	-0.7712	10	0.41790	T	0.15	-13.6949	16.2661	0.82579	0.0:1.0:0.0:0.0	.	215;215;202;215	B7Z4U8;B7ZA58;Q6STE5-2;Q6STE5	.;.;.;SMRD3_HUMAN	N	215;202;202;167	ENSP00000262188:D215N;ENSP00000376558:D202N;ENSP00000349254:D202N	ENSP00000262188:D215N	D	-	1	0	SMARCD3	150570188	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.818000	0.86416	2.423000	0.82170	0.561000	0.74099	GAT	.	.		0.542	SMARCD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348825.1	NM_001003801		T	150939255	C	T	150939255	3	4	115	1	0	0	0	0	1	0	0	0	14794	913	32	3	840	3	SMARCD3	7	150939255	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	3824	150939255	8199408	183	19722										
MLL3	58508	hgsc.bcm.edu	37	chr7	151919143	151919143	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgaagattcacagcagtctgAggaaggcactgaaacgaaaa	11	7	2	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr7:151919143A>G	ENST00000262189.6	-	22	3660	c.3442T>C	c.(3442-3444)Tca>Cca	p.S1148P	KMT2C_ENST00000355193.2_Missense_Mutation_p.S1148P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1148					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CAGCAGTCTGAGGAAGGCACT	0.274																																					p.S1148P		Atlas-SNP	.											.	MLL3	1564	.	0			c.T3442C						.						53	60	58					7																	151919143		2198	4294	6492	SO:0001583	missense	58508	exon22			AGTCTGAGGAAGG	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.3442T>C	chr7.hg19:g.151919143A>G	ENSP00000262189:p.Ser1148Pro	76.0	0.0		63.0	4.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.903787	0.33628	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.83837	-1.77;-1.76	5.58	5.58	0.84498	.	0.202603	0.24542	N	0.037639	T	0.79299	0.4422	N	0.19112	0.55	0.80722	D	1	P;D	0.64830	0.93;0.994	P;P	0.56088	0.462;0.791	T	0.76490	-0.2940	10	0.25751	T	0.34	.	10.2621	0.43434	0.8529:0.0:0.0:0.1471	.	1148;209	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	P	1148	ENSP00000262189:S1148P;ENSP00000347325:S1148P	ENSP00000262189:S1148P	S	-	1	0	MLL3	151550076	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.252000	0.58785	2.119000	0.64992	0.528000	0.53228	TCA	.	.		0.274	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			G	151919143	A	G	151919143	3	3	115	1	0	0	0	0	1	0	0	0	9631	304	11	2	11445	2	MLL3	7	151919143	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	979888	151919143	7219520	184	19723										
DEFA4	1669	hgsc.bcm.edu	37	chr8	6794324	6794324	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggtcttctggcccacgctgcTcctggcctggagcctcatca	11	16	4	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:6794324T>C	ENST00000297435.2	-	2	222	c.98A>G	c.(97-99)gAg>gGg	p.E33G		NM_001925.1	NP_001916.1	P12838	DEF4_HUMAN	defensin, alpha 4, corticostatin	33					antibacterial humoral response (GO:0019731)|defense response to fungus (GO:0050832)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	10				COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		CCCACGCTGCTCCTGGCCTGG	0.552																																					p.E33G		Atlas-SNP	.											.	DEFA4	19	.	0			c.A98G						.						74	70	71					8																	6794324		2203	4300	6503	SO:0001583	missense	1669	exon2			CGCTGCTCCTGGC	X65977	CCDS5961.1	8p23.1	2007-02-20			ENSG00000164821	ENSG00000164821		"Defensins, alpha"	2763	protein-coding gene	gene with protein product		601157		DEF4		8469233	Standard	NM_001925		Approved	HP-4	uc003wqu.1	P12838	OTTHUMG00000090382	ENST00000297435.2:c.98A>G	chr8.hg19:g.6794324T>C	ENSP00000297435:p.Glu33Gly	74.0	0.0		118.0	5.0	NM_001925	Q6EZF8	Missense_Mutation	SNP	ENST00000297435.2	hg19	CCDS5961.1	.	.	.	.	.	.	.	.	.	.	.	12.76	2.033554	0.35893	.	.	ENSG00000164821	ENST00000297435	T	0.37411	1.2	1.66	1.66	0.24008	Defensin propeptide (1);	0.601645	0.12414	U	0.471030	T	0.51873	0.1700	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.78314	0.991	T	0.28202	-1.0051	9	0.87932	D	0	.	5.4467	0.16539	0.0:0.0:0.0:1.0	.	33	P12838	DEF4_HUMAN	G	33	ENSP00000297435:E33G	ENSP00000297435:E33G	E	-	2	0	DEFA4	6781734	0.001000	0.12720	0.005000	0.12908	0.020000	0.10135	0.074000	0.14662	1.014000	0.39417	0.456000	0.33151	GAG	.	.		0.552	DEFA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206754.1	NM_001925		C	6794324	T	C	6794324	3	2	115	1	0	0	0	0	1	0	0	0	4393	1551	54	2	203	2	DEFA4	8	6794324	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10		6794324	139569698	185	19724										
XPO7	23039	hgsc.bcm.edu	37	chr8	21848320	21848320	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttcttttctttttttcaatAgagcgagcacttttcatttt	4	8	4	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:21848320A>G	ENST00000252512.9	+	18	2032		c.e18-1		XPO7_ENST00000433566.4_Splice_Site|XPO7_ENST00000434536.1_Splice_Site	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7						mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		TTTTTTCAATAGAGCGAGCAC	0.418																																					.		Atlas-SNP	.											.	XPO7	79	.	0			c.1933-2A>G						.						135	131	132					8																	21848320		1844	4091	5935	SO:0001630	splice_region_variant	23039	exon18			TTCAATAGAGCGA	AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"Exportins"	14108	protein-coding gene	gene with protein product		606140	"RAN binding protein 16"	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.1933-1A>G	chr8.hg19:g.21848320A>G		56.0	0.0		112.0	5.0	NM_015024	O94846|Q6PJK9|Q8NEK7	Splice_Site	SNP	ENST00000252512.9	hg19	CCDS47818.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.335284	0.81801	.	.	ENSG00000130227	ENST00000434536;ENST00000252512;ENST00000433566	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0637	0.80856	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	XPO7	21904266	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.313000	0.96297	2.274000	0.75844	0.528000	0.53228	.	.	.		0.418	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024	Intron	G	21848320	A	G	21848320	5	3	115	1	0	0	0	0	0	0	1	0	17464	434	15	2	2053	2	XPO7	8	21848320	Splice_Site	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	15053996	21848320	124515702	186	19725										
NEFM	4741	hgsc.bcm.edu	37	chr8	24775101	24775101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agaagctgaagctgaaggagAggaagccgaagctaaagagg	16	5	0	5			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:24775101A>G	ENST00000221166.5	+	3	2515	c.1733A>G	c.(1732-1734)gAg>gGg	p.E578G	GS1-72M22.1_ENST00000607058.1_RNA|NEFM_ENST00000518131.1_Missense_Mutation_p.E578G|NEFM_ENST00000433454.2_Missense_Mutation_p.E202G|NEFM_ENST00000437366.2_Missense_Mutation_p.E578G|NEFM_ENST00000521540.1_Intron			P07197	NFM_HUMAN	neurofilament, medium polypeptide	578	Tail.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		gctgaaggagaggaagccgaa	0.507																																					p.E578G		Atlas-SNP	.											.	NEFM	115	.	0			c.A1733G						.						35	39	37					8																	24775101		2203	4300	6503	SO:0001583	missense	4741	exon3			AAGGAGAGGAAGC	BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"Intermediate filaments type IV"	7734	protein-coding gene	gene with protein product		162250	"neurofilament, medium polypeptide 150kDa"	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.1733A>G	chr8.hg19:g.24775101A>G	ENSP00000221166:p.Glu578Gly	107.0	0.0		105.0	5.0	NM_005382	B4DGN2|E9PBF7|Q4QRK6	Missense_Mutation	SNP	ENST00000221166.5	hg19	CCDS6046.1	.	.	.	.	.	.	.	.	.	.	A	1.383	-0.582978	0.03827	.	.	ENSG00000104722	ENST00000221166;ENST00000518131;ENST00000437366;ENST00000433454	D;D;D;D	0.95069	-1.88;-1.89;-1.94;-3.6	4.08	2.8	0.32819	.	0.000000	0.45867	D	0.000340	D	0.90580	0.7047	M	0.73598	2.24	0.48395	D	0.99964	B;P	0.44734	0.421;0.842	B;B	0.35859	0.08;0.212	D	0.87160	0.2214	10	0.26408	T	0.33	.	6.8428	0.23973	0.7047:0.1495:0.0:0.1457	.	578;578	E7EMV2;P07197	.;NFM_HUMAN	G	578;578;578;202	ENSP00000221166:E578G;ENSP00000427872:E578G;ENSP00000410137:E578G;ENSP00000412295:E202G	ENSP00000221166:E578G	E	+	2	0	NEFM	24831006	1.000000	0.71417	0.959000	0.39883	0.018000	0.09664	4.704000	0.61831	1.793000	0.52555	0.260000	0.18958	GAG	.	.		0.507	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382		G	24775101	A	G	24775101	3	3	115	1	0	0	0	0	1	0	0	0	10325	304	11	2	1743	2	NEFM	8	24775101	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2926781	24775101	121588921	187	19726										
C8orf80	389643	hgsc.bcm.edu	37	chr8	27887829	27887829	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtcctccgcagcccccacctTcgtaacagagcttcaggtca	8	17	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:27887829T>C	ENST00000413272.2	-	16	2157	c.2015A>G	c.(2014-2016)gAa>gGa	p.E672G	NUGGC_ENST00000341513.6_Missense_Mutation_p.E672G	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	672					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										GCCCCCACCTTCGTAACAGAG	0.577																																					p.E672G		Atlas-SNP	.											.	.	.	.	0			c.A2015G						.						40	47	44					8																	27887829		2053	4178	6231	SO:0001583	missense	389643	exon16			CCACCTTCGTAAC	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"speckled-like pattern in the germinal center"		"chromosome 8 open reading frame 80"	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.2015A>G	chr8.hg19:g.27887829T>C	ENSP00000408697:p.Glu672Gly	49.0	0.0		95.0	4.0	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	hg19	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.619518	0.46736	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.17854	2.25;2.25	5.04	5.04	0.67666	.	0.124363	0.56097	D	0.000039	T	0.28400	0.0702	L	0.34521	1.04	0.40530	D	0.980926	D	0.89917	1.0	D	0.69307	0.963	T	0.03503	-1.1030	10	0.66056	D	0.02	-26.059	11.4644	0.50230	0.0:0.0:0.0:1.0	.	672	Q68CJ6	SLIP_HUMAN	G	672	ENSP00000408697:E672G;ENSP00000345031:E672G	ENSP00000345031:E672G	E	-	2	0	C8orf80	27943748	1.000000	0.71417	0.998000	0.56505	0.024000	0.10985	4.119000	0.57891	2.011000	0.59026	0.460000	0.39030	GAA	.	.		0.577	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		C	27887829	T	C	27887829	3	2	115	1	0	0	0	0	1	0	0	0	2441	1783	62	2	391	2	C8orf80	8	27887829	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3112728	27887829	118476193	188	19727										
ZNF395	55893	hgsc.bcm.edu	37	chr8	28210089	28210089	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aggccctgggctcgcacataCcccagatggagggctttgac	13	13	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:28210089C>T	ENST00000344423.5	-	6	1052		c.e6+1		ZNF395_ENST00000523202.1_Splice_Site|ZNF395_ENST00000523095.1_Splice_Site	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		CTCGCACATACCCCAGATGGA	0.587																																					.		Atlas-SNP	.											.	ZNF395	54	.	0			c.920+1G>A						.						126	109	115					8																	28210089		2203	4300	6503	SO:0001630	splice_region_variant	55893	exon7			CACATACCCCAGA	AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"Zinc fingers, C2H2-type"	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.920+1G>A	chr8.hg19:g.28210089C>T		51.0	0.0		106.0	31.0	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Splice_Site	SNP	ENST00000344423.5	hg19	CCDS6067.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.815622	0.70912	.	.	ENSG00000186918	ENST00000344423;ENST00000523202;ENST00000523095	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4092	0.83701	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF395	28266008	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	7.608000	0.82898	2.466000	0.83321	0.561000	0.74099	.	.	.		0.587	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1		Intron	T	28210089	C	T	28210089	5	4	115	1	0	0	0	0	0	0	1	0	17896	521	18	3	640	3	ZNF395	8	28210089	Splice_Site	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	322260	28210089	118153933	189	19728										
FUT10	84750	hgsc.bcm.edu	37	chr8	33230111	33230111	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaaatcagtccttgaatactAggccccaaaactcttgagat	7	10	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:33230111A>G	ENST00000327671.5	-	5	2055	c.1424T>C	c.(1423-1425)cTa>cCa	p.L475P	FUT10_ENST00000518672.1_Missense_Mutation_p.L447P|FUT10_ENST00000524021.1_Missense_Mutation_p.L447P	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	475					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		CTTGAATACTAGGCCCCAAAA	0.378																																					p.L475P		Atlas-SNP	.											.	FUT10	62	.	0			c.T1424C						.						62	58	59					8																	33230111		2203	4300	6503	SO:0001583	missense	84750	exon5			AATACTAGGCCCC	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"Fucosyltransferases"	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1424T>C	chr8.hg19:g.33230111A>G	ENSP00000332757:p.Leu475Pro	121.0	0.0		140.0	6.0	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Missense_Mutation	SNP	ENST00000327671.5	hg19	CCDS6088.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.851326	0.51270	.	.	ENSG00000172728	ENST00000327671;ENST00000380081;ENST00000518672;ENST00000524021	T;T;T	0.40756	1.02;1.02;1.02	5.54	5.54	0.83059	.	0.211836	0.32819	N	0.005620	T	0.55986	0.1955	M	0.76574	2.34	0.37732	D	0.925325	D;D;D	0.57899	0.976;0.963;0.981	P;P;P	0.53689	0.656;0.48;0.732	T	0.63954	-0.6520	10	0.46703	T	0.11	-13.4589	13.6262	0.62165	1.0:0.0:0.0:0.0	.	525;475;517	B4E056;Q6P4F1;E7EU36	.;FUT10_HUMAN;.	P	475;517;447;447	ENSP00000332757:L475P;ENSP00000430428:L447P;ENSP00000429870:L447P	ENSP00000332757:L475P	L	-	2	0	FUT10	33349653	0.991000	0.36638	0.491000	0.27477	0.817000	0.46193	4.014000	0.57145	2.112000	0.64535	0.533000	0.62120	CTA	.	.		0.378	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664		G	33230111	A	G	33230111	3	3	115	1	0	0	0	0	1	0	0	0	6110	420	15	2	19	2	FUT10	8	33230111	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5020022	33230111	113133911	190	19729										
C8orf41	80185	hgsc.bcm.edu	37	chr8	33358008	33358008	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	accacaagtctgcaggaaacTctggaatcaggaagaaaagc	10	9	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:33358008T>C	ENST00000431156.2	-	7	1878	c.1260A>G	c.(1258-1260)agA>agG	p.R420R	TTI2_ENST00000519356.1_5'UTR|TTI2_ENST00000520636.1_Splice_Site_p.R389R|MAK16_ENST00000360128.6_3'UTR|TTI2_ENST00000360742.5_Splice_Site_p.R420R	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	420																	TGCAGGAAACTCTGGAATCAG	0.408																																					p.R420R		Atlas-SNP	.											.	.	.	.	0			c.A1260G						.						79	72	75					8																	33358008		2203	4300	6503	SO:0001630	splice_region_variant	80185	exon7			GGAAACTCTGGAA	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1260-1A>G	chr8.hg19:g.33358008T>C		70.0	0.0		92.0	6.0	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Silent	SNP	ENST00000431156.2	hg19	CCDS6090.1																																																																																			.	.		0.408	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115	Silent	C	33358008	T	C	33358008	5	2	115	1	0	0	0	0	0	0	1	0	2429	1565	54	2	274	2	C8orf41	8	33358008	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	127897	33358008	113006014	191	19730										
ADAM32	203102	hgsc.bcm.edu	37	chr8	39091581	39091581	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cactggctgtcaaaaatggcTctcagtgtgatattgggagg	13	7	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:39091581T>C	ENST00000379907.4	+	16	1925	c.1798T>C	c.(1798-1800)Tct>Cct	p.S600P	ADAM32_ENST00000437682.2_Missense_Mutation_p.S501P|ADAM32_ENST00000519315.1_Missense_Mutation_p.S494P	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	600						integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			CAAAAATGGCTCTCAGTGTGA	0.299																																					p.S600P		Atlas-SNP	.											.	ADAM32	70	.	0			c.T1798C						.						51	43	46					8																	39091581		1806	4030	5836	SO:0001583	missense	203102	exon16			AATGGCTCTCAGT	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"ADAM metallopeptidase domain containing"	15479	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 32"			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1798T>C	chr8.hg19:g.39091581T>C	ENSP00000369238:p.Ser600Pro	69.0	0.0		81.0	4.0	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	hg19	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.663685	0.47572	.	.	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907	T;T;T	0.03413	3.94;4.0;4.33	5.0	-7.23	0.01480	ADAM, cysteine-rich (1);	2.562630	0.02191	N	0.061394	T	0.07683	0.0193	M	0.64997	1.995	0.09310	N	1	D;D;P	0.61080	0.989;0.974;0.928	P;P;P	0.50791	0.648;0.601;0.65	T	0.47328	-0.9126	10	0.87932	D	0	.	6.7453	0.23458	0.4605:0.0:0.3779:0.1616	.	501;494;600	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	P	501;494;600	ENSP00000405978:S501P;ENSP00000429422:S494P;ENSP00000369238:S600P	ENSP00000369238:S600P	S	+	1	0	ADAM32	39210738	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-1.038000	0.03553	-0.884000	0.03976	-0.451000	0.05528	TCT	.	.		0.299	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		C	39091581	T	C	39091581	3	2	115	1	0	0	0	0	1	0	0	0	249	1551	54	2	1860	2	ADAM32	8	39091581	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	5733573	39091581	107272441	192	19731										
IDO2	169355	hgsc.bcm.edu	37	chr8	39836687	39836687	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggttatgtctggcaggaaggAgaggcgcagcctgcagaggt	18	7	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:39836687A>G	ENST00000389060.4	+	3	297	c.297A>G	c.(295-297)ggA>ggG	p.G99G	IDO2_ENST00000343295.4_3'UTR|RP11-44K6.3_ENST00000517623.1_RNA|IDO2_ENST00000502986.2_Silent_p.G112G			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	99					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						GGCAGGAAGGAGAGGCGCAGC	0.637																																					p.G112G		Atlas-SNP	.											.	IDO2	78	.	0			c.A336G						.						28	32	30					8																	39836687		2034	4189	6223	SO:0001819	synonymous_variant	169355	exon4			GGAAGGAGAGGCG	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"indoleamine-pyrrole 2,3 dioxygenase-like 1"	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.297A>G	chr8.hg19:g.39836687A>G		62.0	0.0		128.0	6.0	NM_194294	A4UD41	Silent	SNP	ENST00000389060.4	hg19																																																																																				.	.		0.637	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294		G	39836687	A	G	39836687	2	3	115	1	0	0	0	0	0	0	0	1	7511	291	11	2		2	IDO2	8	39836687	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	745106	39836687	106527335	193	19732										
CHRNA6	8973	hgsc.bcm.edu	37	chr8	42611844	42611844	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaacagttttgatgatcaaaAgggaaaaaggtgatatccat	10	4	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:42611844A>G	ENST00000276410.2	-	5	853	c.498T>C	c.(496-498)ccT>ccC	p.P166P	CHRNA6_ENST00000534622.1_Silent_p.P151P|CHRNA6_ENST00000530869.1_5'Flank	NM_004198.3	NP_004189.1	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6 (neuronal)	166					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|membrane depolarization (GO:0051899)|regulation of dopamine secretion (GO:0014059)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)			endometrium(2)|large_intestine(3)|liver(1)|lung(15)|ovary(1)	22	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)|Varenicline(DB01273)	GATGATCAAAAGGGAAAAAGG	0.363																																					p.P166P		Atlas-SNP	.											.	CHRNA6	60	.	0			c.T498C						.						133	133	133					8																	42611844		2203	4300	6503	SO:0001819	synonymous_variant	8973	exon5			ATCAAAAGGGAAA	U62435	CCDS6135.1, CCDS56536.1	8p22	2012-02-11	2012-02-07					"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	15963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 6 (neuronal)"	606888	"cholinergic receptor, nicotinic, alpha polypeptide 6"			8906617	Standard	NM_004198		Approved		uc003xpj.3	Q15825		ENST00000276410.2:c.498T>C	chr8.hg19:g.42611844A>G		74.0	0.0		94.0	4.0	NM_004198	B2R8V4|B4DQH1	Silent	SNP	ENST00000276410.2	hg19	CCDS6135.1																																																																																			.	.		0.363	CHRNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383156.1			G	42611844	A	G	42611844	2	3	115	1	0	0	0	0	0	0	0	1	3389	59	3	2		2	CHRNA6	8	42611844	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2775157	42611844	103752178	194	19733										
THAP1	55145	hgsc.bcm.edu	37	chr8	42693397	42693397	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaagaggcggcattagtaatCcaatagcagcatcaacctgg	11	9	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:42693397C>A	ENST00000254250.3	-	3	580	c.350G>T	c.(349-351)gGa>gTa	p.G117V	THAP1_ENST00000345117.2_Missense_Mutation_p.D52Y|THAP1_ENST00000532093.1_5'Flank	NM_018105.2	NP_060575.1	Q9NVV9	THAP1_HUMAN	THAP domain containing, apoptosis associated protein 1	117					cell cycle (GO:0007049)|endothelial cell proliferation (GO:0001935)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|lung(4)|prostate(1)|skin(1)	7	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Acute lymphoblastic leukemia(644;0.000299)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0377)|LUSC - Lung squamous cell carcinoma(45;0.0869)			CATTAGTAATCCAATAGCAGC	0.453																																					p.G117V		Atlas-SNP	.											.	THAP1	18	.	0			c.G350T						.						115	129	124					8																	42693397		2203	4300	6503	SO:0001583	missense	55145	exon3			AGTAATCCAATAG	BC021721	CCDS6136.1, CCDS6137.1	8p11.1	2013-01-25			ENSG00000131931	ENSG00000131931		"THAP (C2CH-type zinc finger) domain containing"	20856	protein-coding gene	gene with protein product		609520	"dystonia 6, torsion (autosomal dominant)"	DYT6		12575992, 12717420, 19182804	Standard	NM_018105		Approved	FLJ10477, 4833431A01Rik	uc003xpk.3	Q9NVV9	OTTHUMG00000165276	ENST00000254250.3:c.350G>T	chr8.hg19:g.42693397C>A	ENSP00000254250:p.Gly117Val	135.0	0.0		124.0	66.0	NM_018105	A6NCB6|D3DSY5|H9KV49|Q53FQ1|Q6IA99	Missense_Mutation	SNP	ENST00000254250.3	hg19	CCDS6136.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.73|13.73	2.325825|2.325825	0.41197|0.41197	.|.	.|.	ENSG00000131931|ENSG00000131931	ENST00000345117|ENST00000254250	D|D	0.97575|0.97811	-4.44|-4.55	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|0.164655	.|0.52532	.|D	.|0.000063	D|D	0.97210|0.97210	0.9088|0.9088	.|.	.|.	.|.	0.38563|0.38563	D|D	0.949741|0.949741	.|D	.|0.59357	.|0.985	.|P	.|0.50270	.|0.636	D|D	0.96583|0.96583	0.9432|0.9432	6|9	0.87932|0.24483	D|T	0|0.36	-35.9057|-35.9057	19.7971|19.7971	0.96490|0.96490	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|117	.|Q9NVV9	.|THAP1_HUMAN	Y|V	52|117	ENSP00000344966:D52Y|ENSP00000254250:G117V	ENSP00000344966:D52Y|ENSP00000254250:G117V	D|G	-|-	1|2	0|0	THAP1|THAP1	42812554|42812554	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.978000|0.978000	0.69477|0.69477	3.393000|3.393000	0.52544|0.52544	2.757000|2.757000	0.94681|0.94681	0.585000|0.585000	0.79938|0.79938	GAT|GGA	.	.		0.453	THAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383161.1	NM_018105		A	42693397	C	A	42693397	3	1	115	1	0	0	0	0	1	0	0	0	15856	855	30	3	295	3	THAP1	8	42693397	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	81553	42693397	103670625	195	19734										
EYA1	2138	hgsc.bcm.edu	37	chr8	72267072	72267072	+	Frame_Shift_Del	DEL	G	G	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atatgagagttaccgagtttGgggccactgggggattcact							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:72267072delG	ENST00000340726.3	-	3	708	c.69delC	c.(67-69)cccfs	p.P23fs	EYA1_ENST00000388742.4_Frame_Shift_Del_p.P23fs|EYA1_ENST00000388740.3_Intron|EYA1_ENST00000388741.2_Intron|EYA1_ENST00000388743.2_Frame_Shift_Del_p.P23fs|EYA1_ENST00000303824.7_Frame_Shift_Del_p.P23fs|EYA1_ENST00000419131.1_Frame_Shift_Del_p.P23fs	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	23					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			TACCGAGTTTGGGGCCACTGG	0.463																																					p.K24fs		Atlas-INDEL	.											.	EYA1	108	.	0			c.70delA						.						160	165	164					8																	72267072		2203	4300	6503	SO:0001589	frameshift_variant	2138	exon2			.	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"Protein tyrosine phosphatases / Asp-based PTPs"	3519	protein-coding gene	gene with protein product		601653	"eyes absent (Drosophila) homolog 1", "eyes absent homolog 1 (Drosophila)"	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.69delC	chr8.hg19:g.72267072delG	ENSP00000342626:p.Pro23fs	127.0	0.0		177.0	11.0	NM_172059	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Frame_Shift_Del	DEL	ENST00000340726.3	hg19	CCDS34906.1																																																																																			.	.		0.463	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		-	72267072	G	-	72267072	7	5	115	1	0	1	0	1	0	0	0	0	5330	1335	47	0	1773	0	EYA1	8	72267072	Frame_Shift_Del	DEL	G	TCGA-DD-A3A1-01A-11D-A20W-10	29573675	72267072	74096950	196	19735										
GDAP1	54332	hgsc.bcm.edu	37	chr8	75262703	75262703	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcgcgcaccccaagatggctGagaggcaggaagagcagaga	15	10	0	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:75262703G>A	ENST00000220822.7	+	1	87	c.7G>A	c.(7-9)Gag>Aag	p.E3K	GDAP1_ENST00000521096.1_Intron|GDAP1_ENST00000434412.2_5'UTR|CTD-2320G14.2_ENST00000521872.1_RNA	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	3				E -> R (in Ref. 1; CAA76892). {ECO:0000305}.	cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)		p.E3K(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			CAAGATGGCTGAGAGGCAGGA	0.642																																					p.E3K		Atlas-SNP	.											GDAP1,ear,malignant_melanoma,0,1	GDAP1	36	.	1	Substitution - Missense(1)	skin(1)	c.G7A						.						30	31	31					8																	75262703		2203	4300	6503	SO:0001583	missense	54332	exon1			ATGGCTGAGAGGC		CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"Charcot-Marie-Tooth neuropathy 4A"	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.7G>A	chr8.hg19:g.75262703G>A	ENSP00000220822:p.Glu3Lys	47.0	0.0		50.0	2.0	NM_018972	A8K957|E7FJF3|E7FJF4	Missense_Mutation	SNP	ENST00000220822.7	hg19	CCDS34911.1	.	.	.	.	.	.	.	.	.	.	G	2.310	-0.358159	0.05138	.	.	ENSG00000104381	ENST00000220822	D	0.98914	-5.23	5.08	4.21	0.49690	.	0.798663	0.11092	N	0.600649	D	0.94315	0.8173	N	0.08118	0	0.47153	D	0.999334	B	0.02656	0.0	B	0.01281	0.0	D	0.89313	0.3634	10	0.11485	T	0.65	.	11.907	0.52717	0.0:0.641:0.359:0.0	.	3	Q8TB36	GDAP1_HUMAN	K	3	ENSP00000220822:E3K	ENSP00000220822:E3K	E	+	1	0	GDAP1	75425258	0.879000	0.30193	0.946000	0.38457	0.369000	0.29798	0.716000	0.25836	1.360000	0.45960	-0.165000	0.13383	GAG	.	.		0.642	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379061.1	NM_018972		A	75262703	G	A	75262703	3	1	115	1	0	0	0	0	1	0	0	0	6315	1291	45	3	9	3	GDAP1	8	75262703	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	2995631	75262703	71101319	197	19736										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77617351	77617351	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggaaccaaaaaaatccacttCtgtttatccccatttttcta	3	11	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:77617351C>T	ENST00000521891.2	+	2	1476	c.1028C>T	c.(1027-1029)tCt>tTt	p.S343F	ZFHX4_ENST00000050961.6_Missense_Mutation_p.S343F|ZFHX4_ENST00000455469.2_Missense_Mutation_p.S343F|ZFHX4_ENST00000518282.1_Missense_Mutation_p.S343F|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAATCCACTTCTGTTTATCCC	0.433										HNSCC(33;0.089)																											p.S343F		Atlas-SNP	.											.	ZFHX4	878	.	0			c.C1028T						.						111	105	107					8																	77617351		1819	4089	5908	SO:0001583	missense	79776	exon2			CCACTTCTGTTTA		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.1028C>T	chr8.hg19:g.77617351C>T	ENSP00000430497:p.Ser343Phe	57.0	0.0		64.0	5.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357254	0.41801	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.49720	0.77;0.82;0.79;0.78	5.53	5.53	0.82687	.	0.000000	0.44285	U	0.000474	T	0.56731	0.2005	N	0.20685	0.6	0.80722	D	1	D;D;D;B	0.76494	0.998;0.999;0.999;0.012	D;D;D;B	0.83275	0.991;0.996;0.996;0.005	T	0.56625	-0.7948	10	0.44086	T	0.13	.	19.6556	0.95837	0.0:1.0:0.0:0.0	.	343;343;343;343	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	F	343	ENSP00000430497:S343F;ENSP00000399605:S343F;ENSP00000050961:S343F;ENSP00000430848:S343F	ENSP00000050961:S343F	S	+	2	0	ZFHX4	77779906	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.127000	0.77210	2.882000	0.98803	0.655000	0.94253	TCT	.	.		0.433	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77617351	C	T	77617351	3	4	115	1	0	0	0	0	1	0	0	0	17650	913	32	3	1030	3	ZFHX4	8	77617351	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	2354648	77617351	68746671	198	19737										
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885079	88885079	+	Frame_Shift_Del	DEL	C	C	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gccctggtgctcctcggaagCccccgaggcgagaagagaag							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:88885079delC	ENST00000319675.3	-	1	1217	c.1121delG	c.(1120-1122)ggcfs	p.G374fs		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	374										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						TCCTCGGAAGCCCCCGAGGCG	0.592																																					p.G374fs		Atlas-INDEL	.											.	DCAF4L2	187	.	0			c.1122delC						.						56	62	60					8																	88885079		2203	4300	6503	SO:0001589	frameshift_variant	138009	exon1			.	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.1121delG	chr8.hg19:g.88885079delC	ENSP00000316496:p.Gly374fs	75.0	0.0		172.0	13.0	NM_152418		Frame_Shift_Del	DEL	ENST00000319675.3	hg19	CCDS6245.1																																																																																			.	.		0.592	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		-	88885079	C	-	88885079	7	5	115	1	0	1	0	1	0	0	0	0	4274	739	26	0	70	0	DCAF4L2	8	88885079	Frame_Shift_Del	DEL	C	TCGA-DD-A3A1-01A-11D-A20W-10	11267728	88885079	57478943	199	19738										
RAD54B	25788	hgsc.bcm.edu	37	chr8	95384468	95384468	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tttctgttattctttcaagaAaaggatctgtaagatttaaa	6	4	4	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:95384468A>G	ENST00000336148.5	-	15	2787	c.2663T>C	c.(2662-2664)tTt>tCt	p.F888S	RAD54B_ENST00000519348.1_5'UTR	NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	888					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			TCTTTCAAGAAAAGGATCTGT	0.363								Direct reversal of damage;Homologous recombination																													p.F888S		Atlas-SNP	.											.	RAD54B	88	.	0			c.T2663C						.						67	64	65					8																	95384468		2203	4300	6503	SO:0001583	missense	25788	exon15			TCAAGAAAAGGAT	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.2663T>C	chr8.hg19:g.95384468A>G	ENSP00000336606:p.Phe888Ser	76.0	0.0		92.0	4.0	NM_012415	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	hg19	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	A	18.02	3.530772	0.64860	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	D	0.88586	-2.4	5.65	5.65	0.86999	.	0.050385	0.85682	D	0.000000	D	0.82976	0.5154	L	0.27053	0.805	0.80722	D	1	P	0.50156	0.932	B	0.41813	0.367	T	0.82538	-0.0407	10	0.28530	T	0.3	-25.1253	15.8801	0.79197	1.0:0.0:0.0:0.0	.	888	Q9Y620	RA54B_HUMAN	S	888;560	ENSP00000336606:F888S	ENSP00000336606:F888S	F	-	2	0	RAD54B	95453644	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	4.096000	0.57734	2.166000	0.68216	0.460000	0.39030	TTT	.	.		0.363	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		G	95384468	A	G	95384468	3	3	115	1	0	0	0	0	1	0	0	0	13007	14	1	2	73	2	RAD54B	8	95384468	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6499389	95384468	50979554	200	19739										
SPAG1	6674	hgsc.bcm.edu	37	chr8	101252681	101252681	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cctgcaggggaggtctccatGggatgccttgcttctgagaa	14	10	2	1	rs150966245	byFrequency	TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:101252681G>C	ENST00000388798.2	+	18	2522	c.2331G>C	c.(2329-2331)atG>atC	p.M777I	SPAG1_ENST00000251809.3_Missense_Mutation_p.M777I	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	777			M -> T (in dbSNP:rs6511). {ECO:0000269|PubMed:11517287}.		axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.M777I(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		AGGTCTCCATGGGATGCCTTG	0.488																																					p.M777I		Atlas-SNP	.											SPAG1,pharynx,carcinoma,0,1	SPAG1	80	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G2331C						.						82	89	87					8																	101252681		2203	4300	6503	SO:0001583	missense	6674	exon18			CTCCATGGGATGC	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.2331G>C	chr8.hg19:g.101252681G>C	ENSP00000373450:p.Met777Ile	65.0	0.0		91.0	0.0	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	hg19	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	G	10.17	1.276558	0.23307	.	.	ENSG00000104450	ENST00000251809;ENST00000388798	T;T	0.60171	0.21;0.21	5.68	-11.4	0.00090	.	1.659360	0.03303	N	0.189258	T	0.33556	0.0867	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09997	-1.0649	10	0.25106	T	0.35	2.3277	5.144	0.14975	0.1545:0.2189:0.4807:0.146	.	777	Q07617	SPAG1_HUMAN	I	777	ENSP00000251809:M777I;ENSP00000373450:M777I	ENSP00000251809:M777I	M	+	3	0	SPAG1	101321857	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.832000	0.00743	-3.203000	0.00216	-1.334000	0.01262	ATG	.	G|0.997;A|0.003		0.488	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		C	101252681	G	C	101252681	3	2	115	1	0	0	0	0	1	0	0	0	14990	1348	47	4	2397	4	SPAG1	8	101252681	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	5868213	101252681	45111341	201	19740										
LRP12	29967	hgsc.bcm.edu	37	chr8	105503084	105503084	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agcccttgtccttgatctgaGgcaagatcaagaagaggtct	11	9	3	5			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:105503084G>A	ENST00000276654.5	-	7	2505	c.2397C>T	c.(2395-2397)gcC>gcT	p.A799A	LRP12_ENST00000518375.1_5'UTR|LRP12_ENST00000424843.2_Silent_p.A780A	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	799					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CTTGATCTGAGGCAAGATCAA	0.438																																					p.A799A		Atlas-SNP	.											.	LRP12	124	.	0			c.C2397T						.						161	132	142					8																	105503084		2203	4300	6503	SO:0001819	synonymous_variant	29967	exon7			ATCTGAGGCAAGA	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.2397C>T	chr8.hg19:g.105503084G>A		131.0	0.0		159.0	37.0	NM_013437	A8K137|B4DRQ2	Silent	SNP	ENST00000276654.5	hg19	CCDS6303.1																																																																																			.	.		0.438	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		A	105503084	G	A	105503084	2	1	115	1	0	0	0	0	0	0	0	1	8963	987	35	3		3	LRP12	8	105503084	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	4250403	105503084	40860938	202	19741										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113585826	113585826	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	actactaagtgtcagtccgcGcatagatgcaccagtaaaag	9	10	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:113585826G>T	ENST00000297405.5	-	24	4190	c.3946C>A	c.(3946-3948)Cgc>Agc	p.R1316S	CSMD3_ENST00000343508.3_Missense_Mutation_p.R1276S|CSMD3_ENST00000455883.2_Missense_Mutation_p.R1212S|CSMD3_ENST00000352409.3_Missense_Mutation_p.R1316S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1316	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GTCAGTCCGCGCATAGATGCA	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.R1316S		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,0,2	CSMD3	2325	.	0			c.C3946A						.						123	124	123					8																	113585826		2203	4300	6503	SO:0001583	missense	114788	exon24			GTCCGCGCATAGA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3946C>A	chr8.hg19:g.113585826G>T	ENSP00000297405:p.Arg1316Ser	116.0	0.0		131.0	34.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	10.67	1.415716	0.25552	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.27557	1.66;1.66;1.66;1.66;1.66	4.85	-2.53	0.06326	CUB (5);	0.191183	0.33572	N	0.004775	T	0.22085	0.0532	N	0.10760	0.04	0.25265	N	0.98957	P;P;D	0.53619	0.706;0.75;0.961	B;P;P	0.51582	0.421;0.557;0.674	T	0.34700	-0.9818	10	0.19147	T	0.46	.	18.8933	0.92413	0.0:0.0:0.2404:0.7596	.	1212;1316;1276	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	S	1276;1316;656;1212;1316	ENSP00000345799:R1276S;ENSP00000297405:R1316S;ENSP00000341558:R656S;ENSP00000412263:R1212S;ENSP00000343124:R1316S	ENSP00000297405:R1316S	R	-	1	0	CSMD3	113655002	0.485000	0.25972	0.985000	0.45067	0.986000	0.74619	-0.233000	0.09041	-0.337000	0.08426	0.591000	0.81541	CGC	.	.		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113585826	G	T	113585826	3	4	115	1	0	0	0	0	1	0	0	0	3948	1087	38	1	7369	1	CSMD3	8	113585826	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	8082742	113585826	32778196	203	19742										
RNF139	83940	hgsc.bcm.edu	37	chr8	125498418	125498418	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctaccattacacatcagagaGactttactgtttacttcttc	4	11	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:125498418G>T	ENST00000276692.6	-	0	1018				RNF139_ENST00000303545.3_Missense_Mutation_p.E176D|RP11-158K1.3_ENST00000518639.1_RNA	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1						DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ACATCAGAGAGACTTTACTGT	0.353																																					p.E176D		Atlas-SNP	.											.	RNF139	57	.	0			c.G528T						.						143	141	142					8																	125498418		2203	4300	6503	SO:0001628	intergenic_variant	11236	exon2			CAGAGAGACTTTA	AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068		chr8.hg19:g.125498418G>T		120.0	0.0		192.0	104.0	NM_007218	B2R5J0|Q8TD02|Q9BY40	Missense_Mutation	SNP	ENST00000276692.6	hg19	CCDS6351.1	.	.	.	.	.	.	.	.	.	.	G	7.633	0.679177	0.14907	.	.	ENSG00000170881	ENST00000303545;ENST00000517684	T	0.23754	1.89	5.34	4.45	0.53987	.	0.059734	0.64402	D	0.000003	T	0.13927	0.0337	N	0.14661	0.345	0.32414	N	0.550302	B	0.33777	0.425	B	0.34418	0.182	T	0.11665	-1.0578	10	0.21540	T	0.41	-13.5081	9.5266	0.39169	0.2098:0.0:0.7902:0.0	.	176	Q8WU17	RN139_HUMAN	D	176;49	ENSP00000304051:E176D	ENSP00000304051:E176D	E	+	3	2	RNF139	125567599	1.000000	0.71417	1.000000	0.80357	0.526000	0.34562	2.903000	0.48711	2.642000	0.89623	0.650000	0.86243	GAG	.	.		0.353	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026		T	125498418	G	T	125498418	1	4	115	0	1	0	0	0	0	0	0	0	13457	933	33	3		3	RNF139	8	125498418	IGR	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	11912592	125498418	20865604	204	19743										
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126059515	126059515	+	Frame_Shift_Del	DEL	G	G	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acgttacagactcatccacaGgggtaaacttgggtattgga							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:126059515delG	ENST00000318410.7	-	20	2787	c.2438delC	c.(2437-2439)cctfs	p.P813fs	KIAA0196-AS1_ENST00000519140.1_RNA|KIAA0196_ENST00000517845.1_Frame_Shift_Del_p.P665fs	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	813					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			CTCATCCACAGGGGTAAACTT	0.408																																					p.P813fs		Atlas-INDEL	.											.	KIAA0196	90	.	0			c.2439delT						.						118	107	111					8																	126059515		2203	4300	6503	SO:0001589	frameshift_variant	9897	exon20			.		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.2438delC	chr8.hg19:g.126059515delG	ENSP00000318016:p.Pro813fs	123.0	0.0		141.0	10.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Frame_Shift_Del	DEL	ENST00000318410.7	hg19	CCDS6355.1																																																																																			.	.		0.408	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		-	126059515	G	-	126059515	7	5	115	1	0	1	0	1	0	0	0	0	8170	1000	35	0	1081	0	KIAA0196	8	126059515	Frame_Shift_Del	DEL	G	TCGA-DD-A3A1-01A-11D-A20W-10	561097	126059515	20304507	205	19744										
CYP11B2	1585	hgsc.bcm.edu	37	chr8	143996601	143996601	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gggaggaacctctgcacggcCttgggcgacagcacatctgg	15	12	2	0	rs552105650		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:143996601C>G	ENST00000323110.2	-	3	458	c.456G>C	c.(454-456)aaG>aaC	p.K152N		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	152					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	TCTGCACGGCCTTGGGCGACA	0.642									Familial Hyperaldosteronism type I				.|||	1	0.000199681	0	0	5008	,	,		19898	0		0	False		,,,				2504	0.001				p.K152N		Atlas-SNP	.											.	CYP11B2	107	.	0			c.G456C						.						62	52	55					8																	143996601		2203	4300	6503	SO:0001583	missense	1585	exon3	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	CACGGCCTTGGGC	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"Cytochrome P450s"	2592	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	124080	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.456G>C	chr8.hg19:g.143996601C>G	ENSP00000325822:p.Lys152Asn	194.0	0.0		294.0	23.0	NM_000498	B0ZBE4|Q16726	Missense_Mutation	SNP	ENST00000323110.2	hg19	CCDS6393.1	.	.	.	.	.	.	.	.	.	.	.	8.417	0.845455	0.16963	.	.	ENSG00000179142	ENST00000323110	T	0.69685	-0.42	3.44	-4.07	0.03975	.	0.994613	0.08154	N	0.989473	T	0.56156	0.1966	L	0.58810	1.83	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.51212	-0.8734	10	0.56958	D	0.05	.	5.076	0.14632	0.2202:0.1889:0.0:0.5909	.	152	P19099	C11B2_HUMAN	N	152	ENSP00000325822:K152N	ENSP00000325822:K152N	K	-	3	2	CYP11B2	143993603	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.715000	0.04997	-0.723000	0.04915	-0.258000	0.10820	AAG	.	.		0.642	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1			G	143996601	C	G	143996601	3	3	115	1	0	0	0	0	1	0	0	0	4148	680	24	4	1083	4	CYP11B2	8	143996601	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	17937086	143996601	2367421	206	19745										
COMMD5	28991	hgsc.bcm.edu	37	chr8	146076709	146076709	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgcaggtatggagttgcagcCcccacagcagacattgctgc	12	12	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr8:146076709C>T	ENST00000305103.3	-	2	267	c.15G>A	c.(13-15)ggG>ggA	p.G5G	ZNF250_ENST00000543949.1_3'UTR|AF235103.1_ENST00000578937.1_RNA|COMMD5_ENST00000450361.2_Silent_p.G5G|COMMD5_ENST00000402718.3_Silent_p.G5G	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	5						nucleus (GO:0005634)		p.G5G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			GAGTTGCAGCCCCCACAGCAG	0.597																																					p.G5G		Atlas-SNP	.											COMMD5,colon,carcinoma,0,2	COMMD5	18	.	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G15A						.						63	66	65					8																	146076709		2203	4300	6503	SO:0001819	synonymous_variant	28991	exon2			TGCAGCCCCCACA	AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.15G>A	chr8.hg19:g.146076709C>T		249.0	0.0		386.0	0.0	NM_001081004	D3DWN7|Q9NVN6|Q9UHX5	Silent	SNP	ENST00000305103.3	hg19	CCDS6436.1																																																																																			.	.		0.597	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382962.1	NM_014066		T	146076709	C	T	146076709	2	4	115	1	0	0	0	0	0	0	0	1	3721	610	22	3		3	COMMD5	8	146076709	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	2080108	146076709	287313	207	19746										
DOCK8	81704	hgsc.bcm.edu	37	chr9	334272	334272	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctccaagctgaatccttctgCcagcgtttggggaaataccg	10	12	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:334272C>G	ENST00000453981.1	+	11	1285	c.1173C>G	c.(1171-1173)tgC>tgG	p.C391W	DOCK8_ENST00000432829.2_Missense_Mutation_p.C323W|DOCK8_ENST00000469391.1_Missense_Mutation_p.C323W			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	391					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		AATCCTTCTGCCAGCGTTTGG	0.453																																					p.C391W		Atlas-SNP	.											.	DOCK8	401	.	0			c.C1173G						.						91	88	89					9																	334272		2203	4300	6503	SO:0001583	missense	81704	exon11			CTTCTGCCAGCGT	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.1173C>G	chr9.hg19:g.334272C>G	ENSP00000408464:p.Cys391Trp	86.0	0.0		118.0	5.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812358	0.70912	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391	T;T;T	0.03635	3.86;3.86;3.86	5.87	5.87	0.94306	.	0.086767	0.85682	D	0.000000	T	0.21962	0.0529	M	0.89715	3.055	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.982	T	0.00170	-1.1961	10	0.87932	D	0	.	11.5446	0.50685	0.0:0.8931:0.0:0.1069	.	323;391	E9PH09;Q8NF50	.;DOCK8_HUMAN	W	391;391;323;323	ENSP00000408464:C391W;ENSP00000394888:C323W;ENSP00000419438:C323W	ENSP00000287364:C391W	C	+	3	2	DOCK8	324272	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.747000	0.26290	2.941000	0.99782	0.655000	0.94253	TGC	.	.		0.453	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		G	334272	C	G	334272	3	3	115	1	0	0	0	0	1	0	0	0	4695	747	26	4	1215	4	DOCK8	9	334272	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10		334272	140879159	208	19747										
KANK1	23189	hgsc.bcm.edu	37	chr9	713074	713074	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agataaatattaacgacaacTatctggttggtctcaaaatg	7	6	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:713074T>C	ENST00000382303.1	+	7	2960	c.2308T>C	c.(2308-2310)Tat>Cat	p.Y770H	KANK1_ENST00000382297.2_Missense_Mutation_p.Y770H|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Missense_Mutation_p.Y612H	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	770					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		TAACGACAACTATCTGGTTGG	0.522																																					p.Y770H		Atlas-SNP	.											.	KANK1	231	.	0			c.T2308C						.						90	92	91					9																	713074		2203	4300	6503	SO:0001583	missense	23189	exon7			GACAACTATCTGG	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.2308T>C	chr9.hg19:g.713074T>C	ENSP00000371740:p.Tyr770His	109.0	0.0		106.0	40.0	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	hg19	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.642458	0.87859	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.18016	2.24;2.24;2.24	5.97	5.97	0.96955	.	0.000000	0.51477	D	0.000094	T	0.41488	0.1161	M	0.67953	2.075	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.71184	0.972;0.909	T	0.23833	-1.0177	10	0.87932	D	0	-12.1515	16.4608	0.84044	0.0:0.0:0.0:1.0	.	770;770	Q5W0W1;Q14678	.;KANK1_HUMAN	H	770;770;770;612	ENSP00000371740:Y770H;ENSP00000371734:Y770H;ENSP00000371730:Y612H	ENSP00000346479:Y770H	Y	+	1	0	KANK1	703074	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.950000	0.87804	2.288000	0.76882	0.533000	0.62120	TAT	.	.		0.522	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		C	713074	T	C	713074	3	2	115	1	0	0	0	0	1	0	0	0	7985	1522	53	2	2314	2	KANK1	9	713074	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	378802	713074	140500357	209	19748										
MLLT3	4300	hgsc.bcm.edu	37	chr9	20620823	20620823	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gccccagctccagcttcaccTgcacggcacactgcgggcag	11	18	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:20620823T>G	ENST00000380338.4	-	2	309	c.23A>C	c.(22-24)cAg>cCg	p.Q8P	MLLT3_ENST00000429426.2_Missense_Mutation_p.Q5P|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	8	YEATS. {ECO:0000255|PROSITE- ProRule:PRU00376}.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		CAGCTTCACCTGCACGGCACA	0.612			T	MLL	ALL																																p.Q8P		Atlas-SNP	.		Dom	yes		9	9p22	4300	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"		L	.	MLLT3	125	.	0			c.A23C						.						60	61	61					9																	20620823		2203	4300	6503	SO:0001583	missense	4300	exon2			TTCACCTGCACGG	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.23A>C	chr9.hg19:g.20620823T>G	ENSP00000369695:p.Gln8Pro	71.0	0.0		84.0	5.0	NM_004529	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Missense_Mutation	SNP	ENST00000380338.4	hg19	CCDS6494.1	.	.	.	.	.	.	.	.	.	.	T	17.32	3.358821	0.61403	.	.	ENSG00000171843	ENST00000380338;ENST00000429426;ENST00000540751	.	.	.	5.38	4.22	0.49857	.	0.085068	0.48767	D	0.000164	T	0.67887	0.2941	L	0.47716	1.5	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.79784	0.993;0.983	T	0.68981	-0.5266	9	0.87932	D	0	-7.8369	11.3969	0.49847	0.1357:0.0:0.0:0.8643	.	5;8	B7Z755;P42568	.;AF9_HUMAN	P	8;5;47	.	ENSP00000369695:Q8P	Q	-	2	0	MLLT3	20610823	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.029000	0.88807	0.842000	0.35045	0.459000	0.35465	CAG	.	.		0.612	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		G	20620823	T	G	20620823	3	3	115	1	0	0	0	0	1	0	0	0	9637	1580	55	5	1723	5	MLLT3	9	20620823	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	19907749	20620823	120592608	210	19749										
DDX58	23586	hgsc.bcm.edu	37	chr9	32466317	32466317	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaatactgcttcgtcccatgTctgaaggcgtaaaatagagt	9	8	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:32466317T>C	ENST00000379883.2	-	16	2465	c.2308A>G	c.(2308-2310)Aca>Gca	p.T770A	DDX58_ENST00000379868.1_Missense_Mutation_p.T567A|DDX58_ENST00000379882.1_Missense_Mutation_p.T725A|DDX58_ENST00000542096.1_Missense_Mutation_p.T699A	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	770	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TCGTCCCATGTCTGAAGGCGT	0.373																																					p.T770A		Atlas-SNP	.											.	DDX58	82	.	0			c.A2308G						.						222	210	214					9																	32466317		2203	4300	6503	SO:0001583	missense	23586	exon16			CCCATGTCTGAAG	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2308A>G	chr9.hg19:g.32466317T>C	ENSP00000369213:p.Thr770Ala	115.0	0.0		110.0	5.0	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	hg19	CCDS6526.1	.	.	.	.	.	.	.	.	.	.	T	2.042	-0.419821	0.04734	.	.	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.18	-7.18	0.01505	Helicase, C-terminal (1);	1.666380	0.02946	N	0.141105	T	0.29749	0.0743	N	0.26042	0.785	0.28708	N	0.903694	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.31138	-0.9954	10	0.11485	T	0.65	4.5695	17.0152	0.86416	0.0:0.6194:0.0:0.3806	.	725;699;770	O95786-2;B3KWW1;O95786	.;.;DDX58_HUMAN	A	725;770;567;699	ENSP00000369212:T725A;ENSP00000369213:T770A;ENSP00000369197:T567A;ENSP00000442160:T699A	ENSP00000369197:T567A	T	-	1	0	DDX58	32456317	0.002000	0.14202	0.002000	0.10522	0.113000	0.19764	-0.618000	0.05578	-1.649000	0.01508	-0.256000	0.11100	ACA	.	.		0.373	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		C	32466317	T	C	32466317	3	2	115	1	0	0	0	0	1	0	0	0	4377	1667	58	2	481	2	DDX58	9	32466317	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	11845494	32466317	108747114	211	19750										
FXN	2395	hgsc.bcm.edu	37	chr9	71661353	71661353	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaatgtcaaaaagcagagtgTctatttgatgaatttgagga	11	3	2	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:71661353T>C	ENST00000377270.3	+	2	742	c.218T>C	c.(217-219)gTc>gCc	p.V73A	FXN_ENST00000498653.1_5'UTR|FXN_ENST00000396366.2_Missense_Mutation_p.V73A|FXN_ENST00000396364.3_Missense_Mutation_p.V73A	NM_000144.4	NP_000135.2	Q16595	FRDA_HUMAN	frataxin	73					adult walking behavior (GO:0007628)|aerobic respiration (GO:0009060)|cellular iron ion homeostasis (GO:0006879)|cellular response to hydrogen peroxide (GO:0070301)|embryo development ending in birth or egg hatching (GO:0009792)|heme biosynthetic process (GO:0006783)|ion transport (GO:0006811)|iron incorporation into metallo-sulfur cluster (GO:0018283)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|oxidative phosphorylation (GO:0006119)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)|proprioception (GO:0019230)|protein autoprocessing (GO:0016540)|regulation of ferrochelatase activity (GO:0010722)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)|iron chaperone activity (GO:0034986)|iron-sulfur cluster binding (GO:0051536)			large_intestine(1)|lung(1)	2						AAGCAGAGTGTCTATTTGATG	0.418																																					p.V73A		Atlas-SNP	.											.	FXN	9	.	0			c.T218C						.						110	102	105					9																	71661353		2203	4300	6503	SO:0001583	missense	2395	exon2			AGAGTGTCTATTT	U43752	CCDS6626.1, CCDS43834.1, CCDS55313.1	9q21.11	2014-09-17	2004-08-16	2004-08-19	ENSG00000165060	ENSG00000165060			3951	protein-coding gene	gene with protein product		606829	"Friedreich ataxia"	FRDA		8596916, 8841185	Standard	NM_000144		Approved	FA, FARR, X25, CyaY	uc004aha.2	Q16595	OTTHUMG00000019977	ENST00000377270.3:c.218T>C	chr9.hg19:g.71661353T>C	ENSP00000366482:p.Val73Ala	105.0	0.0		115.0	5.0	NM_000144	A8MXJ6|C9JJ89|O15545|O95656|Q15294|Q5VZ01	Missense_Mutation	SNP	ENST00000377270.3	hg19	CCDS6626.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.266|4.266	0.048515|0.048515	0.08243|0.08243	.|.	.|.	ENSG00000165060|ENSG00000165060	ENST00000484259|ENST00000377270;ENST00000396364;ENST00000396366	.|D;D;D	.|0.88354	.|-2.37;-2.37;-2.37	4.94|4.94	2.57|2.57	0.30868|0.30868	.|.	.|0.391028	.|0.24409	.|N	.|0.038780	T|T	0.78786|0.78786	0.4338|0.4338	L|L	0.38175|0.38175	1.15|1.15	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.12630	.|0.005;0.002;0.006	.|B;B;B	.|0.09377	.|0.004;0.002;0.004	T|T	0.58103|0.58103	-0.7695|-0.7695	5|10	.|0.07813	.|T	.|0.8	-12.7372|-12.7372	6.9731|6.9731	0.24660|0.24660	0.0:0.1863:0.0:0.8137|0.0:0.1863:0.0:0.8137	.|.	.|73;73;73	.|Q16595-2;Q16595;A8MXJ6	.|.;FRDA_HUMAN;.	P|A	11|73	.|ENSP00000366482:V73A;ENSP00000379650:V73A;ENSP00000379652:V73A	.|ENSP00000366482:V73A	S|V	+|+	1|2	0|0	FXN|FXN	70851173|70851173	0.932000|0.932000	0.31603|0.31603	0.049000|0.049000	0.19019|0.19019	0.047000|0.047000	0.14425|0.14425	1.790000|1.790000	0.38734|0.38734	0.319000|0.319000	0.23209|0.23209	-0.421000|-0.421000	0.06004|0.06004	TCT|GTC	.	.		0.418	FXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052568.2	NM_000144		C	71661353	T	C	71661353	3	2	115	1	0	0	0	0	1	0	0	0	6122	1667	58	2	224	2	FXN	9	71661353	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	39195036	71661353	69552078	212	19751										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79321218	79321218	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	actgatttgtttcttgacctTcattagttgaaacattagat	6	6	2	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:79321218T>C	ENST00000376718.3	-	8	6095	c.5972A>G	c.(5971-5973)gAa>gGa	p.E1991G	PRUNE2_ENST00000428286.1_Missense_Mutation_p.E1632G	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1991					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TTCTTGACCTTCATTAGTTGA	0.423																																					p.E1991G		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A5972G						.						121	105	109					9																	79321218		1568	3582	5150	SO:0001583	missense	158471	exon8			TGACCTTCATTAG	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.5972A>G	chr9.hg19:g.79321218T>C	ENSP00000365908:p.Glu1991Gly	99.0	0.0		87.0	4.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.21|13.21	2.168361|2.168361	0.38315|0.38315	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.53857|.	0.6;0.6|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.132018|.	0.34700|.	N|.	0.003750|.	T|.	0.72455|.	0.3462|.	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D|.	0.65815|.	0.995|.	P|.	0.57425|.	0.82|.	T|.	0.71265|.	-0.4644|.	10|.	0.87932|.	D|.	0|.	-15.6032|-15.6032	16.3305|16.3305	0.83010|0.83010	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1991|.	Q8WUY3|.	PRUN2_HUMAN|.	G|W	1991;1632;1990|1312	ENSP00000365908:E1991G;ENSP00000397425:E1632G|.	ENSP00000365908:E1991G|.	E|X	-|-	2|3	0|0	PRUNE2|PRUNE2	78511038|78511038	0.000000|0.000000	0.05858|0.05858	0.103000|0.103000	0.21229|0.21229	0.027000|0.027000	0.11550|0.11550	0.597000|0.597000	0.24059|0.24059	2.317000|2.317000	0.78254|0.78254	0.459000|0.459000	0.35465|0.35465	GAA|TGA	.	.		0.423	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		C	79321218	T	C	79321218	3	2	115	1	0	0	0	0	1	0	0	0	12653	1783	62	2	3342	2	PRUNE2	9	79321218	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	7659865	79321218	61892213	213	19752										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79322807	79322807	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcttcagttttctcaagatcCttttcaggtacagatacata	5	9	4	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:79322807C>T	ENST00000376718.3	-	8	4506	c.4383G>A	c.(4381-4383)aaG>aaA	p.K1461K	PRUNE2_ENST00000428286.1_Silent_p.K1102K	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1461					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TCTCAAGATCCTTTTCAGGTA	0.428																																					p.K1461K		Atlas-SNP	.											.	PRUNE2	331	.	0			c.G4383A						.						63	64	64					9																	79322807		1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			AAGATCCTTTTCA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.4383G>A	chr9.hg19:g.79322807C>T		141.0	0.0		160.0	45.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	C	0.015	-1.539480	0.00942	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.35	2.52	0.30459	.	.	.	.	.	T	0.35480	0.0933	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.21177	-1.0253	4	.	.	.	-0.0249	8.6948	0.34289	0.0:0.6754:0.0:0.3246	.	.	.	.	R	783	.	.	G	-	1	0	PRUNE2	78512627	0.400000	0.25295	0.001000	0.08648	0.007000	0.05969	0.798000	0.27014	0.348000	0.23949	-0.258000	0.10820	GGA	.	.		0.428	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		T	79322807	C	T	79322807	2	4	115	1	0	0	0	0	0	0	0	1	12653	680	24	3		3	PRUNE2	9	79322807	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	1589	79322807	61890624	214	19753										
C9orf79	286234	hgsc.bcm.edu	37	chr9	90501957	90501957	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcacagctggggtacagaccTccagtccctggagcccataa	11	14	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:90501957T>C	ENST00000325643.5	+	4	2621	c.2555T>C	c.(2554-2556)cTc>cCc	p.L852P		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	852					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGTACAGACCTCCAGTCCCTG	0.577																																					p.L852P		Atlas-SNP	.											.	.	.	.	0			c.T2555C						.						47	45	45					9																	90501957		2203	4300	6503	SO:0001583	missense	286234	exon4			CAGACCTCCAGTC	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.2555T>C	chr9.hg19:g.90501957T>C	ENSP00000322640:p.Leu852Pro	67.0	0.0		111.0	7.0	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	hg19	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	t	11.03	1.519447	0.27211	.	.	ENSG00000177992	ENST00000325643;ENST00000539327	T	0.06068	3.35	2.57	-0.148	0.13424	.	1.489590	0.04472	N	0.376278	T	0.13457	0.0326	L	0.41573	1.285	0.09310	N	0.999999	D;D	0.71674	0.998;0.994	D;P	0.65443	0.935;0.737	T	0.17992	-1.0351	10	0.51188	T	0.08	.	3.0452	0.06151	0.248:0.0:0.2551:0.4969	.	852;504	Q6ZUB1;Q8NA33	CI079_HUMAN;.	P	852;504	ENSP00000322640:L852P	ENSP00000322640:L852P	L	+	2	0	C9orf79	89691777	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	0.016000	0.13377	-0.032000	0.13758	0.455000	0.32223	CTC	.	.		0.577	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		C	90501957	T	C	90501957	3	2	115	1	0	0	0	0	1	0	0	0	2499	1551	54	2	2569	2	C9orf79	9	90501957	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	11179150	90501957	50711474	215	19754										
NFIL3	4783	hgsc.bcm.edu	37	chr9	94171681	94171681	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggctataagtctcttgagtgAgacaacctctgcagataagt	10	8	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:94171681A>G	ENST00000297689.3	-	2	1730	c.1336T>C	c.(1336-1338)Tca>Cca	p.S446P		NM_005384.2	NP_005375.2	Q16649	NFIL3_HUMAN	nuclear factor, interleukin 3 regulated	446					cellular response to interleukin-4 (GO:0071353)|circadian rhythm (GO:0007623)|immune response (GO:0006955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	16						CTCTTGAGTGAGACAACCTCT	0.413																																					p.S446P	Esophageal Squamous(152;732 1832 10053 26981 51762)	Atlas-SNP	.											.	NFIL3	43	.	0			c.T1336C						.						124	119	120					9																	94171681		2203	4300	6503	SO:0001583	missense	4783	exon2			TGAGTGAGACAAC	X64318	CCDS6690.1	9q22	2013-01-10			ENSG00000165030	ENSG00000165030		"basic leucine zipper proteins"	7787	protein-coding gene	gene with protein product		605327		IL3BP1		7565758, 1620116	Standard	NM_005384		Approved	E4BP4, NFIL3A, NF-IL3A	uc004arh.3	Q16649	OTTHUMG00000020209	ENST00000297689.3:c.1336T>C	chr9.hg19:g.94171681A>G	ENSP00000297689:p.Ser446Pro	203.0	0.0		206.0	9.0	NM_005384	B2R9Y8|Q14211|Q6FGQ8|Q96HS0	Missense_Mutation	SNP	ENST00000297689.3	hg19	CCDS6690.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.886342	0.51908	.	.	ENSG00000165030	ENST00000375724;ENST00000297689	.	.	.	5.17	5.17	0.71159	Vertebrate interleukin-3 regulated transcription factor (1);	0.221649	0.30401	N	0.009703	T	0.65606	0.2707	L	0.60455	1.87	0.37761	D	0.92631	D	0.53462	0.96	P	0.56514	0.8	T	0.72257	-0.4346	9	0.72032	D	0.01	-5.0822	10.424	0.44367	0.8545:0.0:0.0:0.1455	.	446	Q16649	NFIL3_HUMAN	P	446	.	ENSP00000297689:S446P	S	-	1	0	NFIL3	93211502	1.000000	0.71417	0.315000	0.25238	0.629000	0.37895	4.739000	0.62080	2.153000	0.67306	0.533000	0.62120	TCA	.	.		0.413	NFIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053038.2	NM_005384		G	94171681	A	G	94171681	3	3	115	1	0	0	0	0	1	0	0	0	10382	304	11	2	56	2	NFIL3	9	94171681	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3669724	94171681	47041750	216	19755										
SMC2	10592	hgsc.bcm.edu	37	chr9	106896730	106896730	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgggtctattttttctactcTtttgcctggtgctaatgcta	8	8	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:106896730T>C	ENST00000286398.7	+	23	3431	c.3143T>C	c.(3142-3144)cTt>cCt	p.L1048P	SMC2_ENST00000374787.3_Missense_Mutation_p.L1048P|SMC2_ENST00000374793.3_Missense_Mutation_p.L1048P|SMC2_ENST00000303219.8_Missense_Mutation_p.L1048P	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	1048					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						TTTTCTACTCTTTTGCCTGGT	0.383																																					p.L1048P		Atlas-SNP	.											.	SMC2	127	.	0			c.T3143C						.						123	120	121					9																	106896730		2203	4300	6503	SO:0001583	missense	10592	exon23			CTACTCTTTTGCC	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.3143T>C	chr9.hg19:g.106896730T>C	ENSP00000286398:p.Leu1048Pro	98.0	0.0		117.0	5.0	NM_006444	Q6IEE0|Q9P1P2	Missense_Mutation	SNP	ENST00000286398.7	hg19	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.235396	0.79800	.	.	ENSG00000136824	ENST00000286398;ENST00000374793;ENST00000303219;ENST00000374787	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	5.58	5.58	0.84498	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.42086	0.1187	M	0.91249	3.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.53027	-0.8496	10	0.87932	D	0	-7.5375	14.5857	0.68322	0.0:0.0:0.0:1.0	.	1048	O95347	SMC2_HUMAN	P	1048	ENSP00000286398:L1048P;ENSP00000363925:L1048P;ENSP00000306152:L1048P;ENSP00000363919:L1048P	ENSP00000286398:L1048P	L	+	2	0	SMC2	105936551	1.000000	0.71417	0.998000	0.56505	0.951000	0.60555	8.040000	0.89188	2.126000	0.65437	0.397000	0.26171	CTT	.	.		0.383	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			C	106896730	T	C	106896730	3	2	115	1	0	0	0	0	1	0	0	0	14798	1609	56	2	3229	2	SMC2	9	106896730	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	12725049	106896730	34316701	217	19756										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114213757	114213757	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtttgagcaaaacaggaggaAggaatttagatataatattc	10	3	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:114213757A>G	ENST00000338205.5	-	2	320	c.101T>C	c.(100-102)cTt>cCt	p.L34P	KIAA0368_ENST00000259335.4_Missense_Mutation_p.L212P			Q5VYK3	ECM29_HUMAN	KIAA0368	40					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						AACAGGAGGAAGGAATTTAGA	0.353																																					p.L212P		Atlas-SNP	.											.	KIAA0368	144	.	0			c.T635C						.						60	56	57					9																	114213757		1834	4091	5925	SO:0001583	missense	23392	exon4			GGAGGAAGGAATT	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.101T>C	chr9.hg19:g.114213757A>G	ENSP00000339889:p.Leu34Pro	101.0	0.0		60.0	4.0	NM_001080398	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	hg19		.	.	.	.	.	.	.	.	.	.	A	24.1	4.497710	0.85069	.	.	ENSG00000136813	ENST00000338205;ENST00000259335	T	0.79845	-1.31	5.55	5.55	0.83447	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.89529	0.6741	M	0.79011	2.435	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.90891	0.4761	10	0.87932	D	0	.	15.6977	0.77512	1.0:0.0:0.0:0.0	.	40	Q5VYK3	ECM29_HUMAN	P	34;212	ENSP00000259335:L212P	ENSP00000259335:L212P	L	-	2	0	KIAA0368	113253578	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.923000	0.92808	2.107000	0.64212	0.482000	0.46254	CTT	.	.		0.353	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		G	114213757	A	G	114213757	3	3	115	1	0	0	0	0	1	0	0	0	8180	72	3	2	5610	2	KIAA0368	9	114213757	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	7317027	114213757	26999674	218	19757										
DFNB31	25861	hgsc.bcm.edu	37	chr9	117186678	117186678	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cctccacagagacgctgccaCcacggtactcatccaggtag	9	16	1	1	rs117352600	byFrequency	TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:117186678C>G	ENST00000362057.3	-	6	1520	c.1352G>C	c.(1351-1353)gGt>gCt	p.G451A	DFNB31_ENST00000265134.6_Missense_Mutation_p.G68A|DFNB31_ENST00000374059.3_Missense_Mutation_p.G100A	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	451					inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GACGCTGCCACCACGGTACTC	0.627																																					p.G451A		Atlas-SNP	.											DFNB31,NS,carcinoma,0,1	DFNB31	100	.	0			c.G1352C						.						98	79	86					9																	117186678		2203	4300	6503	SO:0001583	missense	25861	exon6			CTGCCACCACGGT	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"whirlin"	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.1352G>C	chr9.hg19:g.117186678C>G	ENSP00000354623:p.Gly451Ala	198.0	0.0		235.0	0.0	NM_001173425	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Missense_Mutation	SNP	ENST00000362057.3	hg19	CCDS6806.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.736298	0.30774	.	.	ENSG00000095397	ENST00000265134;ENST00000374059;ENST00000362057	T;T;T	0.06294	4.21;4.2;3.32	5.49	2.08	0.27032	.	0.580016	0.18819	N	0.130285	T	0.05273	0.0140	L	0.43152	1.355	0.80722	D	1	B;B;B	0.28512	0.139;0.139;0.214	B;B;B	0.30572	0.05;0.034;0.117	T	0.39165	-0.9627	10	0.33141	T	0.24	-2.7096	2.0825	0.03638	0.2411:0.3747:0.0:0.3842	.	451;451;100	B9EGE6;Q9P202;Q9P202-4	.;WHRN_HUMAN;.	A	68;100;451	ENSP00000265134:G68A;ENSP00000363172:G100A;ENSP00000354623:G451A	ENSP00000265134:G68A	G	-	2	0	DFNB31	116226499	0.453000	0.25721	0.081000	0.20488	0.944000	0.59088	2.923000	0.48868	0.771000	0.33359	0.561000	0.74099	GGT	.	C|0.997;T|0.003		0.627	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404		G	117186678	C	G	117186678	3	3	115	1	0	0	0	0	1	0	0	0	4457	507	18	4	1399	4	DFNB31	9	117186678	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	2972921	117186678	24026753	219	19758										
GOLGA2	2801	hgsc.bcm.edu	37	chr9	131022366	131022366	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cggggttaccgtttccttcaGctcgctcagcttctcctgca	9	15	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:131022366G>A	ENST00000421699.2	-	18	1792	c.1780C>T	c.(1780-1782)Ctg>Ttg	p.L594L	GOLGA2_ENST00000609374.1_Silent_p.L582L|AL590708.1_ENST00000408370.1_RNA	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	594					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						GTTTCCTTCAGCTCGCTCAGC	0.632																																					p.L594L		Atlas-SNP	.											.	GOLGA2	69	.	0			c.C1780T						.						87	82	84					9																	131022366		2203	4300	6503	SO:0001819	synonymous_variant	2801	exon18			CCTTCAGCTCGCT	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"Golgi matrix protein GM130", "SY11 protein"	602580	"golgi autoantigen, golgin subfamily a, 2"			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.1780C>T	chr9.hg19:g.131022366G>A		33.0	0.0		40.0	8.0	NM_004486	Q6GRM9|Q9BRB0|Q9NYF9	Silent	SNP	ENST00000421699.2	hg19	CCDS6896.2																																																																																			.	.		0.632	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486		A	131022366	G	A	131022366	2	1	115	1	0	0	0	0	0	0	0	1	6560	962	34	3		3	GOLGA2	9	131022366	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	13835688	131022366	10191065	220	19759										
PPAPDC3	84814	hgsc.bcm.edu	37	chr9	134183331	134183331	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cctgctcctggacatcatgaCggtggccggcgtgcagaagc	14	13	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:134183331C>T	ENST00000372264.3	+	2	777	c.473C>T	c.(472-474)aCg>aTg	p.T158M		NM_032728.3	NP_116117.3	Q8NBV4	PPAC3_HUMAN	phosphatidic acid phosphatase type 2 domain containing 3	158					negative regulation of myotube differentiation (GO:0010832)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	hydrolase activity (GO:0016787)			breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	16	all_hematologic(7;0.0119)			OV - Ovarian serous cystadenocarcinoma(145;1.22e-05)|Epithelial(140;0.000173)		GACATCATGACGGTGGCCGGC	0.682																																					p.T158M		Atlas-SNP	.											.	PPAPDC3	24	.	0			c.C473T						.						23	22	23					9																	134183331		2200	4296	6496	SO:0001583	missense	84814	exon2			TCATGACGGTGGC	AK027568	CCDS6942.1	9q34.2-q34.3	2008-02-26	2005-07-15	2005-07-15	ENSG00000160539	ENSG00000160539			28174	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 67"	C9orf67		12958361	Standard	NM_032728		Approved	MGC12921, FLJ14662, NET39	uc004cal.2	Q8NBV4	OTTHUMG00000020822	ENST00000372264.3:c.473C>T	chr9.hg19:g.134183331C>T	ENSP00000361338:p.Thr158Met	11.0	0.0		31.0	9.0	NM_032728	Q5T6P0|Q96SS7|Q9BRC3	Missense_Mutation	SNP	ENST00000372264.3	hg19	CCDS6942.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.771215	0.49680	.	.	ENSG00000160539	ENST00000372264	T	0.75260	-0.92	4.68	4.68	0.58851	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.051238	0.85682	D	0.000000	T	0.77718	0.4172	L	0.45352	1.415	0.80722	D	1	D	0.71674	0.998	D	0.63033	0.91	T	0.76639	-0.2885	10	0.41790	T	0.15	-18.2091	10.6287	0.45523	0.0:0.8993:0.0:0.1007	.	158	Q8NBV4	PPAC3_HUMAN	M	158	ENSP00000361338:T158M	ENSP00000361338:T158M	T	+	2	0	PPAPDC3	133173152	1.000000	0.71417	0.978000	0.43139	0.032000	0.12392	4.316000	0.59178	2.296000	0.77279	0.505000	0.49811	ACG	.	.		0.682	PPAPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054724.1	NM_032728		T	134183331	C	T	134183331	3	4	115	1	0	0	0	0	1	0	0	0	12305	536	19	1	479	1	PPAPDC3	9	134183331	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	3160965	134183331	7030100	221	19760										
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134497361	134497361	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gctgcggctccgagtagtccTccagcaactgcatgtaggcc	12	14	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:134497361T>C	ENST00000372189.3	-	11	1799	c.1676A>G	c.(1675-1677)gAg>gGg	p.E559G	RAPGEF1_ENST00000372195.1_Missense_Mutation_p.E576G|RAPGEF1_ENST00000372190.3_Missense_Mutation_p.E577G	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	559					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		CGAGTAGTCCTCCAGCAACTG	0.582																																					p.E577G		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.A1730G						.						56	63	60					9																	134497361		2077	4206	6283	SO:0001583	missense	2889	exon11			TAGTCCTCCAGCA	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1676A>G	chr9.hg19:g.134497361T>C	ENSP00000361263:p.Glu559Gly	167.0	0.0		215.0	9.0	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	hg19	CCDS48047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.9|20.9	4.059388|4.059388	0.76074|0.76074	.|.	.|.	ENSG00000107263|ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000372191;ENST00000357686|ENST00000419442	T;T;T|.	0.27256|.	1.68;1.68;1.68|.	5.57|5.57	5.57|5.57	0.84162|0.84162	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71178|0.71178	0.3309|0.3309	M|M	0.64997|0.64997	1.995|1.995	0.50467|0.50467	D|D	0.999879|0.999879	D;D;D;D;D;D;D|.	0.89917|.	1.0;0.996;0.985;1.0;0.985;0.985;0.991|.	D;D;P;D;P;P;D|.	0.87578|.	0.996;0.986;0.831;0.998;0.831;0.831;0.919|.	T|T	0.70630|0.70630	-0.4819|-0.4819	10|5	0.18276|.	T|.	0.48|.	.|.	14.9117|14.9117	0.70761|0.70761	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	254;17;539;520;576;559;577|.	E9PDT1;Q5JUE7;C9JL20;Q13905-2;Q68DL3;Q13905;Q13905-3|.	.;.;.;.;.;RPGF1_HUMAN;.|.	G|G	559;576;453;559;577;539;485;254;576|18	ENSP00000361269:E576G;ENSP00000361263:E559G;ENSP00000361264:E577G|.	ENSP00000266110:E559G|.	E|R	-|-	2|1	0|2	RAPGEF1|RAPGEF1	133487182|133487182	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.957000|0.957000	0.61999|0.61999	7.392000|7.392000	0.79840|0.79840	2.117000|2.117000	0.64856|0.64856	0.459000|0.459000	0.35465|0.35465	GAG|AGG	.	.		0.582	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		C	134497361	T	C	134497361	3	2	115	1	0	0	0	0	1	0	0	0	13058	1551	54	2	1613	2	RAPGEF1	9	134497361	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	314030	134497361	6716070	222	19761										
REXO4	57109	hgsc.bcm.edu	37	chr9	136277557	136277557	+	Frame_Shift_Del	DEL	C	C	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acgggcggccatgctctcctCccccttagggcccacgccca							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:136277557delC	ENST00000371942.3	-	4	971	c.772delG	c.(772-774)gagfs	p.E259fs	REXO4_ENST00000478037.1_5'UTR|REXO4_ENST00000371935.2_Intron	NM_020385.2	NP_065118.2	Q9GZR2	REXO4_HUMAN	REX4, RNA exonuclease 4 homolog (S. cerevisiae)	259	Exonuclease.				regulation of transcription, DNA-templated (GO:0006355)	nucleolus (GO:0005730)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	15				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		ATGCTCTCCTCCCCCTTAGGG	0.547																																					p.E258fs		Atlas-INDEL	.											.	REXO4	27	.	0			c.773delA						.						172	153	159					9																	136277557		2203	4300	6503	SO:0001589	frameshift_variant	57109	exon4			.	AF273304	CCDS6969.1, CCDS65179.1	9q34	2008-02-05	2005-08-22	2005-08-22	ENSG00000148300	ENSG00000148300			12820	protein-coding gene	gene with protein product		602930	"Xenopus prevents mitotic catatrophe 2 homolog", "XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)"	XPMC2H		9325058	Standard	NM_020385		Approved		uc004cdm.3	Q9GZR2	OTTHUMG00000020870	ENST00000371942.3:c.772delG	chr9.hg19:g.136277557delC	ENSP00000361010:p.Glu259fs	113.0	0.0		152.0	10.0	NM_020385	B2RAT2|Q5T8S4|Q5T8S5|Q5T8S6|Q9GZW3	Frame_Shift_Del	DEL	ENST00000371942.3	hg19	CCDS6969.1																																																																																			.	.		0.547	REXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054899.1			-	136277557	C	-	136277557	7	5	115	1	0	1	0	1	0	0	0	0	13258	864	30	0	516	0	REXO4	9	136277557	Frame_Shift_Del	DEL	C	TCGA-DD-A3A1-01A-11D-A20W-10	1780196	136277557	4935874	223	19762										
SOHLH1	402381	hgsc.bcm.edu	37	chr9	138590847	138590847	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcaccaccactcacctgcgcTccctctcgctgatcacgttc	6	20	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:138590847T>C	ENST00000298466.5	-	2	251	c.191A>G	c.(190-192)gAg>gGg	p.E64G	SOHLH1_ENST00000425225.1_Missense_Mutation_p.E64G	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1	64	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(5)|prostate(1)	12		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		TCACCTGCGCTCCCTCTCGCT	0.697																																					p.E64G		Atlas-SNP	.											.	SOHLH1	70	.	0			c.A191G						.						49	47	48					9																	138590847		2203	4295	6498	SO:0001583	missense	402381	exon2			CTGCGCTCCCTCT	BC031861	CCDS35174.1, CCDS48054.1	9q34.3	2013-05-21	2006-03-16	2006-03-16	ENSG00000165643	ENSG00000165643		"Basic helix-loop-helix proteins"	27845	protein-coding gene	gene with protein product	"spermatogenesis associated 27"	610224	"chromosome 9 open reading frame 157"	C9orf157		12477932	Standard	NM_001012415		Approved	NOHLH, TEB2, bA100C15.3, bHLHe80, SPATA27	uc010nbe.3	Q5JUK2	OTTHUMG00000020915	ENST00000298466.5:c.191A>G	chr9.hg19:g.138590847T>C	ENSP00000298466:p.Glu64Gly	109.0	0.0		171.0	7.0	NM_001012415	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Missense_Mutation	SNP	ENST00000298466.5	hg19	CCDS35174.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.465171	0.63513	.	.	ENSG00000165643	ENST00000298466;ENST00000425225	D;D	0.97831	-4.56;-4.56	3.13	1.91	0.25777	Helix-loop-helix DNA-binding (5);	0.000000	0.33057	N	0.005321	D	0.97031	0.9030	L	0.44542	1.39	0.27971	N	0.936395	D;D	0.76494	0.998;0.999	D;D	0.70487	0.947;0.969	D	0.92293	0.5843	10	0.66056	D	0.02	-17.4684	6.1749	0.20439	0.0:0.0:0.2615:0.7385	.	64;64	Q5JUK2-2;Q5JUK2	.;SOLH1_HUMAN	G	64	ENSP00000298466:E64G;ENSP00000404438:E64G	ENSP00000298466:E64G	E	-	2	0	SOHLH1	137730668	1.000000	0.71417	0.988000	0.46212	0.945000	0.59286	0.975000	0.29449	0.361000	0.24292	0.454000	0.30748	GAG	.	.		0.697	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		C	138590847	T	C	138590847	3	2	115	1	0	0	0	0	1	0	0	0	14938	1551	54	2	1041	2	SOHLH1	9	138590847	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2313290	138590847	2622584	224	19763										
GPSM1	26086	hgsc.bcm.edu	37	chr9	139232412	139232412	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctttgacgtggccgccgagtActacaagtaggtggtcccca	12	12	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr9:139232412A>G	ENST00000440944.1	+	6	1032	c.812A>G	c.(811-813)tAc>tGc	p.Y271C	GPSM1_ENST00000392945.3_Missense_Mutation_p.Y271C	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	271	Mediates association with membranes. {ECO:0000250}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GCCGCCGAGTACTACAAGTAG	0.627																																					p.Y271C		Atlas-SNP	.											.	GPSM1	50	.	0			c.A812G						.						47	40	43					9																	139232412		2192	4295	6487	SO:0001583	missense	26086	exon6			CCGAGTACTACAA	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"Tetratricopeptide (TTC) repeat domain containing"	17858	protein-coding gene	gene with protein product	"AGS3 homolog (C. elegans)"	609491	"G-protein signalling modulator 1 (AGS3-like, C. elegans)"			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.812A>G	chr9.hg19:g.139232412A>G	ENSP00000392828:p.Tyr271Cys	61.0	0.0		99.0	4.0	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Missense_Mutation	SNP	ENST00000440944.1	hg19	CCDS48055.1	.	.	.	.	.	.	.	.	.	.	A	16.45	3.126089	0.56721	.	.	ENSG00000160360	ENST00000392945;ENST00000440944;ENST00000354753	T;T;T	0.75260	-0.92;-0.92;-0.92	4.1	4.1	0.47936	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.286251	0.29087	U	0.013182	T	0.79828	0.4513	L	0.43646	1.37	0.80722	D	1	D;D	0.76494	0.999;0.961	D;P	0.70716	0.97;0.569	T	0.80099	-0.1524	10	0.49607	T	0.09	-16.0651	12.5816	0.56393	1.0:0.0:0.0:0.0	.	271;271	Q86YR5;Q86YR5-3	GPSM1_HUMAN;.	C	271;271;248	ENSP00000376674:Y271C;ENSP00000392828:Y271C;ENSP00000346797:Y248C	ENSP00000346797:Y248C	Y	+	2	0	GPSM1	138352233	1.000000	0.71417	0.993000	0.49108	0.755000	0.42902	7.299000	0.78831	1.624000	0.50355	0.379000	0.24179	TAC	.	.		0.627	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		G	139232412	A	G	139232412	3	3	115	1	0	0	0	0	1	0	0	0	6743	391	14	2	834	2	GPSM1	9	139232412	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	641565	139232412	1981019	225	19764										
NET1	10276	hgsc.bcm.edu	37	chr10	5496244	5496244	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcagttaccgcgcttgaatgCctacagaggttactgtagta	10	9	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:5496244C>T	ENST00000355029.4	+	9	927	c.785C>T	c.(784-786)gCc>gTc	p.A262V	NET1_ENST00000380359.3_Missense_Mutation_p.A208V|NET1_ENST00000542715.1_Missense_Mutation_p.A81V	NM_001047160.2	NP_001040625.1	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming 1	262	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|myoblast migration (GO:0051451)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|kidney(2)|large_intestine(9)|lung(5)|prostate(2)|skin(1)	23						CGCTTGAATGCCTACAGAGGT	0.433																																					p.A262V		Atlas-SNP	.											.	NET1	82	.	0			c.C785T						.						83	85	84					10																	5496244		2203	4300	6503	SO:0001583	missense	10276	exon9			TGAATGCCTACAG	AJ010046	CCDS7067.1, CCDS41483.1	10p15	2013-01-10	2008-09-12		ENSG00000173848	ENSG00000173848		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14592	protein-coding gene	gene with protein product		606450				8649828	Standard	NR_073040		Approved	ARHGEF8, NET1A	uc001iia.4	Q7Z628	OTTHUMG00000017596	ENST00000355029.4:c.785C>T	chr10.hg19:g.5496244C>T	ENSP00000347134:p.Ala262Val	108.0	0.0		82.0	4.0	NM_001047160	Q12773|Q96D82|Q99903|Q9UEN6	Missense_Mutation	SNP	ENST00000355029.4	hg19	CCDS41483.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815264	0.50527	.	.	ENSG00000173848	ENST00000355029;ENST00000542715;ENST00000449083;ENST00000380359;ENST00000380337	T;T;T;T	0.61742	0.08;0.08;0.08;0.08	6.07	5.16	0.70880	Dbl homology (DH) domain (5);	0.000000	0.41712	D	0.000834	T	0.42154	0.1190	L	0.31476	0.935	0.80722	D	1	P;B	0.38335	0.627;0.428	B;B	0.32465	0.146;0.146	T	0.27938	-1.0059	10	0.22109	T	0.4	-21.8148	14.564	0.68162	0.0:0.9282:0.0:0.0718	.	208;262	Q5SQI7;Q7Z628	.;ARHG8_HUMAN	V	262;81;80;208;80	ENSP00000347134:A262V;ENSP00000446452:A81V;ENSP00000403101:A80V;ENSP00000369717:A208V	ENSP00000347134:A262V	A	+	2	0	NET1	5486244	1.000000	0.71417	1.000000	0.80357	0.508000	0.34012	7.688000	0.84153	2.884000	0.98904	0.655000	0.94253	GCC	.	.		0.433	NET1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046553.3	NM_005863		T	5496244	C	T	5496244	3	4	115	1	0	0	0	0	1	0	0	0	10347	739	26	3	916	3	NET1	10	5496244	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10		5496244	130038503	226	19765										
NSUN6	221078	hgsc.bcm.edu	37	chr10	18937549	18937549	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tttcaaacttcctttctgctTcttgtttacctaaagcagtc	4	11	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:18937549T>C	ENST00000377304.4	-	2	519	c.101A>G	c.(100-102)gAa>gGa	p.E34G	RP11-139J15.7_ENST00000606425.1_Missense_Mutation_p.E22G	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	34							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						CCTTTCTGCTTCTTGTTTACC	0.343																																					p.E34G		Atlas-SNP	.											.	NSUN6	46	.	0			c.A101G						.						178	165	170					10																	18937549		2203	4299	6502	SO:0001583	missense	221078	exon2			TCTGCTTCTTGTT	BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"NOP2/Sun domain containing"	23529	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 6", "NOL1/NOP2/Sun domain family, member 6", "ARL5B antisense RNA 1"	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.101A>G	chr10.hg19:g.18937549T>C	ENSP00000366519:p.Glu34Gly	111.0	0.0		97.0	4.0	NM_182543	B0YJ54	Missense_Mutation	SNP	ENST00000377304.4	hg19	CCDS7130.1	.	.	.	.	.	.	.	.	.	.	T	12.74	2.027944	0.35797	.	.	ENSG00000241058	ENST00000377304	T	0.32988	1.43	4.84	-0.992	0.10232	.	0.400925	0.28393	N	0.015505	T	0.28863	0.0716	L	0.53249	1.67	0.47547	D	0.999452	B	0.22604	0.072	B	0.26969	0.075	T	0.25984	-1.0116	10	0.56958	D	0.05	.	13.6389	0.62237	0.0:0.0:0.5206:0.4794	.	34	Q8TEA1	NSUN6_HUMAN	G	34	ENSP00000366519:E34G	ENSP00000366519:E34G	E	-	2	0	NSUN6	18977555	0.334000	0.24739	0.763000	0.31416	0.665000	0.39181	0.134000	0.15932	-0.092000	0.12417	0.383000	0.25322	GAA	.	.		0.343	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543		C	18937549	T	C	18937549	3	2	115	1	0	0	0	0	1	0	0	0	10691	1783	62	2	1348	2	NSUN6	10	18937549	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	13441305	18937549	116597198	227	19766										
TMEM72	643236	hgsc.bcm.edu	37	chr10	45429185	45429185	+	5'UTR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgctgctgtcggtggcctgcTtcctccacccggtcctggtc	12	16	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:45429185T>C	ENST00000544540.1	+	0	440				TMEM72-AS1_ENST00000450287.2_RNA			A0PK05	TMM72_HUMAN	transmembrane protein 72							integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						GGTGGCCTGCTTCCTCCACCC	0.617																																					p.F104L		Atlas-SNP	.											.	TMEM72	25	.	0			c.T310C						.						52	55	54					10																	45429185		1568	3582	5150	SO:0001623	5_prime_UTR_variant	643236	exon4			GCCTGCTTCCTCC	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 127"	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.-45T>C	chr10.hg19:g.45429185T>C		108.0	0.0		142.0	6.0	NM_001123376	A1L181|Q5T740	Missense_Mutation	SNP	ENST00000544540.1	hg19		.	.	.	.	.	.	.	.	.	.	T	27.0	4.787913	0.90367	.	.	ENSG00000187783	ENST00000389583	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.77205	0.4096	M	0.74258	2.255	0.80722	D	1	D	0.67145	0.996	D	0.73380	0.98	T	0.79259	-0.1877	9	0.59425	D	0.04	-18.8848	12.4511	0.55677	0.0:0.0:0.0:1.0	.	104	A0PK05	TMM72_HUMAN	L	104	.	ENSP00000374234:F104L	F	+	1	0	TMEM72	44749191	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.661000	0.68025	2.254000	0.74563	0.533000	0.62120	TTC	.	.		0.617	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376		C	45429185	T	C	45429185	1	2	115	0	1	0	0	0	0	0	0	0	16216	1609	56	2		2	TMEM72	10	45429185	5'UTR	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	26491636	45429185	90105562	228	19767										
ANXA8L2	728113	hgsc.bcm.edu	37	chr10	47756662	47756662	+	Frame_Shift_Del	DEL	T	T	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgtatgcggcaggcgagaaTattcgtgggactgatgagat					rs202221168		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:47756662delT	ENST00000374277.5	+	8	698	c.576delT	c.(574-576)aatfs	p.N192fs	AL603965.1_ENST00000335083.5_Intron|ANXA8L2_ENST00000538825.1_Frame_Shift_Del_p.N130fs|ANXA8L2_ENST00000449464.2_3'UTR|ANXA8L2_ENST00000340243.6_Frame_Shift_Del_p.N173fs	NM_001630.2	NP_001621.2														endometrium(1)|pancreas(1)	2						CAGGCGAGAATATTCGTGGGA	0.597																																					p.N192fs		Atlas-INDEL	.											.	ANXA8L2	8	.	0			c.575delA						.						71	42	52					10																	47756662		1990	3787	5777	SO:0001589	frameshift_variant	244	exon8			.																												ENST00000374277.5:c.576delT	chr10.hg19:g.47756662delT	ENSP00000363395:p.Asn192fs	136.0	0.0		161.0	10.0	NM_001630		Frame_Shift_Del	DEL	ENST00000374277.5	hg19	CCDS7216.1																																																																																			.	.		0.597	ANXA8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047866.1			-	47756662	T	-	47756662	7	5	115	1	0	1	0	1	0	0	0	0	724	1403	49	0	606	0	ANXA8L2	10	47756662	Frame_Shift_Del	DEL	T	TCGA-DD-A3A1-01A-11D-A20W-10	2327477	47756662	87778085	229	19768										
ZNF488	118738	hgsc.bcm.edu	37	chr10	48371474	48371474	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cattctcagaagcggagagaAgaggcccttgcctgccctgt	12	12	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:48371474A>G	ENST00000395702.2	+	2	1169	c.942A>G	c.(940-942)gaA>gaG	p.E314E	ZNF488_ENST00000494156.1_3'UTR|ZNF488_ENST00000586537.1_Silent_p.E207E			Q96MN9	ZN488_HUMAN	zinc finger protein 488	314					negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte development (GO:0014003)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|ovary(2)	14						AGCGGAGAGAAGAGGCCCTTG	0.597																																					p.E314E		Atlas-SNP	.											.	ZNF488	38	.	0			c.A942G						.						94	93	93					10																	48371474		2203	4300	6503	SO:0001819	synonymous_variant	118738	exon2			GAGAGAAGAGGCC	AK056666	CCDS73120.1	10q11.22	2014-04-10			ENSG00000165388	ENSG00000265763		"Zinc fingers, C2H2-type"	23535	protein-coding gene	gene with protein product							Standard	NM_153034		Approved	FLJ32104	uc001jex.3	Q96MN9	OTTHUMG00000188322	ENST00000395702.2:c.942A>G	chr10.hg19:g.48371474A>G		55.0	0.0		95.0	4.0	NM_153034	Q05CE0	Silent	SNP	ENST00000395702.2	hg19	CCDS7217.1																																																																																			.	.		0.597	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034		G	48371474	A	G	48371474	2	3	115	1	0	0	0	0	0	0	0	1	17955	69	3	2		2	ZNF488	10	48371474	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	614812	48371474	87163273	230	19769										
C10orf72	196740	hgsc.bcm.edu	37	chr10	50315774	50315774	+	Frame_Shift_Del	DEL	C	C	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gacggagagcctgtagagcgCcccccgctgctcctccagca					rs368171376		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:50315774delC	ENST00000332853.4	-	2	345	c.322delG	c.(322-324)gcgfs	p.A108fs	VSTM4_ENST00000298454.3_Frame_Shift_Del_p.A108fs	NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	108	Ig-like.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A108S(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						CTGTAGAGCGCCCCCCGCTGC	0.612																																					p.A108fs		Atlas-INDEL	.											.	VSTM4	83	.	1	Substitution - Missense(1)	liver(1)	c.323delC						.						72	76	75					10																	50315774		2203	4300	6503	SO:0001589	frameshift_variant	196740	exon2			.	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"Immunoglobulin superfamily / V-set domain containing"	26470	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 72"	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.322delG	chr10.hg19:g.50315774delC	ENSP00000331062:p.Ala108fs	111.0	0.0		145.0	10.0	NM_144984	B4DNI6|Q96MX7	Frame_Shift_Del	DEL	ENST00000332853.4	hg19	CCDS31198.1																																																																																			.	.		0.612	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984		-	50315774	C	-	50315774	7	5	115	1	0	1	0	1	0	0	0	0	1617	739	26	0	791	0	C10orf72	10	50315774	Frame_Shift_Del	DEL	C	TCGA-DD-A3A1-01A-11D-A20W-10	1944300	50315774	85218973	231	19770										
SGMS1	259230	hgsc.bcm.edu	37	chr10	52087035	52087035	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acattgtaatacaccgatacAggtacagcgtgccaactatg	8	10	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:52087035A>G	ENST00000361781.2	-	8	1630	c.671T>C	c.(670-672)cTg>cCg	p.L224P	SGMS1_ENST00000429490.1_Missense_Mutation_p.L55P	NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	230					apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						ACACCGATACAGGTACAGCGT	0.398																																					p.L224P		Atlas-SNP	.											.	SGMS1	40	.	0			c.T671C						.						99	92	95					10																	52087035		2203	4300	6503	SO:0001583	missense	259230	exon8			CGATACAGGTACA	AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	2.7.8.27	"Sterile alpha motif (SAM) domain containing"	29799	protein-coding gene	gene with protein product		611573	"transmembrane protein 23"	TMEM23		11841947, 14976195	Standard	NM_147156		Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.671T>C	chr10.hg19:g.52087035A>G	ENSP00000354829:p.Leu224Pro	91.0	0.0		112.0	5.0	NM_147156	Q68U43|Q6EKK0|Q75SP1	Missense_Mutation	SNP	ENST00000361781.2	hg19	CCDS7240.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.715522	0.89112	.	.	ENSG00000198964	ENST00000412547;ENST00000361781;ENST00000429490	T	0.55760	0.5	5.73	5.73	0.89815	.	0.073707	0.56097	D	0.000030	T	0.67906	0.2943	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.68621	0.959;0.95	T	0.70777	-0.4780	10	0.87932	D	0	-13.7289	14.2815	0.66216	1.0:0.0:0.0:0.0	.	55;230	B4DJU2;Q86VZ5	.;SMS1_HUMAN	P	24;224;55	ENSP00000354829:L224P	ENSP00000354829:L224P	L	-	2	0	SGMS1	51757041	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.324000	0.78689	0.533000	0.62120	CTG	.	.		0.398	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048074.2	NM_147156		G	52087035	A	G	52087035	3	3	115	1	0	0	0	0	1	0	0	0	14229	188	7	2	586	2	SGMS1	10	52087035	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1771261	52087035	83447712	232	19771										
BICC1	80114	hgsc.bcm.edu	37	chr10	60549107	60549107	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcctaattccccctctattcAgcatatatcacaaacgtaca	2	14	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:60549107A>G	ENST00000373886.3	+	7	690	c.686A>G	c.(685-687)cAg>cGg	p.Q229R		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	229					multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						CCCTCTATTCAGCATATATCA	0.403																																					p.Q229R		Atlas-SNP	.											.	BICC1	121	.	0			c.A686G						.						144	136	139					10																	60549107		2203	4300	6503	SO:0001583	missense	80114	exon7			CTATTCAGCATAT	AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"Sterile alpha motif (SAM) domain containing"	19351	protein-coding gene	gene with protein product		614295	"bicaudal C homolog 1 (Drosophila)"				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.686A>G	chr10.hg19:g.60549107A>G	ENSP00000362993:p.Gln229Arg	202.0	0.0		175.0	8.0	NM_001080512		Missense_Mutation	SNP	ENST00000373886.3	hg19	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	A	16.98	3.271918	0.59649	.	.	ENSG00000122870	ENST00000373886	T	0.30714	1.52	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.39835	0.1093	L	0.56769	1.78	0.80722	D	1	D	0.59357	0.985	P	0.50537	0.643	T	0.13335	-1.0513	10	0.19590	T	0.45	-9.024	15.9023	0.79387	1.0:0.0:0.0:0.0	.	229	Q9H694	BICC1_HUMAN	R	229	ENSP00000362993:Q229R	ENSP00000362993:Q229R	Q	+	2	0	BICC1	60219113	1.000000	0.71417	0.997000	0.53966	0.963000	0.63663	7.043000	0.76572	2.153000	0.67306	0.533000	0.62120	CAG	.	.		0.403	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		G	60549107	A	G	60549107	3	3	115	1	0	0	0	0	1	0	0	0	1427	188	7	2	712	2	BICC1	10	60549107	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	8462072	60549107	74985640	233	19772										
CHST3	9469	hgsc.bcm.edu	37	chr10	73767842	73767842	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgcgagagcatccgcctgtcCgcggagctggggctgcggca	17	13	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:73767842C>T	ENST00000373115.4	+	3	1490	c.1053C>T	c.(1051-1053)tcC>tcT	p.S351S		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	351					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						TCCGCCTGTCCGCGGAGCTGG	0.706																																					p.S351S		Atlas-SNP	.											.	CHST3	36	.	0			c.C1053T						.						6	5	5					10																	73767842		1770	3355	5125	SO:0001819	synonymous_variant	9469	exon3			CCTGTCCGCGGAG	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"Sulfotransferases, membrane-bound"	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.1053C>T	chr10.hg19:g.73767842C>T		28.0	0.0		39.0	19.0	NM_004273	O75099|Q52M30	Silent	SNP	ENST00000373115.4	hg19	CCDS7312.1																																																																																			.	.		0.706	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273		T	73767842	C	T	73767842	2	4	115	1	0	0	0	0	0	0	0	1	3407	639	23	1		1	CHST3	10	73767842	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	13218735	73767842	61766905	234	19773										
USP54	159195	hgsc.bcm.edu	37	chr10	75264616	75264616	+	Frame_Shift_Del	DEL	G	G	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gattctacttacaaaactgtGggaagaaaccggagcttcct					rs376012785		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:75264616delG	ENST00000339859.4	-	21	4403	c.4303delC	c.(4303-4305)cacfs	p.H1435fs	RP11-137L10.6_ENST00000596320.1_RNA|USP54_ENST00000408019.1_Frame_Shift_Del_p.H1435fs|RP11-137L10.6_ENST00000595935.1_RNA|RP11-137L10.6_ENST00000600607.1_RNA|RP11-137L10.6_ENST00000600206.1_RNA|USP54_ENST00000497106.1_5'UTR|USP54_ENST00000428547.1_Frame_Shift_Del_p.H1285fs|USP54_ENST00000422491.2_Intron|RP11-137L10.6_ENST00000593790.1_RNA|RP11-137L10.6_ENST00000442133.4_RNA|USP54_ENST00000394811.2_Intron|RP11-137L10.6_ENST00000595069.1_RNA|RP11-137L10.6_ENST00000597958.1_RNA			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1435					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					ACAAAACTGTGGGAAGAAACC	0.502																																					p.H1435fs	Colon(195;880 2046 8854 25025 38456)	Atlas-INDEL	.											.	USP54	178	.	0			c.4304delA						.						117	99	106					10																	75264616		2203	4300	6503	SO:0001589	frameshift_variant	159195	exon20			.	AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"Ubiquitin-specific peptidases"	23513	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 29", "ubiquitin specific protease 54"	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.4303delC	chr10.hg19:g.75264616delG	ENSP00000345216:p.His1435fs	130.0	0.0		166.0	10.0	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Frame_Shift_Del	DEL	ENST00000339859.4	hg19	CCDS7329.2																																																																																			.	.		0.502	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		-	75264616	G	-	75264616	7	5	115	1	0	1	0	1	0	0	0	0	17100	1348	47	0	763	0	USP54	10	75264616	Frame_Shift_Del	DEL	G	TCGA-DD-A3A1-01A-11D-A20W-10	1496774	75264616	60270131	235	19774										
IFIT1B	439996	hgsc.bcm.edu	37	chr10	91144454	91144454	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atgctttgctgtgctatgagAgggctctgaggctggctgct	15	8	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:91144454A>G	ENST00000371809.3	+	2	1464	c.1384A>G	c.(1384-1386)Agg>Ggg	p.R462G	LIPA_ENST00000371837.1_Intron	NM_001010987.2	NP_001010987.1	Q5T764	IFT1B_HUMAN	interferon-induced protein with tetratricopeptide repeats 1B	462										endometrium(2)|large_intestine(3)|lung(8)	13						GTGCTATGAGAGGGCTCTGAG	0.408																																					p.R462G		Atlas-SNP	.											.	IFIT1B	39	.	0			c.A1384G						.						152	159	157					10																	91144454		2203	4300	6503	SO:0001583	missense	439996	exon2			TATGAGAGGGCTC		CCDS31242.1	10q23.31	2014-05-22	2010-03-22	2010-03-22	ENSG00000204010	ENSG00000204010		"Tetratricopeptide (TTC) repeat domain containing"	23442	protein-coding gene	gene with protein product			"interferon-induced protein with tetratricopeptide repeats 1-like"	IFIT1L			Standard	NM_001010987		Approved	bA149I23.6	uc001kgh.3	Q5T764	OTTHUMG00000018709	ENST00000371809.3:c.1384A>G	chr10.hg19:g.91144454A>G	ENSP00000360874:p.Arg462Gly	105.0	0.0		134.0	6.0	NM_001010987	A7E245	Missense_Mutation	SNP	ENST00000371809.3	hg19	CCDS31242.1	.	.	.	.	.	.	.	.	.	.	A	19.34	3.809643	0.70797	.	.	ENSG00000204010	ENST00000371809	T	0.68331	-0.32	4.13	-3.3	0.05003	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.546343	0.16394	N	0.216346	T	0.57007	0.2024	L	0.59436	1.845	0.24518	N	0.99418	P	0.45768	0.866	P	0.46208	0.507	T	0.53795	-0.8388	10	0.72032	D	0.01	.	1.4588	0.02391	0.4588:0.2558:0.1562:0.1292	.	462	Q5T764	IFT1B_HUMAN	G	462	ENSP00000360874:R462G	ENSP00000360874:R462G	R	+	1	2	IFIT1B	91134434	0.141000	0.22595	0.008000	0.14137	0.582000	0.36321	0.280000	0.18790	-0.907000	0.03862	0.456000	0.33151	AGG	.	.		0.408	IFIT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049296.3	NM_001010987		G	91144454	A	G	91144454	3	3	115	1	0	0	0	0	1	0	0	0	7531	295	11	2	1390	2	IFIT1B	10	91144454	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	15879838	91144454	44390293	236	19775										
KIF20B	9585	hgsc.bcm.edu	37	chr10	91522426	91522426	+	Missense_Mutation	SNP	T	T	C													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agtccttgactcttgtgaagTgtcaacagaaaatgatcaaa							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:91522426T>C	ENST00000371728.3	+	29	4888	c.4823T>C	c.(4822-4824)gTg>gCg	p.V1608A	KIF20B_ENST00000394289.2_Missense_Mutation_p.V1608A|KIF20B_ENST00000416354.1_Missense_Mutation_p.V1638A|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.V1568A	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1608	Interaction with PIN1.			V -> A (in Ref. 1; BAB69456). {ECO:0000305}.	ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						TCTTGTGAAGTGTCAACAGAA	0.338																																					p.V1568A		Atlas-SNP	.											.	KIF20B	191	.	0			c.T4703C						.						90	85	87					10																	91522426		2203	4300	6503	SO:0001583	missense	9585	exon29			GTGAAGTGTCAAC	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.4823T>C	chr10.hg19:g.91522426T>C	ENSP00000360793:p.Val1608Ala	91.0	0.0		86.0	4.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	hg19		.	.	.	.	.	.	.	.	.	.	T	26.6	4.752730	0.89753	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	6.06	6.06	0.98353	.	0.000000	0.45606	D	0.000355	T	0.68449	0.3002	M	0.62723	1.935	0.41059	D	0.985363	D;D	0.69078	0.996;0.997	P;D	0.64042	0.836;0.921	T	0.71087	-0.4694	10	0.62326	D	0.03	-11.1571	15.5919	0.76537	0.0:0.0:0.0:1.0	.	1608;1568	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	A	1568;1638;1608;1608	ENSP00000260753:V1568A;ENSP00000411545:V1638A;ENSP00000377830:V1608A;ENSP00000360793:V1608A	ENSP00000260753:V1568A	V	+	2	0	KIF20B	91512406	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.010000	0.76353	2.324000	0.78689	0.533000	0.62120	GTG	.	.		0.338	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		C	91522426	T	C	91522426	3	2	115	1	0	0	0	0	1	0	0	0	8296	1696	59	2	4813	2	KIF20B	10	91522426	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	377972	91522426	44012321	237	19776	84	2								
KIF20B	9585	hgsc.bcm.edu	37	chr10	91522431	91522431	+	Missense_Mutation	SNP	A	A	G													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttgactcttgtgaagtgtcaAcagaaaatgatcaaagcact							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:91522431A>G	ENST00000371728.3	+	29	4893	c.4828A>G	c.(4828-4830)Aca>Gca	p.T1610A	KIF20B_ENST00000394289.2_Missense_Mutation_p.T1610A|KIF20B_ENST00000416354.1_Missense_Mutation_p.T1640A|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.T1570A	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1610	Interaction with PIN1.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						TGAAGTGTCAACAGAAAATGA	0.348																																					p.T1570A		Atlas-SNP	.											.	KIF20B	191	.	0			c.A4708G						.						90	85	86					10																	91522431		2203	4300	6503	SO:0001583	missense	9585	exon29			GTGTCAACAGAAA	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.4828A>G	chr10.hg19:g.91522431A>G	ENSP00000360793:p.Thr1610Ala	95.0	0.0		91.0	4.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	hg19		.	.	.	.	.	.	.	.	.	.	A	13.92	2.381615	0.42207	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	6.06	0.978	0.19740	.	0.122710	0.37053	N	0.002270	T	0.44265	0.1285	M	0.66939	2.045	0.36363	D	0.860849	B;B	0.12630	0.003;0.006	B;B	0.14578	0.005;0.011	T	0.36744	-0.9735	10	0.56958	D	0.05	-7.7027	4.3202	0.11013	0.5109:0.0:0.1349:0.3542	.	1610;1570	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	A	1570;1640;1610;1610	ENSP00000260753:T1570A;ENSP00000411545:T1640A;ENSP00000377830:T1610A;ENSP00000360793:T1610A	ENSP00000260753:T1570A	T	+	1	0	KIF20B	91512411	0.989000	0.36119	0.993000	0.49108	0.995000	0.86356	1.233000	0.32648	-0.077000	0.12752	-0.274000	0.10170	ACA	.	.		0.348	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		G	91522431	A	G	91522431	3	3	115	1	0	0	0	0	1	0	0	0	8296	43	2	2	4818	2	KIF20B	10	91522431	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5	91522431	44012316	238	19777	84	2								
TNKS2	80351	hgsc.bcm.edu	37	chr10	93609348	93609348	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atggatatatttgagagagaAcaggtgagtagataaatcat	11	2	1	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:93609348A>G	ENST00000371627.4	+	20	3070	c.2691A>G	c.(2689-2691)gaA>gaG	p.E897E		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	897	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				TTGAGAGAGAACAGGTGAGTA	0.338																																					p.E897E		Atlas-SNP	.											.	TNKS2	103	.	0			c.A2691G						.						101	97	98					10																	93609348		2203	4299	6502	SO:0001819	synonymous_variant	80351	exon20			GAGAGAACAGGTG	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.2691A>G	chr10.hg19:g.93609348A>G		104.0	0.0		71.0	4.0	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Silent	SNP	ENST00000371627.4	hg19	CCDS7417.1																																																																																			.	.		0.338	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		G	93609348	A	G	93609348	2	3	115	1	0	0	0	0	0	0	0	1	16336	40	2	2		2	TNKS2	10	93609348	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2086917	93609348	41925399	239	19778										
TLX1NB	100038246	hgsc.bcm.edu	37	chr10	102849600	102849600	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atggcctcttgggaaaggagAgagtgctgacttgcccatgc	14	9	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:102849600A>G	ENST00000445873.1	-	3	1339	c.63T>C	c.(61-63)tcT>tcC	p.S21S	TLX1NB_ENST00000425505.1_5'Flank	NM_001085398.1	NP_001078867.1	P0CAT3	TLXNB_HUMAN	TLX1 neighbor	21																	GGGAAAGGAGAGAGTGCTGAC	0.652																																					p.S21S		Atlas-SNP	.											.	.	.	.	0			c.T63C						.						15	18	17					10																	102849600		1924	4113	6037	SO:0001819	synonymous_variant	100038246	exon3			AAGGAGAGAGTGC	BC019674	CCDS60615.1	10q24	2014-04-01			ENSG00000236311	ENSG00000236311			37183	protein-coding gene	gene with protein product		612734				17303350	Standard	NM_001085398		Approved	TD1, TDI, APT-B7	uc001ksv.3	P0CAT3	OTTHUMG00000018925	ENST00000445873.1:c.63T>C	chr10.hg19:g.102849600A>G		75.0	0.0		78.0	4.0	NM_001085398		Silent	SNP	ENST00000445873.1	hg19																																																																																				.	.		0.652	TLX1NB-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000049925.2	NM_001085398		G	102849600	A	G	102849600	2	3	115	1	0	0	0	0	0	0	0	1	15975	291	11	2		2	TLX1NB	10	102849600	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	9240252	102849600	32685147	240	19779										
USMG5	84833	hgsc.bcm.edu	37	chr10	105152185	105152185	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tttttaataccagtgaactgGtattgcgcatcactttctgg	8	8	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:105152185G>T	ENST00000369825.1	-	3	512	c.30C>A	c.(28-30)taC>taA	p.Y10*	MIR1307_ENST00000408840.1_RNA|USMG5_ENST00000337003.4_Nonsense_Mutation_p.Y10*|USMG5_ENST00000309579.3_Nonsense_Mutation_p.Y10*|USMG5_ENST00000369811.1_Nonsense_Mutation_p.Y10*|USMG5_ENST00000369815.1_Nonsense_Mutation_p.Y10*			Q96IX5	USMG5_HUMAN	up-regulated during skeletal muscle growth 5 homolog (mouse)	10						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)				breast(1)	1		Colorectal(252;0.142)		Epithelial(162;3.94e-09)|all cancers(201;2.76e-08)|BRCA - Breast invasive adenocarcinoma(275;0.197)		CAGTGAACTGGTATTGCGCAT	0.269																																					p.Y10X		Atlas-SNP	.											.	USMG5	5	.	0			c.C30A						.						35	40	38					10																	105152185		2193	4291	6484	SO:0001587	stop_gained	84833	exon3			GAACTGGTATTGC	BC007087	CCDS7548.1	10q24.33	2011-04-13	2008-06-05		ENSG00000173915	ENSG00000173915			30889	protein-coding gene	gene with protein product		615204	"upregulated during skeletal muscle growth 5", "upregulated during skeletal muscle growth 5 homolog (mouse)"			12477932	Standard	NM_032747		Approved	MGC14697, bA792D24.4, DAPIT	uc001kwx.2	Q96IX5	OTTHUMG00000018984	ENST00000369825.1:c.30C>A	chr10.hg19:g.105152185G>T	ENSP00000358840:p.Tyr10*	98.0	0.0		117.0	6.0	NM_001206427	B2R4N2|D3DR92	Nonsense_Mutation	SNP	ENST00000369825.1	hg19	CCDS7548.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.722614	0.48728	.	.	ENSG00000173915	ENST00000369825;ENST00000369815;ENST00000309579;ENST00000337003;ENST00000369811	.	.	.	6.17	2.96	0.34315	.	0.192756	0.37348	N	0.002122	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	10.9458	0.47299	0.2742:0.0:0.7258:0.0	.	.	.	.	X	10	.	ENSP00000311245:Y10X	Y	-	3	2	USMG5	105142175	1.000000	0.71417	0.996000	0.52242	0.473000	0.32948	3.199000	0.51043	0.954000	0.37851	-0.137000	0.14449	TAC	.	.		0.269	USMG5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050142.1	NM_032747		T	105152185	G	T	105152185	4	4	115	1	0	0	0	0	0	1	0	0	17053	1256	44	3	154	3	USMG5	10	105152185	Nonsense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	2302585	105152185	30382562	241	19780										
GPAM	57678	hgsc.bcm.edu	37	chr10	113920573	113920585	+	Frame_Shift_Del	DEL	GACTTCCTCTTTC	GACTTCCTCTTTC	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aggtcaaaatcacgagccagGacttcctctttcatcacaaa							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	GACTTCCTCTTTC	GACTTCCTCTTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:113920573_113920585delGACTTCCTCTTTC	ENST00000348367.4	-	16	1733_1745	c.1536_1548delGAAAGAGGAAGTC	c.(1534-1548)atgaaagaggaagtcfs	p.MKEEV512fs	GPAM_ENST00000423155.1_Frame_Shift_Del_p.MKEEV512fs|GPAM_ENST00000369425.1_Frame_Shift_Del_p.MKEEV512fs			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	512					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		CACGAGCCAGGACTTCCTCTTTCATCACAAAGA	0.432																																					p.513_517del	Ovarian(161;1017 2606 18293 52943)	Atlas-INDEL	.											.	GPAM	68	.	0			c.1537_1549del						.																																			SO:0001589	frameshift_variant	57678	exon16			.	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"glycerol-3-phosphate acyltransferase 1, mitochondrial"	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.1536_1548delGAAAGAGGAAGTC	chr10.hg19:g.113920573_113920585delGACTTCCTCTTTC	ENSP00000265276:p.Met512fs	115.0	0.0		96.0	12.0	NM_001244949	Q5VW51|Q86TA3	Frame_Shift_Del	DEL	ENST00000348367.4	hg19	CCDS7570.1																																																																																			.	.		0.432	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		-	113920585	GACTTCCTCTTTC	-	113920573	7	5	115	1	0	1	0	1	0	0	0	0	6596	1161	41	0	966	0	GPAM	10	113920573	Frame_Shift_Del	DEL	GACTTCCTCTTTC	TCGA-DD-A3A1-01A-11D-A20W-10	8768388	113920573	21614174	242	19781										
GPAM	57678	hgsc.bcm.edu	37	chr10	113920588	113920593	+	In_Frame_Del	DEL	CACAAA	CACAAA	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gccaggacttcctctttcatCacaaagaagtcttcgaccaa					rs187077125		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	CACAAA	CACAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:113920588_113920593delCACAAA	ENST00000348367.4	-	16	1725_1730	c.1528_1533delTTTGTG	c.(1528-1533)tttgtgdel	p.FV510del	GPAM_ENST00000423155.1_In_Frame_Del_p.FV510del|GPAM_ENST00000369425.1_In_Frame_Del_p.FV510del			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	510					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		CCTCTTTCATCACAAAGAAGTCTTCG	0.437																																					p.510_512del	Ovarian(161;1017 2606 18293 52943)	Atlas-INDEL	.											.	GPAM	68	.	0			c.1529_1534del						.																																			SO:0001651	inframe_deletion	57678	exon16			.	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"glycerol-3-phosphate acyltransferase 1, mitochondrial"	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.1528_1533delTTTGTG	chr10.hg19:g.113920588_113920593delCACAAA	ENSP00000265276:p.Phe510_Val511del	91.0	0.0		84.0	12.0	NM_001244949	Q5VW51|Q86TA3	In_Frame_Del	DEL	ENST00000348367.4	hg19	CCDS7570.1																																																																																			.	.		0.437	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		-	113920593	CACAAA	-	113920588	7	5	115	1	0	1	0	1	0	0	0	0	6596	813	29	0	981	0	GPAM	10	113920588	In_Frame_Del	DEL	CACAAA	TCGA-DD-A3A1-01A-11D-A20W-10	15	113920588	21614159	243	19782										
CUZD1	50624	hgsc.bcm.edu	37	chr10	124593456	124593456	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caagtttcatctcgactacaTctggaacagaatttatgaac	6	9	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:124593456T>C	ENST00000368904.1	-	10	2332	c.1383A>G	c.(1381-1383)ggA>ggG	p.G461G	CUZD1_ENST00000392790.1_Splice_Site_p.G461G|CUZD1_ENST00000545804.1_Splice_Site_p.G461G					CUB and zona pellucida-like domains 1											NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|stomach(1)	39		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		CTCGACTACATCTGGAACAGA	0.338																																					p.G461G		Atlas-SNP	.											.	CUZD1	82	.	0			c.A1383G						.						72	73	72					10																	124593456		2203	4300	6503	SO:0001630	splice_region_variant	50624	exon8			ACTACATCTGGAA	AF305835	CCDS7631.1	10q26.13	2003-11-18			ENSG00000138161	ENSG00000138161			17937	protein-coding gene	gene with protein product						10542259	Standard	NM_022034		Approved	ERG-1, UO-44		Q86UP6	OTTHUMG00000019195	ENST00000368904.1:c.1383-1A>G	chr10.hg19:g.124593456T>C		121.0	0.0		144.0	7.0	NM_022034		Silent	SNP	ENST00000368904.1	hg19	CCDS7631.1																																																																																			.	.		0.338	CUZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050829.2	NM_022034	Silent	C	124593456	T	C	124593456	5	2	115	1	0	0	0	0	0	0	1	0	4068	1449	50	2	448	2	CUZD1	10	124593456	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	10672868	124593456	10941291	244	19783										
PSTK	118672	hgsc.bcm.edu	37	chr10	124742793	124742793	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttaaactgttttcagattcgTtgggcttttgccagctcttt	8	8	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:124742793T>A	ENST00000368887.3	+	3	954	c.514T>A	c.(514-516)Ttg>Atg	p.L172M	PSTK_ENST00000405485.1_Missense_Mutation_p.L172M|PSTK_ENST00000497219.1_3'UTR	NM_153336.2	NP_699167.2	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	172					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|tRNA binding (GO:0000049)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|skin(1)|stomach(2)	13		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		TTCAGATTCGTTGGGCTTTTG	0.378																																					p.L172M		Atlas-SNP	.											PSTK,NS,lymphoid_neoplasm,0,1	PSTK	34	.	0			c.T514A						.						52	51	52					10																	124742793		2203	4300	6503	SO:0001583	missense	118672	exon3			GATTCGTTGGGCT	AK127173	CCDS7633.1	10q26.13	2007-04-17	2007-04-17	2007-04-17	ENSG00000179988	ENSG00000179988			28578	protein-coding gene	gene with protein product		611310	"chromosome 10 open reading frame 89"	C10orf89		15317934	Standard	NM_153336		Approved	MGC35392	uc001lgy.1	Q8IV42	OTTHUMG00000019191	ENST00000368887.3:c.514T>A	chr10.hg19:g.124742793T>A	ENSP00000357882:p.Leu172Met	109.0	0.0		96.0	0.0	NM_153336	Q6ZSS9	Missense_Mutation	SNP	ENST00000368887.3	hg19	CCDS7633.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.987176	0.53934	.	.	ENSG00000179988	ENST00000368887;ENST00000405485	T;T	0.30448	1.53;1.53	5.86	0.849	0.18972	.	0.153654	0.41605	D	0.000841	T	0.45175	0.1329	M	0.73962	2.25	0.09310	N	1	P	0.52692	0.955	P	0.57244	0.816	T	0.34900	-0.9810	10	0.52906	T	0.07	-19.4718	9.706	0.40216	0.0:0.3732:0.0:0.6268	.	172	Q8IV42	PSTK_HUMAN	M	172	ENSP00000357882:L172M;ENSP00000384764:L172M	ENSP00000357882:L172M	L	+	1	2	PSTK	124732783	0.114000	0.22134	0.002000	0.10522	0.932000	0.56968	0.517000	0.22832	-0.087000	0.12528	0.460000	0.39030	TTG	.	.		0.378	PSTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050811.1	NM_153336		A	124742793	T	A	124742793	3	1	115	1	0	0	0	0	1	0	0	0	12732	1722	60	4	524	4	PSTK	10	124742793	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	149337	124742793	10791954	245	19784										
MKI67	4288	hgsc.bcm.edu	37	chr10	129899525	129899525	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aacagtaaatggcttaccttCtttggattttctgcacacct	6	10	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:129899525C>T	ENST00000368654.3	-	14	10077	c.9702G>A	c.(9700-9702)aaG>aaA	p.K3234K	MKI67_ENST00000368653.3_Silent_p.K2874K	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3234					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGCTTACCTTCTTTGGATTTT	0.408																																					p.K3234K		Atlas-SNP	.											.	MKI67	363	.	0			c.G9702A						.						115	108	110					10																	129899525		2203	4300	6503	SO:0001819	synonymous_variant	4288	exon14			TACCTTCTTTGGA	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.9702G>A	chr10.hg19:g.129899525C>T		77.0	0.0		103.0	5.0	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	hg19	CCDS7659.1																																																																																			.	.		0.408	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129899525	C	T	129899525	2	4	115	1	0	0	0	0	0	0	0	1	9607	912	32	3		3	MKI67	10	129899525	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	5156732	129899525	5635222	246	19785										
LRRC27	80313	hgsc.bcm.edu	37	chr10	134151182	134151182	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agaattaaagcgcttccttcTgggattggagctcaccagta	10	9	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr10:134151182T>C	ENST00000368614.3	+	3	429	c.324T>C	c.(322-324)tcT>tcC	p.S108S	LRRC27_ENST00000356571.4_Silent_p.S108S|LRRC27_ENST00000368610.3_Silent_p.S46S|LRRC27_ENST00000368612.1_Silent_p.S46S|LRRC27_ENST00000432555.2_5'UTR|LRRC27_ENST00000368613.4_Silent_p.S108S|LRRC27_ENST00000368615.3_Silent_p.S108S|LRRC27_ENST00000392638.2_Silent_p.S108S|LRRC27_ENST00000344079.5_Silent_p.S108S	NM_030626.2	NP_085129.1	Q9C0I9	LRC27_HUMAN	leucine rich repeat containing 27	108										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	18		all_cancers(35;6.28e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;9.12e-05)|Epithelial(32;0.000116)|all cancers(32;0.000145)|BRCA - Breast invasive adenocarcinoma(275;0.218)		CGCTTCCTTCTGGGATTGGAG	0.433																																					p.S108S		Atlas-SNP	.											.	LRRC27	64	.	0			c.T324C						.						78	76	76					10																	134151182		2203	4300	6503	SO:0001819	synonymous_variant	80313	exon3			TCCTTCTGGGATT	AB051461	CCDS31316.1, CCDS44496.1	10q26.3	2013-09-20			ENSG00000148814	ENSG00000148814			29346	protein-coding gene	gene with protein product						11214970	Standard	NM_030626		Approved	KIAA1674	uc010quw.1	Q9C0I9	OTTHUMG00000019284	ENST00000368614.3:c.324T>C	chr10.hg19:g.134151182T>C		85.0	0.0		104.0	5.0	NM_001143757	A6NE72|A6NJB4|A6NKD3|D3DRH0|Q5SZH6|Q5SZH8|Q5SZH9|Q86XT5|Q8N7C8|Q8NA21	Silent	SNP	ENST00000368614.3	hg19	CCDS31316.1	.	.	.	.	.	.	.	.	.	.	T	0.034	-1.317225	0.01331	.	.	ENSG00000148814	ENST00000450442	.	.	.	4.84	-2.8	0.05823	.	.	.	.	.	T	0.39064	0.1064	.	.	.	0.52501	D	0.999958	.	.	.	.	.	.	T	0.25363	-1.0134	4	.	.	.	-0.2086	2.1069	0.03693	0.1194:0.2763:0.1221:0.4822	.	.	.	.	P	60	.	.	L	+	2	0	LRRC27	134001172	0.150000	0.22732	0.024000	0.17045	0.003000	0.03518	-0.586000	0.05787	-1.201000	0.02659	-1.676000	0.00740	CTG	.	.		0.433	LRRC27-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051058.2	XM_290462		C	134151182	T	C	134151182	2	2	115	1	0	0	0	0	0	0	0	1	8990	1567	55	2		2	LRRC27	10	134151182	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4251657	134151182	1383565	247	19786										
BET1L	60626	hgsc.bcm.edu	37	chr11	205324	205324	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acgtccttgccctggacaagAagtaggagaggatgaagaag	14	7	0	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:205324A>G	ENST00000526104.1	+	0	0				BET1L_ENST00000410108.1_Intron|BET1L_ENST00000529614.2_Missense_Mutation_p.F86S|RP11-304M2.5_ENST00000526963.1_RNA|BET1L_ENST00000332865.6_3'UTR|BET1L_ENST00000325147.9_3'UTR|BET1L_ENST00000486280.1_Missense_Mutation_p.F82S|BET1L_ENST00000382762.3_Missense_Mutation_p.F105S			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CCTGGACAAGAAGTAGGAGAG	0.572																																					p.F105S		Atlas-SNP	.											.	BET1L	7	.	0			c.T314C						.						52	57	55					11																	205324		2202	4300	6502	SO:0001631	upstream_gene_variant	51272	exon4			GACAAGAAGTAGG	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069		chr11.hg19:g.205324A>G	Exception_encountered	97.0	0.0		123.0	5.0	NM_001098787	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Missense_Mutation	SNP	ENST00000526104.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.18	3.050211	0.55218	.	.	ENSG00000177951	ENST00000382762;ENST00000529614;ENST00000486280	.	.	.	5.2	5.2	0.72013	.	0.319896	0.28241	N	0.016069	T	0.46054	0.1373	L	0.27053	0.805	0.34001	D	0.650324	B	0.06786	0.001	B	0.10450	0.005	T	0.55231	-0.8173	9	0.44086	T	0.13	.	14.2391	0.65945	1.0:0.0:0.0:0.0	.	105	Q9NYM9	BET1L_HUMAN	S	105;86;82	.	ENSP00000372210:F105S	F	-	2	0	BET1L	195324	1.000000	0.71417	0.990000	0.47175	0.567000	0.35839	9.093000	0.94163	1.964000	0.57103	0.379000	0.24179	TTC	.	.		0.572	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		G	205324	A	G	205324	1	3	115	0	1	0	0	0	0	0	0	0	1409	246	9	2		2	BET1L	11	205324	5'Flank	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10		205324	134801192	248	19787										
MRGPRE	116534	hgsc.bcm.edu	37	chr11	3249741	3249741	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcgcagcgttgccaggctggTctgcacgaagcccgggaagt	16	12	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:3249741T>C	ENST00000389832.5	-	2	595	c.289A>G	c.(289-291)Acc>Gcc	p.T97A	MRGPRE_ENST00000436689.2_Missense_Mutation_p.T96A|AC109309.4_ENST00000418995.2_RNA			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	97						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCCAGGCTGGTCTGCACGAAG	0.667																																					p.T97A		Atlas-SNP	.											.	MRGPRE	35	.	0			c.A289G						.						44	54	51					11																	3249741		2178	4274	6452	SO:0001583	missense	116534	exon2			GGCTGGTCTGCAC	AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"GPCR / Class A : Orphans"	30694	protein-coding gene	gene with protein product		607232	"G protein-coupled receptor 167"	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.289A>G	chr11.hg19:g.3249741T>C	ENSP00000374482:p.Thr97Ala	73.0	0.0		134.0	6.0	NM_001039165	Q2M1V7	Missense_Mutation	SNP	ENST00000389832.5	hg19		.	.	.	.	.	.	.	.	.	.	t	4.323	0.059308	0.08339	.	.	ENSG00000184350	ENST00000436689;ENST00000389832	.	.	.	3.48	-4.87	0.03123	GPCR, rhodopsin-like superfamily (1);	1.230950	0.06196	N	0.682246	T	0.15609	0.0376	N	0.04880	-0.145	0.09310	N	1	B	0.18610	0.029	B	0.28232	0.087	T	0.33214	-0.9877	9	0.13108	T	0.6	-6.0187	6.3775	0.21515	0.0:0.4025:0.163:0.4345	.	96	Q86SM8	MRGRE_HUMAN	A	97;96	.	ENSP00000374482:T96A	T	-	1	0	MRGPRE	3206317	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.162000	0.03141	-0.657000	0.05373	-0.425000	0.05940	ACC	.	.		0.667	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536		C	3249741	T	C	3249741	3	2	115	1	0	0	0	0	1	0	0	0	9773	1667	58	2	653	2	MRGPRE	11	3249741	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3044417	3249741	131756775	249	19788										
SMPD1	6609	hgsc.bcm.edu	37	chr11	6412065	6412065	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttacatcgcatagtgccccgGctccgagatgtctttgggtg	12	11	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:6412065G>A	ENST00000342245.4	+	1	405	c.237G>A	c.(235-237)cgG>cgA	p.R79R	SMPD1_ENST00000527275.1_Silent_p.R79R|SMPD1_ENST00000533196.1_Intron|SMPD1_ENST00000356761.2_Silent_p.R79R|SMPD1_ENST00000299397.3_Silent_p.R79R	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	77					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	TAGTGCCCCGGCTCCGAGATG	0.607																																					p.R79R		Atlas-SNP	.											.	SMPD1	108	.	0			c.G237A						.						56	59	58					11																	6412065		2201	4296	6497	SO:0001819	synonymous_variant	6609	exon1			GCCCCGGCTCCGA	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.237G>A	chr11.hg19:g.6412065G>A		88.0	0.0		89.0	23.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	hg19	CCDS44531.1																																																																																			.	.		0.607	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		A	6412065	G	A	6412065	2	1	115	1	0	0	0	0	0	0	0	1	14819	1190	42	3		3	SMPD1	11	6412065	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	3162324	6412065	128594451	250	19789										
RBMXL2	27288	hgsc.bcm.edu	37	chr11	7111267	7111267	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cgccatcttacggaggaggaGgccgctacgaggagtaccgg	16	11	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:7111267G>T	ENST00000306904.5	+	1	1103	c.916G>T	c.(916-918)Ggc>Tgc	p.G306C		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	306	Arg/Gly/Pro-rich.					nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CGGAGGAGGAGGCCGCTACGA	0.667																																					p.G306C		Atlas-SNP	.											.	RBMXL2	47	.	0			c.G916T						.						18	21	20					11																	7111267		2198	4293	6491	SO:0001583	missense	27288	exon1			GGAGGAGGCCGCT	AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"RNA binding motif (RRM) containing"	17886	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein G T"	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.916G>T	chr11.hg19:g.7111267G>T	ENSP00000304139:p.Gly306Cys	86.0	0.0		109.0	48.0	NM_014469	Q6PEZ2|Q9NQU0	Missense_Mutation	SNP	ENST00000306904.5	hg19	CCDS7777.1	.	.	.	.	.	.	.	.	.	.	g	12.81	2.050157	0.36181	.	.	ENSG00000170748	ENST00000306904	T	0.78816	-1.21	3.51	-0.579	0.11720	.	0.220955	0.46145	U	0.000308	T	0.74642	0.3743	L	0.38531	1.155	0.30422	N	0.777987	D	0.76494	0.999	D	0.65573	0.936	T	0.68416	-0.5414	10	0.36615	T	0.2	.	4.0236	0.09677	0.4188:0.1771:0.404:0.0	.	306	O75526	HNRGT_HUMAN	C	306	ENSP00000304139:G306C	ENSP00000304139:G306C	G	+	1	0	RBMXL2	7067843	1.000000	0.71417	0.470000	0.27216	0.848000	0.48234	3.677000	0.54619	-0.098000	0.12285	-1.096000	0.02151	GGC	.	.		0.667	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469		T	7111267	G	T	7111267	3	4	115	1	0	0	0	0	1	0	0	0	13169	1000	35	3	918	3	RBMXL2	11	7111267	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	699202	7111267	127895249	251	19790										
SCUBE2	57758	hgsc.bcm.edu	37	chr11	9052315	9052315	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aagtactcacctctggtttcAcagtcctgaaaggaagtagc	9	10	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:9052315A>G	ENST00000309263.3	-	17	2316	c.2244T>C	c.(2242-2244)tgT>tgC	p.C748C	SCUBE2_ENST00000520467.1_Silent_p.C720C|SCUBE2_ENST00000457346.2_Silent_p.C777C|RP11-467K18.2_ENST00000531592.1_RNA|SCUBE2_ENST00000450649.2_Silent_p.C622C			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	748						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		CTCTGGTTTCACAGTCCTGAA	0.547																																					p.C720C		Atlas-SNP	.											.	SCUBE2	102	.	0			c.T2160C						.						114	114	114					11																	9052315		2201	4296	6497	SO:0001819	synonymous_variant	57758	exon17			GGTTTCACAGTCC	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.2244T>C	chr11.hg19:g.9052315A>G		64.0	0.0		58.0	4.0	NM_020974	Q2NKQ8|Q6ZWI1	Silent	SNP	ENST00000309263.3	hg19																																																																																				.	.		0.547	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974		G	9052315	A	G	9052315	2	3	115	1	0	0	0	0	0	0	0	1	13960	157	6	2		2	SCUBE2	11	9052315	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1941048	9052315	125954201	252	19791										
SCUBE2	57758	hgsc.bcm.edu	37	chr11	9082018	9082018	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acaactgcagtggacacctgTcgaagtatccttacaggtgc	10	11	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:9082018T>C	ENST00000309263.3	-	8	976	c.904A>G	c.(904-906)Aca>Gca	p.T302A	SCUBE2_ENST00000520467.1_Missense_Mutation_p.T302A|SCUBE2_ENST00000457346.2_Missense_Mutation_p.T302A|SCUBE2_ENST00000450649.2_Missense_Mutation_p.T302A|RP11-467K18.2_ENST00000521394.2_RNA			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	302	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		TGGACACCTGTCGAAGTATCC	0.512																																					p.T302A		Atlas-SNP	.											.	SCUBE2	102	.	0			c.A904G						.						172	154	160					11																	9082018		2201	4296	6497	SO:0001583	missense	57758	exon8			CACCTGTCGAAGT	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.904A>G	chr11.hg19:g.9082018T>C	ENSP00000310658:p.Thr302Ala	72.0	0.0		87.0	6.0	NM_001170690	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	hg19		.	.	.	.	.	.	.	.	.	.	T	21.7	4.184039	0.78677	.	.	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22	5.94	5.94	0.96194	Epidermal growth factor-like (1);	0.000000	0.85682	D	0.000000	D	0.92071	0.7487	L	0.56769	1.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.998	D	0.91709	0.5380	10	0.45353	T	0.12	.	16.4075	0.83691	0.0:0.0:0.0:1.0	.	302;302;302	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	A	302	ENSP00000390481:T302A;ENSP00000310658:T302A;ENSP00000415187:T302A;ENSP00000429969:T302A	ENSP00000310658:T302A	T	-	1	0	SCUBE2	9038594	1.000000	0.71417	0.943000	0.38184	0.979000	0.70002	8.040000	0.89188	2.275000	0.75901	0.528000	0.53228	ACA	.	.		0.512	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974		C	9082018	T	C	9082018	3	2	115	1	0	0	0	0	1	0	0	0	13960	1667	58	2	2246	2	SCUBE2	11	9082018	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	29703	9082018	125924498	253	19792										
WEE1	7465	hgsc.bcm.edu	37	chr11	9598196	9598196	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caaaaaagccattggcgggcTctgttgatgagtatgtatta	11	6	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:9598196T>C	ENST00000450114.2	+	4	1262	c.1009T>C	c.(1009-1011)Tct>Cct	p.S337P	snoU13_ENST00000458785.1_RNA|WEE1_ENST00000299613.6_Missense_Mutation_p.S123P	NM_003390.3	NP_003381.1	P30291	WEE1_HUMAN	WEE1 G2 checkpoint kinase	337	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|establishment of cell polarity (GO:0030010)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neuron projection morphogenesis (GO:0048812)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	23				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		ATTGGCGGGCTCTGTTGATGA	0.398																																					p.S337P		Atlas-SNP	.											.	WEE1	54	.	0			c.T1009C						.						92	97	95					11																	9598196		2201	4294	6495	SO:0001583	missense	7465	exon4			GCGGGCTCTGTTG	X62048	CCDS7800.1, CCDS44536.1	11p15.4	2013-10-21	2013-10-21		ENSG00000166483	ENSG00000166483			12761	protein-coding gene	gene with protein product		193525	"wee1+ (S. pombe) homolog", "WEE1 homolog (S. pombe)"			1840647	Standard	NM_003390		Approved		uc001mhs.3	P30291	OTTHUMG00000165863	ENST00000450114.2:c.1009T>C	chr11.hg19:g.9598196T>C	ENSP00000402084:p.Ser337Pro	157.0	0.0		149.0	6.0	NM_003390	B3KVE1|D3DQV0	Missense_Mutation	SNP	ENST00000450114.2	hg19	CCDS7800.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.945667	0.92593	.	.	ENSG00000166483	ENST00000450114;ENST00000299613	T;T	0.67865	-0.29;-0.29	5.61	5.61	0.85477	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.72985	0.3529	L	0.52126	1.63	0.80722	D	1	P;P	0.45715	0.865;0.772	P;P	0.54431	0.752;0.52	T	0.71520	-0.4568	10	0.36615	T	0.2	-12.1839	15.8077	0.78527	0.0:0.0:0.0:1.0	.	145;337	Q6MZL0;P30291	.;WEE1_HUMAN	P	337;123	ENSP00000402084:S337P;ENSP00000299613:S123P	ENSP00000299613:S123P	S	+	1	0	WEE1	9554772	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.655000	0.83696	2.132000	0.65825	0.528000	0.53228	TCT	.	.		0.398	WEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386757.1	NM_003390		C	9598196	T	C	9598196	3	2	115	1	0	0	0	0	1	0	0	0	17359	1551	54	2	1023	2	WEE1	11	9598196	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	516178	9598196	125408320	254	19793										
SWAP70	23075	hgsc.bcm.edu	37	chr11	9761767	9761767	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aacaggttgctcaaaagtccTctgaactggaacagtattta	8	8	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:9761767T>C	ENST00000318950.6	+	9	1331	c.1228T>C	c.(1228-1230)Tct>Cct	p.S410P	SWAP70_ENST00000447399.2_Missense_Mutation_p.S352P	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	410					isotype switching (GO:0045190)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	11				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		TCAAAAGTCCTCTGAACTGGA	0.468																																					p.S410P		Atlas-SNP	.											.	SWAP70	40	.	0			c.T1228C						.						89	83	85					11																	9761767		2201	4294	6495	SO:0001583	missense	23075	exon9			AAGTCCTCTGAAC	AB014540	CCDS31426.1, CCDS73257.1	11p15	2013-01-10			ENSG00000133789	ENSG00000133789		"Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	17070	protein-coding gene	gene with protein product		604762				9734811, 10681448	Standard	XM_005252829		Approved	KIAA0640, SWAP-70	uc001mhw.3	Q9UH65	OTTHUMG00000165865	ENST00000318950.6:c.1228T>C	chr11.hg19:g.9761767T>C	ENSP00000315630:p.Ser410Pro	60.0	0.0		106.0	5.0	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	hg19	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.533453	0.45073	.	.	ENSG00000133789	ENST00000447399;ENST00000318950	T;T	0.30448	1.95;1.53	5.25	5.25	0.73442	.	0.244803	0.40064	N	0.001183	T	0.25005	0.0607	N	0.19112	0.55	0.34726	D	0.729236	P;P;D	0.56521	0.875;0.641;0.976	B;B;P	0.47864	0.276;0.188;0.559	T	0.34179	-0.9839	10	0.44086	T	0.13	-3.496	10.4245	0.44369	0.1455:0.0:0.0:0.8545	.	352;410;352	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	P	352;410	ENSP00000399056:S352P;ENSP00000315630:S410P	ENSP00000315630:S410P	S	+	1	0	SWAP70	9718343	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	3.807000	0.55591	1.980000	0.57719	0.482000	0.46254	TCT	.	.		0.468	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055		C	9761767	T	C	9761767	3	2	115	1	0	0	0	0	1	0	0	0	15440	1551	54	2	1262	2	SWAP70	11	9761767	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	163571	9761767	125244749	255	19794										
KCNJ11	3767	hgsc.bcm.edu	37	chr11	17409184	17409184	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcatgagccccacgatgttcTgcacgatgaggatcaggatg	12	10	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:17409184T>C	ENST00000339994.4	-	1	1022	c.455A>G	c.(454-456)cAg>cGg	p.Q152R	KCNJ11_ENST00000526747.1_5'Flank|KCNJ11_ENST00000528731.1_Missense_Mutation_p.Q65R	NM_000525.3	NP_000516.3	Q14654	KCJ11_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 11	152					cellular response to glucose stimulus (GO:0071333)|cellular response to nicotine (GO:0071316)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|negative regulation of insulin secretion (GO:0046676)|neurological system process (GO:0050877)|positive regulation of cation channel activity (GO:2001259)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ischemia (GO:0002931)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	ATP-sensitive potassium channel complex (GO:0008282)|axolemma (GO:0030673)|cell body fiber (GO:0070852)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|ion channel binding (GO:0044325)|potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(3)|skin(2)	16				READ - Rectum adenocarcinoma(2;0.0276)|Colorectal(2;0.0633)	Diazoxide(DB01119)|Glimepiride(DB00222)|Glyburide(DB01016)|Ibutilide(DB00308)|Levosimendan(DB00922)|Thiamylal(DB01154)|Verapamil(DB00661)|Yohimbine(DB01392)	CACGATGTTCTGCACGATGAG	0.557											OREG0020810	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q152R		Atlas-SNP	.											.	KCNJ11	39	.	0			c.A455G						.						115	92	100					11																	17409184		2200	4293	6493	SO:0001583	missense	3767	exon1			ATGTTCTGCACGA	D50582	CCDS31436.1, CCDS53606.1	11p15.1	2011-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6257	protein-coding gene	gene with protein product		600937				7502040, 16382105	Standard	NM_001166290		Approved	Kir6.2, BIR	uc001mna.3	Q14654		ENST00000339994.4:c.455A>G	chr11.hg19:g.17409184T>C	ENSP00000345708:p.Gln152Arg	63.0	0.0	717	84.0	4.0	NM_000525	B4DWI4|E9PNK0|Q2M1H7|Q58EX3|Q8IW96	Missense_Mutation	SNP	ENST00000339994.4	hg19	CCDS31436.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.943577	0.73672	.	.	ENSG00000187486	ENST00000339994;ENST00000528731;ENST00000526912	D;D;D	0.96136	-3.92;-3.92;-3.92	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.98340	0.9449	H	0.95679	3.705	0.58432	D	0.999995	D	0.65815	0.995	D	0.81914	0.995	D	0.99612	1.0981	10	0.87932	D	0	.	14.5548	0.68094	0.0:0.0:0.0:1.0	.	152	B2RC52	.	R	152;65;65	ENSP00000345708:Q152R;ENSP00000434755:Q65R;ENSP00000432729:Q65R	ENSP00000345708:Q152R	Q	-	2	0	KCNJ11	17365760	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.040000	0.89188	1.850000	0.53721	0.379000	0.24179	CAG	.	.		0.557	KCNJ11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387037.1	NM_000525		C	17409184	T	C	17409184	3	2	115	1	0	0	0	0	1	0	0	0	8054	1580	55	2	721	2	KCNJ11	11	17409184	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	7647417	17409184	117597332	256	19795										
PRMT3	10196	hgsc.bcm.edu	37	chr11	20409581	20409581	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttaggcggccggggcgctgtGgagaatgaggaggacctgcc	19	9	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:20409581G>T	ENST00000331079.6	+	2	262	c.45G>T	c.(43-45)gtG>gtT	p.V15V	PRMT3_ENST00000437750.2_Intron	NM_001145167.1|NM_005788.3	NP_001138639.1|NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3	15					histone arginine methylation (GO:0034969)|negative regulation of protein ubiquitination (GO:0031397)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ribosome (GO:0005840)	histone-arginine N-methyltransferase activity (GO:0008469)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|modified amino acid binding (GO:0072341)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|prostate(1)	17						GGGGCGCTGTGGAGAATGAGG	0.667																																					p.V15V		Atlas-SNP	.											.	PRMT3	50	.	0			c.G45T						.						55	51	53					11																	20409581		2202	4300	6502	SO:0001819	synonymous_variant	10196	exon2			CGCTGTGGAGAAT	AF059531	CCDS7853.1, CCDS44554.1	11p15.1	2008-02-05	2006-02-16	2006-02-16	ENSG00000185238	ENSG00000185238		"Protein arginine methyltransferases"	30163	protein-coding gene	gene with protein product		603190	"HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"	HRMT1L3		9642256	Standard	NM_005788		Approved		uc001mqb.3	O60678	OTTHUMG00000166022	ENST00000331079.6:c.45G>T	chr11.hg19:g.20409581G>T		185.0	0.0		212.0	76.0	NM_005788	B4DUC7	Silent	SNP	ENST00000331079.6	hg19	CCDS7853.1																																																																																			.	.		0.667	PRMT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387489.1	NM_005788		T	20409581	G	T	20409581	2	4	115	1	0	0	0	0	0	0	0	1	12550	1335	47	3		3	PRMT3	11	20409581	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	3000397	20409581	114596935	257	19796										
FANCF	2188	hgsc.bcm.edu	37	chr11	22646565	22646565	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gacagcgctgggtggcggctAgtcactaaagtcaaaagccc	13	11	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:22646565A>G	ENST00000327470.3	-	1	822	c.792T>C	c.(790-792)acT>acC	p.T264T	AC103801.2_ENST00000428556.2_5'Flank	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	264					DNA repair (GO:0006281)|ovarian follicle development (GO:0001541)|spermatogenesis (GO:0007283)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						GGTGGCGGCTAGTCACTAAAG	0.552			"N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T264T		Atlas-SNP	.	yes	Rec		Fanconi anaemia F	11	11p15	2188	"Fanconi anemia, complementation group F"		L	.	FANCF	24	.	0			c.T792C						.						51	61	58					11																	22646565		2203	4300	6503	SO:0001819	synonymous_variant	2188	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GCGGCTAGTCACT		CCDS7857.1	11p15	2014-09-17				ENSG00000183161		"Fanconi anemia, complementation groups"	3587	protein-coding gene	gene with protein product		613897				9382107	Standard	NM_022725		Approved	FAF	uc001mql.1	Q9NPI8		ENST00000327470.3:c.792T>C	chr11.hg19:g.22646565A>G		67.0	0.0	757	108.0	33.0	NM_022725	Q52LM0	Silent	SNP	ENST00000327470.3	hg19	CCDS7857.1																																																																																			.	.		0.552	FANCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387712.2	NM_022725		G	22646565	A	G	22646565	2	3	115	1	0	0	0	0	0	0	0	1	5675	407	15	2		2	FANCF	11	22646565	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2236984	22646565	112359951	258	19797										
BDNF	627	hgsc.bcm.edu	37	chr11	27695819	27695819	+	5'UTR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcactcatggagaaaactggTggctccacacatccagttgt	10	11	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:27695819T>C	ENST00000420794.1	-	0	153				BDNF_ENST00000438929.1_Missense_Mutation_p.T5A|BDNF_ENST00000314915.6_Intron|BDNF_ENST00000533131.1_Intron|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000395980.2_Intron|BDNF_ENST00000525950.1_Intron|BDNF_ENST00000418212.1_Intron|BDNF_ENST00000530861.1_Intron|BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000395978.3_Intron|BDNF-AS_ENST00000501663.2_RNA|BDNF_ENST00000395986.2_Intron|BDNF-AS_ENST00000499008.3_RNA|BDNF_ENST00000395981.3_Intron|BDNF_ENST00000356660.4_Intron|BDNF-AS_ENST00000502161.2_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF_ENST00000584049.1_Intron|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000395983.3_Intron|BDNF_ENST00000533246.1_Intron|BDNF_ENST00000532997.1_Intron	NM_001143811.1	NP_001137283.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor						axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						AGAAAACTGGTGGCTCCACAC	0.408																																					p.T5A		Atlas-SNP	.											.	BDNF	63	.	0			c.A13G						.						72	66	68					11																	27695819		1567	3577	5144	SO:0001623	5_prime_UTR_variant	627	exon2			AACTGGTGGCTCC	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"Endogenous ligands"	1033	protein-coding gene	gene with protein product	"neurotrophin"	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000420794.1:c.-351A>G	chr11.hg19:g.27695819T>C		91.0	0.0		94.0	4.0	NM_001143810	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Missense_Mutation	SNP	ENST00000420794.1	hg19	CCDS7866.1	.	.	.	.	.	.	.	.	.	.	T	3.356	-0.131525	0.06753	.	.	ENSG00000176697	ENST00000438929	T	0.56275	0.47	5.92	0.773	0.18516	.	.	.	.	.	T	0.37320	0.0999	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17776	-1.0358	8	0.87932	D	0	.	3.3116	0.07018	0.2581:0.2254:0.0:0.5166	.	5	P23560-4	.	A	5	ENSP00000414303:T5A	ENSP00000414303:T5A	T	-	1	0	BDNF	27652395	0.993000	0.37304	0.561000	0.28357	0.009000	0.06853	0.277000	0.18734	-0.118000	0.11851	-0.256000	0.11100	ACC	.	.		0.408	BDNF-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_170735		C	27695819	T	C	27695819	1	2	115	0	1	0	0	0	0	0	0	0	1394	1696	59	2		2	BDNF	11	27695819	5'UTR	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	5049254	27695819	107310697	259	19798										
TTC17	55761	hgsc.bcm.edu	37	chr11	43411338	43411338	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggacctggatctatatgatgGcacatacataactttggaga	10	7	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:43411338G>C	ENST00000039989.4	+	3	400	c.386G>C	c.(385-387)gGc>gCc	p.G129A	TTC17_ENST00000299240.6_Missense_Mutation_p.G129A|RP11-484D2.4_ENST00000394183.2_RNA	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	129					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						CTATATGATGGCACATACATA	0.393																																					p.G129A		Atlas-SNP	.											.	TTC17	112	.	0			c.G386C						.						136	133	134					11																	43411338		2203	4300	6503	SO:0001583	missense	55761	exon3			ATGATGGCACATA	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"Tetratricopeptide (TTC) repeat domain containing"	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.386G>C	chr11.hg19:g.43411338G>C	ENSP00000039989:p.Gly129Ala	215.0	0.0		198.0	57.0	NM_018259	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	hg19	CCDS31466.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.476333	0.84640	.	.	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.31510	1.49;1.49	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.45776	0.1359	L	0.51422	1.61	0.80722	D	1	D;D;D	0.76494	0.994;0.999;0.998	P;D;D	0.75020	0.792;0.985;0.948	T	0.27938	-1.0059	10	0.02654	T	1	-14.4097	18.713	0.91664	0.0:0.0:1.0:0.0	.	129;129;129	Q8NEC0;Q96AE7;G3XAB3	.;TTC17_HUMAN;.	A	129	ENSP00000299240:G129A;ENSP00000039989:G129A	ENSP00000039989:G129A	G	+	2	0	TTC17	43367914	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.813000	0.99286	2.477000	0.83638	0.563000	0.77884	GGC	.	.		0.393	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259		C	43411338	G	C	43411338	3	2	115	1	0	0	0	0	1	0	0	0	16699	1203	42	4	396	4	TTC17	11	43411338	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	15715519	43411338	91595178	260	19799										
ACCS	84680	hgsc.bcm.edu	37	chr11	44102738	44102738	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcttcctgcaggacttcgggAtgtctgggctccgctttggc	13	12	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:44102738A>G	ENST00000263776.8	+	12	1413	c.979A>G	c.(979-981)Atg>Gtg	p.M327V		NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	327					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						GGACTTCGGGATGTCTGGGCT	0.632																																					p.M327V	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											.	ACCS	64	.	0			c.A979G						.						96	91	93					11																	44102738		2203	4300	6503	SO:0001583	missense	84680	exon12			TTCGGGATGTCTG	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.979A>G	chr11.hg19:g.44102738A>G	ENSP00000263776:p.Met327Val	101.0	0.0		140.0	6.0	NM_032592	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	hg19	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	A	1.320	-0.599861	0.03744	.	.	ENSG00000110455	ENST00000263776	D	0.90133	-2.62	5.31	2.98	0.34508	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.153558	0.64402	D	0.000007	T	0.80369	0.4610	N	0.20845	0.615	0.80722	D	1	B	0.16166	0.016	B	0.24006	0.05	T	0.69202	-0.5207	10	0.27785	T	0.31	-26.1217	4.9596	0.14059	0.6855:0.1684:0.1462:0.0	.	327	Q96QU6	1A1L1_HUMAN	V	327	ENSP00000263776:M327V	ENSP00000263776:M327V	M	+	1	0	ACCS	44059314	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	4.031000	0.57267	0.844000	0.35094	-0.316000	0.08728	ATG	.	.		0.632	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		G	44102738	A	G	44102738	3	3	115	1	0	0	0	0	1	0	0	0	133	333	12	2	1021	2	ACCS	11	44102738	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	691400	44102738	90903778	261	19800										
CKAP5	9793	hgsc.bcm.edu	37	chr11	46818446	46818446	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttcaaagcagtacccaatgcTtcaaatgcggcatctctgac	7	12	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:46818446T>C	ENST00000529230.1	-	12	1429	c.1383A>G	c.(1381-1383)gaA>gaG	p.E461E	CKAP5_ENST00000415402.1_Silent_p.E461E|CKAP5_ENST00000532321.1_5'Flank|CKAP5_ENST00000312055.5_Silent_p.E461E|CKAP5_ENST00000354558.3_Silent_p.E461E			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	461					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						TACCCAATGCTTCAAATGCGG	0.413																																					p.E461E	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.A1383G						.						153	131	139					11																	46818446		2201	4299	6500	SO:0001819	synonymous_variant	9793	exon12			CAATGCTTCAAAT		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.1383A>G	chr11.hg19:g.46818446T>C		142.0	0.0		145.0	6.0	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Silent	SNP	ENST00000529230.1	hg19	CCDS31477.1																																																																																			.	.		0.413	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		C	46818446	T	C	46818446	2	2	115	1	0	0	0	0	0	0	0	1	3447	1606	56	2		2	CKAP5	11	46818446	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2715708	46818446	88188070	262	19801										
FNBP4	23360	hgsc.bcm.edu	37	chr11	47758184	47758184	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atactttcaaatcctgttctTcttctacttttggtgttgtc	5	9	4	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:47758184T>C	ENST00000263773.5	-	9	1577	c.1565A>G	c.(1564-1566)gAa>gGa	p.E522G	FNBP4_ENST00000534003.1_5'UTR	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	522						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						ATCCTGTTCTTCTTCTACTTT	0.313																																					p.E522G		Atlas-SNP	.											.	FNBP4	99	.	0			c.A1565G						.						157	133	140					11																	47758184		1792	4062	5854	SO:0001583	missense	23360	exon9			TGTTCTTCTTCTA	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.1565A>G	chr11.hg19:g.47758184T>C	ENSP00000263773:p.Glu522Gly	87.0	0.0		81.0	4.0	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	hg19	CCDS41644.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.069603	0.76301	.	.	ENSG00000109920	ENST00000263773	T	0.13089	2.62	6.16	6.16	0.99307	.	0.285900	0.43579	D	0.000555	T	0.16041	0.0386	N	0.19112	0.55	0.58432	D	0.999996	D	0.59767	0.986	P	0.50970	0.655	T	0.01283	-1.1396	10	0.72032	D	0.01	-11.1806	14.1793	0.65564	0.0:0.0:0.0:1.0	.	522	Q8N3X1	FNBP4_HUMAN	G	522	ENSP00000263773:E522G	ENSP00000263773:E522G	E	-	2	0	FNBP4	47714760	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	4.233000	0.58651	2.367000	0.80283	0.528000	0.53228	GAA	.	.		0.313	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			C	47758184	T	C	47758184	3	2	115	1	0	0	0	0	1	0	0	0	5975	1783	62	2	1524	2	FNBP4	11	47758184	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	939738	47758184	87248332	263	19802										
OR4C15	81309	hgsc.bcm.edu	37	chr11	55322070	55322070	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	actgttgggggcaacatgctAattgtagtaaccattctcag	10	8	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:55322070A>G	ENST00000314644.2	+	1	288	c.288A>G	c.(286-288)ctA>ctG	p.L96L		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	42						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						GCAACATGCTAATTGTAGTAA	0.438										HNSCC(20;0.049)																											p.L96L		Atlas-SNP	.											.	OR4C15	145	.	0			c.A288G						.						161	134	143					11																	55322070		2201	4296	6497	SO:0001819	synonymous_variant	81309	exon1			CATGCTAATTGTA	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"GPCR / Class A : Olfactory receptors"	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.288A>G	chr11.hg19:g.55322070A>G		59.0	0.0		77.0	4.0	NM_001001920	Q6IFE2	Silent	SNP	ENST00000314644.2	hg19	CCDS31501.1																																																																																			.	.		0.438	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		G	55322070	A	G	55322070	2	3	115	1	0	0	0	0	0	0	0	1	11057	349	13	2		2	OR4C15	11	55322070	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	7563886	55322070	79684446	264	19803										
OR5F1	338674	hgsc.bcm.edu	37	chr11	55761365	55761365	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	catagaacagaattatggctGtcaggtgagaggcacacgtg	13	7	1	3	rs377087548		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:55761365G>A	ENST00000278409.1	-	1	736	c.737C>T	c.(736-738)aCa>aTa	p.T246I		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	246					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					AATTATGGCTGTCAGGTGAGA	0.493													G|||	1	0.000199681	0	0	5008	,	,		18311	0		0	False		,,,				2504	0.001				p.T246I		Atlas-SNP	.											.	OR5F1	116	.	0			c.C737T						.						86	82	84					11																	55761365		2201	4296	6497	SO:0001583	missense	338674	exon1			ATGGCTGTCAGGT	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"GPCR / Class A : Olfactory receptors"	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.737C>T	chr11.hg19:g.55761365G>A	ENSP00000278409:p.Thr246Ile	92.0	0.0		84.0	34.0	NM_003697	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	hg19	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	G	3.668	-0.068137	0.07228	.	.	ENSG00000149133	ENST00000278409	T	0.36157	1.27	2.99	-1.74	0.08056	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.33760	0.0874	L	0.52266	1.64	0.09310	N	1	P	0.39601	0.68	B	0.43155	0.41	T	0.30504	-0.9976	9	0.51188	T	0.08	.	8.5481	0.33435	0.5023:0.0:0.4977:0.0	.	246	O95221	OR5F1_HUMAN	I	246	ENSP00000278409:T246I	ENSP00000278409:T246I	T	-	2	0	OR5F1	55517941	0.000000	0.05858	0.028000	0.17463	0.115000	0.19883	-0.029000	0.12329	-0.336000	0.08438	-0.738000	0.03535	ACA	.	.		0.493	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697		A	55761365	G	A	55761365	3	1	115	1	0	0	0	0	1	0	0	0	11167	1377	48	3	210	3	OR5F1	11	55761365	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	439295	55761365	79245151	265	19804										
OR5T2	219464	hgsc.bcm.edu	37	chr11	56000212	56000212	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	attgcagccaagagaaagcaTtctgtggttccaaaactaca	8	9	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:56000212T>A	ENST00000313264.4	-	1	525	c.450A>T	c.(448-450)gaA>gaT	p.E150D		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					AGAGAAAGCATTCTGTGGTTC	0.423																																					p.E150D		Atlas-SNP	.											.	OR5T2	107	.	0			c.A450T						.						178	153	161					11																	56000212		2201	4296	6497	SO:0001583	missense	219464	exon1			AAAGCATTCTGTG	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.450A>T	chr11.hg19:g.56000212T>A	ENSP00000323688:p.Glu150Asp	177.0	0.0		208.0	77.0	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	hg19	CCDS31523.1	.	.	.	.	.	.	.	.	.	.	T	18.28	3.588863	0.66105	.	.	ENSG00000181718	ENST00000313264	T	0.00354	7.92	5.07	-1.8	0.07907	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42682	U	0.000668	T	0.00271	0.0008	L	0.55481	1.735	0.09310	N	0.999995	P	0.44690	0.841	B	0.41412	0.356	T	0.50533	-0.8817	10	0.62326	D	0.03	.	11.3966	0.49845	0.0:0.5914:0.0:0.4086	.	150	Q8NGG2	OR5T2_HUMAN	D	150	ENSP00000323688:E150D	ENSP00000323688:E150D	E	-	3	2	OR5T2	55756788	0.000000	0.05858	0.938000	0.37757	0.731000	0.41821	-1.558000	0.02164	-0.164000	0.10927	0.386000	0.25728	GAA	.	.		0.423	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		A	56000212	T	A	56000212	3	1	115	1	0	0	0	0	1	0	0	0	11191	1490	52	4	628	4	OR5T2	11	56000212	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	238847	56000212	79006304	266	19805										
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57081166	57081166	+	Frame_Shift_Del	DEL	G	G	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggagctgatggagtcacagcGgggcagggagaagcctggga							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:57081166delG	ENST00000532437.1	-	4	1307	c.996delC	c.(994-996)cccfs	p.P332fs	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Frame_Shift_Del_p.P332fs			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	332	Acidic.|Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				GAGTCACAGCGGGGCAGGGAG	0.667																																					p.A333fs		Atlas-INDEL	.											TNKS1BP1,NS,carcinoma,0,1	TNKS1BP1	148	.	0			c.997delG						.						20	24	22					11																	57081166		2185	4289	6474	SO:0001589	frameshift_variant	85456	exon5			.	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.996delC	chr11.hg19:g.57081166delG	ENSP00000437271:p.Pro332fs	194.0	0.0		208.0	13.0	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Frame_Shift_Del	DEL	ENST00000532437.1	hg19	CCDS7951.1																																																																																			.	.		0.667	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		-	57081166	G	-	57081166	7	5	115	1	0	1	0	1	0	0	0	0	16335	1103	39	0	4221	0	TNKS1BP1	11	57081166	Frame_Shift_Del	DEL	G	TCGA-DD-A3A1-01A-11D-A20W-10	1080954	57081166	77925350	267	19806										
FAM111B	374393	hgsc.bcm.edu	37	chr11	58892143	58892143	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctttttcatgttgttgctatAggaaggacaagaaagaagat	10	4	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:58892143A>G	ENST00000343597.3	+	4	764	c.573A>G	c.(571-573)atA>atG	p.I191M	FAM111B_ENST00000411426.1_Missense_Mutation_p.I161M|FAM111B_ENST00000529618.1_Missense_Mutation_p.I161M	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	191							catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						TTGTTGCTATAGGAAGGACAA	0.353																																					p.I191M		Atlas-SNP	.											.	FAM111B	84	.	0			c.A573G						.						105	100	101					11																	58892143		2201	4294	6495	SO:0001583	missense	374393	exon4			TGCTATAGGAAGG	BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.573A>G	chr11.hg19:g.58892143A>G	ENSP00000341565:p.Ile191Met	119.0	0.0		125.0	5.0	NM_198947	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	hg19	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	A	12.60	1.985973	0.35036	.	.	ENSG00000189057	ENST00000411426;ENST00000529618;ENST00000534403;ENST00000343597	T;T;T	0.33216	1.42;1.42;1.42	4.52	-4.46	0.03536	.	1.601420	0.04307	U	0.348379	T	0.27134	0.0665	L	0.52573	1.65	0.09310	N	1	P	0.44578	0.838	P	0.44990	0.466	T	0.35674	-0.9779	10	0.87932	D	0	.	0.5444	0.00651	0.2481:0.233:0.123:0.3959	.	191	Q6SJ93	F111B_HUMAN	M	161;161;161;191	ENSP00000393855:I161M;ENSP00000432875:I161M;ENSP00000341565:I191M	ENSP00000341565:I191M	I	+	3	3	FAM111B	58648719	0.010000	0.17322	0.001000	0.08648	0.004000	0.04260	-0.181000	0.09740	-0.510000	0.06523	-1.870000	0.00554	ATA	.	.		0.353	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		G	58892143	A	G	58892143	3	3	115	1	0	0	0	0	1	0	0	0	5405	410	15	2	579	2	FAM111B	11	58892143	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1810977	58892143	76114373	268	19807										
DAGLA	747	hgsc.bcm.edu	37	chr11	61502340	61502340	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggtgttgcctgtgtcctgcgAggccgcggttcgcccctgga	16	13	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:61502340A>G	ENST00000257215.5	+	10	1110	c.994A>G	c.(994-996)Agg>Ggg	p.R332G		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	332					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		GTGTCCTGCGAGGCCGCGGTT	0.607																																					p.R332G		Atlas-SNP	.											.	DAGLA	109	.	0			c.A994G						.						143	120	128					11																	61502340		2202	4299	6501	SO:0001583	missense	747	exon10			CCTGCGAGGCCGC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"neural stem cell-derived dendrite regulator"	614015	"chromosome 11 open reading frame 11"	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.994A>G	chr11.hg19:g.61502340A>G	ENSP00000257215:p.Arg332Gly	86.0	0.0		113.0	5.0	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	hg19	CCDS31578.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.461936	0.26248	.	.	ENSG00000134780	ENST00000257215	T	0.25579	1.79	4.01	2.0	0.26442	.	0.125473	0.53938	D	0.000058	T	0.12305	0.0299	N	0.25094	0.71	0.34086	D	0.660161	P	0.43477	0.808	B	0.30179	0.112	T	0.26815	-1.0092	10	0.25751	T	0.34	-28.0368	11.5875	0.50927	0.5275:0.4725:0.0:0.0	.	332	Q9Y4D2	DGLA_HUMAN	G	332	ENSP00000257215:R332G	ENSP00000257215:R332G	R	+	1	2	DAGLA	61258916	0.058000	0.20735	0.438000	0.26821	0.974000	0.67602	0.343000	0.19944	0.394000	0.25230	0.459000	0.35465	AGG	.	.		0.607	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		G	61502340	A	G	61502340	3	3	115	1	0	0	0	0	1	0	0	0	4228	295	11	2	1028	2	DAGLA	11	61502340	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2610197	61502340	73504176	269	19808										
SLC22A20	823	hgsc.bcm.edu	37	chr11	64981537	64981537	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgaggcctccaccaacgactCgggggcctggctgagggcca	15	14	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:64981537C>T	ENST00000527323.1	+	0	3086				SLC22A20_ENST00000525437.1_RNA			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		ACCAACGACTCGGGGGCCTGG	0.697																																					p.S65L		Atlas-SNP	.											.	SLC22A20	36	.	0			c.C194T						.						9	12	11					11																	64981537		1865	4064	5929	SO:0001628	intergenic_variant	440044	exon1			ACGACTCGGGGGC	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"EF-hand domain containing"	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614		chr11.hg19:g.64981537C>T		65.0	0.0		63.0	20.0	NM_001004326	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	hg19	CCDS44644.1																																																																																			.	.		0.697	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1			T	64981537	C	T	64981537	1	4	115	0	1	0	0	0	0	0	0	0	14466	893	31	1		1	SLC22A20	11	64981537	IGR	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	3479197	64981537	70024979	270	19809										
LTBP3	4054	hgsc.bcm.edu	37	chr11	65306671	65306671	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcgctcttgcacagcagcccGcgctggttcagctctcggca	11	16	3	0	rs575913813	byFrequency	TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:65306671G>T	ENST00000301873.5	-	28	4060	c.3792C>A	c.(3790-3792)cgC>cgA	p.R1264R	LTBP3_ENST00000530785.1_Silent_p.R267R|LTBP3_ENST00000532932.1_Silent_p.R694R|LTBP3_ENST00000536982.1_Silent_p.R843R|LTBP3_ENST00000322147.4_Silent_p.R1217R|LTBP3_ENST00000529189.1_Silent_p.R220R	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	1264	EGF-like 13; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						ACAGCAGCCCGCGCTGGTTCA	0.711																																					p.R1264R		Atlas-SNP	.											.	LTBP3	55	.	0			c.C3792A						.						5	4	4					11																	65306671		2056	4014	6070	SO:0001819	synonymous_variant	4054	exon28			CAGCCCGCGCTGG	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.3792C>A	chr11.hg19:g.65306671G>T		55.0	0.0		70.0	4.0	NM_001130144	O15107|Q96HB9|Q9H7K2|Q9UFN4	Silent	SNP	ENST00000301873.5	hg19	CCDS44647.1																																																																																			.	.		0.711	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070		T	65306671	G	T	65306671	2	4	115	1	0	0	0	0	0	0	0	1	9084	1074	38	1		1	LTBP3	11	65306671	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	325134	65306671	69699845	271	19810										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65347712	65347712	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cactctttccggggtgctgcTgcgggagggccgtgccacgt	16	13	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:65347712T>C	ENST00000309295.4	+	5	738	c.473T>C	c.(472-474)cTg>cCg	p.L158P		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	158						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GGGGTGCTGCTGCGGGAGGGC	0.642																																					p.L158P		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.T473C						.						77	86	83					11																	65347712		2195	4288	6483	SO:0001583	missense	254102	exon5			TGCTGCTGCGGGA	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.473T>C	chr11.hg19:g.65347712T>C	ENSP00000312671:p.Leu158Pro	101.0	0.0		146.0	6.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.209837	0.79240	.	.	ENSG00000173442	ENST00000309295;ENST00000533237	T;T	0.52057	0.68;0.68	5.56	5.56	0.83823	.	0.260438	0.26460	N	0.024252	T	0.66597	0.2805	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.70124	-0.4958	10	0.87932	D	0	.	12.0941	0.53744	0.0:0.0:0.0:1.0	.	158	Q8N3D4	EH1L1_HUMAN	P	158	ENSP00000312671:L158P;ENSP00000431996:L158P	ENSP00000312671:L158P	L	+	2	0	EHBP1L1	65104288	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.676000	0.61627	2.115000	0.64714	0.454000	0.30748	CTG	.	.		0.642	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		C	65347712	T	C	65347712	3	2	115	1	0	0	0	0	1	0	0	0	4978	1580	55	2	491	2	EHBP1L1	11	65347712	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	41041	65347712	69658804	272	19811										
TPCN2	219931	hgsc.bcm.edu	37	chr11	68835002	68835002	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcaggacagggagaggctgaCctacttccagaacctgcctg	13	12	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:68835002C>G	ENST00000294309.3	+	8	859	c.758C>G	c.(757-759)aCc>aGc	p.T253S	TPCN2_ENST00000542467.1_Missense_Mutation_p.T253S|TPCN2_ENST00000442692.2_3'UTR	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	253					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GAGAGGCTGACCTACTTCCAG	0.657																																					p.T253S		Atlas-SNP	.											.	TPCN2	63	.	0			c.C758G						.						134	104	114					11																	68835002		2200	4294	6494	SO:0001583	missense	219931	exon8			GGCTGACCTACTT	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"Voltage-gated ion channels / Two-pore channels"	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.758C>G	chr11.hg19:g.68835002C>G	ENSP00000294309:p.Thr253Ser	46.0	0.0		56.0	11.0	NM_139075	Q9NT82	Missense_Mutation	SNP	ENST00000294309.3	hg19	CCDS8189.1	.	.	.	.	.	.	.	.	.	.	c	6.762	0.509544	0.12883	.	.	ENSG00000162341	ENST00000356782;ENST00000294309;ENST00000535009;ENST00000542467	D;D	0.98531	-4.98;-4.98	4.97	-1.68	0.08212	Ion transport (1);	1.166550	0.05931	N	0.635100	D	0.93119	0.7809	N	0.22421	0.69	0.09310	N	1	P;B;B	0.40360	0.714;0.238;0.317	B;B;B	0.37550	0.253;0.186;0.164	D	0.90096	0.4181	10	0.10111	T	0.7	-14.4464	4.1192	0.10098	0.1654:0.3636:0.0:0.471	.	253;253;168	E7ETX0;Q8NHX9;F5H1G5	.;TPC2_HUMAN;.	S	183;253;168;253	ENSP00000294309:T253S;ENSP00000445551:T253S	ENSP00000294309:T253S	T	+	2	0	TPCN2	68591578	0.000000	0.05858	0.910000	0.35882	0.815000	0.46073	-0.007000	0.12810	0.002000	0.14630	0.643000	0.83706	ACC	.	.		0.657	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075		G	68835002	C	G	68835002	3	3	115	1	0	0	0	0	1	0	0	0	16411	507	18	4	788	4	TPCN2	11	68835002	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	3487290	68835002	66171514	273	19812										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78498080	78498080	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agccatcctcgcagcggcagGtgccccctacgcacacgcca	10	19	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:78498080G>A	ENST00000278550.7	-	16	2690	c.2228C>T	c.(2227-2229)aCc>aTc	p.T743I		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	743	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.T743N(2)									GCAGCGGCAGGTGCCCCCTAC	0.697																																					p.T743I		Atlas-SNP	.											ODZ4_ENST00000278550,NS,carcinoma,0,2	.	.	.	2	Substitution - Missense(2)	breast(2)	c.C2228T						.						6	9	8					11																	78498080		2027	4089	6116	SO:0001583	missense	26011	exon16			CGGCAGGTGCCCC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.2228C>T	chr11.hg19:g.78498080G>A	ENSP00000278550:p.Thr743Ile	58.0	0.0		74.0	3.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.39|14.39	2.519797|2.519797	0.44866|0.44866	.|.	.|.	ENSG00000149256|ENSG00000149256	ENST00000533525|ENST00000278550	.|T	.|0.03330	.|3.97	5.07|5.07	5.07|5.07	0.68467|0.68467	.|EGF, extracellular (1);Epidermal growth factor-like (1);	.|0.106709	.|0.64402	.|D	.|0.000012	T|T	0.06690|0.06690	0.0171|0.0171	L|L	0.39514|0.39514	1.22|1.22	0.36346|0.36346	D|D	0.859766|0.859766	.|P	.|0.52316	.|0.952	.|P	.|0.49226	.|0.603	T|T	0.42965|0.42965	-0.9420|-0.9420	5|9	.|.	.|.	.|.	.|.	14.2704|14.2704	0.66149|0.66149	0.0:0.1486:0.8514:0.0|0.0:0.1486:0.8514:0.0	.|.	.|743	.|Q6N022	.|TEN4_HUMAN	S|I	57|743	.|ENSP00000278550:T743I	.|.	P|T	-|-	1|2	0|0	ODZ4|ODZ4	78175728|78175728	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.881000|0.881000	0.50899|0.50899	2.801000|2.801000	0.47908|0.47908	2.653000|2.653000	0.90120|0.90120	0.561000|0.561000	0.74099|0.74099	CCT|ACC	.	.		0.697	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78498080	G	A	78498080	3	1	115	1	0	0	0	0	1	0	0	0	10846	1261	44	3	6157	3	ODZ4	11	78498080	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	9663078	78498080	56508436	274	19813										
SLC36A4	120103	hgsc.bcm.edu	37	chr11	92917643	92917643	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tggaagtcctaaaaggccagTtccaatatttcctttaagaa	7	8	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:92917643T>C	ENST00000326402.4	-	3	353	c.223A>G	c.(223-225)Act>Gct	p.T75A	SLC36A4_ENST00000529184.1_5'UTR	NM_152313.2	NP_689526.2	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 4	75					L-alanine transport (GO:0015808)|proline transport (GO:0015824)|tryptophan transport (GO:0015827)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	25		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				AAAAGGCCAGTTCCAATATTT	0.313																																					p.T75A		Atlas-SNP	.											.	SLC36A4	61	.	0			c.A223G						.						179	188	185					11																	92917643		2201	4298	6499	SO:0001583	missense	120103	exon3			GGCCAGTTCCAAT	AY162216	CCDS8291.1, CCDS66202.1	11q21	2013-05-22			ENSG00000180773	ENSG00000180773		"Solute carriers"	19660	protein-coding gene	gene with protein product		613760					Standard	XM_005273758		Approved	PAT4, FLJ38932	uc001pdn.3	Q6YBV0	OTTHUMG00000167368	ENST00000326402.4:c.223A>G	chr11.hg19:g.92917643T>C	ENSP00000317382:p.Thr75Ala	64.0	0.0		68.0	4.0	NM_152313	Q86X30|Q8IVM5|Q8N8S6	Missense_Mutation	SNP	ENST00000326402.4	hg19	CCDS8291.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.501790	0.85176	.	.	ENSG00000180773	ENST00000326402	T	0.01821	4.62	6.06	6.06	0.98353	.	0.071003	0.64402	D	0.000016	T	0.10423	0.0255	M	0.70842	2.15	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00195	-1.1932	10	0.87932	D	0	-20.5103	16.286	0.82722	0.0:0.0:0.0:1.0	.	75	Q6YBV0	S36A4_HUMAN	A	75	ENSP00000317382:T75A	ENSP00000317382:T75A	T	-	1	0	SLC36A4	92557291	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.303000	0.72794	2.323000	0.78572	0.528000	0.53228	ACT	.	.		0.313	SLC36A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394329.2			C	92917643	T	C	92917643	3	2	115	1	0	0	0	0	1	0	0	0	14611	1725	60	2	1327	2	SLC36A4	11	92917643	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	14419563	92917643	42088873	275	19814										
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101833708	101833708	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acaatgctgaaaacagtcatTcactgaagaataaaacagga	7	7	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:101833708T>C	ENST00000263468.8	+	6	2212	c.1942T>C	c.(1942-1944)Tca>Cca	p.S648P	KIAA1377_ENST00000537689.1_Missense_Mutation_p.S449P	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	648										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AAACAGTCATTCACTGAAGAA	0.348																																					p.S648P		Atlas-SNP	.											.	KIAA1377	111	.	0			c.T1942C						.						52	51	51					11																	101833708		2203	4299	6502	SO:0001583	missense	57562	exon6			AGTCATTCACTGA	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.1942T>C	chr11.hg19:g.101833708T>C	ENSP00000263468:p.Ser648Pro	95.0	0.0		96.0	4.0	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	hg19	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	T	0.110	-1.140146	0.01728	.	.	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.08546	3.08;3.08	5.45	3.14	0.36123	.	0.769745	0.11819	N	0.526446	T	0.05044	0.0135	N	0.17674	0.51	0.09310	N	1	B	0.17667	0.023	B	0.18871	0.023	T	0.45352	-0.9267	10	0.23891	T	0.37	-0.5782	3.6374	0.08154	0.1614:0.1798:0.0:0.6587	.	648	Q9P2H0	K1377_HUMAN	P	648;449	ENSP00000263468:S648P;ENSP00000443184:S449P	ENSP00000263468:S648P	S	+	1	0	KIAA1377	101338918	0.016000	0.18221	0.000000	0.03702	0.004000	0.04260	1.921000	0.40035	0.462000	0.27095	-0.250000	0.11733	TCA	.	.		0.348	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		C	101833708	T	C	101833708	3	2	115	1	0	0	0	0	1	0	0	0	8236	1783	62	2	1964	2	KIAA1377	11	101833708	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	8916065	101833708	33172808	276	19815										
IL18	3606	hgsc.bcm.edu	37	chr11	112020884	112020884	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cattcaaatttcttatgactGataatttagattcaagcttg	5	6	3	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:112020884G>C	ENST00000280357.7	-	4	356	c.137C>G	c.(136-138)tCa>tGa	p.S46*	IL18_ENST00000533858.1_5'UTR|IL18_ENST00000528832.1_Nonsense_Mutation_p.S46*|IL18_ENST00000524595.1_Nonsense_Mutation_p.S42*|SDHD_ENST00000532699.1_Intron	NM_001562.3	NP_001553.1	Q14116	IL18_HUMAN	interleukin 18	46					angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|cellular response to organic cyclic compound (GO:0071407)|chemokine biosynthetic process (GO:0042033)|granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0042253)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma biosynthetic process (GO:0042095)|interleukin-13 biosynthetic process (GO:0042231)|interleukin-2 biosynthetic process (GO:0042094)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|natural killer cell activation (GO:0030101)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of tissue remodeling (GO:0034105)|regulation of cell adhesion (GO:0030155)|sleep (GO:0030431)|T-helper 1 type immune response (GO:0042088)|type 2 immune response (GO:0042092)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)						all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		TCTTATGACTGATAATTTAGA	0.299																																					p.S46X		Atlas-SNP	.											.	IL18	10	.	0			c.C137G						.						95	89	91					11																	112020884		1791	4063	5854	SO:0001587	stop_gained	3606	exon4			ATGACTGATAATT	U90434	CCDS44731.1, CCDS58180.1	11q22.2-q22.3	2014-04-04	2014-04-04		ENSG00000150782	ENSG00000150782		"Interleukins and interleukin receptors"	5986	protein-coding gene	gene with protein product	"interferon-gamma-inducing factor"	600953	"interleukin 18 (interferon-gamma-inducing factor)"			7477296, 9693051	Standard	NM_001562		Approved	IGIF, IL1F4, IL-1g, IL-18	uc001pnb.2	Q14116	OTTHUMG00000167006	ENST00000280357.7:c.137C>G	chr11.hg19:g.112020884G>C	ENSP00000280357:p.Ser46*	94.0	0.0		99.0	36.0	NM_001562	O75599|Q6FGY3|Q6WWJ7	Nonsense_Mutation	SNP	ENST00000280357.7	hg19	CCDS44731.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263835	0.80358	.	.	ENSG00000150782	ENST00000280357;ENST00000524595;ENST00000528832	.	.	.	4.97	4.97	0.65823	.	0.642927	0.13849	N	0.358505	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	0.8517	13.9222	0.63940	0.0:0.0:1.0:0.0	.	.	.	.	X	46;42;46	.	ENSP00000280357:S46X	S	-	2	0	IL18	111526094	0.285000	0.24296	0.480000	0.27341	0.287000	0.27160	3.965000	0.56788	2.740000	0.93945	0.650000	0.86243	TCA	.	.		0.299	IL18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392409.1	NM_001562		C	112020884	G	C	112020884	4	2	115	1	0	0	0	0	0	1	0	0	7654	1294	45	4	456	4	IL18	11	112020884	Nonsense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	10187176	112020884	22985632	277	19816										
NCAM1	4684	hgsc.bcm.edu	37	chr11	113105812	113105812	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcccgaaacaacgtacgccgTaaggctggcggcgctcaatg	13	13	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:113105812T>C	ENST00000533760.1	+	13	1966	c.1367T>C	c.(1366-1368)gTa>gCa	p.V456A	NCAM1_ENST00000316851.7_Missense_Mutation_p.V574A|NCAM1_ENST00000401611.2_Missense_Mutation_p.V583A|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	584	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		ACGTACGCCGTAAGGCTGGCG	0.552																																					p.V610A		Atlas-SNP	.											.	NCAM1	372	.	0			c.T1829C						.						26	30	28					11																	113105812		2011	4166	6177	SO:0001583	missense	4684	exon16			ACGCCGTAAGGCT		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.1367T>C	chr11.hg19:g.113105812T>C	ENSP00000473281:p.Val456Ala	83.0	0.0		95.0	4.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.80	2.940991	0.52972	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851;ENST00000433634	T;T	0.61392	0.11;0.11	5.84	5.84	0.93424	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.075248	0.52532	U	0.000070	T	0.76140	0.3946	.	.	.	0.58432	D	0.999995	D;D;D;D	0.61697	0.988;0.988;0.99;0.977	P;D;D;D	0.67548	0.883;0.92;0.952;0.938	T	0.79468	-0.1791	9	0.87932	D	0	-34.9693	16.2087	0.82144	0.0:0.0:0.0:1.0	.	584;574;584;574	P13591-5;P13591-1;P13591;P13591-3	.;.;NCAM1_HUMAN;.	A	456;583;574;18	ENSP00000384055:V583A;ENSP00000318472:V574A	ENSP00000318472:V574A	V	+	2	0	NCAM1	112611022	1.000000	0.71417	0.182000	0.23118	0.006000	0.05464	6.105000	0.71505	2.233000	0.73108	0.482000	0.46254	GTA	.	.		0.552	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		C	113105812	T	C	113105812	3	2	115	1	0	0	0	0	1	0	0	0	10211	1638	57	2	1806	2	NCAM1	11	113105812	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1084928	113105812	21900704	278	19817										
USP28	57646	hgsc.bcm.edu	37	chr11	113683141	113683141	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgtacttgagccagctctgtCggggttgattatagatatag	12	6	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:113683141C>T	ENST00000003302.4	-	16	1897	c.1829G>A	c.(1828-1830)cGa>cAa	p.R610Q	USP28_ENST00000260188.5_Missense_Mutation_p.R610Q|USP28_ENST00000545540.1_Missense_Mutation_p.R485Q|USP28_ENST00000544967.1_Missense_Mutation_p.R318Q	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	610	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		CCAGCTCTGTCGGGGTTGATT	0.438																																					p.R610Q	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	Atlas-SNP	.											.	USP28	135	.	0			c.G1829A						.						151	154	153					11																	113683141		2201	4296	6497	SO:0001583	missense	57646	exon16			CTCTGTCGGGGTT	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.1829G>A	chr11.hg19:g.113683141C>T	ENSP00000003302:p.Arg610Gln	92.0	0.0		94.0	4.0	NM_020886	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	hg19	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.814469	0.32053	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540;ENST00000538475	T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49	5.43	3.45	0.39498	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.178672	0.49305	D	0.000159	T	0.20659	0.0497	N	0.12637	0.245	0.41029	D	0.985143	D;P;D	0.59767	0.986;0.604;0.982	P;B;P	0.49301	0.606;0.183;0.471	T	0.02603	-1.1135	10	0.17832	T	0.49	-12.4082	10.1697	0.42902	0.1355:0.7936:0.0:0.0709	.	485;610;318	B4E3L3;Q96RU2;G3V1N5	.;UBP28_HUMAN;.	Q	610;610;318;485;314	ENSP00000003302:R610Q;ENSP00000260188:R610Q;ENSP00000442431:R318Q;ENSP00000444991:R485Q;ENSP00000442257:R314Q	ENSP00000003302:R610Q	R	-	2	0	USP28	113188351	0.998000	0.40836	0.875000	0.34327	0.061000	0.15899	3.595000	0.54016	1.299000	0.44798	-0.123000	0.14984	CGA	.	.		0.438	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			T	113683141	C	T	113683141	3	4	115	1	0	0	0	0	1	0	0	0	17073	884	31	1	1444	1	USP28	11	113683141	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	577329	113683141	21323375	279	19818										
SLC37A4	51399	hgsc.bcm.edu	37	chr11	118896697	118896697	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttgggggagtcactggtcaCtgttacccggaagaggtaca	14	9	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:118896697C>T	ENST00000533632.1	+	0	1759				SLC37A4_ENST00000545985.1_Missense_Mutation_p.V322M|SLC37A4_ENST00000525102.1_5'UTR|SLC37A4_ENST00000538950.1_Missense_Mutation_p.V249M|SLC37A4_ENST00000357590.5_Missense_Mutation_p.V322M|SLC37A4_ENST00000330775.7_Missense_Mutation_p.V321M	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4						dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)				NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		TCACTGGTCACTGTTACCCGG	0.572																																					p.V322M		Atlas-SNP	.											.	SLC37A4	19	.	0			c.G964A						.						52	58	56					11																	118896697		2080	4221	6301	SO:0001628	intergenic_variant	2542	exon8			TGGTCACTGTTAC	AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"Trafficking protein particle complex"	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296			chr11.hg19:g.118896697C>T		121.0	0.0		139.0	6.0	NM_001467	A8K3A5|B4DME1	Missense_Mutation	SNP	ENST00000533632.1	hg19	CCDS8407.1																																																																																			.	.		0.572	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146		T	118896697	C	T	118896697	1	4	115	0	1	0	0	0	0	0	0	0	14615	565	20	3		3	SLC37A4	11	118896697	IGR	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	5213556	118896697	16109819	280	19819										
OR8G5	219865	hgsc.bcm.edu	37	chr11	124134838	124134838	+	Frame_Shift_Del	DEL	A	A	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcatcaaagaatggcagcagAaaaccattcttttgtgacta							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:124134838delA	ENST00000524943.2	+	1	116	c.116delA	c.(115-117)gaafs	p.E39fs	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		ATGGCAGCAGAAAACCATTCT	0.418																																					p.E39fs	Ovarian(169;523 1969 8640 31295 51256)	Atlas-INDEL	.											.	.	.	.	0			c.115delG						.						52	52	52					11																	124134838		1938	4163	6101	SO:0001589	frameshift_variant	219865	exon1			.	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"GPCR / Class A : Olfactory receptors"	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.116delA	chr11.hg19:g.124134838delA	ENSP00000477014:p.Glu39fs	164.0	0.0		179.0	11.0	NM_001005198	B2RND3|Q6IEU6	Frame_Shift_Del	DEL	ENST00000524943.2	hg19																																																																																				.	.		0.418	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198		-	124134838	A	-	124134838	7	5	115	1	0	1	0	1	0	0	0	0	11245	246	9	0	118	0	OR8G5	11	124134838	Frame_Shift_Del	DEL	A	TCGA-DD-A3A1-01A-11D-A20W-10	5238141	124134838	10871678	281	19820										
SRPR	6734	hgsc.bcm.edu	37	chr11	126135040	126135040	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggcagcaatgaggacactgaAgccattctctaacaaccaga	9	11	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:126135040A>G	ENST00000332118.6	-	11	1493	c.1339T>C	c.(1339-1341)Ttc>Ctc	p.F447L	SRPR_ENST00000530680.1_5'Flank|SRPR_ENST00000532259.1_Missense_Mutation_p.F419L	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	447					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		AGGACACTGAAGCCATTCTCT	0.483																																					p.F447L		Atlas-SNP	.											.	SRPR	60	.	0			c.T1339C						.						51	50	50					11																	126135040		2201	4299	6500	SO:0001583	missense	6734	exon11			CACTGAAGCCATT	BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"signal recognition particle receptor ('docking protein')"			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.1339T>C	chr11.hg19:g.126135040A>G	ENSP00000328023:p.Phe447Leu	72.0	0.0		85.0	4.0	NM_003139	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Missense_Mutation	SNP	ENST00000332118.6	hg19	CCDS31717.1	.	.	.	.	.	.	.	.	.	.	A	19.07	3.755325	0.69648	.	.	ENSG00000182934	ENST00000332118;ENST00000532259	.	.	.	5.26	5.26	0.73747	ATPase, AAA+ type, core (1);Signal recognition particle, SRP54 subunit, GTPase (2);	0.091750	0.85682	D	0.000000	T	0.33731	0.0873	N	0.04636	-0.2	0.80722	D	1	B;B	0.14805	0.005;0.011	B;B	0.18871	0.023;0.023	T	0.24657	-1.0154	9	0.08381	T	0.77	-8.5065	15.3398	0.74287	1.0:0.0:0.0:0.0	.	419;447	E9PJS4;P08240	.;SRPR_HUMAN	L	447;419	.	ENSP00000328023:F447L	F	-	1	0	SRPR	125640250	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.120000	0.77153	2.215000	0.71742	0.528000	0.53228	TTC	.	.		0.483	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139		G	126135040	A	G	126135040	3	3	115	1	0	0	0	0	1	0	0	0	15177	72	3	2	593	2	SRPR	11	126135040	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2000202	126135040	8871476	282	19821										
ST3GAL4	6484	hgsc.bcm.edu	37	chr11	126279255	126279255	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cccttcttcatggagattgcAgctgacaaactgctgagcct	9	12	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:126279255A>G	ENST00000526727.1	+	8	1094	c.720A>G	c.(718-720)gcA>gcG	p.A240A	ST3GAL4_ENST00000227495.6_Silent_p.A236A|ST3GAL4_ENST00000534457.1_Silent_p.A235A|ST3GAL4_ENST00000356132.4_Silent_p.A246A|ST3GAL4_ENST00000449406.2_Silent_p.A229A|ST3GAL4_ENST00000534083.1_Silent_p.A240A|ST3GAL4_ENST00000532243.1_Silent_p.A239A|ST3GAL4_ENST00000530591.1_Silent_p.A236A|ST3GAL4_ENST00000444328.2_Silent_p.A240A|ST3GAL4_ENST00000392669.2_Silent_p.A240A			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	240					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|monosialoganglioside sialyltransferase activity (GO:0047288)			endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)		TGGAGATTGCAGCTGACAAAC	0.527																																					p.A240A		Atlas-SNP	.											.	ST3GAL4	25	.	0			c.A720G						.						105	105	105					11																	126279255		2201	4297	6498	SO:0001819	synonymous_variant	6484	exon9			GATTGCAGCTGAC	X74570	CCDS8474.1, CCDS58193.1, CCDS58194.1	11q23-q24	2013-03-01	2003-01-14	2005-02-07	ENSG00000110080	ENSG00000110080	2.4.99.4	"Sialyltransferases"	10864	protein-coding gene	gene with protein product	"ST3Gal IV"	104240	"sialyltransferase 4C (beta-galactosidase alpha-2,3-sialytransferase)"	CGS23, SIAT4, NANTA3, SIAT4C		8557707, 8288606	Standard	NM_006278		Approved	STZ, SAT3, FLJ11867	uc001qds.3	Q11206	OTTHUMG00000165830	ENST00000526727.1:c.720A>G	chr11.hg19:g.126279255A>G		114.0	0.0		119.0	7.0	NM_001254757	A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	Silent	SNP	ENST00000526727.1	hg19	CCDS58193.1																																																																																			.	.		0.527	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278		G	126279255	A	G	126279255	2	3	115	1	0	0	0	0	0	0	0	1	15232	175	7	2		2	ST3GAL4	11	126279255	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	144215	126279255	8727261	283	19822										
TP53AIP1	63970	hgsc.bcm.edu	37	chr11	128807456	128807456	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agctctgaggacccagatgcTgtcactgggtcctggtgagt	14	10	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:128807456T>C	ENST00000531399.1	-	2	351				TP53AIP1_ENST00000602346.1_Silent_p.T86T|TP53AIP1_ENST00000530777.1_Intron|TP53AIP1_ENST00000458238.2_Intron	NM_022112.2	NP_071395.2	Q9HCN2	TPIP1_HUMAN	tumor protein p53 regulated apoptosis inducing protein 1						apoptotic process (GO:0006915)	mitochondrion (GO:0005739)				large_intestine(1)|lung(1)|skin(1)	3						ACCCAGATGCTGTCACTGGGT	0.577																																					p.T86T		Atlas-SNP	.											.	TP53AIP1	12	.	0			c.A258G						.						64	60	62					11																	128807456		2201	4297	6498	SO:0001627	intron_variant	63970	exon2			AGATGCTGTCACT	AB045831	CCDS8480.1, CCDS8480.2, CCDS55797.1, CCDS55798.1, CCDS58195.1	11q24.3	2011-01-26	2009-03-09		ENSG00000120471	ENSG00000120471			29984	protein-coding gene	gene with protein product		605426				11030628, 12019168	Standard	NM_022112		Approved	p53AIP1	uc021qsd.1	Q9HCN2		ENST00000531399.1:c.141+116A>G	chr11.hg19:g.128807456T>C		51.0	0.0		108.0	5.0	NM_001251964	Q6NT40|Q7Z6F7|Q9HCN0|Q9HCN1	Silent	SNP	ENST00000531399.1	hg19	CCDS8480.2																																																																																			.	.		0.577	TP53AIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386244.1	NM_022112		C	128807456	T	C	128807456	1	2	115	0	1	0	0	0	0	0	0	0	16397	1567	55	2		2	TP53AIP1	11	128807456	Intron	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2528201	128807456	6199060	284	19823										
APLP2	334	hgsc.bcm.edu	37	chr11	130011950	130011950	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaagaggcagtatggcaccaTcagccacgggatcgtggagg	16	9	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:130011950T>G	ENST00000263574.5	+	17	2243	c.2171T>G	c.(2170-2172)aTc>aGc	p.I724S	APLP2_ENST00000539648.1_Missense_Mutation_p.I512S|APLP2_ENST00000278756.7_Missense_Mutation_p.I722S|APLP2_ENST00000338167.5_Missense_Mutation_p.I712S|APLP2_ENST00000345598.5_Missense_Mutation_p.I483S|APLP2_ENST00000528499.1_Missense_Mutation_p.I656S|APLP2_ENST00000543137.1_Missense_Mutation_p.I619S	NM_001642.2	NP_001633.1	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2	724					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0197)|Lung(977;0.24)		TATGGCACCATCAGCCACGGG	0.592																																					p.I724S		Atlas-SNP	.											.	APLP2	71	.	0			c.T2171G						.						75	58	63					11																	130011950		2201	4297	6498	SO:0001583	missense	334	exon17			GCACCATCAGCCA	L19597	CCDS8486.1, CCDS44773.1, CCDS44774.1, CCDS44775.1, CCDS58196.1	11q24	2008-02-05			ENSG00000084234	ENSG00000084234			598	protein-coding gene	gene with protein product		104776		APPL2		10702673	Standard	NM_001642		Approved	APPH	uc021qsg.1	Q06481	OTTHUMG00000165767	ENST00000263574.5:c.2171T>G	chr11.hg19:g.130011950T>G	ENSP00000263574:p.Ile724Ser	91.0	0.0		111.0	33.0	NM_001642	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Missense_Mutation	SNP	ENST00000263574.5	hg19	CCDS8486.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.474193	0.84640	.	.	ENSG00000084234	ENST00000528499;ENST00000539648;ENST00000263574;ENST00000345598;ENST00000338167;ENST00000278756;ENST00000543137	D;D;D;D;D;D;D	0.95885	-3.84;-3.84;-3.84;-3.84;-3.84;-3.84;-3.84	5.75	5.75	0.90469	Beta-amyloid precursor protein C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.97015	0.9025	M	0.63428	1.95	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.91635	0.996;0.999;0.996;0.999;0.999;0.994;0.997	D	0.96843	0.9619	9	.	.	.	-29.7097	15.2493	0.73532	0.0:0.0:0.0:1.0	.	512;724;668;483;650;656;712	F5H845;Q06481;Q06481-2;Q06481-5;B4E3I5;Q06481-4;Q06481-3	.;APLP2_HUMAN;.;.;.;.;.	S	656;512;724;483;712;722;619	ENSP00000435914:I656S;ENSP00000443728:I512S;ENSP00000263574:I724S;ENSP00000263575:I483S;ENSP00000345444:I712S;ENSP00000278756:I722S;ENSP00000444122:I619S	.	I	+	2	0	APLP2	129517160	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.640000	0.83355	2.188000	0.69820	0.528000	0.53228	ATC	.	.		0.592	APLP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386109.1	NM_001642		G	130011950	T	G	130011950	3	3	115	1	0	0	0	0	1	0	0	0	779	1435	50	5	2237	5	APLP2	11	130011950	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1204494	130011950	4994566	285	19824										
NTM	50863	hgsc.bcm.edu	37	chr11	132184537	132184537	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctctgaacatgactatgggAactacacttgcgtggcctcc	9	12	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr11:132184537A>G	ENST00000374786.1	+	6	1353	c.874A>G	c.(874-876)Aac>Gac	p.N292D	NTM_ENST00000374784.1_Missense_Mutation_p.N292D|NTM_ENST00000374791.3_Missense_Mutation_p.N292D|NTM_ENST00000427481.2_Missense_Mutation_p.N283D|NTM_ENST00000539799.1_Missense_Mutation_p.N292D|NTM_ENST00000474900.1_3'UTR|NTM_ENST00000425719.2_Missense_Mutation_p.N292D	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	292	Ig-like C2-type 3.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						TGACTATGGGAACTACACTTG	0.483																																					p.N292D		Atlas-SNP	.											.	NTM	253	.	0			c.A874G						.						104	92	96					11																	132184537		2201	4297	6498	SO:0001583	missense	50863	exon6			TATGGGAACTACA	AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"Immunoglobulin superfamily / I-set domain containing"	17941	protein-coding gene	gene with protein product	"neurotrimin", "IgLON family member 2"	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.874A>G	chr11.hg19:g.132184537A>G	ENSP00000363918:p.Asn292Asp	86.0	0.0		97.0	4.0	NM_001144059	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	hg19	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	A	18.17	3.563689	0.65651	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23;-0.23	5.62	4.48	0.54585	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.038633	0.85682	D	0.000000	T	0.79545	0.4464	M	0.72479	2.2	0.53005	D	0.999967	D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.958;1.0;0.984;0.999	D;D;D;P;D;D;D	0.97110	0.98;1.0;1.0;0.882;1.0;0.924;0.966	T	0.80420	-0.1390	10	0.66056	D	0.02	-32.0373	12.025	0.53365	0.8705:0.0:0.0:0.1295	.	292;283;251;292;292;292;292	B7Z1Z5;B7Z1I4;B7Z1H3;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;.;NTRI_HUMAN;.;.	D	292;292;283;292;292;292	ENSP00000363923:N292D;ENSP00000437668:N292D;ENSP00000416320:N283D;ENSP00000363918:N292D;ENSP00000396722:N292D;ENSP00000363916:N292D	ENSP00000363916:N292D	N	+	1	0	NTM	131689747	1.000000	0.71417	1.000000	0.80357	0.358000	0.29455	8.910000	0.92685	0.946000	0.37632	-0.336000	0.08194	AAC	.	.		0.483	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		G	132184537	A	G	132184537	3	3	115	1	0	0	0	0	1	0	0	0	10708	246	9	2	982	2	NTM	11	132184537	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2172587	132184537	2821979	286	19825										
FBXL14	144699	hgsc.bcm.edu	37	chr12	1702306	1702306	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tggcaggagcagagggagagAgacttgaggccatccagccc	16	10	0	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:1702306A>G	ENST00000339235.3	-	1	1025	c.927T>C	c.(925-927)tcT>tcC	p.S309S	WNT5B_ENST00000537031.1_Intron|FBXL14_ENST00000543278.1_5'Flank	NM_152441.2	NP_689654.1	Q8N1E6	FXL14_HUMAN	F-box and leucine-rich repeat protein 14	309					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	8	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00115)			AGAGGGAGAGAGACTTGAGGC	0.602																																					p.S309S		Atlas-SNP	.											.	FBXL14	19	.	0			c.T927C						.						97	80	86					12																	1702306		2203	4300	6503	SO:0001819	synonymous_variant	144699	exon1			GGAGAGAGACTTG	BC028132	CCDS8509.1	12p13.33	2011-06-09			ENSG00000171823	ENSG00000171823		"F-boxes / Leucine-rich repeats"	28624	protein-coding gene	gene with protein product		609081				12477932	Standard	NM_152441		Approved	MGC40195, Fbl14	uc001qjh.3	Q8N1E6	OTTHUMG00000090369	ENST00000339235.3:c.927T>C	chr12.hg19:g.1702306A>G		60.0	0.0		42.0	4.0	NM_152441		Silent	SNP	ENST00000339235.3	hg19	CCDS8509.1																																																																																			.	.		0.602	FBXL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206741.1	NM_152441		G	1702306	A	G	1702306	2	3	115	1	0	0	0	0	0	0	0	1	5718	291	11	2		2	FBXL14	12	1702306	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10		1702306	132149589	287	19826										
CLEC9A	283420	hgsc.bcm.edu	37	chr12	10213810	10213810	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gctaaactttacagaatggaAgagaagctgtgcccttcaga	10	8	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:10213810A>G	ENST00000355819.1	+	6	870	c.257A>G	c.(256-258)aAg>aGg	p.K86R		NM_207345.2	NP_997228.1	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A	86					positive regulation of cytokine secretion (GO:0050715)|receptor-mediated endocytosis (GO:0006898)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	22						ACAGAATGGAAGAGAAGCTGT	0.408																																					p.K86R		Atlas-SNP	.											.	CLEC9A	41	.	0			c.A257G						.						92	85	88					12																	10213810		2203	4300	6503	SO:0001583	missense	283420	exon6			AATGGAAGAGAAG		CCDS8611.1	12p13.31	2010-04-27				ENSG00000197992		"C-type lectin domain containing"	26705	protein-coding gene	gene with protein product		612252					Standard	NM_207345		Approved	UNQ9341, HEEE9341	uc001qxa.3	Q6UXN8		ENST00000355819.1:c.257A>G	chr12.hg19:g.10213810A>G	ENSP00000348074:p.Lys86Arg	101.0	0.0		82.0	4.0	NM_207345	B0ZBM2	Missense_Mutation	SNP	ENST00000355819.1	hg19	CCDS8611.1	.	.	.	.	.	.	.	.	.	.	A	9.585	1.124688	0.20959	.	.	ENSG00000197992	ENST00000355819	T	0.01455	4.87	4.0	2.83	0.33086	C-type lectin-like (1);	1.095870	0.07076	N	0.836270	T	0.01905	0.0060	L	0.36672	1.1	0.09310	N	1	B	0.10296	0.003	B	0.12837	0.008	T	0.50224	-0.8853	10	0.17369	T	0.5	.	5.7181	0.17972	0.8699:0.0:0.1301:0.0	.	86	Q6UXN8	CLC9A_HUMAN	R	86	ENSP00000348074:K86R	ENSP00000348074:K86R	K	+	2	0	CLEC9A	10105077	0.010000	0.17322	0.001000	0.08648	0.024000	0.10985	0.984000	0.29565	0.854000	0.35336	0.533000	0.62120	AAG	.	.		0.408	CLEC9A-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000399564.1	NM_207345		G	10213810	A	G	10213810	3	3	115	1	0	0	0	0	1	0	0	0	3524	72	3	2	267	2	CLEC9A	12	10213810	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	8511504	10213810	123638085	288	19827										
C12orf59	120939	hgsc.bcm.edu	37	chr12	10342627	10342627	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agctcttcacatgagtcgctTcacagtagccatgtgcgggc	11	12	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:10342627T>C	ENST00000381923.2	+	6	844	c.440T>C	c.(439-441)tTc>tCc	p.F147S	TMEM52B_ENST00000298530.3_Missense_Mutation_p.F127S|TMEM52B_ENST00000536952.1_Missense_Mutation_p.F147S			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	147						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											ATGAGTCGCTTCACAGTAGCC	0.562																																					p.F127S		Atlas-SNP	.											.	.	.	.	0			c.T380C						.						57	53	54					12																	10342627		2203	4300	6503	SO:0001583	missense	120939	exon4			GTCGCTTCACAGT	AY358845	CCDS8619.1, CCDS66314.1	12p13.2	2012-08-15	2012-08-15	2012-08-15	ENSG00000165685	ENSG00000165685			26438	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 59"	C12orf59		12975309	Standard	XM_005253299		Approved	FLJ31166	uc001qxq.3	Q4KMG9	OTTHUMG00000168410	ENST00000381923.2:c.440T>C	chr12.hg19:g.10342627T>C	ENSP00000371348:p.Phe147Ser	110.0	0.0		99.0	4.0	NM_153022	Q96NA7	Missense_Mutation	SNP	ENST00000381923.2	hg19		.	.	.	.	.	.	.	.	.	.	T	15.16	2.751469	0.49257	.	.	ENSG00000165685	ENST00000381923;ENST00000298530;ENST00000536952	T;T;T	0.28666	1.6;1.6;1.6	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.49253	0.1546	M	0.64997	1.995	0.44754	D	0.997753	D;D	0.76494	0.997;0.999	D;D	0.85130	0.991;0.997	T	0.39231	-0.9624	10	0.27082	T	0.32	-28.7633	12.311	0.54927	0.0:0.0:0.0:1.0	.	147;127	Q4KMG9;Q4KMG9-2	CL059_HUMAN;.	S	147;127;147	ENSP00000371348:F147S;ENSP00000298530:F127S;ENSP00000446102:F147S	ENSP00000298530:F127S	F	+	2	0	C12orf59	10233894	1.000000	0.71417	1.000000	0.80357	0.393000	0.30537	4.880000	0.63107	2.058000	0.61347	0.477000	0.44152	TTC	.	.		0.562	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022		C	10342627	T	C	10342627	3	2	115	1	0	0	0	0	1	0	0	0	1704	1783	62	2	394	2	C12orf59	12	10342627	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	128817	10342627	123509268	289	19828										
SLCO1B3	28234	hgsc.bcm.edu	37	chr12	21015742	21015742	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtcattggctttgcactgggAtctctgtttgctaaaatgta	10	7	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:21015742A>G	ENST00000381545.3	+	8	900	c.681A>G	c.(679-681)ggA>ggG	p.G227G	SLCO1B3_ENST00000553473.1_Silent_p.G227G|LST3_ENST00000540229.1_Silent_p.G227G|SLCO1B3_ENST00000261196.2_Silent_p.G227G|LST3_ENST00000381541.3_Intron|SLCO1B7_ENST00000554957.1_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	227					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TTGCACTGGGATCTCTGTTTG	0.363																																					p.G227G		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.A681G						.						189	164	173					12																	21015742		2203	4300	6503	SO:0001819	synonymous_variant	28234	exon8			ACTGGGATCTCTG		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.681A>G	chr12.hg19:g.21015742A>G		208.0	0.0		91.0	6.0	NM_019844	E7EMT8|Q5JAR4	Silent	SNP	ENST00000381545.3	hg19	CCDS8684.1																																																																																			.	.		0.363	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		G	21015742	A	G	21015742	2	3	115	1	0	0	0	0	0	0	0	1	14739	320	12	2		2	SLCO1B3	12	21015742	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	10673115	21015742	112836153	290	19829										
BHLHE41	79365	hgsc.bcm.edu	37	chr12	26276611	26276611	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgttgctcggttaaggcggTtaaagcttttaagtgtttca	11	6	1	0	rs75677280		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:26276611T>C	ENST00000242728.4	-	4	645	c.298A>G	c.(298-300)Acc>Gcc	p.T100A	RP11-283G6.3_ENST00000535914.1_RNA|RP11-283G6.3_ENST00000545819.1_RNA	NM_030762.2	NP_110389.1	Q9C0J9	BHE41_HUMAN	basic helix-loop-helix family, member e41	100					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|MRF binding (GO:0043426)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)	5						GTTAAGGCGGTTAAAGCTTTT	0.468											OREG0021711	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T100A		Atlas-SNP	.											.	BHLHE41	20	.	0			c.A298G						.						141	133	136					12																	26276611		2203	4300	6503	SO:0001583	missense	79365	exon4			AGGCGGTTAAAGC	AB044088	CCDS8706.1	12p12.1	2011-12-05	2009-01-12	2009-01-12	ENSG00000123095	ENSG00000123095		"Basic helix-loop-helix proteins"	16617	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 2", "Enhancer-of-split and hairy-related protein 1"	606200	"basic helix-loop-helix domain containing, class B, 3"	BHLHB3		11162494, 18557763	Standard	NM_030762		Approved	DEC2, SHARP-1, SHARP1, bHLHe41	uc001rhb.3	Q9C0J9	OTTHUMG00000169174	ENST00000242728.4:c.298A>G	chr12.hg19:g.26276611T>C	ENSP00000242728:p.Thr100Ala	102.0	0.0	785	81.0	4.0	NM_030762	A2I2N8	Missense_Mutation	SNP	ENST00000242728.4	hg19	CCDS8706.1	.	.	.	.	.	.	.	.	.	.	T	16.28	3.078924	0.55753	.	.	ENSG00000123095	ENST00000242728;ENST00000540731	T	0.57107	0.42	4.16	4.16	0.48862	Helix-loop-helix DNA-binding (4);	0.000000	0.85682	U	0.000000	T	0.57080	0.2029	L	0.27053	0.805	0.80722	D	1	D	0.62365	0.991	D	0.67231	0.95	T	0.60105	-0.7328	10	0.54805	T	0.06	-4.4045	12.4975	0.55937	0.0:0.0:0.0:1.0	.	100	Q9C0J9	BHE41_HUMAN	A	100	ENSP00000242728:T100A	ENSP00000242728:T100A	T	-	1	0	BHLHE41	26167878	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.873000	0.69644	1.880000	0.54463	0.533000	0.62120	ACC	.	.		0.468	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762		C	26276611	T	C	26276611	3	2	115	1	0	0	0	0	1	0	0	0	1424	1725	60	2	1158	2	BHLHE41	12	26276611	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	5260869	26276611	107575284	291	19830										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26811016	26811016	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgagttcttgagttacagggAtagcagtggtattagacaca	12	5	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:26811016A>G	ENST00000381340.3	-	17	2350	c.1934T>C	c.(1933-1935)aTc>aCc	p.I645T		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	645					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	AGTTACAGGGATAGCAGTGGT	0.338																																					p.I645T		Atlas-SNP	.											.	ITPR2	270	.	0			c.T1934C						.						102	93	96					12																	26811016		1847	4092	5939	SO:0001583	missense	3709	exon17			ACAGGGATAGCAG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1934T>C	chr12.hg19:g.26811016A>G	ENSP00000370744:p.Ile645Thr	110.0	0.0		73.0	4.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.844189	0.71488	.	.	ENSG00000123104	ENST00000381340	D	0.96716	-4.1	4.8	4.8	0.61643	Intracellular calcium-release channel (1);	0.000000	0.85682	D	0.000000	D	0.98333	0.9447	M	0.91459	3.21	0.80722	D	1	D	0.67145	0.996	D	0.72625	0.978	D	0.99513	1.0956	10	0.87932	D	0	.	14.5354	0.67955	1.0:0.0:0.0:0.0	.	645	Q14571	ITPR2_HUMAN	T	645	ENSP00000370744:I645T	ENSP00000370744:I645T	I	-	2	0	ITPR2	26702283	1.000000	0.71417	0.573000	0.28510	0.837000	0.47467	9.123000	0.94387	2.020000	0.59435	0.533000	0.62120	ATC	.	.		0.338	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		G	26811016	A	G	26811016	3	3	115	1	0	0	0	0	1	0	0	0	7930	333	12	2	6335	2	ITPR2	12	26811016	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	534405	26811016	107040879	292	19831										
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46320825	46320825	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcttttgttctctctagaagTttctcttcttggggacagtg	9	8	5	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:46320825T>C	ENST00000369367.3	-	11	2892	c.2659A>G	c.(2659-2661)Act>Gct	p.T887A	SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000419565.2_Missense_Mutation_p.T887A|SCAF11_ENST00000465950.1_Missense_Mutation_p.T572A|SCAF11_ENST00000549162.1_Missense_Mutation_p.T695A	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	887	Arg-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						TCTCTAGAAGTTTCTCTTCTT	0.448																																					p.T887A		Atlas-SNP	.											.	SCAF11	145	.	0			c.A2659G						.						128	130	129					12																	46320825		2203	4300	6503	SO:0001583	missense	9169	exon11			TAGAAGTTTCTCT	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"RING-type (C3HC4) zinc fingers"	10784	protein-coding gene	gene with protein product		603668	"splicing factor, arginine/serine-rich 2, interacting protein", "serine/arginine-rich splicing factor 2, interacting protein"	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.2659A>G	chr12.hg19:g.46320825T>C	ENSP00000358374:p.Thr887Ala	88.0	0.0		93.0	4.0	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	hg19	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	T	7.397	0.631970	0.14322	.	.	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565;ENST00000547018	T;T;T;T;T	0.47869	1.47;2.2;1.47;2.2;0.83	5.81	3.43	0.39272	.	0.703582	0.13292	N	0.398916	T	0.42245	0.1194	L	0.56769	1.78	0.09310	N	1	B;B	0.17667	0.023;0.003	B;B	0.19946	0.027;0.002	T	0.32719	-0.9896	10	0.29301	T	0.29	-0.7387	7.9723	0.30134	0.0:0.0693:0.3955:0.5353	.	695;887	F8VXG7;Q99590	.;SCAFB_HUMAN	A	572;887;695;887;827	ENSP00000449812:T572A;ENSP00000358374:T887A;ENSP00000448864:T695A;ENSP00000413036:T887A;ENSP00000446746:T827A	ENSP00000358374:T887A	T	-	1	0	SCAF11	44607092	0.070000	0.21116	0.384000	0.26145	0.871000	0.50021	1.161000	0.31773	0.462000	0.27095	0.533000	0.62120	ACT	.	.		0.448	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		C	46320825	T	C	46320825	3	2	115	1	0	0	0	0	1	0	0	0	14192	1725	60	2	1752	2	SFRS2IP	12	46320825	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	19509809	46320825	87531070	293	19832										
LASS5	91012	hgsc.bcm.edu	37	chr12	50536965	50536965	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccagctgctttgacaggcccTccagccttttcttatcagga	8	14	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:50536965T>C	ENST00000317551.6	-	3	450	c.326A>G	c.(325-327)gAg>gGg	p.E109G	CERS5_ENST00000422340.2_Missense_Mutation_p.E51G	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	109					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										TGACAGGCCCTCCAGCCTTTT	0.483																																					p.E109G		Atlas-SNP	.											.	.	.	.	0			c.A326G						.						128	134	132					12																	50536965		2203	4300	6503	SO:0001583	missense	91012	exon3			AGGCCCTCCAGCC		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"Homeoboxes / CERS class"	23749	protein-coding gene	gene with protein product		615335	"LAG1 longevity assurance homolog 5 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 5"	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.326A>G	chr12.hg19:g.50536965T>C	ENSP00000325485:p.Glu109Gly	94.0	0.0		130.0	6.0	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	hg19	CCDS8801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.60|16.60	3.169789|3.169789	0.57584|0.57584	.|.	.|.	ENSG00000139624|ENSG00000139624	ENST00000551005;ENST00000317551;ENST00000422340|ENST00000547800	D;D;D|.	0.96913|.	-4.17;-4.17;-4.17|.	4.53|4.53	4.53|4.53	0.55603|0.55603	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);|.	0.163360|.	0.52532|.	D|.	0.000061|.	T|T	0.75715|0.75715	0.3887|0.3887	M|M	0.80847|0.80847	2.515|2.515	0.53688|0.53688	D|D	0.999976|0.999976	D;B;B|.	0.53885|.	0.963;0.049;0.03|.	P;B;B|.	0.62298|.	0.9;0.051;0.033|.	T|T	0.78028|0.78028	-0.2364|-0.2364	10|5	0.30078|.	T|.	0.28|.	-2.7838|-2.7838	14.3303|14.3303	0.66550|0.66550	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	51;109;28|.	B4DV54;Q8N5B7;F8W0U5|.	.;CERS5_HUMAN;.|.	G|G	28;109;51|44	ENSP00000447556:E28G;ENSP00000325485:E109G;ENSP00000389050:E51G|.	ENSP00000325485:E109G|.	E|R	-|-	2|1	0|2	CERS5|CERS5	48823232|48823232	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	6.035000|6.035000	0.70940|0.70940	2.037000|2.037000	0.60232|0.60232	0.533000|0.533000	0.62120|0.62120	GAG|AGG	.	.		0.483	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190		C	50536965	T	C	50536965	3	2	115	1	0	0	0	0	1	0	0	0	8651	1551	54	2	884	2	LASS5	12	50536965	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4216140	50536965	83314930	294	19833										
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51856125	51856125	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cgtagcatataaggcaaaagAgcgagatgatctcctggcgg	13	8	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:51856125A>G	ENST00000453097.2	+	10	1350	c.1133A>G	c.(1132-1134)gAg>gGg	p.E378G	SLC4A8_ENST00000514353.3_Missense_Mutation_p.E325G|SLC4A8_ENST00000358657.3_Missense_Mutation_p.E405G|SLC4A8_ENST00000535225.2_Missense_Mutation_p.E325G|SLC4A8_ENST00000394856.1_Missense_Mutation_p.E325G	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		AAGGCAAAAGAGCGAGATGAT	0.448																																					p.E378G		Atlas-SNP	.											.	SLC4A8	292	.	0			c.A1133G						.						119	117	118					12																	51856125		2203	4300	6503	SO:0001583	missense	9498	exon10			CAAAAGAGCGAGA	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"Solute carriers"	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1133A>G	chr12.hg19:g.51856125A>G	ENSP00000405812:p.Glu378Gly	92.0	0.0		102.0	5.0	NM_001039960		Missense_Mutation	SNP	ENST00000453097.2	hg19	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.799840	0.70567	.	.	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000551071	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	5.02	5.02	0.67125	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.142197	0.64402	D	0.000009	T	0.68146	0.2969	N	0.20807	0.61	0.58432	D	0.999992	P;B;B;B;B;B	0.36354	0.549;0.004;0.364;0.015;0.021;0.04	B;B;B;B;B;B	0.39935	0.13;0.005;0.209;0.314;0.149;0.149	T	0.71351	-0.4619	10	0.49607	T	0.09	.	14.4078	0.67093	1.0:0.0:0.0:0.0	.	325;405;325;378;378;378	E7EML0;Q2Y0W8-2;F5GZ31;Q2Y0W8;Q2Y0W8-3;Q2Y0W8-6	.;.;.;S4A8_HUMAN;.;.	G	325;405;378;325;378;325;325	ENSP00000441520:E325G;ENSP00000351483:E405G;ENSP00000405812:E378G;ENSP00000378325:E325G;ENSP00000442561:E325G	ENSP00000315789:E378G	E	+	2	0	SLC4A8	50142392	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	9.283000	0.95860	2.185000	0.69588	0.533000	0.62120	GAG	.	.		0.448	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		G	51856125	A	G	51856125	3	3	115	1	0	0	0	0	1	0	0	0	14674	304	11	2	1171	2	SLC4A8	12	51856125	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1319160	51856125	81995770	295	19834										
SP1	6667	hgsc.bcm.edu	37	chr12	53800445	53800445	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gacacagcaggtggagaggaAggagaaaacagcccagatgc	15	8	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:53800445A>G	ENST00000327443.4	+	4	1850	c.1752A>G	c.(1750-1752)gaA>gaG	p.E584E	SP1_ENST00000426431.2_Silent_p.E577E	NM_001251825.1|NM_138473.2	NP_001238754.1|NP_612482.2	P08047	SP1_HUMAN	Sp1 transcription factor	584	Transactivation domain C (highly charged).				cellular lipid metabolic process (GO:0044255)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|gene expression (GO:0010467)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|ossification (GO:0001503)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	bHLH transcription factor binding (GO:0043425)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|histone deacetylase binding (GO:0042826)|HMG box domain binding (GO:0071837)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.00527)		GTGGAGAGGAAGGAGAAAACA	0.547																																					p.E584E		Atlas-SNP	.											.	SP1	57	.	0			c.A1752G						.						95	93	93					12																	53800445		2203	4300	6503	SO:0001819	synonymous_variant	6667	exon4			AGAGGAAGGAGAA	J03133	CCDS8857.1, CCDS44898.1	12q13.1	2013-01-08						"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11205	protein-coding gene	gene with protein product	"specificity protein 1"	189906				1662663	Standard	NM_003109		Approved		uc001scw.3	P08047	OTTHUMG00000170047	ENST00000327443.4:c.1752A>G	chr12.hg19:g.53800445A>G		75.0	0.0		86.0	4.0	NM_138473	E4Z9M7|G5E9M8|Q86TN8|Q9H3Q5|Q9NR51|Q9NY21|Q9NYE7	Silent	SNP	ENST00000327443.4	hg19	CCDS8857.1																																																																																			.	.		0.547	SP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407044.1			G	53800445	A	G	53800445	2	3	115	1	0	0	0	0	0	0	0	1	14974	69	3	2		2	SP1	12	53800445	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1944320	53800445	80051450	296	19835										
AMHR2	269	hgsc.bcm.edu	37	chr12	53823319	53823319	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gatggatcgtgtgccattggAgacctgggccttgccttggt	15	9	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:53823319A>G	ENST00000257863.4	+	8	1130	c.1050A>G	c.(1048-1050)ggA>ggG	p.G350G	AMHR2_ENST00000379791.3_Silent_p.G350G|AMHR2_ENST00000550311.1_Silent_p.G350G	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	350	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	GTGCCATTGGAGACCTGGGCC	0.577																																					p.G350G		Atlas-SNP	.											.	AMHR2	61	.	0			c.A1050G						.						106	95	99					12																	53823319		2203	4300	6503	SO:0001819	synonymous_variant	269	exon8			CATTGGAGACCTG	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"Muellerian inhibiting substance type II receptor"	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.1050A>G	chr12.hg19:g.53823319A>G		132.0	0.0		138.0	7.0	NM_020547	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Silent	SNP	ENST00000257863.4	hg19	CCDS8858.1																																																																																			.	.		0.577	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547		G	53823319	A	G	53823319	2	3	115	1	0	0	0	0	0	0	0	1	573	291	11	2		2	AMHR2	12	53823319	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	22874	53823319	80028576	297	19836										
OR6C1	390321	hgsc.bcm.edu	37	chr12	55714409	55714409	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaaccatacagaaataacagAgtttattcttctgggattaa	6	6	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:55714409A>G	ENST00000379668.2	+	1	64	c.26A>G	c.(25-27)gAg>gGg	p.E9G		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						GAAATAACAGAGTTTATTCTT	0.393																																					p.E9G		Atlas-SNP	.											.	OR6C1	58	.	0			c.A26G						.						62	63	63					12																	55714409		2203	4300	6503	SO:0001583	missense	390321	exon1			TAACAGAGTTTAT	AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"GPCR / Class A : Olfactory receptors"	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.26A>G	chr12.hg19:g.55714409A>G	ENSP00000368990:p.Glu9Gly	86.0	0.0		74.0	4.0	NM_001005182	B2RNM0	Missense_Mutation	SNP	ENST00000379668.2	hg19	CCDS31818.1	.	.	.	.	.	.	.	.	.	.	a	11.67	1.708587	0.30322	.	.	ENSG00000205330	ENST00000379668	T	0.11385	2.78	5.21	4.01	0.46588	.	0.782577	0.11725	N	0.535522	T	0.12092	0.0294	L	0.57130	1.785	0.27404	N	0.954758	B	0.13145	0.007	B	0.19946	0.027	T	0.09885	-1.0654	10	0.52906	T	0.07	.	5.3683	0.16125	0.7615:0.0:0.083:0.1556	.	9	Q96RD1	OR6C1_HUMAN	G	9	ENSP00000368990:E9G	ENSP00000368990:E9G	E	+	2	0	OR6C1	54000676	0.006000	0.16342	0.995000	0.50966	0.775000	0.43874	0.091000	0.15046	2.185000	0.69588	0.374000	0.22700	GAG	.	.		0.393	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182		G	55714409	A	G	55714409	3	3	115	1	0	0	0	0	1	0	0	0	11199	304	11	2	28	2	OR6C1	12	55714409	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1891090	55714409	78137486	298	19837										
DNAJC14	85406	hgsc.bcm.edu	37	chr12	56222422	56222422	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gctccatacaaccctctttcTccggggtgcttctgggccat	9	15	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:56222422T>C	ENST00000357606.3	-	3	310	c.21A>G	c.(19-21)ggA>ggG	p.G7G	DNAJC14_ENST00000317269.3_Silent_p.G7G|TMEM198B_ENST00000478241.1_RNA|DNAJC14_ENST00000317287.5_Silent_p.G7G|RP11-762I7.5_ENST00000546837.1_5'Flank			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14	7					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						ACCCTCTTTCTCCGGGGTGCT	0.562																																					p.G7G		Atlas-SNP	.											.	DNAJC14	52	.	0			c.A21G						.						52	52	52					12																	56222422		2203	4300	6503	SO:0001819	synonymous_variant	85406	exon2			TCTTTCTCCGGGG	AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"Heat shock proteins / DNAJ (HSP40)"	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3		ENST00000357606.3:c.21A>G	chr12.hg19:g.56222422T>C		104.0	0.0		91.0	4.0	NM_032364	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	Silent	SNP	ENST00000357606.3	hg19	CCDS8894.1																																																																																			.	.		0.562	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409095.1	NM_032364		C	56222422	T	C	56222422	2	2	115	1	0	0	0	0	0	0	0	1	4635	1538	54	2		2	DNAJC14	12	56222422	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	508013	56222422	77629473	299	19838										
PRIM1	5557	hgsc.bcm.edu	37	chr12	57135246	57135246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aggatgaacactaaaagggcTcttcagtagatgattgattc	10	6	2	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:57135246T>C	ENST00000338193.6	-	9	991	c.955A>G	c.(955-957)Agc>Ggc	p.S319G		NM_000946.2	NP_000937.1	P49642	PRI1_HUMAN	primase, DNA, polypeptide 1 (49kDa)	319					DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			kidney(1)|lung(6)|prostate(1)	8						CTAAAAGGGCTCTTCAGTAGA	0.403																																					p.S319G		Atlas-SNP	.											.	PRIM1	22	.	0			c.A955G						.						71	64	66					12																	57135246		1836	4106	5942	SO:0001583	missense	5557	exon9			AAGGGCTCTTCAG	BC005266	CCDS44926.1	12q13.3	2007-06-19	2007-06-19			ENSG00000198056			9369	protein-coding gene	gene with protein product		176635				8530050	Standard	NM_000946		Approved		uc001smd.3	P49642	OTTHUMG00000170034	ENST00000338193.6:c.955A>G	chr12.hg19:g.57135246T>C	ENSP00000350491:p.Ser319Gly	89.0	0.0		103.0	6.0	NM_000946		Missense_Mutation	SNP	ENST00000338193.6	hg19	CCDS44926.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.424566	0.83667	.	.	ENSG00000198056	ENST00000537418;ENST00000338193;ENST00000549549;ENST00000550770	T;T;T	0.49432	0.78;0.78;0.78	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.65015	0.2651	M	0.81682	2.555	0.80722	D	1	D	0.54207	0.965	P	0.59643	0.861	T	0.64922	-0.6293	10	0.28530	T	0.3	-12.0557	14.235	0.65919	0.0:0.0:0.0:1.0	.	319	P49642	PRI1_HUMAN	G	326;319;100;322	ENSP00000350491:S319G;ENSP00000449806:S100G;ENSP00000450185:S322G	ENSP00000350491:S319G	S	-	1	0	PRIM1	55421513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.560000	0.82277	2.148000	0.66965	0.533000	0.62120	AGC	.	.		0.403	PRIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406956.1	NM_000946		C	57135246	T	C	57135246	3	2	115	1	0	0	0	0	1	0	0	0	12502	1551	54	2	327	2	PRIM1	12	57135246	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	912824	57135246	76716649	300	19839										
MYO1A	4640	hgsc.bcm.edu	37	chr12	57437910	57437910	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgtacagccctgaagctggAggcgtcgtccatgccatcca	11	14	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:57437910A>G	ENST00000442789.2	-	10	1011	c.724T>C	c.(724-726)Tcc>Ccc	p.S242P	MYO1A_ENST00000544473.1_Missense_Mutation_p.S80P|MYO1A_ENST00000300119.3_Missense_Mutation_p.S242P	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	242	Myosin motor.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						CTGAAGCTGGAGGCGTCGTCC	0.562																																					p.S242P		Atlas-SNP	.											.	MYO1A	122	.	0			c.T724C						.						104	94	97					12																	57437910		2203	4300	6503	SO:0001583	missense	4640	exon9			AGCTGGAGGCGTC	L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.724T>C	chr12.hg19:g.57437910A>G	ENSP00000393392:p.Ser242Pro	157.0	0.0		202.0	9.0	NM_005379	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	hg19	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.671256	0.47781	.	.	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000544473	T;T;T	0.72394	-0.65;-0.65;-0.65	4.81	0.8	0.18672	Myosin head, motor domain (2);	0.269795	0.35013	N	0.003502	T	0.65186	0.2667	L	0.52823	1.66	0.36184	D	0.849593	B	0.30937	0.301	B	0.36418	0.224	T	0.68561	-0.5376	10	0.56958	D	0.05	.	10.5198	0.44912	0.454:0.546:0.0:0.0	.	242	Q9UBC5	MYO1A_HUMAN	P	242;242;80	ENSP00000300119:S242P;ENSP00000393392:S242P;ENSP00000440514:S80P	ENSP00000300119:S242P	S	-	1	0	MYO1A	55724177	0.471000	0.25862	0.738000	0.30950	0.831000	0.47069	1.058000	0.30504	0.385000	0.24970	0.460000	0.39030	TCC	.	.		0.562	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		G	57437910	A	G	57437910	3	3	115	1	0	0	0	0	1	0	0	0	10077	304	11	2	2487	2	MYO1A	12	57437910	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	302664	57437910	76413985	301	19840										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58123479	58123479	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgttgtcaattttttcctccTctgcttcttcaccatgggag	7	11	4	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:58123479T>C	ENST00000547588.1	-	13	2499	c.2500A>G	c.(2500-2502)Agg>Ggg	p.R834G	AGAP2_ENST00000257897.3_Missense_Mutation_p.R498G	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	834	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						TTTTTCCTCCTCTGCTTCTTC	0.577																																					p.R834G		Atlas-SNP	.											.	AGAP2	167	.	0			c.A2500G						.						150	148	148					12																	58123479		2203	4300	6503	SO:0001583	missense	116986	exon13			TCCTCCTCTGCTT	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.2500A>G	chr12.hg19:g.58123479T>C	ENSP00000449241:p.Arg834Gly	100.0	0.0		108.0	7.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	hg19	CCDS44932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.29|17.29	3.352148|3.352148	0.61183|0.61183	.|.	.|.	ENSG00000135439|ENSG00000135439	ENST00000328568|ENST00000257897;ENST00000547588	.|T;T	.|0.35973	.|1.39;1.28	4.39|4.39	4.39|4.39	0.52855|0.52855	.|Pleckstrin homology domain (3);	.|0.359275	.|0.30911	.|N	.|0.008631	T|T	0.54431|0.54431	0.1858|0.1858	L|L	0.59436|0.59436	1.845|1.845	0.47905|0.47905	D|D	0.999545|0.999545	.|D;P;D	.|0.76494	.|0.999;0.917;0.987	.|D;P;P	.|0.78314	.|0.991;0.774;0.9	T|T	0.57711|0.57711	-0.7764|-0.7764	5|10	.|0.66056	.|D	.|0.02	.|.	13.0225|13.0225	0.58796|0.58796	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|498;834;834	.|Q99490-2;F8VVT9;Q99490	.|.;.;AGAP2_HUMAN	G|G	697|498;834	.|ENSP00000257897:R498G;ENSP00000449241:R834G	.|ENSP00000257897:R498G	E|R	-|-	2|1	0|2	AGAP2|AGAP2	56409746|56409746	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.765000|0.765000	0.43378|0.43378	0.647000|0.647000	0.24812|0.24812	1.978000|1.978000	0.57642|0.57642	0.379000|0.379000	0.24179|0.24179	GAG|AGG	.	.		0.577	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		C	58123479	T	C	58123479	3	2	115	1	0	0	0	0	1	0	0	0	368	1550	54	2	1106	2	AGAP2	12	58123479	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	685569	58123479	75728416	302	19841										
C12orf56	115749	hgsc.bcm.edu	37	chr12	64664453	64664453	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agctgaaatgaagctgaaagAcccctcaccacttgtttcac	7	12	2	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:64664453A>G	ENST00000543942.2	-	12	2252	c.1626T>C	c.(1624-1626)ggT>ggC	p.G542G	C12orf56_ENST00000536975.1_5'UTR|RPS11P6_ENST00000535684.1_RNA|C12orf56_ENST00000333722.5_Silent_p.G382G	NM_001170633.1	NP_001164104.1	Q8IXR9	CL056_HUMAN	chromosome 12 open reading frame 56	542										NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)	15			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)		AAGCTGAAAGACCCCTCACCA	0.453																																					p.G542G		Atlas-SNP	.											.	C12orf56	42	.	0			c.T1626C						.						84	78	80					12																	64664453		1888	4128	6016	SO:0001819	synonymous_variant	115749	exon12			TGAAAGACCCCTC		CCDS44935.1, CCDS61182.1	12q14.2	2012-08-15			ENSG00000185306	ENSG00000185306			26967	protein-coding gene	gene with protein product							Standard	NM_001099676		Approved		uc021qzu.1	Q8IXR9	OTTHUMG00000168782	ENST00000543942.2:c.1626T>C	chr12.hg19:g.64664453A>G		72.0	0.0		99.0	4.0	NM_001170633		Silent	SNP	ENST00000543942.2	hg19																																																																																				.	.		0.453	C12orf56-008	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000401058.2	NM_001099676		G	64664453	A	G	64664453	2	3	115	1	0	0	0	0	0	0	0	1	1702	262	10	2		2	C12orf56	12	64664453	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6540974	64664453	69187442	303	19842										
ATP2B1	490	hgsc.bcm.edu	37	chr12	90015351	90015351	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tttttgatgtataagcacaaTtcacagaaattcctgttaca	5	7	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:90015351T>C	ENST00000428670.3	-	10	2018	c.1562A>G	c.(1561-1563)aAt>aGt	p.N521S	ATP2B1_ENST00000359142.3_Missense_Mutation_p.N521S|ATP2B1_ENST00000348959.3_Missense_Mutation_p.N521S|ATP2B1_ENST00000393164.2_Missense_Mutation_p.N264S|ATP2B1_ENST00000261173.2_Missense_Mutation_p.N521S			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	521					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						ATAAGCACAATTCACAGAAAT	0.269																																					p.N521S		Atlas-SNP	.											.	ATP2B1	191	.	0			c.A1562G						.						61	62	61					12																	90015351		2201	4295	6496	SO:0001583	missense	490	exon9			GCACAATTCACAG	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.1562A>G	chr12.hg19:g.90015351T>C	ENSP00000392043:p.Asn521Ser	76.0	0.0		72.0	4.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	hg19	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.386860	0.82902	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	D	0.85504	0.5712	M	0.84683	2.71	0.80722	D	1	D;D;P	0.71674	0.998;0.992;0.9	D;P;P	0.76071	0.987;0.85;0.888	D	0.87143	0.2204	9	.	.	.	-13.7261	16.0337	0.80603	0.0:0.0:0.0:1.0	.	521;521;521	P20020-3;P20020-2;P20020-6	.;.;.	S	521;521;521;521;264	ENSP00000261173:N521S;ENSP00000343599:N521S;ENSP00000352054:N521S;ENSP00000392043:N521S;ENSP00000376869:N264S	.	N	-	2	0	ATP2B1	88539482	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.188000	0.69820	0.460000	0.39030	AAT	.	.		0.269	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		C	90015351	T	C	90015351	3	2	115	1	0	0	0	0	1	0	0	0	1139	1493	52	2	2306	2	ATP2B1	12	90015351	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	25350898	90015351	43836544	304	19843										
FGD6	55785	hgsc.bcm.edu	37	chr12	95603722	95603722	+	Frame_Shift_Del	DEL	A	A	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atagatacagtacatcttatAaaaccggtcccttcgtccac							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:95603722delA	ENST00000343958.4	-	2	1561	c.1338delT	c.(1336-1338)tttfs	p.F446fs	FGD6_ENST00000549499.1_Frame_Shift_Del_p.F446fs|FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000546711.1_Frame_Shift_Del_p.F446fs	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	446					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						TACATCTTATAAAACCGGTCC	0.423																																					p.I447X		Atlas-INDEL	.											.	FGD6	127	.	0			c.1339delA						.						109	107	108					12																	95603722		2203	4300	6503	SO:0001589	frameshift_variant	55785	exon2			.	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.1338delT	chr12.hg19:g.95603722delA	ENSP00000344446:p.Phe446fs	103.0	0.0		163.0	11.0	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Frame_Shift_Del	DEL	ENST00000343958.4	hg19	CCDS31878.1																																																																																			.	.		0.423	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		-	95603722	A	-	95603722	7	5	115	1	0	1	0	1	0	0	0	0	5845	359	13	0	3034	0	FGD6	12	95603722	Frame_Shift_Del	DEL	A	TCGA-DD-A3A1-01A-11D-A20W-10	5588371	95603722	38248173	305	19844										
ALDH1L2	160428	hgsc.bcm.edu	37	chr12	105424187	105424187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtcttccacatctgtgaacaCggtcggctccatgaaaaagc	9	12	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:105424187C>T	ENST00000258494.9	-	21	2571	c.2431G>A	c.(2431-2433)Gtg>Atg	p.V811M	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	811	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.V811M(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						TCTGTGAACACGGTCGGCTCC	0.373																																					p.V811M		Atlas-SNP	.											ALDH1L2,rectum,carcinoma,0,1	ALDH1L2	71	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2431A						.						87	83	84					12																	105424187		2203	4300	6503	SO:0001583	missense	160428	exon21			TGAACACGGTCGG	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2431G>A	chr12.hg19:g.105424187C>T	ENSP00000258494:p.Val811Met	53.0	0.0		84.0	4.0	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	hg19	CCDS31891.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.7|24.7	4.560897|4.560897	0.86335|0.86335	.|.	.|.	ENSG00000136010|ENSG00000136010	ENST00000548418|ENST00000258494	.|D	.|0.82081	.|-1.57	6.06|6.06	6.06|6.06	0.98353|0.98353	.|Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93383|0.93383	0.7890|0.7890	H|H	0.95645|0.95645	3.7|3.7	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.68353	.|0.957	D|D	0.94563|0.94563	0.7764|0.7764	5|10	.|0.87932	.|D	.|0	.|.	14.7322|14.7322	0.69391|0.69391	0.0:0.9314:0.0:0.0686|0.0:0.9314:0.0:0.0686	.|.	.|811	.|Q3SY69	.|AL1L2_HUMAN	H|M	63|811	.|ENSP00000258494:V811M	.|ENSP00000258494:V811M	R|V	-|-	2|1	0|0	ALDH1L2|ALDH1L2	103948317|103948317	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.849000|0.849000	0.48306|0.48306	5.970000|5.970000	0.70431|0.70431	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	CGT|GTG	.	.		0.373	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		T	105424187	C	T	105424187	3	4	115	1	0	0	0	0	1	0	0	0	495	536	19	1	352	1	ALDH1L2	12	105424187	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	9820465	105424187	28427708	306	19845										
MYO1H	283446	hgsc.bcm.edu	37	chr12	109834370	109834370	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cccgtgacagactgctgttcTccaacccagtgctggaggta	11	13	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:109834370T>C	ENST00000431443.2	+	3	424	c.424T>C	c.(424-426)Tcc>Ccc	p.S142P	MYO1H_ENST00000310903.5_Missense_Mutation_p.S142P	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	142	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						ACTGCTGTTCTCCAACCCAGT	0.522																																					p.S142P		Atlas-SNP	.											.	MYO1H	98	.	0			c.T424C						.						67	65	65					12																	109834370		1938	4150	6088	SO:0001583	missense	283446	exon3			CTGTTCTCCAACC		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.424T>C	chr12.hg19:g.109834370T>C	ENSP00000444076:p.Ser142Pro	58.0	0.0		93.0	4.0	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	hg19		.	.	.	.	.	.	.	.	.	.	T	24.0	4.482103	0.84747	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	T;T	0.73469	-0.75;-0.75	4.8	4.8	0.61643	.	.	.	.	.	D	0.90964	0.7159	H	0.98426	4.23	0.47621	D	0.999471	D	0.76494	0.999	D	0.68943	0.961	D	0.94213	0.7460	9	0.87932	D	0	.	14.2704	0.66149	0.0:0.0:0.0:1.0	.	142	F5H3C6	.	P	142	ENSP00000439182:S142P;ENSP00000444076:S142P	ENSP00000439182:S142P	S	+	1	0	MYO1H	108318753	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.184000	0.72008	2.112000	0.64535	0.524000	0.50904	TCC	.	.		0.522	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		C	109834370	T	C	109834370	3	2	115	1	0	0	0	0	1	0	0	0	10084	1551	54	2	434	2	MYO1H	12	109834370	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4410183	109834370	24017525	307	19846										
CLIP1	6249	hgsc.bcm.edu	37	chr12	122826186	122826186	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gctcagctacttcctgtactCtcaatgctaggtctttctcc	6	14	4	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:122826186C>T	ENST00000540338.1	-	10	1606	c.1565G>A	c.(1564-1566)aGa>aAa	p.R522K	CLIP1_ENST00000537178.1_Missense_Mutation_p.R476K|CLIP1_ENST00000358808.2_Missense_Mutation_p.R511K|CLIP1_ENST00000302528.7_Missense_Mutation_p.R511K|CLIP1_ENST00000361654.4_Missense_Mutation_p.R476K|CLIP1_ENST00000545889.1_Missense_Mutation_p.R212K			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	522					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		TTCCTGTACTCTCAATGCTAG	0.418																																					p.R522K		Atlas-SNP	.											.	CLIP1	126	.	0			c.G1565A						.						133	135	134					12																	122826186		2203	4300	6503	SO:0001583	missense	6249	exon11			TGTACTCTCAATG		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"restin"	179838	"restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.1565G>A	chr12.hg19:g.122826186C>T	ENSP00000439093:p.Arg522Lys	69.0	0.0		66.0	4.0	NM_001247997	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	hg19	CCDS58285.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.896467	0.33442	.	.	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304	T;T;T;T;T;T	0.61859	2.64;0.63;0.63;0.64;0.54;0.07	5.01	4.12	0.48240	.	0.177541	0.49916	N	0.000124	T	0.45074	0.1324	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.30584	0.0;0.286;0.184;0.052	B;B;B;B	0.31946	0.004;0.138;0.079;0.047	T	0.26258	-1.0108	10	0.16420	T	0.52	-7.4457	10.1323	0.42687	0.0:0.8465:0.0:0.1535	.	212;476;511;522	F5H0N7;P30622-2;P30622-1;P30622	.;.;.;CLIP1_HUMAN	K	212;511;511;356;476;522;445	ENSP00000438743:R212K;ENSP00000303585:R511K;ENSP00000351665:R511K;ENSP00000445531:R476K;ENSP00000439093:R522K;ENSP00000437786:R445K	ENSP00000303585:R511K	R	-	2	0	CLIP1	121392139	0.609000	0.26975	0.070000	0.20053	0.996000	0.88848	3.046000	0.49846	1.239000	0.43787	0.655000	0.94253	AGA	.	.		0.418	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956		T	122826186	C	T	122826186	3	4	115	1	0	0	0	0	1	0	0	0	3534	913	32	3	2815	3	CLIP1	12	122826186	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	12991816	122826186	11025709	308	19847										
ZCCHC8	55596	hgsc.bcm.edu	37	chr12	122958449	122958449	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcatccagcgtctgcttttcAgatgtttttccctccgggac	8	13	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:122958449A>G	ENST00000336229.4	-	14	1849	c.1719T>C	c.(1717-1719)tcT>tcC	p.S573S	ZCCHC8_ENST00000543897.1_Silent_p.S335S|ZCCHC8_ENST00000536306.1_Silent_p.S335S|ZCCHC8_ENST00000538116.1_Silent_p.S184S	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	573					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		TCTGCTTTTCAGATGTTTTTC	0.493																																					p.S573S		Atlas-SNP	.											.	ZCCHC8	56	.	0			c.T1719C						.						214	208	210					12																	122958449		1962	4166	6128	SO:0001819	synonymous_variant	55596	exon14			CTTTTCAGATGTT	BC017704		12q24.31	2014-04-14				ENSG00000033030		"Zinc fingers, CCHC domain containing"	25265	protein-coding gene	gene with protein product						12477932	Standard	XM_005253581		Approved	DKFZp434E2220	uc001ucn.3	Q6NZY4		ENST00000336229.4:c.1719T>C	chr12.hg19:g.122958449A>G		60.0	0.0		90.0	4.0	NM_017612	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Silent	SNP	ENST00000336229.4	hg19																																																																																				.	.		0.493	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		G	122958449	A	G	122958449	2	3	115	1	0	0	0	0	0	0	0	1	17609	175	7	2		2	ZCCHC8	12	122958449	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	132263	122958449	10893446	309	19848										
RILPL1	353116	hgsc.bcm.edu	37	chr12	123983122	123983122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cctccccattctggctgtgcTccccctgcagcctctctcgc	7	21	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:123983122T>C	ENST00000376874.4	-	4	1005	c.770A>G	c.(769-771)gAg>gGg	p.E257G	RILPL1_ENST00000340724.6_Missense_Mutation_p.E105G	NM_178314.3	NP_847884.2	Q5EBL4	RIPL1_HUMAN	Rab interacting lysosomal protein-like 1	257					epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)|regulation of neuron death (GO:1901214)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)		CTGGCTGTGCTCCCCCTGCAG	0.632																																					p.E257G		Atlas-SNP	.											.	RILPL1	23	.	0			c.A770G						.						42	47	46					12																	123983122		2081	4212	6293	SO:0001583	missense	353116	exon4			CTGTGCTCCCCCT	AK097550	CCDS45006.1	12q24.31	2007-11-27			ENSG00000188026	ENSG00000188026			26814	protein-coding gene	gene with protein product		614092				14668488	Standard	NM_178314		Approved	FLJ39378	uc001ufe.2	Q5EBL4	OTTHUMG00000168686	ENST00000376874.4:c.770A>G	chr12.hg19:g.123983122T>C	ENSP00000366070:p.Glu257Gly	106.0	0.0		179.0	8.0	NM_178314	Q66K36|Q8N1M0	Missense_Mutation	SNP	ENST00000376874.4	hg19	CCDS45006.1	.	.	.	.	.	.	.	.	.	.	T	13.90	2.374324	0.42105	.	.	ENSG00000188026	ENST00000376874;ENST00000340724	T;T	0.23147	1.92;1.92	5.22	1.45	0.22620	.	1.363090	0.04323	N	0.351132	T	0.23965	0.0580	L	0.47716	1.5	0.80722	D	1	B;B;B	0.24258	0.004;0.1;0.0	B;B;B	0.24541	0.006;0.054;0.001	T	0.04708	-1.0932	10	0.25751	T	0.34	-2.2299	6.756	0.23514	0.0:0.1365:0.128:0.7356	.	233;257;106	Q5EBL4-2;Q5EBL4;Q5EBL4-3	.;RIPL1_HUMAN;.	G	257;105	ENSP00000366070:E257G;ENSP00000345874:E105G	ENSP00000345874:E105G	E	-	2	0	RILPL1	122549075	0.997000	0.39634	0.054000	0.19295	0.895000	0.52256	2.778000	0.47726	0.062000	0.16340	0.454000	0.30748	GAG	.	.		0.632	RILPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400595.1	NM_178314		C	123983122	T	C	123983122	3	2	115	1	0	0	0	0	1	0	0	0	13376	1551	54	2	457	2	RILPL1	12	123983122	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1024673	123983122	9868773	310	19849										
POLE	5426	hgsc.bcm.edu	37	chr12	133219191	133219191	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gccagtccaggaccccatagTtgatcttgtcagccacacag	9	14	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr12:133219191T>C	ENST00000320574.5	-	37	4896	c.4853A>G	c.(4852-4854)aAc>aGc	p.N1618S	POLE_ENST00000434528.3_5'Flank|POLE_ENST00000535270.1_Missense_Mutation_p.N1591S	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1618					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GACCCCATAGTTGATCTTGTC	0.582								DNA polymerases (catalytic subunits)																													p.N1618S		Atlas-SNP	.											.	POLE	416	.	0			c.A4853G						.						58	59	59					12																	133219191		2203	4300	6503	SO:0001583	missense	5426	exon37			CCATAGTTGATCT		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.4853A>G	chr12.hg19:g.133219191T>C	ENSP00000322570:p.Asn1618Ser	77.0	0.0		140.0	40.0	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	hg19	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	T	2.489	-0.317887	0.05386	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270	T;T;T	0.20738	2.05;2.05;2.05	5.6	2.78	0.32641	DNA polymerase epsilon, catalytic subunit A, C-terminal (1);	0.108697	0.85682	N	0.000000	T	0.06050	0.0157	N	0.02011	-0.69	0.22521	N	0.999026	B	0.02656	0.0	B	0.06405	0.002	T	0.41034	-0.9531	10	0.02654	T	1	.	8.9578	0.35829	0.0:0.6997:0.0:0.3003	.	1618	Q07864	DPOE1_HUMAN	S	1618;1629;1591	ENSP00000322570:N1618S;ENSP00000406383:N1629S;ENSP00000445753:N1591S	ENSP00000322570:N1618S	N	-	2	0	POLE	131729264	0.999000	0.42202	1.000000	0.80357	0.933000	0.57130	0.721000	0.25911	0.714000	0.32081	-0.248000	0.11899	AAC	.	.		0.582	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		C	133219191	T	C	133219191	3	2	115	1	0	0	0	0	1	0	0	0	12205	1725	60	2	2059	2	POLE	12	133219191	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	9236069	133219191	632704	311	19850										
PARP4	143	hgsc.bcm.edu	37	chr13	25017789	25017789	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tacaatgaaaagaacaaaccTcatgactggtttcattttcg	6	8	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:25017789T>C	ENST00000381989.3	-	28	3551	c.3446A>G	c.(3445-3447)gAg>gGg	p.E1149G		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1149					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		AGAACAAACCTCATGACTGGT	0.398																																					p.E1149G		Atlas-SNP	.											.	PARP4	142	.	0			c.A3446G						.						126	137	133					13																	25017789		2203	4300	6503	SO:0001630	splice_region_variant	143	exon28			CAAACCTCATGAC	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3447+1A>G	chr13.hg19:g.25017789T>C		64.0	0.0		86.0	5.0	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	t	14.92	2.680445	0.47886	.	.	ENSG00000102699	ENST00000381989	T	0.65916	-0.18	4.66	4.66	0.58398	.	0.136282	0.47852	D	0.000216	T	0.65048	0.2654	L	0.48642	1.525	0.45962	D	0.998787	D	0.54047	0.964	P	0.52672	0.706	T	0.68277	-0.5451	10	0.62326	D	0.03	-13.432	12.1286	0.53930	0.0:0.0:0.0:1.0	.	1149	Q9UKK3	PARP4_HUMAN	G	1149	ENSP00000371419:E1149G	ENSP00000371419:E1149G	E	-	2	0	PARP4	23915789	1.000000	0.71417	0.936000	0.37596	0.134000	0.20937	6.219000	0.72231	1.970000	0.57323	0.529000	0.55759	GAG	.	.		0.398	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	Missense_Mutation	C	25017789	T	C	25017789	5	2	115	1	0	0	0	0	0	0	1	0	11472	1565	54	2	1756	2	PARP4	13	25017789	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10		25017789	90152089	312	19851										
ATP12A	479	hgsc.bcm.edu	37	chr13	25274939	25274939	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tccagaaacctactcatttgAcatagacgctatgaactttc	5	11	1	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:25274939A>G	ENST00000381946.3	+	13	1927	c.1760A>G	c.(1759-1761)gAc>gGc	p.D587G	RNY1P7_ENST00000384743.1_RNA|ATP12A_ENST00000218548.6_Missense_Mutation_p.D593G			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	587					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TACTCATTTGACATAGACGCT	0.458																																					p.D593G	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											ATP12A,colon,carcinoma,0,3	ATP12A	172	.	0			c.A1778G						.						137	125	129					13																	25274939		2203	4300	6503	SO:0001583	missense	479	exon13			CATTTGACATAGA	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1760A>G	chr13.hg19:g.25274939A>G	ENSP00000371372:p.Asp587Gly	134.0	0.0		140.0	60.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	A	16.13	3.035648	0.54896	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.80909	-1.43;-1.43	6.17	5.0	0.66597	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.063239	0.64402	D	0.000005	D	0.84070	0.5391	L	0.47716	1.5	0.58432	D	0.999999	D;D	0.67145	0.996;0.996	D;P	0.63597	0.916;0.903	D	0.84454	0.0590	10	0.66056	D	0.02	.	10.5257	0.44948	0.9246:0.0:0.0754:0.0	.	593;587	P54707-2;P54707	.;AT12A_HUMAN	G	593;587	ENSP00000218548:D593G;ENSP00000371372:D587G	ENSP00000218548:D593G	D	+	2	0	ATP12A	24172939	1.000000	0.71417	0.831000	0.32960	0.010000	0.07245	9.228000	0.95250	1.161000	0.42604	-0.250000	0.11733	GAC	.	.		0.458	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		G	25274939	A	G	25274939	3	3	115	1	0	0	0	0	1	0	0	0	1122	275	10	2	1828	2	ATP12A	13	25274939	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	257150	25274939	89894939	313	19852										
CENPJ	55835	hgsc.bcm.edu	37	chr13	25478135	25478135	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcgttctcagctttaaacttTtctatttctgtttccaattc	4	10	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:25478135T>C	ENST00000381884.4	-	8	2939	c.2754A>G	c.(2752-2754)gaA>gaG	p.E918E	CENPJ_ENST00000545981.1_Silent_p.E918E	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	918					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		CTTTAAACTTTTCTATTTCTG	0.373																																					p.E918E		Atlas-SNP	.											.	CENPJ	116	.	0			c.A2754G						.						186	176	179					13																	25478135		2203	4300	6503	SO:0001819	synonymous_variant	55835	exon8			AAACTTTTCTATT	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"centrosomal P4.1-associated protein"	609279	"microcephaly, primary autosomal recessive 6"	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.2754A>G	chr13.hg19:g.25478135T>C		110.0	0.0		110.0	5.0	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Silent	SNP	ENST00000381884.4	hg19	CCDS9310.1																																																																																			.	.		0.373	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		C	25478135	T	C	25478135	2	2	115	1	0	0	0	0	0	0	0	1	3236	1838	64	2		2	CENPJ	13	25478135	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	203196	25478135	89691743	314	19853										
FAM123A	219287	hgsc.bcm.edu	37	chr13	25745556	25745556	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cctcttcttgaataatttgaAggcagctttattaatcttcc	5	9	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:25745556A>G	ENST00000515384.1	-	1	869	c.202T>C	c.(202-204)Ttc>Ctc	p.F68L	AMER2-AS1_ENST00000413501.1_lincRNA|AMER2_ENST00000381853.3_Missense_Mutation_p.F68L|AMER2_ENST00000357816.2_Missense_Mutation_p.F68L			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	68	Gly-rich.				ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)										AATAATTTGAAGGCAGCTTTA	0.587																																					p.F68L		Atlas-SNP	.											.	.	.	.	0			c.T202C						.						47	53	51					13																	25745556		2196	4283	6479	SO:0001583	missense	219287	exon1			ATTTGAAGGCAGC	AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"-"	26360	protein-coding gene	gene with protein product		614659	"family with sequence similarity 123A"	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.202T>C	chr13.hg19:g.25745556A>G	ENSP00000426528:p.Phe68Leu	77.0	0.0		93.0	4.0	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	hg19	CCDS53859.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.198323	0.79015	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.27890	1.64;1.64;1.64	3.4	3.4	0.38934	.	0.000000	0.85682	D	0.000000	T	0.45994	0.1370	L	0.46741	1.465	0.44643	D	0.997625	D;D	0.76494	0.999;0.999	D;D	0.83275	0.991;0.996	T	0.46105	-0.9215	10	0.87932	D	0	-1.9422	11.4533	0.50167	1.0:0.0:0.0:0.0	.	68;68	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	L	68	ENSP00000350469:F68L;ENSP00000371277:F68L;ENSP00000426528:F68L	ENSP00000350469:F68L	F	-	1	0	FAM123A	24643556	1.000000	0.71417	0.982000	0.44146	0.887000	0.51463	6.492000	0.73654	1.546000	0.49388	0.260000	0.18958	TTC	.	.		0.587	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704		G	25745556	A	G	25745556	3	3	115	1	0	0	0	0	1	0	0	0	5427	72	3	2	1817	2	FAM123A	13	25745556	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	267421	25745556	89424322	315	19854										
FLT3	2322	hgsc.bcm.edu	37	chr13	28588598	28588598	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgctacataccgcttcttcTgcatctgccagctgacatcc	6	16	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:28588598T>C	ENST00000241453.7	-	23	2931	c.2850A>G	c.(2848-2850)gcA>gcG	p.A950A	FLT3_ENST00000537084.1_Silent_p.A909A|FLT3_ENST00000380982.4_Silent_p.A953A|FLT3_ENST00000469894.1_5'UTR	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	950					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCGCTTCTTCTGCATCTGCCA	0.413			"Mis, O"		"AML, ALL"																																p.A950A		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.A2850G						.						84	78	80					13																	28588598		2203	4300	6503	SO:0001819	synonymous_variant	2322	exon23			TTCTTCTGCATCT	U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2850A>G	chr13.hg19:g.28588598T>C		102.0	0.0		95.0	4.0	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Silent	SNP	ENST00000241453.7	hg19	CCDS31953.1																																																																																			.	.		0.413	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			C	28588598	T	C	28588598	2	2	115	1	0	0	0	0	0	0	0	1	5950	1567	55	2		2	FLT3	13	28588598	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2843042	28588598	86581280	316	19855										
POSTN	10631	hgsc.bcm.edu	37	chr13	38153044	38153044	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agttgatcatttccaacaggTgtgtctatgaagagaaatat	9	5	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:38153044T>C	ENST00000379747.4	-	15	2016	c.1899A>G	c.(1897-1899)acA>acG	p.T633T	POSTN_ENST00000541481.1_Silent_p.T633T|POSTN_ENST00000379749.4_Silent_p.T633T|POSTN_ENST00000379743.4_Silent_p.T633T|POSTN_ENST00000541179.1_Silent_p.T633T|POSTN_ENST00000379742.4_Silent_p.T633T	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	633					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TTCCAACAGGTGTGTCTATGA	0.249																																					p.T633T		Atlas-SNP	.											.	POSTN	161	.	0			c.A1899G						.						41	46	44					13																	38153044		2195	4294	6489	SO:0001819	synonymous_variant	10631	exon15			AACAGGTGTGTCT	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1899A>G	chr13.hg19:g.38153044T>C		97.0	0.0		77.0	4.0	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Silent	SNP	ENST00000379747.4	hg19	CCDS9364.1																																																																																			.	.		0.249	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		C	38153044	T	C	38153044	2	2	115	1	0	0	0	0	0	0	0	1	12268	1683	59	2		2	POSTN	13	38153044	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	9564446	38153044	77016834	317	19856										
FREM2	341640	hgsc.bcm.edu	37	chr13	39343836	39343836	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cgagtgcggatcctgagtgaTggggagcatgagcagtctga	17	7	1	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:39343836T>C	ENST00000280481.7	+	4	5748	c.5532T>C	c.(5530-5532)gaT>gaC	p.D1844D		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1844	Calx-beta 1.				cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TCCTGAGTGATGGGGAGCATG	0.542																																					p.D1844D		Atlas-SNP	.											.	FREM2	385	.	0			c.T5532C						.						142	115	124					13																	39343836		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon4			GAGTGATGGGGAG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.5532T>C	chr13.hg19:g.39343836T>C		257.0	0.0		302.0	115.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.542	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39343836	T	C	39343836	2	2	115	1	0	0	0	0	0	0	0	1	6053	1461	51	2		2	FREM2	13	39343836	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1190792	39343836	75826042	318	19857										
C13orf31	144811	hgsc.bcm.edu	37	chr13	44455553	44455553	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tttaggggagggctttttaaAcagtccattgaaataaacgt	10	5	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:44455553A>C	ENST00000441843.1	+	2	917	c.432A>C	c.(430-432)aaA>aaC	p.K144N	CCDC122_ENST00000444614.3_5'Flank|LACC1_ENST00000325686.6_Missense_Mutation_p.K144N|CCDC122_ENST00000476570.2_5'Flank	NM_001128303.1	NP_001121775.1	Q8IV20	LACC1_HUMAN	laccase (multicopper oxidoreductase) domain containing 1	144																	GGCTTTTTAAACAGTCCATTG	0.338																																					p.K144N		Atlas-SNP	.											.	.	.	.	0			c.A432C						.						77	82	80					13																	44455553		2203	4300	6503	SO:0001583	missense	144811	exon2			TTTTAAACAGTCC	AK096044	CCDS9391.1	13q14.11	2012-05-11	2011-08-09	2011-08-09	ENSG00000179630	ENSG00000179630			26789	protein-coding gene	gene with protein product		613409	"chromosome 13 open reading frame 31"	C13orf31		16740638, 22504414	Standard	NM_153218		Approved	FLJ38725	uc010acg.3	Q8IV20	OTTHUMG00000016826	ENST00000441843.1:c.432A>C	chr13.hg19:g.44455553A>C	ENSP00000391747:p.Lys144Asn	79.0	0.0		84.0	4.0	NM_001128303	A2A3Z6|Q8N8X5	Missense_Mutation	SNP	ENST00000441843.1	hg19	CCDS9391.1	.	.	.	.	.	.	.	.	.	.	A	8.320	0.824010	0.16678	.	.	ENSG00000179630	ENST00000441843;ENST00000425906;ENST00000325686	T;T	0.46451	0.87;0.87	5.66	1.71	0.24356	.	0.285942	0.41396	D	0.000884	T	0.28863	0.0716	L	0.48877	1.53	0.09310	N	1	B	0.26120	0.142	B	0.15870	0.014	T	0.12091	-1.0561	10	0.30854	T	0.27	-31.9683	6.159	0.20354	0.7199:0.136:0.1442:0.0	.	144	Q8IV20	LACC1_HUMAN	N	144	ENSP00000391747:K144N;ENSP00000317619:K144N	ENSP00000317619:K144N	K	+	3	2	LACC1	43353553	0.763000	0.28462	0.942000	0.38095	0.132000	0.20833	1.171000	0.31896	0.522000	0.28464	0.533000	0.62120	AAA	.	.		0.338	LACC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044726.3	NM_153218		C	44455553	A	C	44455553	3	2	115	1	0	0	0	0	1	0	0	0	1728	40	2	5	434	5	C13orf31	13	44455553	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5111717	44455553	70714325	319	19858										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77740659	77740659	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgagggtcaaattcgattgTcatccacctcacacattctg	7	12	4	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:77740659T>C	ENST00000544440.2	-	41	6048	c.6031A>G	c.(6031-6033)Aca>Gca	p.T2011A	MYCBP2_ENST00000357337.6_Missense_Mutation_p.T2011A|MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000407578.2_Missense_Mutation_p.T2049A					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		AATTCGATTGTCATCCACCTC	0.413																																					p.T2049A		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A6145G						.						115	108	110					13																	77740659		2203	4300	6503	SO:0001583	missense	23077	exon41			CGATTGTCATCCA	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.6031A>G	chr13.hg19:g.77740659T>C	ENSP00000444596:p.Thr2011Ala	119.0	0.0		150.0	6.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.88	3.245090	0.59103	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.29655	1.56;1.56;1.56	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.22936	0.0554	L	0.28400	0.85	0.54753	D	0.999985	B	0.23591	0.088	B	0.21360	0.034	T	0.04752	-1.0929	10	0.37606	T	0.19	.	11.2346	0.48933	0.1366:0.0:0.0:0.8634	.	2011	O75592	MYCB2_HUMAN	A	2011;2049;2011	ENSP00000349892:T2011A;ENSP00000384288:T2049A;ENSP00000444596:T2011A	ENSP00000349892:T2011A	T	-	1	0	MYCBP2	76638660	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.149000	0.71795	2.205000	0.71048	0.528000	0.53228	ACA	.	.		0.413	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77740659	T	C	77740659	3	2	115	1	0	0	0	0	1	0	0	0	10027	1667	58	2	8063	2	MYCBP2	13	77740659	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	33285106	77740659	37429219	320	19859										
RNF219	79596	hgsc.bcm.edu	37	chr13	79213208	79213208	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtaaacaatctatttcgtccTgaaaaagcattgcatagtca	6	8	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:79213208T>C	ENST00000282003.6	-	4	359		c.e4-2			NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219								zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		TATTTCGTCCTGAAAAAGCAT	0.348																																					.		Atlas-SNP	.											.	RNF219	94	.	0			c.301-2A>G						.						63	63	63					13																	79213208		2203	4298	6501	SO:0001630	splice_region_variant	79596	exon5			TCGTCCTGAAAAA	BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.301-2A>G	chr13.hg19:g.79213208T>C		111.0	0.0		89.0	4.0	NM_024546	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Splice_Site	SNP	ENST00000282003.6	hg19	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	T	17.71	3.457593	0.63401	.	.	ENSG00000152193	ENST00000282003	.	.	.	4.66	4.66	0.58398	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7069	0.57065	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RNF219	78111209	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	1.697000	0.37784	2.036000	0.60181	0.533000	0.62120	.	.	.		0.348	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546	Intron	C	79213208	T	C	79213208	5	2	115	1	0	0	0	0	0	0	1	0	13497	1594	55	2	1893	2	RNF219	13	79213208	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1472549	79213208	35956670	321	19860										
FARP1	10160	hgsc.bcm.edu	37	chr13	99043122	99043122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agaaggaggacataagaaggTgcagtttgaaaggtaagaga	15	2	0	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:99043122T>C	ENST00000319562.6	+	11	1341	c.1076T>C	c.(1075-1077)gTg>gCg	p.V359A	FARP1_ENST00000376586.2_Missense_Mutation_p.V359A|FARP1_ENST00000595437.1_Missense_Mutation_p.V359A	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	359					dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CATAAGAAGGTGCAGTTTGAA	0.453																																					p.V359A		Atlas-SNP	.											.	FARP1	207	.	0			c.T1076C						.						151	138	142					13																	99043122		2203	4300	6503	SO:0001583	missense	10160	exon11			AGAAGGTGCAGTT	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.1076T>C	chr13.hg19:g.99043122T>C	ENSP00000322926:p.Val359Ala	99.0	0.0		91.0	4.0	NM_005766	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	hg19	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	T	16.41	3.115770	0.56505	.	.	ENSG00000152767	ENST00000376586;ENST00000376584;ENST00000319562	D;D	0.85629	-2.01;-2.01	5.66	5.66	0.87406	FERM adjacent (FA) (1);	0.197470	0.46145	D	0.000312	D	0.82843	0.5125	N	0.25890	0.77	0.58432	D	0.999999	P;D	0.54964	0.951;0.969	P;P	0.52343	0.696;0.634	T	0.80336	-0.1425	10	0.19590	T	0.45	.	15.8839	0.79226	0.0:0.0:0.0:1.0	.	359;359	Q9Y4F1;C9JME2	FARP1_HUMAN;.	A	359;64;359	ENSP00000365771:V359A;ENSP00000322926:V359A	ENSP00000322926:V359A	V	+	2	0	FARP1	97841123	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	6.251000	0.72441	2.158000	0.67659	0.533000	0.62120	GTG	.	.		0.453	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		C	99043122	T	C	99043122	3	2	115	1	0	0	0	0	1	0	0	0	5684	1696	59	2	1337	2	FARP1	13	99043122	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	19829914	99043122	16126756	322	19861										
DOCK9	23348	hgsc.bcm.edu	37	chr13	99515318	99515318	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gacacatccctcacattgatCcgctggacgttttcaatcag	7	13	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:99515318C>T	ENST00000376460.1	-	32	3614	c.3534G>A	c.(3532-3534)cgG>cgA	p.R1178R	DOCK9_ENST00000442173.1_Silent_p.R1178R|DOCK9_ENST00000461998.1_5'UTR|DOCK9_ENST00000339416.2_Silent_p.R1179R|DOCK9_ENST00000448493.2_Silent_p.R1190R	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1179					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TCACATTGATCCGCTGGACGT	0.522																																					p.R1179R		Atlas-SNP	.											.	DOCK9	311	.	0			c.G3537A						.						54	53	54					13																	99515318		2016	4180	6196	SO:0001819	synonymous_variant	23348	exon32			ATTGATCCGCTGG	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.3534G>A	chr13.hg19:g.99515318C>T		132.0	0.0		117.0	45.0	NM_001130049	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Silent	SNP	ENST00000376460.1	hg19	CCDS45062.1																																																																																			.	.		0.522	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		T	99515318	C	T	99515318	2	4	115	1	0	0	0	0	0	0	0	1	4696	842	30	3		3	DOCK9	13	99515318	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	472196	99515318	15654560	323	19862										
DOCK9	23348	hgsc.bcm.edu	37	chr13	99567709	99567709	+	Frame_Shift_Del	DEL	T	T	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgctgccaagagataactacTtttgtcctgcatcttgagct							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:99567709delT	ENST00000376460.1	-	8	846	c.766delA	c.(766-768)agtfs	p.S257fs	DOCK9_ENST00000442173.1_Frame_Shift_Del_p.S257fs|DOCK9_ENST00000339416.2_Frame_Shift_Del_p.S258fs|DOCK9_ENST00000448493.2_Frame_Shift_Del_p.S269fs	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	258	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AGATAACTACTTTTGTCCTGC	0.373																																					p.S257fs		Atlas-INDEL	.											.	DOCK9	311	.	0			c.770delG						.						85	79	81					13																	99567709		1993	4185	6178	SO:0001589	frameshift_variant	23348	exon8			.	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.766delA	chr13.hg19:g.99567709delT	ENSP00000365643:p.Ser257fs	118.0	0.0		148.0	10.0	NM_001130049	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Frame_Shift_Del	DEL	ENST00000376460.1	hg19	CCDS45062.1																																																																																			.	.		0.373	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		-	99567709	T	-	99567709	7	5	115	1	0	1	0	1	0	0	0	0	4696	1609	56	0	5697	0	DOCK9	13	99567709	Frame_Shift_Del	DEL	T	TCGA-DD-A3A1-01A-11D-A20W-10	52391	99567709	15602169	324	19863										
EFNB2	1948	hgsc.bcm.edu	37	chr13	107148141	107148141	+	Frame_Shift_Del	DEL	C	C	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	catggctcttgtctggcacaCccctccctcctggttatcca							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:107148141delC	ENST00000245323.4	-	3	603	c.454delG	c.(454-456)gtgfs	p.V152fs		NM_004093.3	NP_004084.1	P52799	EFNB2_HUMAN	ephrin-B2	152	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				anatomical structure morphogenesis (GO:0009653)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|lymph vessel development (GO:0001945)|negative regulation of keratinocyte proliferation (GO:0010839)|organ morphogenesis (GO:0009887)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|regulation of chemotaxis (GO:0050920)|viral process (GO:0016032)	focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					GTCTGGCACACCCCTCCCTCC	0.448																																					p.V152fs		Atlas-INDEL	.											.	EFNB2	39	.	0			c.455delT						.						315	276	289					13																	107148141		2203	4300	6503	SO:0001589	frameshift_variant	1948	exon3			.	L38734	CCDS9507.1	13q33	2011-03-09			ENSG00000125266	ENSG00000125266		"Ephrins"	3227	protein-coding gene	gene with protein product	"HTK ligand", "ligand of eph-related kinase 5", "eph-related receptor tyrosine kinase ligand 5"	600527		EPLG5		7833926	Standard	NM_004093		Approved	LERK5, Htk-L, HTKL, MGC126226, MGC126227, MGC126228	uc001vqi.3	P52799	OTTHUMG00000017324	ENST00000245323.4:c.454delG	chr13.hg19:g.107148141delC	ENSP00000245323:p.Val152fs	105.0	0.0		120.0	10.0	NM_004093	Q5JV56	Frame_Shift_Del	DEL	ENST00000245323.4	hg19	CCDS9507.1																																																																																			.	.		0.448	EFNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045733.4	NM_004093		-	107148141	C	-	107148141	7	5	115	1	0	1	0	1	0	0	0	0	4958	507	18	0	559	0	EFNB2	13	107148141	Frame_Shift_Del	DEL	C	TCGA-DD-A3A1-01A-11D-A20W-10	7580432	107148141	8021737	325	19864										
PCID2	55795	hgsc.bcm.edu	37	chr13	113834473	113834473	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaaggatggcatactctaccTcacagctctggttacttccg	9	12	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr13:113834473T>C	ENST00000337344.4	-	11	935	c.859A>G	c.(859-861)Agc>Ggc	p.S287G	PCID2_ENST00000493650.1_5'UTR|PCID2_ENST00000375457.2_Splice_Site_p.S285G|PCID2_ENST00000246505.5_Splice_Site_p.S341G|PCID2_ENST00000375459.1_Splice_Site_p.S285G|PCID2_ENST00000375477.1_Splice_Site_p.S287G|PCID2_ENST00000375479.2_Splice_Site_p.S287G	NM_001127202.2	NP_001120674.1	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	287	PCI.				negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mRNA stability (GO:0043488)|spleen development (GO:0048536)					breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)	20	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)			ATACTCTACCTCACAGCTCTG	0.473																																					p.S341G		Atlas-SNP	.											.	PCID2	30	.	0			c.A1021G						.						131	125	127					13																	113834473		2203	4300	6503	SO:0001630	splice_region_variant	55795	exon11			TCTACCTCACAGC	AK002167	CCDS9532.2, CCDS58301.1, CCDS58302.1	13q34	2006-03-31			ENSG00000126226	ENSG00000126226			25653	protein-coding gene	gene with protein product		613713				12477932	Standard	NM_001127203		Approved	FLJ11305	uc031qnm.1	Q5JVF3	OTTHUMG00000017385	ENST00000337344.4:c.860+1A>G	chr13.hg19:g.113834473T>C		121.0	0.0		103.0	6.0	NM_001258212	A6NK09|Q3ZCX1|Q5TC57|Q5TC58|Q9H7K1|Q9HBZ7|Q9NUK6|Q9NVY1|Q9NW44|Q9NWH3	Missense_Mutation	SNP	ENST00000337344.4	hg19	CCDS9532.2	.	.	.	.	.	.	.	.	.	.	T	15.80	2.940745	0.52972	.	.	ENSG00000126226	ENST00000337344;ENST00000375479;ENST00000375477;ENST00000246505;ENST00000375459;ENST00000375457;ENST00000375462;ENST00000246506;ENST00000351317	T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52	5.76	5.76	0.90799	PCI/PINT associated module (1);Proteasome component (PCI) domain (1);	0.130098	0.64402	D	0.000002	T	0.32823	0.0842	L	0.47716	1.5	0.80722	D	1	P;B	0.35139	0.486;0.16	B;B	0.36922	0.236;0.21	T	0.10245	-1.0638	10	0.59425	D	0.04	-13.4827	16.0776	0.80979	0.0:0.0:0.0:1.0	.	341;287	Q5JVF3-4;Q5JVF3	.;PCID2_HUMAN	G	287;287;287;341;285;285;264;287;264	ENSP00000337405:S287G;ENSP00000364628:S287G;ENSP00000364626:S287G;ENSP00000246505:S341G;ENSP00000364608:S285G;ENSP00000364606:S285G;ENSP00000327335:S264G	ENSP00000246505:S341G	S	-	1	0	PCID2	112882474	1.000000	0.71417	0.970000	0.41538	0.126000	0.20510	7.646000	0.83445	2.200000	0.70718	0.533000	0.62120	AGC	.	.		0.473	PCID2-002	KNOWN	alternative_3_UTR|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045897.1	NM_018386	Missense_Mutation	C	113834473	T	C	113834473	5	2	115	1	0	0	0	0	0	0	1	0	11588	1565	54	2	356	2	PCID2	13	113834473	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	6686332	113834473	1335405	326	19865										
OR4K2	390431	hgsc.bcm.edu	37	chr14	20345276	20345276	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctttactcccactctgaacCcaataatctatactttgagg	4	12	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:20345276C>G	ENST00000298642.2	+	1	886	c.850C>G	c.(850-852)Cca>Gca	p.P284A		NM_001005501.1	NP_001005501.1	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K, member 2	284						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(16)|ovary(2)|skin(9)|upper_aerodigestive_tract(2)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CACTCTGAACCCAATAATCTA	0.368																																					p.P284A		Atlas-SNP	.											.	OR4K2	97	.	0			c.C850G						.						106	112	110					14																	20345276		2203	4300	6503	SO:0001583	missense	390431	exon1			CTGAACCCAATAA		CCDS32023.1	14q11.2	2013-09-23			ENSG00000165762	ENSG00000165762		"GPCR / Class A : Olfactory receptors"	14728	protein-coding gene	gene with protein product							Standard	NM_001005501		Approved		uc001vwh.1	Q8NGD2	OTTHUMG00000170624	ENST00000298642.2:c.850C>G	chr14.hg19:g.20345276C>G	ENSP00000298642:p.Pro284Ala	50.0	0.0		27.0	5.0	NM_001005501	B2RNK8|Q6IFA5	Missense_Mutation	SNP	ENST00000298642.2	hg19	CCDS32023.1	.	.	.	.	.	.	.	.	.	.	.	12.05	1.821532	0.32237	.	.	ENSG00000165762	ENST00000298642	T	0.63255	-0.03	5.16	5.16	0.70880	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000153	T	0.72078	0.3416	M	0.86268	2.805	0.51767	D	0.999932	P	0.41524	0.753	P	0.44647	0.456	T	0.77822	-0.2445	10	0.72032	D	0.01	.	16.183	0.81925	0.0:1.0:0.0:0.0	.	284	Q8NGD2	OR4K2_HUMAN	A	284	ENSP00000298642:P284A	ENSP00000298642:P284A	P	+	1	0	OR4K2	19415116	1.000000	0.71417	0.991000	0.47740	0.058000	0.15608	7.249000	0.78278	2.681000	0.91329	0.591000	0.81541	CCA	.	.		0.368	OR4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409864.1			G	20345276	C	G	20345276	3	3	115	1	0	0	0	0	1	0	0	0	11081	623	22	4	852	4	OR4K2	14	20345276	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10		20345276	87004264	327	19866										
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24530141	24530141	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cccttccttctccagctgttTcccagcctctatgagctggg	8	16	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:24530141T>C	ENST00000342740.5	+	26	2350	c.2196T>C	c.(2194-2196)ttT>ttC	p.F732F	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	732						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TCCAGCTGTTTCCCAGCCTCT	0.587																																					p.F732F		Atlas-SNP	.											LRRC16B,colon,carcinoma,0,1	LRRC16B	120	.	0			c.T2196C						.						50	38	42					14																	24530141		2007	3863	5870	SO:0001819	synonymous_variant	90668	exon26			GCTGTTTCCCAGC	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.2196T>C	chr14.hg19:g.24530141T>C		124.0	1.0		112.0	5.0	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	hg19	CCDS32054.1																																																																																			.	.		0.587	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		C	24530141	T	C	24530141	2	2	115	1	0	0	0	0	0	0	0	1	8981	1780	62	2		2	LRRC16B	14	24530141	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4184865	24530141	82819399	328	19867										
SCFD1	23256	hgsc.bcm.edu	37	chr14	31139491	31139491	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttaaacagggttaatttggaAgaatcttcaggagtggaaaa	11	3	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:31139491A>G	ENST00000458591.2	+	11	1112	c.885A>G	c.(883-885)gaA>gaG	p.E295E	SCFD1_ENST00000541123.1_Silent_p.E110E|SCFD1_ENST00000544052.2_Silent_p.E228E|SCFD1_ENST00000421551.3_Silent_p.E236E|SCFD1_ENST00000396629.2_Silent_p.E203E	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	295					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		TTAATTTGGAAGAATCTTCAG	0.333																																					p.E295E		Atlas-SNP	.											.	SCFD1	43	.	0			c.A885G						.						90	110	103					14																	31139491		2203	4295	6498	SO:0001819	synonymous_variant	23256	exon11			TTTGGAAGAATCT	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 163"	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.885A>G	chr14.hg19:g.31139491A>G		174.0	0.0		93.0	4.0	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Silent	SNP	ENST00000458591.2	hg19	CCDS9639.1																																																																																			.	.		0.333	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835		G	31139491	A	G	31139491	2	3	115	1	0	0	0	0	0	0	0	1	13904	69	3	2		2	SCFD1	14	31139491	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6609350	31139491	76210049	329	19868										
FKBP3	2287	hgsc.bcm.edu	37	chr14	45590787	45590787	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gggaaagttggttttatctcCctttttcagaacagatttag	9	6	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:45590787C>T	ENST00000216330.3	-	5	765	c.355G>A	c.(355-357)Gga>Aga	p.G119R	FKBP3_ENST00000396062.3_Missense_Mutation_p.G119R			Q00688	FKBP3_HUMAN	FK506 binding protein 3, 25kDa	119					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)	p.G119*(1)		NS(1)|biliary_tract(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	12						GTTTTATCTCCCTTTTTCAGA	0.338																																					p.G119R		Atlas-SNP	.											FKBP3,colon,carcinoma,0,1	FKBP3	21	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G355A						.						122	113	116					14																	45590787		2203	4300	6503	SO:0001583	missense	2287	exon4			TATCTCCCTTTTT	M96256	CCDS9683.1	14q21.2	2008-08-11	2002-08-29		ENSG00000100442	ENSG00000100442			3719	protein-coding gene	gene with protein product		186947	"FK506-binding protein 3 (25kD)"			1374240, 1532945	Standard	NM_002013		Approved	FKBP-25, PPIase	uc010tqf.2	Q00688	OTTHUMG00000140267	ENST00000216330.3:c.355G>A	chr14.hg19:g.45590787C>T	ENSP00000216330:p.Gly119Arg	95.0	0.0		48.0	2.0	NM_002013	B2R4Q9|Q14317	Missense_Mutation	SNP	ENST00000216330.3	hg19	CCDS9683.1	.	.	.	.	.	.	.	.	.	.	C	33	5.231659	0.95207	.	.	ENSG00000100442	ENST00000216330;ENST00000396062	T;T	0.63096	-0.02;-0.02	6.17	6.17	0.99709	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (1);	0.000000	0.85682	D	0.000000	T	0.66366	0.2782	M	0.65975	2.015	0.80722	D	1	D	0.59357	0.985	B	0.42851	0.4	T	0.71293	-0.4636	10	0.87932	D	0	-9.0144	20.4745	0.99168	0.0:1.0:0.0:0.0	.	119	Q00688	FKBP3_HUMAN	R	119	ENSP00000216330:G119R;ENSP00000379374:G119R	ENSP00000216330:G119R	G	-	1	0	FKBP3	44660537	1.000000	0.71417	0.996000	0.52242	0.929000	0.56500	7.508000	0.81686	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.338	FKBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276796.1	NM_002013		T	45590787	C	T	45590787	3	4	115	1	0	0	0	0	1	0	0	0	5917	632	22	3	335	3	FKBP3	14	45590787	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	14451296	45590787	61758753	330	19869										
FANCM	57697	hgsc.bcm.edu	37	chr14	45653040	45653040	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	catgttcacaattagaagacTtcaaggtttgtaacgggaat	9	6	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:45653040T>C	ENST00000267430.5	+	17	4535	c.4450T>C	c.(4450-4452)Ttc>Ctc	p.F1484L	FANCM_ENST00000555013.1_3'UTR|FANCM_ENST00000542564.2_Missense_Mutation_p.F1458L	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1484					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						ATTAGAAGACTTCAAGGTTTG	0.328								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.F1484L		Atlas-SNP	.											.	FANCM	225	.	0			c.T4450C						.						68	66	67					14																	45653040		2203	4299	6502	SO:0001583	missense	57697	exon17	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GAAGACTTCAAGG	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.4450T>C	chr14.hg19:g.45653040T>C	ENSP00000267430:p.Phe1484Leu	149.0	0.0		78.0	4.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.65|12.65	2.000561|2.000561	0.35320|0.35320	.|.	.|.	ENSG00000187790|ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250|ENST00000554809	T;T;T|.	0.18338|.	2.82;2.82;2.22|.	5.2|5.2	-0.582|-0.582	0.11709|0.11709	.|.	1.380460|.	0.04154|.	N|.	0.321751|.	T|T	0.39462|0.39462	0.1079|0.1079	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	1|1	P;P|.	0.35745|.	0.518;0.518|.	B;B|.	0.30401|.	0.115;0.115|.	T|T	0.35076|0.35076	-0.9803|-0.9803	10|5	0.10111|.	T|.	0.7|.	.|.	5.3297|5.3297	0.15926|0.15926	0.2918:0.0:0.3021:0.4061|0.2918:0.0:0.3021:0.4061	.|.	1458;1484|.	B2RTQ9;Q8IYD8|.	.;FANCM_HUMAN|.	L|P	1484;1458;1000|416	ENSP00000267430:F1484L;ENSP00000442493:F1458L;ENSP00000452033:F1000L|.	ENSP00000267430:F1484L|.	F|L	+|+	1|2	0|0	FANCM|FANCM	44722790|44722790	0.009000|0.009000	0.17119|0.17119	0.005000|0.005000	0.12908|0.12908	0.005000|0.005000	0.04900|0.04900	0.445000|0.445000	0.21677|0.21677	-0.257000|-0.257000	0.09459|0.09459	-1.286000|-1.286000	0.01371|0.01371	TTC|CTT	.	.		0.328	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		C	45653040	T	C	45653040	3	2	115	1	0	0	0	0	1	0	0	0	5679	1609	56	2	4516	2	FANCM	14	45653040	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	62253	45653040	61696500	331	19870										
POLE2	5427	hgsc.bcm.edu	37	chr14	50120709	50120709	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acaaaatactaattcttaccTgcaaggattagtagtaaaaa	5	6	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:50120709T>C	ENST00000216367.5	-	15	1309	c.1210A>G	c.(1210-1212)Aga>Gga	p.R404G	POLE2_ENST00000556584.1_5'UTR|POLE2_ENST00000554396.1_Splice_Site_p.R404G|POLE2_ENST00000539565.2_Splice_Site_p.R378G	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	404					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	AATTCTTACCTGCAAGGATTA	0.358																																					p.R404G		Atlas-SNP	.											.	POLE2	36	.	0			c.A1210G						.						52	51	51					14																	50120709		2203	4300	6503	SO:0001630	splice_region_variant	5427	exon15			CTTACCTGCAAGG	AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479		"DNA polymerases"	9178	protein-coding gene	gene with protein product	"DNA polymerase epsilon subunit B"	602670	"polymerase (DNA directed), epsilon 2 (p59 subunit)"			9405441, 9443964	Standard	NM_002692		Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.1211+1A>G	chr14.hg19:g.50120709T>C		119.0	0.0		88.0	4.0	NM_001197331	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	Missense_Mutation	SNP	ENST00000216367.5	hg19	CCDS32073.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.923866	0.92319	.	.	ENSG00000100479	ENST00000216367;ENST00000539565;ENST00000554396	T;T;T	0.34667	1.35;1.35;1.35	6.16	6.16	0.99307	DNA polymerase alpha/epsilon, subunit B (1);	0.000000	0.85682	D	0.000000	T	0.71702	0.3371	H	0.94734	3.575	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.80289	-0.1445	10	0.87932	D	0	-25.1949	16.8061	0.85666	0.0:0.0:0.0:1.0	.	404;378;404	A4FU92;B4DDE6;P56282	.;.;DPOE2_HUMAN	G	404;378;404	ENSP00000216367:R404G;ENSP00000446313:R378G;ENSP00000451621:R404G	ENSP00000216367:R404G	R	-	1	2	POLE2	49190459	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.250000	0.72435	2.367000	0.80283	0.528000	0.53228	AGA	.	.		0.358	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410512.1	NM_002692	Missense_Mutation	C	50120709	T	C	50120709	5	2	115	1	0	0	0	0	0	0	1	0	12206	1594	55	2	393	2	POLE2	14	50120709	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4467669	50120709	57228831	332	19871										
ARID4A	5926	hgsc.bcm.edu	37	chr14	58831470	58831470	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atctcaagaaaggaccagtgAttgtattggatctgagggaa	12	5	2	3	rs78751371		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:58831470A>G	ENST00000355431.3	+	20	3036	c.2663A>G	c.(2662-2664)gAt>gGt	p.D888G	ARID4A_ENST00000395168.3_Missense_Mutation_p.D888G|ARID4A_ENST00000348476.3_Missense_Mutation_p.D888G|ARID4A_ENST00000431317.2_Missense_Mutation_p.D888G	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	888					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						AGGACCAGTGATTGTATTGGA	0.348																																					p.D888G		Atlas-SNP	.											.	ARID4A	222	.	0			c.A2663G						.						85	78	80					14																	58831470		2202	4300	6502	SO:0001583	missense	5926	exon20			CCAGTGATTGTAT	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2663A>G	chr14.hg19:g.58831470A>G	ENSP00000347602:p.Asp888Gly	84.0	0.0		53.0	4.0	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	hg19	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.024084	0.35701	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.14893	2.48;2.49;2.48;2.49;2.47	5.59	5.59	0.84812	.	0.562418	0.20407	N	0.092934	T	0.19685	0.0473	L	0.44542	1.39	0.30386	N	0.781438	P;P;P	0.45827	0.867;0.501;0.571	B;B;B	0.42282	0.382;0.154;0.153	T	0.05007	-1.0912	10	0.54805	T	0.06	-23.0368	15.7863	0.78306	1.0:0.0:0.0:0.0	.	888;888;888	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	G	888;888;888;888;566	ENSP00000347602:D888G;ENSP00000344556:D888G;ENSP00000378597:D888G;ENSP00000397368:D888G;ENSP00000416053:D566G	ENSP00000344556:D888G	D	+	2	0	ARID4A	57901223	1.000000	0.71417	0.984000	0.44739	0.993000	0.82548	5.116000	0.64661	2.132000	0.65825	0.528000	0.53228	GAT	.	A|0.999;T|0.001		0.348	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		G	58831470	A	G	58831470	3	3	115	1	0	0	0	0	1	0	0	0	919	333	12	2	2737	2	ARID4A	14	58831470	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	8710761	58831470	48518070	333	19872										
ATP6V1D	51382	hgsc.bcm.edu	37	chr14	67807190	67807190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctcgctctctctcatccagcTctgtgatgatataagcaaga	7	12	3	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:67807190T>C	ENST00000216442.7	-	8	1119	c.569A>G	c.(568-570)gAg>gGg	p.E190G	ATP6V1D_ENST00000555431.1_Missense_Mutation_p.E135G|ATP6V1D_ENST00000555474.1_Missense_Mutation_p.E91G|ATP6V1D_ENST00000554236.1_Missense_Mutation_p.S168G|ATP6V1D_ENST00000553974.1_5'Flank|Y_RNA_ENST00000362885.1_RNA	NM_015994.3	NP_057078.1	Q9Y5K8	VATD_HUMAN	ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D	190					cellular iron ion homeostasis (GO:0006879)|cilium assembly (GO:0042384)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|protein localization to cilium (GO:0061512)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			lung(3)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	7				all cancers(60;0.000739)|OV - Ovarian serous cystadenocarcinoma(108;0.00597)|BRCA - Breast invasive adenocarcinoma(234;0.00957)		CTCATCCAGCTCTGTGATGAT	0.348																																					p.E190G		Atlas-SNP	.											.	ATP6V1D	21	.	0			c.A569G						.						123	118	120					14																	67807190		2203	4300	6503	SO:0001583	missense	51382	exon8			TCCAGCTCTGTGA	AF145316	CCDS9780.1	14q23-q24.2	2010-04-21	2002-08-29	2002-05-10	ENSG00000100554	ENSG00000100554		"ATPases / V-type"	13527	protein-coding gene	gene with protein product		609398	"ATPase, H+ transporting, lysosomal (vacuolar proton pump)"	ATP6M		9442887	Standard	NM_015994		Approved	VATD, VMA8	uc001xjf.3	Q9Y5K8		ENST00000216442.7:c.569A>G	chr14.hg19:g.67807190T>C	ENSP00000216442:p.Glu190Gly	78.0	0.0		58.0	4.0	NM_015994	B2RE33|Q9Y688	Missense_Mutation	SNP	ENST00000216442.7	hg19	CCDS9780.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	33|33	5.261693|5.261693	0.95368|0.95368	.|.	.|.	ENSG00000100554|ENSG00000100554	ENST00000555474;ENST00000216442;ENST00000555431|ENST00000554236	.|.	.|.	.|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88340|0.88340	0.6410|0.6410	H|H	0.97077|0.97077	3.935|3.935	0.36499|0.36499	D|D	0.868894|0.868894	D|.	0.89917|.	1.0|.	D|.	0.79108|.	0.992|.	D|D	0.93908|0.93908	0.7194|0.7194	9|5	0.87932|.	D|.	0|.	-27.3306|-27.3306	16.8222|16.8222	0.85835|0.85835	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	190|.	Q9Y5K8|.	VATD_HUMAN|.	G|G	91;190;135|168	.|.	ENSP00000216442:E190G|.	E|S	-|-	2|1	0|0	ATP6V1D|ATP6V1D	66876943|66876943	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.953000|7.953000	0.87836|0.87836	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	GAG|AGC	.	.		0.348	ATP6V1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412511.1	NM_015994		C	67807190	T	C	67807190	3	2	115	1	0	0	0	0	1	0	0	0	1182	1551	54	2	182	2	ATP6V1D	14	67807190	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	8975720	67807190	39542350	334	19873										
TMEM229B	161145	hgsc.bcm.edu	37	chr14	67940454	67940454	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gccgcgcagccgcaggtacaTgcgctccacgatgaggatgg	15	13	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:67940454T>C	ENST00000557006.1	-	4	469	c.187A>G	c.(187-189)Atg>Gtg	p.M63V	TMEM229B_ENST00000357461.2_Missense_Mutation_p.M63V			Q8NBD8	T229B_HUMAN	transmembrane protein 229B	63						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						CGCAGGTACATGCGCTCCACG	0.637																																					p.M63V		Atlas-SNP	.											.	TMEM229B	20	.	0			c.A187G						.						53	43	47					14																	67940454		2203	4299	6502	SO:0001583	missense	161145	exon3			GGTACATGCGCTC	AK090706	CCDS9783.1	14q23.3-q24.1	2009-09-22	2009-09-22	2009-09-22	ENSG00000198133	ENSG00000198133			20130	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 83"	C14orf83			Standard	NM_182526		Approved	FLJ33387	uc001xjk.3	Q8NBD8		ENST00000557006.1:c.187A>G	chr14.hg19:g.67940454T>C	ENSP00000451774:p.Met63Val	123.0	0.0		78.0	4.0	NM_182526		Missense_Mutation	SNP	ENST00000557006.1	hg19	CCDS9783.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.337029	0.60963	.	.	ENSG00000198133	ENST00000557006;ENST00000357461;ENST00000554278;ENST00000554480	.	.	.	4.69	4.69	0.59074	.	0.261255	0.51477	D	0.000096	T	0.48132	0.1483	L	0.29908	0.895	0.80722	D	1	B	0.34349	0.45	B	0.37198	0.243	T	0.48948	-0.8989	9	0.39692	T	0.17	-32.5338	14.177	0.65549	0.0:0.0:0.0:1.0	.	63	Q8NBD8	T229B_HUMAN	V	63	.	ENSP00000350050:M63V	M	-	1	0	TMEM229B	67010207	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.186000	0.72026	1.758000	0.51981	0.454000	0.30748	ATG	.	.		0.637	TMEM229B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412718.2	NM_182526		C	67940454	T	C	67940454	3	2	115	1	0	0	0	0	1	0	0	0	16163	1464	51	2	320	2	TMEM229B	14	67940454	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	133264	67940454	39409086	335	19874										
SLC8A3	6547	hgsc.bcm.edu	37	chr14	70512763	70512763	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gttgtggcgagcttgcagccAcgggggccaccaagctcccc	14	15	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:70512763A>G	ENST00000381269.2	-	8	3438	c.2685T>C	c.(2683-2685)cgT>cgC	p.R895R	SLC8A3_ENST00000356921.2_Silent_p.R889R|SLC8A3_ENST00000357887.3_Silent_p.R893R|SLC8A3_ENST00000216568.7_Silent_p.R266R|SLC8A3_ENST00000534137.1_Silent_p.R892R|SLC8A3_ENST00000394330.2_Silent_p.R252R|SLC8A3_ENST00000528359.1_Silent_p.R893R	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	895					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		GCTTGCAGCCACGGGGGCCAC	0.567											OREG0022773	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R895R		Atlas-SNP	.											.	SLC8A3	234	.	0			c.T2685C						.						25	27	26					14																	70512763		2203	4299	6502	SO:0001819	synonymous_variant	6547	exon8			GCAGCCACGGGGG	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"Solute carriers"	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.2685T>C	chr14.hg19:g.70512763A>G		124.0	0.0	1122	85.0	4.0	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	hg19	CCDS35498.1																																																																																			.	.		0.567	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			G	70512763	A	G	70512763	2	3	115	1	0	0	0	0	0	0	0	1	14723	146	6	2		2	SLC8A3	14	70512763	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2572309	70512763	36836777	336	19875										
MAP3K9	4293	hgsc.bcm.edu	37	chr14	71201208	71201208	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttatatccatctaccagggActtgaggctgaatcagagga	10	9	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:71201208A>G	ENST00000554752.2	-	10	1920	c.1921T>C	c.(1921-1923)Tcc>Ccc	p.S641P	MAP3K9_ENST00000554146.1_Missense_Mutation_p.S355P|MAP3K9_ENST00000553414.1_Missense_Mutation_p.S360P|MAP3K9_ENST00000381250.4_Missense_Mutation_p.S618P|MAP3K9_ENST00000555993.2_Missense_Mutation_p.S641P	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	641					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		TCTACCAGGGACTTGAGGCTG	0.547																																					p.S641P	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.T1921C						.						101	93	95					14																	71201208		2203	4300	6503	SO:0001583	missense	4293	exon10			CCAGGGACTTGAG	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.1921T>C	chr14.hg19:g.71201208A>G	ENSP00000451612:p.Ser641Pro	84.0	0.0		78.0	4.0	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	ENST00000554752.2	hg19		.	.	.	.	.	.	.	.	.	.	A	9.676	1.147960	0.21288	.	.	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	5.81	3.45	0.39498	.	0.224635	0.48767	D	0.000179	T	0.04003	0.0112	N	0.01874	-0.695	0.42936	D	0.994332	B;B;B;B	0.06786	0.0;0.001;0.001;0.001	B;B;B;B	0.10450	0.002;0.002;0.005;0.005	T	0.35895	-0.9770	10	0.02654	T	1	.	8.7954	0.34876	0.5097:0.3769:0.0:0.1134	.	355;641;641;360	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	P	641;641;360;618;355;346	ENSP00000451612:S641P;ENSP00000451038:S360P;ENSP00000370649:S618P;ENSP00000451921:S355P	ENSP00000005198:S641P	S	-	1	0	MAP3K9	70270961	1.000000	0.71417	0.997000	0.53966	0.969000	0.65631	1.181000	0.32017	0.461000	0.27071	0.379000	0.24179	TCC	.	.		0.547	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			G	71201208	A	G	71201208	3	3	115	1	0	0	0	0	1	0	0	0	9266	275	10	2	1451	2	MAP3K9	14	71201208	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	688445	71201208	36148332	337	19876										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72176082	72176082	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tatctgcaaggcacctctgcTgacagtggcattgacaccac	9	13	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:72176082T>C	ENST00000555818.1	+	15	4320	c.3972T>C	c.(3970-3972)gcT>gcC	p.A1324A	SIPA1L1_ENST00000381232.3_Silent_p.A1303A|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000358550.2_Silent_p.A1303A|SIPA1L1_ENST00000537413.1_Silent_p.A778A	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1324	Ser-rich.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GCACCTCTGCTGACAGTGGCA	0.582																																					p.A1324A		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.T3972C						.						96	78	85					14																	72176082		2203	4300	6503	SO:0001819	synonymous_variant	26037	exon15			CTCTGCTGACAGT	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.3972T>C	chr14.hg19:g.72176082T>C		135.0	0.0		98.0	4.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	hg19	CCDS9807.1																																																																																			.	.		0.582	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		C	72176082	T	C	72176082	2	2	115	1	0	0	0	0	0	0	0	1	14344	1567	55	2		2	SIPA1L1	14	72176082	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	974874	72176082	35173458	338	19877										
RBM25	58517	hgsc.bcm.edu	37	chr14	73566448	73566448	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agagatcagcaaattcagagAcacacataaggtagtattct	8	7	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:73566448A>G	ENST00000261973.7	+	9	1142	c.857A>G	c.(856-858)gAc>gGc	p.D286G	RBM25_ENST00000525321.1_Missense_Mutation_p.D286G|RBM25_ENST00000540173.1_Missense_Mutation_p.D286G|RBM25_ENST00000526754.1_Missense_Mutation_p.D286G|RBM25_ENST00000527432.1_Missense_Mutation_p.D286G	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	286	Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		AAATTCAGAGACACACATAAG	0.348																																					p.D286G		Atlas-SNP	.											.	RBM25	81	.	0			c.A857G						.						135	140	138					14																	73566448		2203	4299	6502	SO:0001583	missense	58517	exon9			TCAGAGACACACA	BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"RNA binding motif (RRM) containing"	23244	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 94"	612427	"RNA-binding region (RNP1, RRM) containing 7"	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.857A>G	chr14.hg19:g.73566448A>G	ENSP00000261973:p.Asp286Gly	103.0	0.0		76.0	4.0	NM_021239	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Missense_Mutation	SNP	ENST00000261973.7	hg19	CCDS32113.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.05|15.05	2.719102|2.719102	0.48622|0.48622	.|.	.|.	ENSG00000119707|ENSG00000119707	ENST00000261973;ENST00000540173;ENST00000527432;ENST00000525321;ENST00000526754|ENST00000532192	T;T;T;T;T|.	0.50001|.	0.76;1.35;0.76;1.29;1.35|.	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68384|0.68384	0.2995|0.2995	L|L	0.55481|0.55481	1.735|1.735	0.80722|0.80722	D|D	1|1	B;D|.	0.60575|.	0.059;0.988|.	B;P|.	0.61940|.	0.059;0.896|.	T|T	0.67126|0.67126	-0.5749|-0.5749	10|5	0.66056|.	D|.	0.02|.	.|.	14.7853|14.7853	0.69800|0.69800	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	286;286|.	P49756;P49756-2|.	RBM25_HUMAN;.|.	G|A	286|65	ENSP00000261973:D286G;ENSP00000437934:D286G;ENSP00000431150:D286G;ENSP00000436868:D286G;ENSP00000436225:D286G|.	ENSP00000261973:D286G|.	D|T	+|+	2|1	0|0	RBM25|RBM25	72636201|72636201	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	9.297000|9.297000	0.96120|0.96120	1.900000|1.900000	0.55004|0.55004	0.397000|0.397000	0.26171|0.26171	GAC|ACA	.	.		0.348	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		G	73566448	A	G	73566448	3	3	115	1	0	0	0	0	1	0	0	0	13140	275	10	2	887	2	RBM25	14	73566448	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1390366	73566448	33783092	339	19878										
NUMB	8650	hgsc.bcm.edu	37	chr14	73743385	73743385	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttattttctaatgcagcccaCtgggcttcaaaaggatccac	7	11	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:73743385C>T	ENST00000355058.3	-	13	2135	c.1857G>A	c.(1855-1857)caG>caA	p.Q619Q	NUMB_ENST00000555238.1_Silent_p.Q619Q|NUMB_ENST00000555394.1_Silent_p.Q571Q|NUMB_ENST00000359560.3_Silent_p.Q608Q|NUMB_ENST00000559312.1_Silent_p.Q424Q|NUMB_ENST00000535282.1_Silent_p.Q608Q|NUMB_ENST00000556772.1_Silent_p.Q475Q|NUMB_ENST00000555738.2_Silent_p.Q462Q|NUMB_ENST00000544991.3_Silent_p.Q424Q|NUMB_ENST00000560335.1_Silent_p.Q473Q|NUMB_ENST00000356296.4_Silent_p.Q571Q|NUMB_ENST00000454166.4_Silent_p.Q473Q|RP4-647C14.3_ENST00000556578.1_RNA|NUMB_ENST00000554546.1_Silent_p.Q560Q|NUMB_ENST00000557597.1_Silent_p.Q608Q|NUMB_ENST00000554521.2_Silent_p.Q413Q			P49757	NUMB_HUMAN	numb homolog (Drosophila)	619					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		ATGCAGCCCACTGGGCTTCAA	0.488																																					p.Q619Q		Atlas-SNP	.											.	NUMB	56	.	0			c.G1857A						.						73	69	70					14																	73743385		2203	4300	6503	SO:0001819	synonymous_variant	8650	exon13			AGCCCACTGGGCT	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"numb (Drosophila) homolog", "chromosome 14 open reading frame 41"	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.1857G>A	chr14.hg19:g.73743385C>T		143.0	0.0		90.0	4.0	NM_001005743	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Silent	SNP	ENST00000355058.3	hg19	CCDS32116.1																																																																																			.	.		0.488	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1			T	73743385	C	T	73743385	2	4	115	1	0	0	0	0	0	0	0	1	10760	564	20	3		3	NUMB	14	73743385	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	176937	73743385	33606155	340	19879										
GTF2A1	2957	hgsc.bcm.edu	37	chr14	81662585	81662585	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgaccacctgaagaagctggCctaaagcaaaaagcatgcat	9	10	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:81662585C>T	ENST00000553612.1	-	6	882	c.479G>A	c.(478-480)gGc>gAc	p.G160D	GTF2A1_ENST00000434192.2_Splice_Site_p.G121D	NM_001278940.1|NM_015859.3	NP_001265869.1|NP_056943.1	P52655	TF2AA_HUMAN	general transcription factor IIA, 1, 19/37kDa	160					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(234;0.0287)		AAGAAGCTGGCCTAAAGCAAA	0.408																																					p.G160D		Atlas-SNP	.											.	GTF2A1	34	.	0			c.G479A						.						120	110	113					14																	81662585		2203	4300	6503	SO:0001630	splice_region_variant	2957	exon6			AGCTGGCCTAAAG	X75383	CCDS9873.1, CCDS9874.1	14q31	2010-03-23	2002-08-29					"General transcription factors"	4646	protein-coding gene	gene with protein product		600520	"glucose regulated protein, 58kD pseudogene"			8224848	Standard	NM_015859		Approved	TFIIA	uc001xvf.2	P52655		ENST00000553612.1:c.479-1G>A	chr14.hg19:g.81662585C>T		94.0	0.0		68.0	4.0	NM_015859	Q3KNQ9	Missense_Mutation	SNP	ENST00000553612.1	hg19	CCDS9873.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.040802	0.93685	.	.	ENSG00000165417	ENST00000553612;ENST00000344860;ENST00000434192	T;T	0.61627	0.09;0.09	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.74275	0.3695	M	0.67953	2.075	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.69457	-0.5140	10	0.23302	T	0.38	.	19.1268	0.93388	0.0:1.0:0.0:0.0	.	160	P52655	TF2AA_HUMAN	D	160;121;121	ENSP00000452454:G160D;ENSP00000409492:G121D	ENSP00000298173:G160D	G	-	2	0	GTF2A1	80732338	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.270000	0.78493	2.503000	0.84419	0.561000	0.74099	GGC	.	.		0.408	GTF2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413309.1	NM_015859	Missense_Mutation	T	81662585	C	T	81662585	5	4	115	1	0	0	0	0	0	0	1	0	6861	753	26	3	667	3	GTF2A1	14	81662585	Splice_Site	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	7919200	81662585	25686955	341	19880										
RPS6KA5	9252	hgsc.bcm.edu	37	chr14	91386646	91386646	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaacacccaaactccaccagTcaactgcctataaaacaaca	3	15	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:91386646T>C	ENST00000261991.3	-	7	883	c.710A>G	c.(709-711)gAc>gGc	p.D237G	RPS6KA5_ENST00000536315.2_Missense_Mutation_p.D158G|RPS6KA5_ENST00000418736.2_Missense_Mutation_p.D237G	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	237	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		ACTCCACCAGTCAACTGCCTA	0.289																																					p.D237G		Atlas-SNP	.											.	RPS6KA5	135	.	0			c.A710G						.						87	93	91					14																	91386646		2203	4299	6502	SO:0001583	missense	9252	exon7			CACCAGTCAACTG	AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"ribosomal protein S6 kinase, 90kD, polypeptide 5"			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.710A>G	chr14.hg19:g.91386646T>C	ENSP00000261991:p.Asp237Gly	189.0	0.0		103.0	5.0	NM_182398	O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	hg19	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.393621	0.83011	.	.	ENSG00000100784	ENST00000261991;ENST00000536315;ENST00000418736	T;T;T	0.75589	-0.95;-0.95;-0.95	5.31	5.31	0.75309	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.099481	0.64402	D	0.000002	D	0.92648	0.7664	H	0.99609	4.655	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.95857	0.8880	10	0.87932	D	0	.	15.2506	0.73542	0.0:0.0:0.0:1.0	.	237;237	O75582-2;O75582	.;KS6A5_HUMAN	G	237;158;237	ENSP00000261991:D237G;ENSP00000442803:D158G;ENSP00000402787:D237G	ENSP00000261991:D237G	D	-	2	0	RPS6KA5	90456399	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.298000	0.78815	1.998000	0.58463	0.528000	0.53228	GAC	.	.		0.289	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		C	91386646	T	C	91386646	3	2	115	1	0	0	0	0	1	0	0	0	13669	1667	58	2	1748	2	RPS6KA5	14	91386646	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	9724061	91386646	15962894	342	19881										
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91792363	91792363	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gctgttcctccagcatggccTtggtttcaattaaaatgata	8	9	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:91792363T>C	ENST00000389857.6	-	11	1174	c.1088A>G	c.(1087-1089)aAg>aGg	p.K363R		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	363					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				CAGCATGGCCTTGGTTTCAAT	0.473																																					p.K363R		Atlas-SNP	.											.	CCDC88C	192	.	0			c.A1088G						.						47	46	46					14																	91792363		1961	4156	6117	SO:0001583	missense	440193	exon11			ATGGCCTTGGTTT		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"Dvl-associating protein with a high frequency of leucine residues", "spinocerebellar ataxia 40"	611204	"KIAA1509"	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.1088A>G	chr14.hg19:g.91792363T>C	ENSP00000374507:p.Lys363Arg	81.0	0.0		75.0	4.0	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	hg19	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.010011	0.93346	.	.	ENSG00000015133	ENST00000389857	T	0.52983	0.64	5.22	5.22	0.72569	.	0.000000	0.49916	U	0.000138	T	0.66538	0.2799	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67688	-0.5606	10	0.46703	T	0.11	-52.4231	15.1049	0.72312	0.0:0.0:0.0:1.0	.	363	Q9P219	DAPLE_HUMAN	R	363	ENSP00000374507:K363R	ENSP00000374507:K363R	K	-	2	0	CCDC88C	90862116	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.542000	0.82095	1.977000	0.57605	0.454000	0.30748	AAG	.	.		0.473	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		C	91792363	T	C	91792363	3	2	115	1	0	0	0	0	1	0	0	0	2867	1609	56	2	5078	2	CCDC88C	14	91792363	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	405717	91792363	15557177	343	19882										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92466343	92466343	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gggcagtattttccatttgtTtttgtttcagggccaacatg	10	7	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:92466343T>C	ENST00000267622.4	-	12	5040	c.4667A>G	c.(4666-4668)aAa>aGa	p.K1556R		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1556					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TTCCATTTGTTTTTGTTTCAG	0.338			T	PDGFRB	AML																																p.K1556R	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.A4667G						.						117	104	108					14																	92466343		2201	4300	6501	SO:0001583	missense	9321	exon12			ATTTGTTTTTGTT	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.4667A>G	chr14.hg19:g.92466343T>C	ENSP00000267622:p.Lys1556Arg	172.0	0.0		92.0	4.0	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	hg19	CCDS9899.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.884533	0.91814	.	.	ENSG00000100815	ENST00000267622;ENST00000542257	T	0.04862	3.54	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.24160	0.0585	M	0.70275	2.135	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.987	T	0.00790	-1.1565	10	0.30854	T	0.27	.	16.2421	0.82418	0.0:0.0:0.0:1.0	.	1292;1556	F5H1Z0;Q15643	.;TRIPB_HUMAN	R	1556;1292	ENSP00000267622:K1556R	ENSP00000267622:K1556R	K	-	2	0	TRIP11	91536096	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	7.873000	0.87193	2.234000	0.73211	0.533000	0.62120	AAA	.	.		0.338	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			C	92466343	T	C	92466343	3	2	115	1	0	0	0	0	1	0	0	0	16570	1841	64	2	1312	2	TRIP11	14	92466343	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	673980	92466343	14883197	344	19883										
CPSF2	53981	hgsc.bcm.edu	37	chr14	92609578	92609578	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	attctaacctacagaactacTcctgggactttagcacgttt	6	11	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:92609578T>C	ENST00000298875.4	+	9	1365	c.1080T>C	c.(1078-1080)acT>acC	p.T360T		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	360					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		ACAGAACTACTCCTGGGACTT	0.388																																					p.T360T	Ovarian(78;28 1788 18702 44111)	Atlas-SNP	.											.	CPSF2	63	.	0			c.T1080C						.						80	75	77					14																	92609578		2203	4300	6503	SO:0001819	synonymous_variant	53981	exon9			AACTACTCCTGGG	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"cleavage and polyadenylation specific factor 2, 100kD subunit"			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.1080T>C	chr14.hg19:g.92609578T>C		131.0	0.0		62.0	4.0	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Silent	SNP	ENST00000298875.4	hg19	CCDS9902.1																																																																																			.	.		0.388	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1			C	92609578	T	C	92609578	2	2	115	1	0	0	0	0	0	0	0	1	3827	1538	54	2		2	CPSF2	14	92609578	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	143235	92609578	14739962	345	19884										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94120353	94120353	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gagctgagctccatcgcagcTctcagtcagctcctagaggt	11	13	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:94120353T>C	ENST00000393151.2	+	38	6381	c.6381T>C	c.(6379-6381)gcT>gcC	p.A2127A	UNC79_ENST00000256339.4_Silent_p.A1950A|UNC79_ENST00000553484.1_Silent_p.A2149A|UNC79_ENST00000555664.1_Silent_p.A2088A			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2127					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CCATCGCAGCTCTCAGTCAGC	0.502																																					p.A1950A		Atlas-SNP	.											.	UNC79	366	.	0			c.T5850C						.						110	105	107					14																	94120353		2203	4300	6503	SO:0001819	synonymous_variant	57578	exon38			CGCAGCTCTCAGT	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.6381T>C	chr14.hg19:g.94120353T>C		127.0	0.0		81.0	6.0	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	hg19																																																																																				.	.		0.502	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		C	94120353	T	C	94120353	2	2	115	1	0	0	0	0	0	0	0	1	8239	1538	54	2		2	KIAA1409	14	94120353	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1510775	94120353	13229187	346	19885										
ASB2	51676	hgsc.bcm.edu	37	chr14	94404109	94404109	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gttccttcagccgcgagcagAgctgcacgttgcccacgtag	12	14	1	1	rs533852407		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:94404109A>G	ENST00000315988.4	-	7	2050	c.1562T>C	c.(1561-1563)cTc>cCc	p.L521P	ASB2_ENST00000555019.1_Missense_Mutation_p.L569P|RP11-131H24.4_ENST00000557646.1_5'Flank|ASB2_ENST00000556337.1_5'Flank	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	521					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		CCGCGAGCAGAGCTGCACGTT	0.592																																					p.L569P		Atlas-SNP	.											.	ASB2	71	.	0			c.T1706C						.						110	91	97					14																	94404109		2203	4300	6503	SO:0001583	missense	51676	exon9			GAGCAGAGCTGCA	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"Ankyrin repeat domain containing"	16012	protein-coding gene	gene with protein product		605759	"ankyrin repeat and SOCS box-containing 2"				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.1562T>C	chr14.hg19:g.94404109A>G	ENSP00000320675:p.Leu521Pro	125.0	0.0		93.0	4.0	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	hg19	CCDS9915.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.056147	0.76074	.	.	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988;ENST00000543546;ENST00000555507	T;T;T	0.73681	-0.77;-0.66;-0.7	5.13	5.13	0.70059	.	0.062950	0.64402	D	0.000004	D	0.84365	0.5456	M	0.69358	2.11	0.80722	D	1	P;D;P	0.89917	0.747;1.0;0.747	B;D;B	0.87578	0.405;0.998;0.405	D	0.85123	0.0970	10	0.49607	T	0.09	-7.9602	14.9326	0.70929	1.0:0.0:0.0:0.0	.	537;569;521	B3KPZ6;B4E166;Q96Q27	.;.;ASB2_HUMAN	P	569;537;521;467;467	ENSP00000451575:L569P;ENSP00000320675:L521P;ENSP00000450940:L467P	ENSP00000320675:L521P	L	-	2	0	ASB2	93473862	1.000000	0.71417	0.999000	0.59377	0.939000	0.58152	7.476000	0.81055	1.933000	0.56026	0.379000	0.24179	CTC	.	.		0.592	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1			G	94404109	A	G	94404109	3	3	115	1	0	0	0	0	1	0	0	0	1023	304	11	2	209	2	ASB2	14	94404109	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	283756	94404109	12945431	347	19886										
EML1	2009	hgsc.bcm.edu	37	chr14	100380523	100380523	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttttcaatgcagattccagAacagtttggtccaatacgga	8	9	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:100380523A>G	ENST00000262233.6	+	14	1641	c.1502A>G	c.(1501-1503)gAa>gGa	p.E501G	EML1_ENST00000334192.4_Missense_Mutation_p.E520G|EML1_ENST00000327921.9_Missense_Mutation_p.E489G	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	501	Tandem atypical propeller in EMLs.				brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				CAGATTCCAGAACAGTTTGGT	0.428																																					p.E520G		Atlas-SNP	.											.	EML1	97	.	0			c.A1559G						.						112	100	104					14																	100380523		2203	4300	6503	SO:0001583	missense	2009	exon15			TTCCAGAACAGTT	AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"WD repeat domain containing"	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.1502A>G	chr14.hg19:g.100380523A>G	ENSP00000262233:p.Glu501Gly	144.0	0.0		83.0	4.0	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	hg19	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.531344	0.64972	.	.	ENSG00000066629	ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138	T;T;T	0.41065	1.01;1.01;1.01	5.04	5.04	0.67666	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.047681	0.85682	D	0.000000	T	0.62648	0.2445	M	0.68952	2.095	0.80722	D	1	D;B;D	0.89917	1.0;0.012;1.0	D;B;D	0.91635	0.996;0.009;0.999	T	0.65841	-0.6070	10	0.59425	D	0.04	-30.6283	14.7834	0.69784	1.0:0.0:0.0:0.0	.	489;501;520	F8W717;O00423;O00423-3	.;EMAL1_HUMAN;.	G	489;501;520;520	ENSP00000327384:E489G;ENSP00000262233:E501G;ENSP00000334314:E520G	ENSP00000262233:E501G	E	+	2	0	EML1	99450276	1.000000	0.71417	1.000000	0.80357	0.246000	0.25737	9.132000	0.94455	1.899000	0.54978	0.477000	0.44152	GAA	.	.		0.428	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		G	100380523	A	G	100380523	3	3	115	1	0	0	0	0	1	0	0	0	5098	246	9	2	1617	2	EML1	14	100380523	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5976414	100380523	6969017	348	19887										
MTA1	9112	hgsc.bcm.edu	37	chr14	105916421	105916421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tagaagaggaaatggagaacCcggaaatggtggacctgccc	14	8	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr14:105916421C>T	ENST00000331320.7	+	5	482	c.268C>T	c.(268-270)Ccg>Tcg	p.P90S	MTA1_ENST00000406191.1_Missense_Mutation_p.P90S|MTA1_ENST00000405646.1_Missense_Mutation_p.P73S	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	90	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		AATGGAGAACCCGGAAATGGT	0.627																																					p.P90S		Atlas-SNP	.											MTA1,NS,carcinoma,0,1	MTA1	61	.	0			c.C268T						.						61	66	64					14																	105916421		2203	4300	6503	SO:0001583	missense	9112	exon5			GAGAACCCGGAAA	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"GATA zinc finger domain containing"	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.268C>T	chr14.hg19:g.105916421C>T	ENSP00000333633:p.Pro90Ser	147.0	0.0		100.0	0.0	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	19.02	3.746070	0.69418	.	.	ENSG00000182979	ENST00000331320;ENST00000406191;ENST00000405646;ENST00000498644	D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02	4.14	4.14	0.48551	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	U	0.000000	D	0.83367	0.5239	L	0.56396	1.775	0.80722	D	1	P	0.38250	0.624	B	0.39465	0.3	D	0.83910	0.0295	10	0.41790	T	0.15	-11.5496	14.9627	0.71169	0.0:1.0:0.0:0.0	.	90	Q13330	MTA1_HUMAN	S	90;90;73;4	ENSP00000333633:P90S;ENSP00000385702:P90S;ENSP00000384180:P73S;ENSP00000448146:P4S	ENSP00000333633:P90S	P	+	1	0	MTA1	104987466	1.000000	0.71417	0.914000	0.36105	0.674000	0.39518	3.448000	0.52943	1.839000	0.53478	0.306000	0.20318	CCG	.	.		0.627	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			T	105916421	C	T	105916421	3	4	115	1	0	0	0	0	1	0	0	0	9917	623	22	3	286	3	MTA1	14	105916421	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	5535898	105916421	1433119	349	19888										
CHRM5	1133	hgsc.bcm.edu	37	chr15	34355738	34355738	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	accaggcctcctggtcatccTcccgcaggagcacctccacc	8	20	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:34355738T>C	ENST00000383263.5	+	3	1490	c.820T>C	c.(820-822)Tcc>Ccc	p.S274P	CHRM5_ENST00000557872.1_Missense_Mutation_p.S274P	NM_012125.3	NP_036257.1	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	274					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|dopamine transport (GO:0015872)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|gastric acid secretion (GO:0001696)|metabolic process (GO:0008152)|regulation of phosphatidylinositol dephosphorylation (GO:0060304)|transmission of nerve impulse (GO:0019226)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	20		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Imipramine(DB00458)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CTGGTCATCCTCCCGCAGGAG	0.622																																					p.S274P		Atlas-SNP	.											.	CHRM5	59	.	0			c.T820C						.						47	47	47					15																	34355738		2201	4298	6499	SO:0001583	missense	1133	exon3			TCATCCTCCCGCA		CCDS10031.1	15q26	2012-08-08			ENSG00000184984	ENSG00000184984		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1954	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 5"	118496					Standard	NM_012125		Approved		uc001zhk.1	P08912	OTTHUMG00000129369	ENST00000383263.5:c.820T>C	chr15.hg19:g.34355738T>C	ENSP00000372750:p.Ser274Pro	33.0	0.0		54.0	24.0	NM_012125	Q96RG7	Missense_Mutation	SNP	ENST00000383263.5	hg19	CCDS10031.1	.	.	.	.	.	.	.	.	.	.	T	11.50	1.656802	0.29425	.	.	ENSG00000184984	ENST00000383263	T	0.63255	-0.03	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.306724	0.32028	N	0.006691	T	0.56702	0.2003	L	0.39085	1.19	0.58432	D	0.999995	B	0.32939	0.391	B	0.37731	0.257	T	0.55296	-0.8163	10	0.33141	T	0.24	-21.8193	15.6252	0.76851	0.0:0.0:0.0:1.0	.	274	P08912	ACM5_HUMAN	P	274	ENSP00000372750:S274P	ENSP00000372750:S274P	S	+	1	0	CHRM5	32143030	1.000000	0.71417	1.000000	0.80357	0.488000	0.33401	7.812000	0.86109	2.275000	0.75901	0.528000	0.53228	TCC	.	.		0.622	CHRM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251521.2			C	34355738	T	C	34355738	3	2	115	1	0	0	0	0	1	0	0	0	3382	1551	54	2	822	2	CHRM5	15	34355738	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10		34355738	68175654	350	19889										
CASC5	57082	hgsc.bcm.edu	37	chr15	40897317	40897317	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcctttttcagtgacaatatAgagagacctgttagaagacg	9	7	1	5			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:40897317A>G	ENST00000346991.5	+	3	435	c.45A>G	c.(43-45)atA>atG	p.I15M	CASC5_ENST00000527044.1_Missense_Mutation_p.I15M|snoU13_ENST00000459027.1_RNA|CASC5_ENST00000399668.2_Missense_Mutation_p.I15M			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	15	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.I15M(2)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GTGACAATATAGAGAGACCTG	0.303																																					p.I15M		Atlas-SNP	.											CASC5_ENST00000346991,NS,carcinoma,0,2	CASC5	269	.	2	Substitution - Missense(2)	kidney(2)	c.A45G						.						140	133	135					15																	40897317		1825	4071	5896	SO:0001583	missense	57082	exon3			CAATATAGAGAGA	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.45A>G	chr15.hg19:g.40897317A>G	ENSP00000335463:p.Ile15Met	144.0	1.0		56.0	3.0	NM_144508	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	hg19	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	A	9.239	1.037721	0.19669	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000527044;ENST00000399668	T;T;T	0.20598	2.06;2.06;2.06	5.1	1.48	0.22813	.	0.666646	0.12871	N	0.432303	T	0.08891	0.0220	N	0.08118	0	0.09310	N	1	B;B;B	0.20780	0.048;0.048;0.048	B;B;B	0.16289	0.015;0.015;0.015	T	0.29027	-1.0025	10	0.41790	T	0.15	.	3.2925	0.06954	0.6458:0.0:0.1844:0.1699	.	15;15;15	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	M	15	ENSP00000335463:I15M;ENSP00000432654:I15M;ENSP00000382576:I15M	ENSP00000260369:I15M	I	+	3	3	CASC5	38684609	0.014000	0.17966	0.186000	0.23195	0.664000	0.39144	0.539000	0.23175	0.079000	0.16929	0.533000	0.62120	ATA	.	.		0.303	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		G	40897317	A	G	40897317	3	3	115	1	0	0	0	0	1	0	0	0	2665	410	15	2	51	2	CASC5	15	40897317	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6541579	40897317	61634075	351	19890										
UBR1	197131	hgsc.bcm.edu	37	chr15	43360145	43360145	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gggcctctgcgagctcacagTcaagagctctttgtaggctg	13	11	4	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:43360145T>C	ENST00000290650.4	-	6	827	c.749A>G	c.(748-750)gAc>gGc	p.D250G	UBR1_ENST00000382177.2_Missense_Mutation_p.D250G	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	250					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GAGCTCACAGTCAAGAGCTCT	0.428																																					p.D250G		Atlas-SNP	.											.	UBR1	124	.	0			c.A749G						.						121	112	115					15																	43360145		2203	4299	6502	SO:0001583	missense	197131	exon6			TCACAGTCAAGAG		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.749A>G	chr15.hg19:g.43360145T>C	ENSP00000290650:p.Asp250Gly	102.0	0.0		78.0	4.0	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	hg19	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.142152	0.37825	.	.	ENSG00000159459	ENST00000290650;ENST00000382177;ENST00000546274	T;T	0.69435	0.41;-0.4	5.73	4.61	0.57282	Adaptor protein ClpS, core (1);Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like (2);	0.268407	0.43260	D	0.000592	T	0.27063	0.0663	N	0.01009	-1.055	0.32079	N	0.593426	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.40627	-0.9553	10	0.05351	T	0.99	-4.8412	4.6682	0.12676	0.0:0.2668:0.0:0.7332	.	250;250	B4DYL2;Q8IWV7	.;UBR1_HUMAN	G	250	ENSP00000290650:D250G;ENSP00000371612:D250G	ENSP00000290650:D250G	D	-	2	0	UBR1	41147437	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.117000	0.41939	2.171000	0.68590	0.528000	0.53228	GAC	.	.		0.428	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		C	43360145	T	C	43360145	3	2	115	1	0	0	0	0	1	0	0	0	16916	1667	58	2	4668	2	UBR1	15	43360145	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2462828	43360145	59171247	352	19891										
ZSCAN29	146050	hgsc.bcm.edu	37	chr15	43661910	43661910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gatctccccaggtaagacggTcaggaactgctctagcacca	10	13	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:43661910T>C	ENST00000396976.2	-	1	336	c.202A>G	c.(202-204)Acc>Gcc	p.T68A	TUBGCP4_ENST00000570081.1_Intron|ZSCAN29_ENST00000396972.1_Missense_Mutation_p.T68A|ZSCAN29_ENST00000563508.1_5'Flank|ZSCAN29_ENST00000568898.1_Missense_Mutation_p.T67A|ZSCAN29_ENST00000562072.1_Missense_Mutation_p.T67A|TUBGCP4_ENST00000564079.1_5'Flank|TUBGCP4_ENST00000260383.7_5'Flank	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	68	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		GGTAAGACGGTCAGGAACTGC	0.527																																					p.T68A		Atlas-SNP	.											.	ZSCAN29	57	.	0			c.A202G						.						101	100	100					15																	43661910		2201	4299	6500	SO:0001583	missense	146050	exon1			AGACGGTCAGGAA	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"-", "Zinc fingers, C2H2-type"	26673	protein-coding gene	gene with protein product			"zinc finger protein 690"	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.202A>G	chr15.hg19:g.43661910T>C	ENSP00000380174:p.Thr68Ala	113.0	0.0		93.0	4.0	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Missense_Mutation	SNP	ENST00000396976.2	hg19	CCDS10095.2	.	.	.	.	.	.	.	.	.	.	T	12.59	1.983983	0.35036	.	.	ENSG00000140265	ENST00000396976;ENST00000396972	T;T	0.04317	3.65;3.65	4.79	2.43	0.29744	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.263624	0.26971	N	0.021565	T	0.05273	0.0140	L	0.53617	1.68	0.80722	D	1	B;B;B;B	0.17038	0.0;0.02;0.008;0.014	B;B;B;B	0.22880	0.001;0.042;0.02;0.017	T	0.33163	-0.9879	10	0.39692	T	0.17	-0.4876	4.1613	0.10285	0.1778:0.1089:0.0:0.7133	.	68;67;68;68	Q8IWY8-4;C9K0J8;Q8IWY8-3;Q8IWY8	.;.;.;ZSC29_HUMAN	A	68	ENSP00000380174:T68A;ENSP00000380170:T68A	ENSP00000380170:T68A	T	-	1	0	ZSCAN29	41449202	0.973000	0.33851	0.990000	0.47175	0.998000	0.95712	1.100000	0.31025	0.393000	0.25203	0.533000	0.62120	ACC	.	.		0.527	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455		C	43661910	T	C	43661910	3	2	115	1	0	0	0	0	1	0	0	0	18251	1667	58	2	2376	2	ZSCAN29	15	43661910	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	301765	43661910	58869482	353	19892										
FBN1	2200	hgsc.bcm.edu	37	chr15	48738934	48738934	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttgttgtgagaaaggatgaaAccatgattgcagcggcagtt	13	5	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:48738934A>G	ENST00000316623.5	-	47	6212	c.5757T>C	c.(5755-5757)ggT>ggC	p.G1919G		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1919	EGF-like 32; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		AAAGGATGAAACCATGATTGC	0.403																																					p.G1919G		Atlas-SNP	.											.	FBN1	310	.	0			c.T5757C						.						114	105	108					15																	48738934		2198	4295	6493	SO:0001819	synonymous_variant	2200	exon47			GATGAAACCATGA	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5757T>C	chr15.hg19:g.48738934A>G		64.0	0.0		61.0	4.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	hg19	CCDS32232.1																																																																																			.	.		0.403	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			G	48738934	A	G	48738934	2	3	115	1	0	0	0	0	0	0	0	1	5710	30	2	2		2	FBN1	15	48738934	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5077024	48738934	53792458	354	19893										
USP50	373509	hgsc.bcm.edu	37	chr15	50833322	50833322	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cgttcttgtaggtgcatttcTcacactttaaacatacgatg	7	9	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:50833322T>C	ENST00000532404.1	-	4	757	c.584A>G	c.(583-585)gAg>gGg	p.E195G	USP50_ENST00000530218.1_Intron	NM_203494.4	NP_987090.2	Q70EL3	UBP50_HUMAN	ubiquitin specific peptidase 50	200	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(5)	13				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)		GGTGCATTTCTCACACTTTAA	0.448																																					p.E195G		Atlas-SNP	.											.	USP50	24	.	0			c.A584G						.						153	147	149					15																	50833322		1964	4151	6115	SO:0001583	missense	373509	exon4			CATTTCTCACACT	AI990110	CCDS53944.1	15q21.1	2008-02-05	2005-08-08			ENSG00000170236		"Ubiquitin-specific peptidases"	20079	protein-coding gene	gene with protein product			"ubiquitin specific protease 50"			12838346	Standard	NM_203494		Approved		uc021sky.1	Q70EL3		ENST00000532404.1:c.584A>G	chr15.hg19:g.50833322T>C	ENSP00000434676:p.Glu195Gly	94.0	0.0		85.0	4.0	NM_203494	E9PP86	Missense_Mutation	SNP	ENST00000532404.1	hg19	CCDS53944.1	.	.	.	.	.	.	.	.	.	.	T	16.96	3.266740	0.59540	.	.	ENSG00000170236	ENST00000532404	T	0.26957	1.7	5.45	5.45	0.79879	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.235440	0.38492	N	0.001677	T	0.23094	0.0558	N	0.16478	0.41	0.34385	D	0.693571	D	0.54964	0.969	P	0.55749	0.783	T	0.04565	-1.0942	10	0.02654	T	1	-24.2808	13.0409	0.58899	0.0:0.0:0.0:1.0	.	200	Q70EL3	UBP50_HUMAN	G	195	ENSP00000434676:E195G	ENSP00000434676:E195G	E	-	2	0	USP50	48620614	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	5.140000	0.64807	2.051000	0.60960	0.459000	0.35465	GAG	.	.		0.448	USP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395249.1			C	50833322	T	C	50833322	3	2	115	1	0	0	0	0	1	0	0	0	17097	1551	54	2	436	2	USP50	15	50833322	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2094388	50833322	51698070	355	19894										
TRPM7	54822	hgsc.bcm.edu	37	chr15	50881855	50881855	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tccatgctatctctgtgtccTttaatagaaaaaaagatgtt	6	7	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:50881855T>C	ENST00000313478.7	-	27	4606		c.e27-2		TRPM7_ENST00000560955.1_Splice_Site	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7						actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		CTCTGTGTCCTTTAATAGAAA	0.289																																					.		Atlas-SNP	.											.	TRPM7	145	.	0			c.4325-2A>G						.						118	109	112					15																	50881855		1783	4056	5839	SO:0001630	splice_region_variant	54822	exon28			GTGTCCTTTAATA	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.4325-2A>G	chr15.hg19:g.50881855T>C		81.0	0.0		56.0	4.0	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Splice_Site	SNP	ENST00000313478.7	hg19	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.985798	0.53934	.	.	ENSG00000092439	ENST00000313478	.	.	.	4.5	3.37	0.38596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8202	0.40878	0.0:0.0823:0.0:0.9177	.	.	.	.	.	-1	.	.	.	-	.	.	TRPM7	48669147	1.000000	0.71417	0.955000	0.39395	0.896000	0.52359	4.107000	0.57811	0.604000	0.29930	0.528000	0.53228	.	.	.		0.289	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672	Intron	C	50881855	T	C	50881855	5	2	115	1	0	0	0	0	0	0	1	0	16606	1623	56	2	1326	2	TRPM7	15	50881855	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	48533	50881855	51649537	356	19895										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52697484	52697484	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaagcttattctgaacttacAggtattgtgcagctgtctgc	9	8	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:52697484A>G	ENST00000399231.3	-	9	1296	c.1053T>C	c.(1051-1053)ccT>ccC	p.P351P	MYO5A_ENST00000399233.2_Splice_Site_p.P351P|MYO5A_ENST00000356338.6_Splice_Site_p.P351P|MYO5A_ENST00000358212.6_Splice_Site_p.P351P|MYO5A_ENST00000553916.1_Splice_Site_p.P351P	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	351	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		CTGAACTTACAGGTATTGTGC	0.363																																					p.P351P		Atlas-SNP	.											.	MYO5A	145	.	0			c.T1053C						.						76	69	71					15																	52697484		1876	4099	5975	SO:0001630	splice_region_variant	4644	exon9			ACTTACAGGTATT		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.1053+1T>C	chr15.hg19:g.52697484A>G		67.0	0.0		88.0	5.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	hg19	CCDS42037.1																																																																																			.	.		0.363	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	Silent	G	52697484	A	G	52697484	5	3	115	1	0	0	0	0	0	0	1	0	10087	202	7	2	4646	2	MYO5A	15	52697484	Splice_Site	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1815629	52697484	49833908	357	19896										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54590036	54590036	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gacagataagtcagctgtatCtggggccatacgattgaaaa	11	7	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:54590036C>A	ENST00000260323.11	+	11	4016	c.4016C>A	c.(4015-4017)tCt>tAt	p.S1339Y	UNC13C_ENST00000537900.1_Missense_Mutation_p.S1337Y|UNC13C_ENST00000545554.1_Missense_Mutation_p.S1339Y	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1339					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCAGCTGTATCTGGGGCCATA	0.363																																					p.S1339Y		Atlas-SNP	.											.	UNC13C	674	.	0			c.C4016A						.						65	64	64					15																	54590036		1856	4087	5943	SO:0001583	missense	440279	exon10			CTGTATCTGGGGC	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.4016C>A	chr15.hg19:g.54590036C>A	ENSP00000260323:p.Ser1339Tyr	340.0	0.0		304.0	104.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.644585	0.87859	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.71579	-0.58;-0.58;-0.58	5.59	5.59	0.84812	C2 calcium/lipid-binding domain, CaLB (1);	0.113447	0.64402	D	0.000009	D	0.85927	0.5811	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.981;0.997	D	0.87560	0.2471	10	0.87932	D	0	.	18.5536	0.91075	0.0:1.0:0.0:0.0	.	1339;1339	F5H090;Q8NB66	.;UN13C_HUMAN	Y	1339;1339;1337	ENSP00000260323:S1339Y;ENSP00000438156:S1339Y;ENSP00000442569:S1337Y	ENSP00000260323:S1339Y	S	+	2	0	UNC13C	52377328	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	7.776000	0.85560	2.605000	0.88082	0.650000	0.86243	TCT	.	.		0.363	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54590036	C	A	54590036	3	1	115	1	0	0	0	0	1	0	0	0	17001	913	32	3	4054	3	UNC13C	15	54590036	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	1892552	54590036	47941356	358	19897										
AQP9	366	hgsc.bcm.edu	37	chr15	58467128	58467128	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctttcatagatggacttatgTcctttgctggtggaaaactg	10	7	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:58467128T>C	ENST00000219919.4	+	4	758	c.388T>C	c.(388-390)Tcc>Ccc	p.S130P	ALDH1A2_ENST00000558231.1_Intron|AQP9_ENST00000536493.1_Missense_Mutation_p.S130P|AQP9_ENST00000558772.1_Missense_Mutation_p.S65P	NM_020980.3	NP_066190.2	O43315	AQP9_HUMAN	aquaporin 9	130					amine transport (GO:0015837)|canalicular bile acid transport (GO:0015722)|carboxylic acid transport (GO:0046942)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|glycerol transport (GO:0015793)|immune response (GO:0006955)|metabolic process (GO:0008152)|polyol transport (GO:0015791)|purine nucleobase transport (GO:0006863)|pyrimidine nucleobase transport (GO:0015855)|pyrimidine-containing compound transmembrane transport (GO:0072531)|response to mercury ion (GO:0046689)|response to organic substance (GO:0010033)|response to osmotic stress (GO:0006970)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water homeostasis (GO:0030104)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carboxylic acid transmembrane transporter activity (GO:0046943)|glycerol channel activity (GO:0015254)|polyol transmembrane transporter activity (GO:0015166)|porin activity (GO:0015288)|purine nucleobase transmembrane transporter activity (GO:0005345)|pyrimidine nucleobase transmembrane transporter activity (GO:0005350)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)	p.S130T(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)	21				GBM - Glioblastoma multiforme(80;0.16)		TGGACTTATGTCCTTTGCTGG	0.478																																					p.S130P		Atlas-SNP	.											AQP9,NS,carcinoma,0,1	AQP9	39	.	1	Substitution - Missense(1)	lung(1)	c.T388C						.						134	120	125					15																	58467128		2192	4292	6484	SO:0001583	missense	366	exon4			CTTATGTCCTTTG	AF016495	CCDS10165.1	15q	2005-09-20			ENSG00000103569	ENSG00000103569		"Ion channels / Aquaporins"	643	protein-coding gene	gene with protein product		602914					Standard	NM_020980		Approved	SSC1, HsT17287	uc002aez.2	O43315	OTTHUMG00000132631	ENST00000219919.4:c.388T>C	chr15.hg19:g.58467128T>C	ENSP00000219919:p.Ser130Pro	108.0	1.0		144.0	6.0	NM_020980	Q9NP32	Missense_Mutation	SNP	ENST00000219919.4	hg19	CCDS10165.1	.	.	.	.	.	.	.	.	.	.	t	7.335	0.619818	0.14193	.	.	ENSG00000103569	ENST00000219919;ENST00000536493	T;T	0.11604	2.76;2.76	5.4	-1.85	0.07784	Aquaporin-like (2);	0.731491	0.12956	N	0.425450	T	0.10035	0.0246	L	0.46157	1.445	0.09310	N	1	B	0.31599	0.33	B	0.37480	0.251	T	0.36286	-0.9754	10	0.27785	T	0.31	.	7.3998	0.26956	0.2668:0.0:0.3994:0.3338	.	130	O43315	AQP9_HUMAN	P	130	ENSP00000219919:S130P;ENSP00000441390:S130P	ENSP00000219919:S130P	S	+	1	0	AQP9	56254420	1.000000	0.71417	0.975000	0.42487	0.039000	0.13416	0.914000	0.28624	-0.108000	0.12066	-1.176000	0.01726	TCC	.	.		0.478	AQP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255878.2	NM_020980		C	58467128	T	C	58467128	3	2	115	1	0	0	0	0	1	0	0	0	833	1667	58	2	402	2	AQP9	15	58467128	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3877092	58467128	44064264	359	19898										
NARG2	79664	hgsc.bcm.edu	37	chr15	60768331	60768331	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctttataattttctcgagagAaaaatgtcttaaggccattt	6	6	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:60768331A>G	ENST00000261520.4	-	3	311	c.77T>C	c.(76-78)tTc>tCc	p.F26S	NARG2_ENST00000439632.1_5'UTR|NARG2_ENST00000561114.1_Missense_Mutation_p.F26S|NARG2_ENST00000558654.1_5'UTR	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						TTCTCGAGAGAAAAATGTCTT	0.308																																					p.F26S		Atlas-SNP	.											.	NARG2	82	.	0			c.T77C						.						46	50	48					15																	60768331		2201	4294	6495	SO:0001583	missense	79664	exon3			CGAGAGAAAAATG																												ENST00000261520.4:c.77T>C	chr15.hg19:g.60768331A>G	ENSP00000261520:p.Phe26Ser	123.0	0.0		85.0	4.0	NM_024611		Missense_Mutation	SNP	ENST00000261520.4	hg19	CCDS10176.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.252236	0.80135	.	.	ENSG00000128915	ENST00000261520	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.66934	0.2840	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.70335	-0.4900	9	0.87932	D	0	-15.953	14.6261	0.68621	1.0:0.0:0.0:0.0	.	26	Q659A1	NARG2_HUMAN	S	26	.	ENSP00000261520:F26S	F	-	2	0	NARG2	58555623	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.812000	0.69194	2.239000	0.73571	0.533000	0.62120	TTC	.	.		0.308	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			G	60768331	A	G	60768331	3	3	115	1	0	0	0	0	1	0	0	0	10178	246	9	2	2927	2	NARG2	15	60768331	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2301203	60768331	41763061	360	19899										
PIF1	80119	hgsc.bcm.edu	37	chr15	65108548	65108548	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaggctgcctcatcatcatcTggggactcctggatcagagc	12	12	5	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:65108548T>C	ENST00000268043.4	-	13	1969	c.1875A>G	c.(1873-1875)ccA>ccG	p.P625P	PIF1_ENST00000333425.6_Intron|PIF1_ENST00000559239.1_Silent_p.P625P					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						CATCATCATCTGGGGACTCCT	0.577																																					p.P625P		Atlas-SNP	.											.	PIF1	43	.	0			c.A1875G						.						94	86	89					15																	65108548		2202	4299	6501	SO:0001819	synonymous_variant	80119	exon13			ATCATCTGGGGAC	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"chromosome 15 open reading frame 20", "PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.1875A>G	chr15.hg19:g.65108548T>C		90.0	0.0		96.0	4.0	NM_025049		Silent	SNP	ENST00000268043.4	hg19	CCDS10195.2																																																																																			.	.		0.577	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049		C	65108548	T	C	65108548	2	2	115	1	0	0	0	0	0	0	0	1	11892	1567	55	2		2	PIF1	15	65108548	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4340217	65108548	37422844	361	19900										
DENND4A	10260	hgsc.bcm.edu	37	chr15	65956954	65956954	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctaaaatctgactcattggTccatagacatcattcatttt	4	9	5	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:65956954T>C	ENST00000431932.2	-	30	5542	c.5334A>G	c.(5332-5334)ggA>ggG	p.G1778G	DENND4A_ENST00000443035.3_Silent_p.G1821G	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1778					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						GACTCATTGGTCCATAGACAT	0.333																																					p.G1821G		Atlas-SNP	.											.	DENND4A	217	.	0			c.A5463G						.						101	95	97					15																	65956954		1830	4081	5911	SO:0001819	synonymous_variant	10260	exon31			CATTGGTCCATAG	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.5334A>G	chr15.hg19:g.65956954T>C		169.0	0.0		149.0	7.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	hg19	CCDS45285.1																																																																																			.	.		0.333	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		C	65956954	T	C	65956954	2	2	115	1	0	0	0	0	0	0	0	1	4435	1654	58	2		2	DENND4A	15	65956954	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	848406	65956954	36574438	362	19901										
CELF6	60677	hgsc.bcm.edu	37	chr15	72581260	72581260	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgcagggggtcagccacgcCggggctctgggctggggaga	20	11	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:72581260C>A	ENST00000569547.1	-	9	1113	c.1042G>T	c.(1042-1044)Ggc>Tgc	p.G348C	RP11-106M3.3_ENST00000570175.1_RNA|CELF6_ENST00000567083.1_Missense_Mutation_p.G348C|RP11-106M3.2_ENST00000379915.4_RNA|CELF6_ENST00000539635.1_Missense_Mutation_p.G209C|CELF6_ENST00000543764.2_Intron|CELF6_ENST00000395258.2_Missense_Mutation_p.G235C|CELF6_ENST00000569311.1_5'Flank|CELF6_ENST00000287202.5_Missense_Mutation_p.G348C			Q96J87	CELF6_HUMAN	CUGBP, Elav-like family member 6	348					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(2)	13						TCAGCCACGCCGGGGCTCTGG	0.677																																					p.G348C		Atlas-SNP	.											.	CELF6	30	.	0			c.G1042T						.						5	5	5					15																	72581260		2019	3993	6012	SO:0001583	missense	60677	exon9			CCACGCCGGGGCT	AF425606	CCDS10242.1, CCDS53955.1, CCDS53956.1	15q24	2013-02-12	2010-02-19	2010-02-19	ENSG00000140488	ENSG00000140488		"RNA binding motif (RRM) containing"	14059	protein-coding gene	gene with protein product		612681	"Bruno (Drosophila) -like 6, RNA binding protein", "bruno-like 6, RNA binding protein (Drosophila)"	BRUNOL6		10893231	Standard	NM_052840		Approved		uc002auh.2	Q96J87	OTTHUMG00000133444	ENST00000569547.1:c.1042G>T	chr15.hg19:g.72581260C>A	ENSP00000454749:p.Gly348Cys	189.0	0.0		204.0	93.0	NM_001172684	B4DG28|B4DJB6|Q6PII4|Q6ZNJ7|Q8N607	Missense_Mutation	SNP	ENST00000569547.1	hg19	CCDS10242.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.063340	0.36373	.	.	ENSG00000140488	ENST00000287202;ENST00000437872;ENST00000379915;ENST00000395258;ENST00000539635	T;T;T	0.24908	1.83;2.07;3.57	4.75	1.26	0.21427	.	0.285626	0.24838	U	0.035190	T	0.37812	0.1017	L	0.57536	1.79	0.27313	N	0.957257	D;D;D;D	0.65815	0.988;0.995;0.994;0.988	P;D;P;P	0.67725	0.687;0.953;0.757;0.687	T	0.09975	-1.0650	10	0.66056	D	0.02	.	5.2205	0.15366	0.0:0.4738:0.0:0.5262	.	348;235;209;348	B4DJB6;Q96J87-2;B3KWE6;Q96J87	.;.;.;CELF6_HUMAN	C	348;348;199;235;209	ENSP00000287202:G348C;ENSP00000378677:G235C;ENSP00000443162:G209C	ENSP00000287202:G348C	G	-	1	0	CELF6	70368314	0.044000	0.20184	0.989000	0.46669	0.986000	0.74619	0.761000	0.26489	0.410000	0.25675	0.561000	0.74099	GGC	.	.		0.677	CELF6-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000420180.1	NM_052840		A	72581260	C	A	72581260	3	1	115	1	0	0	0	0	1	0	0	0	3222	652	23	1	419	1	CELF6	15	72581260	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	6624306	72581260	29950132	363	19902										
HEXA	3073	hgsc.bcm.edu	37	chr15	72638893	72638893	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aatgccaggggttccactatGtagaaatccttccagtcagg	10	10	1	1	rs587779406		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:72638893G>C	ENST00000268097.5	-	11	1808	c.1305C>G	c.(1303-1305)taC>taG	p.Y435*	RP11-106M3.2_ENST00000379915.4_RNA|RP11-106M3.3_ENST00000570175.1_RNA|HEXA_ENST00000457859.2_Intron|HEXA_ENST00000429918.2_Nonsense_Mutation_p.Y262*|HEXA_ENST00000567159.1_Nonsense_Mutation_p.Y435*|HEXA_ENST00000566304.1_Nonsense_Mutation_p.Y446*	NM_000520.4	NP_000511.2	P06865	HEXA_HUMAN	hexosaminidase A (alpha polypeptide)	435					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)	p.Y435Y(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	24						GTTCCACTATGTAGAAATCCT	0.572																																					p.Y435X		Atlas-SNP	.											HEXA,rectum,carcinoma,0,2	HEXA	48	.	1	Substitution - coding silent(1)	ovary(1)	c.C1305G						.						101	109	107					15																	72638893		2199	4297	6496	SO:0001587	stop_gained	3073	exon11			CACTATGTAGAAA	M13520	CCDS10243.1	15q24.1	2012-10-02			ENSG00000213614	ENSG00000213614	3.2.1.52		4878	protein-coding gene	gene with protein product	"Tay Sachs disease", "GM2 gangliosidosis"	606869				2952641, 3013851	Standard	NM_000520		Approved		uc002aun.4	P06865	OTTHUMG00000133445	ENST00000268097.5:c.1305C>G	chr15.hg19:g.72638893G>C	ENSP00000268097:p.Tyr435*	92.0	0.0		133.0	0.0	NM_000520	B4DKE7|E7ENH7|Q53HS8|Q6AI32	Nonsense_Mutation	SNP	ENST00000268097.5	hg19	CCDS10243.1	.	.	.	.	.	.	.	.	.	.	G	38	6.701998	0.97776	.	.	ENSG00000213614	ENST00000268097;ENST00000429918	.	.	.	5.88	2.7	0.31948	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.1925	9.9799	0.41806	0.3062:0.0:0.6938:0.0	.	.	.	.	X	435;262	.	ENSP00000268097:Y435X	Y	-	3	2	HEXA	70425947	1.000000	0.71417	0.067000	0.19924	0.922000	0.55478	3.432000	0.52824	0.267000	0.21916	0.655000	0.94253	TAC	.	.		0.572	HEXA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257317.2	NM_000520		C	72638893	G	C	72638893	4	2	115	1	0	0	0	0	0	1	0	0	7082	1372	48	4	300	4	HEXA	15	72638893	Nonsense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	57633	72638893	29892499	364	19903										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75969161	75969161	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cgaaggccagccgccctgaaTccacatcggcttgcgtgaag	12	14	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:75969161T>C	ENST00000308508.5	-	10	5791	c.5699A>G	c.(5698-5700)gAt>gGt	p.D1900G	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1900	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCGCCCTGAATCCACATCGGC	0.667																																					p.D1900G		Atlas-SNP	.											.	CSPG4	175	.	0			c.A5699G						.						23	24	24					15																	75969161		2197	4291	6488	SO:0001583	missense	1464	exon10			CCTGAATCCACAT	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.5699A>G	chr15.hg19:g.75969161T>C	ENSP00000312506:p.Asp1900Gly	70.0	0.0		85.0	4.0	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	hg19	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.117699	0.56505	.	.	ENSG00000173546	ENST00000308508	T	0.21734	1.99	5.29	5.29	0.74685	.	0.085952	0.49916	D	0.000133	T	0.27098	0.0664	M	0.68593	2.085	0.48236	D	0.999612	P	0.48089	0.905	B	0.41894	0.369	T	0.08186	-1.0734	10	0.62326	D	0.03	.	14.4022	0.67056	0.0:0.0:0.0:1.0	.	1900	Q6UVK1	CSPG4_HUMAN	G	1900	ENSP00000312506:D1900G	ENSP00000312506:D1900G	D	-	2	0	CSPG4	73756216	1.000000	0.71417	0.901000	0.35422	0.263000	0.26337	7.751000	0.85126	1.991000	0.58162	0.459000	0.35465	GAT	.	.		0.667	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		C	75969161	T	C	75969161	3	2	115	1	0	0	0	0	1	0	0	0	3962	1435	50	2	1273	2	CSPG4	15	75969161	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3330268	75969161	26562231	365	19904										
TSPAN3	10099	hgsc.bcm.edu	37	chr15	77348564	77348564	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atcataagtgatgaagacatAggctcccacatagcataaaa	7	8	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:77348564A>G	ENST00000267970.4	-	2	370	c.97T>C	c.(97-99)Tat>Cat	p.Y33H	TSPAN3_ENST00000559494.1_Intron|TSPAN3_ENST00000558394.1_5'UTR|TSPAN3_ENST00000561277.1_5'UTR|TSPAN3_ENST00000346495.2_Missense_Mutation_p.Y33H|TSPAN3_ENST00000424443.3_Intron|TSPAN3_ENST00000558745.1_5'UTR	NM_001168412.1|NM_005724.5|NM_198902.2	NP_001161884.1|NP_005715.1|NP_944492.1	O60637	TSN3_HUMAN	tetraspanin 3	33						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	10				all cancers(203;1.14e-19)		ATGAAGACATAGGCTCCCACA	0.428																																					p.Y33H		Atlas-SNP	.											.	TSPAN3	21	.	0			c.T97C						.						99	99	99					15																	77348564		2196	4294	6490	SO:0001583	missense	10099	exon2			AGACATAGGCTCC		CCDS10292.1, CCDS10293.1, CCDS53963.1	15q23	2013-02-14	2005-03-21	2005-03-21	ENSG00000140391	ENSG00000140391		"Tetraspanins"	17752	protein-coding gene	gene with protein product		613134	"transmembrane 4 superfamily member 8"	TM4SF8			Standard	NM_005724		Approved	TM4-A, TSPAN-3	uc002bcj.3	O60637	OTTHUMG00000143728	ENST00000267970.4:c.97T>C	chr15.hg19:g.77348564A>G	ENSP00000267970:p.Tyr33His	94.0	0.0		97.0	4.0	NM_198902	A6NEH4|B3KQQ2|B4DP19|Q9BW22|Q9NVX9	Missense_Mutation	SNP	ENST00000267970.4	hg19	CCDS10292.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.985404	0.93044	.	.	ENSG00000140391	ENST00000267970;ENST00000346495	T;T	0.80738	-1.41;-1.41	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.89111	0.6622	M	0.85777	2.775	0.80722	D	1	P;P	0.42248	0.774;0.604	P;P	0.54431	0.752;0.566	D	0.89950	0.4079	10	0.59425	D	0.04	.	16.3196	0.82941	1.0:0.0:0.0:0.0	.	33;33	A6NEH4;O60637	.;TSN3_HUMAN	H	33	ENSP00000267970:Y33H;ENSP00000341329:Y33H	ENSP00000267970:Y33H	Y	-	1	0	TSPAN3	75135619	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	9.313000	0.96297	2.248000	0.74166	0.459000	0.35465	TAT	.	.		0.428	TSPAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289792.3	NM_005724		G	77348564	A	G	77348564	3	3	115	1	0	0	0	0	1	0	0	0	16660	420	15	2	688	2	TSPAN3	15	77348564	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1379403	77348564	25182828	366	19905										
AGPHD1	123688	hgsc.bcm.edu	37	chr15	78825563	78825563	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tactttcaggtatcaatcacGgagatcttaatgaccataat	6	8	4	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:78825563G>T	ENST00000569878.1	+	4	673	c.673G>T	c.(673-675)Gga>Tga	p.G225*	HYKK_ENST00000563233.1_Intron|HYKK_ENST00000388988.4_Nonsense_Mutation_p.G225*|HYKK_ENST00000408962.2_Intron			A2RU49	HYKK_HUMAN	hydroxylysine kinase	225						cytoplasm (GO:0005737)	hydroxylysine kinase activity (GO:0047992)										TATCAATCACGGAGATCTTAA	0.353																																					p.G225X		Atlas-SNP	.											AGPHD1,brain,glioma,0,2	AGPHD1	22	.	0			c.G673T						.						56	50	52					15																	78825563		1827	4078	5905	SO:0001587	stop_gained	123688	exon5			AATCACGGAGATC	BC132753, BC144383, BM045979	CCDS42063.1, CCDS45318.1	15q25.1	2013-06-11	2013-06-11	2013-06-11	ENSG00000188266	ENSG00000188266	2.7.1.81		34403	protein-coding gene	gene with protein product	"5-hydroxylysine kinase"	614681	"aminoglycoside phosphotransferase domain containing 1"	AGPHD1		18780872, 22241472	Standard	NM_001013619		Approved	LOC123688	uc010unc.2	A2RU49		ENST00000569878.1:c.673G>T	chr15.hg19:g.78825563G>T	ENSP00000455459:p.Gly225*	125.0	0.0		139.0	0.0	NM_001013619	B7ZMA5|F8W6X5|Q6ZTN0	Nonsense_Mutation	SNP	ENST00000569878.1	hg19	CCDS42063.1	.	.	.	.	.	.	.	.	.	.	G	37	5.995893	0.97184	.	.	ENSG00000188266	ENST00000388988	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	20.1577	0.98120	0.0:0.0:1.0:0.0	.	.	.	.	X	225	.	ENSP00000373640:G225X	G	+	1	0	AGPHD1	76612618	1.000000	0.71417	0.829000	0.32907	0.931000	0.56810	9.610000	0.98337	2.767000	0.95098	0.655000	0.94253	GGA	.	.		0.353	HYKK-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435834.1	NM_001013619		T	78825563	G	T	78825563	4	4	115	1	0	0	0	0	0	1	0	0	393	1117	39	1	687	1	AGPHD1	15	78825563	Nonsense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	1476999	78825563	23705829	367	19906										
WDR93	56964	hgsc.bcm.edu	37	chr15	90281279	90281279	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgtctcgtcacaggagactaTtcacatgaaactgcgtccac	8	12	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:90281279T>C	ENST00000268130.7	+	16	1874	c.1773T>C	c.(1771-1773)taT>taC	p.Y591Y	WDR93_ENST00000560294.1_Silent_p.Y563Y|WDR93_ENST00000444934.2_Silent_p.Y308Y	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	591					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			CAGGAGACTATTCACATGAAA	0.463																																					p.Y591Y		Atlas-SNP	.											.	WDR93	63	.	0			c.T1773C						.						271	268	269					15																	90281279		2200	4299	6499	SO:0001819	synonymous_variant	56964	exon16			AGACTATTCACAT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"WD repeat domain containing"	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1773T>C	chr15.hg19:g.90281279T>C		79.0	0.0		93.0	4.0	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	hg19	CCDS32326.1																																																																																			.	.		0.463	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212		C	90281279	T	C	90281279	2	2	115	1	0	0	0	0	0	0	0	1	17355	1500	52	2		2	WDR93	15	90281279	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	11455716	90281279	12250113	368	19907										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99467825	99467825	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aagctaaaccggctaaacccGgggaactacacagcccggat	10	13	0	0	rs146023463		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr15:99467825G>A	ENST00000268035.6	+	13	3305	c.2694G>A	c.(2692-2694)ccG>ccA	p.P898P	IGF1R_ENST00000558762.1_Silent_p.P898P	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	898	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GGCTAAACCCGGGGAACTACA	0.498																																					p.P898P		Atlas-SNP	.											.	IGF1R	147	.	0			c.G2694A						.	G		0,4394		0,0,2197	138	129	132		2694	-11.8	0.5	15	dbSNP_134	132	2,8592	2.2+/-6.3	0,2,4295	no	coding-synonymous	IGF1R	NM_000875.3		0,2,6492	AA,AG,GG		0.0233,0.0,0.0154		898/1368	99467825	2,12986	2197	4297	6494	SO:0001819	synonymous_variant	3480	exon13			AAACCCGGGGAAC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2694G>A	chr15.hg19:g.99467825G>A		198.0	0.0		195.0	72.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	hg19	CCDS10378.1																																																																																			.	G|1.000;A|0.000		0.498	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99467825	G	A	99467825	2	1	115	1	0	0	0	0	0	0	0	1	7580	1103	39	1		1	IGF1R	15	99467825	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	9186546	99467825	3063567	369	19908										
RHBDF1	64285	hgsc.bcm.edu	37	chr16	113173	113173	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cacggccacgggccagggggTctatgatctggaggagggga	19	9	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:113173T>C	ENST00000262316.6	-	5	612	c.470A>G	c.(469-471)gAc>gGc	p.D157G	RHBDF1_ENST00000454039.2_Missense_Mutation_p.D157G	NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	157					cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				GGCCAGGGGGTCTATGATCTG	0.652																																					p.D157G		Atlas-SNP	.											.	RHBDF1	54	.	0			c.A470G						.						25	30	28					16																	113173		2158	4221	6379	SO:0001583	missense	64285	exon5			AGGGGGTCTATGA	BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"chromosome 16 open reading frame 8", "rhomboid family 1 (Drosophila)"	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.470A>G	chr16.hg19:g.113173T>C	ENSP00000262316:p.Asp157Gly	50.0	0.0		83.0	4.0	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Missense_Mutation	SNP	ENST00000262316.6	hg19	CCDS32344.1	.	.	.	.	.	.	.	.	.	.	.	20.6	4.016199	0.75161	.	.	ENSG00000007384	ENST00000262316;ENST00000454039;ENST00000450643	T;T;T	0.80566	-1.39;-1.39;-1.39	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.88793	0.6533	M	0.76328	2.33	0.80722	D	1	D;D;D	0.71674	0.995;0.998;0.997	P;D;D	0.71414	0.879;0.951;0.973	D	0.90020	0.4127	10	0.72032	D	0.01	-36.921	14.8533	0.70316	0.0:0.0:0.0:1.0	.	157;180;157	F5GWL4;B4E3Q0;Q96CC6	.;.;RHDF1_HUMAN	G	157	ENSP00000262316:D157G;ENSP00000392133:D157G;ENSP00000408915:D157G	ENSP00000262316:D157G	D	-	2	0	RHBDF1	53173	1.000000	0.71417	1.000000	0.80357	0.315000	0.28087	7.953000	0.87836	2.107000	0.64212	0.379000	0.24179	GAC	.	.		0.652	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450		C	113173	T	C	113173	3	2	115	1	0	0	0	0	1	0	0	0	13334	1667	58	2	2153	2	RHBDF1	16	113173	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10		113173	90241580	370	19909										
SOLH	6650	hgsc.bcm.edu	37	chr16	599102	599102	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcagtggctgcgaccccaggAgatcaactgctccgtcttca	11	14	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:599102A>G	ENST00000219611.2	+	5	1922	c.1559A>G	c.(1558-1560)gAg>gGg	p.E520G	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	520	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CGACCCCAGGAGATCAACTGC	0.657																																					p.E520G		Atlas-SNP	.											.	SOLH	47	.	0			c.A1559G						.						94	93	94					16																	599102		2200	4300	6500	SO:0001583	missense	6650	exon5			CCCAGGAGATCAA	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"small optic lobes (Drosophila) homolog", "small optic lobes homolog (Drosophila)"	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.1559A>G	chr16.hg19:g.599102A>G	ENSP00000219611:p.Glu520Gly	86.0	0.0		109.0	5.0	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	hg19	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	a	24.7	4.564817	0.86439	.	.	ENSG00000103326	ENST00000219611	D	0.92099	-2.97	5.04	5.04	0.67666	Peptidase C2, calpain, catalytic domain (3);	0.669254	0.14978	N	0.287444	D	0.95965	0.8686	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95723	0.8768	10	0.87932	D	0	.	13.6292	0.62186	1.0:0.0:0.0:0.0	.	520	O75808	CAN15_HUMAN	G	520	ENSP00000219611:E520G	ENSP00000219611:E520G	E	+	2	0	SOLH	539103	1.000000	0.71417	0.999000	0.59377	0.463000	0.32649	5.938000	0.70170	1.903000	0.55091	0.454000	0.30748	GAG	.	.		0.657	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		G	599102	A	G	599102	3	3	115	1	0	0	0	0	1	0	0	0	14940	304	11	2	1565	2	SOLH	16	599102	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	485929	599102	89755651	371	19910										
TPSAB1	7177	hgsc.bcm.edu	37	chr16	1291189	1291189	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgcagcgagtgggcatcgtcGggggtcaggaggcccccagg	19	11	1	0	rs143010092		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:1291189G>T	ENST00000338844.3	+	3	130	c.97G>T	c.(97-99)Ggg>Tgg	p.G33W	TPSAB1_ENST00000461509.2_Missense_Mutation_p.G40W	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	33	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G33R(1)		NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				GGGCATCGTCGGGGGTCAGGA	0.701																																					p.G33W		Atlas-SNP	.											TPSAB1,NS,carcinoma,0,1	TPSAB1	24	.	1	Substitution - Missense(1)	lung(1)	c.G97T						.						38	39	39					16																	1291189		2199	4300	6499	SO:0001583	missense	7177	exon3			ATCGTCGGGGGTC	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"tryptase alpha II", "tryptase beta I", "tryptase-I", "tryptase-II", "tryptase-III"	191080	"tryptase beta 1"	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.97G>T	chr16.hg19:g.1291189G>T	ENSP00000343577:p.Gly33Trp	153.0	0.0		231.0	0.0	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	hg19	CCDS10431.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.063325	0.55432	.	.	ENSG00000172236	ENST00000338844;ENST00000461509	D;D	0.86562	-2.14;-2.14	3.38	3.38	0.38709	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.48767	D	0.000170	D	0.94085	0.8104	M	0.90870	3.155	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.94990	0.8133	10	0.87932	D	0	.	12.6931	0.56988	0.0:0.0:1.0:0.0	.	33	Q15661	TRYB1_HUMAN	W	33;40	ENSP00000343577:G33W;ENSP00000418247:G40W	ENSP00000343577:G33W	G	+	1	0	TPSAB1	1231190	0.970000	0.33590	0.257000	0.24404	0.160000	0.22226	3.309000	0.51903	1.905000	0.55150	0.479000	0.44913	GGG	.	G|1.000;A|0.000		0.701	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294		T	1291189	G	T	1291189	3	4	115	1	0	0	0	0	1	0	0	0	16438	1116	39	1	103	1	TPSAB1	16	1291189	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	692087	1291189	89063564	372	19911										
TSC2	7249	hgsc.bcm.edu	37	chr16	2103446	2103446	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctgctgaaggccatcgtgcAggggcaggtaaggcccaggg	17	10	1	1	rs137854108		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:2103446A>G	ENST00000219476.3	+	4	959	c.329A>G	c.(328-330)cAg>cGg	p.Q110R	TSC2_ENST00000353929.4_Missense_Mutation_p.Q110R|TSC2_ENST00000382538.6_Missense_Mutation_p.Q61R|TSC2_ENST00000401874.2_Missense_Mutation_p.Q110R|TSC2_ENST00000568454.1_Missense_Mutation_p.Q121R|TSC2_ENST00000350773.4_Missense_Mutation_p.Q110R|TSC2_ENST00000439673.2_Intron	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	110	Required for interaction with TSC1.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				GCCATCGTGCAGGGGCAGGTA	0.687			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.Q110R		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.A329G						.						13	15	14					16																	2103446		2181	4274	6455	SO:0001583	missense	7249	exon4	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TCGTGCAGGGGCA	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.329A>G	chr16.hg19:g.2103446A>G	ENSP00000219476:p.Gln110Arg	63.0	0.0		93.0	4.0	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	.	9.145	1.014873	0.19355	.	.	ENSG00000103197	ENST00000219476;ENST00000432909;ENST00000401874;ENST00000353929;ENST00000382538;ENST00000350773;ENST00000445113	T;T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38;-1.38	4.79	4.79	0.61399	Armadillo-like helical (1);Armadillo-type fold (1);Tuberin, N-terminal (1);	0.208445	0.42172	D	0.000752	D	0.83440	0.5255	L	0.49126	1.545	0.44395	D	0.997305	P;D;P;D;D	0.71674	0.583;0.998;0.776;0.979;0.969	B;D;P;P;D	0.70227	0.37;0.91;0.583;0.61;0.968	T	0.79701	-0.1693	10	0.17369	T	0.5	-20.5712	9.7033	0.40200	0.8452:0.0:0.0:0.1548	.	61;110;110;110;110	B4DIL8;B7Z2B8;P49815-4;P49815-5;P49815	.;.;.;.;TSC2_HUMAN	R	110;61;110;110;61;110;121	ENSP00000219476:Q110R;ENSP00000384468:Q110R;ENSP00000248099:Q110R;ENSP00000371978:Q61R;ENSP00000344383:Q110R	ENSP00000219476:Q110R	Q	+	2	0	TSC2	2043447	1.000000	0.71417	1.000000	0.80357	0.358000	0.29455	7.029000	0.76477	1.801000	0.52704	0.379000	0.24179	CAG	.	.		0.687	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		G	2103446	A	G	2103446	3	3	115	1	0	0	0	0	1	0	0	0	16621	188	7	2	339	2	TSC2	16	2103446	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	812257	2103446	88251307	373	19912										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2813553	2813553	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caaactccaccggggccaagTctttctggatcaaagtcacc	8	14	4	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:2813553T>C	ENST00000301740.8	+	11	3573	c.3024T>C	c.(3022-3024)agT>agC	p.S1008S		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1008	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						CGGGGCCAAGTCTTTCTGGAT	0.473																																					p.S1008S		Atlas-SNP	.											.	SRRM2	263	.	0			c.T3024C						.						110	118	115					16																	2813553		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			GCCAAGTCTTTCT	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.3024T>C	chr16.hg19:g.2813553T>C		107.0	0.0		98.0	4.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.		0.473	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			C	2813553	T	C	2813553	2	2	115	1	0	0	0	0	0	0	0	1	15184	1664	58	2		2	SRRM2	16	2813553	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	710107	2813553	87541200	374	19913										
ZG16B	124220	hgsc.bcm.edu	37	chr16	2881993	2881993	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agcttgatggccagatctccTctgcctaccccagccaagag	9	15	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:2881993T>C	ENST00000382280.3	+	4	539	c.460T>C	c.(460-462)Tct>Cct	p.S154P	ZG16B_ENST00000572863.1_Missense_Mutation_p.S124P	NM_145252.2	NP_660295.2	Q96DA0	ZG16B_HUMAN	zymogen granule protein 16B	154					retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|lung(2)|ovary(1)|prostate(1)	5						CCAGATCTCCTCTGCCTACCC	0.507																																					p.S154P		Atlas-SNP	.											.	ZG16B	16	.	0			c.T460C						.						64	67	66					16																	2881993		1958	4162	6120	SO:0001583	missense	124220	exon4			ATCTCCTCTGCCT	BC009722	CCDS10479.2	16p13.3	2014-02-12	2012-12-07		ENSG00000162078	ENSG00000162078			30456	protein-coding gene	gene with protein product	"jacalin-like lectin domain containing 2"		"zymogen granule protein 16 homolog B (rat)"			12477932	Standard	NM_145252		Approved	HRPE773, PRO1567, JCLN2	uc002cru.3	Q96DA0	OTTHUMG00000128933	ENST00000382280.3:c.460T>C	chr16.hg19:g.2881993T>C	ENSP00000371715:p.Ser154Pro	83.0	0.0		120.0	5.0	NM_145252	A6NIY1|B2R4F6|Q6UW28	Missense_Mutation	SNP	ENST00000382280.3	hg19	CCDS10479.2	.	.	.	.	.	.	.	.	.	.	t	15.35	2.807423	0.50421	.	.	ENSG00000162078	ENST00000382280	T	0.33438	1.41	3.28	-6.56	0.01848	Mannose-binding lectin (3);	2.349280	0.02322	N	0.073045	T	0.30230	0.0758	L	0.42245	1.32	0.09310	N	1	D	0.67145	0.996	P	0.49561	0.615	T	0.49560	-0.8927	10	0.52906	T	0.07	0.022	6.035	0.19702	0.4556:0.0:0.3711:0.1733	.	154	Q96DA0	ZG16B_HUMAN	P	154	ENSP00000371715:S154P	ENSP00000371715:S154P	S	+	1	0	ZG16B	2821994	0.000000	0.05858	0.000000	0.03702	0.457000	0.32468	-2.937000	0.00685	-1.913000	0.01079	0.454000	0.30748	TCT	.	.		0.507	ZG16B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250912.1	NM_145252		C	2881993	T	C	2881993	3	2	115	1	0	0	0	0	1	0	0	0	17687	1551	54	2	474	2	ZG16B	16	2881993	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	68440	2881993	87472760	375	19914										
TIGD7	91151	hgsc.bcm.edu	37	chr16	3349414	3349414	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttcctttttgtaaagaagatTttcccatgcatttgctatgg	7	7	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:3349414T>C	ENST00000396862.1	-	2	3029	c.1201A>G	c.(1201-1203)Aat>Gat	p.N401D	TIGD7_ENST00000268674.2_Missense_Mutation_p.N401D|TIGD7_ENST00000574598.1_5'Flank	NM_033208.3	NP_149985.2	Q6NT04	TIGD7_HUMAN	tigger transposable element derived 7	401						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12						TAAAGAAGATTTTCCCATGCA	0.308																																					p.N401D		Atlas-SNP	.											.	TIGD7	41	.	0			c.A1201G						.						91	101	98					16																	3349414		2197	4299	6496	SO:0001583	missense	91151	exon2			GAAGATTTTCCCA	AF251050	CCDS10500.1	16p13.11	2008-02-05			ENSG00000140993	ENSG00000140993			18331	protein-coding gene	gene with protein product		612969					Standard	NM_033208		Approved	Sancho	uc002cus.3	Q6NT04	OTTHUMG00000129325	ENST00000396862.1:c.1201A>G	chr16.hg19:g.3349414T>C	ENSP00000380071:p.Asn401Asp	240.0	0.0		215.0	81.0	NM_033208	Q9BXZ0	Missense_Mutation	SNP	ENST00000396862.1	hg19	CCDS10500.1	.	.	.	.	.	.	.	.	.	.	T	8.165	0.790433	0.16258	.	.	ENSG00000140993	ENST00000426381;ENST00000396862;ENST00000268674	T;T	0.33865	1.39;1.39	5.32	5.32	0.75619	.	0.000000	0.42682	U	0.000664	T	0.44623	0.1302	L	0.27053	0.805	0.28178	N	0.928306	D	0.63880	0.993	D	0.70227	0.968	T	0.36578	-0.9742	10	0.52906	T	0.07	.	11.6709	0.51401	0.0:0.0:0.0:1.0	.	401	Q6NT04	TIGD7_HUMAN	D	401	ENSP00000380071:N401D;ENSP00000268674:N401D	ENSP00000268674:N401D	N	-	1	0	TIGD7	3289415	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.321000	0.43805	2.006000	0.58801	0.533000	0.62120	AAT	.	.		0.308	TIGD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251465.1	NM_033208		C	3349414	T	C	3349414	3	2	115	1	0	0	0	0	1	0	0	0	15916	1841	64	2	452	2	TIGD7	16	3349414	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	467421	3349414	87005339	376	19915										
SCNN1G	6340	hgsc.bcm.edu	37	chr16	23208690	23208690	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcaggatgagtatcccttcgTcgaagatgtgggaacagaga	14	7	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:23208690T>C	ENST00000300061.2	+	6	1162	c.1019T>C	c.(1018-1020)gTc>gCc	p.V340A	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	340					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	TATCCCTTCGTCGAAGATGTG	0.453																																					p.V340A		Atlas-SNP	.											.	SCNN1G	82	.	0			c.T1019C						.						117	103	108					16																	23208690		2197	4300	6497	SO:0001583	missense	6340	exon6			CCTTCGTCGAAGA	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.1019T>C	chr16.hg19:g.23208690T>C	ENSP00000300061:p.Val340Ala	88.0	0.0		120.0	5.0	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Missense_Mutation	SNP	ENST00000300061.2	hg19	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.054696	0.36277	.	.	ENSG00000166828	ENST00000300061	T	0.64803	-0.12	5.62	5.62	0.85841	.	0.225126	0.38058	N	0.001837	T	0.51176	0.1659	N	0.24115	0.695	0.25077	N	0.990958	B	0.26975	0.165	B	0.28385	0.089	T	0.54289	-0.8316	10	0.87932	D	0	-37.2688	14.9985	0.71451	0.0:0.0:0.0:1.0	.	340	P51170	SCNNG_HUMAN	A	340	ENSP00000300061:V340A	ENSP00000300061:V340A	V	+	2	0	SCNN1G	23116191	1.000000	0.71417	0.979000	0.43373	0.095000	0.18619	5.505000	0.66981	2.151000	0.67156	0.533000	0.62120	GTC	.	.		0.453	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		C	23208690	T	C	23208690	3	2	115	1	0	0	0	0	1	0	0	0	13945	1667	58	2	1037	2	SCNN1G	16	23208690	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	19859276	23208690	67146063	377	19916										
CD2BP2	10421	hgsc.bcm.edu	37	chr16	30365247	30365247	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caatgttgtccagccagctgTctcggatctgagcatcccgg	11	13	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:30365247T>C	ENST00000305596.3	-	4	525	c.350A>G	c.(349-351)gAc>gGc	p.D117G	CD2BP2_ENST00000569466.1_Missense_Mutation_p.D117G|RP11-347C12.10_ENST00000563252.1_lincRNA	NM_006110.2	NP_006101.1	O95400	CD2B2_HUMAN	CD2 (cytoplasmic tail) binding protein 2	117					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of phosphatase activity (GO:0010923)|RNA splicing (GO:0008380)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	ribonucleoprotein complex binding (GO:0043021)			breast(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	15						CAGCCAGCTGTCTCGGATCTG	0.622																																					p.D117G		Atlas-SNP	.											.	CD2BP2	30	.	0			c.A350G						.						66	62	63					16																	30365247		2197	4300	6497	SO:0001583	missense	10421	exon4			CAGCTGTCTCGGA	AF104222	CCDS10675.1	16p11.2	2012-04-17	2006-03-28		ENSG00000169217	ENSG00000169217		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 59"	604470	"CD2 antigen (cytoplasmic tail)-binding protein 2"			9843987	Standard	NM_006110		Approved	LIN1, Snu40, PPP1R59	uc002dxs.3	O95400	OTTHUMG00000132397	ENST00000305596.3:c.350A>G	chr16.hg19:g.30365247T>C	ENSP00000304903:p.Asp117Gly	86.0	0.0		119.0	6.0	NM_006110	B2RDX2|Q9ULP2	Missense_Mutation	SNP	ENST00000305596.3	hg19	CCDS10675.1	.	.	.	.	.	.	.	.	.	.	N	22.1	4.241159	0.79912	.	.	ENSG00000169217	ENST00000305596	T	0.66995	-0.24	4.87	4.87	0.63330	.	0.108415	0.64402	D	0.000002	T	0.72550	0.3474	M	0.86805	2.84	0.80722	D	1	D	0.53885	0.963	B	0.43889	0.435	T	0.80155	-0.1500	10	0.87932	D	0	1.2721	13.591	0.61959	0.0:0.0:0.0:1.0	.	117	O95400	CD2B2_HUMAN	G	117	ENSP00000304903:D117G	ENSP00000304903:D117G	D	-	2	0	CD2BP2	30272748	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.774000	0.75012	2.041000	0.60428	0.456000	0.33151	GAC	.	.		0.622	CD2BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255528.1	NM_006110		C	30365247	T	C	30365247	3	2	115	1	0	0	0	0	1	0	0	0	2997	1667	58	2	691	2	CD2BP2	16	30365247	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	7156557	30365247	59989506	378	19917										
ITGAL	3683	hgsc.bcm.edu	37	chr16	30490673	30490673	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atgtatcaagggcaacgtagAcctggtatttctgtttgatg	11	6	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:30490673A>G	ENST00000356798.6	+	6	647	c.467A>G	c.(466-468)gAc>gGc	p.D156G	RP11-297C4.3_ENST00000562525.1_RNA|ITGAL_ENST00000454514.2_Intron|RP11-297C4.2_ENST00000569459.1_RNA|ITGAL_ENST00000358164.5_Intron|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	156	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	GGCAACGTAGACCTGGTATTT	0.473																																					p.D156G	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.A467G						.						119	107	111					16																	30490673		2197	4300	6497	SO:0001583	missense	3683	exon6			ACGTAGACCTGGT		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.467A>G	chr16.hg19:g.30490673A>G	ENSP00000349252:p.Asp156Gly	62.0	0.0		73.0	4.0	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	hg19	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.590583	0.86851	.	.	ENSG00000005844	ENST00000356798	D	0.93247	-3.19	5.98	5.98	0.97165	von Willebrand factor, type A (3);	0.000000	0.56097	D	0.000021	D	0.97601	0.9214	H	0.95504	3.68	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	D	0.98572	1.0646	10	0.87932	D	0	.	13.9892	0.64355	1.0:0.0:0.0:0.0	.	156	P20701	ITAL_HUMAN	G	156	ENSP00000349252:D156G	ENSP00000349252:D156G	D	+	2	0	ITGAL	30398174	1.000000	0.71417	0.998000	0.56505	0.940000	0.58332	6.040000	0.70980	2.289000	0.77006	0.421000	0.28195	GAC	.	.		0.473	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			G	30490673	A	G	30490673	3	3	115	1	0	0	0	0	1	0	0	0	7895	275	10	2	489	2	ITGAL	16	30490673	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	125426	30490673	59864080	379	19918										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31927599	31927599	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	actctaggtcatacctcactAcacatcggagaagacatact	6	12	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:31927599A>G	ENST00000300870.10	+	4	2238	c.2029A>G	c.(2029-2031)Aca>Gca	p.T677A		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	677					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						ATACCTCACTACACATCGGAG	0.443																																					p.T677A		Atlas-SNP	.											.	ZNF267	94	.	0			c.A2029G						.						108	98	101					16																	31927599		2197	4300	6497	SO:0001583	missense	10308	exon4			CTCACTACACATC	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.2029A>G	chr16.hg19:g.31927599A>G	ENSP00000300870:p.Thr677Ala	56.0	0.0		52.0	4.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Missense_Mutation	SNP	ENST00000300870.10	hg19	CCDS32440.1	.	.	.	.	.	.	.	.	.	.	.	1.653	-0.513380	0.04200	.	.	ENSG00000185947	ENST00000300870	T	0.17213	2.29	0.468	0.468	0.16732	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06962	0.0177	N	0.12853	0.265	0.09310	N	0.999999	B	0.23185	0.081	B	0.15484	0.013	T	0.41875	-0.9484	9	0.09843	T	0.71	.	5.2175	0.15350	0.9999:0.0:1.0E-4:0.0	.	677	Q14586	ZN267_HUMAN	A	677	ENSP00000300870:T677A	ENSP00000300870:T677A	T	+	1	0	ZNF267	31835100	0.000000	0.05858	0.005000	0.12908	0.005000	0.04900	-0.244000	0.08903	0.413000	0.25759	0.402000	0.26972	ACA	.	.		0.443	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		G	31927599	A	G	31927599	3	3	115	1	0	0	0	0	1	0	0	0	17821	391	14	2	2043	2	ZNF267	16	31927599	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1436926	31927599	58427154	380	19919										
SNX20	124460	hgsc.bcm.edu	37	chr16	50707345	50707345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggtattctcgcacagtgagcTccttcagggtgatgcctcgg	13	11	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:50707345T>C	ENST00000330943.4	-	4	1094	c.923A>G	c.(922-924)gAg>gGg	p.E308G	RP11-401P9.5_ENST00000570241.2_RNA|RP11-401P9.5_ENST00000570167.1_RNA|SNX20_ENST00000423026.2_Intron|SNX20_ENST00000300590.3_Intron	NM_182854.2	NP_878274.1	Q7Z614	SNX20_HUMAN	sorting nexin 20	308					protein transport (GO:0015031)	endosome (GO:0005768)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)			kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(2)|stomach(1)	15						CACAGTGAGCTCCTTCAGGGT	0.657																																					p.E308G		Atlas-SNP	.											.	SNX20	50	.	0			c.A923G						.						54	59	57					16																	50707345		2198	4300	6498	SO:0001583	missense	124460	exon4			GTGAGCTCCTTCA	AK055837	CCDS10745.1, CCDS10744.1, CCDS45481.1	16q12.1	2008-03-25	2008-03-25		ENSG00000167208	ENSG00000167208		"Sorting nexins"	30390	protein-coding gene	gene with protein product	"selectin ligand interactor cytoplasmic 1"	613281				18196517, 16782399	Standard	NM_182854		Approved	SLIC-1, SLIC1	uc002egk.2	Q7Z614	OTTHUMG00000133173	ENST00000330943.4:c.923A>G	chr16.hg19:g.50707345T>C	ENSP00000332062:p.Glu308Gly	148.0	0.0		184.0	8.0	NM_182854	A8K9D5|Q08E98|Q6P4H2|Q8IV59	Missense_Mutation	SNP	ENST00000330943.4	hg19	CCDS10745.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.306389	0.60305	.	.	ENSG00000167208	ENST00000330943;ENST00000413750	T	0.46451	0.87	5.67	5.67	0.87782	.	0.115560	0.64402	D	0.000020	T	0.60830	0.2299	M	0.78801	2.425	0.53688	D	0.999975	D	0.65815	0.995	P	0.57425	0.82	T	0.66630	-0.5875	10	0.87932	D	0	-11.9079	14.4848	0.67609	0.0:0.0:0.0:1.0	.	308	Q7Z614	SNX20_HUMAN	G	308;144	ENSP00000332062:E308G	ENSP00000332062:E308G	E	-	2	0	SNX20	49264846	1.000000	0.71417	0.929000	0.37066	0.108000	0.19459	4.560000	0.60802	2.161000	0.67846	0.459000	0.35465	GAG	.	.		0.657	SNX20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256879.2	NM_153337		C	50707345	T	C	50707345	3	2	115	1	0	0	0	0	1	0	0	0	14907	1551	54	2	174	2	SNX20	16	50707345	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	18779746	50707345	39647408	381	19920										
SALL1	6299	hgsc.bcm.edu	37	chr16	51175352	51175352	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agatgttggcaagtctgcatTctgagaagccaacagcaata	10	8	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:51175352T>C	ENST00000251020.4	-	2	814	c.781A>G	c.(781-783)Aat>Gat	p.N261D	SALL1_ENST00000440970.1_Missense_Mutation_p.N164D|SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	261					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			AAGTCTGCATTCTGAGAAGCC	0.488																																					p.N261D	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.A781G						.						87	88	88					16																	51175352		2198	4300	6498	SO:0001583	missense	6299	exon2			CTGCATTCTGAGA	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.781A>G	chr16.hg19:g.51175352T>C	ENSP00000251020:p.Asn261Asp	109.0	0.0		98.0	4.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.482571	0.26598	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.06849	3.25;3.29	4.75	4.75	0.60458	.	0.262921	0.44097	D	0.000491	T	0.06142	0.0159	N	0.14661	0.345	0.31008	N	0.719553	B	0.23377	0.084	B	0.19148	0.024	T	0.07347	-1.0777	10	0.39692	T	0.17	.	14.4208	0.67183	0.0:0.0:0.0:1.0	.	261	Q9NSC2	SALL1_HUMAN	D	261;164;225	ENSP00000251020:N261D;ENSP00000407914:N164D	ENSP00000251020:N261D	N	-	1	0	SALL1	49732853	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	5.012000	0.64017	1.980000	0.57719	0.402000	0.26972	AAT	.	.		0.488	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		C	51175352	T	C	51175352	3	2	115	1	0	0	0	0	1	0	0	0	13825	1783	62	2	3201	2	SALL1	16	51175352	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	468007	51175352	39179401	382	19921										
BBS2	583	hgsc.bcm.edu	37	chr16	56533696	56533696	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agcgagatactcaccctctgTgcccgttctgcaatggtaaa	9	12	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:56533696T>C	ENST00000245157.5	-	12	1941	c.1521A>G	c.(1519-1521)gcA>gcG	p.A507A	BBS2_ENST00000568104.1_Silent_p.A507A|BBS2_ENST00000561951.1_5'Flank	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	507					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						TCACCCTCTGTGCCCGTTCTG	0.423									Bardet-Biedl syndrome																												p.A507A		Atlas-SNP	.											.	BBS2	67	.	0			c.A1521G						.						171	163	166					16																	56533696		2198	4300	6498	SO:0001819	synonymous_variant	583	exon12	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CCTCTGTGCCCGT	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.1521A>G	chr16.hg19:g.56533696T>C		101.0	0.0		100.0	4.0	NM_031885	Q96CM0|Q96SN9	Silent	SNP	ENST00000245157.5	hg19	CCDS32451.1																																																																																			.	.		0.423	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		C	56533696	T	C	56533696	2	2	115	1	0	0	0	0	0	0	0	1	1338	1683	59	2		2	BBS2	16	56533696	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	5358344	56533696	33821057	383	19922										
NLRC5	84166	hgsc.bcm.edu	37	chr16	57060298	57060298	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttctatgcaaaagatattgcTccacccttgatagcttttgg	7	9	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:57060298T>C	ENST00000262510.6	+	6	1668	c.1443T>C	c.(1441-1443)gcT>gcC	p.A481A	NLRC5_ENST00000436936.1_Silent_p.A481A|NLRC5_ENST00000539144.1_Silent_p.A481A|NLRC5_ENST00000308149.7_Silent_p.A481A	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	481	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				AAGATATTGCTCCACCCTTGA	0.597																																					p.A481A		Atlas-SNP	.											.	NLRC5	186	.	0			c.T1443C						.						41	39	40					16																	57060298		2198	4300	6498	SO:0001819	synonymous_variant	84166	exon5			TATTGCTCCACCC	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.1443T>C	chr16.hg19:g.57060298T>C		124.0	0.0		146.0	6.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	hg19	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	T	0.104	-1.147767	0.01714	.	.	ENSG00000140853	ENST00000538805	.	.	.	5.4	-1.34	0.09143	.	.	.	.	.	T	0.18383	0.0441	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.23547	-1.0185	4	.	.	.	.	0.5041	0.00584	0.3299:0.2365:0.1152:0.3184	.	.	.	.	P	234	.	.	S	+	1	0	NLRC5	55617799	0.001000	0.12720	0.003000	0.11579	0.034000	0.12701	-0.119000	0.10676	-0.193000	0.10415	0.459000	0.35465	TCC	.	.		0.597	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		C	57060298	T	C	57060298	2	2	115	1	0	0	0	0	0	0	0	1	10479	1538	54	2		2	NLRC5	16	57060298	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	526602	57060298	33294455	384	19923										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58633211	58633211	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caccaggtagctgatttgagAcaaggccagcgagagcgagt	14	9	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:58633211A>G	ENST00000317147.5	-	2	363	c.31T>C	c.(31-33)Tct>Cct	p.S11P	CNOT1_ENST00000569240.1_Missense_Mutation_p.S11P|CNOT1_ENST00000441024.2_Missense_Mutation_p.S11P	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	11					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CTGATTTGAGACAAGGCCAGC	0.502																																					p.S11P		Atlas-SNP	.											.	CNOT1	359	.	0			c.T31C						.						90	86	88					16																	58633211		2198	4300	6498	SO:0001583	missense	23019	exon2			TTTGAGACAAGGC	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.31T>C	chr16.hg19:g.58633211A>G	ENSP00000320949:p.Ser11Pro	115.0	0.0		100.0	4.0	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.891706	0.52014	.	.	ENSG00000125107	ENST00000317147;ENST00000394200;ENST00000441024	T;T	0.24723	1.84;1.84	5.46	5.46	0.80206	.	0.109719	0.64402	D	0.000005	T	0.45776	0.1359	L	0.54323	1.7	0.80722	D	1	D;D;B	0.57899	0.981;0.978;0.046	D;B;B	0.71184	0.972;0.4;0.032	T	0.27226	-1.0080	9	.	.	.	-13.9785	15.5431	0.76070	1.0:0.0:0.0:0.0	.	11;11;11	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	P	11	ENSP00000320949:S11P;ENSP00000413113:S11P	.	S	-	1	0	CNOT1	57190712	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.312000	0.96287	2.065000	0.61736	0.455000	0.32223	TCT	.	.		0.502	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		G	58633211	A	G	58633211	3	3	115	1	0	0	0	0	1	0	0	0	3619	275	10	2	7513	2	CNOT1	16	58633211	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1572913	58633211	31721542	385	19924										
DYNC1LI2	1783	hgsc.bcm.edu	37	chr16	66783141	66783141	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cactgaggtagagatattctAggcctcttccttttttgcca	8	10	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:66783141A>G	ENST00000258198.2	-	3	463	c.257T>C	c.(256-258)cTa>cCa	p.L86P	RP11-61A14.4_ENST00000501143.1_lincRNA|DYNC1LI2_ENST00000440564.2_Intron|DYNC1LI2_ENST00000443351.2_Missense_Mutation_p.L86P|DYNC1LI2_ENST00000379482.2_Missense_Mutation_p.L86P	NM_006141.2	NP_006132.1	O43237	DC1L2_HUMAN	dynein, cytoplasmic 1, light intermediate chain 2	86					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|centrosome localization (GO:0051642)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based movement (GO:0007018)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			central_nervous_system(3)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(4)|stomach(1)	15		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0907)|Epithelial(162;0.212)		GAGATATTCTAGGCCTCTTCC	0.463																																					p.L86P		Atlas-SNP	.											.	DYNC1LI2	37	.	0			c.T257C						.						243	208	220					16																	66783141		2200	4300	6500	SO:0001583	missense	1783	exon3			TATTCTAGGCCTC	AF035812	CCDS10818.1, CCDS67049.1	16q22.1	2008-02-05	2005-11-25	2005-11-25	ENSG00000135720	ENSG00000135720		"Cytoplasmic dyneins"	2966	protein-coding gene	gene with protein product		611406	"dynein, cytoplasmic, light intermediate polypeptide 2"	DNCLI2		16260502	Standard	NM_006141		Approved		uc002eqb.1	O43237	OTTHUMG00000137523	ENST00000258198.2:c.257T>C	chr16.hg19:g.66783141A>G	ENSP00000258198:p.Leu86Pro	153.0	0.0		150.0	6.0	NM_006141	A8K6V1|B4DZP4|Q8TAT3	Missense_Mutation	SNP	ENST00000258198.2	hg19	CCDS10818.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.445733	0.84101	.	.	ENSG00000135720	ENST00000258198;ENST00000379482;ENST00000443351	T;T;T	0.33865	1.53;1.53;1.39	4.81	4.81	0.61882	.	0.000000	0.64402	D	0.000001	T	0.65460	0.2693	M	0.88310	2.945	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.996	D;P;D	0.81914	0.995;0.899;0.988	T	0.73720	-0.3894	10	0.87932	D	0	-15.6057	14.5285	0.67905	1.0:0.0:0.0:0.0	.	86;86;86	B4DHD8;B4DZP4;O43237	.;.;DC1L2_HUMAN	P	86	ENSP00000258198:L86P;ENSP00000368795:L86P;ENSP00000394289:L86P	ENSP00000258198:L86P	L	-	2	0	DYNC1LI2	65340642	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	9.081000	0.94049	2.018000	0.59344	0.374000	0.22700	CTA	.	.		0.463	DYNC1LI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268846.1	NM_006141		G	66783141	A	G	66783141	3	3	115	1	0	0	0	0	1	0	0	0	4847	420	15	2	1265	2	DYNC1LI2	16	66783141	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	8149930	66783141	23571612	386	19925										
RLTPR	146206	hgsc.bcm.edu	37	chr16	67683061	67683061	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtggcgcttggaaggaacttCaacgtccggtgcaagtgagc	15	9	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:67683061C>T	ENST00000334583.6	+	18	2002	c.1674C>T	c.(1672-1674)ttC>ttT	p.F558F	RLTPR_ENST00000545661.1_Silent_p.F522F	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	558					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		GAAGGAACTTCAACGTCCGGT	0.652																																					p.F558F		Atlas-SNP	.											.	RLTPR	124	.	0			c.C1674T						.						54	64	60					16																	67683061		2067	4193	6260	SO:0001819	synonymous_variant	146206	exon18			GAACTTCAACGTC	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.1674C>T	chr16.hg19:g.67683061C>T		132.0	0.0		143.0	50.0	NM_001013838	B8X2Z3	Silent	SNP	ENST00000334583.6	hg19	CCDS45513.1																																																																																			.	.		0.652	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		T	67683061	C	T	67683061	2	4	115	1	0	0	0	0	0	0	0	1	13409	825	29	3		3	RLTPR	16	67683061	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	899920	67683061	22671692	387	19926										
PSMB10	5699	hgsc.bcm.edu	37	chr16	67970637	67970637	+	Frame_Shift_Del	DEL	G	G	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaagccccctcggggctccaGggctggcttcagcatcttgg							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:67970637delG	ENST00000358514.4	-	1	353	c.16delC	c.(16-18)ctgfs	p.L6fs	CTC-479C5.12_ENST00000573493.1_5'Flank	NM_002801.3	NP_002792.1	P40306	PSB10_HUMAN	proteasome (prosome, macropain) subunit, beta type, 10	6					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cell morphogenesis (GO:0000902)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|humoral immune response (GO:0006959)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			NS(2)|endometrium(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)	Carfilzomib(DB08889)	CGGGGCTCCAGGGCTGGCTTC	0.657																																					p.L6fs		Atlas-INDEL	.											.	PSMB10	19	.	0			c.17delT						.						6	8	8					16																	67970637		2065	4131	6196	SO:0001589	frameshift_variant	5699	exon1			.	Y13640	CCDS10853.1	16q22.1	2008-02-05			ENSG00000205220	ENSG00000205220		"Proteasome (prosome, macropain) subunits"	9538	protein-coding gene	gene with protein product		176847		MECL1		8268911	Standard	NM_002801		Approved	LMP10, MGC1665, beta2i	uc002eux.2	P40306	OTTHUMG00000137553	ENST00000358514.4:c.16delC	chr16.hg19:g.67970637delG	ENSP00000351314:p.Leu6fs	121.0	0.0		156.0	10.0	NM_002801	B2R5J4|Q5U098	Frame_Shift_Del	DEL	ENST00000358514.4	hg19	CCDS10853.1																																																																																			.	.		0.657	PSMB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268887.1	NM_002801		-	67970637	G	-	67970637	7	5	115	1	0	1	0	1	0	0	0	0	12687	991	35	0	837	0	PSMB10	16	67970637	Frame_Shift_Del	DEL	G	TCGA-DD-A3A1-01A-11D-A20W-10	287576	67970637	22384116	388	19927										
SLC7A6OS	84138	hgsc.bcm.edu	37	chr16	68344764	68344764	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cgtttacaagcgagcacaagAgcctccgccggctccgcact	10	16	0	1	rs147089863		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:68344764A>G	ENST00000263997.6	-	1	84	c.66T>C	c.(64-66)gcT>gcC	p.A22A	PRMT7_ENST00000339507.5_5'Flank|PRMT7_ENST00000441236.1_5'Flank|snoU13_ENST00000458872.1_RNA|PRMT7_ENST00000449359.3_5'Flank|PRMT7_ENST00000348497.4_5'Flank	NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	22					hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		CGAGCACAAGAGCCTCCGCCG	0.657																																					p.A22A		Atlas-SNP	.											.	SLC7A6OS	22	.	0			c.T66C						.	A		1,4393	2.1+/-5.4	0,1,2196	32	30	31		66	-10.9	0	16	dbSNP_134	31	0,8600		0,0,4300	no	coding-synonymous	SLC7A6OS	NM_032178.2		0,1,6496	GG,GA,AA		0.0,0.0228,0.0077		22/310	68344764	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	84138	exon1			CACAAGAGCCTCC		CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061			25807	protein-coding gene	gene with protein product							Standard	NM_032178		Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558	ENST00000263997.6:c.66T>C	chr16.hg19:g.68344764A>G		123.0	0.0		112.0	5.0	NM_032178	Q8TCZ3|Q9H8R8	Silent	SNP	ENST00000263997.6	hg19	CCDS10865.1																																																																																			.	A|1.000;G|0.000		0.657	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178		G	68344764	A	G	68344764	2	3	115	1	0	0	0	0	0	0	0	1	14717	291	11	2		2	SLC7A6OS	16	68344764	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	374127	68344764	22009989	389	19928										
CFDP1	10428	hgsc.bcm.edu	37	chr16	75338933	75338933	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccttcttacccctctttcccTcgattatggatggccagttc	6	15	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:75338933T>C	ENST00000283882.3	-	6	930	c.798A>G	c.(796-798)cgA>cgG	p.R266R		NM_006324.2	NP_006315.1	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	266	BCNT-C. {ECO:0000255|PROSITE- ProRule:PRU00610}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|negative regulation of fibroblast apoptotic process (GO:2000270)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)					endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						CCTCTTTCCCTCGATTATGGA	0.458																																					p.R266R		Atlas-SNP	.											.	CFDP1	17	.	0			c.A798G						.						167	163	165					16																	75338933		2198	4300	6498	SO:0001819	synonymous_variant	10428	exon6			TTTCCCTCGATTA	AB009285	CCDS10916.1	16q22.2-q22.3	2011-08-12			ENSG00000153774	ENSG00000153774			1873	protein-coding gene	gene with protein product	"Bucentaur", "centromere protein 29"	608108				9602175, 9006920, 11992732	Standard	NM_006324		Approved	BCNT, p97, CP27, SWC5, Yeti, CENP-29	uc002fdy.3	Q9UEE9	OTTHUMG00000137615	ENST00000283882.3:c.798A>G	chr16.hg19:g.75338933T>C		77.0	0.0		79.0	4.0	NM_006324	O00393|O00404|Q9UEF0|Q9UEF1|Q9UEF8	Silent	SNP	ENST00000283882.3	hg19	CCDS10916.1																																																																																			.	.		0.458	CFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269031.2	NM_006324		C	75338933	T	C	75338933	2	2	115	1	0	0	0	0	0	0	0	1	3284	1538	54	2		2	CFDP1	16	75338933	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	6994169	75338933	15015820	390	19929										
CENPN	55839	hgsc.bcm.edu	37	chr16	81066277	81066277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggacttgtaccttctgtttgTcccattgtatccaagatgtt	8	9	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:81066277T>C	ENST00000393335.3	+	11	1114	c.1040T>C	c.(1039-1041)gTc>gCc	p.V347A	RP11-303E16.2_ENST00000566639.1_RNA|RP11-303E16.3_ENST00000561808.1_RNA|RP11-303E16.3_ENST00000566390.1_RNA	NM_001100625.2	NP_001094095.2	Q96H22	CENPN_HUMAN	centromere protein N	0					CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|large_intestine(5)|lung(4)	10						CTTCTGTTTGTCCCATTGTAT	0.423																																					p.V347A		Atlas-SNP	.											.	CENPN	84	.	0			c.T1040C						.						82	86	85					16																	81066277		1893	4104	5997	SO:0001583	missense	55839	exon11			TGTTTGTCCCATT	AK026313	CCDS10931.1, CCDS42199.1, CCDS42200.1, CCDS58482.1, CCDS58483.1	16q23.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000166451	ENSG00000166451			30873	protein-coding gene	gene with protein product		611509	"chromosome 16 open reading frame 60"	C16orf60		16622419	Standard	NM_001100625		Approved	FLJ13607, FLJ22660, BM039	uc002ffy.4	Q96H22	OTTHUMG00000137628	ENST00000393335.3:c.1040T>C	chr16.hg19:g.81066277T>C	ENSP00000377007:p.Val347Ala	89.0	0.0		100.0	6.0	NM_001100625	A8MZE6|B3KN53|B4DJD1|B4DPY7|C9JJM5|D3DUK8|E7ES30|E7ETS3|Q9NZ83	Missense_Mutation	SNP	ENST00000393335.3	hg19	CCDS42199.1	.	.	.	.	.	.	.	.	.	.	T	7.373	0.627202	0.14257	.	.	ENSG00000166451	ENST00000393335	T	0.26373	1.74	0.559	0.559	0.17272	.	0.000000	0.85682	D	0.000000	T	0.10937	0.0267	N	0.08118	0	0.09310	N	1	B	0.20261	0.043	B	0.09377	0.004	T	0.21484	-1.0244	9	0.87932	D	0	-5.1847	.	.	.	.	347	A8MZE6	.	A	347	ENSP00000377007:V347A	ENSP00000377007:V347A	V	+	2	0	CENPN	79623778	0.006000	0.16342	0.010000	0.14722	0.010000	0.07245	0.449000	0.21744	0.469000	0.27268	0.459000	0.35465	GTC	.	.		0.423	CENPN-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269052.1	NM_018455		C	81066277	T	C	81066277	3	2	115	1	0	0	0	0	1	0	0	0	3240	1667	58	2	1253	2	CENPN	16	81066277	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	5727344	81066277	9288476	391	19930										
CMIP	80790	hgsc.bcm.edu	37	chr16	81703808	81703808	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtacatccttgccttgaacgAgctcaacgcggggatggaag	13	10	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:81703808A>G	ENST00000537098.3	+	8	959	c.887A>G	c.(886-888)gAg>gGg	p.E296G	CMIP_ENST00000539778.2_Missense_Mutation_p.E202G|CMIP_ENST00000566513.1_3'UTR|CMIP_ENST00000398040.4_Missense_Mutation_p.E143G	NM_198390.2	NP_938204.2	Q8IY22	CMIP_HUMAN	c-Maf inducing protein	296						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(5)|kidney(1)|lung(7)	13						GCCTTGAACGAGCTCAACGCG	0.582																																					p.E296G		Atlas-SNP	.											.	CMIP	37	.	0			c.A887G						.						59	64	62					16																	81703808		1996	4175	6171	SO:0001583	missense	80790	exon8			TGAACGAGCTCAA	AB051481	CCDS54044.1, CCDS54045.1	16q23	2011-08-04			ENSG00000153815	ENSG00000153815			24319	protein-coding gene	gene with protein product		610112				11214970, 12939343	Standard	NM_030629		Approved		uc002fgp.3	Q8IY22		ENST00000537098.3:c.887A>G	chr16.hg19:g.81703808A>G	ENSP00000446100:p.Glu296Gly	91.0	0.0		106.0	5.0	NM_198390	Q9C0G9	Missense_Mutation	SNP	ENST00000537098.3	hg19	CCDS54044.1	.	.	.	.	.	.	.	.	.	.	A	14.23	2.472447	0.43942	.	.	ENSG00000153815	ENST00000537098;ENST00000539778;ENST00000398040;ENST00000542097	T;T	0.09817	2.94;2.94	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.17746	0.0426	N	0.24115	0.695	0.58432	D	0.999999	D;D;D	0.61080	0.989;0.989;0.981	D;D;D	0.70487	0.969;0.969;0.954	T	0.13764	-1.0497	10	0.16420	T	0.52	.	14.6727	0.68956	1.0:0.0:0.0:0.0	.	143;202;296	Q8IY22-3;Q8IY22-2;Q8IY22	.;.;CMIP_HUMAN	G	296;202;202;109	ENSP00000446100:E296G;ENSP00000440401:E202G	ENSP00000381120:E202G	E	+	2	0	CMIP	80261309	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.724000	0.91462	1.865000	0.54081	0.383000	0.25322	GAG	.	.		0.582	CMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432399.2	NM_030629		G	81703808	A	G	81703808	3	3	115	1	0	0	0	0	1	0	0	0	3580	304	11	2	939	2	CMIP	16	81703808	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	637531	81703808	8650945	392	19931										
OSGIN1	29948	hgsc.bcm.edu	37	chr16	83994667	83994667	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aggtcaaggactggatgcagAagaagcgaaggtgaggccgc	17	7	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:83994667A>G	ENST00000343939.2	+	6	1110	c.727A>G	c.(727-729)Aag>Gag	p.K243E	OSGIN1_ENST00000393306.1_Missense_Mutation_p.K160E|OSGIN1_ENST00000361711.3_Missense_Mutation_p.K160E|OSGIN1_ENST00000565123.1_Missense_Mutation_p.K160E			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	243					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						CTGGATGCAGAAGAAGCGAAG	0.577																																					p.K160E		Atlas-SNP	.											OSGIN1,NS,carcinoma,0,1	OSGIN1	33	.	0			c.A478G						.						64	65	65					16																	83994667		2200	4300	6500	SO:0001583	missense	29948	exon5			ATGCAGAAGAAGC	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"bone marrow stromal cell-derived growth inhibitor", "pregnancy induced growth inhibitor"	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.727A>G	chr16.hg19:g.83994667A>G	ENSP00000343376:p.Lys243Glu	56.0	0.0		60.0	3.0	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	hg19		.	.	.	.	.	.	.	.	.	.	A	4.652	0.121229	0.08881	.	.	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.22539	1.95;1.95;1.95	4.53	2.13	0.27403	.	0.759254	0.12484	N	0.464825	T	0.13372	0.0324	L	0.38531	1.155	0.09310	N	1	B	0.30146	0.27	B	0.28916	0.096	T	0.31998	-0.9923	10	0.10377	T	0.69	-25.0361	6.5396	0.22372	0.6216:0.2898:0.0886:0.0	.	243	Q9UJX0	OSGI1_HUMAN	E	243;160;160	ENSP00000343376:K243E;ENSP00000355374:K160E;ENSP00000376983:K160E	ENSP00000343376:K243E	K	+	1	0	OSGIN1	82552168	0.008000	0.16893	0.239000	0.24122	0.818000	0.46254	0.955000	0.29188	0.594000	0.29761	0.402000	0.26972	AAG	.	.		0.577	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		G	83994667	A	G	83994667	3	3	115	1	0	0	0	0	1	0	0	0	11298	247	9	2	749	2	OSGIN1	16	83994667	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2290859	83994667	6360086	393	19932										
KLHDC4	54758	hgsc.bcm.edu	37	chr16	87742992	87742992	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cccccatagacgtagagcacCccatgcttcacagccagcat	7	17	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:87742992C>T	ENST00000270583.5	-	10	1384	c.1326G>A	c.(1324-1326)ggG>ggA	p.G442G	KLHDC4_ENST00000353170.5_Silent_p.G385G|KLHDC4_ENST00000566349.1_5'UTR|KLHDC4_ENST00000347925.5_Silent_p.G411G	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	442										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		CGTAGAGCACCCCATGCTTCA	0.672																																					p.G442G		Atlas-SNP	.											.	KLHDC4	45	.	0			c.G1326A						.						87	88	88					16																	87742992		2198	4300	6498	SO:0001819	synonymous_variant	54758	exon10			GAGCACCCCATGC	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.1326G>A	chr16.hg19:g.87742992C>T		78.0	0.0		104.0	5.0	NM_017566	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Silent	SNP	ENST00000270583.5	hg19	CCDS10963.1																																																																																			.	.		0.672	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		T	87742992	C	T	87742992	2	4	115	1	0	0	0	0	0	0	0	1	8367	610	22	3		3	KLHDC4	16	87742992	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	3748325	87742992	2611761	394	19933										
CA5A	763	hgsc.bcm.edu	37	chr16	87960395	87960395	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caaattccacctggaagaggTagccagtgttccagatgtac	10	10	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:87960395T>C	ENST00000309893.2	-	2	364	c.299A>G	c.(298-300)tAc>tGc	p.Y100C	CA5A_ENST00000568801.1_5'UTR	NM_001739.1	NP_001730.1	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial	100					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(80;0.0513)	Brinzolamide(DB01194)|Zonisamide(DB00909)	CTGGAAGAGGTAGCCAGTGTT	0.577																																					p.Y100C		Atlas-SNP	.											.	CA5A	32	.	0			c.A299G						.						77	71	73					16																	87960395		2198	4300	6498	SO:0001583	missense	763	exon2			AAGAGGTAGCCAG	L19297	CCDS10965.1	16q24.2	2012-08-21			ENSG00000174990	ENSG00000174990	4.2.1.1	"Carbonic anhydrases"	1377	protein-coding gene	gene with protein product		114761		CA5		8356065, 7490083	Standard	NM_001739		Approved	CAV, CAVA	uc002fkn.1	P35218	OTTHUMG00000137677	ENST00000309893.2:c.299A>G	chr16.hg19:g.87960395T>C	ENSP00000309649:p.Tyr100Cys	68.0	0.0		86.0	4.0	NM_001739	B2RPF2	Missense_Mutation	SNP	ENST00000309893.2	hg19	CCDS10965.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.947355	0.53186	.	.	ENSG00000174990	ENST00000309893	T	0.68331	-0.32	4.1	2.98	0.34508	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.070438	0.64402	D	0.000016	T	0.80819	0.4696	M	0.84846	2.72	0.52099	D	0.999946	D	0.89917	1.0	D	0.91635	0.999	T	0.80077	-0.1533	10	0.66056	D	0.02	-20.4895	9.1125	0.36737	0.1636:0.0:0.0:0.8364	.	100	P35218	CAH5A_HUMAN	C	100	ENSP00000309649:Y100C	ENSP00000309649:Y100C	Y	-	2	0	CA5A	86517896	1.000000	0.71417	0.995000	0.50966	0.671000	0.39405	5.631000	0.67812	0.457000	0.26962	0.454000	0.30748	TAC	.	.		0.577	CA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269164.1	NM_001739		C	87960395	T	C	87960395	3	2	115	1	0	0	0	0	1	0	0	0	2521	1638	57	2	642	2	CA5A	16	87960395	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	217403	87960395	2394358	395	19934										
FANCA	2175	hgsc.bcm.edu	37	chr16	89849430	89849430	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttgccttgaggtcggccagCcgtgtcttggccaatgagat	13	11	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:89849430C>T	ENST00000389301.3	-	16	1581	c.1551G>A	c.(1549-1551)cgG>cgA	p.R517R	FANCA_ENST00000568369.1_Silent_p.R517R	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	517					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GGTCGGCCAGCCGTGTCTTGG	0.557			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R517R		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.G1551A						.						183	133	150					16																	89849430		2198	4300	6498	SO:0001819	synonymous_variant	2175	exon16	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGCCAGCCGTGTC	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"Fanconi anemia, complementation groups"	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1551G>A	chr16.hg19:g.89849430C>T		326.0	0.0		393.0	157.0	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	hg19	CCDS32515.1																																																																																			.	.		0.557	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			T	89849430	C	T	89849430	2	4	115	1	0	0	0	0	0	0	0	1	5670	726	26	3		3	FANCA	16	89849430	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	1889035	89849430	505323	396	19935										
GAS8	2622	hgsc.bcm.edu	37	chr16	90106894	90106894	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acctggaccctgcagccctgAcgctggtgtcccgcaagctg	12	16	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr16:90106894A>G	ENST00000268699.4	+	9	1320	c.1198A>G	c.(1198-1200)Acg>Gcg	p.T400A	GAS8_ENST00000536122.1_Missense_Mutation_p.T375A|GAS8_ENST00000540721.1_3'UTR|URAHP_ENST00000517889.1_RNA	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	400					cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		TGCAGCCCTGACGCTGGTGTC	0.627																																					p.T400A		Atlas-SNP	.											.	GAS8	29	.	0			c.A1198G						.						47	42	43					16																	90106894		2197	4300	6497	SO:0001583	missense	2622	exon9			GCCCTGACGCTGG	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"growth arrest-specific 11"	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.1198A>G	chr16.hg19:g.90106894A>G	ENSP00000268699:p.Thr400Ala	42.0	0.0		64.0	4.0	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	hg19	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	A	3.350	-0.132786	0.06711	.	.	ENSG00000141013	ENST00000536122;ENST00000268699;ENST00000540721	T;T	0.40476	1.03;1.03	5.66	0.994	0.19832	.	0.386283	0.31438	N	0.007644	T	0.15955	0.0384	N	0.05124	-0.11	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.002	T	0.14172	-1.0482	9	.	.	.	-24.706	4.5345	0.12022	0.4755:0.0:0.1488:0.3757	.	371;400	B7Z1X3;O95995	.;GAS8_HUMAN	A	375;400;371	ENSP00000440977:T375A;ENSP00000268699:T400A	.	T	+	1	0	GAS8	88634395	0.002000	0.14202	0.431000	0.26735	0.810000	0.45777	0.274000	0.18680	0.957000	0.37930	0.454000	0.30748	ACG	.	.		0.627	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2			G	90106894	A	G	90106894	3	3	115	1	0	0	0	0	1	0	0	0	6259	275	10	2	1232	2	GAS8	16	90106894	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	257464	90106894	247859	397	19936										
TUSC5	286753	hgsc.bcm.edu	37	chr17	1198888	1198888	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	catcatgggcatcgtcattaTcatggtggccgtgaccgtca	11	11	4	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:1198888T>C	ENST00000333813.3	+	2	830	c.491T>C	c.(490-492)aTc>aCc	p.I164T		NM_172367.2	NP_758955.2	Q8IXB3	TUSC5_HUMAN	tumor suppressor candidate 5	164					response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|prostate(4)|skin(2)	15				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ATCGTCATTATCATGGTGGCC	0.612																																					p.I164T		Atlas-SNP	.											.	TUSC5	25	.	0			c.T491C						.						94	105	102					17																	1198888		2146	4248	6394	SO:0001583	missense	286753	exon2			TCATTATCATGGT	AB090231	CCDS42225.1	17p13.3	2009-10-16			ENSG00000184811	ENSG00000184811			29592	protein-coding gene	gene with protein product	"located at seventeen p thirteen point three 1", "interferon induced transmembrane protein domain containing 3"	612211				12660825	Standard	NM_172367		Approved	LOST1, IFITMD3	uc002fsi.1	Q8IXB3	OTTHUMG00000132196	ENST00000333813.3:c.491T>C	chr17.hg19:g.1198888T>C	ENSP00000329548:p.Ile164Thr	69.0	0.0		116.0	5.0	NM_172367	A6NMK4	Missense_Mutation	SNP	ENST00000333813.3	hg19	CCDS42225.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.858712	0.51376	.	.	ENSG00000184811	ENST00000333813	D	0.87179	-2.22	5.56	5.56	0.83823	.	0.163511	0.38381	U	0.001712	D	0.92130	0.7505	M	0.81497	2.545	0.44843	D	0.997851	D	0.56968	0.978	P	0.60236	0.871	D	0.92409	0.5936	10	0.51188	T	0.08	-17.1909	13.0902	0.59162	0.0:0.0:0.0:1.0	.	164	Q8IXB3	TUSC5_HUMAN	T	164	ENSP00000329548:I164T	ENSP00000329548:I164T	I	+	2	0	TUSC5	1145638	1.000000	0.71417	0.988000	0.46212	0.060000	0.15804	4.477000	0.60223	2.124000	0.65301	0.496000	0.49642	ATC	.	.		0.612	TUSC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255249.1	NM_172367		C	1198888	T	C	1198888	3	2	115	1	0	0	0	0	1	0	0	0	16794	1435	50	2	497	2	TUSC5	17	1198888	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10		1198888	79996322	398	19937										
PITPNA	5306	hgsc.bcm.edu	37	chr17	1444911	1444911	+	Frame_Shift_Del	DEL	A	A	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caggtttcaattttaatcagAaagtcttctttcatgtactc							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:1444911delA	ENST00000313486.7	-	6	576	c.321delT	c.(319-321)tttfs	p.F107fs	PITPNA_ENST00000539476.1_Frame_Shift_Del_p.F107fs	NM_006224.3	NP_006215.1	Q00169	PIPNA_HUMAN	phosphatidylinositol transfer protein, alpha	107					axon guidance (GO:0007411)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)|phosphatidylcholine transporter activity (GO:0008525)|phosphatidylinositol transporter activity (GO:0008526)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	7				UCEC - Uterine corpus endometrioid carcinoma (25;0.0845)		TTTTAATCAGAAAGTCTTCTT	0.433																																					p.L108X		Atlas-INDEL	.											.	PITPNA	14	.	0			c.322delC						.						89	87	88					17																	1444911		1850	4098	5948	SO:0001589	frameshift_variant	5306	exon6			.	M73704	CCDS45563.1	17p13.3	2012-06-29	2003-05-09	2004-09-03	ENSG00000174238	ENSG00000174238			9001	protein-coding gene	gene with protein product		600174	"phosphotidylinositol transfer protein"	PITPN		8255295	Standard	NM_006224		Approved	VIB1A	uc021tnf.1	Q00169	OTTHUMG00000177779	ENST00000313486.7:c.321delT	chr17.hg19:g.1444911delA	ENSP00000316809:p.Phe107fs	146.0	0.0		177.0	11.0	NM_006224		Frame_Shift_Del	DEL	ENST00000313486.7	hg19	CCDS45563.1																																																																																			.	.		0.433	PITPNA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438927.3			-	1444911	A	-	1444911	7	5	115	1	0	1	0	1	0	0	0	0	11956	243	9	0	515	0	PITPNA	17	1444911	Frame_Shift_Del	DEL	A	TCGA-DD-A3A1-01A-11D-A20W-10	246023	1444911	79750299	399	19938										
MINK1	50488	hgsc.bcm.edu	37	chr17	4791017	4791017	+	Frame_Shift_Del	DEL	A	A	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gagaccccgaggcacacatcAaacacctgctgcaccagcgg							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:4791017delA	ENST00000355280.6	+	12	1358	c.1162delA	c.(1162-1164)aaafs	p.K388fs	MINK1_ENST00000453408.3_Frame_Shift_Del_p.K388fs|MINK1_ENST00000347992.7_Frame_Shift_Del_p.K388fs	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						GGCACACATCAAACACCTGCT	0.632																																					p.I387fs		Atlas-INDEL	.											.	MINK1	110	.	0			c.1161delC						.						8	10	9					17																	4791017		2027	4140	6167	SO:0001589	frameshift_variant	50488	exon12			.	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"misshapen/NIK-related kinase"	609426	"misshapen-like kinase 1 (zebrafish)"			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.1162delA	chr17.hg19:g.4791017delA	ENSP00000347427:p.Lys388fs	95.0	0.0		145.0	11.0	NM_170663		Frame_Shift_Del	DEL	ENST00000355280.6	hg19	CCDS45588.1																																																																																			.	.		0.632	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		-	4791017	A	-	4791017	7	5	115	1	0	1	0	1	0	0	0	0	9596	131	5	0	947	0	MINK1	17	4791017	Frame_Shift_Del	DEL	A	TCGA-DD-A3A1-01A-11D-A20W-10	3346106	4791017	76404193	400	19939										
ACADVL	37	hgsc.bcm.edu	37	chr17	7123814	7123814	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caagtcagattcccacccctCtgacgctctgaccaggaaaa	7	15	3	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:7123814C>A	ENST00000356839.5	+	3	349	c.170C>A	c.(169-171)tCt>tAt	p.S57Y	DLG4_ENST00000399510.2_5'Flank|MIR324_ENST00000362183.1_RNA|ACADVL_ENST00000350303.5_Intron|ACADVL_ENST00000543245.2_Missense_Mutation_p.S80Y|ACADVL_ENST00000581562.1_3'UTR	NM_000018.3|NM_001270448.1	NP_000009.1|NP_001257377.1	P49748	ACADV_HUMAN	acyl-CoA dehydrogenase, very long chain	57	Catalytic.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy derivation by oxidation of organic compounds (GO:0015980)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(1)|ovary(4)|skin(1)	21						TCCCACCCCTCTGACGCTCTG	0.577																																					p.S80Y		Atlas-SNP	.											.	ACADVL	43	.	0			c.C239A						.						68	70	69					17																	7123814		2203	4300	6503	SO:0001583	missense	37	exon4			ACCCCTCTGACGC	BC012912	CCDS11090.1, CCDS42249.1, CCDS58509.1	17p13.1	2010-04-30	2010-04-30		ENSG00000072778	ENSG00000072778			92	protein-coding gene	gene with protein product		609575	"acyl-Coenzyme A dehydrogenase, very long chain"			8921384	Standard	NM_000018		Approved	VLCAD, LCACD, ACAD6	uc002gev.4	P49748	OTTHUMG00000102157	ENST00000356839.5:c.170C>A	chr17.hg19:g.7123814C>A	ENSP00000349297:p.Ser57Tyr	79.0	0.0		101.0	36.0	NM_001270447	B4DEB6|F5H2A9|O76056|Q8WUL0	Missense_Mutation	SNP	ENST00000356839.5	hg19	CCDS11090.1	.	.	.	.	.	.	.	.	.	.	C	18.40	3.616576	0.66672	.	.	ENSG00000072778	ENST00000543245;ENST00000356839;ENST00000322910;ENST00000542255	D	0.96967	-4.19	5.82	2.5	0.30297	.	0.814642	0.11767	N	0.531520	D	0.93661	0.7975	L	0.36672	1.1	0.19300	N	0.99997	P;P;P	0.49635	0.797;0.926;0.8	B;B;B	0.44315	0.332;0.446;0.365	D	0.86613	0.1874	10	0.59425	D	0.04	.	11.3334	0.49490	0.4807:0.5193:0.0:0.0	.	103;80;57	G3V1M7;F5H2A9;P49748	.;.;ACADV_HUMAN	Y	80;103;57;103	ENSP00000438689:S80Y	ENSP00000325395:S57Y	S	+	2	0	ACADVL	7064538	0.000000	0.05858	0.256000	0.24389	0.007000	0.05969	0.662000	0.25038	0.756000	0.33013	0.655000	0.94253	TCT	.	.		0.577	ACADVL-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220001.5	NM_000018		A	7123814	C	A	7123814	3	1	115	1	0	0	0	0	1	0	0	0	116	913	32	3	180	3	ACADVL	17	7123814	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	2332797	7123814	74071396	401	19940										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7699846	7699846	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcttcaggactttgaggaagAggtgaagcccattgggaacg	15	7	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:7699846A>G	ENST00000572933.1	+	50	9199	c.7739A>G	c.(7738-7740)gAg>gGg	p.E2580G	DNAH2_ENST00000389173.2_Missense_Mutation_p.E2580G			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2580	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TTTGAGGAAGAGGTGAAGCCC	0.547																																					p.E2580G		Atlas-SNP	.											.	DNAH2	498	.	0			c.A7739G						.						134	109	117					17																	7699846		2203	4300	6503	SO:0001583	missense	146754	exon49			AGGAAGAGGTGAA	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.7739A>G	chr17.hg19:g.7699846A>G	ENSP00000458355:p.Glu2580Gly	67.0	0.0		96.0	4.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	17.94	3.511578	0.64522	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.35048	1.33	5.4	5.4	0.78164	.	0.056757	0.64402	D	0.000002	T	0.41050	0.1142	M	0.69463	2.115	0.80722	D	1	B	0.27700	0.186	B	0.35688	0.208	T	0.34004	-0.9846	10	0.44086	T	0.13	.	11.0254	0.47743	0.8444:0.1556:0.0:0.0	.	2580	Q9P225	DYH2_HUMAN	G	2580	ENSP00000373825:E2580G	ENSP00000353818:E2580G	E	+	2	0	DNAH2	7640571	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.921000	0.56454	2.264000	0.75181	0.496000	0.49642	GAG	.	.		0.547	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		G	7699846	A	G	7699846	3	3	115	1	0	0	0	0	1	0	0	0	4604	304	11	2	7933	2	DNAH2	17	7699846	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	576032	7699846	73495364	402	19941										
CHD3	1107	hgsc.bcm.edu	37	chr17	7803881	7803881	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcttctggctcttagcaactTggagggcttcctggaggagt	13	9	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:7803881T>C	ENST00000330494.7	+	18	2960	c.2810T>C	c.(2809-2811)tTg>tCg	p.L937S	CHD3_ENST00000358181.4_Missense_Mutation_p.L937S|CHD3_ENST00000380358.4_Missense_Mutation_p.L996S	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	937					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				CTTAGCAACTTGGAGGGCTTC	0.488																																					p.L996S		Atlas-SNP	.											.	CHD3	169	.	0			c.T2987C						.						66	69	68					17																	7803881		2203	4300	6503	SO:0001583	missense	1107	exon18			GCAACTTGGAGGG	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.2810T>C	chr17.hg19:g.7803881T>C	ENSP00000332628:p.Leu937Ser	74.0	0.0		81.0	4.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	T	13.81	2.347084	0.41599	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	D;D;D	0.91945	-2.94;-2.94;-2.94	4.63	4.63	0.57726	DEAD-like helicase (1);SNF2-related (1);	0.000000	0.32901	N	0.005517	D	0.93058	0.7790	L	0.31157	0.91	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.87578	0.996;0.998;0.998	D	0.94084	0.7347	10	0.87932	D	0	-12.0132	14.4958	0.67685	0.0:0.0:0.0:1.0	.	937;937;996	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	S	996;937;937	ENSP00000369716:L996S;ENSP00000350907:L937S;ENSP00000332628:L937S	ENSP00000332628:L937S	L	+	2	0	CHD3	7744606	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	7.825000	0.86693	2.085000	0.62840	0.402000	0.26972	TTG	.	.		0.488	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		C	7803881	T	C	7803881	3	2	115	1	0	0	0	0	1	0	0	0	3328	1821	63	2	3161	2	CHD3	17	7803881	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	104035	7803881	73391329	403	19942										
CNTROB	116840	hgsc.bcm.edu	37	chr17	7851016	7851016	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgccgcctgctcagctggaGggcctcaagaattttttgca	11	12	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:7851016G>C	ENST00000563694.1	+	14	3046	c.2121G>C	c.(2119-2121)gaG>gaC	p.E707D	CNTROB_ENST00000380255.3_3'UTR|CNTROB_ENST00000565740.1_Missense_Mutation_p.E707D|CNTROB_ENST00000380262.3_Missense_Mutation_p.E707D	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	707	Pro-rich.|Required for centrosome localization.				centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				CTCAGCTGGAGGGCCTCAAGA	0.542																																					p.E707D		Atlas-SNP	.											.	CNTROB	61	.	0			c.G2121C						.						82	88	86					17																	7851016		2203	4300	6503	SO:0001583	missense	116840	exon14			GCTGGAGGGCCTC	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"centrobin"	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.2121G>C	chr17.hg19:g.7851016G>C	ENSP00000456335:p.Glu707Asp	105.0	0.0		121.0	71.0	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Missense_Mutation	SNP	ENST00000563694.1	hg19	CCDS11126.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.598749	0.28445	.	.	ENSG00000170037	ENST00000380262	T	0.10192	2.9	5.41	-5.03	0.02973	.	0.536026	0.16924	N	0.193956	T	0.04952	0.0133	L	0.27053	0.805	0.51482	D	0.999927	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.002;0.002;0.002	T	0.30794	-0.9966	10	0.72032	D	0.01	-1.0222	1.0312	0.01538	0.4235:0.1135:0.1943:0.2688	.	707;707;707	Q8N137-3;Q8N137;Q8N137-2	.;CNTRB_HUMAN;.	D	707	ENSP00000369614:E707D	ENSP00000369614:E707D	E	+	3	2	CNTROB	7791741	0.725000	0.28048	0.263000	0.24496	0.490000	0.33462	-0.594000	0.05733	-0.705000	0.05035	-1.210000	0.01631	GAG	.	.		0.542	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051		C	7851016	G	C	7851016	3	2	115	1	0	0	0	0	1	0	0	0	3653	991	35	4	2175	4	CNTROB	17	7851016	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	47135	7851016	73344194	404	19943										
PER1	5187	hgsc.bcm.edu	37	chr17	8051338	8051338	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcttgtggatagccagcatgAggggtcggtcctcaggatgc	15	9	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:8051338A>G	ENST00000317276.4	-	10	1448	c.1211T>C	c.(1210-1212)cTc>cCc	p.L404P	PER1_ENST00000578089.1_5'Flank|PER1_ENST00000581082.1_Missense_Mutation_p.L384P|PER1_ENST00000354903.5_Missense_Mutation_p.L388P	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	404	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AGCCAGCATGAGGGGTCGGTC	0.637			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.L404P		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.T1211C						.						45	40	41					17																	8051338		2203	4300	6503	SO:0001583	missense	5187	exon10			AGCATGAGGGGTC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"period (Drosophila) homolog 1", "period homolog 1 (Drosophila)"	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.1211T>C	chr17.hg19:g.8051338A>G	ENSP00000314420:p.Leu404Pro	101.0	0.0		80.0	4.0	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	hg19	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749661	0.69533	.	.	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.16324	2.35;2.35	5.17	5.17	0.71159	PAS fold-3 (1);PAS (2);	0.286010	0.32819	N	0.005612	T	0.45696	0.1355	M	0.84948	2.725	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.989;0.998	T	0.51756	-0.8665	10	0.87932	D	0	-24.0286	13.0042	0.58694	1.0:0.0:0.0:0.0	.	388;404	B4DI49;O15534	.;PER1_HUMAN	P	404;388	ENSP00000314420:L404P;ENSP00000346979:L388P	ENSP00000314420:L404P	L	-	2	0	PER1	7992063	0.976000	0.34144	1.000000	0.80357	0.978000	0.69477	6.054000	0.71096	2.171000	0.68590	0.460000	0.39030	CTC	.	.		0.637	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			G	8051338	A	G	8051338	3	3	115	1	0	0	0	0	1	0	0	0	11738	304	11	2	2717	2	PER1	17	8051338	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	200322	8051338	73143872	405	19944										
VAMP2	6844	hgsc.bcm.edu	37	chr17	8064968	8064968	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttgcgcttgagcttggctgcGcttgtttcaaactgggaggc	14	9	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:8064968G>A	ENST00000316509.6	-	3	335	c.240C>T	c.(238-240)agC>agT	p.S80S	VAMP2_ENST00000404970.3_Silent_p.S35S|VAMP2_ENST00000481878.1_Silent_p.S80S|VAMP2_ENST00000488857.1_Silent_p.S82S|RP11-599B13.6_ENST00000498285.1_Silent_p.S80S	NM_014232.2	NP_055047.2	P63027	VAMP2_HUMAN	vesicle-associated membrane protein 2 (synaptobrevin 2)	80	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|exocytosis (GO:0006887)|glutamate secretion (GO:0014047)|membrane organization (GO:0061024)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021)	calcium-dependent protein binding (GO:0048306)|protein self-association (GO:0043621)									Botulinum Toxin Type B(DB00042)	GCTTGGCTGCGCTTGTTTCAA	0.567																																					p.S80S		Atlas-SNP	.											VAMP2,colon,carcinoma,0,1	VAMP2	5	.	0			c.C240T						.						129	123	125					17																	8064968		2203	4300	6503	SO:0001819	synonymous_variant	6844	exon3			GGCTGCGCTTGTT		CCDS32561.1	17p13.1	2013-09-19			ENSG00000220205	ENSG00000220205		"Vesicle-associated membrane proteins"	12643	protein-coding gene	gene with protein product		185881		SYB2		1976629	Standard	NM_014232		Approved	VAMP-2	uc010cnt.1	P63027	OTTHUMG00000150254	ENST00000316509.6:c.240C>T	chr17.hg19:g.8064968G>A		138.0	0.0		130.0	13.0	NM_014232	P19065|Q9BUC2	Silent	SNP	ENST00000316509.6	hg19	CCDS32561.1																																																																																			.	.		0.567	VAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317118.1			A	8064968	G	A	8064968	2	1	115	1	0	0	0	0	0	0	0	1	17128	1078	38	1		1	VAMP2	17	8064968	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	13630	8064968	73130242	406	19945										
MYH10	4628	hgsc.bcm.edu	37	chr17	8393813	8393813	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttccagctcctccagctgggTcctcatttcctccacctgct	6	18	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:8393813T>C	ENST00000269243.4	-	33	4774	c.4636A>G	c.(4636-4638)Acc>Gcc	p.T1546A	MYH10_ENST00000360416.3_Missense_Mutation_p.T1577A|MYH10_ENST00000396239.1_Missense_Mutation_p.T1567A|MYH10_ENST00000379980.4_Missense_Mutation_p.T1562A	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1546					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						TCCAGCTGGGTCCTCATTTCC	0.557																																					p.T1577A		Atlas-SNP	.											.	MYH10	148	.	0			c.A4729G						.						121	109	113					17																	8393813		2203	4300	6503	SO:0001583	missense	4628	exon35			GCTGGGTCCTCAT	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.4636A>G	chr17.hg19:g.8393813T>C	ENSP00000269243:p.Thr1546Ala	179.0	0.0		182.0	8.0	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	hg19	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.664519	0.47572	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;T;T	0.82255	-1.59;-1.59;-0.95;-0.95	4.56	4.56	0.56223	Myosin tail (1);	0.000000	0.85682	D	0.000000	T	0.72358	0.3450	N	0.21373	0.66	0.58432	D	0.999999	B;B;B	0.17038	0.02;0.001;0.02	B;B;B	0.25405	0.06;0.017;0.06	T	0.66221	-0.5978	10	0.14252	T	0.57	.	14.3574	0.66748	0.0:0.0:0.0:1.0	.	1555;1577;1546	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	A	1546;1577;1567;1562	ENSP00000269243:T1546A;ENSP00000353590:T1577A;ENSP00000379539:T1567A;ENSP00000369315:T1562A	ENSP00000269243:T1546A	T	-	1	0	MYH10	8334538	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.067000	0.71193	2.037000	0.60232	0.533000	0.62120	ACC	.	.		0.557	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			C	8393813	T	C	8393813	3	2	115	1	0	0	0	0	1	0	0	0	10039	1667	58	2	1330	2	MYH10	17	8393813	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	328845	8393813	72801397	407	19946										
NT5M	56953	hgsc.bcm.edu	37	chr17	17250185	17250185	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccacaaccagcacctgcagcTgcagcccccccgccgcaggc	9	22	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:17250185T>C	ENST00000389022.4	+	5	827	c.611T>C	c.(610-612)cTg>cCg	p.L204P	NT5M_ENST00000582909.1_3'UTR	NM_020201.3	NP_064586.1	Q9NPB1	NT5M_HUMAN	5',3'-nucleotidase, mitochondrial	204					dephosphorylation (GO:0016311)|DNA replication (GO:0006260)|dUMP catabolic process (GO:0046079)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine deoxyribonucleotide catabolic process (GO:0009223)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotidase activity (GO:0008252)|nucleotide binding (GO:0000166)	p.L204P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						CACCTGCAGCTGCAGCCCCCC	0.672																																					p.L204P		Atlas-SNP	.											NT5M,NS,carcinoma,0,1	NT5M	17	.	1	Substitution - Missense(1)	kidney(1)	c.T611C						.						30	36	34					17																	17250185		2202	4298	6500	SO:0001583	missense	56953	exon5			TGCAGCTGCAGCC	AF210652	CCDS32581.1	17p11.2	2007-08-01	2002-05-23		ENSG00000205309	ENSG00000205309	3.1.3.5		15769	protein-coding gene	gene with protein product		605292	"5' nucleotidase, mitochondrial"			10899995	Standard	XM_005256731		Approved	dNT-2, dNT2, mdN	uc002grf.3	Q9NPB1	OTTHUMG00000059277	ENST00000389022.4:c.611T>C	chr17.hg19:g.17250185T>C	ENSP00000373674:p.Leu204Pro	90.0	0.0		107.0	5.0	NM_020201		Missense_Mutation	SNP	ENST00000389022.4	hg19	CCDS32581.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.08|17.08	3.297044|3.297044	0.60086|0.60086	.|.	.|.	ENSG00000205309|ENSG00000205309	ENST00000446264|ENST00000389022	.|T	.|0.49139	.|0.79	5.79|5.79	4.72|4.72	0.59763|0.59763	.|HAD-like domain (2);	0.043809|.	0.85682|.	D|.	0.000000|.	T|T	0.48660|0.48660	0.1512|0.1512	M|M	0.61703|0.61703	1.905|1.905	0.47214|0.47214	D|D	0.999351|0.999351	B|B;B	0.32350|0.28439	0.366|0.212;0.212	B|B;B	0.27796|0.36030	0.083|0.216;0.216	T|T	0.52230|0.52230	-0.8603|-0.8603	9|9	0.72032|0.54805	D|T	0.01|0.06	-30.5484|-30.5484	10.2483|10.2483	0.43354|0.43354	0.0:0.0778:0.0:0.9222|0.0:0.0778:0.0:0.9222	.|.	203|210;204	F6S3X3|Q2I378;Q9NPB1	.|.;NT5M_HUMAN	R|P	203|204	.|ENSP00000373674:L204P	ENSP00000390695:C203R|ENSP00000373674:L204P	C|L	+|+	1|2	0|0	NT5M|NT5M	17190910|17190910	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.892000|0.892000	0.51952|0.51952	3.300000|3.300000	0.51834|0.51834	2.203000|2.203000	0.70933|0.70933	0.459000|0.459000	0.35465|0.35465	TGC|CTG	.	.		0.672	NT5M-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446045.1			C	17250185	T	C	17250185	3	2	115	1	0	0	0	0	1	0	0	0	10703	1580	55	2	629	2	NT5M	17	17250185	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	8856372	17250185	63945025	408	19947										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26961916	26961916	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctccttactttcatccttcaTcagctcgtagttatcatgaa	4	12	4	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:26961916T>C	ENST00000528896.2	-	16	2763	c.2689A>G	c.(2689-2691)Atg>Gtg	p.M897V	RP11-192H23.7_ENST00000577814.1_RNA|KIAA0100_ENST00000544884.1_Missense_Mutation_p.M754V|RP11-192H23.7_ENST00000583787.1_RNA|KIAA0100_ENST00000389003.3_Missense_Mutation_p.M754V	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	897						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					TCATCCTTCATCAGCTCGTAG	0.478																																					p.M897V		Atlas-SNP	.											.	KIAA0100	175	.	0			c.A2689G						.						219	239	232					17																	26961916		2203	4300	6503	SO:0001583	missense	9703	exon16			CCTTCATCAGCTC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.2689A>G	chr17.hg19:g.26961916T>C	ENSP00000436773:p.Met897Val	116.0	0.0		80.0	36.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.493281	0.64186	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.24350	1.86;1.86	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.45856	0.1363	M	0.61703	1.905	0.80722	D	1	P	0.49447	0.924	P	0.60682	0.878	T	0.18178	-1.0345	10	0.30854	T	0.27	.	16.2996	0.82804	0.0:0.0:0.0:1.0	.	897	Q14667	K0100_HUMAN	V	897;867;897;754	ENSP00000436773:M897V;ENSP00000446443:M754V	ENSP00000005905:M897V	M	-	1	0	KIAA0100	23986043	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.828000	0.69307	2.252000	0.74401	0.455000	0.32223	ATG	.	.		0.478	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		C	26961916	T	C	26961916	3	2	115	1	0	0	0	0	1	0	0	0	8163	1435	50	2	4114	2	KIAA0100	17	26961916	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	9711731	26961916	54233294	409	19948										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26961957	26961957	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtttcacctcaaaaacatcaTccaagaaaacccatgagaag	5	11	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:26961957T>C	ENST00000528896.2	-	16	2722	c.2648A>G	c.(2647-2649)gAt>gGt	p.D883G	RP11-192H23.7_ENST00000577814.1_RNA|KIAA0100_ENST00000544884.1_Missense_Mutation_p.D740G|RP11-192H23.7_ENST00000583787.1_RNA|KIAA0100_ENST00000389003.3_Missense_Mutation_p.D740G	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	883						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					AAAAACATCATCCAAGAAAAC	0.473																																					p.D883G		Atlas-SNP	.											.	KIAA0100	175	.	0			c.A2648G						.						184	201	195					17																	26961957		2203	4300	6503	SO:0001583	missense	9703	exon16			ACATCATCCAAGA	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.2648A>G	chr17.hg19:g.26961957T>C	ENSP00000436773:p.Asp883Gly	87.0	0.0		69.0	5.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.928545	0.73327	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.75050	-0.9;-0.79	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.85982	0.5824	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.87526	0.2449	10	0.87932	D	0	.	16.2996	0.82804	0.0:0.0:0.0:1.0	.	883	Q14667	K0100_HUMAN	G	883;853;883;740	ENSP00000436773:D883G;ENSP00000446443:D740G	ENSP00000005905:D883G	D	-	2	0	KIAA0100	23986084	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.554000	0.82212	2.252000	0.74401	0.455000	0.32223	GAT	.	.		0.473	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		C	26961957	T	C	26961957	3	2	115	1	0	0	0	0	1	0	0	0	8163	1435	50	2	4155	2	KIAA0100	17	26961957	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	41	26961957	54233253	410	19949										
MED1	5469	hgsc.bcm.edu	37	chr17	37565247	37565247	+	Frame_Shift_Del	DEL	T	T	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	actgactgtgagaggaaggcTtgcccaccatcactgttccc							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:37565247delT	ENST00000300651.6	-	17	3450	c.3227delA	c.(3226-3228)aagfs	p.K1076fs	CTB-131K11.1_ENST00000582842.1_RNA|MED1_ENST00000394287.3_Intron	NM_004774.3	NP_004765.2	O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		AGAGGAAGGCTTGCCCACCAT	0.522										HNSCC(31;0.082)																											p.K1076fs	Pancreas(21;279 768 2492 4877 24026)	Atlas-INDEL	.											.	MED1	123	.	0			c.3228delG						.						99	95	96					17																	37565247		2203	4300	6503	SO:0001589	frameshift_variant	5469	exon17			.	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"PPAR binding protein"	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000300651.6:c.3227delA	chr17.hg19:g.37565247delT	ENSP00000300651:p.Lys1076fs	110.0	0.0		117.0	10.0	NM_004774	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Frame_Shift_Del	DEL	ENST00000300651.6	hg19	CCDS11336.1																																																																																			.	.		0.522	MED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256943.3	NM_004774		-	37565247	T	-	37565247	7	5	115	1	0	1	0	1	0	0	0	0	9434	1609	56	0	1522	0	MED1	17	37565247	Frame_Shift_Del	DEL	T	TCGA-DD-A3A1-01A-11D-A20W-10	10603290	37565247	43629963	411	19950										
KRT40	125115	hgsc.bcm.edu	37	chr17	39140493	39140493	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gccgtgccacaggactcaggAgagcagtgtgtggaggagca	17	9	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:39140493A>G	ENST00000398486.2	-	3	193	c.33T>C	c.(31-33)tcT>tcC	p.S11S	KRT40_ENST00000377755.4_Silent_p.S11S	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	11	Head.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				AGGACTCAGGAGAGCAGTGTG	0.547																																					p.S11S		Atlas-SNP	.											.	KRT40	27	.	0			c.T33C						.						33	42	39					17																	39140493		2083	4224	6307	SO:0001819	synonymous_variant	125115	exon3			CTCAGGAGAGCAG	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"-", "Intermediate filaments type I, keratins (acidic)"	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.33T>C	chr17.hg19:g.39140493A>G		60.0	0.0		102.0	5.0	NM_182497	Q6IFU5	Silent	SNP	ENST00000398486.2	hg19	CCDS42320.1																																																																																			.	.		0.547	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497		G	39140493	A	G	39140493	2	3	115	1	0	0	0	0	0	0	0	1	8487	291	11	2		2	KRT40	17	39140493	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1575246	39140493	42054717	412	19951										
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42964105	42964105	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctcctacgtcatcgtcgtcgTcatcatcatccatctgaaag	6	14	5	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:42964105T>C	ENST00000426333.2	-	3	416	c.119A>G	c.(118-120)gAc>gGc	p.D40G	RN7SL405P_ENST00000582502.1_RNA|EFTUD2_ENST00000592576.1_Missense_Mutation_p.D40G|EFTUD2_ENST00000591382.1_Missense_Mutation_p.D40G|EFTUD2_ENST00000402521.3_Missense_Mutation_p.D5G|EFTUD2_ENST00000589211.1_5'UTR	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	40					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				atcgtcgtcgtcatcatcatc	0.517																																					p.D40G	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.A119G						.						124	80	95					17																	42964105		2203	4300	6503	SO:0001583	missense	9343	exon3			TCGTCGTCATCAT	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.119A>G	chr17.hg19:g.42964105T>C	ENSP00000392094:p.Asp40Gly	105.0	0.0		121.0	6.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Missense_Mutation	SNP	ENST00000426333.2	hg19	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	T	16.73	3.204630	0.58234	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	T;T	0.72167	-0.57;-0.63	5.87	5.87	0.94306	.	0.305751	0.38272	N	0.001744	T	0.62962	0.2471	L	0.35723	1.085	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.57236	-0.7846	10	0.34782	T	0.22	.	16.2742	0.82636	0.0:0.0:0.0:1.0	.	40;40	B4DMC0;Q15029	.;U5S1_HUMAN	G	40;40;5	ENSP00000392094:D40G;ENSP00000385873:D5G	ENSP00000262414:D40G	D	-	2	0	EFTUD2	40319631	1.000000	0.71417	0.153000	0.22517	0.626000	0.37791	7.642000	0.83385	2.253000	0.74438	0.533000	0.62120	GAC	.	.		0.517	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		C	42964105	T	C	42964105	3	2	115	1	0	0	0	0	1	0	0	0	4963	1667	58	2	2903	2	EFTUD2	17	42964105	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3823612	42964105	38231105	413	19952										
HEXIM1	10614	hgsc.bcm.edu	37	chr17	43227633	43227633	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gccgctttccaagtttggagActagactgaaacttttttgg	10	8	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:43227633A>G	ENST00000332499.2	+	1	2950	c.1076A>G	c.(1075-1077)gAc>gGc	p.D359G	AC002117.1_ENST00000452741.1_RNA|AC002117.1_ENST00000589950.1_RNA	NM_006460.2	NP_006451.1	O94992	HEXI1_HUMAN	hexamethylene bis-acetamide inducible 1	359					heart development (GO:0007507)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|snRNA binding (GO:0017069)			breast(1)|kidney(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AAGTTTGGAGACTAGACTGAA	0.517																																					p.D359G		Atlas-SNP	.											.	HEXIM1	25	.	0			c.A1076G						.						36	44	42					17																	43227633		2079	4166	6245	SO:0001583	missense	10614	exon1			TTGGAGACTAGAC	AB021179	CCDS11495.1	17q21.31	2006-03-28				ENSG00000186834			24953	protein-coding gene	gene with protein product		607328				12119119, 12832472	Standard	NM_006460		Approved	CLP-1, HIS1, MAQ1, EDG1	uc002iig.3	O94992		ENST00000332499.2:c.1076A>G	chr17.hg19:g.43227633A>G	ENSP00000328773:p.Asp359Gly	70.0	0.0		85.0	4.0	NM_006460	B2R8Y5	Missense_Mutation	SNP	ENST00000332499.2	hg19	CCDS11495.1	.	.	.	.	.	.	.	.	.	.	A	19.26	3.793599	0.70452	.	.	ENSG00000186834	ENST00000332499	.	.	.	4.14	4.14	0.48551	.	0.101963	0.39475	N	0.001358	T	0.50616	0.1626	N	0.08118	0	0.37438	D	0.914297	D	0.71674	0.998	D	0.85130	0.997	T	0.62751	-0.6788	9	0.72032	D	0.01	.	10.6538	0.45663	1.0:0.0:0.0:0.0	.	359	O94992	HEXI1_HUMAN	G	359	.	ENSP00000328773:D359G	D	+	2	0	HEXIM1	40583416	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.622000	0.54217	1.747000	0.51819	0.459000	0.35465	GAC	.	.		0.517	HEXIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449821.2	NM_006460		G	43227633	A	G	43227633	3	3	115	1	0	0	0	0	1	0	0	0	7085	275	10	2	1078	2	HEXIM1	17	43227633	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	263528	43227633	37967577	414	19953										
PHOSPHO1	162466	hgsc.bcm.edu	37	chr17	47304050	47304050	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agaaactggaaaacagccacTcattgtcggtgcattaccgt	9	10	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:47304050T>C	ENST00000310544.4	-	2	131	c.4A>G	c.(4-6)Agt>Ggt	p.S2G	PHOSPHO1_ENST00000514112.1_5'UTR|PHOSPHO1_ENST00000413580.1_5'UTR			Q8TCT1	PHOP1_HUMAN	phosphatase, orphan 1	2					bone mineralization involved in bone maturation (GO:0035630)|dephosphorylation (GO:0016311)|endochondral ossification (GO:0001958)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of bone mineralization (GO:0030500)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|phosphocholine phosphatase activity (GO:0052731)|phosphoethanolamine phosphatase activity (GO:0052732)|pyrophosphatase activity (GO:0016462)							Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)		Choline(DB00122)	AAACAGCCACTCATTGTCGGT	0.562																																					p.S2G		Atlas-SNP	.											.	PHOSPHO1	7	.	0			c.A4G						.						116	104	108					17																	47304050		2203	4300	6503	SO:0001583	missense	162466	exon2			AGCCACTCATTGT	AJ457189	CCDS11547.1, CCDS45726.1	17q21.32	2008-05-02				ENSG00000173868			16815	protein-coding gene	gene with protein product						12464021	Standard	NM_178500		Approved		uc010wlv.1	Q8TCT1		ENST00000310544.4:c.4A>G	chr17.hg19:g.47304050T>C	ENSP00000311925:p.Ser2Gly	54.0	0.0		115.0	5.0	NM_178500	E9PAM0|Q17RU6	Missense_Mutation	SNP	ENST00000310544.4	hg19	CCDS11547.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.011403	0.35511	.	.	ENSG00000173868	ENST00000310544;ENST00000511066;ENST00000503902	T	0.43688	0.94	4.92	4.92	0.64577	.	0.349141	0.33419	N	0.004940	T	0.27134	0.0665	N	0.14661	0.345	0.80722	D	1	B	0.20887	0.049	B	0.22386	0.039	T	0.09058	-1.0692	10	0.54805	T	0.06	.	10.8726	0.46891	0.0:0.0:0.0:1.0	.	2	Q8TCT1	PHOP1_HUMAN	G	2	ENSP00000311925:S2G	ENSP00000311925:S2G	S	-	1	0	PHOSPHO1	44659049	0.996000	0.38824	1.000000	0.80357	0.811000	0.45836	3.432000	0.52824	2.071000	0.62044	0.459000	0.35465	AGT	.	.		0.562	PHOSPHO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364467.2			C	47304050	T	C	47304050	3	2	115	1	0	0	0	0	1	0	0	0	11865	1551	54	2	927	2	PHOSPHO1	17	47304050	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4076417	47304050	33891160	415	19954										
TEX14	56155	hgsc.bcm.edu	37	chr17	56692692	56692692	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctttcactgtgaccctgctcCcattccacactaggctacaa	5	16	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:56692692C>T	ENST00000240361.8	-	8	885	c.800G>A	c.(799-801)gGg>gAg	p.G267E	TEX14_ENST00000349033.5_Missense_Mutation_p.G261E|TEX14_ENST00000389934.3_Missense_Mutation_p.G261E			Q8IWB6	TEX14_HUMAN	testis expressed 14	267	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GACCCTGCTCCCATTCCACAC	0.532																																					p.G267E		Atlas-SNP	.											.	TEX14	343	.	0			c.G800A						.						96	83	87					17																	56692692		2203	4300	6503	SO:0001583	missense	56155	exon8			CTGCTCCCATTCC	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.800G>A	chr17.hg19:g.56692692C>T	ENSP00000240361:p.Gly267Glu	92.0	0.0		120.0	5.0	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	C	16.92	3.255705	0.59321	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.53640	0.61;0.61;0.61	5.58	5.58	0.84498	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.156845	0.45867	D	0.000323	T	0.65015	0.2651	M	0.73753	2.245	0.28585	N	0.909916	D;D;D	0.67145	0.996;0.973;0.991	D;P;P	0.64877	0.93;0.885;0.885	T	0.64385	-0.6420	10	0.72032	D	0.01	-20.4935	11.5868	0.50923	0.0:0.9182:0.0:0.0818	.	267;261;261	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	E	267;261;261	ENSP00000240361:G267E;ENSP00000374584:G261E;ENSP00000268910:G261E	ENSP00000240361:G267E	G	-	2	0	TEX14	54047691	0.998000	0.40836	0.996000	0.52242	0.282000	0.26991	3.458000	0.53014	2.646000	0.89796	0.561000	0.74099	GGG	.	.		0.532	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56692692	C	T	56692692	3	4	115	1	0	0	0	0	1	0	0	0	15793	623	22	3	3797	3	TEX14	17	56692692	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	9388642	56692692	24502518	416	19955										
CACNG4	27092	hgsc.bcm.edu	37	chr17	65026831	65026831	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttcctcttctccttatgccaGgatgccgagctacaggtacc	8	14	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:65026831G>A	ENST00000262138.3	+	4	697	c.695G>A	c.(694-696)aGg>aAg	p.R232K	AC005544.1_ENST00000375684.1_5'Flank|RP11-74H8.1_ENST00000579138.1_RNA	NM_014405.3	NP_055220.1	Q9UBN1	CCG4_HUMAN	calcium channel, voltage-dependent, gamma subunit 4	232					membrane depolarization (GO:0051899)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(3)	19	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			CCTTATGCCAGGATGCCGAGC	0.552																																					p.R232K		Atlas-SNP	.											.	CACNG4	44	.	0			c.G695A						.						73	77	76					17																	65026831		2203	4300	6503	SO:0001583	missense	27092	exon4			ATGCCAGGATGCC	AH008289	CCDS11667.1	17q24	2006-01-23				ENSG00000075461		"Calcium channel subunits"	1408	protein-coding gene	gene with protein product		606404				10613843	Standard	NM_014405		Approved	MGC11138, MGC24983	uc002jft.2	Q9UBN1		ENST00000262138.3:c.695G>A	chr17.hg19:g.65026831G>A	ENSP00000262138:p.Arg232Lys	149.0	0.0		173.0	68.0	NM_014405	B2RCK0	Missense_Mutation	SNP	ENST00000262138.3	hg19	CCDS11667.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.537970	0.85917	.	.	ENSG00000075461	ENST00000262138	T	0.58060	0.36	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.56337	0.1978	M	0.79123	2.44	0.80722	D	1	D	0.58268	0.982	B	0.44315	0.446	T	0.59815	-0.7383	10	0.11485	T	0.65	-0.0339	18.0456	0.89331	0.0:0.0:1.0:0.0	.	232	Q9UBN1	CCG4_HUMAN	K	232	ENSP00000262138:R232K	ENSP00000262138:R232K	R	+	2	0	CACNG4	62457293	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.319000	0.96338	2.274000	0.75844	0.556000	0.70494	AGG	.	.		0.552	CACNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447036.1	NM_014405		A	65026831	G	A	65026831	3	1	115	1	0	0	0	0	1	0	0	0	2561	1000	35	3	709	3	CACNG4	17	65026831	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	8334139	65026831	16168379	417	19956										
AMZ2	51321	hgsc.bcm.edu	37	chr17	66246396	66246396	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctcaaagaacccagtgcttgTatcacagtatgagaaattaa	7	8	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:66246396T>C	ENST00000359904.3	+	2	1200	c.68T>C	c.(67-69)gTa>gCa	p.V23A	AMZ2_ENST00000585050.1_Intron|AMZ2_ENST00000577866.1_Missense_Mutation_p.V23A|AMZ2_ENST00000577985.1_Missense_Mutation_p.V23A|AMZ2_ENST00000580753.1_Missense_Mutation_p.V23A|AMZ2_ENST00000577273.1_Missense_Mutation_p.V23A|AMZ2_ENST00000392720.2_Missense_Mutation_p.V23A|RP11-147L13.2_ENST00000577698.1_RNA|AMZ2_ENST00000359783.4_Missense_Mutation_p.V23A	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	23							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			CCAGTGCTTGTATCACAGTAT	0.388																																					p.V23A		Atlas-SNP	.											.	AMZ2	15	.	0			c.T68C						.						111	110	110					17																	66246396		2203	4300	6503	SO:0001583	missense	51321	exon2			TGCTTGTATCACA	CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"archaemetzincin-2"	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.68T>C	chr17.hg19:g.66246396T>C	ENSP00000352976:p.Val23Ala	80.0	0.0		90.0	4.0	NM_001033574	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Missense_Mutation	SNP	ENST00000359904.3	hg19	CCDS11674.1	.	.	.	.	.	.	.	.	.	.	T	5.734	0.319854	0.10845	.	.	ENSG00000196704	ENST00000359904;ENST00000359783;ENST00000392720	T;T;T	0.18810	2.19;2.19;2.19	3.58	2.5	0.30297	.	0.091982	0.42821	D	0.000644	T	0.13286	0.0322	L	0.45137	1.4	0.09310	N	1	B;B	0.29188	0.236;0.132	B;B	0.24848	0.056;0.017	T	0.11012	-1.0605	10	0.38643	T	0.18	-15.743	2.631	0.04945	0.2295:0.1264:0.0:0.6441	.	23;23	A6NLD9;Q86W34	.;AMZ2_HUMAN	A	23	ENSP00000352976:V23A;ENSP00000352831:V23A;ENSP00000376481:V23A	ENSP00000352831:V23A	V	+	2	0	AMZ2	63757991	0.059000	0.20769	0.013000	0.15412	0.715000	0.41141	1.102000	0.31050	1.619000	0.50296	0.254000	0.18369	GTA	.	.		0.388	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627		C	66246396	T	C	66246396	3	2	115	1	0	0	0	0	1	0	0	0	597	1638	57	2	70	2	AMZ2	17	66246396	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1219565	66246396	14948814	418	19957										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76472713	76472713	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caatgtttcctggtctttttCgtcaaccattttgtcaccat	5	11	3	0	rs116230343	byFrequency	TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:76472713C>A	ENST00000585328.1	-	52	8204	c.8080G>T	c.(8080-8082)Gaa>Taa	p.E2694*	DNAH17_ENST00000389840.5_Nonsense_Mutation_p.E2685*|DNAH17_ENST00000586052.1_Intron	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2685					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TGGTCTTTTTCGTCAACCATT	0.488																																					p.E2699X		Atlas-SNP	.											.	DNAH17	347	.	0			c.G8095T						.						156	177	170					17																	76472713		2014	4177	6191	SO:0001587	stop_gained	8632	exon52			CTTTTTCGTCAAC	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.8080G>T	chr17.hg19:g.76472713C>A	ENSP00000465516:p.Glu2694*	279.0	0.0		513.0	297.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Nonsense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	C	49	15.769301	0.99844	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	.	.	.	4.64	2.47	0.30058	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	8.0951	0.30824	0.0:0.6116:0.3066:0.0818	.	.	.	.	X	2694;2685	.	ENSP00000300671:E2694X	E	-	1	0	DNAH17	73984308	0.408000	0.25360	0.141000	0.22245	0.808000	0.45660	1.708000	0.37899	0.935000	0.37341	0.455000	0.32223	GAA	.	C|0.986;T|0.014		0.488	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76472713	C	A	76472713	4	1	115	1	0	0	0	0	0	1	0	0	4603	893	31	1	5413	1	DNAH17	17	76472713	Nonsense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	10226317	76472713	4722497	419	19958										
CARD14	79092	hgsc.bcm.edu	37	chr17	78180851	78180851	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttccccatcgtcatccacgTctctgtcaacgagaagatgg	8	14	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:78180851T>C	ENST00000573882.1	+	22	3310	c.2774T>C	c.(2773-2775)gTc>gCc	p.V925A	CARD14_ENST00000344227.2_Missense_Mutation_p.V925A|RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|RP11-334C17.5_ENST00000576824.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	925	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			GTCATCCACGTCTCTGTCAAC	0.612																																					p.V925A		Atlas-SNP	.											.	CARD14	98	.	0			c.T2774C						.						129	98	108					17																	78180851		2203	4299	6502	SO:0001583	missense	79092	exon20			TCCACGTCTCTGT	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"psoriasis susceptibility 2"	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2774T>C	chr17.hg19:g.78180851T>C	ENSP00000458715:p.Val925Ala	78.0	0.0		136.0	8.0	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	hg19	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.820897	0.32237	.	.	ENSG00000141527	ENST00000344227	T	0.20200	2.09	4.93	4.93	0.64822	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	0.311068	0.31760	N	0.007114	T	0.23330	0.0564	L	0.61218	1.895	0.80722	D	1	B	0.32918	0.39	B	0.29862	0.108	T	0.05305	-1.0893	10	0.87932	D	0	-16.9294	12.5224	0.56067	0.0:0.0:0.0:1.0	.	925	Q9BXL6	CAR14_HUMAN	A	925	ENSP00000344549:V925A	ENSP00000344549:V925A	V	+	2	0	CARD14	75795446	0.650000	0.27331	0.025000	0.17156	0.024000	0.10985	5.939000	0.70179	1.848000	0.53677	0.402000	0.26972	GTC	.	.		0.612	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1			C	78180851	T	C	78180851	3	2	115	1	0	0	0	0	1	0	0	0	2648	1667	58	2	3013	2	CARD14	17	78180851	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1708138	78180851	3014359	420	19959										
FOXK2	3607	hgsc.bcm.edu	37	chr17	80544026	80544026	+	Frame_Shift_Del	DEL	C	C	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	caccccggcagccgtgctggCccctcctaaggcagaggccc							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr17:80544026delC	ENST00000335255.5	+	7	1700	c.1526delC	c.(1525-1527)gccfs	p.A509fs	RP13-638C3.3_ENST00000575085.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	509					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			GCCGTGCTGGCCCCTCCTAAG	0.632																																					p.A509fs		Atlas-INDEL	.											.	FOXK2	46	.	0			c.1525delG						.						22	22	22					17																	80544026		2191	4278	6469	SO:0001589	frameshift_variant	3607	exon7			.	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1526delC	chr17.hg19:g.80544026delC	ENSP00000335677:p.Ala509fs	81.0	0.0		166.0	10.0	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Frame_Shift_Del	DEL	ENST00000335255.5	hg19	CCDS11813.1																																																																																			.	.		0.632	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		-	80544026	C	-	80544026	7	5	115	1	0	1	0	1	0	0	0	0	6023	739	26	0	1552	0	FOXK2	17	80544026	Frame_Shift_Del	DEL	C	TCGA-DD-A3A1-01A-11D-A20W-10	2363175	80544026	651184	421	19960										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2728514	2728514	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttttagttatagaaaatggaAcagctttcccatttcaggtg	8	6	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr18:2728514A>G	ENST00000320876.6	+	23	3171	c.2833A>G	c.(2833-2835)Aca>Gca	p.T945A	SMCHD1_ENST00000609587.1_3'UTR|RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.T945A	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	945					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AGAAAATGGAACAGCTTTCCC	0.333																																					p.T945A		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A2833G						.						92	87	89					18																	2728514		1831	4082	5913	SO:0001583	missense	23347	exon23			AATGGAACAGCTT	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.2833A>G	chr18.hg19:g.2728514A>G	ENSP00000326603:p.Thr945Ala	74.0	0.0		65.0	4.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.619764	0.46736	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.23552	1.9;1.9	5.84	5.84	0.93424	.	0.166789	0.52532	D	0.000069	T	0.21631	0.0521	L	0.50333	1.59	0.30633	N	0.757275	P	0.44006	0.824	B	0.34418	0.182	T	0.34551	-0.9824	10	0.54805	T	0.06	-18.768	11.29	0.49245	0.9295:0.0:0.0705:0.0	.	945	A6NHR9	SMHD1_HUMAN	A	945	ENSP00000326603:T945A;ENSP00000261598:T945A	ENSP00000261598:T945A	T	+	1	0	SMCHD1	2718514	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.074000	0.57577	2.230000	0.72887	0.528000	0.53228	ACA	.	.		0.333	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			G	2728514	A	G	2728514	3	3	115	1	0	0	0	0	1	0	0	0	14803	43	2	2	2923	2	SMCHD1	18	2728514	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10		2728514	75348734	422	19961										
RBBP8	5932	hgsc.bcm.edu	37	chr18	20573440	20573440	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acgttgcccaaagattccccAggggagccctgttcacagga	11	13	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr18:20573440A>G	ENST00000399722.2	+	11	2001	c.1650A>G	c.(1648-1650)ccA>ccG	p.P550P	RBBP8_ENST00000399725.2_Silent_p.P550P|RBBP8_ENST00000360790.5_Silent_p.P550P|RBBP8_ENST00000327155.5_Silent_p.P550P	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	550	Damage-recruitment motif.				blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			AAGATTCCCCAGGGGAGCCCT	0.458								Homologous recombination																													p.P550P		Atlas-SNP	.											.	RBBP8	138	.	0			c.A1650G						.						43	44	44					18																	20573440		2202	4299	6501	SO:0001819	synonymous_variant	5932	exon11			TTCCCCAGGGGAG	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"CTBP-interacting protein"	604124	"retinoblastoma-binding protein 8", "Seckel syndrome 2"	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.1650A>G	chr18.hg19:g.20573440A>G		90.0	0.0		91.0	4.0	NM_203292	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Silent	SNP	ENST00000399722.2	hg19	CCDS11875.1																																																																																			.	.		0.458	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		G	20573440	A	G	20573440	2	3	115	1	0	0	0	0	0	0	0	1	13120	175	7	2		2	RBBP8	18	20573440	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	17844926	20573440	57503808	423	19962										
FAM59A	64762	hgsc.bcm.edu	37	chr18	29867200	29867200	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttcctccagccacagctcttCgtagggaagttctgactttc	8	13	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr18:29867200C>T	ENST00000269209.6	-	4	1363	c.1360G>A	c.(1360-1362)Gaa>Aaa	p.E454K	RP11-344B2.2_ENST00000579580.1_RNA|GAREM_ENST00000399218.4_Missense_Mutation_p.E454K|GAREM_ENST00000578619.1_5'Flank			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	454					cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										CACAGCTCTTCGTAGGGAAGT	0.537																																					p.E454K		Atlas-SNP	.											.	.	.	.	0			c.G1360A						.						97	99	98					18																	29867200		2203	4300	6503	SO:0001583	missense	64762	exon4			GCTCTTCGTAGGG	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.1360G>A	chr18.hg19:g.29867200C>T	ENSP00000269209:p.Glu454Lys	86.0	0.0		103.0	12.0	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	hg19	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480505	0.84747	.	.	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.33438	1.41;1.41	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.44603	0.1301	L	0.43152	1.355	0.80722	D	1	D;D	0.63880	0.982;0.993	B;P	0.56823	0.383;0.807	T	0.25745	-1.0123	10	0.54805	T	0.06	-21.1773	19.0993	0.93268	0.0:1.0:0.0:0.0	.	454;454	Q9H706;Q9H706-3	FA59A_HUMAN;.	K	454	ENSP00000382165:E454K;ENSP00000269209:E454K	ENSP00000269209:E454K	E	-	1	0	FAM59A	28121198	1.000000	0.71417	0.975000	0.42487	0.741000	0.42261	7.220000	0.78008	2.821000	0.97095	0.561000	0.74099	GAA	.	.		0.537	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		T	29867200	C	T	29867200	3	4	115	1	0	0	0	0	1	0	0	0	5600	893	31	1	1279	1	FAM59A	18	29867200	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	9293760	29867200	48210048	424	19963										
DTNA	1837	hgsc.bcm.edu	37	chr18	32428290	32428290	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agttcaaaccggcttgatgaAgaacacaggctaattgccag	10	9	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr18:32428290A>G	ENST00000399113.3	+	13	1296	c.1296A>G	c.(1294-1296)gaA>gaG	p.E432E	DTNA_ENST00000597674.1_Silent_p.E54E|DTNA_ENST00000399121.5_Silent_p.E372E|DTNA_ENST00000601125.1_Silent_p.E54E|DTNA_ENST00000595022.1_Silent_p.E372E|DTNA_ENST00000591182.1_Silent_p.E80E|DTNA_ENST00000283365.9_Silent_p.E375E|DTNA_ENST00000598334.1_Silent_p.E372E|DTNA_ENST00000269192.7_Silent_p.E141E|DTNA_ENST00000598774.1_Silent_p.E375E|DTNA_ENST00000556414.3_Silent_p.E84E|DTNA_ENST00000348997.5_Silent_p.E429E|DTNA_ENST00000269191.6_Silent_p.E432E|DTNA_ENST00000599844.1_Silent_p.E54E|DTNA_ENST00000399097.3_Silent_p.E80E|DTNA_ENST00000597599.1_Silent_p.E372E|DTNA_ENST00000444659.1_Silent_p.E432E|DTNA_ENST00000596745.1_Intron|DTNA_ENST00000598142.1_Silent_p.E375E|DTNA_ENST00000269190.7_Silent_p.E433E			Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	432	Syntrophin-binding region.				neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						GGCTTGATGAAGAACACAGGC	0.463																																					p.E432E		Atlas-SNP	.											.	DTNA	321	.	0			c.A1296G						.						101	94	96					18																	32428290		2203	4300	6503	SO:0001819	synonymous_variant	1837	exon13			TGATGAAGAACAC	U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769			3057	protein-coding gene	gene with protein product	"dystrophin-related protein 3"	601239				8081380, 15834686	Standard	NM_001390		Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399113.3:c.1296A>G	chr18.hg19:g.32428290A>G		96.0	0.0		105.0	5.0	NM_001390	A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	Silent	SNP	ENST00000399113.3	hg19	CCDS59311.1																																																																																			.	.		0.463	DTNA-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255422.2	NM_001390		G	32428290	A	G	32428290	2	3	115	1	0	0	0	0	0	0	0	1	4790	69	3	2		2	DTNA	18	32428290	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2561090	32428290	45648958	425	19964										
ZNF24	7572	hgsc.bcm.edu	37	chr18	32920511	32920512	+	Nonsense_Mutation	DNP	TC	TC	CA													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aggggatacttgatccctctTcgccatcaggatcctcctcc							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr18:32920511_32920512TC>CA	ENST00000261332.6	-	2	282_283	c.103_104GA>TG	c.(103-105)GAa>TGa	p.E35*	ZNF24_ENST00000589881.1_Nonsense_Mutation_p.E35*|ZNF24_ENST00000399061.3_Nonsense_Mutation_p.E35*	NM_006965.2	NP_008896.2	P17028	ZNF24_HUMAN	zinc finger protein 24	35					myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	15						TGATCCCTCTTCGCCATCAGGA	0.495																																					p.E35G|p.E35X	Colon(42;769 913 8916 19469 46270)	Atlas-SNP	.											.	ZNF24	40	.	0			c.A104G|c.G103T						.																																			SO:0001587	stop_gained	7572	exon2			CCCTCTTCGCCAT|CCTCTTCGCCATC	AF016052	CCDS11912.1	18q12	2013-01-09	2006-05-10		ENSG00000172466	ENSG00000172466		"-", "Zinc fingers, C2H2-type"	13032	protein-coding gene	gene with protein product		194534	"zinc finger protein 24 (KOX 17)"	ZNF191			Standard	NM_006965		Approved	ZSCAN3, Zfp191, KOX17	uc002kys.2	P17028	OTTHUMG00000132565	ENST00000261332.6:c.103_104delinsCA	chr18.hg19:g.32920511_32920512delinsCA	ENSP00000261332:p.Glu35*	45.0	0.0		60.0|59.0	22.0|21.0	NM_006965	O14754|Q53YE4|Q6ICR5|Q8IZN4	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000261332.6	hg19	CCDS11912.1																																																																																			.	.		0.495	ZNF24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255769.1	NM_006965		CA	32920512	TC	CA	32920511	4	2	115	1	0	0	0	0	0	1	0	0	17807	1783	62	2	1014	2	ZNF24	18	32920511	Nonsense_Mutation	DNP	TC	TCGA-DD-A3A1-01A-11D-A20W-10	492221	32920511	45156737	426	19965										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34182680	34182680	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atggaaatcctggaggaaaaAgatggagttgatacggagct	14	4	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr18:34182680A>G	ENST00000359247.4	+	8	762	c.762A>G	c.(760-762)aaA>aaG	p.K254K	FHOD3_ENST00000590592.1_Silent_p.K254K|FHOD3_ENST00000591635.1_5'UTR|FHOD3_ENST00000257209.4_Silent_p.K254K|FHOD3_ENST00000445677.1_Silent_p.K254K	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	254	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				TGGAGGAAAAAGATGGAGTTG	0.368																																					p.K254K		Atlas-SNP	.											.	FHOD3	210	.	0			c.A762G						.						214	198	204					18																	34182680		2203	4300	6503	SO:0001819	synonymous_variant	80206	exon8			GGAAAAAGATGGA	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.762A>G	chr18.hg19:g.34182680A>G		236.0	0.0		244.0	22.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Silent	SNP	ENST00000359247.4	hg19																																																																																				.	.		0.368	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		G	34182680	A	G	34182680	2	3	115	1	0	0	0	0	0	0	0	1	5891	69	3	2		2	FHOD3	18	34182680	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1262169	34182680	43894568	427	19966										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43481064	43481064	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aactggcacaggaggcttcgTcgggtgcagagcaaggggag	18	8	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr18:43481064T>C	ENST00000282041.5	-	26	4577	c.4543A>G	c.(4543-4545)Acg>Gcg	p.T1515A	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1515					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						GGAGGCTTCGTCGGGTGCAGA	0.502																																					p.T1515A		Atlas-SNP	.											.	EPG5	199	.	0			c.A4543G						.						64	72	70					18																	43481064		2039	4173	6212	SO:0001583	missense	57724	exon26			GCTTCGTCGGGTG	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.4543A>G	chr18.hg19:g.43481064T>C	ENSP00000282041:p.Thr1515Ala	54.0	0.0		69.0	4.0	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	T	0.556	-0.847236	0.02651	.	.	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.09538	2.97	5.59	-11.2	0.00127	.	.	.	.	.	T	0.03959	0.0111	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32107	-0.9919	9	0.11794	T	0.64	1.4365	7.6007	0.28075	0.1431:0.1185:0.0717:0.6668	.	1515	Q9HCE0	EPG5_HUMAN	A	1515;390	ENSP00000282041:T1515A	ENSP00000282041:T1515A	T	-	1	0	EPG5	41735062	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.313000	0.02718	-2.647000	0.00426	-2.026000	0.00426	ACG	.	.		0.502	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43481064	T	C	43481064	3	2	115	1	0	0	0	0	1	0	0	0	8258	1667	58	2	3272	2	KIAA1632	18	43481064	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	9298384	43481064	34596184	428	19967										
C18orf25	147339	hgsc.bcm.edu	37	chr18	43820148	43820148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctagaggagctgaatgcagAggcaggttggtcttccccat	13	9	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr18:43820148A>G	ENST00000282059.6	+	3	1267	c.893A>G	c.(892-894)gAg>gGg	p.E298G	C18orf25_ENST00000321319.6_Intron	NM_145055.3	NP_659492	Q96B23	CR025_HUMAN	chromosome 18 open reading frame 25	298										central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	11						CTGAATGCAGAGGCAGGTTGG	0.542																																					p.E298G		Atlas-SNP	.											.	C18orf25	27	.	0			c.A893G						.						33	34	34					18																	43820148		1974	4164	6138	SO:0001583	missense	147339	exon3			ATGCAGAGGCAGG	AL713661	CCDS42430.1, CCDS42431.1	18q21.1	2014-01-03			ENSG00000152242	ENSG00000152242			28172	protein-coding gene	gene with protein product	"ARKadia-like 1"					15722956	Standard	NM_001008239		Approved	MGC12909, ARKL1, RNF111L1	uc002lbw.3	Q96B23		ENST00000282059.6:c.893A>G	chr18.hg19:g.43820148A>G	ENSP00000282059:p.Glu298Gly	72.0	0.0		100.0	5.0	NM_145055	A8K123|A8KAB6|Q5XG78|Q6N058|Q86TB5|Q8TCQ5	Missense_Mutation	SNP	ENST00000282059.6	hg19	CCDS42430.1	.	.	.	.	.	.	.	.	.	.	A	14.32	2.499911	0.44455	.	.	ENSG00000152242	ENST00000282059	.	.	.	5.76	5.76	0.90799	.	0.435818	0.25363	N	0.031208	T	0.35941	0.0949	N	0.08118	0	0.80722	D	1	B	0.34290	0.447	B	0.33690	0.168	T	0.37361	-0.9709	9	0.51188	T	0.08	-9.3126	16.0843	0.81031	1.0:0.0:0.0:0.0	.	298	Q96B23	CR025_HUMAN	G	298	.	ENSP00000282059:E298G	E	+	2	0	C18orf25	42074146	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	6.278000	0.72614	2.191000	0.70037	0.533000	0.62120	GAG	.	.		0.542	C18orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445242.1	NM_145055		G	43820148	A	G	43820148	3	3	115	1	0	0	0	0	1	0	0	0	1901	304	11	2	899	2	C18orf25	18	43820148	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	339084	43820148	34257100	429	19968										
DYM	54808	hgsc.bcm.edu	37	chr18	46798653	46798653	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctttcttcaacatgatacagAatctcaagaattggtaaaac	5	8	3	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr18:46798653A>G	ENST00000269445.6	-	11	1603	c.1146T>C	c.(1144-1146)atT>atC	p.I382I	DYM_ENST00000442713.2_Silent_p.I192I	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	382					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						CATGATACAGAATCTCAAGAA	0.294																																					p.I382I		Atlas-SNP	.											.	DYM	52	.	0			c.T1146C						.						72	68	70					18																	46798653		2203	4299	6502	SO:0001819	synonymous_variant	54808	exon11			ATACAGAATCTCA	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.1146T>C	chr18.hg19:g.46798653A>G		128.0	0.0		99.0	4.0	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Silent	SNP	ENST00000269445.6	hg19	CCDS11937.1																																																																																			.	.		0.294	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		G	46798653	A	G	46798653	2	3	115	1	0	0	0	0	0	0	0	1	4842	242	9	2		2	DYM	18	46798653	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2978505	46798653	31278595	430	19969										
CDH7	1005	hgsc.bcm.edu	37	chr18	63525083	63525083	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acagaaacacagacttggagAgatacttcaatattgatgcc	8	8	1	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr18:63525083A>G	ENST00000397968.2	+	8	1693	c.1267A>G	c.(1267-1269)Aga>Gga	p.R423G	CDH7_ENST00000323011.3_Missense_Mutation_p.R423G|CDH7_ENST00000536984.2_Missense_Mutation_p.R423G	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	423	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				AGACTTGGAGAGATACTTCAA	0.368																																					p.R423G		Atlas-SNP	.											.	CDH7	362	.	0			c.A1267G						.						140	128	132					18																	63525083		2203	4300	6503	SO:0001583	missense	1005	exon8			TTGGAGAGATACT	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1267A>G	chr18.hg19:g.63525083A>G	ENSP00000381058:p.Arg423Gly	78.0	0.0		93.0	4.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	hg19	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.526825	0.64860	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.49432	0.78;0.78;0.78	4.42	4.42	0.53409	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.53045	0.1772	L	0.31926	0.97	0.58432	D	0.999999	D;D	0.62365	0.991;0.969	P;P	0.59825	0.864;0.65	T	0.56353	-0.7993	10	0.56958	D	0.05	.	14.1166	0.65159	1.0:0.0:0.0:0.0	.	423;423	F5H5X9;Q9ULB5	.;CADH7_HUMAN	G	423	ENSP00000319166:R423G;ENSP00000443030:R423G;ENSP00000381058:R423G	ENSP00000319166:R423G	R	+	1	2	CDH7	61676063	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.884000	0.48562	1.990000	0.58119	0.454000	0.30748	AGA	.	.		0.368	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		G	63525083	A	G	63525083	3	3	115	1	0	0	0	0	1	0	0	0	3117	296	11	2	1293	2	CDH7	18	63525083	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	16726430	63525083	14552165	431	19970										
APC2	10297	hgsc.bcm.edu	37	chr19	1469059	1469059	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcgcacccttctggcgaagcAgcacaagacgcagagatcgc	12	14	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:1469059A>G	ENST00000535453.1	+	14	7472	c.5759A>G	c.(5758-5760)cAg>cGg	p.Q1920R	APC2_ENST00000238483.4_Missense_Mutation_p.Q1646R|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000233607.2_Missense_Mutation_p.Q1920R			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGGCGAAGCAGCACAAGACG	0.761																																					p.Q1920R		Atlas-SNP	.											.	APC2	50	.	0			c.A5759G						.						2	2	2					19																	1469059		1302	3008	4310	SO:0001583	missense	10297	exon15			CGAAGCAGCACAA		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"Armadillo repeat containing"	24036	protein-coding gene	gene with protein product	"adenomatous polyposis coli like"	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.5759A>G	chr19.hg19:g.1469059A>G	ENSP00000442954:p.Gln1920Arg	25.0	0.0		52.0	4.0	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Missense_Mutation	SNP	ENST00000535453.1	hg19	CCDS12068.1	.	.	.	.	.	.	.	.	.	.	A	17.12	3.307691	0.60305	.	.	ENSG00000115266	ENST00000233607;ENST00000238483;ENST00000535453	D;D;D	0.83419	-1.72;-1.72;-1.72	3.9	2.86	0.33363	Adenomatous polyposis coli protein basic domain (1);	0.625158	0.13820	N	0.360516	T	0.76528	0.4000	L	0.50333	1.59	0.80722	D	1	P;P	0.37176	0.531;0.586	B;B	0.39531	0.201;0.302	T	0.68857	-0.5298	10	0.41790	T	0.15	-16.3218	4.169	0.10320	0.6251:0.2525:0.1224:0.0	.	1919;1920	O95996-3;O95996	.;APC2_HUMAN	R	1920;1646;1920	ENSP00000233607:Q1920R;ENSP00000238483:Q1646R;ENSP00000442954:Q1920R	ENSP00000233607:Q1920R	Q	+	2	0	APC2	1420059	0.699000	0.27786	0.999000	0.59377	0.894000	0.52154	1.878000	0.39608	0.420000	0.25954	0.418000	0.28097	CAG	.	.		0.761	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		G	1469059	A	G	1469059	3	3	115	1	0	0	0	0	1	0	0	0	764	188	7	2	5813	2	APC2	19	1469059	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10		1469059	57659924	432	19971										
ATP8B3	148229	hgsc.bcm.edu	37	chr19	1791983	1791983	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cacccaccctgaggtcctgcTccatctcgttgtacacctgt	7	17	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:1791983T>C	ENST00000310127.6	-	19	2429				ATP8B3_ENST00000539485.1_Missense_Mutation_p.E736G|ATP8B3_ENST00000525591.1_Missense_Mutation_p.E689G	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3						binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGTCCTGCTCCATCTCGTT	0.682																																					p.E689G		Atlas-SNP	.											.	ATP8B3	108	.	0			c.A2066G						.						13	14	14					19																	1791983		1875	4066	5941	SO:0001627	intron_variant	148229	exon19			TCCTGCTCCATCT	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"ATPases / P-type"	13535	protein-coding gene	gene with protein product	"aminophospholipid translocase ATP8B3", "potential phospholipid-transporting ATPase IK"	605866	"ATPase, Class I, type 8B, member 3", "ATPase, class I, type 8B, member 3"			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.2190+16A>G	chr19.hg19:g.1791983T>C		108.0	0.0		102.0	5.0	NM_001178002	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	hg19	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	T	15.65	2.895376	0.52121	.	.	ENSG00000130270	ENST00000539485;ENST00000525591	T;T	0.73681	-0.77;-0.77	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	D	0.85678	0.5752	.	.	.	0.46701	D	0.99916	D	0.89917	1.0	D	0.97110	1.0	D	0.87643	0.2523	9	0.87932	D	0	.	12.7566	0.57339	0.0:0.0:0.0:1.0	.	689	Q7Z485	.	G	736;689	ENSP00000443574:E736G;ENSP00000437115:E689G	ENSP00000437115:E689G	E	-	2	0	ATP8B3	1742983	1.000000	0.71417	0.997000	0.53966	0.009000	0.06853	7.911000	0.87458	1.700000	0.51204	0.459000	0.35465	GAG	.	.		0.682	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		C	1791983	T	C	1791983	1	2	115	0	1	0	0	0	0	0	0	0	1196	1551	54	2		2	ATP8B3	19	1791983	Intron	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	322924	1791983	57337000	433	19972										
ZFR2	23217	hgsc.bcm.edu	37	chr19	3821457	3821457	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgggctccgtggcaatgggAaggtccgggttcactttctt	14	10	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:3821457A>G	ENST00000262961.4	-	10	1522	c.1512T>C	c.(1510-1512)ctT>ctC	p.L504L		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	504							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		TGGCAATGGGAAGGTCCGGGT	0.637																																					p.L504L		Atlas-SNP	.											.	ZFR2	63	.	0			c.T1512C						.						26	29	28					19																	3821457		1967	4144	6111	SO:0001819	synonymous_variant	23217	exon10			AATGGGAAGGTCC	AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"KIAA1086"	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.1512T>C	chr19.hg19:g.3821457A>G		74.0	0.0		95.0	4.0	NM_015174		Silent	SNP	ENST00000262961.4	hg19	CCDS45921.1																																																																																			.	.		0.637	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174		G	3821457	A	G	3821457	2	3	115	1	0	0	0	0	0	0	0	1	17675	233	9	2		2	ZFR2	19	3821457	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2029474	3821457	55307526	434	19973										
HOOK2	29911	hgsc.bcm.edu	37	chr19	12883615	12883615	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgctttttctcgcaactgaTggcacagcccagcaccagct	8	15	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:12883615T>C	ENST00000397668.3	-	5	440	c.367A>G	c.(367-369)Atc>Gtc	p.I123V	HOOK2_ENST00000589965.1_Intron|HOOK2_ENST00000264827.5_Missense_Mutation_p.I123V	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	123	Required for localization to the centrosome and induction of aggresome formation.|Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						TCGCAACTGATGGCACAGCCC	0.602																																					p.I123V		Atlas-SNP	.											.	HOOK2	73	.	0			c.A367G						.						63	64	63					19																	12883615		1941	4144	6085	SO:0001583	missense	29911	exon5			AACTGATGGCACA	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"hook homolog 2 (Drosophila)"			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.367A>G	chr19.hg19:g.12883615T>C	ENSP00000380785:p.Ile123Val	58.0	0.0		66.0	4.0	NM_001100176	O60562	Missense_Mutation	SNP	ENST00000397668.3	hg19	CCDS42508.1	.	.	.	.	.	.	.	.	.	.	T	2.999	-0.206456	0.06180	.	.	ENSG00000095066	ENST00000397668;ENST00000264827	T;T	0.13778	2.56;2.56	3.64	3.64	0.41730	.	0.074612	0.53938	D	0.000060	T	0.07052	0.0179	N	0.16201	0.385	0.36769	D	0.883683	B;B	0.28026	0.165;0.198	B;B	0.30316	0.069;0.114	T	0.13737	-1.0498	10	0.02654	T	1	-14.1091	11.5553	0.50743	0.0:0.0:0.0:1.0	.	123;123	Q96ED9-2;Q96ED9	.;HOOK2_HUMAN	V	123	ENSP00000380785:I123V;ENSP00000264827:I123V	ENSP00000264827:I123V	I	-	1	0	HOOK2	12744615	0.977000	0.34250	0.998000	0.56505	0.969000	0.65631	2.078000	0.41567	1.417000	0.47077	0.374000	0.22700	ATC	.	.		0.602	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312		C	12883615	T	C	12883615	3	2	115	1	0	0	0	0	1	0	0	0	7292	1464	51	2	1868	2	HOOK2	19	12883615	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	9062158	12883615	46245368	435	19974										
STX10	8677	hgsc.bcm.edu	37	chr19	13255480	13255480	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctcttgggcgaaggcatccAgcatgctgccaagaacagga	12	11	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:13255480A>G	ENST00000587230.1	-	7	648	c.584T>C	c.(583-585)cTg>cCg	p.L195P	STX10_ENST00000242770.5_Missense_Mutation_p.W194R|STX10_ENST00000343587.5_Missense_Mutation_p.L146P|STX10_ENST00000589083.1_Missense_Mutation_p.L195P	NM_001271609.1	NP_001258538.1	O60499	STX10_HUMAN	syntaxin 10	195	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion (GO:0006906)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|kidney(1)|lung(2)|prostate(1)	6			OV - Ovarian serous cystadenocarcinoma(19;3.41e-21)			GAAGGCATCCAGCATGCTGCC	0.632																																					p.L195P		Atlas-SNP	.											.	STX10	12	.	0			c.T584C						.						75	67	69					19																	13255480		2203	4300	6503	SO:0001583	missense	8677	exon7			GCATCCAGCATGC	AF035531	CCDS32922.1, CCDS62569.1, CCDS62570.1, CCDS62571.1	19p13.13	2008-07-22				ENSG00000104915			11428	protein-coding gene	gene with protein product		603765				9446797	Standard	NM_003765		Approved	hsyn10, SYN10	uc021upq.2	O60499		ENST00000587230.1:c.584T>C	chr19.hg19:g.13255480A>G	ENSP00000466298:p.Leu195Pro	74.0	0.0		98.0	4.0	NM_003765	A6NC41|Q6IAP4|Q96AE8	Missense_Mutation	SNP	ENST00000587230.1	hg19	CCDS32922.1	.	.	.	.	.	.	.	.	.	.	A	18.06	3.539988	0.65085	.	.	ENSG00000104915	ENST00000343587;ENST00000242770;ENST00000440593	.	.	.	4.07	4.07	0.47477	Syntaxin/epimorphin, conserved site (1);Target SNARE coiled-coil domain (3);	0.000000	0.53938	D	0.000051	T	0.81418	0.4818	M	0.91768	3.24	0.80722	D	1	D;D	0.89917	0.984;1.0	P;D	0.97110	0.882;1.0	D	0.84759	0.0761	9	0.72032	D	0.01	.	11.0367	0.47804	1.0:0.0:0.0:0.0	.	146;195	O60499-2;O60499	.;STX10_HUMAN	P	146;195;195	.	ENSP00000242770:L195P	L	-	2	0	STX10	13116480	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	6.510000	0.73729	1.700000	0.51204	0.379000	0.24179	CTG	.	.		0.632	STX10-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452918.1	NM_003765		G	13255480	A	G	13255480	3	3	115	1	0	0	0	0	1	0	0	0	15351	188	7	2	172	2	STX10	19	13255480	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	371865	13255480	45873503	436	19975										
USHBP1	83878	hgsc.bcm.edu	37	chr19	17370230	17370230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gattaaagcatttgagcttcTcaatgctcctgttcccgaag	8	10	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:17370230T>C	ENST00000252597.3	-	7	1087	c.914A>G	c.(913-915)gAg>gGg	p.E305G	USHBP1_ENST00000431146.2_Missense_Mutation_p.E241G	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						TTTGAGCTTCTCAATGCTCCT	0.557																																					p.E305G		Atlas-SNP	.											.	USHBP1	85	.	0			c.A914G						.						87	86	86					19																	17370230		2203	4300	6503	SO:0001583	missense	83878	exon7			AGCTTCTCAATGC	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.914A>G	chr19.hg19:g.17370230T>C	ENSP00000252597:p.Glu305Gly	100.0	0.0		119.0	5.0	NM_031941		Missense_Mutation	SNP	ENST00000252597.3	hg19	CCDS12353.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.134068	0.77662	.	.	ENSG00000130307	ENST00000252597;ENST00000431146;ENST00000324554	T;T;T	0.61510	0.1;0.1;0.1	5.33	5.33	0.75918	Usher syndrome type-1C protein-binding protein 1, PDZ domain (1);	0.073517	0.49305	D	0.000142	T	0.73768	0.3629	M	0.75777	2.31	0.46298	D	0.998977	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.77557	0.979;0.99;0.979	T	0.76149	-0.3065	10	0.56958	D	0.05	-25.1579	11.9652	0.53031	0.0:0.0:0.0:1.0	.	241;305;305	B4DUE8;Q8N8Y1;Q8N6Y0	.;.;USBP1_HUMAN	G	305;241;305	ENSP00000252597:E305G;ENSP00000407902:E241G;ENSP00000324174:E305G	ENSP00000252597:E305G	E	-	2	0	USHBP1	17231230	1.000000	0.71417	0.997000	0.53966	0.831000	0.47069	4.914000	0.63348	2.144000	0.66660	0.533000	0.62120	GAG	.	.		0.557	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		C	17370230	T	C	17370230	3	2	115	1	0	0	0	0	1	0	0	0	17052	1551	54	2	1225	2	USHBP1	19	17370230	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4114750	17370230	41758753	437	19976										
FCHO1	23149	hgsc.bcm.edu	37	chr19	17881358	17881358	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccaggagcggctgcggagggAgagtaccagccagaaggaga	18	9	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:17881358A>G	ENST00000596536.1	+	8	744	c.461A>G	c.(460-462)gAg>gGg	p.E154G	FCHO1_ENST00000252771.7_Missense_Mutation_p.E154G|FCHO1_ENST00000594202.1_Missense_Mutation_p.E154G|FCHO1_ENST00000596951.1_Missense_Mutation_p.E154G|FCHO1_ENST00000597512.1_Missense_Mutation_p.E161G|FCHO1_ENST00000595033.1_Missense_Mutation_p.E104G|FCHO1_ENST00000539407.1_Missense_Mutation_p.E154G|FCHO1_ENST00000600676.1_Missense_Mutation_p.E154G|FCHO1_ENST00000389133.4_Missense_Mutation_p.E154G	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	154	Mediates membrane-binding.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						CTGCGGAGGGAGAGTACCAGC	0.622																																					p.E154G		Atlas-SNP	.											.	FCHO1	69	.	0			c.A461G						.						35	36	35					19																	17881358		2203	4299	6502	SO:0001583	missense	23149	exon7			GGAGGGAGAGTAC	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.461A>G	chr19.hg19:g.17881358A>G	ENSP00000470731:p.Glu154Gly	55.0	0.0		68.0	6.0	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	hg19	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.478761	0.84747	.	.	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.44083	0.93;0.93;0.93	4.56	4.56	0.56223	.	0.057776	0.64402	D	0.000002	T	0.61350	0.2340	M	0.74647	2.275	0.53688	D	0.999975	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.79108	0.956;0.992;0.991	T	0.65162	-0.6235	10	0.72032	D	0.01	-29.2557	10.202	0.43089	1.0:0.0:0.0:0.0	.	104;154;154	B4E120;O14526;O14526-2	.;FCHO1_HUMAN;.	G	154	ENSP00000252771:E154G;ENSP00000373785:E154G;ENSP00000437978:E154G	ENSP00000252771:E154G	E	+	2	0	FCHO1	17742358	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	8.318000	0.89990	1.925000	0.55765	0.402000	0.26972	GAG	.	.		0.622	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122		G	17881358	A	G	17881358	3	3	115	1	0	0	0	0	1	0	0	0	5795	304	11	2	479	2	FCHO1	19	17881358	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	511128	17881358	41247625	438	19977										
COMP	1311	hgsc.bcm.edu	37	chr19	18899995	18899995	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gttggccttggcgaaagccaGccccacgccctggtgggtgg	16	13	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:18899995G>A	ENST00000222271.2	-	5	546	c.502C>T	c.(502-504)Ctg>Ttg	p.L168L	COMP_ENST00000542601.2_Silent_p.L135L|COMP_ENST00000425807.1_Intron	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	168	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GCGAAAGCCAGCCCCACGCCC	0.647																																					p.L168L		Atlas-SNP	.											.	COMP	62	.	0			c.C502T						.						12	15	14					19																	18899995		2192	4255	6447	SO:0001819	synonymous_variant	1311	exon5			AAGCCAGCCCCAC	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"thrombospondin-5"	600310	"cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.502C>T	chr19.hg19:g.18899995G>A		86.0	0.0		81.0	31.0	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Silent	SNP	ENST00000222271.2	hg19	CCDS12385.1																																																																																			.	.		0.647	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095		A	18899995	G	A	18899995	2	1	115	1	0	0	0	0	0	0	0	1	3726	962	34	3		3	COMP	19	18899995	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	1018637	18899995	40228988	439	19978										
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19764869	19764869	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	catacgaggcaagcacggacAttcgcttcagggcactggca	12	12	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:19764869A>G	ENST00000357324.6	-	14	1924	c.1898T>C	c.(1897-1899)aTg>aCg	p.M633T	ATP13A1_ENST00000496082.1_5'UTR|ATP13A1_ENST00000291503.5_Missense_Mutation_p.M515T	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	633						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						AAGCACGGACATTCGCTTCAG	0.532																																					p.M633T	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.T1898C						.						48	57	54					19																	19764869		2202	4300	6502	SO:0001583	missense	57130	exon14			ACGGACATTCGCT	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"ATPases / P-type"	24215	protein-coding gene	gene with protein product	"cation transporting ATPase"		"ATPase type 13A"	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.1898T>C	chr19.hg19:g.19764869A>G	ENSP00000349877:p.Met633Thr	81.0	0.0		96.0	4.0	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Missense_Mutation	SNP	ENST00000357324.6	hg19	CCDS32970.2	.	.	.	.	.	.	.	.	.	.	A	19.28	3.797441	0.70567	.	.	ENSG00000105726	ENST00000291503;ENST00000357324	T;T	0.74737	-0.87;-0.87	5.04	5.04	0.67666	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.89553	0.6748	H	0.95679	3.705	0.80722	D	1	D;D	0.89917	1.0;0.992	D;P	0.91635	0.999;0.822	D	0.91999	0.5609	10	0.66056	D	0.02	-49.6543	12.7194	0.57134	1.0:0.0:0.0:0.0	.	633;515	Q9HD20;Q9HD20-2	AT131_HUMAN;.	T	515;633	ENSP00000291503:M515T;ENSP00000349877:M633T	ENSP00000291503:M515T	M	-	2	0	ATP13A1	19625869	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.851000	0.92205	1.906000	0.55180	0.379000	0.24179	ATG	.	.		0.532	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		G	19764869	A	G	19764869	3	3	115	1	0	0	0	0	1	0	0	0	1123	217	8	2	1768	2	ATP13A1	19	19764869	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	864874	19764869	39364114	440	19979										
ZNF682	91120	hgsc.bcm.edu	37	chr19	20116962	20116962	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttcacatttatagcgtttgAcggcagtatgaattttctta	7	7	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:20116962A>G	ENST00000397165.2	-	4	1509	c.1349T>C	c.(1348-1350)gTc>gCc	p.V450A	ZNF682_ENST00000358523.5_Missense_Mutation_p.V418A|ZNF682_ENST00000397162.1_Missense_Mutation_p.V418A|ZNF682_ENST00000597972.1_Missense_Mutation_p.V456A|ZNF682_ENST00000595736.1_Missense_Mutation_p.V374A|ZNF682_ENST00000596019.1_Intron	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	450			V -> I (in dbSNP:rs17679334).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						ATAGCGTTTGACGGCAGTATG	0.383																																					p.V450A		Atlas-SNP	.											.	ZNF682	51	.	0			c.T1349C						.						88	97	94					19																	20116962		2169	4289	6458	SO:0001583	missense	91120	exon4			CGTTTGACGGCAG	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"Zinc fingers, C2H2-type", "-"	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.1349T>C	chr19.hg19:g.20116962A>G	ENSP00000380351:p.Val450Ala	53.0	0.0		63.0	5.0	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	hg19	CCDS42533.1	.	.	.	.	.	.	.	.	.	.	a	8.884	0.952446	0.18431	.	.	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000341262;ENST00000358523	T;T;T	0.18502	2.21;2.21;2.21	1.09	-2.18	0.07037	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08403	0.0209	N	0.10837	0.055	0.18873	N	0.999988	B	0.16603	0.018	B	0.26614	0.071	T	0.36625	-0.9740	9	0.87932	D	0	.	4.1969	0.10447	0.5658:0.0:0.0:0.4342	.	450	O95780	ZN682_HUMAN	A	450;418;119;418	ENSP00000380351:V450A;ENSP00000380348:V418A;ENSP00000351324:V418A	ENSP00000340236:V119A	V	-	2	0	ZNF682	19977962	0.138000	0.22547	0.000000	0.03702	0.000000	0.00434	1.357000	0.34090	-0.602000	0.05775	-0.669000	0.03829	GTC	.	.		0.383	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196		G	20116962	A	G	20116962	3	3	115	1	0	0	0	0	1	0	0	0	18104	275	10	2	151	2	ZNF682	19	20116962	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	352093	20116962	39012021	441	19980										
DPY19L3	147991	hgsc.bcm.edu	37	chr19	32944160	32944160	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tatcagttttaacctttcagTattcattgcaagaaaacttc	4	8	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:32944160T>C	ENST00000342179.5	+	9	1180	c.965T>C	c.(964-966)gTa>gCa	p.V322A	DPY19L3_ENST00000392250.2_Missense_Mutation_p.V322A|DPY19L3_ENST00000586987.1_Missense_Mutation_p.V322A	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	322						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					AACCTTTCAGTATTCATTGCA	0.318																																					p.V322A		Atlas-SNP	.											.	DPY19L3	70	.	0			c.T965C						.						112	100	104					19																	32944160		2203	4300	6503	SO:0001583	missense	147991	exon9			TTTCAGTATTCAT		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.965T>C	chr19.hg19:g.32944160T>C	ENSP00000344937:p.Val322Ala	157.0	0.0		83.0	4.0	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Missense_Mutation	SNP	ENST00000342179.5	hg19	CCDS12422.1	.	.	.	.	.	.	.	.	.	.	T	11.09	1.535753	0.27475	.	.	ENSG00000178904	ENST00000392250;ENST00000319326;ENST00000342179	T;T	0.56275	0.47;0.47	5.86	5.86	0.93980	.	0.192172	0.45867	D	0.000324	T	0.31765	0.0807	N	0.12961	0.28	0.30900	N	0.729398	B	0.09022	0.002	B	0.10450	0.005	T	0.28554	-1.0040	10	0.10636	T	0.68	-24.0619	10.0118	0.41990	0.0:0.0754:0.0:0.9246	.	322	Q6ZPD9	D19L3_HUMAN	A	322	ENSP00000376081:V322A;ENSP00000344937:V322A	ENSP00000315672:V322A	V	+	2	0	DPY19L3	37636000	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.793000	0.47845	2.240000	0.73641	0.533000	0.62120	GTA	.	.		0.318	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325		C	32944160	T	C	32944160	3	2	115	1	0	0	0	0	1	0	0	0	4744	1638	57	2	995	2	DPY19L3	19	32944160	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	12827198	32944160	26184823	442	19981										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36352785	36352785	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agacattccctgccccagagAgccgcgggggactgggtccg	15	14	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:36352785A>G	ENST00000360202.5	+	11	1567	c.1369A>G	c.(1369-1371)Agc>Ggc	p.S457G	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Missense_Mutation_p.S457G|KIRREL2_ENST00000262625.7_Missense_Mutation_p.S457G|KIRREL2_ENST00000347900.6_Missense_Mutation_p.S407G	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	457	Ig-like C2-type 5.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGCCCCAGAGAGCCGCGGGGG	0.637																																					p.S457G		Atlas-SNP	.											.	KIRREL2	170	.	0			c.A1369G						.						27	30	29					19																	36352785		2202	4290	6492	SO:0001583	missense	84063	exon11			CCAGAGAGCCGCG	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.1369A>G	chr19.hg19:g.36352785A>G	ENSP00000353331:p.Ser457Gly	112.0	0.0		132.0	6.0	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	hg19	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.985925	0.00443	.	.	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.14391	2.51;2.51;2.51	4.54	2.39	0.29439	Immunoglobulin-like (1);	0.346063	0.20850	N	0.084556	T	0.03959	0.0111	N	0.02011	-0.69	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.43556	-0.9384	10	0.12766	T	0.61	-2.2705	6.2161	0.20656	0.2288:0.0:0.7712:0.0	.	457;437;457;407;457	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	G	457;407;457;437	ENSP00000262625:S457G;ENSP00000345067:S407G;ENSP00000353331:S457G	ENSP00000262625:S457G	S	+	1	0	KIRREL2	41044625	0.001000	0.12720	0.006000	0.13384	0.014000	0.08584	0.594000	0.24014	0.929000	0.37192	-0.239000	0.12128	AGC	.	.		0.637	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		G	36352785	A	G	36352785	3	3	115	1	0	0	0	0	1	0	0	0	8334	304	11	2	1411	2	KIRREL2	19	36352785	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3408625	36352785	22776198	443	19982										
ZNF829	374899	hgsc.bcm.edu	37	chr19	37383232	37383232	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atatcttacattcccatggtTtctcttcactcatagttttt	3	10	4	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:37383232T>C	ENST00000391711.3	-	6	825	c.461A>G	c.(460-462)aAa>aGa	p.K154R	ZNF345_ENST00000432005.2_Intron|ZNF829_ENST00000520965.1_Missense_Mutation_p.K235R|ZNF345_ENST00000526123.1_Intron	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	154					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTCCCATGGTTTCTCTTCACT	0.333																																					p.K235R		Atlas-SNP	.											.	ZNF829	70	.	0			c.A704G						.						67	60	62					19																	37383232		1914	4133	6047	SO:0001583	missense	374899	exon6			CATGGTTTCTCTT	BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"Zinc fingers, C2H2-type", "-"	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.461A>G	chr19.hg19:g.37383232T>C	ENSP00000429266:p.Lys154Arg	83.0	0.0		60.0	4.0	NM_001171979	Q3KNS7|Q6ZNN0|Q7Z657	Missense_Mutation	SNP	ENST00000391711.3	hg19	CCDS42557.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.302019	0.23736	.	.	ENSG00000185869	ENST00000520965;ENST00000391711	T	0.32753	1.44	3.18	3.18	0.36537	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31327	0.0793	M	0.67625	2.065	0.22591	N	0.998954	B	0.28667	0.219	B	0.26864	0.074	T	0.18967	-1.0320	9	0.48119	T	0.1	.	9.7618	0.40537	0.0:0.0:0.0:1.0	.	154	Q3KNS6	ZN829_HUMAN	R	154	ENSP00000429266:K154R	ENSP00000429266:K154R	K	-	2	0	ZNF829	42075072	0.005000	0.15991	0.950000	0.38849	0.718000	0.41266	0.355000	0.20163	1.693000	0.51124	0.528000	0.53228	AAA	.	.		0.333	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232		C	37383232	T	C	37383232	3	2	115	1	0	0	0	0	1	0	0	0	18197	1841	64	2	841	2	ZNF829	19	37383232	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1030447	37383232	21745751	444	19983										
CATSPERG	57828	hgsc.bcm.edu	37	chr19	38834967	38834967	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atatcaacggcttcctgaagAgagaccgggacaataacatc	9	10	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:38834967A>G	ENST00000409235.3	+	6	743	c.628A>G	c.(628-630)Aga>Gga	p.R210G	CATSPERG_ENST00000215069.4_Missense_Mutation_p.R195G|CATSPERG_ENST00000410018.1_Missense_Mutation_p.R210G	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	210					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						CTTCCTGAAGAGAGACCGGGA	0.547																																					p.R210G		Atlas-SNP	.											.	CATSPERG	121	.	0			c.A628G						.						118	104	108					19																	38834967		692	1591	2283	SO:0001583	missense	57828	exon6			CTGAAGAGAGACC	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"chromosome 19 open reading frame 15", "cation channel, sperm-associated, gamma"	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.628A>G	chr19.hg19:g.38834967A>G	ENSP00000386962:p.Arg210Gly	108.0	0.0		149.0	6.0	NM_021185	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	hg19	CCDS12514.2	.	.	.	.	.	.	.	.	.	.	A	12.54	1.967333	0.34754	.	.	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410;ENST00000215069	T;T;T;T	0.35421	1.31;1.31;1.31;1.31	4.84	3.81	0.43845	.	0.706063	0.13360	N	0.393711	T	0.42743	0.1216	M	0.71581	2.175	0.29909	N	0.823736	P;P	0.41848	0.728;0.763	P;B	0.44359	0.447;0.288	T	0.46133	-0.9213	10	0.72032	D	0.01	-6.4806	8.5606	0.33509	0.8048:0.1952:0.0:0.0	.	210;210	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	G	210;210;210;195	ENSP00000387057:R210G;ENSP00000386962:R210G;ENSP00000386950:R210G;ENSP00000215069:R195G	ENSP00000215069:R195G	R	+	1	2	CATSPERG	43526807	0.945000	0.32115	0.713000	0.30519	0.121000	0.20230	2.022000	0.41030	0.851000	0.35264	-0.321000	0.08615	AGA	.	.		0.547	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185		G	38834967	A	G	38834967	3	3	115	1	0	0	0	0	1	0	0	0	2694	296	11	2	646	2	CATSPERG	19	38834967	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1451735	38834967	20294016	445	19984										
ZFP36	7538	hgsc.bcm.edu	37	chr19	39899237	39899239	+	In_Frame_Del	DEL	CTC	CTC	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agcggcagcagcctggggggCtctgactctcccgtcttcga							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:39899237_39899239delCTC	ENST00000248673.3	+	2	937_939	c.879_881delCTC	c.(877-882)ggctct>ggt	p.S294del	ZFP36_ENST00000597629.1_In_Frame_Del_p.S300del|MIR4530_ENST00000581459.1_RNA	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	294					3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of inflammatory response (GO:0050728)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of tumor necrosis factor production (GO:0032680)|response to starvation (GO:0042594)|RNA destabilization (GO:0050779)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|AU-rich element binding (GO:0017091)|C-C chemokine binding (GO:0019957)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(5)|pancreas(1)	7	all_cancers(60;6.54e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.53e-06)|Ovarian(47;0.0512)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GCCTGGGGGGCTCTGACTCTCCC	0.645																																					p.299_300del	NSCLC(67;1164 1324 12056 21056 30097)	Atlas-INDEL	.											.	ZFP36	19	.	0			c.896_898del						.																																			SO:0001651	inframe_deletion	7538	exon2			.	M63625	CCDS12534.1, CCDS12534.2	19q13.1	2012-11-27	2012-11-27			ENSG00000128016		"RING-type (C3HC4) zinc fingers"	12862	protein-coding gene	gene with protein product		190700	"zinc finger protein 36, C3H type, homolog (mouse)"			1699942	Standard	NM_003407		Approved	RNF162A, TIS11, G0S24, TTP, NUP475, tristetraprolin	uc002olh.2	P26651		ENST00000248673.3:c.879_881delCTC	chr19.hg19:g.39899237_39899239delCTC	ENSP00000248673:p.Ser294del	84.0	0.0		93.0	21.0	NM_003407	B2RA54	In_Frame_Del	DEL	ENST00000248673.3	hg19																																																																																				.	.		0.645	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				-	39899239	CTC	-	39899237	7	5	115	1	0	1	0	1	0	0	0	0	17660	784	28	0	885	0	ZFP36	19	39899237	In_Frame_Del	DEL	CTC	TCGA-DD-A3A1-01A-11D-A20W-10	1064270	39899237	19229746	446	19985										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40433636	40433636	+	Frame_Shift_Del	DEL	C	C	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctactagctgtgacctttgaCcccgagagatccactgagct							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:40433636delC	ENST00000221347.6	-	2	640	c.633delG	c.(631-633)gggfs	p.G211fs		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	211	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)		p.G211G(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TGACCTTTGACCCCGAGAGAT	0.547																																					p.S212fs		Atlas-INDEL	.											.	FCGBP	416	.	1	Substitution - coding silent(1)	lung(1)	c.634delT						.						73	72	73					19																	40433636		2203	4300	6503	SO:0001589	frameshift_variant	8857	exon2			.	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.633delG	chr19.hg19:g.40433636delC	ENSP00000221347:p.Gly211fs	159.0	0.0		154.0	10.0	NM_003890	O95784	Frame_Shift_Del	DEL	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.		0.547	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		-	40433636	C	-	40433636	7	5	115	1	0	1	0	1	0	0	0	0	5786	494	18	0	15724	0	FCGBP	19	40433636	Frame_Shift_Del	DEL	C	TCGA-DD-A3A1-01A-11D-A20W-10	534399	40433636	18695347	447	19986										
ZNF780B	163131	hgsc.bcm.edu	37	chr19	40541735	40541735	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtcgaacaagctttgtcagaAgagtaaaggcctttctgcat	10	8	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:40541735A>G	ENST00000434248.1	-	5	1096	c.1031T>C	c.(1030-1032)cTt>cCt	p.L344P	ZNF780B_ENST00000221355.6_Missense_Mutation_p.L196P	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	344					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTTTGTCAGAAGAGTAAAGGC	0.428																																					p.L344P		Atlas-SNP	.											.	ZNF780B	143	.	0			c.T1031C						.						64	66	66					19																	40541735		2203	4300	6503	SO:0001583	missense	163131	exon5			GTCAGAAGAGTAA	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"Zinc fingers, C2H2-type", "-"	33109	protein-coding gene	gene with protein product			"zinc finger protein 779"	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.1031T>C	chr19.hg19:g.40541735A>G	ENSP00000391641:p.Leu344Pro	92.0	0.0		86.0	4.0	NM_001005851	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	hg19	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	A	9.651	1.141618	0.21205	.	.	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.09163	3.01;3.01	1.88	-3.76	0.04359	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21468	0.0517	M	0.70275	2.135	0.09310	N	0.999998	D	0.76494	0.999	D	0.67103	0.949	T	0.06752	-1.0809	9	0.39692	T	0.17	.	4.3998	0.11381	0.4309:0.4122:0.0:0.157	.	344	Q9Y6R6	Z780B_HUMAN	P	344;196	ENSP00000391641:L344P;ENSP00000221355:L196P	ENSP00000221355:L196P	L	-	2	0	ZNF780B	45233575	0.000000	0.05858	0.001000	0.08648	0.057000	0.15508	-2.722000	0.00810	-0.842000	0.04195	0.247000	0.18012	CTT	.	.		0.428	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		G	40541735	A	G	40541735	3	3	115	1	0	0	0	0	1	0	0	0	18168	72	3	2	1474	2	ZNF780B	19	40541735	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	108099	40541735	18587248	448	19987										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41060447	41060447	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	acagagcaccctgcagctgcTcaagaaacacctgcagctgg	10	14	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:41060447T>C	ENST00000352632.3	+	24	5065	c.4979T>C	c.(4978-4980)cTc>cCc	p.L1660P	SPTBN4_ENST00000392023.1_Missense_Mutation_p.L336P|SPTBN4_ENST00000338932.3_Missense_Mutation_p.L1660P|SPTBN4_ENST00000595535.1_Missense_Mutation_p.L1660P|SPTBN4_ENST00000598249.1_Missense_Mutation_p.L1660P|SPTBN4_ENST00000392025.1_Missense_Mutation_p.L403P			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1660					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CTGCAGCTGCTCAAGAAACAC	0.701																																					p.L1660P		Atlas-SNP	.											.	SPTBN4	213	.	0			c.T4979C						.						17	15	16					19																	41060447		2183	4275	6458	SO:0001583	missense	57731	exon24			AGCTGCTCAAGAA	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.4979T>C	chr19.hg19:g.41060447T>C	ENSP00000263373:p.Leu1660Pro	117.0	0.0		168.0	7.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	T	17.34	3.363817	0.61513	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000392025;ENST00000392023	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	4.48	4.48	0.54585	.	0.000000	0.51477	D	0.000083	T	0.72779	0.3503	M	0.90425	3.115	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.995;0.996;0.997;0.998;0.995	T	0.79217	-0.1894	10	0.87932	D	0	.	12.7686	0.57408	0.0:0.0:0.0:1.0	.	403;403;336;1660;1660	Q9H254-3;C9JY79;E9PGQ5;Q9H254;Q71S06	.;.;.;SPTN4_HUMAN;.	P	1660;1660;1660;403;336	ENSP00000263373:L1660P;ENSP00000340345:L1660P;ENSP00000375879:L403P;ENSP00000375877:L336P	ENSP00000340345:L1660P	L	+	2	0	SPTBN4	45752287	1.000000	0.71417	1.000000	0.80357	0.282000	0.26991	7.792000	0.85828	1.653000	0.50694	0.260000	0.18958	CTC	.	.		0.701	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			C	41060447	T	C	41060447	3	2	115	1	0	0	0	0	1	0	0	0	15136	1551	54	2	5069	2	SPTBN4	19	41060447	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	518712	41060447	18068536	449	19988										
ZNF226	7769	hgsc.bcm.edu	37	chr19	44680289	44680289	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtggaaaaggcttctgttacAgcccagttcttcctgttcat	9	10	3	0	rs200035894		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:44680289A>G	ENST00000590089.1	+	7	1241	c.874A>G	c.(874-876)Agc>Ggc	p.S292G	ZNF226_ENST00000454662.2_Missense_Mutation_p.S292G|ZNF226_ENST00000337433.5_Missense_Mutation_p.S292G|ZNF226_ENST00000588883.1_3'UTR			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	292					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)						Prostate(69;0.0352)|all_neural(266;0.202)				CTTCTGTTACAGCCCAGTTCT	0.443																																					p.S292G	Pancreas(115;581 1665 13228 19278 50070)	Atlas-SNP	.											.	.	.	.	0			c.A874G						.						56	57	56					19																	44680289		2071	4224	6295	SO:0001583	missense	7769	exon6			TGTTACAGCCCAG	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"Zinc fingers, C2H2-type", "-"	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.874A>G	chr19.hg19:g.44680289A>G	ENSP00000465121:p.Ser292Gly	140.0	0.0		148.0	6.0	NM_001032372	Q8WWE6|Q96TE6|Q9NS44	Missense_Mutation	SNP	ENST00000590089.1	hg19	CCDS46102.1	.	.	.	.	.	.	.	.	.	.	A	3.628	-0.076071	0.07184	.	.	ENSG00000167380	ENST00000337433;ENST00000454662	T;T	0.16457	2.34;2.34	4.28	3.25	0.37280	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.651325	0.12784	N	0.439434	T	0.11965	0.0291	L	0.39085	1.19	0.09310	N	1	B	0.31241	0.315	B	0.19946	0.027	T	0.19451	-1.0305	10	0.34782	T	0.22	.	8.2416	0.31662	0.8999:0.0:0.1001:0.0	.	292	Q9NYT6	ZN226_HUMAN	G	292	ENSP00000336719:S292G;ENSP00000393265:S292G	ENSP00000336719:S292G	S	+	1	0	ZNF226	49372129	0.000000	0.05858	0.007000	0.13788	0.001000	0.01503	0.255000	0.18333	0.817000	0.34445	0.533000	0.62120	AGC	.	A|0.999;T|0.001		0.443	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1			G	44680289	A	G	44680289	3	3	115	1	0	0	0	0	1	0	0	0	17795	188	7	2	942	2	ZNF226	19	44680289	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3619842	44680289	14448694	450	19989										
ZFP112	7771	hgsc.bcm.edu	37	chr19	44832241	44832241	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgaaactcttaccacactcaTcacattggtatggcttctct	5	12	4	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:44832241T>C	ENST00000337401.4	-	5	2175	c.2087A>G	c.(2086-2088)gAt>gGt	p.D696G	ZNF112_ENST00000354340.4_Missense_Mutation_p.D690G|ZNF112_ENST00000536500.1_Missense_Mutation_p.D713G	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	696					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										ACCACACTCATCACATTGGTA	0.448																																					p.D696G		Atlas-SNP	.											.	ZFP112	219	.	0			c.A2087G						.						103	86	92					19																	44832241		2203	4300	6503	SO:0001583	missense	7771	exon5			CACTCATCACATT	AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.2087A>G	chr19.hg19:g.44832241T>C	ENSP00000337081:p.Asp696Gly	75.0	0.0		88.0	4.0	NM_001083335	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	hg19	CCDS54276.1	.	.	.	.	.	.	.	.	.	.	T	11.03	1.520342	0.27211	.	.	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.19394	2.15;2.15;2.15	5.0	2.74	0.32292	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.731907	0.11185	N	0.590573	T	0.18551	0.0445	L	0.56396	1.775	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.32693	-0.9897	10	0.17832	T	0.49	-1.1888	6.0501	0.19781	0.0:0.0945:0.3356:0.5699	.	695;713;696	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	G	696;696;690;713;695	ENSP00000337081:D696G;ENSP00000346305:D690G;ENSP00000441990:D713G	ENSP00000253426:D695G	D	-	2	0	ZNF285	49524081	0.000000	0.05858	0.447000	0.26932	0.983000	0.72400	-2.525000	0.00948	0.865000	0.35603	0.533000	0.62120	GAT	.	.		0.448	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		C	44832241	T	C	44832241	3	2	115	1	0	0	0	0	1	0	0	0	17653	1435	50	2	658	2	ZFP112	19	44832241	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	151952	44832241	14296742	451	19990										
ZNF180	7733	hgsc.bcm.edu	37	chr19	44988603	44988603	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tggtcagagacccagtgtctTctccctcgactttgatgata	9	11	3	3	rs573184540	byFrequency	TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:44988603T>C	ENST00000221327.4	-	3	457	c.176A>G	c.(175-177)gAa>gGa	p.E59G	ZNF180_ENST00000587047.1_Missense_Mutation_p.K61E|ZNF180_ENST00000592529.1_Missense_Mutation_p.E32G|ZNF180_ENST00000391956.4_Intron|ZNF180_ENST00000585514.1_5'UTR|ZNF180_ENST00000586637.1_Silent_p.R68R	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	59					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				CCCAGTGTCTTCTCCCTCGAC	0.458													T|||	2	0.000399361	0	0	5008	,	,		20243	0.002		0	False		,,,				2504	0				p.E59G	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.A176G						.						105	94	97					19																	44988603		2203	4300	6503	SO:0001583	missense	7733	exon3			GTGTCTTCTCCCT	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.176A>G	chr19.hg19:g.44988603T>C	ENSP00000221327:p.Glu59Gly	72.0	0.0		80.0	4.0	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	hg19	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	T	14.05	2.418925	0.42918	.	.	ENSG00000167384	ENST00000221327	T	0.08193	3.12	3.52	3.52	0.40303	.	0.000000	0.34531	N	0.003882	T	0.04588	0.0125	N	0.19112	0.55	0.21762	N	0.999554	P;P	0.50443	0.935;0.935	B;B	0.39094	0.29;0.29	T	0.42224	-0.9464	10	0.20046	T	0.44	-22.6394	8.7454	0.34583	0.0:0.0:0.0:1.0	.	58;59	Q58F03;Q9UJW8	.;ZN180_HUMAN	G	59	ENSP00000221327:E59G	ENSP00000221327:E59G	E	-	2	0	ZNF180	49680443	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	0.796000	0.26986	1.848000	0.53677	0.528000	0.53228	GAA	.	.		0.458	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		C	44988603	T	C	44988603	3	2	115	1	0	0	0	0	1	0	0	0	17763	1783	62	2	1914	2	ZNF180	19	44988603	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	156362	44988603	14140380	452	19991										
CBLC	23624	hgsc.bcm.edu	37	chr19	45285709	45285709	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttcctcacctatgatgaggTccaagagcgtctgcaggcct	10	13	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:45285709T>C	ENST00000270279.3	+	4	803	c.740T>C	c.(739-741)gTc>gCc	p.V247A	CBLC_ENST00000341505.4_Missense_Mutation_p.V247A	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	247	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|SH2-like.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				TATGATGAGGTCCAAGAGCGT	0.622			M		AML																																p.V247A		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.T740C						.						83	75	78					19																	45285709		2203	4300	6503	SO:0001583	missense	23624	exon4			ATGAGGTCCAAGA	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"RING-type (C3HC4) zinc fingers"	15961	protein-coding gene	gene with protein product		608453	"Cas-Br-M (murine) ectropic retroviral transforming sequence c", "Cas-Br-M (murine) ecotropic retroviral transforming sequence c"			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.740T>C	chr19.hg19:g.45285709T>C	ENSP00000270279:p.Val247Ala	118.0	0.0		207.0	9.0	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	hg19	CCDS12643.1	.	.	.	.	.	.	.	.	.	.	.	14.43	2.533334	0.45073	.	.	ENSG00000142273	ENST00000270279;ENST00000341505	D;D	0.82081	-1.57;-1.57	4.7	4.7	0.59300	Adaptor protein Cbl, PTB domain (1);SH2 motif (2);Adaptor protein Cbl, SH2-like (1);	0.000000	0.49305	D	0.000143	D	0.88808	0.6537	M	0.63843	1.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.89287	0.3616	10	0.59425	D	0.04	-44.9982	12.4184	0.55506	0.0:0.0:0.0:1.0	.	247;247	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	A	247	ENSP00000270279:V247A;ENSP00000340250:V247A	ENSP00000270279:V247A	V	+	2	0	CBLC	49977549	1.000000	0.71417	0.480000	0.27341	0.022000	0.10575	7.449000	0.80643	2.103000	0.63969	0.459000	0.35465	GTC	.	.		0.622	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116		C	45285709	T	C	45285709	3	2	115	1	0	0	0	0	1	0	0	0	2704	1667	58	2	754	2	CBLC	19	45285709	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	297106	45285709	13843274	453	19992										
RSPH6A	81492	hgsc.bcm.edu	37	chr19	46305378	46305378	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggctgagagggcttccttacCtgcatcttctgaaagtggcg	13	10	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:46305378C>A	ENST00000221538.3	-	4	1940	c.1798G>T	c.(1798-1800)Gaa>Taa	p.E600*	RSPH6A_ENST00000600188.1_Splice_Site_p.E336*|RSPH6A_ENST00000597055.1_Splice_Site_p.E600*	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	600	Glu-rich.					intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						GCTTCCTTACCTGCATCTTCT	0.637																																					p.E600X		Atlas-SNP	.											.	RSPH6A	70	.	0			c.G1798T						.						96	69	78					19																	46305378		2203	4300	6503	SO:0001630	splice_region_variant	81492	exon4			CCTTACCTGCATC	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"radial spokehead-like 1"	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.1798+1G>T	chr19.hg19:g.46305378C>A		107.0	0.0		126.0	45.0	NM_030785	Q53FE2|Q6PEZ9	Nonsense_Mutation	SNP	ENST00000221538.3	hg19	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.912655	0.92178	.	.	ENSG00000104941	ENST00000221538	.	.	.	4.15	4.15	0.48705	.	0.165132	0.52532	D	0.000078	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.5686	12.2908	0.54817	0.0:1.0:0.0:0.0	.	.	.	.	X	600	.	.	E	-	1	0	RSPH6A	50997218	1.000000	0.71417	0.998000	0.56505	0.119000	0.20118	4.199000	0.58426	2.606000	0.88127	0.456000	0.33151	GAA	.	.		0.637	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1		Nonsense_Mutation	A	46305378	C	A	46305378	5	1	115	1	0	0	0	0	0	0	1	0	13722	695	24	3	367	3	RSPH6A	19	46305378	Splice_Site	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	1019669	46305378	12823605	454	19993										
MYPOP	339344	hgsc.bcm.edu	37	chr19	46393962	46393962	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gggggggagtcgtgcggaggGagcggggctggggggggccg	29	6	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:46393962G>A	ENST00000322217.5	-	3	1205	c.1119C>T	c.(1117-1119)ctC>ctT	p.L373L		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	373	Pro-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						CGTGCGGAGGGAGCGGGGCTG	0.642																																					p.L373L		Atlas-SNP	.											.	MYPOP	23	.	0			c.C1119T						.						9	11	10					19																	46393962		2117	4202	6319	SO:0001819	synonymous_variant	339344	exon3			CGGAGGGAGCGGG	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"p42 Myb-related transcription factor, partner of profilin"					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.1119C>T	chr19.hg19:g.46393962G>A		64.0	0.0		75.0	25.0	NM_001012643		Silent	SNP	ENST00000322217.5	hg19	CCDS33055.1																																																																																			.	.		0.642	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643		A	46393962	G	A	46393962	2	1	115	1	0	0	0	0	0	0	0	1	10108	1161	41	3		3	MYPOP	19	46393962	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	88584	46393962	12735021	455	19994										
DHX34	9704	hgsc.bcm.edu	37	chr19	47876048	47876048	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cctgtgctcaccatcgcagcCgcacttagcgtccagtcgcc	9	18	1	0	rs562906654	byFrequency	TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:47876048C>A	ENST00000328771.4	+	8	2179	c.1830C>A	c.(1828-1830)gcC>gcA	p.A610A		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	610					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		CCATCGCAGCCGCACTTAGCG	0.682																																					p.A610A		Atlas-SNP	.											.	DHX34	98	.	0			c.C1830A						.						45	41	42					19																	47876048		2202	4300	6502	SO:0001819	synonymous_variant	9704	exon8			CGCAGCCGCACTT	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"DEAH-boxes"	16719	protein-coding gene	gene with protein product		615475	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.1830C>A	chr19.hg19:g.47876048C>A		185.0	0.0		156.0	105.0	NM_014681	B4DMY8	Silent	SNP	ENST00000328771.4	hg19	CCDS12700.1																																																																																			.	.		0.682	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		A	47876048	C	A	47876048	2	1	115	1	0	0	0	0	0	0	0	1	4509	639	23	1		1	DHX34	19	47876048	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	1482086	47876048	11252935	456	19995										
SLC17A7	57030	hgsc.bcm.edu	37	chr19	49937914	49937914	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aagggtggggcccatttgctCcagatcccatggcaggcggg	16	11	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:49937914C>T	ENST00000221485.3	-	5	753	c.582G>A	c.(580-582)tgG>tgA	p.W194*	SLC17A7_ENST00000543531.1_Nonsense_Mutation_p.W182*|SLC17A7_ENST00000600601.1_Nonsense_Mutation_p.W127*	NM_020309.3	NP_064705.1	Q9P2U7	VGLU1_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 7	194					glutamate secretion (GO:0014047)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|long-term memory (GO:0007616)|neurotransmitter secretion (GO:0007269)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sequestering of neurotransmitter (GO:0042137)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|synaptic vesicle membrane (GO:0030672)	inorganic phosphate transmembrane transporter activity (GO:0005315)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:inorganic phosphate symporter activity (GO:0015319)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	26		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(486;0.0245)		CCCATTTGCTCCAGATCCCAT	0.592																																					p.W194X		Atlas-SNP	.											.	SLC17A7	57	.	0			c.G582A						.						60	60	60					19																	49937914		2203	4300	6503	SO:0001587	stop_gained	57030	exon5			TTTGCTCCAGATC	AB032436	CCDS12764.1	19q13.33	2013-07-18	2013-07-18		ENSG00000104888	ENSG00000104888		"Solute carriers"	16704	protein-coding gene	gene with protein product	"vesicular glutamate transporter 1"	605208	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7"			8632143, 10820226	Standard	NM_020309		Approved	BNPI, VGLUT1	uc002pnp.3	Q9P2U7		ENST00000221485.3:c.582G>A	chr19.hg19:g.49937914C>T	ENSP00000221485:p.Trp194*	102.0	0.0		85.0	4.0	NM_020309	B4DFR9|B4DG46|Q6PCD0	Nonsense_Mutation	SNP	ENST00000221485.3	hg19	CCDS12764.1	.	.	.	.	.	.	.	.	.	.	C	37	6.117643	0.97300	.	.	ENSG00000104888	ENST00000221485;ENST00000543531	.	.	.	4.83	4.83	0.62350	.	0.000000	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8135	0.78581	0.0:1.0:0.0:0.0	.	.	.	.	X	194;182	.	ENSP00000221485:W194X	W	-	3	0	SLC17A7	54629726	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.482000	0.81143	2.674000	0.91012	0.650000	0.86243	TGG	.	.		0.592	SLC17A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465367.2			T	49937914	C	T	49937914	4	4	115	1	0	0	0	0	0	1	0	0	14437	856	30	3	1132	3	SLC17A7	19	49937914	Nonsense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	2061866	49937914	9191069	457	19996										
MED25	81857	hgsc.bcm.edu	37	chr19	50338357	50338357	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcccctacgaccagagcggcTtcgtcaacggcatccggcag	11	16	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:50338357T>C	ENST00000312865.6	+	14	1650	c.1597T>C	c.(1597-1599)Ttc>Ctc	p.F533L	MED25_ENST00000538643.1_Missense_Mutation_p.F320L	NM_030973.3	NP_112235.2	Q71SY5	MED25_HUMAN	mediator complex subunit 25	533	Interaction with CREBBP.|Interaction with VP16.				cell death (GO:0008219)|gene expression (GO:0010467)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of chromatin binding (GO:0035563)|positive regulation of mediator complex assembly (GO:2001178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|transcription factor binding (GO:0008134)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	17		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		CCAGAGCGGCTTCGTCAACGG	0.602																																					p.F533L	GBM(51;894 1657 37868)	Atlas-SNP	.											.	MED25	98	.	0			c.T1597C						.						195	170	179					19																	50338357		2203	4300	6503	SO:0001583	missense	81857	exon14			AGCGGCTTCGTCA	AL136746	CCDS33075.1	19q13.3	2014-09-17	2007-07-30			ENSG00000104973			28845	protein-coding gene	gene with protein product		610197	"mediator of RNA polymerase II transcription, subunit 25 homolog (S. cerevisiae)"			9110174, 11230166	Standard	NM_030973		Approved	ARC92, ACID1, TCBAP0758, DKFZp434K0512	uc002ppw.2	Q71SY5		ENST00000312865.6:c.1597T>C	chr19.hg19:g.50338357T>C	ENSP00000326767:p.Phe533Leu	150.0	0.0		122.0	5.0	NM_030973	A8K095|B9TX30|O95783|Q6P143|Q6QMH5|Q707U4|Q8TB55|Q9H0L5|Q9HB34	Missense_Mutation	SNP	ENST00000312865.6	hg19	CCDS33075.1	.	.	.	.	.	.	.	.	.	.	t	19.56	3.850008	0.71603	.	.	ENSG00000104973	ENST00000355584;ENST00000377077;ENST00000312881;ENST00000312865;ENST00000456294;ENST00000538643;ENST00000377070;ENST00000536547	D;D	0.87966	-2.32;-2.27	5.54	5.54	0.83059	Mediator complex, subunit Med25, PTOV activation and synapsin 2 (1);	0.000000	0.85682	D	0.000000	D	0.92024	0.7473	M	0.64567	1.98	0.47698	D	0.99949	D;D;P	0.65815	0.995;0.989;0.866	D;D;P	0.80764	0.994;0.981;0.739	D	0.92293	0.5843	10	0.54805	T	0.06	.	14.6528	0.68811	0.0:0.0:0.0:1.0	.	320;533;533	B9TX30;B5ME50;Q71SY5	.;.;MED25_HUMAN	L	533;533;533;533;533;320;268;22	ENSP00000326767:F533L;ENSP00000437496:F320L	ENSP00000326767:F533L	F	+	1	0	MED25	55030169	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	5.554000	0.67294	2.111000	0.64477	0.260000	0.18958	TTC	.	.		0.602	MED25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465316.1	NM_030973		C	50338357	T	C	50338357	3	2	115	1	0	0	0	0	1	0	0	0	9452	1609	56	2	1651	2	MED25	19	50338357	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	400443	50338357	8790626	458	19997										
PPP2R1A	5518	hgsc.bcm.edu	37	chr19	52709237	52709237	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	taccatctatgatgaagatgAggtcctcctggccctggcag	11	11	1	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:52709237A>G	ENST00000322088.6	+	3	249	c.191A>G	c.(190-192)gAg>gGg	p.E64G	PPP2R1A_ENST00000473455.2_3'UTR|PPP2R1A_ENST00000444322.2_Intron|PPP2R1A_ENST00000462990.1_5'UTR	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha	64	PP2A subunit B binding.|Polyoma small and medium T antigens Binding.				apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)	p.E64G(1)		NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		GATGAAGATGAGGTCCTCCTG	0.552			Mis		clear cell ovarian carcinoma																																p.E64G		Atlas-SNP	.		Dom?	yes		19	19q13.41	5518	"protein phosphatase 2, regulatory subunit A, alpha"		E	PPP2R1A,colon,carcinoma,0,3	PPP2R1A	187	.	1	Substitution - Missense(1)	breast(1)	c.A191G						.						201	162	175					19																	52709237		2203	4300	6503	SO:0001583	missense	5518	exon3			AAGATGAGGTCCT		CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9302	protein-coding gene	gene with protein product	"protein phosphatase 2A, regulatory subunit A, alpha isoform", "protein phosphatase 2, 65kDa regulatory subunit A"	605983	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform"				Standard	NR_033500		Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.191A>G	chr19.hg19:g.52709237A>G	ENSP00000324804:p.Glu64Gly	114.0	2.0		90.0	4.0	NM_014225	Q13773|Q6ICQ3|Q96DH3	Missense_Mutation	SNP	ENST00000322088.6	hg19	CCDS12849.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.2|20.2	3.947972|3.947972	0.73787|0.73787	.|.	.|.	ENSG00000105568|ENSG00000105568	ENST00000454220;ENST00000423369;ENST00000322088|ENST00000391791	T;T|T	0.08984|0.55234	3.03;3.03|0.53	3.47|3.47	3.47|3.47	0.39725|0.39725	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.295679|.	0.25695|.	N|.	0.028915|.	T|T	0.79417|0.79417	0.4442|0.4442	H|H	0.97131|0.97131	3.945|3.945	0.80722|0.80722	D|D	1|1	D;D|.	0.55172|.	0.97;0.97|.	P;P|.	0.61658|.	0.892;0.892|.	D|D	0.84499|0.84499	0.0615|0.0615	10|6	0.87932|.	D|.	0|.	-26.1968|-26.1968	10.5807|10.5807	0.45255|0.45255	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	64;64|.	A8K7B7;P30153|.	.;2AAA_HUMAN|.	G|G	104;64;64|43	ENSP00000391905:E104G;ENSP00000324804:E64G|ENSP00000375668:R43G	ENSP00000324804:E64G|.	E|R	+|+	2|1	0|2	PPP2R1A|PPP2R1A	57401049|57401049	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.932000|0.932000	0.56968|0.56968	7.765000|7.765000	0.85310|0.85310	1.819000|1.819000	0.53055|0.53055	0.402000|0.402000	0.26972|0.26972	GAG|AGG	.	.		0.552	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267967.2	NM_014225		G	52709237	A	G	52709237	3	3	115	1	0	0	0	0	1	0	0	0	12394	304	11	2	201	2	PPP2R1A	19	52709237	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	2370880	52709237	6419746	459	19998										
ZNF808	388558	hgsc.bcm.edu	37	chr19	53057563	53057563	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggtttgtgatacagctttcaCgtgtaattcacagctggcac	10	9	2	1	rs558251598		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:53057563C>T	ENST00000359798.4	+	5	1574	c.1394C>T	c.(1393-1395)aCg>aTg	p.T465M		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	465					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		ACAGCTTTCACGTGTAATTCA	0.413													C|||	1	0.000199681	0	0	5008	,	,		21702	0		0.001	False		,,,				2504	0				p.T465M		Atlas-SNP	.											.	ZNF808	81	.	0			c.C1394T						.						59	64	62					19																	53057563		2201	4298	6499	SO:0001583	missense	388558	exon5			CTTTCACGTGTAA	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.1394C>T	chr19.hg19:g.53057563C>T	ENSP00000352846:p.Thr465Met	102.0	0.0		52.0	4.0	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	hg19	CCDS46167.1	.	.	.	.	.	.	.	.	.	.	.	0.032	-1.326287	0.01309	.	.	ENSG00000198482	ENST00000359798	T	0.07800	3.16	1.4	-2.81	0.05805	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06872	0.0175	L	0.41573	1.285	0.09310	N	1	B	0.17038	0.02	B	0.17098	0.017	T	0.24012	-1.0172	9	0.46703	T	0.11	.	6.3442	0.21341	0.0:0.4066:0.3159:0.2775	.	465	Q8N4W9	ZN808_HUMAN	M	465	ENSP00000352846:T465M	ENSP00000352846:T465M	T	+	2	0	ZNF808	57749375	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.040000	0.00157	-3.307000	0.00191	-2.208000	0.00301	ACG	.	.		0.413	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		T	53057563	C	T	53057563	3	4	115	1	0	0	0	0	1	0	0	0	18188	536	19	1	1404	1	ZNF808	19	53057563	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	348326	53057563	6071420	460	19999										
ZNF808	388558	hgsc.bcm.edu	37	chr19	53058144	53058144	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agtgtaatgagtgtgggaagAccttcagttacaagtcatca	11	6	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:53058144A>G	ENST00000359798.4	+	5	2155	c.1975A>G	c.(1975-1977)Acc>Gcc	p.T659A		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	659					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		GTGTGGGAAGACCTTCAGTTA	0.423																																					p.T659A		Atlas-SNP	.											.	ZNF808	81	.	0			c.A1975G						.						106	110	108					19																	53058144		2202	4300	6502	SO:0001583	missense	388558	exon5			GGGAAGACCTTCA	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.1975A>G	chr19.hg19:g.53058144A>G	ENSP00000352846:p.Thr659Ala	73.0	0.0		35.0	4.0	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	hg19	CCDS46167.1	.	.	.	.	.	.	.	.	.	.	.	0.160	-1.082320	0.01888	.	.	ENSG00000198482	ENST00000359798	T	0.03745	3.82	1.54	-3.09	0.05331	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01661	0.0053	N	0.21194	0.64	0.09310	N	1	B	0.13594	0.008	B	0.13407	0.009	T	0.48151	-0.9060	9	0.02654	T	1	.	0.0785	0.00029	0.3305:0.1668:0.193:0.3097	.	659	Q8N4W9	ZN808_HUMAN	A	659	ENSP00000352846:T659A	ENSP00000352846:T659A	T	+	1	0	ZNF808	57749956	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.297000	0.02759	-0.652000	0.05408	0.254000	0.18369	ACC	.	.		0.423	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		G	53058144	A	G	53058144	3	3	115	1	0	0	0	0	1	0	0	0	18188	275	10	2	1985	2	ZNF808	19	53058144	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	581	53058144	6070839	461	20000										
ZNF765	91661	hgsc.bcm.edu	37	chr19	53911420	53911420	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aattcttcattattcacacaAaaacaggaagtacatatgag	5	7	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:53911420A>G	ENST00000396408.3	+	4	729	c.612A>G	c.(610-612)caA>caG	p.Q204Q	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	204					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		TATTCACACAAAAACAGGAAG	0.358																																					p.Q204Q		Atlas-SNP	.											.	ZNF765	61	.	0			c.A612G						.						65	66	66					19																	53911420		2173	4283	6456	SO:0001819	synonymous_variant	91661	exon4			CACACAAAAACAG	BC017357	CCDS46171.1	19q13.41	2013-01-08				ENSG00000196417		"Zinc fingers, C2H2-type", "-"	25092	protein-coding gene	gene with protein product						12477932	Standard	XR_430215		Approved		uc002qbm.3	Q7L2R6		ENST00000396408.3:c.612A>G	chr19.hg19:g.53911420A>G		155.0	0.0		80.0	4.0	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Silent	SNP	ENST00000396408.3	hg19	CCDS46171.1																																																																																			.	.		0.358	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372		G	53911420	A	G	53911420	2	3	115	1	0	0	0	0	0	0	0	1	18154	11	1	2		2	ZNF765	19	53911420	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	853276	53911420	5217563	462	20001										
ZNF331	55422	hgsc.bcm.edu	37	chr19	54081146	54081146	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcctacgaatgtaaggagtgCgggaaggcatgtaaccacct	12	9	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:54081146C>T	ENST00000253144.9	+	7	2665	c.1332C>T	c.(1330-1332)tgC>tgT	p.C444C	ZNF331_ENST00000511154.1_Silent_p.C444C|ZNF331_ENST00000512387.1_Silent_p.C444C|ZNF331_ENST00000511593.2_Silent_p.C444C|ZNF331_ENST00000411977.2_Silent_p.C444C|ZNF331_ENST00000513999.1_Silent_p.C444C|ZNF331_ENST00000449416.1_Silent_p.C444C	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.C444C(1)		NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		GTAAGGAGTGCGGGAAGGCAT	0.488			T	?	follicular thyroid adenoma																																p.C444C		Atlas-SNP	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	ZNF331_ENST00000253144,NS,carcinoma,0,1	ZNF331	66	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1332T						.						77	64	69					19																	54081146		2203	4300	6503	SO:0001819	synonymous_variant	55422	exon5			GGAGTGCGGGAAG	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"Zinc fingers, C2H2-type", "-"	15489	protein-coding gene	gene with protein product	"rearranged in thyroid adenomas"	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.1332C>T	chr19.hg19:g.54081146C>T		49.0	0.0		40.0	2.0	NM_001253801	Q96GJ4	Silent	SNP	ENST00000253144.9	hg19	CCDS33102.1																																																																																			.	.		0.488	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555		T	54081146	C	T	54081146	2	4	115	1	0	0	0	0	0	0	0	1	17864	776	27	1		1	ZNF331	19	54081146	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	169726	54081146	5047837	463	20002										
ZFP28	140612	hgsc.bcm.edu	37	chr19	57066068	57066068	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttgccactcatcagagaatCcatactggagagaagcccta	8	12	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:57066068C>G	ENST00000301318.3	+	8	1985	c.1914C>G	c.(1912-1914)atC>atG	p.I638M	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	638					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		ATCAGAGAATCCATACTGGAG	0.458																																					p.I638M	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.C1914G						.						82	88	86					19																	57066068		2203	4300	6503	SO:0001583	missense	140612	exon8			GAGAATCCATACT		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.1914C>G	chr19.hg19:g.57066068C>G	ENSP00000301318:p.Ile638Met	77.0	0.0		109.0	31.0	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	hg19	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.143204	0.37825	.	.	ENSG00000196867	ENST00000301318	T	0.08720	3.06	3.78	-2.03	0.07365	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41194	D	0.000929	T	0.18341	0.0440	L	0.52905	1.665	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00175	-1.1955	10	0.59425	D	0.04	.	10.0715	0.42337	0.0:0.4499:0.0:0.5501	.	638	Q8NHY6	ZFP28_HUMAN	M	638	ENSP00000301318:I638M	ENSP00000301318:I638M	I	+	3	3	ZFP28	61757880	0.000000	0.05858	0.987000	0.45799	0.982000	0.71751	-2.749000	0.00793	-0.377000	0.07930	-0.391000	0.06502	ATC	.	.		0.458	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		G	57066068	C	G	57066068	3	3	115	1	0	0	0	0	1	0	0	0	17657	845	30	4	1944	4	ZFP28	19	57066068	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	2984922	57066068	2062915	464	20003										
ZNF551	90233	hgsc.bcm.edu	37	chr19	58198344	58198344	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atacagaaaagcttcaagccAcaaacacacacttgttcagc	5	12	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr19:58198344A>C	ENST00000282296.5	+	3	886	c.701A>C	c.(700-702)cAc>cCc	p.H234P	ZNF551_ENST00000596085.1_Intron|ZNF551_ENST00000356715.4_Missense_Mutation_p.H218P|AC003006.7_ENST00000594684.1_Intron|AC003006.7_ENST00000599221.1_Intron			Q7Z340	ZN551_HUMAN	zinc finger protein 551	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GCTTCAAGCCACAAACACACA	0.428																																					p.H234P		Atlas-SNP	.											.	ZNF551	65	.	0			c.A701C						.						87	89	88					19																	58198344		2203	4300	6503	SO:0001583	missense	90233	exon3			CAAGCCACAAACA	BX538151	CCDS12959.1, CCDS12959.2	19q13.43	2013-09-20			ENSG00000204519	ENSG00000204519		"Zinc fingers, C2H2-type", "-"	25108	protein-coding gene	gene with protein product							Standard	NM_138347		Approved	DKFZp686H1038	uc002qpw.5	Q7Z340	OTTHUMG00000183470	ENST00000282296.5:c.701A>C	chr19.hg19:g.58198344A>C	ENSP00000282296:p.His234Pro	66.0	0.0		99.0	5.0	NM_138347	B4DU22|P17034|Q8N246|Q9BRY1	Missense_Mutation	SNP	ENST00000282296.5	hg19	CCDS12959.2	.	.	.	.	.	.	.	.	.	.	A	2.818	-0.245476	0.05906	.	.	ENSG00000204519	ENST00000356715;ENST00000282296;ENST00000359821	.	.	.	2.34	-0.0395	0.13875	.	.	.	.	.	T	0.27933	0.0688	L	0.36672	1.1	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.20075	-1.0286	8	0.38643	T	0.18	.	4.4502	0.11617	0.6812:0.1971:0.1217:0.0	.	234	Q7Z340	ZN551_HUMAN	P	234;218;128	.	ENSP00000282296:H218P	H	+	2	0	ZNF551	62890156	.	.	0.000000	0.03702	0.008000	0.06430	.	.	-0.236000	0.09753	0.459000	0.35465	CAC	.	.		0.428	ZNF551-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466803.2	NM_138347		C	58198344	A	C	58198344	3	2	115	1	0	0	0	0	1	0	0	0	17998	159	6	5	663	5	ZNF551	19	58198344	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1132276	58198344	930639	465	20004										
SNAP25	6616	hgsc.bcm.edu	37	chr20	10277688	10277688	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agatggccatcagtggcggcTtcatccgcaggtgagcctca	13	12	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr20:10277688T>C	ENST00000254976.2	+	6	608	c.397T>C	c.(397-399)Ttc>Ctc	p.F133L	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000453544.1_RNA|SNAP25_ENST00000495883.1_3'UTR|SNAP25_ENST00000304886.2_Missense_Mutation_p.F133L	NM_130811.2	NP_570824.1	P60880	SNP25_HUMAN	synaptosomal-associated protein, 25kDa	133					energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long-term synaptic potentiation (GO:0060291)|neurotransmitter secretion (GO:0007269)|neurotransmitter uptake (GO:0001504)|regulation of establishment of protein localization (GO:0070201)|regulation of insulin secretion (GO:0050796)|regulation of neuron projection development (GO:0010975)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|SNARE complex (GO:0031201)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|trans-Golgi network (GO:0005802)	calcium-dependent protein binding (GO:0048306)			endometrium(1)|large_intestine(2)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	18					Botulinum Toxin Type A(DB00083)	CAGTGGCGGCTTCATCCGCAG	0.498																																					p.F133L		Atlas-SNP	.											.	SNAP25	79	.	0			c.T397C						.						62	58	60					20																	10277688		2203	4300	6503	SO:0001583	missense	6616	exon6			GGCGGCTTCATCC		CCDS13109.1, CCDS13110.1	20p12-p11.2	2008-08-01	2002-08-29		ENSG00000132639	ENSG00000132639			11132	protein-coding gene	gene with protein product	"resistance to inhibitors of cholinesterase 4 homolog"	600322	"synaptosomal-associated protein, 25kD"	SNAP		8661740, 10692432	Standard	NM_003081		Approved	SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2	uc002wnr.2	P60880	OTTHUMG00000031863	ENST00000254976.2:c.397T>C	chr20.hg19:g.10277688T>C	ENSP00000254976:p.Phe133Leu	106.0	0.0		104.0	5.0	NM_003081	B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45	Missense_Mutation	SNP	ENST00000254976.2	hg19	CCDS13110.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.419042	0.62622	.	.	ENSG00000132639	ENST00000254976;ENST00000304886	.	.	.	5.86	5.86	0.93980	SNAP-25 (1);	0.000000	0.85682	D	0.000000	T	0.52256	0.1723	L	0.46157	1.445	0.80722	D	1	P;P	0.38827	0.649;0.515	B;B	0.36567	0.228;0.197	T	0.52313	-0.8592	9	0.36615	T	0.2	-4.1915	16.2652	0.82574	0.0:0.0:0.0:1.0	.	133;133	P60880-2;P60880	.;SNP25_HUMAN	L	133	.	ENSP00000254976:F133L	F	+	1	0	SNAP25	10225688	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.241000	0.73720	0.528000	0.53228	TTC	.	.		0.498	SNAP25-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077976.3	NM_130811		C	10277688	T	C	10277688	3	2	115	1	0	0	0	0	1	0	0	0	14845	1609	56	2	537	2	SNAP25	20	10277688	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10		10277688	52747832	466	20005										
TTLL9	164395	hgsc.bcm.edu	37	chr20	30510809	30510809	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gaaagatgatattcccgtggAgaactatgtggctcagcgtt	12	7	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr20:30510809A>G	ENST00000375938.4	+	8	870	c.617A>G	c.(616-618)gAg>gGg	p.E206G	TTLL9_ENST00000375921.2_Missense_Mutation_p.E133G|TTLL9_ENST00000535842.1_Missense_Mutation_p.E206G|TTLL9_ENST00000375934.4_Missense_Mutation_p.E188G|TTLL9_ENST00000310998.4_Missense_Mutation_p.E156G|TTLL9_ENST00000375922.4_Missense_Mutation_p.E133G			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	206	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			ATTCCCGTGGAGAACTATGTG	0.403																																					p.E206G		Atlas-SNP	.											.	TTLL9	95	.	0			c.A617G						.						163	160	161					20																	30510809		1997	4170	6167	SO:0001583	missense	164395	exon8			CCGTGGAGAACTA	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"Tubulin tyrosine ligase-like family"	16118	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 125"	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.617A>G	chr20.hg19:g.30510809A>G	ENSP00000365105:p.Glu206Gly	84.0	0.0		124.0	6.0	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Missense_Mutation	SNP	ENST00000375938.4	hg19	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.250781	0.80135	.	.	ENSG00000131044	ENST00000375938;ENST00000535842;ENST00000310998;ENST00000375921;ENST00000375935;ENST00000375934;ENST00000375922	T;T;T;T;T;T	0.05925	3.37;3.37;3.37;3.37;3.37;3.37	4.35	4.35	0.52113	.	0.055930	0.64402	D	0.000001	T	0.21550	0.0519	M	0.66939	2.045	0.58432	D	0.999999	D;D	0.89917	0.992;1.0	D;D	0.77557	0.969;0.99	T	0.00494	-1.1706	10	0.87932	D	0	.	12.5143	0.56024	1.0:0.0:0.0:0.0	.	206;93	Q3SXZ7;B1ANK8	TTLL9_HUMAN;.	G	206;206;156;133;151;188;133	ENSP00000365105:E206G;ENSP00000442515:E206G;ENSP00000308980:E156G;ENSP00000365086:E133G;ENSP00000365100:E188G;ENSP00000365088:E133G	ENSP00000308980:E156G	E	+	2	0	TTLL9	29974470	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.607000	0.74163	1.837000	0.53436	0.459000	0.35465	GAG	.	.		0.403	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409		G	30510809	A	G	30510809	3	3	115	1	0	0	0	0	1	0	0	0	16749	304	11	2	643	2	TTLL9	20	30510809	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	20233121	30510809	32514711	467	20006										
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36874425	36874425	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccccctggaagccagagtccAggagacggaacacctgaccc	11	16	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr20:36874425A>G	ENST00000279024.4	-	2	378	c.107T>C	c.(106-108)cTg>cCg	p.L36P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	36										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GCCAGAGTCCAGGAGACGGAA	0.612																																					p.L36P		Atlas-SNP	.											.	KIAA1755	145	.	0			c.T107C						.						69	61	64					20																	36874425		2203	4300	6503	SO:0001583	missense	85449	exon2			GAGTCCAGGAGAC	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.107T>C	chr20.hg19:g.36874425A>G	ENSP00000279024:p.Leu36Pro	86.0	0.0		88.0	4.0	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.630205	0.87660	.	.	ENSG00000149633	ENST00000279024	T	0.10192	2.9	5.4	5.4	0.78164	.	0.000000	0.38164	N	0.001781	T	0.32912	0.0845	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.04178	-1.0971	10	0.87932	D	0	.	14.9112	0.70758	1.0:0.0:0.0:0.0	.	36	Q5JYT7	K1755_HUMAN	P	36	ENSP00000279024:L36P	ENSP00000279024:L36P	L	-	2	0	KIAA1755	36307839	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.272000	0.95707	2.172000	0.68678	0.533000	0.62120	CTG	.	.		0.612	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		G	36874425	A	G	36874425	3	3	115	1	0	0	0	0	1	0	0	0	8266	188	7	2	3547	2	KIAA1755	20	36874425	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6363616	36874425	26151095	468	20007										
CHD6	84181	hgsc.bcm.edu	37	chr20	40052330	40052330	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	atagaagtctgcttgttctcTcctagtccaccttgagattt	7	10	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr20:40052330T>C	ENST00000373233.3	-	30	4534	c.4357A>G	c.(4357-4359)Aga>Gga	p.R1453G		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1453	Myb-like.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GCTTGTTCTCTCCTAGTCCAC	0.403																																					p.R1453G		Atlas-SNP	.											.	CHD6	312	.	0			c.A4357G						.						107	109	108					20																	40052330		2203	4300	6503	SO:0001583	missense	84181	exon30			GTTCTCTCCTAGT	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.4357A>G	chr20.hg19:g.40052330T>C	ENSP00000362330:p.Arg1453Gly	142.0	0.0		119.0	5.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.955273	0.73902	.	.	ENSG00000124177	ENST00000373233	D	0.94723	-3.5	6.02	0.655	0.17839	SANT domain, DNA binding (1);	0.000000	0.64402	D	0.000003	D	0.97281	0.9111	M	0.90425	3.115	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.97331	0.9950	10	0.87932	D	0	-18.5229	14.5297	0.67915	0.0:0.0:0.4819:0.5181	.	1453	Q8TD26	CHD6_HUMAN	G	1453	ENSP00000362330:R1453G	ENSP00000362330:R1453G	R	-	1	2	CHD6	39485744	1.000000	0.71417	0.858000	0.33744	0.998000	0.95712	3.013000	0.49582	0.113000	0.18004	0.533000	0.62120	AGA	.	.		0.403	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			C	40052330	T	C	40052330	3	2	115	1	0	0	0	0	1	0	0	0	3331	1559	54	2	3822	2	CHD6	20	40052330	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3177905	40052330	22973190	469	20008										
TOX2	84969	hgsc.bcm.edu	37	chr20	42694558	42694558	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgccaggcctcagtgcgtcCccgccgccgccaccctcctt	9	22	1	0	rs199841880|rs34604629	byFrequency	TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr20:42694558C>G	ENST00000358131.5	+	6	1321	c.1113C>G	c.(1111-1113)tcC>tcG	p.S371S	TOX2_ENST00000341197.4_Silent_p.S389S|TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000372999.1_Silent_p.S347S|TOX2_ENST00000423191.2_Silent_p.S347S	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	371					female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S347_P348insR(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			TCAGTGCGTCCCCGCCGCCGC	0.716																																					p.S389S		Atlas-SNP	.											TOX2_ENST00000348077,colon,carcinoma,+2,14	TOX2	158	.	1	Insertion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1167G						.						31	34	33					20																	42694558		2201	4298	6499	SO:0001819	synonymous_variant	84969	exon7			TGCGTCCCCGCCG	BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"granulosa cell HMG box 1"	611163	"chromosome 20 open reading frame 100"	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.1113C>G	chr20.hg19:g.42694558C>G		51.0	1.0		58.0	3.0	NM_001098797	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Silent	SNP	ENST00000358131.5	hg19	CCDS42875.1																																																																																			.	.		0.716	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2			G	42694558	C	G	42694558	2	3	115	1	0	0	0	0	0	0	0	1	16393	610	22	4		4	TOX2	20	42694558	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	2642228	42694558	20330962	470	20009										
KCNB1	3745	hgsc.bcm.edu	37	chr20	47990149	47990149	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gctctcgatgaagaaactagAgtgctggctggcatcagggc	14	9	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr20:47990149A>G	ENST00000371741.4	-	2	2114	c.1948T>C	c.(1948-1950)Tct>Cct	p.S650P		NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1	650					energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	AAGAAACTAGAGTGCTGGCTG	0.577																																					p.S650P		Atlas-SNP	.											.	KCNB1	142	.	0			c.T1948C						.						48	49	49					20																	47990149		2203	4300	6503	SO:0001583	missense	3745	exon2			AACTAGAGTGCTG	AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.1948T>C	chr20.hg19:g.47990149A>G	ENSP00000360806:p.Ser650Pro	49.0	0.0		64.0	5.0	NM_004975	Q14193	Missense_Mutation	SNP	ENST00000371741.4	hg19	CCDS13418.1	.	.	.	.	.	.	.	.	.	.	A	3.966	-0.009393	0.07727	.	.	ENSG00000158445	ENST00000371741;ENST00000538812	T	0.26223	1.75	5.7	5.7	0.88788	.	0.890365	0.09895	N	0.741882	T	0.27313	0.0670	L	0.43152	1.355	0.44098	D	0.99686	B	0.14012	0.009	B	0.16289	0.015	T	0.03364	-1.1044	10	0.29301	T	0.29	.	15.6259	0.76855	1.0:0.0:0.0:0.0	.	650	Q14721	KCNB1_HUMAN	P	650;605	ENSP00000360806:S650P	ENSP00000360806:S650P	S	-	1	0	KCNB1	47423556	1.000000	0.71417	0.197000	0.23402	0.252000	0.25951	6.778000	0.75043	2.173000	0.68751	0.533000	0.62120	TCT	.	.		0.577	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975		G	47990149	A	G	47990149	3	3	115	1	0	0	0	0	1	0	0	0	8021	304	11	2	632	2	KCNB1	20	47990149	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5295591	47990149	15035371	471	20010										
TMEM189	387521	hgsc.bcm.edu	37	chr20	48741638	48741638	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tcatgtcatctgcccgaggcTtctcgcccgtcaggccctgg	11	16	5	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr20:48741638T>C	ENST00000371652.4	-	6	866	c.770A>G	c.(769-771)aAg>aGg	p.K257R	TMEM189_ENST00000371650.5_Missense_Mutation_p.K254R|TMEM189-UBE2V1_ENST00000341698.2_Intron|TMEM189_ENST00000371656.2_Missense_Mutation_p.K182R|TMEM189_ENST00000557021.1_Intron	NM_199129.2	NP_954580			transmembrane protein 189											breast(1)|endometrium(2)|large_intestine(3)|lung(2)	8			BRCA - Breast invasive adenocarcinoma(9;3.02e-07)			TGCCCGAGGCTTCTCGCCCGT	0.582																																					p.K257R	GBM(75;703 1202 5766 12781 15082)	Atlas-SNP	.											.	TMEM189	15	.	0			c.A770G						.						89	75	80					20																	48741638		2203	4300	6503	SO:0001583	missense	387521	exon6			CGAGGCTTCTCGC	AF155120	CCDS13428.1, CCDS54473.1	20q13.13	2007-07-30			ENSG00000240849	ENSG00000240849			16735	protein-coding gene	gene with protein product		610994				11076860	Standard	NM_199129		Approved	Kua		A5PLL7	OTTHUMG00000152625	ENST00000371652.4:c.770A>G	chr20.hg19:g.48741638T>C	ENSP00000360715:p.Lys257Arg	82.0	0.0		100.0	4.0	NM_199129		Missense_Mutation	SNP	ENST00000371652.4	hg19	CCDS13428.1	.	.	.	.	.	.	.	.	.	.	T	14.62	2.590285	0.46214	.	.	ENSG00000240849	ENST00000371650;ENST00000371656;ENST00000371652	T;T	0.45276	0.9;0.91	5.64	5.64	0.86602	Kua-ubiquitin conjugating enzyme hybrid, localisation (1);	.	.	.	.	T	0.32852	0.0843	.	.	.	0.80722	D	1	B;B;B	0.31931	0.015;0.347;0.347	B;B;B	0.28638	0.022;0.092;0.092	T	0.08371	-1.0725	8	0.26408	T	0.33	.	15.8623	0.79035	0.0:0.0:0.0:1.0	.	182;254;257	Q5TGE2;Q5TGE1;A5PLL7	.;.;TM189_HUMAN	R	254;182;257	ENSP00000360713:K254R;ENSP00000360715:K257R	ENSP00000360713:K254R	K	-	2	0	TMEM189	48175045	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.595000	0.82710	2.139000	0.66308	0.533000	0.62120	AAG	.	.		0.582	TMEM189-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080529.1	NM_199129		C	48741638	T	C	48741638	3	2	115	1	0	0	0	0	1	0	0	0	16126	1609	56	2	46	2	TMEM189	20	48741638	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	751489	48741638	14283882	472	20011										
EDN3	1908	hgsc.bcm.edu	37	chr20	57896179	57896179	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctcacatcggccacacttgcGctgcgcttgtgtggggagat	13	12	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr20:57896179G>T	ENST00000337938.2	+	3	859	c.473G>T	c.(472-474)cGc>cTc	p.R158L	EDN3_ENST00000311585.7_Missense_Mutation_p.R158L|EDN3_ENST00000371028.2_Missense_Mutation_p.R158L|EDN3_ENST00000371025.3_Missense_Mutation_p.R158L|EDN3_ENST00000395654.3_Missense_Mutation_p.R158L	NM_207034.1	NP_996917.1	P14138	EDN3_HUMAN	endothelin 3	158					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inositol phosphate-mediated signaling (GO:0048016)|melanocyte differentiation (GO:0030318)|multicellular organismal development (GO:0007275)|neural crest cell migration (GO:0001755)|neuron differentiation (GO:0030182)|neutrophil chemotaxis (GO:0030593)|peptide hormone secretion (GO:0030072)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|regulation of developmental pigmentation (GO:0048070)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|signal transduction (GO:0007165)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	19	all_lung(29;0.0115)					CCACACTTGCGCTGCGCTTGT	0.567																																					p.R158L		Atlas-SNP	.											.	EDN3	83	.	0			c.G473T						.						112	104	107					20																	57896179		2203	4300	6503	SO:0001583	missense	1908	exon3			ACTTGCGCTGCGC	X52001	CCDS13477.1, CCDS13478.1, CCDS13479.1	20q13.2-q13.3	2013-02-26			ENSG00000124205	ENSG00000124205		"Endogenous ligands"	3178	protein-coding gene	gene with protein product		131242					Standard	NM_000114		Approved	ET3	uc002yaq.3	P14138	OTTHUMG00000032867	ENST00000337938.2:c.473G>T	chr20.hg19:g.57896179G>T	ENSP00000337128:p.Arg158Leu	127.0	0.0		187.0	66.0	NM_207034	E1P5I5|Q03229|Q7Z6D2|Q9UGT7	Missense_Mutation	SNP	ENST00000337938.2	hg19	CCDS13477.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.820469	0.50633	.	.	ENSG00000124205	ENST00000337938;ENST00000311585;ENST00000371028;ENST00000371025;ENST00000395654	D;D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1;-2.1	4.87	4.87	0.63330	Endothelin-like toxin (1);	0.000000	0.85682	D	0.000000	D	0.91872	0.7427	M	0.62723	1.935	0.38627	D	0.951288	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;0.999	D	0.93303	0.6678	10	0.87932	D	0	-37.8245	13.8571	0.63534	0.0:0.0:1.0:0.0	.	158;158;158;158	P14138-2;Q7Z6D2;P14138;Q4FAT2	.;.;EDN3_HUMAN;.	L	158	ENSP00000337128:R158L;ENSP00000311854:R158L;ENSP00000360067:R158L;ENSP00000360064:R158L;ENSP00000379015:R158L	ENSP00000311854:R158L	R	+	2	0	EDN3	57329574	1.000000	0.71417	0.933000	0.37362	0.010000	0.07245	5.390000	0.66261	2.409000	0.81822	0.561000	0.74099	CGC	.	.		0.567	EDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079919.2	NM_000114		T	57896179	G	T	57896179	3	4	115	1	0	0	0	0	1	0	0	0	4920	1087	38	1	483	1	EDN3	20	57896179	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	9154541	57896179	5129341	473	20012										
GMEB2	26205	hgsc.bcm.edu	37	chr20	62221981	62221981	+	Frame_Shift_Del	DEL	G	G	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccgcttcacaggcggtggcaGggagaccggcgtcagcgtca							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr20:62221981delG	ENST00000266068.1	-	9	1532	c.1054delC	c.(1054-1056)ctgfs	p.L352fs	GMEB2_ENST00000370077.1_Frame_Shift_Del_p.L352fs|GMEB2_ENST00000370069.1_Frame_Shift_Del_p.L301fs			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	352					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			GGCGGTGGCAGGGAGACCGGC	0.667																																					p.L352fs		Atlas-INDEL	.											.	GMEB2	44	.	0			c.1055delT						.						62	48	53					20																	62221981		2197	4300	6497	SO:0001589	frameshift_variant	26205	exon10			.	AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216			4371	protein-coding gene	gene with protein product		607451				10523663, 11743720	Standard	NM_012384		Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000266068.1:c.1054delC	chr20.hg19:g.62221981delG	ENSP00000266068:p.Leu352fs	71.0	0.0		147.0	10.0	NM_012384	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	Frame_Shift_Del	DEL	ENST00000266068.1	hg19	CCDS13528.1																																																																																			.	.		0.667	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	NM_012384		-	62221981	G	-	62221981	7	5	115	1	0	1	0	1	0	0	0	0	6496	991	35	0	542	0	GMEB2	20	62221981	Frame_Shift_Del	DEL	G	TCGA-DD-A3A1-01A-11D-A20W-10	4325802	62221981	803539	474	20013										
ZGPAT	84619	hgsc.bcm.edu	37	chr20	62340023	62340023	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgggcgccggcctggattcgTctgagcaggctgacctgcgc	16	13	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr20:62340023T>C	ENST00000328969.5	+	2	218	c.91T>C	c.(91-93)Tct>Cct	p.S31P	ARFRP1_ENST00000607873.1_5'Flank|ARFRP1_ENST00000324228.2_5'Flank|ZGPAT_ENST00000355969.6_Missense_Mutation_p.S31P|ARFRP1_ENST00000609142.1_5'Flank|RP4-583P15.15_ENST00000490623.2_5'Flank|ZGPAT_ENST00000357119.4_Missense_Mutation_p.S31P|ARFRP1_ENST00000440854.1_5'Flank|ARFRP1_ENST00000359715.5_5'Flank|ZGPAT_ENST00000369967.3_Missense_Mutation_p.S31P|ZGPAT_ENST00000448100.2_Missense_Mutation_p.S31P	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	31					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					CCTGGATTCGTCTGAGCAGGC	0.652																																					p.S31P		Atlas-SNP	.											.	ZGPAT	57	.	0			c.T91C						.						30	33	32					20																	62340023		2200	4294	6494	SO:0001583	missense	84619	exon2			GATTCGTCTGAGC	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"Zinc fingers, CCCH-type domain containing", "G patch domain containing"	15948	protein-coding gene	gene with protein product			"KIAA1847"	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.91T>C	chr20.hg19:g.62340023T>C	ENSP00000332013:p.Ser31Pro	89.0	0.0		122.0	5.0	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Missense_Mutation	SNP	ENST00000328969.5	hg19	CCDS13534.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.129010	0.37533	.	.	ENSG00000197114	ENST00000448100;ENST00000355969;ENST00000357119;ENST00000431125;ENST00000369967;ENST00000328969	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	4.36	0.139	0.14798	.	0.802747	0.11801	N	0.528115	T	0.40743	0.1129	L	0.39898	1.24	0.09310	N	1	D;D;D	0.60160	0.984;0.987;0.984	P;P;P	0.53146	0.67;0.719;0.67	T	0.24154	-1.0168	10	0.46703	T	0.11	-0.0124	6.4878	0.22099	0.1633:0.0:0.3447:0.492	.	31;31;31	Q8N5A5-3;Q8N5A5;Q8N5A5-2	.;ZGPAT_HUMAN;.	P	31	ENSP00000391176:S31P;ENSP00000348242:S31P;ENSP00000349634:S31P;ENSP00000403966:S31P;ENSP00000358984:S31P;ENSP00000332013:S31P	ENSP00000332013:S31P	S	+	1	0	ZGPAT	61810467	0.000000	0.05858	0.004000	0.12327	0.415000	0.31203	-0.101000	0.10973	0.065000	0.16485	0.459000	0.35465	TCT	.	.		0.652	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		C	62340023	T	C	62340023	3	2	115	1	0	0	0	0	1	0	0	0	17689	1667	58	2	93	2	ZGPAT	20	62340023	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	118042	62340023	685497	475	20014										
CCT8	10694	hgsc.bcm.edu	37	chr21	30439969	30439969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaagtttgtgccatctccaaCttcttgctcttgcatatgag	7	10	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr21:30439969C>T	ENST00000286788.4	-	4	495	c.289G>A	c.(289-291)Gtt>Att	p.V97I	CCT8_ENST00000470450.1_5'UTR|CCT8_ENST00000542732.1_Missense_Mutation_p.V78I|CCT8_ENST00000540844.1_Missense_Mutation_p.V24I	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	97					'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						CCATCTCCAACTTCTTGCTCT	0.408																																					p.V97I		Atlas-SNP	.											.	CCT8	38	.	0			c.G289A						.						90	84	86					21																	30439969		2203	4300	6503	SO:0001583	missense	10694	exon4			CTCCAACTTCTTG	Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"Heat Shock Proteins / Chaperonins"	1623	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 112"	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595	ENST00000286788.4:c.289G>A	chr21.hg19:g.30439969C>T	ENSP00000286788:p.Val97Ile	163.0	0.0		119.0	5.0	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Missense_Mutation	SNP	ENST00000286788.4	hg19	CCDS33528.1	.	.	.	.	.	.	.	.	.	.	C	14.57	2.574101	0.45902	.	.	ENSG00000156261	ENST00000389159;ENST00000286788;ENST00000542732;ENST00000540844	T;T;T	0.80304	-1.36;-1.36;-1.36	5.55	5.55	0.83447	Chaperonin TCP-1, conserved site (1);	0.057626	0.64402	D	0.000002	T	0.79913	0.4528	L	0.55743	1.74	0.80722	D	1	B;B;B;B;B	0.22346	0.065;0.023;0.065;0.053;0.068	B;B;B;B;B	0.28849	0.095;0.03;0.066;0.039;0.033	T	0.73603	-0.3930	10	0.28530	T	0.3	-24.6387	19.8683	0.96840	0.0:1.0:0.0:0.0	.	24;78;97;97;97	B4DQH4;B4DEM7;Q53HU0;G5E9B2;P50990	.;.;.;.;TCPQ_HUMAN	I	97;97;78;24	ENSP00000286788:V97I;ENSP00000444984:V78I;ENSP00000442730:V24I	ENSP00000286788:V97I	V	-	1	0	CCT8	29361840	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.480000	0.81109	2.753000	0.94483	0.655000	0.94253	GTT	.	.		0.408	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1			T	30439969	C	T	30439969	3	4	115	1	0	0	0	0	1	0	0	0	2962	565	20	3	1405	3	CCT8	21	30439969	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10		30439969	17689926	476	20015										
KRTAP26-1	388818	hgsc.bcm.edu	37	chr21	31691918	31691918	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	actcttggacaagcagaattGggggcgataggcattgggca	15	7	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr21:31691918G>T	ENST00000360542.3	-	1	689	c.436C>A	c.(436-438)Caa>Aaa	p.Q146K		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	146						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						AAGCAGAATTGGGGGCGATAG	0.547																																					p.Q146K		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.C436A						.						188	186	187					21																	31691918		2203	4300	6503	SO:0001583	missense	388818	exon1			AGAATTGGGGGCG	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"Keratin associated proteins"	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.436C>A	chr21.hg19:g.31691918G>T	ENSP00000353742:p.Gln146Lys	164.0	0.0		140.0	74.0	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	hg19	CCDS13588.1	.	.	.	.	.	.	.	.	.	.	G	9.470	1.095348	0.20471	.	.	ENSG00000197683	ENST00000360542	T	0.03181	4.02	3.77	-4.27	0.03744	.	1.243450	0.06023	U	0.651676	T	0.02342	0.0072	L	0.32530	0.975	0.09310	N	1	P	0.35307	0.494	B	0.33799	0.17	T	0.42766	-0.9432	10	0.06099	T	0.92	-0.0422	4.7346	0.12982	0.4564:0.31:0.2336:0.0	.	146	Q6PEX3	KR261_HUMAN	K	146	ENSP00000353742:Q146K	ENSP00000353742:Q146K	Q	-	1	0	KRTAP26-1	30613789	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.947000	0.03901	-0.679000	0.05217	-0.140000	0.14226	CAA	.	.		0.547	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405		T	31691918	G	T	31691918	3	4	115	1	0	0	0	0	1	0	0	0	8552	1357	47	3	200	3	KRTAP26-1	21	31691918	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	1251949	31691918	16437977	477	20016										
SON	6651	hgsc.bcm.edu	37	chr21	34923955	34923955	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tccatggactcccagatgttAgcaaccagctccatggactc	8	14	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr21:34923955A>G	ENST00000356577.4	+	3	2893	c.2418A>G	c.(2416-2418)ttA>ttG	p.L806L	SON_ENST00000290239.6_Silent_p.L806L|SON_ENST00000300278.4_Silent_p.L806L|SON_ENST00000381679.4_Silent_p.L806L|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	806	17 X 10 AA tandem repeats of L-A-[ST]- [NSG]-[TS]-MDSQM.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						CCCAGATGTTAGCAACCAGCT	0.512																																					p.L806L		Atlas-SNP	.											.	SON	343	.	0			c.A2418G						.						136	135	135					21																	34923955		2203	4300	6503	SO:0001819	synonymous_variant	6651	exon3			GATGTTAGCAACC	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.2418A>G	chr21.hg19:g.34923955A>G		98.0	0.0		63.0	4.0	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	hg19	CCDS13629.1																																																																																			.	.		0.512	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		G	34923955	A	G	34923955	2	3	115	1	0	0	0	0	0	0	0	1	14941	417	15	2		2	SON	21	34923955	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3232037	34923955	13205940	478	20017										
SIK1	150094	hgsc.bcm.edu	37	chr21	44838373	44838373	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aggtcagacaactgtcagagCtggttccctctgcaggactt	11	11	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr21:44838373C>T	ENST00000270162.6	-	12	1643	c.1511G>A	c.(1510-1512)aGc>aAc	p.S504N		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	504					cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	ACTGTCAGAGCTGGTTCCCTC	0.642																																					p.S504N		Atlas-SNP	.											.	SIK1	65	.	0			c.G1511A						.						37	39	38					21																	44838373		2202	4300	6502	SO:0001583	missense	150094	exon12			TCAGAGCTGGTTC	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"myocardial SNF1-like kinase"	605705	"SNF1-like kinase"	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.1511G>A	chr21.hg19:g.44838373C>T	ENSP00000270162:p.Ser504Asn	86.0	0.0		81.0	7.0	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	hg19	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.799237	0.31869	.	.	ENSG00000142178	ENST00000270162	T	0.73469	-0.75	4.79	4.79	0.61399	.	0.110591	0.64402	D	0.000005	T	0.72867	0.3514	M	0.72118	2.19	0.43688	D	0.996137	B	0.18461	0.028	B	0.13407	0.009	T	0.69558	-0.5113	10	0.17369	T	0.5	.	17.8445	0.88725	0.0:1.0:0.0:0.0	.	504	P57059	SIK1_HUMAN	N	504	ENSP00000270162:S504N	ENSP00000270162:S504N	S	-	2	0	SIK1	43662801	1.000000	0.71417	1.000000	0.80357	0.268000	0.26511	4.562000	0.60816	2.205000	0.71048	0.655000	0.94253	AGC	.	.		0.642	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		T	44838373	C	T	44838373	3	4	115	1	0	0	0	0	1	0	0	0	14332	797	28	3	852	3	SIK1	21	44838373	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	9914418	44838373	3291522	479	20018										
TRAPPC10	7109	hgsc.bcm.edu	37	chr21	45499543	45499543	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccccatcacacacacaaggaAgcagctggccgaatgtcaaa	8	14	2	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr21:45499543A>G	ENST00000291574.4	+	12	1743	c.1568A>G	c.(1567-1569)aAg>aGg	p.K523R		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	523					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						CACACAAGGAAGCAGCTGGCC	0.428																																					p.K523R		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.A1568G						.						76	73	74					21																	45499543		2203	4300	6503	SO:0001583	missense	7109	exon12			CAAGGAAGCAGCT	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"Trafficking protein particle complex"	11868	protein-coding gene	gene with protein product	"trafficking protein particle complex subunit 130", "TRAPP 130 kDa subunit"	602103	"transmembrane protein 1"	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.1568A>G	chr21.hg19:g.45499543A>G	ENSP00000291574:p.Lys523Arg	120.0	0.0		97.0	5.0	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	hg19	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	A	8.423	0.846747	0.16963	.	.	ENSG00000160218	ENST00000291574	T	0.44881	0.91	5.49	4.34	0.51931	Tetratricopeptide-like helical (1);	0.045343	0.85682	D	0.000000	T	0.24470	0.0593	N	0.21448	0.665	0.39839	D	0.973082	B	0.26445	0.149	B	0.20384	0.029	T	0.06162	-1.0842	10	0.07482	T	0.82	.	11.082	0.48066	0.926:0.0:0.074:0.0	.	523	P48553	TPC10_HUMAN	R	523	ENSP00000291574:K523R	ENSP00000291574:K523R	K	+	2	0	TRAPPC10	44323971	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.064000	0.49986	0.908000	0.36671	0.482000	0.46254	AAG	.	.		0.428	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		G	45499543	A	G	45499543	3	3	115	1	0	0	0	0	1	0	0	0	16472	72	3	2	1614	2	TRAPPC10	21	45499543	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	661170	45499543	2630352	480	20019										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26164940	26164940	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agaagacaggtgagcctcagAcccagatggagaagacaagc	13	9	1	7			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:26164940A>G	ENST00000407587.2	+	4	1226	c.1057A>G	c.(1057-1059)Acc>Gcc	p.T353A	MYO18B_ENST00000536101.1_Missense_Mutation_p.T353A|MYO18B_ENST00000335473.7_Missense_Mutation_p.T353A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	353						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TGAGCCTCAGACCCAGATGGA	0.552																																					p.T353A		Atlas-SNP	.											.	MYO18B	322	.	0			c.A1057G						.						35	38	37					22																	26164940		2101	4212	6313	SO:0001583	missense	84700	exon4			CCTCAGACCCAGA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.1057A>G	chr22.hg19:g.26164940A>G	ENSP00000386096:p.Thr353Ala	92.0	0.0		80.0	4.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	a	5.433	0.265000	0.10294	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.85955	-2.03;-2.03;-2.05	4.25	-7.05	0.01573	.	3.844790	0.00897	N	0.002311	T	0.68604	0.3019	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.60110	-0.7327	10	0.21540	T	0.41	.	10.2453	0.43336	0.3672:0.1107:0.5221:0.0	.	353;353;353	Q8IUG5;F5GXR6;F5GYU7	MY18B_HUMAN;.;.	A	353	ENSP00000441229:T353A;ENSP00000334563:T353A;ENSP00000386096:T353A	ENSP00000334563:T353A	T	+	1	0	MYO18B	24494940	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-2.095000	0.01350	-1.568000	0.01670	-0.423000	0.05987	ACC	.	.		0.552	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26164940	A	G	26164940	3	3	115	1	0	0	0	0	1	0	0	0	10075	275	10	2	1067	2	MYO18B	22	26164940	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10		26164940	25139626	481	20020										
EWSR1	2130	hgsc.bcm.edu	37	chr22	29693819	29693819	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctgttgtcttgttccagggAaagattttcaagggagcaaa	11	6	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:29693819A>G	ENST00000397938.2	+	13	1616	c.1297A>G	c.(1297-1299)Aaa>Gaa	p.K433E	EWSR1_ENST00000331029.7_Missense_Mutation_p.K395E|EWSR1_ENST00000414183.2_Missense_Mutation_p.K438E|EWSR1_ENST00000406548.1_Missense_Mutation_p.K432E|EWSR1_ENST00000332035.6_Missense_Mutation_p.K377E|EWSR1_ENST00000332050.6_Missense_Mutation_p.K360E	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1	433	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TGTTCCAGGGAAAGATTTTCA	0.498			T	"FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"	"Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"																																p.K438E		Atlas-SNP	.		Dom	yes		22	22q12	2130	Ewing sarcoma breakpoint region 1 (EWS)		"L, M"	.	EWSR1	104	.	0			c.A1312G						.						93	88	90					22																	29693819		2203	4300	6503	SO:0001583	missense	2130	exon14			CCAGGGAAAGATT		CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944		"RNA binding motif (RRM) containing"	3508	protein-coding gene	gene with protein product		133450	"Ewing sarcoma breakpoint region 1"			1522903	Standard	NM_005243		Approved	EWS	uc003aev.3	Q01844	OTTHUMG00000151107	ENST00000397938.2:c.1297A>G	chr22.hg19:g.29693819A>G	ENSP00000381031:p.Lys433Glu	84.0	0.0		85.0	4.0	NM_013986	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	Missense_Mutation	SNP	ENST00000397938.2	hg19	CCDS13851.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.0|22.0	4.235372|4.235372	0.79800|0.79800	.|.	.|.	ENSG00000182944|ENSG00000182944	ENST00000360091|ENST00000332050;ENST00000397938;ENST00000406548;ENST00000331029;ENST00000414183;ENST00000332035	.|T;T;T;T;T;T	.|0.08193	.|3.12;3.12;3.12;3.12;3.12;3.12	5.79|5.79	5.79|5.79	0.91817|0.91817	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.27384|0.27384	0.0672|0.0672	M|M	0.64676|0.64676	1.99|1.99	0.80722|0.80722	D|D	1|1	.|D;P;D;D;P	.|0.62365	.|0.988;0.947;0.988;0.991;0.947	.|D;D;D;D;D	.|0.78314	.|0.971;0.941;0.971;0.991;0.941	T|T	0.00448|0.00448	-1.1733|-1.1733	5|10	.|0.72032	.|D	.|0.01	.|.	15.7839|15.7839	0.78286|0.78286	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|377;432;377;438;433	.|Q96MN4;Q96FE8;B0QYK1;Q96MX4;Q01844	.|.;.;.;.;EWS_HUMAN	G|E	88|360;433;432;395;438;377	.|ENSP00000330896:K360E;ENSP00000381031:K433E;ENSP00000385726:K432E;ENSP00000330516:K395E;ENSP00000400142:K438E;ENSP00000331699:K377E	.|ENSP00000330516:K395E	E|K	+|+	2|1	0|0	EWSR1|EWSR1	28023819|28023819	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.533000|0.533000	0.34776|0.34776	8.098000|8.098000	0.89540|0.89540	2.208000|2.208000	0.71279|0.71279	0.533000|0.533000	0.62120|0.62120	GAA|AAA	.	.		0.498	EWSR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321345.1	NM_005243		G	29693819	A	G	29693819	3	3	115	1	0	0	0	0	1	0	0	0	5298	247	9	2	1464	2	EWSR1	22	29693819	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3528879	29693819	21610747	482	20021										
C22orf28	51493	hgsc.bcm.edu	37	chr22	32792236	32792236	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tctccatagctaccagcgcaTctggaacaagagccacaaag	8	13	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:32792236T>C	ENST00000216038.5	-	8	913	c.815A>G	c.(814-816)gAt>gGt	p.D272G	RTCB_ENST00000451746.2_Intron|RTCB_ENST00000476619.1_5'Flank	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		TACCAGCGCATCTGGAACAAG	0.453																																					p.D272G		Atlas-SNP	.											.	C22orf28	43	.	0			c.A815G						.						113	109	111					22																	32792236		2203	4300	6503	SO:0001630	splice_region_variant	51493	exon8			AGCGCATCTGGAA	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"focal adhesion-associated protein"	613901	"chromosome 22 open reading frame 28"	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.815-1A>G	chr22.hg19:g.32792236T>C		105.0	0.0		138.0	6.0	NM_014306		Missense_Mutation	SNP	ENST00000216038.5	hg19	CCDS13905.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.171446	0.57584	.	.	ENSG00000100220	ENST00000216038	T	0.31769	1.48	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.41994	0.1183	M	0.76574	2.34	0.80722	D	1	B	0.21071	0.051	B	0.30782	0.12	T	0.35425	-0.9789	10	0.87932	D	0	.	16.3947	0.83586	0.0:0.0:0.0:1.0	.	272	Q9Y3I0	RTCB_HUMAN	G	272	ENSP00000216038:D272G	ENSP00000216038:D272G	D	-	2	0	C22orf28	31122236	1.000000	0.71417	1.000000	0.80357	0.460000	0.32559	7.911000	0.87458	2.272000	0.75746	0.459000	0.35465	GAT	.	.		0.453	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306	Missense_Mutation	C	32792236	T	C	32792236	5	2	115	1	0	0	0	0	0	0	1	0	2142	1449	50	2	722	2	C22orf28	22	32792236	Splice_Site	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3098417	32792236	18512330	483	20022										
KCTD17	79734	hgsc.bcm.edu	37	chr22	37449146	37449146	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cctcacctccataggatgagAccggggcctacctcattgac	9	15	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:37449146A>G	ENST00000403888.3	+	2	218	c.217A>G	c.(217-219)Acc>Gcc	p.T73A	KCTD17_ENST00000402077.3_Missense_Mutation_p.T73A|RN7SKP214_ENST00000364208.1_RNA	NM_001282684.1	NP_001269613.1	Q8N5Z5	KCD17_HUMAN	potassium channel tetramerization domain containing 17	73	BTB.				protein homooligomerization (GO:0051260)		identical protein binding (GO:0042802)			NS(1)|breast(1)|endometrium(1)|lung(1)|prostate(1)	5						ATAGGATGAGACCGGGGCCTA	0.612																																					p.T73A		Atlas-SNP	.											.	KCTD17	17	.	0			c.A217G						.						78	48	58					22																	37449146		2201	4297	6498	SO:0001583	missense	79734	exon2			GATGAGACCGGGG	BC025403	CCDS13940.2, CCDS74854.1, CCDS74855.1	22q12.3	2013-06-20	2013-06-20		ENSG00000100379	ENSG00000100379			25705	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 17"			12477932	Standard	XM_005261741		Approved	FLJ12242	uc011amv.2	Q8N5Z5	OTTHUMG00000150532	ENST00000403888.3:c.217A>G	chr22.hg19:g.37449146A>G	ENSP00000385096:p.Thr73Ala	85.0	0.0		125.0	5.0	NM_024681	B0QYA9|B0QYB0|O95517	Missense_Mutation	SNP	ENST00000403888.3	hg19		.	.	.	.	.	.	.	.	.	.	A	16.64	3.178637	0.57692	.	.	ENSG00000100379	ENST00000402077;ENST00000403888;ENST00000431531	T;T;T	0.76709	-1.04;-1.04;-1.04	4.01	4.01	0.46588	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.49305	D	0.000160	T	0.75140	0.3809	M	0.72353	2.195	0.52099	D	0.999944	B;B;B;B	0.31879	0.344;0.011;0.113;0.004	B;B;B;B	0.35353	0.201;0.022;0.171;0.037	T	0.75230	-0.3391	10	0.49607	T	0.09	-4.8341	8.6704	0.34147	0.8299:0.0:0.0:0.1701	.	73;64;73;27	Q8N5Z5-2;E9PCZ8;Q8N5Z5;B0QYB1	.;.;KCD17_HUMAN;.	A	73;73;34	ENSP00000384391:T73A;ENSP00000385096:T73A;ENSP00000402434:T34A	ENSP00000384391:T73A	T	+	1	0	KCTD17	35779092	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	4.722000	0.61958	1.674000	0.50907	0.482000	0.46254	ACC	.	.		0.612	KCTD17-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318781.1	NM_024681		G	37449146	A	G	37449146	3	3	115	1	0	0	0	0	1	0	0	0	8113	275	10	2	223	2	KCTD17	22	37449146	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	4656910	37449146	13855420	484	20023										
RAC2	5880	hgsc.bcm.edu	37	chr22	37622734	37622734	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tagaggaggctgcaggcgcgCttctgctgccgcgtgggctg	18	11	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:37622734C>T	ENST00000249071.6	-	6	679	c.558G>A	c.(556-558)aaG>aaA	p.K186K	RAC2_ENST00000406508.1_Silent_p.K142K|RAC2_ENST00000405484.1_Silent_p.K179K	NM_002872.3	NP_002863.1	P15153	RAC2_HUMAN	ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)	186					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|cell projection assembly (GO:0030031)|G-protein coupled receptor signaling pathway (GO:0007186)|lymphocyte aggregation (GO:0071593)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neutrophil chemotaxis (GO:0090023)|regulation of cell-substrate adhesion (GO:0010810)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of neutrophil migration (GO:1902622)|regulation of respiratory burst (GO:0060263)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)	12					Dextromethorphan(DB00514)	TGCAGGCGCGCTTCTGCTGCC	0.627																																					p.K186K		Atlas-SNP	.											.	RAC2	22	.	0			c.G558A						.						49	51	50					22																	37622734		2203	4299	6502	SO:0001819	synonymous_variant	5880	exon6			GGCGCGCTTCTGC	M64595	CCDS13945.1	22q13.1	2014-09-17			ENSG00000128340	ENSG00000128340		"Endogenous ligands"	9802	protein-coding gene	gene with protein product		602049				2674130	Standard	NM_002872		Approved	EN-7	uc003arc.3	P15153	OTTHUMG00000150540	ENST00000249071.6:c.558G>A	chr22.hg19:g.37622734C>T		55.0	0.0		70.0	24.0	NM_002872	Q9UDJ4	Silent	SNP	ENST00000249071.6	hg19	CCDS13945.1																																																																																			.	.		0.627	RAC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318812.1			T	37622734	C	T	37622734	2	4	115	1	0	0	0	0	0	0	0	1	12990	796	28	3		3	RAC2	22	37622734	Silent	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	173588	37622734	13681832	485	20024										
GCAT	23464	hgsc.bcm.edu	37	chr22	38208955	38208955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccagcgggaggatgccatccTctatcccagctgttatgacg	11	13	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:38208955T>C	ENST00000248924.6	+	3	445	c.389T>C	c.(388-390)cTc>cCc	p.L130P	GCAT_ENST00000323205.6_Missense_Mutation_p.L156P|GCAT_ENST00000415371.1_3'UTR	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	130					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	GATGCCATCCTCTATCCCAGC	0.552																																					p.L156P		Atlas-SNP	.											.	GCAT	27	.	0			c.T467C						.						92	83	86					22																	38208955		2203	4300	6503	SO:0001583	missense	23464	exon3			CCATCCTCTATCC	AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"2-amino-3-ketobutyrate coenzyme A ligase"	607422	"glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.389T>C	chr22.hg19:g.38208955T>C	ENSP00000248924:p.Leu130Pro	77.0	0.0		95.0	5.0	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Missense_Mutation	SNP	ENST00000248924.6	hg19	CCDS13957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.6|23.6	4.433902|4.433902	0.83776|0.83776	.|.	.|.	ENSG00000100116|ENSG00000100116	ENST00000323205;ENST00000248924;ENST00000445195;ENST00000394944|ENST00000451984	D;D;D|.	0.91945|.	-2.94;-2.94;-2.94|.	5.58|5.58	5.58|5.58	0.84498|0.84498	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.90745|0.90745	0.7095|0.7095	H|H	0.99011|0.99011	4.4|4.4	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.94428|0.94428	0.7647|0.7647	10|5	0.87932|.	D|.	0|.	-27.9058|-27.9058	15.742|15.742	0.77905|0.77905	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	156;130|.	E2QC23;O75600|.	.;KBL_HUMAN|.	P|P	156;130;156;156|115	ENSP00000371110:L156P;ENSP00000248924:L130P;ENSP00000406719:L156P|.	ENSP00000248924:L130P|.	L|S	+|+	2|1	0|0	GCAT|GCAT	36538901|36538901	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.835000|0.835000	0.47333|0.47333	7.359000|7.359000	0.79477|0.79477	2.137000|2.137000	0.66172|0.66172	0.533000|0.533000	0.62120|0.62120	CTC|TCT	.	.		0.552	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2		C	38208955	T	C	38208955	3	2	115	1	0	0	0	0	1	0	0	0	6292	1551	54	2	477	2	GCAT	22	38208955	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	586221	38208955	13095611	486	20025										
TNRC6B	23112	hgsc.bcm.edu	37	chr22	40708594	40708594	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	accccaggaagtgtgctgggGggtacagccacatctcccat	12	13	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:40708594G>T	ENST00000454349.2	+	18	4732	c.4521G>T	c.(4519-4521)ggG>ggT	p.G1507G	TNRC6B_ENST00000301923.9_Silent_p.G703G|TNRC6B_ENST00000402203.1_Silent_p.G703G|TNRC6B_ENST00000335727.9_Silent_p.G1397G	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	1507	Silencing domain; interaction with CNOT1 and PAN3.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						GTGTGCTGGGGGGTACAGCCA	0.488																																					p.G1507G		Atlas-SNP	.											.	TNRC6B	195	.	0			c.G4521T						.						126	124	125					22																	40708594		2014	4191	6205	SO:0001819	synonymous_variant	23112	exon18			GCTGGGGGGTACA	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.4521G>T	chr22.hg19:g.40708594G>T		123.0	0.0		116.0	46.0	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Silent	SNP	ENST00000454349.2	hg19	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	G	9.640	1.138665	0.21123	.	.	ENSG00000100354	ENST00000446273	T	0.15256	2.44	5.16	1.97	0.26223	.	0.000000	0.85682	D	0.000000	T	0.27098	0.0664	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01889	-1.1253	7	0.52906	T	0.07	-0.7393	9.7368	0.40392	0.2229:0.0:0.7771:0.0	.	.	.	.	V	1193	ENSP00000409429:G1193V	ENSP00000409429:G1193V	G	+	2	0	TNRC6B	39038540	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.372000	0.44257	0.580000	0.29522	0.655000	0.94253	GGG	.	.		0.488	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				T	40708594	G	T	40708594	2	4	115	1	0	0	0	0	0	0	0	1	16356	1219	43	3		3	TNRC6B	22	40708594	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	2499639	40708594	10595972	487	20026										
PPPDE2	27351	hgsc.bcm.edu	37	chr22	42003333	42003333	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgtgcacaactatggatgtgTgcctgtcacacagagagaga	12	8	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:42003333T>C	ENST00000263256.6	-	3	369	c.113A>G	c.(112-114)cAc>cGc	p.H38R		NM_015704.2	NP_056519.1	Q6ICB0	DESI1_HUMAN	desumoylating isopeptidase 1	38	PPPDE peptidase.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)										TATGGATGTGTGCCTGTCACA	0.473																																					p.H38R		Atlas-SNP	.											.	.	.	.	0			c.A113G						.						75	58	64					22																	42003333		2203	4300	6503	SO:0001583	missense	27351	exon3			GATGTGTGCCTGT	AF038183	CCDS33652.1	22q13.2	2012-05-16	2012-05-16	2012-05-16	ENSG00000100418	ENSG00000100418			24577	protein-coding gene	gene with protein product		614637	"family with sequence similarity 152, member B", "PPPDE peptidase domain containing 2"	FAM152B, PPPDE2		8619474, 9110174, 22370726	Standard	NM_015704		Approved	D15Wsu75e	uc003bam.2	Q6ICB0	OTTHUMG00000044632	ENST00000263256.6:c.113A>G	chr22.hg19:g.42003333T>C	ENSP00000263256:p.His38Arg	56.0	0.0		86.0	5.0	NM_015704		Missense_Mutation	SNP	ENST00000263256.6	hg19	CCDS33652.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.912565	0.92178	.	.	ENSG00000100418	ENST00000263256	.	.	.	5.98	5.98	0.97165	Domain of unknown function DUF862, eukaryotic (1);	0.152394	0.64402	D	0.000013	D	0.88581	0.6475	H	0.97214	3.96	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92476	0.5989	9	0.87932	D	0	-25.5249	16.4728	0.84119	0.0:0.0:0.0:1.0	.	38	Q6ICB0	PPDE2_HUMAN	R	38	.	ENSP00000263256:H38R	H	-	2	0	PPPDE2	40333279	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.040000	0.89188	2.296000	0.77279	0.482000	0.46254	CAC	.	.		0.473	DESI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000104124.3	NM_015704		C	42003333	T	C	42003333	3	2	115	1	0	0	0	0	1	0	0	0	12421	1696	59	2	409	2	PPPDE2	22	42003333	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1294739	42003333	9301233	488	20027										
PACSIN2	11252	hgsc.bcm.edu	37	chr22	43284655	43284655	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agtgtacagtttaccttaagAacatcttgcttgcacttttc	6	9	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:43284655A>C	ENST00000263246.3	-	5	804	c.603T>G	c.(601-603)gtT>gtG	p.V201V	PACSIN2_ENST00000402229.1_Silent_p.V201V|PACSIN2_ENST00000407585.1_Silent_p.V201V|PACSIN2_ENST00000403744.3_Silent_p.V201V|PACSIN2_ENST00000337959.4_Silent_p.V201V	NM_001184970.1	NP_001171899.1	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in neurons 2	201	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cell projection morphogenesis (GO:0048858)|membrane tubulation (GO:0097320)|negative regulation of endocytosis (GO:0045806)|protein localization to endosome (GO:0036010)	caveola (GO:0005901)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	19		Glioma(61;0.222)				TTACCTTAAGAACATCTTGCT	0.453																																					p.V201V		Atlas-SNP	.											.	PACSIN2	48	.	0			c.T603G						.						252	237	242					22																	43284655		2009	4158	6167	SO:0001819	synonymous_variant	11252	exon5			CTTAAGAACATCT	AF128536	CCDS43023.1, CCDS54536.1	22q13.2-q13.33	2009-05-08			ENSG00000100266	ENSG00000100266			8571	protein-coding gene	gene with protein product	"syndapin II"	604960				10431838, 11082044	Standard	NM_007229		Approved	SDPII	uc003bdg.4	Q9UNF0	OTTHUMG00000150701	ENST00000263246.3:c.603T>G	chr22.hg19:g.43284655A>C		201.0	0.0		235.0	103.0	NM_007229	O95921|Q96HV9|Q9H0D3|Q9NPN1|Q9Y4V2	Silent	SNP	ENST00000263246.3	hg19	CCDS43023.1																																																																																			.	.		0.453	PACSIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319665.1	NM_007229		C	43284655	A	C	43284655	2	2	115	1	0	0	0	0	0	0	0	1	11384	233	9	5		5	PACSIN2	22	43284655	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	1281322	43284655	8019911	489	20028										
MCAT	27349	hgsc.bcm.edu	37	chr22	43538972	43538972	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtttctcgacagcggccagcGatgccacgaagatcgcgggc	14	13	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:43538972G>A	ENST00000290429.6	-	1	428	c.383C>T	c.(382-384)tCg>tTg	p.S128L	MCAT_ENST00000327555.5_Missense_Mutation_p.S128L|MCAT_ENST00000464244.1_5'UTR	NM_173467.4	NP_775738.3	Q8IVS2	FABD_HUMAN	malonyl CoA:ACP acyltransferase (mitochondrial)	128					fatty acid biosynthetic process (GO:0006633)|metabolic process (GO:0008152)	mitochondrion (GO:0005739)	[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)	p.S128L(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	11		Ovarian(80;0.0694)				AGCGGCCAGCGATGCCACGAA	0.682																																					p.S128L		Atlas-SNP	.											MCAT,bladder,carcinoma,0,1	MCAT	26	.	1	Substitution - Missense(1)	urinary_tract(1)	c.C383T						.						18	16	17					22																	43538972		2200	4299	6499	SO:0001583	missense	27349	exon1			GCCAGCGATGCCA	AL359401	CCDS14045.1, CCDS33660.1	22q13.2	2010-04-27			ENSG00000100294	ENSG00000100294	2.3.1.39		29622	protein-coding gene	gene with protein product		614479				12882974	Standard	NM_173467		Approved	MT, MCT, fabD, FASN2C, NET62	uc003bdl.1	Q8IVS2	OTTHUMG00000150704	ENST00000290429.6:c.383C>T	chr22.hg19:g.43538972G>A	ENSP00000290429:p.Ser128Leu	136.0	0.0		197.0	70.0	NM_014507	B0QY72|O95510|O95511	Missense_Mutation	SNP	ENST00000290429.6	hg19	CCDS33660.1	.	.	.	.	.	.	.	.	.	.	G	32	5.190008	0.94923	.	.	ENSG00000100294	ENST00000327555;ENST00000290429	T;T	0.42513	0.97;0.97	4.6	4.6	0.57074	Acyl transferase/acyl hydrolase/lysophospholipase (1);Acyl transferase (1);Acyl transferase domain (1);	0.000000	0.85682	D	0.000000	T	0.76772	0.4034	H	0.96970	3.915	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.85868	0.1414	10	0.87932	D	0	-35.372	17.6259	0.88093	0.0:0.0:1.0:0.0	.	128;128	B0QY72;Q8IVS2	.;FABD_HUMAN	L	128	ENSP00000331306:S128L;ENSP00000290429:S128L	ENSP00000290429:S128L	S	-	2	0	MCAT	41868916	1.000000	0.71417	0.977000	0.42913	0.603000	0.37013	7.895000	0.87343	2.394000	0.81467	0.467000	0.42956	TCG	.	.		0.682	MCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319677.2	NM_173467		A	43538972	G	A	43538972	3	1	115	1	0	0	0	0	1	0	0	0	9381	1059	37	1	805	1	MCAT	22	43538972	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	254317	43538972	7765594	490	20029										
SCUBE1	80274	hgsc.bcm.edu	37	chr22	43614330	43614330	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctccagcgccttggctggccTctgggctacctcgtactcag	11	16	2	0	rs34722413		TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:43614330T>C	ENST00000360835.4	-	15	1948	c.1822A>G	c.(1822-1824)Agg>Ggg	p.R608G		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	608					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				TTGGCTGGCCTCTGGGCTACC	0.632																																					p.R608G		Atlas-SNP	.											.	SCUBE1	105	.	0			c.A1822G						.						97	97	97					22																	43614330		2203	4300	6503	SO:0001583	missense	80274	exon15			CTGGCCTCTGGGC		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.1822A>G	chr22.hg19:g.43614330T>C	ENSP00000354080:p.Arg608Gly	89.0	0.0		146.0	6.0	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	hg19	CCDS14048.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.433707	0.43224	.	.	ENSG00000159307	ENST00000360835;ENST00000381243	D	0.85339	-1.97	4.29	-1.18	0.09617	.	0.580008	0.18197	N	0.148642	T	0.77485	0.4137	L	0.50333	1.59	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.68021	-0.5519	10	0.87932	D	0	.	7.5505	0.27793	0.1022:0.0:0.2212:0.6767	.	608	Q8IWY4	SCUB1_HUMAN	G	608;238	ENSP00000354080:R608G	ENSP00000354080:R608G	R	-	1	2	SCUBE1	41944274	1.000000	0.71417	0.993000	0.49108	0.947000	0.59692	1.207000	0.32333	0.032000	0.15435	-0.459000	0.05422	AGG	.	.		0.632	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050		C	43614330	T	C	43614330	3	2	115	1	0	0	0	0	1	0	0	0	13959	1550	54	2	1176	2	SCUBE1	22	43614330	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	75358	43614330	7690236	491	20030										
FAM116B	414918	hgsc.bcm.edu	37	chr22	50752089	50752089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggatgatgaagctctgggtgAgctccaggaggtgccgccgc	17	10	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chr22:50752089A>G	ENST00000413817.3	-	15	1339	c.1268T>C	c.(1267-1269)cTc>cCc	p.L423P	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	423					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										GCTCTGGGTGAGCTCCAGGAG	0.716																																					p.L423P		Atlas-SNP	.											.	.	.	.	0			c.T1268C						.						10	12	11					22																	50752089		1926	4107	6033	SO:0001583	missense	414918	exon15			TGGGTGAGCTCCA	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"DENN/MADD domain containing"	32690	protein-coding gene	gene with protein product			"family with sequence similarity 116, member B"	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.1268T>C	chr22.hg19:g.50752089A>G	ENSP00000391524:p.Leu423Pro	55.0	0.0		65.0	5.0	NM_001001794	A6X8I5	Missense_Mutation	SNP	ENST00000413817.3	hg19	CCDS46732.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.977222	0.74360	.	.	ENSG00000205593	ENST00000413817	.	.	.	4.82	4.82	0.62117	.	0.212047	0.41605	D	0.000848	T	0.76198	0.3954	M	0.84082	2.675	0.80722	D	1	D;D	0.63880	0.993;0.993	P;P	0.58721	0.844;0.844	T	0.80580	-0.1319	9	0.87932	D	0	-32.2663	12.3145	0.54948	1.0:0.0:0.0:0.0	.	423;423	Q8NEG7;C9JIV6	F116B_HUMAN;.	P	423	.	ENSP00000391524:L423P	L	-	2	0	FAM116B	49094661	1.000000	0.71417	0.998000	0.56505	0.892000	0.51952	6.255000	0.72466	1.793000	0.52555	0.379000	0.24179	CTC	.	.		0.716	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794		G	50752089	A	G	50752089	3	3	115	1	0	0	0	0	1	0	0	0	5413	304	11	2	513	2	FAM116B	22	50752089	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	7137759	50752089	552477	492	20031										
STS	412	hgsc.bcm.edu	37	chrX	7268085	7268085	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttccaaagatcccagagagaGaaacccactaactccagcat	6	13	0	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:7268085G>A	ENST00000217961.4	+	10	1755	c.1535G>A	c.(1534-1536)aGa>aAa	p.R512K		NM_000351.4	NP_000342.2	P08842	STS_HUMAN	steroid sulfatase (microsomal), isozyme S	512					cellular protein metabolic process (GO:0044267)|epidermis development (GO:0008544)|female pregnancy (GO:0007565)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|steroid catabolic process (GO:0006706)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|steryl-sulfatase activity (GO:0004773)|sulfuric ester hydrolase activity (GO:0008484)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(1)	27		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Norelgestromin(DB06713)	CCCAGAGAGAGAAACCCACTA	0.517									Ichthyosis																												p.R512K		Atlas-SNP	.											.	STS	64	.	0			c.G1535A						.						71	61	65					X																	7268085		2203	4299	6502	SO:0001583	missense	412	exon10	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GAGAGAGAAACCC	M16505	CCDS14127.1	Xp22.32	2013-06-10	2007-07-19		ENSG00000101846	ENSG00000101846	3.1.6.2	"Arylsulfatase family"	11425	protein-coding gene	gene with protein product	"arylsulfatase C"	300747	"steroid sulfatase (microsomal), arylsulfatase C, isozyme S"	ARSC1			Standard	NM_000351		Approved	ARSC	uc004cry.4	P08842	OTTHUMG00000021102	ENST00000217961.4:c.1535G>A	chrX.hg19:g.7268085G>A	ENSP00000217961:p.Arg512Lys	43.0	0.0		67.0	6.0	NM_000351	B2RA47	Missense_Mutation	SNP	ENST00000217961.4	hg19	CCDS14127.1	.	.	.	.	.	.	.	.	.	.	G	3.707	-0.060332	0.07317	.	.	ENSG00000101846	ENST00000217961	D	0.88896	-2.44	4.22	1.34	0.21922	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.531849	0.19903	N	0.103469	T	0.70474	0.3228	N	0.12502	0.225	0.09310	N	0.999996	B	0.02656	0.0	B	0.04013	0.001	T	0.54397	-0.8300	10	0.06891	T	0.86	.	3.1784	0.06576	0.4155:0.209:0.3755:0.0	.	512	P08842	STS_HUMAN	K	512	ENSP00000217961:R512K	ENSP00000217961:R512K	R	+	2	0	STS	7278085	0.026000	0.19158	0.009000	0.14445	0.018000	0.09664	0.142000	0.16096	0.143000	0.18926	0.600000	0.82982	AGA	.	.		0.517	STS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055686.1	NM_000351		A	7268085	G	A	7268085	3	1	115	1	0	0	0	0	1	0	0	0	15347	942	33	3	1573	3	STS	23	7268085	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10		7268085	148002475	493	20032										
ARHGAP6	395	hgsc.bcm.edu	37	chrX	11682867	11682867	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctggcgcagcttcctcttggAgaagcccttggccgaggccg	14	14	1	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:11682867A>G	ENST00000337414.4	-	1	954	c.82T>C	c.(82-84)Tcc>Ccc	p.S28P	ARHGAP6_ENST00000380718.1_Missense_Mutation_p.S28P|ARHGAP6_ENST00000380732.3_Missense_Mutation_p.S28P	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	28					actin filament polymerization (GO:0030041)|activation of phospholipase C activity (GO:0007202)|focal adhesion assembly (GO:0048041)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of signal transduction (GO:0009967)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TTCCTCTTGGAGAAGCCCTTG	0.721																																					p.S28P		Atlas-SNP	.											.	ARHGAP6	130	.	0			c.T82C						.						6	8	7					X																	11682867		1808	3559	5367	SO:0001583	missense	395	exon1			TCTTGGAGAAGCC	AF012272	CCDS14140.1, CCDS14141.1, CCDS14142.1	Xp22.3	2008-02-05			ENSG00000047648	ENSG00000047648		"Rho GTPase activating proteins"	676	protein-coding gene	gene with protein product		300118				9417914	Standard	XM_005274507		Approved	rhoGAPX-1	uc004cup.1	O43182	OTTHUMG00000021134	ENST00000337414.4:c.82T>C	chrX.hg19:g.11682867A>G	ENSP00000338967:p.Ser28Pro	50.0	0.0		70.0	4.0	NM_006125	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	hg19	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	A	16.10	3.026337	0.54683	.	.	ENSG00000047648	ENST00000337414;ENST00000380718;ENST00000380732	T;T;T	0.35421	1.75;1.61;1.31	4.29	4.29	0.51040	.	.	.	.	.	T	0.37348	0.1000	N	0.24115	0.695	0.80722	D	1	D;D	0.65815	0.982;0.995	P;P	0.56278	0.764;0.795	T	0.24693	-1.0153	9	0.66056	D	0.02	.	10.4807	0.44691	1.0:0.0:0.0:0.0	.	28;28	O43182-2;O43182	.;RHG06_HUMAN	P	28	ENSP00000338967:S28P;ENSP00000370094:S28P;ENSP00000370108:S28P	ENSP00000338967:S28P	S	-	1	0	ARHGAP6	11592788	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.281000	0.65609	1.596000	0.50062	0.481000	0.45027	TCC	.	.		0.721	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427		G	11682867	A	G	11682867	3	3	115	1	0	0	0	0	1	0	0	0	887	304	11	2	3016	2	ARHGAP6	23	11682867	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	4414782	11682867	143587693	494	20033										
EGFL6	25975	hgsc.bcm.edu	37	chrX	13624532	13624532	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcctctggtaaagtcatctgTccctacaatcgaagatgtgt	9	10	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:13624532T>C	ENST00000361306.1	+	6	812	c.555T>C	c.(553-555)tgT>tgC	p.C185C	EGFL6_ENST00000380602.3_Silent_p.C185C	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	185	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						AAGTCATCTGTCCCTACAATC	0.418																																					p.C185C		Atlas-SNP	.											.	EGFL6	111	.	0			c.T555C						.						208	166	180					X																	13624532		2203	4300	6503	SO:0001819	synonymous_variant	25975	exon6			CATCTGTCCCTAC	AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"MAM and EGF domain containing"	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.555T>C	chrX.hg19:g.13624532T>C		95.0	0.0		88.0	5.0	NM_001167890	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Silent	SNP	ENST00000361306.1	hg19	CCDS14155.1																																																																																			.	.		0.418	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507		C	13624532	T	C	13624532	2	2	115	1	0	0	0	0	0	0	0	1	4965	1673	58	2		2	EGFL6	23	13624532	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1941665	13624532	141646028	495	20034										
RBBP7	5931	hgsc.bcm.edu	37	chrX	16876872	16876872	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtttttgtagcaatgatgtgAggattctgcggcatgtaacg	13	5	1	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:16876872A>G	ENST00000380087.2	-	4	768	c.408T>C	c.(406-408)ccT>ccC	p.P136P	RBBP7_ENST00000404022.1_Silent_p.P127P|RBBP7_ENST00000380084.4_Silent_p.P180P			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7	136					cell proliferation (GO:0008283)|cellular heat acclimation (GO:0070370)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	RNA binding (GO:0003723)			biliary_tract(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	25	Hepatocellular(33;0.0997)					CAATGATGTGAGGATTCTGCG	0.368																																					p.P180P		Atlas-SNP	.											.	RBBP7	58	.	0			c.T540C						.						255	206	222					X																	16876872		2203	4300	6503	SO:0001819	synonymous_variant	5931	exon4			GATGTGAGGATTC	U35143	CCDS14179.1, CCDS56598.1	Xp22.22	2013-01-10	2001-11-28		ENSG00000102054	ENSG00000102054		"WD repeat domain containing"	9890	protein-coding gene	gene with protein product	"G1/S transition control protein-binding protein RbAp46", "retinoblastoma-binding protein 7", "retinoblastoma-binding protein RbAp46", "histone acetyltransferase type B subunit 2", "retinoblastoma-binding protein p46"	300825	"retinoblastoma-binding protein 7"			7503932	Standard	NM_002893		Approved	RbAp46	uc004cxs.2	Q16576	OTTHUMG00000021198	ENST00000380087.2:c.408T>C	chrX.hg19:g.16876872A>G		81.0	0.0		86.0	4.0	NM_001198719	Q5JP00	Silent	SNP	ENST00000380087.2	hg19	CCDS14179.1																																																																																			.	.		0.368	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893		G	16876872	A	G	16876872	2	3	115	1	0	0	0	0	0	0	0	1	13119	291	11	2		2	RBBP7	23	16876872	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	3252340	16876872	138393688	496	20035										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23411617	23411617	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggaaacaaacagagaagaacTctatgatctcttggaaaccc	8	9	2	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:23411617T>C	ENST00000379361.4	+	3	2842	c.1982T>C	c.(1981-1983)cTc>cCc	p.L661P		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	661					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						AGAGAAGAACTCTATGATCTC	0.438																																					p.L661P		Atlas-SNP	.											.	PTCHD1	213	.	0			c.T1982C						.						72	68	69					X																	23411617		2203	4300	6503	SO:0001583	missense	139411	exon3			AAGAACTCTATGA	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.1982T>C	chrX.hg19:g.23411617T>C	ENSP00000368666:p.Leu661Pro	86.0	0.0		94.0	6.0	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	hg19	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	T	16.20	3.055954	0.55325	.	.	ENSG00000165186	ENST00000379361	D	0.85861	-2.04	5.48	5.48	0.80851	.	0.058057	0.64402	D	0.000001	D	0.82641	0.5081	N	0.14661	0.345	0.80722	D	1	D	0.55800	0.973	P	0.56163	0.793	D	0.83714	0.0189	10	0.39692	T	0.17	.	14.5487	0.68050	0.0:0.0:0.0:1.0	.	661	Q96NR3	PTHD1_HUMAN	P	661	ENSP00000368666:L661P	ENSP00000368666:L661P	L	+	2	0	PTCHD1	23321538	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.694000	0.84235	1.816000	0.52996	0.486000	0.48141	CTC	.	.		0.438	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		C	23411617	T	C	23411617	3	2	115	1	0	0	0	0	1	0	0	0	12744	1551	54	2	1992	2	PTCHD1	23	23411617	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	6534745	23411617	131858943	497	20036										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37026590	37026590	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttcgcgaagcgcaagcacaGgcgcctgaggttcccgcctg	13	15	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:37026590G>A	ENST00000358047.3	+	1	159	c.107G>A	c.(106-108)aGg>aAg	p.R36K		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	36										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						CGCAAGCACAGGCGCCTGAGG	0.617																																					p.R36K		Atlas-SNP	.											.	FAM47C	267	.	0			c.G107A						.						27	26	27					X																	37026590		2202	4296	6498	SO:0001583	missense	442444	exon1			AGCACAGGCGCCT	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.107G>A	chrX.hg19:g.37026590G>A	ENSP00000367913:p.Arg36Lys	281.0	0.0		313.0	218.0	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	hg19	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	G	10.99	1.506146	0.26949	.	.	ENSG00000198173	ENST00000358047	T	0.19394	2.15	0.462	-0.569	0.11756	.	.	.	.	.	T	0.16128	0.0388	L	0.56769	1.78	0.09310	N	1	B	0.28783	0.222	B	0.27170	0.077	T	0.35895	-0.9770	8	0.15066	T	0.55	.	.	.	.	.	36	Q5HY64	FA47C_HUMAN	K	36	ENSP00000367913:R36K	ENSP00000367913:R36K	R	+	2	0	FAM47C	36936511	0.000000	0.05858	0.009000	0.14445	0.050000	0.14768	0.040000	0.13905	-0.369000	0.08028	0.287000	0.19450	AGG	.	.		0.617	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		A	37026590	G	A	37026590	3	1	115	1	0	0	0	0	1	0	0	0	5579	1000	35	3	109	3	FAM47C	23	37026590	Missense_Mutation	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	13614973	37026590	118243970	498	20037										
TSPYL2	64061	hgsc.bcm.edu	37	chrX	53115071	53115071	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	actgataacaacgagagtgcTgatgaccacgaaaccactga	9	10	0	5			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:53115071T>C	ENST00000375442.4	+	6	1629	c.1497T>C	c.(1495-1497)gcT>gcC	p.A499A		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	499	Asn-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						acgagagtgctgatgaccacg	0.448																																					p.A499A		Atlas-SNP	.											.	TSPYL2	53	.	0			c.T1497C						.						240	173	196					X																	53115071		2203	4300	6503	SO:0001819	synonymous_variant	64061	exon6			GAGTGCTGATGAC	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.1497T>C	chrX.hg19:g.53115071T>C		78.0	0.0		76.0	4.0	NM_022117	O94799|Q96DG7|Q9BZW6	Silent	SNP	ENST00000375442.4	hg19	CCDS14350.1																																																																																			.	.		0.448	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		C	53115071	T	C	53115071	2	2	115	1	0	0	0	0	0	0	0	1	16675	1567	55	2		2	TSPYL2	23	53115071	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	16088481	53115071	102155489	499	20038										
KDM5C	8242	hgsc.bcm.edu	37	chrX	53228324	53228324	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gcagctcgaaagcctctcgcTcagcctctgtgataccctaa	8	15	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:53228324T>C	ENST00000375401.3	-	15	2610	c.2078A>G	c.(2077-2079)gAg>gGg	p.E693G	KDM5C_ENST00000404049.3_Missense_Mutation_p.E692G|KDM5C_ENST00000465402.1_5'Flank|KDM5C_ENST00000375383.3_Missense_Mutation_p.E652G|KDM5C_ENST00000452825.3_Missense_Mutation_p.E626G|KDM5C_ENST00000375379.3_Missense_Mutation_p.E693G	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	693					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						AGCCTCTCGCTCAGCCTCTGT	0.522			"N, F, S"		clear cell renal carcinoma																																p.E693G		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.A2078G						.						134	113	120					X																	53228324		2203	4300	6503	SO:0001583	missense	8242	exon15			TCTCGCTCAGCCT	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11114	protein-coding gene	gene with protein product		314690	"Jumonji, AT rich interactive domain 1C (RBP2-like)", "Smcy homolog, X-linked (mouse)", "jumonji, AT rich interactive domain 1C", "mental retardation, X-linked 13"	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.2078A>G	chrX.hg19:g.53228324T>C	ENSP00000364550:p.Glu693Gly	101.0	0.0		123.0	6.0	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	hg19	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	t	21.9	4.223376	0.79464	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	D;D;D;D;D	0.87887	-2.31;-2.02;-2.02;-2.02;-2.16	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	D	0.91533	0.7326	M	0.81942	2.565	0.58432	D	0.999997	P;D;D	0.55385	0.735;0.971;0.971	P;P;P	0.58172	0.549;0.834;0.834	D	0.92260	0.5816	10	0.87932	D	0	-6.9073	11.2689	0.49127	0.0:0.0:0.0:1.0	.	626;692;693	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	G	626;693;692;693;652	ENSP00000445176:E626G;ENSP00000364550:E693G;ENSP00000385394:E692G;ENSP00000364528:E693G;ENSP00000364532:E652G	ENSP00000364528:E693G	E	-	2	0	KDM5C	53245049	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.899000	0.87370	1.556000	0.49512	0.422000	0.28245	GAG	.	.		0.522	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		C	53228324	T	C	53228324	3	2	115	1	0	0	0	0	1	0	0	0	8144	1551	54	2	2750	2	KDM5C	23	53228324	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	113253	53228324	102042236	500	20039										
TEX11	56159	hgsc.bcm.edu	37	chrX	69964030	69964030	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	cttaccagcatttctggcccAgtagatttcttatccatctt	5	12	3	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:69964030A>G	ENST00000395889.2	-	11	932	c.777T>C	c.(775-777)acT>acC	p.T259T	TEX11_ENST00000344304.3_Silent_p.T259T|TEX11_ENST00000374333.2_Silent_p.T244T	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	259					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					TTTCTGGCCCAGTAGATTTCT	0.269																																					p.T259T		Atlas-SNP	.											.	TEX11	132	.	0			c.T777C						.						45	39	41					X																	69964030		2203	4289	6492	SO:0001819	synonymous_variant	56159	exon11			TGGCCCAGTAGAT	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.777T>C	chrX.hg19:g.69964030A>G		108.0	0.0		99.0	6.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Silent	SNP	ENST00000395889.2	hg19	CCDS35323.1																																																																																			.	.		0.269	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			G	69964030	A	G	69964030	2	3	115	1	0	0	0	0	0	0	0	1	15789	175	7	2		2	TEX11	23	69964030	Silent	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	16735706	69964030	85306530	501	20040										
ATP7A	538	hgsc.bcm.edu	37	chrX	77284804	77284804	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tacgatttgctttccaagccTctatcacagttctgtgtatt	6	10	3	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:77284804T>C	ENST00000341514.6	+	15	3129	c.2974T>C	c.(2974-2976)Tct>Cct	p.S992P	ATP7A_ENST00000343533.5_Missense_Mutation_p.S914P|ATP7A_ENST00000350425.4_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	992					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TTTCCAAGCCTCTATCACAGT	0.433																																					p.S992P		Atlas-SNP	.											.	ATP7A	248	.	0			c.T2974C						.						192	178	182					X																	77284804		2203	4296	6499	SO:0001583	missense	538	exon15			CAAGCCTCTATCA	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.2974T>C	chrX.hg19:g.77284804T>C	ENSP00000345728:p.Ser992Pro	84.0	0.0		106.0	5.0	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	hg19	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.157467	0.78114	.	.	ENSG00000165240	ENST00000343533;ENST00000341514	D;D	0.89415	-2.51;-2.51	6.06	4.88	0.63580	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.93638	0.7968	M	0.81682	2.555	0.80722	D	1	D	0.54397	0.966	D	0.68943	0.961	D	0.92926	0.6359	10	0.54805	T	0.06	15.81	11.3265	0.49452	0.0:0.0:0.2853:0.7146	.	992	Q04656	ATP7A_HUMAN	P	914;992	ENSP00000343026:S914P;ENSP00000345728:S992P	ENSP00000345728:S992P	S	+	1	0	ATP7A	77171460	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.395000	0.52558	0.857000	0.35407	0.481000	0.45027	TCT	.	.		0.433	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		C	77284804	T	C	77284804	3	2	115	1	0	0	0	0	1	0	0	0	1190	1551	54	2	3028	2	ATP7A	23	77284804	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	7320774	77284804	77985756	502	20041										
TBX22	50945	hgsc.bcm.edu	37	chrX	79282219	79282219	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ccagatcattctgcaatccaTgcataagtacaaaccccgag	6	13	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:79282219T>C	ENST00000373294.5	+	5	678	c.650T>C	c.(649-651)aTg>aCg	p.M217T	TBX22_ENST00000373291.1_Missense_Mutation_p.M97T|TBX22_ENST00000442340.1_Missense_Mutation_p.M97T|TBX22_ENST00000373296.3_Missense_Mutation_p.M217T	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	217					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						CTGCAATCCATGCATAAGTAC	0.483																																					p.M217T		Atlas-SNP	.											.	TBX22	118	.	0			c.T650C						.						148	121	130					X																	79282219		2203	4300	6503	SO:0001583	missense	50945	exon5			AATCCATGCATAA	AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"T-boxes"	11600	protein-coding gene	gene with protein product		300307	"cleft palate and/or ankyloglossia"	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.650T>C	chrX.hg19:g.79282219T>C	ENSP00000362390:p.Met217Thr	71.0	0.0		63.0	44.0	NM_016954	Q5JZ06|Q96LC0|Q9HBF1	Missense_Mutation	SNP	ENST00000373294.5	hg19	CCDS14445.1	.	.	.	.	.	.	.	.	.	.	T	17.24	3.338130	0.60963	.	.	ENSG00000122145	ENST00000373296;ENST00000442340;ENST00000373294;ENST00000373291	D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5	3.88	3.88	0.44766	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95900	0.8665	H	0.98027	4.13	0.80722	D	1	D	0.63046	0.992	D	0.66716	0.946	D	0.96018	0.9007	10	0.87932	D	0	.	9.9835	0.41828	0.0:0.0:0.0:1.0	.	217	Q9Y458	TBX22_HUMAN	T	217;97;217;97	ENSP00000362393:M217T;ENSP00000396394:M97T;ENSP00000362390:M217T;ENSP00000362388:M97T	ENSP00000362388:M97T	M	+	2	0	TBX22	79168875	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.012000	0.76366	1.547000	0.49401	0.486000	0.48141	ATG	.	.		0.483	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954		C	79282219	T	C	79282219	3	2	115	1	0	0	0	0	1	0	0	0	15673	1464	51	2	668	2	TBX22	23	79282219	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	1997415	79282219	75988341	503	20042										
FAM46D	169966	hgsc.bcm.edu	37	chrX	79699173	79699173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttagcttccagccataccacCcactgcactttcgtggatca	6	15	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:79699173C>T	ENST00000308293.5	+	3	1374	c.1135C>T	c.(1135-1137)Cca>Tca	p.P379S	FAM46D_ENST00000538312.1_Missense_Mutation_p.P379S	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	379										kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						GCCATACCACCCACTGCACTT	0.408																																					p.P379S		Atlas-SNP	.											.	FAM46D	69	.	0			c.C1135T						.						36	35	35					X																	79699173		2203	4298	6501	SO:0001583	missense	169966	exon5			TACCACCCACTGC	BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"cancer/testis antigen 112"					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.1135C>T	chrX.hg19:g.79699173C>T	ENSP00000308575:p.Pro379Ser	44.0	0.0		33.0	5.0	NM_001170574	B2R9Q6|Q7Z3F6|Q8NHU1	Missense_Mutation	SNP	ENST00000308293.5	hg19	CCDS14446.1	.	.	.	.	.	.	.	.	.	.	C	2.958	-0.215187	0.06101	.	.	ENSG00000174016	ENST00000538312;ENST00000308293	T;T	0.23348	1.91;1.91	5.21	2.38	0.29361	.	0.331275	0.28393	N	0.015516	T	0.20861	0.0502	L	0.48877	1.53	0.09310	N	0.999994	B	0.17038	0.02	B	0.17979	0.02	T	0.19257	-1.0311	10	0.54805	T	0.06	-0.0106	7.3091	0.26465	0.315:0.5095:0.1755:0.0	.	379	Q8NEK8	FA46D_HUMAN	S	379	ENSP00000443410:P379S;ENSP00000308575:P379S	ENSP00000308575:P379S	P	+	1	0	FAM46D	79585829	0.032000	0.19561	0.002000	0.10522	0.003000	0.03518	0.676000	0.25247	0.065000	0.16485	0.594000	0.82650	CCA	.	.		0.408	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630		T	79699173	C	T	79699173	3	4	115	1	0	0	0	0	1	0	0	0	5576	623	22	3	1137	3	FAM46D	23	79699173	Missense_Mutation	SNP	C	TCGA-DD-A3A1-01A-11D-A20W-10	416954	79699173	75571387	504	20043										
BRWD3	254065	hgsc.bcm.edu	37	chrX	79947359	79947359	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ttgatgccctgaataacccgTtcacattcttcgtctctgga	7	12	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:79947359T>C	ENST00000373275.4	-	30	3660	c.3444A>G	c.(3442-3444)gaA>gaG	p.E1148E	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1148					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						GAATAACCCGTTCACATTCTT	0.463																																					p.E1148E		Atlas-SNP	.											.	BRWD3	251	.	0			c.A3444G						.						99	81	87					X																	79947359		2203	4300	6503	SO:0001819	synonymous_variant	254065	exon30			AACCCGTTCACAT		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.3444A>G	chrX.hg19:g.79947359T>C		76.0	0.0		87.0	5.0	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Silent	SNP	ENST00000373275.4	hg19	CCDS14447.1																																																																																			.	.		0.463	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		C	79947359	T	C	79947359	2	2	115	1	0	0	0	0	0	0	0	1	1528	1722	60	2		2	BRWD3	23	79947359	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	248186	79947359	75323201	505	20044										
DIAPH2	1730	hgsc.bcm.edu	37	chrX	96167500	96167500	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aggcaagaaaatattgacaaGaagaatcagtataaacttat	7	4	1	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:96167500G>A	ENST00000324765.8	+	7	1028	c.681G>A	c.(679-681)aaG>aaA	p.K227K	DIAPH2_ENST00000373061.3_Silent_p.K227K|DIAPH2_ENST00000355827.4_Silent_p.K227K|DIAPH2_ENST00000373049.4_Silent_p.K227K|DIAPH2_ENST00000373054.4_Silent_p.K223K			O60879	DIAP2_HUMAN	diaphanous-related formin 2	227	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						ATATTGACAAGAAGAATCAGT	0.308																																					p.K227K		Atlas-SNP	.											.	DIAPH2	148	.	0			c.G681A						.						34	32	33					X																	96167500		2200	4289	6489	SO:0001819	synonymous_variant	1730	exon7			TGACAAGAAGAAT	Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"diaphanous (Drosophila, homolog) 2", "diaphanous homolog 2 (Drosophila)"			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.681G>A	chrX.hg19:g.96167500G>A		66.0	0.0		75.0	4.0	NM_007309	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Silent	SNP	ENST00000324765.8	hg19	CCDS14467.1																																																																																			.	.		0.308	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		A	96167500	G	A	96167500	2	1	115	1	0	0	0	0	0	0	0	1	4521	933	33	3		3	DIAPH2	23	96167500	Silent	SNP	G	TCGA-DD-A3A1-01A-11D-A20W-10	16220141	96167500	59103060	506	20045										
GPRASP1	9737	hgsc.bcm.edu	37	chrX	101910325	101910325	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	actagcagctgatgatgaacAggtcattattggttcctggt	11	7	1	3			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:101910325A>G	ENST00000361600.5	+	5	2285	c.1484A>G	c.(1483-1485)cAg>cGg	p.Q495R	GPRASP1_ENST00000415986.1_Missense_Mutation_p.Q495R|RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000537097.1_Missense_Mutation_p.Q495R|GPRASP1_ENST00000444152.1_Missense_Mutation_p.Q495R	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	495					endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						GATGATGAACAGGTCATTATT	0.498																																					p.Q495R		Atlas-SNP	.											.	GPRASP1	140	.	0			c.A1484G						.						79	72	74					X																	101910325		2203	4300	6503	SO:0001583	missense	9737	exon3			ATGAACAGGTCAT	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"Armadillo repeat containing"	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.1484A>G	chrX.hg19:g.101910325A>G	ENSP00000355146:p.Gln495Arg	94.0	0.0		113.0	5.0	NM_001099411	O43168|Q96LA1	Missense_Mutation	SNP	ENST00000361600.5	hg19	CCDS35352.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.478813	0.26511	.	.	ENSG00000198932	ENST00000415986;ENST00000444152;ENST00000361600;ENST00000537097	T;T;T;T	0.08193	3.12;3.12;3.12;3.12	2.79	0.371	0.16168	.	.	.	.	.	T	0.04048	0.0113	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40553	-0.9557	9	0.49607	T	0.09	-0.2362	5.6912	0.17831	0.7341:0.0:0.2659:0.0	.	495	Q5JY77	GASP1_HUMAN	R	495	ENSP00000393691:Q495R;ENSP00000409420:Q495R;ENSP00000355146:Q495R;ENSP00000445683:Q495R	ENSP00000355146:Q495R	Q	+	2	0	GPRASP1	101796981	0.000000	0.05858	0.000000	0.03702	0.921000	0.55340	0.386000	0.20702	-0.001000	0.14495	0.422000	0.28245	CAG	.	.		0.498	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		G	101910325	A	G	101910325	3	3	115	1	0	0	0	0	1	0	0	0	6731	188	7	2	1486	2	GPRASP1	23	101910325	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5742825	101910325	53360235	507	20046										
GUCY2F	2986	hgsc.bcm.edu	37	chrX	108708492	108708492	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ctgcatcataggcttcccggAgctttgggttgttccttagg	12	10	1	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:108708492A>G	ENST00000218006.2	-	3	1202	c.911T>C	c.(910-912)cTc>cCc	p.L304P		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	304					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						GGCTTCCCGGAGCTTTGGGTT	0.483																																					p.L304P		Atlas-SNP	.											.	GUCY2F	178	.	0			c.T911C						.						140	120	127					X																	108708492		2203	4300	6503	SO:0001583	missense	2986	exon3			TCCCGGAGCTTTG	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.911T>C	chrX.hg19:g.108708492A>G	ENSP00000218006:p.Leu304Pro	98.0	0.0		114.0	6.0	NM_001522	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	hg19	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	A	17.79	3.475541	0.63737	.	.	ENSG00000101890	ENST00000218006	T	0.75589	-0.95	3.94	3.94	0.45596	Extracellular ligand-binding receptor (1);	0.141402	0.48767	D	0.000161	D	0.83663	0.5303	M	0.80332	2.49	0.80722	D	1	D	0.58970	0.984	D	0.70487	0.969	T	0.82520	-0.0416	10	0.32370	T	0.25	.	10.183	0.42980	1.0:0.0:0.0:0.0	.	304	P51841	GUC2F_HUMAN	P	304	ENSP00000218006:L304P	ENSP00000218006:L304P	L	-	2	0	GUCY2F	108595148	1.000000	0.71417	0.106000	0.21319	0.979000	0.70002	8.513000	0.90542	1.764000	0.52075	0.486000	0.48141	CTC	.	.		0.483	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		G	108708492	A	G	108708492	3	3	115	1	0	0	0	0	1	0	0	0	6907	304	11	2	2483	2	GUCY2F	23	108708492	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	6798167	108708492	46562068	508	20047										
TRPC5	7224	hgsc.bcm.edu	37	chrX	111090642	111090642	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	ggtgccacatttcccattccTcccttggacgagaaccatta	7	14	0	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:111090642T>C	ENST00000262839.2	-	6	2318	c.1400A>G	c.(1399-1401)gAg>gGg	p.E467G		NM_012471.2	NP_036603.1	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel, subfamily C, member 5	467					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			biliary_tract(1)|breast(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(38)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TTCCCATTCCTCCCTTGGACG	0.433																																					p.E467G		Atlas-SNP	.											.	TRPC5	142	.	0			c.A1400G						.						85	71	76					X																	111090642		2203	4300	6503	SO:0001583	missense	7224	exon6			CATTCCTCCCTTG	AF054568	CCDS14561.1	Xq23	2014-06-13			ENSG00000072315	ENSG00000072315		"Voltage-gated ion channels / Transient receptor potential cation channels"	12337	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 159"	300334				10493832, 16382100	Standard	NM_012471		Approved	PPP1R159	uc004epl.1	Q9UL62	OTTHUMG00000022212	ENST00000262839.2:c.1400A>G	chrX.hg19:g.111090642T>C	ENSP00000262839:p.Glu467Gly	24.0	0.0		27.0	4.0	NM_012471	B2RP53|O75233|Q5JXY8|Q9Y514	Missense_Mutation	SNP	ENST00000262839.2	hg19	CCDS14561.1	.	.	.	.	.	.	.	.	.	.	T	19.80	3.894065	0.72639	.	.	ENSG00000072315	ENST00000262839	T	0.71222	-0.55	5.51	5.51	0.81932	Ion transport (1);	0.100743	0.64402	D	0.000003	T	0.64316	0.2587	L	0.33668	1.02	0.80722	D	1	B;B	0.32467	0.075;0.372	B;B	0.36030	0.103;0.216	T	0.66571	-0.5890	10	0.62326	D	0.03	-2.8893	14.7304	0.69377	0.0:0.0:0.0:1.0	.	468;467	Q59G51;Q9UL62	.;TRPC5_HUMAN	G	467	ENSP00000262839:E467G	ENSP00000262839:E467G	E	-	2	0	TRPC5	110977298	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.250000	0.72435	1.860000	0.53959	0.430000	0.28490	GAG	.	.		0.433	TRPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057945.1	NM_012471		C	111090642	T	C	111090642	3	2	115	1	0	0	0	0	1	0	0	0	16597	1551	54	2	1545	2	TRPC5	23	111090642	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	2382150	111090642	44179918	509	20048										
XIAP	331	hgsc.bcm.edu	37	chrX	123019618	123019618	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gattaaaaacttttgctaatTttccaagtggtagtcctgtt	7	6	0	0			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:123019618T>C	ENST00000371199.3	+	2	405	c.106T>C	c.(106-108)Ttt>Ctt	p.F36L	XIAP_ENST00000355640.3_Missense_Mutation_p.F36L|XIAP_ENST00000434753.3_Missense_Mutation_p.F36L|XIAP_ENST00000468691.1_Intron	NM_001167.3	NP_001158.2	P98170	XIAP_HUMAN	X-linked inhibitor of apoptosis	36					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|copper ion homeostasis (GO:0055070)|inhibition of cysteine-type endopeptidase activity involved in apoptotic process (GO:1990001)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of protein ubiquitination (GO:0031398)|protein ubiquitination (GO:0016567)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)	25						TTTTGCTAATTTTCCAAGTGG	0.383									X-linked Lymphoproliferative syndrome																												p.F36L		Atlas-SNP	.											.	XIAP	56	.	0			c.T106C						.						81	83	82					X																	123019618		2201	4299	6500	SO:0001583	missense	331	exon2	Familial Cancer Database	XLP, Duncan syndrome, Familial Fatal Epstein-Barr Infection, incl. XLP2	GCTAATTTTCCAA	U45880	CCDS14606.1	Xq25	2014-09-17	2008-03-04	2008-03-04	ENSG00000101966	ENSG00000101966		"Baculoviral IAP repeat containing"	592	protein-coding gene	gene with protein product		300079	"baculoviral IAP repeat-containing 4"	API3, BIRC4		8552191, 8654366	Standard	NM_001167		Approved	hILP	uc010nqu.3	P98170	OTTHUMG00000022336	ENST00000371199.3:c.106T>C	chrX.hg19:g.123019618T>C	ENSP00000360242:p.Phe36Leu	54.0	0.0		62.0	4.0	NM_001204401	D3DTF2|Q9NQ14	Missense_Mutation	SNP	ENST00000371199.3	hg19	CCDS14606.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.263221	0.80358	.	.	ENSG00000101966	ENST00000434753;ENST00000430625;ENST00000371199;ENST00000355640	T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8	5.81	5.81	0.92471	Baculoviral inhibition of apoptosis protein repeat (5);	0.000000	0.85682	D	0.000000	D	0.85767	0.5773	M	0.78637	2.42	0.54753	D	0.99998	D	0.89917	1.0	D	0.72075	0.976	D	0.86536	0.1825	9	.	.	.	-6.0358	15.1702	0.72865	0.0:0.0:0.0:1.0	.	36	P98170	XIAP_HUMAN	L	36	ENSP00000395230:F36L;ENSP00000400637:F36L;ENSP00000360242:F36L;ENSP00000347858:F36L	.	F	+	1	0	XIAP	122847299	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.509000	0.73725	1.965000	0.57142	0.413000	0.27773	TTT	.	.		0.383	XIAP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058165.5	NM_001167		C	123019618	T	C	123019618	3	2	115	1	0	0	0	0	1	0	0	0	17443	1841	64	2	108	2	XIAP	23	123019618	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	11928976	123019618	32250942	510	20049										
STAG2	10735	hgsc.bcm.edu	37	chrX	123224569	123224569	+	Frame_Shift_Del	DEL	T	T	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgaggatagcttcatgagtgTttatccaatgcagactgaac							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:123224569delT	ENST00000371160.1	+	31	3712	c.3422delT	c.(3421-3423)gttfs	p.V1141fs	STAG2_ENST00000354548.5_Frame_Shift_Del_p.V1072fs|STAG2_ENST00000371145.3_Frame_Shift_Del_p.V1141fs|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Frame_Shift_Del_p.V1141fs|STAG2_ENST00000371157.3_Frame_Shift_Del_p.V1141fs|STAG2_ENST00000371144.3_Frame_Shift_Del_p.V1141fs	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	1141					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TTCATGAGTGTTTATCCAATG	0.373																																					p.V1141fs		Atlas-INDEL	.											.	STAG2	309	.	0			c.3421delG						.						198	149	166					X																	123224569		2203	4300	6503	SO:0001589	frameshift_variant	10735	exon31			.	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.3422delT	chrX.hg19:g.123224569delT	ENSP00000360202:p.Val1141fs	120.0	0.0		129.0	10.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Frame_Shift_Del	DEL	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.		0.373	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		-	123224569	T	-	123224569	7	5	115	1	0	1	0	1	0	0	0	0	15258	1725	60	0	3536	0	STAG2	23	123224569	Frame_Shift_Del	DEL	T	TCGA-DD-A3A1-01A-11D-A20W-10	204951	123224569	32045991	511	20050										
UTP14A	10813	hgsc.bcm.edu	37	chrX	129055252	129055252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	agcctctgagagtgaggaagAggagggaggcacagaagatg	18	5	1	5			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:129055252A>G	ENST00000394422.3	+	11	1065	c.1037A>G	c.(1036-1038)gAg>gGg	p.E346G	RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000425117.2_Missense_Mutation_p.E294G|UTP14A_ENST00000371042.3_Missense_Mutation_p.E178G|UTP14A_ENST00000371051.5_Missense_Mutation_p.E292G|UTP14A_ENST00000498179.1_3'UTR	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	346					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(16)|ovary(3)|urinary_tract(1)	32						AGTGAGGAAGAGGAGGGAGGC	0.507																																					p.E346G		Atlas-SNP	.											.	UTP14A	74	.	0			c.A1037G						.						122	100	107					X																	129055252		2203	4300	6503	SO:0001583	missense	10813	exon11			AGGAAGAGGAGGG	AF039694	CCDS14615.1, CCDS55489.1	Xq26.1	2009-01-15	2004-06-01	2004-06-01	ENSG00000156697	ENSG00000156697			10665	protein-coding gene	gene with protein product		300508	"serologically defined colon cancer antigen 16"	SDCCAG16		9610721, 16354793	Standard	NM_006649		Approved	NY-CO-16	uc004euz.3	Q9BVJ6	OTTHUMG00000022378	ENST00000394422.3:c.1037A>G	chrX.hg19:g.129055252A>G	ENSP00000377944:p.Glu346Gly	118.0	0.0		124.0	6.0	NM_006649	A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Missense_Mutation	SNP	ENST00000394422.3	hg19	CCDS14615.1	.	.	.	.	.	.	.	.	.	.	A	19.46	3.831382	0.71258	.	.	ENSG00000156697	ENST00000425117;ENST00000394422;ENST00000371051;ENST00000427972;ENST00000371042	T;T;T;T;T	0.18960	2.18;2.18;2.18;2.18;2.18	6.08	4.92	0.64577	.	0.301734	0.35040	N	0.003497	T	0.39989	0.1099	M	0.82823	2.61	0.09310	N	0.999996	D;B;B;D	0.65815	0.993;0.197;0.197;0.995	P;B;B;D	0.63957	0.869;0.159;0.159;0.92	T	0.38112	-0.9676	10	0.28530	T	0.3	-12.7787	4.6403	0.12545	0.6713:0.1616:0.1671:0.0	.	292;294;294;346	F8WD00;E9PEL7;B4DQ08;Q9BVJ6	.;.;.;UT14A_HUMAN	G	294;346;292;178;178	ENSP00000388669:E294G;ENSP00000377944:E346G;ENSP00000360090:E292G;ENSP00000413187:E178G;ENSP00000360081:E178G	ENSP00000360081:E178G	E	+	2	0	UTP14A	128882933	0.990000	0.36364	0.054000	0.19295	0.661000	0.39034	2.656000	0.46716	0.900000	0.36469	0.441000	0.28932	GAG	.	.		0.507	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058221.1	NM_006649		G	129055252	A	G	129055252	3	3	115	1	0	0	0	0	1	0	0	0	17110	304	11	2	1079	2	UTP14A	23	129055252	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5830683	129055252	26215308	512	20051										
RBMX2	51634	hgsc.bcm.edu	37	chrX	129546386	129546386	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	aaaagagaaagccgaccgggAggtacaggcagagcaaccat	13	9	0	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:129546386A>G	ENST00000305536.6	+	6	597	c.533A>G	c.(532-534)gAg>gGg	p.E178G		NM_016024.2	NP_057108.2	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2	178	Lys-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(2)|large_intestine(1)|liver(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	19						GCCGACCGGGAGGTACAGGCA	0.413																																					p.E178G		Atlas-SNP	.											.	RBMX2	46	.	0			c.A533G						.						50	49	50					X																	129546386		1895	4105	6000	SO:0001583	missense	51634	exon6			ACCGGGAGGTACA	AF078865	CCDS43993.1	Xq26.1	2013-02-12			ENSG00000134597	ENSG00000134597		"RNA binding motif (RRM) containing"	24282	protein-coding gene	gene with protein product						10810093	Standard	NM_016024		Approved	CGI-79	uc004evt.3	Q9Y388	OTTHUMG00000022395	ENST00000305536.6:c.533A>G	chrX.hg19:g.129546386A>G	ENSP00000339090:p.Glu178Gly	101.0	0.0		130.0	6.0	NM_016024	A8K9Z0|Q5JY82|Q9Y3I8	Missense_Mutation	SNP	ENST00000305536.6	hg19	CCDS43993.1	.	.	.	.	.	.	.	.	.	.	A	7.653	0.683367	0.14907	.	.	ENSG00000134597	ENST00000305536;ENST00000538614	T	0.13657	2.57	4.31	-1.23	0.09465	.	2.194050	0.01991	N	0.045503	T	0.09555	0.0235	N	0.24115	0.695	0.09310	N	1	B	0.29716	0.255	B	0.26614	0.071	T	0.25710	-1.0124	10	0.33940	T	0.23	.	5.9397	0.19186	0.3466:0.5441:0.1092:0.0	.	178	Q9Y388	RBMX2_HUMAN	G	178	ENSP00000339090:E178G	ENSP00000339090:E178G	E	+	2	0	RBMX2	129374067	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.005000	0.13129	-0.161000	0.10983	-0.377000	0.06932	GAG	.	.		0.413	RBMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058265.1	NM_016024		G	129546386	A	G	129546386	3	3	115	1	0	0	0	0	1	0	0	0	13167	304	11	2	555	2	RBMX2	23	129546386	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	491134	129546386	25724174	513	20052										
GPR112	139378	hgsc.bcm.edu	37	chrX	135438310	135438310	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tttcagaggaagagatggtcAtggatcgagctattgtaagt	13	4	2	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:135438310A>G	ENST00000394143.1	+	9	7204	c.6913A>G	c.(6913-6915)Atg>Gtg	p.M2305V	GPR112_ENST00000287534.4_Intron|GPR112_ENST00000394141.1_Missense_Mutation_p.M2100V|GPR112_ENST00000370652.1_Missense_Mutation_p.M2305V|GPR112_ENST00000412101.1_Missense_Mutation_p.M2100V	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2305					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					AGAGATGGTCATGGATCGAGC	0.353																																					p.M2305V		Atlas-SNP	.											.	GPR112	459	.	0			c.A6913G						.						144	131	136					X																	135438310		2203	4300	6503	SO:0001583	missense	139378	exon9			ATGGTCATGGATC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.6913A>G	chrX.hg19:g.135438310A>G	ENSP00000377699:p.Met2305Val	73.0	0.0		73.0	4.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	A	1.397	-0.579115	0.03854	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000394141	T;T;T;T	0.35421	1.35;1.35;1.31;1.31	4.86	0.89	0.19218	.	.	.	.	.	T	0.14141	0.0342	N	0.08118	0	0.09310	N	0.999999	B;B	0.25312	0.123;0.109	B;B	0.18871	0.023;0.021	T	0.21109	-1.0255	9	0.25751	T	0.34	.	1.5052	0.02485	0.5472:0.1776:0.1007:0.1745	.	2100;2305	Q8IZF6-3;Q8IZF6	.;GP112_HUMAN	V	2305;2305;2100;2100	ENSP00000377699:M2305V;ENSP00000359686:M2305V;ENSP00000416526:M2100V;ENSP00000377697:M2100V	ENSP00000359686:M2305V	M	+	1	0	GPR112	135265976	0.829000	0.29322	0.019000	0.16419	0.132000	0.20833	1.024000	0.30077	-0.043000	0.13513	0.481000	0.45027	ATG	.	.		0.353	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			G	135438310	A	G	135438310	3	3	115	1	0	0	0	0	1	0	0	0	6637	217	8	2	6935	2	GPR112	23	135438310	Missense_Mutation	SNP	A	TCGA-DD-A3A1-01A-11D-A20W-10	5891924	135438310	19832250	514	20053										
SOX3	6658	hgsc.bcm.edu	37	chrX	139586972	139586972	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tgggtgtccctacggggttcTtgagttcagtctccagaagg	14	9	3	2			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:139586972T>C	ENST00000370536.2	-	1	253	c.254A>G	c.(253-255)aAg>aGg	p.K85R		NM_005634.2	NP_005625.2	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	85					central nervous system development (GO:0007417)|face development (GO:0060324)|hypothalamus development (GO:0021854)|negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|sensory organ development (GO:0007423)|Sertoli cell development (GO:0060009)|sex determination (GO:0007530)|spermatid differentiation (GO:0048515)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	10	Acute lymphoblastic leukemia(192;7.65e-05)					TACGGGGTTCTTGAGTTCAGT	0.711																																					p.K85R		Atlas-SNP	.											.	SOX3	44	.	0			c.A254G						.						8	7	7					X																	139586972		2132	4105	6237	SO:0001583	missense	6658	exon1			GGGTTCTTGAGTT		CCDS14669.1	Xq27.1	2013-10-17			ENSG00000134595	ENSG00000134595		"SRY (sex determining region Y)-boxes"	11199	protein-coding gene	gene with protein product		313430	"panhypopituitarism"	PHP		15800844	Standard	NM_005634		Approved		uc004fbd.1	P41225	OTTHUMG00000022544	ENST00000370536.2:c.254A>G	chrX.hg19:g.139586972T>C	ENSP00000359567:p.Lys85Arg	28.0	0.0		26.0	4.0	NM_005634	P35714|Q5JWI3|Q9NP49	Missense_Mutation	SNP	ENST00000370536.2	hg19	CCDS14669.1	.	.	.	.	.	.	.	.	.	.	t	24.7	4.558287	0.86231	.	.	ENSG00000134595	ENST00000370536	D	0.97906	-4.6	4.39	4.39	0.52855	.	0.132210	0.48767	U	0.000177	D	0.96688	0.8919	N	0.19112	0.55	0.50632	D	0.999884	D	0.69078	0.997	D	0.75020	0.985	D	0.95521	0.8594	9	.	.	.	.	12.082	0.53675	0.0:0.0:0.0:1.0	.	85	P41225	SOX3_HUMAN	R	85	ENSP00000359567:K85R	.	K	-	2	0	SOX3	139414638	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.435000	0.80391	1.433000	0.47394	0.427000	0.28365	AAG	.	.		0.711	SOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058577.1			C	139586972	T	C	139586972	3	2	115	1	0	0	0	0	1	0	0	0	14966	1609	56	2	1090	2	SOX3	23	139586972	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	4148662	139586972	15683588	515	20054										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142717685	142717685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	tacgtctcccttaatcactgTaatttgattgctgcctaaat	5	10	2	1			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:142717685T>C	ENST00000381779.4	-	2	1465	c.1240A>G	c.(1240-1242)Aca>Gca	p.T414A	SLITRK4_ENST00000356928.1_Missense_Mutation_p.T414A|SLITRK4_ENST00000338017.4_Missense_Mutation_p.T414A	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	414						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					TTAATCACTGTAATTTGATTG	0.398																																					p.T414A		Atlas-SNP	.											.	SLITRK4	162	.	0			c.A1240G						.						141	119	126					X																	142717685		2203	4300	6503	SO:0001583	missense	139065	exon2			TCACTGTAATTTG	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.1240A>G	chrX.hg19:g.142717685T>C	ENSP00000371198:p.Thr414Ala	117.0	0.0		109.0	81.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	T	0.484	-0.878560	0.02550	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.55760	0.5;0.5;0.5	5.29	5.29	0.74685	.	0.270580	0.35739	N	0.003009	T	0.39200	0.1069	L	0.41236	1.265	0.35519	D	0.801312	B	0.02656	0.0	B	0.04013	0.001	T	0.42649	-0.9439	10	0.12430	T	0.62	-2.5162	9.3055	0.37872	0.1627:0.0:0.0:0.8373	.	414	Q8IW52	SLIK4_HUMAN	A	414	ENSP00000371198:T414A;ENSP00000349400:T414A;ENSP00000336627:T414A	ENSP00000336627:T414A	T	-	1	0	SLITRK4	142545351	0.110000	0.22057	0.959000	0.39883	0.990000	0.78478	0.276000	0.18716	1.874000	0.54306	0.437000	0.28790	ACA	.	.		0.398	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		C	142717685	T	C	142717685	3	2	115	1	0	0	0	0	1	0	0	0	14760	1638	57	2	1277	2	SLITRK4	23	142717685	Missense_Mutation	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	3130713	142717685	12552875	516	20055										
PNMA3	29944	hgsc.bcm.edu	37	chrX	152226282	152226282	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gtatcacgtagaaacgtgaaTcagactcgcctgaaacgagt	10	9	2	4			TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:152226282T>C	ENST00000370264.4	+	1	896	c.870T>C	c.(868-870)aaT>aaC	p.N290N	PNMA3_ENST00000447306.1_Silent_p.N290N|PNMA3_ENST00000370265.4_Silent_p.N290N			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	290					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16	Acute lymphoblastic leukemia(192;6.56e-05)					gaaacgtgaatcagactcgcc	0.478																																					p.N290N		Atlas-SNP	.											.	PNMA3	81	.	0			c.T870C						.						109	97	101					X																	152226282		2203	4300	6503	SO:0001819	synonymous_variant	29944	exon2			CGTGAATCAGACT	AF083116	CCDS35435.2, CCDS65344.1	Xq28	2012-02-09	2012-02-09		ENSG00000183837	ENSG00000183837		"Paraneoplastic Ma antigens"	18742	protein-coding gene	gene with protein product	"paraneoplastic cancer-testis-brain antigen"	300675	"paraneoplastic antigen MA3"			11558790	Standard	NM_013364		Approved	MA5, MA3, MGC132756, MGC132758	uc004fhc.2	Q9UL41	OTTHUMG00000024195	ENST00000370264.4:c.870T>C	chrX.hg19:g.152226282T>C		90.0	0.0		83.0	4.0	NM_013364	D3DWT7|Q9H0A4	Silent	SNP	ENST00000370264.4	hg19	CCDS35435.2																																																																																			.	.		0.478	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364		C	152226282	T	C	152226282	2	2	115	1	0	0	0	0	0	0	0	1	12164	1432	50	2		2	PNMA3	23	152226282	Silent	SNP	T	TCGA-DD-A3A1-01A-11D-A20W-10	9508597	152226282	3044278	517	20056										
HCFC1	3054	hgsc.bcm.edu	37	chrX	153217070	153217070	+	Frame_Shift_Del	DEL	T	T	-													0.0309477756286267	16	1	1.25271896518437	1.42670771034887	1.20378463060686	0.0201131343656855	0.288546119938488	0	gactcgatgccattggccacTtcggtcagggtagctgcagc							TCGA-DD-A3A1-01A-11D-A20W-10	TCGA-DD-A3A1-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2249a54-91a5-4996-aa54-8ba33cba817c	c6b1efb7-67ef-47f9-afdd-cad7f1d19a46	g.chrX:153217070delT	ENST00000310441.7	-	21	6315	c.5349delA	c.(5347-5349)gaafs	p.E1783fs	HCFC1_ENST00000354233.3_Frame_Shift_Del_p.E1714fs|HCFC1_ENST00000369984.4_Frame_Shift_Del_p.E1828fs	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1783					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CATTGGCCACTTCGGTCAGGG	0.647																																					p.V1784fs		Atlas-INDEL	.											.	HCFC1	284	.	0			c.5350delG						.						40	52	48					X																	153217070		2082	4158	6240	SO:0001589	frameshift_variant	3054	exon21			.		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"VP16-accessory protein", "protein phosphatase 1, regulatory subunit 89"	300019	"mental retardation, X-linked 3", "host cell factor C1 (VP16-accessory protein)"	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.5349delA	chrX.hg19:g.153217070delT	ENSP00000309555:p.Glu1783fs	110.0	0.0		166.0	10.0	NM_005334	Q6P4G5	Frame_Shift_Del	DEL	ENST00000310441.7	hg19	CCDS44020.1																																																																																			.	.		0.647	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		-	153217070	T	-	153217070	7	5	115	1	0	1	0	1	0	0	0	0	7000	1606	56	0	782	0	HCFC1	23	153217070	Frame_Shift_Del	DEL	T	TCGA-DD-A3A1-01A-11D-A20W-10	990788	153217070	2053490	518	20057										
ROR1	4919	hgsc.bcm.edu	37	chr1	64644486	64644486	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	aaagcaagcatctttactagGagacgccaatattcatggac	8	9	2	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr1:64644486G>A	ENST00000371079.1	+	9	3137	c.2762G>A	c.(2761-2763)gGa>gAa	p.G921E	ROR1_ENST00000545203.1_Missense_Mutation_p.G372E	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	921					peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						TCTTTACTAGGAGACGCCAAT	0.398																																					p.G921E		Atlas-SNP	.											.	ROR1	113	.	0			c.G2762A						.						96	94	95					1																	64644486		2203	4299	6502	SO:0001583	missense	4919	exon9			TACTAGGAGACGC	M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"Immunoglobulin superfamily / I-set domain containing"	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.2762G>A	chr1.hg19:g.64644486G>A	ENSP00000360120:p.Gly921Glu	236.0	0.0		197.0	83.0	NM_005012	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	hg19	CCDS626.1	.	.	.	.	.	.	.	.	.	.	G	8.495	0.862849	0.17178	.	.	ENSG00000185483	ENST00000371079;ENST00000544776;ENST00000545203	T;T	0.78595	-0.89;-1.19	5.45	4.52	0.55395	.	0.000000	0.42420	D	0.000716	T	0.50292	0.1607	L	0.27053	0.805	0.41397	D	0.987651	B	0.06786	0.001	B	0.04013	0.001	T	0.55835	-0.8078	10	0.56958	D	0.05	.	9.817	0.40858	0.0728:0.1411:0.7862:0.0	.	921	Q01973	ROR1_HUMAN	E	921;924;372	ENSP00000360120:G921E;ENSP00000441637:G372E	ENSP00000360120:G921E	G	+	2	0	ROR1	64417074	1.000000	0.71417	1.000000	0.80357	0.407000	0.30961	2.920000	0.48844	1.392000	0.46585	0.655000	0.94253	GGA	.	.		0.398	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		A	64644486	G	A	64644486	3	1	116	1	0	0	0	0	1	0	0	0	13541	1174	41	3	2804	3	ROR1	1	64644486	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10		64644486	184606135	1	20058										
GBP5	115362	hgsc.bcm.edu	37	chr1	89735097	89735097	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	caggtaggatttgccagtgcGatagaggcccacaatcgcta	12	10	0	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr1:89735097G>C	ENST00000370459.3	-	2	269	c.142C>G	c.(142-144)Cgc>Ggc	p.R48G	RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000343435.5_Missense_Mutation_p.R48G			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	48	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		TTGCCAGTGCGATAGAGGCCC	0.498																																					p.R48G		Atlas-SNP	.											.	GBP5	65	.	0			c.C142G						.						264	223	237					1																	89735097		2203	4300	6503	SO:0001583	missense	115362	exon3			CAGTGCGATAGAG	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.142C>G	chr1.hg19:g.89735097G>C	ENSP00000359488:p.Arg48Gly	344.0	0.0		378.0	150.0	NM_052942	B2RCE1|Q86TM5	Missense_Mutation	SNP	ENST00000370459.3	hg19	CCDS722.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.427887	0.62733	.	.	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	T;T;T	0.58358	0.34;0.34;0.34	5.0	5.0	0.66597	Guanylate-binding protein, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.63698	0.2533	M	0.86268	2.805	0.41544	D	0.988535	D	0.53619	0.961	P	0.53809	0.735	T	0.70766	-0.4783	10	0.87932	D	0	-4.7548	16.1665	0.81759	0.0:0.0:1.0:0.0	.	48	Q96PP8	GBP5_HUMAN	G	48	ENSP00000340396:R48G;ENSP00000359488:R48G;ENSP00000403010:R48G	ENSP00000340396:R48G	R	-	1	0	GBP5	89507685	1.000000	0.71417	1.000000	0.80357	0.037000	0.13140	6.780000	0.75063	2.762000	0.94881	0.655000	0.94253	CGC	.	.		0.498	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942		C	89735097	G	C	89735097	3	2	116	1	0	0	0	0	1	0	0	0	6285	1058	37	4	1658	4	GBP5	1	89735097	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	25090611	89735097	159515524	2	20059										
FNDC7	163479	hgsc.bcm.edu	37	chr1	109261510	109261510	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	aattgcattctccgtgtccaTtatgcgagccaatggcttgg	10	10	1	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr1:109261510T>G	ENST00000370017.3	+	4	714	c.437T>G	c.(436-438)aTt>aGt	p.I146S	FNDC7_ENST00000271311.2_Missense_Mutation_p.I147S	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	146	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		TCCGTGTCCATTATGCGAGCC	0.448																																					p.I146S		Atlas-SNP	.											.	FNDC7	113	.	0			c.T437G						.						69	60	63					1																	109261510		692	1591	2283	SO:0001583	missense	163479	exon4			TGTCCATTATGCG		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"Fibronectin type III domain containing"	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.437T>G	chr1.hg19:g.109261510T>G	ENSP00000359034:p.Ile146Ser	227.0	0.0		197.0	75.0	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	hg19	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.519831	0.64634	.	.	ENSG00000143107	ENST00000370017;ENST00000271311	T;T	0.57436	0.4;0.4	5.69	5.69	0.88448	.	0.316835	0.36740	N	0.002439	T	0.41396	0.1157	L	0.46157	1.445	0.30260	N	0.793223	B	0.32653	0.379	B	0.41466	0.358	T	0.49273	-0.8957	10	0.52906	T	0.07	-8.9213	15.9414	0.79756	0.0:0.0:0.0:1.0	.	146	E9PAZ5	.	S	146;147	ENSP00000359034:I146S;ENSP00000271311:I147S	ENSP00000271311:I147S	I	+	2	0	FNDC7	109063033	0.998000	0.40836	0.992000	0.48379	0.744000	0.42396	5.400000	0.66320	2.168000	0.68352	0.533000	0.62120	ATT	.	.		0.448	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532		G	109261510	T	G	109261510	3	3	116	1	0	0	0	0	1	0	0	0	5981	1493	52	5	451	5	FNDC7	1	109261510	Missense_Mutation	SNP	T	TCGA-DD-A3A2-01A-11D-A20W-10	19526413	109261510	139989111	3	20060										
TCHH	7062	hgsc.bcm.edu	37	chr1	152084224	152084224	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gcctctcctcctcctcgagcTtcagccaacgttcgcgcctc	7	20	2	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr1:152084224T>C	ENST00000368804.1	-	2	1468	c.1469A>G	c.(1468-1470)aAg>aGg	p.K490R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	490	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCTCGAGCTTCAGCCAACG	0.672																																					p.K490R		Atlas-SNP	.											.	TCHH	275	.	0			c.A1469G						.						65	71	69					1																	152084224		2109	4224	6333	SO:0001583	missense	7062	exon3			TCGAGCTTCAGCC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1469A>G	chr1.hg19:g.152084224T>C	ENSP00000357794:p.Lys490Arg	133.0	0.0		155.0	15.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	t	8.419	0.845945	0.16963	.	.	ENSG00000159450	ENST00000368804	T	0.04654	3.58	2.98	-5.97	0.02227	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.09590	T	0.72	.	5.0277	0.14393	0.1398:0.4054:0.0:0.4548	.	490	Q07283	TRHY_HUMAN	R	490	ENSP00000357794:K490R	ENSP00000357794:K490R	K	-	2	0	TCHH	150350848	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.247000	0.00266	-1.053000	0.03218	-1.396000	0.01147	AAG	.	.		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084224	T	C	152084224	3	2	116	1	0	0	0	0	1	0	0	0	15715	1609	56	2	4366	2	TCHH	1	152084224	Missense_Mutation	SNP	T	TCGA-DD-A3A2-01A-11D-A20W-10	42822714	152084224	97166397	4	20061										
CTSE	1510	hgsc.bcm.edu	37	chr1	206325312	206325312	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ggccagacctttgtggatgcAgagtttgatggaattctggg	15	6	1	3			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr1:206325312A>C	ENST00000358184.2	+	5	655	c.537A>C	c.(535-537)gcA>gcC	p.A179A	CTSE_ENST00000360218.2_Silent_p.A179A|CTSE_ENST00000361052.3_Silent_p.A184A|CTSE_ENST00000432969.2_Silent_p.A104A|CTSE_ENST00000468617.1_3'UTR	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E	184					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|digestion (GO:0007586)|protein autoprocessing (GO:0016540)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(3)	16			BRCA - Breast invasive adenocarcinoma(75;0.0754)			TTGTGGATGCAGAGTTTGATG	0.537																																					p.A179A		Atlas-SNP	.											.	CTSE	72	.	0			c.A537C						.						166	149	155					1																	206325312		2203	4300	6503	SO:0001819	synonymous_variant	1510	exon5			GGATGCAGAGTTT	BC042537	CCDS73012.1, CCDS73013.1	1q32.1	2008-02-05			ENSG00000196188	ENSG00000196188	3.4.23.5	"Cathepsins"	2530	protein-coding gene	gene with protein product		116890				2369841, 2674141	Standard	NM_001910		Approved		uc001hdu.3	P14091	OTTHUMG00000036121	ENST00000358184.2:c.537A>C	chr1.hg19:g.206325312A>C		253.0	0.0		288.0	112.0	NM_001910	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Silent	SNP	ENST00000358184.2	hg19	CCDS1462.1																																																																																			.	.		0.537	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087998.1	NM_001910		C	206325312	A	C	206325312	2	2	116	1	0	0	0	0	0	0	0	1	4035	175	7	5		5	CTSE	1	206325312	Silent	SNP	A	TCGA-DD-A3A2-01A-11D-A20W-10	54241088	206325312	42925309	5	20062										
URB2	9816	hgsc.bcm.edu	37	chr1	229794870	229794870	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	accttatatccagctgtgaaAagtctgctgcaggagggcat	11	9	1	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr1:229794870A>C	ENST00000258243.2	+	10	4537	c.4401A>C	c.(4399-4401)aaA>aaC	p.K1467N		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1467						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						CAGCTGTGAAAAGTCTGCTGC	0.552																																					p.K1467N		Atlas-SNP	.											.	URB2	152	.	0			c.A4401C						.						125	129	127					1																	229794870		2203	4300	6503	SO:0001583	missense	9816	exon10			TGTGAAAAGTCTG	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"nucleolar preribosomal-associated protein 1"		"KIAA0133"	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.4401A>C	chr1.hg19:g.229794870A>C	ENSP00000258243:p.Lys1467Asn	87.0	0.0		85.0	5.0	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	hg19	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	A	14.59	2.580517	0.46006	.	.	ENSG00000135763	ENST00000258243;ENST00000434387	T;T	0.48201	0.82;0.82	5.29	-7.0	0.01599	Nucleolar 27S pre-rRNA processing, Urb2/Npa2, C-terminal (1);	0.046638	0.85682	D	0.000000	T	0.62478	0.2431	M	0.74258	2.255	0.37457	D	0.915054	D	0.89917	1.0	D	0.80764	0.994	T	0.71928	-0.4444	9	.	.	.	-18.0148	18.6368	0.91382	0.2498:0.0:0.7502:0.0	.	1467	Q14146	URB2_HUMAN	N	1467;83	ENSP00000258243:K1467N;ENSP00000395107:K83N	.	K	+	3	2	URB2	227861493	0.031000	0.19500	0.003000	0.11579	0.148000	0.21650	0.087000	0.14958	-1.359000	0.02174	-0.297000	0.09499	AAA	.	.		0.552	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		C	229794870	A	C	229794870	3	2	116	1	0	0	0	0	1	0	0	0	17040	11	1	5	4435	5	URB2	1	229794870	Missense_Mutation	SNP	A	TCGA-DD-A3A2-01A-11D-A20W-10	23469558	229794870	19455751	6	20063										
TRIM67	440730	hgsc.bcm.edu	37	chr1	231337125	231337125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	tctcagatgctctgatcaagCgcgtccaggtgtctcaggag	12	11	4	2	rs370312974		TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr1:231337125C>T	ENST00000366653.5	+	5	1396	c.1396C>T	c.(1396-1398)Cgc>Tgc	p.R466C	TRIM67_ENST00000444294.3_Missense_Mutation_p.R466C|TRIM67_ENST00000449018.3_Missense_Mutation_p.R404C|TRIM67_ENST00000366652.2_Missense_Mutation_p.R466C			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	466	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				TCTGATCAAGCGCGTCCAGGT	0.537																																					p.R466C		Atlas-SNP	.											.	TRIM67	160	.	0			c.C1396T						.	C	CYS/ARG	0,3918		0,0,1959	36	38	37		1396	5.4	1	1		37	1,8301		0,1,4150	no	missense	TRIM67	NM_001004342.3	180	0,1,6109	TT,TC,CC		0.012,0.0,0.0082	probably-damaging	466/784	231337125	1,12219	1959	4151	6110	SO:0001583	missense	440730	exon5			ATCAAGCGCGTCC	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.1396C>T	chr1.hg19:g.231337125C>T	ENSP00000355613:p.Arg466Cys	113.0	0.0		133.0	48.0	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	hg19	CCDS44333.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.438407	0.83885	0.0	1.2E-4	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000449018;ENST00000366653	T;T;T;T	0.75477	-0.94;-0.83;-0.92;-0.94	5.41	5.41	0.78517	B-box, C-terminal (1);COS domain (1);	0.000000	0.85682	D	0.000000	D	0.85292	0.5663	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86755	0.1963	10	0.87932	D	0	.	14.0761	0.64891	0.1506:0.8493:0.0:0.0	.	466	Q6ZTA4	TRI67_HUMAN	C	466;466;404;466	ENSP00000412124:R466C;ENSP00000355612:R466C;ENSP00000400163:R404C;ENSP00000355613:R466C	ENSP00000355612:R466C	R	+	1	0	TRIM67	229403748	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.784000	0.55416	2.530000	0.85305	0.555000	0.69702	CGC	.	.		0.537	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		T	231337125	C	T	231337125	3	4	116	1	0	0	0	0	1	0	0	0	16555	768	27	1	1414	1	TRIM67	1	231337125	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	1542255	231337125	17913496	7	20064										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33172789	33172789	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ggcagccgccccgttcaccaAacaaggcaggcaagttgtgc	12	14	1	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr2:33172789A>G	ENST00000404816.2	+	1	751	c.398A>G	c.(397-399)aAa>aGa	p.K133R	LTBP1_ENST00000354476.3_Missense_Mutation_p.K133R|Y_RNA_ENST00000384224.1_RNA			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	133					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CCGTTCACCAAACAAGGCAGG	0.731																																					p.K133R		Atlas-SNP	.											.	LTBP1	317	.	0			c.A398G						.						8	8	8					2																	33172789		1560	2936	4496	SO:0001583	missense	4052	exon1			TCACCAAACAAGG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.398A>G	chr2.hg19:g.33172789A>G	ENSP00000386043:p.Lys133Arg	56.0	0.0		70.0	19.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	A	2.223	-0.377905	0.05000	.	.	ENSG00000049323	ENST00000404816;ENST00000354476	T;T	0.81247	-1.47;-1.45	3.86	-1.58	0.08479	.	.	.	.	.	T	0.57873	0.2083	N	0.24115	0.695	0.22226	N	0.999277	B	0.13594	0.008	B	0.09377	0.004	T	0.46091	-0.9216	9	0.02654	T	1	.	4.302	0.10928	0.5491:0.1676:0.2833:0.0	.	133	Q14766-4	.	R	133	ENSP00000386043:K133R;ENSP00000346467:K133R	ENSP00000346467:K133R	K	+	2	0	LTBP1	33026293	0.069000	0.21087	0.177000	0.23020	0.983000	0.72400	-0.075000	0.11431	-0.376000	0.07943	-0.411000	0.06167	AAA	.	.		0.731	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		G	33172789	A	G	33172789	3	3	116	1	0	0	0	0	1	0	0	0	9082	14	1	2	400	2	LTBP1	2	33172789	Missense_Mutation	SNP	A	TCGA-DD-A3A2-01A-11D-A20W-10		33172789	210026584	8	20065										
DYSF	8291	hgsc.bcm.edu	37	chr2	71755439	71755439	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	tcttcccagtggacgatgccGtgatggacaacgtgaaacag	12	10	1	2	rs144202114	byFrequency	TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr2:71755439G>T	ENST00000258104.3	+	13	1469	c.1192G>T	c.(1192-1194)Gtg>Ttg	p.V398L	DYSF_ENST00000429174.2_Missense_Mutation_p.V398L|DYSF_ENST00000409744.1_Missense_Mutation_p.V399L|DYSF_ENST00000409762.1_Missense_Mutation_p.V429L|DYSF_ENST00000409366.1_Missense_Mutation_p.V399L|DYSF_ENST00000394120.2_Missense_Mutation_p.V399L|DYSF_ENST00000409651.1_Missense_Mutation_p.V430L|DYSF_ENST00000410020.3_Missense_Mutation_p.V430L|DYSF_ENST00000410041.1_Missense_Mutation_p.V430L|DYSF_ENST00000409582.3_Missense_Mutation_p.V429L|DYSF_ENST00000413539.2_Missense_Mutation_p.V429L	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	398	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.V398M(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GGACGATGCCGTGATGGACAA	0.542																																					p.V430L		Atlas-SNP	.											DYSF,NS,carcinoma,0,1	DYSF	536	.	1	Substitution - Missense(1)	prostate(1)	c.G1288T						.						120	87	98					2																	71755439		2203	4300	6503	SO:0001583	missense	8291	exon14			GATGCCGTGATGG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1192G>T	chr2.hg19:g.71755439G>T	ENSP00000258104:p.Val398Leu	107.0	0.0		106.0	43.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.733747	0.30684	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.81739	-1.52;-1.51;-1.51;-1.53;-1.52;-1.51;-1.52;-1.52;-1.53;-1.51;-1.51	4.82	4.82	0.62117	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.221133	0.39083	N	0.001466	T	0.60287	0.2257	N	0.03154	-0.405	0.36451	D	0.866098	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.21688	0.047;0.047;0.017;0.009;0.004;0.004;0.004;0.004;0.047;0.05;0.059;0.009;0.017;0.021	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.27380	0.047;0.047;0.047;0.047;0.032;0.021;0.032;0.013;0.047;0.036;0.064;0.047;0.047;0.079	T	0.60737	-0.7204	10	0.07175	T	0.84	-24.9596	15.7634	0.78103	0.0:0.0:1.0:0.0	.	430;430;399;399;430;399;429;398;429;429;398;398;399;398	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	L	429;429;429;398;398;430;399;399;399;430;430	ENSP00000407046:V429L;ENSP00000387137:V429L;ENSP00000386547:V429L;ENSP00000398305:V398L;ENSP00000258104:V398L;ENSP00000386683:V430L;ENSP00000377678:V399L;ENSP00000386285:V399L;ENSP00000386512:V399L;ENSP00000386881:V430L;ENSP00000386617:V430L	ENSP00000258104:V398L	V	+	1	0	DYSF	71608947	0.999000	0.42202	0.990000	0.47175	0.841000	0.47740	2.940000	0.49003	2.407000	0.81776	0.462000	0.41574	GTG	.	G|0.996;A|0.004		0.542	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71755439	G	T	71755439	3	4	116	1	0	0	0	0	1	0	0	0	4861	1145	40	1	1434	1	DYSF	2	71755439	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	38582650	71755439	171443934	9	20066										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84777070	84777070	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	atgcacatcttaacggtaaaTgctgttaattcgcttttgaa	7	7	1	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr2:84777070T>C	ENST00000237449.6	+	8	1382	c.1374T>C	c.(1372-1374)aaT>aaC	p.N458N	DNAH6_ENST00000398278.2_Silent_p.N458N|DNAH6_ENST00000389394.3_Silent_p.N458N			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	458	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TAACGGTAAATGCTGTTAATT	0.348																																					p.N458N		Atlas-SNP	.											.	DNAH6	194	.	0			c.T1374C						.						98	88	92					2																	84777070		2203	4300	6503	SO:0001819	synonymous_variant	1768	exon9			GGTAAATGCTGTT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.1374T>C	chr2.hg19:g.84777070T>C		107.0	0.0		111.0	18.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.348	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		C	84777070	T	C	84777070	2	2	116	1	0	0	0	0	0	0	0	1	4607	1461	51	2		2	DNAH6	2	84777070	Silent	SNP	T	TCGA-DD-A3A2-01A-11D-A20W-10	13021631	84777070	158422303	10	20067										
ZNF142	7701	hgsc.bcm.edu	37	chr2	219513586	219513586	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	cttattggaacaagcaaaatCacagtgggggcagtggaagg	14	6	1	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr2:219513586C>A	ENST00000449707.1	-	6	1466	c.1045G>T	c.(1045-1047)Gat>Tat	p.D349Y	ZNF142_ENST00000411696.2_Missense_Mutation_p.D349Y	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	349					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CAAGCAAAATCACAGTGGGGG	0.562											OREG0015202	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D349Y	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.G1045T						.						57	58	58					2																	219513586		2069	4192	6261	SO:0001583	missense	7701	exon6			CAAAATCACAGTG	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.1045G>T	chr2.hg19:g.219513586C>A	ENSP00000408643:p.Asp349Tyr	97.0	0.0	2259	143.0	53.0	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	hg19	CCDS42817.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.493677	0.84962	.	.	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.14266	2.52;2.52	5.35	5.35	0.76521	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.045033	0.85682	D	0.000000	T	0.44498	0.1296	M	0.87381	2.88	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.67231	0.91;0.95	T	0.44636	-0.9315	10	0.62326	D	0.03	1.9246	19.6142	0.95626	0.0:1.0:0.0:0.0	.	349;186	P52746;A8MWU9	ZN142_HUMAN;.	Y	349	ENSP00000408643:D349Y;ENSP00000398798:D349Y	ENSP00000398798:D349Y	D	-	1	0	ZNF142	219221830	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.774000	0.68906	2.941000	0.99782	0.655000	0.94253	GAT	.	.		0.562	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		A	219513586	C	A	219513586	3	1	116	1	0	0	0	0	1	0	0	0	17746	826	29	3	4038	3	ZNF142	2	219513586	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	134736516	219513586	23685787	11	20068										
ITGA9	3680	hgsc.bcm.edu	37	chr3	37695227	37695227	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	tgtttttgaaaggaattgccGttcagaggactgtgccgcag	13	7	1	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr3:37695227G>A	ENST00000264741.5	+	17	2118	c.1862G>A	c.(1861-1863)cGt>cAt	p.R621H		NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	621					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.R621L(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		AGGAATTGCCGTTCAGAGGAC	0.498																																					p.R621H		Atlas-SNP	.											ITGA9,brain,glioma,0,1	ITGA9	98	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G1862A						.						141	140	140					3																	37695227		2203	4300	6503	SO:0001583	missense	3680	exon17			ATTGCCGTTCAGA	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.1862G>A	chr3.hg19:g.37695227G>A	ENSP00000264741:p.Arg621His	179.0	0.0		164.0	61.0	NM_002207	Q14638	Missense_Mutation	SNP	ENST00000264741.5	hg19	CCDS2669.1	.	.	.	.	.	.	.	.	.	.	G	9.966	1.224044	0.22457	.	.	ENSG00000144668	ENST00000264741	T	0.46063	0.88	5.85	-2.75	0.05914	Integrin alpha-2 (1);	0.660409	0.16331	N	0.219124	T	0.36690	0.0976	L	0.36672	1.1	0.09310	N	0.999999	P	0.38800	0.648	P	0.44477	0.451	T	0.39440	-0.9614	10	0.52906	T	0.07	.	13.4039	0.60900	0.5528:0.0:0.4472:0.0	.	621	Q13797	ITA9_HUMAN	H	621	ENSP00000264741:R621H	ENSP00000264741:R621H	R	+	2	0	ITGA9	37670231	0.024000	0.19004	0.005000	0.12908	0.098000	0.18820	0.106000	0.15354	-0.632000	0.05553	-1.969000	0.00466	CGT	.	.		0.498	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		A	37695227	G	A	37695227	3	1	116	1	0	0	0	0	1	0	0	0	7892	1145	40	1	1928	1	ITGA9	3	37695227	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10		37695227	160327203	12	20069										
HYAL3	8372	hgsc.bcm.edu	37	chr3	50332788	50332788	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gtgcccctgggtccaaagtaGggatagaggccgagttggtt	16	8	0	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr3:50332788G>A	ENST00000336307.1	-	2	518	c.246C>T	c.(244-246)ccC>ccT	p.P82P	IFRD2_ENST00000436390.1_5'Flank|HYAL3_ENST00000450982.1_Silent_p.P82P|IFRD2_ENST00000417626.2_5'Flank|IFRD2_ENST00000429673.2_5'Flank|HYAL3_ENST00000513170.1_Intron|HYAL3_ENST00000415204.1_Intron|IFRD2_ENST00000336089.4_5'Flank|HYAL3_ENST00000359051.3_Silent_p.P82P	NM_001200029.1|NM_003549.3	NP_001186958.1|NP_003540.2	O43820	HYAL3_HUMAN	hyaluronoglucosaminidase 3	82					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|hyaluronan catabolic process (GO:0030214)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)|response to virus (GO:0009615)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|lysosome (GO:0005764)	hyaluronoglucuronidase activity (GO:0033906)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(5)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GTCCAAAGTAGGGATAGAGGC	0.577																																					p.P82P		Atlas-SNP	.											.	HYAL3	34	.	0			c.C246T						.						145	134	138					3																	50332788		2203	4300	6503	SO:0001819	synonymous_variant	8372	exon2			AAAGTAGGGATAG	AF040710	CCDS2815.1, CCDS56259.1, CCDS56260.1, CCDS56257.1	3p21.3	2004-03-12			ENSG00000186792	ENSG00000186792			5322	protein-coding gene	gene with protein product		604038				10493834	Standard	NM_003549		Approved	LUCA-3, LUCA14, Minna14	uc021wyn.1	O43820	OTTHUMG00000156936	ENST00000336307.1:c.246C>T	chr3.hg19:g.50332788G>A		86.0	0.0		61.0	18.0	NM_001200030	O60540|Q8NFK2|Q8NFK3|Q8NFK4|Q96E56|Q9BRW9	Silent	SNP	ENST00000336307.1	hg19	CCDS2815.1																																																																																			.	.		0.577	HYAL3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000346664.1	NM_003549		A	50332788	G	A	50332788	2	1	116	1	0	0	0	0	0	0	0	1	7474	987	35	3		3	HYAL3	3	50332788	Silent	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	12637561	50332788	147689642	13	20070										
KALRN	8997	hgsc.bcm.edu	37	chr3	123987858	123987858	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	caagaaaaaggtgctgaaggCccctgtggaggagctggacc	15	9	0	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr3:123987858C>T	ENST00000240874.3	+	5	876	c.719C>T	c.(718-720)gCc>gTc	p.A240V	KALRN_ENST00000460856.1_Missense_Mutation_p.A240V|KALRN_ENST00000360013.3_Missense_Mutation_p.A240V	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	240					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GTGCTGAAGGCCCCTGTGGAG	0.627																																					p.A240V		Atlas-SNP	.											.	KALRN	556	.	0			c.C719T						.						24	23	24					3																	123987858		2202	4300	6502	SO:0001583	missense	8997	exon5			TGAAGGCCCCTGT	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.719C>T	chr3.hg19:g.123987858C>T	ENSP00000240874:p.Ala240Val	195.0	0.0		230.0	17.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	hg19	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.9|24.9	4.580939|4.580939	0.86748|0.86748	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013|ENST00000448253;ENST00000354186	T;T;T|.	0.67698|.	-0.28;-0.28;-0.28|.	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77471|0.77471	0.4135|0.4135	M|M	0.76170|0.76170	2.325|2.325	0.80722|0.80722	D|D	1|1	D;D;D|.	0.76494|.	0.998;0.993;0.999|.	D;D;D|.	0.77004|.	0.975;0.978;0.989|.	T|T	0.75986|0.75986	-0.3124|-0.3124	10|5	0.28530|.	T|.	0.3|.	.|.	19.5125|19.5125	0.95148|0.95148	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	240;240;240|.	C9IZQ6;O60229;O60229-2|.	.;KALRN_HUMAN;.|.	V|S	240|268;218	ENSP00000418611:A240V;ENSP00000240874:A240V;ENSP00000353109:A240V|.	ENSP00000240874:A240V|.	A|P	+|+	2|1	0|0	KALRN|KALRN	125470548|125470548	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.685000|5.685000	0.68204|0.68204	2.840000|2.840000	0.97914|0.97914	0.655000|0.655000	0.94253|0.94253	GCC|CCC	.	.		0.627	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		T	123987858	C	T	123987858	3	4	116	1	0	0	0	0	1	0	0	0	7984	739	26	3	737	3	KALRN	3	123987858	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	73655070	123987858	74034572	14	20071										
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6595009	6595009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ccaacatcaacctctatgccGaggccctggtggccaacgtg	10	15	2	0	rs552037144		TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr4:6595009G>A	ENST00000285599.3	+	6	826	c.790G>A	c.(790-792)Gag>Aag	p.E264K	MAN2B2_ENST00000504248.1_Missense_Mutation_p.E264K	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	264					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CCTCTATGCCGAGGCCCTGGT	0.622													G|||	1	0.000199681	0	0	5008	,	,		20493	0		0	False		,,,				2504	0.001				p.E264K		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G790A						.						112	91	99					4																	6595009		2203	4300	6503	SO:0001583	missense	23324	exon6			TATGCCGAGGCCC	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"core-specific lysosomal alpha-1,6-Mannosidase"					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.790G>A	chr4.hg19:g.6595009G>A	ENSP00000285599:p.Glu264Lys	125.0	0.0		112.0	7.0	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	hg19	CCDS33951.1	.	.	.	.	.	.	.	.	.	.	G	7.956	0.745897	0.15710	.	.	ENSG00000013288	ENST00000285599;ENST00000504248	T;T	0.24908	1.83;1.83	4.59	-2.69	0.06022	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.892334	0.09864	N	0.745779	T	0.10723	0.0262	N	0.11789	0.175	0.09310	N	1	B;B;B	0.26363	0.012;0.012;0.147	B;B;B	0.15484	0.008;0.005;0.013	T	0.34204	-0.9838	10	0.18710	T	0.47	-2.6284	7.4724	0.27357	0.2368:0.2782:0.4849:0.0	.	264;264;264	E9PCD7;Q9Y2E5;Q9Y2E5-2	.;MA2B2_HUMAN;.	K	264	ENSP00000285599:E264K;ENSP00000423129:E264K	ENSP00000285599:E264K	E	+	1	0	MAN2B2	6645910	0.000000	0.05858	0.000000	0.03702	0.197000	0.23852	-0.595000	0.05727	-0.559000	0.06110	0.549000	0.68633	GAG	.	.		0.622	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		A	6595009	G	A	6595009	3	1	116	1	0	0	0	0	1	0	0	0	9226	1059	37	1	812	1	MAN2B2	4	6595009	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10		6595009	184559267	15	20072										
ENOPH1	58478	hgsc.bcm.edu	37	chr4	83378171	83378171	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ctcaaccaacaacattttgtTtctgacagatgttactcgag	6	10	2	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr4:83378171T>G	ENST00000273920.3	+	5	894	c.626T>G	c.(625-627)tTt>tGt	p.F209C	ENOPH1_ENST00000509635.1_Missense_Mutation_p.F121C	NM_021204.3	NP_067027.1			enolase-phosphatase 1											central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|skin(1)	13						AACATTTTGTTTCTGACAGAT	0.388																																					p.F209C		Atlas-SNP	.											.	ENOPH1	26	.	0			c.T626G						.						147	144	145					4																	83378171		2203	4300	6503	SO:0001583	missense	58478	exon5			TTTTGTTTCTGAC		CCDS3594.1, CCDS75154.1	4q21.3	2013-05-29			ENSG00000145293	ENSG00000145293	3.1.3.77		24599	protein-coding gene	gene with protein product	"Enolase-phosphatase E1", "acireductone synthase"					15843022	Standard	XM_005263168		Approved	MASA, E1, mtnC	uc003hmv.3	Q9UHY7	OTTHUMG00000130295	ENST00000273920.3:c.626T>G	chr4.hg19:g.83378171T>G	ENSP00000273920:p.Phe209Cys	168.0	0.0		176.0	55.0	NM_021204		Missense_Mutation	SNP	ENST00000273920.3	hg19	CCDS3594.1	.	.	.	.	.	.	.	.	.	.	t	22.4	4.283949	0.80803	.	.	ENSG00000145293	ENST00000273920;ENST00000509635	T;T	0.09630	2.96;2.96	5.37	5.37	0.77165	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);2,3-diketo-5-methylthio-1-phosphopentane phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.47544	0.1451	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65340	-0.6192	10	0.87932	D	0	-16.7356	15.6667	0.77236	0.0:0.0:0.0:1.0	.	209	Q9UHY7	ENOPH_HUMAN	C	209;121	ENSP00000273920:F209C;ENSP00000422005:F121C	ENSP00000273920:F209C	F	+	2	0	ENOPH1	83597195	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	7.828000	0.86729	2.158000	0.67659	0.477000	0.44152	TTT	.	.		0.388	ENOPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252638.2	NM_021204		G	83378171	T	G	83378171	3	3	116	1	0	0	0	0	1	0	0	0	5126	1841	64	5	644	5	ENOPH1	4	83378171	Missense_Mutation	SNP	T	TCGA-DD-A3A2-01A-11D-A20W-10	76783162	83378171	107776105	16	20073										
PCDH10	57575	hgsc.bcm.edu	37	chr4	134075516	134075516	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ttgacagacctcgccgagttAacaggtatggactctttttt	9	9	1	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr4:134075516A>C	ENST00000264360.5	+	2	3512	c.2686A>C	c.(2686-2688)Aac>Cac	p.N896H		NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	896					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		TCGCCGAGTTAACAGGTATGG	0.348																																					p.N896H		Atlas-SNP	.											.	PCDH10	290	.	0			c.A2686C						.						79	77	78					4																	134075516		2203	4300	6503	SO:0001583	missense	57575	exon2			CGAGTTAACAGGT	AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.2686A>C	chr4.hg19:g.134075516A>C	ENSP00000264360:p.Asn896His	183.0	0.0		174.0	59.0	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	hg19	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.629686	0.67015	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.54071	0.59	5.95	5.95	0.96441	.	0.142346	0.32328	N	0.006241	T	0.50480	0.1618	N	0.24115	0.695	0.58432	D	0.999996	D	0.56521	0.976	P	0.51016	0.656	T	0.51513	-0.8696	10	0.45353	T	0.12	.	16.0852	0.81042	1.0:0.0:0.0:0.0	.	896	Q9P2E7	PCD10_HUMAN	H	896	ENSP00000264360:N896H	ENSP00000264360:N896H	N	+	1	0	PCDH10	134294966	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.962000	0.93254	2.279000	0.76181	0.533000	0.62120	AAC	.	.		0.348	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		C	134075516	A	C	134075516	3	2	116	1	0	0	0	0	1	0	0	0	11516	362	13	5	2752	5	PCDH10	4	134075516	Missense_Mutation	SNP	A	TCGA-DD-A3A2-01A-11D-A20W-10	50697345	134075516	57078760	17	20074										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155157679	155157679	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	taagtaaaaatgtcccttctCatttccagagatgatgttgt	7	7	1	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr4:155157679C>A	ENST00000357232.4	-	25	6759	c.6760G>T	c.(6760-6762)Gag>Tag	p.E2254*		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2254	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E2254Q(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TGTCCCTTCTCATTTCCAGAG	0.403																																					p.E2254X		Atlas-SNP	.											DCHS2,rectum,carcinoma,0,1	DCHS2	594	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6760T						.						98	102	101					4																	155157679		2203	4300	6503	SO:0001587	stop_gained	54798	exon25			CCTTCTCATTTCC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6760G>T	chr4.hg19:g.155157679C>A	ENSP00000349768:p.Glu2254*	92.0	0.0		73.0	27.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Nonsense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	45	11.837165	0.99608	.	.	ENSG00000197410	ENST00000357232	.	.	.	5.64	5.64	0.86602	.	0.079447	0.51477	D	0.000083	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	19.7012	0.96054	0.0:1.0:0.0:0.0	.	.	.	.	X	2254	.	ENSP00000349768:E2254X	E	-	1	0	DCHS2	155377129	1.000000	0.71417	0.974000	0.42286	0.717000	0.41224	2.582000	0.46085	2.637000	0.89404	0.563000	0.77884	GAG	.	.		0.403	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155157679	C	A	155157679	4	1	116	1	0	0	0	0	0	1	0	0	4290	835	29	3	1994	3	DCHS2	4	155157679	Nonsense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	21082163	155157679	35996597	18	20075										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175896738	175896738	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gtcctgttctggacacatccAggatgagcacccccaatatc	8	14	1	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr4:175896738A>C	ENST00000359240.3	+	5	732	c.62A>C	c.(61-63)cAg>cCg	p.Q21P	RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_Missense_Mutation_p.Q21P|ADAM29_ENST00000404450.4_Missense_Mutation_p.Q21P|ADAM29_ENST00000514159.1_Missense_Mutation_p.Q21P	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	21					spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		GGACACATCCAGGATGAGCAC	0.507																																					p.Q21P	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.A62C						.						104	104	104					4																	175896738		2203	4300	6503	SO:0001583	missense	11086	exon4			ACATCCAGGATGA	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.62A>C	chr4.hg19:g.175896738A>C	ENSP00000352177:p.Gln21Pro	138.0	0.0		142.0	55.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	hg19	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	A	5.858	0.342574	0.11069	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000502940;ENST00000502305;ENST00000404450;ENST00000514159	T;T;T;T;T;T	0.55052	4.54;4.54;0.86;0.54;4.54;4.54	4.36	-1.37	0.09056	.	.	.	.	.	T	0.38506	0.1043	L	0.50333	1.59	0.09310	N	1	B	0.28026	0.198	B	0.22601	0.04	T	0.20739	-1.0266	8	.	.	.	.	4.9876	0.14198	0.7315:0.0:0.1179:0.1506	.	21	Q9UKF5	ADA29_HUMAN	P	21	ENSP00000352177:Q21P;ENSP00000414544:Q21P;ENSP00000427674:Q21P;ENSP00000422537:Q21P;ENSP00000384229:Q21P;ENSP00000423517:Q21P	.	Q	+	2	0	ADAM29	176133313	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.137000	0.15995	-0.285000	0.09089	0.519000	0.50382	CAG	.	.		0.507	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				C	175896738	A	C	175896738	3	2	116	1	0	0	0	0	1	0	0	0	247	188	7	5	64	5	ADAM29	4	175896738	Missense_Mutation	SNP	A	TCGA-DD-A3A2-01A-11D-A20W-10	20739059	175896738	15257538	19	20076										
FCHO2	115548	hgsc.bcm.edu	37	chr5	72347203	72347204	+	Frame_Shift_Ins	INS	-	-	A													0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	tgatgtagatgaagaaggctINSacagtattaaaccagaaaca							TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr5:72347203_72347204insA	ENST00000430046.2	+	12	1083_1084	c.967_968insA	c.(967-969)tacfs	p.Y323fs	FCHO2_ENST00000512348.1_Frame_Shift_Ins_p.Y290fs|FCHO2_ENST00000341845.6_Frame_Shift_Ins_p.Y323fs	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	323					clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		TGAAGAAGGCTACAGTATTAAA	0.297																																					p.Y323_S324delinsX		Atlas-INDEL	.											.	FCHO2	96	.	0			c.967_968insA						.																																			SO:0001589	frameshift_variant	115548	exon12			.	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.968dupA	chr5.hg19:g.72347204_72347204dupA	ENSP00000393776:p.Tyr323fs	116.0	0.0		82.0	16.0	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Frame_Shift_Ins	INS	ENST00000430046.2	hg19	CCDS47230.1																																																																																			.	.		0.297	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		A	72347204	-	A	72347203	7	5	116	1	0	1	1	0	0	0	0	0	5796	1522	53	0	1013	0	FCHO2	5	72347203	Frame_Shift_Ins	INS	-	TCGA-DD-A3A2-01A-11D-A20W-10		72347203	108568057	20	20077	85	2								
FCHO2	115548	hgsc.bcm.edu	37	chr5	72347205	72347205	+	Nonsense_Mutation	SNP	C	C	A													0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gatgtagatgaagaaggctaCagtattaaaccagaaacaaa							TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr5:72347205C>A	ENST00000430046.2	+	12	1085	c.969C>A	c.(967-969)taC>taA	p.Y323*	FCHO2_ENST00000512348.1_Nonsense_Mutation_p.Y290*|FCHO2_ENST00000341845.6_Nonsense_Mutation_p.Y323*	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	323					clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		AAGAAGGCTACAGTATTAAAC	0.289																																					p.Y323X		Atlas-SNP	.											.	FCHO2	96	.	0			c.C969A						.						75	71	72					5																	72347205		1718	3865	5583	SO:0001587	stop_gained	115548	exon12			AGGCTACAGTATT	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.969C>A	chr5.hg19:g.72347205C>A	ENSP00000393776:p.Tyr323*	118.0	0.0		85.0	16.0	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Nonsense_Mutation	SNP	ENST00000430046.2	hg19	CCDS47230.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.815388	0.90790	.	.	ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348	.	.	.	4.87	2.38	0.29361	.	0.209202	0.42172	D	0.000757	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6207	8.5108	0.33215	0.0:0.2614:0.0:0.7386	.	.	.	.	X	323;323;290	.	ENSP00000344034:Y323X	Y	+	3	2	FCHO2	72382961	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.543000	0.36147	0.271000	0.22005	-0.312000	0.09012	TAC	.	.		0.289	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		A	72347205	C	A	72347205	4	1	116	1	0	0	0	0	0	1	0	0	5796	489	17	3	1015	3	FCHO2	5	72347205	Nonsense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	2	72347205	108568055	21	20078	85	2								
GFM2	84340	hgsc.bcm.edu	37	chr5	74026206	74026206	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	atctctatatgtaactccccCataccacacagaacagtctg	4	14	2	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr5:74026206C>G	ENST00000296805.3	-	17	2062	c.1605G>C	c.(1603-1605)atG>atC	p.M535I	GFM2_ENST00000345239.2_Missense_Mutation_p.M488I|GFM2_ENST00000515125.1_Intron|GFM2_ENST00000509430.1_Missense_Mutation_p.M535I	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		GTAACTCCCCCATACCACACA	0.383																																					p.M535I		Atlas-SNP	.											.	GFM2	38	.	0			c.G1605C						.						100	93	95					5																	74026206		2203	4300	6503	SO:0001583	missense	84340	exon17			CTCCCCCATACCA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1605G>C	chr5.hg19:g.74026206C>G	ENSP00000296805:p.Met535Ile	139.0	0.0		133.0	53.0	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.882003	0.91740	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000509430	T;T;T	0.76709	-1.04;-1.04;-1.04	5.64	5.64	0.86602	Elongation factor G/III/V (1);	0.000000	0.85682	D	0.000000	D	0.89262	0.6665	M	0.82056	2.57	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.996;0.994	D	0.89986	0.4104	10	0.87932	D	0	-23.315	19.7116	0.96098	0.0:1.0:0.0:0.0	.	535;488;535	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	I	535;488;535	ENSP00000296805:M535I;ENSP00000296804:M488I;ENSP00000427004:M535I	ENSP00000296805:M535I	M	-	3	0	GFM2	74061962	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.595000	0.82710	2.673000	0.90976	0.555000	0.69702	ATG	.	.		0.383	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		G	74026206	C	G	74026206	3	3	116	1	0	0	0	0	1	0	0	0	6350	594	21	4	754	4	GFM2	5	74026206	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	1679001	74026206	106889054	22	20079										
POLK	51426	hgsc.bcm.edu	37	chr5	74872759	74872759	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gggaagctctgtagaaaatgGtaagcaacttattaagacta	10	5	1	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr5:74872759G>C	ENST00000241436.4	+	6	866		c.e6+1		POLK_ENST00000504026.1_Splice_Site|POLK_ENST00000380481.3_Splice_Site|POLK_ENST00000508526.1_Splice_Site|POLK_ENST00000515295.1_Splice_Site|POLK_ENST00000506928.1_Splice_Site|POLK_ENST00000352007.5_Splice_Site	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa						DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		GTAGAAAATGGTAAGCAACTT	0.328								DNA polymerases (catalytic subunits)																													.		Atlas-SNP	.											.	POLK	123	.	0			c.694+1G>C						.						46	46	46					5																	74872759		2203	4299	6502	SO:0001630	splice_region_variant	51426	exon6			AAAATGGTAAGCA	AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"DNA polymerases"	9183	protein-coding gene	gene with protein product	"polymerase (DNA-directed) kappa", "DINB protein", "DNA polymerase kappa"	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.694+1G>C	chr5.hg19:g.74872759G>C		83.0	0.0		64.0	24.0	NM_016218	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Splice_Site	SNP	ENST00000241436.4	hg19	CCDS4030.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.631977	0.67015	.	.	ENSG00000122008	ENST00000241436;ENST00000352007;ENST00000515295;ENST00000504026;ENST00000508526;ENST00000380481	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.035	0.89298	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	POLK	74908515	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	4.950000	0.63603	2.695000	0.91970	0.563000	0.77884	.	.	.		0.328	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218	Intron	C	74872759	G	C	74872759	5	2	116	1	0	0	0	0	0	0	1	0	12213	1275	44	4	713	4	POLK	5	74872759	Splice_Site	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	846553	74872759	106042501	23	20080										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140203294	140203294	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gaccgaagcaccgcgccaccGccttctggtgctggtgaagg	14	14	1	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr5:140203294G>A	ENST00000529859.1	+	1	1934	c.1934G>A	c.(1933-1935)cGc>cAc	p.R645H	PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.R645H|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.R645H	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	645	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCGCCACCGCCTTCTGGTG	0.662																																					p.R645H		Atlas-SNP	.											PCDHA5_ENST00000529859,caecum,carcinoma,0,2	PCDHA5	361	.	0			c.G1934A						.						54	60	58					5																	140203294		2203	4300	6503	SO:0001583	missense	56143	exon1			GCCACCGCCTTCT	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.1934G>A	chr5.hg19:g.140203294G>A	ENSP00000436557:p.Arg645His	208.0	0.0		275.0	97.0	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	hg19	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.350140	0.24512	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.51817	0.69;0.69;0.69	4.01	0.66	0.17868	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.38957	0.1060	M	0.69463	2.115	0.09310	N	1	B;B;B	0.33739	0.422;0.102;0.024	B;B;B	0.21546	0.035;0.033;0.031	T	0.30149	-0.9988	9	0.62326	D	0.03	.	6.565	0.22507	0.2566:0.1793:0.5641:0.0	.	645;645;645	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	H	645	ENSP00000433416:R645H;ENSP00000436557:R645H;ENSP00000367366:R645H	ENSP00000367366:R645H	R	+	2	0	PCDHA5	140183478	0.000000	0.05858	0.288000	0.24862	0.883000	0.51084	-0.114000	0.10757	0.308000	0.22923	-0.683000	0.03753	CGC	.	.		0.662	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		A	140203294	G	A	140203294	3	1	116	1	0	0	0	0	1	0	0	0	11536	1087	38	1	1936	1	PCDHA5	5	140203294	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	65330535	140203294	40711966	24	20081										
PRELID2	153768	hgsc.bcm.edu	37	chr5	145176020	145176020	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gttaccttctgggctccctgTcgtaagaatgtgctggcaaa	11	10	1	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr5:145176020T>G	ENST00000334744.4	-	6	547	c.495A>C	c.(493-495)cgA>cgC	p.R165R	PRELID2_ENST00000394450.2_Silent_p.R124R|PRELID2_ENST00000510594.1_5'UTR|PRELID2_ENST00000511435.1_Silent_p.R153R|PRELID2_ENST00000358004.2_Silent_p.R153R|PRELID2_ENST00000505416.1_Silent_p.R153R	NM_182960.2	NP_892005.1	Q8N945	PRLD2_HUMAN	PRELI domain containing 2	165	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)			endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGGCTCCCTGTCGTAAGAATG	0.378																																					p.R165R		Atlas-SNP	.											.	PRELID2	16	.	0			c.A495C						.						121	130	127					5																	145176020		2203	4300	6503	SO:0001819	synonymous_variant	153768	exon6			TCCCTGTCGTAAG	AK095695	CCDS34261.1, CCDS34262.1, CCDS43377.1	5q32	2012-04-23			ENSG00000186314	ENSG00000186314			28306	protein-coding gene	gene with protein product						12477932	Standard	NM_182960		Approved	MGC21644, FLJ38376	uc003lnq.1	Q8N945	OTTHUMG00000163384	ENST00000334744.4:c.495A>C	chr5.hg19:g.145176020T>G		62.0	0.0		45.0	20.0	NM_182960	G5EA01|Q96EQ3	Silent	SNP	ENST00000334744.4	hg19	CCDS34262.1																																																																																			.	.		0.378	PRELID2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000372970.1	NM_182960		G	145176020	T	G	145176020	2	3	116	1	0	0	0	0	0	0	0	1	12484	1654	58	5		5	PRELID2	5	145176020	Silent	SNP	T	TCGA-DD-A3A2-01A-11D-A20W-10	4972726	145176020	35739240	25	20082										
GLI3	2737	hgsc.bcm.edu	37	chr7	42005030	42005030	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	tgctgttctccccgagggtcTgatagcccccagcaggcccg	12	16	2	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr7:42005030T>G	ENST00000395925.3	-	15	3725	c.3641A>C	c.(3640-3642)cAg>cCg	p.Q1214P	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1214					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CCCGAGGGTCTGATAGCCCCC	0.652									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.Q1214P		Atlas-SNP	.											.	GLI3	312	.	0			c.A3641C						.						48	57	54					7																	42005030		2203	4300	6503	SO:0001583	missense	2737	exon15	Familial Cancer Database	;	AGGGTCTGATAGC		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.3641A>C	chr7.hg19:g.42005030T>G	ENSP00000379258:p.Gln1214Pro	76.0	0.0		85.0	24.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	T	10.92	1.486905	0.26686	.	.	ENSG00000106571	ENST00000395925	T	0.14391	2.51	5.64	-3.29	0.05017	.	0.803221	0.11869	N	0.521607	T	0.06234	0.0161	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21381	-1.0247	10	0.38643	T	0.18	.	19.6624	0.95878	0.0:0.0:0.7125:0.2875	.	1214	P10071	GLI3_HUMAN	P	1214	ENSP00000379258:Q1214P	ENSP00000379258:Q1214P	Q	-	2	0	GLI3	41971555	0.007000	0.16637	0.000000	0.03702	0.044000	0.14063	0.897000	0.28390	-0.859000	0.04105	0.496000	0.49642	CAG	.	.		0.652	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		G	42005030	T	G	42005030	3	3	116	1	0	0	0	0	1	0	0	0	6447	1580	55	5	1105	5	GLI3	7	42005030	Missense_Mutation	SNP	T	TCGA-DD-A3A2-01A-11D-A20W-10		42005030	117133633	26	20083										
ELN	2006	hgsc.bcm.edu	37	chr7	73477959	73477959	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ctgtctccacaggcctagtgGgagccgctgggctcggagga	16	12	1	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr7:73477959G>A	ENST00000252034.7	+	29	2326	c.1927G>A	c.(1927-1929)Gga>Aga	p.G643R	ELN_ENST00000458204.1_Missense_Mutation_p.G633R|ELN_ENST00000357036.5_Missense_Mutation_p.G648R|ELN_ENST00000320492.7_Missense_Mutation_p.G562R|ELN_ENST00000429192.1_Missense_Mutation_p.G629R|CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000414324.1_Missense_Mutation_p.G619R|ELN_ENST00000445912.1_Missense_Mutation_p.G643R|ELN_ENST00000358929.4_Missense_Mutation_p.G711R|ELN_ENST00000380553.4_Missense_Mutation_p.G507R|ELN_ENST00000380584.4_Missense_Mutation_p.G595R|ELN_ENST00000380575.4_Missense_Mutation_p.G614R|ELN_ENST00000380562.4_Missense_Mutation_p.G649R|ELN_ENST00000380576.5_Missense_Mutation_p.G624R|ELN_ENST00000320399.6_Missense_Mutation_p.G676R	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				AGGCCTAGTGGGAGCCGCTGG	0.612			T	PAX5	B-ALL		"Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"																														p.G648R		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN	81	.	0			c.G1942A						.						113	105	108					7																	73477959		2203	4300	6503	SO:0001583	missense	2006	exon29			CTAGTGGGAGCCG		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"tropoelastin", "supravalvular aortic stenosis", "Williams-Beuren syndrome"	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1927G>A	chr7.hg19:g.73477959G>A	ENSP00000252034:p.Gly643Arg	345.0	0.0		479.0	27.0	NM_001081754	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Missense_Mutation	SNP	ENST00000252034.7	hg19	CCDS5562.2	.	.	.	.	.	.	.	.	.	.	G	11.50	1.657390	0.29425	.	.	ENSG00000049540	ENST00000445912;ENST00000252034;ENST00000358929;ENST00000320492;ENST00000414324;ENST00000380562;ENST00000380575;ENST00000380584;ENST00000458204;ENST00000357036;ENST00000429192;ENST00000442462;ENST00000380553;ENST00000380576;ENST00000320399	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.62941	0.04;0.09;0.49;0.3;0.14;0.11;0.15;0.11;0.17;0.17;0.19;-0.01;0.14;0.17	2.4	2.4	0.29515	.	.	.	.	.	T	0.70666	0.3250	.	.	.	0.09310	N	0.999999	D;D;D;D;D;D;D;D;D;D;D;D;D	0.69078	0.997;0.997;0.997;0.997;0.997;0.997;0.997;0.997;0.997;0.997;0.997;0.997;0.997	P;P;P;P;P;P;P;P;P;P;P;P;P	0.61658	0.892;0.892;0.892;0.892;0.892;0.892;0.892;0.892;0.892;0.892;0.892;0.892;0.892	T	0.57688	-0.7768	8	0.72032	D	0.01	.	8.48	0.33036	0.0:0.0:1.0:0.0	.	643;562;619;633;649;614;629;648;624;507;554;595;643	E7ENM0;G5E950;G3V0G6;E7EN65;P15502-1;P15502-7;P15502-12;P15502-5;P15502-13;P15502-11;B3KRT8;P15502-8;P15502-2	.;.;.;.;.;.;.;.;.;.;.;.;.	R	643;643;711;562;619;649;614;595;633;648;629;582;507;624;676	ENSP00000389857:G643R;ENSP00000252034:G643R;ENSP00000351807:G711R;ENSP00000315607:G562R;ENSP00000392575:G619R;ENSP00000369936:G649R;ENSP00000369949:G614R;ENSP00000369958:G595R;ENSP00000403162:G633R;ENSP00000349540:G648R;ENSP00000391129:G629R;ENSP00000369926:G507R;ENSP00000369950:G624R;ENSP00000313565:G676R	ENSP00000252034:G643R	G	+	1	0	ELN	73115895	0.307000	0.24500	0.200000	0.23457	0.008000	0.06430	2.223000	0.42936	1.667000	0.50832	0.460000	0.39030	GGA	.	.		0.612	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501		A	73477959	G	A	73477959	3	1	116	1	0	0	0	0	1	0	0	0	5073	1233	43	3	2056	3	ELN	7	73477959	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	31472929	73477959	85660704	27	20084										
MGAM	8972	hgsc.bcm.edu	37	chr7	141726934	141726934	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gaggttgtccttcagcctgcGccagccatcacttaccgcac	9	16	2	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr7:141726934G>T	ENST00000549489.2	+	9	1097	c.1002G>T	c.(1000-1002)gcG>gcT	p.A334A	MGAM_ENST00000475668.2_Silent_p.A334A	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	334	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTCAGCCTGCGCCAGCCATCA	0.383																																					p.A334A		Atlas-SNP	.											.	MGAM	767	.	0			c.G1002T						.						132	122	125					7																	141726934		1877	4118	5995	SO:0001819	synonymous_variant	8972	exon9			GCCTGCGCCAGCC	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.1002G>T	chr7.hg19:g.141726934G>T		101.0	0.0		183.0	55.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	hg19	CCDS47727.1																																																																																			.	.		0.383	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141726934	G	T	141726934	2	4	116	1	0	0	0	0	0	0	0	1	9550	1074	38	1		1	MGAM	7	141726934	Silent	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	68248975	141726934	17411729	28	20085										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10469481	10469481	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gaggcctgtgtcctggtgctCgatgagcttccagaatatcg	13	10	0	2	rs367955605		TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr8:10469481C>T	ENST00000382483.3	-	4	2350	c.2127G>A	c.(2125-2127)tcG>tcA	p.S709S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	709					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TCCTGGTGCTCGATGAGCTTC	0.622																																					p.S709S		Atlas-SNP	.											.	RP1L1	453	.	0			c.G2127A						.						48	58	55					8																	10469481		2062	4193	6255	SO:0001819	synonymous_variant	94137	exon4			GGTGCTCGATGAG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2127G>A	chr8.hg19:g.10469481C>T		90.0	0.0		113.0	45.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	hg19	CCDS43708.1																																																																																			.	.		0.622	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10469481	C	T	10469481	2	4	116	1	0	0	0	0	0	0	0	1	13548	871	31	1		1	RP1L1	8	10469481	Silent	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10		10469481	135894541	29	20086										
OTUD6B	51633	hgsc.bcm.edu	37	chr8	92082521	92082620	+	Start_Codon_Del	DEL	CATTTAAGTTTCTCGTCTTTGCAGTGGCTTTGCTTAGATCCGGTGCCGCCTTGAAGGCGGGGCTGGGTCCCAGCCGTAGCCAATGGAGCCCCGGGTGAGG	CATTTAAGTTTCTCGTCTTTGCAGTGGCTTTGCTTAGATCCGGTGCCGCCTTGAAGGCGGGGCTGGGTCCCAGCCGTAGCCAATGGAGCCCCGGGTGAGG	-													0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ggctgggtcccagccgtagcCaatggagccccgggtgaggg					rs375158776|rs201838277|rs556885788|rs186307892|rs112052524|rs375130734|rs199542428	byFrequency	TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	CATTTAAGTTTCTCGTCTTTGCAGTGGCTTTGCTTAGATCCGGTGCCGCCTTGAAGGCGGGGCTGGGTCCCAGCCGTAGCCAATGGAGCCCCGGGTGAGG	CATTTAAGTTTCTCGTCTTTGCAGTGGCTTTGCTTAGATCCGGTGCCGCCTTGAAGGCGGGGCTGGGTCCCAGCCGTAGCCAATGGAGCCCCGGGTGAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr8:92082521_92082620delCATTTAAGTTTCTCGTCTTTGCAGTGGCTTTGCTTAGATCCGGTGCCGCCTTGAAGGCGGGGCTGGGTCCCAGCCGTAGCCAATGGAGCCCCGGGTGAGG	ENST00000285420.4	+	0	98_197				OTUD6B_ENST00000404789.3_5'UTR|GS1-251I9.4_ENST00000524003.1_RNA|GS1-251I9.4_ENST00000522817.1_RNA	NM_016023.3	NP_057107.3	Q8N6M0	OTU6B_HUMAN	OTU domain containing 6B								cysteine-type peptidase activity (GO:0008234)	p.L28L(1)|p.S15R(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11			BRCA - Breast invasive adenocarcinoma(11;0.0187)			CAGCCGTAGCCAATGGAGCCCCGGGTGAGGGTTGAGGGGTGGAAGGTGCCTACTAGCCGGTGCAGGTTTCTTCTAGCGCGTGTGCTGGGGTACCTGGTCGTCATGGAGGCGGTATTGACC	0.59																																					.		Pindel	.											.	OTUD6B	28	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	ovary(1)|lung(1)	.						.																																			SO:0001582	initiator_codon_variant	51633	wholegene			.		CCDS6253.2, CCDS69513.1	8q21.3	2013-01-21			ENSG00000155100	ENSG00000155100		"OTU domain containing"	24281	protein-coding gene	gene with protein product		612021					Standard	NM_016023		Approved	CGI-77, DUBA5	uc003yeu.4	Q8N6M0	OTTHUMG00000150758		chr8.hg19:g.92082521_92082620delCATTTAAGTTTCTCGTCTTTGCAGTGGCTTTGCTTAGATCCGGTGCCGCCTTGAAGGCGGGGCTGGGTCCCAGCCGTAGCCAATGGAGCCCCGGGTGAGG		154.0	0.0		134.0	42.0	NM_016023	A8K6I1|B4DEY0|Q9NTA4|Q9Y387	Frame_Shift_Del	DEL	ENST00000285420.4	hg19	CCDS6253.2																																																																																			.	.		0.59	OTUD6B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000319968.1	NM_016023		-	92082620	CATTTAAGTTTCTCGTCTTTGCAGTGGCTTTGCTTAGATCCGGTGCCGCCTTGAAGGCGGGGCTGGGTCCCAGCCGTAGCCAATGGAGCCCCGGGTGAGG	-	92082521	7	5	116	1	0	1	0	1	0	0	0	0	11326	609	21	0	1	0	OTUD6B	8	92082521	Start_Codon_Del	DEL	CATTTAAGTTTCTCGTCTTTGCAGTGGCTTTGCTTAGATCCGGTGCCGCCTTGAAGGCGGGGCTGGGTCCCAGCCGTAGCCAATGGAGCCCCGGGTGAGG	TCGA-DD-A3A2-01A-11D-A20W-10	81613040	92082521	54281501	30	20087										
FKBP15	23307	hgsc.bcm.edu	37	chr9	115938874	115938876	+	In_Frame_Del	DEL	CAC	CAC	-													0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	agttcctcctccagggatgtCaccttgagttccagttgttt							TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr9:115938874_115938876delCAC	ENST00000238256.3	-	21	2281_2283	c.2164_2166delGTG	c.(2164-2166)gtgdel	p.V722del		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	722					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						CCAGGGATGTCACCTTGAGTTCC	0.468																																					p.722_723del		Atlas-Indel,Pindel	.											.	FKBP15	128	.	0			c.2165_2167del						.																																			SO:0001651	inframe_deletion	23307	exon21			.	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23397	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 76", "WASP and FKBP-like protein"		"KIAA0674"	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2164_2166delGTG	chr9.hg19:g.115938874_115938876delCAC	ENSP00000238256:p.Val722del	313.0	0.0		318.0	101.0	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	In_Frame_Del	DEL	ENST00000238256.3	hg19	CCDS48007.1																																																																																			.	.		0.468	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258		-	115938876	CAC	-	115938874	7	5	116	1	0	1	0	1	0	0	0	0	5913	813	29	0	1525	0	FKBP15	9	115938874	In_Frame_Del	DEL	CAC	TCGA-DD-A3A2-01A-11D-A20W-10		115938874	25274557	31	20088										
ASB6	140459	hgsc.bcm.edu	37	chr9	132400301	132400301	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ccacagggtggatatcgaagTtttcgggcagctggagtttc	14	8	0	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr9:132400301T>G	ENST00000277458.4	-	6	1199	c.1034A>C	c.(1033-1035)aAc>aCc	p.N345T	ASB6_ENST00000277459.4_3'UTR|ASB6_ENST00000450050.2_Missense_Mutation_p.N266T|RP11-483H20.4_ENST00000455074.1_RNA	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	345					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				NS(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	15		Ovarian(14;0.00556)				GATATCGAAGTTTTCGGGCAG	0.597																																					p.N345T		Atlas-SNP	.											.	ASB6	31	.	0			c.A1034C						.						83	79	80					9																	132400301		2203	4300	6503	SO:0001583	missense	140459	exon6			TCGAAGTTTTCGG		CCDS6924.1, CCDS6925.1, CCDS75919.1	9q34.13	2013-01-10	2011-01-25		ENSG00000148331	ENSG00000148331		"Ankyrin repeat domain containing"	17181	protein-coding gene	gene with protein product		615051	"ankyrin repeat and SOCS box-containing 6"				Standard	NM_017873		Approved		uc004byf.2	Q9NWX5	OTTHUMG00000020787	ENST00000277458.4:c.1034A>C	chr9.hg19:g.132400301T>G	ENSP00000277458:p.Asn345Thr	53.0	0.0		67.0	31.0	NM_017873	Q5SZB7|Q9BV15	Missense_Mutation	SNP	ENST00000277458.4	hg19	CCDS6924.1	.	.	.	.	.	.	.	.	.	.	T	12.97	2.098473	0.37048	.	.	ENSG00000148331	ENST00000277458;ENST00000450050	T;T	0.70631	-0.5;0.78	5.06	2.73	0.32206	.	0.350115	0.34362	N	0.004026	T	0.52645	0.1747	N	0.24115	0.695	0.38297	D	0.942871	B;B;B	0.26002	0.005;0.139;0.139	B;B;B	0.22386	0.01;0.039;0.027	T	0.48317	-0.9046	10	0.42905	T	0.14	-41.8137	8.6356	0.33945	0.0:0.157:0.0:0.843	.	266;345;345	B4DRC4;A8K9U2;Q9NWX5	.;.;ASB6_HUMAN	T	345;266	ENSP00000277458:N345T;ENSP00000416172:N266T	ENSP00000277458:N345T	N	-	2	0	ASB6	131440122	1.000000	0.71417	0.840000	0.33206	0.782000	0.44232	2.791000	0.47829	0.411000	0.25702	0.379000	0.24179	AAC	.	.		0.597	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873		G	132400301	T	G	132400301	3	3	116	1	0	0	0	0	1	0	0	0	1027	1725	60	5	235	5	ASB6	9	132400301	Missense_Mutation	SNP	T	TCGA-DD-A3A2-01A-11D-A20W-10	16461427	132400301	8813130	32	20089										
FAM69B	138311	hgsc.bcm.edu	37	chr9	139617874	139617874	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ctacgacttcaagatggccgAcctgcagcaggtggcacccg	12	14	1	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr9:139617874A>C	ENST00000371692.4	+	5	1040	c.944A>C	c.(943-945)gAc>gCc	p.D315A	FAM69B_ENST00000371691.1_Missense_Mutation_p.D228A|SNHG7_ENST00000447221.1_RNA|SNHG7_ENST00000362567.2_RNA|SNHG7_ENST00000436596.1_RNA|SNHG7_ENST00000414282.1_RNA|SNHG7_ENST00000416970.1_RNA	NM_152421.3	NP_689634.2	Q5VUD6	FA69B_HUMAN	family with sequence similarity 69, member B	315						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|large_intestine(2)|lung(1)|prostate(1)	8	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.03e-05)|Epithelial(140;0.00013)		AAGATGGCCGACCTGCAGCAG	0.657																																					p.D315A		Atlas-SNP	.											.	FAM69B	22	.	0			c.A944C						.						34	33	33					9																	139617874		2203	4300	6503	SO:0001583	missense	138311	exon5			TGGCCGACCTGCA		CCDS7004.1	9q34.3	2012-08-03			ENSG00000165716	ENSG00000165716			28290	protein-coding gene	gene with protein product		614543				21334309	Standard	NM_152421		Approved	MGC20262, C9orf136	uc004cik.3	Q5VUD6	OTTHUMG00000020940	ENST00000371692.4:c.944A>C	chr9.hg19:g.139617874A>C	ENSP00000360757:p.Asp315Ala	47.0	0.0		38.0	8.0	NM_152421	Q5VUD7|Q8N5N0|Q8WYU5	Missense_Mutation	SNP	ENST00000371692.4	hg19	CCDS7004.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.891032	0.91889	.	.	ENSG00000165716	ENST00000371692;ENST00000371691	T;T	0.68025	-0.3;-0.28	5.29	5.29	0.74685	.	0.195156	0.53938	D	0.000053	T	0.75072	0.3800	M	0.75615	2.305	0.58432	D	0.999998	P	0.50819	0.939	P	0.51324	0.666	T	0.79415	-0.1813	10	0.87932	D	0	-55.3285	14.3785	0.66895	1.0:0.0:0.0:0.0	.	315	Q5VUD6	FA69B_HUMAN	A	315;228	ENSP00000360757:D315A;ENSP00000360756:D228A	ENSP00000360756:D228A	D	+	2	0	FAM69B	138737695	1.000000	0.71417	0.996000	0.52242	0.965000	0.64279	8.253000	0.89842	1.992000	0.58205	0.459000	0.35465	GAC	.	.		0.657	FAM69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055102.1	NM_152421		C	139617874	A	C	139617874	3	2	116	1	0	0	0	0	1	0	0	0	5611	275	10	5	962	5	FAM69B	9	139617874	Missense_Mutation	SNP	A	TCGA-DD-A3A2-01A-11D-A20W-10	7217573	139617874	1595557	33	20090										
TAF3	83860	hgsc.bcm.edu	37	chr10	8006861	8006861	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	aacctcaagttccgataactCatggacaatggatgcctcca	7	12	2	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr10:8006861C>T	ENST00000344293.5	+	3	1594	c.1388C>T	c.(1387-1389)tCa>tTa	p.S463L		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	463					maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						TCCGATAACTCATGGACAATG	0.468																																					p.S463L		Atlas-SNP	.											.	TAF3	93	.	0			c.C1388T						.						95	93	94					10																	8006861		1943	4151	6094	SO:0001583	missense	83860	exon3			ATAACTCATGGAC	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"Zinc fingers, PHD-type"	17303	protein-coding gene	gene with protein product		606576	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.1388C>T	chr10.hg19:g.8006861C>T	ENSP00000340271:p.Ser463Leu	108.0	0.0		109.0	39.0	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	hg19	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.538434	0.65085	.	.	ENSG00000165632	ENST00000344293	T	0.21734	1.99	5.62	5.62	0.85841	.	0.000000	0.56097	D	0.000033	T	0.50051	0.1593	M	0.79475	2.455	0.54753	D	0.999987	D	0.76494	0.999	D	0.78314	0.991	T	0.41448	-0.9508	10	0.40728	T	0.16	-13.8288	19.6582	0.95853	0.0:1.0:0.0:0.0	.	463	Q5VWG9	TAF3_HUMAN	L	463	ENSP00000340271:S463L	ENSP00000340271:S463L	S	+	2	0	TAF3	8046867	1.000000	0.71417	0.991000	0.47740	0.623000	0.37688	5.308000	0.65768	2.659000	0.90383	0.650000	0.86243	TCA	.	.		0.468	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		T	8006861	C	T	8006861	3	4	116	1	0	0	0	0	1	0	0	0	15540	838	29	3	1398	3	TAF3	10	8006861	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10		8006861	127527886	34	20091										
ANUBL1	93550	hgsc.bcm.edu	37	chr10	46111982	46111982	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ataggtacagccatgagtttCtgcataacgatgagatgcac	10	8	1	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr10:46111982C>G	ENST00000344646.5	-	10	2301	c.2086G>C	c.(2086-2088)Gaa>Caa	p.E696Q	ZFAND4_ENST00000374370.1_5'UTR|ZFAND4_ENST00000374371.2_3'UTR|ZFAND4_ENST00000374366.3_Missense_Mutation_p.E622Q	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	696							zinc ion binding (GO:0008270)										CCATGAGTTTCTGCATAACGA	0.403																																					p.E696Q		Atlas-SNP	.											.	.	.	.	0			c.G2086C						.						175	152	160					10																	46111982		2203	4300	6503	SO:0001583	missense	93550	exon10			GAGTTTCTGCATA	AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"Zinc fingers, AN1-type domain containing"	23504	protein-coding gene	gene with protein product			"AN1, ubiquitin-like, homolog (Xenopus laevis)"	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.2086G>C	chr10.hg19:g.46111982C>G	ENSP00000339484:p.Glu696Gln	224.0	0.0		228.0	71.0	NM_001128324	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	hg19	CCDS7214.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.730709	0.89390	.	.	ENSG00000172671	ENST00000344646;ENST00000374366;ENST00000374370	T;T	0.53640	0.61;0.61	5.86	5.86	0.93980	Zinc finger, AN1-type (4);	0.255515	0.37053	N	0.002261	T	0.69780	0.3149	M	0.74647	2.275	0.80722	D	1	D	0.61697	0.99	D	0.74348	0.983	T	0.71699	-0.4514	10	0.87932	D	0	-23.9616	17.6957	0.88281	0.0:1.0:0.0:0.0	.	696	Q86XD8	ANUB1_HUMAN	Q	696;622;578	ENSP00000339484:E696Q;ENSP00000363486:E622Q	ENSP00000339484:E696Q	E	-	1	0	ANUBL1	45431988	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.452000	0.80683	2.776000	0.95493	0.655000	0.94253	GAA	.	.		0.403	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890		G	46111982	C	G	46111982	3	3	116	1	0	0	0	0	1	0	0	0	713	922	32	4	101	4	ANUBL1	10	46111982	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	38105121	46111982	89422765	35	20092										
HTR7	3363	hgsc.bcm.edu	37	chr10	92509305	92509305	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	catcttcgccatgcatttccCattctgcctcacagggtatg	7	14	3	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr10:92509305C>A	ENST00000336152.3	-	2	612	c.586G>T	c.(586-588)Ggg>Tgg	p.G196W	HTR7_ENST00000277874.6_Missense_Mutation_p.G196W|HTR7_ENST00000371721.3_Missense_Mutation_p.G196W|HTR7_ENST00000371719.2_Missense_Mutation_p.G196W	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	196					blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	ATGCATTTCCCATTCTGCCTC	0.483																																					p.G196W		Atlas-SNP	.											.	HTR7	122	.	0			c.G586T						.						118	120	119					10																	92509305		2203	4300	6503	SO:0001583	missense	3363	exon2			ATTTCCCATTCTG	BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5302	protein-coding gene	gene with protein product		182137	"5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)"			8226867	Standard	NM_000872		Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000336152.3:c.586G>T	chr10.hg19:g.92509305C>A	ENSP00000337949:p.Gly196Trp	92.0	0.0		137.0	52.0	NM_019860	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Missense_Mutation	SNP	ENST00000336152.3	hg19	CCDS7408.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.947014	0.73672	.	.	ENSG00000148680	ENST00000336152;ENST00000277874;ENST00000371719;ENST00000371721	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	5.44	5.44	0.79542	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.86377	0.5918	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.86957	0.2089	10	0.56958	D	0.05	.	19.4432	0.94831	0.0:1.0:0.0:0.0	.	196;196	P34969;P34969-2	5HT7R_HUMAN;.	W	196	ENSP00000337949:G196W;ENSP00000277874:G196W;ENSP00000360784:G196W;ENSP00000360786:G196W	ENSP00000277874:G196W	G	-	1	0	HTR7	92499285	1.000000	0.71417	0.999000	0.59377	0.613000	0.37349	5.932000	0.70121	2.833000	0.97629	0.650000	0.86243	GGG	.	.		0.483	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1	NM_000872		A	92509305	C	A	92509305	3	1	116	1	0	0	0	0	1	0	0	0	7461	594	21	3	869	3	HTR7	10	92509305	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	46397323	92509305	43025442	36	20093										
C10orf81	79949	hgsc.bcm.edu	37	chr10	115528632	115528632	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ttcgccaggatataaaagcaAcacagcagaacacagaggtg	10	9	0	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr10:115528632A>G	ENST00000369310.3	+	5	962	c.400A>G	c.(400-402)Aca>Gca	p.T134A	PLEKHS1_ENST00000361048.1_Missense_Mutation_p.T140A|PLEKHS1_ENST00000369309.1_5'Flank|PLEKHS1_ENST00000369312.4_Missense_Mutation_p.T52A	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	134																	TATAAAAGCAACACAGCAGAA	0.413																																					p.T140A		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.A418G						.						126	117	120					10																	115528632		2203	4300	6503	SO:0001583	missense	79949	exon6			AAAGCAACACAGC	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"Pleckstrin homology (PH) domain containing"	26285	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 81"	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000369310.3:c.400A>G	chr10.hg19:g.115528632A>G	ENSP00000358316:p.Thr134Ala	72.0	0.0		50.0	13.0	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	hg19	CCDS53580.1	.	.	.	.	.	.	.	.	.	.	A	1.606	-0.525172	0.04141	.	.	ENSG00000148735	ENST00000361048;ENST00000369312;ENST00000369310	T;T;T	0.28895	1.59;1.59;1.59	5.61	-9.39	0.00619	.	1.163900	0.05889	N	0.627810	T	0.08626	0.0214	N	0.04768	-0.165	0.09310	N	1	B;B;B	0.16396	0.017;0.001;0.001	B;B;B	0.15484	0.013;0.003;0.006	T	0.19811	-1.0294	10	0.02654	T	1	-33.799	3.4913	0.07638	0.3361:0.3667:0.2092:0.088	.	134;134;140	Q5SXH7-5;Q5SXH7-2;Q5SXH7-4	.;.;.	A	140;52;134	ENSP00000354332:T140A;ENSP00000358318:T52A;ENSP00000358316:T134A	ENSP00000354332:T140A	T	+	1	0	C10orf81	115518622	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.080000	0.03407	-1.835000	0.01191	-2.085000	0.00377	ACA	.	.		0.413	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889		G	115528632	A	G	115528632	3	3	116	1	0	0	0	0	1	0	0	0	1621	43	2	2	436	2	C10orf81	10	115528632	Missense_Mutation	SNP	A	TCGA-DD-A3A2-01A-11D-A20W-10	23019327	115528632	20006115	37	20094										
NLRP10	338322	hgsc.bcm.edu	37	chr11	7981809	7981809	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gcaagtcccaattggtagtcGttactactcaggaaagcggc	11	10	1	0	rs56052845		TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr11:7981809G>A	ENST00000328600.2	-	2	1511	c.1350C>T	c.(1348-1350)aaC>aaT	p.N450N		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	450	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATTGGTAGTCGTTACTACTCA	0.483																																					p.N450N		Atlas-SNP	.											NLRP10,colon,carcinoma,0,2	NLRP10	146	.	0			c.C1350T						.						101	112	108					11																	7981809		2201	4296	6497	SO:0001819	synonymous_variant	338322	exon2			GTAGTCGTTACTA	AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"Nucleotide-binding domain and leucine rich repeat containing"	21464	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"	609662	"NACHT, leucine rich repeat and PYD containing 10"	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.1350C>T	chr11.hg19:g.7981809G>A		69.0	0.0		65.0	21.0	NM_176821	Q2M3C4|Q6JGT0	Silent	SNP	ENST00000328600.2	hg19	CCDS7784.1																																																																																			.	.		0.483	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821		A	7981809	G	A	7981809	2	1	116	1	0	0	0	0	0	0	0	1	10481	1136	40	1		1	NLRP10	11	7981809	Silent	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10		7981809	127024707	38	20095										
CSRP3	8048	hgsc.bcm.edu	37	chr11	19204231	19204231	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	acctcttcattctttcttttCcacttgttgtgtaaggcctc	5	12	4	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr11:19204231C>A	ENST00000533783.1	-	7	811	c.571G>T	c.(571-573)Gaa>Taa	p.E191*	CSRP3_ENST00000265968.3_Nonsense_Mutation_p.E191*	NM_003476.4	NP_003467.1	P50461	CSRP3_HUMAN	cysteine and glycine-rich protein 3 (cardiac LIM protein)	191					cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue development (GO:0048738)|cardiac myofibril assembly (GO:0055003)|cellular calcium ion homeostasis (GO:0006874)|detection of muscle stretch (GO:0035995)|protein localization to organelle (GO:0033365)|regulation of the force of heart contraction (GO:0002026)|skeletal muscle tissue development (GO:0007519)	cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)	actinin binding (GO:0042805)|structural constituent of muscle (GO:0008307)|telethonin binding (GO:0031433)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(2)	10						TCTTTCTTTTCCACTTGTTGT	0.448																																					p.E191X		Atlas-SNP	.											.	CSRP3	24	.	0			c.G571T						.						140	139	139					11																	19204231		2199	4293	6492	SO:0001587	stop_gained	8048	exon7			TCTTTTCCACTTG	U20324	CCDS7848.1	11p15.1	2014-09-17				ENSG00000129170			2472	protein-coding gene	gene with protein product		600824				7490106	Standard	NM_003476		Approved	CLP, MLP, CMD1M	uc001mpk.3	P50461		ENST00000533783.1:c.571G>T	chr11.hg19:g.19204231C>A	ENSP00000431813:p.Glu191*	166.0	0.0		164.0	8.0	NM_003476	Q9P131	Nonsense_Mutation	SNP	ENST00000533783.1	hg19	CCDS7848.1	.	.	.	.	.	.	.	.	.	.	C	38	6.962264	0.97967	.	.	ENSG00000129170	ENST00000265968;ENST00000533783	.	.	.	6.06	6.06	0.98353	.	0.217961	0.47852	D	0.000215	.	.	.	.	.	.	0.53688	D	0.99997	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-10.7291	20.2159	0.98296	0.0:1.0:0.0:0.0	.	.	.	.	X	191	.	ENSP00000265968:E191X	E	-	1	0	CSRP3	19160807	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	3.919000	0.56439	2.882000	0.98803	0.655000	0.94253	GAA	.	.		0.448	CSRP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394484.1	NM_003476		A	19204231	C	A	19204231	4	1	116	1	0	0	0	0	0	1	0	0	3971	864	30	3	17	3	CSRP3	11	19204231	Nonsense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	11222422	19204231	115802285	39	20096										
WT1	7490	hgsc.bcm.edu	37	chr11	32421555	32421555	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gggctccgcagaggatgggcGttgtgtggttatcgctctcg	17	9	1	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr11:32421555G>A	ENST00000379079.2	-	6	674	c.401C>T	c.(400-402)aCg>aTg	p.T134M	WT1_ENST00000448076.3_Missense_Mutation_p.T346M|WT1_ENST00000332351.3_Missense_Mutation_p.T346M|WT1_ENST00000530998.1_Missense_Mutation_p.T117M	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	278					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)		EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			GAGGATGGGCGTTGTGTGGTT	0.557			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																												p.T346M		Atlas-SNP	.	yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	WT1_ENST00000379079,colon,carcinoma,0,2	WT1	744	.	0			c.C1037T						.						303	252	270					11																	32421555		2202	4299	6501	SO:0001583	missense	7490	exon6	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	ATGGGCGTTGTGT		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.401C>T	chr11.hg19:g.32421555G>A	ENSP00000368370:p.Thr134Met	269.0	0.0		261.0	11.0	NM_024424	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000379079.2	hg19	CCDS55751.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.418840	0.42918	.	.	ENSG00000184937	ENST00000379079;ENST00000332351;ENST00000530998;ENST00000452863;ENST00000448076;ENST00000527775	D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.98	5.98	0.97165	Wilm&apos (1);s tumour protein, N-terminal (1);	0.255135	0.30593	U	0.009287	D	0.86908	0.6046	L	0.46157	1.445	0.09310	N	1	P;P;P;P;P	0.48694	0.914;0.668;0.616;0.786;0.616	P;P;P;P;P	0.52109	0.493;0.69;0.562;0.627;0.562	T	0.81116	-0.1079	10	0.48119	T	0.1	.	16.6753	0.85277	0.0:0.1293:0.8707:0.0	.	334;278;351;117;134	P19544-8;P19544;P19544-7;B3KSA5;P19544-6	.;WT1_HUMAN;.;.;.	M	134;346;117;329;346;97	ENSP00000368370:T134M;ENSP00000331327:T346M;ENSP00000435307:T117M;ENSP00000415516:T329M;ENSP00000413452:T346M;ENSP00000435351:T97M	ENSP00000331327:T346M	T	-	2	0	WT1	32378131	0.946000	0.32159	0.011000	0.14972	0.059000	0.15707	4.759000	0.62227	2.835000	0.97688	0.650000	0.86243	ACG	.	.		0.557	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378		A	32421555	G	A	32421555	3	1	116	1	0	0	0	0	1	0	0	0	17423	1145	40	1	536	1	WT1	11	32421555	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	13217324	32421555	102584961	40	20097										
RPS6KA4	8986	hgsc.bcm.edu	37	chr11	64128041	64128041	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	tgtatgggggtgagatcgtgCtggccctggaacacctgcac	15	10	0	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr11:64128041C>A	ENST00000334205.4	+	4	504	c.439C>A	c.(439-441)Ctg>Atg	p.L147M	RPS6KA4_ENST00000528057.1_Missense_Mutation_p.L147M|RPS6KA4_ENST00000294261.4_Missense_Mutation_p.L147M	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	147	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						TGAGATCGTGCTGGCCCTGGA	0.607																																					p.L147M		Atlas-SNP	.											.	RPS6KA4	85	.	0			c.C439A						.						74	51	59					11																	64128041		2200	4297	6497	SO:0001583	missense	8986	exon4			ATCGTGCTGGCCC	AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"ribosomal protein S6 kinase, 90kD, polypeptide 4"			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.439C>A	chr11.hg19:g.64128041C>A	ENSP00000333896:p.Leu147Met	102.0	0.0		94.0	42.0	NM_001006944	A8K7Z8|O75585|Q53ES8	Missense_Mutation	SNP	ENST00000334205.4	hg19	CCDS8073.1	.	.	.	.	.	.	.	.	.	.	c	14.48	2.547112	0.45383	.	.	ENSG00000162302	ENST00000528057;ENST00000334205;ENST00000294261;ENST00000530504	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	3.32	3.32	0.38043	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000018	T	0.72622	0.3483	M	0.72479	2.2	0.37355	D	0.910983	P;D;D;D	0.89917	0.706;1.0;0.994;0.992	P;D;D;D	0.97110	0.465;1.0;0.959;0.931	T	0.75039	-0.3458	10	0.46703	T	0.11	.	6.6173	0.22784	0.0:0.8698:0.0:0.1302	.	147;147;147;147	G3XAA9;E9PJN1;O75676;O75676-2	.;.;KS6A4_HUMAN;.	M	147;147;147;131	ENSP00000435580:L147M;ENSP00000333896:L147M;ENSP00000294261:L147M;ENSP00000432945:L131M	ENSP00000294261:L147M	L	+	1	2	RPS6KA4	63884617	0.769000	0.28531	1.000000	0.80357	0.893000	0.52053	0.318000	0.19504	2.165000	0.68154	0.313000	0.20887	CTG	.	.		0.607	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942		A	64128041	C	A	64128041	3	1	116	1	0	0	0	0	1	0	0	0	13668	796	28	3	453	3	RPS6KA4	11	64128041	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	31706486	64128041	70878475	41	20098										
OR8G5	219865	hgsc.bcm.edu	37	chr11	124135110	124135110	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	agaagaacatcatctcctacCctgaatgcatgactcagctc	6	13	3	4			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr11:124135110C>A	ENST00000524943.2	+	1	388	c.388C>A	c.(388-390)Cct>Act	p.P130T	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	130						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		CATCTCCTACCCTGAATGCAT	0.468																																					p.P130T	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.C388A						.						157	140	146					11																	124135110		2160	4274	6434	SO:0001583	missense	219865	exon1			TCCTACCCTGAAT	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"GPCR / Class A : Olfactory receptors"	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.388C>A	chr11.hg19:g.124135110C>A	ENSP00000477014:p.Pro130Thr	321.0	0.0		283.0	116.0	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	hg19																																																																																				.	.		0.468	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198		A	124135110	C	A	124135110	3	1	116	1	0	0	0	0	1	0	0	0	11245	623	22	3	390	3	OR8G5	11	124135110	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	60007069	124135110	10871406	42	20099										
ITFG2	55846	hgsc.bcm.edu	37	chr12	2933099	2933099	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	taccacagcctgctgcaggaGctgggcgtgggtgagtccca	15	12	0	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr12:2933099G>T	ENST00000228799.2	+	11	1369	c.1230G>T	c.(1228-1230)gaG>gaT	p.E410D	ITFG2_ENST00000542548.1_Missense_Mutation_p.E298D|ITFG2_ENST00000419778.2_Missense_Mutation_p.E233D	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	410					germinal center B cell differentiation (GO:0002314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			TGCTGCAGGAGCTGGGCGTGG	0.607																																					p.E410D		Atlas-SNP	.											.	ITFG2	38	.	0			c.G1230T						.						68	70	70					12																	2933099		2203	4300	6503	SO:0001583	missense	55846	exon11			GCAGGAGCTGGGC	AF220048	CCDS8513.1	12p13.33	2006-11-29		2006-07-25	ENSG00000111203	ENSG00000111203			30879	protein-coding gene	gene with protein product						12477932	Standard	NM_018463		Approved	MDS028	uc001qlb.2	Q969R8	OTTHUMG00000130617	ENST00000228799.2:c.1230G>T	chr12.hg19:g.2933099G>T	ENSP00000228799:p.Glu410Asp	83.0	0.0		85.0	33.0	NM_018463	A8K4Z5|D3DUQ2|Q6PKU5|Q96SX6	Missense_Mutation	SNP	ENST00000228799.2	hg19	CCDS8513.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.52|14.52	2.560129|2.560129	0.45590|0.45590	.|.	.|.	ENSG00000111203|ENSG00000111203	ENST00000228799;ENST00000419778;ENST00000542548|ENST00000540662	T;T;T|.	0.09350|.	2.99;2.99;2.99|.	5.33|5.33	4.43|4.43	0.53597|0.53597	.|.	0.401000|.	0.27802|.	N|.	0.017788|.	T|T	0.70806|0.70806	0.3266|0.3266	M|M	0.67953|0.67953	2.075|2.075	0.44834|0.44834	D|D	0.997845|0.997845	P|.	0.38922|.	0.651|.	B|.	0.33521|.	0.165|.	T|T	0.70385|0.70385	-0.4886|-0.4886	10|5	0.62326|.	D|.	0.03|.	-3.4622|-3.4622	13.4961|13.4961	0.61426|0.61426	0.0772:0.0:0.9228:0.0|0.0772:0.0:0.9228:0.0	.|.	410|.	Q969R8|.	ITFG2_HUMAN|.	D|I	410;233;298|31	ENSP00000228799:E410D;ENSP00000401103:E233D;ENSP00000437870:E298D|.	ENSP00000228799:E410D|.	E|S	+|+	3|2	2|0	ITFG2|ITFG2	2803360|2803360	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	2.236000|2.236000	0.43052|0.43052	2.492000|2.492000	0.84095|0.84095	0.561000|0.561000	0.74099|0.74099	GAG|AGC	.	.		0.607	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	NM_018463		T	2933099	G	T	2933099	3	4	116	1	0	0	0	0	1	0	0	0	7879	962	34	3	1272	3	ITFG2	12	2933099	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10		2933099	130918796	43	20100										
FOXJ2	55810	hgsc.bcm.edu	37	chr12	8205442	8205442	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	cttcgactgggacttgatcaCttagtgcatcacagagtgtg	11	9	2	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr12:8205442C>G	ENST00000162391.3	+	11	2866	c.1721C>G	c.(1720-1722)aCt>aGt	p.T574S	FOXJ2_ENST00000539192.1_3'UTR	NM_018416.2	NP_060886.1	Q9P0K8	FOXJ2_HUMAN	forkhead box J2	574					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	16				Kidney(36;0.0944)		GACTTGATCACTTAGTGCATC	0.562																																					p.T574S		Atlas-SNP	.											.	FOXJ2	43	.	0			c.C1721G						.						78	56	63					12																	8205442		2203	4300	6503	SO:0001583	missense	55810	exon11			TGATCACTTAGTG	AF155132	CCDS8587.1	12p13.31	2006-12-15				ENSG00000065970		"Forkhead boxes"	24818	protein-coding gene	gene with protein product						10777590, 10966786	Standard	NM_018416		Approved	FHX	uc001qtu.3	Q9P0K8		ENST00000162391.3:c.1721C>G	chr12.hg19:g.8205442C>G	ENSP00000162391:p.Thr574Ser	62.0	0.0		69.0	28.0	NM_018416	A0AVK4|B2RMP3|Q96PS9|Q9NSN5	Missense_Mutation	SNP	ENST00000162391.3	hg19	CCDS8587.1	.	.	.	.	.	.	.	.	.	.	C	31	5.103169	0.94245	.	.	ENSG00000065970	ENST00000162391	D	0.94758	-3.51	5.85	5.85	0.93711	.	0.648102	0.13574	N	0.377784	D	0.92996	0.7771	L	0.44542	1.39	0.80722	D	1	P	0.42692	0.787	B	0.41236	0.351	D	0.92897	0.6336	10	0.87932	D	0	.	17.6545	0.88174	0.0:1.0:0.0:0.0	.	574	Q9P0K8	FOXJ2_HUMAN	S	574	ENSP00000162391:T574S	ENSP00000162391:T574S	T	+	2	0	FOXJ2	8096709	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.953000	0.56699	2.772000	0.95346	0.650000	0.86243	ACT	.	.		0.562	FOXJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400088.1	NM_018416		G	8205442	C	G	8205442	3	3	116	1	0	0	0	0	1	0	0	0	6020	565	20	4	1759	4	FOXJ2	12	8205442	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	5272343	8205442	125646453	44	20101										
MLL2	8085	hgsc.bcm.edu	37	chr12	49425236	49425236	+	Frame_Shift_Del	DEL	C	C	-													0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	acatggctcttcccgaggttCctgcttgatgctgagttggg							TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr12:49425236delC	ENST00000301067.7	-	39	13251	c.13252delG	c.(13252-13254)gaafs	p.E4418fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4418					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TCCCGAGGTTCCTGCTTGATG	0.602																																					p.E4418fs		Atlas-Indel,Pindel	.											.	MLL2	1173	.	0			c.13253delA						.						35	36	35					12																	49425236		2018	4180	6198	SO:0001589	frameshift_variant	8085	exon39			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.13252delG	chr12.hg19:g.49425236delC	ENSP00000301067:p.Glu4418fs	137.0	0.0		99.0	34.0	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.602	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49425236	C	-	49425236	7	5	116	1	0	1	0	1	0	0	0	0	9630	864	30	0	3425	0	MLL2	12	49425236	Frame_Shift_Del	DEL	C	TCGA-DD-A3A2-01A-11D-A20W-10	41219794	49425236	84426659	45	20102										
ZDHHC17	23390	hgsc.bcm.edu	37	chr12	77158072	77158072	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ggacggcccggatgagtacgAtaccgaagcgggctgtgtgc	17	10	0	1	rs562629778		TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr12:77158072A>G	ENST00000426126.2	+	1	705	c.56A>G	c.(55-57)gAt>gGt	p.D19G	ZDHHC17_ENST00000359019.4_Missense_Mutation_p.I4V|ZDHHC17_ENST00000334822.5_Missense_Mutation_p.D19G	NM_015336.2	NP_056151.2	Q8IUH5	ZDH17_HUMAN	zinc finger, DHHC-type containing 17	19					lipoprotein transport (GO:0042953)|magnesium ion transport (GO:0015693)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein palmitoylation (GO:0018345)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(3)|liver(2)|lung(14)	23						GATGAGTACGATACCGAAGCG	0.642													A|||	1	0.000199681	0	0	5008	,	,		12138	0		0.001	False		,,,				2504	0				p.D19G		Atlas-SNP	.											.	ZDHHC17	45	.	0			c.A56G						.						41	49	46					12																	77158072		2016	4158	6174	SO:0001583	missense	23390	exon1			AGTACGATACCGA	AB023163	CCDS44946.1	12q21.2	2013-01-10				ENSG00000186908		"Zinc fingers, DHHC-type", "Ankyrin repeat domain containing"	18412	protein-coding gene	gene with protein product		607799				9700202, 18794299	Standard	NM_015336		Approved	HIP14, HYPH, KIAA0946	uc001syk.1	Q8IUH5	OTTHUMG00000169917	ENST00000426126.2:c.56A>G	chr12.hg19:g.77158072A>G	ENSP00000403397:p.Asp19Gly	66.0	0.0		51.0	18.0	NM_015336	B4DR39|O75407|Q7Z2I0|Q86W89|Q86YK0|Q9P088|Q9UPZ8	Missense_Mutation	SNP	ENST00000426126.2	hg19	CCDS44946.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.00|16.00	2.998327|2.998327	0.54147|0.54147	.|.	.|.	ENSG00000186908|ENSG00000186908	ENST00000426126;ENST00000334822|ENST00000359019	T;T|T	0.34072|0.38240	1.38;1.38|1.15	4.24|4.24	4.24|4.24	0.50183|0.50183	.|.	0.473631|.	0.23146|.	N|.	0.051417|.	T|T	0.18087|0.18087	0.0434|0.0434	N|N	0.03608|0.03608	-0.345|-0.345	0.21719|0.21719	N|N	0.999577|0.999577	B|.	0.18741|.	0.03|.	B|.	0.15870|.	0.014|.	T|T	0.16958|0.16958	-1.0385|-1.0385	10|7	0.30854|0.22706	T|T	0.27|0.39	-0.9606|-0.9606	10.9418|10.9418	0.47278|0.47278	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	19|.	Q8IUH5|.	ZDH17_HUMAN|.	G|V	19|4	ENSP00000403397:D19G;ENSP00000334868:D19G|ENSP00000351913:I4V	ENSP00000334868:D19G|ENSP00000351913:I4V	D|I	+|+	2|1	0|0	ZDHHC17|ZDHHC17	75682203|75682203	0.996000|0.996000	0.38824|0.38824	0.868000|0.868000	0.34077|0.34077	0.988000|0.988000	0.76386|0.76386	4.273000|4.273000	0.58914|0.58914	1.773000|1.773000	0.52216|0.52216	0.454000|0.454000	0.30748|0.30748	GAT|ATA	.	.		0.642	ZDHHC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406555.1	NM_015336		G	77158072	A	G	77158072	3	3	116	1	0	0	0	0	1	0	0	0	17622	333	12	2	58	2	ZDHHC17	12	77158072	Missense_Mutation	SNP	A	TCGA-DD-A3A2-01A-11D-A20W-10	27732836	77158072	56693823	46	20103										
GATC	51499	hgsc.bcm.edu	37	chr12	120884359	120884359	+	5'Flank	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gcttcacctccaaggcggatCctcaggtaaaggccagggcc	12	14	2	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr12:120884359C>T	ENST00000546954.1	-	0	0				AL021546.6_ENST00000551806.1_Intron|GATC_ENST00000551765.1_Missense_Mutation_p.P26S|TRIAP1_ENST00000302432.3_5'Flank	NM_016399.2	NP_057483.1	O43715	TRIA1_HUMAN	TP53 regulated inhibitor of apoptosis 1						cellular response to UV (GO:0034644)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of membrane lipid distribution (GO:0097035)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	p53 binding (GO:0002039)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CAAGGCGGATCCTCAGGTAAA	0.687																																					p.P26S		Atlas-SNP	.											.	GATC	12	.	0			c.C76T						.						37	43	41					12																	120884359		2203	4297	6500	SO:0001631	upstream_gene_variant	283459	exon1			GCGGATCCTCAGG		CCDS9198.1	12q24.31	2012-10-15			ENSG00000170855	ENSG00000170855			26937	protein-coding gene	gene with protein product	"p53-inducible cell-survival factor", "mitochondrial distribution and morphology 35 homolog (S. cerevisiae)"	614943				11042152, 15735003	Standard	NM_016399		Approved	P53CSV, WF-1, HSPC132, p53CSV, MDM35	uc001tyg.3	O43715	OTTHUMG00000047787		chr12.hg19:g.120884359C>T	Exception_encountered	54.0	0.0		58.0	6.0	NM_176818	B2R4Z7|Q5RKS5|Q6LCA7	Missense_Mutation	SNP	ENST00000546954.1	hg19	CCDS9198.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.199237	0.38806	.	.	ENSG00000257218	ENST00000551765	T	0.49139	0.79	4.76	-0.362	0.12560	.	0.499402	0.21544	N	0.072857	T	0.31295	0.0792	L	0.50333	1.59	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.16364	-1.0405	10	0.37606	T	0.19	-0.0727	0.2962	0.00266	0.2779:0.3055:0.1566:0.26	.	26	O43716	GATC_HUMAN	S	26	ENSP00000446872:P26S	ENSP00000448397:P26S	P	+	1	0	AL021546.1	119368742	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-1.025000	0.03600	-0.159000	0.11021	0.644000	0.83932	CCT	.	.		0.687	TRIAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108980.3	NM_016399		T	120884359	C	T	120884359	1	4	116	0	1	0	0	0	0	0	0	0	6270	855	30	3		3	GATC	12	120884359	5'Flank	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	43726287	120884359	12967536	47	20104										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121426820	121426820	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	cctggtacgtccgcaagcagCgagaggtggcgcagcgtaag	16	11	0	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr12:121426820C>T	ENST00000257555.6	+	2	737	c.511C>T	c.(511-513)Cga>Tga	p.R171*	HNF1A_ENST00000541395.1_Nonsense_Mutation_p.R171*|HNF1A_ENST00000400024.2_Nonsense_Mutation_p.R171*|HNF1A_ENST00000543427.1_Nonsense_Mutation_p.R54*|HNF1A_ENST00000544413.1_Nonsense_Mutation_p.R171*|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000402929.1_Nonsense_Mutation_p.R171*			P20823	HNF1A_HUMAN	HNF1 homeobox A	171					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCGCAAGCAGCGAGAGGTGGC	0.617									Hepatic Adenoma, Familial Clustering of																												p.R171X		Atlas-SNP	.											.	HNF1A	302	.	0			c.C511T	GRCh37	CM971451	HNF1A	M		.						115	99	104					12																	121426820		2203	4300	6503	SO:0001587	stop_gained	6927	exon2	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	AAGCAGCGAGAGG	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.511C>T	chr12.hg19:g.121426820C>T	ENSP00000257555:p.Arg171*	81.0	0.0		81.0	30.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Nonsense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	C	35	5.547882	0.96488	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543027;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	.	.	.	4.91	4.91	0.64330	.	0.000000	0.53938	D	0.000049	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.1481	17.081	0.86598	0.0:1.0:0.0:0.0	.	.	.	.	X	171;171;171;171;171;171;54;171;171;171;171;171	.	ENSP00000257555:R171X	R	+	1	2	HNF1A	119911203	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.527000	0.35975	2.265000	0.75225	0.530000	0.56133	CGA	.	.		0.617	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		T	121426820	C	T	121426820	4	4	116	1	0	0	0	0	0	1	0	0	7260	760	27	1	517	1	HNF1A	12	121426820	Nonsense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	542461	121426820	12425075	48	20105										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121431506	121431506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gacgctagtggaggagtgcaAtaggtacaacggcgggcggg	19	7	0	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr12:121431506A>G	ENST00000257555.6	+	3	936	c.710A>G	c.(709-711)aAt>aGt	p.N237S	HNF1A_ENST00000541395.1_Missense_Mutation_p.N237S|HNF1A_ENST00000400024.2_Missense_Mutation_p.N237S|HNF1A_ENST00000543427.1_Missense_Mutation_p.N120S|HNF1A_ENST00000544413.1_Missense_Mutation_p.N237S|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000402929.1_Missense_Mutation_p.N237S			P20823	HNF1A_HUMAN	HNF1 homeobox A	237			N -> S (in a hepatic multiple adenoma sample; somatic mutation). {ECO:0000269|PubMed:12355088}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.N237S(4)|p.?(1)|p.N237fs*2(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GAGGAGTGCAATAGGTACAAC	0.587									Hepatic Adenoma, Familial Clustering of																												p.N237S		Atlas-SNP	.											HNF1A,NS,other,0,1	HNF1A	302	.	6	Substitution - Missense(4)|Unknown(1)|Insertion - Frameshift(1)	liver(6)	c.A710G						.						80	82	81					12																	121431506		2203	4300	6503	SO:0001583	missense	6927	exon3	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	AGTGCAATAGGTA	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.710A>G	chr12.hg19:g.121431506A>G	ENSP00000257555:p.Asn237Ser	60.0	0.0		70.0	28.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.818815	0.50633	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D;D	0.95853	-3.83;-3.83;-3.83;-3.83	4.45	4.45	0.53987	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.075184	0.53938	D	0.000051	D	0.95166	0.8433	M	0.70595	2.14	0.80722	D	1	B;B;B;P	0.37864	0.304;0.353;0.353;0.61	B;B;B;B	0.43155	0.12;0.283;0.19;0.41	D	0.95388	0.8479	10	0.87932	D	0	-16.729	12.937	0.58320	1.0:0.0:0.0:0.0	.	237;237;237;237	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	S	237;237;237;237;237;120;237;237;237;237;237	ENSP00000257555:N237S;ENSP00000439721:N120S;ENSP00000443112:N237S;ENSP00000438804:N237S	ENSP00000257555:N237S	N	+	2	0	HNF1A	119915889	1.000000	0.71417	0.982000	0.44146	0.547000	0.35210	8.726000	0.91474	1.662000	0.50781	0.423000	0.28283	AAT	.	.		0.587	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		G	121431506	A	G	121431506	3	3	116	1	0	0	0	0	1	0	0	0	7260	101	4	2	720	2	HNF1A	12	121431506	Missense_Mutation	SNP	A	TCGA-DD-A3A2-01A-11D-A20W-10	4686	121431506	12420389	49	20106										
CUL4A	8451	hgsc.bcm.edu	37	chr13	113898777	113898777	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	acaaagaagccacagacgagGagctggagcggacgttggac	15	9	0	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr13:113898777G>T	ENST00000375440.4	+	12	1366	c.1282G>T	c.(1282-1284)Gag>Tag	p.E428*	CUL4A_ENST00000326335.4_Nonsense_Mutation_p.E328*|CUL4A_ENST00000451881.1_Nonsense_Mutation_p.E328*|CUL4A_ENST00000375441.3_Nonsense_Mutation_p.E328*	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	428					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			CACAGACGAGGAGCTGGAGCG	0.433																																					p.E428X		Atlas-SNP	.											.	CUL4A	50	.	0			c.G1282T						.						76	63	67					13																	113898777		2203	4300	6503	SO:0001587	stop_gained	8451	exon12			GACGAGGAGCTGG	U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.1282G>T	chr13.hg19:g.113898777G>T	ENSP00000364589:p.Glu428*	201.0	0.0		243.0	97.0	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Nonsense_Mutation	SNP	ENST00000375440.4	hg19	CCDS41908.1	.	.	.	.	.	.	.	.	.	.	G	44	11.096330	0.99515	.	.	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	.	.	.	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-49.07	18.1481	0.89665	0.0:0.0:1.0:0.0	.	.	.	.	X	328;328;328;428	.	ENSP00000322132:E328X	E	+	1	0	CUL4A	112946778	1.000000	0.71417	0.974000	0.42286	0.962000	0.63368	9.634000	0.98435	2.368000	0.80403	0.484000	0.47621	GAG	.	.		0.433	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589		T	113898777	G	T	113898777	4	4	116	1	0	0	0	0	0	1	0	0	4059	1175	41	3	1328	3	CUL4A	13	113898777	Nonsense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10		113898777	1271101	50	20107										
SECISBP2L	9728	hgsc.bcm.edu	37	chr15	49284998	49284999	+	In_Frame_Ins	INS	-	-	TGGGGGTGTGTCAAATGGAAGTTG													0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	aatgatggctgcttaccaatINStgggggtgtgtcaaatggaa							TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr15:49284998_49284999insTGGGGGTGTGTCAAATGGAAGTTG	ENST00000559471.1	-	18	3011_3012	c.2748_2749insCAACTTCCATTTGACACACCCCCA	c.(2746-2751)ccaatt>ccaCAACTTCCATTTGACACACCCCCAatt	p.915_916insPQLPFDTP	SECISBP2L_ENST00000261847.3_In_Frame_Ins_p.870_871insPQLPFDTP	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	915							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TGCTTACCAATTGGGGGTGTGT	0.446																																					p.I917delinsQLPFDTPPI		Atlas-INDEL	.											.	SECISBP2L	118	.	0			c.2749_2750insCAACTTCCATTTGACACACCCCCA						.																																			SO:0001652	inframe_insertion	9728	exon18			.	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2748_2749insCAACTTCCATTTGACACACCCCCA	chr15.hg19:g.49284998_49284999insTGGGGGTGTGTCAAATGGAAGTTG	ENSP00000453854:p.Pro915_Pro916insProGlnLeuProPheAspThrPro	190.0	0.0		162.0	14.0	NM_001193489	Q8N767	In_Frame_Ins	INS	ENST00000559471.1	hg19	CCDS53942.1																																																																																			.	.		0.446	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		TGGGGGTGTGTCAAATGGAAGTTG	49284999	-	TGGGGGTGTGTCAAATGGAAGTTG	49284998	7	5	116	1	0	1	1	0	0	0	0	0	14022	1493	52	0	560	0	SECISBP2L	15	49284998	In_Frame_Ins	INS	-	TCGA-DD-A3A2-01A-11D-A20W-10		49284998	53246394	51	20108										
TRIP4	9325	hgsc.bcm.edu	37	chr15	64701814	64701814	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gtgttccctttttctcagtaTtcgaaggacccaagtcattg	8	10	2	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr15:64701814T>C	ENST00000261884.3	+	7	890	c.830T>C	c.(829-831)aTt>aCt	p.I277T	TRIP4_ENST00000559565.1_3'UTR	NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	277					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						TTTCTCAGTATTCGAAGGACC	0.393																																					p.I277T		Atlas-SNP	.											.	TRIP4	43	.	0			c.T830C						.						95	86	89					15																	64701814		2203	4300	6503	SO:0001583	missense	9325	exon7			TCAGTATTCGAAG	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"-"	12310	protein-coding gene	gene with protein product	"zinc finger, C2HC5-type"	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.830T>C	chr15.hg19:g.64701814T>C	ENSP00000261884:p.Ile277Thr	127.0	0.0		149.0	11.0	NM_016213	B2RAS0|Q96ED7|Q9UKH0	Missense_Mutation	SNP	ENST00000261884.3	hg19	CCDS10194.1	.	.	.	.	.	.	.	.	.	.	T	15.26	2.779454	0.49891	.	.	ENSG00000103671	ENST00000261884	.	.	.	5.65	5.65	0.86999	.	0.133960	0.64402	D	0.000011	T	0.42698	0.1214	N	0.24115	0.695	0.53688	D	0.999973	B	0.32717	0.381	B	0.24006	0.05	T	0.36456	-0.9747	9	0.36615	T	0.2	-26.0985	15.884	0.79226	0.0:0.0:0.0:1.0	.	277	Q15650	TRIP4_HUMAN	T	277	.	ENSP00000261884:I277T	I	+	2	0	TRIP4	62488867	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	7.628000	0.83189	2.161000	0.67846	0.454000	0.30748	ATT	.	.		0.393	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213		C	64701814	T	C	64701814	3	2	116	1	0	0	0	0	1	0	0	0	16573	1493	52	2	856	2	TRIP4	15	64701814	Missense_Mutation	SNP	T	TCGA-DD-A3A2-01A-11D-A20W-10	15416816	64701814	37829578	52	20109										
FURIN	5045	hgsc.bcm.edu	37	chr15	91423938	91423938	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	caggccacatgactactccgCagatgggtttaatgactggg	12	10	0	3			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr15:91423938C>T	ENST00000268171.3	+	14	1853	c.1574C>T	c.(1573-1575)gCa>gTa	p.A525V		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	525					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GACTACTCCGCAGATGGGTTT	0.582																																					p.A525V		Atlas-SNP	.											.	FURIN	85	.	0			c.C1574T						.						73	66	68					15																	91423938		2198	4298	6496	SO:0001583	missense	5045	exon14			ACTCCGCAGATGG	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1574C>T	chr15.hg19:g.91423938C>T	ENSP00000268171:p.Ala525Val	137.0	0.0		114.0	41.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	hg19	CCDS10364.1	.	.	.	.	.	.	.	.	.	.	C	18.72	3.684826	0.68157	.	.	ENSG00000140564	ENST00000268171	T	0.63744	-0.06	3.76	3.76	0.43208	Proprotein convertase, P (1);Galactose-binding domain-like (1);	0.058661	0.64402	D	0.000002	T	0.53899	0.1825	L	0.52266	1.64	0.58432	D	0.999996	P	0.39181	0.663	B	0.34301	0.179	T	0.57329	-0.7830	10	0.29301	T	0.29	-13.8803	16.1871	0.81960	0.0:1.0:0.0:0.0	.	525	P09958	FURIN_HUMAN	V	525	ENSP00000268171:A525V	ENSP00000268171:A525V	A	+	2	0	FURIN	89224942	0.998000	0.40836	0.969000	0.41365	0.935000	0.57460	4.612000	0.61169	2.119000	0.64992	0.555000	0.69702	GCA	.	.		0.582	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		T	91423938	C	T	91423938	3	4	116	1	0	0	0	0	1	0	0	0	6107	710	25	3	1624	3	FURIN	15	91423938	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	26722124	91423938	11107454	53	20110										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1251935	1251935	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	aaggtggaccccagtgctgtGcaaggccagggtcccgggca	16	12	0	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr16:1251935G>A	ENST00000348261.5	+	9	1733	c.1485G>A	c.(1483-1485)gtG>gtA	p.V495V	CACNA1H_ENST00000565831.1_Silent_p.V495V|CACNA1H_ENST00000358590.4_Silent_p.V495V	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	495					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCAGTGCTGTGCAAGGCCAGG	0.677																																					p.V495V		Atlas-SNP	.											.	CACNA1H	317	.	0			c.G1485A						.						4	6	5					16																	1251935		1866	3739	5605	SO:0001819	synonymous_variant	8912	exon9			TGCTGTGCAAGGC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1485G>A	chr16.hg19:g.1251935G>A		45.0	0.0		40.0	20.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	hg19	CCDS45375.1																																																																																			.	.		0.677	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		A	1251935	G	A	1251935	2	1	116	1	0	0	0	0	0	0	0	1	2547	1306	46	3		3	CACNA1H	16	1251935	Silent	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10		1251935	89102818	54	20111										
ALG1	56052	hgsc.bcm.edu	37	chr16	5127503	5127503	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ctgtgtgttaccaatgctatGcgagaagacctggcggataa	12	8	0	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr16:5127503G>A	ENST00000262374.5	+	5	628	c.597G>A	c.(595-597)atG>atA	p.M199I	ALG1_ENST00000588623.1_Missense_Mutation_p.M88I|ALG1_ENST00000544428.1_Missense_Mutation_p.M88I	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	199					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				CCAATGCTATGCGAGAAGACC	0.587																																					p.M199I		Atlas-SNP	.											.	ALG1	35	.	0			c.G597A						.						111	102	105					16																	5127503		2197	4300	6497	SO:0001583	missense	56052	exon5			TGCTATGCGAGAA	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"Glycosyltransferase group 1 domain containing"	18294	protein-coding gene	gene with protein product		605907	"asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)", "asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.597G>A	chr16.hg19:g.5127503G>A	ENSP00000262374:p.Met199Ile	104.0	0.0		99.0	35.0	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	hg19	CCDS10528.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534990	0.64972	.	.	ENSG00000033011	ENST00000262374;ENST00000544428	D;D	0.83992	-1.79;-1.79	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.93716	0.7992	H	0.95114	3.625	0.80722	D	1	D;D	0.89917	0.996;1.0	P;D	0.87578	0.905;0.998	D	0.94924	0.8076	10	0.72032	D	0.01	-39.8765	15.5247	0.75894	0.0:0.0:1.0:0.0	.	88;199	B4DP08;Q9BT22	.;ALG1_HUMAN	I	199;88	ENSP00000262374:M199I;ENSP00000440019:M88I	ENSP00000262374:M199I	M	+	3	0	ALG1	5067504	1.000000	0.71417	0.998000	0.56505	0.036000	0.12997	7.942000	0.87708	2.750000	0.94351	0.561000	0.74099	ATG	.	.		0.587	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109		A	5127503	G	A	5127503	3	1	116	1	0	0	0	0	1	0	0	0	510	1319	46	3	615	3	ALG1	16	5127503	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	3875568	5127503	85227250	55	20112										
SH2B1	25970	hgsc.bcm.edu	37	chr16	28877909	28877909	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gggtcgctctgtccgaggctCagtccgtggcatcctgcagt	14	13	2	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr16:28877909C>T	ENST00000322610.8	+	4	933	c.494C>T	c.(493-495)tCa>tTa	p.S165L	SH2B1_ENST00000359285.5_Missense_Mutation_p.S165L|SH2B1_ENST00000395532.4_Missense_Mutation_p.S165L|SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000545570.1_Intron|SH2B1_ENST00000538342.1_Intron|SH2B1_ENST00000337120.5_Missense_Mutation_p.S165L			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	165	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation). {ECO:0000250}.|Interaction with RAC1. {ECO:0000250}.|Required for NGF signaling. {ECO:0000250}.				blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						GTCCGAGGCTCAGTCCGTGGC	0.637																																					p.S165L		Atlas-SNP	.											.	SH2B1	160	.	0			c.C494T						.						91	85	87					16																	28877909		2197	4300	6497	SO:0001583	missense	25970	exon2			GAGGCTCAGTCCG	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	30417	protein-coding gene	gene with protein product	"SH2-B homolog"	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.494C>T	chr16.hg19:g.28877909C>T	ENSP00000321221:p.Ser165Leu	51.0	0.0		57.0	22.0	NM_001145796	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	ENST00000322610.8	hg19	CCDS53996.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156884	0.57259	.	.	ENSG00000178188	ENST00000322610;ENST00000359285;ENST00000395532;ENST00000337120	T;T;T;T	0.58652	0.32;0.34;0.34;0.34	3.95	3.95	0.45737	.	0.538636	0.16187	N	0.225577	T	0.45013	0.1321	N	0.14661	0.345	0.22096	N	0.99937	D;P;P	0.56968	0.978;0.936;0.895	P;B;B	0.50537	0.643;0.445;0.354	T	0.19063	-1.0317	10	0.18276	T	0.48	-12.4079	10.2838	0.43556	0.0:0.6579:0.3421:0.0	.	165;165;165	Q9NRF2-2;Q9NRF2-3;Q9NRF2	.;.;SH2B1_HUMAN	L	165	ENSP00000321221:S165L;ENSP00000352232:S165L;ENSP00000378903:S165L;ENSP00000337163:S165L	ENSP00000321221:S165L	S	+	2	0	SH2B1	28785410	0.771000	0.28555	0.962000	0.40283	0.976000	0.68499	4.347000	0.59373	2.055000	0.61198	0.455000	0.32223	TCA	.	.		0.637	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503		T	28877909	C	T	28877909	3	4	116	1	0	0	0	0	1	0	0	0	14242	838	29	3	496	3	SH2B1	16	28877909	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	23750406	28877909	61476844	56	20113										
TMEM219	124446	hgsc.bcm.edu	37	chr16	29979380	29979380	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	caactggtccttatcacagcCagggtgaccacagaaaggac	10	12	1	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr16:29979380C>T	ENST00000566848.1	+	3	857	c.390C>T	c.(388-390)gcC>gcT	p.A130A	TMEM219_ENST00000561899.2_Silent_p.A130A|TMEM219_ENST00000279396.6_Silent_p.A130A|TMEM219_ENST00000414689.2_Silent_p.A130A			Q86XT9	TM219_HUMAN	transmembrane protein 219	130					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|lung(1)|prostate(2)	4						TTATCACAGCCAGGGTGACCA	0.522																																					p.A130A		Atlas-SNP	.											.	TMEM219	10	.	0			c.C390T						.						100	108	105					16																	29979380		1915	4114	6029	SO:0001819	synonymous_variant	124446	exon4			CACAGCCAGGGTG		CCDS42145.1	16p11.2	2008-08-08			ENSG00000149932	ENSG00000149932			25201	protein-coding gene	gene with protein product							Standard	NM_194280		Approved		uc010bzk.1	Q86XT9		ENST00000566848.1:c.390C>T	chr16.hg19:g.29979380C>T		109.0	0.0		116.0	49.0	NM_001083613	D5FK14|Q8WVV8	Silent	SNP	ENST00000566848.1	hg19	CCDS42145.1																																																																																			.	.		0.522	TMEM219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435307.1	NM_001083613		T	29979380	C	T	29979380	2	4	116	1	0	0	0	0	0	0	0	1	16157	581	21	3		3	TMEM219	16	29979380	Silent	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	1101471	29979380	60375373	57	20114										
C17orf68	80169	hgsc.bcm.edu	37	chr17	8141349	8141349	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	tgcctagagggggaaattacCtgagcctgagcaggcaggaa	15	8	0	3			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr17:8141349C>T	ENST00000315684.8	-	4	654	c.647G>A	c.(646-648)aGa>aAa	p.R216K	CTC1_ENST00000581671.1_5'UTR	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	216					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						GGGAAATTACCTGAGCCTGAG	0.542																																					p.R216K		Atlas-SNP	.											.	CTC1	75	.	0			c.G647A						.						56	58	58					17																	8141349		1982	4146	6128	SO:0001630	splice_region_variant	80169	exon4			AATTACCTGAGCC	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"conserved telomere maintenance component 1", "alpha accessory factor 132", "conserved telomere capping protein 1"	613129	"tmp494178", "chromosome 17 open reading frame 68"	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.647+1G>A	chr17.hg19:g.8141349C>T		76.0	0.0		83.0	24.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Missense_Mutation	SNP	ENST00000315684.8	hg19	CCDS42259.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.138662	0.37728	.	.	ENSG00000178971	ENST00000315684;ENST00000449476	D;D	0.84370	-1.84;-1.84	5.27	4.29	0.51040	.	0.166754	0.42548	D	0.000700	D	0.83991	0.5374	M	0.70595	2.14	0.30941	N	0.725828	P	0.39181	0.663	B	0.40165	0.321	D	0.83658	0.0159	9	.	.	.	-5.416	11.7458	0.51819	0.0:0.8232:0.1768:0.0	.	216	Q2NKJ3	CTC1_HUMAN	K	216	ENSP00000313759:R216K;ENSP00000396018:R216K	.	R	-	2	0	CTC1	8082074	1.000000	0.71417	1.000000	0.80357	0.222000	0.24845	2.793000	0.47845	1.445000	0.47624	0.561000	0.74099	AGA	.	.		0.542	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	Missense_Mutation	T	8141349	C	T	8141349	5	4	116	1	0	0	0	0	0	0	1	0	1878	695	24	3	3086	3	C17orf68	17	8141349	Splice_Site	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10		8141349	73053861	58	20115										
CWC25	54883	hgsc.bcm.edu	37	chr17	36977155	36977155	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	cccccagctcctcacttactTgacggccccaacatcctccg	5	21	1	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr17:36977155T>A	ENST00000225428.5	-	2	487	c.190A>T	c.(190-192)Aag>Tag	p.K64*	CWC25_ENST00000536127.1_5'UTR	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	64										central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						CTCACTTACTTGACGGCCCCA	0.557																																					p.K64X		Atlas-SNP	.											.	CWC25	24	.	0			c.A190T						.						144	140	141					17																	36977155		2107	4239	6346	SO:0001630	splice_region_variant	54883	exon2			CTTACTTGACGGC	AK000298	CCDS45663.1	17q12	2010-01-26	2010-01-26	2010-01-26		ENSG00000273559			25989	protein-coding gene	gene with protein product			"coiled-coil domain containing 49"	CCDC49		19941820	Standard	NM_017748		Approved	FLJ20291	uc002hqu.4	Q9NXE8		ENST00000225428.5:c.191+1A>T	chr17.hg19:g.36977155T>A		122.0	0.0		146.0	51.0	NM_017748	A0JLM3|Q68DK5	Nonsense_Mutation	SNP	ENST00000225428.5	hg19	CCDS45663.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.571373	0.86542	.	.	ENSG00000108296	ENST00000225428	.	.	.	5.2	5.2	0.72013	.	0.147994	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9563	0.64150	0.0:0.0:0.0:1.0	.	.	.	.	X	64	.	ENSP00000225428:K64X	K	-	1	0	CWC25	34230681	1.000000	0.71417	1.000000	0.80357	0.281000	0.26958	4.651000	0.61447	1.974000	0.57490	0.529000	0.55759	AAG	.	.		0.557	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442186.6	NM_017748	Nonsense_Mutation	A	36977155	T	A	36977155	5	1	116	1	0	0	0	0	0	0	1	0	4071	1826	63	4	1123	4	CWC25	17	36977155	Splice_Site	SNP	T	TCGA-DD-A3A2-01A-11D-A20W-10	28835806	36977155	44218055	59	20116										
CCR10	2826	hgsc.bcm.edu	37	chr17	40831634	40831634	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	caggaagaaaggcggggccgGcgggggcagccgcggcgggg	24	10	0	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr17:40831634G>A	ENST00000332438.4	-	2	1045	c.1026C>T	c.(1024-1026)cgC>cgT	p.R342R	CNTNAP1_ENST00000264638.4_5'Flank|CTD-3193K9.4_ENST00000593139.1_RNA|CCR10_ENST00000591765.1_Silent_p.R120R|PLEKHH3_ENST00000412503.1_5'Flank|PLEKHH3_ENST00000591022.1_5'Flank|PLEKHH3_ENST00000293349.6_5'Flank	NM_016602.2	NP_057686.2	P46092	CCR10_HUMAN	chemokine (C-C motif) receptor 10	342					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)			lung(1)|ovary(1)|skin(1)	3		Breast(137;0.000153)		BRCA - Breast invasive adenocarcinoma(366;0.14)		ggcggggccggcgggggcagc	0.701																																					p.R342R		Atlas-SNP	.											.	CCR10	7	.	0			c.C1026T						.						11	14	13					17																	40831634		2169	4234	6403	SO:0001819	synonymous_variant	2826	exon2			GGGCCGGCGGGGG	AF215981	CCDS11435.1	17q21.1-q21.3	2012-08-08	2004-11-12	2004-11-12	ENSG00000184451	ENSG00000184451		"GPCR / Class A : Chemokine receptors : C-C motif"	4474	protein-coding gene	gene with protein product		600240	"G protein-coupled receptor 2"	GPR2		7851889	Standard	NM_016602		Approved		uc002iax.4	P46092	OTTHUMG00000132301	ENST00000332438.4:c.1026C>T	chr17.hg19:g.40831634G>A		31.0	0.0		43.0	20.0	NM_016602	Q4V749|Q6T7X2|Q9NZG2	Silent	SNP	ENST00000332438.4	hg19	CCDS11435.1																																																																																			.	.		0.701	CCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255406.1	NM_016602		A	40831634	G	A	40831634	2	1	116	1	0	0	0	0	0	0	0	1	2942	1190	42	3		3	CCR10	17	40831634	Silent	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	3854479	40831634	40363576	60	20117										
KPNB1	3837	hgsc.bcm.edu	37	chr17	45757446	45757446	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gtctttcattgaccacattgCtggagatgaggatcacacag	10	9	3	3			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr17:45757446C>T	ENST00000290158.4	+	20	2821	c.2414C>T	c.(2413-2415)gCt>gTt	p.A805V	KPNB1_ENST00000537679.1_Missense_Mutation_p.A589V|KPNB1_ENST00000535458.2_Missense_Mutation_p.A660V|RP11-138C9.1_ENST00000578482.1_RNA|KPNB1_ENST00000540627.1_Missense_Mutation_p.A660V	NM_001276453.1|NM_002265.4	NP_001263382.1|NP_002256.2	Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	805					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|protein import into nucleus (GO:0006606)|protein import into nucleus, translocation (GO:0000060)|ribosomal protein import into nucleus (GO:0006610)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|ovary(1)|pancreas(1)|skin(1)	4						GACCACATTGCTGGAGATGAG	0.448																																					p.I805I		Atlas-SNP	.											KPNB1_ENST00000290158,NS,carcinoma,0,1	KPNB1	58	.	0			c.T2414T						.						230	234	233					17																	45757446		2203	4300	6503	SO:0001583	missense	3837	exon20			ACATTGCTGGAGA	L39793	CCDS11513.1, CCDS62228.1	17q21.32	2013-02-14			ENSG00000108424	ENSG00000108424		"Importins", "Armadillo repeat containing"	6400	protein-coding gene	gene with protein product	"importin 1"	602738				7615630, 7627554	Standard	NM_002265		Approved	NTF97, IPOB, MGC2155, MGC2156, MGC2157, IMB1, Impnb, IPO1	uc002ilt.2	Q14974	OTTHUMG00000036957	ENST00000290158.4:c.2414C>T	chr17.hg19:g.45757446C>T	ENSP00000290158:p.Ala805Val	110.0	0.0		111.0	8.0	NM_002265	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	Silent	SNP	ENST00000290158.4	hg19	CCDS11513.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.412134	0.62511	.	.	ENSG00000108424	ENST00000535458;ENST00000290158;ENST00000540627;ENST00000537679	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.28	5.28	0.74379	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72407	0.3456	M	0.67700	2.07	0.40882	D	0.984005	D;P	0.58970	0.984;0.926	P;B	0.48627	0.584;0.304	T	0.74902	-0.3506	9	0.40728	T	0.16	-20.4515	18.9028	0.92449	0.0:1.0:0.0:0.0	.	589;805	F5H4R7;Q14974	.;IMB1_HUMAN	V	660;805;660;589	ENSP00000438253:A660V;ENSP00000290158:A805V;ENSP00000438964:A660V;ENSP00000445006:A589V	ENSP00000290158:A805V	A	+	2	0	KPNB1	43112445	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.588000	0.82629	2.470000	0.83445	0.563000	0.77884	GCT	.	.		0.448	KPNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089755.2	NM_002265		T	45757446	C	T	45757446	3	4	116	1	0	0	0	0	1	0	0	0	8444	797	28	3	2492	3	KPNB1	17	45757446	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	4925812	45757446	35437764	61	20118										
RNF213	57674	hgsc.bcm.edu	37	chr17	78341576	78341576	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	agagaactctgacgtgaagaCgcacgggccttttgaggccg	14	10	1	5			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr17:78341576C>T	ENST00000582970.1	+	43	12043	c.11900C>T	c.(11899-11901)aCg>aTg	p.T3967M	CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.T2040M|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.T4016M	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3967					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T2040M(1)|p.T4016M(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GACGTGAAGACGCACGGGCCT	0.592																																					p.T3967M		Atlas-SNP	.											RNF213_ENST00000411702,caecum,carcinoma,0,2	RNF213	766	.	2	Substitution - Missense(2)	large_intestine(2)	c.C11900T						.						73	67	69					17																	78341576		2203	4300	6503	SO:0001583	missense	57674	exon43			TGAAGACGCACGG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11900C>T	chr17.hg19:g.78341576C>T	ENSP00000464087:p.Thr3967Met	65.0	0.0		48.0	2.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.852345	0.32699	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.25085	1.82	5.08	4.12	0.48240	.	0.169933	0.51477	N	0.000093	T	0.28995	0.0720	M	0.65975	2.015	0.28951	N	0.890382	P;B	0.48294	0.908;0.369	B;B	0.41666	0.363;0.054	T	0.30179	-0.9987	10	0.87932	D	0	.	11.7927	0.52078	0.0:0.9173:0.0:0.0827	.	4016;2040	C9JCP4;Q63HN8	.;RN213_HUMAN	M	3967;4016;2040	ENSP00000338218:T2040M	ENSP00000338218:T2040M	T	+	2	0	RNF213	75956171	0.018000	0.18449	0.777000	0.31699	0.569000	0.35902	0.147000	0.16202	1.150000	0.42419	-0.122000	0.15005	ACG	.	.		0.592	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78341576	C	T	78341576	3	4	116	1	0	0	0	0	1	0	0	0	13492	536	19	1	12385	1	RNF213	17	78341576	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	32584130	78341576	2853634	62	20119										
ESCO1	114799	hgsc.bcm.edu	37	chr18	19144186	19144186	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	taatcaactgtttttcatcaGttttctctgcttcttttagt	4	8	5	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr18:19144186G>T	ENST00000269214.5	-	7	2736	c.1799C>A	c.(1798-1800)aCt>aAt	p.T600N		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	600					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)			breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						TTTTTCATCAGTTTTCTCTGC	0.323																																					p.T600N		Atlas-SNP	.											.	ESCO1	89	.	0			c.C1799A						.						117	108	111					18																	19144186		2203	4297	6500	SO:0001583	missense	114799	exon7			TCATCAGTTTTCT	AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.1799C>A	chr18.hg19:g.19144186G>T	ENSP00000269214:p.Thr600Asn	180.0	0.0		141.0	35.0	NM_052911	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Missense_Mutation	SNP	ENST00000269214.5	hg19	CCDS32800.1	.	.	.	.	.	.	.	.	.	.	G	8.885	0.952685	0.18431	.	.	ENSG00000141446	ENST00000269214;ENST00000383276	T;T	0.57907	0.37;1.96	4.92	-1.32	0.09201	.	0.728086	0.12879	N	0.431624	T	0.26159	0.0638	N	0.19112	0.55	0.22050	N	0.9994	B	0.21520	0.057	B	0.14023	0.01	T	0.12477	-1.0546	10	0.17832	T	0.49	-1.6325	1.2834	0.02046	0.2734:0.1076:0.3938:0.2252	.	600	Q5FWF5	ESCO1_HUMAN	N	600	ENSP00000269214:T600N;ENSP00000372763:T600N	ENSP00000269214:T600N	T	-	2	0	ESCO1	17398184	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	0.360000	0.20250	-0.031000	0.13781	-0.211000	0.12701	ACT	.	.		0.323	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		T	19144186	G	T	19144186	3	4	116	1	0	0	0	0	1	0	0	0	5250	1029	36	3	747	3	ESCO1	18	19144186	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10		19144186	58933062	63	20120										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22807281	22807281	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	acaaatggcacatttatatgGcttgttggacgtgtgagtct	11	6	1	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr18:22807281G>T	ENST00000361524.3	-	4	749	c.601C>A	c.(601-603)Cca>Aca	p.P201T	ZNF521_ENST00000584787.1_5'UTR|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Missense_Mutation_p.P201T	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	201					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CATTTATATGGCTTGTTGGAC	0.498			T	PAX5	ALL																																p.P201T		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.C601A						.						92	88	90					18																	22807281		2203	4300	6503	SO:0001583	missense	25925	exon4			TATATGGCTTGTT	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.601C>A	chr18.hg19:g.22807281G>T	ENSP00000354794:p.Pro201Thr	271.0	0.0		258.0	90.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627694	0.28978	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.16897	2.31;2.31	5.98	5.98	0.97165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.48447	0.1500	M	0.81112	2.525	0.50632	D	0.99988	D	0.89917	1.0	D	0.97110	1.0	T	0.42515	-0.9447	10	0.62326	D	0.03	-12.7935	20.4434	0.99119	0.0:0.0:1.0:0.0	.	201	Q96K83	ZN521_HUMAN	T	201;235;201	ENSP00000354794:P201T;ENSP00000382352:P201T	ENSP00000354794:P201T	P	-	1	0	ZNF521	21061279	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.838000	0.97847	0.655000	0.94253	CCA	.	.		0.498	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		T	22807281	G	T	22807281	3	4	116	1	0	0	0	0	1	0	0	0	17980	1203	42	3	3354	3	ZNF521	18	22807281	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	3663095	22807281	55269967	64	20121										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17115174	17115174	+	Frame_Shift_Del	DEL	G	G	-													0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	aacacaggctggtcggacaaGgggaagctcatgttggtgat							TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr19:17115174delG	ENST00000443236.1	-	8	754	c.723delC	c.(721-723)cccfs	p.P241fs	CPAMD8_ENST00000388925.4_Frame_Shift_Del_p.P194fs	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	194						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GGTCGGACAAGGGGAAGCTCA	0.512																																					p.L242fs		Atlas-Indel,Pindel	.											.	CPAMD8	192	.	0			c.724delT						.						90	91	90					19																	17115174		2003	4171	6174	SO:0001589	frameshift_variant	27151	exon8			.	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.723delC	chr19.hg19:g.17115174delG	ENSP00000402505:p.Pro241fs	113.0	0.0		106.0	26.0	NM_015692	Q8NC09|Q9ULD7	Frame_Shift_Del	DEL	ENST00000443236.1	hg19	CCDS42519.1																																																																																			.	.		0.512	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		-	17115174	G	-	17115174	7	5	116	1	0	1	0	1	0	0	0	0	3797	987	35	0	5215	0	CPAMD8	19	17115174	Frame_Shift_Del	DEL	G	TCGA-DD-A3A2-01A-11D-A20W-10		17115174	42013809	65	20122	86	2								
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17115180	17115180	+	Silent	SNP	G	G	A													0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ggctggtcggacaaggggaaGctcatgttggtgatgcctgt							TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr19:17115180G>A	ENST00000443236.1	-	8	748	c.717C>T	c.(715-717)agC>agT	p.S239S	CPAMD8_ENST00000388925.4_Silent_p.S192S	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	192						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						ACAAGGGGAAGCTCATGTTGG	0.517																																					p.S239S		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C717T						.						88	90	90					19																	17115180		2015	4170	6185	SO:0001819	synonymous_variant	27151	exon8			GGGGAAGCTCATG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.717C>T	chr19.hg19:g.17115180G>A		103.0	0.0		99.0	27.0	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	hg19	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	G	0.242	-1.012692	0.02095	.	.	ENSG00000160111	ENST00000443236	.	.	.	2.73	1.31	0.21738	.	.	.	.	.	T	0.51635	0.1686	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46386	-0.9195	4	.	.	.	.	5.1812	0.15161	0.462:0.0:0.538:0.0	.	.	.	.	V	250	.	.	A	-	2	0	CPAMD8	16976180	0.993000	0.37304	0.993000	0.49108	0.025000	0.11179	0.228000	0.17814	1.269000	0.44280	0.491000	0.48974	GCT	.	.		0.517	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		A	17115180	G	A	17115180	2	1	116	1	0	0	0	0	0	0	0	1	3797	962	34	3		3	CPAMD8	19	17115180	Silent	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	6	17115180	42013803	66	20123	86	2								
CYP2A6	1548	hgsc.bcm.edu	37	chr19	41354235	41354235	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ccaaagacaatggagctgatGacattggagactgtgcggct	13	8	0	4			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr19:41354235G>C	ENST00000301141.5	-	4	563	c.543C>G	c.(541-543)gtC>gtG	p.V181V	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	181					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TGGAGCTGATGACATTGGAGA	0.532																																					p.V181V		Atlas-SNP	.											.	CYP2A6	69	.	0			c.C543G						.						135	125	128					19																	41354235		2203	4298	6501	SO:0001819	synonymous_variant	1548	exon4			GCTGATGACATTG	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.543C>G	chr19.hg19:g.41354235G>C		284.0	0.0		354.0	138.0	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Silent	SNP	ENST00000301141.5	hg19	CCDS12568.1																																																																																			.	.		0.532	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		C	41354235	G	C	41354235	2	2	116	1	0	0	0	0	0	0	0	1	4164	1277	45	4		4	CYP2A6	19	41354235	Silent	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	24239055	41354235	17774748	67	20124										
ZNF611	81856	hgsc.bcm.edu	37	chr19	53208756	53208756	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	gcttgatttacgactgaaaaCcttttcacattcatcacatt	4	10	3	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr19:53208756C>G	ENST00000319783.1	-	7	1868	c.1552G>C	c.(1552-1554)Gtt>Ctt	p.V518L	ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000453741.2_Missense_Mutation_p.V449L|ZNF611_ENST00000602162.1_Missense_Mutation_p.V449L|ZNF611_ENST00000595798.1_Missense_Mutation_p.V449L|ZNF611_ENST00000543227.1_Missense_Mutation_p.V518L|ZNF611_ENST00000540744.1_Missense_Mutation_p.V518L	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	518					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		CGACTGAAAACCTTTTCACAT	0.368																																					p.V518L		Atlas-SNP	.											.	ZNF611	72	.	0			c.G1552C						.						120	119	119					19																	53208756		2203	4300	6503	SO:0001583	missense	81856	exon7			TGAAAACCTTTTC	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"Zinc fingers, C2H2-type", "-"	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.1552G>C	chr19.hg19:g.53208756C>G	ENSP00000322427:p.Val518Leu	143.0	0.0		138.0	60.0	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	hg19	CCDS12855.1	.	.	.	.	.	.	.	.	.	.	.	12.08	1.829947	0.32329	.	.	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	1.51	-1.04	0.10068	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10423	0.0255	N	0.16166	0.38	0.09310	N	1	B	0.14012	0.009	B	0.17979	0.02	T	0.31364	-0.9946	9	0.87932	D	0	.	3.0195	0.06071	0.0:0.2713:0.2395:0.4892	.	518	Q8N823	ZN611_HUMAN	L	518;518;449;518	ENSP00000437616:V518L;ENSP00000439211:V518L;ENSP00000443505:V449L;ENSP00000322427:V518L	ENSP00000322427:V518L	V	-	1	0	ZNF611	57900568	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-4.596000	0.00210	-0.051000	0.13334	0.205000	0.17691	GTT	.	.		0.368	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972		G	53208756	C	G	53208756	3	3	116	1	0	0	0	0	1	0	0	0	18052	507	18	4	569	4	ZNF611	19	53208756	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	11854521	53208756	5920227	68	20125										
TMC2	117532	hgsc.bcm.edu	37	chr20	2582881	2582881	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ggaagtgggtacctcatttaCtttgtggttaagcgatctca	11	7	2	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr20:2582881C>T	ENST00000358864.1	+	11	1362	c.1347C>T	c.(1345-1347)taC>taT	p.Y449Y	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	449					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						ACCTCATTTACTTTGTGGTTA	0.403																																					p.Y449Y		Atlas-SNP	.											.	TMC2	121	.	0			c.C1347T						.						180	155	163					20																	2582881		2203	4300	6503	SO:0001819	synonymous_variant	117532	exon11			CATTTACTTTGTG	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1347C>T	chr20.hg19:g.2582881C>T		252.0	0.0		236.0	73.0	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Silent	SNP	ENST00000358864.1	hg19	CCDS13029.2																																																																																			.	.		0.403	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			T	2582881	C	T	2582881	2	4	116	1	0	0	0	0	0	0	0	1	16000	576	20	3		3	TMC2	20	2582881	Silent	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10		2582881	60442639	69	20126										
RALY	22913	hgsc.bcm.edu	37	chr20	32664559	32664559	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ggagctgacacagatcaagtCcaatatcgatgccctgctga	10	11	1	3			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr20:32664559C>T	ENST00000246194.3	+	7	1098	c.596C>T	c.(595-597)tCc>tTc	p.S199F	RALY_ENST00000375114.3_Missense_Mutation_p.S183F|RALY_ENST00000493399.1_3'UTR	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	199					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						CAGATCAAGTCCAATATCGAT	0.592																																					p.S199F		Atlas-SNP	.											.	RALY	44	.	0			c.C596T						.						75	59	65					20																	32664559		2203	4300	6503	SO:0001583	missense	22913	exon7			TCAAGTCCAATAT	AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"RNA binding motif (RRM) containing"	15921	protein-coding gene	gene with protein product		614663	"RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)", "RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	ENST00000246194.3:c.596C>T	chr20.hg19:g.32664559C>T	ENSP00000246194:p.Ser199Phe	91.0	0.0		88.0	38.0	NM_016732	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	Missense_Mutation	SNP	ENST00000246194.3	hg19	CCDS13230.1	.	.	.	.	.	.	.	.	.	.	C	12.71	2.018308	0.35606	.	.	ENSG00000125970	ENST00000375114;ENST00000246194;ENST00000333552;ENST00000442805	T;T;T;T	0.32988	1.43;1.43;1.48;1.43	5.44	3.36	0.38483	.	0.200152	0.43747	D	0.000533	T	0.38585	0.1046	L	0.43152	1.355	0.37959	D	0.93291	D;D	0.57899	0.959;0.981	P;P	0.53649	0.731;0.597	T	0.44360	-0.9333	10	0.44086	T	0.13	-13.9162	15.4309	0.75099	0.263:0.737:0.0:0.0	.	183;199	Q9UKM9-2;Q9UKM9	.;RALY_HUMAN	F	183;199;133;183	ENSP00000364255:S183F;ENSP00000246194:S199F;ENSP00000327522:S133F;ENSP00000415973:S183F	ENSP00000246194:S199F	S	+	2	0	RALY	32128220	0.997000	0.39634	1.000000	0.80357	0.003000	0.03518	0.847000	0.27696	1.505000	0.48720	-0.302000	0.09304	TCC	.	.		0.592	RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1			T	32664559	C	T	32664559	3	4	116	1	0	0	0	0	1	0	0	0	13034	855	30	3	614	3	RALY	20	32664559	Missense_Mutation	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	30081678	32664559	30360961	70	20127										
PLTP	5360	hgsc.bcm.edu	37	chr20	44531198	44531198	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ggtgcagcgcggtggggccaGgacccgcagctccagcttca	16	14	1	0			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr20:44531198G>C	ENST00000477313.1	-	10	1582	c.988C>G	c.(988-990)Ctg>Gtg	p.L330V	PLTP_ENST00000372420.1_Missense_Mutation_p.L242V|PLTP_ENST00000542937.1_Missense_Mutation_p.L350V|PLTP_ENST00000354050.4_Missense_Mutation_p.L278V|PLTP_ENST00000372431.3_Missense_Mutation_p.L330V|PLTP_ENST00000420868.2_Missense_Mutation_p.L235V			P55058	PLTP_HUMAN	phospholipid transfer protein	330					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)			endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				GGTGGGGCCAGGACCCGCAGC	0.637																																					p.L330V		Atlas-SNP	.											.	PLTP	49	.	0			c.C988G						.						37	33	34					20																	44531198		2203	4300	6503	SO:0001583	missense	5360	exon11			GGGCCAGGACCCG	L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.988C>G	chr20.hg19:g.44531198G>C	ENSP00000417138:p.Leu330Val	203.0	0.0		164.0	64.0	NM_006227	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Missense_Mutation	SNP	ENST00000477313.1	hg19	CCDS13386.1	.	.	.	.	.	.	.	.	.	.	G	0.017	-1.496238	0.01009	.	.	ENSG00000100979	ENST00000372420;ENST00000372431;ENST00000354050;ENST00000477313;ENST00000542937;ENST00000420868	T;T;T;T;T;T	0.09911	2.93;2.93;2.93;2.93;2.93;2.93	5.28	-10.3	0.00346	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.693330	0.02942	N	0.140624	T	0.06645	0.0170	L	0.44542	1.39	0.09310	N	1	B;B;B;B;B;B;B	0.09022	0.002;0.002;0.001;0.001;0.002;0.001;0.002	B;B;B;B;B;B;B	0.14023	0.007;0.007;0.007;0.006;0.003;0.006;0.01	T	0.30765	-0.9967	10	0.27082	T	0.32	1.4431	0.9765	0.01426	0.2809:0.1821:0.3216:0.2154	.	235;235;242;330;278;330;350	E7EV16;B4DRB4;B4DDD5;Q53H91;P55058-2;P55058;B3KUE5	.;.;.;.;.;PLTP_HUMAN;.	V	242;330;278;330;350;235	ENSP00000361497:L242V;ENSP00000361508:L330V;ENSP00000335290:L278V;ENSP00000417138:L330V;ENSP00000440296:L350V;ENSP00000411671:L235V	ENSP00000335290:L278V	L	-	1	2	PLTP	43964605	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.279000	0.08479	-1.656000	0.01495	-1.047000	0.02352	CTG	.	.		0.637	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		C	44531198	G	C	44531198	3	2	116	1	0	0	0	0	1	0	0	0	12123	991	35	4	517	4	PLTP	20	44531198	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	11866639	44531198	18494322	71	20128										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61990961	61990961	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ggaccacgtccgagatgttgGccacgggtcgggaccacttg	15	12	0	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr20:61990961G>A	ENST00000370263.4	-	2	388	c.167C>T	c.(166-168)gCc>gTc	p.A56V	CHRNA4_ENST00000463705.1_Intron|RP11-261N11.8_ENST00000370257.1_RNA	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	56					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	CGAGATGTTGGCCACGGGTCG	0.637																																					p.A56V		Atlas-SNP	.											.	CHRNA4	98	.	0			c.C167T						.						125	106	113					20																	61990961		2198	4293	6491	SO:0001583	missense	1137	exon2			ATGTTGGCCACGG		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.167C>T	chr20.hg19:g.61990961G>A	ENSP00000359285:p.Ala56Val	110.0	0.0		109.0	37.0	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	hg19	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.878939	0.51801	.	.	ENSG00000101204	ENST00000370263	T	0.35789	1.29	4.26	4.26	0.50523	Neurotransmitter-gated ion-channel ligand-binding (3);	0.131051	0.49916	D	0.000130	T	0.24431	0.0592	N	0.20766	0.605	0.44736	D	0.997739	B	0.30824	0.296	B	0.25140	0.058	T	0.05500	-1.0881	10	0.29301	T	0.29	.	16.68	0.85289	0.0:0.0:1.0:0.0	.	56	P43681	ACHA4_HUMAN	V	56	ENSP00000359285:A56V	ENSP00000359285:A56V	A	-	2	0	CHRNA4	61461405	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	2.933000	0.48948	1.929000	0.55896	0.491000	0.48974	GCC	.	.		0.637	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			A	61990961	G	A	61990961	3	1	116	1	0	0	0	0	1	0	0	0	3387	1203	42	3	1736	3	CHRNA4	20	61990961	Missense_Mutation	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10	17459763	61990961	1034559	72	20129										
LARGE	9215	hgsc.bcm.edu	37	chr22	33670561	33670561	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	taatgtcgaagctgggggcaTgaggcatgtggatcatgtag	16	5	1	1			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chr22:33670561T>A	ENST00000354992.2	-	16	2694	c.2123A>T	c.(2122-2124)cAt>cTt	p.H708L	LARGE_ENST00000397394.2_Missense_Mutation_p.H708L|LARGE_ENST00000437602.2_Missense_Mutation_p.H659L|LARGE_ENST00000337431.2_Missense_Mutation_p.H656L|LARGE_ENST00000402320.1_Missense_Mutation_p.H656L|LARGE_ENST00000452586.2_Missense_Mutation_p.H507L	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	708					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				GCTGGGGGCATGAGGCATGTG	0.537											OREG0026497	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H708L	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											.	LARGE	98	.	0			c.A2123T						.						147	120	129					22																	33670561		2203	4300	6503	SO:0001583	missense	9215	exon16			GGGGCATGAGGCA	AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"Glycosyltransferase family 8 domain containing"	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.2123A>T	chr22.hg19:g.33670561T>A	ENSP00000347088:p.His708Leu	146.0	0.0	841	149.0	53.0	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	ENST00000354992.2	hg19	CCDS13912.1	.	.	.	.	.	.	.	.	.	.	T	31	5.059072	0.93846	.	.	ENSG00000133424	ENST00000354992;ENST00000337431;ENST00000397394;ENST00000402320;ENST00000452586;ENST00000437602	T;T;T;T;T;T	0.41758	2.08;0.99;2.08;0.99;2.08;0.99	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.70988	0.3287	M	0.88181	2.935	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;1.0;0.999	D;D;D;D	0.97110	1.0;0.96;1.0;0.978	T	0.75508	-0.3293	10	0.54805	T	0.06	-7.4884	16.8061	0.85666	0.0:0.0:0.0:1.0	.	659;507;656;708	B7Z2I9;E9PH73;O95461-2;O95461	.;.;.;LARGE_HUMAN	L	708;656;708;656;507;659	ENSP00000347088:H708L;ENSP00000336636:H656L;ENSP00000380549:H708L;ENSP00000385223:H656L;ENSP00000407917:H507L;ENSP00000388544:H659L	ENSP00000336636:H656L	H	-	2	0	LARGE	32000561	1.000000	0.71417	0.983000	0.44433	0.984000	0.73092	7.554000	0.82212	2.367000	0.80283	0.528000	0.53228	CAT	.	.		0.537	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		A	33670561	T	A	33670561	3	1	116	1	0	0	0	0	1	0	0	0	8636	1464	51	4	151	4	LARGE	22	33670561	Missense_Mutation	SNP	T	TCGA-DD-A3A2-01A-11D-A20W-10		33670561	17634005	73	20130										
POLA1	5422	hgsc.bcm.edu	37	chrX	24744103	24744103	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	tatctacttacccagccagtGgaaaagaactatgcttttga	7	9	1	2			TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chrX:24744103G>T	ENST00000379059.3	+	13	1320	c.1305G>T	c.(1303-1305)gtG>gtT	p.V435V	POLA1_ENST00000379068.3_Silent_p.V441V	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	435					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	CCCAGCCAGTGGAAAAGAACT	0.313																																					p.V435V		Atlas-SNP	.											.	POLA1	117	.	0			c.G1305T						.						62	62	62					X																	24744103		2203	4300	6503	SO:0001819	synonymous_variant	5422	exon13			GCCAGTGGAAAAG		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1305G>T	chrX.hg19:g.24744103G>T		414.0	0.0		444.0	185.0	NM_016937	Q86UQ7	Silent	SNP	ENST00000379059.3	hg19	CCDS14214.1																																																																																			.	.		0.313	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		T	24744103	G	T	24744103	2	4	116	1	0	0	0	0	0	0	0	1	12196	1335	47	3		3	POLA1	23	24744103	Silent	SNP	G	TCGA-DD-A3A2-01A-11D-A20W-10		24744103	130526457	74	20131										
IDS	3423	hgsc.bcm.edu	37	chrX	148582537	148582537	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0547945205479452	4	1	1.02439024390244	2.24085365853659	0.663956639566396	1	1	0	ggtggaaaagaccagctataCggagaatcatcggtatggtt	13	6	1	2	rs201892132		TCGA-DD-A3A2-01A-11D-A20W-10	TCGA-DD-A3A2-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1b32c222-05fb-4c01-ab8a-be3e922002e7	cefe8443-c2b3-4fd4-a429-423b1e389d33	g.chrX:148582537C>T	ENST00000340855.6	-	4	659	c.450G>A	c.(448-450)ccG>ccA	p.P150P	IDS_ENST00000541269.1_5'UTR|IDS_ENST00000370443.4_Silent_p.P150P|IDS_ENST00000370441.4_Silent_p.P150P|IDS_ENST00000422081.2_5'UTR|IDS_ENST00000427113.2_5'Flank|IDS_ENST00000490775.1_5'UTR	NM_000202.5|NM_001166550.1	NP_000193.1|NP_001160022.1	P22304	IDS_HUMAN	iduronate 2-sulfatase	150					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	lysosomal lumen (GO:0043202)	iduronate-2-sulfatase activity (GO:0004423)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(5)|large_intestine(2)|lung(8)|prostate(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					ACCAGCTATACGGAGAATCAT	0.383																																					p.P150P		Atlas-SNP	.											.	IDS	46	.	0			c.G450A						.	C	,,	0,3835		0,0,1632,571	134	122	126		450,180,450	-2.1	1	X		126	1,6727		0,1,2427,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	IDS	NM_000202.5,NM_001166550.1,NM_006123.4	,,	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	,,	150/551,60/461,150/344	148582537	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	3423	exon4			GCTATACGGAGAA	M58342	CCDS14685.1, CCDS14686.1	Xq27.3-q28	2012-10-02	2008-08-01		ENSG00000010404	ENSG00000010404	3.1.6.13		5389	protein-coding gene	gene with protein product	"Hunter syndrome"	300823		SIDS			Standard	NM_006123		Approved		uc011mxe.2	P22304	OTTHUMG00000022615	ENST00000340855.6:c.450G>A	chrX.hg19:g.148582537C>T		95.0	0.0		99.0	41.0	NM_006123	D3DWT4|Q14604|Q9BRM3	Silent	SNP	ENST00000340855.6	hg19	CCDS14685.1																																																																																			.	.		0.383	IDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058677.3			T	148582537	C	T	148582537	2	4	116	1	0	0	0	0	0	0	0	1	7512	523	19	1		1	IDS	23	148582537	Silent	SNP	C	TCGA-DD-A3A2-01A-11D-A20W-10	123838434	148582537	6688023	75	20132										
PHACTR4	65979	hgsc.bcm.edu	37	chr1	28818225	28818225	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	ttctgaggtttaatgaatatGtagaggtaacagatgctcaa	10	4	2	4			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr1:28818225G>T	ENST00000373839.3	+	12	2203	c.1942G>T	c.(1942-1944)Gta>Tta	p.V648L	PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Missense_Mutation_p.V658L	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	648					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		TAATGAATATGTAGAGGTAAC	0.483																																					p.V658L		Atlas-SNP	.											.	PHACTR4	64	.	0			c.G1972T						.						85	90	88					1																	28818225		1936	4143	6079	SO:0001583	missense	65979	exon11			GAATATGTAGAGG	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1942G>T	chr1.hg19:g.28818225G>T	ENSP00000362945:p.Val648Leu	95.0	0.0		81.0	32.0	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	hg19	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	G	35	5.421743	0.96111	.	.	ENSG00000204138	ENST00000373839;ENST00000373836	T;T	0.38887	1.13;1.11	5.77	5.77	0.91146	.	0.114194	0.64402	D	0.000016	T	0.61073	0.2318	M	0.89968	3.075	0.80722	D	1	P;B	0.37176	0.586;0.181	B;B	0.42495	0.389;0.119	T	0.68273	-0.5452	10	0.87932	D	0	-4.2906	19.0261	0.92932	0.0:0.0:1.0:0.0	.	658;648	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	L	648;658	ENSP00000362945:V648L;ENSP00000362942:V658L	ENSP00000362942:V658L	V	+	1	0	PHACTR4	28690812	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.818000	0.99354	2.737000	0.93849	0.558000	0.71614	GTA	.	.		0.483	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		T	28818225	G	T	28818225	3	4	117	1	0	0	0	0	1	0	0	0	11821	1377	48	3	2034	3	PHACTR4	1	28818225	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10		28818225	220432396	1	20133										
PRDX1	5052	hgsc.bcm.edu	37	chr1	45977016	45977016	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	agcgctcacttctgcttggaGaaatattctttgctcttttg	8	9	4	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr1:45977016G>C	ENST00000262746.1	-	6	924	c.585C>G	c.(583-585)ttC>ttG	p.F195L	PRDX1_ENST00000319248.8_Missense_Mutation_p.F195L|PRDX1_ENST00000372079.1_Missense_Mutation_p.F93L	NM_002574.3|NM_181696.2	NP_002565.1|NP_859047.1	Q06830	PRDX1_HUMAN	peroxiredoxin 1	195					cell proliferation (GO:0008283)|erythrocyte homeostasis (GO:0034101)|hydrogen peroxide catabolic process (GO:0042744)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of NF-kappaB import into nucleus (GO:0042345)|regulation of stress-activated MAPK cascade (GO:0032872)|removal of superoxide radicals (GO:0019430)|retina homeostasis (GO:0001895)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)	heme binding (GO:0020037)|peroxidase activity (GO:0004601)|poly(A) RNA binding (GO:0044822)|thioredoxin peroxidase activity (GO:0008379)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|skin(1)	12	Acute lymphoblastic leukemia(166;0.155)					TCTGCTTGGAGAAATATTCTT	0.453																																					p.F195L		Atlas-SNP	.											.	PRDX1	16	.	0			c.C585G						.						202	212	209					1																	45977016		2203	4300	6503	SO:0001583	missense	5052	exon6			CTTGGAGAAATAT	BC021683	CCDS522.1	1p34.1	2008-02-05			ENSG00000117450	ENSG00000117450			9352	protein-coding gene	gene with protein product		176763		PAGA		8496166	Standard	NM_181697		Approved	NKEFA	uc021omw.1	Q06830	OTTHUMG00000007738	ENST00000262746.1:c.585C>G	chr1.hg19:g.45977016G>C	ENSP00000262746:p.Phe195Leu	95.0	0.0		78.0	28.0	NM_181696	B5BU26|D3DPZ8|P35703|Q2V576|Q5T154|Q5T155	Missense_Mutation	SNP	ENST00000262746.1	hg19	CCDS522.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.640237	0.87859	.	.	ENSG00000117450	ENST00000262746;ENST00000319248;ENST00000372079	T;T;T	0.27720	1.65;1.65;1.65	5.04	3.18	0.36537	Peroxiredoxin, C-terminal (1);Thioredoxin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.38746	0.1052	L	0.52573	1.65	0.80722	D	1	P	0.42692	0.787	P	0.50934	0.654	T	0.18147	-1.0346	10	0.87932	D	0	-10.1385	11.234	0.48929	0.1484:0.0:0.8516:0.0	.	195	Q06830	PRDX1_HUMAN	L	195;195;93	ENSP00000262746:F195L;ENSP00000361152:F195L;ENSP00000361150:F93L	ENSP00000262746:F195L	F	-	3	2	PRDX1	45749603	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	4.000000	0.57039	0.547000	0.28938	0.462000	0.41574	TTC	.	.		0.453	PRDX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020845.1	NM_181697		C	45977016	G	C	45977016	3	2	117	1	0	0	0	0	1	0	0	0	12476	933	33	4	18	4	PRDX1	1	45977016	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	17158791	45977016	203273605	2	20134										
DNASE2B	58511	hgsc.bcm.edu	37	chr1	84864291	84864291	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	actgctaagaacatcctttgCtttgctcttccttggcctct	6	13	2	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr1:84864291C>A	ENST00000370665.3	+	1	77	c.44C>A	c.(43-45)gCt>gAt	p.A15D		NM_021233.2	NP_067056.2	Q8WZ79	DNS2B_HUMAN	deoxyribonuclease II beta	15					apoptotic DNA fragmentation (GO:0006309)	extracellular region (GO:0005576)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)			endometrium(1)|lung(4)|skin(1)	6				all cancers(265;0.00303)|Epithelial(280;0.0112)|OV - Ovarian serous cystadenocarcinoma(397;0.0808)		ACATCCTTTGCTTTGCTCTTC	0.443																																					p.A15D	Pancreas(54;788 1175 11852 16034 30034)	Atlas-SNP	.											.	DNASE2B	40	.	0			c.C44A						.						226	232	230					1																	84864291		2009	4179	6188	SO:0001583	missense	58511	exon1			CCTTTGCTTTGCT	AF274571	CCDS694.1, CCDS44167.1	1p22.3	2008-02-05			ENSG00000137976	ENSG00000137976			28875	protein-coding gene	gene with protein product		608057				12594037, 11376952	Standard	NM_021233		Approved	DLAD	uc001djt.1	Q8WZ79	OTTHUMG00000009860	ENST00000370665.3:c.44C>A	chr1.hg19:g.84864291C>A	ENSP00000359699:p.Ala15Asp	87.0	0.0		89.0	40.0	NM_021233	Q5VXD0|Q5VXD1|Q8WZ80|Q9NQW3	Missense_Mutation	SNP	ENST00000370665.3	hg19	CCDS44167.1	.	.	.	.	.	.	.	.	.	.	C	0.370	-0.934652	0.02340	.	.	ENSG00000137976	ENST00000370665	T	0.12255	2.7	5.23	2.37	0.29283	.	1.288080	0.04783	N	0.430212	T	0.03305	0.0096	L	0.36672	1.1	0.19775	N	0.999953	B	0.27498	0.18	B	0.27076	0.076	T	0.43909	-0.9362	10	0.12766	T	0.61	0.1643	7.2221	0.25994	0.0:0.7282:0.0:0.2718	.	15	Q8WZ79	DNS2B_HUMAN	D	15	ENSP00000359699:A15D	ENSP00000359699:A15D	A	+	2	0	DNASE2B	84636879	0.093000	0.21703	0.056000	0.19401	0.009000	0.06853	0.221000	0.17680	0.459000	0.27016	-0.137000	0.14449	GCT	.	.		0.443	DNASE2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027248.1	NM_021233		A	84864291	C	A	84864291	3	1	117	1	0	0	0	0	1	0	0	0	4667	797	28	3	46	3	DNASE2B	1	84864291	Missense_Mutation	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	38887275	84864291	164386330	3	20135										
GBP2	2634	hgsc.bcm.edu	37	chr1	89575922	89575922	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	agccacatcctccttggactCcaaatattttttcagcacct	4	14	1	0			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr1:89575922C>T	ENST00000370466.3	-	9	1658	c.1390G>A	c.(1390-1392)Gag>Aag	p.E464K	GBP2_ENST00000463660.1_5'UTR	NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN	guanylate binding protein 2, interferon-inducible	464					cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		TCCTTGGACTCCAAATATTTT	0.438																																					p.E464K		Atlas-SNP	.											.	GBP2	58	.	0			c.G1390A						.						185	166	172					1																	89575922		2203	4300	6503	SO:0001583	missense	2634	exon9			TGGACTCCAAATA	BC073163	CCDS719.1	1p22.2	2008-02-05			ENSG00000162645	ENSG00000162645			4183	protein-coding gene	gene with protein product		600412				1715024	Standard	NM_004120		Approved		uc001dmz.1	P32456	OTTHUMG00000010662	ENST00000370466.3:c.1390G>A	chr1.hg19:g.89575922C>T	ENSP00000359497:p.Glu464Lys	149.0	0.0		116.0	54.0	NM_004120	Q6GPH0|Q6IAU2|Q86TB0	Missense_Mutation	SNP	ENST00000370466.3	hg19	CCDS719.1	.	.	.	.	.	.	.	.	.	.	C	6.217	0.408220	0.11754	.	.	ENSG00000162645	ENST00000370466	T	0.53423	0.62	3.68	-5.51	0.02568	Guanylate-binding protein, C-terminal (3);	0.578615	0.12970	U	0.424245	T	0.04679	0.0127	N	0.02721	-0.515	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.37979	-0.9682	10	0.12430	T	0.62	-15.3283	6.0082	0.19559	0.0:0.307:0.354:0.339	.	464	P32456	GBP2_HUMAN	K	464	ENSP00000359497:E464K	ENSP00000359497:E464K	E	-	1	0	GBP2	89348510	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-2.023000	0.01438	-1.131000	0.02910	-0.781000	0.03364	GAG	.	.		0.438	GBP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029406.2	NM_004120		T	89575922	C	T	89575922	3	4	117	1	0	0	0	0	1	0	0	0	6282	864	30	3	397	3	GBP2	1	89575922	Missense_Mutation	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	4711631	89575922	159674699	4	20136										
HFM1	164045	hgsc.bcm.edu	37	chr1	91784735	91784735	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	ttcaatagtacagcaaacttCttttcttgagcagctacaaa	5	9	3	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr1:91784735C>A	ENST00000370425.3	-	25	2810	c.2712G>T	c.(2710-2712)aaG>aaT	p.K904N	HFM1_ENST00000370424.3_Missense_Mutation_p.K583N|HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_Missense_Mutation_p.K136N	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	904	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		CAGCAAACTTCTTTTCTTGAG	0.289																																					p.K904N		Atlas-SNP	.											.	HFM1	188	.	0			c.G2712T						.						49	52	51					1																	91784735		2203	4300	6503	SO:0001583	missense	164045	exon25			AAACTTCTTTTCT	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2712G>T	chr1.hg19:g.91784735C>A	ENSP00000359454:p.Lys904Asn	118.0	0.0		106.0	46.0	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	hg19	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	C	5.078	0.200004	0.09652	.	.	ENSG00000162669	ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	T;T;T	0.58940	0.3;0.3;0.3	5.14	0.635	0.17723	Sec63 domain (2);	0.462331	0.18260	U	0.146668	T	0.20536	0.0494	L	0.36672	1.1	0.23798	N	0.996814	B;B	0.09022	0.002;0.002	B;B	0.11329	0.006;0.003	T	0.21177	-1.0253	10	0.32370	T	0.25	.	5.7659	0.18227	0.1105:0.3413:0.4654:0.0827	.	583;904	A6NGI5;A2PYH4	.;HFM1_HUMAN	N	904;136;583;588	ENSP00000359454:K904N;ENSP00000294696:K136N;ENSP00000359453:K583N	ENSP00000294696:K136N	K	-	3	2	HFM1	91557323	1.000000	0.71417	0.991000	0.47740	0.636000	0.38137	0.958000	0.29227	0.231000	0.21079	0.650000	0.86243	AAG	.	.		0.289	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		A	91784735	C	A	91784735	3	1	117	1	0	0	0	0	1	0	0	0	7092	912	32	3	1655	3	HFM1	1	91784735	Missense_Mutation	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	2208813	91784735	157465886	5	20137										
CEP350	9857	hgsc.bcm.edu	37	chr1	179965731	179965731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	atttcagttccagccatctgGaatcaaagcacgtatactgt	7	10	3	0			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr1:179965731G>A	ENST00000367607.3	+	6	857	c.439G>A	c.(439-441)Gaa>Aaa	p.E147K		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	147					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						CAGCCATCTGGAATCAAAGCA	0.378																																					p.E147K		Atlas-SNP	.											.	CEP350	418	.	0			c.G439A						.						41	39	39					1																	179965731		2202	4300	6502	SO:0001583	missense	9857	exon6			CATCTGGAATCAA	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.439G>A	chr1.hg19:g.179965731G>A	ENSP00000356579:p.Glu147Lys	86.0	0.0		117.0	82.0	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.423465	0.62733	.	.	ENSG00000135837	ENST00000367607;ENST00000491495	T;T	0.57595	0.39;0.99	5.1	5.1	0.69264	.	0.140761	0.31897	N	0.006888	T	0.51787	0.1695	L	0.27053	0.805	0.54753	D	0.999983	B;B;P	0.50272	0.361;0.361;0.933	B;B;P	0.51101	0.039;0.086;0.659	T	0.45891	-0.9230	9	.	.	.	.	18.4523	0.90709	0.0:0.0:1.0:0.0	.	147;147;121	E7EU22;Q5VT06;E9PIK0	.;CE350_HUMAN;.	K	147;121	ENSP00000356579:E147K;ENSP00000435808:E121K	.	E	+	1	0	CEP350	178232354	1.000000	0.71417	0.998000	0.56505	0.629000	0.37895	7.113000	0.77095	2.526000	0.85167	0.579000	0.79373	GAA	.	.		0.378	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		A	179965731	G	A	179965731	3	1	117	1	0	0	0	0	1	0	0	0	3256	1175	41	3	457	3	CEP350	1	179965731	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	88180996	179965731	69284890	6	20138										
CEP350	9857	hgsc.bcm.edu	37	chr1	180003175	180003175	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	ctctcactgatctgaacccgGcagccagcagaacaacgaca	8	15	2	3			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr1:180003175G>A	ENST00000367607.3	+	16	4322	c.3904G>A	c.(3904-3906)Gca>Aca	p.A1302T		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1302					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TCTGAACCCGGCAGCCAGCAG	0.403																																					p.A1302T		Atlas-SNP	.											.	CEP350	418	.	0			c.G3904A						.						79	74	76					1																	180003175		2203	4300	6503	SO:0001583	missense	9857	exon16			AACCCGGCAGCCA	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.3904G>A	chr1.hg19:g.180003175G>A	ENSP00000356579:p.Ala1302Thr	144.0	0.0		249.0	160.0	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902788	0.33628	.	.	ENSG00000135837	ENST00000367607	T	0.56611	0.45	5.44	1.18	0.20946	.	0.635955	0.13753	N	0.365101	T	0.33177	0.0854	L	0.27053	0.805	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.04013	0.001;0.001	T	0.18209	-1.0344	9	.	.	.	.	5.8265	0.18556	0.1741:0.2957:0.5302:0.0	.	1302;1302	E7EU22;Q5VT06	.;CE350_HUMAN	T	1302	ENSP00000356579:A1302T	.	A	+	1	0	CEP350	178269798	0.465000	0.25815	0.002000	0.10522	0.090000	0.18270	0.635000	0.24629	-0.042000	0.13535	0.563000	0.77884	GCA	.	.		0.403	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		A	180003175	G	A	180003175	3	1	117	1	0	0	0	0	1	0	0	0	3256	1203	42	3	3962	3	CEP350	1	180003175	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	37444	180003175	69247446	7	20139										
C1orf21	81563	hgsc.bcm.edu	37	chr1	184446676	184446676	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	tccgccaagcatgttgccacTgttcaaaatgaagaggaagc	10	10	1	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr1:184446676T>A	ENST00000235307.6	+	2	468	c.33T>A	c.(31-33)acT>acA	p.T11T		NM_030806.3	NP_110433.1	Q9H246	CA021_HUMAN	chromosome 1 open reading frame 21	11										breast(1)|lung(1)	2		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)		ATGTTGCCACTGTTCAAAATG	0.478																																					p.T11T		Atlas-SNP	.											.	C1orf21	5	.	0			c.T33A						.						85	76	79					1																	184446676		2203	4300	6503	SO:0001819	synonymous_variant	81563	exon2			TGCCACTGTTCAA	AF312864	CCDS1362.1	1q25	2008-07-18			ENSG00000116667	ENSG00000116667			15494	protein-coding gene	gene with protein product	"proliferation-inducing protein 13"					11318611	Standard	NM_030806		Approved	PIG13	uc001gqv.1	Q9H246	OTTHUMG00000035386	ENST00000235307.6:c.33T>A	chr1.hg19:g.184446676T>A		56.0	0.0		92.0	48.0	NM_030806	B2R551	Silent	SNP	ENST00000235307.6	hg19	CCDS1362.1																																																																																			.	.		0.478	C1orf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085784.2	NM_030806		A	184446676	T	A	184446676	2	1	117	1	0	0	0	0	0	0	0	1	2030	1567	55	4		4	C1orf21	1	184446676	Silent	SNP	T	TCGA-DD-A3A3-01A-11D-A22F-10	4443501	184446676	64803945	8	20140										
TRAF3IP3	80342	hgsc.bcm.edu	37	chr1	209936844	209936844	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	cccgcacccccaggaggcccTacaaagggagctggtcctaa	11	16	0	0			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr1:209936844T>A	ENST00000367024.1	+	8	1130	c.614T>A	c.(613-615)cTa>cAa	p.L205Q	TRAF3IP3_ENST00000400959.3_Missense_Mutation_p.L185Q|TRAF3IP3_ENST00000367026.3_Missense_Mutation_p.L185Q|TRAF3IP3_ENST00000010338.4_Missense_Mutation_p.L185Q|TRAF3IP3_ENST00000367025.3_Missense_Mutation_p.L205Q			Q9Y228	T3JAM_HUMAN	TRAF3 interacting protein 3	205						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32				OV - Ovarian serous cystadenocarcinoma(81;0.045)		CAGGAGGCCCTACAAAGGGAG	0.537																																					p.L205Q		Atlas-SNP	.											.	TRAF3IP3	68	.	0			c.T614A						.						89	94	92					1																	209936844		2203	4300	6503	SO:0001583	missense	80342	exon8			AGGCCCTACAAAG		CCDS1490.1, CCDS1490.2, CCDS73023.1	1q32.3-q41	2008-02-05			ENSG00000009790	ENSG00000009790			30766	protein-coding gene	gene with protein product	"TRAF3 interacting Jun N terminal kinase (JNK) activating modulator"	608255				14572659	Standard	XR_247044		Approved	T3JAM	uc001hho.3	Q9Y228	OTTHUMG00000036480	ENST00000367024.1:c.614T>A	chr1.hg19:g.209936844T>A	ENSP00000355991:p.Leu205Gln	132.0	0.0		200.0	40.0	NM_025228	A1L464|A6NIU9|Q2YDB5|Q4VY06|Q7Z706	Missense_Mutation	SNP	ENST00000367024.1	hg19	CCDS1490.2	.	.	.	.	.	.	.	.	.	.	T	18.86	3.713509	0.68730	.	.	ENSG00000009790	ENST00000400959;ENST00000367025;ENST00000458110;ENST00000367026;ENST00000367024;ENST00000010338	T;T;T;T;T	0.56275	0.51;0.47;0.49;0.47;0.49	4.51	4.51	0.55191	.	0.000000	0.53938	D	0.000051	T	0.69504	0.3118	M	0.76328	2.33	0.47778	D	0.999517	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.73059	-0.4102	10	0.87932	D	0	-5.2705	10.4049	0.44252	0.0:0.0:0.0:1.0	.	205;185;205;185	Q9Y228;Q9Y228-2;Q9Y228-3;E2QRE5	T3JAM_HUMAN;.;.;.	Q	185;205;188;185;205;185	ENSP00000383743:L185Q;ENSP00000355992:L205Q;ENSP00000355993:L185Q;ENSP00000355991:L205Q;ENSP00000010338:L185Q	ENSP00000010338:L185Q	L	+	2	0	TRAF3IP3	208003467	0.999000	0.42202	1.000000	0.80357	0.943000	0.58893	3.797000	0.55514	2.023000	0.59567	0.482000	0.46254	CTA	.	.		0.537	TRAF3IP3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088734.2			A	209936844	T	A	209936844	3	1	117	1	0	0	0	0	1	0	0	0	16457	1522	53	4	636	4	TRAF3IP3	1	209936844	Missense_Mutation	SNP	T	TCGA-DD-A3A3-01A-11D-A22F-10	25490168	209936844	39313777	9	20141										
FABP1	2168	hgsc.bcm.edu	37	chr2	88424070	88424072	+	In_Frame_Del	DEL	CAC	CAC	-													0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	ttgatgtttttgaaagttgtCaccagtttattgtcaccttc							TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr2:88424070_88424072delCAC	ENST00000295834.3	-	3	372_374	c.274_276delGTG	c.(274-276)gtgdel	p.V92del	FABP1_ENST00000495375.1_5'UTR|FABP1_ENST00000393750.3_In_Frame_Del_p.V92del	NM_001443.2	NP_001434.1	P07148	FABPL_HUMAN	fatty acid binding protein 1, liver	92					cellular lipid metabolic process (GO:0044255)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|intestinal absorption (GO:0050892)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)	apical cortex (GO:0045179)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|peroxisomal matrix (GO:0005782)	antioxidant activity (GO:0016209)|bile acid binding (GO:0032052)|chromatin binding (GO:0003682)|drug binding (GO:0008144)|fatty acid binding (GO:0005504)|long-chain fatty acid transporter activity (GO:0005324)|phospholipid binding (GO:0005543)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)|stomach(1)	6						TGAAAGTTGTCACCAGTTTATTG	0.507																																					p.92_93del		Atlas-Indel,Pindel	.											.	FABP1	23	.	0			c.275_277del						.																																			SO:0001651	inframe_deletion	2168	exon3			.	M10617	CCDS2001.1	2p11	2013-03-01			ENSG00000163586	ENSG00000163586		"Fatty acid binding protein family"	3555	protein-coding gene	gene with protein product		134650				3012800, 17698986	Standard	NM_001443		Approved	L-FABP	uc002sst.2	P07148	OTTHUMG00000130312	ENST00000295834.3:c.274_276delGTG	chr2.hg19:g.88424070_88424072delCAC	ENSP00000295834:p.Val92del	80.0	0.0		43.0	16.0	NM_001443		In_Frame_Del	DEL	ENST00000295834.3	hg19	CCDS2001.1																																																																																			.	.		0.507	FABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252660.1	NM_001443		-	88424072	CAC	-	88424070	7	5	117	1	0	1	0	1	0	0	0	0	5360	813	29	0	115	0	FABP1	2	88424070	In_Frame_Del	DEL	CAC	TCGA-DD-A3A3-01A-11D-A22F-10		88424070	154775303	10	20142										
TMEM177	80775	hgsc.bcm.edu	37	chr2	120438937	120438937	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	gcagtaccactgccgtgcacGccctgctggccccagcttgc	11	18	0	0	rs547985745	byFrequency	TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr2:120438937G>T	ENST00000424086.1	+	2	981	c.508G>T	c.(508-510)Gcc>Tcc	p.A170S	TMEM177_ENST00000401466.1_Missense_Mutation_p.A170S|TMEM177_ENST00000272521.6_Missense_Mutation_p.A170S|TMEM177_ENST00000496203.1_Intron|TMEM177_ENST00000409951.1_Intron	NM_001105198.1	NP_001098668.1	Q53S58	TM177_HUMAN	transmembrane protein 177	170						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	13	Colorectal(110;0.196)					TGCCGTGCACGCCCTGCTGGC	0.652																																					p.A170S		Atlas-SNP	.											.	TMEM177	26	.	0			c.G508T						.						53	58	56					2																	120438937		2203	4300	6503	SO:0001583	missense	80775	exon2			GTGCACGCCCTGC	BC004404	CCDS2128.1	2q14.2	2008-02-05			ENSG00000144120	ENSG00000144120			28143	protein-coding gene	gene with protein product						12477932	Standard	NM_001105198		Approved	MGC10993	uc002tmc.1	Q53S58	OTTHUMG00000153312	ENST00000424086.1:c.508G>T	chr2.hg19:g.120438937G>T	ENSP00000402661:p.Ala170Ser	58.0	0.0		53.0	15.0	NM_030577	Q9BT20	Missense_Mutation	SNP	ENST00000424086.1	hg19	CCDS2128.1	.	.	.	.	.	.	.	.	.	.	G	15.66	2.899219	0.52227	.	.	ENSG00000144120	ENST00000401466;ENST00000424086;ENST00000272521;ENST00000415646	T;T;T	0.59224	0.28;0.28;0.28	4.48	0.425	0.16473	.	0.110120	0.64402	N	0.000009	T	0.41766	0.1173	L	0.52206	1.635	0.43919	D	0.996563	P	0.37330	0.59	B	0.34242	0.178	T	0.09684	-1.0663	10	0.36615	T	0.2	-21.526	4.2505	0.10693	0.185:0.0:0.4997:0.3153	.	170	Q53S58	TM177_HUMAN	S	170	ENSP00000385966:A170S;ENSP00000402661:A170S;ENSP00000272521:A170S	ENSP00000272521:A170S	A	+	1	0	TMEM177	120155407	0.000000	0.05858	0.461000	0.27105	0.892000	0.51952	0.734000	0.26101	-0.024000	0.13941	0.549000	0.68633	GCC	.	.		0.652	TMEM177-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330673.1	NM_030577		T	120438937	G	T	120438937	3	4	117	1	0	0	0	0	1	0	0	0	16109	1087	38	1	510	1	TMEM177	2	120438937	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	32014867	120438937	122760436	11	20143										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160901606	160901606	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	gcagttctccagggtcagaaCcgatttacctgcttgaatgc	10	11	2	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr2:160901606C>G	ENST00000283243.7	-	2	378	c.172G>C	c.(172-174)Gtt>Ctt	p.V58L	PLA2R1_ENST00000392771.1_Missense_Mutation_p.V58L	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	58	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						AGGGTCAGAACCGATTTACCT	0.413																																					p.V58L		Atlas-SNP	.											.	PLA2R1	153	.	0			c.G172C						.						64	60	61					2																	160901606		2203	4300	6503	SO:0001583	missense	22925	exon2			TCAGAACCGATTT	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.172G>C	chr2.hg19:g.160901606C>G	ENSP00000283243:p.Val58Leu	126.0	0.0		127.0	44.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	hg19	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	C	4.213	0.038262	0.08148	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.30182	1.54;1.54	6.17	2.36	0.29203	Ricin B-related lectin (1);Ricin B lectin (2);	0.886117	0.10056	N	0.721568	T	0.19208	0.0461	L	0.33485	1.01	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.37430	-0.9706	10	0.10377	T	0.69	.	5.5728	0.17206	0.0:0.5225:0.1284:0.3491	.	58;58;58	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	L	58	ENSP00000283243:V58L;ENSP00000376524:V58L	ENSP00000283243:V58L	V	-	1	0	PLA2R1	160609852	0.041000	0.20044	0.092000	0.20876	0.315000	0.28087	1.120000	0.31271	0.160000	0.19432	-0.136000	0.14681	GTT	.	.		0.413	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			G	160901606	C	G	160901606	3	3	117	1	0	0	0	0	1	0	0	0	12019	507	18	4	4343	4	PLA2R1	2	160901606	Missense_Mutation	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	40462669	160901606	82297767	12	20144										
MAP2	4133	hgsc.bcm.edu	37	chr2	210517999	210517999	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	cctgagattaaggatcaaggCggagcaggggaaggacttgt	16	6	1	1	rs149857613		TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr2:210517999C>A	ENST00000360351.4	+	4	611	c.105C>A	c.(103-105)ggC>ggA	p.G35G	MAP2_ENST00000392194.1_Silent_p.G35G|MAP2_ENST00000199940.6_Silent_p.G35G|MAP2_ENST00000447185.1_Silent_p.G35G|MAP2_ENST00000361559.4_Silent_p.G35G	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	35					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AGGATCAAGGCGGAGCAGGGG	0.537																																					p.G35G	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.C105A						.						110	81	91					2																	210517999		2203	4300	6503	SO:0001819	synonymous_variant	4133	exon5			TCAAGGCGGAGCA		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.105C>A	chr2.hg19:g.210517999C>A		149.0	0.0		121.0	59.0	NM_001039538	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	C|1.000;T|0.000		0.537	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		A	210517999	C	A	210517999	2	1	117	1	0	0	0	0	0	0	0	1	9244	755	27	1		1	MAP2	2	210517999	Silent	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	49616393	210517999	32681374	13	20145										
POLQ	10721	hgsc.bcm.edu	37	chr3	121200622	121200622	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	taactatgctatgaagagtcGgctcctgagaatctggatct	10	8	2	3			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr3:121200622G>A	ENST00000264233.5	-	19	6136	c.6008C>T	c.(6007-6009)cCg>cTg	p.P2003L		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2003					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		ATGAAGAGTCGGCTCCTGAGA	0.438								DNA polymerases (catalytic subunits)																													p.P2003L	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											POLQ,colon,carcinoma,0,1	POLQ	273	.	0			c.C6008T						.						80	80	80					3																	121200622		2203	4300	6503	SO:0001583	missense	10721	exon19			AGAGTCGGCTCCT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.6008C>T	chr3.hg19:g.121200622G>A	ENSP00000264233:p.Pro2003Leu	130.0	1.0		112.0	42.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.049302	0.36181	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.20332	2.08	5.17	5.17	0.71159	Ribonuclease H-like (1);	0.305250	0.33854	N	0.004500	T	0.29321	0.0730	L	0.41236	1.265	0.45025	D	0.998047	D;D	0.89917	1.0;0.998	D;P	0.69654	0.965;0.752	T	0.03166	-1.1065	10	0.10377	T	0.69	.	9.398	0.38415	0.0:0.3111:0.5546:0.1343	.	2003;1175	O75417;O75417-2	DPOLQ_HUMAN;.	L	1626;2003;2139	ENSP00000264233:P2003L	ENSP00000264233:P2003L	P	-	2	0	POLQ	122683312	0.998000	0.40836	0.988000	0.46212	0.993000	0.82548	3.721000	0.54941	2.688000	0.91661	0.650000	0.86243	CCG	.	.		0.438	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121200622	G	A	121200622	3	1	117	1	0	0	0	0	1	0	0	0	12217	1116	39	1	1812	1	POLQ	3	121200622	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10		121200622	76821808	14	20146										
MUC20	200958	hgsc.bcm.edu	37	chr3	195452957	195452957	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	agtcagctgcacctgatgccAcggttgggaccccactcccc	10	17	1	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr3:195452957A>T	ENST00000447234.2	+	2	1609	c.1483A>T	c.(1483-1485)Acg>Tcg	p.T495S	MUC20_ENST00000445522.2_Missense_Mutation_p.T460S|MUC20_ENST00000436408.1_Missense_Mutation_p.T495S|MUC20_ENST00000320736.6_Missense_Mutation_p.T324S	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	495	Involved in oligomerization.		Missing. {ECO:0000269|PubMed:14702039}.		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		ACCTGATGCCACGGTTGGGAC	0.602																																					p.T324S		Atlas-SNP	.											.	MUC20	84	.	0			c.A970T						.						55	50	51					3																	195452957		2182	4279	6461	SO:0001583	missense	200958	exon3			GATGCCACGGTTG	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"Mucins"	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1483A>T	chr3.hg19:g.195452957A>T	ENSP00000414350:p.Thr495Ser	353.0	0.0		302.0	64.0	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	hg19		.	.	.	.	.	.	.	.	.	.	A	11.64	1.697698	0.30142	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.34859	1.86;2.18;2.01;1.34	3.16	0.464	0.16706	.	0.358470	0.20556	N	0.090019	T	0.39627	0.1085	L	0.39245	1.2	0.09310	N	1	D	0.64830	0.994	P	0.60886	0.88	T	0.17228	-1.0376	10	0.38643	T	0.18	-3.511	7.0492	0.25063	0.525:0.475:0.0:0.0	.	324	E9PH32	.	S	495;324;495;460	ENSP00000414350:T495S;ENSP00000325431:T324S;ENSP00000396774:T495S;ENSP00000405629:T460S	ENSP00000325431:T324S	T	+	1	0	MUC20	196938628	0.001000	0.12720	0.003000	0.11579	0.036000	0.12997	0.592000	0.23984	0.089000	0.17243	0.421000	0.28195	ACG	.	.		0.602	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673		T	195452957	A	T	195452957	3	4	117	1	0	0	0	0	1	0	0	0	9985	159	6	4	980	4	MUC20	3	195452957	Missense_Mutation	SNP	A	TCGA-DD-A3A3-01A-11D-A22F-10	74252335	195452957	2569473	15	20147										
C4orf23	152992	hgsc.bcm.edu	37	chr4	8465812	8465812	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	accatggatacctgtcattgCagccaggtgagaagtagagg	13	8	1	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr4:8465812C>T	ENST00000389737.4	+	7	1304	c.1304C>T	c.(1303-1305)gCa>gTa	p.A435V	TRMT44_ENST00000513449.2_Missense_Mutation_p.A194V	NM_152544.2	NP_689757.2	Q8IYL2	TRM44_HUMAN	tRNA methyltransferase 44 homolog (S. cerevisiae)	435					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										CCTGTCATTGCAGCCAGGTGA	0.463																																					p.A435V		Atlas-SNP	.											.	TRMT44	7	.	0			c.C1304T						.						148	133	138					4																	8465812		2203	4300	6503	SO:0001583	missense	152992	exon7			TCATTGCAGCCAG	AK093044	CCDS3402.1, CCDS3402.2	4p16.1	2012-06-12	2012-06-12	2012-06-12	ENSG00000155275	ENSG00000155275			26653	protein-coding gene	gene with protein product	"tRNA methyltransferase 44 homolog (S. cerevisiae)"	614309	"chromosome 4 open reading frame 23", "methyltransferase like 19"	C4orf23, METTL19		21658913	Standard	NM_152544		Approved	FLJ35725, TRM44	uc003glg.2	Q8IYL2	OTTHUMG00000160935	ENST00000389737.4:c.1304C>T	chr4.hg19:g.8465812C>T	ENSP00000374387:p.Ala435Val	107.0	0.0		98.0	40.0	NM_152544	Q8NA95	Missense_Mutation	SNP	ENST00000389737.4	hg19	CCDS3402.2	.	.	.	.	.	.	.	.	.	.	C	28.9	4.960839	0.92791	.	.	ENSG00000155275	ENST00000513449;ENST00000389737;ENST00000285635	T;T	0.47869	0.83;0.83	4.18	4.18	0.49190	.	0.058244	0.64402	D	0.000002	T	0.74450	0.3718	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.81810	-0.0762	10	0.87932	D	0	-19.8751	17.1324	0.86729	0.0:1.0:0.0:0.0	.	435;194	Q8IYL2;Q8IYL2-2	TRM44_HUMAN;.	V	194;435;43	ENSP00000424643:A194V;ENSP00000374387:A435V	ENSP00000285635:A43V	A	+	2	0	METTL19	8516712	1.000000	0.71417	0.547000	0.28179	0.956000	0.61745	6.528000	0.73807	2.350000	0.79820	0.558000	0.71614	GCA	.	.		0.463	TRMT44-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359197.2	NM_152544		T	8465812	C	T	8465812	3	4	117	1	0	0	0	0	1	0	0	0	2258	710	25	3	1330	3	C4orf23	4	8465812	Missense_Mutation	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10		8465812	182688464	16	20148										
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25664369	25664369	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	aaccaagattgaacttctgcCgtcctactccacggctacac	6	15	1	2	rs374467761		TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr4:25664369C>T	ENST00000382051.3	+	3	205	c.155C>T	c.(154-156)cCg>cTg	p.P52L	SLC34A2_ENST00000503434.1_Missense_Mutation_p.P51L|SLC34A2_ENST00000504570.1_Missense_Mutation_p.P51L	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	52					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				GAACTTCTGCCGTCCTACTCC	0.517			T	ROS1	NSCLC																																p.P52L		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	.	SLC34A2	93	.	0			c.C155T						.						141	141	141					4																	25664369		2203	4300	6503	SO:0001583	missense	10568	exon3			TTCTGCCGTCCTA	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.155C>T	chr4.hg19:g.25664369C>T	ENSP00000371483:p.Pro52Leu	168.0	0.0		144.0	47.0	NM_006424	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Missense_Mutation	SNP	ENST00000382051.3	hg19	CCDS3435.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.439479	0.83885	.	.	ENSG00000157765	ENST00000513204;ENST00000504570;ENST00000382051;ENST00000503434;ENST00000507530	T;T;T;T;T	0.74737	-0.87;1.05;1.48;1.05;-0.05	5.45	4.6	0.57074	.	0.000000	0.85682	D	0.000000	D	0.85279	0.5660	M	0.81497	2.545	0.80722	D	1	P;D	0.89917	0.832;1.0	B;D	0.68039	0.337;0.955	D	0.87264	0.2281	10	0.87932	D	0	-16.73	14.284	0.66232	0.0:0.9264:0.0:0.0736	.	51;52	O95436-2;O95436	.;NPT2B_HUMAN	L	51;51;52;51;52	ENSP00000423038:P51L;ENSP00000425501:P51L;ENSP00000371483:P52L;ENSP00000423021:P51L;ENSP00000424266:P52L	ENSP00000371483:P52L	P	+	2	0	SLC34A2	25273467	0.991000	0.36638	0.690000	0.30148	0.014000	0.08584	4.040000	0.57333	2.568000	0.86640	0.650000	0.86243	CCG	.	.		0.517	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		T	25664369	C	T	25664369	3	4	117	1	0	0	0	0	1	0	0	0	14583	652	23	1	161	1	SLC34A2	4	25664369	Missense_Mutation	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	17198557	25664369	165489907	17	20149										
KDR	3791	hgsc.bcm.edu	37	chr4	55976858	55976858	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	tgggtaaccaaggtacttcgCagggattctgacacgctccc	11	12	1	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr4:55976858C>A	ENST00000263923.4	-	8	1349	c.1054G>T	c.(1054-1056)Gcg>Tcg	p.A352S		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	352	Ig-like C2-type 4.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGGTACTTCGCAGGGATTCTG	0.413			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.A352S		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.G1054T						.						78	86	83					4																	55976858		2202	4300	6502	SO:0001583	missense	3791	exon8			ACTTCGCAGGGAT	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.1054G>T	chr4.hg19:g.55976858C>A	ENSP00000263923:p.Ala352Ser	230.0	0.0		184.0	74.0	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	hg19	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.251076	0.59212	.	.	ENSG00000128052	ENST00000263923	T	0.80480	-1.38	5.65	5.65	0.86999	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.060061	0.64402	D	0.000003	T	0.81408	0.4816	L	0.58810	1.83	0.20403	N	0.999908	B;B	0.22211	0.066;0.063	B;B	0.31946	0.068;0.138	T	0.74185	-0.3747	10	0.72032	D	0.01	.	17.8994	0.88899	0.0:1.0:0.0:0.0	.	352;352	P35968-2;P35968	.;VGFR2_HUMAN	S	352	ENSP00000263923:A352S	ENSP00000263923:A352S	A	-	1	0	KDR	55671615	1.000000	0.71417	0.996000	0.52242	0.406000	0.30931	6.474000	0.73578	2.665000	0.90641	0.563000	0.77884	GCG	.	.		0.413	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55976858	C	A	55976858	3	1	117	1	0	0	0	0	1	0	0	0	8148	710	25	3	3108	3	KDR	4	55976858	Missense_Mutation	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	30312489	55976858	135177418	18	20150										
SPATA5	166378	hgsc.bcm.edu	37	chr4	123900511	123900511	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	aatgatatcagacccagtgcCatgagggaaatagcaattga	10	7	1	4			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr4:123900511C>T	ENST00000274008.4	+	10	1908	c.1839C>T	c.(1837-1839)gcC>gcT	p.A613A	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	613					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						GACCCAGTGCCATGAGGGAAA	0.408																																					p.A613A		Atlas-SNP	.											.	SPATA5	62	.	0			c.C1839T						.						166	158	161					4																	123900511		2203	4300	6503	SO:0001819	synonymous_variant	166378	exon10			CAGTGCCATGAGG	AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"ATPases / AAA-type"	18119	protein-coding gene	gene with protein product	"ATPase family gene 2 homolog (S. cerevisiae)"	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.1839C>T	chr4.hg19:g.123900511C>T		135.0	0.0		111.0	38.0	NM_145207	C9JT97|Q86XW1|Q8NI20|Q8TDL7	Silent	SNP	ENST00000274008.4	hg19	CCDS3730.1																																																																																			.	.		0.408	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	NM_145207		T	123900511	C	T	123900511	2	4	117	1	0	0	0	0	0	0	0	1	15026	581	21	3		3	SPATA5	4	123900511	Silent	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	67923653	123900511	67253765	19	20151										
NIPBL	25836	hgsc.bcm.edu	37	chr5	36976173	36976173	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	aatagcaatgtttcagaaaaTgatattccttttaatgtgca	6	5	1	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr5:36976173T>A	ENST00000282516.8	+	9	1663	c.1164T>A	c.(1162-1164)aaT>aaA	p.N388K	NIPBL_ENST00000448238.2_Missense_Mutation_p.N388K|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	388					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TTTCAGAAAATGATATTCCTT	0.393																																					p.N388K		Atlas-SNP	.											.	NIPBL	513	.	0			c.T1164A						.						94	100	98					5																	36976173		2203	4300	6503	SO:0001583	missense	25836	exon9			AGAAAATGATATT	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.1164T>A	chr5.hg19:g.36976173T>A	ENSP00000282516:p.Asn388Lys	162.0	0.0		226.0	121.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	hg19	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	T	13.32	2.201900	0.38905	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.92752	-3.1;-3.1	5.45	3.07	0.35406	.	0.389888	0.28538	N	0.014995	T	0.77611	0.4156	N	0.14661	0.345	0.29618	N	0.846443	B;B	0.09022	0.001;0.002	B;B	0.09377	0.002;0.004	T	0.62455	-0.6851	10	0.06365	T	0.9	.	1.6478	0.02765	0.1379:0.1516:0.1433:0.5672	.	388;388	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	K	388	ENSP00000282516:N388K;ENSP00000406266:N388K	ENSP00000282516:N388K	N	+	3	2	NIPBL	37011930	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.496000	0.35638	0.899000	0.36444	0.383000	0.25322	AAT	.	.		0.393	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		A	36976173	T	A	36976173	3	1	117	1	0	0	0	0	1	0	0	0	10437	1461	51	4	1194	4	NIPBL	5	36976173	Missense_Mutation	SNP	T	TCGA-DD-A3A3-01A-11D-A22F-10		36976173	143939087	20	20152										
CWC27	10283	hgsc.bcm.edu	37	chr5	64314004	64314005	+	Frame_Shift_Ins	INS	-	-	TT													0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	ggatgtcacatgtacttcagINStttgaggataaaagcagaaa							TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr5:64314004_64314005insTT	ENST00000381070.3	+	14	1492_1493	c.1275_1276insTT	c.(1276-1278)tttfs	p.F426fs	RP11-307L14.1_ENST00000607786.1_lincRNA|CWC27_ENST00000545000.1_3'UTR|RP11-307L14.2_ENST00000606057.1_lincRNA	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	426					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						ATGTACTTCAGTTTGAGGATAA	0.376																																					p.Q425fs		Atlas-INDEL	.											.	CWC27	47	.	0			c.1275_1276insTT						.																																			SO:0001589	frameshift_variant	10283	exon14			.	AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"serologically defined colon cancer antigen 10"	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.1276_1277dupTT	chr5.hg19:g.64314005_64314006dupTT	ENSP00000370460:p.Phe426fs	202.0	0.0		264.0	145.0	NM_005869	O60529|O60530|Q96EM3	Frame_Shift_Ins	INS	ENST00000381070.3	hg19	CCDS3982.2																																																																																			.	.		0.376	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869		TT	64314005	-	TT	64314004	7	5	117	1	0	1	1	0	0	0	0	0	4072	1020	36	0	1329	0	CWC27	5	64314004	Frame_Shift_Ins	INS	-	TCGA-DD-A3A3-01A-11D-A22F-10	27337831	64314004	116601256	21	20153										
PCDHGA2	56113	hgsc.bcm.edu	37	chr5	140720406	140720406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	cttctcggtgggtctgcacaCgggcgaggtgcgcacggcgc	17	13	2	0	rs370683887		TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr5:140720406C>T	ENST00000394576.2	+	1	1868	c.1868C>T	c.(1867-1869)aCg>aTg	p.T623M	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	623	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T623M(1)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTCTGCACACGGGCGAGGTG	0.687																																					p.T623M		Atlas-SNP	.											PCDHG_cluster,NS,carcinoma,-1,1	PCDHGA2	205	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1868T						.	C	,MET/THR,MET/THR	1,4389		0,1,2194	34	42	39		,1868,1868	5.1	1	5		39	1,8559		0,1,4279	no	intron,missense,missense	PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_032009.1	,81,81	0,2,6473	TT,TC,CC		0.0117,0.0228,0.0154	,,	,623/933,623/824	140720406	2,12948	2195	4280	6475	SO:0001583	missense	56113	exon1			TGCACACGGGCGA	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"Cadherins / Protocadherins : Clustered"	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.1868C>T	chr5.hg19:g.140720406C>T	ENSP00000378077:p.Thr623Met	27.0	0.0		56.0	22.0	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	hg19	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	12.11	1.840122	0.32513	2.28E-4	1.17E-4	ENSG00000081853	ENST00000394576	T	0.58060	0.36	5.14	5.14	0.70334	Cadherin (4);Cadherin-like (1);	0.179052	0.25951	U	0.027248	T	0.79936	0.4532	H	0.94183	3.505	0.23827	N	0.996738	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	T	0.75764	-0.3203	10	0.87932	D	0	.	15.3383	0.74277	0.0:0.8598:0.1401:0.0	.	623;623	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	M	623	ENSP00000378077:T623M	ENSP00000378077:T623M	T	+	2	0	PCDHGA2	140700590	0.007000	0.16637	0.969000	0.41365	0.150000	0.21749	0.099000	0.15210	2.589000	0.87451	0.485000	0.47835	ACG	.	.		0.687	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		T	140720406	C	T	140720406	3	4	117	1	0	0	0	0	1	0	0	0	11563	536	19	1	1870	1	PCDHGA2	5	140720406	Missense_Mutation	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	76406402	140720406	40194854	22	20154										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38747842	38747842	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	aacttgatgctactaagaagGcaagtgtcatgtttataaat	8	5	1	2	rs376576474		TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr6:38747842G>T	ENST00000359357.3	+	13	1742		c.e13+1		DNAH8_ENST00000449981.2_Splice_Site|DNAH8_ENST00000441566.1_Splice_Site			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8						cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TACTAAGAAGGCAAGTGTCAT	0.353																																					.		Atlas-SNP	.											.	DNAH8	1239	.	0			c.2139+1G>T						.						100	94	96					6																	38747842		2203	4300	6503	SO:0001630	splice_region_variant	1769	exon15			AAGAAGGCAAGTG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.1488+1G>T	chr6.hg19:g.38747842G>T		80.0	0.0		83.0	21.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Splice_Site	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	G	16.43	3.120370	0.56613	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7715	0.88494	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAH8	38855820	1.000000	0.71417	0.991000	0.47740	0.529000	0.34654	7.580000	0.82523	2.720000	0.93068	0.591000	0.81541	.	.	.		0.353	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	Intron	T	38747842	G	T	38747842	5	4	117	1	0	0	0	0	0	0	1	0	4609	1217	42	3	1531	3	DNAH8	6	38747842	Splice_Site	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10		38747842	132367225	23	20155										
OPRM1	4988	hgsc.bcm.edu	37	chr6	154412549	154412549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	acaaaactccactcgaattcGtcagaacactagagaccacc	5	14	1	2	rs199984546		TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr6:154412549G>A	ENST00000330432.7	+	3	1343	c.1106G>A	c.(1105-1107)cGt>cAt	p.R369H	OPRM1_ENST00000434900.2_Missense_Mutation_p.R462H|OPRM1_ENST00000360422.4_Missense_Mutation_p.R369H|OPRM1_ENST00000522555.1_Missense_Mutation_p.R269H|OPRM1_ENST00000524163.1_Missense_Mutation_p.R369H|OPRM1_ENST00000428397.2_Missense_Mutation_p.R369H|OPRM1_ENST00000414028.2_Missense_Mutation_p.R369H|OPRM1_ENST00000435918.2_Missense_Mutation_p.R369H|OPRM1_ENST00000520708.1_Missense_Mutation_p.R269H|OPRM1_ENST00000522236.1_Missense_Mutation_p.R269H|OPRM1_ENST00000518759.1_Missense_Mutation_p.R288H|OPRM1_ENST00000419506.2_Missense_Mutation_p.R369H|OPRM1_ENST00000229768.5_Missense_Mutation_p.R369H|OPRM1_ENST00000452687.2_Missense_Mutation_p.R369H|OPRM1_ENST00000337049.4_Missense_Mutation_p.R369H	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1	369					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)	p.R369H(2)|p.R462H(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	ACTCGAATTCGTCAGAACACT	0.438																																					p.R462H		Atlas-SNP	.											OPRM1_ENST00000434900,scalp,carcinoma,+1,2	OPRM1	241	.	3	Substitution - Missense(3)	kidney(3)	c.G1385A						.						54	53	54					6																	154412549		1915	4123	6038	SO:0001583	missense	4988	exon5			GAATTCGTCAGAA	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.1106G>A	chr6.hg19:g.154412549G>A	ENSP00000328264:p.Arg369His	104.0	0.0		76.0	22.0	NM_001145279	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	hg19	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.237880	0.79800	.	.	ENSG00000112038	ENST00000434900;ENST00000520708;ENST00000518759;ENST00000330432;ENST00000360422;ENST00000428397;ENST00000452687;ENST00000229768;ENST00000419506;ENST00000524163;ENST00000414028;ENST00000435918;ENST00000337049;ENST00000522555;ENST00000522236	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14	6.16	6.16	0.99307	.	0.048138	0.85682	D	0.000000	T	0.57140	0.2033	M	0.76170	2.325	0.80722	D	1	D;B;B;D;P;B;B;P;B;P;P;B	0.76494	0.998;0.187;0.187;0.999;0.713;0.025;0.014;0.738;0.364;0.815;0.738;0.187	D;B;B;D;B;B;B;B;B;B;B;B	0.66716	0.909;0.118;0.118;0.946;0.211;0.013;0.009;0.19;0.055;0.22;0.19;0.118	T	0.57429	-0.7813	10	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	369;369;369;369;462;288;269;369;369;369;369;369	P35372-4;P35372-8;P35372-11;P35372-9;P35372-10;B8Q1L9;Q6UPP1;P35372-5;P35372;P35372-7;P35372-3;P35372-2	.;.;.;.;.;.;.;.;OPRM_HUMAN;.;.;.	H	462;269;288;369;369;369;369;369;369;369;369;369;369;269;269	ENSP00000394624:R462H;ENSP00000430876:R269H;ENSP00000430260:R288H;ENSP00000328264:R369H;ENSP00000353598:R369H;ENSP00000411903:R369H;ENSP00000410497:R369H;ENSP00000229768:R369H;ENSP00000403549:R369H;ENSP00000430097:R369H;ENSP00000399359:R369H;ENSP00000413752:R369H;ENSP00000338381:R369H;ENSP00000429719:R269H;ENSP00000429373:R269H	ENSP00000229768:R369H	R	+	2	0	OPRM1	154454242	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	9.869000	0.99810	2.937000	0.99478	0.650000	0.86243	CGT	.	.		0.438	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		A	154412549	G	A	154412549	3	1	117	1	0	0	0	0	1	0	0	0	10896	1145	40	1	1450	1	OPRM1	6	154412549	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	115664707	154412549	16702518	24	20156										
MPP6	51678	hgsc.bcm.edu	37	chr7	24690139	24690139	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	gttgaaaataatgatctggtAattgcccgaatcctccatgg	9	8	1	2	rs548751295		TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr7:24690139A>G	ENST00000222644.5	+	5	709	c.459A>G	c.(457-459)gtA>gtG	p.V153V	MPP6_ENST00000396475.2_Silent_p.V153V|MPP6_ENST00000409761.1_Silent_p.V41V			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						ATGATCTGGTAATTGCCCGAA	0.358																																					p.V153V		Atlas-SNP	.											.	MPP6	62	.	0			c.A459G						.						79	82	81					7																	24690139		2203	4300	6503	SO:0001819	synonymous_variant	51678	exon6			TCTGGTAATTGCC	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.459A>G	chr7.hg19:g.24690139A>G		69.0	0.0		77.0	29.0	NM_016447	B2RAF0	Silent	SNP	ENST00000222644.5	hg19	CCDS5388.1																																																																																			.	.		0.358	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4			G	24690139	A	G	24690139	2	3	117	1	0	0	0	0	0	0	0	1	9747	349	13	2		2	MPP6	7	24690139	Silent	SNP	A	TCGA-DD-A3A3-01A-11D-A22F-10		24690139	134448524	25	20157										
SAMD9	54809	hgsc.bcm.edu	37	chr7	92733944	92733944	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	ccattgcagaaaatccagctGggttgatggtaaagatttag	11	6	0	3			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr7:92733944G>A	ENST00000379958.2	-	3	1736	c.1467C>T	c.(1465-1467)ccC>ccT	p.P489P		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	489						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			AAATCCAGCTGGGTTGATGGT	0.403																																					p.P489P		Atlas-SNP	.											.	SAMD9	239	.	0			c.C1467T						.						88	91	90					7																	92733944		2203	4299	6502	SO:0001819	synonymous_variant	54809	exon2			CCAGCTGGGTTGA	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1467C>T	chr7.hg19:g.92733944G>A		140.0	0.0		112.0	44.0	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	hg19	CCDS34680.1																																																																																			.	.		0.403	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		A	92733944	G	A	92733944	2	1	117	1	0	0	0	0	0	0	0	1	13841	1335	47	3		3	SAMD9	7	92733944	Silent	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	68043805	92733944	66404719	26	20158										
STK3	6788	hgsc.bcm.edu	37	chr8	99719383	99719383	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	aagttaacttactgttaactGaccagccactccaaaatctg	5	11	1	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr8:99719383G>A	ENST00000419617.2	-	5	648	c.508C>T	c.(508-510)Cag>Tag	p.Q170*	STK3_ENST00000523601.1_Nonsense_Mutation_p.Q198*	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	170	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		ACTGTTAACTGACCAGCCACT	0.328																																					p.Q198X		Atlas-SNP	.											.	STK3	47	.	0			c.C592T						.						55	54	54					8																	99719383		1823	4112	5935	SO:0001587	stop_gained	6788	exon7			TTAACTGACCAGC	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"serine/threonine kinase 3 (Ste20, yeast homolog)"			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.508C>T	chr8.hg19:g.99719383G>A	ENSP00000390500:p.Gln170*	88.0	0.0		228.0	16.0	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Nonsense_Mutation	SNP	ENST00000419617.2	hg19	CCDS47900.1	.	.	.	.	.	.	.	.	.	.	G	39	7.738800	0.98462	.	.	ENSG00000104375	ENST00000419617;ENST00000523601	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.9913	0.92793	0.0:0.0:1.0:0.0	.	.	.	.	X	170;198	.	ENSP00000390500:Q170X	Q	-	1	0	STK3	99788559	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.876000	0.87215	2.493000	0.84123	0.561000	0.74099	CAG	.	.		0.328	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281		A	99719383	G	A	99719383	4	1	117	1	0	0	0	0	0	1	0	0	15310	1299	45	3	995	3	STK3	8	99719383	Nonsense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10		99719383	46644639	27	20159										
COLEC10	10584	hgsc.bcm.edu	37	chr8	120118098	120118103	+	In_Frame_Del	DEL	AACTAC	AACTAC	-													0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	acatcgtgcaggaagagaagAactacagggaatccctaacc					rs57284713		TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	AACTAC	AACTAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr8:120118098_120118103delAACTAC	ENST00000332843.2	+	6	543_548	c.502_507delAACTAC	c.(502-507)aactacdel	p.NY168del		NM_006438.3	NP_006429.2	Q9Y6Z7	COL10_HUMAN	collectin sub-family member 10 (C-type lectin)	168	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21	all_cancers(13;4.13e-26)|Lung NSC(37;1.36e-07)|Ovarian(258;0.018)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00113)			GGAAGAGAAGAACTACAGGGAATCCC	0.471																																					p.167_169del		Atlas-Indel,Pindel	.											.	COLEC10	46	.	0			c.501_506del						.																																			SO:0001651	inframe_deletion	10584	exon6			.	AB002631	CCDS6327.1	8q23-q24.1	2007-12-19				ENSG00000184374		"Collectins"	2220	protein-coding gene	gene with protein product		607620				10224141	Standard	NM_006438		Approved	CL-L1	uc003yoo.3	Q9Y6Z7		ENST00000332843.2:c.502_507delAACTAC	chr8.hg19:g.120118098_120118103delAACTAC	ENSP00000332723:p.Asn168_Tyr169del	84.0	0.0		255.0	17.0	NM_006438	Q3SYH6|Q6UW19	In_Frame_Del	DEL	ENST00000332843.2	hg19	CCDS6327.1																																																																																			.	.		0.471	COLEC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381225.1			-	120118103	AACTAC	-	120118098	7	5	117	1	0	1	0	1	0	0	0	0	3712	246	9	0	524	0	COLEC10	8	120118098	In_Frame_Del	DEL	AACTAC	TCGA-DD-A3A3-01A-11D-A22F-10	20398715	120118098	26245924	28	20160										
WISP1	8840	hgsc.bcm.edu	37	chr8	134232984	134232984	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	cgtctctggtgcccccacccGcggcgcgtgagcatacctgg	13	17	1	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr8:134232984G>A	ENST00000250160.6	+	3	616	c.510G>A	c.(508-510)ccG>ccA	p.P170P	WISP1_ENST00000517423.1_Intron|WISP1_ENST00000377863.2_Intron|WISP1_ENST00000519433.1_Intron|WISP1_ENST00000220856.6_Intron	NM_003882.3	NP_003873.1	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1	170	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21	all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			GCCCCCACCCGCGGCGCGTGA	0.667																																					p.P170P		Atlas-SNP	.											.	WISP1	64	.	0			c.G510A						.						39	39	39					8																	134232984		2202	4300	6502	SO:0001819	synonymous_variant	8840	exon3			CCACCCGCGGCGC	AF100779	CCDS6371.1, CCDS6372.1, CCDS56555.1, CCDS56556.1	8q24.22	2007-05-14			ENSG00000104415	ENSG00000104415			12769	protein-coding gene	gene with protein product		603398				9843955	Standard	NM_003882		Approved	CCN4	uc003yub.3	O95388	OTTHUMG00000164440	ENST00000250160.6:c.510G>A	chr8.hg19:g.134232984G>A		22.0	0.0		102.0	21.0	NM_003882	A8KAG6|E7EMM5|Q5JBS6|Q5JBS7|Q5JBS8|Q9HCS3	Silent	SNP	ENST00000250160.6	hg19	CCDS6371.1																																																																																			.	.		0.667	WISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378794.2	NM_003882		A	134232984	G	A	134232984	2	1	117	1	0	0	0	0	0	0	0	1	17387	1074	38	1		1	WISP1	8	134232984	Silent	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	14114886	134232984	12131038	29	20161										
TBC1D13	54662	hgsc.bcm.edu	37	chr9	131566320	131566320	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	atcaagagcctggatgactcGcagtgtggcatcacctacaa	10	11	2	2	rs373890081		TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr9:131566320G>T	ENST00000372648.5	+	9	990	c.840G>T	c.(838-840)tcG>tcT	p.S280S	TBC1D13_ENST00000539497.1_Silent_p.S99S|TBC1D13_ENST00000223865.8_Intron	NM_018201.3	NP_060671.3	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13	280	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	6						TGGATGACTCGCAGTGTGGCA	0.532																																					p.S280S		Atlas-SNP	.											.	TBC1D13	27	.	0			c.G840T						.						111	99	103					9																	131566320		2203	4300	6503	SO:0001819	synonymous_variant	54662	exon9			TGACTCGCAGTGT	AK001605	CCDS6911.1, CCDS69677.1	9q34.13	2013-07-09			ENSG00000107021	ENSG00000107021			25571	protein-coding gene	gene with protein product						22762500	Standard	XM_005252060		Approved	FLJ10743	uc010myj.3	Q9NVG8	OTTHUMG00000020760	ENST00000372648.5:c.840G>T	chr9.hg19:g.131566320G>T		55.0	0.0		67.0	24.0	NM_018201	A7E2E7|B3KW04|B9EGJ8|Q5T270|Q5T271	Silent	SNP	ENST00000372648.5	hg19	CCDS6911.1																																																																																			.	.		0.532	TBC1D13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054496.1	NM_018201		T	131566320	G	T	131566320	2	4	117	1	0	0	0	0	0	0	0	1	15617	1074	38	1		1	TBC1D13	9	131566320	Silent	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10		131566320	9647111	30	20162										
NDST2	8509	hgsc.bcm.edu	37	chr10	75567215	75567215	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	cgatgtctaccaagatgtagCggtcaaggtccaggcagagg	14	9	2	2	rs377733383		TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr10:75567215C>T	ENST00000309979.6	-	3	1488	c.932G>A	c.(931-933)cGc>cAc	p.R311H	RP11-574K11.31_ENST00000603027.1_Missense_Mutation_p.R311H|NDST2_ENST00000299641.4_Missense_Mutation_p.R188H			P52849	NDST2_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	311	Heparan sulfate N-deacetylase 2.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|hydrolase activity (GO:0016787)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30	Prostate(51;0.0112)					CAAGATGTAGCGGTCAAGGTC	0.488																																					p.R311H		Atlas-SNP	.											.	NDST2	53	.	0			c.G932A						.	C	HIS/ARG	0,4406		0,0,2203	94	89	91		932	5.8	1	10		91	1,8599	1.2+/-3.3	0,1,4299	no	missense	NDST2	NM_003635.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	311/884	75567215	1,13005	2203	4300	6503	SO:0001583	missense	8509	exon3			ATGTAGCGGTCAA	U36601	CCDS7335.1	10q22	2007-03-14			ENSG00000166507	ENSG00000166507		"Sulfotransferases, membrane-bound"	7681	protein-coding gene	gene with protein product		603268				9601056	Standard	NM_003635		Approved	NST2, HSST2	uc001jvk.2	P52849	OTTHUMG00000018489	ENST00000309979.6:c.932G>A	chr10.hg19:g.75567215C>T	ENSP00000310657:p.Arg311His	100.0	0.0		83.0	35.0	NM_003635	Q2TB32|Q59H89	Missense_Mutation	SNP	ENST00000309979.6	hg19	CCDS7335.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.779805	0.90195	0.0	1.16E-4	ENSG00000166507	ENST00000309979;ENST00000299641	T;T	0.60171	0.44;0.21	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.81931	0.4927	M	0.89601	3.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84887	0.0834	10	0.87932	D	0	.	19.9417	0.97165	0.0:1.0:0.0:0.0	.	188;311	B4E139;P52849	.;NDST2_HUMAN	H	311;188	ENSP00000310657:R311H;ENSP00000299641:R188H	ENSP00000299641:R188H	R	-	2	0	NDST2	75237221	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.810000	0.86072	2.720000	0.93068	0.655000	0.94253	CGC	.	.		0.488	NDST2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048710.1	NM_003635		T	75567215	C	T	75567215	3	4	117	1	0	0	0	0	1	0	0	0	10265	768	27	1	1771	1	NDST2	10	75567215	Missense_Mutation	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10		75567215	59967532	31	20163										
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1642677	1642677	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	acacagggacacagcaactaGactgggagcagcagggattg	14	9	0	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr11:1642677G>T	ENST00000399682.1	-	1	691	c.647C>A	c.(646-648)tCt>tAt	p.S216Y		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACAGCAACTAGACTGGGAGCA	0.567																																					p.S216Y		Atlas-SNP	.											.	KRTAP5-4	78	.	0			c.C647A						.						93	81	85					11																	1642677		692	1591	2283	SO:0001583	missense	387267	exon1			CAACTAGACTGGG	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"Keratin associated proteins"	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.647C>A	chr11.hg19:g.1642677G>T	ENSP00000382590:p.Ser216Tyr	82.0	0.0		64.0	18.0	NM_001012709		Missense_Mutation	SNP	ENST00000399682.1	hg19		.	.	.	.	.	.	.	.	.	.	G	4.293	0.053617	0.08291	.	.	ENSG00000241598	ENST00000399682;ENST00000328953	T	0.00922	5.54	2.29	1.25	0.21368	.	.	.	.	.	T	0.04272	0.0118	M	0.92317	3.295	0.21822	N	0.999522	P	0.49185	0.92	P	0.52109	0.69	T	0.12142	-1.0559	9	0.72032	D	0.01	.	7.8919	0.29682	0.0:0.5103:0.4897:0.0	.	276	Q6L8H1	KRA54_HUMAN	Y	216;207	ENSP00000382590:S216Y	ENSP00000331603:S207Y	S	-	2	0	KRTAP5-4	1599253	0.995000	0.38212	0.793000	0.32043	0.028000	0.11728	0.414000	0.21164	0.228000	0.21019	0.580000	0.79431	TCT	.	.		0.567	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		T	1642677	G	T	1642677	3	4	117	1	0	0	0	0	1	0	0	0	8572	942	33	3	43	3	KRTAP5-4	11	1642677	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10		1642677	133363839	32	20164										
TRIM21	6737	hgsc.bcm.edu	37	chr11	4411479	4411479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	tgagcagaaagcgctgccggCacacaggacagacgctgccc	13	14	0	3			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr11:4411479C>T	ENST00000254436.7	-	2	273	c.161G>A	c.(160-162)tGc>tAc	p.C54Y	TRIM21_ENST00000543625.1_Missense_Mutation_p.C54Y	NM_003141.3	NP_003132.2	P19474	RO52_HUMAN	tripartite motif containing 21	54					cell cycle (GO:0007049)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein deubiquitination (GO:0090086)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral entry into host cell (GO:0046598)|protein autoubiquitination (GO:0051865)|protein destabilization (GO:0031648)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)	16		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		GCGCTGCCGGCACACAGGACA	0.577																																					p.C54Y		Atlas-SNP	.											.	TRIM21	45	.	0			c.G161A						.						89	94	92					11																	4411479		2131	4245	6376	SO:0001583	missense	6737	exon2			TGCCGGCACACAG	AF391283	CCDS44525.1	11p15.5-p15.3	2014-02-14	2011-01-25	2004-11-26		ENSG00000132109		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	11312	protein-coding gene	gene with protein product		109092	"Sjogren syndrome antigen A1 (52kDa, ribonucleoprotein autoantigen SS-A/Ro)", "tripartite motif-containing 21"	SSA1		8094596	Standard	NM_003141		Approved	RNF81, RO52, Ro/SSA	uc001lyy.1	P19474		ENST00000254436.7:c.161G>A	chr11.hg19:g.4411479C>T	ENSP00000254436:p.Cys54Tyr	76.0	0.0		62.0	19.0	NM_003141	Q5XPV5|Q96RF8	Missense_Mutation	SNP	ENST00000254436.7	hg19	CCDS44525.1	.	.	.	.	.	.	.	.	.	.	C	19.10	3.761332	0.69763	.	.	ENSG00000132109	ENST00000254436;ENST00000543625	T;T	0.54866	0.55;0.55	4.46	3.54	0.40534	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.56097	D	0.000039	T	0.81903	0.4921	H	0.98542	4.26	0.44129	D	0.996912	D	0.89917	1.0	D	0.91635	0.999	D	0.88231	0.2903	10	0.87932	D	0	.	12.9248	0.58254	0.0:0.8356:0.1644:0.0	.	54	P19474	RO52_HUMAN	Y	54	ENSP00000254436:C54Y;ENSP00000444045:C54Y	ENSP00000254436:C54Y	C	-	2	0	TRIM21	4368055	1.000000	0.71417	0.979000	0.43373	0.832000	0.47134	7.074000	0.76791	1.461000	0.47929	0.655000	0.94253	TGC	.	.		0.577	TRIM21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385842.1	NM_003141		T	4411479	C	T	4411479	3	4	117	1	0	0	0	0	1	0	0	0	16510	710	25	3	1290	3	TRIM21	11	4411479	Missense_Mutation	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	2768802	4411479	130595037	33	20165										
HBG1	3047	hgsc.bcm.edu	37	chr11	5269688	5269688	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	tctttgccgaaatggattgcCaaaacggtcaccagcacatt	8	11	2	0			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr11:5269688C>T	ENST00000330597.3	-	3	432	c.345G>A	c.(343-345)ttG>ttA	p.L115L	CTD-2643I7.1_ENST00000564523.1_RNA	NM_000559.2	NP_000550.2	P69891	HBG1_HUMAN	hemoglobin, gamma A	115					blood coagulation (GO:0007596)	cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			large_intestine(1)|lung(3)|skin(1)	5		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AATGGATTGCCAAAACGGTCA	0.527																																					p.L115L	Ovarian(117;2080 2193 33416 49679)	Atlas-SNP	.											.	HBG1	11	.	0			c.G345A						.						44	44	44					11																	5269688		2201	4294	6495	SO:0001819	synonymous_variant	3047	exon3			GATTGCCAAAACG	M91036	CCDS7754.1	11p15.5	2014-05-19			ENSG00000213934	ENSG00000213934			4831	protein-coding gene	gene with protein product		142200				2649166	Standard	NM_000559		Approved	HBG-T2	uc001mah.1	P69891	OTTHUMG00000066681	ENST00000330597.3:c.345G>A	chr11.hg19:g.5269688C>T		248.0	0.0		214.0	66.0	NM_000559	P02096|P62027|Q549G1|Q8TDA1|Q96FH7	Silent	SNP	ENST00000330597.3	hg19	CCDS7754.1																																																																																			.	.		0.527	HBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142982.1	NM_000559		T	5269688	C	T	5269688	2	4	117	1	0	0	0	0	0	0	0	1	6991	593	21	3		3	HBG1	11	5269688	Silent	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	858209	5269688	129736828	34	20166										
CCDC73	493860	hgsc.bcm.edu	37	chr11	32635624	32635625	+	Frame_Shift_Ins	INS	-	-	T													0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	actcatatttttacacatagINStttttcccccagggcttgag							TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr11:32635624_32635625insT	ENST00000335185.5	-	16	2282_2283	c.2239_2240insA	c.(2239-2241)actfs	p.T747fs	CCDC73_ENST00000534415.1_5'Flank	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	747										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TTTACACATAGTTTTTCCCCCA	0.332																																					p.E747fs		Atlas-INDEL	.											.	CCDC73	136	.	0			c.2240_2241insA						.																																			SO:0001589	frameshift_variant	493860	exon16			.	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.2240dupA	chr11.hg19:g.32635629_32635629dupT	ENSP00000335325:p.Thr747fs	113.0	0.0		81.0	20.0	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Frame_Shift_Ins	INS	ENST00000335185.5	hg19	CCDS41630.1																																																																																			.	.		0.332	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		T	32635625	-	T	32635624	7	5	117	1	0	1	1	0	0	0	0	0	2848	1029	36	0	1011	0	CCDC73	11	32635624	Frame_Shift_Ins	INS	-	TCGA-DD-A3A3-01A-11D-A22F-10	27365936	32635624	102370892	35	20167										
SF3B2	10992	hgsc.bcm.edu	37	chr11	65828070	65828070	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	caggaagaacagaagaccatGaagtcaaaaatgcgagagaa	11	6	1	5			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr11:65828070G>T	ENST00000322535.6	+	14	1696	c.1647G>T	c.(1645-1647)atG>atT	p.M549I	SF3B2_ENST00000528302.1_Missense_Mutation_p.M532I	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	549					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						AGAAGACCATGAAGTCAAAAA	0.443																																					p.M549I		Atlas-SNP	.											.	SF3B2	85	.	0			c.G1647T						.						114	104	108					11																	65828070		2201	4295	6496	SO:0001583	missense	10992	exon14			GACCATGAAGTCA	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"splicing factor 3b, subunit 2, 145kD"			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.1647G>T	chr11.hg19:g.65828070G>T	ENSP00000318861:p.Met549Ile	66.0	0.0		50.0	24.0	NM_006842	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Missense_Mutation	SNP	ENST00000322535.6	hg19	CCDS31612.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519037	0.85495	.	.	ENSG00000087365	ENST00000528302;ENST00000322535;ENST00000355456	.	.	.	5.82	5.82	0.92795	Domain of unknown function DUF382 (1);	0.000000	0.85682	D	0.000000	T	0.61048	0.2316	L	0.28400	0.85	0.80722	D	1	P	0.43352	0.804	P	0.52031	0.688	T	0.61907	-0.6966	9	0.59425	D	0.04	-32.2593	17.5904	0.87994	0.0:0.0:1.0:0.0	.	549	Q13435	SF3B2_HUMAN	I	532;549;453	.	ENSP00000318861:M549I	M	+	3	0	SF3B2	65584646	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.976000	0.76135	2.751000	0.94390	0.650000	0.86243	ATG	.	.		0.443	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2			T	65828070	G	T	65828070	3	4	117	1	0	0	0	0	1	0	0	0	14166	1290	45	3	1701	3	SF3B2	11	65828070	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	33192446	65828070	69178446	36	20168										
BEST3	144453	hgsc.bcm.edu	37	chr12	70049144	70049144	+	Frame_Shift_Del	DEL	C	C	-													0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	tagcggaatcatggtggtagCcccctgatgtgggcactggt							TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr12:70049144delC	ENST00000330891.5	-	10	1776	c.1550delG	c.(1549-1551)ggcfs	p.G517fs	BEST3_ENST00000553096.1_Frame_Shift_Del_p.G411fs|BEST3_ENST00000488961.1_Frame_Shift_Del_p.G304fs|BEST3_ENST00000331471.4_Intron	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	517					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			ATGGTGGTAGCCCCCTGATGT	0.562																																					p.G517fs		Atlas-Indel,Pindel	.											.	BEST3	129	.	0			c.1551delC						.						137	136	136					12																	70049144		2070	4207	6277	SO:0001589	frameshift_variant	144453	exon10			.	AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17105	protein-coding gene	gene with protein product		607337	"vitelliform macular dystrophy 2-like 3"	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.1550delG	chr12.hg19:g.70049144delC	ENSP00000332413:p.Gly517fs	68.0	0.0		61.0	28.0	NM_032735	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Frame_Shift_Del	DEL	ENST00000330891.5	hg19	CCDS8992.2																																																																																			.	.		0.562	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439		-	70049144	C	-	70049144	7	5	117	1	0	1	0	1	0	0	0	0	1406	739	26	0	460	0	BEST3	12	70049144	Frame_Shift_Del	DEL	C	TCGA-DD-A3A3-01A-11D-A22F-10		70049144	63802751	37	20169										
POSTN	10631	hgsc.bcm.edu	37	chr13	38159033	38159033	+	Frame_Shift_Del	DEL	G	G	-													0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	cataatagactcagaacactGgagagtatttaagatgtggt							TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr13:38159033delG	ENST00000379747.4	-	8	1045	c.928delC	c.(928-930)cagfs	p.Q310fs	POSTN_ENST00000379749.4_Frame_Shift_Del_p.Q310fs|POSTN_ENST00000541481.1_Frame_Shift_Del_p.Q310fs|POSTN_ENST00000541179.1_Frame_Shift_Del_p.Q310fs|POSTN_ENST00000379743.4_Frame_Shift_Del_p.Q310fs|POSTN_ENST00000379742.4_Frame_Shift_Del_p.Q310fs	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	310	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TCAGAACACTGGAGAGTATTT	0.388																																					p.Q310fs		Atlas-Indel,Pindel	.											.	POSTN	161	.	0			c.929delA						.						112	105	107					13																	38159033		2203	4300	6503	SO:0001589	frameshift_variant	10631	exon8			.	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.928delC	chr13.hg19:g.38159033delG	ENSP00000369071:p.Gln310fs	142.0	0.0		118.0	41.0	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Frame_Shift_Del	DEL	ENST00000379747.4	hg19	CCDS9364.1																																																																																			.	.		0.388	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		-	38159033	G	-	38159033	7	5	117	1	0	1	0	1	0	0	0	0	12268	1357	47	0	1646	0	POSTN	13	38159033	Frame_Shift_Del	DEL	G	TCGA-DD-A3A3-01A-11D-A22F-10		38159033	77010845	38	20170										
FREM2	341640	hgsc.bcm.edu	37	chr13	39338482	39338482	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	agaattttcgtctgaattggGcatggatctcctttgaaaag	10	6	2	3			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr13:39338482G>C	ENST00000280481.7	+	3	5521	c.5305G>C	c.(5305-5307)Gca>Cca	p.A1769P		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1769	Calx-beta 1.				cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TCTGAATTGGGCATGGATCTC	0.343																																					p.A1769P		Atlas-SNP	.											.	FREM2	385	.	0			c.G5305C						.						93	96	95					13																	39338482		2203	4299	6502	SO:0001583	missense	341640	exon3			AATTGGGCATGGA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.5305G>C	chr13.hg19:g.39338482G>C	ENSP00000280481:p.Ala1769Pro	169.0	0.0		136.0	45.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.583882	0.86748	.	.	ENSG00000150893	ENST00000280481	T	0.26067	1.76	5.34	4.48	0.54585	Na-Ca exchanger/integrin-beta4 (1);	0.000000	0.85682	D	0.000000	T	0.56381	0.1981	M	0.86651	2.83	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.65483	-0.6157	10	0.59425	D	0.04	.	15.6233	0.76829	0.0:0.0:0.8613:0.1387	.	1769	Q5SZK8	FREM2_HUMAN	P	1769	ENSP00000280481:A1769P	ENSP00000280481:A1769P	A	+	1	0	FREM2	38236482	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.781000	0.99029	1.359000	0.45940	0.563000	0.77884	GCA	.	.		0.343	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39338482	G	C	39338482	3	2	117	1	0	0	0	0	1	0	0	0	6053	1203	42	4	5315	4	FREM2	13	39338482	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	1179449	39338482	75831396	39	20171										
MUDENG	55745	hgsc.bcm.edu	37	chr14	57741433	57741433	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	aacttacagaattcattagaTaataccaattttgcatctgt	4	7	2	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr14:57741433T>C	ENST00000261558.3	+	2	952	c.546T>C	c.(544-546)gaT>gaC	p.D182D	AP5M1_ENST00000431972.2_Silent_p.D196D	NM_018229.3	NP_060699.3	Q9H0R1	AP5M1_HUMAN	adaptor-related protein complex 5, mu 1 subunit	182					endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytosol (GO:0005829)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)											ATTCATTAGATAATACCAATT	0.398																																					p.D182D		Atlas-SNP	.											.	.	.	.	0			c.T546C						.						59	62	61					14																	57741433		2203	4299	6502	SO:0001819	synonymous_variant	55745	exon2			ATTAGATAATACC	AF094583	CCDS9729.1	14q22.2	2012-03-20	2012-03-20	2012-03-20	ENSG00000053770	ENSG00000053770			20192	protein-coding gene	gene with protein product	"Mu-2 related death-inducing gene"	614368	"chromosome 14 open reading frame 108", "MU-2/AP1M2 domain containing, death-inducing"	C14orf108, MUDENG		18395520	Standard	NM_018229		Approved	FLJ10813, MuD, mu5	uc001xcv.3	Q9H0R1	OTTHUMG00000140318	ENST00000261558.3:c.546T>C	chr14.hg19:g.57741433T>C		161.0	0.0		125.0	45.0	NM_018229	O95354|Q6ZMD7|Q96DX3|Q9NVC5	Silent	SNP	ENST00000261558.3	hg19	CCDS9729.1																																																																																			.	.		0.398	AP5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276922.1	NM_018229		C	57741433	T	C	57741433	2	2	117	1	0	0	0	0	0	0	0	1	9992	1403	49	2		2	MUDENG	14	57741433	Silent	SNP	T	TCGA-DD-A3A3-01A-11D-A22F-10		57741433	49608107	40	20172										
DOC2A	8448	hgsc.bcm.edu	37	chr16	30018527	30018527	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	tcgaggcagatgttaaaatgCttcttctgcgaaggcttgag	12	7	2	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr16:30018527C>T	ENST00000350119.4	-	6	811	c.621G>A	c.(619-621)aaG>aaA	p.K207K	DOC2A_ENST00000564944.1_Silent_p.K207K|DOC2A_ENST00000564979.1_Silent_p.K207K	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	207					nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						TGTTAAAATGCTTCTTCTGCG	0.632																																					p.K207K		Atlas-SNP	.											.	DOC2A	40	.	0			c.G621A						.						47	48	47					16																	30018527		2197	4300	6497	SO:0001819	synonymous_variant	8448	exon6			AAAATGCTTCTTC	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"Synaptotagmins"	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.621G>A	chr16.hg19:g.30018527C>T		44.0	0.0		49.0	23.0	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Silent	SNP	ENST00000350119.4	hg19	CCDS10666.1																																																																																			.	.		0.632	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586		T	30018527	C	T	30018527	2	4	117	1	0	0	0	0	0	0	0	1	4685	796	28	3		3	DOC2A	16	30018527	Silent	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10		30018527	60336226	41	20173										
DHODH	1723	hgsc.bcm.edu	37	chr16	72058091	72058091	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	tgccattggagcagatcatcGgaggtgaggacagcgtctga	15	8	2	3			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr16:72058091G>C	ENST00000219240.4	+	9	1202	c.1181G>C	c.(1180-1182)cGg>cCg	p.R394P	DHODH_ENST00000572887.1_Missense_Mutation_p.R392P	NM_001361.4	NP_001352.2	Q02127	PYRD_HUMAN	dihydroorotate dehydrogenase (quinone)	394					'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of apoptotic process (GO:0043065)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of mitochondrial fission (GO:0090140)|response to caffeine (GO:0031000)|response to drug (GO:0042493)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|neuronal cell body (GO:0043025)	dihydroorotate dehydrogenase activity (GO:0004152)|dihydroorotate oxidase activity (GO:0004158)|drug binding (GO:0008144)|FMN binding (GO:0010181)|ubiquinone binding (GO:0048039)			breast(1)|endometrium(2)|large_intestine(4)|ovary(1)|skin(1)|stomach(1)	10		Ovarian(137;0.125)			Atovaquone(DB01117)|Leflunomide(DB01097)|Teriflunomide(DB08880)	GCAGATCATCGGAGGTGAGGA	0.537																																					p.R394P		Atlas-SNP	.											.	DHODH	33	.	0			c.G1181C						.						117	125	122					16																	72058091		2163	4285	6448	SO:0001583	missense	1723	exon9			ATCATCGGAGGTG		CCDS42192.1	16q22.2	2012-10-02	2011-09-05		ENSG00000102967	ENSG00000102967	1.3.5.2		2867	protein-coding gene	gene with protein product		126064	"dihydroorotate dehydrogenase"			8211381	Standard	NM_001361		Approved		uc002fbp.3	Q02127	OTTHUMG00000178093	ENST00000219240.4:c.1181G>C	chr16.hg19:g.72058091G>C	ENSP00000219240:p.Arg394Pro	185.0	0.0		162.0	53.0	NM_001361	A8K8C8|Q6P176	Missense_Mutation	SNP	ENST00000219240.4	hg19	CCDS42192.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.533341	0.64972	.	.	ENSG00000102967	ENST00000219240	D	0.94232	-3.38	5.0	0.941	0.19519	Aldolase-type TIM barrel (1);	0.255981	0.43747	D	0.000526	D	0.91216	0.7232	L	0.56340	1.77	0.48632	D	0.999684	P	0.49253	0.921	P	0.48227	0.571	D	0.87868	0.2669	10	0.87932	D	0	-5.4628	7.4792	0.27395	0.3389:0.0:0.6611:0.0	.	394	Q02127	PYRD_HUMAN	P	394	ENSP00000219240:R394P	ENSP00000219240:R394P	R	+	2	0	DHODH	70615592	1.000000	0.71417	0.998000	0.56505	0.953000	0.61014	1.526000	0.35964	0.056000	0.16144	-0.258000	0.10820	CGG	.	.		0.537	DHODH-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001361		C	72058091	G	C	72058091	3	2	117	1	0	0	0	0	1	0	0	0	4486	1116	39	4	1215	4	DHODH	16	72058091	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	42039564	72058091	18296662	42	20174										
TRPV1	7442	hgsc.bcm.edu	37	chr17	3493227	3493227	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	atctcattgtacatgctcgtCacaaacttcgtgttgtcggc	8	11	2	0			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr17:3493227C>A	ENST00000571088.1	-	6	1131	c.918G>T	c.(916-918)gtG>gtT	p.V306V	TRPV1_ENST00000576351.1_Silent_p.V306V|TRPV1_ENST00000399756.4_Silent_p.V306V|TRPV1_ENST00000425167.2_Silent_p.V306V|TRPV1_ENST00000310522.5_Silent_p.V306V|TRPV1_ENST00000399759.3_Silent_p.V306V|SHPK_ENST00000572705.1_Silent_p.V306V|TRPV1_ENST00000174621.6_Silent_p.V304V	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	306					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)	p.V306V(2)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	ACATGCTCGTCACAAACTTcg	0.617																																					p.V306V	Melanoma(38;962 1762 15789)	Atlas-SNP	.											TRPV1_ENST00000399756,NS,carcinoma,0,2	TRPV1	99	.	2	Substitution - coding silent(2)	endometrium(2)	c.G918T						.						39	46	43					17																	3493227		2149	4247	6396	SO:0001819	synonymous_variant	7442	exon6			GCTCGTCACAAAC	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12716	protein-coding gene	gene with protein product		602076	"vanilloid receptor subtype 1"	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.918G>T	chr17.hg19:g.3493227C>A		90.0	0.0		61.0	36.0	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Silent	SNP	ENST00000571088.1	hg19	CCDS45576.1																																																																																			.	.		0.617	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727		A	3493227	C	A	3493227	2	1	117	1	0	0	0	0	0	0	0	1	16610	813	29	3		3	TRPV1	17	3493227	Silent	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10		3493227	77701983	43	20175			1	18		2	2	13	N	G_C	2.170747e-05
TRPV1	7442	hgsc.bcm.edu	37	chr17	3493239	3493239	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	atgctcgtcacaaacttcgtGttgtcggccgtgttgtcggc	12	11	1	0			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr17:3493239G>A	ENST00000571088.1	-	6	1119	c.906C>T	c.(904-906)aaC>aaT	p.N302N	TRPV1_ENST00000576351.1_Silent_p.N302N|TRPV1_ENST00000399756.4_Silent_p.N302N|TRPV1_ENST00000425167.2_Silent_p.N302N|TRPV1_ENST00000310522.5_Silent_p.N302N|TRPV1_ENST00000399759.3_Silent_p.N302N|SHPK_ENST00000572705.1_Silent_p.N302N|TRPV1_ENST00000174621.6_Silent_p.N300N	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	302					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	CAAACTTcgtgttgtcggccg	0.597																																					p.N302N	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.C906T						.						36	43	41					17																	3493239		2148	4245	6393	SO:0001819	synonymous_variant	7442	exon6			CTTCGTGTTGTCG	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12716	protein-coding gene	gene with protein product		602076	"vanilloid receptor subtype 1"	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.906C>T	chr17.hg19:g.3493239G>A		81.0	0.0		48.0	29.0	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Silent	SNP	ENST00000571088.1	hg19	CCDS45576.1																																																																																			.	.		0.597	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727		A	3493239	G	A	3493239	2	1	117	1	0	0	0	0	0	0	0	1	16610	1368	48	3		3	TRPV1	17	3493239	Silent	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	12	3493239	77701971	44	20176			1	18		2	2	13	N	G_C	2.170747e-05
NF1	4763	hgsc.bcm.edu	37	chr17	29541512	29541512	+	Frame_Shift_Del	DEL	A	A	-													0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	aacaagccttaaatttaaagAaaaacctacagacctggaga							TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr17:29541512delA	ENST00000358273.4	+	13	1819	c.1436delA	c.(1435-1437)gaafs	p.E479fs	NF1_ENST00000431387.4_Frame_Shift_Del_p.E479fs|NF1_ENST00000356175.3_Frame_Shift_Del_p.E479fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	479					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(5)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAATTTAAAGAAAAACCTACA	0.328			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.E479fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	13	Whole gene deletion(8)|Unknown(5)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)|lung(1)	c.1435delG						.						33	34	34					17																	29541512		2201	4294	6495	SO:0001589	frameshift_variant	4763	exon13	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	.		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1436delA	chr17.hg19:g.29541512delA	ENSP00000351015:p.Glu479fs	182.0	0.0		202.0	103.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	hg19	CCDS42292.1																																																																																			.	.		0.328	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		-	29541512	A	-	29541512	7	5	117	1	0	1	0	1	0	0	0	0	10365	246	9	0	1486	0	NF1	17	29541512	Frame_Shift_Del	DEL	A	TCGA-DD-A3A3-01A-11D-A22F-10	26048273	29541512	51653698	45	20177										
STAT3	6774	hgsc.bcm.edu	37	chr17	40481576	40481576	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	agctcctcccacataccaagTgtttgaattctgcagagagg	9	11	1	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr17:40481576T>C	ENST00000264657.5	-	13	1541	c.1229A>G	c.(1228-1230)cAc>cGc	p.H410R	STAT3_ENST00000585517.1_Missense_Mutation_p.H410R|STAT3_ENST00000588969.1_Missense_Mutation_p.H410R|STAT3_ENST00000389272.3_Missense_Mutation_p.H312R|STAT3_ENST00000404395.3_Missense_Mutation_p.H410R	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	410					acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		ACATACCAAGTGTTTGAATTC	0.498									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.H410R		Atlas-SNP	.											.	STAT3	268	.	0			c.A1229G						.						114	115	115					17																	40481576		2203	4300	6503	SO:0001583	missense	6774	exon13	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	ACCAAGTGTTTGA	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610		"SH2 domain containing"	11364	protein-coding gene	gene with protein product		102582				7512451	Standard	NM_139276		Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.1229A>G	chr17.hg19:g.40481576T>C	ENSP00000264657:p.His410Arg	141.0	0.0		150.0	79.0	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	hg19	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.699209	0.88830	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.88277	-2.36;-2.36;-2.36	6.02	6.02	0.97574	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.94132	0.8118	M	0.78049	2.395	0.80722	D	1	D;D;D	0.55172	0.962;0.97;0.97	P;D;D	0.66351	0.905;0.943;0.943	D	0.94548	0.7751	10	0.72032	D	0.01	-34.673	16.5446	0.84426	0.0:0.0:0.0:1.0	.	410;410;410	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	R	410;312;410	ENSP00000264657:H410R;ENSP00000373923:H312R;ENSP00000384943:H410R	ENSP00000264657:H410R	H	-	2	0	STAT3	37735102	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	8.040000	0.89188	2.311000	0.77944	0.533000	0.62120	CAC	.	.		0.498	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		C	40481576	T	C	40481576	3	2	117	1	0	0	0	0	1	0	0	0	15281	1696	59	2	1131	2	STAT3	17	40481576	Missense_Mutation	SNP	T	TCGA-DD-A3A3-01A-11D-A22F-10	10940064	40481576	40713634	46	20178										
C17orf104	284071	hgsc.bcm.edu	37	chr17	42744727	42744728	+	Frame_Shift_Ins	INS	-	-	A													0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	acttggatgaatgttcaaacINSaaaaaataacactcctattc							TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr17:42744727_42744728insA	ENST00000409122.2	+	5	1590_1591	c.1448_1449insA	c.(1447-1452)acaaaafs	p.TK483fs	C17orf104_ENST00000409464.1_Frame_Shift_Ins_p.TK317fs|C17orf104_ENST00000359945.3_Frame_Shift_Ins_p.TK483fs	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	483										autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						AATGTTCAAACAAAAAATAACA	0.312																																					p.T483fs		Atlas-INDEL	.											.	C17orf104	75	.	0			c.1448_1449insA						.																																			SO:0001589	frameshift_variant	284071	exon5			.		CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.1454dupA	chr17.hg19:g.42744733_42744733dupA	ENSP00000386452:p.Thr483fs	70.0	0.0		107.0	34.0	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Frame_Shift_Ins	INS	ENST00000409122.2	hg19	CCDS45703.2																																																																																			.	.		0.312	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		A	42744728	-	A	42744727	7	5	117	1	0	1	1	0	0	0	0	0	1853	478	17	0	1466	0	C17orf104	17	42744727	Frame_Shift_Ins	INS	-	TCGA-DD-A3A3-01A-11D-A22F-10	2263151	42744727	38450483	47	20179										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901390	51901390	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	aagggcatttatgctctggtGgcacaggatgtctttctcct	11	9	3	0			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr17:51901390G>T	ENST00000268919.4	+	1	1152	c.996G>T	c.(994-996)gtG>gtT	p.V332V		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	332	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						ATGCTCTGGTGGCACAGGATG	0.488																																					p.V332V		Atlas-SNP	.											.	KIF2B	254	.	0			c.G996T						.						107	109	108					17																	51901390		2203	4300	6503	SO:0001819	synonymous_variant	84643	exon1			TCTGGTGGCACAG	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.996G>T	chr17.hg19:g.51901390G>T		90.0	0.0		109.0	30.0	NM_032559	Q96MA2|Q9BXG6	Silent	SNP	ENST00000268919.4	hg19	CCDS32685.1																																																																																			.	.		0.488	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51901390	G	T	51901390	2	4	117	1	0	0	0	0	0	0	0	1	8307	1335	47	3		3	KIF2B	17	51901390	Silent	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	9156663	51901390	29293820	48	20180										
DYNLL2	140735	hgsc.bcm.edu	37	chr17	56166589	56166589	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	acacacgagacaaagcacttCatctatttttacttgggtca	6	10	3	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr17:56166589C>T	ENST00000579991.2	+	3	497	c.219C>T	c.(217-219)ttC>ttT	p.F73F		NM_080677.2	NP_542408.1	Q96FJ2	DYL2_HUMAN	dynein, light chain, LC8-type 2	73					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|microtubule-based process (GO:0007017)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|synaptic target recognition (GO:0008039)|transport (GO:0006810)	centrosome (GO:0005813)|cytosol (GO:0005829)|dynein complex (GO:0030286)|membrane (GO:0016020)|microtubule (GO:0005874)|myosin complex (GO:0016459)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	motor activity (GO:0003774)			lung(3)	3						CAAAGCACTTCATCTATTTTT	0.478																																					p.F73F		Atlas-SNP	.											.	DYNLL2	7	.	0			c.C219T						.						163	182	175					17																	56166589		2203	4300	6503	SO:0001819	synonymous_variant	140735	exon3			GCACTTCATCTAT	AF112997	CCDS11601.1	17q23.2	2009-11-18				ENSG00000264364		"Cytoplasmic dyneins"	24596	protein-coding gene	gene with protein product	"radial spoke 22 homolog (Chlamydomonas)"	608942				16260502	Standard	NM_080677		Approved	MGC17810, Dlc2, DNCL1B, RSPH22	uc010wnn.1	Q96FJ2		ENST00000579991.2:c.219C>T	chr17.hg19:g.56166589C>T		119.0	0.0		127.0	27.0	NM_080677	B2R5B4	Silent	SNP	ENST00000579991.2	hg19	CCDS11601.1																																																																																			.	.		0.478	DYNLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443338.2	NM_080677		T	56166589	C	T	56166589	2	4	117	1	0	0	0	0	0	0	0	1	4851	825	29	3		3	DYNLL2	17	56166589	Silent	SNP	C	TCGA-DD-A3A3-01A-11D-A22F-10	4265199	56166589	25028621	49	20181										
PRKACA	5566	hgsc.bcm.edu	37	chr19	14208204	14208204	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	cgatcttctcatagatctggAtgggctggtctgcgaagaag	13	8	4	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr19:14208204A>G	ENST00000308677.4	-	8	930	c.734T>C	c.(733-735)aTc>aCc	p.I245T	PRKACA_ENST00000589994.1_Missense_Mutation_p.I237T|PRKACA_ENST00000350356.3_5'UTR|PRKACA_ENST00000590853.1_Intron	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	245	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						ATAGATCTGGATGGGCTGGTC	0.582																																					p.I245T		Atlas-SNP	.											.	PRKACA	65	.	0			c.T734C						.						44	46	45					19																	14208204		2203	4300	6503	SO:0001583	missense	5566	exon8			ATCTGGATGGGCT		CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	2.7.11.1		9380	protein-coding gene	gene with protein product		601639				8884279	Standard	NM_002730		Approved	PKACa	uc002myc.3	P17612		ENST00000308677.4:c.734T>C	chr19.hg19:g.14208204A>G	ENSP00000309591:p.Ile245Thr	65.0	0.0		61.0	22.0	NM_002730	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Missense_Mutation	SNP	ENST00000308677.4	hg19	CCDS12304.1	.	.	.	.	.	.	.	.	.	.	A	15.10	2.733348	0.48939	.	.	ENSG00000072062	ENST00000308677;ENST00000350356;ENST00000535695;ENST00000536649	T	0.65364	-0.15	4.68	3.64	0.41730	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.41823	U	0.000806	T	0.49218	0.1544	N	0.16602	0.42	0.40251	D	0.978076	P;B;B	0.41232	0.743;0.039;0.022	P;B;B	0.44623	0.455;0.409;0.123	T	0.52328	-0.8590	10	0.87932	D	0	.	8.8154	0.34993	0.8315:0.0:0.0:0.1685	.	187;245;237	B7Z708;P17612;P17612-2	.;KAPCA_HUMAN;.	T	245;237;245;187	ENSP00000309591:I245T	ENSP00000309591:I245T	I	-	2	0	PRKACA	14069204	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.134000	0.94467	0.613000	0.30089	0.482000	0.46254	ATC	.	.		0.582	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730		G	14208204	A	G	14208204	3	3	117	1	0	0	0	0	1	0	0	0	12509	333	12	2	333	2	PRKACA	19	14208204	Missense_Mutation	SNP	A	TCGA-DD-A3A3-01A-11D-A22F-10		14208204	44920779	50	20182										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15303036	15303036	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	gagcagaggaagcgtccatcGggccccactgagcagcgggc	16	13	0	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr19:15303036G>A	ENST00000263388.2	-	4	489	c.414C>T	c.(412-414)ccC>ccT	p.P138P		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	138	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			AGCGTCCATCGGGCCCCACTG	0.687																																					p.P138P		Atlas-SNP	.											.	NOTCH3	340	.	0			c.C414T						.						21	23	22					19																	15303036		2198	4295	6493	SO:0001819	synonymous_variant	4854	exon4			TCCATCGGGCCCC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.414C>T	chr19.hg19:g.15303036G>A		54.0	0.0		34.0	15.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	hg19	CCDS12326.1																																																																																			.	.		0.687	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		A	15303036	G	A	15303036	2	1	117	1	0	0	0	0	0	0	0	1	10559	1103	39	1		1	NOTCH3	19	15303036	Silent	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	1094832	15303036	43825947	51	20183										
CATSPERG	57828	hgsc.bcm.edu	37	chr19	38855544	38855544	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	accccagattacgctcaaggAtaaaaagctttgctatgacc	7	11	1	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr19:38855544A>T	ENST00000409235.3	+	21	2604	c.2489A>T	c.(2488-2490)gAt>gTt	p.D830V	AC005625.1_ENST00000590304.1_RNA|CATSPERG_ENST00000410018.1_Missense_Mutation_p.D790V|CATSPERG_ENST00000215069.4_3'UTR	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	830					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						ACGCTCAAGGATAAAAAGCTT	0.498																																					p.D830V		Atlas-SNP	.											.	CATSPERG	121	.	0			c.A2489T						.						110	107	108					19																	38855544		2203	4300	6503	SO:0001583	missense	57828	exon21			TCAAGGATAAAAA	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"chromosome 19 open reading frame 15", "cation channel, sperm-associated, gamma"	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.2489A>T	chr19.hg19:g.38855544A>T	ENSP00000386962:p.Asp830Val	63.0	0.0		58.0	17.0	NM_021185	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	hg19	CCDS12514.2	.	.	.	.	.	.	.	.	.	.	A	16.77	3.214251	0.58452	.	.	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410	T;T	0.39056	1.1;1.1	4.5	4.5	0.54988	.	0.106098	0.40908	D	0.000983	T	0.60612	0.2282	M	0.71581	2.175	0.50813	D	0.999893	D;D	0.89917	1.0;1.0	D;D	0.91635	0.985;0.999	T	0.64054	-0.6497	10	0.72032	D	0.01	-22.5564	10.1172	0.42598	1.0:0.0:0.0:0.0	.	830;790	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	V	790;830;830	ENSP00000387057:D790V;ENSP00000386962:D830V	ENSP00000386962:D830V	D	+	2	0	CATSPERG	43547384	0.972000	0.33761	0.039000	0.18376	0.408000	0.30992	4.007000	0.57093	1.897000	0.54924	0.459000	0.35465	GAT	.	.		0.498	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185		T	38855544	A	T	38855544	3	4	117	1	0	0	0	0	1	0	0	0	2694	333	12	4	2567	4	CATSPERG	19	38855544	Missense_Mutation	SNP	A	TCGA-DD-A3A3-01A-11D-A22F-10	23552508	38855544	20273439	52	20184										
ZNF543	125919	hgsc.bcm.edu	37	chr19	57840110	57840110	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	gaagccttatgaatgcagtgAatgtggaaaggccttcaccc	11	9	1	2			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr19:57840110A>C	ENST00000321545.4	+	4	1625	c.1280A>C	c.(1279-1281)gAa>gCa	p.E427A		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	427					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GAATGCAGTGAATGTGGAAAG	0.478																																					p.E427A		Atlas-SNP	.											.	ZNF543	61	.	0			c.A1280C						.						89	72	78					19																	57840110		2203	4300	6503	SO:0001583	missense	125919	exon4			GCAGTGAATGTGG	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"Zinc fingers, C2H2-type", "-"	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.1280A>C	chr19.hg19:g.57840110A>C	ENSP00000322545:p.Glu427Ala	52.0	0.0		37.0	15.0	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	hg19	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	A	9.958	1.221907	0.22457	.	.	ENSG00000178229	ENST00000321545	T	0.06933	3.24	3.0	3.0	0.34707	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21718	0.0523	L	0.60012	1.86	0.09310	N	1	P	0.48407	0.91	D	0.63283	0.913	T	0.02031	-1.1226	9	0.72032	D	0.01	.	10.5184	0.44903	1.0:0.0:0.0:0.0	.	427	Q08ER8	ZN543_HUMAN	A	427	ENSP00000322545:E427A	ENSP00000322545:E427A	E	+	2	0	ZNF543	62531922	0.000000	0.05858	0.063000	0.19743	0.204000	0.24138	1.130000	0.31393	1.353000	0.45828	0.459000	0.35465	GAA	.	.		0.478	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		C	57840110	A	C	57840110	3	2	117	1	0	0	0	0	1	0	0	0	17991	246	9	5	1294	5	ZNF543	19	57840110	Missense_Mutation	SNP	A	TCGA-DD-A3A3-01A-11D-A22F-10	18984566	57840110	1288873	53	20185										
IL17RA	23765	hgsc.bcm.edu	37	chr22	17577966	17577966	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	ccacaggggctaaactgcacGgtcaagaatagtaagtcatc	10	10	2	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chr22:17577966G>A	ENST00000319363.6	+	2	286	c.153G>A	c.(151-153)acG>acA	p.T51T	IL17RA_ENST00000477874.1_Intron	NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	51					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		TAAACTGCACGGTCAAGAATA	0.463																																					p.T51T		Atlas-SNP	.											IL17RA,NS,carcinoma,0,1	IL17RA	62	.	0			c.G153A						.						223	190	201					22																	17577966		2203	4300	6503	SO:0001819	synonymous_variant	23765	exon2			CTGCACGGTCAAG	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"Interleukins and interleukin receptors", "CD molecules"	5985	protein-coding gene	gene with protein product		605461	"interleukin 17 receptor"	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.153G>A	chr22.hg19:g.17577966G>A		216.0	0.0		191.0	70.0	NM_014339	O43844|Q20WK1	Silent	SNP	ENST00000319363.6	hg19	CCDS13739.1																																																																																			.	.		0.463	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339		A	17577966	G	A	17577966	2	1	117	1	0	0	0	0	0	0	0	1	7648	1103	39	1		1	IL17RA	22	17577966	Silent	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10		17577966	33726600	54	20186										
SRPX	8406	hgsc.bcm.edu	37	chrX	38020249	38020249	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	tctgtcatagactgtgtactGgatcttgtggtctccttctg	10	9	5	1			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chrX:38020249G>A	ENST00000378533.3	-	6	818	c.712C>T	c.(712-714)Cag>Tag	p.Q238*	SRPX_ENST00000479015.1_5'Flank|TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000343800.6_Nonsense_Mutation_p.Q225*|SRPX_ENST00000538295.1_Nonsense_Mutation_p.Q238*|SRPX_ENST00000544439.1_Nonsense_Mutation_p.Q218*|SRPX_ENST00000432886.2_Nonsense_Mutation_p.Q179*	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	238	HYR. {ECO:0000255|PROSITE- ProRule:PRU00113}.				autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						ACTGTGTACTGGATCTTGTGG	0.423																																					p.Q238X		Atlas-SNP	.											.	SRPX	53	.	0			c.C712T						.						120	106	111					X																	38020249		2202	4299	6501	SO:0001587	stop_gained	8406	exon6			TGTACTGGATCTT	U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"sushi-repeat-containing protein, X chromosome", "sushi-repeat-containing protein, X-linked"			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.712C>T	chrX.hg19:g.38020249G>A	ENSP00000367794:p.Gln238*	46.0	0.0		44.0	30.0	NM_001170752	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Nonsense_Mutation	SNP	ENST00000378533.3	hg19	CCDS14245.1	.	.	.	.	.	.	.	.	.	.	g	38	6.975654	0.97975	.	.	ENSG00000101955	ENST00000544439;ENST00000432886;ENST00000538295;ENST00000378533;ENST00000343800	.	.	.	5.86	4.98	0.66077	.	0.153881	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-12.6791	15.7122	0.77641	0.0:0.1366:0.8634:0.0	.	.	.	.	X	218;179;238;238;225	.	ENSP00000339211:Q225X	Q	-	1	0	SRPX	37905193	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.354000	0.66040	1.191000	0.43056	0.597000	0.82753	CAG	.	.		0.423	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307		A	38020249	G	A	38020249	4	1	117	1	0	0	0	0	0	1	0	0	15179	1357	47	3	702	3	SRPX	23	38020249	Nonsense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10		38020249	117250311	55	20187										
ELF4	2000	hgsc.bcm.edu	37	chrX	129200820	129200820	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0535714285714286	3	1	0.746923076923077	1.55608974358974	0.592796092796093	1	1	0	taggctcagccatcagcaggGaccctgagcctgaggagagc	14	12	2	3			TCGA-DD-A3A3-01A-11D-A22F-10	TCGA-DD-A3A3-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23566732-cbc1-407d-aa01-5ae509f9fe44	17a04c22-ddc8-4da6-87c4-c27e1b7c6585	g.chrX:129200820G>T	ENST00000308167.5	-	9	2247	c.1868C>A	c.(1867-1869)tCc>tAc	p.S623Y	ELF4_ENST00000335997.7_Missense_Mutation_p.S623Y	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)											breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						CATCAGCAGGGACCCTGAGCC	0.592			T	ERG	AML																																p.S623Y		Atlas-SNP	.		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	.	ELF4	67	.	0			c.C1868A						.						79	88	85					X																	129200820		2203	4300	6503	SO:0001583	missense	2000	exon9			AGCAGGGACCCTG	U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.1868C>A	chrX.hg19:g.129200820G>T	ENSP00000311280:p.Ser623Tyr	78.0	0.0		67.0	47.0	NM_001421		Missense_Mutation	SNP	ENST00000308167.5	hg19	CCDS14617.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.042032	0.55003	.	.	ENSG00000102034	ENST00000335997;ENST00000308167	T;T	0.23552	1.9;1.9	4.96	4.96	0.65561	.	.	.	.	.	T	0.25901	0.0631	L	0.27053	0.805	0.28847	N	0.896242	P	0.50943	0.94	P	0.48030	0.564	T	0.07654	-1.0761	9	0.72032	D	0.01	.	12.6614	0.56815	0.0:0.0:1.0:0.0	.	623	Q99607	ELF4_HUMAN	Y	623	ENSP00000338608:S623Y;ENSP00000311280:S623Y	ENSP00000311280:S623Y	S	-	2	0	ELF4	129028501	1.000000	0.71417	0.958000	0.39756	0.497000	0.33675	5.459000	0.66685	2.040000	0.60383	0.513000	0.50165	TCC	.	.		0.592	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421		T	129200820	G	T	129200820	3	4	117	1	0	0	0	0	1	0	0	0	5058	1174	41	3	127	3	ELF4	23	129200820	Missense_Mutation	SNP	G	TCGA-DD-A3A3-01A-11D-A22F-10	91180571	129200820	26069740	56	20188										
C1orf94	84970	hgsc.bcm.edu	37	chr1	34667861	34667861	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	ctaccttcttgcagtatcagGtcagtgagctggcctggctc	11	12	3	1			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr1:34667861G>T	ENST00000488417.1	+	4	1566		c.e4+1		C1orf94_ENST00000373374.3_Splice_Site	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94											central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				GCAGTATCAGGTCAGTGAGCT	0.547																																					.		Atlas-SNP	.											.	C1orf94	156	.	0			c.876+1G>T						.						138	121	127					1																	34667861		2203	4300	6503	SO:0001630	splice_region_variant	84970	exon4			TATCAGGTCAGTG	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.1446+1G>T	chr1.hg19:g.34667861G>T		103.0	0.0		77.0	27.0	NM_032884	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Splice_Site	SNP	ENST00000488417.1	hg19	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	G	12.25	1.882573	0.33255	.	.	ENSG00000142698	ENST00000373374;ENST00000488417	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3446	0.74327	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C1orf94	34440448	1.000000	0.71417	1.000000	0.80357	0.138000	0.21146	5.405000	0.66351	2.695000	0.91970	0.462000	0.41574	.	.	.		0.547	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	Intron	T	34667861	G	T	34667861	5	4	118	1	0	0	0	0	0	0	1	0	2073	1275	44	3	1461	3	C1orf94	1	34667861	Splice_Site	SNP	G	TCGA-DD-A3A4-01A-11D-A22F-10		34667861	214582760	1	20189										
KIFAP3	22920	hgsc.bcm.edu	37	chr1	170007568	170007568	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	cattaatgttagcaacttcaTcaatctgaaacaaagaggca	6	8	3	2			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr1:170007568T>A	ENST00000361580.2	-	5	607	c.380A>T	c.(379-381)gAt>gTt	p.D127V	KIFAP3_ENST00000367765.1_Missense_Mutation_p.D87V|KIFAP3_ENST00000367767.1_Missense_Mutation_p.D83V|KIFAP3_ENST00000490550.1_5'UTR|KIFAP3_ENST00000538366.1_Missense_Mutation_p.D49V	NM_014970.3	NP_055785.2	Q92845	KIFA3_HUMAN	kinesin-associated protein 3	127					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|membrane organization (GO:0061024)|microtubule-based movement (GO:0007018)|microtubule-based process (GO:0007017)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of calcium-dependent cell-cell adhesion (GO:0046587)|protein complex assembly (GO:0006461)|protein localization (GO:0008104)|signal transduction (GO:0007165)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule cytoskeleton (GO:0015630)	kinesin binding (GO:0019894)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|prostate(2)|skin(3)|urinary_tract(2)	35	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AGCAACTTCATCAATCTGAAA	0.353																																					p.D127V		Atlas-SNP	.											.	KIFAP3	102	.	0			c.A380T						.						95	105	102					1																	170007568		2203	4300	6503	SO:0001583	missense	22920	exon5			ACTTCATCAATCT	U59919	CCDS1288.1, CCDS55659.1, CCDS55660.1, CCDS55661.1	1q24.2	2012-09-20			ENSG00000075945	ENSG00000075945			17060	protein-coding gene	gene with protein product	"Smg GDS"	601836				8900189	Standard	NM_014970		Approved	SMAP, KAP3, FLA3, KAP-1	uc001ggv.3	Q92845	OTTHUMG00000035947	ENST00000361580.2:c.380A>T	chr1.hg19:g.170007568T>A	ENSP00000354560:p.Asp127Val	135.0	0.0		150.0	46.0	NM_014970	B1AKU4|B1AKU5|B2RDL1|B7Z8A3|F5H591|Q8NHU7|Q9H416	Missense_Mutation	SNP	ENST00000361580.2	hg19	CCDS1288.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.162824	0.78226	.	.	ENSG00000075945	ENST00000361580;ENST00000367765;ENST00000367767;ENST00000538366	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.74	5.74	0.90152	Armadillo-like helical (1);	0.043545	0.85682	D	0.000000	T	0.48786	0.1519	L	0.52573	1.65	0.80722	D	1	D;D;P	0.58970	0.984;0.97;0.928	P;P;P	0.57679	0.825;0.697;0.609	T	0.43621	-0.9380	9	.	.	.	-28.1139	16.0039	0.80344	0.0:0.0:0.0:1.0	.	49;83;127	B7Z8A3;B1AKU5;Q92845	.;.;KIFA3_HUMAN	V	127;87;83;49	ENSP00000354560:D127V;ENSP00000356739:D87V;ENSP00000356741:D83V;ENSP00000444622:D49V	.	D	-	2	0	KIFAP3	168274192	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.502000	0.81614	2.317000	0.78254	0.460000	0.39030	GAT	.	.		0.353	KIFAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087568.1	NM_014970		A	170007568	T	A	170007568	3	1	118	1	0	0	0	0	1	0	0	0	8320	1435	50	4	2062	4	KIFAP3	1	170007568	Missense_Mutation	SNP	T	TCGA-DD-A3A4-01A-11D-A22F-10	135339707	170007568	79243053	2	20190										
RGL1	23179	hgsc.bcm.edu	37	chr1	183885770	183885770	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	ctgtttacaaccaacagaatGaagacacctgcataatccgc	6	12	0	3			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr1:183885770G>T	ENST00000360851.3	+	16	2117	c.1939G>T	c.(1939-1941)Gaa>Taa	p.E647*	RGL1_ENST00000539189.1_Nonsense_Mutation_p.E618*|RGL1_ENST00000536277.1_Nonsense_Mutation_p.E645*|RGL1_ENST00000304685.4_Nonsense_Mutation_p.E682*			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	647					cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						CCAACAGAATGAAGACACCTG	0.527																																					p.E682X		Atlas-SNP	.											.	RGL1	91	.	0			c.G2044T						.						142	134	137					1																	183885770		2203	4300	6503	SO:0001587	stop_gained	23179	exon17			CAGAATGAAGACA	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.1939G>T	chr1.hg19:g.183885770G>T	ENSP00000354097:p.Glu647*	99.0	0.0		75.0	30.0	NM_015149	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Nonsense_Mutation	SNP	ENST00000360851.3	hg19		.	.	.	.	.	.	.	.	.	.	G	43	10.299247	0.99378	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000360851;ENST00000539189	.	.	.	5.43	5.43	0.79202	.	0.113427	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	18.8583	0.92262	0.0:0.0:1.0:0.0	.	.	.	.	X	682;682;645;647;618	.	ENSP00000303192:E682X	E	+	1	0	RGL1	182152393	1.000000	0.71417	0.986000	0.45419	0.996000	0.88848	3.633000	0.54295	2.555000	0.86185	0.650000	0.86243	GAA	.	.		0.527	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149		T	183885770	G	T	183885770	4	4	118	1	0	0	0	0	0	1	0	0	13291	1291	45	3	2106	3	RGL1	1	183885770	Nonsense_Mutation	SNP	G	TCGA-DD-A3A4-01A-11D-A22F-10	13878202	183885770	65364851	3	20191										
PGBD2	267002	hgsc.bcm.edu	37	chr1	249211640	249211640	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	ggggtccaagcagctgcacaGggggaagcctgtgcgacttg	17	10	0	0	rs560395632	byFrequency	TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr1:249211640G>T	ENST00000329291.5	+	3	1004	c.857G>T	c.(856-858)aGg>aTg	p.R286M	PGBD2_ENST00000355360.4_Missense_Mutation_p.R35M|PGBD2_ENST00000539153.1_Missense_Mutation_p.R283M	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	286										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CAGCTGCACAGGGGGAAGCCT	0.537																																					p.R286M		Atlas-SNP	.											.	PGBD2	103	.	0			c.G857T						.						78	84	82					1																	249211640		2203	4300	6503	SO:0001583	missense	267002	exon3			TGCACAGGGGGAA	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.857G>T	chr1.hg19:g.249211640G>T	ENSP00000331643:p.Arg286Met	119.0	0.0		122.0	60.0	NM_170725	B3KVR8|Q6MZF8	Missense_Mutation	SNP	ENST00000329291.5	hg19	CCDS31128.1	.	.	.	.	.	.	.	.	.	.	G	1.931	-0.445936	0.04604	.	.	ENSG00000185220	ENST00000355360;ENST00000329291;ENST00000539153	T;T;T	0.18657	2.2;2.2;2.2	3.76	-4.2	0.03823	.	4.769610	0.00824	N	0.001606	T	0.15046	0.0363	L	0.39898	1.24	0.09310	N	1	P;B	0.38250	0.624;0.01	B;B	0.36808	0.233;0.005	T	0.18935	-1.0321	10	0.62326	D	0.03	2.0361	0.8397	0.01147	0.4296:0.222:0.1467:0.2016	.	283;286	F5H4U7;Q6P3X8	.;PGBD2_HUMAN	M	35;286;283	ENSP00000355424:R35M;ENSP00000331643:R286M;ENSP00000439950:R283M	ENSP00000331643:R286M	R	+	2	0	PGBD2	247178263	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.270000	0.08584	-0.572000	0.06006	-0.256000	0.11100	AGG	.	.		0.537	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1			T	249211640	G	T	249211640	3	4	118	1	0	0	0	0	1	0	0	0	11790	1000	35	3	863	3	PGBD2	1	249211640	Missense_Mutation	SNP	G	TCGA-DD-A3A4-01A-11D-A22F-10	65325870	249211640	38981	4	20192										
ITGA4	3676	hgsc.bcm.edu	37	chr2	182350624	182350624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	ctagggagcagtaatgaatgCaatggaaacaaacctcgttg	11	7	0	1			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr2:182350624C>T	ENST00000397033.2	+	10	1488	c.1058C>T	c.(1057-1059)gCa>gTa	p.A353V		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	353					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	GTAATGAATGCAATGGAAACA	0.378																																					p.A353V		Atlas-SNP	.											.	ITGA4	142	.	0			c.C1058T						.						145	136	139					2																	182350624		1860	4108	5968	SO:0001583	missense	3676	exon10			TGAATGCAATGGA		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.1058C>T	chr2.hg19:g.182350624C>T	ENSP00000380227:p.Ala353Val	129.0	0.0		127.0	46.0	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	hg19	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	C	4.075	0.011769	0.07912	.	.	ENSG00000115232	ENST00000425522;ENST00000397033;ENST00000233573	T;T	0.71579	-0.58;-0.58	5.87	3.49	0.39957	.	0.046340	0.85682	D	0.000000	T	0.51346	0.1669	N	0.11364	0.135	0.38330	D	0.94376	B;B	0.24368	0.007;0.102	B;B	0.25884	0.009;0.064	T	0.44128	-0.9348	10	0.31617	T	0.26	.	13.1087	0.59261	0.7457:0.2543:0.0:0.0	.	353;353	E7EP60;P13612	.;ITA4_HUMAN	V	353	ENSP00000380227:A353V;ENSP00000233573:A353V	ENSP00000233573:A353V	A	+	2	0	ITGA4	182058869	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.294000	0.65687	0.467000	0.27218	-1.610000	0.00802	GCA	.	.		0.378	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			T	182350624	C	T	182350624	3	4	118	1	0	0	0	0	1	0	0	0	7887	710	25	3	1096	3	ITGA4	2	182350624	Missense_Mutation	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10		182350624	60848749	5	20193										
ATG16L1	55054	hgsc.bcm.edu	37	chr2	234171807	234171807	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	atggcacatggaatgacaatCagctacaagaaatggcccaa	9	9	1	2			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr2:234171807C>G	ENST00000392017.4	+	3	498	c.241C>G	c.(241-243)Cag>Gag	p.Q81E	ATG16L1_ENST00000347464.5_Intron|ATG16L1_ENST00000392020.4_Missense_Mutation_p.Q81E|ATG16L1_ENST00000373525.5_Intron|ATG16L1_ENST00000392018.1_Missense_Mutation_p.Q81E	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	81					autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		GAATGACAATCAGCTACAAGA	0.458																																					p.Q81E		Atlas-SNP	.											.	ATG16L1	83	.	0			c.C241G						.						136	102	114					2																	234171807		2203	4300	6503	SO:0001583	missense	55054	exon3			GACAATCAGCTAC	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"WD repeat domain containing"	21498	protein-coding gene	gene with protein product		610767	"APG16 autophagy 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like 1 (S. cerevisiae)"	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.241C>G	chr2.hg19:g.234171807C>G	ENSP00000375872:p.Gln81Glu	94.0	0.0		59.0	17.0	NM_017974	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Missense_Mutation	SNP	ENST00000392017.4	hg19	CCDS2503.2	.	.	.	.	.	.	.	.	.	.	C	14.23	2.473236	0.43942	.	.	ENSG00000085978	ENST00000392017;ENST00000417017;ENST00000392020;ENST00000392018	T;T;T	0.50001	0.76;0.8;0.78	5.17	4.28	0.50868	Autophagy-related protein 16 (1);	0.268520	0.30401	U	0.009713	T	0.37073	0.0990	N	0.25890	0.77	0.80722	D	1	B;B	0.29862	0.218;0.259	B;B	0.30943	0.117;0.122	T	0.17167	-1.0378	10	0.38643	T	0.18	.	15.2032	0.73157	0.1419:0.8581:0.0:0.0	.	81;81	Q676U5-2;Q676U5	.;A16L1_HUMAN	E	81	ENSP00000375872:Q81E;ENSP00000375875:Q81E;ENSP00000375873:Q81E	ENSP00000375872:Q81E	Q	+	1	0	ATG16L1	233836546	1.000000	0.71417	0.851000	0.33527	0.874000	0.50279	7.101000	0.76997	1.269000	0.44280	0.650000	0.86243	CAG	.	.		0.458	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974		G	234171807	C	G	234171807	3	3	118	1	0	0	0	0	1	0	0	0	1091	827	29	4	251	4	ATG16L1	2	234171807	Missense_Mutation	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10	51821183	234171807	9027566	6	20194										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41268766	41268766	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	gaggacctatacttacgaaaAactactgtggaccacaagca	8	10	0	0			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr3:41268766A>T	ENST00000349496.5	+	7	1284	c.1004A>T	c.(1003-1005)aAa>aTa	p.K335I	CTNNB1_ENST00000453024.1_Missense_Mutation_p.K328I|CTNNB1_ENST00000396185.3_Missense_Mutation_p.K335I|CTNNB1_ENST00000396183.3_Missense_Mutation_p.K335I|CTNNB1_ENST00000405570.1_Missense_Mutation_p.K335I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	335					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.K335I(8)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACTTACGAAAAACTACTGTGG	0.383		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.K335I	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,colon,carcinoma,-1,11	CTNNB1	4904	.	8	Substitution - Missense(8)	liver(7)|kidney(1)	c.A1004T						.						110	108	109					3																	41268766		2203	4300	6503	SO:0001583	missense	1499	exon7	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACGAAAAACTACT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1004A>T	chr3.hg19:g.41268766A>T	ENSP00000344456:p.Lys335Ile	113.0	0.0		76.0	33.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.040885	0.93685	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.82148	0.4974	M	0.89287	3.02	0.80722	D	1	D;D	0.71674	0.995;0.998	D;D	0.75484	0.97;0.986	D	0.85830	0.1391	10	0.72032	D	0.01	-3.7939	15.5934	0.76558	1.0:0.0:0.0:0.0	.	263;335	B4DSW9;P35222	.;CTNB1_HUMAN	I	335;335;335;328;335	ENSP00000385604:K335I;ENSP00000379486:K335I;ENSP00000344456:K335I;ENSP00000411226:K328I;ENSP00000379488:K335I	ENSP00000344456:K335I	K	+	2	0	CTNNB1	41243770	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	9.339000	0.96797	2.094000	0.63399	0.482000	0.46254	AAA	.	.		0.383	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41268766	A	T	41268766	3	4	118	1	0	0	0	0	1	0	0	0	4018	14	1	4	1026	4	CTNNB1	3	41268766	Missense_Mutation	SNP	A	TCGA-DD-A3A4-01A-11D-A22F-10		41268766	156753664	7	20195										
EIF2B5	8893	hgsc.bcm.edu	37	chr3	183855595	183855595	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	gagcccttgaggaacacaggTcaggatgggaaaatgacagg	15	7	1	2			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr3:183855595T>A	ENST00000273783.3	+	3	628		c.e3+2		EIF2B5_ENST00000498831.1_Splice_Site|RP11-778D9.12_ENST00000608135.1_RNA|RP11-778D9.12_ENST00000608232.1_RNA|EIF2B5_ENST00000444495.1_Splice_Site	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa						astrocyte development (GO:0014002)|astrocyte differentiation (GO:0048708)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|positive regulation of translational initiation (GO:0045948)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)|nucleus (GO:0005634)	guanyl-nucleotide exchange factor activity (GO:0005085)|translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(5)|urinary_tract(1)	27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			GGAACACAGGTCAGGATGGGA	0.483																																					.		Atlas-SNP	.											.	EIF2B5	62	.	0			c.506+2T>A						.						114	100	104					3																	183855595		2203	4300	6503	SO:0001630	splice_region_variant	8893	exon3			CACAGGTCAGGAT	U23028	CCDS3252.1	3q27.3	2006-07-18	2002-08-29		ENSG00000145191	ENSG00000145191			3261	protein-coding gene	gene with protein product		603945	"eukaryotic translation initiation factor 2B, subunit 5 (epsilon, 82kD)"			8688466	Standard	NM_003907		Approved	EIF2Bepsilon, EIF-2B	uc003fmp.3	Q13144	OTTHUMG00000156840	ENST00000273783.3:c.506+2T>A	chr3.hg19:g.183855595T>A		108.0	0.0		119.0	47.0	NM_003907	Q541Z1|Q96D04	Splice_Site	SNP	ENST00000273783.3	hg19	CCDS3252.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.584153	0.65992	.	.	ENSG00000145191	ENST00000273783;ENST00000444495	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1596	0.81693	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF2B5	185338289	1.000000	0.71417	0.995000	0.50966	0.741000	0.42261	7.948000	0.87774	2.216000	0.71823	0.533000	0.62120	.	.	.		0.483	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1		Intron	A	183855595	T	A	183855595	5	1	118	1	0	0	0	0	0	0	1	0	5006	1681	58	4	518	4	EIF2B5	3	183855595	Splice_Site	SNP	T	TCGA-DD-A3A4-01A-11D-A22F-10	142586829	183855595	14166835	8	20196										
ELOVL7	79993	hgsc.bcm.edu	37	chr5	60083199	60083199	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	tatcataaagatgcacagtcCtcgatgtaagatcactgaag	8	8	2	3			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr5:60083199C>A	ENST00000508821.1	-	3	340	c.26G>T	c.(25-27)aGg>aTg	p.R9M	ELOVL7_ENST00000425382.1_Missense_Mutation_p.R9M|ELOVL7_ENST00000505959.1_De_novo_Start_OutOfFrame|ELOVL7_ENST00000438340.1_Missense_Mutation_p.R9M	NM_024930.2	NP_079206.2	A1L3X0	ELOV7_HUMAN	ELOVL fatty acid elongase 7	9					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	9		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)				ATGCACAGTCCTCGATGTAAG	0.338																																					p.R9M		Atlas-SNP	.											.	ELOVL7	24	.	0			c.G26T						.						125	120	122					5																	60083199		2203	4300	6503	SO:0001583	missense	79993	exon2			ACAGTCCTCGATG	AK027216	CCDS34164.1	5q12	2011-05-25	2011-05-25			ENSG00000164181			26292	protein-coding gene	gene with protein product		614451	"ELOVL family member 7, elongation of long chain fatty acids (yeast)"			19826053	Standard	NM_024930		Approved	FLJ23563	uc010iwk.3	A1L3X0		ENST00000508821.1:c.26G>T	chr5.hg19:g.60083199C>A	ENSP00000424123:p.Arg9Met	73.0	0.0		54.0	28.0	NM_001104558	Q589T3|Q9H5D0|Q9NT66	Missense_Mutation	SNP	ENST00000508821.1	hg19	CCDS34164.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.635006	0.47049	.	.	ENSG00000164181	ENST00000508821;ENST00000438340;ENST00000425382;ENST00000507047;ENST00000511799	T;T;T	0.23754	1.89;1.89;1.89	5.54	5.54	0.83059	.	0.268678	0.42682	D	0.000676	T	0.19446	0.0467	L	0.38531	1.155	0.37472	D	0.915655	P	0.37038	0.579	B	0.34418	0.182	T	0.05767	-1.0865	10	0.44086	T	0.13	-13.5378	10.2701	0.43479	0.0:0.9131:0.0:0.0869	.	9	A1L3X0	ELOV7_HUMAN	M	9	ENSP00000424123:R9M;ENSP00000411255:R9M;ENSP00000402634:R9M	ENSP00000402634:R9M	R	-	2	0	ELOVL7	60118956	0.756000	0.28383	0.993000	0.49108	0.991000	0.79684	2.504000	0.45416	2.880000	0.98712	0.650000	0.86243	AGG	.	.		0.338	ELOVL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368195.1			A	60083199	C	A	60083199	3	1	118	1	0	0	0	0	1	0	0	0	5081	681	24	3	847	3	ELOVL7	5	60083199	Missense_Mutation	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10		60083199	120832061	9	20197										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79035108	79035108	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	acaaaaagagctgaaaaagtCccagattgacacatactgtt	7	8	0	4			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr5:79035108C>A	ENST00000446378.2	+	2	10551	c.10520C>A	c.(10519-10521)tCc>tAc	p.S3507Y		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3507					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CTGAAAAAGTCCCAGATTGAC	0.433																																					p.S3507Y		Atlas-SNP	.											.	CMYA5	643	.	0			c.C10520A						.						75	68	70					5																	79035108		1945	4141	6086	SO:0001583	missense	202333	exon2			AAAAGTCCCAGAT	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.10520C>A	chr5.hg19:g.79035108C>A	ENSP00000394770:p.Ser3507Tyr	51.0	0.0		96.0	38.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.447203	0.43429	.	.	ENSG00000164309	ENST00000446378	T	0.24908	1.83	6.03	6.03	0.97812	.	0.949871	0.08775	N	0.895669	T	0.46718	0.1407	L	0.46157	1.445	0.34133	D	0.665476	D	0.69078	0.997	P	0.57283	0.817	T	0.52563	-0.8559	10	0.87932	D	0	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	3507	Q8N3K9	CMYA5_HUMAN	Y	3507	ENSP00000394770:S3507Y	ENSP00000394770:S3507Y	S	+	2	0	CMYA5	79070864	0.595000	0.26857	0.942000	0.38095	0.047000	0.14425	2.171000	0.42453	2.854000	0.98071	0.655000	0.94253	TCC	.	.		0.433	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79035108	C	A	79035108	3	1	118	1	0	0	0	0	1	0	0	0	3592	855	30	3	10526	3	CMYA5	5	79035108	Missense_Mutation	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10	18951909	79035108	101880152	10	20198										
ITGB8	3696	hgsc.bcm.edu	37	chr7	20418810	20418810	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	gttggaaacgatttatctagAaaaatggcatttttctcccg	8	7	2	1			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr7:20418810A>T	ENST00000222573.4	+	4	1209	c.525A>T	c.(523-525)agA>agT	p.R175S	SNORD56_ENST00000363883.1_RNA|ITGB8_ENST00000537992.1_Missense_Mutation_p.R40S	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	175	VWFA.				cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						ATTTATCTAGAAAAATGGCAT	0.348																																					p.R175S		Atlas-SNP	.											.	ITGB8	159	.	0			c.A525T						.						95	98	97					7																	20418810		2203	4300	6503	SO:0001583	missense	3696	exon4			ATCTAGAAAAATG		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.525A>T	chr7.hg19:g.20418810A>T	ENSP00000222573:p.Arg175Ser	113.0	0.0		104.0	47.0	NM_002214	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	hg19	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.569204	0.28003	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	D;D	0.97480	-4.4;-4.4	5.82	4.48	0.54585	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.349225	0.29861	N	0.011001	D	0.90967	0.7160	N	0.11284	0.12	0.24298	N	0.995131	B;B	0.25390	0.077;0.125	B;B	0.24974	0.057;0.053	T	0.82579	-0.0387	10	0.30078	T	0.28	-16.7412	9.6296	0.39772	0.8129:0.0:0.1871:0.0	.	175;175	P26012;Q9BUG9	ITB8_HUMAN;.	S	40;175	ENSP00000441561:R40S;ENSP00000222573:R175S	ENSP00000222573:R175S	R	+	3	2	ITGB8	20385335	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.515000	0.35845	2.216000	0.71823	0.528000	0.53228	AGA	.	.		0.348	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		T	20418810	A	T	20418810	3	4	118	1	0	0	0	0	1	0	0	0	7910	243	9	4	539	4	ITGB8	7	20418810	Missense_Mutation	SNP	A	TCGA-DD-A3A4-01A-11D-A22F-10		20418810	138719853	11	20199										
GUSB	2990	hgsc.bcm.edu	37	chr7	65435332	65435332	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	ggccgggaggggtccaaggaTttggtgtgagcgatcaccat	17	8	1	1			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr7:65435332T>C	ENST00000304895.4	-	9	1543	c.1413A>G	c.(1411-1413)aaA>aaG	p.K471K	GUSB_ENST00000345660.6_Silent_p.K420K|GUSB_ENST00000421103.1_Silent_p.K325K	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	471					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						GGTCCAAGGATTTGGTGTGAG	0.572																																					p.K471K		Atlas-SNP	.											.	GUSB	52	.	0			c.A1413G						.						89	87	88					7																	65435332		2203	4300	6503	SO:0001819	synonymous_variant	2990	exon9			CAAGGATTTGGTG	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1413A>G	chr7.hg19:g.65435332T>C		31.0	0.0		34.0	13.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Silent	SNP	ENST00000304895.4	hg19	CCDS5530.1																																																																																			.	.		0.572	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		C	65435332	T	C	65435332	2	2	118	1	0	0	0	0	0	0	0	1	6911	1490	52	2		2	GUSB	7	65435332	Silent	SNP	T	TCGA-DD-A3A4-01A-11D-A22F-10	45016522	65435332	93703331	12	20200										
ZNF862	643641	hgsc.bcm.edu	37	chr7	149557718	149557719	+	Missense_Mutation	DNP	GC	GC	TA													0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	caaactcttctgctcagcctGcatagaaagacctaatctcc							TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr7:149557718_149557719GC>TA	ENST00000223210.4	+	7	1714_1715	c.1469_1470GC>TA	c.(1468-1470)tGC>tTA	p.C490L	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	490					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						TGCTCAGCCTGCATAGAAAGAC	0.45																																					p.C490F|p.C490X		Atlas-SNP	.											.	ZNF862	97	.	0			c.G1469T|c.C1470A						.																																			SO:0001583	missense	643641	exon7			CAGCCTGCATAGA|AGCCTGCATAGAA	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"Zinc fingers, C2H2-type", "-"	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	Exception_encountered	chr7.hg19:g.149557718_149557719delinsTA	ENSP00000223210:p.Cys490Leu	75.0|76.0	0.0		79.0|78.0	22.0	NM_001099220	A0AUL8	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000223210.4	hg19	CCDS47741.1																																																																																			.	.		0.45	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220		TA	149557719	GC	TA	149557718	3	4	118	1	0	0	0	0	1	0	0	0	18210	1319	46	3	1495	3	ZNF862	7	149557718	Missense_Mutation	DNP	GC	TCGA-DD-A3A4-01A-11D-A22F-10	84122386	149557718	9580945	13	20201										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2876120	2876120	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	gtggccccataaactgtcaaCgttccaatcttgttgccatt	7	12	2	0	rs374916113		TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr8:2876120C>T	ENST00000520002.1	-	53	8466	c.7911G>A	c.(7909-7911)acG>acA	p.T2637T	CSMD1_ENST00000537824.1_Silent_p.T2636T|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000602557.1_Silent_p.T2637T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2637	Sushi 17. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.T2636T(2)|p.T2365T(2)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		AAACTGTCAACGTTCCAATCT	0.453																																					p.T2636T		Atlas-SNP	.											CSMD1_ENST00000537824,colon,carcinoma,0,2	CSMD1	1469	.	4	Substitution - coding silent(4)	large_intestine(2)|prostate(2)	c.G7908A						.	C		1,3869		0,1,1934	146	142	143		7908	-4.7	0	8		143	0,8274		0,0,4137	no	coding-synonymous	CSMD1	NM_033225.5		0,1,6071	TT,TC,CC		0.0,0.0258,0.0082		2636/3565	2876120	1,12143	1935	4137	6072	SO:0001819	synonymous_variant	64478	exon52			TGTCAACGTTCCA			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.7911G>A	chr8.hg19:g.2876120C>T		76.0	0.0		71.0	25.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	C	0.142	-1.101143	0.01843	2.58E-4	0.0	ENSG00000183117	ENST00000335551	.	.	.	5.19	-4.65	0.03339	.	.	.	.	.	T	0.35248	0.0925	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39742	-0.9599	4	.	.	.	.	0.4281	0.00467	0.258:0.1481:0.2267:0.3671	.	.	.	.	I	2054	.	.	V	-	1	0	CSMD1	2863527	0.000000	0.05858	0.013000	0.15412	0.062000	0.15995	-4.050000	0.00305	-0.544000	0.06232	-0.137000	0.14449	GTT	.	.		0.453	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	2876120	C	T	2876120	2	4	118	1	0	0	0	0	0	0	0	1	3946	523	19	1		1	CSMD1	8	2876120	Silent	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10		2876120	143487902	14	20202										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52384855	52384855	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	cctgcggctcaaaagtaattCgggggctctctgcaacaaaa	10	11	2	0			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr8:52384855C>T	ENST00000356297.4	-	8	804	c.704G>A	c.(703-705)cGa>cAa	p.R235Q	PXDNL_ENST00000543296.1_Missense_Mutation_p.R235Q	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	235	Ig-like C2-type 1.				hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				AAAAGTAATTCGGGGGCTCTC	0.413																																					p.R235Q		Atlas-SNP	.											PXDNL_ENST00000356297,NS,carcinoma,0,1	PXDNL	414	.	0			c.G704A						.						96	90	92					8																	52384855		1837	4075	5912	SO:0001583	missense	137902	exon8			GTAATTCGGGGGC		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.704G>A	chr8.hg19:g.52384855C>T	ENSP00000348645:p.Arg235Gln	72.0	0.0		80.0	30.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	8.831	0.940018	0.18281	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.66815	-0.23;-0.23	3.84	2.96	0.34315	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.51975	0.1706	N	0.25332	0.735	0.24906	N	0.992072	P	0.47350	0.894	B	0.42495	0.389	T	0.30909	-0.9962	9	0.27785	T	0.31	.	9.0746	0.36513	0.0:0.8869:0.0:0.1131	.	235	A1KZ92	PXDNL_HUMAN	Q	235	ENSP00000348645:R235Q;ENSP00000444865:R235Q	ENSP00000348645:R235Q	R	-	2	0	PXDNL	52547408	0.542000	0.26426	0.060000	0.19600	0.164000	0.22412	3.613000	0.54152	0.627000	0.30340	-0.350000	0.07774	CGA	.	.		0.413	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		T	52384855	C	T	52384855	3	4	118	1	0	0	0	0	1	0	0	0	12863	884	31	1	3751	1	PXDNL	8	52384855	Missense_Mutation	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10	49508735	52384855	93979167	15	20203										
RGS22	26166	hgsc.bcm.edu	37	chr8	101054142	101054142	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	tgctttctgacatgtactttGacctaaattataaggatgag	8	6	1	3			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr8:101054142G>A	ENST00000360863.6	-	12	2020	c.1826C>T	c.(1825-1827)tCa>tTa	p.S609L	RGS22_ENST00000523287.1_Missense_Mutation_p.S428L|RGS22_ENST00000523437.1_Missense_Mutation_p.S597L	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	609					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			CATGTACTTTGACCTAAATTA	0.338																																					p.S609L		Atlas-SNP	.											.	RGS22	319	.	0			c.C1826T						.						67	61	62					8																	101054142		1851	4098	5949	SO:0001583	missense	26166	exon12			TACTTTGACCTAA	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.1826C>T	chr8.hg19:g.101054142G>A	ENSP00000354109:p.Ser609Leu	80.0	0.0		73.0	26.0	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	hg19	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	G	6.468	0.454593	0.12283	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437	T;T;T	0.32988	1.44;1.43;1.43	5.63	1.8	0.24995	.	0.853073	0.10106	N	0.715279	T	0.17789	0.0427	N	0.14661	0.345	0.27179	N	0.960714	B;B;B	0.10296	0.003;0.003;0.002	B;B;B	0.11329	0.002;0.002;0.006	T	0.26395	-1.0104	10	0.38643	T	0.18	.	7.3362	0.26611	0.3663:0.0:0.6337:0.0	.	597;609;428	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	L	609;597;428;597	ENSP00000354109:S609L;ENSP00000429382:S428L;ENSP00000428212:S597L	ENSP00000354109:S609L	S	-	2	0	RGS22	101123318	0.998000	0.40836	0.590000	0.28732	0.054000	0.15201	1.149000	0.31626	0.046000	0.15833	-0.140000	0.14226	TCA	.	.		0.338	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		A	101054142	G	A	101054142	3	1	118	1	0	0	0	0	1	0	0	0	13320	1294	45	3	2032	3	RGS22	8	101054142	Missense_Mutation	SNP	G	TCGA-DD-A3A4-01A-11D-A22F-10	48669287	101054142	45309880	16	20204										
PSIP1	11168	hgsc.bcm.edu	37	chr9	15506558	15506558	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	tttaaagctaacaggacttaCgtctcatgagttccaaaaaa	6	8	1	1			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr9:15506558C>A	ENST00000380733.4	-	3	493		c.e3+1		PSIP1_ENST00000484265.1_5'UTR|PSIP1_ENST00000397519.2_Splice_Site|PSIP1_ENST00000380738.4_Splice_Site|PSIP1_ENST00000380716.4_Splice_Site|PSIP1_ENST00000380715.1_Splice_Site			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1						establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		ACAGGACTTACGTCTCATGAG	0.373																																					.		Atlas-SNP	.											.	PSIP1	93	.	0			c.149+1G>T						.						92	99	97					9																	15506558		2203	4300	6503	SO:0001630	splice_region_variant	11168	exon4			GACTTACGTCTCA	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"PC4 and SFRS1 interacting protein 2"	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.149+1G>T	chr9.hg19:g.15506558C>A		47.0	0.0		58.0	14.0	NM_001128217	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Splice_Site	SNP	ENST00000380733.4	hg19	CCDS6479.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.102754	0.76983	.	.	ENSG00000164985	ENST00000380733;ENST00000380738;ENST00000380715;ENST00000380716;ENST00000397519	.	.	.	5.88	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.841	0.63439	0.0:0.9257:0.0:0.0743	.	.	.	.	.	-1	.	.	.	-	.	.	PSIP1	15496558	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.718000	0.74713	1.483000	0.48342	0.655000	0.94253	.	.	.		0.373	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222	Intron	A	15506558	C	A	15506558	5	1	118	1	0	0	0	0	0	0	1	0	12675	550	19	1	1527	1	PSIP1	9	15506558	Splice_Site	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10		15506558	125706873	17	20205										
H2AFY2	55506	hgsc.bcm.edu	37	chr10	71835423	71835423	+	Frame_Shift_Del	DEL	C	C	-													0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	aactgaagcaagatgtcgggCcggagtgggaagaagaaaat							TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr10:71835423delC	ENST00000373255.4	+	2	273	c.9delC	c.(7-9)ggcfs	p.G3fs		NM_018649.2	NP_061119.1	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2	3	Histone H2A.				brain development (GO:0007420)|chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(4)|skin(1)	15						AGATGTCGGGCCGGAGTGGGA	0.522																																					p.G3fs		Atlas-Indel,Pindel	.											.	H2AFY2	30	.	0			c.8delG						.						189	160	170					10																	71835423		2203	4300	6503	SO:0001589	frameshift_variant	55506	exon2			.	AF336304	CCDS7296.1	10q22.1	2011-01-27			ENSG00000099284	ENSG00000099284		"Histones / Replication-independent"	14453	protein-coding gene	gene with protein product						11331621, 11262398	Standard	NM_018649		Approved	macroH2A2	uc001jqm.3	Q9P0M6	OTTHUMG00000018396	ENST00000373255.4:c.9delC	chr10.hg19:g.71835423delC	ENSP00000362352:p.Gly3fs	119.0	0.0		88.0	22.0	NM_018649	Q5SQT2	Frame_Shift_Del	DEL	ENST00000373255.4	hg19	CCDS7296.1																																																																																			.	.		0.522	H2AFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048480.2	NM_018649		-	71835423	C	-	71835423	7	5	118	1	0	1	0	1	0	0	0	0	6939	726	26	0	11	0	H2AFY2	10	71835423	Frame_Shift_Del	DEL	C	TCGA-DD-A3A4-01A-11D-A22F-10		71835423	63699324	18	20206										
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72301249	72301249	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	aggtgggtgaggaggagctcGtgagtgtgcctgatgccaag	19	6	0	3			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr10:72301249G>A	ENST00000263563.6	+	17	2348	c.2080G>A	c.(2080-2082)Gtg>Atg	p.V694M		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	694						cytosol (GO:0005829)											GGAGGAGCTCGTGAGTGTGCC	0.627																																					p.V694M		Atlas-SNP	.											.	.	.	.	0			c.G2080A						.						95	77	83					10																	72301249		2203	4300	6503	SO:0001583	missense	27143	exon17			GAGCTCGTGAGTG	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"paladin", "KIAA1274"	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.2080G>A	chr10.hg19:g.72301249G>A	ENSP00000263563:p.Val694Met	50.0	0.0		65.0	20.0	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	hg19	CCDS31215.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.18|18.18	3.566845|3.566845	0.65651|0.65651	.|.	.|.	ENSG00000107719|ENSG00000107719	ENST00000426268|ENST00000263563	.|T	.|0.25749	.|1.78	3.62|3.62	3.62|3.62	0.41486|0.41486	.|.	.|0.221763	.|0.37261	.|U	.|0.002178	T|T	0.36524|0.36524	0.0970|0.0970	M|M	0.74881|0.74881	2.28|2.28	0.58432|0.58432	D|D	0.999997|0.999997	.|D	.|0.54772	.|0.968	.|P	.|0.46885	.|0.53	T|T	0.48258|0.48258	-0.9051|-0.9051	5|10	.|0.59425	.|D	.|0.04	-7.9365|-7.9365	15.1824|15.1824	0.72968|0.72968	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|694	.|Q9ULE6	.|PALD_HUMAN	H|M	74|694	.|ENSP00000263563:V694M	.|ENSP00000263563:V694M	R|V	+|+	2|1	0|0	KIAA1274|KIAA1274	71971255|71971255	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.810000|0.810000	0.45777|0.45777	7.530000|7.530000	0.81962|0.81962	1.890000|1.890000	0.54733|0.54733	0.430000|0.430000	0.28490|0.28490	CGT|GTG	.	.		0.627	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		A	72301249	G	A	72301249	3	1	118	1	0	0	0	0	1	0	0	0	8229	1145	40	1	2142	1	KIAA1274	10	72301249	Missense_Mutation	SNP	G	TCGA-DD-A3A4-01A-11D-A22F-10	465826	72301249	63233498	19	20207										
GPAM	57678	hgsc.bcm.edu	37	chr10	113913361	113913364	+	Frame_Shift_Del	DEL	GAGG	GAGG	-													0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	aagtttttgtcggttgcattGaggtagaaaagtgctgctca							TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	GAGG	GAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr10:113913361_113913364delGAGG	ENST00000348367.4	-	22	2628_2631	c.2431_2434delCCTC	c.(2431-2436)cctcaafs	p.PQ811fs	GPAM_ENST00000423155.1_Frame_Shift_Del_p.PQ811fs			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	811					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		CGGTTGCATTGAGGTAGAAAAGTG	0.373																																					p.811_812del	Ovarian(161;1017 2606 18293 52943)	Atlas-Indel,Pindel	.											.	GPAM	68	.	0			c.2432_2435del						.																																			SO:0001589	frameshift_variant	57678	exon22			.	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"glycerol-3-phosphate acyltransferase 1, mitochondrial"	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.2431_2434delCCTC	chr10.hg19:g.113913361_113913364delGAGG	ENSP00000265276:p.Pro811fs	68.0	0.0		58.0	21.0	NM_020918	Q5VW51|Q86TA3	Frame_Shift_Del	DEL	ENST00000348367.4	hg19	CCDS7570.1																																																																																			.	.		0.373	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		-	113913364	GAGG	-	113913361	7	5	118	1	0	1	0	1	0	0	0	0	6596	1299	45	0	56	0	GPAM	10	113913361	Frame_Shift_Del	DEL	GAGG	TCGA-DD-A3A4-01A-11D-A22F-10	41612112	113913361	21621386	20	20208										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000557334.1_Missense_Mutation_p.G13D|KRAS_ENST00000311936.3_Missense_Mutation_p.G13D|KRAS_ENST00000556131.1_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CTTGCCTACGCCACCAGCTCC	0.338	G13D(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G13D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	KRAS_ENST00000256078,NS,carcinoma,0,2	KRAS	30930	.	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	c.G38A						.						88	78	82					12																	25398281		2203	4300	6503	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	CCTACGCCACCAG	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	chr12.hg19:g.25398281C>T	ENSP00000256078:p.Gly13Asp	190.0	0.0		138.0	65.0	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC	.	.		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	118	1	0	0	0	0	1	0	0	0	8447	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10		25398281	108453614	21	20209										
DTX3	196403	hgsc.bcm.edu	37	chr12	58001190	58001190	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	agacattggagaagtgccggCattcattctgcgagggctgc	14	9	2	2			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr12:58001190C>T	ENST00000548198.1	+	3	2048	c.544C>T	c.(544-546)Cat>Tat	p.H182Y	DTX3_ENST00000548804.1_Missense_Mutation_p.H182Y|DTX3_ENST00000337737.3_Missense_Mutation_p.H182Y|DTX3_ENST00000551632.1_Missense_Mutation_p.H185Y|ARHGEF25_ENST00000333972.7_5'Flank			Q8N9I9	DTX3_HUMAN	deltex 3, E3 ubiquitin ligase	182					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(6)|urinary_tract(1)	12	Melanoma(17;0.122)					GAAGTGCCGGCATTCATTCTG	0.617																																					p.H182Y		Atlas-SNP	.											.	DTX3	27	.	0			c.C544T						.						23	25	25					12																	58001190		1917	4111	6028	SO:0001583	missense	196403	exon5			TGCCGGCATTCAT	AK094385	CCDS41800.1, CCDS66410.1	12q13.2	2014-01-28	2014-01-28			ENSG00000178498		"RING-type (C3HC4) zinc fingers"	24457	protein-coding gene	gene with protein product		613142	"deltex 3 homolog (Drosophila)", "deltex homolog 3 (Drosophila)"			12670957	Standard	XM_005268697		Approved	FLJ34766, RNF154	uc001sow.1	Q8N9I9		ENST00000548198.1:c.544C>T	chr12.hg19:g.58001190C>T	ENSP00000447873:p.His182Tyr	89.0	0.0		85.0	35.0	NM_178502	Q53ZZ2|Q8NAU6|Q8NDS8	Missense_Mutation	SNP	ENST00000548198.1	hg19	CCDS41800.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.602260	0.87055	.	.	ENSG00000178498	ENST00000548804;ENST00000549583;ENST00000337737;ENST00000548198;ENST00000551632;ENST00000548478	D;D;D;D;D;D	0.98012	-4.66;-4.66;-4.66;-4.66;-4.66;-4.66	4.41	4.41	0.53225	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type, conserved site (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.98960	0.9646	H	0.96333	3.805	0.80722	D	1	P	0.51240	0.943	P	0.60415	0.874	D	0.99353	1.0915	10	0.72032	D	0.01	-10.3154	14.9011	0.70681	0.0:1.0:0.0:0.0	.	182	Q8N9I9	DTX3_HUMAN	Y	182;185;182;182;185;175	ENSP00000449294:H182Y;ENSP00000449688:H185Y;ENSP00000338050:H182Y;ENSP00000447873:H182Y;ENSP00000448696:H185Y;ENSP00000448224:H175Y	ENSP00000338050:H182Y	H	+	1	0	DTX3	56287457	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.640000	0.67875	2.189000	0.69895	0.549000	0.68633	CAT	.	.		0.617	DTX3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407848.1	NM_178502		T	58001190	C	T	58001190	3	4	118	1	0	0	0	0	1	0	0	0	4797	710	25	3	550	3	DTX3	12	58001190	Missense_Mutation	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10	32602909	58001190	75850705	22	20210										
CUX2	23316	hgsc.bcm.edu	37	chr12	111746258	111746258	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	ccaagcctgaagactcactgCttattgcaaaggaggccttc	9	12	1	2			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr12:111746258C>A	ENST00000261726.6	+	14	1340	c.1186C>A	c.(1186-1188)Ctt>Att	p.L396I		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	396					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						AGACTCACTGCTTATTGCAAA	0.617																																					p.L396I		Atlas-SNP	.											.	CUX2	145	.	0			c.C1186A						.						46	46	46					12																	111746258		1985	4169	6154	SO:0001583	missense	23316	exon14			TCACTGCTTATTG	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.1186C>A	chr12.hg19:g.111746258C>A	ENSP00000261726:p.Leu396Ile	103.0	0.0		88.0	41.0	NM_015267	A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	hg19	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.479041	0.63849	.	.	ENSG00000111249	ENST00000261726	T	0.60797	0.16	5.04	4.05	0.47172	.	0.070259	0.64402	D	0.000015	T	0.51329	0.1668	M	0.69358	2.11	0.41703	D	0.989411	P	0.39424	0.673	B	0.35813	0.211	T	0.59663	-0.7412	10	0.66056	D	0.02	-26.8714	8.6614	0.34095	0.1636:0.748:0.0:0.0884	.	396	O14529	CUX2_HUMAN	I	396	ENSP00000261726:L396I	ENSP00000261726:L396I	L	+	1	0	CUX2	110230641	1.000000	0.71417	0.711000	0.30485	0.972000	0.66771	1.831000	0.39141	2.344000	0.79699	0.313000	0.20887	CTT	.	.		0.617	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		A	111746258	C	A	111746258	3	1	118	1	0	0	0	0	1	0	0	0	4067	797	28	3	1240	3	CUX2	12	111746258	Missense_Mutation	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10	53745068	111746258	22105637	23	20211										
ZSCAN29	146050	hgsc.bcm.edu	37	chr15	43656356	43656356	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	ctcttcaaagaagggacaggTctctggtgcctggccattct	11	11	4	1			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr15:43656356T>G	ENST00000396976.2	-	4	1581	c.1447A>C	c.(1447-1449)Acc>Ccc	p.T483P	ZSCAN29_ENST00000396972.1_Intron|ZSCAN29_ENST00000568898.1_Intron|ZSCAN29_ENST00000562072.1_Missense_Mutation_p.T482P	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	483					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		AAGGGACAGGTCTCTGGTGCC	0.527																																					p.T483P		Atlas-SNP	.											.	ZSCAN29	57	.	0			c.A1447C						.						95	91	92					15																	43656356		2201	4299	6500	SO:0001583	missense	146050	exon4			GACAGGTCTCTGG	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"-", "Zinc fingers, C2H2-type"	26673	protein-coding gene	gene with protein product			"zinc finger protein 690"	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.1447A>C	chr15.hg19:g.43656356T>G	ENSP00000380174:p.Thr483Pro	63.0	0.0		78.0	28.0	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Missense_Mutation	SNP	ENST00000396976.2	hg19	CCDS10095.2	.	.	.	.	.	.	.	.	.	.	T	12.64	1.999581	0.35320	.	.	ENSG00000140265	ENST00000396976	T	0.44881	0.91	5.22	4.07	0.47477	.	0.083032	0.52532	D	0.000069	T	0.39517	0.1081	N	0.05259	-0.085	0.80722	D	1	B;D	0.89917	0.209;1.0	B;D	0.87578	0.161;0.998	T	0.36817	-0.9732	10	0.41790	T	0.15	-6.2437	9.5918	0.39550	0.1567:0.0:0.0:0.8433	.	482;483	C9K0J8;Q8IWY8	.;ZSC29_HUMAN	P	483	ENSP00000380174:T483P	ENSP00000380174:T483P	T	-	1	0	ZSCAN29	41443648	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.479000	0.35453	0.964000	0.38108	0.533000	0.62120	ACC	.	.		0.527	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455		G	43656356	T	G	43656356	3	3	118	1	0	0	0	0	1	0	0	0	18251	1667	58	5	1119	5	ZSCAN29	15	43656356	Missense_Mutation	SNP	T	TCGA-DD-A3A4-01A-11D-A22F-10		43656356	58875036	24	20212										
ST8SIA2	8128	hgsc.bcm.edu	37	chr15	92988127	92988127	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	gtcaacgtgcgcactgcataCccctcgctgcgcctgctgca	10	17	1	0			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr15:92988127C>T	ENST00000268164.3	+	5	1047	c.810C>T	c.(808-810)taC>taT	p.Y270Y	ST8SIA2_ENST00000539113.1_Silent_p.Y249Y	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	270					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			GCACTGCATACCCCTCGCTGC	0.622																																					p.Y270Y		Atlas-SNP	.											.	ST8SIA2	41	.	0			c.C810T						.						94	79	84					15																	92988127		2198	4298	6496	SO:0001819	synonymous_variant	8128	exon5			TGCATACCCCTCG	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.810C>T	chr15.hg19:g.92988127C>T		43.0	0.0		41.0	19.0	NM_006011	Q4VAZ0|Q92470|Q92746	Silent	SNP	ENST00000268164.3	hg19	CCDS10372.1																																																																																			.	.		0.622	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		T	92988127	C	T	92988127	2	4	118	1	0	0	0	0	0	0	0	1	15247	518	18	3		3	ST8SIA2	15	92988127	Silent	SNP	C	TCGA-DD-A3A4-01A-11D-A22F-10	49331771	92988127	9543265	25	20213										
PHKB	5257	hgsc.bcm.edu	37	chr16	47630379	47630379	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	aaaaacgatttcctagcaacTgtggccgtgatggaaaactg	10	8	0	1			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr16:47630379T>A	ENST00000323584.5	+	13	1324	c.1300T>A	c.(1300-1302)Tgt>Agt	p.C434S	PHKB_ENST00000455779.1_Missense_Mutation_p.C427S|PHKB_ENST00000566044.1_Missense_Mutation_p.C427S|PHKB_ENST00000299167.8_Missense_Mutation_p.C434S	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	434					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				TCCTAGCAACTGTGGCCGTGA	0.388																																					p.C434S		Atlas-SNP	.											.	PHKB	298	.	0			c.T1300A						.						161	164	163					16																	47630379		2201	4300	6501	SO:0001583	missense	5257	exon13			AGCAACTGTGGCC		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.1300T>A	chr16.hg19:g.47630379T>A	ENSP00000313504:p.Cys434Ser	175.0	0.0		168.0	44.0	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	T	7.124	0.578535	0.13686	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.92805	-3.11;-3.11	5.73	4.62	0.57501	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.199255	0.56097	N	0.000035	T	0.72342	0.3448	N	0.01352	-0.895	0.39703	D	0.971213	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.65393	-0.6179	10	0.06494	T	0.89	-14.1591	5.8768	0.18834	0.2753:0.0717:0.0:0.653	.	434;427	Q93100;Q93100-4	KPBB_HUMAN;.	S	427;427;434	ENSP00000414345:C427S;ENSP00000313504:C434S	ENSP00000299167:C427S	C	+	1	0	PHKB	46187880	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.558000	0.36309	0.969000	0.38237	0.533000	0.62120	TGT	.	.		0.388	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			A	47630379	T	A	47630379	3	1	118	1	0	0	0	0	1	0	0	0	11854	1580	55	4	1409	4	PHKB	16	47630379	Missense_Mutation	SNP	T	TCGA-DD-A3A4-01A-11D-A22F-10		47630379	42724374	26	20214										
TMEM132E	124842	hgsc.bcm.edu	37	chr17	32959873	32959873	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	ccttgcacattgagctctcaGatgcccgcctcagccaagtg	9	15	2	2			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr17:32959873G>C	ENST00000321639.5	+	7	1691	c.1363G>C	c.(1363-1365)Gat>Cat	p.D455H		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	455						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TGAGCTCTCAGATGCCCGCCT	0.602																																					p.D455H		Atlas-SNP	.											.	TMEM132E	122	.	0			c.G1363C						.						147	136	140					17																	32959873		2203	4300	6503	SO:0001583	missense	124842	exon7			CTCTCAGATGCCC	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1363G>C	chr17.hg19:g.32959873G>C	ENSP00000316532:p.Asp455His	43.0	0.0		64.0	14.0	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	hg19	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.261448	0.80358	.	.	ENSG00000181291	ENST00000321639	T	0.26660	1.72	4.71	3.75	0.43078	.	0.148429	0.64402	D	0.000019	T	0.45875	0.1364	M	0.86502	2.82	0.80722	D	1	P	0.45126	0.851	P	0.51355	0.667	T	0.54609	-0.8268	10	0.87932	D	0	-16.6363	11.8049	0.52150	0.0841:0.0:0.9159:0.0	.	455	Q6IEE7	T132E_HUMAN	H	455	ENSP00000316532:D455H	ENSP00000316532:D455H	D	+	1	0	TMEM132E	29983986	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.823000	0.86660	1.211000	0.43351	0.551000	0.68910	GAT	.	.		0.602	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		C	32959873	G	C	32959873	3	2	118	1	0	0	0	0	1	0	0	0	16063	942	33	4	1389	4	TMEM132E	17	32959873	Missense_Mutation	SNP	G	TCGA-DD-A3A4-01A-11D-A22F-10		32959873	48235337	27	20215										
KIAA1468	57614	hgsc.bcm.edu	37	chr18	59947916	59947948	+	Splice_Site	DEL	ATTATGGAAACAGTAATTCAAAGAGAGGTAGGA	ATTATGGAAACAGTAATTCAAAGAGAGGTAGGA	-													0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	caattccagcctttggcactAttatggaaacagtaattcaa							TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	ATTATGGAAACAGTAATTCAAAGAGAGGTAGGA	ATTATGGAAACAGTAATTCAAAGAGAGGTAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr18:59947916_59947948delATTATGGAAACAGTAATTCAAAGAGAGGTAGGA	ENST00000398130.2	+	24	3320_3346	c.3088_3114delATTATGGAAACAGTAATTCAAAGAGAGGTAGGA	c.(3088-3114)attatggaaacagtaattcaaagagagdel	p.IMETVIQRE1030del	KIAA1468_ENST00000256858.6_Splice_Site_p.IMETVIQRE1064del	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	1030										autonomic_ganglia(1)|breast(4)|endometrium(4)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47		Colorectal(73;0.186)				CTTTGGCACTATTATGGAAACAGTAATTCAAAGAGAGGTAGGAATAATTGAAA	0.356																																					p.1029_1038del		Atlas-Indel,Pindel	.											.	KIAA1468	93	.	0			c.3087_3114del						.																																			SO:0001630	splice_region_variant	57614	exon24			.	BC011992	CCDS11979.2	18q21.33	2005-11-03			ENSG00000134444	ENSG00000134444			29289	protein-coding gene	gene with protein product						11973628	Standard	NM_020854		Approved	HsT885, HsT3308, FLJ33841	uc002lil.3	Q9P260	OTTHUMG00000132780	ENST00000398130.2:c.3114+1ATTATGGAAACAGTAATTCAAAGAGAGGTAGGA>-	chr18.hg19:g.59947916_59947948delATTATGGAAACAGTAATTCAAAGAGAGGTAGGA		87.0	0.0		71.0	19.0	NM_020854		Frame_Shift_Del	DEL	ENST00000398130.2	hg19	CCDS11979.2																																																																																			.	.		0.356	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854	In_Frame_Del	-	59947948	ATTATGGAAACAGTAATTCAAAGAGAGGTAGGA	-	59947916	8	5	118	1	0	1	0	1	0	0	1	0	8245	449	16	0	3182	0	KIAA1468	18	59947916	Splice_Site	DEL	ATTATGGAAACAGTAATTCAAAGAGAGGTAGGA	TCGA-DD-A3A4-01A-11D-A22F-10		59947916	18129332	28	20216										
ZNF415	55786	hgsc.bcm.edu	37	chr19	53612315	53612315	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	tgccacactctttacatgtgTaaggtttctctccaatatga	6	10	2	1			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr19:53612315T>A	ENST00000500065.4	-	4	1316	c.983A>T	c.(982-984)tAc>tTc	p.Y328F	ZNF415_ENST00000601493.1_Missense_Mutation_p.Y98F|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000421033.1_Missense_Mutation_p.Y340F|ZNF415_ENST00000440291.1_Missense_Mutation_p.Y315F|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.Y376F|ZNF415_ENST00000455735.2_Missense_Mutation_p.Y376F|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000243643.4_Missense_Mutation_p.Y328F	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	376					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		TTTACATGTGTAAGGTTTCTC	0.393																																					p.Y328F		Atlas-SNP	.											.	ZNF415	68	.	0			c.A983T						.						82	76	78					19																	53612315		2203	4300	6503	SO:0001583	missense	55786	exon4			CATGTGTAAGGTT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.983A>T	chr19.hg19:g.53612315T>A	ENSP00000439435:p.Tyr328Phe	79.0	0.0		54.0	19.0	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	hg19	CCDS54313.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.256052	0.39896	.	.	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22	2.78	2.78	0.32641	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15089	0.0364	N	0.02830	-0.485	0.09310	N	1	B;B;B;B;B;P	0.50710	0.131;0.261;0.044;0.005;0.131;0.938	B;P;B;B;B;D	0.64595	0.069;0.641;0.049;0.014;0.069;0.927	T	0.10823	-1.0613	9	0.59425	D	0.04	.	6.2652	0.20922	0.2231:0.0:0.0:0.7769	.	328;376;376;328;315;340	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	F	328;328;376;340;376;315	ENSP00000243643:Y328F;ENSP00000439435:Y328F;ENSP00000396492:Y376F;ENSP00000395055:Y340F;ENSP00000388787:Y376F;ENSP00000414601:Y315F	ENSP00000243643:Y328F	Y	-	2	0	ZNF415	58304127	0.000000	0.05858	0.017000	0.16124	0.118000	0.20060	0.167000	0.16602	1.286000	0.44565	0.402000	0.26972	TAC	.	.		0.393	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		A	53612315	T	A	53612315	3	1	118	1	0	0	0	0	1	0	0	0	17907	1638	57	4	688	4	ZNF415	19	53612315	Missense_Mutation	SNP	T	TCGA-DD-A3A4-01A-11D-A22F-10		53612315	5516668	29	20217										
TCF20	6942	hgsc.bcm.edu	37	chr22	42608580	42608580	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	ccatggacaccaaaccaccaGgaagaatgaccgactgactt	8	13	0	3			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chr22:42608580G>C	ENST00000359486.3	-	1	2868	c.2732C>G	c.(2731-2733)cCt>cGt	p.P911R	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Missense_Mutation_p.P911R	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	911					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						CAAACCACCAGGAAGAATGAC	0.488																																					p.P911R		Atlas-SNP	.											.	TCF20	164	.	0			c.C2732G						.						54	51	52					22																	42608580		2203	4300	6503	SO:0001583	missense	6942	exon1			CCACCAGGAAGAA	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.2732C>G	chr22.hg19:g.42608580G>C	ENSP00000352463:p.Pro911Arg	143.0	0.0		160.0	62.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.578016	0.45902	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.62232	0.05;0.04	5.36	5.36	0.76844	.	0.080565	0.52532	D	0.000062	T	0.70168	0.3193	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.73930	-0.3827	10	0.87932	D	0	-9.6423	19.2789	0.94044	0.0:0.0:1.0:0.0	.	911;911	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	R	911	ENSP00000352463:P911R;ENSP00000335561:P911R	ENSP00000335561:P911R	P	-	2	0	TCF20	40938524	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.355000	0.66046	2.774000	0.95407	0.655000	0.94253	CCT	.	.		0.488	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		C	42608580	G	C	42608580	3	2	118	1	0	0	0	0	1	0	0	0	15705	1000	35	4	3188	4	TCF20	22	42608580	Missense_Mutation	SNP	G	TCGA-DD-A3A4-01A-11D-A22F-10		42608580	8695986	30	20218										
PHF8	23133	hgsc.bcm.edu	37	chrX	54044138	54044138	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	3	1	1.97090909090909	4.81777777777778	0.903333333333333	1	1	0	cagtgaatgatggcgagggcAgcgtcatgcccaacccatcc	12	13	1	2			TCGA-DD-A3A4-01A-11D-A22F-10	TCGA-DD-A3A4-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f5d3f616-5fb1-47a0-9c01-f2fb90568df4	1a2c1ffc-b1b7-48a0-a94a-ecd67bdfe211	g.chrX:54044138A>C	ENST00000357988.5	-	5	876	c.518T>G	c.(517-519)cTg>cGg	p.L173R	PHF8_ENST00000322659.8_Missense_Mutation_p.L137R|PHF8_ENST00000338946.6_Missense_Mutation_p.L137R|PHF8_ENST00000338154.6_Missense_Mutation_p.L137R	NM_001184896.1	NP_001171825.1	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	173					brain development (GO:0007420)|G1/S transition of mitotic cell cycle (GO:0000082)|histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of chromatin silencing at rDNA (GO:0061188)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	40						TGGCGAGGGCAGCGTCATGCC	0.473																																					p.L173R		Atlas-SNP	.											.	PHF8	198	.	0			c.T518G						.						156	105	123					X																	54044138		2203	4300	6503	SO:0001583	missense	23133	exon5			GAGGGCAGCGTCA	AB029034	CCDS14355.1, CCDS55418.1, CCDS55419.1, CCDS55420.1	Xp11.22	2013-01-28			ENSG00000172943	ENSG00000172943		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	20672	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1F"	300560				10470851, 20023638, 20644565	Standard	NM_015107		Approved	ZNF422, KIAA1111, JHDM1F	uc004dsu.3	Q9UPP1	OTTHUMG00000021622	ENST00000357988.5:c.518T>G	chrX.hg19:g.54044138A>C	ENSP00000350676:p.Leu173Arg	63.0	0.0		57.0	42.0	NM_001184896	B3KMV4|B7Z911|Q5H9U5|Q5JPR9|Q5JPS0|Q5JPS2|Q5JPS3|Q5VUJ4|Q7Z6D4|Q9HAH2	Missense_Mutation	SNP	ENST00000357988.5	hg19	CCDS55420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.9|25.9	4.688422|4.688422	0.88639|0.88639	.|.	.|.	ENSG00000172943|ENSG00000172943	ENST00000396282|ENST00000357988;ENST00000338154;ENST00000338946;ENST00000396277;ENST00000322659	.|T;T;T;T	.|0.71579	.|-0.58;-0.58;-0.58;-0.58	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.85327|0.85327	0.5671|0.5671	M|M	0.86651|0.86651	2.83|2.83	0.52501|0.52501	D|D	0.999959|0.999959	.|D;D;D	.|0.71674	.|0.997;0.998;0.998	.|P;D;D	.|0.69307	.|0.83;0.918;0.963	D|D	0.87928|0.87928	0.2708|0.2708	5|10	.|0.87932	.|D	.|0	-8.7688|-8.7688	14.2623|14.2623	0.66092|0.66092	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|137;173;173	.|B7Z911;Q9UPP1-3;Q9UPP1	.|.;.;PHF8_HUMAN	G|R	41|173;137;137;167;137	.|ENSP00000350676:L173R;ENSP00000338868:L137R;ENSP00000340051:L137R;ENSP00000319473:L137R	.|ENSP00000319473:L137R	C|L	-|-	1|2	0|0	PHF8|PHF8	54060863|54060863	0.973000|0.973000	0.33851|0.33851	0.426000|0.426000	0.26672|0.26672	0.992000|0.992000	0.81027|0.81027	9.195000|9.195000	0.94971|0.94971	2.014000|2.014000	0.59158|0.59158	0.486000|0.486000	0.48141|0.48141	TGC|CTG	.	.		0.473	PHF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056784.2	NM_015107		C	54044138	A	C	54044138	3	2	118	1	0	0	0	0	1	0	0	0	11849	188	7	5	2906	5	PHF8	23	54044138	Missense_Mutation	SNP	A	TCGA-DD-A3A4-01A-11D-A22F-10		54044138	101226422	31	20219										
RSC1A1	6248	hgsc.bcm.edu	37	chr1	15986764	15986764	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	aagacaggaagctagtttatCtgtcacatctactaggatgc	9	8	3	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr1:15986764C>A	ENST00000345034.1	+	1	401	c.401C>A	c.(400-402)tCt>tAt	p.S134Y	DDI2_ENST00000480945.1_3'UTR	NM_006511.1	NP_006502.1	Q92681	RSCA1_HUMAN	regulatory solute carrier protein, family 1, member 1	134					intestinal absorption (GO:0050892)|negative regulation of transport (GO:0051051)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	brush border (GO:0005903)|cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel inhibitor activity (GO:0008200)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)	11		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00276)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCTAGTTTATCTGTCACATCT	0.438																																					p.S134Y		Atlas-SNP	.											.	RSC1A1	29	.	0			c.C401A						.						99	97	98					1																	15986764		2203	4300	6503	SO:0001583	missense	6248	exon1			GTTTATCTGTCAC	BN000122, X82877	CCDS161.1	1p36.1	1998-08-25			ENSG00000215695	ENSG00000215695			10458	protein-coding gene	gene with protein product		601966					Standard	NM_006511		Approved	RS1	uc010obn.2	Q92681	OTTHUMG00000067830	ENST00000345034.1:c.401C>A	chr1.hg19:g.15986764C>A	ENSP00000341963:p.Ser134Tyr	128.0	0.0		134.0	65.0	NM_006511	B2RBP5	Missense_Mutation	SNP	ENST00000345034.1	hg19	CCDS161.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631392	0.46944	.	.	ENSG00000215695	ENST00000345034	T	0.48522	0.81	5.46	4.55	0.56014	.	0.460861	0.18123	N	0.150989	T	0.51890	0.1701	L	0.29908	0.895	0.09310	N	1	D	0.89917	1.0	D	0.70935	0.971	T	0.39210	-0.9625	10	0.66056	D	0.02	-13.1966	6.9359	0.24466	0.1728:0.7392:0.0:0.088	.	134	Q92681	RSCA1_HUMAN	Y	134	ENSP00000341963:S134Y	ENSP00000341963:S134Y	S	+	2	0	RSC1A1	15859351	0.305000	0.24481	0.067000	0.19924	0.965000	0.64279	1.199000	0.32235	1.302000	0.44855	0.561000	0.74099	TCT	.	.		0.438	RSC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145500.1	NM_006511		A	15986764	C	A	15986764	3	1	119	1	0	0	0	0	1	0	0	0	13713	913	32	3	403	3	RSC1A1	1	15986764	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10		15986764	233263857	1	20220										
FGGY	55277	hgsc.bcm.edu	37	chr1	60223627	60223627	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	caatggcaaaaatgagcaaaGttgggaaagttgtgttcccg	12	6	0	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr1:60223627G>T	ENST00000303721.7	+	15	1711	c.1537G>T	c.(1537-1539)Gtt>Ttt	p.V513F	FGGY_ENST00000371210.1_Missense_Mutation_p.V214F|FGGY_ENST00000371212.1_Missense_Mutation_p.V425F|FGGY_ENST00000371218.4_Missense_Mutation_p.V537F|RP4-782L23.2_ENST00000443012.1_RNA	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	513					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					AATGAGCAAAGTTGGGAAAGT	0.393																																					p.V537F		Atlas-SNP	.											.	FGGY	99	.	0			c.G1609T						.						118	112	114					1																	60223627		2203	4300	6503	SO:0001583	missense	55277	exon16			AGCAAAGTTGGGA		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.1537G>T	chr1.hg19:g.60223627G>T	ENSP00000305922:p.Val513Phe	61.0	0.0		71.0	27.0	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Missense_Mutation	SNP	ENST00000303721.7	hg19	CCDS611.2	.	.	.	.	.	.	.	.	.	.	G	15.50	2.853128	0.51270	.	.	ENSG00000172456	ENST00000371218;ENST00000303721;ENST00000371212;ENST00000371210	D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7	5.3	5.3	0.74995	.	0.150542	0.44688	D	0.000437	D	0.90947	0.7154	M	0.76002	2.32	0.50632	D	0.999889	P;P;P	0.40909	0.565;0.732;0.585	P;B;B	0.45946	0.498;0.321;0.187	D	0.89622	0.3849	9	.	.	.	-8.0943	9.8208	0.40880	0.0905:0.0:0.9095:0.0	.	537;425;513	Q96C11-3;B1AK94;Q96C11	.;.;FGGY_HUMAN	F	537;513;425;214	ENSP00000360262:V537F;ENSP00000305922:V513F;ENSP00000360256:V425F;ENSP00000360254:V214F	.	V	+	1	0	FGGY	59996215	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.884000	0.39668	2.756000	0.94617	0.563000	0.77884	GTT	.	.		0.393	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411		T	60223627	G	T	60223627	3	4	119	1	0	0	0	0	1	0	0	0	5879	1029	36	3	1667	3	FGGY	1	60223627	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	44236863	60223627	189026994	2	20221										
GNG12	55970	hgsc.bcm.edu	37	chr1	68171260	68171260	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	tccgctgatgccttcgaaacCtgacatggagataaatcaaa	8	10	1	3			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr1:68171260C>G	ENST00000370982.3	-	4	293		c.e4-1			NM_018841.5	NP_061329.3	Q9UBI6	GBG12_HUMAN	guanine nucleotide binding protein (G protein), gamma 12						cellular response to glucagon stimulus (GO:0071377)|cerebral cortex development (GO:0021987)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)			lung(3)	3						CCTTCGAAACCTGACATGGAG	0.413																																					.		Atlas-SNP	.											.	GNG12	11	.	0			c.94-1G>C						.						82	76	78					1																	68171260		2203	4300	6503	SO:0001630	splice_region_variant	55970	exon5			CGAAACCTGACAT	AF119663	CCDS30749.1	1p31.2	2008-02-05			ENSG00000172380	ENSG00000172380			19663	protein-coding gene	gene with protein product		615405				10819326	Standard	NM_018841		Approved		uc001dea.2	Q9UBI6	OTTHUMG00000009545	ENST00000370982.3:c.94-1G>C	chr1.hg19:g.68171260C>G		79.0	0.0		142.0	33.0	NM_018841	Q69YP5|Q9BRV5	Splice_Site	SNP	ENST00000370982.3	hg19	CCDS30749.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.209280	0.58343	.	.	ENSG00000172380	ENST00000370982	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1311	0.89602	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GNG12	67943848	1.000000	0.71417	0.998000	0.56505	0.513000	0.34164	7.063000	0.76714	2.598000	0.87819	0.491000	0.48974	.	.	.		0.413	GNG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026355.2		Intron	G	68171260	C	G	68171260	5	3	119	1	0	0	0	0	0	0	1	0	6533	695	24	4	129	4	GNG12	1	68171260	Splice_Site	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	7947633	68171260	181079361	3	20222										
KCNA2	3737	hgsc.bcm.edu	37	chr1	111147255	111147255	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gtctctggaaactgggctaaGgtctttagctgggtctcaaa	12	8	3	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr1:111147255G>T	ENST00000485317.1	-	3	823	c.150C>A	c.(148-150)acC>acA	p.T50T	KCNA2_ENST00000440270.1_Silent_p.T50T|KCNA2_ENST00000316361.4_Silent_p.T50T|KCNA2_ENST00000369770.3_Silent_p.T50T|KCNA2_ENST00000525120.1_Intron			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	50					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	ACTGGGCTAAGGTCTTTAGCT	0.542																																					p.T50T	Pancreas(18;568 735 10587 23710 36357)	Atlas-SNP	.											.	KCNA2	61	.	0			c.C150A						.						104	110	108					1																	111147255		2203	4300	6503	SO:0001819	synonymous_variant	3737	exon3			GGCTAAGGTCTTT	L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.150C>A	chr1.hg19:g.111147255G>T		105.0	0.0		102.0	46.0	NM_001204269	Q86XG6	Silent	SNP	ENST00000485317.1	hg19	CCDS827.1																																																																																			.	.		0.542	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		T	111147255	G	T	111147255	2	4	119	1	0	0	0	0	0	0	0	1	8012	987	35	3		3	KCNA2	1	111147255	Silent	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	42975995	111147255	138103366	4	20223										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144912287	144912287	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	aggcttgcaccaacttctctGcagcagcctagtaagaggaa	10	11	1	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr1:144912287G>A	ENST00000369354.3	-	15	2177	c.1988C>T	c.(1987-1989)gCa>gTa	p.A663V	PDE4DIP_ENST00000529945.1_Missense_Mutation_p.A826V|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.A800V|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.A663V|PDE4DIP_ENST00000479408.2_Missense_Mutation_p.A450V|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.A663V|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.A826V|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.A800V|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.A663V|PDE4DIP_ENST00000524974.1_5'Flank|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.A729V			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	663					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CAACTTCTCTGCAGCAGCCTA	0.383			T	PDGFRB	MPD																																p.A826V		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C2477T						.						61	57	58					1																	144912287		2203	4300	6503	SO:0001583	missense	9659	exon11			TTCTCTGCAGCAG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.1988C>T	chr1.hg19:g.144912287G>A	ENSP00000358360:p.Ala663Val	133.0	0.0		189.0	42.0	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	10.40	1.340259	0.24339	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	T;T;T;T;T;T;T;T;T;T	0.70749	4.58;4.66;4.66;4.67;4.67;3.66;3.67;2.57;2.57;-0.51	5.5	4.39	0.52855	.	.	.	.	.	T	0.43188	0.1236	L	0.27053	0.805	0.19575	N	0.999967	B;B;P;B;B;B	0.37330	0.01;0.02;0.59;0.016;0.136;0.021	B;B;B;B;B;B	0.39904	0.006;0.009;0.313;0.023;0.028;0.01	T	0.18493	-1.0335	9	0.31617	T	0.26	.	10.1675	0.42888	0.1052:0.0:0.8948:0.0	.	826;450;663;826;729;663	E9PL24;E9PQG4;Q5VU43-7;Q5VU43-2;Q5VU43-3;Q5VU43	.;.;.;.;.;MYOME_HUMAN	V	729;663;663;826;800;800;663;663;826;826;450	ENSP00000327209:A729V;ENSP00000358360:A663V;ENSP00000358363:A663V;ENSP00000435654:A800V;ENSP00000358366:A800V;ENSP00000358357:A663V;ENSP00000358355:A663V;ENSP00000316434:A826V;ENSP00000433392:A826V;ENSP00000436791:A450V	ENSP00000327209:A729V	A	-	2	0	PDE4DIP	143623644	0.953000	0.32496	0.946000	0.38457	0.597000	0.36814	4.150000	0.58098	2.616000	0.88540	0.639000	0.83563	GCA	.	.		0.383	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		A	144912287	G	A	144912287	3	1	119	1	0	0	0	0	1	0	0	0	11652	1319	46	3	5182	3	PDE4DIP	1	144912287	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	33765032	144912287	104338334	5	20224										
C1orf43	25912	hgsc.bcm.edu	37	chr1	154184948	154184948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gcttacccctgtcccatagcGggctgtttcatagccatcca	8	15	1	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr1:154184948G>A	ENST00000368521.5	-	5	691	c.493C>T	c.(493-495)Cgc>Tgc	p.R165C	C1orf43_ENST00000368516.1_Missense_Mutation_p.R131C|C1orf43_ENST00000350592.3_Missense_Mutation_p.R131C|C1orf43_ENST00000362076.4_Missense_Mutation_p.R113C|C1orf43_ENST00000368518.1_Missense_Mutation_p.R165C|C1orf43_ENST00000368519.1_Missense_Mutation_p.R147C	NM_001098616.1	NP_001092086.1	Q9BWL3	CA043_HUMAN	chromosome 1 open reading frame 43	165						integral component of membrane (GO:0016021)	coenzyme binding (GO:0050662)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	10	all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877)					GTCCCATAGCGGGCTGTTTCA	0.488																																					p.R165C		Atlas-SNP	.											.	C1orf43	36	.	0			c.C493T						.						83	79	81					1																	154184948		2203	4300	6503	SO:0001583	missense	25912	exon5			CATAGCGGGCTGT	AF077036	CCDS1061.1, CCDS1062.1, CCDS41404.1, CCDS72924.1	1q21.2	2012-06-25			ENSG00000143612	ENSG00000143612			29876	protein-coding gene	gene with protein product						11042152, 11230159	Standard	XM_005245077		Approved	NICE-3, DKFZp586G1722	uc001fei.2	Q9BWL3	OTTHUMG00000035981	ENST00000368521.5:c.493C>T	chr1.hg19:g.154184948G>A	ENSP00000357507:p.Arg165Cys	88.0	0.0		95.0	4.0	NM_001098616	A8K3G8|D3DV72|D3DV74|Q5M801|Q5VU73|Q5VU83|Q96HP7|Q9UFU2|Q9UGL7|Q9UGL8|Q9Y2R6	Missense_Mutation	SNP	ENST00000368521.5	hg19	CCDS41404.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.657947	0.67586	.	.	ENSG00000143612	ENST00000350592;ENST00000368521;ENST00000362076;ENST00000368519;ENST00000368518;ENST00000368516	.	.	.	5.39	5.39	0.77823	Dehydrogenase, multihelical (1);	0.000000	0.85682	D	0.000000	T	0.63534	0.2519	M	0.80332	2.49	0.80722	D	1	B;B;B;B;B	0.16802	0.015;0.003;0.019;0.001;0.004	B;B;B;B;B	0.21708	0.004;0.002;0.036;0.001;0.003	T	0.65253	-0.6213	9	0.87932	D	0	-12.6106	18.3255	0.90252	0.0:0.0:1.0:0.0	.	147;131;165;113;131	Q9BWL3-5;Q9BWL3-2;Q9BWL3;Q9BWL3-4;Q09GN0	.;.;CA043_HUMAN;.;.	C	131;165;113;147;165;131	.	ENSP00000271925:R131C	R	-	1	0	C1orf43	152451572	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	8.872000	0.92352	2.814000	0.96858	0.585000	0.79938	CGC	.	.		0.488	C1orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087664.2	NM_015449		A	154184948	G	A	154184948	3	1	119	1	0	0	0	0	1	0	0	0	2042	1116	39	1	280	1	C1orf43	1	154184948	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	9272661	154184948	95065673	6	20225										
MNDA	4332	hgsc.bcm.edu	37	chr1	158812126	158812126	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	aagttccaaggcgttgcctgTctagacaaactaatagaact	8	9	1	2			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr1:158812126T>C	ENST00000368141.4	+	2	444	c.183T>C	c.(181-183)tgT>tgC	p.C61C	MNDA_ENST00000491210.1_3'UTR	NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	61	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					GCGTTGCCTGTCTAGACAAAC	0.343																																					p.C61C		Atlas-SNP	.											.	MNDA	147	.	0			c.T183C						.						109	117	114					1																	158812126		2203	4300	6503	SO:0001819	synonymous_variant	4332	exon2			TGCCTGTCTAGAC	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.183T>C	chr1.hg19:g.158812126T>C		137.0	0.0		153.0	66.0	NM_002432		Silent	SNP	ENST00000368141.4	hg19	CCDS1177.1																																																																																			.	.		0.343	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		C	158812126	T	C	158812126	2	2	119	1	0	0	0	0	0	0	0	1	9685	1673	58	2		2	MNDA	1	158812126	Silent	SNP	T	TCGA-DD-A3A5-01A-11D-A22F-10	4627178	158812126	90438495	7	20226										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204394045	204394058	+	Frame_Shift_Del	DEL	GCTCTCGCAGGCGG	GCTCTCGCAGGCGG	-													0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	cttctcctgagccaggtccaGctctcgcaggcggatgttca					rs373485341|rs193298214	byFrequency	TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	GCTCTCGCAGGCGG	GCTCTCGCAGGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr1:204394045_204394058delGCTCTCGCAGGCGG	ENST00000367187.3	-	34	5383_5396	c.4827_4840delCCGCCTGCGAGAGC	c.(4825-4842)atccgcctgcgagagctgfs	p.RLREL1610fs	PIK3C2B_ENST00000424712.2_Frame_Shift_Del_p.RLREL1582fs|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1610					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)	p.R1612*(1)|p.R1610C(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			GCCAGGTCCAGCTCTCGCAGGCGGATGTTCACCT	0.636																																					p.1610_1614del		Pindel	.											.	PIK3C2B	142	.	2	Substitution - Nonsense(1)|Substitution - Missense(1)	lung(2)	c.4828_4841del						.																																			SO:0001589	frameshift_variant	5287	exon34			.	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4827_4840delCCGCCTGCGAGAGC	chr1.hg19:g.204394045_204394058delGCTCTCGCAGGCGG	ENSP00000356155:p.Arg1610fs	79.0	0.0		79.0	22.0	NM_002646	O95666|Q5SW99	Frame_Shift_Del	DEL	ENST00000367187.3	hg19	CCDS1446.1																																																																																			.	.		0.636	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		-	204394058	GCTCTCGCAGGCGG	-	204394045	7	5	119	1	0	1	0	1	0	0	0	0	11919	962	34	0	68	0	PIK3C2B	1	204394045	Frame_Shift_Del	DEL	GCTCTCGCAGGCGG	TCGA-DD-A3A5-01A-11D-A22F-10	45581919	204394045	44856576	8	20227										
RYR2	6262	hgsc.bcm.edu	37	chr1	237758830	237758830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	caactgctatatggtatgtgCgggtgagagcatgagccccg	14	9	0	2			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr1:237758830C>T	ENST00000366574.2	+	34	4786	c.4469C>T	c.(4468-4470)gCg>gTg	p.A1490V	RYR2_ENST00000542537.1_Missense_Mutation_p.A1474V|RYR2_ENST00000360064.6_Missense_Mutation_p.A1488V	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1490	4 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.A1488V(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATGGTATGTGCGGGTGAGAGC	0.463																																					p.A1490V		Atlas-SNP	.											RYR2,NS,carcinoma,0,3	RYR2	1273	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C4469T						.						85	89	88					1																	237758830		2061	4190	6251	SO:0001583	missense	6262	exon34			TATGTGCGGGTGA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.4469C>T	chr1.hg19:g.237758830C>T	ENSP00000355533:p.Ala1490Val	126.0	1.0		130.0	61.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	18.18	3.566525	0.65651	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.60424	0.19;0.19;0.19	5.52	5.52	0.82312	SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	D	0.000006	T	0.46425	0.1392	L	0.39397	1.21	0.80722	D	1	P	0.45827	0.867	B	0.35353	0.201	T	0.52230	-0.8603	10	0.49607	T	0.09	.	14.9817	0.71316	0.0:0.8578:0.1422:0.0	.	1490	Q92736	RYR2_HUMAN	V	1490;1488;1474	ENSP00000355533:A1490V;ENSP00000353174:A1488V;ENSP00000443798:A1474V	ENSP00000353174:A1488V	A	+	2	0	RYR2	235825453	0.997000	0.39634	0.985000	0.45067	0.997000	0.91878	3.478000	0.53158	2.598000	0.87819	0.655000	0.94253	GCG	.	.		0.463	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237758830	C	T	237758830	3	4	119	1	0	0	0	0	1	0	0	0	13784	768	27	1	4603	1	RYR2	1	237758830	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	33364785	237758830	11491791	9	20228										
KCNS3	3790	hgsc.bcm.edu	37	chr2	18113077	18113077	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	tctctattattcccttctatGccacgttggctgtagacacc	6	13	2	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr2:18113077G>T	ENST00000403915.1	+	3	1253	c.802G>T	c.(802-804)Gcc>Tcc	p.A268S	KCNS3_ENST00000304101.4_Missense_Mutation_p.A268S|KCNS3_ENST00000465292.1_Intron	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	268					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TCCCTTCTATGCCACGTTGGC	0.488																																					p.A268S		Atlas-SNP	.											.	KCNS3	85	.	0			c.G802T						.						118	113	115					2																	18113077		2203	4300	6503	SO:0001583	missense	3790	exon3			TTCTATGCCACGT	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.802G>T	chr2.hg19:g.18113077G>T	ENSP00000385968:p.Ala268Ser	140.0	0.0		153.0	60.0	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	hg19	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.931766	0.73442	.	.	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.98649	-5.05;-5.05	6.07	6.07	0.98685	Ion transport (1);	0.202236	0.51477	D	0.000090	D	0.98492	0.9497	L	0.33710	1.025	0.58432	D	0.999998	D	0.71674	0.998	D	0.67725	0.953	D	0.99895	1.1144	10	0.87932	D	0	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	268	Q9BQ31	KCNS3_HUMAN	S	268	ENSP00000385968:A268S;ENSP00000305824:A268S	ENSP00000305824:A268S	A	+	1	0	KCNS3	17976558	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.735000	0.68587	2.884000	0.98904	0.655000	0.94253	GCC	.	.		0.488	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252		T	18113077	G	T	18113077	3	4	119	1	0	0	0	0	1	0	0	0	8099	1319	46	3	804	3	KCNS3	2	18113077	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10		18113077	225086296	10	20229										
C2orf43	60526	hgsc.bcm.edu	37	chr2	20939926	20939926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gccattgggtgactcagacaTtcgttcaattgttggaaaga	11	7	2	3			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr2:20939926T>C	ENST00000237822.3	-	5	587	c.508A>G	c.(508-510)Atg>Gtg	p.M170V	C2orf43_ENST00000403006.2_Missense_Mutation_p.M40V|C2orf43_ENST00000440866.2_Intron|C2orf43_ENST00000541941.1_Missense_Mutation_p.M40V|C2orf43_ENST00000381090.3_Missense_Mutation_p.M170V|C2orf43_ENST00000435420.2_Missense_Mutation_p.M122V	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	170										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GACTCAGACATTCGTTCAATT	0.393																																					p.M170V		Atlas-SNP	.											.	C2orf43	28	.	0			c.A508G						.						102	99	100					2																	20939926		2203	4300	6503	SO:0001583	missense	60526	exon5			CAGACATTCGTTC	AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961			26145	protein-coding gene	gene with protein product		613570				17135363, 24357060	Standard	NM_001282723		Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000237822.3:c.508A>G	chr2.hg19:g.20939926T>C	ENSP00000237822:p.Met170Val	110.0	0.0		169.0	106.0	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Missense_Mutation	SNP	ENST00000237822.3	hg19	CCDS1702.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.210186	0.58343	.	.	ENSG00000118961	ENST00000403006;ENST00000381090;ENST00000237822;ENST00000435420;ENST00000541941;ENST00000432947;ENST00000412261	T;T;T	0.70399	1.05;1.05;-0.48	5.61	0.0619	0.14342	.	0.000000	0.85682	D	0.000000	T	0.76933	0.4057	M	0.80422	2.495	0.80722	D	1	D;B;P;P	0.62365	0.991;0.149;0.642;0.642	P;B;P;P	0.59487	0.858;0.089;0.673;0.579	T	0.72074	-0.4400	10	0.40728	T	0.16	-9.8728	6.4997	0.22162	0.2506:0.0:0.2608:0.4886	.	128;122;170;170	B4DS38;B7ZAJ5;Q9H6V9;B5MDU6	.;.;CB043_HUMAN;.	V	40;170;170;122;40;40;122	ENSP00000384267:M40V;ENSP00000440570:M40V;ENSP00000396911:M40V	ENSP00000237822:M170V	M	-	1	0	C2orf43	20803407	1.000000	0.71417	0.332000	0.25469	0.910000	0.53928	2.108000	0.41854	-0.140000	0.11394	0.528000	0.53228	ATG	.	.		0.393	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925		C	20939926	T	C	20939926	3	2	119	1	0	0	0	0	1	0	0	0	2169	1493	52	2	481	2	C2orf43	2	20939926	Missense_Mutation	SNP	T	TCGA-DD-A3A5-01A-11D-A22F-10	2826849	20939926	222259447	11	20230										
APOB	338	hgsc.bcm.edu	37	chr2	21251347	21251347	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	cctcatcaacataagataggCagccagtcgcttatctcccg	7	14	3	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr2:21251347C>A	ENST00000233242.1	-	13	1808	c.1681G>T	c.(1681-1683)Gcc>Tcc	p.A561S	APOB_ENST00000399256.4_Missense_Mutation_p.A561S	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	561	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATAAGATAGGCAGCCAGTCGC	0.448																																					p.A561S		Atlas-SNP	.											.	APOB	761	.	0			c.G1681T						.						120	119	120					2																	21251347		2203	4300	6503	SO:0001583	missense	338	exon13			GATAGGCAGCCAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1681G>T	chr2.hg19:g.21251347C>A	ENSP00000233242:p.Ala561Ser	86.0	0.0		82.0	35.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.880068	0.91740	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.72051	-0.62;-0.62	5.69	5.69	0.88448	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (2);	0.068821	0.56097	D	0.000033	T	0.80265	0.4591	M	0.78049	2.395	0.51767	D	0.999935	D	0.67145	0.996	P	0.60345	0.873	T	0.79526	-0.1767	10	0.41790	T	0.15	.	10.8827	0.46948	0.132:0.7991:0.0:0.0689	.	561	P04114	APOB_HUMAN	S	561	ENSP00000233242:A561S;ENSP00000382200:A561S	ENSP00000233242:A561S	A	-	1	0	APOB	21104852	0.999000	0.42202	1.000000	0.80357	0.978000	0.69477	3.774000	0.55341	2.865000	0.98341	0.655000	0.94253	GCC	.	.		0.448	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21251347	C	A	21251347	3	1	119	1	0	0	0	0	1	0	0	0	785	710	25	3	12078	3	APOB	2	21251347	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	311421	21251347	221948026	12	20231										
DHX57	90957	hgsc.bcm.edu	37	chr2	39088480	39088480	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	tttgtggtctttagaaaatcGaatttcaagttcatataaaa	6	4	3	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr2:39088480G>A	ENST00000295373.6	-	5	1198	c.1072C>T	c.(1072-1074)Cga>Tga	p.R358*	AC018693.6_ENST00000442829.1_RNA|DHX57_ENST00000479345.2_5'UTR	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	358							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TTAGAAAATCGAATTTCAAGT	0.368																																					p.R358X	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.C1072T						.						48	47	47					2																	39088480		2203	4300	6503	SO:0001587	stop_gained	90957	exon5			AAAATCGAATTTC	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.1072C>T	chr2.hg19:g.39088480G>A	ENSP00000295373:p.Arg358*	85.0	0.0		114.0	41.0	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Nonsense_Mutation	SNP	ENST00000295373.6	hg19	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	G	37	6.283569	0.97440	.	.	ENSG00000163214	ENST00000295373;ENST00000355320	.	.	.	5.55	3.49	0.39957	.	0.000000	0.48767	D	0.000169	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.1348	0.59403	0.0:0.0:0.5552:0.4448	.	.	.	.	X	358;256	.	ENSP00000295373:R358X	R	-	1	2	DHX57	38941984	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.236000	0.51336	1.295000	0.44724	0.655000	0.94253	CGA	.	.		0.368	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		A	39088480	G	A	39088480	4	1	119	1	0	0	0	0	0	1	0	0	4515	1066	37	1	3168	1	DHX57	2	39088480	Nonsense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	17837133	39088480	204110893	13	20232										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54859819	54859819	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	aatgaggagaagatcaatgcTgtggtggagactggccggag	17	5	1	4			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr2:54859819T>C	ENST00000356805.4	+	17	3962	c.3681T>C	c.(3679-3681)gcT>gcC	p.A1227A	SPTBN1_ENST00000333896.5_Silent_p.A1214A	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1227					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			AGATCAATGCTGTGGTGGAGA	0.498																																					p.A1227A		Atlas-SNP	.											.	SPTBN1	378	.	0			c.T3681C						.						120	106	111					2																	54859819		2203	4300	6503	SO:0001819	synonymous_variant	6711	exon17			CAATGCTGTGGTG		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3681T>C	chr2.hg19:g.54859819T>C		96.0	0.0		141.0	54.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	hg19	CCDS33198.1																																																																																			.	.		0.498	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			C	54859819	T	C	54859819	2	2	119	1	0	0	0	0	0	0	0	1	15134	1567	55	2		2	SPTBN1	2	54859819	Silent	SNP	T	TCGA-DD-A3A5-01A-11D-A22F-10	15771339	54859819	188339554	14	20233										
MRPL53	116540	hgsc.bcm.edu	37	chr2	74699318	74699318	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gcccggatgtgggaggcgaaGgcggtgagcatttccagagc	18	9	0	2			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr2:74699318G>C	ENST00000258105.7	-	3	928	c.267C>G	c.(265-267)gcC>gcG	p.A89A	MRPL53_ENST00000409710.1_Missense_Mutation_p.L52V	NM_053050.4	NP_444278.1	Q96EL3	RM53_HUMAN	mitochondrial ribosomal protein L53	89						mitochondrion (GO:0005739)|ribosome (GO:0005840)				central_nervous_system(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5						GGGAGGCGAAGGCGGTGAGCA	0.632																																					p.A89A		Atlas-SNP	.											.	MRPL53	13	.	0			c.C267G						.						36	41	39					2																	74699318		2203	4299	6502	SO:0001819	synonymous_variant	116540	exon3			GGCGAAGGCGGTG	BC012163	CCDS1944.1	2p13.1	2012-09-13			ENSG00000204822	ENSG00000204822		"Mitochondrial ribosomal proteins / large subunits"	16684	protein-coding gene	gene with protein product		611857				11551941	Standard	NM_053050		Approved		uc002sln.3	Q96EL3	OTTHUMG00000129961	ENST00000258105.7:c.267C>G	chr2.hg19:g.74699318G>C		87.0	0.0		90.0	37.0	NM_053050		Silent	SNP	ENST00000258105.7	hg19	CCDS1944.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.651367	0.29336	.	.	ENSG00000204822	ENST00000409710	T	0.55930	0.49	4.99	1.03	0.20045	.	.	.	.	.	T	0.54062	0.1835	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53641	-0.8410	6	0.87932	D	0	-30.6008	4.5993	0.12345	0.2726:0.1603:0.5671:0.0	.	.	.	.	V	52	ENSP00000386920:L52V	ENSP00000386920:L52V	L	-	1	0	MRPL53	74552826	1.000000	0.71417	0.995000	0.50966	0.569000	0.35902	0.772000	0.26647	0.312000	0.23038	0.643000	0.83706	CTT	.	.		0.632	MRPL53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252225.2	NM_053050		C	74699318	G	C	74699318	2	2	119	1	0	0	0	0	0	0	0	1	9826	987	35	4		4	MRPL53	2	74699318	Silent	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	19839499	74699318	168500055	15	20234										
C2orf65	130951	hgsc.bcm.edu	37	chr2	74785860	74785860	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gacttagggccttgagggatCcttctcccactctgaaggca	11	12	2	2			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr2:74785860C>T	ENST00000290536.5	-	11	1692	c.1576G>A	c.(1576-1578)Gat>Aat	p.D526N	M1AP_ENST00000409585.1_Missense_Mutation_p.D522N|M1AP_ENST00000464686.1_5'UTR|M1AP_ENST00000536235.1_Missense_Mutation_p.D522N|M1AP_ENST00000358434.2_Missense_Mutation_p.D175N	NM_001281296.1|NM_138804.3	NP_001268225.1|NP_620159.2	Q8TC57	M1AP_HUMAN	meiosis 1 associated protein	526					cell differentiation (GO:0030154)|chromatin assembly (GO:0031497)|female gamete generation (GO:0007292)|male meiosis chromosome separation (GO:0051308)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											CTTGAGGGATCCTTCTCCCAC	0.557																																					p.D526N		Atlas-SNP	.											.	.	.	.	0			c.G1576A						.						118	112	114					2																	74785860		2203	4300	6503	SO:0001583	missense	130951	exon11			AGGGATCCTTCTC		CCDS33229.1, CCDS62941.1	2p13.1	2013-02-05	2013-02-05	2013-01-16	ENSG00000159374	ENSG00000159374			25183	protein-coding gene	gene with protein product	"meiosis 1 arresting protein", "spermatogenesis associated 37"		"chromosome 2 open reading frame 65"	C2orf65		16881047, 23269666	Standard	NM_138804		Approved	D6Mm5e, SPATA37	uc002smy.3	Q8TC57	OTTHUMG00000152918	ENST00000290536.5:c.1576G>A	chr2.hg19:g.74785860C>T	ENSP00000290536:p.Asp526Asn	114.0	0.0		123.0	64.0	NM_138804	B7Z6E7|E9PGG8|Q6ZP30|Q96L07	Missense_Mutation	SNP	ENST00000290536.5	hg19	CCDS33229.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.725305	0.48833	.	.	ENSG00000159374	ENST00000290536;ENST00000409585;ENST00000536235;ENST00000358434	T;T;T	0.34472	1.39;1.36;1.36	5.24	-5.63	0.02474	.	1.921840	0.02434	N	0.083853	T	0.20536	0.0494	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.0	T	0.24512	-1.0158	10	0.66056	D	0.02	-14.7896	1.5642	0.02601	0.2105:0.4051:0.1605:0.2239	.	522;175;526;278	E9PGG8;Q8TC57-3;Q8TC57;B3KX03	.;.;CB065_HUMAN;.	N	526;522;522;175	ENSP00000290536:D526N;ENSP00000386793:D522N;ENSP00000445662:D522N	ENSP00000290536:D526N	D	-	1	0	C2orf65	74639368	0.005000	0.15991	0.000000	0.03702	0.108000	0.19459	0.268000	0.18571	-0.469000	0.06911	-0.262000	0.10625	GAT	.	.		0.557	M1AP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328569.1	NM_138804		T	74785860	C	T	74785860	3	4	119	1	0	0	0	0	1	0	0	0	2186	855	30	3	20	3	C2orf65	2	74785860	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	86542	74785860	168413513	16	20235										
RGPD5	727851	hgsc.bcm.edu	37	chr2	113147588	113147588	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	aactgaaatccttctcctgaAgttgattttgcaacatctgc	6	10	2	3			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr2:113147588A>C	ENST00000302558.3	-	20	3125	c.2934T>G	c.(2932-2934)acT>acG	p.T978T	RGPD8_ENST00000409750.1_Silent_p.T838T	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	978					protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)			endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						CTTCTCCTGAAGTTGATTTTG	0.423																																					p.T978T		Atlas-SNP	.											.	RGPD8	81	.	0			c.T2934G						.						8	9	8					2																	113147588		675	1517	2192	SO:0001819	synonymous_variant	727851	exon20			TCCTGAAGTTGAT	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"Tetratricopeptide (TTC) repeat domain containing"	9849	protein-coding gene	gene with protein product		602752	"RAN binding protein 2-like 1"	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.2934T>G	chr2.hg19:g.113147588A>C		594.0	0.0		668.0	43.0	NM_001164463	Q5CZA8	Silent	SNP	ENST00000302558.3	hg19	CCDS46394.1																																																																																			.	.		0.423	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279		C	113147588	A	C	113147588	2	2	119	1	0	0	0	0	0	0	0	1	13304	59	3	5		5	RGPD5	2	113147588	Silent	SNP	A	TCGA-DD-A3A5-01A-11D-A22F-10	38361728	113147588	130051785	17	20236										
POTEE	445582	hgsc.bcm.edu	37	chr2	132021205	132021207	+	In_Frame_Del	DEL	CCC	CCC	-													0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	cggctttgcgggcgacgatgCcccccgggctgtcttccctt							TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr2:132021205_132021207delCCC	ENST00000356920.5	+	15	2271_2273	c.2177_2179delCCC	c.(2176-2181)gccccc>gcc	p.P727del	POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	727	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											GGCGACGATGCCCCCCGGGCTGT	0.611																																					p.726_726del		Atlas-INDEL	.											.	.	.	.	0			c.2176_2178del						.																																			SO:0001651	inframe_deletion	445582	exon15			.	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33895	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 2"	608914	"ANKRD26-like family C, member 1A"	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.2177_2179delCCC	chr2.hg19:g.132021208_132021210delCCC	ENSP00000439189:p.Pro727del	279.0	0.0		261.0	73.0	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	In_Frame_Del	DEL	ENST00000356920.5	hg19	CCDS46414.1																																																																																			.	.		0.611	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		-	132021207	CCC	-	132021205	7	5	119	1	0	1	0	1	0	0	0	0	12273	739	26	0	2235	0	POTEE	2	132021205	In_Frame_Del	DEL	CCC	TCGA-DD-A3A5-01A-11D-A22F-10	18873617	132021205	111178168	18	20237										
RUFY4	285180	hgsc.bcm.edu	37	chr2	218940360	218940360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ggtccttcagggacacgcaaCaaaggaagactctaccgtgg	12	11	2	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr2:218940360C>T	ENST00000344321.7	+	9	1663	c.1145C>T	c.(1144-1146)aCa>aTa	p.T382I	RUFY4_ENST00000441828.2_3'UTR|RUFY4_ENST00000463872.1_3'UTR|RUFY4_ENST00000374155.3_Missense_Mutation_p.T402I	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	382							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGACACGCAACAAAGGAAGAC	0.612																																					p.T382I		Atlas-SNP	.											.	RUFY4	59	.	0			c.C1145T						.						55	55	55					2																	218940360		1955	4134	6089	SO:0001583	missense	285180	exon9			ACGCAACAAAGGA	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"Zinc fingers, FYVE domain containing"	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.1145C>T	chr2.hg19:g.218940360C>T	ENSP00000345900:p.Thr382Ile	77.0	0.0		149.0	76.0	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	hg19		.	.	.	.	.	.	.	.	.	.	C	8.675	0.903808	0.17760	.	.	ENSG00000188282	ENST00000344321;ENST00000374155	T;T	0.48522	1.46;0.81	4.41	1.39	0.22231	.	1.548920	0.04048	N	0.304284	T	0.36358	0.0964	N	0.24115	0.695	0.09310	N	1	P	0.44578	0.838	B	0.39299	0.296	T	0.35425	-0.9789	10	0.38643	T	0.18	0.1536	10.0823	0.42397	0.5704:0.4296:0.0:0.0	.	382	Q6ZNE9	RUFY4_HUMAN	I	382;402	ENSP00000345900:T382I;ENSP00000363270:T402I	ENSP00000345900:T382I	T	+	2	0	RUFY4	218648605	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.371000	0.20450	0.075000	0.16796	0.467000	0.42956	ACA	.	.		0.612	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483		T	218940360	C	T	218940360	3	4	119	1	0	0	0	0	1	0	0	0	13756	478	17	3	1171	3	RUFY4	2	218940360	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	86919155	218940360	24259013	19	20238										
NGLY1	55768	hgsc.bcm.edu	37	chr3	25805746	25805746	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	tctatggcaatcaggtcacgAattttttgcagctgctccac	8	11	3	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr3:25805746A>T	ENST00000280700.5	-	3	463	c.303T>A	c.(301-303)atT>atA	p.I101I	NGLY1_ENST00000428257.1_Silent_p.I101I|NGLY1_ENST00000417874.2_Silent_p.I59I|NGLY1_ENST00000396649.3_Silent_p.I101I|NGLY1_ENST00000422724.2_Silent_p.I24I	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	101					glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						TCAGGTCACGAATTTTTTGCA	0.403																																					p.I101I		Atlas-SNP	.											.	NGLY1	57	.	0			c.T303A						.						182	184	183					3																	25805746		2203	4300	6503	SO:0001819	synonymous_variant	55768	exon3			GTCACGAATTTTT	AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.303T>A	chr3.hg19:g.25805746A>T		191.0	0.0		216.0	91.0	NM_018297	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Silent	SNP	ENST00000280700.5	hg19	CCDS33719.1																																																																																			.	.		0.403	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2			T	25805746	A	T	25805746	2	4	119	1	0	0	0	0	0	0	0	1	10407	242	9	4		4	NGLY1	3	25805746	Silent	SNP	A	TCGA-DD-A3A5-01A-11D-A22F-10		25805746	172216684	20	20239										
FLNB	2317	hgsc.bcm.edu	37	chr3	57994556	57994556	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	tggcgctcgagttcctggacCgtgagagcatcaagctcgtg	14	11	1	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr3:57994556C>G	ENST00000295956.4	+	1	430	c.265C>G	c.(265-267)Cgt>Ggt	p.R89G	FLNB_ENST00000490882.1_Missense_Mutation_p.R89G|FLNB_ENST00000358537.3_Missense_Mutation_p.R89G|FLNB_ENST00000357272.4_Missense_Mutation_p.R89G|FLNB_ENST00000429972.2_Missense_Mutation_p.R89G|FLNB_ENST00000348383.5_Missense_Mutation_p.R89G	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	89	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GTTCCTGGACCGTGAGAGCAT	0.667																																					p.R89G		Atlas-SNP	.											.	FLNB	430	.	0			c.C265G						.						101	106	104					3																	57994556		2203	4300	6503	SO:0001583	missense	2317	exon1			CTGGACCGTGAGA	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.265C>G	chr3.hg19:g.57994556C>G	ENSP00000295956:p.Arg89Gly	63.0	0.0		88.0	44.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.652832	0.47362	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272	D;D;D;D;D;D	0.95272	-3.66;-3.66;-3.66;-3.66;-3.66;-3.66	5.34	5.34	0.76211	Calponin homology domain (5);	0.276477	0.32314	N	0.006264	D	0.88952	0.6577	N	0.17594	0.5	0.80722	D	1	B;B;B;B	0.10296	0.001;0.002;0.003;0.003	B;B;B;B	0.19946	0.001;0.027;0.002;0.002	D	0.84940	0.0865	10	0.49607	T	0.09	.	12.4557	0.55702	0.288:0.712:0.0:0.0	.	89;89;89;89	O75369-2;B2ZZ83;Q60FE7;O75369	.;.;.;FLNB_HUMAN	G	89	ENSP00000295956:R89G;ENSP00000420213:R89G;ENSP00000351339:R89G;ENSP00000415599:R89G;ENSP00000232447:R89G;ENSP00000349819:R89G	ENSP00000295956:R89G	R	+	1	0	FLNB	57969596	0.987000	0.35691	0.987000	0.45799	0.956000	0.61745	1.007000	0.29860	2.512000	0.84698	0.585000	0.79938	CGT	.	.		0.667	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		G	57994556	C	G	57994556	3	3	119	1	0	0	0	0	1	0	0	0	5942	652	23	4	267	4	FLNB	3	57994556	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	32188810	57994556	140027874	21	20240										
E2F3	1871	hgsc.bcm.edu	37	chr6	20481646	20481646	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	agaagaagtctaaaaacaacGtccaatggatgtgagtagga	11	5	1	3			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr6:20481646G>A	ENST00000346618.3	+	3	781	c.715G>A	c.(715-717)Gtc>Atc	p.V239I	E2F3_ENST00000535432.1_Missense_Mutation_p.V108I	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	239					mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			TAAAAACAACGTCCAATGGAT	0.478																																					p.V239I		Atlas-SNP	.											.	E2F3	30	.	0			c.G715A						.						109	109	109					6																	20481646		2203	4300	6503	SO:0001583	missense	1871	exon3			AACAACGTCCAAT	Y10479	CCDS4545.1, CCDS58999.1	6p22	2008-08-29			ENSG00000112242	ENSG00000112242			3115	protein-coding gene	gene with protein product		600427				8246996	Standard	NM_001949		Approved		uc003nda.2	O00716	OTTHUMG00000016389	ENST00000346618.3:c.715G>A	chr6.hg19:g.20481646G>A	ENSP00000262904:p.Val239Ile	84.0	0.0		93.0	33.0	NM_001949	Q15000|Q68DT0|Q9BZ44	Missense_Mutation	SNP	ENST00000346618.3	hg19	CCDS4545.1	.	.	.	.	.	.	.	.	.	.	G	7.632	0.679113	0.14907	.	.	ENSG00000112242	ENST00000346618;ENST00000535432	D;D	0.86865	-2.18;-2.18	5.71	5.71	0.89125	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.151897	0.56097	D	0.000037	T	0.36220	0.0959	N	0.00427	-1.505	0.45295	D	0.998294	B;B	0.26902	0.163;0.001	B;B	0.19666	0.026;0.002	T	0.59595	-0.7425	10	0.02654	T	1	.	7.8115	0.29234	0.1913:0.0:0.8087:0.0	.	239;108	O00716;Q68DT0	E2F3_HUMAN;.	I	239;108	ENSP00000262904:V239I;ENSP00000443418:V108I	ENSP00000262904:V239I	V	+	1	0	E2F3	20589625	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.540000	0.82074	2.860000	0.98153	0.655000	0.94253	GTC	.	.		0.478	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1			A	20481646	G	A	20481646	3	1	119	1	0	0	0	0	1	0	0	0	4870	1145	40	1	725	1	E2F3	6	20481646	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10		20481646	150633421	22	20241										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30918729	30918729	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	cagaaaatagagaaaggacaGccaatgagaagaccacacaa	9	8	0	4			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr6:30918729G>A	ENST00000462446.1	+	2	2516	c.2488G>A	c.(2488-2490)Gcc>Acc	p.A830T	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	275						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						AGAAAGGACAGCCAATGAGAA	0.488																																					p.A830T		Atlas-SNP	.											.	DPCR1	99	.	0			c.G2488A						.						71	72	72					6																	30918729		692	1591	2283	SO:0001583	missense	135656	exon2			AGGACAGCCAATG	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2488G>A	chr6.hg19:g.30918729G>A	ENSP00000417182:p.Ala830Thr	91.0	0.0		105.0	33.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	-	0.010	-1.795863	0.00617	.	.	ENSG00000168631	ENST00000462446	T	0.56275	0.47	0.933	-0.246	0.13022	.	.	.	.	.	T	0.11410	0.0278	L	0.29908	0.895	0.09310	N	0.999996	B	0.23058	0.079	B	0.17979	0.02	T	0.32955	-0.9887	9	0.07175	T	0.84	.	5.085	0.14676	0.2731:0.0:0.7269:0.0	.	830	E9PEI6	.	T	830	ENSP00000417182:A830T	ENSP00000417182:A830T	A	+	1	0	DPCR1	31026708	0.000000	0.05858	0.003000	0.11579	0.014000	0.08584	-0.884000	0.04166	-0.052000	0.13311	0.109000	0.15622	GCC	.	.		0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		A	30918729	G	A	30918729	3	1	119	1	0	0	0	0	1	0	0	0	4714	971	34	3	2494	3	DPCR1	6	30918729	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	10437083	30918729	140196338	23	20242										
C6orf174	387104	hgsc.bcm.edu	37	chr6	127796693	127796693	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	atgagccggtcgatggtcttGcccaggcgctcggcctccga	14	14	1	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr6:127796693G>A	ENST00000525778.1	-	6	3223	c.2478C>T	c.(2476-2478)ggC>ggT	p.G826G	SOGA3_ENST00000368268.2_Silent_p.G826G|SOGA3_ENST00000556132.1_Silent_p.G826G|SOGA3_ENST00000465909.2_Silent_p.G826G|SOGA3_ENST00000474293.2_5'UTR|SOGA3_ENST00000481848.2_Silent_p.G826G			Q5TF21	SOGA3_HUMAN	SOGA family member 3	826					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CGATGGTCTTGCCCAGGCGCT	0.672																																					p.G826G		Atlas-SNP	.											.	.	.	.	0			c.C2478T						.						70	80	77					6																	127796693		2152	4249	6401	SO:0001819	synonymous_variant	387104	exon6			GGTCTTGCCCAGG	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.2478C>T	chr6.hg19:g.127796693G>A		24.0	0.0		26.0	10.0	NM_001012279		Silent	SNP	ENST00000525778.1	hg19	CCDS43505.1																																																																																			.	.		0.672	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		A	127796693	G	A	127796693	2	1	119	1	0	0	0	0	0	0	0	1	2347	1306	46	3		3	C6orf174	6	127796693	Silent	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	96877964	127796693	43318374	24	20243										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11676308	11676308	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	tctttctggatgcacgctatCtccctcacctgaataccttc	5	15	4	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr7:11676308C>G	ENST00000423059.4	-	2	722	c.471G>C	c.(469-471)gaG>gaC	p.E157D	THSD7A_ENST00000480061.1_5'UTR	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	157					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TGCACGCTATCTCCCTCACCT	0.498										HNSCC(18;0.044)																											p.E157D		Atlas-SNP	.											.	THSD7A	219	.	0			c.G471C						.						124	118	120					7																	11676308		2005	4202	6207	SO:0001583	missense	221981	exon2			CGCTATCTCCCTC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.471G>C	chr7.hg19:g.11676308C>G	ENSP00000406482:p.Glu157Asp	82.0	0.0		101.0	34.0	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	hg19	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	C	8.040	0.763667	0.15914	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.59502	0.26	5.57	1.78	0.24846	.	0.043316	0.85682	D	0.000000	T	0.30355	0.0762	N	0.16833	0.445	0.44194	D	0.997012	B	0.06786	0.001	B	0.06405	0.002	T	0.04635	-1.0937	10	0.14252	T	0.57	.	1.9432	0.03351	0.1183:0.3959:0.128:0.3578	.	157	Q9UPZ6	THS7A_HUMAN	D	157	ENSP00000406482:E157D	ENSP00000262042:E157D	E	-	3	2	THSD7A	11642833	0.893000	0.30496	0.972000	0.41901	0.565000	0.35776	0.067000	0.14510	0.112000	0.17975	0.650000	0.86243	GAG	.	.		0.498	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		G	11676308	C	G	11676308	3	3	119	1	0	0	0	0	1	0	0	0	15894	912	32	4	4606	4	THSD7A	7	11676308	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10		11676308	147462355	25	20244										
DNAJC1	64215	hgsc.bcm.edu	37	chr10	22207780	22207780	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ttgcatggaagcaaatcatgCcactgtggtttcatcagcaa	9	9	3	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr10:22207780C>T	ENST00000376980.3	-	6	947	c.657G>A	c.(655-657)tgG>tgA	p.W219*		NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	219					negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				GCAAATCATGCCACTGTGGTT	0.373																																					p.W219X		Atlas-SNP	.											.	DNAJC1	42	.	0			c.G657A						.						105	89	95					10																	22207780		2203	4300	6503	SO:0001587	stop_gained	64215	exon6			ATCATGCCACTGT	AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"Heat shock proteins / DNAJ (HSP40)"	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.657G>A	chr10.hg19:g.22207780C>T	ENSP00000366179:p.Trp219*	49.0	0.0		66.0	30.0	NM_022365	B0YIZ8|Q5VX89|Q9H6B8	Nonsense_Mutation	SNP	ENST00000376980.3	hg19	CCDS7136.1	.	.	.	.	.	.	.	.	.	.	C	40	8.263892	0.98732	.	.	ENSG00000136770	ENST00000376980	.	.	.	5.82	5.82	0.92795	.	0.060277	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-3.9738	20.0856	0.97800	0.0:1.0:0.0:0.0	.	.	.	.	X	219	.	ENSP00000366179:W219X	W	-	3	0	DNAJC1	22247786	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.975000	0.76128	2.734000	0.93682	0.655000	0.94253	TGG	.	.		0.373	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047149.1	NM_022365		T	22207780	C	T	22207780	4	4	119	1	0	0	0	0	0	1	0	0	4630	740	26	3	1035	3	DNAJC1	10	22207780	Nonsense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10		22207780	113326967	26	20245										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124390621	124390621	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ggtggtctgcagacagctagGgtgtggacgtgcagtttcag	17	7	2	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr10:124390621G>C	ENST00000338354.3	+	46	5889	c.5783G>C	c.(5782-5784)gGg>gCg	p.G1928A	DMBT1_ENST00000368909.3_Missense_Mutation_p.G1928A|DMBT1_ENST00000344338.3_Missense_Mutation_p.G1918A|DMBT1_ENST00000368956.2_Missense_Mutation_p.G1300A|DMBT1_ENST00000330163.4_Missense_Mutation_p.G1300A|DMBT1_ENST00000368955.3_Missense_Mutation_p.G1918A|DMBT1_ENST00000359586.6_Missense_Mutation_p.G648A			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1928	SRCR 14. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				AGACAGCTAGGGTGTGGACGT	0.552																																					p.G1928A	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G5783C						.						113	115	114					10																	124390621		2071	4214	6285	SO:0001583	missense	1755	exon46			AGCTAGGGTGTGG		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.5783G>C	chr10.hg19:g.124390621G>C	ENSP00000342210:p.Gly1928Ala	136.0	0.0		124.0	35.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	G	12.16	1.854584	0.32791	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000344467;ENST00000359586	T;T;T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43;0.43;0.43	5.41	0.096	0.14488	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.78641	0.4315	H	0.97829	4.085	0.09310	N	1	P;D;B;D;D;D;P	0.76494	0.806;0.999;0.129;0.999;0.991;0.998;0.933	P;D;B;D;P;D;P	0.79784	0.643;0.985;0.02;0.993;0.55;0.99;0.81	T	0.65380	-0.6182	9	0.87932	D	0	.	6.324	0.21232	0.2869:0.1202:0.593:0.0	.	648;1908;1177;2057;1300;1918;1928	F8WEF7;Q9UGM3-5;Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;.;DMBT1_HUMAN	A	1928;2057;1928;1928;1928;1928;1300;1918;1300;1300;1928;1918;1300;74;648	ENSP00000342210:G1928A;ENSP00000343175:G1918A;ENSP00000327747:G1300A;ENSP00000357905:G1928A;ENSP00000357951:G1918A;ENSP00000357952:G1300A;ENSP00000352593:G648A	ENSP00000331522:G1300A	G	+	2	0	DMBT1	124380611	0.000000	0.05858	0.003000	0.11579	0.164000	0.22412	-0.058000	0.11750	-0.267000	0.09325	-0.345000	0.07892	GGG	.	.		0.552	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		C	124390621	G	C	124390621	3	2	119	1	0	0	0	0	1	0	0	0	4579	1232	43	4	5965	4	DMBT1	10	124390621	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	102182841	124390621	11144126	27	20246										
OR56B4	196335	hgsc.bcm.edu	37	chr11	6129479	6129479	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	acagggttcatcatgctcagGaatggcctgttgaccatccc	10	12	3	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr11:6129479G>T	ENST00000316529.3	+	1	566	c.471G>T	c.(469-471)agG>agT	p.R157S	RP11-290F24.3_ENST00000529961.1_RNA	NM_001005181.1	NP_001005181.1	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B, member 4	157						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(1)|lung(10)|skin(6)|urinary_tract(2)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATGCTCAGGAATGGCCTGT	0.502																																					p.R157S		Atlas-SNP	.											.	OR56B4	50	.	0			c.G471T						.						121	109	113					11																	6129479		2201	4296	6497	SO:0001583	missense	196335	exon1			GCTCAGGAATGGC	AB065513	CCDS31406.1	11p15.4	2012-08-09			ENSG00000180919	ENSG00000180919		"GPCR / Class A : Olfactory receptors"	15248	protein-coding gene	gene with protein product							Standard	NM_001005181		Approved		uc010qzx.2	Q8NH76	OTTHUMG00000165531	ENST00000316529.3:c.471G>T	chr11.hg19:g.6129479G>T	ENSP00000321196:p.Arg157Ser	81.0	0.0		110.0	47.0	NM_001005181	Q6IFD7	Missense_Mutation	SNP	ENST00000316529.3	hg19	CCDS31406.1	.	.	.	.	.	.	.	.	.	.	G	9.611	1.131233	0.21041	.	.	ENSG00000180919	ENST00000316529	T	0.36520	1.25	4.06	-0.33	0.12683	GPCR, rhodopsin-like superfamily (1);	0.177648	0.26432	U	0.024405	T	0.56031	0.1958	M	0.89715	3.055	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.47535	-0.9110	10	0.87932	D	0	.	1.8156	0.03099	0.3711:0.1279:0.3709:0.1302	.	157	Q8NH76	O56B4_HUMAN	S	157	ENSP00000321196:R157S	ENSP00000321196:R157S	R	+	3	2	OR56B4	6086055	0.000000	0.05858	0.683000	0.30040	0.030000	0.12068	-2.052000	0.01401	0.052000	0.16007	-0.264000	0.10439	AGG	.	.		0.502	OR56B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384668.1	NM_001005181		T	6129479	G	T	6129479	3	4	119	1	0	0	0	0	1	0	0	0	11147	1165	41	3	473	3	OR56B4	11	6129479	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10		6129479	128877037	28	20247										
DEPDC7	91614	hgsc.bcm.edu	37	chr11	33037511	33037511	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gagcaagggccatggccaccGtgcaggagaaggctgctgcg	17	11	0	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr11:33037511G>A	ENST00000241051.3	+	1	102	c.10G>A	c.(10-12)Gtg>Atg	p.V4M	DEPDC7_ENST00000311388.3_5'Flank	NM_001077242.1	NP_001070710.1	Q96QD5	DEPD7_HUMAN	DEP domain containing 7	4					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17						CATGGCCACCGTGCAGGAGAA	0.697																																					p.V4M		Atlas-SNP	.											.	DEPDC7	94	.	0			c.G10A						.						18	28	25					11																	33037511		2126	4228	6354	SO:0001583	missense	91614	exon1			GCCACCGTGCAGG		CCDS41632.1, CCDS41633.1	11p13	2006-03-24			ENSG00000121690	ENSG00000121690			29899	protein-coding gene	gene with protein product		612294				10568747	Standard	NM_001077242		Approved		uc001mub.3	Q96QD5	OTTHUMG00000166242	ENST00000241051.3:c.10G>A	chr11.hg19:g.33037511G>A	ENSP00000241051:p.Val4Met	97.0	0.0		58.0	20.0	NM_001077242	G5E941|Q8N602|Q8NCU9|Q9UGK5	Missense_Mutation	SNP	ENST00000241051.3	hg19	CCDS41632.1	.	.	.	.	.	.	.	.	.	.	G	34	5.295091	0.95574	.	.	ENSG00000121690	ENST00000241051	T	0.18338	2.22	4.08	3.17	0.36434	.	4.775170	0.00496	N	0.000147	T	0.41190	0.1148	L	0.56769	1.78	0.80722	D	1	B;D;B	0.76494	0.25;0.999;0.25	B;D;B	0.64042	0.044;0.921;0.018	T	0.01319	-1.1386	10	0.87932	D	0	-8.8706	11.9617	0.53011	0.0866:0.0:0.9134:0.0	.	4;4;4	B4DJ78;B4DH51;Q96QD5	.;.;DEPD7_HUMAN	M	4	ENSP00000241051:V4M	ENSP00000241051:V4M	V	+	1	0	DEPDC7	32994087	1.000000	0.71417	0.282000	0.24776	0.848000	0.48234	5.154000	0.64894	1.119000	0.41883	0.472000	0.43445	GTG	.	.		0.697	DEPDC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388655.1	NM_139160		A	33037511	G	A	33037511	3	1	119	1	0	0	0	0	1	0	0	0	4446	1145	40	1	12	1	DEPDC7	11	33037511	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	26908032	33037511	101969005	29	20248										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133815979	133815979	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	catactcagggtccacgtgcGgcgggtagtagccaaacttg	13	11	1	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr11:133815979G>A	ENST00000321016.8	-	2	469	c.239C>T	c.(238-240)cCg>cTg	p.P80L	IGSF9B_ENST00000533871.2_Missense_Mutation_p.P80L			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	80	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GTCCACGTGCGGCGGGTAGTA	0.622																																					p.P80L		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C239T						.						49	60	56					11																	133815979		2122	4224	6346	SO:0001583	missense	22997	exon2			ACGTGCGGCGGGT	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.239C>T	chr11.hg19:g.133815979G>A	ENSP00000317980:p.Pro80Leu	54.0	0.0		72.0	31.0	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	G	28.3	4.912262	0.92178	.	.	ENSG00000080854	ENST00000321016;ENST00000527648;ENST00000533160;ENST00000526663	T;T;T;T	0.65178	-0.14;-0.14;-0.14;1.96	5.68	5.68	0.88126	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000004	T	0.81206	0.4774	M	0.80422	2.495	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81212	-0.1035	10	0.49607	T	0.09	.	19.3986	0.94619	0.0:0.0:1.0:0.0	.	80	Q9UPX0	TUTLB_HUMAN	L	80;80;70;127	ENSP00000317980:P80L;ENSP00000436576:P80L;ENSP00000434026:P70L;ENSP00000435989:P127L	ENSP00000317980:P80L	P	-	2	0	IGSF9B	133321189	1.000000	0.71417	0.187000	0.23214	0.762000	0.43233	9.738000	0.98835	2.693000	0.91896	0.655000	0.94253	CCG	.	.		0.622	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133815979	G	A	133815979	3	1	119	1	0	0	0	0	1	0	0	0	7615	1116	39	1	3882	1	IGSF9B	11	133815979	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	100778468	133815979	1190537	30	20249										
C3AR1	719	hgsc.bcm.edu	37	chr12	8212610	8212610	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gaggtggaggaaccaaattgTgttcactgtccgctgcatct	12	9	2	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr12:8212610T>C	ENST00000307637.4	-	2	375	c.172A>G	c.(172-174)Aca>Gca	p.T58A		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	58					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		AACCAAATTGTGTTCACTGTC	0.577																																					p.T58A		Atlas-SNP	.											.	C3AR1	61	.	0			c.A172G						.						104	87	93					12																	8212610		2203	4300	6503	SO:0001583	missense	719	exon2			AAATTGTGTTCAC	U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"Complement system", "GPCR / Class A : Complement component receptors"	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.172A>G	chr12.hg19:g.8212610T>C	ENSP00000302079:p.Thr58Ala	85.0	0.0		94.0	37.0	NM_004054	O43771|Q92868	Missense_Mutation	SNP	ENST00000307637.4	hg19	CCDS8588.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.132134	0.77662	.	.	ENSG00000171860	ENST00000307637;ENST00000546241	T;T	0.37235	1.21;1.21	5.8	5.8	0.92144	GPCR, rhodopsin-like superfamily (1);	0.079016	0.47455	D	0.000234	T	0.54481	0.1861	L	0.52206	1.635	0.51482	D	0.999928	D	0.89917	1.0	D	0.97110	1.0	T	0.56275	-0.8006	10	0.72032	D	0.01	.	14.1132	0.65137	0.0:0.0:0.0:1.0	.	58	Q16581	C3AR_HUMAN	A	58	ENSP00000302079:T58A;ENSP00000444500:T58A	ENSP00000302079:T58A	T	-	1	0	C3AR1	8103877	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.967000	0.87967	2.213000	0.71641	0.477000	0.44152	ACA	.	.		0.577	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1			C	8212610	T	C	8212610	3	2	119	1	0	0	0	0	1	0	0	0	2207	1696	59	2	1280	2	C3AR1	12	8212610	Missense_Mutation	SNP	T	TCGA-DD-A3A5-01A-11D-A22F-10		8212610	125639285	31	20250										
KLRK1	22914	hgsc.bcm.edu	37	chr12	10525808	10525808	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	atagagtgcacagtctccctTctgcatttcaattattgtta	6	9	3	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr12:10525808T>A	ENST00000240618.6	-	8	696	c.556A>T	c.(556-558)Aag>Tag	p.K186*	RP11-277P12.20_ENST00000500682.1_RNA|KLRK1_ENST00000540818.1_Nonsense_Mutation_p.K186*|KLRC4-KLRK1_ENST00000539300.1_3'UTR	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	186	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.			K -> R (in Ref. 5; BAF84709). {ECO:0000305}.	cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						CAGTCTCCCTTCTGCATTTCA	0.353																																					p.K186X		Atlas-SNP	.											.	.	.	.	0			c.A556T						.						144	132	136					12																	10525808		2203	4300	6503	SO:0001587	stop_gained	0	exon13			CTCCCTTCTGCAT	AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"Killer cell lectin-like receptors", "CD molecules"	18788	protein-coding gene	gene with protein product		611817	"DNA segment on chromosome 12 (unique) 2489 expressed sequence"	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.556A>T	chr12.hg19:g.10525808T>A	ENSP00000240618:p.Lys186*	149.0	0.0		146.0	58.0	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Nonsense_Mutation	SNP	ENST00000240618.6	hg19	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	T	13.52	2.261220	0.39995	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	.	.	.	5.59	4.45	0.53987	.	1.130820	0.06527	N	0.740761	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0858	0.30771	0.0:0.0915:0.0:0.9085	.	.	.	.	X	186	.	ENSP00000240618:K186X	K	-	1	0	KLRK1	10417075	0.129000	0.22400	0.003000	0.11579	0.072000	0.16883	3.105000	0.50314	0.964000	0.38108	0.528000	0.53228	AAG	.	.		0.353	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		A	10525808	T	A	10525808	4	1	119	1	0	0	0	0	0	1	0	0	8432	1792	62	4	98	4	KLRK1	12	10525808	Nonsense_Mutation	SNP	T	TCGA-DD-A3A5-01A-11D-A22F-10	2313198	10525808	123326087	32	20251										
BICD1	636	hgsc.bcm.edu	37	chr12	32369238	32369238	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ctgaagatggagagactcggGaggaaacgcttctgcaggag	16	7	1	3			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr12:32369238G>T	ENST00000281474.5	+	2	374	c.271G>T	c.(271-273)Gag>Tag	p.E91*	BICD1_ENST00000548411.1_Nonsense_Mutation_p.E91*	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	91					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			AGAGACTCGGGAGGAAACGCT	0.512																																					p.E91X		Atlas-SNP	.											.	BICD1	89	.	0			c.G271T						.						99	97	98					12																	32369238		2203	4300	6503	SO:0001587	stop_gained	636	exon2			ACTCGGGAGGAAA	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.271G>T	chr12.hg19:g.32369238G>T	ENSP00000281474:p.Glu91*	98.0	0.0		79.0	27.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Nonsense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	G	38	7.155287	0.98099	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	19.5182	0.95174	0.0:0.0:1.0:0.0	.	.	.	.	X	91	.	ENSP00000281474:E91X	E	+	1	0	BICD1	32260505	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.573000	0.98181	2.603000	0.88011	0.655000	0.94253	GAG	.	.		0.512	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		T	32369238	G	T	32369238	4	4	119	1	0	0	0	0	0	1	0	0	1428	1175	41	3	277	3	BICD1	12	32369238	Nonsense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	21843430	32369238	101482657	33	20252										
IFNG	3458	hgsc.bcm.edu	37	chr12	68553297	68553297	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	cttacaaaatatttcttaagGttttctgcttcttttacata	3	7	3	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr12:68553297G>C	ENST00000229135.3	-	1	230	c.99C>G	c.(97-99)aaC>aaG	p.N33K	IFNG-AS1_ENST00000536914.1_RNA	NM_000619.2	NP_000610.2	P01579	IFNG_HUMAN	interferon, gamma	33					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell cycle arrest (GO:0007050)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to interleukin-18 (GO:0071351)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|extrinsic apoptotic signaling pathway (GO:0097191)|humoral immune response (GO:0006959)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of myelination (GO:0031642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil apoptotic process (GO:0001781)|neutrophil chemotaxis (GO:0030593)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity (GO:0060550)|positive regulation of fructose 1,6-bisphosphate metabolic process (GO:0060552)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|regulation of insulin secretion (GO:0050796)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of the force of heart contraction (GO:0002026)|response to drug (GO:0042493)|response to virus (GO:0009615)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|interferon-gamma receptor binding (GO:0005133)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Glucosamine(DB01296)|Olsalazine(DB01250)	ATTTCTTAAGGTTTTCTGCTT	0.363																																					p.N33K		Atlas-SNP	.											.	IFNG	38	.	0			c.C99G						.						44	42	43					12																	68553297		2203	4298	6501	SO:0001583	missense	3458	exon1			CTTAAGGTTTTCT		CCDS8980.1	12q14	2007-10-17			ENSG00000111537	ENSG00000111537		"Interferons"	5438	protein-coding gene	gene with protein product		147570					Standard	NM_000619		Approved		uc001stw.1	P01579	OTTHUMG00000169113	ENST00000229135.3:c.99C>G	chr12.hg19:g.68553297G>C	ENSP00000229135:p.Asn33Lys	124.0	0.0		111.0	39.0	NM_000619	B5BU88|Q53ZV4	Missense_Mutation	SNP	ENST00000229135.3	hg19	CCDS8980.1	.	.	.	.	.	.	.	.	.	.	G	4.812	0.150979	0.09185	.	.	ENSG00000111537	ENST00000229135	T	0.40476	1.03	5.12	-6.78	0.01721	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.790903	0.12266	N	0.484252	T	0.17152	0.0412	N	0.21448	0.665	0.09310	N	1	B	0.17038	0.02	B	0.12837	0.008	T	0.18871	-1.0323	9	.	.	.	-2.1183	0.4591	0.00513	0.2001:0.2077:0.2774:0.3148	.	33	P01579	IFNG_HUMAN	K	33	ENSP00000229135:N33K	.	N	-	3	2	IFNG	66839564	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.095000	0.03356	-1.531000	0.01749	-0.500000	0.04577	AAC	.	.		0.363	IFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402301.1			C	68553297	G	C	68553297	3	2	119	1	0	0	0	0	1	0	0	0	7557	1252	44	4	417	4	IFNG	12	68553297	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	36184059	68553297	65298598	34	20253										
TPCN1	53373	hgsc.bcm.edu	37	chr12	113704076	113704076	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	acacaatcacctcttctaccTgatggagctggccacggccc	8	16	3	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr12:113704076T>C	ENST00000335509.6	+	4	643	c.329T>C	c.(328-330)cTg>cCg	p.L110P	TPCN1_ENST00000392569.4_Missense_Mutation_p.L42P|TPCN1_ENST00000541517.1_Missense_Mutation_p.L182P|TPCN1_ENST00000550785.1_Missense_Mutation_p.L182P	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	110					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						CTCTTCTACCTGATGGAGCTG	0.612																																					p.L182P		Atlas-SNP	.											.	TPCN1	109	.	0			c.T545C						.						228	224	225					12																	113704076		2203	4300	6503	SO:0001583	missense	53373	exon5			TCTACCTGATGGA	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"Voltage-gated ion channels / Two-pore channels"	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.329T>C	chr12.hg19:g.113704076T>C	ENSP00000335300:p.Leu110Pro	45.0	0.0		60.0	26.0	NM_001143819	A7E258|Q86XS9|Q8NC20	Missense_Mutation	SNP	ENST00000335509.6	hg19	CCDS31908.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.897901	0.72639	.	.	ENSG00000186815	ENST00000552642;ENST00000552985;ENST00000335509;ENST00000552897;ENST00000550785;ENST00000541517;ENST00000392569;ENST00000552542;ENST00000548465	T;D;D;D;D	0.97430	0.69;-4.27;-4.38;-4.38;-4.35	5.29	5.29	0.74685	.	0.201394	0.43579	D	0.000542	D	0.96112	0.8733	L	0.43152	1.355	0.80722	D	1	P;D;P	0.57257	0.911;0.979;0.938	P;P;B	0.50708	0.577;0.648;0.424	D	0.95565	0.8633	10	0.39692	T	0.17	-10.4745	15.2318	0.73395	0.0:0.0:0.0:1.0	.	110;182;110	A5PKY2;Q9ULQ1-3;Q9ULQ1	.;.;TPC1_HUMAN	P	86;196;110;42;182;182;42;42;42	ENSP00000447569:L196P;ENSP00000335300:L110P;ENSP00000448083:L182P;ENSP00000438125:L182P;ENSP00000376350:L42P	ENSP00000335300:L110P	L	+	2	0	TPCN1	112188459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.661000	0.83786	2.001000	0.58596	0.459000	0.35465	CTG	.	.		0.612	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		C	113704076	T	C	113704076	3	2	119	1	0	0	0	0	1	0	0	0	16410	1580	55	2	559	2	TPCN1	12	113704076	Missense_Mutation	SNP	T	TCGA-DD-A3A5-01A-11D-A22F-10	45150779	113704076	20147819	35	20254										
TAOK3	51347	hgsc.bcm.edu	37	chr12	118639247	118639247	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	aatgaggacacgtagtggccGgtctcgtcgaacaaagtcat	12	9	2	1	rs537291817		TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr12:118639247G>T	ENST00000392533.3	-	12	1331	c.841C>A	c.(841-843)Cgg>Agg	p.R281R	TAOK3_ENST00000419821.2_Silent_p.R281R	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	281					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGTAGTGGCCGGTCTCGTCGA	0.393																																					p.R281R		Atlas-SNP	.											.	TAOK3	151	.	0			c.C841A						.						93	86	89					12																	118639247		2203	4300	6503	SO:0001819	synonymous_variant	51347	exon12			GTGGCCGGTCTCG	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.841C>A	chr12.hg19:g.118639247G>T		115.0	0.0		115.0	40.0	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Silent	SNP	ENST00000392533.3	hg19	CCDS9188.1																																																																																			.	.		0.393	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281		T	118639247	G	T	118639247	2	4	119	1	0	0	0	0	0	0	0	1	15564	1115	39	1		1	TAOK3	12	118639247	Silent	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	4935171	118639247	15212648	36	20255										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120578768	120578768	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	tcctcaaggatggggatgatCtcggggaggattttctcccc	13	10	3	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr12:120578768C>A	ENST00000300648.6	-	45	5901	c.5889G>T	c.(5887-5889)gaG>gaT	p.E1963D		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1963					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGGGGATGATCTCGGGGAGGA	0.527																																					p.E1963D		Atlas-SNP	.											.	GCN1L1	207	.	0			c.G5889T						.						152	155	154					12																	120578768		2033	4200	6233	SO:0001583	missense	10985	exon45			GATGATCTCGGGG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.5889G>T	chr12.hg19:g.120578768C>A	ENSP00000300648:p.Glu1963Asp	58.0	0.0		71.0	30.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.879607	0.51801	.	.	ENSG00000089154	ENST00000300648	T	0.65364	-0.15	5.11	3.28	0.37604	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.49372	0.1553	L	0.49455	1.56	0.54753	D	0.999987	P	0.36683	0.565	B	0.34038	0.174	T	0.41770	-0.9490	10	0.29301	T	0.29	.	7.4006	0.26962	0.0:0.7064:0.0:0.2936	.	1963	Q92616	GCN1L_HUMAN	D	1963	ENSP00000300648:E1963D	ENSP00000300648:E1963D	E	-	3	2	GCN1L1	119063151	1.000000	0.71417	0.996000	0.52242	0.976000	0.68499	1.623000	0.37008	1.148000	0.42385	0.462000	0.41574	GAG	.	.		0.527	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			A	120578768	C	A	120578768	3	1	119	1	0	0	0	0	1	0	0	0	6307	912	32	3	2182	3	GCN1L1	12	120578768	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	1939521	120578768	13273127	37	20256										
EP400	57634	hgsc.bcm.edu	37	chr12	132471242	132471242	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	cactatctccagtcacttccCggaccccaggggtggtggca	11	15	2	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr12:132471242C>T	ENST00000333577.4	+	7	2330	c.2221C>T	c.(2221-2223)Cgg>Tgg	p.R741W	EP400_ENST00000332482.4_Missense_Mutation_p.R668W|EP400_ENST00000389562.2_Missense_Mutation_p.R704W|EP400_ENST00000330386.6_Missense_Mutation_p.R705W|EP400_ENST00000389561.2_Missense_Mutation_p.R705W			Q96L91	EP400_HUMAN	E1A binding protein p400	741					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		AGTCACTTCCCGGACCCCAGG	0.587																																					p.R705W		Atlas-SNP	.											.	EP400	370	.	0			c.C2113T						.						114	110	111					12																	132471242		2203	4300	6503	SO:0001583	missense	57634	exon6			ACTTCCCGGACCC	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.2221C>T	chr12.hg19:g.132471242C>T	ENSP00000333602:p.Arg741Trp	41.0	0.0		40.0	14.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	hg19		.	.	.	.	.	.	.	.	.	.	C	10.20	1.285411	0.23478	.	.	ENSG00000183495	ENST00000537902;ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000423130;ENST00000541296;ENST00000542457	D;D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.63;-2.64	5.45	5.45	0.79879	.	0.255650	0.36482	N	0.002565	D	0.93468	0.7916	L	0.56769	1.78	0.37563	D	0.919157	D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;0.999	P;P;P;D;P	0.72075	0.804;0.804;0.804;0.976;0.9	D	0.94370	0.7595	10	0.56958	D	0.05	.	12.4227	0.55529	0.2828:0.7172:0.0:0.0	.	705;705;704;741;668	Q96L91-2;Q96L91-4;Q96L91-5;F8WCN8;Q96L91-3	.;.;.;.;.	W	668;741;705;704;668;705;741;705;705	ENSP00000333602:R741W;ENSP00000374212:R705W;ENSP00000374213:R704W;ENSP00000331737:R668W;ENSP00000330620:R705W	ENSP00000330620:R705W	R	+	1	2	EP400	131037195	1.000000	0.71417	0.998000	0.56505	0.136000	0.21042	3.137000	0.50562	2.562000	0.86427	0.563000	0.77884	CGG	.	.		0.587	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		T	132471242	C	T	132471242	3	4	119	1	0	0	0	0	1	0	0	0	5151	643	23	1	2128	1	EP400	12	132471242	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	11892474	132471242	1380653	38	20257										
C14orf106	55320	hgsc.bcm.edu	37	chr14	45700393	45700393	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gtggtggctctttgagcagtAtctgtttggttttctcgtgc	13	7	3	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr14:45700393A>G	ENST00000310806.4	-	8	2003	c.1545T>C	c.(1543-1545)gaT>gaC	p.D515D		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	515					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						TTTGAGCAGTATCTGTTTGGT	0.368																																					p.D515D		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.T1545C						.						251	200	217					14																	45700393		2203	4300	6503	SO:0001819	synonymous_variant	55320	exon8			AGCAGTATCTGTT	AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"kinetochore null 2 homolog (C. elegans)"		"chromosome 14 open reading frame 106"	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.1545T>C	chr14.hg19:g.45700393A>G		263.0	0.0		251.0	101.0	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Silent	SNP	ENST00000310806.4	hg19	CCDS9684.1																																																																																			.	.		0.368	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			G	45700393	A	G	45700393	2	3	119	1	0	0	0	0	0	0	0	1	1740	446	16	2		2	C14orf106	14	45700393	Silent	SNP	A	TCGA-DD-A3A5-01A-11D-A22F-10		45700393	61649147	39	20258										
NEK9	91754	hgsc.bcm.edu	37	chr14	75580093	75580093	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gaagttcatctgcagtaggtCtctgctcaggatcctaaaaa	9	9	4	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr14:75580093C>T	ENST00000238616.5	-	8	1045	c.887G>A	c.(886-888)aGa>aAa	p.R296K		NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	296	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		TGCAGTAGGTCTCTGCTCAGG	0.398																																					p.R296K		Atlas-SNP	.											.	NEK9	64	.	0			c.G887A						.						133	130	131					14																	75580093		2203	4300	6503	SO:0001583	missense	91754	exon8			GTAGGTCTCTGCT	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"NIMA (never in mitosis gene a)- related kinase 9"			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.887G>A	chr14.hg19:g.75580093C>T	ENSP00000238616:p.Arg296Lys	97.0	0.0		159.0	28.0	NM_033116	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Missense_Mutation	SNP	ENST00000238616.5	hg19	CCDS9839.1	.	.	.	.	.	.	.	.	.	.	C	36	5.769402	0.96914	.	.	ENSG00000119638	ENST00000238616;ENST00000540227	T	0.70869	-0.52	5.86	5.86	0.93980	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91815	0.7410	H	0.99197	4.465	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.94648	0.7836	10	0.87932	D	0	.	20.2019	0.98263	0.0:1.0:0.0:0.0	.	296	Q8TD19	NEK9_HUMAN	K	296;278	ENSP00000238616:R296K	ENSP00000238616:R296K	R	-	2	0	NEK9	74649846	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.050000	0.76620	2.776000	0.95493	0.655000	0.94253	AGA	.	.		0.398	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116		T	75580093	C	T	75580093	3	4	119	1	0	0	0	0	1	0	0	0	10340	913	32	3	2112	3	NEK9	14	75580093	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	29879700	75580093	31769447	40	20259										
NRXN3	9369	hgsc.bcm.edu	37	chr14	80328058	80328058	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ccgggggcctcagaggtgatCcgggagtcgagcagcacaac	16	12	1	2			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr14:80328058C>A	ENST00000557594.1	+	6	2618	c.1665C>A	c.(1663-1665)atC>atA	p.I555I	NRXN3_ENST00000281127.7_Silent_p.I350I|NRXN3_ENST00000335750.5_Silent_p.I979I|NRXN3_ENST00000554719.1_Silent_p.I979I|NRXN3_ENST00000428277.2_Silent_p.I377I|NRXN3_ENST00000556003.1_3'UTR	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3	555					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		CAGAGGTGATCCGGGAGTCGA	0.582																																					p.I979I		Atlas-SNP	.											.	NRXN3	342	.	0			c.C2937A						.						57	57	57					14																	80328058		2203	4300	6503	SO:0001819	synonymous_variant	9369	exon17			GGTGATCCGGGAG	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000557594.1:c.1665C>A	chr14.hg19:g.80328058C>A		56.0	0.0		60.0	30.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Silent	SNP	ENST00000557594.1	hg19																																																																																				.	.		0.582	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250		A	80328058	C	A	80328058	2	1	119	1	0	0	0	0	0	0	0	1	10676	845	30	3		3	NRXN3	14	80328058	Silent	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	4747965	80328058	27021482	41	20260										
PPP4R4	57718	hgsc.bcm.edu	37	chr14	94697004	94697004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	attctgcaggacgaatcagtGtcaattcatgcatataccca	7	10	4	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr14:94697004G>A	ENST00000304338.3	+	4	529	c.375G>A	c.(373-375)gtG>gtA	p.V125V	PPP4R4_ENST00000555690.1_3'UTR	NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	125					negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)			NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						ACGAATCAGTGTCAATTCATG	0.468																																					p.V125V		Atlas-SNP	.											.	PPP4R4	107	.	0			c.G375A						.						142	121	128					14																	94697004		2203	4300	6503	SO:0001819	synonymous_variant	57718	exon4			ATCAGTGTCAATT	AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	23788	protein-coding gene	gene with protein product	"cilia and flagella associated protein 14"		"KIAA1622"	KIAA1622		18715871	Standard	NM_020958		Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.375G>A	chr14.hg19:g.94697004G>A		64.0	0.0		82.0	5.0	NM_058237	Q9BUF8|Q9HCF0	Silent	SNP	ENST00000304338.3	hg19	CCDS9921.1																																																																																			.	.		0.468	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		A	94697004	G	A	94697004	2	1	119	1	0	0	0	0	0	0	0	1	12417	1364	48	3		3	PPP4R4	14	94697004	Silent	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	14368946	94697004	12652536	42	20261										
PLA2G4F	255189	hgsc.bcm.edu	37	chr15	42437866	42437866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	atccaggctggtggcaaaggCgctgccccacatacctaagg	12	13	0	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr15:42437866C>T	ENST00000382396.4	-	16	1773	c.1687G>A	c.(1687-1689)Gcc>Acc	p.A563T	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.A565T			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	563	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		GTGGCAAAGGCGCTGCCCCAC	0.642																																					p.A563T		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.G1687A						.						67	71	70					15																	42437866		2203	4299	6502	SO:0001583	missense	255189	exon16			CAAAGGCGCTGCC		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.1687G>A	chr15.hg19:g.42437866C>T	ENSP00000371833:p.Ala563Thr	50.0	0.0		57.0	29.0	NM_213600	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	hg19	CCDS32204.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.456514	0.63401	.	.	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000443825	T;T	0.08720	3.06;3.06	5.0	5.0	0.66597	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.000000	0.51477	D	0.000091	T	0.37019	0.0988	M	0.89095	3.005	0.48901	D	0.999726	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.37776	-0.9691	10	0.54805	T	0.06	-29.2667	18.6782	0.91537	0.0:1.0:0.0:0.0	.	350;563	A2RRC4;Q68DD2	.;PA24F_HUMAN	T	559;565;563;563	ENSP00000380442:A565T;ENSP00000371833:A563T	ENSP00000290497:A559T	A	-	1	0	PLA2G4F	40225158	1.000000	0.71417	0.962000	0.40283	0.037000	0.13140	5.817000	0.69229	2.499000	0.84300	0.484000	0.47621	GCC	.	.		0.642	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		T	42437866	C	T	42437866	3	4	119	1	0	0	0	0	1	0	0	0	12015	768	27	1	882	1	PLA2G4F	15	42437866	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10		42437866	60093526	43	20262										
JMJD8	339123	hgsc.bcm.edu	37	chr16	733364	733364	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	tggagcggttcccagcaggcCaaatgggggtggggagtagt	19	7	0	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr16:733364C>T	ENST00000293882.4	-	6	678	c.679G>A	c.(679-681)Ggc>Agc	p.G227S	JMJD8_ENST00000562824.1_Missense_Mutation_p.G127S|JMJD8_ENST00000454700.1_Missense_Mutation_p.G197S|JMJD8_ENST00000412368.2_Missense_Mutation_p.G178S|JMJD8_ENST00000562111.1_Missense_Mutation_p.G157S|JMJD8_ENST00000609261.1_Missense_Mutation_p.G157S			Q96S16	JMJD8_HUMAN	jumonji domain containing 8	227	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.					extracellular vesicular exosome (GO:0070062)				breast(1)	1						CCCAGCAGGCCAAATGGGGGT	0.582																																					p.G178S		Atlas-SNP	.											.	JMJD8	14	.	0			c.G532A						.						33	39	37					16																	733364		1938	4101	6039	SO:0001583	missense	339123	exon6			GCAGGCCAAATGG		CCDS45369.1	16p13.3	2008-07-28	2008-07-28	2008-07-28		ENSG00000161999			14148	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 20"	C16orf20			Standard	NM_001005920		Approved		uc002ciw.1	Q96S16		ENST00000293882.4:c.679G>A	chr16.hg19:g.733364C>T	ENSP00000293882:p.Gly227Ser	80.0	0.0		87.0	54.0	NM_001005920	B2RNS7|D3DU58|Q4PKE3|Q4VBY1|Q6GMW5|Q71RB8	Missense_Mutation	SNP	ENST00000293882.4	hg19		.	.	.	.	.	.	.	.	.	.	C	3.053	-0.194890	0.06259	.	.	ENSG00000161999	ENST00000412368;ENST00000293882;ENST00000454700	T;T;T	0.69306	-0.39;-0.39;-0.39	4.09	-2.27	0.06846	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	1.172240	0.05931	N	0.635204	T	0.39279	0.1072	N	0.05441	-0.05	0.09310	N	1	B;B	0.17268	0.017;0.021	B;B	0.21151	0.019;0.033	T	0.30001	-0.9993	10	0.06757	T	0.87	0.0235	6.7022	0.23230	0.0:0.2065:0.3762:0.4173	.	197;227	Q96S16-2;Q96S16	.;JMJD8_HUMAN	S	178;227;197	ENSP00000399475:G178S;ENSP00000293882:G227S;ENSP00000394147:G197S	ENSP00000293882:G227S	G	-	1	0	JMJD8	673365	0.000000	0.05858	0.000000	0.03702	0.308000	0.27856	0.452000	0.21795	-0.186000	0.10533	0.556000	0.70494	GGC	.	.		0.582	JMJD8-201	KNOWN	basic	protein_coding	protein_coding		NM_001005920		T	733364	C	T	733364	3	4	119	1	0	0	0	0	1	0	0	0	7965	594	21	3	341	3	JMJD8	16	733364	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10		733364	89621389	44	20263										
IL21R	50615	hgsc.bcm.edu	37	chr16	27460191	27460191	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	aggatgacggctacccagccCtggacctggatgctggcctg	14	13	0	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr16:27460191C>T	ENST00000337929.3	+	9	1677	c.1204C>T	c.(1204-1206)Ctg>Ttg	p.L402L	IL21R_ENST00000395755.1_Silent_p.L402L|IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000395754.4_Silent_p.L402L|IL21R_ENST00000564089.1_Silent_p.L402L	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	402					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						CTACCCAGCCCTGGACCTGGA	0.632			T	BCL6	NHL																																p.L424L		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.C1270T						.						50	53	52					16																	27460191		2197	4300	6497	SO:0001819	synonymous_variant	50615	exon10			CCAGCCCTGGACC	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1204C>T	chr16.hg19:g.27460191C>T		48.0	0.0		91.0	39.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Silent	SNP	ENST00000337929.3	hg19	CCDS10630.1																																																																																			.	.		0.632	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		T	27460191	C	T	27460191	2	4	119	1	0	0	0	0	0	0	0	1	7680	680	24	3		3	IL21R	16	27460191	Silent	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	26726827	27460191	62894562	45	20264			1	19		2	2	24	N	G_C	4.457734e-05
IL21R	50615	hgsc.bcm.edu	37	chr16	27460214	27460214	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gacctggatgctggcctggaGcccagcccaggcctagagga	15	13	0	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr16:27460214G>T	ENST00000337929.3	+	9	1700	c.1227G>T	c.(1225-1227)gaG>gaT	p.E409D	IL21R_ENST00000395755.1_Missense_Mutation_p.E409D|IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000395754.4_Missense_Mutation_p.E409D|IL21R_ENST00000564089.1_Missense_Mutation_p.E409D	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	409					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						CTGGCCTGGAGCCCAGCCCAG	0.647			T	BCL6	NHL																																p.E431D		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.G1293T						.						46	51	49					16																	27460214		2197	4300	6497	SO:0001583	missense	50615	exon10			CCTGGAGCCCAGC	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1227G>T	chr16.hg19:g.27460214G>T	ENSP00000338010:p.Glu409Asp	45.0	0.0		84.0	30.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	hg19	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	G	12.54	1.968143	0.34754	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.35789	1.29;1.29;1.29	5.19	-1.47	0.08772	.	0.867272	0.10160	N	0.708430	T	0.31796	0.0808	L	0.50919	1.6	0.09310	N	1	D	0.56035	0.974	P	0.44946	0.465	T	0.29640	-1.0005	10	0.33141	T	0.24	-12.5197	8.583	0.33642	0.0:0.3509:0.3847:0.2644	.	409	Q9HBE5	IL21R_HUMAN	D	409	ENSP00000338010:E409D;ENSP00000379104:E409D;ENSP00000379103:E409D	ENSP00000338010:E409D	E	+	3	2	IL21R	27367715	0.016000	0.18221	0.015000	0.15790	0.003000	0.03518	0.337000	0.19841	-0.055000	0.13244	-1.083000	0.02208	GAG	.	.		0.647	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		T	27460214	G	T	27460214	3	4	119	1	0	0	0	0	1	0	0	0	7680	962	34	3	1257	3	IL21R	16	27460214	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	23	27460214	62894539	46	20265			1	19		2	2	24	N	G_C	4.457734e-05
DUSP14	11072	hgsc.bcm.edu	37	chr17	35872856	35872856	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ctggaggcaactgatagactAcgagcgccagctctttggga	13	10	1	2			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr17:35872856A>G	ENST00000487847.1	+	2	1460	c.482A>G	c.(481-483)tAc>tGc	p.Y161C	DUSP14_ENST00000394386.1_Missense_Mutation_p.Y161C|DUSP14_ENST00000394389.4_Missense_Mutation_p.Y161C			O95147	DUS14_HUMAN	dual specificity phosphatase 14	161					peptidyl-tyrosine dephosphorylation (GO:0035335)		MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|poly(A) RNA binding (GO:0044822)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|urinary_tract(1)	9		Breast(25;0.00637)|Ovarian(249;0.15)				CTGATAGACTACGAGCGCCAG	0.537																																					p.Y161C		Atlas-SNP	.											.	DUSP14	16	.	0			c.A482G						.						57	56	56					17																	35872856		2203	4300	6503	SO:0001583	missense	11072	exon3			TAGACTACGAGCG	AF038844	CCDS11320.1	17q12	2014-05-06			ENSG00000161326	ENSG00000276023		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	17007	protein-coding gene	gene with protein product	"MKP-1 like protein tyrosine phosphatase"	606618				11123293	Standard	XM_005256977		Approved	MKP-L, MKP6	uc002hnx.2	O95147	OTTHUMG00000188472	ENST00000487847.1:c.482A>G	chr17.hg19:g.35872856A>G	ENSP00000466299:p.Tyr161Cys	36.0	0.0		31.0	12.0	NM_007026		Missense_Mutation	SNP	ENST00000487847.1	hg19	CCDS11320.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.125984	0.77436	.	.	ENSG00000161326	ENST00000394389;ENST00000394386	T;T	0.63096	-0.02;-0.02	6.06	6.06	0.98353	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.82802	0.5116	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86040	0.1519	10	0.87932	D	0	.	16.6245	0.84952	1.0:0.0:0.0:0.0	.	161	O95147	DUS14_HUMAN	C	161	ENSP00000377912:Y161C;ENSP00000377910:Y161C	ENSP00000377910:Y161C	Y	+	2	0	DUSP14	32946969	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.323000	0.78572	0.528000	0.53228	TAC	.	.		0.537	DUSP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256680.3	NM_007026		G	35872856	A	G	35872856	3	3	119	1	0	0	0	0	1	0	0	0	4816	391	14	2	484	2	DUSP14	17	35872856	Missense_Mutation	SNP	A	TCGA-DD-A3A5-01A-11D-A22F-10		35872856	45322354	47	20266										
GAST	2520	hgsc.bcm.edu	37	chr17	39872101	39872101	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gatggatggacttcggccgcCgcagtgctgaggatgagaac	16	9	0	2			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr17:39872101C>T	ENST00000329402.3	+	3	350	c.283C>T	c.(283-285)Cgc>Tgc	p.R95C	RNA5SP442_ENST00000365050.1_RNA|JUP_ENST00000540235.1_Intron	NM_000805.4	NP_000796.1	P01350	GAST_HUMAN	gastrin	95		Cleavage.			G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.R95S(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7		Breast(137;0.000307)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			CTTCGGCCGCCGCAGTGCTGA	0.557																																					p.R95C		Atlas-SNP	.											GAST,NS,carcinoma,0,1	GAST	13	.	1	Substitution - Missense(1)	kidney(1)	c.C283T						.						64	66	65					17																	39872101		2203	4300	6503	SO:0001583	missense	2520	exon3			GGCCGCCGCAGTG		CCDS11404.1	17q21.2	2013-02-26	2005-06-14	2005-06-14	ENSG00000184502	ENSG00000184502		"Endogenous ligands"	4164	protein-coding gene	gene with protein product	"preprogastrin"	137250		GAS			Standard	NM_000805		Approved		uc002hxl.3	P01350	OTTHUMG00000133496	ENST00000329402.3:c.283C>T	chr17.hg19:g.39872101C>T	ENSP00000331358:p.Arg95Cys	63.0	0.0		59.0	22.0	NM_000805	P78463|P78464	Missense_Mutation	SNP	ENST00000329402.3	hg19	CCDS11404.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.495508	0.44352	.	.	ENSG00000184502	ENST00000329402	T	0.68765	-0.35	4.74	4.74	0.60224	Gastrin/cholecystokinin peptide hormone (2);	0.000000	0.51477	D	0.000084	T	0.80031	0.4549	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.82315	-0.0518	10	0.87932	D	0	-18.3216	13.1178	0.59309	0.0:1.0:0.0:0.0	.	95	P01350	GAST_HUMAN	C	95	ENSP00000331358:R95C	ENSP00000331358:R95C	R	+	1	0	GAST	37125627	0.999000	0.42202	0.998000	0.56505	0.003000	0.03518	3.303000	0.51858	2.455000	0.83008	0.655000	0.94253	CGC	.	.		0.557	GAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257409.1			T	39872101	C	T	39872101	3	4	119	1	0	0	0	0	1	0	0	0	6260	652	23	1	289	1	GAST	17	39872101	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	3999245	39872101	41323109	48	20267										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76462860	76462860	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gggaactttctggctcgtacCcgcagcacggagcccacagg	13	14	1	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr17:76462860C>A	ENST00000585328.1	-	56	8926	c.8802G>T	c.(8800-8802)cgG>cgT	p.R2934R	DNAH17_ENST00000389840.5_Silent_p.R2925R|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2925	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TGGCTCGTACCCGCAGCACGG	0.627																																					p.R2939R		Atlas-SNP	.											.	DNAH17	347	.	0			c.G8817T						.						33	42	39					17																	76462860		2139	4264	6403	SO:0001819	synonymous_variant	8632	exon56			TCGTACCCGCAGC	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.8802G>T	chr17.hg19:g.76462860C>A		37.0	0.0		41.0	21.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	hg19																																																																																				.	.		0.627	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76462860	C	A	76462860	2	1	119	1	0	0	0	0	0	0	0	1	4603	610	22	3		3	DNAH17	17	76462860	Silent	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	36590759	76462860	4732350	49	20268										
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72998476	72998476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ctgagccagcaggaatggccGcagaggtggccctgagtgag	17	10	0	4	rs574385316		TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr18:72998476G>A	ENST00000580243.1	+	2	1462	c.1114G>A	c.(1114-1116)Gca>Aca	p.A372T	TSHZ1_ENST00000322038.5_Missense_Mutation_p.A327T			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	372					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		AGGAATGGCCGCAGAGGTGGC	0.627													G|||	1	0.000199681	0	0.0014	5008	,	,		19208	0		0	False		,,,				2504	0				p.A327T		Atlas-SNP	.											.	TSHZ1	104	.	0			c.G979A						.						74	82	79					18																	72998476		2203	4300	6503	SO:0001583	missense	10194	exon2			ATGGCCGCAGAGG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	10669	protein-coding gene	gene with protein product		614427	"serologically defined colon cancer antigen 33", "teashirt zinc finger 1", "teashirt family zinc finger 1"	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1114G>A	chr18.hg19:g.72998476G>A	ENSP00000464391:p.Ala372Thr	78.0	0.0		79.0	34.0	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	hg19		.	.	.	.	.	.	.	.	.	.	G	1.242	-0.621015	0.03636	.	.	ENSG00000179981	ENST00000322038	T	0.11277	2.79	5.27	-2.73	0.05950	.	0.571079	0.17601	N	0.168404	T	0.04452	0.0122	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.43310	-0.9399	10	0.06757	T	0.87	-2.434	0.0607	0.00015	0.2732:0.1957:0.2408:0.2903	.	372	Q6ZSZ6	TSH1_HUMAN	T	327	ENSP00000323584:A327T	ENSP00000323584:A327T	A	+	1	0	TSHZ1	71127464	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-0.712000	0.05013	1.206000	0.43276	0.561000	0.74099	GCA	.	.		0.627	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	72998476	G	A	72998476	3	1	119	1	0	0	0	0	1	0	0	0	16638	1087	38	1	981	1	TSHZ1	18	72998476	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10		72998476	5078772	50	20269										
C19orf21	126353	hgsc.bcm.edu	37	chr19	758170	758170	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gccccagatgcccgtgcggcCgacccagctccagaagtgag	13	16	0	3	rs530131211		TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr19:758170C>T	ENST00000215582.6	+	2	1327	c.1224C>T	c.(1222-1224)gcC>gcT	p.A408A		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	408					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CCCGTGCGGCCGACCCAGCTC	0.667													C|||	1	0.000199681	8e-04	0	5008	,	,		13659	0		0	False		,,,				2504	0				p.A408A		Atlas-SNP	.											.	C19orf21	56	.	0			c.C1224T						.						19	17	18					19																	758170		2192	4285	6477	SO:0001819	synonymous_variant	126353	exon2			TGCGGCCGACCCA	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.1224C>T	chr19.hg19:g.758170C>T		36.0	0.0		49.0	17.0	NM_173481		Silent	SNP	ENST00000215582.6	hg19	CCDS12042.1																																																																																			.	.		0.667	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		T	758170	C	T	758170	2	4	119	1	0	0	0	0	0	0	0	1	1915	639	23	1		1	C19orf21	19	758170	Silent	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10		758170	58370813	51	20270										
CEACAM6	4680	hgsc.bcm.edu	37	chr19	42266039	42266039	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	agagctctttatccccaacaTcactgtgaataatagcggat	7	10	2	2			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr19:42266039T>C	ENST00000199764.6	+	4	1084	c.866T>C	c.(865-867)aTc>aCc	p.I289T	AC011513.4_ENST00000601409.1_RNA	NM_002483.4	NP_002474.3	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	289	Ig-like C2-type 2.				cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|kidney(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.00575)|all cancers(3;0.0352)|Epithelial(262;0.0797)		ATCCCCAACATCACTGTGAAT	0.498																																					p.I289T		Atlas-SNP	.											.	CEACAM6	52	.	0			c.T866C						.						137	120	126					19																	42266039		2203	4300	6503	SO:0001583	missense	4680	exon4			CCAACATCACTGT	M29541	CCDS12585.1	19q13.1-q13.2	2013-01-29			ENSG00000086548	ENSG00000086548		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1818	protein-coding gene	gene with protein product		163980		NCA			Standard	NM_002483		Approved	CD66c	uc002orm.2	P40199	OTTHUMG00000151064	ENST00000199764.6:c.866T>C	chr19.hg19:g.42266039T>C	ENSP00000199764:p.Ile289Thr	138.0	0.0		150.0	56.0	NM_002483	Q13774|Q14920|Q53XP7	Missense_Mutation	SNP	ENST00000199764.6	hg19	CCDS12585.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.287950	0.40494	.	.	ENSG00000086548	ENST00000199764	T	0.13901	2.55	1.87	1.87	0.25490	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.33118	0.0852	M	0.81179	2.53	0.09310	N	1	D	0.65815	0.995	D	0.71184	0.972	T	0.05566	-1.0877	9	0.87932	D	0	.	5.677	0.17753	0.0:0.0:0.0:1.0	.	289	P40199	CEAM6_HUMAN	T	289	ENSP00000199764:I289T	ENSP00000199764:I289T	I	+	2	0	CEACAM6	46957879	0.004000	0.15560	0.681000	0.30009	0.115000	0.19883	1.621000	0.36986	0.858000	0.35431	0.254000	0.18369	ATC	.	.		0.498	CEACAM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321147.1			C	42266039	T	C	42266039	3	2	119	1	0	0	0	0	1	0	0	0	3198	1435	50	2	880	2	CEACAM6	19	42266039	Missense_Mutation	SNP	T	TCGA-DD-A3A5-01A-11D-A22F-10	41507869	42266039	16862944	52	20271										
CARD8	22900	hgsc.bcm.edu	37	chr19	48718639	48718639	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	tgcagctacaagctggagatCcactacaaaagagggaaaaa	10	8	0	2			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr19:48718639C>A	ENST00000359009.4	-	9	1300	c.988G>T	c.(988-990)Gat>Tat	p.D330Y	CARD8_ENST00000521613.1_Missense_Mutation_p.D386Y|CARD8_ENST00000520153.1_Missense_Mutation_p.D386Y|ZNF114_ENST00000597695.1_Intron|CARD8_ENST00000519940.1_Missense_Mutation_p.D436Y|CARD8_ENST00000447740.2_Missense_Mutation_p.D386Y|CARD8_ENST00000520015.1_Missense_Mutation_p.W388C|CTC-453G23.8_ENST00000595201.1_RNA|CARD8_ENST00000391898.3_Missense_Mutation_p.D436Y|CARD8_ENST00000357778.5_Missense_Mutation_p.D161Y|CARD8_ENST00000520753.1_Missense_Mutation_p.W388C			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	330					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		AGCTGGAGATCCACTACAAAA	0.373																																					p.D436Y		Atlas-SNP	.											.	CARD8	53	.	0			c.G1306T						.						73	69	70					19																	48718639		2203	4300	6503	SO:0001583	missense	22900	exon10			GGAGATCCACTAC	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.988G>T	chr19.hg19:g.48718639C>A	ENSP00000351901:p.Asp330Tyr	72.0	0.0		72.0	26.0	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Missense_Mutation	SNP	ENST00000359009.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.61|10.61	1.397879|1.397879	0.25205|0.25205	.|.	.|.	ENSG00000105483|ENSG00000105483	ENST00000357778;ENST00000447740;ENST00000391898;ENST00000359009;ENST00000520153;ENST00000521613;ENST00000519940|ENST00000520753;ENST00000520015	T;T;T;T;T;T;T|T;T	0.26810|0.16743	1.71;1.71;1.71;1.71;1.71;1.71;1.71|2.32;2.32	1.57|1.57	0.503|0.503	0.16940|0.16940	.|.	.|.	.|.	.|.	.|.	T|T	0.32194|0.32194	0.0821|0.0821	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	D;D;D;D;D|B;D;D	0.76494|0.76494	0.997;0.999;0.999;0.997;0.997|0.013;0.999;0.998	D;D;D;D;D|B;D;D	0.71870|0.74674	0.954;0.975;0.975;0.923;0.954|0.001;0.984;0.938	T|T	0.10109|0.10109	-1.0644|-1.0644	8|8	0.87932|0.87932	D|D	0|0	.|.	4.009|4.009	0.09615|0.09615	0.0:0.7732:0.0:0.2268|0.0:0.7732:0.0:0.2268	.|.	355;436;436;386;330|279;388;282	B5KVR7;E9PEM7;B5KVR6;G3XAM9;Q9Y2G2|Q6MZI8;Q9Y2G2-3;Q9Y2G2-2	.;.;.;.;CARD8_HUMAN|.;.;.	Y|C	161;386;436;330;386;386;436|388	ENSP00000350423:D161Y;ENSP00000391248:D386Y;ENSP00000375767:D436Y;ENSP00000351901:D330Y;ENSP00000428736:D386Y;ENSP00000427858:D386Y;ENSP00000428883:D436Y|ENSP00000429839:W388C;ENSP00000430747:W388C	ENSP00000350423:D161Y|ENSP00000430747:W388C	D|W	-|-	1|3	0|0	CARD8|CARD8	53410451|53410451	0.009000|0.009000	0.17119|0.17119	0.072000|0.072000	0.20136|0.20136	0.061000|0.061000	0.15899|0.15899	0.229000|0.229000	0.17833|0.17833	0.239000|0.239000	0.21243|0.21243	0.313000|0.313000	0.20887|0.20887	GAT|TGG	.	.		0.373	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959		A	48718639	C	A	48718639	3	1	119	1	0	0	0	0	1	0	0	0	2653	856	30	3	315	3	CARD8	19	48718639	Missense_Mutation	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10	6452600	48718639	10410344	53	20272										
ZNF534	147658	hgsc.bcm.edu	37	chr19	52938382	52938382	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ctccatgttggagcaaaagaGagatccctggactctgcaga	11	10	1	3			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr19:52938382G>A	ENST00000332323.6	+	3	291	c.230G>A	c.(229-231)aGa>aAa	p.R77K	ZNF534_ENST00000301085.4_Missense_Mutation_p.R64K|ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000433050.1_Missense_Mutation_p.R64K	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	77	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						GAGCAAAAGAGAGATCCCTGG	0.453																																					p.R77K		Atlas-SNP	.											.	ZNF534	105	.	0			c.G230A						.						126	104	110					19																	52938382		1568	3582	5150	SO:0001583	missense	147658	exon3			AAAAGAGAGATCC	AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"Zinc fingers, C2H2-type", "-"	26337	protein-coding gene	gene with protein product			"KRAB domain only 3"	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.230G>A	chr19.hg19:g.52938382G>A	ENSP00000327538:p.Arg77Lys	143.0	0.0		104.0	44.0	NM_001143939	Q76KX9	Missense_Mutation	SNP	ENST00000332323.6	hg19	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.091411	0.00367	.	.	ENSG00000198633	ENST00000301085;ENST00000332323;ENST00000433050;ENST00000391790	T;T;T	0.05649	5.79;3.41;3.43	1.67	-3.34	0.04943	Krueppel-associated box (2);	.	.	.	.	T	0.01730	0.0055	N	0.02751	-0.505	0.09310	N	1	B;B;B	0.17852	0.001;0.0;0.024	B;B;B	0.11329	0.0;0.0;0.006	T	0.40213	-0.9575	9	0.02654	T	1	.	3.3017	0.06985	0.4699:0.2187:0.3114:0.0	.	64;77;64	Q76KX8-2;Q76KX8;Q1T7F5	.;ZN534_HUMAN;.	K	64;77;64;76	ENSP00000301085:R64K;ENSP00000327538:R77K;ENSP00000391358:R64K	ENSP00000301085:R64K	R	+	2	0	ZNF534	57630194	0.005000	0.15991	0.001000	0.08648	0.024000	0.10985	-0.185000	0.09684	-1.449000	0.01938	-0.474000	0.04947	AGA	.	.		0.453	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512		A	52938382	G	A	52938382	3	1	119	1	0	0	0	0	1	0	0	0	17988	942	33	3	240	3	ZNF534	19	52938382	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	4219743	52938382	6190601	54	20273										
ZNF132	7691	hgsc.bcm.edu	37	chr19	58944869	58944870	+	Frame_Shift_Del	DEL	CT	CT	-													0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gggcctttcttgtgtgtgaaCtctctgatgacgaaccaggt							TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr19:58944869_58944870delCT	ENST00000254166.3	-	3	2341_2342	c.1941_1942delAG	c.(1939-1944)agagttfs	p.RV647fs	CTD-2619J13.17_ENST00000594816.1_lincRNA	NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	647					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		TGTGTGTGAACTCTCTGATGAC	0.465																																					p.648_648del		Atlas-Indel,Pindel	.											.	ZNF132	56	.	0			c.1942_1943del						.																																			SO:0001589	frameshift_variant	7691	exon3			.	U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"Zinc fingers, C2H2-type", "-"	12916	protein-coding gene	gene with protein product		604074	"zinc finger protein 132 (clone pHZ-12)"			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.1941_1942delAG	chr19.hg19:g.58944873_58944874delCT	ENSP00000254166:p.Arg647fs	68.0	0.0		75.0	30.0	NM_003433	Q32MI9	Frame_Shift_Del	DEL	ENST00000254166.3	hg19	CCDS12980.1																																																																																			.	.		0.465	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433		-	58944870	CT	-	58944869	7	5	119	1	0	1	0	1	0	0	0	0	17737	565	20	0	182	0	ZNF132	19	58944869	Frame_Shift_Del	DEL	CT	TCGA-DD-A3A5-01A-11D-A22F-10	6006487	58944869	184114	55	20274										
LCA5L	150082	hgsc.bcm.edu	37	chr21	40794906	40794907	+	Frame_Shift_Ins	INS	-	-	T													0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ccctgaaatacagacctgtaINStttttttgtcatttgcgtcc							TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr21:40794906_40794907insT	ENST00000358268.2	-	5	1360_1361	c.832_833insA	c.(832-834)atafs	p.I278fs	LCA5L_ENST00000485895.2_Frame_Shift_Ins_p.I278fs|LCA5L_ENST00000380671.2_Frame_Shift_Ins_p.I278fs|LCA5L_ENST00000288350.3_Frame_Shift_Ins_p.I278fs			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	278										breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				ACAGACCTGTATTTTTTTGTCA	0.381																																					p.I278fs		Atlas-INDEL	.											.	LCA5L	57	.	0			c.833_834insA						.																																			SO:0001589	frameshift_variant	150082	exon5			.	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 13"	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.833dupA	chr21.hg19:g.40794913_40794913dupT	ENSP00000351008:p.Ile278fs	174.0	0.0		240.0	75.0	NM_152505	D3DSI0|Q3ZCT0	Frame_Shift_Ins	INS	ENST00000358268.2	hg19	CCDS13665.1																																																																																			.	.		0.381	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		T	40794907	-	T	40794906	7	5	119	1	0	1	1	0	0	0	0	0	8666	449	16	0	1203	0	LCA5L	21	40794906	Frame_Shift_Ins	INS	-	TCGA-DD-A3A5-01A-11D-A22F-10		40794906	7334989	56	20275										
SGSM1	129049	hgsc.bcm.edu	37	chr22	25275471	25275471	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	gacaatatgaagtaccagatCctctccagagccttctatgg	8	11	2	3			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr22:25275471C>A	ENST00000400359.4	+	15	1645	c.1638C>A	c.(1636-1638)atC>atA	p.I546I	SGSM1_ENST00000400358.4_Silent_p.I491I	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	546						Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						AGTACCAGATCCTCTCCAGAG	0.488																																					p.I546I		Atlas-SNP	.											.	SGSM1	150	.	0			c.C1638A						.						79	74	76					22																	25275471		1881	4113	5994	SO:0001819	synonymous_variant	129049	exon15			CCAGATCCTCTCC	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"Small G protein signaling modulators"	29410	protein-coding gene	gene with protein product		611417	"RUN and TBC1 domain containing 2"	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.1638C>A	chr22.hg19:g.25275471C>A		84.0	0.0		90.0	44.0	NM_133454	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	hg19	CCDS46674.1																																																																																			.	.		0.488	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318		A	25275471	C	A	25275471	2	1	119	1	0	0	0	0	0	0	0	1	14237	845	30	3		3	SGSM1	22	25275471	Silent	SNP	C	TCGA-DD-A3A5-01A-11D-A22F-10		25275471	26029095	57	20276										
MTMR3	8897	hgsc.bcm.edu	37	chr22	30418642	30418642	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ctggccgcccactgctatgcGtgcgacagtgccttctggct	12	15	1	0			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr22:30418642G>C	ENST00000401950.2	+	19	3723	c.3381G>C	c.(3379-3381)gcG>gcC	p.A1127A	MTMR3_ENST00000351488.3_Silent_p.A1090A|CTA-85E5.10_ENST00000453743.2_RNA|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000333027.3_Silent_p.A1090A|MTMR3_ENST00000406629.1_Silent_p.A1090A|MTMR3_ENST00000323630.5_Silent_p.A991A	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	1127					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			ACTGCTATGCGTGCGACAGTG	0.617																																					p.A1127A		Atlas-SNP	.											MTMR3_ENST00000401950,NS,carcinoma,0,1	MTMR3	106	.	0			c.G3381C						.						81	62	68					22																	30418642		2203	4300	6503	SO:0001819	synonymous_variant	8897	exon19			CTATGCGTGCGAC	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.3381G>C	chr22.hg19:g.30418642G>C		6.0	1.0		21.0	10.0	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Silent	SNP	ENST00000401950.2	hg19	CCDS13870.1																																																																																			.	.		0.617	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		C	30418642	G	C	30418642	2	2	119	1	0	0	0	0	0	0	0	1	9954	1132	40	4		4	MTMR3	22	30418642	Silent	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	5143171	30418642	20885924	58	20277										
RFPL2	10739	hgsc.bcm.edu	37	chr22	32588963	32588963	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	ccagttccttgatgtgggaaGccagcctctctagctgccga	11	13	1	1			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chr22:32588963G>A	ENST00000400237.1	-	4	1417	c.482C>T	c.(481-483)gCt>gTt	p.A161V	RFPL2_ENST00000400236.3_Missense_Mutation_p.A71V|RFPL2_ENST00000489846.1_5'UTR|RFPL2_ENST00000248983.4_Missense_Mutation_p.A71V|RFPL2_ENST00000248980.4_Missense_Mutation_p.A100V			O75678	RFPL2_HUMAN	ret finger protein-like 2	161							zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	21						GATGTGGGAAGCCAGCCTCTC	0.537																																					p.A161V		Atlas-SNP	.											RFPL2_ENST00000400237,NS,neuroblastoma,0,3	RFPL2	81	.	0			c.C482T						.						94	97	96					22																	32588963		2203	4300	6503	SO:0001583	missense	10739	exon4			TGGGAAGCCAGCC	AJ010231	CCDS43009.1, CCDS46694.1, CCDS43009.2	22q12.3	2008-06-12				ENSG00000128253		"RING-type (C3HC4) zinc fingers"	9979	protein-coding gene	gene with protein product		605969				10508838	Standard	NM_001098527		Approved	RNF79	uc003amg.3	O75678		ENST00000400237.1:c.482C>T	chr22.hg19:g.32588963G>A	ENSP00000383096:p.Ala161Val	125.0	0.0		156.0	7.0	NM_001098527		Missense_Mutation	SNP	ENST00000400237.1	hg19	CCDS43009.2	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.303198	0.00240	.	.	ENSG00000128253	ENST00000248980;ENST00000248983;ENST00000400236;ENST00000400237	T;T;T;T	0.11821	2.74;2.74;2.74;2.74	0.636	-0.54	0.11861	Zinc finger, RING/FYVE/PHD-type (1);RDM domain, Ret finger protein-like (1);	.	.	.	.	T	0.02047	0.0064	N	0.00217	-1.83	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.41893	-0.9483	8	0.02654	T	1	.	.	.	.	.	161;100	O75678;O75678-3	RFPL2_HUMAN;.	V	100;71;71;161	ENSP00000248980:A100V;ENSP00000248983:A71V;ENSP00000383095:A71V;ENSP00000383096:A161V	ENSP00000248980:A100V	A	-	2	0	RFPL2	30918963	0.002000	0.14202	0.001000	0.08648	0.006000	0.05464	-0.065000	0.11617	-0.330000	0.08514	-0.606000	0.04082	GCT	.	.		0.537	RFPL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075262.2	NM_006605		A	32588963	G	A	32588963	3	1	119	1	0	0	0	0	1	0	0	0	13269	971	34	3	662	3	RFPL2	22	32588963	Missense_Mutation	SNP	G	TCGA-DD-A3A5-01A-11D-A22F-10	2170321	32588963	18715603	59	20278										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128641995	128641995	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	3	1	0.724242424242424	1.03463203463203	0.629776021080369	1	1	0	aaactttttgaatacagattTttctttaattaccatctcat	2	7	2	2			TCGA-DD-A3A5-01A-11D-A22F-10	TCGA-DD-A3A5-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d536aaa-3e77-409a-a97c-a0e525c3a267	634467ec-6024-4df4-9b0a-399177ac8ba2	g.chrX:128641995T>A	ENST00000371122.4	-	7	1018	c.889A>T	c.(889-891)Aaa>Taa	p.K297*	SMARCA1_ENST00000478420.1_5'Flank|SMARCA1_ENST00000371123.1_Nonsense_Mutation_p.K297*|SMARCA1_ENST00000371121.3_Nonsense_Mutation_p.K297*	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	297	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						AATACAGATTTTTCTTTAATT	0.323																																					p.K297X		Atlas-SNP	.											.	SMARCA1	126	.	0			c.A889T						.						45	39	41					X																	128641995		2203	4296	6499	SO:0001587	stop_gained	6594	exon7			CAGATTTTTCTTT	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.889A>T	chrX.hg19:g.128641995T>A	ENSP00000360163:p.Lys297*	362.0	1.0		349.0	139.0	NM_139035	Q5JV41|Q5JV42	Nonsense_Mutation	SNP	ENST00000371122.4	hg19	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	T	37	6.413170	0.97546	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	.	.	.	5.53	5.53	0.82687	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.4118	14.8541	0.70323	0.0:0.0:0.0:1.0	.	.	.	.	X	297;297;297;276	.	ENSP00000360162:K297X	K	-	1	0	SMARCA1	128469676	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.997000	0.88414	1.958000	0.56883	0.441000	0.28932	AAA	.	.		0.323	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		A	128641995	T	A	128641995	4	1	119	1	0	0	0	0	0	1	0	0	14783	1850	64	4	2347	4	SMARCA1	23	128641995	Nonsense_Mutation	SNP	T	TCGA-DD-A3A5-01A-11D-A22F-10		128641995	26628565	60	20279										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183694627	183694627	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aatgcctcttgtatttagctAtgacagtgaaggtcgtctga	10	7	2	3			TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr4:183694627A>G	ENST00000511685.1	+	23	5018	c.4895A>G	c.(4894-4896)tAt>tGt	p.Y1632C	RP11-18D7.2_ENST00000513255.1_RNA|TENM3_ENST00000406950.2_Missense_Mutation_p.Y1632C			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1632					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTATTTAGCTATGACAGTGAA	0.393																																					p.Y1632C		Atlas-SNP	.											.	.	.	.	0			c.A4895G						.						131	120	123					4																	183694627		1928	4141	6069	SO:0001583	missense	55714	exon22			TTAGCTATGACAG	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.4895A>G	chr4.hg19:g.183694627A>G	ENSP00000424226:p.Tyr1632Cys	278.0	0.0		195.0	22.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	A	19.75	3.886486	0.72410	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.16897	2.31;2.31	5.26	5.26	0.73747	.	.	.	.	.	T	0.48537	0.1505	M	0.88906	2.99	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.58476	-0.7630	9	0.87932	D	0	.	15.3531	0.74405	1.0:0.0:0.0:0.0	.	1632	Q9P273	TEN3_HUMAN	C	1632	ENSP00000424226:Y1632C;ENSP00000385276:Y1632C	ENSP00000385276:Y1632C	Y	+	2	0	ODZ3	183931621	1.000000	0.71417	0.999000	0.59377	0.896000	0.52359	8.761000	0.91691	2.207000	0.71202	0.533000	0.62120	TAT	.	.		0.393	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			G	183694627	A	G	183694627	3	3	120	1	0	0	0	0	1	0	0	0	10845	449	16	2	4981	2	ODZ3	4	183694627	Missense_Mutation	SNP	A	TCGA-DD-A3A6-01A-11D-A22F-10		183694627	7459649	1	20280										
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5209306	5209306	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tatatgatgcaaacacacagTgcaagtggcagttcggagag	12	7	0	2	rs547851789		TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr5:5209306T>A	ENST00000274181.7	+	10	1690	c.1552T>A	c.(1552-1554)Tgc>Agc	p.C518S	ADAMTS16_ENST00000511368.1_Missense_Mutation_p.C518S	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	518	Disintegrin.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						AAACACACAGTGCAAGTGGCA	0.443																																					p.C518S		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.T1552A						.						139	133	135					5																	5209306		1937	4152	6089	SO:0001583	missense	170690	exon10			ACACAGTGCAAGT	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.1552T>A	chr5.hg19:g.5209306T>A	ENSP00000274181:p.Cys518Ser	185.0	0.0		120.0	7.0	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.737295	0.89482	.	.	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	D;D	0.82619	-1.63;-1.63	5.9	5.9	0.94986	Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93916	0.8053	H	0.96301	3.8	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.81914	0.994;0.995;0.971	D	0.95594	0.8657	10	0.87932	D	0	.	15.3148	0.74065	0.0:0.0:0.0:1.0	.	518;518;518	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	S	518	ENSP00000274181:C518S;ENSP00000421631:C518S	ENSP00000274181:C518S	C	+	1	0	ADAMTS16	5262306	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.048000	0.76606	2.251000	0.74343	0.528000	0.53228	TGC	.	.		0.443	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		A	5209306	T	A	5209306	3	1	120	1	0	0	0	0	1	0	0	0	261	1696	59	4	1590	4	ADAMTS16	5	5209306	Missense_Mutation	SNP	T	TCGA-DD-A3A6-01A-11D-A22F-10		5209306	175705954	2	20281										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119327610	119327610	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgcagtagaattatgaaattAcctccacatttaatagagca	6	7	0	3			TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr6:119327610A>G	ENST00000338891.7	-	7	2259		c.e7+1		RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000522284.1_Splice_Site|FAM184A_ENST00000368475.4_Splice_Site|FAM184A_ENST00000352896.5_Splice_Site|FAM184A_ENST00000521531.1_Splice_Site	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A							extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						TTATGAAATTACCTCCACATT	0.363																																					.		Atlas-SNP	.											.	FAM184A	109	.	0			c.1455+2T>C						.						92	88	89					6																	119327610		1837	4080	5917	SO:0001630	splice_region_variant	79632	exon8			GAAATTACCTCCA	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1815+1T>C	chr6.hg19:g.119327610A>G		117.0	0.0		75.0	13.0	NM_001100411	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Splice_Site	SNP	ENST00000338891.7	hg19	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	A	12.96	2.093737	0.36952	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2421	0.82418	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAM184A	119369309	1.000000	0.71417	0.997000	0.53966	0.124000	0.20399	6.603000	0.74145	2.234000	0.73211	0.533000	0.62120	.	.	.		0.363	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581	Intron	G	119327610	A	G	119327610	5	3	120	1	0	0	0	0	0	0	1	0	5516	405	14	2	1653	2	FAM184A	6	119327610	Splice_Site	SNP	A	TCGA-DD-A3A6-01A-11D-A22F-10		119327610	51787457	3	20282										
C6orf118	168090	hgsc.bcm.edu	37	chr6	165715587	165715587	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgggccagtgctgtaagatcGtctccggaggctggtagagc	16	9	1	2			TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr6:165715587G>A	ENST00000230301.8	-	2	244	c.224C>T	c.(223-225)aCg>aTg	p.T75M	C6orf118_ENST00000543069.1_De_novo_Start_InFrame	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	75										breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		CTGTAAGATCGTCTCCGGAGG	0.612																																					p.T75M		Atlas-SNP	.											.	C6orf118	116	.	0			c.C224T						.						96	107	103					6																	165715587		2203	4300	6503	SO:0001583	missense	168090	exon2			AAGATCGTCTCCG		CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.224C>T	chr6.hg19:g.165715587G>A	ENSP00000230301:p.Thr75Met	119.0	0.0		86.0	7.0	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	hg19	CCDS5288.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.584057	0.46110	.	.	ENSG00000112539	ENST00000230301	T	0.12361	2.69	5.31	-1.32	0.09201	.	0.763645	0.11964	N	0.512482	T	0.03520	0.0101	L	0.61218	1.895	0.09310	N	1	B	0.24675	0.109	B	0.18263	0.021	T	0.40079	-0.9582	10	0.49607	T	0.09	-12.8169	0.4604	0.00515	0.2248:0.2465:0.2763:0.2524	.	75	Q5T5N4	CF118_HUMAN	M	75	ENSP00000230301:T75M	ENSP00000230301:T75M	T	-	2	0	C6orf118	165635577	0.000000	0.05858	0.010000	0.14722	0.006000	0.05464	-1.112000	0.03299	-0.278000	0.09180	-0.753000	0.03488	ACG	.	.		0.612	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980		A	165715587	G	A	165715587	3	1	120	1	0	0	0	0	1	0	0	0	2325	1145	40	1	1217	1	C6orf118	6	165715587	Missense_Mutation	SNP	G	TCGA-DD-A3A6-01A-11D-A22F-10	46387977	165715587	5399480	4	20283										
FAM40B	57464	hgsc.bcm.edu	37	chr7	129110535	129110535	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgtaccatccaggatttgccGgagcttactactgaaagtct	9	10	1	1	rs139413732	byFrequency	TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr7:129110535G>C	ENST00000249344.2	+	18	1963	c.1923G>C	c.(1921-1923)ccG>ccC	p.P641P	STRIP2_ENST00000435494.2_Silent_p.P641P	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	641					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											AGGATTTGCCGGAGCTTACTA	0.448																																					p.P641P		Atlas-SNP	.											.	.	.	.	0			c.G1923C						.						148	125	133					7																	129110535		2203	4300	6503	SO:0001819	synonymous_variant	57464	exon18			TTTGCCGGAGCTT	AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog B (yeast)"		"family with sequence similarity 40, member B"	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.1923G>C	chr7.hg19:g.129110535G>C		140.0	0.0		100.0	18.0	NM_020704	Q8WUZ4	Silent	SNP	ENST00000249344.2	hg19	CCDS34752.1																																																																																			.	G|0.999;A|0.001		0.448	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336		C	129110535	G	C	129110535	2	2	120	1	0	0	0	0	0	0	0	1	5569	1103	39	4		4	FAM40B	7	129110535	Silent	SNP	G	TCGA-DD-A3A6-01A-11D-A22F-10		129110535	30028128	5	20284										
CPEB3	22849	hgsc.bcm.edu	37	chr10	93902837	93902837	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttgtgaggccagtctactaCgagaggtccaaacctgcgaa	11	10	1	2			TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr10:93902837C>T	ENST00000265997.4	-	6	1574	c.1402G>A	c.(1402-1404)Gta>Ata	p.V468I	CPEB3_ENST00000412050.4_Missense_Mutation_p.V454I	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	468	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				CAGTCTACTACGAGAGGTCCA	0.393																																					p.V468I		Atlas-SNP	.											.	CPEB3	43	.	0			c.G1402A						.						89	88	88					10																	93902837		2203	4300	6503	SO:0001583	missense	22849	exon6			CTACTACGAGAGG	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.1402G>A	chr10.hg19:g.93902837C>T	ENSP00000265997:p.Val468Ile	66.0	0.0		44.0	5.0	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	hg19	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181730	0.57800	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.15718	2.4;2.4	5.86	5.86	0.93980	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.32133	0.0819	L	0.37897	1.145	0.80722	D	1	B;P;D	0.53885	0.026;0.927;0.963	B;D;D	0.66196	0.017;0.942;0.933	T	0.00804	-1.1559	10	0.19147	T	0.46	-12.1909	20.1823	0.98208	0.0:1.0:0.0:0.0	.	468;454;454	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	I	454;454;468	ENSP00000398310:V454I;ENSP00000265997:V468I	ENSP00000265997:V468I	V	-	1	0	CPEB3	93892817	1.000000	0.71417	0.870000	0.34147	0.948000	0.59901	5.975000	0.70475	2.771000	0.95319	0.650000	0.86243	GTA	.	.		0.393	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		T	93902837	C	T	93902837	3	4	120	1	0	0	0	0	1	0	0	0	3804	536	19	1	714	1	CPEB3	10	93902837	Missense_Mutation	SNP	C	TCGA-DD-A3A6-01A-11D-A22F-10		93902837	41631910	6	20285										
ABLIM1	3983	hgsc.bcm.edu	37	chr10	116417799	116417799	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcaaatgagtgatagtggcaCgcctatgagcggtgaaggag	16	6	0	4			TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr10:116417799C>T	ENST00000277895.5	-	1	258	c.161G>A	c.(160-162)cGt>cAt	p.R54H	ABLIM1_ENST00000533213.2_Intron|snoU13_ENST00000458910.1_RNA|ABLIM1_ENST00000369252.4_Intron	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	54					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		GATAGTGGCACGCCTATGAGC	0.517																																					p.R54H		Atlas-SNP	.											.	ABLIM1	131	.	0			c.G161A						.						99	90	93					10																	116417799		2203	4300	6503	SO:0001583	missense	3983	exon1			GTGGCACGCCTAT	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.161G>A	chr10.hg19:g.116417799C>T	ENSP00000277895:p.Arg54His	122.0	0.0		92.0	10.0	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Missense_Mutation	SNP	ENST00000277895.5	hg19	CCDS7590.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.896022	0.33442	.	.	ENSG00000099204	ENST00000336585;ENST00000369262;ENST00000277895	T	0.28255	1.62	5.77	2.93	0.34026	.	1.263470	0.05929	N	0.634786	T	0.20820	0.0501	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.28396	-1.0045	10	0.56958	D	0.05	.	7.7976	0.29156	0.0:0.6266:0.0:0.3734	.	54	O14639	ABLM1_HUMAN	H	54	ENSP00000277895:R54H	ENSP00000277895:R54H	R	-	2	0	ABLIM1	116407789	0.001000	0.12720	0.028000	0.17463	0.107000	0.19398	0.114000	0.15520	0.372000	0.24591	-0.143000	0.13931	CGT	.	.		0.517	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			T	116417799	C	T	116417799	3	4	120	1	0	0	0	0	1	0	0	0	94	536	19	1	2351	1	ABLIM1	10	116417799	Missense_Mutation	SNP	C	TCGA-DD-A3A6-01A-11D-A22F-10	22514962	116417799	19116948	7	20286										
SERGEF	26297	hgsc.bcm.edu	37	chr11	18010209	18010209	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccttttcattctggaaacaaTgtgcttctattttctggggc	8	9	4	0			TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr11:18010209T>G	ENST00000265965.5	-	8	930	c.779A>C	c.(778-780)cAt>cCt	p.H260P	SERGEF_ENST00000532265.1_Missense_Mutation_p.H146P|SERGEF_ENST00000528200.1_Missense_Mutation_p.H260P	NM_012139.2	NP_036271.1	Q9UGK8	SRGEF_HUMAN	secretion regulating guanine nucleotide exchange factor	260					negative regulation of protein secretion (GO:0050709)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(5)|lung(5)	12						CTGGAAACAATGTGCTTCTAT	0.483																																					p.H260P		Atlas-SNP	.											.	SERGEF	38	.	0			c.A779C						.						154	136	142					11																	18010209		2200	4293	6493	SO:0001583	missense	26297	exon8			AAACAATGTGCTT	AJ243950	CCDS7828.1	11p14.3	2006-03-09			ENSG00000129158	ENSG00000129158			17499	protein-coding gene	gene with protein product		606051				10571079, 12459492	Standard	NM_012139		Approved	DelGEF, Gnefr	uc001mnm.3	Q9UGK8	OTTHUMG00000166420	ENST00000265965.5:c.779A>C	chr11.hg19:g.18010209T>G	ENSP00000265965:p.His260Pro	120.0	0.0		70.0	9.0	NM_012139	Q9UGK9	Missense_Mutation	SNP	ENST00000265965.5	hg19	CCDS7828.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.543|9.543	1.113965|1.113965	0.20795|0.20795	.|.	.|.	ENSG00000129158|ENSG00000129158	ENST00000265965;ENST00000528200;ENST00000532265;ENST00000529728;ENST00000530613|ENST00000529151	T;T;T;T;T|.	0.79454|.	-1.27;-1.27;-1.27;-1.27;-1.27|.	5.63|5.63	-5.82|-5.82	0.02333|0.02333	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);|.	0.695780|.	0.15383|.	N|.	0.265232|.	T|T	0.45696|0.45696	0.1355|0.1355	L|L	0.59436|0.59436	1.845|1.845	0.09310|0.09310	N|N	1|1	B;P;B;B|.	0.41748|.	0.001;0.761;0.001;0.011|.	B;B;B;B|.	0.38562|.	0.001;0.276;0.002;0.002|.	T|T	0.52823|0.52823	-0.8524|-0.8524	10|5	0.30854|.	T|.	0.27|.	0.6702|0.6702	10.0267|10.0267	0.42076|0.42076	0.0:0.4495:0.1007:0.4499|0.0:0.4495:0.1007:0.4499	.|.	146;146;260;260|.	B4DFC0;E9PMV6;Q9UGK8-2;Q9UGK8|.	.;.;.;SRGEF_HUMAN|.	P|L	260;260;146;146;146|124	ENSP00000265965:H260P;ENSP00000434188:H260P;ENSP00000431314:H146P;ENSP00000437297:H146P;ENSP00000436080:H146P|.	ENSP00000265965:H260P|.	H|I	-|-	2|1	0|0	SERGEF|SERGEF	17966785|17966785	0.000000|0.000000	0.05858|0.05858	0.006000|0.006000	0.13384|0.13384	0.820000|0.820000	0.46376|0.46376	-0.306000|-0.306000	0.08178|0.08178	-0.690000|-0.690000	0.05142|0.05142	-0.353000|-0.353000	0.07706|0.07706	CAT|ATT	.	.		0.483	SERGEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389538.1	NM_012139		G	18010209	T	G	18010209	3	3	120	1	0	0	0	0	1	0	0	0	14092	1464	51	5	613	5	SERGEF	11	18010209	Missense_Mutation	SNP	T	TCGA-DD-A3A6-01A-11D-A22F-10		18010209	116996307	8	20287										
DPF2	5977	hgsc.bcm.edu	37	chr11	65111286	65111286	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgaagaagatactcccaagcGtcggggaaaggggaaatcca	13	8	0	3			TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr11:65111286G>A	ENST00000528416.1	+	5	669	c.536G>A	c.(535-537)cGt>cAt	p.R179H	DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000415073.2_Intron|DPF2_ENST00000252268.4_Missense_Mutation_p.R179H	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	179					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						ACTCCCAAGCGTCGGGGAAAG	0.512																																					p.R179H		Atlas-SNP	.											.	DPF2	54	.	0			c.G536A						.						43	40	41					11																	65111286		2201	4297	6498	SO:0001583	missense	5977	exon5			CCAAGCGTCGGGG	U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"Zinc fingers, PHD-type"	9964	protein-coding gene	gene with protein product		601671	"requiem, apoptosis response zinc finger gene"	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.536G>A	chr11.hg19:g.65111286G>A	ENSP00000436901:p.Arg179His	124.0	0.0		90.0	4.0	NM_006268	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	hg19	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	G	35	5.458962	0.96240	.	.	ENSG00000133884	ENST00000528416;ENST00000252268	D;D	0.91464	-2.84;-2.85	5.71	5.71	0.89125	.	0.000000	0.37715	N	0.001967	D	0.91523	0.7323	M	0.82323	2.585	0.54753	D	0.999987	P	0.47604	0.898	B	0.40782	0.34	D	0.92889	0.6329	10	0.72032	D	0.01	-16.6516	17.3563	0.87336	0.0:0.0:1.0:0.0	.	179	Q92785	REQU_HUMAN	H	179	ENSP00000436901:R179H;ENSP00000252268:R179H	ENSP00000252268:R179H	R	+	2	0	DPF2	64867862	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	7.759000	0.85235	2.689000	0.91719	0.655000	0.94253	CGT	.	.		0.512	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		A	65111286	G	A	65111286	3	1	120	1	0	0	0	0	1	0	0	0	4719	1145	40	1	554	1	DPF2	11	65111286	Missense_Mutation	SNP	G	TCGA-DD-A3A6-01A-11D-A22F-10	47101077	65111286	69895230	9	20288										
FUT8	2530	hgsc.bcm.edu	37	chr14	66188664	66188665	+	Frame_Shift_Ins	INS	-	-	A													0	0	1	0	0	0	1	1	0	cagtttgtcaaatacttgatINSccgcccacagccttggctag							TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr14:66188664_66188665insA	ENST00000360689.5	+	8	2734_2735	c.1007_1008insA	c.(1006-1011)atccgcfs	p.R337fs	FUT8_ENST00000394586.2_Frame_Shift_Ins_p.R337fs|FUT8_ENST00000358307.2_Frame_Shift_Ins_p.R208fs|FUT8_ENST00000417683.1_Intron|FUT8_ENST00000557164.1_Frame_Shift_Ins_p.R174fs|FUT8_ENST00000394585.1_Frame_Shift_Ins_p.R337fs	NM_004480.4|NM_178155.2	NP_004471.4|NP_835368.1	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	337	GT23. {ECO:0000255|PROSITE- ProRule:PRU00992}.				cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		AAATACTTGATCCGCCCACAGC	0.455																																					p.I336fs		Atlas-INDEL	.											.	FUT8	101	.	0			c.1007_1008insA						.																																			SO:0001589	frameshift_variant	2530	exon8			.	AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170		"Fucosyltransferases"	4019	protein-coding gene	gene with protein product		602589				9368041	Standard	NM_178155		Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	Exception_encountered	chr14.hg19:g.66188664_66188665insA	ENSP00000353910:p.Arg337fs	129.0	0.0		97.0	11.0	NM_178155	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	Frame_Shift_Ins	INS	ENST00000360689.5	hg19	CCDS9775.1																																																																																			.	.		0.455	FUT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286406.1	NM_004480		A	66188665	-	A	66188664	7	5	120	1	0	1	1	0	0	0	0	0	6118	1435	50	0	1128	0	FUT8	14	66188664	Frame_Shift_Ins	INS	-	TCGA-DD-A3A6-01A-11D-A22F-10		66188664	41160876	10	20289										
PARP16	54956	hgsc.bcm.edu	37	chr15	65563339	65563339	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atccagctcaccaggtcccaGgcccgtttgtggttgtctcc	10	15	2	0			TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr15:65563339G>A	ENST00000261888.6	-	2	691	c.246C>T	c.(244-246)gcC>gcT	p.A82A	PARP16_ENST00000558873.1_5'UTR|PARP16_ENST00000444347.2_Intron	NM_017851.4	NP_060321.3	Q8N5Y8	PAR16_HUMAN	poly (ADP-ribose) polymerase family, member 16	82	PARP alpha-helical.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell death (GO:0060548)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum tubular network (GO:0071782)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	kinase binding (GO:0019900)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|protein serine/threonine kinase activator activity (GO:0043539)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						CCAGGTCCCAGGCCCGTTTGT	0.507																																					p.A82A	NSCLC(50;885 1163 13509 21242 41978)	Atlas-SNP	.											.	PARP16	23	.	0			c.C246T						.						173	169	170					15																	65563339		2201	4299	6500	SO:0001819	synonymous_variant	54956	exon2			GTCCCAGGCCCGT	AK000516	CCDS10204.1	15q22.2	2010-02-16	2004-08-25	2004-08-25	ENSG00000138617	ENSG00000138617		"Poly (ADP-ribose) polymerases"	26040	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 30"	C15orf30		15273990	Standard	NM_017851		Approved	FLJ20509, FLJ25281, pART15	uc002aoq.3	Q8N5Y8	OTTHUMG00000133138	ENST00000261888.6:c.246C>T	chr15.hg19:g.65563339G>A		110.0	0.0		93.0	8.0	NM_017851	Q6PK64|Q9NX03	Silent	SNP	ENST00000261888.6	hg19	CCDS10204.1																																																																																			.	.		0.507	PARP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256827.2	NM_017851		A	65563339	G	A	65563339	2	1	120	1	0	0	0	0	0	0	0	1	11469	987	35	3		3	PARP16	15	65563339	Silent	SNP	G	TCGA-DD-A3A6-01A-11D-A22F-10		65563339	36968053	11	20290										
C20orf96	140680	hgsc.bcm.edu	37	chr20	257508	257508	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	taggagagcctcttcataggGacgctgggtttcctgtggag	15	8	2	1			TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr20:257508G>A	ENST00000360321.2	-	9	976	c.838C>T	c.(838-840)Ccc>Tcc	p.P280S	C20orf96_ENST00000382369.5_Missense_Mutation_p.P245S|C20orf96_ENST00000400269.3_Missense_Mutation_p.P222S	NM_080571.1|NM_153269.2	NP_542138.1|NP_695001.2	Q9NUD7	CT096_HUMAN	chromosome 20 open reading frame 96	280										endometrium(3)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			TCTTCATAGGGACGCTGGGTT	0.577																																					p.P280S		Atlas-SNP	.											.	C20orf96	28	.	0			c.C838T						.						92	82	85					20																	257508		2203	4300	6503	SO:0001583	missense	140680	exon9			CATAGGGACGCTG	AL034548	CCDS12994.1, CCDS74685.1	20p13	2012-10-30			ENSG00000196476	ENSG00000196476			16227	protein-coding gene	gene with protein product							Standard	NM_153269		Approved	dJ1103G7.2	uc002wde.2	Q9NUD7	OTTHUMG00000031626	ENST00000360321.2:c.838C>T	chr20.hg19:g.257508G>A	ENSP00000353470:p.Pro280Ser	110.0	0.0		72.0	10.0	NM_153269	A3KPE0|B2RPH9|Q8N840|Q8NAX5	Missense_Mutation	SNP	ENST00000360321.2	hg19	CCDS12994.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.249955	0.39797	.	.	ENSG00000196476	ENST00000382369;ENST00000360321;ENST00000400269	T;T;T	0.43294	0.95;0.95;0.95	4.52	3.57	0.40892	.	0.440036	0.22871	N	0.054623	T	0.50718	0.1632	L	0.55481	1.735	0.09310	N	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.64595	0.927;0.927;0.927;0.927	T	0.39187	-0.9626	10	0.13108	T	0.6	-13.5247	10.2593	0.43416	0.0:0.2154:0.7846:0.0	.	222;245;280;245	F5GZA9;B7Z971;Q9NUD7;Q5JYC3	.;.;CT096_HUMAN;.	S	245;280;222	ENSP00000371806:P245S;ENSP00000353470:P280S;ENSP00000383128:P222S	ENSP00000353470:P280S	P	-	1	0	C20orf96	205508	0.883000	0.30277	0.008000	0.14137	0.106000	0.19336	2.705000	0.47127	1.129000	0.42072	0.313000	0.20887	CCC	.	.		0.577	C20orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077439.2	NM_153269		A	257508	G	A	257508	3	1	120	1	0	0	0	0	1	0	0	0	2124	1174	41	3	265	3	C20orf96	20	257508	Missense_Mutation	SNP	G	TCGA-DD-A3A6-01A-11D-A22F-10		257508	62768012	12	20291										
NF2	4771	hgsc.bcm.edu	37	chr22	30038257	30038258	+	Frame_Shift_Ins	INS	-	-	A													0	0	1	0	0	0	1	1	0	ttctgtgctcctggcttcttINSacgccgtccaggccaaggta							TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chr22:30038257_30038258insA	ENST00000338641.4	+	4	871_872	c.430_431insA	c.(430-432)tacfs	p.Y144fs	NF2_ENST00000334961.7_Frame_Shift_Ins_p.Y61fs|NF2_ENST00000347330.5_Frame_Shift_Ins_p.Y61fs|NF2_ENST00000361452.4_Frame_Shift_Ins_p.Y103fs|NF2_ENST00000361166.4_Frame_Shift_Ins_p.Y144fs|NF2_ENST00000413209.2_Frame_Shift_Ins_p.Y144fs|NF2_ENST00000353887.4_Frame_Shift_Ins_p.Y61fs|NF2_ENST00000397789.3_Frame_Shift_Ins_p.Y144fs|NF2_ENST00000403999.3_Frame_Shift_Ins_p.Y144fs|NF2_ENST00000403435.1_Frame_Shift_Ins_p.Y144fs|NF2_ENST00000361676.4_Frame_Shift_Ins_p.Y102fs	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	144	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.Y144fs*1(5)|p.V122_K149del(5)|p.?(2)|p.Y144fs*5(1)|p.Y144fs*29(1)|p.K123fs*2(1)|p.A142fs*8(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						CCTGGCTTCTTACGCCGTCCAG	0.45			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.Y144_A145delinsX		Atlas-INDEL	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	NF2_ENST00000403999,rectum,carcinoma,-2,8	NF2	1312	.	16	Deletion - In frame(5)|Insertion - Frameshift(5)|Deletion - Frameshift(4)|Unknown(2)	soft_tissue(8)|meninges(6)|large_intestine(1)|stomach(1)	c.430_431insA	GRCh37	CI045510|CI983522	NF2	I		.																																			SO:0001589	frameshift_variant	4771	exon4	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	.	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.431dupA	chr22.hg19:g.30038258_30038258dupA	ENSP00000344666:p.Tyr144fs	95.0	0.0		67.0	11.0	NM_181832	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Frame_Shift_Ins	INS	ENST00000338641.4	hg19	CCDS13861.1																																																																																			.	.		0.45	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		A	30038258	-	A	30038257	7	5	120	1	0	1	1	0	0	0	0	0	10366	1754	61	0	444	0	NF2	22	30038257	Frame_Shift_Ins	INS	-	TCGA-DD-A3A6-01A-11D-A22F-10		30038257	21266309	13	20292										
RGN	9104	hgsc.bcm.edu	37	chrX	46951499	46951499	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaagttgcctgttgataaaaCaacttcatgctgctttggag	10	7	1	1			TCGA-DD-A3A6-01A-11D-A22F-10	TCGA-DD-A3A6-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f03cb4b-60b1-460c-b761-402e7ca09b0d	a63e3270-347f-4de0-b8f5-494e9b555a9d	g.chrX:46951499C>A	ENST00000352078.4	+	6	1079	c.734C>A	c.(733-735)aCa>aAa	p.T245K	RGN_ENST00000397180.1_Missense_Mutation_p.T245K|RGN_ENST00000457380.1_Missense_Mutation_p.T173K|RGN_ENST00000336169.3_Missense_Mutation_p.T245K	NM_004683.4	NP_004674.1	Q15493	RGN_HUMAN	regucalcin	245					cellular calcium ion homeostasis (GO:0006874)|L-ascorbic acid biosynthetic process (GO:0019853)|positive regulation of ATPase activity (GO:0032781)|regulation of calcium-mediated signaling (GO:0050848)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|enzyme regulator activity (GO:0030234)|gluconolactonase activity (GO:0004341)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	9						GTTGATAAAACAACTTCATGC	0.423																																					p.T245K		Atlas-SNP	.											.	RGN	18	.	0			c.C734A						.						75	69	71					X																	46951499		2203	4300	6503	SO:0001583	missense	9104	exon6			ATAAAACAACTTC	D31815	CCDS14272.1, CCDS75968.1	Xp11.3	2014-03-14	2013-04-26		ENSG00000130988	ENSG00000130988	3.1.1.17		9989	protein-coding gene	gene with protein product	"senescence marker protein-30", "gluconolactonase"	300212	"regucalcin (senescence marker protein-30)"			7548213	Standard	NM_152869		Approved	SMP30, RC	uc004dha.1	Q15493	OTTHUMG00000021435	ENST00000352078.4:c.734C>A	chrX.hg19:g.46951499C>A	ENSP00000253303:p.Thr245Lys	99.0	0.0		72.0	11.0	NM_004683	A4FTW1|A8K271|Q53FC9|Q5JRR5	Missense_Mutation	SNP	ENST00000352078.4	hg19	CCDS14272.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998807	0.74818	.	.	ENSG00000130988	ENST00000397180;ENST00000457380;ENST00000352078;ENST00000336169	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.56	4.69	0.59074	SMP-30/Gluconolaconase/LRE-like region (1);Six-bladed beta-propeller, TolB-like (1);	0.255560	0.44688	D	0.000430	T	0.55784	0.1942	M	0.81112	2.525	0.44807	D	0.997812	D;D	0.89917	1.0;1.0	D;D	0.79784	0.981;0.993	T	0.59043	-0.7528	10	0.51188	T	0.08	-6.6494	13.0624	0.59014	0.0:0.9212:0.0:0.0788	.	173;245	Q15493-2;Q15493	.;RGN_HUMAN	K	245;173;245;245	ENSP00000380365:T245K;ENSP00000406568:T173K;ENSP00000253303:T245K;ENSP00000338400:T245K	ENSP00000338400:T245K	T	+	2	0	RGN	46836443	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	1.650000	0.37292	2.353000	0.79882	0.519000	0.50382	ACA	.	.		0.423	RGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056385.1	NM_004683		A	46951499	C	A	46951499	3	1	120	1	0	0	0	0	1	0	0	0	13297	478	17	3	752	3	RGN	23	46951499	Missense_Mutation	SNP	C	TCGA-DD-A3A6-01A-11D-A22F-10		46951499	108319061	14	20293										
WASF2	10163	hgsc.bcm.edu	37	chr1	27734780	27734780	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	acaagatggtggccacgtcaTtgcccacaacatcccgcttc	8	15	1	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr1:27734780T>C	ENST00000430629.2	-	9	1615	c.1400A>G	c.(1399-1401)aAt>aGt	p.N467S	WASF2_ENST00000536657.1_3'UTR	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	467					actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		GGCCACGTCATTGCCCACAAC	0.527																																					p.N467S		Atlas-SNP	.											.	WASF2	41	.	0			c.A1400G						.						154	130	138					1																	27734780		2203	4300	6503	SO:0001583	missense	10163	exon9			ACGTCATTGCCCA	AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195			12733	protein-coding gene	gene with protein product		605875				10381382	Standard	NM_006990		Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.1400A>G	chr1.hg19:g.27734780T>C	ENSP00000396211:p.Asn467Ser	119.0	0.0		88.0	35.0	NM_006990	B4DZN0|O60794|Q9UDY7	Missense_Mutation	SNP	ENST00000430629.2	hg19	CCDS304.1	.	.	.	.	.	.	.	.	.	.	T	33	5.273046	0.95429	.	.	ENSG00000158195	ENST00000430629	T	0.55052	0.54	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.73009	0.3532	M	0.79475	2.455	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.76798	-0.2826	10	0.72032	D	0.01	-13.095	15.6004	0.76620	0.0:0.0:0.0:1.0	.	467	Q9Y6W5	WASF2_HUMAN	S	467	ENSP00000396211:N467S	ENSP00000396211:N467S	N	-	2	0	WASF2	27607367	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.163000	0.67991	0.528000	0.53228	AAT	.	.		0.527	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009516.1	NM_006990		C	27734780	T	C	27734780	3	2	121	1	0	0	0	0	1	0	0	0	17268	1493	52	2	100	2	WASF2	1	27734780	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10		27734780	221515841	1	20294										
BAI2	576	hgsc.bcm.edu	37	chr1	32206014	32206014	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tcagtgacattcctcagaatGtccacagagaagagcaggtc	10	10	2	4			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr1:32206014G>A	ENST00000373658.3	-	12	2264	c.1923C>T	c.(1921-1923)gaC>gaT	p.D641D	BAI2_ENST00000440175.2_Silent_p.D283D|BAI2_ENST00000398547.1_Silent_p.D574D|BAI2_ENST00000398556.3_Silent_p.D589D|BAI2_ENST00000373655.2_Silent_p.D641D|BAI2_ENST00000398542.1_Silent_p.D574D|BAI2_ENST00000527361.1_Silent_p.D641D|BAI2_ENST00000257070.4_Silent_p.D641D|BAI2_ENST00000398538.1_Silent_p.D629D	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	641					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		TCCTCAGAATGTCCACAGAGA	0.612																																					p.D641D		Atlas-SNP	.											.	BAI2	128	.	0			c.C1923T						.						40	39	40					1																	32206014		2203	4300	6503	SO:0001819	synonymous_variant	576	exon12			CAGAATGTCCACA	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.1923C>T	chr1.hg19:g.32206014G>A		88.0	0.0		65.0	22.0	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	hg19	CCDS346.2																																																																																			.	.		0.612	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		A	32206014	G	A	32206014	2	1	121	1	0	0	0	0	0	0	0	1	1299	1368	48	3		3	BAI2	1	32206014	Silent	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	4471234	32206014	217044607	2	20295										
NRD1	4898	hgsc.bcm.edu	37	chr1	52272522	52272522	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	acaggcaaccttgtggagtaTtcacaattttaactgggtat	9	7	1	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr1:52272522T>C	ENST00000354831.7	-	20	2447	c.2258A>G	c.(2257-2259)aAt>aGt	p.N753S	NRD1_ENST00000544028.1_Missense_Mutation_p.N553S|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000352171.7_Missense_Mutation_p.N685S|NRD1_ENST00000539524.1_Missense_Mutation_p.N621S	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	684					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						TTGTGGAGTATTCACAATTTT	0.383																																					p.N753S		Atlas-SNP	.											.	NRD1	89	.	0			c.A2258G						.						190	191	191					1																	52272522		2203	4300	6503	SO:0001583	missense	4898	exon20			GGAGTATTCACAA	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.2258A>G	chr1.hg19:g.52272522T>C	ENSP00000346890:p.Asn753Ser	288.0	0.0		205.0	80.0	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	11.89	1.773179	0.31411	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.3	4.18	0.49190	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.377447	0.30639	N	0.009195	T	0.28732	0.0712	N	0.24115	0.695	0.29402	N	0.861889	B;B;B	0.13594	0.004;0.004;0.008	B;B;B	0.12837	0.008;0.001;0.003	T	0.09751	-1.0660	10	0.23302	T	0.38	-10.2704	6.4935	0.22130	0.0:0.1836:0.0:0.8164	.	685;684;753	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	S	685;753;621;685;553	ENSP00000262679:N685S;ENSP00000346890:N753S;ENSP00000444416:N621S;ENSP00000442262:N553S	ENSP00000262679:N685S	N	-	2	0	NRD1	52045110	0.961000	0.32948	0.995000	0.50966	0.992000	0.81027	1.441000	0.35035	2.015000	0.59207	0.477000	0.44152	AAT	.	.		0.383	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		C	52272522	T	C	52272522	3	2	121	1	0	0	0	0	1	0	0	0	10654	1493	52	2	1457	2	NRD1	1	52272522	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	20066508	52272522	196978099	3	20296										
HRNR	388697	hgsc.bcm.edu	37	chr1	152191055	152191055	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	agctggaagactgcccggaaCcagacccatgtcggccacgg	13	14	0	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr1:152191055C>G	ENST00000368801.2	-	3	3125	c.3050G>C	c.(3049-3051)gGt>gCt	p.G1017A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1017					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCCCGGAACCAGACCCATG	0.607																																					p.G1017A		Atlas-SNP	.											.	HRNR	403	.	0			c.G3050C						.						134	148	143					1																	152191055		2203	4300	6503	SO:0001583	missense	388697	exon3			CCGGAACCAGACC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.3050G>C	chr1.hg19:g.152191055C>G	ENSP00000357791:p.Gly1017Ala	187.0	0.0		274.0	23.0	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	hg19	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	C	6.450	0.451150	0.12223	.	.	ENSG00000197915	ENST00000368801	T	0.11277	2.79	3.6	2.64	0.31445	.	.	.	.	.	T	0.02193	0.0068	L	0.44542	1.39	0.09310	N	1	P	0.42908	0.793	B	0.35655	0.207	T	0.33214	-0.9877	9	0.08599	T	0.76	.	8.2385	0.31640	0.2376:0.7624:0.0:0.0	.	1017	Q86YZ3	HORN_HUMAN	A	1017	ENSP00000357791:G1017A	ENSP00000357791:G1017A	G	-	2	0	HRNR	150457679	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.260000	0.08708	0.810000	0.34279	0.558000	0.71614	GGT	.	.		0.607	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		G	152191055	C	G	152191055	3	3	121	1	0	0	0	0	1	0	0	0	7368	507	18	4	5506	4	HRNR	1	152191055	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	99918533	152191055	97059566	4	20297										
GON4L	54856	hgsc.bcm.edu	37	chr1	155823310	155823310	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	accttctagaattggtacatTtgtgttctgggtgagcattc	10	7	2	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr1:155823310T>G	ENST00000368331.1	-	2	310	c.262A>C	c.(262-264)Aat>Cat	p.N88H	GON4L_ENST00000361040.5_Missense_Mutation_p.N88H|GON4L_ENST00000437809.1_Missense_Mutation_p.N88H|GON4L_ENST00000271883.5_Missense_Mutation_p.N88H|GON4L_ENST00000471341.1_5'UTR	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	88					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					ATTGGTACATTTGTGTTCTGG	0.463																																					p.N88H		Atlas-SNP	.											.	GON4L	392	.	0			c.A262C						.						183	169	174					1																	155823310		2203	4300	6503	SO:0001583	missense	54856	exon2			GTACATTTGTGTT	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.262A>C	chr1.hg19:g.155823310T>G	ENSP00000357315:p.Asn88His	190.0	0.0		382.0	33.0	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	hg19		.	.	.	.	.	.	.	.	.	.	T	4.081	0.012862	0.07912	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000539959;ENST00000361040	T;T;T;T	0.14640	2.68;2.68;2.68;2.49	4.38	-3.72	0.04411	.	1.396580	0.04648	N	0.406481	T	0.03053	0.0090	L	0.32530	0.975	0.09310	N	1	B;B;B	0.11235	0.004;0.001;0.002	B;B;B	0.08055	0.003;0.001;0.003	T	0.45702	-0.9243	10	0.39692	T	0.17	.	7.1388	0.25543	0.0:0.5516:0.1743:0.2741	.	88;88;88	Q3T8J9-2;Q3T8J9;Q3T8J9-3	.;GON4L_HUMAN;.	H	88	ENSP00000396117:N88H;ENSP00000357315:N88H;ENSP00000271883:N88H;ENSP00000354322:N88H	ENSP00000271883:N88H	N	-	1	0	GON4L	154089934	0.000000	0.05858	0.000000	0.03702	0.119000	0.20118	-0.453000	0.06778	-0.643000	0.05473	0.459000	0.35465	AAT	.	.		0.463	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		G	155823310	T	G	155823310	3	3	121	1	0	0	0	0	1	0	0	0	6580	1841	64	5	6701	5	GON4L	1	155823310	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	3632255	155823310	93427311	5	20298										
OR6K2	81448	hgsc.bcm.edu	37	chr1	158669566	158669566	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ttttatttctttattcctcaGgctatagataatggggttga	8	5	2	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr1:158669566G>A	ENST00000359610.2	-	1	920	c.877C>T	c.(877-879)Ctg>Ttg	p.L293L		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					TTATTCCTCAGGCTATAGATA	0.393																																					p.L293L		Atlas-SNP	.											.	OR6K2	104	.	0			c.C877T						.						73	72	72					1																	158669566		2203	4300	6503	SO:0001819	synonymous_variant	81448	exon1			TCCTCAGGCTATA	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.877C>T	chr1.hg19:g.158669566G>A		194.0	0.0		232.0	157.0	NM_001005279	B9EH33|Q6IFR6	Silent	SNP	ENST00000359610.2	hg19	CCDS30902.1																																																																																			.	.		0.393	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		A	158669566	G	A	158669566	2	1	121	1	0	0	0	0	0	0	0	1	11211	991	35	3		3	OR6K2	1	158669566	Silent	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	2846256	158669566	90581055	6	20299										
PBX1	5087	hgsc.bcm.edu	37	chr1	164789392	164789392	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	atggggattcttaccaagggGcccaggttggagccaacgtg	15	9	1	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr1:164789392G>A	ENST00000420696.2	+	7	1269	c.1081G>A	c.(1081-1083)Gcc>Acc	p.A361T	PBX1_ENST00000560641.1_Missense_Mutation_p.A256T|PBX1_ENST00000401534.1_Intron|PBX1_ENST00000540236.1_Missense_Mutation_p.A361T|PBX1_ENST00000367897.1_Intron|PBX1_ENST00000540246.1_Missense_Mutation_p.A256T|PBX1_ENST00000559240.1_Intron	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	361					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						TTACCAAGGGGCCCAGGTTGG	0.488			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.A361T		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1	60	.	0			c.G1081A						.						84	84	84					1																	164789392		2203	4300	6503	SO:0001583	missense	5087	exon7			CAAGGGGCCCAGG	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"Homeoboxes / TALE class"	8632	protein-coding gene	gene with protein product		176310	"pre-B-cell leukemia transcription factor 1"				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.1081G>A	chr1.hg19:g.164789392G>A	ENSP00000405890:p.Ala361Thr	153.0	0.0		160.0	25.0	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	hg19	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.550454	0.65311	.	.	ENSG00000185630	ENST00000420696;ENST00000540236;ENST00000540246	D;D;D	0.88896	-2.33;-2.33;-2.44	5.61	5.61	0.85477	.	0.207703	0.49916	D	0.000127	T	0.74786	0.3762	N	0.17474	0.49	.	.	.	B;B;B;B	0.25390	0.002;0.002;0.125;0.009	B;B;B;B	0.25614	0.004;0.002;0.062;0.04	T	0.71185	-0.4667	9	0.25751	T	0.34	-10.9742	19.237	0.93864	0.0:0.0:1.0:0.0	.	256;361;361;361	B7Z774;A8K5V0;F5H4U9;P40424	.;.;.;PBX1_HUMAN	T	361;361;256	ENSP00000405890:A361T;ENSP00000439943:A361T;ENSP00000440869:A256T	ENSP00000405890:A361T	A	+	1	0	PBX1	163056016	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	6.170000	0.71920	2.640000	0.89533	0.655000	0.94253	GCC	.	.		0.488	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		A	164789392	G	A	164789392	3	1	121	1	0	0	0	0	1	0	0	0	11501	1203	42	3	1107	3	PBX1	1	164789392	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	6119826	164789392	84461229	7	20300										
NUP133	55746	hgsc.bcm.edu	37	chr1	229636533	229636533	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tgtgcttcacctgagggagaAgagtaagaaagagccactaa	12	7	1	5			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr1:229636533A>G	ENST00000261396.3	-	4	574	c.483T>C	c.(481-483)tcT>tcC	p.S161S	NUP133_ENST00000537506.1_Silent_p.S145S|NUP133_ENST00000366678.3_Silent_p.S161S	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	161					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				CTGAGGGAGAAGAGTAAGAAA	0.403																																					p.S161S		Atlas-SNP	.											.	NUP133	111	.	0			c.T483C						.						60	58	59					1																	229636533		2203	4300	6503	SO:0001819	synonymous_variant	55746	exon4			GGGAGAAGAGTAA		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.483T>C	chr1.hg19:g.229636533A>G		41.0	0.0		102.0	22.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	hg19	CCDS1579.1																																																																																			.	.		0.403	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		G	229636533	A	G	229636533	2	3	121	1	0	0	0	0	0	0	0	1	10763	59	3	2		2	NUP133	1	229636533	Silent	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	64847141	229636533	19614088	8	20301										
ASAP2	8853	hgsc.bcm.edu	37	chr2	9508603	9508603	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	taatgagatcatggaatgttGcctaccagctgaggactcag	11	8	2	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr2:9508603G>A	ENST00000281419.3	+	16	1851	c.1511G>A	c.(1510-1512)tGc>tAc	p.C504Y	ASAP2_ENST00000315273.4_Missense_Mutation_p.C504Y	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	504	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						ATGGAATGTTGCCTACCAGCT	0.428																																					p.C504Y		Atlas-SNP	.											.	ASAP2	91	.	0			c.G1511A						.						99	95	97					2																	9508603		2203	4300	6503	SO:0001583	missense	8853	exon16			AATGTTGCCTACC	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1511G>A	chr2.hg19:g.9508603G>A	ENSP00000281419:p.Cys504Tyr	86.0	0.0		78.0	30.0	NM_001135191	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	hg19	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.105651	0.77096	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.40476	1.03;1.03	5.61	5.61	0.85477	.	0.175663	0.64402	D	0.000005	T	0.50990	0.1648	N	0.20328	0.56	0.80722	D	1	P;D	0.65815	0.778;0.995	B;D	0.65140	0.136;0.932	T	0.53005	-0.8499	10	0.56958	D	0.05	.	20.0086	0.97443	0.0:0.0:1.0:0.0	.	504;504	O43150-2;O43150	.;ASAP2_HUMAN	Y	504	ENSP00000281419:C504Y;ENSP00000316404:C504Y	ENSP00000281419:C504Y	C	+	2	0	ASAP2	9426054	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.613000	0.67688	2.808000	0.96608	0.655000	0.94253	TGC	.	.		0.428	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		A	9508603	G	A	9508603	3	1	121	1	0	0	0	0	1	0	0	0	1011	1319	46	3	1573	3	ASAP2	2	9508603	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10		9508603	233690770	9	20302										
ADAM17	6868	hgsc.bcm.edu	37	chr2	9630394	9630394	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ttctggtgaccggatggtccGtgagatcctcaaatgacttg	12	9	2	3	rs572250428		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr2:9630394G>A	ENST00000310823.3	-	19	2569	c.2387C>T	c.(2386-2388)aCg>aTg	p.T796M	IAH1_ENST00000545602.1_Intron	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	796					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		CGGATGGTCCGTGAGATCCTC	0.498																																					p.T796M		Atlas-SNP	.											.	ADAM17	61	.	0			c.C2387T						.						104	94	97					2																	9630394		2203	4300	6503	SO:0001583	missense	6868	exon19			TGGTCCGTGAGAT	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.2387C>T	chr2.hg19:g.9630394G>A	ENSP00000309968:p.Thr796Met	153.0	0.0		133.0	61.0	NM_003183	O60226	Missense_Mutation	SNP	ENST00000310823.3	hg19	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.758600	0.89843	.	.	ENSG00000151694	ENST00000310823	T	0.29655	1.56	5.35	5.35	0.76521	.	0.102863	0.64402	D	0.000003	T	0.46268	0.1384	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.73380	0.98;0.978;0.978	T	0.47586	-0.9106	10	0.87932	D	0	.	19.0868	0.93206	0.0:0.0:1.0:0.0	.	515;796;796	Q53RS1;B2RNB2;P78536	.;.;ADA17_HUMAN	M	796	ENSP00000309968:T796M	ENSP00000309968:T796M	T	-	2	0	ADAM17	9547845	1.000000	0.71417	0.947000	0.38551	0.988000	0.76386	9.476000	0.97823	2.503000	0.84419	0.561000	0.74099	ACG	.	.		0.498	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			A	9630394	G	A	9630394	3	1	121	1	0	0	0	0	1	0	0	0	238	1145	40	1	91	1	ADAM17	2	9630394	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	121791	9630394	233568979	10	20303										
APOB	338	hgsc.bcm.edu	37	chr2	21251239	21251240	+	Frame_Shift_Ins	INS	-	-	A													0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gagttcaagatattggcaatINSatgggaagccacaaagttct							TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr2:21251239_21251240insA	ENST00000233242.1	-	13	1915_1916	c.1788_1789insT	c.(1786-1791)catattfs	p.I597fs	APOB_ENST00000399256.4_Frame_Shift_Ins_p.I597fs	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	597	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATATTGGCAATATGGGAAGCCA	0.416																																					p.I597fs		Atlas-INDEL	.											.	APOB	761	.	0			c.1789_1790insT						.																																			SO:0001589	frameshift_variant	338	exon13			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1789dupT	chr2.hg19:g.21251240_21251240dupA	ENSP00000233242:p.Ile597fs	157.0	0.0		120.0	49.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.416	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21251240	-	A	21251239	7	5	121	1	0	1	1	0	0	0	0	0	785	1406	49	0	11970	0	APOB	2	21251239	Frame_Shift_Ins	INS	-	TCGA-DD-A3A7-01A-11D-A22F-10	11620845	21251239	221948134	11	20304										
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71043463	71043463	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gtatctgtctggtccagacgGccatttgctttttgggtctg	12	9	3	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr2:71043463G>A	ENST00000272367.2	-	4	1126	c.1050C>T	c.(1048-1050)ggC>ggT	p.G350G	CLEC4F_ENST00000426626.1_Silent_p.G350G	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	350					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						GGTCCAGACGGCCATTTGCTT	0.408																																					p.G350G	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.C1050T						.						86	82	83					2																	71043463		2203	4300	6503	SO:0001819	synonymous_variant	165530	exon4			CAGACGGCCATTT	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.1050C>T	chr2.hg19:g.71043463G>A		213.0	0.0		179.0	69.0	NM_173535	A4QPA5	Silent	SNP	ENST00000272367.2	hg19	CCDS1910.1																																																																																			.	.		0.408	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		A	71043463	G	A	71043463	2	1	121	1	0	0	0	0	0	0	0	1	3518	1190	42	3		3	CLEC4F	2	71043463	Silent	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	49792224	71043463	172155910	12	20305										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73679731	73679731	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ctcacaaatagagaagcccaAgatttcaactgtgattggac	8	9	2	3	rs367904732		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr2:73679731A>G	ENST00000264448.6	+	8	6185	c.6074A>G	c.(6073-6075)aAg>aGg	p.K2025R	ALMS1_ENST00000409009.1_Missense_Mutation_p.K1983R|ALMS1_ENST00000377715.1_Missense_Mutation_p.K2025R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2025	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GAGAAGCCCAAGATTTCAACT	0.388																																					p.K2025R		Atlas-SNP	.											.	ALMS1	384	.	0			c.A6074G						.	A	ARG/LYS	0,3696		0,0,1848	124	119	121		6074	-0.8	0	2		121	1,8169		0,1,4084	no	missense	ALMS1	NM_015120.4	26	0,1,5932	GG,GA,AA		0.0122,0.0,0.0084	probably-damaging	2025/4168	73679731	1,11865	1848	4085	5933	SO:0001583	missense	7840	exon8			AGCCCAAGATTTC	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.6074A>G	chr2.hg19:g.73679731A>G	ENSP00000264448:p.Lys2025Arg	136.0	0.0		80.0	33.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	9.718	1.158894	0.21454	0.0	1.22E-4	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.15603	3.3;3.3;2.41	4.59	-0.788	0.10939	.	0.863437	0.10007	N	0.727676	T	0.26304	0.0642	L	0.54323	1.7	0.09310	N	1	D;D;D	0.67145	0.992;0.992;0.996	D;P;D	0.63192	0.912;0.893;0.912	T	0.17806	-1.0357	10	0.33940	T	0.23	.	4.2435	0.10660	0.4154:0.369:0.2156:0.0	.	2025;1983;2025	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	R	1983;2025;2025	ENSP00000386627:K1983R;ENSP00000264448:K2025R;ENSP00000366944:K2025R	ENSP00000264448:K2025R	K	+	2	0	ALMS1	73533239	0.002000	0.14202	0.001000	0.08648	0.171000	0.22731	0.001000	0.13038	-0.105000	0.12132	-0.417000	0.06048	AAG	.	.		0.388	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		G	73679731	A	G	73679731	3	3	121	1	0	0	0	0	1	0	0	0	535	72	3	2	6104	2	ALMS1	2	73679731	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	2636268	73679731	169519642	13	20306										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73679798	73679798	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	acagcttttcatagttcctaTtctcaaacagtaaagcccaa	4	11	2	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr2:73679798T>A	ENST00000264448.6	+	8	6252	c.6141T>A	c.(6139-6141)taT>taA	p.Y2047*	ALMS1_ENST00000409009.1_Nonsense_Mutation_p.Y2005*|ALMS1_ENST00000377715.1_Nonsense_Mutation_p.Y2047*	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2047	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						ATAGTTCCTATTCTCAAACAG	0.393																																					p.Y2047X		Atlas-SNP	.											.	ALMS1	384	.	0			c.T6141A						.						86	84	85					2																	73679798		1835	4073	5908	SO:0001587	stop_gained	7840	exon8			TTCCTATTCTCAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.6141T>A	chr2.hg19:g.73679798T>A	ENSP00000264448:p.Tyr2047*	144.0	0.0		86.0	35.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Nonsense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	T	44	11.099568	0.99515	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	.	.	.	4.05	1.71	0.24356	.	0.547071	0.15440	N	0.262260	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	.	5.5971	0.17333	0.0:0.2185:0.0:0.7815	.	.	.	.	X	2005;2047;2047	.	ENSP00000264448:Y2047X	Y	+	3	2	ALMS1	73533306	0.017000	0.18338	0.221000	0.23827	0.182000	0.23217	1.050000	0.30404	0.379000	0.24794	0.528000	0.53228	TAT	.	.		0.393	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73679798	T	A	73679798	4	1	121	1	0	0	0	0	0	1	0	0	535	1500	52	4	6171	4	ALMS1	2	73679798	Nonsense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	67	73679798	169519575	14	20307										
ANKRD36	375248	hgsc.bcm.edu	37	chr2	97869996	97869996	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	aaggatggagaaaaaactagGacaggtaattttgaaaagag	12	2	0	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr2:97869996G>T	ENST00000461153.2	+	50	3301	c.3057G>T	c.(3055-3057)agG>agT	p.R1019S	ANKRD36_ENST00000420699.2_Missense_Mutation_p.R1019S			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	1019										endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						AAAAAACTAGGACAGGTAATT	0.358																																					p.R1019S		Atlas-SNP	.											.	ANKRD36	170	.	0			c.G3057T						.						28	33	31					2																	97869996		692	1589	2281	SO:0001583	missense	375248	exon50			AACTAGGACAGGT	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"Ankyrin repeat domain containing"	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.3057G>T	chr2.hg19:g.97869996G>T	ENSP00000419530:p.Arg1019Ser	58.0	0.0		58.0	11.0	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	hg19	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	.	9.403	1.078541	0.20227	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000461694	T;T	0.76186	-1.0;-1.0	0.63	-1.26	0.09376	.	.	.	.	.	T	0.50990	0.1648	N	0.22421	0.69	0.09310	N	1	B	0.16802	0.019	B	0.06405	0.002	T	0.30650	-0.9971	8	0.09338	T	0.73	.	.	.	.	.	1019	A6QL64	AN36A_HUMAN	S	1019;1019;381	ENSP00000419530:R1019S;ENSP00000391950:R1019S	ENSP00000391950:R1019S	R	+	3	2	ANKRD36	97233723	0.009000	0.17119	0.005000	0.12908	0.014000	0.08584	-0.225000	0.09151	-0.424000	0.07382	0.175000	0.17021	AGG	.	.		0.358	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5			T	97869996	G	T	97869996	3	4	121	1	0	0	0	0	1	0	0	0	665	1165	41	3	3255	3	ANKRD36	2	97869996	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	24190198	97869996	145329377	15	20308										
SLC4A10	57282	hgsc.bcm.edu	37	chr2	162799343	162799343	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	taatcccagcaatggcacatTgaaggaatggagggaatcca	11	8	0	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr2:162799343T>G	ENST00000446997.1	+	16	2132	c.2039T>G	c.(2038-2040)tTg>tGg	p.L680W	SLC4A10_ENST00000415876.2_Missense_Mutation_p.L650W|SLC4A10_ENST00000375514.5_Missense_Mutation_p.L661W|SLC4A10_ENST00000421911.1_Missense_Mutation_p.L680W|SLC4A10_ENST00000272716.5_Missense_Mutation_p.L650W	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	680					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	AATGGCACATTGAAGGAATGG	0.388																																					p.L680W		Atlas-SNP	.											.	SLC4A10	309	.	0			c.T2039G						.						72	70	71					2																	162799343		1886	4103	5989	SO:0001583	missense	57282	exon16			GCACATTGAAGGA		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.2039T>G	chr2.hg19:g.162799343T>G	ENSP00000393066:p.Leu680Trp	34.0	0.0		61.0	23.0	NM_001178015	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	hg19	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.714272	0.89112	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	T;T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29;-1.29	5.78	5.78	0.91487	Bicarbonate transporter, C-terminal (1);	0.072239	0.56097	D	0.000028	D	0.89767	0.6810	M	0.84156	2.68	0.54753	D	0.999988	D;D;D	0.67145	0.996;0.996;0.996	D;D;P	0.65987	0.94;0.94;0.895	D	0.91047	0.4875	10	0.66056	D	0.02	.	16.1042	0.81209	0.0:0.0:0.0:1.0	.	661;650;680	F8W675;Q6U841-2;Q6U841	.;.;S4A10_HUMAN	W	661;650;650;649;680;680;679	ENSP00000364664:L661W;ENSP00000395797:L650W;ENSP00000272716:L650W;ENSP00000393066:L680W;ENSP00000404486:L680W	ENSP00000272716:L650W	L	+	2	0	SLC4A10	162507589	0.997000	0.39634	0.903000	0.35520	0.936000	0.57629	5.024000	0.64090	2.211000	0.71520	0.374000	0.22700	TTG	.	.		0.388	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		G	162799343	T	G	162799343	3	3	121	1	0	0	0	0	1	0	0	0	14666	1821	63	5	2186	5	SLC4A10	2	162799343	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	64929347	162799343	80400030	16	20309										
TTN	7273	hgsc.bcm.edu	37	chr2	179560596	179560596	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ttcagtttatacataccttcAtagacctccttttgaacttg	4	10	2	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr2:179560596A>G	ENST00000591111.1	-	112	30476	c.30252T>C	c.(30250-30252)taT>taC	p.Y10084Y	TTN_ENST00000589042.1_Silent_p.Y10401Y|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.Y9157Y|TTN-AS1_ENST00000589487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACATACCTTCATAGACCTCCT	0.373																																					p.Y10401Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T31203C						.						122	117	118					2																	179560596		1346	2805	4151	SO:0001819	synonymous_variant	7273	exon114			ACCTTCATAGACC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30252T>C	chr2.hg19:g.179560596A>G		253.0	0.0		338.0	77.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179560596	A	G	179560596	2	3	121	1	0	0	0	0	0	0	0	1	16750	224	8	2		2	TTN	2	179560596	Silent	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	16761253	179560596	63638777	17	20310										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196682482	196682482	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tcttcaaggtctggcctttcTtgtgccaccacaattcccag	7	14	4	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr2:196682482T>C	ENST00000312428.6	-	50	9463	c.9363A>G	c.(9361-9363)caA>caG	p.Q3121Q		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3121	AAA 5. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CTGGCCTTTCTTGTGCCACCA	0.328																																					p.Q3121Q		Atlas-SNP	.											.	DNAH7	512	.	0			c.A9363G						.						97	91	93					2																	196682482		1852	4095	5947	SO:0001819	synonymous_variant	56171	exon50			CCTTTCTTGTGCC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.9363A>G	chr2.hg19:g.196682482T>C		84.0	0.0		135.0	42.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.328	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196682482	T	C	196682482	2	2	121	1	0	0	0	0	0	0	0	1	4608	1606	56	2		2	DNAH7	2	196682482	Silent	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	17121886	196682482	46516891	18	20311										
IQCF1	132141	hgsc.bcm.edu	37	chr3	51937031	51937031	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gactctgctcctaaggacaaAtgggttggcatctccttctg	10	11	3	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr3:51937031A>G	ENST00000310914.5	-	2	140	c.78T>C	c.(76-78)caT>caC	p.H26H		NM_152397.2	NP_689610.2	Q8N6M8	IQCF1_HUMAN	IQ motif containing F1	26										central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CTAAGGACAAATGGGTTGGCA	0.502																																					p.H26H		Atlas-SNP	.											IQCF1,NS,carcinoma,0,1	IQCF1	26	.	0			c.T78C						.						457	423	435					3																	51937031		2203	4300	6503	SO:0001819	synonymous_variant	132141	exon2			GGACAAATGGGTT	BC029595	CCDS2836.1	3p21.31	2008-02-05			ENSG00000173389	ENSG00000173389			28607	protein-coding gene	gene with protein product						12477932	Standard	NM_152397		Approved	MGC39725	uc003dbv.3	Q8N6M8	OTTHUMG00000156908	ENST00000310914.5:c.78T>C	chr3.hg19:g.51937031A>G		296.0	0.0		240.0	84.0	NM_152397	Q8N711	Silent	SNP	ENST00000310914.5	hg19	CCDS2836.1																																																																																			.	.		0.502	IQCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346568.1	NM_152397		G	51937031	A	G	51937031	2	3	121	1	0	0	0	0	0	0	0	1	7816	98	4	2		2	IQCF1	3	51937031	Silent	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10		51937031	146085399	19	20312										
KCNAB1	7881	hgsc.bcm.edu	37	chr3	156234115	156234115	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gaatcatctcaggaaaatacGgaaacggggtgcctgaaagt	12	7	2	1	rs370046885		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr3:156234115G>A	ENST00000490337.1	+	11	986	c.922G>A	c.(922-924)Gga>Aga	p.G308R	KCNAB1_ENST00000389636.5_Missense_Mutation_p.G279R|KCNAB1_ENST00000302490.8_Missense_Mutation_p.G290R|KCNAB1_ENST00000471742.1_Missense_Mutation_p.G297R|KCNAB1_ENST00000497291.1_3'UTR|KCNAB1_ENST00000389634.5_Missense_Mutation_p.G261R	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	308					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			AGGAAAATACGGAAACGGGGT	0.448																																					p.G308R		Atlas-SNP	.											.	KCNAB1	176	.	0			c.G922A						.	G	ARG/GLY,ARG/GLY,ARG/GLY	0,4406		0,0,2203	100	101	101		889,868,922	4.8	1	3		101	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	KCNAB1	NM_003471.3,NM_172159.3,NM_172160.2	125,125,125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	297/409,290/402,308/420	156234115	1,13005	2203	4300	6503	SO:0001583	missense	7881	exon11			AAATACGGAAACG	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.922G>A	chr3.hg19:g.156234115G>A	ENSP00000419952:p.Gly308Arg	104.0	0.0		72.0	34.0	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	hg19	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.909624	0.52439	0.0	1.16E-4	ENSG00000169282	ENST00000490337;ENST00000389636;ENST00000471742;ENST00000302490;ENST00000389634	T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91	4.77	4.77	0.60923	NADP-dependent oxidoreductase domain (3);	0.056414	0.64402	D	0.000001	T	0.17066	0.0410	N	0.13043	0.29	0.58432	D	0.999993	B;B;B;B;B	0.27380	0.057;0.177;0.016;0.046;0.057	B;B;B;B;B	0.25405	0.022;0.06;0.009;0.013;0.022	T	0.06445	-1.0826	10	0.29301	T	0.29	-0.3472	16.9559	0.86259	0.0:0.0:1.0:0.0	.	279;261;290;297;308	B7Z8E5;F8W6W4;B3KPZ4;Q14722-3;Q14722	.;.;.;.;KCAB1_HUMAN	R	308;279;297;290;261	ENSP00000419952:G308R;ENSP00000374287:G279R;ENSP00000418956:G297R;ENSP00000305858:G290R;ENSP00000374285:G261R	ENSP00000305858:G290R	G	+	1	0	KCNAB1	157716809	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	9.392000	0.97252	2.364000	0.80123	0.561000	0.74099	GGA	.	.		0.448	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		A	156234115	G	A	156234115	3	1	121	1	0	0	0	0	1	0	0	0	8018	1117	39	1	1435	1	KCNAB1	3	156234115	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	104297084	156234115	41788315	20	20313										
SLC26A1	10861	hgsc.bcm.edu	37	chr4	982779	982779	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	aatgtctctcacaggcgggcTgcagcaggctagcagcaggc	14	12	2	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr4:982779T>G	ENST00000361661.2	-	4	2325	c.1948A>C	c.(1948-1950)Agc>Cgc	p.S650R	SLC26A1_ENST00000513138.1_5'Flank|SLC26A1_ENST00000398520.2_Intron|IDUA_ENST00000453894.1_Intron|IDUA_ENST00000509744.1_Intron|SLC26A1_ENST00000398516.2_Missense_Mutation_p.S650R|IDUA_ENST00000247933.4_Intron	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	650	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			ACAGGCGGGCTGCAGCAGGCT	0.677																																					p.S650R		Atlas-SNP	.											.	SLC26A1	44	.	0			c.A1948C						.						19	20	20					4																	982779		2178	4285	6463	SO:0001583	missense	10861	exon3			GCGGGCTGCAGCA	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.1948A>C	chr4.hg19:g.982779T>G	ENSP00000354721:p.Ser650Arg	46.0	0.0		45.0	16.0	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	ENST00000361661.2	hg19	CCDS33934.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.478862	0.63849	.	.	ENSG00000145217	ENST00000361661;ENST00000398516	T;T	0.61392	0.11;0.11	4.25	3.02	0.34903	Sulphate transporter/antisigma-factor antagonist STAS (4);	0.134260	0.64402	D	0.000003	T	0.58047	0.2095	L	0.41415	1.275	0.80722	D	1	P	0.49447	0.924	P	0.55161	0.77	T	0.56842	-0.7912	10	0.66056	D	0.02	.	8.0714	0.30691	0.0:0.1013:0.0:0.8986	.	650	Q9H2B4	S26A1_HUMAN	R	650	ENSP00000354721:S650R;ENSP00000381528:S650R	ENSP00000354721:S650R	S	-	1	0	SLC26A1	972779	1.000000	0.71417	0.996000	0.52242	0.637000	0.38172	4.976000	0.63785	0.483000	0.27608	0.454000	0.30748	AGC	.	.		0.677	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		G	982779	T	G	982779	3	3	121	1	0	0	0	0	1	0	0	0	14529	1580	55	5	264	5	SLC26A1	4	982779	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10		982779	190171497	21	20314										
EVC2	132884	hgsc.bcm.edu	37	chr4	5578055	5578055	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cctttcagaatccacctcccCaggttcgttcagaatcccgg	7	16	2	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr4:5578055C>A	ENST00000344408.5	-	18	3237	c.3184G>T	c.(3184-3186)Ggg>Tgg	p.G1062W	EVC2_ENST00000310917.2_Missense_Mutation_p.G982W|EVC2_ENST00000344938.1_Missense_Mutation_p.G1062W	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	1062					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.G1062W(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TCCACCTCCCCAGGTTCGTTC	0.622																																					p.G1062W		Atlas-SNP	.											.	EVC2	202	.	1	Substitution - Missense(1)	lung(1)	c.G3184T						.						83	77	79					4																	5578055		2203	4300	6503	SO:0001583	missense	132884	exon18			CCTCCCCAGGTTC	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.3184G>T	chr4.hg19:g.5578055C>A	ENSP00000342144:p.Gly1062Trp	79.0	0.0		55.0	6.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561986	0.65538	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74526	-0.85;-0.84;-0.85	5.38	4.53	0.55603	.	2.035800	0.01922	N	0.040580	T	0.76933	0.4057	N	0.19112	0.55	0.24941	N	0.991855	D	0.63880	0.993	P	0.55923	0.787	T	0.65784	-0.6084	10	0.62326	D	0.03	-14.522	12.0681	0.53601	0.0:0.8266:0.1734:0.0	.	1062	Q86UK5	LBN_HUMAN	W	1062;982;1062	ENSP00000339954:G1062W;ENSP00000311683:G982W;ENSP00000342144:G1062W	ENSP00000311683:G982W	G	-	1	0	EVC2	5628956	0.136000	0.22515	0.088000	0.20740	0.296000	0.27459	4.188000	0.58351	1.256000	0.44068	0.491000	0.48974	GGG	.	.		0.622	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		A	5578055	C	A	5578055	3	1	121	1	0	0	0	0	1	0	0	0	5288	594	21	3	762	3	EVC2	4	5578055	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	4595276	5578055	185576221	22	20315										
NCAPG	64151	hgsc.bcm.edu	37	chr4	17841380	17841380	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gctcgccagaaattcgagtcTatacaaaagccttgagttct	8	10	2	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr4:17841380T>C	ENST00000251496.2	+	17	2724	c.2548T>C	c.(2548-2550)Tat>Cat	p.Y850H		NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	850					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		AATTCGAGTCTATACAAAAGC	0.358																																					p.Y850H		Atlas-SNP	.											.	NCAPG	76	.	0			c.T2548C						.						51	52	52					4																	17841380		2203	4300	6503	SO:0001583	missense	64151	exon17			CGAGTCTATACAA	AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"chromosome condensation protein G"	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.2548T>C	chr4.hg19:g.17841380T>C	ENSP00000251496:p.Tyr850His	131.0	0.0		77.0	22.0	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000251496.2	hg19	CCDS3424.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.547545	0.45383	.	.	ENSG00000109805	ENST00000251496	T	0.47528	0.84	5.83	4.65	0.58169	.	0.055206	0.85682	N	0.000000	T	0.65893	0.2735	M	0.72894	2.215	0.58432	D	0.999992	D	0.89917	1.0	D	0.81914	0.995	T	0.68511	-0.5389	10	0.87932	D	0	-10.509	11.8182	0.52224	0.0:0.0682:0.0:0.9318	.	850	Q9BPX3	CND3_HUMAN	H	850	ENSP00000251496:Y850H	ENSP00000251496:Y850H	Y	+	1	0	NCAPG	17450478	1.000000	0.71417	0.998000	0.56505	0.098000	0.18820	4.549000	0.60726	1.045000	0.40225	-0.256000	0.11100	TAT	.	.		0.358	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346		C	17841380	T	C	17841380	3	2	121	1	0	0	0	0	1	0	0	0	10216	1522	53	2	2614	2	NCAPG	4	17841380	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	12263325	17841380	173312896	23	20316										
GRXCR1	389207	hgsc.bcm.edu	37	chr4	42965098	42965098	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tagacgaacgatgccgacgaGtttctgaagctccttccctc	9	13	1	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr4:42965098G>T	ENST00000399770.2	+	2	574	c.574G>T	c.(574-576)Gtt>Ttt	p.V192F		NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	192	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						ATGCCGACGAGTTTCTGAAGC	0.438																																					p.V192F		Atlas-SNP	.											.	GRXCR1	78	.	0			c.G574T						.						355	355	355					4																	42965098		1914	4124	6038	SO:0001583	missense	389207	exon2			CGACGAGTTTCTG		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 88"	613283	"deafness, autosomal recessive 25"	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.574G>T	chr4.hg19:g.42965098G>T	ENSP00000382670:p.Val192Phe	228.0	0.0		158.0	34.0	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	hg19	CCDS43225.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.483960	0.63962	.	.	ENSG00000215203	ENST00000399770	T	0.36157	1.27	6.07	5.24	0.73138	Glutaredoxin (2);Thioredoxin-like fold (2);	0.000000	0.64402	U	0.000009	T	0.42359	0.1199	N	0.22421	0.69	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.19778	-1.0295	10	0.09843	T	0.71	-20.512	14.2764	0.66181	0.0705:0.0:0.9295:0.0	.	192	A8MXD5	GRCR1_HUMAN	F	192	ENSP00000382670:V192F	ENSP00000382670:V192F	V	+	1	0	GRXCR1	42659855	1.000000	0.71417	0.948000	0.38648	0.340000	0.28889	7.658000	0.83755	1.583000	0.49898	0.655000	0.94253	GTT	.	.		0.438	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476		T	42965098	G	T	42965098	3	4	121	1	0	0	0	0	1	0	0	0	6821	1029	36	3	580	3	GRXCR1	4	42965098	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	25123718	42965098	148189178	24	20317			1	20		2	2	14	N	G_C	4.829207e-05
GRXCR1	389207	hgsc.bcm.edu	37	chr4	42965111	42965111	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ccgacgagtttctgaagctcCttccctccctgttgtgttca	8	14	2	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr4:42965111C>T	ENST00000399770.2	+	2	587	c.587C>T	c.(586-588)cCt>cTt	p.P196L		NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	196	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						TCTGAAGCTCCTTCCCTCCCT	0.438																																					p.P196L		Atlas-SNP	.											.	GRXCR1	78	.	0			c.C587T						.						356	356	356					4																	42965111		1916	4125	6041	SO:0001583	missense	389207	exon2			AAGCTCCTTCCCT		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 88"	613283	"deafness, autosomal recessive 25"	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.587C>T	chr4.hg19:g.42965111C>T	ENSP00000382670:p.Pro196Leu	229.0	0.0		155.0	33.0	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	hg19	CCDS43225.1	.	.	.	.	.	.	.	.	.	.	C	4.945	0.175579	0.09391	.	.	ENSG00000215203	ENST00000399770	T	0.32515	1.45	6.07	6.07	0.98685	Glutaredoxin (2);Thioredoxin-like fold (2);	0.077693	0.52532	U	0.000071	T	0.17066	0.0410	N	0.04768	-0.165	0.80722	D	1	P	0.34757	0.467	B	0.33620	0.167	T	0.09907	-1.0653	10	0.08179	T	0.78	-7.83	19.6475	0.95784	0.0:1.0:0.0:0.0	.	196	A8MXD5	GRCR1_HUMAN	L	196	ENSP00000382670:P196L	ENSP00000382670:P196L	P	+	2	0	GRXCR1	42659868	1.000000	0.71417	0.761000	0.31378	0.693000	0.40251	5.741000	0.68638	2.885000	0.99019	0.655000	0.94253	CCT	.	.		0.438	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476		T	42965111	C	T	42965111	3	4	121	1	0	0	0	0	1	0	0	0	6821	681	24	3	593	3	GRXCR1	4	42965111	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	13	42965111	148189165	25	20318			1	20		2	2	14	N	G_C	4.829207e-05
BMP3	651	hgsc.bcm.edu	37	chr4	81967179	81967179	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tgtcctggctgtctaaagatAtcactcaactcttgaggaag	9	9	4	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr4:81967179A>G	ENST00000282701.2	+	2	924	c.604A>G	c.(604-606)Atc>Gtc	p.I202V		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	202					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						GTCTAAAGATATCACTCAACT	0.443																																					p.I202V		Atlas-SNP	.											.	BMP3	59	.	0			c.A604G						.						126	137	133					4																	81967179		2203	4300	6503	SO:0001583	missense	651	exon2			AAAGATATCACTC	M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"Bone morphogenetic proteins"	1070	protein-coding gene	gene with protein product	"osteogenin"	112263	"bone morphogenetic protein 3 (osteogenic)"				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.604A>G	chr4.hg19:g.81967179A>G	ENSP00000282701:p.Ile202Val	76.0	0.0		47.0	23.0	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	hg19	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	A	4.305	0.055947	0.08291	.	.	ENSG00000152785	ENST00000282701	T	0.58652	0.32	5.08	3.89	0.44902	Transforming growth factor-beta, N-terminal (1);	0.089531	0.85682	N	0.000000	T	0.51432	0.1674	M	0.66297	2.02	0.53688	D	0.999977	B	0.28026	0.198	B	0.30316	0.114	T	0.41233	-0.9520	10	0.10377	T	0.69	.	10.8824	0.46946	0.925:0.0:0.075:0.0	.	202	P12645	BMP3_HUMAN	V	202	ENSP00000282701:I202V	ENSP00000282701:I202V	I	+	1	0	BMP3	82186203	1.000000	0.71417	1.000000	0.80357	0.124000	0.20399	3.236000	0.51336	1.058000	0.40530	-0.290000	0.09829	ATC	.	.		0.443	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1			G	81967179	A	G	81967179	3	3	121	1	0	0	0	0	1	0	0	0	1461	449	16	2	610	2	BMP3	4	81967179	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	39002068	81967179	109187097	26	20319										
PRDM5	11107	hgsc.bcm.edu	37	chr4	121737607	121737607	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gaccctccaacgactcctcaCcagtgtggacattttcctgg	8	15	1	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr4:121737607C>A	ENST00000264808.3	-	7	1106		c.e7+1		PRDM5_ENST00000515109.1_Splice_Site|PRDM5_ENST00000428209.2_Splice_Site	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5						histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CGACTCCTCACCAGTGTGGAC	0.547																																					.		Atlas-SNP	.											.	PRDM5	76	.	0			c.865+1G>T						.						108	84	92					4																	121737607		2203	4300	6503	SO:0001630	splice_region_variant	11107	exon8			TCCTCACCAGTGT	AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"Zinc fingers, C2H2-type"	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.865+1G>T	chr4.hg19:g.121737607C>A		116.0	0.0		85.0	36.0	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Splice_Site	SNP	ENST00000264808.3	hg19	CCDS3716.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.964799	0.92791	.	.	ENSG00000138738	ENST00000264808;ENST00000515109;ENST00000428209	.	.	.	6.04	6.04	0.98038	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6396	0.99537	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRDM5	121957057	1.000000	0.71417	0.981000	0.43875	0.929000	0.56500	7.818000	0.86416	2.881000	0.98747	0.650000	0.86243	.	.	.		0.547	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2		Intron	A	121737607	C	A	121737607	5	1	121	1	0	0	0	0	0	0	1	0	12472	521	18	3	1066	3	PRDM5	4	121737607	Splice_Site	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	39770428	121737607	69416669	27	20320										
RNF175	285533	hgsc.bcm.edu	37	chr4	154649420	154649420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gaggatgtaactggtaataaCggagaacatcccccacatag	10	9	0	1	rs370409419		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr4:154649420C>T	ENST00000347063.4	-	4	712	c.340G>A	c.(340-342)Gtt>Att	p.V114I	RNF175_ENST00000274068.4_Intron|RP11-153M7.5_ENST00000505051.1_RNA|RNF175_ENST00000506505.1_Intron	NM_173662.2	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	114						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.V114I(3)		breast(1)|endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	13	all_hematologic(180;0.093)	Renal(120;0.118)				CTGGTAATAACGGAGAACATC	0.478																																					p.V114I		Atlas-SNP	.											RNF175_ENST00000347063,NS,carcinoma,0,3	RNF175	40	.	3	Substitution - Missense(3)	large_intestine(2)|prostate(1)	c.G340A						.	C	ILE/VAL	0,3738		0,0,1869	117	116	116		340	-2.6	0	4		116	1,8203		0,1,4101	no	missense	RNF175	NM_173662.2	29	0,1,5970	TT,TC,CC		0.0122,0.0,0.0084	probably-damaging	114/329	154649420	1,11941	1869	4102	5971	SO:0001583	missense	285533	exon4			TAATAACGGAGAA	BC034385	CCDS47149.1	4q31.3	2008-02-05			ENSG00000145428	ENSG00000145428		"RING-type (C3HC4) zinc fingers"	27735	protein-coding gene	gene with protein product							Standard	NM_173662		Approved	FLJ34190	uc003int.3	Q8N4F7	OTTHUMG00000161557	ENST00000347063.4:c.340G>A	chr4.hg19:g.154649420C>T	ENSP00000340979:p.Val114Ile	82.0	0.0		62.0	31.0	NM_173662	C9JL66|Q8NB61	Missense_Mutation	SNP	ENST00000347063.4	hg19	CCDS47149.1	.	.	.	.	.	.	.	.	.	.	C	1.441	-0.567588	0.03910	0.0	1.22E-4	ENSG00000145428	ENST00000347063;ENST00000508248	T;T	0.61274	0.12;0.12	4.69	-2.58	0.06228	.	0.074861	0.52532	D	0.000078	T	0.17450	0.0419	N	0.02802	-0.49	0.19300	N	0.999973	B	0.15719	0.014	B	0.09377	0.004	T	0.21518	-1.0243	10	0.02654	T	1	-2.9588	0.1241	0.00067	0.2456:0.21:0.2406:0.3038	.	114	Q8N4F7	RN175_HUMAN	I	114;54	ENSP00000340979:V114I;ENSP00000427472:V54I	ENSP00000340979:V114I	V	-	1	0	RNF175	154868870	0.000000	0.05858	0.000000	0.03702	0.889000	0.51656	0.001000	0.13038	-0.602000	0.05775	-0.136000	0.14681	GTT	.	.		0.478	RNF175-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365286.1	NM_173662		T	154649420	C	T	154649420	3	4	121	1	0	0	0	0	1	0	0	0	13478	536	19	1	670	1	RNF175	4	154649420	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	32911813	154649420	36504856	28	20321										
CDH6	1004	hgsc.bcm.edu	37	chr5	31294184	31294184	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cgacatacaggccaccaagaGgctggacagggaagaaaaac	12	10	0	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:31294184G>A	ENST00000265071.2	+	3	609	c.344G>A	c.(343-345)aGg>aAg	p.R115K	CDH6_ENST00000514738.1_Missense_Mutation_p.R60K	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	115	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GCCACCAAGAGGCTGGACAGG	0.458																																					p.R115K		Atlas-SNP	.											.	CDH6	175	.	0			c.G344A						.						107	108	108					5																	31294184		2203	4300	6503	SO:0001583	missense	1004	exon3			CCAAGAGGCTGGA	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"Cadherins / Major cadherins"	1765	protein-coding gene	gene with protein product	"K-Cadherin"	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.344G>A	chr5.hg19:g.31294184G>A	ENSP00000265071:p.Arg115Lys	112.0	0.0		143.0	12.0	NM_004932	A8K5H5|Q9BWS0	Missense_Mutation	SNP	ENST00000265071.2	hg19	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.654749	0.67472	.	.	ENSG00000113361	ENST00000514738;ENST00000265071	T;T	0.52295	0.67;0.67	5.77	5.77	0.91146	Cadherin (5);Cadherin-like (1);	0.040499	0.85682	D	0.000000	T	0.46171	0.1379	L	0.49640	1.575	0.58432	D	0.999997	B;B	0.18166	0.003;0.026	B;B	0.20577	0.014;0.03	T	0.31503	-0.9941	10	0.18710	T	0.47	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	115;115	P55285;P55285-2	CADH6_HUMAN;.	K	60;115	ENSP00000424843:R60K;ENSP00000265071:R115K	ENSP00000265071:R115K	R	+	2	0	CDH6	31329941	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	6.366000	0.73095	2.885000	0.99019	0.655000	0.94253	AGG	.	.		0.458	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		A	31294184	G	A	31294184	3	1	121	1	0	0	0	0	1	0	0	0	3116	1000	35	3	350	3	CDH6	5	31294184	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10		31294184	149621076	29	20322										
JMY	133746	hgsc.bcm.edu	37	chr5	78610232	78610232	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	aaaactgaagaggtgggagaAggaagagtcaagcgtgggcc	17	5	1	4	rs376215787		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:78610232A>C	ENST00000396137.4	+	9	2679	c.2217A>C	c.(2215-2217)gaA>gaC	p.E739D	JMY_ENST00000412001.1_Intron	NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	739					'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		AGGTGGGAGAAGGAAGAGTCA	0.458																																					p.E739D		Atlas-SNP	.											.	JMY	82	.	0			c.A2217C						.						113	121	118					5																	78610232		2100	4251	6351	SO:0001583	missense	133746	exon9			GGGAGAAGGAAGA	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.2217A>C	chr5.hg19:g.78610232A>C	ENSP00000379441:p.Glu739Asp	131.0	0.0		160.0	70.0	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	hg19	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	A	2.652	-0.281736	0.05642	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.74106	-0.81	4.57	2.03	0.26663	.	1.603640	0.04196	N	0.329215	T	0.61949	0.2388	L	0.40543	1.245	0.09310	N	1	B	0.22211	0.066	B	0.18871	0.023	T	0.47114	-0.9142	10	0.13108	T	0.6	.	3.908	0.09191	0.5791:0.1888:0.2321:0.0	.	739	Q8N9B5	JMY_HUMAN	D	739	ENSP00000379441:E739D	ENSP00000282259:E739D	E	+	3	2	JMY	78645988	0.014000	0.17966	0.013000	0.15412	0.173000	0.22820	0.428000	0.21395	1.697000	0.51169	0.477000	0.44152	GAA	.	.		0.458	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405		C	78610232	A	C	78610232	3	2	121	1	0	0	0	0	1	0	0	0	7966	69	3	5	2251	5	JMY	5	78610232	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	47316048	78610232	102305028	30	20323										
RASA1	5921	hgsc.bcm.edu	37	chr5	86685321	86685321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cagatgaacttcgaacgctcAgtaatgagcgtggtgcacag	12	9	1	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:86685321A>G	ENST00000274376.6	+	24	3601	c.3037A>G	c.(3037-3039)Agt>Ggt	p.S1013G	RASA1_ENST00000456692.2_Missense_Mutation_p.S836G|RASA1_ENST00000512763.1_Missense_Mutation_p.S846G|RASA1_ENST00000506290.1_Missense_Mutation_p.S847G	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	1013					blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		TCGAACGCTCAGTAATGAGCG	0.443																																					p.S1013G		Atlas-SNP	.											.	RASA1	213	.	0			c.A3037G						.						137	123	128					5																	86685321		2203	4300	6503	SO:0001583	missense	5921	exon24			ACGCTCAGTAATG		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.3037A>G	chr5.hg19:g.86685321A>G	ENSP00000274376:p.Ser1013Gly	101.0	0.0		115.0	31.0	NM_002890	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	hg19	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.578890	0.86645	.	.	ENSG00000145715	ENST00000274376;ENST00000456692;ENST00000512763;ENST00000506290	T;T;T;T	0.19105	2.17;2.17;2.17;2.17	5.75	5.75	0.90469	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.073152	0.85682	D	0.000000	T	0.43809	0.1264	M	0.71581	2.175	0.80722	D	1	D;D;D;D;D	0.71674	0.997;0.991;0.991;0.998;0.997	P;P;P;P;P	0.62382	0.798;0.729;0.729;0.901;0.77	T	0.30357	-0.9981	10	0.46703	T	0.11	.	16.0379	0.80642	1.0:0.0:0.0:0.0	.	847;846;847;836;1013	E9PGC0;B4DTL2;B4DTX4;P20936-2;P20936	.;.;.;.;RASA1_HUMAN	G	1013;836;846;847	ENSP00000274376:S1013G;ENSP00000411221:S836G;ENSP00000422008:S846G;ENSP00000420905:S847G	ENSP00000274376:S1013G	S	+	1	0	RASA1	86721077	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.691000	0.91279	2.192000	0.70111	0.477000	0.44152	AGT	.	.		0.443	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		G	86685321	A	G	86685321	3	3	121	1	0	0	0	0	1	0	0	0	13075	188	7	2	3143	2	RASA1	5	86685321	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	8075089	86685321	94229939	31	20324										
GIN1	54826	hgsc.bcm.edu	37	chr5	102440400	102440400	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gaacaaatctgtcatgattaTagcatatacatgacttctgt	6	7	3	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:102440400T>C	ENST00000399004.2	-	4	578	c.484A>G	c.(484-486)Ata>Gta	p.I162V	GIN1_ENST00000508629.1_Missense_Mutation_p.I162V|GIN1_ENST00000511400.1_5'Flank	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	162	Integrase catalytic. {ECO:0000255|PROSITE-ProRule:PRU00457}.				DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)	p.I162V(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		GTCATGATTATAGCATATACA	0.358																																					p.I162V		Atlas-SNP	.											GIN1,NS,carcinoma,0,1	GIN1	53	.	1	Substitution - Missense(1)	lung(1)	c.A484G						.						111	103	105					5																	102440400		1857	4097	5954	SO:0001583	missense	54826	exon4			TGATTATAGCATA	BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"gypsy integrase 1", "Ty3/Gypsy integrase 1"		"zinc finger, H2C2 domain containing"	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.484A>G	chr5.hg19:g.102440400T>C	ENSP00000381970:p.Ile162Val	151.0	0.0		166.0	36.0	NM_017676	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Missense_Mutation	SNP	ENST00000399004.2	hg19	CCDS43349.1	.	.	.	.	.	.	.	.	.	.	T	0.843	-0.741096	0.03088	.	.	ENSG00000145723	ENST00000399004;ENST00000508629	T;T	0.40756	1.02;1.02	5.88	-2.62	0.06152	Integrase, catalytic core (2);Ribonuclease H-like (1);	0.731785	0.12470	N	0.466060	T	0.23289	0.0563	N	0.19112	0.55	0.24200	N	0.995515	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.001	T	0.17167	-1.0378	10	0.62326	D	0.03	-20.9525	6.7363	0.23411	0.0:0.3263:0.118:0.5557	.	162;162	Q9NXP7-3;Q9NXP7	.;GIN1_HUMAN	V	162	ENSP00000381970:I162V;ENSP00000427162:I162V	ENSP00000381970:I162V	I	-	1	0	GIN1	102468299	0.923000	0.31300	0.820000	0.32676	0.019000	0.09904	-0.151000	0.10175	-0.366000	0.08064	-1.273000	0.01405	ATA	.	.		0.358	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		C	102440400	T	C	102440400	3	2	121	1	0	0	0	0	1	0	0	0	6394	1406	49	2	1104	2	GIN1	5	102440400	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	15755079	102440400	78474860	32	20325										
ETF1	2107	hgsc.bcm.edu	37	chr5	137844022	137844022	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	catcaaggtcaaaaaattcaTcgtctcctccttggtattcc	5	12	4	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:137844022T>A	ENST00000360541.5	-	11	1507	c.1286A>T	c.(1285-1287)gAt>gTt	p.D429V	ETF1_ENST00000499810.2_Missense_Mutation_p.D396V|ETF1_ENST00000503014.1_Missense_Mutation_p.D415V	NM_004730.3	NP_004721.1	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	429					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)|translation termination factor activity (GO:0008079)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAAAAATTCATCGTCTCCTCC	0.488																																					p.D429V		Atlas-SNP	.											.	ETF1	38	.	0			c.A1286T						.						63	52	56					5																	137844022		2203	4300	6503	SO:0001583	missense	2107	exon11			AATTCATCGTCTC	AF095901	CCDS4207.1, CCDS75313.1, CCDS75314.1	5q31.2	2008-02-05			ENSG00000120705	ENSG00000120705			3477	protein-coding gene	gene with protein product	"sup45 (yeast omnipotent suppressor 45) homolog-like 1", "polypeptide chain release factor 1"	600285		SUP45L1, ERF1, ERF		1546371, 7990965	Standard	NM_004730		Approved	eRF1, TB3-1, RF1	uc003ldc.5	P62495	OTTHUMG00000129199	ENST00000360541.5:c.1286A>T	chr5.hg19:g.137844022T>A	ENSP00000353741:p.Asp429Val	60.0	0.0		77.0	14.0	NM_004730	B2R6B4|D3DQC1|P46055|Q5M7Z7|Q96CG1	Missense_Mutation	SNP	ENST00000360541.5	hg19	CCDS4207.1	.	.	.	.	.	.	.	.	.	.	T	19.65	3.866871	0.72065	.	.	ENSG00000120705	ENST00000499810;ENST00000360541;ENST00000503014	.	.	.	6.17	6.17	0.99709	.	0.043633	0.85682	D	0.000000	T	0.59945	0.2231	L	0.49513	1.565	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.16289	0.001;0.015	T	0.56238	-0.8012	9	0.62326	D	0.03	-8.966	16.4837	0.84171	0.0:0.0:0.0:1.0	.	415;429	B7Z7P8;P62495	.;ERF1_HUMAN	V	396;429;415	.	ENSP00000353741:D429V	D	-	2	0	ETF1	137871921	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.823000	0.86660	2.371000	0.80710	0.533000	0.62120	GAT	.	.		0.488	ETF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251276.2	NM_004730		A	137844022	T	A	137844022	3	1	121	1	0	0	0	0	1	0	0	0	5270	1435	50	4	31	4	ETF1	5	137844022	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	35403622	137844022	43071238	33	20326										
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140187339	140187339	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ccacctgatgacgagctggtAaaaggtcttgggcttatatt	11	8	1	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:140187339A>G	ENST00000530339.1	+	1	567	c.567A>G	c.(565-567)gtA>gtG	p.V189V	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.V189V|PCDHA4_ENST00000512229.2_Silent_p.V189V|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	189	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGAGCTGGTAAAAGGTCTTG	0.478																																					p.V189V		Atlas-SNP	.											.	PCDHA4	419	.	0			c.A567G						.						47	55	52					5																	140187339		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			GCTGGTAAAAGGT	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"Cadherins / Protocadherins : Clustered"	8670	other	complex locus constituent	"ortholog of mouse CNR1, KIAA0345-like 10"	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.567A>G	chr5.hg19:g.140187339A>G		171.0	0.0		191.0	49.0	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	hg19	CCDS54916.1																																																																																			.	.		0.478	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		G	140187339	A	G	140187339	2	3	121	1	0	0	0	0	0	0	0	1	11535	349	13	2		2	PCDHA4	5	140187339	Silent	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	2343317	140187339	40727921	34	20327										
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140724102	140724102	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	atgtaggcattaactccctgCagaactacaagcttagcccc	7	13	0	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:140724102C>A	ENST00000253812.6	+	1	502	c.502C>A	c.(502-504)Cag>Aag	p.Q168K	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	168	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAACTCCCTGCAGAACTACAA	0.483																																					p.Q168K		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.C502A						.						88	86	87					5																	140724102		1959	4144	6103	SO:0001583	missense	56112	exon1			TCCCTGCAGAACT	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.502C>A	chr5.hg19:g.140724102C>A	ENSP00000253812:p.Gln168Lys	113.0	0.0		149.0	34.0	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	hg19	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	14.32	2.498843	0.44455	.	.	ENSG00000254245	ENST00000253812	T	0.19806	2.12	5.65	5.65	0.86999	Cadherin (3);Cadherin-like (1);	0.000000	0.31772	U	0.007086	T	0.32763	0.0840	M	0.78223	2.4	0.25891	N	0.983474	P;B	0.42827	0.791;0.442	B;B	0.40506	0.331;0.178	T	0.30504	-0.9976	10	0.51188	T	0.08	.	19.7068	0.96076	0.0:1.0:0.0:0.0	.	168;168	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	K	168	ENSP00000253812:Q168K	ENSP00000253812:Q168K	Q	+	1	0	PCDHGA3	140704286	0.997000	0.39634	1.000000	0.80357	0.983000	0.72400	2.996000	0.49449	2.824000	0.97209	0.655000	0.94253	CAG	.	.		0.483	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		A	140724102	C	A	140724102	3	1	121	1	0	0	0	0	1	0	0	0	11564	711	25	3	504	3	PCDHGA3	5	140724102	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	536763	140724102	40191158	35	20328										
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156727773	156727773	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gtgaagcggctgtgccatgcCgagcgcaggaaggactttgt	16	9	0	1	rs375762537		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:156727773C>G	ENST00000521420.1	+	5	451	c.360C>G	c.(358-360)gcC>gcG	p.A120A	CYFIP2_ENST00000377576.3_Silent_p.A146A|CYFIP2_ENST00000318218.6_Silent_p.A146A|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000347377.6_Silent_p.A146A|CYFIP2_ENST00000541131.1_Silent_p.A71A					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGTGCCATGCCGAGCGCAGGA	0.577																																					p.A146A		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C438G						.						80	81	81					5																	156727773		2124	4263	6387	SO:0001819	synonymous_variant	26999	exon6			CCATGCCGAGCGC	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.360C>G	chr5.hg19:g.156727773C>G		112.0	0.0		133.0	86.0	NM_001037332		Silent	SNP	ENST00000521420.1	hg19																																																																																				.	.		0.577	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		G	156727773	C	G	156727773	2	3	121	1	0	0	0	0	0	0	0	1	4140	639	23	4		4	CYFIP2	5	156727773	Silent	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	16003671	156727773	24187487	36	20329										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167420042	167420042	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tcaggaacggtttacacgccCccgccccgcctgctgcccag	10	19	1	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:167420042C>G	ENST00000518659.1	+	5	1080	c.1041C>G	c.(1039-1041)ccC>ccG	p.P347P	TENM2_ENST00000545108.1_Silent_p.P347P|TENM2_ENST00000403607.2_Silent_p.P180P|TENM2_ENST00000520394.1_Silent_p.P156P|TENM2_ENST00000519204.1_Silent_p.P226P	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	347	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TTTACACGCCCCCGCCCCGCC	0.587																																					p.P347P		Atlas-SNP	.											.	.	.	.	0			c.C1041G						.						65	68	67					5																	167420042		1896	4100	5996	SO:0001819	synonymous_variant	57451	exon5			CACGCCCCCGCCC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.1041C>G	chr5.hg19:g.167420042C>G		128.0	0.0		122.0	52.0	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	hg19																																																																																				.	.		0.587	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		G	167420042	C	G	167420042	2	3	121	1	0	0	0	0	0	0	0	1	10844	610	22	4		4	ODZ2	5	167420042	Silent	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	10692269	167420042	13495218	37	20330										
FOXI1	2299	hgsc.bcm.edu	37	chr5	169535372	169535372	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gggagccccacgagccacccCttggtcacaccaggactgag	12	16	1	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:169535372C>A	ENST00000306268.6	+	2	955	c.894C>A	c.(892-894)ccC>ccA	p.P298P	FOXI1_ENST00000449804.2_Silent_p.P203P			Q12951	FOXI1_HUMAN	forkhead box I1	298					embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGAGCCACCCCTTGGTCACAC	0.617									Pendred syndrome																												p.P298P		Atlas-SNP	.											.	FOXI1	70	.	0			c.C894A						.						68	65	66					5																	169535372		2203	4300	6503	SO:0001819	synonymous_variant	2299	exon2	Familial Cancer Database	Goiter-Deafness syndrome	CCACCCCTTGGTC	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.894C>A	chr5.hg19:g.169535372C>A		109.0	0.0		128.0	29.0	NM_012188	Q14518|Q66SR7|Q8N6L8	Silent	SNP	ENST00000306268.6	hg19	CCDS4372.1																																																																																			.	.		0.617	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		A	169535372	C	A	169535372	2	1	121	1	0	0	0	0	0	0	0	1	6017	668	24	3		3	FOXI1	5	169535372	Silent	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	2115330	169535372	11379888	38	20331										
MSX2	4488	hgsc.bcm.edu	37	chr5	174151962	174151962	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ccgctggtgaagcccttcgaGaccgcctcggtcaagtcgga	13	14	1	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:174151962G>A	ENST00000239243.6	+	1	427	c.300G>A	c.(298-300)gaG>gaA	p.E100E	MSX2_ENST00000507785.1_Silent_p.E100E	NM_002449.4	NP_002440.2	P35548	MSX2_HUMAN	msh homeobox 2	100					activation of meiosis (GO:0090427)|anagen (GO:0042640)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway involved in heart development (GO:0061312)|bone trabecula formation (GO:0060346)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to estradiol stimulus (GO:0071392)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte development (GO:0002063)|cranial suture morphogenesis (GO:0060363)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic nail plate morphogenesis (GO:0035880)|enamel mineralization (GO:0070166)|endochondral bone growth (GO:0003416)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|frontal suture morphogenesis (GO:0060364)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of catagen (GO:0051795)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|positive regulation of osteoblast differentiation (GO:0045669)|signal transduction involved in regulation of gene expression (GO:0023019)|wound healing, spreading of epidermal cells (GO:0035313)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10	Renal(175;0.000159)|Lung NSC(126;0.0196)|all_lung(126;0.0303)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			AGCCCTTCGAGACCGCCTCGG	0.706																																					p.E100E		Atlas-SNP	.											.	MSX2	24	.	0			c.G300A						.						7	10	9					5																	174151962		2060	4004	6064	SO:0001819	synonymous_variant	4488	exon1			CTTCGAGACCGCC	D26145	CCDS4392.1	5q35.2	2011-06-20	2006-11-21		ENSG00000120149	ENSG00000120149		"Homeoboxes / ANTP class : NKL subclass"	7392	protein-coding gene	gene with protein product	"craniosynostosis, type 2"	123101	"msh (Drosophila) homeo box homolog 2", "parietal foramina 1", "msh homeobox homolog 2 (Drosophila)"	PFM1		8668339, 8786091	Standard	XM_006714868		Approved	CRS2, FPP, HOX8, MSH, PFM	uc003mcy.3	P35548	OTTHUMG00000130556	ENST00000239243.6:c.300G>A	chr5.hg19:g.174151962G>A		39.0	0.0		35.0	7.0	NM_002449	D3DQN1|Q53XM4|Q9UD60	Silent	SNP	ENST00000239243.6	hg19	CCDS4392.1																																																																																			.	.		0.706	MSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252981.3			A	174151962	G	A	174151962	2	1	121	1	0	0	0	0	0	0	0	1	9905	933	33	3		3	MSX2	5	174151962	Silent	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	4616590	174151962	6763298	39	20332										
HK3	3101	hgsc.bcm.edu	37	chr5	176308352	176308352	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cacccccacagacactgccaGctcttccaggccccggttct	7	20	2	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr5:176308352G>T	ENST00000292432.5	-	18	2669	c.2578C>A	c.(2578-2580)Ctg>Atg	p.L860M		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	860	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GACACTGCCAGCTCTTCCAGG	0.677																																					p.L860M		Atlas-SNP	.											.	HK3	210	.	0			c.C2578A						.						101	108	106					5																	176308352		2203	4300	6503	SO:0001583	missense	3101	exon18			CTGCCAGCTCTTC		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.2578C>A	chr5.hg19:g.176308352G>T	ENSP00000292432:p.Leu860Met	59.0	0.0		84.0	21.0	NM_002115	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	hg19	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.096542	0.56075	.	.	ENSG00000160883	ENST00000292432	D	0.98178	-4.77	5.35	3.58	0.41010	Hexokinase, C-terminal (1);	0.000000	0.41605	D	0.000854	D	0.98178	0.9398	M	0.64997	1.995	0.48040	D	0.999572	D	0.54964	0.969	D	0.64144	0.922	D	0.97317	0.9941	10	0.41790	T	0.15	.	11.8579	0.52449	0.1444:0.0:0.8556:0.0	.	860	P52790	HXK3_HUMAN	M	860	ENSP00000292432:L860M	ENSP00000292432:L860M	L	-	1	2	HK3	176240958	1.000000	0.71417	0.940000	0.37924	0.870000	0.49936	4.145000	0.58065	0.755000	0.32990	0.561000	0.74099	CTG	.	.		0.677	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			T	176308352	G	T	176308352	3	4	121	1	0	0	0	0	1	0	0	0	7201	962	34	3	201	3	HK3	5	176308352	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	2156390	176308352	4606908	40	20333										
C6orf150	115004	hgsc.bcm.edu	37	chr6	74161257	74161257	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	aagcagctcaccttcacgtgCtcatagtagctcccggtgtt	9	13	3	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr6:74161257C>A	ENST00000370315.3	-	1	742	c.648G>T	c.(646-648)gaG>gaT	p.E216D	MB21D1_ENST00000370318.1_Missense_Mutation_p.E216D	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	216					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						CCTTCACGTGCTCATAGTAGC	0.662																																					p.E216D		Atlas-SNP	.											.	MB21D1	33	.	0			c.G648T						.						17	17	17					6																	74161257		2186	4278	6464	SO:0001583	missense	115004	exon1			CACGTGCTCATAG	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"chromosome 6 open reading frame 150"	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.648G>T	chr6.hg19:g.74161257C>A	ENSP00000359339:p.Glu216Asp	63.0	0.0		56.0	19.0	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Missense_Mutation	SNP	ENST00000370315.3	hg19	CCDS4978.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.316545	0.60524	.	.	ENSG00000164430	ENST00000370318;ENST00000370315;ENST00000296913	T;T	0.09445	2.98;2.98	4.88	3.09	0.35607	.	0.000000	0.64402	D	0.000005	T	0.17195	0.0413	M	0.80183	2.485	0.31647	N	0.64731	D	0.89917	1.0	D	0.87578	0.998	T	0.03608	-1.1020	10	0.52906	T	0.07	-30.3485	7.0317	0.24970	0.0:0.7908:0.0:0.2092	.	216	Q8N884	M21D1_HUMAN	D	216	ENSP00000359342:E216D;ENSP00000359339:E216D	ENSP00000296913:E216D	E	-	3	2	MB21D1	74217978	0.996000	0.38824	0.949000	0.38748	0.351000	0.29236	0.768000	0.26590	0.487000	0.27698	0.561000	0.74099	GAG	.	.		0.662	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441		A	74161257	C	A	74161257	3	1	121	1	0	0	0	0	1	0	0	0	2339	796	28	3	940	3	C6orf150	6	74161257	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10		74161257	96953810	41	20334										
CD109	135228	hgsc.bcm.edu	37	chr6	74492373	74492373	+	Frame_Shift_Del	DEL	A	A	-													0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tgctgagaggtttatggaggAaaatgaaggacatattgtag							TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr6:74492373delA	ENST00000287097.5	+	18	2112	c.2000delA	c.(1999-2001)gaafs	p.E667fs	CD109_ENST00000422508.2_Frame_Shift_Del_p.E590fs|CD109_ENST00000437994.2_Frame_Shift_Del_p.E667fs			Q6YHK3	CD109_HUMAN	CD109 molecule	667	Bait region (approximate). {ECO:0000250}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTTATGGAGGAAAATGAAGGA	0.373																																					p.E667fs		Atlas-Indel,Pindel	.											.	CD109	170	.	0			c.1999delG						.						179	167	171					6																	74492373		2203	4300	6503	SO:0001589	frameshift_variant	135228	exon18			.	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2000delA	chr6.hg19:g.74492373delA	ENSP00000287097:p.Glu667fs	123.0	0.0		82.0	30.0	NM_001159587	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Frame_Shift_Del	DEL	ENST00000287097.5	hg19	CCDS4982.1																																																																																			.	.		0.373	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		-	74492373	A	-	74492373	7	5	121	1	0	1	0	1	0	0	0	0	2965	246	9	0	2070	0	CD109	6	74492373	Frame_Shift_Del	DEL	A	TCGA-DD-A3A7-01A-11D-A22F-10	331116	74492373	96622694	42	20335										
SENP6	26054	hgsc.bcm.edu	37	chr6	76376479	76376480	+	Frame_Shift_Ins	INS	-	-	TT													0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gacagaactaacagaagagaINSaagcatatctcctcagcctg							TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr6:76376479_76376480insTT	ENST00000447266.2	+	10	1524_1525	c.1046_1047insTT	c.(1045-1050)gaaagcfs	p.ES349fs	SENP6_ENST00000327284.8_Frame_Shift_Ins_p.ES342fs|SENP6_ENST00000541192.1_5'Flank|SENP6_ENST00000370014.3_Frame_Shift_Ins_p.ES349fs|SENP6_ENST00000370010.2_Frame_Shift_Ins_p.ES342fs	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	349					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				AACAGAAGAGAAAGCATATCTC	0.356																																					p.E349fs		Atlas-INDEL	.											.	SENP6	189	.	0			c.1046_1047insTT						.																																			SO:0001589	frameshift_variant	26054	exon10			.		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	Exception_encountered	chr6.hg19:g.76376479_76376480insTT	ENSP00000402527:p.Glu349fs	70.0	0.0		44.0	18.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Frame_Shift_Ins	INS	ENST00000447266.2	hg19	CCDS47454.1																																																																																			.	.		0.356	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		TT	76376480	-	TT	76376479	7	5	121	1	0	1	1	0	0	0	0	0	14065	246	9	0	1084	0	SENP6	6	76376479	Frame_Shift_Ins	INS	-	TCGA-DD-A3A7-01A-11D-A22F-10	1884106	76376479	94738588	43	20336	87	2								
SENP6	26054	hgsc.bcm.edu	37	chr6	76376480	76376481	+	Missense_Mutation	DNP	AA	AA	TC													0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gacagaactaacagaagagaAagcatatctcctcagcctgc							TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr6:76376480_76376481AA>TC	ENST00000447266.2	+	10	1525_1526	c.1047_1048AA>TC	c.(1045-1050)gaAAgc>gaTCgc	p.349_350ES>DR	SENP6_ENST00000327284.8_Missense_Mutation_p.342_343ES>DR|SENP6_ENST00000541192.1_5'Flank|SENP6_ENST00000370014.3_Missense_Mutation_p.349_350ES>DR|SENP6_ENST00000370010.2_Missense_Mutation_p.342_343ES>DR	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	349					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				ACAGAAGAGAAAGCATATCTCC	0.361																																					p.E349D|p.S350R		Atlas-SNP	.											.	SENP6	189	.	0			c.A1047T|c.A1048C						.																																			SO:0001583	missense	26054	exon10			AAGAGAAAGCATA|AGAGAAAGCATAT		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	Exception_encountered	chr6.hg19:g.76376480_76376481delinsTC	ENSP00000402527:p.E349_S350delinsDR	71.0|72.0	0.0		44.0|45.0	19.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	hg19	CCDS47454.1																																																																																			.	.		0.361	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		TC	76376481	AA	TC	76376480	3	4	121	1	0	0	0	0	1	0	0	0	14065	11	1	4	1085	4	SENP6	6	76376480	Missense_Mutation	DNP	AA	TCGA-DD-A3A7-01A-11D-A22F-10	1	76376480	94738587	44	20337	87	2								
INTS1	26173	hgsc.bcm.edu	37	chr7	1525069	1525069	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gggctccttctcctccccgtCccgcaggctgccctccgaaa	9	20	1	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr7:1525069C>A	ENST00000404767.3	-	23	3098	c.3013G>T	c.(3013-3015)Gac>Tac	p.D1005Y	INTS1_ENST00000389470.4_Missense_Mutation_p.D1167Y	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	1005					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		TCCTCCCCGTCCCGCAGGCTG	0.667																																					p.D1005Y		Atlas-SNP	.											.	INTS1	145	.	0			c.G3013T						.						31	40	37					7																	1525069		2078	4205	6283	SO:0001583	missense	26173	exon23			CCCCGTCCCGCAG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.3013G>T	chr7.hg19:g.1525069C>A	ENSP00000385722:p.Asp1005Tyr	40.0	0.0		47.0	33.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.403493	0.62288	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.55588	0.51;0.66	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.68384	0.2995	L	0.54323	1.7	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.67548	0.929;0.952	T	0.71712	-0.4510	10	0.72032	D	0.01	.	18.3337	0.90280	0.0:1.0:0.0:0.0	.	1173;1005	A4D213;Q8N201	.;INT1_HUMAN	Y	1005;1167	ENSP00000385722:D1005Y;ENSP00000374121:D1167Y	ENSP00000374121:D1167Y	D	-	1	0	INTS1	1491595	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	7.420000	0.80191	2.334000	0.79466	0.561000	0.74099	GAC	.	.		0.667	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			A	1525069	C	A	1525069	3	1	121	1	0	0	0	0	1	0	0	0	7784	855	30	3	3663	3	INTS1	7	1525069	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10		1525069	157613594	45	20338										
KLHL7	55975	hgsc.bcm.edu	37	chr7	23207527	23207527	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gcacacaaagcccagcatgcTgacccagcgctgcagccatg	10	16	0	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr7:23207527T>C	ENST00000339077.5	+	9	1493	c.1250T>C	c.(1249-1251)cTg>cCg	p.L417P	KLHL7_ENST00000322231.7_Missense_Mutation_p.L395P|KLHL7_ENST00000542558.1_Missense_Mutation_p.L192P|KLHL7_ENST00000409689.1_Missense_Mutation_p.L369P|KLHL7_ENST00000539124.1_Missense_Mutation_p.L341P|KLHL7_ENST00000545443.1_Missense_Mutation_p.L395P	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	417					protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CCCAGCATGCTGACCCAGCGC	0.463																																					p.L417P		Atlas-SNP	.											.	KLHL7	102	.	0			c.T1250C						.						113	112	112					7																	23207527		2203	4300	6503	SO:0001583	missense	55975	exon9			GCATGCTGACCCA		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"Kelch-like", "BTB/POZ domain containing"	15646	protein-coding gene	gene with protein product	"retinitis pigmentosa 42"	611119	"kelch-like 7 (Drosophila)"			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.1250T>C	chr7.hg19:g.23207527T>C	ENSP00000343273:p.Leu417Pro	127.0	0.0		158.0	32.0	NM_001031710	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Missense_Mutation	SNP	ENST00000339077.5	hg19	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.380654	0.82792	.	.	ENSG00000122550	ENST00000538858;ENST00000322231;ENST00000339077;ENST00000539124;ENST00000542558;ENST00000409689;ENST00000545443	T;T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31;0.31	5.69	5.69	0.88448	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.62901	0.2466	N	0.16567	0.415	0.80722	D	1	D;D	0.71674	0.998;0.996	D;P	0.81914	0.995;0.766	T	0.68387	-0.5422	10	0.62326	D	0.03	.	15.9494	0.79820	0.0:0.0:0.0:1.0	.	417;395	Q8IXQ5;Q8IXQ5-2	KLHL7_HUMAN;.	P	258;395;417;341;192;369;395	ENSP00000322958:L395P;ENSP00000343273:L417P;ENSP00000441136:L341P;ENSP00000442367:L192P;ENSP00000386263:L369P;ENSP00000442366:L395P	ENSP00000322958:L395P	L	+	2	0	KLHL7	23174052	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.698000	0.84413	2.167000	0.68274	0.482000	0.46254	CTG	.	.		0.463	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846		C	23207527	T	C	23207527	3	2	121	1	0	0	0	0	1	0	0	0	8403	1580	55	2	1347	2	KLHL7	7	23207527	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	21682458	23207527	135931136	46	20339										
NPVF	64111	hgsc.bcm.edu	37	chr7	25267920	25267920	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	agagagatttaaaaaacttaCctcagaatatttgtcataat	5	5	2	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr7:25267920C>T	ENST00000222674.2	-	1	185		c.e1+1			NM_022150.3	NP_071433	Q9HCQ7	NPVF_HUMAN	neuropeptide VF precursor						negative regulation of gonadotropin secretion (GO:0032277)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						AAAAAACTTACCTCAGAATAT	0.294																																					.		Atlas-SNP	.											.	NPVF	36	.	0			c.138+1G>A						.						47	52	50					7																	25267920		2199	4292	6491	SO:0001630	splice_region_variant	64111	exon2			AACTTACCTCAGA	AB040290	CCDS5395.1	7p21-p15	2013-02-28	2006-10-06	2006-10-06	ENSG00000105954	ENSG00000105954		"Endogenous ligands"	13782	protein-coding gene	gene with protein product	"RFamide-related peptide precursor", "FMRFamide-related peptide precursor"		"chromosome 7 open reading frame 9"	C7orf9		11951088, 11173868	Standard	NM_022150		Approved	RFRP	uc003sxo.3	Q9HCQ7	OTTHUMG00000128509	ENST00000222674.2:c.138+1G>A	chr7.hg19:g.25267920C>T		154.0	0.0		245.0	63.0	NM_022150	A4D164|Q7LE27|Q96PI9	Splice_Site	SNP	ENST00000222674.2	hg19	CCDS5395.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.776077	0.49786	.	.	ENSG00000105954	ENST00000222674	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7041	0.85367	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NPVF	25234445	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	3.274000	0.51631	2.612000	0.88384	0.650000	0.86243	.	.	.		0.294	NPVF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250315.1	NM_022150	Intron	T	25267920	C	T	25267920	5	4	121	1	0	0	0	0	0	0	1	0	10614	521	18	3	463	3	NPVF	7	25267920	Splice_Site	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	2060393	25267920	133870743	47	20340										
COBL	23242	hgsc.bcm.edu	37	chr7	51098538	51098538	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cttcatcaagttctgcaaggGttttacggaactctccagca	8	11	4	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr7:51098538G>C	ENST00000265136.7	-	9	1640	c.1475C>G	c.(1474-1476)aCc>aGc	p.T492S	COBL_ENST00000395542.2_Missense_Mutation_p.T574S	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	492					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TTCTGCAAGGGTTTTACGGAA	0.438																																					p.T492S	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C1475G						.						188	176	180					7																	51098538		2203	4300	6503	SO:0001583	missense	23242	exon9			GCAAGGGTTTTAC	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.1475C>G	chr7.hg19:g.51098538G>C	ENSP00000265136:p.Thr492Ser	191.0	0.0		201.0	54.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	hg19	CCDS34637.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.00|17.00	3.275753|3.275753	0.59649|0.59649	.|.	.|.	ENSG00000106078|ENSG00000106078	ENST00000452534|ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542	.|T;T;T;T	.|0.22539	.|1.95;1.95;1.95;1.95	5.38|5.38	3.54|3.54	0.40534|0.40534	.|.	.|0.501238	.|0.17011	.|N	.|0.190496	T|T	0.28797|0.28797	0.0714|0.0714	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	.|P;P;D;D;D	.|0.69078	.|0.773;0.773;0.966;0.997;0.986	.|B;B;P;P;P	.|0.61800	.|0.189;0.189;0.77;0.894;0.73	T|T	0.06391|0.06391	-1.0829|-1.0829	5|10	.|0.39692	.|T	.|0.17	.|.	9.7435|9.7435	0.40433|0.40433	0.0782:0.1418:0.78:0.0|0.0782:0.1418:0.78:0.0	.|.	.|492;549;492;574;34	.|O75128-3;O75128-7;O75128;O75128-2;O75128-6	.|.;.;COBL_HUMAN;.;.	K|S	467|492;384;377;574	.|ENSP00000265136:T492S;ENSP00000401204:T384S;ENSP00000413498:T377S;ENSP00000378912:T574S	.|ENSP00000265136:T492S	N|T	-|-	3|2	2|0	COBL|COBL	51066032|51066032	0.671000|0.671000	0.27521|0.27521	0.001000|0.001000	0.08648|0.08648	0.292000|0.292000	0.27327|0.27327	3.204000|3.204000	0.51082|0.51082	0.610000|0.610000	0.30035|0.30035	0.650000|0.650000	0.86243|0.86243	AAC|ACC	.	.		0.438	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		C	51098538	G	C	51098538	3	2	121	1	0	0	0	0	1	0	0	0	3655	1261	44	4	2330	4	COBL	7	51098538	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	25830618	51098538	108040125	48	20341										
AUTS2	26053	hgsc.bcm.edu	37	chr7	70228060	70228060	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gcagacggagccccaactccGagctccttctccggaccctg	10	18	1	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr7:70228060G>A	ENST00000342771.4	+	7	1268	c.947G>A	c.(946-948)cGa>cAa	p.R316Q	AUTS2_ENST00000406775.2_Missense_Mutation_p.R316Q	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	316										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CCCCAACTCCGAGCTCCTTCT	0.627																																					p.R316Q		Atlas-SNP	.											.	AUTS2	173	.	0			c.G947A						.						52	57	55					7																	70228060		2203	4300	6503	SO:0001583	missense	26053	exon7			AACTCCGAGCTCC	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.947G>A	chr7.hg19:g.70228060G>A	ENSP00000344087:p.Arg316Gln	66.0	0.0		67.0	11.0	NM_001127231	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	hg19	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	G	5.070	0.198558	0.09652	.	.	ENSG00000158321	ENST00000406775;ENST00000342771	T;T	0.31247	1.5;1.5	5.58	-8.92	0.00774	.	1.342300	0.04746	N	0.423738	T	0.10208	0.0250	N	0.03608	-0.345	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21415	-1.0246	9	.	.	.	1.0014	6.6852	0.23142	0.5927:0.2215:0.104:0.0818	.	316;316	Q8WXX7-2;Q8WXX7	.;AUTS2_HUMAN	Q	316	ENSP00000385263:R316Q;ENSP00000344087:R316Q	.	R	+	2	0	AUTS2	69865996	0.000000	0.05858	0.000000	0.03702	0.321000	0.28281	-0.381000	0.07417	-1.197000	0.02673	-0.259000	0.10710	CGA	.	.		0.627	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			A	70228060	G	A	70228060	3	1	121	1	0	0	0	0	1	0	0	0	1225	1058	37	1	1118	1	AUTS2	7	70228060	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	19129522	70228060	88910603	49	20342										
ADAM22	53616	hgsc.bcm.edu	37	chr7	87780308	87780308	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tttcctagtgtgcccctaatAttcataaaatggatggatat	7	7	1	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr7:87780308A>T	ENST00000265727.7	+	19	1658	c.1579A>T	c.(1579-1581)Att>Ttt	p.I527F	ADAM22_ENST00000398209.3_Missense_Mutation_p.I527F|ADAM22_ENST00000398204.4_Missense_Mutation_p.I527F|ADAM22_ENST00000315984.7_Missense_Mutation_p.I527F|ADAM22_ENST00000398201.4_Missense_Mutation_p.I527F			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	527	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			TGCCCCTAATATTCATAAAAT	0.333																																					p.I527F		Atlas-SNP	.											.	ADAM22	280	.	0			c.A1579T						.						199	184	189					7																	87780308		1837	4082	5919	SO:0001583	missense	53616	exon19			CCTAATATTCATA	AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277		"ADAM metallopeptidase domain containing"	201	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2"	603709	"a disintegrin and metalloproteinase domain 22"			9693107, 10524237	Standard	NM_021723		Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.1579A>T	chr7.hg19:g.87780308A>T	ENSP00000265727:p.Ile527Phe	314.0	0.0		220.0	83.0	NM_021722	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Missense_Mutation	SNP	ENST00000265727.7	hg19	CCDS47637.1	.	.	.	.	.	.	.	.	.	.	A	15.11	2.735625	0.49045	.	.	ENSG00000008277	ENST00000398204;ENST00000398201;ENST00000265727;ENST00000315984;ENST00000398209;ENST00000398203	T;T;T;T;T;T	0.11385	2.78;2.78;2.78;2.78;2.78;2.78	4.95	-0.117	0.13551	Blood coagulation inhibitor, Disintegrin (5);	0.203493	0.43416	D	0.000568	T	0.07413	0.0187	N	0.20530	0.585	0.45464	D	0.998438	P;B;P;B	0.39920	0.695;0.417;0.472;0.444	B;B;B;B	0.43754	0.43;0.1;0.162;0.19	T	0.30504	-0.9976	10	0.87932	D	0	.	4.9137	0.13835	0.4843:0.2809:0.2348:0.0	.	579;527;527;527	E9PBH5;Q9P0K1-5;Q9P0K1;Q9P0K1-2	.;.;ADA22_HUMAN;.	F	527;527;527;527;527;494	ENSP00000381262:I527F;ENSP00000381260:I527F;ENSP00000265727:I527F;ENSP00000315900:I527F;ENSP00000381267:I527F;ENSP00000381261:I494F	ENSP00000265727:I527F	I	+	1	0	ADAM22	87618244	1.000000	0.71417	0.979000	0.43373	0.996000	0.88848	1.892000	0.39748	0.018000	0.15052	0.533000	0.62120	ATT	.	.		0.333	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723		T	87780308	A	T	87780308	3	4	121	1	0	0	0	0	1	0	0	0	244	449	16	4	1653	4	ADAM22	7	87780308	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	17552248	87780308	71358355	50	20343										
TAS2R38	5726	hgsc.bcm.edu	37	chr7	141672569	141672569	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cagagcagaatggtcatcacAgctctcctcaacttggcatt	8	12	4	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr7:141672569A>T	ENST00000547270.1	-	1	1004	c.921T>A	c.(919-921)gcT>gcA	p.A307A		NM_176817.4	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	307					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			NS(2)|breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)|stomach(1)	21	Melanoma(164;0.0171)					TGGTCATCACAGCTCTCCTCA	0.532																																					p.A307A		Atlas-SNP	.											.	TAS2R38	51	.	0			c.T921A						.						76	65	69					7																	141672569		2203	4300	6503	SO:0001819	synonymous_variant	5726	exon1			CATCACAGCTCTC	AF494231	CCDS34765.1	7q34	2012-10-03	2003-05-29	2003-05-30	ENSG00000257138	ENSG00000257138		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	9584	protein-coding gene	gene with protein product		607751	"phenylthiocarbamide tasting"	PTC		12624758, 12584440	Standard	NM_176817		Approved	T2R61	uc003vwx.1	P59533	OTTHUMG00000158374	ENST00000547270.1:c.921T>A	chr7.hg19:g.141672569A>T		98.0	0.0		67.0	23.0	NM_176817	A4D1U6|P59552|Q2M3E8|Q645W3|Q86UK3	Silent	SNP	ENST00000547270.1	hg19	CCDS34765.1																																																																																			.	.		0.532	TAS2R38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350810.2	NM_176817		T	141672569	A	T	141672569	2	4	121	1	0	0	0	0	0	0	0	1	15590	175	7	4		4	TAS2R38	7	141672569	Silent	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	53892261	141672569	17466094	51	20344										
MLL3	58508	hgsc.bcm.edu	37	chr7	151970850	151970850	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gaagatgtgactgaaatcctGaaaggtgccggctcctgcag	13	9	0	4			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr7:151970850G>T	ENST00000262189.6	-	7	1170	c.952C>A	c.(952-954)Cag>Aag	p.Q318K	KMT2C_ENST00000355193.2_Missense_Mutation_p.Q318K	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	318					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CTGAAATCCTGAAAGGTGCCG	0.423																																					p.Q318K		Atlas-SNP	.											.	MLL3	1564	.	0			c.C952A						.						261	244	249					7																	151970850		2203	4300	6503	SO:0001583	missense	58508	exon7			AATCCTGAAAGGT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.952C>A	chr7.hg19:g.151970850G>T	ENSP00000262189:p.Gln318Lys	484.0	0.0		334.0	20.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.995227	0.74703	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.70749	-0.51;-0.51	4.87	4.87	0.63330	Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);	0.164580	0.28442	N	0.015327	T	0.77294	0.4109	M	0.86502	2.82	0.80722	D	1	P	0.39576	0.679	P	0.45794	0.493	T	0.76735	-0.2850	10	0.02654	T	1	.	18.3751	0.90433	0.0:0.0:1.0:0.0	.	318	Q8NEZ4	MLL3_HUMAN	K	318	ENSP00000262189:Q318K;ENSP00000347325:Q318K	ENSP00000262189:Q318K	Q	-	1	0	MLL3	151601783	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.781000	0.99029	2.423000	0.82170	0.650000	0.86243	CAG	.	.		0.423	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151970850	G	T	151970850	3	4	121	1	0	0	0	0	1	0	0	0	9631	1299	45	3	13995	3	MLL3	7	151970850	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	10298281	151970850	7167813	52	20345										
ZHX2	22882	hgsc.bcm.edu	37	chr8	123963936	123963936	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	aaagaaaacgaagtgatagaGgtgaaatctatgggggaaag	14	2	1	4			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr8:123963936G>A	ENST00000314393.4	+	3	1021	c.186G>A	c.(184-186)gaG>gaA	p.E62E		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	62					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			AAGTGATAGAGGTGAAATCTA	0.498																																					p.E62E	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G186A						.						70	65	67					8																	123963936		2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			GATAGAGGTGAAA	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.186G>A	chr8.hg19:g.123963936G>A		62.0	0.0		82.0	16.0	NM_014943		Silent	SNP	ENST00000314393.4	hg19	CCDS6336.1																																																																																			.	.		0.498	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		A	123963936	G	A	123963936	2	1	121	1	0	0	0	0	0	0	0	1	17691	991	35	3		3	ZHX2	8	123963936	Silent	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10		123963936	22400086	53	20346										
FAM122A	116224	hgsc.bcm.edu	37	chr9	71395649	71395649	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cacccggagaagccagagccCcatcaattgcattagaccaa	8	14	1	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr9:71395649C>A	ENST00000394264.3	+	1	686	c.569C>A	c.(568-570)cCc>cAc	p.P190H	PIP5K1B_ENST00000265382.3_Intron|PIP5K1B_ENST00000541509.1_Intron	NM_138333.3	NP_612206.3	Q96E09	F122A_HUMAN	family with sequence similarity 122A	190										endometrium(1)|lung(2)	3						AGCCAGAGCCCCATCAATTGC	0.458																																					p.P190H		Atlas-SNP	.											.	FAM122A	14	.	0			c.C569A						.						81	80	81					9																	71395649		2203	4300	6503	SO:0001583	missense	116224	exon1			AGAGCCCCATCAA	AK126379	CCDS6623.1	9q21.13	2011-02-10	2006-07-11	2006-07-11	ENSG00000187866	ENSG00000187866			23490	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 42"	C9orf42		12477932	Standard	NM_138333		Approved	MGC17347	uc004agw.1	Q96E09	OTTHUMG00000019971	ENST00000394264.3:c.569C>A	chr9.hg19:g.71395649C>A	ENSP00000377807:p.Pro190His	155.0	0.0		118.0	49.0	NM_138333		Missense_Mutation	SNP	ENST00000394264.3	hg19	CCDS6623.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.145539	0.57044	.	.	ENSG00000187866	ENST00000394264;ENST00000377279	T	0.66995	-0.24	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.83128	0.5187	M	0.88105	2.93	0.43662	D	0.996088	D	0.89917	1.0	D	0.87578	0.998	D	0.85637	0.1274	10	0.87932	D	0	-5.7978	12.8382	0.57786	0.0:1.0:0.0:0.0	.	190	Q96E09	F122A_HUMAN	H	190;174	ENSP00000377807:P190H	ENSP00000366492:P174H	P	+	2	0	FAM122A	70585469	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.382000	0.66213	2.758000	0.94735	0.563000	0.77884	CCC	.	.		0.458	FAM122A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052556.1	NM_138333		A	71395649	C	A	71395649	3	1	121	1	0	0	0	0	1	0	0	0	5424	623	22	3	571	3	FAM122A	9	71395649	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10		71395649	69817782	54	20347										
ZFP37	7539	hgsc.bcm.edu	37	chr9	115805121	115805121	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tttttctccagtgtgggatcGctgatgtataacaagctgtg	11	7	1	1	rs373174435		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr9:115805121G>A	ENST00000374227.3	-	4	1804	c.1777C>T	c.(1777-1779)Cga>Tga	p.R593*	ZFP37_ENST00000553380.1_Nonsense_Mutation_p.R608*|ZFP37_ENST00000555206.1_Nonsense_Mutation_p.R594*	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	593					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						GTGTGGGATCGCTGATGTATA	0.373																																					p.R593X		Atlas-SNP	.											.	ZFP37	93	.	0			c.C1777T						.	G	stop/ARG	0,4406		0,0,2203	188	171	176		1777	3	1	9		176	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	ZFP37	NM_003408.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		593/631	115805121	1,13005	2203	4300	6503	SO:0001587	stop_gained	7539	exon4			GGGATCGCTGATG	AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"Zinc fingers, C2H2-type", "-"	12863	protein-coding gene	gene with protein product		602951	"zinc finger protein homologous to Zfp37 in mouse", "zinc finger protein 37 homolog (mouse)"				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.1777C>T	chr9.hg19:g.115805121G>A	ENSP00000363344:p.Arg593*	126.0	0.0		102.0	39.0	NM_003408	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Nonsense_Mutation	SNP	ENST00000374227.3	hg19	CCDS6787.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.261248	0.80246	0.0	1.16E-4	ENSG00000136866	ENST00000374227;ENST00000555206;ENST00000553380	.	.	.	4.14	3.01	0.34805	.	0.000000	0.44483	D	0.000447	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.1634	9.3304	0.38018	0.0:0.0:0.192:0.808	.	.	.	.	X	593;594;608	.	ENSP00000363344:R593X	R	-	1	2	ZFP37	114844942	0.001000	0.12720	0.994000	0.49952	0.894000	0.52154	-0.032000	0.12266	0.928000	0.37168	-0.262000	0.10625	CGA	.	.		0.373	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		A	115805121	G	A	115805121	4	1	121	1	0	0	0	0	0	1	0	0	17663	1095	38	1	119	1	ZFP37	9	115805121	Nonsense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	44409472	115805121	25408310	55	20348										
TAF3	83860	hgsc.bcm.edu	37	chr10	8006438	8006438	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	caagagccccaagagtcccaAgagccccaaggtcacgactc	9	16	1	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr10:8006438A>G	ENST00000344293.5	+	3	1171	c.965A>G	c.(964-966)aAg>aGg	p.K322R		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	322					maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						aagagtcccaagagccccaag	0.493																																					p.K322R		Atlas-SNP	.											.	TAF3	93	.	0			c.A965G						.						38	39	39					10																	8006438		1870	4094	5964	SO:0001583	missense	83860	exon3			GTCCCAAGAGCCC	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"Zinc fingers, PHD-type"	17303	protein-coding gene	gene with protein product		606576	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.965A>G	chr10.hg19:g.8006438A>G	ENSP00000340271:p.Lys322Arg	47.0	0.0		42.0	18.0	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	hg19	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.267658	0.59540	.	.	ENSG00000165632	ENST00000344293	T	0.28454	1.61	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000001	T	0.31606	0.0802	M	0.71296	2.17	0.51012	D	0.9999	P	0.42409	0.779	B	0.32149	0.141	T	0.23226	-1.0194	10	0.44086	T	0.13	-27.1049	15.7154	0.77663	1.0:0.0:0.0:0.0	.	322	Q5VWG9	TAF3_HUMAN	R	322	ENSP00000340271:K322R	ENSP00000340271:K322R	K	+	2	0	TAF3	8046444	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.730000	0.91510	2.123000	0.65237	0.533000	0.62120	AAG	.	.		0.493	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		G	8006438	A	G	8006438	3	3	121	1	0	0	0	0	1	0	0	0	15540	72	3	2	975	2	TAF3	10	8006438	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10		8006438	127528309	56	20349										
LYZL1	84569	hgsc.bcm.edu	37	chr10	29581509	29581509	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gcccagacggtcctggatgaCggcagcatcgactatggcat	13	12	0	2	rs141824789		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr10:29581509C>T	ENST00000375500.3	+	3	396	c.339C>T	c.(337-339)gaC>gaT	p.D113D		NM_032517.4	NP_115906.3	Q6UWQ5	LYZL1_HUMAN	lysozyme-like 1	67					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			central_nervous_system(1)|cervix(2)|large_intestine(2)|lung(5)|skin(1)	11		Breast(68;0.203)				TCCTGGATGACGGCAGCATCG	0.567													C|||	1	0.000199681	0	0	5008	,	,		18325	0		0.001	False		,,,				2504	0				p.D113D		Atlas-SNP	.											LYZL1,NS,adenocarcinoma,0,1	LYZL1	25	.	0			c.C339T						.	C		1,4405	2.1+/-5.4	0,1,2202	147	114	125		339	-8.8	0	10	dbSNP_134	125	0,8600		0,0,4300	no	coding-synonymous	LYZL1	NM_032517.4		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		113/195	29581509	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	84569	exon3			GGATGACGGCAGC		CCDS31174.1	10p12.1	2004-08-02			ENSG00000120563	ENSG00000120563	3.2.1.1		30502	protein-coding gene	gene with protein product						12477932	Standard	XM_005252627		Approved	MGC33408, LYC2	uc001iul.3	Q6UWQ5	OTTHUMG00000017880	ENST00000375500.3:c.339C>T	chr10.hg19:g.29581509C>T		140.0	0.0		89.0	5.0	NM_032517	Q5T921|Q8WW16	Silent	SNP	ENST00000375500.3	hg19	CCDS31174.1																																																																																			.	C|1.000;T|0.000		0.567	LYZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047381.1	NM_032517		T	29581509	C	T	29581509	2	4	121	1	0	0	0	0	0	0	0	1	9140	535	19	1		1	LYZL1	10	29581509	Silent	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	21575071	29581509	105953238	57	20350										
CCAR1	55749	hgsc.bcm.edu	37	chr10	70508892	70508893	+	Splice_Site	DNP	GC	GC	TT													0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tttttcttttatcttttaaaGctggtttattgcagcctcct							TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr10:70508892_70508893GC>TT	ENST00000265872.6	+	9	945_946	c.826_827GC>TT	c.(826-828)GCt>TTt	p.A276F	CCAR1_ENST00000535016.1_Splice_Site_p.A261F|CCAR1_ENST00000543719.1_Splice_Site_p.A261F	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	276					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						ATCTTTTAAAGCTGGTTTATTG	0.401																																					.|p.A276V		Atlas-SNP	.											.	CCAR1	118	.	0			c.827-1G>T|c.C827T						.																																			SO:0001630	splice_region_variant	55749	exon9			TTTAAAGCTGGTT|TTAAAGCTGGTTT	AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	Exception_encountered	chr10.hg19:g.70508892_70508893delinsTT		34.0	0.0		48.0|49.0	24.0	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Splice_Site|Missense_Mutation	SNP	ENST00000265872.6	hg19	CCDS7282.1																																																																																			.	.		0.401	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237	Missense_Mutation	TT	70508893	GC	TT	70508892	5	4	121	1	0	0	0	0	0	0	1	0	2732	985	34	3	856	3	CCAR1	10	70508892	Splice_Site	DNP	GC	TCGA-DD-A3A7-01A-11D-A22F-10	40927383	70508892	65025855	58	20351										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6579425	6579425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ggcaacctcaggcagtttccCtggccagtacacagaagcag	11	13	1	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:6579425C>T	ENST00000527990.2	+	23	8900	c.8900C>T	c.(8899-8901)cCt>cTt	p.P2967L	DNHD1_ENST00000254579.6_Missense_Mutation_p.P2967L			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2967					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GGCAGTTTCCCTGGCCAGTAC	0.542																																					p.P2967L		Atlas-SNP	.											.	DNHD1	198	.	0			c.C8900T						.						69	59	62					11																	6579425		692	1591	2283	SO:0001583	missense	144132	exon25			GTTTCCCTGGCCA	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.8900C>T	chr11.hg19:g.6579425C>T	ENSP00000436180:p.Pro2967Leu	61.0	0.0		45.0	16.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.925512	0.34002	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210;ENST00000524401	T;T	0.50813	0.73;0.73	5.19	5.19	0.71726	.	.	.	.	.	T	0.53012	0.1770	N	0.14661	0.345	0.49483	D	0.999798	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.60682	-0.7215	9	0.87932	D	0	.	16.0007	0.80290	0.0:1.0:0.0:0.0	.	2967;714	Q96M86;E9PHZ7	DNHD1_HUMAN;.	L	2967;2967;714;32	ENSP00000254579:P2967L;ENSP00000436180:P2967L	ENSP00000254579:P2967L	P	+	2	0	DNHD1	6536001	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.067000	0.57527	2.569000	0.86673	0.650000	0.86243	CCT	.	.		0.542	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		T	6579425	C	T	6579425	3	4	121	1	0	0	0	0	1	0	0	0	4670	681	24	3	8999	3	DNHD1	11	6579425	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10		6579425	128427091	59	20352										
MYOD1	4654	hgsc.bcm.edu	37	chr11	17742472	17742472	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gactacagcggccccccgagCggcgcccggcggcggaactg	16	17	0	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:17742472C>A	ENST00000250003.3	+	2	869	c.654C>A	c.(652-654)agC>agA	p.S218R		NM_002478.4	NP_002469.2	P15172	MYOD1_HUMAN	myogenic differentiation 1	218					cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to oxygen levels (GO:0071453)|cellular response to starvation (GO:0009267)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|myoblast fate determination (GO:0007518)|myotube cell development (GO:0014904)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle fiber adaptation (GO:0043503)|skeletal muscle fiber development (GO:0048741)|skeletal muscle tissue development (GO:0007519)|transcription from RNA polymerase II promoter (GO:0006366)	myofibril (GO:0030016)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|E-box binding (GO:0070888)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	17						gccccccgagcggcgcccggc	0.687																																					p.S218R		Atlas-SNP	.											.	MYOD1	50	.	0			c.C654A						.						12	18	16					11																	17742472		2193	4276	6469	SO:0001583	missense	4654	exon2			CCCGAGCGGCGCC	AF027148	CCDS7826.1	11p15	2013-05-21	2005-09-12			ENSG00000129152		"Basic helix-loop-helix proteins"	7611	protein-coding gene	gene with protein product	"myoblast determination protein 1"	159970	"myogenic factor 3"	MYF3			Standard	NM_002478		Approved	PUM, MYOD, bHLHc1	uc001mni.3	P15172		ENST00000250003.3:c.654C>A	chr11.hg19:g.17742472C>A	ENSP00000250003:p.Ser218Arg	41.0	0.0		40.0	24.0	NM_002478	O75321	Missense_Mutation	SNP	ENST00000250003.3	hg19	CCDS7826.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.475664	0.63737	.	.	ENSG00000129152	ENST00000250003	D	0.97352	-4.35	4.45	0.499	0.16914	.	0.046170	0.85682	D	0.000000	D	0.93628	0.7965	N	0.13003	0.285	0.30094	N	0.808022	D	0.61080	0.989	P	0.56788	0.806	D	0.89911	0.4052	10	0.18710	T	0.47	-29.2492	8.2127	0.31492	0.0:0.5685:0.0:0.4315	.	218	P15172	MYOD1_HUMAN	R	218	ENSP00000250003:S218R	ENSP00000250003:S218R	S	+	3	2	MYOD1	17699048	0.992000	0.36948	0.995000	0.50966	0.975000	0.68041	0.077000	0.14738	-0.067000	0.12976	-0.140000	0.14226	AGC	.	.		0.687	MYOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389387.1	NM_002478		A	17742472	C	A	17742472	3	1	121	1	0	0	0	0	1	0	0	0	10097	767	27	1	660	1	MYOD1	11	17742472	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	11163047	17742472	117264044	60	20353										
IMMP1L	196294	hgsc.bcm.edu	37	chr11	31482231	31482232	+	Frame_Shift_Ins	INS	-	-	A													0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	aagacaatatctgaattttgINSaattgtaggctccattgatg							TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:31482231_31482232insA	ENST00000278200.1	-	4	330_331	c.135_136insT	c.(133-138)attcaafs	p.Q46fs	IMMP1L_ENST00000533642.1_Intron|IMMP1L_ENST00000528161.1_Intron|IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000532287.1_Frame_Shift_Ins_p.Q46fs|IMMP1L_ENST00000526776.1_Intron	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	46					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	serine-type peptidase activity (GO:0008236)			breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					TCTGAATTTTGAATTGTAGGCT	0.277																																					p.Q46fs		Atlas-INDEL	.											.	IMMP1L	16	.	0			c.136_137insT						.																																			SO:0001589	frameshift_variant	196294	exon4			.		CCDS7874.1	11p13	2014-07-30			ENSG00000148950	ENSG00000148950			26317	protein-coding gene	gene with protein product		612323					Standard	NM_144981		Approved	FLJ25059	uc001msy.1	Q96LU5	OTTHUMG00000166226	ENST00000278200.1:c.136dupT	chr11.hg19:g.31482233_31482233dupA	ENSP00000278200:p.Gln46fs	390.0	0.0		286.0	110.0	NM_144981	D3DQZ7|Q96SH9	Frame_Shift_Ins	INS	ENST00000278200.1	hg19	CCDS7874.1																																																																																			.	.		0.277	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981		A	31482232	-	A	31482231	7	5	121	1	0	1	1	0	0	0	0	0	7725	1299	45	0	380	0	IMMP1L	11	31482231	Frame_Shift_Ins	INS	-	TCGA-DD-A3A7-01A-11D-A22F-10	13739759	31482231	103524285	61	20354										
OR5T2	219464	hgsc.bcm.edu	37	chr11	56000436	56000441	+	In_Frame_Del	DEL	AGAGGT	AGAGGT	-													0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	taaatttcccatgagagtgaAgaggtagattgctagaaaca					rs183120088|rs145960242	byFrequency	TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	AGAGGT	AGAGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:56000436_56000441delAGAGGT	ENST00000313264.4	-	1	296_301	c.221_226delACCTCT	c.(220-228)tacctcttc>ttc	p.YL74del		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	74						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					ATGAGAGTGAAGAGGTAGATTGCTAG	0.398																																					p.74_76del		Atlas-Indel,Pindel	.											.	OR5T2	107	.	0			c.222_227del						.																																			SO:0001651	inframe_deletion	219464	exon1			.	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.221_226delACCTCT	chr11.hg19:g.56000436_56000441delAGAGGT	ENSP00000323688:p.Tyr74_Leu75del	123.0	0.0		74.0	19.0	NM_001004746	B9EGX5|Q6IFC8	In_Frame_Del	DEL	ENST00000313264.4	hg19	CCDS31523.1																																																																																			.	.		0.398	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		-	56000441	AGAGGT	-	56000436	7	5	121	1	0	1	0	1	0	0	0	0	11191	72	3	0	852	0	OR5T2	11	56000436	In_Frame_Del	DEL	AGAGGT	TCGA-DD-A3A7-01A-11D-A22F-10	24518205	56000436	79006080	62	20355										
OR5T3	390154	hgsc.bcm.edu	37	chr11	56019970	56019970	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ttcttagtgttttatcattcTtggatgcttgctattctaca	6	7	4	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:56019970T>A	ENST00000303059.3	+	1	295	c.295T>A	c.(295-297)Ttg>Atg	p.L99M		NM_001004747.1	NP_001004747.1	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T, member 3	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(23)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	39	Esophageal squamous(21;0.00448)					TTTATCATTCTTGGATGCTTG	0.383																																					p.L99M		Atlas-SNP	.											.	OR5T3	98	.	0			c.T295A						.						100	100	100					11																	56019970		2201	4296	6497	SO:0001583	missense	390154	exon1			TCATTCTTGGATG	AB065837	CCDS31524.1	11q11	2012-08-09			ENSG00000172489	ENSG00000172489		"GPCR / Class A : Olfactory receptors"	15297	protein-coding gene	gene with protein product							Standard	NM_001004747		Approved	OR5T3Q	uc010rjd.2	Q8NGG3	OTTHUMG00000166852	ENST00000303059.3:c.295T>A	chr11.hg19:g.56019970T>A	ENSP00000305403:p.Leu99Met	284.0	0.0		155.0	61.0	NM_001004747	Q6IFC7	Missense_Mutation	SNP	ENST00000303059.3	hg19	CCDS31524.1	.	.	.	.	.	.	.	.	.	.	t	9.776	1.173895	0.21704	.	.	ENSG00000172489	ENST00000303059	T	0.14391	2.51	4.55	-9.1	0.00714	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31721	U	0.007165	T	0.13286	0.0322	L	0.42008	1.315	0.09310	N	1	P	0.52842	0.956	P	0.60345	0.873	T	0.03728	-1.1009	10	0.66056	D	0.02	.	1.8022	0.03073	0.2488:0.3608:0.1751:0.2153	.	99	Q8NGG3	OR5T3_HUMAN	M	99	ENSP00000305403:L99M	ENSP00000305403:L99M	L	+	1	2	OR5T3	55776546	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-7.641000	0.00032	-1.491000	0.01840	-1.045000	0.02358	TTG	.	.		0.383	OR5T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391599.1	NM_001004747		A	56019970	T	A	56019970	3	1	121	1	0	0	0	0	1	0	0	0	11192	1606	56	4	297	4	OR5T3	11	56019970	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	19534	56019970	78986546	63	20356										
SLC29A2	3177	hgsc.bcm.edu	37	chr11	66135010	66135010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tttattggccaggtagtagcGggcaaacttctgcagaagga	13	7	1	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:66135010G>A	ENST00000357440.2	-	7	886	c.658C>T	c.(658-660)Cgc>Tgc	p.R220C	SLC29A2_ENST00000544554.1_Missense_Mutation_p.R220C|SLC29A2_ENST00000311161.7_Missense_Mutation_p.R220C|SLC29A2_ENST00000546034.1_Missense_Mutation_p.R220C	NM_001532.2	NP_001523.2	Q14542	S29A2_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 2	220					cell proliferation (GO:0008283)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			breast(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10					Didanosine(DB00900)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Zalcitabine(DB00943)|Zidovudine(DB00495)	AGGTAGTAGCGGGCAAACTTC	0.602																																					p.R220C		Atlas-SNP	.											.	SLC29A2	24	.	0			c.C658T						.						124	113	117					11																	66135010		2200	4295	6495	SO:0001583	missense	3177	exon7			AGTAGCGGGCAAA	X86681	CCDS8137.1, CCDS73326.1	11q13	2013-07-17	2013-07-17		ENSG00000174669	ENSG00000174669		"Solute carriers"	11004	protein-coding gene	gene with protein product		602110	"solute carrier family 29 (nucleoside transporters), member 2"	ENT2, HNP36		9192854, 9478986	Standard	NM_001532		Approved	DER12	uc001oht.3	Q14542	OTTHUMG00000169056	ENST00000357440.2:c.658C>T	chr11.hg19:g.66135010G>A	ENSP00000350024:p.Arg220Cys	97.0	0.0		84.0	30.0	NM_001532	B3KPY7|O43530|Q52M84|Q96R00|Q9UPE0	Missense_Mutation	SNP	ENST00000357440.2	hg19	CCDS8137.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.834739	0.71373	.	.	ENSG00000174669	ENST00000311161;ENST00000357440;ENST00000544554;ENST00000546034	T;T;T;T	0.81330	-0.19;-1.48;-1.48;-1.48	4.95	4.95	0.65309	.	0.599930	0.17966	N	0.156010	D	0.87485	0.6189	M	0.82630	2.6	0.51767	D	0.999936	D;D	0.76494	0.999;0.986	P;P	0.57776	0.827;0.625	D	0.88646	0.3179	10	0.87932	D	0	-11.0795	10.935	0.47241	0.0:0.0:0.8127:0.1873	.	220;220	G5E943;Q14542	.;S29A2_HUMAN	C	220	ENSP00000311250:R220C;ENSP00000350024:R220C;ENSP00000439456:R220C;ENSP00000440329:R220C	ENSP00000311250:R220C	R	-	1	0	SLC29A2	65891586	0.971000	0.33674	1.000000	0.80357	0.983000	0.72400	2.182000	0.42556	2.314000	0.78098	0.456000	0.33151	CGC	.	.		0.602	SLC29A2-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402093.1	NM_001532		A	66135010	G	A	66135010	3	1	121	1	0	0	0	0	1	0	0	0	14550	1116	39	1	736	1	SLC29A2	11	66135010	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	10115040	66135010	68871506	64	20357										
PRKRIR	5612	hgsc.bcm.edu	37	chr11	76063257	76063257	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tccccacttctcagttatcaTagtgtgaaatttcacagcca	5	12	3	1	rs148924079		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:76063257T>C	ENST00000260045.3	-	5	1042	c.937A>G	c.(937-939)Atg>Gtg	p.M313V	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	313					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.M313V(1)		cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						TCAGTTATCATAGTGTGAAAT	0.393																																					p.M313V		Atlas-SNP	.											PRKRIR,NS,carcinoma,0,1	PRKRIR	65	.	1	Substitution - Missense(1)	prostate(1)	c.A937G						.	T	VAL/MET	1,4377		0,1,2188	48	51	50		937	5	0.7	11	dbSNP_134	50	1,8559		0,1,4279	no	missense	PRKRIR	NM_004705.2	21	0,2,6467	CC,CT,TT		0.0117,0.0228,0.0155	benign	313/762	76063257	2,12936	2189	4280	6469	SO:0001583	missense	5612	exon5			TTATCATAGTGTG	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"THAP (C2CH-type zinc finger) domain containing"	9440	protein-coding gene	gene with protein product	"THAP domain containing 12"	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.937A>G	chr11.hg19:g.76063257T>C	ENSP00000260045:p.Met313Val	425.0	0.0		347.0	129.0	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	ENST00000260045.3	hg19	CCDS8243.1	.	.	.	.	.	.	.	.	.	.	T	4.484	0.089738	0.08632	2.28E-4	1.17E-4	ENSG00000137492	ENST00000529901;ENST00000260045	T;T	0.17528	2.27;2.27	4.99	4.99	0.66335	Ribonuclease H-like (1);	0.366505	0.33732	N	0.004609	T	0.06690	0.0171	N	0.01874	-0.695	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28106	-1.0054	10	0.31617	T	0.26	.	10.3794	0.44101	0.0:0.0773:0.0:0.9226	.	313	O43422	P52K_HUMAN	V	138;313	ENSP00000436249:M138V;ENSP00000260045:M313V	ENSP00000260045:M313V	M	-	1	0	PRKRIR	75740905	0.747000	0.28283	0.736000	0.30914	0.924000	0.55760	1.077000	0.30741	2.043000	0.60533	0.524000	0.50904	ATG	.	T|1.000;C|0.000		0.393	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705		C	76063257	T	C	76063257	3	2	121	1	0	0	0	0	1	0	0	0	12538	1406	49	2	1352	2	PRKRIR	11	76063257	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	9928247	76063257	58943259	65	20358										
USP35	57558	hgsc.bcm.edu	37	chr11	77920573	77920573	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cgccctctccgcccgaggagCccccggccccaagttcaacc	9	22	2	0	rs202205531		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:77920573C>A	ENST00000529308.1	+	10	1933	c.1672C>A	c.(1672-1674)Ccc>Acc	p.P558T	USP35_ENST00000530535.1_3'UTR|USP35_ENST00000526425.1_Missense_Mutation_p.P289T|USP35_ENST00000441408.2_Missense_Mutation_p.P144T|USP35_ENST00000530267.1_Missense_Mutation_p.P126T	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	558	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			GCCCGAGGAGCCCCCGGCCCC	0.587																																					p.P558T		Atlas-SNP	.											.	USP35	179	.	0			c.C1672A						.						37	42	40					11																	77920573		1946	4120	6066	SO:0001583	missense	57558	exon10			GAGGAGCCCCCGG	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"Ubiquitin-specific peptidases"	20061	protein-coding gene	gene with protein product			"ubiquitin specific protease 35"			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.1672C>A	chr11.hg19:g.77920573C>A	ENSP00000431876:p.Pro558Thr	96.0	0.0		93.0	39.0	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	hg19	CCDS41693.1	.	.	.	.	.	.	.	.	.	.	c	0.901	-0.722173	0.03182	.	.	ENSG00000118369	ENST00000530267;ENST00000529308;ENST00000441408;ENST00000526425	T;T;T;T	0.27402	1.67;1.67;1.67;1.67	4.57	2.59	0.31030	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.298620	0.05240	N	0.511985	T	0.19805	0.0476	N	0.17838	0.53	0.22827	N	0.998683	B;B	0.19445	0.007;0.036	B;B	0.18871	0.014;0.023	T	0.21143	-1.0254	10	0.07325	T	0.83	-12.6195	9.571	0.39427	0.1514:0.5557:0.2929:0.0	.	558;144	Q9P2H5;E7EWV7	UBP35_HUMAN;.	T	126;558;144;289	ENSP00000435468:P126T;ENSP00000431876:P558T;ENSP00000400825:P144T;ENSP00000434942:P289T	ENSP00000400825:P144T	P	+	1	0	USP35	77598221	0.002000	0.14202	0.951000	0.38953	0.059000	0.15707	-0.243000	0.08915	0.475000	0.27415	0.586000	0.80456	CCC	.	C|0.999;T|0.001		0.587	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527		A	77920573	C	A	77920573	3	1	121	1	0	0	0	0	1	0	0	0	17081	739	26	3	1706	3	USP35	11	77920573	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	1857316	77920573	57085943	66	20359										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105789505	105789505	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	aaatgacaagtatgaaggatActgtgtagatttggcatctg	11	4	1	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:105789505A>G	ENST00000530497.1	+	10	1337	c.1337A>G	c.(1336-1338)tAc>tGc	p.Y446C	GRIA4_ENST00000282499.5_Missense_Mutation_p.Y446C|GRIA4_ENST00000525187.1_Missense_Mutation_p.Y446C|GRIA4_ENST00000393127.2_Missense_Mutation_p.Y446C			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	446					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		TATGAAGGATACTGTGTAGAT	0.348																																					p.Y446C		Atlas-SNP	.											.	GRIA4	380	.	0			c.A1337G						.						78	75	76					11																	105789505		2202	4299	6501	SO:0001583	missense	2893	exon11			AAGGATACTGTGT	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1337A>G	chr11.hg19:g.105789505A>G	ENSP00000435775:p.Tyr446Cys	121.0	0.0		81.0	32.0	NM_001077243	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.181026	0.78677	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187	D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11	5.68	5.68	0.88126	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.64402	D	0.000001	D	0.95538	0.8550	H	0.96430	3.82	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.69479	0.964;0.952	D	0.96912	0.9668	10	0.87932	D	0	.	16.2322	0.82352	1.0:0.0:0.0:0.0	.	446;446	P48058;G3V164	GRIA4_HUMAN;.	C	446	ENSP00000282499:Y446C;ENSP00000376835:Y446C;ENSP00000435775:Y446C;ENSP00000432180:Y446C	ENSP00000282499:Y446C	Y	+	2	0	GRIA4	105294715	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.287000	0.95975	2.288000	0.76882	0.528000	0.53228	TAC	.	.		0.348	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			G	105789505	A	G	105789505	3	3	121	1	0	0	0	0	1	0	0	0	6779	391	14	2	1412	2	GRIA4	11	105789505	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	27868932	105789505	29217011	67	20360										
NPAT	4863	hgsc.bcm.edu	37	chr11	108064705	108064714	+	Frame_Shift_Del	DEL	ACTCATTTAA	ACTCATTTAA	-													0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ttttgttttcatagctacatActcatttaaaattgttgtca							TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	ACTCATTTAA	ACTCATTTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:108064705_108064714delACTCATTTAA	ENST00000278612.8	-	3	292_301	c.187_196delTTAAATGAGT	c.(187-198)ttaaatgagtatfs	p.LNEY63fs	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	63	Interaction with MIZF.				positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		ATAGCTACATACTCATTTAAAATTGTTGTC	0.243																																					p.63_66del		Atlas-Indel,Pindel	.											.	NPAT	124	.	0			c.188_197del						.																																			SO:0001589	frameshift_variant	4863	exon3			.	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.187_196delTTAAATGAGT	chr11.hg19:g.108064705_108064714delACTCATTTAA	ENSP00000278612:p.Leu63fs	272.0	0.0		199.0	55.0	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Frame_Shift_Del	DEL	ENST00000278612.8	hg19	CCDS41710.1																																																																																			.	.		0.243	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		-	108064714	ACTCATTTAA	-	108064705	7	5	121	1	0	1	0	1	0	0	0	0	10575	391	14	0	4151	0	NPAT	11	108064705	Frame_Shift_Del	DEL	ACTCATTTAA	TCGA-DD-A3A7-01A-11D-A22F-10	2275200	108064705	26941811	68	20361										
HSPA8	3312	hgsc.bcm.edu	37	chr11	122931847	122931847	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ccaaaaactgtgttggtgggGttcattgcaacttgattctt	10	7	2	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:122931847G>A	ENST00000532636.1	-	2	305	c.186C>T	c.(184-186)aaC>aaT	p.N62N	HSPA8_ENST00000227378.3_Silent_p.N62N|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000534624.1_Silent_p.N62N|SNORD14C_ENST00000365382.1_RNA|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000453788.2_Silent_p.N62N|HSPA8_ENST00000526110.1_Silent_p.N62N|HSPA8_ENST00000534319.1_5'Flank|HSPA8_ENST00000533540.1_Silent_p.N62N|HSPA8_ENST00000526862.1_5'Flank			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	62					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		TGTTGGTGGGGTTCATTGCAA	0.438																																					p.N62N	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.C186T						.						70	61	64					11																	122931847		2202	4299	6501	SO:0001819	synonymous_variant	3312	exon2			GGTGGGGTTCATT	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"Heat shock proteins / HSP70"	5241	protein-coding gene	gene with protein product		600816	"heat shock 70kD protein 8"	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.186C>T	chr11.hg19:g.122931847G>A		62.0	0.0		44.0	6.0	NM_006597	Q9H3R6	Silent	SNP	ENST00000532636.1	hg19	CCDS8440.1																																																																																			.	.		0.438	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			A	122931847	G	A	122931847	2	1	121	1	0	0	0	0	0	0	0	1	7425	1252	44	3		3	HSPA8	11	122931847	Silent	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	14867142	122931847	12074669	69	20362										
GLB1L3	112937	hgsc.bcm.edu	37	chr11	134158769	134158769	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	aataaggataaaacatacatGccgtatctccacaaggtaag	7	8	1	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr11:134158769G>A	ENST00000431683.2	+	7	714	c.714G>A	c.(712-714)atG>atA	p.M238I	GLB1L3_ENST00000389887.5_Missense_Mutation_p.M238I	NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	238					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		AAACATACATGCCGTATCTCC	0.507																																					p.M238I		Atlas-SNP	.											.	GLB1L3	102	.	0			c.G714A						.						69	70	70					11																	134158769		2000	4161	6161	SO:0001583	missense	112937	exon7			ATACATGCCGTAT		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.714G>A	chr11.hg19:g.134158769G>A	ENSP00000396615:p.Met238Ile	38.0	0.0		28.0	11.0	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Missense_Mutation	SNP	ENST00000431683.2	hg19	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.349231	0.61183	.	.	ENSG00000166105	ENST00000389887;ENST00000431683	D;D	0.97994	-4.65;-4.65	5.01	5.01	0.66863	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.	.	.	.	D	0.97864	0.9298	M	0.69358	2.11	0.39725	D	0.971523	P;P	0.49862	0.929;0.786	P;P	0.55222	0.771;0.665	D	0.99013	1.0815	9	0.87932	D	0	.	15.7127	0.77644	0.0:0.0:1.0:0.0	.	238;238	Q8NCI6-4;Q8NCI6	.;GLBL3_HUMAN	I	238	ENSP00000374537:M238I;ENSP00000396615:M238I	ENSP00000374537:M238I	M	+	3	0	GLB1L3	133663979	1.000000	0.71417	0.991000	0.47740	0.038000	0.13279	6.425000	0.73370	2.758000	0.94735	0.655000	0.94253	ATG	.	.		0.507	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416		A	134158769	G	A	134158769	3	1	121	1	0	0	0	0	1	0	0	0	6438	1319	46	3	740	3	GLB1L3	11	134158769	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	11226922	134158769	847747	70	20363										
USP5	8078	hgsc.bcm.edu	37	chr12	6973284	6973284	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	agcgcagcagccgaccccccTcctgaggactgtgtgaccac	11	17	0	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr12:6973284T>G	ENST00000229268.8	+	17	2221	c.2169T>G	c.(2167-2169)ccT>ccG	p.P723P	USP5_ENST00000389231.5_Silent_p.P700P|TPI1_ENST00000229270.4_5'Flank	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	723	UBA 2. {ECO:0000255|PROSITE- ProRule:PRU00212}.|USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						CCGACCCCCCTCCTGAGGACT	0.617																																					p.P723P		Atlas-SNP	.											.	USP5	124	.	0			c.T2169G						.						77	83	81					12																	6973284		2203	4300	6503	SO:0001819	synonymous_variant	8078	exon17			CCCCCCTCCTGAG	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"Ubiquitin-specific peptidases"	12628	protein-coding gene	gene with protein product		601447	"ubiquitin specific protease 5 (isopeptidase T)"			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.2169T>G	chr12.hg19:g.6973284T>G		73.0	0.0		21.0	14.0	NM_001098536	D3DUS7|D3DUS8|Q96J22	Silent	SNP	ENST00000229268.8	hg19	CCDS41743.1																																																																																			.	.		0.617	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1			G	6973284	T	G	6973284	2	3	121	1	0	0	0	0	0	0	0	1	17096	1538	54	5		5	USP5	12	6973284	Silent	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10		6973284	126878611	71	20364										
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14631250	14631251	+	Splice_Site	DNP	GA	GA	TC													0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tatttcacttttaactaacaGaccccaaaaaactaaatcac							TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr12:14631250_14631251GA>TC	ENST00000540793.1	+	11	3096_3097	c.2941_2942GA>TC	c.(2941-2943)GAc>TCc	p.D981S	ATF7IP_ENST00000544627.1_Splice_Site_p.D989S|ATF7IP_ENST00000536444.1_Splice_Site_p.D980S|ATF7IP_ENST00000543189.1_Splice_Site_p.D980S|ATF7IP_ENST00000261168.4_Splice_Site_p.D981S			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	981					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						TTAACTAACAGACCCCAAAAAA	0.396																																					.|p.D981A		Atlas-SNP	.											.	ATF7IP	136	.	0			c.2942-1G>T|c.A2942C						.																																			SO:0001630	splice_region_variant	55729	exon12			CTAACAGACCCCA|TAACAGACCCCAA	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		Exception_encountered	chr12.hg19:g.14631250_14631251delinsTC		100.0|101.0	0.0		39.0	24.0	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Splice_Site|Missense_Mutation	SNP	ENST00000540793.1	hg19	CCDS8663.1																																																																																			.	.		0.396	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	Missense_Mutation	TC	14631251	GA	TC	14631250	5	4	121	1	0	0	0	0	0	0	1	0	1087	956	33	3	2983	3	ATF7IP	12	14631250	Splice_Site	DNP	GA	TCGA-DD-A3A7-01A-11D-A22F-10	7657966	14631250	119220645	72	20365										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40687370	40687370	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gtgaaggctcatttcttgtgAaaaagaaatctaattcaatt	7	5	4	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr12:40687370A>T	ENST00000298910.7	+	21	2771	c.2713A>T	c.(2713-2715)Aaa>Taa	p.K905*	LRRK2_ENST00000343742.2_Nonsense_Mutation_p.K905*	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	905					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				ATTTCTTGTGAAAAAGAAATC	0.328																																					p.K905X		Atlas-SNP	.											.	LRRK2	763	.	0			c.A2713T						.						69	69	69					12																	40687370		2201	4298	6499	SO:0001587	stop_gained	120892	exon21			CTTGTGAAAAAGA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.2713A>T	chr12.hg19:g.40687370A>T	ENSP00000298910:p.Lys905*	118.0	0.0		138.0	101.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Nonsense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	A	41	8.778675	0.98950	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	.	.	.	5.03	5.03	0.67393	.	0.291831	0.37393	N	0.002106	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0591	0.71939	1.0:0.0:0.0:0.0	.	.	.	.	X	905	.	ENSP00000298910:K905X	K	+	1	0	LRRK2	38973637	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.860000	0.69546	2.000000	0.58554	0.528000	0.53228	AAA	.	.		0.328	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40687370	A	T	40687370	4	4	121	1	0	0	0	0	0	1	0	0	9042	247	9	4	2795	4	LRRK2	12	40687370	Nonsense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	26056120	40687370	93164525	73	20366										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41957413	41957413	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tgctgtctaacgatgagtgtAagagaatcgtgctgcttgtt	12	6	1	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr12:41957413A>G	ENST00000402685.2	+	8	1437	c.1429A>G	c.(1429-1431)Aag>Gag	p.K477E	PDZRN4_ENST00000298919.7_Missense_Mutation_p.K217E|PDZRN4_ENST00000539469.2_Missense_Mutation_p.K219E	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	477	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.						ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				CGATGAGTGTAAGAGAATCGT	0.408																																					p.K477E		Atlas-SNP	.											.	PDZRN4	346	.	0			c.A1429G						.						128	118	121					12																	41957413		2203	4300	6503	SO:0001583	missense	29951	exon8			GAGTGTAAGAGAA	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1429A>G	chr12.hg19:g.41957413A>G	ENSP00000384197:p.Lys477Glu	93.0	0.0		98.0	66.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.260997	0.39995	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.30182	1.54;1.54;1.54	5.19	4.03	0.46877	PDZ/DHR/GLGF (3);	0.297133	0.32401	N	0.006156	T	0.17916	0.0430	N	0.17379	0.485	0.36349	D	0.859995	P;B;B	0.44521	0.837;0.061;0.001	B;B;B	0.37387	0.248;0.096;0.015	T	0.13442	-1.0509	10	0.30854	T	0.27	-27.764	12.9161	0.58207	0.8642:0.1357:0.0:0.0	.	477;217;219	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	E	477;219;217	ENSP00000384197:K477E;ENSP00000439990:K219E;ENSP00000298919:K217E	ENSP00000298919:K217E	K	+	1	0	PDZRN4	40243680	1.000000	0.71417	0.633000	0.29310	0.966000	0.64601	3.411000	0.52672	1.042000	0.40150	0.533000	0.62120	AAG	.	.		0.408	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		G	41957413	A	G	41957413	3	3	121	1	0	0	0	0	1	0	0	0	11719	363	13	2	1532	2	PDZRN4	12	41957413	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	1270043	41957413	91894482	74	20367										
MLL2	8085	hgsc.bcm.edu	37	chr12	49416062	49416062	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tccttcctcgtcatctctcaCctggcagggccgccggtcaa	9	17	4	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr12:49416062C>A	ENST00000301067.7	-	52	16412		c.e52+1			NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D						chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TCATCTCTCACCTGGCAGGGC	0.488																																					.		Atlas-SNP	.											.	MLL2	1173	.	0			c.16412+1G>T						.						61	63	63					12																	49416062		2090	4227	6317	SO:0001630	splice_region_variant	8085	exon53			CTCTCACCTGGCA	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.16412+1G>T	chr12.hg19:g.49416062C>A		66.0	0.0		87.0	18.0	NM_003482	O14687	Splice_Site	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.764962	0.90020	.	.	ENSG00000167548	ENST00000301067;ENST00000526209	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7533	0.88441	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MLL2	47702329	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.706000	0.84615	2.565000	0.86533	0.650000	0.86243	.	.	.		0.488	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		Intron	A	49416062	C	A	49416062	5	1	121	1	0	0	0	0	0	0	1	0	9630	521	18	3	212	3	MLL2	12	49416062	Splice_Site	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	7458649	49416062	84435833	75	20368										
RPH3A	22895	hgsc.bcm.edu	37	chr12	113304627	113304627	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tctgtgtggctctgcaaaatCtgcattgagcagagggaggt	14	7	3	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr12:113304627C>G	ENST00000389385.4	+	7	923	c.426C>G	c.(424-426)atC>atG	p.I142M	RPH3A_ENST00000415485.3_Missense_Mutation_p.I142M|RPH3A_ENST00000551052.1_Missense_Mutation_p.I138M|RPH3A_ENST00000420983.2_Missense_Mutation_p.I142M|RPH3A_ENST00000543106.2_Missense_Mutation_p.I142M|RPH3A_ENST00000447659.2_Missense_Mutation_p.I93M|RPH3A_ENST00000548866.1_Missense_Mutation_p.I93M	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	142	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		TCTGCAAAATCTGCATTGAGC	0.532																																					p.I142M		Atlas-SNP	.											.	RPH3A	98	.	0			c.C426G						.						123	95	105					12																	113304627		2203	4300	6503	SO:0001583	missense	22895	exon7			CAAAATCTGCATT	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.426C>G	chr12.hg19:g.113304627C>G	ENSP00000374036:p.Ile142Met	60.0	0.0		60.0	12.0	NM_001143854	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	hg19	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.165785	0.57476	.	.	ENSG00000089169	ENST00000543106;ENST00000551593;ENST00000547728;ENST00000389385;ENST00000447659;ENST00000550901;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983	T;T;T;T;T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	4.69	3.78	0.43462	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.64402	D	0.000011	D	0.83737	0.5319	M	0.72353	2.195	0.53005	D	0.999967	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.87578	0.996;0.995;0.995;0.998	D	0.83907	0.0293	10	0.87932	D	0	.	5.1009	0.14759	0.1889:0.6524:0.0:0.1587	.	93;142;142;138	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	M	142;142;142;142;93;75;138;142;93;142	ENSP00000440384:I142M;ENSP00000446780:I142M;ENSP00000449613:I142M;ENSP00000374036:I142M;ENSP00000413254:I93M;ENSP00000448100:I75M;ENSP00000448297:I138M;ENSP00000405357:I142M;ENSP00000450347:I93M;ENSP00000408889:I142M	ENSP00000374036:I142M	I	+	3	3	RPH3A	111789010	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.500000	0.45381	2.315000	0.78130	0.563000	0.77884	ATC	.	.		0.532	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		G	113304627	C	G	113304627	3	3	121	1	0	0	0	0	1	0	0	0	13566	903	32	4	444	4	RPH3A	12	113304627	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	63888565	113304627	20547268	76	20369										
STARD13	90627	hgsc.bcm.edu	37	chr13	33681023	33681023	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gcttcctcatgctccacggaGagggacaccagggtacacat	11	13	1	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr13:33681023G>C	ENST00000336934.5	-	13	3212	c.3096C>G	c.(3094-3096)ctC>ctG	p.L1032L	STARD13_ENST00000399365.3_Silent_p.L914L|STARD13_ENST00000255486.4_Silent_p.L1024L	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	1032	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GCTCCACGGAGAGGGACACCA	0.532																																					p.L1032L		Atlas-SNP	.											.	STARD13	100	.	0			c.C3096G						.						122	117	119					13																	33681023		2203	4300	6503	SO:0001819	synonymous_variant	90627	exon13			CACGGAGAGGGAC	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19164	protein-coding gene	gene with protein product		609866	"START domain containing 13", "long intergenic non-protein coding RNA 464"	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.3096C>G	chr13.hg19:g.33681023G>C		99.0	0.0		60.0	15.0	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	hg19	CCDS9348.1																																																																																			.	.		0.532	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		C	33681023	G	C	33681023	2	2	121	1	0	0	0	0	0	0	0	1	15271	929	33	4		4	STARD13	13	33681023	Silent	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10		33681023	81488855	77	20370										
WDFY2	115825	hgsc.bcm.edu	37	chr13	52301872	52301872	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	actcaggccaagtaacaatcCtcaaactggagcaagaaaac	7	11	2	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr13:52301872C>A	ENST00000298125.5	+	6	724	c.544C>A	c.(544-546)Ctc>Atc	p.L182I		NM_052950.3	NP_443182.1	Q96P53	WDFY2_HUMAN	WD repeat and FYVE domain containing 2	182							metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	16		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)		AGTAACAATCCTCAAACTGGA	0.413																																					p.L182I		Atlas-SNP	.											.	WDFY2	36	.	0			c.C544A						.						140	124	129					13																	52301872		2203	4300	6503	SO:0001583	missense	115825	exon6			ACAATCCTCAAAC	AF411978	CCDS9429.1	13q14.12	2013-01-09	2003-03-13		ENSG00000139668	ENSG00000139668		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20482	protein-coding gene	gene with protein product		610418	"WD40 and FYVE domain containing 2"				Standard	NM_052950		Approved	ZFYVE22	uc001vfp.3	Q96P53	OTTHUMG00000017407	ENST00000298125.5:c.544C>A	chr13.hg19:g.52301872C>A	ENSP00000298125:p.Leu182Ile	64.0	0.0		62.0	14.0	NM_052950	B1AL86|Q96CS1	Missense_Mutation	SNP	ENST00000298125.5	hg19	CCDS9429.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.918388	0.92249	.	.	ENSG00000139668	ENST00000298125	T	0.65549	-0.16	5.65	5.65	0.86999	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.77011	0.4068	L	0.59912	1.85	0.80722	D	1	D;D	0.63880	0.993;0.993	D;D	0.70016	0.967;0.952	T	0.77781	-0.2459	10	0.66056	D	0.02	-20.9036	18.7245	0.91710	0.0:1.0:0.0:0.0	.	79;182	Q96LK4;Q96P53	.;WDFY2_HUMAN	I	182	ENSP00000298125:L182I	ENSP00000298125:L182I	L	+	1	0	WDFY2	51199873	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	7.440000	0.80464	2.652000	0.90054	0.650000	0.86243	CTC	.	.		0.413	WDFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045985.3	NM_052950		A	52301872	C	A	52301872	3	1	121	1	0	0	0	0	1	0	0	0	17284	681	24	3	566	3	WDFY2	13	52301872	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	18620849	52301872	62868006	78	20371										
ARHGEF7	8874	hgsc.bcm.edu	37	chr13	111927941	111927941	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cagatcctgacggaagccatCcggaactgggagggcgatga	15	10	0	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr13:111927941C>A	ENST00000375741.2	+	13	1648	c.1398C>A	c.(1396-1398)atC>atA	p.I466I	ARHGEF7_ENST00000218789.5_Silent_p.I288I|ARHGEF7_ENST00000483189.1_3'UTR|ARHGEF7_ENST00000544132.1_Silent_p.I122I|ARHGEF7_ENST00000317133.5_Silent_p.I445I|ARHGEF7_ENST00000375736.4_Silent_p.I288I|ARHGEF7_ENST00000478679.1_Silent_p.I210I|ARHGEF7_ENST00000370623.3_Silent_p.I373I|ARHGEF7_ENST00000375737.5_Silent_p.I363I|ARHGEF7_ENST00000375723.1_Silent_p.I288I|ARHGEF7_ENST00000426073.2_Silent_p.I288I|ARHGEF7_ENST00000375739.2_Silent_p.I416I	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	466					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CGGAAGCCATCCGGAACTGGG	0.512																																					p.I466I		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.C1398A						.						181	156	165					13																	111927941		2203	4300	6503	SO:0001819	synonymous_variant	8874	exon13			AGCCATCCGGAAC	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.1398C>A	chr13.hg19:g.111927941C>A		117.0	0.0		118.0	32.0	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Silent	SNP	ENST00000375741.2	hg19	CCDS45068.1																																																																																			.	.		0.512	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511		A	111927941	C	A	111927941	2	1	121	1	0	0	0	0	0	0	0	1	911	845	30	3		3	ARHGEF7	13	111927941	Silent	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	59626069	111927941	3241937	79	20372										
GPHN	10243	hgsc.bcm.edu	37	chr14	67346716	67346716	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gccctggcaatgctgatgggAtcacttaatgttacacctct	9	11	2	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr14:67346716A>T	ENST00000315266.5	+	5	1475	c.354A>T	c.(352-354)ggA>ggT	p.G118G	GPHN_ENST00000543237.1_Silent_p.G131G|GPHN_ENST00000478722.1_Silent_p.G118G|GPHN_ENST00000305960.9_Silent_p.G87G|GPHN_ENST00000459628.1_Silent_p.G100G|GPHN_ENST00000544752.2_3'UTR	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	118	MPT Mo-transferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		TGCTGATGGGATCACTTAATG	0.418			T	MLL	AL																																p.G118G		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.A354T						.						105	98	101					14																	67346716		2203	4300	6503	SO:0001819	synonymous_variant	10243	exon5			GATGGGATCACTT	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.354A>T	chr14.hg19:g.67346716A>T		118.0	0.0		42.0	29.0	NM_001024218	Q9H4E9|Q9P2G2	Silent	SNP	ENST00000315266.5	hg19	CCDS32103.1																																																																																			.	.		0.418	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		T	67346716	A	T	67346716	2	4	121	1	0	0	0	0	0	0	0	1	6618	320	12	4		4	GPHN	14	67346716	Silent	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10		67346716	40002824	80	20373										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51839582	51839582	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ttccaaccagtcataggataCcacactttcaaaagacaatc	4	12	2	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr15:51839582C>T	ENST00000251076.5	-	7	878	c.591G>A	c.(589-591)tgG>tgA	p.W197*	DMXL2_ENST00000449909.3_Nonsense_Mutation_p.W197*|DMXL2_ENST00000560421.1_5'UTR|DMXL2_ENST00000543779.2_Nonsense_Mutation_p.W197*	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	197						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.W197C(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TCATAGGATACCACACTTTCA	0.313																																					p.W197X		Atlas-SNP	.											DMXL2,NS,carcinoma,0,1	DMXL2	262	.	1	Substitution - Missense(1)	kidney(1)	c.G591A						.						77	76	76					15																	51839582		2195	4293	6488	SO:0001587	stop_gained	23312	exon7			AGGATACCACACT	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.591G>A	chr15.hg19:g.51839582C>T	ENSP00000251076:p.Trp197*	72.0	0.0		67.0	14.0	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Nonsense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.467836	0.84533	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.3281	0.94270	0.0:1.0:0.0:0.0	.	.	.	.	X	197	.	ENSP00000251076:W197X	W	-	3	0	DMXL2	49626874	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.398000	0.79919	2.588000	0.87417	0.585000	0.79938	TGG	.	.		0.313	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		T	51839582	C	T	51839582	4	4	121	1	0	0	0	0	0	1	0	0	4597	508	18	3	8670	3	DMXL2	15	51839582	Nonsense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10		51839582	50691810	81	20374										
LACTB	114294	hgsc.bcm.edu	37	chr15	63419842	63419842	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gaaaagtttgaaaattcaatTgaatccctaagattatttaa	5	4	1	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr15:63419842T>G	ENST00000261893.4	+	4	978	c.906T>G	c.(904-906)atT>atG	p.I302M	RPS27L_ENST00000559763.1_Intron|LACTB_ENST00000413507.2_Missense_Mutation_p.I302M	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	302						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						AAAATTCAATTGAATCCCTAA	0.308																																					p.I302M	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											.	LACTB	29	.	0			c.T906G						.						31	37	35					15																	63419842		2187	4278	6465	SO:0001583	missense	114294	exon4			TTCAATTGAATCC	AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"Mitochondrial ribosomal proteins / large subunits"	16468	protein-coding gene	gene with protein product		608440	"mitochondrial ribosomal protein L56"	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.906T>G	chr15.hg19:g.63419842T>G	ENSP00000261893:p.Ile302Met	131.0	0.0		101.0	42.0	NM_171846	P83096	Missense_Mutation	SNP	ENST00000261893.4	hg19	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	T	11.82	1.753315	0.31046	.	.	ENSG00000103642	ENST00000261893;ENST00000413507	T;T	0.42131	0.98;0.98	6.08	1.21	0.21127	Beta-lactamase/transpeptidase-like (2);Beta-lactamase-related (1);	0.046900	0.85682	D	0.000000	T	0.34571	0.0902	L	0.54323	1.7	0.80722	D	1	B	0.22800	0.075	B	0.30251	0.113	T	0.11203	-1.0597	10	0.49607	T	0.09	-12.5011	4.8517	0.13540	0.1275:0.2802:0.0:0.5922	.	302	P83111	LACTB_HUMAN	M	302	ENSP00000261893:I302M;ENSP00000392956:I302M	ENSP00000261893:I302M	I	+	3	3	LACTB	61206895	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	0.856000	0.27818	0.164000	0.19529	-0.353000	0.07706	ATT	.	.		0.308	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857		G	63419842	T	G	63419842	3	3	121	1	0	0	0	0	1	0	0	0	8606	1800	63	5	920	5	LACTB	15	63419842	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	11580260	63419842	39111550	82	20375										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72338583	72338583	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tccatcaaggtttttctctcTcagaaggaagcggtagtcct	9	10	3	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr15:72338583T>G	ENST00000356056.5	-	2	794	c.322A>C	c.(322-324)Aga>Cga	p.R108R	MYO9A_ENST00000444904.1_Silent_p.R108R|MYO9A_ENST00000564571.1_Silent_p.R108R|RNU2-65P_ENST00000410162.1_RNA|MYO9A_ENST00000566885.1_Intron|MYO9A_ENST00000424560.1_Silent_p.R108R|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	108	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTTTTCTCTCTCAGAAGGAAG	0.488																																					p.R108R		Atlas-SNP	.											.	MYO9A	203	.	0			c.A322C						.						92	92	92					15																	72338583		2199	4297	6496	SO:0001819	synonymous_variant	4649	exon2			TCTCTCTCAGAAG	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.322A>C	chr15.hg19:g.72338583T>G		105.0	0.0		101.0	47.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	hg19	CCDS10239.1																																																																																			.	.		0.488	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		G	72338583	T	G	72338583	2	3	121	1	0	0	0	0	0	0	0	1	10093	1559	54	5		5	MYO9A	15	72338583	Silent	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	8918741	72338583	30192809	83	20376										
LMF1	64788	hgsc.bcm.edu	37	chr16	904604	904604	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tcctccaggctgagcggaggGaagtaggctccgatcctctt	13	12	1	1	rs201312320		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr16:904604G>T	ENST00000262301.11	-	11	1650	c.1632C>A	c.(1630-1632)ttC>ttA	p.F544L	LMF1_ENST00000543238.1_Missense_Mutation_p.F307L|LMF1_ENST00000568897.1_Missense_Mutation_p.F327L|LMF1_ENST00000399843.2_Missense_Mutation_p.F544L	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	544					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				TGAGCGGAGGGAAGTAGGCTC	0.652																																					p.F544L		Atlas-SNP	.											.	LMF1	42	.	0			c.C1632A						.						26	32	30					16																	904604		2031	4166	6197	SO:0001583	missense	64788	exon11			CGGAGGGAAGTAG	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"chromosome 16 open reading frame 26", "transmembrane protein 112"	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.1632C>A	chr16.hg19:g.904604G>T	ENSP00000262301:p.Phe544Leu	36.0	0.0		34.0	16.0	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Missense_Mutation	SNP	ENST00000262301.11	hg19	CCDS45373.1	.	.	.	.	.	.	.	.	.	.	G	2.875	-0.233042	0.05983	.	.	ENSG00000103227	ENST00000262301;ENST00000399843;ENST00000540070;ENST00000543238	T;T;T	0.20598	2.06;2.06;2.06	4.4	0.172	0.15031	.	0.000000	0.85682	U	0.000000	T	0.09291	0.0229	N	0.14661	0.345	0.80722	D	1	B	0.15141	0.012	B	0.22880	0.042	T	0.27226	-1.0080	10	0.11485	T	0.65	-4.5933	6.8417	0.23967	0.5242:0.0:0.4758:0.0	.	544	Q96S06	LMF1_HUMAN	L	544;544;327;307	ENSP00000262301:F544L;ENSP00000382737:F544L;ENSP00000437418:F307L	ENSP00000262301:F544L	F	-	3	2	LMF1	844605	1.000000	0.71417	0.966000	0.40874	0.016000	0.09150	1.947000	0.40293	0.024000	0.15214	-0.362000	0.07510	TTC	.	G|0.998;A|0.002		0.652	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773		T	904604	G	T	904604	3	4	121	1	0	0	0	0	1	0	0	0	8854	1165	41	3	75	3	LMF1	16	904604	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10		904604	89450149	84	20377										
PPL	5493	hgsc.bcm.edu	37	chr16	4935181	4935181	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gttctcctcctccaaggcccAtatctttcggagcagctccg	8	16	2	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr16:4935181A>G	ENST00000345988.2	-	22	3564	c.3475T>C	c.(3475-3477)Tgg>Cgg	p.W1159R	PPL_ENST00000590782.2_Missense_Mutation_p.W1157R	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1159					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						TCCAAGGCCCATATCTTTCGG	0.622																																					p.W1159R		Atlas-SNP	.											.	PPL	168	.	0			c.T3475C						.						129	118	122					16																	4935181		2197	4300	6497	SO:0001583	missense	5493	exon22			AGGCCCATATCTT	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3475T>C	chr16.hg19:g.4935181A>G	ENSP00000340510:p.Trp1159Arg	117.0	0.0		68.0	25.0	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	hg19	CCDS10526.1	.	.	.	.	.	.	.	.	.	.	A	0.039	-1.293411	0.01375	.	.	ENSG00000118898	ENST00000345988	T	0.45668	0.89	5.17	2.94	0.34122	.	0.639363	0.15096	N	0.280817	T	0.25531	0.0621	L	0.38531	1.155	0.28266	N	0.924612	B	0.02656	0.0	B	0.04013	0.001	T	0.17899	-1.0354	10	0.15499	T	0.54	.	2.5733	0.04800	0.514:0.0:0.2892:0.1969	.	1159	O60437	PEPL_HUMAN	R	1159	ENSP00000340510:W1159R	ENSP00000340510:W1159R	W	-	1	0	PPL	4875182	0.998000	0.40836	0.962000	0.40283	0.437000	0.31866	1.007000	0.29860	0.823000	0.34589	-0.375000	0.07067	TGG	.	.		0.622	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705		G	4935181	A	G	4935181	3	3	121	1	0	0	0	0	1	0	0	0	12346	217	8	2	1799	2	PPL	16	4935181	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	4030577	4935181	85419572	85	20378										
C16orf89	146556	hgsc.bcm.edu	37	chr16	5108602	5108602	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gagaggccgcagggctcgctGctgtccgtcctgggggaaag	18	11	0	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr16:5108602G>C	ENST00000315997.5	-	4	720	c.519C>G	c.(517-519)agC>agG	p.S173R	C16orf89_ENST00000350219.4_Missense_Mutation_p.S211R|ALG1_ENST00000588623.1_Intron|C16orf89_ENST00000422873.1_Missense_Mutation_p.S211R|C16orf89_ENST00000472572.3_Missense_Mutation_p.S173R|C16orf89_ENST00000474471.3_Missense_Mutation_p.S173R	NM_152459.4	NP_689672.4	Q6UX73	CP089_HUMAN	chromosome 16 open reading frame 89	173						cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	12						AGGGCTCGCTGCTGTCCGTCC	0.612																																					p.S173R		Atlas-SNP	.											.	C16orf89	64	.	0			c.C519G						.						34	43	40					16																	5108602		2104	4234	6338	SO:0001583	missense	146556	exon4			CTCGCTGCTGTCC		CCDS42116.1, CCDS45404.1, CCDS42116.2, CCDS45404.2	16p13.3	2011-12-12			ENSG00000153446	ENSG00000153446			28687	protein-coding gene	gene with protein product						12975309, 20578903	Standard	NM_001098514		Approved	MGC45438	uc010bud.3	Q6UX73	OTTHUMG00000159314	ENST00000315997.5:c.519C>G	chr16.hg19:g.5108602G>C	ENSP00000324672:p.Ser173Arg	20.0	0.0		28.0	9.0	NM_001098514	B4DUM5|Q8N2I3|Q8N4T1	Missense_Mutation	SNP	ENST00000315997.5	hg19	CCDS42116.2	.	.	.	.	.	.	.	.	.	.	G	14.82	2.648958	0.47362	.	.	ENSG00000153446	ENST00000474471;ENST00000472572;ENST00000477550;ENST00000422873;ENST00000350219;ENST00000315997	T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44	5.14	3.17	0.36434	.	0.534254	0.20030	N	0.100730	T	0.35068	0.0919	M	0.63428	1.95	0.09310	N	1	P;P	0.51791	0.944;0.948	B;P	0.52267	0.416;0.694	T	0.11991	-1.0565	10	0.14252	T	0.57	-6.1235	7.1401	0.25552	0.1992:0.0:0.8008:0.0	.	173;211	Q6UX73;G3V0F0	CP089_HUMAN;.	R	173;173;173;211;211;173	ENSP00000417158:S173R;ENSP00000420566:S173R;ENSP00000390402:S211R;ENSP00000283478:S211R;ENSP00000324672:S173R	ENSP00000324672:S173R	S	-	3	2	C16orf89	5048603	0.003000	0.15002	0.030000	0.17652	0.071000	0.16799	0.830000	0.27462	1.164000	0.42652	0.455000	0.32223	AGC	.	.		0.612	C16orf89-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354524.1	NM_152459		C	5108602	G	C	5108602	3	2	121	1	0	0	0	0	1	0	0	0	1844	1310	46	4	844	4	C16orf89	16	5108602	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	173421	5108602	85246151	86	20379										
PALB2	79728	hgsc.bcm.edu	37	chr16	23646316	23646316	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gatgctggggtgcaggctgaTtttctttttcctgtgtatct	12	7	2	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr16:23646316T>C	ENST00000261584.4	-	4	1703	c.1551A>G	c.(1549-1551)aaA>aaG	p.K517K		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	517	DNA-binding (with the preference D loop > dsDNA > ssDNA).				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		TGCAGGCTGATTTTCTTTTTC	0.468			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																													p.K517K		Atlas-SNP	.	yes	Rec		"Fanconi anaemia N, breast cancer susceptibility "	16	16p12.1	79728	partner and localizer of BRCA2		"L, O, E"	.	PALB2	108	.	0			c.A1551G						.						163	155	158					16																	23646316		2197	4300	6497	SO:0001819	synonymous_variant	79728	exon4			GGCTGATTTTCTT		CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"Fanconi anemia, complementation groups"	26144	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group N"	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.1551A>G	chr16.hg19:g.23646316T>C		153.0	0.0		133.0	58.0	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Silent	SNP	ENST00000261584.4	hg19	CCDS32406.1																																																																																			.	.		0.468	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		C	23646316	T	C	23646316	2	2	121	1	0	0	0	0	0	0	0	1	11415	1490	52	2		2	PALB2	16	23646316	Silent	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	18537714	23646316	66708437	87	20380										
JMJD5	79831	hgsc.bcm.edu	37	chr16	27225073	27225073	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ccgtgcatgcagaagtggagGtgggtggtcgctgagggagg	21	6	0	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr16:27225073G>C	ENST00000286096.4	+	3	838		c.e3+1		KDM8_ENST00000568965.1_Intron|CTD-3203P2.1_ENST00000567108.1_RNA|KDM8_ENST00000380948.2_Intron|KDM8_ENST00000441782.2_Splice_Site	NM_024773.2	NP_079049.2	Q8N371	KDM8_HUMAN	lysine (K)-specific demethylase 8						G2/M transition of mitotic cell cycle (GO:0000086)|histone H3-K36 demethylation (GO:0070544)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (H3-K36 specific) (GO:0051864)|metal ion binding (GO:0046872)										AGAAGTGGAGGTGGGTGGTCG	0.592																																					.		Atlas-SNP	.											.	.	.	.	0			c.665+1G>C						.						55	53	54					16																	27225073		2197	4300	6497	SO:0001630	splice_region_variant	79831	exon3			GTGGAGGTGGGTG	AK023860	CCDS10627.1, CCDS45448.1	16p12.1	2012-03-28	2012-03-28	2012-03-28	ENSG00000155666	ENSG00000155666		"Chromatin-modifying enzymes / K-demethylases"	25840	protein-coding gene	gene with protein product		611917	"jumonji domain containing 5"	JMJD5		20457893	Standard	NM_024773		Approved	FLJ13798	uc010vcn.1	Q8N371	OTTHUMG00000131677	ENST00000286096.4:c.665+1G>C	chr16.hg19:g.27225073G>C		59.0	0.0		48.0	17.0	NM_024773	B4DLU9|Q6VAK5|Q9H8B1	Splice_Site	SNP	ENST00000286096.4	hg19	CCDS10627.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.966961	0.74131	.	.	ENSG00000155666	ENST00000286096;ENST00000441782	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4553	0.90718	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	JMJD5	27132574	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.435000	0.90297	2.699000	0.92147	0.609000	0.83330	.	.	.		0.592	KDM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254580.3	NM_024773	Intron	C	27225073	G	C	27225073	5	2	121	1	0	0	0	0	0	0	1	0	7961	1275	44	4	790	4	JMJD5	16	27225073	Splice_Site	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	3578757	27225073	63129680	88	20381										
NLRC5	84166	hgsc.bcm.edu	37	chr16	57054706	57054706	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tcaccaaagacccagaatggCtgaacgccaagatgaagttc	9	11	1	5			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr16:57054706C>A	ENST00000262510.6	+	3	307	c.82C>A	c.(82-84)Ctg>Atg	p.L28M	NLRC5_ENST00000308149.7_Missense_Mutation_p.L28M|NLRC5_ENST00000436936.1_Missense_Mutation_p.L28M|NLRC5_ENST00000539144.1_Missense_Mutation_p.L28M	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	28					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				CCCAGAATGGCTGAACGCCAA	0.567																																					p.L28M		Atlas-SNP	.											.	NLRC5	186	.	0			c.C82A						.						97	87	90					16																	57054706		2198	4300	6498	SO:0001583	missense	84166	exon2			GAATGGCTGAACG	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.82C>A	chr16.hg19:g.57054706C>A	ENSP00000262510:p.Leu28Met	73.0	0.0		55.0	14.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	hg19	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.978607	0.34942	.	.	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000544641;ENST00000539144	T;T;T;T	0.81078	-1.25;-1.29;-1.45;-1.29	4.76	3.79	0.43588	.	.	.	.	.	T	0.72195	0.3430	L	0.43152	1.355	0.24245	N	0.99535	P	0.52061	0.95	B	0.38056	0.264	T	0.63932	-0.6525	9	0.87932	D	0	.	11.7296	0.51728	0.1768:0.8232:0.0:0.0	.	28	Q86WI3	NLRC5_HUMAN	M	28	ENSP00000262510:L28M;ENSP00000308886:L28M;ENSP00000389739:L28M;ENSP00000441727:L28M	ENSP00000262510:L28M	L	+	1	2	NLRC5	55612207	1.000000	0.71417	0.977000	0.42913	0.408000	0.30992	2.004000	0.40854	0.976000	0.38417	0.455000	0.32223	CTG	.	.		0.567	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		A	57054706	C	A	57054706	3	1	121	1	0	0	0	0	1	0	0	0	10479	796	28	3	84	3	NLRC5	16	57054706	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	29829633	57054706	33300047	89	20382										
TPPP3	51673	hgsc.bcm.edu	37	chr16	67424967	67424967	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gggtcaccatggatggcaaaCttgcggaagctctcctccag	12	12	2	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr16:67424967C>T	ENST00000564104.1	-	1	889	c.48G>A	c.(46-48)aaG>aaA	p.K16K	RNU1-123P_ENST00000458950.1_RNA|TPPP3_ENST00000562206.1_Silent_p.K16K|TPPP3_ENST00000393957.2_Silent_p.K16K|TPPP3_ENST00000290942.5_Silent_p.K16K			Q9BW30	TPPP3_HUMAN	tubulin polymerization-promoting protein family member 3	16					microtubule bundle formation (GO:0001578)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	tubulin binding (GO:0015631)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0336)|Epithelial(162;0.0781)		GGATGGCAAACTTGCGGAAGC	0.597																																					p.K16K		Atlas-SNP	.											.	TPPP3	13	.	0			c.G48A						.						124	101	109					16																	67424967		2198	4300	6498	SO:0001819	synonymous_variant	51673	exon3			GGCAAACTTGCGG	BC000691	CCDS10835.1	16q22.1	2008-02-05			ENSG00000159713	ENSG00000159713			24162	protein-coding gene	gene with protein product						15590652, 17105200	Standard	XM_005255979		Approved	CGI-38, p25gamma, p20	uc002etb.3	Q9BW30	OTTHUMG00000137516	ENST00000564104.1:c.48G>A	chr16.hg19:g.67424967C>T		68.0	0.0		57.0	13.0	NM_016140	Q49AH9|Q9Y326|Q9Y6H0	Silent	SNP	ENST00000564104.1	hg19	CCDS10835.1																																																																																			.	.		0.597	TPPP3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421787.2	NM_015964		T	67424967	C	T	67424967	2	4	121	1	0	0	0	0	0	0	0	1	16430	564	20	3		3	TPPP3	16	67424967	Silent	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	10370261	67424967	22929786	90	20383										
GLG1	2734	hgsc.bcm.edu	37	chr16	74487222	74487222	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	caagatcagagaagccatctGctggggccacctagaatgac	11	11	2	4			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr16:74487222G>A	ENST00000422840.2	-	26	3382	c.3383C>T	c.(3382-3384)gCa>gTa	p.A1128V	GLG1_ENST00000205061.5_Missense_Mutation_p.A1128V|GLG1_ENST00000447066.2_Missense_Mutation_p.A1117V	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	1128					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						GAAGCCATCTGCTGGGGCCAC	0.468																																					p.A1128V		Atlas-SNP	.											.	GLG1	106	.	0			c.C3383T						.						85	73	77					16																	74487222		2198	4300	6498	SO:0001583	missense	2734	exon26			CCATCTGCTGGGG		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.3383C>T	chr16.hg19:g.74487222G>A	ENSP00000405984:p.Ala1128Val	108.0	0.0		94.0	39.0	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	hg19	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.437753	0.25900	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.59088	0.2168	L	0.47716	1.5	0.80722	D	1	B;B;P;D	0.55172	0.008;0.296;0.794;0.97	B;B;B;P	0.51833	0.004;0.027;0.31;0.681	T	0.55062	-0.8199	9	0.02654	T	1	-19.2368	19.4724	0.94967	0.0:0.0:1.0:0.0	.	258;1128;1128;1117	Q6ZMF1;Q92896;Q92896-2;B7Z8Y4	.;GSLG1_HUMAN;.;.	V	1128;1117;1128	.	ENSP00000205061:A1128V	A	-	2	0	GLG1	73044723	1.000000	0.71417	0.738000	0.30950	0.426000	0.31534	9.434000	0.97515	2.595000	0.87683	0.514000	0.50259	GCA	.	.		0.468	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		A	74487222	G	A	74487222	3	1	121	1	0	0	0	0	1	0	0	0	6444	1319	46	3	240	3	GLG1	16	74487222	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	7062255	74487222	15867531	91	20384										
YWHAE	7531	hgsc.bcm.edu	37	chr17	1264424	1264424	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gaattaagaatttcgtagtaGaatacggaaaaattgagagc	10	3	0	3	rs148760302		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr17:1264424G>T	ENST00000264335.8	-	4	807	c.540C>A	c.(538-540)ttC>ttA	p.F180L	YWHAE_ENST00000571732.1_Missense_Mutation_p.F158L|YWHAE_ENST00000573026.1_Intron|YWHAE_ENST00000575977.1_Intron	NM_006761.4	NP_006752.1	P62258	1433E_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon	180					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cerebral cortex development (GO:0021987)|G2/M transition of mitotic cell cycle (GO:0000086)|hippo signaling (GO:0035329)|hippocampus development (GO:0021766)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|mitotic cell cycle (GO:0000278)|negative regulation of peptidyl-serine dephosphorylation (GO:1902309)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|substantia nigra development (GO:0021762)|viral process (GO:0016032)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|membrane (GO:0016020)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|ion channel binding (GO:0044325)|MHC class II protein complex binding (GO:0023026)|phosphoprotein binding (GO:0051219)|phosphoserine binding (GO:0050815)|poly(A) RNA binding (GO:0044822)|potassium channel regulator activity (GO:0015459)|protein heterodimerization activity (GO:0046982)			kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(18;0.203)	UCEC - Uterine corpus endometrioid carcinoma (25;0.0887)		TTTCGTAGTAGAATACGGAAA	0.473			T	"FAM22a, FAM22B"	edometrial stromal sarcoma		Miller-Dieker lissencephaly syndrome																														p.F180L		Atlas-SNP	.		Dom	yes		17	17p13.3	7531	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (14-3-3 epsilon)"	yes	M	.	YWHAE	50	.	0			c.C540A						.						93	88	90					17																	1264424		2203	4300	6503	SO:0001583	missense	7531	exon4			GTAGTAGAATACG	U54778	CCDS11001.1	17p13.3	2013-12-03	2013-12-03		ENSG00000108953	ENSG00000108953			12851	protein-coding gene	gene with protein product	"14-3-3 epsilon"	605066	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide"			9371399	Standard	NM_006761		Approved	FLJ45465	uc002fsj.3	P62258	OTTHUMG00000134316	ENST00000264335.8:c.540C>A	chr17.hg19:g.1264424G>T	ENSP00000264335:p.Phe180Leu	104.0	0.0		49.0	35.0	NM_006761	B3KY71|D3DTH5|P29360|P42655|Q4VJB6|Q53XZ5|Q63631|Q7M4R4	Missense_Mutation	SNP	ENST00000264335.8	hg19	CCDS11001.1	.	.	.	.	.	.	.	.	.	.	G	31	5.062852	0.93898	.	.	ENSG00000108953	ENST00000264335;ENST00000414131	T	0.60424	0.19	5.39	4.43	0.53597	14-3-3 domain (4);	0.000000	0.85682	U	0.000000	T	0.79695	0.4490	M	0.92367	3.3	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.84132	0.0412	10	0.87932	D	0	-18.6295	12.2476	0.54578	0.0827:0.0:0.9173:0.0	.	180	P62258	1433E_HUMAN	L	180;158	ENSP00000264335:F180L	ENSP00000264335:F180L	F	-	3	2	YWHAE	1211174	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.713000	0.74686	1.288000	0.44600	0.650000	0.86243	TTC	.	G|1.000;A|0.000		0.473	YWHAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259354.3	NM_006761		T	1264424	G	T	1264424	3	4	121	1	0	0	0	0	1	0	0	0	17517	933	33	3	239	3	YWHAE	17	1264424	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10		1264424	79930786	92	20385										
TP53	7157	hgsc.bcm.edu	37	chr17	7578525	7578525	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gggcaggtcttggccagttgGcaaaacatcttgttgagggc	15	8	2	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr17:7578525G>T	ENST00000269305.4	-	5	594	c.405C>A	c.(403-405)tgC>tgA	p.C135*	TP53_ENST00000455263.2_Nonsense_Mutation_p.C135*|TP53_ENST00000359597.4_Nonsense_Mutation_p.C135*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Nonsense_Mutation_p.C135*|TP53_ENST00000445888.2_Nonsense_Mutation_p.C135*|TP53_ENST00000420246.2_Nonsense_Mutation_p.C135*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	135	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> T (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in sporadic cancers; somatic mutation; decreased E6-mediated binding to E6-AP).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C135W(24)|p.0?(8)|p.C135*(7)|p.C135C(5)|p.C135fs*9(3)|p.N131fs*27(2)|p.Q136fs*13(2)|p.F134_T140>S(1)|p.K132_A138delKMFCQLA(1)|p.S127_Q136del10(1)|p.C135T(1)|p.V73fs*9(1)|p.C135fs*15(1)|p.C135fs*14(1)|p.Y126fs*11(1)|p.C3fs*9(1)|p.C42fs*9(1)|p.C135_A138delCQLA(1)|p.C3W(1)|p.C42W(1)|p.C135_T140delCQLAKT(1)|p.Q136*(1)|p.C135_Q136insXXXXXX(1)|p.C135_Q136insX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGGCCAGTTGGCAAAACATCT	0.567		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.C135X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,0,1	TP53	33396	.	68	Substitution - Missense(27)|Deletion - Frameshift(9)|Substitution - Nonsense(8)|Whole gene deletion(8)|Substitution - coding silent(5)|Deletion - In frame(4)|Insertion - Frameshift(4)|Insertion - In frame(2)|Complex - deletion inframe(1)	urinary_tract(11)|lung(8)|breast(7)|central_nervous_system(6)|oesophagus(6)|ovary(6)|haematopoietic_and_lymphoid_tissue(5)|bone(4)|upper_aerodigestive_tract(3)|large_intestine(3)|stomach(2)|skin(2)|prostate(2)|thyroid(1)|liver(1)|pancreas(1)	c.C405A						.						51	51	51					17																	7578525		2203	4300	6503	SO:0001587	stop_gained	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CAGTTGGCAAAAC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.405C>A	chr17.hg19:g.7578525G>T	ENSP00000269305:p.Cys135*	38.0	0.0		22.0	16.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.678815	0.88542	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	.	.	.	5.48	3.5	0.40072	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.815	10.0222	0.42051	0.1647:0.0:0.8353:0.0	.	.	.	.	X	135;135;135;135;135;135;124;42;3;42;3;135	.	ENSP00000269305:C135X	C	-	3	2	TP53	7519250	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	0.645000	0.24782	0.798000	0.33994	0.655000	0.94253	TGC	.	.		0.567	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578525	G	T	7578525	4	4	121	1	0	0	0	0	0	1	0	0	16396	1195	42	3	893	3	TP53	17	7578525	Nonsense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	6314101	7578525	73616685	93	20386										
GGNBP2	79893	hgsc.bcm.edu	37	chr17	34935776	34935776	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	actgcatcgaatctggcagaAgctacgggcagaagagcaga	13	9	1	4			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr17:34935776A>T	ENST00000304718.4	+	8	1263	c.947A>T	c.(946-948)aAg>aTg	p.K316M		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	316					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		ATCTGGCAGAAGCTACGGGCA	0.438																																					p.K316M		Atlas-SNP	.											.	GGNBP2	72	.	0			c.A947T						.						187	187	187					17																	34935776		2203	4300	6503	SO:0001583	missense	79893	exon8			GGCAGAAGCTACG	AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.947A>T	chr17.hg19:g.34935776A>T	ENSP00000307617:p.Lys316Met	114.0	0.0		197.0	39.0	NM_024835	B2RPK7|Q96T90|Q9GZR8|Q9H767	Missense_Mutation	SNP	ENST00000304718.4	hg19	CCDS11314.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.558246	0.86231	.	.	ENSG00000005955	ENST00000304718	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.76190	0.3953	L	0.56769	1.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.987;0.987;0.98	T	0.78780	-0.2070	9	0.87932	D	0	-18.7483	15.7048	0.77569	1.0:0.0:0.0:0.0	.	316;316;316	A8K3S2;Q9H3C7;Q9H3C7-3	.;GGNB2_HUMAN;.	M	316	.	ENSP00000307617:K316M	K	+	2	0	GGNBP2	32009889	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	8.591000	0.90824	2.113000	0.64589	0.377000	0.23210	AAG	.	.		0.438	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		T	34935776	A	T	34935776	3	4	121	1	0	0	0	0	1	0	0	0	6367	72	3	4	973	4	GGNBP2	17	34935776	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	27357251	34935776	46259434	94	20387										
KRTAP4-2	85291	hgsc.bcm.edu	37	chr17	39334360	39334360	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cagcagctgggacggcagcaGttctctaggccacagccctg	13	14	1	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr17:39334360G>C	ENST00000377726.2	-	1	100	c.57C>G	c.(55-57)aaC>aaG	p.N19K		NM_033062.3	NP_149051	Q9BYR5	KRA42_HUMAN	keratin associated protein 4-2	19	20 X 5 AA repeats OF C-C-[GRQVS]-[SPT]- [VSTQ].					keratin filament (GO:0045095)				kidney(2)|lung(4)|upper_aerodigestive_tract(1)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GACGGCAGCAGTTCTCTAGGC	0.627																																					p.N19K		Atlas-SNP	.											.	KRTAP4-2	93	.	0			c.C57G						.						65	64	64					17																	39334360		2202	4300	6502	SO:0001583	missense	85291	exon1			GCAGCAGTTCTCT	AJ406934	CCDS11384.1	17q21.2	2013-06-25			ENSG00000244537	ENSG00000244537		"Keratin associated proteins"	18900	protein-coding gene	gene with protein product						11279113	Standard	NM_033062		Approved	KAP4.2	uc002hwd.3	Q9BYR5	OTTHUMG00000133437	ENST00000377726.2:c.57C>G	chr17.hg19:g.39334360G>C	ENSP00000366955:p.Asn19Lys	112.0	0.0		144.0	38.0	NM_033062	A0JP64	Missense_Mutation	SNP	ENST00000377726.2	hg19	CCDS11384.1	.	.	.	.	.	.	.	.	.	.	.	11.68	1.709384	0.30322	.	.	ENSG00000244537	ENST00000377726;ENST00000458321	T	0.01295	5.04	4.4	3.42	0.39159	.	5.946940	0.02210	U	0.063068	T	0.01387	0.0045	N	0.08118	0	0.22292	N	0.999225	B	0.11235	0.004	B	0.14578	0.011	T	0.41610	-0.9499	10	0.48119	T	0.1	.	8.6587	0.34079	0.1107:0.0:0.8893:0.0	.	19	Q9BYR5	KRA42_HUMAN	K	19;136	ENSP00000366955:N19K	ENSP00000366955:N19K	N	-	3	2	KRTAP4-2	36587886	0.986000	0.35501	0.951000	0.38953	0.645000	0.38454	1.810000	0.38932	0.952000	0.37798	0.508000	0.49915	AAC	.	.		0.627	KRTAP4-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257305.1			C	39334360	G	C	39334360	3	2	121	1	0	0	0	0	1	0	0	0	8560	1020	36	4	357	4	KRTAP4-2	17	39334360	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	4398584	39334360	41860850	95	20388										
BECN1	8678	hgsc.bcm.edu	37	chr17	40962923	40962923	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cactgcctcctgtgtcttcaAtcttgcctttctccacatcc	4	17	4	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr17:40962923A>G	ENST00000361523.4	-	12	1340	c.1208T>C	c.(1207-1209)aTt>aCt	p.I403T	BECN1_ENST00000590099.1_Missense_Mutation_p.I403T|BECN1_ENST00000438274.3_Silent_p.D279D|CNTD1_ENST00000315066.5_3'UTR	NM_003766.3	NP_003757.1	Q14457	BECN1_HUMAN	beclin 1, autophagy related	403			I -> T.		autophagic vacuole assembly (GO:0000045)|beta-amyloid metabolic process (GO:0050435)|cellular defense response (GO:0006968)|cellular response to aluminum ion (GO:0071275)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokinesis (GO:0000910)|defense response to virus (GO:0051607)|lysosome organization (GO:0007040)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|positive regulation of macroautophagy (GO:0016239)|regulation of catalytic activity (GO:0050790)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to vitamin E (GO:0033197)|viral process (GO:0016032)	dendrite (GO:0030425)|membrane (GO:0016020)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	13		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		TGTGTCTTCAATCTTGCCTTT	0.468																																					p.I403T		Atlas-SNP	.											.	BECN1	23	.	0			c.T1208C						.						75	68	70					17																	40962923		2203	4300	6503	SO:0001583	missense	8678	exon12			TCTTCAATCTTGC	AF077301	CCDS11441.1	17q21	2014-02-12	2008-01-14		ENSG00000126581	ENSG00000126581			1034	protein-coding gene	gene with protein product	"ATG6 autophagy related 6 homolog (S. cerevisiae)"	604378	"beclin 1 (coiled-coil, moesin-like BCL2 interacting protein)"			9765397	Standard	NM_003766		Approved	ATG6, VPS30	uc002ibn.2	Q14457		ENST00000361523.4:c.1208T>C	chr17.hg19:g.40962923A>G	ENSP00000355231:p.Ile403Thr	43.0	0.0		47.0	32.0	NM_003766	B2R6N7|O75595|Q9UNA8	Missense_Mutation	SNP	ENST00000361523.4	hg19	CCDS11441.1	.	.	.	.	.	.	.	.	.	.	A	18.36	3.607506	0.66558	.	.	ENSG00000126581	ENST00000361523;ENST00000543382	T	0.60920	0.15	5.88	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.78904	0.4357	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.82106	-0.0621	10	0.72032	D	0.01	.	11.9132	0.52751	0.9322:0.0:0.0678:0.0	.	403	Q14457	BECN1_HUMAN	T	403;316	ENSP00000355231:I403T	ENSP00000355231:I403T	I	-	2	0	BECN1	38216449	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.300000	0.96151	1.052000	0.40392	0.533000	0.62120	ATT	.	.		0.468	BECN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452405.1	NM_003766		G	40962923	A	G	40962923	3	3	121	1	0	0	0	0	1	0	0	0	1396	101	4	2	148	2	BECN1	17	40962923	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	1628563	40962923	40232287	96	20389										
PTPRM	5797	hgsc.bcm.edu	37	chr18	7906552	7906552	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tcaaggctatctcgctatcgAtgaggtgaaggtgttaggac	13	7	2	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr18:7906552A>C	ENST00000332175.8	+	4	1555	c.518A>C	c.(517-519)gAt>gCt	p.D173A	PTPRM_ENST00000580170.1_Missense_Mutation_p.D173A|PTPRM_ENST00000400060.4_Missense_Mutation_p.D173A|PTPRM_ENST00000400053.4_Missense_Mutation_p.D111A	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	173	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CTCGCTATCGATGAGGTGAAG	0.333																																					p.D173A		Atlas-SNP	.											.	PTPRM	185	.	0			c.A518C						.						178	176	177					18																	7906552		2203	4300	6503	SO:0001583	missense	5797	exon4			CTATCGATGAGGT	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.518A>C	chr18.hg19:g.7906552A>C	ENSP00000331418:p.Asp173Ala	202.0	0.0		170.0	57.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.195315	0.58017	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053	T;T;T	0.09911	2.93;2.93;2.93	5.66	5.66	0.87406	Concanavalin A-like lectin/glucanase (1);MAM domain (4);	0.104180	0.64402	D	0.000003	T	0.41743	0.1172	M	0.91612	3.225	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79784	0.993;0.993	T	0.52373	-0.8584	10	0.87932	D	0	.	14.4722	0.67523	1.0:0.0:0.0:0.0	.	173;173	A7MBN1;P28827	.;PTPRM_HUMAN	A	173;173;111	ENSP00000331418:D173A;ENSP00000382933:D173A;ENSP00000382927:D111A	ENSP00000331418:D173A	D	+	2	0	PTPRM	7896552	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.802000	0.62539	2.167000	0.68274	0.528000	0.53228	GAT	.	.		0.333	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			C	7906552	A	C	7906552	3	2	121	1	0	0	0	0	1	0	0	0	12821	333	12	5	532	5	PTPRM	18	7906552	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10		7906552	70170696	97	20390										
DSEL	92126	hgsc.bcm.edu	37	chr18	65178248	65178248	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tcctaggcgatccatcagagTccagcagatgttttcaatta	8	10	2	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr18:65178248T>A	ENST00000310045.7	-	2	5101	c.3628A>T	c.(3628-3630)Act>Tct	p.T1210S	CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	1200					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				TCCATCAGAGTCCAGCAGATG	0.373																																					p.T1210S		Atlas-SNP	.											.	DSEL	196	.	0			c.A3628T						.						101	97	98					18																	65178248		2203	4300	6503	SO:0001583	missense	92126	exon2			TCAGAGTCCAGCA	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.3628A>T	chr18.hg19:g.65178248T>A	ENSP00000310565:p.Thr1210Ser	140.0	0.0		104.0	36.0	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	hg19	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	T	4.517	0.095997	0.08681	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	D	0.81659	-1.52	5.63	3.21	0.36854	Sulfotransferase domain (1);	0.840505	0.10288	U	0.692741	T	0.60702	0.2289	N	0.16903	0.455	0.24345	N	0.994946	B	0.10296	0.003	B	0.10450	0.005	T	0.48468	-0.9033	10	0.08599	T	0.76	-6.1882	3.6372	0.08153	0.1293:0.0735:0.1563:0.6409	.	1200	Q8IZU8	DSEL_HUMAN	S	1210;1200	ENSP00000310565:T1210S	ENSP00000310565:T1210S	T	-	1	0	DSEL	63329228	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.629000	0.24538	1.002000	0.39104	0.533000	0.62120	ACT	.	.		0.373	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		A	65178248	T	A	65178248	3	1	121	1	0	0	0	0	1	0	0	0	4777	1667	58	4	44	4	DSEL	18	65178248	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	57271696	65178248	12899000	98	20391										
BRD4	23476	hgsc.bcm.edu	37	chr19	15367957	15367957	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ctcctcaggctcgtccggcaTcttggcaaagcgcatttcga	10	14	2	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr19:15367957T>A	ENST00000263377.2	-	8	1590	c.1369A>T	c.(1369-1371)Atg>Ttg	p.M457L	BRD4_ENST00000602230.1_5'UTR|BRD4_ENST00000360016.5_Missense_Mutation_p.M457L|BRD4_ENST00000371835.4_Missense_Mutation_p.M457L	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	457					cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			TCGTCCGGCATCTTGGCAAAG	0.647			T	C15orf55	lethal midline carcinoma of young people																																p.M457L		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.A1369T						.						29	27	28					19																	15367957		2203	4300	6503	SO:0001583	missense	23476	exon8			CCGGCATCTTGGC	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.1369A>T	chr19.hg19:g.15367957T>A	ENSP00000263377:p.Met457Leu	30.0	0.0		25.0	8.0	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	hg19	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.165936	0.78339	.	.	ENSG00000141867	ENST00000263377;ENST00000371835;ENST00000360016	T;T;T	0.15952	2.94;2.38;2.38	5.36	5.36	0.76844	Bromodomain (3);	0.070874	0.64402	D	0.000013	T	0.36744	0.0978	M	0.88906	2.99	0.51233	D	0.999918	B;B;B	0.26081	0.007;0.093;0.141	B;B;B	0.39706	0.005;0.307;0.047	T	0.26155	-1.0111	10	0.44086	T	0.13	-17.2319	14.3739	0.66860	0.0:0.0:0.0:1.0	.	457;457;457	Q4G0X8;O60885-2;O60885	.;.;BRD4_HUMAN	L	457	ENSP00000263377:M457L;ENSP00000360901:M457L;ENSP00000353112:M457L	ENSP00000263377:M457L	M	-	1	0	BRD4	15228957	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	8.040000	0.89188	2.042000	0.60477	0.533000	0.62120	ATG	.	.		0.647	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		A	15367957	T	A	15367957	3	1	121	1	0	0	0	0	1	0	0	0	1506	1435	50	4	2786	4	BRD4	19	15367957	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10		15367957	43761026	99	20392										
LGALS4	3960	hgsc.bcm.edu	37	chr19	39297124	39297124	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gggccggaggggctggcctcCgatgaagttgattgattgaa	17	7	0	4			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr19:39297124C>T	ENST00000307751.4	-	4	928	c.451G>A	c.(451-453)Gga>Aga	p.G151R	LGALS4_ENST00000597803.1_5'UTR	NM_006149.3	NP_006140.1	P56470	LEG4_HUMAN	lectin, galactoside-binding, soluble, 4	151					cell adhesion (GO:0007155)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.G151R(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17	all_cancers(60;1.02e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GGCTGGCCTCCGATGAAGTTG	0.498																																					p.G151R		Atlas-SNP	.											LGALS4,colon,carcinoma,0,2	LGALS4	39	.	1	Substitution - Missense(1)	endometrium(1)	c.G451A						.						74	81	79					19																	39297124		2203	4300	6503	SO:0001583	missense	3960	exon4			GGCCTCCGATGAA		CCDS12521.1	19q13.2	2014-03-19	2008-07-25		ENSG00000171747	ENSG00000171747		"Lectins, galactoside-binding"	6565	protein-coding gene	gene with protein product	"galectin 4"	602518				8063692	Standard	NM_006149		Approved	GAL4	uc002ojg.3	P56470	OTTHUMG00000182608	ENST00000307751.4:c.451G>A	chr19.hg19:g.39297124C>T	ENSP00000302100:p.Gly151Arg	88.0	0.0		76.0	8.0	NM_006149		Missense_Mutation	SNP	ENST00000307751.4	hg19	CCDS12521.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.020850	0.93462	.	.	ENSG00000171747	ENST00000307751	T	0.12569	2.67	5.17	5.17	0.71159	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.056938	0.64402	D	0.000002	T	0.20007	0.0481	N	0.08118	0	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.979	T	0.27905	-1.0060	10	0.59425	D	0.04	-8.8748	16.1626	0.81731	0.0:1.0:0.0:0.0	.	151;151	B4DKK5;P56470	.;LEG4_HUMAN	R	151	ENSP00000302100:G151R	ENSP00000302100:G151R	G	-	1	0	LGALS4	43988964	0.995000	0.38212	0.647000	0.29507	0.541000	0.35023	4.638000	0.61353	2.420000	0.82092	0.462000	0.41574	GGA	.	.		0.498	LGALS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462641.1	NM_006149		T	39297124	C	T	39297124	3	4	121	1	0	0	0	0	1	0	0	0	8754	661	23	1	548	1	LGALS4	19	39297124	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	23929167	39297124	19831859	100	20393										
CEACAM5	1048	hgsc.bcm.edu	37	chr19	42224926	42224926	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cctctcctgccactcggcctCtaacccatccccgcagtatt	5	20	2	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr19:42224926C>T	ENST00000221992.6	+	8	1970	c.1856C>T	c.(1855-1857)tCt>tTt	p.S619F	CEACAM5_ENST00000398599.4_Missense_Mutation_p.S618F|CEACAM5_ENST00000405816.1_Missense_Mutation_p.S619F|CEA_ENST00000598976.1_Intron	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	619	Ig-like 7.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CACTCGGCCTCTAACCCATCC	0.532																																					p.S619F		Atlas-SNP	.											.	CEACAM5	84	.	0			c.C1856T						.						166	149	155					19																	42224926		2203	4300	6503	SO:0001583	missense	1048	exon8			CGGCCTCTAACCC	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1856C>T	chr19.hg19:g.42224926C>T	ENSP00000221992:p.Ser619Phe	189.0	0.0		161.0	71.0	NM_004363	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	hg19	CCDS12584.1	.	.	.	.	.	.	.	.	.	.	C	13.69	2.313133	0.40895	.	.	ENSG00000105388	ENST00000221992;ENST00000405816;ENST00000378181	T;T	0.17370	2.28;2.28	2.17	2.17	0.27698	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.49881	0.1583	H	0.95816	3.725	0.09310	N	1	D;D	0.63880	0.988;0.993	P;D	0.91635	0.903;0.999	T	0.32214	-0.9915	9	0.87932	D	0	.	7.8851	0.29646	0.0:1.0:0.0:0.0	.	619;619	P06731;Q53G30	CEAM5_HUMAN;.	F	619;619;337	ENSP00000221992:S619F;ENSP00000385072:S619F	ENSP00000221992:S619F	S	+	2	0	CEACAM5	46916766	0.964000	0.33143	0.126000	0.21872	0.016000	0.09150	2.935000	0.48963	1.507000	0.48752	0.467000	0.42956	TCT	.	.		0.532	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363		T	42224926	C	T	42224926	3	4	121	1	0	0	0	0	1	0	0	0	3197	913	32	3	1886	3	CEACAM5	19	42224926	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	2927802	42224926	16904057	101	20394										
ZNF226	7769	hgsc.bcm.edu	37	chr19	44681511	44681511	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gcacacaggagaaaaaccatAtaaatgtggggagtgtggta	13	5	0	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr19:44681511A>G	ENST00000590089.1	+	7	2463	c.2096A>G	c.(2095-2097)tAt>tGt	p.Y699C	ZNF226_ENST00000454662.2_Missense_Mutation_p.Y699C|ZNF226_ENST00000337433.5_Missense_Mutation_p.Y699C|ZNF226_ENST00000588883.1_3'UTR			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	699					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)						Prostate(69;0.0352)|all_neural(266;0.202)				GAAAAACCATATAAATGTGGG	0.453																																					p.Y699C	Pancreas(115;581 1665 13228 19278 50070)	Atlas-SNP	.											.	.	.	.	0			c.A2096G						.						121	130	127					19																	44681511		2190	4295	6485	SO:0001583	missense	7769	exon6			AACCATATAAATG	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"Zinc fingers, C2H2-type", "-"	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.2096A>G	chr19.hg19:g.44681511A>G	ENSP00000465121:p.Tyr699Cys	114.0	0.0		89.0	44.0	NM_001032372	Q8WWE6|Q96TE6|Q9NS44	Missense_Mutation	SNP	ENST00000590089.1	hg19	CCDS46102.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.071212	0.36566	.	.	ENSG00000167380	ENST00000337433;ENST00000454662	T;T	0.25414	1.8;1.8	3.89	2.77	0.32553	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.44435	0.1293	M	0.67569	2.06	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.11966	-1.0566	9	0.72032	D	0.01	.	6.6146	0.22771	0.6083:0.0:0.0:0.3917	.	699	Q9NYT6	ZN226_HUMAN	C	699	ENSP00000336719:Y699C;ENSP00000393265:Y699C	ENSP00000336719:Y699C	Y	+	2	0	ZNF226	49373351	0.000000	0.05858	0.970000	0.41538	0.956000	0.61745	-0.025000	0.12413	1.775000	0.52247	0.533000	0.62120	TAT	.	.		0.453	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1			G	44681511	A	G	44681511	3	3	121	1	0	0	0	0	1	0	0	0	17795	449	16	2	2164	2	ZNF226	19	44681511	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10	2456585	44681511	14447472	102	20395										
PLCB1	23236	hgsc.bcm.edu	37	chr20	8698371	8698371	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gatttaatgtataaaattttGgtgaaaaataagaagaaatc	7	1	0	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr20:8698371G>T	ENST00000338037.6	+	14	1416	c.1389G>T	c.(1387-1389)ttG>ttT	p.L463F	PLCB1_ENST00000378641.3_Missense_Mutation_p.L463F|PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378637.2_Missense_Mutation_p.L463F	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	463	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						ATAAAATTTTGGTGAAAAATA	0.388																																					p.K463N		Atlas-SNP	.											.	PLCB1	394	.	0			c.A1389T						.						78	84	82					20																	8698371		2203	4300	6503	SO:0001583	missense	23236	exon14			AATTTTGGTGAAA	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.1389G>T	chr20.hg19:g.8698371G>T	ENSP00000338185:p.Leu463Phe	71.0	0.0		47.0	17.0	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	hg19	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165200	0.78339	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.67523	-0.27;-0.27;-0.27	5.85	5.85	0.93711	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.061993	0.64402	D	0.000003	D	0.86293	0.5898	M	0.93939	3.475	0.53005	D	0.999968	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.89170	0.3536	10	0.87932	D	0	.	15.6322	0.76920	0.0:0.1367:0.8633:0.0	.	463;463	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	F	463;463;463;383;383	ENSP00000367908:L463F;ENSP00000338185:L463F;ENSP00000367904:L463F	ENSP00000338185:L463F	L	+	3	2	PLCB1	8646371	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.707000	0.47143	2.768000	0.95171	0.655000	0.94253	TTG	.	.		0.388	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			T	8698371	G	T	8698371	3	4	121	1	0	0	0	0	1	0	0	0	12036	1339	47	3	1443	3	PLCB1	20	8698371	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10		8698371	54327149	103	20396										
RBM39	9584	hgsc.bcm.edu	37	chr20	34312495	34312495	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	accaacaaaaaaattacctgTgatgcctgtactatgattgg	7	8	0	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr20:34312495T>C	ENST00000253363.6	-	8	707	c.684A>G	c.(682-684)tcA>tcG	p.S228S	RBM39_ENST00000361162.6_Silent_p.S228S|RBM39_ENST00000528062.3_Silent_p.S206S|RBM39_ENST00000407261.4_Silent_p.S71S			Q14498	RBM39_HUMAN	RNA binding motif protein 39	228	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					AAATTACCTGTGATGCCTGTA	0.428																																					p.S228S		Atlas-SNP	.											.	RBM39	68	.	0			c.A684G						.						102	94	97					20																	34312495		2203	4300	6503	SO:0001819	synonymous_variant	9584	exon8			TACCTGTGATGCC	L10910	CCDS13265.1, CCDS13266.1, CCDS56186.1	20q11.22	2014-07-03	2006-07-11	2006-07-11	ENSG00000131051	ENSG00000131051		"RNA binding motif (RRM) containing"	15923	protein-coding gene	gene with protein product	"coactivator of activating protein-1 and estrogen receptors", "functional spliceosome-associated protein 59"	604739	"RNA-binding region (RNP1, RRM) containing 2"	RNPC2		8227358, 15694343, 21551269	Standard	NM_184234		Approved	CC1.3, HCC1, CAPER, fSAP59, CAPERalpha	uc002xeb.3	Q14498	OTTHUMG00000032358	ENST00000253363.6:c.684A>G	chr20.hg19:g.34312495T>C		94.0	0.0		119.0	71.0	NM_184234	A2RRD3|A5D8W2|B0BLV3|E1P5S0|E1P5S1|Q14499	Silent	SNP	ENST00000253363.6	hg19	CCDS13266.1	.	.	.	.	.	.	.	.	.	.	T	10.18	1.279322	0.23307	.	.	ENSG00000131051	ENST00000448303	.	.	.	5.36	1.41	0.22369	.	.	.	.	.	T	0.56140	0.1965	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48958	-0.8988	4	.	.	.	.	8.6434	0.33991	0.1205:0.0:0.3746:0.5049	.	.	.	.	A	101	.	.	T	-	1	0	RBM39	33775909	0.998000	0.40836	1.000000	0.80357	0.991000	0.79684	0.424000	0.21330	0.377000	0.24735	0.456000	0.33151	ACA	.	.		0.428	RBM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078931.2	NM_184237		C	34312495	T	C	34312495	2	2	121	1	0	0	0	0	0	0	0	1	13148	1683	59	2		2	RBM39	20	34312495	Silent	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	25614124	34312495	28713025	104	20397										
GTSF1L	149699	hgsc.bcm.edu	37	chr20	42355239	42355239	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tttttggctttcttggggttCtttctcctgcacgatgccag	10	10	3	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr20:42355239C>G	ENST00000373003.1	-	1	399	c.96G>C	c.(94-96)aaG>aaC	p.K32N	GTSF1L_ENST00000373005.2_Missense_Mutation_p.K32N	NM_001008901.1|NM_176791.3	NP_001008901.1|NP_789761.1	Q9H1H1	GTSFL_HUMAN	gametocyte specific factor 1-like	32							metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TCTTGGGGTTCTTTCTCCTGC	0.498																																					p.K32N		Atlas-SNP	.											.	GTSF1L	14	.	0			c.G96C						.						136	127	130					20																	42355239		2203	4300	6503	SO:0001583	missense	149699	exon1			GGGGTTCTTTCTC	AK058060	CCDS13323.1, CCDS33471.1	20q13.12	2007-11-27	2007-11-27	2007-11-27	ENSG00000124196	ENSG00000124196			16198	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 65", "family with sequence similarity 112, member A"	C20orf65, FAM112A			Standard	NM_176791		Approved	dJ1028D15.4	uc002xld.3	Q9H1H1	OTTHUMG00000032510	ENST00000373003.1:c.96G>C	chr20.hg19:g.42355239C>G	ENSP00000362094:p.Lys32Asn	105.0	0.0		145.0	37.0	NM_001008901	Q5JWH5	Missense_Mutation	SNP	ENST00000373003.1	hg19	CCDS13323.1	.	.	.	.	.	.	.	.	.	.	C	7.988	0.752565	0.15778	.	.	ENSG00000124196	ENST00000373003;ENST00000373005	T;T	0.42900	0.96;0.96	3.68	1.75	0.24633	.	0.095669	0.42420	D	0.000717	T	0.35248	0.0925	N	0.16307	0.4	0.32859	D	0.507739	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	T	0.45160	-0.9280	10	0.02654	T	1	-11.6811	5.8651	0.18771	0.0:0.769:0.0:0.231	.	32;32	Q9H1H1;Q5JWH5	GTSFL_HUMAN;.	N	32	ENSP00000362094:K32N;ENSP00000362096:K32N	ENSP00000362094:K32N	K	-	3	2	GTSF1L	41788653	1.000000	0.71417	0.995000	0.50966	0.957000	0.61999	1.429000	0.34903	0.542000	0.28846	0.430000	0.28490	AAG	.	.		0.498	GTSF1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079313.1	NM_176791		G	42355239	C	G	42355239	3	3	121	1	0	0	0	0	1	0	0	0	6896	912	32	4	354	4	GTSF1L	20	42355239	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	8042744	42355239	20670281	105	20398										
NFATC2	4773	hgsc.bcm.edu	37	chr20	50048694	50048694	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ttggtcactgaccgggggtcCgtttttggcggctctttggc	15	10	2	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr20:50048694C>T	ENST00000396009.3	-	9	2851	c.2632G>A	c.(2632-2634)Gga>Aga	p.G878R	NFATC2_ENST00000609507.1_Missense_Mutation_p.G659R|NFATC2_ENST00000609943.1_Missense_Mutation_p.G858R|NFATC2_ENST00000414705.1_Missense_Mutation_p.G858R|NFATC2_ENST00000371564.3_Missense_Mutation_p.G878R|NFATC2_ENST00000610033.1_Missense_Mutation_p.G659R	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	878					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					ACCGGGGGTCCGTTTTTGGCG	0.572																																					p.G878R		Atlas-SNP	.											.	NFATC2	112	.	0			c.G2632A						.						109	107	107					20																	50048694		2203	4300	6503	SO:0001583	missense	4773	exon9			GGGGTCCGTTTTT	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.2632G>A	chr20.hg19:g.50048694C>T	ENSP00000379330:p.Gly878Arg	169.0	0.0		155.0	11.0	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	hg19	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.482823	0.63962	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	T;T;T	0.14144	2.53;2.54;2.54	5.42	5.42	0.78866	.	0.645829	0.15921	N	0.238110	T	0.32315	0.0825	L	0.44542	1.39	0.35949	D	0.833755	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	P;D;P;P	0.91635	0.852;0.999;0.899;0.863	T	0.09422	-1.0675	10	0.31617	T	0.26	-7.2803	19.2321	0.93843	0.0:1.0:0.0:0.0	.	858;858;878;878	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	R	878;878;858	ENSP00000360619:G878R;ENSP00000379330:G878R;ENSP00000396471:G858R	ENSP00000360619:G878R	G	-	1	0	NFATC2	49482101	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.283000	0.58977	2.533000	0.85409	0.591000	0.81541	GGA	.	.		0.572	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		T	50048694	C	T	50048694	3	4	121	1	0	0	0	0	1	0	0	0	10371	661	23	1	201	1	NFATC2	20	50048694	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	7693455	50048694	12976826	106	20399										
STX16	8675	hgsc.bcm.edu	37	chr20	57251326	57251326	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	attgtgctcattgttgtcctCgttggcgtgaagtctcgata	11	8	2	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr20:57251326C>T	ENST00000371141.4	+	9	1681	c.957C>T	c.(955-957)ctC>ctT	p.L319L	STX16_ENST00000361770.5_Silent_p.L302L|STX16-NPEPL1_ENST00000530122.1_Intron|STX16_ENST00000358029.4_Silent_p.L315L|STX16_ENST00000361830.3_Silent_p.L319L|STX16_ENST00000359617.4_Silent_p.L266L|STX16_ENST00000355957.5_Silent_p.L302L|STX16_ENST00000371132.4_Silent_p.L298L	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	319					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			TTGTTGTCCTCGTTGGCGTGA	0.507																																					p.L319L		Atlas-SNP	.											.	STX16	36	.	0			c.C957T						.						253	225	235					20																	57251326		2203	4300	6503	SO:0001819	synonymous_variant	8675	exon9			TGTCCTCGTTGGC	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.957C>T	chr20.hg19:g.57251326C>T		195.0	0.0		202.0	54.0	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Silent	SNP	ENST00000371141.4	hg19	CCDS13468.1																																																																																			.	.		0.507	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433		T	57251326	C	T	57251326	2	4	121	1	0	0	0	0	0	0	0	1	15354	871	31	1		1	STX16	20	57251326	Silent	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	7202632	57251326	5774194	107	20400										
HRH3	11255	hgsc.bcm.edu	37	chr20	60791849	60791849	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cggcatagcagtggccctcgGggatggagctgcccccggac	16	14	0	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr20:60791849G>C	ENST00000340177.5	-	3	835	c.551C>G	c.(550-552)cCc>cGc	p.P184R	HRH3_ENST00000317393.6_Missense_Mutation_p.P184R	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	184					brain development (GO:0007420)|drinking behavior (GO:0042756)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of serotonin secretion (GO:0014063)|neurotransmitter secretion (GO:0007269)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of norepinephrine secretion (GO:0014061)|response to organic cyclic compound (GO:0014070)	integral component of plasma membrane (GO:0005887)|myelin sheath (GO:0043209)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|histamine receptor activity (GO:0004969)			breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Betahistine(DB06698)|Histamine Phosphate(DB00667)|Mirtazapine(DB00370)	GTGGCCCTCGGGGATGGAGCT	0.602																																					p.P184R		Atlas-SNP	.											.	HRH3	25	.	0			c.C551G						.						67	58	61					20																	60791849		2203	4300	6503	SO:0001583	missense	11255	exon3			CCCTCGGGGATGG	AF140538	CCDS13493.1	20q13.33	2013-09-19			ENSG00000101180	ENSG00000101180		"GPCR / Class A : Histamine receptors"	5184	protein-coding gene	gene with protein product		604525				10347254	Standard	NM_007232		Approved	GPCR97	uc002ycf.2	Q9Y5N1	OTTHUMG00000032899	ENST00000340177.5:c.551C>G	chr20.hg19:g.60791849G>C	ENSP00000342560:p.Pro184Arg	68.0	0.0		65.0	16.0	NM_007232	Q4QRI7|Q9GZX2|Q9H4K8	Missense_Mutation	SNP	ENST00000340177.5	hg19	CCDS13493.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.068747	0.76301	.	.	ENSG00000101180	ENST00000340177;ENST00000317393;ENST00000370797	T;T	0.38722	1.12;1.12	4.53	3.57	0.40892	GPCR, rhodopsin-like superfamily (1);	0.053378	0.85682	D	0.000000	T	0.58004	0.2092	M	0.75085	2.285	0.51233	D	0.99991	D;B;B;B	0.55800	0.973;0.216;0.444;0.444	P;B;B;B	0.59546	0.859;0.345;0.345;0.327	T	0.58808	-0.7571	10	0.38643	T	0.18	-39.9244	12.7758	0.57445	0.0815:0.0:0.9185:0.0	.	184;184;184;184	Q9Y5N1-2;E7EWA7;Q8WXZ9;Q9Y5N1	.;.;.;HRH3_HUMAN	R	184	ENSP00000342560:P184R;ENSP00000321482:P184R	ENSP00000321482:P184R	P	-	2	0	HRH3	60225244	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.492000	0.81482	1.008000	0.39264	0.407000	0.27541	CCC	.	.		0.602	HRH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079994.1	NM_007232		C	60791849	G	C	60791849	3	2	121	1	0	0	0	0	1	0	0	0	7366	1232	43	4	790	4	HRH3	20	60791849	Missense_Mutation	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	3540523	60791849	2233671	108	20401										
BRWD1	54014	hgsc.bcm.edu	37	chr21	40627715	40627715	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cactacgacgcagaccaataTttggaggggactgaatgtct	11	9	1	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr21:40627715T>C	ENST00000333229.2	-	19	2438	c.2111A>G	c.(2110-2112)aAt>aGt	p.N704S	BRWD1_ENST00000380800.3_Missense_Mutation_p.N704S|BRWD1_ENST00000342449.3_Missense_Mutation_p.N704S	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	704					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				CAGACCAATATTTGGAGGGGA	0.433																																					p.N704S	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A2111G						.						101	82	88					21																	40627715		2203	4300	6503	SO:0001583	missense	54014	exon19			CCAATATTTGGAG	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.2111A>G	chr21.hg19:g.40627715T>C	ENSP00000330753:p.Asn704Ser	85.0	0.0		30.0	7.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	hg19	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.700352	0.48307	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.61392	0.11;0.17;0.25	5.7	5.7	0.88788	.	0.065155	0.64402	D	0.000007	T	0.60676	0.2287	L	0.52364	1.645	0.80722	D	1	D;B;P;P	0.57257	0.979;0.046;0.941;0.647	P;B;P;B	0.52881	0.679;0.041;0.712;0.146	T	0.61647	-0.7020	10	0.44086	T	0.13	-15.0161	10.3357	0.43847	0.0:0.0732:0.0:0.9268	.	415;415;704;704	Q5R2U6;Q5R2U8;Q9NSI6-2;Q9NSI6	.;.;.;BRWD1_HUMAN	S	704	ENSP00000330753:N704S;ENSP00000344333:N704S;ENSP00000370178:N704S	ENSP00000330753:N704S	N	-	2	0	BRWD1	39549585	1.000000	0.71417	0.999000	0.59377	0.934000	0.57294	3.822000	0.55708	2.175000	0.68902	0.477000	0.44152	AAT	.	.		0.433	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		C	40627715	T	C	40627715	3	2	121	1	0	0	0	0	1	0	0	0	1527	1493	52	2	5186	2	BRWD1	21	40627715	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10		40627715	7502180	109	20402										
KRTAP10-7	386675	hgsc.bcm.edu	37	chr21	46021639	46021639	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	ccccacctcaacccagaagtCcagctgctgagtgatctcct	7	17	2	3			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr21:46021639C>T	ENST00000380102.2	+	1	1143	c.1118C>T	c.(1117-1119)tCc>tTc	p.S373F	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	373						keratin filament (GO:0045095)				breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						ACCCAGAAGTCCAGCTGCTGA	0.622																																					p.S368F		Atlas-SNP	.											.	KRTAP10-7	41	.	0			c.C1103T						.						29	34	32					21																	46021639		2140	4236	6376	SO:0001583	missense	386675	exon2			AGAAGTCCAGCTG	AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"Keratin associated proteins"	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.1118C>T	chr21.hg19:g.46021639C>T	ENSP00000369445:p.Ser373Phe	70.0	0.0		30.0	12.0	NM_198689	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	hg19		.	.	.	.	.	.	.	.	.	.	c	6.006	0.369505	0.11352	.	.	ENSG00000205441	ENST00000380102	T	0.00840	5.63	3.89	-0.216	0.13153	.	.	.	.	.	T	0.01287	0.0042	M	0.61703	1.905	0.09310	N	1	B	0.14805	0.011	B	0.12837	0.008	T	0.42783	-0.9431	9	0.72032	D	0.01	.	4.2656	0.10761	0.0:0.4324:0.1658:0.4018	.	368	P60409-2	.	F	373	ENSP00000369445:S373F	ENSP00000369445:S373F	S	+	2	0	KRTAP10-7	44846067	0.207000	0.23482	0.001000	0.08648	0.298000	0.27526	0.495000	0.22483	-0.315000	0.08703	-0.373000	0.07131	TCC	.	.		0.622	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689		T	46021639	C	T	46021639	3	4	121	1	0	0	0	0	1	0	0	0	8523	855	30	3	1109	3	KRTAP10-7	21	46021639	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	5393924	46021639	2108256	110	20403										
CABIN1	23523	hgsc.bcm.edu	37	chr22	24564464	24564464	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	tgtgaagttctgccaggtccAtcttggggctgccgcccaga	13	12	2	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr22:24564464A>G	ENST00000398319.2	+	33	6117	c.5732A>G	c.(5731-5733)cAt>cGt	p.H1911R	CABIN1_ENST00000263119.5_Missense_Mutation_p.H1911R|CABIN1_ENST00000337989.7_Missense_Mutation_p.H336R|CABIN1_ENST00000485008.1_3'UTR|CABIN1_ENST00000405822.2_Missense_Mutation_p.H1832R	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1911					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TGCCAGGTCCATCTTGGGGCT	0.597																																					p.H1911R		Atlas-SNP	.											.	CABIN1	153	.	0			c.A5732G						.						56	42	47					22																	24564464		2185	4283	6468	SO:0001583	missense	23523	exon33			AGGTCCATCTTGG	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.5732A>G	chr22.hg19:g.24564464A>G	ENSP00000381364:p.His1911Arg	96.0	0.0		23.0	19.0	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	hg19	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.257453	0.80246	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319;ENST00000337989;ENST00000403176	T;T;T;D	0.86030	0.12;-0.11;0.12;-2.06	5.28	5.28	0.74379	.	0.069207	0.64402	D	0.000005	T	0.75102	0.3804	N	0.24115	0.695	0.49798	D	0.999821	B;P;P	0.38078	0.335;0.617;0.483	B;B;B	0.33960	0.115;0.173;0.084	T	0.75590	-0.3265	10	0.33141	T	0.24	.	14.7596	0.69596	1.0:0.0:0.0:0.0	.	336;1832;1911	B5MEB3;G5E9F3;Q9Y6J0	.;.;CABIN_HUMAN	R	1911;1832;1911;336;336	ENSP00000263119:H1911R;ENSP00000384694:H1832R;ENSP00000381364:H1911R;ENSP00000336991:H336R	ENSP00000263119:H1911R	H	+	2	0	CABIN1	22894464	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	8.304000	0.89958	2.149000	0.67028	0.529000	0.55759	CAT	.	.		0.597	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		G	24564464	A	G	24564464	3	3	121	1	0	0	0	0	1	0	0	0	2530	217	8	2	5858	2	CABIN1	22	24564464	Missense_Mutation	SNP	A	TCGA-DD-A3A7-01A-11D-A22F-10		24564464	26740102	111	20404										
AP1B1	162	hgsc.bcm.edu	37	chr22	29724846	29724846	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gtctcgtaggcctggtacacGtgctgggacacctctggtgc	14	12	2	0	rs147684584		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr22:29724846G>A	ENST00000405198.1	-	22	2845	c.2814C>T	c.(2812-2814)caC>caT	p.H938H	AP1B1_ENST00000432560.2_Silent_p.H928H|AP1B1_ENST00000356015.2_Silent_p.H931H|AP1B1_ENST00000317368.7_Silent_p.H908H|AP1B1_ENST00000472057.1_5'Flank|AP1B1_ENST00000415447.1_Silent_p.H928H|AP1B1_ENST00000402502.1_Silent_p.H928H|AP1B1_ENST00000357586.2_Silent_p.H938H			Q10567	AP1B1_HUMAN	adaptor-related protein complex 1, beta 1 subunit	938					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CCTGGTACACGTGCTGGGACA	0.667													g|||	1	0.000199681	0	0	5008	,	,		14408	0.001		0	False		,,,				2504	0				p.H938H		Atlas-SNP	.											.	AP1B1	72	.	0			c.C2814T						.		,,	1,4405	2.1+/-5.4	0,1,2202	70	56	60		2814,2724,2784	-5.6	0.9	22	dbSNP_134	60	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	AP1B1	NM_001127.3,NM_001166019.1,NM_145730.2	,,	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	,,	938/950,908/920,928/940	29724846	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	162	exon23			GTACACGTGCTGG	L13939	CCDS13855.1, CCDS13856.1, CCDS13856.2, CCDS54515.1	22q12.2	2010-06-18			ENSG00000100280	ENSG00000100280			554	protein-coding gene	gene with protein product		600157		ADTB1, CLAPB2		7987321, 8812422	Standard	NM_145730		Approved	BAM22, AP105A	uc003afj.3	Q10567	OTTHUMG00000151109	ENST00000405198.1:c.2814C>T	chr22.hg19:g.29724846G>A		52.0	0.0		35.0	16.0	NM_001127	C9JRD1|F8WDL0|P78436|Q20WL3|Q86X54	Silent	SNP	ENST00000405198.1	hg19	CCDS13855.1																																																																																			.	G|1.000;A|0.000		0.667	AP1B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321374.1	NM_001127		A	29724846	G	A	29724846	2	1	121	1	0	0	0	0	0	0	0	1	731	1136	40	1		1	AP1B1	22	29724846	Silent	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	5160382	29724846	21579720	112	20405										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46807621	46807621	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	acggccatcttttccccggaCggcccatggggcaggcccag	13	16	1	0	rs577948297		TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chr22:46807621C>T	ENST00000262738.3	-	6	4646	c.4647G>A	c.(4645-4647)ccG>ccA	p.P1549P		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1549	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TTTCCCCGGACGGCCCATGGG	0.587													C|||	1	0.000199681	0	0	5008	,	,		19987	0		0	False		,,,				2504	0.001				p.P1549P		Atlas-SNP	.											.	CELSR1	242	.	0			c.G4647A						.						97	92	93					22																	46807621		2203	4300	6503	SO:0001819	synonymous_variant	9620	exon6			CCCGGACGGCCCA	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.4647G>A	chr22.hg19:g.46807621C>T		57.0	0.0		39.0	13.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	hg19	CCDS14076.1																																																																																			.	.		0.587	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46807621	C	T	46807621	2	4	121	1	0	0	0	0	0	0	0	1	3223	523	19	1		1	CELSR1	22	46807621	Silent	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10	17082775	46807621	4496945	113	20406										
NUDT10	170685	hgsc.bcm.edu	37	chrX	51075989	51075989	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	gcatggagcccgaggaggagCcgggcggtgcggcggtccga	21	11	0	0			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chrX:51075989C>A	ENST00000376006.3	+	2	392	c.172C>A	c.(172-174)Ccg>Acg	p.P58T	NUDT10_ENST00000356450.2_Missense_Mutation_p.P58T	NM_153183.2	NP_694853.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 10	223					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(1)|prostate(3)|upper_aerodigestive_tract(1)	16	Ovarian(276;0.236)					CGAGGAGGAGCCGGGCGGTGC	0.682																																					p.P58T	NSCLC(90;1817 2035 37909 38249)	Atlas-SNP	.											.	NUDT10	28	.	0			c.C172A						.						22	31	28					X																	51075989		2195	4276	6471	SO:0001583	missense	170685	exon2			GAGGAGCCGGGCG	AF469196	CCDS35278.1	Xp11.22-p11.1	2014-05-20			ENSG00000122824	ENSG00000122824		"Nudix motif containing"	17621	protein-coding gene	gene with protein product		300527				12105228	Standard	NM_153183		Approved	DIPP3a, hDIPP3alpha	uc004dph.3	Q8NFP7	OTTHUMG00000021530	ENST00000376006.3:c.172C>A	chrX.hg19:g.51075989C>A	ENSP00000365174:p.Pro58Thr	51.0	0.0		48.0	37.0	NM_153183	Q8NBN1|Q8NCB9|Q8NG25	Missense_Mutation	SNP	ENST00000376006.3	hg19	CCDS35278.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.764907	0.69878	.	.	ENSG00000122824	ENST00000376006;ENST00000356450	T;T	0.51071	0.72;0.72	3.14	2.26	0.28386	NUDIX hydrolase domain (3);NUDIX hydrolase, conserved site (1);NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	T	0.61098	0.2320	M	0.70842	2.15	0.40523	D	0.980859	D	0.89917	1.0	D	0.87578	0.998	T	0.68704	-0.5338	9	0.48119	T	0.1	-13.7387	7.3002	0.26415	0.0:0.8533:0.0:0.1467	.	58	Q8NFP7	NUD10_HUMAN	T	58	ENSP00000365174:P58T;ENSP00000348831:P58T	ENSP00000348831:P58T	P	+	1	0	NUDT10	51092729	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.246000	0.65411	1.602000	0.50124	0.429000	0.28392	CCG	.	.		0.682	NUDT10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056578.1	NM_153183		A	51075989	C	A	51075989	3	1	121	1	0	0	0	0	1	0	0	0	10735	739	26	3	174	3	NUDT10	23	51075989	Missense_Mutation	SNP	C	TCGA-DD-A3A7-01A-11D-A22F-10		51075989	104194571	114	20407										
NXF3	56000	hgsc.bcm.edu	37	chrX	102332620	102332620	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	agggtgaacaaggcactctgGgtcccttggtggctggtatc	15	9	1	1			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chrX:102332620G>C	ENST00000395065.3	-	18	1607	c.1506C>G	c.(1504-1506)acC>acG	p.T502T	NXF3_ENST00000425644.1_Silent_p.T174T	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	502					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)			NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						AGGCACTCTGGGTCCCTTGGT	0.562																																					p.T502T		Atlas-SNP	.											.	NXF3	81	.	0			c.C1506G						.						215	140	166					X																	102332620		2203	4300	6503	SO:0001819	synonymous_variant	56000	exon18			ACTCTGGGTCCCT	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.1506C>G	chrX.hg19:g.102332620G>C		62.0	0.0		38.0	30.0	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Silent	SNP	ENST00000395065.3	hg19	CCDS14503.1																																																																																			.	.		0.562	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		C	102332620	G	C	102332620	2	2	121	1	0	0	0	0	0	0	0	1	10794	1219	43	4		4	NXF3	23	102332620	Silent	SNP	G	TCGA-DD-A3A7-01A-11D-A22F-10	51256631	102332620	52937940	115	20408										
IRAK1	3654	hgsc.bcm.edu	37	chrX	153278076	153278076	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	5	1	0.831496178718401	1.74614197530864	0.465637860082305	1	1	0	cttctgtcgggcagggttgaTgataatctgcggtggctctg	15	8	3	2			TCGA-DD-A3A7-01A-11D-A22F-10	TCGA-DD-A3A7-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29b92b51-7ba3-42a9-97d3-6a9b5e43f928	134e6bf3-534e-4a0e-94e0-37c93f47f72b	g.chrX:153278076T>C	ENST00000369980.3	-	13	2151	c.1984A>G	c.(1984-1986)Atc>Gtc	p.I662V	IRAK1_ENST00000393687.2_Missense_Mutation_p.I632V|IRAK1_ENST00000393682.1_Missense_Mutation_p.I643V|IRAK1_ENST00000369974.2_Missense_Mutation_p.I583V|IRAK1_ENST00000477274.1_Intron|IRAK1_ENST00000429936.2_Missense_Mutation_p.I658V	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	662					activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCAGGGTTGATGATAATCTGC	0.627													T|||	1	0.000264901	8e-04	0	3775	,	,		12908	0		0	False		,,,				2504	0				p.I662V		Atlas-SNP	.											.	IRAK1	107	.	0			c.A1984G						.						118	89	99					X																	153278076		2203	4300	6503	SO:0001583	missense	3654	exon13			GGTTGATGATAAT	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.1984A>G	chrX.hg19:g.153278076T>C	ENSP00000358997:p.Ile662Val	68.0	0.0		59.0	16.0	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Missense_Mutation	SNP	ENST00000369980.3	hg19	CCDS14740.1	.	.	.	.	.	.	.	.	.	.	T	20.0	3.929723	0.73327	.	.	ENSG00000184216	ENST00000369980;ENST00000369974;ENST00000393682;ENST00000393687;ENST00000429936	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	5.96	5.96	0.96718	.	0.114545	0.38959	N	0.001520	T	0.39600	0.1084	L	0.32530	0.975	0.37090	D	0.899404	D;D;D	0.69078	0.994;0.995;0.997	P;D;D	0.80764	0.876;0.984;0.994	T	0.46005	-0.9222	10	0.62326	D	0.03	-19.8813	12.784	0.57493	0.0:0.0:0.0:1.0	.	583;662;632	P51617-4;P51617;P51617-2	.;IRAK1_HUMAN;.	V	662;583;643;632;658	ENSP00000358997:I662V;ENSP00000358991:I583V;ENSP00000377287:I643V;ENSP00000377291:I632V;ENSP00000392662:I658V	ENSP00000358991:I583V	I	-	1	0	IRAK1	152931270	1.000000	0.71417	0.983000	0.44433	0.724000	0.41520	4.861000	0.62969	2.008000	0.58898	0.481000	0.45027	ATC	.	.		0.627	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3			C	153278076	T	C	153278076	3	2	121	1	0	0	0	0	1	0	0	0	7830	1464	51	2	162	2	IRAK1	23	153278076	Missense_Mutation	SNP	T	TCGA-DD-A3A7-01A-11D-A22F-10	50945456	153278076	1992484	116	20409										
KCNAB2	8514	hgsc.bcm.edu	37	chr1	6145274	6145274	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgttttgcagggctgaagtgGtactgggaaacatcattaag	13	5	1	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:6145274G>A	ENST00000164247.1	+	7	856	c.292G>A	c.(292-294)Gta>Ata	p.V98I	KCNAB2_ENST00000378083.3_Missense_Mutation_p.V131I|KCNAB2_ENST00000378092.1_Missense_Mutation_p.V84I|KCNAB2_ENST00000352527.1_Missense_Mutation_p.V84I|KCNAB2_ENST00000602612.1_Missense_Mutation_p.V98I|KCNAB2_ENST00000378111.1_Missense_Mutation_p.V98I|KCNAB2_ENST00000341524.1_Missense_Mutation_p.V98I|KCNAB2_ENST00000378097.1_Missense_Mutation_p.V98I|KCNAB2_ENST00000378087.3_Missense_Mutation_p.V98I|KCNAB2_ENST00000458166.2_Missense_Mutation_p.V31I	NM_001199860.1	NP_001186789.1	Q13303	KCAB2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 2	98					hematopoietic progenitor cell differentiation (GO:0002244)|protein heterooligomerization (GO:0051291)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			large_intestine(1)|lung(4)|skin(3)	8	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)		GGCTGAAGTGGTACTGGGAAA	0.562																																					p.V131I		Atlas-SNP	.											.	KCNAB2	23	.	0			c.G391A						.						204	196	198					1																	6145274		2203	4300	6503	SO:0001583	missense	8514	exon6			GAAGTGGTACTGG	U33429	CCDS55.1, CCDS56.1, CCDS55570.1, CCDS55571.1	1p36.3	2008-02-05			ENSG00000069424	ENSG00000069424		"Potassium channels", "Aldo-keto reductases"	6229	protein-coding gene	gene with protein product		601142				8838324	Standard	NM_003636		Approved	AKR6A5, KCNA2B, HKvbeta2.1, HKvbeta2.2	uc001aly.2	Q13303	OTTHUMG00000000795	ENST00000164247.1:c.292G>A	chr1.hg19:g.6145274G>A	ENSP00000164247:p.Val98Ile	84.0	0.0		141.0	52.0	NM_001199862	A0AVM9|A8K1A4|B0AZR7|O43659|Q5TG82|Q5TG83|Q6ZNE4|Q99411	Missense_Mutation	SNP	ENST00000164247.1	hg19	CCDS55.1	.	.	.	.	.	.	.	.	.	.	G	10.63	1.405294	0.25378	.	.	ENSG00000069424	ENST00000378111;ENST00000378097;ENST00000378092;ENST00000428161;ENST00000389632;ENST00000378087;ENST00000341524;ENST00000352527;ENST00000435937;ENST00000164247;ENST00000378083;ENST00000458166	T;T;T;T;T;T;T;T;T;T;T;T	0.25749	1.78;1.78;1.78;1.78;1.78;1.78;1.78;1.78;1.78;1.78;1.78;1.78	4.93	4.93	0.64822	NADP-dependent oxidoreductase domain (3);	0.000000	0.85682	D	0.000000	T	0.11367	0.0277	N	0.02736	-0.51	0.51767	D	0.99993	B;B;B;B	0.16166	0.001;0.001;0.002;0.016	B;B;B;B	0.15870	0.014;0.002;0.006;0.013	T	0.12502	-1.0545	10	0.06891	T	0.86	-42.1504	17.4755	0.87658	0.0:0.0:1.0:0.0	.	131;84;98;98	Q13303-3;Q13303-2;Q13303;Q2YD85	.;.;KCAB2_HUMAN;.	I	98;98;84;84;98;98;98;84;84;98;131;31	ENSP00000367351:V98I;ENSP00000367337:V98I;ENSP00000367332:V84I;ENSP00000400285:V84I;ENSP00000374283:V98I;ENSP00000367327:V98I;ENSP00000340824:V98I;ENSP00000318772:V84I;ENSP00000389151:V84I;ENSP00000164247:V98I;ENSP00000367323:V131I;ENSP00000396167:V31I	ENSP00000164247:V98I	V	+	1	0	KCNAB2	6067861	1.000000	0.71417	0.972000	0.41901	0.522000	0.34438	3.131000	0.50515	2.416000	0.81992	0.591000	0.81541	GTA	.	.		0.562	KCNAB2-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002114.3	NM_172130		A	6145274	G	A	6145274	3	1	122	1	0	0	0	0	1	0	0	0	8019	1261	44	3	314	3	KCNAB2	1	6145274	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10		6145274	243105347	1	20410										
SPEN	23013	hgsc.bcm.edu	37	chr1	16255449	16255449	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gttgaaagccaagcttgataAtgacactgtcaaatcttctg	8	8	3	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:16255449A>G	ENST00000375759.3	+	11	2918	c.2714A>G	c.(2713-2715)aAt>aGt	p.N905S		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	905					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		AAGCTTGATAATGACACTGTC	0.448																																					p.N905S		Atlas-SNP	.											.	SPEN	374	.	0			c.A2714G						.						150	164	159					1																	16255449		2203	4300	6503	SO:0001583	missense	23013	exon11			TTGATAATGACAC		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.2714A>G	chr1.hg19:g.16255449A>G	ENSP00000364912:p.Asn905Ser	93.0	0.0		101.0	25.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	0.014	-1.572244	0.00887	.	.	ENSG00000065526	ENST00000375759	T	0.51325	0.71	5.38	-1.33	0.09172	.	.	.	.	.	T	0.31482	0.0798	L	0.43152	1.355	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32798	-0.9893	9	0.09084	T	0.74	-9.8138	6.9472	0.24526	0.5567:0.1165:0.3269:0.0	.	905	Q96T58	MINT_HUMAN	S	905	ENSP00000364912:N905S	ENSP00000364912:N905S	N	+	2	0	SPEN	16128036	0.997000	0.39634	0.014000	0.15608	0.014000	0.08584	2.374000	0.44274	-0.391000	0.07763	-0.912000	0.02778	AAT	.	.		0.448	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16255449	A	G	16255449	3	3	122	1	0	0	0	0	1	0	0	0	15053	101	4	2	2756	2	SPEN	1	16255449	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	10110175	16255449	232995172	2	20411										
SDHB	6390	hgsc.bcm.edu	37	chr1	17354296	17354296	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	actgctgcttgccttcctgaGattcatccttcttcttcaaa	5	13	4	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:17354296G>A	ENST00000375499.3	-	5	638	c.488C>T	c.(487-489)tCt>tTt	p.S163F		NM_003000.2	NP_002991.2	P21912	SDHB_HUMAN	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	163			S -> P (in CWS2; uncertain pathological significance; associated with increased manganese superoxide dismutase function and increased levels of reactive oxygen species; associated with a 2.7-fold change in AKT expression and a 1.7-fold increase in MAPK expression; dbSNP:rs33927012). {ECO:0000269|PubMed:18678321}.		aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)|ubiquinone binding (GO:0048039)	p.S163Y(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	10		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0049)|COAD - Colon adenocarcinoma(227;1.18e-05)|BRCA - Breast invasive adenocarcinoma(304;2.41e-05)|Kidney(64;0.000188)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)	Succinic acid(DB00139)	GCCTTCCTGAGATTCATCCTT	0.388			"Mis, N, F"			"paraganglioma, pheochromocytoma"			Familial Paragangliomas;Cowden syndrome;Carney-Stratakis syndrome																												p.S163F		Atlas-SNP	.	yes	Rec		Familial paraganglioma	1	1p36.1-p35	6390	"succinate dehydrogenase complex, subunit B, iron sulfur (Ip)"		O	SDHB,colon,carcinoma,0,1	SDHB	16	.	1	Substitution - Missense(1)	large_intestine(1)	c.C488T						.						160	149	153					1																	17354296		2203	4300	6503	SO:0001583	missense	6390	exon5	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;Carney-Stratakis dyad, Paraganglioma-Gastric Stromal Sarcoma dyad	TCCTGAGATTCAT	U17248	CCDS176.1	1p36.1-p35	2014-09-17			ENSG00000117118	ENSG00000117118	1.3.99.1	"Mitochondrial respiratory chain complex / Complex II"	10681	protein-coding gene	gene with protein product		185470		SDH1, SDH			Standard	NM_003000		Approved		uc001bae.3	P21912	OTTHUMG00000002289	ENST00000375499.3:c.488C>T	chr1.hg19:g.17354296G>A	ENSP00000364649:p.Ser163Phe	108.0	0.0		91.0	35.0	NM_003000	B2R545|Q0QEY7|Q9NQ12	Missense_Mutation	SNP	ENST00000375499.3	hg19	CCDS176.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.796326	0.70567	.	.	ENSG00000117118	ENST00000375499	D	0.96716	-4.1	5.89	5.89	0.94794	Fumarate reductase, C-terminal (1);Alpha-helical ferredoxin (1);	0.052959	0.85682	D	0.000000	D	0.95664	0.8590	M	0.72118	2.19	0.80722	D	1	B	0.26935	0.164	B	0.24269	0.052	D	0.93455	0.6805	10	0.66056	D	0.02	-24.4299	18.8118	0.92061	0.0:0.0:1.0:0.0	.	163	P21912	DHSB_HUMAN	F	163	ENSP00000364649:S163F	ENSP00000364649:S163F	S	-	2	0	SDHB	17226883	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	7.340000	0.79292	2.790000	0.95986	0.655000	0.94253	TCT	.	.		0.388	SDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006603.1	NM_003000		A	17354296	G	A	17354296	3	1	122	1	0	0	0	0	1	0	0	0	13980	942	33	3	370	3	SDHB	1	17354296	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	1098847	17354296	231896325	3	20412										
ARHGEF10L	55160	hgsc.bcm.edu	37	chr1	17942680	17942680	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gcgcaaagtctccttcctgcAcaggaaggacgtcctcggtg	12	13	1	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:17942680A>G	ENST00000361221.3	+	9	977	c.818A>G	c.(817-819)cAc>cGc	p.H273R	ARHGEF10L_ENST00000375408.3_5'Flank|ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.H273R|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.H234R|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000167825.4_5'Flank|ARHGEF10L_ENST00000375420.3_Missense_Mutation_p.H31R|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.H234R	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	273						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		TCCTTCCTGCACAGGAAGGAC	0.627																																					p.H273R		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.A818G						.						93	79	84					1																	17942680		2203	4300	6503	SO:0001583	missense	55160	exon9			TCCTGCACAGGAA	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.818A>G	chr1.hg19:g.17942680A>G	ENSP00000355060:p.His273Arg	98.0	0.0		139.0	51.0	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	hg19	CCDS182.1	.	.	.	.	.	.	.	.	.	.	A	5.613	0.297845	0.10622	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415;ENST00000375420	T;T;T;T;T	0.59224	0.63;0.64;0.44;0.64;0.28	5.19	5.19	0.71726	.	0.204857	0.43110	D	0.000612	T	0.37404	0.1002	N	0.15975	0.35	0.80722	D	1	B;B;B;B;B;B	0.33413	0.0;0.002;0.0;0.002;0.404;0.411	B;B;B;B;B;B	0.36845	0.001;0.007;0.002;0.007;0.234;0.118	T	0.32134	-0.9918	10	0.02654	T	1	-30.851	12.411	0.55468	1.0:0.0:0.0:0.0	.	31;273;39;234;234;273	B4DTE2;Q9HCE6-5;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;ARGAL_HUMAN	R	273;234;273;234;31	ENSP00000355060:H273R;ENSP00000399401:H234R;ENSP00000394621:H273R;ENSP00000364564:H234R;ENSP00000364569:H31R	ENSP00000355060:H273R	H	+	2	0	ARHGEF10L	17815267	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	6.527000	0.73803	1.951000	0.56629	0.460000	0.39030	CAC	.	.		0.627	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		G	17942680	A	G	17942680	3	3	122	1	0	0	0	0	1	0	0	0	895	159	6	2	848	2	ARHGEF10L	1	17942680	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	588384	17942680	231307941	4	20413										
MACF1	23499	hgsc.bcm.edu	37	chr1	39906750	39906750	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttggagcagatttgatttttGcctgtggagaaactgagaag	13	4	0	4			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:39906750G>A	ENST00000372915.3	+	72	18307	c.18220G>A	c.(18220-18222)Gcc>Acc	p.A6074T	MACF1_ENST00000361689.2_Missense_Mutation_p.A4116T|MACF1_ENST00000545844.1_Missense_Mutation_p.A4116T|MACF1_ENST00000564288.1_Missense_Mutation_p.A6175T|MACF1_ENST00000539005.1_Missense_Mutation_p.A3986T|MACF1_ENST00000317713.7_Missense_Mutation_p.A4116T|MACF1_ENST00000289893.4_Missense_Mutation_p.A4618T|MACF1_ENST00000567887.1_Missense_Mutation_p.A6212T			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6074					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TTTGATTTTTGCCTGTGGAGA	0.428																																					p.A4116T		Atlas-SNP	.											.	MACF1	909	.	0			c.G12346A						.						96	99	98					1																	39906750		2203	4300	6503	SO:0001583	missense	23499	exon70			ATTTTTGCCTGTG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18220G>A	chr1.hg19:g.39906750G>A	ENSP00000362006:p.Ala6074Thr	155.0	0.0		161.0	11.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.862234|5.862234	0.97036|0.97036	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.51071|.	0.72;0.72;0.72;0.72;0.72;0.72|.	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	0.000000|.	0.64402|.	D|.	0.000017|.	T|T	0.77837|0.77837	0.4190|0.4190	M|M	0.73598|0.73598	2.24|2.24	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.999;1.0|.	T|T	0.75569|0.75569	-0.3272|-0.3272	10|5	0.72032|.	D|.	0.01|.	.|.	20.2191|20.2191	0.98319|0.98319	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	6074;4116|.	Q9UPN3;F8W8Q1|.	MACF1_HUMAN;.|.	T|Y	4116;6074;4116;4116;3986;4618|3119	ENSP00000439537:A4116T;ENSP00000362006:A6074T;ENSP00000354573:A4116T;ENSP00000313438:A4116T;ENSP00000444364:A3986T;ENSP00000289893:A4618T|.	ENSP00000289893:A4618T|.	A|C	+|+	1|2	0|0	MACF1|MACF1	39679337|39679337	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.869000|9.869000	0.99810|0.99810	2.780000|2.780000	0.95670|0.95670	0.655000|0.655000	0.94253|0.94253	GCC|TGC	.	.		0.428	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39906750	G	A	39906750	3	1	122	1	0	0	0	0	1	0	0	0	9153	1319	46	3	18771	3	MACF1	1	39906750	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	21964070	39906750	209343871	5	20414										
SLC2A1	6513	hgsc.bcm.edu	37	chr1	43394606	43394606	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	agaacctagcaactcaccagCagtgctagcgcgatggtcat	10	12	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:43394606C>A	ENST00000426263.3	-	8	1249	c.1071G>T	c.(1069-1071)ctG>ctT	p.L357L	SLC2A1_ENST00000475162.1_Intron	NM_006516.2	NP_006507.2	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 1	357					carbohydrate metabolic process (GO:0005975)|cellular response to glucose starvation (GO:0042149)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|protein complex assembly (GO:0006461)|regulation of insulin secretion (GO:0050796)|response to osmotic stress (GO:0006970)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|female pronucleus (GO:0001939)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|midbody (GO:0030496)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|identical protein binding (GO:0042802)|protein self-association (GO:0043621)|xenobiotic transporter activity (GO:0042910)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|pancreas(2)	13	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)	AACTCACCAGCAGTGCTAGCG	0.602																																					p.L357L		Atlas-SNP	.											.	SLC2A1	36	.	0			c.G1071T						.						113	111	112					1																	43394606		2203	4300	6503	SO:0001819	synonymous_variant	6513	exon8			CACCAGCAGTGCT	K03195	CCDS477.1	1p34.2	2013-05-22			ENSG00000117394	ENSG00000117394		"Solute carriers"	11005	protein-coding gene	gene with protein product		138140	"human T-cell leukemia virus (I and II) receptor"	GLUT1, GLUT, HTLVR		8839927, 14622599, 18451999	Standard	NM_006516		Approved	DYT18	uc001cik.2	P11166	OTTHUMG00000007657	ENST00000426263.3:c.1071G>T	chr1.hg19:g.43394606C>A		42.0	0.0		55.0	19.0	NM_006516	A8K9S6|B2R620|D3DPX0|O75535|Q147X2	Silent	SNP	ENST00000426263.3	hg19	CCDS477.1																																																																																			.	.		0.602	SLC2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020358.2	NM_006516		A	43394606	C	A	43394606	2	1	122	1	0	0	0	0	0	0	0	1	14553	697	25	3		3	SLC2A1	1	43394606	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	3487856	43394606	205856015	6	20415										
YIPF1	54432	hgsc.bcm.edu	37	chr1	54332448	54332448	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tactgcggtggggatataaaTgaagagggaatatccataga	13	4	0	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:54332448T>C	ENST00000072644.1	-	8	967	c.631A>G	c.(631-633)Att>Gtt	p.I211V	YIPF1_ENST00000469457.1_5'UTR|YIPF1_ENST00000371399.1_Missense_Mutation_p.I28V|YIPF1_ENST00000539954.1_Missense_Mutation_p.I236V	NM_018982.4	NP_061855.1	Q9Y548	YIPF1_HUMAN	Yip1 domain family, member 1	211						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|skin(1)|urinary_tract(2)	19						GGGATATAAATGAAGAGGGAA	0.418																																					p.I211V		Atlas-SNP	.											.	YIPF1	30	.	0			c.A631G						.						99	92	94					1																	54332448		2203	4300	6503	SO:0001583	missense	54432	exon8			TATAAATGAAGAG	BC009674	CCDS584.1	1p33-p32.1	2008-02-05			ENSG00000058799	ENSG00000058799		"Yip1 domain family"	25231	protein-coding gene	gene with protein product						12477932	Standard	NM_018982		Approved	DJ167A19.1, FinGER1	uc001cvu.3	Q9Y548	OTTHUMG00000008074	ENST00000072644.1:c.631A>G	chr1.hg19:g.54332448T>C	ENSP00000072644:p.Ile211Val	68.0	0.0		99.0	14.0	NM_018982	B2RCM7|D3DQ40|Q9NWJ1	Missense_Mutation	SNP	ENST00000072644.1	hg19	CCDS584.1	.	.	.	.	.	.	.	.	.	.	T	11.63	1.694805	0.30052	.	.	ENSG00000058799	ENST00000371399;ENST00000072644;ENST00000539954;ENST00000412288	T	0.39787	1.06	6.01	4.88	0.63580	Yip1 domain (1);	0.185182	0.56097	D	0.000031	T	0.27349	0.0671	L	0.31752	0.955	0.58432	D	0.999999	B	0.14805	0.011	B	0.20184	0.028	T	0.06826	-1.0805	10	0.07482	T	0.82	-7.5382	10.453	0.44533	0.0:0.1574:0.0:0.8426	.	211	Q9Y548	YIPF1_HUMAN	V	28;211;236;211	ENSP00000416507:I211V	ENSP00000072644:I211V	I	-	1	0	YIPF1	54105036	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.347000	0.44036	2.307000	0.77673	0.528000	0.53228	ATT	.	.		0.418	YIPF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022103.5	NM_018982		C	54332448	T	C	54332448	3	2	122	1	0	0	0	0	1	0	0	0	17492	1464	51	2	301	2	YIPF1	1	54332448	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	10937842	54332448	194918173	7	20416										
WDR78	79819	hgsc.bcm.edu	37	chr1	67356850	67356850	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tcattacctgtgaaactagtCaatctttcccgtttatagga	6	9	3	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:67356850C>T	ENST00000371026.3	-	4	685	c.630G>A	c.(628-630)ttG>ttA	p.L210L	WDR78_ENST00000371023.3_Silent_p.L210L|WDR78_ENST00000371022.3_Silent_p.L210L|WDR78_ENST00000431318.1_5'UTR	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	210					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						TGAAACTAGTCAATCTTTCCC	0.343																																					p.L210L		Atlas-SNP	.											.	WDR78	102	.	0			c.G630A						.						169	170	170					1																	67356850		2203	4300	6503	SO:0001819	synonymous_variant	79819	exon4			ACTAGTCAATCTT	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"WD repeat domain containing"	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.630G>A	chr1.hg19:g.67356850C>T		106.0	0.0		119.0	43.0	NM_207014	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Silent	SNP	ENST00000371026.3	hg19	CCDS635.1																																																																																			.	.		0.343	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763		T	67356850	C	T	67356850	2	4	122	1	0	0	0	0	0	0	0	1	17343	825	29	3		3	WDR78	1	67356850	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	13024402	67356850	181893771	8	20417										
RPE65	6121	hgsc.bcm.edu	37	chr1	68903877	68903877	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	agaagcaggttaccttgtcaAtattcaaaggaagtacatat	8	6	2	1	rs62653013		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:68903877A>G	ENST00000262340.5	-	10	1174	c.1121T>C	c.(1120-1122)aTt>aCt	p.I374T		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	374					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						TACCTTGTCAATATTCAAAGG	0.378																																					p.I374T		Atlas-SNP	.											.	RPE65	87	.	0			c.T1121C						.						93	96	95					1																	68903877		2203	4300	6503	SO:0001583	missense	6121	exon10			TTGTCAATATTCA	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.1121T>C	chr1.hg19:g.68903877A>G	ENSP00000262340:p.Ile374Thr	89.0	0.0		112.0	11.0	NM_000329	A8K1L0|Q5T9U3	Missense_Mutation	SNP	ENST00000262340.5	hg19	CCDS643.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.273259	0.40194	.	.	ENSG00000116745	ENST00000262340	D	0.94537	-3.45	5.71	4.57	0.56435	.	0.139429	0.64402	D	0.000006	D	0.86585	0.5968	L	0.51914	1.62	0.53688	D	0.999979	B	0.22146	0.065	B	0.31016	0.123	T	0.81176	-0.1052	10	0.11485	T	0.65	-2.7026	11.8223	0.52245	0.9311:0.0:0.0689:0.0	.	374	Q16518	RPE65_HUMAN	T	374	ENSP00000262340:I374T	ENSP00000262340:I374T	I	-	2	0	RPE65	68676465	1.000000	0.71417	0.811000	0.32455	0.839000	0.47603	5.878000	0.69682	0.984000	0.38629	0.482000	0.46254	ATT	.	.		0.378	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		G	68903877	A	G	68903877	3	3	122	1	0	0	0	0	1	0	0	0	13560	101	4	2	500	2	RPE65	1	68903877	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	1547027	68903877	180346744	9	20418										
GBP2	2634	hgsc.bcm.edu	37	chr1	89583374	89583374	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cacaaatgctggaaaaaagcTcacaaagtcagctgagtcgt	9	9	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:89583374T>G	ENST00000370466.3	-	5	779	c.511A>C	c.(511-513)Agc>Cgc	p.S171R	GBP2_ENST00000463660.1_5'UTR	NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN	guanylate binding protein 2, interferon-inducible	171	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		GGAAAAAAGCTCACAAAGTCA	0.453																																					p.S171R		Atlas-SNP	.											.	GBP2	58	.	0			c.A511C						.						86	78	81					1																	89583374		2203	4300	6503	SO:0001583	missense	2634	exon5			AAAAGCTCACAAA	BC073163	CCDS719.1	1p22.2	2008-02-05			ENSG00000162645	ENSG00000162645			4183	protein-coding gene	gene with protein product		600412				1715024	Standard	NM_004120		Approved		uc001dmz.1	P32456	OTTHUMG00000010662	ENST00000370466.3:c.511A>C	chr1.hg19:g.89583374T>G	ENSP00000359497:p.Ser171Arg	260.0	0.0		263.0	109.0	NM_004120	Q6GPH0|Q6IAU2|Q86TB0	Missense_Mutation	SNP	ENST00000370466.3	hg19	CCDS719.1	.	.	.	.	.	.	.	.	.	.	T	13.38	2.218641	0.39201	.	.	ENSG00000162645	ENST00000370466	T	0.75821	-0.97	3.81	0.312	0.15837	Guanylate-binding protein, N-terminal (1);	0.428344	0.21719	U	0.070156	T	0.44435	0.1293	L	0.41824	1.3	0.24361	N	0.994874	P	0.41748	0.761	B	0.42555	0.391	T	0.37686	-0.9695	10	0.29301	T	0.29	-11.2532	6.6733	0.23080	0.0:0.3537:0.0:0.6463	.	171	P32456	GBP2_HUMAN	R	171	ENSP00000359497:S171R	ENSP00000359497:S171R	S	-	1	0	GBP2	89355962	1.000000	0.71417	0.902000	0.35471	0.003000	0.03518	0.457000	0.21875	0.178000	0.19917	-0.250000	0.11733	AGC	.	.		0.453	GBP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029406.2	NM_004120		G	89583374	T	G	89583374	3	3	122	1	0	0	0	0	1	0	0	0	6282	1551	54	5	1292	5	GBP2	1	89583374	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	20679497	89583374	159667247	10	20419										
DPYD	1806	hgsc.bcm.edu	37	chr1	97564053	97564053	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cataatttttaccttgatggTaggaataggccttttgggga	11	5	0	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:97564053T>C	ENST00000370192.3	-	21	2858	c.2758A>G	c.(2758-2760)Acc>Gcc	p.T920A	DPYD-AS1_ENST00000422980.1_RNA	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	920					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	ACCTTGATGGTAGGAATAGGC	0.294																																					p.T920A		Atlas-SNP	.											.	DPYD	219	.	0			c.A2758G						.						148	157	154					1																	97564053		2203	4300	6503	SO:0001583	missense	1806	exon21			TGATGGTAGGAAT	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2758A>G	chr1.hg19:g.97564053T>C	ENSP00000359211:p.Thr920Ala	148.0	0.0		160.0	40.0	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	T	2.331	-0.353436	0.05173	.	.	ENSG00000188641	ENST00000370192	D	0.89810	-2.57	5.66	-7.03	0.01584	.	0.591910	0.17496	N	0.172164	T	0.43612	0.1255	N	0.01122	-1.005	0.21579	N	0.999635	B	0.02656	0.0	B	0.04013	0.001	T	0.52946	-0.8507	10	0.22109	T	0.4	0.0	13.2935	0.60284	0.0844:0.7307:0.0:0.1848	.	920	Q12882	DPYD_HUMAN	A	920	ENSP00000359211:T920A	ENSP00000359211:T920A	T	-	1	0	DPYD	97336641	0.000000	0.05858	0.009000	0.14445	0.193000	0.23685	-2.454000	0.01004	-1.291000	0.02368	-0.462000	0.05337	ACC	.	.		0.294	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		C	97564053	T	C	97564053	3	2	122	1	0	0	0	0	1	0	0	0	4747	1638	57	2	331	2	DPYD	1	97564053	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	7980679	97564053	151686568	11	20420										
DENND2C	163259	hgsc.bcm.edu	37	chr1	115143496	115143496	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgatggtgcgtccaggagctGggaaaggagcttccatgaca	15	8	0	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:115143496G>T	ENST00000393274.1	-	14	2526	c.1901C>A	c.(1900-1902)cCa>cAa	p.P634Q	DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393276.3_Missense_Mutation_p.P577Q|DENND2C_ENST00000393277.1_Missense_Mutation_p.P634Q	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	634	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCAGGAGCTGGGAAAGGAGC	0.443																																					p.P634Q		Atlas-SNP	.											.	DENND2C	105	.	0			c.C1901A						.						128	124	126					1																	115143496		2203	4300	6503	SO:0001583	missense	163259	exon14			GGAGCTGGGAAAG		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"DENN/MADD domain containing"	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.1901C>A	chr1.hg19:g.115143496G>T	ENSP00000376955:p.Pro634Gln	112.0	0.0		95.0	27.0	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Missense_Mutation	SNP	ENST00000393274.1	hg19	CCDS58018.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.025505	0.93518	.	.	ENSG00000175984	ENST00000393276;ENST00000393274;ENST00000369540;ENST00000393277	T;T;T	0.67171	-0.25;-0.25;-0.25	5.18	5.18	0.71444	DENN (3);	0.000000	0.85682	D	0.000000	D	0.87669	0.6235	H	0.97415	4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.92072	0.5665	10	0.87932	D	0	.	18.7701	0.91888	0.0:0.0:1.0:0.0	.	634;577	Q68D51;Q68D51-3	DEN2C_HUMAN;.	Q	577;634;634;634	ENSP00000376957:P577Q;ENSP00000376955:P634Q;ENSP00000376958:P634Q	ENSP00000358553:P634Q	P	-	2	0	DENND2C	114945019	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.431000	0.82371	0.650000	0.86243	CCA	.	.		0.443	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459		T	115143496	G	T	115143496	3	4	122	1	0	0	0	0	1	0	0	0	4432	1348	47	3	917	3	DENND2C	1	115143496	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	17579443	115143496	134107125	12	20421										
PHGDH	26227	hgsc.bcm.edu	37	chr1	120266059	120266059	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgtggaatgatcatgtgcctGgccaggtaagtccctgactt	12	9	1	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:120266059G>C	ENST00000369409.4	+	3	487	c.351G>C	c.(349-351)ctG>ctC	p.L117L	PHGDH_ENST00000369407.3_Silent_p.L83L	NM_006623.3	NP_006614.2	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase	117					brain development (GO:0007420)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|G1 to G0 transition (GO:0070314)|gamma-aminobutyric acid metabolic process (GO:0009448)|glial cell development (GO:0021782)|glutamine metabolic process (GO:0006541)|glycine metabolic process (GO:0006544)|L-serine biosynthetic process (GO:0006564)|neural tube development (GO:0021915)|neuron projection development (GO:0031175)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|taurine metabolic process (GO:0019530)|threonine metabolic process (GO:0006566)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|phosphoglycerate dehydrogenase activity (GO:0004617)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	18	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)		TCATGTGCCTGGCCAGGTAAG	0.473																																					p.L117L		Atlas-SNP	.											.	PHGDH	51	.	0			c.G351C						.						164	147	153					1																	120266059		2203	4300	6503	SO:0001819	synonymous_variant	26227	exon3			GTGCCTGGCCAGG	BC011262	CCDS904.1	1p12	2008-02-05			ENSG00000092621	ENSG00000092621	1.1.1.95		8923	protein-coding gene	gene with protein product		606879					Standard	NM_006623		Approved	SERA, PGDH, PDG	uc001ehz.3	O43175	OTTHUMG00000012100	ENST00000369409.4:c.351G>C	chr1.hg19:g.120266059G>C		113.0	0.0		122.0	50.0	NM_006623	B2RD08|Q5SZU3|Q9BQ01	Silent	SNP	ENST00000369409.4	hg19	CCDS904.1																																																																																			.	.		0.473	PHGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033464.1	NM_006623		C	120266059	G	C	120266059	2	2	122	1	0	0	0	0	0	0	0	1	11850	1335	47	4		4	PHGDH	1	120266059	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	5122563	120266059	128984562	13	20422										
NES	10763	hgsc.bcm.edu	37	chr1	156641759	156641759	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	taaagacctcagtgatttgtGattctctgtttctagaggtc	9	7	3	4			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:156641759G>T	ENST00000368223.3	-	4	2353	c.2221C>A	c.(2221-2223)Cac>Aac	p.H741N		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	741	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGTGATTTGTGATTCTCTGTT	0.443																																					p.H741N		Atlas-SNP	.											.	NES	196	.	0			c.C2221A						.						121	122	121					1																	156641759		2203	4300	6503	SO:0001583	missense	10763	exon4			ATTTGTGATTCTC	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.2221C>A	chr1.hg19:g.156641759G>T	ENSP00000357206:p.His741Asn	133.0	0.0		267.0	144.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.605578	0.28623	.	.	ENSG00000132688	ENST00000368223	D	0.84660	-1.88	5.12	4.14	0.48551	.	.	.	.	.	T	0.65428	0.2690	L	0.36672	1.1	0.09310	N	1	B	0.25609	0.13	B	0.20184	0.028	T	0.60459	-0.7259	9	0.66056	D	0.02	.	7.9351	0.29925	0.0:0.1742:0.6457:0.1801	.	741	P48681	NEST_HUMAN	N	741	ENSP00000357206:H741N	ENSP00000357206:H741N	H	-	1	0	NES	154908383	0.000000	0.05858	0.014000	0.15608	0.020000	0.10135	0.447000	0.21710	2.356000	0.79943	0.563000	0.77884	CAC	.	.		0.443	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		T	156641759	G	T	156641759	3	4	122	1	0	0	0	0	1	0	0	0	10346	1290	45	3	2648	3	NES	1	156641759	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	36375700	156641759	92608862	14	20423										
PPP1R15B	84919	hgsc.bcm.edu	37	chr1	204378958	204378958	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ctcaggggtctcaggaaggcTtccagactgggaggaattct	14	9	3	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:204378958T>G	ENST00000367188.4	-	1	1961	c.1582A>C	c.(1582-1584)Agc>Cgc	p.S528R	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	528					ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			TCAGGAAGGCTTCCAGACTGG	0.468																																					p.S528R		Atlas-SNP	.											.	PPP1R15B	67	.	0			c.A1582C						.						53	54	54					1																	204378958		2203	4300	6503	SO:0001583	missense	84919	exon1			GAAGGCTTCCAGA	AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14951	protein-coding gene	gene with protein product		613257	"protein phosphatase 1, regulatory (inhibitor) subunit 15B"			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.1582A>C	chr1.hg19:g.204378958T>G	ENSP00000356156:p.Ser528Arg	90.0	0.0		124.0	69.0	NM_032833	Q53GQ4|Q658M2|Q6P156|Q96SN1	Missense_Mutation	SNP	ENST00000367188.4	hg19	CCDS1445.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.326953	0.24080	.	.	ENSG00000158615	ENST00000367188;ENST00000543650	T	0.27720	1.65	5.17	1.35	0.21983	Protein phosphatase 1, regulatory subunit 15A/B, C-terminal (1);	0.961662	0.08634	N	0.916658	T	0.31513	0.0799	M	0.64997	1.995	0.09310	N	1	D	0.54397	0.966	P	0.46629	0.522	T	0.22068	-1.0227	10	0.54805	T	0.06	0.0164	1.4786	0.02432	0.2833:0.0847:0.1565:0.4754	.	528	Q5SWA1	PR15B_HUMAN	R	528;438	ENSP00000356156:S528R	ENSP00000356156:S528R	S	-	1	0	PPP1R15B	202645581	0.000000	0.05858	0.038000	0.18304	0.400000	0.30750	0.521000	0.22893	-0.027000	0.13873	-0.327000	0.08410	AGC	.	.		0.468	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833		G	204378958	T	G	204378958	3	3	122	1	0	0	0	0	1	0	0	0	12376	1609	56	5	567	5	PPP1R15B	1	204378958	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	47737199	204378958	44871663	15	20424										
RYR2	6262	hgsc.bcm.edu	37	chr1	237586488	237586488	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	atggaagacaaaaaccttctActcatggacaaagagaaagc	8	8	2	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:237586488A>T	ENST00000366574.2	+	12	1262	c.945A>T	c.(943-945)ctA>ctT	p.L315L	RYR2_ENST00000360064.6_Silent_p.L313L|RYR2_ENST00000542537.1_Silent_p.L299L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	315	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AAAACCTTCTACTCATGGACA	0.418																																					p.L315L		Atlas-SNP	.											.	RYR2	1273	.	0			c.A945T						.						123	117	119					1																	237586488		1892	4107	5999	SO:0001819	synonymous_variant	6262	exon12			CCTTCTACTCATG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.945A>T	chr1.hg19:g.237586488A>T		243.0	0.0		429.0	27.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.418	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237586488	A	T	237586488	2	4	122	1	0	0	0	0	0	0	0	1	13784	378	14	4		4	RYR2	1	237586488	Silent	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	33207530	237586488	11664133	16	20425										
OR2M5	127059	hgsc.bcm.edu	37	chr1	248308490	248308490	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cttcaactctgacttcatccTcctgggaatcttcaatcaca	4	14	6	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr1:248308490T>C	ENST00000366476.1	+	1	41	c.41T>C	c.(40-42)cTc>cCc	p.L14P		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L14P(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			GACTTCATCCTCCTGGGAATC	0.438																																					p.L14P		Atlas-SNP	.											OR2M5,right_upper_lobe,carcinoma,-1,1	OR2M5	117	.	1	Substitution - Missense(1)	lung(1)	c.T41C						.						225	223	223					1																	248308490		2203	4300	6503	SO:0001583	missense	127059	exon1			TCATCCTCCTGGG		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"GPCR / Class A : Olfactory receptors"	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.41T>C	chr1.hg19:g.248308490T>C	ENSP00000355432:p.Leu14Pro	201.0	0.0		329.0	178.0	NM_001004690		Missense_Mutation	SNP	ENST00000366476.1	hg19	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	t	13.25	2.182311	0.38511	.	.	ENSG00000162727	ENST00000366476	T	0.01215	5.16	3.14	1.93	0.25924	.	0.000000	0.28042	U	0.016823	T	0.11623	0.0283	H	0.98965	4.385	0.19775	N	0.999954	D	0.89917	1.0	D	0.83275	0.996	T	0.15350	-1.0440	10	0.87932	D	0	.	8.1369	0.31061	0.1808:0.0:0.0:0.8192	.	14	A3KFT3	OR2M5_HUMAN	P	14	ENSP00000355432:L14P	ENSP00000355432:L14P	L	+	2	0	OR2M5	246375113	0.052000	0.20516	0.344000	0.25628	0.741000	0.42261	3.154000	0.50693	0.190000	0.20209	0.403000	0.27427	CTC	.	.		0.438	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690		C	248308490	T	C	248308490	3	2	122	1	0	0	0	0	1	0	0	0	11022	1551	54	2	43	2	OR2M5	1	248308490	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	10722002	248308490	942131	17	20426										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1926593	1926593	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cacacctcctcatcgctctcCtccaccatcttttccatgag	3	19	3	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:1926593C>T	ENST00000399161.2	-	10	1695	c.948G>A	c.(946-948)gaG>gaA	p.E316E	MYT1L_ENST00000428368.2_Silent_p.E316E	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	316					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CATCGCTCTCCTCCACCATCT	0.507																																					p.E316E		Atlas-SNP	.											.	MYT1L	241	.	0			c.G948A						.						120	126	124					2																	1926593		2150	4248	6398	SO:0001819	synonymous_variant	23040	exon10			GCTCTCCTCCACC	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.948G>A	chr2.hg19:g.1926593C>T		179.0	0.0		164.0	45.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	hg19																																																																																				.	.		0.507	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		T	1926593	C	T	1926593	2	4	122	1	0	0	0	0	0	0	0	1	10116	680	24	3		3	MYT1L	2	1926593	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10		1926593	241272780	18	20427										
ADI1	55256	hgsc.bcm.edu	37	chr2	3504718	3504718	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cactgccatccaggatgtagCggatctcatcgtccaagtgc	10	13	1	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:3504718C>A	ENST00000327435.6	-	3	535	c.287G>T	c.(286-288)cGc>cTc	p.R96L	ADI1_ENST00000382093.5_Missense_Mutation_p.R90L	NM_018269.3	NP_060739.2			acireductone dioxygenase 1											breast(2)|large_intestine(2)|lung(4)|ovary(1)|stomach(1)	10	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0729)|Epithelial(75;0.173)|all cancers(51;0.228)		CAGGATGTAGCGGATCTCATC	0.532																																					p.R96L		Atlas-SNP	.											.	ADI1	12	.	0			c.G287T						.						223	166	185					2																	3504718		2203	4300	6503	SO:0001583	missense	55256	exon3			ATGTAGCGGATCT		CCDS1653.1	2p25.2	2013-05-29			ENSG00000182551	ENSG00000182551	1.13.11.54		30576	protein-coding gene	gene with protein product	"membrane-type 1 matrix metalloproteinase cytoplasmic tail binding protein-1"	613400				14718544, 15938715	Standard	NM_018269		Approved	SIPL, MTCBP-1, ARD, APL1, FLJ10913, HMFT1638, mtnD	uc002qxp.4	Q9BV57	OTTHUMG00000112441	ENST00000327435.6:c.287G>T	chr2.hg19:g.3504718C>A	ENSP00000333666:p.Arg96Leu	62.0	0.0		66.0	32.0	NM_018269		Missense_Mutation	SNP	ENST00000327435.6	hg19	CCDS1653.1	.	.	.	.	.	.	.	.	.	.	C	35	5.487324	0.96323	.	.	ENSG00000182551	ENST00000327435;ENST00000382093	.	.	.	4.73	4.73	0.59995	Cupin, RmlC-type (1);RmlC-like jelly roll fold (1);	0.049866	0.85682	D	0.000000	D	0.85952	0.5817	H	0.95114	3.625	0.80722	D	1	D	0.71674	0.998	D	0.63381	0.914	D	0.90661	0.4590	9	0.87932	D	0	-24.4714	16.6473	0.85179	0.0:1.0:0.0:0.0	.	96	Q9BV57	MTND_HUMAN	L	96;90	.	ENSP00000333666:R96L	R	-	2	0	ADI1	3483725	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.609000	0.67661	2.339000	0.79563	0.655000	0.94253	CGC	.	.		0.532	ADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000231914.6	NM_018269		A	3504718	C	A	3504718	3	1	122	1	0	0	0	0	1	0	0	0	315	768	27	1	260	1	ADI1	2	3504718	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	1578125	3504718	239694655	19	20428										
C2orf48	348738	hgsc.bcm.edu	37	chr2	10350626	10350626	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	caccaagaatgcacagagggCgctgggctccaagcttcagc	12	13	1	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:10350626C>T	ENST00000381786.3	+	4	672	c.383C>T	c.(382-384)gCg>gTg	p.A128V		NM_182626.2	NP_872432.1	Q96LS8	CB048_HUMAN	chromosome 2 open reading frame 48	128								p.A128V(1)		endometrium(1)|lung(7)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.188)		GCACAGAGGGCGCTGGGCTCC	0.582																																					p.A128V		Atlas-SNP	.											C2orf48,NS,carcinoma,0,1	C2orf48	9	.	1	Substitution - Missense(1)	endometrium(1)	c.C383T						.						63	68	66					2																	10350626		2203	4300	6503	SO:0001583	missense	348738	exon3			AGAGGGCGCTGGG	AK057831	CCDS1670.1	2p25.1	2006-09-01			ENSG00000163009	ENSG00000163009			26322	protein-coding gene	gene with protein product						12477932	Standard	NM_182626		Approved	FLJ25102	uc021vds.1	Q96LS8	OTTHUMG00000119017	ENST00000381786.3:c.383C>T	chr2.hg19:g.10350626C>T	ENSP00000371205:p.Ala128Val	98.0	0.0		114.0	58.0	NM_182626		Missense_Mutation	SNP	ENST00000381786.3	hg19	CCDS1670.1	.	.	.	.	.	.	.	.	.	.	c	8.382	0.837748	0.16891	.	.	ENSG00000163009	ENST00000381786	T	0.38401	1.14	1.51	-1.87	0.07737	.	.	.	.	.	T	0.16599	0.0399	N	0.08118	0	0.09310	N	1	B	0.18863	0.031	B	0.06405	0.002	T	0.17440	-1.0369	9	0.87932	D	0	.	5.813	0.18477	0.0:0.5828:0.0:0.4172	.	128	Q96LS8	CB048_HUMAN	V	128	ENSP00000371205:A128V	ENSP00000371205:A128V	A	+	2	0	C2orf48	10268077	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.740000	0.04861	-0.689000	0.05149	-1.197000	0.01672	GCG	.	.		0.582	C2orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239217.1	NM_182626		T	10350626	C	T	10350626	3	4	122	1	0	0	0	0	1	0	0	0	2172	768	27	1	393	1	C2orf48	2	10350626	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	6845908	10350626	232848747	20	20429										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71591324	71591324	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	aatccatttagaggtagtccAaaatgctttcgatcagttag	8	7	1	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:71591324A>G	ENST00000409544.1	+	5	2289	c.1659A>G	c.(1657-1659)ccA>ccG	p.P553P	ZNF638_ENST00000377802.2_Silent_p.P553P|ZNF638_ENST00000264447.4_Silent_p.P553P|ZNF638_ENST00000355812.3_Silent_p.P553P|ZNF638_ENST00000410075.1_3'UTR	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	553	Arg-rich.				regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GAGGTAGTCCAAAATGCTTTC	0.408																																					p.P553P		Atlas-SNP	.											.	ZNF638	179	.	0			c.A1659G						.						96	91	93					2																	71591324		2203	4300	6503	SO:0001819	synonymous_variant	27332	exon5			TAGTCCAAAATGC	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.1659A>G	chr2.hg19:g.71591324A>G		113.0	0.0		142.0	58.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	hg19	CCDS1917.1																																																																																			.	.		0.408	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		G	71591324	A	G	71591324	2	3	122	1	0	0	0	0	0	0	0	1	18070	117	5	2		2	ZNF638	2	71591324	Silent	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	61240698	71591324	171608049	21	20430										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84832627	84832627	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cttgaattatttctaaggtgGaggactcttggaaaacaact	9	6	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:84832627G>A	ENST00000237449.6	+	19	3093	c.3085G>A	c.(3085-3087)Gag>Aag	p.E1029K	DNAH6_ENST00000389394.3_Missense_Mutation_p.E1029K|DNAH6_ENST00000398278.2_Missense_Mutation_p.E1029K			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1029	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTCTAAGGTGGAGGACTCTTG	0.368																																					p.E1029K		Atlas-SNP	.											.	DNAH6	194	.	0			c.G3085A						.						202	171	181					2																	84832627		692	1591	2283	SO:0001583	missense	1768	exon20			AAGGTGGAGGACT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.3085G>A	chr2.hg19:g.84832627G>A	ENSP00000237449:p.Glu1029Lys	122.0	0.0		132.0	40.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.992448	0.93167	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.60672	0.17;0.17;0.17	5.63	5.63	0.86233	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.53626	0.1808	L	0.38733	1.17	0.51767	D	0.99993	P	0.37370	0.592	B	0.40329	0.326	T	0.49380	-0.8946	9	0.31617	T	0.26	.	18.4531	0.90711	0.0:0.0:1.0:0.0	.	1029	Q9C0G6	DYH6_HUMAN	K	1029	ENSP00000374045:E1029K;ENSP00000381326:E1029K;ENSP00000237449:E1029K	ENSP00000237449:E1029K	E	+	1	0	DNAH6	84686138	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.043000	0.71004	2.654000	0.90174	0.655000	0.94253	GAG	.	.		0.368	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84832627	G	A	84832627	3	1	122	1	0	0	0	0	1	0	0	0	4607	1175	41	3	3159	3	DNAH6	2	84832627	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	13241303	84832627	158366746	22	20431										
SMYD1	150572	hgsc.bcm.edu	37	chr2	88396264	88396264	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gaacactgccagaaaaaactGaaggatgacctcttcctggg	10	10	1	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:88396264G>C	ENST00000419482.2	+	6	934	c.849G>C	c.(847-849)ctG>ctC	p.L283L	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.L270L	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	283					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						AGAAAAAACTGAAGGATGACC	0.498																																					p.L283L		Atlas-SNP	.											.	SMYD1	95	.	0			c.G849C						.						92	86	88					2																	88396264		2203	4300	6503	SO:0001819	synonymous_variant	150572	exon6			AAAACTGAAGGAT	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.849G>C	chr2.hg19:g.88396264G>C		84.0	0.0		88.0	32.0	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	hg19	CCDS33240.1																																																																																			.	.		0.498	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		C	88396264	G	C	88396264	2	2	122	1	0	0	0	0	0	0	0	1	14836	1277	45	4		4	SMYD1	2	88396264	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	3563637	88396264	154803109	23	20432										
FAP	2191	hgsc.bcm.edu	37	chr2	163029733	163029733	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttgccatcacagttgaattcTggaaaagagaaaaaaattaa	7	5	2	2	rs566100960		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:163029733T>C	ENST00000188790.4	-	24	2242		c.e24-2		AC007750.5_ENST00000418968.3_RNA|FAP_ENST00000443424.1_Splice_Site	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						AGTTGAATTCTGGAAAAGAGA	0.353																																					.		Atlas-SNP	.											.	FAP	122	.	0			c.2035-2A>G						.						82	84	83					2																	163029733		2203	4300	6503	SO:0001630	splice_region_variant	2191	exon25			GAATTCTGGAAAA	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.2035-2A>G	chr2.hg19:g.163029733T>C		173.0	0.0		205.0	66.0	NM_004460		Splice_Site	SNP	ENST00000188790.4	hg19	CCDS33311.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.391949	0.62066	.	.	ENSG00000078098	ENST00000188790;ENST00000443424	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1172	0.81314	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAP	162737979	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.316000	0.79007	2.266000	0.75297	0.533000	0.62120	.	.	.		0.353	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2		Intron	C	163029733	T	C	163029733	5	2	122	1	0	0	0	0	0	0	1	0	5681	1594	55	2	261	2	FAP	2	163029733	Splice_Site	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	74633469	163029733	80169640	24	20433										
FAP	2191	hgsc.bcm.edu	37	chr2	163044766	163044766	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgtcaccttggaaagctgttCctcgaccatccaccaaggca	8	14	1	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:163044766C>A	ENST00000188790.4	-	20	1934	c.1727G>T	c.(1726-1728)gGa>gTa	p.G576V	FAP_ENST00000443424.1_Missense_Mutation_p.G551V	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						GAAAGCTGTTCCTCGACCATC	0.458																																					p.G576V		Atlas-SNP	.											.	FAP	122	.	0			c.G1727T						.						165	147	153					2																	163044766		2203	4300	6503	SO:0001583	missense	2191	exon20			GCTGTTCCTCGAC	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.1727G>T	chr2.hg19:g.163044766C>A	ENSP00000188790:p.Gly576Val	113.0	0.0		160.0	61.0	NM_004460		Missense_Mutation	SNP	ENST00000188790.4	hg19	CCDS33311.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.319799	0.81469	.	.	ENSG00000078098	ENST00000188790;ENST00000443424	T;T	0.69175	-0.38;-0.38	6.07	6.07	0.98685	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90349	0.6980	H	0.99026	4.405	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93293	0.6670	10	0.87932	D	0	-16.2334	20.6593	0.99626	0.0:1.0:0.0:0.0	.	551;55;576	B4DLR2;Q12884-2;Q12884	.;.;SEPR_HUMAN	V	576;551	ENSP00000188790:G576V;ENSP00000411391:G551V	ENSP00000188790:G576V	G	-	2	0	FAP	162753012	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.267000	0.78462	2.885000	0.99019	0.655000	0.94253	GGA	.	.		0.458	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			A	163044766	C	A	163044766	3	1	122	1	0	0	0	0	1	0	0	0	5681	855	30	3	583	3	FAP	2	163044766	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	15033	163044766	80154607	25	20434										
TTN	7273	hgsc.bcm.edu	37	chr2	179415808	179415808	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	atccccaggactgagtcctgTaactgtgtactgacattcac	8	12	1	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:179415808T>A	ENST00000591111.1	-	286	86751	c.86527A>T	c.(86527-86529)Aca>Tca	p.T28843S	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T27916S|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T21611S|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T21419S|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T21544S|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T30484S|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28843	Fibronectin type-III 110. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGAGTCCTGTAACTGTGTAC	0.453																																					p.T30484S		Atlas-SNP	.											.	TTN	18412	.	0			c.A91450T						.						89	86	87					2																	179415808		1947	4152	6099	SO:0001583	missense	7273	exon336			GTCCTGTAACTGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.86527A>T	chr2.hg19:g.179415808T>A	ENSP00000465570:p.Thr28843Ser	82.0	0.0		92.0	43.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.37	3.103035	0.56183	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	5.9	4.73	0.59995	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.48114	0.1482	L	0.51422	1.61	0.50632	D	0.999882	B;B;B;B	0.27166	0.17;0.17;0.17;0.099	B;B;B;B	0.26310	0.068;0.068;0.068;0.047	T	0.47315	-0.9127	9	0.87932	D	0	.	12.6321	0.56663	0.1239:0.0:0.0:0.8761	.	21419;21544;21611;28843	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	27916;21419;21611;21544;21416	ENSP00000343764:T27916S;ENSP00000434586:T21419S;ENSP00000340554:T21611S;ENSP00000352154:T21544S	ENSP00000340554:T21611S	T	-	1	0	TTN	179124054	1.000000	0.71417	0.989000	0.46669	0.976000	0.68499	3.275000	0.51639	1.023000	0.39654	0.528000	0.53228	ACA	.	.		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179415808	T	A	179415808	3	1	122	1	0	0	0	0	1	0	0	0	16750	1638	57	4	16637	4	TTN	2	179415808	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	16371042	179415808	63783565	26	20435										
TTN	7273	hgsc.bcm.edu	37	chr2	179544137	179544137	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cctctggcttcttaggaaccTcaggcactttaaagatattg	8	10	3	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:179544137T>A	ENST00000591111.1	-	140	32944	c.32720A>T	c.(32719-32721)gAg>gTg	p.E10907V	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E9980V|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E11224V|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	11678	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTAGGAACCTCAGGCACTTT	0.373																																					p.E11224V		Atlas-SNP	.											.	TTN	18412	.	0			c.A33671T						.						92	86	88					2																	179544137		1829	4086	5915	SO:0001583	missense	7273	exon142			GGAACCTCAGGCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.32720A>T	chr2.hg19:g.179544137T>A	ENSP00000465570:p.Glu10907Val	167.0	0.0		216.0	27.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.07	2.127887	0.37533	.	.	ENSG00000155657	ENST00000342992	T	0.69175	-0.38	5.82	5.82	0.92795	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.74733	0.3755	M	0.90650	3.135	0.80722	D	1	P	0.48911	0.917	P	0.46049	0.502	T	0.80562	-0.1327	9	0.87932	D	0	.	9.7862	0.40677	0.0:0.0763:0.0:0.9237	.	10907	Q8WZ42	TITIN_HUMAN	V	9980	ENSP00000343764:E9980V	ENSP00000343764:E9980V	E	-	2	0	TTN	179252382	0.994000	0.37717	1.000000	0.80357	0.988000	0.76386	2.716000	0.47219	2.207000	0.71202	0.533000	0.62120	GAG	.	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179544137	T	A	179544137	3	1	122	1	0	0	0	0	1	0	0	0	16750	1551	54	4	70742	4	TTN	2	179544137	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	128329	179544137	63655236	27	20436										
NMUR1	10316	hgsc.bcm.edu	37	chr2	232392880	232392880	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ccccgatcgtgctgctggagCctgcaggtgtatctggacct	13	13	1	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr2:232392880C>T	ENST00000305141.4	-	2	985	c.852G>A	c.(850-852)agG>agA	p.R284R		NM_006056.4	NP_006047.3	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	284					activation of phospholipase C activity (GO:0007202)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|chloride transport (GO:0006821)|G-protein coupled receptor signaling pathway (GO:0007186)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|smooth muscle contraction (GO:0006939)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuromedin U receptor activity (GO:0001607)|neuropeptide receptor activity (GO:0008188)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(12)|pancreas(1)|skin(1)	24		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;8.37e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GCTGCTGGAGCCTGCAGGTGT	0.632																																					p.R284R		Atlas-SNP	.											.	NMUR1	46	.	0			c.G852A						.						49	48	49					2																	232392880		2203	4300	6503	SO:0001819	synonymous_variant	10316	exon2			CTGGAGCCTGCAG	AF044600	CCDS2486.1	2q37.1	2012-08-08	2004-05-27	2004-05-28	ENSG00000171596	ENSG00000171596		"GPCR / Class A : Neuromedin U receptors"	4518	protein-coding gene	gene with protein product		604153	"G protein-coupled receptor 66"	GPR66		9782091	Standard	NM_006056		Approved	GPC-R, FM-3, NMU1R	uc002vry.4	Q9HB89	OTTHUMG00000133225	ENST00000305141.4:c.852G>A	chr2.hg19:g.232392880C>T		60.0	0.0		73.0	29.0	NM_006056	O43664|Q7LDP6|Q8NE20	Silent	SNP	ENST00000305141.4	hg19	CCDS2486.1																																																																																			.	.		0.632	NMUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256961.1	NM_006056		T	232392880	C	T	232392880	2	4	122	1	0	0	0	0	0	0	0	1	10515	738	26	3		3	NMUR1	2	232392880	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	52848743	232392880	10806493	28	20437										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47037989	47037989	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gcacccaggacactcggtggGgcagccccacatccctggag	13	16	0	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr3:47037989G>T	ENST00000450053.3	+	16	2559	c.2380G>T	c.(2380-2382)Ggc>Tgc	p.G794C	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Missense_Mutation_p.G794C	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	794					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CACTCGGTGGGGCAGCCCCAC	0.692																																					p.G794C		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G2380T						.						10	13	12					3																	47037989		2009	4180	6189	SO:0001583	missense	23218	exon16			CGGTGGGGCAGCC	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.2380G>T	chr3.hg19:g.47037989G>T	ENSP00000415034:p.Gly794Cys	64.0	0.0		49.0	21.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	hg19	CCDS46817.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.526663	0.85706	.	.	ENSG00000160796	ENST00000292309;ENST00000450053	T;T	0.76839	-1.05;-1.05	4.58	4.58	0.56647	Concanavalin A-like lectin/glucanase (1);	0.000000	0.85682	D	0.000000	D	0.87873	0.6287	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89621	0.3848	10	0.87932	D	0	.	16.1281	0.81408	0.0:0.0:1.0:0.0	.	794	Q6ZNJ1	NBEL2_HUMAN	C	794	ENSP00000292309:G794C;ENSP00000415034:G794C	ENSP00000292309:G794C	G	+	1	0	NBEAL2	47012993	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.713000	0.84693	2.367000	0.80283	0.462000	0.41574	GGC	.	.		0.692	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47037989	G	T	47037989	3	4	122	1	0	0	0	0	1	0	0	0	10198	1232	43	3	2442	3	NBEAL2	3	47037989	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10		47037989	150984441	29	20438										
CSPG5	10675	hgsc.bcm.edu	37	chr3	47618819	47618819	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	agggtggttctctgaggttcCtggtgaccctgggaagctcc	15	10	1	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr3:47618819C>G	ENST00000383738.2	-	2	2795	c.697G>C	c.(697-699)Gga>Cga	p.G233R	CSPG5_ENST00000465441.1_5'Flank|CSPG5_ENST00000264723.4_Missense_Mutation_p.G233R|CSPG5_ENST00000456150.1_Missense_Mutation_p.G95R	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	233					axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		TCTGAGGTTCCTGGTGACCCT	0.537																																					p.G233R		Atlas-SNP	.											.	CSPG5	46	.	0			c.G697C						.						39	40	40					3																	47618819		2203	4300	6503	SO:0001583	missense	10675	exon2			AGGTTCCTGGTGA	AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.697G>C	chr3.hg19:g.47618819C>G	ENSP00000373244:p.Gly233Arg	67.0	0.0		85.0	26.0	NM_006574	Q71M39|Q71M40	Missense_Mutation	SNP	ENST00000383738.2	hg19	CCDS56253.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.679601	0.88542	.	.	ENSG00000114646	ENST00000456150;ENST00000383738;ENST00000264723	T;T;T	0.65178	-0.14;-0.14;-0.14	4.24	4.24	0.50183	Chondroitin sulphate attachment (1);	0.448932	0.22705	N	0.056653	T	0.67258	0.2874	L	0.27053	0.805	0.38227	D	0.94092	D;D	0.64830	0.994;0.993	D;P	0.65987	0.94;0.9	T	0.73471	-0.3972	10	0.62326	D	0.03	-8.3803	15.7135	0.77649	0.0:1.0:0.0:0.0	.	233;233	O95196;O95196-2	CSPG5_HUMAN;.	R	95;233;233	ENSP00000392096:G95R;ENSP00000373244:G233R;ENSP00000264723:G233R	ENSP00000264723:G233R	G	-	1	0	CSPG5	47593823	0.745000	0.28261	1.000000	0.80357	0.999000	0.98932	3.081000	0.50120	2.349000	0.79799	0.643000	0.83706	GGA	.	.		0.537	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574		G	47618819	C	G	47618819	3	3	122	1	0	0	0	0	1	0	0	0	3963	690	24	4	938	4	CSPG5	3	47618819	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	580830	47618819	150403611	30	20439										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78666831	78666831	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gctactttcagaccagcataCtctgccgctgctgcgactgc	9	15	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr3:78666831C>A	ENST00000464233.1	-	27	4349	c.4236G>T	c.(4234-4236)gaG>gaT	p.E1412D	ROBO1_ENST00000467549.1_Missense_Mutation_p.E1312D|ROBO1_ENST00000436010.2_Missense_Mutation_p.E1373D|ROBO1_ENST00000495273.1_Missense_Mutation_p.E1367D	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1412					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GACCAGCATACTCTGCCGCTG	0.502																																					p.E1412D		Atlas-SNP	.											.	ROBO1	833	.	0			c.G4236T						.						65	67	67					3																	78666831		1973	4153	6126	SO:0001583	missense	6091	exon27			AGCATACTCTGCC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.4236G>T	chr3.hg19:g.78666831C>A	ENSP00000420321:p.Glu1412Asp	73.0	0.0		88.0	28.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	5.179	0.218599	0.09810	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.59638	0.32;0.3;0.28;0.25	5.68	2.47	0.30058	.	0.000000	0.85682	D	0.000000	T	0.51975	0.1706	N	0.12746	0.255	0.43777	D	0.996307	D;B;B;B;B	0.61697	0.99;0.013;0.001;0.021;0.023	D;B;B;B;B	0.73380	0.98;0.003;0.001;0.013;0.012	T	0.46034	-0.9220	9	.	.	.	.	7.4685	0.27334	0.0:0.5483:0.0:0.4517	.	1376;1412;1367;1312;1373	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	D	1373;1367;1412;1367;1312;1416	ENSP00000406043:E1373D;ENSP00000420321:E1412D;ENSP00000420637:E1367D;ENSP00000417992:E1312D	.	E	-	3	2	ROBO1	78749521	1.000000	0.71417	1.000000	0.80357	0.065000	0.16274	1.482000	0.35486	0.880000	0.35969	0.591000	0.81541	GAG	.	.		0.502	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78666831	C	A	78666831	3	1	122	1	0	0	0	0	1	0	0	0	13528	564	20	3	739	3	ROBO1	3	78666831	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	31048012	78666831	119355599	31	20440										
CEP97	79598	hgsc.bcm.edu	37	chr3	101445524	101445524	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	atattcacactttgattctgGataaaaatcagattattaaa	4	5	3	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr3:101445524G>T	ENST00000341893.3	+	2	882	c.130G>T	c.(130-132)Gat>Tat	p.D44Y	CEP97_ENST00000494050.1_Missense_Mutation_p.D44Y|CEP97_ENST00000327230.4_Missense_Mutation_p.D44Y			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	44					cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						TTTGATTCTGGATAAAAATCA	0.353																																					p.D44Y		Atlas-SNP	.											.	CEP97	122	.	0			c.G130T						.						67	69	68					3																	101445524		2203	4300	6503	SO:0001583	missense	79598	exon2			ATTCTGGATAAAA	AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504			26244	protein-coding gene	gene with protein product		615864	"leucine-rich repeats and IQ motif containing 2"	LRRIQ2		17719545, 18068367	Standard	NM_024548		Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.130G>T	chr3.hg19:g.101445524G>T	ENSP00000342510:p.Asp44Tyr	61.0	0.0		77.0	18.0	NM_024548	B5MDY8|Q8NA71|Q9H5T9	Missense_Mutation	SNP	ENST00000341893.3	hg19	CCDS2944.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.094659	0.76870	.	.	ENSG00000182504	ENST00000341893;ENST00000327230;ENST00000494050	T;T;T	0.25579	1.79;1.79;2.22	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.39489	0.1080	N	0.21617	0.685	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.997	T	0.41592	-0.9500	10	0.87932	D	0	-20.1694	18.2947	0.90141	0.0:0.0:1.0:0.0	.	44;44;44	E9PG22;Q8IW35-2;Q8IW35	.;.;CEP97_HUMAN	Y	44	ENSP00000342510:D44Y;ENSP00000325881:D44Y;ENSP00000418185:D44Y	ENSP00000325881:D44Y	D	+	1	0	CEP97	102928214	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.514000	0.90545	2.379000	0.81126	0.655000	0.94253	GAT	.	.		0.353	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548		T	101445524	G	T	101445524	3	4	122	1	0	0	0	0	1	0	0	0	3265	1174	41	3	136	3	CEP97	3	101445524	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	22778693	101445524	96576906	32	20441										
IL20RB	53833	hgsc.bcm.edu	37	chr3	136708320	136708320	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gggatggagatcaccaaagaTggcttccacctggttattga	12	8	1	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr3:136708320T>C	ENST00000329582.4	+	4	693	c.444T>C	c.(442-444)gaT>gaC	p.D148D	IL20RB_ENST00000309741.5_Silent_p.D101D|IL20RB_ENST00000484501.1_3'UTR	NM_144717.3	NP_653318.2	Q6UXL0	I20RB_HUMAN	interleukin 20 receptor beta	148	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homeostasis of number of cells within a tissue (GO:0048873)|immune response-inhibiting signal transduction (GO:0002765)|inflammatory response to antigenic stimulus (GO:0002437)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of type IV hypersensitivity (GO:0001808)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-4 production (GO:0032753)	integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14						TCACCAAAGATGGCTTCCACC	0.577																																					p.D148D		Atlas-SNP	.											.	IL20RB	52	.	0			c.T444C						.						87	82	84					3																	136708320		2203	4300	6503	SO:0001819	synonymous_variant	53833	exon4			CAAAGATGGCTTC	BC033292	CCDS3093.1	3q22.3	2013-02-11			ENSG00000174564	ENSG00000174564		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	6004	protein-coding gene	gene with protein product		605621	"fibronectin type III domain containing 6"	FNDC6		11163236, 16703417	Standard	NM_144717		Approved	DIRS1, IL-20R2, MGC34923	uc003eri.2	Q6UXL0	OTTHUMG00000159779	ENST00000329582.4:c.444T>C	chr3.hg19:g.136708320T>C		49.0	0.0		48.0	14.0	NM_144717	B4DL40|Q6P438|Q8IYY5|Q8TAJ7	Silent	SNP	ENST00000329582.4	hg19	CCDS3093.1																																																																																			.	.		0.577	IL20RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357277.2	NM_144717		C	136708320	T	C	136708320	2	2	122	1	0	0	0	0	0	0	0	1	7678	1461	51	2		2	IL20RB	3	136708320	Silent	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	35262796	136708320	61314110	33	20442										
ATR	545	hgsc.bcm.edu	37	chr3	142275233	142275233	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cttagtacatacataagaatCttgggaactctgttacaaga	7	7	2	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr3:142275233C>G	ENST00000350721.4	-	9	2191	c.2070G>C	c.(2068-2070)aaG>aaC	p.K690N	ATR_ENST00000383101.3_Missense_Mutation_p.K626N	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	690					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.K690K(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						ACATAAGAATCTTGGGAACTC	0.368								Other conserved DNA damage response genes																													p.K690N		Atlas-SNP	.											ATR,pharynx,carcinoma,0,1	ATR	285	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.G2070C						.						55	61	59					3																	142275233		2203	4300	6503	SO:0001583	missense	545	exon9			AAGAATCTTGGGA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.2070G>C	chr3.hg19:g.142275233C>G	ENSP00000343741:p.Lys690Asn	146.0	0.0		134.0	43.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	11.70	1.715878	0.30413	.	.	ENSG00000175054	ENST00000350721;ENST00000383101;ENST00000515149	T;T	0.67171	-0.25;-0.25	5.31	4.44	0.53790	Armadillo-like helical (1);Armadillo-type fold (1);	0.175884	0.49305	D	0.000143	T	0.49287	0.1548	L	0.27053	0.805	0.27898	N	0.939099	P	0.38922	0.651	B	0.32677	0.15	T	0.50013	-0.8877	10	0.49607	T	0.09	-3.9732	10.891	0.46996	0.0:0.7998:0.0:0.2002	.	690	Q13535	ATR_HUMAN	N	690;626;307	ENSP00000343741:K690N;ENSP00000372581:K626N	ENSP00000343741:K690N	K	-	3	2	ATR	143757923	1.000000	0.71417	1.000000	0.80357	0.660000	0.38997	0.970000	0.29383	1.382000	0.46385	0.585000	0.79938	AAG	.	.		0.368	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		G	142275233	C	G	142275233	3	3	122	1	0	0	0	0	1	0	0	0	1204	912	32	4	6020	4	ATR	3	142275233	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	5566913	142275233	55747197	34	20443										
RSRC1	51319	hgsc.bcm.edu	37	chr3	157920990	157920990	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	aaagagaaaagagaaaaggaGaaggataaagggaaggacaa	14	1	0	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr3:157920990G>A	ENST00000295930.3	+	4	612	c.450G>A	c.(448-450)gaG>gaA	p.E150E	RSRC1_ENST00000312179.6_Intron|RSRC1_ENST00000496268.1_3'UTR|RSRC1_ENST00000464171.1_Intron|RSRC1_ENST00000480820.1_Silent_p.E150E|RSRC1_ENST00000475278.2_Silent_p.E150E	NM_001271838.1|NM_016625.2	NP_001258767.1|NP_057709.2	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1	150				EK -> GE (in Ref. 3; AAF64267). {ECO:0000305}.	mRNA splicing, via spliceosome (GO:0000398)|nucleocytoplasmic transport (GO:0006913)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)				cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	18			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			gagaaaaggagaaggataaag	0.443																																					p.E150E		Atlas-SNP	.											.	RSRC1	44	.	0			c.G450A						.						116	123	120					3																	157920990		2203	4300	6503	SO:0001819	synonymous_variant	51319	exon4			AAAGGAGAAGGAT	AF208853	CCDS3181.1, CCDS63822.1	3q25.32	2009-09-09			ENSG00000174891	ENSG00000174891			24152	protein-coding gene	gene with protein product	"splicing factor, arginine/serine-rich 21"	613352				15798186, 19065146	Standard	NM_001271838		Approved	MGC12197, BM-011, SRrp53, SFRS21	uc003fbu.2	Q96IZ7	OTTHUMG00000158758	ENST00000295930.3:c.450G>A	chr3.hg19:g.157920990G>A		167.0	0.0		169.0	72.0	NM_016625	A8K2R9|Q96QK2|Q9NZE5	Silent	SNP	ENST00000295930.3	hg19	CCDS3181.1	.	.	.	.	.	.	.	.	.	.	G	4.038	0.004569	0.07866	.	.	ENSG00000174891	ENST00000482822	.	.	.	4.81	2.9	0.33743	.	0.264345	0.39083	N	0.001461	T	0.63803	0.2542	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63346	-0.6658	6	0.72032	D	0.01	.	8.5618	0.33516	0.2745:0.0:0.7255:0.0	.	.	.	.	K	44	.	ENSP00000420464:E44K	E	+	1	0	RSRC1	159403684	1.000000	0.71417	1.000000	0.80357	0.471000	0.32888	1.315000	0.33608	0.484000	0.27630	-0.229000	0.12294	GAA	.	.		0.443	RSRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352063.2	NM_016625		A	157920990	G	A	157920990	2	1	122	1	0	0	0	0	0	0	0	1	13729	933	33	3		3	RSRC1	3	157920990	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	15645757	157920990	40101440	35	20444										
TBCCD1	55171	hgsc.bcm.edu	37	chr3	186281901	186281901	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	caaatatttcgaagtaaagcCacgccaggtccttggccaac	8	12	0	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr3:186281901C>A	ENST00000424280.1	-	2	697	c.218G>T	c.(217-219)tGg>tTg	p.W73L	TBCCD1_ENST00000446782.1_Intron|TBCCD1_ENST00000338733.5_Missense_Mutation_p.W73L	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	73					cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		GAAGTAAAGCCACGCCAGGTC	0.527																																					p.W73L		Atlas-SNP	.											.	TBCCD1	42	.	0			c.G218T						.						68	64	66					3																	186281901		2203	4300	6503	SO:0001583	missense	55171	exon2			TAAAGCCACGCCA	BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.218G>T	chr3.hg19:g.186281901C>A	ENSP00000411253:p.Trp73Leu	51.0	0.0		61.0	24.0	NM_001134415	B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	hg19	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890300	0.91889	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000413695;ENST00000430560	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.66963	0.2843	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.69789	-0.5050	10	0.72032	D	0.01	-7.4769	17.2023	0.86909	0.0:1.0:0.0:0.0	.	73	Q9NVR7	TBCC1_HUMAN	L	73	ENSP00000411253:W73L;ENSP00000341652:W73L;ENSP00000391109:W73L;ENSP00000407506:W73L	ENSP00000341652:W73L	W	-	2	0	TBCCD1	187764595	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	7.336000	0.79245	2.663000	0.90544	0.561000	0.74099	TGG	.	.		0.527	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138		A	186281901	C	A	186281901	3	1	122	1	0	0	0	0	1	0	0	0	15647	595	21	3	1479	3	TBCCD1	3	186281901	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	28360911	186281901	11740529	36	20445										
TMEM128	85013	hgsc.bcm.edu	37	chr4	4248025	4248025	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	agaatccagaatggatattaAgtcttggaagaggtttctcc	10	6	2	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr4:4248025A>C	ENST00000382753.4	-	2	152	c.143T>G	c.(142-144)cTt>cGt	p.L48R	TMEM128_ENST00000254742.2_Missense_Mutation_p.L24R|TMEM128_ENST00000540397.1_Missense_Mutation_p.L48R|TMEM128_ENST00000538516.1_Missense_Mutation_p.L48R			Q5BJH2	TM128_HUMAN	transmembrane protein 128	48						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)		ATGGATATTAAGTCTTGGAAG	0.363																																					p.L24R		Atlas-SNP	.											.	TMEM128	12	.	0			c.T71G						.						126	135	132					4																	4248025		2203	4300	6503	SO:0001583	missense	85013	exon2			ATATTAAGTCTTG	BC007729	CCDS3373.1, CCDS75099.1	4p16.3	2008-02-05			ENSG00000132406	ENSG00000132406			28201	protein-coding gene	gene with protein product							Standard	XM_005248034		Approved	MGC13159	uc003ghq.1	Q5BJH2	OTTHUMG00000125475	ENST00000382753.4:c.143T>G	chr4.hg19:g.4248025A>C	ENSP00000372201:p.Leu48Arg	137.0	0.0		164.0	40.0	NM_032927	B4DHS7|D3DVS3|Q5H9U6|Q96I94	Missense_Mutation	SNP	ENST00000382753.4	hg19		.	.	.	.	.	.	.	.	.	.	A	21.7	4.184129	0.78677	.	.	ENSG00000132406	ENST00000254742;ENST00000382753;ENST00000538516;ENST00000540397	D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6	5.83	4.65	0.58169	.	0.118143	0.56097	D	0.000022	D	0.88481	0.6448	M	0.64997	1.995	0.43527	D	0.995809	D;D;D;D	0.76494	0.999;0.999;0.999;0.998	D;D;D;D	0.73380	0.98;0.961;0.961;0.93	D	0.88548	0.3114	10	0.87932	D	0	-32.5488	10.9313	0.47220	0.9258:0.0:0.0742:0.0	.	48;48;48;24	B7Z3K1;Q5BJH2;D3DVS1;Q5BJH2-2	.;TM128_HUMAN;.;.	R	24;48;48;48	ENSP00000254742:L24R;ENSP00000372201:L48R;ENSP00000442300:L48R;ENSP00000439174:L48R	ENSP00000254742:L24R	L	-	2	0	TMEM128	4298926	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.348000	0.79366	1.043000	0.40175	0.533000	0.62120	CTT	.	.		0.363	TMEM128-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000246798.2	NM_032927		C	4248025	A	C	4248025	3	2	122	1	0	0	0	0	1	0	0	0	16056	72	3	5	366	5	TMEM128	4	4248025	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10		4248025	186906251	37	20446										
CPZ	8532	hgsc.bcm.edu	37	chr4	8621092	8621092	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	aagaaagtcatcatccccgcCcggatgaagagggctggccg	13	12	2	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr4:8621092C>T	ENST00000360986.4	+	11	1881	c.1707C>T	c.(1705-1707)gcC>gcT	p.A569A	CPZ_ENST00000429646.2_Silent_p.A177A|CPZ_ENST00000382480.2_Silent_p.A432A|CPZ_ENST00000315782.6_Silent_p.A558A	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	569					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TCATCCCCGCCCGGATGAAGA	0.577																																					p.A569A		Atlas-SNP	.											.	CPZ	95	.	0			c.C1707T						.						51	45	47					4																	8621092		2203	4300	6503	SO:0001819	synonymous_variant	8532	exon11			CCCCGCCCGGATG	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.1707C>T	chr4.hg19:g.8621092C>T		172.0	0.0		193.0	76.0	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	hg19	CCDS33953.1																																																																																			.	.		0.577	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		T	8621092	C	T	8621092	2	4	122	1	0	0	0	0	0	0	0	1	3841	610	22	3		3	CPZ	4	8621092	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	4373067	8621092	182533184	38	20447										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20535249	20535249	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gagggagcatttgaaggagcAtctggtgtaaatgaaatact	13	4	1	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr4:20535249A>G	ENST00000504154.1	+	18	1995	c.1743A>G	c.(1741-1743)gcA>gcG	p.A581A	SLIT2_ENST00000273739.5_Silent_p.A585A|SLIT2_ENST00000503823.1_Silent_p.A573A|SLIT2_ENST00000503837.1_Silent_p.A577A	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	581					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						TTGAAGGAGCATCTGGTGTAA	0.323																																					p.A581A		Atlas-SNP	.											.	SLIT2	290	.	0			c.A1743G						.						129	130	130					4																	20535249		2203	4300	6503	SO:0001819	synonymous_variant	9353	exon18			AGGAGCATCTGGT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1743A>G	chr4.hg19:g.20535249A>G		449.0	0.0		505.0	188.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	hg19	CCDS3426.1																																																																																			.	.		0.323	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			G	20535249	A	G	20535249	2	3	122	1	0	0	0	0	0	0	0	1	14755	204	8	2		2	SLIT2	4	20535249	Silent	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	11914157	20535249	170619027	39	20448										
YIPF7	285525	hgsc.bcm.edu	37	chr4	44637980	44637980	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	catcaaaactgtcaatgtaaGgagattgtgaataataatct	7	5	3	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr4:44637980G>A	ENST00000332990.5	-	3	327	c.311C>T	c.(310-312)cCt>cTt	p.P104L	YIPF7_ENST00000415895.4_Missense_Mutation_p.P80L	NM_182592.2	NP_872398.2	Q8N8F6	YIPF7_HUMAN	Yip1 domain family, member 7	104						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(1)	12						GTCAATGTAAGGAGATTGTGA	0.388																																					p.P104L		Atlas-SNP	.											.	YIPF7	33	.	0			c.C311T						.						91	91	91					4																	44637980		1891	4129	6020	SO:0001583	missense	285525	exon3			ATGTAAGGAGATT	AK096895	CCDS54766.1	4p13	2008-08-07			ENSG00000177752	ENSG00000177752		"Yip1 domain family"	26825	protein-coding gene	gene with protein product							Standard	NM_182592		Approved	FLJ39576, FinGER9	uc021xnx.1	Q8N8F6	OTTHUMG00000160467	ENST00000332990.5:c.311C>T	chr4.hg19:g.44637980G>A	ENSP00000332772:p.Pro104Leu	98.0	0.0		140.0	8.0	NM_182592	Q3SY21|Q3SY22	Missense_Mutation	SNP	ENST00000332990.5	hg19	CCDS54766.1	.	.	.	.	.	.	.	.	.	.	G	10.46	1.356240	0.24598	.	.	ENSG00000177752	ENST00000332990	T	0.29397	1.57	5.02	5.02	0.67125	.	1.160480	0.06060	N	0.658135	T	0.26955	0.0660	L	0.38175	1.15	0.29390	N	0.862661	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.002	T	0.09079	-1.0691	10	0.27082	T	0.32	-9.1028	8.7405	0.34554	0.0:0.1741:0.6682:0.1576	.	104;104	Q8N8F6-4;Q8N8F6	.;YIPF7_HUMAN	L	104	ENSP00000332772:P104L	ENSP00000332772:P104L	P	-	2	0	YIPF7	44332737	0.990000	0.36364	0.751000	0.31187	0.868000	0.49771	2.478000	0.45189	2.636000	0.89361	0.650000	0.86243	CCT	.	.		0.388	YIPF7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_182592		A	44637980	G	A	44637980	3	1	122	1	0	0	0	0	1	0	0	0	17498	1000	35	3	547	3	YIPF7	4	44637980	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	24102731	44637980	146516296	40	20449										
DCK	1633	hgsc.bcm.edu	37	chr4	71889378	71889378	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	atgaataaccaatttggccaAagccttgaattggatggaat	9	6	0	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr4:71889378A>G	ENST00000286648.5	+	4	901	c.504A>G	c.(502-504)caA>caG	p.Q168Q	DCK_ENST00000504952.1_Silent_p.Q168Q|DCK_ENST00000504730.1_Silent_p.Q168Q	NM_000788.2	NP_000779.1	P27707	DCK_HUMAN	deoxycytidine kinase	168					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxycytidine kinase activity (GO:0004137)|drug binding (GO:0008144)|nucleoside kinase activity (GO:0019206)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)	9			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Cytarabine(DB00987)|Decitabine(DB01262)|Emtricitabine(DB00879)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Lamivudine(DB00709)|Nelarabine(DB01280)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	AATTTGGCCAAAGCCTTGAAT	0.333																																					p.Q168Q		Atlas-SNP	.											.	DCK	23	.	0			c.A504G						.						82	85	84					4																	71889378		2203	4300	6503	SO:0001819	synonymous_variant	1633	exon4			TGGCCAAAGCCTT	M60527	CCDS3548.1	4q13.3-q21.1	2008-02-05			ENSG00000156136	ENSG00000156136	2.7.1.74		2704	protein-coding gene	gene with protein product		125450				8406512	Standard	NM_000788		Approved		uc003hfx.3	P27707	OTTHUMG00000129908	ENST00000286648.5:c.504A>G	chr4.hg19:g.71889378A>G		170.0	0.0		229.0	22.0	NM_000788	B2R8V6|Q5TZY7|Q6FI11	Silent	SNP	ENST00000286648.5	hg19	CCDS3548.1																																																																																			.	.		0.333	DCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252159.2			G	71889378	A	G	71889378	2	3	122	1	0	0	0	0	0	0	0	1	4292	11	1	2		2	DCK	4	71889378	Silent	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	27251398	71889378	119264898	41	20450										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	73990739	73990739	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	atatttccacaacaccaacaTgaccagctgtggcagccaag	7	13	0	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr4:73990739T>C	ENST00000358602.4	-	18	3499	c.3383A>G	c.(3382-3384)cAt>cGt	p.H1128R	ANKRD17_ENST00000330838.6_Missense_Mutation_p.H877R|ANKRD17_ENST00000509867.2_Missense_Mutation_p.H1015R|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1128					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AACACCAACATGACCAGCTGT	0.448																																					p.H1128R		Atlas-SNP	.											.	ANKRD17	214	.	0			c.A3383G						.						124	116	119					4																	73990739		2203	4300	6503	SO:0001583	missense	26057	exon18			CCAACATGACCAG	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.3383A>G	chr4.hg19:g.73990739T>C	ENSP00000351416:p.His1128Arg	114.0	0.0		115.0	43.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	hg19	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.667967	0.88348	.	.	ENSG00000132466	ENST00000358602;ENST00000330838;ENST00000509867;ENST00000411811	T;T;T	0.64803	-0.12;-0.12;-0.12	5.65	5.65	0.86999	Ankyrin repeat-containing domain (3);	0.000000	0.64402	D	0.000001	T	0.64034	0.2562	N	0.11131	0.1	0.53688	D	0.999976	D;D;D;D;D	0.67145	0.996;0.981;0.989;0.985;0.993	D;P;D;P;P	0.75020	0.979;0.854;0.985;0.657;0.867	T	0.72121	-0.4386	10	0.72032	D	0.01	.	15.8728	0.79136	0.0:0.0:0.0:1.0	.	649;1127;877;1128;1015	B4DR08;O75179-2;G5E964;O75179;E7EUV3	.;.;.;ANR17_HUMAN;.	R	1128;877;1015;1128	ENSP00000351416:H1128R;ENSP00000332265:H877R;ENSP00000427151:H1015R	ENSP00000332265:H877R	H	-	2	0	ANKRD17	74209603	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.036000	0.88901	2.143000	0.66587	0.477000	0.44152	CAT	.	.		0.448	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		C	73990739	T	C	73990739	3	2	122	1	0	0	0	0	1	0	0	0	646	1464	51	2	4496	2	ANKRD17	4	73990739	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	2101361	73990739	117163537	42	20451										
ANKRD56	345079	hgsc.bcm.edu	37	chr4	77817627	77817684	+	Frame_Shift_Del	DEL	CTGAGACCCTGAGGGCTCCGGCTGGGGCTGCCCTCCTTCCGAGATACAGAAAGGCCCC	CTGAGACCCTGAGGGCTCCGGCTGGGGCTGCCCTCCTTCCGAGATACAGAAAGGCCCC	-													0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgtgaccatcccctctgtttCtgagaccctgagggctccgg					rs144168746|rs140504486|rs370963563|rs375778128	byFrequency	TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	CTGAGACCCTGAGGGCTCCGGCTGGGGCTGCCCTCCTTCCGAGATACAGAAAGGCCCC	CTGAGACCCTGAGGGCTCCGGCTGGGGCTGCCCTCCTTCCGAGATACAGAAAGGCCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr4:77817627_77817684delCTGAGACCCTGAGGGCTCCGGCTGGGGCTGCCCTCCTTCCGAGATACAGAAAGGCCCC	ENST00000334306.2	-	1	1318_1375	c.1319_1376delGGGGCCTTTCTGTATCTCGGAAGGAGGGCAGCCCCAGCCGGAGCCCTCAGGGTCTCAG	c.(1318-1377)gggggcctttctgtatctcggaaggagggcagccccagccggagccctcagggtctcagafs	p.GGLSVSRKEGSPSRSPQGLR440fs		NM_001029870.1	NP_001025041.1	A6NEL2	SWAHB_HUMAN	sosondowah ankyrin repeat domain family member B	440								p.S450N(1)									CCCTCTGTTTCTGAGACCCTGAGGGCTCCGGCTGGGGCTGCCCTCCTTCCGAGATACAGAAAGGCCCCCAGCTGGATT	0.612																																					p.440_459del		Pindel	.											.	.	.	.	1	Substitution - Missense(1)	skin(1)	c.1320_1377del						.																																			SO:0001589	frameshift_variant	345079	exon1			.		CCDS34017.1	4q21.1	2013-01-10	2012-01-12	2012-01-12	ENSG00000186212	ENSG00000186212		"Ankyrin repeat domain containing"	32958	protein-coding gene	gene with protein product			"ankyrin repeat domain 56"	ANKRD56		22234889	Standard	NM_001029870		Approved		uc003hki.3	A6NEL2	OTTHUMG00000160876	ENST00000334306.2:c.1319_1376delGGGGCCTTTCTGTATCTCGGAAGGAGGGCAGCCCCAGCCGGAGCCCTCAGGGTCTCAG	chr4.hg19:g.77817627_77817684delCTGAGACCCTGAGGGCTCCGGCTGGGGCTGCCCTCCTTCCGAGATACAGAAAGGCCCC	ENSP00000334879:p.Gly440fs	45.0	0.0		45.0	15.0	NM_001029870	B2RP29	Frame_Shift_Del	DEL	ENST00000334306.2	hg19	CCDS34017.1																																																																																			.	.		0.612	SOWAHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362762.1	NM_001029870		-	77817684	CTGAGACCCTGAGGGCTCCGGCTGGGGCTGCCCTCCTTCCGAGATACAGAAAGGCCCC	-	77817627	7	5	122	1	0	1	0	1	0	0	0	0	682	913	32	0	1009	0	ANKRD56	4	77817627	Frame_Shift_Del	DEL	CTGAGACCCTGAGGGCTCCGGCTGGGGCTGCCCTCCTTCCGAGATACAGAAAGGCCCC	TCGA-DD-A3A8-01A-11D-A22F-10	3826888	77817627	113336649	43	20452										
BMP2K	55589	hgsc.bcm.edu	37	chr4	79832589	79832589	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgtgccctttgatgaaataaCggggagccagcagcaaaaag	12	8	0	2	rs370861712		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr4:79832589C>T	ENST00000335016.5	+	16	3054	c.2888C>T	c.(2887-2889)aCg>aTg	p.T963M	PAQR3_ENST00000295462.3_Intron	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	963					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)	p.T963M(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						GATGAAATAACGGGGAGCCAG	0.473													C|||	1	0.000199681	8e-04	0	5008	,	,		20763	0		0	False		,,,				2504	0				p.T963M		Atlas-SNP	.											BMP2K_ENST00000335016,colon,carcinoma,0,1	BMP2K	169	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2888T						.	C	MET/THR	2,3784		0,2,1891	60	57	58		2888	5.4	1	4		58	0,8216		0,0,4108	no	missense	BMP2K	NM_198892.1	81	0,2,5999	TT,TC,CC		0.0,0.0528,0.0167	probably-damaging	963/1162	79832589	2,12000	1893	4108	6001	SO:0001583	missense	55589	exon16			AAATAACGGGGAG	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.2888C>T	chr4.hg19:g.79832589C>T	ENSP00000334836:p.Thr963Met	239.0	0.0		289.0	27.0	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	hg19	CCDS47083.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.744393	0.30865	5.28E-4	0.0	ENSG00000138756	ENST00000335016	T	0.74526	-0.85	5.41	5.41	0.78517	.	0.491893	0.18079	N	0.152346	D	0.82742	0.5103	L	0.57536	1.79	0.80722	D	1	D	0.76494	0.999	P	0.57720	0.826	D	0.84158	0.0427	10	0.87932	D	0	-9.8261	19.1973	0.93695	0.0:1.0:0.0:0.0	.	963	Q9NSY1	BMP2K_HUMAN	M	963	ENSP00000334836:T963M	ENSP00000334836:T963M	T	+	2	0	BMP2K	80051613	0.786000	0.28738	0.978000	0.43139	0.556000	0.35491	3.212000	0.51145	2.538000	0.85594	0.484000	0.47621	ACG	.	.		0.473	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		T	79832589	C	T	79832589	3	4	122	1	0	0	0	0	1	0	0	0	1460	536	19	1	2988	1	BMP2K	4	79832589	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	2014962	79832589	111321687	44	20453										
NDST4	64579	hgsc.bcm.edu	37	chr4	115792014	115792014	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gtttgcaatttcaggttggtCcagctctgcacaaagttgac	10	9	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr4:115792014C>T	ENST00000264363.2	-	7	2307	c.1629G>A	c.(1627-1629)tgG>tgA	p.W543*		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	543	Heparan sulfate N-deacetylase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		TCAGGTTGGTCCAGCTCTGCA	0.443																																					p.W543X		Atlas-SNP	.											.	NDST4	193	.	0			c.G1629A						.						103	112	109					4																	115792014		2203	4299	6502	SO:0001587	stop_gained	64579	exon7			GTTGGTCCAGCTC	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.1629G>A	chr4.hg19:g.115792014C>T	ENSP00000264363:p.Trp543*	201.0	0.0		234.0	22.0	NM_022569	Q2KHM8	Nonsense_Mutation	SNP	ENST00000264363.2	hg19	CCDS3706.1	.	.	.	.	.	.	.	.	.	.	C	39	7.604733	0.98384	.	.	ENSG00000138653	ENST00000264363	.	.	.	5.1	4.25	0.50352	.	0.124042	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1467	0.42769	0.0:0.7858:0.1381:0.0761	.	.	.	.	X	543	.	ENSP00000264363:W543X	W	-	3	0	NDST4	116011463	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.168000	0.50801	2.362000	0.80069	0.561000	0.74099	TGG	.	.		0.443	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		T	115792014	C	T	115792014	4	4	122	1	0	0	0	0	0	1	0	0	10267	856	30	3	1021	3	NDST4	4	115792014	Nonsense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	35959425	115792014	75362262	45	20454										
NR3C2	4306	hgsc.bcm.edu	37	chr4	149002507	149002507	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gcgggcagtcacttccggtgGaagtagagcggcttggcgtt	17	9	1	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr4:149002507G>C	ENST00000358102.3	-	9	3305	c.2943C>G	c.(2941-2943)ttC>ttG	p.F981L	NR3C2_ENST00000355292.3_Missense_Mutation_p.F985L|NR3C2_ENST00000512865.1_Missense_Mutation_p.F864L|NR3C2_ENST00000344721.4_Missense_Mutation_p.F981L|NR3C2_ENST00000511528.1_Missense_Mutation_p.F985L	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	981	Steroid-binding.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	ACTTCCGGTGGAAGTAGAGCG	0.547																																					p.F981L	Melanoma(27;428 957 40335 51025 51111)	Atlas-SNP	.											.	NR3C2	94	.	0			c.C2943G						.						58	55	56					4																	149002507		2203	4300	6503	SO:0001583	missense	4306	exon9			CCGGTGGAAGTAG	M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.2943C>G	chr4.hg19:g.149002507G>C	ENSP00000350815:p.Phe981Leu	78.0	0.0		95.0	15.0	NM_000901	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Missense_Mutation	SNP	ENST00000358102.3	hg19	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.889536	0.52014	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000511528	D;D;D;D;D	0.95447	-3.71;-3.71;-3.71;-3.71;-3.71	5.63	-7.81	0.01210	.	0.000000	0.85682	D	0.000000	D	0.97005	0.9022	M	0.86651	2.83	0.46241	D	0.998942	D;D	0.69078	0.988;0.997	D;D	0.68943	0.936;0.961	D	0.96159	0.9114	9	.	.	.	.	18.4928	0.90853	0.3945:0.0:0.6055:0.0	.	864;981	B0ZBF5;B0ZBF6	.;.	L	981;985;981;864;985	ENSP00000341390:F981L;ENSP00000347441:F985L;ENSP00000350815:F981L;ENSP00000423510:F864L;ENSP00000421481:F985L	.	F	-	3	2	NR3C2	149221957	0.998000	0.40836	0.861000	0.33841	0.170000	0.22686	0.746000	0.26275	-1.513000	0.01789	-0.157000	0.13467	TTC	.	.		0.547	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			C	149002507	G	C	149002507	3	2	122	1	0	0	0	0	1	0	0	0	10640	1165	41	4	15	4	NR3C2	4	149002507	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	33210493	149002507	42151769	46	20455										
ESM1	11082	hgsc.bcm.edu	37	chr5	54281083	54281083	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cttcaccaaaaggatcctccCcattagaaggctgacacctc	6	15	1	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr5:54281083C>A	ENST00000381405.4	-	1	408	c.263G>T	c.(262-264)gGg>gTg	p.G88V	ESM1_ENST00000381403.4_Missense_Mutation_p.G88V|ESM1_ENST00000598310.1_Intron	NM_007036.4	NP_008967.1	Q9NQ30	ESM1_HUMAN	endothelial cell-specific molecule 1	88	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				angiogenesis (GO:0001525)|positive regulation of cell proliferation (GO:0008284)|positive regulation of hepatocyte growth factor receptor signaling pathway (GO:1902204)|regulation of cell growth (GO:0001558)|sprouting angiogenesis (GO:0002040)	extracellular region (GO:0005576)	hepatocyte growth factor receptor binding (GO:0005171)|integrin binding (GO:0005178)			breast(1)|kidney(1)|large_intestine(4)|lung(4)	10		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.116)	Lung(15;0.23)			AGGATCCTCCCCATTAGAAGG	0.572																																					p.G88V		Atlas-SNP	.											.	ESM1	27	.	0			c.G263T						.						97	98	98					5																	54281083		2203	4300	6503	SO:0001583	missense	11082	exon1			TCCTCCCCATTAG	X89426	CCDS3963.1, CCDS47206.1	5q11	2008-02-05			ENSG00000164283	ENSG00000164283			3466	protein-coding gene	gene with protein product		601521				8702785	Standard	NM_001135604		Approved		uc003jpk.3	Q9NQ30	OTTHUMG00000097010	ENST00000381405.4:c.263G>T	chr5.hg19:g.54281083C>A	ENSP00000370812:p.Gly88Val	79.0	0.0		85.0	16.0	NM_001135604	B2R4G3|Q15330|Q3V4E3|Q96ES3	Missense_Mutation	SNP	ENST00000381405.4	hg19	CCDS3963.1	.	.	.	.	.	.	.	.	.	.	C	11.96	1.793817	0.31777	.	.	ENSG00000164283	ENST00000381405;ENST00000381403	T;T	0.66638	-0.22;-0.22	5.56	3.08	0.35506	Insulin-like growth factor-binding protein, IGFBP (2);	0.392618	0.27563	N	0.018808	T	0.58148	0.2102	M	0.61703	1.905	0.48341	D	0.999633	B;B	0.23442	0.029;0.085	B;B	0.19666	0.016;0.026	T	0.54029	-0.8354	10	0.35671	T	0.21	-11.6547	6.8558	0.24040	0.1337:0.0759:0.0:0.7904	.	88;88	Q3V4E3;Q9NQ30	.;ESM1_HUMAN	V	88	ENSP00000370812:G88V;ENSP00000370810:G88V	ENSP00000370810:G88V	G	-	2	0	ESM1	54316840	1.000000	0.71417	1.000000	0.80357	0.334000	0.28698	4.053000	0.57427	0.941000	0.37499	-0.471000	0.05019	GGG	.	.		0.572	ESM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214099.2	NM_007036		A	54281083	C	A	54281083	3	1	122	1	0	0	0	0	1	0	0	0	5254	623	22	3	303	3	ESM1	5	54281083	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10		54281083	126634177	47	20456										
BDP1	55814	hgsc.bcm.edu	37	chr5	70766253	70766253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttttttttagccatcagcatGgtaggaactgacttttctat	7	7	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr5:70766253G>T	ENST00000358731.4	+	7	1214	c.951G>T	c.(949-951)atG>atT	p.M317I	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	317	Myb-like.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		CCATCAGCATGGTAGGAACTG	0.299																																					p.M317I		Atlas-SNP	.											.	BDP1	204	.	0			c.G951T						.						93	85	88					5																	70766253		1811	4073	5884	SO:0001583	missense	55814	exon7			CAGCATGGTAGGA	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.951G>T	chr5.hg19:g.70766253G>T	ENSP00000351575:p.Met317Ile	427.0	0.0		302.0	66.0	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	hg19	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.629902	0.87660	.	.	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000444711	T	0.05081	3.5	5.26	5.26	0.73747	SANT domain, DNA binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.20007	0.0481	L	0.46670	1.46	0.80722	D	1	D;D;P	0.59767	0.986;0.982;0.864	D;D;P	0.70935	0.971;0.961;0.706	T	0.00175	-1.1954	10	0.72032	D	0.01	.	17.6188	0.88075	0.0:0.0:1.0:0.0	.	317;317;317	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	I	317	ENSP00000351575:M317I	ENSP00000351575:M317I	M	+	3	0	BDP1	70802009	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.111000	0.94308	2.438000	0.82558	0.563000	0.77884	ATG	.	.		0.299	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		T	70766253	G	T	70766253	3	4	122	1	0	0	0	0	1	0	0	0	1395	1348	47	3	977	3	BDP1	5	70766253	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	16485170	70766253	110149007	48	20457										
APC	324	hgsc.bcm.edu	37	chr5	112111380	112111380	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	aaggaaaaagactggtattaCgctcaacttcagaatctcac	7	9	3	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr5:112111380C>G	ENST00000457016.1	+	5	857	c.477C>G	c.(475-477)taC>taG	p.Y159*	APC_ENST00000508376.2_Nonsense_Mutation_p.Y159*|APC_ENST00000257430.4_Nonsense_Mutation_p.Y159*|RNU6-482P_ENST00000391068.1_RNA			P25054	APC_HUMAN	adenomatous polyposis coli	159	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACTGGTATTACGCTCAACTTC	0.289		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.Y169X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	0			c.C507G	GRCh37	CM960066	APC	M		.						91	98	95					5																	112111380		2202	4295	6497	SO:0001587	stop_gained	324	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	GTATTACGCTCAA	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.477C>G	chr5.hg19:g.112111380C>G	ENSP00000413133:p.Tyr159*	132.0	0.0		88.0	61.0	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	32	5.141345	0.94560	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.45	4.28	0.50868	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.5197	11.1583	0.48501	0.0:0.0723:0.0:0.9277	.	.	.	.	X	159;169;159;159;159	.	ENSP00000257430:Y159X	Y	+	3	2	APC	112139279	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.763000	0.26517	0.912000	0.36772	-0.238000	0.12139	TAC	.	.		0.289	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112111380	C	G	112111380	4	3	122	1	0	0	0	0	0	1	0	0	763	547	19	4	491	4	APC	5	112111380	Nonsense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	41345127	112111380	68803880	49	20458										
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140347883	140347883	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gacctactcccttctggagaGggagattcaagggctgccag	13	11	2	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr5:140347883G>A	ENST00000289269.5	+	1	2064	c.1532G>A	c.(1531-1533)aGg>aAg	p.R511K	PCDHA12_ENST00000398631.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	511	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTCTGGAGAGGGAGATTCAA	0.498																																					p.R511K	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.G1532A						.						95	90	92					5																	140347883		2203	4300	6503	SO:0001583	missense	56134	exon1			TGGAGAGGGAGAT	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"Cadherins / Protocadherins : Clustered"	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1532G>A	chr5.hg19:g.140347883G>A	ENSP00000289269:p.Arg511Lys	113.0	0.0		204.0	18.0	NM_031883	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	hg19	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	G	2.067	-0.413866	0.04799	.	.	ENSG00000243232	ENST00000289269	T	0.50001	0.76	6.02	2.1	0.27182	Cadherin (4);Cadherin-like (1);	0.304188	0.23795	N	0.044490	T	0.25606	0.0623	N	0.20881	0.62	0.24886	N	0.9922	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.002	T	0.21861	-1.0233	10	0.05959	T	0.93	.	8.2555	0.31754	0.1891:0.0:0.6974:0.1134	.	511;511	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	K	511	ENSP00000289269:R511K	ENSP00000289269:R511K	R	+	2	0	PCDHAC2	140328067	0.621000	0.27077	1.000000	0.80357	0.996000	0.88848	1.266000	0.33039	0.879000	0.35944	0.655000	0.94253	AGG	.	.		0.498	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		A	140347883	G	A	140347883	3	1	122	1	0	0	0	0	1	0	0	0	11542	1000	35	3	1534	3	PCDHAC2	5	140347883	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	28236503	140347883	40567377	50	20459										
EIF4E1B	253314	hgsc.bcm.edu	37	chr5	176070692	176070692	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gccgggcctggcaggacaacCtgcacctggtcaccaaggtg	14	14	1	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr5:176070692C>G	ENST00000318682.6	+	5	837	c.253C>G	c.(253-255)Ctg>Gtg	p.L85V	EIF4E1B_ENST00000504597.1_Missense_Mutation_p.L85V	NM_001099408.1	NP_001092878.1	A6NMX2	I4E1B_HUMAN	eukaryotic translation initiation factor 4E family member 1B	85					regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)	translation initiation factor activity (GO:0003743)			breast(1)|large_intestine(1)|lung(2)|pancreas(1)	5	all_cancers(89;0.00185)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCAGGACAACCTGCACCTGGT	0.632																																					p.L85V		Atlas-SNP	.											.	EIF4E1B	24	.	0			c.C253G						.						29	33	32					5																	176070692		2053	4183	6236	SO:0001583	missense	253314	exon5			GACAACCTGCACC		CCDS47345.1	5q35.2	2008-06-12			ENSG00000175766	ENSG00000175766			33179	protein-coding gene	gene with protein product						16191198	Standard	NM_001099408		Approved	FLJ36951	uc010jkf.1	A6NMX2	OTTHUMG00000163227	ENST00000318682.6:c.253C>G	chr5.hg19:g.176070692C>G	ENSP00000323714:p.Leu85Val	73.0	0.0		83.0	42.0	NM_001099408		Missense_Mutation	SNP	ENST00000318682.6	hg19	CCDS47345.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.443683	0.63067	.	.	ENSG00000175766	ENST00000318682;ENST00000510660;ENST00000504597	T;T;T	0.53640	0.61;0.61;0.61	5.33	2.58	0.30949	Translation Initiation factor eIF- 4e-like  domain (2);	0.000000	0.64402	D	0.000009	T	0.70325	0.3211	M	0.91249	3.19	0.46131	D	0.998884	P	0.48089	0.905	D	0.66979	0.948	T	0.70310	-0.4907	10	0.72032	D	0.01	.	8.53	0.33329	0.0:0.6221:0.0:0.3779	.	85	A6NMX2	I4E1B_HUMAN	V	85	ENSP00000323714:L85V;ENSP00000421009:L85V;ENSP00000427633:L85V	ENSP00000323714:L85V	L	+	1	2	EIF4E1B	176003298	0.927000	0.31430	0.526000	0.27913	0.835000	0.47333	0.952000	0.29149	0.249000	0.21456	0.491000	0.48974	CTG	.	.		0.632	EIF4E1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372187.1	NM_001099408		G	176070692	C	G	176070692	3	3	122	1	0	0	0	0	1	0	0	0	5031	680	24	4	263	4	EIF4E1B	5	176070692	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	35722809	176070692	4844568	51	20460										
OR2Y1	134083	hgsc.bcm.edu	37	chr5	180166444	180166444	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	agtgctgcaggaacagccacGactatgactcgggccacaaa	11	12	0	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr5:180166444G>A	ENST00000307832.2	-	1	655	c.615C>T	c.(613-615)gtC>gtT	p.V205V		NM_001001657.1	NP_001001657.1	Q8NGV0	OR2Y1_HUMAN	olfactory receptor, family 2, subfamily Y, member 1	205						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(89;1.25e-05)|all_epithelial(37;4.36e-06)|Renal(175;0.000159)|Lung NSC(126;0.00317)|all_lung(126;0.0041)|Breast(19;0.114)	all_cancers(40;0.0834)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAACAGCCACGACTATGACTC	0.512																																					p.V205V		Atlas-SNP	.											.	OR2Y1	49	.	0			c.C615T						.						102	92	96					5																	180166444		2203	4300	6503	SO:0001819	synonymous_variant	134083	exon1			AGCCACGACTATG	AB065676	CCDS34323.1	5q35	2012-08-09			ENSG00000174339	ENSG00000174339		"GPCR / Class A : Olfactory receptors"	14837	protein-coding gene	gene with protein product							Standard	NM_001001657		Approved		uc003mmf.1	Q8NGV0	OTTHUMG00000162237	ENST00000307832.2:c.615C>T	chr5.hg19:g.180166444G>A		95.0	0.0		162.0	21.0	NM_001001657	B9EIP1|Q6IFB1|Q96R16	Silent	SNP	ENST00000307832.2	hg19	CCDS34323.1																																																																																			.	.		0.512	OR2Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368059.2	XM_068682		A	180166444	G	A	180166444	2	1	122	1	0	0	0	0	0	0	0	1	11044	1045	37	1		1	OR2Y1	5	180166444	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	4095752	180166444	748816	52	20461										
PPIL1	51645	hgsc.bcm.edu	37	chr6	36839559	36839559	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttctgtggaattttgtgccaTtgtagtaacctcgacgagcc	10	9	1	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr6:36839559T>C	ENST00000373699.5	-	2	397	c.146A>G	c.(145-147)aAt>aGt	p.N49S	C6orf89_ENST00000359359.2_5'Flank|C6orf89_ENST00000510325.2_5'Flank	NM_016059.4	NP_057143.1	Q9Y3C6	PPIL1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 1	49	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			lung(1)|ovary(1)	2						TTTTGTGCCATTGTAGTAACC	0.443																																					p.N49S		Atlas-SNP	.											.	PPIL1	6	.	0			c.A146G						.						181	169	173					6																	36839559		2203	4300	6503	SO:0001583	missense	51645	exon2			GTGCCATTGTAGT	AF090992	CCDS4826.1	6p21.1	2008-08-29			ENSG00000137168	ENSG00000137168			9260	protein-coding gene	gene with protein product		601301				10072585, 8978786	Standard	NM_016059		Approved	CYPL1	uc003omu.2	Q9Y3C6	OTTHUMG00000014612	ENST00000373699.5:c.146A>G	chr6.hg19:g.36839559T>C	ENSP00000362803:p.Asn49Ser	175.0	0.0		292.0	153.0	NM_016059	O15001|Q5TDC9	Missense_Mutation	SNP	ENST00000373699.5	hg19	CCDS4826.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.179993	0.57800	.	.	ENSG00000137168	ENST00000373699	T	0.23348	1.91	5.4	5.4	0.78164	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);Peptidyl-prolyl cis-trans isomerase, cyclophilin-type, conserved site (1);	0.048145	0.85682	D	0.000000	T	0.21718	0.0523	M	0.81112	2.525	0.58432	D	0.999997	B	0.25743	0.133	B	0.24848	0.056	T	0.09997	-1.0649	10	0.72032	D	0.01	.	13.6739	0.62443	0.0:0.0:0.0:1.0	.	49	Q9Y3C6	PPIL1_HUMAN	S	49	ENSP00000362803:N49S	ENSP00000362803:N49S	N	-	2	0	PPIL1	36947537	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.852000	0.55934	2.159000	0.67721	0.533000	0.62120	AAT	.	.		0.443	PPIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040382.1			C	36839559	T	C	36839559	3	2	122	1	0	0	0	0	1	0	0	0	12338	1493	52	2	366	2	PPIL1	6	36839559	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10		36839559	134275508	53	20462										
TJAP1	93643	hgsc.bcm.edu	37	chr6	43471363	43471363	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	acaggtctgtgtctgtaggaGcggtaccggctggactgcaa	15	9	2	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr6:43471363G>C	ENST00000372445.5	+	10	874	c.498G>C	c.(496-498)gaG>gaC	p.E166D	TJAP1_ENST00000372449.1_Missense_Mutation_p.E166D|TJAP1_ENST00000372444.2_Missense_Mutation_p.E156D|TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000372452.1_Missense_Mutation_p.E156D|TJAP1_ENST00000259751.1_Missense_Mutation_p.E156D|TJAP1_ENST00000436109.2_Missense_Mutation_p.E156D|TJAP1_ENST00000438588.2_Missense_Mutation_p.E166D	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	166					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			GTCTGTAGGAGCGGTACCGGC	0.592																																					p.E166D		Atlas-SNP	.											.	TJAP1	35	.	0			c.G498C						.						69	68	68					6																	43471363		2203	4300	6503	SO:0001583	missense	93643	exon10			GTAGGAGCGGTAC	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.498G>C	chr6.hg19:g.43471363G>C	ENSP00000361522:p.Glu166Asp	78.0	0.0		85.0	42.0	NM_001146016	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	ENST00000372445.5	hg19	CCDS55004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.41|18.41	3.618169|3.618169	0.66787|0.66787	.|.	.|.	ENSG00000137221|ENSG00000137221	ENST00000454762|ENST00000372444;ENST00000372445;ENST00000436109;ENST00000442878;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588	.|T;T;T;T;T;T;T;T	.|0.50548	.|0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.65|5.65	1.76|1.76	0.24704|0.24704	.|.	.|0.045264	.|0.85682	.|D	.|0.000000	T|T	0.40767|0.40767	0.1130|0.1130	L|L	0.35414|0.35414	1.06|1.06	0.42677|0.42677	D|D	0.99353|0.99353	.|D;D	.|0.76494	.|0.996;0.999	.|D;D	.|0.76071	.|0.987;0.945	T|T	0.32481|0.32481	-0.9905|-0.9905	5|10	.|0.46703	.|T	.|0.11	-30.4801|-30.4801	9.6221|9.6221	0.39727|0.39727	0.3573:0.0:0.6427:0.0|0.3573:0.0:0.6427:0.0	.|.	.|166;156	.|Q5JTD0;Q5JTD0-2	.|TJAP1_HUMAN;.	P|D	114|156;166;156;166;156;156;156;166;166	.|ENSP00000361521:E156D;ENSP00000361522:E166D;ENSP00000407080:E156D;ENSP00000390981:E166D;ENSP00000259751:E156D;ENSP00000361530:E156D;ENSP00000361527:E166D;ENSP00000408769:E166D	.|ENSP00000259751:E156D	A|E	+|+	1|3	0|2	TJAP1|TJAP1	43579341|43579341	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.807000|0.807000	0.45602|0.45602	0.733000|0.733000	0.26087|0.26087	0.705000|0.705000	0.31890|0.31890	0.462000|0.462000	0.41574|0.41574	GCG|GAG	.	.		0.592	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		C	43471363	G	C	43471363	3	2	122	1	0	0	0	0	1	0	0	0	15943	962	34	4	524	4	TJAP1	6	43471363	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	6631804	43471363	127643704	54	20463										
EYS	346007	hgsc.bcm.edu	37	chr6	64431532	64431532	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgttacatttatcccatctaGatccaggtagccttctgcac	6	12	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr6:64431532G>T	ENST00000370621.3	-	44	8984	c.8458C>A	c.(8458-8460)Cta>Ata	p.L2820I	EYS_ENST00000503581.1_Missense_Mutation_p.L2799I|EYS_ENST00000370616.2_Missense_Mutation_p.L2820I			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2820	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						ATCCCATCTAGATCCAGGTAG	0.368																																					p.L2799I		Atlas-SNP	.											.	EYS	527	.	0			c.C8395A						.						293	231	250					6																	64431532		692	1591	2283	SO:0001583	missense	346007	exon43			CATCTAGATCCAG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.8458C>A	chr6.hg19:g.64431532G>T	ENSP00000359655:p.Leu2820Ile	229.0	0.0		330.0	35.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.72	2.918076	0.52546	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.74947	-0.89;-0.89;-0.89	4.71	-0.644	0.11479	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.000000	0.50627	U	0.000107	T	0.50735	0.1633	L	0.31845	0.965	0.80722	D	1	D;D	0.62365	0.988;0.991	P;P	0.57283	0.721;0.817	T	0.55321	-0.8159	10	0.10902	T	0.67	.	4.7799	0.13197	0.3567:0.1477:0.4956:0.0	.	2799;2820	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	I	2799;2820;2820	ENSP00000424243:L2799I;ENSP00000359655:L2820I;ENSP00000359650:L2820I	ENSP00000359650:L2820I	L	-	1	2	EYS	64489491	0.977000	0.34250	0.920000	0.36463	0.939000	0.58152	0.919000	0.28692	-0.226000	0.09899	0.650000	0.86243	CTA	.	.		0.368	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		T	64431532	G	T	64431532	3	4	122	1	0	0	0	0	1	0	0	0	5334	933	33	3	1043	3	EYS	6	64431532	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	20960169	64431532	106683535	55	20464										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87967391	87967391	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	aaagttaaaaaagaccgtggGcggggcccaaatgggaagga	15	6	0	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr6:87967391G>A	ENST00000369577.3	+	8	4087	c.4044G>A	c.(4042-4044)ggG>ggA	p.G1348G	ZNF292_ENST00000339907.4_Silent_p.G1343G	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1348						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AAGACCGTGGGCGGGGCCCAA	0.423																																					p.G1348G		Atlas-SNP	.											.	ZNF292	479	.	0			c.G4044A						.						31	31	31					6																	87967391		1815	4082	5897	SO:0001819	synonymous_variant	23036	exon8			CCGTGGGCGGGGC	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.4044G>A	chr6.hg19:g.87967391G>A		143.0	0.0		86.0	52.0	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Silent	SNP	ENST00000369577.3	hg19	CCDS47457.1																																																																																			.	.		0.423	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		A	87967391	G	A	87967391	2	1	122	1	0	0	0	0	0	0	0	1	17841	1190	42	3		3	ZNF292	6	87967391	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	23535859	87967391	83147676	56	20465										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160491064	160491064	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ggaaaaagtcaaccaccatcCgattcacctgcagcgagagc	9	13	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr6:160491064C>T	ENST00000356956.1	+	31	4565	c.4417C>T	c.(4417-4419)Cga>Tga	p.R1473*		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1473					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	AACCACCATCCGATTCACCTG	0.532																																					p.R1473X		Atlas-SNP	.											.	IGF2R	251	.	0			c.C4417T						.						100	81	88					6																	160491064		2203	4300	6503	SO:0001587	stop_gained	3482	exon31			ACCATCCGATTCA	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.4417C>T	chr6.hg19:g.160491064C>T	ENSP00000349437:p.Arg1473*	66.0	0.0		39.0	5.0	NM_000876	Q7Z7G9|Q96PT5	Nonsense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	C	46	12.261867	0.99651	.	.	ENSG00000197081	ENST00000356956	.	.	.	5.62	5.62	0.85841	.	0.175470	0.51477	D	0.000087	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.4459	19.6758	0.95932	0.0:1.0:0.0:0.0	.	.	.	.	X	1473	.	ENSP00000349437:R1473X	R	+	1	2	IGF2R	160411054	1.000000	0.71417	0.882000	0.34594	0.810000	0.45777	6.903000	0.75703	2.644000	0.89710	0.561000	0.74099	CGA	.	.		0.532	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		T	160491064	C	T	160491064	4	4	122	1	0	0	0	0	0	1	0	0	7585	644	23	1	4539	1	IGF2R	6	160491064	Nonsense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	72523673	160491064	10624003	57	20466										
SLC22A1	6580	hgsc.bcm.edu	37	chr6	160543147	160543147	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ggggtggctgagctgagccaGcgctgtggctggagccctgc	19	11	0	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr6:160543147G>A	ENST00000366963.4	+	1	327	c.180G>A	c.(178-180)caG>caA	p.Q60Q	SLC22A1_ENST00000457470.2_Silent_p.Q60Q|SLC22A1_ENST00000324965.4_Silent_p.Q60Q	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	60					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|epinephrine transport (GO:0048241)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|norepinephrine transport (GO:0015874)|organic cation transport (GO:0015695)|protein homooligomerization (GO:0051260)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)|dopamine transmembrane transporter activity (GO:0005329)|norepinephrine transmembrane transporter activity (GO:0005333)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)		SLC22A1/CUTA(2)	breast(1)|endometrium(3)|large_intestine(3)|lung(13)|upper_aerodigestive_tract(1)	21		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)	Acebutolol(DB01193)|Acepromazine(DB01614)|Aciclovir(DB00787)|Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Caspofungin(DB00520)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Choline(DB00122)|Cimetidine(DB00501)|Cladribine(DB00242)|Clonidine(DB00575)|Codeine(DB00318)|Cytarabine(DB00987)|Desipramine(DB01151)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Estropipate(DB04574)|Ganciclovir(DB01004)|Gentian Violet(DB00406)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Lamivudine(DB00709)|Latanoprost(DB00654)|Metformin(DB00331)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rocuronium(DB00728)|Saquinavir(DB01232)|Spermine(DB00127)|Testosterone(DB00624)|Thiamine(DB00152)|Thioproperazine(DB01622)|Thiothixene(DB01623)|Tubocurarine(DB01199)|Vecuronium(DB01339)|Verapamil(DB00661)	AGCTGAGCCAGCGCTGTGGCT	0.652																																					p.Q60Q		Atlas-SNP	.											.	SLC22A1	69	.	0			c.G180A						.						63	72	69					6																	160543147		2203	4300	6503	SO:0001819	synonymous_variant	6580	exon1			GAGCCAGCGCTGT	U77086	CCDS5274.1, CCDS5275.1	6q25.3	2013-05-22			ENSG00000175003	ENSG00000175003		"Solute carriers"	10963	protein-coding gene	gene with protein product		602607				9605850	Standard	NM_003057		Approved	OCT1	uc003qtc.3	O15245	OTTHUMG00000015947	ENST00000366963.4:c.180G>A	chr6.hg19:g.160543147G>A		63.0	0.0		66.0	13.0	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	Silent	SNP	ENST00000366963.4	hg19	CCDS5274.1																																																																																			.	.		0.652	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2			A	160543147	G	A	160543147	2	1	122	1	0	0	0	0	0	0	0	1	14455	962	34	3		3	SLC22A1	6	160543147	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	52083	160543147	10571920	58	20467										
DDX56	54606	hgsc.bcm.edu	37	chr7	44609640	44609640	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gctcgatggatgtaggcctcAggggttgggggaagatcaaa	17	6	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr7:44609640A>T	ENST00000258772.5	-	8	1204	c.1098T>A	c.(1096-1098)ccT>ccA	p.P366P	DDX56_ENST00000431640.1_Silent_p.P326P|DDX56_ENST00000485367.1_5'UTR	NM_001257189.1|NM_019082.3	NP_001244118.1|NP_061955.1	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 56	366	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)	16						TGTAGGCCTCAGGGGTTGGGG	0.592																																					p.P366P		Atlas-SNP	.											.	DDX56	36	.	0			c.T1098A						.						92	83	86					7																	44609640		2203	4300	6503	SO:0001819	synonymous_variant	54606	exon8			GGCCTCAGGGGTT	AJ131712	CCDS5492.1, CCDS59053.1	7p13	2012-02-23	2012-02-23		ENSG00000136271	ENSG00000136271		"DEAD-boxes"	18193	protein-coding gene	gene with protein product	"nucleolar helicase of 61 kDa"	608023	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 56"			10749921	Standard	NM_019082		Approved	NOH61	uc003tlg.4	Q9NY93	OTTHUMG00000129211	ENST00000258772.5:c.1098T>A	chr7.hg19:g.44609640A>T		75.0	0.0		64.0	20.0	NM_019082	A4D2K9|C9JV95|Q6IAE2|Q9H9I8	Silent	SNP	ENST00000258772.5	hg19	CCDS5492.1																																																																																			.	.		0.592	DDX56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251291.1	NM_019082		T	44609640	A	T	44609640	2	4	122	1	0	0	0	0	0	0	0	1	4376	175	7	4		4	DDX56	7	44609640	Silent	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10		44609640	114529023	59	20468										
PCLO	27445	hgsc.bcm.edu	37	chr7	82508658	82508658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	attccttattcttaccttccAtaagcttccccgtctgttcc	3	15	2	0	rs556966262		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr7:82508658A>G	ENST00000333891.9	-	10	13986	c.13649T>C	c.(13648-13650)aTg>aCg	p.M4550T	PCLO_ENST00000426442.2_5'UTR|PCLO_ENST00000423517.2_Missense_Mutation_p.M4550T	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTTACCTTCCATAAGCTTCCC	0.373													A|||	1	0.000199681	0	0	5008	,	,		14898	0		0	False		,,,				2504	0.001				p.M4550T		Atlas-SNP	.											.	PCLO	1506	.	0			c.T13649C						.						71	64	67					7																	82508658		1826	4065	5891	SO:0001583	missense	27445	exon10			CCTTCCATAAGCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.13649T>C	chr7.hg19:g.82508658A>G	ENSP00000334319:p.Met4550Thr	168.0	0.0		157.0	67.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	8.233	0.805025	0.16467	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.26373	1.74;1.74	4.8	2.41	0.29592	.	.	.	.	.	T	0.16128	0.0388	N	0.24115	0.695	0.46798	D	0.999205	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.05131	-1.0904	9	0.87932	D	0	.	7.3962	0.26938	0.7486:0.0:0.2514:0.0	.	4550;4550;47	Q9Y6V0-5;Q9Y6V0-6;Q32P40	.;.;.	T	4550;4550;46	ENSP00000334319:M4550T;ENSP00000388393:M4550T	ENSP00000334319:M4550T	M	-	2	0	PCLO	82346594	0.039000	0.19947	0.326000	0.25389	0.893000	0.52053	3.122000	0.50446	0.289000	0.22422	0.482000	0.46254	ATG	.	.		0.373	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82508658	A	G	82508658	3	3	122	1	0	0	0	0	1	0	0	0	11592	217	8	2	1860	2	PCLO	7	82508658	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	37899018	82508658	76630005	60	20469										
PCLO	27445	hgsc.bcm.edu	37	chr7	82582751	82582751	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttgggggcgattggaggtttGcttggctcaggcctgtgggt	19	6	1	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr7:82582751G>T	ENST00000333891.9	-	5	7855	c.7518C>A	c.(7516-7518)agC>agA	p.S2506R	PCLO_ENST00000423517.2_Missense_Mutation_p.S2506R|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTGGAGGTTTGCTTGGCTCAG	0.453																																					p.S2506R		Atlas-SNP	.											.	PCLO	1506	.	0			c.C7518A						.						133	132	132					7																	82582751		1955	4138	6093	SO:0001583	missense	27445	exon5			AGGTTTGCTTGGC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.7518C>A	chr7.hg19:g.82582751G>T	ENSP00000334319:p.Ser2506Arg	91.0	0.0		88.0	13.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	3.030	-0.199928	0.06219	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19806	2.12;2.12	4.52	1.69	0.24217	.	.	.	.	.	T	0.13157	0.0319	L	0.29908	0.895	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.09443	-1.0674	9	0.87932	D	0	.	4.1576	0.10268	0.3449:0.0:0.4963:0.1588	.	2506;2506	Q9Y6V0-5;Q9Y6V0-6	.;.	R	2437;2506;2506	ENSP00000334319:S2506R;ENSP00000388393:S2506R	ENSP00000334319:S2506R	S	-	3	2	PCLO	82420687	0.962000	0.33011	1.000000	0.80357	0.662000	0.39071	0.096000	0.15147	0.355000	0.24131	0.484000	0.47621	AGC	.	.		0.453	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82582751	G	T	82582751	3	4	122	1	0	0	0	0	1	0	0	0	11592	1310	46	3	8011	3	PCLO	7	82582751	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	74093	82582751	76555912	61	20470										
ANKIB1	54467	hgsc.bcm.edu	37	chr7	91936908	91936908	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gagcagctattgatgctgttGataacaaaaaaaacacaccc	7	9	0	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr7:91936908G>C	ENST00000265742.3	+	3	800	c.424G>C	c.(424-426)Gat>Cat	p.D142H		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	142							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TGATGCTGTTGATAACAAAAA	0.368																																					p.D142H		Atlas-SNP	.											.	ANKIB1	92	.	0			c.G424C						.						64	63	63					7																	91936908		1891	4115	6006	SO:0001583	missense	54467	exon3			GCTGTTGATAACA	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"Ankyrin repeat domain containing"	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.424G>C	chr7.hg19:g.91936908G>C	ENSP00000265742:p.Asp142His	38.0	0.0		49.0	22.0	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	hg19	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.744459	0.89663	.	.	ENSG00000001629	ENST00000265742	T	0.62105	0.05	5.71	5.71	0.89125	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.87164	0.6109	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90914	0.4778	10	0.87932	D	0	.	19.8516	0.96743	0.0:0.0:1.0:0.0	.	142	Q9P2G1	AKIB1_HUMAN	H	142	ENSP00000265742:D142H	ENSP00000265742:D142H	D	+	1	0	ANKIB1	91774844	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.476000	0.97823	2.685000	0.91497	0.585000	0.79938	GAT	.	.		0.368	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			C	91936908	G	C	91936908	3	2	122	1	0	0	0	0	1	0	0	0	630	1290	45	4	430	4	ANKIB1	7	91936908	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	9354157	91936908	67201755	62	20471										
GPR37	2861	hgsc.bcm.edu	37	chr7	124386785	124386785	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gagacagaaaaggaggactgGggtgacacaggacttaaaga	15	5	0	4			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr7:124386785G>C	ENST00000303921.2	-	2	2286	c.1636C>G	c.(1636-1638)Cca>Gca	p.P546A		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	546					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AGGAGGACTGGGGTGACACAG	0.488																																					p.P546A		Atlas-SNP	.											.	GPR37	89	.	0			c.C1636G						.						111	104	106					7																	124386785		2203	4300	6503	SO:0001583	missense	2861	exon2			GGACTGGGGTGAC		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.1636C>G	chr7.hg19:g.124386785G>C	ENSP00000306449:p.Pro546Ala	88.0	0.0		103.0	12.0	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Missense_Mutation	SNP	ENST00000303921.2	hg19	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	G	19.83	3.900135	0.72754	.	.	ENSG00000170775	ENST00000303921	D	0.98807	-5.15	5.35	5.35	0.76521	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000023	D	0.98994	0.9657	M	0.71206	2.165	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99893	1.1139	10	0.87932	D	0	-14.4547	18.0541	0.89358	0.0:0.0:1.0:0.0	.	546	O15354	GPR37_HUMAN	A	546	ENSP00000306449:P546A	ENSP00000306449:P546A	P	-	1	0	GPR37	124174021	1.000000	0.71417	0.931000	0.37212	0.995000	0.86356	9.869000	0.99810	2.489000	0.83994	0.655000	0.94253	CCA	.	.		0.488	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		C	124386785	G	C	124386785	3	2	122	1	0	0	0	0	1	0	0	0	6699	1232	43	4	209	4	GPR37	7	124386785	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	32449877	124386785	34751878	63	20472										
JPH1	56704	hgsc.bcm.edu	37	chr8	75233175	75233175	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	taggtctccacgccgtacccGtcttgcagcccgttactcca	8	17	2	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr8:75233175G>T	ENST00000342232.4	-	1	388	c.348C>A	c.(346-348)gaC>gaA	p.D116E		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	116	Gly-rich.				calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			CGCCGTACCCGTCTTGCAGCC	0.711																																					p.D116E		Atlas-SNP	.											.	JPH1	77	.	0			c.C348A						.						46	35	39					8																	75233175		2203	4300	6503	SO:0001583	missense	56704	exon1			GTACCCGTCTTGC	AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.348C>A	chr8.hg19:g.75233175G>T	ENSP00000344488:p.Asp116Glu	26.0	0.0		59.0	9.0	NM_020647	B2RTZ0	Missense_Mutation	SNP	ENST00000342232.4	hg19	CCDS6217.1	.	.	.	.	.	.	.	.	.	.	g	25.3	4.625667	0.87560	.	.	ENSG00000104369	ENST00000342232	T	0.54071	0.59	4.14	4.14	0.48551	.	0.000000	0.85682	D	0.000000	T	0.45377	0.1339	N	0.05608	-0.01	0.58432	D	0.999992	D	0.56746	0.977	P	0.54174	0.744	T	0.51560	-0.8690	10	0.37606	T	0.19	.	16.2109	0.82158	0.0:0.0:1.0:0.0	.	116	Q9HDC5	JPH1_HUMAN	E	116	ENSP00000344488:D116E	ENSP00000344488:D116E	D	-	3	2	JPH1	75395730	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.420000	0.44679	2.120000	0.65058	0.401000	0.26515	GAC	.	.		0.711	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1			T	75233175	G	T	75233175	3	4	122	1	0	0	0	0	1	0	0	0	7969	1136	40	1	1657	1	JPH1	8	75233175	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10		75233175	71130847	64	20473										
PEX2	5828	hgsc.bcm.edu	37	chr8	77895811	77895811	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	taagagaaaaatcagaaattCagcaaaaccatgccagagaa	7	7	2	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr8:77895811C>T	ENST00000419564.2	-	4	1068	c.604G>A	c.(604-606)Gaa>Aaa	p.E202K	PEX2_ENST00000520103.1_Missense_Mutation_p.E202K|PEX2_ENST00000357039.4_Missense_Mutation_p.E202K|PEX2_ENST00000522527.1_Missense_Mutation_p.E202K	NM_001172087.1	NP_001165558.1	P28328	PEX2_HUMAN	peroxisomal biogenesis factor 2	202					bile acid biosynthetic process (GO:0006699)|cholesterol homeostasis (GO:0042632)|fatty acid beta-oxidation (GO:0006635)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|peroxisome organization (GO:0007031)|protein destabilization (GO:0031648)|protein import into peroxisome matrix (GO:0016558)|regulation of cholesterol biosynthetic process (GO:0045540)|very long-chain fatty acid metabolic process (GO:0000038)	Cdc73/Paf1 complex (GO:0016593)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	14						ATCAGAAATTCAGCAAAACCA	0.388																																					p.E202K		Atlas-SNP	.											.	PEX2	44	.	0			c.G604A						.						88	91	90					8																	77895811		2203	4300	6503	SO:0001583	missense	5828	exon4			GAAATTCAGCAAA	M86852	CCDS6221.1	8q21.11	2010-02-09	2010-01-25	2010-01-25		ENSG00000164751		"RING-type (C3HC4) zinc fingers"	9717	protein-coding gene	gene with protein product	"Zellweger syndrome", "peroxin 2"	170993	"peroxisomal membrane protein 3 (35kD, Zellweger syndrome)", "peroxisomal membrane protein 3, 35kDa"	PXMP3		1546315, 8858157	Standard	NM_000318		Approved	PMP35, PAF-1, RNF72, ZWS3	uc022awf.1	P28328		ENST00000419564.2:c.604G>A	chr8.hg19:g.77895811C>T	ENSP00000400984:p.Glu202Lys	43.0	0.0		67.0	16.0	NM_000318	Q567S6|Q9BW41	Missense_Mutation	SNP	ENST00000419564.2	hg19	CCDS6221.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.044970	0.93685	.	.	ENSG00000164751	ENST00000357039;ENST00000419564;ENST00000520103;ENST00000522527	D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68	5.09	5.09	0.68999	Pex, N-terminal (1);	0.051798	0.85682	D	0.000000	D	0.91945	0.7449	M	0.87456	2.885	0.80722	D	1	D	0.67145	0.996	D	0.66602	0.945	D	0.93017	0.6437	10	0.72032	D	0.01	-23.1997	18.6882	0.91573	0.0:1.0:0.0:0.0	.	202	P28328	PEX2_HUMAN	K	202	ENSP00000349543:E202K;ENSP00000400984:E202K;ENSP00000428590:E202K;ENSP00000428638:E202K	ENSP00000349543:E202K	E	-	1	0	PEX2	78058366	1.000000	0.71417	0.957000	0.39632	0.993000	0.82548	5.545000	0.67237	2.663000	0.90544	0.557000	0.71058	GAA	.	.		0.388	PEX2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379122.1	NM_000318		T	77895811	C	T	77895811	3	4	122	1	0	0	0	0	1	0	0	0	11754	835	29	3	317	3	PEX2	8	77895811	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	2662636	77895811	68468211	65	20474										
GEM	2669	hgsc.bcm.edu	37	chr8	95272587	95272587	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gcggcagtggtcctcaggggTagcagaatggcggttgcggt	19	8	1	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr8:95272587T>C	ENST00000297596.2	-	2	409	c.145A>G	c.(145-147)Acc>Gcc	p.T49A	GEM_ENST00000396194.2_Missense_Mutation_p.T49A	NM_005261.3	NP_005252.1	P55040	GEM_HUMAN	GTP binding protein overexpressed in skeletal muscle	49					cell surface receptor signaling pathway (GO:0007166)|chromosome organization (GO:0051276)|immune response (GO:0006955)|metaphase plate congression (GO:0051310)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic side of plasma membrane (GO:0009898)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle midzone (GO:0051233)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			TCCTCAGGGGTAGCAGAATGG	0.602																																					p.T49A	GBM(125;80 1653 28655 32188 47338)|Esophageal Squamous(19;97 579 13602 49091 51766)	Atlas-SNP	.											.	GEM	40	.	0			c.A145G						.						78	76	77					8																	95272587		2203	4300	6503	SO:0001583	missense	2669	exon2			CAGGGGTAGCAGA		CCDS6261.1	8q13-q21	2014-05-09	2001-11-28		ENSG00000164949	ENSG00000164949			4234	protein-coding gene	gene with protein product	"kinase-inducible Ras-like protein"	600164	"GTP-binding protein overexpressed in skeletal muscle"			7912851, 11956230	Standard	NM_005261		Approved	KIR	uc003ygj.3	P55040	OTTHUMG00000164392	ENST00000297596.2:c.145A>G	chr8.hg19:g.95272587T>C	ENSP00000297596:p.Thr49Ala	49.0	0.0		164.0	13.0	NM_181702	B2RA31	Missense_Mutation	SNP	ENST00000297596.2	hg19	CCDS6261.1	.	.	.	.	.	.	.	.	.	.	T	3.852	-0.031678	0.07543	.	.	ENSG00000164949	ENST00000396194;ENST00000297596;ENST00000523433	T;T;T	0.63744	-0.06;-0.06;1.61	5.48	-4.19	0.03835	.	0.720560	0.14061	N	0.344024	T	0.27933	0.0688	N	0.01705	-0.755	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34625	-0.9821	10	0.06365	T	0.9	.	14.7633	0.69621	0.0:0.1648:0.0:0.8352	.	49	P55040	GEM_HUMAN	A	49	ENSP00000379497:T49A;ENSP00000297596:T49A;ENSP00000428258:T49A	ENSP00000297596:T49A	T	-	1	0	GEM	95341763	0.119000	0.22226	0.000000	0.03702	0.655000	0.38815	0.220000	0.17660	-0.733000	0.04850	-0.132000	0.14878	ACC	.	.		0.602	GEM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378566.1	NM_181702		C	95272587	T	C	95272587	3	2	122	1	0	0	0	0	1	0	0	0	6337	1638	57	2	761	2	GEM	8	95272587	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	17376776	95272587	51091435	66	20475										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124382175	124382175	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	atcttcatcatcatcatcatCatcatcatcgtcatcatcat	1	13	12	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr8:124382175C>G	ENST00000287394.5	-	7	924	c.817G>C	c.(817-819)Gat>Cat	p.D273H	ATAD2_ENST00000534257.1_5'Flank|ATAD2_ENST00000521903.1_5'UTR	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	273	Asp-rich.				ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			tcatcatcatcatcatcatcg	0.363																																					p.D273H		Atlas-SNP	.											.	ATAD2	160	.	0			c.G817C						.						251	191	212					8																	124382175		2203	4300	6503	SO:0001583	missense	29028	exon7			CATCATCATCATC	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.817G>C	chr8.hg19:g.124382175C>G	ENSP00000287394:p.Asp273His	134.0	0.0		315.0	18.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	C	2.448	-0.327057	0.05350	.	.	ENSG00000156802	ENST00000287394	T	0.13307	2.6	0.755	0.755	0.18415	.	0.699459	0.15113	N	0.279857	T	0.11324	0.0276	L	0.29908	0.895	0.80722	D	1	P;B	0.44946	0.846;0.0	P;B	0.44946	0.465;0.001	T	0.17561	-1.0365	10	0.49607	T	0.09	.	7.5002	0.27513	0.0:1.0:0.0:0.0	.	103;273	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	H	273	ENSP00000287394:D273H	ENSP00000287394:D273H	D	-	1	0	ATAD2	124451356	1.000000	0.71417	0.113000	0.21522	0.063000	0.16089	2.695000	0.47043	0.731000	0.32448	0.549000	0.68633	GAT	.	.		0.363	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		G	124382175	C	G	124382175	3	3	122	1	0	0	0	0	1	0	0	0	1071	826	29	4	3443	4	ATAD2	8	124382175	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	29109588	124382175	21981847	67	20476										
PTP4A3	11156	hgsc.bcm.edu	37	chr8	142441034	142441034	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cccctcttcccaggaagcgcCgcggagccatcaacagcaag	10	17	2	0	rs145157893		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr8:142441034C>A	ENST00000521578.1	+	6	1357	c.412C>A	c.(412-414)Cgc>Agc	p.R138S	PTP4A3_ENST00000349124.1_Missense_Mutation_p.R113S|PTP4A3_ENST00000329397.1_Missense_Mutation_p.R138S|PTP4A3_ENST00000520105.1_Missense_Mutation_p.R113S|MROH5_ENST00000430863.1_RNA|PTP4A3_ENST00000524028.1_Missense_Mutation_p.R52S			O75365	TP4A3_HUMAN	protein tyrosine phosphatase type IVA, member 3	138	Tyrosine-protein phosphatase.				peptidyl-tyrosine dephosphorylation (GO:0035335)	endosome (GO:0005768)|plasma membrane (GO:0005886)	prenylated protein tyrosine phosphatase activity (GO:0004727)			endometrium(2)|large_intestine(1)|lung(3)	6	all_cancers(97;2.55e-15)|all_epithelial(106;1.39e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0474)			CAGGAAGCGCCGCGGAGCCAT	0.602																																					p.R138S		Atlas-SNP	.											.	PTP4A3	19	.	0			c.C412A						.						97	83	87					8																	142441034		2201	4300	6501	SO:0001583	missense	11156	exon5			AAGCGCCGCGGAG	AF041434	CCDS6382.1, CCDS6383.1	8q24.3	2011-06-09				ENSG00000184489		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"	9636	protein-coding gene	gene with protein product		606449					Standard	NM_032611		Approved	PRL-3, PRL-R, PRL3	uc003ywg.1	O75365		ENST00000521578.1:c.412C>A	chr8.hg19:g.142441034C>A	ENSP00000428976:p.Arg138Ser	25.0	0.0		63.0	14.0	NM_032611	Q8IVN5|Q99849|Q9BTW5	Missense_Mutation	SNP	ENST00000521578.1	hg19	CCDS6383.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.518142	0.64634	.	.	ENSG00000184489	ENST00000521578;ENST00000520105;ENST00000329397;ENST00000349124;ENST00000524028	D;T;D;T	0.83335	-1.71;0.75;-1.71;0.75	4.49	2.53	0.30540	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.056513	0.64402	D	0.000002	D	0.82788	0.5113	M	0.75264	2.295	0.80722	D	1	P;B	0.47191	0.891;0.137	P;B	0.47044	0.535;0.224	T	0.83015	-0.0170	10	0.87932	D	0	-13.2554	7.2761	0.26286	0.2121:0.6933:0.0:0.0947	.	113;138	O75365-2;O75365	.;TP4A3_HUMAN	S	138;113;138;113;52	ENSP00000428976:R138S;ENSP00000428758:R113S;ENSP00000332274:R138S;ENSP00000331730:R113S	ENSP00000332274:R138S	R	+	1	0	PTP4A3	142510216	0.433000	0.25562	0.816000	0.32577	0.708000	0.40852	1.341000	0.33907	1.245000	0.43885	0.555000	0.69702	CGC	.	C|1.000;T|0.000		0.602	PTP4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378977.1	NM_032611		A	142441034	C	A	142441034	3	1	122	1	0	0	0	0	1	0	0	0	12785	652	23	1	430	1	PTP4A3	8	142441034	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	18058859	142441034	3922988	68	20477										
FREM1	158326	hgsc.bcm.edu	37	chr9	14784488	14784488	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gatagtgaacatattcgatcTggccatatcgcggaggggag	14	7	1	1	rs376519870		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr9:14784488T>C	ENST00000380880.3	-	24	5105	c.4322A>G	c.(4321-4323)cAg>cGg	p.Q1441R	FREM1_ENST00000380881.4_Missense_Mutation_p.Q1442R|FREM1_ENST00000422223.2_Missense_Mutation_p.Q1441R			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1441					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		ATATTCGATCTGGCCATATCG	0.493																																					p.Q1441R		Atlas-SNP	.											.	FREM1	261	.	0			c.A4322G						.	T	ARG/GLN	1,3983		0,1,1991	106	104	104		4322	3.2	0.6	9		104	0,8288		0,0,4144	no	missense	FREM1	NM_144966.5	43	0,1,6135	CC,CT,TT		0.0,0.0251,0.0081	benign	1441/2180	14784488	1,12271	1992	4144	6136	SO:0001583	missense	158326	exon25			TCGATCTGGCCAT	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.4322A>G	chr9.hg19:g.14784488T>C	ENSP00000370262:p.Gln1441Arg	106.0	0.0		105.0	28.0	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	hg19	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	T	6.504	0.461183	0.12342	2.51E-4	0.0	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.50001	0.76;0.76;0.76	5.53	3.2	0.36748	.	0.155174	0.64402	N	0.000015	T	0.31918	0.0812	L	0.29908	0.895	0.45452	D	0.998428	B	0.12630	0.006	B	0.12837	0.008	T	0.06197	-1.0840	10	0.16896	T	0.51	-4.7618	10.0584	0.42259	0.0:0.1354:0.0:0.8646	.	1441	Q5H8C1	FREM1_HUMAN	R	1442;1441;1441	ENSP00000370263:Q1442R;ENSP00000412940:Q1441R;ENSP00000370262:Q1441R	ENSP00000370262:Q1441R	Q	-	2	0	FREM1	14774488	1.000000	0.71417	0.550000	0.28217	0.012000	0.07955	2.524000	0.45589	0.478000	0.27488	0.482000	0.46254	CAG	.	.		0.493	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		C	14784488	T	C	14784488	3	2	122	1	0	0	0	0	1	0	0	0	6052	1580	55	2	2323	2	FREM1	9	14784488	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10		14784488	126428943	69	20478										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79320970	79320970	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	caaactgaagggcttcttagCatctatccacaagtcaggcg	9	11	3	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr9:79320970C>T	ENST00000376718.3	-	8	6343	c.6220G>A	c.(6220-6222)Gct>Act	p.A2074T	PRUNE2_ENST00000428286.1_Missense_Mutation_p.A1715T	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2074					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GGCTTCTTAGCATCTATCCAC	0.507																																					p.A2074T		Atlas-SNP	.											.	PRUNE2	331	.	0			c.G6220A						.						166	156	159					9																	79320970		1568	3582	5150	SO:0001583	missense	158471	exon8			TCTTAGCATCTAT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.6220G>A	chr9.hg19:g.79320970C>T	ENSP00000365908:p.Ala2074Thr	109.0	0.0		110.0	22.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.534|5.534	0.283500|0.283500	0.10458|0.10458	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.49432|.	0.78;0.79|.	6.03|6.03	2.81|2.81	0.32909|0.32909	.|.	0.463760|.	0.20212|.	N|.	0.096878|.	T|T	0.22742|0.22742	0.0549|0.0549	N|N	0.17474|0.17474	0.49|0.49	0.09310|0.09310	N|N	0.999998|0.999998	B|.	0.15141|.	0.012|.	B|.	0.14023|.	0.01|.	T|T	0.20806|0.20806	-1.0264|-1.0264	10|5	0.38643|.	T|.	0.18|.	-1.6323|-1.6323	7.7343|7.7343	0.28804|0.28804	0.1183:0.674:0.0:0.2077|0.1183:0.674:0.0:0.2077	.|.	2074|.	Q8WUY3|.	PRUN2_HUMAN|.	T|Y	2074;1715;2073|1395	ENSP00000365908:A2074T;ENSP00000397425:A1715T|.	ENSP00000365908:A2074T|.	A|C	-|-	1|2	0|0	PRUNE2|PRUNE2	78510790|78510790	0.005000|0.005000	0.15991|0.15991	0.659000|0.659000	0.29680|0.29680	0.144000|0.144000	0.21451|0.21451	0.430000|0.430000	0.21428|0.21428	0.889000|0.889000	0.36185|0.36185	0.655000|0.655000	0.94253|0.94253	GCT|TGC	.	.		0.507	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		T	79320970	C	T	79320970	3	4	122	1	0	0	0	0	1	0	0	0	12653	710	25	3	3094	3	PRUNE2	9	79320970	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	64536482	79320970	61892461	70	20479										
OGN	4969	hgsc.bcm.edu	37	chr9	95147921	95147921	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gttaaaagtatgaccctatcGgtaatctttttaagcaaata	6	6	1	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr9:95147921G>C	ENST00000262551.4	-	7	1298	c.878C>G	c.(877-879)cCg>cGg	p.P293R	OGN_ENST00000375561.5_Missense_Mutation_p.P293R|CENPP_ENST00000375587.3_Intron	NM_033014.2	NP_148935.1	P20774	MIME_HUMAN	osteoglycin	293					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|negative regulation of smooth muscle cell proliferation (GO:0048662)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	13						TGACCCTATCGGTAATCTTTT	0.388																																					p.P293R		Atlas-SNP	.											.	OGN	26	.	0			c.C878G						.						120	118	119					9																	95147921		2203	4300	6503	SO:0001583	missense	4969	exon7			CCTATCGGTAATC	AI424992	CCDS6695.1	9q22	2008-02-05	2007-02-16		ENSG00000106809	ENSG00000106809		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8126	protein-coding gene	gene with protein product	"mimecan proteoglycan"	602383	"osteoglycin (osteoinductive factor)"			2372374	Standard	NM_033014		Approved	mimecan, OIF, SLRR3A	uc004asa.3	P20774	OTTHUMG00000020224	ENST00000262551.4:c.878C>G	chr9.hg19:g.95147921G>C	ENSP00000262551:p.Pro293Arg	129.0	0.0		156.0	61.0	NM_033014	Q6FIB0|Q9UF90|Q9UNK5	Missense_Mutation	SNP	ENST00000262551.4	hg19	CCDS6695.1	.	.	.	.	.	.	.	.	.	.	G	19.50	3.839473	0.71488	.	.	ENSG00000106809	ENST00000262551;ENST00000375561	T;T	0.63744	-0.06;-0.06	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.71542	0.3352	L	0.31752	0.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.75175	-0.3410	10	0.87932	D	0	.	18.9675	0.92702	0.0:0.0:1.0:0.0	.	351;293	B4DI63;P20774	.;MIME_HUMAN	R	293	ENSP00000262551:P293R;ENSP00000364711:P293R	ENSP00000262551:P293R	P	-	2	0	OGN	94187742	1.000000	0.71417	0.936000	0.37596	0.490000	0.33462	9.589000	0.98235	2.555000	0.86185	0.650000	0.86243	CCG	.	.		0.388	OGN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053087.1	NM_024416		C	95147921	G	C	95147921	3	2	122	1	0	0	0	0	1	0	0	0	10855	1116	39	4	22	4	OGN	9	95147921	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	15826951	95147921	46065510	71	20480										
TDRD7	23424	hgsc.bcm.edu	37	chr9	100235830	100235830	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	atttgctctgatgggacactCtactgccaggtgccttgtaa	10	10	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr9:100235830C>T	ENST00000355295.4	+	11	2296	c.2001C>T	c.(1999-2001)ctC>ctT	p.L667L	TDRD7_ENST00000422139.2_Silent_p.L593L|TDRD7_ENST00000540902.1_Silent_p.L16L	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	667					germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				ATGGGACACTCTACTGCCAGG	0.438																																					p.L667L		Atlas-SNP	.											.	TDRD7	78	.	0			c.C2001T						.						184	165	171					9																	100235830		2203	4300	6503	SO:0001819	synonymous_variant	23424	exon11			GACACTCTACTGC	AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"Tudor domain containing"	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.2001C>T	chr9.hg19:g.100235830C>T		90.0	0.0		102.0	36.0	NM_014290	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Silent	SNP	ENST00000355295.4	hg19	CCDS6725.1																																																																																			.	.		0.438	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290		T	100235830	C	T	100235830	2	4	122	1	0	0	0	0	0	0	0	1	15750	900	32	3		3	TDRD7	9	100235830	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	5087909	100235830	40977601	72	20481										
CTNNA3	29119	hgsc.bcm.edu	37	chr10	69299302	69299302	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gcacatgacatcaatcatgtCcgcaaggataaggagtctcg	10	10	3	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr10:69299302C>G	ENST00000433211.2	-	4	592	c.418G>C	c.(418-420)Gac>Cac	p.D140H	CTNNA3_ENST00000545309.1_Missense_Mutation_p.D140H|CTNNA3_ENST00000373744.4_Missense_Mutation_p.D140H	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						TCAATCATGTCCGCAAGGATA	0.468																																					p.D140H		Atlas-SNP	.											.	CTNNA3	401	.	0			c.G418C						.						92	81	85					10																	69299302		2203	4300	6503	SO:0001583	missense	29119	exon4			TCATGTCCGCAAG	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.418G>C	chr10.hg19:g.69299302C>G	ENSP00000389714:p.Asp140His	135.0	0.0		186.0	18.0	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	hg19	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.263334	0.80358	.	.	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000545309;ENST00000330298;ENST00000540598	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.18	5.18	0.71444	.	0.000000	0.50627	D	0.000115	T	0.80879	0.4708	M	0.72479	2.2	0.52501	D	0.999952	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.998	T	0.83121	-0.0118	10	0.87932	D	0	-14.108	15.5958	0.76578	0.0:1.0:0.0:0.0	.	140;140;140	F2Z2R0;Q9UI47-2;Q9UI47	.;.;CTNA3_HUMAN	H	140	ENSP00000389714:D140H;ENSP00000362849:D140H;ENSP00000441444:D140H;ENSP00000330570:D140H	ENSP00000330570:D140H	D	-	1	0	CTNNA3	68969308	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	6.084000	0.71335	2.393000	0.81446	0.585000	0.79938	GAC	.	.		0.468	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		G	69299302	C	G	69299302	3	3	122	1	0	0	0	0	1	0	0	0	4016	855	30	4	2329	4	CTNNA3	10	69299302	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10		69299302	66235445	73	20482										
CDHR1	92211	hgsc.bcm.edu	37	chr10	85970872	85970872	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cgactccctctactacgttgCcaggattcctgagaacgccc	8	16	1	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr10:85970872C>A	ENST00000372117.3	+	13	1539	c.1436C>A	c.(1435-1437)gCc>gAc	p.A479D	CDHR1_ENST00000440770.2_Intron|CDHR1_ENST00000332904.3_Missense_Mutation_p.A479D	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	479	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						TACTACGTTGCCAGGATTCCT	0.587																																					p.A479D		Atlas-SNP	.											.	CDHR1	122	.	0			c.C1436A						.						90	87	88					10																	85970872		2203	4300	6503	SO:0001583	missense	92211	exon13			ACGTTGCCAGGAT	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1436C>A	chr10.hg19:g.85970872C>A	ENSP00000361189:p.Ala479Asp	41.0	0.0		58.0	20.0	NM_001171971	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	hg19	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.725952	0.89298	.	.	ENSG00000148600	ENST00000332904;ENST00000372117	T;T	0.56444	0.46;0.46	5.79	5.79	0.91817	Cadherin (3);Cadherin-like (1);	0.050379	0.85682	D	0.000000	T	0.74906	0.3778	M	0.77616	2.38	0.80722	D	1	P;D	0.89917	0.909;1.0	P;D	0.85130	0.61;0.997	T	0.76966	-0.2763	10	0.87932	D	0	-41.2947	18.8083	0.92047	0.0:1.0:0.0:0.0	.	479;479	Q96JP9-2;Q96JP9	.;CDHR1_HUMAN	D	479	ENSP00000331063:A479D;ENSP00000361189:A479D	ENSP00000331063:A479D	A	+	2	0	CDHR1	85960852	1.000000	0.71417	0.999000	0.59377	0.922000	0.55478	5.665000	0.68052	2.735000	0.93741	0.563000	0.77884	GCC	.	.		0.587	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		A	85970872	C	A	85970872	3	1	122	1	0	0	0	0	1	0	0	0	3120	739	26	3	1486	3	CDHR1	10	85970872	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	16671570	85970872	49563875	74	20483										
DUSP5	1847	hgsc.bcm.edu	37	chr10	112262621	112262621	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gtcagctacaggccagcttaTgaccaggtacgtgatgtgat	12	9	1	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr10:112262621T>C	ENST00000369583.3	+	2	806	c.522T>C	c.(520-522)taT>taC	p.Y174Y	DUSP5_ENST00000468749.1_3'UTR	NM_004419.3	NP_004410.3	Q16690	DUS5_HUMAN	dual specificity phosphatase 5	174					endoderm formation (GO:0001706)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			kidney(2)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	13		Breast(234;0.0848)		Epithelial(162;0.000276)|all cancers(201;0.00465)|BRCA - Breast invasive adenocarcinoma(275;0.12)		GGCCAGCTTATGACCAGGTAC	0.502																																					p.Y174Y		Atlas-SNP	.											.	DUSP5	62	.	0			c.T522C						.						187	154	165					10																	112262621		2203	4300	6503	SO:0001819	synonymous_variant	1847	exon2			AGCTTATGACCAG	U16996	CCDS7566.1	10q25	2011-06-09			ENSG00000138166	ENSG00000138166		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3071	protein-coding gene	gene with protein product		603069				7806236	Standard	NM_004419		Approved	HVH3	uc001kzd.3	Q16690	OTTHUMG00000019040	ENST00000369583.3:c.522T>C	chr10.hg19:g.112262621T>C		93.0	0.0		104.0	40.0	NM_004419	Q12997|Q5T603	Silent	SNP	ENST00000369583.3	hg19	CCDS7566.1																																																																																			.	.		0.502	DUSP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050333.1	NM_004419		C	112262621	T	C	112262621	2	2	122	1	0	0	0	0	0	0	0	1	4830	1471	51	2		2	DUSP5	10	112262621	Silent	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	26291749	112262621	23272126	75	20484										
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	380010	380010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gcgggccctgcgcgccgcgcGcctgccccggtaacgacccc	14	21	0	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr11:380010G>A	ENST00000329962.6	+	16	2633	c.2633G>A	c.(2632-2634)cGc>cAc	p.R878H		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	878					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGCGCCGCGCGCCTGCCCCGG	0.692																																					p.R878H		Atlas-SNP	.											B4GALNT4,colon,carcinoma,0,2	B4GALNT4	83	.	0			c.G2633A						.						31	40	37					11																	380010		2200	4298	6498	SO:0001583	missense	338707	exon16			CCGCGCGCCTGCC	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"Beta 4-glycosyltransferases"	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2633G>A	chr11.hg19:g.380010G>A	ENSP00000328277:p.Arg878His	14.0	0.0		7.0	5.0	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	hg19	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	a	2.120	-0.401761	0.04865	.	.	ENSG00000182272	ENST00000329962	T	0.15372	2.43	3.71	-1.89	0.07689	.	0.493753	0.17568	N	0.169575	T	0.08537	0.0212	L	0.40543	1.245	0.09310	N	1	P	0.35383	0.498	B	0.18561	0.022	T	0.18461	-1.0336	10	0.36615	T	0.2	-11.2656	5.1434	0.14971	0.4132:0.2629:0.324:0.0	.	878	Q76KP1	B4GN4_HUMAN	H	878	ENSP00000328277:R878H	ENSP00000328277:R878H	R	+	2	0	B4GALNT4	370010	0.000000	0.05858	0.023000	0.16930	0.016000	0.09150	-0.556000	0.05992	-0.532000	0.06332	-1.028000	0.02416	CGC	.	.		0.692	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		A	380010	G	A	380010	3	1	122	1	0	0	0	0	1	0	0	0	1269	1087	38	1	2695	1	B4GALNT4	11	380010	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10		380010	134626506	76	20485										
TRIM68	55128	hgsc.bcm.edu	37	chr11	4621894	4621894	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cctccacctcccagtagtgcCggcctgaggagatgcactgg	12	15	0	2	rs139399398		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr11:4621894C>T	ENST00000300747.5	-	7	1359	c.1070G>A	c.(1069-1071)cGg>cAg	p.R357Q		NM_018073.6	NP_060543.5	Q6AZZ1	TRI68_HUMAN	tripartite motif containing 68	357	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein autoubiquitination (GO:0051865)|regulation of androgen receptor signaling pathway (GO:0060765)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|histone acetyltransferase binding (GO:0035035)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		CCAGTAGTGCCGGCCTGAGGA	0.542																																					p.R357Q		Atlas-SNP	.											TRIM68,right_lower_lobe,carcinoma,0,1	TRIM68	53	.	0			c.G1070A						.	C	GLN/ARG	1,4401	2.1+/-5.4	0,1,2200	48	50	50		1070	0.8	1	11	dbSNP_134	50	0,8596		0,0,4298	no	missense	TRIM68	NM_018073.5	43	0,1,6498	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	357/486	4621894	1,12997	2201	4298	6499	SO:0001583	missense	55128	exon7			TAGTGCCGGCCTG	AF360739	CCDS31356.1	11p15.4	2013-01-09	2011-01-25	2004-11-17		ENSG00000167333		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21161	protein-coding gene	gene with protein product		613184	"ring finger protein 137", "tripartite motif-containing 68"	RNF137		11597395	Standard	NM_018073		Approved	SS-56, FLJ10369	uc001lzf.2	Q6AZZ1		ENST00000300747.5:c.1070G>A	chr11.hg19:g.4621894C>T	ENSP00000300747:p.Arg357Gln	118.0	0.0		118.0	53.0	NM_018073	A6NI19|A8K551|B3KPM5|B4DVK4|Q8WZ70|Q96LE5|Q96PF7|Q9H9C2|Q9NW18	Missense_Mutation	SNP	ENST00000300747.5	hg19	CCDS31356.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.179112	0.57800	2.27E-4	0.0	ENSG00000167333	ENST00000300747;ENST00000544055;ENST00000526337	T;T	0.70631	-0.5;-0.13	5.52	0.837	0.18896	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.48286	D	0.000193	T	0.66577	0.2803	M	0.80616	2.505	0.30926	N	0.727454	D	0.59357	0.985	B	0.43386	0.418	T	0.68534	-0.5383	10	0.87932	D	0	.	4.214	0.10526	0.1499:0.4915:0.0:0.3586	.	357	Q6AZZ1	TRI68_HUMAN	Q	357;78;134	ENSP00000300747:R357Q;ENSP00000434681:R134Q	ENSP00000300747:R357Q	R	-	2	0	TRIM68	4578470	0.776000	0.28616	0.996000	0.52242	0.994000	0.84299	1.357000	0.34090	0.281000	0.22233	0.561000	0.74099	CGG	.	C|1.000;T|0.000		0.542	TRIM68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385948.1	NM_018073		T	4621894	C	T	4621894	3	4	122	1	0	0	0	0	1	0	0	0	16556	652	23	1	391	1	TRIM68	11	4621894	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	4241884	4621894	130384622	77	20486										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587787	55587787	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tcattgttgtaaccatcctcAagatgcgttcagtcagtggg	10	9	4	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr11:55587787A>G	ENST00000333976.4	+	1	702	c.682A>G	c.(682-684)Aag>Gag	p.K228E		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				AACCATCCTCAAGATGCGTTC	0.493																																					p.K228E		Atlas-SNP	.											.	OR5D18	121	.	0			c.A682G						.						156	130	139					11																	55587787		2200	4296	6496	SO:0001583	missense	219438	exon1			ATCCTCAAGATGC	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.682A>G	chr11.hg19:g.55587787A>G	ENSP00000335025:p.Lys228Glu	142.0	0.0		168.0	62.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	hg19	CCDS31510.1	.	.	.	.	.	.	.	.	.	.	.	12.29	1.892631	0.33442	.	.	ENSG00000186119	ENST00000333976	T	0.00169	8.63	4.73	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	0.177783	0.27302	N	0.019982	T	0.00580	0.0019	M	0.91249	3.19	0.09310	N	1	D	0.63046	0.992	D	0.67900	0.954	T	0.23583	-1.0184	10	0.72032	D	0.01	-20.3675	8.1633	0.31211	0.9029:0.0:0.0971:0.0	.	228	Q8NGL1	OR5DI_HUMAN	E	228	ENSP00000335025:K228E	ENSP00000335025:K228E	K	+	1	0	OR5D18	55344363	0.011000	0.17503	0.866000	0.34008	0.205000	0.24178	2.697000	0.47060	1.945000	0.56424	0.462000	0.41574	AAG	.	.		0.493	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		G	55587787	A	G	55587787	3	3	122	1	0	0	0	0	1	0	0	0	11166	131	5	2	684	2	OR5D18	11	55587787	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	50965893	55587787	79418729	78	20487										
OR5L2	26338	hgsc.bcm.edu	37	chr11	55595156	55595156	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgctacttctgtgggacggtGtgttctctgattcactcgtc	11	10	3	1	rs144734181	byFrequency	TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr11:55595156G>T	ENST00000378397.1	+	1	462	c.462G>T	c.(460-462)gtG>gtT	p.V154V		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				GTGGGACGGTGTGTTCTCTGA	0.493										HNSCC(27;0.073)																											p.V154V		Atlas-SNP	.											OR5L2,NS,carcinoma,0,1	OR5L2	135	.	0			c.G462T						.						222	190	201					11																	55595156		2200	4296	6496	SO:0001819	synonymous_variant	26338	exon1			GACGGTGTGTTCT	AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"GPCR / Class A : Olfactory receptors"	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.462G>T	chr11.hg19:g.55595156G>T		198.0	0.0		231.0	87.0	NM_001004739	Q6IF66|Q96RB2	Silent	SNP	ENST00000378397.1	hg19	CCDS31511.1																																																																																			.	G|0.999;C|0.001		0.493	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739		T	55595156	G	T	55595156	2	4	122	1	0	0	0	0	0	0	0	1	11180	1364	48	3		3	OR5L2	11	55595156	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	7369	55595156	79411360	79	20488										
OR9I1	219954	hgsc.bcm.edu	37	chr11	57886305	57886305	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gcattggccaaaatcacaaaAttgccaaagaagatgatgac	8	8	1	4			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr11:57886305A>T	ENST00000302610.1	-	1	611	c.612T>A	c.(610-612)aaT>aaA	p.N204K	OR9Q1_ENST00000335397.3_Intron	NM_001005211.1	NP_001005211.1	Q8NGQ6	OR9I1_HUMAN	olfactory receptor, family 9, subfamily I, member 1	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|liver(1)|lung(15)|pancreas(1)|skin(1)|urinary_tract(1)	23		Breast(21;0.0589)				AAATCACAAAATTGCCAAAGA	0.448																																					p.N204K		Atlas-SNP	.											.	OR9I1	53	.	0			c.T612A						.						104	94	97					11																	57886305		2201	4296	6497	SO:0001583	missense	219954	exon1			CACAAAATTGCCA	AB065733	CCDS31542.1	11q12.1	2012-08-09			ENSG00000172377	ENSG00000172377		"GPCR / Class A : Olfactory receptors"	14718	protein-coding gene	gene with protein product							Standard	NM_001005211		Approved		uc021qjl.1	Q8NGQ6	OTTHUMG00000167404	ENST00000302610.1:c.612T>A	chr11.hg19:g.57886305A>T	ENSP00000302606:p.Asn204Lys	88.0	0.0		93.0	20.0	NM_001005211	Q6IFH0|Q96RA8	Missense_Mutation	SNP	ENST00000302610.1	hg19	CCDS31542.1	.	.	.	.	.	.	.	.	.	.	A	7.410	0.634607	0.14322	.	.	ENSG00000172377	ENST00000302610	T	0.36878	1.23	4.87	2.86	0.33363	GPCR, rhodopsin-like superfamily (1);	0.118515	0.37761	N	0.001948	T	0.21145	0.0509	N	0.24115	0.695	0.21802	N	0.999533	B	0.09022	0.002	B	0.15052	0.012	T	0.18023	-1.0350	10	0.87932	D	0	-16.8461	4.1634	0.10295	0.2151:0.0:0.6063:0.1787	.	204	Q8NGQ6	OR9I1_HUMAN	K	204	ENSP00000302606:N204K	ENSP00000302606:N204K	N	-	3	2	OR9I1	57642881	0.000000	0.05858	1.000000	0.80357	0.195000	0.23768	0.147000	0.16202	0.660000	0.30964	0.383000	0.25322	AAT	.	.		0.448	OR9I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394539.1	NM_001005211		T	57886305	A	T	57886305	3	4	122	1	0	0	0	0	1	0	0	0	11262	98	4	4	336	4	OR9I1	11	57886305	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	2291149	57886305	77120211	80	20489										
DAGLA	747	hgsc.bcm.edu	37	chr11	61496465	61496465	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	accagaaacaccaagtacctCgacctcaagaattcagtgag	7	12	2	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr11:61496465C>A	ENST00000257215.5	+	8	950	c.834C>A	c.(832-834)ctC>ctA	p.L278L		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	278					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		CCAAGTACCTCGACCTCAAGA	0.547																																					p.L278L		Atlas-SNP	.											.	DAGLA	109	.	0			c.C834A						.						236	190	206					11																	61496465		2202	4299	6501	SO:0001819	synonymous_variant	747	exon8			GTACCTCGACCTC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"neural stem cell-derived dendrite regulator"	614015	"chromosome 11 open reading frame 11"	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.834C>A	chr11.hg19:g.61496465C>A		143.0	0.0		167.0	18.0	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	hg19	CCDS31578.1																																																																																			.	.		0.547	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		A	61496465	C	A	61496465	2	1	122	1	0	0	0	0	0	0	0	1	4228	871	31	1		1	DAGLA	11	61496465	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	3610160	61496465	73510051	81	20490										
POLR2G	5436	hgsc.bcm.edu	37	chr11	62533971	62533971	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tttctggtttcgcagggcttGtaagctgagcctggtggcct	14	9	1	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr11:62533971G>T	ENST00000301788.7	+	8	616	c.511G>T	c.(511-513)Gta>Tta	p.V171L		NM_002696.2	NP_002687.1	P62487	RPB7_HUMAN	polymerase (RNA) II (DNA directed) polypeptide G	171					7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, exonucleolytic (GO:0000291)|nucleotide-excision repair (GO:0006289)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translational initiation (GO:0045948)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)|translation initiation factor binding (GO:0031369)			lung(3)	3						CGCAGGGCTTGTAAGCTGAGC	0.493																																					p.V171L		Atlas-SNP	.											.	POLR2G	6	.	0			c.G511T						.						186	156	166					11																	62533971		2201	4299	6500	SO:0001583	missense	5436	exon8			GGGCTTGTAAGCT	U20659	CCDS31585.1	11q13.1	2013-01-21			ENSG00000168002	ENSG00000168002		"RNA polymerase subunits"	9194	protein-coding gene	gene with protein product		602013				7579693, 9256063	Standard	NM_002696		Approved	hRPB19, hsRPB7, RPB7	uc001nva.3	P62487	OTTHUMG00000167609	ENST00000301788.7:c.511G>T	chr11.hg19:g.62533971G>T	ENSP00000301788:p.Val171Leu	133.0	0.0		122.0	7.0	NM_002696	B2R5C0|P52433|Q2M1Z4	Missense_Mutation	SNP	ENST00000301788.7	hg19	CCDS31585.1	.	.	.	.	.	.	.	.	.	.	G	14.35	2.509114	0.44660	.	.	ENSG00000168002	ENST00000301788	.	.	.	5.94	5.94	0.96194	Nucleic acid-binding, OB-fold-like (1);	0.200778	0.41938	D	0.000789	T	0.49098	0.1537	L	0.37897	1.145	0.54753	D	0.999987	B	0.02656	0.0	B	0.01281	0.0	T	0.44251	-0.9340	9	0.02654	T	1	-22.5135	15.8594	0.79009	0.0:0.0:1.0:0.0	.	171	P62487	RPB7_HUMAN	L	171	.	ENSP00000301788:V171L	V	+	1	0	POLR2G	62290547	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	4.387000	0.59626	2.822000	0.97130	0.557000	0.71058	GTA	.	.		0.493	POLR2G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395344.1	NM_002696		T	62533971	G	T	62533971	3	4	122	1	0	0	0	0	1	0	0	0	12229	1377	48	3	541	3	POLR2G	11	62533971	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	1037506	62533971	72472545	82	20491										
RNF26	79102	hgsc.bcm.edu	37	chr11	119206381	119206381	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ctgtggaggatgacggacgtAgtggctgccttcctagccca	14	11	0	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr11:119206381A>G	ENST00000311413.4	+	1	1145	c.549A>G	c.(547-549)gtA>gtG	p.V183V	RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	183						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.8e-05)		TGACGGACGTAGTGGCTGCCT	0.612																																					p.V183V		Atlas-SNP	.											.	RNF26	23	.	0			c.A549G						.						106	90	95					11																	119206381		2199	4295	6494	SO:0001819	synonymous_variant	79102	exon1			GGACGTAGTGGCT	AB055622	CCDS8419.1	11q23	2008-07-21				ENSG00000173456		"RING-type (C3HC4) zinc fingers"	14646	protein-coding gene	gene with protein product	"ring finger protein with leucine zipper"	606130				11352657	Standard	NM_032015		Approved	MGC2642	uc001pwh.3	Q9BY78		ENST00000311413.4:c.549A>G	chr11.hg19:g.119206381A>G		111.0	0.0		106.0	38.0	NM_032015	Q542Y8	Silent	SNP	ENST00000311413.4	hg19	CCDS8419.1																																																																																			.	.		0.612	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015		G	119206381	A	G	119206381	2	3	122	1	0	0	0	0	0	0	0	1	13501	407	15	2		2	RNF26	11	119206381	Silent	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	56672410	119206381	15800135	83	20492										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26568361	26568361	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ggactgcagttagaataataGagcggccatttcgtgtgaca	12	7	0	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr12:26568361G>C	ENST00000381340.3	-	51	7597	c.7181C>G	c.(7180-7182)tCt>tGt	p.S2394C	RP11-513G19.1_ENST00000535324.1_RNA	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	2394					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TAGAATAATAGAGCGGCCATT	0.383																																					p.S2394C		Atlas-SNP	.											.	ITPR2	270	.	0			c.C7181G						.						141	141	141					12																	26568361		1866	4105	5971	SO:0001583	missense	3709	exon51			ATAATAGAGCGGC	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.7181C>G	chr12.hg19:g.26568361G>C	ENSP00000370744:p.Ser2394Cys	117.0	0.0		132.0	37.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.725769	0.89298	.	.	ENSG00000123104	ENST00000381340	D	0.98684	-5.07	5.08	5.08	0.68730	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99327	0.9764	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98985	1.0806	10	0.87932	D	0	.	18.6686	0.91501	0.0:0.0:1.0:0.0	.	2394	Q14571	ITPR2_HUMAN	C	2394	ENSP00000370744:S2394C	ENSP00000370744:S2394C	S	-	2	0	ITPR2	26459628	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.640000	0.98453	2.636000	0.89361	0.591000	0.81541	TCT	.	.		0.383	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		C	26568361	G	C	26568361	3	2	122	1	0	0	0	0	1	0	0	0	7930	942	33	4	952	4	ITPR2	12	26568361	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10		26568361	107283534	84	20493										
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50186244	50186244	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ctcaccatgggggtcctgggCagcccctccagttgtcgggg	15	14	1	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr12:50186244C>A	ENST00000335999.6	-	12	3978	c.3777G>T	c.(3775-3777)ctG>ctT	p.L1259L		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	1255	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						GGGTCCTGGGCAGCCCCTCCA	0.612																																					p.L1259L		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.G3777T						.						30	34	33					12																	50186244		1931	4124	6055	SO:0001819	synonymous_variant	57701	exon12			CCTGGGCAGCCCC	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.3777G>T	chr12.hg19:g.50186244C>A		61.0	0.0		59.0	21.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	hg19	CCDS41781.2	.	.	.	.	.	.	.	.	.	.	C	8.064	0.768752	0.15983	.	.	ENSG00000167566	ENST00000433948	.	.	.	5.15	0.902	0.19290	.	.	.	.	.	T	0.44582	0.1300	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28004	-1.0057	4	.	.	.	-11.7817	3.7532	0.08575	0.5004:0.288:0.1278:0.0839	.	.	.	.	S	974	.	.	A	-	1	0	NCKAP5L	48472511	0.980000	0.34600	1.000000	0.80357	0.969000	0.65631	-0.086000	0.11233	0.654000	0.30846	0.561000	0.74099	GCC	.	.		0.612	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		A	50186244	C	A	50186244	2	1	122	1	0	0	0	0	0	0	0	1	10233	697	25	3		3	NCKAP5L	12	50186244	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	23617883	50186244	83665651	85	20494										
GRIP1	23426	hgsc.bcm.edu	37	chr12	66742812	66742812	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	agcgttgctataatgtattaGtgggttctcgtgtctccaaa	10	7	2	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr12:66742812G>T	ENST00000398016.3	-	24	3286	c.3218C>A	c.(3217-3219)aCt>aAt	p.T1073N	GRIP1_ENST00000359742.4_Missense_Mutation_p.T1125N|GRIP1_ENST00000286445.7_Missense_Mutation_p.T1110N	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TAATGTATTAGTGGGTTCTCG	0.403																																					p.T1073N		Atlas-SNP	.											.	GRIP1	106	.	0			c.C3218A						.						258	248	251					12																	66742812		1885	4113	5998	SO:0001583	missense	23426	exon24			GTATTAGTGGGTT	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.3218C>A	chr12.hg19:g.66742812G>T	ENSP00000381098:p.Thr1073Asn	275.0	0.0		283.0	30.0	NM_021150	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	hg19	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.452|7.452	0.642881|0.642881	0.14451|0.14451	.|.	.|.	ENSG00000155974|ENSG00000155974	ENST00000538164|ENST00000398016;ENST00000359742;ENST00000286445	.|T;T;T	.|0.21361	.|2.01;2.03;2.03	5.64|5.64	3.75|3.75	0.43078|0.43078	.|.	.|0.185894	.|0.45361	.|D	.|0.000380	T|T	0.22044|0.22044	0.0531|0.0531	L|L	0.29908|0.29908	0.895|0.895	0.44275|0.44275	D|D	0.997131|0.997131	.|P;D	.|0.57571	.|0.95;0.98	.|P;P	.|0.53649	.|0.648;0.731	T|T	0.01621|0.01621	-1.1310|-1.1310	5|9	.|.	.|.	.|.	-7.1406|-7.1406	8.3084|8.3084	0.32055|0.32055	0.0701:0.0:0.6474:0.2826|0.0701:0.0:0.6474:0.2826	.|.	.|1073;1110	.|Q9Y3R0-3;Q9Y3R0-2	.|.;.	I|N	925|1073;1125;1110	.|ENSP00000381098:T1073N;ENSP00000352780:T1125N;ENSP00000286445:T1110N	.|.	L|T	-|-	1|2	2|0	GRIP1|GRIP1	65029079|65029079	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.274000|0.274000	0.26718|0.26718	5.024000|5.024000	0.64090|0.64090	0.693000|0.693000	0.31634|0.31634	0.655000|0.655000	0.94253|0.94253	CTA|ACT	.	.		0.403	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			T	66742812	G	T	66742812	3	4	122	1	0	0	0	0	1	0	0	0	6796	1029	36	3	16	3	GRIP1	12	66742812	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	16556568	66742812	67109083	86	20495										
ATXN2	6311	hgsc.bcm.edu	37	chr12	111951212	111951212	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cgagggactggtccttgctaCtggaggagtagctgcttcac	14	10	1	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr12:111951212C>T	ENST00000377617.3	-	11	2148	c.1987G>A	c.(1987-1989)Gta>Ata	p.V663I	ATXN2_ENST00000389153.4_Missense_Mutation_p.V398I|ATXN2_ENST00000542287.2_Missense_Mutation_p.V398I|ATXN2_ENST00000550104.1_Missense_Mutation_p.V663I|ATXN2_ENST00000535949.1_Missense_Mutation_p.V374I|ATXN2_ENST00000608853.1_Missense_Mutation_p.V503I	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	663	Pro-rich.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						GTCCTTGCTACTGGAGGAGTA	0.507																																					p.V663I		Atlas-SNP	.											.	ATXN2	99	.	0			c.G1987A						.						109	93	98					12																	111951212		2203	4300	6503	SO:0001583	missense	6311	exon11			TTGCTACTGGAGG	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.1987G>A	chr12.hg19:g.111951212C>T	ENSP00000366843:p.Val663Ile	136.0	0.0		142.0	6.0	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Missense_Mutation	SNP	ENST00000377617.3	hg19	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.105245	0.77096	.	.	ENSG00000204842	ENST00000389153;ENST00000377617;ENST00000550104;ENST00000542287;ENST00000535949;ENST00000492467;ENST00000550236	T;T	0.64803	-0.1;-0.12	5.07	3.25	0.37280	.	0.309004	0.34986	N	0.003532	T	0.43411	0.1246	N	0.24115	0.695	0.30602	N	0.760433	B;B;B;B	0.25486	0.127;0.006;0.127;0.012	B;B;B;B	0.24006	0.05;0.005;0.034;0.01	T	0.40098	-0.9581	10	0.37606	T	0.19	-0.8977	7.2842	0.26328	0.1369:0.7164:0.0:0.1467	.	398;663;374;398	B3KT59;Q99700;Q24JQ7;F8VQP2	.;ATX2_HUMAN;.;.	I	398;663;663;398;374;53;78	ENSP00000366843:V663I;ENSP00000446576:V663I	ENSP00000366843:V663I	V	-	1	0	ATXN2	110435595	0.998000	0.40836	0.996000	0.52242	0.994000	0.84299	2.667000	0.46808	0.647000	0.30713	0.650000	0.86243	GTA	.	.		0.507	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		T	111951212	C	T	111951212	3	4	122	1	0	0	0	0	1	0	0	0	1211	565	20	3	2014	3	ATXN2	12	111951212	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	45208400	111951212	21900683	87	20496										
ZMYM5	9205	hgsc.bcm.edu	37	chr13	20426199	20426199	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tcctagatctactgactaaaGgacaagctggatgaccaaat	8	9	1	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr13:20426199G>C	ENST00000337963.4	-	3	386	c.122C>G	c.(121-123)cCt>cGt	p.P41R	ZMYM5_ENST00000382905.4_Missense_Mutation_p.P41R|ZMYM5_ENST00000382907.4_Missense_Mutation_p.P41R	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	41						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		ACTGACTAAAGGACAAGCTGG	0.413																																					p.P41R		Atlas-SNP	.											.	ZMYM5	73	.	0			c.C122G						.						152	147	148					13																	20426199		2203	4300	6503	SO:0001583	missense	9205	exon3			ACTAAAGGACAAG	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.122C>G	chr13.hg19:g.20426199G>C	ENSP00000337034:p.Pro41Arg	75.0	0.0		100.0	34.0	NM_001039650	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	hg19		.	.	.	.	.	.	.	.	.	.	G	7.356	0.623830	0.14193	.	.	ENSG00000132950	ENST00000337963;ENST00000502168;ENST00000382907;ENST00000382905	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	4.25	1.51	0.23008	.	.	.	.	.	T	0.28797	0.0714	L	0.57536	1.79	0.20307	N	0.999916	B;B;B	0.21821	0.061;0.02;0.009	B;B;B	0.19391	0.021;0.025;0.01	T	0.28933	-1.0028	9	0.87932	D	0	-0.4603	7.5323	0.27689	0.1541:0.1363:0.7096:0.0	.	41;41;41	Q9UJ78;Q9UJ78-2;Q9UJ78-1	ZMYM5_HUMAN;.;.	R	41;31;41;41	ENSP00000337034:P41R;ENSP00000445779:P31R;ENSP00000372364:P41R;ENSP00000372361:P41R	ENSP00000337034:P41R	P	-	2	0	ZMYM5	19324199	0.173000	0.23056	0.021000	0.16686	0.002000	0.02628	0.507000	0.22675	0.182000	0.20032	-1.099000	0.02127	CCT	.	.		0.413	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		C	20426199	G	C	20426199	3	2	122	1	0	0	0	0	1	0	0	0	17718	1000	35	4	2022	4	ZMYM5	13	20426199	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10		20426199	94743679	88	20497										
LCP1	3936	hgsc.bcm.edu	37	chr13	46730648	46730649	+	Missense_Mutation	DNP	TC	TC	CA													0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttgggatgacatgccgacaaTcaggatcattttccagggct							TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr13:46730648_46730649TC>CA	ENST00000398576.2	-	8	803_804	c.415_416GA>TG	c.(415-417)GAt>TGt	p.D139C	LCP1_ENST00000323076.2_Missense_Mutation_p.D139C|LCP1_ENST00000460190.1_5'Flank			P13796	PLSL_HUMAN	lymphocyte cytosolic protein 1 (L-plastin)	139	Actin-binding 1.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|organ regeneration (GO:0031100)|protein kinase A signaling (GO:0010737)|regulation of intracellular protein transport (GO:0033157)|T cell activation involved in immune response (GO:0002286)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			breast(2)|kidney(1)|large_intestine(6)|lung(18)|ovary(4)|prostate(2)|skin(1)	34		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)		ATGCCGACAATCAGGATCATTT	0.381			T	BCL6	NHL																																p.D139G|p.D139Y		Atlas-SNP	.		Dom	yes		13	13q14.1-q14.3	3936	lymphocyte cytosolic protein 1 (L-plastin)		L	.	LCP1	69	.	0			c.A416G|c.G415T						.																																			SO:0001583	missense	3936	exon5			CGACAATCAGGAT|GACAATCAGGATC	M22300	CCDS9403.1	13q14.3	2013-01-10			ENSG00000136167	ENSG00000136167		"EF-hand domain containing"	6528	protein-coding gene	gene with protein product	"plastin 2"	153430				2111166	Standard	NM_002298		Approved	PLS2, CP64, L-PLASTIN, LC64P	uc001vba.4	P13796	OTTHUMG00000016864	ENST00000398576.2:c.415_416delinsCA	chr13.hg19:g.46730648_46730649delinsCA	ENSP00000381581:p.Asp139Cys	164.0|165.0	0.0		196.0	23.0|24.0	NM_002298	B2R613|B4DUA0|Q5TBN4	Missense_Mutation	SNP	ENST00000398576.2	hg19	CCDS9403.1																																																																																			.	.		0.381	LCP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044800.3	NM_002298		CA	46730649	TC	CA	46730648	3	2	122	1	0	0	0	0	1	0	0	0	8700	1435	50	2	1515	2	LCP1	13	46730648	Missense_Mutation	DNP	TC	TCGA-DD-A3A8-01A-11D-A22F-10	26304449	46730648	68439230	89	20498										
IPO4	79711	hgsc.bcm.edu	37	chr14	24654742	24654743	+	Frame_Shift_Ins	INS	-	-	ACAC													0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gaggggtcctccaggcccttINSgcacacaatctgcagcagtg							TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr14:24654742_24654743insACAC	ENST00000354464.6	-	13	1376_1377	c.1200_1201insGTGT	c.(1198-1203)tgcaagfs	p.K401fs	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	401					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		TCCAGGCCCTTGCACACAATCT	0.569																																					p.K401_G402delinsVX		Atlas-INDEL	.											.	IPO4	74	.	0			c.1201_1202insGTGT						.																																			SO:0001589	frameshift_variant	79711	exon13			.	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"Importins"	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1200_1201insGTGT	chr14.hg19:g.24654742_24654743insACAC	ENSP00000346453:p.Lys401fs	44.0	0.0		60.0	27.0	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Frame_Shift_Ins	INS	ENST00000354464.6	hg19	CCDS9616.1																																																																																			.	.		0.569	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		ACAC	24654743	-	ACAC	24654742	7	5	122	1	0	1	1	0	0	0	0	0	7804	1821	63	0	2116	0	IPO4	14	24654742	Frame_Shift_Ins	INS	-	TCGA-DD-A3A8-01A-11D-A22F-10		24654742	82694798	90	20499	88	2								
IPO4	79711	hgsc.bcm.edu	37	chr14	24654743	24654743	+	Silent	SNP	G	G	A													0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gaggggtcctccaggcccttGcacacaatctgcagcagtgg							TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr14:24654743G>A	ENST00000354464.6	-	13	1376	c.1200C>T	c.(1198-1200)tgC>tgT	p.C400C	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	400					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CCAGGCCCTTGCACACAATCT	0.567																																					p.C400C		Atlas-SNP	.											.	IPO4	74	.	0			c.C1200T						.						67	70	69					14																	24654743		2021	4187	6208	SO:0001819	synonymous_variant	79711	exon13			GCCCTTGCACACA	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"Importins"	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1200C>T	chr14.hg19:g.24654743G>A		42.0	0.0		59.0	29.0	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	hg19	CCDS9616.1																																																																																			.	.		0.567	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		A	24654743	G	A	24654743	2	1	122	1	0	0	0	0	0	0	0	1	7804	1311	46	3		3	IPO4	14	24654743	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	1	24654743	82694797	91	20500	88	2								
RBM25	58517	hgsc.bcm.edu	37	chr14	73576174	73576174	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gccttctggcagaagggcatCcagatccagatgcagagctc	12	12	1	4			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr14:73576174C>G	ENST00000261973.7	+	14	1951	c.1666C>G	c.(1666-1668)Cca>Gca	p.P556A	RBM25_ENST00000527432.1_Missense_Mutation_p.P556A|RBM25_ENST00000532483.1_3'UTR	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	556	Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		AGAAGGGCATCCAGATCCAGA	0.557																																					p.P556A		Atlas-SNP	.											.	RBM25	81	.	0			c.C1666G						.						89	87	88					14																	73576174		2203	4300	6503	SO:0001583	missense	58517	exon14			GGGCATCCAGATC	BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"RNA binding motif (RRM) containing"	23244	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 94"	612427	"RNA-binding region (RNP1, RRM) containing 7"	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.1666C>G	chr14.hg19:g.73576174C>G	ENSP00000261973:p.Pro556Ala	138.0	0.0		154.0	39.0	NM_021239	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Missense_Mutation	SNP	ENST00000261973.7	hg19	CCDS32113.1	.	.	.	.	.	.	.	.	.	.	C	33	5.268128	0.95429	.	.	ENSG00000119707	ENST00000261973;ENST00000527432	T;T	0.12569	2.67;2.67	5.97	5.97	0.96955	.	0.046120	0.85682	D	0.000000	T	0.19485	0.0468	M	0.66939	2.045	0.80722	D	1	B	0.22541	0.071	B	0.18871	0.023	T	0.08700	-1.0709	10	0.16896	T	0.51	.	20.4388	0.99107	0.0:1.0:0.0:0.0	.	556	P49756	RBM25_HUMAN	A	556	ENSP00000261973:P556A;ENSP00000431150:P556A	ENSP00000261973:P556A	P	+	1	0	RBM25	72645927	1.000000	0.71417	0.995000	0.50966	0.911000	0.54048	7.654000	0.83653	2.836000	0.97738	0.655000	0.94253	CCA	.	.		0.557	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		G	73576174	C	G	73576174	3	3	122	1	0	0	0	0	1	0	0	0	13140	855	30	4	1716	4	RBM25	14	73576174	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	48921431	73576174	33773366	92	20501										
SEL1L	6400	hgsc.bcm.edu	37	chr14	81964803	81964803	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gtcagggcagattcacaactCtggaggacgccgatgccagc	13	12	3	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr14:81964803C>T	ENST00000336735.4	-	9	1043	c.927G>A	c.(925-927)caG>caA	p.Q309Q		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	309	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		ATTCACAACTCTGGAGGACGC	0.428																																					p.Q309Q		Atlas-SNP	.											.	SEL1L	67	.	0			c.G927A						.						101	92	95					14																	81964803		2203	4300	6503	SO:0001819	synonymous_variant	6400	exon9			ACAACTCTGGAGG		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.927G>A	chr14.hg19:g.81964803C>T		74.0	0.0		67.0	17.0	NM_005065	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	hg19	CCDS9876.1																																																																																			.	.		0.428	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		T	81964803	C	T	81964803	2	4	122	1	0	0	0	0	0	0	0	1	14025	912	32	3		3	SEL1L	14	81964803	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	8388629	81964803	25384737	93	20502										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414676	105414676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ggacctccaggtcagcggaaGggggctgaacgctgaggtca	17	10	2	2	rs528075601	byFrequency	TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr14:105414676G>A	ENST00000333244.5	-	7	7231	c.7112C>T	c.(7111-7113)cCt>cTt	p.P2371L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2371						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GTCAGCGGAAGGGGGCTGAAC	0.662													.|||	13	0.00259585	0.0083	0.0014	5008	,	,		5052	0.001		0	False		,,,				2504	0				p.P2371L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C7112T						.						125	138	134					14																	105414676		1960	4148	6108	SO:0001583	missense	113146	exon7			GCGGAAGGGGGCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7112C>T	chr14.hg19:g.105414676G>A	ENSP00000353114:p.Pro2371Leu	87.0	0.0		104.0	34.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	11.96	1.793434	0.31685	.	.	ENSG00000185567	ENST00000333244	T	0.03004	4.08	3.79	2.89	0.33648	.	.	.	.	.	T	0.20292	0.0488	M	0.93328	3.405	0.09310	N	1	D	0.76494	0.999	D	0.72982	0.979	T	0.10497	-1.0627	9	0.66056	D	0.02	.	4.8614	0.13585	0.1144:0.0:0.6724:0.2132	.	2371	Q8IVF2	AHNK2_HUMAN	L	2371	ENSP00000353114:P2371L	ENSP00000353114:P2371L	P	-	2	0	AHNAK2	104485721	0.311000	0.24536	0.003000	0.11579	0.001000	0.01503	3.547000	0.53663	0.571000	0.29365	-0.471000	0.05019	CCT	.	.		0.662	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105414676	G	A	105414676	3	1	122	1	0	0	0	0	1	0	0	0	415	1000	35	3	10279	3	AHNAK2	14	105414676	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	23449873	105414676	1934864	94	20503										
ATP10A	57194	hgsc.bcm.edu	37	chr15	26026303	26026303	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	cgcagggaagatttcgttgcAgcgaagacgcacaaagtctc	12	10	1	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr15:26026303A>G	ENST00000356865.6	-	2	628	c.517T>C	c.(517-519)Tgc>Cgc	p.C173R		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	173					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		ATTTCGTTGCAGCGAAGACGC	0.498																																					p.C173R		Atlas-SNP	.											.	ATP10A	270	.	0			c.T517C						.						107	106	106					15																	26026303		2203	4300	6503	SO:0001583	missense	57194	exon2			CGTTGCAGCGAAG	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.517T>C	chr15.hg19:g.26026303A>G	ENSP00000349325:p.Cys173Arg	86.0	0.0		55.0	11.0	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	A	16.21	3.057409	0.55325	.	.	ENSG00000206190	ENST00000356865	T	0.73047	-0.71	4.67	4.67	0.58626	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.048092	0.85682	D	0.000000	T	0.64450	0.2599	L	0.31752	0.955	0.80722	D	1	B	0.24043	0.096	B	0.36464	0.225	T	0.63139	-0.6704	10	0.40728	T	0.16	-28.913	13.4539	0.61187	1.0:0.0:0.0:0.0	.	173	O60312	AT10A_HUMAN	R	173	ENSP00000349325:C173R	ENSP00000349325:C173R	C	-	1	0	ATP10A	23577396	1.000000	0.71417	0.953000	0.39169	0.310000	0.27922	8.778000	0.91785	1.967000	0.57214	0.459000	0.35465	TGC	.	.		0.498	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		G	26026303	A	G	26026303	3	3	122	1	0	0	0	0	1	0	0	0	1116	188	7	2	4062	2	ATP10A	15	26026303	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10		26026303	76505089	95	20504										
C15orf33	196951	hgsc.bcm.edu	37	chr15	49659729	49659729	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gctcatgcatcttaagataaTataaaatcaatggactctga	6	7	4	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr15:49659729T>C	ENST00000299338.6	-	13	1490	c.1187A>G	c.(1186-1188)tAt>tGt	p.Y396C		NM_152647.2	NP_689860.2	Q96M60	F227B_HUMAN	family with sequence similarity 227, member B	396																	CTTAAGATAATATAAAATCAA	0.358																																					p.Y396C		Atlas-SNP	.											.	.	.	.	0			c.A1187G						.						82	88	86					15																	49659729		2196	4294	6490	SO:0001583	missense	196951	exon13			AGATAATATAAAA		CCDS32237.1	15q21.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000166262	ENSG00000166262			26543	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 33"	C15orf33			Standard	NM_152647		Approved	FLJ32800	uc001zxl.2	Q96M60	OTTHUMG00000172328	ENST00000299338.6:c.1187A>G	chr15.hg19:g.49659729T>C	ENSP00000299338:p.Tyr396Cys	96.0	0.0		109.0	42.0	NM_152647	Q86WS2	Missense_Mutation	SNP	ENST00000299338.6	hg19	CCDS32237.1	.	.	.	.	.	.	.	.	.	.	T	16.80	3.223582	0.58668	.	.	ENSG00000166262	ENST00000299338	.	.	.	5.16	5.16	0.70880	.	0.000000	0.45126	D	0.000388	T	0.76622	0.4013	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.68943	0.961	T	0.79140	-0.1926	9	0.62326	D	0.03	-7.1496	14.1245	0.65210	0.0:0.0:0.0:1.0	.	396	Q96M60	CO033_HUMAN	C	396	.	ENSP00000299338:Y396C	Y	-	2	0	C15orf33	47447021	0.997000	0.39634	0.996000	0.52242	0.589000	0.36550	4.386000	0.59620	2.179000	0.69175	0.528000	0.53228	TAT	.	.		0.358	FAM227B-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417872.1	NM_152647		C	49659729	T	C	49659729	3	2	122	1	0	0	0	0	1	0	0	0	1793	1406	49	2	355	2	C15orf33	15	49659729	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	23633426	49659729	52871663	96	20505										
PAQR5	54852	hgsc.bcm.edu	37	chr15	69695986	69695986	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	catgcagatggaagccatacTtctggacaagactctgagga	11	9	2	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr15:69695986T>A	ENST00000340965.3	+	9	1486	c.818T>A	c.(817-819)cTt>cAt	p.L273H	RP11-253M7.1_ENST00000558617.1_RNA|PAQR5_ENST00000561153.1_Missense_Mutation_p.L273H|Y_RNA_ENST00000384665.1_RNA|PAQR5_ENST00000395407.2_Missense_Mutation_p.L273H|RP11-253M7.1_ENST00000558107.1_RNA|RP11-253M7.1_ENST00000560539.1_RNA	NM_001104554.1	NP_001098024.1	Q9NXK6	MPRG_HUMAN	progestin and adipoQ receptor family member V	273					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)|steroid binding (GO:0005496)			endometrium(3)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|skin(1)	11						GAAGCCATACTTCTGGACAAG	0.517																																					p.L273H		Atlas-SNP	.											.	PAQR5	35	.	0			c.T818A						.						88	77	81					15																	69695986		2199	4298	6497	SO:0001583	missense	54852	exon9			CCATACTTCTGGA		CCDS10232.1	15q22.31	2012-08-10			ENSG00000137819	ENSG00000137819			29645	protein-coding gene	gene with protein product	"membrane progestin receptor gamma"	607781				12574519	Standard	NM_001104554		Approved	FLJ20190, MPRG	uc002arz.2	Q9NXK6	OTTHUMG00000133322	ENST00000340965.3:c.818T>A	chr15.hg19:g.69695986T>A	ENSP00000343877:p.Leu273His	86.0	0.0		74.0	26.0	NM_001104554	Q8IXU2	Missense_Mutation	SNP	ENST00000340965.3	hg19	CCDS10232.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.851145	0.71719	.	.	ENSG00000137819	ENST00000395407;ENST00000340965	T;T	0.27557	1.66;1.66	5.45	4.33	0.51752	.	0.646270	0.16636	N	0.205839	T	0.43678	0.1258	M	0.70275	2.135	0.09310	N	0.99999	D	0.67145	0.996	P	0.54965	0.765	T	0.30001	-0.9993	10	0.44086	T	0.13	-11.9089	7.9719	0.30132	0.0:0.0925:0.0:0.9075	.	273	Q9NXK6	MPRG_HUMAN	H	273	ENSP00000378803:L273H;ENSP00000343877:L273H	ENSP00000343877:L273H	L	+	2	0	PAQR5	67483040	0.220000	0.23631	0.847000	0.33407	0.972000	0.66771	1.982000	0.40638	1.024000	0.39682	0.533000	0.62120	CTT	.	.		0.517	PAQR5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416671.1	NM_017705		A	69695986	T	A	69695986	3	1	122	1	0	0	0	0	1	0	0	0	11447	1609	56	4	844	4	PAQR5	15	69695986	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	20036257	69695986	32835406	97	20506										
MEF2A	4205	hgsc.bcm.edu	37	chr15	100211575	100211575	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgtgagagccctgatgctgaCgattactttgagcacagtcc	11	10	0	4	rs1135561		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr15:100211575C>A	ENST00000557785.1	+	5	655	c.306C>A	c.(304-306)gaC>gaA	p.D102E	MEF2A_ENST00000449277.2_Missense_Mutation_p.D34E|MEF2A_ENST00000453228.2_Missense_Mutation_p.D102E|MEF2A_ENST00000558812.1_Missense_Mutation_p.D34E|MEF2A_ENST00000354410.5_Intron|MEF2A_ENST00000338042.6_Missense_Mutation_p.D102E|MEF2A_ENST00000557942.1_Missense_Mutation_p.D102E	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	102					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			CTGATGCTGACGATTACTTTG	0.378																																					p.D102E		Atlas-SNP	.											MEF2A_ENST00000453228,NS,carcinoma,0,2	MEF2A	138	.	0			c.C306A						.						181	170	173					15																	100211575		1568	3582	5150	SO:0001583	missense	4205	exon4			TGCTGACGATTAC		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"Myocyte enhancer factors"	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.306C>A	chr15.hg19:g.100211575C>A	ENSP00000453441:p.Asp102Glu	188.0	1.0		181.0	66.0	NM_001130926	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Missense_Mutation	SNP	ENST00000557785.1	hg19	CCDS53978.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.203472	0.38905	.	.	ENSG00000068305	ENST00000453228;ENST00000338042;ENST00000449277	T;T;T	0.64438	-0.1;-0.1;-0.1	5.54	5.54	0.83059	.	.	.	.	.	T	0.71434	0.3339	L	0.38733	1.17	0.26035	N	0.981682	B;D;D;B	0.89917	0.417;1.0;0.966;0.375	B;D;P;B	0.87578	0.312;0.998;0.792;0.331	T	0.63310	-0.6666	9	0.39692	T	0.17	.	15.3311	0.74212	0.0:0.8607:0.1393:0.0	.	34;23;102;102	B4DFQ7;Q7Z6C9;Q02078-6;Q02078-2	.;.;.;.	E	102;102;34	ENSP00000404110:D102E;ENSP00000337202:D102E;ENSP00000399460:D34E	ENSP00000337202:D102E	D	+	3	2	MEF2A	98029098	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.794000	0.47853	2.763000	0.94921	0.655000	0.94253	GAC	.	.		0.378	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1			A	100211575	C	A	100211575	3	1	122	1	0	0	0	0	1	0	0	0	9464	535	19	1	316	1	MEF2A	15	100211575	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	30515589	100211575	2319817	98	20507										
TARSL2	123283	hgsc.bcm.edu	37	chr15	102215816	102215816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ctcttaccttctcagcctcaTtccacatctcaatctctcct	1	18	5	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr15:102215816T>C	ENST00000335968.3	-	13	1991	c.1775A>G	c.(1774-1776)aAt>aGt	p.N592S		NM_152334.2	NP_689547.2	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	592					threonyl-tRNA aminoacylation (GO:0006435)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|skin(1)|urinary_tract(1)	29	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CTCAGCCTCATTCCACATCTC	0.433																																					p.N592S		Atlas-SNP	.											.	TARSL2	63	.	0			c.A1775G						.						157	148	151					15																	102215816		2203	4300	6503	SO:0001583	missense	123283	exon13			GCCTCATTCCACA	AL833188	CCDS10394.1	15q26.3	2008-02-05			ENSG00000185418	ENSG00000185418			24728	protein-coding gene	gene with protein product							Standard	NM_152334		Approved	FLJ25005	uc002bxm.3	A2RTX5	OTTHUMG00000149869	ENST00000335968.3:c.1775A>G	chr15.hg19:g.102215816T>C	ENSP00000338093:p.Asn592Ser	64.0	0.0		86.0	23.0	NM_152334	B2RMP7|Q6B0A1|Q6IS76|Q96LW3|Q96MP4	Missense_Mutation	SNP	ENST00000335968.3	hg19	CCDS10394.1	.	.	.	.	.	.	.	.	.	.	T	15.97	2.988934	0.53934	.	.	ENSG00000185418	ENST00000335968;ENST00000333018;ENST00000539112	T;T	0.67171	-0.25;-0.25	5.37	4.24	0.50183	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.397221	0.30762	N	0.008932	T	0.74283	0.3696	M	0.91196	3.185	0.30076	N	0.809608	B;B	0.30605	0.287;0.125	B;B	0.36092	0.217;0.138	T	0.75074	-0.3446	10	0.87932	D	0	-9.2185	10.4461	0.44495	0.0:0.0:0.1806:0.8194	.	592;497	A2RTX5;A2RTX5-2	SYTC2_HUMAN;.	S	592;497;592	ENSP00000338093:N592S;ENSP00000439899:N592S	ENSP00000329291:N497S	N	-	2	0	TARSL2	100033339	1.000000	0.71417	0.988000	0.46212	0.823000	0.46562	6.089000	0.71384	0.872000	0.35775	0.533000	0.62120	AAT	.	.		0.433	TARSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313619.3	NM_152334		C	102215816	T	C	102215816	3	2	122	1	0	0	0	0	1	0	0	0	15576	1493	52	2	661	2	TARSL2	15	102215816	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	2004241	102215816	315576	99	20508										
TFAP4	7023	hgsc.bcm.edu	37	chr16	4308230	4308230	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	agctcctgcttttcctgggtGccctcgatgtgctggattgc	12	12	0	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr16:4308230G>A	ENST00000204517.6	-	7	1171	c.843C>T	c.(841-843)ggC>ggT	p.G281G		NM_003223.2	NP_003214.1	Q01664	TFAP4_HUMAN	transcription factor AP-4 (activating enhancer binding protein 4)	281					cellular response to dexamethasone stimulus (GO:0071549)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	14						TTTCCTGGGTGCCCTCGATGT	0.667																																					p.G281G		Atlas-SNP	.											.	TFAP4	31	.	0			c.C843T						.						44	46	46					16																	4308230		2197	4300	6497	SO:0001819	synonymous_variant	7023	exon7			CTGGGTGCCCTCG	X57435	CCDS10510.1	16p13	2013-05-21	2001-11-28		ENSG00000090447	ENSG00000090447		"Basic helix-loop-helix proteins"	11745	protein-coding gene	gene with protein product		600743	"transcription factor AP-4 (activating enhancer-binding protein 4)"			2123466	Standard	NM_003223		Approved	AP-4, bHLHc41	uc010uxg.2	Q01664	OTTHUMG00000129435	ENST00000204517.6:c.843C>T	chr16.hg19:g.4308230G>A		54.0	0.0		45.0	18.0	NM_003223	O60409	Silent	SNP	ENST00000204517.6	hg19	CCDS10510.1																																																																																			.	.		0.667	TFAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251595.2	NM_003223		A	4308230	G	A	4308230	2	1	122	1	0	0	0	0	0	0	0	1	15807	1306	46	3		3	TFAP4	16	4308230	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10		4308230	86046523	100	20509										
MYH2	4620	hgsc.bcm.edu	37	chr17	10429161	10429161	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tcacagcttctacatgttccTcagctgcctgcagccgctgg	9	15	3	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr17:10429161T>A	ENST00000245503.5	-	31	4604	c.4220A>T	c.(4219-4221)gAg>gTg	p.E1407V	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Missense_Mutation_p.E1407V|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000532183.2_Intron	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1407					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						TACATGTTCCTCAGCTGCCTG	0.483																																					p.E1407V		Atlas-SNP	.											MYH2,NS,carcinoma,0,1	MYH2	390	.	0			c.A4220T						.						57	54	55					17																	10429161		2203	4300	6503	SO:0001583	missense	4620	exon31			TGTTCCTCAGCTG		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.4220A>T	chr17.hg19:g.10429161T>A	ENSP00000245503:p.Glu1407Val	102.0	0.0		109.0	9.0	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	hg19	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.639573	0.87760	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	D;D	0.82344	-1.6;-1.6	5.03	5.03	0.67393	Myosin tail (1);	0.000000	0.39687	U	0.001290	D	0.93792	0.8015	H	0.95884	3.735	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.95626	0.8685	10	0.87932	D	0	.	14.9212	0.70838	0.0:0.0:0.0:1.0	.	1407	Q9UKX2	MYH2_HUMAN	V	1407	ENSP00000245503:E1407V;ENSP00000380367:E1407V	ENSP00000245503:E1407V	E	-	2	0	MYH2	10369886	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.868000	0.87116	2.119000	0.64992	0.379000	0.24179	GAG	.	.		0.483	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		A	10429161	T	A	10429161	3	1	122	1	0	0	0	0	1	0	0	0	10044	1551	54	4	1645	4	MYH2	17	10429161	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10		10429161	70766049	101	20510										
TRIM37	4591	hgsc.bcm.edu	37	chr17	57138433	57138433	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	agctgagagctccagaaacaCagataagtagtaacctcgca	9	10	0	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr17:57138433C>A	ENST00000262294.7	-	12	1238	c.979G>T	c.(979-981)Gtg>Ttg	p.V327L	TRIM37_ENST00000393065.2_Missense_Mutation_p.V293L|TRIM37_ENST00000393066.3_Missense_Mutation_p.V327L|TRIM37_ENST00000376149.3_Missense_Mutation_p.V205L|RN7SL716P_ENST00000580539.1_RNA	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	327	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					TCCAGAAACACAGATAAGTAG	0.353									Mulibrey Nanism																												p.V327L		Atlas-SNP	.											.	TRIM37	105	.	0			c.G979T						.						86	82	83					17																	57138433		2203	4300	6503	SO:0001583	missense	4591	exon12	Familial Cancer Database	Perheentupa syndrome	GAAACACAGATAA	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.979G>T	chr17.hg19:g.57138433C>A	ENSP00000262294:p.Val327Leu	141.0	0.0		183.0	17.0	NM_015294	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000262294.7	hg19	CCDS32694.1	.	.	.	.	.	.	.	.	.	.	C	35	5.508139	0.96386	.	.	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065	T;T;T;T	0.61274	0.12;0.12;0.12;0.12	5.7	5.7	0.88788	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.64402	D	0.000001	T	0.71484	0.3345	L	0.42487	1.325	0.80722	D	1	D;D;P	0.71674	0.998;0.996;0.861	D;D;P	0.76071	0.972;0.987;0.627	T	0.71590	-0.4547	10	0.59425	D	0.04	-45.3867	19.8478	0.96722	0.0:1.0:0.0:0.0	.	293;205;327	F8WEE6;O94972-2;O94972	.;.;TRI37_HUMAN	L	327;327;205;293	ENSP00000376785:V327L;ENSP00000262294:V327L;ENSP00000365319:V205L;ENSP00000376784:V293L	ENSP00000262294:V327L	V	-	1	0	TRIM37	54493215	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.503000	0.81632	2.698000	0.92095	0.655000	0.94253	GTG	.	.		0.353	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		A	57138433	C	A	57138433	3	1	122	1	0	0	0	0	1	0	0	0	16526	478	17	3	1975	3	TRIM37	17	57138433	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	46709272	57138433	24056777	102	20511										
CA4	762	hgsc.bcm.edu	37	chr17	58233977	58233977	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gccagtcccccatcaacatcGtcaccaccaaggcaaaggtg	8	16	2	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr17:58233977G>A	ENST00000300900.4	+	3	268	c.169G>A	c.(169-171)Gtc>Atc	p.V57I		NM_000717.3	NP_000708.1	P22748	CAH4_HUMAN	carbonic anhydrase IV	57					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|organ development (GO:0048513)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)|transport vesicle membrane (GO:0030658)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(2)|lung(5)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.83e-12)|all cancers(12;6.83e-11)		Acetazolamide(DB00819)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diclofenamide(DB01144)|Dorzolamide(DB00869)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Topiramate(DB00273)|Trichlormethiazide(DB01021)|Zonisamide(DB00909)	CATCAACATCGTCACCACCAA	0.557																																					p.V57I		Atlas-SNP	.											.	CA4	20	.	0			c.G169A						.						108	94	99					17																	58233977		2203	4300	6503	SO:0001583	missense	762	exon3			AACATCGTCACCA	L10955	CCDS11624.1	17q23.1	2012-08-21			ENSG00000167434	ENSG00000167434	4.2.1.1	"Carbonic anhydrases"	1375	protein-coding gene	gene with protein product		114760	"retinitis pigmentosa 17 (autosomal dominant)"	RP17		8325641	Standard	NM_000717		Approved	CAIV, Car4	uc002iym.4	P22748		ENST00000300900.4:c.169G>A	chr17.hg19:g.58233977G>A	ENSP00000300900:p.Val57Ile	62.0	0.0		74.0	20.0	NM_000717	B4DQA4|Q6FHI7	Missense_Mutation	SNP	ENST00000300900.4	hg19	CCDS11624.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.565366	0.27915	.	.	ENSG00000167434	ENST00000300900	T	0.66995	-0.24	5.27	4.29	0.51040	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.479266	0.23204	N	0.050749	T	0.53061	0.1773	L	0.48877	1.53	0.09310	N	1	B	0.29835	0.258	B	0.21546	0.035	T	0.34279	-0.9835	10	0.18710	T	0.47	.	9.933	0.41534	0.0932:0.0:0.9068:0.0	.	57	P22748	CAH4_HUMAN	I	57	ENSP00000300900:V57I	ENSP00000300900:V57I	V	+	1	0	CA4	55588759	0.004000	0.15560	0.059000	0.19551	0.305000	0.27757	1.313000	0.33585	2.735000	0.93741	0.655000	0.94253	GTC	.	.		0.557	CA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449189.1	NM_000717		A	58233977	G	A	58233977	3	1	122	1	0	0	0	0	1	0	0	0	2520	1145	40	1	179	1	CA4	17	58233977	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	1095544	58233977	22961233	103	20512										
ABCA8	10351	hgsc.bcm.edu	37	chr17	66920897	66920897	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttgttcaaaagagtcatgaaAtgaaggatcggcatccattt	9	6	2	3			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr17:66920897A>C	ENST00000269080.2	-	10	1524	c.1387T>G	c.(1387-1389)Ttt>Gtt	p.F463V	ABCA8_ENST00000586539.1_Missense_Mutation_p.F463V|ABCA8_ENST00000430352.2_Missense_Mutation_p.F463V	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	463					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GAGTCATGAAATGAAGGATCG	0.463																																					p.F463V		Atlas-SNP	.											.	ABCA8	213	.	0			c.T1387G						.						138	130	133					17																	66920897		2203	4300	6503	SO:0001583	missense	10351	exon10			CATGAAATGAAGG	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.1387T>G	chr17.hg19:g.66920897A>C	ENSP00000269080:p.Phe463Val	69.0	0.0		92.0	32.0	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	hg19	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	A	4.381	0.070372	0.08436	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000542396	D;D	0.85702	-2.02;-2.0	4.42	0.988	0.19796	.	0.270264	0.26272	N	0.025322	T	0.58524	0.2128	N	0.03029	-0.43	0.09310	N	1	B;B;B;B;B	0.09022	0.0;0.002;0.0;0.001;0.001	B;B;B;B;B	0.13407	0.002;0.001;0.001;0.009;0.001	T	0.47071	-0.9145	10	0.10902	T	0.67	.	4.0875	0.09953	0.4553:0.0:0.3786:0.1661	.	402;463;463;463;463	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	V	463;463;402;94	ENSP00000269080:F463V;ENSP00000402814:F463V	ENSP00000269080:F463V	F	-	1	0	ABCA8	64432492	0.000000	0.05858	0.003000	0.11579	0.017000	0.09413	0.451000	0.21779	0.041000	0.15688	0.482000	0.46254	TTT	.	.		0.463	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		C	66920897	A	C	66920897	3	2	122	1	0	0	0	0	1	0	0	0	38	101	4	5	3474	5	ABCA8	17	66920897	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10	8686920	66920897	14274313	104	20513										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21464744	21464744	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gtcttctttcaagctttgccActggctgtgtggtgaatggg	13	8	3	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr18:21464744A>G	ENST00000313654.9	+	41	5471	c.5230A>G	c.(5230-5232)Act>Gct	p.T1744A	LAMA3_ENST00000587184.1_Missense_Mutation_p.T135A|LAMA3_ENST00000399516.3_Missense_Mutation_p.T1744A|LAMA3_ENST00000269217.6_Missense_Mutation_p.T135A	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1744	Domain III A.|Laminin EGF-like 14. {ECO:0000255|PROSITE-ProRule:PRU00460}.			ATG -> GMC (in Ref. 5; CAA59428/ CAA59429). {ECO:0000305}.	cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					AAGCTTTGCCACTGGCTGTGT	0.498																																					p.T1744A		Atlas-SNP	.											.	LAMA3	397	.	0			c.A5230G						.						186	177	180					18																	21464744		2203	4300	6503	SO:0001583	missense	3909	exon41			TTTGCCACTGGCT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.5230A>G	chr18.hg19:g.21464744A>G	ENSP00000324532:p.Thr1744Ala	169.0	0.0		204.0	30.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	A	15.18	2.757797	0.49468	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.62941	-0.01;-0.01;-0.01	6.06	4.89	0.63831	EGF-like, laminin (3);Growth factor, receptor (1);	.	.	.	.	T	0.53433	0.1796	L	0.38838	1.175	0.45594	D	0.998533	P;P;B;P	0.45283	0.822;0.855;0.211;0.65	B;P;B;P	0.44946	0.376;0.456;0.166;0.465	T	0.46359	-0.9197	9	0.22706	T	0.39	.	10.1581	0.42836	0.7197:0.0:0.0:0.2803	.	135;135;1744;1744	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	A	1744;1744;135	ENSP00000324532:T1744A;ENSP00000382432:T1744A;ENSP00000269217:T135A	ENSP00000269217:T135A	T	+	1	0	LAMA3	19718742	0.974000	0.33945	0.993000	0.49108	0.588000	0.36517	1.840000	0.39230	1.088000	0.41272	0.533000	0.62120	ACT	.	.		0.498	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		G	21464744	A	G	21464744	3	3	122	1	0	0	0	0	1	0	0	0	8616	159	6	2	5567	2	LAMA3	18	21464744	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10		21464744	56612504	105	20514										
WDR7	23335	hgsc.bcm.edu	37	chr18	54358487	54358487	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttccttgttgtgttcaggtcCtagtgaaaatggacagacat	10	7	1	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr18:54358487C>G	ENST00000254442.3	+	8	969	c.758C>G	c.(757-759)cCt>cGt	p.P253R	WDR7_ENST00000357574.3_Missense_Mutation_p.P253R|WDR7_ENST00000589935.1_Intron	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	253					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TGTTCAGGTCCTAGTGAAAAT	0.403																																					p.P253R		Atlas-SNP	.											.	WDR7	166	.	0			c.C758G						.						117	125	123					18																	54358487		2203	4300	6503	SO:0001583	missense	23335	exon8			CAGGTCCTAGTGA	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"WD repeat domain containing"	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.758C>G	chr18.hg19:g.54358487C>G	ENSP00000254442:p.Pro253Arg	168.0	0.0		169.0	18.0	NM_052834	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Missense_Mutation	SNP	ENST00000254442.3	hg19	CCDS11962.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.504678	0.26949	.	.	ENSG00000091157	ENST00000254442;ENST00000357574;ENST00000398311	T;T	0.04654	3.58;3.58	5.45	5.45	0.79879	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.165847	0.56097	D	0.000034	T	0.04998	0.0134	L	0.33485	1.01	0.53005	D	0.999966	B;P	0.41265	0.228;0.744	B;B	0.36030	0.054;0.216	T	0.53351	-0.8451	10	0.11485	T	0.65	.	19.2552	0.93943	0.0:1.0:0.0:0.0	.	253;253	Q9Y4E6-2;Q9Y4E6	.;WDR7_HUMAN	R	253	ENSP00000254442:P253R;ENSP00000350187:P253R	ENSP00000254442:P253R	P	+	2	0	WDR7	52509485	0.997000	0.39634	0.995000	0.50966	0.996000	0.88848	4.749000	0.62155	2.729000	0.93468	0.460000	0.39030	CCT	.	.		0.403	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			G	54358487	C	G	54358487	3	3	122	1	0	0	0	0	1	0	0	0	17335	681	24	4	784	4	WDR7	18	54358487	Missense_Mutation	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	32893743	54358487	23718761	106	20515										
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4159733	4159733	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ggacctgtccccacgatgcaAtctcaccgtgaaagacctcc	8	16	1	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr19:4159733A>G	ENST00000078445.2	+	4	677	c.530A>G	c.(529-531)aAt>aGt	p.N177S	CREB3L3_ENST00000602147.1_Missense_Mutation_p.N177S|CREB3L3_ENST00000602257.1_Missense_Mutation_p.N177S|CREB3L3_ENST00000252587.3_Intron|CREB3L3_ENST00000595923.1_Missense_Mutation_p.N176S	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	177					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		CCACGATGCAATCTCACCGTG	0.642																																					p.N177S		Atlas-SNP	.											.	CREB3L3	53	.	0			c.A530G						.						91	84	86					19																	4159733		2203	4300	6503	SO:0001583	missense	84699	exon4			GATGCAATCTCAC		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.530A>G	chr19.hg19:g.4159733A>G	ENSP00000078445:p.Asn177Ser	25.0	0.0		14.0	6.0	NM_001271997	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Missense_Mutation	SNP	ENST00000078445.2	hg19	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	A	3.354	-0.131960	0.06753	.	.	ENSG00000060566	ENST00000078445;ENST00000381943	D	0.82619	-1.63	4.48	-3.74	0.04385	.	3.583700	0.00797	N	0.001389	T	0.64327	0.2588	N	0.17674	0.51	0.23232	N	0.998075	B;B;B;B	0.13594	0.003;0.005;0.008;0.005	B;B;B;B	0.10450	0.005;0.003;0.004;0.002	T	0.55134	-0.8188	10	0.07990	T	0.79	-25.0446	1.213	0.01908	0.3093:0.2114:0.3327:0.1466	.	177;177;176;177	Q68CJ9-3;B7ZL69;Q68CJ9-2;Q68CJ9	.;.;.;CR3L3_HUMAN	S	177	ENSP00000078445:N177S	ENSP00000078445:N177S	N	+	2	0	CREB3L3	4110733	0.012000	0.17670	0.072000	0.20136	0.018000	0.09664	-0.019000	0.12546	-0.424000	0.07382	0.439000	0.28862	AAT	.	.		0.642	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607		G	4159733	A	G	4159733	3	3	122	1	0	0	0	0	1	0	0	0	3860	101	4	2	544	2	CREB3L3	19	4159733	Missense_Mutation	SNP	A	TCGA-DD-A3A8-01A-11D-A22F-10		4159733	54969250	107	20516										
MUC16	94025	hgsc.bcm.edu	37	chr19	9057572	9057572	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gccccaggagaacttttttgGgtggtgatggtcatttgtgt	14	6	1	2	rs367564649		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr19:9057572G>T	ENST00000397910.4	-	3	30077	c.29874C>A	c.(29872-29874)acC>acA	p.T9958T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9960	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AACTTTTTTGGGTGGTGATGG	0.488																																					p.T9958T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C29874A						.						256	249	251					19																	9057572		1970	4167	6137	SO:0001819	synonymous_variant	94025	exon3			TTTTTGGGTGGTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29874C>A	chr19.hg19:g.9057572G>T		280.0	0.0		266.0	108.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9057572	G	T	9057572	2	4	122	1	0	0	0	0	0	0	0	1	9982	1219	43	3		3	MUC16	19	9057572	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	4897839	9057572	50071411	108	20517										
ZNF564	163050	hgsc.bcm.edu	37	chr19	12637749	12637749	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	catacctgacatttataaggTccatctccagtgtgctttat	6	10	1	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr19:12637749T>C	ENST00000339282.7	-	4	1369	c.1173A>G	c.(1171-1173)ggA>ggG	p.G391G	ZNF709_ENST00000428311.1_Intron|CTD-2192J16.21_ENST00000601420.1_RNA|CTD-2192J16.20_ENST00000593682.1_3'UTR	NM_144976.3	NP_659413.1	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	391					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						ATTTATAAGGTCCATCTCCAG	0.448																																					p.G391G		Atlas-SNP	.											.	ZNF564	55	.	0			c.A1173G						.						138	142	141					19																	12637749		2203	4300	6503	SO:0001819	synonymous_variant	163050	exon4			ATAAGGTCCATCT	BC028367	CCDS42505.1	19p13.2	2013-09-19			ENSG00000249709	ENSG00000249709		"Zinc fingers, C2H2-type", "-"	31106	protein-coding gene	gene with protein product							Standard	NM_144976		Approved	MGC26914		Q8TBZ8	OTTHUMG00000156418	ENST00000339282.7:c.1173A>G	chr19.hg19:g.12637749T>C		82.0	0.0		99.0	8.0	NM_144976	B9EGT4|Q6P1K6	Silent	SNP	ENST00000339282.7	hg19	CCDS42505.1																																																																																			.	.		0.448	ZNF564-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344120.2	NM_144976		C	12637749	T	C	12637749	2	2	122	1	0	0	0	0	0	0	0	1	18010	1654	58	2		2	ZNF564	19	12637749	Silent	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	3580177	12637749	46491234	109	20518										
PSMD8	5714	hgsc.bcm.edu	37	chr19	38867031	38867031	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ggcccaatggagcatcctacGcaaggacatcccctccttcg	9	16	0	0	rs200403794		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr19:38867031G>A	ENST00000215071.4	+	3	539	c.473G>A	c.(472-474)cGc>cAc	p.R158H	PSMD8_ENST00000592035.1_5'UTR|PSMD8_ENST00000602911.1_Missense_Mutation_p.R95H	NM_002812.4	NP_002803.2	P48556	PSMD8_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	158					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(1)	6	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGCATCCTACGCAAGGACATC	0.572																																					p.R158H		Atlas-SNP	.											.	PSMD8	31	.	0			c.G473A						.	G	HIS/ARG	0,4318		0,0,2159	56	47	50		473	4.4	1	19		50	2,8384		0,2,4191	yes	missense	PSMD8	NM_002812.4	29	0,2,6350	AA,AG,GG		0.0238,0.0,0.0157	benign	158/351	38867031	2,12702	2159	4193	6352	SO:0001583	missense	5714	exon3			TCCTACGCAAGGA	D38047	CCDS12515.2	19q13.2	2009-05-07			ENSG00000099341	ENSG00000099341		"Proteasome (prosome, macropain) subunits"	9566	protein-coding gene	gene with protein product						7621825	Standard	NM_002812		Approved	S14, Nin1p, p31, HIP6, HYPF, Rpn12	uc002oii.4	P48556	OTTHUMG00000150691	ENST00000215071.4:c.473G>A	chr19.hg19:g.38867031G>A	ENSP00000215071:p.Arg158His	56.0	0.0		83.0	30.0	NM_002812	B4DX18|Q6P1L7	Missense_Mutation	SNP	ENST00000215071.4	hg19	CCDS12515.2	.	.	.	.	.	.	.	.	.	.	G	14.30	2.492809	0.44352	0.0	2.38E-4	ENSG00000099341	ENST00000215071	.	.	.	4.44	4.44	0.53790	.	0.118100	0.56097	D	0.000023	T	0.39036	0.1063	N	0.19112	0.55	0.80722	D	1	B	0.17038	0.02	B	0.04013	0.001	T	0.29305	-1.0016	9	0.45353	T	0.12	-7.3068	8.3919	0.32533	0.1041:0.0:0.8959:0.0	.	158	P48556	PSMD8_HUMAN	H	158	.	ENSP00000215071:R158H	R	+	2	0	PSMD8	43558871	1.000000	0.71417	0.975000	0.42487	0.970000	0.65996	5.746000	0.68681	2.342000	0.79632	0.449000	0.29647	CGC	.	.		0.572	PSMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319627.1	NM_002812		A	38867031	G	A	38867031	3	1	122	1	0	0	0	0	1	0	0	0	12716	1087	38	1	483	1	PSMD8	19	38867031	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	26229282	38867031	20261952	110	20519										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42866314	42866314	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgtcgacgtctccggacctgCagtgagtgcctggcccgcca	13	15	1	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr19:42866314C>T	ENST00000251268.6	+	33	5793	c.5793C>T	c.(5791-5793)tgC>tgT	p.C1931C	MEGF8_ENST00000334370.4_Silent_p.C1864C	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1931	PSI 5.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				TCCGGACCTGCAGTGAGTGCC	0.657																																					p.C1931C		Atlas-SNP	.											.	MEGF8	358	.	0			c.C5793T						.						26	22	24					19																	42866314		2203	4299	6502	SO:0001819	synonymous_variant	1954	exon33			GACCTGCAGTGAG	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.5793C>T	chr19.hg19:g.42866314C>T		19.0	0.0		40.0	15.0	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	hg19																																																																																				.	.		0.657	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		T	42866314	C	T	42866314	2	4	122	1	0	0	0	0	0	0	0	1	9472	718	25	3		3	MEGF8	19	42866314	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	3999283	42866314	16262669	111	20520										
ZNF211	10520	hgsc.bcm.edu	37	chr19	58152126	58152126	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttctgaacagagaatttctgGagaaagagtgccacagttca	10	7	3	4			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr19:58152126G>T	ENST00000347302.3	+	3	451	c.272G>T	c.(271-273)gGa>gTa	p.G91V	ZNF211_ENST00000299871.5_Missense_Mutation_p.G156V|ZNF211_ENST00000541801.1_Missense_Mutation_p.G82V|ZNF211_ENST00000420680.1_Missense_Mutation_p.G95V|ZNF211_ENST00000254182.7_Missense_Mutation_p.G82V|ZNF211_ENST00000240731.4_Missense_Mutation_p.G104V|ZNF211_ENST00000544273.1_Missense_Mutation_p.G103V|ZNF211_ENST00000391703.3_Missense_Mutation_p.G30V	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	91	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AGAATTTCTGGAGAAAGAGTG	0.423																																					p.G156V		Atlas-SNP	.											.	ZNF211	78	.	0			c.G467T						.						94	96	95					19																	58152126		2203	4300	6503	SO:0001583	missense	10520	exon5			TTTCTGGAGAAAG	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"Zinc fingers, C2H2-type", "-"	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.272G>T	chr19.hg19:g.58152126G>T	ENSP00000339562:p.Gly91Val	153.0	0.0		170.0	18.0	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Missense_Mutation	SNP	ENST00000347302.3	hg19	CCDS12957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.006|0.006	-2.039764|-2.039764	0.00402|0.00402	.|.	.|.	ENSG00000121417|ENSG00000121417	ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731|ENST00000407202	T;T;T;T;T;T;T;T|.	0.05996|.	3.36;3.38;3.57;3.5;3.57;3.61;3.39;3.41|.	3.42|3.42	-1.64|-1.64	0.08318|0.08318	Krueppel-associated box (1);|.	.|.	.|.	.|.	.|.	T|T	0.07999|0.07999	0.0200|0.0200	N|N	0.01874|0.01874	-0.695|-0.695	0.09310|0.09310	N|N	1|1	B;B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B;B|.	0.04013|.	0.0;0.0;0.001;0.0;0.0;0.0|.	T|T	0.30416|0.30416	-0.9979|-0.9979	9|5	0.02654|.	T|.	1|.	.|.	0.8611|0.8611	0.01193|0.01193	0.1582:0.2145:0.3266:0.3007|0.1582:0.2145:0.3266:0.3007	.|.	95;103;156;82;91;104|.	Q13398-4;Q13398-3;F8WDV2;Q13398-2;Q13398;B9ZVW1|.	.;.;.;.;ZN211_HUMAN;.|.	V|C	95;91;82;30;82;156;103;104|94	ENSP00000399193:G95V;ENSP00000339562:G91V;ENSP00000254182:G82V;ENSP00000375584:G30V;ENSP00000442601:G82V;ENSP00000299871:G156V;ENSP00000441386:G103V;ENSP00000240731:G104V|.	ENSP00000240731:G104V|.	G|W	+|+	2|3	0|0	ZNF211|ZNF211	62843938|62843938	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.291000|-0.291000	0.08343|0.08343	-0.182000|-0.182000	0.10602|0.10602	-1.214000|-1.214000	0.01621|0.01621	GGA|TGG	.	.		0.423	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1			T	58152126	G	T	58152126	3	4	122	1	0	0	0	0	1	0	0	0	17782	1174	41	3	325	3	ZNF211	19	58152126	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	15285812	58152126	976857	112	20521										
ZNF606	80095	hgsc.bcm.edu	37	chr19	58489764	58489767	+	Frame_Shift_Del	DEL	TCTC	TCTC	-													0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttcactgcatataaagcgttTctctccactatgcattctct							TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr19:58489764_58489767delTCTC	ENST00000341164.4	-	7	2901_2904	c.2281_2284delGAGA	c.(2281-2286)gagaaafs	p.EK761fs	ZNF606_ENST00000536132.1_Frame_Shift_Del_p.EK671fs	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	761					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		ATAAAGCGTTTCTCTCCACTATGC	0.363																																					p.761_762del		Atlas-Indel,Pindel	.											.	ZNF606	155	.	0			c.2282_2285del						.																																			SO:0001589	frameshift_variant	80095	exon7			.	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"Zinc fingers, C2H2-type", "-"	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.2281_2284delGAGA	chr19.hg19:g.58489764_58489767delTCTC	ENSP00000343617:p.Glu761fs	175.0	0.0		168.0	45.0	NM_025027	A8KAN2|Q8NE04|Q96JH5	Frame_Shift_Del	DEL	ENST00000341164.4	hg19	CCDS12968.1																																																																																			.	.		0.363	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		-	58489767	TCTC	-	58489764	7	5	122	1	0	1	0	1	0	0	0	0	18047	1792	62	0	98	0	ZNF606	19	58489764	Frame_Shift_Del	DEL	TCTC	TCGA-DD-A3A8-01A-11D-A22F-10	337638	58489764	639219	113	20522										
SIRPB2	284759	hgsc.bcm.edu	37	chr20	1471995	1471995	+	De_novo_Start_OutOfFrame	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ggcaggtgggggccgacatcGtggagcacatggcatcttct	16	10	2	0	rs372457994		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr20:1471995G>A	ENST00000537284.1	-	0	64				AL109658.1_ENST00000580848.1_RNA|SIRPB2_ENST00000359801.3_Missense_Mutation_p.T4M|SIRPB2_ENST00000444444.2_Missense_Mutation_p.T4M			Q9P1W8	SIRPG_HUMAN	signal-regulatory protein beta 2						blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GGCCGACATCGTGGAGCACAT	0.612																																					p.T4M		Atlas-SNP	.											.	SIRPB2	50	.	0			c.C11T						.	G	MET/THR,MET/THR	0,3136		0,0,1568	39	48	45		11,11	-5	0	20		45	2,7162		0,2,3580	no	missense,missense	SIRPB2	NM_001122962.1,NM_001134836.1	81,81	0,2,5148	AA,AG,GG		0.0279,0.0,0.0194	probably-damaging,probably-damaging	4/343,4/245	1471995	2,10298	1568	3582	5150			284759	exon1			GACATCGTGGAGC	AL109658	CCDS42849.1, CCDS46570.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000196209	ENSG00000196209		"Signal-regulatory proteins", "Immunoglobulin superfamily / V-set domain containing"	16247	protein-coding gene	gene with protein product			"protein tyrosine phosphatase, non-receptor type 1-like", "protein tyrosine phosphatase, non-receptor type substrate 1-like 3"	PTPN1L, PTPNS1L3		16339511	Standard	NM_001122962		Approved	dJ776F14.2	uc002wfg.2	Q5JXA9	OTTHUMG00000031670	ENST00000537284.1:c.-273C>T	chr20.hg19:g.1471995G>A		81.0	0.0		90.0	8.0	NM_001122962	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000537284.1	hg19		.	.	.	.	.	.	.	.	.	.	G	0.534	-0.856574	0.02630	0.0	2.79E-4	ENSG00000196209	ENST00000359801;ENST00000444444;ENST00000381630;ENST00000381628	T;T;T	0.02763	4.52;4.2;4.17	3.39	-4.98	0.03019	.	3.530630	0.00870	N	0.002017	T	0.01353	0.0044	N	0.02539	-0.55	0.18873	N	0.999985	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.46205	-0.9208	10	0.30078	T	0.28	0.0053	5.0559	0.14533	0.459:0.0:0.4007:0.1403	.	4;4	E9PCW6;Q5JXA9	.;SIRB2_HUMAN	M	4	ENSP00000352849:T4M;ENSP00000402438:T4M;ENSP00000371043:T4M	ENSP00000352849:T4M	T	-	2	0	SIRPB2	1419995	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.780000	0.04654	-1.061000	0.03185	-1.130000	0.01982	ACG	.	.		0.612	SIRPB2-201	KNOWN	basic	protein_coding	protein_coding		NM_178459		A	1471995	G	A	1471995	1	1	122	1	0	1	0	0	0	0	0	0	14349	1145	40	1		1	SIRPB2	20	1471995	De_novo_Start_OutOfFrame	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10		1471995	61553525	114	20523										
CHD6	84181	hgsc.bcm.edu	37	chr20	40049297	40049297	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	aaggttcttttaaaagctcaTgcttcactttaaacggctgt	7	8	3	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr20:40049297T>A	ENST00000373233.3	-	31	6155	c.5978A>T	c.(5977-5979)cAt>cTt	p.H1993L		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1993					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				TAAAAGCTCATGCTTCACTTT	0.433																																					p.H1993L		Atlas-SNP	.											.	CHD6	312	.	0			c.A5978T						.						109	110	109					20																	40049297		2203	4300	6503	SO:0001583	missense	84181	exon31			AGCTCATGCTTCA	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.5978A>T	chr20.hg19:g.40049297T>A	ENSP00000362330:p.His1993Leu	186.0	0.0		186.0	12.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	T	5.046	0.194205	0.09599	.	.	ENSG00000124177	ENST00000373233	D	0.85339	-1.97	5.86	-7.08	0.01558	.	0.773311	0.12065	N	0.502733	T	0.68348	0.2991	L	0.41236	1.265	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.58284	-0.7663	10	0.08381	T	0.77	0.0075	5.121	0.14860	0.0919:0.2863:0.4585:0.1633	.	1993	Q8TD26	CHD6_HUMAN	L	1993	ENSP00000362330:H1993L	ENSP00000362330:H1993L	H	-	2	0	CHD6	39482711	0.002000	0.14202	0.008000	0.14137	0.733000	0.41908	-0.156000	0.10100	-1.226000	0.02574	0.533000	0.62120	CAT	.	.		0.433	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40049297	T	A	40049297	3	1	122	1	0	0	0	0	1	0	0	0	3331	1464	51	4	2197	4	CHD6	20	40049297	Missense_Mutation	SNP	T	TCGA-DD-A3A8-01A-11D-A22F-10	38577302	40049297	22976223	115	20524										
PRIC285	85441	hgsc.bcm.edu	37	chr20	62190680	62190680	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tgagcctcgcagaagtccagGaggctacgccagagggggca	16	11	0	3	rs141769251		TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr20:62190680G>A	ENST00000467148.1	-	19	7938	c.7869C>T	c.(7867-7869)ctC>ctT	p.L2623L	HELZ2_ENST00000427522.2_Silent_p.L2054L	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2623	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										AGAAGTCCAGGAGGCTACGCC	0.647																																					p.L2623L		Atlas-SNP	.											.	.	.	.	0			c.C7869T						.	G	,	1,4385		0,1,2192	20	18	19		7869,6162	1.5	0.9	20	dbSNP_134	19	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	0,1,6486	AA,AG,GG		0.0,0.0228,0.0077	,	2623/2650,2054/2081	62190680	1,12973	2193	4294	6487	SO:0001819	synonymous_variant	85441	exon20			GTCCAGGAGGCTA	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.7869C>T	chr20.hg19:g.62190680G>A		45.0	0.0		61.0	19.0	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	hg19	CCDS33508.1																																																																																			.	G|1.000;A|0.000		0.647	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		A	62190680	G	A	62190680	2	1	122	1	0	0	0	0	0	0	0	1	12497	1161	41	3		3	PRIC285	20	62190680	Silent	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	22141383	62190680	834840	116	20525										
GAB4	128954	hgsc.bcm.edu	37	chr22	17443765	17443765	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	acgtgacagagcctatggatGgctgagggacagagggtgga	18	6	0	4			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr22:17443765G>T	ENST00000400588.1	-	10	1690	c.1583C>A	c.(1582-1584)cCa>cAa	p.P528Q		NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	528										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				GCCTATGGATGGCTGAGGGAC	0.577																																					p.P528Q		Atlas-SNP	.											.	GAB4	95	.	0			c.C1583A						.						41	42	41					22																	17443765		2190	4299	6489	SO:0001630	splice_region_variant	128954	exon10			ATGGATGGCTGAG	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"Pleckstrin homology (PH) domain containing"	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.1582-1C>A	chr22.hg19:g.17443765G>T		28.0	0.0		45.0	17.0	NM_001037814		Missense_Mutation	SNP	ENST00000400588.1	hg19	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.587044	0.46110	.	.	ENSG00000215568	ENST00000400588	T	0.22945	1.93	2.55	2.55	0.30701	.	0.055023	0.64402	D	0.000001	T	0.24470	0.0593	L	0.48362	1.52	0.36957	D	0.893157	P	0.47106	0.89	B	0.43413	0.419	T	0.33471	-0.9867	10	0.59425	D	0.04	.	11.2067	0.48773	0.0:0.0:1.0:0.0	.	528	Q2WGN9	GAB4_HUMAN	Q	528	ENSP00000383431:P528Q	ENSP00000383431:P528Q	P	-	2	0	GAB4	15823765	1.000000	0.71417	0.956000	0.39512	0.004000	0.04260	6.907000	0.75724	1.722000	0.51474	0.609000	0.83330	CCA	.	.		0.577	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	Missense_Mutation	T	17443765	G	T	17443765	5	4	122	1	0	0	0	0	0	0	1	0	6159	1362	47	3	145	3	GAB4	22	17443765	Splice_Site	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10		17443765	33860801	117	20526										
SMC1B	26150	hgsc.bcm.edu	37	chr22	45809347	45809347	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	gctgctcagttaccagagccGttggggccgatgatgcaggt	15	10	1	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chr22:45809347G>T	ENST00000342894.3	+	0	0				SMC1B_ENST00000404354.3_Missense_Mutation_p.N34K|RIBC2_ENST00000538017.1_5'Flank|SMC1B_ENST00000357450.4_Missense_Mutation_p.N34K			Q9H4K1	RIBC2_HUMAN	RIB43A domain with coiled-coils 2							nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|skin(2)|urinary_tract(1)	10		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TACCAGAGCCGTTGGGGCCGA	0.682																																					p.N34K		Atlas-SNP	.											.	SMC1B	215	.	0			c.C102A						.						21	27	25					22																	45809347		1931	4134	6065	SO:0001631	upstream_gene_variant	27127	exon1			AGAGCCGTTGGGG	AK098586		22q13.3	2004-08-18	2004-08-18	2004-08-18	ENSG00000128408	ENSG00000128408			13241	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 11"	C22orf11		12477932	Standard	NM_015653		Approved	DKFZp566F0546, FLJ25720	uc011aqs.3	Q9H4K1	OTTHUMG00000151332		chr22.hg19:g.45809347G>T	Exception_encountered	65.0	0.0		50.0	15.0	NM_148674	Q6ICD0|Q9Y413	Missense_Mutation	SNP	ENST00000342894.3	hg19		.	.	.	.	.	.	.	.	.	.	G	12.68	2.011813	0.35511	.	.	ENSG00000077935	ENST00000357450;ENST00000404354	D;T	0.84660	-1.88;1.87	3.58	1.42	0.22433	.	0.000000	0.47455	U	0.000221	D	0.91862	0.7424	M	0.89601	3.045	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89566	0.3810	10	0.87932	D	0	.	7.7074	0.28659	0.4515:0.0:0.5485:0.0	.	34;34	Q8NDV3-2;Q8NDV3-3	.;.	K	34	ENSP00000350036:N34K;ENSP00000385902:N34K	ENSP00000350036:N34K	N	-	3	2	SMC1B	44188011	0.653000	0.27358	0.999000	0.59377	0.136000	0.21042	-0.133000	0.10451	0.010000	0.14839	-1.595000	0.00837	AAC	.	.		0.682	RIBC2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000322250.1	NM_015653		T	45809347	G	T	45809347	1	4	122	0	1	0	0	0	0	0	0	0	14797	1136	40	1		1	SMC1B	22	45809347	5'Flank	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	28365582	45809347	5495219	118	20527										
HDAC8	55869	hgsc.bcm.edu	37	chrX	71788678	71788678	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tctggagatgctgcagataaGcatcagtgtggaaggtggcc	15	7	2	2			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chrX:71788678G>C	ENST00000373573.3	-	3	562	c.221C>G	c.(220-222)gCt>gGt	p.A74G	HDAC8_ENST00000373583.1_Intron|HDAC8_ENST00000373556.3_Missense_Mutation_p.A74G|HDAC8_ENST00000373571.1_Missense_Mutation_p.A74G|HDAC8_ENST00000429103.2_5'UTR|HDAC8_ENST00000373560.2_Missense_Mutation_p.A74G|HDAC8_ENST00000373554.1_Missense_Mutation_p.A74G|HDAC8_ENST00000373589.4_Intron|HDAC8_ENST00000373559.4_Intron|HDAC8_ENST00000478743.1_5'UTR|HDAC8_ENST00000373561.4_Missense_Mutation_p.A74G|HDAC8_ENST00000439122.2_Missense_Mutation_p.A74G	NM_018486.2	NP_060956.1	Q9BY41	HDAC8_HUMAN	histone deacetylase 8	74	Histone deacetylase.				chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cohesin localization to chromatin (GO:0071922)|sister chromatid cohesion (GO:0007062)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(3)|cervix(1)|endometrium(1)|lung(4)|prostate(1)	10	Renal(35;0.156)				Vorinostat(DB02546)	CTGCAGATAAGCATCAGTGTG	0.483																																					p.A74G		Atlas-SNP	.											.	HDAC8	18	.	0			c.C221G						.						111	86	95					X																	71788678		2203	4300	6503	SO:0001583	missense	55869	exon3			AGATAAGCATCAG	AF230097	CCDS14420.1, CCDS55448.1, CCDS55449.1, CCDS55450.1, CCDS55451.1, CCDS55452.1	Xq13	2014-01-29	2002-09-02	2002-09-06	ENSG00000147099	ENSG00000147099			13315	protein-coding gene	gene with protein product		300269	"histone deacetylase-like 1", "Wilson-Turner X-linked mental retardation syndrome"	HDACL1, WTS, MRXS6		10756090, 10922473, 22889856	Standard	NM_001166448		Approved	RPD3	uc004eau.3	Q9BY41	OTTHUMG00000021814	ENST00000373573.3:c.221C>G	chrX.hg19:g.71788678G>C	ENSP00000362674:p.Ala74Gly	31.0	0.0		28.0	17.0	NM_018486	A6ND12|A6ND61|A6NET3|A6NJR3|A8MQ62|B4DKN0|B4DV22|Q86VC8|Q9NP76|Q9NYH4	Missense_Mutation	SNP	ENST00000373573.3	hg19	CCDS14420.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.916005	0.52546	.	.	ENSG00000147099	ENST00000373573;ENST00000415409;ENST00000373571;ENST00000439122;ENST00000373560;ENST00000373561;ENST00000421523;ENST00000373556;ENST00000373554	T;T;T;T;T;T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8	4.59	3.7	0.42460	Histone deacetylase domain (2);	0.231983	0.45361	D	0.000365	T	0.60508	0.2274	N	0.21194	0.64	0.45822	D	0.99869	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.58364	-0.7649	10	0.87932	D	0	-2.9926	11.1601	0.48509	0.0:0.0:0.8142:0.1858	.	74;74	B4DV22;Q9BY41	.;HDAC8_HUMAN	G	74;74;74;74;74;74;35;74;74	ENSP00000362674:A74G;ENSP00000396424:A74G;ENSP00000362672:A74G;ENSP00000414486:A74G;ENSP00000362661:A74G;ENSP00000362662:A74G;ENSP00000398997:A35G;ENSP00000362657:A74G;ENSP00000362655:A74G	ENSP00000362655:A74G	A	-	2	0	HDAC8	71705403	1.000000	0.71417	0.989000	0.46669	0.993000	0.82548	6.236000	0.72339	0.956000	0.37904	0.513000	0.50165	GCT	.	.		0.483	HDAC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057193.2	NM_018486		C	71788678	G	C	71788678	3	2	122	1	0	0	0	0	1	0	0	0	7022	971	34	4	1034	4	HDAC8	23	71788678	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10		71788678	83481882	119	20528										
MTMR1	8776	hgsc.bcm.edu	37	chrX	149905792	149905792	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	tggtggtgcattgcagcgacGgttgggaccgaacagcccag	16	10	0	0			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chrX:149905792G>T	ENST00000370390.3	+	11	1478	c.1321G>T	c.(1321-1323)Ggt>Tgt	p.G441C	MTMR1_ENST00000445323.2_Missense_Mutation_p.G449C|MTMR1_ENST00000451863.2_Missense_Mutation_p.G441C|MTMR1_ENST00000544228.1_Missense_Mutation_p.G441C|MTMR1_ENST00000541925.1_Missense_Mutation_p.G347C|MTMR1_ENST00000538506.1_Missense_Mutation_p.G266C	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	441	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.|Substrate binding. {ECO:0000250}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					TTGCAGCGACGGTTGGGACCG	0.448																																					p.G441C		Atlas-SNP	.											.	MTMR1	82	.	0			c.G1321T						.						148	127	134					X																	149905792		2203	4300	6503	SO:0001583	missense	8776	exon11			AGCGACGGTTGGG	U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.1321G>T	chrX.hg19:g.149905792G>T	ENSP00000359417:p.Gly441Cys	64.0	0.0		71.0	57.0	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Missense_Mutation	SNP	ENST00000370390.3	hg19	CCDS14695.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.140982	0.77775	.	.	ENSG00000063601	ENST00000541925;ENST00000370390;ENST00000445323;ENST00000544228;ENST00000451863;ENST00000538506	D;D;D;D;D;D	0.99121	-5.45;-5.45;-5.45;-5.45;-5.45;-5.45	4.88	4.88	0.63580	Myotubularin phosphatase domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.99635	0.9866	H	0.98883	4.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97274	0.9913	10	0.87932	D	0	.	17.332	0.87267	0.0:0.0:1.0:0.0	.	441;449	Q13613;F8WA39	MTMR1_HUMAN;.	C	347;441;449;441;441;266	ENSP00000441879:G347C;ENSP00000359417:G441C;ENSP00000414178:G449C;ENSP00000440534:G441C;ENSP00000387446:G441C;ENSP00000443444:G266C	ENSP00000359417:G441C	G	+	1	0	MTMR1	149656450	1.000000	0.71417	0.165000	0.22776	0.832000	0.47134	9.869000	0.99810	2.015000	0.59207	0.544000	0.68410	GGT	.	.		0.448	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789		T	149905792	G	T	149905792	3	4	122	1	0	0	0	0	1	0	0	0	9947	1116	39	1	1363	1	MTMR1	23	149905792	Missense_Mutation	SNP	G	TCGA-DD-A3A8-01A-11D-A22F-10	78117114	149905792	5364768	120	20529										
ZNF185	7739	hgsc.bcm.edu	37	chrX	152085856	152085856	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0916666666666667	11	1	1.44334596583732	1.8588546529723	1.21670486376369	1	1	0	ttcaccaagcccatagacagCtcttcccagccccagcagca	6	18	2	1			TCGA-DD-A3A8-01A-11D-A22F-10	TCGA-DD-A3A8-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4cff8590-559e-4204-8635-96e11bfeda68	20e24e02-0caa-4e55-812b-b081b3bb03d8	g.chrX:152085856C>T	ENST00000370268.4	+	5	328	c.291C>T	c.(289-291)agC>agT	p.S97S	ZNF185_ENST00000449285.2_Silent_p.S97S|ZNF185_ENST00000535861.1_Silent_p.S97S|ZNF185_ENST00000318504.7_Silent_p.S97S|ZNF185_ENST00000318529.8_5'Flank|ZNF185_ENST00000539731.1_Silent_p.S97S|ZNF185_ENST00000370270.2_Silent_p.S97S|ZNF185_ENST00000324823.6_5'UTR			O15231	ZN185_HUMAN	zinc finger protein 185 (LIM domain)	97						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(3)	12	Acute lymphoblastic leukemia(192;6.56e-05)					CCATAGACAGCTCTTCCCAGC	0.617																																					p.S97S		Atlas-SNP	.											.	ZNF185	92	.	0			c.C291T						.						62	67	65					X																	152085856		2023	4149	6172	SO:0001819	synonymous_variant	7739	exon5			AGACAGCTCTTCC	AK056517	CCDS48184.1, CCDS55528.1, CCDS55529.1, CCDS55530.1, CCDS55531.1, CCDS55532.1, CCDS69832.1	Xq28	2012-08-08			ENSG00000147394	ENSG00000147394		"Zinc fingers, C2H2-type"	12976	protein-coding gene	gene with protein product		300381				9268636	Standard	NM_001178106		Approved		uc011myg.2	O15231	OTTHUMG00000024187	ENST00000370268.4:c.291C>T	chrX.hg19:g.152085856C>T		92.0	0.0		100.0	27.0	NM_001178109	A4FTV3|A6NME5|B4DLE9|B7Z771|B8K2L9|B8K2M0|B8K2M1|B8K2M2|E9PFR6|F5GXF7|F5GZL4|F8W8V7|H0Y4M8|O00345|Q8N1R8|Q9NSD2	Silent	SNP	ENST00000370268.4	hg19	CCDS48184.1																																																																																			.	.		0.617	ZNF185-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377480.1	NM_007150		T	152085856	C	T	152085856	2	4	122	1	0	0	0	0	0	0	0	1	17767	796	28	3		3	ZNF185	23	152085856	Silent	SNP	C	TCGA-DD-A3A8-01A-11D-A22F-10	2180064	152085856	3184704	121	20530										
PRAMEF2	65122	hgsc.bcm.edu	37	chr1	12919960	12919960	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acctgaaggagatgaagactCtttgcaaactcgttttctcc	8	10	2	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:12919960C>T	ENST00000240189.2	+	3	787	c.700C>T	c.(700-702)Ctt>Ttt	p.L234F		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	234					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GATGAAGACTCTTTGCAAACT	0.423																																					p.L234F		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.C700T						.						110	114	113					1																	12919960		2203	4299	6502	SO:0001583	missense	65122	exon3			AAGACTCTTTGCA		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"-"	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.700C>T	chr1.hg19:g.12919960C>T	ENSP00000240189:p.Leu234Phe	171.0	0.0		145.0	32.0	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	hg19	CCDS149.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.356756	0.24598	.	.	ENSG00000120952	ENST00000240189	T	0.02863	4.13	0.842	-0.495	0.12030	.	0.181875	0.36409	N	0.002604	T	0.13114	0.0318	M	0.90483	3.12	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.04242	-1.0966	10	0.87932	D	0	.	4.5732	0.12219	0.0:0.5898:0.4102:0.0	.	234	O60811	PRAM2_HUMAN	F	234	ENSP00000240189:L234F	ENSP00000240189:L234F	L	+	1	0	PRAMEF2	12842547	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	-1.613000	0.02059	-0.146000	0.11274	0.194000	0.17425	CTT	.	.		0.423	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014		T	12919960	C	T	12919960	3	4	123	1	0	0	0	0	1	0	0	0	12447	913	32	3	706	3	PRAMEF2	1	12919960	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		12919960	236330661	1	20531										
CDA	978	hgsc.bcm.edu	37	chr1	20940334	20940334	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tttgattctttgcttccccaGtgacatgcaagatgatttta	7	8	1	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:20940334G>A	ENST00000375071.3	+	3	448		c.e3-1		CDA_ENST00000461985.1_Intron	NM_001785.2	NP_001776.1	P32320	CDD_HUMAN	cytidine deaminase						cell surface receptor signaling pathway (GO:0007166)|cytidine deamination (GO:0009972)|cytosine metabolic process (GO:0019858)|negative regulation of cell growth (GO:0030308)|negative regulation of nucleotide metabolic process (GO:0045980)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine-containing compound salvage (GO:0008655)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	cytidine deaminase activity (GO:0004126)|nucleoside binding (GO:0001882)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)	TGCTTCCCCAGTGACATGCAA	0.473																																					.	Pancreas(74;49 1356 2772 27818 40529)	Atlas-SNP	.											.	CDA	19	.	0			c.267-1G>A						.						132	110	118					1																	20940334		2203	4300	6503	SO:0001630	splice_region_variant	978	exon3			TCCCCAGTGACAT	BC054036	CCDS210.1	1p36.2-p35	2008-02-05			ENSG00000158825	ENSG00000158825	3.5.4.5		1712	protein-coding gene	gene with protein product		123920				8422236, 9878810	Standard	NM_001785		Approved	CDD	uc001bdk.3	P32320	OTTHUMG00000002845	ENST00000375071.3:c.267-1G>A	chr1.hg19:g.20940334G>A		137.0	0.0		104.0	20.0	NM_001785		Splice_Site	SNP	ENST00000375071.3	hg19	CCDS210.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645639	0.67358	.	.	ENSG00000158825	ENST00000375071	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6118	0.68522	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDA	20812921	1.000000	0.71417	0.997000	0.53966	0.746000	0.42486	8.114000	0.89570	2.523000	0.85059	0.491000	0.48974	.	.	.		0.473	CDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007965.1	NM_001785	Intron	A	20940334	G	A	20940334	5	1	123	1	0	0	0	0	0	0	1	0	3054	1043	36	3	276	3	CDA	1	20940334	Splice_Site	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	8020374	20940334	228310287	2	20532										
HTR1D	3352	hgsc.bcm.edu	37	chr1	23519871	23519871	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gttccagggcactgtcagcaAgcttgattttcacgtggttg	12	9	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:23519871A>T	ENST00000374619.1	-	1	1351	c.842T>A	c.(841-843)cTt>cAt	p.L281H	HTR1D_ENST00000314113.3_Missense_Mutation_p.L281H	NM_000864.4	NP_000855.1	P28221	5HT1D_HUMAN	5-hydroxytryptamine (serotonin) receptor 1D, G protein-coupled	281					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intestine smooth muscle contraction (GO:0014827)|regulation of behavior (GO:0050795)|regulation of locomotion (GO:0040012)|response to toxic substance (GO:0009636)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000779)|all_lung(284;0.00135)|Breast(348;0.0385)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0561)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;4.69e-27)|Colorectal(126;4.86e-08)|COAD - Colon adenocarcinoma(152;2.86e-06)|GBM - Glioblastoma multiforme(114;0.00012)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(1967;0.00122)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.083)|LUSC - Lung squamous cell carcinoma(448;0.185)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Naratriptan(DB00952)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	ACTGTCAGCAAGCTTGATTTT	0.557																																					p.L281H		Atlas-SNP	.											.	HTR1D	36	.	0			c.T842A						.						87	89	89					1																	23519871		2203	4300	6503	SO:0001583	missense	3352	exon1			TCAGCAAGCTTGA	M89955	CCDS231.1	1p36.3-p34.3	2012-08-08	2012-02-03		ENSG00000179546	ENSG00000179546		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5289	protein-coding gene	gene with protein product		182133	"5-hydroxytryptamine (serotonin) receptor 1D"	HTRL		2541503, 1662665	Standard	NM_000864		Approved	RDC4, HT1DA, 5-HT1D	uc001bgn.3	P28221	OTTHUMG00000003235	ENST00000374619.1:c.842T>A	chr1.hg19:g.23519871A>T	ENSP00000363748:p.Leu281His	96.0	0.0		61.0	14.0	NM_000864		Missense_Mutation	SNP	ENST00000374619.1	hg19	CCDS231.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.680737	0.47886	.	.	ENSG00000179546	ENST00000314113;ENST00000374619	T;T	0.70869	-0.52;-0.52	5.34	5.34	0.76211	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.78181	0.4243	L	0.42686	1.345	0.50813	D	0.999899	D	0.76494	0.999	D	0.76071	0.987	T	0.76945	-0.2771	10	0.36615	T	0.2	.	14.5065	0.67755	1.0:0.0:0.0:0.0	.	281	P28221	5HT1D_HUMAN	H	281	ENSP00000313661:L281H;ENSP00000363748:L281H	ENSP00000313661:L281H	L	-	2	0	HTR1D	23392458	1.000000	0.71417	0.997000	0.53966	0.859000	0.49053	7.576000	0.82467	2.037000	0.60232	0.528000	0.53228	CTT	.	.		0.557	HTR1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008924.1	NM_000864		T	23519871	A	T	23519871	3	4	123	1	0	0	0	0	1	0	0	0	7447	72	3	4	295	4	HTR1D	1	23519871	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	2579537	23519871	225730750	3	20533										
C1orf63	57035	hgsc.bcm.edu	37	chr1	25570119	25570119	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccatcttctgttaccttttcCgacagctagacaggttaaga	7	11	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:25570119C>A	ENST00000243189.7	-	4	954	c.678G>T	c.(676-678)tcG>tcT	p.S226S	C1orf63_ENST00000417642.2_Silent_p.S227S	NM_020317.3	NP_064713.3	Q9BUV0	RSRP1_HUMAN		226										breast(1)|large_intestine(1)|lung(4)|pancreas(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TTACCTTTTCCGACAGCTAGA	0.333																																					p.S226S		Atlas-SNP	.											.	C1orf63	17	.	0			c.G678T						.						202	179	187					1																	25570119		2203	4300	6503	SO:0001819	synonymous_variant	57035	exon4			CTTTTCCGACAGC																												ENST00000243189.7:c.678G>T	chr1.hg19:g.25570119C>A		175.0	0.0		108.0	5.0	NM_020317	A8K917|Q49AA4|Q5TH71|Q9GZP6	Silent	SNP	ENST00000243189.7	hg19	CCDS260.1																																																																																			.	.		0.333	C1orf63-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101966.2			A	25570119	C	A	25570119	2	1	123	1	0	0	0	0	0	0	0	1	2055	639	23	1		1	C1orf63	1	25570119	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	2050248	25570119	223680502	4	20534										
HMGB4	127540	hgsc.bcm.edu	37	chr1	34330001	34330001	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggccaaactcgacaaagcccGataccaggaagaaatgatga	10	10	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:34330001G>A	ENST00000522796.1	+	4	2114	c.209G>A	c.(208-210)cGa>cAa	p.R70Q	CSMD2_ENST00000373381.4_Intron|HMGB4_ENST00000425537.1_3'UTR|HMGB4_ENST00000519684.1_Missense_Mutation_p.R70Q			Q8WW32	HMGB4_HUMAN	high mobility group box 4	70						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GACAAAGCCCGATACCAGGAA	0.468																																					p.R70Q		Atlas-SNP	.											HMGB4,NS,malignant_melanoma,0,1	HMGB4	27	.	0			c.G209A						.						123	141	135					1																	34330001		2203	4300	6503	SO:0001583	missense	127540	exon2			AAGCCCGATACCA		CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"High-mobility group / Canonical"	24954	protein-coding gene	gene with protein product			"high-mobility group box 4"				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.209G>A	chr1.hg19:g.34330001G>A	ENSP00000430919:p.Arg70Gln	119.0	0.0		89.0	18.0	NM_145205	B2R4X7|Q0QWA4	Missense_Mutation	SNP	ENST00000522796.1	hg19	CCDS30668.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.244721	0.79912	.	.	ENSG00000176256	ENST00000519684;ENST00000522796	T;T	0.15017	2.46;2.46	5.58	2.7	0.31948	.	0.000000	0.64402	D	0.000001	T	0.19604	0.0471	M	0.72894	2.215	0.43824	D	0.996393	P	0.52170	0.951	B	0.44133	0.442	T	0.01771	-1.1277	10	0.56958	D	0.05	.	5.8675	0.18783	0.1663:0.1562:0.6774:0.0	.	70	B2R4X7	.	Q	70	ENSP00000429214:R70Q;ENSP00000430919:R70Q	ENSP00000429214:R70Q	R	+	2	0	HMGB4	34102588	1.000000	0.71417	0.469000	0.27204	0.989000	0.77384	5.402000	0.66332	0.459000	0.27016	0.609000	0.83330	CGA	.	.		0.468	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205		A	34330001	G	A	34330001	3	1	123	1	0	0	0	0	1	0	0	0	7237	1058	37	1	211	1	HMGB4	1	34330001	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	8759882	34330001	214920620	5	20535										
C1orf94	84970	hgsc.bcm.edu	37	chr1	34667800	34667800	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctgaaccagccactctggctCaacctgaactatccacctcc	5	18	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:34667800C>T	ENST00000488417.1	+	4	1506	c.1386C>T	c.(1384-1386)ctC>ctT	p.L462L	C1orf94_ENST00000373374.3_Silent_p.L272L	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	462										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				CACTCTGGCTCAACCTGAACT	0.532																																					p.L462L		Atlas-SNP	.											.	C1orf94	156	.	0			c.C1386T						.						189	159	169					1																	34667800		2203	4300	6503	SO:0001819	synonymous_variant	84970	exon4			CTGGCTCAACCTG	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.1386C>T	chr1.hg19:g.34667800C>T		293.0	0.0		215.0	47.0	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	hg19	CCDS44108.1																																																																																			.	.		0.532	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884		T	34667800	C	T	34667800	2	4	123	1	0	0	0	0	0	0	0	1	2073	813	29	3		3	C1orf94	1	34667800	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	337799	34667800	214582821	6	20536										
GNL2	29889	hgsc.bcm.edu	37	chr1	38033329	38033329	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aatgttcctgttcctcttccCtttgtgccttccgcttcttt	5	14	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:38033329C>T	ENST00000373062.3	-	15	2086	c.1988G>A	c.(1987-1989)aGg>aAg	p.R663K	GNL2_ENST00000462812.1_5'UTR	NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	663					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				TTCCTCTTCCCTTTGTGCCTT	0.398																																					p.R663K		Atlas-SNP	.											.	GNL2	58	.	0			c.G1988A						.						208	196	200					1																	38033329		2203	4300	6503	SO:0001583	missense	29889	exon15			TCTTCCCTTTGTG	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.1988G>A	chr1.hg19:g.38033329C>T	ENSP00000362153:p.Arg663Lys	142.0	0.0		115.0	24.0	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	hg19	CCDS421.1	.	.	.	.	.	.	.	.	.	.	C	5.665	0.307227	0.10733	.	.	ENSG00000134697	ENST00000373062	T	0.20738	2.05	4.88	2.48	0.30137	.	0.315524	0.36893	N	0.002345	T	0.07279	0.0184	N	0.11427	0.14	0.21256	N	0.999745	B	0.02656	0.0	B	0.04013	0.001	T	0.32587	-0.9901	10	0.08179	T	0.78	-8.7647	2.502	0.04636	0.3076:0.4952:0.0:0.1971	.	663	Q13823	NOG2_HUMAN	K	663	ENSP00000362153:R663K	ENSP00000362153:R663K	R	-	2	0	GNL2	37805916	1.000000	0.71417	0.997000	0.53966	0.521000	0.34408	2.081000	0.41596	1.119000	0.41883	0.591000	0.81541	AGG	.	.		0.398	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285		T	38033329	C	T	38033329	3	4	123	1	0	0	0	0	1	0	0	0	6544	681	24	3	215	3	GNL2	1	38033329	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	3365529	38033329	211217292	7	20537										
LEPR	3953	hgsc.bcm.edu	37	chr1	66102182	66102182	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acgctgatcagcaactctaaAccaagtgaaactggtgaaga	9	9	2	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:66102182A>G	ENST00000349533.6	+	20	3167	c.2982A>G	c.(2980-2982)aaA>aaG	p.K994K	LEPR_ENST00000406510.3_Silent_p.K61K	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		GCAACTCTAAACCAAGTGAAA	0.428																																					p.K994K		Atlas-SNP	.											.	LEPR	284	.	0			c.A2982G						.						66	64	65					1																	66102182		2203	4300	6503	SO:0001819	synonymous_variant	3953	exon20			CTCTAAACCAAGT	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.2982A>G	chr1.hg19:g.66102182A>G		56.0	0.0		36.0	7.0	NM_002303	Q6FHL5	Silent	SNP	ENST00000349533.6	hg19	CCDS631.1																																																																																			.	.		0.428	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		G	66102182	A	G	66102182	2	3	123	1	0	0	0	0	0	0	0	1	8737	40	2	2		2	LEPR	1	66102182	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	28068853	66102182	183148439	8	20538										
MIER1	57708	hgsc.bcm.edu	37	chr1	67436586	67436586	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atgcatctagaagaacaggtGatgagaagggtgtagaagca	14	4	1	5			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:67436586G>A	ENST00000355356.3	+	8	858	c.709G>A	c.(709-711)Gat>Aat	p.D237N	MIER1_ENST00000371016.1_Missense_Mutation_p.D254N|MIER1_ENST00000357692.2_Missense_Mutation_p.D254N|MIER1_ENST00000371018.3_Missense_Mutation_p.D254N|MIER1_ENST00000401041.1_Missense_Mutation_p.D290N|MIER1_ENST00000371014.1_Missense_Mutation_p.D290N|MIER1_ENST00000401042.3_Missense_Mutation_p.D237N|MIER1_ENST00000355977.6_Missense_Mutation_p.D174N	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	237	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interaction with HDAC1.			D -> G (in Ref. 4; CAH10526). {ECO:0000305}.	positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						AAGAACAGGTGATGAGAAGGG	0.363																																					p.D290N		Atlas-SNP	.											.	MIER1	86	.	0			c.G868A						.						107	102	104					1																	67436586		1849	4107	5956	SO:0001583	missense	57708	exon9			ACAGGTGATGAGA		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.709G>A	chr1.hg19:g.67436586G>A	ENSP00000347514:p.Asp237Asn	136.0	0.0		77.0	5.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Missense_Mutation	SNP	ENST00000355356.3	hg19	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.657597	0.47467	.	.	ENSG00000198160	ENST00000371017;ENST00000371018;ENST00000355977;ENST00000357692;ENST00000401041;ENST00000371016;ENST00000371014;ENST00000401042;ENST00000355356	T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.52	5.52	0.82312	ELM2 domain (1);	0.089115	0.85682	D	0.000000	T	0.20129	0.0484	N	0.17379	0.485	0.58432	D	0.999997	B;P;P;P;P;P;P;B;B	0.46395	0.019;0.877;0.873;0.59;0.455;0.799;0.873;0.021;0.007	B;B;B;B;B;B;B;B;B	0.43360	0.016;0.417;0.385;0.223;0.111;0.214;0.298;0.016;0.024	T	0.02371	-1.1169	10	0.16896	T	0.51	-25.6678	19.4162	0.94700	0.0:0.0:1.0:0.0	.	254;254;237;237;174;261;254;290;290	Q5TAD2;Q32NC4;Q8N108-3;Q8N108-6;Q08AE0;Q8N108;Q8N108-10;Q5TAD5;Q5TAD4	.;.;.;.;.;MIER1_HUMAN;.;.;.	N	258;254;174;254;290;254;290;237;237	ENSP00000360057:D254N;ENSP00000348253:D174N;ENSP00000350321:D254N;ENSP00000383820:D290N;ENSP00000360055:D254N;ENSP00000360053:D290N;ENSP00000383821:D237N;ENSP00000347514:D237N	ENSP00000347514:D237N	D	+	1	0	MIER1	67209174	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.629000	0.83207	2.764000	0.94973	0.650000	0.86243	GAT	.	.		0.363	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948		A	67436586	G	A	67436586	3	1	123	1	0	0	0	0	1	0	0	0	9589	1290	45	3	979	3	MIER1	1	67436586	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	1334404	67436586	181814035	9	20539										
ZNHIT6	54680	hgsc.bcm.edu	37	chr1	86123530	86123530	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agaaacaaatttacacttacCttggtgaagaactttcatgt	6	7	1	3	rs139368369		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:86123530C>A	ENST00000370574.3	-	9	1505	c.1372G>T	c.(1372-1374)Gtg>Ttg	p.V458L	ZNHIT6_ENST00000431532.2_Splice_Site_p.V419L			Q9NWK9	BCD1_HUMAN	zinc finger, HIT-type containing 6	458					box C/D snoRNP assembly (GO:0000492)|ribosome biogenesis (GO:0042254)	extracellular vesicular exosome (GO:0070062)|pre-snoRNP complex (GO:0070761)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(2)|cervix(2)|large_intestine(10)|lung(1)|urinary_tract(1)	17						TTACACTTACCTTGGTGAAGA	0.328																																					p.V458L		Atlas-SNP	.											.	ZNHIT6	42	.	0			c.G1372T						.	C	LEU/VAL,LEU/VAL	0,4404		0,0,2202	121	123	122		1255,1372	4.8	1	1	dbSNP_134	122	1,8581	1.2+/-3.3	0,1,4290	no	missense-near-splice,missense-near-splice	ZNHIT6	NM_001170670.1,NM_017953.3	32,32	0,1,6492	AA,AC,CC		0.0117,0.0,0.0077	benign,benign	419/432,458/471	86123530	1,12985	2202	4291	6493	SO:0001630	splice_region_variant	54680	exon9			ACTTACCTTGGTG	AL442074	CCDS707.1, CCDS53338.1	1p22.3	2013-01-17	2010-09-15	2008-06-23	ENSG00000117174	ENSG00000117174		"Zinc fingers, HIT-type"	26089	protein-coding gene	gene with protein product	"box C/D snoRNA essential 1 homolog (S. cerevisiae)"		"chromosome 1 open reading frame 181", "zinc finger, HIT type 6"	C1orf181		12747765	Standard	NM_017953		Approved	FLJ20729, NY-BR-75, BCD1	uc001dlh.3	Q9NWK9	OTTHUMG00000010576	ENST00000370574.3:c.1372+1G>T	chr1.hg19:g.86123530C>A		55.0	0.0		54.0	13.0	NM_017953	B2RBA1|B4DP13|D3DT20|Q9H278|Q9H3X3|Q9NWN0	Missense_Mutation	SNP	ENST00000370574.3	hg19	CCDS707.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.052131	0.36181	0.0	1.17E-4	ENSG00000117174	ENST00000431532;ENST00000370574	T;T	0.45276	0.94;0.9	5.67	4.76	0.60689	.	0.811253	0.11117	N	0.597822	T	0.19685	0.0473	L	0.53249	1.67	0.29441	N	0.859165	B;B	0.26672	0.035;0.156	B;B	0.22386	0.018;0.039	T	0.11155	-1.0599	9	.	.	.	-0.8053	9.9337	0.41539	0.0:0.8427:0.0:0.1573	.	419;458	B4DP13;Q9NWK9	.;BCD1_HUMAN	L	419;458	ENSP00000414344:V419L;ENSP00000359606:V458L	.	V	-	1	0	ZNHIT6	85896118	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.259000	0.43259	1.540000	0.49301	0.655000	0.94253	GTG	.	C|1.000;A|0.000		0.328	ZNHIT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029186.1	NM_017953	Missense_Mutation	A	86123530	C	A	86123530	5	1	123	1	0	0	0	0	0	0	1	0	18224	695	24	3	48	3	ZNHIT6	1	86123530	Splice_Site	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	18686944	86123530	163127091	10	20540										
RPAP2	79871	hgsc.bcm.edu	37	chr1	92789745	92789745	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agatagtcatttccctgcctGgagggaatctcagaacagct	10	10	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:92789745G>A	ENST00000610020.1	+	8	1377	c.1268G>A	c.(1267-1269)tGg>tAg	p.W423*		NM_024813.2	NP_079089.2	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	423					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|snRNA transcription (GO:0009301)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleolus (GO:0005730)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	22		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		TTCCCTGCCTGGAGGGAATCT	0.418																																					p.W423X		Atlas-SNP	.											.	RPAP2	48	.	0			c.G1268A						.						73	76	75					1																	92789745		2203	4300	6503	SO:0001587	stop_gained	79871	exon8			CTGCCTGGAGGGA	AK023212	CCDS740.1	1p22.1	2014-01-28	2007-07-26	2007-07-26	ENSG00000122484	ENSG00000122484			25791	protein-coding gene	gene with protein product		611476	"chromosome 1 open reading frame 82"	C1orf82		17643375	Standard	NM_024813		Approved	FLJ13150	uc001dot.2	Q8IXW5	OTTHUMG00000010288	ENST00000610020.1:c.1268G>A	chr1.hg19:g.92789745G>A	ENSP00000476948:p.Trp423*	110.0	0.0		80.0	21.0	NM_024813	C9JKB5|Q49AS7|Q9H8Y2	Nonsense_Mutation	SNP	ENST00000610020.1	hg19	CCDS740.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.236952	0.58886	.	.	ENSG00000122484	ENST00000370343;ENST00000394482	.	.	.	5.63	-3.36	0.04913	.	1.138040	0.06667	N	0.765441	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	1.4894	2.7472	0.05271	0.278:0.064:0.338:0.32	.	.	.	.	X	423	.	ENSP00000359368:W423X	W	+	2	0	RPAP2	92562333	0.000000	0.05858	0.000000	0.03702	0.985000	0.73830	-0.492000	0.06467	-0.118000	0.11851	0.655000	0.94253	TGG	.	.		0.418	RPAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028368.2	NM_024813		A	92789745	G	A	92789745	4	1	123	1	0	0	0	0	0	1	0	0	13557	1357	47	3	1298	3	RPAP2	1	92789745	Nonsense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	6666215	92789745	156460876	11	20541										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118558673	118558673	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atcctttggtgccgatccgaTttccttcaggtgtggttgta	11	9	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:118558673T>G	ENST00000336338.5	-	29	4267	c.4202A>C	c.(4201-4203)aAt>aCt	p.N1401T		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1401						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GCCGATCCGATTTCCTTCAGG	0.463																																					p.N1401T		Atlas-SNP	.											.	SPAG17	263	.	0			c.A4202C						.						171	177	175					1																	118558673		2203	4300	6503	SO:0001583	missense	200162	exon29			ATCCGATTTCCTT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4202A>C	chr1.hg19:g.118558673T>G	ENSP00000337804:p.Asn1401Thr	320.0	0.0		218.0	49.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	T	3.268	-0.149720	0.06585	.	.	ENSG00000155761	ENST00000336338	T	0.17213	2.29	4.72	0.71	0.18157	.	1.384010	0.04043	N	0.303385	T	0.04227	0.0117	L	0.44542	1.39	0.21064	N	0.999798	B	0.12013	0.005	B	0.09377	0.004	T	0.36089	-0.9762	10	0.29301	T	0.29	.	1.3661	0.02201	0.1536:0.1161:0.3462:0.3841	.	1401	Q6Q759	SPG17_HUMAN	T	1401	ENSP00000337804:N1401T	ENSP00000337804:N1401T	N	-	2	0	SPAG17	118360196	0.505000	0.26131	0.948000	0.38648	0.262000	0.26303	0.556000	0.23438	0.694000	0.31654	0.377000	0.23210	AAT	.	.		0.463	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		G	118558673	T	G	118558673	3	3	123	1	0	0	0	0	1	0	0	0	14994	1493	52	5	2549	5	SPAG17	1	118558673	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	25768928	118558673	130691948	12	20542										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144931551	144931551	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gatcaagcatgaaagcacacTtgctgcaagcgaactcggct	10	11	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:144931551T>C	ENST00000369354.3	-	6	826				PDE4DIP_ENST00000529945.1_Missense_Mutation_p.K53R|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.K53R|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000479408.2_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000530740.1_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein						cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GAAAGCACACTTGCTGCAAGC	0.517			T	PDGFRB	MPD																																p.K53R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A158G						.						98	100	100					1																	144931551		2203	4300	6503	SO:0001627	intron_variant	9659	exon1			GCACACTTGCTGC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.637-7730A>G	chr1.hg19:g.144931551T>C		240.0	0.0		267.0	13.0	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.477935	0.84747	.	.	ENSG00000178104	ENST00000369353;ENST00000313431;ENST00000529945	T;T	0.31247	1.5;1.54	5.3	5.3	0.74995	.	.	.	.	.	T	0.44519	0.1297	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.49331	-0.8951	9	0.87932	D	0	.	13.1866	0.59684	0.0:0.0:0.0:1.0	.	53	Q5VU43-2	.	R	53	ENSP00000316434:K53R;ENSP00000433392:K53R	ENSP00000316434:K53R	K	-	2	0	PDE4DIP	143642908	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	8.040000	0.89188	1.996000	0.58369	0.379000	0.24179	AAG	.	.		0.517	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144931551	T	C	144931551	1	2	123	0	1	0	0	0	0	0	0	0	11652	1609	56	2		2	PDE4DIP	1	144931551	Intron	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	26372878	144931551	104319070	13	20543										
PRKAB2	5565	hgsc.bcm.edu	37	chr1	146634090	146634090	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gatgggtggggatttgaatcTttcctcagatcgaaacgcat	12	7	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:146634090T>C	ENST00000254101.3	-	6	739	c.601A>G	c.(601-603)Aga>Gga	p.R201G	PRKAB2_ENST00000496858.1_5'Flank|PRKAB2_ENST00000425272.2_Missense_Mutation_p.R119G	NM_005399.3	NP_005390.1	O43741	AAKB2_HUMAN	protein kinase, AMP-activated, beta 2 non-catalytic subunit	201					carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)|regulation of fatty acid biosynthetic process (GO:0042304)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)	p.R201*(1)		NS(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(923;0.0487)				Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)	GATTTGAATCTTTCCTCAGAT	0.408																																					p.R201G		Atlas-SNP	.											PRKAB2,mouth,carcinoma,0,1	PRKAB2	26	.	1	Substitution - Nonsense(1)	upper_aerodigestive_tract(1)	c.A601G						.						108	105	106					1																	146634090		2203	4300	6503	SO:0001583	missense	5565	exon6			TGAATCTTTCCTC	BC053610	CCDS925.1	1q21.2	2008-02-05			ENSG00000131791	ENSG00000131791			9379	protein-coding gene	gene with protein product	"AMPK beta 2"	602741				8557660	Standard	NM_005399		Approved		uc001epe.3	O43741	OTTHUMG00000014032	ENST00000254101.3:c.601A>G	chr1.hg19:g.146634090T>C	ENSP00000254101:p.Arg201Gly	104.0	0.0		143.0	14.0	NM_005399	A8K9V5|B4DH06|Q5VXY0	Missense_Mutation	SNP	ENST00000254101.3	hg19	CCDS925.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.959026	0.53400	.	.	ENSG00000131791	ENST00000254101;ENST00000425272	.	.	.	5.74	3.59	0.41128	5-AMP-activated protein kinase, beta subunit, interaction domain (1);	0.048455	0.85682	D	0.000000	T	0.28732	0.0712	L	0.43923	1.385	0.52099	D	0.999943	B;B	0.17465	0.005;0.022	B;B	0.18263	0.008;0.021	T	0.15521	-1.0434	9	0.56958	D	0.05	.	6.3918	0.21591	0.1209:0.0:0.4538:0.4254	.	119;201	B4DH06;O43741	.;AAKB2_HUMAN	G	201;119	.	ENSP00000254101:R201G	R	-	1	2	PRKAB2	145100714	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.991000	0.56973	0.472000	0.27344	0.533000	0.62120	AGA	.	.		0.408	PRKAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039471.1	NM_005399		C	146634090	T	C	146634090	3	2	123	1	0	0	0	0	1	0	0	0	12508	1617	56	2	229	2	PRKAB2	1	146634090	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	1702539	146634090	102616531	14	20544										
VPS45	11311	hgsc.bcm.edu	37	chr1	150054035	150054035	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tggaagattttcagaagaagAaaccaaaagaacagcaaaaa	8	5	1	5			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:150054035A>G	ENST00000369130.3	+	9	1438	c.892A>G	c.(892-894)Aaa>Gaa	p.K298E	VPS45_ENST00000369128.5_Missense_Mutation_p.K193E|VPS45_ENST00000535106.1_Missense_Mutation_p.K229E	NM_001279354.1|NM_007259.3	NP_001266283.1|NP_009190.2	Q9NRW7	VPS45_HUMAN	vacuolar protein sorting 45 homolog (S. cerevisiae)	298				K -> R (in Ref. 1; AAC50931). {ECO:0000305}.	blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|vesicle docking involved in exocytosis (GO:0006904)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			TCAGAAGAAGAAACCAAAAGA	0.338																																					p.K298E		Atlas-SNP	.											.	VPS45	47	.	0			c.A892G						.						71	69	70					1																	150054035		2202	4300	6502	SO:0001583	missense	11311	exon9			AAGAAGAAACCAA	U35246	CCDS944.1, CCDS60244.1, CCDS72904.1	1q21.2	2008-02-05	2006-12-19	2006-12-19	ENSG00000136631	ENSG00000136631			14579	protein-coding gene	gene with protein product		610035	"vacuolar protein sorting 45A (yeast homolog)", "vacuolar protein sorting 45A (yeast)"	VPS45B, VPS45A		8996080	Standard	NM_007259		Approved	h-vps45, H1	uc001etp.3	Q9NRW7	OTTHUMG00000012511	ENST00000369130.3:c.892A>G	chr1.hg19:g.150054035A>G	ENSP00000358126:p.Lys298Glu	129.0	0.0		205.0	14.0	NM_007259	D3DUZ9|F5H8K1|Q15715|Q53FR8|Q5T4P6|Q9Y4Z6	Missense_Mutation	SNP	ENST00000369130.3	hg19	CCDS944.1	.	.	.	.	.	.	.	.	.	.	A	16.30	3.085144	0.55861	.	.	ENSG00000136631	ENST00000369130;ENST00000369128;ENST00000543996;ENST00000535106;ENST00000419023	T;T;T;T	0.76060	1.55;-0.99;1.55;1.55	5.54	5.54	0.83059	.	0.176312	0.64402	D	0.000008	T	0.69477	0.3115	M	0.68952	2.095	0.58432	D	0.999996	P;B;B;B	0.37423	0.594;0.03;0.065;0.03	B;B;B;B	0.43623	0.425;0.102;0.145;0.102	T	0.71384	-0.4609	10	0.38643	T	0.18	.	15.0164	0.71588	1.0:0.0:0.0:0.0	.	193;298;118;298	F5H8K1;Q53FR8;A0AR27;Q9NRW7	.;.;.;VPS45_HUMAN	E	298;193;173;229;229	ENSP00000358126:K298E;ENSP00000358124:K193E;ENSP00000440690:K229E;ENSP00000400143:K229E	ENSP00000358124:K193E	K	+	1	0	VPS45	148320659	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.467000	0.90390	2.326000	0.78906	0.533000	0.62120	AAA	.	.		0.338	VPS45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034964.1	NM_007259		G	150054035	A	G	150054035	3	3	123	1	0	0	0	0	1	0	0	0	17226	247	9	2	926	2	VPS45	1	150054035	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	3419945	150054035	99196586	15	20545										
SETDB1	9869	hgsc.bcm.edu	37	chr1	150915464	150915464	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtggtcgccaaatacaaagaTgggaatcaggtctggctcta	12	8	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:150915464T>C	ENST00000271640.5	+	7	1000	c.810T>C	c.(808-810)gaT>gaC	p.D270D	SETDB1_ENST00000368969.4_Silent_p.D270D|SETDB1_ENST00000368962.2_Silent_p.D270D|SETDB1_ENST00000459773.1_Intron|SETDB1_ENST00000368963.1_Intron	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	270	Tudor 1.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			AATACAAAGATGGGAATCAGG	0.502																																					p.D270D		Atlas-SNP	.											.	SETDB1	204	.	0			c.T810C						.						151	141	144					1																	150915464		2203	4300	6503	SO:0001819	synonymous_variant	9869	exon7			CAAAGATGGGAAT	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.810T>C	chr1.hg19:g.150915464T>C		210.0	0.0		384.0	37.0	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Silent	SNP	ENST00000271640.5	hg19	CCDS44217.1																																																																																			.	.		0.502	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			C	150915464	T	C	150915464	2	2	123	1	0	0	0	0	0	0	0	1	14153	1461	51	2		2	SETDB1	1	150915464	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	861429	150915464	98335157	16	20546										
FLG	2312	hgsc.bcm.edu	37	chr1	152286777	152286777	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcacttagcctcttcctattGtctcctaatctagtattttc	3	12	4	0	rs375267392		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:152286777G>A	ENST00000368799.1	-	3	620	c.585C>T	c.(583-585)gaC>gaT	p.D195D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	195					establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTTCCTATTGTCTCCTAATC	0.318									Ichthyosis																												p.D195D		Atlas-SNP	.											.	FLG	900	.	0			c.C585T						.						87	94	91					1																	152286777		2203	4298	6501	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCTATTGTCTCCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.585C>T	chr1.hg19:g.152286777G>A		143.0	0.0		282.0	31.0	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.318	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152286777	G	A	152286777	2	1	123	1	0	0	0	0	0	0	0	1	5930	1368	48	3		3	FLG	1	152286777	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	1371313	152286777	96963844	17	20547										
FLG2	388698	hgsc.bcm.edu	37	chr1	152327323	152327323	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agccagaggattttcctgagCctgactcatgttgtccaaag	10	10	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:152327323C>G	ENST00000388718.5	-	3	3011	c.2939G>C	c.(2938-2940)gGc>gCc	p.G980A	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	980	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTTTCCTGAGCCTGACTCATG	0.498																																					p.G980A		Atlas-SNP	.											.	FLG2	431	.	0			c.G2939C						.						258	260	259					1																	152327323		2203	4300	6503	SO:0001583	missense	388698	exon3			CCTGAGCCTGACT	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.2939G>C	chr1.hg19:g.152327323C>G	ENSP00000373370:p.Gly980Ala	300.0	0.0		520.0	40.0	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	hg19	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	C	8.274	0.813954	0.16537	.	.	ENSG00000143520	ENST00000388718	T	0.39787	1.06	3.96	2.02	0.26589	.	.	.	.	.	T	0.12603	0.0306	M	0.65498	2.005	0.09310	N	1	P	0.34977	0.478	B	0.30105	0.111	T	0.33085	-0.9882	9	0.05833	T	0.94	1.3468	6.3918	0.21591	0.0:0.7628:0.0:0.2372	.	980	Q5D862	FILA2_HUMAN	A	980	ENSP00000373370:G980A	ENSP00000373370:G980A	G	-	2	0	FLG2	150593947	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	0.317000	0.19487	0.878000	0.35920	0.561000	0.74099	GGC	.	.		0.498	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		G	152327323	C	G	152327323	3	3	123	1	0	0	0	0	1	0	0	0	5931	739	26	4	4240	4	FLG2	1	152327323	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	40546	152327323	96923298	18	20548										
LCE1B	353132	hgsc.bcm.edu	37	chr1	152785131	152785131	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctctgggggttgctgcagttCtgggggaggtggctgctgcc	19	9	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:152785131C>T	ENST00000360090.3	+	1	685	c.209C>T	c.(208-210)tCt>tTt	p.S70F		NM_178349.1	NP_848126.1	Q5T7P3	LCE1B_HUMAN	late cornified envelope 1B	70	Gly-rich.				keratinization (GO:0031424)					breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|skin(2)	18	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGCTGCAGTTCTGGGGGAGGT	0.677																																					p.S70F		Atlas-SNP	.											.	LCE1B	45	.	0			c.C209T						.						44	52	49					1																	152785131		2203	4300	6503	SO:0001583	missense	353132	exon1			GCAGTTCTGGGGG	BI670515	CCDS1027.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000196734	ENSG00000196734		"Late cornified envelopes"	16611	protein-coding gene	gene with protein product		612604	"small proline rich-like (epidermal differentiation complex) 2A"	SPRL2A		11698679	Standard	NM_178349		Approved	LEP2	uc001faq.3	Q5T7P3	OTTHUMG00000014402	ENST00000360090.3:c.209C>T	chr1.hg19:g.152785131C>T	ENSP00000353203:p.Ser70Phe	72.0	0.0		98.0	4.0	NM_178349	A4IF40	Missense_Mutation	SNP	ENST00000360090.3	hg19	CCDS1027.1	.	.	.	.	.	.	.	.	.	.	C	7.359	0.624493	0.14193	.	.	ENSG00000196734	ENST00000360090;ENST00000439693	T	0.06294	3.32	4.35	4.35	0.52113	.	0.000000	0.36519	N	0.002551	T	0.17704	0.0425	M	0.87180	2.865	0.27475	N	0.952748	D	0.76494	0.999	D	0.83275	0.996	T	0.01925	-1.1246	10	0.87932	D	0	.	12.2361	0.54516	0.0:1.0:0.0:0.0	.	70	Q5T7P3	LCE1B_HUMAN	F	70;62	ENSP00000353203:S70F	ENSP00000353203:S70F	S	+	2	0	LCE1B	151051755	1.000000	0.71417	1.000000	0.80357	0.271000	0.26615	1.683000	0.37638	2.256000	0.74724	0.650000	0.86243	TCT	.	.		0.677	LCE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040060.1	NM_178349		T	152785131	C	T	152785131	3	4	123	1	0	0	0	0	1	0	0	0	8669	913	32	3	211	3	LCE1B	1	152785131	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	457808	152785131	96465490	19	20549										
NPR1	4881	hgsc.bcm.edu	37	chr1	153653162	153653162	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atgggcaggatgtcagtgccCgccaggcctttcaggtgagt	15	10	2	1	rs561449958		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:153653162C>T	ENST00000368680.3	+	2	1379	c.907C>T	c.(907-909)Cgc>Tgc	p.R303C		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	303					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	TGTCAGTGCCCGCCAGGCCTT	0.577																																					p.R303C	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											NPR1,caecum,carcinoma,0,1	NPR1	104	.	0			c.C907T						.						34	34	34					1																	153653162		2203	4300	6503	SO:0001583	missense	4881	exon2			AGTGCCCGCCAGG	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"guanylate cyclase A"	108960	"atrionatriuretic peptide receptor A", "natriuretic peptide receptor A"	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.907C>T	chr1.hg19:g.153653162C>T	ENSP00000357669:p.Arg303Cys	44.0	0.0		91.0	19.0	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	hg19	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	C	8.961	0.970610	0.18659	.	.	ENSG00000169418	ENST00000368680	T	0.76186	-1.0	4.47	2.5	0.30297	Extracellular ligand-binding receptor (1);	0.416519	0.22134	N	0.064153	T	0.76364	0.3977	M	0.80982	2.52	0.45097	D	0.998116	D	0.76494	0.999	P	0.59171	0.853	T	0.77792	-0.2455	10	0.62326	D	0.03	.	6.5876	0.22630	0.3253:0.5062:0.1686:0.0	.	303	P16066	ANPRA_HUMAN	C	303	ENSP00000357669:R303C	ENSP00000357669:R303C	R	+	1	0	NPR1	151919786	0.000000	0.05858	0.996000	0.52242	0.037000	0.13140	-0.541000	0.06099	2.317000	0.78254	0.557000	0.71058	CGC	.	.		0.577	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		T	153653162	C	T	153653162	3	4	123	1	0	0	0	0	1	0	0	0	10603	652	23	1	913	1	NPR1	1	153653162	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	868031	153653162	95597459	20	20550										
CHRNB2	1141	hgsc.bcm.edu	37	chr1	154543704	154543704	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtgtccttctattccaatgcCgtggtctcctatgatggcag	10	11	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:154543704C>T	ENST00000368476.3	+	5	669	c.405C>T	c.(403-405)gcC>gcT	p.A135A		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	135					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	ATTCCAATGCCGTGGTCTCCT	0.532																																					p.A135A		Atlas-SNP	.											.	CHRNB2	74	.	0			c.C405T						.						132	121	125					1																	154543704		2203	4300	6503	SO:0001819	synonymous_variant	1141	exon5			CAATGCCGTGGTC	U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1962	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 2 (neuronal)"	118507	"cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.405C>T	chr1.hg19:g.154543704C>T		152.0	0.0		240.0	26.0	NM_000748	Q9UEH9	Silent	SNP	ENST00000368476.3	hg19	CCDS1070.1																																																																																			.	.		0.532	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748		T	154543704	C	T	154543704	2	4	123	1	0	0	0	0	0	0	0	1	3393	639	23	1		1	CHRNB2	1	154543704	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	890542	154543704	94706917	21	20551										
KRTCAP2	80128	hgsc.bcm.edu	37	chr1	155145067	155145067	+	5'Flank	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggaagatctttgcttggaatCctttgccaaagacaagattc	9	8	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:155145067C>A	ENST00000334634.4	+	0	0				TRIM46_ENST00000368382.1_5'Flank|TRIM46_ENST00000368383.3_5'Flank|TRIM46_ENST00000368385.4_5'Flank|RP11-201K10.3_ENST00000473363.2_Missense_Mutation_p.D170Y|TRIM46_ENST00000545012.1_5'Flank|KRTCAP2_ENST00000490672.1_5'UTR|TRIM46_ENST00000392451.2_5'Flank|TRIM46_ENST00000543729.1_5'Flank|KRTCAP2_ENST00000295682.4_Missense_Mutation_p.G92V	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46							intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGCTTGGAATCCTTTGCCAAA	0.443																																					p.G92V		Atlas-SNP	.											.	KRTCAP2	15	.	0			c.G275T						.						112	113	113					1																	155145067		2203	4300	6503	SO:0001631	upstream_gene_variant	200185	exon3			TGGAATCCTTTGC		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19019	protein-coding gene	gene with protein product		600986	"tripartite motif-containing 46"				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680		chr1.hg19:g.155145067C>A	Exception_encountered	157.0	0.0		282.0	16.0	NM_173852	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	hg19	CCDS1097.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.039061	0.93630	.	.	ENSG00000163463	ENST00000295682	T	0.53206	0.63	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.63988	0.2558	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68002	-0.5524	10	0.87932	D	0	-2.9392	13.7846	0.63102	0.0:1.0:0.0:0.0	.	92	Q8N6L1	KTAP2_HUMAN	V	92	ENSP00000295682:G92V	ENSP00000295682:G92V	G	-	2	0	KRTCAP2	153411691	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.172000	0.77604	2.708000	0.92522	0.467000	0.42956	GGA	.	.		0.443	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058		A	155145067	C	A	155145067	1	1	123	0	1	0	0	0	0	0	0	0	8587	855	30	3		3	KRTCAP2	1	155145067	5'Flank	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	601363	155145067	94105554	22	20552										
NES	10763	hgsc.bcm.edu	37	chr1	156639411	156639411	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcccctgggcctgcatcctcCatcccactggggatctctag	10	17	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:156639411C>T	ENST00000368223.3	-	4	4701	c.4569G>A	c.(4567-4569)atG>atA	p.M1523I		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1523	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTGCATCCTCCATCCCACTGG	0.577																																					p.M1523I		Atlas-SNP	.											.	NES	196	.	0			c.G4569A						.						74	66	69					1																	156639411		2203	4300	6503	SO:0001583	missense	10763	exon4			ATCCTCCATCCCA	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.4569G>A	chr1.hg19:g.156639411C>T	ENSP00000357206:p.Met1523Ile	133.0	0.0		297.0	60.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	C	5.254	0.232304	0.09969	.	.	ENSG00000132688	ENST00000368223	D	0.84298	-1.83	4.56	-2.47	0.06442	.	.	.	.	.	T	0.53769	0.1817	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49380	-0.8946	9	0.72032	D	0.01	.	5.5637	0.17158	0.1198:0.5102:0.0:0.37	.	1523	P48681	NEST_HUMAN	I	1523	ENSP00000357206:M1523I	ENSP00000357206:M1523I	M	-	3	0	NES	154906035	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.449000	0.06812	-0.543000	0.06240	0.313000	0.20887	ATG	.	.		0.577	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		T	156639411	C	T	156639411	3	4	123	1	0	0	0	0	1	0	0	0	10346	594	21	3	300	3	NES	1	156639411	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1494344	156639411	92611210	23	20553										
NES	10763	hgsc.bcm.edu	37	chr1	156641300	156641300	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	caggttccatgctcccagagAtctcaatgattcctgattct	7	12	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:156641300A>T	ENST00000368223.3	-	4	2812	c.2680T>A	c.(2680-2682)Tct>Act	p.S894T		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	894	Tail.			QGAMNPLEKEIQEPLESVEVNQETFRLLEEENQESLRSLGA WNLENLRSPEE -> KSGGNESSRKGNSRTTGVCGSEPRDI QTPGRGESGIIEISGSMEPGEFEISRG (in Ref. 1; CAA46780). {ECO:0000305}.	brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GCTCCCAGAGATCTCAATGAT	0.458																																					p.S894T		Atlas-SNP	.											.	NES	196	.	0			c.T2680A						.						65	69	68					1																	156641300		2203	4300	6503	SO:0001583	missense	10763	exon4			CCAGAGATCTCAA	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.2680T>A	chr1.hg19:g.156641300A>T	ENSP00000357206:p.Ser894Thr	129.0	0.0		204.0	17.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	A	15.67	2.903430	0.52333	.	.	ENSG00000132688	ENST00000368223	D	0.90732	-2.72	5.16	-1.46	0.08800	.	.	.	.	.	D	0.82944	0.5147	M	0.65498	2.005	0.09310	N	1	P	0.47409	0.895	P	0.46975	0.533	T	0.75709	-0.3223	9	0.72032	D	0.01	.	5.6531	0.17627	0.2996:0.4436:0.2568:0.0	.	894	P48681	NEST_HUMAN	T	894	ENSP00000357206:S894T	ENSP00000357206:S894T	S	-	1	0	NES	154907924	0.000000	0.05858	0.003000	0.11579	0.012000	0.07955	-0.444000	0.06854	-0.270000	0.09285	-0.371000	0.07208	TCT	.	.		0.458	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		T	156641300	A	T	156641300	3	4	123	1	0	0	0	0	1	0	0	0	10346	333	12	4	2189	4	NES	1	156641300	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	1889	156641300	92609321	24	20554										
OR10T2	128360	hgsc.bcm.edu	37	chr1	158368322	158368322	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttattttttgttagctcatcTtggttgccacaggcattcca	7	9	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:158368322T>G	ENST00000334438.1	-	1	934	c.935A>C	c.(934-936)aAg>aCg	p.K312T		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	312			K -> N (in dbSNP:rs6692949).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					TTAGCTCATCTTGGTTGCCAC	0.358																																					p.K312T		Atlas-SNP	.											.	OR10T2	76	.	0			c.A935C						.						24	23	23					1																	158368322		2203	4300	6503	SO:0001583	missense	128360	exon1			CTCATCTTGGTTG	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"GPCR / Class A : Olfactory receptors"	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.935A>C	chr1.hg19:g.158368322T>G	ENSP00000334115:p.Lys312Thr	57.0	0.0		94.0	12.0	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	hg19	CCDS30895.1	.	.	.	.	.	.	.	.	.	.	T	17.49	3.402698	0.62288	.	.	ENSG00000186306	ENST00000334438	T	0.00305	8.18	4.45	4.45	0.53987	.	0.000000	0.43919	D	0.000520	T	0.00109	0.0003	N	0.08118	0	0.21675	N	0.999599	D	0.76494	0.999	D	0.63488	0.915	T	0.55003	-0.8208	10	0.59425	D	0.04	.	11.3382	0.49516	0.0:0.0:0.0:1.0	.	312	Q8NGX3	O10T2_HUMAN	T	312	ENSP00000334115:K312T	ENSP00000334115:K312T	K	-	2	0	OR10T2	156634946	0.811000	0.29063	0.095000	0.20976	0.394000	0.30568	1.174000	0.31932	1.858000	0.53909	0.533000	0.62120	AAG	.	.		0.358	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475		G	158368322	T	G	158368322	3	3	123	1	0	0	0	0	1	0	0	0	10928	1609	56	5	11	5	OR10T2	1	158368322	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	1727022	158368322	90882299	25	20555										
IGSF9	57549	hgsc.bcm.edu	37	chr1	159901621	159901621	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccttggtccaagagacaacaGgaggagggtccccttgggcg	15	11	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:159901621G>A	ENST00000368094.1	-	11	1540	c.1343C>T	c.(1342-1344)cCt>cTt	p.P448L	IGSF9_ENST00000493195.1_5'UTR|IGSF9_ENST00000361509.3_Missense_Mutation_p.P432L	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	448	Ig-like 5.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			AGAGACAACAGGAGGAGGGTC	0.612																																					p.P448L		Atlas-SNP	.											.	IGSF9	123	.	0			c.C1343T						.						49	55	53					1																	159901621		2203	4300	6503	SO:0001583	missense	57549	exon11			ACAACAGGAGGAG	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.1343C>T	chr1.hg19:g.159901621G>A	ENSP00000357073:p.Pro448Leu	50.0	0.0		113.0	9.0	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	hg19	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.674034	0.47781	.	.	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.71461	-0.57;-0.57	4.41	4.41	0.53225	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.190730	0.25780	N	0.028343	D	0.85526	0.5717	M	0.93328	3.405	0.58432	D	0.999999	D;D	0.89917	0.992;1.0	D;D	0.83275	0.937;0.996	D	0.89524	0.3780	9	.	.	.	-2.2744	14.5219	0.67856	0.0:0.0:1.0:0.0	.	448;448	Q9P2J2;C9JI81	TUTLA_HUMAN;.	L	432;448;448	ENSP00000355049:P432L;ENSP00000357073:P448L	.	P	-	2	0	IGSF9	158168245	1.000000	0.71417	0.366000	0.25914	0.078000	0.17371	8.951000	0.93025	2.003000	0.58678	0.561000	0.74099	CCT	.	.		0.612	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		A	159901621	G	A	159901621	3	1	123	1	0	0	0	0	1	0	0	0	7614	1000	35	3	2240	3	IGSF9	1	159901621	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	1533299	159901621	89349000	26	20556										
ATP1A4	480	hgsc.bcm.edu	37	chr1	160141549	160141549	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcgcagtgcaggaattaaggTaaatacttgcccagaccagg	11	9	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:160141549T>C	ENST00000368081.4	+	12	2325		c.e12+2		ATP1A4_ENST00000418334.1_Splice_Site	NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide						ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGAATTAAGGTAAATACTTGC	0.488																																					.		Atlas-SNP	.											.	ATP1A4	167	.	0			c.1854+2T>C						.						76	79	78					1																	160141549		2203	4300	6503	SO:0001630	splice_region_variant	480	exon12			TTAAGGTAAATAC	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1854+2T>C	chr1.hg19:g.160141549T>C		42.0	0.0		96.0	12.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Splice_Site	SNP	ENST00000368081.4	hg19	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	T	12.94	2.087669	0.36855	.	.	ENSG00000132681	ENST00000368081	.	.	.	4.19	4.19	0.49359	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5356	0.50634	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP1A4	158408173	1.000000	0.71417	0.998000	0.56505	0.311000	0.27955	7.656000	0.83736	1.898000	0.54952	0.533000	0.62120	.	.	.		0.488	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	Intron	C	160141549	T	C	160141549	5	2	123	1	0	0	0	0	0	0	1	0	1131	1652	57	2	1902	2	ATP1A4	1	160141549	Splice_Site	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	239928	160141549	89109072	27	20557										
DNM3	26052	hgsc.bcm.edu	37	chr1	172357765	172357765	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggccaacactaagtgctcccCtcgcaaggcccacatccggc	9	18	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:172357765C>G	ENST00000355305.5	+	20	2513	c.2356C>G	c.(2356-2358)Ctc>Gtc	p.L786V	DNM3_ENST00000367731.1_Missense_Mutation_p.L776V|DNM3_ENST00000358155.4_Missense_Mutation_p.L780V			Q9UQ16	DYN3_HUMAN	dynamin 3	786					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						AAGTGCTCCCCTCGCAAGGCC	0.592																																					p.L780V		Atlas-SNP	.											.	DNM3	85	.	0			c.C2338G						.						52	62	59					1																	172357765		1961	4154	6115	SO:0001583	missense	26052	exon20			GCTCCCCTCGCAA	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.2356C>G	chr1.hg19:g.172357765C>G	ENSP00000347457:p.Leu786Val	67.0	0.0		126.0	11.0	NM_015569	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	hg19		.	.	.	.	.	.	.	.	.	.	C	9.514	1.106573	0.20714	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000355305;ENST00000367731;ENST00000485254	D;D;D;T	0.92397	-3.03;-3.03;-3.03;-0.6	5.32	5.32	0.75619	.	0.489617	0.19509	N	0.112551	T	0.77246	0.4102	N	0.08118	0	0.80722	D	1	B;B;B	0.24258	0.018;0.061;0.1	B;B;B	0.25614	0.004;0.062;0.026	T	0.77180	-0.2682	10	0.59425	D	0.04	.	12.6485	0.56748	0.1653:0.8347:0.0:0.0	.	786;776;780	Q9UQ16;Q9UQ16-2;Q9UQ16-3	DYN3_HUMAN;.;.	V	790;780;786;776;149	ENSP00000350876:L780V;ENSP00000347457:L786V;ENSP00000356705:L776V;ENSP00000429165:L149V	ENSP00000347457:L786V	L	+	1	0	DNM3	170624388	0.537000	0.26386	0.897000	0.35233	0.044000	0.14063	2.298000	0.43602	2.493000	0.84123	0.591000	0.81541	CTC	.	.		0.592	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		G	172357765	C	G	172357765	3	3	123	1	0	0	0	0	1	0	0	0	4675	681	24	4	2416	4	DNM3	1	172357765	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	12216216	172357765	76892856	28	20558										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179659883	179659883	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gatttttctagcagccgtgcTattacattgtacaaagacaa	7	8	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:179659883T>C	ENST00000367614.1	+	17	3110	c.2751T>C	c.(2749-2751)gcT>gcC	p.A917A	TDRD5_ENST00000444136.1_Silent_p.A971A|TDRD5_ENST00000294848.8_Silent_p.A917A	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	917					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						GCAGCCGTGCTATTACATTGT	0.398																																					p.A971A		Atlas-SNP	.											.	TDRD5	149	.	0			c.T2913C						.						85	83	84					1																	179659883		2203	4300	6503	SO:0001819	synonymous_variant	163589	exon18			CCGTGCTATTACA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2751T>C	chr1.hg19:g.179659883T>C		70.0	0.0		148.0	12.0	NM_001199085	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.		0.398	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		C	179659883	T	C	179659883	2	2	123	1	0	0	0	0	0	0	0	1	15748	1509	53	2		2	TDRD5	1	179659883	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	7302118	179659883	69590738	29	20559										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181706682	181706682	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atccggagggcctgccactaCatcgtgaacctgcgctactt	10	14	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:181706682C>T	ENST00000367573.2	+	23	3444	c.3444C>T	c.(3442-3444)taC>taT	p.Y1148Y	CACNA1E_ENST00000367567.4_Silent_p.Y755Y|CACNA1E_ENST00000357570.5_Silent_p.Y1099Y|CACNA1E_ENST00000367570.1_Silent_p.Y1148Y|CACNA1E_ENST00000526775.1_Silent_p.Y1129Y|CACNA1E_ENST00000360108.3_Silent_p.Y1129Y|CACNA1E_ENST00000358338.5_Silent_p.Y1080Y	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1148					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CCTGCCACTACATCGTGAACC	0.627																																					p.Y1148Y		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C3444T						.						59	67	64					1																	181706682		2114	4225	6339	SO:0001819	synonymous_variant	777	exon23			CCACTACATCGTG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3444C>T	chr1.hg19:g.181706682C>T		173.0	0.0		259.0	28.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.627	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181706682	C	T	181706682	2	4	123	1	0	0	0	0	0	0	0	1	2544	489	17	3		3	CACNA1E	1	181706682	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	2046799	181706682	67543939	30	20560										
RGS8	85397	hgsc.bcm.edu	37	chr1	182617399	182617399	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	attccaggttctcctcactgAactccgtcttcaagaaggca	7	13	4	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:182617399A>G	ENST00000483095.2	-	6	490	c.233T>C	c.(232-234)tTc>tCc	p.F78S	RGS8_ENST00000258302.4_Missense_Mutation_p.F96S|RGS8_ENST00000367557.4_Missense_Mutation_p.F78S|RGS8_ENST00000367556.1_Missense_Mutation_p.F78S			P57771	RGS8_HUMAN	regulator of G-protein signaling 8	78	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			haematopoietic_and_lymphoid_tissue(1)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	5						CTCCTCACTGAACTCCGTCTT	0.488																																					p.F96S	Ovarian(189;1262 3804 41973)	Atlas-SNP	.											.	RGS8	51	.	0			c.T287C						.						194	194	194					1																	182617399		2203	4300	6503	SO:0001583	missense	85397	exon5			TCACTGAACTCCG	AF297015	CCDS1349.1, CCDS41443.1	1q25	2008-07-18	2007-08-14		ENSG00000135824	ENSG00000135824		"Regulators of G-protein signaling"	16810	protein-coding gene	gene with protein product		607189	"regulator of G-protein signalling 8"			11318611	Standard	NM_001102450		Approved	MGC119067, MGC119068, MGC119069	uc001gpm.1	P57771	OTTHUMG00000035219	ENST00000483095.2:c.233T>C	chr1.hg19:g.182617399A>G	ENSP00000426289:p.Phe78Ser	121.0	0.0		223.0	20.0	NM_033345	B4DGL9|Q3SYD2	Missense_Mutation	SNP	ENST00000483095.2	hg19	CCDS41443.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.903908	0.92035	.	.	ENSG00000135824	ENST00000483095;ENST00000258302;ENST00000367557;ENST00000367556	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.55	5.55	0.83447	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.66218	0.2767	M	0.93939	3.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.76418	-0.2966	10	0.87932	D	0	.	15.3412	0.74300	1.0:0.0:0.0:0.0	.	78;96	P57771;P57771-2	RGS8_HUMAN;.	S	78;96;78;78	ENSP00000426289:F78S;ENSP00000258302:F96S;ENSP00000356528:F78S;ENSP00000356527:F78S	ENSP00000258302:F96S	F	-	2	0	RGS8	180884022	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.020000	0.93667	2.101000	0.63845	0.460000	0.39030	TTC	.	.		0.488	RGS8-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358979.1	NM_033345		G	182617399	A	G	182617399	3	3	123	1	0	0	0	0	1	0	0	0	13327	246	9	2	317	2	RGS8	1	182617399	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	910717	182617399	66633222	31	20561										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186099815	186099815	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgggcaatggctccctggccAtctatggcactgttgtaagt	12	10	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:186099815A>T	ENST00000271588.4	+	85	13445	c.13216A>T	c.(13216-13218)Atc>Ttc	p.I4406F	HMCN1_ENST00000367492.2_Missense_Mutation_p.I4406F	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4406	Ig-like C2-type 43.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTCCCTGGCCATCTATGGCAC	0.498																																					p.I4406F		Atlas-SNP	.											.	HMCN1	797	.	0			c.A13216T						.						76	78	77					1																	186099815		2203	4300	6503	SO:0001583	missense	83872	exon85			CTGGCCATCTATG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.13216A>T	chr1.hg19:g.186099815A>T	ENSP00000271588:p.Ile4406Phe	51.0	0.0		93.0	11.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.907095	0.92107	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.79247	-1.25;-1.25	5.48	5.48	0.80851	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.87912	0.6297	M	0.78049	2.395	0.80722	D	1	D	0.61697	0.99	D	0.75484	0.986	D	0.88832	0.3306	10	0.56958	D	0.05	.	15.8623	0.79035	1.0:0.0:0.0:0.0	.	4406	Q96RW7	HMCN1_HUMAN	F	4406	ENSP00000271588:I4406F;ENSP00000356462:I4406F	ENSP00000271588:I4406F	I	+	1	0	HMCN1	184366438	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.257000	0.95545	2.205000	0.71048	0.482000	0.46254	ATC	.	.		0.498	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186099815	A	T	186099815	3	4	123	1	0	0	0	0	1	0	0	0	7229	217	8	4	13554	4	HMCN1	1	186099815	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	3482416	186099815	63150806	32	20562										
PDC	5132	hgsc.bcm.edu	37	chr1	186413279	186413279	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atgagttccccacctttataGatgagcagtgtaggaagtac	10	8	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:186413279G>T	ENST00000391997.2	-	4	660	c.573C>A	c.(571-573)atC>atA	p.I191I	PDC_ENST00000340129.5_Silent_p.I191I|PDC_ENST00000456239.2_Silent_p.I139I|PDC_ENST00000497198.1_Silent_p.I139I	NM_002597.4	NP_002588.3	P20941	PHOS_HUMAN	phosducin	191	Thioredoxin fold. {ECO:0000250}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of catalytic activity (GO:0043086)|phototransduction (GO:0007602)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	phospholipase inhibitor activity (GO:0004859)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)	7		Breast(1374;1.53e-05)		KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.0129)		CACCTTTATAGATGAGCAGTG	0.383																																					p.I191I		Atlas-SNP	.											.	PDC	15	.	0			c.C573A						.						82	81	82					1																	186413279		2203	4300	6503	SO:0001819	synonymous_variant	5132	exon4			TTTATAGATGAGC	AF076464	CCDS1370.1, CCDS41447.1	1q25.2	2013-01-08			ENSG00000116703	ENSG00000116703			8759	protein-coding gene	gene with protein product		171490				8288249	Standard	NM_022576		Approved	MEKA	uc001gsa.4	P20941	OTTHUMG00000035575	ENST00000391997.2:c.573C>A	chr1.hg19:g.186413279G>T		92.0	0.0		164.0	13.0	NM_002597	Q14816|Q9UP22|Q9UP23	Silent	SNP	ENST00000391997.2	hg19	CCDS1370.1																																																																																			.	.		0.383	PDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086347.2	NM_022577		T	186413279	G	T	186413279	2	4	123	1	0	0	0	0	0	0	0	1	11623	932	33	3		3	PDC	1	186413279	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	313464	186413279	62837342	33	20563										
CRB1	23418	hgsc.bcm.edu	37	chr1	197403858	197403858	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	attgcaaatgctgtttttaaTggacaaagcggtcaaatatt	8	5	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:197403858T>A	ENST00000367400.3	+	9	3000	c.2865T>A	c.(2863-2865)aaT>aaA	p.N955K	CRB1_ENST00000535699.1_Missense_Mutation_p.N931K|CRB1_ENST00000544212.1_Missense_Mutation_p.N436K|CRB1_ENST00000367399.2_Missense_Mutation_p.N843K|CRB1_ENST00000538660.1_Intron|CRB1_ENST00000367397.1_Missense_Mutation_p.N336K	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	955	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CTGTTTTTAATGGACAAAGCG	0.299																																					p.N955K		Atlas-SNP	.											.	CRB1	284	.	0			c.T2865A						.						66	71	70					1																	197403858		2202	4298	6500	SO:0001583	missense	23418	exon9			TTTTAATGGACAA		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2865T>A	chr1.hg19:g.197403858T>A	ENSP00000356370:p.Asn955Lys	122.0	0.0		181.0	15.0	NM_201253	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	hg19	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	T	4.273	0.049869	0.08243	.	.	ENSG00000134376	ENST00000535699;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	5.34	1.69	0.24217	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.57330	0.2046	M	0.64997	1.995	0.27434	N	0.953926	B;B;P;B	0.35272	0.019;0.287;0.493;0.361	B;B;B;B	0.31101	0.022;0.053;0.124;0.024	T	0.41215	-0.9521	9	0.23891	T	0.37	.	8.9412	0.35731	0.0:0.3398:0.0:0.6602	.	931;843;604;955	F5H0L2;P82279-3;P82279-4;P82279	.;.;.;CRUM1_HUMAN	K	931;955;843;436;336;604	ENSP00000438786:N931K;ENSP00000356370:N955K;ENSP00000356369:N843K;ENSP00000444556:N436K;ENSP00000356367:N336K	ENSP00000356367:N336K	N	+	3	2	CRB1	195670481	0.015000	0.18098	0.870000	0.34147	0.007000	0.05969	-0.067000	0.11579	0.034000	0.15491	-0.408000	0.06270	AAT	.	.		0.299	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		A	197403858	T	A	197403858	3	1	123	1	0	0	0	0	1	0	0	0	3850	1461	51	4	2899	4	CRB1	1	197403858	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	10990579	197403858	51846763	34	20564										
NAV1	89796	hgsc.bcm.edu	37	chr1	201757647	201757647	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cacccgctccaacagcatccCcacccacgaggcggccttcg	8	21	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:201757647C>T	ENST00000367296.4	+	10	3467	c.3047C>T	c.(3046-3048)cCc>cTc	p.P1016L	NAV1_ENST00000367302.1_Intron|NAV1_ENST00000295624.6_Missense_Mutation_p.P1016L|NAV1_ENST00000367297.4_Missense_Mutation_p.P1016L|NAV1_ENST00000367295.1_Missense_Mutation_p.P625L|NAV1_ENST00000367300.3_Intron|NAV1_ENST00000469130.1_3'UTR|IPO9-AS1_ENST00000413035.1_RNA	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1016					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						AACAGCATCCCCACCCACGAG	0.637																																					p.P1016L		Atlas-SNP	.											.	NAV1	143	.	0			c.C3047T						.						115	112	113					1																	201757647		2203	4300	6503	SO:0001583	missense	89796	exon10			GCATCCCCACCCA	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"neuron navigator-1", "pore membrane and/or filament interacting like protein 3"	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.3047C>T	chr1.hg19:g.201757647C>T	ENSP00000356265:p.Pro1016Leu	146.0	0.0		250.0	14.0	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	hg19	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	C	27.7	4.858535	0.91433	.	.	ENSG00000134369	ENST00000367296;ENST00000295624;ENST00000367297;ENST00000391966;ENST00000367295	T;T;T;T	0.10763	2.84;2.85;2.91;2.86	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.35158	0.0922	M	0.72118	2.19	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.994;0.996;0.999	T	0.05468	-1.0883	10	0.87932	D	0	-32.9317	18.7921	0.91978	0.0:1.0:0.0:0.0	.	1016;625;1016;524;1016	Q8NEY1-6;Q8NEY1-5;Q8NEY1;A8MYI2;Q8NEY1-3	.;.;NAV1_HUMAN;.;.	L	1016;1016;1016;524;625	ENSP00000356265:P1016L;ENSP00000295624:P1016L;ENSP00000356266:P1016L;ENSP00000356264:P625L	ENSP00000295624:P1016L	P	+	2	0	NAV1	200024270	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.744000	0.85034	2.526000	0.85167	0.561000	0.74099	CCC	.	.		0.637	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		T	201757647	C	T	201757647	3	4	123	1	0	0	0	0	1	0	0	0	10192	623	22	3	3142	3	NAV1	1	201757647	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	4353789	201757647	47492974	35	20565										
C1orf116	79098	hgsc.bcm.edu	37	chr1	207198319	207198319	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtcagtggacagtccgctgtCagcctccgtgtccagtgagc	13	13	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:207198319C>T	ENST00000359470.5	-	3	445	c.196G>A	c.(196-198)Gac>Aac	p.D66N	C1orf116_ENST00000461135.2_5'UTR	NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	66						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					AGTCCGCTGTCAGCCTCCGTG	0.582																																					p.D66N		Atlas-SNP	.											.	C1orf116	64	.	0			c.G196A						.						82	77	79					1																	207198319		2203	4300	6503	SO:0001583	missense	79098	exon3			CGCTGTCAGCCTC		CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795			28667	protein-coding gene	gene with protein product	"specifically androgen-regulated gene"	611680				15525603, 9389513	Standard	NM_023938		Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.196G>A	chr1.hg19:g.207198319C>T	ENSP00000352447:p.Asp66Asn	87.0	0.0		177.0	8.0	NM_023938	C9JV41|Q658X3	Missense_Mutation	SNP	ENST00000359470.5	hg19	CCDS1475.1	.	.	.	.	.	.	.	.	.	.	C	33	5.267037	0.95399	.	.	ENSG00000182795	ENST00000359470	T	0.15952	2.38	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.42177	0.1191	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.36089	-0.9762	10	0.87932	D	0	-24.9277	17.3149	0.87220	0.0:1.0:0.0:0.0	.	66	Q9BW04	SARG_HUMAN	N	66	ENSP00000352447:D66N	ENSP00000352447:D66N	D	-	1	0	C1orf116	205264942	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	6.452000	0.73485	2.317000	0.78254	0.655000	0.94253	GAC	.	.		0.582	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088973.1	NM_024115		T	207198319	C	T	207198319	3	4	123	1	0	0	0	0	1	0	0	0	1991	826	29	3	1617	3	C1orf116	1	207198319	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	5440672	207198319	42052302	36	20566										
KCNH1	3756	hgsc.bcm.edu	37	chr1	211093070	211093070	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cccacactggtgaggctggtCattgtgaaatacaacgagga	12	9	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:211093070C>A	ENST00000271751.4	-	7	1401	c.1374G>T	c.(1372-1374)atG>atT	p.M458I	KCNH1_ENST00000367007.4_Missense_Mutation_p.M431I			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	458					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		TGAGGCTGGTCATTGTGAAAT	0.493																																					p.M458I		Atlas-SNP	.											.	KCNH1	199	.	0			c.G1374T						.						162	155	157					1																	211093070		2203	4300	6503	SO:0001583	missense	3756	exon7			GCTGGTCATTGTG	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1374G>T	chr1.hg19:g.211093070C>A	ENSP00000271751:p.Met458Ile	247.0	0.0		460.0	23.0	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	hg19	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.735451	0.89482	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.98249	-4.82;-4.82	5.7	5.7	0.88788	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97773	0.9269	L	0.33093	0.98	0.80722	D	1	P;P	0.47034	0.744;0.889	P;P	0.56042	0.626;0.79	D	0.98917	1.0782	10	0.72032	D	0.01	.	18.8226	0.92103	0.0:1.0:0.0:0.0	.	431;458	Q14CL3;O95259	.;KCNH1_HUMAN	I	458;431	ENSP00000271751:M458I;ENSP00000355974:M431I	ENSP00000271751:M458I	M	-	3	0	KCNH1	209159693	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.538000	0.82048	2.692000	0.91855	0.655000	0.94253	ATG	.	.		0.493	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		A	211093070	C	A	211093070	3	1	123	1	0	0	0	0	1	0	0	0	8040	826	29	3	1615	3	KCNH1	1	211093070	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	3894751	211093070	38157551	37	20567										
USH2A	7399	hgsc.bcm.edu	37	chr1	216172333	216172333	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	actccaaattgtaaaatcatGtgtatggtttgacatatata	6	5	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:216172333G>T	ENST00000307340.3	-	34	6939	c.6553C>A	c.(6553-6555)Cat>Aat	p.H2185N	USH2A_ENST00000366943.2_Missense_Mutation_p.H2185N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2185	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GTAAAATCATGTGTATGGTTT	0.323										HNSCC(13;0.011)																											p.H2185N		Atlas-SNP	.											.	USH2A	1168	.	0			c.C6553A						.						146	140	142					1																	216172333		2203	4300	6503	SO:0001583	missense	7399	exon34			AATCATGTGTATG	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.6553C>A	chr1.hg19:g.216172333G>T	ENSP00000305941:p.His2185Asn	115.0	0.0		227.0	22.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	0.400	-0.918967	0.02396	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.52526	0.66;0.66	5.56	1.56	0.23342	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.379718	0.19202	U	0.120144	T	0.40979	0.1139	M	0.62723	1.935	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.32851	-0.9891	10	0.18276	T	0.48	.	10.4517	0.44526	0.1224:0.3076:0.57:0.0	.	2185	O75445	USH2A_HUMAN	N	2185	ENSP00000305941:H2185N;ENSP00000355910:H2185N	ENSP00000305941:H2185N	H	-	1	0	USH2A	214238956	0.004000	0.15560	0.000000	0.03702	0.178000	0.23041	1.456000	0.35201	-0.172000	0.10779	-1.273000	0.01405	CAT	.	.		0.323	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216172333	G	T	216172333	3	4	123	1	0	0	0	0	1	0	0	0	17051	1377	48	3	9211	3	USH2A	1	216172333	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	5079263	216172333	33078288	38	20568										
ESRRG	2104	hgsc.bcm.edu	37	chr1	216850694	216850694	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	catggttgaactgtagctccCactggcgtctgaagagccac	11	12	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:216850694C>T	ENST00000408911.3	-	2	349	c.196G>A	c.(196-198)Ggg>Agg	p.G66R	ESRRG_ENST00000366937.1_Missense_Mutation_p.G71R|ESRRG_ENST00000493603.1_Missense_Mutation_p.G43R|ESRRG_ENST00000366940.2_Missense_Mutation_p.G43R|ESRRG_ENST00000493748.1_Missense_Mutation_p.G43R|ESRRG_ENST00000366938.2_Missense_Mutation_p.G43R|ESRRG_ENST00000360012.3_Missense_Mutation_p.G43R|ESRRG_ENST00000463665.1_Missense_Mutation_p.G43R|ESRRG_ENST00000361395.2_Missense_Mutation_p.G43R|ESRRG_ENST00000359162.2_Missense_Mutation_p.G43R|ESRRG_ENST00000487276.1_Missense_Mutation_p.G43R|ESRRG_ENST00000361525.3_Missense_Mutation_p.G43R|ESRRG_ENST00000391890.3_Missense_Mutation_p.G43R	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	66					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CTGTAGCTCCCACTGGCGTCT	0.577																																					p.G71R		Atlas-SNP	.											.	ESRRG	111	.	0			c.G211A						.						118	105	109					1																	216850694		2203	4300	6503	SO:0001583	missense	2104	exon3			AGCTCCCACTGGC	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"Nuclear hormone receptors"	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.196G>A	chr1.hg19:g.216850694C>T	ENSP00000386171:p.Gly66Arg	387.0	0.0		658.0	57.0	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	hg19	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	C	35	5.473063	0.96274	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748;ENST00000475275;ENST00000469486;ENST00000459955;ENST00000481543	D;D;D;D;D;D;D;D;D;D;D;D;D;D;T;T;T	0.94828	-3.16;-3.16;-3.16;-3.17;-3.16;-3.16;-3.16;-3.16;-3.16;-3.18;-3.53;-3.16;-3.16;-2.98;0.34;0.13;0.07	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	D	0.96568	0.8880	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	0.983;1.0;1.0	P;D;D	0.91635	0.852;0.999;0.996	D	0.94728	0.7907	10	0.32370	T	0.25	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	43;71;66	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	R	43;43;71;66;43;43;43;43;43;43;43;43;43;43;43;43;43;43	ENSP00000355225:G43R;ENSP00000355907:G43R;ENSP00000355904:G71R;ENSP00000386171:G66R;ENSP00000352077:G43R;ENSP00000354584:G43R;ENSP00000355905:G43R;ENSP00000353108:G43R;ENSP00000419594:G43R;ENSP00000375761:G43R;ENSP00000418629:G43R;ENSP00000419155:G43R;ENSP00000417374:G43R;ENSP00000419514:G43R;ENSP00000417900:G43R;ENSP00000420370:G43R;ENSP00000418895:G43R	ENSP00000346386:G43R	G	-	1	0	ESRRG	214917317	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.677000	0.84024	2.937000	0.99478	0.650000	0.86243	GGG	.	.		0.577	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		T	216850694	C	T	216850694	3	4	123	1	0	0	0	0	1	0	0	0	5264	594	21	3	1204	3	ESRRG	1	216850694	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	678361	216850694	32399927	39	20569										
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220387288	220387288	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acaatcttggagccaggaagTtttttgtgttttgcaagtat	10	5	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:220387288T>C	ENST00000358951.2	-	3	330	c.214A>G	c.(214-216)Act>Gct	p.T72A		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	72					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		AGCCAGGAAGTTTTTTGTGTT	0.383																																					p.T72A		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.A214G						.						116	110	112					1																	220387288		2203	4300	6503	SO:0001583	missense	25782	exon3			AGGAAGTTTTTTG	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.214A>G	chr1.hg19:g.220387288T>C	ENSP00000351832:p.Thr72Ala	147.0	0.0		282.0	32.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	hg19	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	T	2.570	-0.299857	0.05532	.	.	ENSG00000118873	ENST00000358951	T	0.29142	1.58	5.7	-9.62	0.00547	.	1.052410	0.07323	N	0.877924	T	0.08179	0.0204	N	0.03608	-0.345	0.09310	N	1	B;B	0.14012	0.009;0.001	B;B	0.11329	0.006;0.001	T	0.19844	-1.0293	10	0.27785	T	0.31	.	0.304	0.00277	0.3453:0.1734:0.1643:0.3169	.	72;72	Q9H2M9-2;Q9H2M9	.;RBGPR_HUMAN	A	72	ENSP00000351832:T72A	ENSP00000351832:T72A	T	-	1	0	RAB3GAP2	218453911	0.131000	0.22433	0.002000	0.10522	0.784000	0.44337	0.207000	0.17395	-1.298000	0.02348	-0.353000	0.07706	ACT	.	.		0.383	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		C	220387288	T	C	220387288	3	2	123	1	0	0	0	0	1	0	0	0	12951	1725	60	2	4099	2	RAB3GAP2	1	220387288	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	3536594	220387288	28863333	40	20570										
MIA3	375056	hgsc.bcm.edu	37	chr1	222822189	222822189	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aggtgaaggatagagtatatCaaggtaaatctttaggcttt	11	3	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:222822189C>T	ENST00000344922.5	+	8	3653	c.3628C>T	c.(3628-3630)Caa>Taa	p.Q1210*	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000340535.7_Nonsense_Mutation_p.Q88*|MIA3_ENST00000344441.6_Intron	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1210					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		TAGAGTATATCAAGGTAAATC	0.264																																					p.Q1210X		Atlas-SNP	.											.	MIA3	167	.	0			c.C3628T						.						159	153	155					1																	222822189		1788	4064	5852	SO:0001587	stop_gained	375056	exon8			GTATATCAAGGTA		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.3628C>T	chr1.hg19:g.222822189C>T	ENSP00000340900:p.Gln1210*	52.0	0.0		68.0	11.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Nonsense_Mutation	SNP	ENST00000344922.5	hg19	CCDS41470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.886492|7.886492	0.98542|0.98542	.|.	.|.	ENSG00000154305|ENSG00000154305	ENST00000344922;ENST00000340535|ENST00000354906	.|.	.|.	.|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|.	.|.	.|.	.|.	.|T	.|0.75004	.|0.3791	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72481	.|-0.4280	.|4	0.06365|.	T|.	0.9|.	.|.	18.5719|18.5719	0.91138|0.91138	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	1210;88|792	.|.	ENSP00000345866:Q88X|.	Q|S	+|+	1|2	0|0	MIA3|MIA3	220888812|220888812	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.906000|0.906000	0.53458|0.53458	4.440000|4.440000	0.59975|0.59975	2.738000|2.738000	0.93877|0.93877	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.	.		0.264	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		T	222822189	C	T	222822189	4	4	123	1	0	0	0	0	0	1	0	0	9574	827	29	3	3658	3	MIA3	1	222822189	Nonsense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	2434901	222822189	26428432	41	20571										
C1orf65	164127	hgsc.bcm.edu	37	chr1	223567373	223567373	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atctaggtcgctggtcccctTcctcagttccctcggagcgg	11	15	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:223567373T>A	ENST00000366875.3	+	1	659	c.556T>A	c.(556-558)Tcc>Acc	p.S186T		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		186										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		CTGGTCCCCTTCCTCAGTTCC	0.602																																					p.S186T		Atlas-SNP	.											.	C1orf65	71	.	0			c.T556A						.						54	55	55					1																	223567373		2203	4300	6503	SO:0001583	missense	164127	exon1			TCCCCTTCCTCAG																												ENST00000366875.3:c.556T>A	chr1.hg19:g.223567373T>A	ENSP00000355840:p.Ser186Thr	244.0	0.0		475.0	50.0	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	hg19	CCDS1537.1	.	.	.	.	.	.	.	.	.	.	T	16.72	3.201684	0.58234	.	.	ENSG00000178395	ENST00000366875	T	0.25250	1.81	4.18	3.03	0.35002	.	.	.	.	.	T	0.40145	0.1105	L	0.56769	1.78	0.19300	N	0.999974	D	0.67145	0.996	D	0.64237	0.923	T	0.11616	-1.0580	9	0.41790	T	0.15	.	7.7188	0.28721	0.0:0.0:0.213:0.787	.	186	Q8N715	CA065_HUMAN	T	186	ENSP00000355840:S186T	ENSP00000355840:S186T	S	+	1	0	C1orf65	221633996	0.077000	0.21312	0.137000	0.22149	0.043000	0.13939	0.076000	0.14712	0.605000	0.29947	0.528000	0.53228	TCC	.	.		0.602	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			A	223567373	T	A	223567373	3	1	123	1	0	0	0	0	1	0	0	0	2057	1783	62	4	558	4	C1orf65	1	223567373	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	745184	223567373	25683248	42	20572										
GNPAT	8443	hgsc.bcm.edu	37	chr1	231411879	231411879	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aaagcttattattttctcctAgaaataataactgtatattt	3	5	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:231411879A>G	ENST00000366647.4	+	15	2106		c.e15-1		GNPAT_ENST00000366646.3_Splice_Site|GNPAT_ENST00000469332.1_Splice_Site	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase						cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				ATTTTCTCCTAGAAATAATAA	0.284																																					.		Atlas-SNP	.											.	GNPAT	73	.	0			c.1938-2A>G						.						19	21	21					1																	231411879		2170	4283	6453	SO:0001630	splice_region_variant	8443	exon15			TCTCCTAGAAATA	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.1938-1A>G	chr1.hg19:g.231411879A>G		201.0	0.0		345.0	33.0	NM_014236	B4DNM9|Q5TBH7|Q9BWC2	Splice_Site	SNP	ENST00000366647.4	hg19	CCDS1592.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.982392	0.53827	.	.	ENSG00000116906	ENST00000366647;ENST00000366646	.	.	.	4.76	4.76	0.60689	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6648	0.56835	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GNPAT	229478502	1.000000	0.71417	0.919000	0.36401	0.838000	0.47535	4.953000	0.63624	2.006000	0.58801	0.460000	0.39030	.	.	.		0.284	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1		Intron	G	231411879	A	G	231411879	5	3	123	1	0	0	0	0	0	0	1	0	6549	434	15	2	1994	2	GNPAT	1	231411879	Splice_Site	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	7844506	231411879	17838742	43	20573										
RYR2	6262	hgsc.bcm.edu	37	chr1	237713919	237713919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gaaccaagaaatccaacaagGacagcctccgcgaggctgtg	11	12	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:237713919G>A	ENST00000366574.2	+	27	3459	c.3142G>A	c.(3142-3144)Gac>Aac	p.D1048N	RYR2_ENST00000360064.6_Missense_Mutation_p.D1046N|RYR2_ENST00000542537.1_Missense_Mutation_p.D1032N	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1048	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATCCAACAAGGACAGCCTCCG	0.507																																					p.D1048N		Atlas-SNP	.											.	RYR2	1273	.	0			c.G3142A						.						111	107	108					1																	237713919		1927	4140	6067	SO:0001583	missense	6262	exon27			AACAAGGACAGCC	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.3142G>A	chr1.hg19:g.237713919G>A	ENSP00000355533:p.Asp1048Asn	180.0	0.0		358.0	50.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	35	5.415136	0.96092	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.91464	-2.85;-2.85;-2.85	5.14	5.14	0.70334	B30.2/SPRY domain (1);Ryanodine receptor Ryr (1);	0.000000	0.56097	U	0.000028	D	0.91153	0.7214	L	0.43554	1.36	0.80722	D	1	P	0.52692	0.955	P	0.51615	0.675	D	0.91388	0.5133	10	0.49607	T	0.09	.	18.6043	0.91261	0.0:0.0:1.0:0.0	.	1048	Q92736	RYR2_HUMAN	N	1048;1046;1032	ENSP00000355533:D1048N;ENSP00000353174:D1046N;ENSP00000443798:D1032N	ENSP00000353174:D1046N	D	+	1	0	RYR2	235780542	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.731000	0.98807	2.393000	0.81446	0.563000	0.77884	GAC	.	.		0.507	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237713919	G	A	237713919	3	1	123	1	0	0	0	0	1	0	0	0	13784	1174	41	3	3248	3	RYR2	1	237713919	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	6302040	237713919	11536702	44	20574										
RYR2	6262	hgsc.bcm.edu	37	chr1	237982484	237982484	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tattgtcattctcttggccaTaatacaaggtaagtatcctc	6	9	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:237982484T>C	ENST00000366574.2	+	101	14899	c.14582T>C	c.(14581-14583)aTa>aCa	p.I4861T	RYR2_ENST00000360064.6_Missense_Mutation_p.I4867T|RYR2_ENST00000542537.1_Missense_Mutation_p.I4845T	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4861					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CTCTTGGCCATAATACAAGGT	0.393																																					p.I4861T		Atlas-SNP	.											.	RYR2	1273	.	0			c.T14582C						.						197	198	198					1																	237982484		1942	4132	6074	SO:0001583	missense	6262	exon101			TGGCCATAATACA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.14582T>C	chr1.hg19:g.237982484T>C	ENSP00000355533:p.Ile4861Thr	122.0	0.0		206.0	12.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.407320	0.83230	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000536033	D;D;D	0.98437	-4.93;-4.93;-4.93	5.58	5.58	0.84498	Ion transport (1);	0.000000	0.64402	U	0.000011	D	0.98868	0.9617	M	0.81179	2.53	0.80722	D	1	P;D	0.62365	0.659;0.991	P;D	0.78314	0.477;0.991	D	0.99850	1.1070	10	0.87932	D	0	.	15.7638	0.78110	0.0:0.0:0.0:1.0	.	294;4861	F5H3C7;Q92736	.;RYR2_HUMAN	T	4861;4867;4845;294	ENSP00000355533:I4861T;ENSP00000353174:I4867T;ENSP00000443798:I4845T	ENSP00000353174:I4867T	I	+	2	0	RYR2	236049107	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.997000	0.88414	2.126000	0.65437	0.533000	0.62120	ATA	.	.		0.393	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237982484	T	C	237982484	3	2	123	1	0	0	0	0	1	0	0	0	13784	1406	49	2	14984	2	RYR2	1	237982484	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	268565	237982484	11268137	45	20575										
RGS7	6000	hgsc.bcm.edu	37	chr1	240966242	240966242	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aagctcctgataggcactggAtcttataaaacgtgggtatg	11	7	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:240966242A>T	ENST00000407727.1	-	15	1320	c.1321T>A	c.(1321-1323)Tcc>Acc	p.S441T	RGS7_ENST00000366565.1_Missense_Mutation_p.S441T|RGS7_ENST00000331110.7_Missense_Mutation_p.S415T|RGS7_ENST00000446183.2_Missense_Mutation_p.S357T|RGS7_ENST00000366564.1_Missense_Mutation_p.S441T|RGS7_ENST00000366562.4_Missense_Mutation_p.S441T|RGS7_ENST00000401882.1_Missense_Mutation_p.S388T|RGS7_ENST00000348120.2_Missense_Mutation_p.S388T|RGS7_ENST00000366563.1_Missense_Mutation_p.S441T			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	441	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			TAGGCACTGGATCTTATAAAA	0.348																																					p.S441T		Atlas-SNP	.											.	RGS7	308	.	0			c.T1321A						.						143	152	149					1																	240966242		2203	4300	6503	SO:0001583	missense	6000	exon16			CACTGGATCTTAT	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"Regulators of G-protein signaling"	10003	protein-coding gene	gene with protein product		602517	"regulator of G-protein signalling 7"			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.1321T>A	chr1.hg19:g.240966242A>T	ENSP00000384428:p.Ser441Thr	76.0	0.0		136.0	10.0	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	hg19		.	.	.	.	.	.	.	.	.	.	A	29.9	5.042600	0.93685	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000440928;ENST00000348120;ENST00000446183;ENST00000366562;ENST00000407727;ENST00000401882	T;T;T;T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81	6.04	6.04	0.98038	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.103098	0.64402	D	0.000001	T	0.72645	0.3486	M	0.86268	2.805	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.998;1.0;0.998;1.0;0.999	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.995;1.0;0.997;1.0;0.998	T	0.77370	-0.2613	10	0.87932	D	0	.	15.7697	0.78157	1.0:0.0:0.0:0.0	.	357;415;388;441;441;441;441	B7Z223;B7Z257;P49802-4;P49802-2;P49802-5;P49802-3;P49802	.;.;.;.;.;.;RGS7_HUMAN	T	415;441;441;441;272;388;357;441;441;388	ENSP00000331485:S415T;ENSP00000355523:S441T;ENSP00000355522:S441T;ENSP00000355521:S441T;ENSP00000404399:S272T;ENSP00000341242:S388T;ENSP00000390138:S357T;ENSP00000355520:S441T;ENSP00000384428:S441T;ENSP00000385508:S388T	ENSP00000331485:S415T	S	-	1	0	RGS7	239032865	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.317000	0.78254	0.460000	0.39030	TCC	.	.		0.348	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		T	240966242	A	T	240966242	3	4	123	1	0	0	0	0	1	0	0	0	13325	333	12	4	154	4	RGS7	1	240966242	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	2983758	240966242	8284379	46	20576										
OR2L2	26246	hgsc.bcm.edu	37	chr1	248202311	248202311	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcacccacctcactgtagtgTccttctactatgcacccttt	5	16	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:248202311T>C	ENST00000366479.2	+	1	838	c.742T>C	c.(742-744)Tcc>Ccc	p.S248P	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			CACTGTAGTGTCCTTCTACTA	0.502																																					p.S248P		Atlas-SNP	.											.	OR2L2	115	.	0			c.T742C						.						206	182	190					1																	248202311		2203	4300	6503	SO:0001583	missense	26246	exon1			GTAGTGTCCTTCT	X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"GPCR / Class A : Olfactory receptors"	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.742T>C	chr1.hg19:g.248202311T>C	ENSP00000355435:p.Ser248Pro	230.0	0.0		471.0	44.0	NM_001004686	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	hg19	CCDS31103.1	.	.	.	.	.	.	.	.	.	.	.	11.36	1.616213	0.28801	.	.	ENSG00000203663	ENST00000366479	T	0.38560	1.13	1.9	-2.83	0.05769	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32287	U	0.006305	T	0.51346	0.1669	M	0.92507	3.315	0.09310	N	1	P	0.37573	0.6	P	0.46850	0.529	T	0.51172	-0.8739	10	0.56958	D	0.05	.	3.1725	0.06558	0.3251:0.0:0.1955:0.4794	.	248	Q8NH16	OR2L2_HUMAN	P	248	ENSP00000355435:S248P	ENSP00000355435:S248P	S	+	1	0	OR2L2	246268934	0.000000	0.05858	0.801000	0.32222	0.060000	0.15804	-2.297000	0.01141	-0.063000	0.13065	-1.636000	0.00776	TCC	.	.		0.502	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686		C	248202311	T	C	248202311	3	2	123	1	0	0	0	0	1	0	0	0	11016	1667	58	2	744	2	OR2L2	1	248202311	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	7236069	248202311	1048310	47	20577										
OR2T1	26696	hgsc.bcm.edu	37	chr1	248569623	248569623	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgcgccttcatacacccatgTacttcctcctcagccacctt	4	18	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:248569623T>A	ENST00000366474.1	+	1	328	c.328T>A	c.(328-330)Tac>Aac	p.Y110N		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TACACCCATGTACTTCCTCCT	0.423																																					p.Y110N		Atlas-SNP	.											.	OR2T1	89	.	0			c.T328A						.						176	159	165					1																	248569623		2203	4300	6503	SO:0001583	missense	26696	exon1			CCCATGTACTTCC	U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"GPCR / Class A : Olfactory receptors"	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.328T>A	chr1.hg19:g.248569623T>A	ENSP00000355430:p.Tyr110Asn	180.0	0.0		337.0	34.0	NM_030904	Q6IEZ9	Missense_Mutation	SNP	ENST00000366474.1	hg19	CCDS31115.1	.	.	.	.	.	.	.	.	.	.	t	19.03	3.746982	0.69418	.	.	ENSG00000175143	ENST00000366474	T	0.15603	2.41	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33534	U	0.004806	T	0.46658	0.1404	M	0.87827	2.91	0.46901	D	0.99924	D	0.89917	1.0	D	0.83275	0.996	T	0.55283	-0.8165	10	0.87932	D	0	.	13.3845	0.60789	0.0:0.0:0.0:1.0	.	110	O43869	OR2T1_HUMAN	N	110	ENSP00000355430:Y110N	ENSP00000355430:Y110N	Y	+	1	0	OR2T1	246636246	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	4.233000	0.58651	1.993000	0.58246	0.528000	0.53228	TAC	.	.		0.423	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2			A	248569623	T	A	248569623	3	1	123	1	0	0	0	0	1	0	0	0	11025	1638	57	4	330	4	OR2T1	1	248569623	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	367312	248569623	680998	48	20578										
OR2G6	391211	hgsc.bcm.edu	37	chr1	248685435	248685435	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cctaattcagtgctccctcaCtgtgcagctgcccctctgtg	8	16	3	0	rs568353162	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:248685435C>A	ENST00000343414.4	+	1	520	c.488C>A	c.(487-489)aCt>aAt	p.T163N		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	163						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGCTCCCTCACTGTGCAGCTG	0.557																																					p.T163N		Atlas-SNP	.											.	OR2G6	124	.	0			c.C488A						.						87	72	77					1																	248685435		2203	4300	6503	SO:0001583	missense	391211	exon1			CCCTCACTGTGCA		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"GPCR / Class A : Olfactory receptors"	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.488C>A	chr1.hg19:g.248685435C>A	ENSP00000341291:p.Thr163Asn	234.0	0.0		448.0	36.0	NM_001013355	B2RP33	Missense_Mutation	SNP	ENST00000343414.4	hg19	CCDS31119.1	.	.	.	.	.	.	.	.	.	.	N	10.77	1.443424	0.25987	.	.	ENSG00000188558	ENST00000343414	T	0.00253	8.43	3.68	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45606	U	0.000345	T	0.00815	0.0027	H	0.97611	4.04	0.09310	N	1	D	0.89917	1.0	D	0.81914	0.995	T	0.19128	-1.0315	10	0.87932	D	0	.	8.3892	0.32518	0.0:0.8869:0.0:0.1131	.	163	Q5TZ20	OR2G6_HUMAN	N	163	ENSP00000341291:T163N	ENSP00000341291:T163N	T	+	2	0	OR2G6	246752058	0.000000	0.05858	0.048000	0.18961	0.274000	0.26718	-0.000000	0.12993	1.869000	0.54173	0.400000	0.26472	ACT	.	.		0.557	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842		A	248685435	C	A	248685435	3	1	123	1	0	0	0	0	1	0	0	0	11009	565	20	3	490	3	OR2G6	1	248685435	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	115812	248685435	565186	49	20579										
OR2T34	127068	hgsc.bcm.edu	37	chr1	248737675	248737675	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agaggtctgcaaacagcagcAtatcggtcataggccatggc	12	10	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:248737675A>C	ENST00000328782.2	-	1	405	c.384T>G	c.(382-384)taT>taG	p.Y128*		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AAACAGCAGCATATCGGTCAT	0.552																																					p.Y128X		Atlas-SNP	.											.	OR2T34	72	.	0			c.T384G						.						22	24	23					1																	248737675		2152	4264	6416	SO:0001587	stop_gained	127068	exon1			AGCAGCATATCGG	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"GPCR / Class A : Olfactory receptors"	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.384T>G	chr1.hg19:g.248737675A>C	ENSP00000330904:p.Tyr128*	651.0	0.0		1219.0	94.0	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Nonsense_Mutation	SNP	ENST00000328782.2	hg19	CCDS31120.1	.	.	.	.	.	.	.	.	.	.	.	14.08	2.427545	0.43122	.	.	ENSG00000183310	ENST00000328782	.	.	.	2.19	-0.611	0.11601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.12	0.20148	0.7399:0.0:0.2601:0.0	.	.	.	.	X	128	.	ENSP00000330904:Y128X	Y	-	3	2	OR2T34	246804298	0.001000	0.12720	0.008000	0.14137	0.119000	0.20118	-0.342000	0.07801	-0.461000	0.06993	0.319000	0.21371	TAT	.	.		0.552	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821		C	248737675	A	C	248737675	4	2	123	1	0	0	0	0	0	1	0	0	11034	224	8	5	576	5	OR2T34	1	248737675	Nonsense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	52240	248737675	512946	50	20580										
NBAS	51594	hgsc.bcm.edu	37	chr2	15307372	15307372	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aatacgtggatagaagggagTggagacacacttcaccagca	12	8	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:15307372T>A	ENST00000281513.5	-	52	6941	c.6916A>T	c.(6916-6918)Act>Tct	p.T2306S	NBAS_ENST00000441750.1_Missense_Mutation_p.T2186S	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2306					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TAGAAGGGAGTGGAGACACAC	0.552																																					p.T2306S		Atlas-SNP	.											.	NBAS	246	.	0			c.A6916T						.						81	73	76					2																	15307372		2203	4300	6503	SO:0001583	missense	51594	exon52			AGGGAGTGGAGAC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.6916A>T	chr2.hg19:g.15307372T>A	ENSP00000281513:p.Thr2306Ser	180.0	0.0		213.0	23.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.010555	0.54361	.	.	ENSG00000151779	ENST00000441750;ENST00000281513;ENST00000433283	T;T	0.30182	1.54;1.54	5.46	5.46	0.80206	.	0.048354	0.85682	D	0.000000	T	0.48892	0.1525	M	0.71581	2.175	0.53688	D	0.999974	D;P	0.57571	0.98;0.489	P;B	0.55455	0.776;0.128	T	0.53725	-0.8398	10	0.87932	D	0	.	14.7106	0.69229	0.0:0.0:0.0:1.0	.	2186;2306	A2RRP1-2;A2RRP1	.;NBAS_HUMAN	S	2186;2306;119	ENSP00000413201:T2186S;ENSP00000281513:T2306S	ENSP00000281513:T2306S	T	-	1	0	NBAS	15224823	1.000000	0.71417	0.740000	0.30986	0.216000	0.24613	5.802000	0.69122	2.062000	0.61559	0.533000	0.62120	ACT	.	.		0.552	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		A	15307372	T	A	15307372	3	1	123	1	0	0	0	0	1	0	0	0	10195	1696	59	4	203	4	NBAS	2	15307372	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10		15307372	227892001	51	20581										
KCNS3	3790	hgsc.bcm.edu	37	chr2	18112349	18112349	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cctgaatgtggggggctttaAgcagtctgttgaccaaagca	13	8	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:18112349A>G	ENST00000403915.1	+	3	525	c.74A>G	c.(73-75)aAg>aGg	p.K25R	KCNS3_ENST00000304101.4_Missense_Mutation_p.K25R|KCNS3_ENST00000465292.1_Intron	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	25					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GGGGGCTTTAAGCAGTCTGTT	0.527																																					p.K25R		Atlas-SNP	.											.	KCNS3	85	.	0			c.A74G						.						106	101	103					2																	18112349		2203	4300	6503	SO:0001583	missense	3790	exon3			GCTTTAAGCAGTC	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.74A>G	chr2.hg19:g.18112349A>G	ENSP00000385968:p.Lys25Arg	273.0	0.0		365.0	128.0	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	hg19	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	A	1.639	-0.516881	0.04200	.	.	ENSG00000170745	ENST00000403915;ENST00000304101;ENST00000419802	T;T;T	0.74632	1.14;1.14;-0.86	5.79	4.44	0.53790	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.159168	0.52532	D	0.000061	T	0.43700	0.1259	N	0.02111	-0.68	0.43394	D	0.995514	B	0.12630	0.006	B	0.15052	0.012	T	0.49808	-0.8900	10	0.02654	T	1	.	12.4181	0.55504	0.9242:0.0:0.0758:0.0	.	25	Q9BQ31	KCNS3_HUMAN	R	25	ENSP00000385968:K25R;ENSP00000305824:K25R;ENSP00000400098:K25R	ENSP00000305824:K25R	K	+	2	0	KCNS3	17975830	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.115000	0.71566	2.226000	0.72624	0.456000	0.33151	AAG	.	.		0.527	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252		G	18112349	A	G	18112349	3	3	123	1	0	0	0	0	1	0	0	0	8099	72	3	2	76	2	KCNS3	2	18112349	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	2804977	18112349	225087024	52	20582										
GALNT14	79623	hgsc.bcm.edu	37	chr2	31178813	31178813	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgcgcaagcatttcaccttgGgcaacttgatgagctgttta	10	9	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:31178813G>A	ENST00000349752.5	-	5	1136	c.497C>T	c.(496-498)cCc>cTc	p.P166L	GALNT14_ENST00000486564.1_5'Flank|GALNT14_ENST00000406653.1_Missense_Mutation_p.P146L|GALNT14_ENST00000324589.5_Missense_Mutation_p.P171L|GALNT14_ENST00000356174.3_Missense_Mutation_p.P133L|GALNT14_ENST00000420311.2_Missense_Mutation_p.P131L	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	166	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					TTTCACCTTGGGCAACTTGAT	0.517																																					p.P171L		Atlas-SNP	.											.	GALNT14	103	.	0			c.C512T						.						215	200	205					2																	31178813		2203	4300	6503	SO:0001583	missense	79623	exon6			ACCTTGGGCAACT	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"Glycosyltransferase family 2 domain containing"	22946	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 14"	608225	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.497C>T	chr2.hg19:g.31178813G>A	ENSP00000288988:p.Pro166Leu	160.0	0.0		215.0	59.0	NM_001253826	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	hg19	CCDS1773.2	.	.	.	.	.	.	.	.	.	.	G	32	5.190093	0.94923	.	.	ENSG00000158089	ENST00000349752;ENST00000324589;ENST00000406653;ENST00000356174;ENST00000420311;ENST00000430167	T;T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14	5.28	5.28	0.74379	Glycosyl transferase, family 2 (1);	0.788526	0.11995	N	0.509410	D	0.82765	0.5108	M	0.85462	2.755	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.994;0.995;0.999;0.999;0.998;0.999	T	0.81178	-0.1051	10	0.44086	T	0.13	.	18.9153	0.92503	0.0:0.0:1.0:0.0	.	131;131;133;171;166;146	F5H263;B7Z5C5;Q96FL9-2;Q96FL9-3;Q96FL9;B3KV89	.;.;.;.;GLT14_HUMAN;.	L	166;171;146;133;131;133	ENSP00000288988:P166L;ENSP00000314500:P171L;ENSP00000385435:P146L;ENSP00000348497:P133L;ENSP00000415514:P131L;ENSP00000406399:P133L	ENSP00000314500:P171L	P	-	2	0	GALNT14	31032317	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.739000	0.91574	2.484000	0.83849	0.561000	0.74099	CCC	.	.		0.517	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572		A	31178813	G	A	31178813	3	1	123	1	0	0	0	0	1	0	0	0	6220	1232	43	3	1205	3	GALNT14	2	31178813	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	13066464	31178813	212020560	53	20583										
LHCGR	3973	hgsc.bcm.edu	37	chr2	48915238	48915238	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	attgccattttcttagcaatCtttgtatctttattggtagc	6	7	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:48915238C>T	ENST00000294954.7	-	11	1719	c.1698G>A	c.(1696-1698)aaG>aaA	p.K566K	LHCGR_ENST00000405626.1_Silent_p.K539K|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000344775.3_Silent_p.K504K|LHCGR_ENST00000403273.1_3'UTR|LHCGR_ENST00000401907.1_3'UTR	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	566					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	TCTTAGCAATCTTTGTATCTT	0.378																																					p.K566K		Atlas-SNP	.											LHCGR,NS,carcinoma,0,1	LHCGR	154	.	0			c.G1698A						.						112	111	111					2																	48915238		2203	4300	6503	SO:0001819	synonymous_variant	3973	exon11			AGCAATCTTTGTA		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"GPCR / Class A : Gonadotropin and TSH receptors"	6585	protein-coding gene	gene with protein product		152790	"hypergonadotropic hypogonadism"	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.1698G>A	chr2.hg19:g.48915238C>T		151.0	0.0		169.0	19.0	NM_000233	Q14751|Q15996|Q9UEW9	Silent	SNP	ENST00000294954.7	hg19	CCDS1842.1																																																																																			.	.		0.378	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3		T	48915238	C	T	48915238	2	4	123	1	0	0	0	0	0	0	0	1	8771	912	32	3		3	LHCGR	2	48915238	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	17736425	48915238	194284135	54	20584										
EFEMP1	2202	hgsc.bcm.edu	37	chr2	56108782	56108782	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctcgcttctgatatccaggaGggcactgacatgcaaaggat	11	10	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:56108782G>A	ENST00000394555.2	-	5	1040	c.605C>T	c.(604-606)cCt>cTt	p.P202L	EFEMP1_ENST00000394554.1_Missense_Mutation_p.P202L|EFEMP1_ENST00000424836.2_Missense_Mutation_p.P144L|EFEMP1_ENST00000355426.3_Missense_Mutation_p.P202L	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	202	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ATATCCAGGAGGGCACTGACA	0.512																																					p.P202L	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											EFEMP1,caecum,carcinoma,0,1	EFEMP1	81	.	0			c.C605T						.						242	178	199					2																	56108782		2203	4300	6503	SO:0001583	missense	2202	exon5			CCAGGAGGGCACT	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"Fibulins"	3218	protein-coding gene	gene with protein product	"fibulin 3"	601548	"fibrillin-like", "EGF-containing fibulin-like extracellular matrix protein 1"	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.605C>T	chr2.hg19:g.56108782G>A	ENSP00000378058:p.Pro202Leu	181.0	0.0		220.0	47.0	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Missense_Mutation	SNP	ENST00000394555.2	hg19	CCDS1857.1	.	.	.	.	.	.	.	.	.	.	G	6.568	0.473090	0.12461	.	.	ENSG00000115380	ENST00000394555;ENST00000394554;ENST00000405693;ENST00000424836;ENST00000355426	D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01	5.71	-2.15	0.07102	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.308277	0.28011	N	0.016958	D	0.84165	0.5412	L	0.55743	1.74	0.22213	N	0.999282	B;B	0.16166	0.016;0.0	B;B	0.10450	0.005;0.004	T	0.67780	-0.5582	10	0.24483	T	0.36	.	2.196	0.03911	0.2975:0.0908:0.4272:0.1846	.	144;202	B4DW75;Q12805	.;FBLN3_HUMAN	L	202;202;58;144;202	ENSP00000378058:P202L;ENSP00000378057:P202L;ENSP00000399145:P144L;ENSP00000347596:P202L	ENSP00000347596:P202L	P	-	2	0	EFEMP1	55962286	0.002000	0.14202	0.053000	0.19242	0.052000	0.14988	-0.135000	0.10420	-0.136000	0.11475	-0.143000	0.13931	CCT	.	.		0.512	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2			A	56108782	G	A	56108782	3	1	123	1	0	0	0	0	1	0	0	0	4943	1000	35	3	904	3	EFEMP1	2	56108782	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	7193544	56108782	187090591	55	20585										
CCDC142	84865	hgsc.bcm.edu	37	chr2	74707914	74707914	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acctggatctgtgcagtcagCttctggatctccaggcccag	11	13	4	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:74707914C>T	ENST00000393965.3	-	5	1881	c.1485G>A	c.(1483-1485)aaG>aaA	p.K495K	CCDC142_ENST00000471713.1_5'UTR|TTC31_ENST00000410003.1_5'Flank|TTC31_ENST00000233623.5_5'Flank|CCDC142_ENST00000290418.4_Silent_p.K488K|TTC31_ENST00000442235.2_5'Flank	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	495										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						GTGCAGTCAGCTTCTGGATCT	0.537																																					p.K488K		Atlas-SNP	.											.	CCDC142	40	.	0			c.G1464A						.						70	68	69					2																	74707914		2203	4300	6503	SO:0001819	synonymous_variant	84865	exon5			AGTCAGCTTCTGG	AK075543	CCDS1945.1	2p13.1	2008-02-05			ENSG00000135637	ENSG00000135637			25889	protein-coding gene	gene with protein product							Standard	NM_032779		Approved	FLJ14397	uc002slq.3	Q17RM4	OTTHUMG00000129962	ENST00000393965.3:c.1485G>A	chr2.hg19:g.74707914C>T		205.0	0.0		251.0	24.0	NM_032779	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Silent	SNP	ENST00000393965.3	hg19																																																																																				.	.		0.537	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779		T	74707914	C	T	74707914	2	4	123	1	0	0	0	0	0	0	0	1	2778	796	28	3		3	CCDC142	2	74707914	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	18599132	74707914	168491459	56	20586										
TACR1	6869	hgsc.bcm.edu	37	chr2	75278382	75278382	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gggttgggatcctcacctgtCattgaggcagcagtagatga	14	8	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:75278382C>T	ENST00000305249.5	-	4	1693	c.928G>A	c.(928-930)Gac>Aac	p.D310N	TACR1_ENST00000409848.3_Missense_Mutation_p.D310N	NM_001058.3	NP_001049.1	P25103	NK1R_HUMAN	tachykinin receptor 1	310					acute inflammatory response (GO:0002526)|aggressive behavior (GO:0002118)|angiotensin-mediated drinking behavior (GO:0003051)|associative learning (GO:0008306)|behavioral response to pain (GO:0048266)|detection of abiotic stimulus (GO:0009582)|eating behavior (GO:0042755)|inflammatory response (GO:0006954)|long-term memory (GO:0007616)|operant conditioning (GO:0035106)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of action potential (GO:0045760)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of ossification (GO:0045778)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of saliva secretion (GO:0046878)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|positive regulation of vasoconstriction (GO:0045907)|regulation of smooth muscle cell migration (GO:0014910)|regulation of smooth muscle cell proliferation (GO:0048660)|response to auditory stimulus (GO:0010996)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to heat (GO:0009408)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to ozone (GO:0010193)|response to progesterone (GO:0032570)|smooth muscle contraction involved in micturition (GO:0060083)|sperm ejaculation (GO:0042713)|tachykinin receptor signaling pathway (GO:0007217)	cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance P receptor activity (GO:0016496)|tachykinin receptor activity (GO:0004995)	p.D310N(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(8)|ovary(1)|skin(1)	24					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)	CCTCACCTGTCATTGAGGCAG	0.532																																					p.D310N	Pancreas(64;62 1268 3653 14826 43765)	Atlas-SNP	.											TACR1,NS,carcinoma,0,1	TACR1	62	.	1	Substitution - Missense(1)	lung(1)	c.G928A						.						187	171	176					2																	75278382		2203	4300	6503	SO:0001583	missense	6869	exon4			ACCTGTCATTGAG	M76675	CCDS1958.1, CCDS46345.1	2p13.1-p12	2012-08-08			ENSG00000115353	ENSG00000115353		"GPCR / Class A : Tachykinin receptors"	11526	protein-coding gene	gene with protein product		162323		TAC1R		1657150	Standard	NM_001058		Approved	SPR, NK1R, NKIR	uc002sng.2	P25103	OTTHUMG00000129973	ENST00000305249.5:c.928G>A	chr2.hg19:g.75278382C>T	ENSP00000303522:p.Asp310Asn	361.0	1.0		383.0	106.0	NM_001058	A8K150	Missense_Mutation	SNP	ENST00000305249.5	hg19	CCDS1958.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.994681	0.74703	.	.	ENSG00000115353	ENST00000305249;ENST00000409848	T;T	0.36878	1.23;1.23	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.41696	0.1170	M	0.65498	2.005	0.80722	D	1	P	0.50066	0.931	B	0.43680	0.427	T	0.19614	-1.0300	10	0.27785	T	0.31	.	17.0229	0.86438	0.0:1.0:0.0:0.0	.	310	P25103	NK1R_HUMAN	N	310	ENSP00000303522:D310N;ENSP00000386448:D310N	ENSP00000303522:D310N	D	-	1	0	TACR1	75131890	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.852000	0.55934	2.880000	0.98712	0.650000	0.86243	GAC	.	.		0.532	TACR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252239.3	NM_001058		T	75278382	C	T	75278382	3	4	123	1	0	0	0	0	1	0	0	0	15520	826	29	3	307	3	TACR1	2	75278382	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	570468	75278382	167920991	57	20587										
AFF3	3899	hgsc.bcm.edu	37	chr2	100194857	100194857	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gagcctggagaccacggcttCgtctgcggccgtgacttgtg	15	12	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:100194857C>T	ENST00000409236.2	-	16	2962	c.2850G>A	c.(2848-2850)acG>acA	p.T950T	AFF3_ENST00000409579.1_Silent_p.T975T|AFF3_ENST00000356421.2_Silent_p.T975T|AFF3_ENST00000317233.4_Silent_p.T950T			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	950					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						ACCACGGCTTCGTCTGCGGCC	0.488																																					p.T975T		Atlas-SNP	.											.	AFF3	164	.	0			c.G2925A						.						131	137	135					2																	100194857		2203	4300	6503	SO:0001819	synonymous_variant	3899	exon17			CGGCTTCGTCTGC	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.2850G>A	chr2.hg19:g.100194857C>T		135.0	0.0		204.0	66.0	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	hg19	CCDS42723.1																																																																																			.	.		0.488	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		T	100194857	C	T	100194857	2	4	123	1	0	0	0	0	0	0	0	1	358	871	31	1		1	AFF3	2	100194857	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	24916475	100194857	143004516	58	20588										
IL1RL1	9173	hgsc.bcm.edu	37	chr2	102968228	102968228	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctccagcatcttatgaaagtAcaggggaccatcaagtggag	11	9	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:102968228A>G	ENST00000233954.1	+	11	1789	c.1518A>G	c.(1516-1518)gtA>gtG	p.V506V		NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1	506	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of macrophage activation (GO:0043032)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|interleukin-1 receptor activity (GO:0004908)|interleukin-33 receptor activity (GO:0002114)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(3)|urinary_tract(1)	16						TTATGAAAGTACAGGGGACCA	0.517																																					p.V506V		Atlas-SNP	.											.	IL1RL1	114	.	0			c.A1518G						.						48	48	48					2																	102968228		2203	4300	6503	SO:0001819	synonymous_variant	9173	exon11			GAAAGTACAGGGG	D12764	CCDS2057.1, CCDS2058.1, CCDS74548.1	2q12	2013-01-29			ENSG00000115602	ENSG00000115602		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5998	protein-coding gene	gene with protein product	"homolog of mouse growth stimulation-expressed"	601203				1482686, 10191101, 16286016	Standard	NM_016232		Approved	ST2, FIT-1, ST2L, ST2V, DER4, T1, IL33R	uc002tbu.1	Q01638	OTTHUMG00000130782	ENST00000233954.1:c.1518A>G	chr2.hg19:g.102968228A>G		176.0	0.0		213.0	37.0	NM_016232	A8K6B3|B4E0I3|Q53TU7|Q8NEJ3|Q9ULV7|Q9UQ44	Silent	SNP	ENST00000233954.1	hg19	CCDS2057.1																																																																																			.	.		0.517	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253296.1	NM_016232		G	102968228	A	G	102968228	2	3	123	1	0	0	0	0	0	0	0	1	7672	378	14	2		2	IL1RL1	2	102968228	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	2773371	102968228	140231145	59	20589										
SLC9A4	389015	hgsc.bcm.edu	37	chr2	103090418	103090418	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgaactggattatgactatgTgcaaattccttatgaggtca	9	6	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:103090418T>C	ENST00000295269.4	+	1	657	c.200T>C	c.(199-201)gTg>gCg	p.V67A		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	67					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						TATGACTATGTGCAAATTCCT	0.418																																					p.V67A		Atlas-SNP	.											.	SLC9A4	115	.	0			c.T200C						.						128	122	124					2																	103090418		2203	4300	6503	SO:0001583	missense	389015	exon1			ACTATGTGCAAAT		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"Solute carriers"	11077	protein-coding gene	gene with protein product		600531	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 4", "solute carrier family 9 (sodium/hydrogen exchanger), member 4"			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.200T>C	chr2.hg19:g.103090418T>C	ENSP00000295269:p.Val67Ala	141.0	0.0		164.0	48.0	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	hg19	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.941453	0.92526	.	.	ENSG00000180251	ENST00000295269	T	0.70749	-0.51	6.04	6.04	0.98038	.	0.122712	0.56097	D	0.000028	D	0.82797	0.5115	M	0.66939	2.045	0.58432	D	0.999996	D	0.71674	0.998	D	0.70935	0.971	D	0.84458	0.0592	10	0.87932	D	0	.	16.5885	0.84745	0.0:0.0:0.0:1.0	.	67	Q6AI14	SL9A4_HUMAN	A	67	ENSP00000295269:V67A	ENSP00000295269:V67A	V	+	2	0	SLC9A4	102456850	1.000000	0.71417	0.991000	0.47740	0.992000	0.81027	7.295000	0.78780	2.317000	0.78254	0.460000	0.39030	GTG	.	.		0.418	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		C	103090418	T	C	103090418	3	2	123	1	0	0	0	0	1	0	0	0	14731	1696	59	2	202	2	SLC9A4	2	103090418	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	122190	103090418	140108955	60	20590										
SLC9A4	389015	hgsc.bcm.edu	37	chr2	103124608	103124608	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tccatcaaggaccagtgcatCattttctacagtggtgttcg	9	10	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:103124608C>A	ENST00000295269.4	+	5	1726	c.1269C>A	c.(1267-1269)atC>atA	p.I423I		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	423					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						ACCAGTGCATCATTTTCTACA	0.433																																					p.I423I		Atlas-SNP	.											.	SLC9A4	115	.	0			c.C1269A						.						171	165	167					2																	103124608		2203	4300	6503	SO:0001819	synonymous_variant	389015	exon5			GTGCATCATTTTC		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"Solute carriers"	11077	protein-coding gene	gene with protein product		600531	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 4", "solute carrier family 9 (sodium/hydrogen exchanger), member 4"			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.1269C>A	chr2.hg19:g.103124608C>A		358.0	0.0		414.0	60.0	NM_001011552	Q69YK0	Silent	SNP	ENST00000295269.4	hg19	CCDS33264.1																																																																																			.	.		0.433	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		A	103124608	C	A	103124608	2	1	123	1	0	0	0	0	0	0	0	1	14731	816	29	3		3	SLC9A4	2	103124608	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	34190	103124608	140074765	61	20591										
SLC9A2	6549	hgsc.bcm.edu	37	chr2	103300730	103300730	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttctccttcctgctgctgtgTttcctcggaaaaaattgttt	7	10	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:103300730T>C	ENST00000233969.2	+	5	1502	c.1360T>C	c.(1360-1362)Ttt>Ctt	p.F454L		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	454					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						TGCTGCTGTGTTTCCTCGGAA	0.438																																					p.F454L		Atlas-SNP	.											.	SLC9A2	112	.	0			c.T1360C						.						259	242	248					2																	103300730		2203	4300	6503	SO:0001583	missense	6549	exon5			GCTGTGTTTCCTC		CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"Solute carriers"	11072	protein-coding gene	gene with protein product		600530	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 2"	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.1360T>C	chr2.hg19:g.103300730T>C	ENSP00000233969:p.Phe454Leu	347.0	0.0		427.0	102.0	NM_003048	B2RMS2	Missense_Mutation	SNP	ENST00000233969.2	hg19	CCDS2062.1	.	.	.	.	.	.	.	.	.	.	T	20.0	3.931198	0.73327	.	.	ENSG00000115616	ENST00000233969	T	0.13196	2.61	5.62	5.62	0.85841	Cation/H+ exchanger (1);	0.059515	0.64402	D	0.000003	T	0.23054	0.0557	L	0.31420	0.93	0.50632	D	0.99988	D	0.69078	0.997	D	0.64877	0.93	T	0.04090	-1.0978	10	0.19590	T	0.45	.	15.8096	0.78547	0.0:0.0:0.0:1.0	.	454	Q9UBY0	SL9A2_HUMAN	L	454	ENSP00000233969:F454L	ENSP00000233969:F454L	F	+	1	0	SLC9A2	102667162	1.000000	0.71417	1.000000	0.80357	0.287000	0.27160	3.184000	0.50926	2.127000	0.65507	0.533000	0.62120	TTT	.	.		0.438	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2			C	103300730	T	C	103300730	3	2	123	1	0	0	0	0	1	0	0	0	14727	1725	60	2	1378	2	SLC9A2	2	103300730	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	176122	103300730	139898643	62	20592										
RGPD4	285190	hgsc.bcm.edu	37	chr2	108489237	108489237	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gttcagtagcccagagtggaTctgaaagcaaagtggaacct	12	8	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:108489237T>A	ENST00000408999.3	+	20	4854	c.4777T>A	c.(4777-4779)Tct>Act	p.S1593T	RGPD4_ENST00000354986.4_Missense_Mutation_p.S1593T	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1593					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						CCAGAGTGGATCTGAAAGCAA	0.383																																					p.S1593T		Atlas-SNP	.											RGPD4,NS,carcinoma,0,1	RGPD4	112	.	0			c.T4777A						.						40	34	35					2																	108489237		691	1591	2282	SO:0001583	missense	285190	exon20			AGTGGATCTGAAA	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.4777T>A	chr2.hg19:g.108489237T>A	ENSP00000386810:p.Ser1593Thr	152.0	0.0		173.0	26.0	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	hg19	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	10.18	1.279615	0.23307	.	.	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.38887	1.11;1.11	2.33	-2.43	0.06522	.	.	.	.	.	T	0.22551	0.0544	L	0.35414	1.06	0.21416	N	0.999698	B	0.10296	0.003	B	0.06405	0.002	T	0.25537	-1.0129	9	0.15499	T	0.54	-8.3036	2.1596	0.03821	0.2529:0.3485:0.0:0.3986	.	1593	Q7Z3J3	RGPD4_HUMAN	T	1593;1593;960	ENSP00000347081:S1593T;ENSP00000386810:S1593T	ENSP00000347081:S1593T	S	+	1	0	RGPD4	107855669	0.009000	0.17119	0.973000	0.42090	0.432000	0.31715	-0.194000	0.09559	-0.198000	0.10333	0.136000	0.15936	TCT	.	.		0.383	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		A	108489237	T	A	108489237	3	1	123	1	0	0	0	0	1	0	0	0	13303	1435	50	4	4855	4	RGPD4	2	108489237	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	5188507	108489237	134710136	63	20593										
KCNH7	90134	hgsc.bcm.edu	37	chr2	163361023	163361023	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	caataatggttttatctgaaGaaggaggtgatgaattcttt	10	3	2	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:163361023G>T	ENST00000332142.5	-	6	1157	c.1058C>A	c.(1057-1059)tCt>tAt	p.S353Y	KCNH7_ENST00000477019.1_5'UTR|KCNH7_ENST00000328032.4_Missense_Mutation_p.S346Y	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	353					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TTTATCTGAAGAAGGAGGTGA	0.373																																					p.S353Y	GBM(196;1492 2208 17507 24132 45496)	Atlas-SNP	.											.	KCNH7	378	.	0			c.C1058A						.						192	189	190					2																	163361023		2203	4300	6503	SO:0001583	missense	90134	exon6			TCTGAAGAAGGAG	AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.1058C>A	chr2.hg19:g.163361023G>T	ENSP00000331727:p.Ser353Tyr	178.0	0.0		228.0	47.0	NM_033272	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	hg19	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.900958	0.92035	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.88664	-2.41;-2.41	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.91212	0.7231	L	0.43152	1.355	0.80722	D	1	P;D	0.61697	0.942;0.99	P;P	0.59703	0.637;0.862	D	0.88900	0.3352	10	0.29301	T	0.29	.	19.775	0.96388	0.0:0.0:1.0:0.0	.	346;353	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	Y	353;346	ENSP00000331727:S353Y;ENSP00000333781:S346Y	ENSP00000333781:S346Y	S	-	2	0	KCNH7	163069269	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.531000	0.73820	2.741000	0.93983	0.585000	0.79938	TCT	.	.		0.373	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		T	163361023	G	T	163361023	3	4	123	1	0	0	0	0	1	0	0	0	8046	942	33	3	2642	3	KCNH7	2	163361023	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	54871786	163361023	79838350	64	20594										
COBLL1	22837	hgsc.bcm.edu	37	chr2	165548775	165548775	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcccgaacggattgcagtcaGcaaactctgtcgcatctgtt	9	12	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:165548775G>A	ENST00000392717.2	-	14	3488	c.3484C>T	c.(3484-3486)Ctg>Ttg	p.L1162L	COBLL1_ENST00000194871.6_Silent_p.L1191L|COBLL1_ENST00000375458.2_Silent_p.L1086L|COBLL1_ENST00000409184.3_Silent_p.L1124L|COBLL1_ENST00000342193.4_Silent_p.L1124L			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	1162	WH2. {ECO:0000255|PROSITE- ProRule:PRU00406}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						ATTGCAGTCAGCAAACTCTGT	0.443																																					p.L1124L		Atlas-SNP	.											.	COBLL1	122	.	0			c.C3370T						.						105	98	101					2																	165548775		2203	4300	6503	SO:0001819	synonymous_variant	22837	exon13			CAGTCAGCAAACT	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.3484C>T	chr2.hg19:g.165548775G>A		150.0	0.0		169.0	56.0	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Silent	SNP	ENST00000392717.2	hg19																																																																																				.	.		0.443	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		A	165548775	G	A	165548775	2	1	123	1	0	0	0	0	0	0	0	1	3656	962	34	3		3	COBLL1	2	165548775	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	2187752	165548775	77650598	65	20595										
TTN	7273	hgsc.bcm.edu	37	chr2	179569674	179569674	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccttttcgtccctctctgacCtctctatttcctcaatttcc	2	17	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:179569674C>A	ENST00000591111.1	-	102	28897	c.28673G>T	c.(28672-28674)aGg>aTg	p.R9558M	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.R8631M|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R9875M			Q8WZ42	TITIN_HUMAN	titin	13643					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTCTCTGACCTCTCTATTTC	0.338																																					p.R9875M		Atlas-SNP	.											.	TTN	18412	.	0			c.G29624T						.						130	128	128					2																	179569674		1821	4090	5911	SO:0001583	missense	7273	exon104			TCTGACCTCTCTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.28673G>T	chr2.hg19:g.179569674C>A	ENSP00000465570:p.Arg9558Met	183.0	0.0		258.0	34.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	8.638	0.895281	0.17613	.	.	ENSG00000155657	ENST00000342992	T	0.62941	-0.01	5.99	4.85	0.62838	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.46852	0.1414	N	0.14661	0.345	0.80722	D	1	B	0.32425	0.371	B	0.36885	0.235	T	0.49969	-0.8882	9	0.87932	D	0	.	9.4026	0.38442	0.0:0.1451:0.0:0.8549	.	9558	Q8WZ42	TITIN_HUMAN	M	8631	ENSP00000343764:R8631M	ENSP00000343764:R8631M	R	-	2	0	TTN	179277919	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	0.957000	0.29215	1.102000	0.41551	-0.302000	0.09304	AGG	.	.		0.338	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179569674	C	A	179569674	3	1	123	1	0	0	0	0	1	0	0	0	16750	681	24	3	74941	3	TTN	2	179569674	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	14020899	179569674	63629699	66	20596										
COL5A2	1290	hgsc.bcm.edu	37	chr2	189901361	189901361	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cctgagaccctctgttcataTcaagaccataccaaacaggt	6	13	3	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:189901361T>A	ENST00000374866.3	-	52	4368	c.4094A>T	c.(4093-4095)gAt>gTt	p.D1365V		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1365	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			TCTGTTCATATCAAGACCATA	0.338																																					p.D1365V		Atlas-SNP	.											.	COL5A2	230	.	0			c.A4094T						.						83	75	78					2																	189901361		2203	4300	6503	SO:0001583	missense	1290	exon52			TTCATATCAAGAC	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.4094A>T	chr2.hg19:g.189901361T>A	ENSP00000364000:p.Asp1365Val	73.0	0.0		100.0	20.0	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	hg19	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.142661	0.57044	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	T	0.73047	-0.71	5.98	5.98	0.97165	Fibrillar collagen, C-terminal (3);	0.000000	0.53938	D	0.000053	T	0.78394	0.4276	L	0.54908	1.71	0.80722	D	1	D;D	0.61080	0.968;0.989	P;P	0.61003	0.757;0.882	T	0.74665	-0.3589	10	0.23302	T	0.38	.	16.4696	0.84102	0.0:0.0:0.0:1.0	.	1005;1365	Q5PR22;P05997	.;CO5A2_HUMAN	V	1365;1005	ENSP00000364000:D1365V	ENSP00000364000:D1365V	D	-	2	0	COL5A2	189609606	1.000000	0.71417	0.974000	0.42286	0.987000	0.75469	4.976000	0.63785	2.289000	0.77006	0.482000	0.46254	GAT	.	.		0.338	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		A	189901361	T	A	189901361	3	1	123	1	0	0	0	0	1	0	0	0	3699	1435	50	4	417	4	COL5A2	2	189901361	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	10331687	189901361	53298012	67	20597										
STAT4	6775	hgsc.bcm.edu	37	chr2	191898231	191898231	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tataccactttcagaatggtCcacccaggtgaaagttattc	7	10	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:191898231C>T	ENST00000392320.2	-	20	2151	c.1837G>A	c.(1837-1839)Gac>Aac	p.D613N	AC067945.4_ENST00000456176.1_RNA|STAT4_ENST00000358470.4_Missense_Mutation_p.D613N|STAT4_ENST00000470708.1_5'Flank	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	613	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			TCAGAATGGTCCACCCAGGTG	0.373																																					p.D613N		Atlas-SNP	.											.	STAT4	85	.	0			c.G1837A						.						54	57	56					2																	191898231		2203	4300	6503	SO:0001583	missense	6775	exon20			AATGGTCCACCCA		CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"SH2 domain containing"	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.1837G>A	chr2.hg19:g.191898231C>T	ENSP00000376134:p.Asp613Asn	92.0	0.0		128.0	36.0	NM_001243835	Q96NZ6	Missense_Mutation	SNP	ENST00000392320.2	hg19	CCDS2310.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.092704	0.76756	.	.	ENSG00000138378	ENST00000358470;ENST00000392320	D;D	0.89050	-2.46;-2.46	5.95	5.95	0.96441	SH2 motif (4);	0.047577	0.85682	D	0.000000	T	0.81597	0.4856	N	0.12182	0.205	0.80722	D	1	P;P;P	0.43938	0.801;0.684;0.822	B;B;B	0.40825	0.272;0.272;0.341	D	0.84977	0.0886	10	0.87932	D	0	-27.3247	15.9301	0.79651	0.1357:0.8643:0.0:0.0	.	522;613;613	Q53S87;B4DV04;Q14765	.;.;STAT4_HUMAN	N	613	ENSP00000351255:D613N;ENSP00000376134:D613N	ENSP00000351255:D613N	D	-	1	0	STAT4	191606476	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.945000	0.70226	2.821000	0.97095	0.650000	0.86243	GAC	.	.		0.373	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151		T	191898231	C	T	191898231	3	4	123	1	0	0	0	0	1	0	0	0	15282	855	30	3	429	3	STAT4	2	191898231	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1996870	191898231	51301142	68	20598										
CCDC150	284992	hgsc.bcm.edu	37	chr2	197521532	197521532	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgcagtccttgaagatgaacAtctttcggctgcaaactgaa	9	9	1	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:197521532A>T	ENST00000389175.4	+	3	487	c.352A>T	c.(352-354)Atc>Ttc	p.I118F	CCDC150_ENST00000472405.2_Missense_Mutation_p.I15F|CCDC150_ENST00000423093.2_Intron|CCDC150_ENST00000272831.7_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	118										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						GAAGATGAACATCTTTCGGCT	0.378																																					p.I118F		Atlas-SNP	.											.	CCDC150	96	.	0			c.A352T						.						107	104	105					2																	197521532		1866	4100	5966	SO:0001583	missense	284992	exon3			ATGAACATCTTTC		CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.352A>T	chr2.hg19:g.197521532A>T	ENSP00000373827:p.Ile118Phe	62.0	0.0		98.0	26.0	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Missense_Mutation	SNP	ENST00000389175.4	hg19	CCDS46478.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.696480	0.30142	.	.	ENSG00000144395	ENST00000389175;ENST00000536389;ENST00000472405	T;T	0.30448	1.53;1.53	4.93	4.93	0.64822	.	0.184719	0.38436	N	0.001687	T	0.48554	0.1506	M	0.65975	2.015	0.80722	D	1	P;D	0.76494	0.566;0.999	B;D	0.80764	0.15;0.994	T	0.44050	-0.9353	10	0.37606	T	0.19	-6.877	8.3768	0.32447	0.9113:0.0:0.0887:0.0	.	118;118	Q8NCX0;F5H6M2	CC150_HUMAN;.	F	118;118;15	ENSP00000373827:I118F;ENSP00000441149:I15F	ENSP00000373827:I118F	I	+	1	0	CCDC150	197229777	1.000000	0.71417	0.998000	0.56505	0.674000	0.39518	1.738000	0.38207	2.082000	0.62665	0.533000	0.62120	ATC	.	.		0.378	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539		T	197521532	A	T	197521532	3	4	123	1	0	0	0	0	1	0	0	0	2787	217	8	4	362	4	CCDC150	2	197521532	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	5623301	197521532	45677841	69	20599										
BMPR2	659	hgsc.bcm.edu	37	chr2	203332240	203332240	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttgtattcatattgatttatAggatgttggtctcacattgg	9	4	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:203332240A>G	ENST00000374580.4	+	3	786		c.e3-1		BMPR2_ENST00000479069.1_Splice_Site|BMPR2_ENST00000374574.2_Splice_Site	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)						activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						ATTGATTTATAGGATGTTGGT	0.348																																					.		Atlas-SNP	.											.	BMPR2	142	.	0			c.248-2A>G						.						97	88	91					2																	203332240		2203	4300	6503	SO:0001630	splice_region_variant	659	exon3			ATTTATAGGATGT	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.248-1A>G	chr2.hg19:g.203332240A>G		85.0	0.0		115.0	47.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Splice_Site	SNP	ENST00000374580.4	hg19	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	A	15.82	2.947200	0.53186	.	.	ENSG00000204217	ENST00000374580;ENST00000374574	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3775	0.74621	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BMPR2	203040485	1.000000	0.71417	0.968000	0.41197	0.575000	0.36095	7.715000	0.84713	2.037000	0.60232	0.533000	0.62120	.	.	.		0.348	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	Intron	G	203332240	A	G	203332240	5	3	123	1	0	0	0	0	0	0	1	0	1471	434	15	2	256	2	BMPR2	2	203332240	Splice_Site	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	5810708	203332240	39867133	70	20600										
IKZF2	22807	hgsc.bcm.edu	37	chr2	213872617	213872617	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agaataagctgagcttataaCtggggccacttcagcgattg	11	8	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:213872617C>G	ENST00000434687.1	-	9	1357	c.1048G>C	c.(1048-1050)Gtt>Ctt	p.V350L	AC079610.1_ENST00000415387.1_RNA|IKZF2_ENST00000342002.2_Missense_Mutation_p.V356L|IKZF2_ENST00000457361.1_Missense_Mutation_p.V350L|IKZF2_ENST00000413091.3_3'UTR|IKZF2_ENST00000374319.4_Missense_Mutation_p.V324L|IKZF2_ENST00000374327.4_Missense_Mutation_p.V205L|IKZF2_ENST00000421754.2_Missense_Mutation_p.V276L|IKZF2_ENST00000451136.2_Missense_Mutation_p.V278L			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)	350					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		GAGCTTATAACTGGGGCCACT	0.493																																					p.V350L		Atlas-SNP	.											.	IKZF2	71	.	0			c.G1048C						.						93	85	88					2																	213872617		2203	4300	6503	SO:0001583	missense	22807	exon8			TTATAACTGGGGC	AF130863	CCDS2395.1, CCDS46507.1	2q13.1	2013-01-08	2006-08-25	2006-08-25	ENSG00000030419	ENSG00000030419		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13177	protein-coding gene	gene with protein product		606234	"zinc finger protein, subfamily 1A, 2 (Helios)"	ZNFN1A2		9512513, 9560339	Standard	NM_001079526		Approved	Helios	uc002vem.3	Q9UKS7	OTTHUMG00000133005	ENST00000434687.1:c.1048G>C	chr2.hg19:g.213872617C>G	ENSP00000412869:p.Val350Leu	155.0	0.0		193.0	41.0	NM_016260	Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1	Missense_Mutation	SNP	ENST00000434687.1	hg19	CCDS2395.1	.	.	.	.	.	.	.	.	.	.	C	13.38	2.221082	0.39201	.	.	ENSG00000030419	ENST00000457361;ENST00000342002;ENST00000434687;ENST00000374319;ENST00000451136;ENST00000421754;ENST00000374327;ENST00000542010	T;T;T;T;T;T;T	0.15603	3.17;3.14;3.17;3.21;3.08;3.22;2.41	6.08	6.08	0.98989	.	0.078533	0.53938	D	0.000052	T	0.34542	0.0901	M	0.77820	2.39	0.80722	D	1	B;P;P;P;P;P	0.48162	0.27;0.717;0.899;0.906;0.803;0.73	B;B;B;P;B;B	0.48571	0.095;0.243;0.419;0.582;0.17;0.205	T	0.03673	-1.1014	10	0.59425	D	0.04	-7.3459	18.844	0.92196	0.0:1.0:0.0:0.0	.	278;276;205;324;350;128	C9JCG7;C9JTM9;F5H8M1;Q9UKS7-2;Q9UKS7;Q96LD7	.;.;.;.;IKZF2_HUMAN;.	L	350;356;350;324;278;276;205;54	ENSP00000410447:V350L;ENSP00000342876:V356L;ENSP00000412869:V350L;ENSP00000363439:V324L;ENSP00000395203:V278L;ENSP00000399574:V276L;ENSP00000363447:V205L	ENSP00000342876:V356L	V	-	1	0	IKZF2	213580862	0.911000	0.30947	1.000000	0.80357	0.990000	0.78478	1.802000	0.38853	2.894000	0.99253	0.655000	0.94253	GTT	.	.		0.493	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256593.3	NM_016260		G	213872617	C	G	213872617	3	3	123	1	0	0	0	0	1	0	0	0	7624	565	20	4	536	4	IKZF2	2	213872617	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	10540377	213872617	29326756	71	20601										
RUFY4	285180	hgsc.bcm.edu	37	chr2	218947924	218947924	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccatgtaccaggaggagcttGgagggcagcgggacttggtc	17	9	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:218947924G>A	ENST00000344321.7	+	11	1965	c.1447G>A	c.(1447-1449)Gga>Aga	p.G483R	RUFY4_ENST00000441828.2_3'UTR|RUFY4_ENST00000374155.3_Missense_Mutation_p.G503R	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	483							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGAGGAGCTTGGAGGGCAGCG	0.602																																					p.G483R		Atlas-SNP	.											.	RUFY4	59	.	0			c.G1447A						.						94	99	97					2																	218947924		2108	4224	6332	SO:0001583	missense	285180	exon11			GAGCTTGGAGGGC	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"Zinc fingers, FYVE domain containing"	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.1447G>A	chr2.hg19:g.218947924G>A	ENSP00000345900:p.Gly483Arg	202.0	0.0		264.0	69.0	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	hg19		.	.	.	.	.	.	.	.	.	.	G	11.12	1.543943	0.27563	.	.	ENSG00000188282	ENST00000344321;ENST00000374155	T;T	0.75367	-0.93;0.9	4.27	-0.116	0.13555	Zinc finger, FYVE/PHD-type (1);	0.995534	0.08141	N	0.991689	T	0.52240	0.1722	N	0.19112	0.55	0.09310	N	1	B	0.24618	0.107	B	0.19148	0.024	T	0.30297	-0.9983	10	0.18710	T	0.47	0.0021	3.2789	0.06908	0.3808:0.2105:0.4087:0.0	.	483	Q6ZNE9	RUFY4_HUMAN	R	483;503	ENSP00000345900:G483R;ENSP00000363270:G503R	ENSP00000345900:G483R	G	+	1	0	RUFY4	218656169	0.000000	0.05858	0.119000	0.21687	0.986000	0.74619	0.563000	0.23547	0.074000	0.16767	0.555000	0.69702	GGA	.	.		0.602	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483		A	218947924	G	A	218947924	3	1	123	1	0	0	0	0	1	0	0	0	13756	1349	47	3	1481	3	RUFY4	2	218947924	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	5075307	218947924	24251449	72	20602										
TUBA4A	7277	hgsc.bcm.edu	37	chr2	220116022	220116022	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctgtggaacaccaggaagccCtgaagtcctgtgcactggtc	12	12	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:220116022C>G	ENST00000248437.4	-	4	572	c.399G>C	c.(397-399)caG>caC	p.Q133H	TUBA4B_ENST00000490341.1_RNA|TUBA4A_ENST00000498660.1_5'UTR|TUBA4A_ENST00000392088.2_Missense_Mutation_p.Q118H	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	133					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	CCAGGAAGCCCTGAAGTCCTG	0.547																																					p.Q133H		Atlas-SNP	.											.	TUBA4A	96	.	0			c.G399C						.						45	49	47					2																	220116022		2189	4299	6488	SO:0001583	missense	7277	exon4			GAAGCCCTGAAGT	AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"Tubulins"	12407	protein-coding gene	gene with protein product		191110	"tubulin, alpha 1 (testis specific)", "tubulin, alpha 1"	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.399G>C	chr2.hg19:g.220116022C>G	ENSP00000248437:p.Gln133His	84.0	0.0		111.0	10.0	NM_006000	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	hg19	CCDS2438.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.672479	0.29693	.	.	ENSG00000127824	ENST00000248437;ENST00000392088;ENST00000427737;ENST00000456818;ENST00000447205	T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68	5.06	3.11	0.35812	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.87374	0.6161	H	0.96430	3.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89404	0.3698	10	0.87932	D	0	.	10.3719	0.44060	0.0:0.772:0.0:0.228	.	133	P68366	TBA4A_HUMAN	H	133;118;118;156;118	ENSP00000248437:Q133H;ENSP00000375938:Q118H;ENSP00000408194:Q118H;ENSP00000416992:Q156H;ENSP00000396061:Q118H	ENSP00000248437:Q133H	Q	-	3	2	TUBA4A	219824266	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.744000	0.26245	1.375000	0.46248	0.655000	0.94253	CAG	.	.		0.547	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000		G	220116022	C	G	220116022	3	3	123	1	0	0	0	0	1	0	0	0	16764	680	24	4	951	4	TUBA4A	2	220116022	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1168098	220116022	23083351	73	20603										
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233710580	233710580	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atgcttcatgcccttaatacGgcaaataacttggatggtaa	8	8	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:233710580G>A	ENST00000409547.1	+	28	3755	c.3444G>A	c.(3442-3444)acG>acA	p.T1148T	GIGYF2_ENST00000409196.3_Silent_p.T1142T|GIGYF2_ENST00000373563.4_Silent_p.T1148T|GIGYF2_ENST00000373566.3_Silent_p.T1170T|GIGYF2_ENST00000409480.1_Silent_p.T1170T|GIGYF2_ENST00000409451.3_Silent_p.T1169T	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1148					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		CCCTTAATACGGCAAATaact	0.463																																					p.T1169T		Atlas-SNP	.											.	GIGYF2	288	.	0			c.G3507A						.						83	79	80					2																	233710580		2203	4300	6503	SO:0001819	synonymous_variant	26058	exon28			TAATACGGCAAAT	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3444G>A	chr2.hg19:g.233710580G>A		94.0	0.0		171.0	26.0	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Silent	SNP	ENST00000409547.1	hg19	CCDS33401.1																																																																																			.	.		0.463	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		A	233710580	G	A	233710580	2	1	123	1	0	0	0	0	0	0	0	1	6386	1103	39	1		1	GIGYF2	2	233710580	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	13594558	233710580	9488793	74	20604										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238274558	238274558	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggccaccgctgcagctgaccCtgtgcatctggctgattctg	12	14	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:238274558C>G	ENST00000295550.4	-	12	6073	c.5621G>C	c.(5620-5622)aGg>aCg	p.R1874T	COL6A3_ENST00000346358.4_Missense_Mutation_p.R1674T|COL6A3_ENST00000409809.1_Missense_Mutation_p.R1668T|COL6A3_ENST00000353578.4_Missense_Mutation_p.R1668T|COL6A3_ENST00000472056.1_Missense_Mutation_p.R1267T|COL6A3_ENST00000347401.3_Missense_Mutation_p.R1673T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1874	Nonhelical region.|VWFA 10. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GCAGCTGACCCTGTGCATCTG	0.597																																					p.R1874T		Atlas-SNP	.											.	COL6A3	608	.	0			c.G5621C						.						74	75	75					2																	238274558		2203	4300	6503	SO:0001583	missense	1293	exon12			CTGACCCTGTGCA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.5621G>C	chr2.hg19:g.238274558C>G	ENSP00000295550:p.Arg1874Thr	46.0	0.0		61.0	17.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	3.575	-0.086856	0.07097	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25	5.34	2.48	0.30137	von Willebrand factor, type A (2);	0.384789	0.22024	N	0.065682	T	0.26085	0.0636	L	0.40543	1.245	0.09310	N	1	P;P;B	0.49090	0.863;0.919;0.094	B;P;B	0.46026	0.428;0.501;0.016	T	0.07102	-1.0790	10	0.16896	T	0.51	.	3.3595	0.07181	0.0:0.4537:0.2013:0.345	.	1267;1668;1874	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	T	1874;1673;1668;1267;1668;1674	ENSP00000295550:R1874T;ENSP00000315609:R1673T;ENSP00000315873:R1668T;ENSP00000418285:R1267T;ENSP00000386844:R1668T;ENSP00000295546:R1674T	ENSP00000295550:R1874T	R	-	2	0	COL6A3	237939297	0.000000	0.05858	0.002000	0.10522	0.037000	0.13140	0.820000	0.27323	0.720000	0.32209	0.655000	0.94253	AGG	.	.		0.597	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238274558	C	G	238274558	3	3	123	1	0	0	0	0	1	0	0	0	3703	681	24	4	4044	4	COL6A3	2	238274558	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	4563978	238274558	4924815	75	20605										
SCLY	51540	hgsc.bcm.edu	37	chr2	238990418	238990418	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acgacatcctcgcggcagtcCgcccgaccacacgcctcgtg	10	19	0	0	rs140009501		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:238990418C>A	ENST00000555827.1	+	5	617	c.553C>A	c.(553-555)Cgc>Agc	p.R185S	SCLY_ENST00000429612.2_Intron|SCLY_ENST00000422984.2_Missense_Mutation_p.R91S|SCLY_ENST00000254663.6_Missense_Mutation_p.R193S|SCLY_ENST00000373332.3_Missense_Mutation_p.R103S|SCLY_ENST00000409736.2_Missense_Mutation_p.R185S			Q96I15	SCLY_HUMAN	selenocysteine lyase	185					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		CGCGGCAGTCCGCCCGACCAC	0.577																																					p.R193S	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	Atlas-SNP	.											.	SCLY	51	.	0			c.C577A						.						109	91	97					2																	238990418		2203	4300	6503	SO:0001583	missense	51540	exon5			GCAGTCCGCCCGA	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"putative selenocysteine lyase"	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.553C>A	chr2.hg19:g.238990418C>A	ENSP00000450613:p.Arg185Ser	101.0	0.0		139.0	30.0	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.7|20.7	4.036739|4.036739	0.75617|0.75617	.|.	.|.	ENSG00000132330|ENSG00000132330	ENST00000437134|ENST00000254663;ENST00000555827;ENST00000373332;ENST00000413463;ENST00000409736;ENST00000422984;ENST00000450965	.|T;T;T;D;T;T;T	.|0.86097	.|2.01;2.01;1.59;-2.07;1.59;2.01;1.59	5.84|5.84	5.84|5.84	0.93424|0.93424	.|Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91492|0.91492	0.7314|0.7314	M|M	0.77486|0.77486	2.375|2.375	0.80722|0.80722	D|D	1|1	.|D;D;P	.|0.60575	.|0.974;0.988;0.92	.|P;P;P	.|0.59012	.|0.731;0.85;0.527	D|D	0.91579|0.91579	0.5277|0.5277	5|10	.|0.59425	.|D	.|0.04	-17.0765|-17.0765	18.9105|18.9105	0.92483|0.92483	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|91;185;185	.|E7ESG3;Q96I15;Q96I15-2	.|.;SCLY_HUMAN;.	Q|S	28|193;185;103;99;185;91;15	.|ENSP00000254663:R193S;ENSP00000450613:R185S;ENSP00000362429:R103S;ENSP00000414165:R99S;ENSP00000387162:R185S;ENSP00000416865:R91S;ENSP00000414053:R15S	.|ENSP00000254663:R185S	P|R	+|+	2|1	0|0	SCLY|SCLY	238655157|238655157	1.000000|1.000000	0.71417|0.71417	0.957000|0.957000	0.39632|0.39632	0.064000|0.064000	0.16182|0.16182	3.095000|3.095000	0.50235|0.50235	2.764000|2.764000	0.94973|0.94973	0.655000|0.655000	0.94253|0.94253	CCG|CGC	.	C|1.000;T|0.000		0.577	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510		A	238990418	C	A	238990418	3	1	123	1	0	0	0	0	1	0	0	0	13922	652	23	1	571	1	SCLY	2	238990418	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	715860	238990418	4208955	76	20606										
GRM7	2917	hgsc.bcm.edu	37	chr3	7620822	7620822	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acaatgaaccctgagcaagcCagaggggttctcaagtgtga	12	9	1	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:7620822C>T	ENST00000357716.4	+	8	2503	c.2229C>T	c.(2227-2229)gcC>gcT	p.A743A	GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000486284.1_Silent_p.A743A|GRM7_ENST00000389336.4_Silent_p.A743A|GRM7_ENST00000403881.1_Silent_p.A743A|GRM7_ENST00000402647.2_Silent_p.A743A	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	743					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						CTGAGCAAGCCAGAGGGGTTC	0.428																																					p.A743A		Atlas-SNP	.											.	GRM7	223	.	0			c.C2229T						.						126	112	117					3																	7620822		2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			GCAAGCCAGAGGG	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.2229C>T	chr3.hg19:g.7620822C>T		225.0	0.0		192.0	44.0	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	hg19	CCDS43042.1																																																																																			.	.		0.428	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		T	7620822	C	T	7620822	2	4	123	1	0	0	0	0	0	0	0	1	6811	581	21	3		3	GRM7	3	7620822	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		7620822	190401608	77	20607										
BRPF1	7862	hgsc.bcm.edu	37	chr3	9776289	9776289	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggcaaacataagaacaaggaGaagcgcaaggactccaacca	10	10	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:9776289G>A	ENST00000457855.1	+	1	476	c.465G>A	c.(463-465)gaG>gaA	p.E155E	BRPF1_ENST00000424362.1_Silent_p.E155E|BRPF1_ENST00000383829.2_Silent_p.E155E|BRPF1_ENST00000302054.3_Silent_p.E155E|BRPF1_ENST00000433861.2_Silent_p.E155E			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	155	Interaction with KAT6A and KAT6B.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					AGAACAAGGAGAAGCGCAAGG	0.562																																					p.E155E		Atlas-SNP	.											.	BRPF1	104	.	0			c.G465A						.						80	79	79					3																	9776289		2203	4300	6503	SO:0001819	synonymous_variant	7862	exon2			CAAGGAGAAGCGC	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"peregrin", "bromodomain-containing protein, 140kD"	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.465G>A	chr3.hg19:g.9776289G>A		245.0	0.0		215.0	37.0	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Silent	SNP	ENST00000457855.1	hg19	CCDS2575.1																																																																																			.	.		0.562	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		A	9776289	G	A	9776289	2	1	123	1	0	0	0	0	0	0	0	1	1522	933	33	3		3	BRPF1	3	9776289	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	2155467	9776289	188246141	78	20608										
LRRC3B	116135	hgsc.bcm.edu	37	chr3	26751290	26751290	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agggctgtctttgttcttccTctgggggtttaaatgtcacc	11	9	4	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:26751290T>G	ENST00000396641.2	+	2	719	c.127T>G	c.(127-129)Tct>Gct	p.S43A	LRRC3B_ENST00000417744.1_Missense_Mutation_p.S43A|LRRC3B_ENST00000456208.2_Missense_Mutation_p.S43A|AC114877.3_ENST00000446601.1_lincRNA	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	43	LRRNT.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						TTGTTCTTCCTCTGGGGGTTT	0.438																																					p.S43A		Atlas-SNP	.											.	LRRC3B	51	.	0			c.T127G						.						148	141	143					3																	26751290		2203	4300	6503	SO:0001583	missense	116135	exon2			TCTTCCTCTGGGG	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.127T>G	chr3.hg19:g.26751290T>G	ENSP00000379880:p.Ser43Ala	177.0	0.0		150.0	36.0	NM_052953	Q5M8T0	Missense_Mutation	SNP	ENST00000396641.2	hg19	CCDS2644.1	.	.	.	.	.	.	.	.	.	.	T	11.53	1.667181	0.29604	.	.	ENSG00000179796	ENST00000396641;ENST00000414619;ENST00000432040;ENST00000417744;ENST00000456208	T;T;T;T	0.62105	0.2;0.05;0.2;0.2	6.17	6.17	0.99709	Leucine-rich repeat-containing N-terminal (2);	0.159349	0.64402	D	0.000019	T	0.45418	0.1341	N	0.16307	0.4	0.42957	D	0.994393	B	0.10296	0.003	B	0.15052	0.012	T	0.39440	-0.9614	10	0.32370	T	0.25	-14.2951	11.1318	0.48351	0.1375:0.0:0.0:0.8625	.	43	Q96PB8	LRC3B_HUMAN	A	43	ENSP00000379880:S43A;ENSP00000398184:S43A;ENSP00000406370:S43A;ENSP00000394940:S43A	ENSP00000379880:S43A	S	+	1	0	LRRC3B	26726294	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.787000	0.38704	2.371000	0.80710	0.533000	0.62120	TCT	.	.		0.438	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953		G	26751290	T	G	26751290	3	3	123	1	0	0	0	0	1	0	0	0	9005	1551	54	5	129	5	LRRC3B	3	26751290	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	16975001	26751290	171271140	79	20609										
DUSP7	1849	hgsc.bcm.edu	37	chr3	52084943	52084943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggctgcttagccccagcgtcCgctcaaagtccagcagctgc	11	16	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:52084943C>T	ENST00000495880.1	-	3	1331	c.1148G>A	c.(1147-1149)cGg>cAg	p.R383Q	DUSP7_ENST00000296483.6_Missense_Mutation_p.R332Q			Q16829	DUS7_HUMAN	dual specificity phosphatase 7	383					inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of MAP kinase activity (GO:0043407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)	p.R332Q(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CCCCAGCGTCCGCTCAAAGTC	0.552																																					p.R383Q		Atlas-SNP	.											DUSP7,NS,carcinoma,0,1	DUSP7	34	.	1	Substitution - Missense(1)	kidney(1)	c.G1148A						.						157	130	139					3																	52084943		2203	4300	6503	SO:0001583	missense	1849	exon3			AGCGTCCGCTCAA	X93921	CCDS33766.1, CCDS33766.2	3p21	2011-06-09			ENSG00000164086	ENSG00000164086		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3073	protein-coding gene	gene with protein product		602749				8626780, 9205128	Standard	NM_001947		Approved	MKP-X, PYST2	uc003dct.3	Q16829	OTTHUMG00000157819	ENST00000495880.1:c.1148G>A	chr3.hg19:g.52084943C>T	ENSP00000417183:p.Arg383Gln	304.0	0.0		234.0	47.0	NM_001947	Q2M3J7|Q8NFJ0	Missense_Mutation	SNP	ENST00000495880.1	hg19	CCDS33766.2	.	.	.	.	.	.	.	.	.	.	c	19.45	3.829829	0.71258	.	.	ENSG00000164086	ENST00000495880;ENST00000296483	D;D	0.85773	-2.03;-2.03	5.75	4.89	0.63831	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.121832	0.56097	D	0.000031	T	0.73418	0.3584	N	0.25485	0.75	0.80722	D	1	P	0.46656	0.882	B	0.33254	0.16	T	0.74542	-0.3631	10	0.37606	T	0.19	.	14.4234	0.67200	0.0:0.9285:0.0:0.0715	.	383	Q16829	DUS7_HUMAN	Q	383;332	ENSP00000417183:R383Q;ENSP00000296483:R332Q	ENSP00000296483:R332Q	R	-	2	0	DUSP7	52059983	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.083000	0.71326	1.448000	0.47680	-0.148000	0.13756	CGG	.	.		0.552	DUSP7-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349697.1	NM_001947		T	52084943	C	T	52084943	3	4	123	1	0	0	0	0	1	0	0	0	4832	652	23	1	115	1	DUSP7	3	52084943	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	25333653	52084943	145937487	80	20610										
BAP1	8314	hgsc.bcm.edu	37	chr3	52441334	52441334	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gaggtggcgtggctcgggccTggggaaaaacagagtcaggg	20	7	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:52441334T>A	ENST00000460680.1	-	7	909		c.e7-2		BAP1_ENST00000296288.5_Splice_Site	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)						anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GGCTCGGGCCTGGGGAAAAAC	0.582			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															.	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.,1	BAP1	371	.	1	Unknown(1)	pleura(1)	c.438-2A>T						.						74	78	77					3																	52441334		2203	4300	6503	SO:0001630	splice_region_variant	8314	exon8			CGGGCCTGGGGAA	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.438-2A>T	chr3.hg19:g.52441334T>A		106.0	0.0		98.0	60.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Splice_Site	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	T	18.68	3.675559	0.67928	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000470173	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.023	0.80512	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	BAP1	52416374	1.000000	0.71417	0.984000	0.44739	0.752000	0.42762	8.005000	0.88553	2.193000	0.70182	0.533000	0.62120	.	.	.		0.582	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		Intron	A	52441334	T	A	52441334	5	1	123	1	0	0	0	0	0	0	1	0	1311	1594	55	4	1797	4	BAP1	3	52441334	Splice_Site	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	356391	52441334	145581096	81	20611										
CADPS	8618	hgsc.bcm.edu	37	chr3	62522190	62522191	+	Missense_Mutation	DNP	TG	TG	AT													0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccatctcaaagagggaagcgTggtcaaagttacaggggttg							TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:62522190_62522191TG>AT	ENST00000383710.4	-	12	2381_2382	c.2032_2033CA>AT	c.(2032-2034)CAc>ATc	p.H678I	CADPS_ENST00000357948.3_Missense_Mutation_p.H678I|CADPS_ENST00000283269.9_Missense_Mutation_p.H678I	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	678					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		GAGGGAAGCGTGGTCAAAGTTA	0.396																																					p.H678L|p.H678N		Atlas-SNP	.											.	CADPS	387	.	0			c.A2033T|c.C2032A						.																																			SO:0001583	missense	8618	exon12			GAAGCGTGGTCAA|AAGCGTGGTCAAA	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.2032_2033delinsAT	chr3.hg19:g.62522190_62522191delinsAT	ENSP00000373215:p.His678Ile	211.0|210.0	0.0		135.0	62.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1																																																																																			.	.		0.396	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		AT	62522191	TG	AT	62522190	3	1	123	1	0	0	0	0	1	0	0	0	2572	1696	59	4	2177	4	CADPS	3	62522190	Missense_Mutation	DNP	TG	TCGA-DD-A3A9-01A-11D-A25V-10	10080856	62522190	135500240	82	20612										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64640083	64640083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tactcaatccactatcttcaCtaatagaacagcttctatag	3	11	4	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:64640083C>T	ENST00000498707.1	-	8	1604	c.1262G>A	c.(1261-1263)aGt>aAt	p.S421N	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.S393N|ADAMTS9_ENST00000459780.1_Missense_Mutation_p.S421N	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	421	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		ACTATCTTCACTAATAGAACA	0.398																																					p.S421N		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G1262A						.						155	166	162					3																	64640083		2203	4300	6503	SO:0001583	missense	56999	exon8			TCTTCACTAATAG	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.1262G>A	chr3.hg19:g.64640083C>T	ENSP00000418735:p.Ser421Asn	192.0	0.0		176.0	31.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.911770	0.33721	.	.	ENSG00000163638	ENST00000295903;ENST00000498707;ENST00000459780	D;D;D	0.86164	-2.08;-2.08;-2.08	5.66	4.78	0.61160	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.105461	0.64402	D	0.000009	T	0.76227	0.3958	N	0.02960	-0.455	0.44736	D	0.997738	P;B;B;P	0.39737	0.685;0.124;0.423;0.549	P;B;B;B	0.45406	0.479;0.105;0.126;0.329	T	0.74740	-0.3563	10	0.10636	T	0.68	.	16.7235	0.85416	0.0:0.8706:0.1294:0.0	.	393;421;421;421	B7ZVX9;Q9P2N4-2;Q9P2N4-1;Q9P2N4	.;.;.;ATS9_HUMAN	N	393;421;421	ENSP00000295903:S393N;ENSP00000418735:S421N;ENSP00000419217:S421N	ENSP00000295903:S393N	S	-	2	0	ADAMTS9	64615123	1.000000	0.71417	0.962000	0.40283	0.755000	0.42902	4.906000	0.63293	1.384000	0.46424	-0.165000	0.13383	AGT	.	.		0.398	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			T	64640083	C	T	64640083	3	4	123	1	0	0	0	0	1	0	0	0	273	565	20	3	4673	3	ADAMTS9	3	64640083	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	2117893	64640083	133382347	83	20613										
HTR1F	3355	hgsc.bcm.edu	37	chr3	88040703	88040703	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	catagcacagtgagaagtctCaggtctgaattcaagcatga	10	8	3	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:88040703C>T	ENST00000319595.4	+	1	858	c.804C>T	c.(802-804)ctC>ctT	p.L268L		NM_000866.3	NP_000857.1	P30939	5HT1F_HUMAN	5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled	268					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(8;0.147)	Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00664)	Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Ketamine(DB01221)|Methysergide(DB00247)|Mianserin(DB06148)|Naratriptan(DB00952)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Zolmitriptan(DB00315)	TGAGAAGTCTCAGGTCTGAAT	0.403																																					p.L268L		Atlas-SNP	.											.	HTR1F	66	.	0			c.C804T						.						61	66	64					3																	88040703		2203	4300	6503	SO:0001819	synonymous_variant	3355	exon2			AAGTCTCAGGTCT	L05597	CCDS2920.1	3p12	2012-08-08	2012-02-03		ENSG00000179097	ENSG00000179097		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5292	protein-coding gene	gene with protein product		182134	"5-hydroxytryptamine (serotonin) receptor 1F"			8384716, 8380639	Standard	NM_000866		Approved	HTR1EL, 5-HT1F	uc003dqr.2	P30939	OTTHUMG00000159008	ENST00000319595.4:c.804C>T	chr3.hg19:g.88040703C>T		59.0	0.0		50.0	8.0	NM_000866		Silent	SNP	ENST00000319595.4	hg19	CCDS2920.1																																																																																			.	.		0.403	HTR1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352890.1	NM_000866		T	88040703	C	T	88040703	2	4	123	1	0	0	0	0	0	0	0	1	7449	813	29	3		3	HTR1F	3	88040703	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	23400620	88040703	109981727	84	20614										
STX19	415117	hgsc.bcm.edu	37	chr3	93733261	93733261	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acagcatggacagcaccaacAacacagtactctgcaaggat	8	12	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:93733261A>C	ENST00000315099.2	-	2	1109	c.853T>G	c.(853-855)Tgt>Ggt	p.C285G	ARL13B_ENST00000303097.7_Intron|ARL13B_ENST00000486562.1_Intron|ARL13B_ENST00000539730.1_Intron|ARL13B_ENST00000394222.3_Intron|ARL13B_ENST00000471138.1_Intron|ARL13B_ENST00000535334.1_Intron	NM_001001850.2	NP_001001850.1	Q8N4C7	STX19_HUMAN	syntaxin 19	285	Cys-rich.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(4)|prostate(1)	9						CAGCACCAACAACACAGTACT	0.318																																					p.C285G		Atlas-SNP	.											.	STX19	19	.	0			c.T853G						.						49	47	48					3																	93733261		2203	4299	6502	SO:0001583	missense	415117	exon2			ACCAACAACACAG	AF461456	CCDS33793.1	3q11	2005-12-30			ENSG00000178750	ENSG00000178750			19300	protein-coding gene	gene with protein product							Standard	NM_001001850		Approved	MGC21382	uc003drh.1	Q8N4C7	OTTHUMG00000159013	ENST00000315099.2:c.853T>G	chr3.hg19:g.93733261A>C	ENSP00000320679:p.Cys285Gly	46.0	0.0		62.0	4.0	NM_001001850		Missense_Mutation	SNP	ENST00000315099.2	hg19	CCDS33793.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.841483	0.51057	.	.	ENSG00000178750	ENST00000315099	T	0.52057	0.68	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.70509	0.3232	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.75258	-0.3381	10	0.72032	D	0.01	-11.8478	15.7642	0.78114	1.0:0.0:0.0:0.0	.	285	Q8N4C7	STX19_HUMAN	G	285	ENSP00000320679:C285G	ENSP00000320679:C285G	C	-	1	0	STX19	95215951	1.000000	0.71417	0.997000	0.53966	0.924000	0.55760	8.678000	0.91211	2.260000	0.74910	0.528000	0.53228	TGT	.	.		0.318	STX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352909.1	NM_001001850		C	93733261	A	C	93733261	3	2	123	1	0	0	0	0	1	0	0	0	15357	130	5	5	35	5	STX19	3	93733261	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	5692558	93733261	104289169	85	20615										
MYH15	22989	hgsc.bcm.edu	37	chr3	108178291	108178291	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttagtcatcaatttattcagGttttcctaaaatggagacca	6	7	3	1	rs372985354		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:108178291G>T	ENST00000273353.3	-	19	2054	c.1998C>A	c.(1996-1998)aaC>aaA	p.N666K	MYH15_ENST00000495753.2_5'UTR	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	666	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						ATTTATTCAGGTTTTCCTAAA	0.328																																					p.N666K		Atlas-SNP	.											.	MYH15	223	.	0			c.C1998A						.						91	84	86					3																	108178291		1830	4079	5909	SO:0001583	missense	22989	exon19			ATTCAGGTTTTCC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1998C>A	chr3.hg19:g.108178291G>T	ENSP00000273353:p.Asn666Lys	61.0	0.0		71.0	6.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.746075	0.69418	.	.	ENSG00000144821	ENST00000273353	T	0.71817	-0.6	5.67	0.301	0.15781	Myosin head, motor domain (2);	.	.	.	.	T	0.79902	0.4526	H	0.95294	3.65	0.33015	D	0.528001	P	0.45957	0.869	P	0.49561	0.615	T	0.80612	-0.1305	9	0.87932	D	0	.	4.0982	0.10002	0.532:0.0:0.2831:0.1848	.	666	Q9Y2K3	MYH15_HUMAN	K	666	ENSP00000273353:N666K	ENSP00000273353:N666K	N	-	3	2	MYH15	109660981	0.997000	0.39634	0.990000	0.47175	0.974000	0.67602	0.654000	0.24918	0.344000	0.23847	0.655000	0.94253	AAC	.	.		0.328	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		T	108178291	G	T	108178291	3	4	123	1	0	0	0	0	1	0	0	0	10043	1252	44	3	3938	3	MYH15	3	108178291	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	14445030	108178291	89844139	86	20616										
MORC1	27136	hgsc.bcm.edu	37	chr3	108833252	108833252	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttgcattgtccagcaattcaGccagtgctccaaaaaggaaa	8	10	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:108833252G>A	ENST00000483760.1	-	2	141	c.98C>T	c.(97-99)gCt>gTt	p.A33V	MORC1_ENST00000232603.5_Missense_Mutation_p.A33V					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						CAGCAATTCAGCCAGTGCTCC	0.348																																					p.A33V		Atlas-SNP	.											.	MORC1	211	.	0			c.C98T						.						101	98	99					3																	108833252		2203	4300	6503	SO:0001583	missense	27136	exon2			AATTCAGCCAGTG	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.98C>T	chr3.hg19:g.108833252G>A	ENSP00000417282:p.Ala33Val	109.0	0.0		93.0	12.0	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	hg19		.	.	.	.	.	.	.	.	.	.	G	22.3	4.265123	0.80358	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	D;D	0.95307	-3.67;-3.67	4.51	4.51	0.55191	ATPase-like, ATP-binding domain (3);	0.000000	0.46145	D	0.000312	D	0.96623	0.8898	M	0.75264	2.295	0.42169	D	0.991635	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96872	0.9640	10	0.87932	D	0	-14.6246	12.8941	0.58089	0.0:0.0:1.0:0.0	.	33;33	E7ERX1;Q86VD1	.;MORC1_HUMAN	V	33	ENSP00000232603:A33V;ENSP00000417282:A33V	ENSP00000232603:A33V	A	-	2	0	MORC1	110315942	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.459000	0.60102	2.478000	0.83669	0.563000	0.77884	GCT	.	.		0.348	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			A	108833252	G	A	108833252	3	1	123	1	0	0	0	0	1	0	0	0	9710	971	34	3	2964	3	MORC1	3	108833252	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	654961	108833252	89189178	87	20617										
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113720448	113720448	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tagacaatactaaccattttCttcagtctcttctcttctcg	3	12	5	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:113720448C>A	ENST00000295878.3	-	13	2303	c.2157G>T	c.(2155-2157)aaG>aaT	p.K719N	KIAA1407_ENST00000545063.1_3'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	719										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						TAACCATTTTCTTCAGTCTCT	0.448																																					p.K719N		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G2157T						.						267	246	253					3																	113720448		2203	4300	6503	SO:0001583	missense	57577	exon13			CATTTTCTTCAGT	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2157G>T	chr3.hg19:g.113720448C>A	ENSP00000295878:p.Lys719Asn	323.0	0.0		330.0	45.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.179453	0.38511	.	.	ENSG00000163617	ENST00000295878	T	0.32988	1.43	5.19	4.32	0.51571	.	0.424673	0.27841	N	0.017626	T	0.37625	0.1010	M	0.63428	1.95	0.80722	D	1	D	0.53462	0.96	P	0.50537	0.643	T	0.19224	-1.0312	10	0.51188	T	0.08	.	8.1568	0.31173	0.0:0.8225:0.0:0.1775	.	719	Q8NCU4	K1407_HUMAN	N	719	ENSP00000295878:K719N	ENSP00000295878:K719N	K	-	3	2	KIAA1407	115203138	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	1.561000	0.36342	1.557000	0.49525	0.650000	0.86243	AAG	.	.		0.448	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		A	113720448	C	A	113720448	3	1	123	1	0	0	0	0	1	0	0	0	8238	912	32	3	673	3	KIAA1407	3	113720448	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	4887196	113720448	84301982	88	20618										
C3orf30	152405	hgsc.bcm.edu	37	chr3	118867060	118867060	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aaattgaccaaggaaagggtTatcatatacgcaatcaaact	7	7	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:118867060T>C	ENST00000295622.1	+	2	1472	c.1432T>C	c.(1432-1434)Tat>Cat	p.Y478H	RP11-484M3.5_ENST00000490594.1_Intron|IGSF11_ENST00000441144.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|IGSF11_ENST00000354673.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	478										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		AGGAAAGGGTTATCATATACG	0.368																																					p.Y478H		Atlas-SNP	.											.	C3orf30	64	.	0			c.T1432C						.						84	90	88					3																	118867060		2203	4300	6503	SO:0001583	missense	152405	exon2			AAGGGTTATCATA	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.1432T>C	chr3.hg19:g.118867060T>C	ENSP00000295622:p.Tyr478His	98.0	0.0		134.0	18.0	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	hg19	CCDS2984.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.769112	0.31320	.	.	ENSG00000163424	ENST00000295622;ENST00000470341	T	0.12672	2.66	3.71	1.33	0.21861	.	1.417150	0.04833	N	0.439075	T	0.18635	0.0447	L	0.36672	1.1	0.09310	N	1	P;D	0.59767	0.845;0.986	B;P	0.53861	0.41;0.736	T	0.17868	-1.0355	10	0.34782	T	0.22	0.0439	5.2338	0.15436	0.0:0.2404:0.0:0.7596	.	478;478	E9PFE5;Q96M34	.;CC030_HUMAN	H	478	ENSP00000295622:Y478H	ENSP00000295622:Y478H	Y	+	1	0	C3orf30	120349750	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.027000	0.13621	0.281000	0.22233	0.533000	0.62120	TAT	.	.		0.368	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539		C	118867060	T	C	118867060	3	2	123	1	0	0	0	0	1	0	0	0	2222	1754	61	2	1438	2	C3orf30	3	118867060	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	5146612	118867060	79155370	89	20619										
DNAJB8	165721	hgsc.bcm.edu	37	chr3	128181553	128181553	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tggacgacatcaccgacttgAaccccgagctgccagaactg	10	14	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:128181553A>C	ENST00000469083.1	-	2	3093	c.536T>G	c.(535-537)tTc>tGc	p.F179C	DNAJB8_ENST00000319153.3_Missense_Mutation_p.F179C|DNAJB8-AS1_ENST00000471626.1_RNA			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	179	Ser-rich.				chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		CACCGACTTGAACCCCGAGCT	0.617																																					p.F179C		Atlas-SNP	.											.	DNAJB8	34	.	0			c.T536G						.						84	81	82					3																	128181553		2203	4300	6503	SO:0001583	missense	165721	exon3			GACTTGAACCCCG		CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"Heat shock proteins / DNAJ (HSP40)"	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.536T>G	chr3.hg19:g.128181553A>C	ENSP00000417418:p.Phe179Cys	136.0	0.0		171.0	22.0	NM_153330	B3KWV7	Missense_Mutation	SNP	ENST00000469083.1	hg19	CCDS3048.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.217198	0.39201	.	.	ENSG00000179407	ENST00000469083;ENST00000319153	T;T	0.52754	0.65;0.65	4.75	3.44	0.39384	.	0.840609	0.10715	N	0.642473	T	0.60117	0.2244	M	0.85945	2.785	0.53688	D	0.999976	D	0.59767	0.986	P	0.49708	0.62	T	0.64210	-0.6461	10	0.49607	T	0.09	.	10.4522	0.44528	0.8439:0.0:0.0:0.1561	.	179	Q8NHS0	DNJB8_HUMAN	C	179	ENSP00000417418:F179C;ENSP00000316053:F179C	ENSP00000316053:F179C	F	-	2	0	DNAJB8	129664243	0.996000	0.38824	0.992000	0.48379	0.165000	0.22458	2.423000	0.44705	1.772000	0.52199	0.459000	0.35465	TTC	.	.		0.617	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330		C	128181553	A	C	128181553	3	2	123	1	0	0	0	0	1	0	0	0	4628	246	9	5	166	5	DNAJB8	3	128181553	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	9314493	128181553	69840877	90	20620										
CEP70	80321	hgsc.bcm.edu	37	chr3	138256157	138256157	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcaatagtttcttcttgctcCgttcgttttttcttataatg	6	8	3	0	rs372060625		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:138256157C>A	ENST00000264982.3	-	7	764	c.498G>T	c.(496-498)acG>acT	p.T166T	CEP70_ENST00000481834.1_Silent_p.T166T|CEP70_ENST00000542237.1_Silent_p.T146T|CEP70_ENST00000464035.1_Silent_p.T166T|CEP70_ENST00000489254.1_Silent_p.T14T|CEP70_ENST00000478673.1_5'UTR|CEP70_ENST00000484888.1_Silent_p.T166T	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	166					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)		p.T166T(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						CTTCTTGCTCCGTTCGTTTTT	0.343																																					p.T166T		Atlas-SNP	.											CEP70,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CEP70	51	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G498T						.						117	105	109					3																	138256157		2202	4300	6502	SO:0001819	synonymous_variant	80321	exon7			TTGCTCCGTTCGT	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.498G>T	chr3.hg19:g.138256157C>A		97.0	0.0		92.0	8.0	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Silent	SNP	ENST00000264982.3	hg19	CCDS3102.1																																																																																			.	.		0.343	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491		A	138256157	C	A	138256157	2	1	123	1	0	0	0	0	0	0	0	1	3261	639	23	1		1	CEP70	3	138256157	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	10074604	138256157	59766273	91	20621										
GRK7	131890	hgsc.bcm.edu	37	chr3	141497352	141497352	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcttccgtgacttcctagccAcagtgcccacgttccgcaag	8	16	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:141497352A>T	ENST00000264952.2	+	1	363	c.226A>T	c.(226-228)Aca>Tca	p.T76S		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	76	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						CTTCCTAGCCACAGTGCCCAC	0.657																																					p.T76S		Atlas-SNP	.											.	GRK7	65	.	0			c.A226T						.						26	25	25					3																	141497352		2201	4292	6493	SO:0001583	missense	131890	exon1			CTAGCCACAGTGC		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.226A>T	chr3.hg19:g.141497352A>T	ENSP00000264952:p.Thr76Ser	97.0	0.0		82.0	11.0	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	hg19	CCDS3120.1	.	.	.	.	.	.	.	.	.	.	A	5.777	0.327664	0.10956	.	.	ENSG00000114124	ENST00000264952	T	0.02258	4.37	4.5	2.02	0.26589	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.277794	0.36665	N	0.002479	T	0.02230	0.0069	L	0.47716	1.5	0.31971	N	0.607198	B	0.18461	0.028	B	0.15052	0.012	T	0.31308	-0.9948	10	0.24483	T	0.36	-6.5237	6.0404	0.19730	0.7748:0.0:0.0804:0.1448	.	76	Q8WTQ7	GRK7_HUMAN	S	76	ENSP00000264952:T76S	ENSP00000264952:T76S	T	+	1	0	GRK7	142980042	0.989000	0.36119	0.551000	0.28230	0.123000	0.20343	1.878000	0.39608	0.113000	0.18004	0.533000	0.62120	ACA	.	.		0.657	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209		T	141497352	A	T	141497352	3	4	123	1	0	0	0	0	1	0	0	0	6803	159	6	4	228	4	GRK7	3	141497352	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	3241195	141497352	56525078	92	20622										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151161336	151161336	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggaccaatgttccgtcaaccGtcaccacagcctgcctactt	7	16	2	0	rs367812916	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:151161336G>T	ENST00000282466.3	-	5	5398	c.5399C>A	c.(5398-5400)aCg>aAg	p.T1800K	IGSF10_ENST00000495443.1_5'Flank	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1800	Ig-like C2-type 4.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TCCGTCAACCGTCACCACAGC	0.507																																					p.T1800K		Atlas-SNP	.											.	IGSF10	279	.	0			c.C5399A						.						101	89	93					3																	151161336		2203	4300	6503	SO:0001583	missense	285313	exon5			TCAACCGTCACCA	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5399C>A	chr3.hg19:g.151161336G>T	ENSP00000282466:p.Thr1800Lys	357.0	0.0		348.0	58.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.481930	0.00163	.	.	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.66815	-0.23	5.26	3.29	0.37713	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.135403	0.32769	N	0.005673	T	0.44561	0.1299	N	0.24115	0.695	0.26731	N	0.970595	B	0.12013	0.005	B	0.19946	0.027	T	0.18808	-1.0325	9	.	.	.	.	2.5263	0.04692	0.1013:0.1253:0.3843:0.3892	.	1800	Q6WRI0	IGS10_HUMAN	K	1800;427	ENSP00000282466:T1800K	.	T	-	2	0	IGSF10	152644026	0.074000	0.21230	0.366000	0.25914	0.026000	0.11368	2.357000	0.44125	0.558000	0.29135	-0.186000	0.12905	ACG	.	.		0.507	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		T	151161336	G	T	151161336	3	4	123	1	0	0	0	0	1	0	0	0	7606	1145	40	1	2528	1	IGSF10	3	151161336	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	9663984	151161336	46861094	93	20623										
SLC33A1	9197	hgsc.bcm.edu	37	chr3	155571758	155571758	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctggccgccgttgccggctgCtgtccttgtgggagatggtg	17	11	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:155571758C>T	ENST00000392845.3	-	1	409	c.29G>A	c.(28-30)aGc>aAc	p.S10N	SLC33A1_ENST00000359479.3_Missense_Mutation_p.S10N|SLC33A1_ENST00000460729.1_5'Flank			O00400	ACATN_HUMAN	solute carrier family 33 (acetyl-CoA transporter), member 1	10					acetyl-CoA transport (GO:0015876)|cell death (GO:0008219)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	acetyl-CoA transporter activity (GO:0008521)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	22			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TTGCCGGCTGCTGTCCTTGTG	0.612																																					p.S10N		Atlas-SNP	.											.	SLC33A1	57	.	0			c.G29A						.						25	30	28					3																	155571758		2187	4268	6455	SO:0001583	missense	9197	exon1			CGGCTGCTGTCCT	D88152	CCDS3173.1	3q25.31	2013-05-22		2002-12-06	ENSG00000169359	ENSG00000169359		"Solute carriers"	95	protein-coding gene	gene with protein product		603690	"acetyl-Coenzyme A transporter", "spastic paraplegia 42 (autosomal dominant)"	ACATN, SPG42		9096318, 19061983	Standard	NM_004733		Approved	AT-1, AT1	uc003fao.2	O00400	OTTHUMG00000158481	ENST00000392845.3:c.29G>A	chr3.hg19:g.155571758C>T	ENSP00000376587:p.Ser10Asn	188.0	0.0		177.0	79.0	NM_004733	B2R5Q2|D3DNK4	Missense_Mutation	SNP	ENST00000392845.3	hg19	CCDS3173.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.777797	0.31502	.	.	ENSG00000169359	ENST00000392845;ENST00000359479	T;T	0.72615	-0.67;-0.67	4.95	-5.36	0.02689	Major facilitator superfamily domain, general substrate transporter (1);	0.631198	0.18395	N	0.142532	T	0.51890	0.1701	N	0.24115	0.695	0.24318	N	0.99506	B	0.02656	0.0	B	0.04013	0.001	T	0.12656	-1.0539	10	0.19147	T	0.46	0.0017	18.1138	0.89543	0.0:0.9078:0.0:0.0922	.	10	O00400	ACATN_HUMAN	N	10	ENSP00000376587:S10N;ENSP00000352456:S10N	ENSP00000352456:S10N	S	-	2	0	SLC33A1	157054452	0.830000	0.29337	0.620000	0.29132	0.833000	0.47200	-0.557000	0.05985	-1.339000	0.02230	-0.355000	0.07637	AGC	.	.		0.612	SLC33A1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351130.3	NM_004733		T	155571758	C	T	155571758	3	4	123	1	0	0	0	0	1	0	0	0	14581	797	28	3	1644	3	SLC33A1	3	155571758	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	4410422	155571758	42450672	94	20624										
FNDC3B	64778	hgsc.bcm.edu	37	chr3	172048416	172048416	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggctggttcgagctggcatcAcatgggtcacgttgcagtgg	16	9	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:172048416A>T	ENST00000336824.4	+	13	1564	c.1465A>T	c.(1465-1467)Aca>Tca	p.T489S	FNDC3B_ENST00000416957.1_Missense_Mutation_p.T489S|FNDC3B_ENST00000415807.2_Missense_Mutation_p.T489S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	489	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AGCTGGCATCACATGGGTCAC	0.478																																					p.T489S		Atlas-SNP	.											.	FNDC3B	118	.	0			c.A1465T						.						133	110	118					3																	172048416		2203	4300	6503	SO:0001583	missense	64778	exon13			GGCATCACATGGG	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.1465A>T	chr3.hg19:g.172048416A>T	ENSP00000338523:p.Thr489Ser	197.0	0.0		218.0	38.0	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	hg19	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.453217	0.43531	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.59502	0.26;0.26;0.26	5.12	5.12	0.69794	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.048827	0.85682	D	0.000000	T	0.45013	0.1321	N	0.17082	0.46	0.80722	D	1	B;B	0.16396	0.008;0.017	B;B	0.28305	0.005;0.088	T	0.34527	-0.9825	10	0.32370	T	0.25	-15.0524	15.2444	0.73497	1.0:0.0:0.0:0.0	.	489;489	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	S	489	ENSP00000411242:T489S;ENSP00000338523:T489S;ENSP00000389094:T489S	ENSP00000338523:T489S	T	+	1	0	FNDC3B	173531110	1.000000	0.71417	0.999000	0.59377	0.697000	0.40408	6.621000	0.74228	2.078000	0.62432	0.533000	0.62120	ACA	.	.		0.478	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		T	172048416	A	T	172048416	3	4	123	1	0	0	0	0	1	0	0	0	5978	159	6	4	1511	4	FNDC3B	3	172048416	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	16476658	172048416	25974014	95	20625										
GNB4	59345	hgsc.bcm.edu	37	chr3	179119095	179119095	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agctcacacggttgtcatgaCcagcaaggacacctgaaaaa	9	11	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:179119095C>G	ENST00000232564.3	-	10	1215	c.929G>C	c.(928-930)gGt>gCt	p.G310A	AC007620.3_ENST00000598857.1_RNA|AC007620.3_ENST00000600539.1_RNA|AC007620.3_ENST00000495081.2_RNA|GNB4_ENST00000468623.1_Missense_Mutation_p.G310A	NM_021629.3	NP_067642.1	Q9HAV0	GBB4_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 4	310					cell death (GO:0008219)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	16	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			GTTGTCATGACCAGCAAGGAC	0.383																																					p.G310A	Melanoma(105;1405 1491 7265 20440 33721)	Atlas-SNP	.											.	GNB4	37	.	0			c.G929C						.						62	57	58					3																	179119095		2203	4300	6503	SO:0001583	missense	59345	exon10			TCATGACCAGCAA	AF300648	CCDS3230.1	3q27.1	2013-01-10			ENSG00000114450	ENSG00000114450		"WD repeat domain containing"	20731	protein-coding gene	gene with protein product		610863				10644457, 11842130	Standard	NM_021629		Approved		uc003fjv.4	Q9HAV0	OTTHUMG00000157440	ENST00000232564.3:c.929G>C	chr3.hg19:g.179119095C>G	ENSP00000232564:p.Gly310Ala	241.0	0.0		228.0	31.0	NM_021629	B3KMH5|D3DNR8	Missense_Mutation	SNP	ENST00000232564.3	hg19	CCDS3230.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446597	0.63178	.	.	ENSG00000114450	ENST00000232564;ENST00000466899;ENST00000468623	T;T	0.67698	-0.28;-0.28	4.92	4.92	0.64577	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.78735	0.4330	L	0.50993	1.605	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.80103	-0.1522	10	0.59425	D	0.04	-12.3924	18.5626	0.91105	0.0:1.0:0.0:0.0	.	310	Q9HAV0	GBB4_HUMAN	A	310;160;310	ENSP00000232564:G310A;ENSP00000419693:G310A	ENSP00000232564:G310A	G	-	2	0	GNB4	180601789	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.702000	0.84576	2.436000	0.82500	0.644000	0.83932	GGT	.	.		0.383	GNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258218.1	NM_021629		G	179119095	C	G	179119095	3	3	123	1	0	0	0	0	1	0	0	0	6528	507	18	4	97	4	GNB4	3	179119095	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	7070679	179119095	18903335	96	20626										
MCCC1	56922	hgsc.bcm.edu	37	chr3	182788806	182788806	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cctcggtgtgtctacaaactTctcgatcagcatagcatcat	7	12	4	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:182788806T>A	ENST00000265594.4	-	7	888	c.742A>T	c.(742-744)Aag>Tag	p.K248*	MCCC1_ENST00000492597.1_Nonsense_Mutation_p.K139*|MCCC1_ENST00000539926.1_Nonsense_Mutation_p.K113*	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	248	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	TCTACAAACTTCTCGATCAGC	0.338																																					p.K248X		Atlas-SNP	.											.	MCCC1	87	.	0			c.A742T						.						89	83	85					3																	182788806		2203	4300	6503	SO:0001587	stop_gained	56922	exon7			CAAACTTCTCGAT	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.742A>T	chr3.hg19:g.182788806T>A	ENSP00000265594:p.Lys248*	150.0	0.0		181.0	26.0	NM_020166	Q59ES4|Q9H959|Q9NS97	Nonsense_Mutation	SNP	ENST00000265594.4	hg19	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	T	36	5.743537	0.96873	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176;ENST00000448585;ENST00000541636	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.0863	0.81056	0.0:0.0:0.0:1.0	.	.	.	.	X	248;139;98;113;201;201;139	.	ENSP00000265594:K248X	K	-	1	0	MCCC1	184271500	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	7.567000	0.82357	2.251000	0.74343	0.528000	0.53228	AAG	.	.		0.338	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		A	182788806	T	A	182788806	4	1	123	1	0	0	0	0	0	1	0	0	9383	1792	62	4	1487	4	MCCC1	3	182788806	Nonsense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	3669711	182788806	15233624	97	20627										
ZNF518B	85460	hgsc.bcm.edu	37	chr4	10445461	10445461	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttggggacatatctattggcCccctttcacttcttaaaggc	8	11	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:10445461C>T	ENST00000326756.3	-	3	2930	c.2492G>A	c.(2491-2493)gGg>gAg	p.G831E		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	831					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						ATCTATTGGCCCCCTTTCACT	0.463																																					p.G831E		Atlas-SNP	.											.	ZNF518B	116	.	0			c.G2492A						.						91	89	90					4																	10445461		2203	4300	6503	SO:0001583	missense	85460	exon3			ATTGGCCCCCTTT	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.2492G>A	chr4.hg19:g.10445461C>T	ENSP00000317614:p.Gly831Glu	127.0	0.0		136.0	27.0	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	hg19	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	C	11.04	1.521364	0.27211	.	.	ENSG00000178163	ENST00000326756	T	0.01406	4.93	6.02	0.754	0.18410	.	0.625953	0.15390	N	0.264864	T	0.01092	0.0036	L	0.33485	1.01	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.49322	-0.8952	10	0.02654	T	1	-8.3179	7.3401	0.26632	0.0:0.4118:0.0:0.5882	.	831	Q9C0D4	Z518B_HUMAN	E	831	ENSP00000317614:G831E	ENSP00000317614:G831E	G	-	2	0	ZNF518B	10054559	0.001000	0.12720	0.001000	0.08648	0.143000	0.21401	0.838000	0.27572	0.160000	0.19432	-0.140000	0.14226	GGG	.	.		0.463	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		T	10445461	C	T	10445461	3	4	123	1	0	0	0	0	1	0	0	0	17978	623	22	3	736	3	ZNF518B	4	10445461	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		10445461	180708815	98	20628										
FAM114A1	92689	hgsc.bcm.edu	37	chr4	38910313	38910313	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cccgggctttaagcggaccaAgacgctcatggagagaactg	13	11	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:38910313A>G	ENST00000358869.2	+	7	934	c.758A>G	c.(757-759)aAg>aGg	p.K253R	FAM114A1_ENST00000515037.1_Missense_Mutation_p.K46R	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	253						cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						AAGCGGACCAAGACGCTCATG	0.388																																					p.K253R		Atlas-SNP	.											.	FAM114A1	42	.	0			c.A758G						.						81	78	79					4																	38910313		2203	4300	6503	SO:0001583	missense	92689	exon7			GGACCAAGACGCT		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.758A>G	chr4.hg19:g.38910313A>G	ENSP00000351740:p.Lys253Arg	141.0	0.0		147.0	22.0	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	hg19	CCDS3447.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.009511	0.93346	.	.	ENSG00000197712	ENST00000515037;ENST00000358869;ENST00000355404	T;T	0.42900	0.96;0.96	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.53965	0.1829	L	0.37697	1.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.43523	-0.9386	10	0.17832	T	0.49	-26.8338	16.8222	0.85835	1.0:0.0:0.0:0.0	.	253	Q8IWE2	NXP20_HUMAN	R	46;253;46	ENSP00000424115:K46R;ENSP00000351740:K253R	ENSP00000347569:K46R	K	+	2	0	FAM114A1	38586708	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.388	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389		G	38910313	A	G	38910313	3	3	123	1	0	0	0	0	1	0	0	0	5408	72	3	2	776	2	FAM114A1	4	38910313	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	28464852	38910313	152243963	99	20629										
GABRA4	2557	hgsc.bcm.edu	37	chr4	46967002	46967002	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aatacctgcagaggggcttcAggatgcttctctctctgcac	10	12	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:46967002A>T	ENST00000264318.3	-	8	2101	c.1119T>A	c.(1117-1119)ccT>ccA	p.P373P		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	373					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	GAGGGGCTTCAGGATGCTTCT	0.408																																					p.P373P	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											.	GABRA4	129	.	0			c.T1119A						.						80	86	84					4																	46967002		2202	4299	6501	SO:0001819	synonymous_variant	2557	exon8			GGCTTCAGGATGC		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4078	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 4"	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.1119T>A	chr4.hg19:g.46967002A>T		128.0	0.0		115.0	12.0	NM_000809	Q8IYR7	Silent	SNP	ENST00000264318.3	hg19	CCDS3473.1																																																																																			.	.		0.408	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			T	46967002	A	T	46967002	2	4	123	1	0	0	0	0	0	0	0	1	6171	175	7	4		4	GABRA4	4	46967002	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	8056689	46967002	144187274	100	20630										
FRYL	285527	hgsc.bcm.edu	37	chr4	48607809	48607809	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aaaccagcaagtgcatgtttTatatctttatctttcacttc	4	9	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:48607809T>A	ENST00000503238.1	-	8	782	c.783A>T	c.(781-783)atA>atT	p.I261I	FRYL_ENST00000506685.1_5'UTR|FRYL_ENST00000507711.1_Silent_p.I261I|FRYL_ENST00000537810.1_Silent_p.I261I|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Silent_p.I261I			O94915	FRYL_HUMAN	FRY-like	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GTGCATGTTTTATATCTTTAT	0.313																																					p.I261I		Atlas-SNP	.											.	FRYL	242	.	0			c.A783T						.						110	113	112					4																	48607809		1824	4090	5914	SO:0001819	synonymous_variant	285527	exon11			ATGTTTTATATCT	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.783A>T	chr4.hg19:g.48607809T>A		149.0	0.0		142.0	32.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	hg19	CCDS43227.1																																																																																			.	.		0.313	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			A	48607809	T	A	48607809	2	1	123	1	0	0	0	0	0	0	0	1	6072	1744	61	4		4	FRYL	4	48607809	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	1640807	48607809	142546467	101	20631										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62800605	62800605	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cttcagccacaagctttgaaTgcatggagagacctgactac	9	11	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:62800605T>A	ENST00000514591.1	+	13	2285	c.1956T>A	c.(1954-1956)aaT>aaA	p.N652K	LPHN3_ENST00000512091.2_Missense_Mutation_p.N652K|LPHN3_ENST00000511324.1_Missense_Mutation_p.N720K|LPHN3_ENST00000504896.1_Missense_Mutation_p.N652K|LPHN3_ENST00000514157.1_Missense_Mutation_p.N652K|LPHN3_ENST00000506746.1_Missense_Mutation_p.N720K|LPHN3_ENST00000509896.1_Missense_Mutation_p.N720K|LPHN3_ENST00000506700.1_Missense_Mutation_p.N652K|LPHN3_ENST00000514996.1_Missense_Mutation_p.N652K|LPHN3_ENST00000508693.1_Missense_Mutation_p.N720K|LPHN3_ENST00000508946.1_Missense_Mutation_p.N652K|LPHN3_ENST00000506720.1_Missense_Mutation_p.N720K|LPHN3_ENST00000507164.1_Missense_Mutation_p.N720K|LPHN3_ENST00000507625.1_Missense_Mutation_p.N720K|LPHN3_ENST00000508078.1_3'UTR|LPHN3_ENST00000545650.1_Missense_Mutation_p.N652K			Q9HAR2	LPHN3_HUMAN	latrophilin 3	639					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						AAGCTTTGAATGCATGGAGAG	0.478																																					p.N652K		Atlas-SNP	.											.	LPHN3	800	.	0			c.T1956A						.						86	89	88					4																	62800605		2058	4215	6273	SO:0001583	missense	23284	exon11			TTTGAATGCATGG	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1956T>A	chr4.hg19:g.62800605T>A	ENSP00000422533:p.Asn652Lys	210.0	0.0		238.0	65.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.289|4.289	0.052855|0.052855	0.08291|0.08291	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000502815|ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.08634	.|3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07	5.43|5.43	3.01|3.01	0.34805|0.34805	.|Domain of unknown function DUF3497 (1);	.|0.276650	.|0.42172	.|D	.|0.000742	T|T	0.02304|0.02304	0.0071|0.0071	N|N	0.01576|0.01576	-0.805|-0.805	0.39293|0.39293	D|D	0.964778|0.964778	.|B;B;B	.|0.11235	.|0.002;0.003;0.004	.|B;B;B	.|0.11329	.|0.006;0.006;0.002	T|T	0.41070|0.41070	-0.9529|-0.9529	5|10	.|0.10636	.|T	.|0.68	.|.	4.8759|4.8759	0.13656|0.13656	0.1267:0.2102:0.0:0.6631|0.1267:0.2102:0.0:0.6631	.|.	.|652;639;652	.|E9PE04;Q9HAR2;Q9HAR2-2	.|.;LPHN3_HUMAN;.	S|K	110|652;652;720;720;652;639;652;639;652;720;720;720;652;652;652;720;720;652	.|ENSP00000423388:N652K;ENSP00000422533:N652K;ENSP00000423787:N720K;ENSP00000425033:N720K;ENSP00000424120:N652K;ENSP00000439831:N652K;ENSP00000421476:N720K;ENSP00000424030:N720K;ENSP00000421372:N720K;ENSP00000425201:N652K;ENSP00000423434:N652K;ENSP00000421627:N652K;ENSP00000420931:N720K;ENSP00000425884:N720K;ENSP00000424258:N652K	.|ENSP00000280009:N652K	C|N	+|+	1|3	0|2	LPHN3|LPHN3	62483200|62483200	0.994000|0.994000	0.37717|0.37717	1.000000|1.000000	0.80357|0.80357	0.965000|0.965000	0.64279|0.64279	0.175000|0.175000	0.16762|0.16762	0.511000|0.511000	0.28236|0.28236	-0.263000|-0.263000	0.10527|0.10527	TGC|AAT	.	.		0.478	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			A	62800605	T	A	62800605	3	1	123	1	0	0	0	0	1	0	0	0	8926	1461	51	4	1998	4	LPHN3	4	62800605	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	14192796	62800605	128353671	102	20632										
ARHGAP24	83478	hgsc.bcm.edu	37	chr4	86852134	86852134	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccggctggtgccttagcctcAactcctttcatccctaaaac	6	16	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:86852134A>T	ENST00000395184.1	+	4	857				ARHGAP24_ENST00000503995.1_Intron|ARHGAP24_ENST00000264343.4_Silent_p.S17S|ARHGAP24_ENST00000395183.2_Intron	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24						activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		CCTTAGCCTCAACTCCTTTCA	0.438																																					p.S17S		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.A51T						.						82	88	86					4																	86852134		2203	4300	6503	SO:0001627	intron_variant	83478	exon1			AGCCTCAACTCCT	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.391+7211A>T	chr4.hg19:g.86852134A>T		159.0	0.0		96.0	21.0	NM_031305	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Silent	SNP	ENST00000395184.1	hg19	CCDS34025.1																																																																																			.	.		0.438	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		T	86852134	A	T	86852134	1	4	123	0	1	0	0	0	0	0	0	0	873	117	5	4		4	ARHGAP24	4	86852134	Intron	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	24051529	86852134	104302142	103	20633										
SEC24B	10427	hgsc.bcm.edu	37	chr4	110442311	110442311	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cggatagtttacttgtgaatCtatatgaaagtaaagaggta	10	3	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:110442311C>T	ENST00000265175.5	+	13	2339	c.2284C>T	c.(2284-2286)Cta>Tta	p.L762L	SEC24B_ENST00000504968.2_Silent_p.L792L|SEC24B_ENST00000399100.2_Silent_p.L727L	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	762					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		ACTTGTGAATCTATATGAAAG	0.244																																					p.L762L		Atlas-SNP	.											.	SEC24B	186	.	0			c.C2284T						.						62	58	59					4																	110442311		1782	4042	5824	SO:0001819	synonymous_variant	10427	exon13			GTGAATCTATATG	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.2284C>T	chr4.hg19:g.110442311C>T		112.0	0.0		62.0	13.0	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Silent	SNP	ENST00000265175.5	hg19	CCDS47124.1																																																																																			.	.		0.244	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			T	110442311	C	T	110442311	2	4	123	1	0	0	0	0	0	0	0	1	14010	912	32	3		3	SEC24B	4	110442311	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	23590177	110442311	80711965	104	20634										
USP53	54532	hgsc.bcm.edu	37	chr4	120192951	120192951	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgaccatatatgaagatgaaAtgaagcaggaaataggaagc	11	4	0	5			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:120192951A>T	ENST00000274030.6	+	16	3115	c.1936A>T	c.(1936-1938)Atg>Ttg	p.M646L	USP53_ENST00000450251.1_Missense_Mutation_p.M646L	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						TGAAGATGAAATGAAGCAGGA	0.363																																					p.M646L		Atlas-SNP	.											.	USP53	69	.	0			c.A1936T						.						117	105	109					4																	120192951		1838	4092	5930	SO:0001583	missense	54532	exon15			GATGAAATGAAGC	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"Ubiquitin-specific peptidases"	29255	protein-coding gene	gene with protein product			"ubiquitin specific protease 53"			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.1936A>T	chr4.hg19:g.120192951A>T	ENSP00000274030:p.Met646Leu	132.0	0.0		101.0	16.0	NM_019050		Missense_Mutation	SNP	ENST00000274030.6	hg19	CCDS43265.1	.	.	.	.	.	.	.	.	.	.	A	7.268	0.606516	0.14002	.	.	ENSG00000145390	ENST00000274030;ENST00000450251	T;T	0.40225	1.04;1.04	5.58	-3.41	0.04839	.	1.734410	0.02229	N	0.064775	T	0.25082	0.0609	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.11916	-1.0568	10	0.11485	T	0.65	1.203	6.2006	0.20573	0.3925:0.2442:0.3634:0.0	.	646	Q70EK8	UBP53_HUMAN	L	646	ENSP00000274030:M646L;ENSP00000409906:M646L	ENSP00000274030:M646L	M	+	1	0	USP53	120412399	0.434000	0.25570	0.486000	0.27416	0.980000	0.70556	0.359000	0.20233	-0.191000	0.10448	-0.376000	0.06991	ATG	.	.		0.363	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597		T	120192951	A	T	120192951	3	4	123	1	0	0	0	0	1	0	0	0	17099	101	4	4	1982	4	USP53	4	120192951	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	9750640	120192951	70961325	105	20635										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158257592	158257592	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gagaagaggtgattgacttcTcaaagcccttcatgagcctc	10	10	2	5			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:158257592T>A	ENST00000264426.9	+	11	1816	c.1537T>A	c.(1537-1539)Tca>Aca	p.S513T	GRIA2_ENST00000449365.1_Missense_Mutation_p.S466T|GRIA2_ENST00000296526.7_Missense_Mutation_p.S513T|GRIA2_ENST00000507898.1_Missense_Mutation_p.S466T|GRIA2_ENST00000393815.2_Missense_Mutation_p.S466T	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	513					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GATTGACTTCTCAAAGCCCTT	0.408																																					p.S513T		Atlas-SNP	.											.	GRIA2	358	.	0			c.T1537A						.						168	167	167					4																	158257592		2203	4300	6503	SO:0001583	missense	2891	exon11			GACTTCTCAAAGC		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.1537T>A	chr4.hg19:g.158257592T>A	ENSP00000264426:p.Ser513Thr	164.0	0.0		144.0	45.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.493758	0.64186	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.46	5.46	0.80206	Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.42017	0.1184	N	0.05554	-0.025	0.80722	D	1	P;B;D	0.54964	0.92;0.292;0.969	B;B;D	0.63381	0.444;0.097;0.914	T	0.44667	-0.9313	10	0.31617	T	0.26	.	15.8205	0.78638	0.0:0.0:0.0:1.0	.	513;513;466	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	T	466;466;513;513;466	ENSP00000426845:S466T;ENSP00000377403:S466T;ENSP00000296526:S513T;ENSP00000264426:S513T;ENSP00000389837:S466T	ENSP00000264426:S513T	S	+	1	0	GRIA2	158477042	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.196000	0.70406	0.533000	0.62120	TCA	.	.		0.408	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			A	158257592	T	A	158257592	3	1	123	1	0	0	0	0	1	0	0	0	6777	1551	54	4	1579	4	GRIA2	4	158257592	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	38064641	158257592	32896684	106	20636										
NAF1	92345	hgsc.bcm.edu	37	chr4	164061471	164061471	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	taatacctttactctcaatgTgatctgaagaattaaaccgt	5	8	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:164061471T>C	ENST00000274054.2	-	5	975	c.782A>G	c.(781-783)cAc>cGc	p.H261R	NAF1_ENST00000509434.1_5'UTR|NAF1_ENST00000422287.2_Missense_Mutation_p.H261R	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	261					pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				ACTCTCAATGTGATCTGAAGA	0.299																																					p.H261R		Atlas-SNP	.											.	NAF1	69	.	0			c.A782G						.						84	92	90					4																	164061471		2203	4292	6495	SO:0001583	missense	92345	exon5			TCAATGTGATCTG		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"nuclear assembly factor 1 homolog (S. cerevisiae)"			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.782A>G	chr4.hg19:g.164061471T>C	ENSP00000274054:p.His261Arg	52.0	0.0		55.0	10.0	NM_138386	D3DP28|E9PAZ2	Missense_Mutation	SNP	ENST00000274054.2	hg19	CCDS3803.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.311775	0.81358	.	.	ENSG00000145414	ENST00000422287;ENST00000274054	T;T	0.32515	1.48;1.45	5.68	5.68	0.88126	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.235594	0.43747	D	0.000528	T	0.47002	0.1422	M	0.65975	2.015	0.46458	D	0.999053	P;D	0.54047	0.897;0.964	P;P	0.57057	0.498;0.812	T	0.33317	-0.9873	10	0.21540	T	0.41	-15.0885	15.1134	0.72380	0.0:0.0:0.0:1.0	.	261;261	E9PAZ2;Q96HR8	.;NAF1_HUMAN	R	261	ENSP00000408963:H261R;ENSP00000274054:H261R	ENSP00000274054:H261R	H	-	2	0	NAF1	164280921	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.880000	0.75578	2.175000	0.68902	0.533000	0.62120	CAC	.	.		0.299	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386		C	164061471	T	C	164061471	3	2	123	1	0	0	0	0	1	0	0	0	10149	1696	59	2	859	2	NAF1	4	164061471	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	5803879	164061471	27092805	107	20637										
TLL1	7092	hgsc.bcm.edu	37	chr4	166976353	166976353	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gacataagatctacctccaaTactttgtggatgaagtttgt	8	7	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:166976353T>C	ENST00000061240.2	+	13	2297	c.1650T>C	c.(1648-1650)aaT>aaC	p.N550N	RNA5SP170_ENST00000517150.1_RNA|TLL1_ENST00000507499.1_Silent_p.N573N	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	550	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		CTACCTCCAATACTTTGTGGA	0.378																																					p.N550N		Atlas-SNP	.											.	TLL1	194	.	0			c.T1650C						.						122	119	120					4																	166976353		2203	4300	6503	SO:0001819	synonymous_variant	7092	exon13			CTCCAATACTTTG	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.1650T>C	chr4.hg19:g.166976353T>C		112.0	0.0		69.0	14.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	hg19	CCDS3811.1																																																																																			.	.		0.378	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			C	166976353	T	C	166976353	2	2	123	1	0	0	0	0	0	0	0	1	15960	1403	49	2		2	TLL1	4	166976353	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	2914882	166976353	24177923	108	20638										
ASB5	140458	hgsc.bcm.edu	37	chr4	177190077	177190077	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aacataccttgtccttgggtTactccataaaattcagctgc	6	11	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:177190077T>C	ENST00000296525.3	-	1	296	c.183A>G	c.(181-183)gtA>gtG	p.V61V		NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	61					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		GTCCTTGGGTTACTCCATAAA	0.393																																					p.V61V		Atlas-SNP	.											.	ASB5	88	.	0			c.A183G						.						105	92	96					4																	177190077		2203	4300	6503	SO:0001819	synonymous_variant	140458	exon1			TTGGGTTACTCCA	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"Ankyrin repeat domain containing"	17180	protein-coding gene	gene with protein product		615050	"ankyrin repeat and SOCS box-containing 5"				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.183A>G	chr4.hg19:g.177190077T>C		120.0	0.0		91.0	14.0	NM_080874	Q8N7B5	Silent	SNP	ENST00000296525.3	hg19	CCDS3827.1																																																																																			.	.		0.393	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1			C	177190077	T	C	177190077	2	2	123	1	0	0	0	0	0	0	0	1	1026	1741	61	2		2	ASB5	4	177190077	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	10213724	177190077	13964199	109	20639										
CCDC110	256309	hgsc.bcm.edu	37	chr4	186366663	186366663	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atcttgaggaatcctaatgaTgcttgagagttctgtcttta	9	6	3	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:186366663T>A	ENST00000307588.3	-	7	2570	c.2495A>T	c.(2494-2496)cAt>cTt	p.H832L	C4orf47_ENST00000378850.4_Intron|CCDC110_ENST00000393540.3_Missense_Mutation_p.H795L	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	832						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		ATCCTAATGATGCTTGAGAGT	0.308																																					p.H832L		Atlas-SNP	.											.	CCDC110	78	.	0			c.A2495T						.						94	94	94					4																	186366663		2203	4300	6503	SO:0001583	missense	256309	exon7			TAATGATGCTTGA	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"cancer/testis antigen 52"	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.2495A>T	chr4.hg19:g.186366663T>A	ENSP00000306776:p.His832Leu	33.0	0.0		31.0	7.0	NM_152775	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	hg19	CCDS3843.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.012950	0.54468	.	.	ENSG00000168491	ENST00000393540;ENST00000307588	T;T	0.07021	3.23;3.24	3.11	-1.6	0.08426	.	2.526390	0.02211	N	0.063204	T	0.08980	0.0222	L	0.40543	1.245	0.09310	N	1	B;B	0.21606	0.058;0.058	B;B	0.17098	0.017;0.017	T	0.41342	-0.9514	10	0.87932	D	0	9.5423	7.001	0.24809	0.0:0.4395:0.0:0.5605	.	795;832	Q8TBZ0-2;Q8TBZ0	.;CC110_HUMAN	L	795;832	ENSP00000377172:H795L;ENSP00000306776:H832L	ENSP00000306776:H832L	H	-	2	0	CCDC110	186603657	0.000000	0.05858	0.000000	0.03702	0.402000	0.30811	-1.131000	0.03238	-0.389000	0.07786	0.383000	0.25322	CAT	.	.		0.308	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775		A	186366663	T	A	186366663	3	1	123	1	0	0	0	0	1	0	0	0	2749	1464	51	4	10	4	CCDC110	4	186366663	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	9176586	186366663	4787613	110	20640										
MTNR1A	4543	hgsc.bcm.edu	37	chr4	187455096	187455096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctgggatcctaggcaccatgCtggcggggtcagaggccacg	16	12	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:187455096C>T	ENST00000307161.5	-	2	1001	c.800G>A	c.(799-801)aGc>aAc	p.S267N	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	267					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	AGGCACCATGCTGGCGGGGTC	0.502																																					p.S267N		Atlas-SNP	.											.	MTNR1A	46	.	0			c.G800A						.						73	79	77					4																	187455096		2203	4300	6503	SO:0001583	missense	4543	exon2			ACCATGCTGGCGG		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"GPCR / Class A : Melatonin receptors"	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.800G>A	chr4.hg19:g.187455096C>T	ENSP00000302811:p.Ser267Asn	113.0	0.0		129.0	32.0	NM_005958	A0AVC5|B0M0L2	Missense_Mutation	SNP	ENST00000307161.5	hg19	CCDS3848.1	.	.	.	.	.	.	.	.	.	.	C	0.029	-1.347024	0.01266	.	.	ENSG00000168412	ENST00000307161	T	0.71934	-0.61	4.71	-3.51	0.04696	GPCR, rhodopsin-like superfamily (1);	1.129860	0.06353	N	0.710224	T	0.59115	0.2170	L	0.42581	1.335	0.09310	N	1	B	0.02656	0.0	B	0.12837	0.008	T	0.41270	-0.9518	10	0.23302	T	0.38	-4.4854	9.5902	0.39541	0.0:0.2529:0.4968:0.2503	.	267	P48039	MTR1A_HUMAN	N	267	ENSP00000302811:S267N	ENSP00000302811:S267N	S	-	2	0	MTNR1A	187692090	0.000000	0.05858	0.009000	0.14445	0.004000	0.04260	-0.404000	0.07205	-0.907000	0.03862	-1.224000	0.01588	AGC	.	.		0.502	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1			T	187455096	C	T	187455096	3	4	123	1	0	0	0	0	1	0	0	0	9960	797	28	3	256	3	MTNR1A	4	187455096	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1088433	187455096	3699180	111	20641										
ADCY2	108	hgsc.bcm.edu	37	chr5	7743819	7743819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctcctttggggctgcgtttcTcttgctggccttcatcctct	9	14	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:7743819T>C	ENST00000338316.4	+	15	1999	c.1910T>C	c.(1909-1911)cTc>cCc	p.L637P	ADCY2_ENST00000537121.1_Missense_Mutation_p.L457P|RP11-711G10.1_ENST00000514105.2_RNA	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	637					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						GCTGCGTTTCTCTTGCTGGCC	0.483																																					p.L637P		Atlas-SNP	.											.	ADCY2	337	.	0			c.T1910C						.						373	332	346					5																	7743819		2203	4300	6503	SO:0001583	missense	108	exon15			CGTTTCTCTTGCT	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1910T>C	chr5.hg19:g.7743819T>C	ENSP00000342952:p.Leu637Pro	260.0	0.0		250.0	47.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	T	9.737	1.163866	0.21538	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	T;D	0.83419	-1.24;-1.72	5.48	5.48	0.80851	.	0.064498	0.64402	D	0.000011	D	0.86167	0.5868	M	0.71581	2.175	0.58432	D	0.999999	P;B	0.45474	0.859;0.003	P;B	0.49708	0.62;0.006	D	0.87327	0.2322	10	0.59425	D	0.04	.	13.3916	0.60827	0.0:0.0:0.0:1.0	.	457;637	B7Z2C1;Q08462	.;ADCY2_HUMAN	P	637;470;457	ENSP00000342952:L637P;ENSP00000444803:L457P	ENSP00000342952:L637P	L	+	2	0	ADCY2	7796819	0.999000	0.42202	0.298000	0.25002	0.266000	0.26442	5.187000	0.65087	2.213000	0.71641	0.454000	0.30748	CTC	.	.		0.483	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		C	7743819	T	C	7743819	3	2	123	1	0	0	0	0	1	0	0	0	294	1551	54	2	1968	2	ADCY2	5	7743819	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10		7743819	173171441	112	20642										
ANKRA2	57763	hgsc.bcm.edu	37	chr5	72857022	72857022	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttggttaaagtggttgactgTtttatgggtgagaaatgctt	13	2	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:72857022T>C	ENST00000296785.3	-	3	1039	c.381A>G	c.(379-381)aaA>aaG	p.K127K		NM_023039.4	NP_075526.1	Q9H9E1	ANRA2_HUMAN	ankyrin repeat, family A (RFXANK-like), 2	127						cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	low-density lipoprotein particle binding (GO:0030169)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		Lung NSC(167;0.0378)|Ovarian(174;0.0908)		OV - Ovarian serous cystadenocarcinoma(47;3.71e-54)		TGGTTGACTGTTTTATGGGTG	0.398																																					p.K127K		Atlas-SNP	.											.	ANKRA2	23	.	0			c.A381G						.						311	279	290					5																	72857022		2203	4300	6503	SO:0001819	synonymous_variant	57763	exon3			TGACTGTTTTATG	AA442702	CCDS4020.1	5q12-q13	2013-01-10			ENSG00000164331	ENSG00000164331		"Ankyrin repeat domain containing"	13208	protein-coding gene	gene with protein product		605787				10965114	Standard	NM_023039		Approved		uc003kcu.2	Q9H9E1	OTTHUMG00000102030	ENST00000296785.3:c.381A>G	chr5.hg19:g.72857022T>C		216.0	0.0		241.0	25.0	NM_023039		Silent	SNP	ENST00000296785.3	hg19	CCDS4020.1																																																																																			.	.		0.398	ANKRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219814.2	NM_023039		C	72857022	T	C	72857022	2	2	123	1	0	0	0	0	0	0	0	1	636	1722	60	2		2	ANKRA2	5	72857022	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	65113203	72857022	108058238	113	20643										
AP3B1	8546	hgsc.bcm.edu	37	chr5	77409598	77409598	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttttcctttggcttttgagtTcctcttggctgttcttttgt	8	8	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:77409598T>C	ENST00000255194.6	-	19	2402	c.2227A>G	c.(2227-2229)Aac>Gac	p.N743D	AP3B1_ENST00000519295.1_Missense_Mutation_p.N694D	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	743	Glu/Ser-rich.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GCTTTTGAGTTCCTCTTGGCT	0.433									Hermansky-Pudlak syndrome																												p.N743D		Atlas-SNP	.											.	AP3B1	94	.	0			c.A2227G						.						190	174	180					5																	77409598		2203	4300	6503	SO:0001583	missense	8546	exon19	Familial Cancer Database	HPS, HPS1-8	TTGAGTTCCTCTT	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.2227A>G	chr5.hg19:g.77409598T>C	ENSP00000255194:p.Asn743Asp	84.0	0.0		66.0	16.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	T	3.780	-0.045885	0.07452	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760	T;T	0.13538	2.58;2.58	5.92	4.75	0.60458	.	1.063530	0.07119	N	0.843528	T	0.10294	0.0252	N	0.22421	0.69	0.09310	N	1	B	0.19817	0.039	B	0.16722	0.016	T	0.37641	-0.9697	10	0.08381	T	0.77	-3.3181	10.549	0.45077	0.0:0.0728:0.0:0.9272	.	743	O00203	AP3B1_HUMAN	D	743;694;743	ENSP00000255194:N743D;ENSP00000430597:N694D	ENSP00000255194:N743D	N	-	1	0	AP3B1	77445354	0.017000	0.18338	0.004000	0.12327	0.755000	0.42902	2.013000	0.40942	1.066000	0.40716	0.459000	0.35465	AAC	.	.		0.433	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			C	77409598	T	C	77409598	3	2	123	1	0	0	0	0	1	0	0	0	744	1783	62	2	1093	2	AP3B1	5	77409598	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	4552576	77409598	103505662	114	20644										
MCTP1	79772	hgsc.bcm.edu	37	chr5	94114816	94114816	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgctgggaaagataattaccTtgtcatctttgtcatcttct	7	8	5	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:94114816T>A	ENST00000515393.1	-	19	2608	c.2609A>T	c.(2608-2610)aAg>aTg	p.K870M	MCTP1_ENST00000312216.8_Splice_Site_p.K649M|MCTP1_ENST00000429576.2_Splice_Site_p.K563M|MCTP1_ENST00000505078.1_Splice_Site_p.K386M|MCTP1_ENST00000514040.1_5'UTR	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	870					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		GATAATTACCTTGTCATCTTT	0.423																																					p.K870M		Atlas-SNP	.											.	MCTP1	110	.	0			c.A2609T						.						184	142	156					5																	94114816		2203	4300	6503	SO:0001630	splice_region_variant	79772	exon19			ATTACCTTGTCAT		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.2610+1A>T	chr5.hg19:g.94114816T>A		186.0	0.0		234.0	36.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Missense_Mutation	SNP	ENST00000515393.1	hg19	CCDS34203.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.084013	0.76642	.	.	ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000505078;ENST00000312216;ENST00000508509	T;T;T;T;T	0.78924	-1.22;-1.04;-0.18;-1.11;-0.93	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.87989	0.6317	M	0.78049	2.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.988	D	0.89320	0.3639	10	0.72032	D	0.01	-16.3989	15.7739	0.78193	0.0:0.0:0.0:1.0	.	870;563;649	Q6DN14;Q6DN14-3;Q6DN14-2	MCTP1_HUMAN;.;.	M	870;563;386;649;590	ENSP00000424126:K870M;ENSP00000391639:K563M;ENSP00000426417:K386M;ENSP00000308957:K649M;ENSP00000423410:K590M	ENSP00000308957:K649M	K	-	2	0	MCTP1	94140572	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.165000	0.77544	2.367000	0.80283	0.528000	0.53228	AAG	.	.		0.423	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717	Missense_Mutation	A	94114816	T	A	94114816	5	1	123	1	0	0	0	0	0	0	1	0	9409	1623	56	4	410	4	MCTP1	5	94114816	Splice_Site	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	16705218	94114816	86800444	115	20645										
FAM81B	153643	hgsc.bcm.edu	37	chr5	94749823	94749823	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttcgaaaagaggaatcgctcGccaggaagttactggaaagc	12	8	0	1	rs202064996		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:94749823G>T	ENST00000283357.5	+	4	512	c.466G>T	c.(466-468)Gcc>Tcc	p.A156S		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	156						nucleus (GO:0005634)		p.A156T(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		GGAATCGCTCGCCAGGAAGTT	0.458																																					p.A156S		Atlas-SNP	.											FAM81B,NS,carcinoma,0,1	FAM81B	51	.	1	Substitution - Missense(1)	large_intestine(1)	c.G466T						.						94	95	95					5																	94749823		1977	4164	6141	SO:0001583	missense	153643	exon4			TCGCTCGCCAGGA		CCDS43341.1	5q15	2008-02-05			ENSG00000153347	ENSG00000153347			26335	protein-coding gene	gene with protein product							Standard	NM_152548		Approved	FLJ25333	uc003kla.1	Q96LP2	OTTHUMG00000162837	ENST00000283357.5:c.466G>T	chr5.hg19:g.94749823G>T	ENSP00000283357:p.Ala156Ser	158.0	0.0		189.0	36.0	NM_152548		Missense_Mutation	SNP	ENST00000283357.5	hg19	CCDS43341.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399513	0.62177	.	.	ENSG00000153347	ENST00000283357	T	0.21932	1.98	5.53	3.72	0.42706	.	0.057016	0.64402	D	0.000002	T	0.37999	0.1024	M	0.66939	2.045	0.34388	D	0.693884	D	0.71674	0.998	P	0.61533	0.89	T	0.50039	-0.8874	10	0.48119	T	0.1	-9.6175	11.8194	0.52230	0.1296:0.0:0.8704:0.0	.	156	Q96LP2	FA81B_HUMAN	S	156	ENSP00000283357:A156S	ENSP00000283357:A156S	A	+	1	0	FAM81B	94775579	1.000000	0.71417	0.985000	0.45067	0.379000	0.30106	3.689000	0.54706	2.602000	0.87976	0.650000	0.86243	GCC	.	G|1.000;A|0.000		0.458	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548		T	94749823	G	T	94749823	3	4	123	1	0	0	0	0	1	0	0	0	5637	1087	38	1	480	1	FAM81B	5	94749823	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	635007	94749823	86165437	116	20646										
CHD1	1105	hgsc.bcm.edu	37	chr5	98212136	98212136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atcactaaatcctttaatatTctcccgaggaatagtccgtg	6	10	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:98212136T>C	ENST00000284049.3	-	23	3513	c.3364A>G	c.(3364-3366)Aat>Gat	p.N1122D		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1122					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	CCTTTAATATTCTCCCGAGGA	0.403																																					p.N1122D		Atlas-SNP	.											.	CHD1	137	.	0			c.A3364G						.						216	217	216					5																	98212136		2203	4300	6503	SO:0001583	missense	1105	exon23			TAATATTCTCCCG	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.3364A>G	chr5.hg19:g.98212136T>C	ENSP00000284049:p.Asn1122Asp	96.0	0.0		107.0	28.0	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.272766	0.40194	.	.	ENSG00000153922	ENST00000284049	D	0.89485	-2.52	5.14	5.14	0.70334	.	0.209202	0.22250	U	0.062567	D	0.85340	0.5674	L	0.48642	1.525	0.58432	D	0.999999	P	0.38863	0.65	B	0.39660	0.306	T	0.82575	-0.0389	10	0.12430	T	0.62	.	15.2607	0.73621	0.0:0.0:0.0:1.0	.	1122	O14646	CHD1_HUMAN	D	1122	ENSP00000284049:N1122D	ENSP00000284049:N1122D	N	-	1	0	CHD1	98240036	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	5.955000	0.70306	2.058000	0.61347	0.528000	0.53228	AAT	.	.		0.403	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		C	98212136	T	C	98212136	3	2	123	1	0	0	0	0	1	0	0	0	3325	1783	62	2	1820	2	CHD1	5	98212136	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	3462313	98212136	82703124	117	20647										
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115811300	115811300	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgtcctgctcaaaagtcagtCttttaaaaaaggaagggaaa	9	6	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:115811300C>G	ENST00000343348.6	-	16	2437		c.e16-1		CTB-118N6.3_ENST00000507558.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|CTB-118N6.3_ENST00000514214.1_RNA|SEMA6A_ENST00000257414.8_Splice_Site|SEMA6A_ENST00000282394.6_Splice_Site|CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000510263.1_Splice_Site	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A						apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		AAAAGTCAGTCTTTTAAAAAA	0.383																																					.		Atlas-SNP	.											.	SEMA6A	93	.	0			c.1650-1G>C						.						50	46	47					5																	115811300		1874	4107	5981	SO:0001630	splice_region_variant	57556	exon17			GTCAGTCTTTTAA	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"Semaphorins"	10738	protein-coding gene	gene with protein product	"sema VIa"	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.1650-1G>C	chr5.hg19:g.115811300C>G		70.0	0.0		80.0	8.0	NM_020796	Q9P2H9	Splice_Site	SNP	ENST00000343348.6	hg19	CCDS47256.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.570226	0.86542	.	.	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000515129;ENST00000282394;ENST00000510263	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4745	0.99168	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEMA6A	115839199	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	7.242000	0.78210	2.941000	0.99782	0.655000	0.94253	.	.	.		0.383	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	Intron	G	115811300	C	G	115811300	5	3	123	1	0	0	0	0	0	0	1	0	14054	927	32	4	1459	4	SEMA6A	5	115811300	Splice_Site	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	17599164	115811300	65103960	118	20648										
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115838016	115838016	+	Frame_Shift_Del	DEL	T	T	-													0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cccacaaacaccggatactgTtttgtatctgtgaaaagagg							TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:115838016delT	ENST00000343348.6	-	3	895	c.108delA	c.(106-108)aaafs	p.K36fs	SEMA6A_ENST00000257414.8_Frame_Shift_Del_p.K36fs|SEMA6A_ENST00000503962.1_5'UTR|CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000510263.1_Frame_Shift_Del_p.K36fs	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	36	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		CCGGATACTGTTTTGTATCTG	0.493																																					p.Q37fs		Pindel	.											.	SEMA6A	93	.	0			c.109delC						.						168	163	165					5																	115838016		1986	4167	6153	SO:0001589	frameshift_variant	57556	exon3			.	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"Semaphorins"	10738	protein-coding gene	gene with protein product	"sema VIa"	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.108delA	chr5.hg19:g.115838016delT	ENSP00000345512:p.Lys36fs	296.0	0.0		323.0	53.0	NM_020796	Q9P2H9	Frame_Shift_Del	DEL	ENST00000343348.6	hg19	CCDS47256.1																																																																																			.	.		0.493	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796		-	115838016	T	-	115838016	7	5	123	1	0	1	0	1	0	0	0	0	14054	1722	60	0	3052	0	SEMA6A	5	115838016	Frame_Shift_Del	DEL	T	TCGA-DD-A3A9-01A-11D-A25V-10	26716	115838016	65077244	119	20649										
ZNF608	57507	hgsc.bcm.edu	37	chr5	123983011	123983011	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttcattccctgcgtgctcccActatttccagctgcaggggc	9	15	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:123983011A>G	ENST00000306315.5	-	4	3501	c.3066T>C	c.(3064-3066)agT>agC	p.S1022S	ZNF608_ENST00000513985.1_5'Flank|ZNF608_ENST00000504926.1_Silent_p.S595S	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1022							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		GCGTGCTCCCACTATTTCCAG	0.468																																					p.S1022S		Atlas-SNP	.											.	ZNF608	117	.	0			c.T3066C						.						166	159	161					5																	123983011		2203	4300	6503	SO:0001819	synonymous_variant	57507	exon4			GCTCCCACTATTT	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.3066T>C	chr5.hg19:g.123983011A>G		161.0	0.0		170.0	31.0	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Silent	SNP	ENST00000306315.5	hg19	CCDS34219.1																																																																																			.	.		0.468	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		G	123983011	A	G	123983011	2	3	123	1	0	0	0	0	0	0	0	1	18049	156	6	2		2	ZNF608	5	123983011	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	8144995	123983011	56932249	120	20650										
PHF15	23338	hgsc.bcm.edu	37	chr5	133914456	133914456	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctgccaagaagaaaccaccaCcaccaccaccgcaggacggg	9	17	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:133914456C>T	ENST00000282605.4	+	12	2040	c.1954C>T	c.(1954-1956)Cca>Tca	p.P652S	PHF15_ENST00000395003.1_Missense_Mutation_p.P608S|PHF15_ENST00000361895.2_Missense_Mutation_p.P609S|PHF15_ENST00000402835.1_3'UTR																NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GAAACCACCACCACCACCACC	0.662																																					p.P608S		Atlas-SNP	.											.	PHF15	60	.	0			c.C1822T						.						38	41	40					5																	133914456		2203	4299	6502	SO:0001583	missense	23338	exon11			CCACCACCACCAC																												ENST00000282605.4:c.1954C>T	chr5.hg19:g.133914456C>T	ENSP00000282605:p.Pro652Ser	92.0	0.0		74.0	19.0	NM_015288		Missense_Mutation	SNP	ENST00000282605.4	hg19		.	.	.	.	.	.	.	.	.	.	c	1.629	-0.519539	0.04171	.	.	ENSG00000043143	ENST00000448712;ENST00000282605;ENST00000361895;ENST00000432594;ENST00000395003	T;T;T	0.40476	1.03;1.05;1.05	2.62	2.62	0.31277	.	1.120060	0.06720	N	0.774630	T	0.16171	0.0389	N	0.02011	-0.69	0.22693	N	0.998845	B;B;P	0.41673	0.421;0.231;0.759	B;B;B	0.37267	0.109;0.037;0.245	T	0.02020	-1.1228	10	0.07813	T	0.8	.	9.2958	0.37815	0.0:1.0:0.0:0.0	.	608;609;668	Q9NQC1;D3DQA3;B3KPL2	JADE2_HUMAN;.;.	S	668;652;609;609;608	ENSP00000282605:P652S;ENSP00000354425:P609S;ENSP00000378451:P608S	ENSP00000282605:P652S	P	+	1	0	PHF15	133942355	0.025000	0.19082	0.137000	0.22149	0.184000	0.23303	0.399000	0.20916	1.401000	0.46761	0.306000	0.20318	CCA	.	.		0.662	PHF15-003	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251170.1			T	133914456	C	T	133914456	3	4	123	1	0	0	0	0	1	0	0	0	11835	507	18	3	1860	3	PHF15	5	133914456	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	9931445	133914456	47000804	121	20651										
DDX46	9879	hgsc.bcm.edu	37	chr5	134121190	134121190	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	caactcgagaactggctttaCagattactaaagagtgtaag	9	7	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:134121190C>G	ENST00000354283.4	+	11	1513	c.1378C>G	c.(1378-1380)Cag>Gag	p.Q460E	DDX46_ENST00000509178.1_3'UTR|DDX46_ENST00000452510.2_Missense_Mutation_p.Q460E			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	460	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACTGGCTTTACAGATTACTAA	0.398																																					p.Q460E	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.C1378G						.						153	154	154					5																	134121190		2203	4300	6503	SO:0001583	missense	9879	exon11			GCTTTACAGATTA		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.1378C>G	chr5.hg19:g.134121190C>G	ENSP00000346236:p.Gln460Glu	88.0	0.0		134.0	11.0	NM_014829	O94894|Q96EI0|Q9Y658	Missense_Mutation	SNP	ENST00000354283.4	hg19	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.671964	0.88348	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	D;D	0.81996	-1.56;-1.56	5.79	5.79	0.91817	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95943	0.8679	H	0.99740	4.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97669	1.0165	10	0.87932	D	0	-18.3815	20.0281	0.97530	0.0:1.0:0.0:0.0	.	460	Q7L014	DDX46_HUMAN	E	460	ENSP00000416534:Q460E;ENSP00000346236:Q460E	ENSP00000346236:Q460E	Q	+	1	0	DDX46	134149089	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.805000	0.86005	2.727000	0.93392	0.655000	0.94253	CAG	.	.		0.398	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		G	134121190	C	G	134121190	3	3	123	1	0	0	0	0	1	0	0	0	4366	479	17	4	1420	4	DDX46	5	134121190	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	206734	134121190	46794070	122	20652										
WNT8A	7478	hgsc.bcm.edu	37	chr5	137426301	137426301	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agacatgctggctgcagctgGctgaattccgggagatggga	16	8	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:137426301G>C	ENST00000398754.1	+	6	600	c.595G>C	c.(595-597)Gct>Cct	p.A199P	WNT8A_ENST00000506684.1_Missense_Mutation_p.A217P	NM_058244.2	NP_490645.1	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family, member 8A	199					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|endoderm development (GO:0007492)|establishment of organ orientation (GO:0048561)|neural crest cell fate commitment (GO:0014034)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|polarity specification of anterior/posterior axis (GO:0009949)|polarity specification of proximal/distal axis (GO:0010085)|regulation of protein localization (GO:0032880)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GCTGCAGCTGGCTGAATTCCG	0.522																																					p.A199P		Atlas-SNP	.											.	WNT8A	36	.	0			c.G595C						.						47	46	46					5																	137426301		1937	4144	6081	SO:0001583	missense	7478	exon6			CAGCTGGCTGAAT	AB057725	CCDS43368.1, CCDS75311.1	5q31	2008-07-18			ENSG00000061492	ENSG00000061492		"Wingless-type MMTV integration sites"	12788	protein-coding gene	gene with protein product		606360				11408932	Standard	XM_005272076		Approved	WNT8D	uc003lcd.1	Q9H1J5	OTTHUMG00000129196	ENST00000398754.1:c.595G>C	chr5.hg19:g.137426301G>C	ENSP00000381739:p.Ala199Pro	124.0	0.0		144.0	17.0	NM_058244	Q96S51	Missense_Mutation	SNP	ENST00000398754.1	hg19	CCDS43368.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.570448	0.28003	.	.	ENSG00000061492	ENST00000506684;ENST00000504809;ENST00000398754	T;T;T	0.74842	-0.88;-0.88;-0.88	4.89	4.89	0.63831	.	0.168053	0.51477	D	0.000084	T	0.58119	0.2100	N	0.04820	-0.15	0.80722	D	1	B;B;P	0.40250	0.18;0.18;0.709	B;B;B	0.42593	0.174;0.174;0.392	T	0.58109	-0.7694	10	0.12103	T	0.63	.	18.2498	0.89998	0.0:0.0:1.0:0.0	.	217;217;199	D6RF47;D6RF94;Q9H1J5	.;.;WNT8A_HUMAN	P	217;217;199	ENSP00000426653:A217P;ENSP00000424809:A217P;ENSP00000381739:A199P	ENSP00000354726:A199P	A	+	1	0	WNT8A	137454200	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.214000	0.42853	2.537000	0.85549	0.557000	0.71058	GCT	.	.		0.522	WNT8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280395.1	NM_058244		C	137426301	G	C	137426301	3	2	123	1	0	0	0	0	1	0	0	0	17411	1203	42	4	617	4	WNT8A	5	137426301	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	3305111	137426301	43488959	123	20653										
PSD2	84249	hgsc.bcm.edu	37	chr5	139219614	139219614	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	caggatttgtctttgcaggaGgagcaactgcggtctcatga	13	8	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:139219614G>A	ENST00000274710.3	+	14	2176	c.1971G>A	c.(1969-1971)gaG>gaA	p.E657E		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	657					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTTGCAGGAGGAGCAACTGC	0.547																																					p.E657E		Atlas-SNP	.											.	PSD2	88	.	0			c.G1971A						.						82	76	78					5																	139219614		2203	4300	6503	SO:0001819	synonymous_variant	84249	exon14			GCAGGAGGAGCAA	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1971G>A	chr5.hg19:g.139219614G>A		173.0	0.0		159.0	18.0	NM_032289	D3DQD3|Q8N3J8	Silent	SNP	ENST00000274710.3	hg19	CCDS4216.1																																																																																			.	.		0.547	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		A	139219614	G	A	139219614	2	1	123	1	0	0	0	0	0	0	0	1	12659	991	35	3		3	PSD2	5	139219614	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	1793313	139219614	41695646	124	20654										
NRG2	9542	hgsc.bcm.edu	37	chr5	139239488	139239488	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcataccctttaattcaaatCcaaggtgctctggcagtgca	7	11	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:139239488C>T	ENST00000361474.1	-	6	1414				NRG2_ENST00000541337.1_Intron|NRG2_ENST00000545385.1_Intron|NRG2_ENST00000358522.3_Missense_Mutation_p.G394E|NRG2_ENST00000289422.7_Missense_Mutation_p.G400E|NRG2_ENST00000340391.3_Intron|NRG2_ENST00000289409.4_Intron|NRG2_ENST00000394770.1_Intron	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2						embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAATTCAAATCCAAGGTGCTC	0.552																																					p.G400E		Atlas-SNP	.											.	NRG2	69	.	0			c.G1199A						.						47	51	50					5																	139239488		1938	4157	6095	SO:0001627	intron_variant	9542	exon6			TCAAATCCAAGGT		CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"Immunoglobulin superfamily / I-set domain containing"	7998	protein-coding gene	gene with protein product	"neural- and thymus-derived activator for ErbB kinases", "divergent of neuregulin-1"	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.1190-4125G>A	chr5.hg19:g.139239488C>T		213.0	0.0		244.0	32.0	NM_013982		Missense_Mutation	SNP	ENST00000361474.1	hg19	CCDS4217.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.92|17.92	3.507888|3.507888	0.64410|0.64410	.|.	.|.	ENSG00000158458|ENSG00000158458	ENST00000544729|ENST00000289422;ENST00000358522	.|T;T	.|0.73681	.|-0.63;-0.77	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	.|.	.|.	.|.	.|.	T|T	0.57125|0.57125	0.2032|0.2032	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|B;P	.|0.39696	.|0.007;0.683	.|B;B	.|0.34385	.|0.001;0.181	T|T	0.63985|0.63985	-0.6513|-0.6513	6|9	0.87932|0.46703	D|T	0|0.11	.|.	19.0293|19.0293	0.92948|0.92948	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|394;400	.|O14511-4;O14511-3	.|.;.	N|E	328|400;394	.|ENSP00000289422:G400E;ENSP00000351323:G394E	ENSP00000444943:D328N|ENSP00000289422:G400E	D|G	-|-	1|2	0|0	NRG2|NRG2	139219672|139219672	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.900000|0.900000	0.52787|0.52787	7.484000|7.484000	0.81180|0.81180	2.509000|2.509000	0.84616|0.84616	0.313000|0.313000	0.20887|0.20887	GAT|GGA	.	.		0.552	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982		T	139239488	C	T	139239488	1	4	123	0	1	0	0	0	0	0	0	0	10657	855	30	3		3	NRG2	5	139239488	Intron	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	19874	139239488	41675772	125	20655										
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140711003	140711003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggcacaataccatataaatgTccccgaaaacgtgccgctgg	9	12	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:140711003T>C	ENST00000517417.1	+	1	752	c.752T>C	c.(751-753)gTc>gCc	p.V251A	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Missense_Mutation_p.V251A	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	251	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATATAAATGTCCCCGAAAAC	0.488																																					p.V251A		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.T752C						.						65	65	65					5																	140711003		2203	4300	6503	SO:0001583	missense	56114	exon1			TAAATGTCCCCGA	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.752T>C	chr5.hg19:g.140711003T>C	ENSP00000431083:p.Val251Ala	65.0	0.0		62.0	14.0	NM_018912	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	hg19	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	T	12.06	1.825319	0.32237	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.58210	0.35;0.35	4.2	4.2	0.49525	Cadherin (4);Cadherin-like (1);	0.000000	0.44483	D	0.000456	T	0.76751	0.4031	M	0.93898	3.47	0.09310	N	1	D;P	0.67145	0.996;0.932	D;P	0.65233	0.933;0.718	T	0.72541	-0.4262	10	0.87932	D	0	.	13.4192	0.60987	0.0:0.0:0.0:1.0	.	251;251	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	A	251	ENSP00000431083:V251A;ENSP00000367345:V251A	ENSP00000367345:V251A	V	+	2	0	PCDHGA1	140691187	0.527000	0.26306	0.073000	0.20177	0.016000	0.09150	4.106000	0.57804	1.905000	0.55150	0.533000	0.62120	GTC	.	.		0.488	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		C	140711003	T	C	140711003	3	2	123	1	0	0	0	0	1	0	0	0	11559	1667	58	2	754	2	PCDHGA1	5	140711003	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	1471515	140711003	40204257	126	20656										
PCDH1	5097	hgsc.bcm.edu	37	chr5	141248811	141248811	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	accatagtcggctgcgaggcTcccaatgagggtgttgggtg	16	9	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:141248811T>A	ENST00000394536.3	-	2	365	c.226A>T	c.(226-228)Agc>Tgc	p.S76C	PCDH1_ENST00000536585.1_Missense_Mutation_p.S54C|PCDH1_ENST00000287008.3_Missense_Mutation_p.S76C|PCDH1_ENST00000503492.1_Missense_Mutation_p.S76C|PCDH1_ENST00000456271.1_Missense_Mutation_p.S76C	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	76	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		GCTGCGAGGCTCCCAATGAGG	0.602																																					p.S76C	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.A226T						.						40	39	40					5																	141248811		2203	4300	6503	SO:0001583	missense	5097	exon2			CGAGGCTCCCAAT	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"Cadherins / Protocadherins : Non-clustered"	8655	protein-coding gene	gene with protein product		603626	"protocadherin 1 (cadherin-like 1)"			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.226A>T	chr5.hg19:g.141248811T>A	ENSP00000378043:p.Ser76Cys	121.0	0.0		102.0	6.0	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000394536.3	hg19	CCDS43375.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.146111	0.57044	.	.	ENSG00000156453	ENST00000503492;ENST00000287008;ENST00000394536;ENST00000456271;ENST00000357517;ENST00000536585;ENST00000514773	T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;1.62	4.21	4.21	0.49690	Cadherin, N-terminal (1);Cadherin (2);	0.000000	0.64402	D	0.000007	T	0.51075	0.1653	M	0.67953	2.075	0.50171	D	0.999852	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.987	T	0.54827	-0.8235	10	0.87932	D	0	.	11.5439	0.50681	0.0:0.0:0.0:1.0	.	76;76	Q08174;Q08174-2	PCDH1_HUMAN;.	C	76;76;76;76;87;54;54	ENSP00000424667:S76C;ENSP00000287008:S76C;ENSP00000378043:S76C;ENSP00000403497:S76C;ENSP00000350122:S87C;ENSP00000438825:S54C;ENSP00000424163:S54C	ENSP00000287008:S76C	S	-	1	0	PCDH1	141228995	1.000000	0.71417	1.000000	0.80357	0.280000	0.26924	7.754000	0.85163	1.895000	0.54865	0.454000	0.30748	AGC	.	.		0.602	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420		A	141248811	T	A	141248811	3	1	123	1	0	0	0	0	1	0	0	0	11515	1551	54	4	3587	4	PCDH1	5	141248811	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	537808	141248811	39666449	127	20657										
KCTD16	57528	hgsc.bcm.edu	37	chr5	143853260	143853260	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcaccctcacactgcgattgCtgctgcaagaatggcaaagg	10	12	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:143853260C>G	ENST00000507359.3	+	3	1961	c.870C>G	c.(868-870)tgC>tgG	p.C290W	KCTD16_ENST00000512467.1_Missense_Mutation_p.C290W	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	290					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)				large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			ACTGCGATTGCTGCTGCAAGA	0.527																																					p.C290W		Atlas-SNP	.											.	KCTD16	70	.	0			c.C870G						.						81	79	80					5																	143853260		2203	4300	6503	SO:0001583	missense	57528	exon4			CGATTGCTGCTGC	AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"potassium channel tetramerisation domain containing 16"			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.870C>G	chr5.hg19:g.143853260C>G	ENSP00000426548:p.Cys290Trp	323.0	0.0		356.0	54.0	NM_020768	Q9P2M9	Missense_Mutation	SNP	ENST00000507359.3	hg19	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.412415	0.42817	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	T;T	0.44083	0.93;0.93	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.27967	0.0689	N	0.08118	0	0.80722	D	1	P	0.45283	0.855	B	0.37780	0.258	T	0.26292	-1.0107	10	0.72032	D	0.01	.	20.04	0.97581	0.0:1.0:0.0:0.0	.	290	Q68DU8	KCD16_HUMAN	W	290	ENSP00000424151:C290W;ENSP00000426548:C290W	ENSP00000426548:C290W	C	+	3	2	KCTD16	143833453	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.758000	0.55220	2.733000	0.93635	0.655000	0.94253	TGC	.	.		0.527	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368		G	143853260	C	G	143853260	3	3	123	1	0	0	0	0	1	0	0	0	8112	805	28	4	876	4	KCTD16	5	143853260	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	2604449	143853260	37062000	128	20658										
SPINK6	404203	hgsc.bcm.edu	37	chr5	147593570	147593570	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gacatatggcaataaatgtgCcttctgtaaggccatagtgt	10	7	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:147593570C>T	ENST00000325630.2	+	3	435	c.179C>T	c.(178-180)gCc>gTc	p.A60V		NM_001195290.1|NM_205841.3	NP_001182219.1|NP_995313.2	Q6UWN8	ISK6_HUMAN	serine peptidase inhibitor, Kazal type 6	60	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATAAATGTGCCTTCTGTAAG	0.428																																					p.A60V		Atlas-SNP	.											.	SPINK6	8	.	0			c.C179T						.						102	84	90					5																	147593570		2203	4300	6503	SO:0001583	missense	404203	exon3			AATGTGCCTTCTG	AY358716	CCDS34268.1	5q32	2011-08-31	2005-08-17		ENSG00000178172	ENSG00000178172		"Serine peptidase inhibitors, Kazal type"	29486	protein-coding gene	gene with protein product	"protease inhibitor H"	615868	"serine protease inhibitor, Kazal type 6"			15060002	Standard	NM_205841		Approved	MGC21394, UNQ844, BUSI2	uc021yff.1	Q6UWN8	OTTHUMG00000163425	ENST00000325630.2:c.179C>T	chr5.hg19:g.147593570C>T	ENSP00000324870:p.Ala60Val	66.0	0.0		73.0	12.0	NM_205841	E0X656|Q8N5P0	Missense_Mutation	SNP	ENST00000325630.2	hg19	CCDS34268.1	.	.	.	.	.	.	.	.	.	.	C	12.89	2.074108	0.36566	.	.	ENSG00000178172	ENST00000325630	T	0.75154	-0.91	5.75	5.75	0.90469	Proteinase inhibitor I1, Kazal (3);	0.343853	0.30159	N	0.010270	T	0.69967	0.3170	.	.	.	0.38896	D	0.957212	B	0.31705	0.336	B	0.37833	0.259	T	0.66716	-0.5853	8	.	.	.	-2.5242	15.8177	0.78615	0.0:1.0:0.0:0.0	.	60	Q6UWN8	ISK6_HUMAN	V	60	ENSP00000324870:A60V	.	A	+	2	0	SPINK6	147573763	0.961000	0.32948	1.000000	0.80357	0.981000	0.71138	2.917000	0.48821	2.885000	0.99019	0.655000	0.94253	GCC	.	.		0.428	SPINK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373332.1	NM_205841		T	147593570	C	T	147593570	3	4	123	1	0	0	0	0	1	0	0	0	15078	739	26	3	189	3	SPINK6	5	147593570	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	3740310	147593570	33321690	129	20659										
FAT2	2196	hgsc.bcm.edu	37	chr5	150945319	150945319	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccatccaagccactgtcatcGtcctgggcagccactacaat	7	16	1	0	rs542235186	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:150945319G>A	ENST00000261800.5	-	1	3186	c.3174C>T	c.(3172-3174)gaC>gaT	p.D1058D		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1058	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CACTGTCATCGTCCTGGGCAG	0.602													G|||	2	0.000399361	8e-04	0	5008	,	,		14351	0		0	False		,,,				2504	0.001				p.D1058D		Atlas-SNP	.											.	FAT2	465	.	0			c.C3174T						.						60	58	59					5																	150945319		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			GTCATCGTCCTGG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3174C>T	chr5.hg19:g.150945319G>A		155.0	0.0		136.0	20.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1																																																																																			.	.		0.602	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150945319	G	A	150945319	2	1	123	1	0	0	0	0	0	0	0	1	5698	1136	40	1		1	FAT2	5	150945319	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	3351749	150945319	29969941	130	20660										
NMUR2	56923	hgsc.bcm.edu	37	chr5	151775082	151775082	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cactccactcctccacaaagCtgaagaagagtcggtcaatg	8	13	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:151775082C>G	ENST00000255262.3	-	3	1040	c.875G>C	c.(874-876)aGc>aCc	p.S292T	NMUR2_ENST00000518933.1_5'UTR	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	292					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			CTCCACAAAGCTGAAGAAGAG	0.473																																					p.S292T		Atlas-SNP	.											.	NMUR2	111	.	0			c.G875C						.						158	137	144					5																	151775082		2203	4300	6503	SO:0001583	missense	56923	exon3			ACAAAGCTGAAGA	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.875G>C	chr5.hg19:g.151775082C>G	ENSP00000255262:p.Ser292Thr	296.0	0.0		322.0	57.0	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	hg19	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.805392	0.50315	.	.	ENSG00000132911	ENST00000255262	T	0.36699	1.24	5.8	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.62986	0.2473	M	0.84585	2.705	0.54753	D	0.999982	D	0.76494	0.999	D	0.76575	0.988	T	0.67530	-0.5647	10	0.48119	T	0.1	-26.0049	13.8172	0.63299	0.0:0.9271:0.0:0.0728	.	292	Q9GZQ4	NMUR2_HUMAN	T	292	ENSP00000255262:S292T	ENSP00000255262:S292T	S	-	2	0	NMUR2	151755275	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.133000	0.77259	1.451000	0.47736	0.655000	0.94253	AGC	.	.		0.473	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		G	151775082	C	G	151775082	3	3	123	1	0	0	0	0	1	0	0	0	10516	797	28	4	380	4	NMUR2	5	151775082	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	829763	151775082	29140178	131	20661										
EBF1	1879	hgsc.bcm.edu	37	chr5	158250310	158250310	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atggccatccacattgactgTcgtagacaccacgacctgga	9	13	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:158250310T>C	ENST00000313708.6	-	8	934	c.652A>G	c.(652-654)Aca>Gca	p.T218A	EBF1_ENST00000380654.4_Missense_Mutation_p.T195A|EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000517373.1_Missense_Mutation_p.T218A	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	218					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACATTGACTGTCGTAGACACC	0.438			T	HMGA2	lipoma																																p.T218A		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	.	EBF1	110	.	0			c.A652G						.						72	58	63					5																	158250310		2203	4300	6503	SO:0001583	missense	1879	exon8			TGACTGTCGTAGA	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"early B-cell factor"	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.652A>G	chr5.hg19:g.158250310T>C	ENSP00000322898:p.Thr218Ala	93.0	0.0		135.0	20.0	NM_024007	Q8IW11	Missense_Mutation	SNP	ENST00000313708.6	hg19	CCDS4343.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.584095	0.65992	.	.	ENSG00000164330	ENST00000318060;ENST00000313708;ENST00000380654;ENST00000517373	T;T;T	0.47869	0.89;0.83;0.9	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.62502	0.2433	M	0.62016	1.91	0.58432	D	0.999997	B;P;B;B	0.45212	0.003;0.853;0.016;0.215	B;P;B;B	0.56127	0.003;0.792;0.022;0.209	T	0.65487	-0.6156	10	0.72032	D	0.01	-4.0874	15.6488	0.77076	0.0:0.0:0.0:1.0	.	218;204;218;195	A8K0Z7;B4E2U8;Q9UH73;Q9UH73-2	.;.;COE1_HUMAN;.	A	218;218;195;218	ENSP00000322898:T218A;ENSP00000370029:T195A;ENSP00000428020:T218A	ENSP00000322898:T218A	T	-	1	0	EBF1	158182888	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	8.036000	0.88901	2.069000	0.61940	0.533000	0.62120	ACA	.	.		0.438	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		C	158250310	T	C	158250310	3	2	123	1	0	0	0	0	1	0	0	0	4882	1667	58	2	1159	2	EBF1	5	158250310	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	6475228	158250310	22664950	132	20662										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161116665	161116665	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cttatcccaaaagtgaaatcAtatatacgtggaaaaaagga	7	6	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:161116665A>G	ENST00000274545.5	+	6	986	c.553A>G	c.(553-555)Ata>Gta	p.I185V	GABRA6_ENST00000523217.1_Missense_Mutation_p.I175V|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	185					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	AAGTGAAATCATATATACGTG	0.343										TCGA Ovarian(5;0.080)																											p.I185V		Atlas-SNP	.											.	GABRA6	139	.	0			c.A553G						.						45	48	47					5																	161116665		2200	4298	6498	SO:0001583	missense	2559	exon6			GAAATCATATATA		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.553A>G	chr5.hg19:g.161116665A>G	ENSP00000274545:p.Ile185Val	72.0	0.0		78.0	12.0	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	hg19	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	A	3.400	-0.122553	0.06795	.	.	ENSG00000145863	ENST00000274545;ENST00000523217;ENST00000517823;ENST00000523691	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.4	5.4	0.78164	Neurotransmitter-gated ion-channel ligand-binding (3);	0.049657	0.85682	D	0.000000	T	0.56934	0.2019	N	0.04686	-0.185	0.43010	D	0.994543	B	0.16603	0.018	B	0.30943	0.122	T	0.53563	-0.8421	10	0.08599	T	0.76	.	9.8755	0.41200	0.9235:0.0:0.0765:0.0	.	185	Q16445	GBRA6_HUMAN	V	185;175;132;105	ENSP00000274545:I185V;ENSP00000430527:I175V;ENSP00000430212:I132V;ENSP00000427989:I105V	ENSP00000274545:I185V	I	+	1	0	GABRA6	161049243	0.998000	0.40836	1.000000	0.80357	0.988000	0.76386	3.568000	0.53820	2.040000	0.60383	0.528000	0.53228	ATA	.	.		0.343	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			G	161116665	A	G	161116665	3	3	123	1	0	0	0	0	1	0	0	0	6173	217	8	2	575	2	GABRA6	5	161116665	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	2866355	161116665	19798595	133	20663										
ZFP2	80108	hgsc.bcm.edu	37	chr5	178359572	178359572	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atcagtgtggaaaagccttcAttaagaattcatcccttaca	6	9	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:178359572A>G	ENST00000361362.2	+	5	1788	c.1258A>G	c.(1258-1260)Att>Gtt	p.I420V	ZFP2_ENST00000523286.1_Missense_Mutation_p.I420V|ZFP2_ENST00000503510.2_Missense_Mutation_p.I420V|ZFP2_ENST00000520301.1_Missense_Mutation_p.I420V	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	420					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		AAAAGCCTTCATTAAGAATTC	0.418																																					p.I420V		Atlas-SNP	.											.	ZFP2	70	.	0			c.A1258G						.						63	66	65					5																	178359572		2203	4300	6503	SO:0001583	missense	80108	exon5			GCCTTCATTAAGA	AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"Zinc fingers, C2H2-type"	26138	protein-coding gene	gene with protein product			"zinc finger protein 2 homolog (mouse)"				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.1258A>G	chr5.hg19:g.178359572A>G	ENSP00000354453:p.Ile420Val	50.0	0.0		52.0	7.0	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Missense_Mutation	SNP	ENST00000361362.2	hg19	CCDS4440.1	.	.	.	.	.	.	.	.	.	.	a	12.02	1.811931	0.32053	.	.	ENSG00000198939	ENST00000361362;ENST00000520301;ENST00000523286;ENST00000503510	T;T;T;T	0.05717	3.4;3.4;3.4;3.4	4.85	4.85	0.62838	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.32719	N	0.005737	T	0.02807	0.0084	N	0.03238	-0.38	0.26509	N	0.974633	P	0.45283	0.855	B	0.38225	0.268	T	0.36672	-0.9738	10	0.51188	T	0.08	-11.7412	7.8747	0.29586	0.816:0.0:0.0:0.184	.	420	Q6ZN57	ZFP2_HUMAN	V	420	ENSP00000354453:I420V;ENSP00000430980:I420V;ENSP00000430531:I420V;ENSP00000438114:I420V	ENSP00000354453:I420V	I	+	1	0	ZFP2	178292178	0.000000	0.05858	1.000000	0.80357	0.999000	0.98932	0.602000	0.24134	2.018000	0.59344	0.533000	0.62120	ATT	.	.		0.418	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613		G	178359572	A	G	178359572	3	3	123	1	0	0	0	0	1	0	0	0	17656	217	8	2	1260	2	ZFP2	5	178359572	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	17242907	178359572	2555688	134	20664										
FOXC1	2296	hgsc.bcm.edu	37	chr6	1612242	1612242	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gaggatcggcttgaacaactCtccagtgaacgggaatagta	12	8	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:1612242C>T	ENST00000380874.2	+	1	1562	c.1562C>T	c.(1561-1563)tCt>tTt	p.S521F		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	521					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		TTGAACAACTCTCCAGTGAAC	0.602																																					p.S521F	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.C1562T						.						63	46	52					6																	1612242		2201	4299	6500	SO:0001583	missense	2296	exon1			ACAACTCTCCAGT	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"Forkhead boxes"	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.1562C>T	chr6.hg19:g.1612242C>T	ENSP00000370256:p.Ser521Phe	137.0	0.0		238.0	21.0	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Missense_Mutation	SNP	ENST00000380874.2	hg19	CCDS4473.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.672562	0.67928	.	.	ENSG00000054598	ENST00000380874	D	0.82433	-1.61	3.52	3.52	0.40303	.	0.000000	0.64402	U	0.000004	D	0.83635	0.5297	L	0.39245	1.2	0.58432	D	0.999995	D	0.65815	0.995	D	0.75484	0.986	D	0.86117	0.1566	10	0.72032	D	0.01	.	14.0047	0.64456	0.0:1.0:0.0:0.0	.	521	Q12948	FOXC1_HUMAN	F	521	ENSP00000370256:S521F	ENSP00000370256:S521F	S	+	2	0	FOXC1	1557241	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	6.548000	0.73896	1.828000	0.53243	0.448000	0.29417	TCT	.	.		0.602	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			T	1612242	C	T	1612242	3	4	123	1	0	0	0	0	1	0	0	0	6002	913	32	3	1564	3	FOXC1	6	1612242	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		1612242	169502825	135	20665										
NRSN1	140767	hgsc.bcm.edu	37	chr6	24146149	24146149	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cactttgtccagggttcaaaAtgtccagcctctactggcaa	8	12	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:24146149A>G	ENST00000378491.4	+	4	864	c.563A>G	c.(562-564)aAt>aGt	p.N188S		NM_080723.4	NP_542454.3			neurensin 1											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	22						AGGGTTCAAAATGTCCAGCCT	0.483																																					p.N188S		Atlas-SNP	.											.	NRSN1	31	.	0			c.A563G						.						58	65	63					6																	24146149		2203	4300	6503	SO:0001583	missense	140767	exon4			TTCAAAATGTCCA	AF418980	CCDS4549.1	6p22.1	2008-02-05	2006-07-04	2006-07-04	ENSG00000152954	ENSG00000152954			17881	protein-coding gene	gene with protein product			"vesicular membrane protein p24"	VMP		12463420	Standard	NM_080723		Approved	p24	uc010jpq.1	Q8IZ57	OTTHUMG00000016406	ENST00000378491.4:c.563A>G	chr6.hg19:g.24146149A>G	ENSP00000367752:p.Asn188Ser	78.0	0.0		119.0	14.0	NM_080723		Missense_Mutation	SNP	ENST00000378491.4	hg19	CCDS4549.1	.	.	.	.	.	.	.	.	.	.	A	14.46	2.540610	0.45280	.	.	ENSG00000152954	ENST00000378491	T	0.19250	2.16	5.35	4.19	0.49359	.	0.042896	0.85682	N	0.000000	T	0.08088	0.0202	L	0.42245	1.32	0.80722	D	1	B	0.21071	0.051	B	0.20955	0.032	T	0.07520	-1.0768	10	0.29301	T	0.29	-9.71	11.1828	0.48638	0.9276:0.0:0.0724:0.0	.	188	Q8IZ57	NRSN1_HUMAN	S	188	ENSP00000367752:N188S	ENSP00000367752:N188S	N	+	2	0	NRSN1	24254128	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	5.652000	0.67959	0.866000	0.35629	0.528000	0.53228	AAT	.	.		0.483	NRSN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043866.1	NM_080723		G	24146149	A	G	24146149	3	3	123	1	0	0	0	0	1	0	0	0	10671	101	4	2	569	2	NRSN1	6	24146149	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	22533907	24146149	146968918	136	20666										
NEU1	4758	hgsc.bcm.edu	37	chr6	31827993	31827993	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcagtggcagtggtagttgtTctggtttcgggcattgatga	16	5	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:31827993T>C	ENST00000375631.4	-	5	976	c.847A>G	c.(847-849)Aac>Gac	p.N283D		NM_000434.3	NP_000425.1	Q99519	NEUR1_HUMAN	sialidase 1 (lysosomal sialidase)	283					glycosphingolipid metabolic process (GO:0006687)|lipid catabolic process (GO:0016042)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	10					Oseltamivir(DB00198)	TGGTAGTTGTTCTGGTTTCGG	0.577																																					p.N283D		Atlas-SNP	.											.	NEU1	21	.	0			c.A847G						.						88	71	77					6																	31827993		1511	2709	4220	SO:0001583	missense	4758	exon5			AGTTGTTCTGGTT	AF040958	CCDS4723.1	6p21	2012-10-02			ENSG00000204386	ENSG00000204386	3.2.1.18		7758	protein-coding gene	gene with protein product		608272		NEU		9054950	Standard	NM_000434		Approved		uc003nxq.4	Q99519	OTTHUMG00000031284	ENST00000375631.4:c.847A>G	chr6.hg19:g.31827993T>C	ENSP00000364782:p.Asn283Asp	219.0	0.0		312.0	39.0	NM_000434		Missense_Mutation	SNP	ENST00000375631.4	hg19	CCDS4723.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.178532	0.38511	.	.	ENSG00000204386	ENST00000375631	D	0.83591	-1.74	5.1	5.1	0.69264	Neuraminidase (2);	0.047002	0.85682	D	0.000000	T	0.73377	0.3579	L	0.39245	1.2	0.45183	D	0.998191	P	0.51147	0.942	P	0.54965	0.765	T	0.71307	-0.4632	10	0.13470	T	0.59	-18.8045	8.4812	0.33043	0.1729:0.0:0.0:0.8271	.	283	Q99519	NEUR1_HUMAN	D	283	ENSP00000364782:N283D	ENSP00000364782:N283D	N	-	1	0	NEU1	31935972	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	5.374000	0.66167	2.270000	0.75569	0.460000	0.39030	AAC	.	.		0.577	NEU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076616.2			C	31827993	T	C	31827993	3	2	123	1	0	0	0	0	1	0	0	0	10350	1783	62	2	408	2	NEU1	6	31827993	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	7681844	31827993	139287074	137	20667										
C2	717	hgsc.bcm.edu	37	chr6	31911759	31911759	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gagacctcaaggcagcacctGtagggaccatggtgagtgct	14	10	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:31911759G>A	ENST00000299367.5	+	14	2075	c.1799G>A	c.(1798-1800)tGt>tAt	p.C600Y	C2_ENST00000469372.1_Missense_Mutation_p.C354Y|C2_ENST00000452323.2_Missense_Mutation_p.C386Y|CFB_ENST00000477310.1_Missense_Mutation_p.C371Y|CFB_ENST00000425368.2_5'Flank|C2_ENST00000442278.2_Missense_Mutation_p.C468Y|CFB_ENST00000556679.1_Missense_Mutation_p.C447Y|CFB_ENST00000456570.1_Missense_Mutation_p.C447Y|C2_ENST00000468407.1_3'UTR	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	600	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		GGCAGCACCTGTAGGGACCAT	0.612																																					p.C600Y		Atlas-SNP	.											.	C2	50	.	0			c.G1799A						.						55	55	55					6																	31911759		1509	2707	4216	SO:0001583	missense	717	exon14			GCACCTGTAGGGA		CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"Complement system"	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.1799G>A	chr6.hg19:g.31911759G>A	ENSP00000299367:p.Cys600Tyr	110.0	0.0		135.0	19.0	NM_000063	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	hg19	CCDS4728.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.3|21.3	4.122491|4.122491	0.77436|0.77436	.|.	.|.	ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000243649;ENSG00000244255;ENSG00000244255|ENSG00000166278	ENST00000469372;ENST00000497706;ENST00000452323;ENST00000299367;ENST00000375493;ENST00000442278;ENST00000556679;ENST00000456570;ENST00000477310|ENST00000383177	T;T;T;T;T;T;T;T|.	0.35048|.	1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33|.	5.21|5.21	5.21|5.21	0.72293|0.72293	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);|.	0.000000|.	0.41194|.	D|.	0.000935|.	T|T	0.75824|0.75824	0.3902|0.3902	M|M	0.88512|0.88512	2.96|2.96	0.39187|0.39187	D|D	0.962896|0.962896	D;D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D;D|.	0.97110|.	1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0|.	T|T	0.80605|0.80605	-0.1308|-0.1308	10|5	0.87932|.	D|.	0|.	-14.3006|-14.3006	14.2644|14.2644	0.66107|0.66107	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	447;571;386;354;468;285;468;600;387|.	B4E1Z4;B4DV48;B4DPF3;B4DQI1;E9PFN7;F8VNY6;B4DV20;P06681;E9PDZ0|.	.;.;.;.;.;.;.;CO2_HUMAN;.|.	Y|I	354;387;386;600;285;468;447;447;371|374	ENSP00000418923:C354Y;ENSP00000417482:C387Y;ENSP00000392322:C386Y;ENSP00000299367:C600Y;ENSP00000395683:C468Y;ENSP00000451848:C447Y;ENSP00000410815:C447Y;ENSP00000418996:C371Y|.	ENSP00000299367:C600Y|.	C|V	+|+	2|1	0|0	CFB;C2;XXbac-BPG116M5.17|C2	32019738|32019738	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.978000|0.978000	0.69477|0.69477	5.559000|5.559000	0.67326|0.67326	2.453000|2.453000	0.82957|0.82957	0.563000|0.563000	0.77884|0.77884	TGT|GTA	.	.		0.612	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9			A	31911759	G	A	31911759	3	1	123	1	0	0	0	0	1	0	0	0	2076	1377	48	3	1930	3	C2	6	31911759	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	83766	31911759	139203308	138	20668										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32188291	32188291	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tccaggttctcctcacagctTgtgccgccccagccactcac	7	19	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:32188291T>A	ENST00000375023.3	-	6	1188	c.1050A>T	c.(1048-1050)acA>acT	p.T350T		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	350	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CCTCACAGCTTGTGCCGCCCC	0.617																																					p.T350T		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A1050T						.						101	101	101					6																	32188291		1511	2709	4220	SO:0001819	synonymous_variant	4855	exon6			ACAGCTTGTGCCG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.1050A>T	chr6.hg19:g.32188291T>A		60.0	0.0		125.0	15.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	hg19	CCDS34420.1																																																																																			.	.		0.617	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32188291	T	A	32188291	2	1	123	1	0	0	0	0	0	0	0	1	10560	1799	63	4		4	NOTCH4	6	32188291	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	276532	32188291	138926776	139	20669										
KCTD20	222658	hgsc.bcm.edu	37	chr6	36449534	36449534	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aatgggggaggaatattcccAaagtaggagcttctggcatg	14	6	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:36449534A>G	ENST00000373731.2	+	6	1245	c.854A>G	c.(853-855)cAa>cGa	p.Q285R	KCTD20_ENST00000544295.1_Missense_Mutation_p.Q39R|KCTD20_ENST00000536244.1_Missense_Mutation_p.Q140R|KCTD20_ENST00000449081.2_Missense_Mutation_p.Q119R|KCTD20_ENST00000474988.1_3'UTR	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	285					protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						GAATATTCCCAAAGTAGGAGC	0.478																																					p.Q285R		Atlas-SNP	.											.	KCTD20	37	.	0			c.A854G						.						78	73	75					6																	36449534		2203	4300	6503	SO:0001583	missense	222658	exon6			ATTCCCAAAGTAG	BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"chromosome 6 open reading frame 69", "potassium channel tetramerisation domain containing 20"	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.854A>G	chr6.hg19:g.36449534A>G	ENSP00000362836:p.Gln285Arg	101.0	0.0		170.0	23.0	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	hg19	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018039	0.75275	.	.	ENSG00000112078	ENST00000373731;ENST00000544295;ENST00000449081;ENST00000536244	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.88108	0.6348	M	0.61703	1.905	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.75484	0.986;0.968	D	0.88993	0.3416	10	0.62326	D	0.03	-19.6228	16.5764	0.84681	1.0:0.0:0.0:0.0	.	119;285	Q7Z5Y7-2;Q7Z5Y7	.;KCD20_HUMAN	R	285;39;119;140	ENSP00000362836:Q285R;ENSP00000440150:Q39R;ENSP00000412205:Q119R;ENSP00000439118:Q140R	ENSP00000362836:Q285R	Q	+	2	0	KCTD20	36557512	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.287000	0.95975	2.371000	0.80710	0.533000	0.62120	CAA	.	.		0.478	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562		G	36449534	A	G	36449534	3	3	123	1	0	0	0	0	1	0	0	0	8117	130	5	2	872	2	KCTD20	6	36449534	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	4261243	36449534	134665533	140	20670										
CPNE5	57699	hgsc.bcm.edu	37	chr6	36730726	36730726	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gaattggctctgcccacgggCcagctcccggtaactggtgg	14	13	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:36730726C>T	ENST00000244751.2	-	12	1447	c.823G>A	c.(823-825)Gcc>Acc	p.A275T		NM_020939.1	NP_065990.1	Q9HCH3	CPNE5_HUMAN	copine V	275						extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(4)|liver(1)|lung(9)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						TGCCCACGGGCCAGCTCCCGG	0.587																																					p.A275T		Atlas-SNP	.											.	CPNE5	56	.	0			c.G823A						.						146	116	126					6																	36730726		2203	4300	6503	SO:0001583	missense	57699	exon12			CACGGGCCAGCTC	H09181	CCDS4825.1	6p21.2	2010-05-28			ENSG00000124772	ENSG00000124772			2318	protein-coding gene	gene with protein product		604209				9430674	Standard	NM_020939		Approved	CPN5, COPN5, KIAA1599	uc003omr.1	Q9HCH3	OTTHUMG00000014602	ENST00000244751.2:c.823G>A	chr6.hg19:g.36730726C>T	ENSP00000244751:p.Ala275Thr	123.0	0.0		166.0	46.0	NM_020939	Q7Z6C8	Missense_Mutation	SNP	ENST00000244751.2	hg19	CCDS4825.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.057349	0.36277	.	.	ENSG00000124772	ENST00000244751	T	0.39406	1.08	5.36	5.36	0.76844	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.166115	0.51477	D	0.000082	T	0.10294	0.0252	N	0.04880	-0.145	0.80722	D	1	B	0.09022	0.002	B	0.11329	0.006	T	0.14200	-1.0481	10	0.18276	T	0.48	.	11.9785	0.53107	0.1732:0.8268:0.0:0.0	.	275	Q9HCH3	CPNE5_HUMAN	T	275	ENSP00000244751:A275T	ENSP00000244751:A275T	A	-	1	0	CPNE5	36838704	0.859000	0.29813	1.000000	0.80357	0.982000	0.71751	0.336000	0.19823	2.693000	0.91896	0.313000	0.20887	GCC	.	.		0.587	CPNE5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040351.1	NM_020939		T	36730726	C	T	36730726	3	4	123	1	0	0	0	0	1	0	0	0	3817	739	26	3	998	3	CPNE5	6	36730726	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	281192	36730726	134384341	141	20671										
MDGA1	266727	hgsc.bcm.edu	37	chr6	37606362	37606362	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	catgggcctgctgccacacaTtgcccttattgccactgaga	9	14	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:37606362T>C	ENST00000434837.3	-	15	3796	c.2618A>G	c.(2617-2619)aAt>aGt	p.N873S	MDGA1_ENST00000297153.7_Missense_Mutation_p.N877S|MDGA1_ENST00000505425.1_Missense_Mutation_p.N873S	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	873	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						CTGCCACACATTGCCCTTATT	0.652																																					p.N873S		Atlas-SNP	.											.	MDGA1	104	.	0			c.A2618G						.						51	57	55					6																	37606362		2046	4181	6227	SO:0001583	missense	266727	exon15			CACACATTGCCCT	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.2618A>G	chr6.hg19:g.37606362T>C	ENSP00000402584:p.Asn873Ser	73.0	0.0		109.0	9.0	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	hg19	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	T	19.73	3.881862	0.72294	.	.	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425	T;T;T	0.02050	4.48;4.48;4.48	5.04	5.04	0.67666	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.234553	0.28600	N	0.014779	T	0.01730	0.0055	L	0.43598	1.365	0.25207	N	0.990003	D;P	0.54964	0.969;0.625	P;B	0.47673	0.554;0.353	T	0.43589	-0.9382	10	0.56958	D	0.05	.	13.0768	0.59091	0.0:0.0:0.0:1.0	.	873;873	Q8NFP4-2;Q8NFP4	.;MDGA1_HUMAN	S	873;877;873	ENSP00000402584:N873S;ENSP00000297153:N877S;ENSP00000422042:N873S	ENSP00000297153:N877S	N	-	2	0	MDGA1	37714340	0.975000	0.34042	0.999000	0.59377	0.997000	0.91878	2.341000	0.43983	2.017000	0.59298	0.529000	0.55759	AAT	.	.		0.652	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			C	37606362	T	C	37606362	3	2	123	1	0	0	0	0	1	0	0	0	9415	1493	52	2	261	2	MDGA1	6	37606362	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	875636	37606362	133508705	142	20672										
TREML4	285852	hgsc.bcm.edu	37	chr6	41196565	41196565	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcctggtgtcagcagacatcTccaagtcggtgtaccttact	9	12	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:41196565T>C	ENST00000341495.2	+	2	281	c.177T>C	c.(175-177)tcT>tcC	p.S59S	TREML4_ENST00000448827.2_Silent_p.S59S	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	59	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					AGCAGACATCTCCAAGTCGGT	0.522																																					p.S59S		Atlas-SNP	.											.	TREML4	25	.	0			c.T177C						.						90	84	86					6																	41196565		2203	4300	6503	SO:0001819	synonymous_variant	285852	exon2			GACATCTCCAAGT	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"Immunoglobulin superfamily / V-set domain containing"	30807	protein-coding gene	gene with protein product	"TREM like transcript 4"	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.177T>C	chr6.hg19:g.41196565T>C		80.0	0.0		125.0	17.0	NM_198153	B7ZL92	Silent	SNP	ENST00000341495.2	hg19	CCDS34446.1																																																																																			.	.		0.522	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2			C	41196565	T	C	41196565	2	2	123	1	0	0	0	0	0	0	0	1	16489	1538	54	2		2	TREML4	6	41196565	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	3590203	41196565	129918502	143	20673										
RSPH9	221421	hgsc.bcm.edu	37	chr6	43623341	43623341	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcttggtgtctgtcattgacCagattgacaaggctgtggcc	13	9	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:43623341C>G	ENST00000372163.4	+	3	489	c.436C>G	c.(436-438)Cag>Gag	p.Q146E	RSPH9_ENST00000372165.4_Intron	NM_152732.4	NP_689945.2	Q9H1X1	RSPH9_HUMAN	radial spoke head 9 homolog (Chlamydomonas)	146					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)				NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						TGTCATTGACCAGATTGACAA	0.607									Kartagener syndrome																												p.Q146E		Atlas-SNP	.											.	RSPH9	60	.	0			c.C436G						.						133	132	132					6																	43623341		2203	4300	6503	SO:0001583	missense	221421	exon3	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATTGACCAGATTG	AK055407	CCDS4905.1, CCDS55005.1	6p21.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000172426	ENSG00000172426			21057	protein-coding gene	gene with protein product		612648	"mitochondrial ribosomal protein S18A-like 1", "chromosome 6 open reading frame 206"	MRPS18AL1, C6orf206		19200523	Standard	NM_152732		Approved	FLJ30845, CILD12	uc003ovx.2	Q9H1X1	OTTHUMG00000014746	ENST00000372163.4:c.436C>G	chr6.hg19:g.43623341C>G	ENSP00000361236:p.Gln146Glu	69.0	0.0		114.0	9.0	NM_152732	A8K5T4|Q96NH9	Missense_Mutation	SNP	ENST00000372163.4	hg19	CCDS4905.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.69|14.69	2.610405|2.610405	0.46527|0.46527	.|.	.|.	ENSG00000172426|ENSG00000172426	ENST00000417236|ENST00000372163;ENST00000372154	.|T	.|0.39997	.|1.05	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	.|.	.|.	.|.	.|.	T|T	0.20941|0.20941	0.0504|0.0504	L|L	0.40543|0.40543	1.245|1.245	0.35723|0.35723	D|D	0.817357|0.817357	.|P	.|0.50369	.|0.934	.|P	.|0.45167	.|0.472	T|T	0.02813|0.02813	-1.1107|-1.1107	5|9	.|0.10111	.|T	.|0.7	.|.	12.2605|12.2605	0.54647|0.54647	0.1697:0.8303:0.0:0.0|0.1697:0.8303:0.0:0.0	.|.	.|146	.|Q9H1X1	.|RSPH9_HUMAN	R|E	70|146;114	.|ENSP00000361236:Q146E	.|ENSP00000361227:Q114E	P|Q	+|+	2|1	0|0	RSPH9|RSPH9	43731319|43731319	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	2.918000|2.918000	0.48829|0.48829	2.672000|2.672000	0.90937|0.90937	0.591000|0.591000	0.81541|0.81541	CCA|CAG	.	.		0.607	RSPH9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040690.1	NM_152732		G	43623341	C	G	43623341	3	3	123	1	0	0	0	0	1	0	0	0	13723	595	21	4	446	4	RSPH9	6	43623341	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	2426776	43623341	127491726	144	20674										
GPR116	221395	hgsc.bcm.edu	37	chr6	46823751	46823751	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttaaatctccttgatattggAgaactcatagaaaacacagg	7	7	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:46823751A>G	ENST00000283296.7	-	20	4209	c.3921T>C	c.(3919-3921)tcT>tcC	p.S1307S	GPR116_ENST00000545669.1_Silent_p.S736S|GPR116_ENST00000265417.7_Silent_p.S1307S|GPR116_ENST00000362015.4_Silent_p.S1287S|GPR116_ENST00000456426.2_Silent_p.S1165S	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	1307					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			TTGATATTGGAGAACTCATAG	0.423																																					p.S1307S	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.T3921C						.						56	50	52					6																	46823751		2203	4296	6499	SO:0001819	synonymous_variant	221395	exon20			TATTGGAGAACTC	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.3921T>C	chr6.hg19:g.46823751A>G		380.0	0.0		547.0	75.0	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	hg19	CCDS4919.1																																																																																			.	.		0.423	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		G	46823751	A	G	46823751	2	3	123	1	0	0	0	0	0	0	0	1	6641	291	11	2		2	GPR116	6	46823751	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	3200410	46823751	124291316	145	20675										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51609291	51609291	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atccttgaagagatattttcTtggacttgcacagtctaatt	7	7	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:51609291T>C	ENST00000371117.3	-	60	10323	c.10048A>G	c.(10048-10050)Aga>Gga	p.R3350G	PKHD1_ENST00000340994.4_Missense_Mutation_p.R3350G	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3350					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGATATTTTCTTGGACTTGCA	0.423																																					p.R3350G		Atlas-SNP	.											.	PKHD1	927	.	0			c.A10048G						.						91	89	89					6																	51609291		2203	4300	6503	SO:0001583	missense	5314	exon60			ATTTTCTTGGACT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10048A>G	chr6.hg19:g.51609291T>C	ENSP00000360158:p.Arg3350Gly	132.0	0.0		176.0	25.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	10.92	1.488143	0.26686	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87966	-2.11;-2.32	5.21	2.81	0.32909	.	0.573790	0.17845	N	0.160070	T	0.66982	0.2845	L	0.41824	1.3	0.18873	N	0.999988	B;B;B	0.14438	0.003;0.01;0.001	B;B;B	0.12156	0.002;0.007;0.002	T	0.60637	-0.7224	10	0.51188	T	0.08	.	7.7127	0.28688	0.0:0.1666:0.0:0.8334	.	3350;3350;3350	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	G	3350	ENSP00000360158:R3350G;ENSP00000341097:R3350G	ENSP00000341097:R3350G	R	-	1	2	PKHD1	51717250	0.976000	0.34144	0.193000	0.23327	0.673000	0.39480	2.284000	0.43478	0.410000	0.25675	0.528000	0.53228	AGA	.	.		0.423	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		C	51609291	T	C	51609291	3	2	123	1	0	0	0	0	1	0	0	0	11980	1617	56	2	2247	2	PKHD1	6	51609291	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	4785540	51609291	119505776	146	20676										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51917941	51917941	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cccgtctcctgggccagaggGagaaggttgatctgatgaac	14	10	2	5			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:51917941G>A	ENST00000371117.3	-	21	2348	c.2073C>T	c.(2071-2073)ctC>ctT	p.L691L	PKHD1_ENST00000340994.4_Silent_p.L691L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	691					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GGGCCAGAGGGAGAAGGTTGA	0.522																																					p.L691L		Atlas-SNP	.											.	PKHD1	927	.	0			c.C2073T						.						74	75	75					6																	51917941		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon21			CAGAGGGAGAAGG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.2073C>T	chr6.hg19:g.51917941G>A		86.0	0.0		142.0	13.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.		0.522	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51917941	G	A	51917941	2	1	123	1	0	0	0	0	0	0	0	1	11980	1161	41	3		3	PKHD1	6	51917941	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	308650	51917941	119197126	147	20677										
LGSN	51557	hgsc.bcm.edu	37	chr6	63990576	63990576	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggcaatgtaattatatttccTtgccacttctttgacacctg	6	10	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:63990576T>A	ENST00000370657.4	-	4	913	c.880A>T	c.(880-882)Agg>Tgg	p.R294W	LGSN_ENST00000370658.5_Intron			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	294					glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)			NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TTATATTTCCTTGCCACTTCT	0.413																																					p.R294W		Atlas-SNP	.											.	LGSN	82	.	0			c.A880T						.						58	57	57					6																	63990576		2203	4300	6503	SO:0001583	missense	51557	exon4			ATTTCCTTGCCAC	AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"glutamate-ammonia ligase (glutamine synthetase) domain containing 1"	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.880A>T	chr6.hg19:g.63990576T>A	ENSP00000359691:p.Arg294Trp	104.0	0.0		145.0	17.0	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	hg19	CCDS4964.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.258331	0.39896	.	.	ENSG00000146166	ENST00000370657	D	0.86769	-2.17	5.62	4.44	0.53790	Glutamine synthetase, catalytic domain (1);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.083576	0.85682	D	0.000000	D	0.85596	0.5733	M	0.68593	2.085	0.80722	D	1	P	0.40197	0.706	P	0.48815	0.591	D	0.86624	0.1881	10	0.87932	D	0	-25.0044	12.1	0.53778	0.0:0.0:0.1438:0.8562	.	294	Q5TDP6	LGSN_HUMAN	W	294	ENSP00000359691:R294W	ENSP00000359691:R294W	R	-	1	2	LGSN	64048535	1.000000	0.71417	0.981000	0.43875	0.007000	0.05969	4.968000	0.63728	0.936000	0.37367	0.533000	0.62120	AGG	.	.		0.413	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571		A	63990576	T	A	63990576	3	1	123	1	0	0	0	0	1	0	0	0	8768	1608	56	4	653	4	LGSN	6	63990576	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	12072635	63990576	107124491	148	20678										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75884975	75884975	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccccactccaagataatttcAtagtagacgtcgtagggtca	8	11	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:75884975A>G	ENST00000322507.8	-	13	2798	c.2489T>C	c.(2488-2490)aTg>aCg	p.M830T	COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Missense_Mutation_p.M830T|COL12A1_ENST00000416123.2_Missense_Mutation_p.M830T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	830	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						AGATAATTTCATAGTAGACGT	0.413																																					p.M830T		Atlas-SNP	.											.	COL12A1	385	.	0			c.T2489C						.						125	118	120					6																	75884975		1864	4083	5947	SO:0001583	missense	1303	exon13			AATTTCATAGTAG	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2489T>C	chr6.hg19:g.75884975A>G	ENSP00000325146:p.Met830Thr	166.0	0.0		172.0	31.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.869910	0.51588	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.53640	0.61;0.61;0.61	5.79	5.79	0.91817	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.148812	0.48286	D	0.000196	T	0.36358	0.0964	M	0.62266	1.93	0.47153	D	0.999338	B	0.20887	0.049	B	0.23150	0.044	T	0.36696	-0.9737	10	0.72032	D	0.01	.	16.1267	0.81400	1.0:0.0:0.0:0.0	.	830	Q99715	COCA1_HUMAN	T	830	ENSP00000325146:M830T;ENSP00000412864:M830T;ENSP00000421216:M830T	ENSP00000325146:M830T	M	-	2	0	COL12A1	75941695	1.000000	0.71417	0.996000	0.52242	0.771000	0.43674	8.962000	0.93254	2.205000	0.71048	0.455000	0.32223	ATG	.	.		0.413	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		G	75884975	A	G	75884975	3	3	123	1	0	0	0	0	1	0	0	0	3671	217	8	2	6918	2	COL12A1	6	75884975	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	11894399	75884975	95230092	149	20679										
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90581017	90581017	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttcctcctcagaaatgatgaCcgggaaattttattggagtg	10	7	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:90581017C>T	ENST00000551025.1	+	0	7239									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GAAATGATGACCGGGAAATTT	0.368																																					p.D1934D	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.C5802T						.						74	71	72					6																	90581017		1798	4066	5864			9994	exon9			TGATGACCGGGAA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90581017C>T		161.0	0.0		121.0	23.0	NM_001137667		Silent	SNP	ENST00000551025.1	hg19																																																																																				.	.		0.368	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		T	90581017	C	T	90581017	1	4	123	0	1	0	0	0	0	0	0	0	2680	506	18	3		3	CASP8AP2	6	90581017	RNA	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	14696042	90581017	80534050	150	20680										
POU3F2	5454	hgsc.bcm.edu	37	chr6	99283906	99283907	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctcggcccaggagatcacctCcctcgcggacagcttacagc							TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:99283906_99283907CC>AA	ENST00000328345.5	+	1	1327_1328	c.1157_1158CC>AA	c.(1156-1158)tCC>tAA	p.S386*		NM_005604.3	NP_005595.2	P20265	PO3F2_HUMAN	POU class 3 homeobox 2	386					astrocyte development (GO:0014002)|cellular response to organic substance (GO:0071310)|cerebral cortex radially oriented cell migration (GO:0021799)|epidermis development (GO:0008544)|forebrain ventricular zone progenitor cell division (GO:0021869)|hypothalamus cell differentiation (GO:0021979)|myelination in peripheral nervous system (GO:0022011)|neurohypophysis development (GO:0021985)|neuron differentiation (GO:0030182)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of axonogenesis (GO:0050770)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	identical protein binding (GO:0042802)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(5)	10		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0355)		GAGATCACCTCCCTCGCGGACA	0.579																																					p.S386Y|p.S386S		Atlas-SNP	.											.	POU3F2	33	.	0			c.C1157A|c.C1158A						.																																			SO:0001587	stop_gained	5454	exon1			TCACCTCCCTCGC|CACCTCCCTCGCG	Z11933	CCDS5040.1	6q16.2	2011-06-20	2007-07-13		ENSG00000184486	ENSG00000184486		"Homeoboxes / POU class"	9215	protein-coding gene	gene with protein product		600494	"POU domain class 3, transcription factor 2"	OTF7		8441633	Standard	NM_005604		Approved	POUF3, BRN2, OCT7	uc003ppe.3	P20265	OTTHUMG00000015258	Exception_encountered	chr6.hg19:g.99283906_99283907delinsAA	ENSP00000329170:p.Ser386*	78.0	0.0		129.0|126.0	48.0|46.0	NM_005604	Q14960|Q86V54|Q9UJL0	Missense_Mutation|Silent	SNP	ENST00000328345.5	hg19	CCDS5040.1																																																																																			.	.		0.579	POU3F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041586.2			AA	99283907	CC	AA	99283906	4	1	123	1	0	0	0	0	0	1	0	0	12284	855	30	3	1159	3	POU3F2	6	99283906	Nonsense_Mutation	DNP	CC	TCGA-DD-A3A9-01A-11D-A25V-10	8702889	99283906	71831161	151	20681										
ASCC3	10973	hgsc.bcm.edu	37	chr6	100960788	100960788	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tggcaagtgagataagaaatTccatgcctaaataaaaagag	9	5	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:100960788T>A	ENST00000369162.2	-	40	6426	c.6082A>T	c.(6082-6084)Aat>Tat	p.N2028Y		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	2028	SEC63 2.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GATAAGAAATTCCATGCCTAA	0.343																																					p.N2028Y		Atlas-SNP	.											.	ASCC3	205	.	0			c.A6082T						.						62	55	57					6																	100960788		2203	4300	6503	SO:0001583	missense	10973	exon40			AGAAATTCCATGC	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.6082A>T	chr6.hg19:g.100960788T>A	ENSP00000358159:p.Asn2028Tyr	74.0	0.0		118.0	17.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.300595	0.60195	.	.	ENSG00000112249	ENST00000369162	T	0.61392	0.11	5.74	5.74	0.90152	Sec63 domain (3);	0.335977	0.32578	N	0.005906	T	0.63010	0.2475	M	0.77820	2.39	0.80722	D	1	P	0.48834	0.916	P	0.54431	0.752	T	0.69993	-0.4994	10	0.72032	D	0.01	.	12.5418	0.56174	0.0:0.0:0.1388:0.8612	.	2028	Q8N3C0	HELC1_HUMAN	Y	2028	ENSP00000358159:N2028Y	ENSP00000358159:N2028Y	N	-	1	0	ASCC3	101067509	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.136000	0.42121	2.198000	0.70561	0.533000	0.62120	AAT	.	.		0.343	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		A	100960788	T	A	100960788	3	1	123	1	0	0	0	0	1	0	0	0	1033	1783	62	4	538	4	ASCC3	6	100960788	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	1676882	100960788	70154279	152	20682										
AIM1	202	hgsc.bcm.edu	37	chr6	106987360	106987360	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	accctgacttgtccttctggGatacagaagaagcgtacatt	9	10	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:106987360G>A	ENST00000369066.3	+	7	4064	c.3577G>A	c.(3577-3579)Gat>Aat	p.D1193N	AIM1_ENST00000535438.1_5'Flank	NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GTCCTTCTGGGATACAGAAGA	0.443																																					p.D1193N		Atlas-SNP	.											.	AIM1	161	.	0			c.G3577A						.						141	134	137					6																	106987360		2203	4300	6503	SO:0001583	missense	202	exon7			TTCTGGGATACAG	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.3577G>A	chr6.hg19:g.106987360G>A	ENSP00000358062:p.Asp1193Asn	133.0	0.0		176.0	22.0	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.357776	0.41801	.	.	ENSG00000112297	ENST00000369066	T	0.75589	-0.95	5.66	1.95	0.26073	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.521950	0.23966	N	0.042805	T	0.19485	0.0468	N	0.00707	-1.245	0.80722	D	1	B	0.09022	0.002	B	0.11329	0.006	T	0.05289	-1.0894	10	0.20519	T	0.43	.	8.5611	0.33511	0.357:0.0:0.643:0.0	.	1193	Q9Y4K1	AIM1_HUMAN	N	1193	ENSP00000358062:D1193N	ENSP00000358062:D1193N	D	+	1	0	AIM1	107094053	1.000000	0.71417	0.684000	0.30055	0.964000	0.63967	3.315000	0.51951	0.342000	0.23796	0.655000	0.94253	GAT	.	.		0.443	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			A	106987360	G	A	106987360	3	1	123	1	0	0	0	0	1	0	0	0	430	1174	41	3	3603	3	AIM1	6	106987360	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	6026572	106987360	64127707	153	20683										
OSTM1	28962	hgsc.bcm.edu	37	chr6	108372335	108372335	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acagactactcagagttttgTatgcttcacggcagtttttg	9	8	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:108372335T>A	ENST00000193322.3	-	4	768	c.683A>T	c.(682-684)tAc>tTc	p.Y228F		NM_014028.3	NP_054747.2	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1	228					ion transmembrane transport (GO:0034220)|osteoclast differentiation (GO:0030316)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)		CAGAGTTTTGTATGCTTCACG	0.348																																					p.Y228F	Melanoma(162;1427 1909 3096 17430 21396)	Atlas-SNP	.											.	OSTM1	22	.	0			c.A683T						.						155	138	144					6																	108372335		2202	4300	6502	SO:0001583	missense	28962	exon4			GTTTTGTATGCTT	AF533891	CCDS5062.1	6q21	2014-06-17			ENSG00000081087	ENSG00000081087			21652	protein-coding gene	gene with protein product	"CLCN7 accessory beta subunit"	607649				12627228, 21527911	Standard	NM_014028		Approved	HSPC019, GL	uc003psd.3	Q86WC4	OTTHUMG00000015317	ENST00000193322.3:c.683A>T	chr6.hg19:g.108372335T>A	ENSP00000193322:p.Tyr228Phe	172.0	0.0		228.0	31.0	NM_014028	E1P5E3|Q5R391|Q6PCA7|Q7RTW6|Q8NC29|Q8TC82|Q9Y2S9	Missense_Mutation	SNP	ENST00000193322.3	hg19	CCDS5062.1	.	.	.	.	.	.	.	.	.	.	t	25.8	4.678364	0.88542	.	.	ENSG00000081087	ENST00000193322;ENST00000440575	T	0.61392	0.11	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.72260	0.3438	M	0.78223	2.4	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77075	-0.2722	10	0.87932	D	0	-7.8843	16.1376	0.81497	0.0:0.0:0.0:1.0	.	228	Q86WC4	OSTM1_HUMAN	F	228;81	ENSP00000193322:Y228F	ENSP00000193322:Y228F	Y	-	2	0	OSTM1	108479028	1.000000	0.71417	0.430000	0.26722	0.937000	0.57800	6.767000	0.74975	2.212000	0.71576	0.533000	0.62120	TAC	.	.		0.348	OSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041709.3	NM_014028		A	108372335	T	A	108372335	3	1	123	1	0	0	0	0	1	0	0	0	11307	1638	57	4	333	4	OSTM1	6	108372335	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	1384975	108372335	62742732	154	20684										
RFX6	222546	hgsc.bcm.edu	37	chr6	117248312	117248312	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggaggcccccaagtgtgggcCcagtactgtcagctccatca	12	14	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:117248312C>T	ENST00000332958.2	+	17	2024	c.2008C>T	c.(2008-2010)Cca>Tca	p.P670S		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	670					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AAGTGTGGGCCCAGTACTGTC	0.527																																					p.P670S		Atlas-SNP	.											.	RFX6	141	.	0			c.C2008T						.						142	133	136					6																	117248312		2203	4300	6503	SO:0001583	missense	222546	exon17			GTGGGCCCAGTAC	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.2008C>T	chr6.hg19:g.117248312C>T	ENSP00000332208:p.Pro670Ser	146.0	0.0		195.0	15.0	NM_173560	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	hg19	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.334435	0.24253	.	.	ENSG00000185002	ENST00000332958	T	0.55760	0.5	5.68	1.69	0.24217	.	0.558936	0.20589	N	0.089387	T	0.11239	0.0274	N	0.12182	0.205	0.09310	N	0.999995	B	0.09022	0.002	B	0.08055	0.003	T	0.27331	-1.0077	10	0.35671	T	0.21	-1.9504	4.6315	0.12504	0.1296:0.6161:0.1186:0.1356	.	670	Q8HWS3	RFX6_HUMAN	S	670	ENSP00000332208:P670S	ENSP00000332208:P670S	P	+	1	0	RFX6	117355005	0.291000	0.24352	0.020000	0.16555	0.957000	0.61999	1.187000	0.32090	0.018000	0.15052	0.655000	0.94253	CCA	.	.		0.527	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		T	117248312	C	T	117248312	3	4	123	1	0	0	0	0	1	0	0	0	13282	623	22	3	2074	3	RFX6	6	117248312	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	8875977	117248312	53866755	155	20685										
RNF146	81847	hgsc.bcm.edu	37	chr6	127607830	127607830	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aacaggaaagcgaacgagtcCtgttctaatactgcaccttc	8	11	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:127607830C>T	ENST00000368314.1	+	3	496	c.72C>T	c.(70-72)tcC>tcT	p.S24S	RNF146_ENST00000489534.1_3'UTR|RNF146_ENST00000356799.2_3'UTR|RNF146_ENST00000608991.1_Silent_p.S23S|RNF146_ENST00000610153.1_Silent_p.S24S|RNF146_ENST00000309649.3_Silent_p.S23S|RNF146_ENST00000476956.1_3'UTR|RNF146_ENST00000477776.1_3'UTR|RNF146_ENST00000480444.1_3'UTR	NM_001242850.1|NM_001242851.1	NP_001229779.1|NP_001229780.1	Q9NTX7	RN146_HUMAN	ring finger protein 146	24					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly-ADP-D-ribose binding (GO:0072572)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(226;0.0407)|all cancers(137;0.2)		CGAACGAGTCCTGTTCTAATA	0.403																																					p.S24S		Atlas-SNP	.											.	RNF146	31	.	0			c.C72T						.						189	153	165					6																	127607830		2203	4300	6503	SO:0001819	synonymous_variant	81847	exon3			CGAGTCCTGTTCT	AK027558	CCDS5136.1, CCDS56449.1	6q22.1-q22.33	2008-02-05			ENSG00000118518	ENSG00000118518		"RING-type (C3HC4) zinc fingers"	21336	protein-coding gene	gene with protein product		612137					Standard	NM_001242844		Approved	DKFZp434O1427, dactylidin, dJ351K20.1	uc021zes.1	Q9NTX7	OTTHUMG00000015522	ENST00000368314.1:c.72C>T	chr6.hg19:g.127607830C>T		207.0	0.0		326.0	34.0	NM_001242850	E1P572|Q6FIB2|Q7L8H4|Q96K03|Q96T06|Q9NTX6	Silent	SNP	ENST00000368314.1	hg19	CCDS56449.1																																																																																			.	.		0.403	RNF146-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042112.1	NM_030963		T	127607830	C	T	127607830	2	4	123	1	0	0	0	0	0	0	0	1	13463	668	24	3		3	RNF146	6	127607830	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	10359518	127607830	43507237	156	20686										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138655566	138655566	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgttcatctgaggatgaagaCatctttgaggaaaccgccca	10	9	3	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:138655566C>T	ENST00000251691.4	+	33	5749	c.5583C>T	c.(5581-5583)gaC>gaT	p.D1861D		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		AGGATGAAGACATCTTTGAGG	0.562																																					p.D1861D		Atlas-SNP	.											.	KIAA1244	236	.	0			c.C5583T						.						30	29	29					6																	138655566		2203	4300	6503	SO:0001819	synonymous_variant	57221	exon33			TGAAGACATCTTT	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.5583C>T	chr6.hg19:g.138655566C>T		79.0	0.0		106.0	11.0	NM_020340		Silent	SNP	ENST00000251691.4	hg19	CCDS5189.2																																																																																			.	.		0.562	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		T	138655566	C	T	138655566	2	4	123	1	0	0	0	0	0	0	0	1	8226	477	17	3		3	KIAA1244	6	138655566	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	11047736	138655566	32459501	157	20687										
GRM1	2911	hgsc.bcm.edu	37	chr6	146755591	146755591	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgcagatgctgccgctgcagCtgagcacctttggggaggag	16	10	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:146755591C>T	ENST00000282753.1	+	8	3479	c.3244C>T	c.(3244-3246)Ctg>Ttg	p.L1082L	GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000361719.2_Silent_p.L1082L|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000492807.2_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1082					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GCCGCTGCAGCTGAGCACCTT	0.692																																					p.L1082L		Atlas-SNP	.											.	GRM1	419	.	0			c.C3244T						.						47	52	50					6																	146755591		2201	4300	6501	SO:0001819	synonymous_variant	2911	exon9			CTGCAGCTGAGCA	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3244C>T	chr6.hg19:g.146755591C>T		41.0	0.0		44.0	5.0	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	hg19	CCDS5209.1																																																																																			.	.		0.692	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		T	146755591	C	T	146755591	2	4	123	1	0	0	0	0	0	0	0	1	6805	796	28	3		3	GRM1	6	146755591	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	8100025	146755591	24359476	158	20688										
SASH1	23328	hgsc.bcm.edu	37	chr6	148841002	148841002	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctcaccgagggggagatgaaGaagggtctcgggtccctaag	16	9	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:148841002G>A	ENST00000367467.3	+	10	1657	c.1182G>A	c.(1180-1182)aaG>aaA	p.K394K		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	394					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GGGAGATGAAGAAGGGTCTCG	0.567																																					p.K394K		Atlas-SNP	.											.	SASH1	123	.	0			c.G1182A						.						13	15	15					6																	148841002		2199	4295	6494	SO:0001819	synonymous_variant	23328	exon10			GATGAAGAAGGGT	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1182G>A	chr6.hg19:g.148841002G>A		19.0	0.0		22.0	7.0	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	hg19	CCDS5212.1																																																																																			.	.		0.567	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		A	148841002	G	A	148841002	2	1	123	1	0	0	0	0	0	0	0	1	13863	933	33	3		3	SASH1	6	148841002	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	2085411	148841002	22274065	159	20689										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152740828	152740828	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gctcatcaaattgctggtgtTcagcaaccacagactgaaga	9	10	3	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:152740828T>C	ENST00000367255.5	-	40	5898	c.5297A>G	c.(5296-5298)gAa>gGa	p.E1766G	SYNE1_ENST00000423061.1_Missense_Mutation_p.E1773G|SYNE1_ENST00000341594.5_Missense_Mutation_p.E1803G|SYNE1_ENST00000448038.1_Missense_Mutation_p.E1773G|SYNE1_ENST00000265368.4_Missense_Mutation_p.E1766G	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1766					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTGCTGGTGTTCAGCAACCAC	0.348										HNSCC(10;0.0054)																											p.E1773G		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A5318G						.						78	77	78					6																	152740828		2203	4300	6503	SO:0001583	missense	23345	exon40			TGGTGTTCAGCAA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.5297A>G	chr6.hg19:g.152740828T>C	ENSP00000356224:p.Glu1766Gly	140.0	0.0		165.0	15.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	12.96	2.093332	0.36952	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27	5.21	5.21	0.72293	.	0.091701	0.47093	D	0.000256	T	0.40670	0.1126	L	0.54323	1.7	0.80722	D	1	D;P;P;D	0.59767	0.986;0.839;0.839;0.982	P;B;B;P	0.56751	0.494;0.218;0.218;0.805	T	0.38373	-0.9664	10	0.66056	D	0.02	.	15.382	0.74664	0.0:0.0:0.0:1.0	.	1749;1766;1766;1773	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	G	1766;1773;1766;1773;1803	ENSP00000356224:E1766G;ENSP00000396024:E1773G;ENSP00000265368:E1766G;ENSP00000390975:E1773G;ENSP00000341887:E1803G	ENSP00000265368:E1766G	E	-	2	0	SYNE1	152782521	1.000000	0.71417	0.777000	0.31699	0.723000	0.41478	6.047000	0.71038	2.097000	0.63578	0.528000	0.53228	GAA	.	.		0.348	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152740828	T	C	152740828	3	2	123	1	0	0	0	0	1	0	0	0	15460	1783	62	2	21597	2	SYNE1	6	152740828	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	3899826	152740828	18374239	160	20690										
PLG	5340	hgsc.bcm.edu	37	chr6	161137785	161137785	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cgctgggaactttgtgacatCccccgctgcagtgagtatga	12	11	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:161137785C>T	ENST00000308192.9	+	7	840	c.777C>T	c.(775-777)atC>atT	p.I259I		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	259	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	TTTGTGACATCCCCCGCTGCA	0.517																																					p.I259I		Atlas-SNP	.											.	PLG	150	.	0			c.C777T						.						65	61	62					6																	161137785		2203	4300	6503	SO:0001819	synonymous_variant	5340	exon7			TGACATCCCCCGC	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.777C>T	chr6.hg19:g.161137785C>T		76.0	0.0		112.0	6.0	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	hg19	CCDS5279.1																																																																																			.	.		0.517	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		T	161137785	C	T	161137785	2	4	123	1	0	0	0	0	0	0	0	1	12095	845	30	3		3	PLG	6	161137785	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	8396957	161137785	9977282	161	20691										
C6orf118	168090	hgsc.bcm.edu	37	chr6	165715083	165715083	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcagctttctctcgtggcccGcggccgccttgctcccagtg	12	17	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:165715083G>A	ENST00000230301.8	-	2	748	c.728C>T	c.(727-729)gCg>gTg	p.A243V	C6orf118_ENST00000543069.1_Missense_Mutation_p.A139V	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	243										breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		CTCGTGGCCCGCGGCCGCCTT	0.607																																					p.A243V		Atlas-SNP	.											C6orf118,NS,carcinoma,0,1	C6orf118	116	.	0			c.C728T						.						51	53	52					6																	165715083		2203	4300	6503	SO:0001583	missense	168090	exon2			TGGCCCGCGGCCG		CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.728C>T	chr6.hg19:g.165715083G>A	ENSP00000230301:p.Ala243Val	109.0	0.0		122.0	14.0	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	hg19	CCDS5288.1	.	.	.	.	.	.	.	.	.	.	G	7.212	0.595566	0.13875	.	.	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.14266	2.52;2.52	4.92	-9.85	0.00476	.	3.383220	0.00839	N	0.001730	T	0.00724	0.0024	N	0.00841	-1.15	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33803	-0.9854	10	0.28530	T	0.3	0.9594	2.604	0.04873	0.117:0.1644:0.326:0.3926	.	243	Q5T5N4	CF118_HUMAN	V	243;139	ENSP00000230301:A243V;ENSP00000439288:A139V	ENSP00000230301:A243V	A	-	2	0	C6orf118	165635073	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.152000	0.01288	-3.367000	0.00178	-2.617000	0.00157	GCG	.	.		0.607	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980		A	165715083	G	A	165715083	3	1	123	1	0	0	0	0	1	0	0	0	2325	1087	38	1	713	1	C6orf118	6	165715083	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	4577298	165715083	5399984	162	20692										
GPR31	2853	hgsc.bcm.edu	37	chr6	167570796	167570796	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agagtgcttcctgccagatgAtgctgaaggagccgtctgcc	13	11	1	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:167570796A>T	ENST00000366834.1	-	1	1021	c.524T>A	c.(523-525)aTc>aAc	p.I175N		NM_005299.2	NP_005290.2	O00270	GPR31_HUMAN	G protein-coupled receptor 31	175					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(4)|large_intestine(4)|lung(7)|prostate(1)	17		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)		CTGCCAGATGATGCTGAAGGA	0.582																																					p.I175N		Atlas-SNP	.											.	GPR31	44	.	0			c.T524A						.						91	98	96					6																	167570796		2203	4300	6503	SO:0001583	missense	2853	exon1			CAGATGATGCTGA	U65402	CCDS5299.1	6q27	2012-08-21				ENSG00000120436		"GPCR / Class A : Orphans"	4486	protein-coding gene	gene with protein product	"hydroxyeicosatetraenoic (HETE) acid receptor 1", "12-(S)-HETE acid receptor"	602043				9205127, 21712392	Standard	NM_005299		Approved	HETER1, 12-HETER	uc011egq.2	O00270		ENST00000366834.1:c.524T>A	chr6.hg19:g.167570796A>T	ENSP00000355799:p.Ile175Asn	80.0	0.0		95.0	6.0	NM_005299	B0M0K2|Q4VBL3|Q9NQ20	Missense_Mutation	SNP	ENST00000366834.1	hg19	CCDS5299.1	.	.	.	.	.	.	.	.	.	.	A	0.030	-1.342818	0.01277	.	.	ENSG00000120436	ENST00000366834	T	0.37058	1.22	3.51	-7.01	0.01594	GPCR, rhodopsin-like superfamily (1);	2.652600	0.02280	U	0.069294	T	0.07052	0.0179	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.10382	-1.0632	10	0.56958	D	0.05	-6.3835	1.4616	0.02397	0.1533:0.2113:0.3534:0.282	.	175	O00270	GPR31_HUMAN	N	175	ENSP00000355799:I175N	ENSP00000355799:I175N	I	-	2	0	GPR31	167490786	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-1.680000	0.01939	-1.692000	0.01428	-0.981000	0.02577	ATC	.	.		0.582	GPR31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043111.1	NM_005299		T	167570796	A	T	167570796	3	4	123	1	0	0	0	0	1	0	0	0	6695	333	12	4	438	4	GPR31	6	167570796	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	1855713	167570796	3544271	163	20693										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47933628	47933628	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccaggcccacacagtagttgCtgtacaccacactgccttca	7	16	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:47933628C>T	ENST00000289672.2	-	15	2350	c.2300G>A	c.(2299-2301)aGc>aAc	p.S767N		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	767	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						ACAGTAGTTGCTGTACACCAC	0.572																																					p.S767N		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G2300A						.						90	68	75					7																	47933628		2203	4300	6503	SO:0001583	missense	168507	exon15			TAGTTGCTGTACA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.2300G>A	chr7.hg19:g.47933628C>T	ENSP00000289672:p.Ser767Asn	86.0	0.0		66.0	6.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	c	17.73	3.460343	0.63401	.	.	ENSG00000158683	ENST00000289672	T	0.69806	-0.43	5.23	4.35	0.52113	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.104209	0.42682	D	0.000675	T	0.78604	0.4309	M	0.63843	1.955	0.25786	N	0.984675	D	0.89917	1.0	D	0.91635	0.999	T	0.71724	-0.4506	10	0.54805	T	0.06	-11.3743	13.6843	0.62506	0.0:0.8439:0.1561:0.0	.	767	Q8TDX9	PK1L1_HUMAN	N	767	ENSP00000289672:S767N	ENSP00000289672:S767N	S	-	2	0	PKD1L1	47900153	1.000000	0.71417	0.179000	0.23059	0.558000	0.35554	3.411000	0.52672	1.197000	0.43143	0.543000	0.68304	AGC	.	.		0.572	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47933628	C	T	47933628	3	4	123	1	0	0	0	0	1	0	0	0	11973	797	28	3	6421	3	PKD1L1	7	47933628	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		47933628	111205035	164	20694										
CCDC132	55610	hgsc.bcm.edu	37	chr7	92905597	92905597	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acacaaaattccaaaagctgCaatataaggatctctgtaca	5	9	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:92905597C>A	ENST00000305866.5	+	12	1050	c.922C>A	c.(922-924)Caa>Aaa	p.Q308K	CCDC132_ENST00000317751.6_Missense_Mutation_p.Q39K|CCDC132_ENST00000541136.1_Missense_Mutation_p.Q119K|CCDC132_ENST00000544910.1_Missense_Mutation_p.Q278K|CCDC132_ENST00000251739.5_Missense_Mutation_p.Q308K|CCDC132_ENST00000535481.1_Intron	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	308						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.Q308*(2)		endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			CCAAAAGCTGCAATATAAGGA	0.343																																					p.Q308K		Atlas-SNP	.											CCDC132_ENST00000305866,NS,carcinoma,-1,2	CCDC132	136	.	2	Substitution - Nonsense(2)	lung(2)	c.C922A						.						144	136	139					7																	92905597		2203	4300	6503	SO:0001583	missense	55610	exon12			AAGCTGCAATATA	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.922C>A	chr7.hg19:g.92905597C>A	ENSP00000307666:p.Gln308Lys	113.0	0.0		122.0	27.0	NM_024553	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.70|11.70	1.715847|1.715847	0.30413|0.30413	.|.	.|.	ENSG00000004766|ENSG00000004766	ENST00000458707|ENST00000251739;ENST00000305866;ENST00000544910;ENST00000541136;ENST00000317751	.|T	.|0.43688	.|0.94	5.6|5.6	5.6|5.6	0.85130|0.85130	.|Vacuolar protein sorting-associated protein 54 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.40015	.|0.1100	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.33266	.|0.135;0.08;0.404	.|B;B;B	.|0.29440	.|0.051;0.058;0.102	.|T	.|0.42899	.|-0.9424	.|10	.|0.02654	.|T	.|1	-30.2354|-30.2354	19.9884|19.9884	0.97356|0.97356	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|278;308;308	.|F5H5U7;Q96JG6;Q96JG6-2	.|.;CC132_HUMAN;.	X|K	94|308;308;278;119;39	.|ENSP00000325582:Q39K	.|ENSP00000251739:Q308K	C|Q	+|+	3|1	2|0	CCDC132|CCDC132	92743533|92743533	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.770000|7.770000	0.85390|0.85390	2.809000|2.809000	0.96659|0.96659	0.655000|0.655000	0.94253|0.94253	TGC|CAA	.	.		0.343	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		A	92905597	C	A	92905597	3	1	123	1	0	0	0	0	1	0	0	0	2769	711	25	3	968	3	CCDC132	7	92905597	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	44971969	92905597	66233066	165	20695										
DYNC1I1	1780	hgsc.bcm.edu	37	chr7	95614244	95614244	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agccctggctgaagattccgAcatcttttttgactacagcg	9	11	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:95614244A>G	ENST00000324972.6	+	8	942	c.749A>G	c.(748-750)gAc>gGc	p.D250G	DYNC1I1_ENST00000537881.1_Missense_Mutation_p.D213G|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.D233G|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.D230G|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.D233G|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.D213G	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	250					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			GAAGATTCCGACATCTTTTTT	0.393																																					p.D250G		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.A749G						.						111	114	113					7																	95614244		2203	4299	6502	SO:0001583	missense	1780	exon8			ATTCCGACATCTT	AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"Cytoplasmic dyneins", "WD repeat domain containing"	2963	protein-coding gene	gene with protein product		603772	"dynein, cytoplasmic, intermediate polypeptide 1"	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.749A>G	chr7.hg19:g.95614244A>G	ENSP00000320130:p.Asp250Gly	73.0	0.0		70.0	12.0	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	hg19	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.826322	0.90955	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.79454	-1.1;-1.04;-1.27;-1.04;-1.05;-1.1	4.95	4.95	0.65309	WD40 repeat-like-containing domain (1);	0.049011	0.85682	D	0.000000	D	0.82490	0.5048	M	0.79926	2.475	0.80722	D	1	B;B;B;B;B	0.28178	0.029;0.014;0.049;0.008;0.202	B;B;B;B;B	0.38842	0.047;0.101;0.101;0.047;0.283	D	0.83531	0.0091	10	0.66056	D	0.02	-17.9527	15.0944	0.72223	1.0:0.0:0.0:0.0	.	233;230;233;250;213	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	G	233;250;213;230;213;233	ENSP00000392337:D233G;ENSP00000320130:D250G;ENSP00000438377:D213G;ENSP00000398118:D230G;ENSP00000352348:D213G;ENSP00000412444:D233G	ENSP00000320130:D250G	D	+	2	0	DYNC1I1	95452180	1.000000	0.71417	0.993000	0.49108	0.973000	0.67179	7.312000	0.78968	2.209000	0.71365	0.533000	0.62120	GAC	.	.		0.393	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		G	95614244	A	G	95614244	3	3	123	1	0	0	0	0	1	0	0	0	4844	275	10	2	775	2	DYNC1I1	7	95614244	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	2708647	95614244	63524419	166	20696										
IFRD1	3475	hgsc.bcm.edu	37	chr7	112102235	112102235	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtgaagaaaaagcttgagatGtatgtatttttagtttcata	9	2	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:112102235G>A	ENST00000403825.3	+	7	1058		c.e7+1		IFRD1_ENST00000005558.4_Splice_Site|IFRD1_ENST00000535603.1_Splice_Site	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1						adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						AGCTTGAGATGTATGTATTTT	0.338																																					.		Atlas-SNP	.											.	IFRD1	46	.	0			c.647+1G>A						.						94	94	94					7																	112102235		2203	4300	6503	SO:0001630	splice_region_variant	3475	exon7			TGAGATGTATGTA	Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.797+1G>A	chr7.hg19:g.112102235G>A		67.0	0.0		71.0	8.0	NM_001197080	B7Z5G1|O75234|Q5U013|Q9BVE4	Splice_Site	SNP	ENST00000403825.3	hg19	CCDS34736.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.530375	0.64860	.	.	ENSG00000006652	ENST00000005558;ENST00000403825;ENST00000536259;ENST00000535603;ENST00000421296	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8426	0.96695	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IFRD1	111889471	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.914000	0.69964	2.775000	0.95449	0.655000	0.94253	.	.	.		0.338	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550	Intron	A	112102235	G	A	112102235	5	1	123	1	0	0	0	0	0	0	1	0	7562	1391	48	3	824	3	IFRD1	7	112102235	Splice_Site	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	16487991	112102235	47036428	167	20697										
NOS3	4846	hgsc.bcm.edu	37	chr7	150698351	150698351	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	accatcgtggaccaccacgcCgccacggcctctttcatgaa	8	17	2	1	rs534664057		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:150698351C>T	ENST00000484524.1	+	10	1266	c.1266C>T	c.(1264-1266)gcC>gcT	p.A422A	NOS3_ENST00000461406.1_Silent_p.A216A|NOS3_ENST00000297494.3_Silent_p.A422A|NOS3_ENST00000467517.1_Silent_p.A422A	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACCACCACGCCGCCACGGCCT	0.637													C|||	1	0.000199681	0	0	5008	,	,		16148	0		0	False		,,,				2504	0.001				p.A422A		Atlas-SNP	.											.	NOS3	131	.	0			c.C1266T						.						73	77	76					7																	150698351		2203	4300	6503	SO:0001819	synonymous_variant	4846	exon10			CCACGCCGCCACG		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.1266C>T	chr7.hg19:g.150698351C>T		88.0	0.0		96.0	18.0	NM_001160111	Q495E5	Silent	SNP	ENST00000484524.1	hg19	CCDS55182.1																																																																																			.	.		0.637	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		T	150698351	C	T	150698351	2	4	123	1	0	0	0	0	0	0	0	1	10553	639	23	1		1	NOS3	7	150698351	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	38596116	150698351	8440312	168	20698										
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150773389	150773389	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cacagctggatgctaacgagGcagagccggtgtttgatgag	15	8	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:150773389G>A	ENST00000485713.1	+	23	4701	c.3661G>A	c.(3661-3663)Gca>Aca	p.A1221T	SLC4A2_ENST00000392826.2_Missense_Mutation_p.A1212T|SLC4A2_ENST00000461735.1_Missense_Mutation_p.A1207T|SLC4A2_ENST00000413384.2_Missense_Mutation_p.A1221T|RP11-148K1.12_ENST00000485974.1_RNA|FASTK_ENST00000489884.1_5'Flank|SLC4A2_ENST00000310317.5_Missense_Mutation_p.A1139T	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	1221	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGCTAACGAGGCAGAGCCGGT	0.632																																					p.A1221T		Atlas-SNP	.											.	SLC4A2	98	.	0			c.G3661A						.						60	51	54					7																	150773389		2202	4300	6502	SO:0001583	missense	6522	exon23			AACGAGGCAGAGC		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"Solute carriers"	11028	protein-coding gene	gene with protein product	"anion exchanger 2 type a", "anion exchanger 2 type b1", "anion exchanger 2 type b2"	109280	"erythrocyte membrane protein band 3-like 1", "solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.3661G>A	chr7.hg19:g.150773389G>A	ENSP00000419412:p.Ala1221Thr	97.0	0.0		116.0	21.0	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	hg19	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	G	17.42	3.385894	0.61956	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13	5.08	4.13	0.48395	.	0.000000	0.85682	D	0.000000	D	0.86527	0.5954	M	0.91920	3.255	0.54753	D	0.999987	B;P;B	0.36633	0.364;0.562;0.427	B;P;B	0.49829	0.236;0.623;0.418	D	0.86766	0.1970	10	0.40728	T	0.16	.	12.0057	0.53257	0.0:0.0:0.8265:0.1735	.	1212;1207;1221	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	T	1221;1221;1139;1212;1207	ENSP00000419412:A1221T;ENSP00000405600:A1221T;ENSP00000311402:A1139T;ENSP00000376571:A1212T;ENSP00000419164:A1207T	ENSP00000311402:A1139T	A	+	1	0	SLC4A2	150404322	1.000000	0.71417	0.997000	0.53966	0.898000	0.52572	6.630000	0.74272	2.361000	0.80049	0.655000	0.94253	GCA	.	.		0.632	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		A	150773389	G	A	150773389	3	1	123	1	0	0	0	0	1	0	0	0	14669	1203	42	3	3747	3	SLC4A2	7	150773389	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	75038	150773389	8365274	169	20699										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110401347	110401347	+	Frame_Shift_Del	DEL	T	T	-													0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	catccaaatggagatatgggTtctatggtttgtaagacgac							TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr8:110401347delT	ENST00000378402.5	+	8	767	c.663delT	c.(661-663)ggtfs	p.G221fs		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	221	IPT/TIG 2.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GAGATATGGGTTCTATGGTTT	0.313										HNSCC(38;0.096)																											p.G221fs		Atlas-Indel,Pindel	.											.	PKHD1L1	522	.	0			c.662delG						.						203	195	197					8																	110401347		1849	4087	5936	SO:0001589	frameshift_variant	93035	exon8			.	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.663delT	chr8.hg19:g.110401347delT	ENSP00000367655:p.Gly221fs	130.0	0.0		142.0	26.0	NM_177531	Q567P2|Q9UF27	Frame_Shift_Del	DEL	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.		0.313	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		-	110401347	T	-	110401347	7	5	123	1	0	1	0	1	0	0	0	0	11981	1712	60	0	693	0	PKHD1L1	8	110401347	Frame_Shift_Del	DEL	T	TCGA-DD-A3A9-01A-11D-A25V-10		110401347	35962675	170	20700										
CYP11B2	1585	hgsc.bcm.edu	37	chr8	143994784	143994784	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcactgatgctggctgcggcGgccaggctctcctggcgcag	15	14	2	1	rs200388238		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr8:143994784G>A	ENST00000323110.2	-	6	1040	c.1038C>T	c.(1036-1038)gcC>gcT	p.A346A		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	346					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	TGGCTGCGGCGGCCAGGCTCT	0.637									Familial Hyperaldosteronism type I																												p.A346A		Atlas-SNP	.											.	CYP11B2	107	.	0			c.C1038T						.						56	61	60					8																	143994784		2202	4299	6501	SO:0001819	synonymous_variant	1585	exon6	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TGCGGCGGCCAGG	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"Cytochrome P450s"	2592	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	124080	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.1038C>T	chr8.hg19:g.143994784G>A		147.0	0.0		92.0	15.0	NM_000498	B0ZBE4|Q16726	Silent	SNP	ENST00000323110.2	hg19	CCDS6393.1																																																																																			.	G|0.999;A|0.001		0.637	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1			A	143994784	G	A	143994784	2	1	123	1	0	0	0	0	0	0	0	1	4148	1103	39	1		1	CYP11B2	8	143994784	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	33593437	143994784	2369238	171	20701										
DMRT3	58524	hgsc.bcm.edu	37	chr9	990928	990928	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggtgtccatttgtgtcaaagCagtccatttacaccgaggac	10	10	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:990928C>T	ENST00000190165.2	+	2	1380	c.1342C>T	c.(1342-1344)Cag>Tag	p.Q448*		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	448					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		TGTGTCAAAGCAGTCCATTTA	0.542																																					p.Q448X		Atlas-SNP	.											.	DMRT3	83	.	0			c.C1342T						.						93	90	91					9																	990928		2203	4300	6503	SO:0001587	stop_gained	58524	exon2			TCAAAGCAGTCCA	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"testis-specific protein"	614754	"DMRT-like family A3"	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.1342C>T	chr9.hg19:g.990928C>T	ENSP00000190165:p.Gln448*	165.0	0.0		139.0	19.0	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Nonsense_Mutation	SNP	ENST00000190165.2	hg19	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	C	35	5.519543	0.96416	.	.	ENSG00000064218	ENST00000190165	.	.	.	5.22	4.28	0.50868	.	0.218002	0.41396	D	0.000885	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-29.9764	15.1877	0.73016	0.1412:0.8588:0.0:0.0	.	.	.	.	X	448	.	ENSP00000190165:Q448X	Q	+	1	0	DMRT3	980928	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.542000	0.53625	2.424000	0.82194	0.655000	0.94253	CAG	.	.		0.542	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240		T	990928	C	T	990928	4	4	123	1	0	0	0	0	0	1	0	0	4589	711	25	3	1348	3	DMRT3	9	990928	Nonsense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		990928	140222503	172	20702										
FREM1	158326	hgsc.bcm.edu	37	chr9	14824891	14824891	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atgtagctgtttcttagttaTataggccacctcagtttcct	7	9	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:14824891T>A	ENST00000380880.3	-	11	2764	c.1981A>T	c.(1981-1983)Ata>Tta	p.I661L	FREM1_ENST00000380881.4_Missense_Mutation_p.I662L|FREM1_ENST00000422223.2_Missense_Mutation_p.I661L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	661					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TTCTTAGTTATATAGGCCACC	0.433																																					p.I661L		Atlas-SNP	.											.	FREM1	261	.	0			c.A1981T						.						84	79	81					9																	14824891		1834	4082	5916	SO:0001583	missense	158326	exon12			TAGTTATATAGGC	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.1981A>T	chr9.hg19:g.14824891T>A	ENSP00000370262:p.Ile661Leu	111.0	0.0		81.0	21.0	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	hg19	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	T	8.773	0.926378	0.18056	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.52983	0.64;0.64;0.64	5.92	2.25	0.28309	.	0.214563	0.49305	D	0.000158	T	0.24470	0.0593	N	0.17082	0.46	0.37515	D	0.917298	B	0.11235	0.004	B	0.17979	0.02	T	0.22277	-1.0221	10	0.02654	T	1	-13.0527	8.8665	0.35289	0.0:0.0781:0.3598:0.5621	.	661	Q5H8C1	FREM1_HUMAN	L	662;661;661	ENSP00000370263:I662L;ENSP00000412940:I661L;ENSP00000370262:I661L	ENSP00000370257:I664L	I	-	1	0	FREM1	14814891	1.000000	0.71417	0.995000	0.50966	0.964000	0.63967	1.878000	0.39608	0.448000	0.26722	0.533000	0.62120	ATA	.	.		0.433	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		A	14824891	T	A	14824891	3	1	123	1	0	0	0	0	1	0	0	0	6052	1406	49	4	4716	4	FREM1	9	14824891	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	13833963	14824891	126388540	173	20703										
TEK	7010	hgsc.bcm.edu	37	chr9	27173269	27173269	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgtaaagaaaggtgcagtggAcaagagggatgcaagtctta	14	4	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:27173269A>G	ENST00000380036.4	+	6	1252	c.810A>G	c.(808-810)ggA>ggG	p.G270G	TEK_ENST00000406359.4_Silent_p.G270G|TEK_ENST00000519097.1_Silent_p.G166G	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	270	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	GGTGCAGTGGACAAGAGGGAT	0.483																																					p.G270G		Atlas-SNP	.											.	TEK	250	.	0			c.A810G						.						175	143	154					9																	27173269		2203	4300	6503	SO:0001819	synonymous_variant	7010	exon6			CAGTGGACAAGAG	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.810A>G	chr9.hg19:g.27173269A>G		245.0	0.0		234.0	44.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	hg19	CCDS6519.1																																																																																			.	.		0.483	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			G	27173269	A	G	27173269	2	3	123	1	0	0	0	0	0	0	0	1	15766	262	10	2		2	TEK	9	27173269	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	12348378	27173269	114040162	174	20704										
SMC5	23137	hgsc.bcm.edu	37	chr9	72895730	72895730	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aatggttcagaggaatgaaaGatataaacaagatgtggaga	12	2	1	5			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:72895730G>T	ENST00000361138.5	+	6	792	c.734G>T	c.(733-735)aGa>aTa	p.R245I		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	245					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						AGGAATGAAAGATATAAACAA	0.338																																					p.R245I		Atlas-SNP	.											.	SMC5	96	.	0			c.G734T						.						135	142	140					9																	72895730		2203	4300	6503	SO:0001583	missense	23137	exon6			ATGAAAGATATAA	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"Structural maintenance of chromosomes proteins"	20465	protein-coding gene	gene with protein product		609386	"SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.734G>T	chr9.hg19:g.72895730G>T	ENSP00000354957:p.Arg245Ile	31.0	0.0		35.0	5.0	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	hg19	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.465506	0.84425	.	.	ENSG00000198887	ENST00000361138	T	0.80909	-1.43	5.2	5.2	0.72013	RecF/RecN/SMC (1);	0.053403	0.64402	D	0.000001	D	0.89550	0.6747	M	0.76002	2.32	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89234	0.3579	10	0.45353	T	0.12	-15.6154	18.7238	0.91705	0.0:0.0:1.0:0.0	.	245	Q8IY18	SMC5_HUMAN	I	245	ENSP00000354957:R245I	ENSP00000354957:R245I	R	+	2	0	SMC5	72085550	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.556000	0.82233	2.441000	0.82636	0.591000	0.81541	AGA	.	.		0.338	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		T	72895730	G	T	72895730	3	4	123	1	0	0	0	0	1	0	0	0	14801	942	33	3	756	3	SMC5	9	72895730	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	45722461	72895730	68317701	175	20705										
FAM75C1	441452	hgsc.bcm.edu	37	chr9	90535712	90535712	+	RNA	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgccctctcctggtcgcaggAgactaccaaaacctggtgca	10	14	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:90535712A>T	ENST00000602681.1	+	0	1616							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TGGTCGCAGGAGACTACCAAA	0.552																																					p.E297V		Atlas-SNP	.											.	.	.	.	0			c.A890T						.						79	75	76					9																	90535712		692	1591	2283			441452	exon4			CGCAGGAGACTAC	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"family with sequence similarity 75, member C1"	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		chr9.hg19:g.90535712A>T		251.0	0.0		260.0	55.0	NM_001145124		Missense_Mutation	SNP	ENST00000602681.1	hg19																																																																																				.	.		0.552	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124		T	90535712	A	T	90535712	1	4	123	0	1	0	0	0	0	0	0	0	5631	304	11	4		4	FAM75C1	9	90535712	RNA	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	17639982	90535712	50677719	176	20706										
FAM22F	54754	hgsc.bcm.edu	37	chr9	97082514	97082514	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtgacaaagtcttcctgggaAcacagcttgtcaatgtagct	10	9	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:97082514A>G	ENST00000253262.4	-	5	1364	c.1344T>C	c.(1342-1344)tgT>tgC	p.C448C	NUTM2F_ENST00000335456.7_Silent_p.C433C|NUTM2F_ENST00000341207.4_Silent_p.C433C	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	448																	CTTCCTGGGAACACAGCTTGT	0.567																																					p.C448C		Atlas-SNP	.											.	FAM22F	72	.	0			c.T1344C						.						44	54	51					9																	97082514		1897	4108	6005	SO:0001819	synonymous_variant	54754	exon5			CTGGGAACACAGC		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"family with sequence similarity 22, member F"	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.1344T>C	chr9.hg19:g.97082514A>G		150.0	0.0		118.0	24.0	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Silent	SNP	ENST00000253262.4	hg19	CCDS47994.1																																																																																			.	.		0.567	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561		G	97082514	A	G	97082514	2	3	123	1	0	0	0	0	0	0	0	1	5550	41	2	2		2	FAM22F	9	97082514	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	6546802	97082514	44130917	177	20707										
OR13C3	138803	hgsc.bcm.edu	37	chr9	107298487	107298487	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cacatgcgaaatgattgataAtattattcccacagaaaggc	7	8	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:107298487A>G	ENST00000374781.2	-	1	650	c.608T>C	c.(607-609)aTt>aCt	p.I203T		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						ATGATTGATAATATTATTCCC	0.418																																					p.I203T	GBM(86;1248 1274 14222 15028 46219)	Atlas-SNP	.											.	OR13C3	45	.	0			c.T608C						.						116	115	115					9																	107298487		2203	4300	6503	SO:0001583	missense	138803	exon1			TTGATAATATTAT		CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"GPCR / Class A : Olfactory receptors"	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.608T>C	chr9.hg19:g.107298487A>G	ENSP00000363913:p.Ile203Thr	90.0	0.0		98.0	19.0	NM_001001961	Q5VVG1|Q6IF52	Missense_Mutation	SNP	ENST00000374781.2	hg19	CCDS35089.1	.	.	.	.	.	.	.	.	.	.	A	9.459	1.092577	0.20471	.	.	ENSG00000204246	ENST00000374781	T	0.00198	8.57	4.08	4.08	0.47627	GPCR, rhodopsin-like superfamily (1);	1.087510	0.07255	U	0.866611	T	0.00109	0.0003	N	0.16201	0.385	0.09310	N	1	P	0.35821	0.523	B	0.32149	0.141	T	0.29671	-1.0004	10	0.39692	T	0.17	.	7.0004	0.24807	0.7969:0.0:0.0:0.2031	.	203	Q8NGS6	O13C3_HUMAN	T	203	ENSP00000363913:I203T	ENSP00000363913:I203T	I	-	2	0	OR13C3	106338308	0.000000	0.05858	0.986000	0.45419	0.745000	0.42441	0.188000	0.17018	1.843000	0.53566	0.482000	0.46254	ATT	.	.		0.418	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2			G	107298487	A	G	107298487	3	3	123	1	0	0	0	0	1	0	0	0	10944	101	4	2	439	2	OR13C3	9	107298487	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	10215973	107298487	33914944	178	20708										
MUSK	4593	hgsc.bcm.edu	37	chr9	113509954	113509954	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccattcaagagagtgtgaaaGaccgagtgattgactcaaga	11	7	2	6			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:113509954G>A	ENST00000374448.4	+	7	921	c.787G>A	c.(787-789)Gac>Aac	p.D263N	MUSK_ENST00000416899.2_Missense_Mutation_p.D263N|MUSK_ENST00000189978.5_Missense_Mutation_p.D263N	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	263	Ig-like 3.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						GAGTGTGAAAGACCGAGTGAT	0.423																																					p.D273N		Atlas-SNP	.											.	MUSK	112	.	0			c.G817A						.						179	167	170					9																	113509954		1921	4138	6059	SO:0001583	missense	4593	exon8			GTGAAAGACCGAG	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.787G>A	chr9.hg19:g.113509954G>A	ENSP00000363571:p.Asp263Asn	116.0	0.0		126.0	32.0	NM_001166280	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	hg19	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.167133	0.57476	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899	T	0.31510	1.49	5.78	4.89	0.63831	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.049251	0.85682	D	0.000000	T	0.37210	0.0995	N	0.22421	0.69	0.80722	D	1	D;D	0.69078	0.993;0.997	D;D	0.67382	0.951;0.93	T	0.09250	-1.0683	10	0.25106	T	0.35	.	12.7894	0.57523	0.0795:0.0:0.9205:0.0	.	263;273	O15146;F5H6T2	MUSK_HUMAN;.	N	263;263;263;273;273;263	ENSP00000363571:D263N	ENSP00000189978:D263N	D	+	1	0	MUSK	112549775	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.003000	0.70701	1.446000	0.47643	0.655000	0.94253	GAC	.	.		0.423	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	113509954	G	A	113509954	3	1	123	1	0	0	0	0	1	0	0	0	9998	942	33	3	847	3	MUSK	9	113509954	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	6211467	113509954	27703477	179	20709										
PTGR1	22949	hgsc.bcm.edu	37	chr9	114348379	114348379	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccatcagaaatggagtgcgtTgtccagcctggagaagccag	13	10	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:114348379T>A	ENST00000407693.2	-	5	538	c.276A>T	c.(274-276)acA>acT	p.T92T	PTGR1_ENST00000238248.3_5'UTR|PTGR1_ENST00000538962.1_Silent_p.T92T|PTGR1_ENST00000309195.5_Silent_p.T92T	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	92					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						TGGAGTGCGTTGTCCAGCCTG	0.463																																					p.T92T	Ovarian(200;132 2151 7551 19220 46064)	Atlas-SNP	.											.	PTGR1	23	.	0			c.A276T						.						163	131	142					9																	114348379		2203	4300	6503	SO:0001819	synonymous_variant	22949	exon5			GTGCGTTGTCCAG	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.276A>T	chr9.hg19:g.114348379T>A		264.0	0.0		219.0	41.0	NM_001146108	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Silent	SNP	ENST00000407693.2	hg19	CCDS6779.1																																																																																			.	.		0.463	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			A	114348379	T	A	114348379	2	1	123	1	0	0	0	0	0	0	0	1	12766	1799	63	4		4	PTGR1	9	114348379	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	838425	114348379	26865052	180	20710										
COL27A1	85301	hgsc.bcm.edu	37	chr9	116973290	116973290	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tggcgttcctggcaagagggGcaagatgggtatgccggtaa	17	7	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:116973290G>A	ENST00000356083.3	+	12	2742	c.2351G>A	c.(2350-2352)gGc>gAc	p.G784D	MIR455_ENST00000384993.1_RNA	NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	784	Collagen-like 3.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GGCAAGAGGGGCAAGATGGGT	0.642																																					p.G784D		Atlas-SNP	.											.	COL27A1	200	.	0			c.G2351A						.						119	102	108					9																	116973290		2203	4300	6503	SO:0001583	missense	85301	exon12			AGAGGGGCAAGAT	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.2351G>A	chr9.hg19:g.116973290G>A	ENSP00000348385:p.Gly784Asp	141.0	0.0		96.0	14.0	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.855050	0.71719	.	.	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	D;D	0.99619	-5.52;-6.28	5.67	5.67	0.87782	.	.	.	.	.	D	0.99822	0.9921	H	0.98629	4.285	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.85130	0.87;0.997	D	0.96851	0.9625	9	0.87932	D	0	.	17.2564	0.87057	0.0:0.0:1.0:0.0	.	784;680	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	D	784;784;680;680	ENSP00000348385:G784D;ENSP00000391328:G680D	ENSP00000348385:G784D	G	+	2	0	COL27A1	116013111	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.384000	0.97219	2.676000	0.91093	0.561000	0.74099	GGC	.	.		0.642	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	116973290	G	A	116973290	3	1	123	1	0	0	0	0	1	0	0	0	3687	1203	42	3	2397	3	COL27A1	9	116973290	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	2624911	116973290	24240141	181	20711										
FBXW2	26190	hgsc.bcm.edu	37	chr9	123526906	123526906	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctggtggcaaagaccaagccCgtgtcattgtgcccatccag	11	13	1	1	rs377576429		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:123526906C>T	ENST00000608872.1	-	8	1483	c.1296G>A	c.(1294-1296)acG>acA	p.T432T	FBXW2_ENST00000340778.5_Silent_p.T367T|FBXW2_ENST00000493559.1_Intron	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	432					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)	p.T432T(1)		ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						AGACCAAGCCCGTGTCATTGT	0.567																																					p.T432T		Atlas-SNP	.											.	FBXW2	34	.	1	Substitution - coding silent(1)	lung(1)	c.G1296A						.	C		0,4338		0,0,2169	143	155	151		1296	-5.2	0.7	9		151	4,8512		0,4,4254	no	coding-synonymous	FBXW2	NM_012164.3		0,4,6423	TT,TC,CC		0.047,0.0,0.0311		432/455	123526906	4,12850	2169	4258	6427	SO:0001819	synonymous_variant	26190	exon8			CAAGCCCGTGTCA	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"F-boxes / WD-40 domains", "WD repeat domain containing"	13608	protein-coding gene	gene with protein product		609071	"F-box and WD-40 domain protein 2"			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1296G>A	chr9.hg19:g.123526906C>T		202.0	0.0		201.0	39.0	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Silent	SNP	ENST00000608872.1	hg19	CCDS43872.1																																																																																			.	.		0.567	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2			T	123526906	C	T	123526906	2	4	123	1	0	0	0	0	0	0	0	1	5774	639	23	1		1	FBXW2	9	123526906	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	6553616	123526906	17686525	182	20712										
NR6A1	2649	hgsc.bcm.edu	37	chr9	127284984	127284984	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aggagggcgcctggaacaggTcattccttgcccacactggt	13	12	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:127284984T>C	ENST00000487099.2	-	10	1600	c.1443A>G	c.(1441-1443)tgA>tgG	p.*481W	NR6A1_ENST00000344523.4_Nonstop_Mutation_p.*480W|NR6A1_ENST00000416460.2_Nonstop_Mutation_p.*476W|NR6A1_ENST00000373584.3_Nonstop_Mutation_p.*477W	NM_001278546.1	NP_001265475.1	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1	0					cell proliferation (GO:0008283)|gamete generation (GO:0007276)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	17						CTGGAACAGGTCATTCCTTGC	0.592																																					p.X481W	Esophageal Squamous(192;272 2884 6208 20560)	Atlas-SNP	.											.	NR6A1	38	.	0			c.A1443G						.						48	34	39					9																	127284984		2202	4298	6500	SO:0001578	stop_lost	2649	exon10			AACAGGTCATTCC	U64876	CCDS35137.1, CCDS55340.1, CCDS65127.1	9q33.3	2014-01-21			ENSG00000148200	ENSG00000148200		"Nuclear hormone receptors"	7985	protein-coding gene	gene with protein product		602778		GCNF		9134503, 8982251	Standard	NM_001489		Approved	GCNF1, RTR, CT150	uc004bor.1	Q15406	OTTHUMG00000020661	ENST00000487099.2:c.1443A>G	chr9.hg19:g.127284984T>C	ENSP00000420267:p.*481Cysext*66	42.0	0.0		33.0	4.0	NM_033334	O00551|O00603|Q5T6F4|Q8NHQ0|Q92898|Q99802	Missense_Mutation	SNP	ENST00000487099.2	hg19	CCDS35137.1	.	.	.	.	.	.	.	.	.	.	T	19.64	3.864714	0.71949	.	.	ENSG00000148200	ENST00000487099;ENST00000373584;ENST00000416460;ENST00000344523	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2214	0.73313	0.0:0.0:0.0:1.0	.	.	.	.	W	481;477;476;480	.	.	X	-	3	0	NR6A1	126324805	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.412000	0.66392	2.168000	0.68352	0.533000	0.62120	TGA	.	.		0.592	NR6A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054043.4			C	127284984	T	C	127284984	4	2	123	1	0	0	0	0	0	0	0	0	10646	1680	58	2	3	2	NR6A1	9	127284984	Nonstop_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	3758078	127284984	13928447	183	20713										
USP20	10868	hgsc.bcm.edu	37	chr9	132632035	132632035	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccaagctccattcagccatcTaccagaatgtgccggccaag	8	15	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:132632035T>C	ENST00000315480.4	+	14	1635	c.1477T>C	c.(1477-1479)Tac>Cac	p.Y493H	USP20_ENST00000372429.3_Missense_Mutation_p.Y493H|USP20_ENST00000358355.1_Missense_Mutation_p.Y493H			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	493	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				TTCAGCCATCTACCAGAATGT	0.597																																					p.Y493H		Atlas-SNP	.											.	USP20	186	.	0			c.T1477C						.						69	71	71					9																	132632035		1949	4135	6084	SO:0001583	missense	10868	exon14			GCCATCTACCAGA	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.1477T>C	chr9.hg19:g.132632035T>C	ENSP00000313811:p.Tyr493His	260.0	0.0		176.0	8.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	T	4.693	0.128839	0.08981	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.02863	4.13;4.13;4.13	4.84	4.84	0.62591	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.394499	0.28665	N	0.014553	T	0.00906	0.0030	N	0.00599	-1.345	0.46798	D	0.999202	B	0.06786	0.001	B	0.06405	0.002	T	0.48305	-0.9047	10	0.07175	T	0.84	.	8.6795	0.34201	0.0:0.0853:0.0:0.9147	.	493	Q9Y2K6	UBP20_HUMAN	H	493	ENSP00000361506:Y493H;ENSP00000313811:Y493H;ENSP00000351122:Y493H	ENSP00000313811:Y493H	Y	+	1	0	USP20	131671856	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.358000	0.66064	2.165000	0.68154	0.533000	0.62120	TAC	.	.		0.597	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			C	132632035	T	C	132632035	3	2	123	1	0	0	0	0	1	0	0	0	17067	1522	53	2	1523	2	USP20	9	132632035	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	5347051	132632035	8581396	184	20714										
NUP214	8021	hgsc.bcm.edu	37	chr9	134038560	134038560	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttcccagagcagcattcacaGgtgtggagaggacttgcact	12	10	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:134038560G>A	ENST00000359428.5	+	19	2867	c.2723G>A	c.(2722-2724)aGt>aAt	p.S908N	RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000586662.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000589540.1_RNA|NUP214_ENST00000411637.2_Splice_Site_p.S898N|RP11-544A12.4_ENST00000592466.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|NUP214_ENST00000451030.1_Splice_Site_p.S909N|RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000589128.1_RNA|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000589095.1_RNA|RP11-544A12.4_ENST00000417798.2_RNA|RP11-544A12.4_ENST00000588325.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	908	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		AGCATTCACAGGTGTGGAGAG	0.483			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.S908N	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.G2723A						.						79	75	76					9																	134038560		2203	4300	6503	SO:0001630	splice_region_variant	8021	exon19			TTCACAGGTGTGG	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.2723+1G>A	chr9.hg19:g.134038560G>A		103.0	0.0		95.0	17.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.030341	0.54790	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605	T;T;T	0.35605	1.3;1.32;1.31	5.6	5.6	0.85130	.	0.147968	0.31233	N	0.008012	T	0.31482	0.0798	N	0.08118	0	0.80722	D	1	P;D;B;P	0.53312	0.672;0.959;0.057;0.928	B;P;B;P	0.50659	0.412;0.647;0.013;0.647	T	0.27191	-1.0081	10	0.59425	D	0.04	-8.2165	16.757	0.85502	0.0:0.0:1.0:0.0	.	897;502;898;908	P35658-2;Q5JUP9;P35658-4;P35658	.;.;.;NU214_HUMAN	N	908;898;909;897;502;337	ENSP00000352400:S908N;ENSP00000396576:S898N;ENSP00000405014:S909N	ENSP00000352400:S908N	S	+	2	0	NUP214	133028381	1.000000	0.71417	0.970000	0.41538	0.375000	0.29983	5.485000	0.66850	2.636000	0.89361	0.467000	0.42956	AGT	.	.		0.483	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	Missense_Mutation	A	134038560	G	A	134038560	5	1	123	1	0	0	0	0	0	0	1	0	10771	1014	35	3	2797	3	NUP214	9	134038560	Splice_Site	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	1406525	134038560	7174871	185	20715										
SEC16A	9919	hgsc.bcm.edu	37	chr9	139361447	139361447	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgctctctcctgtatgcgtcAtactctgcatcacaccaata	5	14	4	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:139361447A>G	ENST00000371706.3	-	4	3390	c.3357T>C	c.(3355-3357)taT>taC	p.Y1119Y	SEC16A_ENST00000313050.7_Silent_p.Y1297Y|SEC16A_ENST00000431893.2_Silent_p.Y1119Y|SEC16A_ENST00000290037.6_Silent_p.Y1119Y			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	1119	Required for endoplasmic reticulum localization.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		TGTATGCGTCATACTCTGCAT	0.607																																					p.Y1297Y		Atlas-SNP	.											.	SEC16A	249	.	0			c.T3891C						.						74	79	78					9																	139361447		2003	4160	6163	SO:0001819	synonymous_variant	9919	exon6			TGCGTCATACTCT	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"KIAA0310"	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.3357T>C	chr9.hg19:g.139361447A>G		48.0	0.0		62.0	14.0	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	hg19																																																																																				.	.		0.607	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		G	139361447	A	G	139361447	2	3	123	1	0	0	0	0	0	0	0	1	14001	224	8	2		2	SEC16A	9	139361447	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	5322887	139361447	1851984	186	20716										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140880973	140880973	+	Frame_Shift_Del	DEL	G	G	-													0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	attgtggtcttcgccctgctGgggatgcagctgtttggggg							TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:140880973delG	ENST00000371372.1	+	14	2023	c.1878delG	c.(1876-1878)ctgfs	p.L626fs	CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371355.4_Frame_Shift_Del_p.L627fs|CACNA1B_ENST00000277551.2_Frame_Shift_Del_p.L626fs|CACNA1B_ENST00000371363.1_Frame_Shift_Del_p.L626fs|CACNA1B_ENST00000371357.1_Frame_Shift_Del_p.L627fs	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	626					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TCGCCCTGCTGGGGATGCAGC	0.612																																					p.L626fs		Atlas-Indel,Pindel	.											.	CACNA1B	266	.	0			c.1877delT						.						52	54	53					9																	140880973		2065	4229	6294	SO:0001589	frameshift_variant	774	exon14			.	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1878delG	chr9.hg19:g.140880973delG	ENSP00000360423:p.Leu626fs	165.0	0.0		183.0	62.0	NM_001243812	B1AQK5	Frame_Shift_Del	DEL	ENST00000371372.1	hg19	CCDS59522.1																																																																																			.	.		0.612	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		-	140880973	G	-	140880973	7	5	123	1	0	1	0	1	0	0	0	0	2541	1335	47	0	1932	0	CACNA1B	9	140880973	Frame_Shift_Del	DEL	G	TCGA-DD-A3A9-01A-11D-A25V-10	1519526	140880973	332458	187	20717										
CUBN	8029	hgsc.bcm.edu	37	chr10	16967302	16967302	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cattactgtgatcagaaataAactgaacaaacatttgatta	5	6	1	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:16967302A>T	ENST00000377833.4	-	43	6649	c.6584T>A	c.(6583-6585)tTt>tAt	p.F2195Y		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2195	CUB 15. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATCAGAAATAAACTGAACAAA	0.388																																					p.F2195Y		Atlas-SNP	.											.	CUBN	515	.	0			c.T6584A						.						69	70	69					10																	16967302		2203	4300	6503	SO:0001583	missense	8029	exon43			GAAATAAACTGAA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.6584T>A	chr10.hg19:g.16967302A>T	ENSP00000367064:p.Phe2195Tyr	260.0	0.0		298.0	48.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.325243	0.81580	.	.	ENSG00000107611	ENST00000377833	T	0.30182	1.54	5.32	5.32	0.75619	CUB (5);	0.000000	0.48286	D	0.000191	T	0.62660	0.2446	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.69636	-0.5092	10	0.51188	T	0.08	.	15.4412	0.75184	1.0:0.0:0.0:0.0	.	2195	O60494	CUBN_HUMAN	Y	2195	ENSP00000367064:F2195Y	ENSP00000367064:F2195Y	F	-	2	0	CUBN	17007308	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	8.494000	0.90477	2.241000	0.73720	0.533000	0.62120	TTT	.	.		0.388	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	16967302	A	T	16967302	3	4	123	1	0	0	0	0	1	0	0	0	4053	14	1	4	4387	4	CUBN	10	16967302	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10		16967302	118567445	188	20718										
GPR158	57512	hgsc.bcm.edu	37	chr10	25887663	25887663	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tctattgtggcttctgaaatGgagaaaaaccccactttttc	7	9	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:25887663G>T	ENST00000376351.3	+	11	3467	c.3108G>T	c.(3106-3108)atG>atT	p.M1036I	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1036					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.M1036I(1)|p.M1036_E1037>IK(1)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CTTCTGAAATGGAGAAAAACC	0.463																																					p.M1036I		Atlas-SNP	.											GPR158,NS,carcinoma,0,1	GPR158	255	.	2	Substitution - Missense(1)|Complex - compound substitution(1)	lung(2)	c.G3108T						.						72	70	71					10																	25887663		2203	4300	6503	SO:0001583	missense	57512	exon11			TGAAATGGAGAAA	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3108G>T	chr10.hg19:g.25887663G>T	ENSP00000365529:p.Met1036Ile	88.0	0.0		110.0	31.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	G	6.532	0.466459	0.12402	.	.	ENSG00000151025	ENST00000376351	T	0.28454	1.61	5.27	1.02	0.19986	.	0.582024	0.17324	N	0.178381	T	0.19485	0.0468	L	0.36672	1.1	0.22684	N	0.998852	B	0.02656	0.0	B	0.09377	0.004	T	0.13926	-1.0491	10	0.40728	T	0.16	.	4.7247	0.12935	0.3964:0.272:0.3316:0.0	.	1036	Q5T848	GP158_HUMAN	I	1036	ENSP00000365529:M1036I	ENSP00000365529:M1036I	M	+	3	0	GPR158	25927669	0.062000	0.20869	1.000000	0.80357	0.983000	0.72400	-0.120000	0.10660	0.593000	0.29745	0.655000	0.94253	ATG	.	.		0.463	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		T	25887663	G	T	25887663	3	4	123	1	0	0	0	0	1	0	0	0	6671	1348	47	3	3150	3	GPR158	10	25887663	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	8920361	25887663	109647084	189	20719										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37507997	37507997	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atgctaaaactggaaatagcCacactgaaacaccaatacca	5	11	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:37507997C>T	ENST00000602533.1	+	34	3288	c.3189C>T	c.(3187-3189)gcC>gcT	p.A1063A	ANKRD30A_ENST00000361713.1_Silent_p.A1063A|ANKRD30A_ENST00000374660.1_Silent_p.A1182A			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1119					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						TGGAAATAGCCACACTGAAAC	0.313																																					p.A1063A		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.C3189T						.						61	60	61					10																	37507997		1812	4062	5874	SO:0001819	synonymous_variant	91074	exon34			AATAGCCACACTG	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.3189C>T	chr10.hg19:g.37507997C>T		174.0	0.0		203.0	65.0	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	hg19																																																																																				.	.		0.313	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37507997	C	T	37507997	2	4	123	1	0	0	0	0	0	0	0	1	658	581	21	3		3	ANKRD30A	10	37507997	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	11620334	37507997	98026750	190	20720										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55600110	55600110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	catttctatcgatggctctgTtggtttgggggtcaattgca	12	7	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:55600110T>C	ENST00000320301.6	-	29	4347	c.3953A>G	c.(3952-3954)aAc>aGc	p.N1318S	PCDH15_ENST00000395432.2_Missense_Mutation_p.N1281S|PCDH15_ENST00000373965.2_Missense_Mutation_p.N1325S|PCDH15_ENST00000395438.1_Missense_Mutation_p.N1318S|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395445.1_Missense_Mutation_p.N1325S|PCDH15_ENST00000395430.1_Missense_Mutation_p.N1318S|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000437009.1_Missense_Mutation_p.N1247S|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000409834.1_Missense_Mutation_p.N929S|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.N1296S|PCDH15_ENST00000361849.3_Missense_Mutation_p.N1318S|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000414778.1_Missense_Mutation_p.N1323S	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1318					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GATGGCTCTGTTGGTTTGGGG	0.428										HNSCC(58;0.16)																											p.N1323S		Atlas-SNP	.											.	PCDH15	1715	.	0			c.A3968G						.						159	151	153					10																	55600110		2203	4300	6503	SO:0001583	missense	65217	exon30			GCTCTGTTGGTTT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3953A>G	chr10.hg19:g.55600110T>C	ENSP00000322604:p.Asn1318Ser	142.0	0.0		186.0	30.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.456328	0.84317	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T;T;T;T;T;T	0.61392	0.3;0.34;0.24;0.26;0.25;0.14;0.13;0.18;0.13;0.11;0.11	5.43	5.43	0.79202	.	.	.	.	.	T	0.67878	0.2940	L	0.36672	1.1	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.997;1.0;0.999;0.998;0.999;1.0;0.997;0.997;0.998;0.998;0.997;1.0;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D	0.85130	0.989;0.997;0.97;0.952;0.997;0.997;0.989;0.995;0.952;0.952;0.995;0.997;0.97	T	0.70204	-0.4936	9	0.59425	D	0.04	.	15.4284	0.75072	0.0:0.0:0.0:1.0	.	1296;1318;1318;1323;1247;1281;1318;1318;1325;1325;1318;1323;1318	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	S	1325;1323;1318;1318;929;1325;1281;1318;1296;1318;1318;1323;1247	ENSP00000363076:N1325S;ENSP00000410304:N1323S;ENSP00000378826:N1318S;ENSP00000386693:N929S;ENSP00000378832:N1325S;ENSP00000378820:N1281S;ENSP00000354950:N1318S;ENSP00000378821:N1296S;ENSP00000322604:N1318S;ENSP00000378818:N1318S;ENSP00000412628:N1247S	ENSP00000322604:N1318S	N	-	2	0	PCDH15	55270116	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.986000	0.88173	2.182000	0.69389	0.472000	0.43445	AAC	.	.		0.428	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		C	55600110	T	C	55600110	3	2	123	1	0	0	0	0	1	0	0	0	11520	1725	60	2	3553	2	PCDH15	10	55600110	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	18092113	55600110	79934637	191	20721										
CDHR1	92211	hgsc.bcm.edu	37	chr10	85972935	85972935	+	Frame_Shift_Del	DEL	C	C	-													0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	caacgtgttcgacatcaattCccacacgggggagatctggc							TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:85972935delC	ENST00000372117.3	+	16	1974	c.1871delC	c.(1870-1872)tccfs	p.S624fs	CDHR1_ENST00000332904.3_Frame_Shift_Del_p.S624fs|CDHR1_ENST00000440770.2_Frame_Shift_Del_p.S328fs	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	624	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						GACATCAATTCCCACACGGGG	0.577																																					p.S624fs		Atlas-Indel,Pindel	.											.	CDHR1	122	.	0			c.1870delT						.						120	106	111					10																	85972935		2203	4300	6503	SO:0001589	frameshift_variant	92211	exon16			.	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1871delC	chr10.hg19:g.85972935delC	ENSP00000361189:p.Ser624fs	155.0	0.0		163.0	54.0	NM_001171971	Q69YZ8|Q8IXY5	Frame_Shift_Del	DEL	ENST00000372117.3	hg19	CCDS7372.1																																																																																			.	.		0.577	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		-	85972935	C	-	85972935	7	5	123	1	0	1	0	1	0	0	0	0	3120	855	30	0	1933	0	CDHR1	10	85972935	Frame_Shift_Del	DEL	C	TCGA-DD-A3A9-01A-11D-A25V-10	30372825	85972935	49561812	192	20722										
FAM190B	54462	hgsc.bcm.edu	37	chr10	86131874	86131874	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aggaagatgctacagttttgGctaaggacagagctgctaat	12	6	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:86131874G>C	ENST00000224756.8	+	2	1251	c.1066G>C	c.(1066-1068)Gct>Cct	p.A356P	CCSER2_ENST00000372088.2_Missense_Mutation_p.A356P|CCSER2_ENST00000359979.4_Missense_Mutation_p.A356P	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	356					microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)											TACAGTTTTGGCTAAGGACAG	0.373																																					p.A356P		Atlas-SNP	.											.	CCSER2	7	.	0			c.G1066C						.						104	103	103					10																	86131874		2203	4300	6503	SO:0001583	missense	54462	exon2			GTTTTGGCTAAGG		CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771			29197	protein-coding gene	gene with protein product			"KIAA1128", "family with sequence similarity 190, member B"	KIAA1128, FAM190B		10574461	Standard	XM_005269905		Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.1066G>C	chr10.hg19:g.86131874G>C	ENSP00000224756:p.Ala356Pro	104.0	0.0		142.0	23.0	NM_018999	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Missense_Mutation	SNP	ENST00000224756.8	hg19	CCDS31235.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.437135	0.25900	.	.	ENSG00000107771	ENST00000359979;ENST00000224756;ENST00000372088	T;T;T	0.55588	0.51;1.86;1.86	5.73	-0.0679	0.13758	.	0.578352	0.16610	N	0.206949	T	0.41488	0.1161	L	0.44542	1.39	0.09310	N	1	P;B;P	0.46220	0.874;0.437;0.874	B;B;P	0.44990	0.369;0.189;0.466	T	0.27640	-1.0068	10	0.52906	T	0.07	-1.1022	3.7258	0.08474	0.4805:0.0:0.3444:0.1751	.	356;356;356	Q9H7U1-3;Q9H7U1;Q9H7U1-2	.;F190B_HUMAN;.	P	356	ENSP00000353068:A356P;ENSP00000224756:A356P;ENSP00000361160:A356P	ENSP00000224756:A356P	A	+	1	0	FAM190B	86121854	0.000000	0.05858	0.003000	0.11579	0.878000	0.50629	-0.266000	0.08631	0.381000	0.24851	-0.136000	0.14681	GCT	.	.		0.373	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999		C	86131874	G	C	86131874	3	2	123	1	0	0	0	0	1	0	0	0	5527	1203	42	4	1068	4	FAM190B	10	86131874	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	158939	86131874	49402873	193	20723										
OPN4	94233	hgsc.bcm.edu	37	chr10	88419162	88419162	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctgctgcttcgtgttcttccTccctctgcttatcatcatct	5	15	5	0	rs34344653		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:88419162T>C	ENST00000241891.5	+	5	904	c.737T>C	c.(736-738)cTc>cCc	p.L246P	OPN4_ENST00000372071.2_Missense_Mutation_p.L257P	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	246					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						GTGTTCTTCCTCCCTCTGCTT	0.592																																					p.L257P		Atlas-SNP	.											.	OPN4	61	.	0			c.T770C						.						260	190	214					10																	88419162		2203	4300	6503	SO:0001583	missense	94233	exon6			TCTTCCTCCCTCT	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"GPCR / Class A : Opsin receptors"	14449	protein-coding gene	gene with protein product	"melanopsin"	606665	"opsin 4 (melanopsin)"			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.737T>C	chr10.hg19:g.88419162T>C	ENSP00000241891:p.Leu246Pro	101.0	0.0		148.0	26.0	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	hg19	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.369293	0.82463	.	.	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.45668	0.89;0.89;0.89	5.15	5.15	0.70609	GPCR, rhodopsin-like superfamily (1);	0.156406	0.39083	N	0.001476	T	0.66096	0.2755	M	0.81614	2.55	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.997	D;D;D	0.72982	0.979;0.961;0.943	T	0.71971	-0.4431	10	0.87932	D	0	.	14.9869	0.71356	0.0:0.0:0.0:1.0	.	257;246;257	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	P	257;246;257	ENSP00000361141:L257P;ENSP00000241891:L246P;ENSP00000393132:L257P	ENSP00000241891:L246P	L	+	2	0	OPN4	88409142	1.000000	0.71417	0.834000	0.33040	0.928000	0.56348	6.172000	0.71932	1.942000	0.56320	0.533000	0.62120	CTC	.	.		0.592	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282		C	88419162	T	C	88419162	3	2	123	1	0	0	0	0	1	0	0	0	10891	1551	54	2	792	2	OPN4	10	88419162	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	2287288	88419162	47115585	194	20724										
BMPR1A	657	hgsc.bcm.edu	37	chr10	88649933	88649933	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	taccttgccttttttaaagtGctattgctcagggcactgtc	8	10	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:88649933G>A	ENST00000372037.3	+	4	719	c.182G>A	c.(181-183)tGc>tAc	p.C61Y	RNU1-19P_ENST00000363306.1_RNA	NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	61					BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						TTTTTAAAGTGCTATTGCTCA	0.403			"Mis, N, F"			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2																												p.C61Y	Ovarian(190;603 2086 22044 30335 47971)	Atlas-SNP	.	yes	Rec		Juvenile polyposis	10	10q22.3	657	"bone morphogenetic protein receptor, type IA"		E	.	BMPR1A	118	.	0			c.G182A						.						165	151	156					10																	88649933		2203	4300	6503	SO:0001583	missense	657	exon4	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	TAAAGTGCTATTG	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779		"CD molecules"	1076	protein-coding gene	gene with protein product		601299		ACVRLK3		8397373, 9730621	Standard	NM_004329		Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.182G>A	chr10.hg19:g.88649933G>A	ENSP00000361107:p.Cys61Tyr	243.0	0.0		275.0	34.0	NM_004329	A8K6U9|Q8NEN8	Missense_Mutation	SNP	ENST00000372037.3	hg19	CCDS7378.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.805747	0.90623	.	.	ENSG00000107779	ENST00000224764;ENST00000372037	D	0.99940	-8.4	6.01	6.01	0.97437	TGF-beta receptor/activin receptor, type I/II (1);	0.000000	0.85682	D	0.000000	D	0.99951	0.9979	M	0.93283	3.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96378	0.9279	10	0.87932	D	0	.	20.5211	0.99222	0.0:0.0:1.0:0.0	.	61	P36894	BMR1A_HUMAN	Y	61	ENSP00000361107:C61Y	ENSP00000224764:C61Y	C	+	2	0	BMPR1A	88639913	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.065000	0.93941	2.861000	0.98227	0.650000	0.86243	TGC	.	.		0.403	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049170.3	NM_004329		A	88649933	G	A	88649933	3	1	123	1	0	0	0	0	1	0	0	0	1469	1319	46	3	188	3	BMPR1A	10	88649933	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	230771	88649933	46884814	195	20725										
IFIT2	3433	hgsc.bcm.edu	37	chr10	91066441	91066441	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgaagaagccttggagaaagCcccaggtgtaacagatgttc	12	8	0	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:91066441C>T	ENST00000371826.3	+	2	897	c.728C>T	c.(727-729)gCc>gTc	p.A243V	LIPA_ENST00000371837.1_Intron|LIPA_ENST00000487618.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	243					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				TTGGAGAAAGCCCCAGGTGTA	0.438																																					p.A243V		Atlas-SNP	.											.	IFIT2	39	.	0			c.C728T						.						78	78	78					10																	91066441		1981	4180	6161	SO:0001583	missense	3433	exon2			AGAAAGCCCCAGG	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"Tetratricopeptide (TTC) repeat domain containing"	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.728C>T	chr10.hg19:g.91066441C>T	ENSP00000360891:p.Ala243Val	129.0	0.0		137.0	12.0	NM_001547	Q5T767	Missense_Mutation	SNP	ENST00000371826.3	hg19	CCDS41548.1	.	.	.	.	.	.	.	.	.	.	C	8.312	0.822276	0.16678	.	.	ENSG00000119922	ENST00000371826	T	0.38240	1.15	4.58	-2.38	0.06622	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.684102	0.13110	U	0.413079	T	0.26412	0.0645	M	0.62723	1.935	0.09310	N	0.999999	B	0.12630	0.006	B	0.15052	0.012	T	0.25882	-1.0119	10	0.33940	T	0.23	-0.2574	1.7187	0.02907	0.1298:0.3984:0.2394:0.2324	.	243	P09913	IFIT2_HUMAN	V	243	ENSP00000360891:A243V	ENSP00000360891:A243V	A	+	2	0	IFIT2	91056421	0.002000	0.14202	0.012000	0.15200	0.069000	0.16628	0.167000	0.16602	-0.421000	0.07416	0.655000	0.94253	GCC	.	.		0.438	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547		T	91066441	C	T	91066441	3	4	123	1	0	0	0	0	1	0	0	0	7532	739	26	3	734	3	IFIT2	10	91066441	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	2416508	91066441	44468306	196	20726										
PLCE1	51196	hgsc.bcm.edu	37	chr10	95791760	95791760	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gacgcttttaaaagcaaaaaGgagcgatccactttgttagt	9	7	0	0	rs573916830	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:95791760G>A	ENST00000371380.3	+	1	1192	c.957G>A	c.(955-957)aaG>aaA	p.K319K	PLCE1_ENST00000260766.3_Silent_p.K319K			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	319					activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				AAAGCAAAAAGGAGCGATCCA	0.388																																					p.K319K		Atlas-SNP	.											.	PLCE1	543	.	0			c.G957A						.						114	112	113					10																	95791760		1853	4088	5941	SO:0001819	synonymous_variant	51196	exon2			CAAAAAGGAGCGA		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.957G>A	chr10.hg19:g.95791760G>A		110.0	0.0		134.0	13.0	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	hg19	CCDS41552.1																																																																																			.	.		0.388	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		A	95791760	G	A	95791760	2	1	123	1	0	0	0	0	0	0	0	1	12043	991	35	3		3	PLCE1	10	95791760	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	4725319	95791760	39742987	197	20727										
SLK	9748	hgsc.bcm.edu	37	chr10	105763103	105763103	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	actctgacagtggagaaaatAaagaagaaataggttcttta	9	4	2	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:105763103A>G	ENST00000369755.3	+	9	2712	c.2167A>G	c.(2167-2169)Aaa>Gaa	p.K723E	SLK_ENST00000335753.4_Missense_Mutation_p.K723E	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	723					apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TGGAGAAAATAAAGAAGAAAT	0.373																																					p.K723E	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.A2167G						.						48	51	50					10																	105763103		2203	4300	6503	SO:0001583	missense	9748	exon9			GAAAATAAAGAAG		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.2167A>G	chr10.hg19:g.105763103A>G	ENSP00000358770:p.Lys723Glu	40.0	0.0		40.0	12.0	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	hg19	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	8.487	0.861211	0.17178	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.70045	-0.45;-0.45	5.71	5.71	0.89125	Protein kinase-like domain (1);	0.382752	0.29348	N	0.012408	T	0.62196	0.2408	M	0.63428	1.95	0.45108	D	0.99812	B;B	0.19583	0.037;0.022	B;B	0.19148	0.024;0.011	T	0.58624	-0.7604	10	0.31617	T	0.26	.	11.086	0.48086	0.9281:0.0:0.0719:0.0	.	723;723	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	E	723	ENSP00000336824:K723E;ENSP00000358770:K723E	ENSP00000336824:K723E	K	+	1	0	SLK	105753093	1.000000	0.71417	0.994000	0.49952	0.092000	0.18411	4.782000	0.62396	2.184000	0.69523	0.454000	0.30748	AAA	.	.		0.373	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		G	105763103	A	G	105763103	3	3	123	1	0	0	0	0	1	0	0	0	14763	363	13	2	2201	2	SLK	10	105763103	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	9971343	105763103	29771644	198	20728										
C10orf79	80217	hgsc.bcm.edu	37	chr10	105952057	105952057	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agaaatattccttgctgatcAtaactagaaaagaagaaatc	6	6	1	5			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:105952057A>G	ENST00000278064.2	-	12	1564	c.1239T>C	c.(1237-1239)taT>taC	p.Y413Y	WDR96_ENST00000357060.3_Silent_p.Y482Y|WDR96_ENST00000428666.1_Silent_p.Y483Y																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTTGCTGATCATAACTAGAAA	0.363																																					p.Y482Y		Atlas-SNP	.											.	WDR96	183	.	0			c.T1446C						.						97	94	95					10																	105952057		2202	4299	6501	SO:0001819	synonymous_variant	80217	exon12			CTGATCATAACTA																												ENST00000278064.2:c.1239T>C	chr10.hg19:g.105952057A>G		69.0	0.0		75.0	19.0	NM_025145		Silent	SNP	ENST00000278064.2	hg19																																																																																				.	.		0.363	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			G	105952057	A	G	105952057	2	3	123	1	0	0	0	0	0	0	0	1	1620	224	8	2		2	C10orf79	10	105952057	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	188954	105952057	29582690	199	20729										
C10orf137	26098	hgsc.bcm.edu	37	chr10	127434413	127434413	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tatgtaacacgggaaggctcAtgcggatttgtgcgcaggcc	14	9	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:127434413A>G	ENST00000356792.4	+	19	2960	c.2728A>G	c.(2728-2730)Atg>Gtg	p.M910V	RP11-383C5.7_ENST00000594025.1_RNA|RP11-383C5.7_ENST00000449436.1_RNA|RP11-383C5.7_ENST00000593871.1_RNA|RP11-383C5.7_ENST00000601363.1_RNA|RP11-383C5.7_ENST00000602030.1_RNA|C10orf137_ENST00000337623.3_Missense_Mutation_p.M876V|RP11-383C5.7_ENST00000600784.1_RNA	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		910					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GGGAAGGCTCATGCGGATTTG	0.428																																					p.M910V		Atlas-SNP	.											.	C10orf137	153	.	0			c.A2728G						.						118	116	117					10																	127434413		2203	4300	6503	SO:0001583	missense	26098	exon19			AGGCTCATGCGGA																												ENST00000356792.4:c.2728A>G	chr10.hg19:g.127434413A>G	ENSP00000349244:p.Met910Val	128.0	0.0		166.0	50.0	NM_001202438	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	hg19	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.980803	0.53827	.	.	ENSG00000107938	ENST00000356792;ENST00000337623	T;T	0.75589	-0.95;-0.95	5.6	5.6	0.85130	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.84880	0.5570	M	0.71871	2.18	0.80722	D	1	D;D;P	0.71674	0.982;0.998;0.917	D;D;D	0.70016	0.961;0.967;0.915	D	0.85902	0.1435	10	0.54805	T	0.06	.	15.8023	0.78463	1.0:0.0:0.0:0.0	.	910;257;876	Q3B7T1;Q5VZQ1;Q3B7T1-5	EDRF1_HUMAN;.;.	V	910;876	ENSP00000349244:M910V;ENSP00000336727:M876V	ENSP00000336727:M876V	M	+	1	0	C10orf137	127424403	1.000000	0.71417	0.998000	0.56505	0.073000	0.16967	8.962000	0.93254	2.137000	0.66172	0.533000	0.62120	ATG	.	.		0.428	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			G	127434413	A	G	127434413	3	3	123	1	0	0	0	0	1	0	0	0	1596	217	8	2	2696	2	C10orf137	10	127434413	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	21482356	127434413	8100334	200	20730										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135038187	135038187	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atcgcaaaggtggtgagccaGgtgcacgcgttccaggagaa	15	9	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:135038187G>A	ENST00000304613.3	+	30	5064	c.5043G>A	c.(5041-5043)caG>caA	p.Q1681Q	KNDC1_ENST00000368572.2_Silent_p.Q1683Q			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1681	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TGGTGAGCCAGGTGCACGCGT	0.612																																					p.Q1681Q		Atlas-SNP	.											.	KNDC1	155	.	0			c.G5043A						.						86	70	75					10																	135038187		2203	4300	6503	SO:0001819	synonymous_variant	85442	exon30			GAGCCAGGTGCAC	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.5043G>A	chr10.hg19:g.135038187G>A		207.0	0.0		307.0	37.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	hg19	CCDS7674.1																																																																																			.	.		0.612	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	135038187	G	A	135038187	2	1	123	1	0	0	0	0	0	0	0	1	8435	991	35	3		3	KNDC1	10	135038187	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	7603774	135038187	496560	201	20731										
ECHS1	1892	hgsc.bcm.edu	37	chr10	135179489	135179489	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agatcccctacctgcattcaCtgattctttggccatcgcta	6	14	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:135179489C>G	ENST00000368547.3	-	6	1085	c.730G>C	c.(730-732)Gtg>Ctg	p.V244L		NM_004092.3	NP_004083.3	P30084	ECHM_HUMAN	enoyl CoA hydratase, short chain, 1, mitochondrial	244					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	10		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;1.62e-06)|OV - Ovarian serous cystadenocarcinoma(35;5.75e-06)|Epithelial(32;7.58e-06)		CCTGCATTCACTGATTCTTTG	0.483																																					p.V244L	GBM(132;1720 1771 5373 10277 21402)	Atlas-SNP	.											.	ECHS1	31	.	0			c.G730C						.						212	176	188					10																	135179489		2202	4300	6502	SO:0001583	missense	1892	exon6			CATTCACTGATTC		CCDS7681.1	10q26.2-q26.3	2010-05-04	2010-04-30		ENSG00000127884	ENSG00000127884	4.2.1.17		3151	protein-coding gene	gene with protein product		602292	"enoyl Coenzyme A hydratase, short chain, 1, mitochondrial"			8012501	Standard	NM_004092		Approved	SCEH	uc001lmu.3	P30084	OTTHUMG00000019320	ENST00000368547.3:c.730G>C	chr10.hg19:g.135179489C>G	ENSP00000357535:p.Val244Leu	101.0	0.0		100.0	18.0	NM_004092	O00739|Q5VWY1|Q96H54	Missense_Mutation	SNP	ENST00000368547.3	hg19	CCDS7681.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760004	0.69763	.	.	ENSG00000127884	ENST00000368547	T	0.67698	-0.28	5.39	5.39	0.77823	Crontonase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.63604	0.2525	L	0.34521	1.04	0.80722	D	1	B	0.28233	0.204	B	0.38755	0.281	T	0.65076	-0.6256	10	0.72032	D	0.01	.	15.0604	0.71947	0.0:1.0:0.0:0.0	.	244	P30084	ECHM_HUMAN	L	244	ENSP00000357535:V244L	ENSP00000357535:V244L	V	-	1	0	ECHS1	135029479	0.999000	0.42202	0.993000	0.49108	0.944000	0.59088	4.484000	0.60271	2.701000	0.92244	0.555000	0.69702	GTG	.	.		0.483	ECHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051156.1			G	135179489	C	G	135179489	3	3	123	1	0	0	0	0	1	0	0	0	4898	565	20	4	154	4	ECHS1	10	135179489	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	141302	135179489	355258	202	20732										
ODF3	113746	hgsc.bcm.edu	37	chr11	198506	198506	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	catggtaatggggcccaataCcgtcggcaaggcctcccagc	12	14	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:198506C>A	ENST00000325113.4	+	5	772	c.455C>A	c.(454-456)aCc>aAc	p.T152N	BET1L_ENST00000410108.1_Intron|ODF3_ENST00000525282.1_Missense_Mutation_p.T152N	NM_053280.3	NP_444510.2	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3	152					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	outer dense fiber (GO:0001520)				biliary_tract(1)|breast(1)|kidney(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)	9		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		GGGCCCAATACCGTCGGCAAG	0.662																																					p.T152N		Atlas-SNP	.											.	ODF3	27	.	0			c.C455A						.						56	56	56					11																	198506		2203	4300	6503	SO:0001583	missense	113746	exon5			CCAATACCGTCGG	AB067774	CCDS7688.1, CCDS65981.1	11p15.5	2010-04-23			ENSG00000177947	ENSG00000177947			19905	protein-coding gene	gene with protein product	"cancer/testis antigen 135"	608356				11870087	Standard	NM_001286136		Approved	SHIPPO1, hSHIPPO, CT135	uc001lob.3	Q96PU9	OTTHUMG00000119073	ENST00000325113.4:c.455C>A	chr11.hg19:g.198506C>A	ENSP00000325868:p.Thr152Asn	171.0	0.0		159.0	23.0	NM_053280	B7ZLT0|Q69YX0	Missense_Mutation	SNP	ENST00000325113.4	hg19	CCDS7688.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.845103	0.71603	.	.	ENSG00000177947	ENST00000325113;ENST00000540150;ENST00000525282	T;T	0.32272	1.48;1.46	4.87	4.87	0.63330	.	0.127854	0.35407	N	0.003240	T	0.35508	0.0934	N	0.19112	0.55	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.68483	0.939;0.958	T	0.06075	-1.0847	10	0.15952	T	0.53	-21.333	13.5189	0.61555	0.0:1.0:0.0:0.0	.	152;152	B7ZLT0;Q96PU9	.;ODF3A_HUMAN	N	152;69;152	ENSP00000325868:T152N;ENSP00000436588:T152N	ENSP00000325868:T152N	T	+	2	0	ODF3	188506	0.002000	0.14202	0.732000	0.30844	0.854000	0.48673	1.682000	0.37628	2.227000	0.72691	0.561000	0.74099	ACC	.	.		0.662	ODF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239287.1			A	198506	C	A	198506	3	1	123	1	0	0	0	0	1	0	0	0	10838	507	18	3	469	3	ODF3	11	198506	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		198506	134808010	203	20733										
PHRF1	57661	hgsc.bcm.edu	37	chr11	611702	611702	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctggtgaaggcgtacgtggaCaagtacaggcacatgcgcag	15	9	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:611702C>A	ENST00000264555.5	+	18	5003	c.4875C>A	c.(4873-4875)gaC>gaA	p.D1625E	PHRF1_ENST00000413872.2_Missense_Mutation_p.D1623E|PHRF1_ENST00000416188.2_Missense_Mutation_p.D1624E|PHRF1_ENST00000533464.1_Missense_Mutation_p.D1621E	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1625					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CGTACGTGGACAAGTACAGGC	0.617																																					p.D1624E		Atlas-SNP	.											.	PHRF1	188	.	0			c.C4872A						.						55	61	59					11																	611702		2138	4264	6402	SO:0001583	missense	57661	exon18			CGTGGACAAGTAC	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.4875C>A	chr11.hg19:g.611702C>A	ENSP00000264555:p.Asp1625Glu	66.0	0.0		81.0	9.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	C	10.15	1.271567	0.23221	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03	4.58	-0.252	0.12999	.	0.201391	0.24920	N	0.034546	T	0.47303	0.1438	L	0.42245	1.32	0.32907	D	0.514006	B;B;B;B	0.31548	0.15;0.328;0.099;0.06	B;B;B;B	0.37015	0.046;0.239;0.069;0.031	T	0.42816	-0.9429	10	0.30854	T	0.27	-32.3459	2.791	0.05388	0.153:0.3802:0.3095:0.1572	.	1621;1623;1624;1625	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	E	1625;1623;1624;1621	ENSP00000264555:D1625E;ENSP00000388589:D1623E;ENSP00000410626:D1624E;ENSP00000431870:D1621E	ENSP00000264555:D1625E	D	+	3	2	PHRF1	601702	0.974000	0.33945	0.992000	0.48379	0.174000	0.22865	0.139000	0.16036	-0.053000	0.13289	-1.134000	0.01955	GAC	.	.		0.617	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		A	611702	C	A	611702	3	1	123	1	0	0	0	0	1	0	0	0	11870	477	17	3	4938	3	PHRF1	11	611702	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	413196	611702	134394814	204	20734										
MUC2	4583	hgsc.bcm.edu	37	chr11	1081136	1081136	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgcaggtgaacctgccccacGtgaccggtgagttgtgcccc	13	14	0	3	rs555224884		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:1081136G>A	ENST00000441003.2	+	11	1459	c.1432G>A	c.(1432-1434)Gtg>Atg	p.V478M	MUC2_ENST00000359061.5_Missense_Mutation_p.V478M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	478	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCTGCCCCACGTGACCGGTGA	0.652													G|||	1	0.000199681	8e-04	0	5008	,	,		16186	0		0	False		,,,				2504	0				p.V478M		Atlas-SNP	.											.	MUC2	614	.	0			c.G1432A						.						33	38	36					11																	1081136		1979	4161	6140	SO:0001583	missense	4583	exon11			CCCCACGTGACCG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.1432G>A	chr11.hg19:g.1081136G>A	ENSP00000415183:p.Val478Met	96.0	0.0		143.0	27.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	G	14.51	2.558420	0.45590	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.59906	0.23;0.23	3.64	1.6	0.23607	.	1.376200	0.05521	U	0.562127	T	0.65091	0.2658	M	0.62723	1.935	0.21697	N	0.999588	P	0.48764	0.915	P	0.53760	0.734	T	0.54289	-0.8316	10	0.33940	T	0.23	.	8.1327	0.31037	0.0988:0.1638:0.7374:0.0	.	478	E7EUV1	.	M	478	ENSP00000415183:V478M;ENSP00000351956:V478M	ENSP00000351956:V478M	V	+	1	0	MUC2	1071136	0.221000	0.23642	0.987000	0.45799	0.798000	0.45092	1.379000	0.34340	1.878000	0.54408	0.491000	0.48974	GTG	.	.		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1081136	G	A	1081136	3	1	123	1	0	0	0	0	1	0	0	0	9984	1145	40	1	1474	1	MUC2	11	1081136	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	469434	1081136	133925380	205	20735										
KRTAP5-3	387266	hgsc.bcm.edu	37	chr11	1629511	1629511	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cagcagcagacaggtacacaGcagccggagccacagccccc	11	17	0	1	rs371318576		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:1629511G>A	ENST00000399685.1	-	1	182	c.105C>T	c.(103-105)tgC>tgT	p.C35C		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	35	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		CAGGTACACAGCAGCCGGAGC	0.677																																					p.C35C		Atlas-SNP	.											.	KRTAP5-3	33	.	0			c.C105T						.	G		1,4397		0,1,2198	59	77	71		105	1.4	1	11		71	0,8590		0,0,4295	no	coding-synonymous	KRTAP5-3	NM_001012708.2		0,1,6493	AA,AG,GG		0.0,0.0227,0.0077		35/239	1629511	1,12987	2199	4295	6494	SO:0001819	synonymous_variant	387266	exon1			TACACAGCAGCCG	AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"Keratin associated proteins"	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.105C>T	chr11.hg19:g.1629511G>A		49.0	0.0		42.0	10.0	NM_001012708	Q6PL44|Q701N3	Silent	SNP	ENST00000399685.1	hg19	CCDS41591.1																																																																																			.	.		0.677	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1			A	1629511	G	A	1629511	2	1	123	1	0	0	0	0	0	0	0	1	8571	963	34	3		3	KRTAP5-3	11	1629511	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	548375	1629511	133377005	206	20736										
TNNT3	7140	hgsc.bcm.edu	37	chr11	1955022	1955023	+	Silent	DNP	CC	CC	AA													0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atcgacagccactttgaagcCcggaagaaggaggaggagga					rs193178655		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:1955022_1955023CC>AA	ENST00000397301.1	+	11	284_285	c.276_277CC>AA	c.(274-279)gcCCgg>gcAAgg	p.92_93AR>AR	TNNT3_ENST00000446240.1_Silent_p.62_63AR>AR|TNNT3_ENST00000381561.4_Silent_p.84_85AR>AR|TNNT3_ENST00000397304.2_Silent_p.62_63AR>AR|TNNT3_ENST00000360603.3_Silent_p.75_76AR>AR|TNNT3_ENST00000381548.3_Silent_p.83_84AR>AR|TNNT3_ENST00000381549.3_Silent_p.73_74AR>AR|TNNT3_ENST00000381589.3_Silent_p.79_80AR>AR|TNNT3_ENST00000278317.6_Silent_p.81_82AR>AR|TNNT3_ENST00000381579.3_Silent_p.73_74AR>AR|TNNT3_ENST00000381558.1_Silent_p.73_74AR>AR			P45378	TNNT3_HUMAN	troponin T type 3 (skeletal, fast)	92					ATP catabolic process (GO:0006200)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)|regulation of striated muscle contraction (GO:0006942)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium-dependent protein binding (GO:0048306)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)			breast(2)|endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(4)|stomach(1)	19		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00253)|Lung(200;0.0333)|LUSC - Lung squamous cell carcinoma(625;0.0826)		ACTTTGAAGCCCGGAAGAAGGA	0.604																																					p.A81A|p.R82R		Atlas-SNP	.											.	TNNT3	68	.	0			c.C243A|c.C244A						.																																			SO:0001819	synonymous_variant	7140	exon10			TGAAGCCCGGAAG|GAAGCCCGGAAGA	M21984	CCDS7727.1, CCDS41594.1, CCDS41595.1, CCDS41596.1	11p15.5	2014-09-17	2005-09-12		ENSG00000130595	ENSG00000130595			11950	protein-coding gene	gene with protein product	"troponin-T3, skeletal, fast"	600692	"troponin T3, skeletal, fast"			8172653	Standard	NM_001042782		Approved	AMCD2B, DA2B, FSSV, DKFZp779M2348	uc001lup.4	P45378	OTTHUMG00000012475	Exception_encountered	chr11.hg19:g.1955022_1955023delinsAA		178.0|177.0	0.0		218.0|219.0	26.0|25.0	NM_006757	A8MQ76|A8MSW1|B3KPX3|B7WP64|B7ZL26|B7ZVV9|Q12975|Q12976|Q12977|Q12978|Q17RG9|Q6FH29|Q6N056|Q86TH6	Silent	SNP	ENST00000397301.1	hg19																																																																																				.	.|C|1.000;T|0.000		0.604	TNNT3-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000142920.3	NM_006757		AA	1955023	CC	AA	1955022	2	1	123	1	0	0	0	0	0	0	0	1	16347	610	22	3		3	TNNT3	11	1955022	Silent	DNP	CC	TCGA-DD-A3A9-01A-11D-A25V-10	325511	1955022	133051494	207	20737										
INS-IGF2	723961	hgsc.bcm.edu	37	chr11	2170519	2170519	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agcagggggtgccctggctgTggcgtccagaccctctggcc	16	14	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:2170519T>A	ENST00000397270.1	-	3	302	c.244A>T	c.(244-246)Aca>Tca	p.T82S	IGF2-AS_ENST00000381361.3_RNA|INS-IGF2_ENST00000481781.1_5'UTR|IGF2-AS_ENST00000381363.4_RNA|IGF2-AS_ENST00000445504.2_RNA|IGF2_ENST00000300632.5_5'UTR	NM_001042376.2	NP_001035835.1	F8WCM5	INSR2_HUMAN	INS-IGF2 readthrough	82						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	5		all_epithelial(84;0.00018)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.0832)|Lung(200;0.156)		GCCCTGGCTGTGGCGTCCAGA	0.587																																					p.T82S		Atlas-SNP	.											.	INS-IGF2	8	.	0			c.A244T						.						75	85	82					11																	2170519		2036	4167	6203	SO:0001583	missense	723961	exon3			TGGCTGTGGCGTC	DQ104205	CCDS41598.1	11p15.5	2011-03-23			ENSG00000129965	ENSG00000129965			33527	other	readthrough						16531418	Standard	NM_001042376		Approved		uc001lvm.3	F8WCM5	OTTHUMG00000166213	ENST00000397270.1:c.244A>T	chr11.hg19:g.2170519T>A	ENSP00000380440:p.Thr82Ser	60.0	0.0		62.0	11.0	NM_001042376	Q1WM24	Missense_Mutation	SNP	ENST00000397270.1	hg19	CCDS41598.1	.	.	.	.	.	.	.	.	.	.	T	10.58	1.391123	0.25118	.	.	ENSG00000129965	ENST00000397270	D	0.95412	-3.7	3.26	-5.09	0.02920	.	0.526148	0.12594	U	0.455347	D	0.90304	0.6967	L	0.43152	1.355	0.09310	N	1	B	0.16396	0.017	B	0.16289	0.015	T	0.79254	-0.1879	10	0.72032	D	0.01	-6.1421	7.8832	0.29635	0.1511:0.0:0.6126:0.2362	.	82	F8WCM5	.	S	82	ENSP00000380440:T82S	ENSP00000348986:T82S	T	-	1	0	INS-IGF2	2127095	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	-1.544000	0.02192	-1.047000	0.03242	0.454000	0.30748	ACA	.	.		0.587	INS-IGF2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000388404.1	NM_001042376.2		A	2170519	T	A	2170519	3	1	123	1	0	0	0	0	1	0	0	0	7772	1696	59	4	366	4	INS-IGF2	11	2170519	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	215497	2170519	132835997	208	20738										
TSSC4	10078	hgsc.bcm.edu	37	chr11	2424378	2424378	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cagcctggaagatgtgaccgAggtcagcgagcagagcaatc	14	10	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:2424378A>C	ENST00000333256.6	+	3	958	c.515A>C	c.(514-516)gAg>gCg	p.E172A	TSSC4_ENST00000467308.1_3'UTR|TSSC4_ENST00000380996.5_Missense_Mutation_p.E108A|AC124057.5_ENST00000433035.1_RNA|TSSC4_ENST00000451491.2_Missense_Mutation_p.E172A|TSSC4_ENST00000380992.1_Splice_Site_p.E108A			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	172										endometrium(3)|large_intestine(1)|lung(4)	8		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGTGACCGAGGTCAGCGAG	0.667																																					p.E172A		Atlas-SNP	.											.	TSSC4	19	.	0			c.A515C						.						28	28	28					11																	2424378		2201	4298	6499	SO:0001583	missense	10078	exon2			TGACCGAGGTCAG	AF125568	CCDS7735.1, CCDS73241.1	11p15.5	2008-02-05			ENSG00000184281	ENSG00000184281			12386	protein-coding gene	gene with protein product		603852				10072438	Standard	XM_005252722		Approved		uc001lwl.3	Q9Y5U2	OTTHUMG00000009895	ENST00000333256.6:c.515A>C	chr11.hg19:g.2424378A>C	ENSP00000331087:p.Glu172Ala	99.0	0.0		90.0	9.0	NM_005706	C9JS66|Q86VL2|Q9BRS6	Missense_Mutation	SNP	ENST00000333256.6	hg19	CCDS7735.1	.	.	.	.	.	.	.	.	.	.	A	16.45	3.126501	0.56721	.	.	ENSG00000184281	ENST00000380996;ENST00000333256;ENST00000380992;ENST00000437110;ENST00000440813;ENST00000496468;ENST00000451491	T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69	3.52	3.52	0.40303	.	0.144148	0.44902	U	0.000419	T	0.66277	0.2773	M	0.77103	2.36	0.50813	D	0.999895	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.984	T	0.70988	-0.4722	10	0.72032	D	0.01	-19.9944	11.6947	0.51536	1.0:0.0:0.0:0.0	.	172;108	Q9Y5U2;Q9Y5U2-2	TSSC4_HUMAN;.	A	108;172;108;172;108;172;172	ENSP00000370384:E108A;ENSP00000331087:E172A;ENSP00000370380:E108A;ENSP00000396925:E172A;ENSP00000416937:E108A;ENSP00000435013:E172A;ENSP00000411224:E172A	ENSP00000331087:E172A	E	+	2	0	TSSC4	2380954	1.000000	0.71417	0.717000	0.30585	0.362000	0.29581	4.604000	0.61112	1.618000	0.50286	0.379000	0.24179	GAG	.	.		0.667	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706		C	2424378	A	C	2424378	3	2	123	1	0	0	0	0	1	0	0	0	16682	304	11	5	517	5	TSSC4	11	2424378	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	253859	2424378	132582138	209	20739										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6579426	6579426	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcaacctcaggcagtttcccTggccagtacacagaagcaga	10	13	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:6579426T>C	ENST00000527990.2	+	23	8901	c.8901T>C	c.(8899-8901)ccT>ccC	p.P2967P	DNHD1_ENST00000254579.6_Silent_p.P2967P			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2967					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GCAGTTTCCCTGGCCAGTACA	0.537																																					p.P2967P		Atlas-SNP	.											.	DNHD1	198	.	0			c.T8901C						.						68	59	62					11																	6579426		692	1591	2283	SO:0001819	synonymous_variant	144132	exon25			TTTCCCTGGCCAG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.8901T>C	chr11.hg19:g.6579426T>C		147.0	0.0		137.0	69.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	hg19	CCDS44532.1																																																																																			.	.		0.537	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		C	6579426	T	C	6579426	2	2	123	1	0	0	0	0	0	0	0	1	4670	1567	55	2		2	DNHD1	11	6579426	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	4155048	6579426	128427090	210	20740										
OR10A5	144124	hgsc.bcm.edu	37	chr11	6867579	6867579	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttgtgttcctatactcgcatTgctgctgctatcctcaagat	7	11	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:6867579T>C	ENST00000299454.4	+	1	697	c.666T>C	c.(664-666)atT>atC	p.I222I	OR10A5_ENST00000379831.2_Silent_p.I226I			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	222					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		ATACTCGCATTGCTGCTGCTA	0.473																																					p.I222I	Pancreas(44;21 1072 25662 28041 45559)	Atlas-SNP	.											.	OR10A5	48	.	0			c.T666C						.						289	236	254					11																	6867579		2201	4296	6497	SO:0001819	synonymous_variant	144124	exon1			TCGCATTGCTGCT	AF324499	CCDS7773.1	11p15.4	2012-08-09			ENSG00000166363	ENSG00000166363		"GPCR / Class A : Olfactory receptors"	15131	protein-coding gene	gene with protein product		608493		OR10A1			Standard	NM_178168		Approved	OR11-403, JCG6	uc001met.1	Q9H207	OTTHUMG00000165738	ENST00000299454.4:c.666T>C	chr11.hg19:g.6867579T>C		445.0	0.0		452.0	54.0	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	hg19	CCDS7773.1																																																																																			.	.		0.473	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168		C	6867579	T	C	6867579	2	2	123	1	0	0	0	0	0	0	0	1	10902	1800	63	2		2	OR10A5	11	6867579	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	288153	6867579	128138937	211	20741										
SYT9	143425	hgsc.bcm.edu	37	chr11	7334640	7334640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttcaaggcataattcaatccGaagacaactcaacttgtcaa	5	10	4	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:7334640G>A	ENST00000318881.6	+	3	749	c.512G>A	c.(511-513)cGa>cAa	p.R171Q	SYT9_ENST00000396716.2_Missense_Mutation_p.R139Q	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	171					positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		AATTCAATCCGAAGACAACTC	0.388																																					p.R171Q		Atlas-SNP	.											.	SYT9	91	.	0			c.G512A						.						44	42	43					11																	7334640		2201	4296	6497	SO:0001583	missense	143425	exon3			CAATCCGAAGACA	AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.512G>A	chr11.hg19:g.7334640G>A	ENSP00000324419:p.Arg171Gln	95.0	0.0		126.0	25.0	NM_175733		Missense_Mutation	SNP	ENST00000318881.6	hg19	CCDS7778.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.623302	0.87460	.	.	ENSG00000170743	ENST00000396716;ENST00000318881	T;T	0.56103	0.48;0.5	5.85	5.85	0.93711	.	0.000000	0.56097	D	0.000029	T	0.49745	0.1575	L	0.50333	1.59	0.58432	D	0.999998	B	0.23650	0.089	B	0.23716	0.048	T	0.34700	-0.9818	10	0.25106	T	0.35	.	18.0311	0.89285	0.0:0.0:1.0:0.0	.	171	Q86SS6	SYT9_HUMAN	Q	139;171	ENSP00000379944:R139Q;ENSP00000324419:R171Q	ENSP00000324419:R171Q	R	+	2	0	SYT9	7291216	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.814000	0.86154	2.932000	0.99384	0.643000	0.83706	CGA	.	.		0.388	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		A	7334640	G	A	7334640	3	1	123	1	0	0	0	0	1	0	0	0	15496	1058	37	1	522	1	SYT9	11	7334640	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	467061	7334640	127671876	212	20742										
COMMD9	29099	hgsc.bcm.edu	37	chr11	36296268	36296268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgtttctttgctcagctccaCggtgacagctgagatggagg	13	9	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:36296268C>T	ENST00000263401.5	-	6	527	c.511G>A	c.(511-513)Gtg>Atg	p.V171M	LINC00610_ENST00000355500.1_lincRNA|COMMD9_ENST00000452374.2_Missense_Mutation_p.V129M|COMMD9_ENST00000533308.1_5'Flank|COMMD9_ENST00000532705.1_Missense_Mutation_p.R159H	NM_014186.3	NP_054905.2	Q9P000	COMD9_HUMAN	COMM domain containing 9	171	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.									kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	5	all_lung(20;0.211)	all_hematologic(20;0.107)				CTCAGCTCCACGGTGACAGCT	0.547																																					p.V171M		Atlas-SNP	.											.	COMMD9	21	.	0			c.G511A						.						165	135	145					11																	36296268		2202	4298	6500	SO:0001583	missense	29099	exon6			GCTCCACGGTGAC	AY542164	CCDS7900.1, CCDS44571.1	11p13	2008-02-05			ENSG00000110442	ENSG00000110442			25014	protein-coding gene	gene with protein product		612299				15799966	Standard	NM_014186		Approved	HSPC166, FLJ31106	uc001mwn.4	Q9P000	OTTHUMG00000166333	ENST00000263401.5:c.511G>A	chr11.hg19:g.36296268C>T	ENSP00000263401:p.Val171Met	248.0	0.0		345.0	173.0	NM_014186	E9PAN2|Q96FI2|Q9H0R0	Missense_Mutation	SNP	ENST00000263401.5	hg19	CCDS7900.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.65|13.65	2.301182|2.301182	0.40694|0.40694	.|.	.|.	ENSG00000110442|ENSG00000110442	ENST00000532705|ENST00000263401;ENST00000452374	.|T;T	.|0.09723	.|2.95;2.95	5.66|5.66	-8.51|-8.51	0.00923|0.00923	.|COMM domain (1);	.|0.383306	.|0.33772	.|N	.|0.004574	T|T	0.03305|0.03305	0.0096|0.0096	N|N	0.10916|0.10916	0.065|0.065	0.18873|0.18873	N|N	0.999989|0.999989	.|P;B	.|0.48230	.|0.907;0.031	.|B;B	.|0.32022	.|0.139;0.018	T|T	0.24870|0.24870	-1.0148|-1.0148	6|10	0.87932|0.27082	D|T	0|0.32	-16.116|-16.116	16.1983|16.1983	0.82046|0.82046	0.0:0.5707:0.0:0.4293|0.0:0.5707:0.0:0.4293	.|.	.|129;171	.|Q9P000-2;Q9P000	.|.;COMD9_HUMAN	H|M	159|171;129	.|ENSP00000263401:V171M;ENSP00000392510:V129M	ENSP00000435599:R159H|ENSP00000263401:V171M	R|V	-|-	2|1	0|0	COMMD9|COMMD9	36252844|36252844	0.001000|0.001000	0.12720|0.12720	0.443000|0.443000	0.26883|0.26883	0.938000|0.938000	0.57974|0.57974	-0.637000|-0.637000	0.05459|0.05459	-1.794000|-1.794000	0.01256|0.01256	-0.290000|-0.290000	0.09829|0.09829	CGT|GTG	.	.		0.547	COMMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389196.1	NM_014186		T	36296268	C	T	36296268	3	4	123	1	0	0	0	0	1	0	0	0	3725	536	19	1	89	1	COMMD9	11	36296268	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	28961628	36296268	98710248	213	20743										
RAG1	5896	hgsc.bcm.edu	37	chr11	36596385	36596385	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atgcccttcggaatgctgagAaggtacttctgccaggctac	11	11	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:36596385A>T	ENST00000299440.5	+	2	1643	c.1531A>T	c.(1531-1533)Aag>Tag	p.K511*		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	511					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				GAATGCTGAGAAGGTACTTCT	0.502									Familial Hemophagocytic Lymphohistiocytosis																												p.K511X	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.A1531T						.						120	113	115					11																	36596385		2202	4298	6500	SO:0001587	stop_gained	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCTGAGAAGGTAC	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.1531A>T	chr11.hg19:g.36596385A>T	ENSP00000299440:p.Lys511*	152.0	0.0		205.0	41.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Nonsense_Mutation	SNP	ENST00000299440.5	hg19	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	A	34	5.298417	0.95574	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7965	0.78416	1.0:0.0:0.0:0.0	.	.	.	.	X	511	.	ENSP00000299440:K511X	K	+	1	0	RAG1	36552961	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	8.962000	0.93254	2.140000	0.66376	0.529000	0.55759	AAG	.	.		0.502	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		T	36596385	A	T	36596385	4	4	123	1	0	0	0	0	0	1	0	0	13018	247	9	4	1533	4	RAG1	11	36596385	Nonsense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	300117	36596385	98410131	214	20744										
RAG2	5897	hgsc.bcm.edu	37	chr11	36614459	36614459	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atatccacatcacaagtaggGcagcatgtaatccagtagcc	8	11	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:36614459G>T	ENST00000311485.3	-	2	1421	c.1260C>A	c.(1258-1260)tgC>tgA	p.C420*	C11orf74_ENST00000446510.2_5'Flank|RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000347206.4_5'Flank|C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000334307.5_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	420					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				CACAAGTAGGGCAGCATGTAA	0.443									Familial Hemophagocytic Lymphohistiocytosis																												p.C420X		Atlas-SNP	.											.	RAG2	92	.	0			c.C1260A						.						147	133	138					11																	36614459		2202	4298	6500	SO:0001587	stop_gained	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AGTAGGGCAGCAT	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.1260C>A	chr11.hg19:g.36614459G>T	ENSP00000308620:p.Cys420*	113.0	0.0		104.0	14.0	NM_001243785	A8K9E9|Q8TBL4	Nonsense_Mutation	SNP	ENST00000311485.3	hg19	CCDS7903.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.576484	0.86645	.	.	ENSG00000175097	ENST00000311485	.	.	.	5.23	0.144	0.14824	.	0.048134	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.072	8.5692	0.33558	0.6253:0.0:0.3747:0.0	.	.	.	.	X	420	.	ENSP00000308620:C420X	C	-	3	2	RAG2	36571035	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	0.778000	0.26732	0.053000	0.16036	0.650000	0.86243	TGC	.	.		0.443	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536		T	36614459	G	T	36614459	4	4	123	1	0	0	0	0	0	1	0	0	13020	1195	42	3	327	3	RAG2	11	36614459	Nonsense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	18074	36614459	98392057	215	20745										
TP53I11	9537	hgsc.bcm.edu	37	chr11	44958391	44958391	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tagaggcggatgggggtcttGctggtcacctgggctccatc	16	10	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:44958391G>T	ENST00000533940.1	-	8	901	c.297C>A	c.(295-297)agC>agA	p.S99R	TP53I11_ENST00000525680.1_Missense_Mutation_p.S99R|TP53I11_ENST00000531928.2_Missense_Mutation_p.S99R|TP53I11_ENST00000308212.5_Missense_Mutation_p.S99R|TP53I11_ENST00000395648.3_Missense_Mutation_p.S99R|TP53I11_ENST00000531130.2_5'UTR	NM_001258320.1	NP_001245249.1	O14683	P5I11_HUMAN	tumor protein p53 inducible protein 11	99					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5						TGGGGGTCTTGCTGGTCACCT	0.687											OREG0020923	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S99R		Atlas-SNP	.											.	TP53I11	17	.	0			c.C297A						.						30	30	30					11																	44958391		2203	4297	6500	SO:0001583	missense	9537	exon5			GGTCTTGCTGGTC	AF010315	CCDS7911.1	11p11.2	2005-09-22				ENSG00000175274			16842	protein-coding gene	gene with protein product						9305847	Standard	NM_006034		Approved	PIG11	uc001myk.3	O14683		ENST00000533940.1:c.297C>A	chr11.hg19:g.44958391G>T	ENSP00000436152:p.Ser99Arg	80.0	0.0	115	97.0	4.0	NM_001258324	Q3ZCS0	Missense_Mutation	SNP	ENST00000533940.1	hg19	CCDS7911.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.744191	0.69418	.	.	ENSG00000175274	ENST00000395648;ENST00000308212;ENST00000308220;ENST00000533940;ENST00000525680;ENST00000528473	.	.	.	4.96	3.05	0.35203	.	.	.	.	.	T	0.45577	0.1349	L	0.59436	1.845	0.42510	D	0.992965	P;B	0.42203	0.773;0.062	B;B	0.37304	0.246;0.075	T	0.47548	-0.9109	8	0.48119	T	0.1	-0.4843	10.0393	0.42148	0.2226:0.0:0.7774:0.0	.	46;99	Q8N8U5;O14683	.;P5I11_HUMAN	R	99;99;46;99;99;99	.	ENSP00000309532:S99R	S	-	3	2	TP53I11	44914967	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	2.144000	0.42197	1.087000	0.41251	0.561000	0.74099	AGC	.	.		0.687	TP53I11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389909.1	NM_006034		T	44958391	G	T	44958391	3	4	123	1	0	0	0	0	1	0	0	0	16400	1310	46	3	284	3	TP53I11	11	44958391	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	8343932	44958391	90048125	216	20746										
MADD	8567	hgsc.bcm.edu	37	chr11	47315515	47315515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cagcgcagacagtggtgtgaGcctgacgtctagttcccagg	14	11	1	3	rs375878509		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:47315515G>A	ENST00000311027.5	+	22	3662	c.3497G>A	c.(3496-3498)aGc>aAc	p.S1166N	MADD_ENST00000342922.4_Missense_Mutation_p.S1128N|MADD_ENST00000406482.1_Missense_Mutation_p.S1085N|MADD_ENST00000405573.2_5'UTR|MADD_ENST00000402799.1_Missense_Mutation_p.S1085N|MADD_ENST00000395336.3_Missense_Mutation_p.S1166N|MADD_ENST00000395344.3_Missense_Mutation_p.S1085N|MADD_ENST00000402192.2_Missense_Mutation_p.S1128N|MADD_ENST00000407859.3_Missense_Mutation_p.S1105N|MADD_ENST00000349238.3_Missense_Mutation_p.S1148N	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		AGTGGTGTGAGCCTGACGTCT	0.428																																					p.S1166N		Atlas-SNP	.											.	MADD	172	.	0			c.G3497A						.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	0,4402		0,0,2201	152	140	144		3254,3254,3497,3383,3314,3254,3443,3254,3497,3383	5.6	1	11		144	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	MADD	NM_001135943.1,NM_001135944.1,NM_003682.3,NM_130470.2,NM_130471.2,NM_130472.2,NM_130473.2,NM_130474.2,NM_130475.2,NM_130476.2	46,46,46,46,46,46,46,46,46,46	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1085/1545,1085/1542,1166/1648,1128/1589,1105/1566,1085/1546,1148/1609,1085/1480,1166/1582,1128/1588	47315515	1,12997	2201	4298	6499	SO:0001583	missense	8567	exon22			GTGTGAGCCTGAC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.3497G>A	chr11.hg19:g.47315515G>A	ENSP00000310933:p.Ser1166Asn	128.0	0.0		132.0	32.0	NM_130475		Missense_Mutation	SNP	ENST00000311027.5	hg19	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.987413	0.93106	0.0	1.16E-4	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T	0.08458	3.33;3.13;3.13;3.34;3.22;3.14;3.09;3.22;3.33	5.56	5.56	0.83823	.	0.039078	0.85682	D	0.000000	T	0.16214	0.0390	L	0.32530	0.975	0.80722	D	1	P;P;P;P;P;P;P;P;P;P	0.48911	0.839;0.745;0.917;0.835;0.9;0.9;0.855;0.915;0.864;0.855	B;B;P;P;P;P;P;P;P;P	0.54460	0.445;0.445;0.753;0.648;0.648;0.648;0.697;0.697;0.571;0.697	T	0.01051	-1.1468	10	0.36615	T	0.2	-16.3602	19.5211	0.95185	0.0:0.0:1.0:0.0	.	1085;1085;1166;1085;1085;1085;1148;1105;1166;1128	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	N	1128;1085;1085;1085;1148;1166;1105;1085;1166;1128	ENSP00000343902:S1128N;ENSP00000385585:S1085N;ENSP00000384435:S1085N;ENSP00000304505:S1148N;ENSP00000310933:S1166N;ENSP00000384204:S1105N;ENSP00000378753:S1085N;ENSP00000378745:S1166N;ENSP00000384287:S1128N	ENSP00000310933:S1166N	S	+	2	0	MADD	47272091	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.598000	0.82745	2.589000	0.87451	0.655000	0.94253	AGC	.	.		0.428	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			A	47315515	G	A	47315515	3	1	123	1	0	0	0	0	1	0	0	0	9161	971	34	3	3579	3	MADD	11	47315515	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	2357124	47315515	87691001	217	20747										
SPI1	6688	hgsc.bcm.edu	37	chr11	47376978	47376978	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtgcgccagcgcctccttgtGcttggacgagaactggaagg	15	11	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:47376978G>C	ENST00000378538.3	-	5	835	c.613C>G	c.(613-615)Cac>Gac	p.H205D	MYBPC3_ENST00000256993.4_5'Flank|MYBPC3_ENST00000545968.1_5'Flank|SPI1_ENST00000533030.1_3'UTR|MYBPC3_ENST00000399249.2_5'Flank|SPI1_ENST00000227163.4_Missense_Mutation_p.H206D	NM_001080547.1|NM_003120.2	NP_001074016.1|NP_003111.2	P17947	SPI1_HUMAN	Spi-1 proto-oncogene	205					anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|histone H3 acetylation (GO:0043966)|hypermethylation of CpG island (GO:0044027)|lymphocyte differentiation (GO:0030098)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of erythrocyte differentiation (GO:0045646)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somatic stem cell maintenance (GO:0035019)	nuclear chromatin (GO:0000790)	core promoter binding (GO:0001047)|NFAT protein binding (GO:0051525)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(4)|ovary(1)	8				Lung(87;0.0967)		GCCTCCTTGTGCTTGGACGAG	0.617																																					p.H206D		Atlas-SNP	.											.	SPI1	21	.	0			c.C616G						.						96	83	87					11																	47376978		2201	4298	6499	SO:0001583	missense	6688	exon5			CCTTGTGCTTGGA	X52056	CCDS7933.2, CCDS44591.1	11p12-p11.22	2014-06-25	2014-06-25		ENSG00000066336	ENSG00000066336			11241	protein-coding gene	gene with protein product	"hematopoietic transcription factor PU.1", "31 kDa transforming protein"	165170	"spleen focus forming virus (SFFV) proviral integration oncogene"			1693183	Standard	NM_003120		Approved	PU.1, SPI-A, OF, SFPI1, SPI-1	uc001nfb.1	P17947	OTTHUMG00000150150	ENST00000378538.3:c.613C>G	chr11.hg19:g.47376978G>C	ENSP00000367799:p.His205Asp	117.0	0.0		109.0	19.0	NM_001080547		Missense_Mutation	SNP	ENST00000378538.3	hg19	CCDS7933.2	.	.	.	.	.	.	.	.	.	.	g	22.0	4.226466	0.79576	.	.	ENSG00000066336	ENST00000378538;ENST00000227163	T;T	0.10099	2.91;2.91	4.23	3.31	0.37934	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.85682	D	0.000000	T	0.13500	0.0327	N	0.17345	0.48	0.80722	D	1	D;D	0.69078	0.992;0.997	D;D	0.66351	0.943;0.932	T	0.10291	-1.0636	10	0.10111	T	0.7	-18.2234	12.2235	0.54447	0.0845:0.0:0.9155:0.0	.	205;206	P17947;P17947-2	SPI1_HUMAN;.	D	205;206	ENSP00000367799:H205D;ENSP00000227163:H206D	ENSP00000227163:H206D	H	-	1	0	SPI1	47333554	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.542000	0.82095	0.896000	0.36366	0.479000	0.44913	CAC	.	.		0.617	SPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316571.1	NM_003120		C	47376978	G	C	47376978	3	2	123	1	0	0	0	0	1	0	0	0	15064	1319	46	4	203	4	SPI1	11	47376978	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	61463	47376978	87629538	218	20748										
OR4A5	81318	hgsc.bcm.edu	37	chr11	51412084	51412084	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aagacctcagccccaccaaaGaaatggtctataaatagctg	7	11	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:51412084G>A	ENST00000319760.6	-	1	364	c.312C>T	c.(310-312)ttC>ttT	p.F104F		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				CCCCACCAAAGAAATGGTCTA	0.448																																					p.F104F		Atlas-SNP	.											OR4A5,NS,carcinoma,0,1	OR4A5	116	.	0			c.C312T						.						66	67	67					11																	51412084		2201	4296	6497	SO:0001819	synonymous_variant	81318	exon1			ACCAAAGAAATGG	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"GPCR / Class A : Olfactory receptors"	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.312C>T	chr11.hg19:g.51412084G>A		276.0	0.0		250.0	36.0	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	hg19	CCDS31497.1																																																																																			.	.		0.448	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		A	51412084	G	A	51412084	2	1	123	1	0	0	0	0	0	0	0	1	11052	933	33	3		3	OR4A5	11	51412084	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	4035106	51412084	83594432	219	20749										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587463	55587463	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cctttttattagctgtgatgGcctatgaccgcttcgtggcc	10	11	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:55587463G>A	ENST00000333976.4	+	1	378	c.358G>A	c.(358-360)Gcc>Acc	p.A120T		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	120						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				AGCTGTGATGGCCTATGACCG	0.453																																					p.A120T		Atlas-SNP	.											OR5D18,right_upper_lobe,carcinoma,0,1	OR5D18	121	.	0			c.G358A						.						167	162	164					11																	55587463		2200	4296	6496	SO:0001583	missense	219438	exon1			GTGATGGCCTATG	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.358G>A	chr11.hg19:g.55587463G>A	ENSP00000335025:p.Ala120Thr	288.0	1.0		338.0	70.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	hg19	CCDS31510.1	.	.	.	.	.	.	.	.	.	.	.	20.7	4.036021	0.75617	.	.	ENSG00000186119	ENST00000333976	T	0.54071	0.59	4.84	3.91	0.45181	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39210	N	0.001428	T	0.68869	0.3048	H	0.96365	3.81	0.35287	D	0.781833	P	0.50369	0.934	P	0.44696	0.458	D	0.84873	0.0826	10	0.87932	D	0	-38.6253	13.543	0.61686	0.0:0.0:0.8427:0.1573	.	120	Q8NGL1	OR5DI_HUMAN	T	120	ENSP00000335025:A120T	ENSP00000335025:A120T	A	+	1	0	OR5D18	55344039	1.000000	0.71417	0.996000	0.52242	0.870000	0.49936	3.767000	0.55288	1.190000	0.43042	0.560000	0.71715	GCC	.	.		0.453	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		A	55587463	G	A	55587463	3	1	123	1	0	0	0	0	1	0	0	0	11166	1203	42	3	360	3	OR5D18	11	55587463	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	4175379	55587463	79419053	220	20750										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62290481	62290481	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcattttcaccttgggcatcTtcaggtgccagtctgggcct	11	12	4	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:62290481T>C	ENST00000378024.4	-	5	11682	c.11408A>G	c.(11407-11409)aAg>aGg	p.K3803R	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3803					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CTTGGGCATCTTCAGGTGCCA	0.522																																					p.K3803R		Atlas-SNP	.											.	AHNAK	532	.	0			c.A11408G						.						255	262	260					11																	62290481		2202	4299	6501	SO:0001583	missense	79026	exon5			GGCATCTTCAGGT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11408A>G	chr11.hg19:g.62290481T>C	ENSP00000367263:p.Lys3803Arg	140.0	0.0		209.0	41.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	12.17	1.856915	0.32791	.	.	ENSG00000124942	ENST00000378024	T	0.01538	4.79	4.61	3.48	0.39840	.	0.000000	0.42964	D	0.000635	T	0.06005	0.0156	H	0.95539	3.685	0.36755	D	0.882988	B	0.19073	0.033	B	0.19946	0.027	T	0.01472	-1.1346	10	0.35671	T	0.21	.	9.8977	0.41329	0.0:0.0829:0.0:0.9171	.	3803	Q09666	AHNK_HUMAN	R	3803	ENSP00000367263:K3803R	ENSP00000367263:K3803R	K	-	2	0	AHNAK	62047057	0.970000	0.33590	1.000000	0.80357	0.979000	0.70002	1.794000	0.38774	0.743000	0.32719	0.444000	0.29173	AAG	.	.		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62290481	T	C	62290481	3	2	123	1	0	0	0	0	1	0	0	0	414	1609	56	2	6384	2	AHNAK	11	62290481	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	6703018	62290481	72716035	221	20751										
MAP3K11	10089	hgsc.bcm.edu	37	chr11	65365896	65365896	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtctgagtccgggaacaaggTccagggtgctcggcggggtg	19	9	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:65365896T>C	ENST00000340313.4	-	0	0				KCNK7_ENST00000394217.2_5'Flank|KCNK7_ENST00000342202.4_5'Flank|MAP3K11_ENST00000534432.1_5'Flank|MAP3K11_ENST00000309100.3_Missense_Mutation_p.T804A|MAP3K11_ENST00000530153.1_Missense_Mutation_p.T547A|MAP3K11_ENST00000532507.1_Missense_Mutation_p.T220A|KCNK7_ENST00000394216.2_5'Flank	NM_033347.1	NP_203133.1	Q9Y2U2	KCNK7_HUMAN	potassium channel, subfamily K, member 7						potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|liver(1)|lung(1)	3						GGGAACAAGGTCCAGGGTGCT	0.667																																					p.T804A		Atlas-SNP	.											.	MAP3K11	67	.	0			c.A2410G						.						43	41	41					11																	65365896		2201	4297	6498	SO:0001631	upstream_gene_variant	4296	exon10			ACAAGGTCCAGGG	AF110522	CCDS8106.1, CCDS31608.1, CCDS41673.1	11q13	2012-03-07			ENSG00000173338	ENSG00000173338		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6282	protein-coding gene	gene with protein product		603940				10206991, 11256078, 16382106	Standard	NM_033347		Approved	K2p7.1	uc001oes.3	Q9Y2U2	OTTHUMG00000166528		chr11.hg19:g.65365896T>C	Exception_encountered	36.0	0.0		42.0	5.0	NM_002419	Q3SYI2|Q9Y2U3|Q9Y2U4	Missense_Mutation	SNP	ENST00000340313.4	hg19	CCDS31608.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.760226	0.69763	.	.	ENSG00000173327	ENST00000309100;ENST00000532507;ENST00000530153	T;T	0.75938	-0.87;-0.98	5.3	4.09	0.47781	.	0.078766	0.49916	D	0.000129	T	0.58538	0.2129	N	0.22421	0.69	0.30055	N	0.811426	B;B	0.24768	0.111;0.023	B;B	0.27170	0.077;0.009	T	0.56842	-0.7912	10	0.40728	T	0.16	.	7.9927	0.30250	0.1818:0.0:0.0:0.8182	.	293;804	B3KQY4;Q16584	.;M3K11_HUMAN	A	804;220;547	ENSP00000309597:T804A;ENSP00000433886:T547A	ENSP00000309597:T804A	T	-	1	0	MAP3K11	65122472	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.632000	0.37102	2.126000	0.65437	0.533000	0.62120	ACC	.	.		0.667	KCNK7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390206.1	NM_005714		C	65365896	T	C	65365896	1	2	123	0	1	0	0	0	0	0	0	0	9254	1667	58	2		2	MAP3K11	11	65365896	5'Flank	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	3075415	65365896	69640620	222	20752										
RBM14	10432	hgsc.bcm.edu	37	chr11	66392861	66392861	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tggtgccgcagcagcctacgGggcccaaccttctgccaccc	11	18	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:66392861G>A	ENST00000310137.4	+	2	1653	c.1514G>A	c.(1513-1515)gGg>gAg	p.G505E	RBM14-RBM4_ENST00000511114.1_Intron|RBM14_ENST00000409738.4_Intron|RBM4_ENST00000503028.2_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM4_ENST00000514361.3_Intron|RBM14-RBM4_ENST00000500635.2_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	505	Ala-rich.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						GCAGCCTACGGGGCCCAACCT	0.627																																					p.G505E		Atlas-SNP	.											RBM14,colon,carcinoma,0,1	RBM14	59	.	0			c.G1514A						.						45	44	44					11																	66392861		2200	4295	6495	SO:0001583	missense	10432	exon2			CCTACGGGGCCCA	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"RNA binding motif (RRM) containing"	14219	protein-coding gene	gene with protein product	"coactivator activator", "SYT interacting protein"	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.1514G>A	chr11.hg19:g.66392861G>A	ENSP00000311747:p.Gly505Glu	59.0	0.0		69.0	11.0	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	hg19	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	G	13.46	2.244440	0.39697	.	.	ENSG00000239306	ENST00000310137	D	0.84370	-1.84	5.75	5.75	0.90469	.	0.173489	0.49916	D	0.000127	D	0.86847	0.6031	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.88458	0.3053	10	0.87932	D	0	-3.9247	15.4418	0.75190	0.0:0.0:1.0:0.0	.	505	Q96PK6	RBM14_HUMAN	E	505	ENSP00000311747:G505E	ENSP00000311747:G505E	G	+	2	0	RBM14	66149437	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	2.738000	0.47401	2.720000	0.93068	0.655000	0.94253	GGG	.	.		0.627	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		A	66392861	G	A	66392861	3	1	123	1	0	0	0	0	1	0	0	0	13130	1232	43	3	1520	3	RBM14	11	66392861	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	1026965	66392861	68613655	223	20753										
TMEM135	65084	hgsc.bcm.edu	37	chr11	86782616	86782616	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cctggctttggtgccgctctGccagcatcttatgtggccat	11	13	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:86782616G>A	ENST00000305494.5	+	3	360	c.321G>A	c.(319-321)ctG>ctA	p.L107L	TMEM135_ENST00000532959.1_Intron|TMEM135_ENST00000355734.4_Silent_p.L107L|TMEM135_ENST00000340353.7_Silent_p.L107L|TMEM135_ENST00000535167.1_5'UTR	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	107					peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GTGCCGCTCTGCCAGCATCTT	0.373																																					p.L107L		Atlas-SNP	.											.	TMEM135	40	.	0			c.G321A						.						69	73	72					11																	86782616		2201	4299	6500	SO:0001819	synonymous_variant	65084	exon3			CGCTCTGCCAGCA	BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.321G>A	chr11.hg19:g.86782616G>A		73.0	0.0		62.0	7.0	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Silent	SNP	ENST00000305494.5	hg19	CCDS8280.1																																																																																			.	.		0.373	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918		A	86782616	G	A	86782616	2	1	123	1	0	0	0	0	0	0	0	1	16066	1306	46	3		3	TMEM135	11	86782616	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	20389755	86782616	48223900	224	20754										
NAALAD2	10003	hgsc.bcm.edu	37	chr11	89896533	89896533	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgggtatttggagctattgaCccaaccagtggggttgctgt	14	7	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:89896533C>G	ENST00000534061.1	+	10	1361	c.1131C>G	c.(1129-1131)gaC>gaG	p.D377E	NAALAD2_ENST00000525171.1_Missense_Mutation_p.D284E|NAALAD2_ENST00000375944.3_Intron|NAALAD2_ENST00000321955.4_Missense_Mutation_p.D344E	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	377	NAALADase.				neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)	p.D377E(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GAGCTATTGACCCAACCAGTG	0.413																																					p.D377E		Atlas-SNP	.											NAALAD2,NS,carcinoma,0,1	NAALAD2	113	.	1	Substitution - Missense(1)	lung(1)	c.C1131G						.						118	126	123					11																	89896533		2201	4299	6500	SO:0001583	missense	10003	exon10			TATTGACCCAACC	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1131C>G	chr11.hg19:g.89896533C>G	ENSP00000432481:p.Asp377Glu	67.0	1.0		74.0	10.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Missense_Mutation	SNP	ENST00000534061.1	hg19	CCDS8288.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.761927	0.49468	.	.	ENSG00000077616	ENST00000534061;ENST00000321955;ENST00000525171	D;D;D	0.90844	-2.74;-2.74;-2.74	5.51	2.53	0.30540	Peptidase M28 (1);	0.000000	0.85682	D	0.000000	D	0.95014	0.8386	M	0.89715	3.055	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.93788	0.7090	9	.	.	.	-20.3126	7.9396	0.29950	0.0:0.6005:0.0:0.3995	.	377;284	Q9Y3Q0;E9PKX5	NALD2_HUMAN;.	E	377;344;284	ENSP00000432481:D377E;ENSP00000320083:D344E;ENSP00000435249:D284E	.	D	+	3	2	NAALAD2	89536181	0.980000	0.34600	1.000000	0.80357	0.996000	0.88848	0.098000	0.15189	0.755000	0.32990	0.591000	0.81541	GAC	.	.		0.413	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		G	89896533	C	G	89896533	3	3	123	1	0	0	0	0	1	0	0	0	10137	506	18	4	1169	4	NAALAD2	11	89896533	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	3113917	89896533	45109983	225	20755										
MMP1	4312	hgsc.bcm.edu	37	chr11	102662135	102662135	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gaaagagcagcatcgatatgCttcacagttctagggaagcc	11	9	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:102662135C>T	ENST00000315274.6	-	8	1192	c.1125G>A	c.(1123-1125)aaG>aaA	p.K375K	WTAPP1_ENST00000525739.2_RNA	NM_001145938.1|NM_002421.3	NP_001139410.1|NP_002412.1	P03956	MMP1_HUMAN	matrix metallopeptidase 1 (interstitial collagenase)	375					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|proteolysis (GO:0006508)|viral process (GO:0016032)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)	Marimastat(DB00786)	CATCGATATGCTTCACAGTTC	0.453																																					p.K375K		Atlas-SNP	.											.	MMP1	74	.	0			c.G1125A						.						233	221	225					11																	102662135		2203	4299	6502	SO:0001819	synonymous_variant	4312	exon8			GATATGCTTCACA	X54925	CCDS8322.1	11q21-q22	2014-01-30	2005-08-08		ENSG00000196611	ENSG00000196611	3.4.24.7	"Endogenous ligands"	7155	protein-coding gene	gene with protein product		120353	"matrix metalloproteinase 1 (interstitial collagenase)"	CLG			Standard	NM_002421		Approved		uc001phi.2	P03956	OTTHUMG00000048192	ENST00000315274.6:c.1125G>A	chr11.hg19:g.102662135C>T		135.0	0.0		149.0	23.0	NM_002421	P08156	Silent	SNP	ENST00000315274.6	hg19	CCDS8322.1																																																																																			.	.		0.453	MMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109632.1	NM_002421		T	102662135	C	T	102662135	2	4	123	1	0	0	0	0	0	0	0	1	9657	796	28	3		3	MMP1	11	102662135	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	12765602	102662135	32344381	226	20756										
ALG9	79796	hgsc.bcm.edu	37	chr11	111740961	111740961	+	3'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aagaaatcacctactggctcCcagtagttgaatgtttcatc	7	10	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:111740961C>T	ENST00000524880.1	-	0	1256				ALG9_ENST00000531154.1_5'UTR|ALG9_ENST00000527377.1_5'Flank|ALG9_ENST00000527228.1_5'UTR|ALG9_ENST00000398006.2_5'UTR			Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dol-P-Man:Man(6)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052926)|dol-P-Man:Man(8)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052918)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)		CTACTGGCTCCCAGTAGTTGA	0.403																																					p.W88X		Atlas-SNP	.											.	ALG9	77	.	0			c.G264A						.						74	73	73					11																	111740961		1837	4102	5939	SO:0001624	3_prime_UTR_variant	79796	exon3			TGGCTCCCAGTAG		CCDS41714.1, CCDS53709.1, CCDS73379.1, CCDS73380.1	11q23	2013-02-26	2013-02-26	2004-08-26	ENSG00000086848	ENSG00000086848	2.4.1.259, 2.4.1.261	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	15672	protein-coding gene	gene with protein product	"dolichyl-P-Man:Man(6)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase", "dolichyl-P-Man:Man(8)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase", "dol-P-Man dependent alpha-1,2-mannosyltransferase"	606941	"disrupted in bipolar affective disorder 1", "asparagine-linked glycosylation 9 homolog (yeast, alpha 1,2 mannosyltransferase)", "asparagine-linked glycosylation 9, alpha- 1,2-mannosyltransferase homolog (S. cerevisiae, alpha- 1,2-mannosyltransferase)", "asparagine-linked glycosylation 9, alpha-1,2-mannosyltransferase homolog (S. cerevisiae)"	DIBD1		12030331, 15148656	Standard	NM_024740		Approved		uc021qql.1	Q9H6U8	OTTHUMG00000166819	ENST00000524880.1:c.*94G>A	chr11.hg19:g.111740961C>T		97.0	0.0		113.0	20.0	NM_001077690	Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	Nonsense_Mutation	SNP	ENST00000524880.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.68	2.308016	0.40895	.	.	ENSG00000086848	ENST00000428306	.	.	.	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7951	18.9101	0.92479	0.0:1.0:0.0:0.0	.	.	.	.	X	321	.	ENSP00000387627:W321X	W	-	3	0	ALG9	111246171	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	7.336000	0.79245	2.539000	0.85634	0.655000	0.94253	TGG	.	.		0.403	ALG9-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000413376.1	NM_024740		T	111740961	C	T	111740961	1	4	123	0	1	0	0	0	0	0	0	0	524	624	22	3		3	ALG9	11	111740961	3'UTR	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	9078826	111740961	23265555	227	20757										
MLL	4297	hgsc.bcm.edu	37	chr11	118374789	118374789	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atggtgttgatgatgggacaGagagtgatactagtgtcaca	14	4	1	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:118374789G>A	ENST00000389506.5	+	27	8173	c.8173G>A	c.(8173-8175)Gag>Aag	p.E2725K	KMT2A_ENST00000534358.1_Missense_Mutation_p.E2728K|KMT2A_ENST00000354520.4_Missense_Mutation_p.E2687K			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2725					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TGATGGGACAGAGAGTGATAC	0.423																																					p.E2728K		Atlas-SNP	.											.	MLL	548	.	0			c.G8182A						.						65	61	62					11																	118374789		2200	4296	6496	SO:0001583	missense	4297	exon27			GGGACAGAGAGTG	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.8173G>A	chr11.hg19:g.118374789G>A	ENSP00000374157:p.Glu2725Lys	109.0	0.0		127.0	26.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250792	0.59212	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.87966	-2.32;-2.32;-2.27	5.65	5.65	0.86999	.	0.049407	0.85682	D	0.000000	D	0.93015	0.7777	M	0.67569	2.06	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.75020	0.985;0.985	D	0.92890	0.6330	10	0.87932	D	0	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	2728;2725	E9PQG7;Q03164	.;MLL1_HUMAN	K	2728;2725;2687;1635	ENSP00000436786:E2728K;ENSP00000374157:E2725K;ENSP00000346516:E2687K	ENSP00000346516:E2687K	E	+	1	0	MLL	117879999	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.144000	0.94629	2.941000	0.99782	0.655000	0.94253	GAG	.	.		0.423	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118374789	G	A	118374789	3	1	123	1	0	0	0	0	1	0	0	0	9629	943	33	3	8279	3	MLL	11	118374789	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	6633828	118374789	16631727	228	20758										
BLID	414899	hgsc.bcm.edu	37	chr11	121986461	121986461	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctgtttccttaggcaacataGgttctttgttggaacccaag	9	9	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:121986461G>T	ENST00000560104.1	-	1	462	c.170C>A	c.(169-171)cCt>cAt	p.P57H		NM_001001786.2	NP_001001786.2	Q8IZY5	BLID_HUMAN	BH3-like motif containing, cell death inducer	57					apoptotic process (GO:0006915)	mitochondrion (GO:0005739)				NS(1)|large_intestine(4)|lung(6)|pancreas(1)	12		Breast(109;0.0164)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;2.08e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.101)		AGGCAACATAGGTTCTTTGTT	0.502											OREG0021435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P57H		Atlas-SNP	.											.	BLID	20	.	0			c.C170A						.						141	141	141					11																	121986461		2202	4299	6501	SO:0001583	missense	414899	exon1			AACATAGGTTCTT	AF303179	CCDS31693.1	11q24.1	2007-06-22				ENSG00000259571			33495	protein-coding gene	gene with protein product	"breast cancer cell 2"	608853				15069058, 17220890	Standard	NM_001001786		Approved	BRCC2	uc001pyf.3	Q8IZY5		ENST00000560104.1:c.170C>A	chr11.hg19:g.121986461G>T	ENSP00000453153:p.Pro57His	162.0	0.0	1515	183.0	29.0	NM_001001786	A1L416	Missense_Mutation	SNP	ENST00000560104.1	hg19	CCDS31693.1	.	.	.	.	.	.	.	.	.	.	G	8.767	0.924959	0.18056	.	.	ENSG00000258606;ENSG00000258574	ENST00000553434;ENST00000556841	.	.	.	3.92	1.85	0.25348	.	.	.	.	.	T	0.17238	0.0414	N	0.08118	0	0.09310	N	1	B	0.20261	0.043	B	0.21546	0.035	T	0.21724	-1.0237	8	0.87932	D	0	.	2.5933	0.04847	0.1789:0.0:0.5378:0.2833	.	57	Q8IZY5	BLID_HUMAN	H	57	.	ENSP00000448995:P57H	P	-	2	0	BLID;AP001924.1	121491671	0.007000	0.16637	0.002000	0.10522	0.022000	0.10575	0.717000	0.25851	0.494000	0.27859	-0.293000	0.09583	CCT	.	.		0.502	BLID-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387656.1	NM_001001786		T	121986461	G	T	121986461	3	4	123	1	0	0	0	0	1	0	0	0	1443	1000	35	3	160	3	BLID	11	121986461	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	3611672	121986461	13020055	229	20759										
OPCML	4978	hgsc.bcm.edu	37	chr11	132306092	132306092	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtcagagtggacatgcggccTttgttttcaatcctcattcc	9	11	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:132306092T>C	ENST00000331898.7	-	6	1403	c.825A>G	c.(823-825)aaA>aaG	p.K275K	OPCML_ENST00000524381.1_Silent_p.K268K|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000374778.4_Silent_p.K234K|OPCML_ENST00000541867.1_Silent_p.K275K	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	275	Ig-like C2-type 3.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		ACATGCGGCCTTTGTTTTCAA	0.458																																					p.K275K		Atlas-SNP	.											.	OPCML	166	.	0			c.A825G						.						159	145	150					11																	132306092		2201	4297	6498	SO:0001819	synonymous_variant	4978	exon6			GCGGCCTTTGTTT	BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.825A>G	chr11.hg19:g.132306092T>C		125.0	0.0		146.0	21.0	NM_002545	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Silent	SNP	ENST00000331898.7	hg19	CCDS8492.1																																																																																			.	.		0.458	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		C	132306092	T	C	132306092	2	2	123	1	0	0	0	0	0	0	0	1	10883	1606	56	2		2	OPCML	11	132306092	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	10319631	132306092	2700424	230	20760										
A2M	2	hgsc.bcm.edu	37	chr12	9258835	9258835	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	actggaaaatactccacctgCccaaagaagggaattccctg	8	12	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:9258835C>T	ENST00000318602.7	-	10	1408	c.1101G>A	c.(1099-1101)ggG>ggA	p.G367G		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	367					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	ACTCCACCTGCCCAAAGAAGG	0.408																																					p.G367G		Atlas-SNP	.											.	A2M	180	.	0			c.G1101A						.						134	126	128					12																	9258835		1880	4107	5987	SO:0001819	synonymous_variant	2	exon10			CACCTGCCCAAAG	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.1101G>A	chr12.hg19:g.9258835C>T		82.0	0.0		107.0	12.0	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Silent	SNP	ENST00000318602.7	hg19	CCDS44827.1																																																																																			.	.		0.408	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		T	9258835	C	T	9258835	2	4	123	1	0	0	0	0	0	0	0	1	4	726	26	3		3	A2M	12	9258835	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		9258835	124593060	231	20761										
C12orf59	120939	hgsc.bcm.edu	37	chr12	10339065	10339065	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttctcctgtgtggcctgacgTccctgtgcttccgctgctgc	11	15	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:10339065T>C	ENST00000381923.2	+	5	588	c.184T>C	c.(184-186)Tcc>Ccc	p.S62P	TMEM52B_ENST00000298530.3_Missense_Mutation_p.S42P|TMEM52B_ENST00000536952.1_Missense_Mutation_p.S62P			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	62						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											TGGCCTGACGTCCCTGTGCTT	0.597																																					p.S42P		Atlas-SNP	.											.	.	.	.	0			c.T124C						.						106	89	95					12																	10339065		2203	4300	6503	SO:0001583	missense	120939	exon3			CTGACGTCCCTGT	AY358845	CCDS8619.1, CCDS66314.1	12p13.2	2012-08-15	2012-08-15	2012-08-15	ENSG00000165685	ENSG00000165685			26438	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 59"	C12orf59		12975309	Standard	XM_005253299		Approved	FLJ31166	uc001qxq.3	Q4KMG9	OTTHUMG00000168410	ENST00000381923.2:c.184T>C	chr12.hg19:g.10339065T>C	ENSP00000371348:p.Ser62Pro	125.0	0.0		152.0	24.0	NM_153022	Q96NA7	Missense_Mutation	SNP	ENST00000381923.2	hg19		.	.	.	.	.	.	.	.	.	.	T	15.10	2.732160	0.48939	.	.	ENSG00000165685	ENST00000381923;ENST00000298530;ENST00000543484;ENST00000536952	T;T;T;T	0.35789	1.29;1.29;1.29;1.29	5.45	4.29	0.51040	.	0.278907	0.31404	N	0.007708	T	0.47078	0.1426	M	0.62723	1.935	0.09310	N	0.999991	D;D	0.57571	0.98;0.98	P;P	0.55303	0.773;0.698	T	0.39035	-0.9633	10	0.59425	D	0.04	-16.9785	9.589	0.39534	0.1699:0.0:0.0:0.8301	.	62;42	Q4KMG9;Q4KMG9-2	CL059_HUMAN;.	P	62;42;62;62	ENSP00000371348:S62P;ENSP00000298530:S42P;ENSP00000445582:S62P;ENSP00000446102:S62P	ENSP00000298530:S42P	S	+	1	0	C12orf59	10230332	0.460000	0.25776	0.041000	0.18516	0.316000	0.28119	3.312000	0.51927	1.041000	0.40125	0.528000	0.53228	TCC	.	.		0.597	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022		C	10339065	T	C	10339065	3	2	123	1	0	0	0	0	1	0	0	0	1704	1667	58	2	134	2	C12orf59	12	10339065	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	1080230	10339065	123512830	232	20762										
PLBD1	79887	hgsc.bcm.edu	37	chr12	14706133	14706133	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	actgggatacttacggggcaGtgaggtaaccctccaaaaag	12	9	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:14706133G>C	ENST00000240617.5	-	2	981	c.329C>G	c.(328-330)aCt>aGt	p.T110S	RN7SKP134_ENST00000363960.1_RNA	NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	110					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						TTACGGGGCAGTGAGGTAACC	0.532																																					p.T110S		Atlas-SNP	.											.	PLBD1	36	.	0			c.C329G						.						68	59	62					12																	14706133		2203	4300	6503	SO:0001583	missense	79887	exon2			GGGGCAGTGAGGT	BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"PLB homolog 1 (Dictyostelium)"					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.329C>G	chr12.hg19:g.14706133G>C	ENSP00000240617:p.Thr110Ser	100.0	0.0		137.0	13.0	NM_024829	A8K4E9|Q9BVV3|Q9H625	Missense_Mutation	SNP	ENST00000240617.5	hg19	CCDS31751.1	.	.	.	.	.	.	.	.	.	.	G	32	5.122416	0.94429	.	.	ENSG00000121316	ENST00000240617;ENST00000540572	T;T	0.21734	1.99;1.99	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	M	0.69248	2.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.33033	-0.9884	10	0.87932	D	0	-21.8403	19.0599	0.93085	0.0:0.0:1.0:0.0	.	110	Q6P4A8	PLBL1_HUMAN	S	110;63	ENSP00000240617:T110S;ENSP00000438367:T63S	ENSP00000240617:T110S	T	-	2	0	PLBD1	14597400	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.506000	0.90518	2.941000	0.99782	0.655000	0.94253	ACT	.	.		0.532	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829		C	14706133	G	C	14706133	3	2	123	1	0	0	0	0	1	0	0	0	12034	1029	36	4	1372	4	PLBD1	12	14706133	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	4367068	14706133	119145762	233	20763										
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18552717	18552717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aaaggactgtttcagaaatgCataccattttgagaagatgg	10	5	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:18552717C>T	ENST00000266497.5	+	14	2166	c.2128C>T	c.(2128-2130)Cat>Tat	p.H710Y	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.H751Y|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.H710Y			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	710	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TTCAGAAATGCATACCATTTT	0.408																																					p.H710Y		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.C2128T						.						87	86	86					12																	18552717		1850	4095	5945	SO:0001583	missense	5288	exon15			GAAATGCATACCA	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2128C>T	chr12.hg19:g.18552717C>T	ENSP00000266497:p.His710Tyr	100.0	0.0		84.0	4.0	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	C	1.214	-0.628771	0.03610	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.61158	0.13;0.13;0.13	5.08	3.13	0.36017	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.255174	0.32970	N	0.005432	T	0.22820	0.0551	N	0.05230	-0.09	0.33701	D	0.614569	B;B;B	0.29955	0.263;0.222;0.15	B;B;B	0.26770	0.073;0.044;0.041	T	0.32613	-0.9900	10	0.02654	T	1	-8.4714	1.4909	0.02456	0.1841:0.4398:0.2092:0.1669	.	750;751;710	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	Y	710;710;751	ENSP00000404845:H710Y;ENSP00000266497:H710Y;ENSP00000445381:H751Y	ENSP00000266497:H710Y	H	+	1	0	PIK3C2G	18443984	1.000000	0.71417	0.971000	0.41717	0.803000	0.45373	1.742000	0.38248	1.330000	0.45394	0.585000	0.79938	CAT	.	.		0.408	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		T	18552717	C	T	18552717	3	4	123	1	0	0	0	0	1	0	0	0	11920	710	25	3	2182	3	PIK3C2G	12	18552717	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	3846584	18552717	115299178	234	20764										
BICD1	636	hgsc.bcm.edu	37	chr12	32260378	32260378	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gatccaggctgccgagtacgGgctggtggtgctggaggaga	19	8	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:32260378G>A	ENST00000281474.5	+	1	216	c.113G>A	c.(112-114)gGg>gAg	p.G38E	RP11-843B15.2_ENST00000551974.1_RNA|BICD1_ENST00000548411.1_Missense_Mutation_p.G38E|BICD1_ENST00000551086.1_Missense_Mutation_p.G38E|BICD1_ENST00000551848.1_Missense_Mutation_p.G38E|BICD1_ENST00000550207.1_Missense_Mutation_p.G38E	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	38					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GCCGAGTACGGGCTGGTGGTG	0.547																																					p.G38E		Atlas-SNP	.											.	BICD1	89	.	0			c.G113A						.						73	63	66					12																	32260378		2203	4300	6503	SO:0001583	missense	636	exon1			AGTACGGGCTGGT	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.113G>A	chr12.hg19:g.32260378G>A	ENSP00000281474:p.Gly38Glu	139.0	0.0		125.0	11.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	G	33	5.197433	0.94960	.	.	ENSG00000151746	ENST00000551848;ENST00000550207;ENST00000548411;ENST00000281474;ENST00000551086	T;T;T;T;T	0.75477	1.27;1.27;-0.9;-0.94;1.27	4.01	4.01	0.46588	.	0.000000	0.64402	D	0.000010	D	0.84973	0.5591	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.83652	0.0156	10	0.24483	T	0.36	.	16.2917	0.82756	0.0:0.0:1.0:0.0	.	38;38	F8W113;Q96G01	.;BICD1_HUMAN	E	38	ENSP00000448933:G38E;ENSP00000447663:G38E;ENSP00000446793:G38E;ENSP00000281474:G38E;ENSP00000447238:G38E	ENSP00000281474:G38E	G	+	2	0	BICD1	32151645	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.971000	0.93419	2.067000	0.61834	0.561000	0.74099	GGG	.	.		0.547	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		A	32260378	G	A	32260378	3	1	123	1	0	0	0	0	1	0	0	0	1428	1232	43	3	115	3	BICD1	12	32260378	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	13707661	32260378	101591517	235	20765										
TUBA1A	7846	hgsc.bcm.edu	37	chr12	49578875	49578875	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aatccttctcaagggcagccAtgtcctcacgggcctctgaa	9	14	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:49578875A>G	ENST00000295766.5	-	4	1753	c.1274T>C	c.(1273-1275)aTg>aCg	p.M425T	TUBA1A_ENST00000550767.1_Missense_Mutation_p.M390T|TUBA1A_ENST00000301071.7_Missense_Mutation_p.M425T	NM_001270399.1	NP_001257328.1	Q71U36	TBA1A_HUMAN	tubulin, alpha 1a	425					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			stomach(1)|upper_aerodigestive_tract(1)	2					Albendazole(DB00518)|Mebendazole(DB00643)|Vinblastine(DB00570)	AAGGGCAGCCATGTCCTCACG	0.493																																					p.M425T	Pancreas(111;782 2307 24613 44561)|NSCLC(165;1667 2752 9496 39006)|Ovarian(19;24 776 10875 37451)	Atlas-SNP	.											.	TUBA1A	32	.	0			c.T1274C						.						167	163	164					12																	49578875		2203	4300	6503	SO:0001583	missense	7846	exon4			GCAGCCATGTCCT	AF141347	CCDS8781.1, CCDS58226.1, CCDS58227.1	12q13.12	2007-02-07						"Tubulins"	20766	protein-coding gene	gene with protein product	"tubulin, alpha, brain-specific"	602529				11504633, 3839072	Standard	NM_006009		Approved	TUBA3, B-ALPHA-1, FLJ25113	uc010smg.1	Q71U36	OTTHUMG00000169511	ENST00000295766.5:c.1274T>C	chr12.hg19:g.49578875A>G	ENSP00000439020:p.Met425Thr	348.0	0.0		336.0	90.0	NM_001270399	A8K0B8|G3V1U9|P04687|P05209	Missense_Mutation	SNP	ENST00000295766.5	hg19	CCDS58227.1	.	.	.	.	.	.	.	.	.	.	a	9.610	1.131008	0.21041	.	.	ENSG00000167552	ENST00000301071;ENST00000552597;ENST00000548405;ENST00000295766;ENST00000550767	D;D;D	0.83914	-1.78;-1.78;-1.78	5.51	5.51	0.81932	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83147	0.5191	M	0.76433	2.335	0.80722	D	1	B	0.02656	0.0	B	0.15870	0.014	T	0.81116	-0.1079	10	0.87932	D	0	.	14.6291	0.68643	1.0:0.0:0.0:0.0	.	425	Q71U36	TBA1A_HUMAN	T	425;156;272;425;390	ENSP00000301071:M425T;ENSP00000439020:M425T;ENSP00000446637:M390T	ENSP00000439020:M425T	M	-	2	0	TUBA1A	47865142	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.879000	0.92398	2.088000	0.63022	0.533000	0.62120	ATG	.	.		0.493	TUBA1A-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404547.2	NM_006009		G	49578875	A	G	49578875	3	3	123	1	0	0	0	0	1	0	0	0	16758	217	8	2	85	2	TUBA1A	12	49578875	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	17318497	49578875	84273020	236	20766										
HELB	92797	hgsc.bcm.edu	37	chr12	66704296	66704296	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aaagtcaactagaggcggacAaggctatagaagttttgctc	11	7	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:66704296A>T	ENST00000247815.4	+	4	1647	c.1588A>T	c.(1588-1590)Aag>Tag	p.K530*		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	530					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		AGAGGCGGACAAGGCTATAGA	0.423																																					p.K530X		Atlas-SNP	.											.	HELB	90	.	0			c.A1588T						.						125	134	131					12																	66704296		2203	4300	6503	SO:0001587	stop_gained	92797	exon4			GCGGACAAGGCTA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.1588A>T	chr12.hg19:g.66704296A>T	ENSP00000247815:p.Lys530*	101.0	0.0		144.0	18.0	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Nonsense_Mutation	SNP	ENST00000247815.4	hg19	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.197075	0.79015	.	.	ENSG00000127311	ENST00000247815	.	.	.	6.04	3.63	0.41609	.	0.237672	0.41500	D	0.000878	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.5058	2.2931	0.04144	0.6062:0.1353:0.1293:0.1292	.	.	.	.	X	530	.	.	K	+	1	0	HELB	64990563	0.386000	0.25180	0.469000	0.27204	0.083000	0.17756	1.723000	0.38053	0.492000	0.27815	0.459000	0.35465	AAG	.	.		0.423	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1			T	66704296	A	T	66704296	4	4	123	1	0	0	0	0	0	1	0	0	7054	131	5	4	1602	4	HELB	12	66704296	Nonsense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	17125421	66704296	67147599	237	20767										
TRHDE	29953	hgsc.bcm.edu	37	chr12	72936136	72936136	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gttttccagaggggtttgcaAgtaagtaaaatgctttttat	10	4	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:72936136A>G	ENST00000261180.4	+	7	1749	c.1653A>G	c.(1651-1653)caA>caG	p.Q551Q		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	551					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						GGGGTTTGCAAGTAAGTAAAA	0.318																																					p.Q551Q		Atlas-SNP	.											.	TRHDE	194	.	0			c.A1653G						.						99	97	98					12																	72936136		2203	4299	6502	SO:0001630	splice_region_variant	29953	exon7			TTTGCAAGTAAGT	AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"pyroglutamyl-peptidase II", "pyroglutamyl aminopeptidase II", "TRH-specific aminopeptidase"	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.1653+1A>G	chr12.hg19:g.72936136A>G		26.0	0.0		35.0	9.0	NM_013381	A5PL19|Q6UWJ4	Silent	SNP	ENST00000261180.4	hg19	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.906348	0.33628	.	.	ENSG00000072657	ENST00000547300	.	.	.	5.25	4.09	0.47781	.	.	.	.	.	T	0.62368	0.2422	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59343	-0.7472	4	.	.	.	.	11.2667	0.49114	0.9276:0.0:0.0724:0.0	.	.	.	.	G	139	.	.	R	+	1	2	TRHDE	71222403	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	3.790000	0.55461	0.928000	0.37168	0.459000	0.35465	AGA	.	.		0.318	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381	Silent	G	72936136	A	G	72936136	5	3	123	1	0	0	0	0	0	0	1	0	16494	86	3	2	1679	2	TRHDE	12	72936136	Splice_Site	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	6231840	72936136	60915759	238	20768										
NR2C1	7181	hgsc.bcm.edu	37	chr12	95422248	95422248	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atgctgttacaaaactcctgTagtttgaagatgtgctccat	8	8	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:95422248T>C	ENST00000333003.5	-	12	1776	c.1446A>G	c.(1444-1446)ctA>ctG	p.L482L	NR2C1_ENST00000545833.1_5'UTR	NM_003297.3	NP_003288.2	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	482					gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	DNA binding (GO:0003677)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13						AAAACTCCTGTAGTTTGAAGA	0.318																																					p.L482L		Atlas-SNP	.											.	NR2C1	56	.	0			c.A1446G						.						132	120	124					12																	95422248		2203	4300	6503	SO:0001819	synonymous_variant	7181	exon12			CTCCTGTAGTTTG	M29960	CCDS9051.1, CCDS41821.1, CCDS44953.1	12q22	2013-01-16				ENSG00000120798		"Nuclear hormone receptors"	7971	protein-coding gene	gene with protein product		601529		TR2		2597158	Standard	NM_001032287		Approved	TR2-11	uc001tdm.5	P13056	OTTHUMG00000170131	ENST00000333003.5:c.1446A>G	chr12.hg19:g.95422248T>C		63.0	0.0		64.0	6.0	NM_003297	A8K5K4|Q15625|Q15626	Silent	SNP	ENST00000333003.5	hg19	CCDS9051.1																																																																																			.	.		0.318	NR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407565.2	NM_003297		C	95422248	T	C	95422248	2	2	123	1	0	0	0	0	0	0	0	1	10631	1625	57	2		2	NR2C1	12	95422248	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	22486112	95422248	38429647	239	20769										
CMKLR1	1240	hgsc.bcm.edu	37	chr12	108686719	108686719	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	taactgatggaagtgttgtaAtcttcatcctccattctctg	7	9	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:108686719A>T	ENST00000312143.7	-	3	384	c.21T>A	c.(19-21)gaT>gaA	p.D7E	CMKLR1_ENST00000412676.1_Missense_Mutation_p.D7E|CMKLR1_ENST00000397688.2_Missense_Mutation_p.D5E|CMKLR1_ENST00000552995.1_Missense_Mutation_p.D5E|CMKLR1_ENST00000550402.1_Missense_Mutation_p.D7E	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	7					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						AAGTGTTGTAATCTTCATCCT	0.453																																					p.D7E		Atlas-SNP	.											.	CMKLR1	67	.	0			c.T21A						.						57	53	55					12																	108686719		1921	4137	6058	SO:0001583	missense	1240	exon3			GTTGTAATCTTCA	U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"GPCR / Class A : Resolvin receptors"	2121	protein-coding gene	gene with protein product	"resolvin E1 receptor", "chemerin receptor"	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.21T>A	chr12.hg19:g.108686719A>T	ENSP00000311733:p.Asp7Glu	136.0	0.0		119.0	6.0	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Missense_Mutation	SNP	ENST00000312143.7	hg19	CCDS44965.1	.	.	.	.	.	.	.	.	.	.	A	13.85	2.359097	0.41801	.	.	ENSG00000174600	ENST00000312143;ENST00000412676;ENST00000397688;ENST00000552995;ENST00000550402;ENST00000550573;ENST00000549466	T;T;T;T;T;T;T	0.68765	-0.35;-0.35;-0.34;-0.34;-0.35;1.24;1.25	5.26	-3.64	0.04515	.	2.205920	0.02384	U	0.079066	T	0.51261	0.1664	L	0.59436	1.845	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39035	-0.9633	10	0.02654	T	1	.	0.4293	0.00468	0.3752:0.13:0.2427:0.2521	.	7	Q99788	CML1_HUMAN	E	7;7;5;5;7;7;7	ENSP00000311733:D7E;ENSP00000401293:D7E;ENSP00000380803:D5E;ENSP00000447579:D5E;ENSP00000449716:D7E;ENSP00000448925:D7E;ENSP00000448362:D7E	ENSP00000311733:D7E	D	-	3	2	CMKLR1	107210849	0.005000	0.15991	0.001000	0.08648	0.203000	0.24098	-0.209000	0.09358	-1.005000	0.03417	-0.378000	0.06908	GAT	.	.		0.453	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1			T	108686719	A	T	108686719	3	4	123	1	0	0	0	0	1	0	0	0	3581	98	4	4	1104	4	CMKLR1	12	108686719	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	13264471	108686719	25165176	240	20770										
TRPV4	59341	hgsc.bcm.edu	37	chr12	110230527	110230527	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agtaaagggcattcatccagCccaggaccagggcaaagacc	11	12	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:110230527C>A	ENST00000418703.2	-	10	1848	c.1754G>T	c.(1753-1755)gGc>gTc	p.G585V	TRPV4_ENST00000346520.2_Missense_Mutation_p.G525V|TRPV4_ENST00000544971.1_Missense_Mutation_p.G478V|TRPV4_ENST00000536838.1_Missense_Mutation_p.G551V|TRPV4_ENST00000541794.1_Missense_Mutation_p.G538V|TRPV4_ENST00000392719.2_Missense_Mutation_p.G538V|TRPV4_ENST00000261740.2_Missense_Mutation_p.G585V|TRPV4_ENST00000537083.1_Missense_Mutation_p.G525V	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	585					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						ATTCATCCAGCCCAGGACCAG	0.587																																					p.G585V		Atlas-SNP	.											.	TRPV4	88	.	0			c.G1754T						.						89	70	77					12																	110230527		2203	4300	6503	SO:0001583	missense	59341	exon11			ATCCAGCCCAGGA	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18083	protein-coding gene	gene with protein product	"osmosensitive transient receptor potential channel 4"	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.1754G>T	chr12.hg19:g.110230527C>A	ENSP00000406191:p.Gly585Val	123.0	0.0		155.0	17.0	NM_021625	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Missense_Mutation	SNP	ENST00000418703.2	hg19	CCDS9134.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055045	0.93793	.	.	ENSG00000111199	ENST00000418703;ENST00000261740;ENST00000392719;ENST00000346520;ENST00000544971;ENST00000537083;ENST00000541794;ENST00000536838	D;D;D;D;D;D;D;D	0.98437	-4.93;-4.93;-4.93;-4.93;-4.93;-4.93;-4.93;-4.93	6.06	6.06	0.98353	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99146	0.9705	M	0.89095	3.005	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.997;0.995	D	0.99406	1.0929	10	0.59425	D	0.04	-1.2413	19.6125	0.95613	0.0:1.0:0.0:0.0	.	525;585;478;538;551	Q9HBA0-2;Q9HBA0;Q9HBA0-6;Q9HBA0-4;Q9HBA0-5	.;TRPV4_HUMAN;.;.;.	V	585;585;538;525;478;525;538;551	ENSP00000406191:G585V;ENSP00000261740:G585V;ENSP00000376480:G538V;ENSP00000319003:G525V;ENSP00000443611:G478V;ENSP00000442738:G525V;ENSP00000442167:G538V;ENSP00000444336:G551V	ENSP00000261740:G585V	G	-	2	0	TRPV4	108714910	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.879000	0.98667	0.650000	0.86243	GGC	.	.		0.587	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625		A	110230527	C	A	110230527	3	1	123	1	0	0	0	0	1	0	0	0	16613	739	26	3	885	3	TRPV4	12	110230527	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1543808	110230527	23621368	241	20771										
RBM19	9904	hgsc.bcm.edu	37	chr12	114296692	114296692	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aggcggaccgtcttcaactcCccaaaggtgctagaaacaaa	9	12	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:114296692C>T	ENST00000545145.2	-	22	2646	c.2568G>A	c.(2566-2568)ggG>ggA	p.G856G	RBM19_ENST00000261741.5_Silent_p.G856G|RBM19_ENST00000392561.3_Silent_p.G856G	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	856	RRM 6. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TCTTCAACTCCCCAAAGGTGC	0.527																																					p.G856G		Atlas-SNP	.											.	RBM19	117	.	0			c.G2568A						.						86	83	84					12																	114296692		2203	4300	6503	SO:0001819	synonymous_variant	9904	exon22			CAACTCCCCAAAG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"RNA binding motif (RRM) containing"	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.2568G>A	chr12.hg19:g.114296692C>T		99.0	0.0		88.0	31.0	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	hg19	CCDS9172.1																																																																																			.	.		0.527	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		T	114296692	C	T	114296692	2	4	123	1	0	0	0	0	0	0	0	1	13136	610	22	3		3	RBM19	12	114296692	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	4066165	114296692	19555203	242	20772										
HIP1R	9026	hgsc.bcm.edu	37	chr12	123338690	123338690	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atccaggactgcagccacctCtaccactacacggtcaagct	7	16	2	0	rs35154568		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:123338690C>T	ENST00000253083.4	+	8	803	c.678C>T	c.(676-678)ctC>ctT	p.L226L		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	226					receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		GCAGCCACCTCTACCACTACA	0.582																																					p.L226L		Atlas-SNP	.											.	HIP1R	68	.	0			c.C678T						.						117	103	108					12																	123338690		2203	4300	6503	SO:0001819	synonymous_variant	9026	exon8			CCACCTCTACCAC	AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.678C>T	chr12.hg19:g.123338690C>T		88.0	0.0		61.0	5.0	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Silent	SNP	ENST00000253083.4	hg19	CCDS31922.1																																																																																			.	.		0.582	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959		T	123338690	C	T	123338690	2	4	123	1	0	0	0	0	0	0	0	1	7124	900	32	3		3	HIP1R	12	123338690	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	9041998	123338690	10513205	243	20773										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	129559407	129559407	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tggcaggattcactaataacCatttccaccttgaccagggt	8	11	1	1	rs577207277		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:129559407C>G	ENST00000422113.2	-	9	2639	c.2313G>C	c.(2311-2313)atG>atC	p.M771I	TMEM132D_ENST00000389441.4_Missense_Mutation_p.M309I	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	771					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CACTAATAACCATTTCCACCT	0.468																																					p.M771I		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G2313C						.						153	134	141					12																	129559407		2203	4300	6503	SO:0001583	missense	121256	exon9			AATAACCATTTCC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.2313G>C	chr12.hg19:g.129559407C>G	ENSP00000408581:p.Met771Ile	251.0	0.0		269.0	14.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.804071	0.50315	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.13778	2.56;2.56	4.2	4.2	0.49525	.	0.110120	0.56097	D	0.000021	T	0.21145	0.0509	M	0.79805	2.47	0.50171	D	0.999852	P;P	0.40834	0.631;0.73	B;B	0.40506	0.31;0.331	T	0.03840	-1.0999	9	.	.	.	-46.7885	12.7483	0.57293	0.0:0.8344:0.1656:0.0	.	771;309	Q14C87;Q14C87-2	T132D_HUMAN;.	I	309;771	ENSP00000374092:M309I;ENSP00000408581:M771I	.	M	-	3	0	TMEM132D	128125360	1.000000	0.71417	0.596000	0.28811	0.475000	0.33008	3.701000	0.54793	2.033000	0.60031	0.462000	0.41574	ATG	.	.		0.468	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		G	129559407	C	G	129559407	3	3	123	1	0	0	0	0	1	0	0	0	16062	594	21	4	990	4	TMEM132D	12	129559407	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	6220717	129559407	4292488	244	20774										
FAM123A	219287	hgsc.bcm.edu	37	chr13	25743926	25743926	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggttggtcaggtgcttgatgCtaatagggatcttagagtcc	14	6	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr13:25743926C>G	ENST00000515384.1	-	1	2499	c.1832G>C	c.(1831-1833)aGc>aCc	p.S611T	AMER2_ENST00000381853.3_Missense_Mutation_p.S492T|AMER2_ENST00000357816.2_Missense_Mutation_p.S492T			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	611					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)										GTGCTTGATGCTAATAGGGAT	0.547																																					p.S611T		Atlas-SNP	.											.	.	.	.	0			c.G1832C						.						196	169	178					13																	25743926		2203	4300	6503	SO:0001583	missense	219287	exon1			TTGATGCTAATAG	AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"-"	26360	protein-coding gene	gene with protein product		614659	"family with sequence similarity 123A"	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1832G>C	chr13.hg19:g.25743926C>G	ENSP00000426528:p.Ser611Thr	366.0	0.0		257.0	59.0	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	hg19	CCDS53859.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507438	0.85282	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.50813	0.81;0.81;0.73	5.97	5.97	0.96955	.	0.105202	0.64402	D	0.000001	T	0.59609	0.2206	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.994;0.997	T	0.60885	-0.7174	10	0.66056	D	0.02	-18.8671	19.4162	0.94700	0.0:1.0:0.0:0.0	.	611;492	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	T	492;492;611	ENSP00000350469:S492T;ENSP00000371277:S492T;ENSP00000426528:S611T	ENSP00000350469:S492T	S	-	2	0	FAM123A	24641926	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.080000	0.76837	2.837000	0.97791	0.655000	0.94253	AGC	.	.		0.547	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704		G	25743926	C	G	25743926	3	3	123	1	0	0	0	0	1	0	0	0	5427	797	28	4	187	4	FAM123A	13	25743926	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		25743926	89425952	245	20775										
FLT1	2321	hgsc.bcm.edu	37	chr13	28942739	28942739	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gatgatgatgatgatgacgaTgatgatgatgatgacaatgg	14	2	0	10	rs371573097|rs558386334	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr13:28942739T>C	ENST00000282397.4	-	15	2368				FLT1_ENST00000541932.1_Silent_p.S726S	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1						blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	atgatgacgatgatgatgatg	0.343																																					p.S726S		Atlas-SNP	.											.	FLT1	393	.	0			c.A2178G						.						289	303	299					13																	28942739		692	1591	2283	SO:0001627	intron_variant	2321	exon15			TGACGATGATGAT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2117-10917A>G	chr13.hg19:g.28942739T>C		54.0	0.0		99.0	10.0	NM_001160030	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.		0.343	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	28942739	T	C	28942739	1	2	123	0	1	0	0	0	0	0	0	0	5949	1451	51	2		2	FLT1	13	28942739	Intron	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	3198813	28942739	86227139	246	20776										
KLF12	11278	hgsc.bcm.edu	37	chr13	74387348	74387348	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtttcattaacgctatctaaGgtcacatttggcaggtcatc	8	9	4	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr13:74387348G>T	ENST00000377669.2	-	4	773	c.747C>A	c.(745-747)acC>acA	p.T249T	KLF12_ENST00000377666.4_Silent_p.T249T|KLF12_ENST00000472022.1_5'UTR	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	249					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		CGCTATCTAAGGTCACATTTG	0.433																																					p.T249T		Atlas-SNP	.											.	KLF12	42	.	0			c.C747A						.						239	205	216					13																	74387348		2203	4300	6503	SO:0001819	synonymous_variant	11278	exon5			ATCTAAGGTCACA	AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6346	protein-coding gene	gene with protein product	"KLF12 zinc finger transcriptional repressor", "AP-2rep transcription factor", "AP-2 repressor"	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.747C>A	chr13.hg19:g.74387348G>T		222.0	0.0		170.0	38.0	NM_007249	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Silent	SNP	ENST00000377669.2	hg19	CCDS9449.1																																																																																			.	.		0.433	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249		T	74387348	G	T	74387348	2	4	123	1	0	0	0	0	0	0	0	1	8349	987	35	3		3	KLF12	13	74387348	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	45444609	74387348	40782530	247	20777										
MYO16	23026	hgsc.bcm.edu	37	chr13	109792700	109792700	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aagcgcagccccaacaccaaGctcagcggctcctacgagga	10	16	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr13:109792700G>A	ENST00000357550.2	+	31	4115	c.4074G>A	c.(4072-4074)aaG>aaA	p.K1358K	MYO16_ENST00000356711.2_Silent_p.K1358K	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CCAACACCAAGCTCAGCGGCT	0.701																																					p.K1380K		Atlas-SNP	.											.	MYO16	285	.	0			c.G4140A						.						38	32	34					13																	109792700		2198	4283	6481	SO:0001819	synonymous_variant	23026	exon32			CACCAAGCTCAGC		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4074G>A	chr13.hg19:g.109792700G>A		8.0	0.0		6.0	4.0	NM_001198950		Silent	SNP	ENST00000357550.2	hg19	CCDS32008.1																																																																																			.	.		0.701	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		A	109792700	G	A	109792700	2	1	123	1	0	0	0	0	0	0	0	1	10073	962	34	3		3	MYO16	13	109792700	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	35405352	109792700	5377178	248	20778										
ACTR10	55860	hgsc.bcm.edu	37	chr14	58690343	58690343	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccttttcttccttaaagcgcGtacttgctttgtaagtgatc	7	10	1	1	rs372667907		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:58690343G>A	ENST00000254286.4	+	9	718	c.638G>A	c.(637-639)cGt>cAt	p.R213H		NM_018477.2	NP_060947.1	Q9NZ32	ARP10_HUMAN	actin-related protein 10 homolog (S. cerevisiae)	213					microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|dynactin complex (GO:0005869)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	13						CTTAAAGCGCGTACTTGCTTT	0.333																																					p.R213H		Atlas-SNP	.											.	ACTR10	33	.	0			c.G638A						.	G	HIS/ARG	0,4404		0,0,2202	77	77	77		638	5.7	1	14		77	2,8598	2.2+/-6.3	0,2,4298	no	missense	ACTR10	NM_018477.2	29	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	213/418	58690343	2,13002	2202	4300	6502	SO:0001583	missense	55860	exon9			AAGCGCGTACTTG	AF220190	CCDS32090.1	14q23.1	2014-08-08			ENSG00000131966	ENSG00000131966			17372	protein-coding gene	gene with protein product						12857853	Standard	NM_018477		Approved	HARP11, ACTR11, Arp11	uc001xdf.3	Q9NZ32	OTTHUMG00000171049	ENST00000254286.4:c.638G>A	chr14.hg19:g.58690343G>A	ENSP00000254286:p.Arg213His	65.0	0.0		65.0	20.0	NM_018477	Q9H9Y5|Q9NWY2	Missense_Mutation	SNP	ENST00000254286.4	hg19	CCDS32090.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.034221	0.75617	0.0	2.33E-4	ENSG00000131966	ENST00000543474;ENST00000254286	D	0.94650	-3.48	5.74	5.74	0.90152	.	0.105394	0.64402	D	0.000004	D	0.97219	0.9091	M	0.86864	2.845	0.80722	D	1	D;D	0.69078	0.995;0.997	P;P	0.59012	0.791;0.85	D	0.97628	1.0140	10	0.87932	D	0	-26.2586	18.9079	0.92471	0.0:0.0:1.0:0.0	.	213;213	Q53H79;Q9NZ32	.;ARP10_HUMAN	H	213	ENSP00000254286:R213H	ENSP00000254286:R213H	R	+	2	0	ACTR10	57760096	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	8.926000	0.92839	2.702000	0.92279	0.655000	0.94253	CGT	.	.		0.333	ACTR10-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411405.1			A	58690343	G	A	58690343	3	1	123	1	0	0	0	0	1	0	0	0	208	1145	40	1	672	1	ACTR10	14	58690343	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10		58690343	48659197	249	20779										
RTN1	6252	hgsc.bcm.edu	37	chr14	60074189	60074189	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgcccgtctgcttgatgtccCgccaatacaacaggtcaata	8	13	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:60074189C>T	ENST00000267484.5	-	4	2122	c.1787G>A	c.(1786-1788)cGg>cAg	p.R596Q	RTN1_ENST00000395090.1_Missense_Mutation_p.R13Q|RTN1_ENST00000557422.1_5'UTR|RTN1_ENST00000342503.4_Missense_Mutation_p.R28Q	NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	596	Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		CTTGATGTCCCGCCAATACAA	0.602																																					p.R596Q		Atlas-SNP	.											.	RTN1	139	.	0			c.G1787A						.						31	31	31					14																	60074189		2203	4300	6503	SO:0001583	missense	6252	exon4			ATGTCCCGCCAAT	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.1787G>A	chr14.hg19:g.60074189C>T	ENSP00000267484:p.Arg596Gln	190.0	0.0		134.0	23.0	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	hg19	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	C	37	6.022003	0.97211	.	.	ENSG00000139970	ENST00000432103;ENST00000267484;ENST00000395090;ENST00000342503;ENST00000433623	T;T;T	0.54866	0.55;0.55;0.55	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.77890	0.4198	M	0.85542	2.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.995	T	0.79676	-0.1704	10	0.87932	D	0	.	20.4777	0.99188	0.0:1.0:0.0:0.0	.	13;596;28	A8MT72;Q16799;Q16799-3	.;RTN1_HUMAN;.	Q	176;596;13;28;522	ENSP00000267484:R596Q;ENSP00000378525:R13Q;ENSP00000340716:R28Q	ENSP00000267484:R596Q	R	-	2	0	RTN1	59143942	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.840000	0.97914	0.655000	0.94253	CGG	.	.		0.602	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			T	60074189	C	T	60074189	3	4	123	1	0	0	0	0	1	0	0	0	13740	652	23	1	567	1	RTN1	14	60074189	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1383846	60074189	47275351	250	20780										
PAPLN	89932	hgsc.bcm.edu	37	chr14	73721644	73721644	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtcatctgtgccattgggccGcccagccactgcgggagcct	13	15	2	0	rs369082075		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:73721644G>A	ENST00000554301.1	+	13	1708	c.1545G>A	c.(1543-1545)ccG>ccA	p.P515P	PAPLN_ENST00000340738.5_Silent_p.P488P|PAPLN_ENST00000381166.3_Silent_p.P515P|PAPLN_ENST00000427855.1_Silent_p.P515P|PAPLN_ENST00000555445.1_Silent_p.P515P			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	515	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		CCATTGGGCCGCCCAGCCACT	0.642																																					p.P488P		Atlas-SNP	.											PAPLN_ENST00000427855,NS,carcinoma,0,2	PAPLN	180	.	0			c.G1464A						.	G		1,4405	2.1+/-5.4	0,1,2202	36	37	37		1464	-9.4	0	14		37	0,8600		0,0,4300	no	coding-synonymous	PAPLN	NM_173462.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		488/1252	73721644	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	89932	exon13			TGGGCCGCCCAGC	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"Immunoglobulin superfamily / I-set domain containing"	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1545G>A	chr14.hg19:g.73721644G>A		35.0	1.0		37.0	14.0	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	hg19																																																																																				.	.		0.642	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		A	73721644	G	A	73721644	2	1	123	1	0	0	0	0	0	0	0	1	11437	1074	38	1		1	PAPLN	14	73721644	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	13647455	73721644	33627896	251	20781										
SEL1L	6400	hgsc.bcm.edu	37	chr14	81955626	81955626	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cctctcccatagaggtaggcCattccaagcccactctgtcc	7	17	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:81955626C>A	ENST00000336735.4	-	14	1481	c.1365G>T	c.(1363-1365)atG>atT	p.M455I		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	455	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		AGAGGTAGGCCATTCCAAGCC	0.423																																					p.M455I		Atlas-SNP	.											.	SEL1L	67	.	0			c.G1365T						.						98	90	93					14																	81955626		2203	4300	6503	SO:0001583	missense	6400	exon14			GTAGGCCATTCCA		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.1365G>T	chr14.hg19:g.81955626C>A	ENSP00000337053:p.Met455Ile	160.0	0.0		182.0	25.0	NM_005065	Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	hg19	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.298139	0.60086	.	.	ENSG00000071537	ENST00000336735	T	0.49432	0.78	5.6	5.6	0.85130	Tetratricopeptide-like helical (1);	0.039238	0.85682	D	0.000000	T	0.29914	0.0748	N	0.04994	-0.135	0.80722	D	1	B	0.18310	0.027	B	0.22880	0.042	T	0.11155	-1.0599	10	0.19590	T	0.45	.	17.7997	0.88583	0.0:1.0:0.0:0.0	.	455	Q9UBV2	SE1L1_HUMAN	I	455	ENSP00000337053:M455I	ENSP00000337053:M455I	M	-	3	0	SEL1L	81025379	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.793000	0.75130	2.640000	0.89533	0.655000	0.94253	ATG	.	.		0.423	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		A	81955626	C	A	81955626	3	1	123	1	0	0	0	0	1	0	0	0	14025	594	21	3	1051	3	SEL1L	14	81955626	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	8233982	81955626	25393914	252	20782										
EML5	161436	hgsc.bcm.edu	37	chr14	89202777	89202777	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggacagcaagtgcccaaagtTcaccttcacaatgcccttgc	8	14	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:89202777T>A	ENST00000380664.5	-	7	979	c.980A>T	c.(979-981)gAa>gTa	p.E327V	EML5_ENST00000554922.1_Missense_Mutation_p.E327V|EML5_ENST00000352093.5_Missense_Mutation_p.E327V			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	327						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						TGCCCAAAGTTCACCTTCACA	0.398																																					p.E327V		Atlas-SNP	.											.	EML5	141	.	0			c.A980T						.						211	205	207					14																	89202777		1926	4124	6050	SO:0001583	missense	161436	exon7			CAAAGTTCACCTT	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.980A>T	chr14.hg19:g.89202777T>A	ENSP00000370039:p.Glu327Val	185.0	0.0		185.0	38.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.471295	0.84533	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.60171	0.21;0.21;0.21	5.06	5.06	0.68205	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.121386	0.53938	D	0.000042	T	0.72914	0.3520	M	0.68593	2.085	0.58432	D	0.999998	D	0.71674	0.998	D	0.70016	0.967	T	0.74774	-0.3551	10	0.51188	T	0.08	-27.7062	14.9672	0.71204	0.0:0.0:0.0:1.0	.	327	Q05BV3	EMAL5_HUMAN	V	327	ENSP00000451998:E327V;ENSP00000298315:E327V;ENSP00000370039:E327V	ENSP00000298315:E327V	E	-	2	0	EML5	88272530	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.525000	0.81892	2.128000	0.65567	0.482000	0.46254	GAA	.	.		0.398	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			A	89202777	T	A	89202777	3	1	123	1	0	0	0	0	1	0	0	0	5102	1783	62	4	5101	4	EML5	14	89202777	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	7247151	89202777	18146763	253	20783										
KCNK13	56659	hgsc.bcm.edu	37	chr14	90651207	90651207	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acaaggcctcgttggccatcCtgcagaagcaactgtctgag	11	12	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:90651207C>T	ENST00000282146.4	+	2	1528	c.1087C>T	c.(1087-1089)Ctg>Ttg	p.L363L		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	363					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				GTTGGCCATCCTGCAGAAGCA	0.617																																					p.L363L		Atlas-SNP	.											.	KCNK13	76	.	0			c.C1087T						.						29	31	31					14																	90651207		2200	4299	6499	SO:0001819	synonymous_variant	56659	exon2			GCCATCCTGCAGA	AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.1087C>T	chr14.hg19:g.90651207C>T		169.0	0.0		163.0	26.0	NM_022054	B5TJL8|Q96E79	Silent	SNP	ENST00000282146.4	hg19	CCDS9889.1																																																																																			.	.		0.617	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		T	90651207	C	T	90651207	2	4	123	1	0	0	0	0	0	0	0	1	8070	680	24	3		3	KCNK13	14	90651207	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1448430	90651207	16698333	254	20784										
RTL1	388015	hgsc.bcm.edu	37	chr14	101350875	101350875	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gatcctctatttccttacgtGggccactggatggctcctcc	9	14	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:101350875G>A	ENST00000534062.1	-	1	309	c.251C>T	c.(250-252)cCa>cTa	p.P84L	MIR432_ENST00000606207.1_RNA|MIR433_ENST00000384837.1_RNA|MIR127_ENST00000384876.1_RNA|MIR136_ENST00000385207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	84					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TTCCTTACGTGGGCCACTGGA	0.572																																					p.P84L		Atlas-SNP	.											.	RTL1	120	.	0			c.C251T						.						82	72	75					14																	101350875		1568	3582	5150	SO:0001583	missense	388015	exon1			TTACGTGGGCCAC		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.251C>T	chr14.hg19:g.101350875G>A	ENSP00000435342:p.Pro84Leu	119.0	0.0		103.0	16.0	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	hg19	CCDS53910.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.770758	0.49680	.	.	ENSG00000254656	ENST00000534062	T	0.42131	0.98	3.54	2.63	0.31362	.	.	.	.	.	T	0.43100	0.1232	N	0.24115	0.695	0.33458	D	0.584537	D	0.69078	0.997	P	0.61328	0.887	T	0.55560	-0.8122	9	0.87932	D	0	.	8.2736	0.31860	0.0:0.0:0.7636:0.2364	.	84	E9PKS8	.	L	84	ENSP00000435342:P84L	ENSP00000435342:P84L	P	-	2	0	RTL1	100420628	0.994000	0.37717	0.984000	0.44739	0.957000	0.61999	2.134000	0.42102	1.038000	0.40049	0.561000	0.74099	CCA	.	.		0.572	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		A	101350875	G	A	101350875	3	1	123	1	0	0	0	0	1	0	0	0	13739	1348	47	3	3829	3	RTL1	14	101350875	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	10699668	101350875	5998665	255	20785										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414859	105414859	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgctgtctttggcagtcacgTccttgtcggccagggacatg	13	11	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:105414859T>C	ENST00000333244.5	-	7	7048	c.6929A>G	c.(6928-6930)gAc>gGc	p.D2310G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2310						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGCAGTCACGTCCTTGTCGGC	0.607																																					p.D2310G		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A6929G						.						199	215	210					14																	105414859		2036	4201	6237	SO:0001583	missense	113146	exon7			GTCACGTCCTTGT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.6929A>G	chr14.hg19:g.105414859T>C	ENSP00000353114:p.Asp2310Gly	159.0	0.0		122.0	28.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	11.15	1.553352	0.27739	.	.	ENSG00000185567	ENST00000333244	T	0.01279	5.06	3.54	1.12	0.20585	.	.	.	.	.	T	0.02047	0.0064	M	0.71871	2.18	0.09310	N	1	B	0.13594	0.008	B	0.11329	0.006	T	0.45585	-0.9251	9	0.20046	T	0.44	.	6.1488	0.20301	0.0:0.2236:0.0:0.7764	.	2310	Q8IVF2	AHNK2_HUMAN	G	2310	ENSP00000353114:D2310G	ENSP00000353114:D2310G	D	-	2	0	AHNAK2	104485904	0.013000	0.17824	0.067000	0.19924	0.005000	0.04900	1.221000	0.32503	0.255000	0.21593	-0.760000	0.03462	GAC	.	.		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105414859	T	C	105414859	3	2	123	1	0	0	0	0	1	0	0	0	415	1667	58	2	10462	2	AHNAK2	14	105414859	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	4063984	105414859	1934681	256	20786										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24921553	24921553	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgacgagaaaaggaccccccTtagcagcggagaagcatcgt	12	11	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:24921553T>C	ENST00000329468.2	+	1	1013	c.539T>C	c.(538-540)cTt>cCt	p.L180P		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	180					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.L180H(1)									AGGACCCCCCTTAGCAGCGGA	0.607																																					p.L180P		Atlas-SNP	.											C15orf2,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.T539C						.						47	40	42					15																	24921553		2203	4300	6503	SO:0001583	missense	23742	exon1			CCCCCCTTAGCAG	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.539T>C	chr15.hg19:g.24921553T>C	ENSP00000333735:p.Leu180Pro	85.0	0.0		97.0	15.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	10.21	1.286474	0.23478	.	.	ENSG00000185823	ENST00000329468	T	0.11821	2.74	2.03	-2.41	0.06562	.	5.007880	0.00589	N	0.000348	T	0.14743	0.0356	L	0.29908	0.895	0.09310	N	1	D	0.54772	0.968	P	0.55749	0.783	T	0.15492	-1.0435	10	0.23302	T	0.38	.	0.011	0.00001	0.3043:0.1978:0.1893:0.3085	.	180	Q9NZP6	CO002_HUMAN	P	180	ENSP00000333735:L180P	ENSP00000333735:L180P	L	+	2	0	C15orf2	22472646	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.233000	0.01204	-0.601000	0.05783	0.352000	0.21897	CTT	.	.		0.607	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		C	24921553	T	C	24921553	3	2	123	1	0	0	0	0	1	0	0	0	1786	1609	56	2	541	2	C15orf2	15	24921553	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10		24921553	77609839	257	20787										
GABRB3	2562	hgsc.bcm.edu	37	chr15	26793135	26793135	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aggaatcgcccatgcccttcTcgaggcatgctctgtttcct	9	14	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:26793135T>C	ENST00000311550.5	-	9	1338	c.1227A>G	c.(1225-1227)cgA>cgG	p.R409R	GABRB3_ENST00000400188.3_Silent_p.R338R|GABRB3_ENST00000299267.4_Silent_p.R409R|GABRB3_ENST00000545868.1_Silent_p.R324R|GABRB3_ENST00000541819.2_Silent_p.R465R	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	409					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CATGCCCTTCTCGAGGCATGC	0.488																																					p.R409R		Atlas-SNP	.											.	GABRB3	338	.	0			c.A1227G						.						84	75	78					15																	26793135		2203	4300	6503	SO:0001819	synonymous_variant	2562	exon9			CCCTTCTCGAGGC		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1227A>G	chr15.hg19:g.26793135T>C		167.0	0.0		174.0	37.0	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	hg19	CCDS10019.1																																																																																			.	.		0.488	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			C	26793135	T	C	26793135	2	2	123	1	0	0	0	0	0	0	0	1	6176	1538	54	2		2	GABRB3	15	26793135	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	1871582	26793135	75738257	258	20788										
CHRM5	1133	hgsc.bcm.edu	37	chr15	34356472	34356472	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgccgatggaaaaagaaaaaAgtggaagagaagttgtactg	13	3	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:34356472A>G	ENST00000383263.5	+	3	2224	c.1554A>G	c.(1552-1554)aaA>aaG	p.K518K	CHRM5_ENST00000557872.1_Silent_p.K518K	NM_012125.3	NP_036257.1	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	518					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|dopamine transport (GO:0015872)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|gastric acid secretion (GO:0001696)|metabolic process (GO:0008152)|regulation of phosphatidylinositol dephosphorylation (GO:0060304)|transmission of nerve impulse (GO:0019226)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	20		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Imipramine(DB00458)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Ziprasidone(DB00246)	AAAAGAAAAAAGTGGAAGAGA	0.463																																					p.K518K		Atlas-SNP	.											.	CHRM5	59	.	0			c.A1554G						.						56	62	60					15																	34356472		2201	4298	6499	SO:0001819	synonymous_variant	1133	exon3			GAAAAAAGTGGAA		CCDS10031.1	15q26	2012-08-08			ENSG00000184984	ENSG00000184984		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1954	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 5"	118496					Standard	NM_012125		Approved		uc001zhk.1	P08912	OTTHUMG00000129369	ENST00000383263.5:c.1554A>G	chr15.hg19:g.34356472A>G		99.0	0.0		103.0	11.0	NM_012125	Q96RG7	Silent	SNP	ENST00000383263.5	hg19	CCDS10031.1																																																																																			.	.		0.463	CHRM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251521.2			G	34356472	A	G	34356472	2	3	123	1	0	0	0	0	0	0	0	1	3382	69	3	2		2	CHRM5	15	34356472	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	7563337	34356472	68174920	259	20789										
CASC5	57082	hgsc.bcm.edu	37	chr15	40920293	40920293	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgatcaccatactgaagaggAtatagataaaagtgctaaca	8	6	1	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:40920293A>G	ENST00000346991.5	+	12	5870	c.5480A>G	c.(5479-5481)gAt>gGt	p.D1827G	CASC5_ENST00000399668.2_Missense_Mutation_p.D1801G			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1827					acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		ACTGAAGAGGATATAGATAAA	0.358																																					p.D1827G		Atlas-SNP	.											.	CASC5	269	.	0			c.A5480G						.						84	87	86					15																	40920293		1819	4084	5903	SO:0001583	missense	57082	exon12			AAGAGGATATAGA	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.5480A>G	chr15.hg19:g.40920293A>G	ENSP00000335463:p.Asp1827Gly	113.0	0.0		89.0	17.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	hg19	CCDS42023.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.14|11.14	1.550390|1.550390	0.27739|0.27739	.|.	.|.	ENSG00000137812|ENSG00000137812	ENST00000346991;ENST00000399668|ENST00000532406	T;T|.	0.05580|.	3.42;3.42|.	5.49|5.49	3.15|3.15	0.36227|0.36227	.|.	0.842583|.	0.10359|.	N|.	0.684210|.	T|T	0.35799|0.35799	0.0944|0.0944	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	1|1	B;B|.	0.29646|.	0.253;0.253|.	B;B|.	0.25291|.	0.059;0.059|.	T|T	0.22138|0.22138	-1.0225|-1.0225	10|5	0.33940|.	T|.	0.23|.	.|.	6.819|6.819	0.23847|0.23847	0.6374:0.2864:0.0762:0.0|0.6374:0.2864:0.0762:0.0	.|.	1801;1827|.	Q8NG31-2;Q8NG31|.	.;CASC5_HUMAN|.	G|V	1827;1801|8	ENSP00000335463:D1827G;ENSP00000382576:D1801G|.	ENSP00000335463:D1827G|.	D|I	+|+	2|1	0|0	CASC5|CASC5	38707585|38707585	0.000000|0.000000	0.05858|0.05858	0.122000|0.122000	0.21767|0.21767	0.983000|0.983000	0.72400|0.72400	0.589000|0.589000	0.23939|0.23939	0.373000|0.373000	0.24621|0.24621	0.529000|0.529000	0.55759|0.55759	GAT|ATA	.	.		0.358	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		G	40920293	A	G	40920293	3	3	123	1	0	0	0	0	1	0	0	0	2665	333	12	2	5522	2	CASC5	15	40920293	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	6563821	40920293	61611099	260	20790										
SPINT1	6692	hgsc.bcm.edu	37	chr15	41137074	41137074	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tagtggagctgcagcccgacCgcggggaggacgccatcgcc	16	14	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:41137074C>T	ENST00000344051.4	+	2	556	c.322C>T	c.(322-324)Cgc>Tgc	p.R108C	RP11-532F12.5_ENST00000568525.1_RNA|RP11-532F12.5_ENST00000564302.1_RNA|SPINT1_ENST00000431806.1_Missense_Mutation_p.R108C|RP11-532F12.5_ENST00000565315.1_RNA|RP11-532F12.5_ENST00000568419.1_RNA|SPINT1_ENST00000562057.1_Missense_Mutation_p.R108C			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	108	MANSC. {ECO:0000255|PROSITE- ProRule:PRU00341}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GCAGCCCGACCGCGGGGAGGA	0.657																																					p.R108C		Atlas-SNP	.											.	SPINT1	28	.	0			c.C322T						.						32	31	31					15																	41137074		2203	4299	6502	SO:0001583	missense	6692	exon2			CCCGACCGCGGGG		CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"serine protease inhibitor, Kunitz type 1"				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.322C>T	chr15.hg19:g.41137074C>T	ENSP00000342098:p.Arg108Cys	80.0	0.0		70.0	9.0	NM_181642	Q7Z7D2	Missense_Mutation	SNP	ENST00000344051.4	hg19	CCDS10067.1	.	.	.	.	.	.	.	.	.	.	C	17.70	3.453648	0.63290	.	.	ENSG00000166145	ENST00000344051;ENST00000536281;ENST00000431806	T;T	0.23348	1.91;1.91	4.98	3.1	0.35709	Seven cysteines (1);Seven cysteines, N-terminal (2);	0.853113	0.10682	N	0.646338	T	0.25121	0.0610	L	0.29908	0.895	0.09310	N	1	D;D;D	0.57571	0.975;0.98;0.975	P;P;P	0.52856	0.594;0.711;0.594	T	0.12967	-1.0527	10	0.56958	D	0.05	-7.0573	2.8482	0.05550	0.1646:0.148:0.5449:0.1426	.	108;108;108	B2RBU9;O43278-2;O43278	.;.;SPIT1_HUMAN	C	108;75;108	ENSP00000342098:R108C;ENSP00000409935:R108C	ENSP00000342098:R108C	R	+	1	0	SPINT1	38924366	0.003000	0.15002	0.858000	0.33744	0.838000	0.47535	0.608000	0.24223	0.621000	0.30232	0.563000	0.77884	CGC	.	.		0.657	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710		T	41137074	C	T	41137074	3	4	123	1	0	0	0	0	1	0	0	0	15083	652	23	1	324	1	SPINT1	15	41137074	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	216781	41137074	61394318	261	20791										
INO80	54617	hgsc.bcm.edu	37	chr15	41337196	41337196	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcaggtatctctggtggctcTccccttctggcgctccccag	10	16	4	0	rs115089447	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:41337196T>A	ENST00000361937.3	-	24	3237	c.2813A>T	c.(2812-2814)gAg>gTg	p.E938V	INO80_ENST00000401393.3_Missense_Mutation_p.E938V			Q9ULG1	INO80_HUMAN	INO80 complex subunit	938	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CTGGTGGCTCTCCCCTTCTGG	0.502																																					p.E938V		Atlas-SNP	.											.	INO80	122	.	0			c.A2813T						.						97	99	98					15																	41337196		2203	4300	6503	SO:0001583	missense	54617	exon24			TGGCTCTCCCCTT	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.2813A>T	chr15.hg19:g.41337196T>A	ENSP00000355205:p.Glu938Val	63.0	0.0		66.0	14.0	NM_017553	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	hg19	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.358497	0.41801	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.91464	-2.85;-2.85	4.95	1.29	0.21616	.	0.587060	0.19449	N	0.113990	T	0.78792	0.4339	N	0.14661	0.345	0.34448	D	0.700379	B	0.26445	0.149	B	0.21708	0.036	T	0.71761	-0.4495	10	0.38643	T	0.18	.	6.5731	0.22549	0.0:0.1395:0.1301:0.7304	.	938	Q9ULG1	INO80_HUMAN	V	938	ENSP00000355205:E938V;ENSP00000384686:E938V	ENSP00000355205:E938V	E	-	2	0	INO80	39124488	0.756000	0.28383	0.846000	0.33378	0.928000	0.56348	1.139000	0.31504	0.113000	0.18004	0.459000	0.35465	GAG	.	T|0.989;C|0.011		0.502	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		A	41337196	T	A	41337196	3	1	123	1	0	0	0	0	1	0	0	0	7755	1551	54	4	1909	4	INO80	15	41337196	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	200122	41337196	61194196	262	20792										
FBN1	2200	hgsc.bcm.edu	37	chr15	48719788	48719788	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tccattggtcatgaatcctcGgccatggggacagagtttct	11	10	2	2	rs397515848		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:48719788G>A	ENST00000316623.5	-	58	7635	c.7180C>T	c.(7180-7182)Cga>Tga	p.R2394*		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2394					extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		ATGAATCCTCGGCCATGGGGA	0.463																																					p.R2394X		Atlas-SNP	.											.	FBN1	310	.	0			c.C7180T	GRCh37	CM993162	FBN1	M		.						79	77	78					15																	48719788		2198	4296	6494	SO:0001587	stop_gained	2200	exon58			ATCCTCGGCCATG	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.7180C>T	chr15.hg19:g.48719788G>A	ENSP00000325527:p.Arg2394*	124.0	0.0		137.0	12.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Nonsense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	50	17.109795	0.99879	.	.	ENSG00000166147	ENST00000316623	.	.	.	5.44	4.51	0.55191	.	0.206926	0.42053	D	0.000769	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	13.249	0.60041	0.0:0.0:0.7113:0.2887	.	.	.	.	X	2394	.	ENSP00000325527:R2394X	R	-	1	2	FBN1	46507080	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.625000	0.67770	1.412000	0.46977	0.650000	0.86243	CGA	.	.		0.463	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48719788	G	A	48719788	4	1	123	1	0	0	0	0	0	1	0	0	5710	1124	39	1	1471	1	FBN1	15	48719788	Nonsense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	7382592	48719788	53811604	263	20793										
RFX7	64864	hgsc.bcm.edu	37	chr15	56394441	56394441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agctttttttcttagtccacTgtagcaatatgtaataaaca	5	7	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:56394441T>C	ENST00000559447.2	-	6	509	c.238A>G	c.(238-240)Agt>Ggt	p.S80G	RFX7_ENST00000423270.1_Missense_Mutation_p.S177G|RFX7_ENST00000317318.6_Missense_Mutation_p.S177G|RFX7_ENST00000422057.1_Missense_Mutation_p.S80G			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	80					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CTTAGTCCACTGTAGCAATAT	0.313																																					p.S177G		Atlas-SNP	.											.	RFX7	170	.	0			c.A529G						.						61	59	60					15																	56394441		1787	4060	5847	SO:0001583	missense	64864	exon6			GTCCACTGTAGCA			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.238A>G	chr15.hg19:g.56394441T>C	ENSP00000453281:p.Ser80Gly	54.0	0.0		47.0	10.0	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.47	3.397234	0.62177	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	D;D;D	0.82803	-1.65;-1.65;-1.65	5.89	5.89	0.94794	Winged helix-turn-helix transcription repressor DNA-binding (1);	1.215880	0.05610	N	0.578026	T	0.81029	0.4738	L	0.39020	1.185	0.58432	D	0.999999	B	0.22683	0.073	B	0.20184	0.028	T	0.59434	-0.7455	10	0.54805	T	0.06	0.236	15.4882	0.75584	0.0:0.0:0.0:1.0	.	80	Q2KHR2	RFX7_HUMAN	G	80;177;177	ENSP00000387504:S80G;ENSP00000313299:S177G;ENSP00000397644:S177G	ENSP00000313299:S177G	S	-	1	0	RFX7	54181733	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.040000	0.89188	2.250000	0.74265	0.477000	0.44152	AGT	.	.		0.313	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		C	56394441	T	C	56394441	3	2	123	1	0	0	0	0	1	0	0	0	13283	1580	55	2	3869	2	RFX7	15	56394441	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	7674653	56394441	46136951	264	20794										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62219327	62219327	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctctcttttctctgagaaaaGggcaagcgagcactttcaga	9	10	3	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:62219327G>A	ENST00000261517.5	-	52	6552	c.6479C>T	c.(6478-6480)cCt>cTt	p.P2160L	VPS13C_ENST00000395896.4_Missense_Mutation_p.P2160L|VPS13C_ENST00000249837.3_Missense_Mutation_p.P2117L|VPS13C_ENST00000395898.3_Missense_Mutation_p.P2117L	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TCTGAGAAAAGGGCAAGCGAG	0.428																																					p.P2160L		Atlas-SNP	.											.	VPS13C	506	.	0			c.C6479T						.						123	120	121					15																	62219327		2203	4300	6503	SO:0001583	missense	54832	exon52			AGAAAAGGGCAAG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6479C>T	chr15.hg19:g.62219327G>A	ENSP00000261517:p.Pro2160Leu	142.0	0.0		117.0	17.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	32	5.128849	0.94473	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.61980	0.06;0.06;0.06	5.41	5.41	0.78517	.	0.179966	0.49916	D	0.000129	T	0.74129	0.3676	M	0.76574	2.34	0.80722	D	1	B;P;B;P	0.47191	0.112;0.891;0.38;0.825	B;P;B;P	0.52159	0.197;0.691;0.197;0.493	T	0.73260	-0.4039	10	0.39692	T	0.17	.	19.5612	0.95373	0.0:0.0:1.0:0.0	.	2117;2160;2117;2160	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	L	2117;2160;2160;2160	ENSP00000249837:P2117L;ENSP00000261517:P2160L;ENSP00000379233:P2160L	ENSP00000249837:P2117L	P	-	2	0	VPS13C	60006619	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.173000	0.94815	2.687000	0.91594	0.655000	0.94253	CCT	.	.		0.428	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62219327	G	A	62219327	3	1	123	1	0	0	0	0	1	0	0	0	17206	1000	35	3	4946	3	VPS13C	15	62219327	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	5824886	62219327	40312065	265	20795										
HEXA	3073	hgsc.bcm.edu	37	chr15	72643535	72643535	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aggaaggatcatctaccagaTgccagtggaacacgttcaat	10	9	3	1	rs121907976		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:72643535T>A	ENST00000268097.5	-	6	1114	c.611A>T	c.(610-612)cAt>cTt	p.H204L	RP11-106M3.3_ENST00000570175.1_RNA|HEXA_ENST00000457859.2_Missense_Mutation_p.H12L|HEXA_ENST00000567159.1_Missense_Mutation_p.H204L|RP11-106M3.2_ENST00000379915.4_RNA|HEXA_ENST00000566304.1_Missense_Mutation_p.H215L|HEXA_ENST00000429918.2_Missense_Mutation_p.H31L	NM_000520.4	NP_000511.2	P06865	HEXA_HUMAN	hexosaminidase A (alpha polypeptide)	204			H -> R (in GM2G1; infantile).		carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	24						ATCTACCAGATGCCAGTGGAA	0.453																																					p.H204L		Atlas-SNP	.											.	HEXA	48	.	0			c.A611T	GRCh37	CM930394	HEXA	M	rs121907976	.						174	145	155					15																	72643535		2199	4297	6496	SO:0001583	missense	3073	exon6			ACCAGATGCCAGT	M13520	CCDS10243.1	15q24.1	2012-10-02			ENSG00000213614	ENSG00000213614	3.2.1.52		4878	protein-coding gene	gene with protein product	"Tay Sachs disease", "GM2 gangliosidosis"	606869				2952641, 3013851	Standard	NM_000520		Approved		uc002aun.4	P06865	OTTHUMG00000133445	ENST00000268097.5:c.611A>T	chr15.hg19:g.72643535T>A	ENSP00000268097:p.His204Leu	116.0	0.0		174.0	24.0	NM_000520	B4DKE7|E7ENH7|Q53HS8|Q6AI32	Missense_Mutation	SNP	ENST00000268097.5	hg19	CCDS10243.1	.	.	.	.	.	.	.	.	.	.	T	34	5.303095	0.95601	.	.	ENSG00000213614	ENST00000268097;ENST00000457859;ENST00000429918	D;D;D	0.98602	-5.02;-5.02;-5.02	5.78	5.78	0.91487	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);Glycoside hydrolase, family 20 (1);	0.000000	0.85682	D	0.000000	D	0.99560	0.9842	H	0.99881	4.885	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.97392	0.9990	10	0.87932	D	0	-24.6736	16.1109	0.81263	0.0:0.0:0.0:1.0	.	31;215;31;84;204	E9PGL4;B4DVA7;B4DVL8;Q9BVJ8;P06865	.;.;.;.;HEXA_HUMAN	L	204;12;31	ENSP00000268097:H204L;ENSP00000398026:H12L;ENSP00000416187:H31L	ENSP00000268097:H204L	H	-	2	0	HEXA	70430589	1.000000	0.71417	0.946000	0.38457	0.996000	0.88848	7.940000	0.87693	2.185000	0.69588	0.533000	0.62120	CAT	.	.		0.453	HEXA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257317.2	NM_000520		A	72643535	T	A	72643535	3	1	123	1	0	0	0	0	1	0	0	0	7082	1464	51	4	1014	4	HEXA	15	72643535	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	10424208	72643535	29887857	266	20796										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91043276	91043276	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgcagtcatgaaattatttgAtagagctaaagtaaatgtca	8	4	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:91043276A>C	ENST00000268182.5	+	38	5034	c.4910A>C	c.(4909-4911)gAt>gCt	p.D1637A	IQGAP1_ENST00000560738.1_Missense_Mutation_p.D1065A	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1637	C2.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AAATTATTTGATAGAGCTAAA	0.368																																					p.D1637A		Atlas-SNP	.											.	IQGAP1	140	.	0			c.A4910C						.						95	88	90					15																	91043276		2198	4298	6496	SO:0001583	missense	8826	exon38			TATTTGATAGAGC	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.4910A>C	chr15.hg19:g.91043276A>C	ENSP00000268182:p.Asp1637Ala	76.0	0.0		69.0	5.0	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	hg19	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.148846	0.78001	.	.	ENSG00000140575	ENST00000268182	T	0.03181	4.02	5.7	5.7	0.88788	.	0.051090	0.85682	D	0.000000	T	0.18509	0.0444	M	0.85197	2.74	0.80722	D	1	D;D	0.57899	0.981;0.961	P;P	0.60012	0.867;0.778	T	0.00346	-1.1800	10	0.72032	D	0.01	-22.2177	15.1546	0.72730	1.0:0.0:0.0:0.0	.	258;1637	B4DNP4;P46940	.;IQGA1_HUMAN	A	1637	ENSP00000268182:D1637A	ENSP00000268182:D1637A	D	+	2	0	IQGAP1	88844280	1.000000	0.71417	0.987000	0.45799	0.524000	0.34500	9.173000	0.94815	2.180000	0.69256	0.454000	0.30748	GAT	.	.		0.368	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		C	91043276	A	C	91043276	3	2	123	1	0	0	0	0	1	0	0	0	7823	333	12	5	5060	5	IQGAP1	15	91043276	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	18399741	91043276	11488116	267	20797										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99451929	99451929	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tctaggaattactccttctaCgtcctcgacaaccagaactt	5	13	2	1	rs542546475		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:99451929C>T	ENST00000268035.6	+	6	1874	c.1263C>T	c.(1261-1263)taC>taT	p.Y421Y	IGF1R_ENST00000558762.1_Silent_p.Y421Y	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	421					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)	p.Y421Y(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	ACTCCTTCTACGTCCTCGACA	0.507													C|||	1	0.000199681	0	0.0014	5008	,	,		22331	0		0	False		,,,				2504	0				p.Y421Y		Atlas-SNP	.											IGF1R,colon,carcinoma,0,1	IGF1R	147	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1263T						.						107	91	96					15																	99451929		2197	4297	6494	SO:0001819	synonymous_variant	3480	exon6			CTTCTACGTCCTC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.1263C>T	chr15.hg19:g.99451929C>T		195.0	0.0		190.0	15.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	hg19	CCDS10378.1																																																																																			.	.		0.507	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		T	99451929	C	T	99451929	2	4	123	1	0	0	0	0	0	0	0	1	7580	547	19	1		1	IGF1R	15	99451929	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	8408653	99451929	3079463	268	20798										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101592136	101592136	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccgctgcaggagctggtcccTgaactgttcatgaccgactt	11	13	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:101592136T>A	ENST00000388948.3	+	24	4019	c.3660T>A	c.(3658-3660)ccT>ccA	p.P1220P	RP11-505E24.3_ENST00000558979.1_RNA|LRRK1_ENST00000284395.5_Silent_p.P1217P|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AGCTGGTCCCTGAACTGTTCA	0.637																																					p.P1220P		Atlas-SNP	.											.	LRRK1	310	.	0			c.T3660A						.						43	49	47					15																	101592136		2021	4180	6201	SO:0001819	synonymous_variant	79705	exon24			GGTCCCTGAACTG	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.3660T>A	chr15.hg19:g.101592136T>A		134.0	0.0		108.0	10.0	NM_024652		Silent	SNP	ENST00000388948.3	hg19	CCDS42086.1																																																																																			.	.		0.637	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101592136	T	A	101592136	2	1	123	1	0	0	0	0	0	0	0	1	9041	1567	55	4		4	LRRK1	15	101592136	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	2140207	101592136	939256	269	20799										
PRKCB	5579	hgsc.bcm.edu	37	chr16	24202416	24202416	+	Frame_Shift_Del	DEL	G	G	-													0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttctttctctcgaagctgatGaccaaacacccaggcaaacg							TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:24202416delG	ENST00000321728.7	+	16	1903	c.1728delG	c.(1726-1728)atgfs	p.M576fs	PRKCB_ENST00000303531.7_Frame_Shift_Del_p.M576fs	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	576	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	CGAAGCTGATGACCAAACACC	0.403																																					p.M576fs		Atlas-Indel,Pindel	.											.	PRKCB	383	.	0			c.1727delT						.						79	78	78					16																	24202416		2197	4300	6497	SO:0001589	frameshift_variant	5579	exon16			.	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"protein kinase C, beta 1"	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.1728delG	chr16.hg19:g.24202416delG	ENSP00000318315:p.Met576fs	118.0	0.0		97.0	29.0	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Frame_Shift_Del	DEL	ENST00000321728.7	hg19	CCDS10618.1																																																																																			.	.		0.403	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		-	24202416	G	-	24202416	7	5	123	1	0	1	0	1	0	0	0	0	12520	1290	45	0	1790	0	PRKCB	16	24202416	Frame_Shift_Del	DEL	G	TCGA-DD-A3A9-01A-11D-A25V-10		24202416	66152337	270	20800										
NUP93	9688	hgsc.bcm.edu	37	chr16	56872968	56872968	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtatcatagtggtcatattgAtagagcttttgatgtaagtt	10	3	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:56872968A>T	ENST00000308159.5	+	19	2244	c.2123A>T	c.(2122-2124)gAt>gTt	p.D708V	NUP93_ENST00000564887.1_Missense_Mutation_p.D585V|NUP93_ENST00000542526.1_Missense_Mutation_p.D585V|NUP93_ENST00000569842.1_Missense_Mutation_p.D708V	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	708					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						GGTCATATTGATAGAGCTTTT	0.363																																					p.D708V	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.A2123T						.						173	158	163					16																	56872968		2198	4300	6498	SO:0001583	missense	9688	exon19			ATATTGATAGAGC	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.2123A>T	chr16.hg19:g.56872968A>T	ENSP00000310668:p.Asp708Val	201.0	0.0		223.0	54.0	NM_014669	B3KPQ8|Q14705	Missense_Mutation	SNP	ENST00000308159.5	hg19	CCDS10769.1	.	.	.	.	.	.	.	.	.	.	A	18.11	3.550717	0.65311	.	.	ENSG00000102900	ENST00000308159;ENST00000542526	T;T	0.44881	0.91;0.91	6.14	6.14	0.99180	.	0.080378	0.85682	D	0.000000	T	0.37156	0.0993	L	0.35487	1.065	0.80722	D	1	B	0.20052	0.041	B	0.26416	0.069	T	0.09509	-1.0671	10	0.31617	T	0.26	-14.8164	16.806	0.85666	1.0:0.0:0.0:0.0	.	708	Q8N1F7	NUP93_HUMAN	V	708;585	ENSP00000310668:D708V;ENSP00000440235:D585V	ENSP00000310668:D708V	D	+	2	0	NUP93	55430469	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.813000	0.91963	2.367000	0.80283	0.529000	0.55759	GAT	.	.		0.363	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669		T	56872968	A	T	56872968	3	4	123	1	0	0	0	0	1	0	0	0	10781	333	12	4	2193	4	NUP93	16	56872968	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	32670552	56872968	33481785	271	20801										
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76513378	76513378	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atacttcagggttttactatAtagattcagatggaagtggt	10	4	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:76513378A>G	ENST00000476707.1	+	11	1973	c.1834A>G	c.(1834-1836)Ata>Gta	p.I612V	CNTNAP4_ENST00000377504.4_Missense_Mutation_p.I560V|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.I536V|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.I608V			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	609	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						GTTTTACTATATAGATTCAGA	0.343																																					p.I536V		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.A1606G						.						120	129	126					16																	76513378		2198	4296	6494	SO:0001583	missense	85445	exon11			TACTATATAGATT	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.1834A>G	chr16.hg19:g.76513378A>G	ENSP00000417628:p.Ile612Val	195.0	0.0		171.0	26.0	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.56	1.974835	0.34848	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.57	0.815	0.18763	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (3);	0.157455	0.29087	N	0.013190	T	0.23210	0.0561	.	.	.	0.39091	D	0.961107	B;B;B;B	0.12630	0.006;0.006;0.006;0.001	B;B;B;B	0.21151	0.02;0.02;0.033;0.005	T	0.06972	-1.0797	9	0.44086	T	0.13	.	9.5427	0.39262	0.731:0.0:0.269:0.0	.	536;612;584;609	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	V	608;560;536;612	ENSP00000306893:I608V;ENSP00000439733:I560V;ENSP00000418741:I536V;ENSP00000417628:I612V	ENSP00000306893:I608V	I	+	1	0	CNTNAP4	75070879	0.867000	0.29959	0.934000	0.37439	0.964000	0.63967	1.676000	0.37565	-0.046000	0.13446	0.528000	0.53228	ATA	.	.		0.343	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		G	76513378	A	G	76513378	3	3	123	1	0	0	0	0	1	0	0	0	3651	449	16	2	1884	2	CNTNAP4	16	76513378	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	19640410	76513378	13841375	272	20802										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77398168	77398168	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cttgtctgccaccacgagggTttccacattgaggccctttt	9	13	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:77398168T>C	ENST00000282849.5	-	5	1307	c.889A>G	c.(889-891)Acc>Gcc	p.T297A		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	297	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						ACCACGAGGGTTTCCACATTG	0.493																																					p.T297A		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.A889G						.						132	120	124					16																	77398168		2198	4300	6498	SO:0001583	missense	170692	exon5			CGAGGGTTTCCAC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.889A>G	chr16.hg19:g.77398168T>C	ENSP00000282849:p.Thr297Ala	222.0	0.0		218.0	51.0	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	T	18.69	3.678734	0.68042	.	.	ENSG00000140873	ENST00000282849	T	0.62639	0.01	5.17	5.17	0.71159	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	T	0.71736	0.3375	L	0.41710	1.295	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.74624	-0.3603	10	0.72032	D	0.01	.	14.3522	0.66711	0.0:0.0:0.0:1.0	.	297	Q8TE60	ATS18_HUMAN	A	297	ENSP00000282849:T297A	ENSP00000282849:T297A	T	-	1	0	ADAMTS18	75955669	1.000000	0.71417	0.805000	0.32314	0.301000	0.27625	7.477000	0.81069	2.170000	0.68504	0.482000	0.46254	ACC	.	.		0.493	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			C	77398168	T	C	77398168	3	2	123	1	0	0	0	0	1	0	0	0	263	1725	60	2	2852	2	ADAMTS18	16	77398168	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	884790	77398168	12956585	273	20803										
VAT1L	57687	hgsc.bcm.edu	37	chr16	77859180	77859180	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggcatttgtcaattacaatgCctgggcagaggtggtctgca	13	8	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:77859180C>T	ENST00000302536.2	+	3	554	c.401C>T	c.(400-402)gCc>gTc	p.A134V		NM_020927.1	NP_065978.1	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport 1-like	134							oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(10)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24						AATTACAATGCCTGGGCAGAG	0.522																																					p.A134V		Atlas-SNP	.											.	VAT1L	68	.	0			c.C401T						.						137	120	125					16																	77859180		2198	4300	6498	SO:0001583	missense	57687	exon3			ACAATGCCTGGGC	AB046796	CCDS32492.1	16q23.1	2014-09-09	2013-08-23		ENSG00000171724	ENSG00000171724			29315	protein-coding gene	gene with protein product			"vesicle amine transport protein 1 homolog (T. californica)-like"			10997877	Standard	NM_020927		Approved	KIAA1576	uc002ffg.1	Q9HCJ6	OTTHUMG00000176845	ENST00000302536.2:c.401C>T	chr16.hg19:g.77859180C>T	ENSP00000303129:p.Ala134Val	292.0	0.0		250.0	43.0	NM_020927	Q8IYW8	Missense_Mutation	SNP	ENST00000302536.2	hg19	CCDS32492.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280932	0.95489	.	.	ENSG00000171724	ENST00000302536	T	0.46063	0.88	6.03	6.03	0.97812	GroES-like (1);	0.000000	0.85682	D	0.000000	T	0.63283	0.2498	L	0.54908	1.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60219	-0.7306	10	0.56958	D	0.05	-9.4193	20.1519	0.98089	0.0:1.0:0.0:0.0	.	134	Q9HCJ6	VAT1L_HUMAN	V	134	ENSP00000303129:A134V	ENSP00000303129:A134V	A	+	2	0	VAT1L	76416681	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.861000	0.98227	0.655000	0.94253	GCC	.	.		0.522	VAT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434010.1	NM_020927		T	77859180	C	T	77859180	3	4	123	1	0	0	0	0	1	0	0	0	17145	739	26	3	411	3	VAT1L	16	77859180	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	461012	77859180	12495573	274	20804										
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88643755	88643755	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cgaggaggaccgggcaagtgAgcctaaatcccaagaccagg	14	11	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:88643755A>C	ENST00000301011.5	+	2	424	c.224A>C	c.(223-225)gAg>gCg	p.E75A	ZC3H18_ENST00000452588.2_Missense_Mutation_p.E75A	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	75						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CGGGCAAGTGAGCCTAAATCC	0.637																																					p.E75A	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.A224C						.						37	39	38					16																	88643755		2197	4300	6497	SO:0001583	missense	124245	exon2			CAAGTGAGCCTAA	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.224A>C	chr16.hg19:g.88643755A>C	ENSP00000301011:p.Glu75Ala	83.0	0.0		52.0	9.0	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	hg19	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	A	9.529	1.110385	0.20714	.	.	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588;ENST00000545404	T;T	0.33865	1.4;1.39	4.36	4.36	0.52297	.	0.122077	0.56097	D	0.000040	T	0.32164	0.0820	L	0.44542	1.39	0.30475	N	0.772884	P;P;P	0.45474	0.859;0.859;0.859	B;B;B	0.41917	0.37;0.37;0.37	T	0.26677	-1.0096	10	0.31617	T	0.26	-23.6357	13.55	0.61726	1.0:0.0:0.0:0.0	.	75;75;75	E7ERS3;B4DTK7;Q86VM9	.;.;ZCH18_HUMAN	A	75	ENSP00000301011:E75A;ENSP00000416951:E75A	ENSP00000289509:E75A	E	+	2	0	ZC3H18	87171256	0.989000	0.36119	0.991000	0.47740	0.007000	0.05969	4.375000	0.59549	1.582000	0.49881	0.459000	0.35465	GAG	.	.		0.637	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		C	88643755	A	C	88643755	3	2	123	1	0	0	0	0	1	0	0	0	17583	304	11	5	226	5	ZC3H18	16	88643755	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	10784575	88643755	1710998	275	20805										
PELP1	27043	hgsc.bcm.edu	37	chr17	4576104	4576104	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgagcctgcccggtggttctCagggccaggaagaagccggg	17	11	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:4576104C>T	ENST00000574876.1	-	16	2199	c.2182G>A	c.(2182-2184)Gag>Aag	p.E728K	PELP1_ENST00000301396.4_Missense_Mutation_p.E872K|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000436683.2_Missense_Mutation_p.E581K|PELP1_ENST00000269230.7_Missense_Mutation_p.E638K|PELP1_ENST00000572293.1_Missense_Mutation_p.E778K			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	728	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						CGGTGGTTCTCAGGGCCAGGA	0.627																																					p.E728K		Atlas-SNP	.											.	PELP1	102	.	0			c.G2182A						.						24	27	26					17																	4576104		1906	4114	6020	SO:0001583	missense	27043	exon16			GGTTCTCAGGGCC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"proline, glutamic acid and leucine rich protein 1"			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2182G>A	chr17.hg19:g.4576104C>T	ENSP00000461625:p.Glu728Lys	78.0	0.0		64.0	26.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	hg19	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995978	0.35226	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.56776	0.44;0.64;1.07	5.4	5.4	0.78164	.	0.436543	0.21440	N	0.074508	T	0.32585	0.0834	N	0.24115	0.695	0.32589	N	0.527431	P;P	0.43231	0.664;0.801	B;B	0.38500	0.275;0.275	T	0.31613	-0.9937	10	0.06891	T	0.86	-21.713	10.1651	0.42875	0.0:0.9095:0.0:0.0905	.	581;728	E7EV54;Q8IZL8	.;PELP1_HUMAN	K	872;638;581	ENSP00000301396:E872K;ENSP00000269230:E638K;ENSP00000416231:E581K	ENSP00000269230:E638K	E	-	1	0	AC091153.1	4522853	0.906000	0.30813	1.000000	0.80357	0.948000	0.59901	0.897000	0.28390	2.526000	0.85167	0.561000	0.74099	GAG	.	.		0.627	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		T	4576104	C	T	4576104	3	4	123	1	0	0	0	0	1	0	0	0	11734	835	29	3	1218	3	PELP1	17	4576104	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		4576104	76619106	276	20806										
PELP1	27043	hgsc.bcm.edu	37	chr17	4576404	4576404	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccgggggtgggtcagagcagCacaggtcaccagtgcttctg	16	11	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:4576404C>T	ENST00000574876.1	-	16	1899	c.1882G>A	c.(1882-1884)Gct>Act	p.A628T	PELP1_ENST00000301396.4_Missense_Mutation_p.A772T|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000436683.2_Missense_Mutation_p.A481T|PELP1_ENST00000269230.7_Missense_Mutation_p.A540T|PELP1_ENST00000572293.1_Missense_Mutation_p.A678T			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	628					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GTCAGAGCAGCACAGGTCACC	0.602																																					p.A628T		Atlas-SNP	.											.	PELP1	102	.	0			c.G1882A						.						22	25	24					17																	4576404		1958	4123	6081	SO:0001583	missense	27043	exon16			GAGCAGCACAGGT		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"proline, glutamic acid and leucine rich protein 1"			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.1882G>A	chr17.hg19:g.4576404C>T	ENSP00000461625:p.Ala628Thr	83.0	0.0		74.0	25.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	hg19	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049441	0.36181	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.51817	0.94;0.69;1.58	5.92	4.94	0.65067	Uncharacterised domain NUC202 (1);	0.326300	0.33092	N	0.005282	T	0.21921	0.0528	N	0.01874	-0.695	0.34443	D	0.699862	P;P	0.36683	0.565;0.565	B;B	0.37015	0.239;0.239	T	0.34453	-0.9828	10	0.15952	T	0.53	-14.3778	12.6748	0.56887	0.1642:0.8357:0.0:0.0	.	481;628	E7EV54;Q8IZL8	.;PELP1_HUMAN	T	772;540;481	ENSP00000301396:A772T;ENSP00000269230:A540T;ENSP00000416231:A481T	ENSP00000269230:A540T	A	-	1	0	AC091153.1	4523153	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.864000	0.39469	1.483000	0.48342	0.655000	0.94253	GCT	.	.		0.602	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		T	4576404	C	T	4576404	3	4	123	1	0	0	0	0	1	0	0	0	11734	710	25	3	1518	3	PELP1	17	4576404	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	300	4576404	76618806	277	20807										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7720031	7720031	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggggttggctggcgagaaggCcagatgggaggagacagtcc	20	7	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:7720031C>T	ENST00000572933.1	+	64	11332	c.9872C>T	c.(9871-9873)gCc>gTc	p.A3291V	DNAH2_ENST00000389173.2_Missense_Mutation_p.A3291V			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3291					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GGCGAGAAGGCCAGATGGGAG	0.567																																					p.A3291V		Atlas-SNP	.											DNAH2,NS,carcinoma,0,1	DNAH2	498	.	0			c.C9872T						.						150	127	135					17																	7720031		2203	4300	6503	SO:0001583	missense	146754	exon63			AGAAGGCCAGATG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.9872C>T	chr17.hg19:g.7720031C>T	ENSP00000458355:p.Ala3291Val	134.0	1.0		88.0	27.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.576394	0.28092	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.69175	-0.38	4.45	4.45	0.53987	Dynein heavy chain, coiled coil stalk (1);	0.208171	0.42294	D	0.000737	T	0.35068	0.0919	N	0.01438	-0.865	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.29610	-1.0006	10	0.16896	T	0.51	.	10.6403	0.45590	0.0:0.9059:0.0:0.0941	.	3252;3291	Q9P225-2;Q9P225	.;DYH2_HUMAN	V	3252;3291	ENSP00000373825:A3291V	ENSP00000353818:A3252V	A	+	2	0	DNAH2	7660756	1.000000	0.71417	1.000000	0.80357	0.593000	0.36681	2.897000	0.48664	2.469000	0.83416	0.462000	0.41574	GCC	.	.		0.567	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7720031	C	T	7720031	3	4	123	1	0	0	0	0	1	0	0	0	4604	739	26	3	10122	3	DNAH2	17	7720031	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	3143627	7720031	73475179	278	20808										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12666558	12666558	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctatgccaccgacagtgatgAgcatcttgaagtcttattaa	8	9	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:12666558A>G	ENST00000343344.4	+	13	2414	c.2414A>G	c.(2413-2415)gAg>gGg	p.E805G	MYOCD_ENST00000425538.1_Missense_Mutation_p.E853G|RP11-1090M7.1_ENST00000584772.1_RNA			Q8IZQ8	MYCD_HUMAN	myocardin	805					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		GACAGTGATGAGCATCTTGAA	0.498																																					p.E853G		Atlas-SNP	.											.	MYOCD	291	.	0			c.A2558G						.						98	97	97					17																	12666558		2203	4300	6503	SO:0001583	missense	93649	exon14			GTGATGAGCATCT	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.2414A>G	chr17.hg19:g.12666558A>G	ENSP00000341835:p.Glu805Gly	155.0	0.0		194.0	124.0	NM_001146312	Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	hg19	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.097201	0.56075	.	.	ENSG00000141052	ENST00000395982;ENST00000425538;ENST00000343344;ENST00000443061	T;T	0.42513	0.98;0.97	5.78	5.78	0.91487	.	0.494651	0.23720	N	0.045231	T	0.30978	0.0782	L	0.39898	1.24	0.80722	D	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.15263	-1.0443	10	0.23891	T	0.37	-34.3016	7.5161	0.27602	0.846:0.0:0.154:0.0	.	529;853;805	E9PEP9;Q8IZQ8-3;Q8IZQ8	.;.;MYCD_HUMAN	G	529;853;805;515	ENSP00000341835:E805G;ENSP00000400148:E515G	ENSP00000341835:E805G	E	+	2	0	MYOCD	12607283	0.446000	0.25665	0.994000	0.49952	0.968000	0.65278	2.469000	0.45110	2.333000	0.79357	0.533000	0.62120	GAG	.	.		0.498	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		G	12666558	A	G	12666558	3	3	123	1	0	0	0	0	1	0	0	0	10096	304	11	2	2624	2	MYOCD	17	12666558	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	4946527	12666558	68528652	279	20809										
ADORA2B	136	hgsc.bcm.edu	37	chr17	15878262	15878262	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcttataatgctggtgatctAcattaagatcttcctggtgg	10	7	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:15878262A>G	ENST00000304222.2	+	2	937	c.605A>G	c.(604-606)tAc>tGc	p.Y202C	ZSWIM7_ENST00000399280.2_5'Flank	NM_000676.2	NP_000667.1	P29275	AA2BR_HUMAN	adenosine A2b receptor	202					activation of adenylate cyclase activity (GO:0007190)|activation of MAPK activity (GO:0000187)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular defense response (GO:0006968)|cellular response to extracellular stimulus (GO:0031668)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)|JNK cascade (GO:0007254)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to non-antigenic stimulus (GO:0002882)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation vascular endothelial growth factor production (GO:0010575)|relaxation of vascular smooth muscle (GO:0060087)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			breast(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)	9				UCEC - Uterine corpus endometrioid carcinoma (92;0.0855)	Adenosine(DB00640)|Defibrotide(DB04932)|Enprofylline(DB00824)|Theophylline(DB00277)	CTGGTGATCTACATTAAGATC	0.512																																					p.Y202C		Atlas-SNP	.											.	ADORA2B	23	.	0			c.A605G						.						115	103	107					17																	15878262		2203	4300	6503	SO:0001583	missense	136	exon2			TGATCTACATTAA	M97759	CCDS11173.1	17p12	2012-08-08			ENSG00000170425	ENSG00000170425		"GPCR / Class A : Adenosine receptors"	264	protein-coding gene	gene with protein product		600446				7558011	Standard	NM_000676		Approved		uc002gpd.1	P29275	OTTHUMG00000059140	ENST00000304222.2:c.605A>G	chr17.hg19:g.15878262A>G	ENSP00000304501:p.Tyr202Cys	189.0	1.0		165.0	102.0	NM_000676		Missense_Mutation	SNP	ENST00000304222.2	hg19	CCDS11173.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.106533	0.77096	.	.	ENSG00000170425	ENST00000304222	T	0.60548	0.18	5.59	5.59	0.84812	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.83385	0.5243	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88748	0.3248	10	0.87932	D	0	-15.0911	14.9373	0.70967	1.0:0.0:0.0:0.0	.	202	P29275	AA2BR_HUMAN	C	202	ENSP00000304501:Y202C	ENSP00000304501:Y202C	Y	+	2	0	ADORA2B	15818987	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.128000	0.65567	0.460000	0.39030	TAC	.	.		0.512	ADORA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131032.1			G	15878262	A	G	15878262	3	3	123	1	0	0	0	0	1	0	0	0	328	391	14	2	611	2	ADORA2B	17	15878262	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	3211704	15878262	65316948	280	20810										
SMCR7	125170	hgsc.bcm.edu	37	chr17	18167688	18167688	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcctggcccctggaggggctGgcggggaacctctggctgca	18	13	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:18167688G>A	ENST00000323019.4	+	4	1186	c.975G>A	c.(973-975)ctG>ctA	p.L325L	MIEF2_ENST00000395704.4_3'UTR|MIEF2_ENST00000395706.2_Silent_p.L336L	NM_001144900.1|NM_139162.3	NP_001138372.1|NP_631901.2	Q96C03	MID49_HUMAN	mitochondrial elongation factor 2	325					mitochondrion organization (GO:0007005)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein targeting to membrane (GO:0090314)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)											TGGAGGGGCTGGCGGGGAACC	0.682																																					p.L336L		Atlas-SNP	.											.	SMCR7	20	.	0			c.G1008A						.						47	55	52					17																	18167688		2203	4296	6499	SO:0001819	synonymous_variant	125170	exon4			GGGGCTGGCGGGG	BC014973	CCDS11193.1, CCDS45624.1, CCDS45625.1	17p11.2	2013-09-23	2013-09-23	2013-09-23	ENSG00000177427	ENSG00000177427			17920	protein-coding gene	gene with protein product		615498	"Smith-Magenis syndrome chromosome region, candidate 7"	SMCR7		11997338, 21508961	Standard	NM_001144900		Approved	MGC23130, MiD49	uc010vxq.2	Q96C03	OTTHUMG00000059392	ENST00000323019.4:c.975G>A	chr17.hg19:g.18167688G>A		8.0	0.0		14.0	12.0	NM_148886	J3KPT3|Q6ZRD4|Q96N07	Silent	SNP	ENST00000323019.4	hg19	CCDS11193.1																																																																																			.	.		0.682	MIEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132060.2	NM_139162		A	18167688	G	A	18167688	2	1	123	1	0	0	0	0	0	0	0	1	14805	1335	47	3		3	SMCR7	17	18167688	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	2289426	18167688	63027522	281	20811										
CCR7	1236	hgsc.bcm.edu	37	chr17	38711491	38711491	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aaaggcctccacatgctctgTgatgagagagcatcgcatcg	11	11	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:38711491T>C	ENST00000246657.2	-	3	702	c.640A>G	c.(640-642)Aca>Gca	p.T214A	CCR7_ENST00000579344.1_Missense_Mutation_p.T208A	NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	214					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				ACATGCTCTGTGATGAGAGAG	0.557																																					p.T214A		Atlas-SNP	.											.	CCR7	31	.	0			c.A640G						.						76	67	70					17																	38711491		2203	4300	6503	SO:0001583	missense	1236	exon3			GCTCTGTGATGAG		CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.640A>G	chr17.hg19:g.38711491T>C	ENSP00000246657:p.Thr214Ala	135.0	0.0		205.0	28.0	NM_001838		Missense_Mutation	SNP	ENST00000246657.2	hg19	CCDS11369.1	.	.	.	.	.	.	.	.	.	.	T	5.552	0.286694	0.10513	.	.	ENSG00000126353	ENST00000246657	T	0.36340	1.26	5.31	1.69	0.24217	GPCR, rhodopsin-like superfamily (1);	0.684502	0.14082	N	0.342628	T	0.18551	0.0445	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.13407	0.009	T	0.21280	-1.0250	10	0.25106	T	0.35	.	2.8001	0.05412	0.1484:0.0963:0.4532:0.3021	.	214	P32248	CCR7_HUMAN	A	214	ENSP00000246657:T214A	ENSP00000246657:T214A	T	-	1	0	CCR7	35965017	0.002000	0.14202	0.001000	0.08648	0.916000	0.54674	0.523000	0.22925	0.089000	0.17243	0.459000	0.35465	ACA	.	.		0.557	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1			C	38711491	T	C	38711491	3	2	123	1	0	0	0	0	1	0	0	0	2948	1696	59	2	500	2	CCR7	17	38711491	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	20543803	38711491	42483719	282	20812										
KRT27	342574	hgsc.bcm.edu	37	chr17	38938637	38938637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acttccaatgcctggcacacCgcatgtgtttccagccccaa	7	16	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:38938637C>T	ENST00000301656.3	-	1	149	c.109G>A	c.(109-111)Ggt>Agt	p.G37S		NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				CCTGGCACACCGCATGTGTTT	0.607																																					p.G37S		Atlas-SNP	.											.	KRT27	41	.	0			c.G109A						.						64	59	61					17																	38938637		2203	4300	6503	SO:0001583	missense	342574	exon1			GCACACCGCATGT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.109G>A	chr17.hg19:g.38938637C>T	ENSP00000301656:p.Gly37Ser	117.0	0.0		145.0	13.0	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	hg19	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.451376	0.26074	.	.	ENSG00000171446	ENST00000301656	D	0.85013	-1.93	4.92	-3.33	0.04958	.	0.845034	0.10518	N	0.665346	T	0.72684	0.3491	L	0.34521	1.04	0.18873	N	0.999985	B	0.09022	0.002	B	0.06405	0.002	T	0.55250	-0.8170	10	0.17832	T	0.49	.	9.2104	0.37316	0.0:0.5159:0.0968:0.3874	.	37	Q7Z3Y8	K1C27_HUMAN	S	37	ENSP00000301656:G37S	ENSP00000301656:G37S	G	-	1	0	KRT27	36192163	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.477000	0.06583	-0.383000	0.07858	-1.063000	0.02288	GGT	.	.		0.607	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		T	38938637	C	T	38938637	3	4	123	1	0	0	0	0	1	0	0	0	8473	652	23	1	1302	1	KRT27	17	38938637	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	227146	38938637	42256573	283	20813										
ACE	1636	hgsc.bcm.edu	37	chr17	61573828	61573828	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cagctggccacacgggccccCtgcacaagtgtgacatctac	10	16	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:61573828C>T	ENST00000290866.4	+	23	3478	c.3454C>T	c.(3454-3456)Ctg>Ttg	p.L1152L	ACE_ENST00000290863.6_Silent_p.L578L|ACE_ENST00000490216.2_Silent_p.L578L|ACE_ENST00000577647.1_Silent_p.L578L|ACE_ENST00000413513.3_Intron|ACE_ENST00000428043.1_Intron|ACE_ENST00000421982.2_Intron	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1152	Peptidase M2 2.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	CACGGGCCCCCTGCACAAGTG	0.642																																					p.L1152L		Atlas-SNP	.											.	ACE	187	.	0			c.C3454T						.						69	67	68					17																	61573828		2203	4300	6503	SO:0001819	synonymous_variant	1636	exon23			GGCCCCCTGCACA	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.3454C>T	chr17.hg19:g.61573828C>T		339.0	1.0		335.0	202.0	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Silent	SNP	ENST00000290866.4	hg19	CCDS11637.1																																																																																			.	.		0.642	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			T	61573828	C	T	61573828	2	4	123	1	0	0	0	0	0	0	0	1	136	680	24	3		3	ACE	17	61573828	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	22635191	61573828	19621382	284	20814										
KCNJ2	3759	hgsc.bcm.edu	37	chr17	68171825	68171825	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgtttgatgtggcgagtgggCaatcttcggaaaagccactt	13	7	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:68171825C>T	ENST00000243457.3	+	2	1028	c.645C>T	c.(643-645)ggC>ggT	p.G215G	KCNJ2_ENST00000535240.1_Silent_p.G215G	NM_000891.2	NP_000882.1	P63252	KCNJ2_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 2	215					cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|magnesium ion transport (GO:0015693)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of resting membrane potential (GO:0060075)|regulation of skeletal muscle contraction via regulation of action potential (GO:0014861)|relaxation of cardiac muscle (GO:0055119)|relaxation of skeletal muscle (GO:0090076)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of membrane (GO:0031224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(13)|skin(1)|urinary_tract(1)	25	Breast(10;1.64e-08)					GGCGAGTGGGCAATCTTCGGA	0.478																																					p.G215G		Atlas-SNP	.											.	KCNJ2	74	.	0			c.C645T						.						114	100	105					17																	68171825		2203	4300	6503	SO:0001819	synonymous_variant	3759	exon2			AGTGGGCAATCTT	AF011904	CCDS11688.1	17q24.3	2014-09-17				ENSG00000123700		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6263	protein-coding gene	gene with protein product		600681				7696590, 11240146, 16382105	Standard	NM_000891		Approved	Kir2.1, IRK1, LQT7	uc002jir.3	P63252		ENST00000243457.3:c.645C>T	chr17.hg19:g.68171825C>T		102.0	0.0		144.0	22.0	NM_000891	O15110|P48049	Silent	SNP	ENST00000243457.3	hg19	CCDS11688.1																																																																																			.	.		0.478	KCNJ2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450889.1	NM_000891		T	68171825	C	T	68171825	2	4	123	1	0	0	0	0	0	0	0	1	8060	697	25	3		3	KCNJ2	17	68171825	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	6597997	68171825	13023385	285	20815										
DNAI2	64446	hgsc.bcm.edu	37	chr17	72285791	72285791	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cctggcaccccgatggcaacAggaagttggcagtggcatac	13	12	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:72285791A>G	ENST00000311014.6	+	5	593	c.526A>G	c.(526-528)Agg>Ggg	p.R176G	DNAI2_ENST00000582036.1_Missense_Mutation_p.R176G|DNAI2_ENST00000446837.2_Missense_Mutation_p.R176G|DNAI2_ENST00000579490.1_Missense_Mutation_p.R233G|DNAI2_ENST00000307504.5_Missense_Mutation_p.R33G			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	176					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						CGATGGCAACAGGAAGTTGGC	0.597									Kartagener syndrome																												p.R176G		Atlas-SNP	.											.	DNAI2	102	.	0			c.A526G						.						64	61	62					17																	72285791		2203	4300	6503	SO:0001583	missense	64446	exon5	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGCAACAGGAAGT	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"Axonemal dyneins", "WD repeat domain containing"	18744	protein-coding gene	gene with protein product	"dynein intermediate chain 2"	605483	"dynein, axonemal, intermediate polypeptide 2"			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.526A>G	chr17.hg19:g.72285791A>G	ENSP00000308312:p.Arg176Gly	98.0	0.0		125.0	83.0	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Missense_Mutation	SNP	ENST00000311014.6	hg19	CCDS11697.1	.	.	.	.	.	.	.	.	.	.	A	9.036	0.988394	0.18966	.	.	ENSG00000171595	ENST00000311014;ENST00000307504;ENST00000446837	T;T;T	0.71461	-0.57;-0.57;-0.57	5.01	-1.01	0.10169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.620678	0.17566	N	0.169629	T	0.61185	0.2327	L	0.46741	1.465	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.49624	-0.8920	10	0.23302	T	0.38	-28.5779	16.2683	0.82601	0.4592:0.5408:0.0:0.0	.	176	Q9GZS0	DNAI2_HUMAN	G	176;33;176	ENSP00000308312:R176G;ENSP00000302929:R33G;ENSP00000400252:R176G	ENSP00000302929:R33G	R	+	1	2	DNAI2	69797386	0.037000	0.19845	0.981000	0.43875	0.882000	0.50991	0.262000	0.18460	-0.053000	0.13289	0.260000	0.18958	AGG	.	.		0.597	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036		G	72285791	A	G	72285791	3	3	123	1	0	0	0	0	1	0	0	0	4612	179	7	2	540	2	DNAI2	17	72285791	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	4113966	72285791	8909419	286	20816										
ST6GALNAC2	10610	hgsc.bcm.edu	37	chr17	74569415	74569415	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acagcttggcactctctgagCcgttcagaaggctcagggtg	13	11	3	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:74569415C>T	ENST00000225276.5	-	4	711	c.392G>A	c.(391-393)gGc>gAc	p.G131D	ST6GALNAC2_ENST00000586520.1_5'UTR|RP11-666A8.9_ENST00000588104.1_RNA	NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	131					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						ACTCTCTGAGCCGTTCAGAAG	0.647																																					p.G131D		Atlas-SNP	.											.	ST6GALNAC2	29	.	0			c.G392A						.						24	22	23					17																	74569415		2199	4298	6497	SO:0001583	missense	10610	exon4			TCTGAGCCGTTCA	U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"Sialyltransferases"	10867	protein-coding gene	gene with protein product		610137	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)", "sialyltransferase-like 1"	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.392G>A	chr17.hg19:g.74569415C>T	ENSP00000225276:p.Gly131Asp	52.0	0.0		46.0	9.0	NM_006456	Q12971	Missense_Mutation	SNP	ENST00000225276.5	hg19	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	C	3.794	-0.043111	0.07452	.	.	ENSG00000070731	ENST00000225276	T	0.29142	1.58	4.77	-1.48	0.08745	.	1.506000	0.03537	N	0.223268	T	0.18718	0.0449	L	0.27944	0.81	0.09310	N	1	B	0.14012	0.009	B	0.13407	0.009	T	0.15122	-1.0448	10	0.10902	T	0.67	-0.9537	5.3608	0.16087	0.0:0.3063:0.1658:0.5279	.	131	Q9UJ37	SIA7B_HUMAN	D	131	ENSP00000225276:G131D	ENSP00000225276:G131D	G	-	2	0	ST6GALNAC2	72081010	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.158000	0.03153	0.079000	0.16929	0.591000	0.81541	GGC	.	.		0.647	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456		T	74569415	C	T	74569415	3	4	123	1	0	0	0	0	1	0	0	0	15239	739	26	3	756	3	ST6GALNAC2	17	74569415	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	2283624	74569415	6625795	287	20817										
MFSD11	79157	hgsc.bcm.edu	37	chr17	74774280	74774280	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttgttcttagtctatttgcgCagccgtggcatttttctaca	8	9	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:74774280C>A	ENST00000588460.1	+	13	3238	c.1196C>A	c.(1195-1197)gCa>gAa	p.A399E	MFSD11_ENST00000590514.1_Missense_Mutation_p.A399E|MFSD11_ENST00000590070.1_3'UTR|MFSD11_ENST00000593181.1_Missense_Mutation_p.A347E|MFSD11_ENST00000355954.3_Missense_Mutation_p.A347E|MFSD11_ENST00000586622.1_Missense_Mutation_p.A399E|MFSD11_ENST00000336509.4_Missense_Mutation_p.A399E	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	399						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						TCTATTTGCGCAGCCGTGGCA	0.493																																					p.A399E		Atlas-SNP	.											.	MFSD11	47	.	0			c.C1196A						.						164	149	154					17																	74774280		2203	4300	6503	SO:0001583	missense	79157	exon13			TTTGCGCAGCCGT	BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.1196C>A	chr17.hg19:g.74774280C>A	ENSP00000464932:p.Ala399Glu	203.0	0.0		285.0	31.0	NM_001242532	O43442|Q9NXI5	Missense_Mutation	SNP	ENST00000588460.1	hg19	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	C	36	5.697421	0.96802	.	.	ENSG00000092931	ENST00000336509;ENST00000355954	D;D	0.82167	-1.58;-1.58	6.07	6.07	0.98685	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.91573	0.7338	M	0.85630	2.765	0.80722	D	1	D;D	0.61080	0.989;0.988	P;P	0.61003	0.858;0.882	D	0.91194	0.4986	10	0.54805	T	0.06	-20.4795	20.2544	0.98414	0.0:1.0:0.0:0.0	.	347;399	O43934-2;O43934	.;MFS11_HUMAN	E	399;347	ENSP00000337240:A399E;ENSP00000348225:A347E	ENSP00000337240:A399E	A	+	2	0	MFSD11	72285875	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.711000	0.84669	2.885000	0.99019	0.655000	0.94253	GCA	.	.		0.493	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311		A	74774280	C	A	74774280	3	1	123	1	0	0	0	0	1	0	0	0	9538	710	25	3	1246	3	MFSD11	17	74774280	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	204865	74774280	6420930	288	20818										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9254383	9254383	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgatgatgaagaaattaataAgatgattgatgataggcata	10	1	0	8			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr18:9254383A>G	ENST00000262126.4	+	9	1358	c.1118A>G	c.(1117-1119)aAg>aGg	p.K373R	ANKRD12_ENST00000383440.2_Missense_Mutation_p.K350R|ANKRD12_ENST00000400020.3_Missense_Mutation_p.K350R	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	373						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						GAAATTAATAAGATGATTGAT	0.348																																					p.K373R		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A1118G						.						96	100	98					18																	9254383		2203	4300	6503	SO:0001583	missense	23253	exon9			TTAATAAGATGAT	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.1118A>G	chr18.hg19:g.9254383A>G	ENSP00000262126:p.Lys373Arg	105.0	0.0		95.0	10.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.854741	0.32791	.	.	ENSG00000101745	ENST00000383440;ENST00000546007;ENST00000262126;ENST00000359158	T;T	0.06142	3.44;3.34	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.09862	0.0242	M	0.64997	1.995	0.80722	D	1	B;B	0.25048	0.117;0.071	B;B	0.23018	0.043;0.019	T	0.10042	-1.0647	10	0.25751	T	0.34	-28.0808	15.8893	0.79279	1.0:0.0:0.0:0.0	.	350;373	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	R	350;350;373;80	ENSP00000372932:K350R;ENSP00000262126:K373R	ENSP00000262126:K373R	K	+	2	0	ANKRD12	9244383	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	7.162000	0.77515	2.153000	0.67306	0.528000	0.53228	AAG	.	.		0.348	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		G	9254383	A	G	9254383	3	3	123	1	0	0	0	0	1	0	0	0	640	72	3	2	1148	2	ANKRD12	18	9254383	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10		9254383	68822865	289	20819										
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29511372	29511372	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gctgactgccagaaacaacaTcattcaaaagcttccggatg	8	11	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr18:29511372T>A	ENST00000283351.4	-	2	607	c.272A>T	c.(271-273)gAt>gTt	p.D91V	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.D37V|TRAPPC8_ENST00000584876.1_5'UTR|TRAPPC8_ENST00000582513.1_Missense_Mutation_p.D91V	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	91					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)		p.D91V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AGAAACAACATCATTCAAAAG	0.408																																					p.D91V		Atlas-SNP	.											TRAPPC8,NS,carcinoma,0,1	TRAPPC8	126	.	1	Substitution - Missense(1)	kidney(1)	c.A272T						.						160	156	157					18																	29511372		2203	4300	6503	SO:0001583	missense	22878	exon2			ACAACATCATTCA	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.272A>T	chr18.hg19:g.29511372T>A	ENSP00000283351:p.Asp91Val	165.0	0.0		129.0	18.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	hg19	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.628068	0.46944	.	.	ENSG00000153339	ENST00000283351	T	0.09350	2.99	5.98	5.98	0.97165	.	0.068910	0.64402	D	0.000009	T	0.18964	0.0455	L	0.46157	1.445	0.80722	D	1	P;P	0.52577	0.954;0.919	P;P	0.50754	0.649;0.536	T	0.00349	-1.1798	10	0.39692	T	0.17	.	16.4696	0.84102	0.0:0.0:0.0:1.0	.	91;91	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	V	91	ENSP00000283351:D91V	ENSP00000283351:D91V	D	-	2	0	TRAPPC8	27765370	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.922000	0.75811	2.289000	0.77006	0.482000	0.46254	GAT	.	.		0.408	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		A	29511372	T	A	29511372	3	1	123	1	0	0	0	0	1	0	0	0	8213	1435	50	4	4147	4	KIAA1012	18	29511372	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	20256989	29511372	48565876	290	20820										
TCEB3B	51224	hgsc.bcm.edu	37	chr18	44560523	44560523	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgctcgaattcctcagccatAtctacctcctccacctcaga	4	17	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr18:44560523A>T	ENST00000332567.4	-	1	1465	c.1113T>A	c.(1111-1113)gaT>gaA	p.D371E	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	371					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CCTCAGCCATATCTACCTCCT	0.512																																					p.D371E		Atlas-SNP	.											.	TCEB3B	141	.	0			c.T1113A						.						84	81	82					18																	44560523		2203	4300	6503	SO:0001583	missense	51224	exon1			AGCCATATCTACC	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1113T>A	chr18.hg19:g.44560523A>T	ENSP00000331302:p.Asp371Glu	98.0	0.0		58.0	10.0	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	hg19	CCDS11932.1	.	.	.	.	.	.	.	.	.	.	A	2.337	-0.352039	0.05173	.	.	ENSG00000206181	ENST00000332567	T	0.05199	3.48	1.67	-3.23	0.05109	.	0.233910	0.22976	U	0.053375	T	0.02193	0.0068	N	0.16656	0.425	0.09310	N	1	P	0.36959	0.575	B	0.30782	0.12	T	0.47711	-0.9096	10	0.12766	T	0.61	.	3.5575	0.07870	0.3184:0.4564:0.0:0.2251	.	371	Q8IYF1	ELOA2_HUMAN	E	371	ENSP00000331302:D371E	ENSP00000331302:D371E	D	-	3	2	TCEB3B	42814521	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.910000	0.04054	-0.848000	0.04163	-1.600000	0.00815	GAT	.	.		0.512	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		T	44560523	A	T	44560523	3	4	123	1	0	0	0	0	1	0	0	0	15697	446	16	4	1152	4	TCEB3B	18	44560523	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	15049151	44560523	33516725	291	20821										
FEM1A	55527	hgsc.bcm.edu	37	chr19	4793795	4793795	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtgaccctgcagtgccttgcGgcccgggccctggataagaa	14	13	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:4793795G>A	ENST00000269856.3	+	1	2068	c.1929G>A	c.(1927-1929)gcG>gcA	p.A643A	AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000596170.1_RNA|AC005523.2_ENST00000601192.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	643					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		AGTGCCTTGCGGCCCGGGCCC	0.592																																					p.A643A		Atlas-SNP	.											FEM1A,colon,carcinoma,0,1	FEM1A	41	.	0			c.G1929A						.						31	29	29					19																	4793795		2203	4300	6503	SO:0001819	synonymous_variant	55527	exon1			CCTTGCGGCCCGG	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"Ankyrin repeat domain containing"	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1929G>A	chr19.hg19:g.4793795G>A		42.0	0.0		67.0	11.0	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Silent	SNP	ENST00000269856.3	hg19	CCDS12135.1																																																																																			.	.		0.592	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1			A	4793795	G	A	4793795	2	1	123	1	0	0	0	0	0	0	0	1	5817	1103	39	1		1	FEM1A	19	4793795	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10		4793795	54335188	292	20822										
TMEM146	257062	hgsc.bcm.edu	37	chr19	5766134	5766134	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcgacactgatttcagttggCtgcgacctggataaaaagat	10	8	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:5766134C>G	ENST00000381624.3	+	17	1588	c.1527C>G	c.(1525-1527)ggC>ggG	p.G509G	CATSPERD_ENST00000381614.2_Silent_p.G167G|CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	509					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											TTTCAGTTGGCTGCGACCTGG	0.537																																					p.G509G		Atlas-SNP	.											.	.	.	.	0			c.C1527G						.						119	111	113					19																	5766134		1980	4155	6135	SO:0001819	synonymous_variant	257062	exon17			AGTTGGCTGCGAC	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.1527C>G	chr19.hg19:g.5766134C>G		124.0	0.0		157.0	22.0	NM_152784	Q6ZRP1	Silent	SNP	ENST00000381624.3	hg19	CCDS12149.2																																																																																			.	.		0.537	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		G	5766134	C	G	5766134	2	3	123	1	0	0	0	0	0	0	0	1	16075	784	28	4		4	TMEM146	19	5766134	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	972339	5766134	53362849	293	20823										
MUC16	94025	hgsc.bcm.edu	37	chr19	9056445	9056445	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cagtggtagtgaaggttgaaGaggagaatggcacaggagtg	18	3	0	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:9056445G>A	ENST00000397910.4	-	3	31204	c.31001C>T	c.(31000-31002)tCt>tTt	p.S10334F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10336	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAAGGTTGAAGAGGAGAATGG	0.517																																					p.S10334F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C31001T						.						109	110	110					19																	9056445		2059	4200	6259	SO:0001583	missense	94025	exon3			GTTGAAGAGGAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31001C>T	chr19.hg19:g.9056445G>A	ENSP00000381008:p.Ser10334Phe	200.0	0.0		262.0	31.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	6.711	0.499943	0.12762	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	3.2	0.979	0.19745	.	.	.	.	.	T	0.02083	0.0065	N	0.24115	0.695	.	.	.	P	0.37101	0.582	B	0.34590	0.186	T	0.41179	-0.9523	8	0.87932	D	0	.	3.6769	0.08295	0.1346:0.0:0.6105:0.2549	.	10334	B5ME49	.	F	10334	ENSP00000381008:S10334F	ENSP00000381008:S10334F	S	-	2	0	MUC16	8917445	0.012000	0.17670	0.006000	0.13384	0.151000	0.21798	0.579000	0.23788	0.327000	0.23409	0.461000	0.40582	TCT	.	.		0.517	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9056445	G	A	9056445	3	1	123	1	0	0	0	0	1	0	0	0	9982	942	33	3	12850	3	MUC16	19	9056445	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	3290311	9056445	50072538	294	20824										
ZNF426	79088	hgsc.bcm.edu	37	chr19	9641667	9641667	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tatgcaaatcttaccaattgTatcccaatggatgtctgacc	6	10	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:9641667T>C	ENST00000535489.1	-	5	738	c.402A>G	c.(400-402)atA>atG	p.I134M	ZNF426_ENST00000253115.2_Missense_Mutation_p.I134M|ZNF426_ENST00000593003.1_Missense_Mutation_p.I96M|ZNF426_ENST00000589289.1_Intron			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	134					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						TTACCAATTGTATCCCAATGG	0.368																																					p.I134M		Atlas-SNP	.											ZNF426,NS,carcinoma,0,1	ZNF426	56	.	0			c.A402G						.						101	96	98					19																	9641667		2203	4300	6503	SO:0001583	missense	79088	exon7			CAATTGTATCCCA	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"Zinc fingers, C2H2-type", "-"	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.402A>G	chr19.hg19:g.9641667T>C	ENSP00000439017:p.Ile134Met	87.0	0.0		91.0	9.0	NM_024106	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	hg19	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.465268	0.01053	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.05925	3.37;3.37	1.53	-0.823	0.10815	.	.	.	.	.	T	0.02610	0.0079	N	0.04636	-0.2	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.47086	-0.9144	9	0.23302	T	0.38	.	5.8549	0.18714	0.0:0.3418:0.0:0.6582	.	121;134	Q59EH4;Q9BUY5	.;ZN426_HUMAN	M	121;134;134	ENSP00000253115:I134M;ENSP00000439017:I134M	ENSP00000253115:I134M	I	-	3	3	ZNF426	9502667	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.149000	0.03182	-0.917000	0.03813	-1.811000	0.00612	ATA	.	.		0.368	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106		C	9641667	T	C	9641667	3	2	123	1	0	0	0	0	1	0	0	0	17915	1628	57	2	1270	2	ZNF426	19	9641667	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	585222	9641667	49487316	295	20825										
ZNF441	126068	hgsc.bcm.edu	37	chr19	11888524	11888524	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctctacagagatgtgatgcaGgaaaccatcagaaacctgga	10	9	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:11888524G>A	ENST00000357901.4	+	2	204	c.102G>A	c.(100-102)caG>caA	p.Q34Q	ZNF441_ENST00000454339.2_5'UTR	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	34	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ATGTGATGCAGGAAACCATCA	0.433																																					p.Q34Q		Atlas-SNP	.											.	ZNF441	123	.	0			c.G102A						.						150	125	132					19																	11888524		692	1591	2283	SO:0001819	synonymous_variant	126068	exon2			GATGCAGGAAACC	AK095956	CCDS12266.2	19p13.13	2013-01-08			ENSG00000197044	ENSG00000197044		"Zinc fingers, C2H2-type", "-"	20875	protein-coding gene	gene with protein product							Standard	NM_152355		Approved	FLJ38637	uc010dyj.3	Q8N8Z8	OTTHUMG00000154449	ENST00000357901.4:c.102G>A	chr19.hg19:g.11888524G>A		180.0	0.0		191.0	19.0	NM_152355		Silent	SNP	ENST00000357901.4	hg19	CCDS12266.2																																																																																			.	.		0.433	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355		A	11888524	G	A	11888524	2	1	123	1	0	0	0	0	0	0	0	1	17929	991	35	3		3	ZNF441	19	11888524	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	2246857	11888524	47240459	296	20826										
ZNF439	90594	hgsc.bcm.edu	37	chr19	11978948	11978948	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctctggagaaagaccttatgAatgtaagacatgtgggaaag	12	5	1	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:11978948A>G	ENST00000304030.2	+	3	1264	c.1064A>G	c.(1063-1065)gAa>gGa	p.E355G	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Missense_Mutation_p.E219G	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	355					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						AGACCTTATGAATGTAAGACA	0.368																																					p.E355G		Atlas-SNP	.											.	ZNF439	67	.	0			c.A1064G						.						82	83	83					19																	11978948		2203	4300	6503	SO:0001583	missense	90594	exon3			CTTATGAATGTAA	AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"Zinc fingers, C2H2-type", "-"	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.1064A>G	chr19.hg19:g.11978948A>G	ENSP00000305077:p.Glu355Gly	76.0	0.0		94.0	11.0	NM_152262	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	hg19	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	a	10.93	1.490582	0.26686	.	.	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.07688	3.17;3.17	0.575	0.575	0.17374	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12689	0.0308	L	0.50333	1.59	0.09310	N	0.999994	D	0.53885	0.963	P	0.53146	0.719	T	0.16748	-1.0392	9	0.66056	D	0.02	.	4.5082	0.11898	0.6646:0.3354:0.0:0.0	.	355	Q8NDP4	ZN439_HUMAN	G	219;355	ENSP00000395632:E219G;ENSP00000305077:E355G	ENSP00000305077:E355G	E	+	2	0	ZNF439	11839948	0.000000	0.05858	0.012000	0.15200	0.085000	0.17905	-0.180000	0.09754	0.485000	0.27652	0.163000	0.16589	GAA	.	.		0.368	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			G	11978948	A	G	11978948	3	3	123	1	0	0	0	0	1	0	0	0	17926	246	9	2	1074	2	ZNF439	19	11978948	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	90424	11978948	47150035	297	20827										
OR7C2	26658	hgsc.bcm.edu	37	chr19	15052324	15052324	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gaaagaggaaaccaaacagaAgttggaaactttctcctcct	8	9	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:15052324A>T	ENST00000248072.3	+	1	24	c.24A>T	c.(22-24)gaA>gaT	p.E8D		NM_012377.1	NP_036509.1	O60412	OR7C2_HUMAN	olfactory receptor, family 7, subfamily C, member 2	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(8)|ovary(2)|skin(2)	15	Ovarian(108;0.203)					ACCAAACAGAAGTTGGAAACT	0.483																																					p.E8D		Atlas-SNP	.											.	OR7C2	50	.	0			c.A24T						.						93	98	96					19																	15052324		2203	4300	6503	SO:0001583	missense	26658	exon1			AACAGAAGTTGGA	U86255	CCDS12320.1	19p13.1	2012-08-09				ENSG00000127529		"GPCR / Class A : Olfactory receptors"	8374	protein-coding gene	gene with protein product				OR7C3			Standard	NM_012377		Approved	OR19-18	uc010xoc.2	O60412		ENST00000248072.3:c.24A>T	chr19.hg19:g.15052324A>T	ENSP00000248072:p.Glu8Asp	89.0	0.0		131.0	14.0	NM_012377	O43881|Q6IFP9	Missense_Mutation	SNP	ENST00000248072.3	hg19	CCDS12320.1	.	.	.	.	.	.	.	.	.	.	a	7.967	0.748165	0.15710	.	.	ENSG00000127529	ENST00000248072	T	0.19669	2.13	4.01	1.88	0.25563	.	1.199010	0.06609	U	0.755311	T	0.09862	0.0242	N	0.10645	0.015	0.09310	N	1	B	0.14012	0.009	B	0.17722	0.019	T	0.38908	-0.9639	10	0.19590	T	0.45	.	3.27	0.06878	0.5348:0.0:0.1031:0.3621	.	8	O60412	OR7C2_HUMAN	D	8	ENSP00000248072:E8D	ENSP00000248072:E8D	E	+	3	2	OR7C2	14913324	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.046000	0.01409	0.223000	0.20920	0.416000	0.27883	GAA	.	.		0.483	OR7C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466281.1			T	15052324	A	T	15052324	3	4	123	1	0	0	0	0	1	0	0	0	11227	69	3	4	26	4	OR7C2	19	15052324	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	3073376	15052324	44076659	298	20828										
ELL	8178	hgsc.bcm.edu	37	chr19	18576653	18576653	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gaagctgccctgggggttgtCgcggccgatgttggagaggt	19	8	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:18576653C>T	ENST00000262809.4	-	3	330	c.259G>A	c.(259-261)Gac>Aac	p.D87N	ELL_ENST00000596124.3_5'UTR	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	87					gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of viral transcription (GO:0050434)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	phosphatase binding (GO:0019902)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(5)|prostate(1)	19				GBM - Glioblastoma multiforme(1328;7.81e-07)		TGGGGGTTGTCGCGGCCGATG	0.677			T	MLL	AL																																p.D87N		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.G259A						.						38	41	40					19																	18576653		2203	4300	6503	SO:0001583	missense	8178	exon3			GGTTGTCGCGGCC	U16282	CCDS12380.1	19p13.1	2012-04-17	2005-05-23			ENSG00000105656		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23114	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 68"	600284	"chromosome 19 open reading frame 17"	C19orf17		7991593, 8596958	Standard	NM_006532		Approved	Men, ELL1, PPP1R68	uc002njh.3	P55199		ENST00000262809.4:c.259G>A	chr19.hg19:g.18576653C>T	ENSP00000262809:p.Asp87Asn	75.0	0.0		57.0	7.0	NM_006532		Missense_Mutation	SNP	ENST00000262809.4	hg19	CCDS12380.1	.	.	.	.	.	.	.	.	.	.	c	27.9	4.875515	0.91664	.	.	ENSG00000105656	ENST00000262809	T	0.34472	1.36	3.82	3.82	0.43975	.	0.000000	0.85682	D	0.000000	T	0.58666	0.2138	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.65352	-0.6189	10	0.87932	D	0	-28.1359	14.9121	0.70767	0.0:1.0:0.0:0.0	.	31;87	Q59HG4;P55199	.;ELL_HUMAN	N	87	ENSP00000262809:D87N	ENSP00000262809:D87N	D	-	1	0	ELL	18437653	1.000000	0.71417	0.936000	0.37596	0.835000	0.47333	7.364000	0.79526	1.974000	0.57490	0.479000	0.44913	GAC	.	.		0.677	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532		T	18576653	C	T	18576653	3	4	123	1	0	0	0	0	1	0	0	0	5064	884	31	1	1646	1	ELL	19	18576653	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	3524329	18576653	40552330	299	20829										
ZNF714	148206	hgsc.bcm.edu	37	chr19	21299624	21299624	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttctttcagctatgtgttctTcttttaccagagacctttgg	7	9	4	1	rs371085101		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:21299624T>C	ENST00000596143.1	+	5	479	c.154T>C	c.(154-156)Tct>Cct	p.S52P	ZNF714_ENST00000601416.1_Missense_Mutation_p.F58S|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_Intron	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	52					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						TATGTGTTCTTCTTTTACCAG	0.313																																					p.S52P		Atlas-SNP	.											.	ZNF714	121	.	0			c.T154C						.						55	56	56					19																	21299624		2175	4287	6462	SO:0001583	missense	148206	exon5			TGTTCTTCTTTTA	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.154T>C	chr19.hg19:g.21299624T>C	ENSP00000472368:p.Ser52Pro	79.0	0.0		76.0	42.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	4.151	0.026416	0.08054	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.601	-0.932	0.10435	.	.	.	.	.	T	0.13670	0.0331	N	0.20685	0.6	0.09310	N	1	P;B	0.41041	0.736;0.386	B;B	0.31495	0.131;0.043	T	0.12192	-1.0557	7	0.59425	D	0.04	.	.	.	.	.	52;52	Q96N38-2;A6NEM4	.;.	P	52	.	ENSP00000291770:S52P	S	+	1	0	ZNF714	21091464	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	-0.067000	0.11579	-0.412000	0.07519	0.374000	0.22700	TCT	.	.		0.313	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		C	21299624	T	C	21299624	3	2	123	1	0	0	0	0	1	0	0	0	18133	1783	62	2	164	2	ZNF714	19	21299624	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	2722971	21299624	37829359	300	20830										
CCDC123	84902	hgsc.bcm.edu	37	chr19	33439208	33439208	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctgtggtgcaggaggggagcCtggaaacccatcttgatgag	16	8	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:33439208C>T	ENST00000305768.5	-	5	647	c.559G>A	c.(559-561)Ggc>Agc	p.G187S	CEP89_ENST00000590597.2_Missense_Mutation_p.G187S	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	187					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						GGAGGGGAGCCTGGAAACCCA	0.338																																					p.G187S		Atlas-SNP	.											.	CEP89	82	.	0			c.G559A						.						85	69	75					19																	33439208		2203	4300	6503	SO:0001583	missense	84902	exon5			GGGAGCCTGGAAA	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"coiled-coil domain containing 123"	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.559G>A	chr19.hg19:g.33439208C>T	ENSP00000306105:p.Gly187Ser	38.0	0.0		59.0	9.0	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	hg19	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	C	6.064	0.380213	0.11466	.	.	ENSG00000121289	ENST00000305768	T	0.27720	1.65	4.69	1.43	0.22495	.	1.749320	0.02706	N	0.112223	T	0.32071	0.0817	L	0.42245	1.32	0.09310	N	1	P;B;B	0.51537	0.946;0.026;0.361	P;B;B	0.49597	0.616;0.019;0.097	T	0.28170	-1.0052	10	0.07644	T	0.81	-0.2223	6.5477	0.22414	0.0:0.6995:0.0:0.3005	.	158;187;187	Q8WUL5;Q96ST8-3;Q96ST8	.;.;CEP89_HUMAN	S	187	ENSP00000306105:G187S	ENSP00000306105:G187S	G	-	1	0	CEP89	38131048	0.030000	0.19436	0.097000	0.21041	0.125000	0.20455	-0.140000	0.10342	0.301000	0.22738	0.655000	0.94253	GGC	.	.		0.338	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		T	33439208	C	T	33439208	3	4	123	1	0	0	0	0	1	0	0	0	2761	681	24	3	1852	3	CCDC123	19	33439208	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	12139584	33439208	25689775	301	20831										
ZFP30	22835	hgsc.bcm.edu	37	chr19	38127120	38127120	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aagtccacagcttttaattcTttccattaccttccactgag	4	12	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:38127120T>C	ENST00000351218.2	-	6	879	c.322A>G	c.(322-324)Aga>Gga	p.R108G	ZFP30_ENST00000589018.1_Intron|ZFP30_ENST00000514101.2_Missense_Mutation_p.R108G|ZFP30_ENST00000392144.1_Missense_Mutation_p.R108G	NM_014898.2	NP_055713.1	Q9Y2G7	ZFP30_HUMAN	ZFP30 zinc finger protein	108					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	21			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTTTTAATTCTTTCCATTACC	0.343																																					p.R108G		Atlas-SNP	.											ZFP30,colon,carcinoma,+1,1	ZFP30	68	.	0			c.A322G						.						59	58	58					19																	38127120		2203	4300	6503	SO:0001583	missense	22835	exon6			TAATTCTTTCCAT	AB023178	CCDS33005.1	19q13.13	2013-01-08	2012-11-27		ENSG00000120784	ENSG00000120784		"Zinc fingers, C2H2-type", "-"	29555	protein-coding gene	gene with protein product			"zinc finger protein 30 homolog (mouse)"			10231032	Standard	NM_014898		Approved	ZNF745, KIAA0961	uc002ogx.1	Q9Y2G7	OTTHUMG00000048177	ENST00000351218.2:c.322A>G	chr19.hg19:g.38127120T>C	ENSP00000343581:p.Arg108Gly	121.0	1.0		142.0	38.0	NM_014898	Q58EY8	Missense_Mutation	SNP	ENST00000351218.2	hg19	CCDS33005.1	.	.	.	.	.	.	.	.	.	.	T	9.031	0.987309	0.18889	.	.	ENSG00000120784	ENST00000351218;ENST00000514101;ENST00000392144;ENST00000440715	T;T;T	0.05925	3.37;3.37;3.37	3.82	2.79	0.32731	.	0.655612	0.12653	N	0.450261	T	0.04907	0.0132	N	0.25957	0.775	0.30725	N	0.747856	B;B	0.24258	0.1;0.1	B;B	0.21708	0.036;0.036	T	0.14448	-1.0472	10	0.27082	T	0.32	.	8.4974	0.33136	0.0:0.1033:0.0:0.8967	.	108;108	D3Y2A0;Q9Y2G7	.;ZFP30_HUMAN	G	108;108;108;107	ENSP00000343581:R108G;ENSP00000422930:R108G;ENSP00000375988:R108G	ENSP00000343581:R108G	R	-	1	2	ZFP30	42818960	0.995000	0.38212	0.970000	0.41538	0.875000	0.50365	1.810000	0.38932	1.725000	0.51514	0.459000	0.35465	AGA	.	.		0.343	ZFP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109601.2	NM_014898		C	38127120	T	C	38127120	3	2	123	1	0	0	0	0	1	0	0	0	17659	1617	56	2	1241	2	ZFP30	19	38127120	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	4687912	38127120	21001863	302	20832										
TIMM50	92609	hgsc.bcm.edu	37	chr19	39980382	39980382	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gagcagcagcgcctggccgaGctctccaagtccaacaagca	11	15	1	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:39980382G>A	ENST00000607714.1	+	11	1006	c.984G>A	c.(982-984)gaG>gaA	p.E328E	TIMM50_ENST00000314349.4_Silent_p.E431E|TIMM50_ENST00000599794.1_Silent_p.E132E|TIMM50_ENST00000544017.1_Silent_p.E215E			Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)	328					cellular protein metabolic process (GO:0044267)|mitochondrial membrane organization (GO:0007006)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein targeting to mitochondrion (GO:0006626)|release of cytochrome c from mitochondria (GO:0001836)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)	interleukin-2 receptor binding (GO:0005134)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)			NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GCCTGGCCGAGCTCTCCAAGT	0.632																																					p.E431E		Atlas-SNP	.											.	TIMM50	37	.	0			c.G1293A						.						59	53	55					19																	39980382		2203	4300	6503	SO:0001819	synonymous_variant	92609	exon11			GGCCGAGCTCTCC	BC009072	CCDS33023.1	19q13.2	2010-06-21	2006-04-04		ENSG00000105197	ENSG00000105197		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	23656	protein-coding gene	gene with protein product		607381	"translocase of inner mitochondrial membrane 50 homolog (yeast)"			12437925	Standard	NM_001001563		Approved	TIM50L	uc002olu.1	Q3ZCQ8		ENST00000607714.1:c.984G>A	chr19.hg19:g.39980382G>A		93.0	0.0		162.0	20.0	NM_001001563	Q330K1|Q6QA00|Q96FJ5|Q96GY2|Q9H370	Silent	SNP	ENST00000607714.1	hg19																																																																																				.	.		0.632	TIMM50-021	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470728.1	NM_001001563		A	39980382	G	A	39980382	2	1	123	1	0	0	0	0	0	0	0	1	15928	962	34	3		3	TIMM50	19	39980382	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	1853262	39980382	19148601	303	20833										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42859978	42859978	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tcaatgcttcggtgggctctGcccgctgtgggtcagggggc	17	11	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:42859978G>A	ENST00000251268.6	+	24	4213	c.4213G>A	c.(4213-4215)Gcc>Acc	p.A1405T	MEGF8_ENST00000334370.4_Missense_Mutation_p.A1338T	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1405	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.|EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				GGTGGGCTCTGCCCGCTGTGG	0.677																																					p.A1405T		Atlas-SNP	.											MEGF8_ENST00000334370,caecum,carcinoma,0,3	MEGF8	358	.	0			c.G4213A						.						15	13	14					19																	42859978		2199	4294	6493	SO:0001583	missense	1954	exon24			GGCTCTGCCCGCT	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.4213G>A	chr19.hg19:g.42859978G>A	ENSP00000251268:p.Ala1405Thr	76.0	0.0		57.0	9.0	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	G	15.39	2.820255	0.50633	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.20598	2.06;2.06	4.61	4.61	0.57282	CUB (1);Epidermal growth factor-like, type 3 (1);	0.183165	0.38217	N	0.001775	T	0.16214	0.0390	N	0.08118	0	0.80722	D	1	P;D	0.60575	0.93;0.988	P;P	0.57911	0.48;0.829	T	0.08932	-1.0698	10	0.12103	T	0.63	-19.2081	7.9456	0.29985	0.0:0.1735:0.6472:0.1793	.	1405;1338	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	T	1338;1405	ENSP00000334219:A1338T;ENSP00000251268:A1405T	ENSP00000251268:A1405T	A	+	1	0	MEGF8	47551818	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.566000	0.60843	2.412000	0.81896	0.563000	0.77884	GCC	.	.		0.677	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		A	42859978	G	A	42859978	3	1	123	1	0	0	0	0	1	0	0	0	9472	1319	46	3	4102	3	MEGF8	19	42859978	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	2879596	42859978	16269005	304	20834										
ZNF222	7673	hgsc.bcm.edu	37	chr19	44536345	44536345	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccacatgggagtgaaatgctAtaagtgtgatgtgtgtggta	14	4	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:44536345A>G	ENST00000187879.8	+	4	680	c.518A>G	c.(517-519)tAt>tGt	p.Y173C	ZNF223_ENST00000591793.1_Intron|ZNF222_ENST00000391960.3_Missense_Mutation_p.Y213C	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	173					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				GTGAAATGCTATAAGTGTGAT	0.438																																					p.Y213C		Atlas-SNP	.											.	ZNF222	90	.	0			c.A638G						.						148	153	151					19																	44536345		2203	4300	6503	SO:0001583	missense	7673	exon4			AATGCTATAAGTG	AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.518A>G	chr19.hg19:g.44536345A>G	ENSP00000187879:p.Tyr173Cys	200.0	0.0		267.0	30.0	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Missense_Mutation	SNP	ENST00000187879.8	hg19	CCDS33045.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.552228	0.27739	.	.	ENSG00000159885	ENST00000391960;ENST00000187879;ENST00000251272	T;T	0.20463	3.15;2.07	2.79	-0.744	0.11101	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23014	0.0556	M	0.81497	2.545	0.09310	N	1	B;B	0.15473	0.013;0.008	B;B	0.17098	0.017;0.007	T	0.37314	-0.9711	9	0.72032	D	0.01	.	3.3882	0.07280	0.4917:0.0:0.3321:0.1762	.	213;173	G5E9B9;Q9UK12	.;ZN222_HUMAN	C	213;173;119	ENSP00000375822:Y213C;ENSP00000187879:Y173C	ENSP00000187879:Y173C	Y	+	2	0	ZNF222	49228185	0.000000	0.05858	0.000000	0.03702	0.669000	0.39330	-0.672000	0.05244	-0.409000	0.07553	0.172000	0.16884	TAT	.	.		0.438	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			G	44536345	A	G	44536345	3	3	123	1	0	0	0	0	1	0	0	0	17791	449	16	2	671	2	ZNF222	19	44536345	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	1676367	44536345	14592638	305	20835										
SFRS16	11129	hgsc.bcm.edu	37	chr19	45543521	45543521	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aagcttcgaggcatgatggtCgactacaagaagagggcgga	15	7	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:45543521C>T	ENST00000221455.3	+	2	149	c.51C>T	c.(49-51)gtC>gtT	p.V17V	CLASRP_ENST00000544944.2_Silent_p.V17V|CLASRP_ENST00000391953.4_Silent_p.V17V	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	17					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						GCATGATGGTCGACTACAAGA	0.587																																					p.V17V		Atlas-SNP	.											.	CLASRP	44	.	0			c.C51T						.						139	110	120					19																	45543521		2203	4297	6500	SO:0001819	synonymous_variant	11129	exon2			GATGGTCGACTAC	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"Clk4 associating SR-related protein"		"splicing factor, arginine/serine-rich 16"	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.51C>T	chr19.hg19:g.45543521C>T		183.0	0.0		243.0	24.0	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	hg19	CCDS12652.2																																																																																			.	.		0.587	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056		T	45543521	C	T	45543521	2	4	123	1	0	0	0	0	0	0	0	1	14187	871	31	1		1	SFRS16	19	45543521	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1007176	45543521	13585462	306	20836										
SYNGR4	23546	hgsc.bcm.edu	37	chr19	48879425	48879425	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttcctggatgagggtggcatGgtgctgaccaccctcccctt	12	13	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:48879425G>A	ENST00000344846.2	+	5	805	c.555G>A	c.(553-555)atG>atA	p.M185I	SYNGR4_ENST00000601610.1_3'UTR|SYNGR4_ENST00000595322.1_3'UTR	NM_012451.3	NP_036583.2	O95473	SNG4_HUMAN	synaptogyrin 4	185						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)		AGGGTGGCATGGTGCTGACCA	0.592																																					p.M185I		Atlas-SNP	.											.	SYNGR4	31	.	0			c.G555A						.						168	135	146					19																	48879425		2203	4300	6503	SO:0001583	missense	23546	exon5			TGGCATGGTGCTG	AJ011733	CCDS12717.1	19q13.3	2008-07-04				ENSG00000105467			11502	protein-coding gene	gene with protein product		608373					Standard	NM_012451		Approved		uc002piz.3	O95473		ENST00000344846.2:c.555G>A	chr19.hg19:g.48879425G>A	ENSP00000344041:p.Met185Ile	148.0	0.0		188.0	28.0	NM_012451	Q3KP58	Missense_Mutation	SNP	ENST00000344846.2	hg19	CCDS12717.1	.	.	.	.	.	.	.	.	.	.	G	7.766	0.706462	0.15239	.	.	ENSG00000105467	ENST00000344846	T	0.40756	1.02	5.51	4.46	0.54185	.	0.171029	0.50627	D	0.000115	T	0.26159	0.0638	N	0.19112	0.55	0.24248	N	0.995334	B	0.09022	0.002	B	0.06405	0.002	T	0.12837	-1.0532	10	0.29301	T	0.29	-24.1945	9.5076	0.39056	0.0:0.1558:0.6826:0.1615	.	185	O95473	SNG4_HUMAN	I	185	ENSP00000344041:M185I	ENSP00000344041:M185I	M	+	3	0	SYNGR4	53571237	0.918000	0.31147	0.997000	0.53966	0.250000	0.25880	0.024000	0.13555	1.451000	0.47736	0.555000	0.69702	ATG	.	.		0.592	SYNGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465704.1			A	48879425	G	A	48879425	3	1	123	1	0	0	0	0	1	0	0	0	15466	1348	47	3	569	3	SYNGR4	19	48879425	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	3335904	48879425	10249558	307	20837										
SIGLEC11	114132	hgsc.bcm.edu	37	chr19	50464033	50464033	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	caggagcacccgtctttgggCtggtccgtcctttgaaccag	12	13	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:50464033C>T	ENST00000447370.2	-	2	326	c.236G>A	c.(235-237)aGc>aAc	p.S79N	CTC-326K19.6_ENST00000451973.1_5'Flank|SIGLEC11_ENST00000426971.2_Missense_Mutation_p.S79N	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	79	Ig-like V-type.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		CGTCTTTGGGCTGGTCCGTCC	0.597																																					p.S79N		Atlas-SNP	.											.	SIGLEC11	70	.	0			c.G236A						.						49	43	45					19																	50464033		2202	4300	6502	SO:0001583	missense	114132	exon2			TTTGGGCTGGTCC	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.236G>A	chr19.hg19:g.50464033C>T	ENSP00000412361:p.Ser79Asn	176.0	0.0		221.0	27.0	NM_052884		Missense_Mutation	SNP	ENST00000447370.2	hg19	CCDS12790.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.006|0.006	-2.083052|-2.083052	0.00371|0.00371	.|.	.|.	ENSG00000161640|ENSG00000161640	ENST00000426971|ENST00000447370;ENST00000458019	T|T	0.47177|0.66460	0.85|-0.21	2.63|2.63	-3.85|-3.85	0.04243|0.04243	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.|2.404500	.|0.01193	.|N	.|0.007397	T|T	0.41971|0.41971	0.1182|0.1182	N|N	0.04132|0.04132	-0.27|-0.27	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	T|T	0.37842|0.37842	-0.9688|-0.9688	6|10	.|0.13470	.|T	.|0.59	.|.	9.7995|9.7995	0.40755|0.40755	0.0:0.64:0.0:0.36|0.0:0.64:0.0:0.36	.|.	.|79;79	.|Q96RL6-2;Q96RL6	.|.;SIG11_HUMAN	T|N	69|79	ENSP00000398891:A69T|ENSP00000412361:S79N	.|ENSP00000412361:S79N	A|S	-|-	1|2	0|0	SIGLEC11|SIGLEC11	55155845|55155845	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-2.396000|-2.396000	0.01052|0.01052	-1.250000|-1.250000	0.02497|0.02497	-1.456000|-1.456000	0.01031|0.01031	GCC|AGC	.	.		0.597	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		T	50464033	C	T	50464033	3	4	123	1	0	0	0	0	1	0	0	0	14322	797	28	3	1900	3	SIGLEC11	19	50464033	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1584608	50464033	8664950	308	20838										
KLK9	284366	hgsc.bcm.edu	37	chr19	51506441	51506441	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gactgcggggcgccggggtcTggagcagggctcagcacccc	18	14	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:51506441T>G	ENST00000594211.1	-	5	679	c.679A>C	c.(679-681)Aga>Cga	p.R227R	KLK9_ENST00000376832.4_Silent_p.R227R|KLK8_ENST00000391806.2_5'Flank|KLK8_ENST00000600767.1_5'Flank|KLK8_ENST00000347619.4_5'Flank|CTB-147C22.9_ENST00000594512.1_RNA|KLK8_ENST00000320838.5_5'Flank|KLK8_ENST00000291726.7_5'Flank|KLK8_ENST00000593490.1_5'Flank|KLK9_ENST00000250366.6_Silent_p.R227R			Q9UKQ9	KLK9_HUMAN	kallikrein-related peptidase 9	227	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7		all_neural(266;0.0652)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		CGCCGGGGTCTGGAGCAGGGC	0.642																																					p.R227R		Atlas-SNP	.											.	KLK9	27	.	0			c.A679C						.						62	67	65					19																	51506441		2203	4300	6503	SO:0001819	synonymous_variant	284366	exon5			GGGGTCTGGAGCA	AF135026	CCDS12816.1	19q13.33	2008-02-05	2006-10-27					"Kallikreins"	6370	protein-coding gene	gene with protein product		605504	"kallikrein 9"			16800724, 16800723	Standard	NM_012315		Approved	KLK-L3	uc002pux.1	Q9UKQ9		ENST00000594211.1:c.679A>C	chr19.hg19:g.51506441T>G		65.0	0.0		79.0	9.0	NM_012315	Q6QA55	Silent	SNP	ENST00000594211.1	hg19	CCDS12816.1																																																																																			.	.		0.642	KLK9-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465226.1	NM_012315		G	51506441	T	G	51506441	2	3	123	1	0	0	0	0	0	0	0	1	8420	1588	55	5		5	KLK9	19	51506441	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	1042408	51506441	7622542	309	20839										
ZNF578	147660	hgsc.bcm.edu	37	chr19	53014631	53014631	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	acaagtcatcccttacatgcCatcataggtgtcacactggt	7	12	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:53014631C>T	ENST00000421239.2	+	6	1241	c.997C>T	c.(997-999)Cat>Tat	p.H333Y	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	333					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		CCTTACATGCCATCATAGGTG	0.428																																					p.H333Y		Atlas-SNP	.											.	.	.	.	0			c.C997T						.						112	114	113					19																	53014631		2200	4300	6500	SO:0001583	missense	147660	exon6			ACATGCCATCATA	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.997C>T	chr19.hg19:g.53014631C>T	ENSP00000459216:p.His333Tyr	163.0	0.0		218.0	37.0	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	hg19	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	13.74	2.327480	0.41197	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.48	1.48	0.22813	.	.	.	.	.	T	0.60064	0.2240	H	0.95402	3.665	0.19575	N	0.999962	D	0.54047	0.964	B	0.42798	0.398	T	0.60393	-0.7272	7	.	.	.	.	10.0458	0.42186	0.0:1.0:0.0:0.0	.	333	G3V4F6	.	Y	333	.	.	H	+	1	0	ZNF578	57706443	0.991000	0.36638	0.001000	0.08648	0.011000	0.07611	3.772000	0.55325	0.835000	0.34877	0.297000	0.19635	CAT	.	.		0.428	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		T	53014631	C	T	53014631	3	4	123	1	0	0	0	0	1	0	0	0	18025	594	21	3	1007	3	ZNF578	19	53014631	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1508190	53014631	6114352	310	20840										
RPS9	6203	hgsc.bcm.edu	37	chr19	54705416	54705416	+	Frame_Shift_Del	DEL	C	C	-													0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aaatttaccctggccaagatCcgcaaggccgcccgggaact							TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:54705416delC	ENST00000302907.4	+	3	331	c.159delC	c.(157-159)atcfs	p.I53fs	RPS9_ENST00000402367.1_Frame_Shift_Del_p.I53fs|RPS9_ENST00000391752.1_Frame_Shift_Del_p.I53fs|RPS9_ENST00000391753.2_Frame_Shift_Del_p.I53fs|RPS9_ENST00000441429.1_Frame_Shift_Del_p.I53fs|AC012314.20_ENST00000426213.1_RNA|RPS9_ENST00000391751.3_Frame_Shift_Del_p.I53fs	NM_001013.3	NP_001004.2	P46781	RS9_HUMAN	ribosomal protein S9	53					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of cell proliferation (GO:0008284)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)|translation regulator activity (GO:0045182)			NS(1)|breast(1)|kidney(11)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	20	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.18)		TGGCCAAGATCCGCAAGGCCG	0.607																																					p.I53fs		Atlas-Indel,Pindel	.											.	RPS9	27	.	0			c.158delT						.						38	35	36					19																	54705416		2203	4300	6503	SO:0001589	frameshift_variant	6203	exon3			.	U14971	CCDS12884.1	19q13.4	2011-04-05			ENSG00000170889	ENSG00000170889		"S ribosomal proteins"	10442	protein-coding gene	gene with protein product	"40S ribosomal protein S9"	603631				7772601, 9582194	Standard	XM_005259135		Approved	S9	uc002qdx.3	P46781	OTTHUMG00000066618	ENST00000302907.4:c.159delC	chr19.hg19:g.54705416delC	ENSP00000302896:p.Ile53fs	71.0	0.0		122.0	36.0	NM_001013	A9C4C1|Q4QRK7|Q9BVZ0	Frame_Shift_Del	DEL	ENST00000302907.4	hg19	CCDS12884.1																																																																																			.	.		0.607	RPS9-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142834.3	NM_001013		-	54705416	C	-	54705416	7	5	123	1	0	1	0	1	0	0	0	0	13677	845	30	0	165	0	RPS9	19	54705416	Frame_Shift_Del	DEL	C	TCGA-DD-A3A9-01A-11D-A25V-10	1690785	54705416	4423567	311	20841										
NLRP7	199713	hgsc.bcm.edu	37	chr19	55453072	55453072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gagtccactctagctggggcGatgtcatagtgctccgagta	13	10	2	0	rs142163492		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:55453072G>A	ENST00000590030.1	-	1	48	c.8C>T	c.(7-9)tCg>tTg	p.S3L	NLRP7_ENST00000340844.2_Missense_Mutation_p.S3L|NLRP7_ENST00000592784.1_Missense_Mutation_p.S3L|NLRP7_ENST00000446217.1_Missense_Mutation_p.S31L|NLRP7_ENST00000588756.1_Missense_Mutation_p.S3L|NLRP7_ENST00000328092.5_Missense_Mutation_p.S3L|NLRP7_ENST00000448121.2_Missense_Mutation_p.S3L			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	3	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TAGCTGGGGCGATGTCATAGT	0.458																																					p.S3L		Atlas-SNP	.											.	NLRP7	411	.	0			c.C8T						.	G	LEU/SER,LEU/SER,LEU/SER	0,4406		0,0,2203	33	34	34		8,8,8	0.5	0	19	dbSNP_134	34	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	145,145,145	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign,benign	3/1038,3/1010,3/981	55453072	2,13004	2203	4300	6503	SO:0001583	missense	199713	exon2			TGGGGCGATGTCA	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.8C>T	chr19.hg19:g.55453072G>A	ENSP00000465520:p.Ser3Leu	75.0	0.0		93.0	9.0	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	hg19	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.664353	0.29604	0.0	2.33E-4	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.79033	-1.11;-1.11;-1.19;-1.23	1.53	0.467	0.16721	Pyrin (1);DEATH-like (1);	.	.	.	.	T	0.65217	0.2670	L	0.43152	1.355	0.09310	N	1	B;B;B;B	0.13145	0.004;0.004;0.004;0.007	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.53099	-0.8486	9	0.42905	T	0.14	.	4.1013	0.10015	0.2269:0.0:0.7731:0.0	.	31;3;3;3	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	L	3;3;3;31;3	ENSP00000329568:S3L;ENSP00000409137:S3L;ENSP00000339491:S3L;ENSP00000414273:S31L	ENSP00000329568:S3L	S	-	2	0	NLRP7	60144884	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.502000	0.22594	0.197000	0.20387	-0.657000	0.03884	TCG	.	G|1.000;A|0.000		0.458	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55453072	G	A	55453072	3	1	123	1	0	0	0	0	1	0	0	0	10491	1059	37	1	3145	1	NLRP7	19	55453072	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	747656	55453072	3675911	312	20842										
NLRP4	147945	hgsc.bcm.edu	37	chr19	56369470	56369470	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gacagcttcgaagagctgcaGggcggcttgaacgaacccga	14	11	0	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:56369470G>T	ENST00000301295.6	+	3	1133	c.711G>T	c.(709-711)caG>caT	p.Q237H	NLRP4_ENST00000587891.1_Missense_Mutation_p.Q162H|NLRP4_ENST00000346986.5_Missense_Mutation_p.Q237H	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	237	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		AAGAGCTGCAGGGCGGCTTGA	0.547																																					p.Q237H		Atlas-SNP	.											.	NLRP4	331	.	0			c.G711T						.						81	83	82					19																	56369470		2203	4300	6503	SO:0001583	missense	147945	exon3			GCTGCAGGGCGGC	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.711G>T	chr19.hg19:g.56369470G>T	ENSP00000301295:p.Gln237His	127.0	0.0		189.0	33.0	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	hg19	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	G	10.57	1.387734	0.25031	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.78707	-1.2;-1.2	4.1	-7.69	0.01263	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.65450	0.2692	L	0.27053	0.805	0.09310	N	1	B;B;B	0.25667	0.04;0.032;0.131	B;B;B	0.33196	0.013;0.099;0.159	T	0.57831	-0.7743	9	0.48119	T	0.1	.	13.3597	0.60648	0.1834:0.1283:0.6884:0.0	.	237;162;237	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	H	237	ENSP00000301295:Q237H;ENSP00000344787:Q237H	ENSP00000301295:Q237H	Q	+	3	2	NLRP4	61061282	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.986000	0.00087	-2.061000	0.00892	-0.302000	0.09304	CAG	.	.		0.547	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56369470	G	T	56369470	3	4	123	1	0	0	0	0	1	0	0	0	10488	991	35	3	717	3	NLRP4	19	56369470	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	916398	56369470	2759513	313	20843										
ZNF135	7694	hgsc.bcm.edu	37	chr19	58578913	58578913	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccacactggggagaaaccctAtcagtgtggtgagtgtggca	14	9	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:58578913A>T	ENST00000313434.5	+	5	1162	c.1061A>T	c.(1060-1062)tAt>tTt	p.Y354F	ZNF135_ENST00000506786.1_Missense_Mutation_p.Y312F|RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000511556.1_Missense_Mutation_p.Y366F|ZNF135_ENST00000439855.2_Missense_Mutation_p.Y354F|ZNF135_ENST00000401053.4_Missense_Mutation_p.Y378F|ZNF135_ENST00000359978.6_Missense_Mutation_p.Y366F	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	354					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		GAGAAACCCTATCAGTGTGGT	0.567																																					p.Y378F		Atlas-SNP	.											.	ZNF135	159	.	0			c.A1133T						.						55	47	50					19																	58578913		2203	4300	6503	SO:0001583	missense	7694	exon4			AACCCTATCAGTG	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"Zinc fingers, C2H2-type", "-"	12919	protein-coding gene	gene with protein product		604077	"zinc finger protein 61", "zinc finger protein 135 (clone pHZ-17)"	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.1061A>T	chr19.hg19:g.58578913A>T	ENSP00000321406:p.Tyr354Phe	138.0	0.0		188.0	26.0	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.492|6.492	0.458944|0.458944	0.12342|0.12342	.|.	.|.	ENSG00000176293|ENSG00000176293	ENST00000391699|ENST00000504540;ENST00000401053;ENST00000359978;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	.|T;T;T;T;T;T	.|0.18338	.|2.22;2.22;2.22;2.22;2.22;2.22	2.75|2.75	2.75|2.75	0.32379|0.32379	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	T|T	0.14614|0.14614	0.0353|0.0353	N|N	0.12471|0.12471	0.22|0.22	0.09310|0.09310	N|N	1|1	.|P;P;B	.|0.48294	.|0.491;0.908;0.118	.|B;P;B	.|0.53490	.|0.213;0.727;0.039	T|T	0.11717|0.11717	-1.0576|-1.0576	5|9	.|0.35671	.|T	.|0.21	.|.	6.2384|6.2384	0.20776|0.20776	0.7761:0.0:0.0:0.2239|0.7761:0.0:0.0:0.2239	.|.	.|366;354;366	.|E9PEV2;P52742;Q8N1I7	.|.;ZN135_HUMAN;.	F|F	372|366;378;366;354;354;366;312	.|ENSP00000441410:Y378F;ENSP00000369437:Y366F;ENSP00000444828:Y354F;ENSP00000321406:Y354F;ENSP00000422074:Y366F;ENSP00000427691:Y312F	.|ENSP00000321406:Y354F	I|Y	+|+	1|2	0|0	ZNF135|ZNF135	63270725|63270725	0.001000|0.001000	0.12720|0.12720	0.664000|0.664000	0.29753|0.29753	0.028000|0.028000	0.11728|0.11728	1.281000|1.281000	0.33214|0.33214	1.272000|1.272000	0.44329|0.44329	0.455000|0.455000	0.32223|0.32223	ATC|TAT	.	.		0.567	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		T	58578913	A	T	58578913	3	4	123	1	0	0	0	0	1	0	0	0	17740	449	16	4	1264	4	ZNF135	19	58578913	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	2209443	58578913	550070	314	20844										
RRBP1	6238	hgsc.bcm.edu	37	chr20	17616198	17616198	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aagctcagcttacttgctctCcacctggctcgtggcctggt	10	14	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:17616198C>A	ENST00000377813.1	-	7	2752	c.2449G>T	c.(2449-2451)Gag>Tag	p.E817*	RRBP1_ENST00000246043.4_Nonsense_Mutation_p.E817*|RRBP1_ENST00000360807.4_Nonsense_Mutation_p.E384*|RRBP1_ENST00000377807.2_Nonsense_Mutation_p.E384*|RRBP1_ENST00000455029.2_Nonsense_Mutation_p.E158*			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	817					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						TACTTGCTCTCCACCTGGCTC	0.647																																					p.E384X		Atlas-SNP	.											.	RRBP1	157	.	0			c.G1150T						.						66	58	61					20																	17616198		2203	4300	6503	SO:0001587	stop_gained	6238	exon7			TGCTCTCCACCTG	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"ribosome binding protein 1 (dog 180kD homolog)", "ribosome binding protein 1 homolog 180kDa (dog)"			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.2449G>T	chr20.hg19:g.17616198C>A	ENSP00000367044:p.Glu817*	65.0	0.0		69.0	21.0	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Nonsense_Mutation	SNP	ENST00000377813.1	hg19		.	.	.	.	.	.	.	.	.	.	C	41	9.068143	0.99055	.	.	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000455029	.	.	.	5.69	5.69	0.88448	.	0.000000	0.37906	N	0.001889	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-44.1293	18.3963	0.90499	0.0:1.0:0.0:0.0	.	.	.	.	X	384;817;384;817;158	.	ENSP00000246043:E817X	E	-	1	0	RRBP1	17564198	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.798000	0.85924	2.700000	0.92200	0.561000	0.74099	GAG	.	.		0.647	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576		A	17616198	C	A	17616198	4	1	123	1	0	0	0	0	0	1	0	0	13693	864	30	3	1859	3	RRBP1	20	17616198	Nonsense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		17616198	45409322	315	20845										
THBD	7056	hgsc.bcm.edu	37	chr20	23028767	23028767	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gatgcactcgaaggtaccggGgaggttgtggcacaccccgg	16	11	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:23028767G>A	ENST00000377103.2	-	1	1611	c.1375C>T	c.(1375-1377)Ccc>Tcc	p.P459S		NM_000361.2	NP_000352.1	P07204	TRBM_HUMAN	thrombomodulin	459	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|female pregnancy (GO:0007565)|leukocyte migration (GO:0050900)|negative regulation of blood coagulation (GO:0030195)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|response to cAMP (GO:0051591)|response to lipopolysaccharide (GO:0032496)|response to X-ray (GO:0010165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|large_intestine(3)|ovary(1)|skin(1)	7	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)				Drotrecogin alfa(DB00055)|Ibuprofen(DB01050)	AAGGTACCGGGGAGGTTGTGG	0.647																																					p.P459S		Atlas-SNP	.											.	THBD	26	.	0			c.C1375T						.						37	38	38					20																	23028767		2202	4300	6502	SO:0001583	missense	7056	exon1			TACCGGGGAGGTT		CCDS13148.1	20p11.21	2014-09-17			ENSG00000178726	ENSG00000178726		"CD molecules"	11784	protein-coding gene	gene with protein product		188040					Standard	NM_000361		Approved	CD141	uc002wss.3	P07204	OTTHUMG00000032053	ENST00000377103.2:c.1375C>T	chr20.hg19:g.23028767G>A	ENSP00000366307:p.Pro459Ser	129.0	0.0		129.0	20.0	NM_000361	Q8IV29|Q9UC32	Missense_Mutation	SNP	ENST00000377103.2	hg19	CCDS13148.1	.	.	.	.	.	.	.	.	.	.	G	9.617	1.132738	0.21041	.	.	ENSG00000178726	ENST00000377103;ENST00000503590	D	0.91577	-2.87	4.73	3.78	0.43462	EGF-like calcium-binding, conserved site (1);Epidermal growth factor-like (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.551000	0.17133	U	0.185771	D	0.87055	0.6082	M	0.74467	2.265	0.09310	N	0.999999	P	0.46784	0.884	B	0.34452	0.183	T	0.79468	-0.1791	10	0.44086	T	0.13	-5.1892	9.6227	0.39732	0.0807:0.1418:0.7775:0.0	.	459	P07204	TRBM_HUMAN	S	459;441	ENSP00000366307:P459S	ENSP00000366307:P459S	P	-	1	0	THBD	22976767	0.006000	0.16342	0.487000	0.27428	0.004000	0.04260	1.581000	0.36558	1.116000	0.41820	0.561000	0.74099	CCC	.	.		0.647	THBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078307.2			A	23028767	G	A	23028767	3	1	123	1	0	0	0	0	1	0	0	0	15867	1232	43	3	356	3	THBD	20	23028767	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	5412569	23028767	39996753	316	20846										
C20orf24	55969	hgsc.bcm.edu	37	chr20	35238002	35238002	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tacttgttctctgttgctccAgattctgcctgatcaatgca	7	11	3	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:35238002A>T	ENST00000373852.5	+	3	353		c.e3-1		C20orf24_ENST00000344795.3_Splice_Site|C20orf24_ENST00000342422.3_Intron|TGIF2-C20orf24_ENST00000558530.1_Splice_Site			Q9BUV8	CT024_HUMAN	chromosome 20 open reading frame 24											breast(1)|kidney(1)|lung(2)	4	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				CTGTTGCTCCAGATTCTGCCT	0.483																																					.		Atlas-SNP	.											.	C20orf24	17	.	0			c.219-2A>T						.						230	200	210					20																	35238002		2203	4300	6503	SO:0001630	splice_region_variant	55969	exon3			TGCTCCAGATTCT	AF112213	CCDS13279.1, CCDS13280.1, CCDS56190.1	20q11.23	2011-01-25			ENSG00000101084	ENSG00000101084			15870	protein-coding gene	gene with protein product						15178406	Standard	NM_018840		Approved	PNAS-11, RIP5		Q9BUV8	OTTHUMG00000032384	ENST00000373852.5:c.219-1A>T	chr20.hg19:g.35238002A>T		180.0	0.0		229.0	26.0	NM_001199534	E1P5U0|O00605|Q5QPG6|Q5QPG7|Q9BT03|Q9BZU7|Q9UI05	Splice_Site	SNP	ENST00000373852.5	hg19	CCDS56190.1	.	.	.	.	.	.	.	.	.	.	A	12.10	1.837778	0.32513	.	.	ENSG00000101084	ENST00000344795;ENST00000373852	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5927	0.61969	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C20orf24	34671416	1.000000	0.71417	1.000000	0.80357	0.031000	0.12232	8.864000	0.92294	2.099000	0.63709	0.533000	0.62120	.	.	.		0.483	C20orf24-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079006.1	NM_018840	Intron	T	35238002	A	T	35238002	5	4	123	1	0	0	0	0	0	0	1	0	2107	202	7	4	227	4	C20orf24	20	35238002	Splice_Site	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	12209235	35238002	27787518	317	20847										
ZHX3	23051	hgsc.bcm.edu	37	chr20	39833219	39833219	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tttttgccagaaaactgcacCcactgcatacaaaggttggg	9	10	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:39833219C>T	ENST00000309060.3	-	4	753	c.338G>A	c.(337-339)gGg>gAg	p.G113E	ZHX3_ENST00000559234.1_Missense_Mutation_p.G113E|ZHX3_ENST00000544979.2_Missense_Mutation_p.G113E|ZHX3_ENST00000432768.2_Missense_Mutation_p.G113E|ZHX3_ENST00000540170.1_Missense_Mutation_p.G113E|ZHX3_ENST00000560361.1_Missense_Mutation_p.G113E|ZHX3_ENST00000557816.1_Missense_Mutation_p.G113E|ZHX3_ENST00000558993.1_Missense_Mutation_p.G113E			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	113					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				AAAACTGCACCCACTGCATAC	0.488																																					p.G113E		Atlas-SNP	.											.	ZHX3	78	.	0			c.G338A						.						107	104	105					20																	39833219		2203	4300	6503	SO:0001583	missense	23051	exon3			CTGCACCCACTGC	AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	15935	protein-coding gene	gene with protein product		609598	"triple homeobox 1"	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.338G>A	chr20.hg19:g.39833219C>T	ENSP00000312222:p.Gly113Glu	84.0	0.0		96.0	20.0	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	hg19	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	C	0.838	-0.742884	0.03088	.	.	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000432768;ENST00000441102;ENST00000419740	T;T;T;T;T	0.24538	1.85;3.28;3.28;3.06;1.85	6.07	2.66	0.31614	Zinc finger, C2H2-like (1);	0.633648	0.17566	N	0.169659	T	0.04998	0.0134	N	0.00408	-1.53	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.001	T	0.40270	-0.9572	10	0.02654	T	1	-5.7801	5.902	0.18972	0.0:0.1905:0.3881:0.4214	.	113;113;113;113	A8K8Q0;Q9H4I2;F5H820;F6R4Q5	.;ZHX3_HUMAN;.;.	E	113	ENSP00000312222:G113E;ENSP00000362360:G113E;ENSP00000442290:G113E;ENSP00000443783:G113E;ENSP00000415498:G113E	ENSP00000312222:G113E	G	-	2	0	ZHX3	39266633	0.046000	0.20272	0.844000	0.33320	0.909000	0.53808	1.051000	0.30417	0.248000	0.21435	-0.165000	0.13383	GGG	.	.		0.488	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035		T	39833219	C	T	39833219	3	4	123	1	0	0	0	0	1	0	0	0	17692	623	22	3	2540	3	ZHX3	20	39833219	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	4595217	39833219	23192301	318	20848										
PABPC1L	80336	hgsc.bcm.edu	37	chr20	43566743	43566743	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tccatgatgtccacacccagCtggctggcaagatcacgggc	11	14	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:43566743C>G	ENST00000217073.2	+	13	1687	c.1687C>G	c.(1687-1689)Ctg>Gtg	p.L563V	PABPC1L_ENST00000372819.1_Missense_Mutation_p.L117V|PABPC1L_ENST00000537323.1_3'UTR|PABPC1L_ENST00000255136.3_Missense_Mutation_p.L563V|PABPC1L_ENST00000217075.2_Missense_Mutation_p.L117V|PABPC1L_ENST00000372824.1_Missense_Mutation_p.L117V|PABPC1L_ENST00000490798.1_Intron			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	563	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.				mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						CCACACCCAGCTGGCTGGCAA	0.567																																					p.L563V		Atlas-SNP	.											.	PABPC1L	59	.	0			c.C1687G						.						72	63	65					20																	43566743		1568	3582	5150	SO:0001583	missense	80336	exon13			ACCCAGCTGGCTG	AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"RNA binding motif (RRM) containing"	15797	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 119"	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.1687C>G	chr20.hg19:g.43566743C>G	ENSP00000217073:p.Leu563Val	140.0	0.0		195.0	38.0	NM_001124756	Q4VY17	Missense_Mutation	SNP	ENST00000217073.2	hg19	CCDS42878.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.68|17.68	3.449107|3.449107	0.63178|0.63178	.|.	.|.	ENSG00000101104|ENSG00000101104	ENST00000255136;ENST00000421240;ENST00000217073;ENST00000372824;ENST00000372819;ENST00000217075|ENST00000372821;ENST00000372826;ENST00000372822	T;T;T;T;T|T	0.50001|0.44083	0.76;0.76;0.76;0.76;0.76|0.93	4.72|4.72	2.74|2.74	0.32292|0.32292	Polyadenylate-binding protein/Hyperplastic disc protein (5);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.57154|0.57154	0.2034|0.2034	M|M	0.82716|0.82716	2.605|2.605	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.85130|.	0.985;0.997|.	T|T	0.61277|0.61277	-0.7095|-0.7095	10|7	0.66056|0.87932	D|D	0.02|0	.|.	8.1996|8.1996	0.31417|0.31417	0.0:0.6888:0.0:0.3112|0.0:0.6888:0.0:0.3112	.|.	563;117|.	Q4VXU2;G5E9L3|.	PAP1L_HUMAN;.|.	V|R	563;117;563;117;117;117|144;98;85	ENSP00000255136:L563V;ENSP00000217073:L563V;ENSP00000361911:L117V;ENSP00000361906:L117V;ENSP00000217075:L117V|ENSP00000361909:S85R	ENSP00000217073:L563V|ENSP00000361908:S144R	L|S	+|+	1|3	2|2	PABPC1L|PABPC1L	43000157|43000157	0.947000|0.947000	0.32204|0.32204	0.905000|0.905000	0.35620|0.35620	0.991000|0.991000	0.79684|0.79684	2.125000|2.125000	0.42016|0.42016	1.224000|1.224000	0.43551|0.43551	0.591000|0.591000	0.81541|0.81541	CTG|AGC	.	.		0.567	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2			G	43566743	C	G	43566743	3	3	123	1	0	0	0	0	1	0	0	0	11373	796	28	4	1737	4	PABPC1L	20	43566743	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	3733524	43566743	19458777	319	20849										
FAM65C	140876	hgsc.bcm.edu	37	chr20	49212742	49212742	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtccagctctggggcaccggCtgtgagttccctggatgacg	15	12	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:49212742C>T	ENST00000327979.2	-	15	2248	c.1837G>A	c.(1837-1839)Gcc>Acc	p.A613T	FAM65C_ENST00000535356.1_Missense_Mutation_p.A617T|FAM65C_ENST00000045083.2_Missense_Mutation_p.A613T			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	613										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGGGCACCGGCTGTGAGTTCC	0.592																																					p.A613T		Atlas-SNP	.											.	FAM65C	87	.	0			c.G1837A						.						67	74	72					20																	49212742		2001	4164	6165	SO:0001583	missense	140876	exon15			CACCGGCTGTGAG	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.1837G>A	chr20.hg19:g.49212742C>T	ENSP00000332663:p.Ala613Thr	115.0	0.0		147.0	19.0	NM_080829	Q5QPB6|Q9NQQ2	Missense_Mutation	SNP	ENST00000327979.2	hg19	CCDS13431.2	.	.	.	.	.	.	.	.	.	.	C	0.062	-1.221873	0.01530	.	.	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	D;D;D	0.82984	-1.67;-1.67;-1.67	5.24	4.3	0.51218	.	0.289381	0.25604	U	0.029529	T	0.65749	0.2721	N	0.22421	0.69	0.09310	N	0.999991	B;B	0.06786	0.0;0.001	B;B	0.10450	0.005;0.003	T	0.49762	-0.8905	10	0.02654	T	1	-16.7173	7.3535	0.26706	0.0:0.7646:0.0:0.2354	.	617;613	F5H0X2;Q96MK2	.;FA65C_HUMAN	T	613;613;617	ENSP00000332663:A613T;ENSP00000045083:A613T;ENSP00000439802:A617T	ENSP00000045083:A613T	A	-	1	0	FAM65C	48646149	0.054000	0.20591	0.889000	0.34880	0.057000	0.15508	0.723000	0.25939	1.210000	0.43336	0.561000	0.74099	GCC	.	.		0.592	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			T	49212742	C	T	49212742	3	4	123	1	0	0	0	0	1	0	0	0	5609	797	28	3	1035	3	FAM65C	20	49212742	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	5645999	49212742	13812778	320	20850										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58489028	58489028	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttgtatcttgcattaagtttAccttcttttgtctccaagca	5	9	3	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:58489028A>G	ENST00000357552.3	-	12	1056		c.e12+1		SYCP2_ENST00000371001.2_Splice_Site			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2						female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			CATTAAGTTTACCTTCTTTTG	0.294																																					.		Atlas-SNP	.											.	SYCP2	204	.	0			c.830+2T>C						.						68	67	67					20																	58489028		2201	4297	6498	SO:0001630	splice_region_variant	10388	exon12			AAGTTTACCTTCT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.830+1T>C	chr20.hg19:g.58489028A>G		83.0	0.0		133.0	22.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Splice_Site	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	A	17.64	3.440185	0.63067	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8546	0.70326	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SYCP2	57922423	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	8.719000	0.91436	1.968000	0.57251	0.533000	0.62120	.	.	.		0.294	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	Intron	G	58489028	A	G	58489028	5	3	123	1	0	0	0	0	0	0	1	0	15447	405	14	2	3896	2	SYCP2	20	58489028	Splice_Site	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	9276286	58489028	4536492	321	20851										
TCFL5	10732	hgsc.bcm.edu	37	chr20	61488865	61488865	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctccgaggactgccaagcgcCttgtgtggcggtggcacctt	14	13	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:61488865C>T	ENST00000335351.3	-	4	1212	c.1120G>A	c.(1120-1122)Ggc>Agc	p.G374S	TCFL5_ENST00000217162.5_Missense_Mutation_p.G326S	NM_006602.2	NP_006593.2	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 (basic helix-loop-helix)	374					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|urinary_tract(1)	9	Breast(26;5.68e-08)					TGCCAAGCGCCTTGTGTGGCG	0.587																																					p.G374S		Atlas-SNP	.											.	TCFL5	43	.	0			c.G1120A						.						123	116	118					20																	61488865		2203	4300	6503	SO:0001583	missense	10732	exon4			AAGCGCCTTGTGT	AB012124	CCDS13506.1	20q13.33	2013-09-19			ENSG00000101190	ENSG00000101190		"Basic helix-loop-helix proteins"	11646	protein-coding gene	gene with protein product	"HPV-16 E2 binding protein 1"	604745				9763657	Standard	XM_005260185		Approved	Figlb, E2BP-1, CHA, bHLHe82	uc002ydp.3	Q9UL49	OTTHUMG00000032939	ENST00000335351.3:c.1120G>A	chr20.hg19:g.61488865C>T	ENSP00000334294:p.Gly374Ser	116.0	0.0		172.0	19.0	NM_006602	O94771|Q9BYW0	Missense_Mutation	SNP	ENST00000335351.3	hg19	CCDS13506.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.910245	0.52439	.	.	ENSG00000101190	ENST00000335351;ENST00000217162	T;T	0.38722	1.15;1.12	5.61	5.61	0.85477	.	0.379291	0.22531	N	0.058854	T	0.32734	0.0839	L	0.32530	0.975	0.32594	N	0.526787	P;P	0.38597	0.525;0.639	B;B	0.33454	0.164;0.122	T	0.50955	-0.8766	10	0.59425	D	0.04	-25.5413	14.8546	0.70326	0.0:0.9293:0.0:0.0707	.	326;374	F8W9A4;Q9UL49	.;TCFL5_HUMAN	S	374;326	ENSP00000334294:G374S;ENSP00000217162:G326S	ENSP00000217162:G326S	G	-	1	0	TCFL5	60959310	0.998000	0.40836	0.962000	0.40283	0.005000	0.04900	2.522000	0.45572	2.651000	0.90000	0.585000	0.79938	GGC	.	.		0.587	TCFL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080079.2	NM_006602		T	61488865	C	T	61488865	3	4	123	1	0	0	0	0	1	0	0	0	15714	681	24	3	394	3	TCFL5	20	61488865	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	2999837	61488865	1536655	322	20852										
LIPI	149998	hgsc.bcm.edu	37	chr21	15579225	15579225	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	atttttggcacaagttattaTgtaaacatttgagcaacata	6	5	0	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr21:15579225T>C	ENST00000536861.1	-	1	46				LIPI_ENST00000344577.2_Missense_Mutation_p.H7R			Q6XZB0	LIPI_HUMAN	lipase, member I						lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		CAAGTTATTATGTAAACATTT	0.378																																					p.H7R		Atlas-SNP	.											.	LIPI	95	.	0			c.A20G						.						97	100	99					21																	15579225		2203	4300	6503	SO:0001627	intron_variant	149998	exon1			TTATTATGTAAAC	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.46+3895A>G	chr21.hg19:g.15579225T>C		48.0	0.0		58.0	14.0	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	hg19		.	.	.	.	.	.	.	.	.	.	T	5.420	0.262683	0.10294	.	.	ENSG00000188992	ENST00000344577	D	0.87729	-2.29	2.02	-0.57	0.11753	.	.	.	.	.	T	0.73289	0.3568	.	.	.	0.09310	N	1	B	0.23540	0.087	B	0.19391	0.025	T	0.57183	-0.7855	8	0.29301	T	0.29	.	1.64	0.02750	0.2944:0.1882:0.0:0.5174	.	7	Q6XZB0-2	.	R	7	ENSP00000343331:H7R	ENSP00000343331:H7R	H	-	2	0	LIPI	14501096	0.001000	0.12720	0.007000	0.13788	0.672000	0.39443	-0.397000	0.07269	-0.143000	0.11334	0.334000	0.21626	CAT	.	.		0.378	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		C	15579225	T	C	15579225	1	2	123	0	1	0	0	0	0	0	0	0	8834	1464	51	2		2	LIPI	21	15579225	Intron	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10		15579225	32550670	323	20853										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32638540	32638540	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agtagcctgcaaatttgctcCccggccccccgtttgctgtc	9	16	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr21:32638540C>A	ENST00000286827.3	-	5	1220	c.749G>T	c.(748-750)gGg>gTg	p.G250V	TIAM1_ENST00000541036.1_Missense_Mutation_p.G250V|TIAM1_ENST00000469412.1_Intron	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	250					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						AAATTTGCTCCCCGGCCCCCC	0.542																																					p.G250V		Atlas-SNP	.											.	TIAM1	522	.	0			c.G749T						.						77	79	78					21																	32638540		2203	4300	6503	SO:0001583	missense	7074	exon5			TTGCTCCCCGGCC		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.749G>T	chr21.hg19:g.32638540C>A	ENSP00000286827:p.Gly250Val	112.0	0.0		73.0	9.0	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	hg19	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.036423	0.35893	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.38401	1.15;1.14	5.4	5.4	0.78164	.	0.227987	0.43919	D	0.000519	T	0.24431	0.0592	N	0.08118	0	0.41091	D	0.985594	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.05632	-1.0873	10	0.48119	T	0.1	.	19.3745	0.94503	0.0:1.0:0.0:0.0	.	250;250;250	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	V	250;91;250	ENSP00000286827:G250V;ENSP00000441570:G250V	ENSP00000286827:G250V	G	-	2	0	TIAM1	31560411	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	3.789000	0.55454	2.803000	0.96430	0.585000	0.79938	GGG	.	.		0.542	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		A	32638540	C	A	32638540	3	1	123	1	0	0	0	0	1	0	0	0	15905	623	22	3	4126	3	TIAM1	21	32638540	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	17059315	32638540	15491355	324	20854										
AIRE	326	hgsc.bcm.edu	37	chr21	45709596	45709596	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tctacactcccagcaagttcGaagactccggcagtgggaag	11	12	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr21:45709596G>A	ENST00000291582.5	+	6	836	c.709G>A	c.(709-711)Gaa>Aaa	p.E237K	AIRE_ENST00000329347.4_5'Flank|AIRE_ENST00000355347.4_5'Flank	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	237	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.				humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		CAGCAAGTTCGAAGACTCCGG	0.662									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy																												p.E237K		Atlas-SNP	.											AIRE,NS,carcinoma,0,1	AIRE	61	.	0			c.G709A						.						46	53	50					21																	45709596		2203	4298	6501	SO:0001583	missense	326	exon6	Familial Cancer Database	APECED	AAGTTCGAAGACT	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"Zinc fingers, PHD-type"	360	protein-coding gene	gene with protein product	"autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"	607358	"autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.709G>A	chr21.hg19:g.45709596G>A	ENSP00000291582:p.Glu237Lys	159.0	1.0		132.0	27.0	NM_000383	B2RP50|O43922|O43932|O75745	Missense_Mutation	SNP	ENST00000291582.5	hg19	CCDS13706.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.560909	0.45590	.	.	ENSG00000160224	ENST00000291582	T	0.67865	-0.29	4.12	3.19	0.36642	SAND domain-like (2);SAND domain (3);	0.132398	0.33631	N	0.004708	T	0.77116	0.4083	M	0.67953	2.075	0.43540	D	0.995837	D	0.89917	1.0	D	0.83275	0.996	T	0.76173	-0.3056	10	0.48119	T	0.1	-42.7415	10.0972	0.42482	0.0:0.2062:0.7938:0.0	.	237	O43918	AIRE_HUMAN	K	237	ENSP00000291582:E237K	ENSP00000291582:E237K	E	+	1	0	AIRE	44534024	1.000000	0.71417	0.060000	0.19600	0.008000	0.06430	4.232000	0.58645	0.981000	0.38548	0.591000	0.81541	GAA	.	.		0.662	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2			A	45709596	G	A	45709596	3	1	123	1	0	0	0	0	1	0	0	0	437	1059	37	1	731	1	AIRE	21	45709596	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	13071056	45709596	2420299	325	20855										
PCNT	5116	hgsc.bcm.edu	37	chr21	47754602	47754602	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aacagcgtgggatgttcacaGtcagtgaccacacaccagaa	10	11	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr21:47754602G>T	ENST00000359568.5	+	3	666	c.559G>T	c.(559-561)Gtc>Ttc	p.V187F	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	187					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GATGTTCACAGTCAGTGACCA	0.507																																					p.V187F		Atlas-SNP	.											.	PCNT	283	.	0			c.G559T						.						202	144	163					21																	47754602		2203	4300	6503	SO:0001583	missense	5116	exon3			TTCACAGTCAGTG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.559G>T	chr21.hg19:g.47754602G>T	ENSP00000352572:p.Val187Phe	309.0	0.0		319.0	38.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	G	1.081	-0.667051	0.03428	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.02177	4.41	0.235	-0.47	0.12131	.	.	.	.	.	T	0.01254	0.0041	L	0.27053	0.805	0.09310	N	1	B;B	0.30236	0.274;0.18	B;B	0.18263	0.021;0.009	T	0.48536	-0.9027	8	0.15952	T	0.53	.	.	.	.	.	69;187	O95613-2;O95613	.;PCNT_HUMAN	F	187;174	ENSP00000352572:V187F	ENSP00000338675:V174F	V	+	1	0	PCNT	46579030	0.019000	0.18553	0.001000	0.08648	0.001000	0.01503	-1.371000	0.02573	-1.906000	0.01089	-1.922000	0.00515	GTC	.	.		0.507	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47754602	G	T	47754602	3	4	123	1	0	0	0	0	1	0	0	0	11599	1029	36	3	569	3	PCNT	21	47754602	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	2045006	47754602	375293	326	20856										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18347690	18347690	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gttctctcagtggagctggcCacggcgttggcccgtccgtt	14	13	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr22:18347690C>T	ENST00000441493.2	-	19	2932	c.2580G>A	c.(2578-2580)gtG>gtA	p.V860V	MICAL3_ENST00000383094.3_Silent_p.V860V|MICAL3_ENST00000400561.2_Silent_p.V860V|MICAL3_ENST00000414725.2_Silent_p.V888V|MICAL3_ENST00000444520.1_Silent_p.V860V|MICAL3_ENST00000207726.7_Silent_p.V888V|MICAL3_ENST00000429452.1_Silent_p.V984V|MICAL3_ENST00000585038.1_Silent_p.V984V	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	860					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		TGGAGCTGGCCACGGCGTTGG	0.597																																					p.V984V		Atlas-SNP	.											.	MICAL3	53	.	0			c.G2952A						.						95	92	93					22																	18347690		1568	3582	5150	SO:0001819	synonymous_variant	57553	exon23			GCTGGCCACGGCG	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.2580G>A	chr22.hg19:g.18347690C>T		129.0	0.0		148.0	29.0	NM_001136004	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.		0.597	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18347690	C	T	18347690	2	4	123	1	0	0	0	0	0	0	0	1	9580	581	21	3		3	MICAL3	22	18347690	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		18347690	32956876	327	20857										
SEC14L4	284904	hgsc.bcm.edu	37	chr22	30899672	30899672	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgcaagcctcacctcgcagcCagcgcaggaggaagtagtca	12	13	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr22:30899672C>T	ENST00000255858.7	-	2	205	c.122G>A	c.(121-123)tGg>tAg	p.W41*	SEC14L4_ENST00000540456.1_Missense_Mutation_p.G10S|SEC14L4_ENST00000381982.3_Nonsense_Mutation_p.W41*|SEC14L4_ENST00000392772.2_5'UTR	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	41						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	ACCTCGCAGCCAGCGCAGGAG	0.612																																					p.W41X		Atlas-SNP	.											.	SEC14L4	43	.	0			c.G122A						.						95	81	86					22																	30899672		2203	4300	6503	SO:0001587	stop_gained	284904	exon2			CGCAGCCAGCGCA	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.122G>A	chr22.hg19:g.30899672C>T	ENSP00000255858:p.Trp41*	62.0	0.0		72.0	13.0	NM_001161368	A5D6W7|A6NCV4	Nonsense_Mutation	SNP	ENST00000255858.7	hg19	CCDS13878.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.1|29.1	4.980158|4.980158	0.92982|0.92982	.|.	.|.	ENSG00000133488|ENSG00000133488	ENST00000540456|ENST00000255858;ENST00000381982	T|.	0.70399|.	-0.48|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.43853|.	0.1266|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|.	0.30179|.	-0.9987|.	8|.	0.52906|0.02654	T|T	0.07|1	2.4821|2.4821	16.8641|16.8641	0.86025|0.86025	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	10|.	G3V1L4|.	.|.	S|X	10|41	ENSP00000440848:G10S|.	ENSP00000440848:G10S|ENSP00000255858:W41X	G|W	-|-	1|2	0|0	SEC14L4|SEC14L4	29229672|29229672	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.635000|0.635000	0.38103|0.38103	6.147000|6.147000	0.71783|0.71783	2.691000|2.691000	0.91804|0.91804	0.585000|0.585000	0.79938|0.79938	GGC|TGG	.	.		0.612	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977		T	30899672	C	T	30899672	4	4	123	1	0	0	0	0	0	1	0	0	13999	595	21	3	1148	3	SEC14L4	22	30899672	Nonsense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	12551982	30899672	20404894	328	20858										
EIF3D	8664	hgsc.bcm.edu	37	chr22	36920731	36920731	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agctactttcatcctcctcaTggaaataagcatattgactt	5	10	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr22:36920731T>C	ENST00000216190.8	-	4	588	c.218A>G	c.(217-219)cAt>cGt	p.H73R	EIF3D_ENST00000541106.1_Intron|EIF3D_ENST00000405442.1_Missense_Mutation_p.H73R	NM_003753.3	NP_003744.1			eukaryotic translation initiation factor 3, subunit D											cervix(1)|endometrium(2)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	15						ATCCTCCTCATGGAAATAAGC	0.498																																					p.H73R		Atlas-SNP	.											.	EIF3D	37	.	0			c.A218G						.						236	208	218					22																	36920731		2203	4300	6503	SO:0001583	missense	8664	exon4			TCCTCATGGAAAT	U54558	CCDS13930.1	22q13.1	2007-07-27	2007-07-27	2007-07-27	ENSG00000100353	ENSG00000100353			3278	protein-coding gene	gene with protein product		603915	"eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDa"	EIF3S7		9341143	Standard	NM_003753		Approved	eIF3-p66, eIF3-zeta, eIF3d	uc003apr.3	O15371	OTTHUMG00000150599	ENST00000216190.8:c.218A>G	chr22.hg19:g.36920731T>C	ENSP00000216190:p.His73Arg	147.0	0.0		210.0	42.0	NM_003753		Missense_Mutation	SNP	ENST00000216190.8	hg19	CCDS13930.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.026903	0.93518	.	.	ENSG00000100353	ENST00000216190;ENST00000397177;ENST00000405442;ENST00000455547;ENST00000457241;ENST00000432675;ENST00000402116	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.83640	0.5298	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83192	-0.0083	9	0.30078	T	0.28	-40.7054	16.5582	0.84512	0.0:0.0:0.0:1.0	.	73	O15371	EIF3D_HUMAN	R	73	.	ENSP00000216190:H73R	H	-	2	0	EIF3D	35250677	1.000000	0.71417	0.976000	0.42696	0.987000	0.75469	7.755000	0.85180	2.308000	0.77769	0.533000	0.62120	CAT	.	.		0.498	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1			C	36920731	T	C	36920731	3	2	123	1	0	0	0	0	1	0	0	0	5016	1464	51	2	1476	2	EIF3D	22	36920731	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	6021059	36920731	14383835	329	20859										
TCF20	6942	hgsc.bcm.edu	37	chr22	42606358	42606358	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggtctgttcttcttcctcagCattgatgattgtacaaacgg	9	9	4	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr22:42606358C>G	ENST00000359486.3	-	1	5090	c.4954G>C	c.(4954-4956)Gct>Cct	p.A1652P	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Missense_Mutation_p.A1652P	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1652					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						TCTTCCTCAGCATTGATGATT	0.488																																					p.A1652P		Atlas-SNP	.											.	TCF20	164	.	0			c.G4954C						.						134	135	134					22																	42606358		2203	4300	6503	SO:0001583	missense	6942	exon1			CCTCAGCATTGAT	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.4954G>C	chr22.hg19:g.42606358C>G	ENSP00000352463:p.Ala1652Pro	317.0	0.0		326.0	34.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.491245	0.64074	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.60920	0.15;0.15	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000001	T	0.76162	0.3949	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.997	T	0.75590	-0.3265	10	0.72032	D	0.01	-15.2709	20.6439	0.99570	0.0:1.0:0.0:0.0	.	1652;1652	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	P	1652	ENSP00000352463:A1652P;ENSP00000335561:A1652P	ENSP00000335561:A1652P	A	-	1	0	TCF20	40936302	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.022000	0.49659	2.884000	0.98904	0.655000	0.94253	GCT	.	.		0.488	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		G	42606358	C	G	42606358	3	3	123	1	0	0	0	0	1	0	0	0	15705	710	25	4	966	4	TCF20	22	42606358	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	5685627	42606358	8698208	330	20860										
GPM6B	2824	hgsc.bcm.edu	37	chrX	13801604	13801604	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccatacaagaagaaaaaggaCgcaattccatagatgacata	7	8	0	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:13801604C>T	ENST00000356942.5	-	3	726	c.285G>A	c.(283-285)gcG>gcA	p.A95A	GPM6B_ENST00000493677.1_Silent_p.A109A|GPM6B_ENST00000398361.3_Silent_p.A9A|GPM6B_ENST00000454189.2_Silent_p.A76A|GPM6B_ENST00000355135.2_Silent_p.A135A|GPM6B_ENST00000316715.4_Silent_p.A135A	NM_005278.3	NP_005269.1	Q13491	GPM6B_HUMAN	glycoprotein M6B	95					cell differentiation (GO:0030154)|extracellular matrix assembly (GO:0085029)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of serotonin uptake (GO:0051612)|nervous system development (GO:0007399)|ossification (GO:0001503)|positive regulation of bone mineralization (GO:0030501)|protein transport (GO:0015031)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of focal adhesion assembly (GO:0051893)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|ovary(1)|pancreas(1)	6						AGAAAAAGGACGCAATTCCAT	0.423																																					p.A135A		Atlas-SNP	.											.	GPM6B	46	.	0			c.G405A						.						159	140	146					X																	13801604		2203	4300	6503	SO:0001819	synonymous_variant	2824	exon4			AAAGGACGCAATT		CCDS14158.1, CCDS35206.1, CCDS35207.1, CCDS48084.1	Xp22.2	2010-08-03			ENSG00000046653	ENSG00000046653			4461	protein-coding gene	gene with protein product		300051				8661015	Standard	NM_001001995		Approved	M6B, MGC17150, MGC54284	uc004cvw.3	Q13491	OTTHUMG00000021162	ENST00000356942.5:c.285G>A	chrX.hg19:g.13801604C>T		209.0	0.0		210.0	29.0	NM_001001995	O76077|Q86X43|Q8N956	Silent	SNP	ENST00000356942.5	hg19	CCDS14158.1																																																																																			.	.		0.423	GPM6B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055822.1	NM_001001995		T	13801604	C	T	13801604	2	4	123	1	0	0	0	0	0	0	0	1	6624	523	19	1		1	GPM6B	23	13801604	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10		13801604	141468956	331	20861										
MOSPD2	158747	hgsc.bcm.edu	37	chrX	14910893	14910893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tgttgaaaggctacaacaagAtgataactgggttgaaagtt	11	4	0	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:14910893A>G	ENST00000380492.3	+	3	216	c.128A>G	c.(127-129)gAt>gGt	p.D43G	MOSPD2_ENST00000482354.1_Missense_Mutation_p.D43G|MOSPD2_ENST00000495110.1_3'UTR	NM_001177475.1|NM_152581.3	NP_001170946.1|NP_689794.1	Q8NHP6	MSPD2_HUMAN	motile sperm domain containing 2	43						integral component of membrane (GO:0016021)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	Hepatocellular(33;0.183)					CTACAACAAGATGATAACTGG	0.343																																					p.D43G		Atlas-SNP	.											.	MOSPD2	46	.	0			c.A128G						.						121	114	117					X																	14910893		2203	4300	6503	SO:0001583	missense	158747	exon3			AACAAGATGATAA	AL834345	CCDS14162.1	Xp22.31	2006-03-16			ENSG00000130150	ENSG00000130150			28381	protein-coding gene	gene with protein product						15533722	Standard	NM_152581		Approved	MGC26706	uc004cwi.3	Q8NHP6	OTTHUMG00000021170	ENST00000380492.3:c.128A>G	chrX.hg19:g.14910893A>G	ENSP00000369860:p.Asp43Gly	179.0	0.0		177.0	25.0	NM_152581	Q8N3H2|Q8NA83	Missense_Mutation	SNP	ENST00000380492.3	hg19	CCDS14162.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.203075	0.79127	.	.	ENSG00000130150	ENST00000380492	T	0.69806	-0.43	5.3	5.3	0.74995	Phosphatidylinositol transfer protein-like, N-terminal (1);	0.051223	0.85682	D	0.000000	T	0.80048	0.4552	M	0.72118	2.19	0.80722	D	1	D	0.76494	0.999	D	0.70487	0.969	T	0.82277	-0.0537	10	0.66056	D	0.02	.	14.3328	0.66569	1.0:0.0:0.0:0.0	.	43	Q8NHP6	MSPD2_HUMAN	G	43	ENSP00000369860:D43G	ENSP00000369860:D43G	D	+	2	0	MOSPD2	14820814	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	8.870000	0.92336	1.763000	0.52060	0.486000	0.48141	GAT	.	.		0.343	MOSPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055837.1	NM_152581		G	14910893	A	G	14910893	3	3	123	1	0	0	0	0	1	0	0	0	9725	333	12	2	138	2	MOSPD2	23	14910893	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	1109289	14910893	140359667	332	20862										
RAI2	10742	hgsc.bcm.edu	37	chrX	17818831	17818831	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aatgaccttggccgcctgggActcgcccaccatctcaatgt	9	15	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:17818831A>G	ENST00000545871.1	-	3	1760	c.1300T>C	c.(1300-1302)Tcc>Ccc	p.S434P	RAI2_ENST00000451717.1_Missense_Mutation_p.S434P|RAI2_ENST00000415486.3_Missense_Mutation_p.S384P|RAI2_ENST00000360011.1_Missense_Mutation_p.S434P|RAI2_ENST00000331511.1_Missense_Mutation_p.S434P	NM_001172739.1|NM_001172743.1	NP_001166210|NP_001166214	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	434					embryo development (GO:0009790)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	22	Hepatocellular(33;0.183)					GCCGCCTGGGACTCGCCCACC	0.542																																					p.S434P		Atlas-SNP	.											.	RAI2	66	.	0			c.T1300C						.						120	118	119					X																	17818831		2203	4300	6503	SO:0001583	missense	10742	exon3			CCTGGGACTCGCC	Z93242	CCDS14183.1, CCDS55374.1	Xp22	2008-02-05			ENSG00000131831	ENSG00000131831			9835	protein-coding gene	gene with protein product		300217				10049581, 10394933	Standard	NR_033348		Approved		uc010nfa.3	Q9Y5P3	OTTHUMG00000021209	ENST00000545871.1:c.1300T>C	chrX.hg19:g.17818831A>G	ENSP00000444210:p.Ser434Pro	58.0	0.0		58.0	12.0	NM_001172739	B1B1K2|B4DQM9|E7EMN4|Q8N6X7	Missense_Mutation	SNP	ENST00000545871.1	hg19	CCDS14183.1	.	.	.	.	.	.	.	.	.	.	A	11.27	1.590116	0.28357	.	.	ENSG00000131831	ENST00000331511;ENST00000360011;ENST00000545871;ENST00000451717;ENST00000415486	T;T;T;T;T	0.50001	0.79;0.79;0.79;0.79;0.76	5.12	5.12	0.69794	.	0.149607	0.46442	D	0.000300	T	0.55449	0.1921	L	0.36672	1.1	0.46113	D	0.998877	D;D	0.67145	0.996;0.969	P;P	0.61070	0.883;0.824	T	0.59778	-0.7390	10	0.87932	D	0	-22.0114	14.0845	0.64947	1.0:0.0:0.0:0.0	.	384;434	E7EMN4;Q9Y5P3	.;RAI2_HUMAN	P	434;434;434;434;384	ENSP00000333456:S434P;ENSP00000353106:S434P;ENSP00000444210:S434P;ENSP00000401323:S434P;ENSP00000392578:S384P	ENSP00000333456:S434P	S	-	1	0	RAI2	17728752	1.000000	0.71417	0.990000	0.47175	0.149000	0.21700	4.641000	0.61375	1.901000	0.55032	0.486000	0.48141	TCC	.	.		0.542	RAI2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055937.1	NM_021785		G	17818831	A	G	17818831	3	3	123	1	0	0	0	0	1	0	0	0	13024	275	10	2	296	2	RAI2	23	17818831	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	2907938	17818831	137451729	333	20863										
MAGEB6	158809	hgsc.bcm.edu	37	chrX	26212302	26212302	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cagggagcttcacccactggCtctcctgatgcaggtgtttc	11	13	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:26212302C>A	ENST00000379034.1	+	2	488	c.339C>A	c.(337-339)ggC>ggA	p.G113G		NM_173523.2	NP_775794.2	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	113	Ser-rich.									breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(18)|ovary(3)|prostate(2)	33						CACCCACTGGCTCTCCTGATG	0.537																																					p.G113G		Atlas-SNP	.											.	MAGEB6	91	.	0			c.C339A						.																																			SO:0001819	synonymous_variant	158809	exon2			CACTGGCTCTCCT	AF320514	CCDS14217.1	Xp22.12	2009-03-17			ENSG00000176746	ENSG00000176746			23796	protein-coding gene	gene with protein product	"cancer/testis antigen family 3, member 4"	300467				10861452	Standard	NM_173523		Approved	FLJ40242, MAGE-B6, MAGEB6A, CT3.4	uc004dbr.3	Q8N7X4	OTTHUMG00000021285	ENST00000379034.1:c.339C>A	chrX.hg19:g.26212302C>A		192.0	0.0		215.0	59.0	NM_173523	Q6GS19|Q9H219	Silent	SNP	ENST00000379034.1	hg19	CCDS14217.1																																																																																			.	.		0.537	MAGEB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056123.1	NM_173523		A	26212302	C	A	26212302	2	1	123	1	0	0	0	0	0	0	0	1	9188	784	28	3		3	MAGEB6	23	26212302	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	8393471	26212302	129058258	334	20864										
UBA1	7317	hgsc.bcm.edu	37	chrX	47062208	47062208	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gcctggctgcccaggaagtcAtgaaggtcagcacgggtggg	17	10	2	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:47062208A>G	ENST00000335972.6	+	11	1411	c.1228A>G	c.(1228-1230)Atg>Gtg	p.M410V	INE1_ENST00000456273.1_RNA|UBA1_ENST00000490869.1_3'UTR|UBA1_ENST00000377351.4_Missense_Mutation_p.M410V	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	410	2 approximate repeats.				cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CCAGGAAGTCATGAAGGTCAG	0.592																																					p.M410V		Atlas-SNP	.											.	UBA1	89	.	0			c.A1228G						.						25	23	23					X																	47062208		2203	4298	6501	SO:0001583	missense	7317	exon11			GAAGTCATGAAGG	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"Ubiquitin-like modifier activating enzymes"	12469	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog (yeast)", "POC20 centriolar protein homolog (Chlamydomonas)"	314370	"ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)", "ubiquitin-activating enzyme E1"	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.1228A>G	chrX.hg19:g.47062208A>G	ENSP00000338413:p.Met410Val	84.0	0.0		102.0	17.0	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	hg19	CCDS14275.1	.	.	.	.	.	.	.	.	.	.	A	11.16	1.556650	0.27827	.	.	ENSG00000130985	ENST00000377351;ENST00000335972	T;T	0.60040	0.22;0.22	4.75	4.75	0.60458	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.41534	0.1163	N	0.17278	0.47	0.80722	D	1	P	0.36495	0.556	B	0.37731	0.257	T	0.32587	-0.9901	10	0.26408	T	0.33	-28.6326	12.5479	0.56210	1.0:0.0:0.0:0.0	.	410	P22314	UBA1_HUMAN	V	410	ENSP00000366568:M410V;ENSP00000338413:M410V	ENSP00000338413:M410V	M	+	1	0	UBA1	46947152	0.998000	0.40836	1.000000	0.80357	0.967000	0.64934	3.453000	0.52978	1.877000	0.54381	0.427000	0.28365	ATG	.	.		0.592	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334		G	47062208	A	G	47062208	3	3	123	1	0	0	0	0	1	0	0	0	16842	217	8	2	1266	2	UBA1	23	47062208	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	20849906	47062208	108208352	335	20865										
CCDC22	28952	hgsc.bcm.edu	37	chrX	49103272	49103272	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	agctggggcctgcttggggcCcccatacaagcccgggacct	14	15	0	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:49103272C>T	ENST00000376227.3	+	7	965	c.795C>T	c.(793-795)gcC>gcT	p.A265A		NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22	265										NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						TGCTTGGGGCCCCCATACAAG	0.657																																					p.A265A		Atlas-SNP	.											.	CCDC22	69	.	0			c.C795T						.						16	14	15					X																	49103272		2178	4270	6448	SO:0001819	synonymous_variant	28952	exon7			TGGGGCCCCCATA	BC000972	CCDS14322.1	Xp11.23	2008-02-05	2005-07-24	2005-07-24	ENSG00000101997	ENSG00000101997			28909	protein-coding gene	gene with protein product		300859	"chromosome X open reading frame 37"	CXorf37		12477932	Standard	NM_014008		Approved	JM1	uc004dnd.2	O60826	OTTHUMG00000024141	ENST00000376227.3:c.795C>T	chrX.hg19:g.49103272C>T		45.0	0.0		33.0	8.0	NM_014008	A8K7G1	Silent	SNP	ENST00000376227.3	hg19	CCDS14322.1																																																																																			.	.		0.657	CCDC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060822.1	NM_014008		T	49103272	C	T	49103272	2	4	123	1	0	0	0	0	0	0	0	1	2799	610	22	3		3	CCDC22	23	49103272	Silent	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	2041064	49103272	106167288	336	20866										
CCNB3	85417	hgsc.bcm.edu	37	chrX	50037910	50037910	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aagaaagaagccaataaagaGtttgtaaaagttgtttccaa	8	4	0	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:50037910G>C	ENST00000376042.1	+	5	550	c.252G>C	c.(250-252)gaG>gaC	p.E84D	CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.E84D			Q8WWL7	CCNB3_HUMAN	cyclin B3	84					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					CCAATAAAGAGTTTGTAAAAG	0.438																																					p.E84D		Atlas-SNP	.											.	CCNB3	367	.	0			c.G252C						.						95	84	88					X																	50037910		2203	4300	6503	SO:0001583	missense	85417	exon4			TAAAGAGTTTGTA	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.252G>C	chrX.hg19:g.50037910G>C	ENSP00000365210:p.Glu84Asp	213.0	0.0		191.0	38.0	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	hg19	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	G	9.184	1.024223	0.19433	.	.	ENSG00000147082	ENST00000376042;ENST00000396540;ENST00000276014	T;T	0.12569	2.67;2.67	3.57	1.79	0.24919	.	.	.	.	.	T	0.24275	0.0588	L	0.46157	1.445	0.09310	N	1	D	0.76494	0.999	D	0.75484	0.986	T	0.08269	-1.0730	8	.	.	.	.	5.1347	0.14928	0.2813:0.0:0.7187:0.0	.	84	Q8WWL7	CCNB3_HUMAN	D	84	ENSP00000365210:E84D;ENSP00000276014:E84D	.	E	+	3	2	CCNB3	50054650	0.363000	0.24989	0.034000	0.17996	0.036000	0.12997	0.489000	0.22387	0.345000	0.23873	0.591000	0.81541	GAG	.	.		0.438	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			C	50037910	G	C	50037910	3	2	123	1	0	0	0	0	1	0	0	0	2916	1020	36	4	262	4	CCNB3	23	50037910	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	934638	50037910	105232650	337	20867										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50345797	50345797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggcccctgaaggaggcgaaaAgtgctgaaactcttgtctgt	13	9	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:50345797A>G	ENST00000289292.7	-	7	4061	c.3778T>C	c.(3778-3780)Ttt>Ctt	p.F1260L	SHROOM4_ENST00000460112.3_Missense_Mutation_p.F1144L|SHROOM4_ENST00000376020.2_Missense_Mutation_p.F1260L			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1260	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					GGAGGCGAAAAGTGCTGAAAC	0.448																																					p.F1260L		Atlas-SNP	.											.	SHROOM4	171	.	0			c.T3778C						.						57	51	53					X																	50345797		2203	4300	6503	SO:0001583	missense	57477	exon7			GCGAAAAGTGCTG	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3778T>C	chrX.hg19:g.50345797A>G	ENSP00000289292:p.Phe1260Leu	152.0	0.0		92.0	19.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	A	5.736	0.320178	0.10845	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.14022	2.96;2.96;2.54	5.25	3.94	0.45596	Apx/shroom, ASD2 (2);	0.146353	0.45867	D	0.000329	T	0.06462	0.0166	N	0.14661	0.345	0.28172	N	0.928549	B	0.06786	0.001	B	0.04013	0.001	T	0.22556	-1.0213	10	0.23302	T	0.38	.	4.3338	0.11076	0.4994:0.1515:0.0:0.3492	.	1260	Q9ULL8	SHRM4_HUMAN	L	1260;1260;1144	ENSP00000289292:F1260L;ENSP00000365188:F1260L;ENSP00000421450:F1144L	ENSP00000289292:F1260L	F	-	1	0	SHROOM4	50362537	0.997000	0.39634	1.000000	0.80357	0.118000	0.20060	0.898000	0.28404	1.869000	0.54173	0.417000	0.27973	TTT	.	.		0.448	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		G	50345797	A	G	50345797	3	3	123	1	0	0	0	0	1	0	0	0	14311	72	3	2	715	2	SHROOM4	23	50345797	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	307887	50345797	104924763	338	20868										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53563161	53563161	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggagacatcattttccagcaGataaaccagaccttggtaga	9	9	1	4			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:53563161G>C	ENST00000342160.3	-	79	12935	c.12478C>G	c.(12478-12480)Ctg>Gtg	p.L4160V	HUWE1_ENST00000262854.6_Missense_Mutation_p.L4160V			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	4160	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TTTTCCAGCAGATAAACCAGA	0.453																																					p.L4160V		Atlas-SNP	.											.	HUWE1	724	.	0			c.C12478G						.						184	127	146					X																	53563161		2203	4300	6503	SO:0001583	missense	10075	exon80			CCAGCAGATAAAC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.12478C>G	chrX.hg19:g.53563161G>C	ENSP00000340648:p.Leu4160Val	294.0	0.0		253.0	56.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.795|7.795	0.712448|0.712448	0.15306|0.15306	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000342160;ENST00000262854|ENST00000427052;ENST00000426907	T;T|.	0.63913|.	-0.07;-0.07|.	5.57|5.57	2.79|2.79	0.32731|0.32731	HECT (4);|.	0.000000|.	0.64402|.	D|.	0.000005|.	T|T	0.58481|0.58481	0.2125|0.2125	M|M	0.64170|0.64170	1.965|1.965	0.58432|0.58432	D|D	0.999998|0.999998	B;B|.	0.26363|.	0.073;0.147|.	B;B|.	0.33339|.	0.162;0.153|.	T|T	0.53507|0.53507	-0.8429|-0.8429	10|5	0.72032|.	D|.	0.01|.	.|.	5.4803|5.4803	0.16719|0.16719	0.2399:0.0:0.611:0.1491|0.2399:0.0:0.611:0.1491	.|.	4160;4144|.	Q7Z6Z7;Q7Z6Z7-2|.	HUWE1_HUMAN;.|.	V|C	4160|3193;982	ENSP00000340648:L4160V;ENSP00000262854:L4160V|.	ENSP00000262854:L4160V|.	L|S	-|-	1|2	2|0	HUWE1|HUWE1	53579886|53579886	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.495000|0.495000	0.33615|0.33615	1.850000|1.850000	0.39328|0.39328	0.624000|0.624000	0.30286|0.30286	-0.232000|-0.232000	0.12228|0.12228	CTG|TCT	.	.		0.453	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		C	53563161	G	C	53563161	3	2	123	1	0	0	0	0	1	0	0	0	7470	933	33	4	666	4	HUWE1	23	53563161	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	3217364	53563161	101707399	339	20869										
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54823434	54823434	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aggtcaaagatggcttcatgGgcttcagcatgtggattaaa	12	6	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:54823434G>A	ENST00000218436.6	-	2	227	c.198C>T	c.(196-198)gcC>gcT	p.A66A		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	66	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										TGGCTTCATGGGCTTCAGCAT	0.463													G|||	1	0.000264901	0	0	3775	,	,		15237	0		0	False		,,,				2504	0.001				p.A66A		Atlas-SNP	.											.	.	.	.	0			c.C198T						.						173	129	144					X																	54823434		2203	4300	6503	SO:0001819	synonymous_variant	347365	exon2			TTCATGGGCTTCA	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.198C>T	chrX.hg19:g.54823434G>A		333.0	0.0		342.0	14.0	NM_198510	A6NN03	Silent	SNP	ENST00000218436.6	hg19	CCDS14361.1																																																																																			.	.		0.463	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		A	54823434	G	A	54823434	2	1	123	1	0	0	0	0	0	0	0	1	7917	1219	43	3		3	ITIH5L	23	54823434	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	1260273	54823434	100447126	340	20870										
SPIN4	139886	hgsc.bcm.edu	37	chrX	62570078	62570078	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ttggacccgtcatctttggcAtgctccacctgcttgcccac	8	16	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:62570078A>G	ENST00000335144.3	-	1	1140	c.621T>C	c.(619-621)caT>caC	p.H207H	SPIN4_ENST00000374884.2_Silent_p.H189H|SPIN4-AS1_ENST00000451979.1_RNA	NM_001012968.2	NP_001012986.2	Q56A73	SPIN4_HUMAN	spindlin family, member 4	207					gamete generation (GO:0007276)					endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	11						CATCTTTGGCATGCTCCACCT	0.453																																					p.H207H		Atlas-SNP	.											.	SPIN4	29	.	0			c.T621C						.						113	109	110					X																	62570078		1978	4141	6119	SO:0001819	synonymous_variant	139886	exon1			TTTGGCATGCTCC	AK126931	CCDS43964.1	Xq11.1	2008-02-05			ENSG00000186767	ENSG00000186767			27040	protein-coding gene	gene with protein product						12477932	Standard	NM_001012968		Approved	FLJ44984	uc004dvf.3	Q56A73	OTTHUMG00000021696	ENST00000335144.3:c.621T>C	chrX.hg19:g.62570078A>G		239.0	0.0		192.0	44.0	NM_001012968	B3KX90|Q5JUL2	Silent	SNP	ENST00000335144.3	hg19	CCDS43964.1																																																																																			.	.		0.453	SPIN4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001012968		G	62570078	A	G	62570078	2	3	123	1	0	0	0	0	0	0	0	1	15071	214	8	2		2	SPIN4	23	62570078	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	7746644	62570078	92700482	341	20871										
FOXO4	4303	hgsc.bcm.edu	37	chrX	70320820	70320820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	cagcccttgctctcgaaaccGtgaagaagccgatatgtgga	11	11	1	2	rs367715683		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:70320820G>A	ENST00000374259.3	+	2	1072	c.740G>A	c.(739-741)cGt>cAt	p.R247H	FOXO4_ENST00000341558.3_Missense_Mutation_p.R192H	NM_001170931.1|NM_005938.3	NP_001164402.1|NP_005929.2	P98177	FOXO4_HUMAN	forkhead box O4	247					cell cycle arrest (GO:0007050)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mitotic G2 DNA damage checkpoint (GO:0007095)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of smooth muscle cell differentiation (GO:0051151)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)	18	Renal(35;0.156)					TCTCGAAACCGTGAAGAAGCC	0.592											OREG0019856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000264901	0	0	3775	,	,		12575	0		0	False		,,,				2504	0.001				p.R247H		Atlas-SNP	.											.	FOXO4	60	.	0			c.G740A						.	G	HIS/ARG,HIS/ARG	0,3458		0,0,1444,570	33	33	33		575,740	1.1	0	X		33	1,6538		0,1,2363,1811	no	missense,missense	FOXO4	NM_001170931.1,NM_005938.3	29,29	0,1,3807,2381	AA,AG,GG,G		0.0153,0.0,0.01	probably-damaging,probably-damaging	192/451,247/506	70320820	1,9996	2014	4175	6189	SO:0001583	missense	4303	exon2			GAAACCGTGAAGA		CCDS43969.1, CCDS55440.1	Xq13.1	2008-02-05	2007-05-02	2007-05-02	ENSG00000184481	ENSG00000184481		"Forkhead boxes"	7139	protein-coding gene	gene with protein product		300033	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 7", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7"	MLLT7		7529552	Standard	NM_005938		Approved	AFX1	uc004dys.2	P98177	OTTHUMG00000021789	ENST00000374259.3:c.740G>A	chrX.hg19:g.70320820G>A	ENSP00000363377:p.Arg247His	140.0	0.0	1121	116.0	30.0	NM_005938	B7WPJ7|O43821|Q13720|Q3KPF1|Q8TDK9	Missense_Mutation	SNP	ENST00000374259.3	hg19	CCDS43969.1	.	.	.	.	.	.	.	.	.	.	G	5.289	0.238767	0.10023	0.0	1.53E-4	ENSG00000184481	ENST00000374259;ENST00000341558	D;D	0.95554	-3.52;-3.74	5.11	1.14	0.20703	.	0.942857	0.08838	N	0.886220	D	0.89687	0.6787	N	0.22421	0.69	0.09310	N	1	B;B;B	0.10296	0.0;0.003;0.0	B;B;B	0.06405	0.0;0.002;0.001	T	0.80044	-0.1547	10	0.52906	T	0.07	-14.3609	5.4224	0.16407	0.2997:0.4218:0.2784:0.0	.	247;192;247	B4DTB6;P98177-2;P98177	.;.;FOXO4_HUMAN	H	247;192	ENSP00000363377:R247H;ENSP00000342209:R192H	ENSP00000342209:R192H	R	+	2	0	FOXO4	70237545	0.002000	0.14202	0.009000	0.14445	0.731000	0.41821	0.603000	0.24149	0.191000	0.20236	0.519000	0.50382	CGT	.	.		0.592	FOXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057115.1	NM_005938		A	70320820	G	A	70320820	3	1	123	1	0	0	0	0	1	0	0	0	6033	1145	40	1	746	1	FOXO4	23	70320820	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	7750742	70320820	84949740	342	20872										
CYSLTR1	10800	hgsc.bcm.edu	37	chrX	77528233	77528233	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ctggaaatgggtttaaactaTactttacatatttcttctcc	5	8	2	0			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:77528233T>C	ENST00000373304.3	-	3	1303	c.1011A>G	c.(1009-1011)gtA>gtG	p.V337V		NM_001282187.1|NM_001282188.1|NM_006639.3	NP_001269116.1|NP_001269117.1|NP_006630.1	Q9Y271	CLTR1_HUMAN	cysteinyl leukotriene receptor 1	337					defense response (GO:0006952)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|respiratory gaseous exchange (GO:0007585)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	leukotriene receptor activity (GO:0004974)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14					Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549)	GTTTAAACTATACTTTACATA	0.308																																					p.V337V		Atlas-SNP	.											.	CYSLTR1	59	.	0			c.A1011G						.						58	54	56					X																	77528233		2193	4295	6488	SO:0001819	synonymous_variant	10800	exon3			AAACTATACTTTA	AF119711	CCDS14439.1	Xq13-q21	2012-08-10			ENSG00000173198	ENSG00000173198		"GPCR / Class A : Leukotriene receptors"	17451	protein-coding gene	gene with protein product		300201				10391245, 10462554	Standard	NM_006639		Approved	CysLT1, CysLT(1), CYSLT1R	uc004edb.3	Q9Y271	OTTHUMG00000021889	ENST00000373304.3:c.1011A>G	chrX.hg19:g.77528233T>C		166.0	0.0		122.0	22.0	NM_006639	B2R954|D3DTE4|Q5JS94|Q8IV19	Silent	SNP	ENST00000373304.3	hg19	CCDS14439.1																																																																																			.	.		0.308	CYSLTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057315.1			C	77528233	T	C	77528233	2	2	123	1	0	0	0	0	0	0	0	1	4203	1393	49	2		2	CYSLTR1	23	77528233	Silent	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	7207413	77528233	77742327	343	20873										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83129239	83129239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aaagaaaggttcaaagaaagAtatcaagaaggatgcaagaa	10	3	2	5			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:83129239A>G	ENST00000329312.4	+	4	1560	c.1523A>G	c.(1522-1524)gAt>gGt	p.D508G		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	508					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						TCAAAGAAAGATATCAAGAAG	0.348																																					p.D508G		Atlas-SNP	.											.	CYLC1	272	.	0			c.A1523G						.						83	73	76					X																	83129239		2202	4299	6501	SO:0001583	missense	1538	exon4			AGAAAGATATCAA	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1523A>G	chrX.hg19:g.83129239A>G	ENSP00000331556:p.Asp508Gly	142.0	0.0		92.0	27.0	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	hg19	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	a	8.594	0.885227	0.17540	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.52754	0.65	3.16	0.613	0.17597	.	.	.	.	.	T	0.35335	0.0928	L	0.50333	1.59	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12156	0.007;0.005	T	0.27640	-1.0068	9	0.32370	T	0.25	.	2.9178	0.05759	0.5928:0.2586:0.1487:0.0	.	508;508	P35663;F5H4V5	CYLC1_HUMAN;.	G	508	ENSP00000331556:D508G	ENSP00000331556:D508G	D	+	2	0	CYLC1	83015895	0.102000	0.21896	0.000000	0.03702	0.003000	0.03518	1.542000	0.36137	0.024000	0.15214	0.486000	0.48141	GAT	.	.		0.348	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		G	83129239	A	G	83129239	3	3	123	1	0	0	0	0	1	0	0	0	4143	333	12	2	1537	2	CYLC1	23	83129239	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	5601006	83129239	72141321	344	20874										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91133861	91133861	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aagaaaaagaaaaagaagaaGaagcattcccctaagaactt	7	6	0	6			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:91133861G>C	ENST00000373094.1	+	2	3467	c.2622G>C	c.(2620-2622)aaG>aaC	p.K874N	PCDH11X_ENST00000395337.2_Missense_Mutation_p.K874N|PCDH11X_ENST00000298274.8_Missense_Mutation_p.K874N|PCDH11X_ENST00000406881.1_Missense_Mutation_p.K874N|PCDH11X_ENST00000361655.2_Missense_Mutation_p.K874N|PCDH11X_ENST00000373097.1_Missense_Mutation_p.K874N|PCDH11X_ENST00000504220.2_Missense_Mutation_p.K874N|PCDH11X_ENST00000361724.1_Missense_Mutation_p.K874N|PCDH11X_ENST00000373088.1_Missense_Mutation_p.K874N	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	874	Poly-Lys.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						aaaagaagaagaagCATTCCC	0.398																																					p.K874N	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.G2622C						.						77	71	73					X																	91133861		2203	4300	6503	SO:0001583	missense	27328	exon2			GAAGAAGAAGCAT	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.2622G>C	chrX.hg19:g.91133861G>C	ENSP00000362186:p.Lys874Asn	502.0	1.0		455.0	94.0	NM_001168363	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	hg19	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.224235	0.39300	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06;1.06;1.06	4.86	4.0	0.46444	Protocadherin (1);	0.121275	0.53938	D	0.000050	T	0.59115	0.2170	M	0.67953	2.075	0.39692	D	0.971066	D;D;D;D;D;D;D;D	0.71674	0.995;0.997;0.997;0.997;0.997;0.998;0.995;0.995	P;D;D;D;D;D;P;P	0.72338	0.905;0.947;0.962;0.962;0.962;0.977;0.905;0.905	T	0.60747	-0.7202	10	0.46703	T	0.11	.	11.2437	0.48985	0.0931:0.0:0.9069:0.0	.	874;874;874;874;874;874;874;874	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	N	874	ENSP00000378746:K874N;ENSP00000362186:K874N;ENSP00000362189:K874N;ENSP00000355040:K874N;ENSP00000362180:K874N;ENSP00000423762:K874N;ENSP00000355105:K874N;ENSP00000384758:K874N;ENSP00000298274:K874N	ENSP00000298274:K874N	K	+	3	2	PCDH11X	91020517	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	5.989000	0.70587	0.953000	0.37825	0.600000	0.82982	AAG	.	.		0.398	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		C	91133861	G	C	91133861	3	2	123	1	0	0	0	0	1	0	0	0	11517	933	33	4	2628	4	PCDH11X	23	91133861	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	8004622	91133861	64136699	345	20875										
ARL13A	392509	hgsc.bcm.edu	37	chrX	100240896	100240896	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	taaaagagtggcagggaaacCcatcttaatgtaagattctg	10	6	2	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:100240896C>A	ENST00000450049.2	+	4	484	c.371C>A	c.(370-372)cCc>cAc	p.P124H		NM_001162491.1	NP_001155963.1	Q5H913	AR13A_HUMAN	ADP-ribosylation factor-like 13A	124					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(1)|ovary(1)	2						GCAGGGAAACCCATCTTAATG	0.443																																					p.P124H		Atlas-SNP	.											.	ARL13A	7	.	0			c.C371A						.						52	46	48					X																	100240896		1911	4118	6029	SO:0001583	missense	392509	exon4			GGAAACCCATCTT		CCDS55463.1	Xq22.1	2014-05-09	2005-11-18	2005-11-18	ENSG00000174225	ENSG00000174225		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	31709	protein-coding gene	gene with protein product			"ADP-ribosylation factor-like 13"	ARL13			Standard	NM_001162491		Approved		uc011mrf.2	Q5H913	OTTHUMG00000022013	ENST00000450049.2:c.371C>A	chrX.hg19:g.100240896C>A	ENSP00000398637:p.Pro124His	65.0	0.0		53.0	12.0	NM_001162490	B2RTT6|B4DX50	Missense_Mutation	SNP	ENST00000450049.2	hg19	CCDS55463.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.556021	0.65425	.	.	ENSG00000174225	ENST00000450049	D	0.85258	-1.96	4.44	4.44	0.53790	.	0.050939	0.85682	D	0.000000	D	0.94145	0.8122	H	0.96048	3.76	0.44807	D	0.997813	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94886	0.8043	10	0.72032	D	0.01	.	11.4066	0.49902	0.0:1.0:0.0:0.0	.	124;124	B2RTT6;Q5H913	.;AR13A_HUMAN	H	124	ENSP00000398637:P124H	ENSP00000398637:P124H	P	+	2	0	ARL13A	100127552	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	3.203000	0.51075	2.464000	0.83262	0.594000	0.82650	CCC	.	.		0.443	ARL13A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000057504.2	XM_373358		A	100240896	C	A	100240896	3	1	123	1	0	0	0	0	1	0	0	0	928	623	22	3	381	3	ARL13A	23	100240896	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	9107035	100240896	55029664	346	20876										
NRK	203447	hgsc.bcm.edu	37	chrX	105179196	105179196	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gtagaagtacctgaggaatcAcctaagcaaccctctgaagt	9	10	2	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:105179196A>G	ENST00000243300.9	+	21	3837	c.3534A>G	c.(3532-3534)tcA>tcG	p.S1178S	NRK_ENST00000428173.2_Silent_p.S1179S	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1178					activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						CTGAGGAATCACCTAAGCAAC	0.403										HNSCC(51;0.14)																											p.S1178S		Atlas-SNP	.											.	NRK	321	.	0			c.A3534G						.						214	188	196					X																	105179196		1899	4117	6016	SO:0001819	synonymous_variant	203447	exon21			GGAATCACCTAAG	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.3534A>G	chrX.hg19:g.105179196A>G		104.0	0.0		94.0	12.0	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Silent	SNP	ENST00000243300.9	hg19																																																																																				.	.		0.403	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		G	105179196	A	G	105179196	2	3	123	1	0	0	0	0	0	0	0	1	10664	146	6	2		2	NRK	23	105179196	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	4938300	105179196	50091364	347	20877										
MORC4	79710	hgsc.bcm.edu	37	chrX	106185319	106185319	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tttcagaatctggaattcagCttggcgataacccatgtgtt	9	8	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:106185319C>A	ENST00000355610.4	-	16	2783	c.2509G>T	c.(2509-2511)Gct>Tct	p.A837S	MORC4_ENST00000255495.7_Missense_Mutation_p.A837S|MORC4_ENST00000535534.1_Missense_Mutation_p.A585S	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	837						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						TGGAATTCAGCTTGGCGATAA	0.443																																					p.A837S		Atlas-SNP	.											.	MORC4	155	.	0			c.G2509T						.						238	199	213					X																	106185319		2203	4300	6503	SO:0001583	missense	79710	exon16			ATTCAGCTTGGCG	AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 2", "zinc finger, CW type with coiled-coil domain 2"	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.2509G>T	chrX.hg19:g.106185319C>A	ENSP00000347821:p.Ala837Ser	181.0	0.0		119.0	26.0	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	hg19	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	c	18.82	3.704564	0.68615	.	.	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.53857	2.62;0.6;1.92	5.4	5.4	0.78164	.	0.206970	0.34802	N	0.003677	T	0.62502	0.2433	L	0.59436	1.845	0.33796	D	0.626066	D;D;D	0.69078	0.997;0.997;0.979	D;D;P	0.75020	0.985;0.985;0.581	T	0.62973	-0.6740	10	0.02654	T	1	-11.638	13.4865	0.61369	0.0:1.0:0.0:0.0	.	585;837;837	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	S	837;585;837	ENSP00000347821:A837S;ENSP00000440359:A585S;ENSP00000255495:A837S	ENSP00000255495:A837S	A	-	1	0	MORC4	106071975	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.282000	0.58971	2.250000	0.74265	0.455000	0.32223	GCT	.	.		0.443	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657		A	106185319	C	A	106185319	3	1	123	1	0	0	0	0	1	0	0	0	9713	797	28	3	312	3	MORC4	23	106185319	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	1006123	106185319	49085241	348	20878										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117752606	117752606	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	aacttccattgctcttcaggAcaattatgagatcagatata	6	8	3	2	rs112023398		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:117752606A>G	ENST00000276202.7	+	31	3449	c.3386A>G	c.(3385-3387)gAc>gGc	p.D1129G	DOCK11_ENST00000276204.6_Missense_Mutation_p.D1129G	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1129					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						GCTCTTCAGGACAATTATGAG	0.363																																					p.D1129G		Atlas-SNP	.											.	DOCK11	185	.	0			c.A3386G						.						105	89	95					X																	117752606		2203	4297	6500	SO:0001583	missense	139818	exon31			TTCAGGACAATTA	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.3386A>G	chrX.hg19:g.117752606A>G	ENSP00000276202:p.Asp1129Gly	325.0	0.0		256.0	57.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	hg19	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.064692	0.55432	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	D;D	0.96459	-4.02;-4.02	5.68	5.68	0.88126	.	0.181876	0.52532	D	0.000069	D	0.91901	0.7436	N	0.17312	0.475	0.44570	D	0.997535	B;B	0.34161	0.439;0.439	B;B	0.33521	0.165;0.165	D	0.91313	0.5076	10	0.40728	T	0.16	-9.5385	15.0808	0.72113	1.0:0.0:0.0:0.0	.	1129;1129	A6NIW2;Q5JSL3	.;DOC11_HUMAN	G	1129	ENSP00000276204:D1129G;ENSP00000276202:D1129G	ENSP00000276202:D1129G	D	+	2	0	DOCK11	117636634	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.778000	0.55371	2.012000	0.59069	0.441000	0.28932	GAC	.	A|0.500;G|0.500		0.363	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		G	117752606	A	G	117752606	3	3	123	1	0	0	0	0	1	0	0	0	4688	275	10	2	3508	2	DOCK11	23	117752606	Missense_Mutation	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	11567287	117752606	37517954	349	20879										
ZNF280C	55609	hgsc.bcm.edu	37	chrX	129349772	129349772	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	taaaagatattaccttatgtTcttcaaagcaaggctcattt	5	7	3	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:129349772T>A	ENST00000370978.4	-	14	1984	c.1831A>T	c.(1831-1833)Aac>Tac	p.N611Y		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	611					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						TACCTTATGTTCTTCAAAGCA	0.313																																					p.N611Y		Atlas-SNP	.											.	ZNF280C	63	.	0			c.A1831T						.						145	131	136					X																	129349772		2203	4300	6503	SO:0001583	missense	55609	exon14			TTATGTTCTTCAA	AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.1831A>T	chrX.hg19:g.129349772T>A	ENSP00000360017:p.Asn611Tyr	82.0	0.0		78.0	14.0	NM_017666	A8K2V8|Q9NXR3	Missense_Mutation	SNP	ENST00000370978.4	hg19	CCDS14622.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.617575	0.46736	.	.	ENSG00000056277	ENST00000066465;ENST00000370978;ENST00000447817	T;T	0.06068	4.13;3.35	5.06	3.81	0.43845	.	.	.	.	.	T	0.18841	0.0452	M	0.72894	2.215	0.21967	N	0.999441	D;P	0.55172	0.97;0.923	P;P	0.62184	0.899;0.762	T	0.03344	-1.1046	9	0.62326	D	0.03	.	8.1169	0.30948	0.1824:0.0:0.0:0.8176	.	562;611	Q9UJJ2;Q8ND82	.;Z280C_HUMAN	Y	562;611;562	ENSP00000360017:N611Y;ENSP00000408521:N562Y	ENSP00000066465:N562Y	N	-	1	0	ZNF280C	129177453	1.000000	0.71417	0.993000	0.49108	0.422000	0.31414	2.283000	0.43470	1.689000	0.51079	0.347000	0.21830	AAC	.	.		0.313	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		A	129349772	T	A	129349772	3	1	123	1	0	0	0	0	1	0	0	0	17831	1783	62	4	406	4	ZNF280C	23	129349772	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	11597166	129349772	25920788	350	20880										
FRMD7	90167	hgsc.bcm.edu	37	chrX	131212020	131212020	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ccagaagacaggcggattctGgccatgggtgaccttatttc	12	10	1	3			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:131212020G>A	ENST00000298542.4	-	12	2200	c.2025C>T	c.(2023-2025)gcC>gcT	p.A675A	FRMD7_ENST00000370879.1_Silent_p.A555A|FRMD7_ENST00000464296.1_Silent_p.A660A	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	675					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					GGCGGATTCTGGCCATGGGTG	0.408																																					p.A675A		Atlas-SNP	.											.	FRMD7	69	.	0			c.C2025T						.						128	117	120					X																	131212020		2203	4300	6503	SO:0001819	synonymous_variant	90167	exon12			GATTCTGGCCATG	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"nystagmus 1, congenital"	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.2025C>T	chrX.hg19:g.131212020G>A		433.0	0.0		346.0	49.0	NM_194277	C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	hg19	CCDS35397.1																																																																																			.	.		0.408	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		A	131212020	G	A	131212020	2	1	123	1	0	0	0	0	0	0	0	1	6063	1335	47	3		3	FRMD7	23	131212020	Silent	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	1862248	131212020	24058540	351	20881										
RBMX	27316	hgsc.bcm.edu	37	chrX	135957309	135957309	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	tctgaatagtcacgatcacgAccatatccatctctatcgct	5	13	4	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:135957309A>G	ENST00000320676.7	-	8	955	c.801T>C	c.(799-801)ggT>ggC	p.G267G	RBMX_ENST00000565438.1_Silent_p.G139G|RBMX_ENST00000431446.3_Missense_Mutation_p.V159A|RBMX_ENST00000496459.2_5'Flank|RBMX_ENST00000562646.1_Silent_p.G267G|RBMX_ENST00000570135.1_Silent_p.G132G	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	267					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CACGATCACGACCATATCCAT	0.388																																					p.V159A		Atlas-SNP	.											.	RBMX	149	.	0			c.T476C						.						169	162	164					X																	135957309		2203	4300	6503	SO:0001819	synonymous_variant	27316	exon6			ATCACGACCATAT		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"RNA binding motif (RRM) containing"	9910	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein G"	300199	"RNA binding motif protein, X chromosome"			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.801T>C	chrX.hg19:g.135957309A>G		183.0	0.0		141.0	23.0	NM_001164803	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	hg19	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	9.651	1.141524	0.21205	.	.	ENSG00000147274	ENST00000431446	T	0.07444	3.19	5.61	5.61	0.85477	.	.	.	.	.	T	0.07279	0.0184	.	.	.	0.80722	D	1	B	0.22276	0.067	B	0.17098	0.017	T	0.19549	-1.0302	8	0.87932	D	0	.	5.5363	0.17013	0.7132:0.1587:0.1281:0.0	.	159	B4E3U4	.	A	159	ENSP00000411989:V159A	ENSP00000411989:V159A	V	-	2	0	RBMX	135784975	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.576000	0.46033	1.989000	0.58080	0.486000	0.48141	GTC	.	.		0.388	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139		G	135957309	A	G	135957309	2	3	123	1	0	0	0	0	0	0	0	1	13166	275	10	2		2	RBMX	23	135957309	Silent	SNP	A	TCGA-DD-A3A9-01A-11D-A25V-10	4745289	135957309	19313251	352	20882										
MAMLD1	10046	hgsc.bcm.edu	37	chrX	149638231	149638231	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	gggagtggctggccagtcatTactgctggagaataacccta	13	9	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:149638231T>C	ENST00000370401.2	+	4	696	c.386T>C	c.(385-387)tTa>tCa	p.L129S	MAMLD1_ENST00000262858.5_Missense_Mutation_p.L129S|MAMLD1_ENST00000455522.2_5'Flank|MAMLD1_ENST00000432680.2_Missense_Mutation_p.L104S|MAMLD1_ENST00000426613.2_Missense_Mutation_p.L104S|MAMLD1_ENST00000468306.1_3'UTR			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	129					male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					GGCCAGTCATTACTGCTGGAG	0.517																																					p.L129S		Atlas-SNP	.											.	MAMLD1	263	.	0			c.T386C						.						85	77	80					X																	149638231		2203	4300	6503	SO:0001583	missense	10046	exon3			AGTCATTACTGCT	U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"chromosome X open reading frame 6"	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.386T>C	chrX.hg19:g.149638231T>C	ENSP00000359428:p.Leu129Ser	130.0	0.0		141.0	19.0	NM_005491	B2RCQ4|B4DG93|B9EGA5	Missense_Mutation	SNP	ENST00000370401.2	hg19	CCDS14693.2	.	.	.	.	.	.	.	.	.	.	T	9.822	1.185984	0.21870	.	.	ENSG00000013619	ENST00000445612;ENST00000370401;ENST00000432680;ENST00000358892;ENST00000262858;ENST00000426613	T;T;T;T	0.70164	-0.06;-0.46;-0.06;-0.06	5.36	4.17	0.49024	.	0.202399	0.30383	N	0.009744	T	0.67813	0.2933	L	0.54323	1.7	0.25087	N	0.990884	P;D;P;D	0.56746	0.763;0.959;0.904;0.977	B;P;P;P	0.53593	0.288;0.647;0.625;0.73	T	0.58418	-0.7640	10	0.16896	T	0.51	-3.1352	10.9972	0.47582	0.1415:0.0:0.0:0.8585	.	91;104;104;129	F6WVG1;Q13495-4;Q13495-3;Q13495	.;.;.;MAMD1_HUMAN	S	91;129;104;129;129;104	ENSP00000359428:L129S;ENSP00000414517:L104S;ENSP00000262858:L129S;ENSP00000397438:L104S	ENSP00000262858:L129S	L	+	2	0	MAMLD1	149388889	0.081000	0.21417	0.001000	0.08648	0.004000	0.04260	1.883000	0.39658	0.650000	0.30769	0.486000	0.48141	TTA	.	.		0.517	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491		C	149638231	T	C	149638231	3	2	123	1	0	0	0	0	1	0	0	0	9217	1764	61	2	396	2	MAMLD1	23	149638231	Missense_Mutation	SNP	T	TCGA-DD-A3A9-01A-11D-A25V-10	13680922	149638231	5632329	353	20883										
IRAK1	3654	hgsc.bcm.edu	37	chrX	153284220	153284220	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggctccctgcaggagggacaCtgagctctctgggcctggct	15	13	1	1			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:153284220C>T	ENST00000369980.3	-	5	726	c.559G>A	c.(559-561)Gtg>Atg	p.V187M	IRAK1_ENST00000393687.2_Missense_Mutation_p.V187M|IRAK1_ENST00000429936.2_Missense_Mutation_p.V213M|IRAK1_ENST00000393682.1_Missense_Mutation_p.V213M|MIR718_ENST00000390190.2_RNA|IRAK1_ENST00000369974.2_Missense_Mutation_p.V187M|IRAK1_ENST00000477274.1_5'Flank	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	187	ProST region.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGGAGGGACACTGAGCTCTCT	0.637																																					p.V187M		Atlas-SNP	.											.	IRAK1	107	.	0			c.G559A						.						27	27	27					X																	153284220		2202	4294	6496	SO:0001583	missense	3654	exon5			GGGACACTGAGCT	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.559G>A	chrX.hg19:g.153284220C>T	ENSP00000358997:p.Val187Met	190.0	0.0		192.0	28.0	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Missense_Mutation	SNP	ENST00000369980.3	hg19	CCDS14740.1	.	.	.	.	.	.	.	.	.	.	.	9.937	1.216444	0.22373	.	.	ENSG00000184216	ENST00000369980;ENST00000369974;ENST00000393682;ENST00000393687;ENST00000429936	T;T;T;T;T	0.74315	-0.83;-0.83;-0.79;-0.8;-0.82	3.82	-0.987	0.10249	Protein kinase-like domain (1);	1.564670	0.04105	N	0.313659	T	0.58293	0.2112	N	0.22421	0.69	0.09310	N	1	B;B;B	0.26081	0.141;0.049;0.081	B;B;B	0.21151	0.03;0.015;0.033	T	0.43147	-0.9409	10	0.38643	T	0.18	-0.1308	5.2916	0.15729	0.0:0.4002:0.3677:0.2321	.	187;187;187	P51617-4;P51617;P51617-2	.;IRAK1_HUMAN;.	M	187;187;213;187;213	ENSP00000358997:V187M;ENSP00000358991:V187M;ENSP00000377287:V213M;ENSP00000377291:V187M;ENSP00000392662:V213M	ENSP00000358990:V213M	V	-	1	0	IRAK1	152937414	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.090000	0.11163	-0.126000	0.11682	0.529000	0.55759	GTG	.	.		0.637	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3			T	153284220	C	T	153284220	3	4	123	1	0	0	0	0	1	0	0	0	7830	565	20	3	1619	3	IRAK1	23	153284220	Missense_Mutation	SNP	C	TCGA-DD-A3A9-01A-11D-A25V-10	3645989	153284220	1986340	354	20884										
FLNA	2316	hgsc.bcm.edu	37	chrX	153580981	153580981	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0619718309859155	22	1	0.955179037580653	0.823190661478599	0.979988882712618	2.22492236283006e-05	0.00276632013778537	0	ggccactgaaggagcccgacGcctgcgggtgatgctctctt	14	13	1	2			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:153580981G>T	ENST00000369850.3	-	40	6678	c.6442C>A	c.(6442-6444)Cgt>Agt	p.R2148S	FLNA_ENST00000369856.3_Missense_Mutation_p.R281S|FLNA_ENST00000344736.4_Missense_Mutation_p.R2108S|FLNA_ENST00000498491.1_5'Flank|FLNA_ENST00000360319.4_Missense_Mutation_p.R2140S|FLNA_ENST00000422373.1_Missense_Mutation_p.R2140S	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	2148					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGAGCCCGACGCCTGCGGGTG	0.637																																					p.R2148S		Atlas-SNP	.											.	FLNA	373	.	0			c.C6442A						.						37	38	38					X																	153580981		1951	4131	6082	SO:0001583	missense	2316	exon40			CCCGACGCCTGCG	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.6442C>A	chrX.hg19:g.153580981G>T	ENSP00000358866:p.Arg2148Ser	228.0	0.0		162.0	28.0	NM_001110556	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	hg19	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.338146	0.24253	.	.	ENSG00000196924	ENST00000360319;ENST00000422373;ENST00000369850;ENST00000369856;ENST00000344736	D;D;D;T;D	0.86366	-2.1;-2.1;-2.11;-0.81;-2.1	5.64	3.89	0.44902	.	0.075157	0.50627	D	0.000117	D	0.83142	0.5190	M	0.64997	1.995	0.45390	D	0.998375	B;B;B;B	0.26975	0.006;0.01;0.165;0.165	B;B;B;B	0.29716	0.012;0.018;0.106;0.106	T	0.75419	-0.3324	10	0.33940	T	0.23	.	6.6402	0.22904	0.1591:0.0:0.6565:0.1844	.	281;2140;2148;2148	E9PHF0;P21333-2;P21333;E9KL45	.;.;FLNA_HUMAN;.	S	2140;2140;2148;281;2108	ENSP00000353467:R2140S;ENSP00000416926:R2140S;ENSP00000358866:R2148S;ENSP00000358872:R281S;ENSP00000358863:R2108S	ENSP00000358863:R2108S	R	-	1	0	FLNA	153234175	0.008000	0.16893	1.000000	0.80357	0.785000	0.44390	0.602000	0.24134	0.564000	0.29238	-0.305000	0.09177	CGT	.	.		0.637	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			T	153580981	G	T	153580981	3	4	123	1	0	0	0	0	1	0	0	0	5941	1087	38	1	1537	1	FLNA	23	153580981	Missense_Mutation	SNP	G	TCGA-DD-A3A9-01A-11D-A25V-10	296761	153580981	1689579	355	20885										
IVL	3713	hgsc.bcm.edu	37	chr1	152883644	152883644	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	gaggtcccagagcagcaggtGgggcagccaaagaacctgga	16	10	0	2			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr1:152883644G>C	ENST00000368764.3	+	2	1435	c.1371G>C	c.(1369-1371)gtG>gtC	p.V457V	IVL_ENST00000392667.2_Silent_p.V311V			P07476	INVO_HUMAN	involucrin	457	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCAGCAGGTGGGGCAGCCAA	0.622																																					p.V457V		Atlas-SNP	.											.	IVL	100	.	0			c.G1371C						.						29	36	34					1																	152883644		2176	4270	6446	SO:0001819	synonymous_variant	3713	exon2			GCAGGTGGGGCAG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1371G>C	chr1.hg19:g.152883644G>C		160.0	0.0		167.0	61.0	NM_005547	Q5T7P4	Silent	SNP	ENST00000368764.3	hg19	CCDS1030.1																																																																																			.	.		0.622	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		C	152883644	G	C	152883644	2	2	124	1	0	0	0	0	0	0	0	1	7938	1335	47	4		4	IVL	1	152883644	Silent	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10		152883644	96366977	1	20886										
THBS3	7059	hgsc.bcm.edu	37	chr1	155170766	155170766	+	Frame_Shift_Del	DEL	C	C	-													0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	tcattatcagcatcttcctgCccagagttgggtgtcaaaag							TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr1:155170766delC	ENST00000368378.3	-	13	1490	c.1470delG	c.(1468-1470)gggfs	p.G490fs	RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000457183.2_Frame_Shift_Del_p.G370fs|THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000422665.1_RNA|RP11-263K19.4_ENST00000454348.1_RNA|THBS3_ENST00000541990.1_Frame_Shift_Del_p.G19fs|RP11-263K19.4_ENST00000436772.1_RNA|THBS3_ENST00000541576.1_5'UTR	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	490					bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CATCTTCCTGCCCAGAGTTGG	0.552																																					p.Q491fs		Atlas-Indel,Pindel	.											.	THBS3	70	.	0			c.1471delC						.						304	269	281					1																	155170766		2203	4300	6503	SO:0001589	frameshift_variant	7059	exon13			.	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.1470delG	chr1.hg19:g.155170766delC	ENSP00000357362:p.Gly490fs	240.0	0.0		306.0	107.0	NM_007112	B1AVR8|B4DQ20|Q8WV34	Frame_Shift_Del	DEL	ENST00000368378.3	hg19	CCDS1099.1																																																																																			.	.		0.552	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		-	155170766	C	-	155170766	7	5	124	1	0	1	0	1	0	0	0	0	15870	726	26	0	1444	0	THBS3	1	155170766	Frame_Shift_Del	DEL	C	TCGA-DD-A4NA-01A-11D-A25V-10	2287122	155170766	94079855	2	20887										
THBS3	7059	hgsc.bcm.edu	37	chr1	155175006	155175006	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	gctgggtctggagggacctcGgagtcgcaggagaactgtgt	18	8	1	1	rs552940002		TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr1:155175006G>A	ENST00000368378.3	-	3	408	c.388C>T	c.(388-390)Cga>Tga	p.R130*	THBS3_ENST00000457183.2_Intron|THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000422665.1_RNA|THBS3_ENST00000541990.1_5'UTR	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	130	Laminin G-like.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GAGGGACCTCGGAGTCGCAGG	0.622																																					p.R130X		Atlas-SNP	.											.	THBS3	70	.	0			c.C388T						.						108	92	98					1																	155175006		2203	4300	6503	SO:0001587	stop_gained	7059	exon3			GACCTCGGAGTCG	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.388C>T	chr1.hg19:g.155175006G>A	ENSP00000357362:p.Arg130*	176.0	0.0		146.0	59.0	NM_007112	B1AVR8|B4DQ20|Q8WV34	Nonsense_Mutation	SNP	ENST00000368378.3	hg19	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.481439	0.44147	.	.	ENSG00000169231	ENST00000368378	.	.	.	4.85	4.85	0.62838	.	0.070640	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-6.8032	10.8234	0.46619	0.0:0.0:0.8114:0.1886	.	.	.	.	X	130	.	ENSP00000357362:R130X	R	-	1	2	THBS3	153441630	1.000000	0.71417	0.999000	0.59377	0.538000	0.34931	1.809000	0.38922	2.679000	0.91253	0.579000	0.79373	CGA	.	.		0.622	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		A	155175006	G	A	155175006	4	1	124	1	0	0	0	0	0	1	0	0	15870	1124	39	1	2566	1	THBS3	1	155175006	Nonsense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10	4240	155175006	94075615	3	20888										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172571313	172571313	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	ttctcaatttgatggagattAtatttcaaaacttcctaaaa	4	6	2	2			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr1:172571313A>T	ENST00000263688.3	+	21	3347	c.3128A>T	c.(3127-3129)tAt>tTt	p.Y1043F	SUCO_ENST00000608151.1_Missense_Mutation_p.Y1195F|SUCO_ENST00000367723.4_Missense_Mutation_p.Y1194F|SUCO_ENST00000610051.1_Missense_Mutation_p.Y672F	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	1043					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											GATGGAGATTATATTTCAAAA	0.313																																					p.Y1043F		Atlas-SNP	.											.	.	.	.	0			c.A3128T						.						93	85	88					1																	172571313		2201	4300	6501	SO:0001583	missense	51430	exon21			GAGATTATATTTC	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.3128A>T	chr1.hg19:g.172571313A>T	ENSP00000263688:p.Tyr1043Phe	70.0	0.0		81.0	28.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	hg19	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	A	16.99	3.274443	0.59649	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.54	5.54	0.83059	.	0.434355	0.24975	N	0.034111	T	0.29976	0.0750	L	0.56769	1.78	0.31651	N	0.646754	B;B;B;B	0.24882	0.113;0.005;0.007;0.001	B;B;B;B	0.19148	0.024;0.007;0.004;0.004	T	0.17715	-1.0360	9	0.16896	T	0.51	-4.0466	14.505	0.67746	1.0:0.0:0.0:0.0	.	672;1043;1195;1043	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	F	1195;1043	.	ENSP00000263688:Y1043F	Y	+	2	0	C1orf9	170837936	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	3.074000	0.50065	2.090000	0.63153	0.528000	0.53228	TAT	.	.		0.313	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		T	172571313	A	T	172571313	3	4	124	1	0	0	0	0	1	0	0	0	2069	449	16	4	3210	4	C1orf9	1	172571313	Missense_Mutation	SNP	A	TCGA-DD-A4NA-01A-11D-A25V-10	17396307	172571313	76679308	4	20889										
EML4	27436	hgsc.bcm.edu	37	chr2	42488346	42488346	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	atgatcaaagtccacaaattCgagcatcaccttctccccag	5	14	3	1			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr2:42488346C>T	ENST00000318522.5	+	4	686	c.424C>T	c.(424-426)Cga>Tga	p.R142*	EML4_ENST00000401738.3_Nonsense_Mutation_p.R142*|EML4_ENST00000402711.2_Intron	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	142					microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						TCCACAAATTCGAGCATCACC	0.388			T	ALK	NSCLC																																p.R142X		Atlas-SNP	.		Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	.	EML4	92	.	0			c.C424T						.						144	142	143					2																	42488346		2203	4300	6503	SO:0001587	stop_gained	27436	exon4			CAAATTCGAGCAT	AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924		"WD repeat domain containing"	1316	protein-coding gene	gene with protein product		607442		C2orf2			Standard	NM_019063		Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.424C>T	chr2.hg19:g.42488346C>T	ENSP00000320663:p.Arg142*	37.0	0.0		54.0	9.0	NM_019063	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	Nonsense_Mutation	SNP	ENST00000318522.5	hg19	CCDS1807.1	.	.	.	.	.	.	.	.	.	.	C	30	5.052548	0.93793	.	.	ENSG00000143924	ENST00000318522;ENST00000401738	.	.	.	5.52	5.52	0.82312	.	0.993065	0.08186	N	0.984631	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.6849	19.4311	0.94768	0.0:1.0:0.0:0.0	.	.	.	.	X	142	.	ENSP00000320663:R142X	R	+	1	2	EML4	42341850	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.677000	0.68142	2.591000	0.87537	0.555000	0.69702	CGA	.	.		0.388	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250463.3	NM_019063		T	42488346	C	T	42488346	4	4	124	1	0	0	0	0	0	1	0	0	5101	876	31	1	438	1	EML4	2	42488346	Nonsense_Mutation	SNP	C	TCGA-DD-A4NA-01A-11D-A25V-10		42488346	200711027	5	20890										
IL18R1	8809	hgsc.bcm.edu	37	chr2	103013028	103013028	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	cactcactgatagagaaaagCcgaagactaatcattgtcct	7	10	2	3			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr2:103013028C>T	ENST00000409599.1	+	12	1664	c.1308C>T	c.(1306-1308)agC>agT	p.S436S	IL18R1_ENST00000233957.1_Silent_p.S436S			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	436	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						TAGAGAAAAGCCGAAGACTAA	0.353																																					p.S436S		Atlas-SNP	.											.	IL18R1	72	.	0			c.C1308T						.						52	53	53					2																	103013028		2203	4300	6503	SO:0001819	synonymous_variant	8809	exon10			GAAAAGCCGAAGA	U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.1308C>T	chr2.hg19:g.103013028C>T		64.0	0.0		97.0	5.0	NM_003855	B2R9Y5|Q52LC9	Silent	SNP	ENST00000409599.1	hg19	CCDS2060.1																																																																																			.	.		0.353	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855		T	103013028	C	T	103013028	2	4	124	1	0	0	0	0	0	0	0	1	7656	738	26	3		3	IL18R1	2	103013028	Silent	SNP	C	TCGA-DD-A4NA-01A-11D-A25V-10	60524682	103013028	140186345	6	20891										
MYO7B	4648	hgsc.bcm.edu	37	chr2	128366325	128366325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	aggggcagaaaagccaaggcGctctccctgccaagaagcgc	13	13	1	2	rs531750826		TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr2:128366325G>A	ENST00000409816.2	+	21	2718	c.2686G>A	c.(2686-2688)Gct>Act	p.A896T	MYO7B_ENST00000389524.4_Missense_Mutation_p.A896T|MYO7B_ENST00000428314.1_Missense_Mutation_p.A896T			Q6PIF6	MYO7B_HUMAN	myosin VIIB	896						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		AAGCCAAGGCGCTCTCCCTGC	0.652																																					p.A896T		Atlas-SNP	.											.	MYO7B	359	.	0			c.G2686A						.						37	43	41					2																	128366325		2090	4197	6287	SO:0001583	missense	4648	exon22			CAAGGCGCTCTCC		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.2686G>A	chr2.hg19:g.128366325G>A	ENSP00000386461:p.Ala896Thr	149.0	0.0		146.0	48.0	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.072437	0.36566	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.87650	-2.28;-2.28;-2.28	4.81	2.97	0.34412	.	0.660604	0.14594	N	0.310077	T	0.79545	0.4464	L	0.56769	1.78	0.09310	N	1	P	0.37158	0.585	B	0.19666	0.026	T	0.65331	-0.6194	10	0.30078	T	0.28	.	8.4557	0.32897	0.0839:0.1539:0.7622:0.0	.	896	Q6PIF6	MYO7B_HUMAN	T	896	ENSP00000374175:A896T;ENSP00000415090:A896T;ENSP00000386461:A896T	ENSP00000374175:A896T	A	+	1	0	MYO7B	128082795	0.001000	0.12720	0.000000	0.03702	0.627000	0.37826	0.777000	0.26718	0.596000	0.29794	0.462000	0.41574	GCT	.	.		0.652	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		A	128366325	G	A	128366325	3	1	124	1	0	0	0	0	1	0	0	0	10092	1087	38	1	2768	1	MYO7B	2	128366325	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10	25353297	128366325	114833048	7	20892										
LRP2	4036	hgsc.bcm.edu	37	chr2	170029679	170029679	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	gcccactttgggatgcagcgGtaatttgttttgcagctgaa	12	8	0	1			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr2:170029679G>A	ENST00000263816.3	-	57	11355	c.11070C>T	c.(11068-11070)taC>taT	p.Y3690Y		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3690	LDL-receptor class A 30. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GGATGCAGCGGTAATTTGTTT	0.517																																					p.Y3690Y		Atlas-SNP	.											.	LRP2	751	.	0			c.C11070T						.						127	117	120					2																	170029679		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon57			GCAGCGGTAATTT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11070C>T	chr2.hg19:g.170029679G>A		167.0	0.0		185.0	70.0	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.		0.517	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170029679	G	A	170029679	2	1	124	1	0	0	0	0	0	0	0	1	8965	1256	44	3		3	LRP2	2	170029679	Silent	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10	41663354	170029679	73169694	8	20893										
IDH1	3417	hgsc.bcm.edu	37	chr2	209113113	209113113	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	ttgatccccataagcatgacGacctatgatgataggtttta	8	8	0	4	rs121913499		TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr2:209113113G>C	ENST00000415913.1	-	4	775	c.394C>G	c.(394-396)Cgt>Ggt	p.R132G	IDH1_ENST00000345146.2_Missense_Mutation_p.R132G|IDH1_ENST00000446179.1_Missense_Mutation_p.R132G	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																p.R132G	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	IDH1,NS,haematopoietic_neoplasm,0,788	IDH1	6310	.	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)	c.C394G						.						81	74	76					2																	209113113		2203	4300	6503	SO:0001583	missense	3417	exon4			CATGACGACCTAT		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>G	chr2.hg19:g.209113113G>C	ENSP00000390265:p.Arg132Gly	185.0	0.0		186.0	86.0	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	hg19	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286370	0.80803	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.96636	0.8902	H	0.99379	4.54	0.80722	D	1	D	0.57899	0.981	P	0.62813	0.907	D	0.98312	1.0524	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	G	132	ENSP00000260985:R132G;ENSP00000410513:R132G;ENSP00000390265:R132G;ENSP00000391075:R132G	ENSP00000260985:R132G	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT	.	.		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			C	209113113	G	C	209113113	3	2	124	1	0	0	0	0	1	0	0	0	7503	1058	37	4	878	4	IDH1	2	209113113	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10	39083434	209113113	34086260	9	20894										
BAP1	8314	hgsc.bcm.edu	37	chr3	52440918	52440918	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	ccactcctcgtcctccccccAgggccctagtggagaccaag	9	19	0	1			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr3:52440918A>C	ENST00000460680.1	-	8	1057	c.586T>G	c.(586-588)Tgg>Ggg	p.W196G	BAP1_ENST00000296288.5_Missense_Mutation_p.W196G	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TCCTCCCCCCAGGGCCCTAGT	0.612			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.W196G	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	BAP1,colon,carcinoma,+1,1	BAP1	371	.	0			c.T586G						.						40	34	36					3																	52440918		2197	4297	6494	SO:0001583	missense	8314	exon8			CCCCCCAGGGCCC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.586T>G	chr3.hg19:g.52440918A>C	ENSP00000417132:p.Trp196Gly	135.0	0.0		98.0	54.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.077545	0.76528	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.54279	0.58;0.58	6.04	6.04	0.98038	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	T	0.72859	0.3513	M	0.75447	2.3	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.75300	-0.3366	10	0.62326	D	0.03	-8.1917	16.2573	0.82524	1.0:0.0:0.0:0.0	.	196	Q92560	BAP1_HUMAN	G	196	ENSP00000417132:W196G;ENSP00000296288:W196G	ENSP00000296288:W196G	W	-	1	0	BAP1	52415958	1.000000	0.71417	1.000000	0.80357	0.618000	0.37518	9.297000	0.96120	2.319000	0.78375	0.528000	0.53228	TGG	.	.		0.612	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			C	52440918	A	C	52440918	3	2	124	1	0	0	0	0	1	0	0	0	1311	188	7	5	1643	5	BAP1	3	52440918	Missense_Mutation	SNP	A	TCGA-DD-A4NA-01A-11D-A25V-10		52440918	145581512	10	20895										
TECRL	253017	hgsc.bcm.edu	37	chr4	65240925	65240925	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	tttgcttaacatcatgaataGtagatgattgtgtcacctga	8	6	2	4			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr4:65240925G>T	ENST00000381210.3	-	2	361	c.251C>A	c.(250-252)aCt>aAt	p.T84N	TECRL_ENST00000507440.1_Missense_Mutation_p.T84N	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	84					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(2)|kidney(5)|large_intestine(7)|lung(30)|prostate(1)|skin(1)|stomach(1)	47						ATCATGAATAGTAGATGATTG	0.204																																					p.T84N		Atlas-SNP	.											.	TECRL	106	.	0			c.C251A						.						10	10	10					4																	65240925		2086	4143	6229	SO:0001583	missense	253017	exon2			TGAATAGTAGATG	AL833108	CCDS33990.1	4q13.1	2009-07-21			ENSG00000205678	ENSG00000205678			27365	protein-coding gene	gene with protein product	"glycoprotein, synaptic 2-like"					12477932	Standard	NM_001010874		Approved	GPSN2L, SRD5A2L2, DKFZp313D0829, DKFZp313B2333, TERL	uc003hcv.3	Q5HYJ1	OTTHUMG00000160680	ENST00000381210.3:c.251C>A	chr4.hg19:g.65240925G>T	ENSP00000370607:p.Thr84Asn	71.0	0.0		92.0	4.0	NM_001010874		Missense_Mutation	SNP	ENST00000381210.3	hg19	CCDS33990.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.054221	0.75960	.	.	ENSG00000205678	ENST00000507440;ENST00000381210;ENST00000509536	T;T;T	0.42513	0.97;0.97;0.97	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.70727	0.3257	M	0.89904	3.07	0.51233	D	0.999919	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.991	T	0.76629	-0.2889	10	0.72032	D	0.01	-4.6574	15.0845	0.72142	0.0:0.0:1.0:0.0	.	84;84	Q6IN47;Q5HYJ1	.;TECRL_HUMAN	N	84	ENSP00000426043:T84N;ENSP00000370607:T84N;ENSP00000422497:T84N	ENSP00000370607:T84N	T	-	2	0	TECRL	64923520	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.105000	0.64591	2.638000	0.89438	0.585000	0.79938	ACT	.	.		0.204	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874		T	65240925	G	T	65240925	3	4	124	1	0	0	0	0	1	0	0	0	15761	1029	36	3	884	3	TECRL	4	65240925	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10		65240925	125913351	11	20896										
USP38	84640	hgsc.bcm.edu	37	chr4	144134995	144134995	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	ctttcgcttgccttttgtccTtcctcttctttggaaaacat	5	12	2	0			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr4:144134995T>C	ENST00000307017.4	+	9	2372	c.1866T>C	c.(1864-1866)ccT>ccC	p.P622P	USP38_ENST00000510377.1_Silent_p.P622P	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	622	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					CCTTTTGTCCTTCCTCTTCTT	0.448																																					p.P622P		Atlas-SNP	.											.	USP38	92	.	0			c.T1866C						.						116	118	117					4																	144134995		2203	4299	6502	SO:0001819	synonymous_variant	84640	exon9			TTGTCCTTCCTCT	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.1866T>C	chr4.hg19:g.144134995T>C		103.0	0.0		144.0	57.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Silent	SNP	ENST00000307017.4	hg19	CCDS3758.1																																																																																			.	.		0.448	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		C	144134995	T	C	144134995	2	2	124	1	0	0	0	0	0	0	0	1	17084	1596	56	2		2	USP38	4	144134995	Silent	SNP	T	TCGA-DD-A4NA-01A-11D-A25V-10	78894070	144134995	47019281	12	20897										
DMGDH	29958	hgsc.bcm.edu	37	chr5	78322295	78322295	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	tccaggcgtaaggcattcatGgcataggttccaaaattgtc	10	9	1	0			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr5:78322295G>A	ENST00000255189.3	-	13	2170	c.2142C>T	c.(2140-2142)gcC>gcT	p.A714A	DMGDH_ENST00000380311.4_Silent_p.A513A|DMGDH_ENST00000540686.1_Silent_p.A334A	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	714					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		AGGCATTCATGGCATAGGTTC	0.433																																					p.A714A		Atlas-SNP	.											.	DMGDH	88	.	0			c.C2142T						.						119	109	113					5																	78322295		2203	4300	6503	SO:0001819	synonymous_variant	29958	exon13			ATTCATGGCATAG	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.2142C>T	chr5.hg19:g.78322295G>A		241.0	0.0		278.0	100.0	NM_013391	B2RBN0|B4E1J9	Silent	SNP	ENST00000255189.3	hg19	CCDS4044.1																																																																																			.	.		0.433	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391		A	78322295	G	A	78322295	2	1	124	1	0	0	0	0	0	0	0	1	4583	1335	47	3		3	DMGDH	5	78322295	Silent	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10		78322295	102592965	13	20898										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135692416	135692416	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	ctcgccagtcctttgtaggcGttcatgcgcgagcgcgagtg	14	12	1	0			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr5:135692416G>A	ENST00000513104.1	-	2	942	c.660C>T	c.(658-660)aaC>aaT	p.N220N	TRPC7_ENST00000355180.3_Silent_p.N220N|TRPC7_ENST00000426057.2_Silent_p.N220N	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	220					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.N220N(2)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTTTGTAGGCGTTCATGCGCG	0.607																																					p.N220N		Atlas-SNP	.											TRPC7,NS,NS,0,2	TRPC7	126	.	2	Substitution - coding silent(2)	NS(2)	c.C660T						.						50	57	55					5																	135692416		2143	4255	6398	SO:0001819	synonymous_variant	57113	exon2			GTAGGCGTTCATG	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.660C>T	chr5.hg19:g.135692416G>A		235.0	1.0		238.0	103.0	NM_001167576	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Silent	SNP	ENST00000513104.1	hg19	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	G	8.513	0.866919	0.17250	.	.	ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753	.	.	.	5.26	-9.63	0.00544	.	.	.	.	.	T	0.60919	0.2306	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70842	-0.4762	4	.	.	.	-22.007	15.4967	0.75658	0.434:0.0:0.566:0.0	.	.	.	.	C	220	.	.	R	-	1	0	TRPC7	135720315	0.372000	0.25064	0.657000	0.29651	0.994000	0.84299	-0.116000	0.10724	-2.153000	0.00793	-0.157000	0.13467	CGC	.	.		0.607	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135692416	G	A	135692416	2	1	124	1	0	0	0	0	0	0	0	1	16599	1136	40	1		1	TRPC7	5	135692416	Silent	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10	57370121	135692416	45222844	14	20899										
TLX3	30012	hgsc.bcm.edu	37	chr5	170736726	170736726	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	tccgtgcccacggtctccagCcttggcggtctcaatttccc	9	17	2	0			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr5:170736726C>A	ENST00000296921.5	+	1	439	c.357C>A	c.(355-357)agC>agA	p.S119R		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	119					central nervous system development (GO:0007417)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|respiratory gaseous exchange (GO:0007585)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CGGTCTCCAGCCTTGGCGGTC	0.706			T	BCL11B	T-ALL																																p.S119R	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"T-cell leukemia, homeobox 3 (HOX11L2)"		L	.	TLX3	23	.	0			c.C357A						.						14	17	16					5																	170736726		2181	4258	6439	SO:0001583	missense	30012	exon1			CTCCAGCCTTGGC	AJ223798	CCDS34288.1	5q35.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000164438	ENSG00000164438		"Homeoboxes / ANTP class : NKL subclass"	13532	protein-coding gene	gene with protein product		604640	"homeo box 11-like 2", "T-cell leukemia, homeobox 3"	HOX11L2		11435718, 11435716	Standard	NM_021025		Approved	RNX	uc003mbf.3	O43711	OTTHUMG00000163207	ENST00000296921.5:c.357C>A	chr5.hg19:g.170736726C>A	ENSP00000296921:p.Ser119Arg	61.0	0.0		32.0	10.0	NM_021025	Q96AD3	Missense_Mutation	SNP	ENST00000296921.5	hg19	CCDS34288.1	.	.	.	.	.	.	.	.	.	.	C	10.79	1.448559	0.26074	.	.	ENSG00000164438	ENST00000296921	D	0.91407	-2.84	4.16	3.28	0.37604	.	0.057883	0.64402	D	0.000001	D	0.85440	0.5697	L	0.29908	0.895	0.35207	D	0.774832	B	0.30584	0.286	B	0.40199	0.322	T	0.81435	-0.0934	10	0.13108	T	0.6	.	11.1602	0.48512	0.0:0.9065:0.0:0.0935	.	119	O43711	TLX3_HUMAN	R	119	ENSP00000296921:S119R	ENSP00000296921:S119R	S	+	3	2	TLX3	170669331	0.278000	0.24230	1.000000	0.80357	0.360000	0.29518	0.101000	0.15251	0.950000	0.37743	0.555000	0.69702	AGC	.	.		0.706	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3			A	170736726	C	A	170736726	3	1	124	1	0	0	0	0	1	0	0	0	15977	738	26	3	359	3	TLX3	5	170736726	Missense_Mutation	SNP	C	TCGA-DD-A4NA-01A-11D-A25V-10	35044310	170736726	10178534	15	20900										
RPP40	10799	hgsc.bcm.edu	37	chr6	4996590	4996590	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	ctcaacgtgctcagtgctacTtttggctgatgctcctgaat	9	11	2	2			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr6:4996590T>G	ENST00000380051.2	-	6	668	c.624A>C	c.(622-624)aaA>aaC	p.K208N	RPP40_ENST00000464646.1_Missense_Mutation_p.K148N|RPP40_ENST00000319533.5_Missense_Mutation_p.K185N	NM_006638.2	NP_006629.2	O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	208					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			NS(1)|breast(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	14	Ovarian(93;0.11)	all_hematologic(90;0.0895)				TCAGTGCTACTTTTGGCTGAT	0.502																																					p.K208N		Atlas-SNP	.											.	RPP40	36	.	0			c.A624C						.						98	94	95					6																	4996590		2203	4300	6503	SO:0001583	missense	10799	exon6			TGCTACTTTTGGC	U94317	CCDS34333.1, CCDS69040.1, CCDS75391.1	6p25.1	2012-05-21	2007-06-26	2004-03-19	ENSG00000124787	ENSG00000124787			20992	protein-coding gene	gene with protein product		606117	"ribonuclease P1", "ribonuclease P 40kDa subunit"	RNASEP1		9630247	Standard	NM_006638		Approved	bA428J1.3	uc003mwl.3	O75818	OTTHUMG00000014168	ENST00000380051.2:c.624A>C	chr6.hg19:g.4996590T>G	ENSP00000369391:p.Lys208Asn	94.0	0.0		125.0	49.0	NM_006638	Q5VX97|Q8WVK8	Missense_Mutation	SNP	ENST00000380051.2	hg19	CCDS34333.1	.	.	.	.	.	.	.	.	.	.	T	11.11	1.541448	0.27563	.	.	ENSG00000124787	ENST00000380051;ENST00000319533;ENST00000464646	T;T;T	0.43294	0.95;0.95;0.95	5.33	4.15	0.48705	.	0.263661	0.43919	D	0.000520	T	0.31040	0.0784	M	0.80028	2.48	0.40610	D	0.981662	P;P	0.42296	0.775;0.72	B;B	0.40901	0.295;0.343	T	0.12682	-1.0538	10	0.31617	T	0.26	-6.1148	11.7027	0.51579	0.0:0.0:0.1483:0.8517	.	185;208	O75818-2;O75818	.;RPP40_HUMAN	N	208;185;148	ENSP00000369391:K208N;ENSP00000317998:K185N;ENSP00000419431:K148N	ENSP00000317998:K185N	K	-	3	2	RPP40	4941589	0.938000	0.31826	0.097000	0.21041	0.398000	0.30690	1.747000	0.38298	0.845000	0.35118	0.528000	0.53228	AAA	.	.		0.502	RPP40-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039733.2	NM_006638		G	4996590	T	G	4996590	3	3	124	1	0	0	0	0	1	0	0	0	13629	1606	56	5	479	5	RPP40	6	4996590	Missense_Mutation	SNP	T	TCGA-DD-A4NA-01A-11D-A25V-10		4996590	166118477	16	20901										
HLA-E	3133	hgsc.bcm.edu	37	chr6	30457628	30457628	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	tcgacaacgacgccgcgagtCcgaggatggtgccgcgggcg	17	13	0	0			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr6:30457628C>A	ENST00000376630.4	+	2	255	c.190C>A	c.(190-192)Ccg>Acg	p.P64T		NM_005516.5	NP_005507.3	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	64	Alpha-1.				antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protection from natural killer cell mediated cytotoxicity (GO:0042270)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)|ovary(3)|skin(1)|urinary_tract(1)	18						CGCCGCGAGTCCGAGGATGGT	0.677																																					p.P64T		Atlas-SNP	.											.	HLA-E	35	.	0			c.C190A						.						62	69	66					6																	30457628		1510	2707	4217	SO:0001583	missense	3133	exon2			GCGAGTCCGAGGA	M20022	CCDS34379.1	6p21.3	2013-01-11			ENSG00000204592	ENSG00000204592		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4962	protein-coding gene	gene with protein product		143010				3131426	Standard	NM_005516		Approved		uc003nqg.3	P13747	OTTHUMG00000031155	ENST00000376630.4:c.190C>A	chr6.hg19:g.30457628C>A	ENSP00000365817:p.Pro64Thr	96.0	0.0		47.0	14.0	NM_005516	Q30169|Q9BT83|Q9GIY7|Q9GIY8	Missense_Mutation	SNP	ENST00000376630.4	hg19	CCDS34379.1	.	.	.	.	.	.	.	.	.	.	.	15.34	2.803154	0.50315	.	.	ENSG00000204592	ENST00000376630	T	0.00832	5.64	1.67	1.67	0.24075	.	.	.	.	.	T	0.01870	0.0059	H	0.95982	3.75	0.09310	N	1	P;P	0.43578	0.811;0.698	P;B	0.48368	0.575;0.402	T	0.24368	-1.0162	9	0.87932	D	0	.	6.7735	0.23607	0.0:1.0:0.0:0.0	.	105;64	E7ENN9;Q6DU44	.;.	T	64	ENSP00000365817:P64T	ENSP00000365817:P64T	P	+	1	0	HLA-E	30565607	0.001000	0.12720	0.128000	0.21923	0.167000	0.22549	0.260000	0.18424	1.235000	0.43724	0.462000	0.41574	CCG	.	.		0.677	HLA-E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076282.2	NM_005516		A	30457628	C	A	30457628	3	1	124	1	0	0	0	0	1	0	0	0	7219	855	30	3	196	3	HLA-E	6	30457628	Missense_Mutation	SNP	C	TCGA-DD-A4NA-01A-11D-A25V-10	25461038	30457628	140657439	17	20902										
PDE7B	27115	hgsc.bcm.edu	37	chr6	136268612	136268612	+	Frame_Shift_Del	DEL	A	A	-													0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	tctatttcagaggtgtggcgAaatcttgtttgagaaccccg							TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr6:136268612delA	ENST00000308191.6	+	2	335	c.32delA	c.(31-33)gaafs	p.E11fs		NM_018945.3	NP_061818.1	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B	11					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	AGGTGTGGCGAAATCTTGTTT	0.368																																					p.E11fs		Atlas-Indel,Pindel	.											PDE7B,NS,carcinoma,0,3	PDE7B	55	.	0			c.31delG						.						117	114	115					6																	136268612		2203	4300	6503	SO:0001589	frameshift_variant	27115	exon2			.	AB038040	CCDS5175.1	6q23-q24	2008-03-18			ENSG00000171408	ENSG00000171408	3.1.4.17	"Phosphodiesterases"	8792	protein-coding gene	gene with protein product		604645				10618442	Standard	XM_005266931		Approved		uc003qgp.3	Q9NP56	OTTHUMG00000015641	ENST00000308191.6:c.32delA	chr6.hg19:g.136268612delA	ENSP00000310661:p.Glu11fs	127.0	0.0		80.0	56.0	NM_018945	Q5W154	Frame_Shift_Del	DEL	ENST00000308191.6	hg19	CCDS5175.1																																																																																			.	.		0.368	PDE7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042371.1			-	136268612	A	-	136268612	7	5	124	1	0	1	0	1	0	0	0	0	11661	246	9	0	38	0	PDE7B	6	136268612	Frame_Shift_Del	DEL	A	TCGA-DD-A4NA-01A-11D-A25V-10	105810984	136268612	34846455	18	20903										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5353127	5353127	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	ggtgacgtgacaccctcgtgGtccagtttgacaagcagctc	12	12	0	3			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr7:5353127G>T	ENST00000430969.1	-	27	7743	c.7395C>A	c.(7393-7395)gaC>gaA	p.D2465E	TNRC18_ENST00000399537.4_Missense_Mutation_p.D2465E	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2465							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CACCCTCGTGGTCCAGTTTGA	0.692																																					p.D2465E		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7395A						.						27	25	26					7																	5353127		1568	3582	5150	SO:0001583	missense	84629	exon27			CTCGTGGTCCAGT	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7395C>A	chr7.hg19:g.5353127G>T	ENSP00000395538:p.Asp2465Glu	92.0	0.0		69.0	4.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	21.6|21.6	4.178561|4.178561	0.78564|0.78564	.|.	.|.	ENSG00000182095|ENSG00000182095	ENST00000399537;ENST00000430969|ENST00000328270	T;T|.	0.54071|.	0.59;0.62|.	5.01|5.01	4.12|4.12	0.48240|0.48240	.|.	0.000000|.	0.40469|.	N|.	0.001096|.	T|T	0.64768|0.64768	0.2628|0.2628	M|M	0.71206|0.71206	2.165|2.165	0.37810|0.37810	D|D	0.928025|0.928025	D|.	0.76494|.	0.999|.	D|.	0.63192|.	0.912|.	T|T	0.67273|0.67273	-0.5712|-0.5712	10|5	0.62326|.	D|.	0.03|.	.|.	9.361|9.361	0.38195|0.38195	0.1638:0.0:0.8362:0.0|0.1638:0.0:0.8362:0.0	.|.	2465|.	O15417|.	TNC18_HUMAN|.	E|T	2465|279	ENSP00000382452:D2465E;ENSP00000395538:D2465E|.	ENSP00000382452:D2465E|.	D|P	-|-	3|1	2|0	TNRC18|TNRC18	5319653|5319653	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.955000|0.955000	0.61496|0.61496	3.819000|3.819000	0.55686|0.55686	1.095000|1.095000	0.41419|0.41419	0.561000|0.561000	0.74099|0.74099	GAC|CCA	.	.		0.692	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	5353127	G	T	5353127	3	4	124	1	0	0	0	0	1	0	0	0	16354	1252	44	3	1527	3	TNRC18	7	5353127	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10		5353127	153785536	19	20904										
C10orf140	387640	hgsc.bcm.edu	37	chr10	21806738	21806738	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	ccacctcttcaaaacctgacTtcaggtctcccatctcgggc	6	17	5	1			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr10:21806738T>A	ENST00000449193.2	-	4	2266	c.14A>T	c.(13-15)aAg>aTg	p.K5M	SKIDA1_ENST00000444772.3_Missense_Mutation_p.K5M|SKIDA1_ENST00000487107.1_5'Flank	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	5						nucleus (GO:0005634)											AAAACCTGACTTCAGGTCTCC	0.458																																					p.K5M		Atlas-SNP	.											.	.	.	.	0			c.A14T						.						26	26	26					10																	21806738		1967	4150	6117	SO:0001583	missense	387640	exon4			CCTGACTTCAGGT	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 140"	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.14A>T	chr10.hg19:g.21806738T>A	ENSP00000410041:p.Lys5Met	79.0	0.0		99.0	4.0	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Missense_Mutation	SNP	ENST00000449193.2	hg19	CCDS44363.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.479672	0.44044	.	.	ENSG00000180592	ENST00000449193;ENST00000444772	.	.	.	4.9	4.9	0.64082	DNA binding domain, putative (1);Transforming protein Ski (1);	0.076598	0.64402	D	0.000020	T	0.53012	0.1770	N	0.08118	0	0.41685	D	0.989314	D;D	0.89917	0.996;1.0	P;D	0.72982	0.905;0.979	T	0.64765	-0.6330	9	0.87932	D	0	.	14.5119	0.67794	0.0:0.0:0.0:1.0	.	5;5	Q1XH10;E9PAX1	DLN1_HUMAN;.	M	5	.	ENSP00000442432:K5M	K	-	2	0	C10orf140	21846744	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.799000	0.69101	1.834000	0.53371	0.254000	0.18369	AAG	.	.		0.458	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		A	21806738	T	A	21806738	3	1	124	1	0	0	0	0	1	0	0	0	1597	1609	56	4	2716	4	C10orf140	10	21806738	Missense_Mutation	SNP	T	TCGA-DD-A4NA-01A-11D-A25V-10		21806738	113728009	20	20905										
RASSF4	83937	hgsc.bcm.edu	37	chr10	45486412	45486412	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	tcagagcggacaaaattaaaAgactgcgagtacccgctgat	10	9	1	3			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr10:45486412A>G	ENST00000340258.5	+	9	815	c.702A>G	c.(700-702)aaA>aaG	p.K234K	RASSF4_ENST00000472561.1_3'UTR|RASSF4_ENST00000334940.6_Silent_p.K243K|RASSF4_ENST00000374417.2_3'UTR	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	0					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						CAAAATTAAAAGACTGCGAGT	0.473																																					p.K234K		Atlas-SNP	.											.	RASSF4	33	.	0			c.A702G						.						76	87	83					10																	45486412		2203	4300	6503	SO:0001819	synonymous_variant	83937	exon9			ATTAAAAGACTGC	BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.702A>G	chr10.hg19:g.45486412A>G		35.0	0.0		41.0	15.0	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000340258.5	hg19	CCDS7208.1																																																																																			.	.		0.473	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023		G	45486412	A	G	45486412	2	3	124	1	0	0	0	0	0	0	0	1	13103	69	3	2		2	RASSF4	10	45486412	Silent	SNP	A	TCGA-DD-A4NA-01A-11D-A25V-10	23679674	45486412	90048335	21	20906										
SAMD8	142891	hgsc.bcm.edu	37	chr10	76910777	76910777	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	atatgtttttatagtatttgGatttacatctttcattatgg	6	3	2	0			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr10:76910777G>T	ENST00000542569.1	+	2	594	c.491G>T	c.(490-492)gGa>gTa	p.G164V	SAMD8_ENST00000372690.3_Missense_Mutation_p.G227V|SAMD8_ENST00000372687.4_Missense_Mutation_p.G164V	NM_001174156.1|NM_144660.2	NP_001167627.1|NP_653261.1	Q96LT4	SAMD8_HUMAN	sterile alpha motif domain containing 8	164					ceramide biosynthetic process (GO:0046513)|regulation of ceramide biosynthetic process (GO:2000303)|sphingomyelin biosynthetic process (GO:0006686)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)	p.G227A(1)|p.G164A(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	12	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					ATAGTATTTGGATTTACATCT	0.358																																					p.G164V		Atlas-SNP	.											SAMD8_ENST00000372690,NS,carcinoma,0,2	SAMD8	57	.	2	Substitution - Missense(2)	lung(2)	c.G491T						.						55	52	53					10																	76910777		2203	4300	6503	SO:0001583	missense	142891	exon2			TATTTGGATTTAC	AK057811	CCDS7347.1, CCDS53543.1	10q22.3	2013-01-10			ENSG00000156671	ENSG00000156671		"Sterile alpha motif (SAM) domain containing"	26320	protein-coding gene	gene with protein product		611575					Standard	NM_144660		Approved	FLJ25082	uc001jwx.2	Q96LT4	OTTHUMG00000018515	ENST00000542569.1:c.491G>T	chr10.hg19:g.76910777G>T	ENSP00000438042:p.Gly164Val	147.0	1.0		111.0	43.0	NM_144660	Q5JSC5|Q5JSC8|Q66K52	Missense_Mutation	SNP	ENST00000542569.1	hg19	CCDS53543.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.159421	0.57368	.	.	ENSG00000156671	ENST00000447533;ENST00000372690;ENST00000542569;ENST00000372687	T;T;T;T	0.11169	2.8;2.8;2.8;2.8	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.14830	0.0358	N	0.21448	0.665	0.80722	D	1	D;B	0.55800	0.973;0.332	P;B	0.53593	0.73;0.147	T	0.12708	-1.0537	10	0.11794	T	0.64	-20.8945	19.8333	0.96644	0.0:0.0:1.0:0.0	.	164;164	Q96LT4-2;Q96LT4	.;SAMD8_HUMAN	V	164;227;164;164	ENSP00000391799:G164V;ENSP00000361775:G227V;ENSP00000438042:G164V;ENSP00000361772:G164V	ENSP00000361772:G164V	G	+	2	0	SAMD8	76580783	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	9.869000	0.99810	2.698000	0.92095	0.491000	0.48974	GGA	.	.		0.358	SAMD8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_144660		T	76910777	G	T	76910777	3	4	124	1	0	0	0	0	1	0	0	0	13840	1174	41	3	493	3	SAMD8	10	76910777	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10	31424365	76910777	58623970	22	20907										
CEP164	22897	hgsc.bcm.edu	37	chr11	117263284	117263284	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	cccagctgcagaagtgccttGggcaagtggagcacagagtt	14	10	0	2			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr11:117263284G>T	ENST00000278935.3	+	19	2581	c.2434G>T	c.(2434-2436)Ggg>Tgg	p.G812W	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	812	Glu-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		GAAGTGCCTTGGGCAAGTGGA	0.577																																					p.G815W		Atlas-SNP	.											.	CEP164	121	.	0			c.G2443T						.						137	129	132					11																	117263284		2201	4296	6497	SO:0001583	missense	22897	exon18			TGCCTTGGGCAAG	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.2434G>T	chr11.hg19:g.117263284G>T	ENSP00000278935:p.Gly812Trp	100.0	0.0		143.0	45.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	hg19	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.569748	0.28003	.	.	ENSG00000110274	ENST00000278935;ENST00000529538;ENST00000375253	T	0.43688	0.94	4.33	3.42	0.39159	.	0.132235	0.35772	N	0.002996	T	0.47021	0.1423	L	0.29908	0.895	0.09310	N	1	D;D;D;D	0.69078	0.996;0.997;0.995;0.997	P;D;D;D	0.74348	0.908;0.958;0.938;0.983	T	0.22208	-1.0223	10	0.72032	D	0.01	-30.7039	7.7052	0.28646	0.0938:0.179:0.7272:0.0	.	786;586;812;815	E9PI34;Q9NTH6;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	W	812;786;693	ENSP00000278935:G812W	ENSP00000278935:G812W	G	+	1	0	CEP164	116768494	0.003000	0.15002	0.899000	0.35326	0.242000	0.25591	1.210000	0.32370	1.044000	0.40200	0.561000	0.74099	GGG	.	.		0.577	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		T	117263284	G	T	117263284	3	4	124	1	0	0	0	0	1	0	0	0	3251	1348	47	3	2500	3	CEP164	11	117263284	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10		117263284	17743232	23	20908										
IRAK4	51135	hgsc.bcm.edu	37	chr12	44176211	44176211	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	gacagtcatgactagcagaaTtgtgggaacaacagcttata	10	7	1	2			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr12:44176211T>C	ENST00000448290.2	+	9	1114	c.1043T>C	c.(1042-1044)aTt>aCt	p.I348T	IRAK4_ENST00000440781.2_Missense_Mutation_p.I224T|IRAK4_ENST00000551736.1_Missense_Mutation_p.I348T|IRAK4_ENST00000431837.1_Missense_Mutation_p.I224T	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	348	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		ACTAGCAGAATTGTGGGAACA	0.418																																					p.I348T		Atlas-SNP	.											.	IRAK4	77	.	0			c.T1043C						.						80	79	79					12																	44176211		2203	4300	6503	SO:0001583	missense	51135	exon9			GCAGAATTGTGGG	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		ENST00000448290.2:c.1043T>C	chr12.hg19:g.44176211T>C	ENSP00000390651:p.Ile348Thr	76.0	0.0		89.0	37.0	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	hg19	CCDS8744.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.518415	0.85495	.	.	ENSG00000198001	ENST00000440781;ENST00000431837;ENST00000448290;ENST00000551736	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.62	5.62	0.85841	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.054522	0.64402	D	0.000001	T	0.66327	0.2778	L	0.48218	1.51	0.80722	D	1	B	0.33637	0.42	P	0.44422	0.449	T	0.69128	-0.5227	10	0.87932	D	0	-23.6069	15.8229	0.78673	0.0:0.0:0.0:1.0	.	348	Q9NWZ3	IRAK4_HUMAN	T	224;224;348;348	ENSP00000408734:I224T;ENSP00000390327:I224T;ENSP00000390651:I348T;ENSP00000446490:I348T	ENSP00000390327:I224T	I	+	2	0	IRAK4	42462478	1.000000	0.71417	0.987000	0.45799	0.988000	0.76386	7.698000	0.84413	2.130000	0.65690	0.477000	0.44152	ATT	.	.		0.418	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1			C	44176211	T	C	44176211	3	2	124	1	0	0	0	0	1	0	0	0	7834	1493	52	2	1073	2	IRAK4	12	44176211	Missense_Mutation	SNP	T	TCGA-DD-A4NA-01A-11D-A25V-10		44176211	89675684	24	20909										
ABCA3	21	hgsc.bcm.edu	37	chr16	2327903	2327903	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	gaaaggtcaggtccacgaagGccttgaactcctccagcgcc	11	14	1	1	rs368905104		TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr16:2327903G>A	ENST00000301732.5	-	31	5586	c.4886C>T	c.(4885-4887)gCc>gTc	p.A1629V	ABCA3_ENST00000382381.3_Missense_Mutation_p.A1571V	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1629					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	GTCCACGAAGGCCTTGAACTC	0.677																																					p.A1629V		Atlas-SNP	.											.	ABCA3	176	.	0			c.C4886T						.	G	VAL/ALA	1,4395	2.1+/-5.4	0,1,2197	26	27	26		4886	3.9	1	16		26	0,8600		0,0,4300	no	missense	ABCA3	NM_001089.2	64	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	benign	1629/1705	2327903	1,12995	2198	4300	6498	SO:0001583	missense	21	exon31			ACGAAGGCCTTGA	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.4886C>T	chr16.hg19:g.2327903G>A	ENSP00000301732:p.Ala1629Val	34.0	0.0		32.0	13.0	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	hg19	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.398143	0.25205	2.27E-4	0.0	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.84370	-1.84	4.96	3.93	0.45458	.	0.192618	0.43747	D	0.000532	T	0.79695	0.4490	M	0.63843	1.955	0.80722	D	1	B;B	0.33135	0.054;0.399	B;B	0.32533	0.065;0.147	T	0.75368	-0.3342	10	0.30078	T	0.28	.	7.1254	0.25469	0.0982:0.0:0.7269:0.1749	.	1633;1629	Q4LE27;Q99758	.;ABCA3_HUMAN	V	1629;1633	ENSP00000301732:A1629V	ENSP00000301732:A1629V	A	-	2	0	ABCA3	2267904	1.000000	0.71417	0.959000	0.39883	0.416000	0.31233	4.548000	0.60718	2.584000	0.87258	0.561000	0.74099	GCC	.	.		0.677	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2327903	G	A	2327903	3	1	124	1	0	0	0	0	1	0	0	0	33	1203	42	3	240	3	ABCA3	16	2327903	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10		2327903	88026850	25	20910										
MAPK7	5598	hgsc.bcm.edu	37	chr17	19285247	19285247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	gcgggagcgaaaggaacgggGggctggggcctctgggggcc	23	9	1	0			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr17:19285247G>A	ENST00000308406.5	+	5	2017	c.1631G>A	c.(1630-1632)gGg>gAg	p.G544E	MAPK7_ENST00000395602.4_Missense_Mutation_p.G544E|MAPK7_ENST00000299612.7_Missense_Mutation_p.G405E|MAPK7_ENST00000571657.1_Intron|MAPK7_ENST00000395604.3_Missense_Mutation_p.G544E|MFAP4_ENST00000574313.2_5'Flank	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	544	May not be required for kinase activity; required to stimulate MEF2C activity. {ECO:0000250}.|Pro-rich.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)			autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					aaggaacggggggctggggcC	0.677																																					p.G544E		Atlas-SNP	.											.	MAPK7	72	.	0			c.G1631A						.						11	23	19					17																	19285247		2028	3994	6022	SO:0001583	missense	5598	exon5			AACGGGGGGCTGG	U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"Mitogen-activated protein kinase cascade / Kinases"	6880	protein-coding gene	gene with protein product	"BMK1 kinase", "extracellular-signal-regulated kinase 5"	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.1631G>A	chr17.hg19:g.19285247G>A	ENSP00000311005:p.Gly544Glu	27.0	0.0		16.0	12.0	NM_002749	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Missense_Mutation	SNP	ENST00000308406.5	hg19	CCDS11206.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.013489	0.35511	.	.	ENSG00000166484	ENST00000308406;ENST00000299612;ENST00000395604;ENST00000395602	T;T;T;T	0.73047	-0.43;-0.71;-0.43;-0.43	5.06	4.07	0.47477	.	0.301968	0.23777	N	0.044675	T	0.52435	0.1734	N	0.22421	0.69	0.30198	N	0.798865	B	0.06786	0.001	B	0.04013	0.001	T	0.48258	-0.9051	10	0.33141	T	0.24	-15.0732	7.2289	0.26030	0.0923:0.1734:0.7342:0.0	.	544	Q13164	MK07_HUMAN	E	544;405;544;544	ENSP00000311005:G544E;ENSP00000299612:G405E;ENSP00000378968:G544E;ENSP00000378966:G544E	ENSP00000299612:G405E	G	+	2	0	MAPK7	19225840	0.440000	0.25618	0.715000	0.30552	0.873000	0.50193	0.886000	0.28241	1.088000	0.41272	0.561000	0.74099	GGG	.	.		0.677	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033		A	19285247	G	A	19285247	3	1	124	1	0	0	0	0	1	0	0	0	9291	1232	43	3	1645	3	MAPK7	17	19285247	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10		19285247	61909963	26	20911										
SDK2	54549	hgsc.bcm.edu	37	chr17	71437017	71437017	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	ccacgctggtgtttttaggtGggatgatgatggtgggtgcg	18	5	0	2			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr17:71437017G>A	ENST00000392650.3	-	6	659	c.659C>T	c.(658-660)cCa>cTa	p.P220L	SDK2_ENST00000388726.3_Missense_Mutation_p.P220L	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	220	Ig-like C2-type 3.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GTTTTTAGGTGGGATGATGAT	0.602																																					p.P220L		Atlas-SNP	.											.	SDK2	219	.	0			c.C659T						.						84	92	90					17																	71437017		692	1591	2283	SO:0001583	missense	54549	exon6			TTAGGTGGGATGA	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.659C>T	chr17.hg19:g.71437017G>A	ENSP00000376421:p.Pro220Leu	175.0	0.0		217.0	63.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.798561	0.90538	.	.	ENSG00000069188	ENST00000392650;ENST00000388726;ENST00000316893	T;T	0.12147	2.71;2.71	4.83	4.83	0.62350	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	U	0.000002	T	0.25717	0.0626	L	0.48877	1.53	0.80722	D	1	D	0.53151	0.958	P	0.55161	0.77	T	0.00792	-1.1564	10	0.38643	T	0.18	.	17.9911	0.89169	0.0:0.0:1.0:0.0	.	220	Q58EX2	SDK2_HUMAN	L	220	ENSP00000376421:P220L;ENSP00000373378:P220L	ENSP00000324967:P220L	P	-	2	0	SDK2	68948612	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	9.173000	0.94815	2.241000	0.73720	0.556000	0.70494	CCA	.	.		0.602	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		A	71437017	G	A	71437017	3	1	124	1	0	0	0	0	1	0	0	0	13984	1348	47	3	6019	3	SDK2	17	71437017	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10	52151770	71437017	9758193	27	20912										
S1PR4	8698	hgsc.bcm.edu	37	chr19	3179635	3179635	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	ctttggctccaacctctgggCccaggagtacctgcggggca	13	14	1	0			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr19:3179635C>A	ENST00000246115.3	+	1	900	c.845C>A	c.(844-846)gCc>gAc	p.A282D		NM_003775.3	NP_003766.1	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4	282					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			breast(1)|kidney(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13						AACCTCTGGGCCCAGGAGTAC	0.647																																					p.A282D	GBM(82;318 1638 33279 49708)	Atlas-SNP	.											.	S1PR4	31	.	0			c.C845A						.						75	76	76					19																	3179635		2203	4300	6503	SO:0001583	missense	8698	exon1			TCTGGGCCCAGGA	AJ000479	CCDS12105.1	19p13.3	2012-08-08	2008-04-30	2008-04-30		ENSG00000125910		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3170	protein-coding gene	gene with protein product		603751	"endothelial differentiation, G-protein-coupled receptor 6", "endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 6"	EDG6		9790765	Standard	NM_003775		Approved		uc002lxg.3	O95977		ENST00000246115.3:c.845C>A	chr19.hg19:g.3179635C>A	ENSP00000246115:p.Ala282Asp	93.0	0.0		56.0	31.0	NM_003775	D6W612	Missense_Mutation	SNP	ENST00000246115.3	hg19	CCDS12105.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.350864	0.61183	.	.	ENSG00000125910	ENST00000246115	T	0.72505	-0.66	4.23	4.23	0.50019	GPCR, rhodopsin-like superfamily (1);	0.122706	0.52532	D	0.000065	T	0.70718	0.3256	L	0.45228	1.405	0.40698	D	0.982457	D	0.57257	0.979	P	0.52343	0.696	T	0.68977	-0.5267	10	0.23302	T	0.38	.	15.1914	0.73047	0.0:1.0:0.0:0.0	.	282	O95977	S1PR4_HUMAN	D	282	ENSP00000246115:A282D	ENSP00000246115:A282D	A	+	2	0	S1PR4	3130635	0.985000	0.35326	0.998000	0.56505	0.624000	0.37722	1.771000	0.38542	1.923000	0.55706	0.462000	0.41574	GCC	.	.		0.647	S1PR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452517.1	NM_003775		A	3179635	C	A	3179635	3	1	124	1	0	0	0	0	1	0	0	0	13811	739	26	3	847	3	S1PR4	19	3179635	Missense_Mutation	SNP	C	TCGA-DD-A4NA-01A-11D-A25V-10		3179635	55949348	28	20913										
LHB	3972	hgsc.bcm.edu	37	chr19	49519408	49519408	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	cccacagtcagaggtgctgcGgcggcagggtccacagcgac	15	14	1	1	rs201749590		TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr19:49519408G>C	ENST00000221421.2	-	3	342	c.343C>G	c.(343-345)Cgc>Ggc	p.R115G	CTB-60B18.10_ENST00000600007.1_lincRNA	NM_000894.2	NP_000885.1	P01229	LSHB_HUMAN	luteinizing hormone beta polypeptide	115					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|male gonad development (GO:0008584)|peptide hormone processing (GO:0016486)|progesterone biosynthetic process (GO:0006701)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		GAGGTGCTGCGGCGGCAGGGT	0.662																																					p.R115G		Atlas-SNP	.											.	LHB	20	.	0			c.C343G						.						56	61	59					19																	49519408		2203	4300	6503	SO:0001583	missense	3972	exon3			TGCTGCGGCGGCA		CCDS12748.1	19q13.3	2013-02-26				ENSG00000104826		"Endogenous ligands"	6584	protein-coding gene	gene with protein product	"lutropin, beta chain", "interstitial cell stimulating hormone, beta chain", "luteinizing hormone beta subunit"	152780				1191677	Standard	NM_000894		Approved	LSH-B, CGB4, hLHB	uc002plt.3	P01229		ENST00000221421.2:c.343C>G	chr19.hg19:g.49519408G>C	ENSP00000221421:p.Arg115Gly	70.0	0.0		54.0	21.0	NM_000894	Q9UDI0	Missense_Mutation	SNP	ENST00000221421.2	hg19	CCDS12748.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.941487	0.34283	.	.	ENSG00000104826	ENST00000221421;ENST00000391870	T	0.57752	0.38	4.71	3.66	0.41972	Cystine knot (1);Gonadotropin, beta subunit, conserved site (1);	0.298608	0.34025	N	0.004337	T	0.62672	0.2447	L	0.55481	1.735	0.26806	N	0.969103	P	0.44344	0.833	P	0.58873	0.847	T	0.56323	-0.7998	10	0.72032	D	0.01	-14.5685	10.529	0.44965	0.0:0.0:0.8059:0.1941	.	115	P01229	LSHB_HUMAN	G	115;131	ENSP00000221421:R115G	ENSP00000221421:R115G	R	-	1	0	LHB	54211220	1.000000	0.71417	0.997000	0.53966	0.003000	0.03518	2.930000	0.48924	1.090000	0.41315	0.462000	0.41574	CGC	.	G|1.000;A|0.000		0.662	LHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466246.1	NM_000894		C	49519408	G	C	49519408	3	2	124	1	0	0	0	0	1	0	0	0	8770	1116	39	4	86	4	LHB	19	49519408	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10	46339773	49519408	9609575	29	20914										
HRC	3270	hgsc.bcm.edu	37	chr19	49657916	49657916	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	tcctcctcctcctcctcctcTtctccttcatcatcttcccc	0	23	5	0	rs7409255		TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr19:49657916T>C	ENST00000252825.4	-	1	765	c.579A>G	c.(577-579)gaA>gaG	p.E193E	HRC_ENST00000595625.1_Silent_p.E193E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	193	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cctcctcctcttcTCCTTCAT	0.557																																					p.E193E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A579G						.						119	95	103					19																	49657916		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCTCCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.579A>G	chr19.hg19:g.49657916T>C		190.0	0.0		276.0	13.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.557	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657916	T	C	49657916	2	2	124	1	0	0	0	0	0	0	0	1	7361	1606	56	2		2	HRC	19	49657916	Silent	SNP	T	TCGA-DD-A4NA-01A-11D-A25V-10	138508	49657916	9471067	30	20915										
SDCBP2	27111	hgsc.bcm.edu	37	chr20	1299029	1299029	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	tggagagggaaagacccataTaattttccagttctgccaag	10	8	1	2			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr20:1299029T>A	ENST00000360779.3	-	4	331	c.158A>T	c.(157-159)tAt>tTt	p.Y53F	SDCBP2_ENST00000339987.3_Missense_Mutation_p.Y53F|SDCBP2_ENST00000381812.1_Missense_Mutation_p.Y53F	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	53					intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						AAGACCCATATAATTTTCCAG	0.488																																					p.Y53F		Atlas-SNP	.											.	SDCBP2	78	.	0			c.A158T						.						78	79	78					20																	1299029		1863	4107	5970	SO:0001583	missense	27111	exon4			CCCATATAATTTT	AF131809	CCDS13013.1, CCDS42848.1	20p13	2008-07-02			ENSG00000125775	ENSG00000125775			15756	protein-coding gene	gene with protein product						11152476	Standard	NM_080489		Approved	ST-2, SITAC18	uc021vzn.1	Q9H190	OTTHUMG00000031661	ENST00000360779.3:c.158A>T	chr20.hg19:g.1299029T>A	ENSP00000354013:p.Tyr53Phe	66.0	0.0		58.0	20.0	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Missense_Mutation	SNP	ENST00000360779.3	hg19	CCDS42848.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.226551	0.58668	.	.	ENSG00000125775	ENST00000381812;ENST00000360779;ENST00000339987	T;T;T	0.39406	1.08;1.08;1.08	4.82	4.82	0.62117	.	0.000000	0.64402	D	0.000001	T	0.58552	0.2130	M	0.65320	2	0.50313	D	0.999867	D;P	0.89917	1.0;0.568	D;B	0.85130	0.997;0.355	T	0.58634	-0.7602	10	0.45353	T	0.12	-0.8873	10.7034	0.45942	0.0:0.0:0.0:1.0	.	53;53	B4DKI5;Q9H190	.;SDCB2_HUMAN	F	53	ENSP00000371233:Y53F;ENSP00000354013:Y53F;ENSP00000342935:Y53F	ENSP00000342935:Y53F	Y	-	2	0	SDCBP2	1247029	1.000000	0.71417	0.713000	0.30519	0.984000	0.73092	6.295000	0.72744	2.021000	0.59480	0.533000	0.62120	TAT	.	.		0.488	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489		A	1299029	T	A	1299029	3	1	124	1	0	0	0	0	1	0	0	0	13971	1406	49	4	744	4	SDCBP2	20	1299029	Missense_Mutation	SNP	T	TCGA-DD-A4NA-01A-11D-A25V-10		1299029	61726491	31	20916										
TRPM2	7226	hgsc.bcm.edu	37	chr21	45810827	45810827	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	tttggccacgagaactgggaCcaccagctgaaactggcagt	12	11	0	2			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr21:45810827C>G	ENST00000397928.1	+	10	1804	c.1359C>G	c.(1357-1359)gaC>gaG	p.D453E	TRPM2_ENST00000300481.9_Missense_Mutation_p.D453E|TRPM2_ENST00000397932.2_Missense_Mutation_p.D453E|TRPM2_ENST00000300482.5_Missense_Mutation_p.D453E|TRPM2_ENST00000498430.1_3'UTR	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	453					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						AGAACTGGGACCACCAGCTGA	0.557																																					p.D453E		Atlas-SNP	.											.	TRPM2	196	.	0			c.C1359G						.						155	136	142					21																	45810827		2203	4300	6503	SO:0001583	missense	7226	exon10			CTGGGACCACCAG	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.1359C>G	chr21.hg19:g.45810827C>G	ENSP00000381023:p.Asp453Glu	106.0	0.0		132.0	53.0	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	hg19	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	C	11.43	1.635726	0.29068	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	4.6	3.71	0.42584	.	0.118260	0.64402	D	0.000016	T	0.62270	0.2414	L	0.49699	1.58	0.42064	D	0.991179	B;B	0.15719	0.014;0.007	B;B	0.16289	0.015;0.009	T	0.58901	-0.7554	10	0.40728	T	0.16	-43.3468	9.7382	0.40401	0.0:0.8375:0.0:0.1625	.	453;453	E9PGK7;O94759	.;TRPM2_HUMAN	E	453	ENSP00000300482:D453E;ENSP00000381023:D453E;ENSP00000300481:D453E;ENSP00000381026:D453E	ENSP00000300481:D453E	D	+	3	2	TRPM2	44635255	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.682000	0.25335	1.047000	0.40274	0.655000	0.94253	GAC	.	.		0.557	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		G	45810827	C	G	45810827	3	3	124	1	0	0	0	0	1	0	0	0	16601	506	18	4	1397	4	TRPM2	21	45810827	Missense_Mutation	SNP	C	TCGA-DD-A4NA-01A-11D-A25V-10		45810827	2319068	32	20917										
MED15	51586	hgsc.bcm.edu	37	chr22	20939289	20939289	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	cagccatgaccgccattcacGgcccacccatcacgtatgtc	7	18	2	1	rs147995933		TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chr22:20939289G>T	ENST00000263205.7	+	15	2020	c.1951G>T	c.(1951-1953)Ggc>Tgc	p.G651C	MED15_ENST00000382974.2_Missense_Mutation_p.G540C|MED15_ENST00000541476.1_Missense_Mutation_p.G585C|MED15_ENST00000406969.1_Missense_Mutation_p.G585C|MED15_ENST00000425759.2_Missense_Mutation_p.G500C|MED15_ENST00000542773.1_3'UTR|MED15_ENST00000292733.7_Missense_Mutation_p.G611C	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	651					gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.G611S(1)|p.G651S(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			CGCCATTCACGGCCCACCCAT	0.657																																					p.G651C		Atlas-SNP	.											PCQAP,bladder,carcinoma,0,2	MED15	68	.	2	Substitution - Missense(2)	urinary_tract(2)	c.G1951T						.						130	124	126					22																	20939289		2203	4300	6503	SO:0001583	missense	51586	exon15			ATTCACGGCCCAC	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"trinucleotide repeat containing 7", "PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.1951G>T	chr22.hg19:g.20939289G>T	ENSP00000263205:p.Gly651Cys	78.0	0.0		75.0	4.0	NM_001003891	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Missense_Mutation	SNP	ENST00000263205.7	hg19	CCDS33602.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.692122	0.88735	.	.	ENSG00000099917	ENST00000425759;ENST00000292733;ENST00000263205;ENST00000406969;ENST00000382974;ENST00000541476;ENST00000542312	.	.	.	5.04	5.04	0.67666	Mediator complex, subunit Med15, metazoa (1);	0.000000	0.85682	D	0.000000	T	0.80105	0.4562	M	0.80982	2.52	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;0.995;1.0;0.998;1.0	T	0.83231	-0.0063	9	0.87932	D	0	.	15.8666	0.79069	0.0:0.0:1.0:0.0	.	581;630;267;585;611;651	B4DGD6;Q6PKB8;B3KWF1;G3V1P5;Q96RN5-2;Q96RN5	.;.;.;.;.;MED15_HUMAN	C	500;611;651;585;540;585;581	.	ENSP00000263205:G651C	G	+	1	0	MED15	19269289	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	9.316000	0.96319	2.355000	0.79922	0.561000	0.74099	GGC	.	G|1.000;A|0.000		0.657	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		T	20939289	G	T	20939289	3	4	124	1	0	0	0	0	1	0	0	0	9442	1116	39	1	2009	1	MED15	22	20939289	Missense_Mutation	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10		20939289	30365277	33	20918										
HCCS	3052	hgsc.bcm.edu	37	chrX	11139831	11139831	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	gatggtggtgaagtcaacaaGgactaccagttcaccatcct	10	10	2	1			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chrX:11139831G>A	ENST00000321143.4	+	7	910	c.708G>A	c.(706-708)aaG>aaA	p.K236K	HCCS_ENST00000380762.4_Silent_p.K236K|ARHGAP6_ENST00000534860.1_Intron|HCCS_ENST00000380763.3_Silent_p.K236K	NM_001122608.2|NM_001171991.2|NM_005333.4	NP_001116080.1|NP_001165462.1|NP_005324.3	P53701	CCHL_HUMAN	holocytochrome c synthase	236					organ morphogenesis (GO:0009887)|oxidation-reduction process (GO:0055114)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	holocytochrome-c synthase activity (GO:0004408)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(3)	7						AAGTCAACAAGGACTACCAGT	0.463																																					p.K236K	Ovarian(86;1338 1347 1462 10340 37882)	Atlas-SNP	.											.	HCCS	17	.	0			c.G708A						.						186	149	162					X																	11139831		2203	4300	6503	SO:0001819	synonymous_variant	3052	exon7			CAACAAGGACTAC		CCDS14139.1	Xp22	2014-01-31	2010-05-11		ENSG00000004961	ENSG00000004961	4.4.1.17		4837	protein-coding gene	gene with protein product	"cytochrome c heme-lyase"	300056	"holocytochrome c synthase (cytochrome c heme-lyase)", "microphthalamia with linear skin defects"	MLS		8364577, 12444108	Standard	NM_001122608		Approved	CCHL	uc004cuj.3	P53701	OTTHUMG00000021128	ENST00000321143.4:c.708G>A	chrX.hg19:g.11139831G>A		226.0	0.0		205.0	70.0	NM_001122608	B3KUS1|Q502X8	Silent	SNP	ENST00000321143.4	hg19	CCDS14139.1																																																																																			.	.		0.463	HCCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055742.1			A	11139831	G	A	11139831	2	1	124	1	0	0	0	0	0	0	0	1	6999	991	35	3		3	HCCS	23	11139831	Silent	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10		11139831	144130729	34	20919										
GEMIN8	54960	hgsc.bcm.edu	37	chrX	14027050	14027050	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	gctcagaacttcagggggatGaccggccagtacttgggctg	15	10	2	2			TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chrX:14027050G>A	ENST00000380523.4	-	5	1029	c.711C>T	c.(709-711)gtC>gtT	p.V237V	GEMIN8_ENST00000398355.3_Silent_p.V237V	NM_017856.2	NP_060326.1	Q9NWZ8	GEMI8_HUMAN	gem (nuclear organelle) associated protein 8	237					spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	9						TCAGGGGGATGACCGGCCAGT	0.557																																					p.V237V		Atlas-SNP	.											.	GEMIN8	19	.	0			c.C711T						.						74	69	71					X																	14027050		2203	4300	6503	SO:0001819	synonymous_variant	54960	exon5			GGGGATGACCGGC	BC020785	CCDS14159.1	Xp22	2010-03-16	2006-11-24	2006-11-24	ENSG00000046647	ENSG00000046647			26044	protein-coding gene	gene with protein product			"family with sequence similarity 51, member A1"	FAM51A1		16434402	Standard	NM_017856		Approved	FLJ20514	uc004cwd.3	Q9NWZ8	OTTHUMG00000021160	ENST00000380523.4:c.711C>T	chrX.hg19:g.14027050G>A		257.0	0.0		233.0	83.0	NM_017856	C4AMC4|Q2LJ66|Q6ZV27	Silent	SNP	ENST00000380523.4	hg19	CCDS14159.1																																																																																			.	.		0.557	GEMIN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055815.1	NM_017856		A	14027050	G	A	14027050	2	1	124	1	0	0	0	0	0	0	0	1	6342	1277	45	3		3	GEMIN8	23	14027050	Silent	SNP	G	TCGA-DD-A4NA-01A-11D-A25V-10	2887219	14027050	141243510	35	20920										
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765399	27765399	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	1	1	0.51717032967033	0	0.68956043956044	1	1	0	gagggaggggaggaggaggaAgaggaggaggaggaggagga	27	0	0	1	rs371896121		TCGA-DD-A4NA-01A-11D-A25V-10	TCGA-DD-A4NA-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ead73fe-1c34-48ed-b20d-89fc3c82dbd6	85fa6efb-2977-466f-b260-4e95585f2e37	g.chrX:27765399A>G	ENST00000451261.2	+	5	786	c.387A>G	c.(385-387)gaA>gaG	p.E129E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	129	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aggaggaggaagaggaggagg	0.572																																					p.E129E		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.A387G						.						24	21	22					X																	27765399		692	1589	2281	SO:0001819	synonymous_variant	347442	exon1			GGAGGAAGAGGAG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.387A>G	chrX.hg19:g.27765399A>G		39.0	0.0		70.0	12.0	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.572	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		G	27765399	A	G	27765399	2	3	124	1	0	0	0	0	0	0	0	1	4280	69	3	2		2	DCAF8L2	23	27765399	Silent	SNP	A	TCGA-DD-A4NA-01A-11D-A25V-10	13738349	27765399	127505161	36	20921										
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150532541	150532541	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	ctcctctgtccccagatgatCaatgcaaggacagctctcca	7	15	3	2			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr1:150532541C>A	ENST00000369038.2	+	17	3295	c.3094C>A	c.(3094-3096)Caa>Aaa	p.Q1032K	ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.Q1032K|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.Q1055K|RP11-54A4.2_ENST00000442435.2_RNA			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	1032	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CCCAGATGATCAATGCAAGGA	0.597											OREG0013787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q1032K		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.C3094A						.						148	139	142					1																	150532541		2203	4300	6503	SO:0001583	missense	54507	exon19			GATGATCAATGCA	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.3094C>A	chr1.hg19:g.150532541C>A	ENSP00000358034:p.Gln1032Lys	185.0	0.0	1733	188.0	46.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	hg19	CCDS955.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.496385	0.26861	.	.	ENSG00000143382	ENST00000271643;ENST00000369039;ENST00000369038	T;T;T	0.39229	1.09;1.09;1.09	4.73	3.8	0.43715	PLAC (2);	.	.	.	.	T	0.07188	0.0182	N	0.02539	-0.55	0.33920	D	0.640772	B;B;B	0.31351	0.32;0.012;0.27	B;B;B	0.31101	0.124;0.022;0.059	T	0.11179	-1.0598	9	0.33141	T	0.24	.	7.7469	0.28875	0.1867:0.6328:0.1805:0.0	.	993;1055;1032	B7ZMJ3;F8WAD0;Q6UY14	.;.;ATL4_HUMAN	K	1032;1055;1032	ENSP00000271643:Q1032K;ENSP00000358035:Q1055K;ENSP00000358034:Q1032K	ENSP00000271643:Q1032K	Q	+	1	0	ADAMTSL4	148799165	0.992000	0.36948	0.951000	0.38953	0.946000	0.59487	3.127000	0.50484	1.175000	0.42826	0.561000	0.74099	CAA	.	.		0.597	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		A	150532541	C	A	150532541	3	1	125	1	0	0	0	0	1	0	0	0	277	827	29	3	3235	3	ADAMTSL4	1	150532541	Missense_Mutation	SNP	C	TCGA-DD-A4NB-01A-12D-A25V-10		150532541	98718080	1	20922										
SLC35F3	148641	hgsc.bcm.edu	37	chr1	234041461	234041461	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	gaggagcggatcctgcgcatCactggctactatggctacca	12	12	1	0			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr1:234041461C>T	ENST00000366618.3	+	2	385	c.240C>T	c.(238-240)atC>atT	p.I80I		NM_173508.2	NP_775779.1	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	0					thiamine transport (GO:0015888)	integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			TCCTGCGCATCACTGGCTACT	0.582																																					p.I80I		Atlas-SNP	.											.	SLC35F3	81	.	0			c.C240T						.						61	57	58					1																	234041461		2203	4300	6503	SO:0001819	synonymous_variant	148641	exon2			GCGCATCACTGGC		CCDS1600.1, CCDS73050.1	1q42.3	2013-05-22			ENSG00000183780	ENSG00000183780		"Solute carriers"	23616	protein-coding gene	gene with protein product							Standard	XM_005273070		Approved	FLJ37712	uc001hvy.1	Q8IY50	OTTHUMG00000037929	ENST00000366618.3:c.240C>T	chr1.hg19:g.234041461C>T		230.0	0.0		292.0	75.0	NM_173508	Q5TDD6|Q8N9C9	Silent	SNP	ENST00000366618.3	hg19	CCDS1600.1																																																																																			.	.		0.582	SLC35F3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092579.2	NM_173508		T	234041461	C	T	234041461	2	4	125	1	0	0	0	0	0	0	0	1	14605	816	29	3		3	SLC35F3	1	234041461	Silent	SNP	C	TCGA-DD-A4NB-01A-12D-A25V-10	83508920	234041461	15209160	2	20923										
SCN3A	6328	hgsc.bcm.edu	37	chr2	165946841	165946841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	tgtcaataatcatgtcttgtTttataggtaagtcaatcctc	6	7	4	0			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr2:165946841T>C	ENST00000360093.3	-	28	6313	c.5822A>G	c.(5821-5823)aAa>aGa	p.K1941R	SCN3A_ENST00000409101.3_Missense_Mutation_p.K1892R|SCN3A_ENST00000465043.1_5'Flank|SCN3A_ENST00000283254.7_Missense_Mutation_p.K1941R|SCN3A_ENST00000540861.1_Missense_Mutation_p.K424R|AC013463.2_ENST00000431341.1_RNA	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1941					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CATGTCTTGTTTTATAGGTAA	0.348																																					p.K1941R		Atlas-SNP	.											.	SCN3A	544	.	0			c.A5822G						.						93	92	92					2																	165946841		2203	4300	6503	SO:0001583	missense	6328	exon28			TCTTGTTTTATAG	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.5822A>G	chr2.hg19:g.165946841T>C	ENSP00000353206:p.Lys1941Arg	271.0	0.0		335.0	84.0	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	hg19		.	.	.	.	.	.	.	.	.	.	T	5.697	0.313120	0.10789	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000540861	D;D;D;D	0.96940	-3.95;-3.95;-3.9;-4.18	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000002	D	0.92110	0.7499	L	0.31578	0.945	0.44562	D	0.997529	B;B;B	0.20261	0.011;0.011;0.043	B;B;B	0.20577	0.009;0.009;0.03	D	0.88047	0.2785	10	0.25751	T	0.34	.	10.8274	0.46640	0.0:0.0699:0.0:0.9301	.	1892;1892;1941	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	R	1941;1941;1892;424	ENSP00000353206:K1941R;ENSP00000283254:K1941R;ENSP00000386726:K1892R;ENSP00000439920:K424R	ENSP00000283254:K1941R	K	-	2	0	SCN3A	165655087	1.000000	0.71417	1.000000	0.80357	0.397000	0.30659	3.240000	0.51368	2.308000	0.77769	0.533000	0.62120	AAA	.	.		0.348	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		C	165946841	T	C	165946841	3	2	125	1	0	0	0	0	1	0	0	0	13933	1841	64	2	184	2	SCN3A	2	165946841	Missense_Mutation	SNP	T	TCGA-DD-A4NB-01A-12D-A25V-10		165946841	77252532	3	20924										
NEUROD1	4760	hgsc.bcm.edu	37	chr2	182542873	182542885	+	Frame_Shift_Del	DEL	CATGGGAGCTGTC	CATGGGAGCTGTC	-													0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	cggaggcttaacgtggaagaCatgggagctgtccatggtac					rs145050582		TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	CATGGGAGCTGTC	CATGGGAGCTGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr2:182542873_182542885delCATGGGAGCTGTC	ENST00000295108.3	-	2	1160_1172	c.703_715delGACAGCTCCCATG	c.(703-717)gacagctcccatgtcfs	p.DSSHV235fs	NEUROD1_ENST00000496876.1_Intron|CERKL_ENST00000479558.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	235					amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.H238H(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			ACGTGGAAGACATGGGAGCTGTCCATGGTACCG	0.629											OREG0005604	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=NEUROD1|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.235_239del		Atlas-INDEL	.											.	NEUROD1	67	.	1	Substitution - coding silent(1)	lung(1)	c.704_716del						.																																			SO:0001589	frameshift_variant	4760	exon2			.	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"Basic helix-loop-helix proteins"	7762	protein-coding gene	gene with protein product	"beta-cell E-box transactivator 2", "neurogenic helix-loop-helix protein NEUROD"	601724	"neurogenic differentiation 1"	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.703_715delGACAGCTCCCATG	chr2.hg19:g.182542873_182542885delCATGGGAGCTGTC	ENSP00000295108:p.Asp235fs	142.0	0.0	1977	99.0	10.0	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Frame_Shift_Del	DEL	ENST00000295108.3	hg19	CCDS2283.1																																																																																			.	.		0.629	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		-	182542885	CATGGGAGCTGTC	-	182542873	7	5	125	1	0	1	0	1	0	0	0	0	10357	478	17	0	359	0	NEUROD1	2	182542873	Frame_Shift_Del	DEL	CATGGGAGCTGTC	TCGA-DD-A4NB-01A-12D-A25V-10	16596032	182542873	60656500	4	20925										
CASP8	841	hgsc.bcm.edu	37	chr2	202131436	202131437	+	Frame_Shift_Ins	INS	-	-	AG													0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	aatagactggatttgctgatINStacctacctaaacactagaa							TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr2:202131436_202131437insAG	ENST00000432109.2	+	3	416_417	c.227_228insAG	c.(226-231)attaccfs	p.T77fs	CASP8_ENST00000323492.7_Frame_Shift_Ins_p.T77fs|CASP8_ENST00000358485.4_Frame_Shift_Ins_p.T136fs|CASP8_ENST00000392258.3_Frame_Shift_Ins_p.T77fs|CASP8_ENST00000264275.5_Frame_Shift_Ins_p.T77fs|CASP8_ENST00000264274.9_Frame_Shift_Ins_p.T77fs|CASP8_ENST00000392259.2_Frame_Shift_Ins_p.T77fs|CASP8_ENST00000392266.3_Frame_Shift_Ins_p.T77fs	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	77	DED 1. {ECO:0000255|PROSITE- ProRule:PRU00065}.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						GATTTGCTGATTACCTACCTAA	0.46										HNSCC(4;0.00038)																											p.I135fs	Melanoma(82;831 1348 20716 36952 40159)	Atlas-INDEL	.											.	CASP8	272	.	0			c.404_405insAG						.																																			SO:0001589	frameshift_variant	841	exon2			.	U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"Caspases"	1509	protein-coding gene	gene with protein product		601763	"caspase 8, apoptosis-related cysteine protease"			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	Exception_encountered	chr2.hg19:g.202131436_202131437insAG	ENSP00000412523:p.Thr77fs	150.0	0.0		154.0	31.0	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Frame_Shift_Ins	INS	ENST00000432109.2	hg19	CCDS2342.1																																																																																			.	.		0.46	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228		AG	202131437	-	AG	202131436	7	5	125	1	0	1	1	0	0	0	0	0	2679	1493	52	0	410	0	CASP8	2	202131436	Frame_Shift_Ins	INS	-	TCGA-DD-A4NB-01A-12D-A25V-10	19588563	202131436	41067937	5	20926										
CPS1	1373	hgsc.bcm.edu	37	chr2	211507320	211507322	+	In_Frame_Del	DEL	TGA	TGA	-													0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	gagactgtgagcacagacttTgatgagtgtgacaaactgta							TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr2:211507320_211507322delTGA	ENST00000233072.5	+	25	3268_3270	c.3072_3074delTGA	c.(3070-3075)tttgat>ttt	p.D1025del	CPS1_ENST00000430249.2_In_Frame_Del_p.D1031del|CPS1_ENST00000451903.2_In_Frame_Del_p.D574del|CPS1_ENST00000497121.1_3'UTR	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1025					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GCACAGACTTTGATGAGTGTGAC	0.414																																					p.1030_1031del		Atlas-Indel,Pindel	.											.	CPS1	485	.	0			c.3089_3091del						.																																			SO:0001651	inframe_deletion	1373	exon26			.	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3072_3074delTGA	chr2.hg19:g.211507323_211507325delTGA	ENSP00000233072:p.Asp1025del	383.0	0.0		299.0	24.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	In_Frame_Del	DEL	ENST00000233072.5	hg19	CCDS2393.1																																																																																			.	.		0.414	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			-	211507322	TGA	-	211507320	7	5	125	1	0	1	0	1	0	0	0	0	3825	1809	63	0	3192	0	CPS1	2	211507320	In_Frame_Del	DEL	TGA	TCGA-DD-A4NB-01A-12D-A25V-10	9375884	211507320	31692053	6	20927										
MYH15	22989	hgsc.bcm.edu	37	chr3	108203986	108203986	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	ttctctaggtttctgtttaaAtttcatatttccaaagtgca	5	7	3	0			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr3:108203986A>G	ENST00000273353.3	-	12	1182	c.1126T>C	c.(1126-1128)Ttt>Ctt	p.F376L		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	376	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TTCTGTTTAAATTTCATATTT	0.398																																					p.F376L		Atlas-SNP	.											.	MYH15	223	.	0			c.T1126C						.						134	124	127					3																	108203986		1867	4103	5970	SO:0001583	missense	22989	exon12			GTTTAAATTTCAT	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1126T>C	chr3.hg19:g.108203986A>G	ENSP00000273353:p.Phe376Leu	173.0	0.0		150.0	38.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.968019	0.92855	.	.	ENSG00000144821	ENST00000273353	D	0.89939	-2.59	6.05	4.87	0.63330	Myosin head, motor domain (2);	.	.	.	.	D	0.95655	0.8587	M	0.93507	3.425	0.52099	D	0.999945	D	0.89917	1.0	D	0.97110	1.0	D	0.96062	0.9039	9	0.87932	D	0	.	13.328	0.60471	0.8681:0.1319:0.0:0.0	.	376	Q9Y2K3	MYH15_HUMAN	L	376	ENSP00000273353:F376L	ENSP00000273353:F376L	F	-	1	0	MYH15	109686676	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.354000	0.79424	1.077000	0.40990	0.528000	0.53228	TTT	.	.		0.398	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		G	108203986	A	G	108203986	3	3	125	1	0	0	0	0	1	0	0	0	10043	101	4	2	4838	2	MYH15	3	108203986	Missense_Mutation	SNP	A	TCGA-DD-A4NB-01A-12D-A25V-10		108203986	89818444	7	20928										
ECE2	9718	hgsc.bcm.edu	37	chr3	184002776	184002810	+	Frame_Shift_Del	DEL	TTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	TTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	-													0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	ggcgccctccatggactggcTtgagttcctgtctttcttgc							TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	TTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	TTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr3:184002776_184002810delTTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	ENST00000402825.3	+	9	1385_1419	c.1385_1419delTTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	c.(1384-1419)cttgagttcctgtctttcttgctgtcaccattggagfs	p.LEFLSFLLSPLE462fs	EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000359140.4_Frame_Shift_Del_p.LEFLSFLLSPLE315fs|ECE2_ENST00000357474.5_Frame_Shift_Del_p.LEFLSFLLSPLE390fs|ECE2_ENST00000404464.3_Frame_Shift_Del_p.LEFLSFLLSPLE344fs	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	462	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)	p.S319F(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ATGGACTGGCTTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAGTTGAGTGACT	0.553											OREG0015945	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.462_473del		Pindel	.											.	ECE2	303	.	1	Substitution - Missense(1)	large_intestine(1)	c.1384_1418del						.																																			SO:0001589	frameshift_variant	9718	exon9			.	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.1385_1419delTTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	chr3.hg19:g.184002776_184002810delTTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	ENSP00000384223:p.Leu462fs	475.0	0.0	1988	326.0	22.0	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Frame_Shift_Del	DEL	ENST00000402825.3	hg19	CCDS3256.2																																																																																			.	.		0.553	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693		-	184002810	TTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	-	184002776	7	5	125	1	0	1	0	1	0	0	0	0	4892	1609	56	0	1983	0	ECE2	3	184002776	Frame_Shift_Del	DEL	TTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	TCGA-DD-A4NB-01A-12D-A25V-10	75798790	184002776	14019654	8	20929										
AFF1	4299	hgsc.bcm.edu	37	chr4	88012960	88012963	+	Frame_Shift_Del	DEL	AGTT	AGTT	-													0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	tctaggactctcagcatgtcAgttctgtaacccaaaaccaa							TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	AGTT	AGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr4:88012960_88012963delAGTT	ENST00000307808.6	+	6	1606_1609	c.1186_1189delAGTT	c.(1186-1191)agttctfs	p.SS396fs	AFF1_ENST00000544085.1_Frame_Shift_Del_p.SS34fs|AFF1_ENST00000395146.4_Frame_Shift_Del_p.SS403fs	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	396					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TCAGCATGTCAGTTCTGTAACCCA	0.275																																					p.402_403del		Atlas-Indel,Pindel	.											.	AFF1	102	.	0			c.1206_1209del						.																																			SO:0001589	frameshift_variant	4299	exon7			.	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.1186_1189delAGTT	chr4.hg19:g.88012960_88012963delAGTT	ENSP00000305689:p.Ser396fs	124.0	0.0		114.0	18.0	NM_001166693	B4DTU1|E9PBM3	Frame_Shift_Del	DEL	ENST00000307808.6	hg19	CCDS3616.1																																																																																			.	.		0.275	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		-	88012963	AGTT	-	88012960	7	5	125	1	0	1	0	1	0	0	0	0	356	188	7	0	1250	0	AFF1	4	88012960	Frame_Shift_Del	DEL	AGTT	TCGA-DD-A4NB-01A-12D-A25V-10		88012960	103141316	9	20930										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	161903	161903	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	gttccttgggtacagcaatcCtgccagaaaggactacagct	10	11	0	1			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr5:161903C>T	ENST00000283426.6	+	10	1475	c.1425C>T	c.(1423-1425)tcC>tcT	p.S475S		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	475							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		TACAGCAATCCTGCCAGAAAG	0.577																																					p.S475S		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.C1425T						.						75	71	73					5																	161903		2203	4300	6503	SO:0001819	synonymous_variant	153478	exon10			GCAATCCTGCCAG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1425C>T	chr5.hg19:g.161903C>T		129.0	0.0		111.0	16.0	NM_052909		Silent	SNP	ENST00000283426.6	hg19	CCDS34124.1																																																																																			.	.		0.577	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		T	161903	C	T	161903	2	4	125	1	0	0	0	0	0	0	0	1	12081	668	24	3		3	PLEKHG4B	5	161903	Silent	SNP	C	TCGA-DD-A4NB-01A-12D-A25V-10		161903	180753357	10	20931										
ITGA1	3672	hgsc.bcm.edu	37	chr5	52193327	52193327	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	cttcatttgaaatggaaatgTctcagactggcttcagtgct	9	8	3	2			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr5:52193327T>C	ENST00000282588.6	+	10	1590	c.1132T>C	c.(1132-1134)Tct>Cct	p.S378P		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	378					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				AATGGAAATGTCTCAGACTGG	0.383																																					p.S378P		Atlas-SNP	.											.	ITGA1	112	.	0			c.T1132C						.						89	84	85					5																	52193327		2203	4300	6503	SO:0001583	missense	3672	exon10			GAAATGTCTCAGA	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.1132T>C	chr5.hg19:g.52193327T>C	ENSP00000282588:p.Ser378Pro	94.0	0.0		90.0	15.0	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	hg19	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.921172	0.92249	.	.	ENSG00000213949	ENST00000282588	T	0.67345	-0.26	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.81735	0.4885	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.83324	-0.0016	10	0.62326	D	0.03	.	16.4447	0.83919	0.0:0.0:0.0:1.0	.	378	P56199	ITA1_HUMAN	P	378	ENSP00000282588:S378P	ENSP00000282588:S378P	S	+	1	0	ITGA1	52229084	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.857000	0.69525	2.284000	0.76573	0.528000	0.53228	TCT	.	.		0.383	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		C	52193327	T	C	52193327	3	2	125	1	0	0	0	0	1	0	0	0	7881	1667	58	2	1170	2	ITGA1	5	52193327	Missense_Mutation	SNP	T	TCGA-DD-A4NB-01A-12D-A25V-10	52031424	52193327	128721933	11	20932										
ANKRD32	84250	hgsc.bcm.edu	37	chr5	94001726	94001726	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	gtctttagtagaagtccttaTcaggtaaggaatttcacatt	8	6	3	1			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr5:94001726T>G	ENST00000265140.5	+	12	1948	c.1529T>G	c.(1528-1530)aTc>aGc	p.I510S		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	510						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		GAAGTCCTTATCAGGTAAGGA	0.348																																					p.I510S		Atlas-SNP	.											.	ANKRD32	117	.	0			c.T1529G						.						150	119	128					5																	94001726		692	1591	2283	SO:0001583	missense	84250	exon12			TCCTTATCAGGTA	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"Ankyrin repeat domain containing"	25408	protein-coding gene	gene with protein product			"BRCT domain containing 1"	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.1529T>G	chr5.hg19:g.94001726T>G	ENSP00000265140:p.Ile510Ser	43.0	0.0		60.0	5.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Missense_Mutation	SNP	ENST00000265140.5	hg19	CCDS4071.2	.	.	.	.	.	.	.	.	.	.	T	14.23	2.472039	0.43942	.	.	ENSG00000133302	ENST00000265140	T	0.56103	0.48	5.25	5.25	0.73442	.	0.495502	0.16842	N	0.197281	T	0.42108	0.1188	L	0.29908	0.895	0.32464	N	0.543763	B	0.23058	0.079	B	0.26517	0.07	T	0.53954	-0.8365	10	0.87932	D	0	.	9.6422	0.39846	0.0:0.0783:0.0:0.9217	.	510	Q9BQI6	ANR32_HUMAN	S	510	ENSP00000265140:I510S	ENSP00000265140:I510S	I	+	2	0	ANKRD32	94027482	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.821000	0.55700	1.966000	0.57179	0.477000	0.44152	ATC	.	.		0.348	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290		G	94001726	T	G	94001726	3	3	125	1	0	0	0	0	1	0	0	0	660	1435	50	5	1571	5	ANKRD32	5	94001726	Missense_Mutation	SNP	T	TCGA-DD-A4NB-01A-12D-A25V-10	41808399	94001726	86913534	12	20933										
MGAT4B	11282	hgsc.bcm.edu	37	chr5	179226059	179226059	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	tggtatgtcttcaggctcgtGctcacctctgctggcgggtt	13	11	4	0			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr5:179226059G>A	ENST00000292591.7	-	11	1562	c.1212C>T	c.(1210-1212)agC>agT	p.S404S	MGAT4B_ENST00000521305.1_5'Flank|MGAT4B_ENST00000337755.5_Silent_p.S419S|MIR1229_ENST00000408467.1_RNA	NM_014275.4	NP_055090.1	Q9UQ53	MGT4B_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B	404					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	13	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCAGGCTCGTGCTCACCTCTG	0.622																																					p.S419S	GBM(13;414 434 4098 22176 23230)	Atlas-SNP	.											.	MGAT4B	41	.	0			c.C1257T						.						152	146	148					5																	179226059		2203	4300	6503	SO:0001819	synonymous_variant	11282	exon10			GCTCGTGCTCACC	AB000624	CCDS4448.1, CCDS4449.1	5q35	2013-02-25	2005-11-16		ENSG00000161013	ENSG00000161013	2.4.1.145	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7048	protein-coding gene	gene with protein product		604561	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme B"			10372966	Standard	NM_014275		Approved	GnT-Ivb	uc003mks.3	Q9UQ53	OTTHUMG00000130912	ENST00000292591.7:c.1212C>T	chr5.hg19:g.179226059G>A		348.0	0.0		367.0	42.0	NM_054013	A8MPR0|Q86TF1|Q96GH4|Q9NSK6	Silent	SNP	ENST00000292591.7	hg19	CCDS4448.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.194|9.194	1.026686|1.026686	0.19512|0.19512	.|.	.|.	ENSG00000161013|ENSG00000161013	ENST00000520969;ENST00000518980|ENST00000518778;ENST00000520875	.|.	.|.	.|.	4.03|4.03	4.03|4.03	0.46877|0.46877	.|.	.|.	.|.	.|.	.|.	T|T	0.71324|0.71324	0.3326|0.3326	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.71981|0.71981	-0.4428|-0.4428	4|4	.|.	.|.	.|.	-26.1269|-26.1269	16.3834|16.3834	0.83489|0.83489	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	V|Y	101;150|229;185	.|.	.|.	A|H	-|-	2|1	0|0	MGAT4B|MGAT4B	179158665|179158665	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.695000|0.695000	0.40330|0.40330	3.682000|3.682000	0.54656|0.54656	2.072000|2.072000	0.62099|0.62099	0.561000|0.561000	0.74099|0.74099	GCA|CAC	.	.		0.622	MGAT4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253503.3	NM_014275		A	179226059	G	A	179226059	2	1	125	1	0	0	0	0	0	0	0	1	9555	1310	46	3		3	MGAT4B	5	179226059	Silent	SNP	G	TCGA-DD-A4NB-01A-12D-A25V-10	85224333	179226059	1689201	13	20934										
BAT3	7917	hgsc.bcm.edu	37	chr6	31610883	31610883	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	gcggtggagccatacctgggGtcccctgagctgtaagaaac	14	11	0	2			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr6:31610883G>A	ENST00000375964.6	-	14	1989	c.1676C>T	c.(1675-1677)aCc>aTc	p.T559I	BAG6_ENST00000362049.6_Missense_Mutation_p.T553I|BAG6_ENST00000439687.2_Missense_Mutation_p.T552I|BAG6_ENST00000375976.4_Missense_Mutation_p.T553I|BAG6_ENST00000211379.5_Missense_Mutation_p.T553I|BAG6_ENST00000404765.2_Missense_Mutation_p.T589I|BAG6_ENST00000470875.1_5'UTR	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	559	4 X 29 AA approximate repeats.|Pro-rich.				brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						CATACCTGGGGTCCCCTGAGC	0.602																																					p.T559I		Atlas-SNP	.											.	BAG6	73	.	0			c.C1676T						.						8	10	9					6																	31610883		2192	4274	6466	SO:0001583	missense	7917	exon14			CCTGGGGTCCCCT	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"HLA-B associated transcript 3"	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.1676C>T	chr6.hg19:g.31610883G>A	ENSP00000365131:p.Thr559Ile	14.0	0.0		12.0	5.0	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Missense_Mutation	SNP	ENST00000375964.6	hg19	CCDS47403.1	.	.	.	.	.	.	.	.	.	.	G	16.99	3.272818	0.59649	.	.	ENSG00000204463	ENST00000375976;ENST00000375964;ENST00000211379;ENST00000404765;ENST00000439687;ENST00000362049;ENST00000437771;ENST00000438149;ENST00000436214	T;T;T;T;T;T;T;T	0.52295	1.15;1.26;1.15;1.35;0.89;1.27;0.69;0.67	5.17	5.17	0.71159	.	0.304052	0.35615	N	0.003100	T	0.24122	0.0584	N	0.08118	0	0.42030	D	0.991025	B;P;B;P	0.44429	0.319;0.835;0.421;0.557	B;P;B;B	0.44477	0.104;0.451;0.107;0.154	T	0.27191	-1.0081	10	0.72032	D	0.01	.	16.5889	0.84759	0.0:0.0:1.0:0.0	.	552;553;559;553	E7EMZ4;F8VXY4;P46379;P46379-2	.;.;BAG6_HUMAN;.	I	553;559;553;589;552;553;589;147;167	ENSP00000365143:T553I;ENSP00000365131:T559I;ENSP00000211379:T553I;ENSP00000384494:T589I;ENSP00000402856:T552I;ENSP00000354875:T553I;ENSP00000397978:T589I;ENSP00000410280:T147I	ENSP00000211379:T553I	T	-	2	0	BAG6	31718862	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	2.556000	0.45862	2.600000	0.87896	0.650000	0.86243	ACC	.	.		0.602	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703		A	31610883	G	A	31610883	3	1	125	1	0	0	0	0	1	0	0	0	1322	1261	44	3	1770	3	BAT3	6	31610883	Missense_Mutation	SNP	G	TCGA-DD-A4NB-01A-12D-A25V-10		31610883	139504184	14	20935										
LFNG	3955	hgsc.bcm.edu	37	chr7	2566469	2566469	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	cactccgcccgctccccacaGgtgacgctgagctacggtat	10	17	0	2			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr7:2566469G>T	ENST00000222725.5	+	7	1007		c.e7-1		LFNG_ENST00000402506.1_Splice_Site|LFNG_ENST00000402045.1_Splice_Site|LFNG_ENST00000359574.3_Splice_Site|LFNG_ENST00000338732.3_Splice_Site|MIR4648_ENST00000580107.1_RNA	NM_001040167.1	NP_001035257.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase						compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		GCTCCCCACAGGTGACGCTGA	0.677																																					.		Atlas-SNP	.											.	LFNG	57	.	0			c.775-1G>T						.						26	28	27					7																	2566469		2199	4298	6497	SO:0001630	splice_region_variant	3955	exon8			CCCACAGGTGACG	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"Beta 3-glycosyltransferases"	6560	protein-coding gene	gene with protein product		602576	"lunatic fringe (Drosophila) homolog", "lunatic fringe homolog (Drosophila)"			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000222725.5:c.988-1G>T	chr7.hg19:g.2566469G>T		86.0	0.0		65.0	4.0	NM_001166355	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Splice_Site	SNP	ENST00000222725.5	hg19	CCDS34587.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.553078	0.45487	.	.	ENSG00000106003	ENST00000402506;ENST00000402045;ENST00000338732;ENST00000222725;ENST00000359574	.	.	.	4.46	4.46	0.54185	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1069	0.86666	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LFNG	2532995	1.000000	0.71417	0.984000	0.44739	0.700000	0.40528	9.205000	0.95048	2.007000	0.58848	0.561000	0.74099	.	.	.		0.677	LFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325021.1	NM_002304	Intron	T	2566469	G	T	2566469	5	4	125	1	0	0	0	0	0	0	1	0	8746	1014	35	3	1289	3	LFNG	7	2566469	Splice_Site	SNP	G	TCGA-DD-A4NB-01A-12D-A25V-10		2566469	156572194	15	20936										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20740268	20740268	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	ttgataaaagccattatgcaCttactacaaatgcaagctct	5	9	1	1			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr9:20740268C>T	ENST00000380249.1	+	7	685	c.321C>T	c.(319-321)caC>caT	p.H107H	FOCAD_ENST00000338382.6_Silent_p.H107H	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	107						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											CCATTATGCACTTACTACAAA	0.303																																					p.H107H		Atlas-SNP	.											.	.	.	.	0			c.C321T						.						78	80	79					9																	20740268		2203	4297	6500	SO:0001819	synonymous_variant	54914	exon7			TATGCACTTACTA	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.321C>T	chr9.hg19:g.20740268C>T		232.0	0.0		226.0	53.0	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Silent	SNP	ENST00000380249.1	hg19	CCDS34993.1																																																																																			.	.		0.303	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		T	20740268	C	T	20740268	2	4	125	1	0	0	0	0	0	0	0	1	8267	564	20	3		3	KIAA1797	9	20740268	Silent	SNP	C	TCGA-DD-A4NB-01A-12D-A25V-10		20740268	120473163	16	20937										
PAX5	5079	hgsc.bcm.edu	37	chr9	37002701	37002701	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	gggacgtgatgcccaggatgCcgctgatggagtacgacgag	17	9	0	2			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr9:37002701C>T	ENST00000358127.4	-	5	622	c.548G>A	c.(547-549)gGc>gAc	p.G183D	PAX5_ENST00000446742.1_Missense_Mutation_p.G117D|PAX5_ENST00000520154.1_Missense_Mutation_p.G183D|PAX5_ENST00000522003.1_Missense_Mutation_p.G75D|PAX5_ENST00000523145.1_Missense_Mutation_p.G75D|PAX5_ENST00000523241.1_Missense_Mutation_p.G183D|PAX5_ENST00000377852.2_Missense_Mutation_p.G183D|PAX5_ENST00000377847.2_Missense_Mutation_p.G183D|RP11-297B17.3_ENST00000509911.2_RNA|PAX5_ENST00000520281.1_Intron|PAX5_ENST00000414447.1_Intron|PAX5_ENST00000377853.2_Missense_Mutation_p.G183D	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	183			G -> S (in ALL3; confers susceptibility to ALL3; reduced transcription factor activity). {ECO:0000269|PubMed:24013638}.|G -> V. {ECO:0000269|PubMed:24013638}.		humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.?(40)	PAX5/JAK2(18)	NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(151)|kidney(1)|lung(10)|prostate(1)|skin(1)	171		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		GCCCAGGATGCCGCTGATGGA	0.677			"T, Mis, D, F, S"	"IGH@, ETV6, PML, FOXP1, ZNF521, ELN"	"NHL, ALL, B-ALL"																																p.G183D		Atlas-SNP	.		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	.	PAX5	250	.	40	Unknown(40)	haematopoietic_and_lymphoid_tissue(40)	c.G548A						.						48	37	41					9																	37002701		2202	4296	6498	SO:0001583	missense	5079	exon5			AGGATGCCGCTGA		CCDS6607.1, CCDS65039.1, CCDS65040.1, CCDS65041.1, CCDS65042.1, CCDS65043.1, CCDS65044.1, CCDS65045.1, CCDS65046.1, CCDS65047.1, CCDS65048.1	9p13.2	2011-06-20	2007-07-12		ENSG00000196092	ENSG00000196092		"Paired boxes", "Homeoboxes / PRD class"	8619	protein-coding gene	gene with protein product	"B-cell lineage specific activator"	167414	"paired box gene 5 (B-cell lineage specific activator protein)", "paired box gene 5 (B-cell lineage specific activator)"			1516825, 8431641	Standard	NM_016734		Approved	BSAP	uc003zzo.1	Q02548	OTTHUMG00000019907	ENST00000358127.4:c.548G>A	chr9.hg19:g.37002701C>T	ENSP00000350844:p.Gly183Asp	182.0	0.0		132.0	6.0	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	hg19	CCDS6607.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.097231|5.097231	0.94197|0.94197	.|.	.|.	ENSG00000196092|ENSG00000196092	ENST00000522932|ENST00000358127;ENST00000377849;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000446742;ENST00000522003;ENST00000523145;ENST00000377847	.|D;D;D;D;D;D;D;D;D	.|0.98234	.|-4.29;-4.29;-4.31;-4.8;-4.79;-3.97;-2.13;-2.71;-4.81	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	.|0.316779	.|0.32258	.|N	.|0.006354	D|D	0.98896|0.98896	0.9626|0.9626	M|M	0.76938|0.76938	2.355|2.355	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;0.965;0.999;1.0;1.0;1.0	.|D;D;P;D;D;D;D	.|0.87578	.|0.998;0.992;0.806;0.98;0.998;0.992;0.992	D|D	0.99858|0.99858	1.1080|1.1080	5|10	.|0.72032	.|D	.|0.01	.|.	18.9629|18.9629	0.92684|0.92684	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|117;183;183;183;183;183;183	.|C0KTF9;C0KTF6;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.|.;.;.;.;.;.;PAX5_HUMAN	T|D	17|183;75;183;183;183;183;117;75;75;183	.|ENSP00000350844:G183D;ENSP00000367084:G183D;ENSP00000367083:G183D;ENSP00000429637:G183D;ENSP00000429291:G183D;ENSP00000404687:G117D;ENSP00000429359:G75D;ENSP00000429197:G75D;ENSP00000367078:G183D	.|ENSP00000350844:G183D	A|G	-|-	1|2	0|0	PAX5|PAX5	36992701|36992701	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.902000|0.902000	0.53008|0.53008	6.942000|6.942000	0.75928|0.75928	2.553000|2.553000	0.86117|0.86117	0.555000|0.555000	0.69702|0.69702	GCA|GGC	.	.		0.677	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1			T	37002701	C	T	37002701	3	4	125	1	0	0	0	0	1	0	0	0	11491	739	26	3	651	3	PAX5	9	37002701	Missense_Mutation	SNP	C	TCGA-DD-A4NB-01A-12D-A25V-10	16262433	37002701	104210730	17	20938										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1263483	1263484	+	Frame_Shift_Del	DEL	AG	AG	-													0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	caaccgaagtgtgagtggacAgagtggtttgacgtggactt							TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr11:1263483_1263484delAG	ENST00000529681.1	+	31	5431_5432	c.5373_5374delAG	c.(5371-5376)acagagfs	p.E1792fs	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Frame_Shift_Del_p.E1795fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1792	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GTGAGTGGACAGAGTGGTTTGA	0.594																																					p.1791_1791del		Atlas-Indel,Pindel	.											.	MUC5B	473	.	0			c.5372_5373del						.																																			SO:0001589	frameshift_variant	727897	exon31			.	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.5373_5374delAG	chr11.hg19:g.1263485_1263486delAG	ENSP00000436812:p.Glu1792fs	290.0	0.0		234.0	42.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.594	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		-	1263484	AG	-	1263483	7	5	125	1	0	1	0	1	0	0	0	0	9988	175	7	0	5504	0	MUC5B	11	1263483	Frame_Shift_Del	DEL	AG	TCGA-DD-A4NB-01A-12D-A25V-10		1263483	133743033	18	20939										
KRAS	3845	hgsc.bcm.edu	37	chr12	25380255	25380255	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	cagtcctcatgtactggtccCtcattgcactgtactcctct	6	15	3	0			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr12:25380255C>A	ENST00000256078.4	-	3	266	c.203G>T	c.(202-204)aGg>aTg	p.R68M	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Missense_Mutation_p.R68M	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	68					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GTACTGGTCCCTCATTGCACT	0.408		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.R68M	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	.	KRAS	30930	.	0			c.G203T						.						119	107	111					12																	25380255		2203	4300	6503	SO:0001583	missense	3845	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TGGTCCCTCATTG	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.203G>T	chr12.hg19:g.25380255C>A	ENSP00000256078:p.Arg68Met	144.0	0.0		151.0	34.0	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	31	5.062554	0.93898	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	T;T	0.80909	-1.43;-0.63	5.77	5.77	0.91146	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.92014	0.7470	M	0.89785	3.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92760	0.6223	10	0.87932	D	0	.	19.3504	0.94381	0.0:1.0:0.0:0.0	.	68;68	P01116-2;P01116	.;RASK_HUMAN	M	68	ENSP00000308495:R68M;ENSP00000256078:R68M	ENSP00000256078:R68M	R	-	2	0	KRAS	25271522	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.805000	0.86005	2.885000	0.99019	0.655000	0.94253	AGG	.	.		0.408	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25380255	C	A	25380255	3	1	125	1	0	0	0	0	1	0	0	0	8447	681	24	3	499	3	KRAS	12	25380255	Missense_Mutation	SNP	C	TCGA-DD-A4NB-01A-12D-A25V-10		25380255	108471640	19	20940										
SYT16	83851	hgsc.bcm.edu	37	chr14	62547559	62547559	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	ctgcctgcaacaggaacaggAcaggaccaatttgcaggtgc	12	11	0	0			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr14:62547559A>G	ENST00000430451.2	+	4	1198	c.1001A>G	c.(1000-1002)gAc>gGc	p.D334G	RP11-355I22.5_ENST00000553990.1_lincRNA|SYT16_ENST00000446982.2_Missense_Mutation_p.T364A	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	334					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		CAGGAACAGGACAGGACCAAT	0.488																																					p.D334G		Atlas-SNP	.											.	SYT16	144	.	0			c.A1001G						.						15	15	15					14																	62547559		1972	4155	6127	SO:0001583	missense	83851	exon4			AACAGGACAGGAC	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1001A>G	chr14.hg19:g.62547559A>G	ENSP00000394700:p.Asp334Gly	214.0	0.0		159.0	39.0	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	hg19	CCDS45121.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.226|8.226	0.803502|0.803502	0.16467|0.16467	.|.	.|.	ENSG00000139973|ENSG00000139973	ENST00000430451|ENST00000446982	T|T	0.04194|0.32272	3.68|1.46	5.27|5.27	2.92|2.92	0.33932|0.33932	.|.	0.721021|.	0.13603|.	N|.	0.375717|.	T|T	0.18841|0.18841	0.0452|0.0452	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.13145	0.0|0.007	B|B	0.01281|0.09377	0.0|0.004	T|T	0.21075|0.21075	-1.0256|-1.0256	10|9	0.46703|0.72032	T|D	0.11|0.01	-26.0138|-26.0138	5.8678|5.8678	0.18786|0.18786	0.7175:0.1393:0.1432:0.0|0.7175:0.1393:0.1432:0.0	.|.	334|364	Q17RD7|B4DZH2	SYT16_HUMAN|.	G|A	334|364	ENSP00000394700:D334G|ENSP00000388023:T364A	ENSP00000394700:D334G|ENSP00000388023:T364A	D|T	+|+	2|1	0|0	SYT16|SYT16	61617312|61617312	0.082000|0.082000	0.21442|0.21442	0.559000|0.559000	0.28332|0.28332	0.277000|0.277000	0.26821|0.26821	1.197000|1.197000	0.32211|0.32211	0.453000|0.453000	0.26858|0.26858	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.		0.488	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		G	62547559	A	G	62547559	3	3	125	1	0	0	0	0	1	0	0	0	15487	275	10	2	1015	2	SYT16	14	62547559	Missense_Mutation	SNP	A	TCGA-DD-A4NB-01A-12D-A25V-10		62547559	44801981	20	20941										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94038399	94038399	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	tcagaacagaagtcccagatAatcagttaaaagaattcagg	8	7	3	4			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr14:94038399A>T	ENST00000393151.2	+	15	1915	c.1915A>T	c.(1915-1917)Aat>Tat	p.N639Y	UNC79_ENST00000555664.1_Missense_Mutation_p.N639Y|UNC79_ENST00000256339.4_Missense_Mutation_p.N462Y|UNC79_ENST00000553484.1_Missense_Mutation_p.N639Y			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	639					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AGTCCCAGATAATCAGTTAAA	0.398																																					p.N462Y		Atlas-SNP	.											.	UNC79	366	.	0			c.A1384T						.						55	57	56					14																	94038399		2203	4300	6503	SO:0001583	missense	57578	exon15			CCAGATAATCAGT	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.1915A>T	chr14.hg19:g.94038399A>T	ENSP00000376858:p.Asn639Tyr	62.0	0.0		42.0	15.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	A	13.02	2.112003	0.37242	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.73	4.56	0.56223	.	0.346019	0.29178	N	0.012905	T	0.09992	0.0245	N	0.08118	0	0.25971	N	0.9825	B	0.28998	0.23	B	0.26864	0.074	T	0.17319	-1.0373	10	0.62326	D	0.03	-6.924	13.1509	0.59488	0.8569:0.1431:0.0:0.0	.	639	C9JQL1	.	Y	462;639;639;639;639	ENSP00000256339:N462Y;ENSP00000450868:N639Y;ENSP00000451360:N639Y;ENSP00000376858:N639Y	ENSP00000256339:N462Y	N	+	1	0	KIAA1409	93108152	1.000000	0.71417	0.273000	0.24645	0.899000	0.52679	3.159000	0.50731	0.956000	0.37904	0.528000	0.53228	AAT	.	.		0.398	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94038399	A	T	94038399	3	4	125	1	0	0	0	0	1	0	0	0	8239	362	13	4	1430	4	KIAA1409	14	94038399	Missense_Mutation	SNP	A	TCGA-DD-A4NB-01A-12D-A25V-10	31490840	94038399	13311141	21	20942										
PIGQ	9091	hgsc.bcm.edu	37	chr16	633549	633549	+	Frame_Shift_Del	DEL	C	C	-													0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	gggattgaagcagtcgctgaCccccgtccccagcgggcccg							TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr16:633549delC	ENST00000026218.5	+	10	2286	c.2198delC	c.(2197-2199)accfs	p.T733fs	PIGQ_ENST00000321878.5_3'UTR	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	733					C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				CAGTCGCTGACCCCCGTCCCC	0.627																																					p.T733fs		Atlas-Indel,Pindel	.											.	PIGQ	43	.	0			c.2197delA						.						38	39	39					16																	633549		2200	4300	6500	SO:0001589	frameshift_variant	9091	exon10			.	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"Phosphatidylinositol glycan anchor biosynthesis"	14135	protein-coding gene	gene with protein product		605754	"phosphatidylinositol glycan, class Q"			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.2198delC	chr16.hg19:g.633549delC	ENSP00000026218:p.Thr733fs	93.0	0.0		112.0	19.0	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Frame_Shift_Del	DEL	ENST00000026218.5	hg19	CCDS10411.1																																																																																			.	.		0.627	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204		-	633549	C	-	633549	7	5	125	1	0	1	0	1	0	0	0	0	11905	507	18	0	2298	0	PIGQ	16	633549	Frame_Shift_Del	DEL	C	TCGA-DD-A4NB-01A-12D-A25V-10		633549	89721204	22	20943										
SNAI3	333929	hgsc.bcm.edu	37	chr16	88747899	88747899	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	tctttgaggggtacaatggcGgcccggctggcccgagggtc	17	11	1	1	rs531621935	byFrequency	TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr16:88747899G>T	ENST00000332281.5	-	2	386	c.300C>A	c.(298-300)gcC>gcA	p.A100A	SNAI3-AS1_ENST00000563261.1_RNA	NM_178310.3	NP_840101.1	Q3KNW1	SNAI3_HUMAN	snail family zinc finger 3	100					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	copper ion binding (GO:0005507)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(1)|kidney(1)|lung(1)|ovary(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(80;0.048)		GTACAATGGCGGCCCGGCTGG	0.687																																					p.A100A	Colon(27;366 710 19748 23199 27567)	Atlas-SNP	.											.	SNAI3	23	.	0			c.C300A						.						57	67	64					16																	88747899		2198	4299	6497	SO:0001819	synonymous_variant	333929	exon2			AATGGCGGCCCGG	BC041461	CCDS32505.1	16q24.3	2013-05-23	2013-05-23			ENSG00000185669		"Snail homologs", "Zinc fingers, C2H2-type"	18411	protein-coding gene	gene with protein product		612741	"zinc finger protein 293", "snail homolog 3 (Drosophila)"	ZNF293		12579345	Standard	NM_178310		Approved	SMUC, Zfp293	uc002flj.3	Q3KNW1		ENST00000332281.5:c.300C>A	chr16.hg19:g.88747899G>T		94.0	0.0		88.0	4.0	NM_178310	Q86SU5	Silent	SNP	ENST00000332281.5	hg19	CCDS32505.1																																																																																			.	.		0.687	SNAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422582.1			T	88747899	G	T	88747899	2	4	125	1	0	0	0	0	0	0	0	1	14843	1103	39	1		1	SNAI3	16	88747899	Silent	SNP	G	TCGA-DD-A4NB-01A-12D-A25V-10	88114350	88747899	1606854	23	20944										
PTPRM	5797	hgsc.bcm.edu	37	chr18	7888162	7888162	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	gggcagagagcccacctgctCttaccccaacttaaagaaaa	8	13	1	2			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr18:7888162C>T	ENST00000332175.8	+	3	1292	c.255C>T	c.(253-255)ctC>ctT	p.L85L	PTPRM_ENST00000400053.4_Silent_p.L23L|PTPRM_ENST00000580170.1_Silent_p.L85L|PTPRM_ENST00000400060.4_Silent_p.L85L	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	85	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CCCACCTGCTCTTACCCCAAC	0.463																																					p.L85L		Atlas-SNP	.											.	PTPRM	185	.	0			c.C255T						.						157	162	161					18																	7888162		2203	4300	6503	SO:0001819	synonymous_variant	5797	exon3			CCTGCTCTTACCC	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.255C>T	chr18.hg19:g.7888162C>T		186.0	0.0		147.0	37.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	hg19	CCDS11840.1																																																																																			.	.		0.463	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	7888162	C	T	7888162	2	4	125	1	0	0	0	0	0	0	0	1	12821	900	32	3		3	PTPRM	18	7888162	Silent	SNP	C	TCGA-DD-A4NB-01A-12D-A25V-10		7888162	70189086	24	20945										
ZNF519	162655	hgsc.bcm.edu	37	chr18	14105585	14105585	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	cattccttacacttgaaaggCttctctccagtatggattct	6	11	2	1			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr18:14105585C>T	ENST00000590202.1	-	3	1106	c.954G>A	c.(952-954)aaG>aaA	p.K318K	ZNF519_ENST00000589498.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589203.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	318					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						ACTTGAAAGGCTTCTCTCCAG	0.393																																					p.K318K		Atlas-SNP	.											ZNF519,NS,carcinoma,0,1	ZNF519	53	.	0			c.G954A						.						82	84	83					18																	14105585		2203	4300	6503	SO:0001819	synonymous_variant	162655	exon3			GAAAGGCTTCTCT	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"Zinc fingers, C2H2-type", "-"	30574	protein-coding gene	gene with protein product	"similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.954G>A	chr18.hg19:g.14105585C>T		64.0	0.0		78.0	4.0	NM_145287		Silent	SNP	ENST00000590202.1	hg19	CCDS32797.1																																																																																			.	.		0.393	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		T	14105585	C	T	14105585	2	4	125	1	0	0	0	0	0	0	0	1	17979	796	28	3		3	ZNF519	18	14105585	Silent	SNP	C	TCGA-DD-A4NB-01A-12D-A25V-10	6217423	14105585	63971663	25	20946										
ZNF426	79088	hgsc.bcm.edu	37	chr19	9643591	9643591	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	gagattagactgggtttgatGatctgacctcctgagcacag	12	8	1	6			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:9643591G>C	ENST00000535489.1	-	4	591	c.255C>G	c.(253-255)atC>atG	p.I85M	ZNF426_ENST00000593003.1_Missense_Mutation_p.I47M|ZNF426_ENST00000589289.1_Missense_Mutation_p.I85M|ZNF426_ENST00000253115.2_Missense_Mutation_p.I85M			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	85	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						TGGGTTTGATGATCTGACCTC	0.408																																					p.I85M		Atlas-SNP	.											ZNF426,colon,carcinoma,0,1	ZNF426	56	.	0			c.C255G						.						130	113	119					19																	9643591		2203	4300	6503	SO:0001583	missense	79088	exon6			TTTGATGATCTGA	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"Zinc fingers, C2H2-type", "-"	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.255C>G	chr19.hg19:g.9643591G>C	ENSP00000439017:p.Ile85Met	96.0	0.0		97.0	21.0	NM_024106	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	hg19	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	G	8.902	0.956519	0.18507	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.00864	5.6;5.6	1.9	-3.81	0.04294	Krueppel-associated box (3);	.	.	.	.	T	0.00695	0.0023	L	0.35487	1.065	0.09310	N	1	B;B	0.24186	0.099;0.099	B;B	0.12837	0.008;0.008	T	0.46707	-0.9172	9	0.36615	T	0.2	.	0.0214	0.00003	0.3038:0.2151:0.1805:0.3005	.	72;85	Q59EH4;Q9BUY5	.;ZN426_HUMAN	M	72;85;85	ENSP00000253115:I85M;ENSP00000439017:I85M	ENSP00000253115:I85M	I	-	3	3	ZNF426	9504591	0.000000	0.05858	0.000000	0.03702	0.917000	0.54804	-4.119000	0.00291	-1.544000	0.01721	0.313000	0.20887	ATC	.	.		0.408	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106		C	9643591	G	C	9643591	3	2	125	1	0	0	0	0	1	0	0	0	17915	1280	45	4	1421	4	ZNF426	19	9643591	Missense_Mutation	SNP	G	TCGA-DD-A4NB-01A-12D-A25V-10		9643591	49485392	26	20947										
ZNF585A	199704	hgsc.bcm.edu	37	chr19	37643714	37643714	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	caactctgacctgtaggtaaAggccttcccacactcagtac	7	14	2	1			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:37643714A>C	ENST00000356958.4	-	5	1345	c.1087T>G	c.(1087-1089)Ttt>Gtt	p.F363V	ZNF585A_ENST00000392157.2_Missense_Mutation_p.F308V|ZNF585A_ENST00000292841.5_Missense_Mutation_p.F308V|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000355533.2_Missense_Mutation_p.F308V			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	363					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTGTAGGTAAAGGCCTTCCCA	0.418																																					p.F308V		Atlas-SNP	.											.	ZNF585A	117	.	0			c.T922G						.						91	90	90					19																	37643714		2203	4298	6501	SO:0001583	missense	199704	exon6			AGGTAAAGGCCTT	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.1087T>G	chr19.hg19:g.37643714A>C	ENSP00000349440:p.Phe363Val	180.0	0.0		207.0	45.0	NM_199126	Q8TE95|Q96MV3	Missense_Mutation	SNP	ENST00000356958.4	hg19		.	.	.	.	.	.	.	.	.	.	A	13.85	2.358830	0.41801	.	.	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157;ENST00000355533	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	2.83	2.83	0.33086	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38326	N	0.001726	T	0.66177	0.2763	M	0.90309	3.105	0.40621	D	0.981766	D	0.71674	0.998	D	0.79784	0.993	T	0.71928	-0.4444	10	0.87932	D	0	.	9.0963	0.36640	1.0:0.0:0.0:0.0	.	363	Q6P3V2	Z585A_HUMAN	V	363;308;308;308	ENSP00000349440:F363V;ENSP00000292841:F308V;ENSP00000375998:F308V;ENSP00000347724:F308V	ENSP00000292841:F308V	F	-	1	0	ZNF585A	42335554	1.000000	0.71417	0.995000	0.50966	0.266000	0.26442	8.306000	0.89962	1.295000	0.44724	0.459000	0.35465	TTT	.	.		0.418	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		C	37643714	A	C	37643714	3	2	125	1	0	0	0	0	1	0	0	0	18032	72	3	5	1226	5	ZNF585A	19	37643714	Missense_Mutation	SNP	A	TCGA-DD-A4NB-01A-12D-A25V-10	28000123	37643714	21485269	27	20948										
MAP3K10	4294	hgsc.bcm.edu	37	chr19	40698304	40698304	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	ctgtggcgtggcgaggaggtGgcagtcaaggccgcccggct	19	11	1	0			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:40698304G>A	ENST00000253055.3	+	1	654	c.366G>A	c.(364-366)gtG>gtA	p.V122V	MAP3K10_ENST00000593906.1_3'UTR	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	122	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GCGAGGAGGTGGCAGTCAAGG	0.667																																					p.V122V		Atlas-SNP	.											.	MAP3K10	70	.	0			c.G366A						.						32	38	36					19																	40698304		2203	4299	6502	SO:0001819	synonymous_variant	4294	exon1			GGAGGTGGCAGTC	X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6849	protein-coding gene	gene with protein product	"MKN28 kinase", "mixed lineage kinase 2", "MKN28 derived nonreceptor_type serine/threonine kinase"	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.366G>A	chr19.hg19:g.40698304G>A		38.0	0.0		31.0	14.0	NM_002446	Q12761|Q14871	Silent	SNP	ENST00000253055.3	hg19	CCDS12549.1																																																																																			.	.		0.667	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446		A	40698304	G	A	40698304	2	1	125	1	0	0	0	0	0	0	0	1	9253	1335	47	3		3	MAP3K10	19	40698304	Silent	SNP	G	TCGA-DD-A4NB-01A-12D-A25V-10	3054590	40698304	18430679	28	20949										
HRC	3270	hgsc.bcm.edu	37	chr19	49657886	49657886	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	ccatactcagtggaggcctcCtcttcctcctcctcctcctc	5	20	2	0			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:49657886C>T	ENST00000252825.4	-	1	795	c.609G>A	c.(607-609)gaG>gaA	p.E203E	HRC_ENST00000595625.1_Silent_p.E203E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	203	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		TGGAGGcctcctcttcctcct	0.572																																					p.E203E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G609A						.						123	91	102					19																	49657886		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			GGCCTCCTCTTCC		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.609G>A	chr19.hg19:g.49657886C>T		294.0	0.0		353.0	19.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.572	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		T	49657886	C	T	49657886	2	4	125	1	0	0	0	0	0	0	0	1	7361	680	24	3		3	HRC	19	49657886	Silent	SNP	C	TCGA-DD-A4NB-01A-12D-A25V-10	8959582	49657886	9471097	29	20950			1	21		3	2	38	N	T_C	4.063651e-05
HRC	3270	hgsc.bcm.edu	37	chr19	49657916	49657916	+	Silent	SNP	T	T	C													0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	tcctcctcctcctcctcctcTtctccttcatcatcttcccc					rs7409255		TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:49657916T>C	ENST00000252825.4	-	1	765	c.579A>G	c.(577-579)gaA>gaG	p.E193E	HRC_ENST00000595625.1_Silent_p.E193E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	193	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cctcctcctcttcTCCTTCAT	0.557																																					p.E193E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A579G						.						119	95	103					19																	49657916		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCTCCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.579A>G	chr19.hg19:g.49657916T>C		284.0	0.0		287.0	43.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.557	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657916	T	C	49657916	2	2	125	1	0	0	0	0	0	0	0	1	7361	1606	56	2		2	HRC	19	49657916	Silent	SNP	T	TCGA-DD-A4NB-01A-12D-A25V-10	30	49657916	9471067	30	20951	89	2	1	21		3	2	38	N	T_C	4.063651e-05
HRC	3270	hgsc.bcm.edu	37	chr19	49657923	49657923	+	Missense_Mutation	SNP	T	T	C													0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	cctcctcctcctcttctcctTcatcatcttccccatcatgg							TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:49657923T>C	ENST00000252825.4	-	1	758	c.572A>G	c.(571-573)gAa>gGa	p.E191G	HRC_ENST00000595625.1_Missense_Mutation_p.E191G	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	191	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		ctcttcTCCTTCATCATCTTC	0.562																																					p.E191G	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A572G						.						125	99	108					19																	49657923		2203	4300	6503	SO:0001583	missense	3270	exon1			TCTCCTTCATCAT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.572A>G	chr19.hg19:g.49657923T>C	ENSP00000252825:p.Glu191Gly	289.0	0.0		273.0	17.0	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	hg19	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	t	12.02	1.813186	0.32053	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.07327	3.2	2.91	1.86	0.25419	.	.	.	.	.	T	0.07728	0.0194	L	0.58428	1.81	0.18873	N	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.41770	-0.9490	9	0.22109	T	0.4	-0.1912	2.7058	0.05162	0.2254:0.1385:0.0:0.6361	.	191	P23327	SRCH_HUMAN	G	191;161	ENSP00000252825:E191G	ENSP00000252825:E191G	E	-	2	0	HRC	54349735	0.229000	0.23729	0.215000	0.23724	0.196000	0.23810	0.207000	0.17395	0.305000	0.22832	0.375000	0.23000	GAA	.	.		0.562	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657923	T	C	49657923	3	2	125	1	0	0	0	0	1	0	0	0	7361	1783	62	2	1551	2	HRC	19	49657923	Missense_Mutation	SNP	T	TCGA-DD-A4NB-01A-12D-A25V-10	7	49657923	9471060	31	20952	89	2	1	21		3	2	38	N	T_C	4.063651e-05
ZNF841	284371	hgsc.bcm.edu	37	chr19	52569235	52569235	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	taggcatgagtagtaactgaAgaccttgccgcattcgttac	10	9	0	3			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:52569235A>T	ENST00000426391.2	-	5	2103	c.1552T>A	c.(1552-1554)Ttc>Atc	p.F518I	ZNF841_ENST00000594295.1_Missense_Mutation_p.F634I|ZNF841_ENST00000359973.2_Intron|ZNF841_ENST00000389534.4_Missense_Mutation_p.F634I|CTC-471J1.2_ENST00000569091.1_RNA|ZNF432_ENST00000598446.1_Intron			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	518					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						TAGTAACTGAAGACCTTGCCG	0.438																																					p.F634I		Atlas-SNP	.											.	ZNF841	183	.	0			c.T1900A						.						121	104	109					19																	52569235		692	1591	2283	SO:0001583	missense	284371	exon7			AACTGAAGACCTT	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"Zinc fingers, C2H2-type", "-"	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.1552T>A	chr19.hg19:g.52569235A>T	ENSP00000415453:p.Phe518Ile	199.0	0.0		220.0	20.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	hg19		.	.	.	.	.	.	.	.	.	.	A	24.0	4.487668	0.84854	.	.	ENSG00000197608	ENST00000389534;ENST00000426391	T;T	0.47528	0.84;0.84	1.75	1.75	0.24633	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.71074	0.3297	M	0.93854	3.465	0.80722	D	1	D;D	0.71674	0.961;0.998	D;D	0.70935	0.958;0.971	T	0.74012	-0.3801	9	0.87932	D	0	.	8.2942	0.31976	1.0:0.0:0.0:0.0	.	634;518	Q6ZN19-3;Q6ZN19	.;ZN841_HUMAN	I	634;518	ENSP00000374185:F634I;ENSP00000415453:F518I	ENSP00000374185:F634I	F	-	1	0	ZNF841	57261047	0.350000	0.24878	0.001000	0.08648	0.819000	0.46315	4.733000	0.62036	0.795000	0.33922	0.260000	0.18958	TTC	.	.		0.438	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		T	52569235	A	T	52569235	3	4	125	1	0	0	0	0	1	0	0	0	18204	72	3	4	878	4	ZNF841	19	52569235	Missense_Mutation	SNP	A	TCGA-DD-A4NB-01A-12D-A25V-10	2911312	52569235	6559748	32	20953										
ZNF83	55769	hgsc.bcm.edu	37	chr19	53117500	53117500	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	atttgatgtatagtaaaatgTaagccttgatgaaaggcctt	9	4	0	3			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:53117500T>C	ENST00000597597.1	-	2	2571	c.318A>G	c.(316-318)ttA>ttG	p.L106L	ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Silent_p.L106L|ZNF83_ENST00000544146.1_Silent_p.L106L|ZNF83_ENST00000391789.4_Silent_p.L106L|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_Silent_p.L106L|ZNF83_ENST00000545872.1_Silent_p.L106L|ZNF83_ENST00000301096.3_Silent_p.L106L			P51522	ZNF83_HUMAN	zinc finger protein 83	106					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		TAGTAAAATGTAAGCCTTGAT	0.333																																					p.L106L		Atlas-SNP	.											.	ZNF83	73	.	0			c.A318G						.						70	70	70					19																	53117500		2203	4300	6503	SO:0001819	synonymous_variant	55769	exon3			AAAATGTAAGCCT	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"Zinc fingers, C2H2-type"	13158	protein-coding gene	gene with protein product		194558	"zinc finger protein 83 (HPF1)", "zinc finger protein 816B"	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.318A>G	chr19.hg19:g.53117500T>C		219.0	0.0		232.0	31.0	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Silent	SNP	ENST00000597597.1	hg19	CCDS12854.1																																																																																			.	.		0.333	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300		C	53117500	T	C	53117500	2	2	125	1	0	0	0	0	0	0	0	1	18198	1635	57	2		2	ZNF83	19	53117500	Silent	SNP	T	TCGA-DD-A4NB-01A-12D-A25V-10	548265	53117500	6011483	33	20954										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34017978	34017978	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	gaaggcggaggaggtctctgTgggggagccgggcgtgtggg	24	6	1	0	rs368850131	byFrequency	TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr21:34017978T>C	ENST00000322229.7	-	24	3368	c.3369A>G	c.(3367-3369)ccA>ccG	p.P1123P	SYNJ1_ENST00000357345.3_Silent_p.P1123P|SYNJ1_ENST00000382491.3_Silent_p.P1118P|SYNJ1_ENST00000382499.2_Silent_p.P1162P|SYNJ1_ENST00000433931.2_Silent_p.P1162P			O43426	SYNJ1_HUMAN	synaptojanin 1	1123	Pro-rich.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						GAGGTCTCTGTGGGGGAGCCG	0.577													T|||	6	0.00119808	8e-04	0.0014	5008	,	,		11289	0		0.004	False		,,,				2504	0				p.P1162P		Atlas-SNP	.											.	SYNJ1	253	.	0			c.A3486G						.	T	,,,	3,4355		0,3,2176	6	8	7		3369,3354,3486,3486	-2.6	1	21		7	22,8474		0,22,4226	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYNJ1	NM_001160302.1,NM_001160306.1,NM_003895.3,NM_203446.2	,,,	0,25,6402	CC,CT,TT		0.2589,0.0688,0.1945	,,,	1123/1296,1118/1527,1162/1613,1162/1351	34017978	25,12829	2179	4248	6427	SO:0001819	synonymous_variant	8867	exon25			TCTCTGTGGGGGA	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.3369A>G	chr21.hg19:g.34017978T>C		4.0	0.0		10.0	7.0	NM_203446	O43425|O94984|Q4KMR1	Silent	SNP	ENST00000322229.7	hg19	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.441088	0.25900	6.88E-4	0.002589	ENSG00000159082	ENST00000438952;ENST00000416083	.	.	.	5.55	-2.63	0.06133	.	.	.	.	.	T	0.49406	0.1555	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41928	-0.9481	4	.	.	.	.	5.8028	0.18424	0.0:0.2566:0.233:0.5104	.	.	.	.	A	15;18	.	.	T	-	1	0	SYNJ1	32939849	0.974000	0.33945	0.979000	0.43373	0.816000	0.46133	-0.063000	0.11655	-0.461000	0.06993	-0.441000	0.05720	ACA	.	.		0.577	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				C	34017978	T	C	34017978	2	2	125	1	0	0	0	0	0	0	0	1	15467	1683	59	2		2	SYNJ1	21	34017978	Silent	SNP	T	TCGA-DD-A4NB-01A-12D-A25V-10		34017978	14111917	34	20955										
TMPRSS2	7113	hgsc.bcm.edu	37	chr21	42851169	42851169	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	3	1	1.8	7.2	1.30909090909091	1	1	0	tttcataaagctggtggatcCgctgtcatccactattcctt	7	11	2	0			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr21:42851169C>T	ENST00000332149.5	-	7	747	c.613G>A	c.(613-615)Gga>Aga	p.G205R	TMPRSS2_ENST00000398585.3_Missense_Mutation_p.G242R|TMPRSS2_ENST00000458356.1_Missense_Mutation_p.G205R	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	205	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)		TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				CTGGTGGATCCGCTGTCATCC	0.348			T	"ERG, ETV1, ETV4, ETV5"	prostate																																p.G242R		Atlas-SNP	.		Dom	yes		21	21q22.3	7113	"transmembrane protease, serine 2"		E	.	TMPRSS2	148	.	0			c.G724A						.						138	138	138					21																	42851169		2203	4300	6503	SO:0001583	missense	7113	exon7			TGGATCCGCTGTC	U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"Serine peptidases / Transmembrane"	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.613G>A	chr21.hg19:g.42851169C>T	ENSP00000330330:p.Gly205Arg	82.0	0.0		90.0	4.0	NM_001135099	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Missense_Mutation	SNP	ENST00000332149.5	hg19	CCDS33564.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.327559	0.24080	.	.	ENSG00000184012	ENST00000332149;ENST00000398585;ENST00000458356;ENST00000454499;ENST00000424093	T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03	5.43	5.43	0.79202	Speract/scavenger receptor (1);Speract/scavenger receptor-related (2);	0.264721	0.30979	N	0.008486	T	0.75280	0.3828	M	0.74881	2.28	0.09310	N	0.999998	D;D	0.76494	0.999;0.999	P;D	0.65010	0.906;0.931	T	0.67473	-0.5662	10	0.21540	T	0.41	.	14.7197	0.69297	0.0:1.0:0.0:0.0	.	242;205	F8WES1;O15393	.;TMPS2_HUMAN	R	205;242;205;205;165	ENSP00000330330:G205R;ENSP00000381588:G242R;ENSP00000391216:G205R;ENSP00000389006:G205R;ENSP00000397846:G165R	ENSP00000330330:G205R	G	-	1	0	TMPRSS2	41773039	0.000000	0.05858	0.214000	0.23707	0.001000	0.01503	0.744000	0.26245	2.553000	0.86117	0.549000	0.68633	GGA	.	.		0.348	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1			T	42851169	C	T	42851169	3	4	125	1	0	0	0	0	1	0	0	0	16262	661	23	1	897	1	TMPRSS2	21	42851169	Missense_Mutation	SNP	C	TCGA-DD-A4NB-01A-12D-A25V-10	8833191	42851169	5278726	35	20956										
NASP	4678	hgsc.bcm.edu	37	chr1	46073649	46073649	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cagaggctgcagaggcctcaGctgtagaggctggatcagaa	15	9	2	4			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr1:46073649G>T	ENST00000350030.3	+	6	1153	c.1066G>T	c.(1066-1068)Gct>Tct	p.A356S	NASP_ENST00000351223.3_Intron|NASP_ENST00000537798.1_Missense_Mutation_p.A292S|NASP_ENST00000372052.4_Intron|NASP_ENST00000402363.3_Missense_Mutation_p.A358S	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	356	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					AGAGGCCTCAGCTGTAGAGGC	0.532																																					p.A356S		Atlas-SNP	.											.	NASP	77	.	0			c.G1066T						.						80	89	86					1																	46073649		2203	4300	6503	SO:0001583	missense	4678	exon6			GCCTCAGCTGTAG	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"Tetratricopeptide (TTC) repeat domain containing"	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.1066G>T	chr1.hg19:g.46073649G>T	ENSP00000255120:p.Ala356Ser	339.0	0.0		339.0	57.0	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Missense_Mutation	SNP	ENST00000350030.3	hg19	CCDS524.1	.	.	.	.	.	.	.	.	.	.	G	9.209	1.030338	0.19512	.	.	ENSG00000132780	ENST00000537798;ENST00000402363;ENST00000341288;ENST00000350030	D;D;D	0.94576	-3.46;-3.46;-3.46	4.93	2.92	0.33932	.	0.737124	0.11710	N	0.537043	D	0.87265	0.6134	N	0.19112	0.55	0.09310	N	1	B;B;P;B;B	0.37061	0.16;0.437;0.58;0.099;0.253	B;B;B;B;B	0.35114	0.088;0.081;0.196;0.04;0.088	T	0.78375	-0.2228	9	.	.	.	-0.8291	7.0467	0.25050	0.1626:0.1426:0.6948:0.0	.	292;356;256;356;358	F5H3J2;Q53H03;B4DS57;P49321;P49321-3	.;.;.;NASP_HUMAN;.	S	292;358;256;356	ENSP00000438871:A292S;ENSP00000384529:A358S;ENSP00000255120:A356S	.	A	+	1	0	NASP	45846236	0.001000	0.12720	0.088000	0.20740	0.385000	0.30292	0.912000	0.28597	1.219000	0.43474	0.508000	0.49915	GCT	.	.		0.532	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		T	46073649	G	T	46073649	3	4	126	1	0	0	0	0	1	0	0	0	10181	971	34	3	1165	3	NASP	1	46073649	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10		46073649	203176972	1	20957										
FOXD2	2306	hgsc.bcm.edu	37	chr1	47904363	47904363	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tctctctcaacgactgcttcGtcaagatcccccgcgagccg	8	17	3	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr1:47904363G>C	ENST00000334793.5	+	1	2675	c.556G>C	c.(556-558)Gtc>Ctc	p.V186L		NM_004474.3	NP_004465.3	O60548	FOXD2_HUMAN	forkhead box D2	186					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(4)	4				READ - Rectum adenocarcinoma(2;0.0908)		CGACTGCTTCGTCAAGATCCC	0.642																																					p.V186L		Atlas-SNP	.											.	FOXD2	16	.	0			c.G556C						.						69	84	79					1																	47904363		2203	4300	6503	SO:0001583	missense	2306	exon1			TGCTTCGTCAAGA	AF042832	CCDS30708.1	1p34-p32	2008-02-05			ENSG00000186564	ENSG00000186564		"Forkhead boxes"	3803	protein-coding gene	gene with protein product		602211		FKHL17		9403061, 12621056	Standard	NM_004474		Approved	FREAC9	uc001crm.3	O60548	OTTHUMG00000007950	ENST00000334793.5:c.556G>C	chr1.hg19:g.47904363G>C	ENSP00000335493:p.Val186Leu	191.0	0.0		268.0	45.0	NM_004474	Q5SVZ3	Missense_Mutation	SNP	ENST00000334793.5	hg19	CCDS30708.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248075	0.80024	.	.	ENSG00000186564	ENST00000334793	D	0.95656	-3.77	4.2	4.2	0.49525	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.063541	0.64402	U	0.000008	D	0.96929	0.8997	M	0.81497	2.545	0.80722	D	1	P	0.38582	0.638	P	0.52217	0.693	D	0.97614	1.0131	10	0.59425	D	0.04	.	15.3129	0.74048	0.0:0.0:1.0:0.0	.	186	O60548	FOXD2_HUMAN	L	186	ENSP00000335493:V186L	ENSP00000335493:V186L	V	+	1	0	FOXD2	47676950	1.000000	0.71417	1.000000	0.80357	0.711000	0.40976	9.101000	0.94219	1.866000	0.54105	0.436000	0.28706	GTC	.	.		0.642	FOXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021831.1	NM_004474		C	47904363	G	C	47904363	3	2	126	1	0	0	0	0	1	0	0	0	6005	1145	40	4	558	4	FOXD2	1	47904363	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	1830714	47904363	201346258	2	20958										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109794691	109794691	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ccatcaccagccaaagtggtGgtgggctggtatcccttgcc	12	13	1	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr1:109794691G>A	ENST00000271332.3	+	1	2051	c.1990G>A	c.(1990-1992)Ggt>Agt	p.G664S		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	664	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CCAAAGTGGTGGTGGGCTGGT	0.567																																					p.G664S	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.G1990A						.						131	124	127					1																	109794691		2203	4300	6503	SO:0001583	missense	1952	exon1			AGTGGTGGTGGGC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.1990G>A	chr1.hg19:g.109794691G>A	ENSP00000271332:p.Gly664Ser	374.0	0.0		322.0	63.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	N	11.12	1.545429	0.27652	.	.	ENSG00000143126	ENST00000271332	T	0.04317	3.65	4.95	4.95	0.65309	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.02533	0.0077	N	0.01874	-0.695	0.58432	D	0.999998	D	0.65815	0.995	D	0.67382	0.951	T	0.61691	-0.7011	9	0.09084	T	0.74	.	18.4313	0.90627	0.0:0.0:1.0:0.0	.	664	Q9HCU4	CELR2_HUMAN	S	664	ENSP00000271332:G664S	ENSP00000271332:G664S	G	+	1	0	CELSR2	109596214	1.000000	0.71417	0.842000	0.33263	0.992000	0.81027	7.393000	0.79851	2.600000	0.87896	0.650000	0.86243	GGT	.	.		0.567	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		A	109794691	G	A	109794691	3	1	126	1	0	0	0	0	1	0	0	0	3224	1348	47	3	1992	3	CELSR2	1	109794691	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	61890328	109794691	139455930	3	20959										
SEMA4A	64218	hgsc.bcm.edu	37	chr1	156146462	156146462	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tggccctggatcctgaactgGcaggcatcccccgggagcat	13	14	0	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr1:156146462G>C	ENST00000368285.3	+	15	2227	c.1960G>C	c.(1960-1962)Gca>Cca	p.A654P	SEMA4A_ENST00000368284.1_Missense_Mutation_p.A522P|SEMA4A_ENST00000355014.2_Missense_Mutation_p.A654P|SEMA4A_ENST00000368286.2_Missense_Mutation_p.A522P|SEMA4A_ENST00000368282.1_Missense_Mutation_p.A654P	NM_001193300.1|NM_022367.3	NP_001180229.1|NP_071762.2	Q9H3S1	SEM4A_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	654					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|regulation of cell shape (GO:0008360)|regulation of endothelial cell migration (GO:0010594)|semaphorin-plexin signaling pathway (GO:0071526)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|ovary(2)|skin(2)	5	Hepatocellular(266;0.158)					TCCTGAACTGGCAGGCATCCC	0.612																																					p.A654P		Atlas-SNP	.											.	SEMA4A	75	.	0			c.G1960C						.						72	73	73					1																	156146462		2203	4300	6503	SO:0001583	missense	64218	exon15			GAACTGGCAGGCA	AK022416	CCDS1132.1, CCDS53378.1	1q22	2014-01-28			ENSG00000196189	ENSG00000196189		"Semaphorins"	10729	protein-coding gene	gene with protein product		607292		SEMAB		7748561	Standard	NM_022367		Approved	SemB, FLJ12287, CORD10	uc009wrq.3	Q9H3S1	OTTHUMG00000014042	ENST00000368285.3:c.1960G>C	chr1.hg19:g.156146462G>C	ENSP00000357268:p.Ala654Pro	151.0	0.0		143.0	34.0	NM_001193300	B2RDH8|B3KR76|Q5TCI5|Q5TCJ6|Q8WUA9	Missense_Mutation	SNP	ENST00000368285.3	hg19	CCDS1132.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.112164	0.56398	.	.	ENSG00000196189	ENST00000355014;ENST00000368285;ENST00000368284;ENST00000368283;ENST00000544376;ENST00000368286;ENST00000368282	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.01	4.06	0.47325	.	0.583196	0.16753	N	0.200945	T	0.25158	0.0611	M	0.65975	2.015	0.34490	D	0.704919	P;P	0.48998	0.863;0.918	P;P	0.44477	0.451;0.451	T	0.08269	-1.0730	10	0.23302	T	0.38	.	8.0996	0.30848	0.1216:0.0:0.8784:0.0	.	522;654	Q5TCJ6;Q9H3S1	.;SEM4A_HUMAN	P	654;654;522;616;616;522;654	ENSP00000347117:A654P;ENSP00000357268:A654P;ENSP00000357267:A522P;ENSP00000357269:A522P;ENSP00000357265:A654P	ENSP00000347117:A654P	A	+	1	0	SEMA4A	154413086	0.305000	0.24481	0.937000	0.37676	0.688000	0.40055	3.500000	0.53318	1.032000	0.39892	0.313000	0.20887	GCA	.	.		0.612	SEMA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039484.2	NM_022367		C	156146462	G	C	156146462	3	2	126	1	0	0	0	0	1	0	0	0	14046	1203	42	4	2014	4	SEMA4A	1	156146462	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	46351771	156146462	93104159	4	20960										
ARHGAP25	9938	hgsc.bcm.edu	37	chr2	69049534	69049534	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	agcgatgcgtttccggaggaCagcagcaaagtacccaggga	14	10	0	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr2:69049534C>T	ENST00000295381.3	+	10	1679	c.1260C>T	c.(1258-1260)gaC>gaT	p.D420D	ARHGAP25_ENST00000409202.3_Silent_p.D421D|ARHGAP25_ENST00000409220.1_Silent_p.D414D|ARHGAP25_ENST00000409030.3_Silent_p.D413D|ARHGAP25_ENST00000479844.1_Silent_p.D114D|ARHGAP25_ENST00000467265.1_Silent_p.D381D	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	420					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						TTCCGGAGGACAGCAGCAAAG	0.498																																					p.D421D		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.C1263T						.						103	109	107					2																	69049534		2203	4300	6503	SO:0001819	synonymous_variant	9938	exon10			GGAGGACAGCAGC	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1260C>T	chr2.hg19:g.69049534C>T		104.0	0.0		108.0	9.0	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Silent	SNP	ENST00000295381.3	hg19		.	.	.	.	.	.	.	.	.	.	C	9.663	1.144592	0.21288	.	.	ENSG00000163219	ENST00000497259	.	.	.	5.17	-9.02	0.00741	.	.	.	.	.	T	0.17152	0.0412	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.20739	-1.0266	4	.	.	.	.	4.1065	0.10038	0.0785:0.2033:0.3431:0.3751	.	.	.	.	I	280	.	.	T	+	2	0	ARHGAP25	68903038	0.000000	0.05858	0.000000	0.03702	0.479000	0.33129	-1.819000	0.01716	-1.394000	0.02077	0.557000	0.71058	ACA	.	.		0.498	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882		T	69049534	C	T	69049534	2	4	126	1	0	0	0	0	0	0	0	1	874	477	17	3		3	ARHGAP25	2	69049534	Silent	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10		69049534	174149839	5	20961										
NEB	4703	hgsc.bcm.edu	37	chr2	152506778	152506778	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tgtttctgtctggaggctgaCgatatttcttctcactgatg	10	8	4	2	rs373589529		TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr2:152506778C>T	ENST00000172853.10	-	54	7490	c.7343G>A	c.(7342-7344)cGt>cAt	p.R2448H	NEB_ENST00000409198.1_Missense_Mutation_p.R2448H|NEB_ENST00000397345.3_Missense_Mutation_p.R2448H|NEB_ENST00000603639.1_Missense_Mutation_p.R2448H|NEB_ENST00000604864.1_Missense_Mutation_p.R2448H|NEB_ENST00000427231.2_Missense_Mutation_p.R2448H			P20929	NEBU_HUMAN	nebulin	2448					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGGAGGCTGACGATATTTCTT	0.463																																					p.R2448H		Atlas-SNP	.											NEB_ENST00000427231,rectum,carcinoma,0,3	NEB	1697	.	0			c.G7343A						.	C	HIS/ARG,HIS/ARG,HIS/ARG	1,3839		0,1,1919	159	150	153		7343,7343,7343	5.2	1	2		153	0,8262		0,0,4131	no	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	29,29,29	0,1,6050	TT,TC,CC		0.0,0.026,0.0083	probably-damaging,probably-damaging,probably-damaging	2448/8526,2448/8526,2448/6670	152506778	1,12101	1920	4131	6051	SO:0001583	missense	4703	exon54			GGCTGACGATATT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.7343G>A	chr2.hg19:g.152506778C>T	ENSP00000172853:p.Arg2448His	255.0	1.0		215.0	31.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.255863	0.95336	2.6E-4	0.0	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.09538	3.0;3.0;3.0;2.97	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.38931	0.1059	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.30822	-0.9965	10	0.59425	D	0.04	.	18.7871	0.91960	0.0:1.0:0.0:0.0	.	2448	P20929	NEBU_HUMAN	H	2448	ENSP00000386259:R2448H;ENSP00000380505:R2448H;ENSP00000416578:R2448H;ENSP00000172853:R2448H	ENSP00000172853:R2448H	R	-	2	0	NEB	152215024	1.000000	0.71417	0.980000	0.43619	0.989000	0.77384	7.770000	0.85390	2.456000	0.83038	0.650000	0.86243	CGT	.	.		0.463	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152506778	C	T	152506778	3	4	126	1	0	0	0	0	1	0	0	0	10311	536	19	1	18859	1	NEB	2	152506778	Missense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	83457244	152506778	90692595	6	20962										
G6PC2	57818	hgsc.bcm.edu	37	chr2	169757874	169757874	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cacaggaatggagtgctcatAattcagcatttgcagaagga	11	7	2	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr2:169757874A>C	ENST00000375363.3	+	1	125	c.33A>C	c.(31-33)atA>atC	p.I11I	SPC25_ENST00000472216.2_Intron|G6PC2_ENST00000421979.1_Silent_p.I11I|G6PC2_ENST00000429379.2_Silent_p.I11I	NM_021176.2	NP_066999.1	Q9NQR9	G6PC2_HUMAN	glucose-6-phosphatase, catalytic, 2	11					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)			breast(1)|endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	13						GAGTGCTCATAATTCAGCATT	0.383																																					p.I11I		Atlas-SNP	.											.	G6PC2	44	.	0			c.A33C						.						122	120	121					2																	169757874		2203	4300	6503	SO:0001819	synonymous_variant	57818	exon1			GCTCATAATTCAG	AF283575	CCDS2230.1, CCDS46443.1	2q24-q31	2008-02-05			ENSG00000152254	ENSG00000152254			28906	protein-coding gene	gene with protein product	"islet specific glucose 6 phosphatase catalytic subunit related protein"	608058				10078553, 10078554	Standard	NM_021176		Approved	IGRP	uc002uem.3	Q9NQR9	OTTHUMG00000132182	ENST00000375363.3:c.33A>C	chr2.hg19:g.169757874A>C		80.0	0.0		94.0	21.0	NM_021176	E9PAX2|Q6AHZ0	Silent	SNP	ENST00000375363.3	hg19	CCDS2230.1																																																																																			.	.		0.383	G6PC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255234.2	NM_021176		C	169757874	A	C	169757874	2	2	126	1	0	0	0	0	0	0	0	1	6152	352	13	5		5	G6PC2	2	169757874	Silent	SNP	A	TCGA-DD-A4ND-01A-11D-A25V-10	17251096	169757874	73441499	7	20963										
CHST13	166012	hgsc.bcm.edu	37	chr3	126255177	126255182	+	In_Frame_Del	DEL	AGCTCT	AGCTCT	-													0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	gaagagaagccccctgcagaAgctctatgacctggatcagg					rs562208555	byFrequency	TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	AGCTCT	AGCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr3:126255177_126255182delAGCTCT	ENST00000319340.2	+	2	211_216	c.161_166delAGCTCT	c.(160-168)aagctctat>aat	p.54_56KLY>N		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	54					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			central_nervous_system(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(114;0.151)		CCCCTGCAGAAGCTCTATGACCTGGA	0.592																																					p.54_55del		Atlas-Indel,Pindel	.											.	CHST13	21	.	0			c.160_165del						.																																			SO:0001651	inframe_deletion	166012	exon2			.	AY120869	CCDS3039.1	3q21.3	2008-02-05			ENSG00000180767	ENSG00000180767	2.8.2.5	"Sulfotransferases, membrane-bound"	21755	protein-coding gene	gene with protein product		610124				12080076	Standard	NM_152889		Approved	C4ST3	uc003eja.3	Q8NET6	OTTHUMG00000162721	ENST00000319340.2:c.161_166delAGCTCT	chr3.hg19:g.126255177_126255182delAGCTCT	ENSP00000317404:p.Lys54_Tyr56delinsAsn	158.0	0.0		159.0	17.0	NM_152889	Q3SYA3|Q3SYA5	In_Frame_Del	DEL	ENST00000319340.2	hg19	CCDS3039.1																																																																																			.	.		0.592	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889		-	126255182	AGCTCT	-	126255177	7	5	126	1	0	1	0	1	0	0	0	0	3403	72	3	0	167	0	CHST13	3	126255177	In_Frame_Del	DEL	AGCTCT	TCGA-DD-A4ND-01A-11D-A25V-10		126255177	71767253	8	20964										
TRPC1	7220	hgsc.bcm.edu	37	chr3	142499740	142499740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	aggatttacttgcacaagccCggaattctcgtgaattggaa	10	8	1	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr3:142499740C>T	ENST00000476941.1	+	6	1315	c.829C>T	c.(829-831)Cgg>Tgg	p.R277W	TRPC1_ENST00000273482.6_Missense_Mutation_p.R243W	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	277					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						TGCACAAGCCCGGAATTCTCG	0.383																																					p.R277W		Atlas-SNP	.											TRPC1,NS,carcinoma,-1,1	TRPC1	82	.	0			c.C829T						.						91	89	90					3																	142499740		2203	4300	6503	SO:0001583	missense	7220	exon6			CAAGCCCGGAATT	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"Voltage-gated ion channels / Transient receptor potential cation channels"	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.829C>T	chr3.hg19:g.142499740C>T	ENSP00000419313:p.Arg277Trp	106.0	0.0		83.0	4.0	NM_001251845	Q14CE4	Missense_Mutation	SNP	ENST00000476941.1	hg19	CCDS58856.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689611	0.88735	.	.	ENSG00000144935	ENST00000476941;ENST00000273482	T;T	0.63913	-0.07;-0.07	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.76941	0.4058	M	0.64567	1.98	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.74023	0.982;0.947	T	0.78275	-0.2267	10	0.87932	D	0	-19.4836	16.338	0.83073	0.1324:0.8676:0.0:0.0	.	277;243	P48995;P48995-2	TRPC1_HUMAN;.	W	277;243	ENSP00000419313:R277W;ENSP00000273482:R243W	ENSP00000273482:R243W	R	+	1	2	TRPC1	143982430	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	5.768000	0.68858	2.733000	0.93635	0.655000	0.94253	CGG	.	.		0.383	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304		T	142499740	C	T	142499740	3	4	126	1	0	0	0	0	1	0	0	0	16593	643	23	1	745	1	TRPC1	3	142499740	Missense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	16244563	142499740	55522690	9	20965										
GPR171	29909	hgsc.bcm.edu	37	chr3	150916346	150916346	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ataggatcaaagcacaggttCgacacagccaggagcagtgt	12	9	1	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr3:150916346C>A	ENST00000309180.5	-	3	1058	c.828G>T	c.(826-828)tcG>tcT	p.S276S	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_013308.3	NP_037440.3	O14626	GP171_HUMAN	G protein-coupled receptor 171	276					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(4)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	15			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGCACAGGTTCGACACAGCCA	0.478																																					p.S276S		Atlas-SNP	.											GPR171,NS,carcinoma,0,1	GPR171	36	.	0			c.G828T						.						87	86	87					3																	150916346		2203	4300	6503	SO:0001819	synonymous_variant	29909	exon3			CAGGTTCGACACA	AF002986	CCDS3155.1	3q25.1	2012-08-21			ENSG00000174946	ENSG00000174946		"GPCR / Class A : Orphans"	30057	protein-coding gene	gene with protein product	"platelet activating receptor homolog"					9370294	Standard	NM_013308		Approved	H963	uc003eyq.4	O14626	OTTHUMG00000159861	ENST00000309180.5:c.828G>T	chr3.hg19:g.150916346C>A		158.0	1.0		173.0	22.0	NM_013308	D3DNJ4|Q8IV06	Silent	SNP	ENST00000309180.5	hg19	CCDS3155.1																																																																																			.	.		0.478	GPR171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357793.1	NM_013308		A	150916346	C	A	150916346	2	1	126	1	0	0	0	0	0	0	0	1	6676	871	31	1		1	GPR171	3	150916346	Silent	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	8416606	150916346	47106084	10	20966										
RGS12	6002	hgsc.bcm.edu	37	chr4	3318591	3318591	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ttttaaacgtggcgatgatcGtgggctacttaggctccatt	11	8	0	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr4:3318591G>A	ENST00000344733.5	+	2	1598	c.694G>A	c.(694-696)Gtg>Atg	p.V232M	RGS12_ENST00000382788.3_Missense_Mutation_p.V232M|RGS12_ENST00000336727.3_Missense_Mutation_p.V232M|RGS12_ENST00000543385.1_Missense_Mutation_p.V232M	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	232	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GGCGATGATCGTGGGCTACTT	0.493																																					p.V232M		Atlas-SNP	.											.	RGS12	128	.	0			c.G694A						.						76	70	72					4																	3318591		2203	4300	6503	SO:0001583	missense	6002	exon2			ATGATCGTGGGCT	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"Regulators of G-protein signaling"	9994	protein-coding gene	gene with protein product		602512	"regulator of G-protein signalling 12"			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.694G>A	chr4.hg19:g.3318591G>A	ENSP00000339381:p.Val232Met	167.0	0.0		199.0	39.0	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	hg19	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.939510	0.52972	.	.	ENSG00000159788	ENST00000543385;ENST00000344733;ENST00000336727;ENST00000382788	T;T;T;T	0.31510	1.49;1.91;1.91;1.91	4.54	4.54	0.55810	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.068416	0.56097	D	0.000022	T	0.60534	0.2276	M	0.84846	2.72	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.69300	-0.5181	10	0.87932	D	0	-27.967	16.2746	0.82638	0.0:0.0:1.0:0.0	.	232;232;232	Q8WX97;O14924;O14924-4	.;RGS12_HUMAN;.	M	232	ENSP00000440566:V232M;ENSP00000339381:V232M;ENSP00000338509:V232M;ENSP00000372238:V232M	ENSP00000338509:V232M	V	+	1	0	RGS12	3288389	1.000000	0.71417	0.997000	0.53966	0.124000	0.20399	9.493000	0.97960	2.071000	0.62044	0.491000	0.48974	GTG	.	.		0.493	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926		A	3318591	G	A	3318591	3	1	126	1	0	0	0	0	1	0	0	0	13310	1145	40	1	696	1	RGS12	4	3318591	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10		3318591	187835685	11	20967										
PCDH10	57575	hgsc.bcm.edu	37	chr4	134072907	134072907	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tcgactatgagcagctgaagGacttcagttttcaggtggaa	12	7	2	2	rs568804747	byFrequency	TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr4:134072907G>A	ENST00000264360.5	+	1	2438	c.1612G>A	c.(1612-1614)Gac>Aac	p.D538N	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	538	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		GCAGCTGAAGGACTTCAGTTT	0.557																																					p.D538N		Atlas-SNP	.											.	PCDH10	290	.	0			c.G1612A						.						56	61	59					4																	134072907		2160	4209	6369	SO:0001583	missense	57575	exon1			CTGAAGGACTTCA	AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.1612G>A	chr4.hg19:g.134072907G>A	ENSP00000264360:p.Asp538Asn	193.0	0.0		194.0	44.0	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	hg19	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.321144	0.23994	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.51574	0.7	4.51	4.51	0.55191	Cadherin (5);Cadherin-like (1);	0.000000	0.45867	D	0.000336	T	0.37571	0.1008	N	0.21583	0.68	0.44890	D	0.9979	P;B	0.36683	0.565;0.0	B;B	0.42282	0.382;0.004	T	0.09885	-1.0654	10	0.09338	T	0.73	.	16.1677	0.81782	0.0:0.0:1.0:0.0	.	538;538	Q9P2E7;Q96SF0	PCD10_HUMAN;.	N	538	ENSP00000264360:D538N	ENSP00000264360:D538N	D	+	1	0	PCDH10	134292357	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.736000	0.62059	2.329000	0.79093	0.655000	0.94253	GAC	.	.		0.557	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		A	134072907	G	A	134072907	3	1	126	1	0	0	0	0	1	0	0	0	11516	1174	41	3	1614	3	PCDH10	4	134072907	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	130754316	134072907	57081369	12	20968										
NPY5R	4889	hgsc.bcm.edu	37	chr4	164271585	164271585	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tctatacatttgtaagtcttCttggctttatggggaatcta	8	6	4	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr4:164271585C>A	ENST00000515560.1	+	4	1682	c.160C>A	c.(160-162)Ctt>Att	p.L54I	NPY5R_ENST00000338566.3_Missense_Mutation_p.L54I|NPY5R_ENST00000506953.1_Missense_Mutation_p.L54I			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	54					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				TGTAAGTCTTCTTGGCTTTAT	0.393																																					p.L54I	Melanoma(139;1287 1774 9781 19750 25599)	Atlas-SNP	.											.	NPY5R	101	.	0			c.C160A						.						135	131	132					4																	164271585		2203	4300	6503	SO:0001583	missense	4889	exon4			AGTCTTCTTGGCT	BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"GPCR / Class A : Neuropeptide receptors : Y"	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.160C>A	chr4.hg19:g.164271585C>A	ENSP00000423917:p.Leu54Ile	165.0	0.0		196.0	33.0	NM_006174	Q6GTR7|Q92916	Missense_Mutation	SNP	ENST00000515560.1	hg19	CCDS3804.1	.	.	.	.	.	.	.	.	.	.	C	13.78	2.339472	0.41398	.	.	ENSG00000164129	ENST00000338566;ENST00000515560;ENST00000506953	T;T;T	0.39056	1.1;1.1;1.1	5.35	5.35	0.76521	.	0.252536	0.27122	N	0.020832	T	0.32941	0.0846	L	0.29908	0.895	0.34337	D	0.688297	B	0.24576	0.106	B	0.17433	0.018	T	0.40175	-0.9577	10	0.42905	T	0.14	.	15.3271	0.74172	0.0:0.8208:0.1792:0.0	.	54	Q15761	NPY5R_HUMAN	I	54	ENSP00000339377:L54I;ENSP00000423917:L54I;ENSP00000423474:L54I	ENSP00000339377:L54I	L	+	1	0	NPY5R	164491035	0.996000	0.38824	1.000000	0.80357	0.998000	0.95712	1.974000	0.40559	2.668000	0.90789	0.655000	0.94253	CTT	.	.		0.393	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174		A	164271585	C	A	164271585	3	1	126	1	0	0	0	0	1	0	0	0	10619	913	32	3	162	3	NPY5R	4	164271585	Missense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	30198678	164271585	26882691	13	20969										
PAPD7	11044	hgsc.bcm.edu	37	chr5	6754921	6754921	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	acggccacacccaaggcggcGgctacagctctgtgggtagc	14	14	1	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr5:6754921G>A	ENST00000230859.6	+	13	1621	c.1492G>A	c.(1492-1494)Ggc>Agc	p.G498S		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	728					double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)			cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CCAAGGCGGCGGCTACAGCTC	0.602																																					p.G498S	NSCLC(7;212 333 5667 23379 46547)	Atlas-SNP	.											.	PAPD7	69	.	0			c.G1492A						.						34	34	34					5																	6754921		2203	4300	6503	SO:0001583	missense	11044	exon13			GGCGGCGGCTACA	AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"topoisomerase-related function protein 4-1", "polymerase (DNA-directed) sigma", "DNA polymerase kappa", "TUTase5"	605198	"polymerase (DNA directed) sigma"	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.1492G>A	chr5.hg19:g.6754921G>A	ENSP00000230859:p.Gly498Ser	210.0	0.0		268.0	51.0	NM_006999	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Missense_Mutation	SNP	ENST00000230859.6	hg19	CCDS3871.1	.	.	.	.	.	.	.	.	.	.	G	9.341	1.063081	0.19987	.	.	ENSG00000112941	ENST00000230859	T	0.28255	1.62	4.76	-1.76	0.08006	.	0.630262	0.15298	N	0.269800	T	0.10551	0.0258	N	0.04508	-0.205	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36529	-0.9744	10	0.05620	T	0.96	-7.3183	10.6449	0.45615	0.402:0.0:0.598:0.0	.	497;498	B7ZLL4;Q5XG87	.;PAPD7_HUMAN	S	498	ENSP00000230859:G498S	ENSP00000230859:G498S	G	+	1	0	PAPD7	6807921	0.047000	0.20315	0.174000	0.22961	0.989000	0.77384	0.099000	0.15210	-0.243000	0.09653	-0.345000	0.07892	GGC	.	.		0.602	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		A	6754921	G	A	6754921	3	1	126	1	0	0	0	0	1	0	0	0	11435	1116	39	1	1538	1	PAPD7	5	6754921	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10		6754921	174160339	14	20970										
UTP15	84135	hgsc.bcm.edu	37	chr5	72874667	72874667	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	gatctctaaggcactcgataGagttcttgatgtgagtgagc	12	7	2	4			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr5:72874667G>T	ENST00000296792.4	+	10	1391	c.1136G>T	c.(1135-1137)aGa>aTa	p.R379I	UTP15_ENST00000543251.1_Missense_Mutation_p.R189I|UTP15_ENST00000508491.1_Missense_Mutation_p.R360I	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	379					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		GCACTCGATAGAGTTCTTGAT	0.353																																					p.R379I		Atlas-SNP	.											.	UTP15	30	.	0			c.G1136T						.						99	102	101					5																	72874667		2203	4300	6503	SO:0001583	missense	84135	exon10			TCGATAGAGTTCT	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"WD repeat domain containing"	25758	protein-coding gene	gene with protein product			"UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.1136G>T	chr5.hg19:g.72874667G>T	ENSP00000296792:p.Arg379Ile	116.0	0.0		151.0	47.0	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Missense_Mutation	SNP	ENST00000296792.4	hg19	CCDS34186.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.54|18.54	3.645207|3.645207	0.67358|0.67358	.|.	.|.	ENSG00000164338|ENSG00000164338	ENST00000509005|ENST00000296792;ENST00000543251;ENST00000508491	.|T;T;T	.|0.42900	.|0.96;0.96;0.96	5.98|5.98	5.98|5.98	0.97165|0.97165	.|U3 small nucleolar RNA-associated protein 15, C-terminal (1);	.|0.135767	.|0.64402	.|D	.|0.000011	.|T	.|0.35711	.|0.0941	L|L	0.50333|0.50333	1.59|1.59	0.52099|0.52099	D|D	0.999941|0.999941	.|P;P	.|0.38677	.|0.512;0.642	.|B;B	.|0.30855	.|0.121;0.121	.|T	.|0.15065	.|-1.0450	.|10	.|0.39692	.|T	.|0.17	.|.	14.7797|14.7797	0.69756|0.69756	0.0:0.2529:0.7471:0.0|0.0:0.2529:0.7471:0.0	.|.	.|360;379	.|B4DXK8;Q8TED0	.|.;UTP15_HUMAN	X|I	406|379;189;360	.|ENSP00000296792:R379I;ENSP00000440796:R189I;ENSP00000424609:R360I	.|ENSP00000296792:R379I	E|R	+|+	1|2	0|0	UTP15|UTP15	72910423|72910423	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	3.615000|3.615000	0.54167|0.54167	2.838000|2.838000	0.97847|0.97847	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.		0.353	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175		T	72874667	G	T	72874667	3	4	126	1	0	0	0	0	1	0	0	0	17112	942	33	3	1170	3	UTP15	5	72874667	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	66119746	72874667	108040593	15	20971										
PCDHGA6	56109	hgsc.bcm.edu	37	chr5	140755726	140755726	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	gattcggacctcactctgtaCctggtggtggcggtggccgc	15	12	2	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr5:140755726C>T	ENST00000517434.1	+	1	2076	c.2076C>T	c.(2074-2076)taC>taT	p.Y692Y	PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	692					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCACTCTGTACCTGGTGGTGG	0.677																																					p.Y692Y		Atlas-SNP	.											PCDHGA6_ENST00000517434,NS,carcinoma,0,1	PCDHGA6	219	.	0			c.C2076T						.						61	70	67					5																	140755726		2203	4293	6496	SO:0001819	synonymous_variant	56109	exon1			TCTGTACCTGGTG	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"Cadherins / Protocadherins : Clustered"	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.2076C>T	chr5.hg19:g.140755726C>T		73.0	0.0		85.0	21.0	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Silent	SNP	ENST00000517434.1	hg19	CCDS54926.1																																																																																			.	.		0.677	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		T	140755726	C	T	140755726	2	4	126	1	0	0	0	0	0	0	0	1	11567	518	18	3		3	PCDHGA6	5	140755726	Silent	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	67881059	140755726	40159534	16	20972										
MYO6	4646	hgsc.bcm.edu	37	chr6	76589582	76589582	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	gcagggtggttacccatcacGagcttcatttcatgaactct	9	11	4	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr6:76589582G>A	ENST00000369977.3	+	21	2262	c.2123G>A	c.(2122-2124)cGa>cAa	p.R708Q	MYO6_ENST00000369981.3_Missense_Mutation_p.R708Q|MYO6_ENST00000369975.1_Missense_Mutation_p.R708Q|MYO6_ENST00000369985.4_Missense_Mutation_p.R708Q|MYO6_ENST00000462633.1_3'UTR	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	708	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		TACCCATCACGAGCTTCATTT	0.408																																					p.R708Q		Atlas-SNP	.											MYO6,colon,carcinoma,0,1	MYO6	124	.	0			c.G2123A						.						174	158	163					6																	76589582		2203	4300	6503	SO:0001583	missense	4646	exon21			CATCACGAGCTTC	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.2123G>A	chr6.hg19:g.76589582G>A	ENSP00000358994:p.Arg708Gln	210.0	0.0		240.0	39.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	hg19	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.747060	0.89663	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	D;D;D;D	0.91996	-2.95;-2.95;-2.95;-2.95	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.97529	0.9191	H	0.96111	3.77	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.983	D	0.98450	1.0591	10	0.87932	D	0	.	19.2649	0.93982	0.0:0.0:1.0:0.0	.	708;708	Q9UM54-2;Q9UM54-1	.;.	Q	708	ENSP00000358998:R708Q;ENSP00000359002:R708Q;ENSP00000358994:R708Q;ENSP00000358992:R708Q	ENSP00000358992:R708Q	R	+	2	0	MYO6	76646302	1.000000	0.71417	1.000000	0.80357	0.446000	0.32137	9.392000	0.97252	2.632000	0.89209	0.655000	0.94253	CGA	.	.		0.408	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		A	76589582	G	A	76589582	3	1	126	1	0	0	0	0	1	0	0	0	10090	1058	37	1	2201	1	MYO6	6	76589582	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10		76589582	94525485	17	20973										
GBAS	2631	hgsc.bcm.edu	37	chr7	56049254	56049254	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cgtggtatggcgagcaggacCaagctggtaggaagcgaagt	17	7	0	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr7:56049254C>T	ENST00000322090.3	+	4	396	c.367C>T	c.(367-369)Caa>Taa	p.Q123*	GBAS_ENST00000446778.1_Silent_p.T107T	NM_001483.2	NP_001474.1	O75323	NIPS2_HUMAN	glioblastoma amplified sequence	123					ATP biosynthetic process (GO:0006754)|negative regulation of ATP citrate synthase activity (GO:2000984)|oxidative phosphorylation (GO:0006119)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CGAGCAGGACCAAGCTGGTAG	0.398																																					p.Q123X		Atlas-SNP	.											.	GBAS	16	.	0			c.C367T						.						153	141	145					7																	56049254		2203	4300	6503	SO:0001587	stop_gained	2631	exon4			CAGGACCAAGCTG	AF029786	CCDS5521.1, CCDS56488.1	7p12	2014-03-11			ENSG00000146729	ENSG00000146729			4179	protein-coding gene	gene with protein product		603004				9615231, 9661659, 20888800	Standard	NM_001483		Approved	NIPSNAP2	uc003tre.2	O75323	OTTHUMG00000022932	ENST00000322090.3:c.367C>T	chr7.hg19:g.56049254C>T	ENSP00000313050:p.Gln123*	144.0	0.0		184.0	64.0	NM_001483	C9IYJ3|O43801|Q53X96	Nonsense_Mutation	SNP	ENST00000322090.3	hg19	CCDS5521.1	.	.	.	.	.	.	.	.	.	.	C	30	5.057879	0.93846	.	.	ENSG00000146729	ENST00000322090	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-9.5334	19.0063	0.92852	0.0:1.0:0.0:0.0	.	.	.	.	X	123	.	ENSP00000313050:Q123X	Q	+	1	0	GBAS	56016748	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	7.478000	0.81082	2.809000	0.96659	0.467000	0.42956	CAA	.	.		0.398	GBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251524.1	NM_001483		T	56049254	C	T	56049254	4	4	126	1	0	0	0	0	0	1	0	0	6277	595	21	3	381	3	GBAS	7	56049254	Nonsense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10		56049254	103089409	18	20974										
MAGI2	9863	hgsc.bcm.edu	37	chr7	77885584	77885584	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cgtgccgtctagctgaccatCagttggcatggagtgcagag	14	10	2	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr7:77885584C>A	ENST00000354212.4	-	10	1976	c.1723G>T	c.(1723-1725)Gat>Tat	p.D575Y	MAGI2_ENST00000522391.1_Missense_Mutation_p.D575Y|MAGI2_ENST00000536571.1_Missense_Mutation_p.D407Y|MAGI2_ENST00000419488.1_Missense_Mutation_p.D575Y|MAGI2_ENST00000535697.1_Missense_Mutation_p.D412Y	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	575					cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				AGCTGACCATCAGTTGGCATG	0.488																																					p.D575Y		Atlas-SNP	.											.	MAGI2	246	.	0			c.G1723T						.						111	95	100					7																	77885584		2203	4300	6503	SO:0001583	missense	9863	exon10			GACCATCAGTTGG	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1723G>T	chr7.hg19:g.77885584C>A	ENSP00000346151:p.Asp575Tyr	391.0	0.0		479.0	161.0	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	hg19	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.010687	0.75046	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	T;T;T;T;T	0.12147	2.81;2.8;2.71;3.72;3.73	5.94	5.94	0.96194	.	0.000000	0.37530	U	0.002044	T	0.40498	0.1119	M	0.72894	2.215	0.80722	D	1	D;B;D;D;D;D	0.89917	0.997;0.376;1.0;1.0;0.997;1.0	D;B;D;D;D;D	0.87578	0.946;0.293;0.998;0.998;0.964;0.997	T	0.07177	-1.0786	10	0.87932	D	0	.	19.3473	0.94370	0.0:1.0:0.0:0.0	.	412;407;575;575;575;575	F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8	.;.;.;.;.;MAGI2_HUMAN	Y	575;575;575;575;407;412	ENSP00000405766:D575Y;ENSP00000346151:D575Y;ENSP00000428389:D575Y;ENSP00000441584:D407Y;ENSP00000441603:D412Y	ENSP00000346151:D575Y	D	-	1	0	MAGI2	77723520	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	7.818000	0.86416	2.816000	0.96949	0.561000	0.74099	GAT	.	.		0.488	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		A	77885584	C	A	77885584	3	1	126	1	0	0	0	0	1	0	0	0	9200	826	29	3	2696	3	MAGI2	7	77885584	Missense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	21836330	77885584	81253079	19	20975										
TGS1	96764	hgsc.bcm.edu	37	chr8	56699053	56699053	+	Frame_Shift_Del	DEL	A	A	-													0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	agaaattacagagaaatgggAaaagtattggaatgaatatg							TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr8:56699053delA	ENST00000260129.5	+	4	1073	c.596delA	c.(595-597)gaafs	p.E199fs		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	199					7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			GAGAAATGGGAAAAGTATTGG	0.378																																					p.E199fs	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-Indel,Pindel	.											.	TGS1	66	.	0			c.595delG						.						100	103	102					8																	56699053		2203	4300	6503	SO:0001589	frameshift_variant	96764	exon4			.	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"nuclear receptor coactivator 6 interacting protein", "trimethylguanosine synthase homolog (S. cerevisiae)"	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.596delA	chr8.hg19:g.56699053delA	ENSP00000260129:p.Glu199fs	83.0	0.0		93.0	39.0	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Frame_Shift_Del	DEL	ENST00000260129.5	hg19	CCDS34894.1																																																																																			.	.		0.378	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831		-	56699053	A	-	56699053	7	5	126	1	0	1	0	1	0	0	0	0	15852	246	9	0	610	0	TGS1	8	56699053	Frame_Shift_Del	DEL	A	TCGA-DD-A4ND-01A-11D-A25V-10		56699053	89664969	20	20976										
GLDC	2731	hgsc.bcm.edu	37	chr9	6558589	6558589	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	aggtgaactgcatcgatattCccatatttatccacctccac	5	13	0	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr9:6558589C>A	ENST00000321612.6	-	17	2172	c.2022G>T	c.(2020-2022)ggG>ggT	p.G674G	GLDC_ENST00000460457.1_5'UTR	NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	674					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	CATCGATATTCCCATATTTAT	0.527																																					p.G674G		Atlas-SNP	.											.	GLDC	118	.	0			c.G2022T						.						218	193	202					9																	6558589		2203	4300	6503	SO:0001819	synonymous_variant	2731	exon17			GATATTCCCATAT	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"glycine cleavage system protein P", "glycine decarboxylase"	238300	"glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.2022G>T	chr9.hg19:g.6558589C>A		137.0	0.0		132.0	25.0	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	hg19	CCDS34987.1																																																																																			.	.		0.527	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170		A	6558589	C	A	6558589	2	1	126	1	0	0	0	0	0	0	0	1	6441	842	30	3		3	GLDC	9	6558589	Silent	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10		6558589	134654842	21	20977										
CHCHD1	118487	hgsc.bcm.edu	37	chr10	75542873	75542873	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	atacaggaaaccctgggagaGtctgggagtttacttccaaa	11	8	1	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr10:75542873G>T	ENST00000372833.5	+	3	298	c.285G>T	c.(283-285)gaG>gaT	p.E95D	ZSWIM8_ENST00000603114.1_5'Flank|CHCHD1_ENST00000372837.3_3'UTR|ZSWIM8_ENST00000604729.1_5'Flank|ZSWIM8_ENST00000605216.1_5'Flank|ZSWIM8_ENST00000604524.1_5'Flank|ZSWIM8_ENST00000398706.2_5'Flank	NM_203298.2	NP_976043.1	Q96BP2	CHCH1_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 1	95						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)	1	Prostate(51;0.0112)					CCCTGGGAGAGTCTGGGAGTT	0.378																																					p.E95D		Atlas-SNP	.											.	CHCHD1	6	.	0			c.G285T						.						110	116	114					10																	75542873		2203	4300	6503	SO:0001583	missense	118487	exon3			GGGAGAGTCTGGG	AK098720	CCDS7334.1	10q22.3	2014-02-12	2004-01-19		ENSG00000172586	ENSG00000172586		"Coiled-coil-helix-coiled-coil-helix domain containing"	23518	protein-coding gene	gene with protein product		608842	"chromosome 10 open reading frame 34"	C10orf34			Standard	NM_203298		Approved	FLJ25854	uc001jvc.4	Q96BP2	OTTHUMG00000018475	ENST00000372833.5:c.285G>T	chr10.hg19:g.75542873G>T	ENSP00000361923:p.Glu95Asp	63.0	0.0		45.0	4.0	NM_203298		Missense_Mutation	SNP	ENST00000372833.5	hg19	CCDS7334.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118352	0.37339	.	.	ENSG00000172586	ENST00000372833	.	.	.	5.03	0.342	0.15996	.	0.490245	0.20613	N	0.088933	T	0.26412	0.0645	L	0.44542	1.39	0.09310	N	0.999999	B	0.23937	0.094	B	0.19666	0.026	T	0.11767	-1.0574	9	0.21014	T	0.42	-9.0645	4.045	0.09768	0.3358:0.2275:0.4367:0.0	.	95	Q96BP2	CHCH1_HUMAN	D	95	.	ENSP00000361923:E95D	E	+	3	2	CHCHD1	75212879	0.009000	0.17119	0.574000	0.28523	0.969000	0.65631	0.006000	0.13152	0.217000	0.20800	0.655000	0.94253	GAG	.	.		0.378	CHCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048676.1	XM_058325		T	75542873	G	T	75542873	3	4	126	1	0	0	0	0	1	0	0	0	3316	1020	36	3	295	3	CHCHD1	10	75542873	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10		75542873	59991874	22	20978										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6588587	6588587	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tgcaagcaacagggaaagcaTcagagctggaaagactggca	13	8	1	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr11:6588587T>A	ENST00000527990.2	+	34	11848	c.11848T>A	c.(11848-11850)Tca>Aca	p.S3950T	DNHD1_ENST00000254579.6_Missense_Mutation_p.S3950T			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3950					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AGGGAAAGCATCAGAGCTGGA	0.612																																					p.S3950T		Atlas-SNP	.											.	DNHD1	198	.	0			c.T11848A						.						48	56	53					11																	6588587		2073	4198	6271	SO:0001583	missense	144132	exon36			AAAGCATCAGAGC	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.11848T>A	chr11.hg19:g.6588587T>A	ENSP00000436180:p.Ser3950Thr	132.0	0.0		142.0	25.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	T	8.284	0.816116	0.16607	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000525883;ENST00000530197	T;T	0.26373	1.74;1.74	4.54	0.767	0.18482	.	0.274240	0.28841	N	0.013968	T	0.10121	0.0248	N	0.14661	0.345	0.21861	N	0.999506	B;B;B;B	0.09022	0.0;0.002;0.0;0.001	B;B;B;B	0.06405	0.001;0.002;0.001;0.002	T	0.30995	-0.9959	10	0.11182	T	0.66	-0.9633	3.8379	0.08902	0.1658:0.5054:0.0:0.3287	.	3038;218;3;3950	B0I1S4;D3DQT9;Q9NSW8;Q96M86	.;.;.;DNHD1_HUMAN	T	3950;3950;218;218	ENSP00000254579:S3950T;ENSP00000436180:S3950T	ENSP00000254579:S3950T	S	+	1	0	DNHD1	6545163	0.903000	0.30736	0.774000	0.31636	0.874000	0.50279	0.007000	0.13174	-0.055000	0.13244	0.459000	0.35465	TCA	.	.		0.612	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6588587	T	A	6588587	3	1	126	1	0	0	0	0	1	0	0	0	4670	1435	50	4	11991	4	DNHD1	11	6588587	Missense_Mutation	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10		6588587	128417929	23	20979										
OR8H1	219469	hgsc.bcm.edu	37	chr11	56058048	56058048	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ttgagtcgcagaaatgcagtCtgctcatccaaaccacattg	8	11	2	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr11:56058048C>T	ENST00000313022.2	-	1	518	c.491G>A	c.(490-492)aGa>aAa	p.R164K		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	164						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					GAAATGCAGTCTGCTCATCCA	0.438																																					p.R164K		Atlas-SNP	.											.	OR8H1	89	.	0			c.G491A						.						95	87	90					11																	56058048		2201	4296	6497	SO:0001583	missense	219469	exon1			TGCAGTCTGCTCA	AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"GPCR / Class A : Olfactory receptors"	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.491G>A	chr11.hg19:g.56058048C>T	ENSP00000323595:p.Arg164Lys	158.0	0.0		254.0	51.0	NM_001005199	B2RNI7|Q6IFC5	Missense_Mutation	SNP	ENST00000313022.2	hg19	CCDS31526.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.513805	0.27123	.	.	ENSG00000181693	ENST00000313022;ENST00000395186	T	0.00123	8.7	3.64	0.239	0.15484	GPCR, rhodopsin-like superfamily (1);	0.342922	0.25425	N	0.030778	T	0.00073	0.0002	N	0.16903	0.455	0.09310	N	1	B	0.12013	0.005	B	0.17979	0.02	T	0.25745	-1.0123	10	0.54805	T	0.06	.	6.1335	0.20219	0.0:0.3043:0.4796:0.2161	.	164	Q8NGG4	OR8H1_HUMAN	K	164;160	ENSP00000323595:R164K	ENSP00000323595:R164K	R	-	2	0	OR8H1	55814624	0.000000	0.05858	0.004000	0.12327	0.029000	0.11900	-4.223000	0.00271	0.284000	0.22305	0.446000	0.29264	AGA	.	.		0.438	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199		T	56058048	C	T	56058048	3	4	126	1	0	0	0	0	1	0	0	0	11246	913	32	3	446	3	OR8H1	11	56058048	Missense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	49469461	56058048	78948468	24	20980										
OR5M10	390167	hgsc.bcm.edu	37	chr11	56344846	56344847	+	Missense_Mutation	DNP	TT	TT	AG													0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tacatagcgatccaatgccaTtgaagcaaggaagtaaaact					rs148438199	byFrequency	TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr11:56344846_56344847TT>AG	ENST00000526812.2	-	1	416_417	c.351_352AA>CT	c.(349-354)tcAAtg>tcCTtg	p.M118L		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						TCCAATGCCATTGAAGCAAGGA	0.45																																					p.M118L|p.S117S		Atlas-SNP	.											.,1|.	OR5M10	56	.	0			c.A352T|c.A351C						.																																			SO:0001583	missense	390167	exon1			ATGCCATTGAAGC|TGCCATTGAAGCA	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"GPCR / Class A : Olfactory receptors"	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.351_352delinsAG	chr11.hg19:g.56344846_56344847delinsAG	ENSP00000436004:p.Met118Leu	149.0|148.0	0.0		396.0|395.0	18.0|16.0	NM_001004741	B9EIL9	Missense_Mutation|Silent	SNP	ENST00000526812.2	hg19	CCDS53630.1																																																																																			.	.		0.45	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		AG	56344847	TT	AG	56344846	3	1	126	1	0	0	0	0	1	0	0	0	11182	1493	52	4	599	4	OR5M10	11	56344846	Missense_Mutation	DNP	TT	TCGA-DD-A4ND-01A-11D-A25V-10	286798	56344846	78661670	25	20981										
GSTP1	2950	hgsc.bcm.edu	37	chr11	67352223	67352223	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ccagtccaataccatcctgcGtcacctgggccgcacccttg	8	18	1	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr11:67352223G>A	ENST00000398606.3	+	4	461	c.212G>A	c.(211-213)cGt>cAt	p.R71H	GSTP1_ENST00000498765.1_3'UTR|GSTP1_ENST00000398603.1_Missense_Mutation_p.R71H	NM_000852.3	NP_000843.1	P09211	GSTP1_HUMAN	glutathione S-transferase pi 1	71	GST N-terminal.				cellular response to lipopolysaccharide (GO:0071222)|central nervous system development (GO:0007417)|common myeloid progenitor cell proliferation (GO:0035726)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biosynthetic process (GO:0009890)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of leukocyte proliferation (GO:0070664)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|nitric oxide storage (GO:0035732)|positive regulation of superoxide anion generation (GO:0032930)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of stress-activated MAPK cascade (GO:0032872)|response to reactive oxygen species (GO:0000302)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|TRAF2-GSTP1 complex (GO:0097057)|vesicle (GO:0031982)	dinitrosyl-iron complex binding (GO:0035731)|glutathione transferase activity (GO:0004364)|JUN kinase binding (GO:0008432)|kinase regulator activity (GO:0019207)|nitric oxide binding (GO:0070026)|S-nitrosoglutathione binding (GO:0035730)			central_nervous_system(1)|cervix(1)|endometrium(4)|lung(2)|ovary(1)	9					Busulfan(DB01008)|Carboplatin(DB00958)|Chlorambucil(DB00291)|Cisplatin(DB00515)|Clomipramine(DB01242)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	ACCATCCTGCGTCACCTGGGC	0.617																																					p.R71H		Atlas-SNP	.											.	GSTP1	21	.	0			c.G212A						.						82	90	88					11																	67352223		2005	4157	6162	SO:0001583	missense	2950	exon4			TCCTGCGTCACCT	U12472	CCDS41679.1	11q13.2	2014-09-17	2008-07-18		ENSG00000084207	ENSG00000084207	2.5.1.18	"Glutathione S-transferases / Soluble"	4638	protein-coding gene	gene with protein product		134660		FAEES3, GST3		1885604, 7587384, 19915149	Standard	NM_000852		Approved	GSTP	uc001omf.3	P09211	OTTHUMG00000137430	ENST00000398606.3:c.212G>A	chr11.hg19:g.67352223G>A	ENSP00000381607:p.Arg71His	115.0	0.0		533.0	26.0	NM_000852	O00460|Q15690|Q5TZY3	Missense_Mutation	SNP	ENST00000398606.3	hg19	CCDS41679.1	.	.	.	.	.	.	.	.	.	.	G	19.98	3.927369	0.73327	.	.	ENSG00000084207	ENST00000398606;ENST00000398603	T;T	0.09163	3.01;3.01	5.65	5.65	0.86999	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.143985	0.38492	N	0.001670	T	0.40015	0.1100	M	0.88640	2.97	0.42107	D	0.991360	D	0.89917	1.0	D	0.80764	0.994	T	0.51371	-0.8714	9	0.87932	D	0	-17.2282	15.2846	0.73819	0.0:0.0:1.0:0.0	.	71	P09211	GSTP1_HUMAN	H	71	ENSP00000381607:R71H;ENSP00000381604:R71H	ENSP00000381604:R71H	R	+	2	0	GSTP1	67108799	0.998000	0.40836	0.607000	0.28956	0.154000	0.21943	6.886000	0.75611	2.675000	0.91044	0.650000	0.86243	CGT	.	.		0.617	GSTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268504.1	NM_000852		A	67352223	G	A	67352223	3	1	126	1	0	0	0	0	1	0	0	0	6853	1145	40	1	226	1	GSTP1	11	67352223	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	11007377	67352223	67654293	26	20982										
ACAT1	38	hgsc.bcm.edu	37	chr11	108010844	108010844	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	gaatattgcacgaaatgaacAggacgcttatgctattaatt	8	6	0	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr11:108010844A>G	ENST00000265838.4	+	7	723	c.632A>G	c.(631-633)cAg>cGg	p.Q211R		NM_000019.3	NP_000010.1	P24752	THIL_HUMAN	acetyl-CoA acetyltransferase 1	211					adipose tissue development (GO:0060612)|brain development (GO:0007420)|branched-chain amino acid catabolic process (GO:0009083)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular nitrogen compound metabolic process (GO:0034641)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|metanephric proximal convoluted tubule development (GO:0072229)|protein homooligomerization (GO:0051260)|response to hormone (GO:0009725)|response to organic cyclic compound (GO:0014070)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acetyl-CoA C-acetyltransferase activity (GO:0003985)|coenzyme binding (GO:0050662)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|prostate(2)	10		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	CGAAATGAACAGGACGCTTAT	0.348																																					p.Q211R		Atlas-SNP	.											.	ACAT1	35	.	0			c.A632G						.						67	70	69					11																	108010844		2201	4298	6499	SO:0001583	missense	38	exon7			ATGAACAGGACGC	D90228	CCDS8339.1	11q22.3	2010-04-30	2010-04-30		ENSG00000075239	ENSG00000075239	2.3.1.9		93	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	607809	"acetyl-Coenzyme A acetyltransferase 1"	ACAT		1979337	Standard	NM_000019		Approved	THIL	uc001pjy.3	P24752	OTTHUMG00000166381	ENST00000265838.4:c.632A>G	chr11.hg19:g.108010844A>G	ENSP00000265838:p.Gln211Arg	127.0	0.0		104.0	22.0	NM_000019	B2R6H1|G3XAB4|Q96FG8	Missense_Mutation	SNP	ENST00000265838.4	hg19	CCDS8339.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.552267	0.86127	.	.	ENSG00000075239	ENST00000265838	D	0.94000	-3.33	5.99	5.99	0.97316	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	D	0.98131	0.9383	H	0.98218	4.175	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.99612	1.0981	10	0.87932	D	0	-26.3074	16.4943	0.84223	1.0:0.0:0.0:0.0	.	211	P24752	THIL_HUMAN	R	211	ENSP00000265838:Q211R	ENSP00000265838:Q211R	Q	+	2	0	ACAT1	107516054	1.000000	0.71417	1.000000	0.80357	0.628000	0.37860	8.923000	0.92808	2.291000	0.77112	0.533000	0.62120	CAG	.	.		0.348	ACAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389474.1	NM_000019		G	108010844	A	G	108010844	3	3	126	1	0	0	0	0	1	0	0	0	121	188	7	2	658	2	ACAT1	11	108010844	Missense_Mutation	SNP	A	TCGA-DD-A4ND-01A-11D-A25V-10	40658621	108010844	26995672	27	20983										
HMBS	3145	hgsc.bcm.edu	37	chr11	118955777	118955777	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	gcaatgcggctgcaacggcgGtgagtgctgagccggtgacc	17	11	0	3			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr11:118955777G>A	ENST00000278715.3	+	1	184		c.e1+1		HMBS_ENST00000442944.2_Splice_Site|HMBS_ENST00000392841.1_5'Flank|HMBS_ENST00000542729.1_5'UTR|HMBS_ENST00000544387.1_Splice_Site|HMBS_ENST00000537841.1_5'UTR|HMBS_ENST00000543090.1_Splice_Site	NM_000190.3	NP_000181.2	P08397	HEM3_HUMAN	hydroxymethylbilane synthase						heme biosynthetic process (GO:0006783)|peptidyl-pyrromethane cofactor linkage (GO:0018160)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	hydroxymethylbilane synthase activity (GO:0004418)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		TGCAACGGCGGTGAGTGCTGA	0.642																																					.		Atlas-SNP	.											.	HMBS	27	.	0			c.33+1G>A	GRCh37	CS003342|CS890127	HMBS	S		.						42	36	38					11																	118955777		2200	4295	6495	SO:0001630	splice_region_variant	3145	exon1			ACGGCGGTGAGTG	X04808	CCDS8409.1, CCDS41726.1, CCDS58186.1, CCDS58187.1	11q23.3	2013-07-10			ENSG00000256269	ENSG00000256269	2.5.1.61		4982	protein-coding gene	gene with protein product		609806	"uroporphyrinogen I synthase", "porphobilinogen deaminase", "porphyria, acute; Chester type"	PBGD, UPS, PORC		8432552, 17298217	Standard	NM_001258208		Approved		uc001puz.1	P08397	OTTHUMG00000168295	ENST00000278715.3:c.33+1G>A	chr11.hg19:g.118955777G>A		135.0	0.0		110.0	31.0	NM_000190	A8K2L0|G3V1P4|G5EA58|P08396|Q16012	Splice_Site	SNP	ENST00000278715.3	hg19	CCDS8409.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.311067	0.81358	.	.	ENSG00000256269	ENST00000278715;ENST00000536813;ENST00000546302;ENST00000544387;ENST00000543090	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7169	0.77674	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HMBS	118460987	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	4.484000	0.60271	2.785000	0.95823	0.650000	0.86243	.	.	.		0.642	HMBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399188.1	NM_000190	Intron	A	118955777	G	A	118955777	5	1	126	1	0	0	0	0	0	0	1	0	7228	1275	44	3	36	3	HMBS	11	118955777	Splice_Site	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	10944933	118955777	16050739	28	20984										
PARP11	57097	hgsc.bcm.edu	37	chr12	3939151	3939151	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cacttcattgtttgttgtttTagaaaataattcttctgctt	5	6	3	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr12:3939151T>C	ENST00000228820.4	-	2	196	c.52A>G	c.(52-54)Aaa>Gaa	p.K18E	PARP11_ENST00000397096.2_Missense_Mutation_p.K11E|PARP11_ENST00000427057.2_5'UTR|PARP11_ENST00000447133.3_5'UTR	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	11	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.						NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	17			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			TTTGTTGTTTTAGAAAATAAT	0.393																																					p.K18E		Atlas-SNP	.											.	PARP11	39	.	0			c.A52G						.						134	122	126					12																	3939151		2203	4300	6503	SO:0001583	missense	57097	exon2			TTGTTTTAGAAAA	AF263540	CCDS8523.2, CCDS66281.1	12p13.3	2014-01-28	2004-08-25	2004-08-26	ENSG00000111224	ENSG00000111224		"Poly (ADP-ribose) polymerases"	1186	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 6"	C12orf6		15273990	Standard	NM_001286522		Approved		uc001qml.2	Q9NR21	OTTHUMG00000156442	ENST00000228820.4:c.52A>G	chr12.hg19:g.3939151T>C	ENSP00000228820:p.Lys18Glu	123.0	0.0		107.0	19.0	NM_020367	B4DRQ0|Q68DS1|Q8N5Y9	Missense_Mutation	SNP	ENST00000228820.4	hg19	CCDS8523.2	.	.	.	.	.	.	.	.	.	.	T	10.10	1.258544	0.23051	.	.	ENSG00000111224	ENST00000397096;ENST00000228820	T;T	0.32988	1.43;2.62	5.52	0.326	0.15908	.	0.404709	0.29537	N	0.011876	T	0.10294	0.0252	N	0.08118	0	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.31586	-0.9938	10	0.06757	T	0.87	.	4.6244	0.12470	0.0:0.2302:0.287:0.4827	.	18;11	Q9NR21-4;Q9NR21	.;PAR11_HUMAN	E	11;18	ENSP00000380284:K11E;ENSP00000228820:K18E	ENSP00000228820:K18E	K	-	1	0	PARP11	3809412	0.068000	0.21057	0.000000	0.03702	0.005000	0.04900	1.101000	0.31037	-0.079000	0.12707	0.460000	0.39030	AAA	.	.		0.393	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1			C	3939151	T	C	3939151	3	2	126	1	0	0	0	0	1	0	0	0	11465	1763	61	2	992	2	PARP11	12	3939151	Missense_Mutation	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10		3939151	129912744	29	20985										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40707956	40707956	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	aatgagcttcctcacgcagtTcactttctaaatgaatcagg	7	10	4	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr12:40707956T>G	ENST00000298910.7	+	32	4777	c.4719T>G	c.(4717-4719)gtT>gtG	p.V1573V	LRRK2_ENST00000481256.1_3'UTR	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1573					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CTCACGCAGTTCACTTTCTAA	0.343																																					p.V1573V		Atlas-SNP	.											.	LRRK2	763	.	0			c.T4719G						.						64	54	57					12																	40707956		2203	4299	6502	SO:0001819	synonymous_variant	120892	exon32			CGCAGTTCACTTT	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4719T>G	chr12.hg19:g.40707956T>G		148.0	0.0		197.0	50.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	hg19	CCDS31774.1																																																																																			.	.		0.343	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		G	40707956	T	G	40707956	2	3	126	1	0	0	0	0	0	0	0	1	9042	1770	62	5		5	LRRK2	12	40707956	Silent	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10	36768805	40707956	93143939	30	20986										
CSAD	51380	hgsc.bcm.edu	37	chr12	53553482	53553482	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ggtacgaaccagaaacacacAttgacaaactcaggctgaga	9	10	1	3			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr12:53553482A>G	ENST00000444623.1	-	16	1500	c.1233T>C	c.(1231-1233)aaT>aaC	p.N411N	RP11-1136G11.8_ENST00000550908.1_lincRNA|CSAD_ENST00000379843.3_Silent_p.N264N|CSAD_ENST00000453446.2_Silent_p.N411N|CSAD_ENST00000379846.1_Silent_p.N264N|CSAD_ENST00000267085.4_Silent_p.N438N	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	411					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	AGAAACACACATTGACAAACT	0.557											OREG0021859	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N438N	Ovarian(109;252 1546 16882 28524 44645)	Atlas-SNP	.											.	CSAD	66	.	0			c.T1314C						.						103	88	93					12																	53553482		2203	4300	6503	SO:0001819	synonymous_variant	51380	exon16			ACACACATTGACA	AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"P-selectin cytoplasmic tail-associated protein"					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.1233T>C	chr12.hg19:g.53553482A>G		96.0	0.0	993	130.0	41.0	NM_015989	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Silent	SNP	ENST00000444623.1	hg19	CCDS58235.1	.	.	.	.	.	.	.	.	.	.	A	9.792	1.178061	0.21787	.	.	ENSG00000139631	ENST00000379850	.	.	.	4.67	-1.42	0.08913	.	.	.	.	.	T	0.55705	0.1937	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51748	-0.8666	4	.	.	.	-29.7639	10.1078	0.42544	0.5876:0.0:0.4124:0.0	.	.	.	.	R	437	.	.	C	-	1	0	CSAD	51839749	0.283000	0.24277	0.995000	0.50966	0.959000	0.62525	-0.344000	0.07780	-0.163000	0.10946	-0.366000	0.07423	TGT	.	.		0.557	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343697.1	NM_015989		G	53553482	A	G	53553482	2	3	126	1	0	0	0	0	0	0	0	1	3927	214	8	2		2	CSAD	12	53553482	Silent	SNP	A	TCGA-DD-A4ND-01A-11D-A25V-10	12845526	53553482	80298413	31	20987										
AVPR1A	552	hgsc.bcm.edu	37	chr12	63544481	63544481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tttggccagctcctcgttgcGcacgtccctcggtgggccgt	13	15	0	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr12:63544481G>A	ENST00000299178.2	-	1	241	c.136C>T	c.(136-138)Cgc>Tgc	p.R46C		NM_000706.4	NP_000697.1	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	46					activation of phospholipase C activity (GO:0007202)|blood circulation (GO:0008015)|calcium-mediated signaling (GO:0019722)|cellular response to water deprivation (GO:0042631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|grooming behavior (GO:0007625)|maternal aggressive behavior (GO:0002125)|maternal behavior (GO:0042711)|myotube differentiation (GO:0014902)|negative regulation of female receptivity (GO:0007621)|negative regulation of transmission of nerve impulse (GO:0051970)|penile erection (GO:0043084)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glutamate secretion (GO:0014049)|positive regulation of heart rate (GO:0010460)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of vasoconstriction (GO:0045907)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to corticosterone (GO:0051412)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|telencephalon development (GO:0021537)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)	p.R46C(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|prostate(2)|skin(1)	26			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	TCCTCGTTGCGCACGTCCCTC	0.697																																					p.R46C		Atlas-SNP	.											AVPR1A,colon,carcinoma,0,1	AVPR1A	85	.	1	Substitution - Missense(1)	large_intestine(1)	c.C136T						.						45	39	41					12																	63544481		2190	4283	6473	SO:0001583	missense	552	exon1			CGTTGCGCACGTC	L25615	CCDS8965.1	12q14-q15	2012-08-08				ENSG00000166148		"GPCR / Class A : Vasopressin and oxytocin receptors"	895	protein-coding gene	gene with protein product		600821		AVPR1		8106369	Standard	NM_000706		Approved		uc001sro.2	P37288		ENST00000299178.2:c.136C>T	chr12.hg19:g.63544481G>A	ENSP00000299178:p.Arg46Cys	13.0	0.0		26.0	3.0	NM_000706		Missense_Mutation	SNP	ENST00000299178.2	hg19	CCDS8965.1	.	.	.	.	.	.	.	.	.	.	G	17.42	3.383896	0.61845	.	.	ENSG00000166148	ENST00000299178	T	0.37752	1.18	5.33	3.43	0.39272	.	0.183434	0.45606	D	0.000342	T	0.56485	0.1988	M	0.86651	2.83	0.80722	D	1	D	0.71674	0.998	P	0.59487	0.858	T	0.61505	-0.7049	9	.	.	.	-23.816	9.1136	0.36744	0.0779:0.0:0.7762:0.1458	.	46	P37288	V1AR_HUMAN	C	46	ENSP00000299178:R46C	.	R	-	1	0	AVPR1A	61830748	1.000000	0.71417	0.906000	0.35671	0.227000	0.25037	6.485000	0.73625	1.250000	0.43966	0.561000	0.74099	CGC	.	.		0.697	AVPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406734.1			A	63544481	G	A	63544481	3	1	126	1	0	0	0	0	1	0	0	0	1231	1087	38	1	1128	1	AVPR1A	12	63544481	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	9990999	63544481	70307414	32	20988										
MYO1H	283446	hgsc.bcm.edu	37	chr12	109879426	109879426	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ttgtgtattaccagatgcagCaaaaggtagttacaagtgaa	10	5	0	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr12:109879426C>T	ENST00000431443.2	+	25	2527	c.2527C>T	c.(2527-2529)Caa>Taa	p.Q843*	MYO1H_ENST00000310903.5_Nonsense_Mutation_p.Q833*	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	843	Myosin tail. {ECO:0000255}.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						CCAGATGCAGCAAAAGGTAGT	0.408																																					p.Q833X		Atlas-SNP	.											.	MYO1H	98	.	0			c.C2497T						.						83	72	76					12																	109879426		1858	4096	5954	SO:0001587	stop_gained	283446	exon25			ATGCAGCAAAAGG		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.2527C>T	chr12.hg19:g.109879426C>T	ENSP00000444076:p.Gln843*	207.0	0.0		270.0	41.0	NM_001101421	F5H3C6	Nonsense_Mutation	SNP	ENST00000431443.2	hg19		.	.	.	.	.	.	.	.	.	.	C	39	7.598883	0.98381	.	.	ENSG00000174527	ENST00000310903;ENST00000431443;ENST00000542268	.	.	.	5.09	3.12	0.35913	.	0.158082	0.30109	N	0.010391	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	14.7318	0.69388	0.0:0.7276:0.2723:0.0	.	.	.	.	X	833;843;24	.	ENSP00000439182:Q833X	Q	+	1	0	MYO1H	108363809	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.340000	0.52143	1.258000	0.44101	0.655000	0.94253	CAA	.	.		0.408	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		T	109879426	C	T	109879426	4	4	126	1	0	0	0	0	0	1	0	0	10084	711	25	3	2595	3	MYO1H	12	109879426	Nonsense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	46334945	109879426	23972469	33	20989										
RAD9B	144715	hgsc.bcm.edu	37	chr12	110956742	110956742	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tttattttgatttccctgggAagtaggtccttgagaatttt	9	5	0	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr12:110956742A>G	ENST00000409778.3	+	6	583	c.559A>G	c.(559-561)Aaa>Gaa	p.K187E	RAD9B_ENST00000392672.4_Splice_Site_p.K256E|RAD9B_ENST00000409246.1_Splice_Site_p.K184E|RAD9B_ENST00000409425.1_Splice_Site_p.K184E|RAD9B_ENST00000409300.1_Splice_Site_p.K256E			Q6WBX8	RAD9B_HUMAN	RAD9 homolog B (S. pombe)	242					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	checkpoint clamp complex (GO:0030896)|nucleoplasm (GO:0005654)				endometrium(1)|large_intestine(2)|lung(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	7						TTTCCCTGGGAAGTAGGTCCT	0.308																																					p.K256E		Atlas-SNP	.											.	RAD9B	50	.	0			c.A766G						.						69	66	67					12																	110956742		2201	4293	6494	SO:0001630	splice_region_variant	144715	exon8			CCTGGGAAGTAGG		CCDS9148.2, CCDS66469.1, CCDS73526.1, CCDS73527.1	12q24.13	2008-12-15	2008-12-15		ENSG00000151164	ENSG00000151164			21700	protein-coding gene	gene with protein product		608368					Standard	NM_152442		Approved	FLJ40346	uc001trf.4	Q6WBX8	OTTHUMG00000152952	ENST00000409778.3:c.560+1A>G	chr12.hg19:g.110956742A>G		38.0	0.0		80.0	4.0	NM_152442	Q5U5K0|Q6NVJ1|Q6ZVT7|Q8N7T9|Q96LI8	Missense_Mutation	SNP	ENST00000409778.3	hg19		.	.	.	.	.	.	.	.	.	.	A	20.9	4.061386	0.76187	.	.	ENSG00000151164	ENST00000409246;ENST00000392672;ENST00000409300;ENST00000409425;ENST00000409778	T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.49029	0.1533	M	0.68317	2.08	0.36502	D	0.869083	D;P;P	0.71674	0.998;0.941;0.941	D;P;P	0.77557	0.99;0.779;0.779	T	0.59144	-0.7509	10	0.62326	D	0.03	-22.9381	13.7178	0.62708	1.0:0.0:0.0:0.0	.	187;256;253	B4DYM6;B4DX60;Q6WBX8	.;.;RAD9B_HUMAN	E	184;256;256;184;187	ENSP00000387329:K184E;ENSP00000376440:K256E;ENSP00000386434:K256E;ENSP00000386629:K184E;ENSP00000386697:K187E	ENSP00000376440:K256E	K	+	1	0	RAD9B	109441125	1.000000	0.71417	0.995000	0.50966	0.630000	0.37929	5.339000	0.65953	2.254000	0.74563	0.467000	0.42956	AAA	.	.		0.308	RAD9B-009	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404634.1	NM_152442	Missense_Mutation	G	110956742	A	G	110956742	5	3	126	1	0	0	0	0	0	0	1	0	13011	260	9	2	796	2	RAD9B	12	110956742	Splice_Site	SNP	A	TCGA-DD-A4ND-01A-11D-A25V-10	1077316	110956742	22895153	34	20990										
SACS	26278	hgsc.bcm.edu	37	chr13	23912521	23912521	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tccactctcactcagggaaaActtcagagcctctcctgtgt	7	14	4	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr13:23912521A>T	ENST00000382292.3	-	9	5767	c.5494T>A	c.(5494-5496)Ttt>Att	p.F1832I	SACS_ENST00000402364.1_Missense_Mutation_p.F1082I|SACS_ENST00000382298.3_Missense_Mutation_p.F1832I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1832					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CTCAGGGAAAACTTCAGAGCC	0.488																																					p.F1832I		Atlas-SNP	.											.	SACS	871	.	0			c.T5494A						.						133	130	131					13																	23912521		2203	4299	6502	SO:0001583	missense	26278	exon10			GGGAAAACTTCAG	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.5494T>A	chr13.hg19:g.23912521A>T	ENSP00000371729:p.Phe1832Ile	91.0	0.0		89.0	8.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	A	34	5.296623	0.95574	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87412	-2.15;-2.25;-2.15	5.75	5.75	0.90469	.	0.052901	0.85682	N	0.000000	D	0.89171	0.6639	M	0.65975	2.015	0.53005	D	0.999968	D	0.54601	0.967	P	0.50314	0.637	D	0.87984	0.2745	10	0.31617	T	0.26	.	16.0591	0.80826	1.0:0.0:0.0:0.0	.	1832	Q9NZJ4	SACS_HUMAN	I	1832;1082;1832	ENSP00000371729:F1832I;ENSP00000385844:F1082I;ENSP00000371735:F1832I	ENSP00000371729:F1832I	F	-	1	0	SACS	22810521	1.000000	0.71417	0.973000	0.42090	0.960000	0.62799	8.962000	0.93254	2.190000	0.69967	0.482000	0.46254	TTT	.	.		0.488	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23912521	A	T	23912521	3	4	126	1	0	0	0	0	1	0	0	0	13819	43	2	4	8249	4	SACS	13	23912521	Missense_Mutation	SNP	A	TCGA-DD-A4ND-01A-11D-A25V-10		23912521	91257357	35	20991										
DCLK1	9201	hgsc.bcm.edu	37	chr13	36428640	36428640	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ttgcttatttccttaccctcTgcttccgcaggcttcctggg	8	14	1	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr13:36428640T>G	ENST00000360631.3	-	6	1242	c.1031A>C	c.(1030-1032)cAg>cCg	p.Q344P	DCLK1_ENST00000379892.4_Missense_Mutation_p.Q344P|DCLK1_ENST00000379893.1_Missense_Mutation_p.Q37P|DCLK1_ENST00000460982.1_5'UTR|DCLK1_ENST00000255448.4_Missense_Mutation_p.Q344P			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	344					axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		CCTTACCCTCTGCTTCCGCAG	0.552																																					p.Q344P		Atlas-SNP	.											.	DCLK1	350	.	0			c.A1031C						.						122	100	107					13																	36428640		2203	4300	6503	SO:0001583	missense	9201	exon6			ACCCTCTGCTTCC	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1031A>C	chr13.hg19:g.36428640T>G	ENSP00000353846:p.Gln344Pro	124.0	0.0		144.0	30.0	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	hg19		.	.	.	.	.	.	.	.	.	.	T	13.57	2.277968	0.40294	.	.	ENSG00000133083	ENST00000399319;ENST00000255448;ENST00000360631;ENST00000379893;ENST00000539451;ENST00000379892	T;T;T;T	0.68181	-0.27;-0.26;-0.31;1.89	5.67	5.67	0.87782	.	0.090520	0.48286	D	0.000195	T	0.59321	0.2185	L	0.34521	1.04	0.48087	D	0.999589	B;P;B	0.37423	0.439;0.594;0.439	B;B;B	0.39660	0.306;0.225;0.306	T	0.57376	-0.7822	10	0.27082	T	0.32	.	15.9173	0.79531	0.0:0.0:0.0:1.0	.	37;344;37	O15075-4;O15075-2;O15075-3	.;.;.	P	36;344;344;37;344;344	ENSP00000255448:Q344P;ENSP00000353846:Q344P;ENSP00000369223:Q37P;ENSP00000369222:Q344P	ENSP00000255448:Q344P	Q	-	2	0	DCLK1	35326640	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.035000	0.64158	2.170000	0.68504	0.533000	0.62120	CAG	.	.		0.552	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		G	36428640	T	G	36428640	3	3	126	1	0	0	0	0	1	0	0	0	4293	1580	55	5	1210	5	DCLK1	13	36428640	Missense_Mutation	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10	12516119	36428640	78741238	36	20992										
LMO7	4008	hgsc.bcm.edu	37	chr13	76382095	76382095	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	aattcaagcaaaatttctctGtgtacttgaaaggacatgcc	7	8	2	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr13:76382095G>A	ENST00000321797.8	+	8	1698	c.977G>A	c.(976-978)tGt>tAt	p.C326Y	LMO7_ENST00000357063.3_Missense_Mutation_p.C611Y|LMO7_ENST00000341547.4_Intron|LMO7_ENST00000526202.1_Intron|LMO7_ENST00000377534.3_Missense_Mutation_p.C611Y|LMO7_ENST00000465261.2_Missense_Mutation_p.C326Y|RP11-29G8.3_ENST00000563635.1_RNA			Q8WWI1	LMO7_HUMAN	LIM domain 7	611					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AAATTTCTCTGTGTACTTGAA	0.443																																					p.C326Y		Atlas-SNP	.											.	LMO7	334	.	0			c.G977A						.						85	86	86					13																	76382095		1568	3582	5150	SO:0001583	missense	4008	exon7			TTCTCTGTGTACT	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"F-box only protein 20"	604362	"LIM domain only 7"	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.977G>A	chr13.hg19:g.76382095G>A	ENSP00000317802:p.Cys326Tyr	56.0	0.0		52.0	8.0	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.	.	.	.	.	.	.	.	.	.	G	19.06	3.754485	0.69648	.	.	ENSG00000136153	ENST00000357063;ENST00000377534;ENST00000321797;ENST00000465261	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	5.67	4.81	0.61882	.	0.046152	0.85682	D	0.000000	T	0.67552	0.2905	M	0.62723	1.935	0.47153	D	0.999334	D;D	0.76494	0.999;0.999	P;P	0.60789	0.879;0.879	T	0.72151	-0.4377	10	0.72032	D	0.01	-11.125	16.6107	0.84882	0.0:0.1345:0.8655:0.0	.	611;326	Q8WWI1;E9PLH4	LMO7_HUMAN;.	Y	611;611;326;326	ENSP00000349571:C611Y;ENSP00000366757:C611Y;ENSP00000317802:C326Y;ENSP00000433352:C326Y	ENSP00000317802:C326Y	C	+	2	0	LMO7	75280096	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	6.233000	0.72320	1.495000	0.48549	0.655000	0.94253	TGT	.	.		0.443	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		A	76382095	G	A	76382095	3	1	126	1	0	0	0	0	1	0	0	0	8864	1377	48	3	1874	3	LMO7	13	76382095	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	39953455	76382095	38787783	37	20993										
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58965663	58965663	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ctaaaccattatctcggcaaTttgacacagtttcaggtaga	7	9	2	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr14:58965663T>G	ENST00000556134.1	+	28	4382	c.4108T>G	c.(4108-4110)Ttt>Gtt	p.F1370V	KIAA0586_ENST00000261244.5_Missense_Mutation_p.F1309V|KIAA0586_ENST00000354386.6_Missense_Mutation_p.F1438V|KIAA0586_ENST00000423743.3_Missense_Mutation_p.F1341V|KIAA0586_ENST00000538571.2_3'UTR	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	1370					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						ATCTCGGCAATTTGACACAGT	0.373																																					p.F1438V		Atlas-SNP	.											.	KIAA0586	180	.	0			c.T4312G						.						60	52	55					14																	58965663		1882	4118	6000	SO:0001583	missense	9786	exon29			CGGCAATTTGACA	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.4108T>G	chr14.hg19:g.58965663T>G	ENSP00000452351:p.Phe1370Val	107.0	0.0		148.0	49.0	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	hg19	CCDS58321.1	.	.	.	.	.	.	.	.	.	.	T	7.543	0.661055	0.14645	.	.	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000423743;ENST00000261244;ENST00000555397	T;T;T;T	0.41400	1.0;1.02;1.01;1.01	4.83	0.828	0.18841	.	1.342700	0.04864	N	0.444663	T	0.30727	0.0774	.	.	.	0.09310	N	1	B;B;P;B;B	0.38370	0.012;0.023;0.628;0.012;0.021	B;B;B;B;B	0.40066	0.006;0.013;0.318;0.006;0.009	T	0.20505	-1.0273	9	0.26408	T	0.33	.	4.7549	0.13078	0.0:0.2631:0.1554:0.5815	.	1245;1438;1309;1370;1341	B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20	.;.;.;K0586_HUMAN;.	V	1438;1370;1341;1309;67	ENSP00000346359:F1438V;ENSP00000452351:F1370V;ENSP00000399427:F1341V;ENSP00000261244:F1309V	ENSP00000261244:F1309V	F	+	1	0	KIAA0586	58035416	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.019000	0.13444	0.203000	0.20529	0.533000	0.62120	TTT	.	.		0.373	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		G	58965663	T	G	58965663	3	3	126	1	0	0	0	0	1	0	0	0	8195	1493	52	5	4027	5	KIAA0586	14	58965663	Missense_Mutation	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10		58965663	48383877	38	20994										
NUMB	8650	hgsc.bcm.edu	37	chr14	73746111	73746111	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ctggcttagcaagcacatggAaggctgagtcagtgccatta	12	9	1	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr14:73746111A>C	ENST00000355058.3	-	12	1396	c.1118T>G	c.(1117-1119)tTc>tGc	p.F373C	NUMB_ENST00000454166.4_Intron|NUMB_ENST00000544991.3_Intron|NUMB_ENST00000557597.1_Missense_Mutation_p.F362C|NUMB_ENST00000556772.1_Missense_Mutation_p.F229C|NUMB_ENST00000560335.1_Intron|NUMB_ENST00000555238.1_Missense_Mutation_p.F373C|NUMB_ENST00000359560.3_Missense_Mutation_p.F362C|NUMB_ENST00000559312.1_Intron|NUMB_ENST00000535282.1_Missense_Mutation_p.F362C|NUMB_ENST00000555738.2_Intron|NUMB_ENST00000555394.1_Intron|NUMB_ENST00000554521.2_Intron|NUMB_ENST00000554546.1_Intron|NUMB_ENST00000356296.4_Intron			P49757	NUMB_HUMAN	numb homolog (Drosophila)	373					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		AAGCACATGGAAGGCTGAGTC	0.532																																					p.F373C		Atlas-SNP	.											.	NUMB	56	.	0			c.T1118G						.						112	92	99					14																	73746111		2203	4300	6503	SO:0001583	missense	8650	exon12			ACATGGAAGGCTG	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"numb (Drosophila) homolog", "chromosome 14 open reading frame 41"	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.1118T>G	chr14.hg19:g.73746111A>C	ENSP00000347169:p.Phe373Cys	160.0	0.0		218.0	33.0	NM_001005743	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Missense_Mutation	SNP	ENST00000355058.3	hg19	CCDS32116.1	.	.	.	.	.	.	.	.	.	.	A	16.59	3.164946	0.57476	.	.	ENSG00000133961	ENST00000557597;ENST00000555238;ENST00000556772;ENST00000355058;ENST00000359560;ENST00000535282	T;T;T;T;T;T	0.49432	0.78;0.78;1.39;0.78;0.78;0.78	5.51	3.09	0.35607	.	0.101870	0.64402	D	0.000002	T	0.33235	0.0856	N	0.08118	0	0.48511	D	0.999662	P;P	0.45428	0.858;0.778	P;B	0.48368	0.575;0.371	T	0.09796	-1.0658	10	0.40728	T	0.16	-0.3505	10.3063	0.43683	0.8649:0.0:0.1351:0.0	.	362;373	P49757-3;P49757	.;NUMB_HUMAN	C	362;373;229;373;362;362	ENSP00000451117:F362C;ENSP00000451300:F373C;ENSP00000451513:F229C;ENSP00000347169:F373C;ENSP00000352563:F362C;ENSP00000441258:F362C	ENSP00000347169:F373C	F	-	2	0	NUMB	72815864	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.611000	0.54132	0.487000	0.27698	0.459000	0.35465	TTC	.	.		0.532	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1			C	73746111	A	C	73746111	3	2	126	1	0	0	0	0	1	0	0	0	10760	246	9	5	845	5	NUMB	14	73746111	Missense_Mutation	SNP	A	TCGA-DD-A4ND-01A-11D-A25V-10	14780448	73746111	33603429	39	20995										
KIAA1024	23251	hgsc.bcm.edu	37	chr15	79748973	79748973	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cgtccaagtgccggaagatgGactgcaaggactgcccacag	13	12	0	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr15:79748973G>T	ENST00000305428.3	+	2	559	c.484G>T	c.(484-486)Gac>Tac	p.D162Y		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	162						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						CCGGAAGATGGACTGCAAGGA	0.572																																					p.D162Y		Atlas-SNP	.											.	KIAA1024	146	.	0			c.G484T						.						68	72	71					15																	79748973		2196	4293	6489	SO:0001583	missense	23251	exon2			AAGATGGACTGCA	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.484G>T	chr15.hg19:g.79748973G>T	ENSP00000307461:p.Asp162Tyr	85.0	0.0		66.0	14.0	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	hg19	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.716867	0.68844	.	.	ENSG00000169330	ENST00000305428	T	0.35973	1.28	5.24	5.24	0.73138	.	0.153847	0.64402	D	0.000017	T	0.45013	0.1321	L	0.60455	1.87	0.53005	D	0.999966	P	0.43094	0.799	P	0.45946	0.498	T	0.30475	-0.9977	9	.	.	.	.	18.8308	0.92139	0.0:0.0:1.0:0.0	.	162	Q9UPX6	K1024_HUMAN	Y	162	ENSP00000307461:D162Y	.	D	+	1	0	KIAA1024	77536028	1.000000	0.71417	0.642000	0.29436	0.994000	0.84299	8.248000	0.89832	2.443000	0.82685	0.591000	0.81541	GAC	.	.		0.572	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		T	79748973	G	T	79748973	3	4	126	1	0	0	0	0	1	0	0	0	8214	1174	41	3	486	3	KIAA1024	15	79748973	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10		79748973	22782419	40	20996										
MAN2A2	4122	hgsc.bcm.edu	37	chr15	91461902	91461902	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ccctaccctcggcggagaccGcactcatcttacaccgcaag	8	18	2	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr15:91461902G>A	ENST00000559717.1	+	22	3676	c.3217G>A	c.(3217-3219)Gca>Aca	p.A1073T	MAN2A2_ENST00000430376.2_Missense_Mutation_p.A263T|MAN2A2_ENST00000558538.1_3'UTR|MAN2A2_ENST00000360468.3_Missense_Mutation_p.A1073T|MAN2A2_ENST00000431652.2_Missense_Mutation_p.A581T|AC068831.15_ENST00000560522.1_RNA			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	1073					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GGCGGAGACCGCACTCATCTT	0.607																																					p.A1073T		Atlas-SNP	.											.	MAN2A2	99	.	0			c.G3217A						.						49	41	44					15																	91461902		2198	4298	6496	SO:0001583	missense	4122	exon21			GAGACCGCACTCA	L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.3217G>A	chr15.hg19:g.91461902G>A	ENSP00000452948:p.Ala1073Thr	48.0	0.0		54.0	10.0	NM_006122	A6NH12|A8K1E8|Q13754	Missense_Mutation	SNP	ENST00000559717.1	hg19	CCDS32332.1	.	.	.	.	.	.	.	.	.	.	G	35	5.528441	0.96446	.	.	ENSG00000196547	ENST00000360468;ENST00000431652;ENST00000430376	D;D;D	0.83673	-1.75;-1.75;-1.75	5.95	5.95	0.96441	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.85682	D	0.000000	D	0.92293	0.7555	M	0.82517	2.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.989;0.995;0.997	D	0.91919	0.5546	10	0.59425	D	0.04	-17.2714	20.458	0.99154	0.0:0.0:1.0:0.0	.	581;701;1073	B4DEU9;B4DIK4;P49641	.;.;MA2A2_HUMAN	T	1073;581;263	ENSP00000353655:A1073T;ENSP00000388221:A581T;ENSP00000394372:A263T	ENSP00000353655:A1073T	A	+	1	0	MAN2A2	89262906	1.000000	0.71417	0.206000	0.23566	0.062000	0.15995	7.414000	0.80117	2.835000	0.97688	0.650000	0.86243	GCA	.	.		0.607	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122		A	91461902	G	A	91461902	3	1	126	1	0	0	0	0	1	0	0	0	9224	1087	38	1	3299	1	MAN2A2	15	91461902	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	11712929	91461902	11069490	41	20997										
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85697087	85697087	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	acaattcagagcaagcggcaGacgccttcaccgagactggc	11	13	2	3			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr16:85697087G>A	ENST00000253458.7	+	11	2687	c.2511G>A	c.(2509-2511)caG>caA	p.Q837Q	GSE1_ENST00000405402.2_Silent_p.Q733Q|GSE1_ENST00000393243.1_Silent_p.Q764Q	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	837																	GCAAGCGGCAGACGCCTTCAC	0.562																																					p.Q837Q		Atlas-SNP	.											.	.	.	.	0			c.G2511A						.						82	82	82					16																	85697087		2198	4300	6498	SO:0001819	synonymous_variant	23199	exon11			GCGGCAGACGCCT	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.2511G>A	chr16.hg19:g.85697087G>A		112.0	0.0		107.0	26.0	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Silent	SNP	ENST00000253458.7	hg19	CCDS10952.1	.	.	.	.	.	.	.	.	.	.	G	9.872	1.199131	0.22121	.	.	ENSG00000131149	ENST00000412692;ENST00000438180	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	T	0.71230	0.3315	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70008	-0.4990	4	.	.	.	-30.1443	15.0773	0.72087	0.0:0.1425:0.8575:0.0	.	.	.	.	K	644;39	.	.	R	+	2	0	KIAA0182	84254588	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.959000	0.56744	2.438000	0.82558	0.561000	0.74099	AGA	.	.		0.562	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		A	85697087	G	A	85697087	2	1	126	1	0	0	0	0	0	0	0	1	8168	933	33	3		3	KIAA0182	16	85697087	Silent	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10		85697087	4657666	42	20998										
USP6	9098	hgsc.bcm.edu	37	chr17	5042895	5042895	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cccccattatgattttgaatGgagctgctgggtccgtgcca	11	11	0	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr17:5042895G>A	ENST00000574788.1	+	22	3654	c.1424G>A	c.(1423-1425)tGg>tAg	p.W475*	USP6_ENST00000250066.6_Nonsense_Mutation_p.W475*|USP6_ENST00000304328.5_Nonsense_Mutation_p.W158*|USP6_ENST00000332776.4_Nonsense_Mutation_p.W475*			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	475			W -> R (in dbSNP:rs8073787). {ECO:0000269|PubMed:1565468}.		cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.W475*(1)|p.R475Q(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GATTTTGAATGGAGCTGCTGG	0.592			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																p.W475X		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	USP6_ENST00000250066,NS,carcinoma,0,2	USP6	213	.	2	Substitution - Missense(1)|Substitution - Nonsense(1)	breast(2)	c.G1424A						.						47	52	51					17																	5042895		2203	4300	6503	SO:0001587	stop_gained	9098	exon14			TTGAATGGAGCTG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.1424G>A	chr17.hg19:g.5042895G>A	ENSP00000460380:p.Trp475*	29.0	0.0		46.0	8.0	NM_004505	Q15634|Q86WP6|Q8IWT4	Nonsense_Mutation	SNP	ENST00000574788.1	hg19	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	G	48	14.206262	0.99784	.	.	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	.	.	.	0.266	-0.532	0.11890	.	0.115600	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	.	.	.	.	.	.	.	X	475;475;158	.	ENSP00000250066:W475X	W	+	2	0	USP6	4983619	0.121000	0.22262	0.003000	0.11579	0.003000	0.03518	-0.046000	0.11983	-1.259000	0.02468	-1.242000	0.01536	TGG	.	.		0.592	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		A	5042895	G	A	5042895	4	1	126	1	0	0	0	0	0	1	0	0	17101	1357	47	3	1474	3	USP6	17	5042895	Nonsense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10		5042895	76152315	43	20999										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33486549	33486549	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	atgacaactcacgtaccatcTatgtggtggataatggtgag	11	7	2	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr17:33486549T>A	ENST00000268876.5	+	8	1061	c.964T>A	c.(964-966)Tat>Aat	p.Y322N	UNC45B_ENST00000378449.1_Missense_Mutation_p.Y322N|UNC45B_ENST00000433649.1_Missense_Mutation_p.Y322N|UNC45B_ENST00000591048.1_Missense_Mutation_p.Y322N|UNC45B_ENST00000394570.2_Missense_Mutation_p.Y322N	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	322					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				ACGTACCATCTATGTGGTGGA	0.512																																					p.Y322N		Atlas-SNP	.											.	UNC45B	133	.	0			c.T964A						.						104	89	94					17																	33486549		2203	4300	6503	SO:0001583	missense	146862	exon8			ACCATCTATGTGG	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.964T>A	chr17.hg19:g.33486549T>A	ENSP00000268876:p.Tyr322Asn	71.0	0.0		76.0	16.0	NM_001267052	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	hg19	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.325637	0.81580	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T;T	0.06933	3.24;3.24;3.24;3.25	5.61	5.61	0.85477	Armadillo-like helical (1);	0.108919	0.64402	D	0.000006	T	0.12263	0.0298	N	0.08118	0	0.52501	D	0.999956	D;D;P	0.67145	0.996;0.963;0.642	P;P;B	0.62184	0.899;0.532;0.366	T	0.30238	-0.9985	10	0.87932	D	0	-8.8596	15.283	0.73801	0.0:0.0:0.0:1.0	.	322;322;322	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	N	322	ENSP00000378071:Y322N;ENSP00000268876:Y322N;ENSP00000412840:Y322N;ENSP00000367710:Y322N	ENSP00000268876:Y322N	Y	+	1	0	UNC45B	30510662	1.000000	0.71417	0.675000	0.29917	0.968000	0.65278	7.055000	0.76656	2.254000	0.74563	0.533000	0.62120	TAT	.	.		0.512	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		A	33486549	T	A	33486549	3	1	126	1	0	0	0	0	1	0	0	0	17004	1522	53	4	990	4	UNC45B	17	33486549	Missense_Mutation	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10	28443654	33486549	47708661	44	21000										
CDK12	51755	hgsc.bcm.edu	37	chr17	37619175	37619175	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cccttacaaggagccttcggCctaccagtccagcacccggt	9	17	0	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr17:37619175C>T	ENST00000447079.4	+	1	884	c.851C>T	c.(850-852)gCc>gTc	p.A284V	CDK12_ENST00000430627.2_Missense_Mutation_p.A284V	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	284					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						GAGCCTTCGGCCTACCAGTCC	0.552			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																											p.A284V		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	161	.	0			c.C851T						.						59	61	60					17																	37619175		2203	4300	6503	SO:0001583	missense	51755	exon1			CTTCGGCCTACCA	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"Cyclin-dependent kinases"	24224	protein-coding gene	gene with protein product	"CDC2 related protein kinase 7"	615514	"Cdc2-related kinase, arginine/serine-rich"	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.851C>T	chr17.hg19:g.37619175C>T	ENSP00000398880:p.Ala284Val	105.0	0.0		114.0	15.0	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	hg19	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822495	0.71028	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.46063	0.88;1.53	5.3	5.3	0.74995	.	0.000000	0.46145	D	0.000304	T	0.54549	0.1865	L	0.36672	1.1	0.42644	D	0.993424	D;D;D	0.69078	0.995;0.997;0.991	D;D;D	0.70716	0.952;0.97;0.964	T	0.56306	-0.8001	10	0.59425	D	0.04	-8.0147	16.0239	0.80528	0.0:0.8659:0.1341:0.0	.	284;284;284	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	V	284	ENSP00000407720:A284V;ENSP00000398880:A284V	ENSP00000407720:A284V	A	+	2	0	CDK12	34872701	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	2.674000	0.46867	2.490000	0.84030	0.655000	0.94253	GCC	.	.		0.552	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		T	37619175	C	T	37619175	3	4	126	1	0	0	0	0	1	0	0	0	3130	739	26	3	853	3	CDK12	17	37619175	Missense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	4132626	37619175	43576035	45	21001										
KRT27	342574	hgsc.bcm.edu	37	chr17	38935981	38935981	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	gaaccaggcctccgcgtcccTgcggttctgctctgcgaggg	14	15	2	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr17:38935981T>A	ENST00000301656.3	-	4	857	c.817A>T	c.(817-819)Agg>Tgg	p.R273W	KRT27_ENST00000540723.1_5'Flank	NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				TCCGCGTCCCTGCGGTTCTGC	0.642																																					p.R273W		Atlas-SNP	.											.	KRT27	41	.	0			c.A817T						.						38	37	37					17																	38935981		2203	4300	6503	SO:0001583	missense	342574	exon4			CGTCCCTGCGGTT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.817A>T	chr17.hg19:g.38935981T>A	ENSP00000301656:p.Arg273Trp	82.0	0.0		80.0	17.0	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	hg19	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.032164	0.75504	.	.	ENSG00000171446	ENST00000301656	D	0.89343	-2.5	5.51	1.73	0.24493	Filament (1);	0.000000	0.64402	D	0.000004	D	0.94019	0.8084	M	0.91354	3.2	0.39113	D	0.961502	D	0.71674	0.998	D	0.67382	0.951	D	0.93288	0.6666	10	0.87932	D	0	.	8.5883	0.33670	0.0:0.0698:0.4034:0.5268	.	273	Q7Z3Y8	K1C27_HUMAN	W	273	ENSP00000301656:R273W	ENSP00000301656:R273W	R	-	1	2	KRT27	36189507	0.000000	0.05858	1.000000	0.80357	0.809000	0.45718	-0.122000	0.10627	0.433000	0.26313	0.477000	0.44152	AGG	.	.		0.642	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		A	38935981	T	A	38935981	3	1	126	1	0	0	0	0	1	0	0	0	8473	1579	55	4	582	4	KRT27	17	38935981	Missense_Mutation	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10	1316806	38935981	42259229	46	21002										
LPIN2	9663	hgsc.bcm.edu	37	chr18	2939526	2939526	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	gtccactccatgtgagactcTgatctgagcaggctctccgc	10	14	3	3			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr18:2939526T>C	ENST00000261596.4	-	6	1012	c.774A>G	c.(772-774)tcA>tcG	p.S258S		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	258					cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		TGTGAGACTCTGATCTGAGCA	0.507																																					p.S258S		Atlas-SNP	.											.	LPIN2	75	.	0			c.A774G						.						130	119	123					18																	2939526		2203	4300	6503	SO:0001819	synonymous_variant	9663	exon6			AGACTCTGATCTG	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.774A>G	chr18.hg19:g.2939526T>C		58.0	0.0		59.0	15.0	NM_014646	A7MD25|D3DUH3	Silent	SNP	ENST00000261596.4	hg19	CCDS11829.1																																																																																			.	.		0.507	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		C	2939526	T	C	2939526	2	2	126	1	0	0	0	0	0	0	0	1	8928	1567	55	2		2	LPIN2	18	2939526	Silent	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10		2939526	75137722	47	21003										
DSC2	1824	hgsc.bcm.edu	37	chr18	28650775	28650775	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	aggaattacttttggttgttTagacgtcccagaagccccac	9	10	0	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr18:28650775T>A	ENST00000280904.6	-	14	2610	c.2167A>T	c.(2167-2169)Aaa>Taa	p.K723*	snoU13_ENST00000459603.1_RNA|DSC2_ENST00000251081.6_Nonsense_Mutation_p.K723*	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	723					bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			TTTGGTTGTTTAGACGTCCCA	0.388																																					p.K723X		Atlas-SNP	.											.	DSC2	168	.	0			c.A2167T						.						117	119	118					18																	28650775		2203	4300	6503	SO:0001587	stop_gained	1824	exon14			GTTGTTTAGACGT	X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"Cadherins / Major cadherins"	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.2167A>T	chr18.hg19:g.28650775T>A	ENSP00000280904:p.Lys723*	93.0	0.0		80.0	13.0	NM_024422		Nonsense_Mutation	SNP	ENST00000280904.6	hg19	CCDS11892.1	.	.	.	.	.	.	.	.	.	.	T	32	5.157194	0.94686	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000438199;ENST00000399347	.	.	.	6.08	2.21	0.28008	.	0.491568	0.15119	N	0.279484	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.3855	0.16216	0.0:0.1725:0.2733:0.5542	.	.	.	.	X	723;723;489;736	.	ENSP00000251081:K723X	K	-	1	0	DSC2	26904773	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.283000	0.18846	0.528000	0.28580	-0.435000	0.05868	AAA	.	.		0.388	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		A	28650775	T	A	28650775	4	1	126	1	0	0	0	0	0	1	0	0	4768	1763	61	4	590	4	DSC2	18	28650775	Nonsense_Mutation	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10	25711249	28650775	49426473	48	21004										
OR7A5	26659	hgsc.bcm.edu	37	chr19	14938783	14938783	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	gcaggctatgtaggtgatgaCtttgttctgtgtctggatgt	14	5	2	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr19:14938783C>A	ENST00000322301.3	-	2	358	c.271G>T	c.(271-273)Gtc>Ttc	p.V91F	OR7A5_ENST00000594432.1_Missense_Mutation_p.V91F|OR7A5_ENST00000601611.1_Intron			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	91					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						TAGGTGATGACTTTGTTCTGT	0.443																																					p.V91F		Atlas-SNP	.											.	OR7A5	43	.	0			c.G271T						.						204	182	190					19																	14938783		2203	4300	6503	SO:0001583	missense	26659	exon1			TGATGACTTTGTT	X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"GPCR / Class A : Olfactory receptors"	8368	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily A, member 5 pseudogene"				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.271G>T	chr19.hg19:g.14938783C>A	ENSP00000316955:p.Val91Phe	125.0	0.0		171.0	8.0	NM_017506	B2R682|Q6IFP1|Q96R96	Missense_Mutation	SNP	ENST00000322301.3	hg19	CCDS12318.1	.	.	.	.	.	.	.	.	.	.	c	8.052	0.766170	0.15983	.	.	ENSG00000188269	ENST00000322301	T	0.00555	6.63	3.13	2.02	0.26589	GPCR, rhodopsin-like superfamily (1);	1.152260	0.07204	U	0.857959	T	0.00754	0.0025	M	0.72353	2.195	0.09310	N	1	B	0.23937	0.094	B	0.25614	0.062	T	0.47169	-0.9138	10	0.40728	T	0.16	.	4.4453	0.11595	0.0:0.6307:0.2373:0.1319	.	91	Q15622	OR7A5_HUMAN	F	91	ENSP00000316955:V91F	ENSP00000316955:V91F	V	-	1	0	OR7A5	14799783	0.000000	0.05858	0.001000	0.08648	0.193000	0.23685	0.004000	0.13106	0.642000	0.30620	0.134000	0.15878	GTC	.	.		0.443	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506		A	14938783	C	A	14938783	3	1	126	1	0	0	0	0	1	0	0	0	11225	565	20	3	692	3	OR7A5	19	14938783	Missense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10		14938783	44190200	49	21005										
OR7A10	390892	hgsc.bcm.edu	37	chr19	14952139	14952139	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cagaacaggcaaggtggaccAcctgattaatttcacagaaa	9	9	1	3			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr19:14952139A>G	ENST00000248058.1	-	1	550	c.551T>C	c.(550-552)gTg>gCg	p.V184A		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	184						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E180fs*7(1)		NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					AAGGTGGACCACCTGATTAAT	0.448																																					p.V184A		Atlas-SNP	.											.	OR7A10	33	.	1	Deletion - Frameshift(1)	breast(1)	c.T551C						.						80	79	79					19																	14952139		2203	4300	6503	SO:0001583	missense	390892	exon1			TGGACCACCTGAT		CCDS32936.1	19p13.1	2012-08-09						"GPCR / Class A : Olfactory receptors"	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.551T>C	chr19.hg19:g.14952139A>G	ENSP00000248058:p.Val184Ala	169.0	0.0		189.0	20.0	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	hg19	CCDS32936.1	.	.	.	.	.	.	.	.	.	.	a	13.14	2.146903	0.37923	.	.	ENSG00000127515	ENST00000248058	T	0.00231	8.49	2.57	2.57	0.30868	GPCR, rhodopsin-like superfamily (1);	0.495796	0.14495	U	0.316089	T	0.00552	0.0018	M	0.93016	3.37	0.09310	N	1	P	0.52463	0.953	P	0.58331	0.837	T	0.28202	-1.0051	10	0.59425	D	0.04	.	8.7704	0.34728	1.0:0.0:0.0:0.0	.	184	O76100	OR7AA_HUMAN	A	184	ENSP00000248058:V184A	ENSP00000248058:V184A	V	-	2	0	OR7A10	14813139	0.451000	0.25705	0.932000	0.37286	0.325000	0.28411	5.638000	0.67861	1.210000	0.43336	0.113000	0.15668	GTG	.	.		0.448	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190		G	14952139	A	G	14952139	3	3	126	1	0	0	0	0	1	0	0	0	11223	159	6	2	382	2	OR7A10	19	14952139	Missense_Mutation	SNP	A	TCGA-DD-A4ND-01A-11D-A25V-10	13356	14952139	44176844	50	21006										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15291637	15291637	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cggctgcaccaatccaccagCgtctggaggggaagcactca	12	14	2	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr19:15291637C>A	ENST00000263388.2	-	19	3072	c.2997G>T	c.(2995-2997)acG>acT	p.T999T		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	999					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			AATCCACCAGCGTCTGGAGGG	0.627																																					p.T999T		Atlas-SNP	.											.	NOTCH3	340	.	0			c.G2997T						.						26	26	26					19																	15291637		2203	4299	6502	SO:0001819	synonymous_variant	4854	exon19			CACCAGCGTCTGG	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.2997G>T	chr19.hg19:g.15291637C>A		64.0	0.0		96.0	4.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	hg19	CCDS12326.1																																																																																			.	.		0.627	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		A	15291637	C	A	15291637	2	1	126	1	0	0	0	0	0	0	0	1	10559	755	27	1		1	NOTCH3	19	15291637	Silent	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	339498	15291637	43837346	51	21007										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52198139	52198139	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tgcctcccgtccacagacatGgtgggcgactccgcgccggc	13	17	0	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr20:52198139G>C	ENST00000371471.2	-	2	1652	c.1227C>G	c.(1225-1227)acC>acG	p.T409T	ZNF217_ENST00000302342.3_Silent_p.T409T|ZNF217_ENST00000540425.1_5'Flank			O75362	ZN217_HUMAN	zinc finger protein 217	409					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			CCACAGACATGGTGGGCGACT	0.632																																					p.T409T		Atlas-SNP	.											.	ZNF217	227	.	0			c.C1227G						.						45	48	47					20																	52198139		2203	4300	6503	SO:0001819	synonymous_variant	7764	exon1			AGACATGGTGGGC	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1227C>G	chr20.hg19:g.52198139G>C		58.0	0.0		76.0	10.0	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	hg19	CCDS13443.1																																																																																			.	.		0.632	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		C	52198139	G	C	52198139	2	2	126	1	0	0	0	0	0	0	0	1	17787	1335	47	4		4	ZNF217	20	52198139	Silent	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10		52198139	10827381	52	21008										
RBM11	54033	hgsc.bcm.edu	37	chr21	15599354	15599354	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ggactcaccaacaaccaagtGactctgacctttatcagatg	7	12	3	3	rs139439630	byFrequency	TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr21:15599354G>T	ENST00000400577.3	+	5	595	c.586G>T	c.(586-588)Gac>Tac	p.D196Y	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	196					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(U) RNA binding (GO:0008266)|protein homodimerization activity (GO:0042803)			endometrium(3)|kidney(3)|lung(7)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		ACAACCAAGTGACTCTGACCT	0.468																																					p.D196Y		Atlas-SNP	.											.	RBM11	41	.	0			c.G586T						.						326	307	313					21																	15599354		1981	4164	6145	SO:0001583	missense	54033	exon5			CCAAGTGACTCTG	AF130358	CCDS46635.1	21q11	2013-02-12			ENSG00000185272	ENSG00000185272		"RNA binding motif (RRM) containing"	9897	protein-coding gene	gene with protein product						12036298	Standard	NM_144770		Approved		uc002yjo.4	P57052	OTTHUMG00000074263	ENST00000400577.3:c.586G>T	chr21.hg19:g.15599354G>T	ENSP00000383421:p.Asp196Tyr	406.0	0.0		434.0	89.0	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	hg19	CCDS46635.1	.	.	.	.	.	.	.	.	.	.	G	6.836	0.523440	0.13066	.	.	ENSG00000185272	ENST00000400577	T	0.09350	2.99	1.87	1.87	0.25490	.	0.067005	0.64402	D	0.000010	T	0.12689	0.0308	N	0.08118	0	0.25653	N	0.986073	D	0.71674	0.998	D	0.69654	0.965	T	0.09443	-1.0674	10	0.59425	D	0.04	.	11.1988	0.48728	0.0:0.0:1.0:0.0	.	196	P57052	RBM11_HUMAN	Y	196	ENSP00000383421:D196Y	ENSP00000383421:D196Y	D	+	1	0	RBM11	14521225	0.107000	0.21998	0.112000	0.21494	0.343000	0.28985	1.259000	0.32956	1.330000	0.45394	0.195000	0.17529	GAC	.	G|0.988;A|0.012		0.468	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770		T	15599354	G	T	15599354	3	4	126	1	0	0	0	0	1	0	0	0	13127	1290	45	3	604	3	RBM11	21	15599354	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10		15599354	32530541	53	21009										
RNF160	26046	hgsc.bcm.edu	37	chr21	30343736	30343736	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	tggaatgcgctggcacaatgCagagactaactcaaaataag	10	8	1	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr21:30343736C>A	ENST00000361371.5	-	7	920	c.841G>T	c.(841-843)Gca>Tca	p.A281S	LTN1_ENST00000389194.2_Missense_Mutation_p.A327S|LTN1_ENST00000389195.2_Missense_Mutation_p.A327S			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	281					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						TGGCACAATGCAGAGACTAAC	0.373																																					p.A327S		Atlas-SNP	.											.	LTN1	141	.	0			c.G979T						.						192	184	187					21																	30343736		2203	4300	6503	SO:0001583	missense	26046	exon7			ACAATGCAGAGAC	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"RING-type (C3HC4) zinc fingers"	13082	protein-coding gene	gene with protein product	"listerin"	613083	"chromosome 21 open reading frame 98", "zinc finger protein 294", "ring finger protein 160"	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.841G>T	chr21.hg19:g.30343736C>A	ENSP00000354977:p.Ala281Ser	126.0	0.0		113.0	28.0	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	hg19		.	.	.	.	.	.	.	.	.	.	C	24.7	4.561382	0.86335	.	.	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000446611;ENST00000389195	T;T;T	0.65916	3.63;3.63;-0.18	4.66	4.66	0.58398	Armadillo-like helical (1);Armadillo-type fold (1);	0.065142	0.64402	D	0.000010	T	0.65933	0.2739	L	0.46157	1.445	0.58432	D	0.999995	D	0.58620	0.983	P	0.53313	0.723	T	0.60647	-0.7222	10	0.19590	T	0.45	.	18.1081	0.89526	0.0:1.0:0.0:0.0	.	281	O94822	LTN1_HUMAN	S	327;281;283;327	ENSP00000373846:A327S;ENSP00000354977:A281S;ENSP00000373847:A327S	ENSP00000354977:A281S	A	-	1	0	LTN1	29265607	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.794000	0.47853	2.579000	0.87056	0.650000	0.86243	GCA	.	.		0.373	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		A	30343736	C	A	30343736	3	1	126	1	0	0	0	0	1	0	0	0	13470	710	25	3	4555	3	RNF160	21	30343736	Missense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	14744382	30343736	17786159	54	21010										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37618218	37618218	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	cccactctctgctcctggagCtgctcacctacctctgcctg	7	19	3	0			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr21:37618218C>T	ENST00000399151.3	+	19	4025	c.3940C>T	c.(3940-3942)Ctg>Ttg	p.L1314L		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1314					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GCTCCTGGAGCTGCTCACCTA	0.607																																					p.L1314L		Atlas-SNP	.											.	DOPEY2	184	.	0			c.C3940T						.						112	112	112					21																	37618218		2203	4300	6503	SO:0001819	synonymous_variant	9980	exon19			CTGGAGCTGCTCA	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.3940C>T	chr21.hg19:g.37618218C>T		101.0	0.0		117.0	28.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	hg19	CCDS13643.1																																																																																			.	.		0.607	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		T	37618218	C	T	37618218	2	4	126	1	0	0	0	0	0	0	0	1	4710	796	28	3		3	DOPEY2	21	37618218	Silent	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10	7274482	37618218	10511677	55	21011										
FOXRED2	80020	hgsc.bcm.edu	37	chr22	36902221	36902221	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ttagccttgcccgtgtaccgCttgttgatgctgatgagctt	11	10	0	3			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr22:36902221C>G	ENST00000397224.4	-	2	342	c.249G>C	c.(247-249)aaG>aaC	p.K83N	FOXRED2_ENST00000397223.4_Missense_Mutation_p.K83N|FOXRED2_ENST00000216187.6_Missense_Mutation_p.K83N	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	83					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CCGTGTACCGCTTGTTGATGC	0.652																																					p.K83N		Atlas-SNP	.											.	FOXRED2	48	.	0			c.G249C						.						123	87	99					22																	36902221		2203	4300	6503	SO:0001583	missense	80020	exon2			GTACCGCTTGTTG	BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.249G>C	chr22.hg19:g.36902221C>G	ENSP00000380401:p.Lys83Asn	95.0	0.0		119.0	33.0	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Missense_Mutation	SNP	ENST00000397224.4	hg19	CCDS13929.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.644565	0.87859	.	.	ENSG00000100350	ENST00000397224;ENST00000216187;ENST00000397223;ENST00000423980	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	5.04	5.04	0.67666	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.56171	0.1967	M	0.90705	3.14	0.54753	D	0.999989	D	0.89917	1.0	D	0.97110	1.0	T	0.64279	-0.6445	10	0.87932	D	0	-34.3659	11.1032	0.48188	0.0:0.9142:0.0:0.0858	.	83	Q8IWF2	FXRD2_HUMAN	N	83	ENSP00000380401:K83N;ENSP00000216187:K83N;ENSP00000380400:K83N;ENSP00000409692:K83N	ENSP00000216187:K83N	K	-	3	2	FOXRED2	35232167	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	2.007000	0.40883	2.337000	0.79520	0.561000	0.74099	AAG	.	.		0.652	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955		G	36902221	C	G	36902221	3	3	126	1	0	0	0	0	1	0	0	0	6042	796	28	4	1837	4	FOXRED2	22	36902221	Missense_Mutation	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10		36902221	14402345	56	21012										
ZC3H7B	23264	hgsc.bcm.edu	37	chr22	41752683	41752683	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ctggctctgcggcaagaacaGcaacagcaagaagcagtggc	13	11	1	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chr22:41752683G>C	ENST00000352645.4	+	22	2809	c.2552G>C	c.(2551-2553)aGc>aCc	p.S851T	ZC3H7B_ENST00000351589.4_Missense_Mutation_p.S851T	NM_017590.4	NP_060060.3	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	867					viral process (GO:0016032)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						GGCAAGAACAGCAACAGCAAG	0.627																																					p.S851T		Atlas-SNP	.											.	ZC3H7B	82	.	0			c.G2552C						.						112	97	102					22																	41752683		2203	4300	6503	SO:0001583	missense	23264	exon22			AGAACAGCAACAG		CCDS14013.1	22q13.2	2013-01-10		2005-08-09	ENSG00000100403	ENSG00000100403		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30869	protein-coding gene	gene with protein product						10470851, 11230166	Standard	NM_017590		Approved	RoXaN, FLJ13787, DKFZp434K0920, KIAA1031	uc003azw.4	Q9UGR2	OTTHUMG00000150969	ENST00000352645.4:c.2552G>C	chr22.hg19:g.41752683G>C	ENSP00000345793:p.Ser851Thr	93.0	0.0		117.0	10.0	NM_017590	A7YY88|B2RCA4|Q5TFX9|Q8TBT9|Q9H8B6|Q9UGQ9|Q9UGR0|Q9UGR1|Q9UK03|Q9UPW9	Missense_Mutation	SNP	ENST00000352645.4	hg19	CCDS14013.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.218823	0.79464	.	.	ENSG00000100403	ENST00000352645;ENST00000351589	T;T	0.40756	1.02;1.02	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.58821	0.2149	L	0.43152	1.355	0.54753	D	0.999987	D	0.63046	0.992	D	0.69824	0.966	T	0.57493	-0.7802	10	0.52906	T	0.07	-31.4131	19.4454	0.94844	0.0:0.0:1.0:0.0	.	851	Q9UGR2-2	.	T	851	ENSP00000345793:S851T;ENSP00000263243:S851T	ENSP00000263243:S851T	S	+	2	0	ZC3H7B	40082629	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.762000	0.98944	2.586000	0.87340	0.655000	0.94253	AGC	.	.		0.627	ZC3H7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320696.1	NM_017590		C	41752683	G	C	41752683	3	2	126	1	0	0	0	0	1	0	0	0	17588	971	34	4	2634	4	ZC3H7B	22	41752683	Missense_Mutation	SNP	G	TCGA-DD-A4ND-01A-11D-A25V-10	4850462	41752683	9551883	57	21013										
SYP	6855	hgsc.bcm.edu	37	chrX	49049852	49049852	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	gtggccatcttcacatctgaCagccccttggcccatgccga	9	16	3	1	rs140804164		TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chrX:49049852C>A	ENST00000263233.4	-	5	564	c.492G>T	c.(490-492)ctG>ctT	p.L164L	SYP_ENST00000479808.1_Silent_p.L164L|SYP_ENST00000538567.1_Silent_p.L46L	NM_003179.2	NP_003170.1	P08247	SYPH_HUMAN	synaptophysin	164	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cellular response to organic substance (GO:0071310)|endocytosis (GO:0006897)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle membrane organization (GO:0048499)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	cholesterol binding (GO:0015485)|protein self-association (GO:0043621)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)	15		all_lung(315;0.00016)				TCACATCTGACAGCCCCTTGG	0.562																																					p.L164L		Atlas-SNP	.											.	SYP	71	.	0			c.G492T						.						101	66	78					X																	49049852		2203	4300	6503	SO:0001819	synonymous_variant	6855	exon5			ATCTGACAGCCCC	X06389	CCDS14321.1	Xp11.23-p11.22	2014-02-19			ENSG00000102003	ENSG00000102003			11506	protein-coding gene	gene with protein product		313475				3120152, 19377476	Standard	NM_003179		Approved	MRX96	uc004dmz.1	P08247	OTTHUMG00000034557	ENST00000263233.4:c.492G>T	chrX.hg19:g.49049852C>A		297.0	0.0		271.0	43.0	NM_003179	B2R7L6|B7Z359|Q6P2F7	Silent	SNP	ENST00000263233.4	hg19	CCDS14321.1	.	.	.	.	.	.	.	.	.	.	C	8.367	0.834533	0.16820	.	.	ENSG00000102003	ENST00000472598	.	.	.	5.11	2.3	0.28687	.	.	.	.	.	T	0.45696	0.1355	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29518	-1.0009	4	.	.	.	-22.3663	3.0343	0.06117	0.1432:0.5503:0.1373:0.1692	.	.	.	.	F	54	.	.	C	-	2	0	SYP	48936796	1.000000	0.71417	0.997000	0.53966	0.967000	0.64934	1.089000	0.30890	0.539000	0.28788	-0.192000	0.12808	TGT	.	C|1.000;T|0.000		0.562	SYP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083625.2	NM_003179		A	49049852	C	A	49049852	2	1	126	1	0	0	0	0	0	0	0	1	15476	465	17	3		3	SYP	23	49049852	Silent	SNP	C	TCGA-DD-A4ND-01A-11D-A25V-10		49049852	106220708	58	21014										
P2RY4	5030	hgsc.bcm.edu	37	chrX	69478612	69478612	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ccaggggccgagtcactttaTagaccacgttgacaatgttc	10	11	1	2			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chrX:69478612T>C	ENST00000374519.2	-	1	1042	c.863A>G	c.(862-864)tAt>tGt	p.Y288C		NM_002565.3	NP_002556.1	P51582	P2RY4_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 4	288					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|transepithelial chloride transport (GO:0030321)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|uridine nucleotide receptor activity (GO:0015065)|UTP-activated nucleotide receptor activity (GO:0045030)			cervix(2)|endometrium(2)|large_intestine(8)|lung(6)	18						AGTCACTTTATAGACCACGTT	0.552																																					p.Y288C		Atlas-SNP	.											.	P2RY4	39	.	0			c.A863G						.						57	45	49					X																	69478612		2203	4300	6503	SO:0001583	missense	5030	exon1			ACTTTATAGACCA	X91852	CCDS14398.1	Xq13	2012-08-08			ENSG00000186912	ENSG00000186912		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8542	protein-coding gene	gene with protein product		300038				8537336	Standard	NM_002565		Approved	NRU, P2Y4, UNR, P2P	uc004dxz.1	P51582	OTTHUMG00000021769	ENST00000374519.2:c.863A>G	chrX.hg19:g.69478612T>C	ENSP00000363643:p.Tyr288Cys	474.0	0.0		431.0	95.0	NM_002565	Q4VBB7|Q4VBB8|Q502W2|Q5JT22	Missense_Mutation	SNP	ENST00000374519.2	hg19	CCDS14398.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618634	0.66787	.	.	ENSG00000186912	ENST00000374519	T	0.25414	1.8	4.7	4.7	0.59300	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000001	T	0.59985	0.2234	M	0.93854	3.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70956	-0.4731	10	0.87932	D	0	.	12.4838	0.55859	0.0:0.0:0.0:1.0	.	288	P51582	P2RY4_HUMAN	C	288	ENSP00000363643:Y288C	ENSP00000363643:Y288C	Y	-	2	0	P2RY4	69395337	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.659000	0.68010	1.737000	0.51674	0.477000	0.44152	TAT	.	.		0.552	P2RY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057058.2	NM_002565		C	69478612	T	C	69478612	3	2	126	1	0	0	0	0	1	0	0	0	11362	1406	49	2	238	2	P2RY4	23	69478612	Missense_Mutation	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10	20428760	69478612	85791948	59	21015										
RNF113A	7737	hgsc.bcm.edu	37	chrX	119005302	119005302	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ccacgccgagactctcgggcTcattttcctcttcctcttcg	7	17	4	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chrX:119005302T>A	ENST00000371442.2	-	1	489	c.275A>T	c.(274-276)gAg>gTg	p.E92V	NDUFA1_ENST00000371437.4_5'Flank	NM_006978.2	NP_008909.1	O15541	R113A_HUMAN	ring finger protein 113A	92	Poly-Glu.						zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(6)	15						ACTCTCGGGCTCATTTTCCTC	0.547																																					p.E92V		Atlas-SNP	.											.	RNF113A	39	.	0			c.A275T						.						163	162	162					X																	119005302		2203	4300	6503	SO:0001583	missense	7737	exon1			TCGGGCTCATTTT	X98253	CCDS14589.1	Xq24	2013-10-22	2005-03-22	2005-03-22	ENSG00000125352	ENSG00000125352		"RING-type (C3HC4) zinc fingers"	12974	protein-coding gene	gene with protein product			"zinc finger protein 183 (RING finger, C3HC4 type)"	ZNF183		9224902	Standard	NM_006978		Approved	RNF113, Cwc24	uc004esb.3	O15541	OTTHUMG00000022283	ENST00000371442.2:c.275A>T	chrX.hg19:g.119005302T>A	ENSP00000360497:p.Glu92Val	178.0	0.0		167.0	10.0	NM_006978	B2RBR7	Missense_Mutation	SNP	ENST00000371442.2	hg19	CCDS14589.1	.	.	.	.	.	.	.	.	.	.	T	8.051	0.766053	0.15983	.	.	ENSG00000125352	ENST00000371442	T	0.34275	1.37	5.49	3.04	0.35103	.	0.582240	0.18241	N	0.147224	T	0.34106	0.0886	M	0.73962	2.25	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31475	-0.9942	10	0.35671	T	0.21	-33.4748	5.5105	0.16878	0.0:0.0898:0.332:0.5783	.	92	O15541	R113A_HUMAN	V	92	ENSP00000360497:E92V	ENSP00000360497:E92V	E	-	2	0	RNF113A	118889330	0.001000	0.12720	0.001000	0.08648	0.304000	0.27724	0.693000	0.25497	0.235000	0.21160	-0.378000	0.06908	GAG	.	.		0.547	RNF113A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058071.1	NM_006978		A	119005302	T	A	119005302	3	1	126	1	0	0	0	0	1	0	0	0	13442	1551	54	4	760	4	RNF113A	23	119005302	Missense_Mutation	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10	49526690	119005302	36265258	60	21016										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135309506	135309506	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0327868852459016	2	1	0.565934065934066	0	0.700680272108844	0.454545454545454	1	0	ttctttttagtctcattttgTtgctgcccatctttgagttt	6	8	3	1			TCGA-DD-A4ND-01A-11D-A25V-10	TCGA-DD-A4ND-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d9c5493e-f969-4c04-a646-9a3134011021	40381948-7dff-4254-8b81-bb6f34579ebf	g.chrX:135309506T>C	ENST00000316077.9	-	12	2191	c.1971A>G	c.(1969-1971)caA>caG	p.Q657Q	MAP7D3_ENST00000370663.5_Silent_p.Q639Q|MAP7D3_ENST00000370661.1_Silent_p.Q622Q|MAP7D3_ENST00000495432.1_5'UTR	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	657					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					TCTCATTTTGTTGCTGCCCAT	0.438																																					p.Q657Q		Atlas-SNP	.											.	MAP7D3	102	.	0			c.A1971G						.						232	203	212					X																	135309506		1948	4136	6084	SO:0001819	synonymous_variant	79649	exon12			ATTTTGTTGCTGC	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1971A>G	chrX.hg19:g.135309506T>C		251.0	0.0		283.0	46.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Silent	SNP	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.438	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			C	135309506	T	C	135309506	2	2	126	1	0	0	0	0	0	0	0	1	9278	1722	60	2		2	MAP7D3	23	135309506	Silent	SNP	T	TCGA-DD-A4ND-01A-11D-A25V-10	16304204	135309506	19961054	61	21017										
RPL22	6146	hgsc.bcm.edu	37	chr1	6257754	6257754	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ccatcttctacagggtgggtGcaatcaagagtgaacttcag	11	9	4	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr1:6257754G>T	ENST00000234875.4	-	2	113	c.75C>A	c.(73-75)tgC>tgA	p.C25*	RPL22_ENST00000484532.1_5'UTR|RPL22_ENST00000497965.1_5'UTR	NM_000983.3	NP_000974.1	P35268	RL22_HUMAN	ribosomal protein L22	25					alpha-beta T cell differentiation (GO:0046632)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	heparin binding (GO:0008201)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	Ovarian(185;0.0634)	all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		CAGGGTGGGTGCAATCAAGAG	0.403			T	RUNX1	"AML, CML"																																p.C25X		Atlas-SNP	.		Dom	yes		1	1p36.31	6146	ribosomal protein L22 (EAP)		L	.	RPL22	24	.	0			c.C75A						.						75	65	68					1																	6257754		2203	4300	6503	SO:0001587	stop_gained	6146	exon2			GTGGGTGCAATCA	BC058887	CCDS58.1	1p36.31	2011-04-06			ENSG00000116251	ENSG00000116251		"L ribosomal proteins"	10315	protein-coding gene	gene with protein product		180474				8395054	Standard	NM_000983		Approved	EAP, L22	uc001amd.3	P35268	OTTHUMG00000000953	ENST00000234875.4:c.75C>A	chr1.hg19:g.6257754G>T	ENSP00000346088:p.Cys25*	42.0	0.0		57.0	36.0	NM_000983	B2R495|Q6IBD1	Nonsense_Mutation	SNP	ENST00000234875.4	hg19	CCDS58.1	.	.	.	.	.	.	.	.	.	.	G	33	5.214143	0.95104	.	.	ENSG00000116251	ENST00000234875	.	.	.	4.35	0.596	0.17496	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3432	0.32256	0.4593:0.0:0.5407:0.0	.	.	.	.	X	25	.	ENSP00000346088:C25X	C	-	3	2	RPL22	6180341	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	1.080000	0.30779	0.241000	0.21283	-0.459000	0.05422	TGC	.	.		0.403	RPL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002830.1	NM_000983		T	6257754	G	T	6257754	4	4	127	1	0	0	0	0	0	1	0	0	13583	1311	46	3	323	3	RPL22	1	6257754	Nonsense_Mutation	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10		6257754	242992867	1	21018										
THAP3	90326	hgsc.bcm.edu	37	chr1	6688628	6688628	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ggccggggcaacttcaagccCaagcagcacacggtcatctg	12	14	3	0			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr1:6688628C>T	ENST00000054650.4	+	3	302	c.144C>T	c.(142-144)ccC>ccT	p.P48P	THAP3_ENST00000307896.6_Silent_p.P48P|THAP3_ENST00000377627.3_Silent_p.P48P	NM_001195753.1	NP_001182682.1	Q8WTV1	THAP3_HUMAN	THAP domain containing, apoptosis associated protein 3	48							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|large_intestine(1)|prostate(1)	4	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		ACTTCAAGCCCAAGCAGCACA	0.612																																					p.P48P		Atlas-SNP	.											.	THAP3	43	.	0			c.C144T						.						67	56	60					1																	6688628		2203	4300	6503	SO:0001819	synonymous_variant	90326	exon2			CAAGCCCAAGCAG	BC022081	CCDS86.1, CCDS55572.1, CCDS55573.1	1p36.1	2013-01-25			ENSG00000041988	ENSG00000041988		"THAP (C2CH-type zinc finger) domain containing"	20855	protein-coding gene	gene with protein product		612532				12575992	Standard	NM_138350		Approved		uc001aod.3	Q8WTV1	OTTHUMG00000001440	ENST00000054650.4:c.144C>T	chr1.hg19:g.6688628C>T		116.0	0.0		188.0	84.0	NM_001195752	Q569K1|Q5TH66|Q5TH67|Q8N8T6|Q9BSC7|Q9Y3H2|Q9Y3H3	Silent	SNP	ENST00000054650.4	hg19	CCDS55572.1																																																																																			.	.		0.612	THAP3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004203.1	NM_138350		T	6688628	C	T	6688628	2	4	127	1	0	0	0	0	0	0	0	1	15860	581	21	3		3	THAP3	1	6688628	Silent	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	430874	6688628	242561993	2	21019										
CELF3	11189	hgsc.bcm.edu	37	chr1	151688481	151688481	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ccccacaaacagcttgatggCatccggctccttcattgagg	9	14	1	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr1:151688481C>G	ENST00000290583.4	-	1	809	c.16G>C	c.(16-18)Gcc>Ccc	p.A6P	AL589765.1_ENST00000442233.2_Intron|RIIAD1_ENST00000326413.3_Intron|CELF3_ENST00000290585.4_Missense_Mutation_p.A6P	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	6					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						AGCTTGATGGCATCCGGCTCC	0.597																																					p.A6P		Atlas-SNP	.											.	CELF3	49	.	0			c.G16C						.						69	62	64					1																	151688481		2203	4300	6503	SO:0001583	missense	11189	exon1			TGATGGCATCCGG	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.16G>C	chr1.hg19:g.151688481C>G	ENSP00000290583:p.Ala6Pro	58.0	0.0		122.0	53.0	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	hg19	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.608560	0.87258	.	.	ENSG00000159409	ENST00000290585;ENST00000290583;ENST00000368833	T;T	0.74106	-0.81;1.33	4.88	4.88	0.63580	Nucleotide-binding, alpha-beta plait (1);	.	.	.	.	T	0.78830	0.4345	L	0.46567	1.45	0.80722	D	1	D;D;D;D	0.76494	0.981;0.999;0.999;0.999	P;D;D;D	0.81914	0.709;0.97;0.983;0.995	T	0.81156	-0.1061	9	0.87932	D	0	.	15.6407	0.76997	0.0:1.0:0.0:0.0	.	6;6;6;6	Q5SZQ7;Q5SZQ8-2;Q5SZQ8;Q5SZQ8-3	.;.;CELF3_HUMAN;.	P	6	ENSP00000290585:A6P;ENSP00000290583:A6P	ENSP00000290583:A6P	A	-	1	0	CELF3	149955105	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.255000	0.78338	2.558000	0.86282	0.478000	0.44815	GCC	.	.		0.597	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		G	151688481	C	G	151688481	3	3	127	1	0	0	0	0	1	0	0	0	3219	710	25	4	1437	4	CELF3	1	151688481	Missense_Mutation	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	144999853	151688481	97562140	3	21020										
IGSF9	57549	hgsc.bcm.edu	37	chr1	159898638	159898638	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	caaagcgcccgtctgggcccCggcaaatgggctccagaggt	14	14	1	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr1:159898638C>T	ENST00000368094.1	-	19	2737	c.2540G>A	c.(2539-2541)cGg>cAg	p.R847Q	IGSF9_ENST00000493195.1_5'UTR|IGSF9_ENST00000361509.3_Missense_Mutation_p.R831Q	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	847	Pro-rich.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GTCTGGGCCCCGGCAAATGGG	0.692																																					p.R847Q		Atlas-SNP	.											.	IGSF9	123	.	0			c.G2540A						.						6	7	7					1																	159898638		2153	4237	6390	SO:0001583	missense	57549	exon19			GGGCCCCGGCAAA	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.2540G>A	chr1.hg19:g.159898638C>T	ENSP00000357073:p.Arg847Gln	13.0	0.0		26.0	4.0	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	hg19	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079536	0.94050	.	.	ENSG00000085552	ENST00000361509;ENST00000368094	T;T	0.78816	-1.21;-1.14	5.15	5.15	0.70609	.	0.000000	0.35179	N	0.003397	D	0.83193	0.5201	M	0.66939	2.045	0.33031	D	0.53016	D	0.89917	1.0	D	0.79108	0.992	T	0.83312	-0.0022	9	.	.	.	-20.9578	16.1159	0.81304	0.0:1.0:0.0:0.0	.	847	Q9P2J2	TUTLA_HUMAN	Q	831;847	ENSP00000355049:R831Q;ENSP00000357073:R847Q	.	R	-	2	0	IGSF9	158165262	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	4.681000	0.61663	2.378000	0.81104	0.655000	0.94253	CGG	.	.		0.692	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		T	159898638	C	T	159898638	3	4	127	1	0	0	0	0	1	0	0	0	7614	652	23	1	1011	1	IGSF9	1	159898638	Missense_Mutation	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	8210157	159898638	89351983	4	21021										
GORAB	92344	hgsc.bcm.edu	37	chr1	170508682	170508682	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ctacctccaaagccagattgCaaattggagaaaaagaaagt	8	8	0	3			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr1:170508682C>A	ENST00000367763.3	+	2	488	c.468C>A	c.(466-468)tgC>tgA	p.C156*	GORAB_ENST00000367762.1_Nonsense_Mutation_p.C156*|GORAB_ENST00000465717.1_3'UTR	NM_152281.2	NP_689494.2	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	156						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|liver(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	17						AGCCAGATTGCAAATTGGAGA	0.398																																					p.C156X		Atlas-SNP	.											.	GORAB	41	.	0			c.C468A						.						55	57	56					1																	170508682		2203	4300	6503	SO:0001587	stop_gained	92344	exon2			AGATTGCAAATTG	AK021814	CCDS1289.1, CCDS53428.1	1q24.2	2009-02-13	2009-02-13	2009-02-13	ENSG00000120370	ENSG00000120370			25676	protein-coding gene	gene with protein product	"gerodermia osteodysplastica"	607983	"SCY1-like 1 binding protein 1"	SCYL1BP1		12783284, 15781263, 18997784	Standard	NM_152281		Approved	FLJ11752, NTKL-BP1, GO	uc001gha.2	Q5T7V8	OTTHUMG00000035228	ENST00000367763.3:c.468C>A	chr1.hg19:g.170508682C>A	ENSP00000356737:p.Cys156*	54.0	0.0		139.0	31.0	NM_152281	Q49A22|Q6P1P9|Q9HAE6|Q9Y350	Nonsense_Mutation	SNP	ENST00000367763.3	hg19	CCDS1289.1	.	.	.	.	.	.	.	.	.	.	C	11.87	1.768546	0.31320	.	.	ENSG00000120370	ENST00000367763;ENST00000367762	.	.	.	5.51	3.31	0.37934	.	0.393945	0.31092	N	0.008267	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-19.1541	7.7954	0.29143	0.1349:0.7046:0.0:0.1605	.	.	.	.	X	156	.	ENSP00000356736:C156X	C	+	3	2	GORAB	168775306	0.990000	0.36364	1.000000	0.80357	0.088000	0.18126	2.401000	0.44513	1.325000	0.45301	-0.237000	0.12165	TGC	.	.		0.398	GORAB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085226.1	NM_152281		A	170508682	C	A	170508682	4	1	127	1	0	0	0	0	0	1	0	0	6582	718	25	3	474	3	GORAB	1	170508682	Nonsense_Mutation	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	10610044	170508682	78741939	5	21022										
TNN	63923	hgsc.bcm.edu	37	chr1	175105078	175105078	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	catgaaggagttctggcttgGtatgatctcagaatccagga	12	7	2	3			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr1:175105078G>C	ENST00000239462.4	+	16	3540		c.e16+1			NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N						axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		TTCTGGCTTGGTATGATCTCA	0.562																																					.		Atlas-SNP	.											.	TNN	297	.	0			c.3427+1G>C						.						106	108	107					1																	175105078		2203	4300	6503	SO:0001630	splice_region_variant	63923	exon16			GGCTTGGTATGAT	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.3427+1G>C	chr1.hg19:g.175105078G>C		61.0	0.0		191.0	41.0	NM_022093	B9EGP3|Q5R360	Splice_Site	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.757290	0.89843	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.003	0.92841	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TNN	173371701	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.538000	0.98072	2.555000	0.86185	0.655000	0.94253	.	.	.		0.562	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	Intron	C	175105078	G	C	175105078	5	2	127	1	0	0	0	0	0	0	1	0	16338	1275	44	4	3486	4	TNN	1	175105078	Splice_Site	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10	4596396	175105078	74145543	6	21023										
GEN1	348654	hgsc.bcm.edu	37	chr2	17954051	17954051	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	agtagagaacaatattaagaAgtaagtttttttaaaaactc	6	3	0	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr2:17954051A>G	ENST00000381254.2	+	8	1167	c.953A>G	c.(952-954)aAg>aGg	p.K318R	GEN1_ENST00000317402.7_Splice_Site_p.K318R|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	318					DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AATATTAAGAAGTAAGTTTTT	0.348								Homologous recombination																													p.K318R		Atlas-SNP	.											.	GEN1	79	.	0			c.A953G						.						47	48	48					2																	17954051		2203	4299	6502	SO:0001630	splice_region_variant	348654	exon8			TTAAGAAGTAAGT	AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"Holliday junction resolvase"	612449	"Gen endonuclease homolog 1 (Drosophila)"			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.953+1A>G	chr2.hg19:g.17954051A>G		82.0	0.0		63.0	31.0	NM_182625	Q17RS9|Q6ZN37	Missense_Mutation	SNP	ENST00000381254.2	hg19	CCDS1691.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.573219	0.28092	.	.	ENSG00000178295	ENST00000317402;ENST00000381254;ENST00000528873	T;T;T	0.44083	0.93;0.93;0.93	5.63	0.528	0.17089	-3&apos (1); exonuclease, C-terminal domain (1);5&apos (1);	0.213792	0.36444	N	0.002582	T	0.31263	0.0791	L	0.42245	1.32	0.34778	D	0.734472	B	0.19200	0.034	B	0.15052	0.012	T	0.27536	-1.0071	10	0.41790	T	0.15	-11.5345	9.7716	0.40593	0.5839:0.0:0.4161:0.0	.	318	Q17RS7	GEN_HUMAN	R	318;318;89	ENSP00000318977:K318R;ENSP00000370653:K318R;ENSP00000431542:K89R	ENSP00000318977:K318R	K	+	2	0	GEN1	17817532	1.000000	0.71417	0.927000	0.36925	0.710000	0.40934	1.486000	0.35530	0.098000	0.17522	-0.290000	0.09829	AAG	.	.		0.348	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625	Missense_Mutation	G	17954051	A	G	17954051	5	3	127	1	0	0	0	0	0	0	1	0	6343	86	3	2	979	2	GEN1	2	17954051	Splice_Site	SNP	A	TCGA-DD-A4NE-01A-11D-A27I-10		17954051	225245322	7	21024										
SPAST	6683	hgsc.bcm.edu	37	chr2	32341263	32341263	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ttgcaagaaattgttattctTccttctctgaggcctgaggt	9	8	2	3			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr2:32341263T>C	ENST00000315285.3	+	7	1205	c.1080T>C	c.(1078-1080)ctT>ctC	p.L360L	SPAST_ENST00000345662.1_Silent_p.L328L	NM_014946.3	NP_055761.2			spastin											breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TTGTTATTCTTCCTTCTCTGA	0.328																																					p.L360L		Atlas-SNP	.											.	SPAST	61	.	0			c.T1080C						.						134	129	131					2																	32341263		2203	4300	6503	SO:0001819	synonymous_variant	6683	exon7			TATTCTTCCTTCT	AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"ATPases / AAA-type"	11233	protein-coding gene	gene with protein product		604277	"spastic paraplegia 4 (autosomal dominant; spastin)"	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.1080T>C	chr2.hg19:g.32341263T>C		68.0	0.0		54.0	21.0	NM_014946		Silent	SNP	ENST00000315285.3	hg19	CCDS1778.1																																																																																			.	.		0.328	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436		C	32341263	T	C	32341263	2	2	127	1	0	0	0	0	0	0	0	1	15012	1770	62	2		2	SPAST	2	32341263	Silent	SNP	T	TCGA-DD-A4NE-01A-11D-A27I-10	14387212	32341263	210858110	8	21025										
VIT	5212	hgsc.bcm.edu	37	chr2	36982183	36982183	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	cctaccacgatggagagaatCctttatcgtcttaggtatga	9	9	1	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr2:36982183C>T	ENST00000389975.3	+	5	697	c.395C>T	c.(394-396)tCc>tTc	p.S132F	VIT_ENST00000497382.1_5'UTR|VIT_ENST00000379241.3_Missense_Mutation_p.S132F|VIT_ENST00000379242.3_Missense_Mutation_p.S132F|VIT_ENST00000457137.2_Missense_Mutation_p.S132F|VIT_ENST00000401530.1_Missense_Mutation_p.S132F|VIT_ENST00000404084.1_Missense_Mutation_p.S110F	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	132	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				TGGAGAGAATCCTTTATCGTC	0.438																																					p.S132F		Atlas-SNP	.											.	VIT	138	.	0			c.C395T						.						131	113	119					2																	36982183		2203	4300	6503	SO:0001583	missense	5212	exon5			GAGAATCCTTTAT	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.395C>T	chr2.hg19:g.36982183C>T	ENSP00000374625:p.Ser132Phe	202.0	0.0		244.0	87.0	NM_001177969	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	hg19	CCDS54347.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.311984	0.81358	.	.	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000402257;ENST00000457137;ENST00000404084;ENST00000379241;ENST00000401530	D;D;D;D;D;D	0.91180	-2.8;-2.8;-2.8;-2.8;-2.8;-2.8	5.63	5.63	0.86233	LCCL (4);	0.110275	0.64402	D	0.000004	D	0.96408	0.8828	M	0.90705	3.14	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.998;0.999;0.999;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.977;0.961;0.989;0.989;0.999	D	0.96719	0.9531	10	0.72032	D	0.01	-25.1552	19.3047	0.94157	0.0:1.0:0.0:0.0	.	132;132;132;132;132;132	B4DRU4;E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4;Q6UXI7-3	.;.;.;VITRN_HUMAN;.;.	F	132;132;132;132;110;132;132	ENSP00000368544:S132F;ENSP00000374625:S132F;ENSP00000393561:S132F;ENSP00000384154:S110F;ENSP00000368543:S132F;ENSP00000385658:S132F	ENSP00000368543:S132F	S	+	2	0	VIT	36835687	1.000000	0.71417	0.994000	0.49952	0.710000	0.40934	4.588000	0.60999	2.652000	0.90054	0.655000	0.94253	TCC	.	.		0.438	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				T	36982183	C	T	36982183	3	4	127	1	0	0	0	0	1	0	0	0	17186	855	30	3	409	3	VIT	2	36982183	Missense_Mutation	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	4640920	36982183	206217190	9	21026										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99012481	99012481	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ccgcctactgaagttttcccGgctctttgaattctttgacc	7	13	2	3	rs104893614		TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr2:99012481G>T	ENST00000272602.2	+	7	887	c.848G>T	c.(847-849)cGg>cTg	p.R283L	CNGA3_ENST00000409937.1_Missense_Mutation_p.R287L|CNGA3_ENST00000436404.2_Missense_Mutation_p.R265L|CNGA3_ENST00000393504.1_Missense_Mutation_p.R283L			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	283			R -> Q (in ACHM2; does not reveal any detectable calcium influx upon agonist application at 37 degrees Celsius; the channel function could be restored by incubating the transfected cells at 27 degrees Celsius; the dose-response relationship for cGMP-activation is not significantly different from that of wild-type CNGA3; the dose-response relationship of the mutant CNGA3 + CNGB3 is similar to that of the wild-type protein; a substantial reduction of macroscopic cGMP maximum current to only one-third of the mean value for wild-type CNGA3 + CNGB3 is observed for the mutant CNGA3 + CNGB3; the channel density into the cell membrane is considerably improved by decreasing the cultivation temparature). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:18521937, ECO:0000269|PubMed:9662398}.|R -> W (in ACHM2; also found in patients with cone-rod dystrophy). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:24903488, ECO:0000269|PubMed:9662398}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AAGTTTTCCCGGCTCTTTGAA	0.493																																					p.R283L		Atlas-SNP	.											CNGA3,colon,carcinoma,+1,1	CNGA3	118	.	0			c.G848T	GRCh37	CM980375	CNGA3	M	rs104893614	.						84	79	81					2																	99012481		2203	4300	6503	SO:0001583	missense	1261	exon8			TTTCCCGGCTCTT	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.848G>T	chr2.hg19:g.99012481G>T	ENSP00000272602:p.Arg283Leu	180.0	1.0		238.0	125.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474010	0.84640	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.99515	-6.06;-6.06;-6.06;-6.06	5.15	5.15	0.70609	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99722	0.9892	H	0.96970	3.915	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	0.998;1.0;0.995	D	0.97335	0.9953	10	0.87932	D	0	.	17.5731	0.87940	0.0:0.0:1.0:0.0	.	287;265;283	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	L	283;265;283;287	ENSP00000377140:R283L;ENSP00000410070:R265L;ENSP00000272602:R283L;ENSP00000386761:R287L	ENSP00000272602:R283L	R	+	2	0	CNGA3	98378913	0.999000	0.42202	1.000000	0.80357	0.972000	0.66771	9.263000	0.95617	2.677000	0.91161	0.563000	0.77884	CGG	.	G|1.000;A|0.000		0.493	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		T	99012481	G	T	99012481	3	4	127	1	0	0	0	0	1	0	0	0	3600	1116	39	1	874	1	CNGA3	2	99012481	Missense_Mutation	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10	62030298	99012481	144186892	10	21027										
STEAP3	55240	hgsc.bcm.edu	37	chr2	120005536	120005536	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	gtgtccgtggtcaacaccacActgccgtgcgtggcctacgt	12	14	1	0			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr2:120005536A>T	ENST00000354888.5	+	4	1278	c.774A>T	c.(772-774)acA>acT	p.T258T	STEAP3_ENST00000393106.2_Silent_p.T258T|STEAP3_ENST00000450943.2_Silent_p.T258T|STEAP3_ENST00000409811.1_Silent_p.T258T|STEAP3-AS1_ENST00000454260.1_RNA|STEAP3_ENST00000393108.2_Silent_p.T258T|STEAP3_ENST00000393107.2_Silent_p.T258T|STEAP3_ENST00000425223.2_Silent_p.T258T|STEAP3_ENST00000393110.2_Silent_p.T268T	NM_182915.2	NP_878919.2	Q658P3	STEA3_HUMAN	STEAP family member 3, metalloreductase	258					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cellular iron ion homeostasis (GO:0006879)|copper ion import (GO:0015677)|exosomal secretion (GO:1990182)|ferric iron import into cell (GO:0097461)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|protein secretion (GO:0009306)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	17						TCAACACCACACTGCCGTGCG	0.622																																					p.T268T		Atlas-SNP	.											.	STEAP3	44	.	0			c.A804T						.						107	102	104					2																	120005536		2203	4300	6503	SO:0001819	synonymous_variant	55240	exon4			CACCACACTGCCG	AY029585	CCDS2125.1, CCDS42738.1	2q14.2	2011-09-30	2011-09-30		ENSG00000115107	ENSG00000115107			24592	protein-coding gene	gene with protein product		609671				12606722	Standard	NM_182915		Approved	TSAP6, dudlin-2, STMP3	uc002tlr.3	Q658P3	OTTHUMG00000131402	ENST00000354888.5:c.774A>T	chr2.hg19:g.120005536A>T		43.0	0.0		57.0	27.0	NM_182915	A8K6E3|Q4VBR2|Q4ZG36|Q53SQ8|Q7Z389|Q86SF6|Q8NEW6|Q8TDP3|Q8TF03|Q9NVB5	Silent	SNP	ENST00000354888.5	hg19	CCDS2125.1																																																																																			.	.		0.622	STEAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254193.1	NM_018234		T	120005536	A	T	120005536	2	4	127	1	0	0	0	0	0	0	0	1	15294	146	6	4		4	STEAP3	2	120005536	Silent	SNP	A	TCGA-DD-A4NE-01A-11D-A27I-10	20993055	120005536	123193837	11	21028										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141747101	141747101	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	atatccaagcaaacctttacCtgtgcaagtttgattggatt	7	8	0	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr2:141747101C>G	ENST00000389484.3	-	17	3741	c.2770G>C	c.(2770-2772)Gcc>Ccc	p.A924P		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	924					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AAACCTTTACCTGTGCAAGTT	0.393										TSP Lung(27;0.18)																											p.A924P	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,right_upper_lobe,carcinoma,0,1	LRP1B	1315	.	0			c.G2770C						.						122	117	119					2																	141747101		2203	4300	6503	SO:0001630	splice_region_variant	53353	exon17			CTTTACCTGTGCA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2770+1G>C	chr2.hg19:g.141747101C>G		42.0	1.0		77.0	31.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.245185	0.80024	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91068	-2.78	5.69	5.69	0.88448	.	0.000000	0.64402	U	0.000001	D	0.87087	0.6090	N	0.04090	-0.28	0.80722	D	1	D	0.57257	0.979	P	0.55222	0.771	D	0.86281	0.1667	9	.	.	.	.	20.181	0.98201	0.0:1.0:0.0:0.0	.	924	Q9NZR2	LRP1B_HUMAN	P	924;862	ENSP00000374135:A924P	.	A	-	1	0	LRP1B	141463571	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	7.727000	0.84838	2.840000	0.97914	0.655000	0.94253	GCC	.	.		0.393	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Missense_Mutation	G	141747101	C	G	141747101	5	3	127	1	0	0	0	0	0	0	1	0	8964	695	24	4	11329	4	LRP1B	2	141747101	Splice_Site	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	21741565	141747101	101452272	12	21029										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160807872	160807872	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tctgtggtgaacagtccaatCcagtgggcatatcctagccg	11	11	1	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr2:160807872C>A	ENST00000283243.7	-	24	3725	c.3519G>T	c.(3517-3519)tgG>tgT	p.W1173C	PLA2R1_ENST00000392771.1_Missense_Mutation_p.W1173C	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	1173	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)	p.W1173*(1)	PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						ACAGTCCAATCCAGTGGGCAT	0.468																																					p.W1173C		Atlas-SNP	.											PLA2R1,trunk,malignant_melanoma,0,1	PLA2R1	153	.	1	Substitution - Nonsense(1)	skin(1)	c.G3519T						.						183	168	173					2																	160807872		2203	4300	6503	SO:0001583	missense	22925	exon24			TCCAATCCAGTGG	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.3519G>T	chr2.hg19:g.160807872C>A	ENSP00000283243:p.Trp1173Cys	182.0	0.0		200.0	86.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	hg19	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.267346	0.80469	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.54071	0.59;0.59	5.88	5.88	0.94601	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.85682	D	0.000000	D	0.83774	0.5327	H	0.97491	4.015	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88760	0.3256	10	0.87932	D	0	.	20.2366	0.98359	0.0:1.0:0.0:0.0	.	1173;1173;1173	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	C	1173	ENSP00000283243:W1173C;ENSP00000376524:W1173C	ENSP00000283243:W1173C	W	-	3	0	PLA2R1	160516118	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.163000	0.77524	2.792000	0.96026	0.557000	0.71058	TGG	.	.		0.468	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			A	160807872	C	A	160807872	3	1	127	1	0	0	0	0	1	0	0	0	12019	856	30	3	908	3	PLA2R1	2	160807872	Missense_Mutation	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	19060771	160807872	82391501	13	21030										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57475398	57475398	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ttatttctgaggcaagactgAgaaatttttctataaacttg	7	5	2	3			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr3:57475398A>T	ENST00000351747.2	-	12	1532	c.1352T>A	c.(1351-1353)cTc>cAc	p.L451H	DNAH12_ENST00000389536.4_Missense_Mutation_p.L451H	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	451	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						GGCAAGACTGAGAAATTTTTC	0.303																																					p.L451H		Atlas-SNP	.											.	DNAH12	182	.	0			c.T1352A						.						45	34	37					3																	57475398		692	1590	2282	SO:0001583	missense	201625	exon12			AGACTGAGAAATT	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.1352T>A	chr3.hg19:g.57475398A>T	ENSP00000295937:p.Leu451His	39.0	0.0		49.0	18.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	hg19		.	.	.	.	.	.	.	.	.	.	A	13.24	2.178049	0.38511	.	.	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536	T;T;T	0.21543	2.16;2.0;3.66	5.42	4.24	0.50183	.	0.330734	0.28166	N	0.016350	T	0.15219	0.0367	N	0.24115	0.695	0.80722	D	1	B	0.26876	0.162	B	0.33890	0.172	T	0.10109	-1.0644	10	0.18710	T	0.47	.	11.2534	0.49039	0.9259:0.0:0.0741:0.0	.	451	Q6ZR08	DYH12_HUMAN	H	451	ENSP00000295937:L451H;ENSP00000418137:L451H;ENSP00000374187:L451H	ENSP00000295937:L451H	L	-	2	0	DNAH12	57450438	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.944000	0.40263	2.058000	0.61347	0.533000	0.62120	CTC	.	.		0.303	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		T	57475398	A	T	57475398	3	4	127	1	0	0	0	0	1	0	0	0	4602	304	11	4	8118	4	DNAH12	3	57475398	Missense_Mutation	SNP	A	TCGA-DD-A4NE-01A-11D-A27I-10		57475398	140547032	14	21031										
SHOX2	6474	hgsc.bcm.edu	37	chr3	157820590	157820590	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tgttccagggtgaaattggtCcgacttcgcctctgcttgat	11	10	1	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr3:157820590C>G	ENST00000425436.3	-	2	457	c.432G>C	c.(430-432)cgG>cgC	p.R144R	SHOX2_ENST00000483851.2_Silent_p.R144R|SHOX2_ENST00000554685.1_5'UTR|SHOX2_ENST00000441443.2_Silent_p.R15R|SHOX2_ENST00000490689.2_Silent_p.R15R|SHOX2_ENST00000389589.4_Silent_p.R168R	NM_001163678.1|NM_006884.3	NP_001157150.1|NP_006875.2	O60902	SHOX2_HUMAN	short stature homeobox 2	144					cardiac atrium morphogenesis (GO:0003209)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte development (GO:0002063)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|heart development (GO:0007507)|heart valve development (GO:0003170)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of axonogenesis (GO:0050772)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of chondrocyte differentiation (GO:0032330)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(10)|skin(3)|upper_aerodigestive_tract(1)	20			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)			TGAAATTGGTCCGACTTCGCC	0.567																																					p.R168R		Atlas-SNP	.											.	SHOX2	84	.	0			c.G504C						.						186	151	163					3																	157820590		2203	4300	6503	SO:0001819	synonymous_variant	6474	exon3			ATTGGTCCGACTT	AJ002368	CCDS33884.1, CCDS43164.1, CCDS33884.2, CCDS54664.1	3q25.32	2011-06-20			ENSG00000168779	ENSG00000168779		"Homeoboxes / PRD class"	10854	protein-coding gene	gene with protein product		602504				9482898, 9466998	Standard	NM_006884		Approved	SHOT, OG12X, OG12	uc003fbs.3	O60902	OTTHUMG00000158755	ENST00000425436.3:c.432G>C	chr3.hg19:g.157820590C>G		178.0	0.0		225.0	110.0	NM_003030	O60465|O60467|O60903	Silent	SNP	ENST00000425436.3	hg19	CCDS43164.1	.	.	.	.	.	.	.	.	.	.	C	9.984	1.228986	0.22542	.	.	ENSG00000168779	ENST00000555977	.	.	.	5.49	4.62	0.57501	.	.	.	.	.	T	0.62146	0.2404	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60291	-0.7292	4	.	.	.	.	10.6737	0.45772	0.0:0.7959:0.1323:0.0718	.	.	.	.	H	48	.	.	D	-	1	0	SHOX2	159303284	0.930000	0.31532	1.000000	0.80357	0.986000	0.74619	0.108000	0.15396	1.320000	0.45209	-0.140000	0.14226	GAC	.	.		0.567	SHOX2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352057.2			G	157820590	C	G	157820590	2	3	127	1	0	0	0	0	0	0	0	1	14304	842	30	4		4	SHOX2	3	157820590	Silent	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	100345192	157820590	40201840	15	21032										
SENP2	59343	hgsc.bcm.edu	37	chr3	185332412	185332412	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tgtcggcccgactccgcctgGgcagtggaagcaatggctta	14	12	0	0			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr3:185332412G>C	ENST00000296257.5	+	11	1234	c.994G>C	c.(994-996)Ggc>Cgc	p.G332R	SENP2_ENST00000545472.1_Missense_Mutation_p.G322R|SENP2_ENST00000427465.2_Missense_Mutation_p.G156R	NM_021627.2	NP_067640.2	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 2	332					cellular protein metabolic process (GO:0044267)|dorsal/ventral axis specification (GO:0009950)|heart development (GO:0007507)|labyrinthine layer development (GO:0060711)|mRNA transport (GO:0051028)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein binding (GO:0032091)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|protein transport (GO:0015031)|regulation of DNA endoreduplication (GO:0032875)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of Wnt signaling pathway (GO:0030111)|spongiotrophoblast layer development (GO:0060712)|trophoblast giant cell differentiation (GO:0060707)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	SUMO-specific protease activity (GO:0016929)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(3)	12	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			ACTCCGCCTGGGCAGTGGAAG	0.458																																					p.G332R		Atlas-SNP	.											.	SENP2	88	.	0			c.G994C						.						78	76	77					3																	185332412		2203	4300	6503	SO:0001583	missense	59343	exon11			CGCCTGGGCAGTG	AF151697	CCDS33902.1	3q28	2005-08-17	2005-08-17		ENSG00000163904	ENSG00000163904			23116	protein-coding gene	gene with protein product		608261	"SUMO1/sentrin/SMT3 specific protease 2"			11896061, 11489887	Standard	XM_005247690		Approved	SMT3IP2, KIAA1331, DKFZp762A2316, AXAM2	uc003fpn.3	Q9HC62	OTTHUMG00000156658	ENST00000296257.5:c.994G>C	chr3.hg19:g.185332412G>C	ENSP00000296257:p.Gly332Arg	150.0	0.0		225.0	91.0	NM_021627	B4DQ42|Q8IW97|Q96SR2|Q9P2L5	Missense_Mutation	SNP	ENST00000296257.5	hg19	CCDS33902.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.757549	0.69648	.	.	ENSG00000163904	ENST00000545472;ENST00000296257;ENST00000437107;ENST00000427465;ENST00000444509	T;T;T;T	0.30981	1.94;1.95;1.97;1.51	5.46	5.46	0.80206	.	0.073866	0.50627	D	0.000111	T	0.37544	0.1007	N	0.19112	0.55	0.41142	D	0.985961	D;D	0.89917	1.0;1.0	D;D	0.71414	0.973;0.973	T	0.05869	-1.0859	10	0.12430	T	0.62	-6.0382	16.619	0.84925	0.0:0.0:1.0:0.0	.	322;332	B4DQ42;Q9HC62	.;SENP2_HUMAN	R	322;332;203;156;39	ENSP00000439653:G322R;ENSP00000296257:G332R;ENSP00000394562:G156R;ENSP00000399201:G39R	ENSP00000296257:G332R	G	+	1	0	SENP2	186815106	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.182000	0.65059	2.734000	0.93682	0.655000	0.94253	GGC	.	.		0.458	SENP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345159.1	NM_021627		C	185332412	G	C	185332412	3	2	127	1	0	0	0	0	1	0	0	0	14062	1232	43	4	1036	4	SENP2	3	185332412	Missense_Mutation	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10	27511822	185332412	12690018	16	21033										
LCORL	254251	hgsc.bcm.edu	37	chr4	17886148	17886148	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tttctttactgtccttatatGaataactatcatggaaatct	4	7	3	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr4:17886148G>A	ENST00000382226.5	-	7	1112	c.1004C>T	c.(1003-1005)tCa>tTa	p.S335L	LCORL_ENST00000382224.1_Missense_Mutation_p.S251L|LCORL_ENST00000539056.1_Intron|LCORL_ENST00000326877.4_Intron	NM_001166139.1	NP_001159611.1	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor corepressor-like	335					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						GTCCTTATATGAATAACTATC	0.393																																					p.S335L		Atlas-SNP	.											.	LCORL	60	.	0			c.C1004T						.						95	79	84					4																	17886148		692	1590	2282	SO:0001583	missense	254251	exon7			TTATATGAATAAC		CCDS3425.1, CCDS54749.1	4p15.32	2006-06-14			ENSG00000178177	ENSG00000178177			30776	protein-coding gene	gene with protein product		611799				12560079	Standard	NM_153686		Approved	MLR1, FLJ30696	uc021xmr.1	Q8N3X6	OTTHUMG00000128538	ENST00000382226.5:c.1004C>T	chr4.hg19:g.17886148G>A	ENSP00000371661:p.Ser335Leu	55.0	0.0		67.0	15.0	NM_001166139	Q96NK1	Missense_Mutation	SNP	ENST00000382226.5	hg19	CCDS54749.1	.	.	.	.	.	.	.	.	.	.	G	11.11	1.540920	0.27563	.	.	ENSG00000178177	ENST00000382224;ENST00000382226	.	.	.	5.34	5.34	0.76211	.	0.545546	0.19569	N	0.111135	T	0.40791	0.1131	N	0.08118	0	0.44816	D	0.997821	.	.	.	.	.	.	T	0.39603	-0.9606	7	0.42905	T	0.14	.	12.716	0.57115	0.0755:0.0:0.9245:0.0	.	.	.	.	L	251;335	.	ENSP00000371659:S251L	S	-	2	0	LCORL	17495246	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.904000	0.63279	2.664000	0.90586	0.655000	0.94253	TCA	.	.		0.393	LCORL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_153686		A	17886148	G	A	17886148	3	1	127	1	0	0	0	0	1	0	0	0	8699	1294	45	3	993	3	LCORL	4	17886148	Missense_Mutation	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10		17886148	173268128	17	21034										
AASDH	132949	hgsc.bcm.edu	37	chr4	57244474	57244474	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	attgacatgctcagaacttaTgctttttattttttcttttt	4	6	2	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr4:57244474T>G	ENST00000205214.6	-	4	688	c.508A>C	c.(508-510)Ata>Cta	p.I170L	AASDH_ENST00000513376.1_Missense_Mutation_p.I70L|AASDH_ENST00000451613.1_Missense_Mutation_p.I170L|AASDH_ENST00000510762.1_5'UTR|AASDH_ENST00000502617.1_Missense_Mutation_p.I170L|AASDH_ENST00000602986.1_Missense_Mutation_p.I17L|AASDH_ENST00000434343.2_Intron	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	170					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TCAGAACTTATGCTTTTTATT	0.363																																					p.I170L		Atlas-SNP	.											.	AASDH	101	.	0			c.A508C						.						144	127	133					4																	57244474		2203	4300	6503	SO:0001583	missense	132949	exon4			AACTTATGCTTTT	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.508A>C	chr4.hg19:g.57244474T>G	ENSP00000205214:p.Ile170Leu	109.0	0.0		108.0	46.0	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	hg19	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	T	3.624	-0.076847	0.07184	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T	0.46451	0.87;1.2;2.92;0.87	5.54	-11.1	0.00147	AMP-dependent synthetase/ligase (1);	2.811710	0.00824	N	0.001603	T	0.15652	0.0377	N	0.04705	-0.18	0.09310	N	1	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.08055	0.001;0.002;0.0;0.003	T	0.08722	-1.0708	10	0.17832	T	0.49	5.9387	4.5148	0.11930	0.1769:0.4522:0.0901:0.2809	.	17;170;170;170	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	L	170;70;170;17;170	ENSP00000205214:I170L;ENSP00000423760:I70L;ENSP00000409656:I170L;ENSP00000421171:I170L	ENSP00000205214:I170L	I	-	1	0	AASDH	56939231	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.565000	0.02150	-2.426000	0.00560	-3.672000	0.00025	ATA	.	.		0.363	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		G	57244474	T	G	57244474	3	3	127	1	0	0	0	0	1	0	0	0	22	1464	51	5	2836	5	AASDH	4	57244474	Missense_Mutation	SNP	T	TCGA-DD-A4NE-01A-11D-A27I-10	39358326	57244474	133909802	18	21035										
HMGCS1	3157	hgsc.bcm.edu	37	chr5	43297200	43297200	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ggagagttttccatctactaTaggatattcagatagcatat	8	6	2	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr5:43297200T>C	ENST00000325110.6	-	5	849	c.643A>G	c.(643-645)Ata>Gta	p.I215V	HMGCS1_ENST00000433297.2_Missense_Mutation_p.I215V	NM_001098272.2	NP_001091742.1	Q01581	HMCS1_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)	215					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|lipid metabolic process (GO:0006629)|liver development (GO:0001889)|male gonad development (GO:0008584)|response to acid chemical (GO:0001101)|response to drug (GO:0042493)|response to lipoprotein particle (GO:0055094)|response to low light intensity stimulus (GO:0009645)|response to purine-containing compound (GO:0014074)|response to tellurium ion (GO:0046690)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hydroxymethylglutaryl-CoA synthase activity (GO:0004421)|isomerase activity (GO:0016853)|organic acid binding (GO:0043177)			NS(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|stomach(1)|urinary_tract(1)	15						CCATCTACTATAGGATATTCA	0.408																																					p.I215V		Atlas-SNP	.											.	HMGCS1	33	.	0			c.A643G						.						142	144	143					5																	43297200		2203	4300	6503	SO:0001583	missense	3157	exon5			CTACTATAGGATA		CCDS34154.1	5p14-p13	2012-10-02	2010-04-30			ENSG00000112972	2.3.3.10		5007	protein-coding gene	gene with protein product	"3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase"	142940	"3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)"	HMGCS			Standard	NM_001098272		Approved		uc003jnq.5	Q01581		ENST00000325110.6:c.643A>G	chr5.hg19:g.43297200T>C	ENSP00000322706:p.Ile215Val	91.0	0.0		121.0	54.0	NM_001098272	B2RDL8	Missense_Mutation	SNP	ENST00000325110.6	hg19	CCDS34154.1	.	.	.	.	.	.	.	.	.	.	T	5.960	0.361052	0.11296	.	.	ENSG00000112972	ENST00000325110;ENST00000433297;ENST00000545275	T;T	0.73789	-0.78;-0.78	5.96	0.595	0.17490	Hydroxymethylglutaryl-coenzyme A synthase C-terminal (1);Thiolase-like (1);	0.148550	0.64402	N	0.000009	T	0.36826	0.0981	N	0.01015	-1.05	0.33260	D	0.559621	B	0.02656	0.0	B	0.01281	0.0	T	0.48990	-0.8985	10	0.02654	T	1	-21.6477	10.3788	0.44099	0.0:0.7213:0.0:0.2787	.	215	Q01581	HMCS1_HUMAN	V	215;215;204	ENSP00000322706:I215V;ENSP00000399402:I215V	ENSP00000322706:I215V	I	-	1	0	HMGCS1	43332957	0.684000	0.27642	0.694000	0.30210	0.991000	0.79684	1.248000	0.32827	0.097000	0.17492	0.533000	0.62120	ATA	.	.		0.408	HMGCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368022.1			C	43297200	T	C	43297200	3	2	127	1	0	0	0	0	1	0	0	0	7241	1406	49	2	947	2	HMGCS1	5	43297200	Missense_Mutation	SNP	T	TCGA-DD-A4NE-01A-11D-A27I-10		43297200	137618060	19	21036										
ACOT12	134526	hgsc.bcm.edu	37	chr5	80628350	80628350	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ctaccaagtctttgggtttgTcatcattcagtataggacag	9	8	4	0			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr5:80628350T>C	ENST00000307624.3	-	13	1365	c.1337A>G	c.(1336-1338)gAc>gGc	p.D446G	ACOT12_ENST00000508234.1_5'UTR	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	446	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		TTTGGGTTTGTCATCATTCAG	0.398																																					p.D446G		Atlas-SNP	.											.	ACOT12	57	.	0			c.A1337G						.						166	136	146					5																	80628350		2203	4300	6503	SO:0001583	missense	134526	exon13			GGTTTGTCATCAT	AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	24436	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 15"	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.1337A>G	chr5.hg19:g.80628350T>C	ENSP00000303246:p.Asp446Gly	76.0	0.0		100.0	42.0	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	hg19	CCDS4055.1	.	.	.	.	.	.	.	.	.	.	T	2.930	-0.221319	0.06061	.	.	ENSG00000172497	ENST00000307624	T	0.78003	-1.14	5.55	3.15	0.36227	Lipid-binding START (2);START-like domain (1);	0.359428	0.30667	N	0.009126	T	0.63058	0.2479	L	0.39020	1.185	0.33951	D	0.644393	B	0.06786	0.001	B	0.11329	0.006	T	0.59542	-0.7435	10	0.15499	T	0.54	-4.9178	7.3925	0.26917	0.0:0.1802:0.0:0.8198	.	446	Q8WYK0	ACO12_HUMAN	G	446	ENSP00000303246:D446G	ENSP00000303246:D446G	D	-	2	0	ACOT12	80664106	0.921000	0.31238	0.878000	0.34440	0.205000	0.24178	1.362000	0.34148	1.049000	0.40321	0.459000	0.35465	GAC	.	.		0.398	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767		C	80628350	T	C	80628350	3	2	127	1	0	0	0	0	1	0	0	0	150	1667	58	2	342	2	ACOT12	5	80628350	Missense_Mutation	SNP	T	TCGA-DD-A4NE-01A-11D-A27I-10	37331150	80628350	100286910	20	21037										
EPB41L4A	64097	hgsc.bcm.edu	37	chr5	111643179	111643179	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tcaaggacaacggaacctttCgttgacttctgcaaaaataa	7	9	2	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr5:111643179C>G	ENST00000261486.5	-	2	384	c.108G>C	c.(106-108)acG>acC	p.T36T		NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	36	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		CGGAACCTTTCGTTGACTTCT	0.383																																					p.T36T		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.G108C						.						91	85	87					5																	111643179		1861	4100	5961	SO:0001819	synonymous_variant	64097	exon2			ACCTTTCGTTGAC	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.108G>C	chr5.hg19:g.111643179C>G		72.0	0.0		102.0	47.0	NM_022140	A4FUI6	Silent	SNP	ENST00000261486.5	hg19	CCDS43350.1																																																																																			.	.		0.383	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			G	111643179	C	G	111643179	2	3	127	1	0	0	0	0	0	0	0	1	5157	871	31	4		4	EPB41L4A	5	111643179	Silent	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	31014829	111643179	69272081	21	21038										
CEP120	153241	hgsc.bcm.edu	37	chr5	122722352	122722353	+	Frame_Shift_Del	DEL	AT	AT	-													0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	gctgcacttccaaagaatggAtatgagtacctagaatttaa							TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr5:122722352_122722353delAT	ENST00000306467.5	-	10	1743_1744	c.1439_1440delAT	c.(1438-1440)tatfs	p.Y480fs	CEP120_ENST00000306481.6_Frame_Shift_Del_p.Y454fs|CEP120_ENST00000328236.5_Frame_Shift_Del_p.Y480fs			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	480					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						CAAAGAATGGATATGAGTACCT	0.307																																					p.480_481del		Atlas-Indel,Pindel	.											.	CEP120	72	.	0			c.1440_1441del						.																																			SO:0001589	frameshift_variant	153241	exon11			.	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"coiled-coil domain containing 100"	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.1439_1440delAT	chr5.hg19:g.122722354_122722355delAT	ENSP00000303058:p.Tyr480fs	57.0	0.0		65.0	29.0	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Frame_Shift_Del	DEL	ENST00000306467.5	hg19	CCDS4134.2																																																																																			.	.		0.307	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223		-	122722353	AT	-	122722352	7	5	127	1	0	1	0	1	0	0	0	0	3248	340	12	0	1564	0	CEP120	5	122722352	Frame_Shift_Del	DEL	AT	TCGA-DD-A4NE-01A-11D-A27I-10	11079173	122722352	58192908	22	21039										
CDKN1A	1026	hgsc.bcm.edu	37	chr6	36652323	36652323	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ggcggcagaccagcatgacaGgtgcggacatgtgcacggaa	16	10	0	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr6:36652323G>C	ENST00000405375.1	+	2	680	c.445G>C	c.(445-447)Gat>Cat	p.D149H	CDKN1A_ENST00000244741.5_Splice_Site_p.D149H|CDKN1A_ENST00000373711.2_Splice_Site_p.D149H|CDKN1A_ENST00000448526.2_Splice_Site_p.D183H	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	149			D -> G (in dbSNP:rs1801724).		cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						CAGCATGACAGGTGCGGACAT	0.597																																					p.D149H		Atlas-SNP	.											.	CDKN1A	27	.	0			c.G445C						.						46	49	48					6																	36652323		2203	4300	6503	SO:0001630	splice_region_variant	1026	exon2			ATGACAGGTGCGG	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.445+1G>C	chr6.hg19:g.36652323G>C		55.0	0.0		154.0	116.0	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	hg19	CCDS4824.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.070817	0.76301	.	.	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99	5.08	5.08	0.68730	.	0.000000	0.49916	D	0.000129	T	0.77003	0.4067	L	0.47190	1.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.75631	-0.3251	9	.	.	.	-14.614	13.8526	0.63506	0.0:0.0:1.0:0.0	.	183;149	B4DQP9;P38936	.;CDN1A_HUMAN	H	183;149;149;149	ENSP00000409259:D183H;ENSP00000244741:D149H;ENSP00000384849:D149H;ENSP00000362815:D149H	.	D	+	1	0	CDKN1A	36760301	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	5.849000	0.69465	2.644000	0.89710	0.561000	0.74099	GAT	.	.		0.597	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467	Missense_Mutation	C	36652323	G	C	36652323	5	2	127	1	0	0	0	0	0	0	1	0	3160	1014	35	4	447	4	CDKN1A	6	36652323	Splice_Site	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10		36652323	134462744	23	21040										
TREML2	79865	hgsc.bcm.edu	37	chr6	41166123	41166123	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ctgcacagacagagtctcccCttcaaggagcctcacttttg	8	14	3	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr6:41166123C>T	ENST00000483722.1	-	2	285	c.100G>A	c.(100-102)Ggg>Agg	p.G34R		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	34	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					AGAGTCTCCCCTTCAAGGAGC	0.493																																					p.G34R		Atlas-SNP	.											.	TREML2	41	.	0			c.G100A						.						127	130	129					6																	41166123		2203	4300	6503	SO:0001583	missense	79865	exon2			TCTCCCCTTCAAG	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"Immunoglobulin superfamily / V-set domain containing"	21092	protein-coding gene	gene with protein product	"TREM-like transcript 2"	609715	"chromosome 6 open reading frame 76"	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.100G>A	chr6.hg19:g.41166123C>T	ENSP00000418767:p.Gly34Arg	55.0	0.0		157.0	7.0	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	hg19	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	14.59	2.581804	0.46006	.	.	ENSG00000112195	ENST00000483722	D	0.81499	-1.5	4.75	4.75	0.60458	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000044	D	0.86623	0.5977	M	0.75085	2.285	0.40423	D	0.979861	D	0.89917	1.0	D	0.97110	1.0	D	0.88269	0.2928	10	0.72032	D	0.01	-23.1011	13.6225	0.62144	0.0:1.0:0.0:0.0	.	34	Q5T2D2	TRML2_HUMAN	R	34	ENSP00000418767:G34R	ENSP00000418767:G34R	G	-	1	0	TREML2	41274101	1.000000	0.71417	0.998000	0.56505	0.028000	0.11728	3.388000	0.52509	2.344000	0.79699	0.563000	0.77884	GGG	.	.		0.493	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807		T	41166123	C	T	41166123	3	4	127	1	0	0	0	0	1	0	0	0	16488	681	24	3	881	3	TREML2	6	41166123	Missense_Mutation	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	4513800	41166123	129948944	24	21041										
PRDM13	59336	hgsc.bcm.edu	37	chr6	100062539	100062539	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	cccggctatcccccggagccTggggatcccaagagcgacga	13	16	0	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr6:100062539T>C	ENST00000369215.4	+	4	2333	c.2028T>C	c.(2026-2028)ccT>ccC	p.P676P		NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	676					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1)	17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		CCCCGGAGCCTGGGGATCCCA	0.692																																					p.P676P		Atlas-SNP	.											.	PRDM13	65	.	0			c.T2028C						.						20	24	23					6																	100062539		1764	3846	5610	SO:0001819	synonymous_variant	59336	exon4			GGAGCCTGGGGAT	AY004253	CCDS43487.1	6q16.2	2012-03-28			ENSG00000112238	ENSG00000112238			13998	protein-coding gene	gene with protein product							Standard	NM_021620		Approved		uc003pqg.1	Q9H4Q3	OTTHUMG00000015269	ENST00000369215.4:c.2028T>C	chr6.hg19:g.100062539T>C		32.0	0.0		28.0	6.0	NM_021620	Q5TGC1|Q5TGC2	Silent	SNP	ENST00000369215.4	hg19	CCDS43487.1																																																																																			.	.		0.692	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2			C	100062539	T	C	100062539	2	2	127	1	0	0	0	0	0	0	0	1	12466	1567	55	2		2	PRDM13	6	100062539	Silent	SNP	T	TCGA-DD-A4NE-01A-11D-A27I-10	58896416	100062539	71052528	25	21042										
EZR	7430	hgsc.bcm.edu	37	chr6	159206580	159206580	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ttggcccggaacttgaactgGaggggattctccttcctgac	12	11	1	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr6:159206580G>T	ENST00000367075.3	-	5	396	c.228C>A	c.(226-228)ctC>ctA	p.L76L	EZR_ENST00000337147.7_Silent_p.L76L|EZR_ENST00000476189.1_5'UTR|EZR_ENST00000392177.4_Silent_p.L44L	NM_001111077.1	NP_001104547.1	P15311	EZRI_HUMAN	ezrin	76	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of endothelial barrier (GO:0061028)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|filopodium assembly (GO:0046847)|leukocyte cell-cell adhesion (GO:0007159)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|receptor internalization (GO:0031623)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|astrocyte projection (GO:0097449)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell tip (GO:0051286)|ciliary basal body (GO:0036064)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|microspike (GO:0044393)|microvillus (GO:0005902)|microvillus membrane (GO:0031528)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|Schwann cell microvillus (GO:0097454)|T-tubule (GO:0030315)|uropod (GO:0001931)|vesicle (GO:0031982)	actin filament binding (GO:0051015)|cell adhesion molecule binding (GO:0050839)|poly(A) RNA binding (GO:0044822)		EZR/ROS1(4)	breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	15		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)		ACTTGAACTGGAGGGGATTCT	0.537			T	ROS1	NSCLC																																p.L76L		Atlas-SNP	.		Dom	yes		6	6q25.3	7430	ezrin		E	.	EZR	44	.	0			c.C228A						.						68	63	65					6																	159206580		2203	4300	6503	SO:0001819	synonymous_variant	7430	exon4			GAACTGGAGGGGA	AF187552	CCDS5258.1	6q25.3	2010-12-10	2007-11-29	2007-11-29	ENSG00000092820	ENSG00000092820		"A-kinase anchor proteins"	12691	protein-coding gene	gene with protein product	"cytovillin 2"	123900	"villin 2 (ezrin)"	VIL2			Standard	NM_003379		Approved		uc003qrt.4	P15311	OTTHUMG00000015917	ENST00000367075.3:c.228C>A	chr6.hg19:g.159206580G>T		128.0	0.0		202.0	78.0	NM_003379	E1P5A8|P23714|Q4VX75|Q96CU8|Q9NSJ4	Silent	SNP	ENST00000367075.3	hg19	CCDS5258.1																																																																																			.	.		0.537	EZR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042878.1	NM_003379		T	159206580	G	T	159206580	2	4	127	1	0	0	0	0	0	0	0	1	5337	1161	41	3		3	EZR	6	159206580	Silent	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10	59144041	159206580	11908487	26	21043										
GPR85	54329	hgsc.bcm.edu	37	chr7	112723996	112723996	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	gcctgtggtgtttgcattttGcctgatgcccagcaaggtgg	14	9	0	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr7:112723996G>T	ENST00000297146.3	-	3	1384	c.781C>A	c.(781-783)Caa>Aaa	p.Q261K	GPR85_ENST00000424100.1_Missense_Mutation_p.Q261K|GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000501255.2_Missense_Mutation_p.Q261K|GPR85_ENST00000449591.1_Missense_Mutation_p.Q261K	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	261					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						TTTGCATTTTGCCTGATGCCC	0.483																																					p.Q261K		Atlas-SNP	.											.	GPR85	49	.	0			c.C781A						.						139	151	147					7																	112723996		2203	4300	6503	SO:0001583	missense	54329	exon3			CATTTTGCCTGAT	AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604		"GPCR / Class A : Orphans"	4536	protein-coding gene	gene with protein product		605188				10978537, 10833454	Standard	NM_018970		Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.781C>A	chr7.hg19:g.112723996G>T	ENSP00000297146:p.Gln261Lys	82.0	0.0		97.0	20.0	NM_001146265	Q9JHI6|Q9NPD1	Missense_Mutation	SNP	ENST00000297146.3	hg19	CCDS5758.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.987347	0.35036	.	.	ENSG00000164604	ENST00000501255;ENST00000297146;ENST00000424100;ENST00000449591	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.52	5.52	0.82312	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.36908	0.0984	L	0.44542	1.39	0.80722	D	1	B	0.14805	0.011	B	0.26693	0.072	T	0.08166	-1.0735	10	0.27082	T	0.32	.	19.8176	0.96576	0.0:0.0:1.0:0.0	.	261	P60893	GPR85_HUMAN	K	261	ENSP00000445808:Q261K;ENSP00000297146:Q261K;ENSP00000396763:Q261K;ENSP00000401178:Q261K	ENSP00000297146:Q261K	Q	-	1	0	GPR85	112511232	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.813000	0.99286	2.765000	0.95021	0.650000	0.86243	CAA	.	.		0.483	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2			T	112723996	G	T	112723996	3	4	127	1	0	0	0	0	1	0	0	0	6723	1328	46	3	335	3	GPR85	7	112723996	Missense_Mutation	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10		112723996	46414667	27	21044										
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138602612	138602612	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	gactataaggcgtaaaaacaCtcgggtctctgacggcaagc	11	10	1	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr7:138602612C>A	ENST00000422774.1	-	2	1808	c.1760G>T	c.(1759-1761)aGt>aTt	p.S587I	KIAA1549_ENST00000242365.4_Missense_Mutation_p.S537I|KIAA1549_ENST00000440172.1_Missense_Mutation_p.S587I			Q9HCM3	K1549_HUMAN	KIAA1549	587	Ser-rich.					integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CGTAAAAACACTCGGGTCTCT	0.458			O	BRAF	pilocytic astrocytoma																																p.S587I	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.G1760T						.						65	67	67					7																	138602612		1954	4137	6091	SO:0001583	missense	57670	exon2			AAAACACTCGGGT		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1760G>T	chr7.hg19:g.138602612C>A	ENSP00000416040:p.Ser587Ile	104.0	0.0		129.0	61.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	hg19	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	C	10.35	1.325024	0.24080	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.26373	1.74;1.75;1.74	3.97	-2.86	0.05717	.	0.972477	0.08440	N	0.945558	T	0.13927	0.0337	N	0.19112	0.55	0.09310	N	1	P;P	0.39157	0.531;0.662	B;B	0.37304	0.125;0.246	T	0.20240	-1.0281	10	0.46703	T	0.11	.	5.8241	0.18544	0.0:0.2031:0.5028:0.2942	.	587;587	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	I	587;537;587	ENSP00000406661:S587I;ENSP00000242365:S537I;ENSP00000416040:S587I	ENSP00000242365:S537I	S	-	2	0	KIAA1549	138253152	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.807000	0.04520	-0.572000	0.06006	-0.188000	0.12872	AGT	.	.		0.458	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			A	138602612	C	A	138602612	3	1	127	1	0	0	0	0	1	0	0	0	8253	565	20	3	4168	3	KIAA1549	7	138602612	Missense_Mutation	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	25878616	138602612	20536051	28	21045										
CHD7	55636	hgsc.bcm.edu	37	chr8	61749438	61749438	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ccgccaggcagctatcgacaGattctccaaacctgattctg	8	14	2	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr8:61749438G>A	ENST00000423902.2	+	17	4531	c.4052G>A	c.(4051-4053)aGa>aAa	p.R1351K	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1351	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GCTATCGACAGATTCTCCAAA	0.488																																					p.R1351K		Atlas-SNP	.											.	CHD7	534	.	0			c.G4052A						.						172	168	169					8																	61749438		2012	4192	6204	SO:0001583	missense	55636	exon17			TCGACAGATTCTC	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.4052G>A	chr8.hg19:g.61749438G>A	ENSP00000392028:p.Arg1351Lys	99.0	0.0		144.0	62.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	35	5.597348	0.96602	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	T	0.75154	-0.91	5.79	5.79	0.91817	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.82875	0.5132	L	0.41415	1.275	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.83705	0.0184	10	0.87932	D	0	-15.0825	20.0411	0.97590	0.0:0.0:1.0:0.0	.	1351	Q9P2D1	CHD7_HUMAN	K	1351	ENSP00000392028:R1351K	ENSP00000307304:R1351K	R	+	2	0	CHD7	61911992	1.000000	0.71417	1.000000	0.80357	0.769000	0.43574	9.869000	0.99810	2.739000	0.93911	0.655000	0.94253	AGA	.	.		0.488	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		A	61749438	G	A	61749438	3	1	127	1	0	0	0	0	1	0	0	0	3332	942	33	3	4114	3	CHD7	8	61749438	Missense_Mutation	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10		61749438	84614584	29	21046										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77618153	77618153	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ggaggagacggctcaccgggCagtggcatcgagtgtccaaa	16	10	1	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr8:77618153C>T	ENST00000521891.2	+	2	2278	c.1830C>T	c.(1828-1830)ggC>ggT	p.G610G	ZFHX4_ENST00000518282.1_Silent_p.G610G|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Silent_p.G610G|ZFHX4_ENST00000050961.6_Silent_p.G610G	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	610					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GCTCACCGGGCAGTGGCATCG	0.577										HNSCC(33;0.089)																											p.G610G		Atlas-SNP	.											.	ZFHX4	878	.	0			c.C1830T						.						74	80	78					8																	77618153		2085	4211	6296	SO:0001819	synonymous_variant	79776	exon2			ACCGGGCAGTGGC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.1830C>T	chr8.hg19:g.77618153C>T		92.0	0.0		110.0	60.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.577	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77618153	C	T	77618153	2	4	127	1	0	0	0	0	0	0	0	1	17650	697	25	3		3	ZFHX4	8	77618153	Silent	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	15868715	77618153	68745869	30	21047										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139824126	139824126	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	gtgggaggccgctggggtggGggtggaggtggaggctctgt	25	5	1	0	rs548885226	byFrequency	TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr8:139824126G>A	ENST00000303045.6	-	9	1811	c.1365C>T	c.(1363-1365)ccC>ccT	p.P455P	COL22A1_ENST00000435777.1_Silent_p.P455P	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	455	Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GCTGGGGTGGGGGTGGAGGTG	0.602										HNSCC(7;0.00092)																											p.P455P		Atlas-SNP	.											.	COL22A1	390	.	0			c.C1365T						.						16	16	16					8																	139824126		2200	4289	6489	SO:0001819	synonymous_variant	169044	exon9			GGGTGGGGGTGGA	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1365C>T	chr8.hg19:g.139824126G>A		18.0	0.0		31.0	6.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.602	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139824126	G	A	139824126	2	1	127	1	0	0	0	0	0	0	0	1	3683	1219	43	3		3	COL22A1	8	139824126	Silent	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10	62205973	139824126	6539896	31	21048										
CUBN	8029	hgsc.bcm.edu	37	chr10	17026254	17026254	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	cagttgggctattctgggagAgtggaaatcggggcctccat	15	8	1	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr10:17026254A>G	ENST00000377833.4	-	30	4440	c.4375T>C	c.(4375-4377)Tct>Cct	p.S1459P		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1459	CUB 9. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATTCTGGGAGAGTGGAAATCG	0.448																																					p.S1459P		Atlas-SNP	.											.	CUBN	515	.	0			c.T4375C						.						80	77	78					10																	17026254		2203	4300	6503	SO:0001583	missense	8029	exon30			TGGGAGAGTGGAA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.4375T>C	chr10.hg19:g.17026254A>G	ENSP00000367064:p.Ser1459Pro	89.0	0.0		122.0	45.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.314155	0.60414	.	.	ENSG00000107611	ENST00000377833	T	0.33438	1.41	5.96	0.561	0.17285	CUB (5);	0.310980	0.23466	N	0.047874	T	0.39358	0.1075	M	0.82923	2.615	0.80722	D	1	P	0.43231	0.801	B	0.41619	0.361	T	0.53436	-0.8439	10	0.66056	D	0.02	.	14.7668	0.69646	0.5262:0.4738:0.0:0.0	.	1459	O60494	CUBN_HUMAN	P	1459	ENSP00000367064:S1459P	ENSP00000367064:S1459P	S	-	1	0	CUBN	17066260	0.005000	0.15991	0.961000	0.40146	0.960000	0.62799	0.129000	0.15830	-0.137000	0.11455	-0.316000	0.08728	TCT	.	.		0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17026254	A	G	17026254	3	3	127	1	0	0	0	0	1	0	0	0	4053	304	11	2	6648	2	CUBN	10	17026254	Missense_Mutation	SNP	A	TCGA-DD-A4NE-01A-11D-A27I-10		17026254	118508493	32	21049										
SPAG6	9576	hgsc.bcm.edu	37	chr10	22700061	22700070	+	Frame_Shift_Del	DEL	ATACATCAAC	ATACATCAAC	-													0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	cctggttctctccttcaagaAtacatcaacagtattaacag					rs541658599		TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	ATACATCAAC	ATACATCAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr10:22700061_22700070delATACATCAAC	ENST00000376624.3	+	10	1558_1567	c.1416_1425delATACATCAAC	c.(1414-1425)gaatacatcaacfs	p.EYIN472fs	SPAG6_ENST00000490361.1_3'UTR|SPAG6_ENST00000538630.1_Frame_Shift_Del_p.EYIN447fs|SPAG6_ENST00000376601.1_Frame_Shift_Del_p.EYIN233fs|RP11-301N24.3_ENST00000422675.1_RNA|SPAG6_ENST00000313311.6_Intron|SPAG6_ENST00000376603.2_Frame_Shift_Del_p.EYIN548fs	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	472					cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						TCCTTCAAGAATACATCAACAGTATTAACA	0.39																																					p.472_475del		Atlas-Indel,Pindel	.											.	SPAG6	90	.	0			c.1415_1424del						.																																			SO:0001589	frameshift_variant	9576	exon10			.	AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"Armadillo repeat containing"	11215	protein-coding gene	gene with protein product	"axoneme central apparatus protein"	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.1416_1425delATACATCAAC	chr10.hg19:g.22700061_22700070delATACATCAAC	ENSP00000365811:p.Glu472fs	76.0	0.0		60.0	17.0	NM_012443	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Frame_Shift_Del	DEL	ENST00000376624.3	hg19	CCDS7139.1																																																																																			.	.		0.39	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1			-	22700070	ATACATCAAC	-	22700061	7	5	127	1	0	1	0	1	0	0	0	0	14997	98	4	0	1454	0	SPAG6	10	22700061	Frame_Shift_Del	DEL	ATACATCAAC	TCGA-DD-A4NE-01A-11D-A27I-10	5673807	22700061	112834686	33	21050										
MYOZ1	58529	hgsc.bcm.edu	37	chr10	75391726	75391726	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tccatccaaggggatgccaaTatccacgttgtagtctacag	9	11	1	0			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr10:75391726T>C	ENST00000359322.4	-	6	1226	c.862A>G	c.(862-864)Att>Gtt	p.I288V	RP11-464F9.22_ENST00000609434.1_lincRNA	NM_021245.3	NP_067068.1			myozenin 1											central_nervous_system(1)|large_intestine(5)|lung(2)|ovary(2)|skin(2)	12	Prostate(51;0.0112)					GGGATGCCAATATCCACGTTG	0.517																																					p.I288V		Atlas-SNP	.											.	MYOZ1	24	.	0			c.A862G						.						81	80	80					10																	75391726		2203	4300	6503	SO:0001583	missense	58529	exon6			TGCCAATATCCAC	AF240633	CCDS7330.1	10q22.1	2008-07-03	2002-01-10	2002-01-11	ENSG00000177791	ENSG00000177791			13752	protein-coding gene	gene with protein product	"calsarcin-2"	605603	"myozenin"	MYOZ		11171996, 10984498	Standard	NM_021245		Approved	FATZ, CS-2	uc001jur.4	Q9NP98	OTTHUMG00000018466	ENST00000359322.4:c.862A>G	chr10.hg19:g.75391726T>C	ENSP00000352272:p.Ile288Val	115.0	0.0		167.0	8.0	NM_021245		Missense_Mutation	SNP	ENST00000359322.4	hg19	CCDS7330.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.562961	0.27915	.	.	ENSG00000177791	ENST00000359322	T	0.63580	-0.05	6.06	-0.764	0.11027	.	0.502966	0.23189	N	0.050926	T	0.41743	0.1172	L	0.36672	1.1	0.25549	N	0.987101	B	0.02656	0.0	B	0.04013	0.001	T	0.23154	-1.0196	10	0.10902	T	0.67	-1.8793	7.0617	0.25129	0.0:0.3859:0.1216:0.4925	.	288	Q9NP98	MYOZ1_HUMAN	V	288	ENSP00000352272:I288V	ENSP00000352272:I288V	I	-	1	0	MYOZ1	75061732	0.291000	0.24352	0.970000	0.41538	0.983000	0.72400	-0.352000	0.07701	-0.079000	0.12707	-0.256000	0.11100	ATT	.	.		0.517	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048654.1			C	75391726	T	C	75391726	3	2	127	1	0	0	0	0	1	0	0	0	10104	1406	49	2	41	2	MYOZ1	10	75391726	Missense_Mutation	SNP	T	TCGA-DD-A4NE-01A-11D-A27I-10	52691665	75391726	60143021	34	21051										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717712	89717712	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	gtactttgagttccctcagcCgttacctgtgtgtggtgata	11	9	1	2	rs587782350		TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr10:89717712C>G	ENST00000371953.3	+	7	2094	c.737C>G	c.(736-738)cCg>cGg	p.P246R	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	246	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.		P -> L (in CWS1 and BRRS). {ECO:0000269|PubMed:10400993}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.P246L(7)|p.R55fs*1(5)|p.L247fs*10(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.L247fs*11(1)|p.L247fs*12(1)|p.G165_*404del(1)|p.?(1)|p.F243fs*9(1)|p.P246fs*11(1)|p.P246_L247insGP(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TTCCCTCAGCCGTTACCTGTG	0.418		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.P246R		Atlas-SNP	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,NS,carcinoma,-1,8	PTEN	3652	.	62	Whole gene deletion(37)|Deletion - Frameshift(10)|Substitution - Missense(7)|Insertion - Frameshift(5)|Deletion - In frame(1)|Insertion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(14)|haematopoietic_and_lymphoid_tissue(8)|skin(8)|lung(5)|breast(3)|ovary(3)|urinary_tract(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|endometrium(1)	c.C737G	GRCh37	CM991083	PTEN	M		.						136	117	124					10																	89717712		2203	4300	6503	SO:0001583	missense	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	CTCAGCCGTTACC	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.737C>G	chr10.hg19:g.89717712C>G	ENSP00000361021:p.Pro246Arg	193.0	0.0		139.0	110.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.768419	0.90020	.	.	ENSG00000171862	ENST00000371953	D	0.85702	-2.02	5.15	5.15	0.70609	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.103668	0.64402	D	0.000002	D	0.89701	0.6791	L	0.59436	1.845	0.80722	D	1	D	0.59767	0.986	P	0.59595	0.86	D	0.89005	0.3424	9	.	.	.	-5.2284	18.6161	0.91303	0.0:1.0:0.0:0.0	.	246	P60484	PTEN_HUMAN	R	246	ENSP00000361021:P246R	.	P	+	2	0	PTEN	89707692	1.000000	0.71417	0.961000	0.40146	0.992000	0.81027	7.452000	0.80683	2.380000	0.81148	0.585000	0.79938	CCG	.	.		0.418	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89717712	C	G	89717712	3	3	127	1	0	0	0	0	1	0	0	0	12750	652	23	4	763	4	PTEN	10	89717712	Missense_Mutation	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	14325986	89717712	45817035	35	21052										
OR5M3	219482	hgsc.bcm.edu	37	chr11	56237770	56237770	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	acattggaagaaaaccacacAtcaacaaatgacaagtgact	6	9	1	3			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr11:56237770A>G	ENST00000312240.2	-	1	244	c.204T>C	c.(202-204)gaT>gaC	p.D68D		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	68						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					AAAACCACACATCAACAAATG	0.388																																					p.D68D		Atlas-SNP	.											.	OR5M3	103	.	0			c.T204C						.						114	101	105					11																	56237770		2201	4296	6497	SO:0001819	synonymous_variant	219482	exon1			CCACACATCAACA	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"GPCR / Class A : Olfactory receptors"	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.204T>C	chr11.hg19:g.56237770A>G		247.0	0.0		435.0	67.0	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Silent	SNP	ENST00000312240.2	hg19	CCDS31532.1																																																																																			.	.		0.388	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		G	56237770	A	G	56237770	2	3	127	1	0	0	0	0	0	0	0	1	11184	214	8	2		2	OR5M3	11	56237770	Silent	SNP	A	TCGA-DD-A4NE-01A-11D-A27I-10		56237770	78768746	36	21053										
GLYAT	10249	hgsc.bcm.edu	37	chr11	58491955	58491955	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tgcagcatctgggcaccttgCaatggtaacatcatggagga	12	9	2	0			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr11:58491955C>T	ENST00000344743.3	-	2	156	c.15G>A	c.(13-15)ttG>ttA	p.L5L	GLYAT_ENST00000278400.3_Silent_p.L5L|GLYAT_ENST00000529732.1_Silent_p.L5L	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase	5					acyl-CoA metabolic process (GO:0006637)|glycine metabolic process (GO:0006544)|monocarboxylic acid metabolic process (GO:0032787)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)|glycine N-benzoyltransferase activity (GO:0047962)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	GGGCACCTTGCAATGGTAACA	0.438																																					p.L5L		Atlas-SNP	.											.,1	GLYAT	53	.	0			c.G15A						.						105	106	106					11																	58491955		2201	4295	6496	SO:0001819	synonymous_variant	10249	exon2			ACCTTGCAATGGT	AF023466	CCDS7970.1, CCDS7971.1	11q12.1	2008-03-11					2.3.1.13		13734	protein-coding gene	gene with protein product		607424					Standard	NM_201648		Approved	GAT, ACGNAT	uc001nnb.3	Q6IB77		ENST00000344743.3:c.15G>A	chr11.hg19:g.58491955C>T		27.0	0.0		76.0	21.0	NM_005838	O14833|Q96QK7	Silent	SNP	ENST00000344743.3	hg19	CCDS7970.1																																																																																			.	.		0.438	GLYAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394593.1			T	58491955	C	T	58491955	2	4	127	1	0	0	0	0	0	0	0	1	6487	709	25	3		3	GLYAT	11	58491955	Silent	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	2254185	58491955	76514561	37	21054										
SSH3	54961	hgsc.bcm.edu	37	chr11	67077629	67077629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tacaccattcccacctcttcCgccagaacctgagggtggtg	9	15	1	2	rs370197853		TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr11:67077629C>T	ENST00000308127.4	+	13	1680	c.1502C>T	c.(1501-1503)cCg>cTg	p.P501L	SSH3_ENST00000308298.7_Intron|SSH3_ENST00000376757.5_Intron	NM_017857.3	NP_060327.3	Q8TE77	SSH3_HUMAN	slingshot protein phosphatase 3	501					protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|DNA binding (GO:0003677)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CCACCTCTTCCGCCAGAACCT	0.617																																					p.P501L		Atlas-SNP	.											.	SSH3	54	.	0			c.C1502T						.	C	LEU/PRO	0,4400		0,0,2200	64	70	68		1502	3.7	0.7	11		68	1,8589	1.2+/-3.3	0,1,4294	no	missense	SSH3	NM_017857.3	98	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	501/660	67077629	1,12989	2200	4295	6495	SO:0001583	missense	54961	exon13			CTCTTCCGCCAGA	AF085851	CCDS8157.1	11q13	2013-03-05	2013-03-05		ENSG00000172830	ENSG00000172830		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30581	protein-coding gene	gene with protein product		606780	"slingshot homolog 3 (Drosophila)"			11832213	Standard	NM_017857		Approved	FLJ20515, FLJ10928	uc001okj.3	Q8TE77	OTTHUMG00000167105	ENST00000308127.4:c.1502C>T	chr11.hg19:g.67077629C>T	ENSP00000312081:p.Pro501Leu	53.0	0.0		121.0	38.0	NM_017857	Q6PK42|Q76I75|Q8N9L8|Q8WYL0|Q9NV45|Q9NWZ7	Missense_Mutation	SNP	ENST00000308127.4	hg19	CCDS8157.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.778533	0.49786	0.0	1.16E-4	ENSG00000172830	ENST00000308127;ENST00000527821	T;T	0.19532	3.67;2.14	4.65	3.72	0.42706	.	0.201018	0.25172	N	0.032584	T	0.11965	0.0291	N	0.19112	0.55	0.80722	D	1	P;P	0.47106	0.89;0.824	B;B	0.36719	0.231;0.116	T	0.05699	-1.0869	10	0.51188	T	0.08	-18.832	10.4151	0.44316	0.2098:0.7902:0.0:0.0	.	355;501	Q8TE77-3;Q8TE77	.;SSH3_HUMAN	L	501;204	ENSP00000312081:P501L;ENSP00000433902:P204L	ENSP00000312081:P501L	P	+	2	0	SSH3	66834205	0.005000	0.15991	0.727000	0.30756	0.982000	0.71751	0.398000	0.20899	1.062000	0.40625	0.555000	0.69702	CCG	.	.		0.617	SSH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393167.1	NM_018276		T	67077629	C	T	67077629	3	4	127	1	0	0	0	0	1	0	0	0	15201	652	23	1	1552	1	SSH3	11	67077629	Missense_Mutation	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	8585674	67077629	67928887	38	21055										
CD4	920	hgsc.bcm.edu	37	chr12	6927621	6927621	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tccaccccggtgcagccaatGgccctgattgtgctgggggg	15	13	0	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr12:6927621G>T	ENST00000011653.4	+	8	1449	c.1191G>T	c.(1189-1191)atG>atT	p.M397I		NM_000616.4|NM_001195015.2|NM_001195016.2|NM_001195017.2	NP_000607.1|NP_001181944.1|NP_001181945.1|NP_001181946.1	P01730	CD4_HUMAN	CD4 molecule	397					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cytokine production (GO:0001816)|defense response to Gram-negative bacterium (GO:0050829)|entry into host cell (GO:0030260)|enzyme linked receptor protein signaling pathway (GO:0007167)|immune response (GO:0006955)|induction by virus of host cell-cell fusion (GO:0006948)|innate immune response (GO:0045087)|maintenance of protein location in cell (GO:0032507)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase activity (GO:0045860)|protein palmitoleylation (GO:0045234)|regulation of defense response to virus by virus (GO:0050690)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|T cell selection (GO:0045058)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|enzyme binding (GO:0019899)|extracellular matrix structural constituent (GO:0005201)|glycoprotein binding (GO:0001948)|MHC class II protein binding (GO:0042289)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|zinc ion binding (GO:0008270)	p.M397I(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	23		Myeloproliferative disorder(1001;0.0122)			Antithymocyte globulin(DB00098)	TGCAGCCAATGGCCCTGATTG	0.627																																					p.M397I		Atlas-SNP	.											CD4,NS,carcinoma,0,1	CD4	47	.	1	Substitution - Missense(1)	lung(1)	c.G1191T						.						85	78	80					12																	6927621		2203	4300	6503	SO:0001583	missense	920	exon8			GCCAATGGCCCTG	M35160	CCDS8562.1	12p13.31	2013-01-11	2006-03-28		ENSG00000010610	ENSG00000010610		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	1678	protein-coding gene	gene with protein product		186940	"CD4 antigen (p55)", "T-cell surface glycoprotein CD4"				Standard	NM_000616		Approved		uc001qqv.2	P01730	OTTHUMG00000168514	ENST00000011653.4:c.1191G>T	chr12.hg19:g.6927621G>T	ENSP00000011653:p.Met397Ile	43.0	0.0		44.0	26.0	NM_000616	B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5	Missense_Mutation	SNP	ENST00000011653.4	hg19	CCDS8562.1	.	.	.	.	.	.	.	.	.	.	G	8.289	0.817381	0.16607	.	.	ENSG00000010610	ENST00000011653	T	0.21361	2.01	3.66	1.8	0.24995	.	0.690196	0.14121	N	0.340009	T	0.13713	0.0332	L	0.36672	1.1	0.09310	N	0.999999	B;P	0.35328	0.444;0.495	B;B	0.31442	0.052;0.13	T	0.15607	-1.0431	10	0.41790	T	0.15	-6.2454	5.9876	0.19442	0.2457:0.0:0.7543:0.0	.	218;397	B0AZV7;P01730	.;CD4_HUMAN	I	397	ENSP00000011653:M397I	ENSP00000011653:M397I	M	+	3	0	CD4	6797882	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.036000	0.12185	0.333000	0.23563	-0.258000	0.10820	ATG	.	.		0.627	CD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399978.1	NM_000616		T	6927621	G	T	6927621	3	4	127	1	0	0	0	0	1	0	0	0	3016	1348	47	3	1217	3	CD4	12	6927621	Missense_Mutation	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10		6927621	126924274	39	21056										
C12orf68	387856	hgsc.bcm.edu	37	chr12	48577984	48577984	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tggaggtgtccaccgtgccgGcagtgggggacgtgatctcc	17	11	1	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr12:48577984G>C	ENST00000316554.3	+	1	619	c.79G>C	c.(79-81)Gca>Cca	p.A27P		NM_001013635.3	NP_001013657.3	Q52MB2	CC184_HUMAN		27						cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)	4						CACCGTGCCGGCAGTGGGGGA	0.647																																					p.A27P		Atlas-SNP	.											.	C12orf68	11	.	0			c.G79C						.						46	55	52					12																	48577984		2203	4299	6502	SO:0001583	missense	387856	exon1			GTGCCGGCAGTGG																												ENST00000316554.3:c.79G>C	chr12.hg19:g.48577984G>C	ENSP00000320849:p.Ala27Pro	23.0	0.0		15.0	6.0	NM_001013635	Q96MK5|Q96N39	Missense_Mutation	SNP	ENST00000316554.3	hg19	CCDS31785.1	.	.	.	.	.	.	.	.	.	.	G	10.72	1.428343	0.25726	.	.	ENSG00000177875	ENST00000316554	T	0.57752	0.38	4.97	4.08	0.47627	.	0.000000	0.51477	D	0.000093	T	0.50803	0.1637	N	0.08118	0	0.34301	D	0.684382	D	0.76494	0.999	D	0.85130	0.997	T	0.66152	-0.5995	10	0.87932	D	0	-20.2082	10.6866	0.45846	0.0:0.0:0.8096:0.1904	.	27	Q52MB2	CL068_HUMAN	P	27	ENSP00000320849:A27P	ENSP00000320849:A27P	A	+	1	0	C12orf68	46864251	0.998000	0.40836	0.993000	0.49108	0.610000	0.37248	2.864000	0.48404	1.306000	0.44926	-0.158000	0.13435	GCA	.	.		0.647	C12orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406514.1			C	48577984	G	C	48577984	3	2	127	1	0	0	0	0	1	0	0	0	1712	1203	42	4	81	4	C12orf68	12	48577984	Missense_Mutation	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10	41650363	48577984	85273911	40	21057										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58121724	58121738	+	In_Frame_Del	DEL	ACCTTGCTGCTCTCA	ACCTTGCTGCTCTCA	-													0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	cacctcaaactcttaccttgAccttgctgctctcacagcat							TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	ACCTTGCTGCTCTCA	ACCTTGCTGCTCTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr12:58121724_58121738delACCTTGCTGCTCTCA	ENST00000547588.1	-	15	2747_2761	c.2748_2762delTGAGAGCAGCAAGGT	c.(2746-2763)tgtgagagcagcaaggtc>tgc	p.ESSKV917del	AGAP2-AS1_ENST00000542466.2_3'UTR|AGAP2_ENST00000257897.3_In_Frame_Del_p.ESSKV561del|RP11-571M6.8_ENST00000548410.2_RNA	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	917					axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)	p.V565I(1)		breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						TCTTACCTTGACCTTGCTGCTCTCACAGCATTGCA	0.595																																					p.917_921del		Pindel	.											.	AGAP2	167	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.2749_2763del						.																																			SO:0001651	inframe_deletion	116986	exon15			.	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.2748_2762delTGAGAGCAGCAAGGT	chr12.hg19:g.58121724_58121738delACCTTGCTGCTCTCA	ENSP00000449241:p.Glu917_Val921del	66.0	0.0		75.0	20.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	In_Frame_Del	DEL	ENST00000547588.1	hg19	CCDS44932.1																																																																																			.	.		0.595	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		-	58121738	ACCTTGCTGCTCTCA	-	58121724	7	5	127	1	0	1	0	1	0	0	0	0	368	275	10	0	836	0	AGAP2	12	58121724	In_Frame_Del	DEL	ACCTTGCTGCTCTCA	TCGA-DD-A4NE-01A-11D-A27I-10	9543740	58121724	75730171	41	21058										
LUM	4060	hgsc.bcm.edu	37	chr12	91498002	91498002	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tacatatccggtggaagactGgtttctgagatgcgattgcc	12	8	1	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr12:91498002G>A	ENST00000266718.4	-	3	1411	c.957C>T	c.(955-957)acC>acT	p.T319T	LUM_ENST00000548071.1_5'UTR	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	319					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						GTGGAAGACTGGTTTCTGAGA	0.388																																					p.T319T		Atlas-SNP	.											.	LUM	65	.	0			c.C957T						.						117	111	113					12																	91498002		2203	4300	6503	SO:0001819	synonymous_variant	4060	exon3			AAGACTGGTTTCT	BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6724	protein-coding gene	gene with protein product	"lumican proteoglycan"	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.957C>T	chr12.hg19:g.91498002G>A		64.0	0.0		89.0	4.0	NM_002345	B2R6R5|Q96QM7	Silent	SNP	ENST00000266718.4	hg19	CCDS9038.1																																																																																			.	.		0.388	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345		A	91498002	G	A	91498002	2	1	127	1	0	0	0	0	0	0	0	1	9094	1335	47	3		3	LUM	12	91498002	Silent	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10	33376278	91498002	42353893	42	21059										
KNTC1	9735	hgsc.bcm.edu	37	chr12	123055421	123055433	+	Splice_Site	DEL	TTTCAGATAATTC	TTTCAGATAATTC	-													0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	atttttaaataatctatttcAgataattcttgcaaaatggt							TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	TTTCAGATAATTC	TTTCAGATAATTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr12:123055421_123055433delTTTCAGATAATTC	ENST00000333479.7	+	23	2037_2048	c.1860_1871delTTTCAGATAATTC	c.(1858-1872)catttcagataattc>cac	p.FR*F621fs	KNTC1_ENST00000450485.2_Splice_Site_p.FR*F584fs	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	621					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		AATCTATTTCAGATAATTCTTGCAAAATGGTTG	0.291																																					p.621_622del		Atlas-INDEL	.											.	KNTC1	182	.	0			c.1861_1866del						.																																			SO:0001630	splice_region_variant	9735	exon23			.		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.1861-1TTTCAGATAATTC>-	chr12.hg19:g.123055421_123055433delTTTCAGATAATTC		99.0	0.0		65.0	16.0	NM_014708	A7E2C4|B3KSG2	In_Frame_Del	DEL	ENST00000333479.7	hg19	CCDS45002.1																																																																																			.	.		0.291	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		Frame_Shift_Del	-	123055433	TTTCAGATAATTC	-	123055421	8	5	127	1	0	1	0	1	0	0	1	0	8437	202	7	0	1945	0	KNTC1	12	123055421	Splice_Site	DEL	TTTCAGATAATTC	TCGA-DD-A4NE-01A-11D-A27I-10	31557419	123055421	10796474	43	21060										
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26145823	26145823	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	aacaccattctcagtcatcaTagaagcggtgagtaacatgc	8	10	3	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr13:26145823T>C	ENST00000381655.2	+	18	1797	c.1655T>C	c.(1654-1656)aTa>aCa	p.I552T	ATP8A2_ENST00000255283.8_Missense_Mutation_p.I512T|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	512					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TCAGTCATCATAGAAGCGGTG	0.423																																					p.I552T		Atlas-SNP	.											.	ATP8A2	181	.	0			c.T1655C						.						136	131	133					13																	26145823		1950	4143	6093	SO:0001583	missense	51761	exon18			TCATCATAGAAGC	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.1655T>C	chr13.hg19:g.26145823T>C	ENSP00000371070:p.Ile552Thr	69.0	0.0		63.0	28.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	hg19	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.479606	0.63849	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	T;T	0.68181	-0.31;-0.31	4.42	4.42	0.53409	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.82001	0.4942	M	0.84846	2.72	0.58432	D	0.999992	P;D;D;P	0.71674	0.954;0.979;0.998;0.92	P;P;D;P	0.68192	0.904;0.905;0.956;0.833	D	0.85529	0.1208	10	0.87932	D	0	.	13.7782	0.63066	0.0:0.0:0.0:1.0	.	512;332;512;512	B7Z880;F5GZN5;Q9NTI2-3;Q9NTI2	.;.;.;AT8A2_HUMAN	T	552;512;332	ENSP00000371070:I552T;ENSP00000255283:I512T	ENSP00000255283:I512T	I	+	2	0	ATP8A2	25043823	1.000000	0.71417	0.996000	0.52242	0.614000	0.37383	6.407000	0.73280	1.985000	0.57927	0.533000	0.62120	ATA	.	.		0.423	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		C	26145823	T	C	26145823	3	2	127	1	0	0	0	0	1	0	0	0	1193	1406	49	2	1725	2	ATP8A2	13	26145823	Missense_Mutation	SNP	T	TCGA-DD-A4NE-01A-11D-A27I-10		26145823	89024055	44	21061										
RB1	5925	hgsc.bcm.edu	37	chr13	48919320	48919321	+	Frame_Shift_Ins	INS	-	-	A													0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	gatgtattgtttgcactcttINScagcaaattggaaaggtaaa							TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr13:48919320_48919321insA	ENST00000267163.4	+	4	623_624	c.485_486insA	c.(484-489)ttcagcfs	p.FS162fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	162					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(6)|p.F162fs*13(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TTTGCACTCTTCAGCAAATTGG	0.282		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.F162fs		Atlas-INDEL	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	RB1_ENST00000267163,colon,carcinoma,-1,2	RB1	1068	.	22	Whole gene deletion(15)|Unknown(6)|Complex - frameshift(1)	bone(11)|breast(6)|eye(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.485_486insA						.																																			SO:0001589	frameshift_variant	5925	exon4	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	Exception_encountered	chr13.hg19:g.48919320_48919321insA	ENSP00000267163:p.Phe162fs	40.0	0.0		32.0	26.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Ins	INS	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.282	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			A	48919321	-	A	48919320	7	5	127	1	0	1	1	0	0	0	0	0	13113	1783	62	0	499	0	RB1	13	48919320	Frame_Shift_Ins	INS	-	TCGA-DD-A4NE-01A-11D-A27I-10	22773497	48919320	66250558	45	21062										
CTSG	1511	hgsc.bcm.edu	37	chr14	25044580	25044580	+	Frame_Shift_Del	DEL	G	G	-													0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	aagatacgccatgtaggggcGggagtggggcctgctctccc							TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr14:25044580delG	ENST00000216336.2	-	2	130	c.94delC	c.(94-96)cgcfs	p.R32fs		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	32	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|defense response to fungus (GO:0050832)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|negative regulation of growth of symbiont in host (GO:0044130)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|positive regulation of immune response (GO:0050778)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	heparin binding (GO:0008201)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(265;0.0269)		ATGTAGGGGCGGGAGTGGGGC	0.562																																					p.R32fs		Atlas-Indel,Pindel	.											CTSG,NS,carcinoma,0,1	CTSG	63	.	0			c.95delG						.						111	112	112					14																	25044580		2203	4300	6503	SO:0001589	frameshift_variant	1511	exon2			.	M16117	CCDS9631.1	14q12	2013-02-25			ENSG00000100448	ENSG00000100448		"Cathepsins", "Endogenous ligands"	2532	protein-coding gene	gene with protein product		116830				2569462	Standard	NM_001911		Approved	CG	uc001wpq.3	P08311	OTTHUMG00000140182	ENST00000216336.2:c.94delC	chr14.hg19:g.25044580delG	ENSP00000216336:p.Arg32fs	38.0	0.0		73.0	34.0	NM_001911	Q6IBJ6|Q9UCA5|Q9UCU6	Frame_Shift_Del	DEL	ENST00000216336.2	hg19	CCDS9631.1																																																																																			.	.		0.562	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2	NM_001911		-	25044580	G	-	25044580	7	5	127	1	0	1	0	1	0	0	0	0	4037	1116	39	0	689	0	CTSG	14	25044580	Frame_Shift_Del	DEL	G	TCGA-DD-A4NE-01A-11D-A27I-10		25044580	82304960	46	21063										
C16orf42	84572	hgsc.bcm.edu	37	chr16	1400190	1400190	+	5'Flank	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tcaggtccaagaagcccttgCcccatttaaacttccgcagc	7	15	1	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr16:1400190C>G	ENST00000204679.4	+	0	0				TSR3_ENST00000007390.2_Missense_Mutation_p.G191A	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit						carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				GAAGCCCTTGCCCCATTTAAA	0.582																																					p.G191A		Atlas-SNP	.											.	.	.	.	0			c.G572C						.						42	42	42					16																	1400190		2197	4298	6495	SO:0001631	upstream_gene_variant	115939	exon4			CCCTTGCCCCATT	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"GlcNAc-phosphotransferase gamma-subunit"	607838	"N-acetylglucosamine-1-phosphotransferase, gamma subunit", "chromosome 16 open reading frame 27"	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835		chr16.hg19:g.1400190C>G	Exception_encountered	19.0	0.0		26.0	11.0	NM_001001410	B2R556|Q6XYD7|Q96L13	Missense_Mutation	SNP	ENST00000204679.4	hg19	CCDS10436.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.342791	0.61073	.	.	ENSG00000007520	ENST00000007390	.	.	.	5.12	5.12	0.69794	Domain of unknown function DUF367 (2);	0.000000	0.85682	D	0.000000	D	0.83454	0.5258	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86432	0.1761	9	0.87932	D	0	-29.85	16.0339	0.80608	0.0:1.0:0.0:0.0	.	191	Q9UJK0	TSR3_HUMAN	A	191	.	ENSP00000007390:G191A	G	-	2	0	C16orf42	1340191	1.000000	0.71417	1.000000	0.80357	0.032000	0.12392	5.719000	0.68462	2.374000	0.81015	0.561000	0.74099	GGC	.	.		0.582	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520		G	1400190	C	G	1400190	1	3	127	0	1	0	0	0	0	0	0	0	1815	739	26	4		4	C16orf42	16	1400190	5'Flank	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10		1400190	88954563	47	21064										
MYH8	4626	hgsc.bcm.edu	37	chr17	10304673	10304673	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tctgcctgcaggtcatccagGgtctgctggtgggtctcttg	14	11	4	0			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr17:10304673G>A	ENST00000403437.2	-	24	3121	c.3027C>T	c.(3025-3027)acC>acT	p.T1009T	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1009					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GGTCATCCAGGGTCTGCTGGT	0.458									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.T1009T		Atlas-SNP	.											.	MYH8	346	.	0			c.C3027T						.						155	153	154					17																	10304673		2203	4300	6503	SO:0001819	synonymous_variant	4626	exon24	Familial Cancer Database	Carney Complex Variant	ATCCAGGGTCTGC		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.3027C>T	chr17.hg19:g.10304673G>A		80.0	0.0		111.0	51.0	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	hg19	CCDS11153.1																																																																																			.	.		0.458	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		A	10304673	G	A	10304673	2	1	127	1	0	0	0	0	0	0	0	1	10050	1219	43	3		3	MYH8	17	10304673	Silent	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10		10304673	70890537	48	21065										
MYH4	4622	hgsc.bcm.edu	37	chr17	10352333	10352333	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	cacagcttctacatgttcttCtgcatcctgcagacgctggg	9	13	3	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr17:10352333C>A	ENST00000255381.2	-	31	4323	c.4213G>T	c.(4213-4215)Gaa>Taa	p.E1405*	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1405					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						ACATGTTCTTCTGCATCCTGC	0.458																																					p.E1405X		Atlas-SNP	.											.	MYH4	349	.	0			c.G4213T						.						66	61	63					17																	10352333		2203	4300	6503	SO:0001587	stop_gained	4622	exon31			GTTCTTCTGCATC		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.4213G>T	chr17.hg19:g.10352333C>A	ENSP00000255381:p.Glu1405*	55.0	0.0		75.0	24.0	NM_017533		Nonsense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	C	43	10.139128	0.99345	.	.	ENSG00000141048	ENST00000255381	.	.	.	5.11	5.11	0.69529	.	0.000000	0.37761	U	0.001955	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.8931	0.92413	0.0:1.0:0.0:0.0	.	.	.	.	X	1405	.	ENSP00000255381:E1405X	E	-	1	0	MYH4	10293058	1.000000	0.71417	0.997000	0.53966	0.948000	0.59901	7.773000	0.85462	2.553000	0.86117	0.555000	0.69702	GAA	.	.		0.458	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		A	10352333	C	A	10352333	4	1	127	1	0	0	0	0	0	1	0	0	10046	922	32	3	1646	3	MYH4	17	10352333	Nonsense_Mutation	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	47660	10352333	70842877	49	21066										
ITGB3	3690	hgsc.bcm.edu	37	chr17	45361990	45361990	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ctgcggattggcttcggggcAtttgtggacaagcctgtgtc	15	9	0	0			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr17:45361990A>G	ENST00000559488.1	+	4	559	c.543A>G	c.(541-543)gcA>gcG	p.A181A	ITGB3_ENST00000571680.1_Silent_p.A181A|ITGB3_ENST00000560629.1_Missense_Mutation_p.I170V|ITGB3_ENST00000435993.2_Silent_p.A134A	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	181	VWFA.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	GCTTCGGGGCATTTGTGGACA	0.552																																					p.A181A		Atlas-SNP	.											.	ITGB3	157	.	0			c.A543G						.						121	126	124					17																	45361990		2203	4300	6503	SO:0001819	synonymous_variant	3690	exon4			CGGGGCATTTGTG		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.543A>G	chr17.hg19:g.45361990A>G		122.0	0.0		136.0	49.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	hg19	CCDS11511.1																																																																																			.	.		0.552	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		G	45361990	A	G	45361990	2	3	127	1	0	0	0	0	0	0	0	1	7904	204	8	2		2	ITGB3	17	45361990	Silent	SNP	A	TCGA-DD-A4NE-01A-11D-A27I-10	35009657	45361990	35833220	50	21067										
DNMT1	1786	hgsc.bcm.edu	37	chr19	10286294	10286295	+	Splice_Site	DNP	GC	GC	AA													0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tgaggtttccgtttggcaggGctgtcacacacagtgaggcc							TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr19:10286294_10286295GC>AA	ENST00000340748.4	-	6	757	c.522_522GC>TT	c.(520-522)ggGC>ggTTc	p.G174G	DNMT1_ENST00000359526.4_Splice_Site_p.G190G|DNMT1_ENST00000540357.1_Splice_Site_p.G174G			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	174	Interaction with DNMT3B.|Interaction with PCNA.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	GTTTGGCAGGGCTGTCACACAC	0.515																																					p.G190G|.		Atlas-SNP	.											.	DNMT1	148	.	0			c.C570T|c.522-1G>T						.																																			SO:0001630	splice_region_variant	1786	exon7			GGCAGGGCTGTCA|GCAGGGCTGTCAC	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.522_522delinsAA	chr19.hg19:g.10286294_10286295delinsAA		94.0|96.0	0.0		158.0|156.0	62.0|61.0	NM_001130823|NM_001379	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Silent|Splice_Site	SNP	ENST00000340748.4	hg19	CCDS12228.1																																																																																			.	.		0.515	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	Silent	AA	10286295	GC	AA	10286294	5	1	127	1	0	0	0	0	0	0	1	0	4677	1217	42	3	4468	3	DNMT1	19	10286294	Splice_Site	DNP	GC	TCGA-DD-A4NE-01A-11D-A27I-10		10286294	48842689	51	21068										
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13936368	13936368	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	cccgcccttcacccaggagaCcccaagtggctgcacacggt	10	18	1	1			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr19:13936368C>T	ENST00000254323.2	+	11	2058	c.1869C>T	c.(1867-1869)gaC>gaT	p.D623D	ZSWIM4_ENST00000440752.2_Silent_p.D457D	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	623							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			ACCCAGGAGACCCCAAGTGGC	0.622																																					p.D623D		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.C1869T						.						91	93	92					19																	13936368		2203	4300	6503	SO:0001819	synonymous_variant	65249	exon11			AGGAGACCCCAAG	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.1869C>T	chr19.hg19:g.13936368C>T		73.0	0.0		112.0	55.0	NM_023072		Silent	SNP	ENST00000254323.2	hg19	CCDS32924.1																																																																																			.	.		0.622	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		T	13936368	C	T	13936368	2	4	127	1	0	0	0	0	0	0	0	1	18258	506	18	3		3	ZSWIM4	19	13936368	Silent	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10	3650074	13936368	45192615	52	21069										
UNC13A	23025	hgsc.bcm.edu	37	chr19	17758169	17758169	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tgtgcgccgtcttggtcaccGcgaagatctcctggatgagc	13	12	3	2			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr19:17758169G>A	ENST00000519716.2	-	17	1948	c.1949C>T	c.(1948-1950)gCg>gTg	p.A650V	UNC13A_ENST00000252773.7_Missense_Mutation_p.A650V|UNC13A_ENST00000552293.1_Missense_Mutation_p.A650V|UNC13A_ENST00000428389.2_Missense_Mutation_p.A738V|UNC13A_ENST00000550896.1_Missense_Mutation_p.A648V|UNC13A_ENST00000551649.1_Missense_Mutation_p.A650V	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	650					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CTTGGTCACCGCGAAGATCTC	0.597																																					p.A650V		Atlas-SNP	.											.	UNC13A	299	.	0			c.C1949T						.						65	69	68					19																	17758169		2134	4269	6403	SO:0001583	missense	23025	exon16			GTCACCGCGAAGA	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.1949C>T	chr19.hg19:g.17758169G>A	ENSP00000429562:p.Ala650Val	77.0	0.0		106.0	59.0	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	13.59	2.281348	0.40394	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	3.76	3.76	0.43208	.	0.325270	0.27406	U	0.019517	T	0.35941	0.0949	N	0.03608	-0.345	0.35689	D	0.814717	B	0.11235	0.004	B	0.09377	0.004	T	0.40365	-0.9567	10	0.40728	T	0.16	-23.5748	9.6831	0.40082	0.0:0.2137:0.7863:0.0	.	650	Q9UPW8	UN13A_HUMAN	V	650;738;650;650;650;648	ENSP00000429562:A650V;ENSP00000400409:A738V;ENSP00000252773:A650V;ENSP00000447236:A650V;ENSP00000447572:A650V;ENSP00000446831:A648V	ENSP00000252773:A650V	A	-	2	0	UNC13A	17619169	0.923000	0.31300	0.986000	0.45419	0.967000	0.64934	2.077000	0.41557	1.812000	0.52913	0.313000	0.20887	GCG	.	.		0.597	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17758169	G	A	17758169	3	1	127	1	0	0	0	0	1	0	0	0	16999	1087	38	1	3270	1	UNC13A	19	17758169	Missense_Mutation	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10	3821801	17758169	41370814	53	21070										
RTEL1	51750	hgsc.bcm.edu	37	chr20	62324187	62324187	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	gtggctggtgcacagacggaCagggccaagctcttcatggt	15	10	2	1	rs535831345		TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr20:62324187C>T	ENST00000360203.5	+	29	3007	c.2682C>T	c.(2680-2682)gaC>gaT	p.D894D	RTEL1_ENST00000508582.2_Silent_p.D918D|RTEL1_ENST00000318100.4_Silent_p.D894D|RTEL1_ENST00000370018.3_Silent_p.D894D|RTEL1_ENST00000370003.1_Silent_p.D139D|RTEL1-TNFRSF6B_ENST00000482936.1_Silent_p.D894D					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			CACAGACGGACAGGGCCAAGC	0.627													C|||	1	0.000199681	0	0	5008	,	,		17078	0.001		0	False		,,,				2504	0				p.D918D		Atlas-SNP	.											.	RTEL1	114	.	0			c.C2754T						.						60	53	55					20																	62324187		2188	4287	6475	SO:0001819	synonymous_variant	51750	exon29			GACGGACAGGGCC	AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"chromosome 20 open reading frame 41"	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.2682C>T	chr20.hg19:g.62324187C>T		66.0	0.0		86.0	44.0	NM_032957		Silent	SNP	ENST00000360203.5	hg19																																																																																				.	.		0.627	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957		T	62324187	C	T	62324187	2	4	127	1	0	0	0	0	0	0	0	1	13735	477	17	3		3	RTEL1	20	62324187	Silent	SNP	C	TCGA-DD-A4NE-01A-11D-A27I-10		62324187	701333	54	21071										
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62597492	62597583	+	Splice_Site	DEL	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	-													0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	gacctgggacgagcccccatAccttttcttaccactgttcc					rs200518817|rs376642783|rs540039560|rs200940725|rs371234637|rs139142804|rs146666443	byFrequency	TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr20:62597492_62597583delGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	ENST00000450537.1	-	5	1005_1095	c.945_1035delAGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTCGGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTC	c.(943-1035)agagggaggaacagtggtaagaaaaggtatgggggctcgtcccaggtcggggaggaacagtggtaagaaaaggtatgggggctcgtcccaggt>ag	p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs	ZNF512B_ENST00000217130.3_Splice_Site_p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs|ZNF512B_ENST00000369888.1_Splice_Site_p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGTCTGCTGATAGCAA	0.575																																					p.338_345del		Pindel	.											.	ZNF512B	72	.	0			c.1012_1034del						.																																			SO:0001630	splice_region_variant	57473	exon5			.	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.1034+1AGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTCGGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTC>-	chr20.hg19:g.62597492_62597583delGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT		111.0	0.0		211.0	19.0	NM_020713	Q08AK9|Q9ULM4	Frame_Shift_Del	DEL	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	.		0.575	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	Frame_Shift_Del	-	62597583	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	-	62597492	8	5	127	1	0	1	0	1	0	0	1	0	17972	405	14	0	1694	0	ZNF512B	20	62597492	Splice_Site	DEL	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	TCGA-DD-A4NE-01A-11D-A27I-10	273305	62597492	428028	55	21072										
NCF4	4689	hgsc.bcm.edu	37	chr22	37271708	37271708	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	tctgcagggcactgtccgggGagccacgggcatcttccctc	13	15	2	0			TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chr22:37271708G>C	ENST00000248899.6	+	8	825	c.641G>C	c.(640-642)gGa>gCa	p.G214A	NCF4_ENST00000397147.4_Missense_Mutation_p.G214A	NM_000631.4	NP_000622.2	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4, 40kDa	214	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of catalytic activity (GO:0043085)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|membrane (GO:0016020)|NADPH oxidase complex (GO:0043020)|phagolysosome (GO:0032010)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein dimerization activity (GO:0046983)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16					Dextromethorphan(DB00514)	ACTGTCCGGGGAGCCACGGGC	0.597																																					p.G214A		Atlas-SNP	.											.	NCF4	66	.	0			c.G641C						.						56	51	53					22																	37271708		2203	4300	6503	SO:0001583	missense	4689	exon8			TCCGGGGAGCCAC	X77094	CCDS13934.1, CCDS13935.1	22q13.1	2014-09-17	2002-08-29		ENSG00000100365	ENSG00000100365			7662	protein-coding gene	gene with protein product	"neutrophil NADPH oxidase factor 4"	601488	"neutrophil cytosolic factor 4 (40kD)"			8839867	Standard	NM_013416		Approved	p40phox, SH3PXD4	uc003apy.4	Q15080	OTTHUMG00000150548	ENST00000248899.6:c.641G>C	chr22.hg19:g.37271708G>C	ENSP00000248899:p.Gly214Ala	36.0	0.0		41.0	20.0	NM_000631	A8K4F9|O60808|Q86U56|Q9BU98|Q9NP45	Missense_Mutation	SNP	ENST00000248899.6	hg19	CCDS13934.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.784470	0.49997	.	.	ENSG00000100365	ENST00000447071;ENST00000248899;ENST00000397147	T;T;T	0.42900	0.96;0.96;0.96	4.45	3.43	0.39272	Src homology-3 domain (4);	0.161554	0.52532	D	0.000061	T	0.58424	0.2121	M	0.90425	3.115	0.26018	N	0.981908	P;P	0.49961	0.93;0.67	P;B	0.53313	0.723;0.403	T	0.54735	-0.8249	10	0.41790	T	0.15	-11.5148	8.3181	0.32113	0.249:0.0:0.751:0.0	.	214;214	A8K4F9;Q15080	.;NCF4_HUMAN	A	111;214;214	ENSP00000414958:G111A;ENSP00000248899:G214A;ENSP00000380334:G214A	ENSP00000248899:G214A	G	+	2	0	NCF4	35601654	1.000000	0.71417	0.814000	0.32528	0.954000	0.61252	3.831000	0.55776	1.005000	0.39183	0.650000	0.86243	GGA	.	.		0.597	NCF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318863.1	NM_000631		C	37271708	G	C	37271708	3	2	127	1	0	0	0	0	1	0	0	0	10227	1174	41	4	671	4	NCF4	22	37271708	Missense_Mutation	SNP	G	TCGA-DD-A4NE-01A-11D-A27I-10		37271708	14032858	56	21073										
NXF2	56001	hgsc.bcm.edu	37	chrX	101573497	101573497	+	Frame_Shift_Del	DEL	C	C	-													0.0350877192982456	2	1	0.574957888826502	0	0.996593673965937	0.4	1	0	ctccagaatctccgctttgaCccaggtaaggctgacagcag							TCGA-DD-A4NE-01A-11D-A27I-10	TCGA-DD-A4NE-11A-11D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	343fcbc2-f30c-4ffa-a0b3-f5bb21e5e70b	2f595b57-7cf4-4499-bec6-497a4e241e01	g.chrX:101573497delC	ENST00000372758.1	+	13	1570	c.720delC	c.(718-720)gacfs	p.D240fs	NXF2_ENST00000372763.1_Frame_Shift_Del_p.D152fs|NXF2_ENST00000330252.5_Frame_Shift_Del_p.D240fs|NXF2_ENST00000372757.1_Frame_Shift_Del_p.D240fs|NXF2_ENST00000395088.2_Frame_Shift_Del_p.D240fs			Q9GZY0	NXF2_HUMAN	nuclear RNA export factor 2	240					mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|lung(2)	4						TCCGCTTTGACCCAGGTAAGG	0.532																																					p.D240fs		Atlas-INDEL	.											.	NXF2B	20	.	0			c.719delA						.						2	4	3					X																	101573497		755	1760	2515	SO:0001589	frameshift_variant	728343	exon9			.	AJ277526	CCDS14497.1	Xq22.1	2011-05-25			ENSG00000185554				8072	protein-coding gene	gene with protein product	"cancer/testis antigen 39", "TAP like protein 2"	300315				11073998, 11279525	Standard	NM_022053		Approved	CT39, TAPL-2	uc004eix.4	Q9GZY0		ENST00000372758.1:c.720delC	chrX.hg19:g.101573497delC	ENSP00000361844:p.Asp240fs	606.0	0.0		990.0	141.0	NM_001099686	Q9BXU4|Q9NSS1|Q9NX66	Frame_Shift_Del	DEL	ENST00000372758.1	hg19	CCDS14497.1																																																																																			.	.		0.532	NXF2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057618.1	NM_017809		-	101573497	C	-	101573497	7	5	127	1	0	1	0	1	0	0	0	0	10792	506	18	0	746	0	NXF2	23	101573497	Frame_Shift_Del	DEL	C	TCGA-DD-A4NE-01A-11D-A27I-10		101573497	53697063	57	21074										
C1orf127	148345	hgsc.bcm.edu	37	chr1	11008624	11008624	+	Frame_Shift_Del	DEL	G	G	-													0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	attcaggtcgttcaggcctcGgggctggcggtgaaggagag							TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:11008624delG	ENST00000377008.4	-	11	1513	c.1067delC	c.(1066-1068)ccgfs	p.P356fs	C1orf127_ENST00000377004.4_Frame_Shift_Del_p.P523fs			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	356	Pro-rich.									NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TTCAGGCCTCGGGGCTGGCGG	0.622																																					p.P523fs		Atlas-INDEL	.											.	C1orf127	134	.	0			c.1569delG						.						57	54	55					1																	11008624		2203	4300	6503	SO:0001589	frameshift_variant	148345	exon12			.	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1067delC	chr1.hg19:g.11008624delG	ENSP00000366207:p.Pro356fs	169.0	0.0		130.0	10.0	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Frame_Shift_Del	DEL	ENST00000377008.4	hg19																																																																																				.	.		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		-	11008624	G	-	11008624	7	5	128	1	0	1	0	1	0	0	0	0	1996	1116	39	0	907	0	C1orf127	1	11008624	Frame_Shift_Del	DEL	G	TCGA-DD-A4NF-01A-11D-A27I-10		11008624	238241997	1	21075										
RPE65	6121	hgsc.bcm.edu	37	chr1	68910330	68910330	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	aagggcattgtcagtaacctCtactcctcgaaagtaagaaa	8	9	2	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:68910330C>T	ENST00000262340.5	-	5	432	c.379G>A	c.(379-381)Gag>Aag	p.E127K		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	127					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						TCAGTAACCTCTACTCCTCGA	0.368																																					p.E127K		Atlas-SNP	.											.	RPE65	87	.	0			c.G379A						.						64	67	66					1																	68910330		2203	4300	6503	SO:0001583	missense	6121	exon5			TAACCTCTACTCC	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.379G>A	chr1.hg19:g.68910330C>T	ENSP00000262340:p.Glu127Lys	119.0	0.0		73.0	22.0	NM_000329	A8K1L0|Q5T9U3	Missense_Mutation	SNP	ENST00000262340.5	hg19	CCDS643.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.185934	0.57909	.	.	ENSG00000116745	ENST00000262340	D	0.94232	-3.38	5.05	5.05	0.67936	.	0.431282	0.19527	N	0.112134	D	0.85186	0.5639	L	0.46157	1.445	0.80722	D	1	B	0.13145	0.007	B	0.17098	0.017	T	0.81243	-0.1021	10	0.06891	T	0.86	-15.4338	18.5839	0.91181	0.0:1.0:0.0:0.0	.	127	Q16518	RPE65_HUMAN	K	127	ENSP00000262340:E127K	ENSP00000262340:E127K	E	-	1	0	RPE65	68682918	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.320000	0.79064	2.627000	0.88993	0.655000	0.94253	GAG	.	.		0.368	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		T	68910330	C	T	68910330	3	4	128	1	0	0	0	0	1	0	0	0	13560	922	32	3	1262	3	RPE65	1	68910330	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	57901706	68910330	180340291	2	21076										
AHCYL1	10768	hgsc.bcm.edu	37	chr1	110560140	110560140	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ggcaagggctgctgtgctgcTctcaaagctcttggagcaat	13	10	2	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:110560140T>A	ENST00000369799.5	+	10	1354	c.987T>A	c.(985-987)gcT>gcA	p.A329A	AHCYL1_ENST00000393614.4_Silent_p.A282A|AHCYL1_ENST00000359172.3_Silent_p.A282A	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	329	NAD binding. {ECO:0000250}.				mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		GCTGTGCTGCTCTCAAAGCTC	0.438																																					p.A329A		Atlas-SNP	.											.	AHCYL1	49	.	0			c.T987A						.						131	123	125					1																	110560140		2203	4300	6503	SO:0001819	synonymous_variant	10768	exon10			TGCTGCTCTCAAA	U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"inositol 1,4,5-trisphosphate receptor-binding protein", "protein phosphatase 1, regulatory subunit 78"	607826	"S-adenosylhomocysteine hydrolase-like 1"			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.987T>A	chr1.hg19:g.110560140T>A		152.0	0.0		92.0	28.0	NM_006621	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Silent	SNP	ENST00000369799.5	hg19	CCDS818.1																																																																																			.	.		0.438	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1			A	110560140	T	A	110560140	2	1	128	1	0	0	0	0	0	0	0	1	410	1538	54	4		4	AHCYL1	1	110560140	Silent	SNP	T	TCGA-DD-A4NF-01A-11D-A27I-10	41649810	110560140	138690481	3	21077										
ZNF687	5298	hgsc.bcm.edu	37	chr1	151261996	151261997	+	IGR	INS	-	-	C													0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gctctttgcccaaaaaaggaINSccatgctggaacatctcaag							TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:151261996_151261997insC	ENST00000368873.1	-	0	3340				ZNF687_ENST00000368879.2_Frame_Shift_Ins_p.T872fs			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta						phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CCAAAAAAGGACCATGCTGGAA	0.564																																					p.T872fs	Colon(154;765 1838 9854 28443 37492)	Pindel	.											.	ZNF687	94	.	0			c.2614_2615insC						.																																			SO:0001628	intergenic_variant	57592	exon5			.	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348		chr1.hg19:g.151261998_151261998dupC		251.0	0.0		311.0	65.0	NM_020832	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	Frame_Shift_Ins	INS	ENST00000368873.1	hg19																																																																																				.	.		0.564	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651		C	151261997	-	C	151261996	6	5	128	0	1	1	1	0	0	0	0	0	18107	275	10	0		0	ZNF687	1	151261996	IGR	INS	-	TCGA-DD-A4NF-01A-11D-A27I-10	40701856	151261996	97988625	4	21078										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158604337	158604337	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tcttcctgttcctcacctgaGtagcagctaatgtatctcca	6	13	3	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:158604337G>A	ENST00000368147.4	-	39	5741	c.5561C>T	c.(5560-5562)aCt>aTt	p.T1854I		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1854					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CCTCACCTGAGTAGCAGCTAA	0.383																																					p.T1854I		Atlas-SNP	.											.	SPTA1	720	.	0			c.C5561T						.						188	171	177					1																	158604337		1928	4134	6062	SO:0001583	missense	6708	exon39			ACCTGAGTAGCAG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5561C>T	chr1.hg19:g.158604337G>A	ENSP00000357129:p.Thr1854Ile	125.0	0.0		134.0	56.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	6.497	0.459910	0.12342	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.46819	0.86;0.86	5.64	2.81	0.32909	.	0.252307	0.20832	N	0.084865	T	0.12263	0.0298	N	0.21373	0.66	0.30554	N	0.765147	B	0.14438	0.01	B	0.17979	0.02	T	0.23547	-1.0185	10	0.19147	T	0.46	.	7.8622	0.29516	0.3011:0.0:0.6989:0.0	.	1854	P02549	SPTA1_HUMAN	I	1854	ENSP00000357130:T1854I;ENSP00000357129:T1854I	ENSP00000357129:T1854I	T	-	2	0	SPTA1	156870961	1.000000	0.71417	0.997000	0.53966	0.906000	0.53458	3.524000	0.53495	0.501000	0.28013	-0.157000	0.13467	ACT	.	.		0.383	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158604337	G	A	158604337	3	1	128	1	0	0	0	0	1	0	0	0	15131	1029	36	3	1754	3	SPTA1	1	158604337	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	7342341	158604337	90646284	5	21079										
OR6N2	81442	hgsc.bcm.edu	37	chr1	158746653	158746653	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tcttctttagccgcacatacAtgaagatgatgctcccaaag	7	11	2	3			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:158746653A>T	ENST00000339258.1	-	1	772	c.773T>A	c.(772-774)aTg>aAg	p.M258K		NM_001005278.1	NP_001005278.1	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N, member 2	258						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(6)|lung(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(112;0.0378)					CCGCACATACATGAAGATGAT	0.438																																					p.M258K		Atlas-SNP	.											.	OR6N2	78	.	0			c.T773A						.						99	94	96					1																	158746653		2203	4300	6503	SO:0001583	missense	81442	exon1			ACATACATGAAGA	BK004200	CCDS30906.1	1q23.1	2012-08-09			ENSG00000188340	ENSG00000188340		"GPCR / Class A : Olfactory receptors"	15035	protein-coding gene	gene with protein product							Standard	NM_001005278		Approved		uc010pir.2	Q8NGY6	OTTHUMG00000022775	ENST00000339258.1:c.773T>A	chr1.hg19:g.158746653A>T	ENSP00000344101:p.Met258Lys	337.0	0.0		507.0	132.0	NM_001005278	Q6IFR2	Missense_Mutation	SNP	ENST00000339258.1	hg19	CCDS30906.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.084886	0.76642	.	.	ENSG00000188340	ENST00000339258	T	0.00198	8.57	4.94	4.94	0.65067	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000274	T	0.00300	0.0009	M	0.83483	2.645	0.44042	D	0.996773	D	0.58970	0.984	P	0.58620	0.842	T	0.75733	-0.3214	10	0.87932	D	0	-19.8763	13.7168	0.62702	1.0:0.0:0.0:0.0	.	258	Q8NGY6	OR6N2_HUMAN	K	258	ENSP00000344101:M258K	ENSP00000344101:M258K	M	-	2	0	OR6N2	157013277	0.340000	0.24792	1.000000	0.80357	0.914000	0.54420	2.807000	0.47955	2.059000	0.61396	0.528000	0.53228	ATG	.	.		0.438	OR6N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059068.1			T	158746653	A	T	158746653	3	4	128	1	0	0	0	0	1	0	0	0	11216	217	8	4	183	4	OR6N2	1	158746653	Missense_Mutation	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	142316	158746653	90503968	6	21080										
CASQ1	844	hgsc.bcm.edu	37	chr1	160165717	160165717	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	agctgaccctgaagctgaatGagattgatttctacgaggcc	11	9	1	5			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:160165717G>A	ENST00000368078.3	+	6	878	c.682G>A	c.(682-684)Gag>Aag	p.E228K	CASQ1_ENST00000467691.1_5'Flank|CASQ1_ENST00000368079.3_Missense_Mutation_p.E222K			P31415	CASQ1_HUMAN	calsequestrin 1 (fast-twitch, skeletal muscle)	228					endoplasmic reticulum organization (GO:0007029)|ion transmembrane transport (GO:0034220)|protein polymerization (GO:0051258)|regulation of sequestering of calcium ion (GO:0051282)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to heat (GO:0009408)|response to organic substance (GO:0010033)|sarcomere organization (GO:0045214)|skeletal muscle tissue development (GO:0007519)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna lumen (GO:0014804)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	21	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GAAGCTGAATGAGATTGATTT	0.532																																					p.E228K		Atlas-SNP	.											.	CASQ1	55	.	0			c.G682A						.						102	102	102					1																	160165717		2203	4300	6503	SO:0001583	missense	844	exon6			CTGAATGAGATTG	S73775	CCDS1198.1, CCDS1198.2	1q21	2011-10-19			ENSG00000143318	ENSG00000143318		"Protein disulfide isomerases"	1512	protein-coding gene	gene with protein product	"calsequestrin 1, fast-twitch, skeletal muscle", "calmitine"	114250		CASQ		8406504, 2321095	Standard	NM_001231		Approved	PDIB1	uc010pja.2	P31415	OTTHUMG00000031607	ENST00000368078.3:c.682G>A	chr1.hg19:g.160165717G>A	ENSP00000357057:p.Glu228Lys	135.0	0.0		177.0	27.0	NM_001231	B1AKZ2|B2R863|Q8TBW7	Missense_Mutation	SNP	ENST00000368078.3	hg19	CCDS1198.2	.	.	.	.	.	.	.	.	.	.	G	24.9	4.579380	0.86645	.	.	ENSG00000143318	ENST00000368079;ENST00000368078;ENST00000441151	T;T	0.79033	-1.23;-1.23	5.35	4.37	0.52481	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	D	0.87010	0.6071	M	0.84683	2.71	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.88309	0.2955	10	0.72032	D	0.01	.	14.7545	0.69552	0.0:0.1454:0.8546:0.0	.	228	P31415	CASQ1_HUMAN	K	222;228;143	ENSP00000357058:E222K;ENSP00000357057:E228K	ENSP00000357057:E228K	E	+	1	0	CASQ1	158432341	1.000000	0.71417	0.995000	0.50966	0.656000	0.38851	7.258000	0.78371	2.660000	0.90430	0.555000	0.69702	GAG	.	.		0.532	CASQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077412.1	NM_001231		A	160165717	G	A	160165717	3	1	128	1	0	0	0	0	1	0	0	0	2682	1291	45	3	704	3	CASQ1	1	160165717	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	1419064	160165717	89084904	7	21081										
PKP1	5317	hgsc.bcm.edu	37	chr1	201282409	201282409	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ctgtaacaccaccggcgcagGcagcgacatctgcttcatgc	10	15	2	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:201282409G>T	ENST00000352845.3	+	3	422	c.422G>T	c.(421-423)gGc>gTc	p.G141V	PKP1_ENST00000263946.3_Missense_Mutation_p.G141V|PKP1_ENST00000367324.3_Missense_Mutation_p.G141V			Q13835	PKP1_HUMAN	plakophilin 1	141					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						ACCGGCGCAGGCAGCGACATC	0.647																																					p.G141V		Atlas-SNP	.											.	PKP1	127	.	0			c.G422T						.						20	23	22					1																	201282409		2203	4300	6503	SO:0001583	missense	5317	exon3			GCGCAGGCAGCGA	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"Armadillo repeat containing"	9023	protein-coding gene	gene with protein product	"ectodermal dysplasia/skin fragility syndrome"	601975	"plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.422G>T	chr1.hg19:g.201282409G>T	ENSP00000295597:p.Gly141Val	265.0	1.0		328.0	137.0	NM_001005337	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	hg19	CCDS30966.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.398373	0.62177	.	.	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.73789	-0.78;-0.68;-0.68	4.25	4.25	0.50352	.	0.000000	0.64402	D	0.000019	T	0.77638	0.4160	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.74674	0.974;0.984	T	0.75566	-0.3273	10	0.27785	T	0.31	-24.1646	17.1769	0.86844	0.0:0.0:1.0:0.0	.	141;141	Q13835-2;Q13835	.;PKP1_HUMAN	V	141	ENSP00000356293:G141V;ENSP00000263946:G141V;ENSP00000295597:G141V	ENSP00000263946:G141V	G	+	2	0	PKP1	199549032	1.000000	0.71417	0.997000	0.53966	0.626000	0.37791	4.666000	0.61554	2.373000	0.80994	0.491000	0.48974	GGC	.	.		0.647	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		T	201282409	G	T	201282409	3	4	128	1	0	0	0	0	1	0	0	0	11993	1203	42	3	432	3	PKP1	1	201282409	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	41116692	201282409	47968212	8	21082										
CD46	4179	hgsc.bcm.edu	37	chr1	207940538	207940538	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cccagttccaaagtgtcttaAaggtacaaaggttatctttt	7	8	2	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:207940538A>C	ENST00000358170.2	+	6	1010	c.854A>C	c.(853-855)aAa>aCa	p.K285T	CD46_ENST00000441839.2_Missense_Mutation_p.K285T|CD46_ENST00000360212.2_Missense_Mutation_p.K285T|CD46_ENST00000357714.1_Missense_Mutation_p.K285T|CD46_ENST00000367041.1_Missense_Mutation_p.K285T|CD46_ENST00000322918.5_Missense_Mutation_p.K285T|CD46_ENST00000361067.1_Missense_Mutation_p.K285T|CD46_ENST00000354848.1_Missense_Mutation_p.K285T|CD46_ENST00000322875.4_Missense_Mutation_p.K285T|CD46_ENST00000367042.1_Missense_Mutation_p.K285T|CD46_ENST00000469535.1_3'UTR|CD46_ENST00000367047.1_Missense_Mutation_p.K222T|CD46_ENST00000480003.1_Missense_Mutation_p.K285T	NM_002389.4	NP_002380.3	P15529	MCP_HUMAN	CD46 molecule, complement regulatory protein	285	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adaptive immune response (GO:0002250)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|interleukin-10 production (GO:0032613)|negative regulation of complement activation (GO:0045916)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transforming growth factor beta production (GO:0071636)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)|regulation of Notch signaling pathway (GO:0008593)|sequestering of extracellular ligand from receptor (GO:0035581)|single fertilization (GO:0007338)|T cell mediated immunity (GO:0002456)|viral process (GO:0016032)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|inner acrosomal membrane (GO:0002079)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cadherin binding (GO:0045296)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	19						AAGTGTCTTAAAGGTACAAAG	0.353																																					p.K285T		Atlas-SNP	.											.	CD46	34	.	0			c.A854C						.						86	83	84					1																	207940538		2203	4299	6502	SO:0001583	missense	4179	exon6			GTCTTAAAGGTAC	BC030594	CCDS1479.1, CCDS1480.1, CCDS1481.1, CCDS1482.1, CCDS1484.1, CCDS1485.1, CCDS31008.1, CCDS31009.1	1q32	2014-09-17	2006-03-28	2006-02-09	ENSG00000117335	ENSG00000117335		"CD molecules", "Complement system"	6953	protein-coding gene	gene with protein product		120920	"antigen identified by monoclonal antibody TRA-2-10", "membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)", "CD46 antigen, complement regulatory protein"	MIC10, MCP		7929741	Standard	NM_002389		Approved	TRA2.10, MGC26544, TLX	uc001hgj.3	P15529	OTTHUMG00000036397	ENST00000358170.2:c.854A>C	chr1.hg19:g.207940538A>C	ENSP00000350893:p.Lys285Thr	239.0	0.0		325.0	137.0	NM_172352	A0T1T0|A0T1T1|A0T1T2|Q15429|Q53GV9|Q5HY94|Q5VWS6|Q5VWS7|Q5VWS8|Q5VWS9|Q5VWT0|Q5VWT1|Q5VWT2|Q6N0A1|Q7Z3R5|Q9NNW2|Q9NNW3|Q9NNW4|Q9UCJ4	Missense_Mutation	SNP	ENST00000358170.2	hg19	CCDS1485.1	.	.	.	.	.	.	.	.	.	.	A	12.27	1.886394	0.33348	.	.	ENSG00000117335	ENST00000358170;ENST00000354848;ENST00000322918;ENST00000367042;ENST00000367041;ENST00000357714;ENST00000322875;ENST00000367047;ENST00000441839;ENST00000361067;ENST00000360212;ENST00000480003	T;T;T;T;T;T;T;T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;0.6;-0.81	5.05	1.28	0.21552	Complement control module (1);Sushi/SCR/CCP (1);	0.644228	0.13704	N	0.368573	D	0.86843	0.6030	H	0.95004	3.61	0.29160	N	0.877823	D;D;P;D;D;D;D;P;D;P;D;D;D;P	0.64830	0.984;0.988;0.858;0.994;0.988;0.973;0.98;0.944;0.984;0.885;0.984;0.973;0.973;0.954	D;P;P;D;P;D;P;P;D;P;D;D;D;P	0.69479	0.916;0.898;0.472;0.964;0.898;0.957;0.843;0.771;0.916;0.476;0.916;0.957;0.957;0.907	T	0.77905	-0.2413	10	0.87932	D	0	.	5.4453	0.16531	0.5664:0.3432:0.0904:0.0	.	285;285;285;285;285;285;285;285;285;285;285;285;285;285	P15529-4;P15529-5;P15529-14;P15529-3;P15529-12;P15529-13;P15529-2;P15529-11;P15529-7;P15529-9;P15529-15;P15529-6;P15529-8;P15529	.;.;.;.;.;.;.;.;.;.;.;.;.;MCP_HUMAN	T	285;285;285;285;285;285;285;222;285;285;285;285	ENSP00000350893:K285T;ENSP00000346912:K285T;ENSP00000314664:K285T;ENSP00000356009:K285T;ENSP00000356008:K285T;ENSP00000350346:K285T;ENSP00000313875:K285T;ENSP00000356014:K222T;ENSP00000413543:K285T;ENSP00000354358:K285T;ENSP00000353342:K285T;ENSP00000418471:K285T	ENSP00000313875:K285T	K	+	2	0	CD46	206007161	0.798000	0.28890	0.242000	0.24170	0.192000	0.23643	1.167000	0.31847	0.110000	0.17919	0.533000	0.62120	AAA	.	.		0.353	CD46-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088588.3	NM_172361		C	207940538	A	C	207940538	3	2	128	1	0	0	0	0	1	0	0	0	3020	14	1	5	876	5	CD46	1	207940538	Missense_Mutation	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	6658129	207940538	41310083	9	21083										
LBR	3930	hgsc.bcm.edu	37	chr1	225594411	225594411	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cattggccaagacacttcatTtggatgactgactaaataaa	7	8	1	3			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:225594411T>A	ENST00000338179.2	-	11	1563	c.1438A>T	c.(1438-1440)Aat>Tat	p.N480Y	LBR_ENST00000272163.4_Missense_Mutation_p.N480Y	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	480					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		GACACTTCATTTGGATGACTG	0.363																																					p.N480Y		Atlas-SNP	.											.	LBR	54	.	0			c.A1438T						.						75	78	77					1																	225594411		2203	4300	6503	SO:0001583	missense	3930	exon11			CTTCATTTGGATG	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"Tudor domain containing"	6518	protein-coding gene	gene with protein product	"tudor domain containing 18"	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.1438A>T	chr1.hg19:g.225594411T>A	ENSP00000339883:p.Asn480Tyr	205.0	0.0		294.0	123.0	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	hg19	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.954808	0.34471	.	.	ENSG00000143815	ENST00000272163;ENST00000338179;ENST00000424022	D;D;D	0.97941	-4.62;-4.62;-4.62	5.21	2.92	0.33932	.	0.419880	0.29106	N	0.013133	D	0.94059	0.8096	N	0.25060	0.705	0.09310	N	1	P	0.34826	0.471	B	0.42738	0.396	D	0.86941	0.2079	10	0.16896	T	0.51	-11.6795	7.2851	0.26333	0.0:0.0757:0.3419:0.5824	.	480	Q14739	LBR_HUMAN	Y	480;480;111	ENSP00000272163:N480Y;ENSP00000339883:N480Y;ENSP00000397817:N111Y	ENSP00000272163:N480Y	N	-	1	0	LBR	223661034	0.007000	0.16637	0.503000	0.27626	0.959000	0.62525	1.208000	0.32345	0.417000	0.25871	0.533000	0.62120	AAT	.	.		0.363	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		A	225594411	T	A	225594411	3	1	128	1	0	0	0	0	1	0	0	0	8661	1841	64	4	425	4	LBR	1	225594411	Missense_Mutation	SNP	T	TCGA-DD-A4NF-01A-11D-A27I-10	17653873	225594411	23656210	10	21084										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228467000	228467000	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	aagtggctcctggggaagacGgtgttgcaggctggggggaa	20	6	0	1	rs371761770	byFrequency	TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:228467000G>T	ENST00000422127.1	+	27	7295	c.7251G>T	c.(7249-7251)acG>acT	p.T2417T	OBSCN_ENST00000570156.2_Silent_p.T2846T|OBSCN_ENST00000284548.11_Silent_p.T2417T|OBSCN_ENST00000359599.6_Silent_p.T1264T|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2417					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGGGGAAGACGGTGTTGCAGG	0.667																																					p.T2846T		Atlas-SNP	.											OBSCN_ENST00000570156,caecum,carcinoma,0,4	OBSCN	2142	.	0			c.G8538T						.						61	72	68					1																	228467000		2103	4209	6312	SO:0001819	synonymous_variant	84033	exon32			GAAGACGGTGTTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.7251G>T	chr1.hg19:g.228467000G>T		158.0	0.0		182.0	37.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.667	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228467000	G	T	228467000	2	4	128	1	0	0	0	0	0	0	0	1	10821	1103	39	1		1	OBSCN	1	228467000	Silent	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	2872589	228467000	20783621	11	21085										
OR2T34	127068	hgsc.bcm.edu	37	chr1	248737387	248737387	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tggatgagatgcaggatgagGgtgtatgagctggagatgac	18	3	0	5			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr1:248737387G>C	ENST00000328782.2	-	1	693	c.672C>G	c.(670-672)acC>acG	p.T224T		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCAGGATGAGGGTGTATGAGC	0.562																																					p.T224T		Atlas-SNP	.											.	OR2T34	72	.	0			c.C672G						.						140	158	152					1																	248737387		2173	4300	6473	SO:0001819	synonymous_variant	127068	exon1			GATGAGGGTGTAT	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"GPCR / Class A : Olfactory receptors"	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.672C>G	chr1.hg19:g.248737387G>C		576.0	1.0		703.0	164.0	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Silent	SNP	ENST00000328782.2	hg19	CCDS31120.1																																																																																			.	.		0.562	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821		C	248737387	G	C	248737387	2	2	128	1	0	0	0	0	0	0	0	1	11034	1219	43	4		4	OR2T34	1	248737387	Silent	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	20270387	248737387	513234	12	21086										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37256043	37256043	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	atcagttcgagaactaacccCaggggcaaaaggactgacat	10	10	1	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr2:37256043C>T	ENST00000233099.5	-	23	3477	c.3382G>A	c.(3382-3384)Ggg>Agg	p.G1128R	HEATR5B_ENST00000354531.2_Missense_Mutation_p.G1128R	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1128						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				GAACTAACCCCAGGGGCAAAA	0.403																																					p.G1128R		Atlas-SNP	.											.	HEATR5B	185	.	0			c.G3382A						.						67	71	69					2																	37256043		2203	4300	6503	SO:0001583	missense	54497	exon23			TAACCCCAGGGGC	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.3382G>A	chr2.hg19:g.37256043C>T	ENSP00000233099:p.Gly1128Arg	118.0	0.0		109.0	53.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.469107	0.26423	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.42900	0.96;0.96	4.78	4.78	0.61160	Armadillo-like helical (1);Armadillo-type fold (1);	0.135912	0.32120	N	0.006556	T	0.42675	0.1213	N	0.08118	0	0.44976	D	0.997994	D	0.89917	1.0	D	0.87578	0.998	T	0.39099	-0.9630	10	0.18276	T	0.48	-10.3609	15.9995	0.80280	0.0:1.0:0.0:0.0	.	1128	Q9P2D3	HTR5B_HUMAN	R	1128	ENSP00000233099:G1128R;ENSP00000346531:G1128R	ENSP00000233099:G1128R	G	-	1	0	HEATR5B	37109547	0.992000	0.36948	0.997000	0.53966	0.123000	0.20343	5.038000	0.64177	2.191000	0.70037	0.655000	0.94253	GGG	.	.		0.403	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		T	37256043	C	T	37256043	3	4	128	1	0	0	0	0	1	0	0	0	7041	594	21	3	2889	3	HEATR5B	2	37256043	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10		37256043	205943330	13	21087										
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43980783	43980783	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	atttctcagtgcaagctcgtGgagagactgatagagaaaag	12	6	1	3			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr2:43980783G>A	ENST00000282406.4	+	25	3789	c.3679G>A	c.(3679-3681)Gga>Aga	p.G1227R		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	1227	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GCAAGCTCGTGGAGAGACTGA	0.313																																					p.G1227R		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.G3679A						.						69	76	74					2																	43980783		2202	4299	6501	SO:0001583	missense	130271	exon25			GCTCGTGGAGAGA	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.3679G>A	chr2.hg19:g.43980783G>A	ENSP00000282406:p.Gly1227Arg	164.0	0.0		134.0	49.0	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.183855	0.78677	.	.	ENSG00000152527	ENST00000282406	T	0.71341	-0.56	5.42	5.42	0.78866	FERM central domain (1);Band 4.1 domain (1);FERM domain (1);	0.047839	0.85682	D	0.000000	D	0.84365	0.5456	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.82625	-0.0365	10	0.33141	T	0.24	-23.0345	19.2521	0.93929	0.0:0.0:1.0:0.0	.	1227	Q8IVE3	PKHH2_HUMAN	R	1227	ENSP00000282406:G1227R	ENSP00000282406:G1227R	G	+	1	0	PLEKHH2	43834287	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.585000	0.82584	2.542000	0.85734	0.655000	0.94253	GGA	.	.		0.313	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		A	43980783	G	A	43980783	3	1	128	1	0	0	0	0	1	0	0	0	12086	1349	47	3	3773	3	PLEKHH2	2	43980783	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	6724740	43980783	199218590	14	21088										
GPR148	344561	hgsc.bcm.edu	37	chr2	131486786	131486786	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ttggccggccctgatccagcTcatcagcaagacaccctgca	9	16	2	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr2:131486786T>A	ENST00000309926.4	+	1	144	c.62T>A	c.(61-63)cTc>cAc	p.L21H		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					CTGATCCAGCTCATCAGCAAG	0.607																																					p.L21H		Atlas-SNP	.											.	GPR148	54	.	0			c.T62A						.						99	97	98					2																	131486786		2203	4300	6503	SO:0001583	missense	344561	exon1			TCCAGCTCATCAG	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"GPCR / Class A : Orphans"	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.62T>A	chr2.hg19:g.131486786T>A	ENSP00000308908:p.Leu21His	377.0	0.0		317.0	110.0	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	hg19	CCDS2163.1	.	.	.	.	.	.	.	.	.	.	.	12.47	1.948813	0.34377	.	.	ENSG00000173302	ENST00000309926	T	0.10288	2.89	2.41	-3.59	0.04583	.	1.579220	0.05003	U	0.469570	T	0.04952	0.0133	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.39251	-0.9623	10	0.56958	D	0.05	1.2623	2.5666	0.04784	0.4262:0.2879:0.0:0.2859	.	21	Q8TDV2	GP148_HUMAN	H	21	ENSP00000308908:L21H	ENSP00000308908:L21H	L	+	2	0	GPR148	131203256	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.112000	0.10791	-0.875000	0.04022	0.379000	0.24179	CTC	.	.		0.607	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092		A	131486786	T	A	131486786	3	1	128	1	0	0	0	0	1	0	0	0	6661	1551	54	4	64	4	GPR148	2	131486786	Missense_Mutation	SNP	T	TCGA-DD-A4NF-01A-11D-A27I-10	87506003	131486786	111712587	15	21089										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133540419	133540419	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cagaaggggccttgttgggaGagctttccgtggaagagttc	16	7	0	3			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr2:133540419G>C	ENST00000409261.1	-	14	4338	c.3965C>G	c.(3964-3966)tCt>tGt	p.S1322C	NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.S1322C	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1322										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CTTGTTGGGAGAGCTTTCCGT	0.612																																					p.S1322C		Atlas-SNP	.											.	NCKAP5	322	.	0			c.C3965G						.						56	54	55					2																	133540419		1896	4115	6011	SO:0001583	missense	344148	exon14			TTGGGAGAGCTTT	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.3965C>G	chr2.hg19:g.133540419G>C	ENSP00000387128:p.Ser1322Cys	198.0	0.0		172.0	10.0	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	hg19	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	G	9.339	1.062653	0.19987	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.11277	2.79;2.79	5.5	3.55	0.40652	.	0.456856	0.16109	U	0.229205	T	0.11580	0.0282	L	0.29908	0.895	0.20074	N	0.999934	D	0.61080	0.989	P	0.53313	0.723	T	0.14868	-1.0457	10	0.37606	T	0.19	.	4.0234	0.09677	0.5295:0.0:0.4705:0.0	.	1322	O14513	NCKP5_HUMAN	C	1322	ENSP00000387128:S1322C;ENSP00000380603:S1322C	ENSP00000380603:S1322C	S	-	2	0	NCKAP5	133256889	0.656000	0.27385	0.006000	0.13384	0.118000	0.20060	1.268000	0.33062	0.794000	0.33899	0.655000	0.94253	TCT	.	.		0.612	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		C	133540419	G	C	133540419	3	2	128	1	0	0	0	0	1	0	0	0	10232	942	33	4	1792	4	NCKAP5	2	133540419	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	2053633	133540419	109658954	16	21090										
HDAC4	9759	hgsc.bcm.edu	37	chr2	240056082	240056082	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ggtgccggggaaaagggagaGcctctgctggagggcgggaa	21	7	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr2:240056082G>A	ENST00000345617.3	-	11	1944	c.1153C>T	c.(1153-1155)Ctc>Ttc	p.L385F	HDAC4_ENST00000553145.1_5'UTR|HDAC4_ENST00000543185.1_5'UTR|HDAC4_ENST00000541256.1_Missense_Mutation_p.L354F	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	385					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		AAAAGGGAGAGCCTCTGCTGG	0.672																																					p.L385F		Atlas-SNP	.											.	HDAC4	127	.	0			c.C1153T						.						48	35	39					2																	240056082		2203	4300	6503	SO:0001583	missense	9759	exon11			GGGAGAGCCTCTG	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.1153C>T	chr2.hg19:g.240056082G>A	ENSP00000264606:p.Leu385Phe	51.0	0.0		28.0	11.0	NM_006037	Q9UND6	Missense_Mutation	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	G	6.898	0.535144	0.13188	.	.	ENSG00000068024	ENST00000345617;ENST00000456922;ENST00000541256;ENST00000393621	T;T	0.59364	0.27;1.42	4.32	-1.48	0.08745	.	0.278425	0.39341	N	0.001399	T	0.46889	0.1416	L	0.50333	1.59	0.80722	D	1	B;P;B;P;B;P	0.39717	0.314;0.624;0.011;0.56;0.215;0.684	B;B;B;B;B;B	0.35470	0.098;0.203;0.02;0.19;0.043;0.1	T	0.45071	-0.9286	9	.	.	.	.	16.0252	0.80538	0.0:0.0:0.6934:0.3066	.	380;268;354;354;353;385	B7Z8G5;F5H0Q9;F5H5W4;B7Z8I2;Q53SM2;P56524	.;.;.;.;.;HDAC4_HUMAN	F	385;268;354;268	ENSP00000264606:L385F;ENSP00000443057:L354F	.	L	-	1	0	HDAC4	239721019	0.000000	0.05858	0.729000	0.30791	0.164000	0.22412	-1.220000	0.02971	-0.336000	0.08438	-0.397000	0.06425	CTC	.	.		0.672	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		A	240056082	G	A	240056082	3	1	128	1	0	0	0	0	1	0	0	0	7018	971	34	3	2169	3	HDAC4	2	240056082	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	106515663	240056082	3143291	17	21091										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266097	41266097	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ggcagcaacagtcttacctgGactctggaatccattctggt	10	11	3	0	rs28931588|rs121913416|rs121913417		TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr3:41266097G>T	ENST00000349496.5	+	3	374	c.94G>T	c.(94-96)Gac>Tac	p.D32Y	CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32Y|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32Y|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32Y|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25Y	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32Y(128)|p.D32N(82)|p.A5_A80del(53)|p.D32H(40)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.Q28fs*20(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.D32fs*9(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GTCTTACCTGGACTCTGGAAT	0.478	D32N(KE39_STOMACH)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32Y	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,2	CTNNB1	4904	.	397	Substitution - Missense(250)|Deletion - In frame(120)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Complex - frameshift(1)	liver(155)|central_nervous_system(55)|endometrium(40)|stomach(36)|pancreas(28)|large_intestine(22)|pituitary(22)|skin(11)|ovary(9)|soft_tissue(4)|prostate(4)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|adrenal_gland(1)|biliary_tract(1)|urinary_tract(1)|lung(1)|NS(1)	c.G94T						.						92	77	82					3																	41266097		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TACCTGGACTCTG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.94G>T	chr3.hg19:g.41266097G>T	ENSP00000344456:p.Asp32Tyr	355.0	1.0		301.0	109.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337485	0.81911	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.68210	0.2976	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.70498	-0.4855	10	0.87932	D	0	0.3843	19.9596	0.97236	0.0:0.0:1.0:0.0	rs28931588	32	P35222	CTNB1_HUMAN	Y	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25Y;ENSP00000385604:D32Y;ENSP00000412219:D32Y;ENSP00000379486:D32Y;ENSP00000344456:D32Y;ENSP00000411226:D25Y;ENSP00000379488:D32Y;ENSP00000409302:D32Y;ENSP00000401599:D32Y	ENSP00000344456:D32Y	D	+	1	0	CTNNB1	41241101	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GAC	.	.		0.478	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266097	G	T	41266097	3	4	128	1	0	0	0	0	1	0	0	0	4018	1174	41	3	100	3	CTNNB1	3	41266097	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		41266097	156756333	18	21092										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52360896	52360896	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	acccaatcttccccatctacCtcccactgaaggtgagccgg	7	17	2	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr3:52360896C>G	ENST00000420323.2	+	5	988	c.727C>G	c.(727-729)Ctc>Gtc	p.L243V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	243	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCCCATCTACCTCCCACTGAA	0.592																																					p.L243V		Atlas-SNP	.											.	DNAH1	534	.	0			c.C727G						.						88	106	100					3																	52360896		2091	4217	6308	SO:0001583	missense	25981	exon5			ATCTACCTCCCAC	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.727C>G	chr3.hg19:g.52360896C>G	ENSP00000401514:p.Leu243Val	325.0	0.0		228.0	60.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.173124	0.78452	.	.	ENSG00000114841	ENST00000420323	T	0.35605	1.3	5.51	5.51	0.81932	.	0.308624	0.23243	N	0.050326	T	0.69214	0.3086	M	0.90082	3.085	0.53005	D	0.999964	D;D	0.89917	0.996;1.0	P;D	0.81914	0.8;0.995	T	0.75465	-0.3308	10	0.72032	D	0.01	.	19.4334	0.94781	0.0:1.0:0.0:0.0	.	243;243	C9JXH6;Q9P2D7-3	.;.	V	243	ENSP00000401514:L243V	ENSP00000401514:L243V	L	+	1	0	DNAH1	52335936	1.000000	0.71417	0.974000	0.42286	0.744000	0.42396	4.611000	0.61162	2.591000	0.87537	0.313000	0.20887	CTC	.	.		0.592	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52360896	C	G	52360896	3	3	128	1	0	0	0	0	1	0	0	0	4599	681	24	4	741	4	DNAH1	3	52360896	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	11094799	52360896	145661534	19	21093										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78688976	78688976	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	atggagcagtcattgtggttGttgccagtattaggccacgt	13	7	1	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr3:78688976G>T	ENST00000464233.1	-	22	3068	c.2955C>A	c.(2953-2955)aaC>aaA	p.N985K	ROBO1_ENST00000467549.1_Missense_Mutation_p.N940K|ROBO1_ENST00000436010.2_Missense_Mutation_p.N946K|ROBO1_ENST00000495273.1_Missense_Mutation_p.N940K	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	985					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		CATTGTGGTTGTTGCCAGTAT	0.502																																					p.N985K		Atlas-SNP	.											.	ROBO1	833	.	0			c.C2955A						.						73	73	73					3																	78688976		2012	4190	6202	SO:0001583	missense	6091	exon22			GTGGTTGTTGCCA	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2955C>A	chr3.hg19:g.78688976G>T	ENSP00000420321:p.Asn985Lys	150.0	0.0		123.0	48.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	G	9.202	1.028688	0.19512	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.59502	0.29;0.26;0.27;0.31	5.78	3.97	0.46021	.	0.140197	0.64402	D	0.000004	T	0.44519	0.1297	L	0.36672	1.1	0.46798	D	0.999205	B;B;B;B;B	0.22909	0.069;0.077;0.025;0.019;0.003	B;B;B;B;B	0.22386	0.037;0.028;0.036;0.028;0.039	T	0.27434	-1.0074	9	.	.	.	.	11.5399	0.50661	0.1656:0.0:0.8344:0.0	.	949;985;940;940;946	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	K	946;940;985;940;940;989	ENSP00000406043:N946K;ENSP00000420321:N985K;ENSP00000420637:N940K;ENSP00000417992:N940K	.	N	-	3	2	ROBO1	78771666	1.000000	0.71417	0.994000	0.49952	0.147000	0.21601	3.512000	0.53407	2.732000	0.93576	0.591000	0.81541	AAC	.	.		0.502	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78688976	G	T	78688976	3	4	128	1	0	0	0	0	1	0	0	0	13528	1368	48	3	2040	3	ROBO1	3	78688976	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	26328080	78688976	119333454	20	21094										
NSUN3	63899	hgsc.bcm.edu	37	chr3	93812983	93812983	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tttttaatcctttttatttaGgttatcttcattgtaatgaa	4	4	2	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr3:93812983G>T	ENST00000314622.4	+	4	677		c.e4-1			NM_022072.3	NP_071355.1	Q9H649	NSUN3_HUMAN	NOP2/Sun domain family, member 3								methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	18						TTTTTATTTAGGTTATCTTCA	0.299																																					.		Atlas-SNP	.											NSUN3,right_upper_lobe,carcinoma,0,2	NSUN3	33	.	0			c.467-1G>T						.						56	54	55					3																	93812983		2203	4300	6503	SO:0001630	splice_region_variant	63899	exon4			TATTTAGGTTATC	BC020602	CCDS2927.1	3q11.2	2009-11-23	2009-11-23		ENSG00000178694	ENSG00000178694		"NOP2/Sun domain containing"	26208	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 3", "NOL1/NOP2/Sun domain family, member 3"			12477932	Standard	NM_022072		Approved	FLJ22609	uc003drl.1	Q9H649	OTTHUMG00000159025	ENST00000314622.4:c.467-1G>T	chr3.hg19:g.93812983G>T		82.0	0.0		80.0	4.0	NM_022072	Q6PG41|Q8IXG9|Q9H6M2	Splice_Site	SNP	ENST00000314622.4	hg19	CCDS2927.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.531542	0.27387	.	.	ENSG00000178694	ENST00000314622	.	.	.	5.98	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2548	0.73576	0.0669:0.0:0.9331:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NSUN3	95295673	1.000000	0.71417	1.000000	0.80357	0.046000	0.14306	8.517000	0.90555	1.541000	0.49316	-0.145000	0.13849	.	.	.		0.299	NSUN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352934.1	NM_022072	Intron	T	93812983	G	T	93812983	5	4	128	1	0	0	0	0	0	0	1	0	10688	1014	35	3	480	3	NSUN3	3	93812983	Splice_Site	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	15124007	93812983	104209447	21	21095										
LYAR	55646	hgsc.bcm.edu	37	chr4	4283593	4283593	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	atacttctgatcttcacttaTgcatttcacgtggtttttat	5	8	4	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr4:4283593T>C	ENST00000343470.4	-	4	394	c.154A>G	c.(154-156)Ata>Gta	p.I52V	LYAR_ENST00000452476.1_Missense_Mutation_p.I52V	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	52						nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TCTTCACTTATGCATTTCACG	0.443																																					p.I52V		Atlas-SNP	.											.	LYAR	36	.	0			c.A154G						.						364	323	337					4																	4283593		2203	4300	6503	SO:0001583	missense	55646	exon4			CACTTATGCATTT	AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"Zinc fingers, C2HC-type containing"	26021	protein-coding gene	gene with protein product			"Ly1 antibody reactive homolog (mouse)"			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.154A>G	chr4.hg19:g.4283593T>C	ENSP00000345917:p.Ile52Val	214.0	0.0		188.0	82.0	NM_017816	D3DVS4|Q6FI78|Q9NYS1	Missense_Mutation	SNP	ENST00000343470.4	hg19	CCDS3374.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.523758	0.27299	.	.	ENSG00000145220	ENST00000343470;ENST00000452476;ENST00000513174	T;T	0.39406	1.08;1.08	4.16	2.97	0.34412	Zinc finger, C2H2, LYAR-type (1);	0.156511	0.56097	N	0.000030	T	0.36963	0.0986	L	0.52126	1.63	0.52501	D	0.999954	B	0.19817	0.039	B	0.33960	0.173	T	0.15178	-1.0446	10	0.39692	T	0.17	-14.6164	5.5538	0.17105	0.0:0.0971:0.1731:0.7298	.	52	Q9NX58	LYAR_HUMAN	V	52	ENSP00000345917:I52V;ENSP00000397367:I52V	ENSP00000345917:I52V	I	-	1	0	LYAR	4334494	1.000000	0.71417	0.993000	0.49108	0.599000	0.36880	0.916000	0.28651	0.574000	0.29417	0.172000	0.16884	ATA	.	.		0.443	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816		C	4283593	T	C	4283593	3	2	128	1	0	0	0	0	1	0	0	0	9112	1464	51	2	1013	2	LYAR	4	4283593	Missense_Mutation	SNP	T	TCGA-DD-A4NF-01A-11D-A27I-10		4283593	186870683	22	21096										
ABCG2	9429	hgsc.bcm.edu	37	chr4	89039368	89039368	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	acttgaagatggaatatcgaGgctgatgaatggagaagatg	14	3	0	6			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr4:89039368G>C	ENST00000237612.3	-	7	1279	c.734C>G	c.(733-735)cCt>cGt	p.P245R	ABCG2_ENST00000515655.1_Missense_Mutation_p.P245R	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	245	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	GGAATATCGAGGCTGATGAAT	0.413																																					p.P245R		Atlas-SNP	.											.	ABCG2	151	.	0			c.C734G						.						144	128	134					4																	89039368		2203	4300	6503	SO:0001583	missense	9429	exon7			TATCGAGGCTGAT	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.734C>G	chr4.hg19:g.89039368G>C	ENSP00000237612:p.Pro245Arg	188.0	0.0		120.0	49.0	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	hg19	CCDS3628.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.903431	0.92035	.	.	ENSG00000118777	ENST00000515655;ENST00000237612	T;T	0.56941	0.43;0.43	5.45	5.45	0.79879	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	T	0.77116	0.4083	M	0.84846	2.72	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.80322	-0.1431	10	0.87932	D	0	-35.1969	19.2735	0.94021	0.0:0.0:1.0:0.0	.	245;245;245	Q9UNQ0-2;Q9UNQ0;Q4W5I3	.;ABCG2_HUMAN;.	R	245	ENSP00000426917:P245R;ENSP00000237612:P245R	ENSP00000237612:P245R	P	-	2	0	ABCG2	89258392	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.397000	0.97276	2.716000	0.92895	0.655000	0.94253	CCT	.	.		0.413	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		C	89039368	G	C	89039368	3	2	128	1	0	0	0	0	1	0	0	0	69	1000	35	4	1273	4	ABCG2	4	89039368	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	84755775	89039368	102114908	23	21097										
SNCA	6622	hgsc.bcm.edu	37	chr4	90756778	90756778	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tctcagcagcagccacaactCcctccttggcctttgaaagt	7	15	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr4:90756778C>T	ENST00000394986.1	-	2	462	c.41G>A	c.(40-42)gGa>gAa	p.G14E	RP11-67M1.1_ENST00000501215.1_RNA|SNCA_ENST00000345009.4_Missense_Mutation_p.G14E|SNCA_ENST00000336904.3_Missense_Mutation_p.G14E|SNCA_ENST00000505199.1_Missense_Mutation_p.G14E|RP11-67M1.1_ENST00000513653.1_RNA|SNCA_ENST00000394989.2_Missense_Mutation_p.G14E|SNCA_ENST00000394991.3_Missense_Mutation_p.G14E|SNCA_ENST00000508895.1_Missense_Mutation_p.G14E|SNCA_ENST00000420646.2_Missense_Mutation_p.G14E|SNCA_ENST00000502987.1_Missense_Mutation_p.G14E|SNCA_ENST00000506244.1_Missense_Mutation_p.G14E			P37840	SYUA_HUMAN	synuclein, alpha (non A4 component of amyloid precursor)	14					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adult locomotory behavior (GO:0008344)|aging (GO:0007568)|behavioral response to cocaine (GO:0048148)|cellular response to copper ion (GO:0071280)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to oxidative stress (GO:0034599)|dopamine biosynthetic process (GO:0042416)|dopamine uptake involved in synaptic transmission (GO:0051583)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|long-term synaptic potentiation (GO:0060291)|microglial cell activation (GO:0001774)|mitochondrial ATP synthesis coupled electron transport (GO:0042775)|mitochondrial membrane organization (GO:0007006)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dopamine metabolic process (GO:0045963)|negative regulation of dopamine uptake involved in synaptic transmission (GO:0051585)|negative regulation of exocytosis (GO:0045920)|negative regulation of histone acetylation (GO:0035067)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of monooxygenase activity (GO:0032769)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of norepinephrine uptake (GO:0051622)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of serotonin uptake (GO:0051612)|negative regulation of thrombin receptor signaling pathway (GO:0070495)|negative regulation of transporter activity (GO:0032410)|neutral lipid metabolic process (GO:0006638)|oxidation-reduction process (GO:0055114)|phospholipid metabolic process (GO:0006644)|positive regulation of endocytosis (GO:0045807)|positive regulation of glutathione peroxidase activity (GO:1903284)|positive regulation of hydrogen peroxide catabolic process (GO:1903285)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of receptor recycling (GO:0001921)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein destabilization (GO:0031648)|receptor internalization (GO:0031623)|regulation of acyl-CoA biosynthetic process (GO:0050812)|regulation of dopamine secretion (GO:0014059)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glutamate secretion (GO:0014048)|regulation of locomotion (GO:0040012)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of macrophage activation (GO:0043030)|regulation of neuron death (GO:1901214)|regulation of phospholipase activity (GO:0010517)|response to drug (GO:0042493)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|response to iron(II) ion (GO:0010040)|response to lipopolysaccharide (GO:0032496)|response to magnesium ion (GO:0032026)|synapse organization (GO:0050808)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular region (GO:0005576)|fibril (GO:0043205)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nuclear outer membrane (GO:0005640)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribosome (GO:0005840)|rough endoplasmic reticulum (GO:0005791)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	alpha-tubulin binding (GO:0043014)|calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|dynein binding (GO:0045502)|ferrous iron binding (GO:0008198)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinesin binding (GO:0019894)|magnesium ion binding (GO:0000287)|oxidoreductase activity (GO:0016491)|phospholipid binding (GO:0005543)|phosphoprotein binding (GO:0051219)|tau protein binding (GO:0048156)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)	8		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.42e-05)		AGCCACAACTCCCTCCTTGGC	0.428																																					p.G14E		Atlas-SNP	.											.	SNCA	17	.	0			c.G41A						.						135	124	128					4																	90756778		2203	4300	6503	SO:0001583	missense	6622	exon2			ACAACTCCCTCCT	L08850	CCDS3634.1, CCDS43252.1	4q21.3-q22	2014-05-22			ENSG00000145335	ENSG00000145335		"Parkinson disease"	11138	protein-coding gene	gene with protein product		163890	"Parkinson disease (autosomal dominant, Lewy body) 4"	PARK1, PARK4		8248242, 14593171	Standard	NM_000345		Approved	NACP, PD1, alpha-synuclein	uc003hsr.3	P37840	OTTHUMG00000130948	ENST00000394986.1:c.41G>A	chr4.hg19:g.90756778C>T	ENSP00000378437:p.Gly14Glu	200.0	0.0		154.0	60.0	NM_000345	A8K2A4|Q13701|Q4JHI3|Q6IAU6	Missense_Mutation	SNP	ENST00000394986.1	hg19	CCDS3634.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.917650	0.92249	.	.	ENSG00000145335	ENST00000394989;ENST00000420646;ENST00000345009;ENST00000394986;ENST00000394991;ENST00000336904;ENST00000508895;ENST00000506244;ENST00000505199;ENST00000502987;ENST00000506691	D;D;D;D;D;D;D;D;D;D;D	0.92048	-2.96;-2.96;-2.96;-2.96;-2.96;-2.96;-2.96;-2.96;-2.96;-2.96;-2.96	4.28	4.28	0.50868	.	0.000000	0.64402	D	0.000001	D	0.95623	0.8577	M	0.70595	2.14	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.95931	0.8938	10	0.87932	D	0	-4.8285	18.1022	0.89509	0.0:1.0:0.0:0.0	.	14;14;14	P37840-3;P37840;P37840-2	.;SYUA_HUMAN;.	E	14	ENSP00000378440:G14E;ENSP00000396241:G14E;ENSP00000343683:G14E;ENSP00000378437:G14E;ENSP00000378442:G14E;ENSP00000338345:G14E;ENSP00000426955:G14E;ENSP00000422238:G14E;ENSP00000421485:G14E;ENSP00000426034:G14E;ENSP00000423445:G14E	ENSP00000338345:G14E	G	-	2	0	SNCA	90975801	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.467000	0.80930	2.701000	0.92244	0.644000	0.83932	GGA	.	.		0.428	SNCA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253547.2			T	90756778	C	T	90756778	3	4	128	1	0	0	0	0	1	0	0	0	14855	855	30	3	401	3	SNCA	4	90756778	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	1717410	90756778	100397498	24	21098										
NHEDC1	150159	hgsc.bcm.edu	37	chr4	103912818	103912818	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	acctgaggagttgtagatgtTtggaagttttcatcctccaa	10	7	1	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr4:103912818T>C	ENST00000296422.7	-	2	192	c.51A>G	c.(49-51)caA>caG	p.Q17Q	SLC9B1_ENST00000394789.3_Silent_p.Q17Q	NM_139173.3	NP_631912	Q4ZJI4	SL9B1_HUMAN	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	17					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TTGTAGATGTTTGGAAGTTTT	0.249																																					p.Q17Q		Atlas-SNP	.											.	.	.	.	0			c.A51G						.						48	48	48					4																	103912818		2196	4291	6487	SO:0001819	synonymous_variant	150159	exon2			AGATGTTTGGAAG	AF447585	CCDS34041.1, CCDS47119.1	4q24	2013-05-22	2012-03-22	2011-07-26	ENSG00000164037	ENSG00000164037		"Solute carriers"	24244	protein-coding gene	gene with protein product		611527	"Na+/H+ exchanger domain containing 1", "solute carrier family 9, subfamily B (cation proton antiporter 2), member 1"	NHEDC1		16850186	Standard	NM_139173		Approved	NHA1	uc003hww.3	Q4ZJI4	OTTHUMG00000161114	ENST00000296422.7:c.51A>G	chr4.hg19:g.103912818T>C		18.0	0.0		19.0	9.0	NM_001100874	A1KXV1|B9EH04|C9JBP7|Q49A30|Q8NCV2|Q8WVZ0	Silent	SNP	ENST00000296422.7	hg19	CCDS34041.1																																																																																			.	.		0.249	SLC9B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363841.1	NM_139173		C	103912818	T	C	103912818	2	2	128	1	0	0	0	0	0	0	0	1	10409	1838	64	2		2	NHEDC1	4	103912818	Silent	SNP	T	TCGA-DD-A4NF-01A-11D-A27I-10	13156040	103912818	87241458	25	21099										
LEF1	51176	hgsc.bcm.edu	37	chr4	109084858	109084858	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gcctccatctggatgctttcCtgggaagatccaaagaacaa	9	11	1	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr4:109084858C>T	ENST00000265165.1	-	3	935		c.e3-1		LEF1_ENST00000510624.1_Splice_Site|LEF1_ENST00000512172.1_Splice_Site|LEF1_ENST00000438313.2_Splice_Site|LEF1_ENST00000379951.2_Splice_Site	NM_016269.4	NP_057353.1	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1						alpha-beta T cell differentiation (GO:0046632)|anatomical structure regression (GO:0060033)|apoptotic process involved in morphogenesis (GO:0060561)|apoptotic process involved in patterning of blood vessels (GO:1902262)|B cell proliferation (GO:0042100)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|cellular response to cytokine stimulus (GO:0071345)|cellular response to interleukin-4 (GO:0071353)|chorio-allantoic fusion (GO:0060710)|dentate gyrus development (GO:0021542)|embryonic limb morphogenesis (GO:0030326)|epithelial to mesenchymal transition (GO:0001837)|eye pigmentation (GO:0048069)|face morphogenesis (GO:0060325)|forebrain neuroblast division (GO:0021873)|forebrain neuron differentiation (GO:0021879)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|mammary gland development (GO:0030879)|muscle fiber development (GO:0048747)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process in bone marrow (GO:0071866)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA binding (GO:0043392)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neutrophil differentiation (GO:0030223)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesoderm formation (GO:0048341)|patterning of blood vessels (GO:0001569)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell cycle process (GO:0090068)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell-cell adhesion (GO:0022407)|regulation of striated muscle tissue development (GO:0016202)|sensory perception of taste (GO:0050909)|somitogenesis (GO:0001756)|sprouting angiogenesis (GO:0002040)|steroid hormone mediated signaling pathway (GO:0043401)|T cell receptor V(D)J recombination (GO:0033153)|T-helper 1 cell differentiation (GO:0045063)|tongue development (GO:0043586)|trachea gland development (GO:0061153)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer binding (GO:0035326)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|gamma-catenin binding (GO:0045295)|histone binding (GO:0042393)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	25				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		GGATGCTTTCCTGGGAAGATC	0.393																																					.		Atlas-SNP	.											.	LEF1	93	.	0			c.281-1G>A						.						105	96	99					4																	109084858		2203	4300	6503	SO:0001630	splice_region_variant	51176	exon4			GCTTTCCTGGGAA		CCDS3679.1, CCDS47122.1, CCDS47123.1, CCDS54791.1	4q23-q25	2011-07-08			ENSG00000138795	ENSG00000138795			6551	protein-coding gene	gene with protein product		153245				1783375	Standard	NM_016269		Approved	TCF1ALPHA, TCF10, TCF7L3	uc003hyt.2	Q9UJU2	OTTHUMG00000131809	ENST00000265165.1:c.281-1G>A	chr4.hg19:g.109084858C>T		165.0	0.0		90.0	26.0	NM_016269	B4DG38|B7Z8E2|E9PDK3|Q3ZCU4|Q9HAZ0	Splice_Site	SNP	ENST00000265165.1	hg19	CCDS3679.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812941	0.70912	.	.	ENSG00000138795	ENST00000265165;ENST00000379951;ENST00000438313;ENST00000510624;ENST00000515500;ENST00000512172	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1374	0.98035	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LEF1	109304307	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	5.667000	0.68067	2.763000	0.94921	0.563000	0.77884	.	.	.		0.393	LEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254749.2		Intron	T	109084858	C	T	109084858	5	4	128	1	0	0	0	0	0	0	1	0	8723	695	24	3	1039	3	LEF1	4	109084858	Splice_Site	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	5172040	109084858	82069418	26	21100										
WWC2	80014	hgsc.bcm.edu	37	chr4	184182073	184182073	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tgtctttcagcctctctgccAgcaccctgtccatgtcatct	6	16	5	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr4:184182073A>G	ENST00000403733.3	+	11	1496	c.1297A>G	c.(1297-1299)Agc>Ggc	p.S433G	WWC2_ENST00000504005.1_Missense_Mutation_p.S115G|WWC2_ENST00000378925.3_Missense_Mutation_p.S335G|WWC2_ENST00000513834.1_Missense_Mutation_p.S433G|WWC2_ENST00000448232.2_Missense_Mutation_p.S433G	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	433	Ser-rich.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		CCTCTCTGCCAGCACCCTGTC	0.517																																					p.S433G		Atlas-SNP	.											.	WWC2	78	.	0			c.A1297G						.						31	30	31					4																	184182073		2202	4300	6502	SO:0001583	missense	80014	exon11			TCTGCCAGCACCC	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.1297A>G	chr4.hg19:g.184182073A>G	ENSP00000384222:p.Ser433Gly	97.0	0.0		81.0	33.0	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	hg19	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	A	23.9	4.474497	0.84640	.	.	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232;ENST00000504005	T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.69115	0.3075	M	0.81497	2.545	0.58432	D	0.999998	D	0.69078	0.997	D	0.75020	0.985	T	0.73522	-0.3956	10	0.56958	D	0.05	-20.6401	14.628	0.68635	1.0:0.0:0.0:0.0	.	433	Q6AWC2	WWC2_HUMAN	G	433;335;433;433;115	ENSP00000384222:S433G;ENSP00000368205:S335G;ENSP00000425054:S433G;ENSP00000398577:S433G;ENSP00000427569:S115G	ENSP00000368205:S335G	S	+	1	0	WWC2	184419067	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.097000	0.94193	2.046000	0.60703	0.528000	0.53228	AGC	.	.		0.517	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		G	184182073	A	G	184182073	3	3	128	1	0	0	0	0	1	0	0	0	17427	188	7	2	1339	2	WWC2	4	184182073	Missense_Mutation	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	75097215	184182073	6972203	27	21101										
BDP1	55814	hgsc.bcm.edu	37	chr5	70751716	70751716	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gcctccgccatgttccgcagGgcacgccttagcgtgaagcc	12	16	0	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr5:70751716G>T	ENST00000358731.4	+	1	275	c.12G>T	c.(10-12)agG>agT	p.R4S	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	4	Interaction with ZBTB43.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TGTTCCGCAGGGCACGCCTTA	0.706																																					p.R4S		Atlas-SNP	.											.	BDP1	204	.	0			c.G12T						.						8	10	9					5																	70751716		1921	4128	6049	SO:0001583	missense	55814	exon1			CCGCAGGGCACGC	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.12G>T	chr5.hg19:g.70751716G>T	ENSP00000351575:p.Arg4Ser	69.0	0.0		44.0	20.0	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	hg19	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.941488	0.92526	.	.	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000444711	T	0.24151	1.87	5.2	5.2	0.72013	.	0.063724	0.64402	D	0.000013	T	0.50017	0.1591	M	0.67953	2.075	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.923;0.951;0.997	T	0.50048	-0.8873	10	0.87932	D	0	.	15.7583	0.78054	0.0:0.0:1.0:0.0	.	4;4;4	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	S	4	ENSP00000351575:R4S	ENSP00000351575:R4S	R	+	3	2	BDP1	70787472	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.094000	0.41719	2.693000	0.91896	0.655000	0.94253	AGG	.	.		0.706	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		T	70751716	G	T	70751716	3	4	128	1	0	0	0	0	1	0	0	0	1395	1223	43	3	14	3	BDP1	5	70751716	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		70751716	110163544	28	21102										
LNPEP	4012	hgsc.bcm.edu	37	chr5	96342142	96342142	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tctttacagctacctgtggcAtattccactatcctatgtca	5	12	2	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr5:96342142A>G	ENST00000231368.5	+	11	2650	c.1958A>G	c.(1957-1959)cAt>cGt	p.H653R	LNPEP_ENST00000395770.3_Missense_Mutation_p.H639R	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	653					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		TACCTGTGGCATATTCCACTA	0.318																																					p.H653R		Atlas-SNP	.											.	LNPEP	80	.	0			c.A1958G						.						56	57	57					5																	96342142		2202	4295	6497	SO:0001583	missense	4012	exon11			TGTGGCATATTCC	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"cystinyl aminopeptidase", "placental leucine aminopeptidase"	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.1958A>G	chr5.hg19:g.96342142A>G	ENSP00000231368:p.His653Arg	228.0	0.0		173.0	59.0	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	hg19	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	A	18.17	3.564553	0.65651	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.01252	5.1;5.1	5.33	5.33	0.75918	.	0.293471	0.42053	D	0.000778	T	0.02807	0.0084	M	0.67953	2.075	0.45946	D	0.998776	B	0.27498	0.18	B	0.29942	0.109	T	0.42749	-0.9433	10	0.59425	D	0.04	.	11.6261	0.51147	0.8514:0.1485:0.0:0.0	.	653	Q9UIQ6	LCAP_HUMAN	R	653;639	ENSP00000231368:H653R;ENSP00000379117:H639R	ENSP00000231368:H653R	H	+	2	0	LNPEP	96367898	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.147000	0.71783	2.007000	0.58848	0.459000	0.35465	CAT	.	.		0.318	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		G	96342142	A	G	96342142	3	3	128	1	0	0	0	0	1	0	0	0	8873	217	8	2	2000	2	LNPEP	5	96342142	Missense_Mutation	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	25590426	96342142	84573118	29	21103										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140264081	140264081	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gcccactctagtgtgctccaGcgcggcagggagttggtcgt	15	12	1	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr5:140264081G>T	ENST00000289272.2	+	1	2228	c.2228G>T	c.(2227-2229)aGc>aTc	p.S743I	PCDHA7_ENST00000525929.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.S743I|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	743	6 X 4 AA repeats of P-X-X-P.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGTGCTCCAGCGCGGCAGGG	0.677																																					p.S743I	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.G2228T						.						52	57	55					5																	140264081		2203	4299	6502	SO:0001583	missense	56136	exon1			GCTCCAGCGCGGC	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.2228G>T	chr5.hg19:g.140264081G>T	ENSP00000289272:p.Ser743Ile	64.0	0.0		46.0	14.0	NM_031865	O75277	Missense_Mutation	SNP	ENST00000289272.2	hg19	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.518889	0.44763	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.17213	2.29;2.29	4.61	2.37	0.29283	.	.	.	.	.	T	0.48040	0.1478	H	0.95470	3.675	0.26094	N	0.980912	D;P;D	0.69078	0.992;0.956;0.997	D;P;D	0.72982	0.933;0.771;0.979	T	0.35624	-0.9781	9	0.37606	T	0.19	.	7.5405	0.27735	0.1637:0.1475:0.6888:0.0	.	743;743;743	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	I	743	ENSP00000386821:S743I;ENSP00000289272:S743I	ENSP00000289272:S743I	S	+	2	0	PCDHA13	140244265	0.982000	0.34865	0.999000	0.59377	0.107000	0.19398	2.310000	0.43708	0.886000	0.36113	0.655000	0.94253	AGC	.	.		0.677	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		T	140264081	G	T	140264081	3	4	128	1	0	0	0	0	1	0	0	0	11532	971	34	3	2230	3	PCDHA13	5	140264081	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	43921939	140264081	40651179	30	21104										
FAT2	2196	hgsc.bcm.edu	37	chr5	150911280	150911280	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	aggtggggcgtcctcgggcaCctgcacgctgtgctcggtgt	17	12	0	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr5:150911280C>A	ENST00000261800.5	-	13	9691	c.9679G>T	c.(9679-9681)Gtg>Ttg	p.V3227L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3227	Cadherin 29. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCTCGGGCACCTGCACGCTG	0.677																																					p.V3227L		Atlas-SNP	.											.	FAT2	465	.	0			c.G9679T						.						54	44	47					5																	150911280		2203	4300	6503	SO:0001583	missense	2196	exon13			CGGGCACCTGCAC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.9679G>T	chr5.hg19:g.150911280C>A	ENSP00000261800:p.Val3227Leu	21.0	0.0		14.0	9.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.42|15.42	2.826902|2.826902	0.50739|0.50739	.|.	.|.	ENSG00000086570|ENSG00000086570	ENST00000520200|ENST00000261800	.|T	.|0.55234	.|0.53	5.23|5.23	5.23|5.23	0.72850|0.72850	.|Cadherin (3);Cadherin-like (1);	.|0.000000	.|0.52532	.|D	.|0.000072	T|T	0.50990|0.50990	0.1648|0.1648	L|L	0.43757|0.43757	1.38|1.38	0.39135|0.39135	D|D	0.961928|0.961928	.|B	.|0.31040	.|0.305	.|B	.|0.37692	.|0.256	T|T	0.57033|0.57033	-0.7880|-0.7880	5|10	.|0.59425	.|D	.|0.04	.|.	14.4286|14.4286	0.67233|0.67233	0.0:0.8528:0.1472:0.0|0.0:0.8528:0.1472:0.0	.|.	.|3227	.|Q9NYQ8	.|FAT2_HUMAN	V|L	85|3227	.|ENSP00000261800:V3227L	.|ENSP00000261800:V3227L	G|V	-|-	2|1	0|0	FAT2|FAT2	150891473|150891473	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.807000|0.807000	0.45602|0.45602	1.983000|1.983000	0.40648|0.40648	2.444000|2.444000	0.82710|0.82710	0.555000|0.555000	0.69702|0.69702	GGT|GTG	.	.		0.677	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150911280	C	A	150911280	3	1	128	1	0	0	0	0	1	0	0	0	5698	507	18	3	3414	3	FAT2	5	150911280	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	10647199	150911280	30003980	31	21105										
DUSP1	1843	hgsc.bcm.edu	37	chr5	172197268	172197268	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	catgggggtcgactgtttgcTgcacagctccgggcaggaag	16	10	0	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr5:172197268T>G	ENST00000239223.3	-	2	651	c.409A>C	c.(409-411)Agc>Cgc	p.S137R	RP11-779O18.3_ENST00000523005.1_RNA	NM_004417.3	NP_004408.1	P28562	DUS1_HUMAN	dual specificity phosphatase 1	137	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cellular response to hormone stimulus (GO:0032870)|endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of meiotic cell cycle (GO:0051447)|peptidyl-threonine dephosphorylation (GO:0035970)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|protein dephosphorylation (GO:0006470)|regulation of apoptotic process (GO:0042981)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to light stimulus (GO:0009416)|response to oxidative stress (GO:0006979)|response to retinoic acid (GO:0032526)|response to testosterone (GO:0033574)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|liver(1)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	Renal(175;0.000159)|Lung NSC(126;0.00431)|all_lung(126;0.00729)	all_hematologic(541;4.11e-18)|Breast(839;0.00637)|Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.15)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)	GBM - Glioblastoma multiforme(465;0.0103)		GACTGTTTGCTGCACAGCTCC	0.562																																					p.S137R		Atlas-SNP	.											.	DUSP1	27	.	0			c.A409C						.						51	49	50					5																	172197268		2203	4300	6503	SO:0001583	missense	1843	exon2			GTTTGCTGCACAG	X68277	CCDS4380.1	5q35.1	2011-06-09			ENSG00000120129	ENSG00000120129		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3064	protein-coding gene	gene with protein product		600714		PTPN10		1406996, 7806236	Standard	NM_004417		Approved	HVH1, CL100, MKP-1	uc003mbv.2	P28562	OTTHUMG00000130523	ENST00000239223.3:c.409A>C	chr5.hg19:g.172197268T>G	ENSP00000239223:p.Ser137Arg	281.0	1.0		202.0	79.0	NM_004417	D3DQL9|Q2V508	Missense_Mutation	SNP	ENST00000239223.3	hg19	CCDS4380.1	.	.	.	.	.	.	.	.	.	.	T	16.77	3.216220	0.58452	.	.	ENSG00000120129	ENST00000239223;ENST00000457103;ENST00000434080	T	0.44083	0.93	4.76	4.76	0.60689	Rhodanese-like (3);	0.045960	0.85682	D	0.000000	T	0.38983	0.1061	L	0.57536	1.79	0.40495	D	0.980582	B;P	0.36683	0.286;0.565	B;B	0.35353	0.125;0.201	T	0.29305	-1.0016	10	0.24483	T	0.36	.	14.1266	0.65225	0.0:0.0:0.0:1.0	.	137;94	P28562;B4DNT2	DUS1_HUMAN;.	R	137;110;72	ENSP00000239223:S137R	ENSP00000239223:S137R	S	-	1	0	DUSP1	172129874	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.297000	0.59061	2.003000	0.58678	0.459000	0.35465	AGC	.	.		0.562	DUSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252943.3	NM_004417		G	172197268	T	G	172197268	3	3	128	1	0	0	0	0	1	0	0	0	4811	1580	55	5	706	5	DUSP1	5	172197268	Missense_Mutation	SNP	T	TCGA-DD-A4NF-01A-11D-A27I-10	21285988	172197268	8717992	32	21106										
C6orf62	81688	hgsc.bcm.edu	37	chr6	24714570	24714570	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	acaggcctaaaaggctcatcAgattctttccacctagaaaa	6	11	3	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr6:24714570A>G	ENST00000378119.4	-	3	2572	c.405T>C	c.(403-405)tcT>tcC	p.S135S	C6orf62_ENST00000540769.1_Silent_p.S77S|C6orf62_ENST00000378102.3_Silent_p.S106S	NM_030939.4	NP_112201.1	Q9GZU0	CF062_HUMAN	chromosome 6 open reading frame 62	135						intracellular (GO:0005622)				endometrium(2)|kidney(3)|large_intestine(2)|lung(3)	10						AAGGCTCATCAGATTCTTTCC	0.368																																					p.S135S		Atlas-SNP	.											.	C6orf62	18	.	0			c.T405C						.						78	80	79					6																	24714570		2203	4300	6503	SO:0001819	synonymous_variant	81688	exon3			CTCATCAGATTCT	AL136632	CCDS4559.1	6p22.1	2011-12-13			ENSG00000112308	ENSG00000112308			20998	protein-coding gene	gene with protein product	"HBV X-transactivated protein 12"					11230166	Standard	NM_030939		Approved	FLJ12619, DKFZP564G182, XTP12	uc003nel.3	Q9GZU0	OTTHUMG00000014361	ENST00000378119.4:c.405T>C	chr6.hg19:g.24714570A>G		168.0	0.0		98.0	27.0	NM_030939	Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2	Silent	SNP	ENST00000378119.4	hg19	CCDS4559.1																																																																																			.	.		0.368	C6orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040017.1	NM_030939		G	24714570	A	G	24714570	2	3	128	1	0	0	0	0	0	0	0	1	2370	175	7	2		2	C6orf62	6	24714570	Silent	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10		24714570	146400497	33	21107										
KIAA0240	23506	hgsc.bcm.edu	37	chr6	42832697	42832697	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	agtgcagtaccagagcacgtCtgaagagaaggccagccgga	14	10	1	3			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr6:42832697C>A	ENST00000314073.5	+	13	2929	c.2753C>A	c.(2752-2754)tCt>tAt	p.S918Y	GLTSCR1L_ENST00000394168.1_Missense_Mutation_p.S918Y			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	918																	CAGAGCACGTCTGAAGAGAAG	0.522																																					p.S918Y		Atlas-SNP	.											.	.	.	.	0			c.C2753A						.						46	47	47					6																	42832697		2203	4300	6503	SO:0001583	missense	23506	exon12			GCACGTCTGAAGA	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"KIAA0240"	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.2753C>A	chr6.hg19:g.42832697C>A	ENSP00000313933:p.Ser918Tyr	77.0	0.0		78.0	32.0	NM_015349	A1L3W2|Q5TFZ3|Q92514	Missense_Mutation	SNP	ENST00000314073.5	hg19	CCDS34451.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.723163	0.30503	.	.	ENSG00000112624	ENST00000394167;ENST00000314073;ENST00000394168	T;T	0.48201	0.82;0.82	5.34	3.47	0.39725	.	0.575197	0.17896	N	0.158371	T	0.19327	0.0464	L	0.27053	0.805	0.09310	N	1	P	0.42620	0.785	B	0.44224	0.444	T	0.04650	-1.0936	10	0.72032	D	0.01	-0.0271	6.0454	0.19758	0.1417:0.6502:0.1364:0.0716	.	918	Q6AI39	K0240_HUMAN	Y	918	ENSP00000313933:S918Y;ENSP00000377723:S918Y	ENSP00000313933:S918Y	S	+	2	0	KIAA0240	42940675	0.005000	0.15991	0.004000	0.12327	0.895000	0.52256	1.501000	0.35693	0.662000	0.31006	0.650000	0.86243	TCT	.	.		0.522	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		A	42832697	C	A	42832697	3	1	128	1	0	0	0	0	1	0	0	0	8173	913	32	3	2795	3	KIAA0240	6	42832697	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	18118127	42832697	128282370	34	21108										
CRISP3	10321	hgsc.bcm.edu	37	chr6	49698949	49698949	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tcataagggacatatagtctAttagcccaattaccactgaa	6	9	2	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr6:49698949A>G	ENST00000393666.1	-	6	543	c.537T>C	c.(535-537)aaT>aaC	p.N179N	CRISP3_ENST00000433368.2_Silent_p.N202N|CRISP3_ENST00000371159.4_Silent_p.N210N|CRISP3_ENST00000263045.4_Silent_p.N192N|CRISP3_ENST00000423399.2_Silent_p.N89N			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	179					defense response (GO:0006952)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|specific granule (GO:0042581)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|skin(6)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			CATATAGTCTATTAGCCCAAT	0.338																																					p.N202N		Atlas-SNP	.											.	CRISP3	67	.	0			c.T606C						.						92	85	87					6																	49698949		2203	4300	6503	SO:0001819	synonymous_variant	10321	exon7			TAGTCTATTAGCC	X94323	CCDS4929.1, CCDS4929.2, CCDS55019.1	6p12.3	2008-02-05			ENSG00000096006	ENSG00000096006			16904	protein-coding gene	gene with protein product						8665901, 12223513	Standard	NM_006061		Approved	SGP28, CRISP-3, CRS3, dJ442L6.3, Aeg2	uc003ozs.3	P54108	OTTHUMG00000014823	ENST00000393666.1:c.537T>C	chr6.hg19:g.49698949A>G		258.0	0.0		221.0	91.0	NM_001190986	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Silent	SNP	ENST00000393666.1	hg19																																																																																				.	.		0.338	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061		G	49698949	A	G	49698949	2	3	128	1	0	0	0	0	0	0	0	1	3883	446	16	2		2	CRISP3	6	49698949	Silent	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	6866252	49698949	121416118	35	21109										
MYO6	4646	hgsc.bcm.edu	37	chr6	76595796	76595796	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tcgaatgtggctttgcaagaGgagacacaaacctcggtaag	12	8	0	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr6:76595796G>A	ENST00000369977.3	+	24	2631	c.2492G>A	c.(2491-2493)aGg>aAg	p.R831K	MYO6_ENST00000369981.3_Missense_Mutation_p.R831K|MYO6_ENST00000369975.1_Missense_Mutation_p.R831K|MYO6_ENST00000369985.4_Missense_Mutation_p.R831K	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	831	IQ.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		CTTTGCAAGAGGAGACACAAA	0.308																																					p.R831K		Atlas-SNP	.											.	MYO6	124	.	0			c.G2492A						.						41	41	41					6																	76595796		2203	4298	6501	SO:0001583	missense	4646	exon24			GCAAGAGGAGACA	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.2492G>A	chr6.hg19:g.76595796G>A	ENSP00000358994:p.Arg831Lys	180.0	0.0		113.0	50.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	hg19	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	G	6.782	0.513175	0.12944	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	5.82	5.82	0.92795	.	0.133760	0.64402	D	0.000002	T	0.22742	0.0549	N	0.03917	-0.325	0.48571	D	0.999673	B;B	0.18461	0.028;0.0	B;B	0.16289	0.015;0.001	T	0.30563	-0.9974	10	0.02654	T	1	.	10.4817	0.44698	0.1433:0.0:0.8567:0.0	.	831;831	Q9UM54-2;Q9UM54-1	.;.	K	831	ENSP00000358998:R831K;ENSP00000359002:R831K;ENSP00000358994:R831K;ENSP00000358992:R831K	ENSP00000358992:R831K	R	+	2	0	MYO6	76652516	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.612000	0.61169	2.745000	0.94114	0.655000	0.94253	AGG	.	.		0.308	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		A	76595796	G	A	76595796	3	1	128	1	0	0	0	0	1	0	0	0	10090	1000	35	3	2582	3	MYO6	6	76595796	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	26896847	76595796	94519271	36	21110										
MRAP2	112609	hgsc.bcm.edu	37	chr6	84798909	84798909	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gtattttctcgccaaggcaaCgaggagtccaggtctctctt	10	11	3	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr6:84798909C>G	ENST00000257776.4	+	4	462	c.327C>G	c.(325-327)aaC>aaG	p.N109K		NM_138409.2	NP_612418.2	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	109					energy homeostasis (GO:0097009)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|positive regulation of cAMP biosynthetic process (GO:0030819)|protein localization to cell surface (GO:0034394)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	corticotropin hormone receptor binding (GO:0031780)|identical protein binding (GO:0042802)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)|type 5 melanocortin receptor binding (GO:0031783)	p.N109K(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(4)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	19						GCCAAGGCAACGAGGAGTCCA	0.498																																					p.N109K		Atlas-SNP	.											MRAP2,NS,carcinoma,0,1	MRAP2	40	.	1	Substitution - Missense(1)	breast(1)	c.C327G						.						115	109	111					6																	84798909		2203	4300	6503	SO:0001583	missense	112609	exon4			AGGCAACGAGGAG	AK090775	CCDS5001.1	6q14.3	2009-10-06	2008-07-16	2008-07-16	ENSG00000135324	ENSG00000135324			21232	protein-coding gene	gene with protein product		615410	"chromosome 6 open reading frame 117"	C6orf117			Standard	NM_138409		Approved	bA51G5.2	uc003pkg.4	Q96G30	OTTHUMG00000015121	ENST00000257776.4:c.327C>G	chr6.hg19:g.84798909C>G	ENSP00000257776:p.Asn109Lys	153.0	0.0		107.0	40.0	NM_138409	A8K9M1|Q8IXM9|Q8N2D1	Missense_Mutation	SNP	ENST00000257776.4	hg19	CCDS5001.1	.	.	.	.	.	.	.	.	.	.	C	10.00	1.233279	0.22626	.	.	ENSG00000135324	ENST00000257776	D	0.82344	-1.6	5.33	-5.52	0.02560	.	0.507890	0.21382	N	0.075441	T	0.38692	0.1050	N	0.22421	0.69	0.19945	N	0.999949	B	0.30914	0.3	B	0.23275	0.045	T	0.52177	-0.8610	10	0.15499	T	0.54	-14.7234	6.7356	0.23407	0.0945:0.5015:0.0961:0.3078	.	109	Q96G30	MRAP2_HUMAN	K	109	ENSP00000257776:N109K	ENSP00000257776:N109K	N	+	3	2	MRAP2	84855628	0.003000	0.15002	0.837000	0.33122	0.949000	0.60115	-0.913000	0.04042	-0.789000	0.04498	-0.136000	0.14681	AAC	.	.		0.498	MRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041367.1	NM_138409		G	84798909	C	G	84798909	3	3	128	1	0	0	0	0	1	0	0	0	9763	535	19	4	337	4	MRAP2	6	84798909	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	8203113	84798909	86316158	37	21111										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101296578	101296578	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tgcttctctcccattatcagTtccaactattcaaagacaaa	3	12	3	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr6:101296578T>C	ENST00000369162.2	-	4	591	c.247A>G	c.(247-249)Act>Gct	p.T83A	ASCC3_ENST00000522650.1_Missense_Mutation_p.T83A	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	83					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		CCATTATCAGTTCCAACTATT	0.363																																					p.T83A		Atlas-SNP	.											.	ASCC3	205	.	0			c.A247G						.						67	66	66					6																	101296578		2052	4198	6250	SO:0001583	missense	10973	exon4			TATCAGTTCCAAC	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.247A>G	chr6.hg19:g.101296578T>C	ENSP00000358159:p.Thr83Ala	40.0	0.0		35.0	16.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	T	7.047	0.563727	0.13498	.	.	ENSG00000112249	ENST00000369162;ENST00000522650;ENST00000324723	T;T;T	0.55413	0.58;0.52;0.97	5.85	5.85	0.93711	.	0.786135	0.11911	N	0.517630	T	0.21881	0.0527	L	0.50333	1.59	0.58432	D	0.999996	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.18053	-1.0349	10	0.06365	T	0.9	.	6.367	0.21461	0.1424:0.0791:0.0:0.7785	.	83;83;83	Q4G1A0;E7EW23;Q8N3C0	.;.;HELC1_HUMAN	A	83	ENSP00000358159:T83A;ENSP00000430769:T83A;ENSP00000320777:T83A	ENSP00000320777:T83A	T	-	1	0	ASCC3	101403299	0.928000	0.31464	0.934000	0.37439	0.892000	0.51952	0.323000	0.19593	2.234000	0.73211	0.533000	0.62120	ACT	.	.		0.363	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		C	101296578	T	C	101296578	3	2	128	1	0	0	0	0	1	0	0	0	1033	1725	60	2	6517	2	ASCC3	6	101296578	Missense_Mutation	SNP	T	TCGA-DD-A4NF-01A-11D-A27I-10	16497669	101296578	69818489	38	21112										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47930177	47930177	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gtagggggacaggaacacccGggtctcagaagagttccggc	16	10	1	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr7:47930177G>A	ENST00000289672.2	-	16	2688	c.2638C>T	c.(2638-2640)Cgg>Tgg	p.R880W		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	880	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						AGGAACACCCGGGTCTCAGAA	0.562																																					p.R880W		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C2638T						.						86	78	81					7																	47930177		2203	4300	6503	SO:0001583	missense	168507	exon16			ACACCCGGGTCTC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.2638C>T	chr7.hg19:g.47930177G>A	ENSP00000289672:p.Arg880Trp	87.0	0.0		92.0	34.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.619851	0.28801	.	.	ENSG00000158683	ENST00000289672	T	0.70045	-0.45	5.44	2.57	0.30868	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.630546	0.13935	N	0.352617	T	0.54127	0.1839	N	0.22421	0.69	0.09310	N	1	P	0.51791	0.948	P	0.47376	0.545	T	0.45338	-0.9268	10	0.66056	D	0.02	-7.5742	5.1808	0.15160	0.1885:0.1706:0.6409:0.0	.	880	Q8TDX9	PK1L1_HUMAN	W	880	ENSP00000289672:R880W	ENSP00000289672:R880W	R	-	1	2	PKD1L1	47896702	0.007000	0.16637	0.008000	0.14137	0.045000	0.14185	1.102000	0.31050	0.245000	0.21373	0.643000	0.83706	CGG	.	.		0.562	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47930177	G	A	47930177	3	1	128	1	0	0	0	0	1	0	0	0	11973	1115	39	1	6079	1	PKD1L1	7	47930177	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		47930177	111208486	39	21113										
POM121L12	285877	hgsc.bcm.edu	37	chr7	53103689	53103689	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ttcccggggagaccgctctgGggcgagacctctcctgtgcc	14	15	2	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr7:53103689G>T	ENST00000408890.4	+	1	341	c.325G>T	c.(325-327)Ggg>Tgg	p.G109W		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	109										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GACCGCTCTGGGGCGAGACCT	0.711																																					p.G109W		Atlas-SNP	.											.	POM121L12	146	.	0			c.G325T						.						23	27	26					7																	53103689		1971	4132	6103	SO:0001583	missense	285877	exon1			GCTCTGGGGCGAG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.325G>T	chr7.hg19:g.53103689G>T	ENSP00000386133:p.Gly109Trp	19.0	0.0		17.0	6.0	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	hg19	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	G	11.51	1.660537	0.29515	.	.	ENSG00000221900	ENST00000408890	T	0.58940	0.3	1.84	0.907	0.19321	.	.	.	.	.	T	0.64789	0.2630	L	0.46157	1.445	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.51419	-0.8708	9	0.87932	D	0	.	6.1016	0.20051	0.0:0.3237:0.6763:0.0	.	109	Q8N7R1	P1L12_HUMAN	W	109	ENSP00000386133:G109W	ENSP00000386133:G109W	G	+	1	0	POM121L12	53071183	0.001000	0.12720	0.004000	0.12327	0.007000	0.05969	0.147000	0.16202	0.336000	0.23639	0.462000	0.41574	GGG	.	.		0.711	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		T	53103689	G	T	53103689	3	4	128	1	0	0	0	0	1	0	0	0	12250	1232	43	3	327	3	POM121L12	7	53103689	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	5173512	53103689	106034974	40	21114										
POR	5447	hgsc.bcm.edu	37	chr7	75615486	75615486	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cttggccccaggtctacgtcCagcacctgctaaagcaagac	9	15	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr7:75615486C>G	ENST00000461988.1	+	15	1930	c.1825C>G	c.(1825-1827)Cag>Gag	p.Q609E	POR_ENST00000419840.1_Intron|POR_ENST00000394893.1_Missense_Mutation_p.Q609E|POR_ENST00000545601.1_Missense_Mutation_p.Q417E|POR_ENST00000450476.1_Missense_Mutation_p.Q508E|TMEM120A_ENST00000493111.2_RNA|TMEM120A_ENST00000338761.4_RNA|POR_ENST00000439269.1_Missense_Mutation_p.Q347E	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	606			LKQDREHLW -> R (in ABS1).		carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	GGTCTACGTCCAGCACCTGCT	0.632																																					p.Q609E		Atlas-SNP	.											.	POR	46	.	0			c.C1825G						.						47	59	55					7																	75615486		2106	4222	6328	SO:0001583	missense	5447	exon15			TACGTCCAGCACC	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.1825C>G	chr7.hg19:g.75615486C>G	ENSP00000419970:p.Gln609Glu	189.0	0.0		151.0	55.0	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Missense_Mutation	SNP	ENST00000461988.1	hg19	CCDS5579.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.95|11.95	1.790798|1.790798	0.31685|0.31685	.|.	.|.	ENSG00000127948|ENSG00000127948	ENST00000447222|ENST00000461988;ENST00000394893;ENST00000545601;ENST00000450476;ENST00000439269	.|D;D;D;D;D	.|0.81499	.|-1.5;-1.5;-1.5;-1.5;-1.5	3.59|3.59	2.69|2.69	0.31865|0.31865	.|Oxidoreductase FAD/NAD(P)-binding (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	.|0.058333	.|0.64402	.|D	.|0.000001	D|D	0.93429|0.93429	0.7904|0.7904	H|H	0.99249|0.99249	4.485|4.485	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.999;0.997;0.999	.|D;D;D;D	.|0.91635	.|0.999;0.972;0.942;0.975	D|D	0.94576|0.94576	0.7775|0.7775	5|10	.|0.72032	.|D	.|0.01	-24.618|-24.618	12.1931|12.1931	0.54282|0.54282	0.1726:0.8273:0.0:0.0|0.1726:0.8273:0.0:0.0	.|.	.|606;508;417;615	.|P16435;E7EVY7;F5H468;Q59ED7	.|NCPR_HUMAN;.;.;.	R|E	659|609;609;417;508;347	.|ENSP00000419970:Q609E;ENSP00000378355:Q609E;ENSP00000446149:Q417E;ENSP00000416572:Q508E;ENSP00000412490:Q347E	.|ENSP00000378355:Q609E	P|Q	+|+	2|1	0|0	POR|POR	75453422|75453422	1.000000|1.000000	0.71417|0.71417	0.943000|0.943000	0.38184|0.38184	0.149000|0.149000	0.21700|0.21700	6.572000|6.572000	0.74005|0.74005	1.062000|1.062000	0.40625|0.40625	-0.314000|-0.314000	0.08810|0.08810	CCA|CAG	.	.		0.632	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941		G	75615486	C	G	75615486	3	3	128	1	0	0	0	0	1	0	0	0	12266	595	21	4	1879	4	POR	7	75615486	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	22511797	75615486	83523177	41	21115										
CCDC132	55610	hgsc.bcm.edu	37	chr7	92935245	92935245	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tgtttgagcagtactgtagtGgtgggaatccatttgaaatt	12	4	0	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr7:92935245G>A	ENST00000305866.5	+	18	1686	c.1558G>A	c.(1558-1560)Ggt>Agt	p.G520S	CCDC132_ENST00000317751.6_Missense_Mutation_p.G251S|CCDC132_ENST00000544910.1_Missense_Mutation_p.G490S|CCDC132_ENST00000535481.1_Missense_Mutation_p.G240S|CCDC132_ENST00000541136.1_Missense_Mutation_p.G331S	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	520						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			GTACTGTAGTGGTGGGAATCC	0.413																																					p.G520S		Atlas-SNP	.											.	CCDC132	136	.	0			c.G1558A						.						127	118	121					7																	92935245		1878	4100	5978	SO:0001583	missense	55610	exon18			TGTAGTGGTGGGA	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1558G>A	chr7.hg19:g.92935245G>A	ENSP00000307666:p.Gly520Ser	239.0	0.0		163.0	57.0	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.683303	0.68157	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751	T	0.39592	1.07	5.6	5.6	0.85130	.	0.185421	0.46442	D	0.000283	T	0.33614	0.0869	L	0.27053	0.805	0.58432	D	0.999999	B;B;B	0.25667	0.131;0.122;0.131	B;B;B	0.28305	0.058;0.088;0.058	T	0.11131	-1.0600	10	0.10902	T	0.67	-10.8814	19.9947	0.97381	0.0:0.0:1.0:0.0	.	240;490;520	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	S	520;490;331;240;251	ENSP00000325582:G251S	ENSP00000307666:G520S	G	+	1	0	CCDC132	92773181	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.963000	0.70372	2.794000	0.96219	0.650000	0.86243	GGT	.	.		0.413	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		A	92935245	G	A	92935245	3	1	128	1	0	0	0	0	1	0	0	0	2769	1348	47	3	1670	3	CCDC132	7	92935245	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	17319759	92935245	66203418	42	21116										
DOCK4	9732	hgsc.bcm.edu	37	chr7	111634195	111634195	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	aaaaagctacttaaccacatAgagttgtttccacatggttc	6	9	0	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr7:111634195A>T	ENST00000437633.1	-	5	566	c.310T>A	c.(310-312)Tat>Aat	p.Y104N	DOCK4_ENST00000476846.1_5'UTR|DOCK4_ENST00000428084.1_Missense_Mutation_p.Y104N	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	104					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				TTAACCACATAGAGTTGTTTC	0.338																																					p.Y104N		Atlas-SNP	.											.	DOCK4	365	.	0			c.T310A						.						147	137	141					7																	111634195		1835	4088	5923	SO:0001583	missense	9732	exon5			CCACATAGAGTTG		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.310T>A	chr7.hg19:g.111634195A>T	ENSP00000404179:p.Tyr104Asn	94.0	0.0		61.0	17.0	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	A	18.34	3.603024	0.66445	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	T;T	0.03920	3.76;3.76	5.68	5.68	0.88126	.	0.178935	0.51477	D	0.000093	T	0.18130	0.0435	M	0.87758	2.905	0.80722	D	1	B;B;P;B	0.37985	0.105;0.105;0.613;0.105	B;B;P;B	0.47981	0.028;0.042;0.563;0.042	T	0.00155	-1.1980	10	0.87932	D	0	.	13.6615	0.62370	1.0:0.0:0.0:0.0	.	104;104;104;104	A4D0S8;Q149N6;Q149N5;Q8N1I0	.;.;.;DOCK4_HUMAN	N	92;104;104;92;103	ENSP00000410746:Y104N;ENSP00000404179:Y104N	ENSP00000345432:Y92N	Y	-	1	0	DOCK4	111421431	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.862000	0.92283	2.166000	0.68216	0.533000	0.62120	TAT	.	.		0.338	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		T	111634195	A	T	111634195	3	4	128	1	0	0	0	0	1	0	0	0	4691	420	15	4	5782	4	DOCK4	7	111634195	Missense_Mutation	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	18698950	111634195	47504468	43	21117										
JHDM1D	80853	hgsc.bcm.edu	37	chr7	139824552	139824552	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	aacgtgccaaattttcatctGttggctttattaaataaaaa	5	6	2	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr7:139824552G>A	ENST00000397560.2	-	7	1017	c.920C>T	c.(919-921)aCa>aTa	p.T307I	JHDM1D_ENST00000006967.5_Missense_Mutation_p.T307I	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		307	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					ATTTTCATCTGTTGGCTTTAT	0.353																																					p.T307I		Atlas-SNP	.											.	JHDM1D	54	.	0			c.C920T						.						72	65	67					7																	139824552		1829	4080	5909	SO:0001583	missense	80853	exon7			TCATCTGTTGGCT																												ENST00000397560.2:c.920C>T	chr7.hg19:g.139824552G>A	ENSP00000380692:p.Thr307Ile	91.0	0.0		65.0	20.0	NM_030647	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Missense_Mutation	SNP	ENST00000397560.2	hg19	CCDS43658.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.808622	0.90707	.	.	ENSG00000006459	ENST00000397560;ENST00000006967	T;T	0.72505	-0.66;-0.66	5.49	5.49	0.81192	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.091347	0.85682	D	0.000000	D	0.88481	0.6448	M	0.93678	3.445	0.80722	D	1	D	0.71674	0.998	D	0.68765	0.96	D	0.90913	0.4777	10	0.87932	D	0	-11.0674	19.7073	0.96079	0.0:0.0:1.0:0.0	.	307	Q6ZMT4	KDM7_HUMAN	I	307	ENSP00000380692:T307I;ENSP00000006967:T307I	ENSP00000006967:T307I	T	-	2	0	JHDM1D	139471021	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.813000	0.99286	2.728000	0.93425	0.655000	0.94253	ACA	.	.		0.353	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1			A	139824552	G	A	139824552	3	1	128	1	0	0	0	0	1	0	0	0	7957	1377	48	3	1961	3	JHDM1D	7	139824552	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	28190357	139824552	19314111	44	21118										
PDIA4	9601	hgsc.bcm.edu	37	chr7	148703056	148703056	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	agggggcgcctggtgtagcgCttagcatcgtttgacacctt	14	10	0	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr7:148703056C>T	ENST00000286091.4	-	8	1453	c.1221G>A	c.(1219-1221)aaG>aaA	p.K407K		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	407					cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			TGGTGTAGCGCTTAGCATCGT	0.607											OREG0018420	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K407K		Atlas-SNP	.											.	PDIA4	57	.	0			c.G1221A						.						58	59	59					7																	148703056		2203	4300	6503	SO:0001819	synonymous_variant	9601	exon8			GTAGCGCTTAGCA	BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"Protein disulfide isomerases"	30167	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 4"			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.1221G>A	chr7.hg19:g.148703056C>T		99.0	0.0	1719	65.0	21.0	NM_004911	A8K4K6|Q549T6	Silent	SNP	ENST00000286091.4	hg19	CCDS5893.1																																																																																			.	.		0.607	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911		T	148703056	C	T	148703056	2	4	128	1	0	0	0	0	0	0	0	1	11679	796	28	3		3	PDIA4	7	148703056	Silent	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	8878504	148703056	10435607	45	21119										
HTRA4	203100	hgsc.bcm.edu	37	chr8	38831805	38831805	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gattagacctcagctgcggaCcgcggggctgggacgatgcc	16	12	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr8:38831805C>T	ENST00000302495.4	+	1	123	c.23C>T	c.(22-24)aCc>aTc	p.T8I	CTD-2544N14.3_ENST00000520863.1_RNA	NM_153692.3	NP_710159.1	P83105	HTRA4_HUMAN	HtrA serine peptidase 4	8					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)	11		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)			CAGCTGCGGACCGCGGGGCTG	0.607																																					p.T8I		Atlas-SNP	.											.	HTRA4	25	.	0			c.C23T						.						30	26	27					8																	38831805		2198	4295	6493	SO:0001583	missense	203100	exon1			TGCGGACCGCGGG	AK075205	CCDS6110.1	8p11.23	2008-02-05			ENSG00000169495	ENSG00000169495			26909	protein-coding gene	gene with protein product		610700					Standard	NM_153692		Approved	FLJ90724	uc003xmj.3	P83105	OTTHUMG00000164070	ENST00000302495.4:c.23C>T	chr8.hg19:g.38831805C>T	ENSP00000305919:p.Thr8Ile	102.0	0.0		73.0	32.0	NM_153692	Q542Z4|Q6PF13	Missense_Mutation	SNP	ENST00000302495.4	hg19	CCDS6110.1	.	.	.	.	.	.	.	.	.	.	C	9.892	1.204503	0.22205	.	.	ENSG00000169495	ENST00000302495	D	0.84442	-1.85	4.02	-3.04	0.05412	.	0.951484	0.08588	N	0.923523	T	0.65575	0.2704	N	0.08118	0	0.09310	N	1	B	0.14805	0.011	B	0.11329	0.006	T	0.52852	-0.8520	10	0.72032	D	0.01	5.2858	2.5787	0.04813	0.1354:0.2529:0.4229:0.1888	.	8	P83105	HTRA4_HUMAN	I	8	ENSP00000305919:T8I	ENSP00000305919:T8I	T	+	2	0	HTRA4	38950962	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.691000	0.05133	-0.520000	0.06435	-0.127000	0.14921	ACC	.	.		0.607	HTRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377077.1	NM_153692		T	38831805	C	T	38831805	3	4	128	1	0	0	0	0	1	0	0	0	7465	507	18	3	25	3	HTRA4	8	38831805	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10		38831805	107532217	46	21120										
MCM4	4173	hgsc.bcm.edu	37	chr8	48874204	48874204	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	agagccctgctgcgcaggacGtgctgttttccagccctccc	11	16	0	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr8:48874204G>A	ENST00000262105.2	+	2	408	c.199G>A	c.(199-201)Gtg>Atg	p.V67M	MCM4_ENST00000523944.1_Missense_Mutation_p.V67M|PRKDC_ENST00000523565.1_5'Flank|PRKDC_ENST00000314191.2_5'Flank|PRKDC_ENST00000338368.3_5'Flank	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	67					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			biliary_tract(1)|breast(1)|endometrium(7)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	44		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				TGCGCAGGACGTGCTGTTTTC	0.567																																					p.V67M		Atlas-SNP	.											.	MCM4	97	.	0			c.G199A						.						129	126	127					8																	48874204		2203	4300	6503	SO:0001583	missense	4173	exon3			CAGGACGTGCTGT		CCDS6143.1	8q12-q13	2008-02-05	2007-04-04		ENSG00000104738	ENSG00000104738			6947	protein-coding gene	gene with protein product		602638	"MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)"	CDC21		7601140	Standard	NM_005914		Approved	CDC54, hCdc21, P1-Cdc21, MGC33310	uc003xql.2	P33991	OTTHUMG00000164205	ENST00000262105.2:c.199G>A	chr8.hg19:g.48874204G>A	ENSP00000262105:p.Val67Met	131.0	0.0		126.0	55.0	NM_182746	Q8NEH1|Q99658	Missense_Mutation	SNP	ENST00000262105.2	hg19	CCDS6143.1	.	.	.	.	.	.	.	.	.	.	G	8.912	0.958944	0.18507	.	.	ENSG00000104738	ENST00000518221;ENST00000523944;ENST00000262105;ENST00000396826;ENST00000519170	T;T	0.02916	4.11;4.11	5.55	-6.29	0.02013	.	0.919463	0.09520	N	0.791036	T	0.01627	0.0052	N	0.14661	0.345	0.18873	N	0.999986	B;B	0.30851	0.297;0.297	B;B	0.23574	0.047;0.047	T	0.42916	-0.9423	10	0.30078	T	0.28	-0.2015	10.4414	0.44469	0.2957:0.16:0.5443:0.0	.	67;67	B3KMX0;P33991	.;MCM4_HUMAN	M	67;67;67;67;17	ENSP00000430194:V67M;ENSP00000262105:V67M	ENSP00000262105:V67M	V	+	1	0	MCM4	49036757	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.054000	0.14205	-1.594000	0.01615	-1.020000	0.02445	GTG	.	.		0.567	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377791.1	NM_005914		A	48874204	G	A	48874204	3	1	128	1	0	0	0	0	1	0	0	0	9398	1145	40	1	205	1	MCM4	8	48874204	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	10042399	48874204	97489818	47	21121										
PREX2	80243	hgsc.bcm.edu	37	chr8	69032483	69032483	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ggctgttgtgagggcctttgAccaaaccaagtatctcactc	10	11	1	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr8:69032483A>G	ENST00000288368.4	+	29	3834	c.3557A>G	c.(3556-3558)gAc>gGc	p.D1186G		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1186					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AGGGCCTTTGACCAAACCAAG	0.398																																					p.D1186G		Atlas-SNP	.											.	PREX2	614	.	0			c.A3557G						.						119	119	119					8																	69032483		2203	4300	6503	SO:0001583	missense	80243	exon29			CCTTTGACCAAAC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3557A>G	chr8.hg19:g.69032483A>G	ENSP00000288368:p.Asp1186Gly	121.0	0.0		111.0	51.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.526954	0.64860	.	.	ENSG00000046889	ENST00000288368	T	0.36520	1.25	5.29	5.29	0.74685	.	0.056952	0.64402	D	0.000002	T	0.23965	0.0580	N	0.08118	0	0.43745	D	0.99624	B	0.14438	0.01	B	0.22152	0.038	T	0.07986	-1.0744	10	0.87932	D	0	.	15.5312	0.75964	1.0:0.0:0.0:0.0	.	1186	Q70Z35	PREX2_HUMAN	G	1186	ENSP00000288368:D1186G	ENSP00000288368:D1186G	D	+	2	0	PREX2	69195037	1.000000	0.71417	0.998000	0.56505	0.937000	0.57800	8.678000	0.91211	2.120000	0.65058	0.528000	0.53228	GAC	.	.		0.398	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		G	69032483	A	G	69032483	3	3	128	1	0	0	0	0	1	0	0	0	12489	275	10	2	3900	2	PREX2	8	69032483	Missense_Mutation	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	20158279	69032483	77331539	48	21122										
SLCO5A1	81796	hgsc.bcm.edu	37	chr8	70591818	70591818	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gggtggagtgatcacttggcGactttggacacaggtgcatt	15	7	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr8:70591818G>A	ENST00000260126.4	-	8	2525	c.1819C>T	c.(1819-1821)Cgc>Tgc	p.R607C	SLCO5A1_ENST00000530307.1_Missense_Mutation_p.R552C|SLCO5A1_ENST00000524945.1_Missense_Mutation_p.R607C	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	607						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.R607C(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			ATCACTTGGCGACTTTGGACA	0.453																																					p.R607C		Atlas-SNP	.											SLCO5A1,NS,carcinoma,0,1	SLCO5A1	142	.	1	Substitution - Missense(1)	kidney(1)	c.C1819T						.						142	133	136					8																	70591818		2203	4300	6503	SO:0001583	missense	81796	exon8			CTTGGCGACTTTG	AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"Solute carriers"	19046	protein-coding gene	gene with protein product		613543	"solute carrier family 21 (organic anion transporter), member 15"	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.1819C>T	chr8.hg19:g.70591818G>A	ENSP00000260126:p.Arg607Cys	183.0	1.0		164.0	41.0	NM_030958	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Missense_Mutation	SNP	ENST00000260126.4	hg19	CCDS6205.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.916520	0.73098	.	.	ENSG00000137571	ENST00000260126;ENST00000524945;ENST00000530307	T;T;T	0.42900	1.07;1.44;0.96	5.8	4.92	0.64577	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000005	T	0.54334	0.1852	L	0.31926	0.97	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.991;0.977	T	0.55698	-0.8100	10	0.48119	T	0.1	.	16.2099	0.82148	0.0:0.0:0.8658:0.1342	.	552;607;607	E9PKK5;Q9H2Y9;G3V1C0	.;SO5A1_HUMAN;.	C	607;607;552	ENSP00000260126:R607C;ENSP00000434422:R607C;ENSP00000431611:R552C	ENSP00000260126:R607C	R	-	1	0	SLCO5A1	70754372	1.000000	0.71417	0.993000	0.49108	0.772000	0.43724	4.750000	0.62162	1.425000	0.47237	0.655000	0.94253	CGC	.	.		0.453	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958		A	70591818	G	A	70591818	3	1	128	1	0	0	0	0	1	0	0	0	14746	1058	37	1	739	1	SLCO5A1	8	70591818	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	1559335	70591818	75772204	49	21123										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73480055	73480055	+	Frame_Shift_Del	DEL	G	G	-													0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	agagcctgtggacattatccGgagcaaaacatgctccagga					rs561571977	byFrequency	TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr8:73480055delG	ENST00000523207.1	+	2	674	c.86delG	c.(85-87)cggfs	p.R29fs		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	29					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GACATTATCCGGAGCAAAACA	0.552																																					p.R29fs		Atlas-Indel,Pindel	.											KCNB2,NS,carcinoma,-1,1	KCNB2	228	.	0			c.85delC						.						81	81	81					8																	73480055		2203	4300	6503	SO:0001589	frameshift_variant	9312	exon2			.	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.86delG	chr8.hg19:g.73480055delG	ENSP00000430846:p.Arg29fs	146.0	0.0		155.0	85.0	NM_004770	Q7Z7D0|Q9BXD3	Frame_Shift_Del	DEL	ENST00000523207.1	hg19	CCDS6209.1																																																																																			.	.		0.552	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		-	73480055	G	-	73480055	7	5	128	1	0	1	0	1	0	0	0	0	8022	1116	39	0	88	0	KCNB2	8	73480055	Frame_Shift_Del	DEL	G	TCGA-DD-A4NF-01A-11D-A27I-10	2888237	73480055	72883967	50	21124										
SLC7A13	157724	hgsc.bcm.edu	37	chr8	87229802	87229802	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tgaaaaaaatatagtttatcAaatcaattagacttgttaag	5	3	2	2	rs201235225		TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr8:87229802A>T	ENST00000297524.3	-	3	1179	c.1076T>A	c.(1075-1077)tTg>tAg	p.L359*	SLC7A13_ENST00000419776.2_Nonsense_Mutation_p.L350*|SLC7A13_ENST00000520624.1_5'Flank	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	359						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						ATAGTTTATCAAATCAATTAG	0.328																																					p.L359X		Atlas-SNP	.											.	SLC7A13	97	.	0			c.T1076A						.						46	54	51					8																	87229802		2203	4298	6501	SO:0001587	stop_gained	157724	exon3			TTTATCAAATCAA	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"Solute carriers"	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.1076T>A	chr8.hg19:g.87229802A>T	ENSP00000297524:p.Leu359*	97.0	0.0		99.0	29.0	NM_138817	Q05C37|Q08AH9|Q96N84	Nonsense_Mutation	SNP	ENST00000297524.3	hg19	CCDS34917.1	.	.	.	.	.	.	.	.	.	.	A	15.73	2.918491	0.52546	.	.	ENSG00000164893	ENST00000297524;ENST00000419776	.	.	.	5.27	5.27	0.74061	.	0.000000	0.48767	D	0.000164	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4479	0.61151	1.0:0.0:0.0:0.0	.	.	.	.	X	359;350	.	ENSP00000297524:L359X	L	-	2	0	SLC7A13	87298918	0.997000	0.39634	0.627000	0.29227	0.106000	0.19336	5.073000	0.64395	2.102000	0.63906	0.528000	0.53228	TTG	.	A|0.999;G|0.001		0.328	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817		T	87229802	A	T	87229802	4	4	128	1	0	0	0	0	0	1	0	0	14710	131	5	4	344	4	SLC7A13	8	87229802	Nonsense_Mutation	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	13749747	87229802	59134220	51	21125										
INTS8	55656	hgsc.bcm.edu	37	chr8	95892419	95892419	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	acagctggcagcgcagagaaGgaaaaaaaagtttctccaag	11	8	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr8:95892419G>A	ENST00000523731.1	+	27	3078	c.2945G>A	c.(2944-2946)aGg>aAg	p.R982K	CCNE2_ENST00000520509.1_3'UTR|INTS8_ENST00000447247.1_Missense_Mutation_p.R965K	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	982					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					GCGCAGAGAAGGAAAAAAAAG	0.338																																					p.R982K		Atlas-SNP	.											.	INTS8	92	.	0			c.G2945A						.						78	78	78					8																	95892419		2203	4300	6503	SO:0001583	missense	55656	exon27			AGAGAAGGAAAAA	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2945G>A	chr8.hg19:g.95892419G>A	ENSP00000430338:p.Arg982Lys	146.0	0.0		166.0	38.0	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Missense_Mutation	SNP	ENST00000523731.1	hg19	CCDS34925.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.8|27.8	4.868439|4.868439	0.91587|0.91587	.|.	.|.	ENSG00000164941|ENSG00000164941	ENST00000520526|ENST00000523731;ENST00000447247	.|.	.|.	.|.	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.79269|0.79269	0.4417|0.4417	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	.|D	.|0.61697	.|0.99	.|D	.|0.72982	.|0.979	T|T	0.79764|0.79764	-0.1666|-0.1666	5|9	.|0.87932	.|D	.|0	-16.7756|-16.7756	20.1241|20.1241	0.97973|0.97973	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|982	.|Q75QN2	.|INT8_HUMAN	R|K	787|982;965	.|.	.|ENSP00000398203:R965K	G|R	+|+	1|2	0|0	INTS8|INTS8	95961595|95961595	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.184000|9.184000	0.94893|0.94893	2.760000|2.760000	0.94817|0.94817	0.651000|0.651000	0.88453|0.88453	GGA|AGG	.	.		0.338	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		A	95892419	G	A	95892419	3	1	128	1	0	0	0	0	1	0	0	0	7793	1000	35	3	3051	3	INTS8	8	95892419	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	8662617	95892419	50471603	52	21126										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110393732	110393732	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	agtcattcaactcaaattacAtgctatactaggtctgtttt	5	8	4	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr8:110393732A>G	ENST00000378402.5	+	3	401	c.297A>G	c.(295-297)acA>acG	p.T99T		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	99	IPT/TIG 1.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CTCAAATTACATGCTATACTA	0.284										HNSCC(38;0.096)																											p.T99T		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A297G						.						43	42	43					8																	110393732		1807	4060	5867	SO:0001819	synonymous_variant	93035	exon3			AATTACATGCTAT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.297A>G	chr8.hg19:g.110393732A>G		77.0	0.0		75.0	18.0	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.		0.284	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		G	110393732	A	G	110393732	2	3	128	1	0	0	0	0	0	0	0	1	11981	204	8	2		2	PKHD1L1	8	110393732	Silent	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	14501313	110393732	35970290	53	21127										
INSL6	11172	hgsc.bcm.edu	37	chr9	5164195	5164195	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ttaccaaggggtgaatatccCtttttatccttatactcagg	7	9	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr9:5164195C>A	ENST00000381641.3	-	2	425	c.360G>T	c.(358-360)aaG>aaT	p.K120N	INSL6_ENST00000510407.1_5'UTR	NM_007179.2	NP_009110.2	Q9Y581	INSL6_HUMAN	insulin-like 6	120					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(2)	15	all_hematologic(13;0.137)	Breast(48;0.147)|Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0128)|Lung(218;0.145)		GTGAATATCCCTTTTTATCCT	0.348																																					p.K120N		Atlas-SNP	.											.	INSL6	35	.	0			c.G360T						.						89	89	89					9																	5164195		2203	4298	6501	SO:0001583	missense	11172	exon2			ATATCCCTTTTTA	AF156094	CCDS6458.1	9p24	2008-07-21			ENSG00000120210	ENSG00000120210			6089	protein-coding gene	gene with protein product	"relaxin/insulin-like factor 1"	606414				10819760	Standard	NM_007179		Approved	RIF1	uc003zix.3	Q9Y581	OTTHUMG00000019489	ENST00000381641.3:c.360G>T	chr9.hg19:g.5164195C>A	ENSP00000371054:p.Lys120Asn	54.0	0.0		43.0	13.0	NM_007179	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000381641.3	hg19	CCDS6458.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.132240	0.37630	.	.	ENSG00000120210	ENST00000381641	T	0.59502	0.26	4.2	1.33	0.21861	Insulin-like (3);	0.831249	0.10888	N	0.623067	T	0.64371	0.2592	L	0.50333	1.59	0.09310	N	1	D	0.63046	0.992	D	0.63283	0.913	T	0.51513	-0.8696	10	0.72032	D	0.01	-8.6385	6.5047	0.22188	0.0:0.6929:0.0:0.3071	.	120	Q9Y581	INSL6_HUMAN	N	120	ENSP00000371054:K120N	ENSP00000371054:K120N	K	-	3	2	INSL6	5154195	0.053000	0.20554	0.002000	0.10522	0.026000	0.11368	0.904000	0.28491	0.308000	0.22923	0.591000	0.81541	AAG	.	.		0.348	INSL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051608.3	NM_007179		A	5164195	C	A	5164195	3	1	128	1	0	0	0	0	1	0	0	0	7779	680	24	3	285	3	INSL6	9	5164195	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10		5164195	136049236	54	21128										
ARID3C	138715	hgsc.bcm.edu	37	chr9	34622422	34622422	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gtccataggccccatcagcaCagctctcttctctgggggct	10	15	3	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr9:34622422C>G	ENST00000378909.2	-	5	1062	c.970G>C	c.(970-972)Gtg>Ctg	p.V324L	DCTN3_ENST00000378916.4_5'Flank|DCTN3_ENST00000378913.2_5'Flank|DCTN3_ENST00000259632.7_5'Flank|DCTN3_ENST00000447983.2_5'Flank|DCTN3_ENST00000341694.2_5'Flank|DCTN3_ENST00000477738.2_5'Flank	NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	324	Pro-rich.|REKLES. {ECO:0000255|PROSITE- ProRule:PRU00819}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		CCCATCAGCACAGCTCTCTTC	0.617																																					p.V324L		Atlas-SNP	.											.	ARID3C	33	.	0			c.G970C						.						57	58	58					9																	34622422		2203	4300	6503	SO:0001583	missense	138715	exon5			TCAGCACAGCTCT		CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"-"	21209	protein-coding gene	gene with protein product			"AT rich interactive domain 3C (BRIGHT- like)"				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.970G>C	chr9.hg19:g.34622422C>G	ENSP00000368189:p.Val324Leu	99.0	0.0		65.0	17.0	NM_001017363		Missense_Mutation	SNP	ENST00000378909.2	hg19	CCDS35006.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.026421	0.54683	.	.	ENSG00000205143	ENST00000378909	T	0.43294	0.95	5.02	5.02	0.67125	REKLES domain (1);	0.000000	0.43919	D	0.000514	T	0.35128	0.0921	L	0.43152	1.355	0.30967	N	0.722993	B	0.24823	0.112	B	0.24006	0.05	T	0.24368	-1.0162	10	0.14656	T	0.56	-19.8625	15.6437	0.77029	0.0:1.0:0.0:0.0	.	324	A6NKF2	ARI3C_HUMAN	L	324	ENSP00000368189:V324L	ENSP00000368189:V324L	V	-	1	0	ARID3C	34612422	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	3.934000	0.56553	2.603000	0.88011	0.448000	0.29417	GTG	.	.		0.617	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061		G	34622422	C	G	34622422	3	3	128	1	0	0	0	0	1	0	0	0	918	478	17	4	279	4	ARID3C	9	34622422	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	29458227	34622422	106591009	55	21129										
SMC5	23137	hgsc.bcm.edu	37	chr9	72879295	72879295	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gccaatggaacagggaagtcGagcattgtgtgtgccatttg	14	7	0	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr9:72879295G>T	ENST00000361138.5	+	2	319	c.261G>T	c.(259-261)tcG>tcT	p.S87S		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	87					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						CAGGGAAGTCGAGCATTGTGT	0.373																																					p.S87S		Atlas-SNP	.											.	SMC5	96	.	0			c.G261T						.						143	140	141					9																	72879295		2203	4300	6503	SO:0001819	synonymous_variant	23137	exon2			GAAGTCGAGCATT	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"Structural maintenance of chromosomes proteins"	20465	protein-coding gene	gene with protein product		609386	"SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.261G>T	chr9.hg19:g.72879295G>T		291.0	0.0		170.0	69.0	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Silent	SNP	ENST00000361138.5	hg19	CCDS6632.1																																																																																			.	.		0.373	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		T	72879295	G	T	72879295	2	4	128	1	0	0	0	0	0	0	0	1	14801	1045	37	1		1	SMC5	9	72879295	Silent	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	38256873	72879295	68334136	56	21130										
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134351321	134351322	+	Frame_Shift_Ins	INS	-	-	G													0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ccctgacgcatttggtggccINSggggctttgaggacagccgc					rs370454900		TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr9:134351321_134351322insG	ENST00000357304.4	+	15	3860_3861	c.3805_3806insG	c.(3805-3807)cggfs	p.R1269fs	PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1269							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						ATTTGGTGGCCGGGGCTTTGAG	0.559											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R1269fs		Atlas-Indel,Pindel	.											PRRC2B_ENST00000357304,NS,carcinoma,0,2	PRRC2B	266	.	0			c.3805_3806insG						.																																			SO:0001589	frameshift_variant	84726	exon15			.	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.3809dupG	chr9.hg19:g.134351325_134351325dupG	ENSP00000349856:p.Arg1269fs	95.0	0.0	1610	73.0	25.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Frame_Shift_Ins	INS	ENST00000357304.4	hg19	CCDS48044.1																																																																																			.	.		0.559	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	134351322	-	G	134351321	7	5	128	1	0	1	1	0	0	0	0	0	1320	643	23	0	3863	0	BAT2L1	9	134351321	Frame_Shift_Ins	INS	-	TCGA-DD-A4NF-01A-11D-A27I-10	61472026	134351321	6862110	57	21131										
ABCA2	20	hgsc.bcm.edu	37	chr9	139916820	139916820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tacctcgggcgggtccacacGggcggccaagagtgcttggg	17	12	0	1	rs367828133		TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr9:139916820G>A	ENST00000371605.3	-	5	694	c.547C>T	c.(547-549)Cgt>Tgt	p.R183C	ABCA2_ENST00000492260.1_5'UTR|ABCA2_ENST00000265662.5_Missense_Mutation_p.R184C|ABCA2_ENST00000341511.6_Missense_Mutation_p.R184C			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	183					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GGGTCCACACGGGCGGCCAAG	0.657													g|||	1	0.000199681	8e-04	0	5008	,	,		13373	0		0	False		,,,				2504	0				p.R214C		Atlas-SNP	.											.	ABCA2	113	.	0			c.C640T						.						22	28	26					9																	139916820		2022	4145	6167	SO:0001583	missense	20	exon6			CCACACGGGCGGC	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.547C>T	chr9.hg19:g.139916820G>A	ENSP00000360666:p.Arg183Cys	73.0	0.0		58.0	17.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Missense_Mutation	SNP	ENST00000371605.3	hg19		.	.	.	.	.	.	.	.	.	.	g	7.835	0.720645	0.15372	.	.	ENSG00000107331	ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	D;D;D	0.87103	-2.21;-2.21;-2.21	4.39	0.992	0.19819	.	416.678000	0.01211	U	0.007859	T	0.72407	0.3456	N	0.08118	0	0.09310	N	1	P;P;B	0.47302	0.893;0.876;0.261	B;B;B	0.34452	0.183;0.183;0.083	T	0.70306	-0.4908	10	0.66056	D	0.02	.	6.0741	0.19905	0.0:0.2529:0.2978:0.4493	.	183;213;214	Q9BZC7;E7EU84;E7ETC3	ABCA2_HUMAN;.;.	C	184;183;214;184	ENSP00000265662:R184C;ENSP00000360666:R183C;ENSP00000344155:R184C	ENSP00000265662:R184C	R	-	1	0	ABCA2	139036641	0.002000	0.14202	0.391000	0.26233	0.024000	0.10985	-0.032000	0.12266	0.754000	0.32968	0.486000	0.48141	CGT	.	.		0.657	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		A	139916820	G	A	139916820	3	1	128	1	0	0	0	0	1	0	0	0	32	1116	39	1	6936	1	ABCA2	9	139916820	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	5565499	139916820	1296611	58	21132										
SPAG6	9576	hgsc.bcm.edu	37	chr10	22675715	22675715	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ctgtggtggatgcaggagctGttcctcttttagtactctgt	12	8	2	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr10:22675715G>T	ENST00000376624.3	+	5	647	c.505G>T	c.(505-507)Gtt>Ttt	p.V169F	RP11-301N24.3_ENST00000422675.1_RNA|SPAG6_ENST00000376601.1_Intron|SPAG6_ENST00000313311.6_Missense_Mutation_p.V169F|SPAG6_ENST00000376603.2_Missense_Mutation_p.V245F|SPAG6_ENST00000538630.1_Missense_Mutation_p.V144F	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	169					cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						TGCAGGAGCTGTTCCTCTTTT	0.463																																					p.V169F		Atlas-SNP	.											.	SPAG6	90	.	0			c.G505T						.						111	103	105					10																	22675715		2203	4300	6503	SO:0001583	missense	9576	exon5			GGAGCTGTTCCTC	AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"Armadillo repeat containing"	11215	protein-coding gene	gene with protein product	"axoneme central apparatus protein"	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.505G>T	chr10.hg19:g.22675715G>T	ENSP00000365811:p.Val169Phe	140.0	0.0		101.0	26.0	NM_172242	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Missense_Mutation	SNP	ENST00000376624.3	hg19	CCDS7139.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.895267	0.72639	.	.	ENSG00000077327	ENST00000376624;ENST00000376603;ENST00000538630;ENST00000313311;ENST00000435326	T;T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95;0.53	5.6	3.75	0.43078	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.87916	0.6298	H	0.94771	3.58	0.80722	D	1	P;P;P;P	0.52577	0.925;0.953;0.954;0.911	P;P;P;P	0.62649	0.905;0.807;0.771;0.853	D	0.89225	0.3573	10	0.87932	D	0	-19.2613	10.9645	0.47403	0.2031:0.0:0.7969:0.0	.	144;245;169;169	B4DXZ4;O75602-3;O75602-2;O75602	.;.;.;SPAG6_HUMAN	F	169;245;144;169;245	ENSP00000365811:V169F;ENSP00000365788:V245F;ENSP00000441325:V144F;ENSP00000323599:V169F;ENSP00000406594:V245F	ENSP00000323599:V169F	V	+	1	0	SPAG6	22715721	1.000000	0.71417	0.727000	0.30756	0.977000	0.68977	4.132000	0.57977	0.841000	0.35020	0.563000	0.77884	GTT	.	.		0.463	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1			T	22675715	G	T	22675715	3	4	128	1	0	0	0	0	1	0	0	0	14997	1377	48	3	523	3	SPAG6	10	22675715	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		22675715	112859032	59	21133										
ZNF37A	7587	hgsc.bcm.edu	37	chr10	38406925	38406925	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tgtggaaaaaccttcacccaGaagtcagcccacacaagaca	7	13	2	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr10:38406925G>T	ENST00000361085.5	+	7	1191	c.846G>T	c.(844-846)caG>caT	p.Q282H	ZNF37A_ENST00000351773.3_Missense_Mutation_p.Q282H	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	282					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|prostate(1)	28						CCTTCACCCAGAAGTCAGCCC	0.388																																					p.Q282H		Atlas-SNP	.											.	ZNF37A	118	.	0			c.G846T						.						73	76	75					10																	38406925		2202	4300	6502	SO:0001583	missense	7587	exon7			CACCCAGAAGTCA	X69115	CCDS31183.1	10p11.2	2013-01-08	2006-05-11		ENSG00000075407	ENSG00000075407		"Zinc fingers, C2H2-type", "-"	13102	protein-coding gene	gene with protein product			"zinc finger protein 37a (KOX 21)"			2014798, 8464732	Standard	NM_001178101		Approved	KOX21, ZNF37	uc001izl.3	P17032	OTTHUMG00000017990	ENST00000361085.5:c.846G>T	chr10.hg19:g.38406925G>T	ENSP00000354377:p.Gln282His	57.0	0.0		33.0	11.0	NM_003421	B3KRQ3|D3DRZ3|Q96B88	Missense_Mutation	SNP	ENST00000361085.5	hg19	CCDS31183.1	.	.	.	.	.	.	.	.	.	.	G	7.786	0.710557	0.15239	.	.	ENSG00000075407	ENST00000351773;ENST00000361085	T;T	0.17054	2.3;2.3	2.34	1.41	0.22369	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10723	0.0262	L	0.39085	1.19	0.09310	N	1	B	0.17268	0.021	B	0.14578	0.011	T	0.37220	-0.9715	9	0.20519	T	0.43	.	3.0136	0.06052	0.1588:0.0:0.5766:0.2646	.	282	P17032	ZN37A_HUMAN	H	282	ENSP00000329141:Q282H;ENSP00000354377:Q282H	ENSP00000329141:Q282H	Q	+	3	2	ZNF37A	38446931	0.000000	0.05858	0.981000	0.43875	0.734000	0.41952	-4.049000	0.00305	0.324000	0.23333	0.591000	0.81541	CAG	.	.		0.388	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421		T	38406925	G	T	38406925	3	4	128	1	0	0	0	0	1	0	0	0	17887	933	33	3	860	3	ZNF37A	10	38406925	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	15731210	38406925	97127822	60	21134										
C10orf71	118461	hgsc.bcm.edu	37	chr10	50533616	50533616	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	caccattgctttacccgaggGtgacatagaagaccagccac	9	13	0	3			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr10:50533616G>A	ENST00000374144.3	+	3	3314	c.3026G>A	c.(3025-3027)gGt>gAt	p.G1009D	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1009										endometrium(1)	1						TTACCCGAGGGTGACATAGAA	0.572																																					p.G1009D		Atlas-SNP	.											.	C10orf71	179	.	0			c.G3026A						.						57	59	58					10																	50533616		692	1591	2283	SO:0001583	missense	118461	exon3			CCGAGGGTGACAT	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.3026G>A	chr10.hg19:g.50533616G>A	ENSP00000363259:p.Gly1009Asp	341.0	0.0		240.0	98.0	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	hg19	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	G	2.999	-0.206535	0.06180	.	.	ENSG00000177354	ENST00000374144	T	0.04015	3.73	4.93	-3.73	0.04398	.	0.777423	0.10556	N	0.660827	T	0.03434	0.0099	L	0.38175	1.15	0.09310	N	1	.	.	.	.	.	.	T	0.47686	-0.9098	8	0.12103	T	0.63	.	4.625	0.12474	0.4586:0.0:0.1799:0.3615	.	.	.	.	D	1009	ENSP00000363259:G1009D	ENSP00000363259:G1009D	G	+	2	0	C10orf71	50203622	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	0.224000	0.17738	-0.405000	0.07599	0.491000	0.48974	GGT	.	.		0.572	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		A	50533616	G	A	50533616	3	1	128	1	0	0	0	0	1	0	0	0	1616	1261	44	3	3028	3	C10orf71	10	50533616	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	12126691	50533616	85001131	61	21135										
CHAT	1103	hgsc.bcm.edu	37	chr10	50857589	50857589	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gaagctgatccgagcagactCcgtcagcgagctccccgccc	11	17	1	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr10:50857589C>A	ENST00000337653.2	+	10	1571	c.1418C>A	c.(1417-1419)tCc>tAc	p.S473Y	CHAT_ENST00000339797.1_Missense_Mutation_p.S355Y|CHAT_ENST00000455728.2_Missense_Mutation_p.S355Y|CHAT_ENST00000395562.2_Missense_Mutation_p.S391Y|CHAT_ENST00000395559.2_Missense_Mutation_p.S355Y|CHAT_ENST00000351556.3_Missense_Mutation_p.S355Y	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	473					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	CGAGCAGACTCCGTCAGCGAG	0.617																																					p.S473Y		Atlas-SNP	.											.	CHAT	162	.	0			c.C1418A						.						38	45	42					10																	50857589		2203	4300	6503	SO:0001583	missense	1103	exon10			CAGACTCCGTCAG	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.1418C>A	chr10.hg19:g.50857589C>A	ENSP00000337103:p.Ser473Tyr	187.0	0.0		162.0	79.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	hg19	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.288966	0.59976	.	.	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	D;D;D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7;-2.7;-2.7	5.04	5.04	0.67666	.	0.227258	0.45126	D	0.000396	D	0.94414	0.8203	M	0.64170	1.965	0.54753	D	0.999984	D;D	0.89917	0.994;1.0	P;D	0.75020	0.872;0.985	D	0.94451	0.7667	10	0.52906	T	0.07	-17.3729	18.3655	0.90389	0.0:1.0:0.0:0.0	.	355;473	F8W8I2;P28329	.;CLAT_HUMAN	Y	355;355;355;473;391;355	ENSP00000343486:S355Y;ENSP00000345878:S355Y;ENSP00000378926:S355Y;ENSP00000337103:S473Y;ENSP00000378929:S391Y;ENSP00000390521:S355Y	ENSP00000337103:S473Y	S	+	2	0	CHAT	50527595	1.000000	0.71417	0.917000	0.36280	0.389000	0.30415	5.794000	0.69067	2.322000	0.78497	0.462000	0.41574	TCC	.	.		0.617	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		A	50857589	C	A	50857589	3	1	128	1	0	0	0	0	1	0	0	0	3315	855	30	3	1500	3	CHAT	10	50857589	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	323973	50857589	84677158	62	21136										
OR51L1	119682	hgsc.bcm.edu	37	chr11	5021109	5021109	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gtctatagtgtcagaacaaaGcagattcgtctaggaattct	9	7	4	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr11:5021109G>A	ENST00000321543.1	+	1	897	c.897G>A	c.(895-897)aaG>aaA	p.K299K		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	299						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCAGAACAAAGCAGATTCGTC	0.443																																					p.K299K		Atlas-SNP	.											.	OR51L1	60	.	0			c.G897A						.						97	89	92					11																	5021109		2201	4298	6499	SO:0001819	synonymous_variant	119682	exon1			AACAAAGCAGATT	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"GPCR / Class A : Olfactory receptors"	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.897G>A	chr11.hg19:g.5021109G>A		153.0	0.0		95.0	40.0	NM_001004755	Q6IFE5	Silent	SNP	ENST00000321543.1	hg19	CCDS31369.1																																																																																			.	.		0.443	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755		A	5021109	G	A	5021109	2	1	128	1	0	0	0	0	0	0	0	1	11111	962	34	3		3	OR51L1	11	5021109	Silent	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		5021109	129985407	63	21137										
GLYATL2	219970	hgsc.bcm.edu	37	chr11	58607044	58607044	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	atgctcttttctaaggatttAtacagaatctgcagcttctg	7	8	4	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr11:58607044A>G	ENST00000287275.1	-	2	432	c.42T>C	c.(40-42)taT>taC	p.Y14Y	GLYATL2_ENST00000533636.1_Intron|GLYATL2_ENST00000532258.1_Silent_p.Y14Y	NM_145016.3	NP_659453.3	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	14						endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	23		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	CTAAGGATTTATACAGAATCT	0.413																																					p.Y14Y		Atlas-SNP	.											.	GLYATL2	40	.	0			c.T42C						.						137	125	129					11																	58607044		1865	4102	5967	SO:0001819	synonymous_variant	219970	exon2			GGATTTATACAGA	AF426250	CCDS41649.1	11q12.1	2008-02-05				ENSG00000156689			24178	protein-coding gene	gene with protein product		614762				12477932	Standard	NM_145016		Approved	BXMAS2-10, MGC24009	uc001nnd.4	Q8WU03		ENST00000287275.1:c.42T>C	chr11.hg19:g.58607044A>G		166.0	0.0		88.0	38.0	NM_145016	A5LGC7|Q86WC3|Q96AT2	Silent	SNP	ENST00000287275.1	hg19	CCDS41649.1																																																																																			.	.		0.413	GLYATL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394599.1	NM_145016		G	58607044	A	G	58607044	2	3	128	1	0	0	0	0	0	0	0	1	6489	456	16	2		2	GLYATL2	11	58607044	Silent	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	53585935	58607044	76399472	64	21138										
SDHAF2	79869	hgsc.bcm.edu	37	chr11	61197634	61197634	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ggaaaatggcggtgtctacaGtgttctcgacttcgtcgctg	13	9	2	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr11:61197634G>T	ENST00000394888.4	-	0	0				RP11-286N22.8_ENST00000543044.1_5'UTR|CPSF7_ENST00000340437.4_5'Flank|SDHAF2_ENST00000543265.1_Missense_Mutation_p.V6L|SDHAF2_ENST00000301761.2_Missense_Mutation_p.V6L|CPSF7_ENST00000448745.1_5'Flank|SDHAF2_ENST00000534878.1_Missense_Mutation_p.V6L|RP11-286N22.8_ENST00000544880.1_3'UTR|SDHAF2_ENST00000537782.1_Missense_Mutation_p.V6L|SDHAF2_ENST00000542074.1_Missense_Mutation_p.V6L|CPSF7_ENST00000439958.3_5'Flank|CPSF7_ENST00000541963.1_5'Flank	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						GGTGTCTACAGTGTTCTCGAC	0.637																																					p.V6L		Atlas-SNP	.											.	SDHAF2	26	.	0			c.G16T						.						71	74	73					11																	61197634		2202	4299	6501	SO:0001631	upstream_gene_variant	54949	exon1			TCTACAGTGTTCT		CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"RNA binding motif (RRM) containing"	30098	protein-coding gene	gene with protein product	"pre mRNA cleavage factor I, 59 kDa subunit", "cleavage factor Im complex 59 kDa subunit"					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198		chr11.hg19:g.61197634G>T	Exception_encountered	91.0	0.0		58.0	12.0	NM_017841	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Missense_Mutation	SNP	ENST00000394888.4	hg19	CCDS44619.1	.	.	.	.	.	.	.	.	.	.	g	13.23	2.175354	0.38413	.	.	ENSG00000256591;ENSG00000167985;ENSG00000167985	ENST00000541135;ENST00000301761;ENST00000543265	T;T;T	0.79247	-1.25;-1.09;-1.17	4.72	1.62	0.23740	.	1.596220	0.02981	N	0.145639	T	0.65037	0.2653	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44757	-0.9307	10	0.29301	T	0.29	0.0216	3.692	0.08350	0.2189:0.0:0.5824:0.1986	.	6	Q9NX18	SDHF2_HUMAN	L	6	ENSP00000443130:V6L;ENSP00000301761:V6L;ENSP00000443660:V6L	ENSP00000440939:V6L	V	+	1	0	SDHAF2;RP11-286N22.8	60954210	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.721000	0.25911	0.231000	0.21079	0.556000	0.70494	GTG	.	.		0.637	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811		T	61197634	G	T	61197634	1	4	128	0	1	0	0	0	0	0	0	0	13979	1029	36	3		3	SDHAF2	11	61197634	5'Flank	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	2590590	61197634	73808882	65	21139										
GAL	51083	hgsc.bcm.edu	37	chr11	68458398	68458398	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tttgcagaggccggtgccctCgaccgcctcctggatctccc	11	17	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr11:68458398C>G	ENST00000265643.3	+	6	573	c.315C>G	c.(313-315)ctC>ctG	p.L105L		NM_015973.3	NP_057057.2	P22466	GALA_HUMAN	galanin/GMAP prepropeptide	105					cAMP-mediated signaling (GO:0019933)|feeding behavior (GO:0007631)|inflammatory response (GO:0006954)|insulin secretion (GO:0030073)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of root hair elongation (GO:1902891)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catagen (GO:0051795)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of large conductance calcium-activated potassium channel activity (GO:1902608)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein kinase A signaling (GO:0010737)|regulation of glucocorticoid metabolic process (GO:0031943)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to insulin (GO:0032868)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|secretory granule (GO:0030141)	neuropeptide hormone activity (GO:0005184)|type 1 galanin receptor binding (GO:0031764)|type 2 galanin receptor binding (GO:0031765)|type 3 galanin receptor binding (GO:0031766)			lung(4)	4	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)		CCGGTGCCCTCGACCGCCTCC	0.562																																					p.L105L		Atlas-SNP	.											.	GAL	11	.	0			c.C315G						.						50	52	51					11																	68458398		2200	4294	6494	SO:0001819	synonymous_variant	51083	exon6			TGCCCTCGACCGC	L11144	CCDS8183.1	11q13.2	2013-02-26	2012-10-23		ENSG00000069482	ENSG00000069482		"Endogenous ligands"	4114	protein-coding gene	gene with protein product	"galanin-message-associated peptide", "galanin/GMAP prepropeptide"	137035	"galanin", "galanin prepropeptide"	GALN		7508413	Standard	XM_006718580		Approved	GMAP, GAL-GMAP, GLNN	uc001oob.3	P22466	OTTHUMG00000167890	ENST00000265643.3:c.315C>G	chr11.hg19:g.68458398C>G		94.0	0.0		55.0	19.0	NM_015973	Q14413	Silent	SNP	ENST00000265643.3	hg19	CCDS8183.1																																																																																			.	.		0.562	GAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396843.2	NM_001479		G	68458398	C	G	68458398	2	3	128	1	0	0	0	0	0	0	0	1	6204	871	31	4		4	GAL	11	68458398	Silent	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	7260764	68458398	66548118	66	21140										
FAM76B	143684	hgsc.bcm.edu	37	chr11	95522613	95522613	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ggataacgctgggtacacttGgtgcaggcgtacagggccga	16	9	0	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr11:95522613G>T	ENST00000358780.5	-	1	342	c.30C>A	c.(28-30)acC>acA	p.T10T	CEP57_ENST00000537677.1_5'Flank|FAM76B_ENST00000536839.1_Silent_p.T10T|CEP57_ENST00000325542.5_5'Flank|FAM76B_ENST00000538047.1_5'Flank|CEP57_ENST00000538658.1_5'Flank|CEP57_ENST00000325486.5_5'Flank	NM_144664.4	NP_653265.3	Q5HYJ3	FA76B_HUMAN	family with sequence similarity 76, member B	10						nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(1)|kidney(1)|lung(1)	3		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GGGTACACTTGGTGCAGGCGT	0.711																																					p.T10T		Atlas-SNP	.											.	FAM76B	10	.	0			c.C30A						.						21	29	27					11																	95522613		1959	4176	6135	SO:0001819	synonymous_variant	143684	exon1			ACACTTGGTGCAG		CCDS41700.1	11q21	2008-02-05			ENSG00000077458	ENSG00000077458			28492	protein-coding gene	gene with protein product						12477932	Standard	NM_144664		Approved	MGC33371	uc001pfn.2	Q5HYJ3	OTTHUMG00000167739	ENST00000358780.5:c.30C>A	chr11.hg19:g.95522613G>T		57.0	0.0		70.0	28.0	NM_144664	Q6PIU3|Q8TC53	Silent	SNP	ENST00000358780.5	hg19	CCDS41700.1																																																																																			.	.		0.711	FAM76B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395969.1	NM_144664		T	95522613	G	T	95522613	2	4	128	1	0	0	0	0	0	0	0	1	5633	1335	47	3		3	FAM76B	11	95522613	Silent	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	27064215	95522613	39483903	67	21141										
DENND5B	160518	hgsc.bcm.edu	37	chr12	31586176	31586176	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gcagtggcactccgacttacCcagcgactgaaacaatcaaa	8	13	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr12:31586176C>A	ENST00000389082.5	-	8	2283	c.2019G>T	c.(2017-2019)tgG>tgT	p.W673C	DENND5B_ENST00000306833.6_Missense_Mutation_p.W708C|DENND5B_ENST00000354285.4_Missense_Mutation_p.W695C|DENND5B_ENST00000536562.1_Missense_Mutation_p.W708C	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	673					positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TCCGACTTACCCAGCGACTGA	0.423																																					p.W673C		Atlas-SNP	.											.	DENND5B	114	.	0			c.G2019T						.						140	144	143					12																	31586176		2078	4234	6312	SO:0001583	missense	160518	exon8			ACTTACCCAGCGA	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.2019G>T	chr12.hg19:g.31586176C>A	ENSP00000373734:p.Trp673Cys	100.0	0.0		86.0	33.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	hg19	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.877434	0.51801	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285	T;T;T;T	0.07567	3.75;3.86;3.86;3.18	4.13	4.13	0.48395	.	0.082869	0.52532	D	0.000080	T	0.26448	0.0646	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;0.988;1.0	D;P;D	0.81914	0.995;0.775;0.992	T	0.01829	-1.1265	10	0.36615	T	0.2	-16.4356	16.6004	0.84815	0.0:1.0:0.0:0.0	.	695;673;708	Q6ZUT9-4;Q6ZUT9;G3V1S3	.;DEN5B_HUMAN;.	C	673;708;708;695	ENSP00000373734:W673C;ENSP00000306482:W708C;ENSP00000444889:W708C;ENSP00000346238:W695C	ENSP00000306482:W708C	W	-	3	0	DENND5B	31477443	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.801000	0.75170	2.131000	0.65755	0.655000	0.94253	TGG	.	.		0.423	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		A	31586176	C	A	31586176	3	1	128	1	0	0	0	0	1	0	0	0	4439	624	22	3	1861	3	DENND5B	12	31586176	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10		31586176	102265719	68	21142										
CCDC63	160762	hgsc.bcm.edu	37	chr12	111342552	111342552	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gaacccatcaaagtcatcccCccagtgctgggggctgaccc	10	16	2	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr12:111342552C>T	ENST00000308208.5	+	11	1745	c.1503C>T	c.(1501-1503)ccC>ccT	p.P501P	CCDC63_ENST00000545036.1_Silent_p.P461P|CCDC63_ENST00000552694.1_Silent_p.P422P	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	501								p.P501P(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						AAGTCATCCCCCCAGTGCTGG	0.587																																					p.P501P		Atlas-SNP	.											.	CCDC63	89	.	1	Substitution - coding silent(1)	lung(1)	c.C1503T						.						61	60	60					12																	111342552		2203	4300	6503	SO:0001819	synonymous_variant	160762	exon11			CATCCCCCCAGTG	AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"outer row dynein assembly 5 homolog (Chlamydomonas)"						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1503C>T	chr12.hg19:g.111342552C>T		173.0	0.0		118.0	40.0	NM_152591	B4DY03|Q0P603|Q6P2E1	Silent	SNP	ENST00000308208.5	hg19	CCDS9151.1																																																																																			.	.		0.587	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591		T	111342552	C	T	111342552	2	4	128	1	0	0	0	0	0	0	0	1	2836	610	22	3		3	CCDC63	12	111342552	Silent	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	79756376	111342552	22509343	69	21143										
SACS	26278	hgsc.bcm.edu	37	chr13	23907796	23907796	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	atagcacggaagtgactttaGaatttttatatcatcttggg	9	5	2	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr13:23907796G>A	ENST00000382292.3	-	9	10492	c.10219C>T	c.(10219-10221)Cta>Tta	p.L3407L	SACS_ENST00000402364.1_Silent_p.L2657L|SACS_ENST00000382298.3_Silent_p.L3407L			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3407					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AGTGACTTTAGAATTTTTATA	0.338																																					p.L3407L		Atlas-SNP	.											SACS_ENST00000382298,colon,carcinoma,0,2	SACS	871	.	0			c.C10219T						.						83	86	85					13																	23907796		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			ACTTTAGAATTTT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.10219C>T	chr13.hg19:g.23907796G>A		68.0	1.0		58.0	19.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	.		0.338	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23907796	G	A	23907796	2	1	128	1	0	0	0	0	0	0	0	1	13819	933	33	3		3	SACS	13	23907796	Silent	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		23907796	91262082	70	21144										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24864810	24864810	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	caagagggctttgccatctaTtccgagtactgcaacaacca	8	12	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr13:24864810T>C	ENST00000382095.4	+	8	1400	c.993T>C	c.(991-993)taT>taC	p.Y331Y	SPATA13_ENST00000382108.3_Silent_p.Y956Y|SPATA13_ENST00000343003.6_Silent_p.Y275Y|SPATA13_ENST00000409126.1_Silent_p.Y191Y|SPATA13_ENST00000399949.2_Silent_p.Y253Y|SPATA13_ENST00000424834.2_Silent_p.Y956Y|RP11-307N16.6_ENST00000382141.4_Silent_p.Y834Y	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	331	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		TTGCCATCTATTCCGAGTACT	0.567																																					p.Y956Y		Atlas-SNP	.											.	SPATA13	92	.	0			c.T2868C						.						81	86	84					13																	24864810		2203	4300	6503	SO:0001819	synonymous_variant	221178	exon9			CATCTATTCCGAG	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.993T>C	chr13.hg19:g.24864810T>C		276.0	0.0		185.0	78.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	hg19	CCDS9305.1	.	.	.	.	.	.	.	.	.	.	T	9.558	1.117774	0.20877	.	.	ENSG00000182957	ENST00000424834	.	.	.	5.34	-3.24	0.05094	.	.	.	.	.	T	0.62696	0.2449	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61123	-0.7126	4	.	.	.	.	13.2731	0.60172	0.0:0.4039:0.0:0.5961	.	.	.	.	L	994	.	.	F	+	1	0	SPATA13	23762810	0.926000	0.31397	0.877000	0.34402	0.946000	0.59487	0.031000	0.13710	-0.610000	0.05716	-0.375000	0.07067	TTC	.	.		0.567	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		C	24864810	T	C	24864810	2	2	128	1	0	0	0	0	0	0	0	1	15015	1500	52	2		2	SPATA13	13	24864810	Silent	SNP	T	TCGA-DD-A4NF-01A-11D-A27I-10	957014	24864810	90305068	71	21145										
USPL1	10208	hgsc.bcm.edu	37	chr13	31205167	31205167	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	aagttttgaacagcaaacatAatggagaagtatatgacgaa	9	4	0	3			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr13:31205167A>T	ENST00000255304.4	+	4	766	c.424A>T	c.(424-426)Aat>Tat	p.N142Y	USPL1_ENST00000465952.1_3'UTR	NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	142					Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		CAGCAAACATAATGGAGAAGT	0.363																																					p.N142Y	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.A424T						.						68	69	69					13																	31205167		2203	4300	6503	SO:0001583	missense	10208	exon4			AAACATAATGGAG	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 22"	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.424A>T	chr13.hg19:g.31205167A>T	ENSP00000255304:p.Asn142Tyr	70.0	0.0		67.0	22.0	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	hg19	CCDS9336.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.492378	0.64074	.	.	ENSG00000132952	ENST00000255304	T	0.08720	3.06	6.07	-2.51	0.06365	.	0.799706	0.12362	N	0.475533	T	0.17066	0.0410	L	0.60455	1.87	0.09310	N	1	D	0.65815	0.995	D	0.63192	0.912	T	0.07790	-1.0754	10	0.66056	D	0.02	-7.5718	7.454	0.27255	0.4808:0.0:0.408:0.1112	.	142	Q5W0Q7	USPL1_HUMAN	Y	142	ENSP00000255304:N142Y	ENSP00000255304:N142Y	N	+	1	0	USPL1	30103167	0.000000	0.05858	0.000000	0.03702	0.407000	0.30961	-0.061000	0.11693	-0.279000	0.09167	-0.250000	0.11733	AAT	.	.		0.363	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		T	31205167	A	T	31205167	3	4	128	1	0	0	0	0	1	0	0	0	17107	362	13	4	434	4	USPL1	13	31205167	Missense_Mutation	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	6340357	31205167	83964711	72	21146										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58298754	58298754	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tttgttttgcagaaccagaaGagtgtgttaattgcacagat	10	5	0	4			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr13:58298754G>T	ENST00000377918.3	+	4	2832	c.2806G>T	c.(2806-2808)Gag>Tag	p.E936*		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	936					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		AGAACCAGAAGAGTGTGTTAA	0.428																																					p.E936X	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.G2806T						.						48	49	49					13																	58298754		2203	4300	6503	SO:0001587	stop_gained	27253	exon4			CCAGAAGAGTGTG	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.2806G>T	chr13.hg19:g.58298754G>T	ENSP00000367151:p.Glu936*	92.0	0.0		94.0	40.0	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Nonsense_Mutation	SNP	ENST00000377918.3	hg19	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	G	39	7.732918	0.98459	.	.	ENSG00000118946	ENST00000377918	.	.	.	6.07	6.07	0.98685	.	0.143793	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	.	.	.	X	936	.	.	E	+	1	0	PCDH17	57196755	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.472000	0.97709	2.885000	0.99019	0.655000	0.94253	GAG	.	.		0.428	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		T	58298754	G	T	58298754	4	4	128	1	0	0	0	0	0	1	0	0	11521	943	33	3	2820	3	PCDH17	13	58298754	Nonsense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	27093587	58298754	56871124	73	21147										
SOX21	11166	hgsc.bcm.edu	37	chr13	95364066	95364066	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cagcgtcttgggcttgcgccGcggccggtacttgtagtcgg	16	12	1	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr13:95364066G>A	ENST00000376945.2	-	1	323	c.238C>T	c.(238-240)Cgg>Tgg	p.R80W	SOX21-AS1_ENST00000438290.2_lincRNA	NM_007084.2	NP_009015.1	Q9Y651	SOX21_HUMAN	SRY (sex determining region Y)-box 21	80					hair follicle development (GO:0001942)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6	all_neural(89;0.0646)|Medulloblastoma(90;0.163)					GGCTTGCGCCGCGGCCGGTAC	0.657																																					p.R80W		Atlas-SNP	.											.	SOX21	21	.	0			c.C238T						.						70	65	67					13																	95364066		2203	4300	6503	SO:0001583	missense	11166	exon1			TGCGCCGCGGCCG	AF107044	CCDS9473.1	13q31-q32	2008-07-18			ENSG00000125285	ENSG00000125285		"SRY (sex determining region Y)-boxes"	11197	protein-coding gene	gene with protein product	"SRY-box 21"	604974				10441749	Standard	NM_007084		Approved	SOX25	uc001vma.3	Q9Y651	OTTHUMG00000017209	ENST00000376945.2:c.238C>T	chr13.hg19:g.95364066G>A	ENSP00000366144:p.Arg80Trp	164.0	0.0		154.0	63.0	NM_007084	P35715|Q15504|Q5TBS1	Missense_Mutation	SNP	ENST00000376945.2	hg19	CCDS9473.1	.	.	.	.	.	.	.	.	.	.	g	15.18	2.758392	0.49468	.	.	ENSG00000125285	ENST00000376945	D	0.92348	-3.02	3.04	1.2	0.21068	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);	0.000000	0.64402	U	0.000008	D	0.94032	0.8088	M	0.72479	2.2	0.58432	D	0.999991	D	0.89917	1.0	D	0.91635	0.999	D	0.91498	0.5217	10	0.87932	D	0	.	6.7491	0.23477	0.1009:0.0:0.7251:0.174	.	80	Q9Y651	SOX21_HUMAN	W	80	ENSP00000366144:R80W	ENSP00000366144:R80W	R	-	1	2	SOX21	94162067	0.998000	0.40836	0.999000	0.59377	0.635000	0.38103	2.381000	0.44336	-0.019000	0.14055	-0.348000	0.07805	CGG	.	.		0.657	SOX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045467.4	NM_007084		A	95364066	G	A	95364066	3	1	128	1	0	0	0	0	1	0	0	0	14965	1086	38	1	596	1	SOX21	13	95364066	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	37065312	95364066	19805812	74	21148										
SPTB	6710	hgsc.bcm.edu	37	chr14	65260364	65260364	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gtgcttgcgctgtaagatgaGcacactggtcaggtctttgc	13	9	2	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr14:65260364G>A	ENST00000389721.5	-	13	2049	c.2017C>T	c.(2017-2019)Ctc>Ttc	p.L673F	SPTB_ENST00000556626.1_Missense_Mutation_p.L673F|SPTB_ENST00000542895.1_Missense_Mutation_p.L673F|SPTB_ENST00000389720.3_Missense_Mutation_p.L673F|SPTB_ENST00000389722.3_Missense_Mutation_p.L673F	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	673					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		TGTAAGATGAGCACACTGGTC	0.547																																					p.L673F		Atlas-SNP	.											.	SPTB	378	.	0			c.C2017T						.						119	85	96					14																	65260364		2203	4300	6503	SO:0001583	missense	6710	exon13			AGATGAGCACACT		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.2017C>T	chr14.hg19:g.65260364G>A	ENSP00000374371:p.Leu673Phe	244.0	0.0		183.0	77.0	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	G	9.838	1.190293	0.21954	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	5.02	4.1	0.47936	.	0.000000	0.64402	D	0.000002	T	0.46776	0.1410	M	0.74881	2.28	0.40999	D	0.984916	B;B	0.29037	0.128;0.231	B;B	0.34301	0.179;0.179	T	0.40850	-0.9541	10	0.23302	T	0.38	.	9.058	0.36416	0.0857:0.1517:0.7626:0.0	.	673;677	P11277;Q59FP5	SPTB1_HUMAN;.	F	677;673;673;673;673;673	ENSP00000374372:L673F;ENSP00000451752:L673F;ENSP00000374371:L673F;ENSP00000443882:L673F;ENSP00000374370:L673F	ENSP00000374370:L673F	L	-	1	0	SPTB	64330117	0.737000	0.28175	0.977000	0.42913	0.952000	0.60782	0.797000	0.26999	2.494000	0.84150	0.561000	0.74099	CTC	.	.		0.547	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			A	65260364	G	A	65260364	3	1	128	1	0	0	0	0	1	0	0	0	15133	971	34	3	5130	3	SPTB	14	65260364	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		65260364	42089176	75	21149										
DCAF5	8816	hgsc.bcm.edu	37	chr14	69522154	69522154	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	taccagtgagtcaaagaaggCcatcatccgggggtcttcct	11	11	3	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr14:69522154C>A	ENST00000341516.5	-	9	1396	c.1249G>T	c.(1249-1251)Gcc>Tcc	p.A417S	DCAF5_ENST00000554215.1_Missense_Mutation_p.A335S|DCAF5_ENST00000553293.1_5'UTR|DCAF5_ENST00000556847.1_Missense_Mutation_p.A335S|DCAF5_ENST00000557386.1_Missense_Mutation_p.A416S	NM_001284206.1|NM_001284207.1|NM_003861.2	NP_001271135.1|NP_001271136.1|NP_003852.1	Q96JK2	DCAF5_HUMAN	DDB1 and CUL4 associated factor 5	417					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|upper_aerodigestive_tract(2)	29						TCAAAGAAGGCCATCATCCGG	0.562																																					p.A417S		Atlas-SNP	.											.	DCAF5	67	.	0			c.G1249T						.						89	85	87					14																	69522154		2203	4300	6503	SO:0001583	missense	8816	exon9			AGAAGGCCATCAT	AB058727	CCDS32106.1, CCDS61480.1, CCDS61481.1, CCDS73646.1	14q23-q24.1	2013-01-09	2009-07-17	2009-07-17				"WD repeat domain containing", "DDB1 and CUL4 associated factors"	20224	protein-coding gene	gene with protein product		603812	"WD repeat domain 22"	WDR22		9740667, 9521877	Standard	NM_003861		Approved	BCRP2, D14S1461E, BCRG2, KIAA1824	uc001xkp.3	Q96JK2		ENST00000341516.5:c.1249G>T	chr14.hg19:g.69522154C>A	ENSP00000341351:p.Ala417Ser	167.0	0.0		117.0	54.0	NM_003861	B2RN31|G3V4J7|O60559|Q8N3V3|Q8N3V5	Missense_Mutation	SNP	ENST00000341516.5	hg19	CCDS32106.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530871	0.85706	.	.	ENSG00000139990	ENST00000341516;ENST00000554215;ENST00000556847;ENST00000557386	T;T;T;T	0.75050	-0.9;-0.72;-0.72;-0.21	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.81559	0.4848	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.981	T	0.82460	-0.0446	10	0.62326	D	0.03	-17.0231	19.7989	0.96497	0.0:1.0:0.0:0.0	.	416;417	G3V4J7;Q96JK2	.;DCAF5_HUMAN	S	417;335;335;416	ENSP00000341351:A417S;ENSP00000451551:A335S;ENSP00000452052:A335S;ENSP00000451845:A416S	ENSP00000341351:A417S	A	-	1	0	DCAF5	68591907	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.336000	0.79245	2.683000	0.91414	0.561000	0.74099	GCC	.	.		0.562	DCAF5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414806.2	NM_003861		A	69522154	C	A	69522154	3	1	128	1	0	0	0	0	1	0	0	0	4275	739	26	3	1583	3	DCAF5	14	69522154	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	4261790	69522154	37827386	76	21150										
HERC2	8924	hgsc.bcm.edu	37	chr15	28491165	28491165	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ttgcatgagaccagcattttTactgagcagaagcactatag	9	8	0	3			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr15:28491165T>C	ENST00000261609.7	-	23	3547	c.3439A>G	c.(3439-3441)Aaa>Gaa	p.K1147E		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CCAGCATTTTTACTGAGCAGA	0.413																																					p.K1147E		Atlas-SNP	.											.	HERC2	501	.	0			c.A3439G						.						92	83	86					15																	28491165		2203	4300	6503	SO:0001583	missense	8924	exon23			CATTTTTACTGAG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.3439A>G	chr15.hg19:g.28491165T>C	ENSP00000261609:p.Lys1147Glu	123.0	0.0		110.0	46.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.261445	0.23051	.	.	ENSG00000128731	ENST00000261609	T	0.38401	1.14	5.61	5.61	0.85477	.	0.055128	0.85682	D	0.000000	T	0.24547	0.0595	N	0.19112	0.55	0.39329	D	0.965383	B	0.09022	0.002	B	0.06405	0.002	T	0.10543	-1.0625	10	0.12103	T	0.63	.	16.1042	0.81209	0.0:0.0:0.0:1.0	.	1147	O95714	HERC2_HUMAN	E	1147	ENSP00000261609:K1147E	ENSP00000261609:K1147E	K	-	1	0	HERC2	26164760	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.929000	0.63455	2.270000	0.75569	0.528000	0.53228	AAA	.	.		0.413	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		C	28491165	T	C	28491165	3	2	128	1	0	0	0	0	1	0	0	0	7067	1763	61	2	11349	2	HERC2	15	28491165	Missense_Mutation	SNP	T	TCGA-DD-A4NF-01A-11D-A27I-10		28491165	74040227	77	21151										
CSNK1G1	53944	hgsc.bcm.edu	37	chr15	64508895	64508895	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	acatggtccaaagtaatacaCctgtgggagaccttcacctg	9	11	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr15:64508895C>T	ENST00000303052.7	-	5	733	c.310G>A	c.(310-312)Gtg>Atg	p.V104M	CSNK1G1_ENST00000303032.6_Missense_Mutation_p.V104M|CSNK1G1_ENST00000607537.1_Missense_Mutation_p.V104M|CTD-2116N17.1_ENST00000606793.1_Missense_Mutation_p.V77M	NM_022048.3	NP_071331.2	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	104	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	13						AAGTAATACACCTGTGGGAGA	0.453																																					p.V104M		Atlas-SNP	.											.	CSNK1G1	56	.	0			c.G310A						.						66	58	61					15																	64508895		2203	4300	6503	SO:0001583	missense	53944	exon5			AATACACCTGTGG	AB042562	CCDS10192.2	15q22.1-q22.31	2013-01-17			ENSG00000169118	ENSG00000169118			2454	protein-coding gene	gene with protein product		606274				11124537	Standard	NM_022048		Approved	CK1gamma1	uc002anf.3	Q9HCP0	OTTHUMG00000133019	ENST00000303052.7:c.310G>A	chr15.hg19:g.64508895C>T	ENSP00000305777:p.Val104Met	237.0	0.0		150.0	64.0	NM_022048	Q5JPH1|Q96AE9|Q9HCP1	Missense_Mutation	SNP	ENST00000303052.7	hg19	CCDS10192.2	.	.	.	.	.	.	.	.	.	.	C	31	5.090517	0.94149	.	.	ENSG00000169118	ENST00000303052;ENST00000303032	T;T	0.21361	2.01;2.01	5.51	5.51	0.81932	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.48857	0.1523	M	0.73217	2.22	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.992;0.995;0.994	T	0.43507	-0.9387	10	0.62326	D	0.03	.	19.7866	0.96442	0.0:1.0:0.0:0.0	.	104;104;104	Q9HCP0-2;Q8IXA3;Q9HCP0	.;.;KC1G1_HUMAN	M	104	ENSP00000305777:V104M;ENSP00000307753:V104M	ENSP00000307753:V104M	V	-	1	0	CSNK1G1	62295948	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.056000	0.71111	2.756000	0.94617	0.655000	0.94253	GTG	.	.		0.453	CSNK1G1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256605.1	NM_022048		T	64508895	C	T	64508895	3	4	128	1	0	0	0	0	1	0	0	0	3956	507	18	3	990	3	CSNK1G1	15	64508895	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	36017730	64508895	38022497	78	21152										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72189982	72189982	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tgcccattctgtctgtcttgGataattccttgacagtacta	7	10	3	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr15:72189982G>C	ENST00000356056.5	-	25	5334	c.4862C>G	c.(4861-4863)tCc>tGc	p.S1621C	MYO9A_ENST00000444904.1_Missense_Mutation_p.S1602C|MYO9A_ENST00000564571.1_Missense_Mutation_p.S1621C|MYO9A_ENST00000566885.1_Missense_Mutation_p.S1241C|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000424560.1_Missense_Mutation_p.S1621C	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1621	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GTCTGTCTTGGATAATTCCTT	0.448																																					p.S1621C		Atlas-SNP	.											.	MYO9A	203	.	0			c.C4862G						.						136	122	127					15																	72189982		2199	4297	6496	SO:0001583	missense	4649	exon25			GTCTTGGATAATT	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.4862C>G	chr15.hg19:g.72189982G>C	ENSP00000348349:p.Ser1621Cys	285.0	1.0		264.0	115.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.565776	0.27915	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.84800	-1.9;-1.89;-1.9	5.92	3.66	0.41972	.	.	.	.	.	T	0.77219	0.4098	N	0.24115	0.695	0.09310	N	1	P;P;P	0.45348	0.547;0.547;0.856	B;B;B	0.43331	0.416;0.416;0.319	T	0.67803	-0.5576	9	0.54805	T	0.06	.	9.2093	0.37309	0.0867:0.0:0.7635:0.1498	.	1602;1621;1621	B2RTY4-2;B2RTY4-4;B2RTY4	.;.;MYO9A_HUMAN	C	1621;1621;1602	ENSP00000348349:S1621C;ENSP00000399162:S1621C;ENSP00000398250:S1602C	ENSP00000348349:S1621C	S	-	2	0	MYO9A	69977036	0.942000	0.31987	0.147000	0.22382	0.323000	0.28346	1.757000	0.38400	1.441000	0.47550	0.650000	0.86243	TCC	.	.		0.448	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		C	72189982	G	C	72189982	3	2	128	1	0	0	0	0	1	0	0	0	10093	1174	41	4	2856	4	MYO9A	15	72189982	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	7681087	72189982	30341410	79	21153										
TELO2	9894	hgsc.bcm.edu	37	chr16	1545384	1545384	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tgaagatggcgcggctgctgGccagattcctgcgcgagggc	17	11	0	3			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr16:1545384G>C	ENST00000262319.6	+	3	652	c.373G>C	c.(373-375)Gcc>Ccc	p.A125P		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	125					regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				GCGGCTGCTGGCCAGATTCCT	0.692																																					p.A125P		Atlas-SNP	.											.	TELO2	44	.	0			c.G373C						.						5	6	6					16																	1545384		2111	4145	6256	SO:0001583	missense	9894	exon3			CTGCTGGCCAGAT	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"TEL2, telomere maintenance 2, homolog (S. cerevisiae)"			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.373G>C	chr16.hg19:g.1545384G>C	ENSP00000262319:p.Ala125Pro	19.0	0.0		14.0	7.0	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	hg19	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.570224	0.45798	.	.	ENSG00000100726	ENST00000262319	D	0.85258	-1.96	5.34	2.97	0.34412	.	0.445445	0.23424	N	0.048340	T	0.81293	0.4792	L	0.57536	1.79	0.19300	N	0.999976	P	0.39665	0.682	B	0.40199	0.322	T	0.70995	-0.4720	10	0.33141	T	0.24	-11.1656	10.1187	0.42607	0.086:0.0:0.7725:0.1415	.	125	Q9Y4R8	TELO2_HUMAN	P	125	ENSP00000262319:A125P	ENSP00000262319:A125P	A	+	1	0	TELO2	1485385	1.000000	0.71417	0.837000	0.33122	0.165000	0.22458	4.829000	0.62737	1.222000	0.43521	0.655000	0.94253	GCC	.	.		0.692	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111		C	1545384	G	C	1545384	3	2	128	1	0	0	0	0	1	0	0	0	15772	1203	42	4	379	4	TELO2	16	1545384	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		1545384	88809369	80	21154										
TBL3	10607	hgsc.bcm.edu	37	chr16	2026901	2026901	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	agccttgctgtccaagaacaCagccccagacaacggcccta	8	16	0	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr16:2026901C>T	ENST00000568546.1	+	14	1507	c.1379C>T	c.(1378-1380)aCa>aTa	p.T460I		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	460					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						TCCAAGAACACAGCCCCAGAC	0.607																																					p.T460I	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.C1379T						.						114	91	99					16																	2026901		2198	4300	6498	SO:0001583	missense	10607	exon14			AGAACACAGCCCC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"WD repeat domain containing"	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1379C>T	chr16.hg19:g.2026901C>T	ENSP00000454836:p.Thr460Ile	195.0	0.0		113.0	38.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	hg19	CCDS10453.1	.	.	.	.	.	.	.	.	.	.	C	5.628	0.300504	0.10678	.	.	ENSG00000183751	ENST00000332704	.	.	.	5.27	0.796	0.18648	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.462635	0.20004	N	0.101267	T	0.36331	0.0963	M	0.61703	1.905	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.17137	-1.0379	9	0.19147	T	0.46	-0.2246	5.1339	0.14924	0.3416:0.4733:0.113:0.0721	.	222;460	A0JLS5;Q12788	.;TBL3_HUMAN	I	460	.	ENSP00000331815:T460I	T	+	2	0	TBL3	1966902	0.000000	0.05858	0.001000	0.08648	0.538000	0.34931	0.141000	0.16076	0.588000	0.29660	0.561000	0.74099	ACA	.	.		0.607	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453		T	2026901	C	T	2026901	3	4	128	1	0	0	0	0	1	0	0	0	15658	478	17	3	1433	3	TBL3	16	2026901	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	481517	2026901	88327852	81	21155										
A2BP1	54715	hgsc.bcm.edu	37	chr16	7568314	7568314	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ttcccgagcacacattaaacCtgtaccctcccgcccagacg	6	18	0	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr16:7568314C>T	ENST00000550418.1	+	5	1181	c.193C>T	c.(193-195)Ctg>Ttg	p.L65L	RBFOX1_ENST00000436368.2_Silent_p.L85L|RBFOX1_ENST00000340209.4_Silent_p.L70L|RBFOX1_ENST00000535565.2_Silent_p.L101L|RBFOX1_ENST00000547372.1_Silent_p.L108L|RBFOX1_ENST00000355637.4_Silent_p.L85L|RBFOX1_ENST00000311745.5_Silent_p.L85L|RBFOX1_ENST00000553186.1_Silent_p.L65L|RBFOX1_ENST00000547338.1_Silent_p.L65L|RBFOX1_ENST00000552089.1_Silent_p.L101L|RBFOX1_ENST00000422070.4_Silent_p.L108L	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	65					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						CACATTAAACCTGTACCCTCC	0.652																																					p.L85L	Ovarian(157;934 2567 15163 39509)	Atlas-SNP	.											.	RBFOX1	341	.	0			c.C253T						.						124	117	120					16																	7568314		2197	4300	6497	SO:0001819	synonymous_variant	54715	exon2			TTAAACCTGTACC	AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"RNA binding motif (RRM) containing"	18222	protein-coding gene	gene with protein product	"ataxin 2-binding protein 1", "hexaribonucleotide binding protein 1"	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.193C>T	chr16.hg19:g.7568314C>T		113.0	0.0		91.0	39.0	NM_145891	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Silent	SNP	ENST00000550418.1	hg19	CCDS55983.1																																																																																			.	.		0.652	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		T	7568314	C	T	7568314	2	4	128	1	0	0	0	0	0	0	0	1	3	680	24	3		3	A2BP1	16	7568314	Silent	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	5541413	7568314	82786439	82	21156										
TAOK2	9344	hgsc.bcm.edu	37	chr16	29994582	29994582	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	aggaagaaggccctgaagccCgggagatggccatgatgcag	16	9	0	4			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr16:29994582C>T	ENST00000308893.4	+	12	2232	c.1189C>T	c.(1189-1191)Cgg>Tgg	p.R397W	TAOK2_ENST00000416441.2_Missense_Mutation_p.R224W|TAOK2_ENST00000279394.3_Missense_Mutation_p.R397W|TAOK2_ENST00000543033.1_Missense_Mutation_p.R397W	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	397	Glu-rich.				actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						CCCTGAAGCCCGGGAGATGGC	0.617																																					p.R397W		Atlas-SNP	.											.	TAOK2	142	.	0			c.C1189T						.						45	41	42					16																	29994582		2197	4300	6497	SO:0001583	missense	9344	exon12			GAAGCCCGGGAGA	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.1189C>T	chr16.hg19:g.29994582C>T	ENSP00000310094:p.Arg397Trp	60.0	0.0		54.0	22.0	NM_004783	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Missense_Mutation	SNP	ENST00000308893.4	hg19	CCDS10663.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.509159	0.44660	.	.	ENSG00000149930	ENST00000416441;ENST00000308893;ENST00000543033;ENST00000279394	T;T;T	0.30182	1.54;1.54;1.54	5.24	1.95	0.26073	.	0.131951	0.47852	D	0.000209	T	0.21718	0.0523	N	0.08118	0	0.39578	D	0.969385	D;D;D;P;D	0.71674	0.997;0.998;0.987;0.784;0.983	P;P;B;B;P	0.55923	0.617;0.787;0.432;0.075;0.586	T	0.06180	-1.0841	9	.	.	.	.	6.5214	0.22277	0.3083:0.4626:0.2291:0.0	.	588;224;397;397;397	Q86V37;Q9UL54-3;Q9UL54-2;A0PJ48;Q9UL54	.;.;.;.;TAOK2_HUMAN	W	397	ENSP00000310094:R397W;ENSP00000440336:R397W;ENSP00000279394:R397W	.	R	+	1	2	TAOK2	29902083	0.999000	0.42202	0.999000	0.59377	0.156000	0.22039	0.599000	0.24089	0.551000	0.29008	0.563000	0.77884	CGG	.	.		0.617	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151		T	29994582	C	T	29994582	3	4	128	1	0	0	0	0	1	0	0	0	15563	643	23	1	1231	1	TAOK2	16	29994582	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	22426268	29994582	60360171	83	21157										
FAM192A	80011	hgsc.bcm.edu	37	chr16	57197926	57197926	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cacccaccttgattcttgtcAtctggctcagggtccggttt	9	13	4	1	rs372644692		TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr16:57197926A>T	ENST00000309137.8	-	6	792	c.534T>A	c.(532-534)gaT>gaA	p.D178E	FAM192A_ENST00000569266.1_Missense_Mutation_p.D178E|FAM192A_ENST00000564108.1_Missense_Mutation_p.D178E|FAM192A_ENST00000389447.5_Missense_Mutation_p.D178E|FAM192A_ENST00000566077.1_Missense_Mutation_p.D101E|FAM192A_ENST00000567439.1_Missense_Mutation_p.D178E	NM_024946.2	NP_079222.1	Q9GZU8	F192A_HUMAN	family with sequence similarity 192, member A	178						nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|lung(4)|prostate(2)	11						GATTCTTGTCATCTGGCTCAG	0.453																																					p.D178E		Atlas-SNP	.											.	FAM192A	23	.	0			c.T534A						.						318	308	311					16																	57197926		1969	4157	6126	SO:0001583	missense	80011	exon6			CTTGTCATCTGGC		CCDS42168.1	16q13	2009-08-19	2009-08-19	2009-08-19		ENSG00000172775			29856	protein-coding gene	gene with protein product	"NEFA interacting nuclear protein NIP30"		"chromosome 16 open reading frame 94"	C16orf94		12477932	Standard	NM_024946		Approved	NIP30	uc021tiy.1	Q9GZU8		ENST00000309137.8:c.534T>A	chr16.hg19:g.57197926A>T	ENSP00000335808:p.Asp178Glu	228.0	0.0		168.0	67.0	NM_024946		Missense_Mutation	SNP	ENST00000309137.8	hg19	CCDS42168.1	.	.	.	.	.	.	.	.	.	.	A	7.186	0.590538	0.13812	.	.	ENSG00000172775	ENST00000309137;ENST00000389447	.	.	.	5.97	2.4	0.29515	.	0.563671	0.22381	N	0.060812	T	0.19046	0.0457	N	0.22421	0.69	0.31940	N	0.611055	B	0.02656	0.0	B	0.04013	0.001	T	0.31447	-0.9943	9	0.02654	T	1	-6.0501	2.6359	0.04957	0.4589:0.1217:0.0672:0.3522	.	178	Q9GZU8	F192A_HUMAN	E	178	.	ENSP00000335808:D178E	D	-	3	2	FAM192A	55755427	0.954000	0.32549	1.000000	0.80357	0.970000	0.65996	0.023000	0.13533	0.116000	0.18110	0.477000	0.44152	GAT	.	.		0.453	FAM192A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433022.2	NM_024946		T	57197926	A	T	57197926	3	4	128	1	0	0	0	0	1	0	0	0	5528	214	8	4	238	4	FAM192A	16	57197926	Missense_Mutation	SNP	A	TCGA-DD-A4NF-01A-11D-A27I-10	27203344	57197926	33156827	84	21158										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70896085	70896085	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tgtggggaaccctcggcccaGtggtccatggtgctgtccag	15	12	0	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr16:70896085G>C	ENST00000393567.2	-	69	11793	c.11643C>G	c.(11641-11643)caC>caG	p.H3881Q		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3881					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CCTCGGCCCAGTGGTCCATGG	0.562																																					p.H3881Q		Atlas-SNP	.											.	HYDIN	788	.	0			c.C11643G						.						38	40	40					16																	70896085		1946	4152	6098	SO:0001583	missense	54768	exon69			GGCCCAGTGGTCC	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.11643C>G	chr16.hg19:g.70896085G>C	ENSP00000377197:p.His3881Gln	184.0	0.0		111.0	40.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	hg19	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.763038	0.31228	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00840	5.63	5.97	1.36	0.22044	.	.	.	.	.	T	0.01029	0.0034	L	0.38531	1.155	0.25303	N	0.989268	B	0.27823	0.19	B	0.35550	0.205	T	0.47471	-0.9115	9	0.16420	T	0.52	.	5.3162	0.15856	0.1676:0.0:0.5455:0.2869	.	3880	F8WD23	.	Q	3881;3880	ENSP00000377197:H3881Q	ENSP00000313052:H3880Q	H	-	3	2	HYDIN	69453586	0.933000	0.31639	0.994000	0.49952	0.034000	0.12701	1.479000	0.35453	0.847000	0.35167	0.511000	0.50034	CAC	.	.		0.562	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			C	70896085	G	C	70896085	3	2	128	1	0	0	0	0	1	0	0	0	7476	1020	36	4	3794	4	HYDIN	16	70896085	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	13698159	70896085	19458668	85	21159										
PLCG2	5336	hgsc.bcm.edu	37	chr16	81925146	81925146	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	atgacgcggtggacatgcagGacatgaacaaccccctgtct	11	12	1	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr16:81925146G>A	ENST00000359376.3	+	11	1151	c.937G>A	c.(937-939)Gac>Aac	p.D313N		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	313	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						GGACATGCAGGACATGAACAA	0.493																																					p.D313N		Atlas-SNP	.											.	PLCG2	276	.	0			c.G937A						.						107	110	109					16																	81925146		2111	4226	6337	SO:0001583	missense	5336	exon11			ATGCAGGACATGA		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.937G>A	chr16.hg19:g.81925146G>A	ENSP00000352336:p.Asp313Asn	335.0	0.0		239.0	81.0	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	hg19	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.952333	0.34471	.	.	ENSG00000197943	ENST00000359376	T	0.64085	-0.08	5.61	3.66	0.41972	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);Phospholipase C, phosphatidylinositol-specific , X domain (2);	0.130613	0.64402	N	0.000002	T	0.63022	0.2476	M	0.85630	2.765	0.53688	D	0.999978	B;B	0.22211	0.022;0.066	B;B	0.18263	0.021;0.015	T	0.60576	-0.7236	10	0.38643	T	0.18	.	10.0304	0.42096	0.2057:0.0:0.7943:0.0	.	180;313	B4E3H3;P16885	.;PLCG2_HUMAN	N	313	ENSP00000352336:D313N	ENSP00000352336:D313N	D	+	1	0	PLCG2	80482647	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.107000	0.57811	0.845000	0.35118	-0.880000	0.02959	GAC	.	.		0.493	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			A	81925146	G	A	81925146	3	1	128	1	0	0	0	0	1	0	0	0	12045	1174	41	3	975	3	PLCG2	16	81925146	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	11029061	81925146	8429607	86	21160										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7726895	7726895	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cctttgagcagtaccctcgtGactggcacctgtggtatacc	10	13	0	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr17:7726895G>T	ENST00000572933.1	+	74	12738	c.11278G>T	c.(11278-11280)Gac>Tac	p.D3760Y	DNAH2_ENST00000389173.2_Missense_Mutation_p.D3760Y			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3760					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GTACCCTCGTGACTGGCACCT	0.532																																					p.D3760Y		Atlas-SNP	.											.	DNAH2	498	.	0			c.G11278T						.						156	121	133					17																	7726895		2203	4300	6503	SO:0001583	missense	146754	exon73			CCTCGTGACTGGC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.11278G>T	chr17.hg19:g.7726895G>T	ENSP00000458355:p.Asp3760Tyr	244.0	0.0		214.0	83.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.997407	0.74818	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.56275	0.47	4.89	4.89	0.63831	Dynein heavy chain (1);	0.177492	0.47852	D	0.000220	T	0.77624	0.4158	M	0.91300	3.195	0.80722	D	1	P;D	0.59357	0.845;0.985	P;D	0.66979	0.802;0.948	T	0.82750	-0.0303	10	0.62326	D	0.03	.	16.9793	0.86323	0.0:0.0:1.0:0.0	.	3721;3760	Q9P225-2;Q9P225	.;DYH2_HUMAN	Y	3721;3760	ENSP00000373825:D3760Y	ENSP00000353818:D3721Y	D	+	1	0	DNAH2	7667620	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.627000	0.74258	2.551000	0.86045	0.609000	0.83330	GAC	.	.		0.532	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7726895	G	T	7726895	3	4	128	1	0	0	0	0	1	0	0	0	4604	1290	45	3	11568	3	DNAH2	17	7726895	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		7726895	73468315	87	21161										
RICH2	9912	hgsc.bcm.edu	37	chr17	12852526	12852526	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cggccctggactgctgcgtgGtggatgtgcaggagtactcg	17	10	0	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr17:12852526G>A	ENST00000379672.5	+	11	1231	c.931G>A	c.(931-933)Gtg>Atg	p.V311M	ARHGAP44_ENST00000262444.9_Missense_Mutation_p.V311M|ARHGAP44_ENST00000340825.3_Missense_Mutation_p.V311M	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	311	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						CTGCTGCGTGGTGGATGTGCA	0.622																																					p.V311M		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.G931A						.						31	33	33					17																	12852526		2044	4185	6229	SO:0001583	missense	9912	exon11			TGCGTGGTGGATG		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"Rho GTPase activating proteins"	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.931G>A	chr17.hg19:g.12852526G>A	ENSP00000368994:p.Val311Met	72.0	0.0		65.0	25.0	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Missense_Mutation	SNP	ENST00000379672.5	hg19	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.858092	0.32791	.	.	ENSG00000006740	ENST00000379672;ENST00000340825;ENST00000538915	T;T	0.19250	2.16;2.16	6.05	2.79	0.32731	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.398771	0.27442	N	0.019358	T	0.17066	0.0410	L	0.41632	1.29	0.49299	D	0.999775	B;B	0.15473	0.01;0.013	B;B	0.17722	0.019;0.016	T	0.04885	-1.0920	10	0.34782	T	0.22	.	10.7368	0.46130	0.0:0.3087:0.5714:0.12	.	311;311	A6NCP5;Q17R89	.;RHG44_HUMAN	M	311;311;34	ENSP00000368994:V311M;ENSP00000342566:V311M	ENSP00000342566:V311M	V	+	1	0	ARHGAP44	12793251	0.997000	0.39634	1.000000	0.80357	0.976000	0.68499	0.341000	0.19909	0.839000	0.34971	0.637000	0.83480	GTG	.	.		0.622	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859		A	12852526	G	A	12852526	3	1	128	1	0	0	0	0	1	0	0	0	13372	1261	44	3	973	3	RICH2	17	12852526	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	5125631	12852526	68342684	88	21162										
CDK5R1	8851	hgsc.bcm.edu	37	chr17	30814788	30814788	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cactccatcatctccgtgctGccttggaagagaatcgtggc	10	13	2	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr17:30814788G>A	ENST00000313401.3	+	2	839	c.150G>A	c.(148-150)ctG>ctA	p.L50L		NM_003885.2	NP_003876.1	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	50					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|brain development (GO:0007420)|cell proliferation (GO:0008283)|cerebellum development (GO:0021549)|embryo development (GO:0009790)|ephrin receptor signaling pathway (GO:0048013)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|hippocampus development (GO:0021766)|ionotropic glutamate receptor signaling pathway (GO:0035235)|layer formation in cerebral cortex (GO:0021819)|negative regulation of axon extension (GO:0030517)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of neuron differentiation (GO:0045664)|rhythmic process (GO:0048511)|serine phosphorylation of STAT3 protein (GO:0033136)|superior olivary nucleus maturation (GO:0021722)	axon (GO:0030424)|contractile fiber (GO:0043292)|cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|cyclin-dependent protein kinase 5 activator activity (GO:0016534)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)			cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)			TCTCCGTGCTGCCTTGGAAGA	0.562																																					p.L50L		Atlas-SNP	.											.	CDK5R1	30	.	0			c.G150A						.						108	93	98					17																	30814788		2203	4300	6503	SO:0001819	synonymous_variant	8851	exon2			CGTGCTGCCTTGG	X80343	CCDS11273.1	17q12	2006-03-28			ENSG00000176749	ENSG00000176749			1775	protein-coding gene	gene with protein product		603460				8090221	Standard	NM_003885		Approved	p35nck5a, Nck5a	uc002hhn.3	Q15078	OTTHUMG00000132814	ENST00000313401.3:c.150G>A	chr17.hg19:g.30814788G>A		337.0	0.0		252.0	87.0	NM_003885	E1P664|Q5U0G3	Silent	SNP	ENST00000313401.3	hg19	CCDS11273.1																																																																																			.	.		0.562	CDK5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256264.1	NM_003885		A	30814788	G	A	30814788	2	1	128	1	0	0	0	0	0	0	0	1	3145	1306	46	3		3	CDK5R1	17	30814788	Silent	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	17962262	30814788	50380422	89	21163										
DNAI2	64446	hgsc.bcm.edu	37	chr17	72281284	72281284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tggagcagaccatccgtttcCggaagaaagtggagaaagat	13	7	0	4			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr17:72281284C>T	ENST00000311014.6	+	3	356	c.289C>T	c.(289-291)Cgg>Tgg	p.R97W	DNAI2_ENST00000579490.1_Missense_Mutation_p.R154W|DNAI2_ENST00000446837.2_Missense_Mutation_p.R97W|DNAI2_ENST00000307504.5_5'UTR|DNAI2_ENST00000582036.1_Missense_Mutation_p.R97W			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	97					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						CATCCGTTTCCGGAAGAAAGT	0.582									Kartagener syndrome																												p.R97W		Atlas-SNP	.											.	DNAI2	102	.	0			c.C289T						.						75	64	68					17																	72281284		2203	4300	6503	SO:0001583	missense	64446	exon3	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CGTTTCCGGAAGA	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"Axonemal dyneins", "WD repeat domain containing"	18744	protein-coding gene	gene with protein product	"dynein intermediate chain 2"	605483	"dynein, axonemal, intermediate polypeptide 2"			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.289C>T	chr17.hg19:g.72281284C>T	ENSP00000308312:p.Arg97Trp	204.0	0.0		138.0	7.0	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Missense_Mutation	SNP	ENST00000311014.6	hg19	CCDS11697.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.621425	0.87460	.	.	ENSG00000171595	ENST00000311014;ENST00000446837	T;T	0.15952	2.38;2.38	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.55862	0.1947	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.69591	-0.5104	10	0.87932	D	0	-44.4411	18.6962	0.91601	0.0:1.0:0.0:0.0	.	97	Q9GZS0	DNAI2_HUMAN	W	97	ENSP00000308312:R97W;ENSP00000400252:R97W	ENSP00000308312:R97W	R	+	1	2	DNAI2	69792879	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.701000	0.54793	2.640000	0.89533	0.650000	0.86243	CGG	.	.		0.582	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036		T	72281284	C	T	72281284	3	4	128	1	0	0	0	0	1	0	0	0	4612	643	23	1	295	1	DNAI2	17	72281284	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	41466496	72281284	8913926	90	21164										
CIRBP	1153	hgsc.bcm.edu	37	chr19	1271158	1271158	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gtggtggttgtgaaagacagGgagacccagagatctcgggg	18	6	1	4			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr19:1271158G>C	ENST00000588030.1	+	3	383	c.123G>C	c.(121-123)agG>agC	p.R41S	CIRBP_ENST00000589235.1_Missense_Mutation_p.R41S|CIRBP_ENST00000586472.1_Missense_Mutation_p.R41S|CIRBP_ENST00000587896.1_Missense_Mutation_p.R41S|CIRBP-AS1_ENST00000585832.1_RNA|CIRBP_ENST00000587323.1_Missense_Mutation_p.R41S|CIRBP-AS1_ENST00000600215.1_RNA|CIRBP_ENST00000585630.1_Missense_Mutation_p.R41S|CIRBP_ENST00000586773.1_Missense_Mutation_p.R41S|CIRBP_ENST00000588090.1_Missense_Mutation_p.R41S|CIRBP_ENST00000589710.1_Missense_Mutation_p.R41S|CIRBP_ENST00000588230.1_Missense_Mutation_p.R41S|CIRBP_ENST00000589686.1_Missense_Mutation_p.R41S|CIRBP_ENST00000413636.2_Missense_Mutation_p.R41S|CIRBP_ENST00000589660.1_Missense_Mutation_p.R41S|CIRBP_ENST00000320936.5_Missense_Mutation_p.R41S|CIRBP_ENST00000591935.1_Missense_Mutation_p.R41S|CIRBP_ENST00000444172.2_Intron			Q14011	CIRBP_HUMAN	cold inducible RNA binding protein	41	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA stabilization (GO:0048255)|positive regulation of translation (GO:0045727)|response to cold (GO:0009409)|response to UV (GO:0009411)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|small ribosomal subunit rRNA binding (GO:0070181)|translation repressor activity (GO:0030371)			endometrium(1)|large_intestine(1)|lung(3)	5		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGAAAGACAGGGAGACCCAGA	0.577																																					p.R41S		Atlas-SNP	.											.	CIRBP	19	.	0			c.G123C						.						103	106	105					19																	1271158		2203	4300	6503	SO:0001583	missense	1153	exon3			AGACAGGGAGACC	D78134	CCDS12059.1, CCDS74244.1, CCDS74245.1	19p13.3	2013-02-12	2001-11-28		ENSG00000099622	ENSG00000099622		"RNA binding motif (RRM) containing"	1982	protein-coding gene	gene with protein product	"Cold-inducible RNA-binding protein", "glycine-rich RNA binding protein"	602649	"cold inducible RNA-binding protein"			9434172, 9151692	Standard	NM_001280		Approved	CIRP	uc002lrr.4	Q14011		ENST00000588030.1:c.123G>C	chr19.hg19:g.1271158G>C	ENSP00000468788:p.Arg41Ser	396.0	0.0		264.0	82.0	NM_001280	B3KT17|B4E2X2	Missense_Mutation	SNP	ENST00000588030.1	hg19	CCDS12059.1	.	.	.	.	.	.	.	.	.	.	G	11.98	1.799404	0.31869	.	.	ENSG00000099622	ENST00000320936;ENST00000413636	D;D	0.85339	-1.97;-1.97	4.12	3.08	0.35506	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.058497	0.64402	U	0.000013	D	0.87466	0.6184	L	0.42686	1.345	0.80722	D	1	D;D;D;D	0.89917	0.981;0.989;1.0;0.989	D;D;D;D	0.85130	0.928;0.971;0.997;0.971	D	0.86241	0.1643	10	0.87932	D	0	-3.1252	8.2397	0.31652	0.1998:0.0:0.8002:0.0	.	41;41;41;41	B4E2X2;Q53XX5;D6W5Y5;Q14011	.;.;.;CIRBP_HUMAN	S	41	ENSP00000322887:R41S;ENSP00000412831:R41S	ENSP00000322887:R41S	R	+	3	2	CIRBP	1222158	1.000000	0.71417	0.996000	0.52242	0.006000	0.05464	1.272000	0.33109	0.723000	0.32274	-0.271000	0.10264	AGG	.	.		0.577	CIRBP-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449969.1	NM_001280		C	1271158	G	C	1271158	3	2	128	1	0	0	0	0	1	0	0	0	3435	1223	43	4	129	4	CIRBP	19	1271158	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		1271158	57857825	91	21165										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22362974	22362974	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tcagtaaggatcgaggaccaGctgaaggctttgccacattc	11	10	1	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr19:22362974G>C	ENST00000397121.2	-	3	1862	c.1545C>G	c.(1543-1545)agC>agG	p.S515R		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	515					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TCGAGGACCAGCTGAAGGCTT	0.408																																					p.S515R		Atlas-SNP	.											.	ZNF676	146	.	0			c.C1545G						.						63	66	65					19																	22362974		2151	4273	6424	SO:0001583	missense	163223	exon3			GGACCAGCTGAAG	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.1545C>G	chr19.hg19:g.22362974G>C	ENSP00000380310:p.Ser515Arg	26.0	0.0		27.0	13.0	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	hg19	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	0.014	-1.577780	0.00879	.	.	ENSG00000196109	ENST00000397121	T	0.07216	3.21	0.81	-1.62	0.08372	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05135	0.0137	L	0.38175	1.15	0.09310	N	1	P	0.46621	0.881	B	0.40134	0.32	T	0.34279	-0.9835	9	0.13108	T	0.6	.	4.2702	0.10783	0.1971:0.0:0.587:0.2158	.	515	Q8N7Q3	ZN676_HUMAN	R	515	ENSP00000380310:S515R	ENSP00000380310:S515R	S	-	3	2	ZNF676	22154814	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-8.795000	0.00016	-1.122000	0.02945	-1.109000	0.02080	AGC	.	.		0.408	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		C	22362974	G	C	22362974	3	2	128	1	0	0	0	0	1	0	0	0	18098	962	34	4	225	4	ZNF676	19	22362974	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	21091816	22362974	36766009	92	21166										
DHX34	9704	hgsc.bcm.edu	37	chr19	47861354	47861354	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	tactgccactgcacagcgccCtgtctgtggccgaccaggac	11	16	1	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr19:47861354C>T	ENST00000328771.4	+	4	1598	c.1249C>T	c.(1249-1251)Ctg>Ttg	p.L417L	DHX34_ENST00000471451.1_3'UTR	NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	417	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		GCACAGCGCCCTGTCTGTGGC	0.657																																					p.L417L		Atlas-SNP	.											.	DHX34	98	.	0			c.C1249T						.						26	25	26					19																	47861354		2203	4298	6501	SO:0001819	synonymous_variant	9704	exon4			AGCGCCCTGTCTG	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"DEAH-boxes"	16719	protein-coding gene	gene with protein product		615475	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.1249C>T	chr19.hg19:g.47861354C>T		50.0	0.0		39.0	16.0	NM_014681	B4DMY8	Silent	SNP	ENST00000328771.4	hg19	CCDS12700.1																																																																																			.	.		0.657	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		T	47861354	C	T	47861354	2	4	128	1	0	0	0	0	0	0	0	1	4509	680	24	3		3	DHX34	19	47861354	Silent	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	25498380	47861354	11267629	93	21167										
BACE2	25825	hgsc.bcm.edu	37	chr21	42617961	42617961	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cccagaaggtgtttgatgcgGtggtggaagctgtggcccgc	17	9	0	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chr21:42617961G>A	ENST00000330333.6	+	6	1418	c.955G>A	c.(955-957)Gtg>Atg	p.V319M	BACE2_ENST00000466122.1_3'UTR|BACE2_ENST00000347667.5_Missense_Mutation_p.V319M|BACE2_ENST00000328735.6_Missense_Mutation_p.V319M	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2	319					membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				GTTTGATGCGGTGGTGGAAGC	0.607																																					p.V319M		Atlas-SNP	.											.	BACE2	45	.	0			c.G955A						.						58	43	48					21																	42617961		2203	4300	6503	SO:0001583	missense	25825	exon6			GATGCGGTGGTGG	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.955G>A	chr21.hg19:g.42617961G>A	ENSP00000332979:p.Val319Met	155.0	0.0		138.0	52.0	NM_138992	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	hg19	CCDS13668.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.522968	0.44866	.	.	ENSG00000182240	ENST00000330333;ENST00000347667;ENST00000328735;ENST00000544566	T;T;T	0.58210	0.35;0.35;0.35	5.31	5.31	0.75309	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.133554	0.50627	D	0.000119	T	0.55016	0.1894	L	0.43152	1.355	0.47341	D	0.999393	D;P;D	0.61080	0.989;0.708;0.977	P;B;P	0.53266	0.722;0.294;0.617	T	0.56177	-0.8022	10	0.52906	T	0.07	.	11.4521	0.50158	0.0821:0.0:0.9179:0.0	.	319;319;319	Q9Y5Z0-3;Q9Y5Z0-2;Q9Y5Z0	.;.;BACE2_HUMAN	M	319;319;319;224	ENSP00000332979:V319M;ENSP00000327528:V319M;ENSP00000333854:V319M	ENSP00000333854:V319M	V	+	1	0	BACE2	41539831	1.000000	0.71417	0.942000	0.38095	0.187000	0.23431	3.951000	0.56684	2.482000	0.83794	0.655000	0.94253	GTG	.	.		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			A	42617961	G	A	42617961	3	1	128	1	0	0	0	0	1	0	0	0	1282	1261	44	3	977	3	BACE2	21	42617961	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		42617961	5511934	94	21168										
PHEX	5251	hgsc.bcm.edu	37	chrX	22117127	22117127	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	gttctctctcccctcagttcGactggctgggctacatcaag	9	14	4	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chrX:22117127G>A	ENST00000379374.4	+	9	1502	c.937G>A	c.(937-939)Gac>Aac	p.D313N	PHEX_ENST00000475778.1_3'UTR|PHEX_ENST00000418858.3_Missense_Mutation_p.D16N|PHEX_ENST00000537599.1_Missense_Mutation_p.D313N|PHEX_ENST00000535894.1_Missense_Mutation_p.D216N	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	313					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						CCCTCAGTTCGACTGGCTGGG	0.483																																					p.D313N		Atlas-SNP	.											.	PHEX	95	.	0			c.G937A	GRCh37	CI001586	PHEX	I		.						133	115	121					X																	22117127		2203	4300	6503	SO:0001583	missense	5251	exon9			CAGTTCGACTGGC	U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.937G>A	chrX.hg19:g.22117127G>A	ENSP00000368682:p.Asp313Asn	31.0	0.0		34.0	21.0	NM_000444	O00678|Q13646|Q2M325|Q93032|Q99827	Missense_Mutation	SNP	ENST00000379374.4	hg19	CCDS14204.1	.	.	.	.	.	.	.	.	.	.	G	7.793	0.711926	0.15306	.	.	ENSG00000102174	ENST00000379374;ENST00000537599;ENST00000535894;ENST00000418858	D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66	5.46	5.46	0.80206	Peptidase M13 (1);	0.043010	0.85682	D	0.000000	T	0.69593	0.3128	N	0.12663	0.25	0.47476	D	0.99943	P;P	0.39624	0.631;0.681	B;B	0.36766	0.149;0.232	T	0.69416	-0.5151	10	0.13470	T	0.59	.	18.3838	0.90459	0.0:0.0:1.0:0.0	.	313;313	F5GXU4;P78562	.;PHEX_HUMAN	N	313;313;216;16	ENSP00000368682:D313N;ENSP00000440362:D313N;ENSP00000439418:D216N;ENSP00000443531:D16N	ENSP00000368682:D313N	D	+	1	0	PHEX	22027048	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	5.567000	0.67378	2.282000	0.76494	0.529000	0.55759	GAC	.	.		0.483	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		A	22117127	G	A	22117127	3	1	128	1	0	0	0	0	1	0	0	0	11828	1058	37	1	971	1	PHEX	23	22117127	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10		22117127	133153433	95	21169										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50376662	50376662	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	agttttggtctataggttttGgtctctgggtaaaagtcttg	12	4	3	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chrX:50376662G>A	ENST00000289292.7	-	4	2694	c.2411C>T	c.(2410-2412)cCa>cTa	p.P804L	SHROOM4_ENST00000460112.3_Missense_Mutation_p.P688L|SHROOM4_ENST00000376020.2_Missense_Mutation_p.P804L			Q9ULL8	SHRM4_HUMAN	shroom family member 4	804					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					TATAGGTTTTGGTCTCTGGGT	0.438																																					p.P804L		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C2411T						.						118	109	112					X																	50376662		2203	4300	6503	SO:0001583	missense	57477	exon4			GGTTTTGGTCTCT	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.2411C>T	chrX.hg19:g.50376662G>A	ENSP00000289292:p.Pro804Leu	114.0	0.0		91.0	72.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.557934	0.45590	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	D;D;D	0.87650	-2.28;-2.28;-2.28	5.92	5.06	0.68205	.	0.245301	0.34223	N	0.004145	T	0.80276	0.4593	L	0.32530	0.975	0.35986	D	0.836336	P	0.50272	0.933	B	0.41440	0.357	D	0.84080	0.0384	10	0.72032	D	0.01	.	9.1331	0.36857	0.0:0.1551:0.6808:0.1641	.	804	Q9ULL8	SHRM4_HUMAN	L	804;804;688	ENSP00000289292:P804L;ENSP00000365188:P804L;ENSP00000421450:P688L	ENSP00000289292:P804L	P	-	2	0	SHROOM4	50393402	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.307000	0.51888	1.230000	0.43646	0.600000	0.82982	CCA	.	.		0.438	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		A	50376662	G	A	50376662	3	1	128	1	0	0	0	0	1	0	0	0	14311	1348	47	3	2094	3	SHROOM4	23	50376662	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	28259535	50376662	104893898	96	21170										
PHF8	23133	hgsc.bcm.edu	37	chrX	54022132	54022132	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	cccatgctccttacttccacCaggcggatctccctggccag	8	18	1	0			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chrX:54022132C>T	ENST00000357988.5	-	12	1783	c.1425G>A	c.(1423-1425)ctG>ctA	p.L475L	PHF8_ENST00000322659.8_Silent_p.L439L|PHF8_ENST00000338946.6_Silent_p.L439L|PHF8_ENST00000338154.6_Silent_p.L439L	NM_001184896.1	NP_001171825.1	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	475					brain development (GO:0007420)|G1/S transition of mitotic cell cycle (GO:0000082)|histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of chromatin silencing at rDNA (GO:0061188)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	40						TTACTTCCACCAGGCGGATCT	0.552																																					p.L475L		Atlas-SNP	.											.	PHF8	198	.	0			c.G1425A						.						110	79	89					X																	54022132		2203	4300	6503	SO:0001819	synonymous_variant	23133	exon12			TTCCACCAGGCGG	AB029034	CCDS14355.1, CCDS55418.1, CCDS55419.1, CCDS55420.1	Xp11.22	2013-01-28			ENSG00000172943	ENSG00000172943		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	20672	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1F"	300560				10470851, 20023638, 20644565	Standard	NM_015107		Approved	ZNF422, KIAA1111, JHDM1F	uc004dsu.3	Q9UPP1	OTTHUMG00000021622	ENST00000357988.5:c.1425G>A	chrX.hg19:g.54022132C>T		80.0	0.0		33.0	24.0	NM_001184896	B3KMV4|B7Z911|Q5H9U5|Q5JPR9|Q5JPS0|Q5JPS2|Q5JPS3|Q5VUJ4|Q7Z6D4|Q9HAH2	Silent	SNP	ENST00000357988.5	hg19	CCDS55420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.122|9.122	1.009126|1.009126	0.19199|0.19199	.|.	.|.	ENSG00000172943|ENSG00000172943	ENST00000443302|ENST00000396282;ENST00000448003	.|.	.|.	.|.	5.62|5.62	3.82|3.82	0.43975|0.43975	.|.	.|.	.|.	.|.	.|.	T|.	0.55178|.	0.1904|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.51132|.	-0.8744|.	4|.	.|.	.|.	.|.	-3.5455|-3.5455	6.0766|6.0766	0.19919|0.19919	0.4705:0.44:0.0:0.0894|0.4705:0.44:0.0:0.0894	.|.	.|.	.|.	.|.	S|X	203|343;120	.|.	.|.	G|W	-|-	1|2	0|0	PHF8|PHF8	54038857|54038857	0.978000|0.978000	0.34361|0.34361	1.000000|1.000000	0.80357|0.80357	0.945000|0.945000	0.59286|0.59286	0.044000|0.044000	0.13992|0.13992	1.121000|1.121000	0.41925|0.41925	0.468000|0.468000	0.43344|0.43344	GGT|TGG	.	.		0.552	PHF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056784.2	NM_015107		T	54022132	C	T	54022132	2	4	128	1	0	0	0	0	0	0	0	1	11849	581	21	3		3	PHF8	23	54022132	Silent	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	3645470	54022132	101248428	97	21171										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	105011411	105011411	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	caggctgatctccctgaattCcacccttcagattcaatgca	6	14	3	3			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chrX:105011411C>A	ENST00000372582.1	+	11	2574	c.1818C>A	c.(1816-1818)ttC>ttA	p.F606L	IL1RAPL2_ENST00000344799.4_Missense_Mutation_p.F606L	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	606			F -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.F606L(2)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TCCCTGAATTCCACCCTTCAG	0.478																																					p.F606L		Atlas-SNP	.											.	IL1RAPL2	105	.	2	Substitution - Missense(2)	breast(2)	c.C1818A						.						105	92	97					X																	105011411		2203	4300	6503	SO:0001583	missense	26280	exon11			TGAATTCCACCCT	AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1818C>A	chrX.hg19:g.105011411C>A	ENSP00000361663:p.Phe606Leu	201.0	0.0		260.0	225.0	NM_017416	Q2M3U3|Q9NZN0	Missense_Mutation	SNP	ENST00000372582.1	hg19	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.653126	0.29425	.	.	ENSG00000189108	ENST00000372582;ENST00000344799;ENST00000538500	T;T;T	0.04194	3.96;3.96;3.68	5.89	5.02	0.67125	.	0.419105	0.25380	N	0.031098	T	0.05686	0.0149	L	0.47716	1.5	0.47123	D	0.999328	B	0.02656	0.0	B	0.04013	0.001	T	0.35101	-0.9802	10	0.17369	T	0.5	.	12.5146	0.56026	0.0:0.9191:0.0:0.0809	.	606	Q9NP60	IRPL2_HUMAN	L	606;606;211	ENSP00000361663:F606L;ENSP00000344976:F606L;ENSP00000445576:F211L	ENSP00000344976:F606L	F	+	3	2	IL1RAPL2	104898067	1.000000	0.71417	1.000000	0.80357	0.295000	0.27426	3.029000	0.49712	2.492000	0.84095	0.597000	0.82753	TTC	.	.		0.478	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		A	105011411	C	A	105011411	3	1	128	1	0	0	0	0	1	0	0	0	7671	854	30	3	1856	3	IL1RAPL2	23	105011411	Missense_Mutation	SNP	C	TCGA-DD-A4NF-01A-11D-A27I-10	50989279	105011411	50259149	98	21172										
DCAF12L1	139170	hgsc.bcm.edu	37	chrX	125685361	125685361	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	ccagaaatcattgtggttgaGccagcctctgccacaggcaa	10	12	2	2			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chrX:125685361G>A	ENST00000371126.1	-	1	1473	c.1231C>T	c.(1231-1233)Ctc>Ttc	p.L411F		NM_178470.4	NP_848565.2	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	411										breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(39)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68						TTGTGGTTGAGCCAGCCTCTG	0.557																																					p.L411F		Atlas-SNP	.											.	DCAF12L1	135	.	0			c.C1231T						.						90	84	86					X																	125685361		2203	4300	6503	SO:0001583	missense	139170	exon1			GGTTGAGCCAGCC	BC035674	CCDS14610.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198889	ENSG00000198889		"WD repeat domain containing"	29395	protein-coding gene	gene with protein product			"WD repeat domain 40B"	WDR40B		12477932	Standard	NM_178470		Approved	KIAA1892L	uc004eul.3	Q5VU92	OTTHUMG00000022353	ENST00000371126.1:c.1231C>T	chrX.hg19:g.125685361G>A	ENSP00000360167:p.Leu411Phe	218.0	1.0		281.0	132.0	NM_178470	Q8IYK3	Missense_Mutation	SNP	ENST00000371126.1	hg19	CCDS14610.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.681043	0.29872	.	.	ENSG00000198889	ENST00000371126	T	0.21734	1.99	4.0	2.16	0.27623	.	0.000000	0.32593	N	0.005885	T	0.28067	0.0692	M	0.71581	2.175	0.30613	N	0.759294	D	0.53619	0.961	P	0.50405	0.64	T	0.20240	-1.0281	10	0.51188	T	0.08	.	5.7817	0.18310	0.1115:0.0:0.691:0.1976	.	411	Q5VU92	DC121_HUMAN	F	411	ENSP00000360167:L411F	ENSP00000360167:L411F	L	-	1	0	DCAF12L1	125513042	1.000000	0.71417	0.830000	0.32933	0.073000	0.16967	2.899000	0.48679	0.439000	0.26476	0.513000	0.50165	CTC	.	.		0.557	DCAF12L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058186.1	NM_178470		A	125685361	G	A	125685361	3	1	128	1	0	0	0	0	1	0	0	0	4266	971	34	3	164	3	DCAF12L1	23	125685361	Missense_Mutation	SNP	G	TCGA-DD-A4NF-01A-11D-A27I-10	20673950	125685361	29585199	99	21173										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153129931	153129931	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	4	1	0.589827074741336	0.578484246380925	0.593707516022529	0.569230769230769	1	0	agggaagccccacccttctcTtctgccagggagagagggtg	14	12	2	1			TCGA-DD-A4NF-01A-11D-A27I-10	TCGA-DD-A4NF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22ec33a5-0591-489b-acaa-9a7dae5f9f59	b191ad27-9a0d-4b6e-9e4f-b019a8aa53be	g.chrX:153129931T>C	ENST00000370060.1	-	25	3357	c.3168A>G	c.(3166-3168)gaA>gaG	p.E1056E	L1CAM_ENST00000361981.3_Splice_Site_p.E1051E|L1CAM_ENST00000370055.1_Splice_Site_p.E1051E|L1CAM_ENST00000543994.1_Splice_Site_p.E1058E|L1CAM_ENST00000361699.4_Splice_Site_p.E1056E|L1CAM_ENST00000370057.3_Splice_Site_p.E1056E|L1CAM_ENST00000538883.1_Splice_Site_p.E1058E	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	1056	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CACCCTTCTCTTCTGCCAGGG	0.632																																					p.E1056E		Atlas-SNP	.											.	L1CAM	189	.	0			c.A3168G						.						86	79	81					X																	153129931		2203	4300	6503	SO:0001630	splice_region_variant	3897	exon24			CTTCTCTTCTGCC	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.3167-1A>G	chrX.hg19:g.153129931T>C		98.0	0.0		90.0	44.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Silent	SNP	ENST00000370060.1	hg19	CCDS14733.1																																																																																			.	.		0.632	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003	Silent	C	153129931	T	C	153129931	5	2	128	1	0	0	0	0	0	0	1	0	8597	1623	56	2	625	2	L1CAM	23	153129931	Splice_Site	SNP	T	TCGA-DD-A4NF-01A-11D-A27I-10	27444570	153129931	2140629	100	21174										
CCDC30	728621	hgsc.bcm.edu	37	chr1	43076659	43076659	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tgtttttcagcatgtcaaaaGcaaccaggaattgtcagaga	9	7	3	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr1:43076659G>A	ENST00000340612.4	+	9	1394	c.1394G>A	c.(1393-1395)aGc>aAc	p.S465N	CCDC30_ENST00000342022.4_Missense_Mutation_p.S465N|CCDC30_ENST00000428554.2_Missense_Mutation_p.S465N|CCDC30_ENST00000507855.1_Missense_Mutation_p.S254N|CCDC30_ENST00000390640.4_Missense_Mutation_p.S254N			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	465						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						CATGTCAAAAGCAACCAGGAA	0.353																																					p.S465N		Atlas-SNP	.											.	CCDC30	78	.	0			c.G1394A						.						97	93	94					1																	43076659		2203	4300	6503	SO:0001583	missense	728621	exon10			TCAAAAGCAACCA	AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"prefoldin 6-like"					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1394G>A	chr1.hg19:g.43076659G>A	ENSP00000340378:p.Ser465Asn	62.0	0.0		35.0	9.0	NM_001080850	Q14F06|Q5VVM5	Missense_Mutation	SNP	ENST00000340612.4	hg19	CCDS30690.1	.	.	.	.	.	.	.	.	.	.	G	3.607	-0.080286	0.07141	.	.	ENSG00000186409	ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	5.68	-0.387	0.12463	.	0.599099	0.18985	N	0.125775	T	0.33294	0.0858	L	0.46741	1.465	0.29212	N	0.874542	B;B	0.20368	0.01;0.044	B;B	0.26416	0.015;0.069	T	0.17653	-1.0362	10	0.23891	T	0.37	.	4.1754	0.10349	0.4932:0.1846:0.3222:0.0	.	465;254	Q5VVM6;Q5VVM6-2	CCD30_HUMAN;.	N	465;254;465;465;254	ENSP00000397035:S465N;ENSP00000426711:S254N;ENSP00000340378:S465N;ENSP00000339280:S465N;ENSP00000375051:S254N	ENSP00000340378:S465N	S	+	2	0	CCDC30	42849246	0.997000	0.39634	0.991000	0.47740	0.008000	0.06430	0.388000	0.20735	0.026000	0.15269	-0.251000	0.11542	AGC	.	.		0.353	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030		A	43076659	G	A	43076659	3	1	129	1	0	0	0	0	1	0	0	0	2807	971	34	3	1428	3	CCDC30	1	43076659	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10		43076659	206173962	1	21175										
CD1B	910	hgsc.bcm.edu	37	chr1	158301185	158301185	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	taccaccaggaaagagaacaGctaacagttgaaatggcagc	10	9	0	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr1:158301185G>T	ENST00000368168.3	-	1	136	c.29C>A	c.(28-30)gCt>gAt	p.A10D		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	10					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					AAAGAGAACAGCTAACAGTTG	0.468																																					p.A10D		Atlas-SNP	.											.	CD1B	78	.	0			c.C29A						.						81	73	76					1																	158301185		2203	4300	6503	SO:0001583	missense	910	exon1			AGAACAGCTAACA	M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1635	protein-coding gene	gene with protein product		188360	"CD1B antigen, b polypeptide", "CD1b antigen"	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.29C>A	chr1.hg19:g.158301185G>T	ENSP00000357150:p.Ala10Asp	271.0	0.0		292.0	62.0	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Missense_Mutation	SNP	ENST00000368168.3	hg19	CCDS1176.1	.	.	.	.	.	.	.	.	.	.	G	8.634	0.894454	0.17613	.	.	ENSG00000158485	ENST00000368168	T	0.01388	4.95	3.14	0.839	0.18907	.	0.870979	0.09334	N	0.816454	T	0.00998	0.0033	M	0.72118	2.19	0.09310	N	1	P;D	0.58268	0.947;0.982	P;P	0.48524	0.58;0.521	T	0.48019	-0.9071	10	0.23302	T	0.38	0.0619	5.6837	0.17790	0.3004:0.0:0.6996:0.0	.	10;10	B4E0D2;P29016	.;CD1B_HUMAN	D	10	ENSP00000357150:A10D	ENSP00000357150:A10D	A	-	2	0	CD1B	156567809	0.000000	0.05858	0.001000	0.08648	0.234000	0.25298	-0.905000	0.04075	0.218000	0.20820	0.650000	0.86243	GCT	.	.		0.468	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764		T	158301185	G	T	158301185	3	4	129	1	0	0	0	0	1	0	0	0	2977	971	34	3	996	3	CD1B	1	158301185	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	115224526	158301185	90949436	2	21176										
DARC	2532	hgsc.bcm.edu	37	chr1	159175737	159175737	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	caggcctcaccctggggctcActgtgggaatttggggagtg	16	10	2	0			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr1:159175737A>T	ENST00000368122.2	+	2	1187	c.508A>T	c.(508-510)Act>Tct	p.T170S	CTA-134P22.2_ENST00000609696.1_RNA|DARC_ENST00000537147.1_Missense_Mutation_p.T170S|DARC_ENST00000368121.2_Missense_Mutation_p.T172S	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		170					chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					CCTGGGGCTCACTGTGGGAAT	0.627																																					p.T172S		Atlas-SNP	.											.	DARC	76	.	0			c.A514T						.						38	32	34					1																	159175737		2203	4300	6503	SO:0001583	missense	2532	exon1			GGGCTCACTGTGG																												ENST00000368122.2:c.508A>T	chr1.hg19:g.159175737A>T	ENSP00000357104:p.Thr170Ser	92.0	0.0		104.0	23.0	NM_001122951	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Missense_Mutation	SNP	ENST00000368122.2	hg19	CCDS1183.1	.	.	.	.	.	.	.	.	.	.	A	0.006	-2.116638	0.00349	.	.	ENSG00000213088	ENST00000368122;ENST00000537147;ENST00000359381;ENST00000368121	T;T;T	0.36157	1.27;1.27;1.27	4.8	-6.86	0.01676	.	1.437920	0.05370	N	0.535262	T	0.04048	0.0113	N	0.19112	0.55	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.12837	0.008;0.005	T	0.21518	-1.0243	10	0.08837	T	0.75	-15.3394	1.028	0.01532	0.3298:0.3145:0.1458:0.2099	.	172;170	Q5Y7A1;Q16570	.;DUFFY_HUMAN	S	170;170;170;172	ENSP00000357104:T170S;ENSP00000441985:T170S;ENSP00000357103:T172S	ENSP00000352341:T170S	T	+	1	0	DARC	157442361	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.796000	0.04575	-1.454000	0.01926	-3.678000	0.00024	ACT	.	.		0.627	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2			T	159175737	A	T	159175737	3	4	129	1	0	0	0	0	1	0	0	0	4242	159	6	4	541	4	DARC	1	159175737	Missense_Mutation	SNP	A	TCGA-DD-A4NG-01A-11D-A27I-10	874552	159175737	90074884	3	21177										
ANGPTL1	9068	hgsc.bcm.edu	37	chr1	178822882	178822882	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	atataaatcccactgaccgaAtgcccagcttcttttgcttg	6	12	1	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr1:178822882A>G	ENST00000234816.2	-	4	1311	c.864T>C	c.(862-864)caT>caC	p.H288H	ANGPTL1_ENST00000367629.1_Silent_p.H288H|RALGPS2_ENST00000367635.3_Intron|RALGPS2_ENST00000367634.2_Intron	NM_004673.3	NP_004664.1	O95841	ANGL1_HUMAN	angiopoietin-like 1	288	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(2)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	14						CACTGACCGAATGCCCAGCTT	0.373																																					p.H288H		Atlas-SNP	.											.	ANGPTL1	41	.	0			c.T864C						.						101	97	98					1																	178822882		2203	4300	6503	SO:0001819	synonymous_variant	9068	exon4			GACCGAATGCCCA	AF107253	CCDS1327.1	1q25.2	2013-02-06			ENSG00000116194	ENSG00000116194		"Fibrinogen C domain containing"	489	protein-coding gene	gene with protein product	"angioarrestin"	603874		ANGPT3		10025962, 9286704	Standard	NM_004673		Approved	ANG3, AngY, ARP1	uc001gma.3	O95841	OTTHUMG00000035075	ENST00000234816.2:c.864T>C	chr1.hg19:g.178822882A>G		113.0	0.0		112.0	19.0	NM_004673	Q5T5Z5	Silent	SNP	ENST00000234816.2	hg19	CCDS1327.1																																																																																			.	.		0.373	ANGPTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084924.1	NM_004673		G	178822882	A	G	178822882	2	3	129	1	0	0	0	0	0	0	0	1	613	98	4	2		2	ANGPTL1	1	178822882	Silent	SNP	A	TCGA-DD-A4NG-01A-11D-A27I-10	19647145	178822882	70427739	4	21178										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181767517	181767517	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	cggcagctcccacccgtcccGccaaagccccggcccctcct	8	24	0	0	rs377180948		TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr1:181767517G>A	ENST00000367573.2	+	48	6489	c.6489G>A	c.(6487-6489)ccG>ccA	p.P2163P	CACNA1E_ENST00000360108.3_Silent_p.P2144P|CACNA1E_ENST00000358338.5_Silent_p.P2052P|CACNA1E_ENST00000367570.1_Silent_p.P2120P|CACNA1E_ENST00000526775.1_Silent_p.P2101P|CACNA1E_ENST00000367567.4_Silent_p.P1727P|CACNA1E_ENST00000357570.5_Silent_p.P2114P	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2163					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.P2120P(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CACCCGTCCCGCCAAAGCCCC	0.627													G|||	1	0.000199681	8e-04	0	5008	,	,		16398	0		0	False		,,,				2504	0				p.P2163P		Atlas-SNP	.											CACNA1E_ENST00000367573,caecum,carcinoma,+1,1	CACNA1E	778	.	1	Substitution - coding silent(1)	ovary(1)	c.G6489A						.						79	91	87					1																	181767517		1989	4156	6145	SO:0001819	synonymous_variant	777	exon48			CGTCCCGCCAAAG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6489G>A	chr1.hg19:g.181767517G>A		89.0	1.0		111.0	34.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.627	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181767517	G	A	181767517	2	1	129	1	0	0	0	0	0	0	0	1	2544	1074	38	1		1	CACNA1E	1	181767517	Silent	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	2944635	181767517	67483104	5	21179										
TGFB2	7042	hgsc.bcm.edu	37	chr1	218609331	218609331	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	ggtattgatggcacctccacAtataccagtggtgatcagaa	10	9	1	3			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr1:218609331A>G	ENST00000366930.4	+	5	1241	c.774A>G	c.(772-774)acA>acG	p.T258T	TGFB2_ENST00000479322.1_3'UTR|TGFB2_ENST00000366929.4_Silent_p.T286T	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	258					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		GCACCTCCACATATACCAGTG	0.373																																					p.T286T		Atlas-SNP	.											.	TGFB2	102	.	0			c.A858G						.						82	86	85					1																	218609331		2203	4300	6503	SO:0001819	synonymous_variant	7042	exon6			CTCCACATATACC	M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.774A>G	chr1.hg19:g.218609331A>G		66.0	0.0		73.0	22.0	NM_001135599	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Silent	SNP	ENST00000366930.4	hg19	CCDS1521.1																																																																																			.	.		0.373	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		G	218609331	A	G	218609331	2	3	129	1	0	0	0	0	0	0	0	1	15833	204	8	2		2	TGFB2	1	218609331	Silent	SNP	A	TCGA-DD-A4NG-01A-11D-A27I-10	36841814	218609331	30641290	6	21180										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1093900	1093900	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	agcgcagaactgttacactcCgcagacagccagttggcggc	12	13	0	2	rs192264442	byFrequency	TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr2:1093900C>T	ENST00000308624.5	+	3	358	c.229C>T	c.(229-231)Cgc>Tgc	p.R77C	SNTG2_ENST00000407292.1_Intron	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	77	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		TGTTACACTCCGCAGACAGCC	0.358																																					p.R77C		Atlas-SNP	.											.	SNTG2	125	.	0			c.C229T						.						219	224	223					2																	1093900		1844	4095	5939	SO:0001583	missense	54221	exon3			ACACTCCGCAGAC	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.229C>T	chr2.hg19:g.1093900C>T	ENSP00000311837:p.Arg77Cys	116.0	0.0		88.0	4.0	NM_018968	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	hg19	CCDS46220.1	.	.	.	.	.	.	.	.	.	.	C	6.641	0.486677	0.12641	.	.	ENSG00000172554	ENST00000308624	T	0.27557	1.66	4.68	4.68	0.58851	PDZ/DHR/GLGF (3);	0.191315	0.44483	D	0.000445	T	0.31734	0.0806	L	0.53729	1.69	0.80722	D	1	B	0.21688	0.059	B	0.19666	0.026	T	0.10428	-1.0630	10	0.45353	T	0.12	.	15.3884	0.74723	0.0:1.0:0.0:0.0	.	77	Q9NY99	SNTG2_HUMAN	C	77	ENSP00000311837:R77C	ENSP00000311837:R77C	R	+	1	0	SNTG2	1083900	0.996000	0.38824	1.000000	0.80357	0.026000	0.11368	1.692000	0.37731	2.121000	0.65114	0.563000	0.77884	CGC	.	C|0.998;A|0.002		0.358	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		T	1093900	C	T	1093900	3	4	129	1	0	0	0	0	1	0	0	0	14890	652	23	1	239	1	SNTG2	2	1093900	Missense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10		1093900	242105473	7	21181										
NBAS	51594	hgsc.bcm.edu	37	chr2	15378653	15378653	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gggtttccaggtgggcaagtGatttctccagatgattcaaa	12	7	2	3			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr2:15378653G>C	ENST00000281513.5	-	45	5907	c.5882C>G	c.(5881-5883)tCa>tGa	p.S1961*	NBAS_ENST00000441750.1_Nonsense_Mutation_p.S1841*	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1961					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						GTGGGCAAGTGATTTCTCCAG	0.408																																					p.S1961X		Atlas-SNP	.											.	NBAS	246	.	0			c.C5882G						.						106	107	107					2																	15378653		2203	4300	6503	SO:0001587	stop_gained	51594	exon45			GCAAGTGATTTCT	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.5882C>G	chr2.hg19:g.15378653G>C	ENSP00000281513:p.Ser1961*	120.0	0.0		82.0	35.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Nonsense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	48|48	14.352992|14.352992	0.99791|0.99791	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000442506|ENST00000441750;ENST00000281513;ENST00000417461	.|.	.|.	.|.	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	.|0.101468	.|0.64402	.|D	.|0.000003	D|.	0.82384|.	0.5025|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.83259|.	-0.0049|.	3|.	.|0.87932	.|D	.|0	.|.	20.4238|20.4238	0.99064|0.99064	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	D|X	1009|1841;1961;53	.|.	.|ENSP00000281513:S1961X	H|S	-|-	1|2	0|0	NBAS|NBAS	15296104|15296104	1.000000|1.000000	0.71417|0.71417	0.592000|0.592000	0.28758|0.28758	0.979000|0.979000	0.70002|0.70002	8.491000|8.491000	0.90468|0.90468	2.828000|2.828000	0.97474|0.97474	0.655000|0.655000	0.94253|0.94253	CAC|TCA	.	.		0.408	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		C	15378653	G	C	15378653	4	2	129	1	0	0	0	0	0	1	0	0	10195	1294	45	4	1265	4	NBAS	2	15378653	Nonsense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	14284753	15378653	227820720	8	21182										
APOB	338	hgsc.bcm.edu	37	chr2	21229380	21229381	+	Frame_Shift_Ins	INS	-	-	A													0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	aattccatggaggaagagacINSagtaggttttgacttggtat							TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr2:21229380_21229381insA	ENST00000233242.1	-	26	10486_10487	c.10359_10360insT	c.(10357-10362)actgtcfs	p.V3454fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3454	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGGAAGAGACAGTAGGTTTTG	0.391																																					p.V3454fs		Atlas-Indel,Pindel	.											.	APOB	761	.	0			c.10360_10361insT						.																																			SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10360dupT	chr2.hg19:g.21229381_21229381dupA	ENSP00000233242:p.Val3454fs	196.0	0.0		181.0	58.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.391	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21229381	-	A	21229380	7	5	129	1	0	1	1	0	0	0	0	0	785	478	17	0	3347	0	APOB	2	21229380	Frame_Shift_Ins	INS	-	TCGA-DD-A4NG-01A-11D-A27I-10	5850727	21229380	221969993	9	21183										
LHCGR	3973	hgsc.bcm.edu	37	chr2	48958372	48958372	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	agtaacttacttacatttttAtgacctcattaagtcctctg	4	9	2	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr2:48958372A>C	ENST00000294954.7	-	2	248	c.227T>G	c.(226-228)aTa>aGa	p.I76R	LHCGR_ENST00000405626.1_Missense_Mutation_p.I76R|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000344775.3_Missense_Mutation_p.I76R|LHCGR_ENST00000403273.1_Missense_Mutation_p.I76R|LHCGR_ENST00000401907.1_Missense_Mutation_p.I76R	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	76					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	TTACATTTTTATGACCTCATT	0.328																																					p.I76R		Atlas-SNP	.											LHCGR,NS,carcinoma,0,1	LHCGR	154	.	0			c.T227G						.						90	91	90					2																	48958372		2203	4300	6503	SO:0001583	missense	3973	exon2			ATTTTTATGACCT		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"GPCR / Class A : Gonadotropin and TSH receptors"	6585	protein-coding gene	gene with protein product		152790	"hypergonadotropic hypogonadism"	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.227T>G	chr2.hg19:g.48958372A>C	ENSP00000294954:p.Ile76Arg	31.0	0.0		29.0	11.0	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	hg19	CCDS1842.1	.	.	.	.	.	.	.	.	.	.	A	6.720	0.501628	0.12822	.	.	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000405626;ENST00000403273;ENST00000401907;ENST00000428232	D;D;D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52;-1.52;-1.52	5.89	4.75	0.60458	.	0.993034	0.08199	N	0.982596	T	0.70745	0.3259	N	0.05230	-0.09	0.34550	D	0.711215	P	0.44690	0.841	P	0.49387	0.609	T	0.66712	-0.5854	9	.	.	.	.	9.3413	0.38082	0.9198:0.0:0.0802:0.0	.	76	P22888	LSHR_HUMAN	R	76;76;76;76;76;42	ENSP00000344301:I76R;ENSP00000294954:I76R;ENSP00000386033:I76R;ENSP00000385847:I76R;ENSP00000385406:I76R;ENSP00000403748:I42R	.	I	-	2	0	LHCGR	48811876	0.983000	0.35010	0.934000	0.37439	0.964000	0.63967	3.136000	0.50554	2.247000	0.74100	0.482000	0.46254	ATA	.	.		0.328	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3		C	48958372	A	C	48958372	3	2	129	1	0	0	0	0	1	0	0	0	8771	449	16	5	1912	5	LHCGR	2	48958372	Missense_Mutation	SNP	A	TCGA-DD-A4NG-01A-11D-A27I-10	27728992	48958372	194241001	10	21184										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54876897	54876897	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	cgctgaatggaaggatggccTcaatgaagcctgggccgacc	14	11	1	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr2:54876897T>G	ENST00000356805.4	+	26	5629	c.5348T>G	c.(5347-5349)cTc>cGc	p.L1783R	SPTBN1_ENST00000333896.5_Missense_Mutation_p.L1770R	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1783	Interaction with ANK2.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			AAGGATGGCCTCAATGAAGCC	0.537																																					p.L1783R		Atlas-SNP	.											.	SPTBN1	378	.	0			c.T5348G						.						82	76	78					2																	54876897		2203	4300	6503	SO:0001583	missense	6711	exon26			ATGGCCTCAATGA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.5348T>G	chr2.hg19:g.54876897T>G	ENSP00000349259:p.Leu1783Arg	279.0	0.0		258.0	80.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.576172	0.86645	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.64803	-0.12;-0.12	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.85843	0.5791	H	0.95917	3.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.90388	0.4393	10	0.87932	D	0	.	16.0606	0.80836	0.0:0.0:0.0:1.0	.	1770;1783	Q01082-3;Q01082	.;SPTB2_HUMAN	R	1783;1770	ENSP00000349259:L1783R;ENSP00000334156:L1770R	ENSP00000334156:L1770R	L	+	2	0	SPTBN1	54730401	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.945000	0.87732	2.201000	0.70794	0.454000	0.30748	CTC	.	.		0.537	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			G	54876897	T	G	54876897	3	3	129	1	0	0	0	0	1	0	0	0	15134	1551	54	5	5559	5	SPTBN1	2	54876897	Missense_Mutation	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	5918525	54876897	188322476	11	21185										
TTN	7273	hgsc.bcm.edu	37	chr2	179499955	179499955	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	ggaatgtctgcctctgagatTtctgcatcaaagcttgcact	9	10	4	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr2:179499955T>G	ENST00000591111.1	-	178	37262	c.37038A>C	c.(37036-37038)gaA>gaC	p.E12346D	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E13987D|TTN_ENST00000342175.6_Missense_Mutation_p.E5114D|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E11419D|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E5047D|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E4922D|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12346					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTCTGAGATTTCTGCATCAA	0.388																																					p.E13987D		Atlas-SNP	.											.	TTN	18412	.	0			c.A41961C						.						184	169	174					2																	179499955		1879	4108	5987	SO:0001583	missense	7273	exon228			TGAGATTTCTGCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.37038A>C	chr2.hg19:g.179499955T>G	ENSP00000465570:p.Glu12346Asp	130.0	0.0		119.0	39.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.89	1.773424	0.31411	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.37411	1.2;1.2;1.2;1.2	5.85	2.13	0.27403	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60274	0.2256	M	0.87269	2.87	0.39071	D	0.960718	D;D;D;D	0.69078	0.997;0.997;0.997;0.997	D;D;D;D	0.72625	0.978;0.978;0.978;0.978	T	0.63435	-0.6638	9	0.87932	D	0	.	9.5744	0.39447	0.0:0.2588:0.0:0.7412	.	4922;5047;5114;12346	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	11419;4922;5114;5047;4922	ENSP00000343764:E11419D;ENSP00000434586:E4922D;ENSP00000340554:E5114D;ENSP00000352154:E5047D	ENSP00000340554:E5114D	E	-	3	2	TTN	179208200	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.646000	0.37249	0.125000	0.18397	-0.256000	0.11100	GAA	.	.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179499955	T	G	179499955	3	3	129	1	0	0	0	0	1	0	0	0	16750	1838	64	5	66272	5	TTN	2	179499955	Missense_Mutation	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	124623058	179499955	63699418	12	21186										
CYP27A1	1593	hgsc.bcm.edu	37	chr2	219674376	219674376	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gcacgtgaacctggccagtgCcccgctcttggagcaagtga	13	13	1	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr2:219674376C>T	ENST00000258415.4	+	2	759	c.332C>T	c.(331-333)gCc>gTc	p.A111V		NM_000784.3	NP_000775.1	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A, polypeptide 1	111					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	cholestanetriol 26-monooxygenase activity (GO:0047749)|cholesterol 26-hydroxylase activity (GO:0031073)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(3)|urinary_tract(1)	26		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Chenodeoxycholic acid(DB06777)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Pegvisomant(DB00082)	CTGGCCAGTGCCCCGCTCTTG	0.547																																					p.A111V		Atlas-SNP	.											.	CYP27A1	52	.	0			c.C332T						.						144	127	133					2																	219674376		2203	4300	6503	SO:0001583	missense	1593	exon2			CCAGTGCCCCGCT	BC017044	CCDS2423.1	2q35	2013-09-19	2003-01-14		ENSG00000135929	ENSG00000135929		"Cytochrome P450s"	2605	protein-coding gene	gene with protein product	"cerebrotendinous xanthomatosis"	606530	"cytochrome P450, subfamily XXVIIA (steroid 27-hydroxylase, cerebrotendinous xanthomatosis), polypeptide 1"	CYP27		2019602	Standard	NM_000784		Approved	CTX, CP27	uc002viz.4	Q02318	OTTHUMG00000048238	ENST00000258415.4:c.332C>T	chr2.hg19:g.219674376C>T	ENSP00000258415:p.Ala111Val	211.0	0.0		205.0	73.0	NM_000784	A8K303|Q6LDB4|Q86YQ6	Missense_Mutation	SNP	ENST00000258415.4	hg19	CCDS2423.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.292194	0.59976	.	.	ENSG00000135929	ENST00000258415;ENST00000411688	T;T	0.69040	-0.37;-0.37	5.67	5.67	0.87782	.	0.154974	0.56097	D	0.000021	T	0.57917	0.2086	L	0.43923	1.385	0.47441	D	0.999426	P	0.37370	0.592	B	0.37091	0.241	T	0.56366	-0.7991	10	0.30854	T	0.27	-25.2004	12.112	0.53844	0.0:0.9226:0.0:0.0774	.	111	Q02318	CP27A_HUMAN	V	111;17	ENSP00000258415:A111V;ENSP00000392671:A17V	ENSP00000258415:A111V	A	+	2	0	CYP27A1	219382620	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	6.510000	0.73729	2.677000	0.91161	0.655000	0.94253	GCC	.	.		0.547	CYP27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109734.4			T	219674376	C	T	219674376	3	4	129	1	0	0	0	0	1	0	0	0	4160	739	26	3	338	3	CYP27A1	2	219674376	Missense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10	40174421	219674376	23524997	13	21187										
GADL1	339896	hgsc.bcm.edu	37	chr3	30819694	30819694	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	attaagttttgcccagaactCgggtccttcttccatctctc	6	13	2	1	rs145224145		TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr3:30819694C>A	ENST00000282538.5	-	14	1519	c.1369G>T	c.(1369-1371)Gag>Tag	p.E457*	GADL1_ENST00000498387.1_5'UTR	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	457					carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						GCCCAGAACTCGGGTCCTTCT	0.328																																					p.E457X		Atlas-SNP	.											.	GADL1	91	.	0			c.G1369T						.						78	82	81					3																	30819694		2203	4300	6503	SO:0001587	stop_gained	339896	exon14			AGAACTCGGGTCC	AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644			27949	protein-coding gene	gene with protein product		615601					Standard	NM_207359		Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.1369G>T	chr3.hg19:g.30819694C>A	ENSP00000282538:p.Glu457*	298.0	1.0		230.0	78.0	NM_207359		Nonsense_Mutation	SNP	ENST00000282538.5	hg19	CCDS2649.2	.	.	.	.	.	.	.	.	.	.	C	41	8.641858	0.98897	.	.	ENSG00000144644	ENST00000282538	.	.	.	6.02	5.13	0.70059	.	0.057263	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-11.7558	16.0963	0.81127	0.0:0.8656:0.1344:0.0	.	.	.	.	X	457	.	ENSP00000282538:E457X	E	-	1	0	GADL1	30794698	1.000000	0.71417	0.944000	0.38274	0.996000	0.88848	5.913000	0.69957	1.521000	0.48983	0.655000	0.94253	GAG	.	C|1.000;T|0.000		0.328	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359		A	30819694	C	A	30819694	4	1	129	1	0	0	0	0	0	1	0	0	6193	893	31	1	204	1	GADL1	3	30819694	Nonsense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10		30819694	167202736	14	21188										
SNRK	54861	hgsc.bcm.edu	37	chr3	43381915	43381915	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	cccttgtgtcatacaaaaatCtctcggaagaggagcacaac	8	11	2	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr3:43381915C>G	ENST00000296088.7	+	5	1172	c.868C>G	c.(868-870)Ctc>Gtc	p.L290V	SNRK_ENST00000429705.2_Missense_Mutation_p.L290V|SNRK_ENST00000437827.1_Missense_Mutation_p.L84V|SNRK_ENST00000454177.1_Missense_Mutation_p.L290V	NM_017719.4	NP_060189.3			SNF related kinase											breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(5)|prostate(1)|skin(2)|stomach(1)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)		ATACAAAAATCTCTCGGAAGA	0.478																																					p.L290V		Atlas-SNP	.											.	SNRK	118	.	0			c.C868G						.						87	90	89					3																	43381915		1958	4149	6107	SO:0001583	missense	54861	exon5			AAAAATCTCTCGG	D43636	CCDS43075.1	3p22.1	2005-08-09			ENSG00000163788	ENSG00000163788			30598	protein-coding gene	gene with protein product		612760				8654423, 7788527	Standard	NM_017719		Approved	FLJ20224, HSNFRK, KIAA0096	uc003cmt.4	Q9NRH2	OTTHUMG00000156491	ENST00000296088.7:c.868C>G	chr3.hg19:g.43381915C>G	ENSP00000296088:p.Leu290Val	200.0	0.0		217.0	70.0	NM_017719		Missense_Mutation	SNP	ENST00000296088.7	hg19	CCDS43075.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.844580	0.71488	.	.	ENSG00000163788	ENST00000454177;ENST00000429705;ENST00000296088;ENST00000437827	D;D;D;T	0.82893	-1.66;-1.66;-1.66;-0.81	5.33	5.33	0.75918	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.77685	0.4167	L	0.41573	1.285	0.80722	D	1	B	0.25904	0.137	B	0.31614	0.133	T	0.71751	-0.4498	10	0.06365	T	0.9	.	19.3838	0.94548	0.0:1.0:0.0:0.0	.	290	Q9NRH2	SNRK_HUMAN	V	290;290;290;84	ENSP00000401246:L290V;ENSP00000411375:L290V;ENSP00000296088:L290V;ENSP00000409516:L84V	ENSP00000296088:L290V	L	+	1	0	SNRK	43356919	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	4.920000	0.63390	2.670000	0.90874	0.655000	0.94253	CTC	.	.		0.478	SNRK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344325.1	NM_017719		G	43381915	C	G	43381915	3	3	129	1	0	0	0	0	1	0	0	0	14866	913	32	4	878	4	SNRK	3	43381915	Missense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10	12562221	43381915	154640515	15	21189										
OR5K3	403277	hgsc.bcm.edu	37	chr3	98109590	98109590	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	ccaaagctgaagactgttctGtttgtggtgttctttgccat	10	8	2	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr3:98109590G>C	ENST00000383695.1	+	1	81	c.81G>C	c.(79-81)ctG>ctC	p.L27L	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	27						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						AGACTGTTCTGTTTGTGGTGT	0.418																																					p.L27L		Atlas-SNP	.											.	OR5K3	60	.	0			c.G81C						.						236	216	223					3																	98109590		2203	4300	6503	SO:0001819	synonymous_variant	403277	exon1			TGTTCTGTTTGTG		CCDS33803.1	3q11.2	2013-09-23			ENSG00000206536	ENSG00000206536		"GPCR / Class A : Olfactory receptors"	31290	protein-coding gene	gene with protein product							Standard	NM_001005516		Approved		uc011bgw.2	A6NET4	OTTHUMG00000160077	ENST00000383695.1:c.81G>C	chr3.hg19:g.98109590G>C		289.0	0.0		218.0	58.0	NM_001005516		Silent	SNP	ENST00000383695.1	hg19	CCDS33803.1																																																																																			.	.		0.418	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359110.1			C	98109590	G	C	98109590	2	2	129	1	0	0	0	0	0	0	0	1	11177	1364	48	4		4	OR5K3	3	98109590	Silent	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	54727675	98109590	99912840	16	21190										
ST3GAL6	10402	hgsc.bcm.edu	37	chr3	98487331	98487331	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	cctgagtgctgtcttcctctAttatgtactgcattgcatat	7	10	2	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr3:98487331A>C	ENST00000483910.1	+	2	336	c.47A>C	c.(46-48)tAt>tCt	p.Y16S	ST3GAL6_ENST00000468553.1_Missense_Mutation_p.Y16S|ST3GAL6_ENST00000265261.6_5'UTR|ST3GAL6_ENST00000394162.1_Missense_Mutation_p.Y16S|ST3GAL6_ENST00000462152.1_Intron	NM_001271146.1	NP_001258075.1	Q9Y274	SIA10_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	16					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|cellular response to interleukin-6 (GO:0071354)|glycolipid metabolic process (GO:0006664)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,3-sialyltransferase activity (GO:0052798)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(1)	19						GTCTTCCTCTATTATGTACTG	0.398																																					p.Y69S		Atlas-SNP	.											.	ST3GAL6	41	.	0			c.A206C						.						249	230	237					3																	98487331		2203	4300	6503	SO:0001583	missense	10402	exon2			TCCTCTATTATGT	AF119391	CCDS2933.1, CCDS59452.1, CCDS74968.1	3q12.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000064225	ENSG00000064225		"Sialyltransferases"	18080	protein-coding gene	gene with protein product		607156	"sialyltransferase 10 (alpha-2,3-sialyltransferase VI)"	SIAT10		10206952	Standard	NM_006100		Approved	ST3GALVI	uc010hpd.4	Q9Y274	OTTHUMG00000159047	ENST00000483910.1:c.47A>C	chr3.hg19:g.98487331A>C	ENSP00000417376:p.Tyr16Ser	188.0	0.0		121.0	41.0	NM_001271145	B2RCH2|B3KMI1|D3DN39|F8W6U0	Missense_Mutation	SNP	ENST00000483910.1	hg19	CCDS2933.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.066198	0.55539	.	.	ENSG00000064225	ENST00000483910;ENST00000460774;ENST00000497008;ENST00000486334;ENST00000394162;ENST00000468553;ENST00000485391;ENST00000492254	T;T;T;T	0.53206	0.68;0.63;0.68;0.73	6.06	6.06	0.98353	.	0.194728	0.36740	N	0.002429	T	0.46132	0.1377	L	0.32530	0.975	0.80722	D	1	D;P	0.54397	0.966;0.895	P;B	0.49012	0.598;0.307	T	0.47302	-0.9128	10	0.62326	D	0.03	-7.9031	13.0011	0.58676	1.0:0.0:0.0:0.0	.	39;16	C9J480;Q9Y274	.;SIA10_HUMAN	S	16;16;16;16;16;16;16;39	ENSP00000417376:Y16S;ENSP00000418896:Y16S;ENSP00000377717:Y16S;ENSP00000417201:Y39S	ENSP00000377717:Y16S	Y	+	2	0	ST3GAL6	99970021	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	4.619000	0.61218	2.324000	0.78689	0.533000	0.62120	TAT	.	.		0.398	ST3GAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353013.2	NM_006100		C	98487331	A	C	98487331	3	2	129	1	0	0	0	0	1	0	0	0	15234	449	16	5	49	5	ST3GAL6	3	98487331	Missense_Mutation	SNP	A	TCGA-DD-A4NG-01A-11D-A27I-10	377741	98487331	99535099	17	21191										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376101	113376101	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	cttaactgccctgcttgttgTtgttgctgttgctgctgctg	11	10	0	0			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr3:113376101T>C	ENST00000478658.1	-	5	4445	c.4428A>G	c.(4426-4428)caA>caG	p.Q1476Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1476Q			Q68DE3	K2018_HUMAN	KIAA2018	1476	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						CTGCTtgttgttgttgctgtt	0.488																																					p.Q1476Q		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A4428G						.						98	106	103					3																	113376101		2192	4280	6472	SO:0001819	synonymous_variant	205717	exon7			TTGTTGTTGTTGC	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4428A>G	chr3.hg19:g.113376101T>C		121.0	0.0		115.0	7.0	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.		0.488	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		C	113376101	T	C	113376101	2	2	129	1	0	0	0	0	0	0	0	1	8277	1722	60	2		2	KIAA2018	3	113376101	Silent	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	14888770	113376101	84646329	18	21192										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121416717	121416717	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	ctttttctctagtaagagctGatccatttttgttatttcaa	5	7	2	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr3:121416717G>A	ENST00000340645.5	-	13	2763	c.2638C>T	c.(2638-2640)Cag>Tag	p.Q880*	GOLGB1_ENST00000393667.3_Nonsense_Mutation_p.Q885*	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	880					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		AGTAAGAGCTGATCCATTTTT	0.423																																					p.Q885X		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C2653T						.						152	158	156					3																	121416717		2203	4299	6502	SO:0001587	stop_gained	2804	exon13			AGAGCTGATCCAT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.2638C>T	chr3.hg19:g.121416717G>A	ENSP00000341848:p.Gln880*	137.0	0.0		96.0	29.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Nonsense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	G	37	6.399190	0.97537	.	.	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235	.	.	.	5.35	4.48	0.54585	.	0.000000	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	11.8048	0.52147	0.0842:0.0:0.9158:0.0	.	.	.	.	X	880;885;844;692	.	ENSP00000341848:Q880X	Q	-	1	0	GOLGB1	122899407	0.078000	0.21339	0.994000	0.49952	0.914000	0.54420	0.896000	0.28377	1.494000	0.48533	0.655000	0.94253	CAG	.	.		0.423	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121416717	G	A	121416717	4	1	129	1	0	0	0	0	0	1	0	0	6573	1299	45	3	7181	3	GOLGB1	3	121416717	Nonsense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	8040616	121416717	76605713	19	21193										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173998531	173998531	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	atcaactgacatcactttcaGacctacgagaaaaaattctg	5	10	4	3			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr3:173998531G>T	ENST00000457714.1	+	7	2339	c.1910G>T	c.(1909-1911)aGa>aTa	p.R637I	NLGN1_ENST00000401917.3_Missense_Mutation_p.R677I|NLGN1_ENST00000545397.1_Missense_Mutation_p.R637I|NLGN1_ENST00000361589.4_Missense_Mutation_p.R637I	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	654					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			ATCACTTTCAGACCTACGAGA	0.433																																					p.R637I		Atlas-SNP	.											.	NLGN1	209	.	0			c.G1910T						.						122	121	121					3																	173998531		2203	4300	6503	SO:0001583	missense	22871	exon7			CTTTCAGACCTAC	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.1910G>T	chr3.hg19:g.173998531G>T	ENSP00000392500:p.Arg637Ile	186.0	0.0		157.0	53.0	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	hg19	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.389465	0.25118	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000545397;ENST00000401917	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.59	5.59	0.84812	.	0.049426	0.85682	D	0.000000	T	0.56217	0.1970	L	0.36672	1.1	0.80722	D	1	B	0.16166	0.016	B	0.22152	0.038	T	0.49312	-0.8953	10	0.22109	T	0.4	.	13.2118	0.59830	0.0729:0.0:0.9271:0.0	.	637	Q8N2Q7-2	.	I	637;637;637;677	ENSP00000392500:R637I;ENSP00000354541:R637I;ENSP00000441108:R637I;ENSP00000385750:R677I	ENSP00000354541:R637I	R	+	2	0	NLGN1	175481225	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.090000	0.71397	2.793000	0.96121	0.655000	0.94253	AGA	.	.		0.433	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		T	173998531	G	T	173998531	3	4	129	1	0	0	0	0	1	0	0	0	10470	942	33	3	1928	3	NLGN1	3	173998531	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	52581814	173998531	24023899	20	21194										
KCNMB3	27094	hgsc.bcm.edu	37	chr3	178984440	178984440	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	ttccggaagtgacttacctcCcctggcgcctccggctgccc	10	18	0	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr3:178984440C>T	ENST00000349697.2	-	1	319	c.59G>A	c.(58-60)gGg>gAg	p.G20E	KCNMB3_ENST00000497599.1_Missense_Mutation_p.G20E	NM_171828.1	NP_741979.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	0					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	GACTTACCTCCCCTGGCGCCT	0.577																																					p.G20E		Atlas-SNP	.											.	KCNMB3	46	.	0			c.G59A						.						50	49	49					3																	178984440		2203	4300	6503	SO:0001583	missense	27094	exon1			TACCTCCCCTGGC	AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121		"Potassium channels"	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL		10585773	Standard	NM_001163677		Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000349697.2:c.59G>A	chr3.hg19:g.178984440C>T	ENSP00000327866:p.Gly20Glu	87.0	0.0		69.0	29.0	NM_171828	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000349697.2	hg19	CCDS3225.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.965002	0.53507	.	.	ENSG00000171121	ENST00000497599;ENST00000349697	T;T	0.17854	2.25;2.96	5.38	3.46	0.39613	.	.	.	.	.	T	0.17323	0.0416	N	0.08118	0	0.80722	D	1	D;D	0.67145	0.994;0.996	P;D	0.63381	0.865;0.914	T	0.08249	-1.0731	9	0.87932	D	0	.	8.1343	0.31046	0.1803:0.6457:0.174:0.0	.	20;20	E9PER5;Q9NPA1-2	.;.	E	20	ENSP00000417091:G20E;ENSP00000327866:G20E	ENSP00000327866:G20E	G	-	2	0	KCNMB3	180467134	0.943000	0.32029	1.000000	0.80357	0.380000	0.30137	0.671000	0.25172	1.269000	0.44280	0.505000	0.49811	GGG	.	.		0.577	KCNMB3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358530.1			T	178984440	C	T	178984440	3	4	129	1	0	0	0	0	1	0	0	0	8085	623	22	3	997	3	KCNMB3	3	178984440	Missense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10	4985909	178984440	19037990	21	21195										
EHHADH	1962	hgsc.bcm.edu	37	chr3	184947229	184947229	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tctatactgacctgaggtaaTtaagtcaagtgcagcaggaa	10	7	2	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr3:184947229T>C	ENST00000231887.3	-	4	529	c.454A>G	c.(454-456)Att>Gtt	p.I152V	EHHADH_ENST00000456310.1_Missense_Mutation_p.I56V|EHHADH_ENST00000475987.1_5'UTR	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	152	Enoyl-CoA hydratase / isomerase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CCTGAGGTAATTAAGTCAAGT	0.463																																					p.I152V		Atlas-SNP	.											.	EHHADH	73	.	0			c.A454G						.						74	69	71					3																	184947229		2203	4300	6503	SO:0001583	missense	1962	exon4			AGGTAATTAAGTC	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.454A>G	chr3.hg19:g.184947229T>C	ENSP00000231887:p.Ile152Val	120.0	0.0		106.0	40.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	T	15.28	2.786578	0.49997	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.68025	-0.3;-0.3	6.07	6.07	0.98685	Crotonase, core (1);	0.130265	0.64402	D	0.000001	T	0.70833	0.3269	L	0.52759	1.655	0.80722	D	1	D	0.56746	0.977	P	0.52189	0.692	T	0.70718	-0.4795	10	0.41790	T	0.15	-21.2101	15.6102	0.76710	0.0:0.0:0.0:1.0	.	152	Q08426	ECHP_HUMAN	V	152;152;56	ENSP00000231887:I152V;ENSP00000387746:I56V	ENSP00000231887:I152V	I	-	1	0	EHHADH	186429923	1.000000	0.71417	0.973000	0.42090	0.413000	0.31143	4.471000	0.60182	2.330000	0.79161	0.528000	0.53228	ATT	.	.		0.463	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			C	184947229	T	C	184947229	3	2	129	1	0	0	0	0	1	0	0	0	4984	1493	52	2	1733	2	EHHADH	3	184947229	Missense_Mutation	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	5962789	184947229	13075201	22	21196										
OTOP1	133060	hgsc.bcm.edu	37	chr4	4199475	4199475	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	attccagccagccccgcagcCcccataagcatcagcagggt	9	17	1	0			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr4:4199475C>A	ENST00000296358.4	-	5	1110	c.1086G>T	c.(1084-1086)ggG>ggT	p.G362G		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	362					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GCCCCGCAGCCCCCATAAGCA	0.542																																					p.G362G		Atlas-SNP	.											.	OTOP1	118	.	0			c.G1086T						.						41	44	43					4																	4199475		2203	4300	6503	SO:0001819	synonymous_variant	133060	exon5			CGCAGCCCCCATA	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1086G>T	chr4.hg19:g.4199475C>A		179.0	0.0		176.0	54.0	NM_177998	A1L476	Silent	SNP	ENST00000296358.4	hg19	CCDS3372.1																																																																																			.	.		0.542	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		A	4199475	C	A	4199475	2	1	129	1	0	0	0	0	0	0	0	1	11314	610	22	3		3	OTOP1	4	4199475	Silent	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10		4199475	186954801	23	21197										
CENPE	1062	hgsc.bcm.edu	37	chr4	104066455	104066455	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	aacctcactaatttgttttaTattaaattgttcctctttct	2	8	3	0			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr4:104066455T>C	ENST00000265148.3	-	32	4698	c.4609A>G	c.(4609-4611)Ata>Gta	p.I1537V	CENPE_ENST00000380026.3_Missense_Mutation_p.I1512V	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1537					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		ATTTGTTTTATATTAAATTGT	0.294																																					p.I1537V		Atlas-SNP	.											.	CENPE	253	.	0			c.A4609G						.						53	51	51					4																	104066455		2201	4298	6499	SO:0001583	missense	1062	exon32			GTTTTATATTAAA	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.4609A>G	chr4.hg19:g.104066455T>C	ENSP00000265148:p.Ile1537Val	52.0	0.0		49.0	14.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.934242	0.00053	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.66638	-0.21;-0.22	4.09	-5.37	0.02681	.	.	.	.	.	T	0.37812	0.1017	N	0.11427	0.14	0.09310	N	1	B;B	0.20261	0.043;0.001	B;B	0.17722	0.019;0.001	T	0.44620	-0.9316	9	0.02654	T	1	.	11.6933	0.51529	0.0:0.224:0.0:0.776	.	1512;1537	Q02224-3;Q02224	.;CENPE_HUMAN	V	1537;1537;1512	ENSP00000265148:I1537V;ENSP00000369365:I1512V	ENSP00000265148:I1537V	I	-	1	0	CENPE	104285904	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.273000	0.01164	-1.176000	0.02747	-0.404000	0.06349	ATA	.	.		0.294	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	104066455	T	C	104066455	3	2	129	1	0	0	0	0	1	0	0	0	3232	1406	49	2	3568	2	CENPE	4	104066455	Missense_Mutation	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	99866980	104066455	87087821	24	21198										
ADAM19	8728	hgsc.bcm.edu	37	chr5	156918883	156918885	+	In_Frame_Del	DEL	AAG	AAG	-													0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tcccacagccttcagtttcaAagaaggaggtgttcctgcac					rs146858323	byFrequency	TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr5:156918883_156918885delAAG	ENST00000517905.1	-	17	1988_1990	c.1944_1946delCTT	c.(1942-1947)ttcttt>ttt	p.648_649FF>F	ADAM19_ENST00000257527.4_In_Frame_Del_p.648_649FF>F|ADAM19_ENST00000394020.1_In_Frame_Del_p.650_651FF>F|ADAM19_ENST00000430702.2_In_Frame_Del_p.381_382FF>F			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	648	Cys-rich.				heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTCAGTTTCAAAGAAGGAGGTGT	0.557																																					p.649_649del		Atlas-Indel,Pindel	.											.	ADAM19	216	.	0			c.1945_1947del						.																																			SO:0001651	inframe_deletion	8728	exon17			.	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"ADAM metallopeptidase domain containing"	197	protein-coding gene	gene with protein product	"meltrin beta"	603640	"a disintegrin and metalloproteinase domain 19 (meltrin beta)"			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.1944_1946delCTT	chr5.hg19:g.156918886_156918888delAAG	ENSP00000428654:p.Phe649del	208.0	0.0		157.0	44.0	NM_033274	Q9BZL5|Q9UHP2	In_Frame_Del	DEL	ENST00000517905.1	hg19																																																																																				.	.		0.557	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274		-	156918885	AAG	-	156918883	7	5	129	1	0	1	0	1	0	0	0	0	240	14	1	0	838	0	ADAM19	5	156918883	In_Frame_Del	DEL	AAG	TCGA-DD-A4NG-01A-11D-A27I-10		156918883	23996377	25	21199										
CDYL	9425	hgsc.bcm.edu	37	chr6	4935914	4935914	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gcaaacagaaagtgcctacaGatacagagatattgtggtca	10	7	1	3			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr6:4935914G>C	ENST00000328908.5	+	5	1150	c.1019G>C	c.(1018-1020)aGa>aCa	p.R340T	CDYL_ENST00000343762.5_Missense_Mutation_p.R154T|CDYL_ENST00000449732.2_Missense_Mutation_p.R154T|CDYL_ENST00000472453.1_3'UTR|CDYL_ENST00000397588.3_Missense_Mutation_p.R286T			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	340					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		AGTGCCTACAGATACAGAGAT	0.463																																					p.R286T		Atlas-SNP	.											.	CDYL	74	.	0			c.G857C						.						122	114	117					6																	4935914		2203	4300	6503	SO:0001583	missense	9425	exon3			CCTACAGATACAG	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"CDY-like, autosomal", "testis-specific chromodomain Y-like protein"	603778	"chromodomain protein, Y chromosome-like"			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.1019G>C	chr6.hg19:g.4935914G>C	ENSP00000330512:p.Arg340Thr	170.0	1.0		251.0	167.0	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	hg19		.	.	.	.	.	.	.	.	.	.	G	18.86	3.714257	0.68730	.	.	ENSG00000153046	ENST00000328908;ENST00000440139;ENST00000397588;ENST00000449732;ENST00000343762	T;T;T;T	0.58060	0.75;0.36;0.39;0.39	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.31231	0.0790	N	0.25890	0.77	0.80722	D	1	B;B	0.32245	0.254;0.361	B;B	0.34590	0.139;0.186	T	0.10590	-1.0623	9	.	.	.	.	19.6321	0.95713	0.0:0.0:1.0:0.0	.	286;340	Q9Y232-2;Q9Y232	.;CDYL1_HUMAN	T	340;66;286;154;154	ENSP00000330512:R340T;ENSP00000380718:R286T;ENSP00000394076:R154T;ENSP00000340908:R154T	.	R	+	2	0	CDYL	4880913	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.640000	0.98453	2.884000	0.98904	0.655000	0.94253	AGA	.	.		0.463	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		C	4935914	G	C	4935914	3	2	129	1	0	0	0	0	1	0	0	0	3187	942	33	4	867	4	CDYL	6	4935914	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10		4935914	166179153	26	21200										
KPNA5	3841	hgsc.bcm.edu	37	chr6	117019926	117019927	+	Frame_Shift_Del	DEL	AA	AA	-													0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gagttgtacagagatttgtgAaatttcttgaaagaaatgaa							TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr6:117019926_117019927delAA	ENST00000368564.1	+	5	548_549	c.400_401delAA	c.(400-402)aaafs	p.K134fs	KPNA5_ENST00000356348.1_Frame_Shift_Del_p.K134fs			O15131	IMA6_HUMAN	karyopherin alpha 5 (importin alpha 6)	131					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(6)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		GAGATTTGTGAAATTTCTTGAA	0.287																																					p.133_134del		Atlas-Indel,Pindel	.											.	KPNA5	57	.	0			c.399_400del						.																																			SO:0001589	frameshift_variant	3841	exon5			.	AF005361	CCDS5111.1	6q22.2	2013-02-14			ENSG00000196911	ENSG00000196911		"Importins", "Armadillo repeat containing"	6398	protein-coding gene	gene with protein product		604545				9395085	Standard	NM_002269		Approved	SRP6, IPOA6	uc003pxh.3	O15131	OTTHUMG00000015448	ENST00000368564.1:c.400_401delAA	chr6.hg19:g.117019926_117019927delAA	ENSP00000357552:p.Lys134fs	108.0	0.0		48.0	23.0	NM_002269	B2RAI5|Q86X23	Frame_Shift_Del	DEL	ENST00000368564.1	hg19	CCDS5111.1																																																																																			.	.		0.287	KPNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041967.1	NM_002269		-	117019927	AA	-	117019926	7	5	129	1	0	1	0	1	0	0	0	0	8442	247	9	0	418	0	KPNA5	6	117019926	Frame_Shift_Del	DEL	AA	TCGA-DD-A4NG-01A-11D-A27I-10	112084012	117019926	54095141	27	21201										
LRRN3	54674	hgsc.bcm.edu	37	chr7	110764538	110764538	+	Frame_Shift_Del	DEL	A	A	-													0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	catgctgcgcaaagtgctcgAataccatctgatgtcaaggt							TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr7:110764538delA	ENST00000422987.3	+	2	2541	c.1710delA	c.(1708-1710)cgafs	p.R570fs	LRRN3_ENST00000451085.1_Frame_Shift_Del_p.R570fs|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000415362.1_Intron|LRRN3_ENST00000308478.5_Frame_Shift_Del_p.R570fs|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000405709.2_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	570	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		AAAGTGCTCGAATACCATCTG	0.353																																					p.R570fs		Atlas-Indel,Pindel	.											.	LRRN3	132	.	0			c.1709delG						.						58	55	56					7																	110764538		2203	4300	6503	SO:0001589	frameshift_variant	54674	exon3			.	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17200	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 5"					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1710delA	chr7.hg19:g.110764538delA	ENSP00000412417:p.Arg570fs	59.0	0.0		70.0	20.0	NM_001099658	O43377|Q6I9V8|Q8IYQ6	Frame_Shift_Del	DEL	ENST00000422987.3	hg19	CCDS5754.1																																																																																			.	.		0.353	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		-	110764538	A	-	110764538	7	5	129	1	0	1	0	1	0	0	0	0	9045	233	9	0	1712	0	LRRN3	7	110764538	Frame_Shift_Del	DEL	A	TCGA-DD-A4NG-01A-11D-A27I-10		110764538	48374125	28	21202										
WASL	8976	hgsc.bcm.edu	37	chr7	123334793	123334793	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	cctccgcagttcatttttaaCagcttcaacacctcctgttt	4	14	2	0			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr7:123334793C>T	ENST00000223023.4	-	8	1134	c.802G>A	c.(802-804)Gtt>Att	p.V268I		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	268					actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCATTTTTAACAGCTTCAACA	0.343																																					p.V268I		Atlas-SNP	.											.	WASL	70	.	0			c.G802A						.						108	115	113					7																	123334793		2203	4300	6503	SO:0001583	missense	8976	exon8			TTTTAACAGCTTC	D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.802G>A	chr7.hg19:g.123334793C>T	ENSP00000223023:p.Val268Ile	87.0	0.0		100.0	24.0	NM_003941	A1JUI9|Q7Z746	Missense_Mutation	SNP	ENST00000223023.4	hg19	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872612	0.91587	.	.	ENSG00000106299	ENST00000223023	D	0.95137	-3.62	5.87	4.99	0.66335	Wiscott-Aldrich syndrome, C-terminal (1);	0.056133	0.64402	N	0.000001	D	0.93083	0.7798	M	0.64676	1.99	0.80722	D	1	B	0.10296	0.003	B	0.10450	0.005	D	0.90512	0.4482	10	0.72032	D	0.01	-12.7737	14.8933	0.70625	0.0:0.9312:0.0:0.0688	.	268	O00401	WASL_HUMAN	I	268	ENSP00000223023:V268I	ENSP00000223023:V268I	V	-	1	0	WASL	123122029	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.006000	0.70724	1.494000	0.48533	-0.225000	0.12378	GTT	.	.		0.343	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941		T	123334793	C	T	123334793	3	4	129	1	0	0	0	0	1	0	0	0	17271	478	17	3	731	3	WASL	7	123334793	Missense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10	12570255	123334793	35803870	29	21203										
WEE2	494551	hgsc.bcm.edu	37	chr7	141408580	141408580	+	Frame_Shift_Del	DEL	A	A	-													0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tggatgacaaagatattgacAaagaactaaggcagaaatta							TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr7:141408580delA	ENST00000397541.2	+	1	428	c.22delA	c.(22-24)aaafs	p.K8fs	WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000459753.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	8			K -> T (in dbSNP:rs35672788). {ECO:0000269|PubMed:17344846}.		female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					AGATATTGACAAAGAACTAAG	0.443																																					p.D7fs		Atlas-Indel,Pindel	.											.	WEE2	59	.	0			c.21delC						.						125	120	122					7																	141408580		1876	4110	5986	SO:0001589	frameshift_variant	494551	exon1			.	AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.22delA	chr7.hg19:g.141408580delA	ENSP00000380675:p.Lys8fs	101.0	0.0		96.0	50.0	NM_001105558		Frame_Shift_Del	DEL	ENST00000397541.2	hg19	CCDS43660.1																																																																																			.	.		0.443	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558		-	141408580	A	-	141408580	7	5	129	1	0	1	0	1	0	0	0	0	17360	131	5	0	24	0	WEE2	7	141408580	Frame_Shift_Del	DEL	A	TCGA-DD-A4NG-01A-11D-A27I-10	18073787	141408580	17730083	30	21204										
SNTB1	6641	hgsc.bcm.edu	37	chr8	121824005	121824005	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gcgatcccgcaccaaaacttCcagcagcccgctccgctgcg	9	19	0	0			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr8:121824005C>A	ENST00000395601.3	-	2	493	c.79G>T	c.(79-81)Gaa>Taa	p.E27*	SNTB1_ENST00000517992.1_Nonsense_Mutation_p.E27*|RP11-713M15.2_ENST00000605955.1_RNA|SNTB1_ENST00000519177.1_5'Flank	NM_021021.3	NP_066301.1	Q13884	SNTB1_HUMAN	syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)	27	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|protein complex (GO:0043234)|synapse (GO:0045202)				NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(6)	24	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			ACCAAAACTTCCAGCAGCCCG	0.682																																					p.E27X		Atlas-SNP	.											.	SNTB1	54	.	0			c.G79T						.						13	12	12					8																	121824005		2159	4227	6386	SO:0001587	stop_gained	6641	exon1			AAACTTCCAGCAG	AF028828	CCDS6334.1	8q23-q24	2013-01-10	2002-08-29		ENSG00000172164	ENSG00000172164		"Pleckstrin homology (PH) domain containing"	11168	protein-coding gene	gene with protein product	"tax interaction protein 43"	600026	"syntrophin, beta 1 (dystrophin-associated protein A1, 59kD, basic component 1)"	SNT2B1		8183929, 9482110	Standard	NM_021021		Approved	59-DAP, A1B, BSYN2, TIP-43, SNT2	uc010mdg.3	Q13884	OTTHUMG00000165041	ENST00000395601.3:c.79G>T	chr8.hg19:g.121824005C>A	ENSP00000378965:p.Glu27*	19.0	0.0		42.0	5.0	NM_021021	A8K9E0|O14912|Q4KMG8	Nonsense_Mutation	SNP	ENST00000395601.3	hg19	CCDS6334.1	.	.	.	.	.	.	.	.	.	.	C	39	7.500416	0.98322	.	.	ENSG00000172164	ENST00000395601;ENST00000517992;ENST00000520717	.	.	.	4.97	4.1	0.47936	.	0.233112	0.42420	D	0.000703	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.8622	0.57920	0.0:0.9195:0.0:0.0805	.	.	.	.	X	27	.	ENSP00000378965:E27X	E	-	1	0	SNTB1	121893186	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.878000	0.75567	1.073000	0.40885	0.561000	0.74099	GAA	.	.		0.682	SNTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381535.1	NM_021021		A	121824005	C	A	121824005	4	1	129	1	0	0	0	0	0	1	0	0	14887	864	30	3	1565	3	SNTB1	8	121824005	Nonsense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10		121824005	24540017	31	21205										
PTPLAD2	401494	hgsc.bcm.edu	37	chr9	21008109	21008109	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tggtggaataagtgccaaatGattcaaaataaggcagcgat	11	5	1	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr9:21008109G>A	ENST00000495827.2	-	6	572	c.527C>T	c.(526-528)tCa>tTa	p.S176L	PTPLAD2_ENST00000513293.2_Missense_Mutation_p.S176L	NM_001010915.3	NP_001010915.2	Q5VWC8	HACD4_HUMAN	protein tyrosine phosphatase-like A domain containing 2	176					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)	10				Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10)		AGTGCCAAATGATTCAAAATA	0.363																																					p.S176L		Atlas-SNP	.											.	PTPLAD2	26	.	0			c.C527T						.						118	112	114					9																	21008109		1868	4107	5975	SO:0001583	missense	401494	exon6			CCAAATGATTCAA		CCDS43791.1	9p21.3	2008-02-05			ENSG00000188921	ENSG00000188921			20920	protein-coding gene	gene with protein product		615941					Standard	NM_001010915		Approved	Em:AL662879.1, OTTHUMG00000021016	uc010mir.1	Q5VWC8	OTTHUMG00000021016	ENST00000495827.2:c.527C>T	chr9.hg19:g.21008109G>A	ENSP00000419503:p.Ser176Leu	133.0	0.0		84.0	21.0	NM_001010915	Q7Z385	Missense_Mutation	SNP	ENST00000495827.2	hg19	CCDS43791.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.178924	0.57692	.	.	ENSG00000188921	ENST00000513293;ENST00000495827	T;T	0.31247	1.5;1.5	5.64	4.74	0.60224	.	0.384793	0.26816	N	0.022344	T	0.30262	0.0759	L	0.47716	1.5	0.38633	D	0.951419	B	0.06786	0.001	B	0.10450	0.005	T	0.12218	-1.0556	10	0.52906	T	0.07	-22.4092	14.9311	0.70916	0.0703:0.0:0.9297:0.0	.	176	Q5VWC8	HACD4_HUMAN	L	176	ENSP00000426475:S176L;ENSP00000419503:S176L	ENSP00000419503:S176L	S	-	2	0	PTPLAD2	20998109	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.388000	0.59633	1.494000	0.48533	0.650000	0.86243	TCA	.	.		0.363	PTPLAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055434.3	NM_001010915		A	21008109	G	A	21008109	3	1	129	1	0	0	0	0	1	0	0	0	12789	1294	45	3	179	3	PTPLAD2	9	21008109	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10		21008109	120205322	32	21206										
FAM120A	23196	hgsc.bcm.edu	37	chr9	96233651	96233652	+	Frame_Shift_Ins	INS	-	-	T													0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gaatccaaatcgttttcctaINStttttgctgctctcttaggt					rs368570688		TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr9:96233651_96233652insT	ENST00000277165.6	+	2	897_898	c.703_704insT	c.(703-705)attfs	p.I235fs	FAM120A_ENST00000333936.5_Frame_Shift_Ins_p.I235fs|FAM120A_ENST00000375389.3_Frame_Shift_Ins_p.I235fs|FAM120A_ENST00000340893.4_Frame_Shift_Ins_p.I235fs	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	235						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TCGTTTTCCTATTTTTGCTGCT	0.416																																					p.I235fs		Atlas-Indel,Pindel	.											.	FAM120A	105	.	0			c.703_704insT						.																																			SO:0001589	frameshift_variant	23196	exon2			.	AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"DNA polymerase-transactivated protein 1", "oxidative stess-associated Src activator"	612265	"chromosome 9 open reading frame 10"	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.708dupT	chr9.hg19:g.96233656_96233656dupT	ENSP00000277165:p.Ile235fs	184.0	0.0		162.0	32.0	NM_014612	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Frame_Shift_Ins	INS	ENST00000277165.6	hg19	CCDS6706.1																																																																																			.	.		0.416	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612		T	96233652	-	T	96233651	7	5	129	1	0	1	1	0	0	0	0	0	5420	449	16	0	709	0	FAM120A	9	96233651	Frame_Shift_Ins	INS	-	TCGA-DD-A4NG-01A-11D-A27I-10	75225542	96233651	44979780	33	21207										
DCLRE1C	64421	hgsc.bcm.edu	37	chr10	14951131	14951131	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tttcactgttggattcttcaCaatctacaaagtttgtgaaa	6	7	4	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr10:14951131C>A	ENST00000378278.2	-	14	1392	c.1355G>T	c.(1354-1356)tGt>tTt	p.C452F	DCLRE1C_ENST00000378249.1_Missense_Mutation_p.C337F|DCLRE1C_ENST00000378254.1_Missense_Mutation_p.C332F|DCLRE1C_ENST00000396817.2_Missense_Mutation_p.C332F|DCLRE1C_ENST00000378246.2_Missense_Mutation_p.C337F|DCLRE1C_ENST00000378242.1_Missense_Mutation_p.C105F|DCLRE1C_ENST00000378258.1_Missense_Mutation_p.C332F|DCLRE1C_ENST00000453695.2_Missense_Mutation_p.C332F|DCLRE1C_ENST00000378289.4_Intron|DCLRE1C_ENST00000492201.1_5'UTR|DCLRE1C_ENST00000357717.2_Missense_Mutation_p.C337F|DCLRE1C_ENST00000378255.1_Missense_Mutation_p.C332F			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	452					B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						GGATTCTTCACAATCTACAAA	0.463								Non-homologous end-joining																													p.C452F		Atlas-SNP	.											.	DCLRE1C	136	.	0			c.G1355T						.						108	100	102					10																	14951131		2203	4300	6503	SO:0001583	missense	64421	exon14			TCTTCACAATCTA	BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	605988	"severe combined immunodeficiency, type a (Athabascan)", "DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.1355G>T	chr10.hg19:g.14951131C>A	ENSP00000367527:p.Cys452Phe	99.0	0.0		107.0	31.0	NM_001033855	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Missense_Mutation	SNP	ENST00000378278.2	hg19	CCDS31149.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227083	0.79576	.	.	ENSG00000152457	ENST00000453695;ENST00000378246;ENST00000357717;ENST00000378249;ENST00000396817;ENST00000378255;ENST00000378254;ENST00000378278;ENST00000378258;ENST00000378242	T;T;T;T;T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.55081	0.1898	M	0.76002	2.32	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.56238	-0.8012	10	0.87932	D	0	.	19.9857	0.97347	0.0:1.0:0.0:0.0	.	337;452	Q96SD1-3;Q96SD1	.;DCR1C_HUMAN	F	332;337;337;337;332;332;332;452;332;105	ENSP00000400529:C332F;ENSP00000367492:C337F;ENSP00000350349:C337F;ENSP00000367496:C337F;ENSP00000380030:C332F;ENSP00000367503:C332F;ENSP00000367502:C332F;ENSP00000367527:C452F;ENSP00000367506:C332F;ENSP00000367488:C105F	ENSP00000350349:C337F	C	-	2	0	DCLRE1C	14991137	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	5.359000	0.66074	2.706000	0.92434	0.655000	0.94253	TGT	.	.		0.463	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487		A	14951131	C	A	14951131	3	1	129	1	0	0	0	0	1	0	0	0	4298	478	17	3	727	3	DCLRE1C	10	14951131	Missense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10		14951131	120583616	34	21208										
GAD2	2572	hgsc.bcm.edu	37	chr10	26505807	26505807	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tctggggattccgagaatccCggcacaggtaggaaggagaa	15	8	1	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr10:26505807C>T	ENST00000376261.3	+	1	572	c.69C>T	c.(67-69)ccC>ccT	p.P23P	GAD2_ENST00000259271.3_Silent_p.P23P|GAD2_ENST00000376248.1_5'Flank	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	23					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CCGAGAATCCCGGCACAGGTA	0.607																																					p.P23P		Atlas-SNP	.											.	GAD2	116	.	0			c.C69T						.						51	60	57					10																	26505807		2203	4300	6503	SO:0001819	synonymous_variant	2572	exon1			GAATCCCGGCACA	AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.69C>T	chr10.hg19:g.26505807C>T		52.0	0.0		59.0	4.0	NM_000818	Q9UD87	Silent	SNP	ENST00000376261.3	hg19	CCDS7149.1																																																																																			.	.		0.607	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818		T	26505807	C	T	26505807	2	4	129	1	0	0	0	0	0	0	0	1	6188	639	23	1		1	GAD2	10	26505807	Silent	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10	11554676	26505807	109028940	35	21209										
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46999052	46999052	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	agctgggcgaggccagcaccAgaccccaggccccggaggaa	15	15	0	1	rs147004572		TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr10:46999052A>G	ENST00000374317.1	+	3	445	c.172A>G	c.(172-174)Aga>Gga	p.R58G	GPRIN2_ENST00000374314.4_Missense_Mutation_p.R58G	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	58										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						GGCCAGCACCAGACCCCAGGC	0.697																																					p.R58G		Atlas-SNP	.											.	GPRIN2	94	.	0			c.A172G						.	A	GLY/ARG	0,4400		0,0,2200	29	37	35		172	-10.9	0	10	dbSNP_134	35	2,8588		0,2,4293	no	missense	GPRIN2	NM_014696.3	125	0,2,6493	GG,GA,AA		0.0233,0.0,0.0154	benign	58/459	46999052	2,12988	2200	4295	6495	SO:0001583	missense	9721	exon3			AGCACCAGACCCC	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"KIAA0514"	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.172A>G	chr10.hg19:g.46999052A>G	ENSP00000363436:p.Arg58Gly	4.0	0.0		18.0	5.0	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	hg19	CCDS31192.1	.	.	.	.	.	.	.	.	.	.	A	0.391	-0.923656	0.02377	0.0	2.33E-4	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03413	3.94;3.94	5.64	-10.9	0.00192	.	1.769970	0.03226	N	0.178269	T	0.00998	0.0033	N	0.01109	-1.01	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44190	-0.9344	10	0.06757	T	0.87	5.6082	7.1416	0.25558	0.6422:0.0937:0.1691:0.0949	.	58	O60269	GRIN2_HUMAN	G	58	ENSP00000363436:R58G;ENSP00000363433:R58G	ENSP00000363433:R58G	R	+	1	2	GPRIN2	46419058	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.392000	0.02523	-1.708000	0.01401	-0.911000	0.02809	AGA	.	A|1.000;G|0.000		0.697	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		G	46999052	A	G	46999052	3	3	129	1	0	0	0	0	1	0	0	0	6739	180	7	2	174	2	GPRIN2	10	46999052	Missense_Mutation	SNP	A	TCGA-DD-A4NG-01A-11D-A27I-10	20493245	46999052	88535695	36	21210										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1267292	1267292	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gacaagcacagccaccaaatCcacagctaccagctttacac	5	16	0	0			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr11:1267292C>A	ENST00000529681.1	+	31	9240	c.9182C>A	c.(9181-9183)tCc>tAc	p.S3061Y	MUC5B_ENST00000447027.1_Missense_Mutation_p.S3064Y|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3061	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCCACCAAATCCACAGCTACC	0.592																																					p.S3061Y		Atlas-SNP	.											.	MUC5B	473	.	0			c.C9182A						.						170	189	183					11																	1267292		2093	4205	6298	SO:0001583	missense	727897	exon31			CCAAATCCACAGC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.9182C>A	chr11.hg19:g.1267292C>A	ENSP00000436812:p.Ser3061Tyr	397.0	1.0		409.0	123.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	4.664	0.123473	0.08931	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.20069	2.1;2.29	3.21	2.26	0.28386	.	.	.	.	.	T	0.14442	0.0349	L	0.34521	1.04	0.09310	N	1	P;B	0.36144	0.539;0.386	B;B	0.28011	0.085;0.059	T	0.12218	-1.0556	9	0.87932	D	0	.	9.8854	0.41257	0.2053:0.7946:0.0:0.0	.	3644;3064	A7Y9J9;E9PBJ0	.;.	Y	3061;3064;3033;3021	ENSP00000436812:S3061Y;ENSP00000415793:S3064Y	ENSP00000343037:S3033Y	S	+	2	0	MUC5B	1223868	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.289000	0.08365	0.670000	0.31165	0.523000	0.50628	TCC	.	.		0.592	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1267292	C	A	1267292	3	1	129	1	0	0	0	0	1	0	0	0	9988	855	30	3	9313	3	MUC5B	11	1267292	Missense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10		1267292	133739224	37	21211										
UBQLN3	50613	hgsc.bcm.edu	37	chr11	5529136	5529136	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	cctcctgccacactacccgtCcctgctaggcaaggcatgaa	8	17	0	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr11:5529136C>A	ENST00000311659.4	-	2	1800	c.1653G>T	c.(1651-1653)ggG>ggT	p.G551G	AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_5'Flank|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_5'Flank	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	551										NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACTACCCGTCCCTGCTAGGC	0.572																																					p.G551G	Ovarian(72;684 1260 12332 41642 52180)	Atlas-SNP	.											.	UBQLN3	107	.	0			c.G1653T						.						54	48	50					11																	5529136		2201	4297	6498	SO:0001819	synonymous_variant	50613	exon2			ACCCGTCCCTGCT	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"Ubiquilin family"	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.1653G>T	chr11.hg19:g.5529136C>A		89.0	0.0		95.0	27.0	NM_017481	Q9NRE0	Silent	SNP	ENST00000311659.4	hg19	CCDS7758.1																																																																																			.	.		0.572	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		A	5529136	C	A	5529136	2	1	129	1	0	0	0	0	0	0	0	1	16913	842	30	3		3	UBQLN3	11	5529136	Silent	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10	4261844	5529136	129477380	38	21212										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6567458	6567458	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	ggtgaactgcaccacttgtaTgccccactgtaccaggaggc	11	13	0	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr11:6567458T>C	ENST00000527990.2	+	19	5289	c.5289T>C	c.(5287-5289)taT>taC	p.Y1763Y	DNHD1_ENST00000254579.6_Silent_p.Y1763Y			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1763					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		ACCACTTGTATGCCCCACTGT	0.587																																					p.Y1763Y		Atlas-SNP	.											.	DNHD1	198	.	0			c.T5289C						.						56	50	52					11																	6567458		692	1591	2283	SO:0001819	synonymous_variant	144132	exon21			CTTGTATGCCCCA	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.5289T>C	chr11.hg19:g.6567458T>C		104.0	0.0		116.0	31.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	hg19	CCDS44532.1																																																																																			.	.		0.587	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		C	6567458	T	C	6567458	2	2	129	1	0	0	0	0	0	0	0	1	4670	1471	51	2		2	DNHD1	11	6567458	Silent	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	1038322	6567458	128439058	39	21213										
DKK3	27122	hgsc.bcm.edu	37	chr11	11987381	11987381	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gggctggcagaggaggccacTggcacaagggcatcggtcca	17	11	0	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr11:11987381T>A	ENST00000396505.2	-	7	1043	c.805A>T	c.(805-807)Agt>Tgt	p.S269C	DKK3_ENST00000527132.1_Intron|DKK3_ENST00000326932.4_Missense_Mutation_p.S269C|DKK3_ENST00000525493.1_Missense_Mutation_p.S269C|DKK3_ENST00000450094.2_Missense_Mutation_p.S241C	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	269	DKK-type Cys-2.				adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		AGGAGGCCACTGGCACAAGGG	0.662																																					p.S269C		Atlas-SNP	.											.	DKK3	35	.	0			c.A805T						.						62	60	61					11																	11987381		2201	4294	6495	SO:0001583	missense	27122	exon6			GGCCACTGGCACA	AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"regulated in glioma"	605416	"dickkopf (Xenopus laevis) homolog 3", "dickkopf 3 homolog (Xenopus laevis)"			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.805A>T	chr11.hg19:g.11987381T>A	ENSP00000379762:p.Ser269Cys	58.0	0.0		62.0	19.0	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Missense_Mutation	SNP	ENST00000396505.2	hg19	CCDS7808.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.236128	0.79800	.	.	ENSG00000050165	ENST00000396505;ENST00000326932;ENST00000366345;ENST00000525493;ENST00000450094;ENST00000326914	T;T;T;T	0.33216	2.14;2.14;2.14;1.42	5.65	4.54	0.55810	.	0.410373	0.32671	N	0.005782	T	0.38295	0.1035	L	0.40543	1.245	0.40982	D	0.984786	D;D;D	0.76494	0.999;0.985;0.985	P;P;P	0.62560	0.904;0.628;0.628	T	0.27331	-1.0077	10	0.62326	D	0.03	-21.9131	6.6644	0.23032	0.0:0.0772:0.2795:0.6433	.	269;241;269	F6SYF8;E7EUD0;Q9UBP4	.;.;DKK3_HUMAN	C	269;269;212;269;241;113	ENSP00000379762:S269C;ENSP00000314910:S269C;ENSP00000433112:S269C;ENSP00000398365:S241C	ENSP00000314730:S113C	S	-	1	0	DKK3	11943957	0.982000	0.34865	1.000000	0.80357	0.998000	0.95712	1.876000	0.39588	2.146000	0.66826	0.533000	0.62120	AGT	.	.		0.662	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253		A	11987381	T	A	11987381	3	1	129	1	0	0	0	0	1	0	0	0	4548	1580	55	4	255	4	DKK3	11	11987381	Missense_Mutation	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	5419923	11987381	123019135	40	21214										
HIPK3	10114	hgsc.bcm.edu	37	chr11	33308240	33308240	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	acactgcaggtgctacaaagGtcatagcagctcaggcacag	11	11	2	0			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr11:33308240G>A	ENST00000303296.4	+	2	585	c.280G>A	c.(280-282)Gtc>Atc	p.V94I	HIPK3_ENST00000379016.3_Missense_Mutation_p.V94I|HIPK3_ENST00000525975.1_Missense_Mutation_p.V94I|HIPK3_ENST00000456517.1_Missense_Mutation_p.V94I	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	94					apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						TGCTACAAAGGTCATAGCAGC	0.478																																					p.V94I		Atlas-SNP	.											.	HIPK3	92	.	0			c.G280A						.						79	72	75					11																	33308240		2202	4298	6500	SO:0001583	missense	10114	exon2			ACAAAGGTCATAG	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.280G>A	chr11.hg19:g.33308240G>A	ENSP00000304226:p.Val94Ile	105.0	0.0		100.0	31.0	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.552126	0.27739	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.52057	0.7;0.68;0.7;0.7	5.65	5.65	0.86999	.	0.102900	0.42682	D	0.000670	T	0.31702	0.0805	N	0.14661	0.345	0.32898	D	0.512834	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.001	T	0.33007	-0.9885	10	0.32370	T	0.25	.	13.9438	0.64071	0.0723:0.0:0.9277:0.0	.	94;94	Q9H422-2;Q9H422	.;HIPK3_HUMAN	I	94	ENSP00000431710:V94I;ENSP00000304226:V94I;ENSP00000368301:V94I;ENSP00000398241:V94I	ENSP00000304226:V94I	V	+	1	0	HIPK3	33264816	1.000000	0.71417	0.995000	0.50966	0.947000	0.59692	3.819000	0.55686	2.673000	0.90976	0.585000	0.79938	GTC	.	.		0.478	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		A	33308240	G	A	33308240	3	1	129	1	0	0	0	0	1	0	0	0	7127	1261	44	3	282	3	HIPK3	11	33308240	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	21320859	33308240	101698276	41	21215										
TPCN2	219931	hgsc.bcm.edu	37	chr11	68854594	68854594	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tgccagaacttccttcacaaGtgggacccccgcagccacct	8	17	1	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr11:68854594G>A	ENST00000294309.3	+	24	2201	c.2100G>A	c.(2098-2100)aaG>aaA	p.K700K	TPCN2_ENST00000542467.1_Silent_p.K518K|TPCN2_ENST00000442692.2_3'UTR	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	700					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TCCTTCACAAGTGGGACCCCC	0.652																																					p.K700K		Atlas-SNP	.											.	TPCN2	63	.	0			c.G2100A						.						41	43	43					11																	68854594		2200	4294	6494	SO:0001819	synonymous_variant	219931	exon24			TCACAAGTGGGAC	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"Voltage-gated ion channels / Two-pore channels"	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.2100G>A	chr11.hg19:g.68854594G>A		67.0	0.0		69.0	22.0	NM_139075	Q9NT82	Silent	SNP	ENST00000294309.3	hg19	CCDS8189.1																																																																																			.	.		0.652	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075		A	68854594	G	A	68854594	2	1	129	1	0	0	0	0	0	0	0	1	16411	1020	36	3		3	TPCN2	11	68854594	Silent	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	35546354	68854594	66151922	42	21216										
C11orf63	79864	hgsc.bcm.edu	37	chr11	122774639	122774639	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tctgctttgggcaggcaacaAccaatagaagacaaatattc	8	9	1	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr11:122774639A>G	ENST00000531316.1	+	2	443	c.351A>G	c.(349-351)caA>caG	p.Q117Q	C11orf63_ENST00000307257.6_Silent_p.Q117Q|C11orf63_ENST00000227349.2_Silent_p.Q117Q			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	117					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)					breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		GCAGGCAACAACCAATAGAAG	0.433																																					p.Q117Q		Atlas-SNP	.											.	C11orf63	116	.	0			c.A351G						.						170	191	184					11																	122774639		2202	4299	6501	SO:0001819	synonymous_variant	79864	exon3			GCAACAACCAATA	BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.351A>G	chr11.hg19:g.122774639A>G		86.0	0.0		66.0	24.0	NM_024806	A8K6G0|Q96GB5|Q9H5D6	Silent	SNP	ENST00000531316.1	hg19	CCDS8438.1																																																																																			.	.		0.433	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806		G	122774639	A	G	122774639	2	3	129	1	0	0	0	0	0	0	0	1	1656	40	2	2		2	C11orf63	11	122774639	Silent	SNP	A	TCGA-DD-A4NG-01A-11D-A27I-10	53920045	122774639	12231877	43	21217										
C1RL	51279	hgsc.bcm.edu	37	chr12	7249174	7249174	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	ggcagacactgtgcctttgcGtctcatccccaacacagaac	8	15	1	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr12:7249174G>A	ENST00000266542.4	-	6	1369	c.1277C>T	c.(1276-1278)aCg>aTg	p.T426M	C1RL_ENST00000545280.1_Intron|C1RL_ENST00000504702.2_Intron|C1RL_ENST00000544702.1_3'UTR	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	426	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GTGCCTTTGCGTCTCATCCCC	0.582													G|||	1	0.000199681	8e-04	0	5008	,	,		-128	0		0	False		,,,				2504	0				p.T426M		Atlas-SNP	.											C1RL,colon,carcinoma,0,1	C1RL	39	.	0			c.C1277T						.						151	144	146					12																	7249174		2203	4300	6503	SO:0001583	missense	51279	exon6			CTTTGCGTCTCAT	AF178985	CCDS8573.1, CCDS73431.1	12p13.31	2008-02-05				ENSG00000139178			21265	protein-coding gene	gene with protein product		608974				12838346	Standard	XM_005253385		Approved	C1r-LP, C1RL1	uc001qsn.3	Q9NZP8		ENST00000266542.4:c.1277C>T	chr12.hg19:g.7249174G>A	ENSP00000266542:p.Thr426Met	262.0	2.0		206.0	73.0	NM_016546	Q53GX9	Missense_Mutation	SNP	ENST00000266542.4	hg19	CCDS8573.1	.	.	.	.	.	.	.	.	.	.	G	2.462	-0.323939	0.05350	.	.	ENSG00000139178	ENST00000266542	T	0.44083	0.93	4.98	-5.31	0.02730	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.428750	0.03836	N	0.269762	T	0.36138	0.0956	L	0.47016	1.485	0.09310	N	0.999999	B	0.29612	0.251	B	0.23150	0.044	T	0.25012	-1.0144	10	0.36615	T	0.2	.	14.7057	0.69189	0.7726:0.0:0.2274:0.0	.	426	Q9NZP8	C1RL_HUMAN	M	426	ENSP00000266542:T426M	ENSP00000266542:T426M	T	-	2	0	C1RL	7140316	0.000000	0.05858	0.000000	0.03702	0.120000	0.20174	-3.225000	0.00550	-1.523000	0.01767	-0.409000	0.06214	ACG	.	.		0.582	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	NM_016546		A	7249174	G	A	7249174	3	1	129	1	0	0	0	0	1	0	0	0	1975	1145	40	1	190	1	C1RL	12	7249174	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10		7249174	126602721	44	21218										
RASSF8	11228	hgsc.bcm.edu	37	chr12	26217450	26217450	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	ggtcgaactggaaggtacacCcttatagagaaatggagaga	13	6	0	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr12:26217450C>A	ENST00000405154.2	+	3	322	c.123C>A	c.(121-123)acC>acA	p.T41T	RASSF8_ENST00000542865.1_Silent_p.T41T|RASSF8_ENST00000282884.9_Silent_p.T41T|RASSF8_ENST00000541490.1_Silent_p.T41T|RASSF8_ENST00000381352.3_Silent_p.T41T	NM_001164748.1	NP_001158220.1	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	41	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				signal transduction (GO:0007165)					cervix(2)|endometrium(1)|large_intestine(6)|lung(15)|urinary_tract(1)	25	Colorectal(261;0.0847)					GAAGGTACACCCTTATAGAGA	0.363																																					p.T41T		Atlas-SNP	.											.	RASSF8	56	.	0			c.C123A						.						95	100	98					12																	26217450		2203	4300	6503	SO:0001819	synonymous_variant	11228	exon4			GTACACCCTTATA	U82396	CCDS8705.1, CCDS53765.1	12p12.3	2013-05-30	2008-02-22	2005-09-14	ENSG00000123094	ENSG00000123094			13232	protein-coding gene	gene with protein product		608231	"chromosome 12 open reading frame 2"	C12orf2			Standard	NM_007211		Approved	HoJ-1	uc001rgx.3	Q8NHQ8	OTTHUMG00000169087	ENST00000405154.2:c.123C>A	chr12.hg19:g.26217450C>A		163.0	0.0		104.0	32.0	NM_007211	A8K1Z0|O95647|Q5SCI2|Q76KB6	Silent	SNP	ENST00000405154.2	hg19	CCDS53765.1																																																																																			.	.		0.363	RASSF8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402209.2	NM_007211		A	26217450	C	A	26217450	2	1	129	1	0	0	0	0	0	0	0	1	13107	610	22	3		3	RASSF8	12	26217450	Silent	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10	18968276	26217450	107634445	45	21219										
MRPS35	60488	hgsc.bcm.edu	37	chr12	27908279	27908279	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tccttggtactaaagaaattGaagagtacaaaaagtctgtt	8	5	1	3			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr12:27908279G>A	ENST00000081029.3	+	8	939	c.868G>A	c.(868-870)Gaa>Aaa	p.E290K	MRPS35_ENST00000538315.1_3'UTR|Y_RNA_ENST00000516776.1_RNA	NM_021821.3	NP_068593.2	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S35	0						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	6	Lung SC(9;0.0873)					TAAAGAAATTGAAGAGTACAA	0.338																																					p.E290K		Atlas-SNP	.											.	MRPS35	26	.	0			c.G868A						.						67	79	75					12																	27908279		2202	4296	6498	SO:0001583	missense	60488	exon8			GAAATTGAAGAGT	AF182422	CCDS8714.1, CCDS53769.1	12p11	2012-09-13			ENSG00000061794	ENSG00000061794		"Mitochondrial ribosomal proteins / small subunits"	16635	protein-coding gene	gene with protein product		611995				11279123	Standard	NM_021821		Approved	MRPS28, MDS023	uc001rih.3	P82673	OTTHUMG00000169215	ENST00000081029.3:c.868G>A	chr12.hg19:g.27908279G>A	ENSP00000081029:p.Glu290Lys	120.0	0.0		70.0	27.0	NM_021821	B2RDZ7|Q96Q21	Missense_Mutation	SNP	ENST00000081029.3	hg19	CCDS8714.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.204644	0.38905	.	.	ENSG00000061794	ENST00000081029;ENST00000321446	T	0.46819	0.86	6.05	4.18	0.49190	.	0.485515	0.26210	N	0.025681	T	0.27629	0.0679	N	0.20483	0.58	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.07790	-1.0754	10	0.15499	T	0.54	-16.1596	6.9671	0.24629	0.1411:0.153:0.706:0.0	.	290	P82673	RT35_HUMAN	K	290;254	ENSP00000081029:E290K	ENSP00000081029:E290K	E	+	1	0	MRPS35	27799546	0.731000	0.28111	0.923000	0.36655	0.975000	0.68041	1.612000	0.36889	1.533000	0.49186	0.637000	0.83480	GAA	.	.		0.338	MRPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402897.1	NM_021821		A	27908279	G	A	27908279	3	1	129	1	0	0	0	0	1	0	0	0	9853	1291	45	3	898	3	MRPS35	12	27908279	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	1690829	27908279	105943616	46	21220										
DDX11	1663	hgsc.bcm.edu	37	chr12	31249813	31249813	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	ctcttgcagcccctgcagacGagagtcaggccagcaccctg	11	16	2	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr12:31249813G>A	ENST00000407793.2	+	17	1902	c.1651G>A	c.(1651-1653)Gag>Aag	p.E551K	DDX11_ENST00000228264.6_Missense_Mutation_p.E525K|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000539673.1_3'UTR|DDX11_ENST00000350437.4_Missense_Mutation_p.E551K|DDX11_ENST00000545668.1_Missense_Mutation_p.E551K|DDX11_ENST00000542838.1_Missense_Mutation_p.E551K	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	551					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CCCTGCAGACGAGAGTCAGGC	0.617										Multiple Myeloma(12;0.14)																											p.E551K		Atlas-SNP	.											.	DDX11	188	.	0			c.G1651A						.						49	48	49					12																	31249813		2203	4300	6503	SO:0001583	missense	1663	exon17			GCAGACGAGAGTC	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1651G>A	chr12.hg19:g.31249813G>A	ENSP00000384703:p.Glu551Lys	164.0	0.0		183.0	67.0	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	hg19	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.173169	0.38413	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000404673;ENST00000228264;ENST00000545668;ENST00000350437	T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52	3.56	3.56	0.40772	.	0.579436	0.18328	N	0.144574	T	0.41096	0.1144	L	0.54908	1.71	0.80722	D	1	P;P;P;P	0.50710	0.938;0.929;0.875;0.938	B;B;B;B	0.37267	0.245;0.163;0.173;0.245	T	0.36939	-0.9727	10	0.12430	T	0.62	.	12.707	0.57065	0.0:0.0:1.0:0.0	.	525;551;551;551	Q96FC9-3;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	K	551;551;276;525;551;551	ENSP00000443426:E551K;ENSP00000384703:E551K;ENSP00000228264:E525K;ENSP00000440402:E551K;ENSP00000309965:E551K	ENSP00000228264:E525K	E	+	1	0	DDX11	31141080	1.000000	0.71417	0.016000	0.15963	0.012000	0.07955	4.925000	0.63425	1.813000	0.52934	0.505000	0.49811	GAG	.	.		0.617	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		A	31249813	G	A	31249813	3	1	129	1	0	0	0	0	1	0	0	0	4345	1059	37	1	1713	1	DDX11	12	31249813	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	3341534	31249813	102602082	47	21221										
CEP290	80184	hgsc.bcm.edu	37	chr12	88479875	88479875	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tattcgaatgttctccttaaTtttccttagagcgatctcaa	5	9	2	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr12:88479875T>G	ENST00000552810.1	-	34	4721	c.4378A>C	c.(4378-4380)Att>Ctt	p.I1460L	CEP290_ENST00000397838.3_Missense_Mutation_p.I520L|CEP290_ENST00000309041.7_Missense_Mutation_p.I1462L|CEP290_ENST00000547691.2_Missense_Mutation_p.I520L	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1460					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTCTCCTTAATTTTCCTTAGA	0.343																																					p.I1460L		Atlas-SNP	.											.	CEP290	195	.	0			c.A4378C						.						136	117	123					12																	88479875		1811	4066	5877	SO:0001583	missense	80184	exon34			CCTTAATTTTCCT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.4378A>C	chr12.hg19:g.88479875T>G	ENSP00000448012:p.Ile1460Leu	47.0	0.0		48.0	16.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.114262	0.37339	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.68331	0.25;-0.32;-0.32;0.25	5.78	3.34	0.38264	.	0.199343	0.51477	N	0.000095	T	0.58192	0.2105	L	0.51422	1.61	0.37309	D	0.909023	P	0.46327	0.876	P	0.47134	0.539	T	0.61417	-0.7067	10	0.05351	T	0.99	.	8.5254	0.33302	0.0:0.0652:0.2326:0.7022	.	1460	O15078	CE290_HUMAN	L	520;1460;1462;520	ENSP00000446905:I520L;ENSP00000448012:I1460L;ENSP00000308021:I1462L;ENSP00000380938:I520L	ENSP00000308021:I1462L	I	-	1	0	CEP290	87004006	1.000000	0.71417	1.000000	0.80357	0.525000	0.34531	3.478000	0.53158	0.414000	0.25790	0.455000	0.32223	ATT	.	.		0.343	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		G	88479875	T	G	88479875	3	3	129	1	0	0	0	0	1	0	0	0	3255	1493	52	5	3145	5	CEP290	12	88479875	Missense_Mutation	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	57230062	88479875	45372020	48	21222										
UBE2N	7334	hgsc.bcm.edu	37	chr12	93835657	93835657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gatcctgcggggcagcccggCcatcttgtcagaacccgagt	13	14	2	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr12:93835657C>T	ENST00000318066.2	-	1	381	c.4G>A	c.(4-6)Gcc>Acc	p.A2T	UBE2N_ENST00000552442.1_Missense_Mutation_p.A2T|UBE2N_ENST00000550657.1_Missense_Mutation_p.A2T|UBE2N_ENST00000549833.1_5'Flank	NM_003348.3	NP_003339.1	P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N	2					cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|DNA double-strand break processing (GO:0000729)|double-strand break repair via homologous recombination (GO:0000724)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone ubiquitination (GO:0016574)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone modification (GO:0031058)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|postreplication repair (GO:0006301)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of DNA repair (GO:0006282)|regulation of histone ubiquitination (GO:0033182)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)|UBC13-MMS2 complex (GO:0031372)|UBC13-UEV1A complex (GO:0035370)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|liver(2)|lung(5)	10						GGCAGCCCGGCCATCTTGTCA	0.682								Direct reversal of damage;Rad6 pathway																													p.A2T	Pancreas(197;738 2228 30225 32034 33454)	Atlas-SNP	.											.	UBE2N	20	.	0			c.G4A						.						32	34	33					12																	93835657		2203	4300	6503	SO:0001583	missense	7334	exon1			GCCCGGCCATCTT	D83004	CCDS31875.1	12q22	2011-05-19	2011-05-19			ENSG00000177889		"Ubiquitin-conjugating enzymes E2"	12492	protein-coding gene	gene with protein product		603679	"ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13)", "ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)"			8902611	Standard	NM_003348		Approved	UbcH-ben, UBC13, MGC8489	uc001tcp.3	P61088	OTTHUMG00000170156	ENST00000318066.2:c.4G>A	chr12.hg19:g.93835657C>T	ENSP00000316176:p.Ala2Thr	115.0	0.0		139.0	57.0	NM_003348	Q16781|Q53Y81	Missense_Mutation	SNP	ENST00000318066.2	hg19	CCDS31875.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.073088	0.76415	.	.	ENSG00000177889	ENST00000318066;ENST00000550657;ENST00000552442	T;T;T	0.66460	1.09;-0.21;-0.14	4.79	3.9	0.45041	Ubiquitin-conjugating enzyme/RWD-like (1);	0.000000	0.42682	U	0.000667	T	0.61476	0.2350	L	0.54323	1.7	0.42564	D	0.993154	B	0.09022	0.002	B	0.08055	0.003	T	0.63107	-0.6711	10	0.72032	D	0.01	0.1856	12.7691	0.57410	0.0:0.8348:0.1652:0.0	.	2	P61088	UBE2N_HUMAN	T	2	ENSP00000316176:A2T;ENSP00000449352:A2T;ENSP00000448352:A2T	ENSP00000316176:A2T	A	-	1	0	UBE2N	92359788	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.096000	0.41738	1.368000	0.46115	0.563000	0.77884	GCC	.	.		0.682	UBE2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407710.1	NM_003348		T	93835657	C	T	93835657	3	4	129	1	0	0	0	0	1	0	0	0	16881	739	26	3	470	3	UBE2N	12	93835657	Missense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10	5355782	93835657	40016238	49	21223										
UNC119B	84747	hgsc.bcm.edu	37	chr12	121151187	121151187	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	agattgccaaaccttgcgttTcaggtaggcctctacgttgt	10	10	2	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr12:121151187T>G	ENST00000344651.4	+	2	395	c.355T>G	c.(355-357)Tca>Gca	p.S119A	UNC119B_ENST00000539658.1_3'UTR	NM_001080533.1	NP_001074002.1	A6NIH7	U119B_HUMAN	unc-119 homolog B (C. elegans)	119					cilium morphogenesis (GO:0060271)|lipoprotein transport (GO:0042953)	ciliary transition zone (GO:0035869)	lipid binding (GO:0008289)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)	9	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ACCTTGCGTTTCAGGTAGGCC	0.438											OREG0022197	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S119A		Atlas-SNP	.											.	UNC119B	21	.	0			c.T355G						.						124	109	114					12																	121151187		2203	4300	6503	SO:0001583	missense	84747	exon2			TGCGTTTCAGGTA		CCDS31914.1	12q24	2014-06-16	2001-11-28		ENSG00000175970	ENSG00000175970			16488	protein-coding gene	gene with protein product	"POC7 centriolar protein homolog B (Chlamydomonas)"		"unc119 (C.elegans) homolog B"				Standard	NM_001080533		Approved	MGC5139, POC7B	uc001tyz.4	A6NIH7	OTTHUMG00000169201	ENST00000344651.4:c.355T>G	chr12.hg19:g.121151187T>G	ENSP00000344942:p.Ser119Ala	171.0	0.0	1509	151.0	49.0	NM_001080533		Missense_Mutation	SNP	ENST00000344651.4	hg19	CCDS31914.1	.	.	.	.	.	.	.	.	.	.	T	9.946	1.218750	0.22373	.	.	ENSG00000175970	ENST00000344651;ENST00000537794	.	.	.	5.25	-0.0333	0.13901	Immunoglobulin E-set (1);	1.294440	0.04863	N	0.444469	T	0.40979	0.1139	L	0.42245	1.32	0.18873	N	0.999989	B	0.02656	0.0	B	0.10450	0.005	T	0.29243	-1.0018	9	0.25751	T	0.34	-16.3266	10.1812	0.42968	0.1118:0.0:0.464:0.4242	.	119	A6NIH7	U119B_HUMAN	A	119	.	ENSP00000344942:S119A	S	+	1	0	UNC119B	119635570	1.000000	0.71417	0.190000	0.23270	0.866000	0.49608	0.825000	0.27393	-0.140000	0.11394	0.460000	0.39030	TCA	.	.		0.438	UNC119B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402857.1	NM_001080533		G	121151187	T	G	121151187	3	3	129	1	0	0	0	0	1	0	0	0	16998	1783	62	5	361	5	UNC119B	12	121151187	Missense_Mutation	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	27315530	121151187	12700708	50	21224										
FRY	10129	hgsc.bcm.edu	37	chr13	32850640	32850640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	tggacaagctcaagttcagtGtgttagaactgcaagaatat	10	6	2	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr13:32850640G>A	ENST00000380250.3	+	57	8822	c.8326G>A	c.(8326-8328)Gtg>Atg	p.V2776M	FRY_ENST00000542859.1_Missense_Mutation_p.V146M	NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2776						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CAAGTTCAGTGTGTTAGAACT	0.388																																					p.V2776M		Atlas-SNP	.											.	FRY	312	.	0			c.G8326A						.						175	157	163					13																	32850640		1892	4117	6009	SO:0001583	missense	10129	exon57			TTCAGTGTGTTAG	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.8326G>A	chr13.hg19:g.32850640G>A	ENSP00000369600:p.Val2776Met	161.0	0.0		82.0	35.0	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.7|24.7	4.564999|4.564999	0.86439|0.86439	.|.	.|.	ENSG00000073910|ENSG00000073910	ENST00000380235|ENST00000380250;ENST00000542859	.|T	.|0.28895	.|1.59	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	.|0.058305	.|0.64402	.|D	.|0.000002	T|T	0.52468|0.52468	0.1736|0.1736	L|L	0.58354|0.58354	1.805|1.805	0.80722|0.80722	D|D	1|1	.|D;P	.|0.71674	.|0.998;0.769	.|D;B	.|0.65443	.|0.935;0.297	T|T	0.42682|0.42682	-0.9437|-0.9437	6|10	0.72032|0.41790	D|T	0.01|0.15	.|.	19.616|19.616	0.95634|0.95634	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|557;2776	.|Q8NB82;Q5TBA9	.|.;FRY_HUMAN	Y|M	403|2776;146	.|ENSP00000369600:V2776M	ENSP00000369567:C403Y|ENSP00000369600:V2776M	C|V	+|+	2|1	0|0	FRY|FRY	31748640|31748640	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.777000|0.777000	0.43975|0.43975	9.339000|9.339000	0.96797|0.96797	2.642000|2.642000	0.89623|0.89623	0.555000|0.555000	0.69702|0.69702	TGT|GTG	.	.		0.388	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		A	32850640	G	A	32850640	3	1	129	1	0	0	0	0	1	0	0	0	6071	1377	48	3	8552	3	FRY	13	32850640	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10		32850640	82319238	51	21225										
THBS1	7057	hgsc.bcm.edu	37	chr15	39886581	39886581	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	cctatgctggtggtagactaGggttgtttgtcttctctcaa	11	8	3	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr15:39886581G>A	ENST00000260356.5	+	21	3610	c.3445G>A	c.(3445-3447)Ggg>Agg	p.G1149R	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1149	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		TGGTAGACTAGGGTTGTTTGT	0.418																																					p.G1149R		Atlas-SNP	.											.	THBS1	106	.	0			c.G3445A						.						163	153	157					15																	39886581		2200	4297	6497	SO:0001583	missense	7057	exon21			AGACTAGGGTTGT		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.3445G>A	chr15.hg19:g.39886581G>A	ENSP00000260356:p.Gly1149Arg	108.0	0.0		95.0	29.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	G	33	5.214773	0.95104	.	.	ENSG00000137801	ENST00000260356	D	0.96992	-4.2	5.44	5.44	0.79542	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.35262	N	0.003331	D	0.98529	0.9509	M	0.89601	3.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99285	1.0897	10	0.87932	D	0	-20.1238	19.6125	0.95613	0.0:0.0:1.0:0.0	.	1064;1149	B4E3J7;P07996	.;TSP1_HUMAN	R	1149	ENSP00000260356:G1149R	ENSP00000260356:G1149R	G	+	1	0	THBS1	37673873	1.000000	0.71417	0.813000	0.32504	0.995000	0.86356	9.813000	0.99286	2.698000	0.92095	0.591000	0.81541	GGG	.	.		0.418	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		A	39886581	G	A	39886581	3	1	129	1	0	0	0	0	1	0	0	0	15868	1000	35	3	3523	3	THBS1	15	39886581	Missense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10		39886581	62644811	52	21226										
TMIGD1	388364	hgsc.bcm.edu	37	chr17	28656378	28656378	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gaagagacacagacagagctGgaattgattttgtttccaga	11	6	0	5			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr17:28656378G>A	ENST00000328886.4	-	3	324	c.252C>T	c.(250-252)tcC>tcT	p.S84S	TMIGD1_ENST00000538566.2_Silent_p.S84S	NM_206832.1	NP_996663.1	Q6UXZ0	TMIG1_HUMAN	transmembrane and immunoglobulin domain containing 1	84	Ig-like C2-type 1.					integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	12						AGACAGAGCTGGAATTGATTT	0.493																																					p.S84S		Atlas-SNP	.											.	TMIGD1	38	.	0			c.C252T						.						141	121	128					17																	28656378		2203	4300	6503	SO:0001819	synonymous_variant	388364	exon3			AGAGCTGGAATTG	AY358153	CCDS32605.1	17q11.2	2013-01-29	2006-07-05	2006-07-05		ENSG00000182271		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	32431	protein-coding gene	gene with protein product				TMIGD		12975309	Standard	NM_206832		Approved	UNQ9372	uc002hfa.1	Q6UXZ0		ENST00000328886.4:c.252C>T	chr17.hg19:g.28656378G>A		186.0	0.0		176.0	47.0	NM_206832	A8K2K1|Q6ZMC6	Silent	SNP	ENST00000328886.4	hg19	CCDS32605.1																																																																																			.	.		0.493	TMIGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447955.1	NM_206832		A	28656378	G	A	28656378	2	1	129	1	0	0	0	0	0	0	0	1	16245	1335	47	3		3	TMIGD1	17	28656378	Silent	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10		28656378	52538832	53	21227										
KRT38	8687	hgsc.bcm.edu	37	chr17	39596873	39596873	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	ggtctccttctcatggccatTcagggtgttttcaccatagg	10	11	4	0			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr17:39596873T>C	ENST00000246646.3	-	1	300	c.301A>G	c.(301-303)Aat>Gat	p.N101D		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	101	Head.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				TCATGGCCATTCAGGGTGTTT	0.587																																					p.N101D		Atlas-SNP	.											.	KRT38	63	.	0			c.A301G						.						115	102	107					17																	39596873		2203	4300	6503	SO:0001583	missense	8687	exon1			GGCCATTCAGGGT	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"-", "Intermediate filaments type I, keratins (acidic)"	6456	protein-coding gene	gene with protein product		604542	"keratin, hair, acidic, 8"	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.301A>G	chr17.hg19:g.39596873T>C	ENSP00000246646:p.Asn101Asp	170.0	0.0		153.0	70.0	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	hg19	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	T	19.88	3.908876	0.72868	.	.	ENSG00000171360	ENST00000246646	D	0.81996	-1.56	4.72	4.72	0.59763	.	0.000000	0.52532	D	0.000076	D	0.87811	0.6271	M	0.78049	2.395	0.09310	N	1	D	0.60575	0.988	P	0.57204	0.815	T	0.81506	-0.0902	10	0.66056	D	0.02	.	10.5173	0.44898	0.0:0.0:0.0:1.0	.	101	O76015	KRT38_HUMAN	D	101	ENSP00000246646:N101D	ENSP00000246646:N101D	N	-	1	0	KRT38	36850399	0.000000	0.05858	0.016000	0.15963	0.737000	0.42083	0.286000	0.18902	1.982000	0.57802	0.528000	0.53228	AAT	.	.		0.587	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		C	39596873	T	C	39596873	3	2	129	1	0	0	0	0	1	0	0	0	8484	1783	62	2	1097	2	KRT38	17	39596873	Missense_Mutation	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	10940495	39596873	41598337	54	21228										
C3	718	hgsc.bcm.edu	37	chr19	6693481	6693481	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	agagctgggttgtctgaaggCcagctgctgggtgtaccctg	16	9	1	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr19:6693481C>A	ENST00000245907.6	-	25	3264	c.3172G>T	c.(3172-3174)Gcc>Tcc	p.A1058S		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1058					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGTCTGAAGGCCAGCTGCTGG	0.642																																					p.A1058S		Atlas-SNP	.											.	C3	192	.	0			c.G3172T						.						41	36	38					19																	6693481		2202	4300	6502	SO:0001583	missense	718	exon25			TGAAGGCCAGCTG	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.3172G>T	chr19.hg19:g.6693481C>A	ENSP00000245907:p.Ala1058Ser	39.0	0.0		32.0	9.0	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.608901	0.46527	.	.	ENSG00000125730	ENST00000245907	T	0.30182	1.54	5.52	3.39	0.38822	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.249575	0.46145	D	0.000315	T	0.24314	0.0589	L	0.35288	1.05	0.34864	D	0.742877	B	0.30542	0.284	B	0.40982	0.345	T	0.16188	-1.0411	10	0.06891	T	0.86	.	9.5697	0.39420	0.0:0.8304:0.0:0.1696	.	1058	P01024	CO3_HUMAN	S	1058	ENSP00000245907:A1058S	ENSP00000245907:A1058S	A	-	1	0	C3	6644481	0.019000	0.18553	1.000000	0.80357	0.259000	0.26198	0.315000	0.19451	1.480000	0.48289	0.650000	0.86243	GCC	.	.		0.642	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		A	6693481	C	A	6693481	3	1	129	1	0	0	0	0	1	0	0	0	2206	739	26	3	1887	3	C3	19	6693481	Missense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10		6693481	52435502	55	21229										
ANO8	57719	hgsc.bcm.edu	37	chr19	17443815	17443815	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	cgcaaattctgcagccagaaGcggatgatgctctggcgttc	12	11	2	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr19:17443815G>A	ENST00000159087.4	-	5	668	c.510C>T	c.(508-510)cgC>cgT	p.R170R	GTPBP3_ENST00000361619.5_5'Flank	NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	170					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						GCAGCCAGAAGCGGATGATGC	0.622																																					p.R170R		Atlas-SNP	.											.	ANO8	67	.	0			c.C510T						.						62	56	58					19																	17443815		2203	4300	6503	SO:0001819	synonymous_variant	57719	exon5			CCAGAAGCGGATG	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	29329	protein-coding gene	gene with protein product		610216	"KIAA1623", "transmembrane protein 16H"	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.510C>T	chr19.hg19:g.17443815G>A		98.0	0.0		85.0	29.0	NM_020959	A6NIJ0	Silent	SNP	ENST00000159087.4	hg19	CCDS32949.1																																																																																			.	.		0.622	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644		A	17443815	G	A	17443815	2	1	129	1	0	0	0	0	0	0	0	1	703	958	34	3		3	ANO8	19	17443815	Silent	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	10750334	17443815	41685168	56	21230										
AKT2	208	hgsc.bcm.edu	37	chr19	40742001	40742001	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	cggcccggccatagtcattgTcctccagcacctgaggatgg	12	14	1	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr19:40742001T>C	ENST00000392038.2	-	11	1269	c.971A>G	c.(970-972)gAc>gGc	p.D324G	AKT2_ENST00000579047.1_Missense_Mutation_p.D262G|AKT2_ENST00000311278.6_Missense_Mutation_p.D281G|AKT2_ENST00000424901.1_Missense_Mutation_p.D324G	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	324	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)	p.D324G(1)		breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			ATAGTCATTGTCCTCCAGCAC	0.637			A		"ovarian, pancreatic "																																p.D324G		Atlas-SNP	.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	AKT2,NS,carcinoma,-1,1	AKT2	53	.	1	Substitution - Missense(1)	kidney(1)	c.A971G						.						72	58	62					19																	40742001		2203	4300	6503	SO:0001583	missense	208	exon11			TCATTGTCCTCCA	M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"Pleckstrin homology (PH) domain containing"	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.971A>G	chr19.hg19:g.40742001T>C	ENSP00000375892:p.Asp324Gly	64.0	0.0		86.0	24.0	NM_001626	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	hg19	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.661738	0.88154	.	.	ENSG00000105221	ENST00000392038;ENST00000391844;ENST00000424901;ENST00000311278;ENST00000391845	T;T;T	0.20069	2.1;2.1;2.1	5.66	5.66	0.87406	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.042391	0.85682	D	0.000000	T	0.18173	0.0436	N	0.00778	-1.195	0.80722	D	1	B;B;D	0.76494	0.02;0.11;0.999	B;B;D	0.77004	0.116;0.196;0.989	T	0.56444	-0.7978	10	0.39692	T	0.17	.	14.8659	0.70416	0.0:0.0:0.0:1.0	.	262;281;324	B4DG79;Q0VAN0;P31751	.;.;AKT2_HUMAN	G	324;225;324;281;144	ENSP00000375892:D324G;ENSP00000399532:D324G;ENSP00000309428:D281G	ENSP00000309428:D281G	D	-	2	0	AKT2	45433841	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.994000	0.88315	2.159000	0.67721	0.459000	0.35465	GAC	.	.		0.637	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626		C	40742001	T	C	40742001	3	2	129	1	0	0	0	0	1	0	0	0	480	1667	58	2	490	2	AKT2	19	40742001	Missense_Mutation	SNP	T	TCGA-DD-A4NG-01A-11D-A27I-10	23298186	40742001	18386982	57	21231										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42837807	42837807	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	acttccttttcctggacacaGagtgcacgtatgactacctg	8	12	0	2			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr19:42837807G>T	ENST00000251268.6	+	2	238	c.238G>T	c.(238-240)Gag>Tag	p.E80*	MEGF8_ENST00000334370.4_Nonsense_Mutation_p.E80*	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	80	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CCTGGACACAGAGTGCACGTA	0.617																																					p.E80X		Atlas-SNP	.											.	MEGF8	358	.	0			c.G238T						.						89	93	92					19																	42837807		2073	4195	6268	SO:0001587	stop_gained	1954	exon2			GACACAGAGTGCA	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.238G>T	chr19.hg19:g.42837807G>T	ENSP00000251268:p.Glu80*	120.0	0.0		115.0	35.0	NM_001271938	A8KAY0|O75097	Nonsense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	G	43	10.194334	0.99357	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-8.5856	16.3026	0.82830	0.0:0.0:1.0:0.0	.	.	.	.	X	80	.	ENSP00000251268:E80X	E	+	1	0	MEGF8	47529647	1.000000	0.71417	0.920000	0.36463	0.908000	0.53690	8.684000	0.91242	2.453000	0.82957	0.486000	0.48141	GAG	.	.		0.617	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		T	42837807	G	T	42837807	4	4	129	1	0	0	0	0	0	1	0	0	9472	943	33	3	244	3	MEGF8	19	42837807	Nonsense_Mutation	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	2095806	42837807	16291176	58	21232										
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55598913	55598913	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	caggacaaagagaaagtgtcAgagctggaggcagtgatgga	16	5	1	3			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr19:55598913A>T	ENST00000201647.6	+	20	2159	c.2103A>T	c.(2101-2103)tcA>tcT	p.S701S	EPS8L1_ENST00000586329.1_Silent_p.S526S|EPS8L1_ENST00000540810.1_Silent_p.S637S|EPS8L1_ENST00000588359.1_Silent_p.S387S|EPS8L1_ENST00000245618.5_Silent_p.S574S	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	701					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		AGAAAGTGTCAGAGCTGGAGG	0.582																																					p.S701S	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.A2103T						.						133	130	131					19																	55598913		2203	4300	6503	SO:0001819	synonymous_variant	54869	exon20			AGTGTCAGAGCTG	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.2103A>T	chr19.hg19:g.55598913A>T		226.0	0.0		214.0	67.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Silent	SNP	ENST00000201647.6	hg19	CCDS12914.1																																																																																			.	.		0.582	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		T	55598913	A	T	55598913	2	4	129	1	0	0	0	0	0	0	0	1	5197	175	7	4		4	EPS8L1	19	55598913	Silent	SNP	A	TCGA-DD-A4NG-01A-11D-A27I-10	12761106	55598913	3530070	59	21233										
RBL1	5933	hgsc.bcm.edu	37	chr20	35683995	35683995	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	agtcttcgtgtttcctgaacCattacagtctctagtatttt	6	9	2	1			TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr20:35683995C>T	ENST00000373664.3	-	11	1494	c.1428G>A	c.(1426-1428)atG>atA	p.M476I	RBL1_ENST00000344359.3_Missense_Mutation_p.M476I	NM_002895.2	NP_002886.2	P28749	RBL1_HUMAN	retinoblastoma-like 1	476	Domain A.|Pocket; binds T and E1A.				chromatin modification (GO:0016568)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(7)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	42		Myeloproliferative disorder(115;0.00878)				TTTCCTGAACCATTACAGTCT	0.388																																					p.M476I		Atlas-SNP	.											.	RBL1	114	.	0			c.G1428A						.						112	103	106					20																	35683995		2202	4299	6501	SO:0001583	missense	5933	exon11			CTGAACCATTACA	L14812	CCDS13289.1, CCDS13290.1	20q11.23	2014-03-11	2014-03-11		ENSG00000080839	ENSG00000080839			9893	protein-coding gene	gene with protein product		116957				1833063	Standard	NM_183404		Approved	p107, cp107, PRB1	uc002xgi.3	P28749	OTTHUMG00000032406	ENST00000373664.3:c.1428G>A	chr20.hg19:g.35683995C>T	ENSP00000362768:p.Met476Ile	71.0	0.0		79.0	39.0	NM_183404	A8K2W5|Q4VXA0|Q8N5K6|Q9H1L5|Q9H1M1	Missense_Mutation	SNP	ENST00000373664.3	hg19	CCDS13289.1	.	.	.	.	.	.	.	.	.	.	C	4.373	0.068759	0.08436	.	.	ENSG00000080839	ENST00000373664;ENST00000344359	D;D	0.86366	-2.11;-2.11	4.8	3.84	0.44239	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.140268	0.64402	D	0.000003	T	0.68007	0.2954	N	0.04705	-0.18	0.44946	D	0.997967	P;B	0.38827	0.649;0.005	B;B	0.32624	0.149;0.028	T	0.66248	-0.5971	10	0.14252	T	0.57	-7.3058	10.2705	0.43481	0.1532:0.6992:0.1476:0.0	.	476;476	P28749-2;P28749	.;RBL1_HUMAN	I	476	ENSP00000362768:M476I;ENSP00000343646:M476I	ENSP00000343646:M476I	M	-	3	0	RBL1	35117409	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.408000	0.44574	1.256000	0.44068	-0.181000	0.13052	ATG	.	.		0.388	RBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079067.2	NM_002895		T	35683995	C	T	35683995	3	4	129	1	0	0	0	0	1	0	0	0	13124	594	21	3	1835	3	RBL1	20	35683995	Missense_Mutation	SNP	C	TCGA-DD-A4NG-01A-11D-A27I-10		35683995	27341525	60	21234										
MYT1	4661	hgsc.bcm.edu	37	chr20	62839416	62839416	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gaggaagaggaagaggaggaGgaggaagaggaagaggagga	23	0	0	4	rs544053715	byFrequency	TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr20:62839416G>A	ENST00000328439.1	+	7	1231	c.867G>A	c.(865-867)gaG>gaA	p.E289E	MYT1_ENST00000536311.1_Silent_p.E289E|MYT1_ENST00000360149.4_Intron	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					aagaggaggaggaggaagagg	0.567													g|||	2	0.000399361	0	0.0014	5008	,	,		14500	0		0.001	False		,,,				2504	0				p.E289E	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.G867A						.						37	37	37					20																	62839416		2203	4300	6503	SO:0001819	synonymous_variant	4661	exon7			GGAGGAGGAGGAA	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.867G>A	chr20.hg19:g.62839416G>A		68.0	0.0		80.0	14.0	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000328439.1	hg19	CCDS13558.1																																																																																			.	.		0.567	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		A	62839416	G	A	62839416	2	1	129	1	0	0	0	0	0	0	0	1	10115	991	35	3		3	MYT1	20	62839416	Silent	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	27155421	62839416	186104	61	21235			1	22		2	2	19	G		3.604965e-05
MYT1	4661	hgsc.bcm.edu	37	chr20	62839434	62839434	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0967741935483871	6	1	1.6583850931677	5.38975155279503	0.979954827780915	1	1	0	gaggaggaagaggaagaggaGgaggaagaggaagaggaaga	22	0	0	5	rs537698482	byFrequency	TCGA-DD-A4NG-01A-11D-A27I-10	TCGA-DD-A4NG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03c88506-d72e-4a44-a34e-a7f0564f1799	2b8a07c1-c041-4779-b4df-4bd6a8128dd8	g.chr20:62839434G>A	ENST00000328439.1	+	7	1249	c.885G>A	c.(883-885)gaG>gaA	p.E295E	MYT1_ENST00000536311.1_Silent_p.E295E|MYT1_ENST00000360149.4_Intron	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					aggaagaggaggaggaagagg	0.572																																					p.E295E	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.G885A						.						47	47	47					20																	62839434		2203	4300	6503	SO:0001819	synonymous_variant	4661	exon7			AGAGGAGGAGGAA	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.885G>A	chr20.hg19:g.62839434G>A		89.0	0.0		96.0	8.0	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000328439.1	hg19	CCDS13558.1																																																																																			.	.		0.572	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		A	62839434	G	A	62839434	2	1	129	1	0	0	0	0	0	0	0	1	10115	991	35	3		3	MYT1	20	62839434	Silent	SNP	G	TCGA-DD-A4NG-01A-11D-A27I-10	18	62839434	186086	62	21236			1	22		2	2	19	G		3.604965e-05
C1QA	712	hgsc.bcm.edu	37	chr1	22965369	22965369	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	atccaaggccttaaaggagaCcagggggaacctgggccctc	13	12	0	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr1:22965369C>A	ENST00000374642.3	+	3	411	c.207C>A	c.(205-207)gaC>gaA	p.D69E	C1QA_ENST00000402322.1_Missense_Mutation_p.D69E	NM_015991.2	NP_057075.1	P02745	C1QA_HUMAN	complement component 1, q subcomponent, A chain	69	Collagen-like.				cell-cell signaling (GO:0007267)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	collagen trimer (GO:0005581)|complement component C1 complex (GO:0005602)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|liver(1)|lung(3)|skin(1)	6		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.41e-27)|Colorectal(126;1.52e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.63e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000541)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TTAAAGGAGACCAGGGGGAAC	0.642																																					p.D69E		Atlas-SNP	.											.	C1QA	31	.	0			c.C207A						.						6	8	8					1																	22965369		2141	4246	6387	SO:0001583	missense	712	exon3			AGGAGACCAGGGG	AF135157	CCDS226.1	1p36.3-p34.1	2014-09-17	2006-02-09		ENSG00000173372	ENSG00000173372		"Complement system"	1241	protein-coding gene	gene with protein product		120550	"complement component 1, q subcomponent, alpha polypeptide"			1537612	Standard	NM_015991		Approved		uc001bfy.3	P02745	OTTHUMG00000002893	ENST00000374642.3:c.207C>A	chr1.hg19:g.22965369C>A	ENSP00000363773:p.Asp69Glu	62.0	0.0		63.0	10.0	NM_015991	B2R4X2|Q5T963	Missense_Mutation	SNP	ENST00000374642.3	hg19	CCDS226.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.57|12.57	1.977597|1.977597	0.34848|0.34848	.|.	.|.	ENSG00000173372|ENSG00000173372	ENST00000374642;ENST00000438241;ENST00000402322|ENST00000339353	D;D;D|.	0.90197|.	-2.63;-2.63;-2.63|.	5.48|5.48	1.98|1.98	0.26296|0.26296	.|.	.|0.489945	.|0.15948	.|N	.|0.236865	T|T	0.27027|0.27027	0.0662|0.0662	L|L	0.35542|0.35542	1.07|1.07	0.20403|0.20403	N|N	0.999905|0.999905	P|.	0.37207|.	0.587|.	B|.	0.39027|.	0.288|.	T|T	0.17258|0.17258	-1.0375|-1.0375	9|7	0.09590|0.46703	T|T	0.72|0.11	1.8948|1.8948	3.7723|3.7723	0.08646|0.08646	0.1698:0.4398:0.0:0.3904|0.1698:0.4398:0.0:0.3904	.|.	69|.	P02745|.	C1QA_HUMAN|.	E|N	69|67	ENSP00000363773:D69E;ENSP00000416841:D69E;ENSP00000385564:D69E|.	ENSP00000363773:D69E|ENSP00000341271:T67N	D|T	+|+	3|2	2|0	C1QA|C1QA	22837956|22837956	0.000000|0.000000	0.05858|0.05858	0.447000|0.447000	0.26932|0.26932	0.917000|0.917000	0.54804|0.54804	-0.036000|-0.036000	0.12185|0.12185	0.239000|0.239000	0.21243|0.21243	0.561000|0.561000	0.74099|0.74099	GAC|ACC	.	.		0.642	C1QA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008087.2	NM_015991		A	22965369	C	A	22965369	3	1	130	1	0	0	0	0	1	0	0	0	1956	506	18	3	213	3	C1QA	1	22965369	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10		22965369	226285252	1	21237										
RNF11	26994	hgsc.bcm.edu	37	chr1	51702468	51702468	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	cccccacctcggatgacatcTccctgcttcacgagtctcag	7	18	3	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr1:51702468T>A	ENST00000242719.3	+	1	526	c.40T>A	c.(40-42)Tcc>Acc	p.S14T	RP11-296A18.3_ENST00000366181.2_lincRNA|RNF11_ENST00000494873.1_3'UTR	NM_014372.4	NP_055187.1	Q9Y3C5	RNF11_HUMAN	ring finger protein 11	14					protein autoubiquitination (GO:0051865)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	DNA binding (GO:0003677)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		large_intestine(1)	1						GGATGACATCTCCCTGCTTCA	0.642																																					p.S14T		Atlas-SNP	.											.	RNF11	10	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.T40A						.						53	46	48					1																	51702468		2203	4300	6503	SO:0001583	missense	26994	exon1			GACATCTCCCTGC	AB024703	CCDS556.1	1p32	2013-01-09			ENSG00000123091	ENSG00000123091		"RING-type (C3HC4) zinc fingers"	10056	protein-coding gene	gene with protein product		612598				10673045, 10810093	Standard	NM_014372		Approved	CGI-123, Sid1669p, MGC51169	uc001csi.4	Q9Y3C5	OTTHUMG00000008190	ENST00000242719.3:c.40T>A	chr1.hg19:g.51702468T>A	ENSP00000242719:p.Ser14Thr	227.0	0.0		216.0	44.0	NM_014372	A8KAI2|Q5T7R8	Missense_Mutation	SNP	ENST00000242719.3	hg19	CCDS556.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.529623	0.85706	.	.	ENSG00000123091	ENST00000242719	T	0.18016	2.24	4.64	4.64	0.57946	.	0.174863	0.52532	D	0.000075	T	0.28234	0.0697	L	0.55990	1.75	0.80722	D	1	P	0.47191	0.891	P	0.53006	0.715	T	0.01185	-1.1425	10	0.34782	T	0.22	-1.3414	14.1633	0.65461	0.0:0.0:0.0:1.0	.	14	Q9Y3C5	RNF11_HUMAN	T	14	ENSP00000242719:S14T	ENSP00000242719:S14T	S	+	1	0	RNF11	51475056	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.513000	0.73742	2.073000	0.62155	0.454000	0.30748	TCC	.	.		0.642	RNF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022419.1	NM_014372		A	51702468	T	A	51702468	3	1	130	1	0	0	0	0	1	0	0	0	13439	1551	54	4	42	4	RNF11	1	51702468	Missense_Mutation	SNP	T	TCGA-DD-A4NH-01A-11D-A27I-10	28737099	51702468	197548153	2	21238										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118635840	118635840	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ccacttgtggaacattaataAgctgcatgctttccaaatag	7	9	0	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr1:118635840A>T	ENST00000336338.5	-	8	1177	c.1112T>A	c.(1111-1113)cTt>cAt	p.L371H		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	371						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		AACATTAATAAGCTGCATGCT	0.408																																					p.L371H		Atlas-SNP	.											.	SPAG17	263	.	0			c.T1112A						.						114	105	108					1																	118635840		2203	4300	6503	SO:0001583	missense	200162	exon8			TTAATAAGCTGCA		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.1112T>A	chr1.hg19:g.118635840A>T	ENSP00000337804:p.Leu371His	117.0	0.0		173.0	13.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	A	16.58	3.162470	0.57368	.	.	ENSG00000155761	ENST00000336338	T	0.72167	-0.63	5.64	5.64	0.86602	.	0.059501	0.64402	D	0.000003	T	0.81059	0.4744	M	0.79475	2.455	0.34293	D	0.683427	D	0.89917	1.0	D	0.83275	0.996	D	0.85133	0.0976	10	0.87932	D	0	.	15.8528	0.78947	1.0:0.0:0.0:0.0	.	371	Q6Q759	SPG17_HUMAN	H	371	ENSP00000337804:L371H	ENSP00000337804:L371H	L	-	2	0	SPAG17	118437363	1.000000	0.71417	0.874000	0.34290	0.228000	0.25075	7.742000	0.85008	2.141000	0.66446	0.482000	0.46254	CTT	.	.		0.408	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		T	118635840	A	T	118635840	3	4	130	1	0	0	0	0	1	0	0	0	14994	72	3	4	5723	4	SPAG17	1	118635840	Missense_Mutation	SNP	A	TCGA-DD-A4NH-01A-11D-A27I-10	66933372	118635840	130614781	3	21239										
NOTCH2NL	388677	hgsc.bcm.edu	37	chr1	145273364	145273364	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	atctcatccatgctttgtgtCtcgaccttgcctgaatggcg	9	12	2	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr1:145273364C>G	ENST00000369340.3	+	4	662	c.218C>G	c.(217-219)tCt>tGt	p.S73C	RP11-458D21.5_ENST00000468030.1_Missense_Mutation_p.S73C|NOTCH2NL_ENST00000344859.3_Missense_Mutation_p.S73C|NOTCH2NL_ENST00000362074.6_Missense_Mutation_p.S73C			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	73	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						TGCTTTGTGTCTCGACCTTGC	0.547																																					p.S73C		Atlas-SNP	.											.	NOTCH2NL	100	.	0			c.C218G						.						511	464	480					1																	145273364		2203	4300	6503	SO:0001583	missense	388677	exon3			TTGTGTCTCGACC		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"Notch homolog 2 (Drosophila) N-terminal like"			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.218C>G	chr1.hg19:g.145273364C>G	ENSP00000358346:p.Ser73Cys	2643.0	0.0		3638.0	161.0	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Missense_Mutation	SNP	ENST00000369340.3	hg19	CCDS909.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.509632	0.27036	.	.	ENSG00000213240	ENST00000362074;ENST00000344859;ENST00000369340	D;D;D	0.92397	-3.03;-3.03;-3.03	2.75	1.77	0.24775	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.93746	0.8001	M	0.89968	3.075	0.25140	N	0.990501	D;D	0.67145	0.99;0.996	P;P	0.62649	0.847;0.905	D	0.86894	0.2050	9	0.72032	D	0.01	.	8.4516	0.32873	0.2347:0.7653:0.0:0.0	.	73;73	Q7Z3S9-2;Q7Z3S9	.;NT2NL_HUMAN	C	73	ENSP00000354929:S73C;ENSP00000344557:S73C;ENSP00000358346:S73C	ENSP00000344557:S73C	S	+	2	0	NOTCH2NL	143984721	0.993000	0.37304	0.886000	0.34754	0.179000	0.23085	2.225000	0.42954	0.434000	0.26340	0.394000	0.25966	TCT	.	.		0.547	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458		G	145273364	C	G	145273364	3	3	130	1	0	0	0	0	1	0	0	0	10558	913	32	4	224	4	NOTCH2NL	1	145273364	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	26637524	145273364	103977257	4	21240										
TTC24	164118	hgsc.bcm.edu	37	chr1	156551507	156551507	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	gcacagggcaggcgacacggCgaccaatgtttcaatgtggc	14	11	1	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr1:156551507C>T	ENST00000368237.3	+	1	351	c.351C>T	c.(349-351)ggC>ggT	p.G117G	TTC24_ENST00000368236.3_Silent_p.G117G			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	117										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGCGACACGGCGACCAATGTT	0.637																																					p.G117G		Atlas-SNP	.											TTC24,NS,carcinoma,0,1	TTC24	46	.	0			c.C351T						.						42	50	47					1																	156551507		692	1591	2283	SO:0001819	synonymous_variant	164118	exon2			ACACGGCGACCAA		CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"Tetratricopeptide (TTC) repeat domain containing"	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.351C>T	chr1.hg19:g.156551507C>T		136.0	0.0		228.0	30.0	NM_001105669	Q5T3H7	Silent	SNP	ENST00000368237.3	hg19	CCDS53379.1																																																																																			.	.		0.637	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		T	156551507	C	T	156551507	2	4	130	1	0	0	0	0	0	0	0	1	16707	755	27	1		1	TTC24	1	156551507	Silent	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	11278143	156551507	92699114	5	21241										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200959773	200959773	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	tgcatgacgatgtcaatgatCcgtcgctccagggactgcca	11	12	1	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr1:200959773C>A	ENST00000422435.2	-	19	3082	c.2766G>T	c.(2764-2766)cgG>cgT	p.R922R	KIF21B_ENST00000332129.2_Silent_p.R922R|KIF21B_ENST00000461742.2_Silent_p.R922R|KIF21B_ENST00000360529.5_Silent_p.R922R	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	922					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TGTCAATGATCCGTCGCTCCA	0.562																																					p.R922R		Atlas-SNP	.											.	KIF21B	208	.	0			c.G2766T						.						94	88	90					1																	200959773		2203	4300	6503	SO:0001819	synonymous_variant	23046	exon19			AATGATCCGTCGC	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.2766G>T	chr1.hg19:g.200959773C>A		95.0	0.0		183.0	20.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	.		0.562	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200959773	C	A	200959773	2	1	130	1	0	0	0	0	0	0	0	1	8298	842	30	3		3	KIF21B	1	200959773	Silent	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	44408266	200959773	48290848	6	21242										
LYST	1130	hgsc.bcm.edu	37	chr1	235940366	235940366	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	taagcagtgattcttaccctGgcaaagagaaaaacaaatat	7	7	1	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr1:235940366G>A	ENST00000389794.3	-	17	5631	c.5457C>T	c.(5455-5457)gcC>gcT	p.A1819A	LYST_ENST00000536965.1_3'UTR|LYST_ENST00000389793.2_Silent_p.A1819A			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1819					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TTCTTACCCTGGCAAAGAGAA	0.338																																					p.A1819A		Atlas-SNP	.											.	LYST	370	.	0			c.C5457T						.						65	67	66					1																	235940366		2202	4300	6502	SO:0001819	synonymous_variant	1130	exon17			TACCCTGGCAAAG	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.5457C>T	chr1.hg19:g.235940366G>A		52.0	0.0		68.0	4.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.338	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235940366	G	A	235940366	2	1	130	1	0	0	0	0	0	0	0	1	9137	1335	47	3		3	LYST	1	235940366	Silent	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10	34980593	235940366	13310255	7	21243										
AKT3	10000	hgsc.bcm.edu	37	chr1	243800994	243800994	+	Frame_Shift_Del	DEL	C	C	-													0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	tctcgaaccaaaataactttCccaaaagtgcctttacctag							TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr1:243800994delC	ENST00000366539.1	-	6	680	c.480delG	c.(478-480)gggfs	p.G160fs	AKT3_ENST00000336199.5_Frame_Shift_Del_p.G160fs|AKT3_ENST00000263826.5_Frame_Shift_Del_p.G160fs|AKT3_ENST00000366540.1_Frame_Shift_Del_p.G160fs			Q9Y243	AKT3_HUMAN	v-akt murine thymoma viral oncogene homolog 3	160	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitochondrial genome maintenance (GO:0000002)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|skin(3)|stomach(1)	26	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			AAATAACTTTCCCAAAAGTGC	0.279																																					p.K161fs		Atlas-Indel,Pindel	.											.	AKT3	177	.	0			c.481delA						.						96	94	95					1																	243800994		2201	4297	6498	SO:0001589	frameshift_variant	10000	exon6			.	AF124141	CCDS31076.1, CCDS31077.1	1q44	2013-07-09	2013-07-09		ENSG00000117020	ENSG00000117020	2.7.11.1	"Pleckstrin homology (PH) domain containing"	393	protein-coding gene	gene with protein product	"protein kinase B, gamma"	611223				10092583, 10208883	Standard	NM_005465		Approved	PKBG, RAC-gamma, PRKBG	uc001iab.2	Q9Y243	OTTHUMG00000039994	ENST00000366539.1:c.480delG	chr1.hg19:g.243800994delC	ENSP00000355497:p.Gly160fs	31.0	0.0		59.0	22.0	NM_001206729	Q0VAA6|Q5VTI1|Q5VTI2|Q96QV3|Q9UFP5	Frame_Shift_Del	DEL	ENST00000366539.1	hg19	CCDS31077.1																																																																																			.	.		0.279	AKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096479.1	NM_181690		-	243800994	C	-	243800994	7	5	130	1	0	1	0	1	0	0	0	0	481	842	30	0	1043	0	AKT3	1	243800994	Frame_Shift_Del	DEL	C	TCGA-DD-A4NH-01A-11D-A27I-10	7860628	243800994	5449627	8	21244										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196740508	196740508	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	cactgtctaagtaactcaatGggaggttgagccccatatac	9	10	2	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr2:196740508G>T	ENST00000312428.6	-	38	6277	c.6177C>A	c.(6175-6177)ccC>ccA	p.P2059P		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2059	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GTAACTCAATGGGAGGTTGAG	0.408																																					p.P2059P		Atlas-SNP	.											.	DNAH7	512	.	0			c.C6177A						.						103	95	98					2																	196740508		1877	4105	5982	SO:0001819	synonymous_variant	56171	exon38			CTCAATGGGAGGT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.6177C>A	chr2.hg19:g.196740508G>T		193.0	0.0		201.0	44.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.408	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196740508	G	T	196740508	2	4	130	1	0	0	0	0	0	0	0	1	4608	1335	47	3		3	DNAH7	2	196740508	Silent	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10		196740508	46458865	9	21245										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230632438	230632438	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	tcaaacgtctttcggacaatTgtcaaaggtggattcaaact	8	8	4	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr2:230632438T>A	ENST00000283943.5	-	41	5989	c.5811A>T	c.(5809-5811)acA>acT	p.T1937T	TRIP12_ENST00000389044.4_Silent_p.T1985T|TRIP12_ENST00000389045.3_Silent_p.T1667T	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1937	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TTCGGACAATTGTCAAAGGTG	0.373																																					p.T1937T		Atlas-SNP	.											.	TRIP12	207	.	0			c.A5811T						.						100	101	101					2																	230632438		2203	4300	6503	SO:0001819	synonymous_variant	9320	exon41			GACAATTGTCAAA	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.5811A>T	chr2.hg19:g.230632438T>A		71.0	0.0		88.0	4.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.		0.373	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		A	230632438	T	A	230632438	2	1	130	1	0	0	0	0	0	0	0	1	16571	1799	63	4		4	TRIP12	2	230632438	Silent	SNP	T	TCGA-DD-A4NH-01A-11D-A27I-10	33891930	230632438	12566935	10	21246										
SNED1	25992	hgsc.bcm.edu	37	chr2	242004719	242004719	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	gacccaaaccctgaagagctCttcccaccgacggccctcaa	7	18	2	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr2:242004719C>T	ENST00000310397.8	+	21	2718	c.2718C>T	c.(2716-2718)ctC>ctT	p.L906L	SNED1_ENST00000405547.3_Silent_p.L906L|SNED1_ENST00000342631.6_Silent_p.L906L|SNED1_ENST00000401884.1_Silent_p.L906L|AC005237.4_ENST00000458377.1_RNA	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	906					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		CTGAAGAGCTCTTCCCACCGA	0.617																																					p.L906L		Atlas-SNP	.											.	SNED1	76	.	0			c.C2718T						.						23	27	26					2																	242004719		1978	4158	6136	SO:0001819	synonymous_variant	25992	exon21			AGAGCTCTTCCCA	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"Fibronectin type III domain containing"	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.2718C>T	chr2.hg19:g.242004719C>T		81.0	0.0		112.0	13.0	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	hg19	CCDS46562.1																																																																																			.	.		0.617	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		T	242004719	C	T	242004719	2	4	130	1	0	0	0	0	0	0	0	1	14860	900	32	3		3	SNED1	2	242004719	Silent	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	11372281	242004719	1194654	11	21247										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48610139	48610139	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	cgtggggccaggttctccttTaggtccgacagggccaggca	15	12	1	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr3:48610139T>A	ENST00000328333.8	-	87	6972	c.6865A>T	c.(6865-6867)Aaa>Taa	p.K2289*	COL7A1_ENST00000454817.1_Nonsense_Mutation_p.K2257*	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2289	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GGTTCTCCTTTAGGTCCGACA	0.627																																					p.K2289X		Atlas-SNP	.											.	COL7A1	320	.	0			c.A6865T						.						24	30	28					3																	48610139		2200	4296	6496	SO:0001587	stop_gained	1294	exon87			CTCCTTTAGGTCC	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6865A>T	chr3.hg19:g.48610139T>A	ENSP00000332371:p.Lys2289*	139.0	0.0		152.0	19.0	NM_000094	Q14054|Q16507	Nonsense_Mutation	SNP	ENST00000328333.8	hg19	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	T	46	12.575030	0.99679	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	.	.	.	6.06	6.06	0.98353	.	0.000000	0.49916	D	0.000138	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.1837	0.72982	0.0:0.0:0.0:1.0	.	.	.	.	X	2289;2257	.	ENSP00000332371:K2289X	K	-	1	0	COL7A1	48585143	1.000000	0.71417	1.000000	0.80357	0.187000	0.23431	3.430000	0.52807	2.322000	0.78497	0.528000	0.53228	AAA	.	.		0.627	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48610139	T	A	48610139	4	1	130	1	0	0	0	0	0	1	0	0	3706	1763	61	4	2097	4	COL7A1	3	48610139	Nonsense_Mutation	SNP	T	TCGA-DD-A4NH-01A-11D-A27I-10		48610139	149412291	12	21248										
KBTBD8	84541	hgsc.bcm.edu	37	chr3	67054129	67054129	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	atacgttttcctctgatggaAgatacctttatagagaaaat	7	6	1	3			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr3:67054129A>T	ENST00000417314.2	+	3	787	c.738A>T	c.(736-738)gaA>gaT	p.E246D	KBTBD8_ENST00000469661.1_3'UTR|KBTBD8_ENST00000295568.4_Missense_Mutation_p.E220D|KBTBD8_ENST00000460576.1_Intron			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	246	BACK.					cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		CTCTGATGGAAGATACCTTTA	0.403																																					p.E246D		Atlas-SNP	.											.	KBTBD8	101	.	0			c.A738T						.						97	109	105					3																	67054129		2203	4300	6503	SO:0001583	missense	84541	exon3			GATGGAAGATACC	AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"BTB/POZ domain containing"	30691	protein-coding gene	gene with protein product	"T-cell activation kelch repeat protein"					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.738A>T	chr3.hg19:g.67054129A>T	ENSP00000401878:p.Glu246Asp	65.0	0.0		53.0	12.0	NM_032505	B4DTW6|Q96JI5	Missense_Mutation	SNP	ENST00000417314.2	hg19	CCDS2906.2	.	.	.	.	.	.	.	.	.	.	A	8.216	0.801378	0.16397	.	.	ENSG00000163376	ENST00000295568;ENST00000417314	T;T	0.68765	-0.35;-0.35	4.82	3.65	0.41850	BTB/Kelch-associated (2);	0.096458	0.64402	D	0.000001	T	0.33498	0.0865	N	0.01649	-0.78	0.42321	D	0.992254	B	0.09022	0.002	B	0.10450	0.005	T	0.08764	-1.0706	10	0.44086	T	0.13	.	3.8885	0.09108	0.6678:0.1311:0.0745:0.1265	.	246	Q8NFY9	KBTB8_HUMAN	D	220;246	ENSP00000295568:E220D;ENSP00000401878:E246D	ENSP00000295568:E220D	E	+	3	2	KBTBD8	67136819	0.978000	0.34361	1.000000	0.80357	0.995000	0.86356	0.232000	0.17891	0.777000	0.33496	0.445000	0.29226	GAA	.	.		0.403	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505		T	67054129	A	T	67054129	3	4	130	1	0	0	0	0	1	0	0	0	8008	69	3	4	748	4	KBTBD8	3	67054129	Missense_Mutation	SNP	A	TCGA-DD-A4NH-01A-11D-A27I-10	18443990	67054129	130968301	13	21249										
CASR	846	hgsc.bcm.edu	37	chr3	122003472	122003472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ctgcccgggccacgctgcgcCgcagcaacgtctcccgcaag	12	19	1	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr3:122003472C>T	ENST00000490131.1	+	7	3043	c.2671C>T	c.(2671-2673)Cgc>Tgc	p.R891C	AC068754.1_ENST00000408547.1_RNA|CASR_ENST00000498619.1_Missense_Mutation_p.R901C|CASR_ENST00000296154.5_Missense_Mutation_p.R891C	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	891	Interaction with RNF19A.				anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.R891G(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	CACGCTGCGCCGCAGCAACGT	0.627																																					p.R901C		Atlas-SNP	.											CASR,NS,carcinoma,-1,1	CASR	190	.	1	Substitution - Missense(1)	lung(1)	c.C2701T						.						30	31	31					3																	122003472		2203	4298	6501	SO:0001583	missense	846	exon7			CTGCGCCGCAGCA	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.2671C>T	chr3.hg19:g.122003472C>T	ENSP00000418685:p.Arg891Cys	55.0	0.0		37.0	2.0	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	hg19	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634258	0.87660	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.89343	-2.5;-2.5;-2.5	5.89	5.89	0.94794	.	0.051500	0.85682	D	0.000000	D	0.90283	0.6961	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	P;P	0.60117	0.869;0.791	D	0.91266	0.5040	10	0.87932	D	0	.	19.2448	0.93898	0.0:1.0:0.0:0.0	.	901;891	E7ENE0;P41180	.;CASR_HUMAN	C	891;901;891	ENSP00000418685:R891C;ENSP00000420194:R901C;ENSP00000296154:R891C	ENSP00000296154:R891C	R	+	1	0	CASR	123486162	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.666000	0.83877	2.793000	0.96121	0.561000	0.74099	CGC	.	.		0.627	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		T	122003472	C	T	122003472	3	4	130	1	0	0	0	0	1	0	0	0	2684	652	23	1	2723	1	CASR	3	122003472	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	54949343	122003472	76018958	14	21250										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151166486	151166486	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	aaatttggtcttgcattaacCaagagggatctgctctgaga	10	7	3	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr3:151166486C>A	ENST00000282466.3	-	4	1282	c.1283G>T	c.(1282-1284)tGg>tTg	p.W428L		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	428					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TTGCATTAACCAAGAGGGATC	0.428																																					p.W428L		Atlas-SNP	.											.	IGSF10	279	.	0			c.G1283T						.						117	107	111					3																	151166486		2203	4300	6503	SO:0001583	missense	285313	exon4			ATTAACCAAGAGG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.1283G>T	chr3.hg19:g.151166486C>A	ENSP00000282466:p.Trp428Leu	62.0	0.0		81.0	13.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.407204	0.83230	.	.	ENSG00000152580	ENST00000282466	D	0.96265	-3.96	5.08	5.08	0.68730	.	0.000000	0.44097	D	0.000499	D	0.98040	0.9354	M	0.81802	2.56	0.58432	D	0.999997	D	0.89917	1.0	D	0.85130	0.997	D	0.97943	1.0327	10	0.39692	T	0.17	.	18.4741	0.90785	0.0:1.0:0.0:0.0	.	428	Q6WRI0	IGS10_HUMAN	L	428	ENSP00000282466:W428L	ENSP00000282466:W428L	W	-	2	0	IGSF10	152649176	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.487000	0.81328	2.378000	0.81104	0.555000	0.69702	TGG	.	.		0.428	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151166486	C	A	151166486	3	1	130	1	0	0	0	0	1	0	0	0	7606	595	21	3	6648	3	IGSF10	3	151166486	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	29163014	151166486	46855944	15	21251										
ZNF732	654254	hgsc.bcm.edu	37	chr4	289878	289878	+	Missense_Mutation	SNP	C	C	A													0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	tctatacaaattctgctgggCagggtccaggcatttccact							TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr4:289878C>A	ENST00000419098.1	-	2	80	c.70G>T	c.(70-72)Gcc>Tcc	p.A24S		NM_001137608.1	NP_001131080.1	B4DXR9	ZN732_HUMAN	zinc finger protein 732	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)	3						TTCTGCTGGGCAGGGTCCAGG	0.418																																					p.A23S		Atlas-SNP	.											.	ZNF732	117	.	0			c.G67T						.						33	32	32					4																	289878		692	1590	2282	SO:0001583	missense	654254	exon1			GCTGGGCAGGGTC	AK302099	CCDS46990.1	4p16.3	2014-02-12	2009-07-22		ENSG00000186777	ENSG00000186777		"Zinc fingers, C2H2-type", "-"	37138	protein-coding gene	gene with protein product							Standard	NM_001137608		Approved	FLJ59067	uc011buu.1	B4DXR9	OTTHUMG00000159883	ENST00000419098.1:c.70G>T	chr4.hg19:g.289878C>A	ENSP00000415774:p.Ala24Ser	175.0	0.0		178.0	8.0	NM_001137608		Missense_Mutation	SNP	ENST00000419098.1	hg19	CCDS46990.1	.	.	.	.	.	.	.	.	.	.	C	3.894	-0.023332	0.07634	.	.	ENSG00000186777	ENST00000419098	T	0.02258	4.37	1.22	-2.43	0.06522	Krueppel-associated box (4);	.	.	.	.	T	0.03263	0.0095	M	0.65677	2.01	0.09310	N	1	B	0.32350	0.366	B	0.37692	0.256	T	0.36939	-0.9727	9	0.42905	T	0.14	.	2.9027	0.05711	0.0:0.4666:0.2847:0.2487	.	24	B4DXR9	ZN732_HUMAN	S	24	ENSP00000415774:A24S	ENSP00000415774:A24S	A	-	1	0	ZNF732	279878	0.000000	0.05858	0.085000	0.20634	0.087000	0.18053	-1.157000	0.03157	-0.694000	0.05113	-0.680000	0.03767	GCC	.	.		0.418	ZNF732-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357937.2	NM_001137608		A	289878	C	A	289878	3	1	130	1	0	0	0	0	1	0	0	0	18138	710	25	3	1699	3	ZNF732	4	289878	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10		289878	190864398	16	21252	90	2								
ZNF732	654254	hgsc.bcm.edu	37	chr4	289881	289881	+	Missense_Mutation	SNP	G	G	T													0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	atacaaattctgctgggcagGgtccaggcatttccactctt							TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr4:289881G>T	ENST00000419098.1	-	2	77	c.67C>A	c.(67-69)Cct>Act	p.P23T		NM_001137608.1	NP_001131080.1	B4DXR9	ZN732_HUMAN	zinc finger protein 732	23	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)	3						TGCTGGGCAGGGTCCAGGCAT	0.413																																					p.P22T		Atlas-SNP	.											.	ZNF732	117	.	0			c.C64A						.						35	33	34					4																	289881		692	1590	2282	SO:0001583	missense	654254	exon1			GGGCAGGGTCCAG	AK302099	CCDS46990.1	4p16.3	2014-02-12	2009-07-22		ENSG00000186777	ENSG00000186777		"Zinc fingers, C2H2-type", "-"	37138	protein-coding gene	gene with protein product							Standard	NM_001137608		Approved	FLJ59067	uc011buu.1	B4DXR9	OTTHUMG00000159883	ENST00000419098.1:c.67C>A	chr4.hg19:g.289881G>T	ENSP00000415774:p.Pro23Thr	168.0	0.0		170.0	8.0	NM_001137608		Missense_Mutation	SNP	ENST00000419098.1	hg19	CCDS46990.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.337467	0.00224	.	.	ENSG00000186777	ENST00000419098	T	0.02472	4.28	1.22	1.22	0.21188	Krueppel-associated box (4);	.	.	.	.	T	0.02888	0.0086	L	0.56340	1.77	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	T	0.49771	-0.8904	9	0.08599	T	0.76	.	5.3307	0.15930	0.0:0.0:1.0:0.0	.	23	B4DXR9	ZN732_HUMAN	T	23	ENSP00000415774:P23T	ENSP00000415774:P23T	P	-	1	0	ZNF732	279881	0.000000	0.05858	0.122000	0.21767	0.125000	0.20455	-0.620000	0.05565	0.300000	0.22699	0.305000	0.20034	CCT	.	.		0.413	ZNF732-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357937.2	NM_001137608		T	289881	G	T	289881	3	4	130	1	0	0	0	0	1	0	0	0	18138	1232	43	3	1702	3	ZNF732	4	289881	Missense_Mutation	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10	3	289881	190864395	17	21253	90	2								
ATP10D	57205	hgsc.bcm.edu	37	chr4	47517533	47517533	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	tgttcctagttgtcctgaacTgggtacctttggtagaagcc	11	9	0	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr4:47517533T>C	ENST00000273859.3	+	3	600	c.331T>C	c.(331-333)Tgg>Cgg	p.W111R	ATP10D_ENST00000504445.1_Missense_Mutation_p.W111R	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	111					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						TGTCCTGAACTGGGTACCTTT	0.438																																					p.W111R		Atlas-SNP	.											.	ATP10D	168	.	0			c.T331C						.						168	157	161					4																	47517533		2203	4300	6503	SO:0001583	missense	57205	exon3			CTGAACTGGGTAC	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.331T>C	chr4.hg19:g.47517533T>C	ENSP00000273859:p.Trp111Arg	180.0	0.0		142.0	18.0	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	hg19	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.371132	0.82573	.	.	ENSG00000145246	ENST00000273859;ENST00000504445	T;T	0.80566	-1.39;-1.39	5.38	5.38	0.77491	ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.88804	0.6536	M	0.74881	2.28	0.52099	D	0.999947	D;D	0.89917	0.994;1.0	P;D	0.74674	0.837;0.984	D	0.90062	0.4157	10	0.72032	D	0.01	-10.1816	14.5555	0.68097	0.0:0.0:0.0:1.0	.	111;111	Q9P241;Q6PEW3	AT10D_HUMAN;.	R	111	ENSP00000273859:W111R;ENSP00000420909:W111R	ENSP00000273859:W111R	W	+	1	0	ATP10D	47212290	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.671000	0.83941	2.032000	0.59987	0.533000	0.62120	TGG	.	.		0.438	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		C	47517533	T	C	47517533	3	2	130	1	0	0	0	0	1	0	0	0	1118	1580	55	2	337	2	ATP10D	4	47517533	Missense_Mutation	SNP	T	TCGA-DD-A4NH-01A-11D-A27I-10	47227652	47517533	143636743	18	21254										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79238646	79238646	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ggagagggtttctactctgaCcatggagtctgcaaaggtat	13	7	3	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr4:79238646C>A	ENST00000325942.6	+	17	2384	c.1944C>A	c.(1942-1944)gaC>gaA	p.D648E	FRAS1_ENST00000264899.6_Missense_Mutation_p.D648E|FRAS1_ENST00000264895.6_Missense_Mutation_p.D648E	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	648					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TCTACTCTGACCATGGAGTCT	0.512																																					p.D648E		Atlas-SNP	.											.	FRAS1	779	.	0			c.C1944A						.						67	71	70					4																	79238646		2024	4202	6226	SO:0001583	missense	80144	exon17			CTCTGACCATGGA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1944C>A	chr4.hg19:g.79238646C>A	ENSP00000326330:p.Asp648Glu	84.0	0.0		93.0	16.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	8.989|8.989|8.989	0.977324|0.977324|0.977324	0.18812|0.18812|0.18812	.|.|.	.|.|.	ENSG00000138759|ENSG00000138759|ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000264899|ENST00000508900|ENST00000502446	T;T;T|.|.	0.76186|.|.	-1.0;-1.0;-1.0|.|.	5.71|5.71|5.71	-0.445|-0.445|-0.445	0.12242|0.12242|0.12242	Growth factor, receptor (1);|.|.	0.358875|.|.	0.31102|.|.	N|.|.	0.008242|.|.	T|T|T	0.36608|0.36608|0.36608	0.0973|0.0973|0.0973	L|L|L	0.57536|0.57536|0.57536	1.79|1.79|1.79	0.09310|0.09310|0.09310	N|N|N	0.999998|0.999998|0.999998	P;P;D;B|.|.	0.54772|.|.	0.781;0.781;0.968;0.434|.|.	P;P;P;B|.|.	0.52793|.|.	0.54;0.459;0.709;0.325|.|.	T|T|T	0.35375|0.35375|0.35375	-0.9791|-0.9791|-0.9791	10|5|5	0.48119|.|.	T|.|.	0.1|.|.	.|.|.	1.5182|1.5182|1.5182	0.02510|0.02510|0.02510	0.1444:0.2729:0.1416:0.4412|0.1444:0.2729:0.1416:0.4412|0.1444:0.2729:0.1416:0.4412	.|.|.	648;648;648;648|.|.	E9PHH6;Q86XX4;E7EWM9;A2RRR8|.|.	.;FRAS1_HUMAN;.;.|.|.	E|T|N	648|491|577	ENSP00000326330:D648E;ENSP00000264895:D648E;ENSP00000264899:D648E|.|.	ENSP00000264895:D648E|.|.	D|P|T	+|+|+	3|1|2	2|0|0	FRAS1|FRAS1|FRAS1	79457670|79457670|79457670	0.014000|0.014000|0.014000	0.17966|0.17966|0.17966	0.013000|0.013000|0.013000	0.15412|0.15412|0.15412	0.015000|0.015000|0.015000	0.08874|0.08874|0.08874	-0.286000|-0.286000|-0.286000	0.08399|0.08399|0.08399	0.063000|0.063000|0.063000	0.16370|0.16370|0.16370	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GAC|CCA|ACC	.	.		0.512	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			A	79238646	C	A	79238646	3	1	130	1	0	0	0	0	1	0	0	0	6050	506	18	3	2010	3	FRAS1	4	79238646	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	31721113	79238646	111915630	19	21255										
SLC6A3	6531	hgsc.bcm.edu	37	chr5	1409893	1409893	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	aggacgatgaagagcgtgaaGagctcacggtgtctgtgcag	16	7	2	4			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr5:1409893G>A	ENST00000270349.9	-	10	1468	c.1341C>T	c.(1339-1341)ctC>ctT	p.L447L	SLC6A3_ENST00000453492.2_Silent_p.L447L	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	447					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	AGAGCGTGAAGAGCTCACGGT	0.592																																					p.L447L		Atlas-SNP	.											.	SLC6A3	102	.	0			c.C1341T						.						209	151	170					5																	1409893		2203	4300	6503	SO:0001819	synonymous_variant	6531	exon10			CGTGAAGAGCTCA		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"Solute carriers"	11049	protein-coding gene	gene with protein product	"dopamine transporter"	126455	"solute carrier family 6 (neurotransmitter transporter, dopamine), member 3", "dopamine transporter 1"	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1341C>T	chr5.hg19:g.1409893G>A		169.0	0.0		198.0	35.0	NM_001044	A2RUN4|Q14996	Silent	SNP	ENST00000270349.9	hg19	CCDS3863.1																																																																																			.	.		0.592	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		A	1409893	G	A	1409893	2	1	130	1	0	0	0	0	0	0	0	1	14700	929	33	3		3	SLC6A3	5	1409893	Silent	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10		1409893	179505367	20	21256										
PCDHGC5	56097	hgsc.bcm.edu	37	chr5	140869878	140869878	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ctattggcctctttggccaaCcctgtcctagagagcacacc	8	15	1	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr5:140869878C>T	ENST00000252087.1	+	1	1071	c.1071C>T	c.(1069-1071)aaC>aaT	p.N357N	PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	357	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N357K(2)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTTGGCCAACCCTGTCCTAG	0.542																																					p.N357N		Atlas-SNP	.											PCDHGC5_ENST00000252087,NS,carcinoma,0,2	PCDHGC5	199	.	2	Substitution - Missense(2)	lung(2)	c.C1071T						.						93	94	93					5																	140869878		2203	4300	6503	SO:0001819	synonymous_variant	56097	exon1			GGCCAACCCTGTC	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"Cadherins / Protocadherins : Clustered"	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.1071C>T	chr5.hg19:g.140869878C>T		138.0	0.0		151.0	37.0	NM_018929	Q9Y5C2	Silent	SNP	ENST00000252087.1	hg19	CCDS4263.1																																																																																			.	.		0.542	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929		T	140869878	C	T	140869878	2	4	130	1	0	0	0	0	0	0	0	1	11580	506	18	3		3	PCDHGC5	5	140869878	Silent	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	139459985	140869878	40045382	21	21257										
RIMS2	9699	hgsc.bcm.edu	37	chr8	104897822	104897822	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	agaggaagagtaccagtcacGctaccgaagtgatccgaatt	11	9	1	3			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr8:104897822G>T	ENST00000436393.2	+	2	570	c.329G>T	c.(328-330)cGc>cTc	p.R110L	RIMS2_ENST00000522174.1_3'UTR|RIMS2_ENST00000507740.1_Missense_Mutation_p.R140L|RIMS2_ENST00000262231.10_Missense_Mutation_p.R140L|RIMS2_ENST00000406091.3_Missense_Mutation_p.R332L			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	363	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.R140L(2)|p.R368L(1)|p.R110L(1)|p.R332L(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TACCAGTCACGCTACCGAAGT	0.463										HNSCC(12;0.0054)																											p.R332L		Atlas-SNP	.											RIMS2_ENST00000507740,NS,carcinoma,0,5	RIMS2	1357	.	5	Substitution - Missense(5)	lung(5)	c.G995T						.						97	96	96					8																	104897822		2029	4177	6206	SO:0001583	missense	9699	exon4			AGTCACGCTACCG	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.329G>T	chr8.hg19:g.104897822G>T	ENSP00000390665:p.Arg110Leu	85.0	0.0		94.0	12.0	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	hg19		.	.	.	.	.	.	.	.	.	.	G	28.1	4.889240	0.91889	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.32	5.32	0.75619	.	.	.	.	.	T	0.66954	0.2842	M	0.76574	2.34	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.994;1.0;0.999;1.0	D;D;D;D;D	0.91635	0.99;0.988;0.999;0.997;0.999	T	0.70684	-0.4804	9	0.87932	D	0	.	18.9862	0.92771	0.0:0.0:1.0:0.0	.	363;110;140;140;332	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	L	332;363;332;363;140;140;140;140;110	ENSP00000427018:R332L;ENSP00000384892:R332L;ENSP00000425205:R140L;ENSP00000262231:R140L;ENSP00000423559:R140L;ENSP00000386228:R140L;ENSP00000390665:R110L	ENSP00000262231:R140L	R	+	2	0	RIMS2	104966998	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	9.615000	0.98356	2.479000	0.83701	0.467000	0.42956	CGC	.	.		0.463	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		T	104897822	G	T	104897822	3	4	130	1	0	0	0	0	1	0	0	0	13383	1087	38	1	1135	1	RIMS2	8	104897822	Missense_Mutation	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10		104897822	41466200	22	21258										
TEK	7010	hgsc.bcm.edu	37	chr9	27206595	27206595	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	tccagagggaagaaccagctGtgcagttcaactcagggact	12	10	2	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr9:27206595G>C	ENST00000380036.4	+	15	2822	c.2380G>C	c.(2380-2382)Gtg>Ctg	p.V794L	TEK_ENST00000519097.1_Missense_Mutation_p.V646L|TEK_ENST00000406359.4_Missense_Mutation_p.V751L	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	794					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	AGAACCAGCTGTGCAGTTCAA	0.408																																					p.V794L		Atlas-SNP	.											.	TEK	250	.	0			c.G2380C						.						57	57	57					9																	27206595		2203	4300	6503	SO:0001583	missense	7010	exon15			CCAGCTGTGCAGT	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2380G>C	chr9.hg19:g.27206595G>C	ENSP00000369375:p.Val794Leu	101.0	0.0		109.0	12.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	G	3.020	-0.202071	0.06219	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359	T;T;T	0.72615	-0.65;-0.66;-0.67	5.9	5.01	0.66863	.	0.000000	0.46145	D	0.000305	T	0.57198	0.2037	L	0.29908	0.895	0.49798	D	0.999821	B;B;B;B	0.21606	0.002;0.001;0.004;0.058	B;B;B;B	0.14578	0.002;0.007;0.007;0.011	T	0.54153	-0.8336	10	0.07813	T	0.8	.	16.8258	0.85930	0.0:0.2412:0.7588:0.0	.	646;827;751;794	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	L	646;794;751	ENSP00000430686:V646L;ENSP00000369375:V794L;ENSP00000383977:V751L	ENSP00000369375:V794L	V	+	1	0	TEK	27196595	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.125000	0.57931	1.501000	0.48654	0.637000	0.83480	GTG	.	.		0.408	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			C	27206595	G	C	27206595	3	2	130	1	0	0	0	0	1	0	0	0	15766	1377	48	4	2438	4	TEK	9	27206595	Missense_Mutation	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10		27206595	114006836	23	21259										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79983032	79983032	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ccgatctacagtctgaagtcAtaagacactattcaaaacag	6	10	4	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr9:79983032A>C	ENST00000360280.3	+	62	8793	c.8533A>C	c.(8533-8535)Ata>Cta	p.I2845L	VPS13A_ENST00000376634.4_Missense_Mutation_p.I2845L|VPS13A_ENST00000357409.5_Missense_Mutation_p.I2845L|VPS13A_ENST00000376636.3_Missense_Mutation_p.I2806L	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2845					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GTCTGAAGTCATAAGACACTA	0.338																																					p.I2845L		Atlas-SNP	.											.	VPS13A	735	.	0			c.A8533C						.						69	64	66					9																	79983032		2202	4295	6497	SO:0001583	missense	23230	exon62			GAAGTCATAAGAC	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.8533A>C	chr9.hg19:g.79983032A>C	ENSP00000353422:p.Ile2845Leu	44.0	0.0		44.0	8.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	14.80	2.642606	0.47153	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.93	-0.554	0.11811	.	0.257926	0.43747	D	0.000528	T	0.68412	0.2998	L	0.55834	1.745	0.80722	D	1	B;B;B;B	0.30455	0.029;0.28;0.239;0.121	B;B;B;B	0.29176	0.025;0.077;0.099;0.085	T	0.57271	-0.7840	9	.	.	.	.	11.5912	0.50947	0.6216:0.0:0.3784:0.0	.	2806;2845;2845;2845	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	L	2845;2806;2845;2845	ENSP00000365821:I2845L;ENSP00000365823:I2806L;ENSP00000353422:I2845L;ENSP00000349985:I2845L	.	I	+	1	0	VPS13A	79172852	0.616000	0.27035	0.986000	0.45419	0.907000	0.53573	0.238000	0.18004	-0.325000	0.08577	-0.375000	0.07067	ATA	.	.		0.338	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		C	79983032	A	C	79983032	3	2	130	1	0	0	0	0	1	0	0	0	17204	217	8	5	8779	5	VPS13A	9	79983032	Missense_Mutation	SNP	A	TCGA-DD-A4NH-01A-11D-A27I-10	52776437	79983032	61230399	24	21260										
MED27	9442	hgsc.bcm.edu	37	chr9	134738510	134738510	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	tgatagtggagcagggcagtGgtggcatggtctgtcacctg	17	7	2	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr9:134738510G>A	ENST00000292035.5	-	7	804	c.741C>T	c.(739-741)acC>acT	p.T247T	MED27_ENST00000357028.2_Silent_p.T211T	NM_004269.3	NP_004260.2	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	247					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	18		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		GCAGGGCAGTGGTGGCATGGT	0.532																																					p.T247T	Colon(41;784 923 6932 42329 52483)	Atlas-SNP	.											.	MED27	37	.	0			c.C741T						.						72	64	67					9																	134738510		2203	4300	6503	SO:0001819	synonymous_variant	9442	exon7			GGCAGTGGTGGCA	AF104252	CCDS6945.1, CCDS59153.1, CCDS69689.1	9q34.13	2008-02-05	2007-07-30	2007-07-30	ENSG00000160563	ENSG00000160563			2377	protein-coding gene	gene with protein product		605044	"cofactor required for Sp1 transcriptional activation, subunit 8, 34kDa"	CRSP8		9989412	Standard	NM_004269		Approved	TRAP37, CRSP34	uc004cbe.2	Q6P2C8	OTTHUMG00000020833	ENST00000292035.5:c.741C>T	chr9.hg19:g.134738510G>A		159.0	0.0		180.0	32.0	NM_004269	O95401|Q4F964|Q5VTA4|Q5VTA5|Q9BU57|Q9NYR4|V9GYV9	Silent	SNP	ENST00000292035.5	hg19	CCDS6945.1																																																																																			.	.		0.532	MED27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054770.2	NM_004269		A	134738510	G	A	134738510	2	1	130	1	0	0	0	0	0	0	0	1	9454	1335	47	3		3	MED27	9	134738510	Silent	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10	54755478	134738510	6474921	25	21261										
RPL7A	6130	hgsc.bcm.edu	37	chr9	136216457	136216457	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ccgctttgtgaaatggccccGctatatcaggttgcagcggc	12	12	1	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr9:136216457G>A	ENST00000323345.6	+	3	206	c.176G>A	c.(175-177)cGc>cAc	p.R59H	SNORD24_ENST00000383884.1_RNA|MED22_ENST00000476080.1_5'Flank|RPL7A_ENST00000315731.4_Silent_p.P3P|SNORD36C_ENST00000516733.1_RNA|RPL7A_ENST00000463740.1_3'UTR|SNORD36A_ENST00000362874.1_RNA|SURF1_ENST00000495952.1_5'Flank|MED22_ENST00000344469.5_5'Flank|MED22_ENST00000343730.5_5'Flank|SNORD36B_ENST00000363961.1_RNA|MED22_ENST00000491289.1_5'Flank|MED22_ENST00000371999.1_5'Flank|MED22_ENST00000471524.1_5'Flank	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	59					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		AAATGGCCCCGCTATATCAGG	0.542																																					p.R59H		Atlas-SNP	.											.	RPL7A	9	.	0			c.G176A						.						47	51	49					9																	136216457		2203	4297	6500	SO:0001583	missense	6130	exon3			GGCCCCGCTATAT	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"L ribosomal proteins"	10364	protein-coding gene	gene with protein product	"surfeit 3", "PLA-X polypeptide", "surfeit locus protein 3", "60S ribosomal protein L7a", ";", "thyroid hormone receptor uncoupling protein"	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.176G>A	chr9.hg19:g.136216457G>A	ENSP00000361076:p.Arg59His	112.0	0.0		170.0	43.0	NM_000972	P11518|Q5T8U4	Missense_Mutation	SNP	ENST00000323345.6	hg19	CCDS6965.1	.	.	.	.	.	.	.	.	.	.	G	4.509	0.094398	0.08632	.	.	ENSG00000148303	ENST00000323345;ENST00000426651	T;T	0.56444	0.46;0.84	4.03	3.12	0.35913	.	0.000000	0.85682	D	0.000000	T	0.33352	0.0860	N	0.12182	0.205	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.07501	-1.0769	10	0.40728	T	0.16	.	12.1047	0.53805	0.0:0.0:0.8272:0.1728	.	59	P62424	RL7A_HUMAN	H	59;86	ENSP00000361076:R59H;ENSP00000416638:R86H	ENSP00000361076:R59H	R	+	2	0	RPL7A	135206278	1.000000	0.71417	1.000000	0.80357	0.010000	0.07245	5.826000	0.69293	0.691000	0.31592	-0.823000	0.03104	CGC	.	.		0.542	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972		A	136216457	G	A	136216457	3	1	130	1	0	0	0	0	1	0	0	0	13615	1087	38	1	186	1	RPL7A	9	136216457	Missense_Mutation	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10	1477947	136216457	4996974	26	21262										
BICC1	80114	hgsc.bcm.edu	37	chr10	60573612	60573612	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ctcatccatgtccctttcacGgtccaacagtcgtgagcact	7	15	2	1	rs111922761	byFrequency	TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr10:60573612G>C	ENST00000373886.3	+	18	2403	c.2399G>C	c.(2398-2400)cGg>cCg	p.R800P	BICC1_ENST00000263103.1_Missense_Mutation_p.R426P	NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	800					multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						TCCCTTTCACGGTCCAACAGT	0.458																																					p.R800P		Atlas-SNP	.											.	BICC1	121	.	0			c.G2399C						.						151	140	144					10																	60573612		2203	4300	6503	SO:0001583	missense	80114	exon18			TTTCACGGTCCAA	AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"Sterile alpha motif (SAM) domain containing"	19351	protein-coding gene	gene with protein product		614295	"bicaudal C homolog 1 (Drosophila)"				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.2399G>C	chr10.hg19:g.60573612G>C	ENSP00000362993:p.Arg800Pro	199.0	0.0		248.0	45.0	NM_001080512		Missense_Mutation	SNP	ENST00000373886.3	hg19	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337866	0.81911	.	.	ENSG00000122870	ENST00000373886;ENST00000263103	T;T	0.49139	1.6;0.79	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.64438	0.2598	L	0.50333	1.59	0.58432	D	0.999997	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.995	T	0.57670	-0.7771	10	0.33940	T	0.23	-16.3176	18.4528	0.90710	0.0:0.0:1.0:0.0	.	720;800	E7EU62;Q9H694	.;BICC1_HUMAN	P	800;426	ENSP00000362993:R800P;ENSP00000263103:R426P	ENSP00000263103:R426P	R	+	2	0	BICC1	60243618	1.000000	0.71417	0.973000	0.42090	0.778000	0.44026	9.313000	0.96297	2.793000	0.96121	0.563000	0.77884	CGG	.	G|0.992;A|0.008		0.458	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		C	60573612	G	C	60573612	3	2	130	1	0	0	0	0	1	0	0	0	1427	1116	39	4	2469	4	BICC1	10	60573612	Missense_Mutation	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10		60573612	74961135	27	21263										
OAT	4942	hgsc.bcm.edu	37	chr10	126089485	126089485	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	acaacatcagaaggtagcttCatgagttcatttctcaagat	7	8	4	3			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr10:126089485C>T	ENST00000368845.5	-	9	1175	c.1083G>A	c.(1081-1083)atG>atA	p.M361I	OAT_ENST00000539214.1_Missense_Mutation_p.M223I|OAT_ENST00000467675.1_5'Flank	NM_000274.3	NP_000265.1	P04181	OAT_HUMAN	ornithine aminotransferase	361					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-proline biosynthetic process (GO:0055129)|protein hexamerization (GO:0034214)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ornithine-oxo-acid transaminase activity (GO:0004587)|pyridoxal phosphate binding (GO:0030170)			endometrium(2)|large_intestine(1)|lung(2)	5		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)	AAGGTAGCTTCATGAGTTCAT	0.313																																					p.M361I		Atlas-SNP	.											.	OAT	25	.	0			c.G1083A						.						90	83	86					10																	126089485		2203	4299	6502	SO:0001583	missense	4942	exon9			TAGCTTCATGAGT	BC016928	CCDS7639.1, CCDS53586.1	10q26	2014-09-17	2010-01-20		ENSG00000065154	ENSG00000065154	2.6.1.13		8091	protein-coding gene	gene with protein product	"Ornithine aminotransferase", "ornithine aminotransferase precursor", "gyrate atrophy"	613349				1682785	Standard	NM_000274		Approved	HOGA	uc001lhp.3	P04181	OTTHUMG00000019213	ENST00000368845.5:c.1083G>A	chr10.hg19:g.126089485C>T	ENSP00000357838:p.Met361Ile	118.0	0.0		144.0	31.0	NM_000274	D3DRF0|Q16068|Q16069|Q68CS0|Q6IAV9|Q9UD03	Missense_Mutation	SNP	ENST00000368845.5	hg19	CCDS7639.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.299342	0.40694	.	.	ENSG00000065154	ENST00000539214;ENST00000368845	D;D	0.85484	-1.99;-1.99	4.97	4.04	0.47022	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.194639	0.64402	D	0.000004	T	0.73659	0.3615	N	0.10972	0.075	0.36605	D	0.87488	B	0.10296	0.003	B	0.09377	0.004	T	0.72966	-0.4131	10	0.52906	T	0.07	-23.6061	15.9362	0.79712	0.0:0.8642:0.1358:0.0	.	361	P04181	OAT_HUMAN	I	223;361	ENSP00000439042:M223I;ENSP00000357838:M361I	ENSP00000357838:M361I	M	-	3	0	OAT	126079475	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.789000	0.38724	1.357000	0.45904	0.655000	0.94253	ATG	.	.		0.313	OAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050863.1	NM_000274		T	126089485	C	T	126089485	3	4	130	1	0	0	0	0	1	0	0	0	10812	826	29	3	244	3	OAT	10	126089485	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	65515873	126089485	9445262	28	21264										
SYVN1	84447	hgsc.bcm.edu	37	chr11	64900425	64900425	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	gtcctcagccagccagtggaAacatttgaggaagagaagaa	12	8	1	3			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr11:64900425A>C	ENST00000377190.3	-	4	440	c.346T>G	c.(346-348)Ttc>Gtc	p.F116V	SYVN1_ENST00000307289.6_Missense_Mutation_p.F116V|SYVN1_ENST00000294256.8_Missense_Mutation_p.F116V|SYVN1_ENST00000526060.1_Missense_Mutation_p.F116V|SYVN1_ENST00000526121.1_5'Flank	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	116					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						AGCCAGTGGAAACATTTGAGG	0.557																																					p.F116V		Atlas-SNP	.											.	SYVN1	55	.	0			c.T346G						.						49	48	49					11																	64900425		2201	4297	6498	SO:0001583	missense	84447	exon4			AGTGGAAACATTT	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"RING-type (C3HC4) zinc fingers"	20738	protein-coding gene	gene with protein product	"HMG-coA reductase degradation 1 homolog (S. cerevisiae)"	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.346T>G	chr11.hg19:g.64900425A>C	ENSP00000366395:p.Phe116Val	154.0	0.0		176.0	28.0	NM_172230	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Missense_Mutation	SNP	ENST00000377190.3	hg19	CCDS31605.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.384128	0.82792	.	.	ENSG00000162298	ENST00000377190;ENST00000294256;ENST00000434219;ENST00000307289;ENST00000526060;ENST00000531018;ENST00000528487	T;T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34;-0.34	5.38	5.38	0.77491	.	0.059221	0.64402	N	0.000002	D	0.84329	0.5448	M	0.91612	3.225	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.998	D;D;D	0.74674	0.984;0.93;0.948	D	0.87353	0.2339	10	0.59425	D	0.04	-16.4399	13.3305	0.60483	1.0:0.0:0.0:0.0	.	116;116;116	Q86TM6-2;Q86TM6-3;Q86TM6	.;.;SYVN1_HUMAN	V	116;116;116;116;116;56;101	ENSP00000366395:F116V;ENSP00000294256:F116V;ENSP00000302035:F116V;ENSP00000436984:F116V;ENSP00000431215:F56V;ENSP00000431720:F101V	ENSP00000294256:F116V	F	-	1	0	SYVN1	64657001	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	8.790000	0.91844	2.026000	0.59711	0.460000	0.39030	TTC	.	.		0.557	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431		C	64900425	A	C	64900425	3	2	130	1	0	0	0	0	1	0	0	0	15502	14	1	5	1559	5	SYVN1	11	64900425	Missense_Mutation	SNP	A	TCGA-DD-A4NH-01A-11D-A27I-10		64900425	70106091	29	21265										
C11orf73	51501	hgsc.bcm.edu	37	chr11	86048470	86048470	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	atgaatattgtccgaactccAtctgttgctcagattggaat	8	8	2	2	rs376891384		TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr11:86048470A>G	ENST00000278483.3	+	3	544	c.318A>G	c.(316-318)ccA>ccG	p.P106P	C11orf73_ENST00000533986.1_Silent_p.P106P|C11orf73_ENST00000530208.1_3'UTR	NM_016401.3	NP_057485.2	Q53FT3	HIKES_HUMAN	chromosome 11 open reading frame 73	106					cellular response to heat (GO:0034605)|Golgi organization (GO:0007030)|lung development (GO:0030324)|protein import into nucleus (GO:0006606)|protein transport (GO:0015031)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	Hsp70 protein binding (GO:0030544)|protein transporter activity (GO:0008565)			kidney(1)|large_intestine(1)|urinary_tract(1)	3		Acute lymphoblastic leukemia(157;1.17e-07)|all_hematologic(158;0.000556)				TCCGAACTCCATCTGTTGCTC	0.403																																					p.P106P		Atlas-SNP	.											.	C11orf73	9	.	0			c.A318G						.	A		2,4402	4.2+/-10.8	0,2,2200	176	165	169		318	0.2	1	11		169	0,8598		0,0,4299	no	coding-synonymous	C11orf73	NM_016401.3		0,2,6499	GG,GA,AA		0.0,0.0454,0.0154		106/198	86048470	2,13000	2202	4299	6501	SO:0001819	synonymous_variant	51501	exon3			AACTCCATCTGTT	BC015991	CCDS8275.1	11q14.2	2013-03-12			ENSG00000149196	ENSG00000149196			26938	protein-coding gene	gene with protein product		614908				11042152, 22541429	Standard	NM_016401		Approved	HSPC138, HSPC179, Hikeshi, OPI10	uc001pbu.3	Q53FT3	OTTHUMG00000167212	ENST00000278483.3:c.318A>G	chr11.hg19:g.86048470A>G		132.0	0.0		155.0	35.0	NM_016401	Q8WVE8|Q9NVQ2|Q9NZZ1|Q9P022|Q9P0N1	Silent	SNP	ENST00000278483.3	hg19	CCDS8275.1																																																																																			.	.		0.403	C11orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393747.1	NM_016401		G	86048470	A	G	86048470	2	3	130	1	0	0	0	0	0	0	0	1	1663	204	8	2		2	C11orf73	11	86048470	Silent	SNP	A	TCGA-DD-A4NH-01A-11D-A27I-10	21148045	86048470	48958046	30	21266										
TMEM218	219854	hgsc.bcm.edu	37	chr11	124971201	124971201	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	taaaaaaatgacagagaaccTggggttaaaaagacaaatta	8	4	0	3			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr11:124971201T>A	ENST00000279968.4	-	4	434		c.e4-2		TMEM218_ENST00000529583.1_Splice_Site|TMEM218_ENST00000531909.1_Splice_Site|TMEM218_ENST00000527271.1_Splice_Site|TMEM218_ENST00000526175.1_Splice_Site|TMEM218_ENST00000527766.1_Splice_Site|TMEM218_ENST00000455225.1_Splice_Site|TMEM218_ENST00000532407.1_Splice_Site|TMEM218_ENST00000528724.1_Splice_Site|TMEM218_ENST00000531262.1_Splice_Site|TMEM218_ENST00000529609.1_Intron|TMEM218_ENST00000532156.1_Intron			A2RU14	TM218_HUMAN	transmembrane protein 218							integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						ACAGAGAACCTGGGGTTAAAA	0.408																																					.		Atlas-SNP	.											.	TMEM218	14	.	0			c.216-2A>T						.						50	47	48					11																	124971201		2201	4299	6500	SO:0001630	splice_region_variant	219854	exon5			AGAACCTGGGGTT		CCDS31715.1	11q24.2	2008-08-08			ENSG00000150433	ENSG00000150433			27344	protein-coding gene	gene with protein product							Standard	NM_001258238		Approved		uc031qeu.1	A2RU14		ENST00000279968.4:c.111-2A>T	chr11.hg19:g.124971201T>A		38.0	0.0		33.0	9.0	NM_001258242	B7ZM48	Splice_Site	SNP	ENST00000279968.4	hg19	CCDS31715.1	.	.	.	.	.	.	.	.	.	.	T	17.63	3.436543	0.62955	.	.	ENSG00000150433	ENST00000455225;ENST00000531909;ENST00000528724;ENST00000532407;ENST00000279968;ENST00000526175;ENST00000527766;ENST00000529583;ENST00000527271;ENST00000524373;ENST00000533273;ENST00000529530	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1434	0.59448	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM218	124476411	1.000000	0.71417	0.996000	0.52242	0.849000	0.48306	4.489000	0.60309	2.072000	0.62099	0.533000	0.62120	.	.	.		0.408	TMEM218-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386849.1	NM_001080546	Intron	A	124971201	T	A	124971201	5	1	130	1	0	0	0	0	0	0	1	0	16156	1594	55	4	246	4	TMEM218	11	124971201	Splice_Site	SNP	T	TCGA-DD-A4NH-01A-11D-A27I-10	38922731	124971201	10035315	31	21267										
TMTC1	83857	hgsc.bcm.edu	37	chr12	29920979	29920979	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ttactgcatgaaagtagaatGggttcataccagtcaaaaat	8	6	2	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr12:29920979G>A	ENST00000539277.1	-	2	390	c.332C>T	c.(331-333)cCa>cTa	p.P111L	TMTC1_ENST00000552618.1_Missense_Mutation_p.P111L|TMTC1_ENST00000551659.1_Missense_Mutation_p.P111L|TMTC1_ENST00000381224.2_Missense_Mutation_p.P3L|TMTC1_ENST00000256062.5_Missense_Mutation_p.P3L	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	111						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					AAAGTAGAATGGGTTCATACC	0.343																																					p.P111L		Atlas-SNP	.											.	TMTC1	147	.	0			c.C332T						.						58	53	55					12																	29920979		2203	4300	6503	SO:0001583	missense	83857	exon2			TAGAATGGGTTCA		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.332C>T	chr12.hg19:g.29920979G>A	ENSP00000442046:p.Pro111Leu	77.0	0.0		80.0	11.0	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	hg19	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.787163	0.90367	.	.	ENSG00000133687	ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277;ENST00000381224	D;D;D;D;T	0.94232	-2.12;-3.38;-3.38;-3.38;-0.27	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.96713	0.8927	M	0.84585	2.705	0.80722	D	1	D;D	0.76494	0.999;0.996	D;P	0.70935	0.971;0.847	D	0.96817	0.9601	9	.	.	.	-13.9925	15.7586	0.78058	0.0:0.0:1.0:0.0	.	3;111	Q8IUR5-3;Q8IUR5	.;TMTC1_HUMAN	L	3;111;111;111;3	ENSP00000256062:P3L;ENSP00000448112:P111L;ENSP00000449043:P111L;ENSP00000442046:P111L;ENSP00000370622:P3L	.	P	-	2	0	TMTC1	29812246	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.122000	0.89584	2.500000	0.84329	0.655000	0.94253	CCA	.	.		0.343	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		A	29920979	G	A	29920979	3	1	130	1	0	0	0	0	1	0	0	0	16275	1348	47	3	2384	3	TMTC1	12	29920979	Missense_Mutation	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10		29920979	103930916	32	21268										
DTX3	196403	hgsc.bcm.edu	37	chr12	58001298	58001298	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	gcaaccagccccagaatgggCggatgctggtctctaaggac	13	12	1	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr12:58001298C>T	ENST00000548198.1	+	3	2156	c.652C>T	c.(652-654)Cgg>Tgg	p.R218W	DTX3_ENST00000551632.1_Missense_Mutation_p.R221W|ARHGEF25_ENST00000333972.7_5'Flank|DTX3_ENST00000548804.1_Missense_Mutation_p.R218W|DTX3_ENST00000337737.3_Missense_Mutation_p.R218W			Q8N9I9	DTX3_HUMAN	deltex 3, E3 ubiquitin ligase	218					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(6)|urinary_tract(1)	12	Melanoma(17;0.122)					CCAGAATGGGCGGATGCTGGT	0.632																																					p.R218W		Atlas-SNP	.											.	DTX3	27	.	0			c.C652T						.						49	53	52					12																	58001298		1967	4136	6103	SO:0001583	missense	196403	exon5			AATGGGCGGATGC	AK094385	CCDS41800.1, CCDS66410.1	12q13.2	2014-01-28	2014-01-28			ENSG00000178498		"RING-type (C3HC4) zinc fingers"	24457	protein-coding gene	gene with protein product		613142	"deltex 3 homolog (Drosophila)", "deltex homolog 3 (Drosophila)"			12670957	Standard	XM_005268697		Approved	FLJ34766, RNF154	uc001sow.1	Q8N9I9		ENST00000548198.1:c.652C>T	chr12.hg19:g.58001298C>T	ENSP00000447873:p.Arg218Trp	249.0	0.0		407.0	63.0	NM_178502	Q53ZZ2|Q8NAU6|Q8NDS8	Missense_Mutation	SNP	ENST00000548198.1	hg19	CCDS41800.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.321079	0.60634	.	.	ENSG00000178498	ENST00000548804;ENST00000337737;ENST00000548198;ENST00000551632;ENST00000550300	T;T;T;T;T	0.50548	1.91;1.91;1.91;1.91;0.74	4.29	2.27	0.28462	.	0.288167	0.29814	N	0.011127	T	0.59321	0.2185	L	0.60455	1.87	0.36011	D	0.83809	D	0.76494	0.999	D	0.65684	0.937	T	0.68473	-0.5399	10	0.72032	D	0.01	-11.1105	10.6065	0.45398	0.4482:0.5518:0.0:0.0	.	218	Q8N9I9	DTX3_HUMAN	W	218;218;218;221;6	ENSP00000449294:R218W;ENSP00000338050:R218W;ENSP00000447873:R218W;ENSP00000448696:R221W;ENSP00000446996:R6W	ENSP00000338050:R218W	R	+	1	2	DTX3	56287565	0.352000	0.24895	1.000000	0.80357	0.998000	0.95712	0.576000	0.23744	0.904000	0.36572	0.561000	0.74099	CGG	.	.		0.632	DTX3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407848.1	NM_178502		T	58001298	C	T	58001298	3	4	130	1	0	0	0	0	1	0	0	0	4797	759	27	1	658	1	DTX3	12	58001298	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	28080319	58001298	75850597	33	21269										
ANO4	121601	hgsc.bcm.edu	37	chr12	101490394	101490394	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	agtttgtcaatctgaacagcTccacattttacatcgcattc	5	11	2	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr12:101490394T>A	ENST00000392977.3	+	19	2029	c.1819T>A	c.(1819-1821)Tcc>Acc	p.S607T	ANO4_ENST00000299222.9_Missense_Mutation_p.S127T|ANO4_ENST00000392979.3_Missense_Mutation_p.S572T|ANO4_ENST00000550015.1_Missense_Mutation_p.S127T			Q32M45	ANO4_HUMAN	anoctamin 4	607					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						TCTGAACAGCTCCACATTTTA	0.493										HNSCC(74;0.22)																											p.S572T		Atlas-SNP	.											.	ANO4	183	.	0			c.T1714A						.						130	117	121					12																	101490394		2203	4300	6503	SO:0001583	missense	121601	exon18			AACAGCTCCACAT	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.1819T>A	chr12.hg19:g.101490394T>A	ENSP00000376703:p.Ser607Thr	127.0	0.0		172.0	23.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	hg19		.	.	.	.	.	.	.	.	.	.	T	29.9	5.045246	0.93685	.	.	ENSG00000151572	ENST00000392979;ENST00000299222;ENST00000392977;ENST00000550015	T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.83792	0.5331	M	0.86953	2.85	0.80722	D	1	D;D;D	0.71674	0.992;0.998;0.997	P;D;D	0.76071	0.832;0.987;0.978	D	0.85858	0.1408	10	0.52906	T	0.07	.	15.773	0.78187	0.0:0.0:0.0:1.0	.	127;607;572	Q32M45-3;Q32M45;Q32M45-2	.;ANO4_HUMAN;.	T	572;127;607;127	ENSP00000376705:S572T;ENSP00000299222:S127T;ENSP00000376703:S607T;ENSP00000450192:S127T	ENSP00000299222:S127T	S	+	1	0	ANO4	100014525	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.015000	0.88690	2.207000	0.71202	0.460000	0.39030	TCC	.	.		0.493	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		A	101490394	T	A	101490394	3	1	130	1	0	0	0	0	1	0	0	0	699	1551	54	4	1780	4	ANO4	12	101490394	Missense_Mutation	SNP	T	TCGA-DD-A4NH-01A-11D-A27I-10	43489096	101490394	32361501	34	21270										
DUOX2	50506	hgsc.bcm.edu	37	chr15	45391660	45391660	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	gaagatgtagacattgactgCgtggccagcactgtgcaaaa	12	8	0	3			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr15:45391660C>T	ENST00000603300.1	-	26	3638	c.3436G>A	c.(3436-3438)Gca>Aca	p.A1146T	DUOX2_ENST00000389039.6_Missense_Mutation_p.A1146T	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1146	Ferric oxidoreductase.|Interaction with TXNDC11. {ECO:0000250}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		ACATTGACTGCGTGGCCAGCA	0.537																																					p.A1146T		Atlas-SNP	.											.	DUOX2	137	.	0			c.G3436A						.						78	63	68					15																	45391660		2198	4298	6496	SO:0001583	missense	50506	exon26			TGACTGCGTGGCC	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"EF-hand domain containing"	13273	protein-coding gene	gene with protein product	"dual oxidase-like domains 2", "nicotinamide adenine dinucleotide phosphate oxidase", "flavoprotein NADPH oxidase", "NADPH thyroid oxidase 2", "NADH/NADPH thyroid oxidase p138-tox", "NADPH oxidase/peroxidase DUOX2"	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.3436G>A	chr15.hg19:g.45391660C>T	ENSP00000475084:p.Ala1146Thr	81.0	0.0		92.0	16.0	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	hg19	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.332291	0.41297	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.44	5.44	0.79542	Flavoprotein transmembrane component (1);	0.431830	0.25695	N	0.028918	T	0.25158	0.0611	L	0.31926	0.97	0.09310	N	1	B	0.32203	0.36	B	0.29862	0.108	T	0.20571	-1.0271	9	0.52906	T	0.07	-1.6056	7.0218	0.24918	0.2895:0.63:0.0:0.0806	.	1146	Q9NRD8	DUOX2_HUMAN	T	1146	.	ENSP00000373691:A1146T	A	-	1	0	DUOX2	43178952	0.001000	0.12720	0.336000	0.25522	0.590000	0.36582	0.892000	0.28322	2.561000	0.86390	0.563000	0.77884	GCA	.	.		0.537	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		T	45391660	C	T	45391660	3	4	130	1	0	0	0	0	1	0	0	0	4803	768	27	1	1246	1	DUOX2	15	45391660	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10		45391660	57139732	35	21271										
TSC2	7249	hgsc.bcm.edu	37	chr16	2134406	2134406	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ctcccgagctgcagactctgCaggacatcctcggggaccct	11	16	1	1	rs397514935		TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr16:2134406C>T	ENST00000219476.3	+	34	4813	c.4183C>T	c.(4183-4185)Cag>Tag	p.Q1395*	TSC2_ENST00000439673.2_Nonsense_Mutation_p.Q1292*|TSC2_ENST00000401874.2_Nonsense_Mutation_p.Q1328*|TSC2_ENST00000350773.4_Nonsense_Mutation_p.Q1372*|TSC2_ENST00000353929.4_Nonsense_Mutation_p.Q1352*|TSC2_ENST00000568454.1_Nonsense_Mutation_p.Q1339*|TSC2_ENST00000382538.6_Nonsense_Mutation_p.Q1280*	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1395					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				GCAGACTCTGCAGGACATCCT	0.677			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.Q1395X		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.C4183T						.						31	32	31					16																	2134406		2188	4297	6485	SO:0001587	stop_gained	7249	exon34	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	ACTCTGCAGGACA	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.4183C>T	chr16.hg19:g.2134406C>T	ENSP00000219476:p.Gln1395*	84.0	0.0		60.0	14.0	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Nonsense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	C	42	9.275497	0.99122	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	.	.	.	5.03	5.03	0.67393	.	0.076992	0.56097	D	0.000036	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-24.6107	18.3399	0.90302	0.0:1.0:0.0:0.0	.	.	.	.	X	1395;1329;1352;1292;1280;1372	.	ENSP00000219476:Q1395X	Q	+	1	0	TSC2	2074407	1.000000	0.71417	0.984000	0.44739	0.400000	0.30750	7.328000	0.79160	2.350000	0.79820	0.484000	0.47621	CAG	.	.		0.677	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		T	2134406	C	T	2134406	4	4	130	1	0	0	0	0	0	1	0	0	16621	711	25	3	4313	3	TSC2	16	2134406	Nonsense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10		2134406	88220347	36	21272										
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29889651	29889651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	cttctcttcctggacgtgcaCgccccacacgcagtcttggc	9	17	2	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr16:29889651C>T	ENST00000308713.5	-	10	2196	c.1669G>A	c.(1669-1671)Gtg>Atg	p.V557M	SEZ6L2_ENST00000537485.1_Missense_Mutation_p.V513M|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.V443M|SEZ6L2_ENST00000350527.3_Missense_Mutation_p.V487M	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	557	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGGACGTGCACGCCCCACACG	0.607																																					p.V557M		Atlas-SNP	.											.	SEZ6L2	137	.	0			c.G1669A						.						130	102	111					16																	29889651		2197	4300	6497	SO:0001583	missense	26470	exon10			CGTGCACGCCCCA	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1669G>A	chr16.hg19:g.29889651C>T	ENSP00000312550:p.Val557Met	120.0	0.0		125.0	34.0	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	hg19	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.046680	0.93740	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.42	4.45	0.53987	CUB (5);	0.160446	0.29417	N	0.012211	T	0.32971	0.0847	M	0.76727	2.345	0.09310	N	0.999992	P;P;P;P;P;P	0.52170	0.932;0.728;0.709;0.938;0.914;0.951	B;B;B;B;B;B	0.40659	0.284;0.336;0.128;0.258;0.267;0.326	T	0.36529	-0.9744	10	0.87932	D	0	.	9.049	0.36365	0.0:0.1349:0.457:0.4081	.	513;557;443;487;557;487	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	M	487;557;443;513	ENSP00000310206:V487M;ENSP00000312550:V557M;ENSP00000319215:V443M;ENSP00000439412:V513M	ENSP00000312550:V557M	V	-	1	0	SEZ6L2	29797152	0.995000	0.38212	0.997000	0.53966	0.851000	0.48451	0.679000	0.25291	0.660000	0.30964	-0.120000	0.15030	GTG	.	.		0.607	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		T	29889651	C	T	29889651	3	4	130	1	0	0	0	0	1	0	0	0	14159	536	19	1	1138	1	SEZ6L2	16	29889651	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	27755245	29889651	60465102	37	21273										
RBL2	5934	hgsc.bcm.edu	37	chr16	53524210	53524210	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ctaatgaccgtggttcccacTgaggttagtctcttgtatta	9	9	1	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr16:53524210T>C	ENST00000262133.6	+	22	3555	c.3418T>C	c.(3418-3420)Tga>Cga	p.*1140R	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Nonstop_Mutation_p.*519R	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	0					chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TGGTTCCCACTGAGGTTAGTC	0.408																																					p.X1140R		Atlas-SNP	.											.	RBL2	115	.	0			c.T3418C						.						99	96	97					16																	53524210		2198	4300	6498	SO:0001578	stop_lost	5934	exon22			TCCCACTGAGGTT	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.3418T>C	chr16.hg19:g.53524210T>C	ENSP00000262133:p.*1140Argext*2	115.0	0.0		106.0	23.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	hg19	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	T	19.52	3.843610	0.71488	.	.	ENSG00000103479	ENST00000262133;ENST00000379935;ENST00000544545	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3113	0.74035	0.0:0.0:0.0:1.0	.	.	.	.	R	1140;850;519	.	.	X	+	1	0	RBL2	52081711	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.806000	0.75195	2.263000	0.75096	0.533000	0.62120	TGA	.	.		0.408	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		C	53524210	T	C	53524210	4	2	130	1	0	0	0	0	0	0	0	0	13125	1593	55	2	3504	2	RBL2	16	53524210	Nonstop_Mutation	SNP	T	TCGA-DD-A4NH-01A-11D-A27I-10	23634559	53524210	36830543	38	21274										
STAT5B	6777	hgsc.bcm.edu	37	chr17	40384099	40384100	+	Frame_Shift_Ins	INS	-	-	G													0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	atataacgcttgcatctgatINSgaagggcttctccttggagc							TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr17:40384099_40384100insG	ENST00000293328.3	-	2	214_215	c.46_47insC	c.(46-48)catfs	p.H16fs		NM_012448.3	NP_036580.2	P51692	STA5B_HUMAN	signal transducer and activator of transcription 5B	16					2-oxoglutarate metabolic process (GO:0006103)|acute-phase response (GO:0006953)|allantoin metabolic process (GO:0000255)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|liver development (GO:0001889)|luteinization (GO:0001553)|natural killer cell differentiation (GO:0001779)|negative regulation of apoptotic process (GO:0043066)|negative regulation of erythrocyte differentiation (GO:0045647)|oxaloacetate metabolic process (GO:0006107)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cellular component movement (GO:0051272)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone metabolic process (GO:0042448)|prolactin signaling pathway (GO:0038161)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to lipopolysaccharide (GO:0032496)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription from RNA polymerase II promoter (GO:0006366)|valine metabolic process (GO:0006573)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|glucocorticoid receptor binding (GO:0035259)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)	TTGCATCTGATGAAGGGCTTCT	0.436																																					p.H16fs		Atlas-Indel,Pindel	.											.	STAT5B	89	.	0			c.47_48insC						.																																			SO:0001589	frameshift_variant	6777	exon2			.	BC065227	CCDS11423.1	17q11.2	2014-09-17			ENSG00000173757	ENSG00000173757		"SH2 domain containing"	11367	protein-coding gene	gene with protein product		604260				8631883	Standard	NM_012448		Approved		uc002hzh.3	P51692	OTTHUMG00000150724	ENST00000293328.3:c.47dupC	chr17.hg19:g.40384100_40384100dupG	ENSP00000293328:p.His16fs	199.0	0.0		242.0	48.0	NM_012448	Q8WWS8	Frame_Shift_Ins	INS	ENST00000293328.3	hg19	CCDS11423.1																																																																																			.	.		0.436	STAT5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319797.1	NM_012448		G	40384100	-	G	40384099	7	5	130	1	0	1	1	0	0	0	0	0	15284	1464	51	0	2388	0	STAT5B	17	40384099	Frame_Shift_Ins	INS	-	TCGA-DD-A4NH-01A-11D-A27I-10		40384099	40811111	39	21275										
PGS1	9489	hgsc.bcm.edu	37	chr17	76395500	76395500	+	Frame_Shift_Del	DEL	T	T	-													0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	agcaggtccgagtctccctcTttcacacgccgcacctccgt							TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr17:76395500delT	ENST00000262764.6	+	5	609	c.583delT	c.(583-585)tttfs	p.F195fs	PGS1_ENST00000588281.1_3'UTR|PGS1_ENST00000329897.7_Frame_Shift_Del_p.F60fs|SNORA30_ENST00000363193.1_RNA	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1	195					cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			AGTCTCCCTCTTTCACACGCC	0.602																																					p.L194fs	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-Indel,Pindel	.											.	PGS1	30	.	0			c.582delC						.						91	96	95					17																	76395500		2093	4197	6290	SO:0001589	frameshift_variant	9489	exon5			.		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8		ENST00000262764.6:c.583delT	chr17.hg19:g.76395500delT	ENSP00000262764:p.Phe195fs	124.0	0.0		176.0	46.0	NM_024419	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Frame_Shift_Del	DEL	ENST00000262764.6	hg19	CCDS42391.1																																																																																			.	.		0.602	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419		-	76395500	T	-	76395500	7	5	130	1	0	1	0	1	0	0	0	0	11817	1609	56	0	601	0	PGS1	17	76395500	Frame_Shift_Del	DEL	T	TCGA-DD-A4NH-01A-11D-A27I-10	36011401	76395500	4799710	40	21276										
PPAP2C	8612	hgsc.bcm.edu	37	chr19	288111	288111	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	accggatggagtcatccccgCagtaaaatcctcgcttgtac	9	13	1	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr19:288111C>T	ENST00000269812.3	-	2	162	c.113G>A	c.(112-114)tGc>tAc	p.C38Y	PPAP2C_ENST00000434325.2_5'UTR|PPAP2C_ENST00000327790.3_Missense_Mutation_p.C59Y	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	38					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCATCCCCGCAGTAAAATCC	0.602																																					p.C59Y		Atlas-SNP	.											.	PPAP2C	38	.	0			c.G176A						.						158	124	135					19																	288111		2203	4300	6503	SO:0001583	missense	8612	exon2			TCCCCGCAGTAAA	AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	3.1.3.4		9230	protein-coding gene	gene with protein product		607126				9570154, 9607309	Standard	NM_177543		Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.113G>A	chr19.hg19:g.288111C>T	ENSP00000269812:p.Cys38Tyr	245.0	0.0		272.0	38.0	NM_177543	A6NLV0|E9PAY8	Missense_Mutation	SNP	ENST00000269812.3	hg19	CCDS12023.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.019691	0.54576	.	.	ENSG00000141934	ENST00000269812;ENST00000327790	T;T	0.74526	-0.85;-0.85	4.7	4.7	0.59300	.	0.054186	0.85682	D	0.000000	D	0.88930	0.6571	M	0.91612	3.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.991	D	0.91643	0.5328	10	0.87932	D	0	-1.2756	16.6041	0.84824	0.0:1.0:0.0:0.0	.	38;59	O43688;O43688-2	LPP2_HUMAN;.	Y	38;59	ENSP00000269812:C38Y;ENSP00000329697:C59Y	ENSP00000269812:C38Y	C	-	2	0	PPAP2C	239111	1.000000	0.71417	0.778000	0.31720	0.050000	0.14768	7.105000	0.77031	2.335000	0.79485	0.650000	0.86243	TGC	.	.		0.602	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451777.2			T	288111	C	T	288111	3	4	130	1	0	0	0	0	1	0	0	0	12301	710	25	3	773	3	PPAP2C	19	288111	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10		288111	58840872	41	21277										
ZBTB7A	51341	hgsc.bcm.edu	37	chr19	4055085	4055085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	tgcaggcggccagcaccgagCggtgcgtggggaactcgcgg	19	12	0	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr19:4055085C>T	ENST00000322357.4	-	2	424	c.146G>A	c.(145-147)cGc>cAc	p.R49H	ZBTB7A_ENST00000601588.1_Missense_Mutation_p.R49H	NM_015898.2	NP_056982.1	O95365	ZBT7A_HUMAN	zinc finger and BTB domain containing 7A	49	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	14		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.014)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCACCGAGCGGTGCGTGGG	0.657																																					p.R49H		Atlas-SNP	.											ZBTB7A,NS,carcinoma,0,1	ZBTB7A	35	.	0			c.G146A						.						41	43	42					19																	4055085		2201	4299	6500	SO:0001583	missense	51341	exon2			ACCGAGCGGTGCG	AF000561	CCDS12119.1	19p13.3	2013-01-08		2005-04-07		ENSG00000178951		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	18078	protein-coding gene	gene with protein product	"zinc finger and BTB domain containing 7A, HIV-1 inducer of short transcripts binding protein", "lymphoma related factor"	605878	"zinc finger and BTB domain containing 7"	ZBTB7		9973611, 9927193	Standard	NM_015898		Approved	FBI-1, LRF, DKFZp547O146, pokemon, ZNF857A	uc002lzi.3	O95365		ENST00000322357.4:c.146G>A	chr19.hg19:g.4055085C>T	ENSP00000323670:p.Arg49His	28.0	0.0		9.0	3.0	NM_015898	D6W619|O00456|Q14D41|Q5XG86	Missense_Mutation	SNP	ENST00000322357.4	hg19	CCDS12119.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.309759	0.81247	.	.	ENSG00000178951	ENST00000322357	T	0.75367	-0.93	4.79	4.79	0.61399	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.91932	0.7445	H	0.98738	4.315	0.52501	D	0.999956	D	0.89917	1.0	D	0.80764	0.994	D	0.95394	0.8484	10	0.87932	D	0	.	16.794	0.85597	0.0:1.0:0.0:0.0	.	49	O95365	ZBT7A_HUMAN	H	49	ENSP00000323670:R49H	ENSP00000323670:R49H	R	-	2	0	ZBTB7A	4006085	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.760000	0.62235	2.202000	0.70862	0.462000	0.41574	CGC	.	.		0.657	ZBTB7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457621.2	NM_015898		T	4055085	C	T	4055085	3	4	130	1	0	0	0	0	1	0	0	0	17568	768	27	1	1616	1	ZBTB7A	19	4055085	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	3766974	4055085	55073898	42	21278										
OR10H1	26539	hgsc.bcm.edu	37	chr19	15917988	15917988	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	tgaggctgaagatgatggggCtgaggaagggtgtgaggacc	20	4	0	6			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr19:15917988C>T	ENST00000334920.2	-	1	948	c.860G>A	c.(859-861)aGc>aAc	p.S287N		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	287						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						GATGATGGGGCTGAGGAAGGG	0.502																																					p.S287N		Atlas-SNP	.											.	OR10H1	59	.	0			c.G860A						.						82	70	74					19																	15917988		2203	4297	6500	SO:0001583	missense	26539	exon1			ATGGGGCTGAGGA	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"GPCR / Class A : Olfactory receptors"	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.860G>A	chr19.hg19:g.15917988C>T	ENSP00000335596:p.Ser287Asn	304.0	0.0		310.0	54.0	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	hg19	CCDS12335.1	.	.	.	.	.	.	.	.	.	.	.	9.595	1.127093	0.20959	.	.	ENSG00000186723	ENST00000334920	T	0.19532	2.14	5.06	5.06	0.68205	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000012	T	0.08935	0.0221	N	0.00109	-2.105	0.35034	D	0.75906	D	0.89917	1.0	D	0.91635	0.999	T	0.46871	-0.9160	10	0.02654	T	1	.	9.5425	0.39260	0.0:0.9034:0.0:0.0966	.	287	Q9Y4A9	O10H1_HUMAN	N	287	ENSP00000335596:S287N	ENSP00000335596:S287N	S	-	2	0	OR10H1	15778988	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.321000	0.65846	2.346000	0.79739	0.643000	0.83706	AGC	.	.		0.502	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1			T	15917988	C	T	15917988	3	4	130	1	0	0	0	0	1	0	0	0	10914	797	28	3	100	3	OR10H1	19	15917988	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	11862903	15917988	43210995	43	21279										
ZNF529	57711	hgsc.bcm.edu	37	chr19	37045633	37045633	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	cagtacaagttcctctgagcAgaatccagatattcccattc	6	12	1	3			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr19:37045633A>G	ENST00000591340.1	-	4	332	c.174T>C	c.(172-174)tcT>tcC	p.S58S	ZNF529_ENST00000334116.7_5'UTR	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	58	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1	Esophageal squamous(110;0.198)					TCCTCTGAGCAGAATCCAGAT	0.408																																					p.S58S		Atlas-SNP	.											.	ZNF529	82	.	0			c.T174C						.						119	105	110					19																	37045633		692	1591	2283	SO:0001819	synonymous_variant	57711	exon5			CTGAGCAGAATCC	AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"Zinc fingers, C2H2-type", "-"	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.174T>C	chr19.hg19:g.37045633A>G		146.0	0.0		148.0	35.0	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Silent	SNP	ENST00000591340.1	hg19	CCDS54256.1																																																																																			.	.		0.408	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951		G	37045633	A	G	37045633	2	3	130	1	0	0	0	0	0	0	0	1	17985	175	7	2		2	ZNF529	19	37045633	Silent	SNP	A	TCGA-DD-A4NH-01A-11D-A27I-10	21127645	37045633	22083350	44	21280										
ZNF780B	163131	hgsc.bcm.edu	37	chr19	40540905	40540905	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ctgggtgtgaagactgaaggCcttgccacattccttacatt	10	10	0	3			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr19:40540905C>T	ENST00000434248.1	-	5	1926	c.1861G>A	c.(1861-1863)Gcc>Acc	p.A621T	ZNF780B_ENST00000221355.6_Missense_Mutation_p.A473T	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	621					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					AGACTGAAGGCCTTGCCACAT	0.413																																					p.A621T		Atlas-SNP	.											.	ZNF780B	143	.	0			c.G1861A						.						116	122	120					19																	40540905		2203	4300	6503	SO:0001583	missense	163131	exon5			TGAAGGCCTTGCC	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"Zinc fingers, C2H2-type", "-"	33109	protein-coding gene	gene with protein product			"zinc finger protein 779"	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.1861G>A	chr19.hg19:g.40540905C>T	ENSP00000391641:p.Ala621Thr	134.0	0.0		144.0	26.0	NM_001005851	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	hg19	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	c	13.68	2.308746	0.40895	.	.	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.16897	2.31;2.31	2.56	2.56	0.30785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18882	0.0453	N	0.12502	0.225	0.22489	N	0.999058	D	0.89917	1.0	D	0.91635	0.999	T	0.12863	-1.0531	9	0.33940	T	0.23	.	5.1106	0.14808	0.0:0.83:0.0:0.17	.	621	Q9Y6R6	Z780B_HUMAN	T	621;473	ENSP00000391641:A621T;ENSP00000221355:A473T	ENSP00000221355:A473T	A	-	1	0	ZNF780B	45232745	0.000000	0.05858	0.323000	0.25347	0.505000	0.33919	-0.732000	0.04904	1.259000	0.44117	0.462000	0.41574	GCC	.	.		0.413	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		T	40540905	C	T	40540905	3	4	130	1	0	0	0	0	1	0	0	0	18168	739	26	3	644	3	ZNF780B	19	40540905	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	3495272	40540905	18588078	45	21281										
NLRP7	199713	hgsc.bcm.edu	37	chr19	55450802	55450802	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ggtggatgaaggagtagcagCctttggagactctgtcctgg	16	7	1	2	rs146205567		TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr19:55450802C>T	ENST00000590030.1	-	3	1425	c.1385G>A	c.(1384-1386)gGc>gAc	p.G462D	NLRP7_ENST00000446217.1_Missense_Mutation_p.G490D|NLRP7_ENST00000592784.1_Missense_Mutation_p.G462D|NLRP7_ENST00000448121.2_Missense_Mutation_p.G462D|NLRP7_ENST00000588756.1_Missense_Mutation_p.G462D|NLRP7_ENST00000340844.2_Missense_Mutation_p.G462D|NLRP7_ENST00000328092.5_Missense_Mutation_p.G462D			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	462	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		GGAGTAGCAGCCTTTGGAGAC	0.622																																					p.G462D		Atlas-SNP	.											.	NLRP7	411	.	0			c.G1385A						.						37	36	36					19																	55450802		2203	4297	6500	SO:0001583	missense	199713	exon4			TAGCAGCCTTTGG	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.1385G>A	chr19.hg19:g.55450802C>T	ENSP00000465520:p.Gly462Asp	162.0	0.0		220.0	29.0	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	hg19	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	C	7.834	0.720554	0.15372	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.73897	-0.73;-0.73;-0.79;-0.76	1.81	-1.81	0.07882	.	0.517197	0.14640	N	0.307281	T	0.47414	0.1444	N	0.12182	0.205	0.18873	N	0.999983	B;B;B;B	0.29301	0.156;0.092;0.156;0.241	B;B;B;B	0.34242	0.06;0.086;0.086;0.178	T	0.40627	-0.9553	10	0.11182	T	0.66	.	2.718	0.05193	0.0:0.3924:0.2553:0.3522	.	490;462;462;462	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	D	462;462;462;490;229	ENSP00000329568:G462D;ENSP00000409137:G462D;ENSP00000339491:G462D;ENSP00000414273:G490D	ENSP00000329568:G462D	G	-	2	0	NLRP7	60142614	0.005000	0.15991	0.042000	0.18584	0.110000	0.19582	0.000000	0.12993	-0.426000	0.07360	-0.448000	0.05591	GGC	.	C|1.000;A|0.000		0.622	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		T	55450802	C	T	55450802	3	4	130	1	0	0	0	0	1	0	0	0	10491	739	26	3	1760	3	NLRP7	19	55450802	Missense_Mutation	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	14909897	55450802	3678181	46	21282										
ZNF446	55663	hgsc.bcm.edu	37	chr19	58991841	58991841	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	cagtccccggggctagccacCggggaaagcacagagaagcc	14	14	0	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr19:58991841C>T	ENST00000594369.1	+	7	1482	c.1101C>T	c.(1099-1101)acC>acT	p.T367T	ZNF446_ENST00000335841.4_3'UTR|ZNF446_ENST00000596341.1_Silent_p.T316T	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	367					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		GGCTAGCCACCGGGGAAAGCA	0.662																																					p.T367T		Atlas-SNP	.											.	ZNF446	22	.	0			c.C1101T						.						27	28	28					19																	58991841		2202	4300	6502	SO:0001819	synonymous_variant	55663	exon7			AGCCACCGGGGAA		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"Zinc fingers, C2H2-type", "-", "-", "-"	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.1101C>T	chr19.hg19:g.58991841C>T		123.0	0.0		92.0	4.0	NM_017908		Silent	SNP	ENST00000594369.1	hg19	CCDS12982.1																																																																																			.	.		0.662	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908		T	58991841	C	T	58991841	2	4	130	1	0	0	0	0	0	0	0	1	17934	639	23	1		1	ZNF446	19	58991841	Silent	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	3541039	58991841	137142	47	21283										
ADNP	23394	hgsc.bcm.edu	37	chr20	49508933	49508934	+	Frame_Shift_Del	DEL	TT	TT	-													0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	agggctgtttgttgaaatacTttgttagaaagcttttcctg					rs140169338	byFrequency	TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr20:49508933_49508934delTT	ENST00000396029.3	-	5	2884_2885	c.2317_2318delAA	c.(2317-2319)aagfs	p.K773fs	ADNP_ENST00000349014.3_Frame_Shift_Del_p.K773fs|ADNP_ENST00000371602.4_Frame_Shift_Del_p.K773fs|ADNP_ENST00000396032.3_Frame_Shift_Del_p.K773fs	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	773					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						GTTGAAATACTTTGTTAGAAAG	0.426																																					p.773_773del		Atlas-Indel,Pindel	.											.	ADNP	106	.	0			c.2318_2319del						.																																			SO:0001589	frameshift_variant	23394	exon5			.	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.2317_2318delAA	chr20.hg19:g.49508933_49508934delTT	ENSP00000379346:p.Lys773fs	180.0	0.0		201.0	43.0	NM_015339	E1P5Y2|O94881|Q5BKU2|Q9UG34	Frame_Shift_Del	DEL	ENST00000396029.3	hg19	CCDS13433.1																																																																																			.	.		0.426	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		-	49508934	TT	-	49508933	7	5	130	1	0	1	0	1	0	0	0	0	323	1609	56	0	994	0	ADNP	20	49508933	Frame_Shift_Del	DEL	TT	TCGA-DD-A4NH-01A-11D-A27I-10		49508933	13516587	48	21284										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60887087	60887087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	tcacacggccctgctgcaggGacacctggcatagcccatcc	10	17	1	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chr20:60887087G>A	ENST00000252999.3	-	70	9590	c.9524C>T	c.(9523-9525)tCc>tTc	p.S3175F	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3175	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CTGCTGCAGGGACACCTGGCA	0.647																																					p.S3175F		Atlas-SNP	.											.	LAMA5	268	.	0			c.C9524T						.						48	51	50					20																	60887087		2202	4296	6498	SO:0001583	missense	3911	exon70			TGCAGGGACACCT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.9524C>T	chr20.hg19:g.60887087G>A	ENSP00000252999:p.Ser3175Phe	61.0	0.0		57.0	16.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	g	11.14	1.550027	0.27652	.	.	ENSG00000130702	ENST00000252999	T	0.78707	-1.2	4.62	3.67	0.42095	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.573613	0.19055	N	0.123932	T	0.73923	0.3649	M	0.65498	2.005	0.80722	D	1	B	0.12013	0.005	B	0.12156	0.007	T	0.71830	-0.4474	10	0.37606	T	0.19	.	11.7433	0.51804	0.0879:0.0:0.9121:0.0	.	3175	O15230	LAMA5_HUMAN	F	3175	ENSP00000252999:S3175F	ENSP00000252999:S3175F	S	-	2	0	LAMA5	60320482	0.998000	0.40836	0.999000	0.59377	0.327000	0.28475	1.211000	0.32382	2.118000	0.64928	0.556000	0.70494	TCC	.	.		0.647	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60887087	G	A	60887087	3	1	130	1	0	0	0	0	1	0	0	0	8618	1174	41	3	1607	3	LAMA5	20	60887087	Missense_Mutation	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10	11378154	60887087	2138433	49	21285										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382426	24382426	+	IGR	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	ctgctgctgctgctgctgctGctcctgctcctgctctagct	10	16	1	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chrX:24382426G>C								AC004552.1 (15403 upstream) : PDK3 (100911 downstream)																							tgctgctgctgctcctgctcc	0.627																																					p.A517P		Atlas-SNP	.											.	.	.	.	0			c.G1549C						.						2	2	2					X																	24382426		1073	2483	3556	SO:0001628	intergenic_variant	100130302	exon1			GCTGCTGCTCCTG																													chrX.hg19:g.24382426G>C		198.0	0.0		241.0	12.0	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.627									C	24382426	G	C	24382426	1	2	130	0	1	0	0	0	0	0	0	0	5581	1319	46	4		4	FAM48B1	23	24382426	IGR	SNP	G	TCGA-DD-A4NH-01A-11D-A27I-10		24382426	130888134	50	21286										
BMP15	9210	hgsc.bcm.edu	37	chrX	50658924	50658924	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	acccaaccaaccacttccctTcctcagaaggagattcctca	4	17	2	2			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chrX:50658924T>A	ENST00000252677.3	+	2	496	c.496T>A	c.(496-498)Tcc>Acc	p.S166T		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	166					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					CCACTTCCCTTCCTCAGAAGG	0.483																																					p.S166T		Atlas-SNP	.											.	BMP15	62	.	0			c.T496A						.						103	81	88					X																	50658924		2203	4299	6502	SO:0001583	missense	9210	exon2			TTCCCTTCCTCAG	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"Bone morphogenetic proteins"	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.496T>A	chrX.hg19:g.50658924T>A	ENSP00000252677:p.Ser166Thr	315.0	0.0		379.0	56.0	NM_005448	Q17RM6|Q5JST1|Q9UMS1	Missense_Mutation	SNP	ENST00000252677.3	hg19	CCDS14334.1	.	.	.	.	.	.	.	.	.	.	t	3.406	-0.121129	0.06838	.	.	ENSG00000130385	ENST00000252677	T	0.79749	-1.3	4.69	-4.9	0.03094	.	0.490054	0.23213	N	0.050643	T	0.69124	0.3076	M	0.72118	2.19	0.09310	N	1	P	0.43231	0.801	B	0.37780	0.258	T	0.66830	-0.5824	10	0.11794	T	0.64	.	9.3461	0.38109	0.0:0.6047:0.1455:0.2498	.	166	O95972	BMP15_HUMAN	T	166	ENSP00000252677:S166T	ENSP00000252677:S166T	S	+	1	0	BMP15	50675664	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.586000	0.05787	-0.754000	0.04715	-0.538000	0.04264	TCC	.	.		0.483	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448		A	50658924	T	A	50658924	3	1	130	1	0	0	0	0	1	0	0	0	1458	1783	62	4	502	4	BMP15	23	50658924	Missense_Mutation	SNP	T	TCGA-DD-A4NH-01A-11D-A27I-10	26276498	50658924	104611636	51	21287										
DNASE1L1	1774	hgsc.bcm.edu	37	chrX	153633194	153633194	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	gaagtacacatacgtctccaTgtaggtgctgcgccccagct	10	13	1	0			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chrX:153633194T>C	ENST00000393638.1	-	4	572	c.286A>G	c.(286-288)Atg>Gtg	p.M96V	DNASE1L1_ENST00000369809.1_Missense_Mutation_p.M96V	NM_001009934.1	NP_001009934.1	P49184	DNSL1_HUMAN	deoxyribonuclease I-like 1	96					DNA metabolic process (GO:0006259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			lung(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TACGTCTCCATGTAGGTGCTG	0.627																																					p.M96V		Atlas-SNP	.											.	DNASE1L1	20	.	0			c.A286G						.						35	32	33					X																	153633194		2202	4300	6502	SO:0001583	missense	1774	exon4			TCTCCATGTAGGT	L40817	CCDS14747.1	Xq28	2008-02-05			ENSG00000013563	ENSG00000013563			2957	protein-coding gene	gene with protein product	"DNase X"	300081		DNL1L		8541839, 8654957	Standard	XM_005277829		Approved	DNAS1L1, XIB, DNASEX	uc004fkw.1	P49184	OTTHUMG00000033188	ENST00000393638.1:c.286A>G	chrX.hg19:g.153633194T>C	ENSP00000377255:p.Met96Val	233.0	0.0		293.0	58.0	NM_006730	D3DWW7|Q5HY41	Missense_Mutation	SNP	ENST00000393638.1	hg19	CCDS14747.1	.	.	.	.	.	.	.	.	.	.	T	5.453	0.268755	0.10349	.	.	ENSG00000013563	ENST00000369809;ENST00000393638;ENST00000014935;ENST00000369808;ENST00000369807;ENST00000309585;ENST00000451865;ENST00000424626	T;T;T;T;T;T;T;T	0.79749	0.75;0.75;0.75;0.75;0.75;0.75;-1.3;1.49	4.31	3.13	0.36017	Endonuclease/exonuclease/phosphatase (2);	0.565616	0.17688	N	0.165394	T	0.77685	0.4167	M	0.62723	1.935	0.09310	N	0.999996	B	0.28820	0.224	B	0.33846	0.171	T	0.67530	-0.5647	10	0.59425	D	0.04	-2.9377	8.3694	0.32406	0.0:0.1087:0.0:0.8913	.	96	P49184	DNSL1_HUMAN	V	96	ENSP00000358824:M96V;ENSP00000377255:M96V;ENSP00000014935:M96V;ENSP00000358823:M96V;ENSP00000358822:M96V;ENSP00000309168:M96V;ENSP00000393346:M96V;ENSP00000393000:M96V	ENSP00000014935:M96V	M	-	1	0	DNASE1L1	153286388	1.000000	0.71417	0.854000	0.33618	0.179000	0.23085	0.729000	0.26028	0.001000	0.14605	-1.912000	0.00520	ATG	.	.		0.627	DNASE1L1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080928.2			C	153633194	T	C	153633194	3	2	130	1	0	0	0	0	1	0	0	0	4663	1464	51	2	642	2	DNASE1L1	23	153633194	Missense_Mutation	SNP	T	TCGA-DD-A4NH-01A-11D-A27I-10	102974270	153633194	1637366	52	21288										
MPP1	4354	hgsc.bcm.edu	37	chrX	154010040	154010040	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	4	1	1.1010989010989	1.78928571428571	0.975974025974026	0.485714285714286	1	0	gagataaagtggtactccttCccatcttcctcactcttcct	5	14	3	1			TCGA-DD-A4NH-01A-11D-A27I-10	TCGA-DD-A4NH-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d6e688d-9606-497f-93d0-ab5238450020	2aa64a1b-06d8-4074-ad24-b2c108738bd2	g.chrX:154010040C>T	ENST00000369534.3	-	10	1131	c.984G>A	c.(982-984)ggG>ggA	p.G328G	MPP1_ENST00000462825.1_5'Flank|MPP1_ENST00000413259.3_Silent_p.G298G|MPP1_ENST00000393531.1_Silent_p.G308G	NM_001166460.1|NM_001166461.1|NM_002436.3	NP_001159932.1|NP_001159933.1|NP_002427.1	Q00013	EM55_HUMAN	membrane protein, palmitoylated 1, 55kDa	328	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.|Interaction with MPP5.				nucleotide phosphorylation (GO:0046939)|regulation of neutrophil chemotaxis (GO:0090022)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(9)|ovary(2)|prostate(1)	21	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GGTACTCCTTCCCATCTTCCT	0.507																																					p.G328G		Atlas-SNP	.											.	MPP1	52	.	0			c.G984A						.						258	206	223					X																	154010040		2203	4300	6503	SO:0001819	synonymous_variant	4354	exon10			CTCCTTCCCATCT		CCDS14762.1, CCDS55544.1, CCDS55545.1	Xq28	2008-03-04	2002-08-29		ENSG00000130830	ENSG00000130830			7219	protein-coding gene	gene with protein product		305360	"membrane protein, palmitoylated 1 (55kD)"	DXS552E		1713685	Standard	NM_002436		Approved	PEMP	uc004fmp.2	Q00013	OTTHUMG00000024244	ENST00000369534.3:c.984G>A	chrX.hg19:g.154010040C>T		254.0	0.0		361.0	65.0	NM_002436	B4DZV5|G3XAI1|Q2TSB6|Q5J7V5	Silent	SNP	ENST00000369534.3	hg19	CCDS14762.1																																																																																			.	.		0.507	MPP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061191.3	NM_002436		T	154010040	C	T	154010040	2	4	130	1	0	0	0	0	0	0	0	1	9742	842	30	3		3	MPP1	23	154010040	Silent	SNP	C	TCGA-DD-A4NH-01A-11D-A27I-10	376846	154010040	1260520	53	21289										
MAN1C1	57134	hgsc.bcm.edu	37	chr1	25944335	25944335	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cgtcccggcctccccgtgggGgctgcggctgccgcagaagt	16	16	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:25944335G>A	ENST00000374332.4	+	1	377	c.47G>A	c.(46-48)gGg>gAg	p.G16E	MAN1C1_ENST00000263979.3_5'Flank	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	16					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		TCCCCGTGGGGGCTGCGGCTG	0.692																																					p.G16E		Atlas-SNP	.											.	MAN1C1	48	.	0			c.G47A						.						14	17	16					1																	25944335		2173	4257	6430	SO:0001583	missense	57134	exon1			CGTGGGGGCTGCG	AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.47G>A	chr1.hg19:g.25944335G>A	ENSP00000363452:p.Gly16Glu	69.0	0.0		53.0	20.0	NM_020379	A6NNE2|B2RNP2|Q9Y545	Missense_Mutation	SNP	ENST00000374332.4	hg19	CCDS265.1	.	.	.	.	.	.	.	.	.	.	g	21.8	4.196335	0.78902	.	.	ENSG00000117643	ENST00000374332	D	0.98280	-4.84	3.83	2.88	0.33553	.	0.000000	0.46758	U	0.000272	D	0.96800	0.8955	L	0.29908	0.895	0.80722	D	1	D	0.63880	0.993	P	0.57371	0.819	D	0.95174	0.8293	10	0.46703	T	0.11	.	9.1786	0.37127	0.0:0.2226:0.7774:0.0	.	16	Q9NR34	MA1C1_HUMAN	E	16	ENSP00000363452:G16E	ENSP00000363452:G16E	G	+	2	0	MAN1C1	25816922	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	2.847000	0.48270	0.790000	0.33803	0.546000	0.68486	GGG	.	.		0.692	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379		A	25944335	G	A	25944335	3	1	131	1	0	0	0	0	1	0	0	0	9222	1232	43	3	49	3	MAN1C1	1	25944335	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10		25944335	223306286	1	21290										
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155932460	155932460	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	aggccttgctgtggcggctgCagaactccgagtaggtctta	14	10	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:155932460C>T	ENST00000361247.4	-	9	1124	c.1025G>A	c.(1024-1026)tGc>tAc	p.C342Y	ARHGEF2_ENST00000313695.7_Missense_Mutation_p.C314Y|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.C387Y|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.C341Y|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.C314Y|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.C343Y|ARHGEF2_ENST00000477754.2_Intron	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	342	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GTGGCGGCTGCAGAACTCCGA	0.537																																					p.C342Y	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.G1025A						.						65	66	66					1																	155932460		2203	4300	6503	SO:0001583	missense	9181	exon9			CGGCTGCAGAACT	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	682	protein-coding gene	gene with protein product		607560	"rho/rac guanine nucleotide exchange factor (GEF) 2"			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.1025G>A	chr1.hg19:g.155932460C>T	ENSP00000354837:p.Cys342Tyr	181.0	0.0		287.0	22.0	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	hg19	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.659865	0.88154	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000435736;ENST00000543433;ENST00000313667	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	5.08	5.08	0.68730	Dbl homology (DH) domain (5);	0.000000	0.52532	D	0.000072	D	0.83326	0.5230	M	0.91140	3.18	0.80722	D	1	D;D;P;D	0.76494	0.999;0.984;0.77;0.966	D;D;B;P	0.76071	0.987;0.954;0.424;0.879	D	0.86301	0.1680	10	0.87932	D	0	-27.6171	16.3414	0.83083	0.0:1.0:0.0:0.0	.	387;386;342;341	B7Z977;D3DVA5;Q92974;Q92974-2	.;.;ARHG2_HUMAN;.	Y	314;342;343;314;387;315;341	ENSP00000315325:C314Y;ENSP00000354837:C342Y;ENSP00000357298:C343Y;ENSP00000357299:C314Y;ENSP00000314787:C341Y	ENSP00000314787:C341Y	C	-	2	0	ARHGEF2	154199084	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.156000	0.77453	2.803000	0.96430	0.609000	0.83330	TGC	.	.		0.537	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		T	155932460	C	T	155932460	3	4	131	1	0	0	0	0	1	0	0	0	903	710	25	3	1991	3	ARHGEF2	1	155932460	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	129988125	155932460	93318161	2	21291										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156937793	156937793	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	actcacctggtcaccggttgAggggactgctgcatccgagc	13	13	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:156937793A>C	ENST00000361409.2	-	10	1571	c.829T>G	c.(829-831)Tca>Gca	p.S277A	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.S317A	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	277					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TCACCGGTTGAGGGGACTGCT	0.582																																					p.S317A		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.T949G						.						54	51	52					1																	156937793		2203	4300	6503	SO:0001583	missense	9826	exon11			CGGTTGAGGGGAC	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.829T>G	chr1.hg19:g.156937793A>C	ENSP00000354644:p.Ser277Ala	152.0	0.0		173.0	37.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	hg19	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	A	6.104	0.387446	0.11581	.	.	ENSG00000132694	ENST00000368194;ENST00000361409	T;T	0.66280	-0.2;-0.13	4.81	-3.32	0.04973	.	1.665720	0.03587	N	0.231258	T	0.09992	0.0245	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.03296	-1.1051	10	0.06757	T	0.87	0.9157	0.1917	0.00135	0.2972:0.2247:0.2488:0.2292	.	277;317	O15085;O15085-2	ARHGB_HUMAN;.	A	317;277	ENSP00000357177:S317A;ENSP00000354644:S277A	ENSP00000354644:S277A	S	-	1	0	ARHGEF11	155204417	0.000000	0.05858	0.000000	0.03702	0.355000	0.29361	0.242000	0.18087	-1.007000	0.03408	-1.313000	0.01306	TCA	.	.		0.582	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		C	156937793	A	C	156937793	3	2	131	1	0	0	0	0	1	0	0	0	896	304	11	5	3863	5	ARHGEF11	1	156937793	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	1005333	156937793	92312828	3	21292										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157494326	157494326	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ccctgggagccctgaaggtgAggatgggacgagatactgga	17	8	0	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:157494326A>T	ENST00000361835.3	-	10	2139	c.1982T>A	c.(1981-1983)cTc>cAc	p.L661H	FCRL5_ENST00000368191.3_Missense_Mutation_p.L576H|FCRL5_ENST00000356953.4_Missense_Mutation_p.L661H|FCRL5_ENST00000368190.3_Missense_Mutation_p.L661H|FCRL5_ENST00000461387.1_5'Flank	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	661	Ig-like C2-type 7.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				CCTGAAGGTGAGGATGGGACG	0.507																																					p.L661H		Atlas-SNP	.											.	FCRL5	177	.	0			c.T1982A						.						49	54	52					1																	157494326		2203	4300	6503	SO:0001583	missense	83416	exon10			AAGGTGAGGATGG	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.1982T>A	chr1.hg19:g.157494326A>T	ENSP00000354691:p.Leu661His	140.0	0.0		271.0	16.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	hg19	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.269824	0.59540	.	.	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191	T;T;T;T	0.03951	3.75;3.75;3.75;3.75	4.69	4.69	0.59074	Immunoglobulin-like (1);	17.269200	0.00597	U	0.000372	T	0.27663	0.0680	H	0.97131	3.945	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.81914	0.987;0.951;0.995;0.995	T	0.15093	-1.0449	10	0.72032	D	0.01	.	10.7093	0.45973	1.0:0.0:0.0:0.0	.	576;661;661;661	F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9	.;.;.;FCRL5_HUMAN	H	661;661;661;576	ENSP00000354691:L661H;ENSP00000349434:L661H;ENSP00000357173:L661H;ENSP00000357174:L576H	ENSP00000349434:L661H	L	-	2	0	FCRL5	155760950	0.998000	0.40836	0.224000	0.23877	0.013000	0.08279	4.168000	0.58216	2.097000	0.63578	0.454000	0.30748	CTC	.	.		0.507	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		T	157494326	A	T	157494326	3	4	131	1	0	0	0	0	1	0	0	0	5806	304	11	4	983	4	FCRL5	1	157494326	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	556533	157494326	91756295	4	21293										
SERPINC1	462	hgsc.bcm.edu	37	chr1	173880936	173880936	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ggggtaacatctgcaactcaCcttgaagtccaggggctgga	13	10	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:173880936C>T	ENST00000367698.3	-	3	743		c.e3+1		SERPINC1_ENST00000494024.1_5'Flank	NM_000488.3	NP_000479.1	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C (antithrombin), member 1						blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of inflammatory response (GO:0050728)|regulation of blood coagulation, intrinsic pathway (GO:2000266)|regulation of proteolysis (GO:0030162)|response to nutrient (GO:0007584)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1)	25					Ardeparin(DB00407)|Dalteparin(DB06779)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Nadroparin(DB08813)|Sulodexide(DB06271)|Tinzaparin(DB06822)	CTGCAACTCACCTTGAAGTCC	0.498																																					.		Atlas-SNP	.											.	SERPINC1	57	.	0			c.624+1G>A						.						116	103	108					1																	173880936		2203	4300	6503	SO:0001630	splice_region_variant	462	exon4			AACTCACCTTGAA	X68793	CCDS1313.1	1q25.1	2014-02-18	2005-08-18		ENSG00000117601	ENSG00000117601		"Serine (or cysteine) peptidase inhibitors"	775	protein-coding gene	gene with protein product	"antithrombin III", "signal peptide antithrombin part 1", "coding sequence signal peptide antithrombin part 1", "antithrombin (aa 375-432)"	107300	"serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1"	AT3		3979120, 24172014	Standard	NM_000488		Approved	ATIII, MGC22579	uc001gjt.3	P01008	OTTHUMG00000037276	ENST00000367698.3:c.624+1G>A	chr1.hg19:g.173880936C>T		126.0	0.0		180.0	71.0	NM_000488	B2R6P0|P78439|P78447|Q13815|Q5TC78|Q7KZ43|Q7KZ97|Q9UC78	Splice_Site	SNP	ENST00000367698.3	hg19	CCDS1313.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.705364	0.89018	.	.	ENSG00000117601	ENST00000367698	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7525	0.96273	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SERPINC1	172147559	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.487000	0.81328	2.669000	0.90835	0.591000	0.81541	.	.	.		0.498	SERPINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090734.1	NM_000488	Intron	T	173880936	C	T	173880936	5	4	131	1	0	0	0	0	0	0	1	0	14124	521	18	3	789	3	SERPINC1	1	173880936	Splice_Site	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	16386610	173880936	75369685	5	21294										
NPL	80896	hgsc.bcm.edu	37	chr1	182794948	182794948	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	agatttatcaactttgttgtCaaactaggtaagtgccaccc	7	9	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:182794948C>G	ENST00000367553.1	+	11	815	c.771C>G	c.(769-771)gtC>gtG	p.V257V	NPL_ENST00000367554.3_Silent_p.V238V|NPL_ENST00000367555.1_Silent_p.V213V|NPL_ENST00000463899.1_3'UTR|NPL_ENST00000367552.2_Silent_p.V213V|NPL_ENST00000258317.2_Silent_p.V257V	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	257					carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)			breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						ACTTTGTTGTCAAACTAGGTA	0.348																																					p.S229X		Atlas-SNP	.											.	NPL	55	.	0			c.C686G						.						154	162	159					1																	182794948		2203	4300	6503	SO:0001819	synonymous_variant	80896	exon11			TGTTGTCAAACTA	AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"dihydrodipicolinate synthetase homolog 1 (E. coli)"	611412	"chromosome 1 open reading frame 13"	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.771C>G	chr1.hg19:g.182794948C>G		20.0	0.0		44.0	5.0	NM_001200052	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Nonsense_Mutation	SNP	ENST00000367553.1	hg19	CCDS1350.1																																																																																			.	.		0.348	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769		G	182794948	C	G	182794948	2	3	131	1	0	0	0	0	0	0	0	1	10594	813	29	4		4	NPL	1	182794948	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	8914012	182794948	66455673	6	21295										
PFKFB2	5208	hgsc.bcm.edu	37	chr1	207241653	207241653	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gattctgaatgagattgatgCtgtgagtaggaagctctgaa	13	4	2	5			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:207241653C>T	ENST00000367080.3	+	10	1110	c.986C>T	c.(985-987)gCt>gTt	p.A329V	PFKFB2_ENST00000541914.1_Splice_Site_p.A143V|PFKFB2_ENST00000411990.2_Splice_Site_p.A231V|PFKFB2_ENST00000545806.1_Splice_Site_p.A296V|PFKFB2_ENST00000367079.2_Splice_Site_p.A329V	NM_006212.2	NP_006203.2	O60825	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	329	Fructose-2,6-bisphosphatase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose catabolic process (GO:0006007)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|lactate metabolic process (GO:0006089)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|protein kinase binding (GO:0019901)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	20	Prostate(682;0.19)					GAGATTGATGCTGTGAGTAGG	0.463																																					p.A329V		Atlas-SNP	.											.	PFKFB2	70	.	0			c.C986T						.						70	67	68					1																	207241653		2203	4300	6503	SO:0001630	splice_region_variant	5208	exon10			TTGATGCTGTGAG		CCDS31003.1, CCDS31004.1	1q31-q32.2	2012-07-13			ENSG00000123836	ENSG00000123836	2.7.1.105, 3.1.3.46		8873	protein-coding gene	gene with protein product		171835					Standard	XM_005273162		Approved		uc001hfg.3	O60825	OTTHUMG00000036033	ENST00000367080.3:c.987+1C>T	chr1.hg19:g.207241653C>T		48.0	0.0		89.0	6.0	NM_001018053	O60824|Q5VVQ3|Q5VVQ4|Q9H3P1	Missense_Mutation	SNP	ENST00000367080.3	hg19	CCDS31004.1	.	.	.	.	.	.	.	.	.	.	C	35	5.420605	0.96111	.	.	ENSG00000123836	ENST00000411990;ENST00000367080;ENST00000367079;ENST00000545806;ENST00000541914	T;T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64;-0.64	5.67	4.77	0.60923	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	D	0.000000	T	0.79764	0.4502	L	0.52126	1.63	0.80722	D	1	P;D;D;D	0.89917	0.855;0.996;1.0;0.979	B;P;D;P	0.79784	0.381;0.679;0.993;0.722	T	0.81678	-0.0824	10	0.87932	D	0	.	13.6914	0.62549	0.0:0.9261:0.0:0.0739	.	143;231;329;329	B4DI16;B4DY91;Q5VVQ3;O60825	.;.;.;F262_HUMAN	V	231;329;329;296;143	ENSP00000408717:A231V;ENSP00000356047:A329V;ENSP00000356046:A329V;ENSP00000439420:A296V;ENSP00000440878:A143V	ENSP00000356046:A329V	A	+	2	0	PFKFB2	205308276	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.755000	0.85180	1.414000	0.47017	0.650000	0.86243	GCT	.	.		0.463	PFKFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087838.1		Missense_Mutation	T	207241653	C	T	207241653	5	4	131	1	0	0	0	0	0	0	1	0	11770	811	28	3	1020	3	PFKFB2	1	207241653	Splice_Site	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	24446705	207241653	42008968	7	21296										
USH2A	7399	hgsc.bcm.edu	37	chr1	216040372	216040372	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gtttagcccacctcacgtcgAtggctgtgtggttaaggaca	12	10	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:216040372A>G	ENST00000307340.3	-	44	9208	c.8822T>C	c.(8821-8823)aTc>aCc	p.I2941T	USH2A_ENST00000366943.2_Missense_Mutation_p.I2941T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2941	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CCTCACGTCGATGGCTGTGTG	0.453										HNSCC(13;0.011)																											p.I2941T		Atlas-SNP	.											.	USH2A	1168	.	0			c.T8822C						.						166	136	146					1																	216040372		2203	4300	6503	SO:0001583	missense	7399	exon44			ACGTCGATGGCTG	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.8822T>C	chr1.hg19:g.216040372A>G	ENSP00000305941:p.Ile2941Thr	127.0	0.0		218.0	22.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.436146	0.83885	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.59502	0.26;0.26	5.72	4.56	0.56223	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.142993	0.30949	N	0.008560	T	0.59569	0.2203	M	0.77103	2.36	0.19300	N	0.999976	P	0.39717	0.684	B	0.38378	0.272	T	0.58278	-0.7664	10	0.72032	D	0.01	.	12.7915	0.57537	0.8631:0.1368:0.0:0.0	.	2941	O75445	USH2A_HUMAN	T	2941	ENSP00000305941:I2941T;ENSP00000355910:I2941T	ENSP00000305941:I2941T	I	-	2	0	USH2A	214106995	0.996000	0.38824	0.357000	0.25798	0.840000	0.47671	3.970000	0.56824	0.952000	0.37798	0.455000	0.32223	ATC	.	.		0.453	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	216040372	A	G	216040372	3	3	131	1	0	0	0	0	1	0	0	0	17051	333	12	2	6902	2	USH2A	1	216040372	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	8798719	216040372	33210249	8	21297										
USH2A	7399	hgsc.bcm.edu	37	chr1	216371756	216371756	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cttggtgtatggctccaagcCagtgatggttgtcattgttt	12	7	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:216371756C>T	ENST00000307340.3	-	18	4368	c.3982G>A	c.(3982-3984)Ggc>Agc	p.G1328S	USH2A_ENST00000366942.3_Missense_Mutation_p.G1328S|USH2A_ENST00000366943.2_Missense_Mutation_p.G1328S|RP5-1099E6.3_ENST00000420867.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1328	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GGCTCCAAGCCAGTGATGGTT	0.453										HNSCC(13;0.011)																											p.G1328S		Atlas-SNP	.											.	USH2A	1168	.	0			c.G3982A						.						138	128	131					1																	216371756		2203	4300	6503	SO:0001583	missense	7399	exon18			CCAAGCCAGTGAT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.3982G>A	chr1.hg19:g.216371756C>T	ENSP00000305941:p.Gly1328Ser	115.0	0.0		191.0	13.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.850455	0.71719	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.61274	0.12;0.34;0.34	5.69	5.69	0.88448	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.309756	0.22942	N	0.053763	T	0.66376	0.2783	M	0.76433	2.335	0.35137	D	0.768545	P;P	0.45715	0.837;0.865	P;P	0.49999	0.628;0.61	T	0.73927	-0.3828	10	0.36615	T	0.2	.	13.0738	0.59075	0.0:0.9268:0.0:0.0732	.	1328;1328	O75445-2;O75445	.;USH2A_HUMAN	S	1328	ENSP00000305941:G1328S;ENSP00000355910:G1328S;ENSP00000355909:G1328S	ENSP00000305941:G1328S	G	-	1	0	USH2A	214438379	0.788000	0.28762	0.989000	0.46669	0.449000	0.32228	2.716000	0.47219	2.688000	0.91661	0.650000	0.86243	GGC	.	.		0.453	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216371756	C	T	216371756	3	4	131	1	0	0	0	0	1	0	0	0	17051	594	21	3	11860	3	USH2A	1	216371756	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	331384	216371756	32878865	9	21298										
EPRS	2058	hgsc.bcm.edu	37	chr1	220174520	220174520	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ctttggtcttttcctttgacCctgatgttggcatttccttt	7	10	1	2	rs374231493		TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:220174520C>A	ENST00000366923.3	-	17	2410	c.2141G>T	c.(2140-2142)gGg>gTg	p.G714V		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	714	Glutamate--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	TTCCTTTGACCCTGATGTTGG	0.378																																					p.G714V		Atlas-SNP	.											.	EPRS	140	.	0			c.G2141T						.						167	149	155					1																	220174520		2203	4300	6503	SO:0001583	missense	2058	exon17			TTTGACCCTGATG	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.2141G>T	chr1.hg19:g.220174520C>A	ENSP00000355890:p.Gly714Val	123.0	0.0		249.0	65.0	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Missense_Mutation	SNP	ENST00000366923.3	hg19	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.783887	0.90282	.	.	ENSG00000136628	ENST00000366923;ENST00000536921;ENST00000435048	T	0.06768	3.26	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.29817	0.0745	M	0.67397	2.05	0.80722	D	1	D;P;D;D	0.89917	1.0;0.819;0.995;0.991	D;P;P;P	0.76575	0.988;0.614;0.788;0.858	T	0.00581	-1.1660	10	0.62326	D	0.03	-22.932	19.3764	0.94512	0.0:1.0:0.0:0.0	.	738;721;721;714	E7EMN0;F5H7I7;Q3KQZ8;P07814	.;.;.;SYEP_HUMAN	V	714;721;738	ENSP00000355890:G714V	ENSP00000355890:G714V	G	-	2	0	EPRS	218241143	1.000000	0.71417	0.995000	0.50966	0.931000	0.56810	6.907000	0.75724	2.590000	0.87494	0.563000	0.77884	GGG	.	.		0.378	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		A	220174520	C	A	220174520	3	1	131	1	0	0	0	0	1	0	0	0	5193	623	22	3	2461	3	EPRS	1	220174520	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	3802764	220174520	29076101	10	21299										
NUP133	55746	hgsc.bcm.edu	37	chr1	229596501	229596502	+	Frame_Shift_Ins	INS	-	-	A													0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tccagataccaacggaagagINSaaagtctgaaaaattctaca							TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:229596501_229596502insA	ENST00000261396.3	-	20	2791_2792	c.2700_2701insT	c.(2698-2703)tttctcfs	p.L901fs	NUP133_ENST00000537506.1_Frame_Shift_Ins_p.L885fs	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	901					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				CAACGGAAGAGAAAGTCTGAAA	0.337																																					p.L901fs		Atlas-Indel,Pindel	.											.	NUP133	111	.	0			c.2701_2702insT						.																																			SO:0001589	frameshift_variant	55746	exon20			.		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.2701dupT	chr1.hg19:g.229596504_229596504dupA	ENSP00000261396:p.Leu901fs	65.0	0.0		130.0	33.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Frame_Shift_Ins	INS	ENST00000261396.3	hg19	CCDS1579.1																																																																																			.	.		0.337	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		A	229596502	-	A	229596501	7	5	131	1	0	1	1	0	0	0	0	0	10763	942	33	0	797	0	NUP133	1	229596501	Frame_Shift_Ins	INS	-	TCGA-DD-A4NI-01A-11D-A27I-10	9421981	229596501	19654120	11	21300										
ACTN2	88	hgsc.bcm.edu	37	chr1	236850058	236850058	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	aggaggaggagtgggaccgcGacctgctcctggacccagcc	16	13	0	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:236850058G>A	ENST00000366578.4	+	1	251	c.85G>A	c.(85-87)Gac>Aac	p.D29N	ACTN2_ENST00000492634.1_3'UTR|ACTN2_ENST00000542672.1_Missense_Mutation_p.D29N	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	29	Actin-binding.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			GTGGGACCGCGACCTGCTCCT	0.692																																					p.D29N		Atlas-SNP	.											.	ACTN2	191	.	0			c.G85A						.						48	43	45					1																	236850058		2203	4300	6503	SO:0001583	missense	88	exon1			GACCGCGACCTGC	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.85G>A	chr1.hg19:g.236850058G>A	ENSP00000355537:p.Asp29Asn	92.0	0.0		157.0	11.0	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	hg19	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.247493	0.80024	.	.	ENSG00000077522	ENST00000542672;ENST00000366578	T;T	0.60299	0.2;0.2	3.81	2.86	0.33363	Calponin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.49915	0.1585	L	0.58583	1.82	0.80722	D	1	P;P	0.39157	0.662;0.649	B;B	0.31869	0.137;0.057	T	0.56751	-0.7927	10	0.87932	D	0	.	13.0662	0.59034	0.0:0.163:0.837:0.0	.	29;29	B2RCS5;P35609	.;ACTN2_HUMAN	N	29	ENSP00000443495:D29N;ENSP00000355537:D29N	ENSP00000355537:D29N	D	+	1	0	ACTN2	234916681	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.711000	0.91396	0.757000	0.33036	0.462000	0.41574	GAC	.	.		0.692	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		A	236850058	G	A	236850058	3	1	131	1	0	0	0	0	1	0	0	0	205	1058	37	1	87	1	ACTN2	1	236850058	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	7253557	236850058	12400563	12	21301										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247599337	247599337	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	atcagtattgagcaccagccAttccctgaccagactctatg	7	13	2	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:247599337A>G	ENST00000336119.3	+	6	3310	c.2564A>G	c.(2563-2565)cAt>cGt	p.H855R	NLRP3_ENST00000391827.2_Missense_Mutation_p.H798R|NLRP3_ENST00000366497.2_Intron|NLRP3_ENST00000348069.2_Intron|NLRP3_ENST00000366496.2_Intron|NLRP3_ENST00000391828.3_Missense_Mutation_p.H855R	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	855					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			AGCACCAGCCATTCCCTGACC	0.483																																					p.H855R		Atlas-SNP	.											.	NLRP3	286	.	0			c.A2564G						.						128	111	117					1																	247599337		2203	4300	6503	SO:0001583	missense	114548	exon6			CCAGCCATTCCCT	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.2564A>G	chr1.hg19:g.247599337A>G	ENSP00000337383:p.His855Arg	138.0	0.0		277.0	48.0	NM_004895	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	a	0.828	-0.746385	0.03065	.	.	ENSG00000162711	ENST00000391828;ENST00000336119;ENST00000391827	T;T;T	0.45668	0.89;0.89;0.89	3.63	-4.55	0.03441	.	1.030140	0.07791	N	0.954965	T	0.16041	0.0386	N	0.04373	-0.215	0.09310	N	1	B;B;B	0.12013	0.0;0.0;0.005	B;B;B	0.04013	0.0;0.0;0.001	T	0.20974	-1.0259	10	0.20046	T	0.44	.	5.4132	0.16360	0.3316:0.2976:0.3708:0.0	.	835;798;855	B7ZKS9;Q96P20-4;Q96P20	.;.;NALP3_HUMAN	R	855;855;798	ENSP00000375704:H855R;ENSP00000337383:H855R;ENSP00000375703:H798R	ENSP00000337383:H855R	H	+	2	0	NLRP3	245665960	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.700000	0.05081	-1.155000	0.02822	-2.766000	0.00121	CAT	.	.		0.483	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		G	247599337	A	G	247599337	3	3	131	1	0	0	0	0	1	0	0	0	10487	217	8	2	2586	2	NLRP3	1	247599337	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	10749279	247599337	1651284	13	21302										
OR1C1	26188	hgsc.bcm.edu	37	chr1	247921053	247921053	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gaacagtggagaagataagtCcataagatacgaggatacag	12	5	0	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr1:247921053C>A	ENST00000408896.2	-	1	929	c.656G>T	c.(655-657)gGa>gTa	p.G219V		NM_012353.2	NP_036485.2	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C, member 1	219					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(32)|skin(2)|upper_aerodigestive_tract(1)	46	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)			GAAGATAAGTCCATAAGATAC	0.483																																					p.G219V		Atlas-SNP	.											.	OR1C1	86	.	0			c.G656T						.						55	54	54					1																	247921053		2021	4195	6216	SO:0001583	missense	26188	exon1			ATAAGTCCATAAG	X89674	CCDS41481.1	1q44	2012-08-09			ENSG00000221888	ENSG00000221888		"GPCR / Class A : Olfactory receptors"	8182	protein-coding gene	gene with protein product						9119360	Standard	NM_012353		Approved	TPCR27, HSTPCR27	uc010pza.2	Q15619	OTTHUMG00000040198	ENST00000408896.2:c.656G>T	chr1.hg19:g.247921053C>A	ENSP00000386138:p.Gly219Val	119.0	0.0		180.0	39.0	NM_012353	B9EIR9|Q5VVD2|Q6IF97|Q8NGZ1|Q96R83	Missense_Mutation	SNP	ENST00000408896.2	hg19	CCDS41481.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.788307	0.00628	.	.	ENSG00000221888	ENST00000408896	T	0.00017	9.09	3.22	-2.25	0.06888	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	N	0.02368	-0.58	0.09310	N	1	B	0.10296	0.003	B	0.20184	0.028	T	0.03354	-1.1045	9	0.36615	T	0.2	.	12.9735	0.58525	0.8047:0.1953:0.0:0.0	.	219	Q15619	OR1C1_HUMAN	V	219	ENSP00000386138:G219V	ENSP00000386138:G219V	G	-	2	0	OR1C1	245987676	0.000000	0.05858	0.026000	0.17262	0.096000	0.18686	0.360000	0.20250	-0.166000	0.10890	-0.293000	0.09583	GGA	.	.		0.483	OR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096855.1			A	247921053	C	A	247921053	3	1	131	1	0	0	0	0	1	0	0	0	10961	855	30	3	290	3	OR1C1	1	247921053	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	321716	247921053	1329568	14	21303										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33246001	33246001	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tgtgttccgccatgtcagaaTggagggatgtgtctccggcc	14	10	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:33246001T>C	ENST00000404816.2	+	3	944	c.591T>C	c.(589-591)aaT>aaC	p.N197N	LTBP1_ENST00000354476.3_Silent_p.N197N			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	197	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CATGTCAGAATGGAGGGATGT	0.483																																					p.N197N		Atlas-SNP	.											.	LTBP1	317	.	0			c.T591C						.						197	202	200					2																	33246001		2202	4298	6500	SO:0001819	synonymous_variant	4052	exon3			TCAGAATGGAGGG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.591T>C	chr2.hg19:g.33246001T>C		85.0	0.0		133.0	8.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	hg19	CCDS33177.2																																																																																			.	.		0.483	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		C	33246001	T	C	33246001	2	2	131	1	0	0	0	0	0	0	0	1	9082	1461	51	2		2	LTBP1	2	33246001	Silent	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10		33246001	209953372	15	21304										
SOS1	6654	hgsc.bcm.edu	37	chr2	39249927	39249927	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	aagcatcctttccagtgtacTccggtactgtaaagatatca	7	10	1	1	rs397517149		TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:39249927T>C	ENST00000426016.1	-	11	1728	c.1642A>G	c.(1642-1644)Agt>Ggt	p.S548G	SOS1_ENST00000395038.2_Missense_Mutation_p.S548G|SOS1_ENST00000472480.1_5'Flank|SOS1_ENST00000402219.2_Missense_Mutation_p.S548G			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	548	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		S -> R (in NS4). {ECO:0000269|PubMed:17143282, ECO:0000269|PubMed:17143285, ECO:0000269|PubMed:21387466}.		apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				TCCAGTGTACTCCGGTACTGT	0.383									Noonan syndrome																												p.S548G		Atlas-SNP	.											.	SOS1	134	.	0			c.A1642G	GRCh37	CM070280	SOS1	M		.						141	135	137					2																	39249927		2203	4300	6503	SO:0001583	missense	6654	exon10	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	GTGTACTCCGGTA	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1642A>G	chr2.hg19:g.39249927T>C	ENSP00000387784:p.Ser548Gly	69.0	0.0		123.0	43.0	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	hg19	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.506634	0.64410	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	D;D;D	0.88201	-2.35;-2.35;-2.35	5.78	5.78	0.91487	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	D	0.93861	0.8036	M	0.77820	2.39	0.80722	D	1	D;D	0.65815	0.995;0.994	D;P	0.64042	0.921;0.813	D	0.94446	0.7663	10	0.72032	D	0.01	.	16.1027	0.81194	0.0:0.0:0.0:1.0	.	280;548	F5GX06;Q07889	.;SOS1_HUMAN	G	548;548;280;548;548	ENSP00000387784:S548G;ENSP00000384675:S548G;ENSP00000378479:S548G	ENSP00000263879:S548G	S	-	1	0	SOS1	39103431	0.794000	0.28838	1.000000	0.80357	0.924000	0.55760	1.386000	0.34419	2.198000	0.70561	0.455000	0.32223	AGT	.	.		0.383	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		C	39249927	T	C	39249927	3	2	131	1	0	0	0	0	1	0	0	0	14951	1551	54	2	2415	2	SOS1	2	39249927	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	6003926	39249927	203949446	16	21305										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50464017	50464017	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	acagtgctaaaacctatggcCagtctgtctgctcgtgtact	9	11	2	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:50464017C>A	ENST00000406316.2	-	18	4932	c.3456G>T	c.(3454-3456)ctG>ctT	p.L1152L	NRXN1_ENST00000402717.3_Silent_p.L1144L|NRXN1_ENST00000401710.1_Silent_p.L170L|NRXN1_ENST00000342183.5_Silent_p.L117L|NRXN1_ENST00000401669.2_Silent_p.L1152L|NRXN1_ENST00000405472.3_Silent_p.L1144L|NRXN1_ENST00000404971.1_Silent_p.L1192L|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000406859.3_Silent_p.L1152L	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1152	Laminin G-like 6. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			AACCTATGGCCAGTCTGTCTG	0.468																																					p.L1192L		Atlas-SNP	.											NRXN1_ENST00000536085,NS,carcinoma,0,3	NRXN1	1118	.	0			c.G3576T						.						132	118	123					2																	50464017		2203	4300	6503	SO:0001819	synonymous_variant	9378	exon19			TATGGCCAGTCTG	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3456G>T	chr2.hg19:g.50464017C>A		196.0	1.0		268.0	71.0	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	hg19	CCDS54360.1																																																																																			.	.		0.468	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	50464017	C	A	50464017	2	1	131	1	0	0	0	0	0	0	0	1	10674	581	21	3		3	NRXN1	2	50464017	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	11214090	50464017	192735356	17	21306										
B3GNT2	10678	hgsc.bcm.edu	37	chr2	62449528	62449528	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	atctacccctcccgaggcatActggaaccgagagcaagaga	10	13	1	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:62449528A>T	ENST00000301998.4	+	2	425	c.173A>T	c.(172-174)tAc>tTc	p.Y58F	B3GNT2_ENST00000405767.1_Missense_Mutation_p.Y58F	NM_006577.5	NP_006568.2	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	58					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)	18	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)			CCCGAGGCATACTGGAACCGA	0.502																																					p.Y58F		Atlas-SNP	.											.	B3GNT2	34	.	0			c.A173T						.						146	171	162					2																	62449528		2203	4300	6503	SO:0001583	missense	10678	exon2			AGGCATACTGGAA	AB049584	CCDS1870.1	2p15	2013-02-19	2006-04-12	2006-04-12	ENSG00000170340	ENSG00000170340		"Beta 3-glycosyltransferases"	15629	protein-coding gene	gene with protein product		605581	"UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1"	B3GNT1		9892646, 11042166	Standard	NM_006577		Approved	B3GNT-2, BETA3GNT, B3GN-T2, B3GN-T1	uc002sbs.3	Q9NY97	OTTHUMG00000129444	ENST00000301998.4:c.173A>T	chr2.hg19:g.62449528A>T	ENSP00000305595:p.Tyr58Phe	101.0	0.0		115.0	12.0	NM_006577	Q54AC1|Q9NQQ9|Q9NQR0|Q9NUT9	Missense_Mutation	SNP	ENST00000301998.4	hg19	CCDS1870.1	.	.	.	.	.	.	.	.	.	.	A	12.60	1.988060	0.35036	.	.	ENSG00000170340	ENST00000301998;ENST00000405767	T;T	0.26373	1.74;1.74	6.02	6.02	0.97574	.	0.120536	0.64402	D	0.000019	T	0.27731	0.0682	L	0.58428	1.81	0.58432	D	0.999996	B	0.09022	0.002	B	0.08055	0.003	T	0.07347	-1.0777	10	0.17369	T	0.5	.	16.5446	0.84426	1.0:0.0:0.0:0.0	.	58	Q9NY97	B3GN2_HUMAN	F	58	ENSP00000305595:Y58F;ENSP00000384692:Y58F	ENSP00000305595:Y58F	Y	+	2	0	B3GNT2	62303032	1.000000	0.71417	0.921000	0.36526	0.827000	0.46813	3.663000	0.54518	2.311000	0.77944	0.533000	0.62120	TAC	.	.		0.502	B3GNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251606.2	NM_006577		T	62449528	A	T	62449528	3	4	131	1	0	0	0	0	1	0	0	0	1257	391	14	4	175	4	B3GNT2	2	62449528	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	11985511	62449528	180749845	18	21307										
AUP1	165545	hgsc.bcm.edu	37	chr2	74754135	74754135	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ctgccgggcccaggaagactTggcaaatgttagggctgttg	15	9	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:74754135T>C	ENST00000404568.3	-	0	0				HTRA2_ENST00000352222.3_5'Flank|DQX1_ENST00000393951.2_5'Flank|HTRA2_ENST00000258080.3_5'Flank|AUP1_ENST00000377526.3_Missense_Mutation_p.K377E|DQX1_ENST00000495597.1_5'Flank	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1							nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						CAGGAAGACTTGGCAAATGTT	0.532																																					p.K377E		Atlas-SNP	.											.	AUP1	29	.	0			c.A1129G						.						52	54	54					2																	74754135		1948	4141	6089	SO:0001631	upstream_gene_variant	550	exon11			AAGACTTGGCAAA	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965		chr2.hg19:g.74754135T>C	Exception_encountered	54.0	0.0		105.0	5.0	NM_181575	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	hg19	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	T	21.8	4.202405	0.79127	.	.	ENSG00000115307	ENST00000377526;ENST00000258081	.	.	.	5.36	5.36	0.76844	.	0.159108	0.56097	D	0.000029	T	0.66247	0.2770	L	0.54323	1.7	0.51012	D	0.999902	D;D;D	0.61080	0.988;0.989;0.986	P;P;P	0.58520	0.76;0.775;0.84	T	0.69292	-0.5183	9	0.72032	D	0.01	-15.7148	11.6678	0.51383	0.0:0.0:0.0:1.0	.	434;443;377	E7EU18;Q9Y679;Q9Y679-2	.;AUP1_HUMAN;.	E	377;441	.	ENSP00000258081:K441E	K	-	1	0	AUP1	74607643	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.088000	0.71371	2.246000	0.74042	0.533000	0.62120	AAG	.	.		0.532	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		C	74754135	T	C	74754135	1	2	131	0	1	0	0	0	0	0	0	0	1220	1821	63	2		2	AUP1	2	74754135	5'Flank	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	12304607	74754135	168445238	19	21308										
IL1RL2	8808	hgsc.bcm.edu	37	chr2	102836404	102836404	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	atcaccttcttggaagtgaaAatggaagattatggccttcc	9	8	2	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:102836404A>G	ENST00000264257.2	+	8	1044	c.918A>G	c.(916-918)aaA>aaG	p.K306K	IL1RL2_ENST00000481806.1_3'UTR|IL1RL2_ENST00000539491.1_Silent_p.K306K|IL1RL2_ENST00000441515.2_Silent_p.K188K	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	306	Ig-like C2-type 3.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						TGGAAGTGAAAATGGAAGATT	0.398																																					p.K306K		Atlas-SNP	.											.	IL1RL2	118	.	0			c.A918G						.						131	116	121					2																	102836404		2203	4300	6503	SO:0001819	synonymous_variant	8808	exon8			AGTGAAAATGGAA	U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.918A>G	chr2.hg19:g.102836404A>G		93.0	0.0		156.0	65.0	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Silent	SNP	ENST00000264257.2	hg19	CCDS2056.1																																																																																			.	.		0.398	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		G	102836404	A	G	102836404	2	3	131	1	0	0	0	0	0	0	0	1	7673	11	1	2		2	IL1RL2	2	102836404	Silent	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	28082269	102836404	140362969	20	21309										
GLI2	2736	hgsc.bcm.edu	37	chr2	121747481	121747481	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	agagccatcacctggcagccTccatgagccaggagggctac	12	14	1	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:121747481T>A	ENST00000452319.1	+	14	4051	c.3991T>A	c.(3991-3993)Tcc>Acc	p.S1331T	GLI2_ENST00000361492.4_Missense_Mutation_p.S1331T|GLI2_ENST00000314490.11_Intron					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CCTGGCAGCCTCCATGAGCCA	0.662																																					p.S1331T		Atlas-SNP	.											.	GLI2	187	.	0			c.T3991A						.						19	20	19					2																	121747481		2200	4294	6494	SO:0001583	missense	2736	exon13			GCAGCCTCCATGA		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.3991T>A	chr2.hg19:g.121747481T>A	ENSP00000390436:p.Ser1331Thr	162.0	0.0		181.0	10.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	T	7.290	0.610783	0.14066	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.14391	2.51;2.51	4.35	-7.44	0.01379	.	0.674730	0.15033	N	0.284344	T	0.03520	0.0101	N	0.08118	0	0.33388	D	0.575745	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.34950	-0.9808	9	.	.	.	.	1.2355	0.01952	0.1733:0.2848:0.1717:0.3702	.	1331;986	P10070;P10070-2	GLI2_HUMAN;.	T	1331	ENSP00000390436:S1331T;ENSP00000354586:S1331T	.	S	+	1	0	GLI2	121463951	0.000000	0.05858	0.000000	0.03702	0.958000	0.62258	-2.077000	0.01371	-1.744000	0.01338	-0.415000	0.06103	TCC	.	.		0.662	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		A	121747481	T	A	121747481	3	1	131	1	0	0	0	0	1	0	0	0	6446	1551	54	4	4041	4	GLI2	2	121747481	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	18911077	121747481	121451892	21	21310										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148657133	148657133	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ttccggagatggaagtcacaCagcgtaagttcacagggaaa	12	8	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:148657133C>T	ENST00000241416.7	+	3	1006	c.370C>T	c.(370-372)Cag>Tag	p.Q124*	AC009480.3_ENST00000402410.2_RNA|ACVR2A_ENST00000404590.1_Nonsense_Mutation_p.Q124*|ACVR2A_ENST00000535787.1_Nonsense_Mutation_p.Q16*	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	124					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		GGAAGTCACACAGCGTAAGTT	0.373																																					p.Q124X		Atlas-SNP	.											.	ACVR2A	125	.	0			c.C370T						.						152	160	157					2																	148657133		2202	4300	6502	SO:0001587	stop_gained	92	exon3			GTCACACAGCGTA		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.370C>T	chr2.hg19:g.148657133C>T	ENSP00000241416:p.Gln124*	19.0	0.0		55.0	17.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Nonsense_Mutation	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	C	40	8.231984	0.98717	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	.	.	.	5.56	4.63	0.57726	.	0.426594	0.27572	N	0.018763	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	14.7454	0.69488	0.1435:0.8564:0.0:0.0	.	.	.	.	X	124;16;124	.	ENSP00000241416:Q124X	Q	+	1	0	ACVR2A	148373603	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.585000	0.36600	2.771000	0.95319	0.650000	0.86243	CAG	.	.		0.373	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		T	148657133	C	T	148657133	4	4	131	1	0	0	0	0	0	1	0	0	223	479	17	3	380	3	ACVR2A	2	148657133	Nonsense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	26909652	148657133	94542240	22	21311										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098968	178098968	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ttactccaagatctatatctTgcctccaaagtatgtcaatc	4	11	3	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:178098968T>G	ENST00000397062.3	-	2	631	c.77A>C	c.(76-78)cAa>cCa	p.Q26P	NFE2L2_ENST00000423513.1_Missense_Mutation_p.Q10P|NFE2L2_ENST00000446151.2_Missense_Mutation_p.Q10P|NFE2L2_ENST00000464747.1_Missense_Mutation_p.Q10P|NFE2L2_ENST00000397063.4_Missense_Mutation_p.Q10P	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	26					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q26P(1)|p.Q26L(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ATCTATATCTTGCCTCCAAAG	0.348			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.Q26P		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,-1,2	NFE2L2	225	.	2	Substitution - Missense(2)	lung(2)	c.A77C						.						59	53	55					2																	178098968		1842	4098	5940	SO:0001583	missense	4780	exon2			ATATCTTGCCTCC		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.77A>C	chr2.hg19:g.178098968T>G	ENSP00000380252:p.Gln26Pro	34.0	0.0		64.0	4.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.816192	0.70912	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.66287	0.2774	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	0.999;0.998;1.0;0.999	D;D;D;D	0.85130	0.996;0.986;0.997;0.996	T	0.72959	-0.4133	10	0.87932	D	0	.	16.098	0.81144	0.0:0.0:0.0:1.0	.	10;10;10;26	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	P	10;26;10;10;10;10;10	ENSP00000380253:Q10P;ENSP00000380252:Q26P;ENSP00000411575:Q10P;ENSP00000391590:Q10P;ENSP00000400073:Q10P;ENSP00000412191:Q10P;ENSP00000410015:Q10P	ENSP00000380252:Q26P	Q	-	2	0	NFE2L2	177807214	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.698000	0.84413	2.210000	0.71456	0.460000	0.39030	CAA	.	.		0.348	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		G	178098968	T	G	178098968	3	3	131	1	0	0	0	0	1	0	0	0	10377	1812	63	5	1756	5	NFE2L2	2	178098968	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	29441835	178098968	65100405	23	21312										
COL5A2	1290	hgsc.bcm.edu	37	chr2	189927932	189927932	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ggcctggaaggcccatgctcCcgggctgccctctgattcct	12	16	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:189927932C>T	ENST00000374866.3	-	27	2109	c.1835G>A	c.(1834-1836)gGg>gAg	p.G612E		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	612					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			GCCCATGCTCCCGGGCTGCCC	0.522																																					p.G612E		Atlas-SNP	.											.	COL5A2	230	.	0			c.G1835A						.						81	92	88					2																	189927932		2203	4300	6503	SO:0001583	missense	1290	exon27			ATGCTCCCGGGCT	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.1835G>A	chr2.hg19:g.189927932C>T	ENSP00000364000:p.Gly612Glu	19.0	0.0		41.0	14.0	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	hg19	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.648970	0.87958	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.99619	-6.28	4.56	4.56	0.56223	.	0.000000	0.46442	D	0.000283	D	0.99768	0.9905	H	0.95950	3.745	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.96884	0.9648	9	.	.	.	.	17.7045	0.88304	0.0:1.0:0.0:0.0	.	252;612	Q5PR22;P05997	.;CO5A2_HUMAN	E	612;252	ENSP00000364000:G612E	.	G	-	2	0	COL5A2	189636177	1.000000	0.71417	0.990000	0.47175	0.925000	0.55904	7.445000	0.80570	2.244000	0.73946	0.467000	0.42956	GGG	.	.		0.522	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		T	189927932	C	T	189927932	3	4	131	1	0	0	0	0	1	0	0	0	3699	623	22	3	2776	3	COL5A2	2	189927932	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	11828964	189927932	53271441	24	21313										
HIBCH	26275	hgsc.bcm.edu	37	chr2	191159323	191159323	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tcctcctgctccctttataaTgatcaggaaagtttcaggat	7	10	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:191159323T>C	ENST00000359678.5	-	4	547	c.253A>G	c.(253-255)Att>Gtt	p.I85V	HIBCH_ENST00000392332.3_Missense_Mutation_p.I85V	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	85					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			CCCTTTATAATGATCAGGAAA	0.393																																					p.I85V		Atlas-SNP	.											.	HIBCH	28	.	0			c.A253G						.						83	79	81					2																	191159323		2203	4300	6503	SO:0001583	missense	26275	exon4			TTATAATGATCAG	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"3-hydroxyisobutyryl-Coenzyme A hydrolase"			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.253A>G	chr2.hg19:g.191159323T>C	ENSP00000352706:p.Ile85Val	57.0	0.0		81.0	8.0	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Missense_Mutation	SNP	ENST00000359678.5	hg19	CCDS2304.1	.	.	.	.	.	.	.	.	.	.	T	12.51	1.959275	0.34565	.	.	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000409934	T;T;T	0.67523	-0.26;-0.27;-0.26	5.43	2.93	0.34026	Crotonase, core (1);	0.095807	0.64402	D	0.000001	T	0.48114	0.1482	N	0.17564	0.495	0.80722	D	1	B;B	0.19817	0.01;0.039	B;B	0.24701	0.055;0.025	T	0.20605	-1.0270	10	0.23891	T	0.37	-0.3131	10.6221	0.45487	0.0:0.0:0.3037:0.6963	.	85;85	Q6NVY1-2;Q6NVY1	.;HIBCH_HUMAN	V	85;85;139	ENSP00000376144:I85V;ENSP00000352706:I85V;ENSP00000387247:I139V	ENSP00000352706:I85V	I	-	1	0	HIBCH	190867568	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	1.434000	0.34958	0.314000	0.23086	0.460000	0.39030	ATT	.	.		0.393	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1			C	191159323	T	C	191159323	3	2	131	1	0	0	0	0	1	0	0	0	7109	1464	51	2	951	2	HIBCH	2	191159323	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	1231391	191159323	52040050	25	21314										
STRADB	55437	hgsc.bcm.edu	37	chr2	202344880	202344880	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gattttcctgatgaaaaagaCtcatactgggaattctaggg	10	6	2	3	rs568127362	byFrequency	TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:202344880C>T	ENST00000194530.3	+	12	1604	c.1239C>T	c.(1237-1239)gaC>gaT	p.D413D	STRADB_ENST00000392249.2_3'UTR	NM_001206864.1|NM_018571.5	NP_001193793.1|NP_061041.2	Q9C0K7	STRAB_HUMAN	STE20-related kinase adaptor beta	413					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cell morphogenesis (GO:0000902)|insulin receptor signaling pathway (GO:0008286)|JNK cascade (GO:0007254)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|lung(5)|prostate(1)|skin(3)|stomach(1)	13						ATGAAAAAGACTCATACTGGG	0.393													C|||	61	0.0121805	0.0144	0.0144	5008	,	,		17652	0.004		0.0169	False		,,,				2504	0.0112				p.D413D		Atlas-SNP	.											.	STRADB	33	.	0			c.C1239T						.						139	139	139					2																	202344880		2203	4300	6503	SO:0001819	synonymous_variant	55437	exon12			AAAAGACTCATAC	AB038950	CCDS2348.1, CCDS56161.1	2q33.1	2010-09-30	2008-09-15	2008-09-15	ENSG00000082146	ENSG00000082146			13205	protein-coding gene	gene with protein product		607333	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2"	ALS2CR2		11161814, 14511394	Standard	NM_018571		Approved	CALS-21, PAPK, ILPIPA, ILPIP	uc002uyd.4	Q9C0K7	OTTHUMG00000132831	ENST00000194530.3:c.1239C>T	chr2.hg19:g.202344880C>T		85.0	0.0		144.0	7.0	NM_018571	Q5BKY7|Q9P1L0	Silent	SNP	ENST00000194530.3	hg19	CCDS2348.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.510128	0.00984	.	.	ENSG00000082146	ENST00000415688	.	.	.	5.32	-3.37	0.04898	.	.	.	.	.	T	0.22044	0.0531	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.31420	-0.9944	4	.	.	.	.	5.6468	0.17594	0.2111:0.3213:0.0:0.4677	.	.	.	.	F	84	.	.	L	+	1	0	STRADB	202053125	0.000000	0.05858	0.000000	0.03702	0.191000	0.23601	-0.169000	0.09911	-0.631000	0.05560	-0.142000	0.14014	CTC	.	.		0.393	STRADB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256297.1	NM_018571		T	202344880	C	T	202344880	2	4	131	1	0	0	0	0	0	0	0	1	15340	564	20	3		3	STRADB	2	202344880	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	11185557	202344880	40854493	26	21315										
PECR	55825	hgsc.bcm.edu	37	chr2	216946374	216946397	+	In_Frame_Del	DEL	CGATGCCCGTGGCCCCGCCGGTGA	CGATGCCCGTGGCCCCGCCGGTGA	-													0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ctccttcacgatggcttttcCgatgcccgtggccccgccgg					rs370096306|rs201164160		TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	CGATGCCCGTGGCCCCGCCGGTGA	CGATGCCCGTGGCCCCGCCGGTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:216946374_216946397delCGATGCCCGTGGCCCCGCCGGTGA	ENST00000265322.7	-	1	142_165	c.68_91delTCACCGGCGGGGCCACGGGCATCG	c.(67-93)gtcaccggcggggccacgggcatcgga>gga	p.VTGGATGI23del	PECR_ENST00000497889.1_5'UTR|TMEM169_ENST00000437356.2_5'Flank|TMEM169_ENST00000454545.1_5'Flank|TMEM169_ENST00000295658.4_5'Flank|TMEM169_ENST00000406027.2_5'Flank	NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	23					fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	ATGGCTTTTCCGATGCCCGTGGCCCCGCCGGTGACGATGGCCAC	0.674																																					p.23_31del		Atlas-Indel,Pindel	.											.	PECR	22	.	0			c.69_92del						.																																			SO:0001651	inframe_deletion	55825	exon1			.	AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18281	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 29C, member 1"	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.68_91delTCACCGGCGGGGCCACGGGCATCG	chr2.hg19:g.216946374_216946397delCGATGCCCGTGGCCCCGCCGGTGA	ENSP00000265322:p.Val23_Ile30del	183.0	0.0		226.0	42.0	NM_018441	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	In_Frame_Del	DEL	ENST00000265322.7	hg19	CCDS33375.1																																																																																			.	.		0.674	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441		-	216946397	CGATGCCCGTGGCCCCGCCGGTGA	-	216946374	7	5	131	1	0	1	0	1	0	0	0	0	11726	661	23	0	852	0	PECR	2	216946374	In_Frame_Del	DEL	CGATGCCCGTGGCCCCGCCGGTGA	TCGA-DD-A4NI-01A-11D-A27I-10	14601494	216946374	26252999	27	21316										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220432567	220432567	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gagctgctctggcagatgacCggcagctcctccccatcacg	11	16	2	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:220432567C>A	ENST00000404537.1	-	3	1463	c.1407G>T	c.(1405-1407)ccG>ccT	p.P469P	OBSL1_ENST00000265318.4_Silent_p.P469P|OBSL1_ENST00000491370.1_5'Flank|OBSL1_ENST00000603926.1_Silent_p.P469P|OBSL1_ENST00000373873.4_Silent_p.P469P|OBSL1_ENST00000373876.1_Silent_p.P469P|OBSL1_ENST00000289656.3_Silent_p.P56P	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	469					cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GGCAGATGACCGGCAGCTCCT	0.632																																					p.P469P		Atlas-SNP	.											OBSL1_ENST00000404537,NS,carcinoma,0,1	OBSL1	120	.	0			c.G1407T						.						44	49	47					2																	220432567		2152	4258	6410	SO:0001819	synonymous_variant	23363	exon3			GATGACCGGCAGC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.1407G>T	chr2.hg19:g.220432567C>A		257.0	1.0		276.0	109.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	hg19	CCDS46520.1																																																																																			.	.		0.632	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			A	220432567	C	A	220432567	2	1	131	1	0	0	0	0	0	0	0	1	10822	639	23	1		1	OBSL1	2	220432567	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	3486193	220432567	22766806	28	21317										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230632438	230632438	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tcaaacgtctttcggacaatTgtcaaaggtggattcaaact	8	8	4	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr2:230632438T>A	ENST00000283943.5	-	41	5989	c.5811A>T	c.(5809-5811)acA>acT	p.T1937T	TRIP12_ENST00000389044.4_Silent_p.T1985T|TRIP12_ENST00000389045.3_Silent_p.T1667T	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1937	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TTCGGACAATTGTCAAAGGTG	0.373																																					p.T1937T		Atlas-SNP	.											.	TRIP12	207	.	0			c.A5811T						.						100	101	101					2																	230632438		2203	4300	6503	SO:0001819	synonymous_variant	9320	exon41			GACAATTGTCAAA	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.5811A>T	chr2.hg19:g.230632438T>A		37.0	0.0		71.0	18.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.		0.373	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		A	230632438	T	A	230632438	2	1	131	1	0	0	0	0	0	0	0	1	16571	1799	63	4		4	TRIP12	2	230632438	Silent	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	10199871	230632438	12566935	29	21318										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38138132	38138132	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gtcctggaaatcgaggtgaaAggctcagtagaacctttcca	11	9	1	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr3:38138132A>T	ENST00000308059.6	+	15	2265	c.2244A>T	c.(2242-2244)aaA>aaT	p.K748N	DLEC1_ENST00000346219.3_Missense_Mutation_p.K748N|DLEC1_ENST00000452631.2_Missense_Mutation_p.K748N					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		TCGAGGTGAAAGGCTCAGTAG	0.483																																					p.K748N		Atlas-SNP	.											.	DLEC1	278	.	0			c.A2244T						.						138	134	135					3																	38138132		1935	4144	6079	SO:0001583	missense	9940	exon15			GGTGAAAGGCTCA	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.2244A>T	chr3.hg19:g.38138132A>T	ENSP00000308597:p.Lys748Asn	90.0	0.0		133.0	48.0	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	A	19.51	3.841067	0.71488	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.06449	3.32;3.3;3.55	4.93	-1.51	0.08664	.	0.064020	0.64402	D	0.000012	T	0.18800	0.0451	M	0.77103	2.36	0.50632	D	0.999888	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.70716	0.97;0.954;0.97	T	0.00641	-1.1631	10	0.56958	D	0.05	-18.6292	9.586	0.39517	0.5995:0.0:0.4005:0.0	.	748;748;748	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	N	748	ENSP00000308597:K748N;ENSP00000315914:K748N;ENSP00000410427:K748N	ENSP00000308597:K748N	K	+	3	2	DLEC1	38113136	1.000000	0.71417	0.988000	0.46212	0.919000	0.55068	1.179000	0.31993	-0.202000	0.10268	0.533000	0.62120	AAA	.	.		0.483	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38138132	A	T	38138132	3	4	131	1	0	0	0	0	1	0	0	0	4554	69	3	4	2302	4	DLEC1	3	38138132	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10		38138132	159884298	30	21319										
SCN5A	6331	hgsc.bcm.edu	37	chr3	38622799	38622799	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gttcatctctctgtcctcatCaggggctgtgaggttgtctg	12	10	6	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr3:38622799C>T	ENST00000333535.4	-	17	3000	c.2851G>A	c.(2851-2853)Gat>Aat	p.D951N	SCN5A_ENST00000451551.2_Missense_Mutation_p.D951N|SCN5A_ENST00000413689.1_Missense_Mutation_p.D951N|SCN5A_ENST00000414099.2_Missense_Mutation_p.D951N|SCN5A_ENST00000443581.1_Missense_Mutation_p.D951N|SCN5A_ENST00000425664.1_Missense_Mutation_p.D951N|SCN5A_ENST00000450102.2_Missense_Mutation_p.D951N|SCN5A_ENST00000423572.2_Missense_Mutation_p.D951N|SCN5A_ENST00000455624.2_Missense_Mutation_p.D951N|SCN5A_ENST00000449557.2_Missense_Mutation_p.D951N			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	951					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CTGTCCTCATCAGGGGCTGTG	0.587																																					p.D951N		Atlas-SNP	.											.	SCN5A	634	.	0			c.G2851A						.						37	39	38					3																	38622799		2107	4254	6361	SO:0001583	missense	6331	exon17			CCTCATCAGGGGC	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.2851G>A	chr3.hg19:g.38622799C>T	ENSP00000328968:p.Asp951Asn	219.0	0.0		316.0	29.0	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	hg19	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.146333	0.77888	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.96685	-3.99;-4.02;-4.02;-4.0;-4.02;-3.99;-4.02;-4.09;-4.0;-4.0	4.59	4.59	0.56863	.	0.057015	0.64402	D	0.000002	D	0.98099	0.9373	M	0.83012	2.62	0.58432	D	0.999993	D;D;D;D;D;D;D	0.76494	0.998;0.997;0.999;0.998;0.998;0.995;0.999	P;D;D;P;P;P;D	0.77004	0.82;0.989;0.913;0.82;0.82;0.894;0.913	D	0.99050	1.0827	10	0.72032	D	0.01	.	17.6188	0.88075	0.0:1.0:0.0:0.0	.	951;951;951;951;951;951;951	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	N	951	ENSP00000398962:D951N;ENSP00000398266:D951N;ENSP00000410257:D951N;ENSP00000388797:D951N;ENSP00000397915:D951N;ENSP00000416634:D951N;ENSP00000328968:D951N;ENSP00000399524:D951N;ENSP00000403355:D951N;ENSP00000413996:D951N	ENSP00000328968:D951N	D	-	1	0	SCN5A	38597803	1.000000	0.71417	0.646000	0.29493	0.416000	0.31233	7.651000	0.83577	2.399000	0.81585	0.655000	0.94253	GAT	.	.		0.587	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		T	38622799	C	T	38622799	3	4	131	1	0	0	0	0	1	0	0	0	13937	826	29	3	3247	3	SCN5A	3	38622799	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	484667	38622799	159399631	31	21320										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266110	41266110	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ttacctggactctggaatccAttctggtgccactaccacag	8	13	2	0	rs121913416		TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr3:41266110A>C	ENST00000349496.5	+	3	387	c.107A>C	c.(106-108)cAt>cCt	p.H36P	CTNNB1_ENST00000453024.1_Missense_Mutation_p.H29P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.H36P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.H36P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.H36P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	36					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.H36P(24)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.H36R(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.I35_S37>T(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.S29_H36del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTGGAATCCATTCTGGTGCC	0.498		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.H36P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	159	Deletion - In frame(104)|Substitution - Missense(27)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(119)|large_intestine(20)|stomach(7)|kidney(6)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.A107C						.						95	80	85					3																	41266110		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GAATCCATTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.107A>C	chr3.hg19:g.41266110A>C	ENSP00000344456:p.His36Pro	182.0	0.0		283.0	83.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824526	0.50739	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88	5.76	5.76	0.90799	.	0.093481	0.85682	D	0.000000	T	0.51210	0.1661	M	0.64170	1.965	0.80722	D	1	P	0.40398	0.716	P	0.45946	0.498	T	0.54807	-0.8238	10	0.72032	D	0.01	-2.3155	16.0676	0.80897	1.0:0.0:0.0:0.0	.	36	P35222	CTNB1_HUMAN	P	29;36;36;36;36;29;36;36;36	ENSP00000400508:H29P;ENSP00000385604:H36P;ENSP00000412219:H36P;ENSP00000379486:H36P;ENSP00000344456:H36P;ENSP00000411226:H29P;ENSP00000379488:H36P;ENSP00000409302:H36P;ENSP00000401599:H36P	ENSP00000344456:H36P	H	+	2	0	CTNNB1	41241114	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	CAT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266110	A	C	41266110	3	2	131	1	0	0	0	0	1	0	0	0	4018	217	8	5	113	5	CTNNB1	3	41266110	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	2643311	41266110	156756320	32	21321										
DHX30	22907	hgsc.bcm.edu	37	chr3	47888778	47888778	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cccagtctgaggatgaatgcGcactcgatttggaccttgtg	12	10	1	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr3:47888778G>A	ENST00000445061.1	+	12	2352	c.1945G>A	c.(1945-1947)Gca>Aca	p.A649T	MIR1226_ENST00000408658.1_RNA|DHX30_ENST00000457607.1_Missense_Mutation_p.A677T|DHX30_ENST00000348968.4_Missense_Mutation_p.A621T|DHX30_ENST00000446256.2_Missense_Mutation_p.A610T	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	649						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		GGATGAATGCGCACTCGATTT	0.612																																					p.A649T		Atlas-SNP	.											DHX30,NS,malignant_melanoma,0,1	DHX30	101	.	0			c.G1945A						.						181	144	157					3																	47888778		2203	4300	6503	SO:0001583	missense	22907	exon12			GAATGCGCACTCG	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.1945G>A	chr3.hg19:g.47888778G>A	ENSP00000405620:p.Ala649Thr	248.0	1.0		298.0	20.0	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Missense_Mutation	SNP	ENST00000445061.1	hg19	CCDS2759.1	.	.	.	.	.	.	.	.	.	.	G	8.312	0.822347	0.16678	.	.	ENSG00000132153	ENST00000446256;ENST00000445061;ENST00000348968;ENST00000457607	T;T;T;T	0.02606	4.23;4.23;4.23;4.23	4.23	3.35	0.38373	.	0.502267	0.21404	N	0.075093	T	0.02047	0.0064	N	0.12961	0.28	0.09310	N	1	B;B	0.17852	0.024;0.015	B;B	0.16722	0.003;0.016	T	0.47736	-0.9094	10	0.15066	T	0.55	.	11.3391	0.49523	0.0894:0.0:0.9106:0.0	.	649;610	Q7L2E3;Q7L2E3-3	DHX30_HUMAN;.	T	610;649;621;677	ENSP00000392601:A610T;ENSP00000405620:A649T;ENSP00000343442:A621T;ENSP00000394682:A677T	ENSP00000343442:A621T	A	+	1	0	DHX30	47863782	0.941000	0.31946	0.015000	0.15790	0.858000	0.48976	2.798000	0.47884	0.967000	0.38186	0.462000	0.41574	GCA	.	.		0.612	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		A	47888778	G	A	47888778	3	1	131	1	0	0	0	0	1	0	0	0	4506	1087	38	1	1994	1	DHX30	3	47888778	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	6622668	47888778	150133652	33	21322										
ITIH1	3697	hgsc.bcm.edu	37	chr3	52824922	52824922	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gtcatcggatgtcagcccggAcgcacgggctgctgggtacg	16	12	2	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr3:52824922A>G	ENST00000273283.2	+	20	2503	c.2479A>G	c.(2479-2481)Acg>Gcg	p.T827A	ITIH1_ENST00000537050.1_Missense_Mutation_p.T539A|ITIH1_ENST00000542827.1_3'UTR|ITIH1_ENST00000405128.3_Missense_Mutation_p.T193A|ITIH1_ENST00000540715.1_Missense_Mutation_p.T685A	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	827	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		GTCAGCCCGGACGCACGGGCT	0.622																																					p.T827A		Atlas-SNP	.											.	ITIH1	108	.	0			c.A2479G						.						90	85	87					3																	52824922		2203	4300	6503	SO:0001583	missense	3697	exon20			GCCCGGACGCACG		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"inter-alpha (globulin) inhibitor, H1 polypeptide"			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2479A>G	chr3.hg19:g.52824922A>G	ENSP00000273283:p.Thr827Ala	152.0	0.0		152.0	45.0	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	hg19	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.832067	0.50845	.	.	ENSG00000055957	ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133;ENST00000405128	T;T;T;T;T	0.11821	2.74;2.74;2.74;2.74;2.74	5.75	5.75	0.90469	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.171869	0.52532	D	0.000071	T	0.24661	0.0598	L	0.45744	1.44	0.36445	D	0.865709	B;D;P;D	0.65815	0.324;0.995;0.953;0.995	B;D;P;D	0.68039	0.219;0.93;0.76;0.955	T	0.18209	-1.0344	10	0.19590	T	0.45	-16.1011	9.4056	0.38460	0.9202:0.0:0.0798:0.0	.	685;193;428;827	F5H165;B5MCP1;Q9P1C5;P19827	.;.;.;ITIH1_HUMAN	A	827;685;539;380;193	ENSP00000273283:T827A;ENSP00000443973:T685A;ENSP00000443847:T539A;ENSP00000395836:T380A;ENSP00000384589:T193A	ENSP00000273283:T827A	T	+	1	0	ITIH1	52799962	1.000000	0.71417	0.994000	0.49952	0.877000	0.50540	6.084000	0.71335	2.195000	0.70347	0.533000	0.62120	ACG	.	.		0.622	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		G	52824922	A	G	52824922	3	3	131	1	0	0	0	0	1	0	0	0	7912	275	10	2	2557	2	ITIH1	3	52824922	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	4936144	52824922	145197508	34	21323										
PARP14	54625	hgsc.bcm.edu	37	chr3	122418685	122418685	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	attttgattgagtttgatacActtaaggagatggtaatctt	9	3	1	4			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr3:122418685A>T	ENST00000474629.2	+	6	1550	c.1284A>T	c.(1282-1284)acA>acT	p.T428T		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	428					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		AGTTTGATACACTTAAGGAGA	0.353																																					p.T428T		Atlas-SNP	.											.	PARP14	242	.	0			c.A1284T						.						112	107	109					3																	122418685		1875	4112	5987	SO:0001819	synonymous_variant	54625	exon6			TGATACACTTAAG	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1284A>T	chr3.hg19:g.122418685A>T		87.0	0.0		140.0	31.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.		0.353	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		T	122418685	A	T	122418685	2	4	131	1	0	0	0	0	0	0	0	1	11467	146	6	4		4	PARP14	3	122418685	Silent	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	69593763	122418685	75603745	35	21324										
ITGB5	3693	hgsc.bcm.edu	37	chr3	124592297	124592297	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tcccccacctacatacctctTtggagcaccaggcacatttt	5	16	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr3:124592297T>C	ENST00000296181.4	-	2	448	c.152A>G	c.(151-153)aAa>aGa	p.K51R		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	51	PSI.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		ACATACCTCTTTGGAGCACCA	0.483																																					p.K51R		Atlas-SNP	.											.	ITGB5	66	.	0			c.A152G						.						252	236	241					3																	124592297		2203	4300	6503	SO:0001583	missense	3693	exon2			ACCTCTTTGGAGC	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.152A>G	chr3.hg19:g.124592297T>C	ENSP00000296181:p.Lys51Arg	147.0	0.0		172.0	9.0	NM_002213	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	hg19	CCDS3030.1	.	.	.	.	.	.	.	.	.	.	T	14.59	2.580171	0.46006	.	.	ENSG00000082781	ENST00000296181	D	0.92699	-3.09	5.04	2.36	0.29203	Integrin beta subunit, N-terminal (2);	0.224693	0.47093	N	0.000258	D	0.87849	0.6281	L	0.60067	1.865	0.34810	D	0.737612	B	0.11235	0.004	B	0.13407	0.009	T	0.82583	-0.0385	10	0.38643	T	0.18	.	6.8438	0.23977	0.0:0.2278:0.0:0.7722	.	51	P18084	ITB5_HUMAN	R	51	ENSP00000296181:K51R	ENSP00000296181:K51R	K	-	2	0	ITGB5	126074987	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	2.262000	0.43285	0.300000	0.22699	0.379000	0.24179	AAA	.	.		0.483	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		C	124592297	T	C	124592297	3	2	131	1	0	0	0	0	1	0	0	0	7907	1841	64	2	2303	2	ITGB5	3	124592297	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	2173612	124592297	73430133	36	21325										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	193029676	193029676	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	actcattgcaaaatggtaacAgcttcctccttccccacgag	6	14	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr3:193029676A>G	ENST00000342358.4	-	20	2491	c.2374T>C	c.(2374-2376)Tgt>Cgt	p.C792R	ATP13A5-AS1_ENST00000414634.1_RNA|ATP13A5_ENST00000495496.1_5'UTR	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	792						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.C792R(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		AAATGGTAACAGCTTCCTCCT	0.393																																					p.C792R		Atlas-SNP	.											ATP13A5,NS,carcinoma,0,1	ATP13A5	171	.	1	Substitution - Missense(1)	lung(1)	c.T2374C						.						145	133	137					3																	193029676		2203	4300	6503	SO:0001583	missense	344905	exon20			GGTAACAGCTTCC	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.2374T>C	chr3.hg19:g.193029676A>G	ENSP00000341942:p.Cys792Arg	92.0	0.0		176.0	29.0	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	hg19	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	A	6.688	0.495628	0.12762	.	.	ENSG00000187527	ENST00000342358	D	0.83837	-1.77	5.44	-5.59	0.02505	HAD-like domain (1);	1.552730	0.03177	N	0.171566	T	0.65176	0.2666	N	0.24115	0.695	0.09310	N	0.999997	B	0.17268	0.021	B	0.15052	0.012	T	0.48031	-0.9070	10	0.25106	T	0.35	2.2476	0.4128	0.00444	0.2148:0.264:0.1666:0.3546	.	792	Q4VNC0	AT135_HUMAN	R	792	ENSP00000341942:C792R	ENSP00000341942:C792R	C	-	1	0	ATP13A5	194512370	0.000000	0.05858	0.004000	0.12327	0.192000	0.23643	-1.208000	0.03005	-0.555000	0.06142	0.528000	0.53228	TGT	.	.		0.393	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		G	193029676	A	G	193029676	3	3	131	1	0	0	0	0	1	0	0	0	1127	188	7	2	1324	2	ATP13A5	3	193029676	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	68437379	193029676	4992754	37	21326										
LRRC33	375387	hgsc.bcm.edu	37	chr3	196387008	196387008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gctgcggtccgtgtccctggCggggaacaccatcatgcggc	15	14	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr3:196387008C>T	ENST00000328557.4	+	3	697	c.494C>T	c.(493-495)gCg>gTg	p.A165V		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	165					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											GTGTCCCTGGCGGGGAACACC	0.647																																					p.A165V		Atlas-SNP	.											.	LRRC33	91	.	0			c.C494T						.						36	36	36					3																	196387008		2203	4300	6503	SO:0001583	missense	375387	exon3			CCCTGGCGGGGAA	AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"leucine rich repeat containing 33"	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.494C>T	chr3.hg19:g.196387008C>T	ENSP00000328625:p.Ala165Val	70.0	0.0		93.0	50.0	NM_198565		Missense_Mutation	SNP	ENST00000328557.4	hg19	CCDS3319.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.944793	0.53079	.	.	ENSG00000174004	ENST00000328557	T	0.57752	0.38	5.97	4.19	0.49359	.	0.114073	0.64402	D	0.000009	T	0.39835	0.1093	L	0.35793	1.09	0.80722	D	1	B	0.30973	0.302	B	0.30105	0.111	T	0.30534	-0.9975	10	0.62326	D	0.03	.	7.0601	0.25121	0.1304:0.678:0.1255:0.066	.	165	Q86YC3	LRC33_HUMAN	V	165	ENSP00000328625:A165V	ENSP00000328625:A165V	A	+	2	0	LRRC33	197871405	0.999000	0.42202	0.730000	0.30809	0.196000	0.23810	3.964000	0.56780	0.865000	0.35603	-0.140000	0.14226	GCG	.	.		0.647	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565		T	196387008	C	T	196387008	3	4	131	1	0	0	0	0	1	0	0	0	8997	768	27	1	500	1	LRRC33	3	196387008	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	3357332	196387008	1635422	38	21327										
PDCL2	132954	hgsc.bcm.edu	37	chr4	56422846	56422846	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ttcttccaaatcagtctgtaTtgctccaacttctgctagct	5	12	4	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr4:56422846T>A	ENST00000295645.4	-	6	706	c.604A>T	c.(604-606)Ata>Tta	p.I202L		NM_152401.2	NP_689614.2	Q8N4E4	PDCL2_HUMAN	phosducin-like 2	202	Thioredoxin fold. {ECO:0000250}.									endometrium(1)|kidney(1)|lung(4)|ovary(1)	7	Lung NSC(11;0.00256)|Glioma(25;0.08)|all_epithelial(27;0.0863)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.69e-07)|Lung(4;1.03e-06)|Epithelial(7;0.00669)			TCAGTCTGTATTGCTCCAACT	0.318																																					p.I202L		Atlas-SNP	.											.	PDCL2	21	.	0			c.A604T						.						99	87	91					4																	56422846		1835	4077	5912	SO:0001583	missense	132954	exon6			TCTGTATTGCTCC	BC034431	CCDS47059.1	4q12	2008-02-05			ENSG00000163440	ENSG00000163440			29524	protein-coding gene	gene with protein product		611676				12424248	Standard	NM_152401		Approved	GCPHLP	uc003hbb.3	Q8N4E4	OTTHUMG00000160674	ENST00000295645.4:c.604A>T	chr4.hg19:g.56422846T>A	ENSP00000295645:p.Ile202Leu	72.0	0.0		87.0	25.0	NM_152401	A8MWA2|B9ZVQ9	Missense_Mutation	SNP	ENST00000295645.4	hg19	CCDS47059.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.462565	0.43736	.	.	ENSG00000163440	ENST00000295645	T	0.27557	1.66	5.81	3.4	0.38934	Phosducin, thioredoxin-like domain (1);Thioredoxin-like fold (2);	0.077906	0.56097	D	0.000040	T	0.24044	0.0582	L	0.39566	1.225	0.35652	D	0.811824	B	0.12013	0.005	B	0.30401	0.115	T	0.18272	-1.0342	10	0.14252	T	0.57	-5.8095	8.1421	0.31089	0.0:0.2964:0.0:0.7036	.	202	Q8N4E4	PDCL2_HUMAN	L	202	ENSP00000295645:I202L	ENSP00000295645:I202L	I	-	1	0	PDCL2	56117603	0.969000	0.33509	1.000000	0.80357	0.995000	0.86356	0.763000	0.26517	0.475000	0.27415	0.528000	0.53228	ATA	.	.		0.318	PDCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361659.1	NM_152401		A	56422846	T	A	56422846	3	1	131	1	0	0	0	0	1	0	0	0	11636	1493	52	4	125	4	PDCL2	4	56422846	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10		56422846	134731430	39	21328										
ALB	213	hgsc.bcm.edu	37	chr4	74283832	74283834	+	In_Frame_Del	DEL	GTG	GTG	-													0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tggtcctgaaccagttatgtGtgttgcatgagaaaacgcca							TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	GTG	GTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr4:74283832_74283834delGTG	ENST00000503124.1	+	10	1213_1215	c.1006_1008delGTG	c.(1006-1008)gtgdel	p.V336del	ALB_ENST00000415165.2_In_Frame_Del_p.V294del|ALB_ENST00000401494.3_In_Frame_Del_p.V371del|ALB_ENST00000295897.4_In_Frame_Del_p.V486del|ALB_ENST00000509063.1_In_Frame_Del_p.V486del|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CCAGTTATGTGTGTTGCATGAGA	0.419																																					p.485_486del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.1455_1457del						.																																			SO:0001651	inframe_deletion	213	exon12			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1006_1008delGTG	chr4.hg19:g.74283832_74283834delGTG	ENSP00000421027:p.Val336del	55.0	0.0		96.0	20.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	In_Frame_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.419	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74283834	GTG	-	74283832	7	5	131	1	0	1	0	1	0	0	0	0	486	1377	48	0	1502	0	ALB	4	74283832	In_Frame_Del	DEL	GTG	TCGA-DD-A4NI-01A-11D-A27I-10	17860986	74283832	116870444	40	21329										
BBS7	55212	hgsc.bcm.edu	37	chr4	122747089	122747089	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ttccaatagaaggggtacttTagtttttacattggtgcctt	9	6	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr4:122747089T>C	ENST00000264499.4	-	19	2257	c.2074A>G	c.(2074-2076)Aaa>Gaa	p.K692E	CCNA2_ENST00000274026.5_5'Flank	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	692					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						AGGGGTACTTTAGTTTTTACA	0.318									Bardet-Biedl syndrome																												p.K692E		Atlas-SNP	.											.	BBS7	61	.	0			c.A2074G						.						86	90	89					4																	122747089		2203	4299	6502	SO:0001583	missense	55212	exon19	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GTACTTTAGTTTT	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.2074A>G	chr4.hg19:g.122747089T>C	ENSP00000264499:p.Lys692Glu	18.0	0.0		37.0	10.0	NM_176824	Q4W5P8|Q8N581|Q9NVI4	Missense_Mutation	SNP	ENST00000264499.4	hg19	CCDS3724.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.394128	0.83011	.	.	ENSG00000138686	ENST00000264499;ENST00000507814	T;T	0.77750	-1.12;-1.12	5.81	5.81	0.92471	.	0.049340	0.85682	D	0.000000	D	0.88051	0.6333	M	0.85945	2.785	0.80722	D	1	D	0.69078	0.997	D	0.63113	0.911	D	0.88443	0.3043	10	0.42905	T	0.14	-15.727	16.1773	0.81862	0.0:0.0:0.0:1.0	.	692	Q8IWZ6	BBS7_HUMAN	E	692;115	ENSP00000264499:K692E;ENSP00000423250:K115E	ENSP00000264499:K692E	K	-	1	0	BBS7	122966539	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	6.070000	0.71220	2.217000	0.71921	0.482000	0.46254	AAA	.	.		0.318	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256716.1			C	122747089	T	C	122747089	3	2	131	1	0	0	0	0	1	0	0	0	1341	1763	61	2	77	2	BBS7	4	122747089	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	48463257	122747089	68407187	41	21330										
MARCH6	10299	hgsc.bcm.edu	37	chr5	10403536	10403536	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	caggaaatgtttgatgctacTctgaaagatcgagaactgag	11	6	1	5			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr5:10403536T>A	ENST00000274140.5	+	15	1347	c.1215T>A	c.(1213-1215)acT>acA	p.T405T	MARCH6_ENST00000449913.2_Silent_p.T357T|MARCH6_ENST00000503788.1_Silent_p.T300T|MARCH6_ENST00000510792.1_Silent_p.T103T	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	405					protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						TTGATGCTACTCTGAAAGATC	0.413																																					p.T405T		Atlas-SNP	.											.	MARCH6	89	.	0			c.T1215A						.						139	127	131					5																	10403536		2203	4300	6503	SO:0001819	synonymous_variant	10299	exon15			TGCTACTCTGAAA	AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	30550	protein-coding gene	gene with protein product		613297	"membrane-associated ring finger (C3HC4) 6"			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.1215T>A	chr5.hg19:g.10403536T>A		108.0	0.0		176.0	12.0	NM_005885	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	Silent	SNP	ENST00000274140.5	hg19	CCDS34135.1																																																																																			.	.		0.413	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2	NM_005885		A	10403536	T	A	10403536	2	1	131	1	0	0	0	0	0	0	0	1	9314	1538	54	4		4	MARCH6	5	10403536	Silent	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10		10403536	170511724	42	21331										
NUDT12	83594	hgsc.bcm.edu	37	chr5	102895039	102895039	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	attttcacattcttccacttCattcgttaggaaccaaggct	5	11	3	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr5:102895039C>T	ENST00000230792.2	-	3	433	c.337G>A	c.(337-339)Gaa>Aaa	p.E113K	NUDT12_ENST00000507423.1_Missense_Mutation_p.E95K	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	113					NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		TCTTCCACTTCATTCGTTAGG	0.398																																					p.E113K		Atlas-SNP	.											.	NUDT12	27	.	0			c.G337A						.						62	66	65					5																	102895039		2202	4298	6500	SO:0001583	missense	83594	exon3			CCACTTCATTCGT	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"Nudix motif containing", "Ankyrin repeat domain containing"	18826	protein-coding gene	gene with protein product	"nucleoside diphosphate linked moiety X-type motif 12"	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.337G>A	chr5.hg19:g.102895039C>T	ENSP00000230792:p.Glu113Lys	67.0	0.0		143.0	35.0	NM_031438	B3KUW2|Q8TAL7	Missense_Mutation	SNP	ENST00000230792.2	hg19	CCDS4096.1	.	.	.	.	.	.	.	.	.	.	C	8.284	0.816167	0.16607	.	.	ENSG00000112874	ENST00000230792;ENST00000507423	T;T	0.16897	3.52;2.31	6.16	5.2	0.72013	Ankyrin repeat-containing domain (1);	0.896444	0.10080	N	0.718600	T	0.09069	0.0224	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23332	-1.0191	10	0.13470	T	0.59	-6.0657	10.2597	0.43419	0.0:0.7645:0.1415:0.094	.	95;113	E7EM93;Q9BQG2	.;NUD12_HUMAN	K	113;95	ENSP00000230792:E113K;ENSP00000424521:E95K	ENSP00000230792:E113K	E	-	1	0	NUDT12	102922938	0.016000	0.18221	0.654000	0.29608	0.305000	0.27757	1.315000	0.33608	2.937000	0.99478	0.650000	0.86243	GAA	.	.		0.398	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438		T	102895039	C	T	102895039	3	4	131	1	0	0	0	0	1	0	0	0	10737	835	29	3	1071	3	NUDT12	5	102895039	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	92491503	102895039	78020221	43	21332										
FBN2	2201	hgsc.bcm.edu	37	chr5	127674670	127674670	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gccactttcatagccttcgaAgcactcgcactcaaagctgc	7	15	2	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr5:127674670A>G	ENST00000508053.1	-	32	4401	c.3427T>C	c.(3427-3429)Ttc>Ctc	p.F1143L	FBN2_ENST00000262464.4_Missense_Mutation_p.F1143L|FBN2_ENST00000507835.1_5'UTR|FBN2_ENST00000508989.1_Missense_Mutation_p.F1110L			P35556	FBN2_HUMAN	fibrillin 2	1143	EGF-like 16; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TAGCCTTCGAAGCACTCGCAC	0.498																																					p.F1143L		Atlas-SNP	.											.	FBN2	858	.	0			c.T3427C						.						107	87	94					5																	127674670		2203	4300	6503	SO:0001583	missense	2201	exon26			CTTCGAAGCACTC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.3427T>C	chr5.hg19:g.127674670A>G	ENSP00000424571:p.Phe1143Leu	219.0	0.0		326.0	21.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.235757	0.58886	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.86627	-2.15;-2.15;-2.15	5.13	5.13	0.70059	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.73265	0.3565	N	0.04787	-0.16	0.48762	D	0.999701	B;P	0.39216	0.101;0.664	B;B	0.38194	0.267;0.26	T	0.73892	-0.3839	10	0.10377	T	0.69	.	15.396	0.74794	1.0:0.0:0.0:0.0	.	1110;1143	D6RJI3;P35556	.;FBN2_HUMAN	L	1143;1143;1110	ENSP00000262464:F1143L;ENSP00000424571:F1143L;ENSP00000425596:F1110L	ENSP00000262464:F1143L	F	-	1	0	FBN2	127702569	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.860000	0.69546	2.274000	0.75844	0.477000	0.44152	TTC	.	.		0.498	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		G	127674670	A	G	127674670	3	3	131	1	0	0	0	0	1	0	0	0	5711	72	3	2	5471	2	FBN2	5	127674670	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	24779631	127674670	53240590	44	21333										
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140856170	140856170	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tcgagagcgcgcacgatcccGatgtgggaagcaactcttta	12	11	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr5:140856170G>T	ENST00000308177.3	+	1	591	c.487G>T	c.(487-489)Gat>Tat	p.D163Y	PCDHGA6_ENST00000517434.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB6_ENST00000520790.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	163	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D163N(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCACGATCCCGATGTGGGAAG	0.567																																					p.D163Y		Atlas-SNP	.											PCDHGC3_ENST00000308177,bladder,carcinoma,0,2	PCDHGC3	173	.	2	Substitution - Missense(2)	urinary_tract(2)	c.G487T						.						53	56	55					5																	140856170		2203	4300	6503	SO:0001583	missense	5098	exon1			GATCCCGATGTGG	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.487G>T	chr5.hg19:g.140856170G>T	ENSP00000312070:p.Asp163Tyr	197.0	2.0		274.0	27.0	NM_032402	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	hg19	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.156846	0.78114	.	.	ENSG00000240184	ENST00000308177	T	0.74737	-0.87	5.27	5.27	0.74061	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.93145	0.7817	H	0.99740	4.74	0.48452	D	0.999655	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96057	0.9036	9	0.87932	D	0	.	19.0821	0.93186	0.0:0.0:1.0:0.0	.	163;163	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	Y	163	ENSP00000312070:D163Y	ENSP00000312070:D163Y	D	+	1	0	PCDHGC3	140836354	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.652000	0.98499	2.722000	0.93159	0.655000	0.94253	GAT	.	.		0.567	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		T	140856170	G	T	140856170	3	4	131	1	0	0	0	0	1	0	0	0	11578	1058	37	1	489	1	PCDHGC3	5	140856170	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	13181500	140856170	40059090	45	21334										
C1QTNF2	114898	hgsc.bcm.edu	37	chr5	159797621	159797621	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gcagcagccgggcagagcgtCggccccaggcatagttttcc	14	14	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr5:159797621C>A	ENST00000393975.3	-	1	27	c.24G>T	c.(22-24)ccG>ccT	p.P8P		NM_031908.4	NP_114114.2	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	0					activation of MAPK activity (GO:0000187)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(2)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	13	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGCAGAGCGTCGGCCCCAGGC	0.687																																					p.P8P		Atlas-SNP	.											.	C1QTNF2	33	.	0			c.G24T						.						14	17	16					5																	159797621		1838	4041	5879	SO:0001819	synonymous_variant	114898	exon1			GAGCGTCGGCCCC	AF329836	CCDS4351.2	5q33.3	2008-05-15			ENSG00000145861	ENSG00000145861			14325	protein-coding gene	gene with protein product							Standard	XM_005265815		Approved	CTRP2	uc003lyd.3	Q9BXJ5	OTTHUMG00000130323	ENST00000393975.3:c.24G>T	chr5.hg19:g.159797621C>A		18.0	0.0		39.0	14.0	NM_031908		Silent	SNP	ENST00000393975.3	hg19	CCDS4351.2																																																																																			.	.		0.687	C1QTNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252672.2			A	159797621	C	A	159797621	2	1	131	1	0	0	0	0	0	0	0	1	1965	871	31	1		1	C1QTNF2	5	159797621	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	18941451	159797621	21117639	46	21335										
HK3	3101	hgsc.bcm.edu	37	chr5	176318451	176318451	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ggaccgcaggggcagggctgGcctgtcccctcagcgcctgc	16	16	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr5:176318451G>A	ENST00000292432.5	-	3	288	c.197C>T	c.(196-198)gCc>gTc	p.A66V		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	66	Hexokinase type-1 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCAGGGCTGGCCTGTCCCCT	0.622																																					p.A66V		Atlas-SNP	.											.	HK3	210	.	0			c.C197T						.						95	93	94					5																	176318451		2203	4300	6503	SO:0001583	missense	3101	exon3			GGGCTGGCCTGTC		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.197C>T	chr5.hg19:g.176318451G>A	ENSP00000292432:p.Ala66Val	110.0	0.0		143.0	11.0	NM_002115	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	hg19	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	G	8.237	0.805956	0.16467	.	.	ENSG00000160883	ENST00000292432	D	0.98926	-5.24	4.7	0.41	0.16387	Hexokinase, N-terminal (1);	1.279450	0.05344	N	0.530644	D	0.96334	0.8804	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.19666	0.026	D	0.90777	0.4676	10	0.62326	D	0.03	.	7.5648	0.27872	0.0794:0.0:0.4673:0.4532	.	66	P52790	HXK3_HUMAN	V	66	ENSP00000292432:A66V	ENSP00000292432:A66V	A	-	2	0	HK3	176251057	0.004000	0.15560	0.000000	0.03702	0.015000	0.08874	0.413000	0.21148	-0.164000	0.10927	0.561000	0.74099	GCC	.	.		0.622	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			A	176318451	G	A	176318451	3	1	131	1	0	0	0	0	1	0	0	0	7201	1203	42	3	2642	3	HK3	5	176318451	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	16520830	176318451	4596809	47	21336										
OR2Y1	134083	hgsc.bcm.edu	37	chr5	180166721	180166721	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	aggccatcaccaccaggagcAcacactctgtggagcccagg	11	15	2	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr5:180166721A>C	ENST00000307832.2	-	1	378	c.338T>G	c.(337-339)gTg>gGg	p.V113G		NM_001001657.1	NP_001001657.1	Q8NGV0	OR2Y1_HUMAN	olfactory receptor, family 2, subfamily Y, member 1	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(89;1.25e-05)|all_epithelial(37;4.36e-06)|Renal(175;0.000159)|Lung NSC(126;0.00317)|all_lung(126;0.0041)|Breast(19;0.114)	all_cancers(40;0.0834)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CACCAGGAGCACACACTCTGT	0.597																																					p.V113G		Atlas-SNP	.											.	OR2Y1	49	.	0			c.T338G						.						75	63	67					5																	180166721		2203	4300	6503	SO:0001583	missense	134083	exon1			AGGAGCACACACT	AB065676	CCDS34323.1	5q35	2012-08-09			ENSG00000174339	ENSG00000174339		"GPCR / Class A : Olfactory receptors"	14837	protein-coding gene	gene with protein product							Standard	NM_001001657		Approved		uc003mmf.1	Q8NGV0	OTTHUMG00000162237	ENST00000307832.2:c.338T>G	chr5.hg19:g.180166721A>C	ENSP00000312403:p.Val113Gly	105.0	0.0		141.0	13.0	NM_001001657	B9EIP1|Q6IFB1|Q96R16	Missense_Mutation	SNP	ENST00000307832.2	hg19	CCDS34323.1	.	.	.	.	.	.	.	.	.	.	a	10.38	1.333295	0.24167	.	.	ENSG00000174339	ENST00000307832	T	0.01474	4.85	4.41	3.22	0.36961	GPCR, rhodopsin-like superfamily (1);	0.376195	0.19865	N	0.104328	T	0.04272	0.0118	L	0.46567	1.45	0.09310	N	1	D	0.56746	0.977	P	0.55577	0.779	T	0.27157	-1.0082	10	0.87932	D	0	.	8.7168	0.34416	0.83:0.0:0.0:0.17	.	113	Q8NGV0	OR2Y1_HUMAN	G	113	ENSP00000312403:V113G	ENSP00000312403:V113G	V	-	2	0	OR2Y1	180099327	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	0.998000	0.29744	0.800000	0.34041	0.418000	0.28097	GTG	.	.		0.597	OR2Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368059.2	XM_068682		C	180166721	A	C	180166721	3	2	131	1	0	0	0	0	1	0	0	0	11044	159	6	5	601	5	OR2Y1	5	180166721	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	3848270	180166721	748539	48	21337										
HIST1H1B	3009	hgsc.bcm.edu	37	chr6	27834746	27834746	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cttgggcttggcaggactctTggttgcctttttcggtttgg	14	8	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr6:27834746T>C	ENST00000331442.3	-	1	613	c.562A>G	c.(562-564)Aag>Gag	p.K188E		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	188					chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						GCAGGACTCTTGGTTGCCTTT	0.582																																					p.K188E		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.A562G						.						76	75	75					6																	27834746		2203	4300	6503	SO:0001583	missense	3009	exon1			GACTCTTGGTTGC	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"Histones / Replication-dependent"	4719	protein-coding gene	gene with protein product		142711	"H1 histone family, member 5", "histone 1, H1b"	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.562A>G	chr6.hg19:g.27834746T>C	ENSP00000330074:p.Lys188Glu	90.0	0.0		138.0	30.0	NM_005322	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	hg19	CCDS4635.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.255589	0.39896	.	.	ENSG00000184357	ENST00000331442	T	0.20069	2.1	5.19	5.19	0.71726	.	0.053885	0.64402	D	0.000001	T	0.05640	0.0148	N	0.08118	0	0.58432	D	0.999994	P	0.38473	0.633	B	0.33799	0.17	T	0.17623	-1.0363	10	0.72032	D	0.01	-5.6055	14.5461	0.68032	0.0:0.0:0.0:1.0	.	188	P16401	H15_HUMAN	E	188	ENSP00000330074:K188E	ENSP00000330074:K188E	K	-	1	0	HIST1H1B	27942725	1.000000	0.71417	0.857000	0.33713	0.041000	0.13682	4.536000	0.60636	2.103000	0.63969	0.533000	0.62120	AAG	.	.		0.582	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		C	27834746	T	C	27834746	3	2	131	1	0	0	0	0	1	0	0	0	7132	1821	63	2	122	2	HIST1H1B	6	27834746	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10		27834746	143280321	49	21338										
TNXB	7148	hgsc.bcm.edu	37	chr6	32036335	32036335	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tccattcctgtactggaccaGgaagtggtcaaactgtccct	9	12	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr6:32036335G>C	ENST00000375244.3	-	17	6253	c.6052C>G	c.(6052-6054)Ctg>Gtg	p.L2018V	TNXB_ENST00000375247.2_Missense_Mutation_p.L2018V			P22105	TENX_HUMAN	tenascin XB	2100	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TACTGGACCAGGAAGTGGTCA	0.617																																					p.L2018V		Atlas-SNP	.											.	TNXB	553	.	0			c.C6052G						.						42	46	45					6																	32036335		2005	4172	6177	SO:0001583	missense	7148	exon17			GGACCAGGAAGTG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.6052C>G	chr6.hg19:g.32036335G>C	ENSP00000364393:p.Leu2018Val	163.0	0.0		239.0	37.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	G	9.639	1.138385	0.21123	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.57107	0.42;0.42	5.33	-0.283	0.12874	.	0.809168	0.10468	N	0.671168	T	0.13372	0.0324	N	0.21324	0.655	0.19300	N	0.999979	B	0.22003	0.063	B	0.21360	0.034	T	0.25676	-1.0125	10	0.25751	T	0.34	.	4.2941	0.10892	0.0774:0.3566:0.3359:0.2301	.	2018	P22105-3	.	V	2018	ENSP00000364393:L2018V;ENSP00000364396:L2018V	ENSP00000364393:L2018V	L	-	1	2	TNXB	32144313	0.001000	0.12720	0.999000	0.59377	0.647000	0.38526	-1.333000	0.02667	0.183000	0.20059	0.655000	0.94253	CTG	.	.		0.617	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		C	32036335	G	C	32036335	3	2	131	1	0	0	0	0	1	0	0	0	16361	991	35	4	8773	4	TNXB	6	32036335	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	4201589	32036335	139078732	50	21339										
NFYA	4800	hgsc.bcm.edu	37	chr6	41048594	41048594	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cagttgcagactgaggcccaGgtggcatccgcctcaggcca	13	14	1	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr6:41048594G>A	ENST00000341376.6	+	3	321	c.120G>A	c.(118-120)caG>caA	p.Q40Q	OARD1_ENST00000480585.1_Intron|NFYA_ENST00000353205.5_Intron	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	40	Gln-rich.				cellular lipid metabolic process (GO:0044255)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	9	Ovarian(28;0.0418)|Colorectal(47;0.196)					CTGAGGCCCAGGTGGCATCCG	0.532																																					p.Q40Q		Atlas-SNP	.											.	NFYA	33	.	0			c.G120A						.						103	95	98					6																	41048594		2203	4300	6503	SO:0001819	synonymous_variant	4800	exon3			GGCCCAGGTGGCA		CCDS4849.1, CCDS4850.1	6p21.3	2008-11-11			ENSG00000001167	ENSG00000001167			7804	protein-coding gene	gene with protein product		189903				1774067, 9612081	Standard	NM_002505		Approved	HAP2, CBF-B, NF-YA	uc003opo.3	P23511	OTTHUMG00000014669	ENST00000341376.6:c.120G>A	chr6.hg19:g.41048594G>A		70.0	0.0		134.0	42.0	NM_002505	Q8IXU0	Silent	SNP	ENST00000341376.6	hg19	CCDS4849.1																																																																																			.	.		0.532	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040496.1			A	41048594	G	A	41048594	2	1	131	1	0	0	0	0	0	0	0	1	10398	991	35	3		3	NFYA	6	41048594	Silent	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	9012259	41048594	130066473	51	21340										
AARS2	57505	hgsc.bcm.edu	37	chr6	44273478	44273478	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tcagctctaccatgtccaagGggagtcccaggtctccacac	9	15	3	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr6:44273478G>A	ENST00000244571.4	-	10	1348	c.1346C>T	c.(1345-1347)cCc>cTc	p.P449L	TMEM151B_ENST00000438774.2_Intron|RP11-444E17.6_ENST00000505802.1_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CATGTCCAAGGGGAGTCCCAG	0.552																																					p.P449L		Atlas-SNP	.											.	AARS2	77	.	0			c.C1346T						.						110	111	111					6																	44273478		2203	4300	6503	SO:0001583	missense	57505	exon10			TCCAAGGGGAGTC	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	21022	protein-coding gene	gene with protein product	"alanine tRNA ligase 2, mitochondrial"	612035	"alanyl-tRNA synthetase like", "alanyl-tRNA synthetase 2, mitochondrial (putative)"	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.1346C>T	chr6.hg19:g.44273478G>A	ENSP00000244571:p.Pro449Leu	211.0	0.0		339.0	90.0	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	hg19	CCDS34464.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.413354	0.83449	.	.	ENSG00000124608	ENST00000244571	D	0.82255	-1.59	4.62	4.62	0.57501	Alanyl-tRNA synthetase, class IIc, anti-codon-binding domain (1);Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93132	0.7813	H	0.95402	3.665	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94982	0.8126	10	0.87932	D	0	-24.2296	16.622	0.84933	0.0:0.0:1.0:0.0	.	449	Q5JTZ9	SYAM_HUMAN	L	449	ENSP00000244571:P449L	ENSP00000244571:P449L	P	-	2	0	AARS2	44381456	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	9.538000	0.98072	2.395000	0.81488	0.655000	0.94253	CCC	.	.		0.552	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		A	44273478	G	A	44273478	3	1	131	1	0	0	0	0	1	0	0	0	20	1232	43	3	1663	3	AARS2	6	44273478	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	3224884	44273478	126841589	52	21341										
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83866961	83866961	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tctccattctcaagtgttccTgtttttcagagtgttacttt	6	9	3	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr6:83866961T>C	ENST00000349129.2	+	35	6925	c.6665T>C	c.(6664-6666)cTg>cCg	p.L2222P	DOPEY1_ENST00000369739.3_Missense_Mutation_p.L2213P|DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000237163.5_Intron	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2222					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CAAGTGTTCCTGTTTTTCAGA	0.388																																					p.L2222P		Atlas-SNP	.											.	DOPEY1	190	.	0			c.T6665C						.						165	148	154					6																	83866961		2203	4300	6503	SO:0001583	missense	23033	exon35			TGTTCCTGTTTTT	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.6665T>C	chr6.hg19:g.83866961T>C	ENSP00000195654:p.Leu2222Pro	78.0	0.0		106.0	7.0	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	hg19	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.349059	0.82132	.	.	ENSG00000083097	ENST00000349129	T	0.52754	0.65	6.02	6.02	0.97574	.	0.072326	0.56097	D	0.000023	T	0.63943	0.2554	M	0.74467	2.265	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.997;0.997;0.997	T	0.68926	-0.5280	10	0.87932	D	0	.	16.542	0.84395	0.0:0.0:0.0:1.0	.	2113;2213;2222	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	P	2222	ENSP00000195654:L2222P	ENSP00000195654:L2222P	L	+	2	0	DOPEY1	83923680	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	7.698000	0.84413	2.304000	0.77564	0.528000	0.53228	CTG	.	.		0.388	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		C	83866961	T	C	83866961	3	2	131	1	0	0	0	0	1	0	0	0	4709	1580	55	2	6795	2	DOPEY1	6	83866961	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	39593483	83866961	87248106	53	21342										
OLIG3	167826	hgsc.bcm.edu	37	chr6	137815097	137815097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cgacagctgcttcttgatttTgtacttgctgctctctcccg	8	13	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr6:137815097T>C	ENST00000367734.2	-	1	434	c.211A>G	c.(211-213)Aaa>Gaa	p.K71E		NM_175747.2	NP_786923.1	Q7RTU3	OLIG3_HUMAN	oligodendrocyte transcription factor 3	71					spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron migration (GO:0097476)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II transcription corepressor activity (GO:0001106)			endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	11	Breast(32;0.165)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00161)|OV - Ovarian serous cystadenocarcinoma(155;0.00447)		TTCTTGATTTTGTACTTGCTG	0.597																																					p.K71E		Atlas-SNP	.											.	OLIG3	34	.	0			c.A211G						.						122	108	113					6																	137815097		2203	4300	6503	SO:0001583	missense	167826	exon1			TGATTTTGTACTT	AK096362	CCDS5186.1	6q23.3	2013-05-21			ENSG00000177468	ENSG00000177468		"Basic helix-loop-helix proteins"	18003	protein-coding gene	gene with protein product		609323					Standard	NM_175747		Approved	Bhlhb7, bHLHe20	uc003qhp.1	Q7RTU3	OTTHUMG00000015657	ENST00000367734.2:c.211A>G	chr6.hg19:g.137815097T>C	ENSP00000356708:p.Lys71Glu	100.0	0.0		130.0	7.0	NM_175747	Q8N8Q0	Missense_Mutation	SNP	ENST00000367734.2	hg19	CCDS5186.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.002738	0.74932	.	.	ENSG00000177468	ENST00000367734	T	0.72505	-0.66	5.44	4.25	0.50352	.	0.000000	0.85682	D	0.000000	T	0.59985	0.2234	L	0.29908	0.895	0.58432	D	0.999997	D	0.63880	0.993	P	0.55923	0.787	T	0.65768	-0.6088	10	0.62326	D	0.03	-0.0868	11.6284	0.51160	0.1335:0.0:0.0:0.8665	.	71	Q7RTU3	OLIG3_HUMAN	E	71	ENSP00000356708:K71E	ENSP00000356708:K71E	K	-	1	0	OLIG3	137856790	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.182000	0.71995	0.850000	0.35239	0.482000	0.46254	AAA	.	.		0.597	OLIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042405.1	NM_175747		C	137815097	T	C	137815097	3	2	131	1	0	0	0	0	1	0	0	0	10871	1821	63	2	611	2	OLIG3	6	137815097	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	53948136	137815097	33299970	54	21343										
SUN1	23353	hgsc.bcm.edu	37	chr7	905675	905675	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ttgggatcccgctgtggtacTtctcgcagtccccgcgcgtg	13	14	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr7:905675T>G	ENST00000405266.1	+	17	2086	c.2062T>G	c.(2062-2064)Ttc>Gtc	p.F688V	SUN1_ENST00000452783.2_Missense_Mutation_p.F548V|SUN1_ENST00000389574.3_Missense_Mutation_p.F568V|SUN1_ENST00000456758.2_Missense_Mutation_p.F840V|SUN1_ENST00000425407.2_Missense_Mutation_p.F568V|SUN1_ENST00000413514.2_Missense_Mutation_p.F449V|SUN1_ENST00000401592.1_Missense_Mutation_p.F651V			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	678	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCTGTGGTACTTCTCGCAGTC	0.562																																					p.F651V		Atlas-SNP	.											.	SUN1	157	.	0			c.T1951G						.						89	93	92					7																	905675		2084	4207	6291	SO:0001583	missense	23353	exon16			TGGTACTTCTCGC	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"Sad1 unc-84 domain protein 1"	607723	"unc-84 homolog A (C. elegans)"	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.2062T>G	chr7.hg19:g.905675T>G	ENSP00000384116:p.Phe688Val	82.0	0.0		189.0	87.0	NM_001130965	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.1|22.1	4.239995|4.239995	0.79912|0.79912	.|.	.|.	ENSG00000164828|ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000452783;ENST00000405266;ENST00000401592;ENST00000297445;ENST00000425407;ENST00000429178;ENST00000413514|ENST00000433212	T;T;T;T;T;T;T;T|.	0.43294|.	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95|.	4.94|4.94	4.94|4.94	0.65067|0.65067	Sad1/UNC-like, C-terminal (2);|.	0.252686|.	0.48286|.	D|.	0.000195|.	T|T	0.76300|0.76300	0.3968|0.3968	M|M	0.81682|0.81682	2.555|2.555	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	0.999;0.999;0.996;1.0;0.994;0.994|.	D;D;D;D;P;P|.	0.78314|.	0.985;0.985;0.955;0.991;0.904;0.899|.	T|T	0.78578|0.78578	-0.2150|-0.2150	10|5	0.44086|.	T|.	0.13|.	-27.9778|-27.9778	14.6072|14.6072	0.68489|0.68489	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	449;548;651;840;678;568|.	E7EP45;E9PDU4;E9PF23;A4D2Q0;O94901;O94901-5|.	.;.;.;.;SUN1_HUMAN;.|.	V|R	840;568;548;688;651;678;568;576;449|499	ENSP00000388743:F840V;ENSP00000374225:F568V;ENSP00000413439:F548V;ENSP00000384116:F688V;ENSP00000384015:F651V;ENSP00000392309:F568V;ENSP00000409909:F576V;ENSP00000389313:F449V|.	ENSP00000297445:F678V|.	F|L	+|+	1|2	0|0	SUN1|SUN1	872201|872201	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	2.548000|2.548000	0.45794|0.45794	1.859000|1.859000	0.53934|0.53934	0.533000|0.533000	0.62120|0.62120	TTC|CTT	.	.		0.562	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154		G	905675	T	G	905675	3	3	131	1	0	0	0	0	1	0	0	0	15406	1609	56	5	2196	5	SUN1	7	905675	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10		905675	158232988	55	21344										
SDK1	221935	hgsc.bcm.edu	37	chr7	4091432	4091432	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ctggggacgggcctcccagcAcacctcagctggtctggact	13	15	2	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr7:4091432A>T	ENST00000404826.2	+	19	3020	c.2881A>T	c.(2881-2883)Aca>Tca	p.T961S	SDK1_ENST00000389531.3_Missense_Mutation_p.T961S	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	961	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GCCTCCCAGCACACCTCAGCT	0.527																																					p.T961S		Atlas-SNP	.											.	SDK1	361	.	0			c.A2881T						.						129	120	123					7																	4091432		2203	4300	6503	SO:0001583	missense	221935	exon19			CCCAGCACACCTC	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.2881A>T	chr7.hg19:g.4091432A>T	ENSP00000385899:p.Thr961Ser	127.0	0.0		193.0	16.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	A	0.015	-1.556530	0.00910	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.52983	0.64;0.64	5.62	-3.18	0.05186	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.437089	0.22169	N	0.063673	T	0.16171	0.0389	N	0.11651	0.15	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.27706	-1.0066	10	0.02654	T	1	.	3.7836	0.08690	0.2295:0.3866:0.2959:0.088	.	961;961	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	S	961	ENSP00000385899:T961S;ENSP00000374182:T961S	ENSP00000374182:T961S	T	+	1	0	SDK1	4057958	0.000000	0.05858	0.002000	0.10522	0.586000	0.36452	-0.103000	0.10940	-0.443000	0.07180	-0.256000	0.11100	ACA	.	.		0.527	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4091432	A	T	4091432	3	4	131	1	0	0	0	0	1	0	0	0	13983	159	6	4	2955	4	SDK1	7	4091432	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	3185757	4091432	155047231	56	21345										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18688299	18688299	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ataccagcagcagatccacaTgaacaaagtaagcctccaag	7	12	0	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr7:18688299T>A	ENST00000432645.2	+	10	1451	c.1451T>A	c.(1450-1452)aTg>aAg	p.M484K	HDAC9_ENST00000456174.2_Missense_Mutation_p.M456K|HDAC9_ENST00000524023.1_Missense_Mutation_p.M407K|HDAC9_ENST00000405010.3_Missense_Mutation_p.M484K|HDAC9_ENST00000428307.2_Missense_Mutation_p.M440K|HDAC9_ENST00000401921.1_Missense_Mutation_p.M443K|HDAC9_ENST00000406451.4_Missense_Mutation_p.M484K|HDAC9_ENST00000406072.1_Missense_Mutation_p.M471K|HDAC9_ENST00000441542.2_Missense_Mutation_p.M487K|HDAC9_ENST00000417496.2_Missense_Mutation_p.M482K	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	484					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	CAGATCCACATGAACAAAGTA	0.463																																					p.M487K		Atlas-SNP	.											.	HDAC9	560	.	0			c.T1460A						.						36	37	37					7																	18688299		2021	4180	6201	SO:0001583	missense	9734	exon10			TCCACATGAACAA	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1451T>A	chr7.hg19:g.18688299T>A	ENSP00000410337:p.Met484Lys	78.0	0.0		144.0	42.0	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	hg19	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	T	16.36	3.102219	0.56183	.	.	ENSG00000048052	ENST00000417496;ENST00000262069;ENST00000405010;ENST00000406451;ENST00000428307;ENST00000406072;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000456174;ENST00000524023;ENST00000341009	T;T;T;T;T;T;T;T;T;T	0.58060	0.94;0.95;0.36;0.95;0.95;0.37;0.36;0.36;0.97;0.95	5.28	5.28	0.74379	.	0.121996	0.36972	N	0.002306	T	0.60379	0.2264	L	0.50333	1.59	0.58432	D	0.999996	P;B;D;B;D;D;B;P;D;D;B;D;P;P	0.57899	0.851;0.337;0.978;0.289;0.963;0.978;0.013;0.774;0.981;0.967;0.013;0.981;0.61;0.665	B;B;P;B;B;P;B;B;P;B;B;P;B;B	0.53593	0.11;0.099;0.647;0.045;0.444;0.647;0.01;0.101;0.73;0.439;0.01;0.73;0.201;0.103	T	0.64993	-0.6276	10	0.87932	D	0	-18.3526	15.2052	0.73173	0.0:0.0:0.0:1.0	.	407;456;484;471;482;484;487;443;487;484;456;484;484;462	E7EX34;C9JS87;Q9UKV0-4;B5MCF1;B7Z917;Q9UKV0-2;Q68D71;Q9UKV0-6;Q9UKV0-7;Q9UKV0;B7Z928;Q9UKV0-5;Q9UKV0-3;Q8N879	.;.;.;.;.;.;.;.;.;HDAC9_HUMAN;.;.;.;.	K	482;485;484;484;440;471;443;484;487;456;407;484	ENSP00000401669:M482K;ENSP00000384382:M484K;ENSP00000384657:M484K;ENSP00000395655:M440K;ENSP00000384017:M471K;ENSP00000383912:M443K;ENSP00000410337:M484K;ENSP00000408617:M487K;ENSP00000388568:M456K;ENSP00000430036:M407K	ENSP00000262069:M485K	M	+	2	0	HDAC9	18654824	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.503000	0.81632	2.005000	0.58758	0.455000	0.32223	ATG	.	.		0.463	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			A	18688299	T	A	18688299	3	1	131	1	0	0	0	0	1	0	0	0	7023	1464	51	4	1498	4	HDAC9	7	18688299	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	14596867	18688299	140450364	57	21346										
IGF2BP3	10643	hgsc.bcm.edu	37	chr7	23353255	23353255	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ttttcttctttaatttttccAtaaattcttccctgagcctg	3	10	3	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr7:23353255A>G	ENST00000258729.3	-	13	1769	c.1413T>C	c.(1411-1413)taT>taC	p.Y471Y		NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	471					anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						TAATTTTTCCATAAATTCTTC	0.378																																					p.Y471Y		Atlas-SNP	.											.	IGF2BP3	71	.	0			c.T1413C						.						79	76	77					7																	23353255		2203	4300	6503	SO:0001819	synonymous_variant	10643	exon13			TTTTCCATAAATT	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"RNA binding motif (RRM) containing"	28868	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 3", "cancer/testis antigen 98"	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.1413T>C	chr7.hg19:g.23353255A>G		35.0	0.0		81.0	38.0	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Silent	SNP	ENST00000258729.3	hg19	CCDS5382.1																																																																																			.	.		0.378	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547		G	23353255	A	G	23353255	2	3	131	1	0	0	0	0	0	0	0	1	7584	224	8	2		2	IGF2BP3	7	23353255	Silent	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	4664956	23353255	135785408	58	21347										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83643576	83643576	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gcttttccagagtgttctccAtctattgcattttcacggaa	7	10	3	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr7:83643576A>G	ENST00000265362.4	-	7	1073	c.759T>C	c.(757-759)gaT>gaC	p.D253D	SEMA3A_ENST00000436949.1_Silent_p.D253D	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	253	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						AGTGTTCTCCATCTATTGCAT	0.398																																					p.D253D		Atlas-SNP	.											.	SEMA3A	121	.	0			c.T759C						.						115	111	112					7																	83643576		2203	4300	6503	SO:0001819	synonymous_variant	10371	exon7			TTCTCCATCTATT	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.759T>C	chr7.hg19:g.83643576A>G		64.0	0.0		100.0	46.0	NM_006080		Silent	SNP	ENST00000265362.4	hg19	CCDS5599.1																																																																																			.	.		0.398	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		G	83643576	A	G	83643576	2	3	131	1	0	0	0	0	0	0	0	1	14039	214	8	2		2	SEMA3A	7	83643576	Silent	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	60290321	83643576	75495087	59	21348										
PSMC2	5701	hgsc.bcm.edu	37	chr7	102988211	102988211	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gaccaaagaggatgagaaggAcgacaagcccatccgaggtc	13	10	0	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr7:102988211A>C	ENST00000435765.1	+	2	464	c.53A>C	c.(52-54)gAc>gCc	p.D18A	PSMC2_ENST00000292644.3_Missense_Mutation_p.D18A|DNAJC2_ENST00000379263.3_5'Flank|PSMC2_ENST00000544811.1_5'UTR|DNAJC2_ENST00000412522.1_5'Flank	NM_002803.3	NP_002794.1	P35998	PRS7_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 2	18					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|osteoblast differentiation (GO:0001649)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	21						GATGAGAAGGACGACAAGCCC	0.587																																					p.D18A		Atlas-SNP	.											.	PSMC2	38	.	0			c.A53C						.						132	113	119					7																	102988211		2203	4300	6503	SO:0001583	missense	5701	exon1			AGAAGGACGACAA	D11094	CCDS5731.1	7q22.1-q22.3	2010-04-21			ENSG00000161057	ENSG00000161057		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9548	protein-coding gene	gene with protein product	"proteasome 26S subunit, ATPase, 2", "mammalian suppressor of sgv-1 of yeast", "protease 26S subunit 7", "putative protein product of Nbla10058"	154365				9473509, 1377363	Standard	NM_002803		Approved	MSS1, S7, Nbla10058	uc003vbs.3	P35998	OTTHUMG00000157206	ENST00000435765.1:c.53A>C	chr7.hg19:g.102988211A>C	ENSP00000391211:p.Asp18Ala	155.0	0.0		181.0	79.0	NM_001204453	A4D0Q1|B7Z5E2|Q3LIA5|Q9UDI3	Missense_Mutation	SNP	ENST00000435765.1	hg19	CCDS5731.1	.	.	.	.	.	.	.	.	.	.	A	16.79	3.220807	0.58560	.	.	ENSG00000161057	ENST00000457587;ENST00000425206;ENST00000435765;ENST00000292644	D;D	0.94417	-3.42;-3.42	4.34	4.34	0.51931	.	0.280303	0.40222	N	0.001155	D	0.91466	0.7306	L	0.52126	1.63	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	D	0.88373	0.2996	10	0.30854	T	0.27	-2.853	13.6346	0.62215	1.0:0.0:0.0:0.0	.	18	P35998	PRS7_HUMAN	A	18	ENSP00000391211:D18A;ENSP00000292644:D18A	ENSP00000292644:D18A	D	+	2	0	PSMC2	102775447	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	5.812000	0.69194	1.950000	0.56595	0.533000	0.62120	GAC	.	.		0.587	PSMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347922.1	NM_002803		C	102988211	A	C	102988211	3	2	131	1	0	0	0	0	1	0	0	0	12698	275	10	5	55	5	PSMC2	7	102988211	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	19344635	102988211	56150452	60	21349										
DOCK4	9732	hgsc.bcm.edu	37	chr7	111517084	111517084	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	caaataaaacattatacattAccattttgtgtgagttttgt	5	5	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr7:111517084A>G	ENST00000437633.1	-	17	2001		c.e17+1		DOCK4_ENST00000476846.1_Splice_Site|DOCK4_ENST00000428084.1_Splice_Site	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4						cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				ATTATACATTACCATTTTGTG	0.328																																					.		Atlas-SNP	.											.	DOCK4	365	.	0			c.1744+2T>C						.						53	51	52					7																	111517084		1823	4075	5898	SO:0001630	splice_region_variant	9732	exon18			TACATTACCATTT		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.1744+1T>C	chr7.hg19:g.111517084A>G		41.0	0.0		87.0	6.0	NM_014705	O14584|O94824|Q8NB45	Splice_Site	SNP	ENST00000437633.1	hg19	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	A	19.92	3.915907	0.73098	.	.	ENSG00000128512	ENST00000352877;ENST00000423057;ENST00000428084;ENST00000437633;ENST00000445943;ENST00000342288;ENST00000544250	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DOCK4	111304320	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	8.950000	0.93019	2.367000	0.80283	0.528000	0.53228	.	.	.		0.328	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	Intron	G	111517084	A	G	111517084	5	3	131	1	0	0	0	0	0	0	1	0	4691	405	14	2	4298	2	DOCK4	7	111517084	Splice_Site	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	8528873	111517084	47621579	61	21350										
CADPS2	93664	hgsc.bcm.edu	37	chr7	122526154	122526154	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ctgcaggcggatcctccgctCctgctcatcgtccagctgcc	10	18	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr7:122526154C>G	ENST00000449022.2	-	1	257	c.238G>C	c.(238-240)Gag>Cag	p.E80Q	CADPS2_ENST00000412584.2_Missense_Mutation_p.E80Q|CADPS2_ENST00000334010.7_Missense_Mutation_p.E80Q|CADPS2_ENST00000313070.7_Missense_Mutation_p.E80Q	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	80					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						ATCCTCCGCTCCTGCTCATCG	0.701																																					p.E80Q		Atlas-SNP	.											.	CADPS2	116	.	0			c.G238C						.						13	19	17					7																	122526154		2173	4266	6439	SO:0001583	missense	93664	exon1			TCCGCTCCTGCTC		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.238G>C	chr7.hg19:g.122526154C>G	ENSP00000398481:p.Glu80Gln	94.0	0.0		143.0	29.0	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	hg19	CCDS55158.1	.	.	.	.	.	.	.	.	.	.	C	19.91	3.914146	0.72983	.	.	ENSG00000081803	ENST00000313070;ENST00000334010;ENST00000420900;ENST00000545465;ENST00000412584;ENST00000449022	D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61	4.71	4.71	0.59529	.	0.074039	0.51477	D	0.000087	T	0.81889	0.4918	M	0.69185	2.1	0.58432	D	0.999997	B;B	0.17038	0.02;0.003	B;B	0.17722	0.019;0.004	T	0.80238	-0.1465	10	0.54805	T	0.06	-5.8539	15.1488	0.72681	0.0:1.0:0.0:0.0	.	80;80	Q86UW7-2;Q86UW7	.;CAPS2_HUMAN	Q	80;80;80;47;80;80	ENSP00000325581:E80Q;ENSP00000333940:E80Q;ENSP00000400401:E80Q;ENSP00000398481:E80Q	ENSP00000325581:E80Q	E	-	1	0	CADPS2	122313390	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.225000	0.58600	2.123000	0.65237	0.508000	0.49915	GAG	.	.		0.701	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		G	122526154	C	G	122526154	3	3	131	1	0	0	0	0	1	0	0	0	2573	864	30	4	3816	4	CADPS2	7	122526154	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	11009070	122526154	36612509	62	21351										
MGAM	8972	hgsc.bcm.edu	37	chr7	141764227	141764227	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ctgagcagcaagaccctttgTatggagagtcagcagatcct	11	10	1	4	rs3087317	byFrequency	TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr7:141764227T>C	ENST00000549489.2	+	37	4484	c.4389T>C	c.(4387-4389)tgT>tgC	p.C1463C	MGAM_ENST00000475668.2_Silent_p.C1463C	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1463	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGACCCTTTGTATGGAGAGTC	0.567													N|||	8	0.00159744	0.0045	0	5008	,	,		18881	0		0	False		,,,				2504	0.002				p.C1463C		Atlas-SNP	.											.	MGAM	767	.	0			c.T4389C						.						33	35	35					7																	141764227		1968	4170	6138	SO:0001819	synonymous_variant	8972	exon37			CCTTTGTATGGAG	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4389T>C	chr7.hg19:g.141764227T>C		102.0	0.0		158.0	11.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	hg19	CCDS47727.1																																																																																			.	.		0.567	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			C	141764227	T	C	141764227	2	2	131	1	0	0	0	0	0	0	0	1	9550	1644	57	2		2	MGAM	7	141764227	Silent	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	19238073	141764227	17374436	63	21352										
PCM1	5108	hgsc.bcm.edu	37	chr8	17815276	17815276	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	agttacaagatcttgttgctAtggtacaggtaaatattgct	9	5	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr8:17815276A>G	ENST00000519253.1	+	13	2283	c.2032A>G	c.(2032-2034)Atg>Gtg	p.M678V	PCM1_ENST00000524226.1_Missense_Mutation_p.M679V|PCM1_ENST00000325083.8_Missense_Mutation_p.M678V			Q15154	PCM1_HUMAN	pericentriolar material 1	678					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TCTTGTTGCTATGGTACAGGT	0.323			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.M678V		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.A2032G						.						92	89	89					8																	17815276		1871	4116	5987	SO:0001583	missense	5108	exon13			GTTGCTATGGTAC		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.2032A>G	chr8.hg19:g.17815276A>G	ENSP00000431099:p.Met678Val	98.0	0.0		69.0	8.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.28	2.488814	0.44249	.	.	ENSG00000078674	ENST00000325083;ENST00000517730;ENST00000519253;ENST00000524226	T;T;T;T	0.28454	3.52;2.61;1.61;1.61	5.25	4.08	0.47627	.	0.000000	0.85682	D	0.000000	T	0.41143	0.1146	L	0.52364	1.645	0.80722	D	1	B;P;B;B	0.40834	0.433;0.73;0.433;0.433	B;P;B;B	0.53224	0.164;0.721;0.164;0.164	T	0.10543	-1.0625	10	0.30854	T	0.27	-9.2044	12.1868	0.54243	0.8718:0.0:0.0:0.1282	.	678;717;679;678	E7ETA6;E7EV93;E7EV56;Q15154	.;.;.;PCM1_HUMAN	V	678;717;678;679	ENSP00000327077:M678V;ENSP00000428131:M717V;ENSP00000431099:M678V;ENSP00000430521:M679V	ENSP00000327077:M678V	M	+	1	0	PCM1	17859556	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.609000	0.67661	1.074000	0.40909	0.477000	0.44152	ATG	.	.		0.323	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		G	17815276	A	G	17815276	3	3	131	1	0	0	0	0	1	0	0	0	11593	449	16	2	2074	2	PCM1	8	17815276	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10		17815276	128548746	64	21353										
PDLIM2	64236	hgsc.bcm.edu	37	chr8	22442575	22442575	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gtcagtcctccttaaggtccTcctactccagcccaacctcc	5	19	1	0	rs2294049		TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr8:22442575T>A	ENST00000397760.4	+	5	761	c.361T>A	c.(361-363)Tcc>Acc	p.S121T	PDLIM2_ENST00000409141.1_Missense_Mutation_p.S121T|PDLIM2_ENST00000339162.7_Missense_Mutation_p.S121T|PDLIM2_ENST00000409417.1_Missense_Mutation_p.S121T|PDLIM2_ENST00000448520.1_3'UTR|PDLIM2_ENST00000397761.2_Missense_Mutation_p.S121T|PDLIM2_ENST00000308354.7_Missense_Mutation_p.S371T|PDLIM2_ENST00000265810.4_Missense_Mutation_p.S121T			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)	121	Ser-rich.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		CTTAAGGTCCTCCTACTCCAG	0.647																																					p.S371T		Atlas-SNP	.											.	PDLIM2	42	.	0			c.T1111A						.						79	76	77					8																	22442575		2203	4300	6503	SO:0001583	missense	64236	exon5			AGGTCCTCCTACT	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270	ENST00000397760.4:c.361T>A	chr8.hg19:g.22442575T>A	ENSP00000380867:p.Ser121Thr	192.0	0.0		192.0	12.0	NM_021630	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	hg19		.	.	.	.	.	.	.	.	.	.	T	9.292	1.050862	0.19827	.	.	ENSG00000120913	ENST00000456545;ENST00000308354;ENST00000452226;ENST00000397760;ENST00000339162;ENST00000381194;ENST00000397761;ENST00000436754;ENST00000426493;ENST00000429812;ENST00000409141;ENST00000265810;ENST00000409417	T;T;T;T;T;T;T;T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41	5.52	0.299	0.15771	.	0.278041	0.28821	N	0.014026	T	0.13243	0.0321	L	0.48362	1.52	0.19300	N	0.999979	P;P;P;P	0.40731	0.728;0.728;0.455;0.455	B;B;B;B	0.39339	0.297;0.168;0.081;0.081	T	0.13980	-1.0489	10	0.36615	T	0.2	-14.5621	7.1977	0.25862	0.0:0.0846:0.3846:0.5308	rs2294049;rs2294049	121;121;121;121	Q96JY6-3;Q96JY6-4;Q96JY6;C9JS55	.;.;PDLI2_HUMAN;.	T	121;371;121;121;121;121;121;121;121;121;121;121;121	ENSP00000401992:S121T;ENSP00000312634:S371T;ENSP00000394376:S121T;ENSP00000380867:S121T;ENSP00000342035:S121T;ENSP00000380868:S121T;ENSP00000397738:S121T;ENSP00000392920:S121T;ENSP00000407643:S121T;ENSP00000386868:S121T;ENSP00000265810:S121T;ENSP00000387084:S121T	ENSP00000265810:S121T	S	+	1	0	PDLIM2	22498520	0.234000	0.23783	0.167000	0.22817	0.236000	0.25371	0.037000	0.13840	-0.169000	0.10834	0.533000	0.62120	TCC	.	T|1.000;|0.000		0.647	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1			A	22442575	T	A	22442575	3	1	131	1	0	0	0	0	1	0	0	0	11689	1551	54	4	375	4	PDLIM2	8	22442575	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	4627299	22442575	123921447	65	21354										
RBM12B	389677	hgsc.bcm.edu	37	chr8	94747568	94747568	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	agcatttgttttctagaaatTggatcaatatgaactggacg	9	5	2	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr8:94747568T>C	ENST00000399300.2	-	3	1284	c.1071A>G	c.(1069-1071)ccA>ccG	p.P357P	RBM12B_ENST00000517700.1_Silent_p.P357P|RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	357	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TTCTAGAAATTGGATCAATAT	0.368																																					p.P357P		Atlas-SNP	.											.	RBM12B	78	.	0			c.A1071G						.						95	92	93					8																	94747568		1853	4086	5939	SO:0001819	synonymous_variant	389677	exon3			AGAAATTGGATCA		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.1071A>G	chr8.hg19:g.94747568T>C		33.0	0.0		78.0	4.0	NM_203390	A8MYB5	Silent	SNP	ENST00000399300.2	hg19	CCDS43755.1																																																																																			.	.		0.368	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		C	94747568	T	C	94747568	2	2	131	1	0	0	0	0	0	0	0	1	13129	1799	63	2		2	RBM12B	8	94747568	Silent	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	72304993	94747568	51616454	66	21355										
POU5F1B	5462	hgsc.bcm.edu	37	chr8	128428181	128428181	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gtgggggtgatgggccatggGgggcggagccgggctgggtt	25	6	0	1	rs551358165		TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr8:128428181G>T	ENST00000465342.2	+	2	1227	c.70G>T	c.(70-72)Ggg>Tgg	p.G24W	CASC8_ENST00000523825.1_RNA|CASC8_ENST00000501396.1_RNA|POU5F1B_ENST00000391675.1_Missense_Mutation_p.G24W|CASC8_ENST00000502082.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	24				WGA -> GGP (in Ref. 5; ADE48566/ ADE48597). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|prostate(1)|urinary_tract(1)	3						TGGGCCATGGGGGGCGGAGCC	0.701																																					p.G24W		Atlas-SNP	.											.	POU5F1B	32	.	0			c.G70T						.						2	4	3					8																	128428181		506	1360	1866	SO:0001583	missense	5462	exon1			CCATGGGGGGCGG	AF268615	CCDS55274.1	8q24.21	2011-06-20	2009-04-15	2009-04-15	ENSG00000212993	ENSG00000212993		"Homeoboxes / POU class"	9223	protein-coding gene	gene with protein product		615739	"POU domain class 5, transcription factor 1 pseudogene 1", "POU class 5 homeobox 1 pseudogene 1"	OTF3P1, POU5F1P1		1408763	Standard	NM_001159542		Approved	OTF3C	uc003ysf.3	Q06416	OTTHUMG00000157807	ENST00000465342.2:c.70G>T	chr8.hg19:g.128428181G>T	ENSP00000419298:p.Gly24Trp	11.0	0.0		19.0	4.0	NM_001159542	D5K9S4|D5K9S9|D5K9T0|D5K9T1|D5K9T3|D5K9U3|D5K9U6|D5K9V4|D5K9V6|D5K9W0|D5K9W2|D5K9W7|D5K9X2|D5K9X3|D5K9X5|D5K9X8|D5K9X9|E9LRB1|E9LRB2|E9LRH5|E9LRH6|E9LRH7|E9LRK4|E9LRK5|E9LRK7|E9LRK8|E9LRM7|E9LRM9|E9LRN2|E9LRN4|E9LRN5|E9LRP8|E9LRQ0|E9LRQ2|E9LRQ3|E9LRQ4|E9LRQ5|E9LRS3|Q2VIK6|Q9BZV7|Q9BZV9	Missense_Mutation	SNP	ENST00000465342.2	hg19	CCDS55274.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.451068	0.26074	.	.	ENSG00000212993	ENST00000465342;ENST00000391675	D;D	0.81579	-1.51;-1.51	1.21	-1.52	0.08637	.	0.000000	0.36854	N	0.002366	D	0.82884	0.5134	M	0.66939	2.045	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71932	-0.4443	10	0.87932	D	0	.	1.7722	0.03014	0.2475:0.0:0.4295:0.323	.	24	Q06416	P5F1B_HUMAN	W	24	ENSP00000419298:G24W;ENSP00000375557:G24W	ENSP00000375557:G24W	G	+	1	0	POU5F1B	128497363	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.233000	0.02934	-0.394000	0.07727	0.121000	0.15741	GGG	.	.		0.701	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542		T	128428181	G	T	128428181	3	4	131	1	0	0	0	0	1	0	0	0	12291	1232	43	3	72	3	POU5F1B	8	128428181	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	33680613	128428181	17935841	67	21356										
PTP4A3	11156	hgsc.bcm.edu	37	chr8	142435203	142435203	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tgtgtgtgaagtgacctatgAcaaaacgccgctggagaagg	14	7	0	4			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr8:142435203A>T	ENST00000521578.1	+	3	1106	c.161A>T	c.(160-162)gAc>gTc	p.D54V	PTP4A3_ENST00000520105.1_Missense_Mutation_p.D54V|PTP4A3_ENST00000524028.1_Intron|PTP4A3_ENST00000329397.1_Missense_Mutation_p.D54V|PTP4A3_ENST00000349124.1_Missense_Mutation_p.D54V			O75365	TP4A3_HUMAN	protein tyrosine phosphatase type IVA, member 3	54					peptidyl-tyrosine dephosphorylation (GO:0035335)	endosome (GO:0005768)|plasma membrane (GO:0005886)	prenylated protein tyrosine phosphatase activity (GO:0004727)			endometrium(2)|large_intestine(1)|lung(3)	6	all_cancers(97;2.55e-15)|all_epithelial(106;1.39e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0474)			GTGACCTATGACAAAACGCCG	0.672																																					p.D54V		Atlas-SNP	.											.	PTP4A3	19	.	0			c.A161T						.						138	104	116					8																	142435203		2202	4300	6502	SO:0001583	missense	11156	exon2			CCTATGACAAAAC	AF041434	CCDS6382.1, CCDS6383.1	8q24.3	2011-06-09				ENSG00000184489		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"	9636	protein-coding gene	gene with protein product		606449					Standard	NM_032611		Approved	PRL-3, PRL-R, PRL3	uc003ywg.1	O75365		ENST00000521578.1:c.161A>T	chr8.hg19:g.142435203A>T	ENSP00000428976:p.Asp54Val	69.0	0.0		127.0	26.0	NM_032611	Q8IVN5|Q99849|Q9BTW5	Missense_Mutation	SNP	ENST00000521578.1	hg19	CCDS6383.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.361180	0.61403	.	.	ENSG00000184489	ENST00000521578;ENST00000520105;ENST00000523147;ENST00000329397;ENST00000349124	D;T;D;T	0.83755	-1.76;0.74;-1.76;0.74	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.93588	0.7953	H	0.96048	3.76	0.80722	D	1	D;P	0.89917	1.0;0.951	D;D	0.87578	0.998;0.942	D	0.95282	0.8387	10	0.87932	D	0	-6.4064	13.5462	0.61705	1.0:0.0:0.0:0.0	.	54;54	O75365-2;O75365	.;TP4A3_HUMAN	V	54	ENSP00000428976:D54V;ENSP00000428758:D54V;ENSP00000332274:D54V;ENSP00000331730:D54V	ENSP00000332274:D54V	D	+	2	0	PTP4A3	142504385	1.000000	0.71417	0.999000	0.59377	0.149000	0.21700	5.160000	0.64929	1.945000	0.56424	0.402000	0.26972	GAC	.	.		0.672	PTP4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378977.1	NM_032611		T	142435203	A	T	142435203	3	4	131	1	0	0	0	0	1	0	0	0	12785	275	10	4	167	4	PTP4A3	8	142435203	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	14007022	142435203	3928819	68	21357										
ROR2	4920	hgsc.bcm.edu	37	chr9	94495598	94495598	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cgtcgcggcacagctcacgcGgcttgggtgtccgggagcgc	17	14	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr9:94495598G>C	ENST00000375708.3	-	6	941	c.743C>G	c.(742-744)cCg>cGg	p.P248R	ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Missense_Mutation_p.P108R	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	248	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CAGCTCACGCGGCTTGGGTGT	0.647																																					p.P248R		Atlas-SNP	.											.	ROR2	167	.	0			c.C743G						.						42	40	41					9																	94495598		2203	4300	6503	SO:0001583	missense	4920	exon6			TCACGCGGCTTGG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.743C>G	chr9.hg19:g.94495598G>C	ENSP00000364860:p.Pro248Arg	25.0	0.0		26.0	10.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	hg19	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.547936	0.45383	.	.	ENSG00000169071	ENST00000375715;ENST00000375708	T;T	0.78816	0.48;-1.21	4.37	3.43	0.39272	Frizzled domain (2);Kringle (1);	0.180958	0.25906	N	0.027526	T	0.69269	0.3092	N	0.24115	0.695	0.48571	D	0.999679	B;B;B	0.28512	0.035;0.004;0.214	B;B;B	0.37422	0.088;0.013;0.249	T	0.66548	-0.5896	10	0.27785	T	0.31	.	15.6817	0.77373	0.0:0.1492:0.8508:0.0	.	248;248;108	A1L4F5;Q01974;B1APY4	.;ROR2_HUMAN;.	R	108;248	ENSP00000364867:P108R;ENSP00000364860:P248R	ENSP00000364860:P248R	P	-	2	0	ROR2	93535419	0.951000	0.32395	0.996000	0.52242	0.937000	0.57800	1.499000	0.35671	2.271000	0.75665	0.511000	0.50034	CCG	.	.		0.647	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			C	94495598	G	C	94495598	3	2	131	1	0	0	0	0	1	0	0	0	13542	1116	39	4	2104	4	ROR2	9	94495598	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10		94495598	46717833	69	21358										
OR13C8	138802	hgsc.bcm.edu	37	chr9	107331510	107331510	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ggtagggctttctgcccaccCaaagctccagacagttttct	9	13	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr9:107331510C>A	ENST00000335040.1	+	1	62	c.62C>A	c.(61-63)cCa>cAa	p.P21Q		NM_001004483.1	NP_001004483.1	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C, member 8	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|skin(1)	25						TCTGCCCACCCAAAGCTCCAG	0.418																																					p.P21Q		Atlas-SNP	.											.	OR13C8	77	.	0			c.C62A						.						158	158	158					9																	107331510		2203	4300	6503	SO:0001583	missense	138802	exon1			CCCACCCAAAGCT		CCDS35090.1	9q31.1	2013-09-24			ENSG00000186943	ENSG00000186943		"GPCR / Class A : Olfactory receptors"	15103	protein-coding gene	gene with protein product							Standard	NM_001004483		Approved		uc011lvo.2	Q8NGS7	OTTHUMG00000020409	ENST00000335040.1:c.62C>A	chr9.hg19:g.107331510C>A	ENSP00000334068:p.Pro21Gln	51.0	0.0		55.0	11.0	NM_001004483	Q5VVG0|Q96R44	Missense_Mutation	SNP	ENST00000335040.1	hg19	CCDS35090.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.888628	0.52014	.	.	ENSG00000186943	ENST00000335040	T	0.00428	7.44	4.97	4.97	0.65823	.	0.000000	0.56097	D	0.000024	T	0.01092	0.0036	M	0.73753	2.245	0.31297	N	0.688721	D	0.67145	0.996	D	0.66196	0.942	T	0.37957	-0.9683	10	0.72032	D	0.01	.	16.1185	0.81325	0.0:1.0:0.0:0.0	.	21	Q8NGS7	O13C8_HUMAN	Q	21	ENSP00000334068:P21Q	ENSP00000334068:P21Q	P	+	2	0	OR13C8	106371331	0.000000	0.05858	0.997000	0.53966	0.724000	0.41520	-0.220000	0.09215	2.741000	0.93983	0.655000	0.94253	CCA	.	.		0.418	OR13C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053480.1			A	107331510	C	A	107331510	3	1	131	1	0	0	0	0	1	0	0	0	10947	594	21	3	64	3	OR13C8	9	107331510	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	12835912	107331510	33881921	70	21359										
NUP188	23511	hgsc.bcm.edu	37	chr9	131762026	131762026	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	aggcagtgccacagaggacaAggacagcatggagactgacg	15	9	0	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr9:131762026A>T	ENST00000372577.2	+	34	3806	c.3785A>T	c.(3784-3786)aAg>aTg	p.K1262M		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1262					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						ACAGAGGACAAGGACAGCATG	0.587																																					p.K1262M		Atlas-SNP	.											.	NUP188	140	.	0			c.A3785T						.						90	76	81					9																	131762026		2203	4300	6503	SO:0001583	missense	23511	exon34			AGGACAAGGACAG	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.3785A>T	chr9.hg19:g.131762026A>T	ENSP00000361658:p.Lys1262Met	136.0	0.0		138.0	9.0	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	hg19	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.376764	0.82682	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.35236	1.32	5.28	5.28	0.74379	.	0.052075	0.85682	D	0.000000	T	0.47764	0.1463	M	0.65975	2.015	0.52099	D	0.999947	B;D	0.58620	0.233;0.983	B;P	0.50231	0.062;0.635	T	0.53401	-0.8444	10	0.72032	D	0.01	-1.0364	14.3743	0.66862	1.0:0.0:0.0:0.0	.	595;1262	E9PET9;Q5SRE5	.;NU188_HUMAN	M	1151;1262	ENSP00000361658:K1262M	ENSP00000349125:K1151M	K	+	2	0	NUP188	130801847	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	6.259000	0.72494	2.000000	0.58554	0.460000	0.39030	AAG	.	.		0.587	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			T	131762026	A	T	131762026	3	4	131	1	0	0	0	0	1	0	0	0	10767	72	3	4	3919	4	NUP188	9	131762026	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	24430516	131762026	9451405	71	21360										
CHAT	1103	hgsc.bcm.edu	37	chr10	50863255	50863255	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gcactggcttttgtgagagcCgtgactgaccacaaggctgc	13	11	0	3	rs201580702	byFrequency	TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr10:50863255C>T	ENST00000337653.2	+	12	1902	c.1749C>T	c.(1747-1749)gcC>gcT	p.A583A	CHAT_ENST00000395562.2_Silent_p.A501A|CHAT_ENST00000395559.2_Silent_p.A465A|CHAT_ENST00000455728.2_Silent_p.A465A|CHAT_ENST00000351556.3_Silent_p.A465A|CHAT_ENST00000339797.1_Silent_p.A465A	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	583					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	TTGTGAGAGCCGTGACTGACC	0.632																																					p.A583A		Atlas-SNP	.											.	CHAT	162	.	0			c.C1749T						.						66	62	64					10																	50863255		2203	4300	6503	SO:0001819	synonymous_variant	1103	exon12			GAGAGCCGTGACT	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.1749C>T	chr10.hg19:g.50863255C>T		120.0	0.0		192.0	61.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Silent	SNP	ENST00000337653.2	hg19	CCDS7232.1																																																																																			.	C|0.999;G|0.001		0.632	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		T	50863255	C	T	50863255	2	4	131	1	0	0	0	0	0	0	0	1	3315	639	23	1		1	CHAT	10	50863255	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10		50863255	84671492	72	21361										
PLCE1	51196	hgsc.bcm.edu	37	chr10	95791740	95791740	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	attgtgatgatgtagaagaaGacgcttttaaaagcaaaaag	10	3	0	5			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr10:95791740G>A	ENST00000371380.3	+	1	1172	c.937G>A	c.(937-939)Gac>Aac	p.D313N	PLCE1_ENST00000260766.3_Missense_Mutation_p.D313N			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	313					activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				TGTAGAAGAAGACGCTTTTAA	0.383																																					p.D313N		Atlas-SNP	.											.	PLCE1	543	.	0			c.G937A						.						125	123	124					10																	95791740		1860	4089	5949	SO:0001583	missense	51196	exon2			GAAGAAGACGCTT		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.937G>A	chr10.hg19:g.95791740G>A	ENSP00000360431:p.Asp313Asn	77.0	0.0		84.0	8.0	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	hg19	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.912625	0.52439	.	.	ENSG00000138193	ENST00000260766;ENST00000371380	T;T	0.70631	-0.5;-0.5	5.28	5.28	0.74379	Ras guanine nucleotide exchange factor, domain (1);	0.280907	0.25288	N	0.031748	T	0.66761	0.2822	N	0.24115	0.695	0.80722	D	1	D;D	0.56035	0.974;0.974	P;P	0.47981	0.563;0.563	T	0.72100	-0.4392	10	0.66056	D	0.02	.	18.9486	0.92632	0.0:0.0:1.0:0.0	.	313;313	B7ZM61;Q9P212	.;PLCE1_HUMAN	N	313	ENSP00000260766:D313N;ENSP00000360431:D313N	ENSP00000260766:D313N	D	+	1	0	PLCE1	95781730	1.000000	0.71417	0.864000	0.33941	0.079000	0.17450	7.224000	0.78042	2.479000	0.83701	0.655000	0.94253	GAC	.	.		0.383	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		A	95791740	G	A	95791740	3	1	131	1	0	0	0	0	1	0	0	0	12043	942	33	3	939	3	PLCE1	10	95791740	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	44928485	95791740	39743007	73	21362										
DOCK1	1793	hgsc.bcm.edu	37	chr10	129216713	129216713	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gcatggtgcagcagcacctgGatgaccccagcctgcccatc	11	16	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr10:129216713G>T	ENST00000280333.6	+	45	4646	c.4537G>T	c.(4537-4539)Gat>Tat	p.D1513Y		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1513	DHR-2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GCAGCACCTGGATGACCCCAG	0.572																																					p.D1513Y		Atlas-SNP	.											.	DOCK1	188	.	0			c.G4537T						.						68	81	77					10																	129216713		2202	4300	6502	SO:0001583	missense	1793	exon45			CACCTGGATGACC	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.4537G>T	chr10.hg19:g.129216713G>T	ENSP00000280333:p.Asp1513Tyr	77.0	0.0		96.0	33.0	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	hg19		.	.	.	.	.	.	.	.	.	.	G	12.63	1.994854	0.35226	.	.	ENSG00000150760	ENST00000280333	T	0.03801	3.8	4.8	2.88	0.33553	.	0.286549	0.37012	N	0.002294	T	0.02727	0.0082	N	0.08118	0	0.33355	D	0.571548	B;B;B	0.34015	0.018;0.435;0.085	B;B;B	0.37508	0.011;0.252;0.094	T	0.29305	-1.0016	10	0.56958	D	0.05	.	3.9981	0.09568	0.2509:0.207:0.5421:0.0	.	1513;1579;1513	B2RUU3;A8MU08;Q14185	.;.;DOCK1_HUMAN	Y	1513	ENSP00000280333:D1513Y	ENSP00000280333:D1513Y	D	+	1	0	DOCK1	129106703	0.953000	0.32496	0.989000	0.46669	0.982000	0.71751	2.780000	0.47742	1.230000	0.43646	0.555000	0.69702	GAT	.	.		0.572	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		T	129216713	G	T	129216713	3	4	131	1	0	0	0	0	1	0	0	0	4686	1174	41	3	4715	3	DOCK1	10	129216713	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	33424973	129216713	6318034	74	21363										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6566625	6566625	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	aggccctcaagcaactgcccAagcaaaacaagttgtacctg	8	13	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr11:6566625A>G	ENST00000527990.2	+	19	4456	c.4456A>G	c.(4456-4458)Aag>Gag	p.K1486E	DNHD1_ENST00000254579.6_Missense_Mutation_p.K1486E			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1486					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GCAACTGCCCAAGCAAAACAA	0.577																																					p.K1486E		Atlas-SNP	.											.	DNHD1	198	.	0			c.A4456G						.						32	33	33					11																	6566625		692	1591	2283	SO:0001583	missense	144132	exon21			CTGCCCAAGCAAA	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.4456A>G	chr11.hg19:g.6566625A>G	ENSP00000436180:p.Lys1486Glu	156.0	0.0		181.0	47.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.196522	0.00299	.	.	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.26067	1.76;1.76	4.91	2.92	0.33932	.	1.021260	0.07825	N	0.960421	T	0.07503	0.0189	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.26155	-1.0111	10	0.02654	T	1	.	7.5823	0.27972	0.149:0.5261:0.3249:0.0	.	1486	Q96M86	DNHD1_HUMAN	E	1486	ENSP00000254579:K1486E;ENSP00000436180:K1486E	ENSP00000254579:K1486E	K	+	1	0	DNHD1	6523201	0.015000	0.18098	0.088000	0.20740	0.003000	0.03518	1.633000	0.37113	1.264000	0.44198	-0.619000	0.04042	AAG	.	.		0.577	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		G	6566625	A	G	6566625	3	3	131	1	0	0	0	0	1	0	0	0	4670	131	5	2	4539	2	DNHD1	11	6566625	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10		6566625	128439891	75	21364										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17141377	17141377	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	attagtgggtacaatgcaggCcactggtgaagcaatgagta	13	6	0	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr11:17141377C>T	ENST00000265970.7	-	15	2801	c.2802G>A	c.(2800-2802)tgG>tgA	p.W934*	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Nonsense_Mutation_p.W554*	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	934	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						ACAATGCAGGCCACTGGTGAA	0.368																																					p.W934X		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.G2802A						.						124	126	125					11																	17141377		2200	4293	6493	SO:0001587	stop_gained	5286	exon15			TGCAGGCCACTGG	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.2802G>A	chr11.hg19:g.17141377C>T	ENSP00000265970:p.Trp934*	94.0	0.0		116.0	40.0	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Nonsense_Mutation	SNP	ENST00000265970.7	hg19	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	C	38	6.764357	0.97821	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.337	18.4903	0.90844	0.0:1.0:0.0:0.0	.	.	.	.	X	934;554	.	ENSP00000265970:W934X	W	-	3	0	PIK3C2A	17097953	1.000000	0.71417	1.000000	0.80357	0.446000	0.32137	7.435000	0.80391	2.363000	0.80096	0.585000	0.79938	TGG	.	.		0.368	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		T	17141377	C	T	17141377	4	4	131	1	0	0	0	0	0	1	0	0	11918	740	26	3	2330	3	PIK3C2A	11	17141377	Nonsense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	10574752	17141377	117865139	76	21365										
CAPRIN1	4076	hgsc.bcm.edu	37	chr11	34101204	34101204	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	taaaggaaattgttgagcgtGtttttcagtcaaactacttt	8	5	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr11:34101204G>A	ENST00000341394.4	+	7	907	c.718G>A	c.(718-720)Gtt>Att	p.V240I	CAPRIN1_ENST00000389645.3_Missense_Mutation_p.V240I|CAPRIN1_ENST00000530820.1_Missense_Mutation_p.V240I|CAPRIN1_ENST00000532820.1_Missense_Mutation_p.V240I|CAPRIN1_ENST00000529307.1_Missense_Mutation_p.V159I	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1	240					negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				TGTTGAGCGTGTTTTTCAGTC	0.423																																					p.V240I		Atlas-SNP	.											.	CAPRIN1	110	.	0			c.G718A						.						94	92	93					11																	34101204		2202	4298	6500	SO:0001583	missense	4076	exon7			GAGCGTGTTTTTC	BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"cytoplasmic activation/proliferation-associated protein-1"	601178	"membrane component, chromosome 11, surface marker 1", "GPI-anchored membrane protein 1"	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.718G>A	chr11.hg19:g.34101204G>A	ENSP00000340329:p.Val240Ile	82.0	0.0		72.0	19.0	NM_203364	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	Missense_Mutation	SNP	ENST00000341394.4	hg19	CCDS31453.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.974305	0.34848	.	.	ENSG00000135387	ENST00000341394;ENST00000389645;ENST00000532820;ENST00000530820;ENST00000529307	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	5.56	4.43	0.53597	.	0.104805	0.64402	D	0.000004	T	0.10809	0.0264	N	0.08118	0	0.44395	D	0.9973	B;B	0.15930	0.015;0.008	B;B	0.15484	0.01;0.013	T	0.30650	-0.9971	10	0.02654	T	1	-6.4504	4.1179	0.10090	0.3154:0.0:0.6846:0.0	.	240;240	Q14444;Q14444-2	CAPR1_HUMAN;.	I	240;240;240;240;159	ENSP00000340329:V240I;ENSP00000374296:V240I;ENSP00000434150:V240I;ENSP00000434204:V240I;ENSP00000431581:V159I	ENSP00000340329:V240I	V	+	1	0	CAPRIN1	34057780	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.115000	0.57865	2.779000	0.95612	0.637000	0.83480	GTT	.	.		0.423	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388680.2	NM_005898		A	34101204	G	A	34101204	3	1	131	1	0	0	0	0	1	0	0	0	2637	1377	48	3	740	3	CAPRIN1	11	34101204	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	16959827	34101204	100905312	77	21366										
ACCSL	390110	hgsc.bcm.edu	37	chr11	44073229	44073229	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gttctaaatggctgctgctcTgtcttctgtgccctggccat	10	12	4	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr11:44073229T>A	ENST00000378832.1	+	5	788	c.732T>A	c.(730-732)tcT>tcA	p.S244S		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	244					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						GCTGCTGCTCTGTCTTCTGTG	0.498																																					p.S244S		Atlas-SNP	.											.	ACCSL	57	.	0			c.T732A						.						311	302	305					11																	44073229		2104	4217	6321	SO:0001819	synonymous_variant	390110	exon5			CTGCTCTGTCTTC		CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.732T>A	chr11.hg19:g.44073229T>A		152.0	0.0		234.0	10.0	NM_001031854		Silent	SNP	ENST00000378832.1	hg19	CCDS41636.1																																																																																			.	.		0.498	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854		A	44073229	T	A	44073229	2	1	131	1	0	0	0	0	0	0	0	1	134	1567	55	4		4	ACCSL	11	44073229	Silent	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	9972025	44073229	90933287	78	21367										
SPI1	6688	hgsc.bcm.edu	37	chr11	47381502	47381502	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gagctgctgcagctgcggggGctgcacgctctggagctccg	17	13	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr11:47381502G>T	ENST00000378538.3	-	3	454	c.232C>A	c.(232-234)Ccc>Acc	p.P78T	SPI1_ENST00000533030.1_Intron|SPI1_ENST00000227163.4_Missense_Mutation_p.P79T|SPI1_ENST00000533968.1_Missense_Mutation_p.P78T	NM_001080547.1|NM_003120.2	NP_001074016.1|NP_003111.2	P17947	SPI1_HUMAN	Spi-1 proto-oncogene	78					anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|histone H3 acetylation (GO:0043966)|hypermethylation of CpG island (GO:0044027)|lymphocyte differentiation (GO:0030098)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of erythrocyte differentiation (GO:0045646)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somatic stem cell maintenance (GO:0035019)	nuclear chromatin (GO:0000790)	core promoter binding (GO:0001047)|NFAT protein binding (GO:0051525)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(4)|ovary(1)	8				Lung(87;0.0967)		AGCTGCGGGGGCTGCACGCTC	0.632																																					p.P79T		Atlas-SNP	.											.	SPI1	21	.	0			c.C235A						.						52	44	47					11																	47381502		2201	4298	6499	SO:0001583	missense	6688	exon3			GCGGGGGCTGCAC	X52056	CCDS7933.2, CCDS44591.1	11p12-p11.22	2014-06-25	2014-06-25		ENSG00000066336	ENSG00000066336			11241	protein-coding gene	gene with protein product	"hematopoietic transcription factor PU.1", "31 kDa transforming protein"	165170	"spleen focus forming virus (SFFV) proviral integration oncogene"			1693183	Standard	NM_003120		Approved	PU.1, SPI-A, OF, SFPI1, SPI-1	uc001nfb.1	P17947	OTTHUMG00000150150	ENST00000378538.3:c.232C>A	chr11.hg19:g.47381502G>T	ENSP00000367799:p.Pro78Thr	23.0	0.0		28.0	9.0	NM_001080547		Missense_Mutation	SNP	ENST00000378538.3	hg19	CCDS7933.2	.	.	.	.	.	.	.	.	.	.	G	11.36	1.617186	0.28801	.	.	ENSG00000066336	ENST00000378538;ENST00000227163;ENST00000533968	T;T;T	0.46819	0.86;0.86;0.86	3.59	2.66	0.31614	.	0.190216	0.47093	D	0.000247	T	0.59676	0.2211	M	0.65975	2.015	0.39020	D	0.959725	D;B;B	0.76494	0.999;0.003;0.035	D;B;B	0.69479	0.964;0.008;0.029	T	0.60459	-0.7259	10	0.09843	T	0.71	-13.8829	13.3339	0.60505	0.0:0.1594:0.8406:0.0	.	78;78;79	F5H3K6;P17947;P17947-2	.;SPI1_HUMAN;.	T	78;79;78	ENSP00000367799:P78T;ENSP00000227163:P79T;ENSP00000438846:P78T	ENSP00000227163:P79T	P	-	1	0	SPI1	47338078	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.392000	0.34486	0.821000	0.34540	0.655000	0.94253	CCC	.	.		0.632	SPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316571.1	NM_003120		T	47381502	G	T	47381502	3	4	131	1	0	0	0	0	1	0	0	0	15064	1203	42	3	592	3	SPI1	11	47381502	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	3308273	47381502	87625014	79	21368										
SLC22A8	9376	hgsc.bcm.edu	37	chr11	62768191	62768191	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ggctgtgcccccatgtctcaCctgtcagacaggtctccaag	10	15	3	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr11:62768191C>A	ENST00000336232.2	-	3	573		c.e3+1		SLC22A8_ENST00000535878.1_Splice_Site|SLC22A8_ENST00000545207.1_Splice_Site|SLC22A8_ENST00000311438.8_Splice_Site|SLC22A8_ENST00000430500.2_Splice_Site|SLC22A8_ENST00000542795.1_Splice_Site	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8						glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CCATGTCTCACCTGTCAGACA	0.567																																					.		Atlas-SNP	.											.	SLC22A8	60	.	0			c.437+1G>T						.						127	92	104					11																	62768191		2201	4298	6499	SO:0001630	splice_region_variant	9376	exon4			GTCTCACCTGTCA	AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"Solute carriers"	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.437+1G>T	chr11.hg19:g.62768191C>A		125.0	0.0		184.0	8.0	NM_004254	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Splice_Site	SNP	ENST00000336232.2	hg19	CCDS8042.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.594840	0.46318	.	.	ENSG00000149452	ENST00000336232;ENST00000540631;ENST00000545207;ENST00000535878;ENST00000311438;ENST00000430500	.	.	.	4.45	4.45	0.53987	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7761	0.57448	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC22A8	62524767	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	6.022000	0.70839	2.456000	0.83038	0.313000	0.20887	.	.	.		0.567	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254	Intron	A	62768191	C	A	62768191	5	1	131	1	0	0	0	0	0	0	1	0	14475	521	18	3	1226	3	SLC22A8	11	62768191	Splice_Site	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	15386689	62768191	72238325	80	21369										
SPCS2	9789	hgsc.bcm.edu	37	chr11	74676881	74676881	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cctcaccatctgtacaatctCctgtttctttgccatagtgg	6	13	4	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr11:74676881C>A	ENST00000263672.6	+	3	311	c.272C>A	c.(271-273)tCc>tAc	p.S91Y	SPCS2_ENST00000528265.1_Intron|SPCS2_ENST00000530257.1_Intron|RNU6-216P_ENST00000363282.1_RNA|SPCS2_ENST00000526361.1_Intron	NM_014752.2	NP_055567.2	Q15005	SPCS2_HUMAN	signal peptidase complex subunit 2 homolog (S. cerevisiae)	91					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)			breast(1)	1						TGTACAATCTCCTGTTTCTTT	0.393																																					p.S91Y		Atlas-SNP	.											.	SPCS2	17	.	0			c.C272A						.						142	132	135					11																	74676881		1799	4040	5839	SO:0001583	missense	9789	exon3			CAATCTCCTGTTT	D14658	CCDS44681.1	11q13.4	2008-02-05			ENSG00000118363	ENSG00000118363			28962	protein-coding gene	gene with protein product						7788527	Standard	NM_014752		Approved	KIAA0102	uc001ovu.2	Q15005	OTTHUMG00000165517	ENST00000263672.6:c.272C>A	chr11.hg19:g.74676881C>A	ENSP00000263672:p.Ser91Tyr	66.0	0.0		68.0	22.0	NM_014752	Q15507|Q3KQT0|Q641R4|Q6FG65|Q6IRX0|Q6P1P4|Q96HU9	Missense_Mutation	SNP	ENST00000263672.6	hg19	CCDS44681.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.495202	0.85069	.	.	ENSG00000118363	ENST00000263672;ENST00000532972;ENST00000526883	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.79551	0.4465	M	0.80616	2.505	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	T	0.81422	-0.0940	9	0.62326	D	0.03	-1.6163	14.9491	0.71057	0.0:1.0:0.0:0.0	.	91	Q15005	SPCS2_HUMAN	Y	91;122;95	.	ENSP00000263672:S91Y	S	+	2	0	SPCS2	74354529	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.048000	0.76606	2.665000	0.90641	0.563000	0.77884	TCC	.	.		0.393	SPCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384587.1	NM_014752		A	74676881	C	A	74676881	3	1	131	1	0	0	0	0	1	0	0	0	15039	855	30	3	282	3	SPCS2	11	74676881	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	11908690	74676881	60329635	81	21370										
FAM55B	120406	hgsc.bcm.edu	37	chr11	114577377	114577377	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tcatccgtagggccatcaatAttcaaaaggccattgaacgt	8	10	3	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr11:114577377A>C	ENST00000389586.4	+	6	1595	c.1405A>C	c.(1405-1407)Att>Ctt	p.I469L	NXPE2_ENST00000375475.5_Intron	NM_182495.5	NP_872301.2	Q96DL1	NXPE2_HUMAN	neurexophilin and PC-esterase domain family, member 2	469						integral component of membrane (GO:0016021)											GGCCATCAATATTCAAAAGGC	0.443																																					p.I469L		Atlas-SNP	.											.	.	.	.	0			c.A1405C						.						69	57	61					11																	114577377		692	1591	2283	SO:0001583	missense	120406	exon6			ATCAATATTCAAA	AK057953	CCDS44738.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000204361	ENSG00000204361			26331	protein-coding gene	gene with protein product			"family with sequence similarity 55, member B"	FAM55B			Standard	NM_182495		Approved	FLJ25224	uc009yyy.2	Q96DL1	OTTHUMG00000168293	ENST00000389586.4:c.1405A>C	chr11.hg19:g.114577377A>C	ENSP00000374237:p.Ile469Leu	125.0	0.0		147.0	8.0	NM_182495	Q2NKI8	Missense_Mutation	SNP	ENST00000389586.4	hg19	CCDS44738.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.128198	0.56721	.	.	ENSG00000204361	ENST00000389586	T	0.20881	2.04	5.37	-8.12	0.01078	.	0.463681	0.15942	N	0.237143	T	0.14141	0.0342	L	0.54323	1.7	0.53688	D	0.999979	P	0.36753	0.568	B	0.34093	0.175	T	0.09143	-1.0688	10	0.51188	T	0.08	.	9.6192	0.39710	0.1837:0.0:0.6095:0.2068	.	469	Q96DL1	FA55B_HUMAN	L	469	ENSP00000374237:I469L	ENSP00000374237:I469L	I	+	1	0	FAM55B	114082587	0.025000	0.19082	0.017000	0.16124	0.996000	0.88848	-0.015000	0.12634	-1.517000	0.01780	0.454000	0.30748	ATT	.	.		0.443	NXPE2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399181.1	NM_182495		C	114577377	A	C	114577377	3	2	131	1	0	0	0	0	1	0	0	0	5593	449	16	5	1427	5	FAM55B	11	114577377	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	39900496	114577377	20429139	82	21371										
GPR19	2842	hgsc.bcm.edu	37	chr12	12815347	12815347	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	agtgtaggaataatcaaatgTggcttgctgttatccattct	9	6	2	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr12:12815347T>C	ENST00000540510.1	-	2	228	c.36A>G	c.(34-36)ccA>ccG	p.P12P	GPR19_ENST00000332427.2_Silent_p.P12P			P46093	GPR4_HUMAN	G protein-coupled receptor 19	0					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.048)		TAATCAAATGTGGCTTGCTGT	0.438																																					p.P12P		Atlas-SNP	.											.	GPR19	47	.	0			c.A36G						.						113	109	110					12																	12815347		2203	4300	6503	SO:0001819	synonymous_variant	2842	exon4			CAAATGTGGCTTG		CCDS8652.1	12p12.3	2014-01-30				ENSG00000183150		"GPCR / Class A : Orphans"	4473	protein-coding gene	gene with protein product		602927					Standard	NM_006143		Approved		uc001raq.2	Q15760		ENST00000540510.1:c.36A>G	chr12.hg19:g.12815347T>C		60.0	0.0		66.0	9.0	NM_006143	A8K3T3|B0M0K1|Q6NWM4	Silent	SNP	ENST00000540510.1	hg19	CCDS8652.1																																																																																			.	.		0.438	GPR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400662.1	NM_006143		C	12815347	T	C	12815347	2	2	131	1	0	0	0	0	0	0	0	1	6687	1683	59	2		2	GPR19	12	12815347	Silent	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10		12815347	121036548	83	21372										
CCDC91	55297	hgsc.bcm.edu	37	chr12	28459739	28459739	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	attgggtttaactgatgaaaAaagtaatggaacaattgccc	9	5	0	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr12:28459739A>G	ENST00000545336.1	+	8	751	c.332A>G	c.(331-333)aAa>aGa	p.K111R	CCDC91_ENST00000381256.1_Missense_Mutation_p.K111R|CCDC91_ENST00000539107.1_Missense_Mutation_p.K111R|CCDC91_ENST00000540401.1_3'UTR|CCDC91_ENST00000306172.5_Missense_Mutation_p.K81R|CCDC91_ENST00000381259.1_Missense_Mutation_p.K111R			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	111					protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					ACTGATGAAAAAAGTAATGGA	0.353																																					p.K111R		Atlas-SNP	.											.	CCDC91	63	.	0			c.A332G						.						89	94	93					12																	28459739		2203	4300	6503	SO:0001583	missense	55297	exon4			ATGAAAAAAGTAA	AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"GGA binding partner"					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.332A>G	chr12.hg19:g.28459739A>G	ENSP00000438040:p.Lys111Arg	52.0	0.0		77.0	28.0	NM_018318	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Missense_Mutation	SNP	ENST00000545336.1	hg19	CCDS8716.1	.	.	.	.	.	.	.	.	.	.	A	10.19	1.282892	0.23392	.	.	ENSG00000123106	ENST00000539107;ENST00000536442;ENST00000545336;ENST00000545737;ENST00000381259;ENST00000381256;ENST00000306172	T;T;T;T;T;T;T	0.32988	1.44;1.45;1.44;1.45;1.44;1.44;1.43	5.26	4.17	0.49024	.	0.875326	0.09820	N	0.751623	T	0.17365	0.0417	N	0.14661	0.345	0.21697	N	0.999587	B;B	0.30281	0.144;0.275	B;B	0.27796	0.048;0.083	T	0.23261	-1.0193	10	0.16896	T	0.51	-2.348	8.7619	0.34680	0.7525:0.2475:0.0:0.0	.	111;81	Q7Z6B0;Q7Z6B0-2	CCD91_HUMAN;.	R	111;111;111;111;111;111;81	ENSP00000440513:K111R;ENSP00000445660:K111R;ENSP00000438040:K111R;ENSP00000442544:K111R;ENSP00000370658:K111R;ENSP00000370655:K111R;ENSP00000305075:K81R	ENSP00000305075:K81R	K	+	2	0	CCDC91	28351006	1.000000	0.71417	0.999000	0.59377	0.945000	0.59286	2.074000	0.41529	1.092000	0.41356	0.528000	0.53228	AAA	.	.		0.353	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1	NM_018318		G	28459739	A	G	28459739	3	3	131	1	0	0	0	0	1	0	0	0	2872	14	1	2	346	2	CCDC91	12	28459739	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	15644392	28459739	105392156	84	21373										
CAPRIN2	65981	hgsc.bcm.edu	37	chr12	30863308	30863308	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tcactggcacatccacagggGtcatgctacgggagtctcct	11	13	3	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr12:30863308G>A	ENST00000298892.5	-	17	3512	c.2762C>T	c.(2761-2763)aCc>aTc	p.T921I	CAPRIN2_ENST00000417045.1_3'UTR|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.T971I|CAPRIN2_ENST00000308433.5_Missense_Mutation_p.T637I|CAPRIN2_ENST00000395805.2_3'UTR	NM_023925.3	NP_076414.2			caprin family member 2											breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					ATCCACAGGGGTCATGCTACG	0.542																																					p.T971I		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.C2912T						.						227	230	229					12																	30863308		2203	4300	6503	SO:0001583	missense	65981	exon18			ACAGGGGTCATGC	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000298892.5:c.2762C>T	chr12.hg19:g.30863308G>A	ENSP00000298892:p.Thr921Ile	128.0	0.0		184.0	16.0	NM_001002259		Missense_Mutation	SNP	ENST00000298892.5	hg19	CCDS8720.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.400459	0.83120	.	.	ENSG00000110888	ENST00000298892;ENST00000251071;ENST00000308433	T;T;T	0.76316	-0.65;-0.71;-1.01	5.7	4.76	0.60689	.	0.237281	0.43579	D	0.000548	T	0.77150	0.4088	N	0.19112	0.55	0.36693	D	0.879683	D;D	0.71674	0.997;0.998	P;D	0.65323	0.852;0.934	T	0.81673	-0.0826	10	0.72032	D	0.01	-8.9208	11.2018	0.48745	0.0:0.1374:0.7202:0.1424	.	971;921	Q6IMN6;Q6IMN6-2	CAPR2_HUMAN;.	I	921;971;637	ENSP00000298892:T921I;ENSP00000251071:T971I;ENSP00000309785:T637I	ENSP00000251071:T971I	T	-	2	0	CAPRIN2	30754575	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.337000	0.72958	2.682000	0.91365	0.655000	0.94253	ACC	.	.		0.542	CAPRIN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402778.1	NM_023925		A	30863308	G	A	30863308	3	1	131	1	0	0	0	0	1	0	0	0	2638	1261	44	3	475	3	CAPRIN2	12	30863308	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	2403569	30863308	102988587	85	21374										
GALNT6	11226	hgsc.bcm.edu	37	chr12	51758078	51758078	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	acgatgtctgggctcaccacCactgtcttgtcctcagcgat	9	14	4	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr12:51758078C>T	ENST00000543196.2	-	5	1081	c.876G>A	c.(874-876)gtG>gtA	p.V292V	GALNT6_ENST00000356317.3_Silent_p.V292V			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	292					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GGCTCACCACCACTGTCTTGT	0.607																																					p.V292V		Atlas-SNP	.											.	GALNT6	63	.	0			c.G876A						.						77	73	74					12																	51758078		2203	4300	6503	SO:0001819	synonymous_variant	11226	exon6			CACCACCACTGTC	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.876G>A	chr12.hg19:g.51758078C>T		174.0	0.0		219.0	65.0	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Silent	SNP	ENST00000543196.2	hg19	CCDS8813.1																																																																																			.	.		0.607	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		T	51758078	C	T	51758078	2	4	131	1	0	0	0	0	0	0	0	1	6225	581	21	3		3	GALNT6	12	51758078	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	20894770	51758078	82093817	86	21375										
KRT3	3850	hgsc.bcm.edu	37	chr12	53189359	53189359	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gggccaaagccaccaggactGcccaagctgccaggcccacc	11	18	0	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr12:53189359G>A	ENST00000417996.2	-	1	542	c.468C>T	c.(466-468)ggC>ggT	p.G156G	KRT3_ENST00000309505.3_Silent_p.G156G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	156	Gly-rich.|Head.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						CACCAGGACTGCCCAAGCTGC	0.622																																					p.G156G		Atlas-SNP	.											.	KRT3	65	.	0			c.C468T						.						116	157	143					12																	53189359		2203	4300	6503	SO:0001819	synonymous_variant	3850	exon1			AGGACTGCCCAAG		CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"-", "Intermediate filaments type II, keratins (basic)"	6440	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 3", "cytokeratin 3"	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.468C>T	chr12.hg19:g.53189359G>A		118.0	0.0		174.0	65.0	NM_057088	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	hg19	CCDS44895.1																																																																																			.	.		0.622	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		A	53189359	G	A	53189359	2	1	131	1	0	0	0	0	0	0	0	1	8475	1306	46	3		3	KRT3	12	53189359	Silent	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	1431281	53189359	80662536	87	21376										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70988332	70988332	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tagaggtagccaggggtcagCccgtgaaaagcataggaagt	15	7	1	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr12:70988332C>T	ENST00000261266.5	-	4	806	c.777G>A	c.(775-777)ggG>ggA	p.G259G	PTPRB_ENST00000538708.1_Silent_p.G259G|PTPRB_ENST00000451516.2_Silent_p.G259G|PTPRB_ENST00000334414.6_Silent_p.G477G|PTPRB_ENST00000551525.1_Silent_p.G476G|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550857.1_Silent_p.G259G|PTPRB_ENST00000550358.1_Silent_p.G477G	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	259	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CAGGGGTCAGCCCGTGAAAAG	0.507																																					p.G477G		Atlas-SNP	.											.	PTPRB	676	.	0			c.G1431A						.						152	150	151					12																	70988332		2004	4193	6197	SO:0001819	synonymous_variant	5787	exon6			GGTCAGCCCGTGA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.777G>A	chr12.hg19:g.70988332C>T		222.0	0.0		290.0	82.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.507	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70988332	C	T	70988332	2	4	131	1	0	0	0	0	0	0	0	1	12811	726	26	3		3	PTPRB	12	70988332	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	17798973	70988332	62863563	88	21377										
UTP20	27340	hgsc.bcm.edu	37	chr12	101748856	101748856	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tatccaaggaaccataaccgGggatattctccccaggctac	8	13	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr12:101748856G>T	ENST00000261637.4	+	41	5528	c.5354G>T	c.(5353-5355)gGg>gTg	p.G1785V		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1785					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						ACCATAACCGGGGATATTCTC	0.433																																					p.G1785V		Atlas-SNP	.											.	UTP20	222	.	0			c.G5354T						.						52	53	53					12																	101748856		2203	4300	6503	SO:0001583	missense	27340	exon41			TAACCGGGGATAT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.5354G>T	chr12.hg19:g.101748856G>T	ENSP00000261637:p.Gly1785Val	57.0	0.0		91.0	4.0	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	hg19	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	G	8.233	0.805105	0.16467	.	.	ENSG00000120800	ENST00000261637	T	0.17054	2.3	5.79	4.9	0.64082	Armadillo-type fold (1);	0.555608	0.21383	N	0.075436	T	0.11196	0.0273	N	0.25647	0.755	0.48632	D	0.999683	B	0.19817	0.039	B	0.19391	0.025	T	0.13899	-1.0492	10	0.27785	T	0.31	-18.1894	7.4785	0.27391	0.0861:0.1689:0.745:0.0	.	1785	O75691	UTP20_HUMAN	V	1785	ENSP00000261637:G1785V	ENSP00000261637:G1785V	G	+	2	0	UTP20	100272987	0.996000	0.38824	1.000000	0.80357	0.358000	0.29455	1.285000	0.33261	2.733000	0.93635	0.655000	0.94253	GGG	.	.		0.433	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101748856	G	T	101748856	3	4	131	1	0	0	0	0	1	0	0	0	17114	1232	43	3	5516	3	UTP20	12	101748856	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	30760524	101748856	32103039	89	21378										
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26586735	26586735	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cccccgacgctgttccggggCagctccctgcagcagggcgt	14	17	0	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr13:26586735C>A	ENST00000381655.2	+	36	3586	c.3444C>A	c.(3442-3444)ggC>ggA	p.G1148G	ATP8A2_ENST00000255283.8_Silent_p.G1083G	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	1108					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TGTTCCGGGGCAGCTCCCTGC	0.687																																					p.G1148G		Atlas-SNP	.											.	ATP8A2	181	.	0			c.C3444A						.						9	10	9					13																	26586735		1761	3878	5639	SO:0001819	synonymous_variant	51761	exon36			CCGGGGCAGCTCC	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.3444C>A	chr13.hg19:g.26586735C>A		38.0	0.0		61.0	35.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Silent	SNP	ENST00000381655.2	hg19	CCDS41873.1																																																																																			.	.		0.687	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		A	26586735	C	A	26586735	2	1	131	1	0	0	0	0	0	0	0	1	1193	697	25	3		3	ATP8A2	13	26586735	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10		26586735	88583143	90	21379										
C13orf26	122046	hgsc.bcm.edu	37	chr13	31549019	31549019	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tcgctttattcgtactcactGtgacactaacaaaaagaaga	6	9	1	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr13:31549019G>A	ENST00000380473.3	+	7	858	c.845G>A	c.(844-846)tGt>tAt	p.C282Y	RP11-252M21.6_ENST00000433788.1_RNA|TEX26_ENST00000530916.1_3'UTR	NM_152325.1	NP_689538.1	Q8N6G2	TEX26_HUMAN	testis expressed 26	282																	CGTACTCACTGTGACACTAAC	0.303																																					p.C282Y		Atlas-SNP	.											.	.	.	.	0			c.G845A						.						60	55	57					13																	31549019		2194	4294	6488	SO:0001583	missense	122046	exon7			CTCACTGTGACAC	BC030277	CCDS9339.1	13q12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000175664	ENSG00000175664			28622	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 26"	C13orf26		12477932	Standard	NM_152325		Approved	MGC40178	uc001uti.3	Q8N6G2	OTTHUMG00000016682	ENST00000380473.3:c.845G>A	chr13.hg19:g.31549019G>A	ENSP00000369840:p.Cys282Tyr	58.0	0.0		101.0	20.0	NM_152325		Missense_Mutation	SNP	ENST00000380473.3	hg19	CCDS9339.1	.	.	.	.	.	.	.	.	.	.	G	1.967	-0.437424	0.04636	.	.	ENSG00000175664	ENST00000380473	T	0.41400	1.0	4.09	2.11	0.27256	.	0.722447	0.13951	N	0.351502	T	0.22742	0.0549	L	0.29908	0.895	0.09310	N	1	B	0.20550	0.046	B	0.17722	0.019	T	0.30679	-0.9970	10	0.02654	T	1	-1.8397	5.5663	0.17173	0.2927:0.0:0.7073:0.0	.	282	Q8N6G2	CM026_HUMAN	Y	282	ENSP00000369840:C282Y	ENSP00000369840:C282Y	C	+	2	0	C13orf26	30447019	0.750000	0.28316	0.106000	0.21319	0.035000	0.12851	0.213000	0.17521	0.535000	0.28714	0.655000	0.94253	TGT	.	.		0.303	TEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044380.2	NM_152325		A	31549019	G	A	31549019	3	1	131	1	0	0	0	0	1	0	0	0	1724	1377	48	3	871	3	C13orf26	13	31549019	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	4962284	31549019	83620859	91	21380										
KBTBD7	84078	hgsc.bcm.edu	37	chr13	41766715	41766715	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tttggtcatgattgacaatcTggtagttgtgggtctctgaa	12	5	3	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr13:41766715T>C	ENST00000379483.3	-	1	1987	c.1679A>G	c.(1678-1680)cAg>cGg	p.Q560R		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	560										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		ATTGACAATCTGGTAGTTGTG	0.433																																					p.Q560R		Atlas-SNP	.											.	KBTBD7	60	.	0			c.A1679G						.						172	169	170					13																	41766715		2203	4300	6503	SO:0001583	missense	84078	exon1			ACAATCTGGTAGT	AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"BTB/POZ domain containing"	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.1679A>G	chr13.hg19:g.41766715T>C	ENSP00000368797:p.Gln560Arg	155.0	0.0		187.0	52.0	NM_032138	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Missense_Mutation	SNP	ENST00000379483.3	hg19	CCDS9377.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.755143	0.00663	.	.	ENSG00000120696	ENST00000379483;ENST00000501885	T	0.65732	-0.17	5.37	5.37	0.77165	Kelch-type beta propeller (1);	0.000000	0.64402	U	0.000001	T	0.45696	0.1355	N	0.21448	0.665	0.50171	D	0.999852	B	0.06786	0.001	B	0.06405	0.002	T	0.37709	-0.9694	10	0.12103	T	0.63	.	13.3145	0.60399	0.0:0.0:0.0:1.0	.	560	Q8WVZ9	KBTB7_HUMAN	R	560;462	ENSP00000368797:Q560R	ENSP00000368797:Q560R	Q	-	2	0	KBTBD7	40664715	1.000000	0.71417	1.000000	0.80357	0.121000	0.20230	6.520000	0.73773	2.023000	0.59567	0.455000	0.32223	CAG	.	.		0.433	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138		C	41766715	T	C	41766715	3	2	131	1	0	0	0	0	1	0	0	0	8007	1580	55	2	379	2	KBTBD7	13	41766715	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	10217696	41766715	73403163	92	21381										
DGKH	160851	hgsc.bcm.edu	37	chr13	42763420	42763420	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	agtttaaagaaagcagtgagGcaagtcattgaggaagccgg	14	5	1	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr13:42763420G>T	ENST00000337343.4	+	15	1908	c.1887G>T	c.(1885-1887)agG>agT	p.R629S	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000379274.2_Missense_Mutation_p.R493S|DGKH_ENST00000261491.5_Missense_Mutation_p.R629S|DGKH_ENST00000540693.1_Missense_Mutation_p.R629S|DGKH_ENST00000538674.1_Missense_Mutation_p.R384S|DGKH_ENST00000536612.1_Missense_Mutation_p.R493S	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	629					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		AAGCAGTGAGGCAAGTCATTG	0.438																																					p.R629S		Atlas-SNP	.											.	DGKH	106	.	0			c.G1887T						.						76	73	74					13																	42763420		2203	4300	6503	SO:0001583	missense	160851	exon16			AGTGAGGCAAGTC	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.1887G>T	chr13.hg19:g.42763420G>T	ENSP00000337572:p.Arg629Ser	88.0	0.0		116.0	31.0	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	hg19	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.995550	0.74703	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612;ENST00000538674	D;T;D;D;D;T	0.82711	-1.64;-1.46;-1.64;-1.59;-1.6;1.61	5.72	4.88	0.63580	.	0.000000	0.85682	D	0.000000	D	0.89305	0.6677	M	0.71581	2.175	0.58432	D	0.999991	D;D;D;P	0.71674	0.998;0.998;0.995;0.884	D;D;D;P	0.72075	0.956;0.976;0.91;0.54	D	0.89801	0.3975	10	0.66056	D	0.02	.	11.7184	0.51668	0.1415:0.0:0.8585:0.0	.	384;493;629;629	F5GYP2;Q86XP1-3;Q86XP1-2;Q86XP1	.;.;.;DGKH_HUMAN	S	629;629;629;493;493;384	ENSP00000440823:R629S;ENSP00000337572:R629S;ENSP00000261491:R629S;ENSP00000368576:R493S;ENSP00000445114:R493S;ENSP00000441308:R384S	ENSP00000261491:R629S	R	+	3	2	DGKH	41661420	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.368000	0.52357	1.419000	0.47118	0.655000	0.94253	AGG	.	.		0.438	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		T	42763420	G	T	42763420	3	4	131	1	0	0	0	0	1	0	0	0	4472	1194	42	3	1945	3	DGKH	13	42763420	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	996705	42763420	72406458	93	21382										
NUFIP1	26747	hgsc.bcm.edu	37	chr13	45563368	45563368	+	Frame_Shift_Del	DEL	G	G	-													0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gggagagactgggcctccatGgggggctgcgactcagagga							TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr13:45563368delG	ENST00000379161.4	-	1	250	c.204delC	c.(202-204)cccfs	p.P68fs	RP11-321C24.1_ENST00000437748.2_lincRNA|GPALPP1_ENST00000361121.2_5'Flank|GPALPP1_ENST00000379151.4_5'Flank	NM_012345.2	NP_036477.2	Q9UHK0	NUFP1_HUMAN	nuclear fragile X mental retardation protein interacting protein 1	68	Pro-rich.				box C/D snoRNP assembly (GO:0000492)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA processing (GO:0006396)	cytosolic ribosome (GO:0022626)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|pre-snoRNP complex (GO:0070761)|presynaptic active zone (GO:0048786)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(4)|skin(3)	18		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)		GGGCCTCCATGGGGGGCTGCG	0.672																																					p.M69fs		Atlas-INDEL	.											.	NUFIP1	41	.	0			c.205delA						.						15	18	17					13																	45563368		2198	4292	6490	SO:0001589	frameshift_variant	26747	exon1			.	AF159548	CCDS9393.1	13q14	2008-02-05			ENSG00000083635	ENSG00000083635			8057	protein-coding gene	gene with protein product		604354				10556305, 10894927	Standard	NM_012345		Approved	NUFIP	uc001uzp.2	Q9UHK0	OTTHUMG00000016842	ENST00000379161.4:c.204delC	chr13.hg19:g.45563368delG	ENSP00000368459:p.Pro68fs	38.0	0.0		36.0	11.0	NM_012345	Q8WVM5|Q96SG1	Frame_Shift_Del	DEL	ENST00000379161.4	hg19	CCDS9393.1																																																																																			.	.		0.672	NUFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044755.2	NM_012345		-	45563368	G	-	45563368	7	5	131	1	0	1	0	1	0	0	0	0	10757	1335	47	0	1323	0	NUFIP1	13	45563368	Frame_Shift_Del	DEL	G	TCGA-DD-A4NI-01A-11D-A27I-10	2799948	45563368	69606510	94	21383										
UPF3A	65110	hgsc.bcm.edu	37	chr13	115052106	115052106	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	aagacaagagagctcattggTctgttttgctcatttcttct	8	8	5	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr13:115052106T>C	ENST00000375299.3	+	5	687		c.e5+2		UPF3A_ENST00000351487.5_Splice_Site|UPF3A_ENST00000475218.2_Splice_Site	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)						gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleocytoplasmic transport (GO:0006913)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	16	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		AGCTCATTGGTCTGTTTTGCT	0.408																																					.		Atlas-SNP	.											.	UPF3A	47	.	0			c.532+2T>C						.						52	48	49					13																	115052106		2203	4300	6503	SO:0001630	splice_region_variant	65110	exon4			CATTGGTCTGTTT	AF318575	CCDS9543.1, CCDS9544.1	13q34	2010-04-30			ENSG00000169062	ENSG00000169062			20332	protein-coding gene	gene with protein product		605530				11113196, 11163187	Standard	NM_023011		Approved	RENT3A, UPF3, HUPF3A	uc001vup.3	Q9H1J1	OTTHUMG00000017403	ENST00000375299.3:c.631+2T>C	chr13.hg19:g.115052106T>C		175.0	0.0		237.0	23.0	NM_080687	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Splice_Site	SNP	ENST00000375299.3	hg19	CCDS9543.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.207740	0.39003	.	.	ENSG00000169062	ENST00000375299;ENST00000351487;ENST00000543577	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1071	0.72329	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	UPF3A	114070208	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	7.172000	0.77604	1.978000	0.57642	0.459000	0.35465	.	.	.		0.408	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2		Intron	C	115052106	T	C	115052106	5	2	131	1	0	0	0	0	0	0	1	0	17020	1681	58	2	651	2	UPF3A	13	115052106	Splice_Site	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	69488738	115052106	117772	95	21384										
RNF31	55072	hgsc.bcm.edu	37	chr14	24618693	24618693	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	atcctgtaaacaggccctgtGtccagcctgtgaccacctgt	9	14	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr14:24618693G>T	ENST00000324103.6	+	6	1030	c.710G>T	c.(709-711)tGt>tTt	p.C237F	PSME2_ENST00000471700.2_5'Flank|RP11-468E2.4_ENST00000558468.1_5'Flank|PSME2_ENST00000216802.5_5'Flank|RNF31_ENST00000559275.1_Missense_Mutation_p.C86F|PSME2_ENST00000560410.1_5'Flank|RNF31_ENST00000382687.3_Missense_Mutation_p.C86F	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	237	Polyubiquitin-binding.				CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		CAGGCCCTGTGTCCAGCCTGT	0.637																																					p.C237F		Atlas-SNP	.											.	RNF31	95	.	0			c.G710T						.						88	93	91					14																	24618693		2094	4219	6313	SO:0001583	missense	55072	exon6			CCCTGTGTCCAGC	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"RING-type (C3HC4) zinc fingers"	16031	protein-coding gene	gene with protein product	"HOIL-1-interacting protein"	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.710G>T	chr14.hg19:g.24618693G>T	ENSP00000315112:p.Cys237Phe	106.0	0.0		151.0	44.0	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	hg19	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.185324	0.78677	.	.	ENSG00000092098	ENST00000324103;ENST00000382687	T;T	0.80214	-1.35;-1.31	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.89005	0.6592	L	0.61218	1.895	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.994;0.997	D	0.89095	0.3485	10	0.87932	D	0	-21.2105	19.0767	0.93165	0.0:0.0:1.0:0.0	.	52;237;86	B3KV71;Q96EP0;Q96EP0-3	.;RNF31_HUMAN;.	F	237;86	ENSP00000315112:C237F;ENSP00000372134:C86F	ENSP00000315112:C237F	C	+	2	0	RNF31	23688533	1.000000	0.71417	0.924000	0.36721	0.629000	0.37895	6.467000	0.73547	2.808000	0.96608	0.655000	0.94253	TGT	.	.		0.637	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		T	24618693	G	T	24618693	3	4	131	1	0	0	0	0	1	0	0	0	13502	1377	48	3	732	3	RNF31	14	24618693	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10		24618693	82730847	96	21385										
GPR135	64582	hgsc.bcm.edu	37	chr14	59930690	59930690	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tctggcttgcagacccgggcCctggctgggcaggaaagcgt	16	12	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr14:59930690C>A	ENST00000395116.1	-	1	1370	c.1255G>T	c.(1255-1257)Ggc>Tgc	p.G419C		NM_022571.5	NP_072093.2	Q8IZ08	GP135_HUMAN	G protein-coupled receptor 135	419						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.134)		AGACCCGGGCCCTGGCTGGGC	0.637																																					p.G419C		Atlas-SNP	.											GPR135,NS,carcinoma,0,1	GPR135	26	.	0			c.G1255T						.						40	34	36					14																	59930690		2203	4300	6503	SO:0001583	missense	64582	exon1			CCGGGCCCTGGCT	AY288418	CCDS9738.1	14q23.1	2012-08-21			ENSG00000181619	ENSG00000181619		"GPCR / Class A : Orphans"	19991	protein-coding gene	gene with protein product		607970				14623098	Standard	NM_022571		Approved	HUMNPIIY20, PAFR	uc010apj.3	Q8IZ08	OTTHUMG00000140325	ENST00000395116.1:c.1255G>T	chr14.hg19:g.59930690C>A	ENSP00000378548:p.Gly419Cys	87.0	1.0		88.0	30.0	NM_022571	Q7Z604|Q86SM3|Q8NH39	Missense_Mutation	SNP	ENST00000395116.1	hg19	CCDS9738.1	.	.	.	.	.	.	.	.	.	.	c	18.23	3.578961	0.65878	.	.	ENSG00000181619	ENST00000395116	T	0.63580	-0.05	4.89	1.93	0.25924	.	0.456851	0.20560	U	0.089927	T	0.51753	0.1693	L	0.27053	0.805	0.38467	D	0.947369	D	0.57257	0.979	P	0.46975	0.533	T	0.56780	-0.7922	10	0.52906	T	0.07	-7.6514	11.5851	0.50914	0.0:0.6903:0.2352:0.0745	.	419	Q8IZ08	GP135_HUMAN	C	419	ENSP00000378548:G419C	ENSP00000378548:G419C	G	-	1	0	GPR135	59000443	0.450000	0.25697	0.031000	0.17742	0.138000	0.21146	0.794000	0.26958	0.659000	0.30945	0.651000	0.88453	GGC	.	.		0.637	GPR135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276941.1	NM_022571		A	59930690	C	A	59930690	3	1	131	1	0	0	0	0	1	0	0	0	6652	623	22	3	233	3	GPR135	14	59930690	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	35311997	59930690	47418850	97	21386										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64457170	64457170	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	atgtttgatgagcttatggcAagaagtgaagatatgttaca	11	3	0	5			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr14:64457170A>G	ENST00000344113.4	+	20	2567	c.2355A>G	c.(2353-2355)gcA>gcG	p.A785A	SYNE2_ENST00000554584.1_Silent_p.A785A|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000358025.3_Silent_p.A785A	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	785					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGCTTATGGCAAGAAGTGAAG	0.338																																					p.A785A		Atlas-SNP	.											.	SYNE2	577	.	0			c.A2355G						.						92	88	89					14																	64457170		1835	4098	5933	SO:0001819	synonymous_variant	23224	exon20			TATGGCAAGAAGT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.2355A>G	chr14.hg19:g.64457170A>G		139.0	0.0		144.0	18.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.338	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64457170	A	G	64457170	2	3	131	1	0	0	0	0	0	0	0	1	15461	117	5	2		2	SYNE2	14	64457170	Silent	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	4526480	64457170	42892370	98	21387										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089799	86089799	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	atccccaacaacatgcgataCtgcaacagcagcgtgccaga	8	14	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr14:86089799C>G	ENST00000330753.4	+	2	2708	c.1941C>G	c.(1939-1941)taC>taG	p.Y647*	FLRT2_ENST00000554746.1_Nonsense_Mutation_p.Y647*	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	647					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		ACATGCGATACTGCAACAGCA	0.507																																					p.Y647X		Atlas-SNP	.											.	FLRT2	168	.	0			c.C1941G						.						204	208	207					14																	86089799		2189	4266	6455	SO:0001587	stop_gained	23768	exon2			GCGATACTGCAAC	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1941C>G	chr14.hg19:g.86089799C>G	ENSP00000332879:p.Tyr647*	92.0	0.0		94.0	6.0	NM_013231	A0AV84|B7ZLP3	Nonsense_Mutation	SNP	ENST00000330753.4	hg19	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	C	45	11.932692	0.99618	.	.	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	.	.	.	6.06	6.06	0.98353	.	0.154928	0.48286	D	0.000182	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.7132	14.7494	0.69513	0.0:0.9315:0.0:0.0685	.	.	.	.	X	647;647;300	.	ENSP00000332879:Y647X	Y	+	3	2	FLRT2	85159552	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.311000	0.51919	2.880000	0.98712	0.650000	0.86243	TAC	.	.		0.507	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			G	86089799	C	G	86089799	4	3	131	1	0	0	0	0	0	1	0	0	5947	576	20	4	1943	4	FLRT2	14	86089799	Nonsense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	21632629	86089799	21259741	99	21388										
SNRPN	6638	hgsc.bcm.edu	37	chr15	25221503	25221503	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gaaaagcgggttttgggtctGgtgttgctgcgtggggagaa	19	4	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr15:25221503G>T	ENST00000400100.1	+	9	1097	c.207G>T	c.(205-207)ctG>ctT	p.L69L	SNRPN_ENST00000400097.1_Silent_p.L69L|SNRPN_ENST00000346403.6_Silent_p.L69L|SNURF_ENST00000338094.6_3'UTR|SNRPN_ENST00000400098.1_Silent_p.L69L|SNRPN_ENST00000444203.2_Silent_p.L73L|SNRPN_ENST00000390687.4_Silent_p.L69L|SNURF_ENST00000551312.2_Intron|SNRPN_ENST00000577565.1_Silent_p.L69L|SNRPN_ENST00000554227.2_Silent_p.L73L	NM_022807.2	NP_073718.1	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	69					response to hormone (GO:0009725)|RNA splicing (GO:0008380)	small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U2 snRNP (GO:0005686)	RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(2)	24		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		TTTTGGGTCTGGTGTTGCTGC	0.453									Prader-Willi syndrome																												p.L69L		Atlas-SNP	.											SNRPN,NS,carcinoma,0,2	SNRPN	58	.	0			c.G207T						.						93	100	98					15																	25221503		1926	4134	6060	SO:0001819	synonymous_variant	6638	exon9	Familial Cancer Database	Prader-Labhart-Willi syndrome	GGGTCTGGTGTTG	L80005	CCDS10017.1	15q11.2	2013-07-16			ENSG00000128739	ENSG00000128739			11164	protein-coding gene	gene with protein product	"tissue-specific splicing protein", "SM protein N", "small nuclear ribonucleoprotein N"	182279	"Prader-Willi syndrome chromosome region"	PWCR		1533223	Standard	NM_022805		Approved	SMN, SM-D, HCERN3, SNRNP-N, SNURF-SNRPN, RT-LI	uc001ywt.1	P63162	OTTHUMG00000129180	ENST00000400100.1:c.207G>T	chr15.hg19:g.25221503G>T		128.0	1.0		157.0	7.0	NM_022807	B3KVR1|P14648|P17135|Q0D2Q5	Silent	SNP	ENST00000400100.1	hg19	CCDS10017.1																																																																																			.	.		0.453	SNRPN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413849.10	NM_003097		T	25221503	G	T	25221503	2	4	131	1	0	0	0	0	0	0	0	1	14885	1335	47	3		3	SNRPN	15	25221503	Silent	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10		25221503	77309889	100	21389										
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48533795	48533795	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ttaggggttgcaatttgtgtAggtaagtggtacgtctccag	14	5	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr15:48533795A>G	ENST00000558405.1	+	9	1313	c.1299A>G	c.(1297-1299)gtA>gtG	p.V433V	SLC12A1_ENST00000396577.3_Splice_Site_p.V433V|SLC12A1_ENST00000380993.3_Splice_Site_p.V433V			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	433					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CAATTTGTGTAGGTAAGTGGT	0.433																																					p.V433V		Atlas-SNP	.											.	SLC12A1	243	.	0			c.A1299G						.						205	190	195					15																	48533795		2198	4297	6495	SO:0001630	splice_region_variant	6557	exon10			TTGTGTAGGTAAG		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1300+1A>G	chr15.hg19:g.48533795A>G		100.0	0.0		167.0	58.0	NM_001184832	A8JYA2|E9PDW4	Silent	SNP	ENST00000558405.1	hg19	CCDS10129.2																																																																																			.	.		0.433	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		Silent	G	48533795	A	G	48533795	5	3	131	1	0	0	0	0	0	0	1	0	14397	434	15	2	1433	2	SLC12A1	15	48533795	Splice_Site	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	23312292	48533795	53997597	101	21390										
SHC4	399694	hgsc.bcm.edu	37	chr15	49254841	49254841	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gaggggccgctggaacctggGtcccggctttcctggagctt	16	12	0	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr15:49254841G>T	ENST00000332408.4	-	1	800	c.372C>A	c.(370-372)gaC>gaA	p.D124E		NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	124	CH2.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		TGGAACCTGGGTCCCGGCTTT	0.607																																					p.D124E		Atlas-SNP	.											.	SHC4	70	.	0			c.C372A						.						49	50	49					15																	49254841		2197	4295	6492	SO:0001583	missense	399694	exon1			ACCTGGGTCCCGG	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"SH2 domain containing"	16743	protein-coding gene	gene with protein product	"rai-like protein"						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.372C>A	chr15.hg19:g.49254841G>T	ENSP00000329668:p.Asp124Glu	68.0	0.0		100.0	37.0	NM_203349	Q6UXQ3|Q8IYW3	Missense_Mutation	SNP	ENST00000332408.4	hg19	CCDS10130.1	.	.	.	.	.	.	.	.	.	.	G	0.071	-1.201489	0.01581	.	.	ENSG00000185634	ENST00000332408	T	0.04603	3.59	4.67	-4.35	0.03656	.	0.539396	0.16931	N	0.193641	T	0.01835	0.0058	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.45934	-0.9227	10	0.11485	T	0.65	-18.6904	7.3232	0.26540	0.3112:0.5173:0.1715:0.0	.	124	Q6S5L8	SHC4_HUMAN	E	124	ENSP00000329668:D124E	ENSP00000329668:D124E	D	-	3	2	SHC4	47042133	0.000000	0.05858	0.108000	0.21378	0.114000	0.19823	-2.692000	0.00830	-0.785000	0.04522	-0.165000	0.13383	GAC	.	.		0.607	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349		T	49254841	G	T	49254841	3	4	131	1	0	0	0	0	1	0	0	0	14288	1252	44	3	1568	3	SHC4	15	49254841	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	721046	49254841	53276551	102	21391										
SCAPER	49855	hgsc.bcm.edu	37	chr15	76994169	76994169	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cggcttgctggtgttttctcCctttaacatggctaaaaaga	9	9	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr15:76994169C>G	ENST00000563290.1	-	20	2533	c.2438G>C	c.(2437-2439)gGg>gCg	p.G813A	SCAPER_ENST00000538941.2_Missense_Mutation_p.G567A|SCAPER_ENST00000324767.7_Missense_Mutation_p.G813A			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	813						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						GTGTTTTCTCCCTTTAACATG	0.353																																					p.G813A		Atlas-SNP	.											.	SCAPER	160	.	0			c.G2438C						.						87	85	85					15																	76994169		1857	4126	5983	SO:0001583	missense	49855	exon19			TTTCTCCCTTTAA	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.2438G>C	chr15.hg19:g.76994169C>G	ENSP00000454973:p.Gly813Ala	52.0	0.0		63.0	17.0	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	hg19	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.315415	0.81358	.	.	ENSG00000140386	ENST00000324767;ENST00000538941;ENST00000303521	T;T	0.71103	-0.54;-0.54	5.49	5.49	0.81192	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	D	0.82678	0.5089	M	0.65975	2.015	0.80722	D	1	D;D	0.62365	0.991;0.987	D;P	0.66196	0.942;0.834	T	0.82141	-0.0604	10	0.46703	T	0.11	.	19.3857	0.94555	0.0:1.0:0.0:0.0	.	812;567	Q9BY12;F5H7X8	SCAPE_HUMAN;.	A	813;567;835	ENSP00000326924:G813A;ENSP00000442190:G567A	ENSP00000303560:G835A	G	-	2	0	SCAPER	74781224	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	7.234000	0.78134	2.596000	0.87737	0.557000	0.71058	GGG	.	.		0.353	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		G	76994169	C	G	76994169	3	3	131	1	0	0	0	0	1	0	0	0	13893	623	22	4	1816	4	SCAPER	15	76994169	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	27739328	76994169	25537223	103	21392										
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79350802	79350802	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ttctgcattaatgcctcatgCtctgtggcgagggtcctgta	11	10	3	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr15:79350802C>T	ENST00000419573.3	-	3	679	c.405G>A	c.(403-405)gaG>gaA	p.E135E	RASGRF1_ENST00000558480.2_Silent_p.E135E|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	135					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ATGCCTCATGCTCTGTGGCGA	0.572																																					p.E135E		Atlas-SNP	.											.	RASGRF1	168	.	0			c.G405A						.						121	100	107					15																	79350802		2196	4293	6489	SO:0001819	synonymous_variant	5923	exon3			CTCATGCTCTGTG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.405G>A	chr15.hg19:g.79350802C>T		97.0	0.0		154.0	46.0	NM_001145648	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	hg19	CCDS10309.1																																																																																			.	.		0.572	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		T	79350802	C	T	79350802	2	4	131	1	0	0	0	0	0	0	0	1	13087	796	28	3		3	RASGRF1	15	79350802	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	2356633	79350802	23180590	104	21393										
AP3B2	8120	hgsc.bcm.edu	37	chr15	83357541	83357541	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cagggccaggtcttgctgctCctcagcgtagcgtaccaggt	13	13	2	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr15:83357541C>G	ENST00000261722.3	-	4	514	c.307G>C	c.(307-309)Gag>Cag	p.E103Q	AP3B2_ENST00000535348.1_Intron|AP3B2_ENST00000542200.1_Missense_Mutation_p.E103Q|RP11-752G15.3_ENST00000560650.1_RNA|AP3B2_ENST00000561455.1_5'UTR|AP3B2_ENST00000535359.1_Missense_Mutation_p.E103Q	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	103					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			TCTTGCTGCTCCTCAGCGTAG	0.602																																					p.E103Q		Atlas-SNP	.											.	AP3B2	103	.	0			c.G307C						.						78	84	82					15																	83357541		2117	4237	6354	SO:0001583	missense	8120	exon4			GCTGCTCCTCAGC	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.307G>C	chr15.hg19:g.83357541C>G	ENSP00000261722:p.Glu103Gln	152.0	0.0		170.0	31.0	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Missense_Mutation	SNP	ENST00000261722.3	hg19	CCDS45331.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.225169	0.79576	.	.	ENSG00000103723	ENST00000261722;ENST00000535359;ENST00000541693;ENST00000542200;ENST00000535513	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	5.76	5.76	0.90799	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.108228	0.64402	N	0.000007	T	0.33702	0.0872	L	0.31476	0.935	0.80722	D	1	P;P;B	0.40000	0.698;0.592;0.236	B;P;B	0.45276	0.222;0.475;0.349	T	0.02294	-1.1181	10	0.42905	T	0.14	-24.8029	19.5631	0.95380	0.0:1.0:0.0:0.0	.	103;103;103	F5H0E6;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	Q	103;103;59;103;103	ENSP00000261722:E103Q;ENSP00000440984:E103Q;ENSP00000441961:E59Q;ENSP00000440719:E103Q	ENSP00000261722:E103Q	E	-	1	0	AP3B2	81154595	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.693000	0.84214	2.710000	0.92621	0.655000	0.94253	GAG	.	.		0.602	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			G	83357541	C	G	83357541	3	3	131	1	0	0	0	0	1	0	0	0	745	864	30	4	2957	4	AP3B2	15	83357541	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	4006739	83357541	19173851	105	21394										
ACSM2A	123876	hgsc.bcm.edu	37	chr16	20494379	20494379	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tggccttcatcttttttgcaGgtggtgaaggcatttgtggt	13	6	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr16:20494379G>A	ENST00000573854.1	+	13	1623		c.e13-1		ACSM2A_ENST00000575690.1_Splice_Site|ACSM2A_ENST00000396104.2_Splice_Site|ACSM2A_ENST00000417235.2_Splice_Site|ACSM2A_ENST00000219054.6_Splice_Site|ACSM2A_ENST00000536134.1_Splice_Site	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A						fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						CTTTTTTGCAGGTGGTGAAGG	0.498																																					.		Atlas-SNP	.											.	ACSM2A	120	.	0			c.1510-1G>A						.						195	177	183					16																	20494379		2203	4300	6503	SO:0001630	splice_region_variant	123876	exon14			TTTGCAGGTGGTG	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"Acyl-CoA synthetase family"	32017	protein-coding gene	gene with protein product		614358	"acyl-CoA synthetase medium-chain family member 2"	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.1510-1G>A	chr16.hg19:g.20494379G>A		137.0	0.0		199.0	46.0	NM_001010845	B3KTT9|O75202	Splice_Site	SNP	ENST00000573854.1	hg19	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.636470	0.29068	.	.	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000536134;ENST00000396104	.	.	.	3.26	3.26	0.37387	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.417	0.67158	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACSM2A	20401880	1.000000	0.71417	0.927000	0.36925	0.359000	0.29487	7.884000	0.87274	1.507000	0.48752	0.305000	0.20034	.	.	.		0.498	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845	Intron	A	20494379	G	A	20494379	5	1	131	1	0	0	0	0	0	0	1	0	183	1014	35	3	1555	3	ACSM2A	16	20494379	Splice_Site	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10		20494379	69860374	106	21395										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24834929	24834929	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	attctccagccggaccgatcTcaatcactggaatggtgctg	10	12	3	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr16:24834929T>G	ENST00000395799.3	+	25	5819	c.5690T>G	c.(5689-5691)cTc>cGc	p.L1897R	TNRC6A_ENST00000432286.2_Missense_Mutation_p.L375R|TNRC6A_ENST00000315183.7_Missense_Mutation_p.L1848R	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1897	Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		CGGACCGATCTCAATCACTGG	0.612																																					p.L1897R		Atlas-SNP	.											.	TNRC6A	171	.	0			c.T5690G						.						114	113	114					16																	24834929		2197	4300	6497	SO:0001583	missense	27327	exon25			CCGATCTCAATCA	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.5690T>G	chr16.hg19:g.24834929T>G	ENSP00000379144:p.Leu1897Arg	122.0	0.0		138.0	27.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	t	8.042	0.764075	0.15914	.	.	ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286	T;T	0.13089	2.63;2.62	5.64	5.64	0.86602	.	0.227351	0.39341	N	0.001385	T	0.15089	0.0364	L	0.39898	1.24	0.33298	D	0.564448	D;B	0.54207	0.965;0.412	P;B	0.47981	0.563;0.121	T	0.16808	-1.0390	10	0.21540	T	0.41	-0.1468	10.9817	0.47499	0.0:0.0724:0.0:0.9276	.	1848;1897	Q8NDV7-6;Q8NDV7	.;TNR6A_HUMAN	R	1848;1897;375	ENSP00000326900:L1848R;ENSP00000379144:L1897R	ENSP00000326900:L1848R	L	+	2	0	TNRC6A	24742430	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.545000	0.60698	2.132000	0.65825	0.529000	0.55759	CTC	.	.		0.612	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24834929	T	G	24834929	3	3	131	1	0	0	0	0	1	0	0	0	16355	1551	54	5	5788	5	TNRC6A	16	24834929	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	4340550	24834929	65519824	107	21396										
TGFB1I1	7041	hgsc.bcm.edu	37	chr16	31487440	31487440	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gagaaggatggagcccccttCtgccccgagtgctactttga	12	12	1	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr16:31487440C>A	ENST00000394863.3	+	8	952	c.822C>A	c.(820-822)ttC>ttA	p.F274L	TGFB1I1_ENST00000361773.3_Missense_Mutation_p.F257L|TGFB1I1_ENST00000394858.2_Missense_Mutation_p.F257L|TGFB1I1_ENST00000567607.1_Missense_Mutation_p.F257L	NM_001042454.2	NP_001035919.1	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced transcript 1	274	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|cell adhesion (GO:0007155)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|response to heat (GO:0009408)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|I-SMAD binding (GO:0070411)|Roundabout binding (GO:0048495)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(8)|upper_aerodigestive_tract(1)	9						GAGCCCCCTTCTGCCCCGAGT	0.677																																					p.F274L		Atlas-SNP	.											.	TGFB1I1	60	.	0			c.C822A						.						66	59	61					16																	31487440		2197	4300	6497	SO:0001583	missense	7041	exon8			CCCCTTCTGCCCC	AB007836	CCDS10713.1, CCDS42156.1	16p11	2008-02-05			ENSG00000140682	ENSG00000140682			11767	protein-coding gene	gene with protein product		602353				9422762, 10075738	Standard	NM_015927		Approved	Hic-5, TSC-5, ARA55, HIC-5	uc002ecd.2	O43294	OTTHUMG00000132467	ENST00000394863.3:c.822C>A	chr16.hg19:g.31487440C>A	ENSP00000378332:p.Phe274Leu	63.0	0.0		76.0	19.0	NM_001042454	B2R8D5|Q9BPW3|Q9Y2V5	Missense_Mutation	SNP	ENST00000394863.3	hg19	CCDS42156.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.767115	0.69878	.	.	ENSG00000140682	ENST00000394863;ENST00000361773;ENST00000394858	D;D;D	0.87412	-2.25;-2.25;-2.25	5.4	2.06	0.26882	Zinc finger, LIM-type (4);	0.054439	0.85682	D	0.000000	T	0.77198	0.4095	N	0.16066	0.365	0.46774	D	0.999196	B	0.26445	0.149	B	0.36766	0.232	T	0.66364	-0.5942	10	0.39692	T	0.17	.	7.5762	0.27937	0.0:0.623:0.0:0.377	.	274	O43294	TGFI1_HUMAN	L	274;257;257	ENSP00000378332:F274L;ENSP00000355117:F257L;ENSP00000378327:F257L	ENSP00000355117:F257L	F	+	3	2	TGFB1I1	31394941	0.999000	0.42202	1.000000	0.80357	0.988000	0.76386	0.719000	0.25881	0.240000	0.21263	0.655000	0.94253	TTC	.	.		0.677	TGFB1I1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255630.3			A	31487440	C	A	31487440	3	1	131	1	0	0	0	0	1	0	0	0	15832	912	32	3	852	3	TGFB1I1	16	31487440	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	6652511	31487440	58867313	108	21397										
PSKH1	5681	hgsc.bcm.edu	37	chr16	67943502	67943502	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cagtggacatgtgggcgctgGgcgtcattgcctacatccta	13	11	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr16:67943502G>T	ENST00000291041.5	+	2	1020	c.850G>T	c.(850-852)Ggc>Tgc	p.G284C		NM_006742.2	NP_006733.1	P11801	KPSH1_HUMAN	protein serine kinase H1	284	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|large_intestine(1)|lung(7)|pancreas(1)	12		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0044)|Epithelial(162;0.0197)|all cancers(182;0.128)		GTGGGCGCTGGGCGTCATTGC	0.567																																					p.G284C		Atlas-SNP	.											.	PSKH1	28	.	0			c.G850T						.						98	83	88					16																	67943502		2198	4300	6498	SO:0001583	missense	5681	exon2			GCGCTGGGCGTCA	M14504	CCDS10851.1	16q22.1	2008-02-05			ENSG00000159792	ENSG00000159792			9529	protein-coding gene	gene with protein product		177015				8268911	Standard	NM_006742		Approved		uc002euv.3	P11801	OTTHUMG00000137548	ENST00000291041.5:c.850G>T	chr16.hg19:g.67943502G>T	ENSP00000291041:p.Gly284Cys	104.0	0.0		130.0	38.0	NM_006742	Q9NY19	Missense_Mutation	SNP	ENST00000291041.5	hg19	CCDS10851.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.253978	0.80135	.	.	ENSG00000159792	ENST00000291041	D	0.82167	-1.58	5.45	5.45	0.79879	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95642	0.8583	H	0.99379	4.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97744	1.0210	10	0.87932	D	0	-17.3627	18.8712	0.92315	0.0:0.0:1.0:0.0	.	284	P11801	KPSH1_HUMAN	C	284	ENSP00000291041:G284C	ENSP00000291041:G284C	G	+	1	0	PSKH1	66501003	1.000000	0.71417	0.909000	0.35828	0.685000	0.39939	9.869000	0.99810	2.561000	0.86390	0.655000	0.94253	GGC	.	.		0.567	PSKH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268882.3	NM_006742		T	67943502	G	T	67943502	3	4	131	1	0	0	0	0	1	0	0	0	12676	1232	43	3	852	3	PSKH1	16	67943502	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	36456062	67943502	22411251	109	21398										
PDPR	55066	hgsc.bcm.edu	37	chr16	70170122	70170122	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ctgttgagttcccttctgagGaggatgccagaattagagac	12	8	1	4			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr16:70170122G>A	ENST00000288050.4	+	10	1980	c.1023G>A	c.(1021-1023)agG>agA	p.R341R	PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000398122.3_Silent_p.R241R|PDPR_ENST00000568530.1_Silent_p.R341R	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	341					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		CCCTTCTGAGGAGGATGCCAG	0.463																																					p.R341R		Atlas-SNP	.											.	PDPR	66	.	0			c.G1023A						.						31	34	33					16																	70170122		1875	4116	5991	SO:0001819	synonymous_variant	55066	exon10			TCTGAGGAGGATG		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1023G>A	chr16.hg19:g.70170122G>A		148.0	0.0		158.0	7.0	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Silent	SNP	ENST00000288050.4	hg19	CCDS45520.1																																																																																			.	.		0.463	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990		A	70170122	G	A	70170122	2	1	131	1	0	0	0	0	0	0	0	1	11698	1165	41	3		3	PDPR	16	70170122	Silent	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	2226620	70170122	20184631	110	21399										
ANKFY1	51479	hgsc.bcm.edu	37	chr17	4086813	4086825	+	Frame_Shift_Del	DEL	GAGCCCAGCAGCT	GAGCCCAGCAGCT	-													0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tgtcattgatggcggctccaGagcccagcagctgggctgcg							TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	GAGCCCAGCAGCT	GAGCCCAGCAGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr17:4086813_4086825delGAGCCCAGCAGCT	ENST00000341657.4	-	14	1855_1867	c.1820_1832delAGCTGCTGGGCTC	c.(1819-1833)cagctgctgggctctfs	p.QLLGS607fs	CYB5D2_ENST00000573984.1_Intron|ANKFY1_ENST00000573722.1_5'Flank|ANKFY1_ENST00000570535.1_Frame_Shift_Del_p.QLLGS649fs|Y_RNA_ENST00000516003.1_RNA|ANKFY1_ENST00000574367.1_Frame_Shift_Del_p.QLLGS607fs	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	607					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GGCGGCTCCAGAGCCCAGCAGCTGGGCTGCGAT	0.592																																					p.649_653del		Pindel	.											.	ANKFY1	81	.	0			c.1947_1959del						.																																			SO:0001589	frameshift_variant	51479	exon14			.	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"Zinc fingers, FYVE domain containing", "BTB/POZ domain containing", "Ankyrin repeat domain containing"	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.1820_1832delAGCTGCTGGGCTC	chr17.hg19:g.4086813_4086825delGAGCCCAGCAGCT	ENSP00000343362:p.Gln607fs	83.0	0.0		85.0	13.0	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Frame_Shift_Del	DEL	ENST00000341657.4	hg19																																																																																				.	.		0.592	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		-	4086825	GAGCCCAGCAGCT	-	4086813	7	5	131	1	0	1	0	1	0	0	0	0	626	942	33	0	1728	0	ANKFY1	17	4086813	Frame_Shift_Del	DEL	GAGCCCAGCAGCT	TCGA-DD-A4NI-01A-11D-A27I-10		4086813	77108397	111	21400										
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4446343	4446343	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gcgttgaagtggtagagggcGgtgggggagtcgggctggcg	24	5	0	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr17:4446343G>A	ENST00000254718.4	-	20	3063	c.2757C>T	c.(2755-2757)acC>acT	p.T919T	MYBBP1A_ENST00000381556.2_Silent_p.T919T			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	919					cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						GGTAGAGGGCGGTGGGGGAGT	0.667																																					p.T919T		Atlas-SNP	.											MYBBP1A,right_upper_lobe,carcinoma,0,1	MYBBP1A	69	.	0			c.C2757T						.						50	59	56					17																	4446343		2203	4300	6503	SO:0001819	synonymous_variant	10514	exon20			GAGGGCGGTGGGG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"p53-activated protein-2"	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.2757C>T	chr17.hg19:g.4446343G>A		54.0	0.0		85.0	7.0	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	hg19	CCDS11046.1																																																																																			.	.		0.667	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		A	4446343	G	A	4446343	2	1	131	1	0	0	0	0	0	0	0	1	10017	1103	39	1		1	MYBBP1A	17	4446343	Silent	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	359530	4446343	76748867	112	21401										
ZBTB4	57659	hgsc.bcm.edu	37	chr17	7370078	7370078	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	attgagctggcgcaggacggCgggggcatgggacgggtccg	21	9	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr17:7370078C>T	ENST00000311403.4	-	3	382	c.43G>A	c.(43-45)Gcc>Acc	p.A15T	ZBTB4_ENST00000380599.4_Missense_Mutation_p.A15T	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	15					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		CGCAGGACGGCGGGGGCATGG	0.657																																					p.A15T		Atlas-SNP	.											.	ZBTB4	163	.	0			c.G43A						.						20	17	18					17																	7370078		2199	4299	6498	SO:0001583	missense	57659	exon3			GGACGGCGGGGGC	AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.43G>A	chr17.hg19:g.7370078C>T	ENSP00000307858:p.Ala15Thr	40.0	0.0		45.0	13.0	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Missense_Mutation	SNP	ENST00000311403.4	hg19	CCDS11107.1	.	.	.	.	.	.	.	.	.	.	C	4.358	0.065871	0.08388	.	.	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.70282	-0.47;-0.47	5.0	5.0	0.66597	BTB/POZ fold (2);	0.178800	0.37483	N	0.002077	T	0.46795	0.1411	N	0.05230	-0.09	0.34910	D	0.747394	D	0.58620	0.983	P	0.44422	0.449	T	0.54873	-0.8228	10	0.25106	T	0.35	-16.4127	6.3793	0.21525	0.1828:0.7267:0.0:0.0905	.	15	Q9P1Z0	ZBTB4_HUMAN	T	15	ENSP00000307858:A15T;ENSP00000369973:A15T	ENSP00000307858:A15T	A	-	1	0	ZBTB4	7310802	0.121000	0.22262	0.850000	0.33497	0.302000	0.27658	0.590000	0.23954	2.605000	0.88082	0.561000	0.74099	GCC	.	.		0.657	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899		T	7370078	C	T	7370078	3	4	131	1	0	0	0	0	1	0	0	0	17556	768	27	1	3006	1	ZBTB4	17	7370078	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	2923735	7370078	73825132	113	21402										
PER1	5187	hgsc.bcm.edu	37	chr17	8047144	8047144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gtggcgtgagcgcttggcttTggatcggcagtggtgtcggc	19	8	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr17:8047144T>C	ENST00000317276.4	-	19	2749	c.2512A>G	c.(2512-2514)Aaa>Gaa	p.K838E	PER1_ENST00000578089.1_5'UTR|PER1_ENST00000581082.1_Missense_Mutation_p.K815E	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	838					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CGCTTGGCTTTGGATCGGCAG	0.672			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.K838E		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.A2512G						.						43	52	49					17																	8047144		2203	4300	6503	SO:0001583	missense	5187	exon19			TGGCTTTGGATCG	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"period (Drosophila) homolog 1", "period homolog 1 (Drosophila)"	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2512A>G	chr17.hg19:g.8047144T>C	ENSP00000314420:p.Lys838Glu	36.0	0.0		41.0	6.0	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	hg19	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	T	16.68	3.191104	0.58017	.	.	ENSG00000179094	ENST00000317276	T	0.16743	2.32	5.24	5.24	0.73138	.	0.197963	0.42053	D	0.000767	T	0.15739	0.0379	L	0.35854	1.095	0.80722	D	1	P	0.47409	0.895	B	0.41236	0.351	T	0.01553	-1.1326	10	0.54805	T	0.06	-7.4453	13.0668	0.59038	0.0:0.0:0.0:1.0	.	838	O15534	PER1_HUMAN	E	838	ENSP00000314420:K838E	ENSP00000314420:K838E	K	-	1	0	PER1	7987869	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.189000	0.58358	1.982000	0.57802	0.460000	0.39030	AAA	.	.		0.672	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			C	8047144	T	C	8047144	3	2	131	1	0	0	0	0	1	0	0	0	11738	1821	63	2	1380	2	PER1	17	8047144	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	677066	8047144	73148066	114	21403										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27023949	27023949	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gatggagaccatggaccaggGtgatgtgattatccgaccaa	13	8	0	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr17:27023949G>A	ENST00000314616.6	+	30	4341	c.4058G>A	c.(4057-4059)gGt>gAt	p.G1353D	SUPT6H_ENST00000347486.4_Missense_Mutation_p.G1353D	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1353	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					ATGGACCAGGGTGATGTGATT	0.498																																					p.G1353D		Atlas-SNP	.											.	SUPT6H	165	.	0			c.G4058A						.						169	140	150					17																	27023949		2203	4300	6503	SO:0001583	missense	6830	exon30			ACCAGGGTGATGT	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.4058G>A	chr17.hg19:g.27023949G>A	ENSP00000319104:p.Gly1353Asp	183.0	0.0		265.0	91.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	hg19	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	34	5.399209	0.96030	.	.	ENSG00000109111	ENST00000314616	D	0.81739	-1.53	5.94	5.94	0.96194	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.93426	0.7903	H	0.95114	3.625	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94444	0.7661	10	0.87932	D	0	-18.8388	20.3594	0.98849	0.0:0.0:1.0:0.0	.	1353	Q7KZ85	SPT6H_HUMAN	D	1353	ENSP00000319104:G1353D	ENSP00000319104:G1353D	G	+	2	0	SUPT6H	24048076	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.359000	0.97115	2.816000	0.96949	0.563000	0.77884	GGT	.	.		0.498	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		A	27023949	G	A	27023949	3	1	131	1	0	0	0	0	1	0	0	0	15415	1261	44	3	4172	3	SUPT6H	17	27023949	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	18976805	27023949	54171261	115	21404										
TEX2	55852	hgsc.bcm.edu	37	chr17	62248484	62248484	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gtgatcaacgtaaggcttgaAggcctggaggatttttggca	14	6	1	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr17:62248484A>T	ENST00000583097.1	-	7	2819	c.2647T>A	c.(2647-2649)Ttc>Atc	p.F883I	TEX2_ENST00000584379.1_Missense_Mutation_p.F883I|TEX2_ENST00000258991.3_Missense_Mutation_p.F890I			Q8IWB9	TEX2_HUMAN	testis expressed 2	883					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TAAGGCTTGAAGGCCTGGAGG	0.448																																					p.F890I		Atlas-SNP	.											.	TEX2	89	.	0			c.T2668A						.						130	106	114					17																	62248484		2203	4300	6503	SO:0001583	missense	55852	exon7			GCTTGAAGGCCTG	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"transmembrane protein 96"		"testis expressed sequence 2"			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.2647T>A	chr17.hg19:g.62248484A>T	ENSP00000462665:p.Phe883Ile	131.0	0.0		219.0	30.0	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.10	3.302815	0.60195	.	.	ENSG00000136478	ENST00000258991	T	0.42900	0.96	6.03	6.03	0.97812	Domain of unknown function DUF2404 (1);	0.052460	0.85682	D	0.000000	T	0.42040	0.1185	N	0.22421	0.69	0.58432	D	0.999998	P;P	0.42375	0.778;0.719	P;P	0.48738	0.452;0.588	T	0.25779	-1.0122	10	0.41790	T	0.15	-21.5077	16.5602	0.84551	1.0:0.0:0.0:0.0	.	890;883	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	I	890	ENSP00000258991:F890I	ENSP00000258991:F890I	F	-	1	0	TEX2	59602216	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.932000	0.92897	2.313000	0.78055	0.454000	0.30748	TTC	.	.		0.448	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		T	62248484	A	T	62248484	3	4	131	1	0	0	0	0	1	0	0	0	15796	72	3	4	760	4	TEX2	17	62248484	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	35224535	62248484	18946726	116	21405										
KIF19	124602	hgsc.bcm.edu	37	chr17	72342641	72342641	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gtacatcaactatcgcgacaGcaagctcacccggctcctga	8	15	2	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr17:72342641G>T	ENST00000389916.4	+	8	1040	c.902G>T	c.(901-903)aGc>aTc	p.S301I		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	301	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						TATCGCGACAGCAAGCTCACC	0.577																																					p.S301I		Atlas-SNP	.											.	KIF19	102	.	0			c.G902T						.						68	42	51					17																	72342641		2049	3985	6034	SO:0001583	missense	124602	exon8			GCGACAGCAAGCT	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.902G>T	chr17.hg19:g.72342641G>T	ENSP00000374566:p.Ser301Ile	168.0	0.0		303.0	166.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	G	27.1	4.803380	0.90623	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	D;D	0.86297	-2.1;-2.1	5.8	5.8	0.92144	Kinesin, motor domain (4);	.	.	.	.	D	0.97081	0.9046	H	0.99726	4.73	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98541	1.0632	9	0.87932	D	0	.	19.7033	0.96063	0.0:0.0:1.0:0.0	.	301;259;259;301	Q2TAC6;F8VW50;Q2TAC6-3;Q2TAC6-2	KIF19_HUMAN;.;.;.	I	259;301	ENSP00000449134:S259I;ENSP00000374566:S301I	ENSP00000374566:S301I	S	+	2	0	KIF19	69854236	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	6.141000	0.71744	2.764000	0.94973	0.556000	0.70494	AGC	.	.		0.577	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		T	72342641	G	T	72342641	3	4	131	1	0	0	0	0	1	0	0	0	8291	971	34	3	932	3	KIF19	17	72342641	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	10094157	72342641	8852569	117	21406										
ACTG1	71	hgsc.bcm.edu	37	chr17	79479128	79479128	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gcttgctctgggcctcgtcgCccacgtaggagtccttctgg	13	14	2	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr17:79479128C>A	ENST00000575842.1	-	2	590	c.164G>T	c.(163-165)gGc>gTc	p.G55V	AC139149.1_ENST00000584254.1_RNA|ACTG1_ENST00000575087.1_Missense_Mutation_p.G55V|ACTG1_ENST00000573283.1_Missense_Mutation_p.G55V|RP13-766D20.2_ENST00000430912.1_RNA|ACTG1_ENST00000331925.2_Missense_Mutation_p.G55V			P63261	ACTG_HUMAN	actin, gamma 1	55					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1)	29	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			GGCCTCGTCGCCCACGTAGGA	0.642																																					p.G55V		Atlas-SNP	.											.	ACTG1	55	.	0			c.G164T						.						65	64	65					17																	79479128		2203	4300	6503	SO:0001583	missense	71	exon3			TCGTCGCCCACGT		CCDS11782.1	17q25	2010-04-23	2004-05-19		ENSG00000184009	ENSG00000184009			144	protein-coding gene	gene with protein product		102560	"deafness, autosomal dominant 20; deafness, autosomal dominant 26"	ACTG, DFNA20, DFNA26		14684684	Standard	NM_001614		Approved		uc002kal.2	P63261		ENST00000575842.1:c.164G>T	chr17.hg19:g.79479128C>A	ENSP00000458162:p.Gly55Val	43.0	0.0		68.0	16.0	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000575842.1	hg19	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.237185	0.58886	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	D	0.96459	-4.02	3.88	3.88	0.44766	Actin, conserved site (1);	0.000000	0.64402	U	0.000001	D	0.99004	0.9660	H	0.99573	4.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98686	1.0694	10	0.87932	D	0	.	14.8003	0.69909	0.0:1.0:0.0:0.0	.	55	P63261	ACTG_HUMAN	V	55	ENSP00000331514:G55V	ENSP00000331514:G55V	G	-	2	0	ACTG1	77093723	1.000000	0.71417	0.995000	0.50966	0.966000	0.64601	7.227000	0.78070	2.007000	0.58848	0.563000	0.77884	GGC	.	.		0.642	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614		A	79479128	C	A	79479128	3	1	131	1	0	0	0	0	1	0	0	0	196	739	26	3	979	3	ACTG1	17	79479128	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	7136487	79479128	1716082	118	21407										
CEP76	79959	hgsc.bcm.edu	37	chr18	12699183	12699183	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	acctgaaggtaaagatacctCcgtgttggatcaatattagc	9	8	1	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr18:12699183C>T	ENST00000262127.2	-	4	540	c.315G>A	c.(313-315)cgG>cgA	p.R105R	CEP76_ENST00000423709.2_Intron|CEP76_ENST00000586887.1_Intron|PSMG2_ENST00000585331.2_Intron	NM_024899.2	NP_079175.2	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	105					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AAAGATACCTCCGTGTTGGAT	0.353																																					p.R105R		Atlas-SNP	.											.	CEP76	45	.	0			c.G315A						.						84	84	84					18																	12699183		2203	4300	6503	SO:0001819	synonymous_variant	79959	exon4			ATACCTCCGTGTT	BC026307	CCDS11861.1, CCDS62390.1	18p11.21	2014-02-20	2005-12-01	2005-12-01	ENSG00000101624	ENSG00000101624			25727	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 9"	C18orf9		14654843	Standard	NM_024899		Approved	HsT1705, FLJ12542	uc002kri.4	Q8TAP6	OTTHUMG00000131701	ENST00000262127.2:c.315G>A	chr18.hg19:g.12699183C>T		65.0	0.0		104.0	24.0	NM_024899	B0YJB2|B4DXG5|B4DZW1|Q658N5|Q9H9U7	Silent	SNP	ENST00000262127.2	hg19	CCDS11861.1																																																																																			.	.		0.353	CEP76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254611.1	NM_024899		T	12699183	C	T	12699183	2	4	131	1	0	0	0	0	0	0	0	1	3263	842	30	3		3	CEP76	18	12699183	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10		12699183	65378065	119	21408										
DSG4	147409	hgsc.bcm.edu	37	chr18	28971168	28971168	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	taatttccccaccttagagaAaacttcagtaagtttgtatt	5	8	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr18:28971168A>C	ENST00000308128.4	+	7	947	c.812A>C	c.(811-813)aAa>aCa	p.K271T	RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.K271T|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	271	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Missing (in HYPT6). {ECO:0000269|PubMed:12705872, ECO:0000269|PubMed:15191570}.		anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACCTTAGAGAAAACTTCAGTA	0.403																																					p.K271T		Atlas-SNP	.											.	DSG4	343	.	0			c.A812C						.						131	117	122					18																	28971168		2203	4300	6503	SO:0001583	missense	147409	exon7			TAGAGAAAACTTC	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.812A>C	chr18.hg19:g.28971168A>C	ENSP00000311859:p.Lys271Thr	50.0	0.0		93.0	30.0	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	hg19	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	A	11.89	1.774648	0.31411	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.60920	0.15;0.15	5.9	4.75	0.60458	Cadherin (3);Cadherin-like (1);	0.000000	0.36972	N	0.002316	T	0.47395	0.1443	L	0.33753	1.03	0.32633	N	0.521715	P;B	0.36392	0.551;0.255	B;B	0.37550	0.253;0.122	T	0.59172	-0.7504	10	0.44086	T	0.13	.	11.8916	0.52633	0.9319:0.0:0.0681:0.0	.	271;271	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	T	271	ENSP00000311859:K271T;ENSP00000352785:K271T	ENSP00000311859:K271T	K	+	2	0	DSG4	27225166	1.000000	0.71417	0.999000	0.59377	0.872000	0.50106	5.965000	0.70387	1.061000	0.40601	0.482000	0.46254	AAA	.	.		0.403	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		C	28971168	A	C	28971168	3	2	131	1	0	0	0	0	1	0	0	0	4781	14	1	5	838	5	DSG4	18	28971168	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	16271985	28971168	49106080	120	21409										
DSG2	1829	hgsc.bcm.edu	37	chr18	29115251	29115251	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	agatatgtaaaattagaagaTagagataattggatctctgt	9	2	1	4	rs367548984		TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr18:29115251T>C	ENST00000261590.8	+	10	1508	c.1299T>C	c.(1297-1299)gaT>gaC	p.D433D		NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	433	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			AATTAGAAGATAGAGATAATT	0.308																																					p.D433D		Atlas-SNP	.											.	DSG2	115	.	0			c.T1299C						.	T		1,3575		0,1,1787	38	35	36		1299	-4.4	0	18		36	0,8102		0,0,4051	no	coding-synonymous	DSG2	NM_001943.3		0,1,5838	CC,CT,TT		0.0,0.028,0.0086		433/1119	29115251	1,11677	1788	4051	5839	SO:0001819	synonymous_variant	1829	exon10			AGAAGATAGAGAT	Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"Cadherins / Major cadherins"	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.1299T>C	chr18.hg19:g.29115251T>C		88.0	0.0		81.0	19.0	NM_001943	Q4KKU6	Silent	SNP	ENST00000261590.8	hg19	CCDS42423.1																																																																																			.	.		0.308	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943		C	29115251	T	C	29115251	2	2	131	1	0	0	0	0	0	0	0	1	4779	1403	49	2		2	DSG2	18	29115251	Silent	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	144083	29115251	48961997	121	21410										
RPRD1A	55197	hgsc.bcm.edu	37	chr18	33573185	33573185	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	agtgacattgggcaatcgagAtaagtctggcaggctctgga	14	7	2	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr18:33573185A>G	ENST00000399022.4	-	7	1039	c.868T>C	c.(868-870)Tct>Cct	p.S290P	RPRD1A_ENST00000337059.5_Missense_Mutation_p.S254P|RPRD1A_ENST00000357384.4_Missense_Mutation_p.S290P|RPRD1A_ENST00000590898.1_Missense_Mutation_p.S254P|RPRD1A_ENST00000588737.1_Missense_Mutation_p.S254P	NM_018170.3	NP_060640.2	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing 1A	290					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(2)	12						GGCAATCGAGATAAGTCTGGC	0.537																																					p.S290P		Atlas-SNP	.											.	RPRD1A	30	.	0			c.T868C						.						110	100	103					18																	33573185		2203	4300	6503	SO:0001583	missense	55197	exon7			ATCGAGATAAGTC	AF419845	CCDS11917.1	18q12.2	2012-02-09	2008-08-15		ENSG00000141425	ENSG00000141425			25560	protein-coding gene	gene with protein product	"cyclin-dependent kinase 2B-inhibitor-related protein", "Cyclin-dependent kinase inhibitor 2B-related protein (p15INK4B-related protein)"	610347				12470661, 22231121	Standard	NM_018170		Approved	P15RS, FLJ10656, HsT3101	uc002kzg.3	Q96P16	OTTHUMG00000132591	ENST00000399022.4:c.868T>C	chr18.hg19:g.33573185A>G	ENSP00000381984:p.Ser290Pro	101.0	0.0		127.0	40.0	NM_018170	A8KA42|B2RBA3|Q7Z5G8|Q96FY9|Q9NVL4	Missense_Mutation	SNP	ENST00000399022.4	hg19	CCDS11917.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.040668	0.75732	.	.	ENSG00000141425	ENST00000399022;ENST00000357384;ENST00000337059	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.76572	0.4006	M	0.66939	2.045	0.80722	D	1	D;D	0.76494	0.99;0.999	P;D	0.74348	0.811;0.983	T	0.78163	-0.2311	9	0.56958	D	0.05	-10.0903	14.0823	0.64932	1.0:0.0:0.0:0.0	.	290;254	Q96P16;Q96P16-3	RPR1A_HUMAN;.	P	290;290;254	.	ENSP00000337476:S254P	S	-	1	0	RPRD1A	31827183	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.157000	0.94714	2.218000	0.71995	0.533000	0.62120	TCT	.	.		0.537	RPRD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255802.1	NM_018170		G	33573185	A	G	33573185	3	3	131	1	0	0	0	0	1	0	0	0	13630	333	12	2	74	2	RPRD1A	18	33573185	Missense_Mutation	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	4457934	33573185	44504063	122	21411										
TUBB4	10382	hgsc.bcm.edu	37	chr19	6495192	6495193	+	Missense_Mutation	DNP	CC	CC	GG													0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	agcctaggccacctcctcctCcgcctcctcctcgaactcgc					rs201070507		TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr19:6495192_6495193CC>GG	ENST00000264071.2	-	4	1688_1689	c.1317_1318GG>CC	c.(1315-1320)gcGGag>gcCCag	p.E440Q	CTD-2396E7.9_ENST00000599292.1_RNA|TUBB4A_ENST00000540257.1_Missense_Mutation_p.E440Q|CTD-2396E7.10_ENST00000596027.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	440					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)										ACCTCCTCCTCCGCCTCCTCCT	0.624																																					p.E440Q|p.A439A		Atlas-SNP	.											.	.	.	.	0			c.G1318C|c.G1317C						.																																			SO:0001583	missense	10382	exon4			CCTCCTCCGCCTC|CTCCTCCGCCTCC	AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"Tubulins"	20774	protein-coding gene	gene with protein product	"class IVa beta-tubulin"	602662	"tubulin, beta 4", "tubulin, beta 4 class IVa", "dystonia 4, torsion (autosomal dominant)"	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.1317_1318delinsGG	chr19.hg19:g.6495192_6495193delinsGG	ENSP00000264071:p.Glu440Gln	142.0	0.0		164.0|165.0	35.0|38.0	NM_006087	B3KQP4|Q969E5	Missense_Mutation|Silent	SNP	ENST00000264071.2	hg19	CCDS12168.1																																																																																			.	.|C|0.999;T|0.001		0.624	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		GG	6495193	CC	GG	6495192	3	3	131	1	0	0	0	0	1	0	0	0	16773	864	30	4	20	4	TUBB4	19	6495192	Missense_Mutation	DNP	CC	TCGA-DD-A4NI-01A-11D-A27I-10		6495192	52633791	123	21412										
C3	718	hgsc.bcm.edu	37	chr19	6693493	6693493	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tctgaaggccagctgctgggTgtaccctgcagagaagagag	15	9	1	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr19:6693493T>C	ENST00000245907.6	-	25	3252	c.3160A>G	c.(3160-3162)Acc>Gcc	p.T1054A		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1054					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	AGCTGCTGGGTGTACCCTGCA	0.652																																					p.T1054A		Atlas-SNP	.											.	C3	192	.	0			c.A3160G						.						36	33	34					19																	6693493		2202	4300	6502	SO:0001583	missense	718	exon25			GCTGGGTGTACCC	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.3160A>G	chr19.hg19:g.6693493T>C	ENSP00000245907:p.Thr1054Ala	29.0	0.0		40.0	21.0	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.450423	0.01080	.	.	ENSG00000125730	ENST00000245907	T	0.31510	1.49	5.52	2.25	0.28309	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.309452	0.39020	N	0.001481	T	0.14399	0.0348	N	0.20881	0.62	0.09310	N	0.999998	B	0.11235	0.004	B	0.12156	0.007	T	0.16958	-1.0385	10	0.16896	T	0.51	.	1.7163	0.02902	0.1373:0.1575:0.1423:0.5629	.	1054	P01024	CO3_HUMAN	A	1054	ENSP00000245907:T1054A	ENSP00000245907:T1054A	T	-	1	0	C3	6644493	0.567000	0.26626	0.998000	0.56505	0.235000	0.25334	0.338000	0.19858	0.461000	0.27071	-0.280000	0.10049	ACC	.	.		0.652	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		C	6693493	T	C	6693493	3	2	131	1	0	0	0	0	1	0	0	0	2206	1696	59	2	1899	2	C3	19	6693493	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	198301	6693493	52435490	124	21413										
ZNF99	7652	hgsc.bcm.edu	37	chr19	22940609	22940610	+	Missense_Mutation	DNP	CC	CC	AA													0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cacatttgtagggtttctttCcagtatgaattatcttatgt							TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr19:22940609_22940610CC>AA	ENST00000596209.1	-	4	2191_2192	c.2101_2102GG>TT	c.(2101-2103)GGa>TTa	p.G701L	CTC-451A6.4_ENST00000442497.2_lincRNA|ZNF99_ENST00000397104.3_Missense_Mutation_p.G610L	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	701					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GGGTTTCTTTCCAGTATGAATT	0.361																																					p.G701V|p.G701X		Atlas-SNP	.											.	ZNF99	273	.	0			c.G2102T|c.G2101T						.																																			SO:0001583	missense	7652	exon4			TTCTTTCCAGTAT|TCTTTCCAGTATG	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2101_2102delinsAA	chr19.hg19:g.22940609_22940610delinsAA	ENSP00000472969:p.Gly701Leu	21.0	0.0		33.0	9.0	NM_001080409	M0R335	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1																																																																																			.	.		0.361	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		AA	22940610	CC	AA	22940609	3	1	131	1	0	0	0	0	1	0	0	0	18219	855	30	3	1295	3	ZNF99	19	22940609	Missense_Mutation	DNP	CC	TCGA-DD-A4NI-01A-11D-A27I-10	16247116	22940609	36188374	125	21414										
SARS2	54938	hgsc.bcm.edu	37	chr19	39421333	39421333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cccggggccggaacccccgaCgagtcagcaaaggccacaag	13	16	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr19:39421333C>T	ENST00000221431.6	-	1	203	c.44G>A	c.(43-45)cGt>cAt	p.R15H	SARS2_ENST00000430193.3_Missense_Mutation_p.R15H|SARS2_ENST00000594171.1_5'Flank|SARS2_ENST00000600042.1_Missense_Mutation_p.R15H|CTC-360G5.8_ENST00000599996.1_Intron|MRPS12_ENST00000407800.2_5'Flank|MRPS12_ENST00000402029.3_5'Flank|MRPS12_ENST00000308018.4_5'UTR|SARS2_ENST00000448145.2_Intron	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	15					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			GAACCCCCGACGAGTCAGCAA	0.602											OREG0025455	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R15H		Atlas-SNP	.											.	SARS2	33	.	0			c.G44A						.						40	38	39					19																	39421333		2203	4299	6502	SO:0001583	missense	54938	exon1			CCCCGACGAGTCA	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"Aminoacyl tRNA synthetases / Class II"	17697	protein-coding gene	gene with protein product	"serine tRNA ligase 2, mitochondrial"	612804	"serine-tRNA ligase, mitochondrial", "seryl-tRNA synthetase 2"	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.44G>A	chr19.hg19:g.39421333C>T	ENSP00000221431:p.Arg15His	56.0	0.0	885	67.0	33.0	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Missense_Mutation	SNP	ENST00000221431.6	hg19	CCDS33017.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028488	0.54790	.	.	ENSG00000104835	ENST00000430193;ENST00000221431;ENST00000455102	T;T;T	0.56941	0.44;0.43;1.28	5.35	-0.894	0.10563	.	1.643000	0.02821	N	0.125534	T	0.44095	0.1277	L	0.44542	1.39	.	.	.	B;B;B	0.21753	0.06;0.019;0.019	B;B;B	0.12837	0.008;0.001;0.001	T	0.34129	-0.9841	9	0.59425	D	0.04	.	5.3226	0.15889	0.1352:0.3443:0.4405:0.08	.	15;15;15	B4DJP6;B4DE10;Q9NP81	.;.;SYSM_HUMAN	H	15	ENSP00000406754:R15H;ENSP00000221431:R15H;ENSP00000414954:R15H	ENSP00000221431:R15H	R	-	2	0	FBXO17	44113173	0.000000	0.05858	0.000000	0.03702	0.209000	0.24338	-0.042000	0.12063	-0.065000	0.13021	-0.140000	0.14226	CGT	.	.		0.602	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827		T	39421333	C	T	39421333	3	4	131	1	0	0	0	0	1	0	0	0	13860	536	19	1	1657	1	SARS2	19	39421333	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	16480724	39421333	19707650	126	21415										
ZNF180	7733	hgsc.bcm.edu	37	chr19	44980916	44980916	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ccagtatgagttctctgatgTacaacaagaacataactctg	7	9	2	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr19:44980916T>A	ENST00000221327.4	-	5	2063	c.1782A>T	c.(1780-1782)gtA>gtT	p.V594V	ZNF180_ENST00000592529.1_Silent_p.V567V|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Silent_p.V569V	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	594					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				TTCTCTGATGTACAACAAGAA	0.418																																					p.V594V	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.A1782T						.						108	110	109					19																	44980916		2203	4300	6503	SO:0001819	synonymous_variant	7733	exon5			CTGATGTACAACA	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1782A>T	chr19.hg19:g.44980916T>A		62.0	0.0		92.0	39.0	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	hg19	CCDS12639.1																																																																																			.	.		0.418	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		A	44980916	T	A	44980916	2	1	131	1	0	0	0	0	0	0	0	1	17763	1625	57	4		4	ZNF180	19	44980916	Silent	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	5559583	44980916	14148067	127	21416										
KCNA7	3743	hgsc.bcm.edu	37	chr19	49573780	49573780	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cacgcatggaggcccgaagcGtctggcccaagatttgcagg	14	12	1	1	rs376824241		TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr19:49573780G>A	ENST00000221444.1	-	2	1266	c.911C>T	c.(910-912)aCg>aTg	p.T304M		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	304					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	GGCCCGAAGCGTCTGGCCCAA	0.577																																					p.T304M	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											KCNA7,NS,carcinoma,0,1	KCNA7	30	.	0			c.C911T						.	G	MET/THR	0,4406		0,0,2203	59	57	57		911	4.5	1	19		57	1,8599	1.2+/-3.3	0,1,4299	no	missense	KCNA7	NM_031886.2	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	304/457	49573780	1,13005	2203	4300	6503	SO:0001583	missense	3743	exon2			CGAAGCGTCTGGC	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.911C>T	chr19.hg19:g.49573780G>A	ENSP00000221444:p.Thr304Met	115.0	1.0		133.0	10.0	NM_031886	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	hg19	CCDS12755.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.437991	0.83885	0.0	1.16E-4	ENSG00000104848	ENST00000221444	D	0.98512	-4.97	4.54	4.54	0.55810	Ion transport (1);	0.101147	0.64402	D	0.000003	D	0.99381	0.9782	H	0.97940	4.11	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.98294	1.0515	10	0.87932	D	0	.	16.4224	0.83771	0.0:0.0:1.0:0.0	.	304	Q96RP8	KCNA7_HUMAN	M	304	ENSP00000221444:T304M	ENSP00000221444:T304M	T	-	2	0	KCNA7	54265592	1.000000	0.71417	0.954000	0.39281	0.994000	0.84299	9.820000	0.99359	2.264000	0.75181	0.491000	0.48974	ACG	.	.		0.577	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886		A	49573780	G	A	49573780	3	1	131	1	0	0	0	0	1	0	0	0	8017	1145	40	1	463	1	KCNA7	19	49573780	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	4592864	49573780	9555203	128	21417										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53644386	53644386	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ttacatttgtaaggtttttcTccagtatggatgacctgatg	9	6	1	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr19:53644386T>A	ENST00000334197.7	-	5	1763	c.1695A>T	c.(1693-1695)ggA>ggT	p.G565G	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000452676.2_Silent_p.G566G|ZNF347_ENST00000601469.2_Silent_p.G566G	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	565					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		AAGGTTTTTCTCCAGTATGGA	0.408																																					p.G566G	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											ZNF347,NS,carcinoma,0,1	ZNF347	87	.	0			c.A1698T						.						156	149	152					19																	53644386		2203	4300	6503	SO:0001819	synonymous_variant	84671	exon5			TTTTTCTCCAGTA	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.1695A>T	chr19.hg19:g.53644386T>A		90.0	0.0		104.0	6.0	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Silent	SNP	ENST00000334197.7	hg19	CCDS33097.1																																																																																			.	.		0.408	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		A	53644386	T	A	53644386	2	1	131	1	0	0	0	0	0	0	0	1	17876	1538	54	4		4	ZNF347	19	53644386	Silent	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10	4070606	53644386	5484597	129	21418										
LENG8	114823	hgsc.bcm.edu	37	chr19	54967843	54967843	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tggcgcccaccaagcgcagtCgaaagaagatggcggcgctg	15	12	0	2			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr19:54967843C>A	ENST00000326764.5	+	11	1953	c.1474C>A	c.(1474-1476)Cga>Aga	p.R492R	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	455										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		CAAGCGCAGTCGAAAGAAGAT	0.677																																					p.R492R		Atlas-SNP	.											.	LENG8	73	.	0			c.C1474A						.						16	21	19					19																	54967843		2196	4291	6487	SO:0001819	synonymous_variant	114823	exon11			CGCAGTCGAAAGA	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1474C>A	chr19.hg19:g.54967843C>A		60.0	0.0		93.0	29.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Silent	SNP	ENST00000326764.5	hg19	CCDS12894.1																																																																																			.	.		0.677	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		A	54967843	C	A	54967843	2	1	131	1	0	0	0	0	0	0	0	1	8733	876	31	1		1	LENG8	19	54967843	Silent	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	1323457	54967843	4161140	130	21419										
SYT5	6861	hgsc.bcm.edu	37	chr19	55686689	55686689	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	catgaccagcaccctgccccCcagctccacgtaggggacct	9	19	0	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr19:55686689C>A	ENST00000354308.3	-	6	928	c.559G>T	c.(559-561)Ggg>Tgg	p.G187W	SYT5_ENST00000592935.1_5'Flank|SYT5_ENST00000537500.1_Missense_Mutation_p.G187W|CTD-2587H24.5_ENST00000591665.1_RNA|SYT5_ENST00000590851.1_Missense_Mutation_p.G184W	NM_003180.2	NP_003171.2	O00445	SYT5_HUMAN	synaptotagmin V	187	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|dense core granule (GO:0031045)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		ACCCTGCCCCCCAGCTCCACG	0.617																																					p.G187W		Atlas-SNP	.											.	SYT5	45	.	0			c.G559T						.						35	30	32					19																	55686689		2202	4300	6502	SO:0001583	missense	6861	exon6			TGCCCCCCAGCTC	X96783	CCDS12919.1, CCDS74455.1	19q13.42	2014-07-02			ENSG00000129990	ENSG00000129990		"Synaptotagmins"	11513	protein-coding gene	gene with protein product	"synaptotagmin 5"	600782				9177789	Standard	XM_006723338		Approved		uc002qjn.1	O00445	OTTHUMG00000180669	ENST00000354308.3:c.559G>T	chr19.hg19:g.55686689C>A	ENSP00000346265:p.Gly187Trp	35.0	0.0		56.0	12.0	NM_003180	B3KWJ8|B7Z300|Q86X72	Missense_Mutation	SNP	ENST00000354308.3	hg19	CCDS12919.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.016193	0.93404	.	.	ENSG00000129990	ENST00000537500;ENST00000354308;ENST00000543844	T;T	0.69435	-0.4;-0.4	4.26	4.26	0.50523	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	0.000000	0.85682	D	0.000000	T	0.76877	0.4049	L	0.46947	1.48	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	0.995;1.0;0.995	T	0.79490	-0.1782	10	0.66056	D	0.02	.	16.3268	0.82986	0.0:1.0:0.0:0.0	.	184;187;187	B7Z300;Q4FD32;O00445	.;.;SYT5_HUMAN	W	187;187;184	ENSP00000442896:G187W;ENSP00000346265:G187W	ENSP00000346265:G187W	G	-	1	0	SYT5	60378501	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	5.861000	0.69553	2.329000	0.79093	0.555000	0.69702	GGG	.	.		0.617	SYT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452501.1	NM_003180		A	55686689	C	A	55686689	3	1	131	1	0	0	0	0	1	0	0	0	15492	623	22	3	617	3	SYT5	19	55686689	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	718846	55686689	3442294	131	21420										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33334661	33334661	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tagggcctgagttatccaagTtaattccttgttctccaggc	9	10	1	1	rs17092079	byFrequency	TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr20:33334661T>G	ENST00000374796.2	-	11	5434	c.2864A>C	c.(2863-2865)aAc>aCc	p.N955T	NCOA6_ENST00000359003.2_Missense_Mutation_p.N955T			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	955	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.		N -> S (in dbSNP:rs17092079). {ECO:0000269|PubMed:10567404, ECO:0000269|PubMed:10681503, ECO:0000269|PubMed:10823961, ECO:0000269|PubMed:10866662, ECO:0000269|PubMed:8724849}.		brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						GTTATCCAAGTTAATTCCTTG	0.418																																					p.N955T		Atlas-SNP	.											.	NCOA6	219	.	0			c.A2864C						.						93	91	92					20																	33334661		2203	4300	6503	SO:0001583	missense	23054	exon10			TCCAAGTTAATTC	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.2864A>C	chr20.hg19:g.33334661T>G	ENSP00000363929:p.Asn955Thr	59.0	0.0		58.0	6.0	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	hg19	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.939720	0.73557	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.23552	1.9;1.9	5.89	4.73	0.59995	.	0.163888	0.42420	D	0.000713	T	0.14227	0.0344	N	0.19112	0.55	0.36170	P	0.15127199999999996	B	0.22346	0.068	B	0.13407	0.009	T	0.12218	-1.0556	9	0.26408	T	0.33	-6.7525	7.6213	0.28187	0.0:0.0698:0.2543:0.6758	.	955	Q14686	NCOA6_HUMAN	T	955	ENSP00000363929:N955T;ENSP00000351894:N955T	ENSP00000351894:N955T	N	-	2	0	NCOA6	32798322	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.065000	0.30592	2.246000	0.74042	0.533000	0.62120	AAC	.	T|0.927;C|0.073		0.418	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		G	33334661	T	G	33334661	3	3	131	1	0	0	0	0	1	0	0	0	10242	1725	60	5	3351	5	NCOA6	20	33334661	Missense_Mutation	SNP	T	TCGA-DD-A4NI-01A-11D-A27I-10		33334661	29690859	132	21421										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46255749	46255749	+	Frame_Shift_Del	DEL	T	T	-													0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	aacatatcctattttaggcaTtggatggtttcctatttgtg							TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr20:46255749delT	ENST00000371998.3	+	6	552	c.361delT	c.(361-363)ttgfs	p.L121fs	NCOA3_ENST00000372004.3_Frame_Shift_Del_p.L121fs|NCOA3_ENST00000497292.1_3'UTR|NCOA3_ENST00000341724.6_Frame_Shift_Del_p.L121fs|NCOA3_ENST00000371997.3_Frame_Shift_Del_p.L121fs			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	121	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						ATTTTAGGCATTGGATGGTTT	0.363																																					p.A120fs		Pindel	.											.	NCOA3	156	.	0			c.360delA						.						131	122	125					20																	46255749		2203	4300	6503	SO:0001589	frameshift_variant	8202	exon6			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.361delT	chr20.hg19:g.46255749delT	ENSP00000361066:p.Leu121fs	156.0	0.0		248.0	52.0	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Frame_Shift_Del	DEL	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.		0.363	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		-	46255749	T	-	46255749	7	5	131	1	0	1	0	1	0	0	0	0	10239	1490	52	0	375	0	NCOA3	20	46255749	Frame_Shift_Del	DEL	T	TCGA-DD-A4NI-01A-11D-A27I-10	12921088	46255749	16769771	133	21422										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50273555	50273555	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tcagcctgatcagtcacaccGttggactcatacacgggagt	10	12	4	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr20:50273555G>T	ENST00000338821.5	-	14	1692	c.1428C>A	c.(1426-1428)aaC>aaA	p.N476K	ATP9A_ENST00000311637.5_Missense_Mutation_p.N340K|ATP9A_ENST00000402822.1_Missense_Mutation_p.N355K	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	476					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.N476N(1)		breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CAGTCACACCGTTGGACTCAT	0.617																																					p.N476K		Atlas-SNP	.											ATP9A,colon,carcinoma,0,1	ATP9A	135	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1428A						.						113	83	93					20																	50273555		2203	4300	6503	SO:0001583	missense	10079	exon14			CACACCGTTGGAC	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1428C>A	chr20.hg19:g.50273555G>T	ENSP00000342481:p.Asn476Lys	152.0	0.0		209.0	22.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	hg19	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.375881	0.42105	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	D;D;D	0.96011	-3.88;-3.88;-3.88	5.02	-5.71	0.02413	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.86781	0.6015	N	0.04768	-0.165	0.58432	D	0.999997	B;P	0.46512	0.325;0.879	B;P	0.44597	0.072;0.454	T	0.81874	-0.0732	10	0.32370	T	0.25	-27.125	13.0906	0.59166	0.5748:0.0:0.4252:0.0	.	355;476	O75110-2;O75110	.;ATP9A_HUMAN	K	340;476;355	ENSP00000309086:N340K;ENSP00000342481:N476K;ENSP00000385875:N355K	ENSP00000309086:N340K	N	-	3	2	ATP9A	49706962	0.932000	0.31603	0.799000	0.32177	0.299000	0.27559	-0.051000	0.11885	-0.976000	0.03542	-1.595000	0.00837	AAC	.	.		0.617	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		T	50273555	G	T	50273555	3	4	131	1	0	0	0	0	1	0	0	0	1198	1136	40	1	1775	1	ATP9A	20	50273555	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10	4017806	50273555	12751965	134	21423										
KRTAP6-3	337968	hgsc.bcm.edu	37	chr21	31964987	31964987	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	tctgtggctgtggctacagaGgcctggactgtggctatggc	16	9	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr21:31964987G>C	ENST00000391624.1	+	1	229	c.202G>C	c.(202-204)Ggc>Cgc	p.G68R	KRTAP22-2_ENST00000382830.2_5'Flank	NM_181605.3	NP_853636.3	Q3LI67	KRA63_HUMAN	keratin associated protein 6-3	68						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(7)	10						tggctacagaggcctggactg	0.602																																					p.G75R		Atlas-SNP	.											.	KRTAP6-3	30	.	0			c.G223C						.						53	64	61					21																	31964987		2203	4300	6503	SO:0001583	missense	337968	exon1			TACAGAGGCCTGG	AP001708		21q22.1	2012-04-19			ENSG00000212938	ENSG00000212938		"Keratin associated proteins"	18933	protein-coding gene	gene with protein product						12359730	Standard	NM_181605		Approved	KAP6.3	uc002yom.3	Q3LI67	OTTHUMG00000057791	ENST00000391624.1:c.202G>C	chr21.hg19:g.31964987G>C	ENSP00000375482:p.Gly68Arg	132.0	0.0		175.0	13.0	NM_181605	A4IF26	Missense_Mutation	SNP	ENST00000391624.1	hg19		.	.	.	.	.	.	.	.	.	.	G	0.204	-1.042036	0.01997	.	.	ENSG00000212938	ENST00000391624	T	0.32023	1.47	3.62	-4.04	0.04010	.	.	.	.	.	T	0.13372	0.0324	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.26710	-1.0095	9	0.87932	D	0	.	6.1497	0.20304	0.2934:0.1799:0.5267:0.0	.	68	Q3LI67	KRA63_HUMAN	R	68	ENSP00000375482:G68R	ENSP00000375482:G68R	G	+	1	0	KRTAP6-3	30886858	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.584000	0.05800	-0.714000	0.04975	-1.295000	0.01343	GGC	.	.		0.602	KRTAP6-3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128243.2	NM_181605		C	31964987	G	C	31964987	3	2	131	1	0	0	0	0	1	0	0	0	8580	1000	35	4	225	4	KRTAP6-3	21	31964987	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10		31964987	16164908	135	21424										
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26706735	26706735	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ggcctgctgagcgaaggcaaCaccatccgcatcgagttcac	11	14	1	1			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr22:26706735C>A	ENST00000248933.6	+	7	1709	c.1614C>A	c.(1612-1614)aaC>aaA	p.N538K	SEZ6L_ENST00000402979.1_Missense_Mutation_p.N311K|SEZ6L_ENST00000529632.2_Missense_Mutation_p.N538K|SEZ6L_ENST00000360929.3_Missense_Mutation_p.N538K|SEZ6L_ENST00000403121.1_Missense_Mutation_p.N311K|SEZ6L_ENST00000404234.3_Missense_Mutation_p.N538K|SEZ6L_ENST00000343706.4_Missense_Mutation_p.N538K			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	538	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GCGAAGGCAACACCATCCGCA	0.582																																					p.N538K		Atlas-SNP	.											.	SEZ6L	174	.	0			c.C1614A						.						146	114	125					22																	26706735		2203	4300	6503	SO:0001583	missense	23544	exon7			AGGCAACACCATC	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1614C>A	chr22.hg19:g.26706735C>A	ENSP00000248933:p.Asn538Lys	182.0	0.0		194.0	58.0	NM_021115	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	hg19	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	C	1.004	-0.689938	0.03328	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17;1.17;1.17	5.04	-3.65	0.04502	CUB (5);	0.757438	0.11620	N	0.545850	T	0.29620	0.0739	M	0.78456	2.415	0.20563	N	0.999886	B;B;B;B;B;B;B	0.31274	0.125;0.149;0.109;0.317;0.317;0.149;0.149	B;B;B;B;B;B;B	0.31390	0.129;0.079;0.049;0.108;0.108;0.079;0.079	T	0.29088	-1.0023	10	0.25751	T	0.34	.	2.7657	0.05319	0.1145:0.3387:0.1123:0.4345	.	538;538;311;538;538;538;538	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	K	538;538;538;538;538;311;311	ENSP00000384772:N538K;ENSP00000437037:N538K;ENSP00000354185:N538K;ENSP00000248933:N538K;ENSP00000342661:N538K;ENSP00000384838:N311K;ENSP00000384733:N311K	ENSP00000248933:N538K	N	+	3	2	SEZ6L	25036735	0.007000	0.16637	0.000000	0.03702	0.065000	0.16274	0.181000	0.16880	-0.192000	0.10432	0.561000	0.74099	AAC	.	.		0.582	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26706735	C	A	26706735	3	1	131	1	0	0	0	0	1	0	0	0	14158	477	17	3	1640	3	SEZ6L	22	26706735	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10		26706735	24597831	136	21425										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885446	29885446	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	gtctccagagaaggccaagtCcccagtgaaggaagaagcaa	12	10	1	3			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr22:29885446C>A	ENST00000310624.6	+	4	1850	c.1817C>A	c.(1816-1818)tCc>tAc	p.S606Y		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	606	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAGGCCAAGtccccagtgaag	0.562																																					p.S606Y		Atlas-SNP	.											.	NEFH	178	.	0			c.C1817A						.						66	63	64					22																	29885446		2203	4300	6503	SO:0001583	missense	4744	exon4			CCAAGTCCCCAGT		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1817C>A	chr22.hg19:g.29885446C>A	ENSP00000311997:p.Ser606Tyr	155.0	0.0		217.0	61.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	hg19	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.457677	0.43634	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	T	0.42900	0.96	5.81	4.79	0.61399	.	0.137016	0.34088	N	0.004264	T	0.55289	0.1911	M	0.68952	2.095	0.33210	D	0.553233	D	0.71674	0.998	D	0.66196	0.942	T	0.67280	-0.5710	10	0.87932	D	0	.	6.2363	0.20764	0.1565:0.6961:0.0:0.1474	.	606	P12036	NFH_HUMAN	Y	606	ENSP00000311997:S606Y	ENSP00000311997:S606Y	S	+	2	0	NEFH	28215446	0.134000	0.22483	0.984000	0.44739	0.598000	0.36846	1.971000	0.40530	2.747000	0.94245	0.650000	0.86243	TCC	.	.		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885446	C	A	29885446	3	1	131	1	0	0	0	0	1	0	0	0	10323	855	30	3	1831	3	NEFH	22	29885446	Missense_Mutation	SNP	C	TCGA-DD-A4NI-01A-11D-A27I-10	3178711	29885446	21419120	137	21426										
GRAMD4	23151	hgsc.bcm.edu	37	chr22	47073042	47073042	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	ggtggcatttcttccctgccAgccgctcgtgtttggtgcca	12	13	1	0			TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chr22:47073042A>T	ENST00000406902.1	+	19	1845		c.e19-1		GRAMD4_ENST00000408031.1_Splice_Site|GRAMD4_ENST00000361034.3_Splice_Site			Q6IC98	GRAM4_HUMAN	GRAM domain containing 4						apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	12		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)		CTTCCCTGCCAGCCGCTCGTG	0.627																																					.		Atlas-SNP	.											.	GRAMD4	53	.	0			c.1633-2A>T						.						97	87	90					22																	47073042		2202	4300	6502	SO:0001630	splice_region_variant	23151	exon18			CCTGCCAGCCGCT		CCDS33672.1	22q13.31	2008-03-03			ENSG00000075240	ENSG00000075240			29113	protein-coding gene	gene with protein product	"death-inducing-protein"	613691				15565177	Standard	NM_015124		Approved	KIAA0767, DIP	uc003bhx.3	Q6IC98	OTTHUMG00000150402	ENST00000406902.1:c.1633-1A>T	chr22.hg19:g.47073042A>T		71.0	0.0		93.0	6.0	NM_015124	A9IN51|A9IN57|Q68EN0|Q9UGE6|Q9Y4B9	Splice_Site	SNP	ENST00000406902.1	hg19	CCDS33672.1	.	.	.	.	.	.	.	.	.	.	.	16.55	3.154112	0.57259	.	.	ENSG00000075240	ENST00000406902;ENST00000361034;ENST00000408031	.	.	.	4.7	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0257	0.58814	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GRAMD4	45451706	1.000000	0.71417	0.998000	0.56505	0.553000	0.35397	6.328000	0.72915	1.748000	0.51833	0.374000	0.22700	.	.	.		0.627	GRAMD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317969.1	NM_015124	Intron	T	47073042	A	T	47073042	5	4	131	1	0	0	0	0	0	0	1	0	6761	202	7	4	1701	4	GRAMD4	22	47073042	Splice_Site	SNP	A	TCGA-DD-A4NI-01A-11D-A27I-10	17187596	47073042	4231524	138	21427										
CHM	1121	hgsc.bcm.edu	37	chrX	85302520	85302520	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0287769784172662	4	1	0.751606705095077	1.00997150997151	0.692551892551893	0.523809523809524	1	0	cgatcacatcaaactccgaaGggagagtatccgccatcttg	9	12	3	1	rs201252021		TCGA-DD-A4NI-01A-11D-A27I-10	TCGA-DD-A4NI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c154a63e-d2e1-4abb-83fe-62a5a5a70b33	63af893a-b381-43ba-8feb-c3221799df94	g.chrX:85302520G>A	ENST00000357749.2	-	1	46	c.17C>T	c.(16-18)cCt>cTt	p.P6L	CHM_ENST00000537751.1_5'UTR|CHM_ENST00000358786.4_Missense_Mutation_p.P6L|CHM_ENST00000467744.2_5'Flank	NM_000390.2	NP_000381.1	P24386	RAE1_HUMAN	choroideremia (Rab escort protein 1)	6					blood vessel development (GO:0001568)|protein geranylgeranylation (GO:0018344)|protein targeting to membrane (GO:0006612)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytosol (GO:0005829)|Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|prostate(1)	20		all_lung(315;5.41e-06)				AAACTCCGAAGGGAGAGTATC	0.458																																					p.P6L		Atlas-SNP	.											.	CHM	57	.	0			c.C17T	GRCh37	CD022133	CHM	D		.						123	72	89					X																	85302520		2203	4300	6503	SO:0001583	missense	1121	exon1			TCCGAAGGGAGAG	X78121	CCDS14454.1, CCDS48139.1	Xq21.1-q21.3	2014-09-17			ENSG00000188419	ENSG00000188419			1940	protein-coding gene	gene with protein product		300390		TCD, DXS540		1373238	Standard	XM_006724615		Approved	REP-1	uc004eet.3	P24386	OTTHUMG00000021937	ENST00000357749.2:c.17C>T	chrX.hg19:g.85302520G>A	ENSP00000350386:p.Pro6Leu	154.0	0.0		188.0	117.0	NM_001145414	A1L4D2|O43732	Missense_Mutation	SNP	ENST00000357749.2	hg19	CCDS14454.1	.	.	.	.	.	.	.	.	.	.	G	18.69	3.677800	0.68042	.	.	ENSG00000188419	ENST00000357749;ENST00000358786	T;T	0.61627	0.09;0.09	5.06	4.19	0.49359	.	0.130770	0.53938	D	0.000060	T	0.74966	0.3786	M	0.76002	2.32	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.78489	-0.2184	10	0.87932	D	0	-10.0809	14.3456	0.66662	0.0:0.1453:0.8547:0.0	.	6;6	A1L4D2;P24386	.;RAE1_HUMAN	L	6	ENSP00000350386:P6L;ENSP00000362228:P6L	ENSP00000350386:P6L	P	-	2	0	CHM	85189176	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	4.355000	0.59424	1.096000	0.41439	0.600000	0.82982	CCT	.	.		0.458	CHM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057396.3	NM_000390		A	85302520	G	A	85302520	3	1	131	1	0	0	0	0	1	0	0	0	3352	1000	35	3	2027	3	CHM	23	85302520	Missense_Mutation	SNP	G	TCGA-DD-A4NI-01A-11D-A27I-10		85302520	69968040	139	21428										
PIK3CD	5293	hgsc.bcm.edu	37	chr1	9777146	9777146	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	agaaaccgcgtgccaaaccaCctcccattcctgcgaagaag	8	15	0	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr1:9777146C>T	ENST00000377346.4	+	7	1105	c.910C>T	c.(910-912)Cct>Tct	p.P304S	PIK3CD_ENST00000543390.1_5'Flank|PIK3CD_ENST00000536656.1_Missense_Mutation_p.P269S|PIK3CD_ENST00000361110.2_Missense_Mutation_p.P269S	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	304					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	TGCCAAACCACCTCCCATTCC	0.622																																					p.P304S		Atlas-SNP	.											.	PIK3CD	86	.	0			c.C910T						.						125	113	117					1																	9777146		2203	4300	6503	SO:0001583	missense	5293	exon7			AAACCACCTCCCA		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase, catalytic, delta polypeptide", "phosphoinositide-3-kinase C"	602839	"phosphoinositide-3-kinase, catalytic, delta polypeptide"			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.910C>T	chr1.hg19:g.9777146C>T	ENSP00000366563:p.Pro304Ser	238.0	0.0		260.0	94.0	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	hg19	CCDS104.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.186683	0.57909	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	T;T;T	0.66638	-0.22;-0.12;-0.22	5.16	5.16	0.70880	.	0.105658	0.64402	D	0.000003	T	0.67069	0.2854	N	0.19112	0.55	0.80722	D	1	B;D;P	0.76494	0.047;0.999;0.599	B;D;B	0.68765	0.024;0.96;0.356	T	0.60687	-0.7214	10	0.08837	T	0.75	-40.6061	16.807	0.85708	0.0:1.0:0.0:0.0	.	304;269;304	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	S	269;304;269;269	ENSP00000446444:P269S;ENSP00000366563:P304S;ENSP00000354410:P269S	ENSP00000353766:P269S	P	+	1	0	PIK3CD	9699733	1.000000	0.71417	0.971000	0.41717	0.009000	0.06853	7.264000	0.78432	2.415000	0.81967	0.491000	0.48974	CCT	.	.		0.622	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		T	9777146	C	T	9777146	3	4	132	1	0	0	0	0	1	0	0	0	11924	507	18	3	928	3	PIK3CD	1	9777146	Missense_Mutation	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10		9777146	239473475	1	21429										
SPEN	23013	hgsc.bcm.edu	37	chr1	16261862	16261862	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tcccaagggcaagccaccccAgcagtactgcatctacggcg	10	16	1	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr1:16261862A>G	ENST00000375759.3	+	11	9331	c.9127A>G	c.(9127-9129)Agc>Ggc	p.S3043G		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	3043					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		AAGCCACCCCAGCAGTACTGC	0.587																																					p.S3043G		Atlas-SNP	.											.	SPEN	374	.	0			c.A9127G						.						125	111	116					1																	16261862		2203	4300	6503	SO:0001583	missense	23013	exon11			CACCCCAGCAGTA		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.9127A>G	chr1.hg19:g.16261862A>G	ENSP00000364912:p.Ser3043Gly	691.0	0.0		785.0	160.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	6.109	0.388362	0.11581	.	.	ENSG00000065526	ENST00000375759	T	0.10573	2.86	5.54	5.54	0.83059	.	.	.	.	.	T	0.10294	0.0252	L	0.38838	1.175	0.30659	N	0.754629	B	0.31599	0.33	B	0.34779	0.189	T	0.09292	-1.0681	9	0.33940	T	0.23	-8.8625	8.3787	0.32457	0.8834:0.0:0.1166:0.0	.	3043	Q96T58	MINT_HUMAN	G	3043	ENSP00000364912:S3043G	ENSP00000364912:S3043G	S	+	1	0	SPEN	16134449	1.000000	0.71417	1.000000	0.80357	0.229000	0.25112	5.693000	0.68264	2.113000	0.64589	0.454000	0.30748	AGC	.	.		0.587	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16261862	A	G	16261862	3	3	132	1	0	0	0	0	1	0	0	0	15053	188	7	2	9169	2	SPEN	1	16261862	Missense_Mutation	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10	6484716	16261862	232988759	2	21430										
CD101	9398	hgsc.bcm.edu	37	chr1	117554255	117554255	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	cattagccctcacctgtgagGcatccaaagccacagcccaa	7	16	1	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr1:117554255G>C	ENST00000256652.4	+	3	566	c.508G>C	c.(508-510)Gca>Cca	p.A170P	CD101_ENST00000369470.1_Missense_Mutation_p.A170P	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	170	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CACCTGTGAGGCATCCAAAGC	0.502																																					p.A170P		Atlas-SNP	.											.	CD101	95	.	0			c.G508C						.						109	93	99					1																	117554255		2203	4300	6503	SO:0001583	missense	9398	exon3			TGTGAGGCATCCA	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.508G>C	chr1.hg19:g.117554255G>C	ENSP00000256652:p.Ala170Pro	139.0	0.0		234.0	33.0	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	hg19	CCDS891.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.097884	0.56075	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.64803	-0.12;-0.12	5.33	3.42	0.39159	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.500066	0.19450	N	0.113957	T	0.56702	0.2003	M	0.76170	2.325	0.30716	N	0.748722	D	0.54397	0.966	P	0.52386	0.697	T	0.57365	-0.7824	10	0.72032	D	0.01	0.0208	8.897	0.35470	0.0804:0.0:0.7719:0.1477	.	170	Q93033	IGSF2_HUMAN	P	170	ENSP00000256652:A170P;ENSP00000358482:A170P	ENSP00000256652:A170P	A	+	1	0	CD101	117355778	1.000000	0.71417	0.019000	0.16419	0.323000	0.28346	6.423000	0.73361	0.609000	0.30018	0.650000	0.86243	GCA	.	.		0.502	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		C	117554255	G	C	117554255	3	2	132	1	0	0	0	0	1	0	0	0	2964	1203	42	4	518	4	CD101	1	117554255	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	101292393	117554255	131696366	3	21431										
PYHIN1	149628	hgsc.bcm.edu	37	chr1	158906744	158906744	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tgttctactgaaaggattagAggtcatcaatgattatcatt	8	5	4	3			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr1:158906744A>G	ENST00000368140.1	+	2	289	c.44A>G	c.(43-45)gAg>gGg	p.E15G	PYHIN1_ENST00000368135.4_Missense_Mutation_p.E15G|PYHIN1_ENST00000368138.3_Missense_Mutation_p.E15G|PYHIN1_ENST00000392252.3_Missense_Mutation_p.E15G|PYHIN1_ENST00000392254.2_Missense_Mutation_p.E15G	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	15	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					AAAGGATTAGAGGTCATCAAT	0.294																																					p.E15G		Atlas-SNP	.											.	PYHIN1	208	.	0			c.A44G						.						51	54	53					1																	158906744		2203	4300	6503	SO:0001583	missense	149628	exon2			GATTAGAGGTCAT	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.44A>G	chr1.hg19:g.158906744A>G	ENSP00000357122:p.Glu15Gly	136.0	0.0		196.0	24.0	NM_152501	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Missense_Mutation	SNP	ENST00000368140.1	hg19	CCDS1178.1	.	.	.	.	.	.	.	.	.	.	A	13.51	2.259972	0.39995	.	.	ENSG00000163564	ENST00000458222;ENST00000368140;ENST00000368138;ENST00000392254;ENST00000392252;ENST00000368135	T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38	2.83	1.62	0.23740	Pyrin (2);	.	.	.	.	T	0.51041	0.1651	M	0.66297	2.02	0.09310	N	1	D;D;D;D;D	0.71674	0.998;0.998;0.998;0.998;0.978	D;D;D;D;P	0.76575	0.979;0.979;0.979;0.988;0.806	T	0.35351	-0.9792	9	0.87932	D	0	.	5.2315	0.15424	0.7443:0.0:0.0:0.2556	.	15;15;15;15;15	Q6K0P9-4;Q6K0P9-3;Q6K0P9-2;Q6K0P9;Q6K0P9-5	.;.;.;IFIX_HUMAN;.	G	15	ENSP00000407616:E15G;ENSP00000357122:E15G;ENSP00000357120:E15G;ENSP00000376083:E15G;ENSP00000376082:E15G;ENSP00000357117:E15G	ENSP00000357117:E15G	E	+	2	0	PYHIN1	157173368	0.003000	0.15002	0.000000	0.03702	0.004000	0.04260	2.003000	0.40844	0.262000	0.21774	0.460000	0.39030	GAG	.	.		0.294	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		G	158906744	A	G	158906744	3	3	132	1	0	0	0	0	1	0	0	0	12880	304	11	2	46	2	PYHIN1	1	158906744	Missense_Mutation	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10	41352489	158906744	90343877	4	21432										
FBXO28	23219	hgsc.bcm.edu	37	chr1	224345363	224345363	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ttcctcagggtccgggcagaAtgaggagtctcctcggaaac	13	11	2	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr1:224345363A>T	ENST00000366862.5	+	5	1065	c.1022A>T	c.(1021-1023)aAt>aTt	p.N341I	FBXO28_ENST00000424254.2_3'UTR	NM_015176.3	NP_055991.1	Q9NVF7	FBX28_HUMAN	F-box protein 28	341										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(2)|skin(1)	10	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		TCCGGGCAGAATGAGGAGTCT	0.453																																					p.N341I		Atlas-SNP	.											.	FBXO28	34	.	0			c.A1022T						.						93	99	97					1																	224345363		2203	4300	6503	SO:0001583	missense	23219	exon5			GGCAGAATGAGGA	AK001628	CCDS1539.1, CCDS44320.1	1q42.12	2011-08-12			ENSG00000143756	ENSG00000143756		"F-boxes /  "other""	29046	protein-coding gene	gene with protein product	"centromere protein 30"	609100				9455484	Standard	NM_015176		Approved	FLJ10766, KIAA0483, Fbx28, CENP-30	uc001hoh.3	Q9NVF7	OTTHUMG00000037495	ENST00000366862.5:c.1022A>T	chr1.hg19:g.224345363A>T	ENSP00000355827:p.Asn341Ile	156.0	0.0		244.0	11.0	NM_015176	E9PEM8|O75070	Missense_Mutation	SNP	ENST00000366862.5	hg19	CCDS1539.1	.	.	.	.	.	.	.	.	.	.	A	10.88	1.474774	0.26511	.	.	ENSG00000143756	ENST00000366862	.	.	.	5.97	-7.04	0.01578	.	0.777393	0.13127	N	0.411734	T	0.27933	0.0688	N	0.08118	0	0.25137	N	0.990525	B	0.19445	0.036	B	0.23018	0.043	T	0.02115	-1.1211	9	0.48119	T	0.1	-0.5652	20.0911	0.97820	0.3305:0.0:0.6695:0.0	.	341	Q9NVF7	FBX28_HUMAN	I	341	.	ENSP00000355827:N341I	N	+	2	0	FBXO28	222411986	0.030000	0.19436	0.008000	0.14137	0.966000	0.64601	0.228000	0.17814	-1.816000	0.01221	-0.256000	0.11100	AAT	.	.		0.453	FBXO28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091283.2	NM_015176		T	224345363	A	T	224345363	3	4	132	1	0	0	0	0	1	0	0	0	5746	101	4	4	1040	4	FBXO28	1	224345363	Missense_Mutation	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10	65438619	224345363	24905258	5	21433										
ASTL	431705	hgsc.bcm.edu	37	chr2	96803391	96803391	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ggccatctgggaagctggtaCcacaggctcctgcgcagctg	14	13	1	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr2:96803391C>T	ENST00000342380.2	-	2	103	c.104G>A	c.(103-105)gGt>gAt	p.G35D		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						GAAGCTGGTACCACAGGCTCC	0.612																																					p.G35D		Atlas-SNP	.											.	ASTL	59	.	0			c.G104A						.						101	92	95					2																	96803391		2203	4300	6503	SO:0001583	missense	431705	exon2			CTGGTACCACAGG	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"sperm acrosomal SLLP1 binding"	608860	"astacin-like metalloendopeptidase (M12 family)"			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.104G>A	chr2.hg19:g.96803391C>T	ENSP00000343674:p.Gly35Asp	66.0	0.0		80.0	11.0	NM_001002036		Missense_Mutation	SNP	ENST00000342380.2	hg19	CCDS33249.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.235015	0.22626	.	.	ENSG00000188886	ENST00000342380	T	0.63744	-0.06	4.51	-3.66	0.04489	.	0.851198	0.09622	N	0.777472	T	0.34978	0.0916	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.21314	-1.0249	10	0.13470	T	0.59	-0.5391	1.1629	0.01809	0.1376:0.2796:0.1849:0.3979	.	35	Q6HA08	ASTL_HUMAN	D	35	ENSP00000343674:G35D	ENSP00000343674:G35D	G	-	2	0	ASTL	96167118	0.000000	0.05858	0.031000	0.17742	0.937000	0.57800	-2.120000	0.01323	-0.411000	0.07530	0.558000	0.71614	GGT	.	.		0.612	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			T	96803391	C	T	96803391	3	4	132	1	0	0	0	0	1	0	0	0	1063	507	18	3	1222	3	ASTL	2	96803391	Missense_Mutation	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10		96803391	146395982	6	21434										
IL1F8	27177	hgsc.bcm.edu	37	chr2	113786633	113786633	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tcactgaattctgtgtctctAcaggctattaaatgaagagt	8	7	3	3			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr2:113786633A>T	ENST00000259213.4	-	4	251	c.144T>A	c.(142-144)tgT>tgA	p.C48*	IL36B_ENST00000327407.2_Nonsense_Mutation_p.C48*	NM_014438.3	NP_055253.2	Q9NZH7	IL36B_HUMAN	interleukin 36, beta	48					immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-1 receptor binding (GO:0005149)			kidney(1)|ovary(1)|pancreas(1)	3						CTGTGTCTCTACAGGCTATTA	0.433																																					p.C48X		Atlas-SNP	.											.	IL36B	69	.	0			c.T144A						.						118	110	113					2																	113786633		2203	4300	6503	SO:0001587	stop_gained	27177	exon4			GTCTCTACAGGCT	AF201833	CCDS2109.1, CCDS2110.1	2q14	2011-07-14	2011-06-06	2011-06-06	ENSG00000136696	ENSG00000136696		"Interleukins and interleukin receptors"	15564	protein-coding gene	gene with protein product		605508	"interleukin 1 family, member 8 (eta)"	IL1F8		10625660, 10512743, 16646978	Standard	NM_173178		Approved	FIL1, IL-1H2, IL-1F8, FILI-(ETA), IL1-ETA, IL1H2, MGC126880, MGC126882	uc002tiq.1	Q9NZH7	OTTHUMG00000131338	ENST00000259213.4:c.144T>A	chr2.hg19:g.113786633A>T	ENSP00000259213:p.Cys48*	101.0	0.0		117.0	19.0	NM_173178	Q3MIH0|Q53SR6|Q7RTZ7|Q9UHA5	Nonsense_Mutation	SNP	ENST00000259213.4	hg19	CCDS2109.1	.	.	.	.	.	.	.	.	.	.	a	12.08	1.831231	0.32329	.	.	ENSG00000136696	ENST00000259213;ENST00000327407	.	.	.	3.75	-3.18	0.05186	.	0.377475	0.22942	N	0.053769	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1773	0.42946	0.5189:0.0:0.4811:0.0	.	.	.	.	X	48	.	ENSP00000259213:C48X	C	-	3	2	IL36B	113503104	0.003000	0.15002	0.000000	0.03702	0.026000	0.11368	-0.660000	0.05317	-1.235000	0.02545	-1.470000	0.01010	TGT	.	.		0.433	IL36B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254110.1	NM_014438		T	113786633	A	T	113786633	4	4	132	1	0	0	0	0	0	1	0	0	7665	389	14	4	579	4	IL1F8	2	113786633	Nonsense_Mutation	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10	16983242	113786633	129412740	7	21435										
GLI2	2736	hgsc.bcm.edu	37	chr2	121747764	121747764	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	gggagcgatgggcaacatggGgtcggtgcctccccagccgc	17	13	0	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr2:121747764G>T	ENST00000452319.1	+	14	4334	c.4274G>T	c.(4273-4275)gGg>gTg	p.G1425V	GLI2_ENST00000314490.11_Intron|GLI2_ENST00000361492.4_Missense_Mutation_p.G1425V					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GGCAACATGGGGTCGGTGCCT	0.652																																					p.G1425V		Atlas-SNP	.											.	GLI2	187	.	0			c.G4274T						.						37	40	39					2																	121747764		2202	4300	6502	SO:0001583	missense	2736	exon13			ACATGGGGTCGGT		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.4274G>T	chr2.hg19:g.121747764G>T	ENSP00000390436:p.Gly1425Val	93.0	0.0		140.0	55.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	0.017	-1.488371	0.01018	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.12984	2.63;2.63	4.57	-6.78	0.01721	.	1.596530	0.04137	N	0.318884	T	0.08358	0.0208	L	0.27053	0.805	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.30563	-0.9974	9	.	.	.	.	7.4423	0.27190	0.0:0.2279:0.4972:0.2749	.	1425;1080	P10070;P10070-2	GLI2_HUMAN;.	V	1425	ENSP00000390436:G1425V;ENSP00000354586:G1425V	.	G	+	2	0	GLI2	121464234	0.397000	0.25270	0.000000	0.03702	0.020000	0.10135	-0.232000	0.09055	-1.610000	0.01583	-0.538000	0.04264	GGG	.	.		0.652	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121747764	G	T	121747764	3	4	132	1	0	0	0	0	1	0	0	0	6446	1232	43	3	4324	3	GLI2	2	121747764	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	7961131	121747764	121451609	8	21436										
TTN	7273	hgsc.bcm.edu	37	chr2	179424403	179424403	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ttaatgtgtactttccagagTcatttctgttggcattttca	7	7	3	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr2:179424403T>C	ENST00000591111.1	-	276	81757	c.81533A>G	c.(81532-81534)gAc>gGc	p.D27178G	TTN_ENST00000342175.6_Missense_Mutation_p.D19946G|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D19754G|TTN_ENST00000589042.1_Missense_Mutation_p.D28819G|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D19879G|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D26251G|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592689.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27178	Ig-like 129.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTCCAGAGTCATTTCTGTT	0.423																																					p.D28819G		Atlas-SNP	.											.	TTN	18412	.	0			c.A86456G						.						172	161	165					2																	179424403		1984	4173	6157	SO:0001583	missense	7273	exon326			CCAGAGTCATTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.81533A>G	chr2.hg19:g.179424403T>C	ENSP00000465570:p.Asp27178Gly	164.0	0.0		134.0	22.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.50	2.552581	0.45487	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.93556	0.7943	H	0.97635	4.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.95666	0.8719	9	0.87932	D	0	.	16.383	0.83481	0.0:0.0:0.0:1.0	.	19754;19879;19946;27178	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	26251;19754;19946;19879;19751	ENSP00000343764:D26251G;ENSP00000434586:D19754G;ENSP00000340554:D19946G;ENSP00000352154:D19879G	ENSP00000340554:D19946G	D	-	2	0	TTN	179132649	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	8.040000	0.89188	2.326000	0.78906	0.533000	0.62120	GAC	.	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179424403	T	C	179424403	3	2	132	1	0	0	0	0	1	0	0	0	16750	1667	58	2	21671	2	TTN	2	179424403	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	57676639	179424403	63774970	9	21437										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189873705	189873705	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tggacctcctggtgcccctgGtccttgctgtggtggtgttg	15	11	0	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr2:189873705G>A	ENST00000304636.3	+	48	3751	c.3581G>A	c.(3580-3582)gGt>gAt	p.G1194D	COL3A1_ENST00000317840.5_Missense_Mutation_p.G891D	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	1194	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	GGTGCCCCTGGTCCTTGCTGT	0.552																																					p.G1194D		Atlas-SNP	.											.	COL3A1	292	.	0			c.G3581A						.						67	75	72					2																	189873705		2203	4300	6503	SO:0001583	missense	1281	exon48			CCCCTGGTCCTTG	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.3581G>A	chr2.hg19:g.189873705G>A	ENSP00000304408:p.Gly1194Asp	131.0	0.0		110.0	16.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	hg19	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.542311	0.85917	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.99429	-5.89;-5.89	5.54	5.54	0.83059	.	0.000000	0.52532	D	0.000068	D	0.99725	0.9893	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97543	1.0087	10	0.59425	D	0.04	.	19.4783	0.94998	0.0:0.0:1.0:0.0	.	1194	P02461	CO3A1_HUMAN	D	1194;891	ENSP00000304408:G1194D;ENSP00000315243:G891D	ENSP00000304408:G1194D	G	+	2	0	COL3A1	189581950	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.917000	0.75782	2.601000	0.87937	0.655000	0.94253	GGT	.	.		0.552	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		A	189873705	G	A	189873705	3	1	132	1	0	0	0	0	1	0	0	0	3690	1261	44	3	3771	3	COL3A1	2	189873705	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	10449302	189873705	53325668	10	21438										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220500541	220500541	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tgcgagatgcgctgcactccCagtgtgtggccgctgtgctc	14	13	0	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr2:220500541C>T	ENST00000358055.3	+	14	2631	c.2119C>T	c.(2119-2121)Cag>Tag	p.Q707*	SLC4A3_ENST00000273063.6_Nonsense_Mutation_p.Q734*|SLC4A3_ENST00000317151.3_Nonsense_Mutation_p.Q707*|SLC4A3_ENST00000373762.3_Nonsense_Mutation_p.Q734*|SLC4A3_ENST00000373760.2_Nonsense_Mutation_p.Q707*			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	707					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCTGCACTCCCAGTGTGTGGC	0.657																																					p.Q734X		Atlas-SNP	.											.	SLC4A3	144	.	0			c.C2200T						.						33	31	32					2																	220500541		2203	4300	6503	SO:0001587	stop_gained	6508	exon14			CACTCCCAGTGTG		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2119C>T	chr2.hg19:g.220500541C>T	ENSP00000350756:p.Gln707*	96.0	0.0		85.0	4.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Nonsense_Mutation	SNP	ENST00000358055.3	hg19	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	C	40	8.062091	0.98635	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151	.	.	.	4.09	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.8706	0.86039	0.0:1.0:0.0:0.0	.	.	.	.	X	707;707;734;734;707	.	ENSP00000273063:Q734X	Q	+	1	0	SLC4A3	220208785	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.602000	0.82796	2.264000	0.75181	0.643000	0.83706	CAG	.	.		0.657	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		T	220500541	C	T	220500541	4	4	132	1	0	0	0	0	0	1	0	0	14670	595	21	3	2250	3	SLC4A3	2	220500541	Nonsense_Mutation	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10	30626836	220500541	22698832	11	21439										
CIDEC	63924	hgsc.bcm.edu	37	chr3	9911995	9911995	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ggcttgtctgccagcatcagAgtgtcccggacctggggaat	14	11	2	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr3:9911995A>G	ENST00000336832.2	-	4	358	c.219T>C	c.(217-219)acT>acC	p.T73T	CIDEC_ENST00000430427.1_Silent_p.T83T|CIDEC_ENST00000423850.1_5'UTR|CIDEC_ENST00000443115.1_Intron|CIDEC_ENST00000455015.1_5'UTR|CIDEC_ENST00000383817.1_Intron	NM_001199552.1|NM_001199623.1|NM_022094.3	NP_001186481.1|NP_001186552.1|NP_071377.2	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	73	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|lipid particle organization (GO:0034389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	8	Medulloblastoma(99;0.227)					CCAGCATCAGAGTGTCCCGGA	0.562																																					p.T86T		Atlas-SNP	.											.	CIDEC	22	.	0			c.T258C						.						47	47	47					3																	9911995		2203	4300	6503	SO:0001819	synonymous_variant	63924	exon4			CATCAGAGTGTCC		CCDS2587.1, CCDS56239.1, CCDS74897.1	3p25	2004-07-26			ENSG00000187288	ENSG00000187288			24229	protein-coding gene	gene with protein product		612120				12429024	Standard	NM_001199623		Approved	CIDE-3, FLJ20871, Fsp27	uc021wsw.1	Q96AQ7	OTTHUMG00000128522	ENST00000336832.2:c.219T>C	chr3.hg19:g.9911995A>G		46.0	0.0		68.0	11.0	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Silent	SNP	ENST00000336832.2	hg19	CCDS2587.1																																																																																			.	.		0.562	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094		G	9911995	A	G	9911995	2	3	132	1	0	0	0	0	0	0	0	1	3429	291	11	2		2	CIDEC	3	9911995	Silent	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10		9911995	188110435	12	21440										
CAND2	23066	hgsc.bcm.edu	37	chr3	12861637	12861638	+	Missense_Mutation	DNP	GG	GG	CT													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	gcggtcaagttccttatctcGgaccagccccatcccattga					rs145134860	byFrequency	TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr3:12861637_12861638GG>CT	ENST00000456430.2	+	11	3038_3039	c.2997_2998GG>CT	c.(2995-3000)tcGGac>tcCTac	p.D1000Y	CAND2_ENST00000295989.5_Missense_Mutation_p.D907Y	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	1000					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TCCTTATCTCGGACCAGCCCCA	0.604																																					p.S999S|p.D1000Y	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.G2997C|c.G2998T						.																																			SO:0001583	missense	23066	exon11			TATCTCGGACCAG|ATCTCGGACCAGC		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	Exception_encountered	chr3.hg19:g.12861637_12861638delinsCT	ENSP00000387641:p.Asp1000Tyr	129.0|127.0	0.0		194.0	52.0	NM_001162499	B9EGM9|E9KL24	Silent|Missense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1																																																																																			.	G|0.999;A|0.001|.		0.604	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		CT	12861638	GG	CT	12861637	3	2	132	1	0	0	0	0	1	0	0	0	2618	1103	39	4	3039	4	CAND2	3	12861637	Missense_Mutation	DNP	GG	TCGA-DD-A4NJ-01A-11D-A27I-10	2949642	12861637	185160793	13	21441										
C3orf23	285343	hgsc.bcm.edu	37	chr3	44442771	44442771	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	gtgatccagcaaatctccagTggtttattctcaccaaagct	7	11	2	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr3:44442771T>A	ENST00000342649.4	+	10	1622	c.1195T>A	c.(1195-1197)Tgg>Agg	p.W399R	TCAIM_ENST00000417237.1_Missense_Mutation_p.W399R	NM_001282913.1|NM_173826.3	NP_001269842.1|NP_776187.2	Q8N3R3	TCAIM_HUMAN	T cell activation inhibitor, mitochondrial	399						mitochondrion (GO:0005739)											AAATCTCCAGTGGTTTATTCT	0.398																																					p.W399R		Atlas-SNP	.											.	.	.	.	0			c.T1195A						.						128	120	122					3																	44442771		2203	4300	6503	SO:0001583	missense	285343	exon10			CTCCAGTGGTTTA		CCDS2712.1, CCDS43076.1	3p21.33-p21.32	2012-08-22	2012-08-22	2012-08-22	ENSG00000179152	ENSG00000179152			25241	protein-coding gene	gene with protein product	"tolerance associated gene-1"		"chromosome 3 open reading frame 23"	C3orf23		12477932	Standard	NM_001029840		Approved	DKFZp313N0621, TOAG-1	uc003cnd.4	Q8N3R3	OTTHUMG00000133049	ENST00000342649.4:c.1195T>A	chr3.hg19:g.44442771T>A	ENSP00000341539:p.Trp399Arg	49.0	0.0		83.0	29.0	NM_173826	A8K9P1|Q0P5T9|Q495R1|Q495R3|Q4G0M4|Q6GMU8	Missense_Mutation	SNP	ENST00000342649.4	hg19	CCDS2712.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.686955	0.48097	.	.	ENSG00000179152	ENST00000417237;ENST00000342649	T;T	0.40476	1.03;1.03	5.6	5.6	0.85130	.	0.201692	0.46145	D	0.000315	T	0.41119	0.1145	L	0.51422	1.61	0.33990	D	0.649012	P	0.42203	0.773	B	0.40009	0.316	T	0.57423	-0.7814	10	0.40728	T	0.16	.	15.7878	0.78322	0.0:0.0:0.0:1.0	.	399	Q8N3R3	CC023_HUMAN	R	399	ENSP00000402581:W399R;ENSP00000341539:W399R	ENSP00000341539:W399R	W	+	1	0	C3orf23	44417775	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	3.058000	0.49939	2.135000	0.66039	0.454000	0.30748	TGG	.	.		0.398	TCAIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256655.2	NM_173826		A	44442771	T	A	44442771	3	1	132	1	0	0	0	0	1	0	0	0	2218	1696	59	4	1281	4	C3orf23	3	44442771	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	31581134	44442771	153579659	14	21442										
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101383939	101383939	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tctataagtatcatcatcagGgccaaagtctgtctttgctg	8	9	6	0	rs370264120		TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr3:101383939G>A	ENST00000312938.4	-	4	2072	c.1492C>T	c.(1492-1494)Cct>Tct	p.P498S	Y_RNA_ENST00000364251.1_RNA	NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TCATCATCAGGGCCAAAGTCT	0.408																																					p.P498S		Atlas-SNP	.											.	ZBTB11	77	.	0			c.C1492T						.	G	SER/PRO	1,4405	2.1+/-5.4	0,1,2202	205	188	194		1492	4.2	0	3		194	0,8600		0,0,4300	no	missense	ZBTB11	NM_014415.3	74	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	498/1054	101383939	1,13005	2203	4300	6503	SO:0001583	missense	27107	exon4			CATCAGGGCCAAA	U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.1492C>T	chr3.hg19:g.101383939G>A	ENSP00000326200:p.Pro498Ser	126.0	0.0		176.0	21.0	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	hg19	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	G	4.089	0.014463	0.07959	2.27E-4	0.0	ENSG00000066422	ENST00000312938	T	0.09630	2.96	6.03	4.24	0.50183	.	0.556311	0.21502	N	0.073515	T	0.06826	0.0174	N	0.14661	0.345	0.36524	D	0.870317	B	0.02656	0.0	B	0.04013	0.001	T	0.28235	-1.0050	10	0.26408	T	0.33	-2.6158	11.291	0.49250	0.0651:0.0:0.8069:0.128	.	498	O95625	ZBT11_HUMAN	S	498	ENSP00000326200:P498S	ENSP00000326200:P498S	P	-	1	0	ZBTB11	102866629	0.999000	0.42202	0.016000	0.15963	0.196000	0.23810	4.360000	0.59455	0.875000	0.35847	0.655000	0.94253	CCT	.	.		0.408	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		A	101383939	G	A	101383939	3	1	132	1	0	0	0	0	1	0	0	0	17539	1232	43	3	1701	3	ZBTB11	3	101383939	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	56941168	101383939	96638491	15	21443										
HTR3C	170572	hgsc.bcm.edu	37	chr3	183777775	183777776	+	Missense_Mutation	DNP	CC	CC	AA													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	cagcccagggagatgctgtcCcactgcgccccagaagggaa					rs556123764|rs575185101		TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr3:183777775_183777776CC>AA	ENST00000318351.1	+	8	1119_1120	c.1085_1086CC>AA	c.(1084-1086)cCC>cAA	p.P362Q		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	362					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	AGATGCTGTCCCACTGCGCCCC	0.639																																					p.P362H|p.P362P		Atlas-SNP	.											.	HTR3C	65	.	0			c.C1085A|c.C1086A						.																																			SO:0001583	missense	170572	exon8			GCTGTCCCACTGC|CTGTCCCACTGCG	AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24003	protein-coding gene	gene with protein product		610121	"5-hydroxytryptamine (serotonin) receptor 3, family member C"			12801637, 15157181	Standard	NM_130770		Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	Exception_encountered	chr3.hg19:g.183777775_183777776delinsAA	ENSP00000322617:p.Pro362Gln	66.0	0.0		65.0|66.0	26.0|28.0	NM_130770	A2RRR5	Missense_Mutation|Silent	SNP	ENST00000318351.1	hg19	CCDS3250.1																																																																																			.	.		0.639	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770		AA	183777776	CC	AA	183777775	3	1	132	1	0	0	0	0	1	0	0	0	7455	623	22	3	1115	3	HTR3C	3	183777775	Missense_Mutation	DNP	CC	TCGA-DD-A4NJ-01A-11D-A27I-10	82393836	183777775	14244655	16	21444										
DNAJB14	79982	hgsc.bcm.edu	37	chr4	100844269	100844270	+	Frame_Shift_Ins	INS	-	-	T													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	aaagcaagctttctataagcINSttttttcaaatcttcatcac							TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr4:100844269_100844270insT	ENST00000442697.2	-	3	532_533	c.378_379insA	c.(376-381)aaagctfs	p.A127fs	DNAJB14_ENST00000471738.1_5'Flank	NM_001031723.2|NM_001278310.1	NP_001026893.1|NP_001265239.1	Q8TBM8	DJB14_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 14	127	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5				OV - Ovarian serous cystadenocarcinoma(123;4.59e-09)		TTTCTATAAGCTTTTTTCAAAT	0.322																																					p.A127fs		Atlas-Indel,Pindel	.											.	DNAJB14	25	.	0			c.379_380insA						.																																			SO:0001589	frameshift_variant	79982	exon3			.	BC022248	CCDS34035.1, CCDS75171.1	4q23	2011-09-02			ENSG00000164031	ENSG00000164031		"Heat shock proteins / DNAJ (HSP40)"	25881	protein-coding gene	gene with protein product							Standard	NM_001031723		Approved	FLJ14281	uc003hvl.4	Q8TBM8	OTTHUMG00000131049	ENST00000442697.2:c.379dupA	chr4.hg19:g.100844275_100844275dupT	ENSP00000404381:p.Ala127fs	155.0	0.0		170.0	50.0	NM_001031723	Q6UXN1|Q7Z3P0|Q86TA7|Q86TM0|Q9GZU9	Frame_Shift_Ins	INS	ENST00000442697.2	hg19	CCDS34035.1																																																																																			.	.		0.322	DNAJB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253696.2	NM_001031723.2		T	100844270	-	T	100844269	7	5	132	1	0	1	1	0	0	0	0	0	4621	797	28	0	784	0	DNAJB14	4	100844269	Frame_Shift_Ins	INS	-	TCGA-DD-A4NJ-01A-11D-A27I-10		100844269	90310007	17	21445										
PCDH18	54510	hgsc.bcm.edu	37	chr4	138450774	138450774	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	acctcaacagcaggagtggcGtgggtgagttctaatgagaa	14	7	2	2	rs375416110		TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr4:138450774G>T	ENST00000344876.4	-	1	2855	c.2469C>A	c.(2467-2469)caC>caA	p.H823Q	PCDH18_ENST00000412923.2_Missense_Mutation_p.H823Q|PCDH18_ENST00000510305.1_Missense_Mutation_p.H34Q|PCDH18_ENST00000507846.1_Missense_Mutation_p.H603Q|PCDH18_ENST00000511115.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	823					brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					CAGGAGTGGCGTGGGTGAGTT	0.433																																					p.H823Q		Atlas-SNP	.											.	PCDH18	229	.	0			c.C2469A						.						115	98	104					4																	138450774		2203	4300	6503	SO:0001583	missense	54510	exon1			AGTGGCGTGGGTG	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2469C>A	chr4.hg19:g.138450774G>T	ENSP00000355082:p.His823Gln	180.0	0.0		170.0	56.0	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	hg19	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	G	3.416	-0.119248	0.06838	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846;ENST00000510305	T;T;T;T	0.53857	0.7;0.7;0.6;1.54	5.29	-3.59	0.04583	.	0.152169	0.30109	N	0.010383	T	0.41026	0.1141	L	0.57536	1.79	0.80722	D	1	P;B;P	0.43169	0.525;0.017;0.8	B;B;B	0.39503	0.117;0.017;0.301	T	0.48246	-0.9052	10	0.14252	T	0.57	.	12.94	0.58337	0.7311:0.0:0.2689:0.0	.	603;823;823	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	Q	823;823;603;34	ENSP00000355082:H823Q;ENSP00000390688:H823Q;ENSP00000425903:H603Q;ENSP00000424269:H34Q	ENSP00000355082:H823Q	H	-	3	2	PCDH18	138670224	0.046000	0.20272	0.922000	0.36590	0.997000	0.91878	-0.491000	0.06474	-0.906000	0.03866	-0.140000	0.14226	CAC	.	.		0.433	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		T	138450774	G	T	138450774	3	4	132	1	0	0	0	0	1	0	0	0	11522	1136	40	1	954	1	PCDH18	4	138450774	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	37606505	138450774	52703502	18	21446										
IRX1	79192	hgsc.bcm.edu	37	chr5	3599429	3599429	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	cttattacccctacggccagTtccaatacggggaccccggg	10	15	0	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr5:3599429T>A	ENST00000302006.3	+	2	419	c.367T>A	c.(367-369)Ttc>Atc	p.F123I	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	123					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CTACGGCCAGTTCCAATACGG	0.657																																					p.F123I		Atlas-SNP	.											.	IRX1	106	.	0			c.T367A						.						45	49	47					5																	3599429		2203	4300	6503	SO:0001583	missense	79192	exon2			GGCCAGTTCCAAT	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.367T>A	chr5.hg19:g.3599429T>A	ENSP00000305244:p.Phe123Ile	89.0	0.0		116.0	13.0	NM_024337	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	hg19	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.305560	0.81247	.	.	ENSG00000170549	ENST00000302006	T	0.57907	0.37	4.83	4.83	0.62350	Homeodomain-like (1);	0.152306	0.64402	D	0.000014	T	0.62986	0.2473	L	0.40543	1.245	0.58432	D	0.999998	D	0.76494	0.999	D	0.70227	0.968	T	0.64554	-0.6380	10	0.51188	T	0.08	.	14.3661	0.66807	0.0:0.0:0.0:1.0	.	123	P78414	IRX1_HUMAN	I	123	ENSP00000305244:F123I	ENSP00000305244:F123I	F	+	1	0	IRX1	3652429	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.672000	0.83956	1.902000	0.55061	0.533000	0.62120	TTC	.	.		0.657	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		A	3599429	T	A	3599429	3	1	132	1	0	0	0	0	1	0	0	0	7852	1725	60	4	373	4	IRX1	5	3599429	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10		3599429	177315831	19	21447										
C1QTNF3	114899	hgsc.bcm.edu	37	chr5	34024046	34024056	+	Frame_Shift_Del	DEL	CATAAGGTACA	CATAAGGTACA	-													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	aagactgtgttgccattgtgCataaggtacacatacacttc							TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	CATAAGGTACA	CATAAGGTACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr5:34024046_34024056delCATAAGGTACA	ENST00000231338.7	-	5	626_636	c.539_549delTGTACCTTATG	c.(538-549)gtgtaccttatgfs	p.VYLM180fs	C1QTNF3_ENST00000513065.1_5'UTR|C1QTNF3_ENST00000382065.3_Frame_Shift_Del_p.VYLM253fs|RP11-1084J3.4_ENST00000382079.3_Frame_Shift_Del_p.VYLM164fs	NM_030945.3	NP_112207.1	Q9BXJ4	C1QT3_HUMAN	C1q and tumor necrosis factor related protein 3	180	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				cellular triglyceride homeostasis (GO:0035356)|fat cell differentiation (GO:0045444)|negative regulation of gene expression (GO:0010629)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of cytokine secretion (GO:0050715)|protein trimerization (GO:0070206)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|prostate(3)|stomach(1)|urinary_tract(1)	17	all_lung(31;0.0207)					TGCCATTGTGCATAAGGTACACATACACTTC	0.412																																					p.253_257del		Pindel	.											.	C1QTNF3	31	.	0			c.759_769del						.																																			SO:0001589	frameshift_variant	114899	exon5			.	AF329837	CCDS3904.1, CCDS34141.1	5p13	2009-05-20			ENSG00000082196	ENSG00000082196			14326	protein-coding gene	gene with protein product	"cartonectin"	612045				18421280	Standard	NM_030945		Approved	CTRP3, Cors, Corcs, 2310005P21Rik, Cors-26	uc003jio.3	Q9BXJ4	OTTHUMG00000090735	ENST00000231338.7:c.539_549delTGTACCTTATG	chr5.hg19:g.34024046_34024056delCATAAGGTACA	ENSP00000231338:p.Val180fs	174.0	0.0		211.0	10.0	NM_181435	Q0VAN4|Q542Y2|Q6MZN1|Q96KY1	Frame_Shift_Del	DEL	ENST00000231338.7	hg19	CCDS3904.1																																																																																			.	.		0.412	C1QTNF3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207469.1	NM_030945		-	34024056	CATAAGGTACA	-	34024046	7	5	132	1	0	1	0	1	0	0	0	0	1966	710	25	0	199	0	C1QTNF3	5	34024046	Frame_Shift_Del	DEL	CATAAGGTACA	TCGA-DD-A4NJ-01A-11D-A27I-10	30424617	34024046	146891214	20	21448										
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79733987	79733987	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	atgtcccagagtcttctgatTgttgtgaaggttttattaat	9	5	2	3			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr5:79733987T>G	ENST00000338008.5	+	3	1663	c.1483T>G	c.(1483-1485)Tgt>Ggt	p.C495G	ZFYVE16_ENST00000505560.1_Missense_Mutation_p.C495G|ZFYVE16_ENST00000510158.1_Missense_Mutation_p.C495G	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	495					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		GTCTTCTGATTGTTGTGAAGG	0.403																																					p.C495G	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.T1483G						.						77	79	78					5																	79733987		2182	4294	6476	SO:0001583	missense	9765	exon4			TCTGATTGTTGTG	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"Zinc fingers, FYVE domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20756	protein-coding gene	gene with protein product	"endofin", "protein phosphatase 1, regulatory subunit 69"	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.1483T>G	chr5.hg19:g.79733987T>G	ENSP00000337159:p.Cys495Gly	89.0	0.0		139.0	7.0	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Missense_Mutation	SNP	ENST00000338008.5	hg19	CCDS4050.1	.	.	.	.	.	.	.	.	.	.	T	0.029	-1.346999	0.01266	.	.	ENSG00000039319	ENST00000338008;ENST00000510158;ENST00000505560	T;T;T	0.37584	1.19;1.19;1.19	5.41	-10.8	0.00216	.	2.616210	0.00923	N	0.002609	T	0.15522	0.0374	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.11891	-1.0569	10	0.18710	T	0.47	23.4448	14.2774	0.66189	0.0:0.4891:0.4265:0.0845	.	495;495	Q7Z3T8-3;Q7Z3T8	.;ZFY16_HUMAN	G	495	ENSP00000337159:C495G;ENSP00000423663:C495G;ENSP00000426848:C495G	ENSP00000337159:C495G	C	+	1	0	ZFYVE16	79769743	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-3.111000	0.00599	-1.981000	0.00989	0.533000	0.62120	TGT	.	.		0.403	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		G	79733987	T	G	79733987	3	3	132	1	0	0	0	0	1	0	0	0	17679	1812	63	5	1489	5	ZFYVE16	5	79733987	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	45709941	79733987	101181273	21	21449										
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140348025	140348025	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	caggacaaggggagcccaccActgagcagcactgtgactgc	13	13	0	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr5:140348025A>G	ENST00000289269.5	+	1	2206	c.1674A>G	c.(1672-1674)ccA>ccG	p.P558P	PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA12_ENST00000398631.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	558	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGCCCACCACTGAGCAGCA	0.527																																					p.P558P	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.A1674G						.						107	98	101					5																	140348025		2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			CCCACCACTGAGC	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"Cadherins / Protocadherins : Clustered"	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1674A>G	chr5.hg19:g.140348025A>G		129.0	0.0		160.0	55.0	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	hg19	CCDS4242.1																																																																																			.	.		0.527	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		G	140348025	A	G	140348025	2	3	132	1	0	0	0	0	0	0	0	1	11542	146	6	2		2	PCDHAC2	5	140348025	Silent	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10	60614038	140348025	40567235	22	21450										
DST	667	hgsc.bcm.edu	37	chr6	56494239	56494239	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tcatctacttcagatctccaTtgctaaaatacattaattgg	4	9	4	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr6:56494239T>A	ENST00000361203.3	-	28	3658	c.3651A>T	c.(3649-3651)caA>caT	p.Q1217H	DST_ENST00000370769.4_Missense_Mutation_p.Q1217H|DST_ENST00000312431.6_Missense_Mutation_p.Q1217H|DST_ENST00000421834.2_Missense_Mutation_p.Q1217H|DST_ENST00000370754.5_Missense_Mutation_p.Q1395H|DST_ENST00000370765.6_Missense_Mutation_p.Q891H|DST_ENST00000370788.2_Missense_Mutation_p.Q1217H|DST_ENST00000244364.6_Missense_Mutation_p.Q891H|DST_ENST00000518935.1_Missense_Mutation_p.Q891H|DST_ENST00000446842.2_Missense_Mutation_p.Q891H			Q03001	DYST_HUMAN	dystonin	1217					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CAGATCTCCATTGCTAAAATA	0.303																																					p.Q891H		Atlas-SNP	.											.	DST	1427	.	0			c.A2673T						.						83	79	80					6																	56494239		2203	4300	6503	SO:0001583	missense	667	exon18			TCTCCATTGCTAA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.3651A>T	chr6.hg19:g.56494239T>A	ENSP00000354508:p.Gln1217His	48.0	0.0		61.0	23.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	T	15.19	2.758896	0.49468	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;T;T;T;T;T;T;T	0.76709	-1.04;-0.04;-0.04;0.09;0.91;-1.04;0.06;-0.06;-1.04;-1.04;-1.04;-1.04	5.7	4.53	0.55603	.	0.000000	0.51477	D	0.000096	T	0.62036	0.2395	L	0.45228	1.405	0.29745	N	0.836787	P;P;P;B;B;B;P;B	0.49961	0.93;0.93;0.93;0.001;0.178;0.185;0.93;0.009	P;P;P;B;B;B;P;B	0.50440	0.635;0.641;0.635;0.002;0.108;0.281;0.635;0.012	T	0.60801	-0.7191	9	0.23302	T	0.38	.	8.245	0.31682	0.1327:0.0:0.1391:0.7281	.	1217;1217;1395;891;891;891;1217;891	Q5TBT1;E7ERU2;E9PEB9;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;DYST_HUMAN;.	H	891;1395;1217;1217;891;1217;1217;1217;891;1257;891;891	ENSP00000244364:Q891H;ENSP00000359790:Q1395H;ENSP00000359805:Q1217H;ENSP00000400883:Q1217H;ENSP00000393645:Q891H;ENSP00000307959:Q1217H;ENSP00000359824:Q1217H;ENSP00000354508:Q1217H;ENSP00000404924:Q891H;ENSP00000431030:Q1257H;ENSP00000359801:Q891H;ENSP00000431003:Q891H	ENSP00000244364:Q891H	Q	-	3	2	DST	56602198	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.112000	0.50368	0.968000	0.38212	0.533000	0.62120	CAA	.	.		0.303	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56494239	T	A	56494239	3	1	132	1	0	0	0	0	1	0	0	0	4785	1490	52	4	17750	4	DST	6	56494239	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10		56494239	114620828	23	21451										
ROS1	6098	hgsc.bcm.edu	37	chr6	117709158	117709158	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tctgccaggcagaagggcctAattcaaagagttcaataata	9	8	3	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr6:117709158A>C	ENST00000368508.3	-	13	1997	c.1799T>G	c.(1798-1800)tTa>tGa	p.L600*	ROS1_ENST00000368507.3_Intron|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	600	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AGAAGGGCCTAATTCAAAGAG	0.438			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.L600X		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.T1799G						.						100	101	101					6																	117709158		2203	4300	6503	SO:0001587	stop_gained	6098	exon13			GGGCCTAATTCAA	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.1799T>G	chr6.hg19:g.117709158A>C	ENSP00000357494:p.Leu600*	76.0	0.0		77.0	43.0	NM_002944	Q15368|Q5TDB5	Nonsense_Mutation	SNP	ENST00000368508.3	hg19	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	A	39	7.850165	0.98525	.	.	ENSG00000047936	ENST00000368508	.	.	.	4.56	0.781	0.18561	.	0.214637	0.23896	N	0.043500	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.5213	0.04681	0.4986:0.0:0.2954:0.206	.	.	.	.	X	600	.	ENSP00000357494:L600X	L	-	2	0	ROS1	117815851	0.846000	0.29590	0.978000	0.43139	0.960000	0.62799	0.993000	0.29680	0.224000	0.20940	0.459000	0.35465	TTA	.	.		0.438	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			C	117709158	A	C	117709158	4	2	132	1	0	0	0	0	0	1	0	0	13546	372	13	5	5368	5	ROS1	6	117709158	Nonsense_Mutation	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10	61214919	117709158	53405909	24	21452										
DPY19L1	23333	hgsc.bcm.edu	37	chr7	35013135	35013135	+	Missense_Mutation	SNP	T	T	C													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	gtcaaagttacctgagaataTgagtcactagcaacatctga							TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr7:35013135T>C	ENST00000310974.4	-	8	830	c.686A>G	c.(685-687)cAt>cGt	p.H229R	DPY19L1_ENST00000462134.2_5'UTR	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	229						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						CCTGAGAATATGAGTCACTAG	0.303																																					p.H229R		Atlas-SNP	.											.	DPY19L1	56	.	0			c.A686G						.						53	47	49					7																	35013135		1871	4119	5990	SO:0001583	missense	23333	exon8			AGAATATGAGTCA	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.686A>G	chr7.hg19:g.35013135T>C	ENSP00000308695:p.His229Arg	113.0	0.0		132.0	37.0	NM_015283	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	hg19	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	T	12.86	2.064056	0.36373	.	.	ENSG00000173852	ENST00000310974;ENST00000446375	T;T	0.54071	0.59;0.59	4.8	3.65	0.41850	.	0.130194	0.53938	N	0.000058	T	0.39306	0.1073	L	0.40543	1.245	0.27765	N	0.94369	B	0.06786	0.001	B	0.08055	0.003	T	0.23368	-1.0190	10	0.25751	T	0.34	-9.4722	8.1742	0.31272	0.0:0.0968:0.0:0.9032	.	229	Q2PZI1	D19L1_HUMAN	R	229;28	ENSP00000308695:H229R;ENSP00000400510:H28R	ENSP00000308695:H229R	H	-	2	0	DPY19L1	34979660	1.000000	0.71417	1.000000	0.80357	0.685000	0.39939	3.340000	0.52143	0.711000	0.32018	0.260000	0.18958	CAT	.	.		0.303	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			C	35013135	T	C	35013135	3	2	132	1	0	0	0	0	1	0	0	0	4742	1464	51	2	1401	2	DPY19L1	7	35013135	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10		35013135	124125528	25	21453	91	2								
DPY19L1	23333	hgsc.bcm.edu	37	chr7	35013143	35013143	+	Silent	SNP	T	T	C													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tacctgagaatatgagtcacTagcaacatctgaagaacaag					rs199681894	byFrequency	TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr7:35013143T>C	ENST00000310974.4	-	8	822	c.678A>G	c.(676-678)ctA>ctG	p.L226L	DPY19L1_ENST00000462134.2_5'UTR	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	226						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						TATGAGTCACTAGCAACATCT	0.313																																					p.L226L		Atlas-SNP	.											.	DPY19L1	56	.	0			c.A678G						.						53	48	50					7																	35013143		1876	4135	6011	SO:0001819	synonymous_variant	23333	exon8			AGTCACTAGCAAC	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.678A>G	chr7.hg19:g.35013143T>C		114.0	0.0		133.0	38.0	NM_015283	O94954|Q4G151	Silent	SNP	ENST00000310974.4	hg19	CCDS43567.1																																																																																			.	T|0.974;A|0.026		0.313	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			C	35013143	T	C	35013143	2	2	132	1	0	0	0	0	0	0	0	1	4742	1509	53	2		2	DPY19L1	7	35013143	Silent	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	8	35013143	124125520	26	21454	91	2								
PEG10	23089	hgsc.bcm.edu	37	chr7	94293118	94293118	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	agtgcccagaagacctcccaGagaagttcgatggcaaccca	10	13	0	3			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr7:94293118G>A	ENST00000482108.1	+	2	729	c.250G>A	c.(250-252)Gag>Aag	p.E84K	PEG10_ENST00000488574.1_Missense_Mutation_p.E84K	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	84	Necessary for interaction with ALK1.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			AGACCTCCCAGAGAAGTTCGA	0.572																																					p.E160K		Atlas-SNP	.											.	PEG10	36	.	0			c.G478A						.						56	60	59					7																	94293118		1991	4146	6137	SO:0001583	missense	23089	exon2			CTCCCAGAGAAGT	AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.250G>A	chr7.hg19:g.94293118G>A	ENSP00000417587:p.Glu84Lys	116.0	0.0		173.0	37.0	NM_001172438	Q96A68|Q9UPV1	Missense_Mutation	SNP	ENST00000482108.1	hg19	CCDS55126.1	.	.	.	.	.	.	.	.	.	.	G	17.52	3.410267	0.62399	.	.	ENSG00000242265	ENST00000482108;ENST00000488574	T;T	0.12361	2.69;2.69	4.25	4.25	0.50352	.	.	.	.	.	T	0.17492	0.0420	N	0.24115	0.695	0.25870	N	0.983723	D;D	0.61080	0.989;0.989	P;P	0.57548	0.823;0.823	T	0.10800	-1.0614	9	0.21540	T	0.41	.	12.3761	0.55281	0.0:0.0:1.0:0.0	.	160;84	B4DSP0;Q86TG7	.;PEG10_HUMAN	K	84	ENSP00000417587:E84K;ENSP00000418944:E84K	ENSP00000417587:E84K	E	+	1	0	PEG10	94131054	1.000000	0.71417	0.938000	0.37757	0.757000	0.42996	4.022000	0.57203	2.382000	0.81193	0.555000	0.69702	GAG	.	.		0.572	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340751.1	NM_015068		A	94293118	G	A	94293118	3	1	132	1	0	0	0	0	1	0	0	0	11728	943	33	3	484	3	PEG10	7	94293118	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	59279975	94293118	64845545	27	21455										
ASB10	136371	hgsc.bcm.edu	37	chr7	150878543	150878543	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	acctgaggagcagctccgcaCacctattggggggagacggt	15	11	0	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr7:150878543C>T	ENST00000420175.2	-	3	611	c.587G>A	c.(586-588)tGt>tAt	p.C196Y	ASB10_ENST00000422024.1_Missense_Mutation_p.C241Y|ASB10_ENST00000434669.1_Missense_Mutation_p.C241Y|ASB10_ENST00000377867.3_Missense_Mutation_p.C181Y|ASB10_ENST00000275838.1_Missense_Mutation_p.C196Y			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	196					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGCTCCGCACACCTATTGGG	0.642																																					p.C196Y		Atlas-SNP	.											.	ASB10	99	.	0			c.G587A						.						20	19	19					7																	150878543		2192	4279	6471	SO:0001583	missense	136371	exon3			TCCGCACACCTAT	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"Ankyrin repeat domain containing"	17185	protein-coding gene	gene with protein product		615054	"ankyrin repeat and SOCS box-containing 10", "glaucoma 1, open angle, F (adult-onset)"	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.587G>A	chr7.hg19:g.150878543C>T	ENSP00000391137:p.Cys196Tyr	82.0	0.0		111.0	41.0	NM_001142459	A0AVH0|Q6ZUL6	Missense_Mutation	SNP	ENST00000420175.2	hg19	CCDS47750.2	.	.	.	.	.	.	.	.	.	.	C	17.54	3.414789	0.62511	.	.	ENSG00000146926	ENST00000275838;ENST00000377867;ENST00000422024;ENST00000434669;ENST00000420175	T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17	5.14	5.14	0.70334	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.78426	0.4281	M	0.69463	2.115	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.80598	-0.1311	10	0.87932	D	0	-5.1831	17.951	0.89053	0.0:1.0:0.0:0.0	.	181;196;241	Q8WXI3-3;Q8WXI3;D5MNW9	.;ASB10_HUMAN;.	Y	196;181;241;241;196	ENSP00000275838:C196Y;ENSP00000367098:C181Y;ENSP00000401369:C241Y;ENSP00000398247:C241Y;ENSP00000391137:C196Y	ENSP00000275838:C196Y	C	-	2	0	ASB10	150509476	1.000000	0.71417	0.995000	0.50966	0.344000	0.29017	7.326000	0.79133	2.549000	0.85964	0.655000	0.94253	TGT	.	.		0.642	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871		T	150878543	C	T	150878543	3	4	132	1	0	0	0	0	1	0	0	0	1014	478	17	3	828	3	ASB10	7	150878543	Missense_Mutation	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10	56585425	150878543	8260120	28	21456										
UBR5	51366	hgsc.bcm.edu	37	chr8	103324043	103324043	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tgtaggaaaattattttcctGttctgcttttcctgtagcaa	7	7	1	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr8:103324043G>C	ENST00000520539.1	-	19	2944	c.2338C>G	c.(2338-2340)Cag>Gag	p.Q780E	UBR5_ENST00000220959.4_Missense_Mutation_p.Q780E|UBR5_ENST00000521922.1_Missense_Mutation_p.Q774E	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	780				Q -> R (in Ref. 2; AAF88143). {ECO:0000305}.	cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TTATTTTCCTGTTCTGCTTTT	0.403																																					p.Q780E	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.C2338G						.						99	96	97					8																	103324043		2203	4300	6503	SO:0001583	missense	51366	exon19			TTTCCTGTTCTGC	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.2338C>G	chr8.hg19:g.103324043G>C	ENSP00000429084:p.Gln780Glu	195.0	0.0		386.0	58.0	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	hg19	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.156767	0.78114	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	T;T;T	0.49432	0.78;0.78;0.78	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.57829	0.2080	L	0.54323	1.7	0.80722	D	1	P;P	0.40332	0.713;0.713	P;P	0.48654	0.585;0.585	T	0.60105	-0.7328	10	0.72032	D	0.01	.	19.2083	0.93744	0.0:0.0:1.0:0.0	.	774;780	E7EMW7;O95071	.;UBR5_HUMAN	E	780;780;774	ENSP00000429084:Q780E;ENSP00000220959:Q780E;ENSP00000427819:Q774E	ENSP00000220959:Q780E	Q	-	1	0	UBR5	103393219	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.563000	0.86464	0.655000	0.94253	CAG	.	.		0.403	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		C	103324043	G	C	103324043	3	2	132	1	0	0	0	0	1	0	0	0	16920	1386	48	4	6225	4	UBR5	8	103324043	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10		103324043	43039979	29	21457										
ADCY8	114	hgsc.bcm.edu	37	chr8	131949435	131949435	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	cccaggattttaatacgaagGcagtgatgctcctggaagga	12	8	0	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr8:131949435G>A	ENST00000286355.5	-	5	3457	c.1365C>T	c.(1363-1365)tgC>tgT	p.C455C	ADCY8_ENST00000377928.3_Silent_p.C455C|RP11-737F9.1_ENST00000523318.1_RNA	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	455					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TAATACGAAGGCAGTGATGCT	0.522										HNSCC(32;0.087)																											p.C455C		Atlas-SNP	.											.	ADCY8	291	.	0			c.C1365T						.						61	57	58					8																	131949435		2203	4300	6503	SO:0001819	synonymous_variant	114	exon5			ACGAAGGCAGTGA	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1365C>T	chr8.hg19:g.131949435G>A		135.0	0.0		225.0	50.0	NM_001115		Silent	SNP	ENST00000286355.5	hg19	CCDS6363.1																																																																																			.	.		0.522	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	131949435	G	A	131949435	2	1	132	1	0	0	0	0	0	0	0	1	300	1195	42	3		3	ADCY8	8	131949435	Silent	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	28625392	131949435	14414587	30	21458										
SLC45A4	57210	hgsc.bcm.edu	37	chr8	142231676	142231676	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ggtgtggccgagaaacttacCgatggcagagccgttaagga	15	8	0	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr8:142231676C>T	ENST00000024061.3	-	2	584	c.277G>A	c.(277-279)Ggt>Agt	p.G93S	SLC45A4_ENST00000433583.2_Splice_Site_p.G86S|SLC45A4_ENST00000517878.1_Splice_Site_p.G144S|SLC45A4_ENST00000519067.1_Splice_Site_p.G93S	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			AGAAACTTACCGATGGCAGAG	0.592																																					p.G93S		Atlas-SNP	.											.	SLC45A4	71	.	0			c.G277A						.						55	62	60					8																	142231676		2203	4300	6503	SO:0001630	splice_region_variant	57210	exon2			ACTTACCGATGGC	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"Solute carriers"	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.277+1G>A	chr8.hg19:g.142231676C>T		113.0	0.0		231.0	46.0	NM_001080431	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	hg19	CCDS34948.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.823106	0.71143	.	.	ENSG00000022567	ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061;ENST00000519986	D;D;D;D;D	0.96913	-4.17;-4.17;-4.17;-4.17;-4.17	5.46	4.59	0.56863	.	0.000000	0.85682	D	0.000000	D	0.95893	0.8663	M	0.67953	2.075	0.80722	D	1	D;D;P	0.58620	0.975;0.983;0.566	P;P;B	0.48368	0.518;0.575;0.127	D	0.94898	0.8054	9	.	.	.	-17.6448	14.4562	0.67418	0.0:0.9286:0.0:0.0714	.	144;93;93	E7EV90;Q5BKX6-3;Q5BKX6-2	.;.;.	S	93;144;86;93;75	ENSP00000429059:G93S;ENSP00000428137:G144S;ENSP00000400799:G86S;ENSP00000024061:G93S;ENSP00000429974:G75S	.	G	-	1	0	SLC45A4	142300858	1.000000	0.71417	0.998000	0.56505	0.807000	0.45602	5.877000	0.69675	1.308000	0.44962	-0.448000	0.05591	GGT	.	.		0.592	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	Missense_Mutation	T	142231676	C	T	142231676	5	4	132	1	0	0	0	0	0	0	1	0	14658	666	23	1	2147	1	SLC45A4	8	142231676	Splice_Site	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10	10282241	142231676	4132346	31	21459										
MTAP	4507	hgsc.bcm.edu	37	chr9	21838002	21838002	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tgagccgttttgccccaaaaCgagagaggtgtgtagtcttt	12	8	1	2	rs368718537		TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr9:21838002C>T	ENST00000460874.2	+	5	719	c.494C>T	c.(493-495)aCg>aTg	p.T165M	MTAP_ENST00000580900.1_Missense_Mutation_p.T148M|MTAP_ENST00000380172.4_Missense_Mutation_p.T148M|RP11-145E5.5_ENST00000404796.2_Intron					methylthioadenosine phosphorylase									p.0(1)|p.0?(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|lung(3)|pancreas(1)	10		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)		TGCCCCAAAACGAGAGAGGTG	0.498																																					p.T148M		Atlas-SNP	.											.	MTAP	23	.	2	Whole gene deletion(2)	lung(2)	c.C443T						.						229	227	228					9																	21838002		2203	4300	6503	SO:0001583	missense	4507	exon5			CCAAAACGAGAGA	AB062485	CCDS6509.1	9p21	2013-05-29			ENSG00000099810	ENSG00000099810	2.4.2.28		7413	protein-coding gene	gene with protein product	"S-methyl-5'-thioadenosine phosphorylase"	156540				11126361	Standard	NM_002451		Approved	MSAP, c86fus	uc003zph.3	Q13126	OTTHUMG00000019690	ENST00000460874.2:c.494C>T	chr9.hg19:g.21838002C>T	ENSP00000461932:p.Thr165Met	109.0	0.0		152.0	61.0	NM_002451		Missense_Mutation	SNP	ENST00000460874.2	hg19		.	.	.	.	.	.	.	.	.	.	C	14.17	2.454968	0.43634	.	.	ENSG00000099810	ENST00000380172	D	0.86366	-2.11	5.54	5.54	0.83059	Nucleoside phosphorylase domain (1);	0.000000	0.85682	D	0.000000	D	0.90130	0.6916	L	0.39020	1.185	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.66716	0.946;0.921	D	0.89885	0.4033	10	0.46703	T	0.11	-22.4499	18.2739	0.90077	0.0:1.0:0.0:0.0	.	165;148	B4DUC8;Q13126	.;MTAP_HUMAN	M	148	ENSP00000369519:T148M	ENSP00000369519:T148M	T	+	2	0	MTAP	21828002	1.000000	0.71417	0.976000	0.42696	0.894000	0.52154	5.608000	0.67654	2.607000	0.88179	0.655000	0.94253	ACG	.	.		0.498	MTAP-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000051929.2	NM_002451		T	21838002	C	T	21838002	3	4	132	1	0	0	0	0	1	0	0	0	9920	536	19	1	461	1	MTAP	9	21838002	Missense_Mutation	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10		21838002	119375429	32	21460										
PHF2	5253	hgsc.bcm.edu	37	chr9	96435949	96435949	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tgcaggcctccgactcctgcCtgcagaccacgtggggagct	13	15	0	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr9:96435949C>T	ENST00000359246.4	+	18	2798	c.2431C>T	c.(2431-2433)Ctg>Ttg	p.L811L	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	811					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		CGACTCCTGCCTGCAGACCAC	0.667																																					p.L811L		Atlas-SNP	.											.	PHF2	113	.	0			c.C2431T						.						34	37	36					9																	96435949		2203	4300	6503	SO:0001819	synonymous_variant	5253	exon18			TCCTGCCTGCAGA	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	8920	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1E", "centromere protein 35"	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.2431C>T	chr9.hg19:g.96435949C>T		182.0	0.0		233.0	78.0	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	hg19	CCDS35069.1																																																																																			.	.		0.667	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		T	96435949	C	T	96435949	2	4	132	1	0	0	0	0	0	0	0	1	11839	680	24	3		3	PHF2	9	96435949	Silent	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10	74597947	96435949	44777482	33	21461										
KCNMA1	3778	hgsc.bcm.edu	37	chr10	78761222	78761222	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	agaagaaagtgggaaggctcTctcaagggtgtccacgttac	13	8	2	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr10:78761222T>A	ENST00000286628.8	-	19	2208	c.2209A>T	c.(2209-2211)Aga>Tga	p.R737*	KCNMA1_ENST00000406533.3_Nonsense_Mutation_p.R741*|KCNMA1_ENST00000404857.1_Intron|KCNMA1_ENST00000286627.5_Intron|KCNMA1_ENST00000372443.1_Intron|KCNMA1_ENST00000404771.3_Nonsense_Mutation_p.R737*|KCNMA1_ENST00000354353.5_Intron|KCNMA1_ENST00000372440.1_Intron	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	737					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	GGGAAGGCTCTCTCAAGGGTG	0.498																																					p.R737X		Atlas-SNP	.											.	KCNMA1	370	.	0			c.A2209T						.						159	131	140					10																	78761222		692	1591	2283	SO:0001587	stop_gained	3778	exon19			AGGCTCTCTCAAG	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.2209A>T	chr10.hg19:g.78761222T>A	ENSP00000286628:p.Arg737*	228.0	0.0		302.0	39.0	NM_001161352	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Nonsense_Mutation	SNP	ENST00000286628.8	hg19		.	.	.	.	.	.	.	.	.	.	T	38	6.954715	0.97960	.	.	ENSG00000156113	ENST00000372437;ENST00000457953;ENST00000404771;ENST00000286628;ENST00000406533	.	.	.	5.93	3.51	0.40186	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-10.1658	12.7381	0.57236	0.0:0.0:0.398:0.602	.	.	.	.	X	672;711;674;711;741	.	ENSP00000286628:R711X	R	-	1	2	KCNMA1	78431228	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.717000	0.47227	0.447000	0.26695	0.533000	0.62120	AGA	.	.		0.498	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247		A	78761222	T	A	78761222	4	1	132	1	0	0	0	0	0	1	0	0	8082	1559	54	4	1697	4	KCNMA1	10	78761222	Nonsense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10		78761222	56773525	34	21462										
PAX2	5076	hgsc.bcm.edu	37	chr10	102509535	102509535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	gtgtgaaccagctcggggggGtgtttgtgaacggccggccc	18	10	0	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr10:102509535G>A	ENST00000428433.1	+	2	626	c.76G>A	c.(76-78)Gtg>Atg	p.V26M	PAX2_ENST00000556085.1_Missense_Mutation_p.V25M|PAX2_ENST00000370296.2_Missense_Mutation_p.V26M|PAX2_ENST00000361791.3_Missense_Mutation_p.V26M|PAX2_ENST00000355243.3_Missense_Mutation_p.V26M|PAX2_ENST00000553492.1_Intron	NM_003987.3|NM_003990.3	NP_003978|NP_003981.2	Q02962	PAX2_HUMAN	paired box 2	26	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				aging (GO:0007568)|axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cell fate determination (GO:0001709)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucose stimulus (GO:0071333)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|glial cell differentiation (GO:0010001)|inner ear morphogenesis (GO:0042472)|mesenchymal to epithelial transition (GO:0060231)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|mesonephric duct development (GO:0072177)|mesonephric tubule formation (GO:0072172)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric nephron tubule formation (GO:0072289)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytolysis (GO:0045918)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of programmed cell death (GO:0043069)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|neural tube closure (GO:0001843)|optic chiasma development (GO:0061360)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|optic nerve development (GO:0021554)|optic nerve morphogenesis (GO:0021631)|optic nerve structural organization (GO:0021633)|pancreas development (GO:0031016)|paramesonephric duct development (GO:0061205)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of optic nerve formation (GO:2000597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|protein kinase B signaling (GO:0043491)|reactive oxygen species metabolic process (GO:0072593)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of metanephros size (GO:0035566)|response to nutrient levels (GO:0031667)|retinal pigment epithelium development (GO:0003406)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|ureter development (GO:0072189)|ureter maturation (GO:0035799)|ureter morphogenesis (GO:0072197)|urogenital system development (GO:0001655)|vestibulocochlear nerve formation (GO:0021650)|visual perception (GO:0007601)	centriolar satellite (GO:0034451)|lysosome (GO:0005764)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|superoxide-generating NADPH oxidase activity (GO:0016175)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		GCTCGGGGGGGTGTTTGTGAA	0.657																																					p.V26M		Atlas-SNP	.											.	PAX2	83	.	0			c.G76A						.						30	36	34					10																	102509535		2196	4294	6490	SO:0001583	missense	5076	exon2			GGGGGGGTGTTTG		CCDS7499.1, CCDS41561.1	10q24.31	2011-06-20	2007-07-12		ENSG00000075891	ENSG00000075891		"Paired boxes", "Homeoboxes / PRD class"	8616	protein-coding gene	gene with protein product		167409	"paired box gene 2"			8431641, 7981748	Standard	NM_003990		Approved		uc001krk.4	Q02962	OTTHUMG00000018913	ENST00000428433.1:c.76G>A	chr10.hg19:g.102509535G>A	ENSP00000396259:p.Val26Met	24.0	0.0		28.0	9.0	NM_000278	Q15105|Q15110|Q15837|Q5SZP2|Q5SZP3	Missense_Mutation	SNP	ENST00000428433.1	hg19	CCDS53569.1	.	.	.	.	.	.	.	.	.	.	G	35	5.561159	0.96527	.	.	ENSG00000075891	ENST00000370296;ENST00000428433;ENST00000361791;ENST00000355243;ENST00000556085;ENST00000427256;ENST00000554172	D;D;D;D;D;D;D	0.99656	-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31	6.17	6.17	0.99709	Paired box protein, N-terminal (4);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99447	0.9804	L	0.48174	1.505	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;0.958;0.999;1.0;1.0;0.999;1.0	D;P;D;D;D;D;D	0.91635	0.988;0.726;0.995;0.999;0.999;0.998;0.999	D	0.99727	1.1011	10	0.51188	T	0.08	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	25;26;26;30;26;26;30	G3V5U4;Q02962-2;Q02962-3;Q6YFJ8;Q02962;Q02962-4;G3V5S4	.;.;.;.;PAX2_HUMAN;.;.	M	26;26;26;26;25;26;30	ENSP00000359319:V26M;ENSP00000396259:V26M;ENSP00000355069:V26M;ENSP00000347385:V26M;ENSP00000452527:V25M;ENSP00000398652:V26M;ENSP00000452489:V30M	ENSP00000347385:V26M	V	+	1	0	PAX2	102499525	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.862000	0.99564	2.941000	0.99782	0.655000	0.94253	GTG	.	.		0.657	PAX2-202	KNOWN	basic|CCDS	protein_coding	protein_coding				A	102509535	G	A	102509535	3	1	132	1	0	0	0	0	1	0	0	0	11488	1261	44	3	82	3	PAX2	10	102509535	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	23748313	102509535	33025212	35	21463										
ADAM12	8038	hgsc.bcm.edu	37	chr10	127798378	127798378	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ccacgatcaccagctccacaTacttagttgccttgagggtc	8	14	1	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr10:127798378T>C	ENST00000368679.4	-	7	953	c.644A>G	c.(643-645)tAt>tGt	p.Y215C	ADAM12_ENST00000368676.4_Missense_Mutation_p.Y215C	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	215	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CAGCTCCACATACTTAGTTGC	0.403																																					p.Y215C		Atlas-SNP	.											.	ADAM12	388	.	0			c.A644G						.						171	147	155					10																	127798378		2203	4300	6503	SO:0001583	missense	8038	exon7			TCCACATACTTAG	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.644A>G	chr10.hg19:g.127798378T>C	ENSP00000357668:p.Tyr215Cys	78.0	0.0		68.0	21.0	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	hg19	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.679847	0.68042	.	.	ENSG00000148848	ENST00000368679;ENST00000368676;ENST00000448723	T;T;T	0.73152	-0.72;-0.72;-0.72	5.39	5.39	0.77823	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.64402	D	0.000001	D	0.88325	0.6406	H	0.94183	3.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.983;0.983;0.983;1.0	D	0.91227	0.5011	10	0.62326	D	0.03	.	15.5813	0.76445	0.0:0.0:0.0:1.0	.	212;215;212;215	O43184-3;O43184-2;O43184-4;O43184	.;.;.;ADA12_HUMAN	C	215;215;212	ENSP00000357668:Y215C;ENSP00000357665:Y215C;ENSP00000391268:Y212C	ENSP00000357665:Y215C	Y	-	2	0	ADAM12	127788368	1.000000	0.71417	0.980000	0.43619	0.476000	0.33039	7.459000	0.80802	2.267000	0.75376	0.528000	0.53228	TAT	.	.		0.403	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			C	127798378	T	C	127798378	3	2	132	1	0	0	0	0	1	0	0	0	236	1406	49	2	2261	2	ADAM12	10	127798378	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	25288843	127798378	7736369	36	21464										
EBF3	253738	hgsc.bcm.edu	37	chr10	131665456	131665456	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	gcagaactgcttggatttgtAggagagggtcacttcgacga	14	7	1	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr10:131665456A>G	ENST00000355311.5	-	10	1060	c.988T>C	c.(988-990)Tac>Cac	p.Y330H	EBF3_ENST00000368648.3_Missense_Mutation_p.Y321H			Q9H4W6	COE3_HUMAN	early B-cell factor 3	330	IPT/TIG.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		TTGGATTTGTAGGAGAGGGTC	0.577																																					p.Y321H		Atlas-SNP	.											.	EBF3	193	.	0			c.T961C						.						92	80	84					10																	131665456		2203	4300	6503	SO:0001583	missense	253738	exon10			ATTTGTAGGAGAG		CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.988T>C	chr10.hg19:g.131665456A>G	ENSP00000347463:p.Tyr330His	117.0	0.0		154.0	49.0	NM_001005463	A0AUY1|Q5T6H9|Q9H4W5	Missense_Mutation	SNP	ENST00000355311.5	hg19		.	.	.	.	.	.	.	.	.	.	A	21.6	4.178812	0.78564	.	.	ENSG00000108001	ENST00000355311;ENST00000368648	T;T	0.75938	-0.98;-0.98	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.80391	0.4614	L	0.41824	1.3	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.79475	-0.1788	10	0.37606	T	0.19	-18.3429	15.1986	0.73116	1.0:0.0:0.0:0.0	.	321	Q9H4W6-2	.	H	330;321	ENSP00000347463:Y330H;ENSP00000357637:Y321H	ENSP00000347463:Y330H	Y	-	1	0	EBF3	131555446	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.196000	0.94978	2.127000	0.65507	0.533000	0.62120	TAC	.	.		0.577	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		G	131665456	A	G	131665456	3	3	132	1	0	0	0	0	1	0	0	0	4884	420	15	2	722	2	EBF3	10	131665456	Missense_Mutation	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10	3867078	131665456	3869291	37	21465										
HPX	3263	hgsc.bcm.edu	37	chr11	6453126	6453127	+	Frame_Shift_Del	DEL	AT	AT	-													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ccaatacacacctggaccagAtagagtttttcttcccagga							TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr11:6453126_6453127delAT	ENST00000265983.3	-	8	1056_1057	c.956_957delAT	c.(955-957)tatfs	p.Y319fs		NM_000613.2	NP_000604.1	P02790	HEMO_HUMAN	hemopexin	319					cellular iron ion homeostasis (GO:0006879)|heme metabolic process (GO:0042168)|heme transport (GO:0015886)|hemoglobin metabolic process (GO:0020027)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|viral process (GO:0016032)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme transporter activity (GO:0015232)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(11)|prostate(1)	15		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)		CCTGGACCAGATAGAGTTTTTC	0.54																																					p.319_320del		Atlas-Indel,Pindel	.											.	HPX	33	.	0			c.957_958del						.																																			SO:0001589	frameshift_variant	3263	exon8			.	J03048	CCDS7763.1	11p15.5-p15.4	2012-10-02			ENSG00000110169	ENSG00000110169			5171	protein-coding gene	gene with protein product		142290				2989777, 2842511	Standard	NM_000613		Approved		uc001mdg.2	P02790	OTTHUMG00000133399	ENST00000265983.3:c.956_957delAT	chr11.hg19:g.6453126_6453127delAT	ENSP00000265983:p.Tyr319fs	67.0	0.0		51.0	15.0	NM_000613	B2R957	Frame_Shift_Del	DEL	ENST00000265983.3	hg19	CCDS7763.1																																																																																			.	.		0.54	HPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257256.1	NM_000613		-	6453127	AT	-	6453126	7	5	132	1	0	1	0	1	0	0	0	0	7355	340	12	0	443	0	HPX	11	6453126	Frame_Shift_Del	DEL	AT	TCGA-DD-A4NJ-01A-11D-A27I-10		6453126	128553390	38	21466										
UEVLD	55293	hgsc.bcm.edu	37	chr11	18579874	18579874	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	gaggacaagcctgtctgcaaTaccctgtacagtaagagaaa	10	9	1	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr11:18579874T>G	ENST00000541984.1	-	5	378	c.316A>C	c.(316-318)Att>Ctt	p.I106L	UEVLD_ENST00000320750.6_Missense_Mutation_p.I184L|UEVLD_ENST00000543987.1_Missense_Mutation_p.I206L|UEVLD_ENST00000540666.1_5'UTR|UEVLD_ENST00000535484.1_Missense_Mutation_p.I168L|UEVLD_ENST00000396197.3_Missense_Mutation_p.I206L|UEVLD_ENST00000379387.4_Missense_Mutation_p.I184L	NM_001261386.1	NP_001248315.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						CTGTCTGCAATACCCTGTACA	0.428																																					p.I206L		Atlas-SNP	.											.	UEVLD	58	.	0			c.A616C						.						95	77	83					11																	18579874		2199	4293	6492	SO:0001583	missense	55293	exon7			CTGCAATACCCTG	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000541984.1:c.316A>C	chr11.hg19:g.18579874T>G	ENSP00000437538:p.Ile106Leu	62.0	0.0		69.0	8.0	NM_001040697		Missense_Mutation	SNP	ENST00000541984.1	hg19	CCDS58125.1	.	.	.	.	.	.	.	.	.	.	T	0.111	-1.138511	0.01742	.	.	ENSG00000151116	ENST00000543987;ENST00000535484;ENST00000396197;ENST00000320750;ENST00000379387;ENST00000541984	D;D;D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2;-2.2;-2.2	5.38	-0.809	0.10864	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.412612	0.27816	N	0.017728	T	0.66809	0.2827	N	0.11927	0.2	0.80722	D	1	B;B;B;B	0.18013	0.025;0.0;0.003;0.011	B;B;B;B	0.31442	0.13;0.003;0.025;0.13	T	0.55134	-0.8188	10	0.02654	T	1	-11.122	1.6526	0.02775	0.1295:0.2584:0.1333:0.4787	.	184;184;206;206	B4DL43;Q8IX04-3;Q8IX04-2;Q8IX04	.;.;.;UEVLD_HUMAN	L	206;168;206;184;184;106	ENSP00000442974:I206L;ENSP00000441092:I168L;ENSP00000379500:I206L;ENSP00000323353:I184L;ENSP00000368697:I184L;ENSP00000437538:I106L	ENSP00000323353:I184L	I	-	1	0	UEVLD	18536450	1.000000	0.71417	0.998000	0.56505	0.152000	0.21847	0.598000	0.24074	0.037000	0.15575	-0.332000	0.08345	ATT	.	.		0.428	UEVLD-015	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000395928.1	NM_018314		G	18579874	T	G	18579874	3	3	132	1	0	0	0	0	1	0	0	0	16948	1406	49	5	823	5	UEVLD	11	18579874	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	12126748	18579874	116426642	39	21467										
SHANK2	22941	hgsc.bcm.edu	37	chr11	70348970	70348970	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	caccttaaggaccaggtgatTccctccctgccggatcatgt	9	14	1	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr11:70348970T>A	ENST00000423696.2	-	8	1027	c.991A>T	c.(991-993)Aat>Tat	p.N331Y	SHANK2_ENST00000449833.2_Missense_Mutation_p.N122Y|SHANK2_ENST00000409530.1_Missense_Mutation_p.N121Y|SHANK2_ENST00000338508.4_Missense_Mutation_p.N711Y|SHANK2_ENST00000357171.3_Missense_Mutation_p.N122Y|SHANK2_ENST00000409161.1_Missense_Mutation_p.N121Y|SHANK2_ENST00000449116.2_Missense_Mutation_p.N122Y			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	331	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			ACCAGGTGATTCCCTCCCTGC	0.572																																					p.N122Y		Atlas-SNP	.											.	SHANK2	340	.	0			c.A364T						.						155	125	135					11																	70348970		2200	4294	6494	SO:0001583	missense	22941	exon3			GGTGATTCCCTCC	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14295	protein-coding gene	gene with protein product		603290	"cortactin binding protein 1"	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.991A>T	chr11.hg19:g.70348970T>A	ENSP00000394536:p.Asn331Tyr	102.0	0.0		148.0	43.0	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.9|22.9	4.350054|4.350054	0.82132|0.82132	.|.	.|.	ENSG00000162105|ENSG00000162105	ENST00000412252|ENST00000449833;ENST00000409161;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018;ENST00000409530;ENST00000449116;ENST00000357171	.|T;T;T;T;T;T;T;T	.|0.27890	.|1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64	4.46|4.46	4.46|4.46	0.54185|0.54185	.|PDZ/DHR/GLGF (4);	.|0.136203	.|0.64402	.|D	.|0.000004	T|T	0.53158|0.53158	0.1779|0.1779	M|M	0.69185|0.69185	2.1|2.1	0.58432|0.58432	D|D	0.999995|0.999995	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.999;1.0;0.999;0.999	T|T	0.58312|0.58312	-0.7658|-0.7658	5|10	.|0.87932	.|D	.|0	.|.	14.0594|14.0594	0.64790|0.64790	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|122;331;710;122	.|B7ZKU9;Q9UPX8;Q9UPX8-3;Q9UPX8-4	.|.;SHAN2_HUMAN;.;.	V|Y	120|122;121;711;331;345;341;121;122;122	.|ENSP00000399423:N122Y;ENSP00000386491:N121Y;ENSP00000345193:N711Y;ENSP00000394536:N331Y;ENSP00000294018:N341Y;ENSP00000387324:N121Y;ENSP00000394939:N122Y;ENSP00000349694:N122Y	.|ENSP00000294018:N341Y	E|N	-|-	2|1	0|0	SHANK2|SHANK2	70026618|70026618	1.000000|1.000000	0.71417|0.71417	0.947000|0.947000	0.38551|0.38551	0.940000|0.940000	0.58332|0.58332	5.716000|5.716000	0.68437|0.68437	1.789000|1.789000	0.52484|0.52484	0.379000|0.379000	0.24179|0.24179	GAA|AAT	.	.		0.572	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		A	70348970	T	A	70348970	3	1	132	1	0	0	0	0	1	0	0	0	14280	1783	62	4	3457	4	SHANK2	11	70348970	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	51769096	70348970	64657546	40	21468										
KRTAP5-7	440050	hgsc.bcm.edu	37	chr11	71238649	71238675	+	In_Frame_Del	DEL	CTGCTGCTCCTCAGGCTGTGGGTCATC	CTGCTGCTCCTCAGGCTGTGGGTCATC	-													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tgcagctgctataagccctgCtgctgctcctcaggctgtgg					rs200832929|rs549981674		TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	CTGCTGCTCCTCAGGCTGTGGGTCATC	CTGCTGCTCCTCAGGCTGTGGGTCATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr11:71238649_71238675delCTGCTGCTCCTCAGGCTGTGGGTCATC	ENST00000398536.4	+	1	337_363	c.303_329delCTGCTGCTCCTCAGGCTGTGGGTCATC	c.(301-330)tgctgctgctcctcaggctgtgggtcatcc>tgc	p.CCSSGCGSS102del		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	102	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.G108W(1)		breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						ataagccctgctgctgctcctcaggctgtgggtcatcctgctgccag	0.634																																					p.101_110del		Atlas-INDEL	.											.	KRTAP5-7	23	.	1	Substitution - Missense(1)	lung(1)	c.302_328del						.																																			SO:0001651	inframe_deletion	440050	exon1			.	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"Keratin associated proteins"	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.303_329delCTGCTGCTCCTCAGGCTGTGGGTCATC	chr11.hg19:g.71238649_71238675delCTGCTGCTCCTCAGGCTGTGGGTCATC	ENSP00000417330:p.Cys102_Ser110del	157.0	0.0		194.0	35.0	NM_001012503	B2RNM3|Q701N5	In_Frame_Del	DEL	ENST00000398536.4	hg19	CCDS41682.1																																																																																			.	.		0.634	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1			-	71238675	CTGCTGCTCCTCAGGCTGTGGGTCATC	-	71238649	7	5	132	1	0	1	0	1	0	0	0	0	8575	805	28	0	305	0	KRTAP5-7	11	71238649	In_Frame_Del	DEL	CTGCTGCTCCTCAGGCTGTGGGTCATC	TCGA-DD-A4NJ-01A-11D-A27I-10	889679	71238649	63767867	41	21469										
C11orf70	85016	hgsc.bcm.edu	37	chr11	101952001	101952001	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ttacctcttctgtctttaaaGtttcagcttatgtaagtgtg	7	7	4	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr11:101952001G>A	ENST00000434758.2	+	6	692	c.664G>A	c.(664-666)Gtt>Att	p.V222I	C11orf70_ENST00000526781.1_Missense_Mutation_p.V222I	NM_032930.2	NP_116319.2	Q9BRQ4	CK070_HUMAN	chromosome 11 open reading frame 70	222										breast(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|skin(2)	12	all_epithelial(12;0.0137)	Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0335)		TGTCTTTAAAGTTTCAGCTTA	0.308																																					p.V222I		Atlas-SNP	.											.	C11orf70	33	.	0			c.G664A						.						84	86	86					11																	101952001		2203	4295	6498	SO:0001583	missense	85016	exon6			TTTAAAGTTTCAG	AK094851	CCDS8313.1, CCDS8313.2, CCDS53698.1	11q22.1	2012-05-31			ENSG00000137691	ENSG00000137691			28188	protein-coding gene	gene with protein product							Standard	NM_032930		Approved	MGC13040	uc001pgp.3	Q9BRQ4	OTTHUMG00000167320	ENST00000434758.2:c.664G>A	chr11.hg19:g.101952001G>A	ENSP00000414390:p.Val222Ile	28.0	0.0		34.0	7.0	NM_032930	E9PJU1	Missense_Mutation	SNP	ENST00000434758.2	hg19	CCDS8313.2	.	.	.	.	.	.	.	.	.	.	G	23.2	4.387631	0.82902	.	.	ENSG00000137691	ENST00000434758;ENST00000526781;ENST00000423732	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.77598	0.4154	M	0.64630	1.985	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.74948	-0.3490	9	0.42905	T	0.14	-24.4378	18.8612	0.92273	0.0:0.0:1.0:0.0	.	222	Q9BRQ4	CK070_HUMAN	I	222;222;184	.	ENSP00000392150:V184I	V	+	1	0	C11orf70	101457211	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.693000	0.84214	2.873000	0.98535	0.563000	0.77884	GTT	.	.		0.308	C11orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394144.1	NM_032930		A	101952001	G	A	101952001	3	1	132	1	0	0	0	0	1	0	0	0	1661	1029	36	3	568	3	C11orf70	11	101952001	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	30713352	101952001	33054515	42	21470										
NFRKB	4798	hgsc.bcm.edu	37	chr11	129762747	129762747	+	5'UTR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	atggtctaaggaatccattgTttcttctccacaggtactct	7	10	4	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr11:129762747T>C	ENST00000446488.3	-	0	101				NFRKB_ENST00000304521.5_5'UTR|NFRKB_ENST00000524746.1_5'UTR|NFRKB_ENST00000524794.1_Missense_Mutation_p.T13A|NFRKB_ENST00000526940.1_5'UTR	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein						DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		GAATCCATTGTTTCTTCTCCA	0.493																																					p.T13A		Atlas-SNP	.											.	NFRKB	101	.	0			c.A37G						.						180	153	162					11																	129762747		2201	4297	6498	SO:0001623	5_prime_UTR_variant	4798	exon1			CCATTGTTTCTTC		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"INO80 complex subunits"	7802	protein-coding gene	gene with protein product	"nuclear factor related to kappa B binding protein", "DNA-binding protein R kappa B", "INO80 complex subunit G"	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.-3A>G	chr11.hg19:g.129762747T>C		153.0	0.0		174.0	24.0	NM_006165	Q12869|Q15312|Q9H048	Missense_Mutation	SNP	ENST00000446488.3	hg19	CCDS44770.1	.	.	.	.	.	.	.	.	.	.	T	14.93	2.680946	0.47886	.	.	ENSG00000170322	ENST00000524794	.	.	.	4.66	-4.82	0.03171	.	.	.	.	.	T	0.22936	0.0554	.	.	.	0.18873	N	0.999987	B	0.02656	0.0	B	0.01281	0.0	T	0.19095	-1.0316	7	0.25106	T	0.35	1.0065	7.5933	0.28033	0.0:0.3595:0.1127:0.5278	.	13	Q6P4R8-2	.	A	13	.	ENSP00000436926:T13A	T	-	1	0	NFRKB	129267957	0.007000	0.16637	0.016000	0.15963	0.968000	0.65278	-0.148000	0.10219	-1.404000	0.02050	0.477000	0.44152	ACA	.	.		0.493	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		C	129762747	T	C	129762747	1	2	132	0	1	0	0	0	0	0	0	0	10393	1725	60	2		2	NFRKB	11	129762747	5'UTR	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	27810746	129762747	5243769	43	21471										
IQSEC3	440073	hgsc.bcm.edu	37	chr12	271125	271125	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	cgctgacatccccagggagcTggtggtaggcatctatgaga	14	10	1	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr12:271125T>A	ENST00000538872.1	+	8	2595	c.2477T>A	c.(2476-2478)cTg>cAg	p.L826Q	IQSEC3_ENST00000382841.2_Missense_Mutation_p.L523Q|IQSEC3_ENST00000326261.4_Missense_Mutation_p.L826Q|RP11-598F7.5_ENST00000540136.1_RNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	826	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		CCCAGGGAGCTGGTGGTAGGC	0.592																																					p.L826Q		Atlas-SNP	.											.	IQSEC3	154	.	0			c.T2477A						.						96	68	78					12																	271125		2203	4299	6502	SO:0001583	missense	440073	exon8			GGGAGCTGGTGGT	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2477T>A	chr12.hg19:g.271125T>A	ENSP00000437554:p.Leu826Gln	232.0	0.0		215.0	106.0	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Missense_Mutation	SNP	ENST00000538872.1	hg19	CCDS53728.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.811973	0.90707	.	.	ENSG00000120645	ENST00000538872;ENST00000326261;ENST00000382841	T;T;T	0.56103	0.48;0.48;0.48	5.54	5.54	0.83059	SEC7-like, alpha orthogonal bundle (1);SEC7-like (4);	0.100056	0.64402	D	0.000004	T	0.69468	0.3114	M	0.64997	1.995	0.58432	D	0.999995	P;D	0.63880	0.82;0.993	P;D	0.69479	0.465;0.964	T	0.72896	-0.4153	10	0.87932	D	0	.	15.6811	0.77371	0.0:0.0:0.0:1.0	.	826;523	Q9UPP2;Q9UPP2-2	IQEC3_HUMAN;.	Q	826;826;523	ENSP00000437554:L826Q;ENSP00000315662:L826Q;ENSP00000372292:L523Q	ENSP00000315662:L826Q	L	+	2	0	IQSEC3	141386	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.209000	0.72171	2.105000	0.64084	0.459000	0.35465	CTG	.	.		0.592	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		A	271125	T	A	271125	3	1	132	1	0	0	0	0	1	0	0	0	7828	1580	55	4	2507	4	IQSEC3	12	271125	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10		271125	133580770	44	21472										
KRT2	3849	hgsc.bcm.edu	37	chr12	53045641	53045642	+	In_Frame_Ins	INS	-	-	GCCGCTGCCGCCTCCAAA													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	aagctgctgccgcctccaaaINSaccacctcctctgccaccaa							TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr12:53045641_53045642insGCCGCTGCCGCCTCCAAA	ENST00000309680.3	-	1	306_307	c.285_286insTTTGGAGGCGGCAGCGGC	c.(283-288)ggtttt>ggtTTTGGAGGCGGCAGCGGCttt	p.95_96GF>GFGGGSGF		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	95	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		ccgcctccaaaaccacctcctc	0.619																																					p.F96delinsFGGGSGF		Atlas-INDEL	.											.	KRT2	94	.	0			c.286_287insTTTGGAGGCGGCAGCGGC						.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.285_286insTTTGGAGGCGGCAGCGGC	chr12.hg19:g.53045641_53045642insGCCGCTGCCGCCTCCAAA	ENSP00000310861:p.Gly95_Phe96insPheGlyGlyGlySerGly	136.0	0.0		222.0	81.0	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.619	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		GCCGCTGCCGCCTCCAAA	53045642	-	GCCGCTGCCGCCTCCAAA	53045641	7	5	132	1	0	1	1	0	0	0	0	0	8466	14	1	0	1669	0	KRT2	12	53045641	In_Frame_Ins	INS	-	TCGA-DD-A4NJ-01A-11D-A27I-10	52774516	53045641	80806254	45	21473										
KRT1	3848	hgsc.bcm.edu	37	chr12	53074087	53074087	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	agcagagccagagctgaagcCccctccacttcggtacccag	10	16	0	3			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr12:53074087C>A	ENST00000252244.3	-	1	104	c.46G>T	c.(46-48)Ggc>Tgc	p.G16C		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	16	Gly/Phe/Ser-rich.|Head.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						GAGCTGAAGCCCCCTCCACTT	0.542																																					p.G16C		Atlas-SNP	.											.	KRT1	110	.	0			c.G46T						.						73	81	78					12																	53074087		2203	4300	6503	SO:0001583	missense	3848	exon1			TGAAGCCCCCTCC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.46G>T	chr12.hg19:g.53074087C>A	ENSP00000252244:p.Gly16Cys	172.0	0.0		187.0	22.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	hg19	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	C	10.79	1.450651	0.26074	.	.	ENSG00000167768	ENST00000252244	D	0.85773	-2.03	4.36	2.48	0.30137	.	.	.	.	.	D	0.89887	0.6845	M	0.91354	3.2	0.09310	N	1	D	0.59767	0.986	P	0.51487	0.671	T	0.81693	-0.0817	9	0.87932	D	0	.	8.0051	0.30321	0.0:0.7248:0.0:0.2752	.	16	P04264	K2C1_HUMAN	C	16	ENSP00000252244:G16C	ENSP00000252244:G16C	G	-	1	0	KRT1	51360354	0.000000	0.05858	0.034000	0.17996	0.900000	0.52787	0.042000	0.13949	0.402000	0.25451	0.491000	0.48974	GGC	.	.		0.542	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		A	53074087	C	A	53074087	3	1	132	1	0	0	0	0	1	0	0	0	8456	623	22	3	1924	3	KRT1	12	53074087	Missense_Mutation	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10	28446	53074087	80777808	46	21474										
OR6C75	390323	hgsc.bcm.edu	37	chr12	55759405	55759405	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tggatttctgtgcctccaatGtaattgatcattttatctgt	7	7	3	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr12:55759405G>T	ENST00000343399.3	+	1	511	c.511G>T	c.(511-513)Gta>Tta	p.V171L		NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C, member 75	171						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)	25						TGCCTCCAATGTAATTGATCA	0.428																																					p.V171L		Atlas-SNP	.											.	OR6C75	67	.	0			c.G511T						.						170	144	153					12																	55759405		2203	4300	6503	SO:0001583	missense	390323	exon1			TCCAATGTAATTG		CCDS31820.1	12q13.2	2013-09-23			ENSG00000187857	ENSG00000187857		"GPCR / Class A : Olfactory receptors"	31304	protein-coding gene	gene with protein product							Standard	NM_001005497		Approved		uc010spk.2	A6NL08	OTTHUMG00000169886	ENST00000343399.3:c.511G>T	chr12.hg19:g.55759405G>T	ENSP00000368987:p.Val171Leu	106.0	0.0		117.0	42.0	NM_001005497		Missense_Mutation	SNP	ENST00000343399.3	hg19	CCDS31820.1	.	.	.	.	.	.	.	.	.	.	g	12.84	2.059306	0.36373	.	.	ENSG00000187857	ENST00000343399	T	0.00145	8.67	5.22	-7.39	0.01402	GPCR, rhodopsin-like superfamily (1);	0.248995	0.27056	N	0.021146	T	0.00144	0.0004	L	0.56340	1.77	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.49978	-0.8881	10	0.51188	T	0.08	.	15.0283	0.71687	0.1842:0.1111:0.7047:0.0	.	171	A6NL08	O6C75_HUMAN	L	171	ENSP00000368987:V171L	ENSP00000368987:V171L	V	+	1	0	OR6C75	54045672	0.000000	0.05858	0.618000	0.29105	0.952000	0.60782	-3.774000	0.00370	-1.261000	0.02462	-0.331000	0.08364	GTA	.	.		0.428	OR6C75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406418.1			T	55759405	G	T	55759405	3	4	132	1	0	0	0	0	1	0	0	0	11208	1377	48	3	513	3	OR6C75	12	55759405	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	2685318	55759405	78092490	47	21475										
SUOX	6821	hgsc.bcm.edu	37	chr12	56398608	56398608	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tggctaagctggatggagagGaacagcgccccaggaaggcc	16	10	0	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr12:56398608G>A	ENST00000394109.3	+	3	2159	c.1435G>A	c.(1435-1437)Gaa>Aaa	p.E479K	IKZF4_ENST00000262032.5_5'Flank|SUOX_ENST00000394115.2_Missense_Mutation_p.E479K|SUOX_ENST00000266971.3_Missense_Mutation_p.E479K|SUOX_ENST00000356124.4_Missense_Mutation_p.E479K|SUOX_ENST00000548274.1_Missense_Mutation_p.E479K			P51687	SUOX_HUMAN	sulfite oxidase	479	Homodimerization. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|sulfite oxidase activity (GO:0008482)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)	15			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)			GGATGGAGAGGAACAGCGCCC	0.587																																					p.E479K		Atlas-SNP	.											.	SUOX	33	.	0			c.G1435A						.						191	170	177					12																	56398608		2203	4300	6503	SO:0001583	missense	6821	exon6			GGAGAGGAACAGC	BC065193	CCDS8901.2	12q13.13	2011-02-10			ENSG00000139531	ENSG00000139531	1.8.3.1		11460	protein-coding gene	gene with protein product		606887				7599189	Standard	XM_005269112		Approved		uc001siz.3	P51687	OTTHUMG00000128503	ENST00000394109.3:c.1435G>A	chr12.hg19:g.56398608G>A	ENSP00000377668:p.Glu479Lys	169.0	0.0		210.0	22.0	NM_000456		Missense_Mutation	SNP	ENST00000394109.3	hg19	CCDS8901.2	.	.	.	.	.	.	.	.	.	.	G	6.200	0.405137	0.11754	.	.	ENSG00000139531	ENST00000356124;ENST00000266971;ENST00000394115;ENST00000548274;ENST00000394109	D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83	4.76	2.94	0.34122	Immunoglobulin E-set (1);Moybdenum cofactor oxidoreductase, dimerisation (2);	0.279645	0.32533	N	0.005965	T	0.72993	0.3530	N	0.25789	0.76	0.39350	D	0.965732	B	0.14012	0.009	B	0.14023	0.01	T	0.65026	-0.6268	10	0.38643	T	0.18	-24.5556	6.6168	0.22780	0.2885:0.0:0.7115:0.0	.	479	P51687	SUOX_HUMAN	K	479	ENSP00000348440:E479K;ENSP00000266971:E479K;ENSP00000377674:E479K;ENSP00000450245:E479K;ENSP00000377668:E479K	ENSP00000266971:E479K	E	+	1	0	SUOX	54684875	1.000000	0.71417	0.994000	0.49952	0.645000	0.38454	1.954000	0.40362	0.745000	0.32763	0.467000	0.42956	GAA	.	.		0.587	SUOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250309.1	NM_000456		A	56398608	G	A	56398608	3	1	132	1	0	0	0	0	1	0	0	0	15410	1175	41	3	1445	3	SUOX	12	56398608	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	639203	56398608	77453287	48	21476										
RB1	5925	hgsc.bcm.edu	37	chr13	48941636	48941636	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ttttttctttcaaggttgaaAatctttctaaacgatacgaa	5	6	4	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr13:48941636A>T	ENST00000267163.4	+	10	1084	c.946A>T	c.(946-948)Aat>Tat	p.N316Y		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	316					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(7)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CAAGGTTGAAAATCTTTCTAA	0.289		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.N316Y		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	22	Whole gene deletion(15)|Unknown(7)	bone(11)|breast(5)|adrenal_gland(1)|eye(1)|soft_tissue(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.A946T						.						50	59	56					13																	48941636		2198	4287	6485	SO:0001583	missense	5925	exon10	Familial Cancer Database		GTTGAAAATCTTT	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.946A>T	chr13.hg19:g.48941636A>T	ENSP00000267163:p.Asn316Tyr	23.0	0.0		11.0	5.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	13.57	2.276232	0.40294	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.92752	-3.1	5.43	5.43	0.79202	.	0.549651	0.21267	N	0.077382	D	0.84897	0.5574	N	0.22421	0.69	0.26717	N	0.970859	P	0.34837	0.472	B	0.31245	0.126	T	0.79257	-0.1878	10	0.48119	T	0.1	.	10.6562	0.45675	0.923:0.0:0.077:0.0	.	316	P06400	RB_HUMAN	Y	295;316	ENSP00000267163:N316Y	ENSP00000267163:N316Y	N	+	1	0	RB1	47839637	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	2.334000	0.43920	2.039000	0.60335	0.482000	0.46254	AAT	.	.		0.289	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			T	48941636	A	T	48941636	3	4	132	1	0	0	0	0	1	0	0	0	13113	14	1	4	984	4	RB1	13	48941636	Missense_Mutation	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10		48941636	66228242	49	21477										
RB1	5925	hgsc.bcm.edu	37	chr13	48951170	48951170	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tgtgtcgaaattggatcacaGgtaacttgaattcattgtaa	9	5	2	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr13:48951170G>A	ENST00000267163.4	+	13	1470	c.1332G>A	c.(1330-1332)caG>caA	p.Q444Q		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	444	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(9)|p.Q444H(2)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TTGGATCACAGGTAACTTGAA	0.328		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.Q444Q		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	RB1,fibrous_tissue_and_uncertain_origin,malignant_fibrous_histiocytoma-pleomorphic_sarcoma,0,2	RB1	1068	.	26	Whole gene deletion(15)|Unknown(9)|Substitution - Missense(2)	bone(11)|breast(5)|central_nervous_system(3)|soft_tissue(2)|adrenal_gland(1)|eye(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|lung(1)	c.G1332A	GRCh37	CS004738|CS081960	RB1	S		.						102	110	107					13																	48951170		2203	4299	6502	SO:0001630	splice_region_variant	5925	exon13	Familial Cancer Database		ATCACAGGTAACT	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1332+1G>A	chr13.hg19:g.48951170G>A		47.0	0.0		43.0	21.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.328	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		Silent	A	48951170	G	A	48951170	5	1	132	1	0	0	0	0	0	0	1	0	13113	1014	35	3	1382	3	RB1	13	48951170	Splice_Site	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	9534	48951170	66218708	50	21478										
C13orf34	79866	hgsc.bcm.edu	37	chr13	73312100	73312100	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tatgactttaattttcctagTttttcactaaagatgtcatc	4	7	2	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr13:73312100T>C	ENST00000390667.5	+	5	404	c.307T>C	c.(307-309)Ttt>Ctt	p.F103L	BORA_ENST00000377815.3_Splice_Site_p.F33L|BORA_ENST00000464754.1_3'UTR	NM_024808.2	NP_079084.2	Q6PGQ7	BORA_HUMAN	bora, aurora kinase A activator	103					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of mitosis (GO:0007088)|regulation of mitotic spindle organization (GO:0060236)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)	protein kinase binding (GO:0019901)										ATTTTCCTAGTTTTTCACTAA	0.343																																					p.F103L		Atlas-SNP	.											.	.	.	.	0			c.T307C						.						133	123	126					13																	73312100		1829	4085	5914	SO:0001630	splice_region_variant	79866	exon5			TCCTAGTTTTTCA	BC025367	CCDS9446.1, CCDS66560.1, CCDS9446.2, CCDS73583.1	13q22.1	2013-08-13	2011-08-09	2011-08-09	ENSG00000136122	ENSG00000136122			24724	protein-coding gene	gene with protein product		610510	"chromosome 13 open reading frame 34"	C13orf34		16890155, 18378770, 18566290, 19487276	Standard	NM_001286746		Approved	FLJ22624	uc001viv.1	Q6PGQ7	OTTHUMG00000017068	ENST00000390667.5:c.307-1T>C	chr13.hg19:g.73312100T>C		96.0	0.0		71.0	18.0	NM_024808	B4DQ30|Q5W0P3|Q5W0P4|Q86YC6|Q96IW9|Q9H640	Missense_Mutation	SNP	ENST00000390667.5	hg19	CCDS9446.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.118751|5.118751	0.94385|0.94385	.|.	.|.	ENSG00000136122|ENSG00000136122	ENST00000377815;ENST00000390667|ENST00000377814	T;T|.	0.62788|.	0.08;0.0|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.047164|.	0.85682|.	D|.	0.000000|.	T|T	0.77765|0.77765	0.4179|0.4179	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.998;0.999;0.999;0.999|.	D;D;D;D|.	0.76071|.	0.987;0.986;0.987;0.986|.	T|T	0.79145|0.79145	-0.1924|-0.1924	9|5	.|.	.|.	.|.	-26.6439|-26.6439	16.1668|16.1668	0.81768|0.81768	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	33;103;163;103|.	B4DQ30;A8K631;B5LMG6;Q6PGQ7|.	.;.;.;BORA_HUMAN|.	L|A	33;103|80	ENSP00000367046:F33L;ENSP00000375082:F103L|.	.|.	F|V	+|+	1|2	0|0	BORA|BORA	72210101|72210101	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	6.725000|6.725000	0.74752|0.74752	2.210000|2.210000	0.71456|0.71456	0.533000|0.533000	0.62120|0.62120	TTT|GTT	.	.		0.343	BORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045245.3	NM_024808	Missense_Mutation	C	73312100	T	C	73312100	5	2	132	1	0	0	0	0	0	0	1	0	1730	1739	60	2	321	2	C13orf34	13	73312100	Splice_Site	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	24360930	73312100	41857778	51	21479										
SNW1	22938	hgsc.bcm.edu	37	chr14	78202323	78202323	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	caggcgcaggaggagaaggtGgtccccggggaattttctta	16	8	1	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr14:78202323G>C	ENST00000261531.7	-	7	727	c.665C>G	c.(664-666)cCa>cGa	p.P222R	SLIRP_ENST00000557431.1_Intron|SNW1_ENST00000554775.1_Missense_Mutation_p.P60R|SNW1_ENST00000555761.1_Missense_Mutation_p.P222R	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	222	Pro-rich.|SNW.				cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)			NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		AGGAGAAGGTGGTCCCCGGGG	0.388																																					p.P222R		Atlas-SNP	.											.	SNW1	44	.	0			c.C665G						.						55	66	62					14																	78202323		2203	4300	6503	SO:0001583	missense	22938	exon7			GAAGGTGGTCCCC	AF045184	CCDS9867.1	14q22.1-q22.3	2005-09-13	2005-09-13	2005-09-13		ENSG00000100603			16696	protein-coding gene	gene with protein product		603055	"SKI interacting protein"	SKIIP		8973337, 9632709	Standard	NM_012245		Approved	NCoA-62, SKIP, Prp45, PRPF45, Bx42	uc001xuf.3	Q13573		ENST00000261531.7:c.665C>G	chr14.hg19:g.78202323G>C	ENSP00000261531:p.Pro222Arg	35.0	0.0		30.0	9.0	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Missense_Mutation	SNP	ENST00000261531.7	hg19	CCDS9867.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.945465	0.92593	.	.	ENSG00000100603	ENST00000261531;ENST00000554775;ENST00000555761;ENST00000416259	.	.	.	5.65	5.65	0.86999	SKI-interacting protein SKIP, SNW domain (1);	0.000000	0.85682	D	0.000000	D	0.87382	0.6163	M	0.93550	3.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.89682	0.3891	9	0.87932	D	0	.	20.1398	0.98056	0.0:0.0:1.0:0.0	.	222;222	G3V3A4;Q13573	.;SNW1_HUMAN	R	222;60;222;222	.	ENSP00000261531:P222R	P	-	2	0	SNW1	77272076	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.770000	0.98971	2.843000	0.97960	0.585000	0.79938	CCA	.	.		0.388	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245		C	78202323	G	C	78202323	3	2	132	1	0	0	0	0	1	0	0	0	14894	1348	47	4	977	4	SNW1	14	78202323	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10		78202323	29147217	52	21480										
NRXN3	9369	hgsc.bcm.edu	37	chr14	79434590	79434590	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tcgtggcctctcgagatggcTttcagggctgtctagcatca	12	11	4	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr14:79434590T>A	ENST00000554719.1	+	11	2415	c.1924T>A	c.(1924-1926)Ttt>Att	p.F642I	NRXN3_ENST00000335750.5_Missense_Mutation_p.F642I	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	248					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TCGAGATGGCTTTCAGGGCTG	0.527																																					p.F642I		Atlas-SNP	.											.	NRXN3	342	.	0			c.T1924A						.						134	117	123					14																	79434590		2203	4300	6503	SO:0001583	missense	9369	exon11			GATGGCTTTCAGG	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.1924T>A	chr14.hg19:g.79434590T>A	ENSP00000451648:p.Phe642Ile	169.0	0.0		196.0	49.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	hg19	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	T	36	5.777289	0.96929	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750	D;D	0.90620	-2.7;-2.7	6.03	6.03	0.97812	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.108331	0.64402	D	0.000006	D	0.94932	0.8361	.	.	.	0.58432	D	0.999999	D;D	0.69078	0.997;0.971	D;P	0.67548	0.952;0.774	D	0.94735	0.7913	8	.	.	.	.	16.5655	0.84588	0.0:0.0:0.0:1.0	.	1015;642	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	I	1015;1004;642;642	ENSP00000451648:F642I;ENSP00000338349:F642I	.	F	+	1	0	NRXN3	78504343	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	8.040000	0.89188	2.302000	0.77476	0.533000	0.62120	TTT	.	.		0.527	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250		A	79434590	T	A	79434590	3	1	132	1	0	0	0	0	1	0	0	0	10676	1609	56	4	1958	4	NRXN3	14	79434590	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	1232267	79434590	27914950	53	21481										
KCNK13	56659	hgsc.bcm.edu	37	chr14	90651290	90651290	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	gacaatgaattctcagggggGgtgggagcctttgcaatcat	14	7	2	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr14:90651290G>T	ENST00000282146.4	+	2	1611	c.1170G>T	c.(1168-1170)ggG>ggT	p.G390G		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	390					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				TCTCAGGGGGGGTGGGAGCCT	0.592																																					p.G390G		Atlas-SNP	.											.	KCNK13	76	.	0			c.G1170T						.						17	19	19					14																	90651290		2202	4296	6498	SO:0001819	synonymous_variant	56659	exon2			AGGGGGGGTGGGA	AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.1170G>T	chr14.hg19:g.90651290G>T		55.0	0.0		63.0	16.0	NM_022054	B5TJL8|Q96E79	Silent	SNP	ENST00000282146.4	hg19	CCDS9889.1																																																																																			.	.		0.592	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		T	90651290	G	T	90651290	2	4	132	1	0	0	0	0	0	0	0	1	8070	1219	43	3		3	KCNK13	14	90651290	Silent	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	11216700	90651290	16698250	54	21482										
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102551156	102551178	+	Frame_Shift_Del	DEL	CTTAATCTTCTTCTTCTTCTTCT	CTTAATCTTCTTCTTCTTCTTCT	-													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tcttgatcgatgtacttttcCttaatcttcttcttcttctt					rs371838714|rs372518751|rs55793809	byFrequency	TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	CTTAATCTTCTTCTTCTTCTTCT	CTTAATCTTCTTCTTCTTCTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr14:102551156_102551178delCTTAATCTTCTTCTTCTTCTTCT	ENST00000216281.8	-	5	1026_1048	c.821_843delAGAAGAAGAAGAAGAAGATTAAG	c.(820-843)aagaagaagaagaagaagattaagfs	p.KKKKKKIK274fs	HSP90AA1_ENST00000334701.7_Frame_Shift_Del_p.KKKKKKIK396fs|HSP90AA1_ENST00000441629.2_Frame_Shift_Del_p.KKKKKKIK95fs	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	274					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	TGTActtttccttaatcttcttcttcttcttcttgtcaccatc	0.372																																					p.396_404del		Atlas-Indel,Pindel	.											.	HSP90AA1	65	.	0			c.1188_1210del						.																																			SO:0001589	frameshift_variant	3320	exon6			.	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.821_843delAGAAGAAGAAGAAGAAGATTAAG	chr14.hg19:g.102551156_102551178delCTTAATCTTCTTCTTCTTCTTCT	ENSP00000216281:p.Lys274fs	76.0	0.0		90.0	11.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Frame_Shift_Del	DEL	ENST00000216281.8	hg19	CCDS9967.1																																																																																			.	.		0.372	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		-	102551178	CTTAATCTTCTTCTTCTTCTTCT	-	102551156	7	5	132	1	0	1	0	1	0	0	0	0	7410	680	24	0	1383	0	HSP90AA1	14	102551156	Frame_Shift_Del	DEL	CTTAATCTTCTTCTTCTTCTTCT	TCGA-DD-A4NJ-01A-11D-A27I-10	11899866	102551156	4798384	55	21483										
KIF26A	26153	hgsc.bcm.edu	37	chr14	104642627	104642628	+	Missense_Mutation	DNP	AG	AG	CT													0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tggggccagacagacctgacAgtcctgggccaacctggggt							TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr14:104642627_104642628AG>CT	ENST00000423312.2	+	12	3502_3503	c.3502_3503AG>CT	c.(3502-3504)AGt>CTt	p.S1168L	KIF26A_ENST00000315264.7_Missense_Mutation_p.S1029L	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1168					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		CAGACCTGACAGTCCTGGGCCA	0.728																																					p.S1168R|p.S1168I		Atlas-SNP	.											.	KIF26A	84	.	0			c.A3502C|c.G3503T						.																																			SO:0001583	missense	26153	exon12			CCTGACAGTCCTG|CTGACAGTCCTGG	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"Kinesins"	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	Exception_encountered	chr14.hg19:g.104642627_104642628delinsCT	ENSP00000388241:p.Ser1168Leu	20.0|21.0	0.0		41.0|40.0	7.0	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	hg19	CCDS45171.1																																																																																			.	.		0.728	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			CT	104642628	AG	CT	104642627	3	2	132	1	0	0	0	0	1	0	0	0	8303	188	7	5	3548	5	KIF26A	14	104642627	Missense_Mutation	DNP	AG	TCGA-DD-A4NJ-01A-11D-A27I-10	2091471	104642627	2706913	56	21484										
ADAMTS17	170691	hgsc.bcm.edu	37	chr15	100594228	100594228	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	agctctatcttccagtcactGttgatggaccccttacccga	7	14	3	1	rs368641530		TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr15:100594228G>A	ENST00000268070.4	-	16	2274	c.2169C>T	c.(2167-2169)aaC>aaT	p.N723N		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	723	Spacer.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		TCCAGTCACTGTTGATGGACC	0.532																																					p.N723N		Atlas-SNP	.											.	ADAMTS17	127	.	0			c.C2169T						.	G		0,4406		0,0,2203	141	145	144		2169	4.9	1	15		144	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADAMTS17	NM_139057.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		723/1096	100594228	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	170691	exon16			GTCACTGTTGATG	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.2169C>T	chr15.hg19:g.100594228G>A		101.0	0.0		301.0	143.0	NM_139057	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	hg19	CCDS10383.1																																																																																			.	.		0.532	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		A	100594228	G	A	100594228	2	1	132	1	0	0	0	0	0	0	0	1	262	1368	48	3		3	ADAMTS17	15	100594228	Silent	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10		100594228	1937164	57	21485										
FLYWCH2	114984	hgsc.bcm.edu	37	chr16	2946481	2946481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ccgagcccagcgagcaggagGgtgagagtgtgaaggccagc	18	10	0	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr16:2946481G>A	ENST00000396958.3	+	3	411	c.31G>A	c.(31-33)Ggt>Agt	p.G11S	FLYWCH2_ENST00000572006.1_Missense_Mutation_p.G11S|FLYWCH2_ENST00000293981.6_Missense_Mutation_p.G11S	NM_001142500.1|NM_138439.2	NP_001135972.1|NP_612448.1	Q96CP2	FWCH2_HUMAN	FLYWCH family member 2	11							poly(A) RNA binding (GO:0044822)	p.G11F(2)		central_nervous_system(1)|lung(3)|ovary(1)|skin(1)	6						CGAGCAGGAGGGTGAGAGTGT	0.657																																					p.G11S		Atlas-SNP	.											.,2	FLYWCH2	12	.	2	Substitution - Missense(2)	lung(2)	c.G31A						.						44	54	51					16																	2946481		2198	4300	6498	SO:0001583	missense	114984	exon3			CAGGAGGGTGAGA	BC014089	CCDS10482.1	16p13.3	2014-02-12	2007-06-21		ENSG00000162076	ENSG00000162076			25178	protein-coding gene	gene with protein product						12477932	Standard	NM_138439		Approved		uc010uwk.2	Q96CP2	OTTHUMG00000128962	ENST00000396958.3:c.31G>A	chr16.hg19:g.2946481G>A	ENSP00000380159:p.Gly11Ser	48.0	0.0		55.0	11.0	NM_001142499		Missense_Mutation	SNP	ENST00000396958.3	hg19	CCDS10482.1	.	.	.	.	.	.	.	.	.	.	G	12.27	1.886527	0.33348	.	.	ENSG00000162076	ENST00000396958;ENST00000293981	.	.	.	3.36	2.41	0.29592	.	0.000000	0.35805	N	0.002962	T	0.22205	0.0535	L	0.34521	1.04	0.20307	N	0.999912	P	0.36909	0.573	B	0.32090	0.14	T	0.16630	-1.0396	9	0.72032	D	0.01	.	6.4655	0.21980	0.1344:0.0:0.8656:0.0	.	11	Q96CP2	FWCH2_HUMAN	S	11	.	ENSP00000293981:G11S	G	+	1	0	FLYWCH2	2886482	0.757000	0.28394	0.470000	0.27216	0.729000	0.41735	0.742000	0.26216	1.008000	0.39264	0.407000	0.27541	GGT	.	.		0.657	FLYWCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250944.1	NM_138439		A	2946481	G	A	2946481	3	1	132	1	0	0	0	0	1	0	0	0	5956	1232	43	3	33	3	FLYWCH2	16	2946481	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10		2946481	87408272	58	21486										
CDH3	1001	hgsc.bcm.edu	37	chr16	68721498	68721498	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	gcccagtccctgagccccgtCagatcaccatctgcaaccaa	7	18	3	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr16:68721498C>A	ENST00000264012.4	+	12	2198	c.1654C>A	c.(1654-1656)Cag>Aag	p.Q552K	CDH3_ENST00000581171.1_Missense_Mutation_p.Q497K|CDH3_ENST00000429102.2_Missense_Mutation_p.Q552K	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	552	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		TGAGCCCCGTCAGATCACCAT	0.572																																					p.Q552K		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.C1654A						.						147	126	133					16																	68721498		2198	4300	6498	SO:0001583	missense	1001	exon12			CCCCGTCAGATCA	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"Cadherins / Major cadherins"	1762	protein-coding gene	gene with protein product		114021	"cadherin 3, P-cadherin (placental)"			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.1654C>A	chr16.hg19:g.68721498C>A	ENSP00000264012:p.Gln552Lys	247.0	0.0		214.0	112.0	NM_001793	B2R6F4|Q05DI6	Missense_Mutation	SNP	ENST00000264012.4	hg19	CCDS10868.1	.	.	.	.	.	.	.	.	.	.	C	8.630	0.893409	0.17613	.	.	ENSG00000062038	ENST00000429102;ENST00000264012;ENST00000542274	T;T	0.60672	0.17;0.17	5.29	1.02	0.19986	Cadherin (1);Cadherin-like (2);	0.854162	0.09735	N	0.762654	T	0.40956	0.1138	L	0.31664	0.95	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.24190	-1.0167	10	0.35671	T	0.21	.	5.0474	0.14490	0.2286:0.4738:0.227:0.0706	.	552	P22223	CADH3_HUMAN	K	552;552;497	ENSP00000398485:Q552K;ENSP00000264012:Q552K	ENSP00000264012:Q552K	Q	+	1	0	CDH3	67278999	0.000000	0.05858	0.009000	0.14445	0.725000	0.41563	-0.241000	0.08940	-0.257000	0.09459	-1.255000	0.01485	CAG	.	.		0.572	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793		A	68721498	C	A	68721498	3	1	132	1	0	0	0	0	1	0	0	0	3113	827	29	3	1700	3	CDH3	16	68721498	Missense_Mutation	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10	65775017	68721498	21633255	59	21487										
NF1	4763	hgsc.bcm.edu	37	chr17	29553694	29553694	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tgcctctgtcagcaatatgaTgtcaacaggtaaatgtgaat	9	7	3	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr17:29553694T>G	ENST00000358273.4	+	18	2626	c.2243T>G	c.(2242-2244)aTg>aGg	p.M748R	NF1_ENST00000356175.3_Missense_Mutation_p.M748R	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	748					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AGCAATATGATGTCAACAGGT	0.413			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.M748R		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.T2243G						.						124	111	115					17																	29553694		2203	4300	6503	SO:0001583	missense	4763	exon18	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	ATATGATGTCAAC		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.2243T>G	chr17.hg19:g.29553694T>G	ENSP00000351015:p.Met748Arg	65.0	0.0		91.0	40.0	NM_000267	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	T	15.68	2.905559	0.52333	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.07567	3.36;3.49;3.18	5.78	5.78	0.91487	Armadillo-type fold (1);	0.088921	0.85682	D	0.000000	T	0.05227	0.0139	N	0.04508	-0.205	0.80722	D	1	B;B;B	0.29716	0.004;0.255;0.0	B;B;B	0.28784	0.005;0.094;0.001	T	0.50767	-0.8789	10	0.38643	T	0.18	.	16.1254	0.81392	0.0:0.0:0.0:1.0	.	748;748;748	E1P657;P21359-2;P21359	.;.;NF1_HUMAN	R	748;748;414	ENSP00000351015:M748R;ENSP00000348498:M748R;ENSP00000389907:M414R	ENSP00000348498:M748R	M	+	2	0	NF1	26577820	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.828000	0.69307	2.195000	0.70347	0.528000	0.53228	ATG	.	.		0.413	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29553694	T	G	29553694	3	3	132	1	0	0	0	0	1	0	0	0	10365	1464	51	5	2374	5	NF1	17	29553694	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10		29553694	51641516	60	21488										
FBXL20	84961	hgsc.bcm.edu	37	chr17	37421707	37421707	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	attaatgtgctatctgttatCtgaaagaaataacgtatgtt	7	4	2	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr17:37421707C>A	ENST00000264658.6	-	13	1194		c.e13-1		FBXL20_ENST00000583610.1_Splice_Site|FBXL20_ENST00000577399.1_Splice_Site|FBXL20_ENST00000394294.3_Splice_Site	NM_032875.2	NP_116264.2	Q96IG2	FXL20_HUMAN	F-box and leucine-rich repeat protein 20						behavioral fear response (GO:0001662)	cytoplasm (GO:0005737)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22			LUAD - Lung adenocarcinoma(14;0.146)			TATCTGTTATCTGAAAGAAAT	0.328																																					.		Atlas-SNP	.											.	FBXL20	36	.	0			c.838-1G>T						.						101	92	95					17																	37421707		2203	4300	6503	SO:0001630	splice_region_variant	84961	exon13			TGTTATCTGAAAG	BC007557	CCDS32640.1, CCDS54116.1	17q21.2	2011-06-09				ENSG00000108306		"F-boxes / Leucine-rich repeats"	24679	protein-coding gene	gene with protein product		609086				12477932	Standard	NM_032875		Approved	MGC15482, Fbl2, Fbl20	uc002hrt.3	Q96IG2		ENST00000264658.6:c.934-1G>T	chr17.hg19:g.37421707C>A		56.0	0.0		83.0	36.0	NM_001184906	A8K729|Q38J52	Splice_Site	SNP	ENST00000264658.6	hg19	CCDS32640.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.543465	0.86022	.	.	ENSG00000108306	ENST00000264658;ENST00000394294	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7207	0.91692	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FBXL20	34675233	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.677000	0.84024	2.530000	0.85305	0.563000	0.77884	.	.	.		0.328	FBXL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444315.2	NM_032875	Intron	A	37421707	C	A	37421707	5	1	132	1	0	0	0	0	0	0	1	0	5725	927	32	3	389	3	FBXL20	17	37421707	Splice_Site	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10	7868013	37421707	43773503	61	21489										
FZD2	2535	hgsc.bcm.edu	37	chr17	42635258	42635258	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tgggccacacgaaccaggagGacgcaggcctagaggtgcac	15	12	0	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr17:42635258G>T	ENST00000315323.3	+	1	334	c.202G>T	c.(202-204)Gac>Tac	p.D68Y		NM_001466.3	NP_001457.1	Q14332	FZD2_HUMAN	frizzled class receptor 2	68	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cell-cell signaling (GO:0007267)|cochlea morphogenesis (GO:0090103)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|inner ear receptor cell development (GO:0060119)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|sensory perception of smell (GO:0007608)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(8)	33		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GAACCAGGAGGACGCAGGCCT	0.617																																					p.D68Y		Atlas-SNP	.											.	FZD2	81	.	0			c.G202T						.						161	144	150					17																	42635258		2203	4300	6503	SO:0001583	missense	2535	exon1			CAGGAGGACGCAG	L37882	CCDS11484.1	17q21.1	2014-01-29	2014-01-29			ENSG00000180340		"GPCR / Class F : Frizzled receptors"	4040	protein-coding gene	gene with protein product		600667	"frizzled (Drosophila) homolog 2", "frizzled homolog 2 (Drosophila)", "frizzled 2, seven transmembrane spanning receptor", "frizzled family receptor 2"			7558010, 9813155	Standard	NM_001466		Approved		uc002igx.2	Q14332		ENST00000315323.3:c.202G>T	chr17.hg19:g.42635258G>T	ENSP00000323901:p.Asp68Tyr	255.0	0.0		349.0	22.0	NM_001466	Q0VG82	Missense_Mutation	SNP	ENST00000315323.3	hg19	CCDS11484.1	.	.	.	.	.	.	.	.	.	.	g	18.49	3.634772	0.67130	.	.	ENSG00000180340	ENST00000541149;ENST00000315323	T	0.80214	-1.35	4.14	4.14	0.48551	Frizzled domain (5);	0.050318	0.85682	D	0.000000	D	0.90126	0.6915	M	0.85777	2.775	0.80722	D	1	D	0.69078	0.997	D	0.72075	0.976	D	0.92264	0.5819	10	0.87932	D	0	.	16.0247	0.80536	0.0:0.0:1.0:0.0	.	68	Q14332	FZD2_HUMAN	Y	144;68	ENSP00000323901:D68Y	ENSP00000323901:D68Y	D	+	1	0	FZD2	39990784	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.534000	0.98061	1.848000	0.53677	0.462000	0.41574	GAC	.	.		0.617	FZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457806.1	NM_001466		T	42635258	G	T	42635258	3	4	132	1	0	0	0	0	1	0	0	0	6138	1174	41	3	204	3	FZD2	17	42635258	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	5213551	42635258	38559952	62	21490										
ANKFN1	162282	hgsc.bcm.edu	37	chr17	54558126	54558126	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tgcaattgttcttctacgagCtccagatggcagtgaaagct	10	9	2	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr17:54558126C>T	ENST00000318698.2	+	16	2082	c.2047C>T	c.(2047-2049)Ctc>Ttc	p.L683F	ANKFN1_ENST00000566473.2_Missense_Mutation_p.L683F	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	683										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						CTTCTACGAGCTCCAGATGGC	0.423																																					p.L683F		Atlas-SNP	.											.	ANKFN1	115	.	0			c.C2047T						.						200	194	196					17																	54558126		2203	4300	6503	SO:0001583	missense	162282	exon16			TACGAGCTCCAGA	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.2047C>T	chr17.hg19:g.54558126C>T	ENSP00000321627:p.Leu683Phe	71.0	0.0		129.0	22.0	NM_153228		Missense_Mutation	SNP	ENST00000318698.2	hg19	CCDS32686.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182945	0.78677	.	.	ENSG00000153930	ENST00000318698	T	0.45668	0.89	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.68943	0.3056	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.72261	-0.4345	10	0.54805	T	0.06	-8.0775	19.1091	0.93310	0.0:1.0:0.0:0.0	.	683	Q8N957	ANKF1_HUMAN	F	683	ENSP00000321627:L683F	ENSP00000321627:L683F	L	+	1	0	ANKFN1	51913125	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.176000	0.77643	2.496000	0.84212	0.655000	0.94253	CTC	.	.		0.423	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		T	54558126	C	T	54558126	3	4	132	1	0	0	0	0	1	0	0	0	625	797	28	3	2109	3	ANKFN1	17	54558126	Missense_Mutation	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10	11922868	54558126	26637084	63	21491										
APCDD1	147495	hgsc.bcm.edu	37	chr18	10468488	10468488	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ctgggagagggttctgccctCcttcatccagacagcaggtc	12	13	2	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr18:10468488C>T	ENST00000355285.5	+	2	435	c.81C>T	c.(79-81)ctC>ctT	p.L27L	APCDD1_ENST00000578882.1_Silent_p.L27L	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		GTTCTGCCCTCCTTCATCCAG	0.488																																					p.L27L		Atlas-SNP	.											.	APCDD1	57	.	0			c.C81T						.						148	152	151					18																	10468488		2203	4300	6503	SO:0001819	synonymous_variant	147495	exon2			TGCCCTCCTTCAT	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.81C>T	chr18.hg19:g.10468488C>T		110.0	0.0		135.0	51.0	NM_153000		Silent	SNP	ENST00000355285.5	hg19	CCDS11849.1																																																																																			.	.		0.488	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		T	10468488	C	T	10468488	2	4	132	1	0	0	0	0	0	0	0	1	765	842	30	3		3	APCDD1	18	10468488	Silent	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10		10468488	67608760	64	21492										
C19orf35	374872	hgsc.bcm.edu	37	chr19	2280897	2280897	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ccaggtggggttgtcgggctCggggggctctgtggggggct	23	8	1	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr19:2280897C>T	ENST00000342063.3	-	2	127	c.34G>A	c.(34-36)Gag>Aag	p.E12K		NM_198532.2	NP_940934.1	Q6ZS72	CS035_HUMAN	chromosome 19 open reading frame 35	12										large_intestine(1)|lung(5)|pancreas(1)|prostate(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTGTCGGGCTCGGGGGGCTCT	0.687																																					p.E12K		Atlas-SNP	.											.	C19orf35	18	.	0			c.G34A						.						20	23	22					19																	2280897		2202	4298	6500	SO:0001583	missense	374872	exon2			CGGGCTCGGGGGG	AK127680	CCDS12087.1	19p13.3	2012-10-26			ENSG00000188305	ENSG00000188305			24793	protein-coding gene	gene with protein product							Standard	NM_198532		Approved	FLJ45778	uc002lvn.2	Q6ZS72	OTTHUMG00000178460	ENST00000342063.3:c.34G>A	chr19.hg19:g.2280897C>T	ENSP00000345102:p.Glu12Lys	28.0	0.0		44.0	4.0	NM_198532		Missense_Mutation	SNP	ENST00000342063.3	hg19	CCDS12087.1	.	.	.	.	.	.	.	.	.	.	c	9.616	1.132482	0.21041	.	.	ENSG00000188305	ENST00000342063	T	0.14391	2.51	2.84	1.8	0.24995	.	.	.	.	.	T	0.07188	0.0182	N	0.22421	0.69	0.09310	N	1	P	0.36660	0.564	B	0.27262	0.078	T	0.26224	-1.0109	9	0.33141	T	0.24	.	7.3986	0.26950	0.0:0.8567:0.0:0.1433	.	12	Q6ZS72	CS035_HUMAN	K	12	ENSP00000345102:E12K	ENSP00000345102:E12K	E	-	1	0	C19orf35	2231897	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.140000	0.16056	1.589000	0.49982	0.556000	0.70494	GAG	.	.		0.687	C19orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442080.1	NM_198532		T	2280897	C	T	2280897	3	4	132	1	0	0	0	0	1	0	0	0	1922	893	31	1	1399	1	C19orf35	19	2280897	Missense_Mutation	SNP	C	TCGA-DD-A4NJ-01A-11D-A27I-10		2280897	56848086	65	21493										
THOP1	7064	hgsc.bcm.edu	37	chr19	2794767	2794767	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tctcccctgttttagttcagAggaatatccttgacttcccc	6	13	2	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr19:2794767A>C	ENST00000307741.6	+	3	438	c.235A>C	c.(235-237)Agg>Cgg	p.R79R	THOP1_ENST00000586677.1_5'Flank	NM_003249.3	NP_003240.1	P52888	THOP1_HUMAN	thimet oligopeptidase 1	79					intracellular signal transduction (GO:0035556)|peptide metabolic process (GO:0006518)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			NS(1)|central_nervous_system(1)|endometrium(1)|lung(8)|ovary(2)|skin(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTTAGTTCAGAGGAATATCCT	0.577																																					p.R79R		Atlas-SNP	.											.	THOP1	49	.	0			c.A235C						.						160	170	167					19																	2794767		2203	4300	6503	SO:0001819	synonymous_variant	7064	exon3			GTTCAGAGGAATA		CCDS12095.1	19p13.3	2008-02-05				ENSG00000172009	3.4.24.15		11793	protein-coding gene	gene with protein product		601117				9790774	Standard	NM_003249		Approved		uc002lwj.3	P52888		ENST00000307741.6:c.235A>C	chr19.hg19:g.2794767A>C		88.0	0.0		77.0	12.0	NM_003249	B3KSE2|Q9UCB3	Silent	SNP	ENST00000307741.6	hg19	CCDS12095.1																																																																																			.	.		0.577	THOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451587.2			C	2794767	A	C	2794767	2	2	132	1	0	0	0	0	0	0	0	1	15886	295	11	5		5	THOP1	19	2794767	Silent	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10	513870	2794767	56334216	66	21494										
RYR1	6261	hgsc.bcm.edu	37	chr19	39018424	39018424	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	gtgctctactacctggaccaGgtgggtggggccggaggggt	19	9	1	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr19:39018424G>T	ENST00000359596.3	+	73	10824	c.10824G>T	c.(10822-10824)caG>caT	p.Q3608H	AC067969.1_ENST00000597015.1_RNA|RYR1_ENST00000355481.4_Splice_Site_p.Q3603H|RYR1_ENST00000360985.3_Splice_Site_p.Q3608H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3608					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACCTGGACCAGGTGGGTGGGG	0.642																																					p.Q3608H		Atlas-SNP	.											.	RYR1	708	.	0			c.G10824T						.						35	38	37					19																	39018424		2202	4300	6502	SO:0001630	splice_region_variant	6261	exon73			GGACCAGGTGGGT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.10824+1G>T	chr19.hg19:g.39018424G>T		113.0	0.0		120.0	29.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.916766	0.33815	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985;ENST00000538206	D;D;D	0.97066	-4.22;-4.22;-4.23	4.42	4.42	0.53409	.	0.228705	0.28790	U	0.014134	D	0.97408	0.9152	M	0.68593	2.085	0.58432	D	0.999998	D;D;D	0.59767	0.965;0.986;0.976	P;P;P	0.56216	0.723;0.794;0.628	D	0.97767	1.0224	10	0.59425	D	0.04	.	15.94	0.79747	0.0:0.0:1.0:0.0	.	3608;3603;3608	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	H	3608;3603;3608;528	ENSP00000352608:Q3608H;ENSP00000347667:Q3603H;ENSP00000354254:Q3608H	ENSP00000347667:Q3603H	Q	+	3	2	RYR1	43710264	1.000000	0.71417	1.000000	0.80357	0.425000	0.31504	7.338000	0.79269	2.289000	0.77006	0.313000	0.20887	CAG	.	.		0.642	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		Missense_Mutation	T	39018424	G	T	39018424	5	4	132	1	0	0	0	0	0	0	1	0	13783	1014	35	3	11114	3	RYR1	19	39018424	Splice_Site	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	36223657	39018424	20110559	67	21495										
SYT5	6861	hgsc.bcm.edu	37	chr19	55687105	55687105	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	cgaaggtctccccaaagtgaGggttcagcgtctgccgatgc	13	12	3	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr19:55687105G>C	ENST00000354308.3	-	5	881	c.512C>G	c.(511-513)cCt>cGt	p.P171R	CTD-2587H24.5_ENST00000591665.1_RNA|SYT5_ENST00000590851.1_Missense_Mutation_p.P168R|SYT5_ENST00000592935.1_5'Flank|SYT5_ENST00000537500.1_Missense_Mutation_p.P171R	NM_003180.2	NP_003171.2	O00445	SYT5_HUMAN	synaptotagmin V	171	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|dense core granule (GO:0031045)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		CCCAAAGTGAGGGTTCAGCGT	0.617																																					p.P171R		Atlas-SNP	.											.	SYT5	45	.	0			c.C512G						.						129	119	122					19																	55687105		2203	4300	6503	SO:0001583	missense	6861	exon5			AAGTGAGGGTTCA	X96783	CCDS12919.1, CCDS74455.1	19q13.42	2014-07-02			ENSG00000129990	ENSG00000129990		"Synaptotagmins"	11513	protein-coding gene	gene with protein product	"synaptotagmin 5"	600782				9177789	Standard	XM_006723338		Approved		uc002qjn.1	O00445	OTTHUMG00000180669	ENST00000354308.3:c.512C>G	chr19.hg19:g.55687105G>C	ENSP00000346265:p.Pro171Arg	273.0	0.0		351.0	67.0	NM_003180	B3KWJ8|B7Z300|Q86X72	Missense_Mutation	SNP	ENST00000354308.3	hg19	CCDS12919.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.534800	0.85812	.	.	ENSG00000129990	ENST00000537500;ENST00000354308;ENST00000543844	D;D	0.91407	-2.84;-2.84	4.54	4.54	0.55810	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.97813	0.9282	H	0.99825	4.815	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99509	1.0955	10	0.87932	D	0	.	16.9441	0.86226	0.0:0.0:1.0:0.0	.	168;171;171	B7Z300;Q4FD32;O00445	.;.;SYT5_HUMAN	R	171;171;168	ENSP00000442896:P171R;ENSP00000346265:P171R	ENSP00000346265:P171R	P	-	2	0	SYT5	60378917	1.000000	0.71417	0.989000	0.46669	0.853000	0.48598	7.775000	0.85489	2.480000	0.83734	0.555000	0.69702	CCT	.	.		0.617	SYT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452501.1	NM_003180		C	55687105	G	C	55687105	3	2	132	1	0	0	0	0	1	0	0	0	15492	1000	35	4	668	4	SYT5	19	55687105	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	16668681	55687105	3441878	68	21496										
NLRP9	338321	hgsc.bcm.edu	37	chr19	56244429	56244429	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ttttgcaacaaactgctcagGataattggcattggctgccg	10	9	1	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr19:56244429G>C	ENST00000332836.2	-	2	795	c.768C>G	c.(766-768)atC>atG	p.I256M		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	256	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		AACTGCTCAGGATAATTGGCA	0.418																																					p.I256M		Atlas-SNP	.											.	NLRP9	163	.	0			c.C768G						.						48	49	49					19																	56244429		2203	4300	6503	SO:0001583	missense	338321	exon2			GCTCAGGATAATT	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.768C>G	chr19.hg19:g.56244429G>C	ENSP00000331857:p.Ile256Met	48.0	0.0		49.0	13.0	NM_176820	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	hg19	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.894510	0.52121	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.79033	-1.23	2.46	2.46	0.29980	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.80696	0.4672	L	0.53249	1.67	0.26881	N	0.967537	D	0.54397	0.966	P	0.61477	0.889	T	0.68655	-0.5351	9	0.72032	D	0.01	.	5.254	0.15537	0.1587:0.0:0.8413:0.0	.	256	Q7RTR0	NALP9_HUMAN	M	256	ENSP00000331857:I256M	ENSP00000331857:I256M	I	-	3	3	NLRP9	60936241	0.089000	0.21612	0.100000	0.21137	0.643000	0.38383	-0.143000	0.10296	1.731000	0.51592	0.644000	0.83932	ATC	.	.		0.418	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		C	56244429	G	C	56244429	3	2	132	1	0	0	0	0	1	0	0	0	10493	1164	41	4	2239	4	NLRP9	19	56244429	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	557324	56244429	2884554	69	21497										
ANGPT4	51378	hgsc.bcm.edu	37	chr20	861812	861812	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	agttcccagggagccccctaAccttcctgggcttcgttgca	10	15	0	0			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr20:861812A>C	ENST00000381922.3	-	5	1054		c.e5+1		ANGPT4_ENST00000546022.1_Splice_Site	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						GAGCCCCCTAACCTTCCTGGG	0.597																																					.	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											.	ANGPT4	77	.	0			c.951+2T>G						.						53	44	47					20																	861812		2203	4300	6503	SO:0001630	splice_region_variant	51378	exon6			CCCCTAACCTTCC	AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"Fibrinogen C domain containing"	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.951+1T>G	chr20.hg19:g.861812A>C		118.0	0.0		144.0	51.0	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Splice_Site	SNP	ENST00000381922.3	hg19	CCDS13009.1	.	.	.	.	.	.	.	.	.	.	A	17.54	3.414167	0.62511	.	.	ENSG00000101280	ENST00000381922;ENST00000546022	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5025	0.61465	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ANGPT4	809812	1.000000	0.71417	0.982000	0.44146	0.589000	0.36550	8.892000	0.92491	2.069000	0.61940	0.459000	0.35465	.	.	.		0.597	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985	Intron	C	861812	A	C	861812	5	2	132	1	0	0	0	0	0	0	1	0	612	57	2	5	578	5	ANGPT4	20	861812	Splice_Site	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10		861812	62163708	70	21498										
TMC2	117532	hgsc.bcm.edu	37	chr20	2591138	2591138	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	catcgctgccctggagaattAccacccacgcactggactga	9	15	0	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr20:2591138A>T	ENST00000358864.1	+	12	1502	c.1487A>T	c.(1486-1488)tAc>tTc	p.Y496F	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	496					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						CTGGAGAATTACCACCCACGC	0.527																																					p.Y496F		Atlas-SNP	.											.	TMC2	121	.	0			c.A1487T						.						258	214	229					20																	2591138		2203	4300	6503	SO:0001583	missense	117532	exon12			AGAATTACCACCC	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1487A>T	chr20.hg19:g.2591138A>T	ENSP00000351732:p.Tyr496Phe	224.0	0.0		259.0	34.0	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	hg19	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	A	26.6	4.752008	0.89753	.	.	ENSG00000149488	ENST00000358864	D	0.87412	-2.25	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.93226	0.7842	M	0.83774	2.66	0.80722	D	1	D;D;D;D	0.89917	0.993;0.998;0.999;1.0	D;D;D;D	0.79784	0.926;0.993;0.977;0.968	D	0.93994	0.7269	10	0.72032	D	0.01	-14.4871	13.0887	0.59156	1.0:0.0:0.0:0.0	.	327;328;496;496	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	F	496	ENSP00000351732:Y496F	ENSP00000351732:Y496F	Y	+	2	0	TMC2	2539138	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.265000	0.95647	2.033000	0.60031	0.528000	0.53228	TAC	.	.		0.527	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			T	2591138	A	T	2591138	3	4	132	1	0	0	0	0	1	0	0	0	16000	391	14	4	1533	4	TMC2	20	2591138	Missense_Mutation	SNP	A	TCGA-DD-A4NJ-01A-11D-A27I-10	1729326	2591138	60434382	71	21499										
PHACTR3	116154	hgsc.bcm.edu	37	chr20	58416548	58416548	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	aaagcgcaggactatgacagGagggcagacaaaccctggac	13	10	0	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr20:58416548G>A	ENST00000371015.1	+	11	2012	c.1545G>A	c.(1543-1545)agG>agA	p.R515R	PHACTR3_ENST00000361300.4_Silent_p.R404R|PHACTR3_ENST00000541461.1_Silent_p.R474R|PHACTR3_ENST00000395639.4_Silent_p.R404R|PHACTR3_ENST00000359926.3_Silent_p.R512R|PHACTR3_ENST00000395636.2_Silent_p.R474R|PHACTR3_ENST00000355648.4_Silent_p.R474R	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	515	Required for PP1CA binding and inhibition of PP1 activity.					nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			ACTATGACAGGAGGGCAGACA	0.448																																					p.R515R		Atlas-SNP	.											PHACTR3,NS,carcinoma,0,1	PHACTR3	104	.	0			c.G1545A						.						91	81	84					20																	58416548		2203	4300	6503	SO:0001819	synonymous_variant	116154	exon11			TGACAGGAGGGCA	AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"Phosphatase and actin regulators"	15833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 123"	608725	"chromosome 20 open reading frame 101"	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.1545G>A	chr20.hg19:g.58416548G>A		218.0	0.0		256.0	38.0	NM_080672	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Silent	SNP	ENST00000371015.1	hg19	CCDS13480.1																																																																																			.	.		0.448	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		A	58416548	G	A	58416548	2	1	132	1	0	0	0	0	0	0	0	1	11820	1165	41	3		3	PHACTR3	20	58416548	Silent	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	55825410	58416548	4608972	72	21500										
STMN3	50861	hgsc.bcm.edu	37	chr20	62275626	62275626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	agaagcaggagcagatgagcGacagcaccgacagctccttc	12	12	0	3			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr20:62275626G>A	ENST00000370053.1	-	2	137	c.56C>T	c.(55-57)tCg>tTg	p.S19L	STMN3_ENST00000540534.1_Missense_Mutation_p.S8L	NM_001276310.1|NM_015894.2	NP_001263239.1|NP_056978.2	Q9NZ72	STMN3_HUMAN	stathmin-like 3	19					cytoplasmic microtubule organization (GO:0031122)|negative regulation of Rac protein signal transduction (GO:0035021)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|regulation of cytoskeleton organization (GO:0051493)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of Rac GTPase activity (GO:0032314)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	protein domain specific binding (GO:0019904)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)	8	all_cancers(38;2.31e-11)|all_epithelial(29;7.76e-13)		Epithelial(9;1.9e-09)|all cancers(9;1.22e-08)|BRCA - Breast invasive adenocarcinoma(10;8.86e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.00559)			GCAGATGAGCGACAGCACCGA	0.642																																					p.S19L		Atlas-SNP	.											.	STMN3	19	.	0			c.C56T						.						186	143	157					20																	62275626		2203	4300	6503	SO:0001583	missense	50861	exon2			ATGAGCGACAGCA	AF069709	CCDS13529.1, CCDS63330.1	20q13.3	2007-01-22			ENSG00000197457	ENSG00000197457			15926	protein-coding gene	gene with protein product		608362				9603203, 10655513	Standard	NM_001276310		Approved	SCLIP	uc002yfr.2	Q9NZ72	OTTHUMG00000032985	ENST00000370053.1:c.56C>T	chr20.hg19:g.62275626G>A	ENSP00000359070:p.Ser19Leu	85.0	0.0		126.0	41.0	NM_015894	B3KSQ5|B7WP52|B7Z5G4|O75527|Q969Y4	Missense_Mutation	SNP	ENST00000370053.1	hg19	CCDS13529.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.813781	0.70912	.	.	ENSG00000197457	ENST00000370053;ENST00000540534	.	.	.	4.2	4.2	0.49525	.	0.229124	0.28036	U	0.016847	T	0.52224	0.1721	M	0.78456	2.415	0.43292	D	0.995278	P	0.43352	0.804	B	0.29942	0.109	T	0.64245	-0.6453	9	0.87932	D	0	-7.9244	11.7791	0.52003	0.0:0.0:0.8241:0.1759	.	19	Q9NZ72	STMN3_HUMAN	L	19;8	.	ENSP00000359070:S19L	S	-	2	0	STMN3	61746070	1.000000	0.71417	0.835000	0.33067	0.705000	0.40729	9.664000	0.98607	1.904000	0.55121	0.313000	0.20887	TCG	.	.		0.642	STMN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080163.1	NM_015894		A	62275626	G	A	62275626	3	1	132	1	0	0	0	0	1	0	0	0	15325	1059	37	1	502	1	STMN3	20	62275626	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	3859078	62275626	749894	73	21501										
TTC3	7267	hgsc.bcm.edu	37	chr21	38538717	38538717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	atgttgctggtcaccagattGcctctgaaacacagatcctt	8	11	2	3			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr21:38538717G>A	ENST00000399017.2	+	33	6948	c.4201G>A	c.(4201-4203)Gcc>Acc	p.A1401T	TTC3_ENST00000355666.1_Missense_Mutation_p.A1401T|TTC3_ENST00000354749.2_Missense_Mutation_p.A1401T|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1401					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TCACCAGATTGCCTCTGAAAC	0.453																																					p.A1401T	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.G4201A						.						124	115	118					21																	38538717		2203	4300	6503	SO:0001583	missense	7267	exon33			CAGATTGCCTCTG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.4201G>A	chr21.hg19:g.38538717G>A	ENSP00000381981:p.Ala1401Thr	148.0	0.0		210.0	61.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	G	12.52	1.963456	0.34659	.	.	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.08720	3.06;3.06;3.06	4.65	1.63	0.23807	.	0.921456	0.09160	N	0.840330	T	0.08802	0.0218	L	0.44542	1.39	0.09310	N	1	P;P	0.49559	0.925;0.914	B;B	0.44044	0.439;0.355	T	0.31475	-0.9942	9	.	.	.	-0.0035	5.1944	0.15227	0.2043:0.1747:0.621:0.0	.	459;1401	Q5GIT6;P53804	.;TTC3_HUMAN	T	1401	ENSP00000347889:A1401T;ENSP00000381981:A1401T;ENSP00000346791:A1401T	.	A	+	1	0	TTC3	37460587	0.000000	0.05858	0.001000	0.08648	0.109000	0.19521	-0.036000	0.12185	0.456000	0.26937	0.655000	0.94253	GCC	.	.		0.453	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			A	38538717	G	A	38538717	3	1	132	1	0	0	0	0	1	0	0	0	16712	1319	46	3	4327	3	TTC3	21	38538717	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10		38538717	9591178	74	21502										
TMPRSS3	64699	hgsc.bcm.edu	37	chr21	43808542	43808542	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	ccagttgggcacaggcaacaTttgcgtagtgacccttccag	11	12	0	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chr21:43808542T>C	ENST00000291532.3	-	5	1371	c.416A>G	c.(415-417)aAt>aGt	p.N139S	TMPRSS3_ENST00000398405.1_Missense_Mutation_p.N137S|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.N223S|TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000433957.2_Missense_Mutation_p.N139S|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.N139S	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	139	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						ACAGGCAACATTTGCGTAGTG	0.517																																					p.N139S		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.A416G						.						152	135	141					21																	43808542		2203	4300	6503	SO:0001583	missense	64699	exon5			GCAACATTTGCGT	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"Serine peptidases / Transmembrane"	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.416A>G	chr21.hg19:g.43808542T>C	ENSP00000291532:p.Asn139Ser	172.0	0.0		288.0	94.0	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	hg19	CCDS13686.1	.	.	.	.	.	.	.	.	.	.	T	5.536	0.283860	0.10458	.	.	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21	4.94	-4.17	0.03857	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	1.597180	0.03547	N	0.224911	T	0.49830	0.1580	M	0.70595	2.14	0.09310	N	1	B;B;B	0.14012	0.009;0.0;0.0	B;B;B	0.11329	0.006;0.001;0.003	T	0.25537	-1.0129	9	.	.	.	.	1.7632	0.02996	0.1097:0.2292:0.2109:0.4502	.	139;139;139	P57727-3;P57727-5;P57727	.;.;TMPS3_HUMAN	S	139;139;137;223;139	ENSP00000291532:N139S;ENSP00000411013:N139S;ENSP00000381442:N137S;ENSP00000369762:N223S;ENSP00000381434:N139S	.	N	-	2	0	TMPRSS3	42681611	0.000000	0.05858	0.000000	0.03702	0.836000	0.47400	0.097000	0.15168	-0.391000	0.07763	0.402000	0.26972	AAT	.	.		0.517	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1			C	43808542	T	C	43808542	3	2	132	1	0	0	0	0	1	0	0	0	16263	1493	52	2	1067	2	TMPRSS3	21	43808542	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	5269825	43808542	4321353	75	21503										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5821238	5821238	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tggggatgccgaagacatagGggacctcatcaccatgggcc	14	11	2	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chrX:5821238G>T	ENST00000381095.3	-	5	2108	c.1481C>A	c.(1480-1482)cCc>cAc	p.P494H	NLGN4X_ENST00000381093.2_Missense_Mutation_p.P514H|NLGN4X_ENST00000538097.1_Missense_Mutation_p.P494H|NLGN4X_ENST00000275857.6_Missense_Mutation_p.P494H|NLGN4X_ENST00000381092.1_Missense_Mutation_p.P494H	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	494					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						GAAGACATAGGGGACCTCATC	0.557																																					p.P494H		Atlas-SNP	.											.	NLGN4X	191	.	0			c.C1481A						.						97	81	86					X																	5821238		2203	4300	6503	SO:0001583	missense	57502	exon5			ACATAGGGGACCT	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1481C>A	chrX.hg19:g.5821238G>T	ENSP00000370485:p.Pro494His	431.0	0.0		589.0	134.0	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.398700	0.42512	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	3.93	3.93	0.45458	Carboxylesterase, type B (1);	.	.	.	.	D	0.84620	0.5512	M	0.91872	3.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.989;1.0;0.998	D	0.88636	0.3172	9	0.87932	D	0	.	14.4947	0.67678	0.0:0.0:1.0:0.0	.	551;494;514	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	H	494;514;494;494;494	ENSP00000370485:P494H;ENSP00000370483:P514H;ENSP00000275857:P494H;ENSP00000370482:P494H;ENSP00000439203:P494H	ENSP00000275857:P494H	P	-	2	0	NLGN4X	5831238	1.000000	0.71417	0.547000	0.28179	0.082000	0.17680	8.442000	0.90317	1.579000	0.49836	0.600000	0.82982	CCC	.	.		0.557	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		T	5821238	G	T	5821238	3	4	132	1	0	0	0	0	1	0	0	0	10473	1232	43	3	977	3	NLGN4X	23	5821238	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10		5821238	149449322	76	21504										
PFKFB1	5207	hgsc.bcm.edu	37	chrX	54978366	54978366	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	cgcgaactgagaggccagagTcacctccgatgcggcctctg	13	14	2	2			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chrX:54978366T>G	ENST00000375006.3	-	8	888	c.818A>C	c.(817-819)gAc>gCc	p.D273A	PFKFB1_ENST00000374992.2_Intron|PFKFB1_ENST00000545676.1_Missense_Mutation_p.D208A	NM_002625.2	NP_002616.2	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	273	Fructose-2,6-bisphosphatase.				carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|intracellular signal transduction (GO:0035556)|organ regeneration (GO:0031100)|positive regulation of glucokinase activity (GO:0033133)|response to cAMP (GO:0051591)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex (GO:0043540)|cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|fructose-6-phosphate binding (GO:0070095)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)	24						GAGGCCAGAGTCACCTCCGAT	0.582																																					p.D273A		Atlas-SNP	.											.	PFKFB1	64	.	0			c.A818C						.						102	65	78					X																	54978366		2202	4299	6501	SO:0001583	missense	5207	exon8			CCAGAGTCACCTC		CCDS14364.1, CCDS65273.1	Xp11.21	2012-07-13			ENSG00000158571	ENSG00000158571	2.7.1.105, 3.1.3.46		8872	protein-coding gene	gene with protein product		311790		PFRX		9119406	Standard	NM_002625		Approved		uc004dty.2	P16118	OTTHUMG00000021643	ENST00000375006.3:c.818A>C	chrX.hg19:g.54978366T>G	ENSP00000364145:p.Asp273Ala	206.0	0.0		235.0	70.0	NM_002625	B2RA88|B4DUN5|Q5JXS5|Q99951	Missense_Mutation	SNP	ENST00000375006.3	hg19	CCDS14364.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.257593	0.80246	.	.	ENSG00000158571	ENST00000375006;ENST00000545676	T;T	0.73152	-0.72;-0.72	4.53	4.53	0.55603	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	D	0.000000	D	0.90827	0.7119	H	0.99642	4.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93746	0.7054	10	0.87932	D	0	-23.1119	12.3464	0.55124	0.0:0.0:0.0:1.0	.	208;273	B4DUN5;P16118	.;F261_HUMAN	A	273;208	ENSP00000364145:D273A;ENSP00000444074:D208A	ENSP00000364145:D273A	D	-	2	0	PFKFB1	54995091	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	7.841000	0.86834	1.618000	0.50286	0.422000	0.28245	GAC	.	.		0.582	PFKFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056847.1			G	54978366	T	G	54978366	3	3	132	1	0	0	0	0	1	0	0	0	11769	1667	58	5	625	5	PFKFB1	23	54978366	Missense_Mutation	SNP	T	TCGA-DD-A4NJ-01A-11D-A27I-10	49157128	54978366	100292194	77	21505										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153034490	153034490	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.012987012987013	1	1	0.258531356083616	0	0.312392055267703	1	1	0	tcagcccagacctgctgctgGacagcagtggcagtcacctc	11	15	2	1			TCGA-DD-A4NJ-01A-11D-A27I-10	TCGA-DD-A4NJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e0b2f481-ccfb-4dcb-a3a4-56eb06e6623e	5a036ee2-e439-437a-8708-f758a33834ac	g.chrX:153034490G>A	ENST00000361971.5	+	5	1468	c.1354G>A	c.(1354-1356)Gac>Aac	p.D452N	PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538282.1_Intron|U52111.14_ENST00000434284.1_RNA|PLXNB3_ENST00000538776.1_Missense_Mutation_p.D105N|PLXNB3_ENST00000538966.1_Missense_Mutation_p.D475N|U52111.14_ENST00000416854.1_RNA	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	452	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CCTGCTGCTGGACAGCAGTGG	0.647																																					p.D475N		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G1423A						.						63	54	57					X																	153034490		2202	4300	6502	SO:0001583	missense	5365	exon6			CTGCTGGACAGCA	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.1354G>A	chrX.hg19:g.153034490G>A	ENSP00000355378:p.Asp452Asn	141.0	0.0		183.0	10.0	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.296121	0.60086	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776	T;T;T	0.05447	3.44;3.44;3.44	5.27	5.27	0.74061	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (3);	0.054815	0.64402	D	0.000001	T	0.16300	0.0392	M	0.85630	2.765	0.34413	D	0.696535	B;P;P;B	0.40578	0.237;0.722;0.474;0.108	B;B;B;B	0.42386	0.255;0.267;0.386;0.144	T	0.24012	-1.0172	10	0.59425	D	0.04	.	15.2028	0.73153	0.0:0.0:1.0:0.0	.	105;134;475;452	B7Z3H9;B7Z9A5;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	N	475;452;105	ENSP00000442736:D475N;ENSP00000355378:D452N;ENSP00000445569:D105N	ENSP00000355378:D452N	D	+	1	0	PLXNB3	152687684	1.000000	0.71417	0.991000	0.47740	0.693000	0.40251	2.956000	0.49129	2.178000	0.69098	0.513000	0.50165	GAC	.	.		0.647	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			A	153034490	G	A	153034490	3	1	132	1	0	0	0	0	1	0	0	0	12134	1174	41	3	1486	3	PLXNB3	23	153034490	Missense_Mutation	SNP	G	TCGA-DD-A4NJ-01A-11D-A27I-10	98056124	153034490	2236070	78	21506										
MACF1	23499	hgsc.bcm.edu	37	chr1	39920643	39920643	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gccttgtcagaactggtggcTaatgctgagctcctggaaga	13	9	1	3			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr1:39920643T>A	ENST00000372915.3	+	88	20733	c.20646T>A	c.(20644-20646)gcT>gcA	p.A6882A	MACF1_ENST00000545844.1_Silent_p.A4924A|MACF1_ENST00000289893.4_Silent_p.A5426A|MACF1_ENST00000361689.2_Silent_p.A4924A|MACF1_ENST00000564288.1_Silent_p.A6983A|MACF1_ENST00000567887.1_Silent_p.A7020A|MACF1_ENST00000539005.1_Silent_p.A4794A|MACF1_ENST00000317713.7_Silent_p.A4924A			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6882					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AACTGGTGGCTAATGCTGAGC	0.542																																					p.A4924A		Atlas-SNP	.											.	MACF1	909	.	0			c.T14772A						.						98	86	90					1																	39920643		2203	4300	6503	SO:0001819	synonymous_variant	23499	exon86			GGTGGCTAATGCT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.20646T>A	chr1.hg19:g.39920643T>A		135.0	0.0		92.0	6.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.18|10.18	1.279980|1.279980	0.23392|0.23392	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000360115|ENST00000372925	.|.	.|.	.|.	5.51|5.51	-6.37|-6.37	0.01963|0.01963	.|.	.|.	.|.	.|.	.|.	T|.	0.33059|.	0.0850|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.44513|.	-0.9323|.	4|.	.|.	.|.	.|.	.|.	0.1858|0.1858	0.00128|0.00128	0.3236:0.2168:0.2266:0.2331|0.3236:0.2168:0.2266:0.2331	.|.	.|.	.|.	.|.	Q|K	26|3928	.|.	.|.	L|X	+|+	2|1	0|0	MACF1|MACF1	39693230|39693230	0.489000|0.489000	0.26004|0.26004	0.952000|0.952000	0.39060|0.39060	0.968000|0.968000	0.65278|0.65278	-0.291000|-0.291000	0.08343|0.08343	-0.604000|-0.604000	0.05760|0.05760	-0.408000|-0.408000	0.06270|0.06270	CTA|TAA	.	.		0.542	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39920643	T	A	39920643	2	1	133	1	0	0	0	0	0	0	0	1	9153	1509	53	4		4	MACF1	1	39920643	Silent	SNP	T	TCGA-DD-A4NK-01A-11D-A28X-10		39920643	209329978	1	21507										
IPO13	9670	hgsc.bcm.edu	37	chr1	44415602	44415602	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gcctggcggtggaatgtgggGctgtcttcccgctgctggag	18	10	1	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr1:44415602G>A	ENST00000372343.3	+	2	1260	c.598G>A	c.(598-600)Gct>Act	p.A200T		NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	200					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				GGAATGTGGGGCTGTCTTCCC	0.622																																					p.A200T		Atlas-SNP	.											.	IPO13	86	.	0			c.G598A						.						15	17	16					1																	44415602		2203	4298	6501	SO:0001583	missense	9670	exon2			TGTGGGGCTGTCT	AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"Importins"	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.598G>A	chr1.hg19:g.44415602G>A	ENSP00000361418:p.Ala200Thr	58.0	0.0		51.0	21.0	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Missense_Mutation	SNP	ENST00000372343.3	hg19	CCDS503.1	.	.	.	.	.	.	.	.	.	.	G	2.188	-0.385964	0.04966	.	.	ENSG00000117408	ENST00000372343	T	0.41065	1.01	5.46	4.54	0.55810	Exportin-1/Importin-beta-like (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.275968	0.41396	N	0.000890	T	0.20941	0.0504	N	0.12182	0.205	0.80722	D	1	B	0.26602	0.154	B	0.27380	0.079	T	0.05852	-1.0860	10	0.08381	T	0.77	-7.8459	8.0028	0.30308	0.0808:0.0:0.6636:0.2557	.	200	O94829	IPO13_HUMAN	T	200	ENSP00000361418:A200T	ENSP00000361418:A200T	A	+	1	0	IPO13	44188189	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	2.050000	0.41297	1.290000	0.44636	0.491000	0.48974	GCT	.	.		0.622	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652		A	44415602	G	A	44415602	3	1	133	1	0	0	0	0	1	0	0	0	7803	1203	42	3	604	3	IPO13	1	44415602	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	4494959	44415602	204835019	2	21508										
BEND5	79656	hgsc.bcm.edu	37	chr1	49208383	49208383	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cttcctcactgaaagtgctcCgtaactccggctcgggctcg	10	15	1	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr1:49208383C>T	ENST00000371833.3	-	4	892	c.806G>A	c.(805-807)cGg>cAg	p.R269Q	AGBL4_ENST00000371839.1_Intron|AGBL4_ENST00000371838.1_Intron|BEND5_ENST00000476096.1_Intron	NM_024603.2	NP_078879.2	Q7L4P6	BEND5_HUMAN	BEN domain containing 5	269						Golgi apparatus (GO:0005794)				large_intestine(5)|lung(2)|skin(1)	8						GAAAGTGCTCCGTAACTCCGG	0.473																																					p.R269Q		Atlas-SNP	.											BEND5_ENST00000371833,colon,carcinoma,0,2	BEND5	93	.	0			c.G806A						.						113	105	108					1																	49208383		2203	4300	6503	SO:0001583	missense	79656	exon4			GTGCTCCGTAACT	BC007932	CCDS552.2	1p33	2012-11-22	2008-10-03	2008-10-03	ENSG00000162373	ENSG00000162373		"BEN domain containing"	25668	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 165"	C1orf165		12477932	Standard	NM_024603		Approved	FLJ11588	uc001crx.4	Q7L4P6	OTTHUMG00000008153	ENST00000371833.3:c.806G>A	chr1.hg19:g.49208383C>T	ENSP00000360899:p.Arg269Gln	79.0	0.0		61.0	11.0	NM_024603	D3DQ27|Q96A62|Q9HAI3	Missense_Mutation	SNP	ENST00000371833.3	hg19	CCDS552.2	.	.	.	.	.	.	.	.	.	.	C	11.83	1.754417	0.31046	.	.	ENSG00000162373	ENST00000371833	.	.	.	5.45	3.52	0.40303	.	0.119122	0.56097	N	0.000023	T	0.21761	0.0524	N	0.04880	-0.145	0.35690	D	0.814756	B	0.06786	0.001	B	0.01281	0.0	T	0.15838	-1.0423	8	.	.	.	-15.8643	7.2545	0.26168	0.0:0.6867:0.0:0.3133	.	269	Q7L4P6	BEND5_HUMAN	Q	269	.	.	R	-	2	0	BEND5	48980970	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.122000	0.50446	1.510000	0.48803	0.591000	0.81541	CGG	.	.		0.473	BEND5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022323.1	NM_024603		T	49208383	C	T	49208383	3	4	133	1	0	0	0	0	1	0	0	0	1401	652	23	1	471	1	BEND5	1	49208383	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	4792781	49208383	200042238	3	21509										
HFE2	148738	hgsc.bcm.edu	37	chr1	145416462	145416462	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ttgtcgattcaaactgctaaCcctgggaaccatgtggagat	10	9	1	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr1:145416462C>A	ENST00000336751.5	+	4	1045	c.807C>A	c.(805-807)aaC>aaA	p.N269K	HFE2_ENST00000357836.5_Missense_Mutation_p.N156K|HFE2_ENST00000475797.1_Missense_Mutation_p.N43K|HFE2_ENST00000497365.1_Missense_Mutation_p.N43K	NM_213653.3	NP_998818.1	Q6ZVN8	RGMC_HUMAN	hemochromatosis type 2 (juvenile)	269					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|iron ion homeostasis (GO:0055072)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	14	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AAACTGCTAACCCTGGGAACC	0.502																																					p.N269K		Atlas-SNP	.											.	HFE2	48	.	0			c.C807A						.						107	108	108					1																	145416462		2203	4300	6503	SO:0001583	missense	148738	exon4			TGCTAACCCTGGG	AY372521	CCDS72877.1, CCDS72878.1, CCDS72879.1	1q21.2	2014-06-26			ENSG00000168509	ENSG00000168509			4887	protein-coding gene	gene with protein product	"repulsive guidance molecule c"	608374				10205270, 14647275	Standard	NM_213653		Approved	JH, HFE2A, RGMC, HJV, hemojuvelin, haemojuvelin	uc001eni.2	Q6ZVN8	OTTHUMG00000013748	ENST00000336751.5:c.807C>A	chr1.hg19:g.145416462C>A	ENSP00000337014:p.Asn269Lys	148.0	0.0		132.0	38.0	NM_213653	B1ALI7|Q2PQ63|Q6IMF6|Q8NAH2|Q8WVJ5	Missense_Mutation	SNP	ENST00000336751.5	hg19	CCDS910.1	.	.	.	.	.	.	.	.	.	.	C	4.206	0.036975	0.08148	.	.	ENSG00000168509	ENST00000357836;ENST00000336751;ENST00000497365;ENST00000475797	D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76	5.18	3.23	0.37069	Repulsive guidance molecule, C-terminal (1);	0.541229	0.19997	N	0.101436	T	0.42698	0.1214	N	0.22421	0.69	0.29765	N	0.835266	B	0.23185	0.081	B	0.21917	0.037	T	0.29761	-1.0001	10	0.06099	T	0.92	-18.4474	4.1701	0.10326	0.1604:0.5972:0.1555:0.0868	.	269	Q6ZVN8	RGMC_HUMAN	K	156;269;43;43	ENSP00000350495:N156K;ENSP00000337014:N269K;ENSP00000421820:N43K;ENSP00000425716:N43K	ENSP00000337014:N269K	N	+	3	2	HFE2	144127819	0.474000	0.25886	0.992000	0.48379	0.991000	0.79684	0.833000	0.27504	1.417000	0.47077	0.655000	0.94253	AAC	.	.		0.502	HFE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038527.1	NM_145277		A	145416462	C	A	145416462	3	1	133	1	0	0	0	0	1	0	0	0	7091	506	18	3	817	3	HFE2	1	145416462	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	96208079	145416462	103834159	4	21510										
DISP1	84976	hgsc.bcm.edu	37	chr1	223177045	223177045	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gcgttatgatgctgaatacaAaaagcttttcatgtttgaac	8	6	1	3			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr1:223177045A>G	ENST00000284476.6	+	8	2470	c.2306A>G	c.(2305-2307)aAa>aGa	p.K769R		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	769					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		GCTGAATACAAAAAGCTTTTC	0.478																																					p.K769R		Atlas-SNP	.											.	DISP1	145	.	0			c.A2306G						.						65	63	64					1																	223177045		2203	4300	6503	SO:0001583	missense	84976	exon10			AATACAAAAAGCT	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.2306A>G	chr1.hg19:g.223177045A>G	ENSP00000284476:p.Lys769Arg	181.0	0.0		198.0	114.0	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	hg19	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	A	8.000	0.755284	0.15846	.	.	ENSG00000154309	ENST00000284476	D	0.92199	-2.99	5.61	4.46	0.54185	.	0.041993	0.85682	N	0.000000	T	0.82181	0.4981	N	0.13098	0.295	0.49915	D	0.999836	B	0.20052	0.041	B	0.25405	0.06	T	0.72087	-0.4396	10	0.14252	T	0.57	-21.409	7.3385	0.26623	0.8006:0.0:0.0697:0.1298	.	769	Q96F81	DISP1_HUMAN	R	769	ENSP00000284476:K769R	ENSP00000284476:K769R	K	+	2	0	DISP1	221243668	1.000000	0.71417	0.976000	0.42696	0.997000	0.91878	6.343000	0.72986	1.028000	0.39785	0.533000	0.62120	AAA	.	.		0.478	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		G	223177045	A	G	223177045	3	3	133	1	0	0	0	0	1	0	0	0	4541	14	1	2	2332	2	DISP1	1	223177045	Missense_Mutation	SNP	A	TCGA-DD-A4NK-01A-11D-A28X-10	77760583	223177045	26073576	5	21511										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228526698	228526698	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	aaggcagtcatcttccgcaaTgtgcgggacatcggccgctt	12	12	2	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr1:228526698T>C	ENST00000422127.1	+	69	17273	c.17229T>C	c.(17227-17229)aaT>aaC	p.N5743N	OBSCN_ENST00000570156.2_Silent_p.N6700N|OBSCN_ENST00000366709.4_Silent_p.N2862N|OBSCN_ENST00000366707.4_Silent_p.N3377N|OBSCN_ENST00000284548.11_Silent_p.N5743N	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5743	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TCTTCCGCAATGTGCGGGACA	0.627																																					p.N6700N		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T20100C						.						11	14	13					1																	228526698		1887	3764	5651	SO:0001819	synonymous_variant	84033	exon80			CCGCAATGTGCGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.17229T>C	chr1.hg19:g.228526698T>C		259.0	0.0		278.0	86.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	T	11.89	1.774647	0.31411	.	.	ENSG00000154358	ENST00000441106	.	.	.	5.19	-3.62	0.04543	.	.	.	.	.	T	0.62672	0.2447	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60657	-0.7220	4	.	.	.	.	13.5375	0.61653	0.0:0.3254:0.0:0.6746	.	.	.	.	R	359	.	.	C	+	1	0	OBSCN	226593321	0.009000	0.17119	0.323000	0.25347	0.650000	0.38633	-0.800000	0.04555	-0.887000	0.03961	-0.285000	0.09966	TGT	.	.		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228526698	T	C	228526698	2	2	133	1	0	0	0	0	0	0	0	1	10821	1461	51	2		2	OBSCN	1	228526698	Silent	SNP	T	TCGA-DD-A4NK-01A-11D-A28X-10	5349653	228526698	20723923	6	21512										
MDH1	4190	hgsc.bcm.edu	37	chr2	63832431	63832431	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cagactgtgcagcagcgtggCgctgctgtcatcaaggctcg	14	12	2	1	rs542095115		TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr2:63832431C>T	ENST00000233114.8	+	7	1128	c.693C>T	c.(691-693)ggC>ggT	p.G231G	MDH1_ENST00000409476.1_Silent_p.G107G|MDH1_ENST00000539945.1_Silent_p.G249G|MDH1_ENST00000544381.1_Silent_p.G142G|MDH1_ENST00000394423.1_Silent_p.G231G|MDH1_ENST00000409908.1_Silent_p.G66G	NM_005917.3	NP_005908.1	P40925	MDHC_HUMAN	malate dehydrogenase 1, NAD (soluble)	231					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	diiodophenylpyruvate reductase activity (GO:0047860)|L-malate dehydrogenase activity (GO:0030060)|malic enzyme activity (GO:0004470)|NAD binding (GO:0051287)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(4)	13						AGCAGCGTGGCGCTGCTGTCA	0.517													c|||	1	0.000199681	0	0	5008	,	,		18924	0		0	False		,,,				2504	0.001				p.G249G		Atlas-SNP	.											.	MDH1	29	.	0			c.C747T						.						49	47	47					2																	63832431		2203	4300	6503	SO:0001819	synonymous_variant	4190	exon7			GCGTGGCGCTGCT		CCDS1874.1, CCDS56121.1, CCDS56122.1	2p23	2012-10-02			ENSG00000014641	ENSG00000014641	1.1.1.37		6970	protein-coding gene	gene with protein product		154200					Standard	NM_005917		Approved		uc010ypv.2	P40925	OTTHUMG00000129512	ENST00000233114.8:c.693C>T	chr2.hg19:g.63832431C>T		124.0	0.0		119.0	50.0	NM_001199111	B2R5V5|B4DUN2|B7Z3I7|F5H098|Q6I9V0	Silent	SNP	ENST00000233114.8	hg19	CCDS1874.1																																																																																			.	.		0.517	MDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251687.1			T	63832431	C	T	63832431	2	4	133	1	0	0	0	0	0	0	0	1	9417	755	27	1		1	MDH1	2	63832431	Silent	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10		63832431	179366942	7	21513										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80801440	80801440	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	aggctgtgctgatgatcaggGtatgtgaggcctctgtagct	15	7	2	3			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr2:80801440G>T	ENST00000402739.4	+	12	1898		c.e12+1		CTNNA2_ENST00000466387.1_Splice_Site|CTNNA2_ENST00000361291.4_Splice_Site|CTNNA2_ENST00000496558.1_Splice_Site|CTNNA2_ENST00000540488.1_Splice_Site|AC008067.2_ENST00000430876.1_RNA|CTNNA2_ENST00000541047.1_Splice_Site|CTNNA2_ENST00000343114.3_Splice_Site|AC008067.2_ENST00000609950.1_RNA	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2						axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GATGATCAGGGTATGTGAGGC	0.438																																					.		Atlas-SNP	.											.	CTNNA2	462	.	0			c.1893+1G>T						.						144	138	140					2																	80801440		2125	4264	6389	SO:0001630	splice_region_variant	1496	exon13			ATCAGGGTATGTG		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1893+1G>T	chr2.hg19:g.80801440G>T		148.0	0.0		128.0	43.0	NM_004389	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Splice_Site	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	G	26.2	4.718590	0.89205	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488;ENST00000343114	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1825	0.86858	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CTNNA2	80654951	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.799000	0.99117	2.510000	0.84645	0.491000	0.48974	.	.	.		0.438	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	Intron	T	80801440	G	T	80801440	5	4	133	1	0	0	0	0	0	0	1	0	4015	1275	44	3	1732	3	CTNNA2	2	80801440	Splice_Site	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	16969009	80801440	162397933	8	21514										
FER1L5	90342	hgsc.bcm.edu	37	chr2	97360146	97360146	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	aagcgttccctggaagaatgGggcatacacactccccaaga	10	12	0	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr2:97360146G>A	ENST00000457909.1	+	0	2145							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						TGGAAGAATGGGGCATACACA	0.622																																					p.G1256E		Atlas-SNP	.											.	FER1L5	113	.	0			c.G3767A						.						91	83	86					2																	97360146		692	1591	2283			90342	exon33			AGAATGGGGCATA	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		chr2.hg19:g.97360146G>A		103.0	0.0		83.0	28.0	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.52	1.372537	0.24857	.	.	ENSG00000214272	ENST00000414152;ENST00000436930	.	.	.	4.69	1.71	0.24356	.	.	.	.	.	T	0.62319	0.2418	L	0.61036	1.89	.	.	.	D	0.76494	0.999	D	0.65874	0.939	T	0.66060	-0.6017	7	0.44086	T	0.13	-7.1371	7.0607	0.25123	0.3273:0.0:0.6727:0.0	.	1256	A0AVI2	FR1L5_HUMAN	E	1256;1214	.	ENSP00000444148:G1256E	G	+	2	0	FER1L5	96723873	0.565000	0.26610	0.000000	0.03702	0.867000	0.49689	2.110000	0.41873	0.165000	0.19558	0.462000	0.41574	GGG	.	.		0.622	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		A	97360146	G	A	97360146	1	1	133	0	1	0	0	0	0	0	0	0	5822	1232	43	3		3	FER1L5	2	97360146	RNA	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	16558706	97360146	145839227	9	21515										
DPP10	57628	hgsc.bcm.edu	37	chr2	116534805	116534805	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gtaaaagtgagcaaattaccGtgcggcatctgacatcagga	11	8	2	2	rs150929011		TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr2:116534805G>A	ENST00000410059.1	+	14	1723	c.1243G>A	c.(1243-1245)Gtg>Atg	p.V415M	DPP10_ENST00000310323.8_Missense_Mutation_p.V408M|DPP10_ENST00000409163.1_Missense_Mutation_p.V365M|DPP10_ENST00000393147.2_Missense_Mutation_p.V419M	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	415						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.V408M(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						GCAAATTACCGTGCGGCATCT	0.378																																					p.V419M		Atlas-SNP	.											DPP10_ENST00000410059,rectum,carcinoma,0,5	DPP10	415	.	1	Substitution - Missense(1)	ovary(1)	c.G1255A						.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	3,4403	6.2+/-15.9	0,3,2200	108	105	106		1222,1255,1093,1231,1243	4.1	0.9	2	dbSNP_134	106	0,8598		0,0,4299	no	missense,missense,missense,missense,missense	DPP10	NM_001004360.3,NM_001178034.1,NM_001178036.1,NM_001178037.1,NM_020868.3	21,21,21,21,21	0,3,6499	AA,AG,GG		0.0,0.0681,0.0231	benign,benign,benign,benign,benign	408/790,419/801,365/747,411/793,415/797	116534805	3,13001	2203	4299	6502	SO:0001583	missense	57628	exon14			ATTACCGTGCGGC	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1243G>A	chr2.hg19:g.116534805G>A	ENSP00000386565:p.Val415Met	205.0	0.0		185.0	10.0	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.493314	0.44352	6.81E-4	0.0	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	4.97	4.1	0.47936	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.202355	0.42548	N	0.000696	T	0.20536	0.0494	L	0.29908	0.895	0.44946	D	0.997961	B;P;B;P	0.38677	0.385;0.524;0.439;0.642	B;B;B;B	0.36378	0.063;0.086;0.104;0.223	T	0.04115	-1.0976	10	0.62326	D	0.03	-14.5709	7.6174	0.28167	0.1874:0.0:0.8126:0.0	.	408;419;411;415	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	M	415;365;419;408;365	ENSP00000386565:V415M;ENSP00000387038:V365M;ENSP00000376855:V419M;ENSP00000309066:V408M	ENSP00000309066:V408M	V	+	1	0	DPP10	116251275	1.000000	0.71417	0.893000	0.35052	0.992000	0.81027	3.538000	0.53597	1.452000	0.47756	0.655000	0.94253	GTG	.	G|1.000;A|0.000		0.378	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		A	116534805	G	A	116534805	3	1	133	1	0	0	0	0	1	0	0	0	4729	1145	40	1	1468	1	DPP10	2	116534805	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	19174659	116534805	126664568	10	21516										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148684653	148684659	+	Frame_Shift_Del	DEL	TGGCAAT	TGGCAAT	-													0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gtttttctccttttagggaaTggcaatgctctgtgaaacca							TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	TGGCAAT	TGGCAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr2:148684653_148684659delTGGCAAT	ENST00000241416.7	+	11	1988_1994	c.1352_1358delTGGCAAT	c.(1351-1359)atggcaatgfs	p.MAM451fs	ACVR2A_ENST00000535787.1_Frame_Shift_Del_p.MAM343fs|ACVR2A_ENST00000495775.1_3'UTR|ACVR2A_ENST00000404590.1_Frame_Shift_Del_p.MAM451fs	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	451	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TTTTAGGGAATGGCAATGCTCTGTGAA	0.386																																					p.451_453del		Atlas-Indel,Pindel	.											.	ACVR2A	125	.	0			c.1351_1357del						.																																			SO:0001589	frameshift_variant	92	exon11			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1352_1358delTGGCAAT	chr2.hg19:g.148684653_148684659delTGGCAAT	ENSP00000241416:p.Met451fs	114.0	0.0		66.0	13.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Frame_Shift_Del	DEL	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.386	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		-	148684659	TGGCAAT	-	148684653	7	5	133	1	0	1	0	1	0	0	0	0	223	1464	51	0	1394	0	ACVR2A	2	148684653	Frame_Shift_Del	DEL	TGGCAAT	TCGA-DD-A4NK-01A-11D-A28X-10	32149848	148684653	94514720	11	21517										
GPR1	2825	hgsc.bcm.edu	37	chr2	207040977	207040977	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gttcactcactgtgccagaaCagctgacttcccacagtgtg	9	13	2	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr2:207040977C>T	ENST00000407325.2	-	3	1357	c.995G>A	c.(994-996)tGt>tAt	p.C332Y	GPR1_ENST00000437420.1_Missense_Mutation_p.C332Y	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	332					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		TGTGCCAGAACAGCTGACTTC	0.433																																					p.C332Y		Atlas-SNP	.											.	GPR1	38	.	0			c.G995A						.						76	74	74					2																	207040977		2203	4300	6503	SO:0001583	missense	2825	exon3			CCAGAACAGCTGA		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"GPCR / Class A : Orphans"	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.995G>A	chr2.hg19:g.207040977C>T	ENSP00000384345:p.Cys332Tyr	123.0	0.0		110.0	45.0	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Missense_Mutation	SNP	ENST00000407325.2	hg19	CCDS2368.1	.	.	.	.	.	.	.	.	.	.	C	3.201	-0.163738	0.06502	.	.	ENSG00000183671	ENST00000407325;ENST00000437420	T;T	0.72282	-0.64;-0.64	5.45	5.45	0.79879	.	0.593736	0.18045	N	0.153470	T	0.49830	0.1580	N	0.08118	0	0.38126	D	0.938004	B	0.25007	0.116	B	0.19391	0.025	T	0.51545	-0.8692	10	0.26408	T	0.33	.	12.6099	0.56546	0.0:0.9245:0.0:0.0755	.	332	P46091	GPR1_HUMAN	Y	332	ENSP00000384345:C332Y;ENSP00000397535:C332Y	ENSP00000384345:C332Y	C	-	2	0	GPR1	206749222	0.977000	0.34250	0.996000	0.52242	0.855000	0.48748	3.329000	0.52060	2.579000	0.87056	0.655000	0.94253	TGT	.	.		0.433	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199		T	207040977	C	T	207040977	3	4	133	1	0	0	0	0	1	0	0	0	6629	478	17	3	76	3	GPR1	2	207040977	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	58356324	207040977	36158396	12	21518										
ECEL1	9427	hgsc.bcm.edu	37	chr2	233345176	233345176	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ggactgcgaccgccgcttgaTgcaccagttctgggtccagg	14	13	1	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr2:233345176T>C	ENST00000304546.1	-	17	2371	c.2161A>G	c.(2161-2163)Atc>Gtc	p.I721V	ECEL1_ENST00000409941.1_Missense_Mutation_p.I719V	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	721					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		CGCCGCTTGATGCACCAGTTC	0.657																																					p.I721V		Atlas-SNP	.											.	ECEL1	73	.	0			c.A2161G						.						43	47	46					2																	233345176		2203	4300	6503	SO:0001583	missense	9427	exon17			GCTTGATGCACCA	Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.2161A>G	chr2.hg19:g.233345176T>C	ENSP00000302051:p.Ile721Val	138.0	0.0		112.0	47.0	NM_004826	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Missense_Mutation	SNP	ENST00000304546.1	hg19	CCDS2493.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.672103	0.47781	.	.	ENSG00000171551	ENST00000411860;ENST00000304546;ENST00000409941	D;D;D	0.81739	-1.53;-1.53;-1.53	5.4	5.4	0.78164	Peptidase M13, neprilysin, C-terminal (1);Metallopeptidase, catalytic domain (1);	0.157721	0.53938	D	0.000042	T	0.68054	0.2959	N	0.05608	-0.01	0.53688	D	0.999978	B;B	0.25351	0.011;0.124	B;B	0.30943	0.007;0.122	T	0.68032	-0.5516	10	0.56958	D	0.05	-0.7302	15.4627	0.75373	0.0:0.0:0.0:1.0	.	719;721	O95672-2;O95672	.;ECEL1_HUMAN	V	114;721;719	ENSP00000412683:I114V;ENSP00000302051:I721V;ENSP00000386333:I719V	ENSP00000302051:I721V	I	-	1	0	ECEL1	233053420	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.946000	0.87746	2.067000	0.61834	0.370000	0.22315	ATC	.	.		0.657	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		C	233345176	T	C	233345176	3	2	133	1	0	0	0	0	1	0	0	0	4893	1464	51	2	174	2	ECEL1	2	233345176	Missense_Mutation	SNP	T	TCGA-DD-A4NK-01A-11D-A28X-10	26304199	233345176	9854197	13	21519										
CNOT10	25904	hgsc.bcm.edu	37	chr3	32757737	32757737	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	actggtaataacaacaacaaAgatggatctaatcataaagc	6	7	2	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr3:32757737A>G	ENST00000328834.5	+	6	910	c.594A>G	c.(592-594)aaA>aaG	p.K198K	CNOT10_ENST00000331889.6_Silent_p.K198K|CNOT10_ENST00000538368.1_5'UTR|CNOT10_ENST00000454516.2_Silent_p.K258K|CNOT10_ENST00000463697.1_3'UTR	NM_015442.2	NP_056257.1	Q9H9A5	CNO10_HUMAN	CCR4-NOT transcription complex, subunit 10	198					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(3)	23						ACAACAACAAAGATGGATCTA	0.318																																					p.K258K		Atlas-SNP	.											.	CNOT10	57	.	0			c.A774G						.						98	99	98					3																	32757737		2203	4299	6502	SO:0001819	synonymous_variant	25904	exon6			CAACAAAGATGGA	BC002928	CCDS2655.1, CCDS58821.1, CCDS58822.1	3p23	2013-01-10			ENSG00000182973	ENSG00000182973		"Tetratricopeptide (TTC) repeat domain containing"	23817	protein-coding gene	gene with protein product							Standard	NR_046352		Approved	FLJ12890, FLJ13165	uc011axj.2	Q9H9A5	OTTHUMG00000130748	ENST00000328834.5:c.594A>G	chr3.hg19:g.32757737A>G		173.0	0.0		126.0	56.0	NM_001256742	B7Z7L1|F8WAF2|Q9BU30|Q9H5J7|Q9H8X1|Q9H9W0|Q9HAH3|Q9UFJ2	Silent	SNP	ENST00000328834.5	hg19	CCDS2655.1																																																																																			.	.		0.318	CNOT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253248.2	NM_015442		G	32757737	A	G	32757737	2	3	133	1	0	0	0	0	0	0	0	1	3620	69	3	2		2	CNOT10	3	32757737	Silent	SNP	A	TCGA-DD-A4NK-01A-11D-A28X-10		32757737	165264693	14	21520										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266137	41266137	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tgccactaccacagctccttCtctgagtggtaaaggcaatc	8	13	1	1	rs121913409		TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr3:41266137C>A	ENST00000349496.5	+	3	414	c.134C>A	c.(133-135)tCt>tAt	p.S45Y	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38Y|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45Y|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45Y|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45Y	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45F(384)|p.S45del(53)|p.A5_A80del(53)|p.S45C(19)|p.S45Y(17)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.S45fs*2(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACAGCTCCTTCTCTGAGTGGT	0.498	S45F(HCC15_LUNG)|S45F(LS180_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45Y	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+1,2	CTNNB1	4904	.	601	Substitution - Missense(421)|Deletion - In frame(152)|Complex - deletion inframe(20)|Unknown(7)|Deletion - Frameshift(1)	soft_tissue(233)|liver(141)|large_intestine(85)|kidney(74)|endometrium(16)|skin(11)|adrenal_gland(9)|stomach(7)|biliary_tract(5)|ovary(4)|lung(3)|central_nervous_system(2)|cervix(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(1)|pituitary(1)|prostate(1)|bone(1)|pancreas(1)	c.C134A						.						84	74	77					3																	41266137		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTCCTTCTCTGAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.134C>A	chr3.hg19:g.41266137C>A	ENSP00000344456:p.Ser45Tyr	225.0	0.0		118.0	57.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519229	0.85495	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.68659	0.3025	M	0.65677	2.01	0.80722	D	1	D	0.76494	0.999	D	0.67231	0.95	T	0.69320	-0.5176	10	0.87932	D	0	-13.6823	20.2983	0.98569	0.0:1.0:0.0:0.0	.	45	P35222	CTNB1_HUMAN	Y	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38Y;ENSP00000385604:S45Y;ENSP00000412219:S45Y;ENSP00000379486:S45Y;ENSP00000344456:S45Y;ENSP00000411226:S38Y;ENSP00000379488:S45Y;ENSP00000409302:S45Y;ENSP00000401599:S45Y	ENSP00000344456:S45Y	S	+	2	0	CTNNB1	41241141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266137	C	A	41266137	3	1	133	1	0	0	0	0	1	0	0	0	4018	913	32	3	140	3	CTNNB1	3	41266137	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	8508400	41266137	156756293	15	21521										
SPATA16	83893	hgsc.bcm.edu	37	chr3	172643141	172643141	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gttcagatgatttacctgtgAatatcggcagcttcctgctt	9	9	1	3			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr3:172643141A>T	ENST00000351008.3	-	7	1406	c.1223T>A	c.(1222-1224)tTc>tAc	p.F408Y		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	408					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			TTTACCTGTGAATATCGGCAG	0.363																																					p.F408Y		Atlas-SNP	.											.	SPATA16	111	.	0			c.T1223A						.						61	62	62					3																	172643141		2203	4299	6502	SO:0001583	missense	83893	exon7			CCTGTGAATATCG	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.1223T>A	chr3.hg19:g.172643141A>T	ENSP00000341765:p.Phe408Tyr	103.0	0.0		93.0	33.0	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	hg19	CCDS3221.1	.	.	.	.	.	.	.	.	.	.	A	12.54	1.968609	0.34754	.	.	ENSG00000144962	ENST00000351008	T	0.16897	2.31	5.3	2.77	0.32553	.	0.175750	0.40728	N	0.001040	T	0.10852	0.0265	N	0.19112	0.55	0.23210	N	0.998114	B	0.15930	0.015	B	0.14578	0.011	T	0.22626	-1.0211	10	0.49607	T	0.09	-4.8638	9.5057	0.39044	0.7197:0.0:0.0:0.2803	.	408	Q9BXB7	SPT16_HUMAN	Y	408	ENSP00000341765:F408Y	ENSP00000341765:F408Y	F	-	2	0	SPATA16	174125835	1.000000	0.71417	0.946000	0.38457	0.328000	0.28507	3.020000	0.49643	0.331000	0.23511	0.460000	0.39030	TTC	.	.		0.363	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955		T	172643141	A	T	172643141	3	4	133	1	0	0	0	0	1	0	0	0	15016	246	9	4	506	4	SPATA16	3	172643141	Missense_Mutation	SNP	A	TCGA-DD-A4NK-01A-11D-A28X-10	131377004	172643141	25379289	16	21522										
CLDN16	10686	hgsc.bcm.edu	37	chr3	190126207	190126207	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ttggtatccaatataaatttGgttggtcctgttggctcgga	11	6	0	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr3:190126207G>A	ENST00000264734.2	+	4	945	c.697G>A	c.(697-699)Ggt>Agt	p.G233S	CLDN16_ENST00000456423.1_Intron	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	233			G -> D (in HOMG3). {ECO:0000269|PubMed:10390358}.		calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		ATATAAATTTGGTTGGTCCTG	0.413																																					p.G233S		Atlas-SNP	.											.	CLDN16	59	.	0			c.G697A	GRCh37	CM056565	CLDN16	M		.						213	204	207					3																	190126207		2203	4300	6503	SO:0001583	missense	10686	exon4			AAATTTGGTTGGT	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"Claudins"	2037	protein-coding gene	gene with protein product	"paracellin-1", "hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.697G>A	chr3.hg19:g.190126207G>A	ENSP00000264734:p.Gly233Ser	136.0	0.0		110.0	38.0	NM_006580		Missense_Mutation	SNP	ENST00000264734.2	hg19	CCDS3296.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.010989	0.93346	.	.	ENSG00000113946	ENST00000264734	D	0.94232	-3.38	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.96833	0.8966	M	0.83953	2.67	0.80722	D	1	D	0.76494	0.999	D	0.68192	0.956	D	0.97198	0.9862	10	0.87932	D	0	-6.0599	18.5953	0.91227	0.0:0.0:1.0:0.0	.	233	Q9Y5I7	CLD16_HUMAN	S	233	ENSP00000264734:G233S	ENSP00000264734:G233S	G	+	1	0	CLDN16	191608901	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.124000	0.77185	2.624000	0.88883	0.557000	0.71058	GGT	.	.		0.413	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580		A	190126207	G	A	190126207	3	1	133	1	0	0	0	0	1	0	0	0	3479	1348	47	3	711	3	CLDN16	3	190126207	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	17483066	190126207	7896223	17	21523										
BST1	683	hgsc.bcm.edu	37	chr4	15709230	15709230	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	atgttctgtatggcagggttGcagatttcttgagctggtgt	14	5	2	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr4:15709230G>A	ENST00000265016.4	+	3	607	c.412G>A	c.(412-414)Gca>Aca	p.A138T	BST1_ENST00000382346.3_Missense_Mutation_p.A153T	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	138					humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)			central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						TGGCAGGGTTGCAGATTTCTT	0.448																																					p.A138T		Atlas-SNP	.											.	BST1	30	.	0			c.G412A						.						137	132	133					4																	15709230		2203	4300	6503	SO:0001583	missense	683	exon3			AGGGTTGCAGATT	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"CD molecules"	1118	protein-coding gene	gene with protein product	"NAD(+) nucleosidase", "ADP-ribosyl cyclase 2"	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.412G>A	chr4.hg19:g.15709230G>A	ENSP00000265016:p.Ala138Thr	140.0	0.0		115.0	44.0	NM_004334	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Missense_Mutation	SNP	ENST00000265016.4	hg19	CCDS3416.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.060012	0.36373	.	.	ENSG00000109743	ENST00000265016;ENST00000382346	T;T	0.15952	2.38;2.38	5.44	4.6	0.57074	.	0.395559	0.26328	N	0.025019	T	0.17874	0.0429	L	0.55213	1.73	0.09310	N	1	P	0.47253	0.892	B	0.41412	0.356	T	0.10706	-1.0618	10	0.44086	T	0.13	-7.5596	10.3528	0.43945	0.0915:0.0:0.9085:0.0	.	138	Q10588	BST1_HUMAN	T	138;153	ENSP00000265016:A138T;ENSP00000371783:A153T	ENSP00000265016:A138T	A	+	1	0	BST1	15318328	0.246000	0.23909	0.004000	0.12327	0.552000	0.35366	3.957000	0.56730	1.287000	0.44583	0.591000	0.81541	GCA	.	.		0.448	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334		A	15709230	G	A	15709230	3	1	133	1	0	0	0	0	1	0	0	0	1535	1319	46	3	422	3	BST1	4	15709230	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10		15709230	175445046	18	21524										
ALB	213	hgsc.bcm.edu	37	chr4	74274521	74274524	+	Splice_Site	DEL	AAGT	AAGT	-													0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	atgaagagacatttttgaaaAagtaagtaatcagatgttta					rs17853494		TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr4:74274521_74274524delAAGT	ENST00000295897.4	+	4	570_571	c.481_482delAAGT	c.(481-483)aag>g	p.K161fs	ALB_ENST00000505649.1_3'UTR|ALB_ENST00000509063.1_Splice_Site_p.K161fs|ALB_ENST00000415165.2_Intron|ALB_ENST00000401494.3_Intron|ALB_ENST00000503124.1_Intron	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATTTTTGAAAAAGTAAGTAATCAG	0.348																																					p.160_161del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.480_482del						.																																			SO:0001630	splice_region_variant	213	exon4			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.482+1AAGT>-	chr4.hg19:g.74274525_74274528delAAGT		57.0	0.0		46.0	13.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	In_Frame_Del	DEL	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.348	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477	Frame_Shift_Del	-	74274524	AAGT	-	74274521	8	5	133	1	0	1	0	1	0	0	1	0	486	28	1	0	495	0	ALB	4	74274521	Splice_Site	DEL	AAGT	TCGA-DD-A4NK-01A-11D-A28X-10	58565291	74274521	116879755	19	21525										
ADH1B	125	hgsc.bcm.edu	37	chr4	100235183	100235183	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ctgctttacagcccataacaGcagataggccgacccctccc	7	17	0	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr4:100235183G>A	ENST00000305046.8	-	6	690	c.623C>T	c.(622-624)gCt>gTt	p.A208V	ADH1B_ENST00000394887.3_Missense_Mutation_p.A168V			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	208					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	GCCCATAACAGCAGATAGGCC	0.483																																					p.A208V		Atlas-SNP	.											.	ADH1B	68	.	0			c.C623T						.						230	231	230					4																	100235183		2203	4300	6503	SO:0001583	missense	125	exon6			ATAACAGCAGATA	AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"Alcohol dehydrogenases"	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.623C>T	chr4.hg19:g.100235183G>A	ENSP00000306606:p.Ala208Val	331.0	0.0		217.0	49.0	NM_000668	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Missense_Mutation	SNP	ENST00000305046.8	hg19	CCDS34033.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.109666	0.00353	.	.	ENSG00000196616	ENST00000305046;ENST00000394887;ENST00000412614	T;T	0.07688	3.17;3.17	3.81	0.982	0.19762	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.267496	0.36519	N	0.002557	T	0.02848	0.0085	N	0.05124	-0.11	0.29370	N	0.864081	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.003	T	0.46775	-0.9167	10	0.02654	T	1	-5.9832	7.8235	0.29300	0.8179:0.0:0.1821:0.0	.	195;168;208	F5HB16;A8MYN5;P00325	.;.;ADH1B_HUMAN	V	208;168;195	ENSP00000306606:A208V;ENSP00000378351:A168V	ENSP00000306606:A208V	A	-	2	0	ADH1B	100454206	0.955000	0.32602	0.105000	0.21289	0.048000	0.14542	2.017000	0.40981	-0.035000	0.13691	-0.459000	0.05422	GCT	.	.		0.483	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668		A	100235183	G	A	100235183	3	1	133	1	0	0	0	0	1	0	0	0	308	971	34	3	520	3	ADH1B	4	100235183	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	25960662	100235183	90919093	20	21526										
FAT4	79633	hgsc.bcm.edu	37	chr4	126372517	126372517	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cttcatcggatcagggaatgAaaatggtgccttttctatta	9	7	3	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr4:126372517A>T	ENST00000394329.3	+	9	10359	c.10346A>T	c.(10345-10347)gAa>gTa	p.E3449V	FAT4_ENST00000335110.5_Missense_Mutation_p.E1747V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3449	Cadherin 33. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TCAGGGAATGAAAATGGTGCC	0.463																																					p.E3449V		Atlas-SNP	.											.	FAT4	1752	.	0			c.A10346T						.						101	103	102					4																	126372517		2203	4300	6503	SO:0001583	missense	79633	exon9			GGAATGAAAATGG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.10346A>T	chr4.hg19:g.126372517A>T	ENSP00000377862:p.Glu3449Val	134.0	0.0		93.0	4.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	11.01	1.514615	0.27123	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.62498	0.02;0.02	4.76	4.76	0.60689	Cadherin (4);Cadherin-like (1);	0.211286	0.22657	U	0.057258	T	0.40222	0.1108	N	0.04275	-0.24	0.41292	D	0.986981	B;P;P	0.41265	0.253;0.714;0.744	B;B;B	0.38880	0.118;0.284;0.275	T	0.43637	-0.9379	10	0.30078	T	0.28	.	14.4679	0.67497	1.0:0.0:0.0:0.0	.	1747;3449;3449	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	V	3449;1747	ENSP00000377862:E3449V;ENSP00000335169:E1747V	ENSP00000335169:E1747V	E	+	2	0	FAT4	126591967	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.906000	0.63293	2.003000	0.58678	0.459000	0.35465	GAA	.	.		0.463	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126372517	A	T	126372517	3	4	133	1	0	0	0	0	1	0	0	0	5700	246	9	4	10380	4	FAT4	4	126372517	Missense_Mutation	SNP	A	TCGA-DD-A4NK-01A-11D-A28X-10	26137334	126372517	64781759	21	21527										
FAT4	79633	hgsc.bcm.edu	37	chr4	126400895	126400895	+	Splice_Site	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tctcattatgatttattttaGatgccctaggctggaaggcg	10	7	1	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr4:126400895G>A	ENST00000394329.3	+	14	12486		c.e14-1		FAT4_ENST00000335110.5_Intron	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4						branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATTTATTTTAGATGCCCTAGG	0.408																																					.		Atlas-SNP	.											.	FAT4	1752	.	0			c.12474-1G>A						.						59	53	55					4																	126400895		1568	3582	5150	SO:0001630	splice_region_variant	79633	exon14			ATTTTAGATGCCC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.12474-1G>A	chr4.hg19:g.126400895G>A		58.0	0.0		43.0	14.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Splice_Site	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	11.03	1.518891	0.27211	.	.	ENSG00000196159	ENST00000394329	.	.	.	4.89	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0825	0.89445	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAT4	126620345	1.000000	0.71417	0.536000	0.28039	0.018000	0.09664	7.577000	0.82486	2.262000	0.75019	0.460000	0.39030	.	.	.		0.408	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	Intron	A	126400895	G	A	126400895	5	1	133	1	0	0	0	0	0	0	1	0	5700	956	33	3	12527	3	FAT4	4	126400895	Splice_Site	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	28378	126400895	64753381	22	21528										
PPAP2A	8611	hgsc.bcm.edu	37	chr5	54763977	54763977	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cagggtttctccaagaataaTctgaaaaagaaacagaaaaa	7	6	2	4			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr5:54763977T>C	ENST00000307259.8	-	3	631	c.211A>G	c.(211-213)Att>Gtt	p.I71V	PPAP2A_ENST00000515132.1_5'UTR|PPAP2A_ENST00000264775.5_Splice_Site_p.I72V	NM_003711.2	NP_003702.2	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A	71					androgen receptor signaling pathway (GO:0030521)|germ cell migration (GO:0008354)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|phospholipid dephosphorylation (GO:0046839)|protein dephosphorylation (GO:0006470)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of lipid metabolic process (GO:0019216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	9		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				CCAAGAATAATCTGAAAAAGA	0.333																																					p.I72V		Atlas-SNP	.											.	PPAP2A	42	.	0			c.A214G						.						59	66	63					5																	54763977		2203	4299	6502	SO:0001630	splice_region_variant	8611	exon3			GAATAATCTGAAA	AB000888	CCDS34159.1, CCDS34160.1	5q11	2009-05-27			ENSG00000067113	ENSG00000067113	3.1.3.4		9228	protein-coding gene	gene with protein product		607124				9305923	Standard	NM_003711		Approved	PAP-2a, LPP1	uc003jpz.4	O14494	OTTHUMG00000162240	ENST00000307259.8:c.211-1A>G	chr5.hg19:g.54763977T>C		62.0	0.0		77.0	21.0	NM_176895	B7ZKN8|G3XA95|O60457|O60463|Q17RZ4	Missense_Mutation	SNP	ENST00000307259.8	hg19	CCDS34159.1	.	.	.	.	.	.	.	.	.	.	T	12.78	2.040158	0.35989	.	.	ENSG00000067113	ENST00000264775;ENST00000307259	T;T	0.74106	-0.81;-0.81	5.63	4.46	0.54185	.	0.288085	0.22170	N	0.063660	T	0.67487	0.2898	L	0.49699	1.58	0.34975	D	0.753528	B;B	0.06786	0.001;0.0	B;B	0.15484	0.013;0.003	T	0.68078	-0.5504	10	0.30854	T	0.27	-15.5351	11.6628	0.51356	0.0:0.0697:0.0:0.9303	.	71;72	O14494;G3XA95	LPP1_HUMAN;.	V	72;71	ENSP00000264775:I72V;ENSP00000302229:I71V	ENSP00000264775:I72V	I	-	1	0	PPAP2A	54799734	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.936000	0.70153	1.071000	0.40834	0.467000	0.42956	ATT	.	.		0.333	PPAP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368073.1		Missense_Mutation	C	54763977	T	C	54763977	5	2	133	1	0	0	0	0	0	0	1	0	12299	1449	50	2	659	2	PPAP2A	5	54763977	Splice_Site	SNP	T	TCGA-DD-A4NK-01A-11D-A28X-10		54763977	126151283	23	21529										
POC5	134359	hgsc.bcm.edu	37	chr5	74981292	74981292	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	accatactcttcctttttatTatttgtggagtctatcccta	4	10	2	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr5:74981292T>G	ENST00000428202.2	-	10	1336	c.1147A>C	c.(1147-1149)Aat>Cat	p.N383H	POC5_ENST00000510798.1_Missense_Mutation_p.N266H|POC5_ENST00000380475.2_Missense_Mutation_p.N266H|POC5_ENST00000446329.2_Missense_Mutation_p.N358H|POC5_ENST00000514838.2_Missense_Mutation_p.N355H	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	383					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TCCTTTTTATTATTTGTGGAG	0.383																																					p.N383H		Atlas-SNP	.											.	POC5	82	.	0			c.A1147C						.						158	164	162					5																	74981292		1888	4125	6013	SO:0001583	missense	134359	exon10			TTTTATTATTTGT	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 37", "POC5 centriolar protein homolog (Chlamydomonas)"	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.1147A>C	chr5.hg19:g.74981292T>G	ENSP00000410216:p.Asn383His	67.0	0.0		87.0	50.0	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	hg19	CCDS47236.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.980825	0.53827	.	.	ENSG00000152359	ENST00000428202;ENST00000514838;ENST00000380475;ENST00000510798;ENST00000446329	T;T;T;T;T	0.46819	1.89;1.47;0.86;0.86;1.89	4.36	4.36	0.52297	.	0.552273	0.21013	N	0.081660	T	0.62563	0.2438	M	0.70595	2.14	0.09310	N	1	D;D;D	0.71674	0.995;0.993;0.998	P;P;D	0.64877	0.885;0.878;0.93	T	0.54536	-0.8279	10	0.52906	T	0.07	-6.8685	10.2513	0.43370	0.0:0.0:0.0:1.0	.	266;383;358	Q8NA72-2;Q8NA72;Q8NA72-3	.;POC5_HUMAN;.	H	383;355;266;266;358	ENSP00000410216:N383H;ENSP00000420971:N355H;ENSP00000369842:N266H;ENSP00000426796:N266H;ENSP00000399481:N358H	ENSP00000369842:N266H	N	-	1	0	POC5	75017048	0.007000	0.16637	0.004000	0.12327	0.636000	0.38137	1.189000	0.32114	2.185000	0.69588	0.459000	0.35465	AAT	.	.		0.383	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408		G	74981292	T	G	74981292	3	3	133	1	0	0	0	0	1	0	0	0	12186	1754	61	5	592	5	POC5	5	74981292	Missense_Mutation	SNP	T	TCGA-DD-A4NK-01A-11D-A28X-10	20217315	74981292	105933968	24	21530										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112926896	112926896	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cgagccttttgggaaagcagCatagtttacttggtattttc	10	7	0	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr5:112926896C>T	ENST00000161863.4	+	27	4197	c.3984C>T	c.(3982-3984)agC>agT	p.S1328S		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1328	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GGGAAAGCAGCATAGTTTACT	0.403																																					p.S1328S		Atlas-SNP	.											.	YTHDC2	118	.	0			c.C3984T						.						158	159	159					5																	112926896		2202	4300	6502	SO:0001819	synonymous_variant	64848	exon27			AAGCAGCATAGTT	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.3984C>T	chr5.hg19:g.112926896C>T		158.0	0.0		147.0	38.0	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	hg19	CCDS4113.1																																																																																			.	.		0.403	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		T	112926896	C	T	112926896	2	4	133	1	0	0	0	0	0	0	0	1	17512	709	25	3		3	YTHDC2	5	112926896	Silent	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	37945604	112926896	67988364	25	21531										
KDM3B	51780	hgsc.bcm.edu	37	chr5	137734001	137734001	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	agatctagagacctcaaaatAcatcctggccaatgttgggg	10	9	2	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr5:137734001A>G	ENST00000314358.5	+	10	3166	c.2966A>G	c.(2965-2967)tAc>tGc	p.Y989C	KDM3B_ENST00000394866.1_Missense_Mutation_p.Y645C|KDM3B_ENST00000542866.1_Missense_Mutation_p.Y21C	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	989					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						ACCTCAAAATACATCCTGGCC	0.517																																					p.Y989C		Atlas-SNP	.											.	KDM3B	177	.	0			c.A2966G						.						133	126	128					5																	137734001		2203	4300	6503	SO:0001583	missense	51780	exon10			CAAAATACATCCT	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.2966A>G	chr5.hg19:g.137734001A>G	ENSP00000326563:p.Tyr989Cys	204.0	0.0		228.0	76.0	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.501133	0.85176	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	T;T;T	0.73897	-0.22;-0.79;-0.75	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.85613	0.5737	M	0.74647	2.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.87568	0.2476	10	0.87932	D	0	-23.0814	15.102	0.72288	1.0:0.0:0.0:0.0	.	645;989	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	C	989;779;645;21	ENSP00000326563:Y989C;ENSP00000378335:Y645C;ENSP00000439462:Y21C	ENSP00000326563:Y989C	Y	+	2	0	KDM3B	137761900	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	1.963000	0.57068	0.454000	0.30748	TAC	.	.		0.517	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		G	137734001	A	G	137734001	3	3	133	1	0	0	0	0	1	0	0	0	8136	391	14	2	3004	2	KDM3B	5	137734001	Missense_Mutation	SNP	A	TCGA-DD-A4NK-01A-11D-A28X-10	24807105	137734001	43181259	26	21532										
PPP2R5D	5528	hgsc.bcm.edu	37	chr6	42957352	42957352	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tcatcttttcctttcaggagCcccccaaggttgccaaatgc	7	14	3	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr6:42957352C>T	ENST00000485511.1	+	2	210	c.31C>T	c.(31-33)Ccc>Tcc	p.P11S	PPP2R5D_ENST00000394110.3_Missense_Mutation_p.P11S|PPP2R5D_ENST00000472118.1_Missense_Mutation_p.P11S|PPP2R5D_ENST00000461010.1_Intron	NM_001270476.1|NM_006245.3	NP_001257405.1|NP_006236.1	Q14738	2A5D_HUMAN	protein phosphatase 2, regulatory subunit B', delta	11					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of catalytic activity (GO:0050790)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	25			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CTTTCAGGAGCCCCCCAAGGT	0.502																																					p.P11S	Melanoma(63;587 1613 29742 31770)	Atlas-SNP	.											.,2	PPP2R5D	47	.	0			c.C31T						.						52	49	50					6																	42957352		2203	4300	6503	SO:0001583	missense	5528	exon2			CAGGAGCCCCCCA	L76702	CCDS4878.1, CCDS43464.1, CCDS55002.1	6p21.1	2010-06-18	2010-04-14		ENSG00000112640	ENSG00000112640		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9312	protein-coding gene	gene with protein product		601646	"protein phosphatase 2, regulatory subunit B (B56), delta isoform", "protein phosphatase 2, regulatory subunit B', delta isoform"			7592815	Standard	NM_006245		Approved	B56D	uc003oth.4	Q14738	OTTHUMG00000014716	ENST00000485511.1:c.31C>T	chr6.hg19:g.42957352C>T	ENSP00000417963:p.Pro11Ser	87.0	0.0		69.0	20.0	NM_180976	A8K3I9|B5BUA6|O00494|O00696|Q15171|Q5TC39	Missense_Mutation	SNP	ENST00000485511.1	hg19	CCDS4878.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.425611	0.62733	.	.	ENSG00000112640	ENST00000485511;ENST00000394110;ENST00000472118;ENST00000541610	T;T;T	0.41065	1.05;1.01;1.05	5.84	4.02	0.46733	.	3.298050	0.01007	N	0.003778	T	0.19087	0.0458	L	0.31664	0.95	0.80722	D	1	B;B	0.31209	0.001;0.313	B;B	0.23419	0.001;0.046	T	0.01245	-1.1407	10	0.52906	T	0.07	-9.3292	11.6182	0.51102	0.3237:0.6763:0.0:0.0	.	11;11	Q14738;Q14738-2	2A5D_HUMAN;.	S	11	ENSP00000417963:P11S;ENSP00000377669:P11S;ENSP00000420550:P11S	ENSP00000230402:P11S	P	+	1	0	PPP2R5D	43065330	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	0.978000	0.29488	0.780000	0.33566	0.655000	0.94253	CCC	.	.		0.502	PPP2R5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040573.3	NM_006245		T	42957352	C	T	42957352	3	4	133	1	0	0	0	0	1	0	0	0	12407	739	26	3	37	3	PPP2R5D	6	42957352	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10		42957352	128157715	27	21533										
CYP39A1	51302	hgsc.bcm.edu	37	chr6	46620284	46620284	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	aagaacagagcaaggcaaccCaggattataatcactgttgg	10	8	1	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr6:46620284C>T	ENST00000275016.2	-	1	239	c.36G>A	c.(34-36)ctG>ctA	p.L12L	SLC25A27_ENST00000411689.2_5'Flank|SLC25A27_ENST00000452689.2_5'Flank|SLC25A27_ENST00000371347.5_5'Flank	NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	12					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)	p.L12L(1)	EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						CAAGGCAACCCAGGATTATAA	0.468																																					p.L12L		Atlas-SNP	.											.	CYP39A1	41	.	1	Substitution - coding silent(1)	kidney(1)	c.G36A						.						198	207	204					6																	46620284		2203	4300	6503	SO:0001819	synonymous_variant	51302	exon1			GCAACCCAGGATT	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"Cytochrome P450s"	17449	protein-coding gene	gene with protein product		605994	"cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.36G>A	chr6.hg19:g.46620284C>T		97.0	0.0		125.0	36.0	NM_016593	Q5VTT0|Q96FW5	Silent	SNP	ENST00000275016.2	hg19	CCDS4916.1																																																																																			.	.		0.468	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1			T	46620284	C	T	46620284	2	4	133	1	0	0	0	0	0	0	0	1	4179	581	21	3		3	CYP39A1	6	46620284	Silent	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	3662932	46620284	124494783	28	21534										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146275926	146275926	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tttcaccactgaaggatgacTccaccagaatacccttgtca	6	13	2	3			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr6:146275926T>A	ENST00000367505.2	-	2	797	c.533A>T	c.(532-534)gAg>gTg	p.E178V	SHPRH_ENST00000438092.2_Missense_Mutation_p.E178V|SHPRH_ENST00000367503.3_Missense_Mutation_p.E178V|SHPRH_ENST00000275233.7_Missense_Mutation_p.E178V			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	178					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		GAAGGATGACTCCACCAGAAT	0.363																																					p.E178V		Atlas-SNP	.											.	SHPRH	169	.	0			c.A533T						.						119	111	113					6																	146275926		1836	4098	5934	SO:0001583	missense	257218	exon2			GATGACTCCACCA	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.533A>T	chr6.hg19:g.146275926T>A	ENSP00000356475:p.Glu178Val	50.0	0.0		35.0	26.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	hg19	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	T	21.7	4.190428	0.78789	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233;ENST00000444767	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.66	5.66	0.87406	.	0.072072	0.53938	D	0.000045	T	0.75079	0.3801	M	0.61703	1.905	0.58432	D	0.999998	D;D;D;D	0.89917	0.989;0.996;0.998;1.0	P;P;P;D	0.91635	0.839;0.67;0.823;0.999	T	0.76900	-0.2788	10	0.51188	T	0.08	-14.8336	15.8839	0.79226	0.0:0.0:0.0:1.0	.	67;178;178;67	Q149N8-2;Q149N8;Q149N8-4;F8WEL0	.;SHPRH_HUMAN;.;.	V	178;178;178;178;67	ENSP00000356475:E178V;ENSP00000356473:E178V;ENSP00000412797:E178V;ENSP00000275233:E178V	ENSP00000275233:E178V	E	-	2	0	SHPRH	146317619	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	3.635000	0.54309	2.158000	0.67659	0.533000	0.62120	GAG	.	.		0.363	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		A	146275926	T	A	146275926	3	1	133	1	0	0	0	0	1	0	0	0	14306	1551	54	4	4678	4	SHPRH	6	146275926	Missense_Mutation	SNP	T	TCGA-DD-A4NK-01A-11D-A28X-10	99655642	146275926	24839141	29	21535										
SNX8	29886	hgsc.bcm.edu	37	chr7	2294745	2294745	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cacggtggggtcagggtgctGtgtggtcccgcaaagaggca	18	9	1	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr7:2294745G>C	ENST00000222990.3	-	11	1386	c.1344C>G	c.(1342-1344)caC>caG	p.H448Q		NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	448					early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)	early endosome membrane (GO:0031901)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(2)|skin(3)	26		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		TCAGGGTGCTGTGTGGTCCCG	0.637																																					p.H448Q		Atlas-SNP	.											.	SNX8	46	.	0			c.C1344G						.						66	52	57					7																	2294745		2185	4293	6478	SO:0001583	missense	29886	exon11			GGTGCTGTGTGGT	AF121858	CCDS5331.1	7p22.3	2010-08-05			ENSG00000106266	ENSG00000106266		"Sorting nexins"	14972	protein-coding gene	gene with protein product		614905					Standard	NM_013321		Approved	Mvp1	uc003slw.3	Q9Y5X2	OTTHUMG00000151512	ENST00000222990.3:c.1344C>G	chr7.hg19:g.2294745G>C	ENSP00000222990:p.His448Gln	152.0	0.0		189.0	34.0	NM_013321	A4D207|Q96I67	Missense_Mutation	SNP	ENST00000222990.3	hg19	CCDS5331.1	.	.	.	.	.	.	.	.	.	.	G	8.955	0.969170	0.18659	.	.	ENSG00000106266	ENST00000222990	.	.	.	5.15	1.25	0.21368	.	0.397901	0.26258	N	0.025414	T	0.24392	0.0591	N	0.22421	0.69	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.16630	-1.0396	9	0.23302	T	0.38	.	8.9545	0.35809	0.3008:0.0:0.6992:0.0	.	448	Q9Y5X2	SNX8_HUMAN	Q	448	.	ENSP00000222990:H448Q	H	-	3	2	SNX8	2261271	0.025000	0.19082	0.000000	0.03702	0.146000	0.21551	1.663000	0.37429	0.198000	0.20407	-0.259000	0.10710	CAC	.	.		0.637	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322949.2			C	2294745	G	C	2294745	3	2	133	1	0	0	0	0	1	0	0	0	14923	1368	48	4	57	4	SNX8	7	2294745	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10		2294745	156843918	30	21536										
SDK1	221935	hgsc.bcm.edu	37	chr7	4153733	4153733	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ctacaggattaagtactggcGctcagacctccagtcctcag	9	13	2	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr7:4153733G>A	ENST00000404826.2	+	25	3789	c.3650G>A	c.(3649-3651)cGc>cAc	p.R1217H	SDK1_ENST00000389531.3_Missense_Mutation_p.R1217H	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1217	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AAGTACTGGCGCTCAGACCTC	0.582																																					p.R1217H		Atlas-SNP	.											.	SDK1	361	.	0			c.G3650A						.						70	68	69					7																	4153733		2203	4300	6503	SO:0001583	missense	221935	exon25			ACTGGCGCTCAGA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.3650G>A	chr7.hg19:g.4153733G>A	ENSP00000385899:p.Arg1217His	165.0	0.0		188.0	42.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.586943	0.86851	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.56941	0.43;0.43	5.38	5.38	0.77491	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.158761	0.42682	D	0.000676	T	0.77322	0.4113	M	0.87269	2.87	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.73708	0.981;0.976	T	0.81369	-0.0964	10	0.72032	D	0.01	.	19.1613	0.93533	0.0:0.0:1.0:0.0	.	1217;1217	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	H	1217	ENSP00000385899:R1217H;ENSP00000374182:R1217H	ENSP00000374182:R1217H	R	+	2	0	SDK1	4120259	1.000000	0.71417	0.938000	0.37757	0.523000	0.34469	8.296000	0.89940	2.507000	0.84556	0.655000	0.94253	CGC	.	.		0.582	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		A	4153733	G	A	4153733	3	1	133	1	0	0	0	0	1	0	0	0	13983	1087	38	1	3748	1	SDK1	7	4153733	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	1858988	4153733	154984930	31	21537										
DFNA5	1687	hgsc.bcm.edu	37	chr7	24758744	24758744	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tgctcagagatcacacacttCtgcatcgtcgtgatcttctg	8	12	5	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr7:24758744C>T	ENST00000342947.3	-	4	923	c.498G>A	c.(496-498)caG>caA	p.Q166Q	DFNA5_ENST00000409775.3_Silent_p.Q166Q|DFNA5_ENST00000419307.1_Silent_p.Q2Q|DFNA5_ENST00000409970.1_Silent_p.Q2Q|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000545231.1_Silent_p.Q2Q	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	166					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						TCACACACTTCTGCATCGTCG	0.537																																					p.Q166Q	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.G498A						.						234	185	202					7																	24758744		2203	4300	6503	SO:0001819	synonymous_variant	1687	exon4			ACACTTCTGCATC	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.498G>A	chr7.hg19:g.24758744C>T		145.0	0.0		178.0	26.0	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Silent	SNP	ENST00000342947.3	hg19	CCDS5389.1																																																																																			.	.		0.537	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		T	24758744	C	T	24758744	2	4	133	1	0	0	0	0	0	0	0	1	4456	912	32	3		3	DFNA5	7	24758744	Silent	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	20605011	24758744	134379919	32	21538										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48287835	48287835	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	atatcttcttttcttgttaaGgatcgtattttgcaagaggt	8	5	3	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr7:48287835G>T	ENST00000435803.1	+	14	1683		c.e14-1			NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13						transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TTCTTGTTAAGGATCGTATTT	0.383																																					.		Atlas-SNP	.											.	ABCA13	1192	.	0			c.1660-1G>T						.						51	50	50					7																	48287835		1827	4085	5912	SO:0001630	splice_region_variant	154664	exon14			TGTTAAGGATCGT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.1660-1G>T	chr7.hg19:g.48287835G>T		88.0	0.0		106.0	74.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Splice_Site	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.929143	0.34096	.	.	ENSG00000179869	ENST00000435803	.	.	.	4.29	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5891	0.56434	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ABCA13	48258381	1.000000	0.71417	0.073000	0.20177	0.568000	0.35870	4.428000	0.59894	2.074000	0.62210	0.655000	0.94253	.	.	.		0.383	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	Intron	T	48287835	G	T	48287835	5	4	133	1	0	0	0	0	0	0	1	0	31	1014	35	3	1542	3	ABCA13	7	48287835	Splice_Site	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	23529091	48287835	110850828	33	21539										
STEAP4	79689	hgsc.bcm.edu	37	chr7	87912273	87912273	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ataaacataagggtagattaCgtctcttataacacaataga	6	6	1	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr7:87912273C>T	ENST00000380079.4	-	3	768	c.667G>A	c.(667-669)Gta>Ata	p.V223I	AC003991.3_ENST00000595121.1_RNA|AC003991.3_ENST00000434733.1_RNA|STEAP4_ENST00000301959.5_Intron|AC003991.3_ENST00000600908.1_RNA|AC003991.3_ENST00000447758.1_RNA|STEAP4_ENST00000414498.1_Missense_Mutation_p.V223I	NM_001205315.1|NM_024636.3	NP_001192244.1|NP_078912.2	Q687X5	STEA4_HUMAN	STEAP family member 4	223					copper ion import (GO:0015677)|fat cell differentiation (GO:0045444)|ferric iron import into cell (GO:0097461)|iron ion homeostasis (GO:0055072)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(3)	15	Esophageal squamous(14;0.00802)					GGGTAGATTACGTCTCTTATA	0.378																																					p.V223I		Atlas-SNP	.											.	STEAP4	54	.	0			c.G667A						.						90	86	87					7																	87912273		1884	4107	5991	SO:0001583	missense	79689	exon4			AGATTACGTCTCT	AK026806	CCDS43611.1, CCDS56494.1	7q21.13	2014-01-28	2005-06-15	2005-06-15	ENSG00000127954	ENSG00000127954			21923	protein-coding gene	gene with protein product		611098	"tumor necrosis factor, alpha-induced protein 9"	TNFAIP9		11443137, 15897894	Standard	NM_024636		Approved	FLJ23153, TIARP, STAMP2	uc003ujs.3	Q687X5	OTTHUMG00000153853	ENST00000380079.4:c.667G>A	chr7.hg19:g.87912273C>T	ENSP00000369419:p.Val223Ile	104.0	0.0		131.0	63.0	NM_001205315	Q658Q9|Q687X4|Q8WWB0|Q9H5R1	Missense_Mutation	SNP	ENST00000380079.4	hg19	CCDS43611.1	.	.	.	.	.	.	.	.	.	.	C	1.263	-0.615247	0.03663	.	.	ENSG00000127954	ENST00000380079;ENST00000414498	T;T	0.11063	3.16;2.81	6.08	1.24	0.21308	.	0.325818	0.35838	N	0.002950	T	0.06554	0.0168	N	0.25144	0.715	0.28116	N	0.930817	B;B	0.24675	0.109;0.109	B;B	0.16722	0.016;0.01	T	0.33471	-0.9867	10	0.22706	T	0.39	-6.2203	10.7338	0.46113	0.0:0.5653:0.0:0.4347	.	223;223	C9JS50;Q687X5	.;STEA4_HUMAN	I	223	ENSP00000369419:V223I;ENSP00000394399:V223I	ENSP00000369419:V223I	V	-	1	0	STEAP4	87750209	0.005000	0.15991	0.056000	0.19401	0.073000	0.16967	0.196000	0.17176	0.167000	0.19631	0.591000	0.81541	GTA	.	.		0.378	STEAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332712.4	NM_024636		T	87912273	C	T	87912273	3	4	133	1	0	0	0	0	1	0	0	0	15295	536	19	1	724	1	STEAP4	7	87912273	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	39624438	87912273	71226390	34	21540										
PTCD1	26024	hgsc.bcm.edu	37	chr7	99022509	99022509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gcaggttggggacgaggcccCtctttgccaggaccggcaac	15	13	1	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr7:99022509C>T	ENST00000292478.4	-	6	1896	c.1646G>A	c.(1645-1647)aGg>aAg	p.R549K	ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.R598K|PTCD1_ENST00000555673.1_Missense_Mutation_p.R598K	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	549					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			GACGAGGCCCCTCTTTGCCAG	0.592																																					p.R598K		Atlas-SNP	.											.	.	.	.	0			c.G1793A						.						75	71	72					7																	99022509		2203	4300	6503	SO:0001583	missense	100526740	exon7			AGGCCCCTCTTTG	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.1646G>A	chr7.hg19:g.99022509C>T	ENSP00000292478:p.Arg549Lys	92.0	0.0		98.0	28.0	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	hg19	CCDS34691.1	.	.	.	.	.	.	.	.	.	.	C	8.495	0.862955	0.17178	.	.	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000438524;ENST00000555673;ENST00000413834	T;T;T	0.64438	-0.1;-0.08;-0.08	5.91	4.1	0.47936	.	0.134995	0.64402	N	0.000004	T	0.42810	0.1219	L	0.35542	1.07	0.34009	D	0.651271	B;B	0.31193	0.312;0.028	B;B	0.25884	0.064;0.015	T	0.47289	-0.9129	10	0.09843	T	0.71	-26.2877	8.3548	0.32324	0.0:0.7031:0.0:0.2969	.	598;549	G3V325;O75127	.;PTCD1_HUMAN	K	549;331;598;598	ENSP00000292478:R549K;ENSP00000450995:R598K;ENSP00000400168:R598K	ENSP00000400168:R598K	R	-	2	0	ATP5J2-PTCD1;PTCD1	98860445	0.960000	0.32886	0.971000	0.41717	0.050000	0.14768	1.496000	0.35638	0.829000	0.34733	-0.379000	0.06801	AGG	.	.		0.592	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		T	99022509	C	T	99022509	3	4	133	1	0	0	0	0	1	0	0	0	12739	681	24	3	468	3	PTCD1	7	99022509	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	11110236	99022509	60116154	35	21541										
RGS20	8601	hgsc.bcm.edu	37	chr8	54792096	54792096	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tcggggggtcgtccgctgagGcccccccatccggtagccaa	14	16	0	1	rs35570213		TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr8:54792096G>A	ENST00000297313.3	+	2	536	c.444G>A	c.(442-444)agG>agA	p.R148R	RGS20_ENST00000344277.6_Intron|RP11-1070A24.2_ENST00000606037.1_RNA|RGS20_ENST00000522225.1_5'Flank|RGS20_ENST00000276500.4_5'Flank	NM_170587.2	NP_733466.1	O76081	RGS20_HUMAN	regulator of G-protein signaling 20	148					positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			GTCCGCTGAGGCCCCCCCATC	0.736																																					p.R148R		Atlas-SNP	.											.	RGS20	51	.	0			c.G444A						.						7	7	7					8																	54792096		1958	3860	5818	SO:0001819	synonymous_variant	8601	exon2			GCTGAGGCCCCCC	AF074979	CCDS6155.1, CCDS6156.1, CCDS69482.1	8q11.23	2008-07-25	2007-08-14		ENSG00000147509	ENSG00000147509		"Regulators of G-protein signaling"	14600	protein-coding gene	gene with protein product		607193	"regulator of G-protein signalling 20"			9748279, 9748280	Standard	NM_003702		Approved	RGSZ1, ZGAP1	uc003xrp.3	O76081	OTTHUMG00000164750	ENST00000297313.3:c.444G>A	chr8.hg19:g.54792096G>A		131.0	0.0		142.0	81.0	NM_170587	Q96BG9	Silent	SNP	ENST00000297313.3	hg19	CCDS6155.1																																																																																			.	.		0.736	RGS20-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380058.1			A	54792096	G	A	54792096	2	1	133	1	0	0	0	0	0	0	0	1	13318	1194	42	3		3	RGS20	8	54792096	Silent	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10		54792096	91571926	36	21542										
RP1	6101	hgsc.bcm.edu	37	chr8	55540553	55540553	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gaggtgatgacattcagaaaGatctaaatattttgacagac	9	5	2	6			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr8:55540553G>C	ENST00000220676.1	+	4	4259	c.4111G>C	c.(4111-4113)Gat>Cat	p.D1371H		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1371					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CATTCAGAAAGATCTAAATAT	0.333																																					p.D1371H	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G4111C						.						55	60	59					8																	55540553		2202	4300	6502	SO:0001583	missense	6101	exon4			CAGAAAGATCTAA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.4111G>C	chr8.hg19:g.55540553G>C	ENSP00000220676:p.Asp1371His	67.0	0.0		63.0	35.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.896347	0.52121	.	.	ENSG00000104237	ENST00000220676	T	0.26957	1.7	5.89	5.01	0.66863	.	0.588335	0.16177	N	0.226015	T	0.30417	0.0764	L	0.32530	0.975	0.09310	N	1	D	0.62365	0.991	P	0.52710	0.707	T	0.09707	-1.0662	10	0.87932	D	0	.	11.7279	0.51720	0.1338:0.0:0.8662:0.0	.	1371	P56715	RP1_HUMAN	H	1371	ENSP00000220676:D1371H	ENSP00000220676:D1371H	D	+	1	0	RP1	55703106	0.819000	0.29175	0.895000	0.35142	0.648000	0.38561	2.279000	0.43435	2.793000	0.96121	0.655000	0.94253	GAT	.	.		0.333	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		C	55540553	G	C	55540553	3	2	133	1	0	0	0	0	1	0	0	0	13547	942	33	4	4121	4	RP1	8	55540553	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	748457	55540553	90823469	37	21543										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18777771	18777771	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	agctctcagcctcggaggtgGtcacccacctggggcagacg	14	14	2	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr9:18777771G>A	ENST00000380548.4	+	19	3883	c.3544G>A	c.(3544-3546)Gtc>Atc	p.V1182I		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1182	Ig-like C2-type 2.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CTCGGAGGTGGTCACCCACCT	0.682																																					p.V1182I		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.G3544A						.						23	28	27					9																	18777771		2118	4237	6355	SO:0001583	missense	92949	exon19			GAGGTGGTCACCC	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.3544G>A	chr9.hg19:g.18777771G>A	ENSP00000369921:p.Val1182Ile	199.0	0.0		185.0	33.0	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	hg19	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827372	0.50845	.	.	ENSG00000178031	ENST00000380548	T	0.62639	0.01	5.94	5.94	0.96194	Immunoglobulin-like (1);	0.096148	0.43579	D	0.000545	T	0.51126	0.1656	N	0.12569	0.235	0.80722	D	1	P	0.42296	0.775	B	0.43658	0.426	T	0.45220	-0.9276	10	0.19147	T	0.46	.	20.3552	0.98837	0.0:0.0:1.0:0.0	.	1182	Q8N6G6	ATL1_HUMAN	I	1182	ENSP00000369921:V1182I	ENSP00000369921:V1182I	V	+	1	0	ADAMTSL1	18767771	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.199000	0.51043	2.812000	0.96745	0.557000	0.71058	GTC	.	.		0.682	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			A	18777771	G	A	18777771	3	1	133	1	0	0	0	0	1	0	0	0	274	1261	44	3	3622	3	ADAMTSL1	9	18777771	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10		18777771	122435660	38	21544										
APBA1	320	hgsc.bcm.edu	37	chr9	72131731	72131731	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tcggcgtgctcggcctctgcCtgctccgtgtactcctcggc	12	17	1	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr9:72131731C>T	ENST00000265381.4	-	2	618	c.396G>A	c.(394-396)caG>caA	p.Q132Q		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	132					axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						CGGCCTCTGCCTGCTCCGTGT	0.706																																					p.Q132Q		Atlas-SNP	.											.	APBA1	96	.	0			c.G396A						.						36	32	33					9																	72131731		2201	4296	6497	SO:0001819	synonymous_variant	320	exon2			CTCTGCCTGCTCC	AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.396G>A	chr9.hg19:g.72131731C>T		56.0	0.0		27.0	12.0	NM_001163	O14914|O60570|Q5VYR8	Silent	SNP	ENST00000265381.4	hg19	CCDS6630.1																																																																																			.	.		0.706	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		T	72131731	C	T	72131731	2	4	133	1	0	0	0	0	0	0	0	1	756	680	24	3		3	APBA1	9	72131731	Silent	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	53353960	72131731	69081700	39	21545										
MUSK	4593	hgsc.bcm.edu	37	chr9	113509934	113509934	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ctgtcaggtttcttctgggtCcattcaagagagtgtgaaag	12	7	4	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr9:113509934C>G	ENST00000374448.4	+	7	901	c.767C>G	c.(766-768)tCc>tGc	p.S256C	MUSK_ENST00000189978.5_Missense_Mutation_p.S256C|MUSK_ENST00000416899.2_Missense_Mutation_p.S256C	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	256	Ig-like 3.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						TCTTCTGGGTCCATTCAAGAG	0.413																																					p.S266C		Atlas-SNP	.											.	MUSK	112	.	0			c.C797G						.						168	155	159					9																	113509934		1867	4119	5986	SO:0001583	missense	4593	exon8			CTGGGTCCATTCA	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.767C>G	chr9.hg19:g.113509934C>G	ENSP00000363571:p.Ser256Cys	84.0	0.0		85.0	32.0	NM_001166280	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	hg19	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.521598	0.64747	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899	T	0.12984	2.63	5.68	5.68	0.88126	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.40423	0.1116	M	0.87971	2.92	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79784	0.976;0.993	T	0.32903	-0.9889	10	0.59425	D	0.04	.	10.6852	0.45839	0.0:0.9133:0.0:0.0867	.	256;266	O15146;F5H6T2	MUSK_HUMAN;.	C	256;256;256;266;266;256	ENSP00000363571:S256C	ENSP00000189978:S256C	S	+	2	0	MUSK	112549755	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.256000	0.51492	2.675000	0.91044	0.655000	0.94253	TCC	.	.		0.413	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	113509934	C	G	113509934	3	3	133	1	0	0	0	0	1	0	0	0	9998	855	30	4	827	4	MUSK	9	113509934	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	41378203	113509934	27703497	40	21546										
TMEM203	94107	hgsc.bcm.edu	37	chr9	140099480	140099491	+	In_Frame_Del	DEL	CATGAGCAGCTG	CATGAGCAGCTG	-													0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ttgacccgacaggcgcggatCatgagcagctgcaggagaat					rs201112261|rs143273542		TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	CATGAGCAGCTG	CATGAGCAGCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr9:140099480_140099491delCATGAGCAGCTG	ENST00000343666.5	-	1	599_610	c.376_387delCAGCTGCTCATG	c.(376-387)cagctgctcatgdel	p.QLLM126del	NDOR1_ENST00000458322.2_5'Flank|TPRN_ENST00000541945.1_5'Flank|NDOR1_ENST00000427047.2_5'Flank|NDOR1_ENST00000371521.4_5'Flank|TMEM203_ENST00000537254.1_In_Frame_Del_p.QLLM126del|NDOR1_ENST00000344894.5_5'Flank	NM_053045.1	NP_444273.1	Q969S6	TM203_HUMAN	transmembrane protein 203	126						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(1)	2	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		AGGCGCGGATCATGAGCAGCTGCAGGAGAATG	0.599																																					p.126_130del		Atlas-Indel,Pindel	.											.	TMEM203	8	.	0			c.377_388del						.																																			SO:0001651	inframe_deletion	94107	exon1			.	BC009283	CCDS35185.1	9q34.3	2007-12-18			ENSG00000187713	ENSG00000187713			28217	protein-coding gene	gene with protein product	"HBeAg-binding protein 1"					12477932	Standard	NM_053045		Approved	MGC14327, HBEBP1	uc004clv.3	Q969S6	OTTHUMG00000020985	ENST00000343666.5:c.376_387delCAGCTGCTCATG	chr9.hg19:g.140099480_140099491delCATGAGCAGCTG	ENSP00000375053:p.Gln126_Met129del	103.0	0.0		61.0	16.0	NM_053045	Q6NW08	In_Frame_Del	DEL	ENST00000343666.5	hg19	CCDS35185.1																																																																																			.	.		0.599	TMEM203-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055325.2	NM_053045		-	140099491	CATGAGCAGCTG	-	140099480	7	5	133	1	0	1	0	1	0	0	0	0	16143	826	29	0	27	0	TMEM203	9	140099480	In_Frame_Del	DEL	CATGAGCAGCTG	TCGA-DD-A4NK-01A-11D-A28X-10	26589546	140099480	1113951	41	21547										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55591092	55591092	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tactgtctgtagctgaccaaAaccaccaagatggcaggaat	9	10	1	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr10:55591092A>G	ENST00000320301.6	-	30	4579	c.4185T>C	c.(4183-4185)gtT>gtC	p.V1395V	PCDH15_ENST00000395438.1_Silent_p.V1395V|PCDH15_ENST00000437009.1_Silent_p.V1324V|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373965.2_Silent_p.V1402V|PCDH15_ENST00000409834.1_Silent_p.V1006V|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000414778.1_Silent_p.V1400V|PCDH15_ENST00000361849.3_Silent_p.V1395V|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395432.2_Silent_p.V1358V|PCDH15_ENST00000395430.1_Silent_p.V1395V|PCDH15_ENST00000395445.1_Silent_p.V1402V|PCDH15_ENST00000395433.1_Silent_p.V1373V	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1395					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				AGCTGACCAAAACCACCAAGA	0.458										HNSCC(58;0.16)																											p.V1400V		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T4200C						.						225	198	207					10																	55591092		2203	4300	6503	SO:0001819	synonymous_variant	65217	exon31			GACCAAAACCACC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4185T>C	chr10.hg19:g.55591092A>G		168.0	0.0		107.0	40.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.		0.458	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		G	55591092	A	G	55591092	2	3	133	1	0	0	0	0	0	0	0	1	11520	1	1	2		2	PCDH15	10	55591092	Silent	SNP	A	TCGA-DD-A4NK-01A-11D-A28X-10		55591092	79943655	42	21548										
RBP4	5950	hgsc.bcm.edu	37	chr10	95360550	95360550	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tcttggccatggcgtaccagGtcccagagaactgtgagaag	13	10	1	2	rs367834906		TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr10:95360550G>A	ENST00000371467.1	-	3	441	c.122C>T	c.(121-123)aCc>aTc	p.T41I	FFAR4_ENST00000604414.1_Intron|RBP4_ENST00000371469.2_Missense_Mutation_p.T39I|RBP4_ENST00000371464.3_Missense_Mutation_p.T41I			P02753	RET4_HUMAN	retinol binding protein 4, plasma	41					cardiac muscle tissue development (GO:0048738)|detection of light stimulus involved in visual perception (GO:0050908)|embryonic organ morphogenesis (GO:0048562)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic skeletal system development (GO:0048706)|eye development (GO:0001654)|female genitalia morphogenesis (GO:0048807)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|lung development (GO:0030324)|maintenance of gastrointestinal epithelium (GO:0030277)|male gonad development (GO:0008584)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|phototransduction, visible light (GO:0007603)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of insulin secretion (GO:0032024)|response to ethanol (GO:0045471)|response to insulin (GO:0032868)|response to retinoic acid (GO:0032526)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|retinol transport (GO:0034633)|spermatogenesis (GO:0007283)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	retinal binding (GO:0016918)|retinol binding (GO:0019841)|retinol transporter activity (GO:0034632)			large_intestine(1)|lung(3)|skin(1)	5		Colorectal(252;0.122)			Vitamin A(DB00162)	GGCGTACCAGGTCCCAGAGAA	0.687																																					p.T41I	Pancreas(5;160 256 1117 46697 50185)	Atlas-SNP	.											.	RBP4	10	.	0			c.C122T						.	G	ILE/THR	1,4405	2.1+/-5.4	0,1,2202	25	26	26		122	1	0.5	10		26	0,8598		0,0,4299	no	missense	RBP4	NM_006744.3	89	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	benign	41/202	95360550	1,13003	2203	4299	6502	SO:0001583	missense	5950	exon3			TACCAGGTCCCAG	BC020633	CCDS31249.1	10q23.33	2014-01-22	2001-11-28		ENSG00000138207	ENSG00000138207		"Lipocalins"	9922	protein-coding gene	gene with protein product		180250	"retinol-binding protein 4, plasma"				Standard	XM_005270023		Approved		uc001kit.3	P02753	OTTHUMG00000018773	ENST00000371467.1:c.122C>T	chr10.hg19:g.95360550G>A	ENSP00000360522:p.Thr41Ile	311.0	0.0		208.0	32.0	NM_006744	D3DR38|O43478|O43479|Q5VY24|Q8WWA3|Q9P178	Missense_Mutation	SNP	ENST00000371467.1	hg19	CCDS31249.1	.	.	.	.	.	.	.	.	.	.	G	7.025	0.559526	0.13436	2.27E-4	0.0	ENSG00000138207	ENST00000371464;ENST00000371469;ENST00000371467;ENST00000371463	T;T	0.10763	2.84;2.84	5.25	1.05	0.20165	Lipocalin conserved site (1);Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.317296	0.37809	N	0.001921	T	0.08088	0.0202	L	0.45581	1.43	0.22710	N	0.998824	B	0.19073	0.033	B	0.23419	0.046	T	0.35773	-0.9775	10	0.19147	T	0.46	-6.019	4.4617	0.11669	0.3928:0.0:0.4625:0.1447	.	41	P02753	RET4_HUMAN	I	41;39;41;39	ENSP00000360519:T41I;ENSP00000360522:T41I	ENSP00000360518:T39I	T	-	2	0	RBP4	95350540	0.243000	0.23878	0.467000	0.27180	0.398000	0.30690	0.267000	0.18552	0.220000	0.20860	0.306000	0.20318	ACC	.	.		0.687	RBP4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049431.1	NM_006744		A	95360550	G	A	95360550	3	1	133	1	0	0	0	0	1	0	0	0	13173	1261	44	3	499	3	RBP4	10	95360550	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	39769458	95360550	40174197	43	21549										
OR5M8	219484	hgsc.bcm.edu	37	chr11	56258001	56258001	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	taaattataaggttcagcatAgggattactgtggtataaaa	9	3	1	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr11:56258001A>T	ENST00000327216.2	-	1	870	c.846T>A	c.(844-846)ccT>ccA	p.P282P		NM_001005282.1	NP_001005282.1	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M, member 8	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(22)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Esophageal squamous(21;0.00352)					GGTTCAGCATAGGGATTACTG	0.323																																					p.P282P		Atlas-SNP	.											.	OR5M8	74	.	0			c.T846A						.						45	52	49					11																	56258001		2201	4295	6496	SO:0001819	synonymous_variant	219484	exon1			CAGCATAGGGATT	AB065744	CCDS31533.1	11q11	2012-08-09			ENSG00000181371	ENSG00000181371		"GPCR / Class A : Olfactory receptors"	14846	protein-coding gene	gene with protein product							Standard	NM_001005282		Approved		uc001nix.1	Q8NGP6	OTTHUMG00000166877	ENST00000327216.2:c.846T>A	chr11.hg19:g.56258001A>T		45.0	0.0		46.0	15.0	NM_001005282	B2RNM5|Q6IEW3|Q96RB8	Silent	SNP	ENST00000327216.2	hg19	CCDS31533.1																																																																																			.	.		0.323	OR5M8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391641.1	NM_001005282		T	56258001	A	T	56258001	2	4	133	1	0	0	0	0	0	0	0	1	11185	407	15	4		4	OR5M8	11	56258001	Silent	SNP	A	TCGA-DD-A4NK-01A-11D-A28X-10		56258001	78748515	44	21550										
UBXN1	51035	hgsc.bcm.edu	37	chr11	62445539	62445539	+	Frame_Shift_Del	DEL	T	T	-													0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tcccgttccaatgcctcccgTtcctctctttcttcacgctc							TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr11:62445539delT	ENST00000301935.5	-	5	508	c.342delA	c.(340-342)gaafs	p.E114fs	UBXN1_ENST00000533000.1_5'Flank|UBXN1_ENST00000529640.1_Frame_Shift_Del_p.E114fs|UBXN1_ENST00000294119.2_Frame_Shift_Del_p.E114fs|UBXN1_ENST00000524762.1_5'UTR			Q04323	UBXN1_HUMAN	UBX domain protein 1	114	Interaction with BRCA1.				negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|K6-linked polyubiquitin binding (GO:0071796)|polyubiquitin binding (GO:0031593)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|lung(12)	17						ATGCCTCCCGTTCCTCTCTTT	0.582																																					p.R115fs		Atlas-Indel,Pindel	.											.	UBXN1	28	.	0			c.343delC						.						100	80	87					11																	62445539		2202	4299	6501	SO:0001589	frameshift_variant	51035	exon5			.		CCDS8029.1, CCDS66105.1, CCDS73307.1	11q23	2014-02-12	2008-07-25		ENSG00000162191	ENSG00000162191		"UBX domain containing"	18402	protein-coding gene	gene with protein product	"SAPK substrate protein 1"					12838346, 20351172	Standard	NM_001286078		Approved	LOC51035, 2B28, UBXD10, SAKS1	uc001nuj.3	Q04323	OTTHUMG00000167580	ENST00000301935.5:c.342delA	chr11.hg19:g.62445539delT	ENSP00000303991:p.Glu114fs	92.0	0.0		66.0	28.0	NM_015853	Q9BV93|Q9BVV5	Frame_Shift_Del	DEL	ENST00000301935.5	hg19																																																																																				.	.		0.582	UBXN1-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000395153.1	NM_015853		-	62445539	T	-	62445539	7	5	133	1	0	1	0	1	0	0	0	0	16926	1722	60	0	612	0	UBXN1	11	62445539	Frame_Shift_Del	DEL	T	TCGA-DD-A4NK-01A-11D-A28X-10	6187538	62445539	72560977	45	21551										
CTTN	2017	hgsc.bcm.edu	37	chr11	70269063	70269063	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cagactactccaaaggattcGgcgggaagtatggggtgcag	15	8	0	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr11:70269063G>A	ENST00000301843.8	+	12	1125	c.919G>A	c.(919-921)Ggc>Agc	p.G307S	CTTN_ENST00000346329.3_Missense_Mutation_p.G270S|CTTN_ENST00000376561.3_Missense_Mutation_p.G270S|CTTN_ENST00000538675.1_5'UTR	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	307					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)				breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		CAAAGGATTCGGCGGGAAGTA	0.562																																					p.G307S		Atlas-SNP	.											.	CTTN	162	.	0			c.G919A						.						174	147	157					11																	70269063		2200	4294	6494	SO:0001583	missense	2017	exon12			GGATTCGGCGGGA	AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.919G>A	chr11.hg19:g.70269063G>A	ENSP00000301843:p.Gly307Ser	413.0	0.0		350.0	137.0	NM_005231	Q8N707|Q96H99	Missense_Mutation	SNP	ENST00000301843.8	hg19	CCDS41680.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.960680	0.92791	.	.	ENSG00000085733	ENST00000346329;ENST00000301843;ENST00000376561	T;T;T	0.54279	0.76;1.08;0.58	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.80534	0.4641	M	0.93283	3.4	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.97110	0.96;0.992;1.0	D	0.85586	0.1243	10	0.62326	D	0.03	-24.7659	18.7266	0.91716	0.0:0.0:1.0:0.0	.	270;307;270	Q96H99;Q14247;Q8N707	.;SRC8_HUMAN;.	S	270;307;270	ENSP00000317189:G270S;ENSP00000301843:G307S;ENSP00000365745:G270S	ENSP00000301843:G307S	G	+	1	0	CTTN	69946711	1.000000	0.71417	0.193000	0.23327	0.800000	0.45204	8.942000	0.92970	2.426000	0.82243	0.655000	0.94253	GGC	.	.		0.562	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		A	70269063	G	A	70269063	3	1	133	1	0	0	0	0	1	0	0	0	4046	1116	39	1	957	1	CTTN	11	70269063	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	7823524	70269063	64737453	46	21552										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73020363	73020363	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ctcccaaccgcaggccggggCccgggcctcctgctcctcct	11	21	0	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr11:73020363C>A	ENST00000263674.3	+	1	1030	c.680C>A	c.(679-681)gCc>gAc	p.A227D	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	227					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CAGGCCGGGGCCCGGGCCTCC	0.687																																					p.A227D		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.C680A						.						19	23	22					11																	73020363		2060	3983	6043	SO:0001583	missense	9828	exon1			CCGGGGCCCGGGC	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.680C>A	chr11.hg19:g.73020363C>A	ENSP00000263674:p.Ala227Asp	191.0	0.0		138.0	55.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.512317	0.64522	.	.	ENSG00000110237	ENST00000263674	T	0.61040	0.14	4.39	3.46	0.39613	.	0.213571	0.23780	N	0.044626	T	0.37705	0.1013	N	0.24115	0.695	0.30306	N	0.788983	B	0.33694	0.421	B	0.29267	0.1	T	0.45527	-0.9255	10	0.62326	D	0.03	-8.0287	7.2727	0.26266	0.0:0.8809:0.0:0.1191	.	227	Q96PE2	ARHGH_HUMAN	D	227	ENSP00000263674:A227D	ENSP00000263674:A227D	A	+	2	0	ARHGEF17	72698011	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	1.404000	0.34623	2.010000	0.58986	0.462000	0.41574	GCC	.	.		0.687	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		A	73020363	C	A	73020363	3	1	133	1	0	0	0	0	1	0	0	0	900	739	26	3	682	3	ARHGEF17	11	73020363	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	2751300	73020363	61986153	47	21553										
FREM2	341640	hgsc.bcm.edu	37	chr13	39264849	39264849	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	aaacatttctccagcaccagGctctgagaaatcaagagcag	8	11	3	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr13:39264849G>A	ENST00000280481.7	+	1	3584	c.3368G>A	c.(3367-3369)gGc>gAc	p.G1123D		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1123					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CCAGCACCAGGCTCTGAGAAA	0.438																																					p.G1123D		Atlas-SNP	.											.	FREM2	385	.	0			c.G3368A						.						61	61	61					13																	39264849		2203	4300	6503	SO:0001583	missense	341640	exon1			CACCAGGCTCTGA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.3368G>A	chr13.hg19:g.39264849G>A	ENSP00000280481:p.Gly1123Asp	64.0	0.0		51.0	6.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.061662	0.76187	.	.	ENSG00000150893	ENST00000280481	T	0.26373	1.74	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.61451	0.2348	H	0.94734	3.575	0.80722	D	1	D	0.64830	0.994	P	0.58013	0.831	T	0.71056	-0.4703	10	0.66056	D	0.02	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	1123	Q5SZK8	FREM2_HUMAN	D	1123	ENSP00000280481:G1123D	ENSP00000280481:G1123D	G	+	2	0	FREM2	38162849	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.864000	0.99589	2.890000	0.99128	0.650000	0.86243	GGC	.	.		0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39264849	G	A	39264849	3	1	133	1	0	0	0	0	1	0	0	0	6053	1203	42	3	3370	3	FREM2	13	39264849	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10		39264849	75905029	48	21554										
PIBF1	10464	hgsc.bcm.edu	37	chr13	73468073	73468073	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	aattggaatgtgaaaaatatCagaaaaaattggaggtacat	9	2	1	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr13:73468073C>A	ENST00000326291.6	+	11	1812	c.1474C>A	c.(1474-1476)Cag>Aag	p.Q492K		NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	492						centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		TGAAAAATATCAGAAAAAATT	0.328																																					p.Q492K		Atlas-SNP	.											.	PIBF1	65	.	0			c.C1474A						.						77	80	79					13																	73468073		2203	4300	6503	SO:0001583	missense	10464	exon11			AAATATCAGAAAA	AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"progesterone-induced blocking factor 1"	607532	"chromosome 13 open reading frame 24"	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.1474C>A	chr13.hg19:g.73468073C>A	ENSP00000317144:p.Gln492Lys	148.0	0.0		115.0	35.0	NM_006346	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Missense_Mutation	SNP	ENST00000326291.6	hg19	CCDS31991.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.670586	0.67814	.	.	ENSG00000083535	ENST00000326291	T	0.24151	1.87	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.45196	0.1330	L	0.50333	1.59	0.58432	D	0.999999	D;D	0.67145	0.996;0.996	D;D	0.72982	0.979;0.979	T	0.12915	-1.0529	10	0.25106	T	0.35	-10.5628	18.6527	0.91437	0.0:1.0:0.0:0.0	.	492;492	Q8WXW3;Q4G0R1	PIBF1_HUMAN;.	K	492	ENSP00000317144:Q492K	ENSP00000317144:Q492K	Q	+	1	0	PIBF1	72366074	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.680000	0.74518	2.477000	0.83638	0.650000	0.86243	CAG	.	.		0.328	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346		A	73468073	C	A	73468073	3	1	133	1	0	0	0	0	1	0	0	0	11888	827	29	3	1512	3	PIBF1	13	73468073	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	34203224	73468073	41701805	49	21555										
C13orf39	196541	hgsc.bcm.edu	37	chr13	103343267	103343267	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gtagctggcgtaatctgtagGaacaaatttctggaggctat	12	6	2	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr13:103343267G>T	ENST00000267273.6	-	2	183	c.178C>A	c.(178-180)Cct>Act	p.P60T		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	60					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)			breast(1)|large_intestine(3)|lung(2)|skin(1)	7						TAATCTGTAGGAACAAATTTC	0.433																																					p.P60T		Atlas-SNP	.											METTL21C,NS,carcinoma,0,1	METTL21C	23	.	0			c.C178A						.						154	142	146					13																	103343267		2203	4300	6503	SO:0001583	missense	196541	exon2			CTGTAGGAACAAA		CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"chromosome 13 open reading frame 39"	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.178C>A	chr13.hg19:g.103343267G>T	ENSP00000267273:p.Pro60Thr	192.0	0.0		119.0	51.0	NM_001010977		Missense_Mutation	SNP	ENST00000267273.6	hg19	CCDS32003.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.242805	0.79912	.	.	ENSG00000139780	ENST00000267273	T	0.16597	2.33	6.16	6.16	0.99307	.	0.204155	0.52532	D	0.000064	T	0.31513	0.0799	L	0.29908	0.895	0.44424	D	0.997345	D	0.69078	0.997	D	0.64042	0.921	T	0.00496	-1.1705	10	0.56958	D	0.05	-24.158	19.848	0.96722	0.0:0.0:1.0:0.0	.	60	Q5VZV1	MT21C_HUMAN	T	60	ENSP00000267273:P60T	ENSP00000267273:P60T	P	-	1	0	METTL21C	102141268	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.459000	0.80802	2.937000	0.99478	0.650000	0.86243	CCT	.	.		0.433	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977		T	103343267	G	T	103343267	3	4	133	1	0	0	0	0	1	0	0	0	1734	1174	41	3	628	3	C13orf39	13	103343267	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	29875194	103343267	11826611	50	21556										
PPIL5	122769	hgsc.bcm.edu	37	chr14	50074175	50074175	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tgagactggctcatagaggcTgtaatgttgatacaccagtt	11	7	1	3			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr14:50074175T>A	ENST00000298288.6	+	3	664	c.340T>A	c.(340-342)Tgt>Agt	p.C114S	LRR1_ENST00000318317.4_Intron|LRR1_ENST00000557531.1_3'UTR	NM_152329.3	NP_689542.2	Q96L50	LLR1_HUMAN	leucine rich repeat protein 1	114					protein ubiquitination (GO:0016567)					kidney(2)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TCATAGAGGCTGTAATGTTGA	0.353																																					p.C114S		Atlas-SNP	.											.	LRR1	35	.	0			c.T340A						.						60	66	64					14																	50074175		2203	4300	6503	SO:0001583	missense	122769	exon3			AGAGGCTGTAATG	BC030142	CCDS9686.1, CCDS9687.1	14q21.3	2011-02-02	2011-02-02	2011-02-02	ENSG00000165501	ENSG00000165501			19742	protein-coding gene	gene with protein product	"LRR-repeat protein 1"	609193	"peptidylprolyl isomerase (cyclophilin)-like 5"	PPIL5		11804328, 21074724	Standard	NR_037792		Approved	MGC20689, LRR-1	uc001wwn.3	Q96L50	OTTHUMG00000140273	ENST00000298288.6:c.340T>A	chr14.hg19:g.50074175T>A	ENSP00000298288:p.Cys114Ser	64.0	0.0		63.0	17.0	NM_152329	A5D6X3|B4DDE0|Q52M24|Q86SZ1|Q8N6H9	Missense_Mutation	SNP	ENST00000298288.6	hg19	CCDS9686.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.691893	0.00731	.	.	ENSG00000165501	ENST00000298288;ENST00000361579	T	0.17213	2.29	5.58	5.58	0.84498	.	0.392987	0.34110	N	0.004248	T	0.08582	0.0213	N	0.14661	0.345	0.09310	N	0.999996	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.36335	-0.9752	10	0.09338	T	0.73	-1.303	8.3678	0.32397	0.1301:0.0:0.1359:0.734	.	136;114	A8MSW2;Q96L50	.;LLR1_HUMAN	S	114;136	ENSP00000298288:C114S	ENSP00000298288:C114S	C	+	1	0	LRR1	49143925	0.634000	0.27190	0.393000	0.26258	0.116000	0.19942	1.132000	0.31418	2.262000	0.75019	0.529000	0.55759	TGT	.	.		0.353	LRR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410790.1	NM_203467		A	50074175	T	A	50074175	3	1	133	1	0	0	0	0	1	0	0	0	12342	1580	55	4	350	4	PPIL5	14	50074175	Missense_Mutation	SNP	T	TCGA-DD-A4NK-01A-11D-A28X-10		50074175	57275365	51	21557										
SPTB	6710	hgsc.bcm.edu	37	chr14	65252575	65252575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tcaagaccttatcccggttgTtctccatagaccccaagaaa	6	13	2	3	rs368552247		TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr14:65252575T>C	ENST00000389721.5	-	16	3688	c.3656A>G	c.(3655-3657)aAc>aGc	p.N1219S	SPTB_ENST00000556626.1_Missense_Mutation_p.N1219S|SPTB_ENST00000389722.3_Missense_Mutation_p.N1219S|SPTB_ENST00000542895.1_Missense_Mutation_p.N1219S|SPTB_ENST00000389720.3_Missense_Mutation_p.N1219S	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1219					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		ATCCCGGTTGTTCTCCATAGA	0.517																																					p.N1219S		Atlas-SNP	.											.	SPTB	378	.	0			c.A3656G						.	T	SER/ASN,SER/ASN	1,4405	2.1+/-5.4	0,1,2202	192	196	195		3656,3656	3.7	1	14		195	0,8600		0,0,4300	no	missense,missense	SPTB	NM_000347.5,NM_001024858.2	46,46	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign	1219/2138,1219/2329	65252575	1,13005	2203	4300	6503	SO:0001583	missense	6710	exon16			CGGTTGTTCTCCA		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.3656A>G	chr14.hg19:g.65252575T>C	ENSP00000374371:p.Asn1219Ser	67.0	0.0		55.0	25.0	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	T	13.69	2.313233	0.40895	2.27E-4	0.0	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78	4.94	3.7	0.42460	.	0.205937	0.43919	D	0.000501	T	0.26991	0.0661	N	0.11560	0.145	0.44515	D	0.997468	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08617	-1.0713	10	0.44086	T	0.13	.	9.7829	0.40660	0.0:0.0:0.3506:0.6494	.	1219;1223	P11277;Q59FP5	SPTB1_HUMAN;.	S	1223;1219;3;1219;1219;1219;1219	ENSP00000374372:N1219S;ENSP00000451752:N1219S;ENSP00000374371:N1219S;ENSP00000443882:N1219S;ENSP00000374370:N1219S	ENSP00000334218:N3S	N	-	2	0	SPTB	64322328	0.995000	0.38212	1.000000	0.80357	0.994000	0.84299	1.599000	0.36751	1.983000	0.57843	0.443000	0.29094	AAC	.	.		0.517	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			C	65252575	T	C	65252575	3	2	133	1	0	0	0	0	1	0	0	0	15133	1725	60	2	3479	2	SPTB	14	65252575	Missense_Mutation	SNP	T	TCGA-DD-A4NK-01A-11D-A28X-10	15178400	65252575	42096965	52	21558										
LTK	4058	hgsc.bcm.edu	37	chr15	41796253	41796253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gaggcccctggatttgagggGcttgaggccagaggacagcc	17	10	0	3			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr15:41796253G>T	ENST00000263800.6	-	20	2632	c.2536C>A	c.(2536-2538)Ccc>Acc	p.P846T	LTK_ENST00000561619.1_Missense_Mutation_p.P544T|LTK_ENST00000355166.5_Missense_Mutation_p.P785T|LTK_ENST00000453182.2_Missense_Mutation_p.P716T	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	846					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.P846T(1)|p.P785T(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		GATTTGAGGGGCTTGAGGCCA	0.607										TSP Lung(18;0.14)																											p.P846T		Atlas-SNP	.											LTK_ENST00000263800,NS,carcinoma,0,2	LTK	117	.	2	Substitution - Missense(2)	lung(2)	c.C2536A						.						39	45	43					15																	41796253		2203	4300	6503	SO:0001583	missense	4058	exon20			TGAGGGGCTTGAG	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.2536C>A	chr15.hg19:g.41796253G>T	ENSP00000263800:p.Pro846Thr	100.0	0.0		82.0	4.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	G	7.360	0.624684	0.14193	.	.	ENSG00000062524	ENST00000355166;ENST00000263800;ENST00000453182	T;T;T	0.75477	-0.94;-0.71;-0.89	4.52	-1.19	0.09585	.	0.556043	0.13481	N	0.384684	T	0.43233	0.1238	N	0.08118	0	0.18873	N	0.999986	B;B;B;B	0.12013	0.005;0.001;0.004;0.001	B;B;B;B	0.12156	0.003;0.002;0.007;0.003	T	0.21177	-1.0253	10	0.12766	T	0.61	.	1.5061	0.02486	0.1688:0.1316:0.3873:0.3123	.	716;716;785;846	E9PFX4;B4DL89;P29376-4;P29376	.;.;.;LTK_HUMAN	T	785;846;716	ENSP00000347293:P785T;ENSP00000263800:P846T;ENSP00000392196:P716T	ENSP00000263800:P846T	P	-	1	0	LTK	39583545	0.522000	0.26266	0.939000	0.37840	0.848000	0.48234	1.317000	0.33631	-0.308000	0.08792	-0.136000	0.14681	CCC	.	.		0.607	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			T	41796253	G	T	41796253	3	4	133	1	0	0	0	0	1	0	0	0	9089	1203	42	3	62	3	LTK	15	41796253	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10		41796253	60735139	53	21559										
MGA	23269	hgsc.bcm.edu	37	chr15	41988802	41988802	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	aatcagaaaatggtcttagaAaacattcaccagatctcaga	6	8	4	4			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr15:41988802A>T	ENST00000570161.1	+	2	1594	c.1594A>T	c.(1594-1596)Aaa>Taa	p.K532*	MGA_ENST00000219905.7_Nonsense_Mutation_p.K532*|MGA_ENST00000545763.1_Nonsense_Mutation_p.K532*|MGA_ENST00000389936.4_Nonsense_Mutation_p.K532*|MGA_ENST00000566586.1_Nonsense_Mutation_p.K532*			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGGTCTTAGAAAACATTCACC	0.373																																					p.K532X		Atlas-SNP	.											.	MGA	264	.	0			c.A1594T						.						74	66	68					15																	41988802		1842	4088	5930	SO:0001587	stop_gained	23269	exon3			CTTAGAAAACATT	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1594A>T	chr15.hg19:g.41988802A>T	ENSP00000457035:p.Lys532*	65.0	0.0		79.0	8.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Nonsense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	A	35	5.545638	0.96488	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	.	.	.	5.54	5.54	0.83059	.	0.470570	0.22266	N	0.062322	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.68	0.77360	1.0:0.0:0.0:0.0	.	.	.	.	X	532	.	ENSP00000219905:K532X	K	+	1	0	MGA	39776094	0.999000	0.42202	0.998000	0.56505	0.821000	0.46438	2.947000	0.49058	2.107000	0.64212	0.379000	0.24179	AAA	.	.		0.373	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	41988802	A	T	41988802	4	4	133	1	0	0	0	0	0	1	0	0	9549	15	1	4	1600	4	MGA	15	41988802	Nonsense_Mutation	SNP	A	TCGA-DD-A4NK-01A-11D-A28X-10	192549	41988802	60542590	54	21560										
LDHAL6B	92483	hgsc.bcm.edu	37	chr15	59499173	59499173	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tgcctgttgtgcgggccagcCagagagtgagctcggtggga	18	9	0	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr15:59499173C>A	ENST00000307144.4	+	1	132	c.34C>A	c.(34-36)Cag>Aag	p.Q12K	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	12					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						GCGGGCCAGCCAGAGAGTGAG	0.582																																					p.Q12K		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.C34A						.						37	36	36					15																	59499173		2191	4290	6481	SO:0001583	missense	92483	exon1			GCCAGCCAGAGAG	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"lactate dehydrogenase A-like 6"	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.34C>A	chr15.hg19:g.59499173C>A	ENSP00000302393:p.Gln12Lys	121.0	0.0		104.0	38.0	NM_033195	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	hg19	CCDS10171.1	.	.	.	.	.	.	.	.	.	.	C	1.967	-0.437395	0.04636	.	.	ENSG00000171989	ENST00000307144	T	0.66638	-0.22	0.827	-0.333	0.12671	.	.	.	.	.	T	0.42877	0.1222	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17992	-1.0351	9	0.21014	T	0.42	.	3.2405	0.06779	0.0:0.6516:0.0:0.3484	.	12	Q9BYZ2	LDH6B_HUMAN	K	12	ENSP00000302393:Q12K	ENSP00000302393:Q12K	Q	+	1	0	LDHAL6B	57286465	0.070000	0.21116	0.001000	0.08648	0.069000	0.16628	0.149000	0.16243	-0.143000	0.11334	0.305000	0.20034	CAG	.	.		0.582	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195		A	59499173	C	A	59499173	3	1	133	1	0	0	0	0	1	0	0	0	8709	595	21	3	36	3	LDHAL6B	15	59499173	Missense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	17510371	59499173	43032219	55	21561										
OR1F1	4992	hgsc.bcm.edu	37	chr16	3254987	3254987	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tgtggttctcacctggctgtGgttctcctcttctacagcac	9	13	4	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr16:3254987G>A	ENST00000304646.2	+	1	741	c.741G>A	c.(739-741)gtG>gtA	p.V247V	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	247					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(2)|lung(7)	11						ACCTGGCTGTGGTTCTCCTCT	0.493																																					p.V247V		Atlas-SNP	.											.	OR1F1	36	.	0			c.G741A						.						208	191	197					16																	3254987		2197	4300	6497	SO:0001819	synonymous_variant	4992	exon1			GGCTGTGGTTCTC	Y14442	CCDS10496.1	16p13.3	2012-08-09			ENSG00000168124	ENSG00000168124		"GPCR / Class A : Olfactory receptors"	8194	protein-coding gene	gene with protein product		603232		OR1F4, OR1F6, OR1F7, OR1F8, OR1F9, OR1F5, OR1F10, OR1F13P		9288094, 9500546	Standard	NM_012360		Approved	Olfmf, OR16-36, OR16-37, OR16-88, OR16-89, OR16-90, OLFMF, OR3-145	uc010uwu.2	O43749	OTTHUMG00000133153	ENST00000304646.2:c.741G>A	chr16.hg19:g.3254987G>A		217.0	0.0		155.0	44.0	NM_012360	O15246|Q6IFL5	Silent	SNP	ENST00000304646.2	hg19	CCDS10496.1																																																																																			.	.		0.493	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1			A	3254987	G	A	3254987	2	1	133	1	0	0	0	0	0	0	0	1	10965	1335	47	3		3	OR1F1	16	3254987	Silent	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10		3254987	87099766	56	21562										
ATXN2L	11273	hgsc.bcm.edu	37	chr16	28846465	28846465	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	atcgtgtcatcctctaccccTcagtacccttctgcagagca	6	16	4	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr16:28846465T>A	ENST00000336783.4	+	19	2687	c.2520T>A	c.(2518-2520)ccT>ccA	p.P840P	ATXN2L_ENST00000382686.4_Silent_p.P840P|ATXN2L_ENST00000570200.1_Silent_p.P840P|ATXN2L_ENST00000565845.1_3'UTR|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000395547.2_Silent_p.P840P|ATXN2L_ENST00000564304.1_Silent_p.P846P|ATXN2L_ENST00000340394.8_Silent_p.P840P|ATXN2L_ENST00000325215.6_Silent_p.P840P	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like	840					regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						CCTCTACCCCTCAGTACCCTT	0.642																																					p.P840P		Atlas-SNP	.											.	ATXN2L	159	.	0			c.T2520A						.						154	130	138					16																	28846465		2197	4300	6497	SO:0001819	synonymous_variant	11273	exon19			TACCCCTCAGTAC		CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.2520T>A	chr16.hg19:g.28846465T>A		154.0	0.0		118.0	38.0	NM_148414	A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Silent	SNP	ENST00000336783.4	hg19	CCDS10641.1																																																																																			.	.		0.642	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245		A	28846465	T	A	28846465	2	1	133	1	0	0	0	0	0	0	0	1	1212	1538	54	4		4	ATXN2L	16	28846465	Silent	SNP	T	TCGA-DD-A4NK-01A-11D-A28X-10	25591478	28846465	61508288	57	21563										
HIRIP3	8479	hgsc.bcm.edu	37	chr16	30005727	30005728	+	Frame_Shift_Ins	INS	-	-	T													0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tcctcatcctcttctttctcINSttcctcctccacttcctcct							TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr16:30005727_30005728insT	ENST00000279392.3	-	4	1568_1569	c.738_739insA	c.(736-741)gaagagfs	p.E247fs	INO80E_ENST00000567254.1_5'Flank|INO80E_ENST00000304516.7_5'Flank|INO80E_ENST00000567705.1_5'Flank|INO80E_ENST00000563197.1_5'Flank|HIRIP3_ENST00000566471.1_5'Flank|HIRIP3_ENST00000564026.1_Intron	NM_003609.4	NP_003600.2	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3	247	Glu-rich.				chromatin assembly or disassembly (GO:0006333)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(9)	17						tcttctttctcttcctcctcca	0.49																																					p.E247fs		Atlas-Indel,Pindel	.											.	HIRIP3	45	.	0			c.739_740insA						.																																			SO:0001589	frameshift_variant	8479	exon4			.	AJ223351	CCDS10664.1, CCDS58449.1	16p12.1	2008-02-05	2001-11-29		ENSG00000149929	ENSG00000149929			4917	protein-coding gene	gene with protein product		603365	"HIRA-interacting protein 3"			9710638	Standard	NM_003609		Approved		uc002dve.3	Q9BW71	OTTHUMG00000132118	ENST00000279392.3:c.739dupA	chr16.hg19:g.30005729_30005729dupT	ENSP00000279392:p.Glu247fs	70.0	0.0		55.0	22.0	NM_003609	H3BSR3|O75707|O75708	Frame_Shift_Ins	INS	ENST00000279392.3	hg19	CCDS10664.1																																																																																			.	.		0.49	HIRIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255160.2	NM_003609		T	30005728	-	T	30005727	7	5	133	1	0	1	1	0	0	0	0	0	7130	922	32	0	947	0	HIRIP3	16	30005727	Frame_Shift_Ins	INS	-	TCGA-DD-A4NK-01A-11D-A28X-10	1159262	30005727	60349026	58	21564										
SIAH1	6477	hgsc.bcm.edu	37	chr16	48396330	48396330	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	aggtaatgctgtagcagtctGacggctcatttctgaaataa	10	7	3	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr16:48396330G>A	ENST00000380006.2	-	1	1463	c.10C>T	c.(10-12)Cag>Tag	p.Q4*	SIAH1_ENST00000573005.1_5'Flank|SIAH1_ENST00000356721.3_Nonsense_Mutation_p.Q35*|SIAH1_ENST00000394725.2_Nonsense_Mutation_p.Q4*			Q8IUQ4	SIAH1_HUMAN	siah E3 ubiquitin protein ligase 1	4					anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell cycle (GO:0007049)|nervous system development (GO:0007399)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein catabolic process (GO:0030163)|protein destabilization (GO:0031648)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	beta-catenin destruction complex (GO:0030877)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|stomach(1)	7		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)				GTAGCAGTCTGACGGCTCATT	0.428																																					p.Q35X		Atlas-SNP	.											SIAH1_ENST00000356721,NS,carcinoma,0,2	SIAH1	33	.	0			c.C103T						.						61	58	59					16																	48396330		2200	4300	6500	SO:0001587	stop_gained	6477	exon2			CAGTCTGACGGCT	U76247	CCDS10735.1, CCDS32444.1	16q12.1	2013-06-03	2012-02-23		ENSG00000196470	ENSG00000196470			10857	protein-coding gene	gene with protein product		602212	"seven in absentia homolog 1 (Drosophila)"			9403064, 9334332	Standard	NM_001006610		Approved	hSIAH1	uc002efo.1	Q8IUQ4	OTTHUMG00000175417	ENST00000380006.2:c.10C>T	chr16.hg19:g.48396330G>A	ENSP00000369343:p.Gln4*	237.0	0.0		186.0	71.0	NM_001006610	A0FKF3|O43269|Q49A58|Q92880	Nonsense_Mutation	SNP	ENST00000380006.2	hg19	CCDS10735.1	.	.	.	.	.	.	.	.	.	.	G	48	14.140680	0.99781	.	.	ENSG00000196470	ENST00000356721;ENST00000394725;ENST00000380006	.	.	.	5.43	5.43	0.79202	.	0.142052	0.48286	U	0.000183	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	-0.6805	19.2389	0.93873	0.0:0.0:1.0:0.0	.	.	.	.	X	35;4;20	.	ENSP00000349156:Q35X	Q	-	1	0	SIAH1	46953831	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.714000	0.98744	2.555000	0.86185	0.655000	0.94253	CAG	.	.		0.428	SIAH1-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256842.12			A	48396330	G	A	48396330	4	1	133	1	0	0	0	0	0	1	0	0	14314	1299	45	3	842	3	SIAH1	16	48396330	Nonsense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	18390603	48396330	41958423	59	21565										
CDH1	999	hgsc.bcm.edu	37	chr16	68842624	68842624	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	caacaaagacaaagaaggcaAggttttctacagcatcactg	8	9	2	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr16:68842624A>G	ENST00000261769.5	+	5	751	c.560A>G	c.(559-561)aAg>aGg	p.K187R	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.K187R	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	187	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(2)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		AAAGAAGGCAAGGTTTTCTAC	0.428			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												p.K187R		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	.	CDH1	535	.	2	Unknown(2)	breast(2)	c.A560G						.						58	57	57					16																	68842624		2198	4300	6498	SO:0001583	missense	999	exon5	Familial Cancer Database	HDGC	AAGGCAAGGTTTT	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.560A>G	chr16.hg19:g.68842624A>G	ENSP00000261769:p.Lys187Arg	76.0	0.0		54.0	23.0	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	hg19	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	A	12.07	1.826294	0.32329	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.51071	0.72;0.72	5.78	3.5	0.40072	Cadherin (4);Cadherin-like (1);	0.669534	0.13536	N	0.380600	T	0.34308	0.0893	N	0.21545	0.675	0.32195	N	0.5786	B;B	0.21225	0.025;0.053	B;B	0.29663	0.022;0.105	T	0.40194	-0.9576	10	0.35671	T	0.21	.	8.4372	0.32795	0.7979:0.1329:0.0692:0.0	.	187;187	Q9UII8;P12830	.;CADH1_HUMAN	R	187	ENSP00000261769:K187R;ENSP00000414946:K187R	ENSP00000261769:K187R	K	+	2	0	CDH1	67400125	0.077000	0.21312	0.792000	0.32020	0.957000	0.61999	0.780000	0.26760	1.087000	0.41251	0.533000	0.62120	AAG	.	.		0.428	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		G	68842624	A	G	68842624	3	3	133	1	0	0	0	0	1	0	0	0	3097	72	3	2	578	2	CDH1	16	68842624	Missense_Mutation	SNP	A	TCGA-DD-A4NK-01A-11D-A28X-10	20446294	68842624	21512129	60	21566										
MLLT6	4302	hgsc.bcm.edu	37	chr17	36876674	36876674	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ctgcagaaggagaaccagcgGctgcaagagcagatcctgag	14	10	0	5			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr17:36876674G>A	ENST00000325718.7	+	15	2296	c.2205G>A	c.(2203-2205)cgG>cgA	p.R735R	MIR4726_ENST00000577947.1_RNA|CTB-58E17.9_ENST00000579499.1_RNA	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	735	Leucine-zipper.			R -> W (in Ref. 4; BAD92870). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					AGAACCAGCGGCTGCAAGAGC	0.662			T	MLL	AL																																p.R735R		Atlas-SNP	.		Dom	yes		17	17q21	4302	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"		L	.	MLLT6	80	.	0			c.G2205A						.						34	29	31					17																	36876674		2200	4286	6486	SO:0001819	synonymous_variant	4302	exon15			CCAGCGGCTGCAA		CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"Zinc fingers, PHD-type"	7138	protein-coding gene	gene with protein product	"Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6", "trithorax homolog"	600328	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.2205G>A	chr17.hg19:g.36876674G>A		109.0	0.0		112.0	41.0	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Silent	SNP	ENST00000325718.7	hg19	CCDS11327.1																																																																																			.	.		0.662	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937		A	36876674	G	A	36876674	2	1	133	1	0	0	0	0	0	0	0	1	9639	1190	42	3		3	MLLT6	17	36876674	Silent	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10		36876674	44318536	61	21567										
MAPT	4137	hgsc.bcm.edu	37	chr17	44060964	44060964	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cttcccagcggagggtgccaTccccctccctgtggatttcc	10	17	0	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr17:44060964T>A	ENST00000571987.1	+	5	794	c.794T>A	c.(793-795)aTc>aAc	p.I265N	MAPT_ENST00000576518.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.I265N|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.I265N|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.I265N|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000446361.3_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	265					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GAGGGTGCCATCCCCCTCCCT	0.672																																					p.I265N		Atlas-SNP	.											.	MAPT	135	.	0			c.T794A						.						31	30	30					17																	44060964		2202	4299	6501	SO:0001583	missense	4137	exon6			GTGCCATCCCCCT	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.794T>A	chr17.hg19:g.44060964T>A	ENSP00000458742:p.Ile265Asn	94.0	0.0		77.0	26.0	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	hg19	CCDS11501.1	.	.	.	.	.	.	.	.	.	.	T	9.722	1.159964	0.21454	.	.	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.15139	2.45;2.47;2.45	5.47	2.0	0.26442	.	0.732533	0.11787	N	0.529564	T	0.13586	0.0329	L	0.50333	1.59	0.09310	N	1	P;P	0.45474	0.859;0.638	B;B	0.40534	0.332;0.178	T	0.16453	-1.0402	10	0.23891	T	0.37	-1.5043	4.2549	0.10712	0.0:0.1789:0.1734:0.6477	.	265;265	P10636-9;P10636	.;TAU_HUMAN	N	265	ENSP00000340820:I265N;ENSP00000262410:I265N;ENSP00000410838:I265N	ENSP00000262410:I265N	I	+	2	0	MAPT	41416801	0.007000	0.16637	0.715000	0.30552	0.007000	0.05969	0.016000	0.13377	0.353000	0.24079	0.459000	0.35465	ATC	.	.		0.672	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		A	44060964	T	A	44060964	3	1	133	1	0	0	0	0	1	0	0	0	9306	1435	50	4	812	4	MAPT	17	44060964	Missense_Mutation	SNP	T	TCGA-DD-A4NK-01A-11D-A28X-10	7184290	44060964	37134246	62	21568										
CDK3	1018	hgsc.bcm.edu	37	chr17	73998495	73998495	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gcccctgcgcacctacacccAtgaggtattgtgagacaaag	10	13	0	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr17:73998495A>G	ENST00000425876.2	+	4	570	c.482A>G	c.(481-483)cAt>cGt	p.H161R	TEN1-CDK3_ENST00000567351.1_RNA|CDK3_ENST00000448471.1_Missense_Mutation_p.H161R			Q00526	CDK3_HUMAN	cyclin-dependent kinase 3	161	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|G0 to G1 transition (GO:0045023)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			central_nervous_system(1)	1						ACCTACACCCATGAGGTATTG	0.592																																					p.H161R		Atlas-SNP	.											.	CDK3	31	.	0			c.A482G						.						44	37	39					17																	73998495		2203	4300	6503	SO:0001583	missense	1018	exon5			ACACCCATGAGGT	X66357	CCDS11736.1	17q25.1	2012-09-20			ENSG00000250506	ENSG00000250506		"Cyclin-dependent kinases"	1772	protein-coding gene	gene with protein product		123828				1639063	Standard	NM_001258		Approved		uc010dgt.3	Q00526	OTTHUMG00000154861	ENST00000425876.2:c.482A>G	chr17.hg19:g.73998495A>G	ENSP00000410561:p.His161Arg	82.0	0.0		62.0	21.0	NM_001258		Missense_Mutation	SNP	ENST00000425876.2	hg19	CCDS11736.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.362987	0.82353	.	.	ENSG00000250506	ENST00000448471;ENST00000425876	T;T	0.41758	0.99;0.99	4.51	4.51	0.55191	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000023	T	0.48132	0.1483	N	0.21282	0.65	0.58432	D	0.999998	D	0.67145	0.996	D	0.67548	0.952	T	0.53436	-0.8439	10	0.87932	D	0	-13.1552	13.162	0.59550	1.0:0.0:0.0:0.0	.	161	Q00526	CDK3_HUMAN	R	161	ENSP00000400088:H161R;ENSP00000410561:H161R	ENSP00000410561:H161R	H	+	2	0	CDK3	71510090	1.000000	0.71417	0.999000	0.59377	0.921000	0.55340	9.083000	0.94067	1.905000	0.55150	0.454000	0.30748	CAT	.	.		0.592	CDK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337389.2	NM_001258		G	73998495	A	G	73998495	3	3	133	1	0	0	0	0	1	0	0	0	3142	217	8	2	496	2	CDK3	17	73998495	Missense_Mutation	SNP	A	TCGA-DD-A4NK-01A-11D-A28X-10	29937531	73998495	7196715	63	21569										
RASGRP4	115727	hgsc.bcm.edu	37	chr19	38912649	38912649	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tccagcagctcatcttcgctGcagccgccctcactcagcag	8	18	4	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr19:38912649G>A	ENST00000587738.1	-	2	238	c.168C>T	c.(166-168)tgC>tgT	p.C56C	RASGRP4_ENST00000454404.2_Silent_p.C56C|RASGRP4_ENST00000587753.1_Silent_p.C56C|RASGRP4_ENST00000433821.2_Silent_p.C56C|RASGRP4_ENST00000426920.2_Silent_p.C56C|RASGRP4_ENST00000586305.1_Silent_p.C56C|RASGRP4_ENST00000293062.9_Silent_p.C56C			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	56	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CATCTTCGCTGCAGCCGCCCT	0.627																																					p.C56C		Atlas-SNP	.											.	RASGRP4	54	.	0			c.C168T						.						34	39	37					19																	38912649		2057	4199	6256	SO:0001819	synonymous_variant	115727	exon2			TTCGCTGCAGCCG	AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"EF-hand domain containing"	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.168C>T	chr19.hg19:g.38912649G>A		81.0	0.0		81.0	34.0	NM_001146206	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Silent	SNP	ENST00000587738.1	hg19	CCDS46068.1																																																																																			.	.		0.627	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1	NM_170604		A	38912649	G	A	38912649	2	1	133	1	0	0	0	0	0	0	0	1	13092	1311	46	3		3	RASGRP4	19	38912649	Silent	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10		38912649	20216334	64	21570										
ZNF226	7769	hgsc.bcm.edu	37	chr19	44676265	44676265	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cagtgaccttcaaggacgtgGctgtggccttcacggaggag	15	10	2	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr19:44676265G>T	ENST00000590089.1	+	5	407	c.40G>T	c.(40-42)Gct>Tct	p.A14S	ZNF226_ENST00000588742.1_Missense_Mutation_p.A14S|ZNF226_ENST00000588795.1_Missense_Mutation_p.A14S|ZNF226_ENST00000589160.1_Missense_Mutation_p.A14S|ZNF226_ENST00000300823.6_Missense_Mutation_p.A14S|ZNF226_ENST00000454662.2_Missense_Mutation_p.A14S|ZNF226_ENST00000337433.5_Missense_Mutation_p.A14S|ZNF226_ENST00000588883.1_Missense_Mutation_p.A14S|ZNF226_ENST00000413984.2_Missense_Mutation_p.A14S			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	14	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)						Prostate(69;0.0352)|all_neural(266;0.202)				CAAGGACGTGGCTGTGGCCTT	0.512																																					p.A14S	Pancreas(115;581 1665 13228 19278 50070)	Atlas-SNP	.											.	.	.	.	0			c.G40T						.						165	164	165					19																	44676265		2203	4300	6503	SO:0001583	missense	7769	exon4			GACGTGGCTGTGG	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"Zinc fingers, C2H2-type", "-"	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.40G>T	chr19.hg19:g.44676265G>T	ENSP00000465121:p.Ala14Ser	172.0	0.0		130.0	52.0	NM_015919	Q8WWE6|Q96TE6|Q9NS44	Missense_Mutation	SNP	ENST00000590089.1	hg19	CCDS46102.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.038600	0.75617	.	.	ENSG00000167380	ENST00000300823;ENST00000337433;ENST00000413984;ENST00000454662	T;T;T;T	0.03181	4.02;4.02;4.02;4.02	4.32	3.28	0.37604	Krueppel-associated box (4);	.	.	.	.	T	0.18087	0.0434	M	0.85197	2.74	0.28737	N	0.902177	D;D	0.76494	0.979;0.999	P;D	0.74674	0.822;0.984	T	0.01930	-1.1245	9	0.66056	D	0.02	.	9.9256	0.41489	0.1011:0.0:0.8989:0.0	.	14;14	Q9NYT6;Q8WWE6	ZN226_HUMAN;.	S	14	ENSP00000300823:A14S;ENSP00000336719:A14S;ENSP00000407474:A14S;ENSP00000393265:A14S	ENSP00000300823:A14S	A	+	1	0	ZNF226	49368105	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.797000	0.38804	1.177000	0.42855	0.650000	0.86243	GCT	.	.		0.512	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1			T	44676265	G	T	44676265	3	4	133	1	0	0	0	0	1	0	0	0	17795	1203	42	3	46	3	ZNF226	19	44676265	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	5763616	44676265	14452718	65	21571										
NR1H2	7376	hgsc.bcm.edu	37	chr19	50881836	50881836	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tcggaaacagcagcaggagtCacagtcacagtcgcagtcac	11	12	3	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr19:50881836C>A	ENST00000253727.5	+	6	765	c.530C>A	c.(529-531)tCa>tAa	p.S177*	NR1H2_ENST00000411902.2_Nonsense_Mutation_p.S80*|NR1H2_ENST00000542413.1_5'UTR|NR1H2_ENST00000593926.1_Nonsense_Mutation_p.S177*|NR1H2_ENST00000599105.1_Nonsense_Mutation_p.S177*|NR1H2_ENST00000598168.1_Nonsense_Mutation_p.S177*	NM_007121.5	NP_009052	P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2	177					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pinocytosis (GO:0048550)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	apolipoprotein A-I receptor binding (GO:0034191)|ATPase binding (GO:0051117)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	8		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		CAGCAGGAGTCACAGTCACAG	0.632																																					p.S177X		Atlas-SNP	.											.	NR1H2	47	.	0			c.C530A						.						35	46	42					19																	50881836		2163	4263	6426	SO:0001587	stop_gained	7376	exon6			AGGAGTCACAGTC	U14534	CCDS42593.1, CCDS58673.1	19q13.3	2013-01-16				ENSG00000131408		"Nuclear hormone receptors"	7965	protein-coding gene	gene with protein product	"liver X receptor-beta"	600380	"ubiquitously-expressed nuclear receptor"	UNR		7782080, 7971966	Standard	NM_007121		Approved	NER, NER-I, RIP15, LXR-b	uc010enw.4	P55055		ENST00000253727.5:c.530C>A	chr19.hg19:g.50881836C>A	ENSP00000253727:p.Ser177*	91.0	0.0		65.0	27.0	NM_007121	A8K490|B4DNM6|E7EWA6|Q12970|Q5I0Y1	Nonsense_Mutation	SNP	ENST00000253727.5	hg19	CCDS42593.1	.	.	.	.	.	.	.	.	.	.	C	18.94	3.729108	0.69074	.	.	ENSG00000131408	ENST00000253727;ENST00000411902;ENST00000376942	.	.	.	1.62	0.529	0.17095	.	0.346219	0.24391	N	0.038939	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	6.1298	0.20199	0.4374:0.5625:0.0:0.0	.	.	.	.	X	177;80;177	.	ENSP00000253727:S177X	S	+	2	0	NR1H2	55573648	0.018000	0.18449	0.995000	0.50966	0.250000	0.25880	-0.173000	0.09854	0.127000	0.18452	-0.755000	0.03482	TCA	.	.		0.632	NR1H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464724.2			A	50881836	C	A	50881836	4	1	133	1	0	0	0	0	0	1	0	0	10626	838	29	3	544	3	NR1H2	19	50881836	Nonsense_Mutation	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	6205571	50881836	8247147	66	21572										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41416175	41416175	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ggtttctcgctgtgggcccaGccttggcattcctcctggtg	13	13	1	0			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr21:41416175G>T	ENST00000400454.1	-	31	5690	c.5213C>A	c.(5212-5214)gCt>gAt	p.A1738D		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1738					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TGTGGGCCCAGCCTTGGCATT	0.592																																					p.A1738D	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C5213A						.						75	82	80					21																	41416175		2132	4238	6370	SO:0001583	missense	1826	exon31			GGCCCAGCCTTGG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.5213C>A	chr21.hg19:g.41416175G>T	ENSP00000383303:p.Ala1738Asp	141.0	0.0		113.0	45.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	g	16.72	3.200941	0.58234	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.60672	0.17;0.27	5.53	4.6	0.57074	.	0.109142	0.64402	D	0.000006	T	0.47248	0.1435	L	0.27053	0.805	0.39184	D	0.962836	P	0.38250	0.624	B	0.37267	0.245	T	0.52953	-0.8506	10	0.40728	T	0.16	.	18.011	0.89224	0.0:0.1306:0.8694:0.0	.	1738	O60469	DSCAM_HUMAN	D	1738;1490	ENSP00000383303:A1738D;ENSP00000385342:A1490D	ENSP00000383303:A1738D	A	-	2	0	DSCAM	40338045	1.000000	0.71417	0.936000	0.37596	0.718000	0.41266	7.806000	0.86020	2.605000	0.88082	0.655000	0.94253	GCT	.	.		0.592	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		T	41416175	G	T	41416175	3	4	133	1	0	0	0	0	1	0	0	0	4770	971	34	3	837	3	DSCAM	21	41416175	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10		41416175	6713720	67	21573										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19211532	19211532	+	Frame_Shift_Del	DEL	G	G	-													0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tgtatttcagatgcacatctGggtcttggctgaagttcacg							TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr22:19211532delG	ENST00000263200.10	-	14	2246	c.2174delC	c.(2173-2175)ccafs	p.P725fs	CLTCL1_ENST00000427926.1_Frame_Shift_Del_p.P725fs|CLTCL1_ENST00000353891.5_Frame_Shift_Del_p.P725fs	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	725	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					ATGCACATCTGGGTCTTGGCT	0.512			T	?	ALCL																																p.P725fs		Atlas-INDEL	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.2175delA						.						91	95	94					22																	19211532		2036	4192	6228	SO:0001589	frameshift_variant	8218	exon14			.		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.2174delC	chr22.hg19:g.19211532delG	ENSP00000445677:p.Pro725fs	267.0	0.0		174.0	11.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Frame_Shift_Del	DEL	ENST00000263200.10	hg19	CCDS46662.1																																																																																			.	.		0.512	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		-	19211532	G	-	19211532	7	5	133	1	0	1	0	1	0	0	0	0	3569	1348	47	0	2824	0	CLTCL1	22	19211532	Frame_Shift_Del	DEL	G	TCGA-DD-A4NK-01A-11D-A28X-10		19211532	32093034	68	21574										
CDC45	8318	hgsc.bcm.edu	37	chr22	19481906	19481906	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cgagagtgggaggcccggagGtgagtctgtgcttccagctg	18	9	1	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr22:19481906G>T	ENST00000407835.1	+	7	798		c.e7+1		CDC45_ENST00000437685.2_Splice_Site|CDC45_ENST00000483431.1_Splice_Site|CDC45_ENST00000404724.3_Splice_Site|CDC45_ENST00000263201.1_Splice_Site			O75419	CDC45_HUMAN	cell division cycle 45						DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						AGGCCCGGAGGTGAGTCTGTG	0.562																																					.		Atlas-SNP	.											.	CDC45	48	.	0			c.404+1G>T						.						67	68	67					22																	19481906		2203	4300	6503	SO:0001630	splice_region_variant	8318	exon5			CCGGAGGTGAGTC	AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"human CDC45"	603465	"CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like", "CDC45 cell division cycle 45-like (S. cerevisiae)", "cell division cycle 45 homolog (S. cerevisiae)"	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.542+1G>T	chr22.hg19:g.19481906G>T		199.0	0.0		139.0	46.0	NM_001178011	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Splice_Site	SNP	ENST00000407835.1	hg19	CCDS13762.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.884035	0.33255	.	.	ENSG00000093009	ENST00000407835;ENST00000437685;ENST00000263201;ENST00000404724	.	.	.	4.46	4.46	0.54185	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9561	0.64150	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDC45	17861906	1.000000	0.71417	1.000000	0.80357	0.221000	0.24807	5.264000	0.65513	2.295000	0.77249	0.563000	0.77884	.	.	.		0.562	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504	Intron	T	19481906	G	T	19481906	5	4	133	1	0	0	0	0	0	0	1	0	3083	1275	44	3	565	3	CDC45	22	19481906	Splice_Site	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	270374	19481906	31822660	69	21575										
GCAT	23464	hgsc.bcm.edu	37	chr22	38212648	38212648	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	tccgggtacagatctcagcaGtgcatagcgaggaagacatt	12	9	1	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr22:38212648G>A	ENST00000248924.6	+	9	1239	c.1183G>A	c.(1183-1185)Gtg>Atg	p.V395M	GCAT_ENST00000323205.6_Missense_Mutation_p.V421M	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	395					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	GATCTCAGCAGTGCATAGCGA	0.617																																					p.V421M		Atlas-SNP	.											.	GCAT	27	.	0			c.G1261A						.						81	72	75					22																	38212648		2203	4300	6503	SO:0001583	missense	23464	exon9			TCAGCAGTGCATA	AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"2-amino-3-ketobutyrate coenzyme A ligase"	607422	"glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.1183G>A	chr22.hg19:g.38212648G>A	ENSP00000248924:p.Val395Met	127.0	0.0		126.0	44.0	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Missense_Mutation	SNP	ENST00000248924.6	hg19	CCDS13957.1	.	.	.	.	.	.	.	.	.	.	g	19.66	3.869526	0.72065	.	.	ENSG00000100116	ENST00000323205;ENST00000248924	D;D	0.90620	-2.7;-2.7	5.42	4.41	0.53225	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.116625	0.64402	N	0.000017	D	0.90410	0.6998	L	0.33339	1.005	0.36264	D	0.854711	B;D	0.56035	0.007;0.974	B;P	0.55749	0.034;0.783	D	0.93296	0.6672	10	0.72032	D	0.01	-21.3337	14.3991	0.67031	0.0712:0.0:0.9288:0.0	.	421;395	E2QC23;O75600	.;KBL_HUMAN	M	421;395	ENSP00000371110:V421M;ENSP00000248924:V395M	ENSP00000248924:V395M	V	+	1	0	GCAT	36542594	1.000000	0.71417	0.838000	0.33150	0.470000	0.32858	5.387000	0.66243	1.325000	0.45301	-0.119000	0.15052	GTG	.	.		0.617	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2		A	38212648	G	A	38212648	3	1	133	1	0	0	0	0	1	0	0	0	6292	1029	36	3	1295	3	GCAT	22	38212648	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	18730742	38212648	13091918	70	21576										
SOX10	6663	hgsc.bcm.edu	37	chr22	38369604	38369604	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	gagatggccgtgtagaggggCcgctgcgagggccccatata	17	10	0	2			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr22:38369604C>T	ENST00000396884.2	-	4	1581	c.1299G>A	c.(1297-1299)cgG>cgA	p.R433R	POLR2F_ENST00000405557.1_Intron|SOX10_ENST00000360880.2_Silent_p.R433R|POLR2F_ENST00000407936.1_Intron	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	433					anatomical structure morphogenesis (GO:0009653)|cell maturation (GO:0048469)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|enteric nervous system development (GO:0048484)|in utero embryonic development (GO:0001701)|melanocyte differentiation (GO:0030318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system development (GO:0007422)|positive regulation of gliogenesis (GO:0014015)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extrinsic component of mitochondrial outer membrane (GO:0031315)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|transcription coactivator activity (GO:0003713)			NS(6)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|skin(2)	20	Melanoma(58;0.045)					TGTAGAGGGGCCGCTGCGAGG	0.637																																					p.R433R	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)	Atlas-SNP	.											.	SOX10	48	.	0			c.G1299A						.						23	28	27					22																	38369604		2192	4290	6482	SO:0001819	synonymous_variant	6663	exon4			GAGGGGCCGCTGC		CCDS13964.1	22q13.1	2014-09-17			ENSG00000100146	ENSG00000100146		"SRY (sex determining region Y)-boxes"	11190	protein-coding gene	gene with protein product	"dominant megacolon, mouse, human homolog of"	602229				9462749, 10441344, 12944398	Standard	NM_006941		Approved	DOM, WS4, WS2E	uc003aun.1	P56693	OTTHUMG00000149913	ENST00000396884.2:c.1299G>A	chr22.hg19:g.38369604C>T		40.0	0.0		38.0	14.0	NM_006941	B4DV62|Q6FHW7	Silent	SNP	ENST00000396884.2	hg19	CCDS13964.1																																																																																			.	.		0.637	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941		T	38369604	C	T	38369604	2	4	133	1	0	0	0	0	0	0	0	1	14956	726	26	3		3	SOX10	22	38369604	Silent	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	156956	38369604	12934962	71	21577										
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50664565	50664566	+	Frame_Shift_Ins	INS	-	-	GTCCTCCACCTCTTTGGAGATGAGCACGTAGCCATGTGTCCAGTACGAC													0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ttcagaaacacgggaacacaINSgtcctccacctctttggaga					rs202112234		TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chr22:50664565_50664566insGTCCTCCACCTCTTTGGAGATGAGCACGTAGCCATGTGTCCAGTACGAC	ENST00000248846.5	-	9	1850_1851	c.1746_1747insGTCGTACTGGACACATGGCTACGTGCTCATCTCCAAAGAGGTGGAGGAC	c.(1744-1749)gactgtfs	p.C583fs	TUBGCP6_ENST00000439308.2_Frame_Shift_Ins_p.C583fs|TUBGCP6_ENST00000491449.1_De_novo_Start_OutOfFrame			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	583					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		ACGGGAACACAGTCCTCCACCT	0.559																																					p.C583fs		Pindel	.											.	TUBGCP6	132	.	0			c.1747_1748insGTCGTACTGGACACATGGCTACGTGCTCATCTCCAAAGAGGTGGAGGAC						.																																			SO:0001589	frameshift_variant	85378	exon9			.	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.1746_1747insGTCGTACTGGACACATGGCTACGTGCTCATCTCCAAAGAGGTGGAGGAC	chr22.hg19:g.50664565_50664566insGTCCTCCACCTCTTTGGAGATGAGCACGTAGCCATGTGTCCAGTACGAC	ENSP00000248846:p.Cys583fs	325.0	0.0		264.0	23.0	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Frame_Shift_Ins	INS	ENST00000248846.5	hg19	CCDS14087.1																																																																																			.	.		0.559	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		GTCCTCCACCTCTTTGGAGATGAGCACGTAGCCATGTGTCCAGTACGAC	50664566	-	GTCCTCCACCTCTTTGGAGATGAGCACGTAGCCATGTGTCCAGTACGAC	50664565	7	5	133	1	0	1	1	0	0	0	0	0	16785	188	7	0	3780	0	TUBGCP6	22	50664565	Frame_Shift_Ins	INS	-	TCGA-DD-A4NK-01A-11D-A28X-10	12294961	50664565	640001	72	21578										
GNL3L	54552	hgsc.bcm.edu	37	chrX	54566597	54566597	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	caaaatgggaagaaagcaacCtccaaagtgccctctgcacc	8	13	1	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chrX:54566597C>A	ENST00000336470.4	+	4	250	c.111C>A	c.(109-111)acC>acA	p.T37T	GNL3L_ENST00000360845.2_Silent_p.T37T|GNL3L_ENST00000489691.1_3'UTR	NM_019067.5	NP_061940.1	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)-like	37					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	30						AGAAAGCAACCTCCAAAGTGC	0.453																																					p.T37T		Atlas-SNP	.											.	GNL3L	73	.	0			c.C111A						.						110	96	101					X																	54566597		2203	4300	6503	SO:0001819	synonymous_variant	54552	exon4			AGCAACCTCCAAA	AK001475	CCDS14360.1	Xp11.22	2010-03-17			ENSG00000130119	ENSG00000130119			25553	protein-coding gene	gene with protein product		300873				12477932	Standard	NM_019067		Approved	FLJ10613	uc004dth.2	Q9NVN8	OTTHUMG00000021629	ENST00000336470.4:c.111C>A	chrX.hg19:g.54566597C>A		342.0	0.0		288.0	99.0	NM_001184819		Silent	SNP	ENST00000336470.4	hg19	CCDS14360.1																																																																																			.	.		0.453	GNL3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056805.1	NM_019067		A	54566597	C	A	54566597	2	1	133	1	0	0	0	0	0	0	0	1	6546	668	24	3		3	GNL3L	23	54566597	Silent	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10		54566597	100703963	73	21579										
ATRX	546	hgsc.bcm.edu	37	chrX	76938217	76938217	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cagaagagtcaaaatcttttGtatttggaattctttttttg	7	4	3	2	rs139131007	byFrequency	TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chrX:76938217G>A	ENST00000373344.5	-	9	2745	c.2531C>T	c.(2530-2532)aCa>aTa	p.T844I	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Missense_Mutation_p.T806I	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	844					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						AAAATCTTTTGTATTTGGAAT	0.348			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.T844I		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.C2531T						.						179	195	190					X																	76938217		2203	4294	6497	SO:0001583	missense	546	exon9			TCTTTTGTATTTG	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.2531C>T	chrX.hg19:g.76938217G>A	ENSP00000362441:p.Thr844Ile	12.0	0.0		14.0	5.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	hg19	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.350013	0.00219	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.92099	-2.96;-2.97	5.73	2.03	0.26663	.	0.119448	0.56097	D	0.000027	T	0.79528	0.4461	N	0.08118	0	0.22401	N	0.999134	B;B;B;B	0.31040	0.052;0.305;0.053;0.052	B;B;B;B	0.28232	0.028;0.087;0.039;0.028	T	0.70461	-0.4865	10	0.59425	D	0.04	-8.419	4.9467	0.13993	0.0:0.2218:0.2756:0.5025	.	844;776;806;844	A4LAA3;P46100-6;P46100-4;P46100	.;.;.;ATRX_HUMAN	I	844;806;771	ENSP00000362441:T844I;ENSP00000378967:T806I	ENSP00000362441:T844I	T	-	2	0	ATRX	76824873	0.859000	0.29813	0.216000	0.23742	0.031000	0.12232	0.246000	0.18160	0.003000	0.14656	-0.625000	0.03995	ACA	.	G|0.999;T|0.001		0.348	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		A	76938217	G	A	76938217	3	1	133	1	0	0	0	0	1	0	0	0	1208	1377	48	3	5055	3	ATRX	23	76938217	Missense_Mutation	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	22371620	76938217	78332343	74	21580										
MAMLD1	10046	hgsc.bcm.edu	37	chrX	149671633	149671633	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	ccgtcctgccaggccctgggGagtgagtccttcctgcccgg	14	16	0	1			TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chrX:149671633G>C	ENST00000370401.2	+	6	2440	c.2130G>C	c.(2128-2130)ggG>ggC	p.G710G	MAMLD1_ENST00000455522.2_Silent_p.G150G|MAMLD1_ENST00000262858.5_Silent_p.G710G|MAMLD1_ENST00000432680.2_Intron|MAMLD1_ENST00000426613.2_Silent_p.G685G			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	710					male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					AGGCCCTGGGGAGTGAGTCCT	0.652																																					p.G710G		Atlas-SNP	.											.	MAMLD1	263	.	0			c.G2130C						.						73	73	73					X																	149671633		2203	4299	6502	SO:0001819	synonymous_variant	10046	exon5			CCTGGGGAGTGAG	U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"chromosome X open reading frame 6"	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.2130G>C	chrX.hg19:g.149671633G>C		412.0	0.0		355.0	130.0	NM_005491	B2RCQ4|B4DG93|B9EGA5	Silent	SNP	ENST00000370401.2	hg19	CCDS14693.2																																																																																			.	.		0.652	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491		C	149671633	G	C	149671633	2	2	133	1	0	0	0	0	0	0	0	1	9217	1161	41	4		4	MAMLD1	23	149671633	Silent	SNP	G	TCGA-DD-A4NK-01A-11D-A28X-10	72733416	149671633	5598927	75	21581										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153135689	153135689	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	4	1	0.812378031781433	1.72630331753555	0.690521327014218	0.559440559440559	1	0	cgcagccatttgatggtgggCgtgggactgcccgggaggca	18	10	0	1	rs201381558		TCGA-DD-A4NK-01A-11D-A28X-10	TCGA-DD-A4NK-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85d5f17f-7a02-4e34-aeb5-0a41708f9af4	fecea418-1023-458d-aac6-ce383901f30a	g.chrX:153135689C>A	ENST00000370060.1	-	9	1002	c.813G>T	c.(811-813)acG>acT	p.T271T	L1CAM_ENST00000370055.1_Silent_p.T266T|L1CAM_ENST00000361699.4_Silent_p.T271T|L1CAM_ENST00000538883.1_Silent_p.T273T|L1CAM_ENST00000543994.1_Silent_p.T273T|L1CAM_ENST00000370057.3_Silent_p.T271T|L1CAM_ENST00000361981.3_Silent_p.T266T	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	271	Ig-like C2-type 3.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGATGGTGGGCGTGGGACTGC	0.637																																					p.T271T		Atlas-SNP	.											.	L1CAM	189	.	0			c.G813T						.						112	112	112					X																	153135689		2203	4300	6503	SO:0001819	synonymous_variant	3897	exon8			GGTGGGCGTGGGA	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.813G>T	chrX.hg19:g.153135689C>A		133.0	0.0		105.0	29.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Silent	SNP	ENST00000370060.1	hg19	CCDS14733.1																																																																																			.	.		0.637	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		A	153135689	C	A	153135689	2	1	133	1	0	0	0	0	0	0	0	1	8597	755	27	1		1	L1CAM	23	153135689	Silent	SNP	C	TCGA-DD-A4NK-01A-11D-A28X-10	3464056	153135689	2134871	76	21582										
NKAIN1	79570	hgsc.bcm.edu	37	chr1	31654558	31654558	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcggggcagaggctaccccgAcctgcgggaaacaaaggcag	16	12	0	1			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr1:31654558A>T	ENST00000373736.2	-	7	622	c.616T>A	c.(616-618)Tcg>Acg	p.S206T	NKAIN1_ENST00000398657.2_Splice_Site_p.S135T|NKAIN1_ENST00000263693.1_Splice_Site_p.S162T|NKAIN1_ENST00000528449.1_5'Flank	NM_024522.2	NP_078798.2	Q4KMZ8	NKAI1_HUMAN	Na+/K+ transporting ATPase interacting 1	206						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|ovary(1)|prostate(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|Breast(348;0.141)|all_neural(195;0.146)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0184)|READ - Rectum adenocarcinoma(331;0.148)		GGCTACCCCGACCTGCGGGAA	0.701																																					p.S206T		Atlas-SNP	.											.	NKAIN1	21	.	0			c.T616A						.						17	23	21					1																	31654558		2016	3954	5970	SO:0001630	splice_region_variant	79570	exon7			ACCCCGACCTGCG	AK022712	CCDS339.1, CCDS339.2	1p35.2	2010-06-25	2007-10-04	2007-10-04	ENSG00000084628	ENSG00000084628		"Na+/K+ transporting ATPase interacting"	25743	protein-coding gene	gene with protein product		612871	"family with sequence similarity 77, member C"	FAM77C		17606467	Standard	NM_024522		Approved	FLJ12650	uc010ogd.2	Q4KMZ8	OTTHUMG00000003788	ENST00000373736.2:c.615-1T>A	chr1.hg19:g.31654558A>T		274.0	0.0		291.0	82.0	NM_024522	A2VDJ3|B7Z5F5|B7Z5W9|Q9H9M7	Missense_Mutation	SNP	ENST00000373736.2	hg19	CCDS339.2	.	.	.	.	.	.	.	.	.	.	A	10.65	1.408859	0.25378	.	.	ENSG00000084628	ENST00000373736;ENST00000263693;ENST00000398657	T;T;T	0.15952	2.38;2.38;2.38	4.29	3.14	0.36123	.	0.277557	0.29995	N	0.010670	T	0.05777	0.0151	N	0.02011	-0.69	0.39686	D	0.970977	B;B	0.15473	0.013;0.0	B;B	0.22880	0.042;0.003	T	0.29181	-1.0020	10	0.14252	T	0.57	-27.1254	8.0726	0.30697	0.7949:0.2051:0.0:0.0	.	206;135	Q4KMZ8;B7Z5F5	NKAI1_HUMAN;.	T	206;162;135	ENSP00000362841:S206T;ENSP00000263693:S162T;ENSP00000381650:S135T	ENSP00000263693:S162T	S	-	1	0	NKAIN1	31427145	1.000000	0.71417	0.997000	0.53966	0.237000	0.25408	1.852000	0.39348	0.774000	0.33427	0.459000	0.35465	TCG	.	.		0.701	NKAIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010655.2	NM_024522	Missense_Mutation	T	31654558	A	T	31654558	5	4	134	1	0	0	0	0	0	0	1	0	10444	289	10	4	11	4	NKAIN1	1	31654558	Splice_Site	SNP	A	TCGA-DD-A4NL-01A-11D-A28X-10		31654558	217596063	1	21583										
ABCA4	24	hgsc.bcm.edu	37	chr1	94476865	94476865	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctggctcagtgcaaggtcaAtgaggccccggcccaggcag	14	14	2	1	rs61750575		TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr1:94476865A>G	ENST00000370225.3	-	39	5623	c.5537T>C	c.(5536-5538)aTt>aCt	p.I1846T	ABCA4_ENST00000535881.1_5'UTR|ABCA4_ENST00000536513.1_Missense_Mutation_p.I116T|ABCA4_ENST00000465352.1_5'Flank	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1846			I -> T. {ECO:0000269|PubMed:11527935}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TGCAAGGTCAATGAGGCCCCG	0.597																																					p.I1846T		Atlas-SNP	.											.	ABCA4	275	.	0			c.T5537C	GRCh37	CM990067	ABCA4	M	rs61750575	.						77	77	77					1																	94476865		2203	4300	6503	SO:0001583	missense	24	exon39			AGGTCAATGAGGC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.5537T>C	chr1.hg19:g.94476865A>G	ENSP00000359245:p.Ile1846Thr	377.0	0.0		317.0	17.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	A	18.27	3.586442	0.66105	.	.	ENSG00000198691	ENST00000546054;ENST00000370225;ENST00000536513	D;D	0.87256	-2.23;-2.23	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	D	0.91195	0.7226	M	0.78637	2.42	0.80722	D	1	P;D	0.69078	0.566;0.997	B;D	0.65140	0.403;0.932	D	0.92581	0.6074	10	0.87932	D	0	.	14.5621	0.68148	1.0:0.0:0.0:0.0	rs61750575	116;1846	B4DWY6;P78363	.;ABCA4_HUMAN	T	638;1846;116	ENSP00000359245:I1846T;ENSP00000439707:I116T	ENSP00000359245:I1846T	I	-	2	0	ABCA4	94249453	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.099000	0.94207	2.074000	0.62210	0.477000	0.44152	ATT	.	.		0.597	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		G	94476865	A	G	94476865	3	3	134	1	0	0	0	0	1	0	0	0	34	101	4	2	1332	2	ABCA4	1	94476865	Missense_Mutation	SNP	A	TCGA-DD-A4NL-01A-11D-A28X-10	62822307	94476865	154773756	2	21584										
AMY2B	280	hgsc.bcm.edu	37	chr1	104120169	104120169	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gagtaattaaagaagttactAttaatccagacactacttgt	6	6	0	2			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr1:104120169A>G	ENST00000361355.4	+	10	1775	c.1159A>G	c.(1159-1161)Att>Gtt	p.I387V	AMY2B_ENST00000491397.1_Intron	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	387					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)	p.I387F(1)		breast(1)|endometrium(7)|kidney(4)|large_intestine(1)|lung(30)|prostate(1)|skin(1)|urinary_tract(1)	46		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		AGAAGTTACTATTAATCCAGA	0.353																																					p.I387V		Atlas-SNP	.											AMY2B,NS,carcinoma,0,1	AMY2B	80	.	1	Substitution - Missense(1)	lung(1)	c.A1159G						.						95	99	98					1																	104120169		2202	4297	6499	SO:0001583	missense	280	exon10			GTTACTATTAATC	M24895	CCDS782.1	1p21	2010-08-02	2006-04-27		ENSG00000240038	ENSG00000240038	3.2.1.1		478	protein-coding gene	gene with protein product		104660	"amylase, alpha 2B; pancreatic"	AMY2		8268204	Standard	NM_020978		Approved		uc001duq.3	P19961	OTTHUMG00000011024	ENST00000361355.4:c.1159A>G	chr1.hg19:g.104120169A>G	ENSP00000354610:p.Ile387Val	515.0	2.0		387.0	137.0	NM_020978	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	hg19	CCDS782.1	.	.	.	.	.	.	.	.	.	.	A	15.68	2.905330	0.52333	.	.	ENSG00000240038	ENST00000361355	.	.	.	4.82	4.82	0.62117	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.47488	0.1448	M	0.63843	1.955	0.80722	D	1	B	0.09022	0.002	B	0.10450	0.005	T	0.55192	-0.8179	9	0.59425	D	0.04	.	14.3577	0.66748	1.0:0.0:0.0:0.0	.	387	P19961	AMY2B_HUMAN	V	387	.	ENSP00000354610:I387V	I	+	1	0	AMY2B	103921692	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.274000	0.78538	1.789000	0.52484	0.372000	0.22366	ATT	.	.		0.353	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1	NM_020978		G	104120169	A	G	104120169	3	3	134	1	0	0	0	0	1	0	0	0	595	449	16	2	1189	2	AMY2B	1	104120169	Missense_Mutation	SNP	A	TCGA-DD-A4NL-01A-11D-A28X-10	9643304	104120169	145130452	3	21585										
SCAMP3	10067	hgsc.bcm.edu	37	chr1	155226183	155226183	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgggccttctgaaagctggCacctgtgcggcggtataagg	15	10	1	1			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr1:155226183C>G	ENST00000302631.3	-	9	1032	c.925G>C	c.(925-927)Gcc>Ccc	p.A309P	FAM189B_ENST00000361361.2_5'Flank|FAM189B_ENST00000472550.1_5'Flank|FAM189B_ENST00000368368.3_5'Flank|SCAMP3_ENST00000355379.3_Missense_Mutation_p.A283P|FAM189B_ENST00000350210.2_5'Flank|SCAMP3_ENST00000472397.1_5'UTR	NM_005698.3	NP_005689.2	O14828	SCAM3_HUMAN	secretory carrier membrane protein 3	309					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|response to retinoic acid (GO:0032526)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|large_intestine(3)|lung(7)|ovary(4)|urinary_tract(1)	19	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGAAAGCTGGCACCTGTGCGG	0.572																																					p.A309P		Atlas-SNP	.											.	SCAMP3	33	.	0			c.G925C						.						97	108	104					1																	155226183		2203	4300	6503	SO:0001583	missense	10067	exon9			AGCTGGCACCTGT	AF005039	CCDS1105.1, CCDS1106.1	1q21	2013-02-21			ENSG00000116521	ENSG00000116521		"Secretory carrier membrane proteins"	10565	protein-coding gene	gene with protein product	"Propin 1"	606913		C1orf3		9331372, 9658162	Standard	NM_005698		Approved		uc001fjs.3	O14828	OTTHUMG00000035874	ENST00000302631.3:c.925G>C	chr1.hg19:g.155226183C>G	ENSP00000307275:p.Ala309Pro	84.0	0.0		80.0	20.0	NM_005698	A9Z1W6|B1AVS6|O15128|Q96FR8|Q9BPY0	Missense_Mutation	SNP	ENST00000302631.3	hg19	CCDS1105.1	.	.	.	.	.	.	.	.	.	.	C	35	5.570658	0.96540	.	.	ENSG00000116521	ENST00000302631;ENST00000355379	T;T	0.20881	2.32;2.04	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.41650	0.1168	M	0.81341	2.54	0.80722	D	1	D;D;D	0.64830	0.99;0.994;0.994	D;D;P	0.66602	0.945;0.93;0.821	T	0.31724	-0.9933	10	0.87932	D	0	-12.5227	16.9918	0.86356	0.0:1.0:0.0:0.0	.	309;283;309	Q6FHJ5;O14828-2;O14828	.;.;SCAM3_HUMAN	P	309;283	ENSP00000307275:A309P;ENSP00000347540:A283P	ENSP00000307275:A309P	A	-	1	0	SCAMP3	153492807	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.629000	0.83207	2.880000	0.98712	0.655000	0.94253	GCC	.	.		0.572	SCAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087399.1	NM_005698		G	155226183	C	G	155226183	3	3	134	1	0	0	0	0	1	0	0	0	13887	710	25	4	122	4	SCAMP3	1	155226183	Missense_Mutation	SNP	C	TCGA-DD-A4NL-01A-11D-A28X-10	51106014	155226183	94024438	4	21586										
RYR2	6262	hgsc.bcm.edu	37	chr1	237947912	237947912	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctcttgcacttcgtggccagCgttttcagaggctttttccg	10	12	2	1			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr1:237947912C>T	ENST00000366574.2	+	90	13217	c.12900C>T	c.(12898-12900)agC>agT	p.S4300S	RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Silent_p.S4306S|RYR2_ENST00000542537.1_Silent_p.S4284S	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4300					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TCGTGGCCAGCGTTTTCAGAG	0.463																																					p.S4300S		Atlas-SNP	.											RYR2,NS,carcinoma,0,1	RYR2	1273	.	0			c.C12900T						.						73	72	73					1																	237947912		1913	4121	6034	SO:0001819	synonymous_variant	6262	exon90			GGCCAGCGTTTTC	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.12900C>T	chr1.hg19:g.237947912C>T		89.0	0.0		63.0	16.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.463	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237947912	C	T	237947912	2	4	134	1	0	0	0	0	0	0	0	1	13784	767	27	1		1	RYR2	1	237947912	Silent	SNP	C	TCGA-DD-A4NL-01A-11D-A28X-10	82721729	237947912	11302709	5	21587										
IL1R1	3554	hgsc.bcm.edu	37	chr2	102792895	102792895	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agagaaacatcaggcttcagCtggctgggtggttcatctga	13	8	4	2			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr2:102792895C>G	ENST00000410023.1	+	12	1704	c.1386C>G	c.(1384-1386)agC>agG	p.S462R	IL1R1_ENST00000409589.1_Intron|IL1R1_ENST00000409929.1_Missense_Mutation_p.S431R|IL1R1_ENST00000233946.3_Missense_Mutation_p.S462R|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000424272.1_3'UTR			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	462	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	CAGGCTTCAGCTGGCTGGGTG	0.398																																					p.S462R		Atlas-SNP	.											.	IL1R1	52	.	0			c.C1386G						.						64	63	63					2																	102792895		2203	4300	6503	SO:0001583	missense	3554	exon11			CTTCAGCTGGCTG	M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.1386C>G	chr2.hg19:g.102792895C>G	ENSP00000386380:p.Ser462Arg	123.0	0.0		97.0	28.0	NM_000877	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	hg19	CCDS2055.1	.	.	.	.	.	.	.	.	.	.	C	2.225	-0.377546	0.05000	.	.	ENSG00000115594	ENST00000409929;ENST00000410023;ENST00000233946	T;T;T	0.08193	3.12;3.12;3.12	5.61	1.51	0.23008	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.858674	0.11190	N	0.589973	T	0.04407	0.0121	N	0.14661	0.345	0.09310	N	1	B;B	0.17038	0.02;0.009	B;B	0.23716	0.048;0.02	T	0.47235	-0.9133	10	0.16896	T	0.51	.	4.4235	0.11492	0.1098:0.5981:0.1069:0.1852	.	431;462	B8ZZW4;P14778	.;IL1R1_HUMAN	R	431;462;462	ENSP00000386776:S431R;ENSP00000386380:S462R;ENSP00000233946:S462R	ENSP00000233946:S462R	S	+	3	2	IL1R1	102159327	0.000000	0.05858	0.007000	0.13788	0.086000	0.17979	0.157000	0.16402	0.730000	0.32425	-0.244000	0.11960	AGC	.	.		0.398	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1			G	102792895	C	G	102792895	3	3	134	1	0	0	0	0	1	0	0	0	7667	796	28	4	1424	4	IL1R1	2	102792895	Missense_Mutation	SNP	C	TCGA-DD-A4NL-01A-11D-A28X-10		102792895	140406478	6	21588										
KIF1A	547	hgsc.bcm.edu	37	chr2	241697828	241697828	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	catagaaggggtctccgccgGtcaccacgttgtcacagtcc	11	14	3	1			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr2:241697828G>T	ENST00000320389.7	-	25	2662	c.2504C>A	c.(2503-2505)aCc>aAc	p.T835N	KIF1A_ENST00000498729.2_Missense_Mutation_p.T844N	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	835					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		GTCTCCGCCGGTCACCACGTT	0.637																																					p.T844N		Atlas-SNP	.											.	KIF1A	152	.	0			c.C2531A						.						61	71	68					2																	241697828		2162	4260	6422	SO:0001583	missense	547	exon26			CCGCCGGTCACCA	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"Kinesins", "Pleckstrin homology (PH) domain containing"	888	protein-coding gene	gene with protein product		601255	"axonal transport of synaptic vesicles", "chromosome 2 open reading frame 20", "spastic paraplegia 30 (autosomal recessive)"	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.2504C>A	chr2.hg19:g.241697828G>T	ENSP00000322791:p.Thr835Asn	262.0	0.0		206.0	15.0	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	hg19	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.064681	0.76187	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	T;T;T	0.76060	-0.99;-0.99;-0.99	5.28	5.28	0.74379	.	0.059531	0.64402	U	0.000003	T	0.75613	0.3873	L	0.59436	1.845	0.80722	D	1	B;P;B	0.48764	0.182;0.915;0.07	B;P;B	0.45232	0.127;0.474;0.056	T	0.77281	-0.2646	10	0.45353	T	0.12	.	18.4813	0.90812	0.0:0.0:1.0:0.0	.	844;844;835	F5H045;Q12756-2;Q12756	.;.;KIF1A_HUMAN	N	835;844;844;844	ENSP00000322791:T835N;ENSP00000438388:T844N;ENSP00000384231:T844N	ENSP00000322791:T835N	T	-	2	0	KIF1A	241346501	1.000000	0.71417	0.995000	0.50966	0.963000	0.63663	9.545000	0.98095	2.473000	0.83533	0.591000	0.81541	ACC	.	.		0.637	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		T	241697828	G	T	241697828	3	4	134	1	0	0	0	0	1	0	0	0	8292	1261	44	3	2660	3	KIF1A	2	241697828	Missense_Mutation	SNP	G	TCGA-DD-A4NL-01A-11D-A28X-10	138904933	241697828	1501545	7	21589										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41268766	41268766	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaggacctatacttacgaaaAactactgtggaccacaagca	8	10	0	0			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr3:41268766A>T	ENST00000349496.5	+	7	1284	c.1004A>T	c.(1003-1005)aAa>aTa	p.K335I	CTNNB1_ENST00000396185.3_Missense_Mutation_p.K335I|CTNNB1_ENST00000405570.1_Missense_Mutation_p.K335I|CTNNB1_ENST00000396183.3_Missense_Mutation_p.K335I|CTNNB1_ENST00000453024.1_Missense_Mutation_p.K328I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	335					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.K335I(8)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACTTACGAAAAACTACTGTGG	0.383		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.K335I	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,colon,carcinoma,-1,11	CTNNB1	4904	.	8	Substitution - Missense(8)	liver(7)|kidney(1)	c.A1004T						.						110	108	109					3																	41268766		2203	4300	6503	SO:0001583	missense	1499	exon7	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACGAAAAACTACT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1004A>T	chr3.hg19:g.41268766A>T	ENSP00000344456:p.Lys335Ile	81.0	0.0		66.0	19.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.040885	0.93685	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.82148	0.4974	M	0.89287	3.02	0.80722	D	1	D;D	0.71674	0.995;0.998	D;D	0.75484	0.97;0.986	D	0.85830	0.1391	10	0.72032	D	0.01	-3.7939	15.5934	0.76558	1.0:0.0:0.0:0.0	.	263;335	B4DSW9;P35222	.;CTNB1_HUMAN	I	335;335;335;328;335	ENSP00000385604:K335I;ENSP00000379486:K335I;ENSP00000344456:K335I;ENSP00000411226:K328I;ENSP00000379488:K335I	ENSP00000344456:K335I	K	+	2	0	CTNNB1	41243770	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	9.339000	0.96797	2.094000	0.63399	0.482000	0.46254	AAA	.	.		0.383	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41268766	A	T	41268766	3	4	134	1	0	0	0	0	1	0	0	0	4018	14	1	4	1026	4	CTNNB1	3	41268766	Missense_Mutation	SNP	A	TCGA-DD-A4NL-01A-11D-A28X-10		41268766	156753664	8	21590										
CHST2	9435	hgsc.bcm.edu	37	chr3	142840928	142840928	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agggccactacctggtggtgCggtacgaggacctggtggga	18	9	0	0	rs539420111		TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr3:142840928C>T	ENST00000309575.3	+	2	2654	c.1270C>T	c.(1270-1272)Cgg>Tgg	p.R424W		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	424					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)	p.R424R(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						CCTGGTGGTGCGGTACGAGGA	0.592																																					p.R424W		Atlas-SNP	.											CHST2,NS,carcinoma,0,1	CHST2	67	.	1	Substitution - coding silent(1)	breast(1)	c.C1270T						.						56	56	56					3																	142840928		2203	4300	6503	SO:0001583	missense	9435	exon2			GTGGTGCGGTACG	BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"Sulfotransferases, membrane-bound"	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.1270C>T	chr3.hg19:g.142840928C>T	ENSP00000307911:p.Arg424Trp	143.0	1.0		148.0	10.0	NM_004267	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	hg19	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	C	17.30	3.354834	0.61293	.	.	ENSG00000175040	ENST00000309575	D	0.84070	-1.8	4.33	3.42	0.39159	Sulfotransferase domain (1);	0.000000	0.64402	D	0.000001	D	0.91841	0.7418	M	0.91459	3.21	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92401	0.5929	10	0.87932	D	0	-15.3322	11.2518	0.49031	0.3442:0.6558:0.0:0.0	.	424	Q9Y4C5	CHST2_HUMAN	W	424	ENSP00000307911:R424W	ENSP00000307911:R424W	R	+	1	2	CHST2	144323618	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.686000	0.61700	0.964000	0.38108	0.407000	0.27541	CGG	.	.		0.592	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		T	142840928	C	T	142840928	3	4	134	1	0	0	0	0	1	0	0	0	3406	759	27	1	1272	1	CHST2	3	142840928	Missense_Mutation	SNP	C	TCGA-DD-A4NL-01A-11D-A28X-10	101572162	142840928	55181502	9	21591										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6083468	6083468	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttcagctgaacctcggtctcTcgtgagcgtttcagctgtgg	12	11	3	2			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr4:6083468T>C	ENST00000282924.5	-	6	1454	c.969A>G	c.(967-969)cgA>cgG	p.R323R	JAKMIP1_ENST00000409371.3_Silent_p.R158R|JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000410077.2_Silent_p.R158R|JAKMIP1_ENST00000409831.1_Silent_p.R323R|JAKMIP1_ENST00000409021.3_Silent_p.R323R	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	323	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCTCGGTCTCTCGTGAGCGTT	0.537																																					p.R323R		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.A969G						.						96	94	95					4																	6083468		2203	4300	6503	SO:0001819	synonymous_variant	152789	exon6			GGTCTCTCGTGAG	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.969A>G	chr4.hg19:g.6083468T>C		94.0	0.0		68.0	5.0	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Silent	SNP	ENST00000282924.5	hg19	CCDS3385.1																																																																																			.	.		0.537	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		C	6083468	T	C	6083468	2	2	134	1	0	0	0	0	0	0	0	1	7949	1538	54	2		2	JAKMIP1	4	6083468	Silent	SNP	T	TCGA-DD-A4NL-01A-11D-A28X-10		6083468	185070808	10	21592										
KCTD8	386617	hgsc.bcm.edu	37	chr4	44176930	44176930	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atttcttcttccacacttagCttctcacagactttcttttt	2	12	4	1			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr4:44176930C>T	ENST00000360029.3	-	2	1582	c.1299G>A	c.(1297-1299)aaG>aaA	p.K433K		NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	433					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						CCACACTTAGCTTCTCACAGA	0.418										HNSCC(17;0.042)																											p.K433K		Atlas-SNP	.											.	KCTD8	96	.	0			c.G1299A						.						188	197	194					4																	44176930		2203	4300	6503	SO:0001819	synonymous_variant	386617	exon2			ACTTAGCTTCTCA	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.1299G>A	chr4.hg19:g.44176930C>T		57.0	0.0		53.0	6.0	NM_198353	A2RU39	Silent	SNP	ENST00000360029.3	hg19	CCDS3467.1																																																																																			.	.		0.418	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			T	44176930	C	T	44176930	2	4	134	1	0	0	0	0	0	0	0	1	8124	796	28	3		3	KCTD8	4	44176930	Silent	SNP	C	TCGA-DD-A4NL-01A-11D-A28X-10	38093462	44176930	146977346	11	21593										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32074424	32074424	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggcccccaaggggagccctgGaagctggtggaagaaggaac	17	10	0	1			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr5:32074424G>T	ENST00000438447.1	+	18	3600	c.3212G>T	c.(3211-3213)gGa>gTa	p.G1071V	PDZD2_ENST00000282493.3_Missense_Mutation_p.G1071V			O15018	PDZD2_HUMAN	PDZ domain containing 2	1071					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GGGAGCCCTGGAAGCTGGTGG	0.577																																					p.G1071V		Atlas-SNP	.											.	PDZD2	306	.	0			c.G3212T						.						112	130	124					5																	32074424		2203	4300	6503	SO:0001583	missense	23037	exon17			GCCCTGGAAGCTG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3212G>T	chr5.hg19:g.32074424G>T	ENSP00000402033:p.Gly1071Val	66.0	0.0		55.0	14.0	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.852549	0.51270	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.06687	3.27;3.27	5.67	2.79	0.32731	.	0.433620	0.19808	N	0.105600	T	0.09423	0.0232	L	0.57536	1.79	0.20196	N	0.99993	P;B	0.42785	0.79;0.451	B;B	0.36719	0.231;0.086	T	0.10870	-1.0611	10	0.62326	D	0.03	.	10.6122	0.45429	0.0:0.2679:0.5935:0.1386	.	897;1071	B4E3P2;O15018	.;PDZD2_HUMAN	V	1071;873;1071	ENSP00000402033:G1071V;ENSP00000282493:G1071V	ENSP00000282493:G1071V	G	+	2	0	PDZD2	32110181	0.042000	0.20092	0.001000	0.08648	0.007000	0.05969	2.314000	0.43743	0.273000	0.22049	0.563000	0.77884	GGA	.	.		0.577	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32074424	G	T	32074424	3	4	134	1	0	0	0	0	1	0	0	0	11710	1174	41	3	3278	3	PDZD2	5	32074424	Missense_Mutation	SNP	G	TCGA-DD-A4NL-01A-11D-A28X-10		32074424	148840836	12	21594										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55260056	55260067	+	In_Frame_Del	DEL	GACAAAATACAC	GACAAAATACAC	-													0	0	1	0	0	0	1	1	0	tctacccagacttcaatgttGacaaaatacacagtagaata							TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	GACAAAATACAC	GACAAAATACAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr5:55260056_55260067delGACAAAATACAC	ENST00000381298.2	-	6	877_888	c.565_576delGTGTATTTTGTC	c.(565-576)gtgtattttgtcdel	p.VYFV189del	IL6ST_ENST00000522633.2_In_Frame_Del_p.VYFV189del|IL6ST_ENST00000577363.1_5'UTR|IL6ST_ENST00000336909.5_In_Frame_Del_p.VYFV189del|IL6ST_ENST00000381287.4_In_Frame_Del_p.VYFV189del|IL6ST_ENST00000381294.3_In_Frame_Del_p.VYFV189del|IL6ST_ENST00000502326.3_In_Frame_Del_p.VYFV189del|IL6ST_ENST00000536319.1_In_Frame_Del_p.VYFV189del|IL6ST_ENST00000396816.1_In_Frame_Del_p.CILS47del|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000381293.2_Intron	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	189	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)	p.Y186_Y190delYSTVY(1)		breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				CTTCAATGTTGACAAAATACACAGTAGAATAA	0.373			O		hepatocellular ca																																p.189_193del		Atlas-Indel,Pindel	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	1	Deletion - In frame(1)	liver(1)	c.566_577del						.																																			SO:0001651	inframe_deletion	3572	exon6			.	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.565_576delGTGTATTTTGTC	chr5.hg19:g.55260056_55260067delGACAAAATACAC	ENSP00000370698:p.Val189_Val192del	210.0	0.0		119.0	13.0	NM_001190981	A0N0L4|Q5FC04|Q9UQ41	In_Frame_Del	DEL	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.		0.373	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		-	55260067	GACAAAATACAC	-	55260056	7	5	134	1	0	1	0	1	0	0	0	0	7712	1277	45	0	2228	0	IL6ST	5	55260056	In_Frame_Del	DEL	GACAAAATACAC	TCGA-DD-A4NL-01A-11D-A28X-10	23185632	55260056	125655204	13	21595										
HSD17B3	3293	hgsc.bcm.edu	37	chr9	99007649	99007649	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tggaagctgagtacatggagTagagaggccaaggaaacagg	16	5	0	2			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr9:99007649T>C	ENST00000375263.3	-	8	631	c.584A>G	c.(583-585)tAc>tGc	p.Y195C	RP11-240L7.4_ENST00000448857.1_RNA|HSD17B3_ENST00000375262.2_Missense_Mutation_p.Y195C|HSD17B3_ENST00000464104.1_5'UTR	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	195					androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				GTACATGGAGTAGAGAGGCCA	0.463																																					p.Y195C		Atlas-SNP	.											.	HSD17B3	32	.	0			c.A584G						.						151	139	143					9																	99007649		2203	4300	6503	SO:0001583	missense	3293	exon8			ATGGAGTAGAGAG		CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5212	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 12C, member 2"	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.584A>G	chr9.hg19:g.99007649T>C	ENSP00000364412:p.Tyr195Cys	139.0	0.0		102.0	6.0	NM_000197	Q5U0Q6	Missense_Mutation	SNP	ENST00000375263.3	hg19	CCDS6716.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.640933	0.47153	.	.	ENSG00000130948	ENST00000375263;ENST00000375262	D;D	0.87571	-2.27;-2.27	5.01	3.84	0.44239	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.057949	0.64402	D	0.000001	D	0.87010	0.6071	N	0.24115	0.695	0.21473	N	0.999671	P;D	0.71674	0.946;0.998	P;D	0.68192	0.886;0.956	T	0.79050	-0.1962	10	0.66056	D	0.02	-14.3891	10.4102	0.44289	0.1467:0.0:0.0:0.8533	.	195;195	Q5U0Q6;P37058	.;DHB3_HUMAN	C	195	ENSP00000364412:Y195C;ENSP00000364411:Y195C	ENSP00000364411:Y195C	Y	-	2	0	HSD17B3	98047470	0.807000	0.29009	0.007000	0.13788	0.937000	0.57800	1.906000	0.39887	1.009000	0.39289	0.533000	0.62120	TAC	.	.		0.463	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197		C	99007649	T	C	99007649	3	2	134	1	0	0	0	0	1	0	0	0	7394	1638	57	2	364	2	HSD17B3	9	99007649	Missense_Mutation	SNP	T	TCGA-DD-A4NL-01A-11D-A28X-10		99007649	42205782	14	21596										
ZNF462	58499	hgsc.bcm.edu	37	chr9	109687663	109687663	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaacttggggctcacaaacaGtgtcacacgggtacaacgtc	10	11	2	0			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr9:109687663G>T	ENST00000277225.5	+	3	1759	c.1470G>T	c.(1468-1470)caG>caT	p.Q490H	ZNF462_ENST00000457913.1_Missense_Mutation_p.Q490H|ZNF462_ENST00000441147.2_5'Flank			Q96JM2	ZN462_HUMAN	zinc finger protein 462	490					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						CTCACAAACAGTGTCACACGG	0.443																																					p.Q490H		Atlas-SNP	.											.	ZNF462	322	.	0			c.G1470T						.						105	94	98					9																	109687663		2203	4300	6503	SO:0001583	missense	58499	exon3			CAAACAGTGTCAC	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.1470G>T	chr9.hg19:g.109687663G>T	ENSP00000277225:p.Gln490His	236.0	0.0		148.0	47.0	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	hg19	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.302067	0.40694	.	.	ENSG00000148143	ENST00000277225;ENST00000457913	T;T	0.06371	3.31;3.76	5.69	5.69	0.88448	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.17831	0.0428	L	0.47716	1.5	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.81914	0.995;0.99	T	0.00229	-1.1898	9	.	.	.	.	13.3323	0.60495	0.0752:0.0:0.9248:0.0	.	490;490	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	H	490	ENSP00000277225:Q490H;ENSP00000414570:Q490H	.	Q	+	3	2	ZNF462	108727484	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.764000	0.47613	2.681000	0.91329	0.561000	0.74099	CAG	.	.		0.443	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		T	109687663	G	T	109687663	3	4	134	1	0	0	0	0	1	0	0	0	17941	1020	36	3	1476	3	ZNF462	9	109687663	Missense_Mutation	SNP	G	TCGA-DD-A4NL-01A-11D-A28X-10	10680014	109687663	31525768	15	21597										
KLRK1	22914	hgsc.bcm.edu	37	chr12	10541390	10541390	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cccagctgtgtcgagacctcCgaccacgaatccaccccatc	7	19	0	1			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr12:10541390C>T	ENST00000240618.6	-	2	160	c.20G>A	c.(19-21)cGg>cAg	p.R7Q	KLRK1_ENST00000540818.1_Missense_Mutation_p.R7Q|KLRC4-KLRK1_ENST00000539300.1_3'UTR|RP11-277P12.20_ENST00000500682.1_RNA	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	7					cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						TCGAGACCTCCGACCACGAAT	0.373																																					p.R7Q		Atlas-SNP	.											.	.	.	.	0			c.G20A						.						103	94	97					12																	10541390		2203	4300	6503	SO:0001583	missense	0	exon7			GACCTCCGACCAC	AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"Killer cell lectin-like receptors", "CD molecules"	18788	protein-coding gene	gene with protein product		611817	"DNA segment on chromosome 12 (unique) 2489 expressed sequence"	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.20G>A	chr12.hg19:g.10541390C>T	ENSP00000240618:p.Arg7Gln	67.0	0.0		41.0	10.0	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Missense_Mutation	SNP	ENST00000240618.6	hg19	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.761786	0.49468	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	T;T	0.01933	4.55;4.55	3.62	0.78	0.18556	.	0.444127	0.16886	N	0.195506	T	0.03263	0.0095	L	0.46157	1.445	0.09310	N	1	P;D	0.69078	0.454;0.997	B;P	0.50825	0.049;0.651	T	0.44329	-0.9335	10	0.33940	T	0.23	.	4.028	0.09697	0.0:0.5853:0.1952:0.2194	.	7;7	Q8WZ67;P26718	.;NKG2D_HUMAN	Q	7	ENSP00000240618:R7Q;ENSP00000446003:R7Q	ENSP00000240618:R7Q	R	-	2	0	KLRK1	10432657	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.393000	0.07305	0.164000	0.19529	-0.837000	0.03062	CGG	.	.		0.373	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		T	10541390	C	T	10541390	3	4	134	1	0	0	0	0	1	0	0	0	8432	652	23	1	658	1	KLRK1	12	10541390	Missense_Mutation	SNP	C	TCGA-DD-A4NL-01A-11D-A28X-10		10541390	123310505	16	21598										
TAS2R20	259295	hgsc.bcm.edu	37	chr12	11150077	11150077	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaaagaacaaagaccccaacActatcaccagaactacactc	3	14	1	3			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr12:11150077A>G	ENST00000538986.1	-	1	397	c.398T>C	c.(397-399)gTg>gCg	p.V133A	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	133					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						AGACCCCAACACTATCACCAG	0.373																																					p.V133A		Atlas-SNP	.											.	TAS2R20	17	.	0			c.T398C						.						118	108	111					12																	11150077		2203	4300	6503	SO:0001583	missense	259295	exon1			CCCAACACTATCA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19109	protein-coding gene	gene with protein product		613962	"taste receptor, type 2, member 49"	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.398T>C	chr12.hg19:g.11150077A>G	ENSP00000441624:p.Val133Ala	96.0	0.0		49.0	9.0	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	hg19	CCDS8639.1	.	.	.	.	.	.	.	.	.	.	A	9.802	1.180714	0.21787	.	.	ENSG00000255837	ENST00000538986	T	0.37411	1.2	2.93	2.93	0.34026	.	0.830641	0.09582	U	0.782738	T	0.25531	0.0621	N	0.22421	0.69	0.09310	N	1	B	0.23377	0.084	B	0.29524	0.103	T	0.27673	-1.0067	10	0.87932	D	0	.	4.7748	0.13173	0.8524:0.0:0.1476:0.0	.	133	P59543	T2R20_HUMAN	A	133	ENSP00000441624:V133A	ENSP00000441624:V133A	V	-	2	0	TAS2R20	11041344	0.001000	0.12720	0.004000	0.12327	0.002000	0.02628	1.455000	0.35190	1.349000	0.45751	0.482000	0.46254	GTG	.	.		0.373	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889		G	11150077	A	G	11150077	3	3	134	1	0	0	0	0	1	0	0	0	15586	159	6	2	535	2	TAS2R20	12	11150077	Missense_Mutation	SNP	A	TCGA-DD-A4NL-01A-11D-A28X-10	608687	11150077	122701818	17	21599										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54914613	54914613	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggagatcataaagtcactgtAaaaggtatacttctggtcta	9	6	4	1			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr15:54914613A>G	ENST00000260323.11	+	30	6195	c.6195A>G	c.(6193-6195)gtA>gtG	p.V2065V	UNC13C_ENST00000539562.2_5'UTR|UNC13C_ENST00000537900.1_Silent_p.V2063V|UNC13C_ENST00000545554.1_Silent_p.V2065V	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	2065	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AAGTCACTGTAAAAGGTATAC	0.408																																					p.V2065V		Atlas-SNP	.											.	UNC13C	674	.	0			c.A6195G						.						86	85	85					15																	54914613		1900	4117	6017	SO:0001819	synonymous_variant	440279	exon29			CACTGTAAAAGGT	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.6195A>G	chr15.hg19:g.54914613A>G		85.0	0.0		70.0	15.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.408	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		G	54914613	A	G	54914613	2	3	134	1	0	0	0	0	0	0	0	1	17001	349	13	2		2	UNC13C	15	54914613	Silent	SNP	A	TCGA-DD-A4NL-01A-11D-A28X-10		54914613	47616779	18	21600										
KIAA0427	9811	hgsc.bcm.edu	37	chr18	46385908	46385908	+	Frame_Shift_Del	DEL	C	C	-													0	0	1	0	0	0	1	1	0	cacgcagtactacaacagaaCcatccagaaactgacagcct							TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr18:46385908delC	ENST00000256413.3	+	12	2070	c.1775delC	c.(1774-1776)accfs	p.T592fs	CTIF_ENST00000382998.4_Frame_Shift_Del_p.T594fs	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	592					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						TACAACAGAACCATCCAGAAA	0.647																																					p.T594fs		Pindel	.											.	CTIF	102	.	0			c.1780delA						.						63	55	58					18																	46385908		2203	4300	6503	SO:0001589	frameshift_variant	9811	exon13			.	AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"KIAA0427"	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.1775delC	chr18.hg19:g.46385908delC	ENSP00000256413:p.Thr592fs	262.0	0.0		225.0	11.0	NM_001142397	B3KTR8|Q8IVD5	Frame_Shift_Del	DEL	ENST00000256413.3	hg19	CCDS11935.1																																																																																			.	.		0.647	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772		-	46385908	C	-	46385908	7	5	134	1	0	1	0	1	0	0	0	0	8185	507	18	0	1823	0	KIAA0427	18	46385908	Frame_Shift_Del	DEL	C	TCGA-DD-A4NL-01A-11D-A28X-10		46385908	31691340	19	21601										
FAM129C	199786	hgsc.bcm.edu	37	chr19	17664297	17664297	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgttcttggttcagcttgcAgagggactttcacactccct	10	11	3	1	rs199532721		TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr19:17664297A>G	ENST00000335393.4	+	16	2157	c.2019A>G	c.(2017-2019)gcA>gcG	p.A673A	FAM129C_ENST00000449408.2_Silent_p.A399A|FAM129C_ENST00000601861.1_Silent_p.A642A|COLGALT1_ENST00000252599.4_5'Flank	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	673										autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						TTCAGCTTGCAGAGGGACTTT	0.512																																					p.A673A		Atlas-SNP	.											.	FAM129C	110	.	0			c.A2019G						.						187	162	171					19																	17664297		2203	4300	6503	SO:0001819	synonymous_variant	199786	exon16			GCTTGCAGAGGGA	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.2019A>G	chr19.hg19:g.17664297A>G		140.0	0.0		108.0	5.0	NM_173544	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Silent	SNP	ENST00000335393.4	hg19	CCDS12362.1																																																																																			.	A|1.000;C|0.000		0.512	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544		G	17664297	A	G	17664297	2	3	134	1	0	0	0	0	0	0	0	1	5443	175	7	2		2	FAM129C	19	17664297	Silent	SNP	A	TCGA-DD-A4NL-01A-11D-A28X-10		17664297	41464686	20	21602										
MZF1	7593	hgsc.bcm.edu	37	chr19	59074590	59074612	+	Frame_Shift_Del	DEL	CCCCGCCCCCAGTGCTGGGGCGG	CCCCGCCCCCAGTGCTGGGGCGG	-													0	0	1	0	0	0	1	1	0	gcaacggccgcccctaaccaCcccgcccccagtgctggggc					rs545452499|rs200541260|rs146251309|rs375810541		TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	CCCCGCCCCCAGTGCTGGGGCGG	CCCCGCCCCCAGTGCTGGGGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr19:59074590_59074612delCCCCGCCCCCAGTGCTGGGGCGG	ENST00000215057.2	-	6	1592_1614	c.1032_1054delCCGCCCCAGCACTGGGGGCGGGG	c.(1030-1056)ggccgccccagcactgggggcggggtgfs	p.RPSTGGGV345fs	MZF1_ENST00000599369.1_Frame_Shift_Del_p.RPSTGGGV345fs|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000600534.1_RNA|MZF1_ENST00000594234.1_Frame_Shift_Del_p.AAPALGAG263fs	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	345					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		CCCCTAACCACCCCGCCCCCAGTGCTGGGGCGGCCCCGGCTCC	0.682																																					p.345_352del		Atlas-Indel,Pindel	.											.	MZF1	37	.	0			c.1033_1055del						.																																			SO:0001589	frameshift_variant	7593	exon6			.	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"-", "Zinc fingers, C2H2-type"	13108	protein-coding gene	gene with protein product		194550	"zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.1032_1054delCCGCCCCAGCACTGGGGGCGGGG	chr19.hg19:g.59074590_59074612delCCCCGCCCCCAGTGCTGGGGCGG	ENSP00000215057:p.Arg345fs	26.0	0.0		64.0	10.0	NM_003422	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Frame_Shift_Del	DEL	ENST00000215057.2	hg19	CCDS12988.1																																																																																			.	.		0.682	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		-	59074612	CCCCGCCCCCAGTGCTGGGGCGG	-	59074590	7	5	134	1	0	1	0	1	0	0	0	0	10117	507	18	0	1154	0	MZF1	19	59074590	Frame_Shift_Del	DEL	CCCCGCCCCCAGTGCTGGGGCGG	TCGA-DD-A4NL-01A-11D-A28X-10	41410293	59074590	54393	21	21603										
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45242105	45242105	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttacctgttcttacctggccGgctggactccaacaagcatc	8	14	1	0			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr20:45242105G>C	ENST00000279027.4	-	2	389	c.371C>G	c.(370-372)cCg>cGg	p.P124R	SLC13A3_ENST00000413164.2_Missense_Mutation_p.P124R|SLC13A3_ENST00000495082.1_Missense_Mutation_p.P77R|SLC13A3_ENST00000339636.3_Missense_Mutation_p.P124R|SLC13A3_ENST00000417157.2_Missense_Mutation_p.P77R|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000472148.1_Missense_Mutation_p.P77R|SLC13A3_ENST00000372121.1_Missense_Mutation_p.P124R|SLC13A3_ENST00000290317.5_Missense_Mutation_p.P77R|SLC13A3_ENST00000396360.1_Missense_Mutation_p.P77R	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	124					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	TTACCTGGCCGGCTGGACTCC	0.567																																					p.P124R		Atlas-SNP	.											.	SLC13A3	88	.	0			c.C371G						.						59	55	57					20																	45242105		2203	4300	6503	SO:0001583	missense	64849	exon2			CTGGCCGGCTGGA	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.371C>G	chr20.hg19:g.45242105G>C	ENSP00000279027:p.Pro124Arg	138.0	0.0		126.0	26.0	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	hg19	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	G	31	5.099054	0.94197	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082;ENST00000468915;ENST00000420568;ENST00000372121;ENST00000417157;ENST00000339636	T;T;T;T;T;T;T;T;T;T;T	0.03607	3.87;3.87;3.87;3.87;3.87;3.87;3.87;3.87;3.87;3.87;3.87	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.33059	0.0850	H	0.96048	3.76	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.44711	-0.9310	10	0.87932	D	0	-21.7825	20.8794	0.99867	0.0:0.0:1.0:0.0	.	124;77;77;77;124	B4DIR8;Q8WWT9-3;F6WI18;C9J4A3;Q8WWT9	.;.;.;.;S13A3_HUMAN	R	77;77;124;77;124;77;77;87;124;77;124	ENSP00000290317:P77R;ENSP00000379648:P77R;ENSP00000279027:P124R;ENSP00000420177:P77R;ENSP00000415852:P124R;ENSP00000419621:P77R;ENSP00000417784:P77R;ENSP00000395095:P87R;ENSP00000361193:P124R;ENSP00000397955:P77R;ENSP00000344912:P124R	ENSP00000279027:P124R	P	-	2	0	SLC13A3	44675512	1.000000	0.71417	0.979000	0.43373	0.972000	0.66771	9.813000	0.99286	2.941000	0.99782	0.655000	0.94253	CCG	.	.		0.567	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			C	45242105	G	C	45242105	3	2	134	1	0	0	0	0	1	0	0	0	14408	1116	39	4	1485	4	SLC13A3	20	45242105	Missense_Mutation	SNP	G	TCGA-DD-A4NL-01A-11D-A28X-10		45242105	17783415	22	21604										
TUBA8	51807	hgsc.bcm.edu	37	chr22	18604415	18604415	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctttttcagcgagactggcaAtgggaagcatgtgccccggg	14	10	1	1			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr22:18604415A>T	ENST00000330423.3	+	2	246	c.173A>T	c.(172-174)aAt>aTt	p.N58I	TUBA8_ENST00000316027.6_De_novo_Start_OutOfFrame	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	58					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	14						GAGACTGGCAATGGGAAGCAT	0.552																																					p.N58I		Atlas-SNP	.											.	TUBA8	36	.	0			c.A173T						.						88	76	80					22																	18604415		2203	4300	6503	SO:0001583	missense	51807	exon2			CTGGCAATGGGAA	AJ245922	CCDS13751.1, CCDS54495.1	22q11	2005-06-11			ENSG00000183785	ENSG00000183785		"Tubulins"	12410	protein-coding gene	gene with protein product		605742		TUBAL2		10772959, 10591208	Standard	NM_001193414		Approved		uc002znv.2	Q9NY65	OTTHUMG00000150097	ENST00000330423.3:c.173A>T	chr22.hg19:g.18604415A>T	ENSP00000333326:p.Asn58Ile	248.0	0.0		212.0	56.0	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Missense_Mutation	SNP	ENST00000330423.3	hg19	CCDS13751.1	.	.	.	.	.	.	.	.	.	.	A	13.94	2.386705	0.42308	.	.	ENSG00000183785	ENST00000330423;ENST00000416740	T;T	0.70164	-0.46;-0.46	5.06	3.92	0.45320	Tubulin/FtsZ, GTPase domain (4);	0.423476	0.26696	N	0.022964	T	0.66458	0.2791	M	0.81614	2.55	0.44728	D	0.997724	B;B;B	0.28783	0.0;0.019;0.222	B;B;B	0.29440	0.01;0.063;0.102	T	0.71009	-0.4716	10	0.72032	D	0.01	.	9.8108	0.40822	0.6205:0.3795:0.0:0.0	.	82;58;57	C9J2C0;Q9NY65;Q7Z3M3	.;TBA8_HUMAN;.	I	58;82	ENSP00000333326:N58I;ENSP00000412646:N82I	ENSP00000333326:N58I	N	+	2	0	TUBA8	16984415	1.000000	0.71417	1.000000	0.80357	0.686000	0.39977	4.519000	0.60517	2.030000	0.59900	0.459000	0.35465	AAT	.	.		0.552	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943		T	18604415	A	T	18604415	3	4	134	1	0	0	0	0	1	0	0	0	16765	101	4	4	179	4	TUBA8	22	18604415	Missense_Mutation	SNP	A	TCGA-DD-A4NL-01A-11D-A28X-10		18604415	32700151	23	21605										
ZNF280B	140883	hgsc.bcm.edu	37	chr22	22843497	22843497	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cagtatcttttctaaggtgaTcatacttttttctccttgac	5	9	4	2			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr22:22843497T>A	ENST00000406426.1	-	4	969	c.227A>T	c.(226-228)gAt>gTt	p.D76V	ZNF280B_ENST00000360412.2_Missense_Mutation_p.D76V			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	76					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TCTAAGGTGATCATACTTTTT	0.438																																					p.D76V		Atlas-SNP	.											.	ZNF280B	67	.	0			c.A227T						.						173	155	161					22																	22843497		2203	4300	6503	SO:0001583	missense	140883	exon4			AGGTGATCATACT	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"zinc finger protein 279", "suppressor of hairy wing homolog 2 (Drosophila)"	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.227A>T	chr22.hg19:g.22843497T>A	ENSP00000385998:p.Asp76Val	69.0	0.0		69.0	5.0	NM_080764		Missense_Mutation	SNP	ENST00000406426.1	hg19	CCDS13799.1	.	.	.	.	.	.	.	.	.	.	t	10.54	1.378456	0.24944	.	.	ENSG00000198477	ENST00000406426;ENST00000360412	T;T	0.23147	1.92;1.92	4.55	1.37	0.22104	.	.	.	.	.	T	0.17408	0.0418	N	0.19112	0.55	0.09310	N	1	B	0.32010	0.351	B	0.37015	0.239	T	0.27434	-1.0074	9	0.72032	D	0.01	.	6.1309	0.20204	0.0:0.6848:0.0:0.3152	.	76	Q86YH2	Z280B_HUMAN	V	76	ENSP00000385998:D76V;ENSP00000353586:D76V	ENSP00000353586:D76V	D	-	2	0	ZNF280B	21173497	0.132000	0.22450	0.002000	0.10522	0.408000	0.30992	0.164000	0.16542	0.654000	0.30846	-0.221000	0.12465	GAT	.	.		0.438	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764		A	22843497	T	A	22843497	3	1	134	1	0	0	0	0	1	0	0	0	17830	1435	50	4	1408	4	ZNF280B	22	22843497	Missense_Mutation	SNP	T	TCGA-DD-A4NL-01A-11D-A28X-10	4239082	22843497	28461069	24	21606										
LDOC1L	84247	hgsc.bcm.edu	37	chr22	44892793	44892793	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctggatgcactgggcaaggcCccgtgcccgcagaggccagc	15	15	0	1			TCGA-DD-A4NL-01A-11D-A28X-10	TCGA-DD-A4NL-11A-11D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d09e93b-51df-4683-a2fa-94c85cc1c0ab	04c60928-59b2-44bf-9d49-57bfbdd82528	g.chr22:44892793C>A	ENST00000341255.3	-	2	1153	c.644G>T	c.(643-645)gGg>gTg	p.G215V		NM_032287.2	NP_115663.2	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	215										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(3)|prostate(2)	11		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)		TGGGCAAGGCCCCGTGCCCGC	0.637																																					p.G215V		Atlas-SNP	.											.	LDOC1L	24	.	0			c.G644T						.						36	40	39					22																	44892793		2203	4300	6503	SO:0001583	missense	84247	exon2			CAAGGCCCCGTGC	CR456439	CCDS33662.1	22q13.3	2006-09-06			ENSG00000188636	ENSG00000188636			13343	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_032287		Approved	dJ1033E15.2, DKFZp761O17121, Mart6, Mar6	uc003beu.1	Q6ICC9	OTTHUMG00000150465	ENST00000341255.3:c.644G>T	chr22.hg19:g.44892793C>A	ENSP00000340434:p.Gly215Val	53.0	0.0		47.0	14.0	NM_032287	Q6ZTR1	Missense_Mutation	SNP	ENST00000341255.3	hg19	CCDS33662.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.766037	0.49574	.	.	ENSG00000188636	ENST00000341255	T	0.18338	2.22	3.18	-0.452	0.12205	.	0.486110	0.16542	N	0.209910	T	0.06690	0.0171	N	0.08118	0	0.30495	N	0.771008	P	0.35077	0.483	B	0.29267	0.1	T	0.18524	-1.0334	10	0.72032	D	0.01	-5.4003	6.5729	0.22549	0.1869:0.3686:0.4446:0.0	.	215	Q6ICC9	LDOCL_HUMAN	V	215	ENSP00000340434:G215V	ENSP00000340434:G215V	G	-	2	0	LDOC1L	43271457	0.221000	0.23642	0.244000	0.24202	0.879000	0.50718	0.591000	0.23969	0.011000	0.14865	0.555000	0.69702	GGG	.	.		0.637	LDOC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318222.1	NM_032287		A	44892793	C	A	44892793	3	1	134	1	0	0	0	0	1	0	0	0	8719	623	22	3	79	3	LDOC1L	22	44892793	Missense_Mutation	SNP	C	TCGA-DD-A4NL-01A-11D-A28X-10	22049296	44892793	6411773	25	21607										
ERRFI1	54206	hgsc.bcm.edu	37	chr1	8074333	8074340	+	Frame_Shift_Del	DEL	TCCTCTTC	TCCTCTTC	-													0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	taaaaccacatacaacttgaTcctcttcatgtggtcccaag					rs34781518	byFrequency	TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	TCCTCTTC	TCCTCTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:8074333_8074340delTCCTCTTC	ENST00000377482.5	-	4	542_549	c.319_326delGAAGAGGA	c.(319-327)gaagaggatfs	p.EED107fs	ERRFI1_ENST00000474874.1_Intron|ERRFI1_ENST00000469499.1_3'UTR|ERRFI1_ENST00000467067.1_3'UTR	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	107					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		TACAACTTGATCCTCTTCATGTGGTCCC	0.476																																					p.107_109del		Atlas-INDEL	.											.	ERRFI1	42	.	0			c.320_327del						.																																			SO:0001589	frameshift_variant	54206	exon4			.	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.319_326delGAAGAGGA	chr1.hg19:g.8074333_8074340delTCCTCTTC	ENSP00000366702:p.Glu107fs	123.0	0.0		28.0	15.0	NM_018948	B2RDX9|Q9NTG9|Q9UD05	Frame_Shift_Del	DEL	ENST00000377482.5	hg19	CCDS94.1																																																																																			.	.		0.476	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948		-	8074340	TCCTCTTC	-	8074333	7	5	135	1	0	1	0	1	0	0	0	0	5246	1435	50	0	1066	0	ERRFI1	1	8074333	Frame_Shift_Del	DEL	TCCTCTTC	TCGA-DD-A4NN-01A-11D-A28X-10		8074333	241176288	1	21608	92	2								
ERRFI1	54206	hgsc.bcm.edu	37	chr1	8074342	8074343	+	Frame_Shift_Del	DEL	TG	TG	-													0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	atacaacttgatcctcttcaTgtggtcccaagttttcactt							TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:8074342_8074343delTG	ENST00000377482.5	-	4	539_540	c.316_317delCA	c.(316-318)catfs	p.H106fs	ERRFI1_ENST00000474874.1_Intron|ERRFI1_ENST00000469499.1_3'UTR|ERRFI1_ENST00000467067.1_3'UTR	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	106					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		ATCCTCTTCATGTGGTCCCAAG	0.47																																					p.106_106del		Atlas-INDEL	.											.	ERRFI1	42	.	0			c.317_318del						.																																			SO:0001589	frameshift_variant	54206	exon4			.	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.316_317delCA	chr1.hg19:g.8074344_8074345delTG	ENSP00000366702:p.His106fs	115.0	0.0		26.0	15.0	NM_018948	B2RDX9|Q9NTG9|Q9UD05	Frame_Shift_Del	DEL	ENST00000377482.5	hg19	CCDS94.1																																																																																			.	.		0.47	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948		-	8074343	TG	-	8074342	7	5	135	1	0	1	0	1	0	0	0	0	5246	1464	51	0	1075	0	ERRFI1	1	8074342	Frame_Shift_Del	DEL	TG	TCGA-DD-A4NN-01A-11D-A28X-10	9	8074342	241176279	2	21609	92	2								
SEMA6C	10500	hgsc.bcm.edu	37	chr1	151110260	151110260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ggtctccatgctccaaggccTggacaaagtgtggctctaag	12	11	2	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:151110260T>C	ENST00000341697.3	-	10	2374	c.683A>G	c.(682-684)cAg>cGg	p.Q228R				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	228	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CTCCAAGGCCTGGACAAAGTG	0.562																																					p.Q228R		Atlas-SNP	.											.	SEMA6C	70	.	0			c.A683G						.						116	98	104					1																	151110260		2203	4300	6503	SO:0001583	missense	10500	exon10			AAGGCCTGGACAA	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"Semaphorins"	10740	protein-coding gene	gene with protein product	"m-Sema Y2"	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.683A>G	chr1.hg19:g.151110260T>C	ENSP00000344148:p.Gln228Arg	186.0	0.0		552.0	29.0	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	hg19	CCDS984.1	.	.	.	.	.	.	.	.	.	.	T	17.00	3.276700	0.59758	.	.	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697;ENST00000392792	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	4.48	4.48	0.54585	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.209202	0.49305	D	0.000146	T	0.05731	0.0150	N	0.16656	0.425	0.25473	N	0.987806	P;B;B;B	0.41710	0.76;0.001;0.036;0.0	B;B;B;B	0.37451	0.25;0.0;0.035;0.0	T	0.10268	-1.0637	10	0.66056	D	0.02	.	11.7802	0.52010	0.0:0.0:0.0:1.0	.	228;188;228;228	B4DZD4;Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;.;SEM6C_HUMAN	R	228;188;228;228;228	ENSP00000357910:Q228R;ENSP00000357908:Q188R;ENSP00000357909:Q228R;ENSP00000344148:Q228R	ENSP00000344148:Q228R	Q	-	2	0	SEMA6C	149376884	1.000000	0.71417	0.953000	0.39169	0.965000	0.64279	7.735000	0.84939	1.884000	0.54569	0.459000	0.35465	CAG	.	.		0.562	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		C	151110260	T	C	151110260	3	2	135	1	0	0	0	0	1	0	0	0	14056	1580	55	2	2249	2	SEMA6C	1	151110260	Missense_Mutation	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10	143035918	151110260	98140361	3	21610										
TCHH	7062	hgsc.bcm.edu	37	chr1	152084221	152084221	+	Missense_Mutation	SNP	A	A	C													0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	cgcgcctctcctcctcctcgAgcttcagccaacgttcgcgc					rs202112040		TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:152084221A>C	ENST00000368804.1	-	2	1471	c.1472T>G	c.(1471-1473)cTc>cGc	p.L491R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	491	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCTCCTCGAGCTTCAGCCA	0.672																																					p.L491R		Atlas-SNP	.											.	TCHH	275	.	0			c.T1472G						.						63	70	68					1																	152084221		2106	4220	6326	SO:0001583	missense	7062	exon3			TCCTCGAGCTTCA	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1472T>G	chr1.hg19:g.152084221A>C	ENSP00000357794:p.Leu491Arg	80.0	0.0		263.0	17.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	a	0.064	-1.216147	0.01542	.	.	ENSG00000159450	ENST00000368804	T	0.04603	3.59	2.11	-4.23	0.03789	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43491	-0.9388	9	0.12430	T	0.62	.	7.0185	0.24900	0.2982:0.5613:0.0:0.1406	.	491	Q07283	TRHY_HUMAN	R	491	ENSP00000357794:L491R	ENSP00000357794:L491R	L	-	2	0	TCHH	150350845	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-1.154000	0.03166	-2.764000	0.00368	-1.533000	0.00918	CTC	.	.		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084221	A	C	152084221	3	2	135	1	0	0	0	0	1	0	0	0	15715	304	11	5	4363	5	TCHH	1	152084221	Missense_Mutation	SNP	A	TCGA-DD-A4NN-01A-11D-A28X-10	973961	152084221	97166400	4	21611	93	2								
TCHH	7062	hgsc.bcm.edu	37	chr1	152084224	152084224	+	Missense_Mutation	SNP	T	T	C													0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gcctctcctcctcctcgagcTtcagccaacgttcgcgcctc							TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:152084224T>C	ENST00000368804.1	-	2	1468	c.1469A>G	c.(1468-1470)aAg>aGg	p.K490R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	490	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCTCGAGCTTCAGCCAACG	0.672																																					p.K490R		Atlas-SNP	.											.	TCHH	275	.	0			c.A1469G						.						65	71	69					1																	152084224		2109	4224	6333	SO:0001583	missense	7062	exon3			TCGAGCTTCAGCC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1469A>G	chr1.hg19:g.152084224T>C	ENSP00000357794:p.Lys490Arg	79.0	0.0		267.0	12.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	t	8.419	0.845945	0.16963	.	.	ENSG00000159450	ENST00000368804	T	0.04654	3.58	2.98	-5.97	0.02227	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.09590	T	0.72	.	5.0277	0.14393	0.1398:0.4054:0.0:0.4548	.	490	Q07283	TRHY_HUMAN	R	490	ENSP00000357794:K490R	ENSP00000357794:K490R	K	-	2	0	TCHH	150350848	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.247000	0.00266	-1.053000	0.03218	-1.396000	0.01147	AAG	.	.		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084224	T	C	152084224	3	2	135	1	0	0	0	0	1	0	0	0	15715	1609	56	2	4366	2	TCHH	1	152084224	Missense_Mutation	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10	3	152084224	97166397	5	21612	93	2								
PGLYRP3	114771	hgsc.bcm.edu	37	chr1	153277442	153277442	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	cctatcttattgccaaagaaGgcgatgcccagggaaatgtt	10	9	1	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:153277442G>T	ENST00000290722.1	-	3	409	c.357C>A	c.(355-357)gcC>gcA	p.A119A		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	119					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGCCAAAGAAGGCGATGCCCA	0.537																																					p.A119A		Atlas-SNP	.											.	PGLYRP3	55	.	0			c.C357A						.						155	130	138					1																	153277442		2203	4300	6503	SO:0001819	synonymous_variant	114771	exon3			AAAGAAGGCGATG	AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I alpha precursor"	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.357C>A	chr1.hg19:g.153277442G>T		198.0	0.0		590.0	113.0	NM_052891	A1A4U8|Q5SY65	Silent	SNP	ENST00000290722.1	hg19	CCDS1035.1																																																																																			.	.		0.537	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891		T	153277442	G	T	153277442	2	4	135	1	0	0	0	0	0	0	0	1	11804	987	35	3		3	PGLYRP3	1	153277442	Silent	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	1193218	153277442	95973179	6	21613										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155429586	155429586	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tggtaaaacaaatagcactaGcctgttgaagaagtactctc	8	8	1	2			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:155429586G>T	ENST00000368346.3	-	4	5726		c.e4+1		ASH1L_ENST00000392403.3_Splice_Site			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)						cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AATAGCACTAGCCTGTTGAAG	0.408																																					.		Atlas-SNP	.											.	ASH1L	279	.	0			c.5086+2C>A						.						72	70	70					1																	155429586		2203	4300	6503	SO:0001630	splice_region_variant	55870	exon5			GCACTAGCCTGTT	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.5086+1C>A	chr1.hg19:g.155429586G>T		34.0	0.0		95.0	4.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Splice_Site	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.78	2.935610	0.52972	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	.	.	.	4.39	1.48	0.22813	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.0436	0.25033	0.3899:0.0:0.6101:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ASH1L	153696210	1.000000	0.71417	0.961000	0.40146	0.986000	0.74619	0.467000	0.22035	0.139000	0.18822	0.591000	0.81541	.	.	.		0.408	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	Intron	T	155429586	G	T	155429586	5	4	135	1	0	0	0	0	0	0	1	0	1041	985	34	3	3906	3	ASH1L	1	155429586	Splice_Site	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	2152144	155429586	93821035	7	21614										
INSRR	3645	hgsc.bcm.edu	37	chr1	156828374	156828381	+	Frame_Shift_Del	DEL	GCAGGCAT	GCAGGCAT	-													0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	caaggagaggaagatcacagGcaggcatgctccccagggcc					rs2644597		TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	GCAGGCAT	GCAGGCAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:156828374_156828381delGCAGGCAT	ENST00000368195.3	-	1	429_436	c.33_40delATGCCTGC	c.(31-42)gcatgcctgcctfs	p.CLP12fs	NTRK1_ENST00000392302.2_Intron|NTRK1_ENST00000368196.3_5'Flank|NTRK1_ENST00000524377.1_5'Flank|NTRK1_ENST00000358660.3_5'Flank	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	12					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AAGATCACAGGCAGGCATGCTCCCCAGG	0.62																																					p.12_14del		Atlas-Indel,Pindel	.											.	INSRR	309	.	0			c.34_41del						.																																			SO:0001589	frameshift_variant	3645	exon1			.	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.33_40delATGCCTGC	chr1.hg19:g.156828374_156828381delGCAGGCAT	ENSP00000357178:p.Cys12fs	133.0	0.0		350.0	28.0	NM_014215	O60724|Q5VZS3	Frame_Shift_Del	DEL	ENST00000368195.3	hg19	CCDS1160.1																																																																																			.	.		0.62	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		-	156828381	GCAGGCAT	-	156828374	7	5	135	1	0	1	0	1	0	0	0	0	7783	1203	42	0	3940	0	INSRR	1	156828374	Frame_Shift_Del	DEL	GCAGGCAT	TCGA-DD-A4NN-01A-11D-A28X-10	1398788	156828374	92422247	8	21615										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158622406	158622406	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ataacgttgcaatagacgacGtctgcgttcttctgcccgat	9	11	3	1	rs372281474		TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:158622406G>A	ENST00000368147.4	-	23	3406	c.3226C>T	c.(3226-3228)Cgt>Tgt	p.R1076C		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1076					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AATAGACGACGTCTGCGTTCT	0.438																																					p.R1076C		Atlas-SNP	.											.	SPTA1	720	.	0			c.C3226T						.						108	99	102					1																	158622406		1887	4112	5999	SO:0001583	missense	6708	exon23			GACGACGTCTGCG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3226C>T	chr1.hg19:g.158622406G>A	ENSP00000357129:p.Arg1076Cys	127.0	0.0		300.0	106.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.339932	0.41398	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.68025	-0.3;-0.3	5.3	4.39	0.52855	.	0.000000	0.32703	N	0.005759	T	0.65481	0.2695	L	0.54323	1.7	0.49389	D	0.999783	D	0.76494	0.999	D	0.63703	0.917	T	0.70733	-0.4791	10	0.72032	D	0.01	.	7.9373	0.29937	0.0843:0.2521:0.6635:0.0	.	1076	P02549	SPTA1_HUMAN	C	1076	ENSP00000357130:R1076C;ENSP00000357129:R1076C	ENSP00000357129:R1076C	R	-	1	0	SPTA1	156889030	1.000000	0.71417	0.251000	0.24312	0.016000	0.09150	3.757000	0.55212	1.479000	0.48272	0.655000	0.94253	CGT	.	.		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158622406	G	A	158622406	3	1	135	1	0	0	0	0	1	0	0	0	15131	1145	40	1	4153	1	SPTA1	1	158622406	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	1794032	158622406	90628215	9	21616										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158624516	158624516	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tttgttctccagcaactcccTccactggtgcagcctgttgt	8	14	1	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:158624516T>C	ENST00000368147.4	-	21	3101	c.2921A>G	c.(2920-2922)gAg>gGg	p.E974G		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	974					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGCAACTCCCTCCACTGGTGC	0.517																																					p.E974G		Atlas-SNP	.											.	SPTA1	720	.	0			c.A2921G						.						64	63	63					1																	158624516		1953	4157	6110	SO:0001583	missense	6708	exon21			ACTCCCTCCACTG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2921A>G	chr1.hg19:g.158624516T>C	ENSP00000357129:p.Glu974Gly	79.0	0.0		227.0	35.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	11.64	1.699723	0.30142	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.55588	0.68;0.51	5.31	4.2	0.49525	Src homology-3 domain (1);	0.261227	0.20064	N	0.100008	T	0.21841	0.0526	L	0.28274	0.84	0.36718	D	0.881012	B	0.02656	0.0	B	0.09377	0.004	T	0.05954	-1.0854	10	0.48119	T	0.1	.	9.9468	0.41613	0.0:0.0796:0.0:0.9204	.	974	P02549	SPTA1_HUMAN	G	974	ENSP00000357130:E974G;ENSP00000357129:E974G	ENSP00000357129:E974G	E	-	2	0	SPTA1	156891140	1.000000	0.71417	0.614000	0.29051	0.674000	0.39518	5.375000	0.66173	1.061000	0.40601	0.482000	0.46254	GAG	.	.		0.517	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158624516	T	C	158624516	3	2	135	1	0	0	0	0	1	0	0	0	15131	1551	54	2	4466	2	SPTA1	1	158624516	Missense_Mutation	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10	2110	158624516	90626105	10	21617										
PVRL4	81607	hgsc.bcm.edu	37	chr1	161044015	161044015	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	cccagtactcactatttctgGgtcatctgctgggccttgcg	10	13	4	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:161044015G>A	ENST00000368012.3	-	6	1451	c.1149C>T	c.(1147-1149)acC>acT	p.T383T	PVRL4_ENST00000486694.1_5'UTR|PVRL4_ENST00000453926.2_Silent_p.T117T	NM_030916.2	NP_112178.2	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4	383					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|urinary_tract(1)	20	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			ACTATTTCTGGGTCATCTGCT	0.577																																					p.T383T	NSCLC(76;1160 1387 14476 16172 29359)	Atlas-SNP	.											.	PVRL4	48	.	0			c.C1149T						.						120	115	117					1																	161044015		2203	4300	6503	SO:0001819	synonymous_variant	81607	exon6			TTTCTGGGTCATC	AF426163	CCDS1216.1	1q22-q23.2	2013-01-14			ENSG00000143217	ENSG00000143217		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	19688	protein-coding gene	gene with protein product		609607				11544254	Standard	NM_030916		Approved	nectin-4, PRR4, LNIR	uc001fxo.2	Q96NY8	OTTHUMG00000031475	ENST00000368012.3:c.1149C>T	chr1.hg19:g.161044015G>A		204.0	0.0		620.0	126.0	NM_030916	B4DQW3|Q96K15	Silent	SNP	ENST00000368012.3	hg19	CCDS1216.1																																																																																			.	.		0.577	PVRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077074.1	NM_030916		A	161044015	G	A	161044015	2	1	135	1	0	0	0	0	0	0	0	1	12857	1219	43	3		3	PVRL4	1	161044015	Silent	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	2419499	161044015	88206606	11	21618										
GPR52	9293	hgsc.bcm.edu	37	chr1	174417683	174417683	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tcgttatcttgcaataaccaAgcctctttcctacaatcaac	3	13	3	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:174417683A>T	ENST00000367685.2	+	1	472	c.434A>T	c.(433-435)aAg>aTg	p.K145M	RABGAP1L_ENST00000251507.4_Intron|RABGAP1L_ENST00000357444.6_Intron|RABGAP1L_ENST00000367689.3_Intron	NM_005684.4	NP_005675.3	Q9Y2T5	GPR52_HUMAN	G protein-coupled receptor 52	145					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(3)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|prostate(1)|skin(2)	20						GCAATAACCAAGCCTCTTTCC	0.393																																					p.K145M	Ovarian(92;924 1390 1930 16467 40583)	Atlas-SNP	.											.	GPR52	40	.	0			c.A434T						.						198	196	197					1																	174417683		2203	4300	6503	SO:0001583	missense	9293	exon1			TAACCAAGCCTCT	AF096784	CCDS30941.1	1q24	2012-08-21			ENSG00000203737	ENSG00000203737		"GPCR / Class A : Orphans"	4508	protein-coding gene	gene with protein product		604106				9931487	Standard	NM_005684		Approved		uc001gka.1	Q9Y2T5	OTTHUMG00000034901	ENST00000367685.2:c.434A>T	chr1.hg19:g.174417683A>T	ENSP00000356658:p.Lys145Met	135.0	0.0		410.0	157.0	NM_005684	O75654|Q4VBL6|Q6ISM0	Missense_Mutation	SNP	ENST00000367685.2	hg19	CCDS30941.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.452566	0.63290	.	.	ENSG00000203737	ENST00000367685	T	0.39406	1.08	5.9	5.9	0.94986	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.63307	0.2500	M	0.68593	2.085	0.43489	D	0.995729	D	0.89917	1.0	D	0.71656	0.974	T	0.65776	-0.6086	10	0.66056	D	0.02	-11.7665	16.3322	0.83039	1.0:0.0:0.0:0.0	.	145	Q9Y2T5	GPR52_HUMAN	M	145	ENSP00000356658:K145M	ENSP00000356658:K145M	K	+	2	0	GPR52	172684306	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.930000	0.92872	2.251000	0.74343	0.528000	0.53228	AAG	.	.		0.393	GPR52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084511.1	NM_005684		T	174417683	A	T	174417683	3	4	135	1	0	0	0	0	1	0	0	0	6706	72	3	4	436	4	GPR52	1	174417683	Missense_Mutation	SNP	A	TCGA-DD-A4NN-01A-11D-A28X-10	13373668	174417683	74832938	12	21619										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181479711	181479711	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tgacaagacccccatgtcccGaagactggtatgtgattccc	9	13	0	4	rs369308237		TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:181479711G>A	ENST00000367573.2	+	2	365	c.365G>A	c.(364-366)cGa>cAa	p.R122Q	CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R122Q|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R122Q|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R73Q|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R122Q|CACNA1E_ENST00000358338.5_Missense_Mutation_p.R73Q	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	122					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.R122Q(2)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CCCATGTCCCGAAGACTGGTA	0.527																																					p.R122Q		Atlas-SNP	.											CACNA1E_ENST00000367573,NS,carcinoma,0,2	CACNA1E	778	.	2	Substitution - Missense(2)	lung(2)	c.G365A						.	G	GLN/ARG,GLN/ARG,GLN/ARG	0,4106		0,0,2053	111	112	112		365,365,365	5.3	1	1		112	1,8363		0,1,4181	no	missense,missense,missense	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	43,43,43	0,1,6234	AA,AG,GG		0.012,0.0,0.0080	probably-damaging,probably-damaging,probably-damaging	122/2271,122/2314,122/2252	181479711	1,12469	2053	4182	6235	SO:0001583	missense	777	exon2			TGTCCCGAAGACT	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.365G>A	chr1.hg19:g.181479711G>A	ENSP00000356545:p.Arg122Gln	167.0	0.0		418.0	69.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267351	0.80469	0.0	1.2E-4	ENSG00000198216	ENST00000524607;ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.97430	-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38	5.27	5.27	0.74061	.	0.067055	0.64402	D	0.000015	D	0.87099	0.6093	N	0.00771	-1.2	0.80722	D	1	P;P	0.47762	0.9;0.9	B;B	0.32583	0.148;0.148	D	0.89417	0.3707	10	0.27785	T	0.31	.	18.4942	0.90858	0.0:0.0:1.0:0.0	.	122;122	Q15878-2;Q15878-3	.;.	Q	122;122;122;73;73;122;122	ENSP00000432038:R122Q;ENSP00000356542:R122Q;ENSP00000434814:R122Q;ENSP00000350183:R73Q;ENSP00000351101:R73Q;ENSP00000353222:R122Q;ENSP00000356545:R122Q	ENSP00000350183:R73Q	R	+	2	0	CACNA1E	179746334	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.942000	0.63547	2.456000	0.83038	0.561000	0.74099	CGA	.	.		0.527	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181479711	G	A	181479711	3	1	135	1	0	0	0	0	1	0	0	0	2544	1058	37	1	371	1	CACNA1E	1	181479711	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	7062028	181479711	67770910	13	21620										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186086707	186086707	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	caattcactggaccaaaaatGgtataagactgcttcccagg	8	10	1	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:186086707G>A	ENST00000271588.4	+	77	12029	c.11800G>A	c.(11800-11802)Ggt>Agt	p.G3934S	HMCN1_ENST00000367492.2_Missense_Mutation_p.G3934S	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3934	Ig-like C2-type 38.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GACCAAAAATGGTATAAGACT	0.423																																					p.G3934S		Atlas-SNP	.											.	HMCN1	797	.	0			c.G11800A						.						105	102	103					1																	186086707		2203	4300	6503	SO:0001583	missense	83872	exon77			AAAAATGGTATAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11800G>A	chr1.hg19:g.186086707G>A	ENSP00000271588:p.Gly3934Ser	104.0	0.0		307.0	101.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.810564	0.90707	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.81821	-1.54;-1.54	5.65	5.65	0.86999	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.097934	0.64402	D	0.000001	D	0.88962	0.6580	M	0.76328	2.33	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.89400	0.3695	10	0.62326	D	0.03	.	14.5656	0.68173	0.0:0.0:0.8539:0.1461	.	3934	Q96RW7	HMCN1_HUMAN	S	3934	ENSP00000271588:G3934S;ENSP00000356462:G3934S	ENSP00000271588:G3934S	G	+	1	0	HMCN1	184353330	1.000000	0.71417	0.992000	0.48379	0.988000	0.76386	7.871000	0.87180	2.655000	0.90218	0.655000	0.94253	GGT	.	.		0.423	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186086707	G	A	186086707	3	1	135	1	0	0	0	0	1	0	0	0	7229	1348	47	3	12106	3	HMCN1	1	186086707	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	4606996	186086707	63163914	14	21621										
TP53BP2	7159	hgsc.bcm.edu	37	chr1	223968572	223968572	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gtttcaggccaagctcctttGtcttggtttaattcttgggt	10	8	3	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr1:223968572G>C	ENST00000343537.7	-	18	3679	c.3388C>G	c.(3388-3390)Caa>Gaa	p.Q1130E	TP53BP2_ENST00000391879.2_Missense_Mutation_p.Q363E|TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391878.2_Missense_Mutation_p.Q1001E	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	1124					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		AAGCTCCTTTGTCTTGGTTTA	0.303																																					p.Q1130E		Atlas-SNP	.											.	TP53BP2	144	.	0			c.C3388G						.						91	92	92					1																	223968572		2203	4300	6503	SO:0001583	missense	7159	exon18			TCCTTTGTCTTGG	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.3388C>G	chr1.hg19:g.223968572G>C	ENSP00000341957:p.Gln1130Glu	61.0	0.0		83.0	6.0	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	hg19	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	G	32	5.171968	0.94807	.	.	ENSG00000143514	ENST00000391878;ENST00000343537;ENST00000391879	T;T;T	0.56611	0.45;0.63;0.45	5.48	5.48	0.80851	Src homology-3 domain (1);	0.053329	0.85682	D	0.000000	T	0.73233	0.3561	M	0.70595	2.14	0.80722	D	1	D;D	0.61080	0.989;0.98	D;D	0.72338	0.977;0.966	T	0.74836	-0.3529	10	0.72032	D	0.01	.	19.7152	0.96115	0.0:0.0:1.0:0.0	.	1130;1124	B4DG66;Q13625	.;ASPP2_HUMAN	E	1001;1130;363	ENSP00000375750:Q1001E;ENSP00000341957:Q1130E;ENSP00000375751:Q363E	ENSP00000341957:Q1130E	Q	-	1	0	TP53BP2	222035195	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.420000	0.97426	2.733000	0.93635	0.591000	0.81541	CAA	.	.		0.303	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		C	223968572	G	C	223968572	3	2	135	1	0	0	0	0	1	0	0	0	16399	1386	48	4	20	4	TP53BP2	1	223968572	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	37881865	223968572	25282049	15	21622										
NPAS2	4862	hgsc.bcm.edu	37	chr2	101580582	101580590	+	In_Frame_Del	DEL	GGAAAGGAG	GGAAAGGAG	-													0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gaccttgccgggtgccactaGgaaaggaggtttgcttcatt							TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	GGAAAGGAG	GGAAAGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr2:101580582_101580590delGGAAAGGAG	ENST00000335681.5	+	8	946_954	c.661_669delGGAAAGGAG	c.(661-669)ggaaaggagdel	p.GKE221del	NPAS2_ENST00000542504.1_In_Frame_Del_p.GKE286del|NPAS2_ENST00000486017.1_3'UTR	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	221					cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGTGCCACTAGGAAAGGAGGTTTGCTTCA	0.512																																					p.220_223del		Atlas-Indel,Pindel	.											NPAS2,colon,carcinoma,+1,1	NPAS2	88	.	0			c.660_668del						.																																			SO:0001651	inframe_deletion	4862	exon8			.	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"Basic helix-loop-helix proteins"	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.661_669delGGAAAGGAG	chr2.hg19:g.101580582_101580590delGGAAAGGAG	ENSP00000338283:p.Gly221_Glu223del	87.0	0.0		91.0	24.0	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	In_Frame_Del	DEL	ENST00000335681.5	hg19	CCDS2048.1																																																																																			.	.		0.512	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3			-	101580590	GGAAAGGAG	-	101580582	7	5	135	1	0	1	0	1	0	0	0	0	10572	1001	35	0	687	0	NPAS2	2	101580582	In_Frame_Del	DEL	GGAAAGGAG	TCGA-DD-A4NN-01A-11D-A28X-10		101580582	141618791	16	21623										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196891544	196891544	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ttcatcagataatgtaactaTgctgtcagtgaagactttca	7	7	4	3			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr2:196891544T>C	ENST00000312428.6	-	7	707	c.607A>G	c.(607-609)Ata>Gta	p.I203V	DNAH7_ENST00000410072.1_Missense_Mutation_p.I203V	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	203	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AATGTAACTATGCTGTCAGTG	0.353																																					p.I203V		Atlas-SNP	.											.	DNAH7	512	.	0			c.A607G						.						129	122	124					2																	196891544		1874	4102	5976	SO:0001583	missense	56171	exon7			TAACTATGCTGTC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.607A>G	chr2.hg19:g.196891544T>C	ENSP00000311273:p.Ile203Val	108.0	0.0		129.0	67.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	T	13.18	2.160789	0.38119	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.22539	1.95;2.78	5.92	5.92	0.95590	.	0.057481	0.64402	D	0.000005	T	0.21841	0.0526	M	0.61703	1.905	0.41309	D	0.987093	B	0.13145	0.007	B	0.14023	0.01	T	0.06844	-1.0804	10	0.18710	T	0.47	.	11.1289	0.48334	0.0:0.0722:0.0:0.9278	.	203	Q8WXX0	DYH7_HUMAN	V	203	ENSP00000311273:I203V;ENSP00000386260:I203V	ENSP00000311273:I203V	I	-	1	0	DNAH7	196599789	1.000000	0.71417	0.952000	0.39060	0.698000	0.40448	2.314000	0.43743	2.260000	0.74910	0.528000	0.53228	ATA	.	.		0.353	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196891544	T	C	196891544	3	2	135	1	0	0	0	0	1	0	0	0	4608	1464	51	2	11703	2	DNAH7	2	196891544	Missense_Mutation	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10	95310962	196891544	46307829	17	21624										
AGAP1	116987	hgsc.bcm.edu	37	chr2	237032725	237032725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	acctgtccaggagaaacaatAaccggaacaacagcagtggg	11	10	0	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr2:237032725A>G	ENST00000304032.8	+	18	3113	c.2533A>G	c.(2533-2535)Aac>Gac	p.N845D	AGAP1_ENST00000428334.2_Missense_Mutation_p.N684D|AGAP1_ENST00000336665.5_Missense_Mutation_p.N792D|AGAP1_ENST00000409538.1_Missense_Mutation_p.N1057D	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	845					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						GAGAAACAATAACCGGAACAA	0.652																																					p.N845D		Atlas-SNP	.											.	AGAP1	95	.	0			c.A2533G						.						60	66	64					2																	237032725		2203	4300	6503	SO:0001583	missense	116987	exon18			AACAATAACCGGA	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16922	protein-coding gene	gene with protein product		608651	"centaurin, gamma 2"	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.2533A>G	chr2.hg19:g.237032725A>G	ENSP00000307634:p.Asn845Asp	293.0	0.0		382.0	174.0	NM_001037131	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	hg19	CCDS33408.1	.	.	.	.	.	.	.	.	.	.	A	12.44	1.937476	0.34189	.	.	ENSG00000157985	ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	T;T;T;T	0.70516	-0.49;-0.47;-0.46;0.59	4.2	1.68	0.24146	.	0.307764	0.32357	N	0.006201	T	0.59932	0.2230	L	0.58101	1.795	0.28518	N	0.913215	B;B	0.22541	0.004;0.071	B;B	0.18263	0.01;0.021	T	0.52793	-0.8528	10	0.45353	T	0.12	.	4.8536	0.13549	0.7462:0.0:0.0907:0.1631	.	792;845	Q9UPQ3-2;Q9UPQ3	.;AGAP1_HUMAN	D	845;792;1057;684	ENSP00000307634:N845D;ENSP00000338378:N792D;ENSP00000386897:N1057D;ENSP00000411824:N684D	ENSP00000307634:N845D	N	+	1	0	AGAP1	236697464	0.994000	0.37717	0.765000	0.31456	0.993000	0.82548	2.956000	0.49129	0.053000	0.16036	0.460000	0.39030	AAC	.	.		0.652	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914		G	237032725	A	G	237032725	3	3	135	1	0	0	0	0	1	0	0	0	366	362	13	2	2603	2	AGAP1	2	237032725	Missense_Mutation	SNP	A	TCGA-DD-A4NN-01A-11D-A28X-10	40141181	237032725	6166648	18	21625										
ROBO1	6091	hgsc.bcm.edu	37	chr3	79174651	79174651	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gttatcagaggtggggattgGcgtcccgtggtcgttccccc	15	11	1	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr3:79174651G>A	ENST00000464233.1	-	3	240	c.127C>T	c.(127-129)Cca>Tca	p.P43S		NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	43					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GTGGGGATTGGCGTCCCGTGG	0.507																																					p.P43S		Atlas-SNP	.											.	ROBO1	833	.	0			c.C127T						.						146	143	144					3																	79174651		2006	4172	6178	SO:0001583	missense	6091	exon3			GGATTGGCGTCCC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.127C>T	chr3.hg19:g.79174651G>A	ENSP00000420321:p.Pro43Ser	269.0	0.0		334.0	149.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.971632	0.34754	.	.	ENSG00000169855	ENST00000464233;ENST00000398414	T	0.59502	0.26	5.43	5.43	0.79202	.	0.357864	0.26159	N	0.025988	T	0.35740	0.0942	N	0.08118	0	0.80722	D	1	B	0.30793	0.295	B	0.26310	0.068	T	0.25012	-1.0144	9	.	.	.	.	15.1257	0.72481	0.0:0.141:0.859:0.0	.	43	Q9Y6N7	ROBO1_HUMAN	S	43	ENSP00000420321:P43S	.	P	-	1	0	ROBO1	79257341	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	5.108000	0.64609	2.699000	0.92147	0.655000	0.94253	CCA	.	.		0.507	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	79174651	G	A	79174651	3	1	135	1	0	0	0	0	1	0	0	0	13528	1203	42	3	5016	3	ROBO1	3	79174651	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10		79174651	118847779	19	21626										
AGPAT9	84803	hgsc.bcm.edu	37	chr4	84457903	84457903	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gatctacatgaagatcctagTgaaaactttagaggtgagtg	11	5	1	5	rs150911365		TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr4:84457903T>A	ENST00000395226.2	+	2	346	c.128T>A	c.(127-129)gTg>gAg	p.V43E	AGPAT9_ENST00000264409.4_Missense_Mutation_p.V43E	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	43					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				AAGATCCTAGTGAAAACTTTA	0.572																																					p.V43E		Atlas-SNP	.											.	AGPAT9	41	.	0			c.T128A						.						51	48	49					4																	84457903		2203	4300	6503	SO:0001583	missense	84803	exon2			TCCTAGTGAAAAC	AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	28157	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, theta"	610958	"1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.128T>A	chr4.hg19:g.84457903T>A	ENSP00000378651:p.Val43Glu	47.0	0.0		36.0	28.0	NM_001256421	Q68CJ4|Q6GPI6|Q96NA3	Missense_Mutation	SNP	ENST00000395226.2	hg19	CCDS3606.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.091865	0.36952	.	.	ENSG00000138678	ENST00000395226;ENST00000264409	T;T	0.49720	0.77;0.77	4.68	4.68	0.58851	.	0.079233	0.49916	D	0.000130	T	0.42653	0.1212	L	0.58101	1.795	0.50632	D	0.999885	P	0.37423	0.594	B	0.33750	0.169	T	0.39231	-0.9624	10	0.35671	T	0.21	-11.887	13.1799	0.59649	0.0:0.0:0.0:1.0	.	43	Q53EU6	GPAT3_HUMAN	E	43	ENSP00000378651:V43E;ENSP00000264409:V43E	ENSP00000264409:V43E	V	+	2	0	AGPAT9	84676927	1.000000	0.71417	1.000000	0.80357	0.050000	0.14768	5.148000	0.64857	1.760000	0.52011	0.374000	0.22700	GTG	.	T|1.000;C|0.000		0.572	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717		A	84457903	T	A	84457903	3	1	135	1	0	0	0	0	1	0	0	0	392	1696	59	4	130	4	AGPAT9	4	84457903	Missense_Mutation	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10		84457903	106696373	20	21627										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85724505	85724505	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	catggcaagcatggctccagGatgaatgatgactgcatcag	12	9	1	3			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr4:85724505G>A	ENST00000295888.4	-	16	2952	c.2545C>T	c.(2545-2547)Cct>Tct	p.P849S	WDFY3_ENST00000512267.1_5'UTR|WDFY3-AS1_ENST00000510449.1_RNA|WDFY3_ENST00000322366.6_Missense_Mutation_p.P849S	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	849					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		ATGGCTCCAGGATGAATGATG	0.473																																					p.P849S		Atlas-SNP	.											.	WDFY3	314	.	0			c.C2545T						.						84	77	79					4																	85724505		2203	4300	6503	SO:0001583	missense	23001	exon16			CTCCAGGATGAAT	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.2545C>T	chr4.hg19:g.85724505G>A	ENSP00000295888:p.Pro849Ser	345.0	0.0		233.0	170.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.789935	0.90367	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.39406	1.08;1.08	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.52306	0.1726	M	0.66378	2.025	0.80722	D	1	D	0.54772	0.968	P	0.46885	0.53	T	0.56450	-0.7977	10	0.62326	D	0.03	.	19.9403	0.97159	0.0:0.0:1.0:0.0	.	849	Q8IZQ1	WDFY3_HUMAN	S	849	ENSP00000318466:P849S;ENSP00000295888:P849S	ENSP00000295888:P849S	P	-	1	0	WDFY3	85943529	1.000000	0.71417	0.999000	0.59377	0.865000	0.49528	7.344000	0.79328	2.712000	0.92718	0.650000	0.86243	CCT	.	.		0.473	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85724505	G	A	85724505	3	1	135	1	0	0	0	0	1	0	0	0	17285	1174	41	3	8247	3	WDFY3	4	85724505	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	1266602	85724505	105429771	21	21628										
WDR17	116966	hgsc.bcm.edu	37	chr4	177058704	177058704	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tattgctgggggaacttcccGaaatggtgcttttatttgga	12	6	0	0	rs200199041		TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr4:177058704G>A	ENST00000280190.4	+	10	1529	c.1373G>A	c.(1372-1374)cGa>cAa	p.R458Q	WDR17_ENST00000393643.2_Missense_Mutation_p.R434Q|WDR17_ENST00000507824.2_Missense_Mutation_p.R441Q|WDR17_ENST00000508596.1_Missense_Mutation_p.R434Q			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	458										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		GGAACTTCCCGAAATGGTGCT	0.279																																					p.R458Q		Atlas-SNP	.											.	WDR17	198	.	0			c.G1373A						.	G	GLN/ARG,GLN/ARG	0,4404		0,0,2202	76	80	79		1301,1373	2.2	1	4		79	1,8593	1.2+/-3.3	0,1,4296	yes	missense,missense	WDR17	NM_181265.3,NM_170710.4	43,43	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	434/1284,458/1323	177058704	1,12997	2202	4297	6499	SO:0001583	missense	116966	exon10			CTTCCCGAAATGG	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.1373G>A	chr4.hg19:g.177058704G>A	ENSP00000280190:p.Arg458Gln	61.0	0.0		32.0	26.0	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	hg19	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.448909	0.43531	0.0	1.16E-4	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.04758	3.57;3.56;3.57	5.08	2.22	0.28083	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.216830	0.36268	N	0.002682	T	0.03434	0.0099	N	0.24115	0.695	0.39331	D	0.96541	B;B	0.20368	0.011;0.044	B;B	0.12156	0.007;0.007	T	0.49679	-0.8914	10	0.32370	T	0.25	-3.5877	8.1747	0.31275	0.3317:0.0:0.6683:0.0	.	434;458	E7EQX0;Q8IZU2	.;WDR17_HUMAN	Q	434;434;458;441	ENSP00000422763:R434Q;ENSP00000377258:R434Q;ENSP00000280190:R458Q	ENSP00000280190:R458Q	R	+	2	0	WDR17	177295698	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	1.545000	0.36169	0.193000	0.20303	-0.140000	0.14226	CGA	.	.		0.279	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			A	177058704	G	A	177058704	3	1	135	1	0	0	0	0	1	0	0	0	17292	1058	37	1	1407	1	WDR17	4	177058704	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	91334199	177058704	14095572	22	21629										
ADCY2	108	hgsc.bcm.edu	37	chr5	7706898	7706910	+	Frame_Shift_Del	DEL	TGGGCGTGCATTC	TGGGCGTGCATTC	-													0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	agttgatatcaacatgcgcgTgggcgtgcattctgggaatg					rs35209447	byFrequency	TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	TGGGCGTGCATTC	TGGGCGTGCATTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr5:7706898_7706910delTGGGCGTGCATTC	ENST00000338316.4	+	8	1240_1252	c.1151_1163delTGGGCGTGCATTC	c.(1150-1164)gtgggcgtgcattctfs	p.VGVHS384fs	ADCY2_ENST00000537121.1_Frame_Shift_Del_p.VGVHS204fs|RP11-711G10.1_ENST00000514105.2_RNA	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	384					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.G385D(2)|p.V384V(1)|p.V386A(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						AACATGCGCGTGGGCGTGCATTCTGGGAATGTC	0.479																																					p.384_388del		Atlas-Indel,Pindel	.											.	ADCY2	337	.	4	Substitution - Missense(3)|Substitution - coding silent(1)	lung(2)|prostate(1)|large_intestine(1)	c.1150_1162del						.																																			SO:0001589	frameshift_variant	108	exon8			.	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1151_1163delTGGGCGTGCATTC	chr5.hg19:g.7706898_7706910delTGGGCGTGCATTC	ENSP00000342952:p.Val384fs	227.0	0.0		258.0	59.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Frame_Shift_Del	DEL	ENST00000338316.4	hg19	CCDS3872.2																																																																																			.	.		0.479	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		-	7706910	TGGGCGTGCATTC	-	7706898	7	5	135	1	0	1	0	1	0	0	0	0	294	1696	59	0	1181	0	ADCY2	5	7706898	Frame_Shift_Del	DEL	TGGGCGTGCATTC	TCGA-DD-A4NN-01A-11D-A28X-10		7706898	173208362	23	21630										
MARCH6	10299	hgsc.bcm.edu	37	chr5	10391780	10391780	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	aggcagaagaggaggaggagGacaatgaggaggaagatgac	19	3	0	5			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr5:10391780G>C	ENST00000274140.5	+	7	835	c.703G>C	c.(703-705)Gac>Cac	p.D235H	MARCH6_ENST00000449913.2_Missense_Mutation_p.D187H|MARCH6_ENST00000503788.1_Missense_Mutation_p.D130H	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	235					protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						ggaggaggaggacaatgagga	0.557																																					p.D235H		Atlas-SNP	.											.,1	MARCH6	89	.	0			c.G703C						.						129	97	108					5																	10391780		2203	4300	6503	SO:0001583	missense	10299	exon7			GAGGAGGACAATG	AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	30550	protein-coding gene	gene with protein product		613297	"membrane-associated ring finger (C3HC4) 6"			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.703G>C	chr5.hg19:g.10391780G>C	ENSP00000274140:p.Asp235His	168.0	0.0		246.0	55.0	NM_005885	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	Missense_Mutation	SNP	ENST00000274140.5	hg19	CCDS34135.1	.	.	.	.	.	.	.	.	.	.	G	19.50	3.838704	0.71373	.	.	ENSG00000145495	ENST00000449913;ENST00000503788;ENST00000274140	T;T;T	0.46451	1.89;0.87;1.91	6.02	6.02	0.97574	.	0.307377	0.38381	N	0.001714	T	0.54191	0.1843	M	0.62723	1.935	0.80722	D	1	P;P;B	0.41748	0.526;0.761;0.291	P;B;B	0.47673	0.554;0.365;0.058	T	0.48990	-0.8985	10	0.48119	T	0.1	-4.0438	20.1511	0.98086	0.0:0.0:1.0:0.0	.	130;187;235	B4DKJ2;B4DT33;O60337	.;.;MARH6_HUMAN	H	187;130;235	ENSP00000414643:D187H;ENSP00000425930:D130H;ENSP00000274140:D235H	ENSP00000274140:D235H	D	+	1	0	MARCH6	10444780	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.135000	0.71696	2.865000	0.98341	0.655000	0.94253	GAC	.	.		0.557	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2	NM_005885		C	10391780	G	C	10391780	3	2	135	1	0	0	0	0	1	0	0	0	9314	1174	41	4	729	4	MARCH6	5	10391780	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	2684882	10391780	170523480	24	21631										
SV2C	22987	hgsc.bcm.edu	37	chr5	75427868	75427868	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ggagtatcagggcatccccaGtatgaaccaagcgaaggaca	12	10	1	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr5:75427868G>T	ENST00000502798.2	+	2	735	c.293G>T	c.(292-294)aGt>aTt	p.S98I	SV2C_ENST00000322285.7_Missense_Mutation_p.S98I	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	98					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		GGCATCCCCAGTATGAACCAA	0.547																																					p.S98I		Atlas-SNP	.											.	SV2C	97	.	0			c.G293T						.						78	82	81					5																	75427868		2110	4255	6365	SO:0001583	missense	22987	exon2			TCCCCAGTATGAA	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.293G>T	chr5.hg19:g.75427868G>T	ENSP00000423541:p.Ser98Ile	151.0	0.0		192.0	80.0	NM_014979	Q496K1|Q9UPU8	Missense_Mutation	SNP	ENST00000502798.2	hg19	CCDS43331.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.917387	0.33815	.	.	ENSG00000122012	ENST00000502798;ENST00000322285	T;T	0.30448	1.53;1.53	5.76	1.29	0.21616	Major facilitator superfamily domain, general substrate transporter (1);	0.396707	0.30630	N	0.009208	T	0.21347	0.0514	L	0.36672	1.1	0.22240	N	0.99927	B	0.18013	0.025	B	0.21708	0.036	T	0.18335	-1.0340	10	0.56958	D	0.05	-6.8884	6.6107	0.22749	0.2254:0.27:0.5047:0.0	.	98	Q496J9	SV2C_HUMAN	I	98	ENSP00000423541:S98I;ENSP00000316983:S98I	ENSP00000316983:S98I	S	+	2	0	SV2C	75463624	0.000000	0.05858	0.310000	0.25168	0.873000	0.50193	0.566000	0.23593	0.319000	0.23209	0.655000	0.94253	AGT	.	.		0.547	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4			T	75427868	G	T	75427868	3	4	135	1	0	0	0	0	1	0	0	0	15434	1029	36	3	295	3	SV2C	5	75427868	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	65036088	75427868	105487392	25	21632										
CXXC5	51523	hgsc.bcm.edu	37	chr5	139060853	139060853	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	agtaccccatgcagggagagCtggcctctgccatcagctcc	11	15	2	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr5:139060853C>G	ENST00000302517.3	+	2	1459	c.745C>G	c.(745-747)Ctg>Gtg	p.L249V	CXXC5_ENST00000511048.1_Missense_Mutation_p.L249V|CXXC5_ENST00000515038.1_3'UTR	NM_016463.7	NP_057547.5	Q7LFL8	CXXC5_HUMAN	CXXC finger protein 5	249					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGGGAGAGCTGGCCTCTGC	0.647																																					p.L249V		Atlas-SNP	.											.	CXXC5	27	.	0			c.C745G						.						31	37	35					5																	139060853		2065	4220	6285	SO:0001583	missense	51523	exon2			GGAGAGCTGGCCT	AK024338	CCDS43370.1	5q31.3	2014-02-18	2011-12-01						26943	protein-coding gene	gene with protein product	"retinoid-inducible nuclear factor", "WT1-induced Inhibitor of Dishevelled"	612752				11042152, 19001364, 19182210, 20220130	Standard	NM_016463		Approved	HSPC195, RINF, WID	uc010jfg.1	Q7LFL8		ENST00000302517.3:c.745C>G	chr5.hg19:g.139060853C>G	ENSP00000302543:p.Leu249Val	99.0	0.0		115.0	8.0	NM_016463	B3KND0|C8CBA8|Q8TB79|Q9NV51|Q9P0S8	Missense_Mutation	SNP	ENST00000302517.3	hg19	CCDS43370.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.154667	0.57259	.	.	ENSG00000171604	ENST00000302517;ENST00000511048	.	.	.	5.04	5.04	0.67666	.	0.000000	0.64402	D	0.000002	T	0.33644	0.0870	N	0.24115	0.695	0.51012	D	0.999901	P	0.47841	0.901	P	0.44696	0.458	T	0.05257	-1.0896	9	0.27082	T	0.32	-9.0229	7.7398	0.28835	0.0:0.8536:0.0:0.1464	.	249	Q7LFL8	CXXC5_HUMAN	V	249	.	ENSP00000302543:L249V	L	+	1	2	CXXC5	139041037	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.821000	0.48065	2.343000	0.79666	0.505000	0.49811	CTG	.	.		0.647	CXXC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372744.1	NM_016463		G	139060853	C	G	139060853	3	3	135	1	0	0	0	0	1	0	0	0	4101	796	28	4	747	4	CXXC5	5	139060853	Missense_Mutation	SNP	C	TCGA-DD-A4NN-01A-11D-A28X-10	63632985	139060853	41854407	26	21633										
DDX41	51428	hgsc.bcm.edu	37	chr5	176940709	176940709	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gaagtaggagaagatggtacGgatgtcaccctcgaagccca	13	9	1	2			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr5:176940709G>T	ENST00000507955.1	-	10	1598	c.1075C>A	c.(1075-1077)Cgt>Agt	p.R359S	DDX41_ENST00000506965.1_5'Flank	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	359	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				apoptotic process (GO:0006915)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)|RNA processing (GO:0006396)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)					all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			AAGATGGTACGGATGTCACCC	0.632																																					p.R359S		Atlas-SNP	.											.	DDX41	49	.	0			c.C1075A						.						108	87	94					5																	176940709		2203	4300	6503	SO:0001583	missense	51428	exon10			TGGTACGGATGTC	AF195417	CCDS4427.1	5q35.3	2008-02-05			ENSG00000183258	ENSG00000183258		"DEAD-boxes"	18674	protein-coding gene	gene with protein product		608170				10607561	Standard	NM_016222		Approved	ABS, MGC8828	uc003mho.3	Q9UJV9	OTTHUMG00000130858	ENST00000507955.1:c.1075C>A	chr5.hg19:g.176940709G>T	ENSP00000422753:p.Arg359Ser	183.0	0.0		212.0	105.0	NM_016222	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Missense_Mutation	SNP	ENST00000507955.1	hg19	CCDS4427.1	.	.	.	.	.	.	.	.	.	.	G	13.69	2.312097	0.40895	.	.	ENSG00000183258	ENST00000330503;ENST00000507955	T;T	0.15256	2.44;2.44	5.8	4.9	0.64082	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.056560	0.64402	D	0.000002	T	0.28034	0.0691	L	0.50919	1.6	0.80722	D	1	B;B	0.28933	0.228;0.064	P;B	0.44359	0.447;0.131	T	0.07328	-1.0778	10	0.72032	D	0.01	-11.9076	13.9359	0.64026	0.0:0.0:0.7267:0.2733	.	233;359	B3KRK2;Q9UJV9	.;DDX41_HUMAN	S	377;359	ENSP00000330349:R377S;ENSP00000422753:R359S	ENSP00000330349:R377S	R	-	1	0	DDX41	176873315	1.000000	0.71417	1.000000	0.80357	0.167000	0.22549	2.483000	0.45233	2.749000	0.94314	0.655000	0.94253	CGT	.	.		0.632	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222		T	176940709	G	T	176940709	3	4	135	1	0	0	0	0	1	0	0	0	4363	1116	39	1	825	1	DDX41	5	176940709	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	37879856	176940709	3974551	27	21634										
OR10C1	442194	hgsc.bcm.edu	37	chr6	29408254	29408254	+	Frame_Shift_Del	DEL	G	G	-													0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tgggcctgtggggtgctggtGgggctgggccacaccccttt							TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr6:29408254delG	ENST00000444197.2	+	1	1172	c.462delG	c.(460-462)gtgfs	p.V154fs	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GGGTGCTGGTGGGGCTGGGCC	0.617																																					p.V154fs		Atlas-Indel,Pindel	.											.	OR10C1	58	.	0			c.461delT						.						96	109	104					6																	29408254		1510	2709	4219	SO:0001589	frameshift_variant	442194	exon1			.		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"GPCR / Class A : Olfactory receptors"	8165	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily C, member 2", "olfactory receptor, family 10, subfamily C, member 1"	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.462delG	chr6.hg19:g.29408254delG	ENSP00000419119:p.Val154fs	98.0	0.0		172.0	52.0	NM_013941	Q5SUN7|Q96R18	Frame_Shift_Del	DEL	ENST00000444197.2	hg19	CCDS34364.1																																																																																			.	.		0.617	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			-	29408254	G	-	29408254	7	5	135	1	0	1	0	1	0	0	0	0	10907	1335	47	0	464	0	OR10C1	6	29408254	Frame_Shift_Del	DEL	G	TCGA-DD-A4NN-01A-11D-A28X-10		29408254	141706813	28	21635										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136589436	136589436	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gagaagaaggtgatgctgaaGaggatgaagatcgagaatga	16	2	0	9			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr6:136589436G>A	ENST00000531224.1	-	10	2513	c.2261C>T	c.(2260-2262)tCt>tTt	p.S754F	BCLAF1_ENST00000353331.4_Missense_Mutation_p.S752F|BCLAF1_ENST00000527759.1_Missense_Mutation_p.S752F|BCLAF1_ENST00000031135.9_5'UTR|BCLAF1_ENST00000392348.2_Missense_Mutation_p.S752F|BCLAF1_ENST00000530767.1_Missense_Mutation_p.S581F|BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000527536.1_Missense_Mutation_p.S754F	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	754	Poly-Ser.				apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		TGATGCTGAAGAGGATGAAGA	0.338																																					p.S754F	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.C2261T						.						124	108	114					6																	136589436		2203	4300	6503	SO:0001583	missense	9774	exon10			GCTGAAGAGGATG	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.2261C>T	chr6.hg19:g.136589436G>A	ENSP00000435210:p.Ser754Phe	106.0	0.0		94.0	11.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.238426	0.79800	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348	T;T;T;T;T;T	0.12569	2.67;2.67;2.67;2.67;2.67;2.67	4.87	4.87	0.63330	.	0.000000	0.56097	D	0.000028	T	0.23492	0.0568	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.89917	0.987;1.0;0.994;0.987;0.987	P;D;P;P;P	0.74023	0.775;0.982;0.865;0.775;0.775	T	0.00948	-1.1504	10	0.31617	T	0.26	-6.0919	18.3705	0.90405	0.0:0.0:1.0:0.0	.	752;82;752;754;581	Q9NYF8-2;B7Z8J9;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;.;BCLF1_HUMAN;.	F	754;752;754;581;752;752	ENSP00000435210:S754F;ENSP00000229446:S752F;ENSP00000435441:S754F;ENSP00000436501:S581F;ENSP00000434826:S752F;ENSP00000376159:S752F	ENSP00000229446:S752F	S	-	2	0	BCLAF1	136631129	1.000000	0.71417	0.999000	0.59377	0.936000	0.57629	7.615000	0.83006	2.431000	0.82371	0.484000	0.47621	TCT	.	.		0.338	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		A	136589436	G	A	136589436	3	1	135	1	0	0	0	0	1	0	0	0	1383	942	33	3	517	3	BCLAF1	6	136589436	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	107181182	136589436	34525631	29	21636										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11633070	11633070	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ctgaccactcggaaacctggCactctttggtgatcacacag	9	13	2	2	rs558393471		TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr7:11633070C>T	ENST00000423059.4	-	3	1333	c.1082G>A	c.(1081-1083)tGc>tAc	p.C361Y		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	361	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		GGAAACCTGGCACTCTTTGGT	0.507										HNSCC(18;0.044)																											p.C361Y		Atlas-SNP	.											.	THSD7A	219	.	0			c.G1082A						.						110	108	109					7																	11633070		1936	4141	6077	SO:0001583	missense	221981	exon3			ACCTGGCACTCTT		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.1082G>A	chr7.hg19:g.11633070C>T	ENSP00000406482:p.Cys361Tyr	128.0	0.0		136.0	61.0	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	hg19	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.571129	0.86542	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.22336	1.96	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.64046	0.2563	H	0.97587	4.035	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77316	-0.2633	10	0.52906	T	0.07	.	18.8995	0.92437	0.0:1.0:0.0:0.0	.	361	Q9UPZ6	THS7A_HUMAN	Y	361	ENSP00000406482:C361Y	ENSP00000262042:C361Y	C	-	2	0	THSD7A	11599595	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.814000	0.86154	2.458000	0.83093	0.655000	0.94253	TGC	.	.		0.507	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		T	11633070	C	T	11633070	3	4	135	1	0	0	0	0	1	0	0	0	15894	710	25	3	3991	3	THSD7A	7	11633070	Missense_Mutation	SNP	C	TCGA-DD-A4NN-01A-11D-A28X-10		11633070	147505593	30	21637										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47876604	47876604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	acacggtgaggcgcggcgtgTgcaggtagcggctggaggag	21	8	0	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr7:47876604T>C	ENST00000289672.2	-	37	5908	c.5858A>G	c.(5857-5859)cAc>cGc	p.H1953R		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1953					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GCGCGGCGTGTGCAGGTAGCG	0.587																																					p.H1953R		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A5858G						.						63	56	58					7																	47876604		2203	4300	6503	SO:0001583	missense	168507	exon37			GGCGTGTGCAGGT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5858A>G	chr7.hg19:g.47876604T>C	ENSP00000289672:p.His1953Arg	291.0	0.0		373.0	84.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	7.390	0.630661	0.14322	.	.	ENSG00000158683	ENST00000289672	T	0.09817	2.94	5.1	1.38	0.22167	.	0.352176	0.24945	N	0.034351	T	0.03136	0.0092	N	0.11560	0.145	0.28076	N	0.932385	P	0.40660	0.726	B	0.33890	0.172	T	0.35968	-0.9767	10	0.02654	T	1	-23.5721	5.0943	0.14725	0.0:0.1689:0.1544:0.6767	.	1953	Q8TDX9	PK1L1_HUMAN	R	1953	ENSP00000289672:H1953R	ENSP00000289672:H1953R	H	-	2	0	PKD1L1	47843129	1.000000	0.71417	0.051000	0.19133	0.776000	0.43924	1.101000	0.31037	-0.004000	0.14419	0.533000	0.62120	CAC	.	.		0.587	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		C	47876604	T	C	47876604	3	2	135	1	0	0	0	0	1	0	0	0	11973	1696	59	2	2775	2	PKD1L1	7	47876604	Missense_Mutation	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10	36243534	47876604	111262059	31	21638										
POM121L12	285877	hgsc.bcm.edu	37	chr7	53103948	53103948	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	aagcgctaggttcgacgggcCgttgtggttcgaggtctcag	16	9	1	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr7:53103948C>G	ENST00000408890.4	+	1	600	c.584C>G	c.(583-585)cCg>cGg	p.P195R		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	195										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						TTCGACGGGCCGTTGTGGTTC	0.687																																					p.P195R		Atlas-SNP	.											.	POM121L12	146	.	0			c.C584G						.						48	56	53					7																	53103948		1974	4144	6118	SO:0001583	missense	285877	exon1			ACGGGCCGTTGTG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.584C>G	chr7.hg19:g.53103948C>G	ENSP00000386133:p.Pro195Arg	43.0	0.0		71.0	33.0	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	hg19	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.533585	0.27387	.	.	ENSG00000221900	ENST00000408890	T	0.12984	2.63	2.21	0.295	0.15752	.	.	.	.	.	T	0.22627	0.0546	L	0.46157	1.445	0.09310	N	1	D	0.76494	0.999	D	0.79784	0.993	T	0.12167	-1.0558	9	0.54805	T	0.06	.	2.6712	0.05067	0.2815:0.5508:0.0:0.1677	.	195	Q8N7R1	P1L12_HUMAN	R	195	ENSP00000386133:P195R	ENSP00000386133:P195R	P	+	2	0	POM121L12	53071442	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	0.515000	0.22801	0.057000	0.16193	0.561000	0.74099	CCG	.	.		0.687	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		G	53103948	C	G	53103948	3	3	135	1	0	0	0	0	1	0	0	0	12250	652	23	4	586	4	POM121L12	7	53103948	Missense_Mutation	SNP	C	TCGA-DD-A4NN-01A-11D-A28X-10	5227344	53103948	106034715	32	21639										
JHDM1D	80853	hgsc.bcm.edu	37	chr7	139876582	139876582	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ttgcagatatcgcactcgatCatgaagcggttcacgtcgta	10	10	2	2			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr7:139876582C>G	ENST00000397560.2	-	1	253	c.156G>C	c.(154-156)atG>atC	p.M52I	JHDM1D_ENST00000006967.5_Missense_Mutation_p.M52I|JHDM1D-AS1_ENST00000566699.1_RNA	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		52					histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					CGCACTCGATCATGAAGCGGT	0.711																																					p.M52I		Atlas-SNP	.											.	JHDM1D	54	.	0			c.G156C						.						20	27	25					7																	139876582		2184	4283	6467	SO:0001583	missense	80853	exon1			CTCGATCATGAAG																												ENST00000397560.2:c.156G>C	chr7.hg19:g.139876582C>G	ENSP00000380692:p.Met52Ile	49.0	0.0		75.0	29.0	NM_030647	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Missense_Mutation	SNP	ENST00000397560.2	hg19	CCDS43658.1	.	.	.	.	.	.	.	.	.	.	c	20.6	4.013461	0.75161	.	.	ENSG00000006459	ENST00000397560;ENST00000006967	T;T	0.11495	2.77;2.77	2.14	1.14	0.20703	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	U	0.000000	T	0.45935	0.1367	H	0.99325	4.515	0.48830	D	0.999716	D	0.64830	0.994	D	0.77004	0.989	T	0.51044	-0.8755	10	0.56958	D	0.05	.	8.1229	0.30982	0.2432:0.7568:0.0:0.0	.	52	Q6ZMT4	KDM7_HUMAN	I	52	ENSP00000380692:M52I;ENSP00000006967:M52I	ENSP00000006967:M52I	M	-	3	0	JHDM1D	139523051	1.000000	0.71417	0.886000	0.34754	0.958000	0.62258	5.473000	0.66774	0.040000	0.15660	0.282000	0.19409	ATG	.	.		0.711	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1			G	139876582	C	G	139876582	3	3	135	1	0	0	0	0	1	0	0	0	7957	826	29	4	2749	4	JHDM1D	7	139876582	Missense_Mutation	SNP	C	TCGA-DD-A4NN-01A-11D-A28X-10	86772634	139876582	19262081	33	21640										
MYOM2	9172	hgsc.bcm.edu	37	chr8	2054129	2054129	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gcgtctcagttcacctggtgTaaatcctacgaggagatttc	10	10	2	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr8:2054129T>C	ENST00000262113.4	+	22	2973	c.2832T>C	c.(2830-2832)tgT>tgC	p.C944C	MYOM2_ENST00000523438.1_Silent_p.C369C	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	944	Ig-like C2-type 3.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		TCACCTGGTGTAAATCCTACG	0.473																																					p.C944C		Atlas-SNP	.											.	MYOM2	251	.	0			c.T2832C						.						127	123	124					8																	2054129		2203	4300	6503	SO:0001819	synonymous_variant	9172	exon22			CTGGTGTAAATCC		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.2832T>C	chr8.hg19:g.2054129T>C		128.0	0.0		172.0	105.0	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	hg19	CCDS5957.1																																																																																			.	.		0.473	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		C	2054129	T	C	2054129	2	2	135	1	0	0	0	0	0	0	0	1	10101	1644	57	2		2	MYOM2	8	2054129	Silent	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10		2054129	144309893	34	21641										
FGF20	26281	hgsc.bcm.edu	37	chr8	16850701	16850701	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gcgccatctcttggagttccGtctttgttaagtgccacaaa	9	11	2	0	rs376980441		TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr8:16850701G>A	ENST00000180166.5	-	3	664	c.516C>T	c.(514-516)gaC>gaT	p.D172D		NM_019851.2	NP_062825.1	Q9NP95	FGF20_HUMAN	fibroblast growth factor 20	172					cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of cardiac muscle cell proliferation (GO:0060043)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	11				Colorectal(111;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		TTGGAGTTCCGTCTTTGTTAA	0.428																																					p.D172D		Atlas-SNP	.											.	FGF20	16	.	0			c.C516T						.	G		1,4405	2.1+/-5.4	0,1,2202	182	162	169		516	-2.2	1	8		169	0,8600		0,0,4300	no	coding-synonymous	FGF20	NM_019851.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		172/212	16850701	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	26281	exon3			AGTTCCGTCTTTG	AB030648	CCDS5998.1	8p22	2008-05-15			ENSG00000078579	ENSG00000078579			3677	protein-coding gene	gene with protein product		605558				10913340	Standard	NM_019851		Approved		uc003wxc.1	Q9NP95	OTTHUMG00000096964	ENST00000180166.5:c.516C>T	chr8.hg19:g.16850701G>A		114.0	0.0		151.0	51.0	NM_019851	B2RPH5	Silent	SNP	ENST00000180166.5	hg19	CCDS5998.1	.	.	.	.	.	.	.	.	.	.	G	6.030	0.373895	0.11409	2.27E-4	0.0	ENSG00000078579	ENST00000519941	.	.	.	5.85	-2.23	0.06930	.	.	.	.	.	T	0.62913	0.2467	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59799	-0.7386	4	.	.	.	.	12.901	0.58125	0.5672:0.0:0.4328:0.0	.	.	.	.	W	74	.	.	R	-	1	2	FGF20	16895072	0.614000	0.27017	0.979000	0.43373	0.791000	0.44710	0.002000	0.13061	-0.536000	0.06298	-0.302000	0.09304	CGG	.	.		0.428	FGF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214030.1			A	16850701	G	A	16850701	2	1	135	1	0	0	0	0	0	0	0	1	5857	1136	40	1		1	FGF20	8	16850701	Silent	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	14796572	16850701	129513321	35	21642										
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48309166	48309166	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	cccaggactccagaaaattcAgcaaagaagaagcttttaag	8	9	1	3			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr8:48309166A>T	ENST00000297423.4	+	6	1140	c.756A>T	c.(754-756)tcA>tcT	p.S252S	SPIDR_ENST00000518074.1_Silent_p.S192S|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Silent_p.S182S	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	252	Necessary for interaction with RAD51.				cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)		p.S252S(1)									CAGAAAATTCAGCAAAGAAGA	0.313																																					p.S252S		Atlas-SNP	.											KIAA0146,NS,carcinoma,0,1	KIAA0146	64	.	1	Substitution - coding silent(1)	lung(1)	c.A756T						.						134	134	134					8																	48309166		1799	4069	5868	SO:0001819	synonymous_variant	23514	exon6			AAATTCAGCAAAG	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"KIAA0146"	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.756A>T	chr8.hg19:g.48309166A>T		100.0	0.0		92.0	38.0	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Silent	SNP	ENST00000297423.4	hg19	CCDS43737.1																																																																																			.	.		0.313	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		T	48309166	A	T	48309166	2	4	135	1	0	0	0	0	0	0	0	1	8166	175	7	4		4	KIAA0146	8	48309166	Silent	SNP	A	TCGA-DD-A4NN-01A-11D-A28X-10	31458465	48309166	98054856	36	21643										
RECQL4	9684	hgsc.bcm.edu	37	chr8	145741755	145741755	+	5'Flank	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gctgctgggctgggggctccCcacacggatgctgacttctt	14	13	1	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr8:145741755C>G	ENST00000292524.1	+	0	0				RECQL4_ENST00000532237.1_5'UTR|LRRC14_ENST00000529022.1_5'Flank|CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000428558.2_Missense_Mutation_p.G250R	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TGGGGGCTCCCCACACGGATG	0.642																																					p.G250R		Atlas-SNP	.											.	RECQL4	75	.	0			c.G748C						.						18	20	19					8																	145741755		2016	4173	6189	SO:0001631	upstream_gene_variant	9401	exon5			GGCTCCCCACACG	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		chr8.hg19:g.145741755C>G	Exception_encountered	22.0	0.0		41.0	13.0	NM_004260	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1																																																																																			.	.		0.642	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		G	145741755	C	G	145741755	1	3	135	0	1	0	0	0	0	0	0	0	13217	623	22	4		4	RECQL4	8	145741755	5'Flank	SNP	C	TCGA-DD-A4NN-01A-11D-A28X-10	97432589	145741755	622267	37	21644										
CIZ1	25792	hgsc.bcm.edu	37	chr9	130941315	130941315	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tgcctcctgctgcagctgcaCctgccttgggccctgtgaat	11	15	0	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr9:130941315C>T	ENST00000393608.1	-	8	1373	c.1171G>A	c.(1171-1173)Gtg>Atg	p.V391M	CIZ1_ENST00000325721.8_Missense_Mutation_p.V362M|CIZ1_ENST00000372948.3_Intron|CIZ1_ENST00000372954.1_Intron|CIZ1_ENST00000541172.1_Missense_Mutation_p.V290M|CIZ1_ENST00000538431.1_Missense_Mutation_p.V391M|CIZ1_ENST00000372938.5_Missense_Mutation_p.V391M|CIZ1_ENST00000357558.5_Missense_Mutation_p.V391M|CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000277465.4_Missense_Mutation_p.V391M	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	391	Gln-rich.				maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						tgcagctgcacctgccttggg	0.642																																					p.V421M		Atlas-SNP	.											.	CIZ1	75	.	0			c.G1261A						.						61	50	54					9																	130941315		2203	4300	6503	SO:0001583	missense	25792	exon8			GCTGCACCTGCCT	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.1171G>A	chr9.hg19:g.130941315C>T	ENSP00000377232:p.Val391Met	110.0	0.0		174.0	81.0	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Missense_Mutation	SNP	ENST00000393608.1	hg19	CCDS6894.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.085356	0.36758	.	.	ENSG00000148337	ENST00000393608;ENST00000538431;ENST00000357558;ENST00000325721;ENST00000537314;ENST00000541172;ENST00000277465;ENST00000372941;ENST00000372938;ENST00000415526	T;T;T;T;T;T;T;T	0.34275	1.37;1.52;1.57;1.55;1.96;1.57;1.37;1.95	2.13	-0.265	0.12946	.	.	.	.	.	T	0.29126	0.0724	N	0.08118	0	0.09310	N	1	D;P;P;P;P	0.57571	0.98;0.662;0.842;0.599;0.94	P;B;B;B;B	0.61397	0.888;0.217;0.36;0.039;0.36	T	0.13335	-1.0513	9	0.48119	T	0.1	.	4.3	0.10920	0.4649:0.3243:0.2108:0.0	.	391;391;391;362;391	B7Z3U7;F5H2X7;Q9ULV3;Q9ULV3-2;Q5SYW2	.;.;CIZ1_HUMAN;.;.	M	391;391;391;362;358;290;391;367;391;313	ENSP00000377232:V391M;ENSP00000439244:V391M;ENSP00000350169:V391M;ENSP00000320374:V362M;ENSP00000445057:V290M;ENSP00000277465:V391M;ENSP00000362029:V391M;ENSP00000398011:V313M	ENSP00000277465:V391M	V	-	1	0	CIZ1	129981136	0.000000	0.05858	0.003000	0.11579	0.204000	0.24138	-0.972000	0.03802	-0.057000	0.13199	0.462000	0.41574	GTG	.	.		0.642	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		T	130941315	C	T	130941315	3	4	135	1	0	0	0	0	1	0	0	0	3443	507	18	3	1565	3	CIZ1	9	130941315	Missense_Mutation	SNP	C	TCGA-DD-A4NN-01A-11D-A28X-10		130941315	10272116	38	21645										
NAV2	89797	hgsc.bcm.edu	37	chr11	20083871	20083871	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	agttcatggatcctcactctCcttggtttccagcacatcgt	7	13	3	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr11:20083871C>T	ENST00000396087.3	+	22	5117	c.5018C>T	c.(5017-5019)tCc>tTc	p.S1673F	NAV2_ENST00000533917.1_Missense_Mutation_p.S681F|NAV2_ENST00000349880.4_Missense_Mutation_p.S1617F|NAV2_ENST00000396085.1_Missense_Mutation_p.S1617F|NAV2_ENST00000360655.4_Missense_Mutation_p.S1553F|NAV2_ENST00000540292.1_Missense_Mutation_p.S1604F|NAV2_ENST00000527559.2_Missense_Mutation_p.S1602F|NAV2_ENST00000311043.8_Missense_Mutation_p.S681F	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1673	Ser-rich.				glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TCCTCACTCTCCTTGGTTTCC	0.403																																					p.S1673F		Atlas-SNP	.											NAV2,NS,malignant_melanoma,0,1	NAV2	255	.	0			c.C5018T						.						123	115	117					11																	20083871		2203	4300	6503	SO:0001583	missense	89797	exon22			CACTCTCCTTGGT	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.5018C>T	chr11.hg19:g.20083871C>T	ENSP00000379396:p.Ser1673Phe	22.0	0.0		41.0	22.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	hg19	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.765749	0.90020	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000525322;ENST00000311043;ENST00000536595	T;T;T;T;T;T;T;T;T	0.61040	0.14;0.27;0.21;0.34;0.25;0.25;1.81;0.38;1.81	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000010	T	0.77191	0.4094	M	0.76170	2.325	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.998;0.996;0.997;1.0;0.999	T	0.76329	-0.2999	9	.	.	.	.	19.7522	0.96271	0.0:1.0:0.0:0.0	.	1617;1673;681;666;1617;1553	A7E2D6;Q8IVL1;Q8IVL1-5;E9PNV5;Q8IVL1-3;Q8IVL1-4	.;NAV2_HUMAN;.;.;.;.	F	1553;1617;1617;1673;1602;1604;681;666;681;666	ENSP00000353871:S1553F;ENSP00000379394:S1617F;ENSP00000309577:S1617F;ENSP00000379396:S1673F;ENSP00000435395:S1602F;ENSP00000443489:S1604F;ENSP00000437316:S681F;ENSP00000437136:S666F;ENSP00000312169:S681F	.	S	+	2	0	NAV2	20040447	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.041000	0.76558	2.730000	0.93505	0.644000	0.83932	TCC	.	.		0.403	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		T	20083871	C	T	20083871	3	4	135	1	0	0	0	0	1	0	0	0	10193	855	30	3	5037	3	NAV2	11	20083871	Missense_Mutation	SNP	C	TCGA-DD-A4NN-01A-11D-A28X-10		20083871	114922645	39	21646										
GAS2	2620	hgsc.bcm.edu	37	chr11	22777439	22777439	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tgcaaatgcccaaacaagttCtgtgtggagcggctctccca	10	12	2	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr11:22777439C>G	ENST00000454584.2	+	7	968	c.663C>G	c.(661-663)ttC>ttG	p.F221L	GAS2_ENST00000433790.1_Missense_Mutation_p.F221L|GAS2_ENST00000278187.3_Missense_Mutation_p.F221L	NM_001143830.1	NP_001137302.1	O43903	GAS2_HUMAN	growth arrest-specific 2	221	GAR. {ECO:0000255|PROSITE- ProRule:PRU00792}.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|regulation of cell shape (GO:0008360)	actin filament (GO:0005884)|cytosol (GO:0005829)|membrane (GO:0016020)				breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(4)|stomach(1)	24						CAAACAAGTTCTGTGTGGAGC	0.403																																					p.F221L		Atlas-SNP	.											.	GAS2	46	.	0			c.C663G						.						81	79	80					11																	22777439		2203	4300	6503	SO:0001583	missense	2620	exon7			CAAGTTCTGTGTG	BC040470	CCDS7858.1	11p14.3	2005-10-11			ENSG00000148935	ENSG00000148935			4167	protein-coding gene	gene with protein product		602835				9521882	Standard	NM_005256		Approved		uc001mqo.3	O43903	OTTHUMG00000166071	ENST00000454584.2:c.663C>G	chr11.hg19:g.22777439C>G	ENSP00000401145:p.Phe221Leu	95.0	0.0		137.0	38.0	NM_177553	B2R9C8|D3DQZ0|Q6ICV8|Q7Z3X8	Missense_Mutation	SNP	ENST00000454584.2	hg19	CCDS7858.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.201848	0.58234	.	.	ENSG00000148935	ENST00000454584;ENST00000278187;ENST00000433790	T;T;T	0.51817	0.69;0.69;0.69	5.61	4.69	0.59074	Growth-arrest-specific protein 2 domain (5);	0.000000	0.85682	D	0.000000	T	0.45276	0.1334	L	0.50993	1.605	0.54753	D	0.999985	B	0.14805	0.011	B	0.34180	0.177	T	0.39643	-0.9604	10	0.38643	T	0.18	-15.0215	9.6024	0.39612	0.0:0.7924:0.0:0.2076	.	221	O43903	GAS2_HUMAN	L	221	ENSP00000401145:F221L;ENSP00000278187:F221L;ENSP00000396708:F221L	ENSP00000278187:F221L	F	+	3	2	GAS2	22734015	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.065000	0.41442	2.639000	0.89480	0.655000	0.94253	TTC	.	.		0.403	GAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387717.1	NM_177553		G	22777439	C	G	22777439	3	3	135	1	0	0	0	0	1	0	0	0	6253	912	32	4	685	4	GAS2	11	22777439	Missense_Mutation	SNP	C	TCGA-DD-A4NN-01A-11D-A28X-10	2693568	22777439	112229077	40	21647										
LASS5	91012	hgsc.bcm.edu	37	chr12	50529577	50529577	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ctgaagatcacaaaaagggtGtcacagagccgctgatactt	10	9	2	4			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr12:50529577G>A	ENST00000317551.6	-	8	934	c.810C>T	c.(808-810)gaC>gaT	p.D270D	CERS5_ENST00000422340.2_Silent_p.D212D	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	270	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										CAAAAAGGGTGTCACAGAGCC	0.458																																					p.D270D		Atlas-SNP	.											.	.	.	.	0			c.C810T						.						123	114	117					12																	50529577		2203	4300	6503	SO:0001819	synonymous_variant	91012	exon8			AAGGGTGTCACAG		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"Homeoboxes / CERS class"	23749	protein-coding gene	gene with protein product		615335	"LAG1 longevity assurance homolog 5 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 5"	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.810C>T	chr12.hg19:g.50529577G>A		107.0	0.0		117.0	46.0	NM_147190	B4DV54	Silent	SNP	ENST00000317551.6	hg19	CCDS8801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.302|9.302	1.053327|1.053327	0.19907|0.19907	.|.	.|.	ENSG00000139624|ENSG00000139624	ENST00000550919|ENST00000550547;ENST00000547800	.|.	.|.	.|.	4.56|4.56	4.56|4.56	0.56223|0.56223	.|.	.|.	.|.	.|.	.|.	T|T	0.59729|0.59729	0.2215|0.2215	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.56757|0.56757	-0.7926|-0.7926	4|4	.|.	.|.	.|.	-8.7566|-8.7566	9.0655|9.0655	0.36460|0.36460	0.1345:0.0:0.8655:0.0|0.1345:0.0:0.8655:0.0	.|.	.|.	.|.	.|.	Y|I	40|72;174	.|.	.|.	H|T	-|-	1|2	0|0	CERS5|CERS5	48815844|48815844	0.992000|0.992000	0.36948|0.36948	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.157000|2.157000	0.42320|0.42320	2.515000|2.515000	0.84797|0.84797	0.655000|0.655000	0.94253|0.94253	CAC|ACA	.	.		0.458	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190		A	50529577	G	A	50529577	2	1	135	1	0	0	0	0	0	0	0	1	8651	1368	48	3		3	LASS5	12	50529577	Silent	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10		50529577	83322318	41	21648										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58125709	58125709	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ccaacattcggtgaggacggGagggaagaagagtagtcgct	16	7	0	3			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr12:58125709G>A	ENST00000547588.1	-	8	1835	c.1836C>T	c.(1834-1836)ctC>ctT	p.L612L	AGAP2_ENST00000257897.3_Silent_p.L276L	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	612					axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						GTGAGGACGGGAGGGAAGAAG	0.622																																					p.L612L		Atlas-SNP	.											.	AGAP2	167	.	0			c.C1836T						.						56	51	53					12																	58125709		2203	4300	6503	SO:0001819	synonymous_variant	116986	exon8			GGACGGGAGGGAA	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.1836C>T	chr12.hg19:g.58125709G>A		81.0	0.0		109.0	50.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Silent	SNP	ENST00000547588.1	hg19	CCDS44932.1	.	.	.	.	.	.	.	.	.	.	G	9.201	1.028449	0.19512	.	.	ENSG00000135439	ENST00000328568	.	.	.	4.63	-0.156	0.13391	.	.	.	.	.	T	0.41696	0.1170	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24693	-1.0153	4	.	.	.	.	1.6027	0.02678	0.3342:0.1377:0.3884:0.1397	.	.	.	.	S	476	.	.	P	-	1	0	AGAP2	56411976	0.996000	0.38824	0.996000	0.52242	0.962000	0.63368	0.351000	0.20096	-0.010000	0.14271	0.561000	0.74099	CCC	.	.		0.622	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		A	58125709	G	A	58125709	2	1	135	1	0	0	0	0	0	0	0	1	368	1161	41	3		3	AGAP2	12	58125709	Silent	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	7596132	58125709	75726186	42	21649										
EDNRB	1910	hgsc.bcm.edu	37	chr13	78474006	78474006	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tctcttaccttaaagcagttTttgaatcttttgctcaccaa	4	10	3	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr13:78474006T>C	ENST00000334286.5	-	6	1418	c.1182A>G	c.(1180-1182)aaA>aaG	p.K394K	EDNRB_ENST00000377211.4_Silent_p.K484K|EDNRB_ENST00000446573.1_Silent_p.K394K	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	394					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TAAAGCAGTTTTTGAATCTTT	0.348																																					p.K484K		Atlas-SNP	.											.	EDNRB	172	.	0			c.A1452G						.						83	78	79					13																	78474006		2203	4299	6502	SO:0001819	synonymous_variant	1910	exon7			GCAGTTTTTGAAT	L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.1182A>G	chr13.hg19:g.78474006T>C		34.0	0.0		20.0	16.0	NM_001201397	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Silent	SNP	ENST00000334286.5	hg19	CCDS9461.1																																																																																			.	.		0.348	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			C	78474006	T	C	78474006	2	2	135	1	0	0	0	0	0	0	0	1	4922	1838	64	2		2	EDNRB	13	78474006	Silent	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10		78474006	36695872	43	21650										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54914531	54914531	+	Frame_Shift_Del	DEL	C	C	-													0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ctgcttattttcaggtcgttCctccaaagatgccgtgggtc							TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr15:54914531delC	ENST00000260323.11	+	30	6113	c.6113delC	c.(6112-6114)tccfs	p.S2039fs	UNC13C_ENST00000545554.1_Frame_Shift_Del_p.S2039fs|UNC13C_ENST00000539562.2_5'UTR|UNC13C_ENST00000537900.1_Frame_Shift_Del_p.S2037fs	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	2039					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCAGGTCGTTCCTCCAAAGAT	0.403																																					p.S2038fs		Atlas-Indel,Pindel	.											.	UNC13C	674	.	0			c.6112delT						.						110	112	111					15																	54914531		1972	4165	6137	SO:0001589	frameshift_variant	440279	exon29			.	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.6113delC	chr15.hg19:g.54914531delC	ENSP00000260323:p.Ser2039fs	90.0	0.0		110.0	43.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Frame_Shift_Del	DEL	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.403	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		-	54914531	C	-	54914531	7	5	135	1	0	1	0	1	0	0	0	0	17001	855	30	0	6227	0	UNC13C	15	54914531	Frame_Shift_Del	DEL	C	TCGA-DD-A4NN-01A-11D-A28X-10		54914531	47616861	44	21651										
ITGAM	3684	hgsc.bcm.edu	37	chr16	31282347	31282347	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	catcatcccacatgactttcGgcggatgaaggagtttgtct	10	10	2	2			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr16:31282347G>A	ENST00000287497.8	+	6	575	c.500G>A	c.(499-501)cGg>cAg	p.R167Q	ITGAM_ENST00000544665.3_Missense_Mutation_p.R167Q			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	167	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						CATGACTTTCGGCGGATGAAG	0.502																																					p.R167Q		Atlas-SNP	.											.	ITGAM	137	.	0			c.G500A						.						186	171	176					16																	31282347		1934	4142	6076	SO:0001583	missense	3684	exon6			ACTTTCGGCGGAT	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.500G>A	chr16.hg19:g.31282347G>A	ENSP00000287497:p.Arg167Gln	151.0	0.0		203.0	63.0	NM_000632	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	hg19	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.743449	0.00675	.	.	ENSG00000169896	ENST00000544665;ENST00000287497	D;D	0.82619	-1.63;-1.63	5.5	-4.45	0.03546	von Willebrand factor, type A (3);	.	.	.	.	T	0.49558	0.1564	N	0.00808	-1.17	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.09377	0.004;0.004	T	0.50617	-0.8807	9	0.10111	T	0.7	.	8.8614	0.35261	0.4229:0.0:0.4706:0.1065	.	167;167	Q4VAK1;P11215	.;ITAM_HUMAN	Q	167	ENSP00000441691:R167Q;ENSP00000287497:R167Q	ENSP00000287497:R167Q	R	+	2	0	ITGAM	31189848	0.000000	0.05858	0.008000	0.14137	0.001000	0.01503	-0.176000	0.09811	-0.658000	0.05366	-2.069000	0.00389	CGG	.	.		0.502	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		A	31282347	G	A	31282347	3	1	135	1	0	0	0	0	1	0	0	0	7896	1116	39	1	522	1	ITGAM	16	31282347	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10		31282347	59072406	45	21652										
BBS2	583	hgsc.bcm.edu	37	chr16	56548459	56548459	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	catcatagccaagctcagggTtcaatacgcctgcagtcaga	9	12	4	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr16:56548459T>A	ENST00000245157.5	-	2	671	c.251A>T	c.(250-252)aAc>aTc	p.N84I	BBS2_ENST00000568104.1_Missense_Mutation_p.N84I	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	84					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						AAGCTCAGGGTTCAATACGCC	0.473									Bardet-Biedl syndrome																												p.N84I		Atlas-SNP	.											.	BBS2	67	.	0			c.A251T						.						96	95	95					16																	56548459		2198	4300	6498	SO:0001583	missense	583	exon2	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TCAGGGTTCAATA	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.251A>T	chr16.hg19:g.56548459T>A	ENSP00000245157:p.Asn84Ile	256.0	0.0		140.0	109.0	NM_031885	Q96CM0|Q96SN9	Missense_Mutation	SNP	ENST00000245157.5	hg19	CCDS32451.1	.	.	.	.	.	.	.	.	.	.	T	15.14	2.744079	0.49151	.	.	ENSG00000125124	ENST00000245157	T	0.67523	-0.27	5.4	1.81	0.25067	WD40 repeat-like-containing domain (1);	0.449158	0.27424	N	0.019429	T	0.56381	0.1981	L	0.47716	1.5	0.32435	N	0.547476	P;P	0.38250	0.624;0.624	B;B	0.41332	0.354;0.354	T	0.58601	-0.7608	10	0.38643	T	0.18	-4.298	5.4598	0.16610	0.1184:0.2048:0.0:0.6768	.	84;84	A8K0N9;Q9BXC9	.;BBS2_HUMAN	I	84	ENSP00000245157:N84I	ENSP00000245157:N84I	N	-	2	0	BBS2	55105960	1.000000	0.71417	0.979000	0.43373	0.975000	0.68041	1.485000	0.35519	0.030000	0.15379	0.482000	0.46254	AAC	.	.		0.473	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		A	56548459	T	A	56548459	3	1	135	1	0	0	0	0	1	0	0	0	1338	1725	60	4	1978	4	BBS2	16	56548459	Missense_Mutation	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10	25266112	56548459	33806294	46	21653										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34340646	34340647	+	Frame_Shift_Ins	INS	-	-	GT													0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ctatgcggaggacgcggctgINSagcacgagaacatgaaggct							TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr18:34340646_34340647insGT	ENST00000359247.4	+	22	3925_3926	c.3925_3926insGT	c.(3925-3927)gagfs	p.E1309fs	FHOD3_ENST00000590592.1_Frame_Shift_Ins_p.E1509fs|FHOD3_ENST00000592128.1_Frame_Shift_Ins_p.E305fs|FHOD3_ENST00000445677.1_Frame_Shift_Ins_p.E1288fs|FHOD3_ENST00000257209.4_Frame_Shift_Ins_p.E1326fs|FHOD3_ENST00000591635.1_Frame_Shift_Ins_p.E522fs	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1309					actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GGACGCGGCTGAGCACGAGAAC	0.653																																					p.E1326fs		Atlas-Indel,Pindel	.											.	FHOD3	210	.	0			c.3976_3977insGT						.																																			SO:0001589	frameshift_variant	80206	exon23			.	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		Exception_encountered	chr18.hg19:g.34340646_34340647insGT	ENSP00000352186:p.Glu1309fs	85.0	0.0		157.0	89.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Frame_Shift_Ins	INS	ENST00000359247.4	hg19																																																																																				.	.		0.653	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		GT	34340647	-	GT	34340646	7	5	135	1	0	1	1	0	0	0	0	0	5891	1291	45	0	4066	0	FHOD3	18	34340646	Frame_Shift_Ins	INS	-	TCGA-DD-A4NN-01A-11D-A28X-10		34340646	43736602	47	21654										
CDH19	28513	hgsc.bcm.edu	37	chr18	64239420	64239420	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	aggaattcccaacataaaacGcagcagtaaataacagttca	6	9	1	0	rs368840152		TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr18:64239420G>C	ENST00000540086.1	-	2	268	c.22C>G	c.(22-24)Cgt>Ggt	p.R8G	CDH19_ENST00000262150.2_Missense_Mutation_p.R8G	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	0					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				AACATAAAACGCAGCAGTAAA	0.393																																					p.R8G		Atlas-SNP	.											.	CDH19	141	.	0			c.C22G						.						86	80	82					18																	64239420		2203	4300	6503	SO:0001583	missense	28513	exon2			TAAAACGCAGCAG	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"Cadherins / Major cadherins"	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000540086.1:c.22C>G	chr18.hg19:g.64239420G>C	ENSP00000439593:p.Arg8Gly	103.0	0.0		142.0	76.0	NM_021153	O15098	Missense_Mutation	SNP	ENST00000540086.1	hg19	CCDS59325.1	.	.	.	.	.	.	.	.	.	.	G	7.595	0.671478	0.14776	.	.	ENSG00000071991	ENST00000262150;ENST00000540086	T;T	0.55930	0.49;0.51	5.85	3.0	0.34707	.	2.735250	0.00958	N	0.003060	T	0.33000	0.0848	N	0.08118	0	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.16289	0.015;0.003	T	0.19257	-1.0311	10	0.26408	T	0.33	.	3.5124	0.07713	0.139:0.2473:0.4863:0.1274	.	8;8	F5H1K0;Q9H159	.;CAD19_HUMAN	G	8	ENSP00000262150:R8G;ENSP00000439593:R8G	ENSP00000262150:R8G	R	-	1	0	CDH19	62390400	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	0.215000	0.17562	0.341000	0.23771	0.563000	0.77884	CGT	.	.		0.393	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153		C	64239420	G	C	64239420	3	2	135	1	0	0	0	0	1	0	0	0	3106	1087	38	4	2340	4	CDH19	18	64239420	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	29898774	64239420	13837828	48	21655										
APC2	10297	hgsc.bcm.edu	37	chr19	1456316	1456316	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tccctgcaggccttgctggcGgtgaagtcggtgccggtgga	17	11	0	1	rs138830892	byFrequency	TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr19:1456316G>A	ENST00000535453.1	+	7	2442	c.729G>A	c.(727-729)gcG>gcA	p.A243A	CTB-25B13.12_ENST00000588225.1_RNA|APC2_ENST00000238483.4_Intron|APC2_ENST00000233607.2_Silent_p.A243A			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTTGCTGGCGGTGAAGTCGG	0.682																																					p.A243A		Atlas-SNP	.											.	APC2	50	.	0			c.G729A						.						25	26	26					19																	1456316		2194	4297	6491	SO:0001819	synonymous_variant	10297	exon8			GCTGGCGGTGAAG		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"Armadillo repeat containing"	24036	protein-coding gene	gene with protein product	"adenomatous polyposis coli like"	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.729G>A	chr19.hg19:g.1456316G>A		159.0	0.0		201.0	68.0	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	hg19	CCDS12068.1																																																																																			.	G|1.000;C|0.000		0.682	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		A	1456316	G	A	1456316	2	1	135	1	0	0	0	0	0	0	0	1	764	1103	39	1		1	APC2	19	1456316	Silent	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10		1456316	57672667	49	21656										
BRD4	23476	hgsc.bcm.edu	37	chr19	15349580	15349580	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ccggcgtcttcgctcctgctCccgcttccgggccaactccc	9	21	1	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr19:15349580C>A	ENST00000263377.2	-	19	4215	c.3994G>T	c.(3994-3996)Gag>Tag	p.E1332*	AC004257.3_ENST00000602793.1_lincRNA	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1332	C-terminal (CTD) region.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			CGCTCCTGCTCCCGCTTCCGG	0.677			T	C15orf55	lethal midline carcinoma of young people																																p.E1332X		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.G3994T						.						11	12	12					19																	15349580		2198	4292	6490	SO:0001587	stop_gained	23476	exon19			CCTGCTCCCGCTT	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.3994G>T	chr19.hg19:g.15349580C>A	ENSP00000263377:p.Glu1332*	62.0	0.0		135.0	66.0	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Nonsense_Mutation	SNP	ENST00000263377.2	hg19	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	c	45	11.288583	0.99542	.	.	ENSG00000141867	ENST00000263377	.	.	.	5.16	5.16	0.70880	.	0.000000	0.50627	D	0.000114	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.0666	17.4346	0.87548	0.0:1.0:0.0:0.0	.	.	.	.	X	1332	.	ENSP00000263377:E1332X	E	-	1	0	BRD4	15210580	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.148000	0.64857	2.396000	0.81511	0.645000	0.84053	GAG	.	.		0.677	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		A	15349580	C	A	15349580	4	1	135	1	0	0	0	0	0	1	0	0	1506	864	30	3	102	3	BRD4	19	15349580	Nonsense_Mutation	SNP	C	TCGA-DD-A4NN-01A-11D-A28X-10	13893264	15349580	43779403	50	21657										
CHERP	10523	hgsc.bcm.edu	37	chr19	16636060	16636060	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	cccgtacactcaccggcaggGaagtccccctgggggtagtc	13	15	1	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr19:16636060G>C	ENST00000198939.6	-	10	1803	c.1767C>G	c.(1765-1767)ttC>ttG	p.F589L	CHERP_ENST00000544299.1_5'UTR|CTD-3222D19.2_ENST00000409035.1_Intron|CHERP_ENST00000546361.2_Missense_Mutation_p.F578L					calcium homeostasis endoplasmic reticulum protein											endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						CACCGGCAGGGAAGTCCCCCT	0.716																																					p.F578L		Atlas-SNP	.											.	CHERP	70	.	0			c.C1734G						.						6	9	8					19																	16636060		1761	3768	5529	SO:0001583	missense	10523	exon10			GGCAGGGAAGTCC	U94836	CCDS42518.1	19p13.1	2013-01-28				ENSG00000085872		"G patch domain containing"	16930	protein-coding gene	gene with protein product						8896557, 10794731	Standard	NM_006387		Approved	ERPROT213-21, DAN16	uc002nei.1	Q8IWX8	OTTHUMG00000169304	ENST00000198939.6:c.1767C>G	chr19.hg19:g.16636060G>C	ENSP00000198939:p.Phe589Leu	98.0	0.0		187.0	67.0	NM_006387		Missense_Mutation	SNP	ENST00000198939.6	hg19		.	.	.	.	.	.	.	.	.	.	G	13.77	2.335910	0.41398	.	.	ENSG00000085872	ENST00000546361;ENST00000198939	D;D	0.89123	-2.47;-2.47	5.13	-1.55	0.08558	.	.	.	.	.	T	0.79429	0.4444	L	0.41236	1.265	0.80722	D	1	P	0.38504	0.634	B	0.36186	0.219	T	0.69113	-0.5231	9	0.12430	T	0.62	-17.0758	9.0272	0.36236	0.5637:0.0:0.4363:0.0	.	578	Q8IWX8	CHERP_HUMAN	L	578;589	ENSP00000439856:F578L;ENSP00000198939:F589L	ENSP00000198939:F589L	F	-	3	2	CHERP	16497060	1.000000	0.71417	0.791000	0.31998	0.576000	0.36127	0.962000	0.29280	-0.051000	0.13334	-0.291000	0.09656	TTC	.	.		0.716	CHERP-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000403372.1	NM_006387		C	16636060	G	C	16636060	3	2	135	1	0	0	0	0	1	0	0	0	3338	1165	41	4	1048	4	CHERP	19	16636060	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	1286480	16636060	42492923	51	21658										
ZNF431	170959	hgsc.bcm.edu	37	chr19	21366647	21366647	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	aggagagaaatcttacaaatGtgaagaatgtggtaaagcct	11	4	1	3			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr19:21366647G>A	ENST00000311048.7	+	5	1685	c.1541G>A	c.(1540-1542)tGt>tAt	p.C514Y	ZNF431_ENST00000594425.1_Intron|ZNF431_ENST00000600692.1_3'UTR	NM_133473.2	NP_597730.2	Q8TF32	ZN431_HUMAN	zinc finger protein 431	514					cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23						TCTTACAAATGTGAAGAATGT	0.343																																					p.C514Y		Atlas-SNP	.											.	ZNF431	71	.	0			c.G1541A						.						53	59	57					19																	21366647		2203	4298	6501	SO:0001583	missense	170959	exon5			ACAAATGTGAAGA	AB075849	CCDS32979.1	19p12	2013-01-08				ENSG00000196705		"Zinc fingers, C2H2-type", "-"	20809	protein-coding gene	gene with protein product						11853319	Standard	NM_133473		Approved	KIAA1969	uc002npp.2	Q8TF32		ENST00000311048.7:c.1541G>A	chr19.hg19:g.21366647G>A	ENSP00000308578:p.Cys514Tyr	37.0	0.0		78.0	26.0	NM_133473	A8KAK7|Q8IWC4	Missense_Mutation	SNP	ENST00000311048.7	hg19	CCDS32979.1	.	.	.	.	.	.	.	.	.	.	.	18.54	3.645636	0.67358	.	.	ENSG00000196705	ENST00000311048	D	0.85088	-1.94	0.421	0.421	0.16451	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93452	0.7911	H	0.96175	3.78	0.30199	N	0.798821	D	0.89917	1.0	D	0.97110	1.0	D	0.87170	0.2220	9	0.54805	T	0.06	.	8.3187	0.32115	0.0:0.0:1.0:0.0	.	514	Q8TF32	ZN431_HUMAN	Y	514	ENSP00000308578:C514Y	ENSP00000308578:C514Y	C	+	2	0	ZNF431	21158487	0.995000	0.38212	0.866000	0.34008	0.846000	0.48090	4.672000	0.61597	0.452000	0.26830	0.455000	0.32223	TGT	.	.		0.343	ZNF431-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463943.1	XM_086098		A	21366647	G	A	21366647	3	1	135	1	0	0	0	0	1	0	0	0	17920	1377	48	3	1559	3	ZNF431	19	21366647	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	4730587	21366647	37762336	52	21659										
ZNF461	92283	hgsc.bcm.edu	37	chr19	37130125	37130125	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ccagtatgaattctctgatgTatagtaagatgtgagcgatg	11	5	1	4			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr19:37130125T>A	ENST00000588268.1	-	6	1349	c.1122A>T	c.(1120-1122)atA>atT	p.I374I	ZNF461_ENST00000540605.2_5'UTR|ZNF461_ENST00000360357.4_Silent_p.I351I	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	374					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TTCTCTGATGTATAGTAAGAT	0.408																																					p.I374I		Atlas-SNP	.											.	ZNF461	73	.	0			c.A1122T						.						80	88	86					19																	37130125		2197	4296	6493	SO:0001819	synonymous_variant	92283	exon6			CTGATGTATAGTA	BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"Zinc fingers, C2H2-type", "-"	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.1122A>T	chr19.hg19:g.37130125T>A		81.0	0.0		90.0	38.0	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Silent	SNP	ENST00000588268.1	hg19	CCDS54257.1																																																																																			.	.		0.408	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		A	37130125	T	A	37130125	2	1	135	1	0	0	0	0	0	0	0	1	17940	1628	57	4		4	ZNF461	19	37130125	Silent	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10	15763478	37130125	21998858	53	21660										
ZNF585A	199704	hgsc.bcm.edu	37	chr19	37642633	37642633	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tgtcagtaaaggccttcccaCactcagcacacacgtaaggc	8	14	2	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr19:37642633C>A	ENST00000356958.4	-	5	2426	c.2168G>T	c.(2167-2169)tGt>tTt	p.C723F	ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000392157.2_Missense_Mutation_p.C668F|ZNF585A_ENST00000292841.5_Missense_Mutation_p.C668F|ZNF585A_ENST00000355533.2_Missense_Mutation_p.C360F			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	723					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGCCTTCCCACACTCAGCACA	0.463																																					p.C668F		Atlas-SNP	.											.	ZNF585A	117	.	0			c.G2003T						.						169	136	147					19																	37642633		2203	4300	6503	SO:0001583	missense	199704	exon6			TTCCCACACTCAG	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.2168G>T	chr19.hg19:g.37642633C>A	ENSP00000349440:p.Cys723Phe	226.0	0.0		358.0	130.0	NM_199126	Q8TE95|Q96MV3	Missense_Mutation	SNP	ENST00000356958.4	hg19		.	.	.	.	.	.	.	.	.	.	C	18.56	3.651114	0.67472	.	.	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157;ENST00000355533	D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04	3.05	3.05	0.35203	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40640	N	0.001059	D	0.91616	0.7351	.	.	.	0.49389	D	0.999788	D	0.89917	1.0	D	0.91635	0.999	D	0.92766	0.6228	9	0.87932	D	0	.	13.3213	0.60434	0.0:1.0:0.0:0.0	.	723	Q6P3V2	Z585A_HUMAN	F	723;668;668;360	ENSP00000349440:C723F;ENSP00000292841:C668F;ENSP00000375998:C668F;ENSP00000347724:C360F	ENSP00000292841:C668F	C	-	2	0	ZNF585A	42334473	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	3.336000	0.52113	1.697000	0.51169	0.655000	0.94253	TGT	.	.		0.463	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		A	37642633	C	A	37642633	3	1	135	1	0	0	0	0	1	0	0	0	18032	478	17	3	145	3	ZNF585A	19	37642633	Missense_Mutation	SNP	C	TCGA-DD-A4NN-01A-11D-A28X-10	512508	37642633	21486350	54	21661										
TSEN34	79042	hgsc.bcm.edu	37	chr19	54696036	54696036	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	cagatctgctctccttgtccAgctggccactgccaggcctc	9	17	2	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr19:54696036A>G	ENST00000396383.1	+	4	868	c.557A>G	c.(556-558)cAg>cGg	p.Q186R	CTD-3093M3.1_ENST00000594382.1_lincRNA|MBOAT7_ENST00000391754.1_5'Flank|MBOAT7_ENST00000245615.1_5'Flank|MBOAT7_ENST00000431666.2_5'Flank|TSEN34_ENST00000396388.2_Missense_Mutation_p.Q186R|TSEN34_ENST00000429671.2_Missense_Mutation_p.Q186R|MBOAT7_ENST00000338624.6_5'Flank|MBOAT7_ENST00000474910.1_5'Flank|TSEN34_ENST00000302937.4_Missense_Mutation_p.Q186R			Q9BSV6	SEN34_HUMAN	TSEN34 tRNA splicing endonuclease subunit	186					mRNA processing (GO:0006397)|tRNA-type intron splice site recognition and cleavage (GO:0000379)	tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	10	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CTCCTTGTCCAGCTGGCCACT	0.647																																					p.Q186R	Esophageal Squamous(37;841 964 4869 42824)	Atlas-SNP	.											.	TSEN34	17	.	0			c.A557G						.						65	68	67					19																	54696036		1877	4093	5970	SO:0001583	missense	79042	exon4			TTGTCCAGCTGGC	AF211970	CCDS42609.1, CCDS74446.1	19q13.4	2013-08-06	2013-08-06	2005-03-12	ENSG00000170892	ENSG00000170892		"tRNA splicing endonuclease subunits"	15506	protein-coding gene	gene with protein product		608754	"leukocyte receptor cluster (LRC) member 5", "tRNA splicing endonuclease 34 homolog (SEN34, S. cerevisiae)", "tRNA splicing endonuclease 34 homolog (S. cerevisiae)"	LENG5		10941842, 15109492	Standard	NM_024075		Approved	SEN34, SEN34L	uc002qdw.3	Q9BSV6	OTTHUMG00000066515	ENST00000396383.1:c.557A>G	chr19.hg19:g.54696036A>G	ENSP00000379667:p.Gln186Arg	206.0	1.0		259.0	126.0	NM_024075	A6NNB1|B0V3J1|Q9BVT1|Q9H6H5	Missense_Mutation	SNP	ENST00000396383.1	hg19	CCDS42609.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.477569	0.84640	.	.	ENSG00000170892	ENST00000455798;ENST00000456872;ENST00000302937;ENST00000429671;ENST00000396383;ENST00000396388	T;T;T;T;T;T	0.66995	-0.24;-0.13;-0.11;-0.13;-0.11;-0.11	4.56	4.56	0.56223	.	0.057122	0.64402	D	0.000001	T	0.75102	0.3804	L	0.59436	1.845	0.42751	D	0.993776	D;D	0.76494	0.999;0.999	D;D	0.66196	0.922;0.942	T	0.74281	-0.3716	10	0.34782	T	0.22	.	11.7599	0.51896	1.0:0.0:0.0:0.0	.	186;186	E7EQB3;Q9BSV6	.;SEN34_HUMAN	R	186;189;186;186;186;186	ENSP00000400743:Q186R;ENSP00000408689:Q189R;ENSP00000305524:Q186R;ENSP00000397402:Q186R;ENSP00000379667:Q186R;ENSP00000379671:Q186R	ENSP00000305524:Q186R	Q	+	2	0	TSEN34	59387848	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.334000	0.79224	1.842000	0.53543	0.459000	0.35465	CAG	.	.		0.647	TSEN34-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142200.1	NM_024075		G	54696036	A	G	54696036	3	3	135	1	0	0	0	0	1	0	0	0	16628	188	7	2	567	2	TSEN34	19	54696036	Missense_Mutation	SNP	A	TCGA-DD-A4NN-01A-11D-A28X-10	17053403	54696036	4432947	55	21662										
BCL2L1	598	hgsc.bcm.edu	37	chr20	30309743	30309743	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	cgcagttcaaactcgtcgccTgcctccctcagcgcttgctt	8	17	2	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr20:30309743T>A	ENST00000307677.4	-	2	689	c.279A>T	c.(277-279)gcA>gcT	p.A93A	BCL2L1_ENST00000376055.4_Silent_p.A93A|BCL2L1_ENST00000420653.1_Silent_p.A93A|BCL2L1_ENST00000376062.2_Silent_p.A93A	NM_138578.1	NP_612815.1	Q07817	B2CL1_HUMAN	BCL2-like 1	93					apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process in bone marrow (GO:0071839)|cell proliferation (GO:0008283)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to alkaloid (GO:0071312)|cellular response to amino acid stimulus (GO:0071230)|cellular response to gamma radiation (GO:0071480)|cytokinesis (GO:0000910)|endocytosis (GO:0006897)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fertilization (GO:0009566)|germ cell development (GO:0007281)|growth (GO:0040007)|hepatocyte apoptotic process (GO:0097284)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male gonad development (GO:0008584)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of execution phase of apoptosis (GO:1900118)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|release of cytochrome c from mitochondria (GO:0001836)|response to cycloheximide (GO:0046898)|response to cytokine (GO:0034097)|spermatogenesis (GO:0007283)|suppression by virus of host apoptotic process (GO:0019050)	Bcl-2 family protein complex (GO:0097136)|cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synapse (GO:0045202)	BH3 domain binding (GO:0051434)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	all_cancers(5;3.47e-06)|all_epithelial(3;1.83e-06)|Lung NSC(7;2.08e-06)|all_lung(7;3.63e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;2.97e-06)|all cancers(5;3.21e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00052)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			ACTCGTCGCCTGCCTCCCTCA	0.602																																					p.A93A	Colon(51;693 1004 1401 20431 21026)	Atlas-SNP	.											.	BCL2L1	23	.	0			c.A279T						.						95	83	87					20																	30309743		2203	4300	6503	SO:0001819	synonymous_variant	598	exon2			GTCGCCTGCCTCC	Z23115	CCDS13188.1, CCDS13189.1	20q11.21	2014-03-07			ENSG00000171552	ENSG00000171552		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	992	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 52"	600039				8358789	Standard	NM_001191		Approved	BCLX, BCL2L, Bcl-X, bcl-xL, bcl-xS, PPP1R52	uc002wwl.3	Q07817	OTTHUMG00000032192	ENST00000307677.4:c.279A>T	chr20.hg19:g.30309743T>A		141.0	0.0		279.0	83.0	NM_138578	E1P5L6|Q5CZ89|Q5TE65|Q92976	Silent	SNP	ENST00000307677.4	hg19	CCDS13189.1																																																																																			.	.		0.602	BCL2L1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078575.1	NM_138578		A	30309743	T	A	30309743	2	1	135	1	0	0	0	0	0	0	0	1	1367	1567	55	4		4	BCL2L1	20	30309743	Silent	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10		30309743	32715777	56	21663										
ADNP	23394	hgsc.bcm.edu	37	chr20	49508566	49508566	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ttaggttcaacttcaaaaacAgggtcaaaagggctaccact	8	9	3	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr20:49508566A>C	ENST00000396029.3	-	5	3252	c.2685T>G	c.(2683-2685)ccT>ccG	p.P895P	ADNP_ENST00000371602.4_Silent_p.P895P|ADNP_ENST00000349014.3_Silent_p.P895P|ADNP_ENST00000396032.3_Silent_p.P895P	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	895					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						CTTCAAAAACAGGGTCAAAAG	0.413																																					p.P895P		Atlas-SNP	.											.	ADNP	106	.	0			c.T2685G						.						142	143	143					20																	49508566		2203	4300	6503	SO:0001819	synonymous_variant	23394	exon5			AAAAACAGGGTCA	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.2685T>G	chr20.hg19:g.49508566A>C		112.0	0.0		161.0	84.0	NM_015339	E1P5Y2|O94881|Q5BKU2|Q9UG34	Silent	SNP	ENST00000396029.3	hg19	CCDS13433.1																																																																																			.	.		0.413	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		C	49508566	A	C	49508566	2	2	135	1	0	0	0	0	0	0	0	1	323	175	7	5		5	ADNP	20	49508566	Silent	SNP	A	TCGA-DD-A4NN-01A-11D-A28X-10	19198823	49508566	13516954	57	21664										
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28210546	28210546	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	ctctggttccgctgtttcacTtcgatgttggtggctccagt	11	11	2	0			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr21:28210546T>C	ENST00000284984.3	-	9	2710	c.2256A>G	c.(2254-2256)gaA>gaG	p.E752E		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	752	Spacer.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		GCTGTTTCACTTCGATGTTGG	0.433																																					p.E752E		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.A2256G						.						87	71	76					21																	28210546		2203	4292	6495	SO:0001819	synonymous_variant	9510	exon9			TTTCACTTCGATG	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.2256A>G	chr21.hg19:g.28210546T>C		69.0	0.0		83.0	35.0	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Silent	SNP	ENST00000284984.3	hg19	CCDS33524.1																																																																																			.	.		0.433	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			C	28210546	T	C	28210546	2	2	135	1	0	0	0	0	0	0	0	1	255	1606	56	2		2	ADAMTS1	21	28210546	Silent	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10		28210546	19919349	58	21665										
IFNAR1	3454	hgsc.bcm.edu	37	chr21	34721747	34721747	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	tcccttagtgattcattccaTatctatatcggtgctccaaa	5	11	2	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chr21:34721747T>C	ENST00000270139.3	+	8	1193	c.1041T>C	c.(1039-1041)caT>caC	p.H347H	IFNAR1_ENST00000442357.2_Silent_p.H347H|IFNAR1_ENST00000416947.2_Silent_p.H278H	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	347	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""Interferon Alfa-2a(DB00034)|""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"	ATTCATTCCATATCTATATCG	0.328																																					p.H347H	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											.	IFNAR1	44	.	0			c.T1041C						.						56	56	56					21																	34721747		2203	4300	6503	SO:0001819	synonymous_variant	3454	exon8			ATTCCATATCTAT		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"Interferons"	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.1041T>C	chr21.hg19:g.34721747T>C		106.0	0.0		101.0	45.0	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Silent	SNP	ENST00000270139.3	hg19	CCDS13624.1																																																																																			.	.		0.328	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4			C	34721747	T	C	34721747	2	2	135	1	0	0	0	0	0	0	0	1	7553	1403	49	2		2	IFNAR1	21	34721747	Silent	SNP	T	TCGA-DD-A4NN-01A-11D-A28X-10	6511201	34721747	13408148	59	21666										
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765414	27765414	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	gaggaagaggaggaggaggaGgaggaggaggaggaggagga	26	0	0	1			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chrX:27765414G>A	ENST00000451261.2	+	5	801	c.402G>A	c.(400-402)gaG>gaA	p.E134E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	134	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aggaggaggaggaggaggagg	0.582																																					p.E134E		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G402A						.						16	15	15					X																	27765414		692	1587	2279	SO:0001819	synonymous_variant	347442	exon1			GGAGGAGGAGGAG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.402G>A	chrX.hg19:g.27765414G>A		45.0	0.0		76.0	11.0	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.582	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		A	27765414	G	A	27765414	2	1	135	1	0	0	0	0	0	0	0	1	4280	991	35	3		3	DCAF8L2	23	27765414	Silent	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10		27765414	127505146	60	21667										
MAGEE1	57692	hgsc.bcm.edu	37	chrX	75649900	75649900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.762142857142857	1.58074074074074	0.374385964912281	1	1	0	atatattgttaaagaatatcGcaaccagtttcctgagatac	6	7	0	2			TCGA-DD-A4NN-01A-11D-A28X-10	TCGA-DD-A4NN-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	472abc15-0124-4700-8026-8eed68cbcde9	7d51dd41-e8be-488c-bbfe-66156768782f	g.chrX:75649900G>A	ENST00000361470.2	+	1	1855	c.1577G>A	c.(1576-1578)cGc>cAc	p.R526H		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	526	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						AAAGAATATCGCAACCAGTTT	0.478																																					p.R526H		Atlas-SNP	.											.	MAGEE1	236	.	0			c.G1577A						.						48	46	47					X																	75649900		2203	4300	6503	SO:0001583	missense	57692	exon1			AATATCGCAACCA	AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.1577G>A	chrX.hg19:g.75649900G>A	ENSP00000354912:p.Arg526His	118.0	0.0		105.0	30.0	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Missense_Mutation	SNP	ENST00000361470.2	hg19	CCDS14433.1	.	.	.	.	.	.	.	.	.	.	G	5.695	0.312811	0.10789	.	.	ENSG00000198934	ENST00000361470	T	0.05382	3.45	2.13	0.28	0.15682	.	.	.	.	.	T	0.12646	0.0307	L	0.39514	1.22	0.09310	N	1	D	0.76494	0.999	D	0.77557	0.99	T	0.19386	-1.0307	9	0.62326	D	0.03	.	4.1776	0.10360	0.4006:0.0:0.5994:0.0	.	526	Q9HCI5	MAGE1_HUMAN	H	526	ENSP00000354912:R526H	ENSP00000354912:R526H	R	+	2	0	MAGEE1	75566304	0.070000	0.21116	0.037000	0.18230	0.001000	0.01503	0.239000	0.18023	-0.044000	0.13491	-0.215000	0.12644	CGC	.	.		0.478	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		A	75649900	G	A	75649900	3	1	135	1	0	0	0	0	1	0	0	0	9194	1087	38	1	1579	1	MAGEE1	23	75649900	Missense_Mutation	SNP	G	TCGA-DD-A4NN-01A-11D-A28X-10	47884486	75649900	79620660	61	21668										
C1orf187	374946	hgsc.bcm.edu	37	chr1	11771928	11771928	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	caggcacagcccaggtctgaCggggaggtgatgcccacgct	15	13	1	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:11771928C>A	ENST00000294485.5	+	4	798	c.663C>A	c.(661-663)gaC>gaA	p.D221E		NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein																		CCAGGTCTGACGGGGAGGTGA	0.547																																					p.D221E		Atlas-SNP	.											.	.	.	.	0			c.C663A						.						67	49	55					1																	11771928		2203	4300	6503	SO:0001583	missense	374946	exon4			GTCTGACGGGGAG	AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"dorsal repulsive axon guidance protein", "neural tissue-specific cysteine-rich protein"	612682	"chromosome 1 open reading frame 187"	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.663C>A	chr1.hg19:g.11771928C>A	ENSP00000294485:p.Asp221Glu	109.0	0.0		126.0	19.0	NM_198545		Missense_Mutation	SNP	ENST00000294485.5	hg19	CCDS135.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.798461	0.31777	.	.	ENSG00000162490	ENST00000294485	T	0.44881	0.91	5.7	-9.64	0.00541	.	0.259259	0.38436	N	0.001683	T	0.26011	0.0634	M	0.67953	2.075	0.28339	N	0.921429	P	0.40970	0.734	B	0.34779	0.189	T	0.12578	-1.0542	10	0.23891	T	0.37	-20.7068	8.5413	0.33395	0.0779:0.2014:0.0775:0.6432	.	221	Q8NBI3	DRAXI_HUMAN	E	221	ENSP00000294485:D221E	ENSP00000294485:D221E	D	+	3	2	C1orf187	11694515	0.000000	0.05858	0.095000	0.20976	0.643000	0.38383	-3.031000	0.00637	-2.447000	0.00545	-2.939000	0.00087	GAC	.	.		0.547	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545		A	11771928	C	A	11771928	3	1	136	1	0	0	0	0	1	0	0	0	2023	535	19	1	673	1	C1orf187	1	11771928	Missense_Mutation	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10		11771928	237478693	1	21669										
GDAP2	54834	hgsc.bcm.edu	37	chr1	118455267	118455268	+	Missense_Mutation	DNP	TG	TG	AT													0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gatgaaccgggcagctagatTgaatccttttgtcaattttg							TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:118455267_118455268TG>AT	ENST00000369443.5	-	4	603_604	c.354_355CA>AT	c.(352-357)ttCAat>ttATat	p.118_119FN>LY	GDAP2_ENST00000369442.3_Missense_Mutation_p.118_119FN>LY	NM_017686.3	NP_060156.1	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated protein 2	118	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				response to retinoic acid (GO:0032526)	lysosomal membrane (GO:0005765)				kidney(2)|large_intestine(3)|lung(9)|ovary(2)	16		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		GCAGCTAGATTGAATCCTTTTG	0.416																																					p.N119Y|p.F118L		Atlas-SNP	.											.	GDAP2	37	.	0			c.A355T|c.C354A						.																																			SO:0001583	missense	54834	exon4			CTAGATTGAATCC|TAGATTGAATCCT	AK000149	CCDS897.1, CCDS44201.1	1q11	2011-10-20			ENSG00000196505	ENSG00000196505			18010	protein-coding gene	gene with protein product						1021725	Standard	NM_017686		Approved	FLJ20142, dJ776P7.1, MACROD3	uc001ehf.3	Q9NXN4	OTTHUMG00000012199	ENST00000369443.5:c.354_355delinsAT	chr1.hg19:g.118455267_118455268delinsAT	ENSP00000358451:p.F118_N119delinsLY	97.0|95.0	0.0		129.0|130.0	63.0	NM_017686	Q96DZ0	Missense_Mutation	SNP	ENST00000369443.5	hg19	CCDS897.1																																																																																			.	.		0.416	GDAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033732.2	NM_017686		AT	118455268	TG	AT	118455267	3	1	136	1	0	0	0	0	1	0	0	0	6317	1812	63	4	1227	4	GDAP2	1	118455267	Missense_Mutation	DNP	TG	TCGA-DD-A4NO-01A-11D-A28X-10	106683339	118455267	130795354	2	21670										
OR6N2	81442	hgsc.bcm.edu	37	chr1	158747387	158747387	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	acactggcaaagccaaggaaCacaaattcagccaggcttga	9	11	1	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:158747387C>A	ENST00000339258.1	-	1	38	c.39G>T	c.(37-39)gtG>gtT	p.V13V		NM_001005278.1	NP_001005278.1	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N, member 2	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(6)|lung(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(112;0.0378)					AGCCAAGGAACACAAATTCAG	0.463																																					p.V13V		Atlas-SNP	.											.	OR6N2	78	.	0			c.G39T						.						63	66	65					1																	158747387		2203	4300	6503	SO:0001819	synonymous_variant	81442	exon1			AAGGAACACAAAT	BK004200	CCDS30906.1	1q23.1	2012-08-09			ENSG00000188340	ENSG00000188340		"GPCR / Class A : Olfactory receptors"	15035	protein-coding gene	gene with protein product							Standard	NM_001005278		Approved		uc010pir.2	Q8NGY6	OTTHUMG00000022775	ENST00000339258.1:c.39G>T	chr1.hg19:g.158747387C>A		292.0	0.0		468.0	134.0	NM_001005278	Q6IFR2	Silent	SNP	ENST00000339258.1	hg19	CCDS30906.1																																																																																			.	.		0.463	OR6N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059068.1			A	158747387	C	A	158747387	2	1	136	1	0	0	0	0	0	0	0	1	11216	465	17	3		3	OR6N2	1	158747387	Silent	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10	40292120	158747387	90503234	3	21671										
ATP2B4	493	hgsc.bcm.edu	37	chr1	203702358	203702358	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	tgattctttgcagatcgacgTaattaacacattccagacgg	8	9	1	3			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:203702358T>C	ENST00000341360.2	+	20	3714	c.3317T>C	c.(3316-3318)gTa>gCa	p.V1106A	ATP2B4_ENST00000357681.5_Intron|ATP2B4_ENST00000391954.2_Missense_Mutation_p.V1070A|ATP2B4_ENST00000367218.3_Missense_Mutation_p.V1106A|ATP2B4_ENST00000367219.3_Missense_Mutation_p.V1094A			P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	1106	Calmodulin-binding subdomain B. {ECO:0000250}.				blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CAGATCGACGTAATTAACACA	0.473																																					p.V1106A		Atlas-SNP	.											.	ATP2B4	226	.	0			c.T3317C						.						110	107	108					1																	203702358		2203	4300	6503	SO:0001583	missense	493	exon21			TCGACGTAATTAA	M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"ATPases / P-type"	817	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 4"	108732	"matrix-remodelling associated 1"	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000341360.2:c.3317T>C	chr1.hg19:g.203702358T>C	ENSP00000340930:p.Val1106Ala	70.0	0.0		140.0	23.0	NM_001001396	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Missense_Mutation	SNP	ENST00000341360.2	hg19	CCDS30977.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.9|25.9	4.689658|4.689658	0.88735|0.88735	.|.	.|.	ENSG00000058668|ENSG00000058668	ENST00000367218;ENST00000367219;ENST00000391954;ENST00000341360|ENST00000356729	D;D;D;D|.	0.92911|.	-3.13;-3.13;-3.13;-3.13|.	5.01|5.01	5.01|5.01	0.66863|0.66863	.|.	0.212421|.	0.23742|.	N|.	0.045009|.	T|.	0.70544|.	0.3236|.	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	D|D	1|1	D;D|.	0.69078|.	0.997;0.985|.	D;D|.	0.79108|.	0.992;0.981|.	T|.	0.70139|.	-0.4954|.	10|.	0.87932|.	D|.	0|.	.|.	14.5464|14.5464	0.68032|0.68032	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1106;1106|.	P23634;B1APW5|.	AT2B4_HUMAN;.|.	A|Q	1106;1094;1070;1106|71	ENSP00000356187:V1106A;ENSP00000356188:V1094A;ENSP00000375816:V1070A;ENSP00000340930:V1106A|.	ENSP00000340930:V1106A|.	V|X	+|+	2|1	0|0	ATP2B4|ATP2B4	201968981|201968981	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.843000|7.843000	0.86859|0.86859	2.108000|2.108000	0.64289|0.64289	0.533000|0.533000	0.62120|0.62120	GTA|TAA	.	.		0.473	ATP2B4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087463.1	NM_001001396		C	203702358	T	C	203702358	3	2	136	1	0	0	0	0	1	0	0	0	1142	1638	57	2	3395	2	ATP2B4	1	203702358	Missense_Mutation	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10	44954971	203702358	45548263	4	21672										
RCOR3	55758	hgsc.bcm.edu	37	chr1	211486854	211486854	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	aacagcccctattgccactcTgaaccagcctccaccacttc	4	19	1	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:211486854T>A	ENST00000367005.4	+	11	1373	c.1232T>A	c.(1231-1233)cTg>cAg	p.L411Q	RCOR3_ENST00000526255.1_3'UTR|RCOR3_ENST00000367006.4_Silent_p.S388S|RCOR3_ENST00000419091.2_Missense_Mutation_p.L469Q	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	411	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		ATTGCCACTCTGAACCAGCCT	0.627																																					p.L469Q		Atlas-SNP	.											.	RCOR3	51	.	0			c.T1406A						.						143	108	120					1																	211486854		2203	4300	6503	SO:0001583	missense	55758	exon12			CCACTCTGAACCA	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.1232T>A	chr1.hg19:g.211486854T>A	ENSP00000355972:p.Leu411Gln	97.0	0.0		203.0	68.0	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	hg19	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	T	10.87	1.472798	0.26423	.	.	ENSG00000117625	ENST00000419091;ENST00000367005;ENST00000529763	T;T	0.31510	1.49;1.53	5.07	5.07	0.68467	.	0.380245	0.23893	N	0.043536	T	0.40119	0.1104	.	.	.	0.30833	N	0.736454	D;P	0.58620	0.983;0.79	P;B	0.58331	0.837;0.202	T	0.28073	-1.0055	9	0.13470	T	0.59	-7.4012	14.8169	0.70041	0.0:0.0:0.0:1.0	.	469;411	Q9P2K3-3;Q9P2K3	.;RCOR3_HUMAN	Q	469;411;187	ENSP00000413929:L469Q;ENSP00000355972:L411Q	ENSP00000355972:L411Q	L	+	2	0	RCOR3	209553477	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.712000	0.74681	1.910000	0.55303	0.528000	0.53228	CTG	.	.		0.627	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		A	211486854	T	A	211486854	3	1	136	1	0	0	0	0	1	0	0	0	13199	1580	55	4	1485	4	RCOR3	1	211486854	Missense_Mutation	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10	7784496	211486854	37763767	5	21673										
ZNF238	10472	hgsc.bcm.edu	37	chr1	244218375	244218375	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	actttctcttgcatgtacacCctcaagcgccacgagaggac	8	14	2	1	rs375286592		TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:244218375C>A	ENST00000358704.4	+	2	1448	c.1299C>A	c.(1297-1299)acC>acA	p.T433T		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	424					cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCATGTACACCCTCAAGCGCC	0.632																																					p.T433T		Atlas-SNP	.											.	.	.	.	0			c.C1299A						.	C	,	0,4406		0,0,2203	71	73	72		1272,1299	-1.3	1	1		72	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ZNF238	NM_006352.3,NM_205768.2	,	0,2,6501	AA,AC,CC		0.0233,0.0,0.0154	,	424/523,433/532	244218375	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10472	exon2			GTACACCCTCAAG	U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13030	protein-coding gene	gene with protein product		608433	"zinc finger protein 238"	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.1299C>A	chr1.hg19:g.244218375C>A		205.0	0.0		528.0	246.0	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Silent	SNP	ENST00000358704.4	hg19	CCDS1622.1																																																																																			.	.		0.632	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768		A	244218375	C	A	244218375	2	1	136	1	0	0	0	0	0	0	0	1	17805	610	22	3		3	ZNF238	1	244218375	Silent	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10	32731521	244218375	5032246	6	21674										
C2orf63	130162	hgsc.bcm.edu	37	chr2	55402927	55402927	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	agctggttaagatatagaacTaccaaaacacatgttccatt	6	8	0	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:55402927T>C	ENST00000401408.1	-	13	2105	c.1760A>G	c.(1759-1761)tAg>tGg	p.*587W	CLHC1_ENST00000494539.1_5'UTR|CLHC1_ENST00000406076.1_Nonstop_Mutation_p.*465W|CLHC1_ENST00000407122.1_Nonstop_Mutation_p.*587W|CLHC1_ENST00000406437.2_Nonstop_Mutation_p.*138W	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	0																	GATATAGAACTACCAAAACAC	0.368																																					p.X587W		Atlas-SNP	.											.	.	.	.	0			c.A1760G						.						100	91	94					2																	55402927		2203	4300	6503	SO:0001578	stop_lost	130162	exon13			TAGAACTACCAAA		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 63"	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.1760A>G	chr2.hg19:g.55402927T>C	ENSP00000384869:p.*587Serext*7	105.0	0.0		136.0	58.0	NM_152385	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	hg19	CCDS33201.1	.	.	.	.	.	.	.	.	.	.	T	19.55	3.848614	0.71603	.	.	ENSG00000162994	ENST00000406437;ENST00000407122;ENST00000401408;ENST00000406076	.	.	.	5.8	4.63	0.57726	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2414	0.43314	0.1477:0.0:0.0:0.8523	.	.	.	.	W	138;587;587;465	.	.	X	-	2	0	C2orf63	55256431	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.888000	0.63164	1.010000	0.39314	0.528000	0.53228	TAG	.	.		0.368	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385		C	55402927	T	C	55402927	4	2	136	1	0	0	0	0	0	0	0	0	2184	1535	53	2	4	2	C2orf63	2	55402927	Nonstop_Mutation	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10		55402927	187796446	7	21675										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73681090	73681090	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	tggtagcagtgtagattcacTggctgcacatgtgaaaaacc	11	8	1	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:73681090T>A	ENST00000264448.6	+	8	7544	c.7433T>A	c.(7432-7434)cTg>cAg	p.L2478Q	ALMS1_ENST00000377715.1_Missense_Mutation_p.L2478Q|ALMS1_ENST00000409009.1_Missense_Mutation_p.L2436Q|ALMS1-IT1_ENST00000441587.2_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2478					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GTAGATTCACTGGCTGCACAT	0.453																																					p.L2478Q		Atlas-SNP	.											.	ALMS1	384	.	0			c.T7433A						.						116	115	115					2																	73681090		1949	4140	6089	SO:0001583	missense	7840	exon8			ATTCACTGGCTGC	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7433T>A	chr2.hg19:g.73681090T>A	ENSP00000264448:p.Leu2478Gln	125.0	0.0		195.0	10.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	T	18.50	3.638306	0.67130	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.35605	2.22;2.22;1.3	5.9	5.9	0.94986	.	0.000000	0.39146	N	0.001453	T	0.52725	0.1752	L	0.48642	1.525	0.41976	D	0.990779	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.55515	-0.8129	10	0.87932	D	0	.	12.7235	0.57156	0.0:0.0:0.0:1.0	.	2478;2436;2478	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	Q	2436;2478;2478	ENSP00000386627:L2436Q;ENSP00000264448:L2478Q;ENSP00000366944:L2478Q	ENSP00000264448:L2478Q	L	+	2	0	ALMS1	73534598	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	4.517000	0.60503	2.264000	0.75181	0.533000	0.62120	CTG	.	.		0.453	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73681090	T	A	73681090	3	1	136	1	0	0	0	0	1	0	0	0	535	1580	55	4	7463	4	ALMS1	2	73681090	Missense_Mutation	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10	18278163	73681090	169518283	8	21676										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098809	178098810	+	Missense_Mutation	DNP	TC	TC	AA													0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ttgggagaaattcacctgtcTcttcatctagttgtaactga							TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:178098809_178098810TC>AA	ENST00000397062.3	-	2	789_790	c.235_236GA>TT	c.(235-237)GAg>TTg	p.E79L	NFE2L2_ENST00000423513.1_Missense_Mutation_p.E63L|NFE2L2_ENST00000446151.2_Missense_Mutation_p.E63L|NFE2L2_ENST00000464747.1_Missense_Mutation_p.E63L|NFE2L2_ENST00000397063.4_Missense_Mutation_p.E63L	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	79					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E79K(10)|p.E79Q(10)|p.E79G(1)|p.E79_T80insE(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			TTCACCTGTCTCTTCATCTAGT	0.441			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.E79V|p.E79X		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,bladder,carcinoma,-1,3|NFE2L2,bladder,carcinoma,0,21	NFE2L2	225	.	22	Substitution - Missense(21)|Insertion - In frame(1)	lung(13)|oesophagus(5)|upper_aerodigestive_tract(2)|urinary_tract(1)|cervix(1)	c.A236T|c.G235T						.																																			SO:0001583	missense	4780	exon2			CCTGTCTCTTCAT|CTGTCTCTTCATC		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.235_236delinsAA	chr2.hg19:g.178098809_178098810delinsAA	ENSP00000380252:p.Glu79Leu	47.0|48.0	0.0		64.0	26.0|27.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1																																																																																			.	.		0.441	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		AA	178098810	TC	AA	178098809	3	1	136	1	0	0	0	0	1	0	0	0	10377	1551	54	4	1597	4	NFE2L2	2	178098809	Missense_Mutation	DNP	TC	TCGA-DD-A4NO-01A-11D-A28X-10	104417719	178098809	65100564	9	21677										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209217426	209217426	+	Frame_Shift_Del	DEL	A	A	-													0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gagtttacagaattggttatAagaactctcagaacaacact							TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:209217426delA	ENST00000264380.4	+	39	5922	c.5764delA	c.(5764-5766)aagfs	p.K1922fs		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1922	Catalytic.|PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						AATTGGTTATAAGAACTCTCA	0.373																																					p.Y1921X		Atlas-INDEL	.											.	PIKFYVE	223	.	0			c.5763delT						.						80	83	82					2																	209217426		2202	4300	6502	SO:0001589	frameshift_variant	200576	exon39			.	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.5764delA	chr2.hg19:g.209217426delA	ENSP00000264380:p.Lys1922fs	45.0	0.0		43.0	16.0	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Frame_Shift_Del	DEL	ENST00000264380.4	hg19	CCDS2382.1																																																																																			.	.		0.373	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		-	209217426	A	-	209217426	7	5	136	1	0	1	0	1	0	0	0	0	11933	363	13	0	5925	0	PIKFYVE	2	209217426	Frame_Shift_Del	DEL	A	TCGA-DD-A4NO-01A-11D-A28X-10	31118617	209217426	33981947	10	21678										
SPEG	10290	hgsc.bcm.edu	37	chr2	220342149	220342149	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gtgaggtctcctgcaaagcaGagttggctgtgcattcaggt	14	8	2	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:220342149G>T	ENST00000312358.7	+	20	4843	c.4711G>T	c.(4711-4713)Gag>Tag	p.E1571*	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1571	Ig-like 8.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CTGCAAAGCAGAGTTGGCTGT	0.612																																					p.E1571X		Atlas-SNP	.											.	SPEG	272	.	0			c.G4711T						.						32	38	36					2																	220342149		2082	4217	6299	SO:0001587	stop_gained	10290	exon20			AAAGCAGAGTTGG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.4711G>T	chr2.hg19:g.220342149G>T	ENSP00000311684:p.Glu1571*	105.0	0.0		120.0	50.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Nonsense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	47	13.211917	0.99727	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	.	.	.	5.35	5.35	0.76521	.	0.457119	0.16376	N	0.217101	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	19.0677	0.93119	0.0:0.0:1.0:0.0	.	.	.	.	X	1571	.	ENSP00000265327:E1571X	E	+	1	0	SPEG	220050393	1.000000	0.71417	0.967000	0.41034	0.995000	0.86356	9.613000	0.98350	2.506000	0.84524	0.655000	0.94253	GAG	.	.		0.612	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220342149	G	T	220342149	4	4	136	1	0	0	0	0	0	1	0	0	15051	943	33	3	4801	3	SPEG	2	220342149	Nonsense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	11124723	220342149	22857224	11	21679										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225653873	225653873	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gctcaaaaaagctggccatcCcatagagaacatgccttggg	10	11	1	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:225653873C>A	ENST00000258390.7	-	48	5393	c.5326G>T	c.(5326-5328)Gga>Tga	p.G1776*	DOCK10_ENST00000409592.3_Nonsense_Mutation_p.G1770*	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1776	DHR-2.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GCTGGCCATCCCATAGAGAAC	0.383																																					p.G1776X		Atlas-SNP	.											.	DOCK10	308	.	0			c.G5326T						.						138	117	123					2																	225653873		1877	4103	5980	SO:0001587	stop_gained	55619	exon48			GCCATCCCATAGA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.5326G>T	chr2.hg19:g.225653873C>A	ENSP00000258390:p.Gly1776*	86.0	0.0		110.0	54.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Nonsense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	47	13.299214	0.99733	.	.	ENSG00000135905	ENST00000409592;ENST00000258390;ENST00000373702	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.2079	0.98282	0.0:1.0:0.0:0.0	.	.	.	.	X	1770;1776;281	.	ENSP00000258390:G1776X	G	-	1	0	DOCK10	225362117	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.476000	0.81055	2.781000	0.95711	0.655000	0.94253	GGA	.	.		0.383	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			A	225653873	C	A	225653873	4	1	136	1	0	0	0	0	0	1	0	0	4687	632	22	3	1270	3	DOCK10	2	225653873	Nonsense_Mutation	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10	5311724	225653873	17545500	12	21680										
LRIG1	26018	hgsc.bcm.edu	37	chr3	66465346	66465346	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gtaggtttctgtactcacagTtgtgtcagcctgggtagctt	12	8	3	0			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr3:66465346T>C	ENST00000273261.3	-	5	1169	c.645A>G	c.(643-645)caA>caG	p.Q215Q	LRIG1_ENST00000383703.3_Silent_p.Q215Q	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	215					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		GTACTCACAGTTGTGTCAGCC	0.488																																					p.Q215Q		Atlas-SNP	.											.	LRIG1	138	.	0			c.A645G						.						172	158	163					3																	66465346		2203	4300	6503	SO:0001819	synonymous_variant	26018	exon5			TCACAGTTGTGTC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.645A>G	chr3.hg19:g.66465346T>C		73.0	0.0		114.0	32.0	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	hg19	CCDS33783.1																																																																																			.	.		0.488	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		C	66465346	T	C	66465346	2	2	136	1	0	0	0	0	0	0	0	1	8953	1722	60	2		2	LRIG1	3	66465346	Silent	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10		66465346	131557084	13	21681										
ZNF654	55279	hgsc.bcm.edu	37	chr3	88189316	88189316	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ttaagctgccgttccagcttGcccagcacacaaaaagtcac	7	14	1	0			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr3:88189316G>A	ENST00000309495.5	+	1	1063	c.856G>A	c.(856-858)Gcc>Acc	p.A286T	CGGBP1_ENST00000462901.1_Intron	NM_018293.2	NP_060763.2	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	286					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(3)	12		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		GTTCCAGCTTGCCCAGCACAC	0.393																																					p.A286T		Atlas-SNP	.											.	ZNF654	56	.	0			c.G856A						.						117	108	111					3																	88189316		1874	4112	5986	SO:0001583	missense	55279	exon1			CAGCTTGCCCAGC	AF543494	CCDS46874.1	3p11.1	2005-01-10			ENSG00000175105	ENSG00000175105			25612	protein-coding gene	gene with protein product							Standard	NM_018293		Approved	FLJ10997, FLJ21142	uc003dqv.3	Q8IZM8	OTTHUMG00000159097	ENST00000309495.5:c.856G>A	chr3.hg19:g.88189316G>A	ENSP00000312141:p.Ala286Thr	74.0	0.0		70.0	19.0	NM_018293	Q9H791|Q9NV14	Missense_Mutation	SNP	ENST00000309495.5	hg19	CCDS46874.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.871297	0.33069	.	.	ENSG00000175105	ENST00000309495	T	0.36157	1.27	5.87	4.99	0.66335	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.617472	0.17613	N	0.167998	T	0.19127	0.0459	N	0.12831	0.26	0.80722	D	1	B	0.29909	0.261	B	0.20577	0.03	T	0.07347	-1.0777	10	0.10636	T	0.68	.	14.4059	0.67081	0.0715:0.0:0.9285:0.0	.	286	Q8IZM8	ZN654_HUMAN	T	286	ENSP00000312141:A286T	ENSP00000312141:A286T	A	+	1	0	ZNF654	88272006	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.261000	0.43276	2.785000	0.95823	0.655000	0.94253	GCC	.	.		0.393	ZNF654-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353285.2	NM_018293		A	88189316	G	A	88189316	3	1	136	1	0	0	0	0	1	0	0	0	18082	1319	46	3	858	3	ZNF654	3	88189316	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	21723970	88189316	109833114	14	21682										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108373044	108373044	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ggaaagaacaagcaaatccaCactcagtcagtagacttata	7	9	2	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr3:108373044C>T	ENST00000361582.3	+	19	2316	c.2086C>T	c.(2086-2088)Cac>Tac	p.H696Y	DZIP3_ENST00000463306.1_Missense_Mutation_p.H696Y	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	696					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						AGCAAATCCACACTCAGTCAG	0.378																																					p.H696Y		Atlas-SNP	.											.	DZIP3	111	.	0			c.C2086T						.						154	136	142					3																	108373044		2203	4300	6503	SO:0001583	missense	9666	exon19			AATCCACACTCAG	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2086C>T	chr3.hg19:g.108373044C>T	ENSP00000355028:p.His696Tyr	143.0	0.0		149.0	43.0	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	hg19	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	C	11.19	1.566819	0.28003	.	.	ENSG00000198919	ENST00000361582;ENST00000463306	T;T	0.30714	1.52;1.52	4.81	0.747	0.18371	.	1.249520	0.05584	N	0.573414	T	0.15089	0.0364	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23904	-1.0175	10	0.38643	T	0.18	0.0012	3.1826	0.06589	0.1921:0.4828:0.0:0.3251	.	314;696	D3DN61;Q86Y13	.;DZIP3_HUMAN	Y	696	ENSP00000355028:H696Y;ENSP00000419981:H696Y	ENSP00000355028:H696Y	H	+	1	0	DZIP3	109855734	0.000000	0.05858	0.000000	0.03702	0.613000	0.37349	-0.670000	0.05256	-0.052000	0.13311	0.585000	0.79938	CAC	.	.		0.378	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		T	108373044	C	T	108373044	3	4	136	1	0	0	0	0	1	0	0	0	4867	478	17	3	2156	3	DZIP3	3	108373044	Missense_Mutation	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10	20183728	108373044	89649386	15	21683										
HTT	3064	hgsc.bcm.edu	37	chr4	3123007	3123007	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ccaagaccacaatgttgtgaCcggagccctggagctgttgc	12	12	0	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr4:3123007C>A	ENST00000355072.5	+	9	1266	c.1121C>A	c.(1120-1122)aCc>aAc	p.T374N		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	374					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AATGTTGTGACCGGAGCCCTG	0.522																																					p.T374N		Atlas-SNP	.											.	HTT	221	.	0			c.C1121A						.						66	68	67					4																	3123007		1965	4170	6135	SO:0001583	missense	3064	exon9			TTGTGACCGGAGC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1121C>A	chr4.hg19:g.3123007C>A	ENSP00000347184:p.Thr374Asn	85.0	0.0		115.0	45.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	C	19.86	3.905103	0.72868	.	.	ENSG00000197386	ENST00000355072	T	0.64618	-0.11	4.52	4.52	0.55395	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69251	0.3090	L	0.33624	1.015	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.65985	-0.6035	10	0.25106	T	0.35	.	17.2061	0.86918	0.0:1.0:0.0:0.0	.	374	P42858	HD_HUMAN	N	374	ENSP00000347184:T374N	ENSP00000347184:T374N	T	+	2	0	HTT	3092805	1.000000	0.71417	0.965000	0.40720	0.976000	0.68499	7.260000	0.78391	2.233000	0.73108	0.655000	0.94253	ACC	.	.		0.522	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3123007	C	A	3123007	3	1	136	1	0	0	0	0	1	0	0	0	7466	507	18	3	1155	3	HTT	4	3123007	Missense_Mutation	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10		3123007	188031269	16	21684										
UGT2B4	7363	hgsc.bcm.edu	37	chr4	70352328	70352330	+	Splice_Site	DEL	AAG	AAG	-													0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ttgttcttcagagacttaccAagaagatcattctggggtat							TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr4:70352328_70352330delAAG	ENST00000305107.6	-	4	1133_1135	c.1087_1089delCTT	c.(1087-1089)cttdel	p.L363del	UGT2B4_ENST00000506580.1_5'UTR|UGT2B4_ENST00000381096.3_Splice_Site_p.L227del|UGT2B4_ENST00000512583.1_Splice_Site_p.L363del	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	363					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	GAGACTTACCAAGAAGATCATTC	0.34																																					p.363_364del		Atlas-Indel,Pindel	.											.	UGT2B4	105	.	0			c.1088_1090del						.																																			SO:0001630	splice_region_variant	7363	exon4			.	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"UDP glucuronosyltransferases"	12553	protein-coding gene	gene with protein product		600067	"UDP glycosyltransferase 2 family, polypeptide B4"			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.1090+1CTT>-	chr4.hg19:g.70352331_70352333delAAG		100.0	0.0		84.0	22.0	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	In_Frame_Del	DEL	ENST00000305107.6	hg19	CCDS43234.1																																																																																			.	.		0.34	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	In_Frame_Del	-	70352330	AAG	-	70352328	8	5	136	1	0	1	0	1	0	0	1	0	16976	144	5	0	509	0	UGT2B4	4	70352328	Splice_Site	DEL	AAG	TCGA-DD-A4NO-01A-11D-A28X-10	67229321	70352328	120801948	17	21685										
ZNF827	152485	hgsc.bcm.edu	37	chr4	146695657	146695657	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	aggacagacaggaatggtcaCctgtgtgcttggtgccaatg	14	8	1	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr4:146695657C>G	ENST00000508784.1	-	11	3088		c.e11+1		ZNF827_ENST00000379448.4_Splice_Site|ZNF827_ENST00000513320.1_Splice_Site			Q17R98	ZN827_HUMAN	zinc finger protein 827						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					GGAATGGTCACCTGTGTGCTT	0.562																																					.		Atlas-SNP	.											.	ZNF827	102	.	0			c.2860+1G>C						.						258	174	202					4																	146695657		2203	4300	6503	SO:0001630	splice_region_variant	152485	exon12			TGGTCACCTGTGT	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.2860+1G>C	chr4.hg19:g.146695657C>G		132.0	0.0		148.0	42.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Splice_Site	SNP	ENST00000508784.1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.8	4.331918	0.81801	.	.	ENSG00000151612	ENST00000508784;ENST00000513320;ENST00000379448;ENST00000281318;ENST00000511659;ENST00000440280	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2789	0.98501	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF827	146915107	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.412000	0.80091	2.788000	0.95919	0.650000	0.86243	.	.	.		0.562	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835	Intron	G	146695657	C	G	146695657	5	3	136	1	0	0	0	0	0	0	1	0	18195	521	18	4	384	4	ZNF827	4	146695657	Splice_Site	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10	76343329	146695657	44458619	18	21686										
CDH9	1007	hgsc.bcm.edu	37	chr5	26881251	26881251	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gtcaaacaatcctcttagtcTcggtcactatcatcaccccc	4	16	6	0			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr5:26881251T>G	ENST00000231021.4	-	12	2536	c.2364A>C	c.(2362-2364)cgA>cgC	p.R788R		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	788					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CCTCTTAGTCTCGGTCACTAT	0.413																																					p.R788R	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A2364C						.						135	129	131					5																	26881251		2203	4300	6503	SO:0001819	synonymous_variant	1007	exon12			TTAGTCTCGGTCA	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.2364A>C	chr5.hg19:g.26881251T>G		89.0	0.0		152.0	56.0	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	hg19	CCDS3893.1																																																																																			.	.		0.413	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		G	26881251	T	G	26881251	2	3	136	1	0	0	0	0	0	0	0	1	3119	1538	54	5		5	CDH9	5	26881251	Silent	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10		26881251	154034009	19	21687										
GZMA	3001	hgsc.bcm.edu	37	chr5	54401400	54401400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gaaaaaccatctgtgctgggGctttgattgcaaaagactgg	12	7	1	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr5:54401400G>A	ENST00000274306.6	+	2	204	c.169G>A	c.(169-171)Gct>Act	p.A57T		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	57	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				CTGTGCTGGGGCTTTGATTGC	0.388																																					p.A57T		Atlas-SNP	.											.	GZMA	60	.	0			c.G169A						.						104	96	99					5																	54401400		2203	4300	6503	SO:0001583	missense	3001	exon2			GCTGGGGCTTTGA		CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"CTL tryptase", "Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.169G>A	chr5.hg19:g.54401400G>A	ENSP00000274306:p.Ala57Thr	51.0	0.0		45.0	21.0	NM_006144	A4PHN1|Q6IB36	Missense_Mutation	SNP	ENST00000274306.6	hg19	CCDS3965.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.468773	0.26335	.	.	ENSG00000145649	ENST00000274306	D	0.89196	-2.48	5.07	5.07	0.68467	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.235594	0.41605	D	0.000858	T	0.66557	0.2801	N	0.00859	-1.14	0.40122	D	0.976618	P	0.37158	0.585	B	0.30105	0.111	T	0.73332	-0.4016	10	0.24483	T	0.36	.	12.6488	0.56749	0.0801:0.0:0.9199:0.0	.	57	P12544	GRAA_HUMAN	T	57	ENSP00000274306:A57T	ENSP00000274306:A57T	A	+	1	0	GZMA	54437157	0.628000	0.27138	0.987000	0.45799	0.442000	0.32017	1.022000	0.30052	2.615000	0.88500	0.655000	0.94253	GCT	.	.		0.388	GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144		A	54401400	G	A	54401400	3	1	136	1	0	0	0	0	1	0	0	0	6924	1203	42	3	175	3	GZMA	5	54401400	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	27520149	54401400	126513860	20	21688										
NR3C1	2908	hgsc.bcm.edu	37	chr5	142779486	142779486	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	accaattatatttgctccagGaaagcttgcctgacagtaaa	7	9	0	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr5:142779486G>C	ENST00000343796.2	-	2	1912	c.919C>G	c.(919-921)Cct>Gct	p.P307A	NR3C1_ENST00000231509.3_Missense_Mutation_p.P307A|NR3C1_ENST00000416954.2_Intron|NR3C1_ENST00000415690.2_Missense_Mutation_p.P307A|NR3C1_ENST00000394466.2_Missense_Mutation_p.P307A|NR3C1_ENST00000503201.1_Missense_Mutation_p.P307A|NR3C1_ENST00000504572.1_Missense_Mutation_p.P307A|NR3C1_ENST00000394464.2_Missense_Mutation_p.P307A|NR3C1_ENST00000424646.2_Missense_Mutation_p.P307A	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	307	Modulating.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	TTTGCTCCAGGAAAGCTTGCC	0.428																																					p.P307A		Atlas-SNP	.											.	NR3C1	124	.	0			c.C919G						.						77	80	79					5																	142779486		2203	4300	6503	SO:0001583	missense	2908	exon2			CTCCAGGAAAGCT	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.919C>G	chr5.hg19:g.142779486G>C	ENSP00000343205:p.Pro307Ala	72.0	0.0		87.0	4.0	NM_001018074	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	hg19	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.402063	0.25291	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000361001;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000503201	T;T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6	5.65	2.04	0.26737	.	0.290828	0.39544	N	0.001337	T	0.16769	0.0403	N	0.19112	0.55	0.80722	D	1	B;B;B	0.21147	0.052;0.012;0.015	B;B;B	0.23574	0.047;0.014;0.028	T	0.07829	-1.0752	10	0.14252	T	0.57	.	8.8019	0.34914	0.707:0.0:0.293:0.0	.	307;307;307	E5KQF5;P04150;E5KQF6	.;GCR_HUMAN;.	A	307	ENSP00000377977:P307A;ENSP00000343205:P307A;ENSP00000387672:P307A;ENSP00000405282:P307A;ENSP00000422518:P307A;ENSP00000377979:P307A;ENSP00000231509:P307A;ENSP00000427672:P307A	ENSP00000231509:P307A	P	-	1	0	NR3C1	142759679	0.998000	0.40836	1.000000	0.80357	0.878000	0.50629	0.620000	0.24403	0.421000	0.25980	-0.312000	0.09012	CCT	.	.		0.428	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			C	142779486	G	C	142779486	3	2	136	1	0	0	0	0	1	0	0	0	10639	1174	41	4	1501	4	NR3C1	5	142779486	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	88378086	142779486	38135774	21	21689										
PHIP	55023	hgsc.bcm.edu	37	chr6	79752610	79752610	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	agttacacagtacacagatgAcaagtgtccaagaattcgtt	8	8	0	3			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr6:79752610A>T	ENST00000275034.4	-	7	717	c.550T>A	c.(550-552)Tca>Aca	p.S184T		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	184					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TACACAGATGACAAGTGTCCA	0.353																																					p.S184T		Atlas-SNP	.											.	PHIP	177	.	0			c.T550A						.						165	159	161					6																	79752610		2203	4299	6502	SO:0001583	missense	55023	exon7			CAGATGACAAGTG	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.550T>A	chr6.hg19:g.79752610A>T	ENSP00000275034:p.Ser184Thr	70.0	0.0		75.0	4.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.961330	0.92791	.	.	ENSG00000146247	ENST00000275034	T	0.27720	1.65	5.29	5.29	0.74685	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000013	T	0.34571	0.0902	L	0.41356	1.27	0.80722	D	1	D;D	0.57257	0.979;0.979	D;D	0.74023	0.982;0.982	T	0.07271	-1.0781	9	.	.	.	-9.4383	14.3835	0.66926	1.0:0.0:0.0:0.0	.	184;184	A7J992;Q8WWQ0	.;PHIP_HUMAN	T	184	ENSP00000275034:S184T	.	S	-	1	0	PHIP	79809329	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	8.880000	0.92407	1.994000	0.58287	0.533000	0.62120	TCA	.	.		0.353	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			T	79752610	A	T	79752610	3	4	136	1	0	0	0	0	1	0	0	0	11851	275	10	4	5051	4	PHIP	6	79752610	Missense_Mutation	SNP	A	TCGA-DD-A4NO-01A-11D-A28X-10		79752610	91362457	22	21690										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157522055	157522055	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ggcagatccagacacacggaAtcccgcctcagatgatgggc	12	13	1	4			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr6:157522055A>G	ENST00000350026.5	+	17	4289	c.4288A>G	c.(4288-4290)Atc>Gtc	p.I1430V	ARID1B_ENST00000275248.4_Missense_Mutation_p.I1425V|ARID1B_ENST00000367148.1_Missense_Mutation_p.I1483V|ARID1B_ENST00000346085.5_Missense_Mutation_p.I1443V	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1430					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GACACACGGAATCCCGCCTCA	0.637																																					p.I1443V		Atlas-SNP	.											.	ARID1B	320	.	0			c.A4327G						.						28	32	31					6																	157522055		2203	4296	6499	SO:0001583	missense	57492	exon18			CACGGAATCCCGC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.4288A>G	chr6.hg19:g.157522055A>G	ENSP00000055163:p.Ile1430Val	179.0	0.0		216.0	90.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	1.491	-0.554755	0.03996	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.01981	4.86;4.86;4.85;4.85;4.52	5.08	-4.85	0.03142	.	0.267066	0.41823	N	0.000816	T	0.00440	0.0014	N	0.22421	0.69	0.09310	N	0.999995	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.46748	-0.9169	10	0.16896	T	0.51	.	8.7325	0.34507	0.4103:0.4637:0.126:0.0	.	1430;1443;1425	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	V	1443;1430;1483;1425;952	ENSP00000344546:I1443V;ENSP00000055163:I1430V;ENSP00000356116:I1483V;ENSP00000275248:I1425V;ENSP00000412835:I952V	ENSP00000275248:I1425V	I	+	1	0	ARID1B	157563747	0.589000	0.26807	0.017000	0.16124	0.037000	0.13140	1.471000	0.35365	-0.553000	0.06158	-0.326000	0.08463	ATC	.	.		0.637	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		G	157522055	A	G	157522055	3	3	136	1	0	0	0	0	1	0	0	0	914	101	4	2	4397	2	ARID1B	6	157522055	Missense_Mutation	SNP	A	TCGA-DD-A4NO-01A-11D-A28X-10	77769445	157522055	13593012	23	21691										
LPA	4018	hgsc.bcm.edu	37	chr6	161016508	161016508	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	acctgacactgggatccatgGtgtaacaccaagggcgaatc	11	11	0	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr6:161016508G>T	ENST00000316300.5	-	21	3391	c.3347C>A	c.(3346-3348)aCc>aAc	p.T1116N	LPA_ENST00000447678.1_Missense_Mutation_p.T1116N			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3624	Kringle 10. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GGGATCCATGGTGTAACACCA	0.517																																					p.T1116N		Atlas-SNP	.											.	LPA	237	.	0			c.C3347A						.						107	105	106					6																	161016508		2123	4259	6382	SO:0001583	missense	4018	exon22			TCCATGGTGTAAC	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.3347C>A	chr6.hg19:g.161016508G>T	ENSP00000321334:p.Thr1116Asn	84.0	0.0		143.0	29.0	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	hg19	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	g	11.47	1.648034	0.29336	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.70986	-0.53;-0.53	2.31	2.31	0.28768	Kringle (4);Kringle-like fold (1);	.	.	.	.	D	0.82416	0.5032	H	0.95816	3.725	0.23739	N	0.996974	D	0.76494	0.999	D	0.97110	1.0	T	0.70454	-0.4867	9	0.87932	D	0	.	8.0392	0.30511	0.0:0.0:1.0:0.0	.	3624	P08519	APOA_HUMAN	N	1116	ENSP00000321334:T1116N;ENSP00000395608:T1116N	ENSP00000321334:T1116N	T	-	2	0	LPA	160936498	1.000000	0.71417	0.217000	0.23759	0.314000	0.28054	5.905000	0.69893	1.265000	0.44215	0.205000	0.17691	ACC	.	.		0.517	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	161016508	G	T	161016508	3	4	136	1	0	0	0	0	1	0	0	0	8912	1261	44	3	2851	3	LPA	6	161016508	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	3494453	161016508	10098559	24	21692										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11446000	11446000	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ataatgagttcaatgtcagcAcagaattcctcatccaccac	5	12	3	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr7:11446000A>G	ENST00000423059.4	-	22	4415	c.4164T>C	c.(4162-4164)tgT>tgC	p.C1388C	AC004538.3_ENST00000445839.1_RNA|AC004160.4_ENST00000425837.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1388	TSP type-1 14. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CAATGTCAGCACAGAATTCCT	0.443										HNSCC(18;0.044)																											p.C1388C		Atlas-SNP	.											.	THSD7A	219	.	0			c.T4164C						.						114	116	115					7																	11446000		1923	4154	6077	SO:0001819	synonymous_variant	221981	exon21			GTCAGCACAGAAT		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.4164T>C	chr7.hg19:g.11446000A>G		71.0	0.0		155.0	56.0	NM_015204		Silent	SNP	ENST00000423059.4	hg19	CCDS47543.1																																																																																			.	.		0.443	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		G	11446000	A	G	11446000	2	3	136	1	0	0	0	0	0	0	0	1	15894	157	6	2		2	THSD7A	7	11446000	Silent	SNP	A	TCGA-DD-A4NO-01A-11D-A28X-10		11446000	147692663	25	21693										
FKBP9	11328	hgsc.bcm.edu	37	chr7	33014908	33014908	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	caagcccccgagttgccctcGgaccatccaggtgtctgatt	10	15	1	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr7:33014908G>A	ENST00000242209.4	+	3	651	c.482G>A	c.(481-483)cGg>cAg	p.R161Q	AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Missense_Mutation_p.R214Q|FKBP9_ENST00000538443.1_Missense_Mutation_p.R23Q	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	161					chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			AGTTGCCCTCGGACCATCCAG	0.473																																					p.R161Q		Atlas-SNP	.											FKBP9,brain,glioma,0,9	FKBP9	335	.	0			c.G482A						.						99	87	91					7																	33014908		2203	4300	6503	SO:0001583	missense	11328	exon3			GCCCTCGGACCAT	AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"EF-hand domain containing"	3725	protein-coding gene	gene with protein product			"FK506-binding protein 9 (63 kD)"			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.482G>A	chr7.hg19:g.33014908G>A	ENSP00000242209:p.Arg161Gln	93.0	2.0		140.0	6.0	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Missense_Mutation	SNP	ENST00000242209.4	hg19	CCDS5439.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.720086	0.89205	.	.	ENSG00000122642	ENST00000242209;ENST00000538336;ENST00000538443	D;D;D	0.86164	-2.08;-2.08;-2.08	5.36	5.36	0.76844	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (1);	0.000000	0.85682	D	0.000000	D	0.92714	0.7684	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.92752	0.6217	10	0.56958	D	0.05	-4.2611	19.0957	0.93249	0.0:0.0:1.0:0.0	.	214;161;161	B7Z6H3;O95302;B3KQQ0	.;FKBP9_HUMAN;.	Q	161;214;23	ENSP00000242209:R161Q;ENSP00000439250:R214Q;ENSP00000437504:R23Q	ENSP00000242209:R161Q	R	+	2	0	FKBP9	32981433	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	9.809000	0.99208	2.524000	0.85096	0.650000	0.86243	CGG	.	.		0.473	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270		A	33014908	G	A	33014908	3	1	136	1	0	0	0	0	1	0	0	0	5923	1116	39	1	492	1	FKBP9	7	33014908	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	21568908	33014908	126123755	26	21694										
GSR	2936	hgsc.bcm.edu	37	chr8	30538494	30538494	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	tggtaactgcgtgatacatcGgggtaaagctcgttgaatag	13	6	0	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr8:30538494G>T	ENST00000221130.5	-	12	1436	c.1346C>A	c.(1345-1347)cCg>cAg	p.P449Q	GSR_ENST00000546342.1_Missense_Mutation_p.P420Q|GSR_ENST00000537535.1_Missense_Mutation_p.P367Q|GSR_ENST00000414019.1_Missense_Mutation_p.P406Q|GSR_ENST00000541648.1_Missense_Mutation_p.P396Q	NM_000637.3|NM_001195102.1|NM_001195103.1	NP_000628.2|NP_001182031.1|NP_001182032.1	P00390	GSHR_HUMAN	glutathione reductase	449					cell redox homeostasis (GO:0045454)|glutathione metabolic process (GO:0006749)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|glutathione-disulfide reductase activity (GO:0004362)|NADP binding (GO:0050661)	p.P449Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	23				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Flavin adenine dinucleotide(DB03147)|Glutathione(DB00143)	GTGATACATCGGGGTAAAGCT	0.338																																					p.P449Q		Atlas-SNP	.											.	GSR	53	.	1	Substitution - Missense(1)	lung(1)	c.C1346A						.						253	240	244					8																	30538494		2201	4300	6501	SO:0001583	missense	2936	exon12			TACATCGGGGTAA		CCDS34877.1, CCDS56530.1, CCDS56531.1, CCDS56532.1	8p21.1	2012-10-02			ENSG00000104687	ENSG00000104687	1.8.1.7		4623	protein-coding gene	gene with protein product		138300					Standard	NM_000637		Approved		uc003xih.2	P00390	OTTHUMG00000163946	ENST00000221130.5:c.1346C>A	chr8.hg19:g.30538494G>T	ENSP00000221130:p.Pro449Gln	81.0	0.0		82.0	4.0	NM_000637	C8KIL8|C8KIL9|C8KIM0|D3DSV3|Q7Z5C9|Q9NP63	Missense_Mutation	SNP	ENST00000221130.5	hg19	CCDS34877.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611051	0.66558	.	.	ENSG00000104687	ENST00000221130;ENST00000414019;ENST00000546342;ENST00000541648;ENST00000537535	D;D;D;D;D	0.92446	-3.04;-3.04;-3.04;-3.04;-3.04	5.35	5.35	0.76521	FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (2);	0.000000	0.85682	D	0.000000	D	0.96987	0.9016	M	0.92880	3.355	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97760	1.0220	10	0.72032	D	0.01	-25.7309	16.6411	0.85127	0.0:0.0:1.0:0.0	.	449	P00390	GSHR_HUMAN	Q	449;406;420;396;367	ENSP00000221130:P449Q;ENSP00000390065:P406Q;ENSP00000445516:P420Q;ENSP00000444559:P396Q;ENSP00000438845:P367Q	ENSP00000221130:P449Q	P	-	2	0	GSR	30658036	1.000000	0.71417	1.000000	0.80357	0.276000	0.26787	8.914000	0.92735	2.511000	0.84671	0.650000	0.86243	CCG	.	.		0.338	GSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376519.1			T	30538494	G	T	30538494	3	4	136	1	0	0	0	0	1	0	0	0	6837	1116	39	1	230	1	GSR	8	30538494	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10		30538494	115825528	27	21695										
OPLAH	26873	hgsc.bcm.edu	37	chr8	145106719	145106719	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gtttaggccgcgggcgccagGctcgccccctgcggagggag	18	14	0	0			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr8:145106719G>C	ENST00000426825.1	-	27	3712	c.3631C>G	c.(3631-3633)Cct>Gct	p.P1211A	CTD-3065J16.6_ENST00000561181.1_RNA|CTD-3065J16.6_ENST00000528912.1_RNA|OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	1211					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CGGGCGCCAGGCTCGCCCCCT	0.741																																					p.P1211A		Atlas-SNP	.											.	OPLAH	78	.	0			c.C3631G						.						13	15	14					8																	145106719		1811	4057	5868	SO:0001583	missense	26873	exon27			CGCCAGGCTCGCC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.3631C>G	chr8.hg19:g.145106719G>C	ENSP00000475943:p.Pro1211Ala	29.0	0.0		47.0	15.0	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	hg19		.	.	.	.	.	.	.	.	.	.	g	8.918	0.960411	0.18507	.	.	ENSG00000178814	ENST00000426825	.	.	.	4.64	3.72	0.42706	.	0.447039	0.24242	N	0.040254	T	0.40015	0.1100	L	0.33339	1.005	0.31266	N	0.6923779999999999	B	0.14805	0.011	B	0.16289	0.015	T	0.51020	-0.8758	8	0.41790	T	0.15	.	10.7779	0.46361	0.0:0.1917:0.8083:0.0	.	1211	O14841	OPLA_HUMAN	A	1211	.	ENSP00000412071:P1211A	P	-	1	0	OPLAH	145178707	0.900000	0.30661	0.953000	0.39169	0.259000	0.26198	1.523000	0.35932	2.126000	0.65437	0.472000	0.43445	CCT	.	.		0.741	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		C	145106719	G	C	145106719	3	2	136	1	0	0	0	0	1	0	0	0	10885	1203	42	4	243	4	OPLAH	8	145106719	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	114568225	145106719	1257303	28	21696										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113173981	113173981	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	actccacttgccgtcggccaGgcattcaatggtgtcaagac	10	13	2	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr9:113173981G>T	ENST00000401783.2	-	37	6346	c.6010C>A	c.(6010-6012)Ctg>Atg	p.L2004M	SVEP1_ENST00000374469.1_Missense_Mutation_p.L1981M|SVEP1_ENST00000297826.5_De_novo_Start_InFrame	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2004	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CCGTCGGCCAGGCATTCAATG	0.493																																					p.L2004M		Atlas-SNP	.											.	SVEP1	326	.	0			c.C6010A						.						27	29	28					9																	113173981		1953	4144	6097	SO:0001583	missense	79987	exon37			CGGCCAGGCATTC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.6010C>A	chr9.hg19:g.113173981G>T	ENSP00000384917:p.Leu2004Met	89.0	0.0		100.0	4.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.934540	0.34189	.	.	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.66460	-0.21;-0.21	5.58	2.75	0.32379	Complement control module (2);Sushi/SCR/CCP (3);	0.140827	0.48286	D	0.000193	T	0.53610	0.1807	L	0.55213	1.73	0.80722	D	1	P	0.35192	0.489	B	0.33620	0.167	T	0.49969	-0.8882	10	0.42905	T	0.14	.	3.2306	0.06747	0.3981:0.0:0.4234:0.1785	.	2004	Q4LDE5	SVEP1_HUMAN	M	2004;1981	ENSP00000384917:L2004M;ENSP00000363593:L1981M	ENSP00000363593:L1981M	L	-	1	2	SVEP1	112213802	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.370000	0.44240	0.726000	0.32339	-0.218000	0.12543	CTG	.	.		0.493	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113173981	G	T	113173981	3	4	136	1	0	0	0	0	1	0	0	0	15435	991	35	3	4753	3	SVEP1	9	113173981	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10		113173981	28039450	29	21697										
SEC31B	25956	hgsc.bcm.edu	37	chr10	102265220	102265221	+	Frame_Shift_Ins	INS	-	-	A													0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ctggcacctgcagtggtgggINSagaggctggcctttgctgaa							TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr10:102265220_102265221insA	ENST00000370345.3	-	10	1173_1174	c.1076_1077insT	c.(1075-1077)ctcfs	p.L359fs	SEC31B_ENST00000451524.1_Frame_Shift_Ins_p.L359fs	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	359					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GCAGTGGTGGGAGAGGCTGGCC	0.515																																					p.L359fs		Atlas-Indel,Pindel	.											.	SEC31B	84	.	0			c.1077_1078insT						.																																			SO:0001589	frameshift_variant	25956	exon10			.	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.1077dupT	chr10.hg19:g.102265221_102265221dupA	ENSP00000359370:p.Leu359fs	55.0	0.0		95.0	23.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Frame_Shift_Ins	INS	ENST00000370345.3	hg19	CCDS7495.1																																																																																			.	.		0.515	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		A	102265221	-	A	102265220	7	5	136	1	0	1	1	0	0	0	0	0	14014	1161	41	0	2530	0	SEC31B	10	102265220	Frame_Shift_Ins	INS	-	TCGA-DD-A4NO-01A-11D-A28X-10		102265220	33269527	30	21698										
ABTB2	25841	hgsc.bcm.edu	37	chr11	34189528	34189528	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gcagcgcaggcgtacatcagTggcgtcataccctgagcaaa	12	12	2	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr11:34189528T>G	ENST00000435224.2	-	6	1999	c.1575A>C	c.(1573-1575)ccA>ccC	p.P525P	ABTB2_ENST00000298992.2_Silent_p.P339P	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	525					cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				CGTACATCAGTGGCGTCATAC	0.542																																					p.P525P		Atlas-SNP	.											.	ABTB2	101	.	0			c.A1575C						.						155	94	115					11																	34189528		2202	4298	6500	SO:0001819	synonymous_variant	25841	exon6			CATCAGTGGCGTC	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.1575A>C	chr11.hg19:g.34189528T>G		84.0	0.0		121.0	18.0	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Silent	SNP	ENST00000435224.2	hg19	CCDS7890.2																																																																																			.	.		0.542	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804		G	34189528	T	G	34189528	2	3	136	1	0	0	0	0	0	0	0	1	103	1683	59	5		5	ABTB2	11	34189528	Silent	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10		34189528	100816988	31	21699										
LRP4	4038	hgsc.bcm.edu	37	chr11	46921839	46921839	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	cctgctcatccgagtcatccTcacagtcgttgtccccgtca	7	17	4	0			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr11:46921839T>A	ENST00000378623.1	-	3	532	c.290A>T	c.(289-291)gAg>gTg	p.E97V		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	97	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		CGAGTCATCCTCACAGTCGTT	0.532																																					p.E97V		Atlas-SNP	.											.	LRP4	160	.	0			c.A290T						.						131	114	120					11																	46921839		2201	4299	6500	SO:0001583	missense	4038	exon3			TCATCCTCACAGT	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.290A>T	chr11.hg19:g.46921839T>A	ENSP00000367888:p.Glu97Val	120.0	0.0		190.0	74.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	T	15.73	2.918894	0.52546	.	.	ENSG00000134569	ENST00000378623;ENST00000534404	D;D	0.95690	-3.78;-3.78	5.63	5.63	0.86233	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.140677	0.47852	D	0.000201	D	0.94411	0.8202	L	0.38649	1.16	0.52501	D	0.999956	P;D	0.59357	0.692;0.985	B;P	0.51453	0.22;0.67	D	0.93936	0.7219	10	0.38643	T	0.18	.	15.841	0.78845	0.0:0.0:0.0:1.0	.	142;97	C9JRN7;O75096	.;LRP4_HUMAN	V	97;48	ENSP00000367888:E97V;ENSP00000434763:E48V	ENSP00000367888:E97V	E	-	2	0	LRP4	46878415	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.209000	0.58493	2.146000	0.66826	0.459000	0.35465	GAG	.	.		0.532	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		A	46921839	T	A	46921839	3	1	136	1	0	0	0	0	1	0	0	0	8968	1551	54	4	5571	4	LRP4	11	46921839	Missense_Mutation	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10	12732311	46921839	88084677	32	21700										
C11orf9	745	hgsc.bcm.edu	37	chr11	61547742	61547742	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ctgagcctgcgcacagaggaGgacctggtagacactgatgg	15	10	0	4			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr11:61547742G>C	ENST00000278836.5	+	18	2481	c.2385G>C	c.(2383-2385)gaG>gaC	p.E795D	MYRF_ENST00000327797.1_Missense_Mutation_p.G478R|MYRF_ENST00000265460.5_Missense_Mutation_p.E786D|MYRF_ENST00000389602.4_Missense_Mutation_p.E186D|TMEM258_ENST00000535042.1_Intron	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	795					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCACAGAGGAGGACCTGGTAG	0.612																																					p.E795D		Atlas-SNP	.											.	.	.	.	0			c.G2385C						.						87	68	75					11																	61547742		2202	4299	6501	SO:0001583	missense	745	exon18			AGAGGAGGACCTG		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"myelin gene regulatory factor"	608329	"chromosome 11 open reading frame 9"	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.2385G>C	chr11.hg19:g.61547742G>C	ENSP00000278836:p.Glu795Asp	241.0	0.0		387.0	71.0	NM_001127392	O43582|Q9P1Q6	Missense_Mutation	SNP	ENST00000278836.5	hg19	CCDS44622.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.15|11.15	1.554032|1.554032	0.27739|0.27739	.|.	.|.	ENSG00000124920|ENSG00000124920	ENST00000278836;ENST00000265460;ENST00000389602|ENST00000327797	T;T;T|T	0.32988|0.40225	1.44;1.45;1.43|1.04	4.86|4.86	1.92|1.92	0.25849|0.25849	.|.	0.109296|.	0.64402|.	D|.	0.000007|.	T|T	0.33323|0.33323	0.0859|0.0859	L|L	0.29908|0.29908	0.895|0.895	0.26322|0.26322	N|N	0.977664|0.977664	P;P;B|.	0.37688|.	0.605;0.459;0.011|.	B;B;B|.	0.39590|.	0.18;0.304;0.01|.	T|T	0.29731|0.29731	-1.0002|-1.0002	10|7	0.22109|0.87932	T|D	0.4|0	-34.3974|-34.3974	5.9653|5.9653	0.19322|0.19322	0.225:0.0:0.6412:0.1338|0.225:0.0:0.6412:0.1338	.|.	186;786;795|.	B4DHB2;Q9Y2G1-2;Q9Y2G1|.	.;.;MRF_HUMAN|.	D|R	795;786;186|478	ENSP00000278836:E795D;ENSP00000265460:E786D;ENSP00000374253:E186D|ENSP00000333261:G478R	ENSP00000265460:E786D|ENSP00000333261:G478R	E|G	+|+	3|1	2|0	C11orf9|C11orf9	61304318|61304318	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.816000|0.816000	0.46133|0.46133	1.460000|1.460000	0.35244|0.35244	0.587000|0.587000	0.29643|0.29643	-0.258000|-0.258000	0.10820|0.10820	GAG|GGA	.	.		0.612	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		C	61547742	G	C	61547742	3	2	136	1	0	0	0	0	1	0	0	0	1673	991	35	4	2478	4	C11orf9	11	61547742	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	14625903	61547742	73458774	33	21701										
KRT79	338785	hgsc.bcm.edu	37	chr12	53216820	53216820	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ctgctctcctcgctctccagAagcttgcggtaggtggcaat	11	13	2	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr12:53216820A>G	ENST00000330553.5	-	7	1381	c.1347T>C	c.(1345-1347)ctT>ctC	p.L449L		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	449	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CGCTCTCCAGAAGCTTGCGGT	0.657																																					p.L449L		Atlas-SNP	.											.	KRT79	78	.	0			c.T1347C						.						58	55	56					12																	53216820		2203	4300	6503	SO:0001819	synonymous_variant	338785	exon7			CTCCAGAAGCTTG	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"-", "Intermediate filaments type II, keratins (basic)"	28930	protein-coding gene	gene with protein product	"keratin 6-like"	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.1347T>C	chr12.hg19:g.53216820A>G		60.0	0.0		65.0	18.0	NM_175834	Q6P465|Q7Z793	Silent	SNP	ENST00000330553.5	hg19	CCDS8839.1																																																																																			.	.		0.657	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		G	53216820	A	G	53216820	2	3	136	1	0	0	0	0	0	0	0	1	8501	233	9	2		2	KRT79	12	53216820	Silent	SNP	A	TCGA-DD-A4NO-01A-11D-A28X-10		53216820	80635075	34	21702										
CRY1	1407	hgsc.bcm.edu	37	chr12	107393336	107393336	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ttagaacacttaccttcattCcttcttcccaactaatccac	1	15	2	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr12:107393336C>G	ENST00000008527.5	-	7	1997	c.1130G>C	c.(1129-1131)gGa>gCa	p.G377A		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	377	Required for inhibition of CLOCK- ARNTL/BMAL1-mediated transcription. {ECO:0000250}.				blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						TACCTTCATTCCTTCTTCCCA	0.413																																					p.G377A		Atlas-SNP	.											.	CRY1	74	.	0			c.G1130C						.						84	78	80					12																	107393336		2203	4300	6503	SO:0001583	missense	1407	exon7			TTCATTCCTTCTT	BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"cryptochrome 1 (photolyase-like)"	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.1130G>C	chr12.hg19:g.107393336C>G	ENSP00000008527:p.Gly377Ala	93.0	0.0		80.0	29.0	NM_004075		Missense_Mutation	SNP	ENST00000008527.5	hg19	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708209	0.89018	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.79	5.79	0.91817	DNA photolyase, FAD-binding/Cryptochrome, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.90017	0.6883	H	0.96489	3.83	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92455	0.5973	9	0.87932	D	0	-17.7008	20.0308	0.97536	0.0:1.0:0.0:0.0	.	377	Q16526	CRY1_HUMAN	A	377	.	ENSP00000008527:G377A	G	-	2	0	CRY1	105917466	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.818000	0.86416	2.732000	0.93576	0.585000	0.79938	GGA	.	.		0.413	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075		G	107393336	C	G	107393336	3	3	136	1	0	0	0	0	1	0	0	0	3905	855	30	4	654	4	CRY1	12	107393336	Missense_Mutation	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10	54176516	107393336	26458559	35	21703										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112601506	112601506	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gctcccgcagccgcaggctcCggatggctgccgcgtagatg	15	15	0	1	rs564542020		TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr12:112601506C>T	ENST00000430131.2	-	73	12616	c.11471G>A	c.(11470-11472)cGg>cAg	p.R3824Q	HECTD4_ENST00000549141.1_5'Flank|HECTD4_ENST00000550722.1_Missense_Mutation_p.R4100Q|HECTD4_ENST00000377560.5_Missense_Mutation_p.R4074Q			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3824	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CCGCAGGCTCCGGATGGCTGC	0.682													C|||	1	0.000199681	8e-04	0	5008	,	,		17361	0		0	False		,,,				2504	0				p.R4112Q		Atlas-SNP	.											.	.	.	.	0			c.G12335A						.						5	9	7					12																	112601506		1490	2933	4423	SO:0001583	missense	283450	exon74			AGGCTCCGGATGG	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.11471G>A	chr12.hg19:g.112601506C>T	ENSP00000404379:p.Arg3824Gln	70.0	0.0		64.0	22.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.822958	0.96989	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722;ENST00000547085	T;T;T	0.57436	0.4;0.4;0.4	5.73	5.73	0.89815	HECT (4);	.	.	.	.	T	0.64416	0.2596	L	0.31664	0.95	0.58432	D	0.999999	D	0.69078	0.997	D	0.72982	0.979	T	0.66432	-0.5925	9	0.72032	D	0.01	.	19.8984	0.96975	0.0:1.0:0.0:0.0	.	3824	Q9Y4D8	K0614_HUMAN	Q	4074;3824;4100;289	ENSP00000366783:R4074Q;ENSP00000404379:R3824Q;ENSP00000449784:R4100Q	ENSP00000366783:R4074Q	R	-	2	0	C12orf51	111085889	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.597000	0.67577	2.713000	0.92767	0.655000	0.94253	CGG	.	.		0.682	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112601506	C	T	112601506	3	4	136	1	0	0	0	0	1	0	0	0	1698	652	23	1	531	1	C12orf51	12	112601506	Missense_Mutation	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10	5208170	112601506	21250389	36	21704										
EBPL	84650	hgsc.bcm.edu	37	chr13	50235138	50235138	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	tcactgaactggtttctttcTgatgcattttcttgagttct	7	8	5	3			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr13:50235138T>G	ENST00000242827.6	-	4	637	c.587A>C	c.(586-588)cAg>cCg	p.Q196P	EBPL_ENST00000495963.2_5'UTR|EBPL_ENST00000378270.5_3'UTR|EBPL_ENST00000378284.2_3'UTR|EBPL_ENST00000378272.5_3'UTR	NM_032565.3	NP_115954.1	Q9BY08	EBPL_HUMAN	emopamil binding protein-like	196					sterol metabolic process (GO:0016125)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholestenol delta-isomerase activity (GO:0047750)	p.Q196P(2)		endometrium(8)|kidney(6)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		GGTTTCTTTCTGATGCATTTT	0.383																																					p.Q196P	NSCLC(39;857 1083 36109 42364 51411)	Atlas-SNP	.											EBPL,NS,carcinoma,0,2	EBPL	44	.	2	Substitution - Missense(2)	endometrium(2)	c.A587C						.						73	73	73					13																	50235138		2203	4300	6503	SO:0001583	missense	84650	exon4			TCTTTCTGATGCA	AF243433	CCDS9420.1, CCDS61334.1	13q12-q13	2008-02-05			ENSG00000123179	ENSG00000123179			18061	protein-coding gene	gene with protein product							Standard	NM_032565		Approved	EBRP	uc001vdg.3	Q9BY08	OTTHUMG00000016920	ENST00000242827.6:c.587A>C	chr13.hg19:g.50235138T>G	ENSP00000242827:p.Gln196Pro	96.0	1.0		82.0	4.0	NM_032565	A6NJ59|Q569H7|Q5JVN2|Q5JVN3|Q5JVN4|Q5JVN5|Q5JVN6	Missense_Mutation	SNP	ENST00000242827.6	hg19	CCDS9420.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.722268	0.48728	.	.	ENSG00000123179	ENST00000242827	D	0.97994	-4.65	5.61	-2.45	0.06481	.	1.466260	0.03646	N	0.240220	D	0.94876	0.8344	L	0.47716	1.5	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	D	0.86530	0.1821	10	0.30078	T	0.28	-0.1548	6.1064	0.20075	0.3657:0.0:0.2518:0.3825	.	196	Q9BY08	EBPL_HUMAN	P	196	ENSP00000242827:Q196P	ENSP00000242827:Q196P	Q	-	2	0	EBPL	49133139	0.002000	0.14202	0.003000	0.11579	0.996000	0.88848	-0.059000	0.11731	-0.151000	0.11176	0.528000	0.53228	CAG	.	.		0.383	EBPL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044932.2	NM_032565		G	50235138	T	G	50235138	3	3	136	1	0	0	0	0	1	0	0	0	4889	1580	55	5	37	5	EBPL	13	50235138	Missense_Mutation	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10		50235138	64934740	37	21705										
CLN5	1203	hgsc.bcm.edu	37	chr13	77566254	77566254	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	atggcgcaggaggtagacacGgcacagggcgccgagatgcg	18	10	0	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr13:77566254G>C	ENST00000377453.3	+	1	1460	c.168G>C	c.(166-168)acG>acC	p.T56T	CLN5_ENST00000485938.1_3'UTR	NM_006493.2	NP_006484.1	O75503	CLN5_HUMAN	ceroid-lipofuscinosis, neuronal 5	7					brain development (GO:0007420)|cell death (GO:0008219)|glycosylation (GO:0070085)|lysosomal lumen acidification (GO:0007042)|neurogenesis (GO:0022008)|neuron maturation (GO:0042551)|protein catabolic process (GO:0030163)|signal peptide processing (GO:0006465)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|vacuolar lumen (GO:0005775)	mannose binding (GO:0005537)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0503)		AGGTAGACACGGCACAGGGCG	0.741																																					p.T56T		Atlas-SNP	.											.	CLN5	32	.	0			c.G168C						.						11	14	13					13																	77566254		2161	4235	6396	SO:0001819	synonymous_variant	1203	exon1			AGACACGGCACAG		CCDS9456.1	13q21.2-q32	2014-09-17			ENSG00000102805	ENSG00000102805			2076	protein-coding gene	gene with protein product		608102				7942847, 8661106	Standard	NM_006493		Approved		uc001vkc.3	O75503	OTTHUMG00000017100	ENST00000377453.3:c.168G>C	chr13.hg19:g.77566254G>C		25.0	0.0		32.0	5.0	NM_006493	B3KQK7	Silent	SNP	ENST00000377453.3	hg19	CCDS9456.1																																																																																			.	.		0.741	CLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045318.1	NM_006493		C	77566254	G	C	77566254	2	2	136	1	0	0	0	0	0	0	0	1	3546	1103	39	4		4	CLN5	13	77566254	Silent	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	27331116	77566254	37603624	38	21706										
SLC10A2	6555	hgsc.bcm.edu	37	chr13	103705045	103705045	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gaaacaggaacaacgagagaAaccagagatgtacctaaaga	10	7	0	3			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr13:103705045A>T	ENST00000245312.3	-	3	1106	c.510T>A	c.(508-510)gtT>gtA	p.V170V		NM_000452.2	NP_000443	Q12908	NTCP2_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 2	170					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	bile acid:sodium symporter activity (GO:0008508)			breast(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)				Aciclovir(DB00787)|Cyclosporine(DB00091)|Ursodeoxycholic acid(DB01586)|Valaciclovir(DB00577)	CAACGAGAGAAACCAGAGATG	0.398																																					p.V170V		Atlas-SNP	.											.	SLC10A2	67	.	0			c.T510A						.						167	152	157					13																	103705045		2203	4300	6503	SO:0001819	synonymous_variant	6555	exon3			GAGAGAAACCAGA	U10417	CCDS9506.1	13q33	2013-07-18	2013-07-18		ENSG00000125255	ENSG00000125255		"Solute carriers"	10906	protein-coding gene	gene with protein product		601295		ASBT, ISBT		8661017	Standard	NM_000452		Approved		uc001vpy.4	Q12908	OTTHUMG00000017313	ENST00000245312.3:c.510T>A	chr13.hg19:g.103705045A>T		87.0	0.0		94.0	25.0	NM_000452	A1L4F4|Q13839	Silent	SNP	ENST00000245312.3	hg19	CCDS9506.1																																																																																			.	.		0.398	SLC10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045716.1			T	103705045	A	T	103705045	2	4	136	1	0	0	0	0	0	0	0	1	14389	1	1	4		4	SLC10A2	13	103705045	Silent	SNP	A	TCGA-DD-A4NO-01A-11D-A28X-10	26138791	103705045	11464833	39	21707										
BAZ1A	11177	hgsc.bcm.edu	37	chr14	35255190	35255190	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	agtgcagctatcaagatccaAacttttcaaactgcagccta	6	11	2	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr14:35255190A>G	ENST00000382422.2	-	13	1951	c.1624T>C	c.(1624-1626)Ttg>Ctg	p.L542L	BAZ1A_ENST00000358716.4_Silent_p.L510L|BAZ1A_ENST00000360310.1_Silent_p.L542L			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	542					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		TCAAGATCCAAACTTTTCAAA	0.313																																					p.L542L		Atlas-SNP	.											.	BAZ1A	128	.	0			c.T1624C						.						44	43	43					14																	35255190		2203	4300	6503	SO:0001819	synonymous_variant	11177	exon14			GATCCAAACTTTT	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.1624T>C	chr14.hg19:g.35255190A>G		30.0	0.0		16.0	4.0	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	hg19	CCDS9651.1																																																																																			.	.		0.313	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			G	35255190	A	G	35255190	2	3	136	1	0	0	0	0	0	0	0	1	1329	11	1	2		2	BAZ1A	14	35255190	Silent	SNP	A	TCGA-DD-A4NO-01A-11D-A28X-10		35255190	72094350	40	21708										
TLN2	83660	hgsc.bcm.edu	37	chr15	63029258	63029258	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gccctgattgcacctggagaTgcagagcgtcaacaaagact	11	11	1	4			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr15:63029258T>G	ENST00000561311.1	+	28	3770	c.3540T>G	c.(3538-3540)gaT>gaG	p.D1180E	TLN2_ENST00000559908.1_3'UTR|TLN2_ENST00000306829.6_Missense_Mutation_p.D1180E			Q9Y4G6	TLN2_HUMAN	talin 2	1180	Ala-rich.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CACCTGGAGATGCAGAGCGTC	0.557																																					p.D1180E		Atlas-SNP	.											.	TLN2	253	.	0			c.T3540G						.						63	57	59					15																	63029258		2203	4300	6503	SO:0001583	missense	83660	exon26			TGGAGATGCAGAG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.3540T>G	chr15.hg19:g.63029258T>G	ENSP00000453508:p.Asp1180Glu	141.0	0.0		279.0	55.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.610404	0.46527	.	.	ENSG00000171914	ENST00000306829	T	0.16073	2.37	5.12	-1.57	0.08506	.	0.000000	0.85682	D	0.000000	T	0.18841	0.0452	M	0.64630	1.985	0.43133	D	0.994872	B	0.32731	0.382	B	0.35607	0.206	T	0.06215	-1.0839	10	0.45353	T	0.12	-17.8071	13.5526	0.61740	0.0:0.5273:0.0:0.4727	.	1180	Q9Y4G6	TLN2_HUMAN	E	1180	ENSP00000303476:D1180E	ENSP00000303476:D1180E	D	+	3	2	TLN2	60816550	0.361000	0.24972	0.892000	0.35008	0.972000	0.66771	-0.357000	0.07651	-0.486000	0.06744	-0.347000	0.07816	GAT	.	.		0.557	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			G	63029258	T	G	63029258	3	3	136	1	0	0	0	0	1	0	0	0	15963	1461	51	5	3642	5	TLN2	15	63029258	Missense_Mutation	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10		63029258	39502134	41	21709										
CELF6	60677	hgsc.bcm.edu	37	chr15	72582280	72582280	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	cccagggaacccgccctcacCgccatggtccggctgccgtg	12	19	1	0			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr15:72582280C>T	ENST00000569547.1	-	5	674	c.603G>A	c.(601-603)gcG>gcA	p.A201A	RP11-106M3.2_ENST00000379915.4_RNA|RP11-106M3.3_ENST00000570175.1_RNA|CELF6_ENST00000569311.1_5'UTR|CELF6_ENST00000543764.2_Splice_Site_p.A86A|CELF6_ENST00000567083.1_Splice_Site_p.A201A|CELF6_ENST00000395258.2_Splice_Site_p.A88A|CELF6_ENST00000287202.5_Splice_Site_p.A201A|CELF6_ENST00000539635.1_Splice_Site_p.A62A			Q96J87	CELF6_HUMAN	CUGBP, Elav-like family member 6	201	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(2)	13						CCGCCCTCACCGCCATGGTCC	0.687																																					p.A201A		Atlas-SNP	.											.	CELF6	30	.	0			c.G603A						.						12	14	13					15																	72582280		2163	4258	6421	SO:0001630	splice_region_variant	60677	exon5			CCTCACCGCCATG	AF425606	CCDS10242.1, CCDS53955.1, CCDS53956.1	15q24	2013-02-12	2010-02-19	2010-02-19	ENSG00000140488	ENSG00000140488		"RNA binding motif (RRM) containing"	14059	protein-coding gene	gene with protein product		612681	"Bruno (Drosophila) -like 6, RNA binding protein", "bruno-like 6, RNA binding protein (Drosophila)"	BRUNOL6		10893231	Standard	NM_052840		Approved		uc002auh.2	Q96J87	OTTHUMG00000133444	ENST00000569547.1:c.603+1G>A	chr15.hg19:g.72582280C>T		78.0	0.0		91.0	5.0	NM_001172684	B4DG28|B4DJB6|Q6PII4|Q6ZNJ7|Q8N607	Silent	SNP	ENST00000569547.1	hg19	CCDS10242.1																																																																																			.	.		0.687	CELF6-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000420180.1	NM_052840	Silent	T	72582280	C	T	72582280	5	4	136	1	0	0	0	0	0	0	1	0	3222	666	23	1	874	1	CELF6	15	72582280	Splice_Site	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10	9553022	72582280	29949112	42	21710										
GFOD2	81577	hgsc.bcm.edu	37	chr16	67709857	67709857	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ggaagcgcagcacgttccctAccaggctcatgagctgcggg	14	13	1	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr16:67709857A>G	ENST00000268797.7	-	3	704	c.359T>C	c.(358-360)gTa>gCa	p.V120A	GFOD2_ENST00000602377.1_5'UTR	NM_030819.3	NP_110446.3	Q3B7J2	GFOD2_HUMAN	glucose-fructose oxidoreductase domain containing 2	120					extracellular matrix organization (GO:0030198)	proteinaceous extracellular matrix (GO:0005578)	oxidoreductase activity (GO:0016491)			breast(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0151)|Epithelial(162;0.0505)|all cancers(182;0.242)		CACGTTCCCTACCAGGCTCAT	0.567																																					p.V120A		Atlas-SNP	.											.	GFOD2	36	.	0			c.T359C						.						95	72	80					16																	67709857		2198	4300	6498	SO:0001583	missense	81577	exon3			TTCCCTACCAGGC	AK074382	CCDS10845.1, CCDS59268.1	16q22.1	2008-02-05			ENSG00000141098	ENSG00000141098			28159	protein-coding gene	gene with protein product						12975309	Standard	NM_030819		Approved	FLJ23802, MGC11335	uc002eub.3	Q3B7J2	OTTHUMG00000137537	ENST00000268797.7:c.359T>C	chr16.hg19:g.67709857A>G	ENSP00000268797:p.Val120Ala	128.0	0.0		146.0	45.0	NM_030819	Q69YL9|Q6UXX6|Q7L648|Q8TE86|Q9BQ07|R4GNG5	Missense_Mutation	SNP	ENST00000268797.7	hg19	CCDS10845.1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.583781	0.65992	.	.	ENSG00000141098	ENST00000268797	T	0.29655	1.56	5.01	5.01	0.66863	NAD(P)-binding domain (1);	0.049892	0.85682	D	0.000000	T	0.41190	0.1148	M	0.68317	2.08	0.58432	D	0.999999	P	0.42203	0.773	P	0.45794	0.493	T	0.42565	-0.9444	10	0.72032	D	0.01	-30.6441	14.6786	0.69001	1.0:0.0:0.0:0.0	.	120	Q3B7J2	GFOD2_HUMAN	A	120	ENSP00000268797:V120A	ENSP00000268797:V120A	V	-	2	0	GFOD2	66267358	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	9.307000	0.96226	2.007000	0.58848	0.460000	0.39030	GTA	.	.		0.567	GFOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268868.2	NM_030819		G	67709857	A	G	67709857	3	3	136	1	0	0	0	0	1	0	0	0	6352	391	14	2	802	2	GFOD2	16	67709857	Missense_Mutation	SNP	A	TCGA-DD-A4NO-01A-11D-A28X-10		67709857	22644896	43	21711										
MED13	9969	hgsc.bcm.edu	37	chr17	60064481	60064481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	acgggcatgactagtagggcGtggagcatctacaaaagtca	13	8	2	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr17:60064481G>A	ENST00000397786.2	-	12	2348	c.2272C>T	c.(2272-2274)Cgc>Tgc	p.R758C		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	758					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CTAGTAGGGCGTGGAGCATCT	0.433																																					p.R758C		Atlas-SNP	.											.	MED13	181	.	0			c.C2272T						.						61	57	58					17																	60064481		1862	4100	5962	SO:0001583	missense	9969	exon12			TAGGGCGTGGAGC	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.2272C>T	chr17.hg19:g.60064481G>A	ENSP00000380888:p.Arg758Cys	134.0	0.0		189.0	57.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100342	0.56183	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.74947	-0.89	5.12	5.12	0.69794	.	0.059122	0.64402	D	0.000002	T	0.69646	0.3134	L	0.43152	1.355	0.80722	D	1	B	0.22983	0.078	B	0.11329	0.006	T	0.67317	-0.5701	10	0.56958	D	0.05	-20.273	18.9313	0.92566	0.0:0.0:1.0:0.0	.	758	Q9UHV7	MED13_HUMAN	C	758;757	ENSP00000380888:R758C	ENSP00000262436:R757C	R	-	1	0	MED13	57419263	1.000000	0.71417	0.992000	0.48379	0.901000	0.52897	7.277000	0.78572	2.560000	0.86352	0.655000	0.94253	CGC	.	.		0.433	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		A	60064481	G	A	60064481	3	1	136	1	0	0	0	0	1	0	0	0	9439	1145	40	1	4328	1	MED13	17	60064481	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10		60064481	21130729	44	21712										
KIAA1328	57536	hgsc.bcm.edu	37	chr18	34647263	34647263	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	atgacccctcaacatcctaaGacacatccagaatcatgcag	5	14	2	3			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr18:34647263G>C	ENST00000280020.5	+	7	1009	c.987G>C	c.(985-987)aaG>aaC	p.K329N	KIAA1328_ENST00000543923.1_Missense_Mutation_p.K221N|KIAA1328_ENST00000435985.2_Missense_Mutation_p.K45N|KIAA1328_ENST00000586135.1_Missense_Mutation_p.K45N|KIAA1328_ENST00000586501.1_Missense_Mutation_p.K45N|KIAA1328_ENST00000591619.1_Missense_Mutation_p.K325N	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	329										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		AACATCCTAAGACACATCCAG	0.468																																					p.K329N		Atlas-SNP	.											.	KIAA1328	39	.	0			c.G987C						.						111	106	108					18																	34647263		2089	4215	6304	SO:0001583	missense	57536	exon7			TCCTAAGACACAT	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.987G>C	chr18.hg19:g.34647263G>C	ENSP00000280020:p.Lys329Asn	196.0	0.0		229.0	18.0	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Missense_Mutation	SNP	ENST00000280020.5	hg19	CCDS45855.1	.	.	.	.	.	.	.	.	.	.	G	7.573	0.667232	0.14710	.	.	ENSG00000150477	ENST00000543923;ENST00000280020;ENST00000383055;ENST00000435985	T;T;T	0.45276	0.9;0.9;0.9	6.17	-0.189	0.13260	.	0.681821	0.14788	N	0.298395	T	0.36331	0.0963	L	0.50333	1.59	0.09310	N	1	B;B;P;B	0.46142	0.023;0.023;0.873;0.01	B;B;P;B	0.44990	0.023;0.023;0.466;0.007	T	0.18840	-1.0324	10	0.41790	T	0.15	.	6.9251	0.24410	0.4411:0.0:0.4455:0.1135	.	45;329;45;329	Q86T90-4;A8K8C3;Q86T90-3;Q86T90	.;.;.;K1328_HUMAN	N	221;329;329;45	ENSP00000441359:K221N;ENSP00000280020:K329N;ENSP00000390515:K45N	ENSP00000280020:K329N	K	+	3	2	KIAA1328	32901261	0.007000	0.16637	0.017000	0.16124	0.028000	0.11728	-0.117000	0.10708	-0.080000	0.12685	-0.150000	0.13652	AAG	.	.		0.468	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776		C	34647263	G	C	34647263	3	2	136	1	0	0	0	0	1	0	0	0	8234	933	33	4	1013	4	KIAA1328	18	34647263	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10		34647263	43429985	45	21713										
TIMM13	26517	hgsc.bcm.edu	37	chr19	2427289	2427289	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	cagggagcccccaggtttccCtatacacttccggaaacact	8	15	0	0			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr19:2427289C>T	ENST00000215570.3	-	2	514	c.154G>A	c.(154-156)Ggg>Agg	p.G52R	LMNB2_ENST00000475819.1_5'Flank|TIMM13_ENST00000591871.1_Missense_Mutation_p.G37R	NM_012458.2	NP_036590.1	Q9Y5L4	TIM13_HUMAN	translocase of inner mitochondrial membrane 13 homolog (yeast)	52					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein transport (GO:0072321)|protein targeting to mitochondrion (GO:0006626)|sensory perception of sound (GO:0007605)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space protein transporter complex (GO:0042719)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	zinc ion binding (GO:0008270)			endometrium(1)|prostate(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGGTTTCCCTATACACTTC	0.667																																					p.G52R		Atlas-SNP	.											.	TIMM13	7	.	0			c.G154A						.						96	110	105					19																	2427289		2203	4300	6503	SO:0001583	missense	26517	exon2			GTTTCCCTATACA	AF152352	CCDS12089.1	19p13.3	2008-07-04	2001-11-28	2002-03-17		ENSG00000099800			11816	protein-coding gene	gene with protein product		607383	"translocase of inner mitochondrial membrane 13 (yeast) homolog B"	TIMM13B		10552927, 17329230	Standard	NM_012458		Approved	Tim13	uc002lvx.1	Q9Y5L4		ENST00000215570.3:c.154G>A	chr19.hg19:g.2427289C>T	ENSP00000215570:p.Gly52Arg	39.0	0.0		73.0	25.0	NM_012458	P62206|Q9UHL8|Q9WTL1	Missense_Mutation	SNP	ENST00000215570.3	hg19	CCDS12089.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.493180	0.44352	.	.	ENSG00000099800	ENST00000215570	T	0.62498	0.02	3.44	3.44	0.39384	.	0.000000	0.85682	D	0.000000	T	0.48169	0.1485	.	.	.	0.58432	D	0.999999	B	0.21753	0.06	B	0.23716	0.048	T	0.41716	-0.9493	9	0.23302	T	0.38	-23.6549	12.7718	0.57426	0.0:1.0:0.0:0.0	.	52	Q9Y5L4	TIM13_HUMAN	R	52	ENSP00000215570:G52R	ENSP00000215570:G52R	G	-	1	0	TIMM13	2378289	1.000000	0.71417	0.999000	0.59377	0.870000	0.49936	4.117000	0.57877	1.922000	0.55676	0.491000	0.48974	GGG	.	.		0.667	TIMM13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451333.1			T	2427289	C	T	2427289	3	4	136	1	0	0	0	0	1	0	0	0	15921	681	24	3	141	3	TIMM13	19	2427289	Missense_Mutation	SNP	C	TCGA-DD-A4NO-01A-11D-A28X-10		2427289	56701694	46	21714										
UNC13A	23025	hgsc.bcm.edu	37	chr19	17720864	17720864	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gttgacctcgatgaacggccGgaagatgccagaagtctgcc	13	11	1	4			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr19:17720864G>A	ENST00000519716.2	-	43	4695	c.4696C>T	c.(4696-4698)Cgg>Tgg	p.R1566W	UNC13A_ENST00000252773.7_Missense_Mutation_p.R1566W|UNC13A_ENST00000428389.2_Missense_Mutation_p.R1654W|UNC13A_ENST00000550896.1_Missense_Mutation_p.R1539W|UNC13A_ENST00000552293.1_Missense_Mutation_p.R1560W|UNC13A_ENST00000551649.1_Missense_Mutation_p.R1585W	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1566	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						ATGAACGGCCGGAAGATGCCA	0.517																																					p.R1566W		Atlas-SNP	.											.	UNC13A	299	.	0			c.C4696T						.						122	130	127					19																	17720864		2154	4277	6431	SO:0001583	missense	23025	exon41			ACGGCCGGAAGAT	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.4696C>T	chr19.hg19:g.17720864G>A	ENSP00000429562:p.Arg1566Trp	118.0	0.0		199.0	73.0	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007738	0.75046	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42;-0.42	4.13	4.13	0.48395	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	U	0.000000	D	0.84005	0.5377	M	0.89968	3.075	0.46981	D	0.999273	D	0.89917	1.0	D	0.85130	0.997	D	0.87780	0.2611	10	0.87932	D	0	-17.1577	13.9527	0.64129	0.0:0.0:1.0:0.0	.	1566	Q9UPW8	UN13A_HUMAN	W	1566;1654;1566;1585;1560;1539	ENSP00000429562:R1566W;ENSP00000400409:R1654W;ENSP00000252773:R1566W;ENSP00000447236:R1585W;ENSP00000447572:R1560W;ENSP00000446831:R1539W	ENSP00000252773:R1566W	R	-	1	2	UNC13A	17581864	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.923000	0.56469	1.869000	0.54173	0.478000	0.44815	CGG	.	.		0.517	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17720864	G	A	17720864	3	1	136	1	0	0	0	0	1	0	0	0	16999	1115	39	1	423	1	UNC13A	19	17720864	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	15293575	17720864	41408119	47	21715										
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39914693	39914693	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	cggctcttacaactttctctGatcaaggccacccagaaatc	6	14	3	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr19:39914693G>A	ENST00000409794.3	+	19	3770	c.2920G>A	c.(2920-2922)Gat>Aat	p.D974N	CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.D945N|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.D915N	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	974					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AACTTTCTCTGATCAAGGCCA	0.567																																					p.D974N		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G2920A						.						93	97	96					19																	39914693		2203	4300	6503	SO:0001583	missense	64857	exon19			TTCTCTGATCAAG	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.2920G>A	chr19.hg19:g.39914693G>A	ENSP00000386733:p.Asp974Asn	130.0	0.0		167.0	82.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	hg19	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	G	16.20	3.056851	0.55325	.	.	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000458508	T;T;T	0.78816	-1.03;-1.1;-1.21	3.82	2.75	0.32379	.	0.949809	0.08659	N	0.912730	T	0.77691	0.4168	L	0.39898	1.24	0.09310	N	0.999999	D;P;P	0.55385	0.971;0.952;0.952	P;P;P	0.52514	0.701;0.505;0.601	T	0.65331	-0.6194	10	0.87932	D	0	.	9.3484	0.38122	0.0:0.2186:0.7814:0.0	.	945;974;915	Q9H7P9-3;Q9H7P9;E7ESZ3	.;PKHG2_HUMAN;.	N	974;945;915	ENSP00000386733:D974N;ENSP00000392906:D945N;ENSP00000408857:D915N	ENSP00000386733:D974N	D	+	1	0	PLEKHG2	44606533	0.000000	0.05858	0.011000	0.14972	0.042000	0.13812	0.588000	0.23924	1.165000	0.42670	0.591000	0.81541	GAT	.	.		0.567	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		A	39914693	G	A	39914693	3	1	136	1	0	0	0	0	1	0	0	0	12078	1290	45	3	2990	3	PLEKHG2	19	39914693	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10	22193829	39914693	19214290	48	21716										
BPIL1	80341	hgsc.bcm.edu	37	chr20	31600638	31600638	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	tctgaatgtccatgtgccccGcctccacctgaaattcattg	7	14	2	2			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr20:31600638G>A	ENST00000170150.3	+	4	428	c.233G>A	c.(232-234)cGc>cAc	p.R78H		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	78						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										CATGTGCCCCGCCTCCACCTG	0.537																																					p.R78H		Atlas-SNP	.											.	.	.	.	0			c.G233A						.						197	187	190					20																	31600638		2203	4300	6503	SO:0001583	missense	80341	exon4			TGCCCCGCCTCCA	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"BPI fold containing"	16177	protein-coding gene	gene with protein product		614108	"bactericidal/permeability-increasing protein-like 1"	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.233G>A	chr20.hg19:g.31600638G>A	ENSP00000170150:p.Arg78His	126.0	0.0		280.0	36.0	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	hg19	CCDS13210.1	.	.	.	.	.	.	.	.	.	.	G	3.151	-0.174123	0.06421	.	.	ENSG00000078898	ENST00000170150	T	0.05786	3.39	4.41	-5.21	0.02815	.	1.608980	0.03461	N	0.212134	T	0.02380	0.0073	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44436	-0.9328	10	0.13470	T	0.59	0.0364	7.6161	0.28158	0.2661:0.0:0.5834:0.1505	.	78	Q8N4F0	BPIB2_HUMAN	H	78	ENSP00000170150:R78H	ENSP00000170150:R78H	R	+	2	0	BPIFB2	31064299	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.003000	0.03682	-1.155000	0.02822	-0.302000	0.09304	CGC	.	.		0.537	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227		A	31600638	G	A	31600638	3	1	136	1	0	0	0	0	1	0	0	0	1493	1087	38	1	243	1	BPIL1	20	31600638	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10		31600638	31424882	49	21717										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60893664	60893664	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	gtgtggccagtgcctggttcTcctcccagaggctgctcagc	13	14	2	1			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr20:60893664T>G	ENST00000252999.3	-	53	7151	c.7085A>C	c.(7084-7086)gAg>gCg	p.E2362A		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2362	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TGCCTGGTTCTCCTCCCAGAG	0.672																																					p.E2362A		Atlas-SNP	.											.	LAMA5	268	.	0			c.A7085C						.						30	37	35					20																	60893664		2183	4270	6453	SO:0001583	missense	3911	exon53			TGGTTCTCCTCCC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7085A>C	chr20.hg19:g.60893664T>G	ENSP00000252999:p.Glu2362Ala	129.0	0.0		251.0	27.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	-	11.66	1.706313	0.30232	.	.	ENSG00000130702	ENST00000252999	T	0.14144	2.53	3.88	2.73	0.32206	Laminin I (1);	0.993490	0.08172	U	0.986761	T	0.13114	0.0318	L	0.43923	1.385	0.31105	N	0.710572	B	0.29481	0.245	B	0.31946	0.138	T	0.28681	-1.0036	10	0.48119	T	0.1	.	4.6545	0.12611	0.0:0.1485:0.407:0.4445	.	2362	O15230	LAMA5_HUMAN	A	2362	ENSP00000252999:E2362A	ENSP00000252999:E2362A	E	-	2	0	LAMA5	60327059	0.985000	0.35326	0.993000	0.49108	0.428000	0.31595	2.380000	0.44327	0.467000	0.27218	0.358000	0.22013	GAG	.	.		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		G	60893664	T	G	60893664	3	3	136	1	0	0	0	0	1	0	0	0	8618	1551	54	5	4114	5	LAMA5	20	60893664	Missense_Mutation	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10	29293026	60893664	2131856	50	21718										
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29440871	29440871	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	aatcaagctgaagcagcgacGcagtcaggtagtgcctctgt	12	10	3	1	rs372884606		TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr22:29440871G>A	ENST00000544604.2	+	5	912	c.737G>A	c.(736-738)cGc>cAc	p.R246H	ZNRF3_ENST00000332811.4_Missense_Mutation_p.R146H|ZNRF3_ENST00000402174.1_Missense_Mutation_p.R146H|ZNRF3_ENST00000406323.3_Missense_Mutation_p.R146H	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	246					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						AAGCAGCGACGCAGTCAGGTA	0.517																																					p.R246H		Atlas-SNP	.											.	ZNRF3	75	.	0			c.G737A						.	G	HIS/ARG,HIS/ARG	1,4143		0,1,2071	111	113	113		737,437	5.3	1	22		113	0,8382		0,0,4191	no	missense,missense	ZNRF3	NM_001206998.1,NM_032173.3	29,29	0,1,6262	AA,AG,GG		0.0,0.0241,0.0080	probably-damaging,probably-damaging	246/937,146/837	29440871	1,12525	2072	4191	6263	SO:0001583	missense	84133	exon5			AGCGACGCAGTCA	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"RING-type (C3HC4) zinc fingers"	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.737G>A	chr22.hg19:g.29440871G>A	ENSP00000443824:p.Arg246His	103.0	0.0		158.0	47.0	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	hg19	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.835791	0.91117	2.41E-4	0.0	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000402174;ENST00000406323	T;T;T;T	0.12039	2.82;2.72;2.72;2.72	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.25269	0.0614	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.02743	-1.1116	10	0.33940	T	0.23	-14.7992	18.0498	0.89344	0.0:0.0:1.0:0.0	.	246	Q9ULT6	ZNRF3_HUMAN	H	246;146;146;146	ENSP00000443824:R246H;ENSP00000328614:R146H;ENSP00000384456:R146H;ENSP00000384553:R146H	ENSP00000328614:R146H	R	+	2	0	ZNRF3	27770871	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.814000	0.91968	2.515000	0.84797	0.655000	0.94253	CGC	.	.		0.517	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		A	29440871	G	A	29440871	3	1	136	1	0	0	0	0	1	0	0	0	18228	1087	38	1	451	1	ZNRF3	22	29440871	Missense_Mutation	SNP	G	TCGA-DD-A4NO-01A-11D-A28X-10		29440871	21863695	51	21719										
BMX	660	hgsc.bcm.edu	37	chrX	15560134	15560134	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	ccatcccaagctggttaaatTctatggagtgtgttcaaagg	10	8	2	0			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chrX:15560134T>A	ENST00000357607.2	+	15	1612	c.1424T>A	c.(1423-1425)tTc>tAc	p.F475Y	BMX_ENST00000342014.6_Missense_Mutation_p.F475Y|BMX_ENST00000348343.6_Missense_Mutation_p.F475Y			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	475	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					CTGGTTAAATTCTATGGAGTG	0.393																																					p.F475Y		Atlas-SNP	.											.	BMX	73	.	0			c.T1424A						.						123	117	119					X																	15560134		2203	4299	6502	SO:0001583	missense	660	exon15			TTAAATTCTATGG	AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1079	protein-coding gene	gene with protein product	"BTK-like on X chromosome"	300101				7970727	Standard	NM_203281		Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.1424T>A	chrX.hg19:g.15560134T>A	ENSP00000350224:p.Phe475Tyr	98.0	0.0		124.0	93.0	NM_001721	A6NIH9|O60564|Q12871	Missense_Mutation	SNP	ENST00000357607.2	hg19	CCDS14168.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.455164	0.84209	.	.	ENSG00000102010	ENST00000357607;ENST00000348343;ENST00000342014	D;D;D	0.89270	-2.49;-2.49;-2.49	4.84	4.84	0.62591	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.134965	0.37669	N	0.001999	D	0.89192	0.6645	L	0.39147	1.195	0.40456	D	0.98019	P	0.49783	0.928	P	0.54372	0.75	D	0.90436	0.4428	10	0.87932	D	0	.	12.3781	0.55291	0.0:0.0:0.0:1.0	.	475	P51813	BMX_HUMAN	Y	475	ENSP00000350224:F475Y;ENSP00000308774:F475Y;ENSP00000340082:F475Y	ENSP00000340082:F475Y	F	+	2	0	BMX	15470055	1.000000	0.71417	0.998000	0.56505	0.821000	0.46438	7.837000	0.86796	1.593000	0.50029	0.481000	0.45027	TTC	.	.		0.393	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	NM_001721		A	15560134	T	A	15560134	3	1	136	1	0	0	0	0	1	0	0	0	1473	1783	62	4	1478	4	BMX	23	15560134	Missense_Mutation	SNP	T	TCGA-DD-A4NO-01A-11D-A28X-10		15560134	139710426	52	21720										
CYSLTR1	10800	hgsc.bcm.edu	37	chrX	77528826	77528827	+	Frame_Shift_Ins	INS	-	-	T													0.0377358490566038	2	1	0.759985069055618	1.03140830800405	0.601654846335697	1	1	0	cctacacacacaaacctggcINSttttttctgtgtaaccaaat							TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chrX:77528826_77528827insT	ENST00000373304.3	-	3	709_710	c.417_418insA	c.(415-420)aaagccfs	p.A140fs		NM_001282187.1|NM_001282188.1|NM_006639.3	NP_001269116.1|NP_001269117.1|NP_006630.1	Q9Y271	CLTR1_HUMAN	cysteinyl leukotriene receptor 1	140					defense response (GO:0006952)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|respiratory gaseous exchange (GO:0007585)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	leukotriene receptor activity (GO:0004974)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14					Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549)	ACAAACCTGGCTTTTTTCTGTG	0.366																																					p.A140fs		Atlas-Indel,Pindel	.											.	CYSLTR1	59	.	0			c.418_419insA						.																																			SO:0001589	frameshift_variant	10800	exon3			.	AF119711	CCDS14439.1	Xq13-q21	2012-08-10			ENSG00000173198	ENSG00000173198		"GPCR / Class A : Leukotriene receptors"	17451	protein-coding gene	gene with protein product		300201				10391245, 10462554	Standard	NM_006639		Approved	CysLT1, CysLT(1), CYSLT1R	uc004edb.3	Q9Y271	OTTHUMG00000021889	ENST00000373304.3:c.418dupA	chrX.hg19:g.77528832_77528832dupT	ENSP00000362401:p.Ala140fs	71.0	0.0		62.0	41.0	NM_006639	B2R954|D3DTE4|Q5JS94|Q8IV19	Frame_Shift_Ins	INS	ENST00000373304.3	hg19	CCDS14439.1																																																																																			.	.		0.366	CYSLTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057315.1			T	77528827	-	T	77528826	7	5	136	1	0	1	1	0	0	0	0	0	4203	797	28	0	599	0	CYSLTR1	23	77528826	Frame_Shift_Ins	INS	-	TCGA-DD-A4NO-01A-11D-A28X-10	61968692	77528826	77741734	53	21721										
RPS6KA1	6195	hgsc.bcm.edu	37	chr1	26881119	26881119	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	gcaaagaggccattgaccacGagaagaaggcctattctttc	10	10	1	4			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr1:26881119G>A	ENST00000374168.2	+	9	800	c.646G>A	c.(646-648)Gag>Aag	p.E216K	MIR1976_ENST00000459548.1_RNA|RPS6KA1_ENST00000530003.1_Missense_Mutation_p.E200K|RPS6KA1_ENST00000374166.4_Missense_Mutation_p.E216K|RPS6KA1_ENST00000374162.2_Missense_Mutation_p.E124K|RPS6KA1_ENST00000526792.1_Missense_Mutation_p.E124K|RPS6KA1_ENST00000531382.1_Missense_Mutation_p.E225K	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	216	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		CATTGACCACGAGAAGAAGGC	0.587																																					p.E225K		Atlas-SNP	.											.	RPS6KA1	65	.	0			c.G673A						.						171	170	170					1																	26881119		2203	4300	6503	SO:0001583	missense	6195	exon8			GACCACGAGAAGA	BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"ribosomal protein S6 kinase, 90kD, polypeptide 1"			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.646G>A	chr1.hg19:g.26881119G>A	ENSP00000363283:p.Glu216Lys	150.0	0.0		232.0	75.0	NM_001006665	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Missense_Mutation	SNP	ENST00000374168.2	hg19	CCDS284.1	.	.	.	.	.	.	.	.	.	.	G	36	5.845293	0.97016	.	.	ENSG00000117676	ENST00000374168;ENST00000374166;ENST00000526792;ENST00000374162;ENST00000530003;ENST00000531382	T;T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1;-0.1	5.65	5.65	0.86999	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.71953	0.3401	L	0.33137	0.985	0.80722	D	1	P;P;D	0.67145	0.824;0.76;0.996	P;B;D	0.74348	0.531;0.144;0.983	T	0.74093	-0.3776	10	0.72032	D	0.01	.	18.6893	0.91577	0.0:0.0:1.0:0.0	.	200;225;216	B7Z2K7;Q15418-2;Q15418	.;.;KS6A1_HUMAN	K	216;216;124;124;200;225	ENSP00000363283:E216K;ENSP00000363281:E216K;ENSP00000431651:E124K;ENSP00000363277:E124K;ENSP00000432281:E200K;ENSP00000435412:E225K	ENSP00000363277:E124K	E	+	1	0	RPS6KA1	26753706	1.000000	0.71417	0.978000	0.43139	0.994000	0.84299	9.869000	0.99810	2.655000	0.90218	0.563000	0.77884	GAG	.	.		0.587	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011431.1	NM_002953		A	26881119	G	A	26881119	3	1	137	1	0	0	0	0	1	0	0	0	13665	1059	37	1	819	1	RPS6KA1	1	26881119	Missense_Mutation	SNP	G	TCGA-DD-A4NP-01A-11D-A28X-10		26881119	222369502	1	21722										
TMEM79	84283	hgsc.bcm.edu	37	chr1	156255146	156255146	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	ggtggggccgaatccccgggAgctgagtccctcagagtggg	18	11	1	2			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr1:156255146A>C	ENST00000405535.2	+	2	300	c.129A>C	c.(127-129)ggA>ggC	p.G43G	SMG5_ENST00000361813.5_5'Flank|SMG5_ENST00000368267.5_5'Flank|TMEM79_ENST00000357501.2_Intron|TMEM79_ENST00000295694.5_Silent_p.G43G|TMEM79_ENST00000495881.1_3'UTR	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	43					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					AATCCCCGGGAGCTGAGTCCC	0.607																																					p.G43G		Atlas-SNP	.											.	TMEM79	43	.	0			c.A129C						.						35	40	39					1																	156255146		2203	4300	6503	SO:0001819	synonymous_variant	84283	exon2			CCCGGGAGCTGAG	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"mattrin"	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.129A>C	chr1.hg19:g.156255146A>C		92.0	0.0		121.0	38.0	NM_032323	B2RE22|D3DVB8	Silent	SNP	ENST00000405535.2	hg19	CCDS1138.1																																																																																			.	.		0.607	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		C	156255146	A	C	156255146	2	2	137	1	0	0	0	0	0	0	0	1	16218	291	11	5		5	TMEM79	1	156255146	Silent	SNP	A	TCGA-DD-A4NP-01A-11D-A28X-10	129374027	156255146	92995475	2	21723										
PPP1R12B	4660	hgsc.bcm.edu	37	chr1	202462434	202462434	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	agcagccctggggcaggagtCtggatgaagaggtgagctca	17	8	2	3			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr1:202462434C>A	ENST00000608999.1	+	15	2287	c.2134C>A	c.(2134-2136)Ctg>Atg	p.L712M	PPP1R12B_ENST00000367270.4_5'UTR|PPP1R12B_ENST00000336894.4_Missense_Mutation_p.L712M|PPP1R12B_ENST00000290419.5_3'UTR|PPP1R12B_ENST00000391959.3_5'UTR	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	712					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			GGGCAGGAGTCTGGATGAAGA	0.537																																					p.L712M		Atlas-SNP	.											.	PPP1R12B	100	.	0			c.C2134A						.						20	22	21					1																	202462434		2203	4299	6502	SO:0001583	missense	4660	exon15			AGGAGTCTGGATG	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7619	protein-coding gene	gene with protein product	"myosin phosphatase regulatory subunit", "myosin phosphatase, target subunit 2"	603768	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.2134C>A	chr1.hg19:g.202462434C>A	ENSP00000476755:p.Leu712Met	277.0	0.0		394.0	144.0	NM_002481	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Missense_Mutation	SNP	ENST00000608999.1	hg19	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.364616	0.41902	.	.	ENSG00000077157	ENST00000406302;ENST00000336894	T;T	0.03358	3.96;3.96	5.47	2.22	0.28083	.	0.785958	0.11171	N	0.592005	T	0.08492	0.0211	L	0.56769	1.78	0.20563	N	0.999881	P;P	0.47484	0.761;0.896	B;P	0.53988	0.275;0.739	T	0.29243	-1.0018	10	0.36615	T	0.2	.	5.2635	0.15586	0.0:0.5498:0.0:0.4502	.	712;712	O60237;F8W8M3	MYPT2_HUMAN;.	M	712	ENSP00000384496:L712M;ENSP00000337897:L712M	ENSP00000337897:L712M	L	+	1	2	PPP1R12B	200729057	0.000000	0.05858	0.016000	0.15963	0.965000	0.64279	0.034000	0.13776	0.692000	0.31613	-0.136000	0.14681	CTG	.	.		0.537	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105		A	202462434	C	A	202462434	3	1	137	1	0	0	0	0	1	0	0	0	12367	912	32	3	2282	3	PPP1R12B	1	202462434	Missense_Mutation	SNP	C	TCGA-DD-A4NP-01A-11D-A28X-10	46207288	202462434	46788187	3	21724										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38791583	38791583	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	ccctcaaggacggaggttatGatactgacaacactcattgc	9	11	2	2			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr3:38791583G>T	ENST00000449082.2	-	12	1847	c.1848C>A	c.(1846-1848)atC>atA	p.I616I		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	616					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CGGAGGTTATGATACTGACAA	0.463																																					p.I616I		Atlas-SNP	.											.	SCN10A	359	.	0			c.C1848A						.						178	148	158					3																	38791583		2203	4300	6503	SO:0001819	synonymous_variant	6336	exon12			GGTTATGATACTG	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1848C>A	chr3.hg19:g.38791583G>T		105.0	0.0		134.0	38.0	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.		0.463	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38791583	G	T	38791583	2	4	137	1	0	0	0	0	0	0	0	1	13927	1280	45	3		3	SCN10A	3	38791583	Silent	SNP	G	TCGA-DD-A4NP-01A-11D-A28X-10		38791583	159230847	4	21725										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55260044	55260049	+	In_Frame_Del	DEL	GACTTC	GACTTC	-													0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	gcattctctgcttctacccaGacttcaatgttgacaaaata							TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	GACTTC	GACTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr5:55260044_55260049delGACTTC	ENST00000381298.2	-	6	895_900	c.583_588delGAAGTC	c.(583-588)gaagtcdel	p.EV195del	IL6ST_ENST00000536319.1_In_Frame_Del_p.EV195del|IL6ST_ENST00000502326.3_In_Frame_Del_p.EV195del|IL6ST_ENST00000577363.1_5'UTR|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000522633.2_In_Frame_Del_p.EV195del|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000381287.4_In_Frame_Del_p.EV195del|IL6ST_ENST00000396816.1_In_Frame_Del_p.52_54LKS>F|IL6ST_ENST00000336909.5_In_Frame_Del_p.EV195del|IL6ST_ENST00000381294.3_In_Frame_Del_p.EV195del	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	195	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				CTTCTACCCAGACTTCAATGTTGACA	0.379			O		hepatocellular ca																																p.195_197del		Atlas-Indel,Pindel	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.584_589del						.																																			SO:0001651	inframe_deletion	3572	exon6			.	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.583_588delGAAGTC	chr5.hg19:g.55260044_55260049delGACTTC	ENSP00000370698:p.Glu195_Val196del	112.0	0.0		125.0	14.0	NM_001190981	A0N0L4|Q5FC04|Q9UQ41	In_Frame_Del	DEL	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.		0.379	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		-	55260049	GACTTC	-	55260044	7	5	137	1	0	1	0	1	0	0	0	0	7712	929	33	0	2216	0	IL6ST	5	55260044	In_Frame_Del	DEL	GACTTC	TCGA-DD-A4NP-01A-11D-A28X-10		55260044	125655216	5	21726										
APC	324	hgsc.bcm.edu	37	chr5	112111324	112111324	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	ttttttaaaaaaaaaaaaatAggtcattgcttcttgctgat	5	4	2	1			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr5:112111324A>G	ENST00000457016.1	+	5	802		c.e5-1		APC_ENST00000257430.4_Splice_Site|RNU6-482P_ENST00000391068.1_RNA|APC_ENST00000508376.2_Splice_Site			P25054	APC_HUMAN	adenomatous polyposis coli						anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		aaaaaaaaataGGTCATTGCT	0.313		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											.	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	APC,colon,carcinoma,0,1	APC	4158	.	0			c.453-2A>G	GRCh37	CS043351|CS051678	APC	S		.						47	53	51					5																	112111324		2202	4288	6490	SO:0001630	splice_region_variant	324	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AAAAATAGGTCAT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.423-1A>G	chr5.hg19:g.112111324A>G		49.0	0.0		49.0	21.0	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Splice_Site	SNP	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.313	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	Intron	G	112111324	A	G	112111324	5	3	137	1	0	0	0	0	0	0	1	0	763	434	15	2	435	2	APC	5	112111324	Splice_Site	SNP	A	TCGA-DD-A4NP-01A-11D-A28X-10	56851280	112111324	68803936	6	21727										
TUBB2A	7280	hgsc.bcm.edu	37	chr6	3154966	3154966	+	Frame_Shift_Del	DEL	C	C	-													0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	gatgcggtctgggtactcttCccggatcttgctgatgagca							TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr6:3154966delC	ENST00000333628.3	-	4	531	c.469delG	c.(469-471)gaafs	p.E158fs	TUBB2A_ENST00000489942.1_5'UTR|RP1-40E16.11_ENST00000447644.1_RNA	NM_001069.2	NP_001060.1	Q13885	TBB2A_HUMAN	tubulin, beta 2A class IIa	158					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|large_intestine(4)|lung(2)|skin(1)	9	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				GGGTACTCTTCCCGGATCTTG	0.622																																					p.E157fs		Atlas-INDEL	.											.	TUBB2A	23	.	0			c.470delA						.						33	23	26					6																	3154966		2202	4276	6478	SO:0001589	frameshift_variant	7280	exon4			.	AY159127	CCDS4484.1	6p25.2	2012-10-02	2011-10-10	2005-11-03	ENSG00000137267	ENSG00000137267		"Tubulins"	12412	protein-coding gene	gene with protein product	"class IIa beta-tubulin"	615101	"tubulin, beta polypeptide", "tubulin, beta 2", "tubulin, beta 2A"	TUBB, TUBB2		14574404	Standard	NM_001069		Approved	dJ40E16.7	uc003mvc.3	Q13885	OTTHUMG00000014135	ENST00000333628.3:c.469delG	chr6.hg19:g.3154966delC	ENSP00000369703:p.Glu158fs	222.0	0.0		320.0	69.0	NM_001069	Q6FGZ8|Q8IWR2	Frame_Shift_Del	DEL	ENST00000333628.3	hg19	CCDS4484.1																																																																																			.	.		0.622	TUBB2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039662.1	NM_001069		-	3154966	C	-	3154966	7	5	137	1	0	1	0	1	0	0	0	0	16769	864	30	0	872	0	TUBB2A	6	3154966	Frame_Shift_Del	DEL	C	TCGA-DD-A4NP-01A-11D-A28X-10		3154966	167960101	7	21728										
ZNF451	26036	hgsc.bcm.edu	37	chr6	57012123	57012123	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	ggaacaaggatccttcttctGacttgcatttattgttggat	9	7	2	1			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr6:57012123G>A	ENST00000370706.4	+	10	1484	c.1240G>A	c.(1240-1242)Gac>Aac	p.D414N	RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|ZNF451_ENST00000491832.2_Missense_Mutation_p.D414N|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|ZNF451_ENST00000357489.3_Missense_Mutation_p.D414N|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000589549.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TCCTTCTTCTGACTTGCATTT	0.383																																					p.D414N		Atlas-SNP	.											.	ZNF451	181	.	0			c.G1240A						.						64	67	66					6																	57012123		2203	4300	6503	SO:0001583	missense	26036	exon10			TCTTCTGACTTGC	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"Zinc fingers, C2H2-type"	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.1240G>A	chr6.hg19:g.57012123G>A	ENSP00000359740:p.Asp414Asn	65.0	0.0		82.0	7.0	NM_001031623	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Missense_Mutation	SNP	ENST00000370706.4	hg19	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.784441	0.49997	.	.	ENSG00000112200	ENST00000370706;ENST00000357489;ENST00000491832	T;T;T	0.06687	3.27;3.27;3.27	5.2	5.2	0.72013	.	0.265926	0.37906	N	0.001894	T	0.14614	0.0353	M	0.72118	2.19	0.80722	D	1	D;D;P;D	0.71674	0.998;0.963;0.536;0.963	D;P;B;P	0.65573	0.936;0.704;0.152;0.704	T	0.10359	-1.0633	10	0.16896	T	0.51	-16.8979	14.7166	0.69275	0.0:0.1883:0.8117:0.0	.	414;414;414;414	Q9Y4E5-2;Q9Y4E5;E9PH99;Q4KMR5	.;ZN451_HUMAN;.;.	N	414	ENSP00000359740:D414N;ENSP00000350083:D414N;ENSP00000421645:D414N	ENSP00000350083:D414N	D	+	1	0	ZNF451	57120082	1.000000	0.71417	0.988000	0.46212	0.765000	0.43378	3.019000	0.49635	2.419000	0.82065	0.650000	0.86243	GAC	.	.		0.383	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555		A	57012123	G	A	57012123	3	1	137	1	0	0	0	0	1	0	0	0	17937	1290	45	3	1278	3	ZNF451	6	57012123	Missense_Mutation	SNP	G	TCGA-DD-A4NP-01A-11D-A28X-10	53857157	57012123	114102944	8	21729										
BET1	10282	hgsc.bcm.edu	37	chr7	93628605	93628605	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	ttgccaggaggtactccttcAcctgcaaggatcagagtcac	10	12	3	1			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr7:93628605A>G	ENST00000222547.3	-	2	179	c.21T>C	c.(19-21)ggT>ggC	p.G7G	BET1_ENST00000425626.1_Splice_Site_p.G7G|BET1_ENST00000471446.1_5'Flank|AC006378.2_ENST00000426193.2_RNA|AC006378.2_ENST00000426634.1_RNA|BET1_ENST00000433727.1_Splice_Site_p.G7G	NM_005868.4	NP_005859.1	O15155	BET1_HUMAN	Bet1 golgi vesicular membrane trafficking protein	7					ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)|vesicle fusion with Golgi apparatus (GO:0048280)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				large_intestine(2)|lung(1)|prostate(1)|skin(1)	5	all_cancers(62;2.22e-10)|all_epithelial(64;1.38e-09)|Lung NSC(181;0.218)	Breast(660;0.000162)|Ovarian(593;0.000626)	STAD - Stomach adenocarcinoma(171;0.000967)			GTACTCCTTCACCTGCAAGGA	0.453																																					p.G7G		Atlas-SNP	.											.	BET1	12	.	0			c.T21C						.						63	57	59					7																	93628605		2203	4300	6503	SO:0001630	splice_region_variant	10282	exon2			TCCTTCACCTGCA	AF007551	CCDS5635.1	7q21.1-q22	2013-03-08	2013-03-08		ENSG00000105829	ENSG00000105829			14562	protein-coding gene	gene with protein product	"Golgi vesicular membrane trafficking protein p18", "Bet1p homolog"	605456	"Bet1 (S. cerevisiae) homolog", "BET1 homolog (S. cerevisiae)", "blocked early in transport 1 homolog (S. cerevisiae)"			9382863, 10449330	Standard	XM_005250109		Approved	hbet1	uc003unf.1	O15155	OTTHUMG00000023487	ENST00000222547.3:c.20-1T>C	chr7.hg19:g.93628605A>G		40.0	0.0		46.0	16.0	NM_005868	Q96EA0	Silent	SNP	ENST00000222547.3	hg19	CCDS5635.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.478612	0.44044	.	.	ENSG00000105829	ENST00000457139	.	.	.	5.35	4.18	0.49190	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.354	0.43954	0.8534:0.0:0.0:0.1466	.	.	.	.	R	22	.	.	X	-	1	0	BET1	93466541	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	3.650000	0.54424	0.964000	0.38108	0.533000	0.62120	TGA	.	.		0.453	BET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255181.2	NM_005868	Silent	G	93628605	A	G	93628605	5	3	137	1	0	0	0	0	0	0	1	0	1408	173	6	2	347	2	BET1	7	93628605	Splice_Site	SNP	A	TCGA-DD-A4NP-01A-11D-A28X-10		93628605	65510058	9	21730										
ZNF800	168850	hgsc.bcm.edu	37	chr7	127026146	127026146	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	actcaattatttgttgaataCcagatttggatgtctgtagt	8	5	2	2			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr7:127026146C>G	ENST00000393313.1	-	3	716	c.125G>C	c.(124-126)gGt>gCt	p.G42A	ZNF800_ENST00000265827.3_Missense_Mutation_p.G42A|ZNF800_ENST00000393312.1_Missense_Mutation_p.G42A			Q2TB10	ZN800_HUMAN	zinc finger protein 800	42					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						TTGTTGAATACCAGATTTGGA	0.378																																					p.G42A		Atlas-SNP	.											ZNF800,NS,carcinoma,0,2	ZNF800	78	.	0			c.G125C						.						112	106	108					7																	127026146		2203	4300	6503	SO:0001583	missense	168850	exon3			TGAATACCAGATT	AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"Zinc fingers, C2H2-type"	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.125G>C	chr7.hg19:g.127026146C>G	ENSP00000376989:p.Gly42Ala	34.0	0.0		41.0	10.0	NM_176814	Q9HBN0	Missense_Mutation	SNP	ENST00000393313.1	hg19	CCDS5795.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.821552	0.90873	.	.	ENSG00000048405	ENST00000393313;ENST00000265827;ENST00000393312;ENST00000434602;ENST00000436992;ENST00000439506	T;T;T;T;T;T	0.54675	2.08;2.08;2.08;0.56;0.69;1.28	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.61689	0.2367	N	0.24115	0.695	0.38778	D	0.954700	D	0.76494	0.999	D	0.80764	0.994	T	0.66941	-0.5796	9	0.72032	D	0.01	-6.8906	18.2091	0.89864	0.0:1.0:0.0:0.0	.	42	Q2TB10	ZN800_HUMAN	A	42	ENSP00000376989:G42A;ENSP00000265827:G42A;ENSP00000376988:G42A;ENSP00000403945:G42A;ENSP00000401109:G42A;ENSP00000389776:G42A	ENSP00000265827:G42A	G	-	2	0	ZNF800	126813382	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.240000	0.78192	2.546000	0.85860	0.655000	0.94253	GGT	.	.		0.378	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814		G	127026146	C	G	127026146	3	3	137	1	0	0	0	0	1	0	0	0	18184	507	18	4	1885	4	ZNF800	7	127026146	Missense_Mutation	SNP	C	TCGA-DD-A4NP-01A-11D-A28X-10	33397541	127026146	32112517	10	21731										
PTN	5764	hgsc.bcm.edu	37	chr7	136938301	136938301	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	tccagtccgagtgccctcccGtgtgcccagcccacagtctc	9	19	1	0	rs149012204		TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr7:136938301G>T	ENST00000348225.2	-	3	626	c.199C>A	c.(199-201)Cgg>Agg	p.R67R	PTN_ENST00000393083.2_Silent_p.R67R	NM_002825.5	NP_002816.1	P21246	PTN_HUMAN	pleiotrophin	67					bone mineralization (GO:0030282)|learning (GO:0007612)|negative regulation of catalytic activity (GO:0043086)|nervous system development (GO:0007399)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	heparin binding (GO:0008201)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23						GTGCCCTCCCGTGTGCCCAGC	0.522																																					p.R67R		Atlas-SNP	.											.	PTN	38	.	0			c.C199A						.						105	88	94					7																	136938301		2203	4300	6503	SO:0001819	synonymous_variant	5764	exon3			CCTCCCGTGTGCC	M57399	CCDS5844.1	7q33	2014-01-30	2008-07-31		ENSG00000105894	ENSG00000105894		"Endogenous ligands"	9630	protein-coding gene	gene with protein product	"heparin binding growth factor 8"	162095	"neurite growth-promoting factor 1"	NEGF1		1457401, 1768439	Standard	NM_002825		Approved	HBNF, HBGF8	uc003vtq.2	P21246	OTTHUMG00000155709	ENST00000348225.2:c.199C>A	chr7.hg19:g.136938301G>T		60.0	0.0		82.0	4.0	NM_002825	Q5U0B0|Q6ICQ5|Q9UCC6	Silent	SNP	ENST00000348225.2	hg19	CCDS5844.1																																																																																			.	G|1.000;A|0.000		0.522	PTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341339.1	NM_002825		T	136938301	G	T	136938301	2	4	137	1	0	0	0	0	0	0	0	1	12781	1144	40	1		1	PTN	7	136938301	Silent	SNP	G	TCGA-DD-A4NP-01A-11D-A28X-10	9912155	136938301	22200362	11	21732										
WHSC1L1	54904	hgsc.bcm.edu	37	chr8	38133282	38133282	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	cagaggcggccttccagtgcAgagggaaccagggccccctt	14	14	0	2			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr8:38133282A>T	ENST00000317025.8	-	24	4708	c.4191T>A	c.(4189-4191)tcT>tcA	p.S1397S	RP11-513D5.5_ENST00000529325.1_RNA|WHSC1L1_ENST00000433384.2_Silent_p.S1348S|WHSC1L1_ENST00000527502.1_Silent_p.S1386S	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	1397					histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			CTTCCAGTGCAGAGGGAACCA	0.498			T	NUP98	AML																																p.S1397S		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.T4191A						.						81	76	77					8																	38133282		1917	4153	6070	SO:0001819	synonymous_variant	54904	exon24			CAGTGCAGAGGGA	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.4191T>A	chr8.hg19:g.38133282A>T		45.0	0.0		70.0	23.0	NM_023034	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Silent	SNP	ENST00000317025.8	hg19	CCDS43729.1																																																																																			.	.		0.498	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		T	38133282	A	T	38133282	2	4	137	1	0	0	0	0	0	0	0	1	17378	175	7	4		4	WHSC1L1	8	38133282	Silent	SNP	A	TCGA-DD-A4NP-01A-11D-A28X-10		38133282	108230740	12	21733										
LRRTM3	347731	hgsc.bcm.edu	37	chr10	68686847	68686847	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	attacaggagataccctcaaGtatatctgctggttgcttag	9	8	2	1			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr10:68686847G>C	ENST00000361320.4	+	2	751	c.173G>C	c.(172-174)aGt>aCt	p.S58T	CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.2_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	58	LRRNT.				positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						ATACCCTCAAGTATATCTGCT	0.423																																					p.S58T		Atlas-SNP	.											.	LRRTM3	241	.	0			c.G173C						.						126	129	128					10																	68686847		2203	4300	6503	SO:0001583	missense	347731	exon2			CCTCAAGTATATC	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.173G>C	chr10.hg19:g.68686847G>C	ENSP00000355187:p.Ser58Thr	48.0	0.0		59.0	21.0	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	hg19	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.916752	0.33815	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	D	0.95949	-3.86	5.53	5.53	0.82687	Leucine-rich repeat-containing N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.93471	0.7917	L	0.39085	1.19	0.43761	D	0.996272	B;B	0.34200	0.441;0.387	B;B	0.41723	0.365;0.196	D	0.92422	0.5946	10	0.44086	T	0.13	.	13.9266	0.63966	0.0:0.1526:0.8474:0.0	.	58;58	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	T	58	ENSP00000355187:S58T	ENSP00000355187:S58T	S	+	2	0	LRRTM3	68356853	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.912000	0.56386	2.613000	0.88420	0.655000	0.94253	AGT	.	.		0.423	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011		C	68686847	G	C	68686847	3	2	137	1	0	0	0	0	1	0	0	0	9050	1029	36	4	179	4	LRRTM3	10	68686847	Missense_Mutation	SNP	G	TCGA-DD-A4NP-01A-11D-A28X-10		68686847	66847900	13	21734										
NRAP	4892	hgsc.bcm.edu	37	chr10	115374663	115374663	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	ggcatccaacctcagtttatAgccaccatctcgaagtttgc	7	13	2	0			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr10:115374663A>T	ENST00000359988.3	-	28	3365	c.3121T>A	c.(3121-3123)Tat>Aat	p.Y1041N	NRAP_ENST00000369360.3_Missense_Mutation_p.Y1014N|NRAP_ENST00000369358.4_Missense_Mutation_p.Y1049N|NRAP_ENST00000360478.3_Missense_Mutation_p.Y1006N	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CTCAGTTTATAGCCACCATCT	0.458																																					p.Y1041N		Atlas-SNP	.											.	NRAP	208	.	0			c.T3121A						.						190	168	175					10																	115374663		2203	4300	6503	SO:0001583	missense	4892	exon28			GTTTATAGCCACC		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3121T>A	chr10.hg19:g.115374663A>T	ENSP00000353078:p.Tyr1041Asn	146.0	0.0		235.0	73.0	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	hg19	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	A	14.24	2.476461	0.44044	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.35048	2.01;2.13;1.38;1.33	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.64549	0.2608	M	0.86502	2.82	0.46701	D	0.99916	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.987;0.994;0.99	T	0.67201	-0.5730	10	0.34782	T	0.22	.	15.7107	0.77626	1.0:0.0:0.0:0.0	.	1041;1006;1041	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	N	1049;1014;1041;1006	ENSP00000358365:Y1049N;ENSP00000358367:Y1014N;ENSP00000353078:Y1041N;ENSP00000353666:Y1006N	ENSP00000353078:Y1041N	Y	-	1	0	NRAP	115364653	1.000000	0.71417	0.155000	0.22561	0.331000	0.28603	8.551000	0.90678	2.112000	0.64535	0.533000	0.62120	TAT	.	.		0.458	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		T	115374663	A	T	115374663	3	4	137	1	0	0	0	0	1	0	0	0	10647	420	15	4	2131	4	NRAP	10	115374663	Missense_Mutation	SNP	A	TCGA-DD-A4NP-01A-11D-A28X-10	46687816	115374663	20160084	14	21735										
STT3A	3703	hgsc.bcm.edu	37	chr11	125476211	125476211	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	cataggtctcgtcatggggaGgttatgtgttcctgatcaac	12	8	3	1			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr11:125476211G>T	ENST00000529196.1	+	9	837	c.631G>T	c.(631-633)Ggt>Tgt	p.G211C	STT3A_ENST00000531491.1_Missense_Mutation_p.G119C|STT3A_ENST00000392708.4_Missense_Mutation_p.G211C			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	211					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		GTCATGGGGAGGTTATGTGTT	0.468																																					p.G211C		Atlas-SNP	.											.	STT3A	52	.	0			c.G631T						.						368	320	337					11																	125476211		2201	4299	6500	SO:0001583	missense	3703	exon8			TGGGGAGGTTATG	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"dolichyl-diphosphooligosaccharide protein glycotransferase"	601134	"integral membrane protein 1", "STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)", "STT3A, cataylic subunit of the oligosaccharyltransferase complex"	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.631G>T	chr11.hg19:g.125476211G>T	ENSP00000436962:p.Gly211Cys	63.0	0.0		99.0	4.0	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Missense_Mutation	SNP	ENST00000529196.1	hg19	CCDS8458.1	.	.	.	.	.	.	.	.	.	.	G	34	5.308801	0.95629	.	.	ENSG00000134910	ENST00000392708;ENST00000529196;ENST00000531491	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.90089	0.6904	H	0.96460	3.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92186	0.5755	9	0.87932	D	0	-15.9493	20.177	0.98182	0.0:0.0:1.0:0.0	.	119;211	E9PNQ1;P46977	.;STT3A_HUMAN	C	211;211;119	.	ENSP00000376472:G211C	G	+	1	0	STT3A	124981421	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.869000	0.99810	2.854000	0.98071	0.655000	0.94253	GGT	.	.		0.468	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713		T	125476211	G	T	125476211	3	4	137	1	0	0	0	0	1	0	0	0	15348	1000	35	3	657	3	STT3A	11	125476211	Missense_Mutation	SNP	G	TCGA-DD-A4NP-01A-11D-A28X-10		125476211	9530305	15	21736										
WNT1	7471	hgsc.bcm.edu	37	chr12	49374348	49374348	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	cgggggccccgactggcactGggggggctgcagcgacaaca	18	13	0	0			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr12:49374348G>T	ENST00000293549.3	+	3	536	c.500G>T	c.(499-501)tGg>tTg	p.W167L		NM_005430.3	NP_005421.1	P04628	WNT1_HUMAN	wingless-type MMTV integration site family, member 1	167					bone development (GO:0060348)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to peptide hormone stimulus (GO:0071375)|central nervous system morphogenesis (GO:0021551)|cerebellum formation (GO:0021588)|diencephalon development (GO:0021536)|embryonic axis specification (GO:0000578)|forebrain anterior/posterior pattern specification (GO:0021797)|hematopoietic stem cell proliferation (GO:0071425)|hepatocyte differentiation (GO:0070365)|inner ear morphogenesis (GO:0042472)|midbrain development (GO:0030901)|midbrain-hindbrain boundary maturation during brain development (GO:0022004)|myoblast fusion (GO:0007520)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell aging (GO:0090344)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|neuron fate determination (GO:0048664)|organ regeneration (GO:0031100)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dermatome development (GO:0061184)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to wounding (GO:0009611)|signal transduction in response to DNA damage (GO:0042770)|Spemann organizer formation (GO:0060061)|spinal cord association neuron differentiation (GO:0021527)|T cell differentiation in thymus (GO:0033077)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription regulatory region DNA binding (GO:0044212)	p.G169fs*30(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(357;0.244)		gACTGGCACTGGGGGGGCTGC	0.682																																					p.W167L		Atlas-SNP	.											.,1	WNT1	13	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.G500T						.						9	11	11					12																	49374348		2195	4281	6476	SO:0001583	missense	7471	exon3			GGCACTGGGGGGG	X03072	CCDS8776.1	12q13	2013-02-28				ENSG00000125084		"Wingless-type MMTV integration sites", "Endogenous ligands"	12774	protein-coding gene	gene with protein product		164820		INT1		2998762, 3281802	Standard	NM_005430		Approved		uc001rsu.3	P04628	OTTHUMG00000170403	ENST00000293549.3:c.500G>T	chr12.hg19:g.49374348G>T	ENSP00000293549:p.Trp167Leu	92.0	0.0		145.0	52.0	NM_005430	Q5U0N2	Missense_Mutation	SNP	ENST00000293549.3	hg19	CCDS8776.1	.	.	.	.	.	.	.	.	.	.	G	34	5.389170	0.95988	.	.	ENSG00000125084	ENST00000293549;ENST00000380414	D	0.81739	-1.53	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.92792	0.7708	H	0.95437	3.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94755	0.7931	10	0.87932	D	0	.	17.1121	0.86678	0.0:0.0:1.0:0.0	.	167	P04628	WNT1_HUMAN	L	167;3	ENSP00000293549:W167L	ENSP00000293549:W167L	W	+	2	0	WNT1	47660615	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.816000	0.86201	2.574000	0.86865	0.655000	0.94253	TGG	.	.		0.682	WNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408937.1			T	49374348	G	T	49374348	3	4	137	1	0	0	0	0	1	0	0	0	17396	1357	47	3	510	3	WNT1	12	49374348	Missense_Mutation	SNP	G	TCGA-DD-A4NP-01A-11D-A28X-10		49374348	84477547	16	21737										
HOXC6	3223	hgsc.bcm.edu	37	chr12	54423712	54423712	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	gggcggaaaagaggaaaagcGggaagagacagaagaggaga	19	3	0	5			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr12:54423712G>T	ENST00000243108.4	+	2	838	c.674G>T	c.(673-675)cGg>cTg	p.R225L	RP11-834C11.12_ENST00000513209.1_Intron|HOXC5_ENST00000312492.2_5'Flank|HOXC4_ENST00000303406.4_Intron|HOXC6_ENST00000394331.3_Missense_Mutation_p.R143L|RP11-834C11.14_ENST00000512206.1_RNA	NM_004503.3	NP_004494.1	P09630	HXC6_HUMAN	homeobox C6	225	Glu/Lys-rich.				anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GAGGAAAAGCGGGAAGAGACA	0.587																																					p.R225L		Atlas-SNP	.											.	HOXC6	30	.	0			c.G674T						.						130	158	149					12																	54423712		2202	4300	6502	SO:0001583	missense	3223	exon2			AAAAGCGGGAAGA		CCDS8871.1, CCDS41792.1	12q13.13	2011-06-20	2005-12-22		ENSG00000197757	ENSG00000197757		"Homeoboxes / ANTP class : HOXL subclass"	5128	protein-coding gene	gene with protein product		142972	"homeo box C6"	HOX3C, HOX3		1973146, 1358459	Standard	NM_153693		Approved		uc001sev.3	P09630	OTTHUMG00000160027	ENST00000243108.4:c.674G>T	chr12.hg19:g.54423712G>T	ENSP00000243108:p.Arg225Leu	90.0	0.0		84.0	4.0	NM_004503	B2RBV2|Q6DK09	Missense_Mutation	SNP	ENST00000243108.4	hg19	CCDS8871.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.277602	0.40294	.	.	ENSG00000197757	ENST00000394331;ENST00000243108	D;D	0.92699	-3.09;-3.03	4.96	4.96	0.65561	.	0.233443	0.37304	N	0.002155	D	0.84115	0.5401	N	0.08118	0	0.80722	D	1	B	0.14012	0.009	B	0.06405	0.002	T	0.79448	-0.1799	10	0.42905	T	0.14	.	17.1341	0.86734	0.0:0.0:1.0:0.0	.	225	P09630	HXC6_HUMAN	L	143;225	ENSP00000377864:R143L;ENSP00000243108:R225L	ENSP00000243108:R225L	R	+	2	0	HOXC6	52709979	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.396000	0.59684	2.584000	0.87258	0.561000	0.74099	CGG	.	.		0.587	HOXC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358943.2			T	54423712	G	T	54423712	3	4	137	1	0	0	0	0	1	0	0	0	7324	1116	39	1	680	1	HOXC6	12	54423712	Missense_Mutation	SNP	G	TCGA-DD-A4NP-01A-11D-A28X-10	5049364	54423712	79428183	17	21738										
SART3	9733	hgsc.bcm.edu	37	chr12	108929239	108929239	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	ttctgcatgttattgcacagTcgagcctaaagtgcatcagc	9	10	2	0			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr12:108929239T>C	ENST00000228284.3	-	12	1686	c.1452A>G	c.(1450-1452)cgA>cgG	p.R484R	SART3_ENST00000431469.2_Silent_p.R448R	NM_014706.3	NP_055521.1	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T cells 3	484					cell morphogenesis (GO:0000902)|hematopoietic stem cell proliferation (GO:0071425)|homeostasis of number of cells (GO:0048872)|regulation of gene expression (GO:0010468)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|stomach(1)	25						TATTGCACAGTCGAGCCTAAA	0.478									Porokeratosis																												p.R484R		Atlas-SNP	.											.	SART3	64	.	0			c.A1452G						.						231	210	217					12																	108929239		2203	4300	6503	SO:0001819	synonymous_variant	9733	exon12	Familial Cancer Database	incl.: Porokeratosis of Mibelli, Disseminated Superficial Actinic Porokertosis, Porokeratosis Palmaris Plantaris et Disseminata, Porokeratosis Punctata Palmaris et Plantaris, Linear Porokeratosis	GCACAGTCGAGCC	AB020880	CCDS9117.1	12q24.11	2013-02-12	2006-12-07			ENSG00000075856		"RNA binding motif (RRM) containing"	16860	protein-coding gene	gene with protein product		611684	"squamous cell carcinoma antigen recognised by T cells 3"			12032085, 15840095, 20595234	Standard	NM_014706		Approved	KIAA0156, RP11-13G14, TIP110, p110	uc001tmz.1	Q15020	OTTHUMG00000169449	ENST00000228284.3:c.1452A>G	chr12.hg19:g.108929239T>C		99.0	0.0		163.0	25.0	NM_014706	A8K2E4|Q2M2H0|Q58F06|Q8IUS1|Q96J95	Silent	SNP	ENST00000228284.3	hg19	CCDS9117.1																																																																																			.	.		0.478	SART3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404094.1			C	108929239	T	C	108929239	2	2	137	1	0	0	0	0	0	0	0	1	13862	1654	58	2		2	SART3	12	108929239	Silent	SNP	T	TCGA-DD-A4NP-01A-11D-A28X-10	54505527	108929239	24922656	18	21739										
SBNO1	55206	hgsc.bcm.edu	37	chr12	123815842	123815842	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	tcatagatgattcctgctatCgtccttccttttcctacacc	4	14	1	2	rs74679372	byFrequency	TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr12:123815842C>T	ENST00000602398.1	-	8	1117	c.990G>A	c.(988-990)acG>acA	p.T330T	SBNO1_ENST00000602750.1_Silent_p.T329T|SBNO1_ENST00000420886.2_Silent_p.T330T|SBNO1_ENST00000267176.4_Silent_p.T329T			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	330					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TTCCTGCTATCGTCCTTCCTT	0.443																																					p.T330T		Atlas-SNP	.											.	SBNO1	138	.	0			c.G990A						.						158	142	148					12																	123815842		2203	4300	6503	SO:0001819	synonymous_variant	55206	exon7			TGCTATCGTCCTT	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.990G>A	chr12.hg19:g.123815842C>T		63.0	0.0		104.0	39.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	hg19	CCDS53844.1																																																																																			.	C|0.999;A|0.001		0.443	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		T	123815842	C	T	123815842	2	4	137	1	0	0	0	0	0	0	0	1	13877	871	31	1		1	SBNO1	12	123815842	Silent	SNP	C	TCGA-DD-A4NP-01A-11D-A28X-10	14886603	123815842	10036053	19	21740										
OR4M2	390538	hgsc.bcm.edu	37	chr15	22369299	22369299	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	ccaacagggccatgtccaccTgctattcccacattaccatt	5	16	0	0			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr15:22369299T>A	ENST00000332663.2	+	1	822	c.724T>A	c.(724-726)Tgc>Agc	p.C242S	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	242						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CATGTCCACCTGCTATTCCCA	0.458																																					p.C242S		Atlas-SNP	.											.	OR4M2	140	.	0			c.T724A						.						276	196	223					15																	22369299		2203	4300	6503	SO:0001583	missense	390538	exon1			TCCACCTGCTATT	AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"GPCR / Class A : Olfactory receptors"	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.724T>A	chr15.hg19:g.22369299T>A	ENSP00000329467:p.Cys242Ser	272.0	0.0		333.0	69.0	NM_001004719	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	hg19	CCDS32172.1	.	.	.	.	.	.	.	.	.	.	.	17.54	3.413917	0.62511	.	.	ENSG00000182974	ENST00000332663	T	0.00369	7.74	2.28	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000046	T	0.01320	0.0043	H	0.96111	3.77	0.43632	D	0.996026	D	0.89917	1.0	D	0.97110	1.0	T	0.41324	-0.9515	10	0.87932	D	0	-12.2555	8.1829	0.31322	0.0:0.0:0.0:1.0	.	242	Q8NGB6	OR4M2_HUMAN	S	242	ENSP00000329467:C242S	ENSP00000329467:C242S	C	+	1	0	OR4M2	19870663	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.243000	0.78219	1.068000	0.40764	0.368000	0.22195	TGC	.	.		0.458	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1			A	22369299	T	A	22369299	3	1	137	1	0	0	0	0	1	0	0	0	11085	1580	55	4	726	4	OR4M2	15	22369299	Missense_Mutation	SNP	T	TCGA-DD-A4NP-01A-11D-A28X-10		22369299	80162093	20	21741										
MYH14	79784	hgsc.bcm.edu	37	chr19	50794186	50794186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	gggatgaggagcggaagcagCgcactctggccgtggctgcc	18	11	1	1	rs369826983		TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr19:50794186C>T	ENST00000596571.1	+	33	4885	c.4885C>T	c.(4885-4887)Cgc>Tgc	p.R1629C	MYH14_ENST00000425460.1_Missense_Mutation_p.R1637C|MYH14_ENST00000440075.2_Missense_Mutation_p.R1670C|MYH14_ENST00000262269.8_Missense_Mutation_p.R1670C|MYH14_ENST00000376970.2_Missense_Mutation_p.R1662C|MYH14_ENST00000601313.1_Missense_Mutation_p.R1670C|MYH14_ENST00000598205.1_Missense_Mutation_p.R1637C			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1629					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GCGGAAGCAGCGCACTCTGGC	0.657																																					p.R1670C		Atlas-SNP	.											.	MYH14	261	.	0			c.C5008T						.	C	CYS/ARG,CYS/ARG,CYS/ARG	1,4141		0,1,2070	19	25	23		4909,5008,4885	0.7	1	19		23	0,8398		0,0,4199	no	missense,missense,missense	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	180,180,180	0,1,6269	TT,TC,CC		0.0,0.0241,0.0080	probably-damaging,probably-damaging,probably-damaging	1637/2004,1670/2037,1629/1996	50794186	1,12539	2071	4199	6270	SO:0001583	missense	79784	exon36			AAGCAGCGCACTC	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.4885C>T	chr19.hg19:g.50794186C>T	ENSP00000472819:p.Arg1629Cys	165.0	0.0		270.0	86.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530049	0.45073	2.41E-4	0.0	ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	4.42	0.697	0.18081	Myosin tail (1);	.	.	.	.	D	0.88804	0.6536	M	0.84773	2.715	0.54753	D	0.99998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88589	0.3142	9	0.87932	D	0	.	11.0492	0.47876	0.68:0.32:0.0:0.0	.	1670;1629;1637	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	C	1670;1662;1637;1413;1670	ENSP00000406273:R1670C;ENSP00000366169:R1662C;ENSP00000407879:R1637C;ENSP00000262269:R1670C	ENSP00000262269:R1670C	R	+	1	0	MYH14	55485998	0.405000	0.25336	1.000000	0.80357	0.358000	0.29455	-0.374000	0.07484	0.493000	0.27837	0.491000	0.48974	CGC	.	.		0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50794186	C	T	50794186	3	4	137	1	0	0	0	0	1	0	0	0	10042	768	27	1	5146	1	MYH14	19	50794186	Missense_Mutation	SNP	C	TCGA-DD-A4NP-01A-11D-A28X-10		50794186	8334797	21	21742										
SLC19A1	6573	hgsc.bcm.edu	37	chr21	46951887	46951887	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	tgacgctgtagaagagctccAtgagctgcatgtgcgccacc	12	12	0	4			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr21:46951887A>G	ENST00000311124.4	-	3	517	c.365T>C	c.(364-366)aTg>aCg	p.M122T	SLC19A1_ENST00000485649.2_Missense_Mutation_p.M82T|SLC19A1_ENST00000380010.4_Missense_Mutation_p.M122T|SLC19A1_ENST00000567670.1_Missense_Mutation_p.M122T	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	122					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	Methotrexate(DB00563)|Pralatrexate(DB06813)	GAAGAGCTCCATGAGCTGCAT	0.657																																					p.M122T		Atlas-SNP	.											.	SLC19A1	53	.	0			c.T365C						.						23	25	25					21																	46951887		2198	4300	6498	SO:0001583	missense	6573	exon3			AGCTCCATGAGCT	U15939	CCDS13725.1, CCDS56217.1, CCDS56218.1	21q22.3	2013-05-22			ENSG00000173638	ENSG00000173638		"Solute carriers"	10937	protein-coding gene	gene with protein product		600424				9570943	Standard	NM_194255		Approved	FOLT	uc002zhl.2	P41440	OTTHUMG00000090397	ENST00000311124.4:c.365T>C	chr21.hg19:g.46951887A>G	ENSP00000308895:p.Met122Thr	40.0	0.0		55.0	7.0	NM_001205206	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000311124.4	hg19	CCDS13725.1	.	.	.	.	.	.	.	.	.	.	A	14.37	2.513930	0.44763	.	.	ENSG00000173638	ENST00000311124;ENST00000380010;ENST00000485649;ENST00000427839;ENST00000443742	T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;0.36;0.36	4.95	4.95	0.65309	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.90484	0.7019	M	0.90814	3.15	0.58432	D	0.999998	D;D;D;D	0.67145	0.996;0.996;0.996;0.996	D;D;D;D	0.67725	0.953;0.953;0.936;0.953	D	0.92332	0.5874	10	0.72032	D	0.01	-67.9873	13.7172	0.62705	1.0:0.0:0.0:0.0	.	82;144;122;122	B7Z8C3;D3DSM6;E9PFY4;P41440	.;.;.;S19A1_HUMAN	T	122;122;82;122;122	ENSP00000308895:M122T;ENSP00000369347:M122T;ENSP00000441772:M82T;ENSP00000401850:M122T;ENSP00000411345:M122T	ENSP00000308895:M122T	M	-	2	0	SLC19A1	45776315	1.000000	0.71417	0.993000	0.49108	0.006000	0.05464	8.830000	0.92063	1.989000	0.58080	0.379000	0.24179	ATG	.	.		0.657	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1			G	46951887	A	G	46951887	3	3	137	1	0	0	0	0	1	0	0	0	14443	217	8	2	1426	2	SLC19A1	21	46951887	Missense_Mutation	SNP	A	TCGA-DD-A4NP-01A-11D-A28X-10		46951887	1178008	22	21743										
LIF	3976	hgsc.bcm.edu	37	chr22	30640773	30640773	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	1.0632318501171	0	1.48852459016393	1	1	0	aaagagggcattggcactgcCattgagctgtgccagttggc	14	9	0	2			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr22:30640773C>T	ENST00000249075.3	-	2	324	c.169G>A	c.(169-171)Ggc>Agc	p.G57S	RP1-102K2.8_ENST00000593843.1_RNA|LIF_ENST00000403987.3_Intron|RP1-102K2.8_ENST00000608354.1_RNA	NM_002309.4	NP_002300.1	P15018	LIF_HUMAN	leukemia inhibitory factor	57					blood vessel remodeling (GO:0001974)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|immune response (GO:0006955)|leukemia inhibitory factor signaling pathway (GO:0048861)|lung alveolus development (GO:0048286)|lung lobe morphogenesis (GO:0060463)|lung vasculature development (GO:0060426)|multicellular organismal development (GO:0007275)|muscle organ morphogenesis (GO:0048644)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of hormone secretion (GO:0046888)|negative regulation of meiosis (GO:0045835)|neuron development (GO:0048666)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cell proliferation (GO:0008284)|positive regulation of histone H3-K27 acetylation (GO:1901676)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|spongiotrophoblast differentiation (GO:0060708)|stem cell maintenance (GO:0019827)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|leukemia inhibitory factor receptor binding (GO:0005146)|receptor binding (GO:0005102)|RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001135)			breast(1)|lung(3)|skin(3)	7			Epithelial(10;0.171)			TTGGCACTGCCATTGAGCTGT	0.542																																					p.G57S		Atlas-SNP	.											.	LIF	18	.	0			c.G169A						.						176	150	159					22																	30640773		2203	4300	6503	SO:0001583	missense	3976	exon2			CACTGCCATTGAG		CCDS13872.1, CCDS58799.1	22q12.2	2012-02-09	2012-02-09		ENSG00000128342	ENSG00000128342			6596	protein-coding gene	gene with protein product	"differentiation inhibitory activity", "differentiation-inducing factor", "hepatocyte-stimulating factor III", "cholinergic differentiation factor", "human interleukin in DA cells"	159540				1714745, 8058719	Standard	NM_002309		Approved	CDF, DIA, HILDA	uc003agz.3	P15018	OTTHUMG00000150910	ENST00000249075.3:c.169G>A	chr22.hg19:g.30640773C>T	ENSP00000249075:p.Gly57Ser	157.0	0.0		221.0	11.0	NM_002309	B2RCW7|B5MC23|Q52LZ2	Missense_Mutation	SNP	ENST00000249075.3	hg19	CCDS13872.1	.	.	.	.	.	.	.	.	.	.	C	5.385	0.256288	0.10185	.	.	ENSG00000128342	ENST00000249075	T	0.74842	-0.88	4.56	-0.535	0.11879	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.637394	0.14132	N	0.339333	T	0.51415	0.1673	N	0.14661	0.345	0.52099	D	0.999949	B	0.17038	0.02	B	0.19946	0.027	T	0.17715	-1.0360	10	0.16896	T	0.51	-3.3473	7.6763	0.28488	0.0:0.4459:0.0:0.5541	.	57	P15018	LIF_HUMAN	S	57	ENSP00000249075:G57S	ENSP00000249075:G57S	G	-	1	0	LIF	28970773	0.003000	0.15002	0.768000	0.31515	0.974000	0.67602	-0.678000	0.05209	-0.253000	0.09514	0.563000	0.77884	GGC	.	.		0.542	LIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320508.1	NM_002309		T	30640773	C	T	30640773	3	4	137	1	0	0	0	0	1	0	0	0	8788	594	21	3	447	3	LIF	22	30640773	Missense_Mutation	SNP	C	TCGA-DD-A4NP-01A-11D-A28X-10		30640773	20663793	23	21744										
DVL1	1855	hgsc.bcm.edu	37	chr1	1277480	1277480	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gctcccgccggtgactgaccAtggactccgtgcctgtctcg	12	16	1	2	rs147424815		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:1277480A>G	ENST00000378888.5	-	4	703	c.419T>C	c.(418-420)aTg>aCg	p.M140T	DVL1_ENST00000378891.5_Missense_Mutation_p.M140T			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	140					axon extension (GO:0048675)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|collateral sprouting (GO:0048668)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|cytoplasmic microtubule organization (GO:0031122)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|negative regulation of protein binding (GO:0032091)|negative regulation of protein kinase activity (GO:0006469)|neural tube development (GO:0021915)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prepulse inhibition (GO:0060134)|protein localization to microtubule (GO:0035372)|protein localization to nucleus (GO:0034504)|receptor clustering (GO:0043113)|regulation of neurotransmitter levels (GO:0001505)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|social behavior (GO:0035176)|synapse organization (GO:0050808)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	axon (GO:0030424)|cell cortex (GO:0005938)|clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|growth cone (GO:0030426)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	enzyme binding (GO:0019899)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|Rac GTPase binding (GO:0048365)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GTGACTGACCATGGACTCCGT	0.687																																					p.M140T		Atlas-SNP	.											.	DVL1	36	.	0			c.T419C						.	A	THR/MET	0,4386		0,0,2193	26	24	25		419	3.6	1	1	dbSNP_134	25	1,8581		0,1,4290	no	missense	DVL1	NM_004421.2	81	0,1,6483	GG,GA,AA		0.0117,0.0,0.0077	benign	140/671	1277480	1,12967	2193	4291	6484	SO:0001583	missense	1855	exon4			CTGACCATGGACT	AF006011	CCDS22.1	1p36	2013-05-22	2013-05-22		ENSG00000107404	ENSG00000107404		"Dishevelled homologs"	3084	protein-coding gene	gene with protein product		601365	"dishevelled 1 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 1 (Drosophila)"			8817329	Standard	NM_004421		Approved		uc001aer.4	O14640	OTTHUMG00000003069	ENST00000378888.5:c.419T>C	chr1.hg19:g.1277480A>G	ENSP00000368166:p.Met140Thr	153.0	0.0		150.0	27.0	NM_004421	Q5TA33|Q5TA35	Missense_Mutation	SNP	ENST00000378888.5	hg19		.	.	.	.	.	.	.	.	.	.	A	10.31	1.314796	0.23908	0.0	1.17E-4	ENSG00000107404	ENST00000378891;ENST00000378888;ENST00000345100	T;T	0.04551	3.61;3.6	3.59	3.59	0.41128	.	0.193497	0.41712	D	0.000827	T	0.03564	0.0102	N	0.14661	0.345	0.41865	D	0.990246	B	0.22146	0.065	B	0.17098	0.017	T	0.47100	-0.9143	10	0.52906	T	0.07	.	11.5538	0.50735	1.0:0.0:0.0:0.0	.	140	O14640-2	.	T	140	ENSP00000368169:M140T;ENSP00000368166:M140T	ENSP00000340031:M140T	M	-	2	0	DVL1	1267343	0.946000	0.32159	0.987000	0.45799	0.607000	0.37147	8.619000	0.90938	1.629000	0.50426	0.155000	0.16302	ATG	.	A|1.000;G|0.000		0.687	DVL1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008490.1	NM_004421		G	1277480	A	G	1277480	3	3	138	1	0	0	0	0	1	0	0	0	4837	217	8	2	1641	2	DVL1	1	1277480	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10		1277480	247973141	1	21745										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7700465	7700465	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ctgctctccccacagaacccCgacatcgtcctggtgcacta	7	18	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:7700465C>T	ENST00000303635.7	+	7	723	c.516C>T	c.(514-516)ccC>ccT	p.P172P	CAMTA1_ENST00000439411.2_Silent_p.P172P	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	172					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CACAGAACCCCGACATCGTCC	0.647			T	WWTR1	epitheliod hemangioendothelioma																																p.P172P		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.C516T						.						86	76	80					1																	7700465		2203	4300	6503	SO:0001819	synonymous_variant	23261	exon7			GAACCCCGACATC	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.516C>T	chr1.hg19:g.7700465C>T		137.0	0.0		130.0	27.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	hg19	CCDS30576.1																																																																																			.	.		0.647	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		T	7700465	C	T	7700465	2	4	138	1	0	0	0	0	0	0	0	1	2615	639	23	1		1	CAMTA1	1	7700465	Silent	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	6422985	7700465	241550156	2	21746										
MFAP2	4237	hgsc.bcm.edu	37	chr1	17301519	17301519	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cttgtcccgacagaggtcagCtattgggggcaggaaggagg	17	8	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:17301519C>G	ENST00000375535.3	-	9	738		c.e9-1		MFAP2_ENST00000375534.3_Splice_Site|MFAP2_ENST00000438542.1_Splice_Site|MFAP2_ENST00000490075.1_Splice_Site			P55001	MFAP2_HUMAN	microfibrillar-associated protein 2						extracellular matrix organization (GO:0030198)|platelet formation (GO:0030220)	extracellular region (GO:0005576)|microfibril (GO:0001527)				kidney(1)|lung(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000118)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000538)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|COAD - Colon adenocarcinoma(227;1.07e-05)|BRCA - Breast invasive adenocarcinoma(304;3.04e-05)|Kidney(64;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00544)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CAGAGGTCAGCTATTGGGGGC	0.617																																					.		Atlas-SNP	.											.	MFAP2	8	.	0			c.446-1G>C						.						8	8	8					1																	17301519		2090	4073	6163	SO:0001630	splice_region_variant	4237	exon10			GGTCAGCTATTGG	BC015039	CCDS174.1, CCDS44071.1	1p36.1-p35	2008-02-05			ENSG00000117122	ENSG00000117122			7033	protein-coding gene	gene with protein product		156790				7759096	Standard	NM_017459		Approved	MAGP, MAGP-1	uc001azw.3	P55001	OTTHUMG00000002290	ENST00000375535.3:c.449-1G>C	chr1.hg19:g.17301519C>G		125.0	0.0		114.0	19.0	NM_001135248	Q53X60|Q5JXY0	Splice_Site	SNP	ENST00000375535.3	hg19	CCDS174.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.838766	0.51057	.	.	ENSG00000117122	ENST00000375535;ENST00000375534;ENST00000438542	.	.	.	3.87	3.87	0.44632	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7093	0.62659	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MFAP2	17174106	1.000000	0.71417	0.998000	0.56505	0.653000	0.38743	6.821000	0.75272	1.905000	0.55150	0.491000	0.48974	.	.	.		0.617	MFAP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006609.1	NM_002403	Intron	G	17301519	C	G	17301519	5	3	138	1	0	0	0	0	0	0	1	0	9523	811	28	4	107	4	MFAP2	1	17301519	Splice_Site	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	9601054	17301519	231949102	3	21747										
FGR	2268	hgsc.bcm.edu	37	chr1	27941376	27941376	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gttacctgggctgccatgtcCaccaattggggcagcctcaa	11	13	1	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:27941376C>A	ENST00000374005.3	-	10	1368	c.1080G>T	c.(1078-1080)gtG>gtT	p.V360V	FGR_ENST00000399173.1_Silent_p.V360V|FGR_ENST00000545953.1_Silent_p.V294V|FGR_ENST00000374004.1_Silent_p.V360V	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	360	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CTGCCATGTCCACCAATTGGG	0.562																																					p.V360V		Atlas-SNP	.											.	FGR	39	.	0			c.G1080T						.						26	24	25					1																	27941376		2203	4298	6501	SO:0001819	synonymous_variant	2268	exon10			CATGTCCACCAAT	BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"SH2 domain containing"	3697	protein-coding gene	gene with protein product		164940	"Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog", "v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog", "feline Gardner-Rasheed sarcoma viral oncogene homolog"	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.1080G>T	chr1.hg19:g.27941376C>A		204.0	0.0		147.0	19.0	NM_001042729	D3DPL7|Q9UIQ3	Silent	SNP	ENST00000374005.3	hg19	CCDS305.1																																																																																			.	.		0.562	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248		A	27941376	C	A	27941376	2	1	138	1	0	0	0	0	0	0	0	1	5882	581	21	3		3	FGR	1	27941376	Silent	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	10639857	27941376	221309245	4	21748										
IPP	3652	hgsc.bcm.edu	37	chr1	46165836	46165836	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	atgcctgctctaggcactttCattgaggcaacttcaaccca	7	13	3	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:46165836C>A	ENST00000396478.3	-	9	1659	c.1557G>T	c.(1555-1557)atG>atT	p.M519I	IPP_ENST00000495072.1_5'UTR	NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	519						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TAGGCACTTTCATTGAGGCAA	0.408																																					p.M519I		Atlas-SNP	.											.	IPP	66	.	0			c.G1557T						.						117	120	119					1																	46165836		2203	4300	6503	SO:0001583	missense	3652	exon9			CACTTTCATTGAG	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.1557G>T	chr1.hg19:g.46165836C>A	ENSP00000379739:p.Met519Ile	38.0	0.0		34.0	6.0	NM_001145349	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	hg19	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.020667	0.93462	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	D;D	0.84070	-1.8;-1.8	5.77	5.77	0.91146	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.91831	0.7415	M	0.81341	2.54	0.80722	D	1	D;D	0.69078	0.997;0.971	D;D	0.75020	0.985;0.93	D	0.92163	0.5737	10	0.87932	D	0	.	19.9946	0.97381	0.0:1.0:0.0:0.0	.	519;519	Q9Y573;A2A6V3	IPP_HUMAN;.	I	519	ENSP00000353024:M519I;ENSP00000379739:M519I	ENSP00000353024:M519I	M	-	3	0	IPP	45938423	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.212000	0.77941	2.728000	0.93425	0.591000	0.81541	ATG	.	.		0.408	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		A	46165836	C	A	46165836	3	1	138	1	0	0	0	0	1	0	0	0	7809	826	29	3	303	3	IPP	1	46165836	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	18224460	46165836	203084785	5	21749										
PTPN22	26191	hgsc.bcm.edu	37	chr1	114380848	114380848	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ctgccatttcatggttgtgtCagcatttttgtcaaaactgt	8	8	3	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:114380848C>T	ENST00000359785.5	-	13	1309	c.1174G>A	c.(1174-1176)Gac>Aac	p.D392N	PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000538253.1_Missense_Mutation_p.D148N|PTPN22_ENST00000528414.1_Missense_Mutation_p.D337N|PTPN22_ENST00000525799.1_Missense_Mutation_p.D265N|PTPN22_ENST00000420377.2_Missense_Mutation_p.D392N	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	392					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATGGTTGTGTCAGCATTTTTG	0.398																																					p.D392N		Atlas-SNP	.											.	PTPN22	90	.	0			c.G1174A						.						91	90	90					1																	114380848		2203	4300	6503	SO:0001583	missense	26191	exon13			TTGTGTCAGCATT	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.1174G>A	chr1.hg19:g.114380848C>T	ENSP00000352833:p.Asp392Asn	53.0	0.0		52.0	8.0	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	hg19	CCDS863.1	.	.	.	.	.	.	.	.	.	.	C	8.609	0.888604	0.17540	.	.	ENSG00000134242	ENST00000359785;ENST00000528414;ENST00000538253;ENST00000420377;ENST00000525799;ENST00000354605	T;T;T;T;T	0.32515	3.72;3.33;1.45;3.6;3.03	5.82	1.82	0.25136	.	0.575346	0.17597	N	0.168558	T	0.10937	0.0267	M	0.65975	2.015	0.09310	N	1	B;P;B;B;B;B	0.35050	0.122;0.482;0.007;0.013;0.012;0.007	B;B;B;B;B;B	0.27262	0.045;0.078;0.006;0.005;0.015;0.006	T	0.11494	-1.0585	10	0.48119	T	0.1	.	5.7786	0.18294	0.0:0.6253:0.1414:0.2334	.	148;265;392;337;392;392	F5H2S8;E9PPI1;E9PMT0;E9PLD8;G5E984;Q9Y2R2	.;.;.;.;.;PTN22_HUMAN	N	392;337;148;392;265;392	ENSP00000352833:D392N;ENSP00000435176:D337N;ENSP00000439372:D148N;ENSP00000388229:D392N;ENSP00000432674:D265N	ENSP00000346621:D392N	D	-	1	0	PTPN22	114182371	0.000000	0.05858	0.017000	0.16124	0.088000	0.18126	0.196000	0.17176	0.354000	0.24105	0.655000	0.94253	GAC	.	.		0.398	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		T	114380848	C	T	114380848	3	4	138	1	0	0	0	0	1	0	0	0	12802	826	29	3	1308	3	PTPN22	1	114380848	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	68215012	114380848	134869773	6	21750										
OR10J5	127385	hgsc.bcm.edu	37	chr1	159504893	159504893	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	aaatatttctgcccacaactCtgcatagggcatcctttacc	5	13	2	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:159504893C>G	ENST00000334857.2	-	1	949	c.905G>C	c.(904-906)aGa>aCa	p.R302T		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					GCCCACAACTCTGCATAGGGC	0.418																																					p.R302T		Atlas-SNP	.											.	OR10J5	68	.	0			c.G905C						.						63	59	61					1																	159504893		2203	4300	6503	SO:0001583	missense	127385	exon1			ACAACTCTGCATA		CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"GPCR / Class A : Olfactory receptors"	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.905G>C	chr1.hg19:g.159504893C>G	ENSP00000334441:p.Arg302Thr	46.0	0.0		52.0	7.0	NM_001004469	B9EH35|Q6IFH2	Missense_Mutation	SNP	ENST00000334857.2	hg19	CCDS30910.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.416895	0.42918	.	.	ENSG00000184155	ENST00000334857	T	0.40476	1.03	4.4	3.48	0.39840	.	.	.	.	.	T	0.51381	0.1671	M	0.84219	2.685	0.30806	N	0.739329	D	0.69078	0.997	D	0.64687	0.928	T	0.52586	-0.8556	9	0.87932	D	0	.	10.3544	0.43956	0.0:0.9025:0.0:0.0975	.	302	Q8NHC4	O10J5_HUMAN	T	302	ENSP00000334441:R302T	ENSP00000334441:R302T	R	-	2	0	OR10J5	157771517	0.429000	0.25530	0.201000	0.23476	0.694000	0.40290	1.296000	0.33389	1.180000	0.42898	0.591000	0.81541	AGA	.	.		0.418	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469		G	159504893	C	G	159504893	3	3	138	1	0	0	0	0	1	0	0	0	10921	913	32	4	26	4	OR10J5	1	159504893	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	45124045	159504893	89745728	7	21751										
FCRLB	127943	hgsc.bcm.edu	37	chr1	161697408	161697408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	agacccccacctctcactttGctgtgagcccgggaacccca	8	18	1	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:161697408G>A	ENST00000367948.2	+	8	1452	c.1237G>A	c.(1237-1239)Gct>Act	p.A413T	FCRLB_ENST00000367944.3_3'UTR|FCRLB_ENST00000392158.1_Missense_Mutation_p.A413T|FCRLB_ENST00000367945.1_3'UTR|FCRLB_ENST00000336830.5_3'UTR|FCRLB_ENST00000495397.1_3'UTR|FCRLB_ENST00000367946.3_3'UTR			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	413					negative regulation of immune response (GO:0050777)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|skin(1)	17	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			CTCTCACTTTGCTGTGAGCCC	0.647																																					p.A413T		Atlas-SNP	.											.	FCRLB	35	.	0			c.G1237A						.						23	29	27					1																	161697408		2201	4300	6501	SO:0001583	missense	127943	exon6			CACTTTGCTGTGA	AY670683	CCDS30927.1, CCDS72962.1, CCDS72963.1, CCDS72964.1, CCDS72965.1	1q23.3	2013-01-11	2006-09-26	2006-09-26	ENSG00000162746	ENSG00000162746		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26431	protein-coding gene	gene with protein product		609251	"Fc receptor-like and mucin-like 2"	FCRLM2		15676285	Standard	NM_001288829		Approved	FLJ31052, FCRL2, FREB-2, FCRLY	uc001gbi.3	Q6BAA4	OTTHUMG00000133629	ENST00000367948.2:c.1237G>A	chr1.hg19:g.161697408G>A	ENSP00000356925:p.Ala413Thr	115.0	0.0		123.0	8.0	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Missense_Mutation	SNP	ENST00000367948.2	hg19	CCDS30927.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.515373	0.44763	.	.	ENSG00000162746	ENST00000367948;ENST00000392158	T;T	0.01599	4.74;4.74	4.45	2.52	0.30459	.	0.502419	0.16507	N	0.211401	T	0.00384	0.0012	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.44375	-0.9332	10	0.19590	T	0.45	.	5.3593	0.16079	0.1152:0.2079:0.6769:0.0	.	413	Q6BAA4	FCRLB_HUMAN	T	413	ENSP00000356925:A413T;ENSP00000375999:A413T	ENSP00000356925:A413T	A	+	1	0	FCRLB	159964032	0.060000	0.20803	0.007000	0.13788	0.221000	0.24807	0.620000	0.24403	0.471000	0.27319	0.455000	0.32223	GCT	.	.		0.647	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378		A	161697408	G	A	161697408	3	1	138	1	0	0	0	0	1	0	0	0	5809	1319	46	3	1259	3	FCRLB	1	161697408	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	2192515	161697408	87553213	8	21752										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181767462	181767462	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	aagtgagagctccatcccctCtgtctctgacaccagcaccc	7	17	2	2	rs189356042		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:181767462C>G	ENST00000367573.2	+	48	6434	c.6434C>G	c.(6433-6435)tCt>tGt	p.S2145C	CACNA1E_ENST00000360108.3_Missense_Mutation_p.S2126C|CACNA1E_ENST00000367567.4_Missense_Mutation_p.S1709C|CACNA1E_ENST00000367570.1_Missense_Mutation_p.S2102C|CACNA1E_ENST00000358338.5_Missense_Mutation_p.S2034C|CACNA1E_ENST00000357570.5_Missense_Mutation_p.S2096C|CACNA1E_ENST00000526775.1_Missense_Mutation_p.S2083C	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2145					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TCCATCCCCTCTGTCTCTGAC	0.572																																					p.S2145C		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C6434G						.						126	135	132					1																	181767462		2024	4177	6201	SO:0001583	missense	777	exon48			TCCCCTCTGTCTC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6434C>G	chr1.hg19:g.181767462C>G	ENSP00000356545:p.Ser2145Cys	33.0	0.0		36.0	9.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.573979	0.86542	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98135	-4.62;-4.61;-4.29;-4.61;-4.74;-4.29;-4.29	5.59	5.59	0.84812	.	0.447086	0.24172	N	0.040899	D	0.98372	0.9459	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.995	D	0.99659	1.0993	10	0.87932	D	0	.	17.3853	0.87414	0.0:1.0:0.0:0.0	.	2083;2102	Q15878-2;Q15878-3	.;.	C	2102;2083;2096;2034;1709;2126;2145	ENSP00000356542:S2102C;ENSP00000434814:S2083C;ENSP00000350183:S2096C;ENSP00000351101:S2034C;ENSP00000356539:S1709C;ENSP00000353222:S2126C;ENSP00000356545:S2145C	ENSP00000350183:S2096C	S	+	2	0	CACNA1E	180034085	1.000000	0.71417	0.986000	0.45419	0.985000	0.73830	6.836000	0.75349	2.622000	0.88805	0.563000	0.77884	TCT	.	C|1.000;T|0.000		0.572	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		G	181767462	C	G	181767462	3	3	138	1	0	0	0	0	1	0	0	0	2544	913	32	4	6491	4	CACNA1E	1	181767462	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	20070054	181767462	67483159	9	21753										
TRIM67	440730	hgsc.bcm.edu	37	chr1	231344856	231344857	+	Frame_Shift_Ins	INS	-	-	A													0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	tgcacgtggaccggtacgacINSaaccacccagaccccgcctt							TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:231344856_231344857insA	ENST00000366653.5	+	8	1983_1984	c.1983_1984insA	c.(1984-1986)aacfs	p.N662fs	TRIM67_ENST00000444294.3_Frame_Shift_Ins_p.N660fs|TRIM67_ENST00000366652.2_Frame_Shift_Ins_p.N662fs|TRIM67_ENST00000449018.3_Frame_Shift_Ins_p.N600fs			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	662	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				ACCGGTACGACAACCACCCAGA	0.629																																					p.D661fs		Atlas-Indel,Pindel	.											.	TRIM67	160	.	0			c.1983_1984insA						.																																			SO:0001589	frameshift_variant	440730	exon8			.	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.1985dupA	chr1.hg19:g.231344858_231344858dupA	ENSP00000355613:p.Asn662fs	246.0	0.0		275.0	85.0	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Frame_Shift_Ins	INS	ENST00000366653.5	hg19	CCDS44333.1																																																																																			.	.		0.629	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		A	231344857	-	A	231344856	7	5	138	1	0	1	1	0	0	0	0	0	16555	477	17	0	2013	0	TRIM67	1	231344856	Frame_Shift_Ins	INS	-	TCGA-DD-A4NQ-01A-21D-A28X-10	49577394	231344856	17905765	10	21754										
LYST	1130	hgsc.bcm.edu	37	chr1	235973623	235973623	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gaattggcttctgaatctgaGgtggagagctgtgtctttct	13	6	4	3			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:235973623G>T	ENST00000389794.3	-	5	669	c.495C>A	c.(493-495)acC>acA	p.T165T	LYST_ENST00000536965.1_Silent_p.T165T|LYST_ENST00000389793.2_Silent_p.T165T			Q99698	LYST_HUMAN	lysosomal trafficking regulator	165					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			CTGAATCTGAGGTGGAGAGCT	0.393																																					p.T165T		Atlas-SNP	.											.	LYST	370	.	0			c.C495A						.						151	147	148					1																	235973623		2203	4300	6503	SO:0001819	synonymous_variant	1130	exon5			ATCTGAGGTGGAG	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.495C>A	chr1.hg19:g.235973623G>T		83.0	0.0		92.0	20.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.393	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			T	235973623	G	T	235973623	2	4	138	1	0	0	0	0	0	0	0	1	9137	987	35	3		3	LYST	1	235973623	Silent	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	4628767	235973623	13276998	11	21755										
RYR2	6262	hgsc.bcm.edu	37	chr1	237778097	237778097	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	caaggggggcaagcggcccaAggaaggcctgctccaaatga	15	11	0	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr1:237778097A>C	ENST00000366574.2	+	37	5986	c.5669A>C	c.(5668-5670)aAg>aCg	p.K1890T	RYR2_ENST00000542537.1_Missense_Mutation_p.K1874T|RYR2_ENST00000360064.6_Missense_Mutation_p.K1888T	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1890	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AAGCGGCCCAAGGAAGGCCTG	0.507																																					p.K1890T		Atlas-SNP	.											.	RYR2	1273	.	0			c.A5669C						.						41	44	43					1																	237778097		1967	4148	6115	SO:0001583	missense	6262	exon37			GGCCCAAGGAAGG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.5669A>C	chr1.hg19:g.237778097A>C	ENSP00000355533:p.Lys1890Thr	185.0	0.0		156.0	31.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	7.093	0.572537	0.13623	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.72942	-0.7;-0.7;-0.7	5.33	5.33	0.75918	.	0.310145	0.24674	N	0.036523	T	0.51244	0.1663	N	0.14661	0.345	0.43326	D	0.995351	B	0.06786	0.001	B	0.04013	0.001	T	0.47142	-0.9140	10	0.15499	T	0.54	.	11.9117	0.52743	0.8546:0.1454:0.0:0.0	.	1890	Q92736	RYR2_HUMAN	T	1890;1888;1874	ENSP00000355533:K1890T;ENSP00000353174:K1888T;ENSP00000443798:K1874T	ENSP00000353174:K1888T	K	+	2	0	RYR2	235844720	0.994000	0.37717	0.880000	0.34516	0.949000	0.60115	3.016000	0.49607	2.012000	0.59069	0.528000	0.53228	AAG	.	.		0.507	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237778097	A	C	237778097	3	2	138	1	0	0	0	0	1	0	0	0	13784	72	3	5	5815	5	RYR2	1	237778097	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10	1804474	237778097	11472524	12	21756										
GRHL1	29841	hgsc.bcm.edu	37	chr2	10095217	10095217	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cgctgcgctgggcctgctctAtgactactacaaggtgggtt	13	11	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr2:10095217A>G	ENST00000324907.9	+	2	330	c.194A>G	c.(193-195)tAt>tGt	p.Y65C	GRHL1_ENST00000324883.5_5'UTR|GRHL1_ENST00000405379.2_Missense_Mutation_p.Y65C	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	65	Transcription activation.				cellular lipid metabolic process (GO:0044255)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		GGCCTGCTCTATGACTACTAC	0.498																																					p.Y65C		Atlas-SNP	.											.	GRHL1	95	.	0			c.A194G						.						47	52	50					2																	10095217		2053	4240	6293	SO:0001583	missense	29841	exon2			TGCTCTATGACTA	AF198489	CCDS33144.1, CCDS33144.2	2p25.2	2008-02-05	2005-07-11	2005-07-11	ENSG00000134317	ENSG00000134317			17923	protein-coding gene	gene with protein product		609786	"transcription factor CP2-like 2"	TFCP2L2		10644752, 12393799	Standard	NM_198182		Approved	LBP-32, MGR	uc002raa.3	Q9NZI5	OTTHUMG00000151704	ENST00000324907.9:c.194A>G	chr2.hg19:g.10095217A>G	ENSP00000324693:p.Tyr65Cys	132.0	0.0		110.0	16.0	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Missense_Mutation	SNP	ENST00000324907.9	hg19	CCDS33144.2	.	.	.	.	.	.	.	.	.	.	A	19.57	3.852336	0.71719	.	.	ENSG00000134317	ENST00000405379;ENST00000324907	T;T	0.55760	0.5;0.5	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.75206	0.3818	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78979	-0.1990	10	0.66056	D	0.02	-6.483	16.1205	0.81351	1.0:0.0:0.0:0.0	.	65	Q9NZI5	GRHL1_HUMAN	C	65	ENSP00000384209:Y65C;ENSP00000324693:Y65C	ENSP00000324693:Y65C	Y	+	2	0	GRHL1	10012668	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	9.339000	0.96797	2.205000	0.71048	0.533000	0.62120	TAT	.	.		0.498	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		G	10095217	A	G	10095217	3	3	138	1	0	0	0	0	1	0	0	0	6772	449	16	2	200	2	GRHL1	2	10095217	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10		10095217	233104156	13	21757										
DQX1	165545	hgsc.bcm.edu	37	chr2	74745708	74745708	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ggcaagttactcaggaagtaTggaggggccaattccaccag	13	9	1	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr2:74745708T>A	ENST00000404568.3	-	12	2238	c.2019A>T	c.(2017-2019)ccA>ccT	p.P673P	DQX1_ENST00000393951.2_Silent_p.P673P	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	673						nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						TCAGGAAGTATGGAGGGGCCA	0.483																																					p.P673P		Atlas-SNP	.											.	DQX1	95	.	0			c.A2019T						.						100	91	94					2																	74745708		2203	4300	6503	SO:0001819	synonymous_variant	165545	exon12			GAAGTATGGAGGG	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.2019A>T	chr2.hg19:g.74745708T>A		147.0	0.0		139.0	24.0	NM_133637	Q6B017|Q8NAM8	Silent	SNP	ENST00000404568.3	hg19	CCDS1949.2																																																																																			.	.		0.483	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		A	74745708	T	A	74745708	2	1	138	1	0	0	0	0	0	0	0	1	4753	1451	51	4		4	DQX1	2	74745708	Silent	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	64650491	74745708	168453665	14	21758										
LMAN2L	81562	hgsc.bcm.edu	37	chr2	97405772	97405772	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ccaaggggtcccagagtcgcCgccatctttcccaccaacga	9	17	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr2:97405772C>T	ENST00000264963.4	-	1	28	c.6G>A	c.(4-6)gcG>gcA	p.A2A	LMAN2L_ENST00000377079.4_Silent_p.A2A|LMAN2L_ENST00000426463.2_5'UTR|LMAN2L_ENST00000534882.1_5'UTR|LMAN2L_ENST00000537039.1_5'UTR	NM_030805.3	NP_110432.1	Q9H0V9	LMA2L_HUMAN	lectin, mannose-binding 2-like	2					ER to Golgi vesicle-mediated transport (GO:0006888)|protein folding (GO:0006457)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|lung(2)|skin(1)|urinary_tract(1)	7						CCAGAGTCGCCGCCATCTTTC	0.602																																					p.A2A		Atlas-SNP	.											.	LMAN2L	27	.	0			c.G6A						.						48	54	52					2																	97405772		2203	4300	6503	SO:0001819	synonymous_variant	81562	exon1			AGTCGCCGCCATC	AL136617	CCDS2023.1, CCDS46365.1	2q11.1	2008-02-05			ENSG00000114988	ENSG00000114988			19263	protein-coding gene	gene with protein product		609552				12609988	Standard	NM_001142292		Approved	DKFZp564L2423, VIPL	uc002swv.3	Q9H0V9	OTTHUMG00000130453	ENST00000264963.4:c.6G>A	chr2.hg19:g.97405772C>T		22.0	0.0		37.0	9.0	NM_030805	B4DSH3|D3DXH6|Q53GV3|Q53S67|Q63HN6|Q8NBQ6|Q9BQ14	Silent	SNP	ENST00000264963.4	hg19	CCDS2023.1																																																																																			.	.		0.602	LMAN2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252844.1	NM_030805		T	97405772	C	T	97405772	2	4	138	1	0	0	0	0	0	0	0	1	8848	639	23	1		1	LMAN2L	2	97405772	Silent	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	22660064	97405772	145793601	15	21759										
GLI2	2736	hgsc.bcm.edu	37	chr2	121554929	121554929	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gcctcagccactgcctccgaGaagcaagaagccaaaagtgg	11	13	1	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr2:121554929G>T	ENST00000452319.1	+	2	93	c.33G>T	c.(31-33)gaG>gaT	p.E11D	GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_5'UTR|GLI2_ENST00000361492.4_Missense_Mutation_p.E11D					GLI family zinc finger 2									p.E11E(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CTGCCTCCGAGAAGCAAGAAG	0.597																																					p.E11D		Atlas-SNP	.											GLI2,NS,carcinoma,0,1	GLI2	187	.	1	Substitution - coding silent(1)	breast(1)	c.G33T						.						120	138	132					2																	121554929		2203	4300	6503	SO:0001583	missense	2736	exon1			CTCCGAGAAGCAA		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.33G>T	chr2.hg19:g.121554929G>T	ENSP00000390436:p.Glu11Asp	73.0	0.0		68.0	15.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274804	0.23307	.	.	ENSG00000074047	ENST00000418323;ENST00000452319;ENST00000361492;ENST00000440937;ENST00000360874	T;T	0.16324	2.35;2.35	5.86	4.98	0.66077	.	0.000000	0.53938	D	0.000051	T	0.12561	0.0305	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.12013	0.003;0.002;0.0;0.005	B;B;B;B	0.11329	0.004;0.002;0.0;0.006	T	0.04509	-1.0946	10	0.87932	D	0	.	15.2895	0.73854	0.0:0.2779:0.7221:0.0	.	11;11;11;11	B4DT63;P10070;Q0VGA0;F5H4D9	.;GLI2_HUMAN;.;.	D	11;11;11;11;3	ENSP00000390436:E11D;ENSP00000354586:E11D	ENSP00000344473:E11D	E	+	3	2	GLI2	121271399	1.000000	0.71417	0.999000	0.59377	0.336000	0.28762	1.875000	0.39578	1.467000	0.48044	0.655000	0.94253	GAG	.	.		0.597	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121554929	G	T	121554929	3	4	138	1	0	0	0	0	1	0	0	0	6446	933	33	3	35	3	GLI2	2	121554929	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	24149157	121554929	121644444	16	21760										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160242941	160242941	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	caagtcttgtacttcacccaTgctgtcccctatatttagca	5	13	2	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr2:160242941T>A	ENST00000392783.2	-	22	3889	c.3394A>T	c.(3394-3396)Atg>Ttg	p.M1132L	BAZ2B_ENST00000355831.2_Missense_Mutation_p.M1098L|BAZ2B_ENST00000392782.1_Missense_Mutation_p.M1096L|AC008277.1_ENST00000420020.1_RNA|BAZ2B_ENST00000343439.5_Missense_Mutation_p.M1032L	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1132	DDT. {ECO:0000255|PROSITE- ProRule:PRU00063}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						ACTTCACCCATGCTGTCCCCT	0.383																																					p.M1132L		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A3394T						.						96	88	90					2																	160242941		1890	4135	6025	SO:0001583	missense	29994	exon22			CACCCATGCTGTC	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.3394A>T	chr2.hg19:g.160242941T>A	ENSP00000376534:p.Met1132Leu	98.0	0.0		61.0	10.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.08|17.08	3.298867|3.298867	0.60195|0.60195	.|.	.|.	ENSG00000123636|ENSG00000123636	ENST00000294905|ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	.|T;T;T;T	.|0.57436	.|0.46;0.46;0.46;0.4	6.08|6.08	6.08|6.08	0.98989|0.98989	.|DDT domain superfamily (1);DDT domain, subgroup (1);DDT domain (1);	.|0.000000	.|0.44902	.|U	.|0.000420	T|T	0.40862|0.40862	0.1134|0.1134	N|N	0.08118|0.08118	0|0	0.47094|0.47094	D|D	0.999317|0.999317	.|B;P	.|0.45176	.|0.367;0.852	.|B;P	.|0.46389	.|0.106;0.515	T|T	0.35251|0.35251	-0.9796|-0.9796	5|9	.|.	.|.	.|.	-12.1071|-12.1071	16.6512|16.6512	0.85203|0.85203	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1096;1132	.|Q9UIF8-5;Q9UIF8	.|.;BAZ2B_HUMAN	L|L	192|1096;1132;1098;1032	.|ENSP00000376533:M1096L;ENSP00000376534:M1132L;ENSP00000348087:M1098L;ENSP00000339670:M1032L	.|.	H|M	-|-	2|1	0|0	BAZ2B|BAZ2B	159951187|159951187	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.081000|5.081000	0.64444|0.64444	2.333000|2.333000	0.79357|0.79357	0.482000|0.482000	0.46254|0.46254	CAT|ATG	.	.		0.383	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			A	160242941	T	A	160242941	3	1	138	1	0	0	0	0	1	0	0	0	1332	1464	51	4	3176	4	BAZ2B	2	160242941	Missense_Mutation	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	38688012	160242941	82956432	17	21761										
HOXD9	3235	hgsc.bcm.edu	37	chr2	176988265	176988265	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	tcccaggctgttcgctgaagGaggaggagaagcagcattcg	15	9	0	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr2:176988265G>C	ENST00000249499.6	+	1	1178	c.769G>C	c.(769-771)Gag>Cag	p.E257Q	HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	257					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal system morphogenesis (GO:0048704)|hindlimb morphogenesis (GO:0035137)|mammary gland development (GO:0030879)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		TTCGCTGAAGGAGGAGGAGAA	0.612																																					p.E257Q	GBM(47;924 952 7959 9248 12176)	Atlas-SNP	.											.	HOXD9	49	.	0			c.G769C						.						14	14	14					2																	176988265		2195	4271	6466	SO:0001583	missense	3235	exon1			CTGAAGGAGGAGG		CCDS2267.2	2q31.1	2011-06-20	2005-12-22		ENSG00000128709	ENSG00000128709		"Homeoboxes / ANTP class : HOXL subclass"	5140	protein-coding gene	gene with protein product		142982	"homeo box D9"	HOX4C, HOX4		1973146, 1358459	Standard	NM_014213		Approved		uc010zex.2	P28356	OTTHUMG00000132516	ENST00000249499.6:c.769G>C	chr2.hg19:g.176988265G>C	ENSP00000249499:p.Glu257Gln	91.0	0.0		70.0	12.0	NM_014213	Q86ST1	Missense_Mutation	SNP	ENST00000249499.6	hg19	CCDS2267.2	.	.	.	.	.	.	.	.	.	.	G	16.56	3.157721	0.57368	.	.	ENSG00000128709	ENST00000249499	D	0.94046	-3.34	4.91	2.95	0.34219	.	5.085380	0.00541	N	0.000224	D	0.91637	0.7357	L	0.43152	1.355	0.32337	N	0.560278	D	0.54601	0.967	B	0.44044	0.439	D	0.84295	0.0502	10	0.35671	T	0.21	.	9.8521	0.41064	0.0773:0.1403:0.7824:0.0	.	257	P28356	HXD9_HUMAN	Q	257	ENSP00000249499:E257Q	ENSP00000249499:E257Q	E	+	1	0	HOXD9	176696511	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.728000	0.74769	1.176000	0.42840	0.555000	0.69702	GAG	.	.		0.612	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255698.4			C	176988265	G	C	176988265	3	2	138	1	0	0	0	0	1	0	0	0	7335	1175	41	4	771	4	HOXD9	2	176988265	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	16745324	176988265	66211108	18	21762										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186673299	186673299	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gaaaggatttatcaggttgtCgattccgtttatagtaacat	9	5	1	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr2:186673299C>T	ENST00000424728.1	+	17	19266	c.19266C>T	c.(19264-19266)gtC>gtT	p.V6422V	FSIP2_ENST00000343098.5_Silent_p.V6511V			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6422										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						ATCAGGTTGTCGATTCCGTTT	0.328																																					p.V6511V		Atlas-SNP	.											.	FSIP2	251	.	0			c.C19533T						.						65	59	61					2																	186673299		1811	4072	5883	SO:0001819	synonymous_variant	401024	exon17			GGTTGTCGATTCC	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.19266C>T	chr2.hg19:g.186673299C>T		127.0	0.0		98.0	16.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Silent	SNP	ENST00000424728.1	hg19																																																																																				.	.		0.328	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		T	186673299	C	T	186673299	2	4	138	1	0	0	0	0	0	0	0	1	6083	871	31	1		1	FSIP2	2	186673299	Silent	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	9685034	186673299	56526074	19	21763										
ITGAV	3685	hgsc.bcm.edu	37	chr2	187465066	187465066	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	catcctcaatacacaaatgcTcctaggcaccctccttctga	4	16	2	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr2:187465066T>C	ENST00000261023.3	+	2	459				ITGAV_ENST00000433736.2_Missense_Mutation_p.L2P|ITGAV_ENST00000374907.3_Intron	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V						angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	ACACAAATGCTCCTAGGCACC	0.463																																					p.L2P	Melanoma(58;108 1995 6081)	Atlas-SNP	.											.	ITGAV	124	.	0			c.T5C						.						189	160	169					2																	187465066		692	1591	2283	SO:0001627	intron_variant	3685	exon1			AAATGCTCCTAGG		CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"CD molecules", "Integrins"	6150	protein-coding gene	gene with protein product		193210	"antigen identified by monoclonal antibody L230", "vitronectin receptor", "integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.186-1682T>C	chr2.hg19:g.187465066T>C		71.0	0.0		49.0	7.0	NM_001144999	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Missense_Mutation	SNP	ENST00000261023.3	hg19	CCDS2292.1	.	.	.	.	.	.	.	.	.	.	T	2.665	-0.278942	0.05642	.	.	ENSG00000138448	ENST00000433736	T	0.69175	-0.38	2.58	1.34	0.21922	.	.	.	.	.	T	0.41834	0.1176	N	0.08118	0	0.09310	N	1	B	0.21309	0.054	B	0.15052	0.012	T	0.33266	-0.9875	9	0.87932	D	0	.	4.6264	0.12481	0.0:0.1604:0.0:0.8396	.	2	E7EWZ6	.	P	2	ENSP00000404291:L2P	ENSP00000404291:L2P	L	+	2	0	ITGAV	187173311	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.046000	0.14035	0.365000	0.24400	0.528000	0.53228	CTC	.	.		0.463	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		C	187465066	T	C	187465066	1	2	138	0	1	0	0	0	0	0	0	0	7897	1551	54	2		2	ITGAV	2	187465066	Intron	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	791767	187465066	55734307	20	21764										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227906897	227906897	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	aggacctggtatccctggatCcccctggaggcctcttggcc	12	15	1	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr2:227906897C>A	ENST00000396625.3	-	37	3679	c.3472G>T	c.(3472-3474)Gat>Tat	p.D1158Y	COL4A4_ENST00000329662.7_Missense_Mutation_p.D1158Y	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1158	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		ATCCCTGGATCCCCCTGGAGG	0.542																																					p.D1158Y		Atlas-SNP	.											.	COL4A4	215	.	0			c.G3472T						.						142	138	139					2																	227906897		1865	4101	5966	SO:0001583	missense	1286	exon37			CTGGATCCCCCTG		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.3472G>T	chr2.hg19:g.227906897C>A	ENSP00000379866:p.Asp1158Tyr	56.0	0.0		45.0	7.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	hg19	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	C	0.913	-0.718288	0.03182	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.93547	-2.63;-3.24	6.17	1.24	0.21308	.	.	.	.	.	D	0.87529	0.6200	L	0.39020	1.185	0.09310	N	0.999999	B	0.15930	0.015	B	0.19946	0.027	T	0.75602	-0.3261	9	0.41790	T	0.15	.	4.9584	0.14054	0.2304:0.3074:0.3921:0.0702	.	1158	P53420	CO4A4_HUMAN	Y	1158	ENSP00000379866:D1158Y;ENSP00000328553:D1158Y	ENSP00000328553:D1158Y	D	-	1	0	COL4A4	227615141	0.000000	0.05858	0.003000	0.11579	0.906000	0.53458	-0.023000	0.12456	-0.053000	0.13289	0.655000	0.94253	GAT	.	.		0.542	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		A	227906897	C	A	227906897	3	1	138	1	0	0	0	0	1	0	0	0	3695	855	30	3	1648	3	COL4A4	2	227906897	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	40441831	227906897	15292476	21	21765										
LTF	4057	hgsc.bcm.edu	37	chr3	46492064	46492064	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	caacggcatgagaagggaccCgggccagatggcagtctttg	15	10	1	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr3:46492064C>A	ENST00000231751.4	-	7	1098	c.803G>T	c.(802-804)cGg>cTg	p.R268L	LTF_ENST00000426532.2_Missense_Mutation_p.R224L|LTF_ENST00000417439.1_Missense_Mutation_p.R268L	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	268	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		AGAAGGGACCCGGGCCAGATG	0.562																																					p.R268L		Atlas-SNP	.											.	LTF	98	.	0			c.G803T						.						105	93	97					3																	46492064		2203	4296	6499	SO:0001583	missense	4057	exon7			GGGACCCGGGCCA		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.803G>T	chr3.hg19:g.46492064C>A	ENSP00000231751:p.Arg268Leu	178.0	0.0		150.0	25.0	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Missense_Mutation	SNP	ENST00000231751.4	hg19	CCDS33747.1	.	.	.	.	.	.	.	.	.	.	C	10.14	1.267941	0.23136	.	.	ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	4.79	0.439	0.16567	.	0.239958	0.48767	D	0.000161	T	0.43986	0.1272	L	0.55743	1.74	0.40246	D	0.978013	B;D;B	0.59357	0.1;0.985;0.1	B;P;B	0.59424	0.086;0.857;0.086	T	0.25745	-1.0123	10	0.44086	T	0.13	-10.4148	8.2006	0.31421	0.0:0.4907:0.0:0.5093	.	268;255;268	E7ER44;E7EQB2;P02788	.;.;TRFL_HUMAN	L	268;224;268;255	ENSP00000231751:R268L;ENSP00000405719:R224L;ENSP00000405546:R268L;ENSP00000397427:R255L	ENSP00000231751:R268L	R	-	2	0	LTF	46467068	0.064000	0.20934	0.008000	0.14137	0.223000	0.24884	0.419000	0.21247	-0.047000	0.13423	0.655000	0.94253	CGG	.	.		0.562	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		A	46492064	C	A	46492064	3	1	138	1	0	0	0	0	1	0	0	0	9088	652	23	1	1373	1	LTF	3	46492064	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10		46492064	151530366	22	21766										
C3orf67	200844	hgsc.bcm.edu	37	chr3	58849427	58849427	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	tccatgaggtgctgatcgtgGtcttgatgaaaaagtgaaaa	12	5	1	5			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr3:58849427G>A	ENST00000482387.1	-	8	1171	c.1075C>T	c.(1075-1077)Cca>Tca	p.P359S	RP11-147N17.1_ENST00000492031.1_RNA|RP11-147N17.1_ENST00000463703.1_RNA|C3orf67_ENST00000472469.1_Missense_Mutation_p.P266S|RP11-147N17.1_ENST00000482372.1_RNA|RP11-147N17.1_ENST00000493123.1_RNA|C3orf67_ENST00000295966.7_Missense_Mutation_p.P359S			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	359										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(3)|prostate(2)|skin(1)	19		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		GCTGATCGTGGTCTTGATGAA	0.468																																					p.P359S		Atlas-SNP	.											.	C3orf67	45	.	0			c.C1075T						.						148	142	144					3																	58849427		2203	4300	6503	SO:0001583	missense	200844	exon12			ATCGTGGTCTTGA	AK124920	CCDS33776.1	3p14.2	2011-01-25			ENSG00000163689	ENSG00000163689			24763	protein-coding gene	gene with protein product							Standard	NM_198463		Approved	FLJ42117, FLJ42930	uc003dkt.1	Q6ZVT6	OTTHUMG00000159151	ENST00000482387.1:c.1075C>T	chr3.hg19:g.58849427G>A	ENSP00000417122:p.Pro359Ser	94.0	0.0		77.0	13.0	NM_198463	B9EKV6|Q6ZV69	Missense_Mutation	SNP	ENST00000482387.1	hg19		.	.	.	.	.	.	.	.	.	.	G	22.3	4.275456	0.80580	.	.	ENSG00000163689	ENST00000295966;ENST00000482387;ENST00000394474;ENST00000472469	T;T;T	0.37058	1.64;1.35;1.22	5.39	5.39	0.77823	.	0.068735	0.64402	D	0.000018	T	0.62109	0.2401	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.64402	-0.6416	10	0.66056	D	0.02	-15.996	17.7005	0.88293	0.0:0.0:1.0:0.0	.	266;359;359	C9J3M8;Q6ZVT6-2;Q6ZVT6	.;.;CC067_HUMAN	S	359;359;64;266	ENSP00000295966:P359S;ENSP00000417122:P359S;ENSP00000417271:P266S	ENSP00000295966:P359S	P	-	1	0	C3orf67	58824467	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.688000	0.74557	2.678000	0.91216	0.655000	0.94253	CCA	.	.		0.468	C3orf67-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000353803.1	NM_198463		A	58849427	G	A	58849427	3	1	138	1	0	0	0	0	1	0	0	0	2243	1261	44	3	636	3	C3orf67	3	58849427	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	12357363	58849427	139173003	23	21767										
OR5H14	403273	hgsc.bcm.edu	37	chr3	97868812	97868812	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cttatactgattcctctattAactttctaatggtttttatt	3	7	2	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr3:97868812A>T	ENST00000437310.1	+	1	643	c.583A>T	c.(583-585)Aac>Tac	p.N195Y	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						TTCCTCTATTAACTTTCTAAT	0.284																																					p.N195Y		Atlas-SNP	.											.	OR5H14	56	.	0			c.A583T						.						64	68	67					3																	97868812		2200	4295	6495	SO:0001583	missense	403273	exon1			TCTATTAACTTTC		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"GPCR / Class A : Olfactory receptors"	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.583A>T	chr3.hg19:g.97868812A>T	ENSP00000401706:p.Asn195Tyr	62.0	0.0		52.0	15.0	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	hg19	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.665736	0.47677	.	.	ENSG00000236032	ENST00000437310	T	0.00224	8.51	2.49	2.49	0.30216	GPCR, rhodopsin-like superfamily (1);	0.128437	0.35378	N	0.003241	T	0.00440	0.0014	M	0.75777	2.31	0.27419	N	0.954332	D	0.89917	1.0	D	0.83275	0.996	T	0.37820	-0.9689	10	0.87932	D	0	.	6.7194	0.23323	1.0:0.0:0.0:0.0	.	195	A6NHG9	O5H14_HUMAN	Y	195	ENSP00000401706:N195Y	ENSP00000401706:N195Y	N	+	1	0	OR5H14	99351502	0.000000	0.05858	0.133000	0.22050	0.049000	0.14656	0.830000	0.27462	1.132000	0.42129	0.164000	0.16699	AAC	.	.		0.284	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			T	97868812	A	T	97868812	3	4	138	1	0	0	0	0	1	0	0	0	11169	362	13	4	585	4	OR5H14	3	97868812	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10	39019385	97868812	100153618	24	21768										
AFAP1	60312	hgsc.bcm.edu	37	chr4	7787959	7787959	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gacatcgtcataatgaagtgCcgtcccgctggggtgggcat	14	10	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr4:7787959C>T	ENST00000360265.4	-	11	1726	c.1492G>A	c.(1492-1494)Gca>Aca	p.A498T	AFAP1_ENST00000382543.3_Missense_Mutation_p.A498T|AFAP1_ENST00000420658.1_Missense_Mutation_p.A498T|AFAP1_ENST00000513842.1_5'UTR|AFAP1_ENST00000358461.2_Missense_Mutation_p.A498T			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	498						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TAATGAAGTGCCGTCCCGCTG	0.498																																					p.A498T		Atlas-SNP	.											.	AFAP1	93	.	0			c.G1492A						.						117	113	115					4																	7787959		2203	4300	6503	SO:0001583	missense	60312	exon12			GAAGTGCCGTCCC	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1492G>A	chr4.hg19:g.7787959C>T	ENSP00000353402:p.Ala498Thr	137.0	0.0		98.0	19.0	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	hg19	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.847265	0.91277	.	.	ENSG00000196526	ENST00000360265;ENST00000420658;ENST00000358461;ENST00000382543	T;T;T;T	0.16743	2.32;2.34;2.32;2.34	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.40297	0.1111	M	0.70595	2.14	0.80722	D	1	D;B	0.89917	1.0;0.226	D;B	0.87578	0.998;0.132	T	0.18524	-1.0334	10	0.10902	T	0.67	-44.1013	18.916	0.92506	0.0:1.0:0.0:0.0	.	498;498	E9PDT7;Q8N556	.;AFAP1_HUMAN	T	498	ENSP00000353402:A498T;ENSP00000410689:A498T;ENSP00000351245:A498T;ENSP00000371983:A498T	ENSP00000351245:A498T	A	-	1	0	AFAP1	7838859	1.000000	0.71417	0.748000	0.31131	0.689000	0.40095	5.266000	0.65525	2.462000	0.83206	0.650000	0.86243	GCA	.	.		0.498	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		T	7787959	C	T	7787959	3	4	138	1	0	0	0	0	1	0	0	0	353	739	26	3	980	3	AFAP1	4	7787959	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10		7787959	183366317	25	21769										
TRPC3	7222	hgsc.bcm.edu	37	chr4	122853884	122853884	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gatggcgagcagcagggcgtCgccaatgcgcgccaggttct	16	12	1	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr4:122853884C>T	ENST00000379645.3	-	2	602	c.529G>A	c.(529-531)Gac>Aac	p.D177N	TRPC3_ENST00000513531.1_Missense_Mutation_p.D104N|TRPC3_ENST00000264811.5_Missense_Mutation_p.D104N	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	92					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						AGCAGGGCGTCGCCAATGCGC	0.647																																					p.D177N		Atlas-SNP	.											.	TRPC3	201	.	0			c.G529A						.						66	57	60					4																	122853884		2203	4300	6503	SO:0001583	missense	7222	exon2			GGGCGTCGCCAAT	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.529G>A	chr4.hg19:g.122853884C>T	ENSP00000368966:p.Asp177Asn	152.0	0.0		132.0	28.0	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	hg19	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	C	34	5.311162	0.95629	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	T;T;T	0.63580	-0.05;-0.05;-0.05	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.75384	0.3842	L	0.45137	1.4	0.80722	D	1	D;D	0.89917	0.995;1.0	P;D	0.97110	0.881;1.0	T	0.74172	-0.3751	10	0.54805	T	0.06	0.0055	20.3932	0.98965	0.0:1.0:0.0:0.0	.	104;177	E9PCJ9;Q5G1L5	.;.	N	104;177;104	ENSP00000264811:D104N;ENSP00000368966:D177N;ENSP00000426899:D104N	ENSP00000264811:D104N	D	-	1	0	TRPC3	123073334	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.755000	0.85180	2.824000	0.97209	0.655000	0.94253	GAC	.	.		0.647	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		T	122853884	C	T	122853884	3	4	138	1	0	0	0	0	1	0	0	0	16594	884	31	1	2280	1	TRPC3	4	122853884	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	115065925	122853884	68300392	26	21770										
SPEF2	79925	hgsc.bcm.edu	37	chr5	35704679	35704679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	aagaattgtcctataaaactGctcacgaagatatcagtcaa	6	8	3	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr5:35704679G>A	ENST00000356031.3	+	17	2576	c.2422G>A	c.(2422-2424)Gct>Act	p.A808T	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000509059.1_Missense_Mutation_p.A803T|SPEF2_ENST00000440995.2_Missense_Mutation_p.A803T	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	808					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTATAAAACTGCTCACGAAGA	0.313																																					p.A808T		Atlas-SNP	.											.	SPEF2	324	.	0			c.G2422A						.						112	103	106					5																	35704679		1824	4075	5899	SO:0001583	missense	79925	exon17			AAAACTGCTCACG	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.2422G>A	chr5.hg19:g.35704679G>A	ENSP00000348314:p.Ala808Thr	63.0	0.0		40.0	7.0	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	hg19	CCDS43309.1	.	.	.	.	.	.	.	.	.	.	G	10.54	1.379416	0.24944	.	.	ENSG00000152582	ENST00000356031;ENST00000509059;ENST00000440995;ENST00000504054	T;T;T;T	0.31510	3.4;3.25;3.39;1.49	5.76	-11.0	0.00169	.	1.975980	0.01835	N	0.034961	T	0.17662	0.0424	L	0.43152	1.355	0.09310	N	1	B;B;B	0.18610	0.017;0.029;0.017	B;B;B	0.16289	0.006;0.015;0.006	T	0.10636	-1.0621	10	0.19147	T	0.46	.	3.0789	0.06255	0.1595:0.0925:0.3132:0.4347	.	803;803;808	D6REZ4;Q9C093-2;Q9C093	.;.;SPEF2_HUMAN	T	808;803;803;314	ENSP00000348314:A808T;ENSP00000421593:A803T;ENSP00000412125:A803T;ENSP00000421744:A314T	ENSP00000348314:A808T	A	+	1	0	SPEF2	35740436	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.874000	0.00718	-1.549000	0.01710	-0.293000	0.09583	GCT	.	.		0.313	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		A	35704679	G	A	35704679	3	1	138	1	0	0	0	0	1	0	0	0	15050	1319	46	3	2509	3	SPEF2	5	35704679	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10		35704679	145210581	27	21771										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140182464	140182464	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cgtgctggacgagaacgacaAcgcgccggcactgctgatgc	14	13	0	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr5:140182464A>G	ENST00000522353.2	+	1	1682	c.1682A>G	c.(1681-1683)aAc>aGc	p.N561S	PCDHA3_ENST00000532566.2_Missense_Mutation_p.N561S|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	561	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGAACGACAACGCGCCGGCA	0.682																																					p.N561S		Atlas-SNP	.											.	PCDHA3	396	.	0			c.A1682G						.						91	91	91					5																	140182464		2203	4298	6501	SO:0001583	missense	56145	exon1			ACGACAACGCGCC	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1682A>G	chr5.hg19:g.140182464A>G	ENSP00000429808:p.Asn561Ser	41.0	0.0		133.0	14.0	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	hg19	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	a	16.41	3.114673	0.56505	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.52754	0.65;0.65	4.5	4.5	0.54988	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.45126	U	0.000383	T	0.74129	0.3676	M	0.91459	3.21	0.34191	D	0.672095	D;D	0.89917	0.999;1.0	D;D	0.85130	0.997;0.983	D	0.86083	0.1545	10	0.87932	D	0	.	14.1425	0.65329	1.0:0.0:0.0:0.0	.	561;561	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	S	561	ENSP00000429808:N561S;ENSP00000434086:N561S	ENSP00000429808:N561S	N	+	2	0	PCDHA3	140162648	1.000000	0.71417	1.000000	0.80357	0.367000	0.29736	6.679000	0.74513	1.814000	0.52955	0.254000	0.18369	AAC	.	.		0.682	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		G	140182464	A	G	140182464	3	3	138	1	0	0	0	0	1	0	0	0	11534	43	2	2	1684	2	PCDHA3	5	140182464	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10	104477785	140182464	40732796	28	21772										
FYN	2534	hgsc.bcm.edu	37	chr6	112035597	112035597	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cctttgtgaaaactcaggtcAtcttctgtccgtgcttcata	7	11	5	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr6:112035597A>G	ENST00000354650.3	-	5	903	c.297T>C	c.(295-297)gaT>gaC	p.D99D	FYN_ENST00000538466.1_Silent_p.D99D|FYN_ENST00000229471.4_Silent_p.D99D|FYN_ENST00000368667.2_Silent_p.D99D|FYN_ENST00000368678.4_Silent_p.D99D|FYN_ENST00000229470.5_Splice_Site|FYN_ENST00000356013.2_Silent_p.D99D|FYN_ENST00000368682.3_Silent_p.D99D	NM_002037.5	NP_002028.1	P06241	FYN_HUMAN	FYN proto-oncogene, Src family tyrosine kinase	99	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				activated T cell proliferation (GO:0050798)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular response to peptide hormone stimulus (GO:0071375)|dendrite morphogenesis (GO:0048813)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|feeding behavior (GO:0007631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|leukocyte migration (GO:0050900)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein localization to nucleus (GO:1900182)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|glycoprotein binding (GO:0001948)|growth factor receptor binding (GO:0070851)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(17)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	30		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	AACTCAGGTCATCTTCTGTCC	0.423																																					p.D99D		Atlas-SNP	.											.	FYN	108	.	0			c.T297C						.						95	91	93					6																	112035597		2203	4300	6503	SO:0001819	synonymous_variant	2534	exon2			CAGGTCATCTTCT	AK056699	CCDS5094.1, CCDS5095.1, CCDS5096.1	6q21	2014-06-25	2014-06-25		ENSG00000010810	ENSG00000010810		"SH2 domain containing"	4037	protein-coding gene	gene with protein product		137025	"FYN oncogene related to SRC, FGR, YES"			3526330	Standard	NM_002037		Approved	SYN, SLK, MGC45350	uc003pvh.3	P06241	OTTHUMG00000016305	ENST00000354650.3:c.297T>C	chr6.hg19:g.112035597A>G		60.0	0.0		40.0	5.0	NM_153047	B5BU57|E1P557|H0UI48|Q16248|Q5R3A6|Q5R3A7|Q8N5D7	Silent	SNP	ENST00000354650.3	hg19	CCDS5094.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.517835	0.64634	.	.	ENSG00000010810	ENST00000229470	.	.	.	5.77	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.477	0.55821	0.8744:0.0:0.0:0.1256	.	.	.	.	.	-1	.	.	.	-	.	.	FYN	112142290	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.351000	0.66022	1.089000	0.41292	0.533000	0.62120	.	.	.		0.423	FYN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043655.1			G	112035597	A	G	112035597	2	3	138	1	0	0	0	0	0	0	0	1	6134	214	8	2		2	FYN	6	112035597	Silent	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10		112035597	59079470	29	21773										
TUBE1	51175	hgsc.bcm.edu	37	chr6	112408473	112408484	+	In_Frame_Del	DEL	CAGAAGCAGCAG	CAGAAGCAGCAG	-													0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gctcccttagtgccaggtccCagaagcagcagccgatctgg					rs146077743		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	CAGAAGCAGCAG	CAGAAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr6:112408473_112408484delCAGAAGCAGCAG	ENST00000368662.5	-	2	129_140	c.51_62delCTGCTGCTTCTG	c.(49-63)ggctgctgcttctgg>ggg	p.CCFW18del	FAM229B_ENST00000368656.2_5'Flank|FAM229B_ENST00000604268.1_5'Flank|TUBE1_ENST00000604814.1_5'Flank	NM_016262.4	NP_057346.1	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1	18					centrosome cycle (GO:0007098)|protein polymerization (GO:0051258)	microtubule (GO:0005874)|pericentriolar material (GO:0000242)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	12		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)	Vinblastine(DB00570)	TGCCAGGTCCCAGAAGCAGCAGCCGATCTGGT	0.642											OREG0017625	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.18_21del		Atlas-Indel,Pindel	.											.	TUBE1	49	.	0			c.52_63del						.																																			SO:0001651	inframe_deletion	51175	exon2			.	AF201334	CCDS5100.1	6q21	2005-11-03			ENSG00000074935	ENSG00000074935		"Tubulins"	20775	protein-coding gene	gene with protein product		607345				10620804	Standard	NM_016262		Approved	dJ142L7.2, FLJ22589, TUBE	uc003pvq.3	Q9UJT0	OTTHUMG00000015382	ENST00000368662.5:c.51_62delCTGCTGCTTCTG	chr6.hg19:g.112408473_112408484delCAGAAGCAGCAG	ENSP00000357651:p.Cys18_Trp21del	305.0	0.0	1442	258.0	22.0	NM_016262	Q5H8W8|Q8NEG3	In_Frame_Del	DEL	ENST00000368662.5	hg19	CCDS5100.1																																																																																			.	.		0.642	TUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041867.1	NM_016262		-	112408484	CAGAAGCAGCAG	-	112408473	7	5	138	1	0	1	0	1	0	0	0	0	16778	595	21	0	1409	0	TUBE1	6	112408473	In_Frame_Del	DEL	CAGAAGCAGCAG	TCGA-DD-A4NQ-01A-21D-A28X-10	372876	112408473	58706594	30	21774			1	23		2	2	17	N	T_CAGAAGCAGCAG	4.031352e-05
TUBE1	51175	hgsc.bcm.edu	37	chr6	112408489	112408489	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gtcccagaagcagcagccgaTctggtttccgcactggccga	12	14	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr6:112408489T>A	ENST00000368662.5	-	2	124	c.46A>T	c.(46-48)Atc>Ttc	p.I16F	FAM229B_ENST00000368656.2_5'Flank|FAM229B_ENST00000604268.1_5'Flank|TUBE1_ENST00000604814.1_5'Flank	NM_016262.4	NP_057346.1	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1	16					centrosome cycle (GO:0007098)|protein polymerization (GO:0051258)	microtubule (GO:0005874)|pericentriolar material (GO:0000242)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	12		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)	Vinblastine(DB00570)	CAGCAGCCGATCTGGTTTCCG	0.642											OREG0017625	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I16F		Atlas-SNP	.											.	TUBE1	49	.	0			c.A46T						.						14	13	14					6																	112408489		2119	4132	6251	SO:0001583	missense	51175	exon2			AGCCGATCTGGTT	AF201334	CCDS5100.1	6q21	2005-11-03			ENSG00000074935	ENSG00000074935		"Tubulins"	20775	protein-coding gene	gene with protein product		607345				10620804	Standard	NM_016262		Approved	dJ142L7.2, FLJ22589, TUBE	uc003pvq.3	Q9UJT0	OTTHUMG00000015382	ENST00000368662.5:c.46A>T	chr6.hg19:g.112408489T>A	ENSP00000357651:p.Ile16Phe	336.0	0.0	1442	280.0	31.0	NM_016262	Q5H8W8|Q8NEG3	Missense_Mutation	SNP	ENST00000368662.5	hg19	CCDS5100.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.556665	0.86231	.	.	ENSG00000074935	ENST00000368662;ENST00000368657	T	0.73469	-0.75	5.48	5.48	0.80851	Tubulin/FtsZ, GTPase domain (3);	0.218932	0.47852	D	0.000215	D	0.88533	0.6462	H	0.97564	4.03	0.58432	D	0.999998	D	0.59767	0.986	D	0.70227	0.968	D	0.91661	0.5342	10	0.87932	D	0	.	11.0503	0.47882	0.0:0.0748:0.0:0.9252	.	16	Q9UJT0	TBE_HUMAN	F	16	ENSP00000357651:I16F	ENSP00000357646:I16F	I	-	1	0	TUBE1	112515182	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.829000	0.39121	2.219000	0.72066	0.472000	0.43445	ATC	.	.		0.642	TUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041867.1	NM_016262		A	112408489	T	A	112408489	3	1	138	1	0	0	0	0	1	0	0	0	16778	1435	50	4	1425	4	TUBE1	6	112408489	Missense_Mutation	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	16	112408489	58706578	31	21775			1	23		2	2	17	N	T_CAGAAGCAGCAG	4.031352e-05
LAMA4	3910	hgsc.bcm.edu	37	chr6	112435307	112435307	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cctccaacaaacacaggctcCctgtgatcaattggttttgg	8	12	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr6:112435307C>G	ENST00000230538.7	-	38	5695	c.5298G>C	c.(5296-5298)agG>agC	p.R1766S	LAMA4_ENST00000522006.1_Missense_Mutation_p.R1759S|LAMA4_ENST00000389463.4_Missense_Mutation_p.R1759S|LAMA4_ENST00000424408.2_Missense_Mutation_p.R1759S	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1766	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		ACACAGGCTCCCTGTGATCAA	0.398																																					p.R1766S		Atlas-SNP	.											.	LAMA4	227	.	0			c.G5298C						.						109	104	106					6																	112435307		2203	4300	6503	SO:0001583	missense	3910	exon38			AGGCTCCCTGTGA		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.5298G>C	chr6.hg19:g.112435307C>G	ENSP00000230538:p.Arg1766Ser	55.0	0.0		54.0	8.0	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	hg19	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465153	0.43839	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	5.6	3.76	0.43208	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.135590	0.64402	N	0.000003	T	0.46718	0.1407	N	0.25647	0.755	0.80722	D	1	B;B	0.24426	0.103;0.084	B;B	0.25614	0.062;0.037	T	0.47381	-0.9122	10	0.29301	T	0.29	.	7.4671	0.27328	0.0:0.7175:0.1416:0.1409	.	1766;1759	Q16363;Q16363-2	LAMA4_HUMAN;.	S	1766;1759;1759;1759	ENSP00000230538:R1766S;ENSP00000429488:R1759S;ENSP00000374114:R1759S;ENSP00000416470:R1759S	ENSP00000230538:R1766S	R	-	3	2	LAMA4	112542000	0.980000	0.34600	1.000000	0.80357	0.996000	0.88848	0.152000	0.16302	1.468000	0.48064	0.655000	0.94253	AGG	.	.		0.398	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		G	112435307	C	G	112435307	3	3	138	1	0	0	0	0	1	0	0	0	8617	622	22	4	181	4	LAMA4	6	112435307	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	26818	112435307	58679760	32	21776										
AMZ1	155185	hgsc.bcm.edu	37	chr7	2740124	2740124	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gcacaggagttcagcttcggGccccgggccttgaaggacgc	15	13	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr7:2740124G>A	ENST00000312371.4	+	2	407	c.39G>A	c.(37-39)ggG>ggA	p.G13G	AMZ1_ENST00000407112.1_Silent_p.G13G	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	13							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		TCAGCTTCGGGCCCCGGGCCT	0.692																																					p.G13G		Atlas-SNP	.											.	AMZ1	41	.	0			c.G39A						.						61	67	65					7																	2740124		2203	4300	6503	SO:0001819	synonymous_variant	155185	exon2			CTTCGGGCCCCGG	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"archaemetzincin-1"	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.39G>A	chr7.hg19:g.2740124G>A		55.0	0.0		62.0	13.0	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	hg19	CCDS34589.1																																																																																			.	.		0.692	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463		A	2740124	G	A	2740124	2	1	138	1	0	0	0	0	0	0	0	1	596	1190	42	3		3	AMZ1	7	2740124	Silent	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10		2740124	156398539	33	21777										
SDK1	221935	hgsc.bcm.edu	37	chr7	4285345	4285345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gccccggcggcctgcactacTcagacgaggacatctgcaac	11	16	2	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr7:4285345T>C	ENST00000404826.2	+	44	6428	c.6289T>C	c.(6289-6291)Tca>Cca	p.S2097P	SDK1_ENST00000389531.3_Missense_Mutation_p.S2077P|SDK1_ENST00000466611.1_3'UTR	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	2097					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CCTGCACTACTCAGACGAGGA	0.607																																					p.S2097P		Atlas-SNP	.											.	SDK1	361	.	0			c.T6289C						.						71	63	66					7																	4285345		2203	4300	6503	SO:0001583	missense	221935	exon44			CACTACTCAGACG	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.6289T>C	chr7.hg19:g.4285345T>C	ENSP00000385899:p.Ser2097Pro	157.0	0.0		140.0	17.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.905832	0.92107	.	.	ENSG00000146555	ENST00000404826;ENST00000446104;ENST00000389531	T;T	0.73681	-0.76;-0.77	5.3	5.3	0.74995	.	0.000000	0.64402	D	0.000004	D	0.86581	0.5967	M	0.83012	2.62	0.53688	D	0.999977	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.994;0.998;0.99;0.997	D	0.88628	0.3167	10	0.87932	D	0	.	13.8091	0.63252	0.0:0.0:0.0:1.0	.	2077;157;584;2097	F8W6X9;Q7Z5N4-2;F2Z3E9;Q7Z5N4	.;.;.;SDK1_HUMAN	P	2097;345;2077	ENSP00000385899:S2097P;ENSP00000374182:S2077P	ENSP00000374182:S2077P	S	+	1	0	SDK1	4251871	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.480000	0.81109	1.992000	0.58205	0.533000	0.62120	TCA	.	.		0.607	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		C	4285345	T	C	4285345	3	2	138	1	0	0	0	0	1	0	0	0	13983	1551	54	2	6463	2	SDK1	7	4285345	Missense_Mutation	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	1545221	4285345	154853318	34	21778										
HOXA3	3200	hgsc.bcm.edu	37	chr7	27148273	27148273	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ccaccagctgcgcgctcgtgTaggccgtgcgcgcgcgcttg	15	16	0	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr7:27148273T>C	ENST00000396352.4	-	3	792	c.593A>G	c.(592-594)tAc>tGc	p.Y198C	HOXA3_ENST00000317201.2_Missense_Mutation_p.Y198C|HOXA-AS2_ENST00000518088.1_RNA|HOXA3_ENST00000521401.1_5'Flank	NM_030661.4	NP_109377.1	O43365	HXA3_HUMAN	homeobox A3	198					angiogenesis (GO:0001525)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(18)|skin(1)	29						CGCGCTCGTGTAGGCCGTGCG	0.667																																					p.Y198C	Esophageal Squamous(136;1368 1743 5685 7935 50360)	Atlas-SNP	.											.	HOXA3	62	.	0			c.A593G						.						49	50	50					7																	27148273		2203	4300	6503	SO:0001583	missense	3200	exon3			CTCGTGTAGGCCG		CCDS5404.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105997	ENSG00000105997		"Homeoboxes / ANTP class : HOXL subclass"	5104	protein-coding gene	gene with protein product		142954	"homeo box A3"	HOX1E, HOX1		1973146, 1358459	Standard	XM_005249730		Approved		uc011jzl.2	O43365	OTTHUMG00000023209	ENST00000396352.4:c.593A>G	chr7.hg19:g.27148273T>C	ENSP00000379640:p.Tyr198Cys	39.0	0.0		55.0	8.0	NM_030661	A4D181	Missense_Mutation	SNP	ENST00000396352.4	hg19	CCDS5404.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.987286	0.53934	.	.	ENSG00000105997	ENST00000396352;ENST00000317201;ENST00000396350	D;D	0.96365	-3.99;-3.99	5.03	5.03	0.67393	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.113080	0.64402	D	0.000007	D	0.98466	0.9489	M	0.92077	3.27	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99694	1.1002	10	0.87932	D	0	.	14.9447	0.71020	0.0:0.0:0.0:1.0	.	198	O43365	HXA3_HUMAN	C	198;198;40	ENSP00000379640:Y198C;ENSP00000324884:Y198C	ENSP00000324884:Y198C	Y	-	2	0	HOXA3	27114798	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.011000	0.70760	2.118000	0.64928	0.533000	0.62120	TAC	.	.		0.667	HOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358708.2			C	27148273	T	C	27148273	3	2	138	1	0	0	0	0	1	0	0	0	7302	1638	57	2	742	2	HOXA3	7	27148273	Missense_Mutation	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	22862928	27148273	131990390	35	21779										
CCDC129	223075	hgsc.bcm.edu	37	chr7	31683502	31683502	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	tgtgttcactaactggtcacCaggaagcccagttcatgacg	10	11	3	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr7:31683502C>A	ENST00000407970.3	+	11	2556	c.2518C>A	c.(2518-2520)Cag>Aag	p.Q840K	CCDC129_ENST00000451887.2_Missense_Mutation_p.Q866K|CCDC129_ENST00000319386.3_Missense_Mutation_p.Q692K|CCDC129_ENST00000409210.1_Missense_Mutation_p.Q748K	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	840										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AACTGGTCACCAGGAAGCCCA	0.547																																					p.Q866K		Atlas-SNP	.											.	CCDC129	127	.	0			c.C2596A						.						79	74	76					7																	31683502		2203	4300	6503	SO:0001583	missense	223075	exon11			GGTCACCAGGAAG	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.2518C>A	chr7.hg19:g.31683502C>A	ENSP00000384416:p.Gln840Lys	57.0	0.0		75.0	11.0	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	hg19	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	C	0.046	-1.265142	0.01433	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.56	1.72	0.24424	.	1.779550	0.03023	N	0.151011	T	0.18800	0.0451	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.12013	0.005;0.002;0.002;0.002	B;B;B;B	0.13407	0.006;0.003;0.003;0.009	T	0.16630	-1.0396	10	0.07030	T	0.85	2.9476	4.5407	0.12056	0.1534:0.6:0.0:0.2466	.	866;850;840;692	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	K	692;840;866;850;748	ENSP00000313062:Q692K;ENSP00000384416:Q840K;ENSP00000395835:Q866K;ENSP00000387214:Q748K	ENSP00000313062:Q692K	Q	+	1	0	CCDC129	31650027	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	1.013000	0.29937	0.102000	0.17638	-0.742000	0.03525	CAG	.	.		0.547	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		A	31683502	C	A	31683502	3	1	138	1	0	0	0	0	1	0	0	0	2766	595	21	3	2556	3	CCDC129	7	31683502	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	4535229	31683502	127455161	36	21780										
GIGYF1	64599	hgsc.bcm.edu	37	chr7	100284048	100284048	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ccgccagccagcagagcgggGaccaccatctgcacaggaaa	12	15	1	1	rs542492951		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr7:100284048G>T	ENST00000275732.5	-	8	1912	c.703C>A	c.(703-705)Ccc>Acc	p.P235T	GIGYF1_ENST00000471340.2_Intron	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	235					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					GCAGAGCGGGGACCACCATCT	0.632																																					p.P235T		Atlas-SNP	.											.	GIGYF1	113	.	0			c.C703A						.						40	39	39					7																	100284048		2181	4252	6433	SO:0001583	missense	64599	exon8			AGCGGGGACCACC	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"GYF domain containing 1"	612064	"PERQ amino acid rich, with GYF domain 1"	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.703C>A	chr7.hg19:g.100284048G>T	ENSP00000275732:p.Pro235Thr	50.0	0.0		60.0	5.0	NM_022574	Q6Y7W7|Q8WZ38	Missense_Mutation	SNP	ENST00000275732.5	hg19	CCDS34708.1	.	.	.	.	.	.	.	.	.	.	.	21.2	4.108888	0.77096	.	.	ENSG00000146830	ENST00000275732	D	0.84730	-1.89	5.15	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.82130	0.4970	L	0.54323	1.7	0.80722	D	1	P	0.48589	0.912	P	0.45310	0.476	T	0.78558	-0.2158	10	0.20519	T	0.43	-18.0463	11.3205	0.49419	0.0876:0.0:0.9124:0.0	.	235	O75420	PERQ1_HUMAN	T	235	ENSP00000275732:P235T	ENSP00000275732:P235T	P	-	1	0	GIGYF1	100121984	1.000000	0.71417	1.000000	0.80357	0.758000	0.43043	9.604000	0.98317	1.401000	0.46761	0.563000	0.77884	CCC	.	.		0.632	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		T	100284048	G	T	100284048	3	4	138	1	0	0	0	0	1	0	0	0	6385	1174	41	3	2472	3	GIGYF1	7	100284048	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	68600546	100284048	58854615	37	21781										
EPHA1	2041	hgsc.bcm.edu	37	chr7	143096483	143096483	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	atggggtgtgtccatgtccaTccggtaggagccgctagggc	16	10	0	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr7:143096483T>A	ENST00000275815.3	-	5	945	c.859A>T	c.(859-861)Atg>Ttg	p.M287L		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	287	Cys-rich.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				TCCATGTCCATCCGGTAGGAG	0.592																																					p.M287L		Atlas-SNP	.											.	EPHA1	193	.	0			c.A859T						.						42	36	38					7																	143096483		2203	4300	6503	SO:0001583	missense	2041	exon5			TGTCCATCCGGTA	M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.859A>T	chr7.hg19:g.143096483T>A	ENSP00000275815:p.Met287Leu	144.0	0.0		144.0	44.0	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	hg19	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	T	8.001	0.755414	0.15846	.	.	ENSG00000146904	ENST00000275815	D	0.97186	-4.28	5.22	-0.761	0.11038	Growth factor, receptor (1);	1.983880	0.02089	N	0.052968	D	0.91290	0.7254	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	D	0.84449	0.0587	10	0.87932	D	0	.	4.208	0.10498	0.1061:0.5117:0.1488:0.2334	.	287	P21709	EPHA1_HUMAN	L	287	ENSP00000275815:M287L	ENSP00000275815:M287L	M	-	1	0	EPHA1	142806605	0.000000	0.05858	0.005000	0.12908	0.045000	0.14185	0.073000	0.14640	-0.024000	0.13941	0.533000	0.62120	ATG	.	.		0.592	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			A	143096483	T	A	143096483	3	1	138	1	0	0	0	0	1	0	0	0	5167	1435	50	4	2127	4	EPHA1	7	143096483	Missense_Mutation	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	42812435	143096483	16042180	38	21782										
OR2A2	442361	hgsc.bcm.edu	37	chr7	143807041	143807041	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gtgatgtcctatgataggtaTgtggccatctgccacccttt	10	10	1	2	rs201869620		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr7:143807041T>A	ENST00000408979.2	+	1	435	c.366T>A	c.(364-366)taT>taA	p.Y122*		NM_001005480.2	NP_001005480.2	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A, member 2	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)|skin(4)	22	Melanoma(164;0.0783)					ATGATAGGTATGTGGCCATCT	0.483																																					p.Y122X		Atlas-SNP	.											.	OR2A2	48	.	0			c.T366A						.						184	171	175					7																	143807041		2109	4264	6373	SO:0001587	stop_gained	442361	exon1			TAGGTATGTGGCC		CCDS43671.1	7q35	2013-09-20		2004-03-10	ENSG00000221989	ENSG00000221989		"GPCR / Class A : Olfactory receptors"	8230	protein-coding gene	gene with protein product				OR2A2P, OR2A17P			Standard	NM_001005480		Approved	OST008	uc011ktz.2	Q6IF42	OTTHUMG00000158001	ENST00000408979.2:c.366T>A	chr7.hg19:g.143807041T>A	ENSP00000386209:p.Tyr122*	143.0	0.0		159.0	21.0	NM_001005480	B2RN85|Q8NGT6	Nonsense_Mutation	SNP	ENST00000408979.2	hg19	CCDS43671.1	.	.	.	.	.	.	.	.	.	.	T	14.62	2.588865	0.46110	.	.	ENSG00000221989	ENST00000408979	.	.	.	3.61	-5.37	0.02681	.	0.597987	0.12654	U	0.450208	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.5284	11.4922	0.50387	0.0:0.5836:0.0:0.4164	.	.	.	.	X	122	.	ENSP00000386209:Y122X	Y	+	3	2	OR2A2	143437974	0.001000	0.12720	0.083000	0.20561	0.466000	0.32739	-1.711000	0.01886	-1.305000	0.02327	-0.315000	0.08773	TAT	.	T|0.999;C|0.001		0.483	OR2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349978.1			A	143807041	T	A	143807041	4	1	138	1	0	0	0	0	0	1	0	0	10986	1471	51	4	368	4	OR2A2	7	143807041	Nonsense_Mutation	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	710558	143807041	15331622	39	21783										
BLK	640	hgsc.bcm.edu	37	chr8	11420535	11420535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ccccggaagccatccacttcGgggtcttcaccatcaaagca	8	16	3	0	rs376140772		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr8:11420535G>A	ENST00000259089.4	+	12	1820	c.1228G>A	c.(1228-1230)Ggg>Agg	p.G410R	BLK_ENST00000529894.1_Missense_Mutation_p.G339R	NM_001715.2	NP_001706.2	P51451	BLK_HUMAN	BLK proto-oncogene, Src family tyrosine kinase	410	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell receptor signaling pathway (GO:0050853)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of insulin secretion (GO:0032024)	plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(4)|stomach(1)	27			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		CATCCACTTCGGGGTCTTCAC	0.607																																					p.G410R		Atlas-SNP	.											.	BLK	78	.	0			c.G1228A						.	G	ARG/GLY	0,4406		0,0,2203	98	77	84		1228	4.2	0.9	8		84	1,8599	1.2+/-3.3	0,1,4299	no	missense	BLK	NM_001715.2	125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	410/506	11420535	1,13005	2203	4300	6503	SO:0001583	missense	640	exon12			CACTTCGGGGTCT	BC004473	CCDS5982.1	8p23-p22	2014-06-25	2014-06-25		ENSG00000136573	ENSG00000136573		"SH2 domain containing"	1057	protein-coding gene	gene with protein product		191305	"B lymphoid tyrosine kinase"			7845672	Standard	NM_001715		Approved	MGC10442	uc003wty.3	P51451	OTTHUMG00000090729	ENST00000259089.4:c.1228G>A	chr8.hg19:g.11420535G>A	ENSP00000259089:p.Gly410Arg	152.0	0.0		172.0	32.0	NM_001715	Q16291|Q96IN1	Missense_Mutation	SNP	ENST00000259089.4	hg19	CCDS5982.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.441544	0.83993	0.0	1.16E-4	ENSG00000136573	ENST00000259089;ENST00000427279;ENST00000529894;ENST00000526097	D;D	0.82526	-1.62;-1.62	4.22	4.22	0.49857	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43919	D	0.000508	D	0.84275	0.5436	N	0.16708	0.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87386	0.2360	10	0.87932	D	0	.	16.1153	0.81302	0.0:0.0:1.0:0.0	.	246;410	E9PM44;P51451	.;BLK_HUMAN	R	410;410;339;246	ENSP00000259089:G410R;ENSP00000433663:G339R	ENSP00000259089:G410R	G	+	1	0	BLK	11457944	1.000000	0.71417	0.914000	0.36105	0.654000	0.38779	9.312000	0.96287	2.325000	0.78763	0.455000	0.32223	GGG	.	.		0.607	BLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207460.1			A	11420535	G	A	11420535	3	1	138	1	0	0	0	0	1	0	0	0	1444	1116	39	1	1270	1	BLK	8	11420535	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10		11420535	134943487	40	21784										
SLC39A14	23516	hgsc.bcm.edu	37	chr8	22273745	22273745	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ctgtgtcagttttccaaggcAtcagcacctcggtggccatc	10	13	2	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr8:22273745A>G	ENST00000381237.1	+	7	1218	c.1099A>G	c.(1099-1101)Atc>Gtc	p.I367V	SLC39A14_ENST00000240095.6_Missense_Mutation_p.I367V|SLC39A14_ENST00000359741.5_Missense_Mutation_p.I367V|SLC39A14_ENST00000289952.5_Missense_Mutation_p.I367V	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	367					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		TTTCCAAGGCATCAGCACCTC	0.587																																					p.I367V		Atlas-SNP	.											.	SLC39A14	59	.	0			c.A1099G						.						112	100	104					8																	22273745		2203	4300	6503	SO:0001583	missense	23516	exon7			CAAGGCATCAGCA	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"Solute carriers"	20858	protein-coding gene	gene with protein product		608736	"solute carrier family 39 (metal ion transporter), member 14"			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.1099A>G	chr8.hg19:g.22273745A>G	ENSP00000370635:p.Ile367Val	140.0	0.0		147.0	23.0	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Missense_Mutation	SNP	ENST00000381237.1	hg19	CCDS47823.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.624006	0.46840	.	.	ENSG00000104635	ENST00000359741;ENST00000240095;ENST00000381237;ENST00000289952;ENST00000517370	T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56	5.99	5.99	0.97316	.	0.151633	0.64402	D	0.000012	T	0.38878	0.1057	L	0.28192	0.835	0.44295	D	0.997163	B;B;B	0.31893	0.081;0.198;0.345	B;B;B	0.33392	0.051;0.074;0.163	T	0.29427	-1.0012	10	0.29301	T	0.29	-41.9697	9.8955	0.41316	0.9236:0.0:0.0764:0.0	.	367;367;367	Q15043-2;Q15043;B6EU88	.;S39AE_HUMAN;.	V	367;367;367;367;190	ENSP00000352779:I367V;ENSP00000240095:I367V;ENSP00000370635:I367V;ENSP00000289952:I367V;ENSP00000427981:I190V	ENSP00000240095:I367V	I	+	1	0	SLC39A14	22329690	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.627000	0.54252	2.291000	0.77112	0.533000	0.62120	ATC	.	.		0.587	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677		G	22273745	A	G	22273745	3	3	138	1	0	0	0	0	1	0	0	0	14632	217	8	2	1295	2	SLC39A14	8	22273745	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10	10853210	22273745	124090277	41	21785										
FNTA	2339	hgsc.bcm.edu	37	chr8	42911627	42911627	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gcggccgaggctggggaagcCgtggcgtcccccatggacga	18	13	0	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr8:42911627C>T	ENST00000302279.3	+	1	332	c.138C>T	c.(136-138)gcC>gcT	p.A46A	FNTA_ENST00000529687.1_5'Flank|FNTA_ENST00000524546.1_3'UTR|RP11-598P20.5_ENST00000534420.1_Intron|FNTA_ENST00000342116.4_Silent_p.A46A	NM_002027.2	NP_002018.1	P49354	FNTA_HUMAN	farnesyltransferase, CAAX box, alpha	46					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|phototransduction, visible light (GO:0007603)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of tubulin deacetylation (GO:0090044)|protein farnesylation (GO:0018343)|protein geranylgeranylation (GO:0018344)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transforming growth factor beta receptor signaling pathway (GO:0007179)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|protein farnesyltransferase complex (GO:0005965)	alpha-tubulin binding (GO:0043014)|CAAX-protein geranylgeranyltransferase activity (GO:0004662)|microtubule binding (GO:0008017)|protein farnesyltransferase activity (GO:0004660)|protein geranylgeranyltransferase activity (GO:0004661)			cervix(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	16	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			CTGGGGAAGCCGTGGCGTCCC	0.741																																					p.A46A		Atlas-SNP	.											.	FNTA	34	.	0			c.C138T						.						12	12	12					8																	42911627		2173	4256	6429	SO:0001819	synonymous_variant	2339	exon1			GGAAGCCGTGGCG	L10413	CCDS6140.1	8p11.21	2011-06-27			ENSG00000168522	ENSG00000168522		"Prenyltransferase alpha subunit repeat containing"	3782	protein-coding gene	gene with protein product	"protein prenyltransferase alpha subunit repeat containing 2"	134635				8276393	Standard	NR_033698		Approved	FPTA, PGGT1A, PTAR2	uc003xps.3	P49354	OTTHUMG00000165279	ENST00000302279.3:c.138C>T	chr8.hg19:g.42911627C>T		33.0	0.0		52.0	14.0	NM_002027	A6NJW0|Q53XJ9|Q9UDC1	Silent	SNP	ENST00000302279.3	hg19	CCDS6140.1																																																																																			.	.		0.741	FNTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383178.1	NM_002027		T	42911627	C	T	42911627	2	4	138	1	0	0	0	0	0	0	0	1	5985	639	23	1		1	FNTA	8	42911627	Silent	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	20637882	42911627	103452395	42	21786										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77767616	77767616	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	caccaccggagacgagggaaAcactgaaatggaaagcacca	11	11	0	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr8:77767616A>C	ENST00000521891.2	+	10	8907	c.8459A>C	c.(8458-8460)aAc>aCc	p.N2820T	ZFHX4_ENST00000050961.6_Missense_Mutation_p.N2775T|ZFHX4_ENST00000518282.1_Missense_Mutation_p.N2794T|ZFHX4_ENST00000455469.2_Missense_Mutation_p.N2775T	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2775					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GACGAGGGAAACACTGAAATG	0.483										HNSCC(33;0.089)																											p.N2820T		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A8459C						.						56	56	56					8																	77767616		1959	4154	6113	SO:0001583	missense	79776	exon10			AGGGAAACACTGA		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.8459A>C	chr8.hg19:g.77767616A>C	ENSP00000430497:p.Asn2820Thr	82.0	0.0		43.0	11.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	0.220	-1.029708	0.02045	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.61859	0.07;0.16;0.13;0.11	5.13	1.29	0.21616	.	0.801294	0.10398	U	0.679569	T	0.60547	0.2277	L	0.55990	1.75	0.09310	N	1	B;B;B	0.23591	0.053;0.088;0.063	B;B;B	0.38683	0.144;0.279;0.128	T	0.59337	-0.7473	10	0.46703	T	0.11	.	12.8967	0.58104	0.5955:0.4045:0.0:0.0	.	2775;2775;2820	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	T	2820;2804;2775;2775;2794	ENSP00000430497:N2820T;ENSP00000399605:N2775T;ENSP00000050961:N2775T;ENSP00000430848:N2794T	ENSP00000050961:N2775T	N	+	2	0	ZFHX4	77930171	1.000000	0.71417	0.000000	0.03702	0.015000	0.08874	5.986000	0.70563	0.067000	0.16545	-0.488000	0.04728	AAC	.	.		0.483	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77767616	A	C	77767616	3	2	138	1	0	0	0	0	1	0	0	0	17650	43	2	5	8493	5	ZFHX4	8	77767616	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10	34855989	77767616	68596406	43	21787										
CISD1	55847	hgsc.bcm.edu	37	chr10	60037077	60037077	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	actgccgttgttggaggtccAaaaaggtgaggaaagcaatt	13	6	0	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr10:60037077A>T	ENST00000333926.5	+	2	448	c.232A>T	c.(232-234)Aaa>Taa	p.K78*	CISD1_ENST00000488388.2_3'UTR	NM_018464.4	NP_060934.1	Q9NZ45	CISD1_HUMAN	CDGSH iron sulfur domain 1	78					regulation of cellular respiration (GO:0043457)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)			breast(1)	1						TTGGAGGTCCAAAAAGGTGAG	0.363																																					p.K78X		Atlas-SNP	.											.	CISD1	7	.	0			c.A232T						.						56	50	52					10																	60037077		2203	4300	6503	SO:0001587	stop_gained	55847	exon2			AGGTCCAAAAAGG	AY960578	CCDS7251.1	10q21.3	2011-01-05	2007-08-10	2007-08-10	ENSG00000122873	ENSG00000122873		"CDGSH iron sulfur domain containing"	30880	protein-coding gene	gene with protein product		611932	"chromosome 10 open reading frame 70", "zinc finger, CDGSH-type domain 1"	C10orf70, ZCD1		17376863, 17584744	Standard	NM_018464		Approved	MDS029, mitoNEET	uc001jkc.5	Q9NZ45	OTTHUMG00000018266	ENST00000333926.5:c.232A>T	chr10.hg19:g.60037077A>T	ENSP00000363041:p.Lys78*	217.0	0.0		181.0	28.0	NM_018464	Q1X902	Nonsense_Mutation	SNP	ENST00000333926.5	hg19	CCDS7251.1	.	.	.	.	.	.	.	.	.	.	A	38	7.116879	0.98074	.	.	ENSG00000122873	ENST00000333926	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.8936	14.3757	0.66874	1.0:0.0:0.0:0.0	.	.	.	.	X	78	.	ENSP00000363041:K78X	K	+	1	0	CISD1	59707083	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.958000	0.87877	2.279000	0.76181	0.533000	0.62120	AAA	.	.		0.363	CISD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048137.1	NM_018464		T	60037077	A	T	60037077	4	4	138	1	0	0	0	0	0	1	0	0	3437	131	5	4	238	4	CISD1	10	60037077	Nonsense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10		60037077	75497670	44	21788										
TNKS2	80351	hgsc.bcm.edu	37	chr10	93558647	93558647	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cccgctgcacttcgccgcagGtaaccggggccagcgtcccc	12	19	0	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr10:93558647G>T	ENST00000371627.4	+	1	578		c.e1+1		TNKS2-AS1_ENST00000432246.1_RNA|TNKS2-AS1_ENST00000432938.1_RNA	NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2						multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				TTCGCCGCAGGTAACCGGGGC	0.677																																					.		Atlas-SNP	.											.	TNKS2	103	.	0			c.199+1G>T						.						10	12	11					10																	93558647		2107	4161	6268	SO:0001630	splice_region_variant	80351	exon1			CCGCAGGTAACCG	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.199+1G>T	chr10.hg19:g.93558647G>T		67.0	0.0		75.0	12.0	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Splice_Site	SNP	ENST00000371627.4	hg19	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	G	33	5.223708	0.95139	.	.	ENSG00000107854	ENST00000371627	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7371	0.88396	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TNKS2	93548627	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.952000	0.93031	2.513000	0.84729	0.561000	0.74099	.	.	.		0.677	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235	Intron	T	93558647	G	T	93558647	5	4	138	1	0	0	0	0	0	0	1	0	16336	1275	44	3	202	3	TNKS2	10	93558647	Splice_Site	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	33521570	93558647	41976100	45	21789										
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643105	1643105	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ccccccttggagcccccacaGgagccacagctggagcagga	12	17	0	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr11:1643105G>C	ENST00000399682.1	-	1	263	c.219C>G	c.(217-219)tcC>tcG	p.S73S		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.S73S(1)		NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AGCCCCCACAGGAGCCACAGC	0.667																																					p.S73S		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	.	1	Substitution - coding silent(1)	lung(1)	c.C219G						.						7	15	12					11																	1643105		657	1539	2196	SO:0001819	synonymous_variant	387267	exon1			CCCACAGGAGCCA	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"Keratin associated proteins"	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.219C>G	chr11.hg19:g.1643105G>C		96.0	1.0		121.0	7.0	NM_001012709		Silent	SNP	ENST00000399682.1	hg19																																																																																				.	.		0.667	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		C	1643105	G	C	1643105	2	2	138	1	0	0	0	0	0	0	0	1	8572	987	35	4		4	KRTAP5-4	11	1643105	Silent	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10		1643105	133363411	46	21790										
OR51D1	390038	hgsc.bcm.edu	37	chr11	4661048	4661048	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	agccccagctcttggtccctAtcatagccacttcaaatgga	7	14	3	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr11:4661048A>G	ENST00000357605.2	+	1	104	c.28A>G	c.(28-30)Atc>Gtc	p.I10V		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	10						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTTGGTCCCTATCATAGCCAC	0.483																																					p.I10V		Atlas-SNP	.											.	OR51D1	49	.	0			c.A28G						.						145	139	141					11																	4661048		2201	4298	6499	SO:0001583	missense	390038	exon1			GTCCCTATCATAG	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"GPCR / Class A : Olfactory receptors"	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.28A>G	chr11.hg19:g.4661048A>G	ENSP00000350222:p.Ile10Val	79.0	0.0		50.0	8.0	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	hg19	CCDS31357.1	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.513722	0.00975	.	.	ENSG00000197428	ENST00000357605	T	0.00003	9.84	4.59	-2.29	0.06805	.	1.292380	0.05750	N	0.602973	T	0.00039	0.0001	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.01188	-1.1424	10	0.08837	T	0.75	.	4.4669	0.11694	0.3978:0.3084:0.2937:0.0	.	10	Q8NGF3	O51D1_HUMAN	V	10	ENSP00000350222:I10V	ENSP00000350222:I10V	I	+	1	0	OR51D1	4617624	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.645000	0.05409	-0.281000	0.09141	-1.229000	0.01577	ATC	.	.		0.483	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751		G	4661048	A	G	4661048	3	3	138	1	0	0	0	0	1	0	0	0	11102	449	16	2	30	2	OR51D1	11	4661048	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10	3017943	4661048	130345468	47	21791										
OR51T1	401665	hgsc.bcm.edu	37	chr11	4903313	4903313	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ggagactccacaaacccatgTattatttcctctccatgctg	6	13	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr11:4903313T>A	ENST00000322049.1	+	1	184	c.184T>A	c.(184-186)Tat>Aat	p.Y62N	MMP26_ENST00000380390.1_Intron|OR51T1_ENST00000380378.1_Missense_Mutation_p.Y89N|MMP26_ENST00000477339.1_Intron			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAAACCCATGTATTATTTCCT	0.478																																					p.Y89N		Atlas-SNP	.											.	OR51T1	92	.	0			c.T265A						.						192	174	180					11																	4903313		2201	4298	6499	SO:0001583	missense	401665	exon1			CCCATGTATTATT	BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"GPCR / Class A : Olfactory receptors"	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.184T>A	chr11.hg19:g.4903313T>A	ENSP00000322679:p.Tyr62Asn	97.0	0.0		79.0	16.0	NM_001004759	Q6IFH9	Missense_Mutation	SNP	ENST00000322049.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.61	3.170651	0.57584	.	.	ENSG00000176900	ENST00000380378;ENST00000322049	T;T	0.15603	2.41;2.41	4.4	4.4	0.53042	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36628	N	0.002493	T	0.59851	0.2224	H	0.99182	4.46	0.53688	D	0.999975	D	0.89917	1.0	D	0.97110	1.0	T	0.76618	-0.2893	10	0.87932	D	0	.	12.5837	0.56406	0.0:0.0:0.0:1.0	.	62	Q8NGJ9	O51T1_HUMAN	N	89;62	ENSP00000369738:Y89N;ENSP00000322679:Y62N	ENSP00000322679:Y62N	Y	+	1	0	OR51T1	4859889	1.000000	0.71417	1.000000	0.80357	0.422000	0.31414	6.059000	0.71133	1.838000	0.53458	0.397000	0.26171	TAT	.	.		0.478	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759		A	4903313	T	A	4903313	3	1	138	1	0	0	0	0	1	0	0	0	11115	1638	57	4	267	4	OR51T1	11	4903313	Missense_Mutation	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	242265	4903313	130103203	48	21792										
NAALADL1	10004	hgsc.bcm.edu	37	chr11	64820704	64820704	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cctcacccttcttcagcaggGtccccaggacacgggagagc	11	16	3	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr11:64820704G>A	ENST00000358658.3	-	8	1211	c.1184C>T	c.(1183-1185)aCc>aTc	p.T395I	NAALADL1_ENST00000355721.3_Missense_Mutation_p.T354I|NAALADL1_ENST00000340252.4_Missense_Mutation_p.T446I|NAALADL1_ENST00000355369.2_Missense_Mutation_p.T395I|NAALADL1_ENST00000356632.3_Missense_Mutation_p.T360I|NAALADL1_ENST00000339885.2_Missense_Mutation_p.T395I	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	395	NAALADase.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						CTTCAGCAGGGTCCCCAGGAC	0.677																																					p.T395I		Atlas-SNP	.											.	NAALADL1	58	.	0			c.C1184T						.						15	13	14					11																	64820704		2146	4210	6356	SO:0001583	missense	10004	exon8			AGCAGGGTCCCCA	AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"ileal peptidase I100"	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.1184C>T	chr11.hg19:g.64820704G>A	ENSP00000351484:p.Thr395Ile	191.0	0.0		206.0	31.0	NM_005468	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Missense_Mutation	SNP	ENST00000358658.3	hg19	CCDS31604.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.348152	0.61183	.	.	ENSG00000168060	ENST00000358658;ENST00000355369;ENST00000339885;ENST00000453486;ENST00000340252;ENST00000355721;ENST00000356632	T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04	4.38	4.38	0.52667	Peptidase M28 (1);	1.058390	0.07396	N	0.889930	T	0.54935	0.1889	M	0.69823	2.125	0.36556	D	0.872157	P	0.39311	0.667	P	0.45232	0.474	T	0.58160	-0.7685	10	0.59425	D	0.04	-41.2916	14.4677	0.67494	0.0:0.0:1.0:0.0	.	395	Q9UQQ1	NALDL_HUMAN	I	395;395;395;395;446;354;360	ENSP00000351484:T395I;ENSP00000347530:T395I;ENSP00000340111:T395I;ENSP00000344244:T446I;ENSP00000347955:T354I;ENSP00000349045:T360I	ENSP00000340111:T395I	T	-	2	0	NAALADL1	64577280	0.978000	0.34361	1.000000	0.80357	0.976000	0.68499	1.144000	0.31565	2.265000	0.75225	0.655000	0.94253	ACC	.	.		0.677	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468		A	64820704	G	A	64820704	3	1	138	1	0	0	0	0	1	0	0	0	10138	1261	44	3	1082	3	NAALADL1	11	64820704	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	59917391	64820704	70185812	49	21793										
GRAMD1B	57476	hgsc.bcm.edu	37	chr11	123489506	123489506	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cagggtctaaggctccaagaAaggtaatcctggcctcgtcc	11	12	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr11:123489506A>T	ENST00000529750.1	+	18	2334	c.2007A>T	c.(2005-2007)gaA>gaT	p.E669D	GRAMD1B_ENST00000450171.2_Missense_Mutation_p.E356D|GRAMD1B_ENST00000322282.7_Missense_Mutation_p.E669D|GRAMD1B_ENST00000456860.2_Missense_Mutation_p.E676D	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	669						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		GGCTCCAAGAAAGGTAATCCT	0.557																																					p.E669D		Atlas-SNP	.											.	GRAMD1B	122	.	0			c.A2007T						.						44	46	46					11																	123489506		2053	4196	6249	SO:0001583	missense	57476	exon18			CCAAGAAAGGTAA	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.2007A>T	chr11.hg19:g.123489506A>T	ENSP00000436500:p.Glu669Asp	102.0	0.0		98.0	16.0	NM_020716	Q6UW85|Q9ULL9	Missense_Mutation	SNP	ENST00000529750.1	hg19	CCDS53720.1	.	.	.	.	.	.	.	.	.	.	A	11.56	1.675970	0.29783	.	.	ENSG00000023171	ENST00000539133;ENST00000456860;ENST00000322282;ENST00000529750;ENST00000529432;ENST00000450171	T;T;T;T;T	0.48522	1.84;1.84;1.84;1.84;0.81	4.83	-0.351	0.12602	.	0.242826	0.40469	N	0.001083	T	0.26774	0.0655	N	0.21194	0.64	0.58432	D	0.999999	B;B;B;B	0.14805	0.002;0.011;0.0;0.001	B;B;B;B	0.16722	0.005;0.016;0.002;0.002	T	0.03221	-1.1059	10	0.32370	T	0.25	.	5.7251	0.18008	0.3925:0.3943:0.2132:0.0	.	625;356;669;676	B7Z4N9;Q3KR37-3;Q3KR37;E7EPH8	.;.;GRM1B_HUMAN;.	D	676;676;669;669;629;356	ENSP00000402457:E676D;ENSP00000325628:E669D;ENSP00000436500:E669D;ENSP00000432987:E629D;ENSP00000388458:E356D	ENSP00000325628:E669D	E	+	3	2	GRAMD1B	122994716	0.995000	0.38212	1.000000	0.80357	0.942000	0.58702	0.342000	0.19926	0.285000	0.22329	0.374000	0.22700	GAA	.	.		0.557	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		T	123489506	A	T	123489506	3	4	138	1	0	0	0	0	1	0	0	0	6757	11	1	4	2077	4	GRAMD1B	11	123489506	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10	58668802	123489506	11517010	50	21794										
SPATS2	65244	hgsc.bcm.edu	37	chr12	49919817	49919817	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	accaagggcggcatgacagtAtgggtcgttacagaaacagc	13	9	0	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr12:49919817A>G	ENST00000553127.1	+	15	1930	c.1417A>G	c.(1417-1419)Atg>Gtg	p.M473V	SPATS2_ENST00000552918.1_Missense_Mutation_p.M473V|SPATS2_ENST00000321898.6_Missense_Mutation_p.M473V			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	473						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						GCATGACAGTATGGGTCGTTA	0.512																																					p.M473V		Atlas-SNP	.											.	SPATS2	43	.	0			c.A1417G						.						149	120	130					12																	49919817		2203	4300	6503	SO:0001583	missense	65244	exon14			GACAGTATGGGTC	AK023179	CCDS31794.1	12q13.12	2009-06-12							18650	protein-coding gene	gene with protein product		611667				11944913, 17989879	Standard	NM_023071		Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000553127.1:c.1417A>G	chr12.hg19:g.49919817A>G	ENSP00000448228:p.Met473Val	309.0	0.0		231.0	49.0	NM_023071	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	Missense_Mutation	SNP	ENST00000553127.1	hg19	CCDS31794.1	.	.	.	.	.	.	.	.	.	.	A	5.619	0.298877	0.10622	.	.	ENSG00000123352	ENST00000553127;ENST00000321898;ENST00000552918;ENST00000395063	.	.	.	4.8	-0.7	0.11273	.	1.755980	0.02754	N	0.117782	T	0.17109	0.0411	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19192	-1.0313	9	0.12430	T	0.62	5.7897	8.9139	0.35570	0.5259:0.0:0.4741:0.0	.	473	Q86XZ4	SPAS2_HUMAN	V	473	.	ENSP00000326841:M473V	M	+	1	0	SPATS2	48206084	0.002000	0.14202	0.245000	0.24217	0.744000	0.42396	-0.164000	0.09983	-0.008000	0.14320	-0.483000	0.04790	ATG	.	.		0.512	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404023.1	NM_023071		G	49919817	A	G	49919817	3	3	138	1	0	0	0	0	1	0	0	0	15034	449	16	2	1463	2	SPATS2	12	49919817	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10		49919817	83932078	51	21795										
ACCN2	41	hgsc.bcm.edu	37	chr12	50473752	50473752	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	tgcaacctgacccgctatggCaaagagctgtccatggtcaa	10	12	1	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr12:50473752C>T	ENST00000447966.2	+	8	1348	c.1119C>T	c.(1117-1119)ggC>ggT	p.G373G	ASIC1_ENST00000228468.4_Silent_p.G373G|ASIC1_ENST00000552438.1_Silent_p.G407G	NM_001095.3	NP_001086.2	P78348	ASIC1_HUMAN	acid-sensing (proton-gated) ion channel 1	373					associative learning (GO:0008306)|calcium ion transmembrane transport (GO:0070588)|cellular response to pH (GO:0071467)|ion transmembrane transport (GO:0034220)|memory (GO:0007613)|negative regulation of neurotransmitter secretion (GO:0046929)|protein homotrimerization (GO:0070207)|regulation of membrane potential (GO:0042391)|response to acidic pH (GO:0010447)|response to pH (GO:0009268)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acid-sensing ion channel activity (GO:0044736)|ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)									Amiloride(DB00594)|Diclofenac(DB00586)	CCCGCTATGGCAAAGAGCTGT	0.532																																					p.G407G		Atlas-SNP	.											.	.	.	.	0			c.C1221T						.						167	141	149					12																	50473752		2203	4300	6503	SO:0001819	synonymous_variant	41	exon6			CTATGGCAAAGAG	U78181	CCDS8796.1, CCDS44876.1, CCDS58228.1	12q12	2012-02-23	2012-02-22	2012-02-22		ENSG00000110881		"Ion channels / Acid-sensing (proton-gated) ion channels"	100	protein-coding gene	gene with protein product		602866	"amiloride-sensitive cation channel 2, neuronal"	ACCN2		9037075	Standard	NM_001095		Approved	BNaC2, hBNaC2	uc001rvv.4	P78348	OTTHUMG00000169812	ENST00000447966.2:c.1119C>T	chr12.hg19:g.50473752C>T		325.0	0.0		324.0	53.0	NM_001256830	A3KN86|E5KBL7|P78349|Q96CV2	Silent	SNP	ENST00000447966.2	hg19	CCDS44876.1	.	.	.	.	.	.	.	.	.	.	C	9.786	1.176565	0.21704	.	.	ENSG00000110881	ENST00000453327	.	.	.	4.74	3.79	0.43588	.	.	.	.	.	T	0.69079	0.3071	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67352	-0.5692	4	.	.	.	-18.821	14.5079	0.67764	0.0:0.7524:0.2476:0.0	.	.	.	.	V	241	.	.	A	+	2	0	ACCN2	48760019	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.092000	0.30927	2.653000	0.90120	0.561000	0.74099	GCA	.	.		0.532	ASIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406004.2	NM_020039		T	50473752	C	T	50473752	2	4	138	1	0	0	0	0	0	0	0	1	129	697	25	3		3	ACCN2	12	50473752	Silent	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	553935	50473752	83378143	52	21796										
RAB3IP	117177	hgsc.bcm.edu	37	chr12	70206599	70206599	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gagtaagtcctgtaaacacaGaattaaattaggggactcaa	9	6	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr12:70206599G>A	ENST00000247833.7	+	9	1548	c.1172G>A	c.(1171-1173)aGa>aAa	p.R391K	RAB3IP_ENST00000325555.9_Missense_Mutation_p.R185K|AC025263.3_ENST00000550437.1_Missense_Mutation_p.R32K|RAB3IP_ENST00000553099.1_Missense_Mutation_p.R185K|RAB3IP_ENST00000483530.2_Intron|RAB3IP_ENST00000550847.1_Missense_Mutation_p.R98K|RAB3IP_ENST00000362025.5_Intron|RAB3IP_ENST00000551641.1_Missense_Mutation_p.R185K|RAB3IP_ENST00000550536.1_Missense_Mutation_p.R407K					RAB3A interacting protein											NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			TGTAAACACAGAATTAAATTA	0.333																																					p.R407K		Atlas-SNP	.											.	RAB3IP	48	.	0			c.G1220A						.						82	88	86					12																	70206599		2203	4300	6503	SO:0001583	missense	117177	exon9			AACACAGAATTAA		CCDS8993.1, CCDS8995.1, CCDS8996.1, CCDS41811.1, CCDS44942.1	12q15	2013-01-22	2013-01-22		ENSG00000127328	ENSG00000127328			16508	protein-coding gene	gene with protein product	"rabin3"	608686					Standard	NM_175623		Approved	RABIN3	uc001svm.3	Q96QF0	OTTHUMG00000169437	ENST00000247833.7:c.1172G>A	chr12.hg19:g.70206599G>A	ENSP00000247833:p.Arg391Lys	116.0	0.0		75.0	13.0	NM_175623		Missense_Mutation	SNP	ENST00000247833.7	hg19	CCDS8995.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	31|31	5.082839|5.082839	0.94050|0.94050	.|.	.|.	ENSG00000127328|ENSG00000127328	ENST00000526994|ENST00000247833;ENST00000325555;ENST00000550536;ENST00000551641;ENST00000553099;ENST00000550847	.|T;T;T;T;T;T	.|0.51071	.|0.72;0.72;0.72;0.72;0.72;0.72	6.01|6.01	5.1|5.1	0.69264|0.69264	.|.	.|0.042490	.|0.85682	.|D	.|0.000000	T|T	0.54447|0.54447	0.1859|0.1859	M|M	0.88310|0.88310	2.945|2.945	0.58432|0.58432	D|D	0.999999|0.999999	.|P	.|0.38195	.|0.622	.|B	.|0.30179	.|0.112	T|T	0.65994|0.65994	-0.6033|-0.6033	5|10	.|0.87932	.|D	.|0	.|.	17.1091|17.1091	0.86670|0.86670	0.0:0.1267:0.8733:0.0|0.0:0.1267:0.8733:0.0	.|.	.|407	.|Q96QF0	.|RAB3I_HUMAN	K|K	123|391;185;407;185;185;98	.|ENSP00000247833:R391K;ENSP00000323349:R185K;ENSP00000447300:R407K;ENSP00000448773:R185K;ENSP00000448027:R185K;ENSP00000448102:R98K	.|ENSP00000447336:R32K	E|R	+|+	1|2	0|0	RAB3IP|RAB3IP	68492866|68492866	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.476000|9.476000	0.97823|0.97823	1.515000|1.515000	0.48885|0.48885	0.650000|0.650000	0.86243|0.86243	GAA|AGA	.	.		0.333	RAB3IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280671.2	NM_022456		A	70206599	G	A	70206599	3	1	138	1	0	0	0	0	1	0	0	0	12953	942	33	3	1254	3	RAB3IP	12	70206599	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	19732847	70206599	63645296	53	21797										
GLT8D2	83468	hgsc.bcm.edu	37	chr12	104388181	104388181	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	tgcttccattctgtcatgttGgcaacaatcacaccaggatt	7	11	3	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr12:104388181G>C	ENST00000360814.4	-	9	1104	c.699C>G	c.(697-699)gcC>gcG	p.A233A	GLT8D2_ENST00000546436.1_Silent_p.A233A|GLT8D2_ENST00000548660.1_Silent_p.A233A	NM_031302.3	NP_112592.1	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	233						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						CTGTCATGTTGGCAACAATCA	0.473																																					p.A233A		Atlas-SNP	.											.	GLT8D2	40	.	0			c.C699G						.						138	116	123					12																	104388181		2203	4300	6503	SO:0001819	synonymous_variant	83468	exon9			CATGTTGGCAACA	BC022343	CCDS9096.1	12q23.3	2013-02-22			ENSG00000120820	ENSG00000120820		"Glycosyltransferase family 8 domain containing"	24890	protein-coding gene	gene with protein product							Standard	NM_031302		Approved	FLJ31494	uc001tkh.1	Q9H1C3	OTTHUMG00000170120	ENST00000360814.4:c.699C>G	chr12.hg19:g.104388181G>C		132.0	0.0		130.0	18.0	NM_031302	Q96KA2	Silent	SNP	ENST00000360814.4	hg19	CCDS9096.1																																																																																			.	.		0.473	GLT8D2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407371.1	NM_031302		C	104388181	G	C	104388181	2	2	138	1	0	0	0	0	0	0	0	1	6478	1335	47	4		4	GLT8D2	12	104388181	Silent	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	34181582	104388181	29463714	54	21798										
BTBD11	121551	hgsc.bcm.edu	37	chr12	108012091	108012091	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gccaaactgagggccctgagGgaggccatgtatcacagcgc	14	12	1	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr12:108012091G>T	ENST00000280758.5	+	10	2916	c.2388G>T	c.(2386-2388)agG>agT	p.R796S	RP11-128P10.1_ENST00000548473.1_RNA|BTBD11_ENST00000357167.4_Missense_Mutation_p.R333S|BTBD11_ENST00000420571.2_Intron|BTBD11_ENST00000490090.2_Missense_Mutation_p.R796S	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	796						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						GGGCCCTGAGGGAGGCCATGT	0.627																																					p.R796S		Atlas-SNP	.											.	BTBD11	122	.	0			c.G2388T						.						64	53	57					12																	108012091		2203	4300	6503	SO:0001583	missense	121551	exon10			CCTGAGGGAGGCC	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2388G>T	chr12.hg19:g.108012091G>T	ENSP00000280758:p.Arg796Ser	86.0	0.0		83.0	12.0	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	hg19	CCDS31893.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.683482	0.68157	.	.	ENSG00000151136	ENST00000280758;ENST00000490090;ENST00000357167	T;T;T	0.39056	1.2;1.24;1.1	5.07	3.21	0.36854	.	0.204155	0.51477	D	0.000088	T	0.39809	0.1092	L	0.51422	1.61	0.80722	D	1	B;P;P	0.49090	0.018;0.919;0.914	B;B;P	0.46026	0.016;0.324;0.501	T	0.34354	-0.9832	10	0.72032	D	0.01	.	8.6922	0.34273	0.2323:0.0:0.7677:0.0	.	333;796;796	E9PHS4;A6QL63;A6QL63-3	.;BTBDB_HUMAN;.	S	796;796;333	ENSP00000280758:R796S;ENSP00000447319:R796S;ENSP00000349690:R333S	ENSP00000280758:R796S	R	+	3	2	BTBD11	106536221	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.920000	0.40025	1.257000	0.44085	0.563000	0.77884	AGG	.	.		0.627	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		T	108012091	G	T	108012091	3	4	138	1	0	0	0	0	1	0	0	0	1541	1223	43	3	2531	3	BTBD11	12	108012091	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	3623910	108012091	25839804	55	21799										
DAAM1	23002	hgsc.bcm.edu	37	chr14	59821978	59821978	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gaaattatatgaataaaggtCaaagagggaatgcatatgga	11	2	1	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr14:59821978C>G	ENST00000395125.1	+	20	2505	c.2482C>G	c.(2482-2484)Caa>Gaa	p.Q828E	DAAM1_ENST00000553966.1_3'UTR|DAAM1_ENST00000360909.3_Missense_Mutation_p.Q818E|DAAM1_ENST00000351081.1_Missense_Mutation_p.Q828E	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	828	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		GAATAAAGGTCAAAGAGGGAA	0.413																																					p.Q828E		Atlas-SNP	.											.	DAAM1	95	.	0			c.C2482G						.						156	146	149					14																	59821978		2203	4300	6503	SO:0001583	missense	23002	exon20			AAAGGTCAAAGAG	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.2482C>G	chr14.hg19:g.59821978C>G	ENSP00000378557:p.Gln828Glu	109.0	0.0		63.0	12.0	NM_014992	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	hg19	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.320873	0.81469	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000358498;ENST00000395125	T;T;T	0.16743	2.32;2.32;2.32	5.81	5.81	0.92471	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.45054	0.1323	M	0.79475	2.455	0.80722	D	1	D;D	0.67145	0.975;0.996	P;D	0.64687	0.658;0.928	T	0.22417	-1.0217	10	0.54805	T	0.06	.	20.4375	0.99097	0.0:1.0:0.0:0.0	.	818;828	Q9Y4D1-2;Q9Y4D1	.;DAAM1_HUMAN	E	818;828;797;828	ENSP00000354162:Q818E;ENSP00000247170:Q828E;ENSP00000378557:Q828E	ENSP00000247170:Q828E	Q	+	1	0	DAAM1	58891731	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.776000	0.85560	2.906000	0.99361	0.655000	0.94253	CAA	.	.		0.413	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		G	59821978	C	G	59821978	3	3	138	1	0	0	0	0	1	0	0	0	4217	827	29	4	2560	4	DAAM1	14	59821978	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10		59821978	47527562	56	21800										
DHRS7	51635	hgsc.bcm.edu	37	chr14	60631900	60631900	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ttggccggtcctcacctgggCgtcgtccctgccactcggcc	12	18	1	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr14:60631900C>T	ENST00000216500.5	-	2	583	c.128G>A	c.(127-129)cGc>cAc	p.R43H	DHRS7_ENST00000536410.2_Intron|PCNXL4_ENST00000553898.1_Intron|DHRS7_ENST00000557185.1_Missense_Mutation_p.R43H|PCNXL4_ENST00000406949.1_Intron			Q9Y394	DHRS7_HUMAN	dehydrogenase/reductase (SDR family) member 7	43						membrane (GO:0016020)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	5				OV - Ovarian serous cystadenocarcinoma(108;0.121)		CTCACCTGGGCGTCGTCCCTG	0.697																																					p.R43H		Atlas-SNP	.											.	DHRS7	31	.	0			c.G128A						.						18	19	19					14																	60631900		2199	4294	6493	SO:0001583	missense	51635	exon1			CCTGGGCGTCGTC	AF151844	CCDS9743.1	14q23.1	2011-09-20			ENSG00000100612	ENSG00000100612		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	21524	protein-coding gene	gene with protein product	"retinal short-chain dehydrogenase/reductase 4", "short chain dehydrogenase/reductase family 34C, member 1"	612833				10800688, 10810093, 19027726	Standard	NM_016029		Approved	retDSR4, SDR34C1	uc001xes.3	Q9Y394	OTTHUMG00000140331	ENST00000216500.5:c.128G>A	chr14.hg19:g.60631900C>T	ENSP00000216500:p.Arg43His	219.0	0.0		220.0	27.0	NM_016029	B2R896|Q9UKU2	Missense_Mutation	SNP	ENST00000216500.5	hg19	CCDS9743.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.3|28.3	4.903943|4.903943	0.92035|0.92035	.|.	.|.	ENSG00000100612|ENSG00000100612	ENST00000554101;ENST00000557137|ENST00000216500;ENST00000360557;ENST00000557185;ENST00000557326	.|D;D	.|0.85013	.|-1.93;-1.93	5.02|5.02	5.02|5.02	0.67125|0.67125	.|.	.|0.244896	.|0.38959	.|N	.|0.001510	D|D	0.85474|0.85474	0.5705|0.5705	L|L	0.47716|0.47716	1.5|1.5	0.34921|0.34921	D|D	0.748429|0.748429	.|D;D	.|0.71674	.|0.998;0.992	.|P;P	.|0.58013	.|0.831;0.574	D|D	0.87741|0.87741	0.2585|0.2585	5|10	.|0.48119	.|T	.|0.1	.|.	7.0958|7.0958	0.25309|0.25309	0.0:0.7347:0.1751:0.0902|0.0:0.7347:0.1751:0.0902	.|.	.|43;43	.|F8W9Q4;Q9Y394	.|.;DHRS7_HUMAN	T|H	38;43|43	.|ENSP00000216500:R43H;ENSP00000451882:R43H	.|ENSP00000216500:R43H	A|R	-|-	1|2	0|0	DHRS7|DHRS7	59701653|59701653	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	1.748000|1.748000	0.38308|0.38308	2.602000|2.602000	0.87976|0.87976	0.557000|0.557000	0.71058|0.71058	GCC|CGC	.	.		0.697	DHRS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276947.2	NM_016029		T	60631900	C	T	60631900	3	4	138	1	0	0	0	0	1	0	0	0	4497	768	27	1	919	1	DHRS7	14	60631900	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	809922	60631900	46717640	57	21801										
C15orf33	196951	hgsc.bcm.edu	37	chr15	49620847	49620850	+	Frame_Shift_Del	DEL	TCTC	TCTC	-													0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	acgatagtgatgccacacatTctctctcaatttcagcttcg							TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr15:49620847_49620850delTCTC	ENST00000299338.6	-	16	1745_1748	c.1442_1445delGAGA	c.(1441-1446)agagaafs	p.RE481fs	GALK2_ENST00000327171.3_3'UTR	NM_152647.2	NP_689860.2	Q96M60	F227B_HUMAN	family with sequence similarity 227, member B	481																	tgCCACACATTCTCTCTCAATTTC	0.348																																					p.481_482del		Atlas-INDEL	.											.	.	.	.	0			c.1443_1446del						.																																			SO:0001589	frameshift_variant	196951	exon16			.		CCDS32237.1	15q21.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000166262	ENSG00000166262			26543	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 33"	C15orf33			Standard	NM_152647		Approved	FLJ32800	uc001zxl.2	Q96M60	OTTHUMG00000172328	ENST00000299338.6:c.1442_1445delGAGA	chr15.hg19:g.49620851_49620854delTCTC	ENSP00000299338:p.Arg481fs	74.0	0.0		66.0	10.0	NM_152647	Q86WS2	Frame_Shift_Del	DEL	ENST00000299338.6	hg19	CCDS32237.1																																																																																			.	.		0.348	FAM227B-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417872.1	NM_152647		-	49620850	TCTC	-	49620847	7	5	138	1	0	1	0	1	0	0	0	0	1793	1783	62	0	85	0	C15orf33	15	49620847	Frame_Shift_Del	DEL	TCTC	TCGA-DD-A4NQ-01A-21D-A28X-10		49620847	52910545	58	21802										
TSC2	7249	hgsc.bcm.edu	37	chr16	2136306	2136311	+	In_Frame_Del	DEL	TGTACC	TGTACC	-													0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ggactgccagccggacaaggTgtacctgggaggcctggacg					rs397514889|rs45517368|rs137854039|rs45511204		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	TGTACC	TGTACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr16:2136306_2136311delTGTACC	ENST00000219476.3	+	37	5405_5410	c.4775_4780delTGTACC	c.(4774-4782)gtgtacctg>gtg	p.YL1593del	TSC2_ENST00000353929.4_In_Frame_Del_p.YL1550del|TSC2_ENST00000401874.2_In_Frame_Del_p.YL1526del|TSC2_ENST00000439673.2_In_Frame_Del_p.YL1490del|TSC2_ENST00000350773.4_In_Frame_Del_p.YL1570del|TSC2_ENST00000568454.1_In_Frame_Del_p.YL1537del|TSC2_ENST00000382538.6_In_Frame_Del_p.YL1478del	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1593	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CCGGACAAGGTGTACCTGGGAGGCCT	0.631			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.1592_1593del		Atlas-Indel,Pindel	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.4774_4779del	GRCh37	CM054165|CM971528	TSC2	M	rs45511204|rs45517368	.																																			SO:0001651	inframe_deletion	7249	exon37	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	.	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.4775_4780delTGTACC	chr16.hg19:g.2136306_2136311delTGTACC	ENSP00000219476:p.Tyr1593_Leu1594del	239.0	0.0		156.0	20.0	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	In_Frame_Del	DEL	ENST00000219476.3	hg19	CCDS10458.1																																																																																			.	.		0.631	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		-	2136311	TGTACC	-	2136306	7	5	138	1	0	1	0	1	0	0	0	0	16621	1696	59	0	4917	0	TSC2	16	2136306	In_Frame_Del	DEL	TGTACC	TCGA-DD-A4NQ-01A-21D-A28X-10		2136306	88218447	59	21803										
NLRC5	84166	hgsc.bcm.edu	37	chr16	57060281	57060281	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	agacagggaaggttatcttcTatgcaaaagatattgctcca	9	7	2	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr16:57060281T>A	ENST00000262510.6	+	6	1651	c.1426T>A	c.(1426-1428)Tat>Aat	p.Y476N	NLRC5_ENST00000308149.7_Missense_Mutation_p.Y476N|NLRC5_ENST00000436936.1_Missense_Mutation_p.Y476N|NLRC5_ENST00000539144.1_Missense_Mutation_p.Y476N	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	476	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GGTTATCTTCTATGCAAAAGA	0.617																																					p.Y476N		Atlas-SNP	.											.	NLRC5	186	.	0			c.T1426A						.						38	35	36					16																	57060281		2198	4300	6498	SO:0001583	missense	84166	exon5			ATCTTCTATGCAA	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.1426T>A	chr16.hg19:g.57060281T>A	ENSP00000262510:p.Tyr476Asn	94.0	0.0		66.0	15.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	hg19	CCDS10773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.67|12.67	2.006408|2.006408	0.35415|0.35415	.|.	.|.	ENSG00000140853|ENSG00000140853	ENST00000538805|ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144	.|D;D;D;D	.|0.88201	.|-2.35;-2.35;-2.35;-2.35	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.533360	.|0.14204	.|N	.|0.334531	D|D	0.87301|0.87301	0.6143|0.6143	L|L	0.46157|0.46157	1.445|1.445	0.33805|0.33805	D|D	0.627167|0.627167	.|P;D;B;B	.|0.54964	.|0.799;0.969;0.222;0.19	.|B;P;B;B	.|0.46253	.|0.386;0.509;0.037;0.028	D|D	0.87584|0.87584	0.2486|0.2486	5|10	.|0.22706	.|T	.|0.39	.|.	14.5996|14.5996	0.68432|0.68432	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|476;476;476;476	.|Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3	.|.;.;.;NLRC5_HUMAN	Q|N	228|476	.|ENSP00000262510:Y476N;ENSP00000308886:Y476N;ENSP00000389739:Y476N;ENSP00000441727:Y476N	.|ENSP00000262510:Y476N	L|Y	+|+	2|1	0|0	NLRC5|NLRC5	55617782|55617782	1.000000|1.000000	0.71417|0.71417	0.870000|0.870000	0.34147|0.34147	0.281000|0.281000	0.26958|0.26958	3.025000|3.025000	0.49681|0.49681	2.047000|2.047000	0.60756|0.60756	0.459000|0.459000	0.35465|0.35465	CTA|TAT	.	.		0.617	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		A	57060281	T	A	57060281	3	1	138	1	0	0	0	0	1	0	0	0	10479	1522	53	4	1440	4	NLRC5	16	57060281	Missense_Mutation	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	54923975	57060281	33294472	60	21804										
SLC2A4	6517	hgsc.bcm.edu	37	chr17	7187403	7187403	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ttgttatcggcattctgatcGcccaggtgaccggagcaagc	12	11	1	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr17:7187403G>T	ENST00000317370.8	+	5	827	c.559G>T	c.(559-561)Gcc>Tcc	p.A187S	SLC2A4_ENST00000571308.1_Missense_Mutation_p.A187S|RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000424875.2_Missense_Mutation_p.A177S	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	187					amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						CATTCTGATCGCCCAGGTGAC	0.612																																					p.A187S		Atlas-SNP	.											.	SLC2A4	44	.	0			c.G559T						.						35	33	34					17																	7187403		2200	4298	6498	SO:0001583	missense	6517	exon5			CTGATCGCCCAGG	M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"Solute carriers"	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.559G>T	chr17.hg19:g.7187403G>T	ENSP00000320935:p.Ala187Ser	86.0	0.0		58.0	10.0	NM_001042	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	hg19	CCDS11097.1	.	.	.	.	.	.	.	.	.	.	G	6.982	0.551300	0.13374	.	.	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.81415	-1.49;-1.49	5.66	5.66	0.87406	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.060310	0.64402	N	0.000004	T	0.77143	0.4087	L	0.58583	1.82	0.80722	D	1	P;P	0.45672	0.741;0.864	B;B	0.41466	0.358;0.244	T	0.74411	-0.3674	10	0.09590	T	0.72	.	17.2301	0.86982	0.0:0.0:1.0:0.0	.	187;177	P14672;F5H081	GTR4_HUMAN;.	S	187;177	ENSP00000320935:A187S;ENSP00000396887:A177S	ENSP00000320935:A187S	A	+	1	0	SLC2A4	7128127	0.840000	0.29493	0.966000	0.40874	0.608000	0.37181	4.227000	0.58612	2.665000	0.90641	0.655000	0.94253	GCC	.	.		0.612	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3			T	7187403	G	T	7187403	3	4	138	1	0	0	0	0	1	0	0	0	14561	1087	38	1	577	1	SLC2A4	17	7187403	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10		7187403	74007807	61	21805										
TP53	7157	hgsc.bcm.edu	37	chr17	7576633	7576633	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ttcatgctctctttaacaatTttctttttgaaagctggtct	5	8	4	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr17:7576633T>C	ENST00000269305.4	-	9	1183				TP53_ENST00000445888.2_Intron|TP53_ENST00000359597.4_Intron|TP53_ENST00000455263.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.N340D	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.I332fs*49(1)|p.?(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTTTAACAATTTTCTTTTTGA	0.368		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.N340D	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	.	TP53	33396	.	10	Whole gene deletion(8)|Unknown(1)|Insertion - Frameshift(1)	bone(4)|haematopoietic_and_lymphoid_tissue(2)|central_nervous_system(2)|stomach(1)|breast(1)	c.A1018G						.						69	61	63					17																	7576633		1567	3581	5148	SO:0001627	intron_variant	7157	exon10	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AACAATTTTCTTT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.993+219A>G	chr17.hg19:g.7576633T>C		109.0	0.0		42.0	16.0	NM_001126114	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	18.91	3.723503	0.68959	.	.	ENSG00000141510	ENST00000420246	D	0.99311	-5.73	2.36	1.2	0.21068	.	.	.	.	.	D	0.97343	0.9131	.	.	.	0.19300	N	0.999976	B	0.30889	0.299	B	0.38616	0.277	D	0.95034	0.8172	7	.	.	.	.	4.4007	0.11385	0.2965:0.0:0.0:0.7035	.	340	P04637-2	.	D	340	ENSP00000391127:N340D	.	N	-	1	0	TP53	7517358	0.162000	0.22906	0.336000	0.25522	0.965000	0.64279	0.105000	0.15333	0.301000	0.22738	0.459000	0.35465	AAT	.	.		0.368	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7576633	T	C	7576633	1	2	138	0	1	0	0	0	0	0	0	0	16396	1841	64	2		2	TP53	17	7576633	Intron	SNP	T	TCGA-DD-A4NQ-01A-21D-A28X-10	389230	7576633	73618577	62	21806										
NCLN	56926	hgsc.bcm.edu	37	chr19	3206308	3206308	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	tgatggactggctcaccaacCagccgcgggccgcgcagctg	14	15	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr19:3206308C>T	ENST00000246117.4	+	12	1815	c.1384C>T	c.(1384-1386)Cag>Tag	p.Q462*	NCLN_ENST00000590671.1_Nonsense_Mutation_p.Q388*	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	462					regulation of signal transduction (GO:0009966)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				kidney(1)|lung(3)|skin(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.83e-113)|Epithelial(107;1.65e-111)|all cancers(105;1.53e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00139)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTCACCAACCAGCCGCGGGC	0.662																																					p.Q462X		Atlas-SNP	.											.	NCLN	27	.	0			c.C1384T						.						26	20	22					19																	3206308		1963	3775	5738	SO:0001587	stop_gained	56926	exon12			ACCAACCAGCCGC	BC025926	CCDS32869.1	19p13.3	2010-08-13	2010-08-13			ENSG00000125912			26923	protein-coding gene	gene with protein product	"nicastrin-like protein"	609156	"nicalin homolog (zebrafish)"			11230166	Standard	NM_020170		Approved	NICALIN, NET59	uc002lxi.3	Q969V3		ENST00000246117.4:c.1384C>T	chr19.hg19:g.3206308C>T	ENSP00000246117:p.Gln462*	105.0	0.0		109.0	27.0	NM_020170	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Nonsense_Mutation	SNP	ENST00000246117.4	hg19	CCDS32869.1	.	.	.	.	.	.	.	.	.	.	C	38	7.255656	0.98168	.	.	ENSG00000125912	ENST00000246117	.	.	.	4.05	4.05	0.47172	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	-12.412	14.7949	0.69870	0.0:1.0:0.0:0.0	.	.	.	.	X	462	.	ENSP00000246117:Q462X	Q	+	1	0	NCLN	3157308	1.000000	0.71417	0.979000	0.43373	0.859000	0.49053	7.090000	0.76916	1.802000	0.52723	0.549000	0.68633	CAG	.	.		0.662	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1	NM_020170		T	3206308	C	T	3206308	4	4	138	1	0	0	0	0	0	1	0	0	10236	595	21	3	1430	3	NCLN	19	3206308	Nonsense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10		3206308	55922675	63	21807										
C19orf10	56005	hgsc.bcm.edu	37	chr19	4664897	4664897	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ccgagtctcacctccagatgGtgcaggtgaagtgctggtgg	15	10	1	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr19:4664897G>T	ENST00000262947.3	-	3	313	c.278C>A	c.(277-279)aCc>aAc	p.T93N	C19orf10_ENST00000599630.1_Missense_Mutation_p.T93N	NM_019107.3	NP_061980.1	Q969H8	CS010_HUMAN	chromosome 19 open reading frame 10	93					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.015)		CCTCCAGATGGTGCAGGTGAA	0.637																																					p.T93N		Atlas-SNP	.											.	C19orf10	9	.	0			c.C278A						.						119	75	90					19																	4664897		2200	4298	6498	SO:0001583	missense	56005	exon3			CAGATGGTGCAGG	AF282264	CCDS12133.1	19p13.3	2013-11-27	2003-06-25	2003-06-27	ENSG00000074842	ENSG00000074842			16948	protein-coding gene	gene with protein product		606746	"interleukin 27 working designation"	IL27, IL27w		17362502, 21128247	Standard	NM_019107		Approved	R33729_1, IL25, SF20, IL-25, IL-27	uc002may.3	Q969H8		ENST00000262947.3:c.278C>A	chr19.hg19:g.4664897G>T	ENSP00000262947:p.Thr93Asn	143.0	0.0		94.0	13.0	NM_019107	D6W628|O75256|O75272|Q9BTK7|Q9NP69	Missense_Mutation	SNP	ENST00000262947.3	hg19	CCDS12133.1	.	.	.	.	.	.	.	.	.	.	g	13.36	2.215345	0.39102	.	.	ENSG00000074842	ENST00000262947	T	0.46819	0.86	4.54	3.25	0.37280	.	0.133303	0.51477	D	0.000094	T	0.39358	0.1075	L	0.34521	1.04	0.20764	N	0.999851	P	0.43826	0.818	P	0.44732	0.459	T	0.27123	-1.0083	10	0.49607	T	0.09	-16.6686	10.3755	0.44079	0.1152:0.0:0.8848:0.0	.	93	Q969H8	CS010_HUMAN	N	93	ENSP00000262947:T93N	ENSP00000262947:T93N	T	-	2	0	C19orf10	4615897	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.515000	0.60489	2.118000	0.64928	0.550000	0.68814	ACC	.	.		0.637	C19orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458937.1	NM_019107		T	4664897	G	T	4664897	3	4	138	1	0	0	0	0	1	0	0	0	1910	1261	44	3	259	3	C19orf10	19	4664897	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	1458589	4664897	54464086	64	21808										
JAK3	3718	hgsc.bcm.edu	37	chr19	17943612	17943612	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	accttaccttgcccagctgtGagatgtacttgaggtgtctc	10	11	1	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr19:17943612G>A	ENST00000527670.1	-	17	2506	c.2477C>T	c.(2476-2478)tCa>tTa	p.S826L	JAK3_ENST00000458235.1_Missense_Mutation_p.S826L|JAK3_ENST00000534444.1_Missense_Mutation_p.S826L			P52333	JAK3_HUMAN	Janus kinase 3	826	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GCCCAGCTGTGAGATGTACTT	0.627		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.S826L		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	JAK3	341	.	0			c.C2477T						.						185	154	164					19																	17943612		2203	4300	6503	SO:0001583	missense	3718	exon18			AGCTGTGAGATGT	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.2477C>T	chr19.hg19:g.17943612G>A	ENSP00000432511:p.Ser826Leu	263.0	0.0		198.0	35.0	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	hg19	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.752414	0.89753	.	.	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	T;T;D	0.89552	-0.02;-0.02;-2.53	5.11	5.11	0.69529	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92126	0.7504	L	0.48935	1.535	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.71414	0.936;0.973	D	0.92798	0.6254	10	0.66056	D	0.02	-15.1052	15.9996	0.80285	0.0:0.0:1.0:0.0	.	826;826	P52333-2;P52333	.;JAK3_HUMAN	L	826	ENSP00000391676:S826L;ENSP00000432511:S826L;ENSP00000436421:S826L	ENSP00000391676:S826L	S	-	2	0	JAK3	17804612	0.999000	0.42202	0.989000	0.46669	0.987000	0.75469	2.893000	0.48633	2.385000	0.81259	0.478000	0.44815	TCA	.	.		0.627	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		A	17943612	G	A	17943612	3	1	138	1	0	0	0	0	1	0	0	0	7948	1294	45	3	925	3	JAK3	19	17943612	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	13278715	17943612	41185371	65	21809										
RYR1	6261	hgsc.bcm.edu	37	chr19	39071081	39071081	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gtggccttcaacttcttccgCaagttctacaacaagagcga	8	12	3	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr19:39071081C>T	ENST00000359596.3	+	101	14583	c.14583C>T	c.(14581-14583)cgC>cgT	p.R4861R	RYR1_ENST00000355481.4_Silent_p.R4856R|RYR1_ENST00000360985.3_Silent_p.R4856R			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4861			R -> C (in CCD). {ECO:0000269|PubMed:12565913, ECO:0000269|PubMed:17226826}.|R -> H (in CCD and MHS1; release of calcium from intracellular stores in the absence of any pharmacological activator of RYR). {ECO:0000269|PubMed:11709545, ECO:0000269|PubMed:11741831, ECO:0000269|PubMed:12565913, ECO:0000269|PubMed:14670767, ECO:0000269|PubMed:14985404, ECO:0000269|PubMed:17226826, ECO:0000269|PubMed:23558838, ECO:0000269|PubMed:24561095}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACTTCTTCCGCAAGTTCTACA	0.582																																					p.R4861R		Atlas-SNP	.											.	RYR1	708	.	0			c.C14583T						.						205	161	175					19																	39071081		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon101			CTTCCGCAAGTTC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14583C>T	chr19.hg19:g.39071081C>T		246.0	0.0		264.0	46.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.582	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	39071081	C	T	39071081	2	4	138	1	0	0	0	0	0	0	0	1	13783	697	25	3		3	RYR1	19	39071081	Silent	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	21127469	39071081	20057902	66	21810										
CD37	951	hgsc.bcm.edu	37	chr19	49841271	49841271	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gcggccgaggagagctgggaCtatgtgcagttccaggtaag	17	8	0	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr19:49841271C>G	ENST00000323906.4	+	5	573	c.432C>G	c.(430-432)gaC>gaG	p.D144E	CD37_ENST00000426897.2_Missense_Mutation_p.D76E|CD37_ENST00000535669.2_Missense_Mutation_p.D144E|CD37_ENST00000598095.1_Missense_Mutation_p.D76E|CD37_ENST00000596426.1_3'UTR|CTC-301O7.4_ENST00000358234.4_lincRNA	NM_001774.2	NP_001765.1	P11049	CD37_HUMAN	CD37 molecule	144					defense response to protozoan (GO:0042832)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid dendritic cell activation (GO:0030886)|positive regulation of immunoglobulin production (GO:0002639)|regulation of defense response to virus (GO:0050688)|regulation of humoral immune response (GO:0002920)	extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	11		all_lung(116;2.81e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00088)|GBM - Glioblastoma multiforme(486;0.0443)		AGAGCTGGGACTATGTGCAGT	0.637																																					p.D144E		Atlas-SNP	.											.	CD37	33	.	0			c.C432G						.						98	89	92					19																	49841271		2203	4300	6503	SO:0001583	missense	951	exon5			CTGGGACTATGTG		CCDS12760.1, CCDS46139.1	19p13-q13.4	2013-02-14	2006-03-28			ENSG00000104894		"CD molecules", "Tetraspanins"	1666	protein-coding gene	gene with protein product		151523	"CD37 antigen"			8436422	Standard	XM_005259435		Approved	TSPAN26	uc002pnd.3	P11049		ENST00000323906.4:c.432C>G	chr19.hg19:g.49841271C>G	ENSP00000325708:p.Asp144Glu	180.0	0.0		194.0	62.0	NM_001774	B4DVC1|Q3KPF9	Missense_Mutation	SNP	ENST00000323906.4	hg19	CCDS12760.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.818360	0.50633	.	.	ENSG00000104894	ENST00000323906;ENST00000426897;ENST00000535669	D;D;D	0.81908	-1.55;-1.55;-1.55	3.69	2.3	0.28687	Tetraspanin, EC2 domain (1);	0.000000	0.56097	D	0.000029	D	0.89065	0.6609	M	0.85859	2.78	0.40891	D	0.984078	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.91635	0.999;0.998;0.998;0.997	D	0.86897	0.2052	10	0.87932	D	0	.	4.127	0.10131	0.0:0.6288:0.0:0.3712	.	76;144;144;144	B4DVC1;B7ZAN3;B4DW15;P11049	.;.;.;CD37_HUMAN	E	144;76;144	ENSP00000325708:D144E;ENSP00000413151:D76E;ENSP00000441037:D144E	ENSP00000325708:D144E	D	+	3	2	CD37	54533083	0.765000	0.28485	1.000000	0.80357	0.345000	0.29048	-0.105000	0.10907	0.686000	0.31488	0.313000	0.20887	GAC	.	.		0.637	CD37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465532.1			G	49841271	C	G	49841271	3	3	138	1	0	0	0	0	1	0	0	0	3010	564	20	4	450	4	CD37	19	49841271	Missense_Mutation	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	10770190	49841271	9287712	67	21811										
A1BG	1	hgsc.bcm.edu	37	chr19	58862780	58862780	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cgctcagaatcagctcgaccGgcgcgctgtccccggaccag	12	17	2	1	rs542119157		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr19:58862780G>A	ENST00000263100.3	-	5	948	c.887C>T	c.(886-888)cCg>cTg	p.P296L	A1BG-AS1_ENST00000599728.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000595302.1_RNA	NM_130786.3	NP_570602.2	P04217	A1BG_HUMAN	alpha-1-B glycoprotein	296	Ig-like V-type 3.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)	15		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)		CAGCTCGACCGGCGCGCTGTC	0.657													G|||	1	0.000199681	0	0	5008	,	,		14169	0		0	False		,,,				2504	0.001				p.P296L		Atlas-SNP	.											A1BG,NS,carcinoma,0,1	A1BG	40	.	0			c.C887T						.						54	59	57					19																	58862780		2202	4300	6502	SO:0001583	missense	1	exon5			TCGACCGGCGCGC		CCDS12976.1	19q13.43	2013-10-15			ENSG00000121410	ENSG00000121410		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5	protein-coding gene	gene with protein product		138670				2591067	Standard	NM_130786		Approved		uc002qsd.4	P04217	OTTHUMG00000183507	ENST00000263100.3:c.887C>T	chr19.hg19:g.58862780G>A	ENSP00000263100:p.Pro296Leu	68.0	0.0		96.0	27.0	NM_130786	A8K052|Q68CK0|Q8IYJ6|Q96P39	Missense_Mutation	SNP	ENST00000263100.3	hg19	CCDS12976.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.431997	0.62844	.	.	ENSG00000121410	ENST00000263100;ENST00000453054	T	0.13538	2.58	3.42	3.42	0.39159	Immunoglobulin-like fold (1);	0.000000	0.45361	D	0.000380	T	0.36880	0.0983	M	0.82823	2.61	0.50467	D	0.999871	D	0.89917	1.0	D	0.76071	0.987	T	0.26849	-1.0091	10	0.87932	D	0	.	10.6418	0.45596	0.0:0.0:1.0:0.0	.	296	P04217	A1BG_HUMAN	L	296;174	ENSP00000263100:P296L	ENSP00000263100:P296L	P	-	2	0	A1BG	63554592	0.000000	0.05858	0.755000	0.31263	0.003000	0.03518	0.558000	0.23469	2.217000	0.71921	0.462000	0.41574	CCG	.	.		0.657	A1BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466930.1	NM_130786		A	58862780	G	A	58862780	3	1	138	1	0	0	0	0	1	0	0	0	1	1116	39	1	616	1	A1BG	19	58862780	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	9021509	58862780	266203	68	21812										
SEC23B	10483	hgsc.bcm.edu	37	chr20	18505223	18505223	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ggtctgatcacatttggaagGatggtgcaggttcatgagct	14	6	3	2			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr20:18505223G>C	ENST00000336714.3	+	5	945	c.513G>C	c.(511-513)agG>agC	p.R171S	SEC23B_ENST00000377475.3_Missense_Mutation_p.R171S|SEC23B_ENST00000377465.1_Missense_Mutation_p.R171S|SEC23B_ENST00000262544.2_Missense_Mutation_p.R171S	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	171					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						CATTTGGAAGGATGGTGCAGG	0.478																																					p.R171S		Atlas-SNP	.											.	SEC23B	70	.	0			c.G513C						.						145	127	133					20																	18505223		2203	4300	6503	SO:0001583	missense	10483	exon5			TGGAAGGATGGTG	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"Sec23 (S. cerevisiae) homolog B", "congenital dyserythropoietic anemia, type II"	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.513G>C	chr20.hg19:g.18505223G>C	ENSP00000338844:p.Arg171Ser	153.0	0.0		99.0	17.0	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	hg19	CCDS13137.1	.	.	.	.	.	.	.	.	.	.	G	16.17	3.046011	0.55110	.	.	ENSG00000101310	ENST00000450074;ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	T;T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95;-0.95	4.91	-0.753	0.11068	Sec23/Sec24, trunk domain (1);	0.000000	0.85682	D	0.000000	T	0.58424	0.2121	L	0.35593	1.075	0.80722	D	1	B;B	0.15930	0.015;0.004	B;B	0.17098	0.017;0.017	T	0.42916	-0.9423	10	0.30078	T	0.28	-19.7662	9.812	0.40828	0.5316:0.0:0.4684:0.0	.	153;171	B4DJW8;Q15437	.;SC23B_HUMAN	S	171	ENSP00000403971:R171S;ENSP00000338844:R171S;ENSP00000262544:R171S;ENSP00000366695:R171S;ENSP00000366685:R171S	ENSP00000262544:R171S	R	+	3	2	SEC23B	18453223	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	2.130000	0.42064	0.020000	0.15106	0.591000	0.81541	AGG	.	.		0.478	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			C	18505223	G	C	18505223	3	2	138	1	0	0	0	0	1	0	0	0	14007	1165	41	4	527	4	SEC23B	20	18505223	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10		18505223	44520297	69	21813										
PYGB	5834	hgsc.bcm.edu	37	chr20	25261588	25261588	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ctgtgttttggcaccagcacGtggccgcgctgtttcccggc	13	14	0	0	rs201813153		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr20:25261588G>A	ENST00000216962.4	+	11	1353	c.1243G>A	c.(1243-1245)Gtg>Atg	p.V415M		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	415					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						GCACCAGCACGTGGCCGCGCT	0.642													G|||	1	0.000199681	8e-04	0	5008	,	,		18121	0		0	False		,,,				2504	0				p.V415M		Atlas-SNP	.											.	PYGB	84	.	0			c.G1243A						.						114	102	106					20																	25261588		2203	4300	6503	SO:0001583	missense	5834	exon11			CAGCACGTGGCCG		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"Glycogen phosphorylases"	9723	protein-coding gene	gene with protein product	"glycogen phosphorylase, brain form"	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.1243G>A	chr20.hg19:g.25261588G>A	ENSP00000216962:p.Val415Met	173.0	0.0		169.0	24.0	NM_002862	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	hg19	CCDS13171.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.141304	0.37825	.	.	ENSG00000100994	ENST00000216962	D	0.95035	-3.59	4.02	3.06	0.35304	.	0.251138	0.39341	N	0.001398	D	0.95130	0.8422	M	0.81942	2.565	0.44462	D	0.997395	D	0.60575	0.988	P	0.53401	0.725	D	0.94246	0.7489	10	0.87932	D	0	-26.065	8.2363	0.31627	0.1881:0.0:0.8119:0.0	.	415	P11216	PYGB_HUMAN	M	415	ENSP00000216962:V415M	ENSP00000216962:V415M	V	+	1	0	PYGB	25209588	0.998000	0.40836	0.834000	0.33040	0.026000	0.11368	3.100000	0.50275	1.027000	0.39758	0.462000	0.41574	GTG	.	.		0.642	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862		A	25261588	G	A	25261588	3	1	138	1	0	0	0	0	1	0	0	0	12875	1145	40	1	1285	1	PYGB	20	25261588	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	6756365	25261588	37763932	70	21814										
CPNE1	8904	hgsc.bcm.edu	37	chr20	34220601	34220601	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	gggcttgagcagttccgcacCcgttcagtccggccaagctg	13	14	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr20:34220601C>A	ENST00000317619.3	-	5	541	c.147G>T	c.(145-147)cgG>cgT	p.R49R	CPNE1_ENST00000397445.1_Silent_p.R49R|CPNE1_ENST00000397446.1_Silent_p.R49R|CPNE1_ENST00000397443.1_Silent_p.R49R|RP1-309K20.6_ENST00000541176.2_3'UTR|CPNE1_ENST00000352393.4_Silent_p.R49R|CPNE1_ENST00000397442.1_Silent_p.R49R|CPNE1_ENST00000317677.5_Silent_p.R54R			Q99829	CPNE1_HUMAN	copine I	49	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			AGTTCCGCACCCGTTCAGTCC	0.532																																					p.R54R		Atlas-SNP	.											.	CPNE1	44	.	0			c.G162T						.						128	126	127					20																	34220601		2203	4300	6503	SO:0001819	synonymous_variant	8904	exon3			CCGCACCCGTTCA	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.147G>T	chr20.hg19:g.34220601C>A		186.0	0.0		125.0	10.0	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Silent	SNP	ENST00000317619.3	hg19	CCDS13260.1																																																																																			.	.		0.532	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930		A	34220601	C	A	34220601	2	1	138	1	0	0	0	0	0	0	0	1	3813	610	22	3		3	CPNE1	20	34220601	Silent	SNP	C	TCGA-DD-A4NQ-01A-21D-A28X-10	8959013	34220601	28804919	71	21815										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50287714	50287714	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ctcaggaatcgtgctggagcGaaccacggtcccggggattt	14	11	1	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr20:50287714G>A	ENST00000338821.5	-	12	1384	c.1120C>T	c.(1120-1122)Cgc>Tgc	p.R374C	ATP9A_ENST00000311637.5_Missense_Mutation_p.R238C|ATP9A_ENST00000402822.1_Missense_Mutation_p.R253C	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	374					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GTGCTGGAGCGAACCACGGTC	0.552																																					p.R374C		Atlas-SNP	.											.	ATP9A	135	.	0			c.C1120T						.						94	79	84					20																	50287714		2203	4300	6503	SO:0001583	missense	10079	exon12			TGGAGCGAACCAC	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1120C>T	chr20.hg19:g.50287714G>A	ENSP00000342481:p.Arg374Cys	123.0	0.0		100.0	7.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	hg19	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.867084	0.51588	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	D;D;D	0.91577	-2.87;-2.87;-2.87	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.97244	0.9099	H	0.98818	4.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.978	D	0.98312	1.0524	10	0.87932	D	0	-15.1513	13.6168	0.62112	0.0:0.0:0.8447:0.1553	.	253;374	O75110-2;O75110	.;ATP9A_HUMAN	C	238;374;253	ENSP00000309086:R238C;ENSP00000342481:R374C;ENSP00000385875:R253C	ENSP00000309086:R238C	R	-	1	0	ATP9A	49721121	1.000000	0.71417	0.999000	0.59377	0.230000	0.25150	4.694000	0.61760	2.397000	0.81536	0.313000	0.20887	CGC	.	.		0.552	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		A	50287714	G	A	50287714	3	1	138	1	0	0	0	0	1	0	0	0	1198	1058	37	1	2091	1	ATP9A	20	50287714	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	16067113	50287714	12737806	72	21816										
PHACTR3	116154	hgsc.bcm.edu	37	chr20	58322830	58322830	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cagcgctggagaagaagatgGccggcaggcaaggccgagag	18	9	0	4			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr20:58322830G>T	ENST00000371015.1	+	3	765	c.298G>T	c.(298-300)Gcc>Tcc	p.A100S	PHACTR3_ENST00000395639.4_Missense_Mutation_p.A59S|PHACTR3_ENST00000359926.3_Missense_Mutation_p.A97S|PHACTR3_ENST00000395636.2_Missense_Mutation_p.A59S|PHACTR3_ENST00000541461.1_Missense_Mutation_p.A59S|PHACTR3_ENST00000355648.4_Missense_Mutation_p.A59S|PHACTR3_ENST00000361300.4_Missense_Mutation_p.A59S	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	100						nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			GAAGAAGATGGCCGGCAGGCA	0.607																																					p.A100S		Atlas-SNP	.											.	PHACTR3	104	.	0			c.G298T						.						146	133	138					20																	58322830		2203	4300	6503	SO:0001583	missense	116154	exon3			AAGATGGCCGGCA	AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"Phosphatase and actin regulators"	15833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 123"	608725	"chromosome 20 open reading frame 101"	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.298G>T	chr20.hg19:g.58322830G>T	ENSP00000360054:p.Ala100Ser	183.0	0.0		103.0	15.0	NM_080672	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Missense_Mutation	SNP	ENST00000371015.1	hg19	CCDS13480.1	.	.	.	.	.	.	.	.	.	.	G	1.196	-0.633917	0.03584	.	.	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000395639;ENST00000541461;ENST00000355648;ENST00000395636;ENST00000361300	T;T;T;T;T;T;T	0.19532	2.87;2.91;2.14;2.78;2.78;2.78;2.14	4.26	2.28	0.28536	.	0.351081	0.33199	N	0.005169	T	0.06508	0.0167	N	0.04705	-0.18	0.30950	N	0.724849	B;B;B	0.15141	0.012;0.001;0.001	B;B;B	0.14578	0.011;0.003;0.002	T	0.35968	-0.9767	10	0.02654	T	1	-5.5525	3.4531	0.07506	0.3106:0.0:0.5107:0.1787	.	59;100;97	Q96KR7-3;Q96KR7;B1AKX0	.;PHAR3_HUMAN;.	S	97;100;59;59;59;59;59	ENSP00000353002:A97S;ENSP00000360054:A100S;ENSP00000379001:A59S;ENSP00000442483:A59S;ENSP00000347866:A59S;ENSP00000378998:A59S;ENSP00000354555:A59S	ENSP00000347866:A59S	A	+	1	0	PHACTR3	57756225	1.000000	0.71417	0.954000	0.39281	0.933000	0.57130	1.266000	0.33039	0.359000	0.24239	0.563000	0.77884	GCC	.	.		0.607	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		T	58322830	G	T	58322830	3	4	138	1	0	0	0	0	1	0	0	0	11820	1203	42	3	308	3	PHACTR3	20	58322830	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	8035116	58322830	4702690	73	21817										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61978125	61978125	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cagccagggcggcaggaagaGgcccaccgtccccagcaggc	15	16	0	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr20:61978125G>A	ENST00000370263.4	-	6	2070	c.1849C>T	c.(1849-1851)Ctc>Ttc	p.L617F	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	617					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GGCAGGAAGAGGCCCACCGTC	0.657																																					p.L617F		Atlas-SNP	.											.	CHRNA4	98	.	0			c.C1849T						.						98	61	73					20																	61978125		2202	4299	6501	SO:0001583	missense	1137	exon6			GGAAGAGGCCCAC		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1849C>T	chr20.hg19:g.61978125G>A	ENSP00000359285:p.Leu617Phe	130.0	0.0		130.0	23.0	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	hg19	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	G	33	5.227201	0.95173	.	.	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	D	0.87809	-2.3	4.43	4.43	0.53597	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.179987	0.49916	D	0.000123	D	0.92867	0.7731	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.999	D	0.93943	0.7225	10	0.87932	D	0	.	17.3789	0.87399	0.0:0.0:1.0:0.0	.	546;617	Q4VAQ5;P43681	.;ACHA4_HUMAN	F	523;617;546	ENSP00000359285:L617F	ENSP00000359280:L523F	L	-	1	0	CHRNA4	61448569	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.546000	0.98097	2.177000	0.69029	0.511000	0.50034	CTC	.	.		0.657	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			A	61978125	G	A	61978125	3	1	138	1	0	0	0	0	1	0	0	0	3387	1000	35	3	38	3	CHRNA4	20	61978125	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10	3655295	61978125	1047395	74	21818										
RSPH1	89765	hgsc.bcm.edu	37	chr21	43896039	43896039	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	tcatagcggaactcctcctgGtcatactcccggctctcttc	7	16	3	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr21:43896039G>A	ENST00000291536.3	-	8	1013	c.846C>T	c.(844-846)gaC>gaT	p.D282D	RSPH1_ENST00000398352.3_Silent_p.D244D	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	282					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)				large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						ACTCCTCCTGGTCATACTCCC	0.627																																					p.D282D	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-SNP	.											.	RSPH1	36	.	0			c.C846T						.						186	143	157					21																	43896039		2203	4300	6503	SO:0001819	synonymous_variant	89765	exon8			CTCCTGGTCATAC	AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"meichroacidin"	609314	"testis specific A2 homolog (mouse)"	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.846C>T	chr21.hg19:g.43896039G>A		114.0	0.0		104.0	24.0	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Silent	SNP	ENST00000291536.3	hg19	CCDS13688.1																																																																																			.	.		0.627	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1			A	43896039	G	A	43896039	2	1	138	1	0	0	0	0	0	0	0	1	13717	1252	44	3		3	RSPH1	21	43896039	Silent	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10		43896039	4233856	75	21819										
THAP7	80764	hgsc.bcm.edu	37	chr22	21354333	21354333	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cttgcaggcctgcagctggcGctgggccttgtcaagggcat	15	12	1	0			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr22:21354333G>A	ENST00000215742.4	-	4	940	c.766C>T	c.(766-768)Cgc>Tgc	p.R256C	THAP7-AS1_ENST00000429962.1_RNA|THAP7_ENST00000399133.2_Missense_Mutation_p.R256C|THAP7-AS1_ENST00000452284.1_RNA|THAP7-AS1_ENST00000436079.1_RNA	NM_030573.2	NP_085050.2	Q9BT49	THAP7_HUMAN	THAP domain containing 7	256					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nuclear speck (GO:0016607)	C2H2 zinc finger domain binding (GO:0070742)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)			cervix(1)|lung(2)|prostate(3)|skin(1)|stomach(1)	8	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			TGCAGCTGGCGCTGGGCCTTG	0.662																																					p.R256C		Atlas-SNP	.											.	THAP7	15	.	0			c.C766T						.						21	23	22					22																	21354333		2194	4292	6486	SO:0001583	missense	80764	exon4			GCTGGCGCTGGGC	BC004346	CCDS13787.1	22q11.2	2013-01-25			ENSG00000184436	ENSG00000184436		"THAP (C2CH-type zinc finger) domain containing"	23190	protein-coding gene	gene with protein product		609518				12575992	Standard	NM_030573		Approved	MGC10963	uc002ztr.1	Q9BT49	OTTHUMG00000150879	ENST00000215742.4:c.766C>T	chr22.hg19:g.21354333G>A	ENSP00000215742:p.Arg256Cys	92.0	0.0		122.0	23.0	NM_030573	B2RD97|D3DX40	Missense_Mutation	SNP	ENST00000215742.4	hg19	CCDS13787.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.901273	0.72754	.	.	ENSG00000184436	ENST00000215742;ENST00000399133	D;D	0.97256	-4.31;-4.31	4.96	3.95	0.45737	.	0.198258	0.33534	N	0.004811	D	0.91978	0.7459	N	0.24115	0.695	0.58432	D	0.999998	B	0.19331	0.035	B	0.06405	0.002	D	0.88075	0.2803	10	0.87932	D	0	-18.3688	6.1901	0.20520	0.0935:0.0:0.7229:0.1836	.	256	Q9BT49	THAP7_HUMAN	C	256	ENSP00000215742:R256C;ENSP00000382084:R256C	ENSP00000215742:R256C	R	-	1	0	THAP7	19684333	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.031000	0.41117	1.303000	0.44873	0.655000	0.94253	CGC	.	.		0.662	THAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320405.1	NM_030573		A	21354333	G	A	21354333	3	1	138	1	0	0	0	0	1	0	0	0	15864	1087	38	1	167	1	THAP7	22	21354333	Missense_Mutation	SNP	G	TCGA-DD-A4NQ-01A-21D-A28X-10		21354333	29950233	76	21820										
H1F0	3005	hgsc.bcm.edu	37	chr22	38201683	38201684	+	Frame_Shift_Ins	INS	-	-	T													0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	ccgagaagaaccgcgctggcINStcctcgcgccagtccattca							TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chr22:38201683_38201684insT	ENST00000340857.2	+	1	570_571	c.132_133insT	c.(133-135)tccfs	p.S45fs	GCAT_ENST00000323205.6_5'Flank|GCAT_ENST00000248924.6_5'Flank	NM_005318.3	NP_005309.1	P07305	H10_HUMAN	H1 histone family, member 0	45	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|nucleosome assembly (GO:0006334)	actin cytoskeleton (GO:0015629)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(2)|prostate(2)|urinary_tract(1)	7	Melanoma(58;0.045)					ACCGCGCTGGCTCCTCGCGCCA	0.574																																					p.G44fs	NSCLC(191;1872 2984 30230 41544)|Esophageal Squamous(4;11 371 39444 52196)	Atlas-INDEL	.											.	H1F0	12	.	0			c.132_133insT						.																																			SO:0001589	frameshift_variant	3005	exon1			.	X03473	CCDS13956.1	22q13.1	2011-01-27			ENSG00000189060	ENSG00000189060		"Histones / Replication-independent"	4714	protein-coding gene	gene with protein product	"H1.0, H1(0), H1-0"	142708		H1FV		3084796	Standard	NM_005318		Approved	H10	uc003aty.3	P07305	OTTHUMG00000150659	ENST00000340857.2:c.133dupT	chr22.hg19:g.38201684_38201684dupT	ENSP00000344504:p.Ser45fs	176.0	0.0		111.0	11.0	NM_005318	B2R6I0|B4DRD6|Q6FG88|Q8N6R3	Frame_Shift_Ins	INS	ENST00000340857.2	hg19	CCDS13956.1																																																																																			.	.		0.574	H1F0-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319453.1	NM_005318		T	38201684	-	T	38201683	7	5	138	1	0	1	1	0	0	0	0	0	6929	784	28	0	134	0	H1F0	22	38201683	Frame_Shift_Ins	INS	-	TCGA-DD-A4NQ-01A-21D-A28X-10	16847350	38201683	13102883	77	21821										
COL4A6	1288	hgsc.bcm.edu	37	chrX	107681209	107681209	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	6	1	1.62279293739968	2.83988764044944	1.13595505617978	1	1	0	cggtcaggcacaacgtaaccAggagcagccacaacctgaaa	10	13	1	1			TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	g.chrX:107681209A>T	ENST00000372216.4	-	2	129	c.29T>A	c.(28-30)cTg>cAg	p.L10Q	COL4A6_ENST00000545689.1_Missense_Mutation_p.L9Q|COL4A6_ENST00000334504.7_Missense_Mutation_p.L9Q|COL4A6_ENST00000538570.1_Missense_Mutation_p.L9Q|COL4A5_ENST00000328300.6_5'Flank|COL4A6_ENST00000461897.1_5'UTR|COL4A6_ENST00000394872.2_Missense_Mutation_p.L9Q|COL4A5_ENST00000361603.2_5'Flank	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	10					cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						CAACGTAACCAGGAGCAGCCA	0.597									Alport syndrome with Diffuse Leiomyomatosis																												p.L10Q	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.T29A						.						63	52	56					X																	107681209		2203	4300	6503	SO:0001583	missense	1288	exon2	Familial Cancer Database		GTAACCAGGAGCA	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.29T>A	chrX.hg19:g.107681209A>T	ENSP00000361290:p.Leu10Gln	268.0	0.0		226.0	64.0	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	hg19	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.879269	0.33162	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D;D	0.92249	-3.0;-2.97;-2.98;-2.93;-2.93	5.18	5.18	0.71444	.	0.000000	0.30252	N	0.010047	D	0.91246	0.7241	N	0.19112	0.55	0.32529	N	0.535172	D;D;D;D	0.69078	0.997;0.997;0.994;0.997	D;D;P;D	0.66351	0.943;0.943;0.879;0.943	D	0.92142	0.5721	10	0.56958	D	0.05	.	10.7064	0.45958	1.0:0.0:0.0:0.0	.	9;9;10;9	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	Q	10;9;9;9;9;9	ENSP00000361290:L10Q;ENSP00000334733:L9Q;ENSP00000378340:L9Q;ENSP00000443707:L9Q;ENSP00000445236:L9Q	ENSP00000334733:L9Q	L	-	2	0	COL4A6	107567865	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	3.848000	0.55903	1.992000	0.58205	0.486000	0.48141	CTG	.	.		0.597	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			T	107681209	A	T	107681209	3	4	138	1	0	0	0	0	1	0	0	0	3697	188	7	4	5222	4	COL4A6	23	107681209	Missense_Mutation	SNP	A	TCGA-DD-A4NQ-01A-21D-A28X-10		107681209	47589351	78	21822										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27101142	27101142	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	tggcaccaatgcccagcaaaAcatgccaccacaaatgatgg	8	13	0	1			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr1:27101142A>C	ENST00000324856.7	+	18	4795	c.4424A>C	c.(4423-4425)aAc>aCc	p.N1475T	ARID1A_ENST00000457599.2_Intron|ARID1A_ENST00000374152.2_Missense_Mutation_p.N1092T|ARID1A_ENST00000540690.1_Intron	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1475					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCCCAGCAAAACATGCCACCA	0.572			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.N1475T		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.A4424C						.						63	66	65					1																	27101142		2203	4300	6503	SO:0001583	missense	8289	exon18			AGCAAAACATGCC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4424A>C	chr1.hg19:g.27101142A>C	ENSP00000320485:p.Asn1475Thr	38.0	0.0		57.0	11.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.640|8.640	0.895675|0.895675	0.17686|0.17686	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000430799|ENST00000324856;ENST00000374152	.|T;T	.|0.02369	.|4.49;4.32	5.54|5.54	3.18|3.18	0.36537|0.36537	.|.	.|0.405053	.|0.30528	.|N	.|0.009435	T|T	0.01800|0.01800	0.0057|0.0057	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.25904	.|0.137;0.0;0.001	.|B;B;B	.|0.28011	.|0.085;0.001;0.002	T|T	0.58216|0.58216	-0.7675|-0.7675	5|10	.|0.39692	.|T	.|0.17	-6.5561|-6.5561	7.475|7.475	0.27371|0.27371	0.6555:0.2689:0.0756:0.0|0.6555:0.2689:0.0756:0.0	.|.	.|1092;1475;1128	.|O14497-3;O14497;Q4LE49	.|.;ARI1A_HUMAN;.	N|T	371|1475;1092	.|ENSP00000320485:N1475T;ENSP00000363267:N1092T	.|ENSP00000320485:N1475T	K|N	+|+	3|2	2|0	ARID1A|ARID1A	26973729|26973729	0.935000|0.935000	0.31712|0.31712	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.698000|1.698000	0.37794|0.37794	1.104000|1.104000	0.41587|0.41587	0.528000|0.528000	0.53228|0.53228	AAA|AAC	.	.		0.572	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		C	27101142	A	C	27101142	3	2	139	1	0	0	0	0	1	0	0	0	913	43	2	5	4494	5	ARID1A	1	27101142	Missense_Mutation	SNP	A	TCGA-DD-A4NR-01A-11D-A30V-10		27101142	222149479	1	21823										
ADCY10	55811	hgsc.bcm.edu	37	chr1	167849404	167849404	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	gatcccacagaagacaatccCactggcaacaccgatggata	8	13	0	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr1:167849404C>T	ENST00000367851.4	-	11	1349	c.1165G>A	c.(1165-1167)Ggg>Agg	p.G389R	ADCY10_ENST00000545172.1_Missense_Mutation_p.G236R|ADCY10_ENST00000367848.1_Missense_Mutation_p.G297R	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	389	Guanylate cyclase 2. {ECO:0000255|PROSITE-ProRule:PRU00099}.				cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						AAGACAATCCCACTGGCAACA	0.498																																					p.G389R		Atlas-SNP	.											.	ADCY10	175	.	0			c.G1165A						.						72	63	66					1																	167849404		2203	4299	6502	SO:0001583	missense	55811	exon11			CAATCCCACTGGC	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.1165G>A	chr1.hg19:g.167849404C>T	ENSP00000356825:p.Gly389Arg	103.0	0.0		144.0	18.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	hg19	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.559390	0.45590	.	.	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	D;D;D	0.97831	-4.56;-4.56;-4.56	5.25	4.34	0.51931	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.000000	0.64402	D	0.000010	D	0.98792	0.9593	H	0.95780	3.72	0.32132	N	0.5866290000000001	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99917	1.1230	9	0.87932	D	0	-19.6578	9.8299	0.40934	0.0:0.9049:0.0:0.0951	.	236;297;389	F5GWS5;Q96PN6-2;Q96PN6	.;.;ADCYA_HUMAN	R	236;389;297	ENSP00000441992:G236R;ENSP00000356825:G389R;ENSP00000356822:G297R	ENSP00000356822:G297R	G	-	1	0	ADCY10	166116028	0.993000	0.37304	0.939000	0.37840	0.054000	0.15201	4.672000	0.61597	1.214000	0.43395	0.655000	0.94253	GGG	.	.		0.498	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		T	167849404	C	T	167849404	3	4	139	1	0	0	0	0	1	0	0	0	293	594	21	3	3759	3	ADCY10	1	167849404	Missense_Mutation	SNP	C	TCGA-DD-A4NR-01A-11D-A30V-10	140748262	167849404	81401217	2	21824										
ASTN1	460	hgsc.bcm.edu	37	chr1	176999968	176999968	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ctttgttgttgatccgctttCtctggctgctggaggtgtga	13	8	1	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr1:176999968C>T	ENST00000367654.3	-	4	1197	c.986G>A	c.(985-987)aGa>aAa	p.R329K	ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Missense_Mutation_p.R329K|MIR488_ENST00000365739.2_RNA|ASTN1_ENST00000361833.2_Missense_Mutation_p.R329K|ASTN1_ENST00000367657.3_Missense_Mutation_p.R329K	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	329					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GATCCGCTTTCTCTGGCTGCT	0.468																																					p.R329K		Atlas-SNP	.											.	ASTN1	314	.	0			c.G986A						.						162	154	157					1																	176999968		2203	4300	6503	SO:0001583	missense	460	exon4			CGCTTTCTCTGGC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.986G>A	chr1.hg19:g.176999968C>T	ENSP00000356626:p.Arg329Lys	79.0	0.0		84.0	15.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	C	18.15	3.560504	0.65538	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.16457	2.34;2.75;2.75;2.34	5.76	5.76	0.90799	.	0.107611	0.64402	D	0.000016	T	0.10637	0.0260	N	0.19112	0.55	0.44603	D	0.997574	P;B;B	0.36837	0.571;0.218;0.218	B;B;B	0.33620	0.167;0.12;0.12	T	0.26430	-1.0103	10	0.17832	T	0.49	-24.8203	12.8744	0.57982	0.0:0.9253:0.0:0.0747	.	329;329;329	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	K	329	ENSP00000356629:R329K;ENSP00000354536:R329K;ENSP00000356626:R329K;ENSP00000395041:R329K	ENSP00000354536:R329K	R	-	2	0	ASTN1	175266591	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.651000	0.67951	2.706000	0.92434	0.655000	0.94253	AGA	.	.		0.468	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		T	176999968	C	T	176999968	3	4	139	1	0	0	0	0	1	0	0	0	1064	913	32	3	2982	3	ASTN1	1	176999968	Missense_Mutation	SNP	C	TCGA-DD-A4NR-01A-11D-A30V-10	9150564	176999968	72250653	3	21825										
C1orf14	81626	hgsc.bcm.edu	37	chr1	182922155	182922155	+	Frame_Shift_Del	DEL	G	G	-													0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	atcgcggtgcccttcagggtGgtcgcggccgccgtgtcccc							TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr1:182922155delG	ENST00000367547.3	-	1	350	c.114delC	c.(112-114)accfs	p.T39fs	SHCBP1L_ENST00000423786.1_5'Flank|SHCBP1L_ENST00000488956.1_5'UTR	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	111										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						CCTTCAGGGTGGTCGCGGCCG	0.736																																					p.T39fs		Atlas-INDEL	.											.	SHCBP1L	64	.	0			c.115delA						.						3	3	3					1																	182922155		1775	3719	5494	SO:0001589	frameshift_variant	81626	exon1			.	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.114delC	chr1.hg19:g.182922155delG	ENSP00000356518:p.Thr39fs	45.0	0.0		63.0	14.0	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Frame_Shift_Del	DEL	ENST00000367547.3	hg19	CCDS30955.1																																																																																			.	.		0.736	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		-	182922155	G	-	182922155	7	5	139	1	0	1	0	1	0	0	0	0	2002	1335	47	0	1887	0	C1orf14	1	182922155	Frame_Shift_Del	DEL	G	TCGA-DD-A4NR-01A-11D-A30V-10	5922187	182922155	66328466	4	21826										
C1orf107	27042	hgsc.bcm.edu	37	chr1	210015748	210015748	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	gggcccttcaggatgcccagAtcaactcagtgttcaacaag	10	12	4	1			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr1:210015748A>G	ENST00000491415.2	+	9	1681	c.1624A>G	c.(1624-1626)Atc>Gtc	p.I542V		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	542					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						GGATGCCCAGATCAACTCAGT	0.478																																					p.I542V		Atlas-SNP	.											.	DIEXF	97	.	0			c.A1624G						.						138	138	138					1																	210015748		2203	4300	6503	SO:0001583	missense	27042	exon9			GCCCAGATCAACT	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.1624A>G	chr1.hg19:g.210015748A>G	ENSP00000419005:p.Ile542Val	53.0	0.0		115.0	15.0	NM_014388	O75992|Q4VY00|Q63HL9	Missense_Mutation	SNP	ENST00000491415.2	hg19	CCDS1493.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.583532	0.46006	.	.	ENSG00000117597	ENST00000491415	T	0.50001	0.76	6.17	2.68	0.31781	.	0.084250	0.85682	N	0.000000	T	0.48187	0.1486	M	0.80422	2.495	0.49798	D	0.999822	B	0.25105	0.118	B	0.27796	0.083	T	0.43750	-0.9372	10	0.39692	T	0.17	-23.2262	9.5562	0.39339	0.804:0.0:0.196:0.0	.	542	Q68CQ4	DIEXF_HUMAN	V	542	ENSP00000419005:I542V	ENSP00000419005:I542V	I	+	1	0	DIEXF	208082371	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.491000	0.53252	0.566000	0.29273	-0.290000	0.09829	ATC	.	.		0.478	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		G	210015748	A	G	210015748	3	3	139	1	0	0	0	0	1	0	0	0	1983	333	12	2	1658	2	C1orf107	1	210015748	Missense_Mutation	SNP	A	TCGA-DD-A4NR-01A-11D-A30V-10	27093593	210015748	39234873	5	21827										
SLC4A5	57835	hgsc.bcm.edu	37	chr2	74482906	74482906	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	tttcaatggctctcacctggTggggacaggcacctcggtca	12	12	3	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr2:74482906T>A	ENST00000377634.4	-	13	1420	c.1021A>T	c.(1021-1023)Acc>Tcc	p.T341S	SLC4A5_ENST00000346834.4_Missense_Mutation_p.T341S|SLC4A5_ENST00000483195.1_5'UTR|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Missense_Mutation_p.T341S|SLC4A5_ENST00000358683.4_Missense_Mutation_p.T277S|SLC4A5_ENST00000423644.1_Missense_Mutation_p.T341S|SLC4A5_ENST00000394019.2_Missense_Mutation_p.T341S|SLC4A5_ENST00000357822.5_Missense_Mutation_p.T341S|SLC4A5_ENST00000359484.4_Missense_Mutation_p.T277S					solute carrier family 4 (sodium bicarbonate cotransporter), member 5											breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						TCTCACCTGGTGGGGACAGGC	0.592																																					p.T341S		Atlas-SNP	.											.	SLC4A5	215	.	0			c.A1021T						.						100	86	91					2																	74482906		2203	4300	6503	SO:0001583	missense	57835	exon8			ACCTGGTGGGGAC	AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"Solute carriers"	18168	protein-coding gene	gene with protein product		606757	"solute carrier family 4, sodium bicarbonate cotransporter, member 5"			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.1021A>T	chr2.hg19:g.74482906T>A	ENSP00000366861:p.Thr341Ser	32.0	0.0		38.0	9.0	NM_021196		Missense_Mutation	SNP	ENST00000377634.4	hg19	CCDS1936.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.583538	0.65992	.	.	ENSG00000188687	ENST00000394019;ENST00000451608;ENST00000346834;ENST00000359484;ENST00000423644;ENST00000358683;ENST00000357822;ENST00000377632;ENST00000377634;ENST00000425249	T;T;T;T;T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37	5.1	5.1	0.69264	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	T	0.78817	0.4343	L	0.52126	1.63	0.58432	D	0.999997	B;B;B;B;B	0.26445	0.126;0.149;0.022;0.073;0.105	B;B;B;B;B	0.37144	0.052;0.21;0.119;0.242;0.199	T	0.75263	-0.3379	10	0.33141	T	0.24	.	12.8856	0.58042	0.0:0.0:0.0:1.0	.	341;341;277;341;341	Q9BY07-4;E7EQT3;Q9BY07-7;Q9BY07;Q9BY07-3	.;.;.;S4A5_HUMAN;.	S	341;341;341;277;341;277;341;341;341;341	ENSP00000377587:T341S;ENSP00000251768:T341S;ENSP00000352461:T277S;ENSP00000395804:T341S;ENSP00000351513:T277S;ENSP00000350475:T341S;ENSP00000366859:T341S;ENSP00000366861:T341S;ENSP00000405678:T341S	ENSP00000251768:T341S	T	-	1	0	SLC4A5	74336414	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.868000	0.87116	2.144000	0.66660	0.533000	0.62120	ACC	.	.		0.592	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3			A	74482906	T	A	74482906	3	1	139	1	0	0	0	0	1	0	0	0	14672	1696	59	4	2468	4	SLC4A5	2	74482906	Missense_Mutation	SNP	T	TCGA-DD-A4NR-01A-11D-A30V-10		74482906	168716467	6	21828										
ACVR2B	93	hgsc.bcm.edu	37	chr3	38519668	38519668	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	cccgacagcccccaccctgcTcacggtgctggcctactcac	8	21	2	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr3:38519668T>C	ENST00000352511.4	+	4	879	c.407T>C	c.(406-408)cTc>cCc	p.L136P		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	136					activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		CCCACCCTGCTCACGGTGCTG	0.632																																					p.L136P		Atlas-SNP	.											.	ACVR2B	88	.	0			c.T407C						.						49	49	49					3																	38519668		2203	4300	6503	SO:0001583	missense	93	exon4			CCCTGCTCACGGT	X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	ENST00000352511.4:c.407T>C	chr3.hg19:g.38519668T>C	ENSP00000340361:p.Leu136Pro	28.0	0.0		42.0	8.0	NM_001106	Q4VAV0	Missense_Mutation	SNP	ENST00000352511.4	hg19	CCDS2679.1	.	.	.	.	.	.	.	.	.	.	T	19.87	3.906625	0.72868	.	.	ENSG00000114739	ENST00000352511	D	0.84873	-1.91	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	D	0.83667	0.5304	M	0.76574	2.34	0.80722	D	1	B	0.28552	0.215	B	0.22601	0.04	T	0.81953	-0.0697	10	0.36615	T	0.2	.	14.2824	0.66221	0.0:0.0:0.0:1.0	.	136	Q13705	AVR2B_HUMAN	P	136	ENSP00000340361:L136P	ENSP00000340361:L136P	L	+	2	0	ACVR2B	38494672	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	6.096000	0.71446	1.788000	0.52465	0.379000	0.24179	CTC	.	.		0.632	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106		C	38519668	T	C	38519668	3	2	139	1	0	0	0	0	1	0	0	0	224	1551	54	2	421	2	ACVR2B	3	38519668	Missense_Mutation	SNP	T	TCGA-DD-A4NR-01A-11D-A30V-10		38519668	159502762	7	21829										
AADAC	13	hgsc.bcm.edu	37	chr3	151545468	151545468	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ccgtcatatcaagaaaattcAaattttctatttctatccaa	2	9	5	1			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr3:151545468A>G	ENST00000232892.7	+	5	834	c.708A>G	c.(706-708)tcA>tcG	p.S236S	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	236					positive regulation of triglyceride catabolic process (GO:0010898)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|deacetylase activity (GO:0019213)|lipase activity (GO:0016298)|serine hydrolase activity (GO:0017171)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(5)|skin(2)	19		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			AAGAAAATTCAAATTTTCTAT	0.363																																					p.S236S	Ovarian(30;839 841 2699 32801 46334)	Atlas-SNP	.											.	AADAC	49	.	0			c.A708G						.						66	68	67					3																	151545468		2203	4299	6502	SO:0001819	synonymous_variant	13	exon5			AAATTCAAATTTT	L32179	CCDS33877.1	3q25.1	2014-03-18	2012-07-13		ENSG00000114771	ENSG00000114771	3.1.1.3		17	protein-coding gene	gene with protein product		600338	"arylacetamide deacetylase (esterase)"			8063807	Standard	XM_005247103		Approved	DAC, CES5A1	uc003eze.3	P22760	OTTHUMG00000159876	ENST00000232892.7:c.708A>G	chr3.hg19:g.151545468A>G		111.0	0.0		122.0	21.0	NM_001086	A8K3L3|D3DNJ6|Q8N1A9	Silent	SNP	ENST00000232892.7	hg19	CCDS33877.1																																																																																			.	.		0.363	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086		G	151545468	A	G	151545468	2	3	139	1	0	0	0	0	0	0	0	1	10	117	5	2		2	AADAC	3	151545468	Silent	SNP	A	TCGA-DD-A4NR-01A-11D-A30V-10	113025800	151545468	46476962	8	21830										
CDS1	1040	hgsc.bcm.edu	37	chr4	85540553	85540553	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	tttttaaattataggtacttTctattgtgtgtaaactactt	5	4	1	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr4:85540553T>C	ENST00000295887.5	+	5	870	c.447T>C	c.(445-447)ttT>ttC	p.F149F		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		ATAGGTACTTTCTATTGTGTG	0.318																																					p.F149F		Atlas-SNP	.											.	CDS1	58	.	0			c.T447C						.						71	75	74					4																	85540553		2201	4294	6495	SO:0001819	synonymous_variant	1040	exon5			GTACTTTCTATTG	U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.447T>C	chr4.hg19:g.85540553T>C		93.0	0.0		106.0	13.0	NM_001263	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000295887.5	hg19	CCDS3608.1																																																																																			.	.		0.318	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2			C	85540553	T	C	85540553	2	2	139	1	0	0	0	0	0	0	0	1	3179	1780	62	2		2	CDS1	4	85540553	Silent	SNP	T	TCGA-DD-A4NR-01A-11D-A30V-10		85540553	105613723	9	21831										
SEC24A	10802	hgsc.bcm.edu	37	chr5	133997208	133997208	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	aactgtatctggaaatacaaGtttaaccacaaatcatcaat	4	8	3	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr5:133997208G>T	ENST00000398844.2	+	2	785	c.497G>T	c.(496-498)aGt>aTt	p.S166I	SEC24A_ENST00000322887.4_Missense_Mutation_p.S166I	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	166	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGAAATACAAGTTTAACCACA	0.368																																					p.S166I		Atlas-SNP	.											.	SEC24A	77	.	0			c.G497T						.						96	92	93					5																	133997208		1938	4141	6079	SO:0001583	missense	10802	exon2			ATACAAGTTTAAC	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.497G>T	chr5.hg19:g.133997208G>T	ENSP00000381823:p.Ser166Ile	93.0	0.0		113.0	15.0	NM_001252231	A8MVW3|Q8WUV2|Q96GP7	Missense_Mutation	SNP	ENST00000398844.2	hg19	CCDS43363.1	.	.	.	.	.	.	.	.	.	.	G	7.939	0.742462	0.15642	.	.	ENSG00000113615	ENST00000398844;ENST00000322887	D;D	0.97232	-4.3;-4.3	5.55	0.504	0.16946	.	1.193380	0.05767	N	0.605952	D	0.91851	0.7421	N	0.22421	0.69	0.09310	N	1	B	0.15473	0.013	B	0.13407	0.009	T	0.82147	-0.0601	10	0.37606	T	0.19	-0.1978	1.1954	0.01874	0.475:0.143:0.2437:0.1383	.	166	O95486	SC24A_HUMAN	I	166	ENSP00000381823:S166I;ENSP00000321749:S166I	ENSP00000321749:S166I	S	+	2	0	SEC24A	134025107	0.995000	0.38212	0.258000	0.24420	0.328000	0.28507	1.315000	0.33608	0.062000	0.16340	0.655000	0.94253	AGT	.	.		0.368	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			T	133997208	G	T	133997208	3	4	139	1	0	0	0	0	1	0	0	0	14009	1029	36	3	503	3	SEC24A	5	133997208	Missense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10		133997208	46918052	10	21832										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140792839	140792839	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ttccatgggaggctggagccCggcagatctcctactcaatt	11	12	2	1			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr5:140792839C>T	ENST00000398610.2	+	1	97	c.97C>T	c.(97-99)Cgg>Tgg	p.R33W	PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	33	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCTGGAGCCCGGCAGATCTC	0.567											OREG0016862	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R33W		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.C97T						.						45	51	49					5																	140792839		1897	4149	6046	SO:0001583	missense	56106	exon1			GGAGCCCGGCAGA		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.97C>T	chr5.hg19:g.140792839C>T	ENSP00000381611:p.Arg33Trp	64.0	0.0	1659	81.0	17.0	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	hg19	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	c	8.061	0.768209	0.15983	.	.	ENSG00000253846	ENST00000398610	T	0.49139	0.79	5.49	1.19	0.21007	.	.	.	.	.	T	0.40322	0.1112	L	0.54323	1.7	0.09310	N	1	B;B	0.18741	0.016;0.03	B;B	0.20955	0.013;0.032	T	0.41822	-0.9487	9	0.72032	D	0.01	.	6.0171	0.19608	0.1108:0.3842:0.426:0.079	.	33;33	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	W	33	ENSP00000381611:R33W	ENSP00000381611:R33W	R	+	1	2	PCDHGA10	140773023	0.636000	0.27207	0.876000	0.34364	0.324000	0.28378	0.851000	0.27751	0.640000	0.30582	0.460000	0.39030	CGG	.	.		0.567	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		T	140792839	C	T	140792839	3	4	139	1	0	0	0	0	1	0	0	0	11560	643	23	1	99	1	PCDHGA10	5	140792839	Missense_Mutation	SNP	C	TCGA-DD-A4NR-01A-11D-A30V-10	6795631	140792839	40122421	11	21833										
GEMIN5	25929	hgsc.bcm.edu	37	chr5	154311018	154311018	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	aaaagaaagatcaatcttacCtcggcctctagaacagctcc	6	12	3	3			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr5:154311018C>T	ENST00000285873.7	-	5	856	c.781G>A	c.(781-783)Ggg>Agg	p.G261R		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	261					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCAATCTTACCTCGGCCTCTA	0.433																																					p.G261R		Atlas-SNP	.											GEMIN5,NS,carcinoma,0,1	GEMIN5	120	.	0			c.G781A						.						162	142	149					5																	154311018		2203	4300	6503	SO:0001630	splice_region_variant	25929	exon5			TCTTACCTCGGCC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.781+1G>A	chr5.hg19:g.154311018C>T		53.0	0.0		91.0	27.0	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	hg19	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103299	0.76983	.	.	ENSG00000082516	ENST00000285873	T	0.48201	0.82	5.28	5.28	0.74379	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.190178	0.45126	D	0.000383	T	0.51193	0.1660	L	0.44542	1.39	0.53005	D	0.999965	D;D	0.60575	0.988;0.988	P;P	0.54026	0.74;0.74	T	0.45687	-0.9244	9	.	.	.	-9.4696	12.7256	0.57168	0.0:0.9148:0.0:0.0852	.	260;261	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	R	261	ENSP00000285873:G261R	.	G	-	1	0	GEMIN5	154291211	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.939000	0.56591	2.469000	0.83416	0.655000	0.94253	GGG	.	.		0.433	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1		Missense_Mutation	T	154311018	C	T	154311018	5	4	139	1	0	0	0	0	0	0	1	0	6339	695	24	3	3841	3	GEMIN5	5	154311018	Splice_Site	SNP	C	TCGA-DD-A4NR-01A-11D-A30V-10	13518179	154311018	26604242	12	21834										
JARID2	3720	hgsc.bcm.edu	37	chr6	15452356	15452356	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	tactcagatatcagacctctCtaaaaggaagcctaagacag	7	10	3	3			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr6:15452356C>G	ENST00000341776.2	+	4	687	c.443C>G	c.(442-444)tCt>tGt	p.S148C	JARID2_ENST00000397311.3_5'UTR|JARID2_ENST00000541660.1_Missense_Mutation_p.S110C	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	148					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				TCAGACCTCTCTAAAAGGAAG	0.473																																					p.S148C		Atlas-SNP	.											.	JARID2	135	.	0			c.C443G						.						99	94	96					6																	15452356		2203	4300	6503	SO:0001583	missense	3720	exon4			ACCTCTCTAAAAG	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.443C>G	chr6.hg19:g.15452356C>G	ENSP00000341280:p.Ser148Cys	55.0	0.0		71.0	21.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	hg19	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.773059	0.90108	.	.	ENSG00000008083	ENST00000341776;ENST00000541660	T;T	0.38240	1.15;1.15	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.47021	0.1423	L	0.42245	1.32	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.992	T	0.41963	-0.9479	10	0.52906	T	0.07	-7.0486	19.1821	0.93628	0.0:1.0:0.0:0.0	.	110;148	F5H590;Q92833	.;JARD2_HUMAN	C	148;110	ENSP00000341280:S148C;ENSP00000444623:S110C	ENSP00000341280:S148C	S	+	2	0	JARID2	15560335	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.294000	0.78760	2.513000	0.84729	0.655000	0.94253	TCT	.	.		0.473	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		G	15452356	C	G	15452356	3	3	139	1	0	0	0	0	1	0	0	0	7954	913	32	4	457	4	JARID2	6	15452356	Missense_Mutation	SNP	C	TCGA-DD-A4NR-01A-11D-A30V-10		15452356	155662711	13	21835										
RUNX2	860	hgsc.bcm.edu	37	chr6	45390432	45390432	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	tgcgcaacagcagcagcaacAgcagcagcagcaacagcagc	11	14	0	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr6:45390432A>C	ENST00000371438.1	+	2	519	c.161A>C	c.(160-162)cAg>cCg	p.Q54P	RUNX2_ENST00000371432.3_Missense_Mutation_p.Q40P|RUNX2_ENST00000465038.2_Missense_Mutation_p.Q54P|RUNX2_ENST00000359524.5_Missense_Mutation_p.Q40P|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000541979.1_Missense_Mutation_p.Q122P|RUNX2_ENST00000352853.5_Missense_Mutation_p.Q122P|RUNX2_ENST00000576263.1_Missense_Mutation_p.Q54P|RUNX2_ENST00000371436.6_Missense_Mutation_p.Q54P	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	54	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						cagcagcaacagcagcagcag	0.731																																					p.Q54P		Atlas-SNP	.											.	RUNX2	128	.	0			c.A161C						.						20	28	25					6																	45390432		1745	3566	5311	SO:0001583	missense	860	exon3			AGCAACAGCAGCA	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.161A>C	chr6.hg19:g.45390432A>C	ENSP00000360493:p.Gln54Pro	58.0	0.0		73.0	11.0	NM_001024630	O14614|O14615|O95181	Missense_Mutation	SNP	ENST00000371438.1	hg19	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	A	6.074	0.382044	0.11524	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	T;T;T;T;T;T;T	0.50277	0.86;1.08;1.08;0.86;0.75;0.75;0.75	1.8	1.8	0.24995	.	0.397823	0.18432	N	0.141408	T	0.11922	0.0290	N	0.19112	0.55	0.37120	D	0.900762	B;B;B	0.29909	0.027;0.046;0.261	B;B;B	0.17979	0.02;0.009;0.009	T	0.05370	-1.0889	10	0.27082	T	0.32	.	7.3175	0.26509	1.0:0.0:0.0:0.0	.	122;54;40	F6RGB9;Q13950;Q13950-2	.;RUNX2_HUMAN;.	P	54;122;122;54;54;40;40	ENSP00000420707:Q54P;ENSP00000319087:Q122P;ENSP00000446290:Q122P;ENSP00000360493:Q54P;ENSP00000360491:Q54P;ENSP00000352514:Q40P;ENSP00000360486:Q40P	ENSP00000319087:Q122P	Q	+	2	0	RUNX2	45498410	0.814000	0.29104	1.000000	0.80357	0.899000	0.52679	0.000000	0.12993	1.094000	0.41399	0.334000	0.21626	CAG	.	.		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		C	45390432	A	C	45390432	3	2	139	1	0	0	0	0	1	0	0	0	13763	188	7	5	183	5	RUNX2	6	45390432	Missense_Mutation	SNP	A	TCGA-DD-A4NR-01A-11D-A30V-10	29938076	45390432	125724635	14	21836										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76023702	76023702	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ggtgagctcagacccttttcGtgaccttcctcttgttattt	8	11	2	3			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr6:76023702G>A	ENST00000237172.7	-	5	2176	c.1846C>T	c.(1846-1848)Cga>Tga	p.R616*	FILIP1_ENST00000393004.2_Nonsense_Mutation_p.R616*|FILIP1_ENST00000370020.1_Nonsense_Mutation_p.R517*|FILIP1_ENST00000498523.1_5'UTR	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	616								p.R616*(1)		breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GACCCTTTTCGTGACCTTCCT	0.398																																					p.R616X		Atlas-SNP	.											FILIP1,rectum,carcinoma,0,1	FILIP1	173	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1846T						.						264	273	270					6																	76023702		2203	4300	6503	SO:0001587	stop_gained	27145	exon5			CTTTTCGTGACCT	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.1846C>T	chr6.hg19:g.76023702G>A	ENSP00000237172:p.Arg616*	73.0	0.0		97.0	4.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Nonsense_Mutation	SNP	ENST00000237172.7	hg19	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	G	37	6.036074	0.97221	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	.	.	.	6.11	4.29	0.51040	.	0.249082	0.40064	N	0.001184	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-5.9393	8.1643	0.31217	0.076:0.0:0.4741:0.4499	.	.	.	.	X	616;616;517	.	ENSP00000237172:R616X	R	-	1	2	FILIP1	76080422	0.025000	0.19082	0.647000	0.29507	0.410000	0.31052	1.616000	0.36933	0.861000	0.35504	0.655000	0.94253	CGA	.	.		0.398	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76023702	G	A	76023702	4	1	139	1	0	0	0	0	0	1	0	0	5902	1153	40	1	1803	1	FILIP1	6	76023702	Nonsense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10	30633270	76023702	95091365	15	21837										
BMPER	168667	hgsc.bcm.edu	37	chr7	34014331	34014331	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	caggctgtgtgtttgagggtGtgcagtatcaagaaggggag	18	4	1	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr7:34014331G>A	ENST00000297161.2	+	7	885	c.511G>A	c.(511-513)Gtg>Atg	p.V171M	BMPER_ENST00000426693.1_Missense_Mutation_p.V171M	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	171	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GTTTGAGGGTGTGCAGTATCA	0.478																																					p.V171M		Atlas-SNP	.											.	BMPER	131	.	0			c.G511A						.						292	257	269					7																	34014331		2203	4300	6503	SO:0001583	missense	168667	exon7			GAGGGTGTGCAGT		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"crossveinless-2"	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.511G>A	chr7.hg19:g.34014331G>A	ENSP00000297161:p.Val171Met	127.0	0.0		129.0	14.0	NM_133468	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	hg19	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.673789	0.29693	.	.	ENSG00000164619	ENST00000297161;ENST00000426693	T;T	0.72835	-0.69;-0.69	5.33	3.52	0.40303	von Willebrand factor, type C (3);	0.416166	0.23928	N	0.043176	T	0.52354	0.1729	L	0.28504	0.86	0.25377	N	0.988647	B	0.12013	0.005	B	0.13407	0.009	T	0.43814	-0.9368	10	0.48119	T	0.1	.	2.7243	0.05209	0.1587:0.1467:0.5429:0.1517	.	171	Q8N8U9	BMPER_HUMAN	M	171	ENSP00000297161:V171M;ENSP00000393950:V171M	ENSP00000297161:V171M	V	+	1	0	BMPER	33980856	0.997000	0.39634	1.000000	0.80357	0.632000	0.37999	1.595000	0.36708	0.725000	0.32318	0.655000	0.94253	GTG	.	.		0.478	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		A	34014331	G	A	34014331	3	1	139	1	0	0	0	0	1	0	0	0	1468	1377	48	3	533	3	BMPER	7	34014331	Missense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10		34014331	125124332	16	21838										
PUS7	54517	hgsc.bcm.edu	37	chr7	105121549	105121549	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	gttccaaatctttgcattccAtagtagttaataaatccaat	4	8	1	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr7:105121549A>G	ENST00000356362.2	-	9	1339	c.1125T>C	c.(1123-1125)taT>taC	p.Y375Y	PUS7_ENST00000469408.1_Silent_p.Y375Y	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	375	TRUD. {ECO:0000255|PROSITE- ProRule:PRU00342}.				pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|pancreas(1)|skin(1)	23						TTTGCATTCCATAGTAGTTAA	0.363																																					p.Y375Y	Colon(138;2387 3051 17860)	Atlas-SNP	.											.	PUS7	59	.	0			c.T1125C						.						139	132	134					7																	105121549		2203	4300	6503	SO:0001819	synonymous_variant	54517	exon9			CATTCCATAGTAG	AK128629	CCDS34725.1	7q22.3	2014-02-14	2014-02-14		ENSG00000091127	ENSG00000091127			26033	protein-coding gene	gene with protein product			"pseudouridylate synthase 7 homolog (S. cerevisiae)"			11572484	Standard	NM_019042		Approved	FLJ20485	uc003vcx.3	Q96PZ0	OTTHUMG00000157399	ENST00000356362.2:c.1125T>C	chr7.hg19:g.105121549A>G		98.0	0.0		122.0	24.0	NM_019042	Q75MG4|Q9NX19	Silent	SNP	ENST00000356362.2	hg19	CCDS34725.1																																																																																			.	.		0.363	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042		G	105121549	A	G	105121549	2	3	139	1	0	0	0	0	0	0	0	1	12848	224	8	2		2	PUS7	7	105121549	Silent	SNP	A	TCGA-DD-A4NR-01A-11D-A30V-10	71107218	105121549	54017114	17	21839										
XKR6	286046	hgsc.bcm.edu	37	chr8	10782237	10782237	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	gaaggtctccaggaggcgcaGcatgttgacgtctgcatatt	13	9	2	1			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr8:10782237G>T	ENST00000416569.2	-	2	894	c.868C>A	c.(868-870)Ctg>Atg	p.L290M	XKR6_ENST00000304437.2_Missense_Mutation_p.L11M	NM_173683.3	NP_775954.2	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related family, member 6	290						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(8)|ovary(2)|prostate(1)|skin(3)	31				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		AGGAGGCGCAGCATGTTGACG	0.577																																					p.L290M		Atlas-SNP	.											.	XKR6	85	.	0			c.C868A						.						117	106	110					8																	10782237		2203	4300	6503	SO:0001583	missense	286046	exon2			GGCGCAGCATGTT	BC024146	CCDS5978.2	8p23.1	2009-05-27	2006-01-12	2005-07-28	ENSG00000171044	ENSG00000171044			27806	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 7", "chromosome 8 open reading frame 21", "X Kell blood group precursor-related family, member 6", "chromosome 8 open reading frame 5"	C8orf7, C8orf21, C8orf5			Standard	NM_173683		Approved		uc003wtk.1	Q5GH73	OTTHUMG00000129351	ENST00000416569.2:c.868C>A	chr8.hg19:g.10782237G>T	ENSP00000416707:p.Leu290Met	27.0	0.0		44.0	10.0	NM_173683	Q8TBA0	Missense_Mutation	SNP	ENST00000416569.2	hg19	CCDS5978.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	18.26|18.26	3.584910|3.584910	0.65992|0.65992	.|.	.|.	ENSG00000171044|ENSG00000171044	ENST00000382461|ENST00000304437;ENST00000416569	.|T;T	.|0.72394	.|-0.65;-0.65	4.84|4.84	0.119|0.119	0.14685|0.14685	.|.	.|0.000000	.|0.64402	.|D	.|0.000003	.|D	.|0.84092	.|0.5396	M|M	0.88450|0.88450	2.955|2.955	0.44042|0.44042	D|D	0.996774|0.996774	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	.|D	.|0.85008	.|0.0904	.|10	.|0.56958	.|D	.|0.05	-13.5137|-13.5137	13.0399|13.0399	0.58893|0.58893	0.2207:0.0:0.7793:0.0|0.2207:0.0:0.7793:0.0	.|.	.|290	.|Q5GH73	.|XKR6_HUMAN	X|M	66|11;290	.|ENSP00000307120:L11M;ENSP00000416707:L290M	.|ENSP00000307120:L11M	C|L	-|-	3|1	2|2	XKR6|XKR6	10819647|10819647	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.919000|1.919000	0.40015|0.40015	0.105000|0.105000	0.17753|0.17753	0.457000|0.457000	0.33378|0.33378	TGC|CTG	.	.		0.577	XKR6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383958.1	NM_173683		T	10782237	G	T	10782237	3	4	139	1	0	0	0	0	1	0	0	0	17450	962	34	3	1065	3	XKR6	8	10782237	Missense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10		10782237	135581785	18	21840										
CSMD3	114788	hgsc.bcm.edu	37	chr8	114031312	114031312	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ataccttgatagggagcactAaatccacggtatcgatgatt	9	8	0	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr8:114031312A>G	ENST00000297405.5	-	6	1258	c.1014T>C	c.(1012-1014)ttT>ttC	p.F338F	CSMD3_ENST00000343508.3_Silent_p.F298F|CSMD3_ENST00000455883.2_Silent_p.F338F|CSMD3_ENST00000352409.3_Silent_p.F338F	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	338	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F338fs*11(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AGGGAGCACTAAATCCACGGT	0.358										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.F338F		Atlas-SNP	.											.,1	CSMD3	2325	.	1	Deletion - Frameshift(1)	liver(1)	c.T1014C						.						204	181	189					8																	114031312		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon6			AGCACTAAATCCA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1014T>C	chr8.hg19:g.114031312A>G		63.0	0.0		97.0	6.0	NM_052900	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.358	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	114031312	A	G	114031312	2	3	139	1	0	0	0	0	0	0	0	1	3948	359	13	2		2	CSMD3	8	114031312	Silent	SNP	A	TCGA-DD-A4NR-01A-11D-A30V-10	103249075	114031312	32332710	19	21841										
ITIH2	3698	hgsc.bcm.edu	37	chr10	7765447	7765447	+	Frame_Shift_Del	DEL	C	C	-													0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	attttgtccacttctttgctCctgacaacctggacccaatt							TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr10:7765447delC	ENST00000358415.4	+	9	1067	c.901delC	c.(901-903)cctfs	p.P301fs	ITIH2_ENST00000379587.4_Frame_Shift_Del_p.P290fs	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	301					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CTTCTTTGCTCCTGACAACCT	0.413																																					p.A300fs		Pindel	.											.	ITIH2	144	.	0			c.900delT						.						154	135	141					10																	7765447		2203	4300	6503	SO:0001589	frameshift_variant	3698	exon9			.	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.901delC	chr10.hg19:g.7765447delC	ENSP00000351190:p.Pro301fs	105.0	0.0		147.0	14.0	NM_002216	Q14659|Q15484|Q5T986	Frame_Shift_Del	DEL	ENST00000358415.4	hg19	CCDS31141.1																																																																																			.	.		0.413	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		-	7765447	C	-	7765447	7	5	139	1	0	1	0	1	0	0	0	0	7913	855	30	0	935	0	ITIH2	10	7765447	Frame_Shift_Del	DEL	C	TCGA-DD-A4NR-01A-11D-A30V-10		7765447	127769300	20	21842										
CAMK1D	57118	hgsc.bcm.edu	37	chr10	12391854	12391854	+	Frame_Shift_Del	DEL	A	A	-													0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	gcgagagcagctcctcctggAaaaagcaagctgaagacatc							TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr10:12391854delA	ENST00000378847.3	+	1	374	c.37delA	c.(37-39)aaafs	p.K14fs	CAMK1D_ENST00000487696.1_3'UTR|CAMK1D_ENST00000378845.1_Frame_Shift_Del_p.K14fs	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	14					inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		CTCCTCCTGGAAAAAGCAAGC	0.701																																					p.W12X		Pindel	.											.	CAMK1D	99	.	0			c.36delG						.						30	31	30					10																	12391854		2201	4300	6501	SO:0001589	frameshift_variant	57118	exon1			.	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.37delA	chr10.hg19:g.12391854delA	ENSP00000368124:p.Lys14fs	144.0	0.0		223.0	26.0	NM_153498	B0YIY0|Q9HD31	Frame_Shift_Del	DEL	ENST00000378847.3	hg19	CCDS7091.1																																																																																			.	.		0.701	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		-	12391854	A	-	12391854	7	5	139	1	0	1	0	1	0	0	0	0	2599	247	9	0	39	0	CAMK1D	10	12391854	Frame_Shift_Del	DEL	A	TCGA-DD-A4NR-01A-11D-A30V-10	4626407	12391854	123142893	21	21843										
WEE1	7465	hgsc.bcm.edu	37	chr11	9597784	9597784	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	acattttttttagttcctgtGgtgaagacatggaagccagt	10	6	0	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr11:9597784G>A	ENST00000450114.2	+	3	1043	c.790G>A	c.(790-792)Ggt>Agt	p.G264S	WEE1_ENST00000299613.6_Missense_Mutation_p.G50S|snoU13_ENST00000458785.1_RNA	NM_003390.3	NP_003381.1	P30291	WEE1_HUMAN	WEE1 G2 checkpoint kinase	264					blood coagulation (GO:0007596)|establishment of cell polarity (GO:0030010)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neuron projection morphogenesis (GO:0048812)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	23				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		tagttcctgtggtgaagacat	0.289																																					p.G264S		Atlas-SNP	.											.	WEE1	54	.	0			c.G790A						.						57	67	63					11																	9597784		1327	2308	3635	SO:0001583	missense	7465	exon3			TCCTGTGGTGAAG	X62048	CCDS7800.1, CCDS44536.1	11p15.4	2013-10-21	2013-10-21		ENSG00000166483	ENSG00000166483			12761	protein-coding gene	gene with protein product		193525	"wee1+ (S. pombe) homolog", "WEE1 homolog (S. pombe)"			1840647	Standard	NM_003390		Approved		uc001mhs.3	P30291	OTTHUMG00000165863	ENST00000450114.2:c.790G>A	chr11.hg19:g.9597784G>A	ENSP00000402084:p.Gly264Ser	143.0	0.0		149.0	21.0	NM_003390	B3KVE1|D3DQV0	Missense_Mutation	SNP	ENST00000450114.2	hg19	CCDS7800.1	.	.	.	.	.	.	.	.	.	.	G	3.025	-0.200901	0.06219	.	.	ENSG00000166483	ENST00000450114;ENST00000299613	T;T	0.53640	0.74;0.61	3.63	2.67	0.31697	.	0.158692	0.56097	N	0.000031	T	0.34542	0.0901	L	0.46157	1.445	0.80722	D	1	B;B	0.17268	0.0;0.021	B;B	0.17979	0.002;0.02	T	0.08006	-1.0743	10	0.16420	T	0.52	-9.2048	6.8148	0.23824	0.0959:0.0:0.7139:0.1902	.	72;264	Q6MZL0;P30291	.;WEE1_HUMAN	S	264;50	ENSP00000402084:G264S;ENSP00000299613:G50S	ENSP00000299613:G50S	G	+	1	0	WEE1	9554360	1.000000	0.71417	0.992000	0.48379	0.240000	0.25518	2.219000	0.42899	0.442000	0.26555	-0.397000	0.06425	GGT	.	.		0.289	WEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386757.1	NM_003390		A	9597784	G	A	9597784	3	1	139	1	0	0	0	0	1	0	0	0	17359	1348	47	3	800	3	WEE1	11	9597784	Missense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10		9597784	125408732	22	21844										
PITPNM1	9600	hgsc.bcm.edu	37	chr11	67261260	67261260	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ctgaagaccacagcctccgtGccgcgggccaccacagtcag	11	17	1	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr11:67261260G>T	ENST00000534749.1	-	20	3245	c.3057C>A	c.(3055-3057)ggC>ggA	p.G1019G	PITPNM1_ENST00000526450.1_5'UTR|PITPNM1_ENST00000436757.2_Silent_p.G1018G|PITPNM1_ENST00000356404.3_Silent_p.G1019G			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	1019					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						CAGCCTCCGTGCCGCGGGCCA	0.716																																					p.G1019G	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.C3057A						.						15	15	15					11																	67261260		2089	4084	6173	SO:0001819	synonymous_variant	9600	exon21			CTCCGTGCCGCGG	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"PYK2 N-terminal domain-interacting receptor 2", "retinal degeneration B alpha 1"	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.3057C>A	chr11.hg19:g.67261260G>T		58.0	0.0		59.0	9.0	NM_004910	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Silent	SNP	ENST00000534749.1	hg19	CCDS31620.1																																																																																			.	.		0.716	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		T	67261260	G	T	67261260	2	4	139	1	0	0	0	0	0	0	0	1	11959	1306	46	3		3	PITPNM1	11	67261260	Silent	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10	57663476	67261260	67745256	23	21845										
OVCH1	341350	hgsc.bcm.edu	37	chr12	29598311	29598311	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ggactcatgaaagtcattgaGtaaagtcttcttccatgtaa	8	7	4	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr12:29598311G>T	ENST00000318184.5	-	23	2780	c.2781C>A	c.(2779-2781)taC>taA	p.Y927*	OVCH1-AS1_ENST00000549411.1_Intron|OVCH1-AS1_ENST00000551108.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	927	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AAGTCATTGAGTAAAGTCTTC	0.398																																					p.Y927X		Atlas-SNP	.											.	OVCH1	195	.	0			c.C2781A						.						89	84	86					12																	29598311		1854	4098	5952	SO:0001587	stop_gained	341350	exon23			CATTGAGTAAAGT	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.2781C>A	chr12.hg19:g.29598311G>T	ENSP00000326708:p.Tyr927*	55.0	0.0		91.0	14.0	NM_183378		Nonsense_Mutation	SNP	ENST00000318184.5	hg19		.	.	.	.	.	.	.	.	.	.	G	16.50	3.140303	0.56936	.	.	ENSG00000187950	ENST00000318184	.	.	.	2.2	-0.713	0.11223	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.0496	0.14501	0.4856:0.0:0.5144:0.0	.	.	.	.	X	927	.	ENSP00000326708:Y927X	Y	-	3	2	OVCH1	29489578	0.015000	0.18098	0.001000	0.08648	0.002000	0.02628	-0.048000	0.11944	-0.186000	0.10533	-0.251000	0.11542	TAC	.	.		0.398	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		T	29598311	G	T	29598311	4	4	139	1	0	0	0	0	0	1	0	0	11332	1024	36	3	647	3	OVCH1	12	29598311	Nonsense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10		29598311	104253584	24	21846										
SP7	121340	hgsc.bcm.edu	37	chr12	53722106	53722106	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	gcctggttctccatgggtgcGctggtgtttgctcaggtggt	16	9	2	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr12:53722106G>A	ENST00000536324.2	-	3	1403	c.1120C>T	c.(1120-1122)Cgc>Tgc	p.R374C	SP7_ENST00000303846.3_Missense_Mutation_p.R374C|SP7_ENST00000537210.2_Missense_Mutation_p.R356C	NM_001173467.1	NP_001166938.1	Q8TDD2	SP7_HUMAN	Sp7 transcription factor	374					hematopoietic stem cell differentiation (GO:0060218)|osteoblast differentiation (GO:0001649)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(2)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	14						CCATGGGTGCGCTGGTGTTTG	0.672											OREG0021867	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R374C		Atlas-SNP	.											.	SP7	30	.	0			c.C1120T						.						38	45	43					12																	53722106		2124	4246	6370	SO:0001583	missense	121340	exon2			GGGTGCGCTGGTG	AF477981	CCDS44897.1, CCDS73475.1	12q13.13	2013-01-08				ENSG00000170374		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	17321	protein-coding gene	gene with protein product		606633				11792318	Standard	NM_152860		Approved	osterix, OSX	uc001sct.3	Q8TDD2		ENST00000536324.2:c.1120C>T	chr12.hg19:g.53722106G>A	ENSP00000443827:p.Arg374Cys	39.0	0.0	994	45.0	18.0	NM_152860	B3KY26|Q3MJ72|Q7Z718	Missense_Mutation	SNP	ENST00000536324.2	hg19	CCDS44897.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.829160	0.50845	.	.	ENSG00000170374	ENST00000536324;ENST00000303846;ENST00000537210	T;T;T	0.36157	1.27;1.27;1.27	4.66	4.66	0.58398	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.067164	0.56097	D	0.000034	T	0.56645	0.1999	M	0.70842	2.15	0.52501	D	0.999953	D	0.89917	1.0	D	0.69142	0.962	T	0.60439	-0.7263	10	0.87932	D	0	.	12.9159	0.58205	0.0:0.0:0.8366:0.1634	.	374	Q8TDD2	SP7_HUMAN	C	374;374;356	ENSP00000443827:R374C;ENSP00000302812:R374C;ENSP00000441367:R356C	ENSP00000302812:R374C	R	-	1	0	SP7	52008373	1.000000	0.71417	1.000000	0.80357	0.595000	0.36748	3.697000	0.54764	2.509000	0.84616	0.561000	0.74099	CGC	.	.		0.672	SP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406917.1			A	53722106	G	A	53722106	3	1	139	1	0	0	0	0	1	0	0	0	14984	1087	38	1	179	1	SP7	12	53722106	Missense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10	24123795	53722106	80129789	25	21847										
MYBPC1	4604	hgsc.bcm.edu	37	chr12	102076403	102076403	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	gatatatcaaggagtaaataCccctggacaaccagtcttcc	7	11	2	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr12:102076403C>T	ENST00000550270.1	+	29	3412				MYBPC1_ENST00000545503.2_Missense_Mutation_p.T1127I|MYBPC1_ENST00000550501.1_3'UTR|MYBPC1_ENST00000536007.1_Missense_Mutation_p.T1108I|MYBPC1_ENST00000547405.1_Missense_Mutation_p.T1101I|MYBPC1_ENST00000549145.1_Intron|MYBPC1_ENST00000541119.1_Missense_Mutation_p.T1115I|MYBPC1_ENST00000441232.1_Missense_Mutation_p.T1145I|MYBPC1_ENST00000360610.2_Intron|MYBPC1_ENST00000361685.2_Intron|MYBPC1_ENST00000551300.1_Intron|MYBPC1_ENST00000361466.2_Missense_Mutation_p.T1152I|MYBPC1_ENST00000553190.1_Intron|MYBPC1_ENST00000392934.3_Intron|MYBPC1_ENST00000547509.1_Missense_Mutation_p.T1113I|MYBPC1_ENST00000452455.2_Missense_Mutation_p.T1145I			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type						cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						GGAGTAAATACCCCTGGACAA	0.363																																					p.T1152I		Atlas-SNP	.											.	MYBPC1	235	.	0			c.C3455T						.						72	74	73					12																	102076403		2203	4300	6503	SO:0001627	intron_variant	4604	exon30			TAAATACCCCTGG		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7549	protein-coding gene	gene with protein product		160794	"myosin-binding protein C, slow-type"			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.3413-1757C>T	chr12.hg19:g.102076403C>T		99.0	0.0		144.0	31.0	NM_002465	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	hg19	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	C	14.57	2.575572	0.45902	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000547509;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466	T;T;T;T;T;T;T;T	0.59224	0.3;0.31;0.29;0.29;0.28;0.32;0.29;0.3	5.92	5.92	0.95590	.	0.363133	0.19907	N	0.103391	T	0.41050	0.1142	N	0.08118	0	0.80722	D	1	B;B;B;B;B;P	0.36909	0.002;0.437;0.294;0.437;0.0;0.573	B;B;B;B;B;B	0.37833	0.002;0.132;0.084;0.132;0.001;0.259	T	0.45804	-0.9236	10	0.52906	T	0.07	.	14.3366	0.66595	0.1568:0.8432:0.0:0.0	.	1108;1115;1145;1127;1101;1152	B7ZL02;B7ZL10;E7EWS6;B7ZL09;Q17RR7;G3XAE8	.;.;.;.;.;.	I	1101;1145;1145;1113;1127;1108;1115;1152	ENSP00000448175:T1101I;ENSP00000400908:T1145I;ENSP00000388989:T1145I;ENSP00000447362:T1113I;ENSP00000440034:T1127I;ENSP00000446128:T1108I;ENSP00000442847:T1115I;ENSP00000354849:T1152I	ENSP00000354849:T1152I	T	+	2	0	MYBPC1	100600534	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.228000	0.51270	2.809000	0.96659	0.655000	0.94253	ACC	.	.		0.363	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1			T	102076403	C	T	102076403	1	4	139	0	1	0	0	0	0	0	0	0	10020	507	18	3		3	MYBPC1	12	102076403	Intron	SNP	C	TCGA-DD-A4NR-01A-11D-A30V-10	48354297	102076403	31775492	26	21848										
SPTB	6710	hgsc.bcm.edu	37	chr14	65241980	65241980	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	cccggccgctgcctcccgcaGcctgtcccaggagctctgca	11	20	1	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr14:65241980G>A	ENST00000389721.5	-	22	4737	c.4705C>T	c.(4705-4707)Ctg>Ttg	p.L1569L	SPTB_ENST00000389722.3_Silent_p.L1569L|SPTB_ENST00000556626.1_Silent_p.L1569L|SPTB_ENST00000542895.1_Silent_p.L1569L|SPTB_ENST00000389720.3_Silent_p.L1569L	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1569					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GCCTCCCGCAGCCTGTCCCAG	0.677																																					p.L1569L		Atlas-SNP	.											.	SPTB	378	.	0			c.C4705T						.						38	30	33					14																	65241980		2203	4299	6502	SO:0001819	synonymous_variant	6710	exon22			CCCGCAGCCTGTC		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4705C>T	chr14.hg19:g.65241980G>A		35.0	0.0		45.0	9.0	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	hg19	CCDS32100.1																																																																																			.	.		0.677	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			A	65241980	G	A	65241980	2	1	139	1	0	0	0	0	0	0	0	1	15133	962	34	3		3	SPTB	14	65241980	Silent	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10		65241980	42107560	27	21849										
RPAP1	26015	hgsc.bcm.edu	37	chr15	41816168	41816168	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	agaggctggcctcagcagaaTcactacaaaagtgccaaagg	11	10	2	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr15:41816168T>C	ENST00000304330.4	-	17	2353	c.2237A>G	c.(2236-2238)gAt>gGt	p.D746G	RPAP1_ENST00000561603.1_Missense_Mutation_p.D746G	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	746						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CTCAGCAGAATCACTACAAAA	0.597																																					p.D746G		Atlas-SNP	.											.	RPAP1	111	.	0			c.A2237G						.						33	32	33					15																	41816168		2203	4300	6503	SO:0001583	missense	26015	exon17			GCAGAATCACTAC	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.2237A>G	chr15.hg19:g.41816168T>C	ENSP00000306123:p.Asp746Gly	44.0	0.0		59.0	8.0	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	hg19	CCDS10079.1	.	.	.	.	.	.	.	.	.	.	T	6.315	0.426283	0.11987	.	.	ENSG00000103932	ENST00000304330	T	0.11930	2.73	4.47	3.35	0.38373	.	0.937786	0.09133	N	0.844107	T	0.07773	0.0195	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33624	-0.9861	10	0.87932	D	0	-17.8935	3.3007	0.06982	0.2026:0.1116:0.0:0.6857	.	746	Q9BWH6	RPAP1_HUMAN	G	746	ENSP00000306123:D746G	ENSP00000306123:D746G	D	-	2	0	RPAP1	39603460	0.415000	0.25416	0.255000	0.24374	0.204000	0.24138	0.785000	0.26830	0.762000	0.33152	0.460000	0.39030	GAT	.	.		0.597	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		C	41816168	T	C	41816168	3	2	139	1	0	0	0	0	1	0	0	0	13556	1435	50	2	1980	2	RPAP1	15	41816168	Missense_Mutation	SNP	T	TCGA-DD-A4NR-01A-11D-A30V-10		41816168	60715224	28	21850										
FBXL19	54620	hgsc.bcm.edu	37	chr16	30938694	30938694	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	gggaaggaggacacggtggaGggagaggaagagaaatttgg	21	2	0	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr16:30938694G>T	ENST00000380310.2	+	3	461	c.303G>T	c.(301-303)gaG>gaT	p.E101D	FBXL19_ENST00000565690.1_Missense_Mutation_p.E81D|FBXL19_ENST00000338343.4_Missense_Mutation_p.E81D|FBXL19_ENST00000471231.2_5'UTR|FBXL19_ENST00000562319.1_Missense_Mutation_p.E81D	NM_001099784.2	NP_001093254.2	Q6PCT2	FXL19_HUMAN	F-box and leucine-rich repeat protein 19	101					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)	SCF ubiquitin ligase complex (GO:0019005)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						ACACGGTGGAGGGAGAGGAAG	0.617																																					p.E101D		Atlas-SNP	.											.	FBXL19	74	.	0			c.G303T						.						119	141	134					16																	30938694		2019	4168	6187	SO:0001583	missense	54620	exon3			GGTGGAGGGAGAG	AK127701	CCDS45465.1, CCDS73873.1	16p11.2	2014-02-20			ENSG00000099364	ENSG00000099364		"F-boxes / Leucine-rich repeats"	25300	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1C"	609085					Standard	NM_001099784		Approved	DKFZp434K0410, Fbl19, JHDM1C, CXXC11	uc002eab.2	Q6PCT2	OTTHUMG00000132403	ENST00000380310.2:c.303G>T	chr16.hg19:g.30938694G>T	ENSP00000369666:p.Glu101Asp	64.0	0.0		71.0	4.0	NM_001099784	A8MT10|Q8N789|Q9NT14	Missense_Mutation	SNP	ENST00000380310.2	hg19	CCDS45465.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.02|16.02	3.003941|3.003941	0.54254|0.54254	.|.	.|.	ENSG00000099364|ENSG00000099364	ENST00000338343;ENST00000380310|ENST00000427128	T;T|.	0.25250|.	1.81;2.12|.	5.12|5.12	3.13|3.13	0.36017|0.36017	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);|.	0.239273|.	0.32785|.	N|.	0.005652|.	T|T	0.37237|0.37237	0.0996|0.0996	N|N	0.22421|0.22421	0.69|0.69	0.31755|0.31755	N|N	0.63407|0.63407	B;B|.	0.27351|.	0.176;0.041|.	B;B|.	0.20955|.	0.026;0.032|.	T|T	0.41822|0.41822	-0.9487|-0.9487	10|5	0.24483|.	T|.	0.36|.	-8.3682|-8.3682	11.1158|11.1158	0.48259|0.48259	0.1567:0.0:0.8433:0.0|0.1567:0.0:0.8433:0.0	.|.	101;101|.	Q6PCT2;Q6PCT2-2|.	FXL19_HUMAN;.|.	D|W	81;101|36	ENSP00000339712:E81D;ENSP00000369666:E101D|.	ENSP00000339712:E81D|.	E|G	+|+	3|1	2|0	FBXL19|FBXL19	30846195|30846195	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	0.422000|0.422000	0.21296|0.21296	0.669000|0.669000	0.31146|0.31146	0.448000|0.448000	0.29417|0.29417	GAG|GGG	.	.		0.617	FBXL19-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_019085		T	30938694	G	T	30938694	3	4	139	1	0	0	0	0	1	0	0	0	5723	991	35	3	313	3	FBXL19	16	30938694	Missense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10		30938694	59416059	29	21851										
SPG7	6687	hgsc.bcm.edu	37	chr16	89574985	89574985	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ggcctccgggggacctcgccGaggctggaggccgagctctg	18	14	1	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr16:89574985G>A	ENST00000268704.2	+	1	175	c.160G>A	c.(160-162)Gag>Aag	p.E54K	SPG7_ENST00000341316.2_Missense_Mutation_p.E54K	NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	54					anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		GGACCTCGCCGAGGCTGGAGG	0.776																																					p.E54K		Atlas-SNP	.											.	SPG7	75	.	0			c.G160A						.						1	2	2					16																	89574985		1024	2194	3218	SO:0001583	missense	6687	exon1			CTCGCCGAGGCTG	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"ATPases / AAA-type"	11237	protein-coding gene	gene with protein product	"paraplegin"	602783	"cell matrix adhesion regulator"	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.160G>A	chr16.hg19:g.89574985G>A	ENSP00000268704:p.Glu54Lys	16.0	0.0		34.0	6.0	NM_199367	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	hg19	CCDS10977.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.119339	0.37436	.	.	ENSG00000197912	ENST00000268704;ENST00000341316	T;T	0.80909	-1.43;-1.43	3.77	-0.85	0.10720	Peptidase M41, FtsH (1);	0.786859	0.11029	N	0.607463	T	0.53899	0.1825	N	0.08118	0	0.09310	N	1	B;B	0.26120	0.011;0.142	B;B	0.14578	0.001;0.011	T	0.37957	-0.9683	10	0.17369	T	0.5	.	4.2676	0.10771	0.226:0.3729:0.4011:0.0	.	54;54	Q9UQ90;Q9UQ90-2	SPG7_HUMAN;.	K	54	ENSP00000268704:E54K;ENSP00000341157:E54K	ENSP00000268704:E54K	E	+	1	0	SPG7	88102486	0.156000	0.22821	0.000000	0.03702	0.055000	0.15305	1.380000	0.34351	-0.087000	0.12528	0.467000	0.42956	GAG	.	.		0.776	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119		A	89574985	G	A	89574985	3	1	139	1	0	0	0	0	1	0	0	0	15059	1059	37	1	162	1	SPG7	16	89574985	Missense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10	58636291	89574985	779768	30	21852										
MYH1	4619	hgsc.bcm.edu	37	chr17	10395803	10395803	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	gcttgttgacctgggactcaGcaatgtcagcccgttcctcg	11	13	2	1			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr17:10395803G>A	ENST00000226207.5	-	40	5844	c.5750C>T	c.(5749-5751)gCt>gTt	p.A1917V	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1917					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CTGGGACTCAGCAATGTCAGC	0.488																																					p.A1917V		Atlas-SNP	.											.	MYH1	403	.	0			c.C5750T						.						190	173	179					17																	10395803		2203	4300	6503	SO:0001583	missense	4619	exon40			GACTCAGCAATGT		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.5750C>T	chr17.hg19:g.10395803G>A	ENSP00000226207:p.Ala1917Val	75.0	0.0		124.0	20.0	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	G	34	5.317651	0.95682	.	.	ENSG00000109061	ENST00000226207	T	0.81247	-1.47	4.63	4.63	0.57726	Myosin tail (1);	0.000000	0.39909	U	0.001232	D	0.92967	0.7762	H	0.96175	3.78	0.58432	D	0.999999	D	0.71674	0.998	D	0.73708	0.981	D	0.95159	0.8280	10	0.87932	D	0	.	18.0186	0.89249	0.0:0.0:1.0:0.0	.	1917	P12882	MYH1_HUMAN	V	1917	ENSP00000226207:A1917V	ENSP00000226207:A1917V	A	-	2	0	MYH1	10336528	1.000000	0.71417	0.787000	0.31911	0.976000	0.68499	9.548000	0.98103	2.546000	0.85860	0.655000	0.94253	GCT	.	.		0.488	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		A	10395803	G	A	10395803	3	1	139	1	0	0	0	0	1	0	0	0	10038	971	34	3	73	3	MYH1	17	10395803	Missense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10		10395803	70799407	31	21853										
AATK	9625	hgsc.bcm.edu	37	chr17	79100253	79100253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	acgaaattgttgcgatgaagGtgcaggacgccacaggccac	13	10	0	1			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr17:79100253G>T	ENST00000326724.4	-	7	753	c.729C>A	c.(727-729)caC>caA	p.H243Q	AATK_ENST00000417379.1_Missense_Mutation_p.H140Q|MIR338_ENST00000390137.2_RNA|MIR657_ENST00000385003.1_RNA|AATK_ENST00000572339.1_5'UTR	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	243	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			TGCGATGAAGGTGCAGGACGC	0.701																																					p.H243Q		Atlas-SNP	.											.	AATK	102	.	0			c.C729A						.						8	10	9					17																	79100253		1996	4136	6132	SO:0001583	missense	9625	exon7			ATGAAGGTGCAGG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.729C>A	chr17.hg19:g.79100253G>T	ENSP00000324196:p.His243Gln	68.0	0.0		90.0	14.0	NM_001080395	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	hg19	CCDS45807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.33|10.33	1.321035|1.321035	0.23994|0.23994	.|.	.|.	ENSG00000181409|ENSG00000181409	ENST00000326724;ENST00000374792|ENST00000417379	D;D|.	0.82893|.	-1.66;-1.66|.	4.07|4.07	-0.25|-0.25	0.13007|0.13007	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.060881|.	0.64402|.	D|.	0.000006|.	T|T	0.60143|0.60143	0.2246|0.2246	M|M	0.74389|0.74389	2.26|2.26	0.41250|0.41250	D|D	0.986704|0.986704	P|.	0.45240|.	0.854|.	P|.	0.51866|.	0.682|.	T|T	0.55276|0.55276	-0.8166|-0.8166	10|5	0.72032|.	D|.	0.01|.	.|.	4.6142|4.6142	0.12417|0.12417	0.4434:0.0:0.4113:0.1453|0.4434:0.0:0.4113:0.1453	.|.	243|.	Q6ZMQ8|.	LMTK1_HUMAN|.	Q|N	243|196	ENSP00000324196:H243Q;ENSP00000363924:H243Q|.	ENSP00000324196:H243Q|.	H|T	-|-	3|2	2|0	AATK|AATK	76714848|76714848	1.000000|1.000000	0.71417|0.71417	0.806000|0.806000	0.32338|0.32338	0.035000|0.035000	0.12851|0.12851	1.533000|1.533000	0.36040|0.36040	-0.180000|-0.180000	0.10637|0.10637	-0.363000|-0.363000	0.07495|0.07495	CAC|ACC	.	.		0.701	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		T	79100253	G	T	79100253	3	4	139	1	0	0	0	0	1	0	0	0	26	1252	44	3	3427	3	AATK	17	79100253	Missense_Mutation	SNP	G	TCGA-DD-A4NR-01A-11D-A30V-10	68704450	79100253	2094957	32	21854										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610300	10610300	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	aggccgtgtaggcgaattcaAtgaggcgctccatgaccttg	13	10	1	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr19:10610300A>G	ENST00000171111.5	-	2	957	c.410T>C	c.(409-411)aTt>aCt	p.I137T	KEAP1_ENST00000393623.2_Missense_Mutation_p.I137T|KEAP1_ENST00000588024.1_5'Flank	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	137	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GGCGAATTCAATGAGGCGCTC	0.587																																					p.I137T		Atlas-SNP	.											.	KEAP1	182	.	0			c.T410C						.						144	117	126					19																	10610300		2203	4300	6503	SO:0001583	missense	9817	exon2			AATTCAATGAGGC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.410T>C	chr19.hg19:g.10610300A>G	ENSP00000171111:p.Ile137Thr	41.0	0.0		53.0	5.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.161918	0.78226	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.69685	-0.42;-0.42	4.68	4.68	0.58851	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.060634	0.64402	D	0.000002	T	0.78648	0.4316	M	0.89534	3.04	0.50632	D	0.999886	P	0.51537	0.946	P	0.51550	0.673	D	0.83575	0.0114	10	0.87932	D	0	.	12.0934	0.53739	1.0:0.0:0.0:0.0	.	137	Q14145	KEAP1_HUMAN	T	137	ENSP00000171111:I137T;ENSP00000377245:I137T	ENSP00000171111:I137T	I	-	2	0	KEAP1	10471300	1.000000	0.71417	0.950000	0.38849	0.931000	0.56810	9.135000	0.94478	1.756000	0.51951	0.379000	0.24179	ATT	.	.		0.587	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		G	10610300	A	G	10610300	3	3	139	1	0	0	0	0	1	0	0	0	8150	101	4	2	1484	2	KEAP1	19	10610300	Missense_Mutation	SNP	A	TCGA-DD-A4NR-01A-11D-A30V-10		10610300	48518683	33	21855										
TST	7263	hgsc.bcm.edu	37	chr22	37414605	37414605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ctcttctatgtcaaagaaagAggcgccgggtacgtggcgct	13	10	3	2			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chr22:37414605A>G	ENST00000403892.3	-	1	903	c.169T>C	c.(169-171)Tct>Cct	p.S57P	MPST_ENST00000401419.3_5'Flank|MPST_ENST00000397129.1_5'Flank|MPST_ENST00000429360.2_5'Flank|MPST_ENST00000404802.3_5'Flank|MPST_ENST00000341116.3_5'Flank|MPST_ENST00000404393.1_5'Flank|TST_ENST00000249042.3_Missense_Mutation_p.S57P	NM_001270483.1	NP_001257412.1	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase (rhodanese)	57	Rhodanese 1. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cellular nitrogen compound metabolic process (GO:0034641)|cyanate catabolic process (GO:0009440)|epithelial cell differentiation (GO:0030855)|rRNA import into mitochondrion (GO:0035928)|rRNA transport (GO:0051029)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|thiosulfate sulfurtransferase activity (GO:0004792)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	7						TCAAAGAAAGAGGCGCCGGGT	0.672																																					p.S57P		Atlas-SNP	.											.	TST	22	.	0			c.T169C						.						7	7	7					22																	37414605		2158	4235	6393	SO:0001583	missense	7263	exon2			AGAAAGAGGCGCC	Z73420	CCDS13938.1	22q13.1	2002-02-05			ENSG00000128311	ENSG00000128311	2.8.1.1		12388	protein-coding gene	gene with protein product		180370				1953758	Standard	NM_003312		Approved	RDS	uc003aqh.4	Q16762	OTTHUMG00000150533	ENST00000403892.3:c.169T>C	chr22.hg19:g.37414605A>G	ENSP00000385828:p.Ser57Pro	41.0	0.0		40.0	4.0	NM_003312	B3KRM1|Q6IB06	Missense_Mutation	SNP	ENST00000403892.3	hg19	CCDS13938.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.845606	0.71603	.	.	ENSG00000128311	ENST00000403892;ENST00000249042;ENST00000413912;ENST00000438203	T;T;T	0.25250	1.81;1.81;1.81	4.94	4.94	0.65067	Rhodanese-like (5);Thiosulphate sulfurtransferase, conserved site (1);	0.127399	0.64402	D	0.000016	T	0.32010	0.0815	L	0.42245	1.32	0.49798	D	0.999827	P	0.49358	0.923	P	0.56563	0.801	T	0.05517	-1.0880	10	0.35671	T	0.21	-28.9281	6.6314	0.22859	0.7653:0.1554:0.0793:0.0	.	57	Q16762	THTR_HUMAN	P	57	ENSP00000385828:S57P;ENSP00000249042:S57P;ENSP00000400764:S57P	ENSP00000249042:S57P	S	-	1	0	TST	35744551	0.998000	0.40836	1.000000	0.80357	0.949000	0.60115	1.480000	0.35464	1.853000	0.53794	0.459000	0.35465	TCT	.	.		0.672	TST-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318790.1			G	37414605	A	G	37414605	3	3	139	1	0	0	0	0	1	0	0	0	16688	304	11	2	732	2	TST	22	37414605	Missense_Mutation	SNP	A	TCGA-DD-A4NR-01A-11D-A30V-10		37414605	13889961	34	21856										
CLCN5	1184	hgsc.bcm.edu	37	chrX	49853423	49853444	+	Frame_Shift_Del	DEL	AATGGAACAGCTGGCTTATTAC	AATGGAACAGCTGGCTTATTAC	-													0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ggtcgacttctaggagtaggAatggaacagctggcttatta					rs148124447		TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	AATGGAACAGCTGGCTTATTAC	AATGGAACAGCTGGCTTATTAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chrX:49853423_49853444delAATGGAACAGCTGGCTTATTAC	ENST00000307367.2	+	9	1707_1728	c.1416_1437delAATGGAACAGCTGGCTTATTAC	c.(1414-1437)ggaatggaacagctggcttattacfs	p.GMEQLAYY472fs	CLCN5_ENST00000376091.3_Frame_Shift_Del_p.GMEQLAYY542fs|CLCN5_ENST00000376108.3_Frame_Shift_Del_p.GMEQLAYY472fs|CLCN5_ENST00000376088.3_Frame_Shift_Del_p.GMEQLAYY542fs			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	472					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					TAGGAGTAGGAATGGAACAGCTGGCTTATTACCACCAGGAAT	0.509																																					p.542_549del		Atlas-Indel,Pindel	.											.	CLCN5	137	.	0			c.1625_1646del						.																																			SO:0001589	frameshift_variant	1184	exon12			.	X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.1416_1437delAATGGAACAGCTGGCTTATTAC	chrX.hg19:g.49853423_49853444delAATGGAACAGCTGGCTTATTAC	ENSP00000304257:p.Gly472fs	122.0	0.0		91.0	10.0	NM_001127898	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Frame_Shift_Del	DEL	ENST00000307367.2	hg19	CCDS14328.1																																																																																			.	.		0.509	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			-	49853444	AATGGAACAGCTGGCTTATTAC	-	49853423	7	5	139	1	0	1	0	1	0	0	0	0	3468	233	9	0	1664	0	CLCN5	23	49853423	Frame_Shift_Del	DEL	AATGGAACAGCTGGCTTATTAC	TCGA-DD-A4NR-01A-11D-A30V-10		49853423	105417137	35	21857										
AR	367	hgsc.bcm.edu	37	chrX	66765514	66765515	+	Frame_Shift_Del	DEL	AG	AG	-													0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	ccactttccccggcttaagcAgctgctccgctgaccttaaa							TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chrX:66765514_66765515delAG	ENST00000374690.3	+	1	1050_1051	c.526_527delAG	c.(526-528)agcfs	p.S176fs	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Frame_Shift_Del_p.S176fs|AR_ENST00000504326.1_Frame_Shift_Del_p.S176fs	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	174	Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CGGCTTAAGCAGCTGCTCCGCT	0.629									Androgen Insensitivity Syndrome																												p.175_176del		Atlas-INDEL	.											.	AR	249	.	0			c.525_526del						.																																			SO:0001589	frameshift_variant	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	.	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.526_527delAG	chrX.hg19:g.66765514_66765515delAG	ENSP00000363822:p.Ser176fs	53.0	0.0		78.0	13.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Frame_Shift_Del	DEL	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.		0.629	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		-	66765515	AG	-	66765514	7	5	139	1	0	1	0	1	0	0	0	0	836	188	7	0	528	0	AR	23	66765514	Frame_Shift_Del	DEL	AG	TCGA-DD-A4NR-01A-11D-A30V-10	16912091	66765514	88505046	36	21858										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73960186	73960186	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	2	1	1.11204013377926	7.22826086956522	0.602355072463768	1	1	0	tcacctattgctgttttcccAttgcttttgctcacaccctt	4	14	2	0			TCGA-DD-A4NR-01A-11D-A30V-10	TCGA-DD-A4NR-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	083000f9-e8e4-4d44-a4b3-74a624a24186	ba98edfd-3301-4ba6-8d12-38e87d1f6bfa	g.chrX:73960186A>G	ENST00000055682.6	-	3	4817	c.4206T>C	c.(4204-4206)aaT>aaC	p.N1402N		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1402					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						CTGTTTTCCCATTGCTTTTGC	0.448																																					p.N1402N		Atlas-SNP	.											.	KIAA2022	262	.	0			c.T4206C						.						197	161	173					X																	73960186		2203	4300	6503	SO:0001819	synonymous_variant	340533	exon3			TTTCCCATTGCTT		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.4206T>C	chrX.hg19:g.73960186A>G		39.0	0.0		76.0	14.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Silent	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	A	0.827	-0.746596	0.03065	.	.	ENSG00000050030	ENST00000424929	.	.	.	5.36	0.149	0.14863	.	.	.	.	.	T	0.55097	0.1899	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46233	-0.9206	4	.	.	.	-8.4146	8.451	0.32871	0.4603:0.0:0.5397:0.0	.	.	.	.	R	4	.	.	W	-	1	0	KIAA2022	73876911	0.951000	0.32395	0.989000	0.46669	0.591000	0.36615	0.438000	0.21559	-0.076000	0.12775	0.441000	0.28932	TGG	.	.		0.448	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		G	73960186	A	G	73960186	2	3	139	1	0	0	0	0	0	0	0	1	8278	214	8	2		2	KIAA2022	23	73960186	Silent	SNP	A	TCGA-DD-A4NR-01A-11D-A30V-10	7194672	73960186	81310374	37	21859										
ZBTB40	9923	hgsc.bcm.edu	37	chr1	22838185	22838185	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gcaggtgtccttactaaggaAgatggagagaaggaaacgtg	15	5	0	2			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr1:22838185A>C	ENST00000375647.4	+	11	2226	c.2019A>C	c.(2017-2019)gaA>gaC	p.E673D	ZBTB40_ENST00000404138.1_Missense_Mutation_p.E673D|ZBTB40_ENST00000374651.4_Missense_Mutation_p.E561D	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	673					bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		TTACTAAGGAAGATGGAGAGA	0.428																																					p.E673D		Atlas-SNP	.											.	ZBTB40	87	.	0			c.A2019C						.						50	49	49					1																	22838185		2203	4300	6503	SO:0001583	missense	9923	exon12			TAAGGAAGATGGA	AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.2019A>C	chr1.hg19:g.22838185A>C	ENSP00000364798:p.Glu673Asp	175.0	0.0		209.0	18.0	NM_001083621	O75066|Q5TFU5|Q8N1R1	Missense_Mutation	SNP	ENST00000375647.4	hg19	CCDS224.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.164371	0.38217	.	.	ENSG00000184677	ENST00000404138;ENST00000375647;ENST00000374651	D;D;D	0.82081	-1.57;-1.57;-1.57	5.23	-3.38	0.04883	.	0.000000	0.50627	D	0.000107	T	0.71651	0.3365	L	0.48642	1.525	0.09310	N	1	B;B	0.25609	0.13;0.079	B;B	0.24006	0.05;0.037	T	0.60414	-0.7268	10	0.51188	T	0.08	-7.6673	7.8705	0.29563	0.4598:0.1196:0.4205:0.0	.	561;673	F8WAI8;Q9NUA8	.;ZBT40_HUMAN	D	673;673;561	ENSP00000384527:E673D;ENSP00000364798:E673D;ENSP00000363782:E561D	ENSP00000363782:E561D	E	+	3	2	ZBTB40	22710772	0.452000	0.25713	0.008000	0.14137	0.002000	0.02628	0.956000	0.29202	-0.588000	0.05882	-1.119000	0.02030	GAA	.	.		0.428	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870		C	22838185	A	C	22838185	3	2	140	1	0	0	0	0	1	0	0	0	17557	69	3	5	2057	5	ZBTB40	1	22838185	Missense_Mutation	SNP	A	TCGA-DD-A4NS-01A-11D-A30V-10		22838185	226412436	1	21860										
EPHA10	284656	hgsc.bcm.edu	37	chr1	38227457	38227457	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	cctgcgtgaagctctcgtccGccgcgatcgtgtcgattttg	12	13	1	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr1:38227457G>A	ENST00000373048.4	-	3	469	c.470C>T	c.(469-471)gCg>gTg	p.A157V	EPHA10_ENST00000319637.6_Missense_Mutation_p.A157V|EPHA10_ENST00000427468.2_Missense_Mutation_p.A157V	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	157	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GCTCTCGTCCGCCGCGATCGT	0.662																																					p.A157V		Atlas-SNP	.											EPHA10,colon,carcinoma,0,2	EPHA10	120	.	0			c.C470T						.						27	33	31					1																	38227457		2195	4296	6491	SO:0001583	missense	284656	exon3			TCGTCCGCCGCGA	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.470C>T	chr1.hg19:g.38227457G>A	ENSP00000362139:p.Ala157Val	80.0	0.0		74.0	8.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	hg19	CCDS41305.1	.	.	.	.	.	.	.	.	.	.	G	34	5.330075	0.95733	.	.	ENSG00000183317	ENST00000427468;ENST00000373048;ENST00000319637	T;T;T	0.05925	3.37;3.37;3.37	4.75	4.75	0.60458	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.41500	D	0.000875	T	0.35770	0.0943	M	0.93197	3.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.965;0.998	T	0.50048	-0.8873	10	0.87932	D	0	.	17.2504	0.87041	0.0:0.0:1.0:0.0	.	157;157	Q5JZY3;Q5JZY3-2	EPHAA_HUMAN;.	V	157	ENSP00000397746:A157V;ENSP00000362139:A157V;ENSP00000316395:A157V	ENSP00000316395:A157V	A	-	2	0	EPHA10	38000044	1.000000	0.71417	0.630000	0.29268	0.966000	0.64601	9.511000	0.98006	2.598000	0.87819	0.643000	0.83706	GCG	.	.		0.662	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		A	38227457	G	A	38227457	3	1	140	1	0	0	0	0	1	0	0	0	5168	1087	38	1	2654	1	EPHA10	1	38227457	Missense_Mutation	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10	15389272	38227457	211023164	2	21861										
CD46	4179	hgsc.bcm.edu	37	chr1	207934716	207934716	+	Frame_Shift_Del	DEL	T	T	-													0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	ctgcacctggaccagatccaTtttcacttattggagagagc							TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr1:207934716delT	ENST00000358170.2	+	5	754	c.598delT	c.(598-600)tttfs	p.F200fs	CD46_ENST00000361067.1_Frame_Shift_Del_p.F200fs|CD46_ENST00000480003.1_Frame_Shift_Del_p.F200fs|CD46_ENST00000367041.1_Frame_Shift_Del_p.F200fs|CD46_ENST00000367042.1_Frame_Shift_Del_p.F200fs|CD46_ENST00000367047.1_Frame_Shift_Del_p.F137fs|CD46_ENST00000360212.2_Frame_Shift_Del_p.F200fs|CD46_ENST00000354848.1_Frame_Shift_Del_p.F200fs|CD46_ENST00000357714.1_Frame_Shift_Del_p.F200fs|CD46_ENST00000322918.5_Frame_Shift_Del_p.F200fs|CD46_ENST00000469535.1_3'UTR|CD46_ENST00000322875.4_Frame_Shift_Del_p.F200fs|CD46_ENST00000441839.2_Frame_Shift_Del_p.F200fs	NM_002389.4	NP_002380.3	P15529	MCP_HUMAN	CD46 molecule, complement regulatory protein	200	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adaptive immune response (GO:0002250)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|interleukin-10 production (GO:0032613)|negative regulation of complement activation (GO:0045916)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transforming growth factor beta production (GO:0071636)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)|regulation of Notch signaling pathway (GO:0008593)|sequestering of extracellular ligand from receptor (GO:0035581)|single fertilization (GO:0007338)|T cell mediated immunity (GO:0002456)|viral process (GO:0016032)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|inner acrosomal membrane (GO:0002079)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cadherin binding (GO:0045296)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	19						ACCAGATCCATTTTCACTTAT	0.373																																					p.P199fs		Atlas-Indel,Pindel	.											.	CD46	34	.	0			c.597delA						.						152	130	137					1																	207934716		2203	4300	6503	SO:0001589	frameshift_variant	4179	exon5			.	BC030594	CCDS1479.1, CCDS1480.1, CCDS1481.1, CCDS1482.1, CCDS1484.1, CCDS1485.1, CCDS31008.1, CCDS31009.1	1q32	2014-09-17	2006-03-28	2006-02-09	ENSG00000117335	ENSG00000117335		"CD molecules", "Complement system"	6953	protein-coding gene	gene with protein product		120920	"antigen identified by monoclonal antibody TRA-2-10", "membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)", "CD46 antigen, complement regulatory protein"	MIC10, MCP		7929741	Standard	NM_002389		Approved	TRA2.10, MGC26544, TLX	uc001hgj.3	P15529	OTTHUMG00000036397	ENST00000358170.2:c.598delT	chr1.hg19:g.207934716delT	ENSP00000350893:p.Phe200fs	115.0	0.0		130.0	22.0	NM_172352	A0T1T0|A0T1T1|A0T1T2|Q15429|Q53GV9|Q5HY94|Q5VWS6|Q5VWS7|Q5VWS8|Q5VWS9|Q5VWT0|Q5VWT1|Q5VWT2|Q6N0A1|Q7Z3R5|Q9NNW2|Q9NNW3|Q9NNW4|Q9UCJ4	Frame_Shift_Del	DEL	ENST00000358170.2	hg19	CCDS1485.1																																																																																			.	.		0.373	CD46-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088588.3	NM_172361		-	207934716	T	-	207934716	7	5	140	1	0	1	0	1	0	0	0	0	3020	1493	52	0	616	0	CD46	1	207934716	Frame_Shift_Del	DEL	T	TCGA-DD-A4NS-01A-11D-A30V-10	169707259	207934716	41315905	3	21862										
OR2W5	441932	hgsc.bcm.edu	37	chr1	247655366	247655366	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gggtgggagaaaggggctggGgagcctcaacgaggggaaca	21	6	1	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr1:247655366G>T	ENST00000522351.1	+	0	997							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G313R(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			AAGGGGCTGGGGAGCCTCAAC	0.493																																					p.G313X		Atlas-SNP	.											OR2W5,extremity,malignant_melanoma,0,1	OR2W5	97	.	1	Substitution - Missense(1)	skin(1)	c.G937T						.						55	59	57					1																	247655366		2203	4300	6503			441932	exon1			GGCTGGGGAGCCT			1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"GPCR / Class A : Olfactory receptors"	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		chr1.hg19:g.247655366G>T		74.0	0.0		81.0	6.0	NM_001004698	B9EH85	Nonsense_Mutation	SNP	ENST00000522351.1	hg19																																																																																				.	.		0.493	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698		T	247655366	G	T	247655366	1	4	140	0	1	0	0	0	0	0	0	0	11043	1233	43	3		3	OR2W5	1	247655366	RNA	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10	39720650	247655366	1595255	4	21863										
APOB	338	hgsc.bcm.edu	37	chr2	21233945	21233945	+	Frame_Shift_Del	DEL	A	A	-													0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	ccagaggttctgctttcaacAggaatttgctatacagctgc							TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr2:21233945delA	ENST00000233242.1	-	26	5922	c.5795delT	c.(5794-5796)ctgfs	p.L1933fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1933					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTTTCAACAGGAATTTGCT	0.458																																					p.L1932fs		Atlas-Indel,Pindel	.											.	APOB	761	.	0			c.5796delG						.						205	189	195					2																	21233945		2203	4300	6503	SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.5795delT	chr2.hg19:g.21233945delA	ENSP00000233242:p.Leu1933fs	146.0	0.0		153.0	13.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.458	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21233945	A	-	21233945	7	5	140	1	0	1	0	1	0	0	0	0	785	188	7	0	7912	0	APOB	2	21233945	Frame_Shift_Del	DEL	A	TCGA-DD-A4NS-01A-11D-A30V-10		21233945	221965428	5	21864										
CXCR4	7852	hgsc.bcm.edu	37	chr2	136872511	136872511	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	ccacctcgctttcctttggaGaggatcttgaggctggaccc	11	13	1	2			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr2:136872511G>A	ENST00000241393.3	-	2	1091	c.987C>T	c.(985-987)ctC>ctT	p.L329L	CXCR4_ENST00000409817.1_Silent_p.L333L|CXCR4_ENST00000466288.1_5'UTR	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	329					activation of MAPK activity (GO:0000187)|ameboidal cell migration (GO:0001667)|apoptotic process (GO:0006915)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular response to cytokine stimulus (GO:0071345)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|inflammatory response (GO:0006954)|motor neuron axon guidance (GO:0008045)|myelin maintenance (GO:0043217)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|neutrophil activation (GO:0042119)|patterning of blood vessels (GO:0001569)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of chemotaxis (GO:0050920)|response to hypoxia (GO:0001666)|response to virus (GO:0009615)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)|myosin light chain binding (GO:0032027)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)|Plerixafor(DB06809)	TTCCTTTGGAGAGGATCTTGA	0.463																																					p.L333L		Atlas-SNP	.											.	CXCR4	51	.	0			c.C999T						.						266	252	256					2																	136872511		2203	4300	6503	SO:0001819	synonymous_variant	7852	exon1			TTTGGAGAGGATC	AF005058	CCDS33295.1, CCDS46420.1	2q21	2014-09-17	2002-08-22		ENSG00000121966	ENSG00000121966		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	2561	protein-coding gene	gene with protein product		162643	"chemokine (C-X-C motif), receptor 4 (fusin)"			9599023, 9379028	Standard	NM_001008540		Approved	LESTR, NPY3R, HM89, NPYY3R, D2S201E, fusin, HSY3RR, NPYR, CD184	uc002tuz.3	P61073	OTTHUMG00000153583	ENST00000241393.3:c.987C>T	chr2.hg19:g.136872511G>A		176.0	0.0		218.0	24.0	NM_001008540	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Silent	SNP	ENST00000241393.3	hg19	CCDS46420.1																																																																																			.	.		0.463	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1			A	136872511	G	A	136872511	2	1	140	1	0	0	0	0	0	0	0	1	4095	929	33	3		3	CXCR4	2	136872511	Silent	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10	115638566	136872511	106326862	6	21865										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160310259	160310259	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gctgaccattgggaaggcacTcgacactgtggacaggttaa	13	9	0	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr2:160310259T>G	ENST00000392783.2	-	4	694	c.199A>C	c.(199-201)Agt>Cgt	p.S67R	BAZ2B_ENST00000392782.1_Missense_Mutation_p.S67R|BAZ2B_ENST00000355831.2_Missense_Mutation_p.S67R|BAZ2B_ENST00000343439.5_Missense_Mutation_p.S67R	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	67					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						GGGAAGGCACTCGACACTGTG	0.468																																					p.S67R		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A199C						.						81	77	78					2																	160310259		1891	4131	6022	SO:0001583	missense	29994	exon4			AGGCACTCGACAC	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.199A>C	chr2.hg19:g.160310259T>G	ENSP00000376534:p.Ser67Arg	107.0	0.0		124.0	10.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	T	18.34	3.602272	0.66445	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000437839	T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35	5.46	5.46	0.80206	.	.	.	.	.	T	0.56645	0.1999	L	0.56769	1.78	0.48632	D	0.999685	D;D;D	0.76494	0.994;0.999;0.998	D;D;D	0.83275	0.983;0.996;0.991	T	0.59878	-0.7371	9	0.87932	D	0	-7.7425	14.5001	0.67716	0.0:0.0:0.0:1.0	.	67;67;67	Q6MZK7;Q9UIF8-5;Q9UIF8	.;.;BAZ2B_HUMAN	R	67	ENSP00000376533:S67R;ENSP00000376534:S67R;ENSP00000348087:S67R;ENSP00000339670:S67R;ENSP00000415613:S67R	ENSP00000339670:S67R	S	-	1	0	BAZ2B	160018505	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.401000	0.66326	2.066000	0.61787	0.533000	0.62120	AGT	.	.		0.468	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			G	160310259	T	G	160310259	3	3	140	1	0	0	0	0	1	0	0	0	1332	1551	54	5	6443	5	BAZ2B	2	160310259	Missense_Mutation	SNP	T	TCGA-DD-A4NS-01A-11D-A30V-10	23437748	160310259	82889114	7	21866										
SCN3A	6328	hgsc.bcm.edu	37	chr2	165947139	165947139	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gtggatccggtcaccactgaCcatgggcagatccatggcaa	12	12	1	2			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr2:165947139C>G	ENST00000360093.3	-	28	6015	c.5524G>C	c.(5524-5526)Gtc>Ctc	p.V1842L	SCN3A_ENST00000465043.1_5'Flank|SCN3A_ENST00000283254.7_Missense_Mutation_p.V1842L|SCN3A_ENST00000409101.3_Missense_Mutation_p.V1793L|SCN3A_ENST00000540861.1_Missense_Mutation_p.V325L|AC013463.2_ENST00000431341.1_RNA	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1842					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCACCACTGACCATGGGCAGA	0.463																																					p.V1842L		Atlas-SNP	.											.	SCN3A	544	.	0			c.G5524C						.						100	99	99					2																	165947139		2203	4300	6503	SO:0001583	missense	6328	exon28			CACTGACCATGGG	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.5524G>C	chr2.hg19:g.165947139C>G	ENSP00000353206:p.Val1842Leu	229.0	0.0		269.0	22.0	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	hg19		.	.	.	.	.	.	.	.	.	.	C	22.8	4.334371	0.81801	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000540861	D;D;D;D	0.97016	-4.0;-4.0;-3.93;-4.21	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000019	D	0.98798	0.9595	H	0.94542	3.55	0.80722	D	1	P;B;D	0.67145	0.642;0.308;0.996	P;B;D	0.77004	0.898;0.335;0.989	D	0.99007	1.0813	10	0.87932	D	0	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	1793;1793;1842	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	L	1842;1842;1793;325	ENSP00000353206:V1842L;ENSP00000283254:V1842L;ENSP00000386726:V1793L;ENSP00000439920:V325L	ENSP00000283254:V1842L	V	-	1	0	SCN3A	165655385	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.884000	0.98904	0.655000	0.94253	GTC	.	.		0.463	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		G	165947139	C	G	165947139	3	3	140	1	0	0	0	0	1	0	0	0	13933	507	18	4	482	4	SCN3A	2	165947139	Missense_Mutation	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10	5636880	165947139	77252234	8	21867										
TTN	7273	hgsc.bcm.edu	37	chr2	179584040	179584040	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	actgacatttgggcccactaAcaatctcatttccatcctga	5	13	1	2			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr2:179584040A>G	ENST00000591111.1	-	81	23350	c.23126T>C	c.(23125-23127)gTt>gCt	p.V7709A	TTN_ENST00000342992.6_Missense_Mutation_p.V6782A|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V8026A			Q8WZ42	TITIN_HUMAN	titin	13252	Ig-like 59.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGGCCCACTAACAATCTCATT	0.517																																					p.V8026A		Atlas-SNP	.											.	TTN	18412	.	0			c.T24077C						.						126	126	126					2																	179584040		1901	4116	6017	SO:0001583	missense	7273	exon83			CCACTAACAATCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.23126T>C	chr2.hg19:g.179584040A>G	ENSP00000465570:p.Val7709Ala	100.0	0.0		110.0	7.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.28	1.305304	0.23736	.	.	ENSG00000155657	ENST00000342992	T	0.65178	-0.14	6.08	6.08	0.98989	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50599	0.1625	N	0.12502	0.225	0.25870	N	0.983712	B	0.15141	0.012	B	0.24701	0.055	T	0.52358	-0.8586	9	0.87932	D	0	.	16.6438	0.85155	1.0:0.0:0.0:0.0	.	7709	Q8WZ42	TITIN_HUMAN	A	6782	ENSP00000343764:V6782A	ENSP00000343764:V6782A	V	-	2	0	TTN	179292285	0.000000	0.05858	0.823000	0.32752	0.912000	0.54170	0.918000	0.28678	2.333000	0.79357	0.533000	0.62120	GTT	.	.		0.517	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179584040	A	G	179584040	3	3	140	1	0	0	0	0	1	0	0	0	16750	43	2	2	80572	2	TTN	2	179584040	Missense_Mutation	SNP	A	TCGA-DD-A4NS-01A-11D-A30V-10	13636901	179584040	63615333	9	21868										
SESTD1	91404	hgsc.bcm.edu	37	chr2	179997118	179997118	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	atgccccactgggctcttagTtgttctgatccaggcccttc	9	14	2	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr2:179997118T>C	ENST00000428443.3	-	10	1201	c.885A>G	c.(883-885)caA>caG	p.Q295Q		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	295							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			GGGCTCTTAGTTGTTCTGATC	0.443																																					p.Q295Q		Atlas-SNP	.											.	SESTD1	66	.	0			c.A885G						.						129	138	135					2																	179997118		2203	4300	6503	SO:0001819	synonymous_variant	91404	exon10			TCTTAGTTGTTCT	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.885A>G	chr2.hg19:g.179997118T>C		74.0	0.0		98.0	5.0	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Silent	SNP	ENST00000428443.3	hg19	CCDS33338.1																																																																																			.	.		0.443	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		C	179997118	T	C	179997118	2	2	140	1	0	0	0	0	0	0	0	1	14142	1722	60	2		2	SESTD1	2	179997118	Silent	SNP	T	TCGA-DD-A4NS-01A-11D-A30V-10	413078	179997118	63202255	10	21869										
OXTR	5021	hgsc.bcm.edu	37	chr3	8809008	8809008	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	tctgcacgaagaagaaaggcGtccagcacacgatgaaggcc	12	11	1	3			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr3:8809008G>A	ENST00000316793.3	-	3	1490	c.866C>T	c.(865-867)aCg>aTg	p.T289M	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	289					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	GAAGAAAGGCGTCCAGCACAC	0.612																																					p.T289M		Atlas-SNP	.											.	OXTR	31	.	0			c.C866T						.						46	40	42					3																	8809008		2203	4300	6503	SO:0001583	missense	5021	exon3			AAAGGCGTCCAGC		CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"GPCR / Class A : Vasopressin and oxytocin receptors"	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.866C>T	chr3.hg19:g.8809008G>A	ENSP00000324270:p.Thr289Met	86.0	0.0		119.0	9.0	NM_000916	Q15071	Missense_Mutation	SNP	ENST00000316793.3	hg19	CCDS2570.1	.	.	.	.	.	.	.	.	.	.	G	32	5.111847	0.94339	.	.	ENSG00000180914	ENST00000316793	T	0.72615	-0.67	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.81470	0.4829	M	0.76002	2.32	0.80722	D	1	D	0.62365	0.991	P	0.58077	0.832	D	0.84171	0.0434	10	0.72032	D	0.01	-40.8917	17.1817	0.86857	0.0:0.0:1.0:0.0	.	289	P30559	OXYR_HUMAN	M	289	ENSP00000324270:T289M	ENSP00000324270:T289M	T	-	2	0	OXTR	8784008	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.731000	0.98807	2.466000	0.83321	0.561000	0.74099	ACG	.	.		0.612	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2			A	8809008	G	A	8809008	3	1	140	1	0	0	0	0	1	0	0	0	11347	1145	40	1	311	1	OXTR	3	8809008	Missense_Mutation	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10		8809008	189213422	11	21870										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57488148	57488148	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	acacgtgttcaggaagttctGtgtcaagatttactggtgtt	11	6	3	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr3:57488148G>T	ENST00000351747.2	-	10	1325	c.1145C>A	c.(1144-1146)aCa>aAa	p.T382K	DNAH12_ENST00000311202.6_Missense_Mutation_p.T382K|DNAH12_ENST00000389536.4_Missense_Mutation_p.T382K	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	382	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						AGGAAGTTCTGTGTCAAGATT	0.378																																					p.T382K		Atlas-SNP	.											.	DNAH12	182	.	0			c.C1145A						.						224	199	207					3																	57488148		2203	4300	6503	SO:0001583	missense	201625	exon10			AGTTCTGTGTCAA	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.1145C>A	chr3.hg19:g.57488148G>T	ENSP00000295937:p.Thr382Lys	129.0	0.0		155.0	12.0	NM_198564	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	hg19		.	.	.	.	.	.	.	.	.	.	G	15.51	2.854469	0.51376	.	.	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536;ENST00000311202	T;T;T;T	0.23147	2.09;1.92;3.48;2.95	5.21	4.28	0.50868	.	0.315781	0.27591	N	0.018693	T	0.35740	0.0942	M	0.61703	1.905	0.80722	D	1	D;P	0.53745	0.962;0.651	P;B	0.49421	0.61;0.122	T	0.19778	-1.0295	10	0.62326	D	0.03	.	14.0674	0.64839	0.0:0.0:0.8505:0.1495	.	382;382	Q6ZR08-4;Q6ZR08	.;DYH12_HUMAN	K	382	ENSP00000295937:T382K;ENSP00000418137:T382K;ENSP00000374187:T382K;ENSP00000312554:T382K	ENSP00000312554:T382K	T	-	2	0	DNAH12	57463188	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.338000	0.65947	2.581000	0.87130	0.655000	0.94253	ACA	.	.		0.378	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		T	57488148	G	T	57488148	3	4	140	1	0	0	0	0	1	0	0	0	4602	1377	48	3	8376	3	DNAH12	3	57488148	Missense_Mutation	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10	48679140	57488148	140534282	12	21871										
PCDHGB7	56099	hgsc.bcm.edu	37	chr5	140799054	140799054	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	ccagggctcgcccgcgctcaGcgccaatgtgagcctgcgcg	14	17	1	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr5:140799054G>T	ENST00000398594.2	+	1	1628	c.1628G>T	c.(1627-1629)aGc>aTc	p.S543I	PCDHGA8_ENST00000398604.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	543	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCGCGCTCAGCGCCAATGTG	0.711																																					p.S543I		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.G1628T						.						26	32	30					5																	140799054		2059	4181	6240	SO:0001583	missense	56099	exon1			CGCTCAGCGCCAA	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1628G>T	chr5.hg19:g.140799054G>T	ENSP00000381594:p.Ser543Ile	85.0	0.0		92.0	8.0	NM_018927	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	hg19	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	g	17.39	3.376355	0.61735	.	.	ENSG00000254122	ENST00000398594	T	0.55930	0.49	5.38	5.38	0.77491	Cadherin (4);Cadherin-like (1);	0.489979	0.14288	U	0.329061	T	0.67896	0.2942	M	0.75264	2.295	0.25114	N	0.990695	D;P	0.53151	0.958;0.907	P;P	0.58210	0.835;0.751	T	0.62609	-0.6818	10	0.87932	D	0	.	12.1429	0.54008	0.0793:0.0:0.9207:0.0	.	543;543	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	I	543	ENSP00000381594:S543I	ENSP00000381594:S543I	S	+	2	0	PCDHGB7	140779238	0.992000	0.36948	1.000000	0.80357	0.858000	0.48976	4.904000	0.63279	2.513000	0.84729	0.491000	0.48974	AGC	.	.		0.711	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		T	140799054	G	T	140799054	3	4	140	1	0	0	0	0	1	0	0	0	11577	971	34	3	1630	3	PCDHGB7	5	140799054	Missense_Mutation	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10		140799054	40116206	13	21872										
ZNF300	91975	hgsc.bcm.edu	37	chr5	150275398	150275398	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	agaatgtctttccacattcaGtacattcataaggtttttcc	5	9	3	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr5:150275398G>T	ENST00000274599.5	-	6	1823	c.1403C>A	c.(1402-1404)aCt>aAt	p.T468N	ZNF300_ENST00000418587.2_Missense_Mutation_p.T432N|ZNF300_ENST00000427179.1_3'UTR|ZNF300_ENST00000446148.2_Missense_Mutation_p.T484N|ZNF300_ENST00000394226.2_Missense_Mutation_p.T468N	NM_052860.2	NP_443092.1	Q96RE9	ZN300_HUMAN	zinc finger protein 300	468					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)	27		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCACATTCAGTACATTCATA	0.413																																					p.T484N		Atlas-SNP	.											.	ZNF300	69	.	0			c.C1451A						.						84	79	81					5																	150275398		2203	4300	6503	SO:0001583	missense	91975	exon7			CATTCAGTACATT	AF395541	CCDS4311.2, CCDS54939.1, CCDS54940.1	5q33.1	2013-01-08			ENSG00000145908	ENSG00000145908		"Zinc fingers, C2H2-type", "-"	13091	protein-coding gene	gene with protein product		612429				14746915	Standard	NM_052860		Approved		uc021yfx.1	Q96RE9	OTTHUMG00000130076	ENST00000274599.5:c.1403C>A	chr5.hg19:g.150275398G>T	ENSP00000274599:p.Thr468Asn	73.0	0.0		95.0	5.0	NM_001172831	A8MY91|B3KU35|B4DU78|F5GWS1|Q06DQ3|Q17RP3|Q5H9N5	Missense_Mutation	SNP	ENST00000274599.5	hg19	CCDS4311.2	.	.	.	.	.	.	.	.	.	.	G	7.908	0.735880	0.15574	.	.	ENSG00000145908	ENST00000446148;ENST00000274599;ENST00000418587;ENST00000394226	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	3.64	2.68	0.31781	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09555	0.0235	N	0.21240	0.645	0.09310	N	1	B	0.17465	0.022	B	0.15870	0.014	T	0.33163	-0.9879	9	0.08381	T	0.77	.	8.0772	0.30722	0.0:0.0:0.6383:0.3617	.	468	Q96RE9	ZN300_HUMAN	N	484;468;432;468	ENSP00000397178:T484N;ENSP00000274599:T468N;ENSP00000392593:T432N;ENSP00000377773:T468N	ENSP00000274599:T468N	T	-	2	0	ZNF300	150255591	0.000000	0.05858	1.000000	0.80357	0.992000	0.81027	-1.130000	0.03241	2.059000	0.61396	0.591000	0.81541	ACT	.	.		0.413	ZNF300-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_052860		T	150275398	G	T	150275398	3	4	140	1	0	0	0	0	1	0	0	0	17846	1029	36	3	415	3	ZNF300	5	150275398	Missense_Mutation	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10	9476344	150275398	30639862	14	21873										
GFPT2	9945	hgsc.bcm.edu	37	chr5	179780211	179780211	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	cgggcgggcgcggcactcacCgcacatcgtggctgcttctc	14	16	2	0			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr5:179780211C>T	ENST00000253778.8	-	1	176	c.7G>A	c.(7-9)Gga>Aga	p.G3R		NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	3	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	CGGCACTCACCGCACATCGTG	0.776																																					p.G3R		Atlas-SNP	.											.	GFPT2	74	.	0			c.G7A						.						3	6	5					5																	179780211		1400	3242	4642	SO:0001630	splice_region_variant	9945	exon1			ACTCACCGCACAT	AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"glutamine: fructose-6-phosphate aminotransferase 2"	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.7+1G>A	chr5.hg19:g.179780211C>T		55.0	0.0		70.0	7.0	NM_005110	Q53XM2|Q9BWS4	Missense_Mutation	SNP	ENST00000253778.8	hg19	CCDS43411.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.449614	0.84101	.	.	ENSG00000131459	ENST00000253778	D	0.83506	-1.73	3.8	3.8	0.43715	Glutamine amidotransferase, type II (1);Glutamine amidotransferase, class-II (1);	0.000000	0.85682	D	0.000000	D	0.94265	0.8158	H	0.98833	4.345	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95435	0.8520	9	.	.	.	-14.9935	11.8895	0.52620	0.0:1.0:0.0:0.0	.	3	O94808	GFPT2_HUMAN	R	3	ENSP00000253778:G3R	.	G	-	1	0	GFPT2	179712817	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	2.086000	0.41643	2.066000	0.61787	0.555000	0.69702	GGA	.	.		0.776	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110	Missense_Mutation	T	179780211	C	T	179780211	5	4	140	1	0	0	0	0	0	0	1	0	6354	666	23	1	2117	1	GFPT2	5	179780211	Splice_Site	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10	29504813	179780211	1135049	15	21874										
SLC13A1	6561	hgsc.bcm.edu	37	chr7	122774465	122774465	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	acatgaaatatttacttactTgaatcctaggaaaagccact	5	8	0	2			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr7:122774465T>A	ENST00000194130.2	-	8	970	c.931A>T	c.(931-933)Aat>Tat	p.N311Y	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	311					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	TTTACTTACTTGAATCCTAGG	0.418																																					p.N311Y		Atlas-SNP	.											.	SLC13A1	110	.	0			c.A931T						.						92	84	87					7																	122774465		2203	4300	6503	SO:0001630	splice_region_variant	6561	exon8			CTTACTTGAATCC		CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"Solute carriers"	10916	protein-coding gene	gene with protein product		606193	"solute carrier family 13 (sodium/sulphate symporters), member 1"			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.932+1A>T	chr7.hg19:g.122774465T>A		90.0	0.0		116.0	8.0	NM_022444	Q9H5Z0	Missense_Mutation	SNP	ENST00000194130.2	hg19	CCDS5786.1	.	.	.	.	.	.	.	.	.	.	T	18.22	3.574810	0.65878	.	.	ENSG00000081800	ENST00000194130	T	0.03035	4.07	6.04	0.868	0.19090	.	0.352689	0.35805	N	0.002978	T	0.15349	0.0370	M	0.85373	2.75	0.80722	D	1	D;D	0.60160	0.987;0.987	D;D	0.67900	0.954;0.954	T	0.00218	-1.1908	10	0.54805	T	0.06	.	9.2357	0.37464	0.0:0.3702:0.0:0.6298	.	311;311	A4D0X1;Q9BZW2	.;S13A1_HUMAN	Y	311	ENSP00000194130:N311Y	ENSP00000194130:N311Y	N	-	1	0	SLC13A1	122561701	0.998000	0.40836	0.998000	0.56505	0.961000	0.63080	0.286000	0.18902	-0.070000	0.12908	-0.376000	0.06991	AAT	.	.		0.418	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444	Missense_Mutation	A	122774465	T	A	122774465	5	1	140	1	0	0	0	0	0	0	1	0	14406	1826	63	4	888	4	SLC13A1	7	122774465	Splice_Site	SNP	T	TCGA-DD-A4NS-01A-11D-A30V-10		122774465	36364198	16	21875										
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138768681	138768681	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	ggcagttgggaaaacgacagTtccctcgggtgaagtggtca	15	8	1	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr7:138768681T>C	ENST00000242351.5	-	3	858	c.542A>G	c.(541-543)aAc>aGc	p.N181S	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.N181S|ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.N181S	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	181	N-terminal domain.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						AAAACGACAGTTCCCTCGGGT	0.542																																					p.N181S		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.A542G						.						135	120	125					7																	138768681		2203	4300	6503	SO:0001583	missense	56829	exon3			CGACAGTTCCCTC	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.542A>G	chr7.hg19:g.138768681T>C	ENSP00000242351:p.Asn181Ser	74.0	0.0		94.0	4.0	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	hg19	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.887148	0.33348	.	.	ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652	T;T;T	0.40756	1.02;1.02;1.02	4.77	2.3	0.28687	Zinc finger, CCCH-type (1);	0.675658	0.14201	N	0.334673	T	0.39332	0.1074	L	0.57536	1.79	0.09310	N	1	P;P	0.52316	0.952;0.816	P;B	0.45881	0.496;0.307	T	0.18903	-1.0322	10	0.39692	T	0.17	.	5.4739	0.16686	0.1743:0.0:0.1823:0.6434	.	181;181	Q7Z2W4-2;Q7Z2W4	.;ZCCHV_HUMAN	S	181	ENSP00000242351:N181S;ENSP00000418385:N181S;ENSP00000419855:N181S	ENSP00000242351:N181S	N	-	2	0	ZC3HAV1	138419221	0.017000	0.18338	0.004000	0.12327	0.211000	0.24417	1.903000	0.39858	0.375000	0.24679	0.533000	0.62120	AAC	.	.		0.542	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		C	138768681	T	C	138768681	3	2	140	1	0	0	0	0	1	0	0	0	17590	1725	60	2	2214	2	ZC3HAV1	7	138768681	Missense_Mutation	SNP	T	TCGA-DD-A4NS-01A-11D-A30V-10	15994216	138768681	20369982	17	21876										
KLHL9	55958	hgsc.bcm.edu	37	chr9	21334572	21334572	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gaccaaccttgttcaccccaTgaagcttaatgcacatcaaa	5	13	2	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr9:21334572T>G	ENST00000359039.4	-	1	807	c.287A>C	c.(286-288)cAt>cCt	p.H96P	KLHL9_ENST00000537938.1_Missense_Mutation_p.H28P			Q9P2J3	KLHL9_HUMAN	kelch-like family member 9	96	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|midbody (GO:0030496)				endometrium(9)|large_intestine(7)|lung(10)|ovary(4)|skin(2)	32				Lung(24;8.52e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.118)		GTTCACCCCATGAAGCTTAAT	0.383																																					p.H96P		Atlas-SNP	.											.	KLHL9	61	.	0			c.A287C						.						138	128	132					9																	21334572		2203	4300	6503	SO:0001583	missense	55958	exon1			ACCCCATGAAGCT	AB037775	CCDS6503.1	9p22	2013-01-30	2013-01-30		ENSG00000198642	ENSG00000198642		"Kelch-like", "BTB/POZ domain containing"	18732	protein-coding gene	gene with protein product		611201	"kelch-like 9 (Drosophila)"				Standard	NM_018847		Approved	KIAA1354, FLJ13568	uc003zoy.3	Q9P2J3	OTTHUMG00000019669	ENST00000359039.4:c.287A>C	chr9.hg19:g.21334572T>G	ENSP00000351933:p.His96Pro	197.0	0.0		193.0	14.0	NM_018847	Q8TCQ2	Missense_Mutation	SNP	ENST00000359039.4	hg19	CCDS6503.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.471571	0.43942	.	.	ENSG00000198642	ENST00000359039;ENST00000537938	T;T	0.65549	-0.16;-0.16	5.49	5.49	0.81192	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.71643	0.3364	L	0.43598	1.365	0.80722	D	1	D	0.65815	0.995	D	0.70227	0.968	T	0.73260	-0.4039	10	0.56958	D	0.05	.	13.8561	0.63527	0.0:0.0:0.0:1.0	.	96	Q9P2J3	KLHL9_HUMAN	P	96;28	ENSP00000351933:H96P;ENSP00000437733:H28P	ENSP00000351933:H96P	H	-	2	0	KLHL9	21324572	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.217000	0.72218	2.222000	0.72286	0.533000	0.62120	CAT	.	.		0.383	KLHL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051898.2	NM_018847		G	21334572	T	G	21334572	3	3	140	1	0	0	0	0	1	0	0	0	8405	1464	51	5	1570	5	KLHL9	9	21334572	Missense_Mutation	SNP	T	TCGA-DD-A4NS-01A-11D-A30V-10		21334572	119878859	18	21877										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113192621	113192621	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gtgattttggttactcccatCaactggtatccttcctgaca	7	11	1	2			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr9:113192621C>A	ENST00000401783.2	-	33	5799	c.5463G>T	c.(5461-5463)ttG>ttT	p.L1821F	SVEP1_ENST00000374469.1_Missense_Mutation_p.L1798F|SVEP1_ENST00000297826.5_5'Flank	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1821	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TTACTCCCATCAACTGGTATC	0.398																																					p.L1821F		Atlas-SNP	.											.	SVEP1	326	.	0			c.G5463T						.						87	79	81					9																	113192621		1877	4114	5991	SO:0001583	missense	79987	exon33			TCCCATCAACTGG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.5463G>T	chr9.hg19:g.113192621C>A	ENSP00000384917:p.Leu1821Phe	120.0	0.0		163.0	12.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	14.93	2.683181	0.47991	.	.	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.70749	-0.51;-0.51	5.27	4.34	0.51931	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.86883	0.6040	M	0.92077	3.27	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.88723	0.3231	10	0.51188	T	0.08	.	15.4306	0.75092	0.1391:0.8609:0.0:0.0	.	1821	Q4LDE5	SVEP1_HUMAN	F	1821;1798	ENSP00000384917:L1821F;ENSP00000363593:L1798F	ENSP00000363593:L1798F	L	-	3	2	SVEP1	112232442	0.909000	0.30893	0.958000	0.39756	0.548000	0.35241	1.564000	0.36375	2.735000	0.93741	0.655000	0.94253	TTG	.	.		0.398	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113192621	C	A	113192621	3	1	140	1	0	0	0	0	1	0	0	0	15435	825	29	3	5316	3	SVEP1	9	113192621	Missense_Mutation	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10	91858049	113192621	28020810	19	21878										
CPN1	1369	hgsc.bcm.edu	37	chr10	101823465	101823465	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	aacatccatccatgtgcataGgagtagaccttggccagcta	9	11	0	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr10:101823465G>T	ENST00000370418.3	-	5	1028	c.777C>A	c.(775-777)tcC>tcA	p.S259S		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	259	Catalytic.				response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.S259S(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		CATGTGCATAGGAGTAGACCT	0.493																																					p.S259S		Atlas-SNP	.											CPN1,colon,carcinoma,0,1	CPN1	62	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C777A						.						100	91	94					10																	101823465		2203	4300	6503	SO:0001819	synonymous_variant	1369	exon5			TGCATAGGAGTAG	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"anaphylatoxin inactivator", "arginine carboxypeptidase", "carboxypeptidase K", "kininase I", "lysine carboxypeptidase"	603103	"carboxypeptidase N, polypeptide 1, 50kD"			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.777C>A	chr10.hg19:g.101823465G>T		53.0	0.0		80.0	10.0	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	hg19	CCDS7486.1																																																																																			.	.		0.493	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		T	101823465	G	T	101823465	2	4	140	1	0	0	0	0	0	0	0	1	3811	987	35	3		3	CPN1	10	101823465	Silent	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10		101823465	33711282	20	21879										
MUC2	4583	hgsc.bcm.edu	37	chr11	1080902	1080902	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	caacgattcctacgctctccTgggcgagctggccccctgtg	11	16	1	0			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr11:1080902T>A	ENST00000441003.2	+	10	1313	c.1286T>A	c.(1285-1287)cTg>cAg	p.L429Q	MUC2_ENST00000359061.5_Missense_Mutation_p.L429Q	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	429	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TACGCTCTCCTGGGCGAGCTG	0.647																																					p.L429Q		Atlas-SNP	.											.	MUC2	614	.	0			c.T1286A						.						58	66	63					11																	1080902		2080	4207	6287	SO:0001583	missense	4583	exon10			CTCTCCTGGGCGA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.1286T>A	chr11.hg19:g.1080902T>A	ENSP00000415183:p.Leu429Gln	65.0	0.0		95.0	7.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	T	10.23	1.292151	0.23564	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.61627	0.09;0.09	3.57	3.57	0.40892	.	0.000000	0.48286	U	0.000200	T	0.70509	0.3232	M	0.68593	2.085	0.34140	D	0.666289	D	0.56035	0.974	D	0.64877	0.93	T	0.80708	-0.1262	10	0.72032	D	0.01	.	12.305	0.54898	0.0:0.0:0.0:1.0	.	429	E7EUV1	.	Q	429	ENSP00000415183:L429Q;ENSP00000351956:L429Q	ENSP00000351956:L429Q	L	+	2	0	MUC2	1070902	1.000000	0.71417	0.977000	0.42913	0.174000	0.22865	3.746000	0.55127	1.513000	0.48852	0.358000	0.22013	CTG	.	.		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1080902	T	A	1080902	3	1	140	1	0	0	0	0	1	0	0	0	9984	1580	55	4	1324	4	MUC2	11	1080902	Missense_Mutation	SNP	T	TCGA-DD-A4NS-01A-11D-A30V-10		1080902	133925614	21	21880										
OR51S1	119692	hgsc.bcm.edu	37	chr11	4869689	4869689	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	aggagcactgcagagaggtgGgcagcacaggtttgaccagc	16	9	0	2			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr11:4869689G>T	ENST00000322101.2	-	1	825	c.750C>A	c.(748-750)gcC>gcA	p.A250A	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	250						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGAGAGGTGGGCAGCACAGG	0.512																																					p.A250A		Atlas-SNP	.											.	OR51S1	83	.	0			c.C750A						.						97	83	88					11																	4869689		2201	4298	6499	SO:0001819	synonymous_variant	119692	exon1			GAGGTGGGCAGCA	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"GPCR / Class A : Olfactory receptors"	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.750C>A	chr11.hg19:g.4869689G>T		101.0	0.0		124.0	13.0	NM_001004758	B9EGZ1|Q6IFI2	Silent	SNP	ENST00000322101.2	hg19	CCDS31362.1																																																																																			.	.		0.512	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758		T	4869689	G	T	4869689	2	4	140	1	0	0	0	0	0	0	0	1	11114	1219	43	3		3	OR51S1	11	4869689	Silent	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10	3788787	4869689	130136827	22	21881										
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1949905	1949905	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	accacaagggccgttcctacCtgcagcaatggctgtcctct	9	15	1	0			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr12:1949905C>T	ENST00000382722.5	-	26	2913	c.2551G>A	c.(2551-2553)Gcc>Acc	p.A851T	CACNA2D4_ENST00000585708.1_Splice_Site_p.A787T|CACNA2D4_ENST00000586184.1_Splice_Site_p.A851T|CACNA2D4_ENST00000585732.1_Splice_Site_p.A712T|CACNA2D4_ENST00000587995.1_Splice_Site_p.A826T|CACNA2D4_ENST00000588077.1_Splice_Site_p.A787T	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	851					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		CCGTTCCTACCTGCAGCAATG	0.592																																					p.A851T	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.G2551A						.						69	75	73					12																	1949905		2157	4249	6406	SO:0001630	splice_region_variant	93589	exon26			TCCTACCTGCAGC	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"Calcium channel subunits"	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.2551+1G>A	chr12.hg19:g.1949905C>T		37.0	0.0		21.0	6.0	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	hg19	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.259698	0.80246	.	.	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.69926	-0.44	4.97	4.97	0.65823	.	0.146062	0.45126	N	0.000397	T	0.73697	0.3620	M	0.63428	1.95	0.58432	D	0.999994	P;P	0.49090	0.912;0.919	P;P	0.52159	0.691;0.543	T	0.74237	-0.3730	9	.	.	.	.	17.0724	0.86578	0.0:1.0:0.0:0.0	.	851;851	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	T	787;851;851	ENSP00000372169:A851T	.	A	-	1	0	CACNA2D4	1820166	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	7.172000	0.77604	2.319000	0.78375	0.555000	0.69702	GCC	.	.		0.592	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		Missense_Mutation	T	1949905	C	T	1949905	5	4	140	1	0	0	0	0	0	0	1	0	2553	695	24	3	914	3	CACNA2D4	12	1949905	Splice_Site	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10		1949905	131901990	23	21882										
KRT73	319101	hgsc.bcm.edu	37	chr12	53007536	53007536	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	cgatctcctcatactgggcaCggacctcagcaatgatgctg	10	13	3	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr12:53007536C>T	ENST00000305748.3	-	5	954	c.920G>A	c.(919-921)cGt>cAt	p.R307H	RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000551089.1_RNA|RP11-641A6.2_ENST00000549180.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	307	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		ATACTGGGCACGGACCTCAGC	0.582																																					p.R307H		Atlas-SNP	.											.	KRT73	101	.	0			c.G920A						.						144	121	129					12																	53007536		2203	4300	6503	SO:0001583	missense	319101	exon5			TGGGCACGGACCT	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"-", "Intermediate filaments type II, keratins (basic)"	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.920G>A	chr12.hg19:g.53007536C>T	ENSP00000307014:p.Arg307His	77.0	0.0		93.0	6.0	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	hg19	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.199922	0.58126	.	.	ENSG00000186049	ENST00000305748;ENST00000552855	D;D	0.93307	-3.2;-3.2	5.07	4.16	0.48862	Filament (1);	0.000000	0.49916	D	0.000133	D	0.93789	0.8014	H	0.95745	3.715	0.09310	N	1	P	0.36633	0.562	B	0.36186	0.219	D	0.90605	0.4547	10	0.87932	D	0	.	4.0	0.09576	0.2031:0.6029:0.0:0.194	.	307	Q86Y46	K2C73_HUMAN	H	307;52	ENSP00000307014:R307H;ENSP00000449081:R52H	ENSP00000307014:R307H	R	-	2	0	KRT73	51293803	0.000000	0.05858	0.287000	0.24848	0.941000	0.58515	0.199000	0.17237	1.240000	0.43803	0.655000	0.94253	CGT	.	.		0.582	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		T	53007536	C	T	53007536	3	4	140	1	0	0	0	0	1	0	0	0	8495	536	19	1	722	1	KRT73	12	53007536	Missense_Mutation	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10	51057631	53007536	80844359	24	21883										
MYO1A	4640	hgsc.bcm.edu	37	chr12	57442030	57442030	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	tcatagcgaagctgaagattCttgagcagtgactcctccac	9	11	2	4			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr12:57442030C>A	ENST00000442789.2	-	3	365	c.78G>T	c.(76-78)aaG>aaT	p.K26N	MYO1A_ENST00000544473.1_5'Flank|MYO1A_ENST00000300119.3_Missense_Mutation_p.K26N	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	26	Myosin motor.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.K26N(1)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						GCTGAAGATTCTTGAGCAGTG	0.542																																					p.K26N		Atlas-SNP	.											MYO1A,colon,carcinoma,0,1	MYO1A	122	.	1	Substitution - Missense(1)	large_intestine(1)	c.G78T						.						83	72	76					12																	57442030		2203	4300	6503	SO:0001583	missense	4640	exon2			AAGATTCTTGAGC	L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.78G>T	chr12.hg19:g.57442030C>A	ENSP00000393392:p.Lys26Asn	59.0	1.0		77.0	5.0	NM_005379	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	hg19	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	C	10.08	1.251435	0.22880	.	.	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000433964	D;D;D	0.86956	-2.19;-2.19;-2.19	4.76	3.8	0.43715	Myosin head, motor domain (2);	0.317552	0.28977	N	0.013536	T	0.67078	0.2855	N	0.01668	-0.77	0.80722	D	1	B	0.31413	0.322	B	0.31191	0.125	T	0.67917	-0.5546	10	0.22109	T	0.4	.	12.4003	0.55410	0.0:0.8288:0.1711:0.0	.	26	Q9UBC5	MYO1A_HUMAN	N	26	ENSP00000300119:K26N;ENSP00000393392:K26N;ENSP00000400991:K26N	ENSP00000300119:K26N	K	-	3	2	MYO1A	55728297	0.197000	0.23362	1.000000	0.80357	0.582000	0.36321	-0.021000	0.12504	2.368000	0.80403	0.462000	0.41574	AAG	.	.		0.542	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		A	57442030	C	A	57442030	3	1	140	1	0	0	0	0	1	0	0	0	10077	912	32	3	3161	3	MYO1A	12	57442030	Missense_Mutation	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10	4434494	57442030	76409865	25	21884										
KSR2	283455	hgsc.bcm.edu	37	chr12	118198839	118198839	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	ggcgtgtgggcctcgtccacGcggtgccccagctggaactc	15	15	0	0			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr12:118198839G>A	ENST00000339824.5	-	4	1690	c.963C>T	c.(961-963)cgC>cgT	p.R321R	KSR2_ENST00000425217.1_Silent_p.R292R			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	321					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCTCGTCCACGCGGTGCCCCA	0.677																																					p.R292R		Atlas-SNP	.											.	KSR2	208	.	0			c.C876T						.						44	54	51					12																	118198839		1973	4161	6134	SO:0001819	synonymous_variant	283455	exon4			GTCCACGCGGTGC	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.963C>T	chr12.hg19:g.118198839G>A		99.0	0.0		104.0	7.0	NM_173598	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	hg19																																																																																				.	.		0.677	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		A	118198839	G	A	118198839	2	1	140	1	0	0	0	0	0	0	0	1	8591	1074	38	1		1	KSR2	12	118198839	Silent	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10	60756809	118198839	15653056	26	21885										
FREM2	341640	hgsc.bcm.edu	37	chr13	39264479	39264479	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	aaatcttggtcaatggcattCcagcagagcagtttactcaa	8	9	3	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr13:39264479C>G	ENST00000280481.7	+	1	3214	c.2998C>G	c.(2998-3000)Cca>Gca	p.P1000A		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1000					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CAATGGCATTCCAGCAGAGCA	0.438																																					p.P1000A		Atlas-SNP	.											.	FREM2	385	.	0			c.C2998G						.						137	140	139					13																	39264479		2203	4300	6503	SO:0001583	missense	341640	exon1			GGCATTCCAGCAG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.2998C>G	chr13.hg19:g.39264479C>G	ENSP00000280481:p.Pro1000Ala	147.0	0.0		148.0	13.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	9.052	0.992225	0.18966	.	.	ENSG00000150893	ENST00000280481	T	0.22539	1.95	5.79	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.28466	0.0704	M	0.81179	2.53	0.80722	D	1	B	0.32338	0.365	B	0.30401	0.115	T	0.05599	-1.0875	10	0.29301	T	0.29	.	14.9625	0.71166	0.0:0.9314:0.0:0.0686	.	1000	Q5SZK8	FREM2_HUMAN	A	1000	ENSP00000280481:P1000A	ENSP00000280481:P1000A	P	+	1	0	FREM2	38162479	1.000000	0.71417	0.997000	0.53966	0.586000	0.36452	4.942000	0.63547	1.461000	0.47929	0.650000	0.86243	CCA	.	.		0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39264479	C	G	39264479	3	3	140	1	0	0	0	0	1	0	0	0	6053	855	30	4	3000	4	FREM2	13	39264479	Missense_Mutation	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10		39264479	75905399	27	21886										
GPR137C	283554	hgsc.bcm.edu	37	chr14	53098899	53098899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gtatgtctctgtgccagactGtcgtcgtgggctctgtagtc	13	10	2	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr14:53098899G>A	ENST00000321662.6	+	4	739	c.739G>A	c.(739-741)Gtc>Atc	p.V247I		NM_001099652.1	NP_001093122.1	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C	247						integral component of membrane (GO:0016021)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8	Breast(41;0.0716)					GTGCCAGACTGTCGTCGTGGG	0.378																																					p.V247I		Atlas-SNP	.											.	GPR137C	24	.	0			c.G739A						.						159	159	159					14																	53098899		1896	4123	6019	SO:0001583	missense	283554	exon4			CAGACTGTCGTCG	BX647179	CCDS45106.1	14q22.1	2012-08-10				ENSG00000180998			25445	protein-coding gene	gene with protein product							Standard	NM_001099652		Approved	DKFZp762F0713, TM7SF1L2	uc001wzu.4	Q8N3F9		ENST00000321662.6:c.739G>A	chr14.hg19:g.53098899G>A	ENSP00000315106:p.Val247Ile	150.0	0.0		146.0	12.0	NM_001099652	Q86SM2	Missense_Mutation	SNP	ENST00000321662.6	hg19	CCDS45106.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.43|14.43	2.533958|2.533958	0.45073|0.45073	.|.	.|.	ENSG00000180998|ENSG00000180998	ENST00000542169|ENST00000321662	.|T	.|0.42513	.|0.97	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	.|0.155710	.|0.64402	.|D	.|0.000020	T|T	0.24431|0.24431	0.0592|0.0592	L|L	0.27053|0.27053	0.805|0.805	0.35697|0.35697	D|D	0.81531|0.81531	.|B;B	.|0.24721	.|0.11;0.11	.|B;B	.|0.20184	.|0.028;0.028	T|T	0.16305|0.16305	-1.0407|-1.0407	5|10	.|0.05620	.|T	.|0.96	-20.8916|-20.8916	9.6536|9.6536	0.39912|0.39912	0.0807:0.1451:0.7741:0.0|0.0807:0.1451:0.7741:0.0	.|.	.|247;76	.|Q8N3F9;B3KW22	.|G137C_HUMAN;.	Y|I	216|247	.|ENSP00000315106:V247I	.|ENSP00000315106:V247I	C|V	+|+	2|1	0|0	GPR137C|GPR137C	52168649|52168649	0.994000|0.994000	0.37717|0.37717	0.985000|0.985000	0.45067|0.45067	0.984000|0.984000	0.73092|0.73092	2.651000|2.651000	0.46674|0.46674	2.789000|2.789000	0.95967|0.95967	0.591000|0.591000	0.81541|0.81541	TGT|GTC	.	.		0.378	GPR137C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411685.1	XM_290615		A	53098899	G	A	53098899	3	1	140	1	0	0	0	0	1	0	0	0	6655	1377	48	3	753	3	GPR137C	14	53098899	Missense_Mutation	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10		53098899	54250641	28	21887										
MAPK6	5597	hgsc.bcm.edu	37	chr15	52342240	52342240	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	tggtacagatctccacgtctTttactttctcctaataatta	4	10	3	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr15:52342240T>G	ENST00000261845.5	+	3	1413	c.606T>G	c.(604-606)ctT>ctG	p.L202L		NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	202	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		CTCCACGTCTTTTACTTTCTC	0.363																																					p.L202L		Atlas-SNP	.											.	MAPK6	70	.	0			c.T606G						.						92	98	96					15																	52342240		2195	4293	6488	SO:0001819	synonymous_variant	5597	exon3			ACGTCTTTTACTT	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"Mitogen-activated protein kinase cascade / Kinases"	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.606T>G	chr15.hg19:g.52342240T>G		118.0	0.0		115.0	6.0	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Silent	SNP	ENST00000261845.5	hg19	CCDS10147.1																																																																																			.	T|1.000;|0.000		0.363	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748		G	52342240	T	G	52342240	2	3	140	1	0	0	0	0	0	0	0	1	9290	1828	64	5		5	MAPK6	15	52342240	Silent	SNP	T	TCGA-DD-A4NS-01A-11D-A30V-10		52342240	50189152	29	21888										
POLG	5428	hgsc.bcm.edu	37	chr15	89866679	89866679	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gcagccagggatgtccacgtCgttgtaaggtccattgccat	12	11	0	0			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr15:89866679C>A	ENST00000268124.5	-	13	2554	c.2221G>T	c.(2221-2223)Gac>Tac	p.D741Y	POLG_ENST00000442287.2_Missense_Mutation_p.D741Y	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	741					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			ATGTCCACGTCGTTGTAAGGT	0.582								DNA polymerases (catalytic subunits)																													p.D741Y	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.G2221T						.						182	127	145					15																	89866679		2200	4299	6499	SO:0001583	missense	5428	exon13			CCACGTCGTTGTA	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"DNA polymerases"	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.2221G>T	chr15.hg19:g.89866679C>A	ENSP00000268124:p.Asp741Tyr	98.0	0.0		100.0	4.0	NM_002693	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	hg19	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890552	0.91889	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.97016	-4.21;-4.21	5.57	5.57	0.84162	DNA-directed DNA polymerase, family A, palm domain (1);	0.000000	0.85682	D	0.000000	D	0.97983	0.9336	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.98539	1.0631	10	0.72032	D	0.01	-15.7528	19.5413	0.95275	0.0:1.0:0.0:0.0	.	741	P54098	DPOG1_HUMAN	Y	741	ENSP00000268124:D741Y;ENSP00000399851:D741Y	ENSP00000268124:D741Y	D	-	1	0	POLG	87667683	1.000000	0.71417	0.763000	0.31416	0.953000	0.61014	7.649000	0.83500	2.640000	0.89533	0.650000	0.86243	GAC	.	.		0.582	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		A	89866679	C	A	89866679	3	1	140	1	0	0	0	0	1	0	0	0	12209	884	31	1	1542	1	POLG	15	89866679	Missense_Mutation	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10	37524439	89866679	12664713	30	21889										
NF1	4763	hgsc.bcm.edu	37	chr17	29592318	29592318	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	tttctaccaagctgggacttCcaaagctgggaatcctattt	8	10	1	0			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr17:29592318C>A	ENST00000358273.4	+	36	5179	c.4796C>A	c.(4795-4797)tCc>tAc	p.S1599Y	NF1_ENST00000356175.3_Missense_Mutation_p.S1578Y	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1599	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GCTGGGACTTCCAAAGCTGGG	0.313			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.S1599Y		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.C4796A	GRCh37	CM077303	NF1	M		.						66	68	67					17																	29592318		2203	4297	6500	SO:0001583	missense	4763	exon36	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	GGACTTCCAAAGC		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4796C>A	chr17.hg19:g.29592318C>A	ENSP00000351015:p.Ser1599Tyr	268.0	0.0		303.0	19.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.887938	0.91814	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.60548	0.18;0.18;0.18	5.9	5.9	0.94986	Cellular retinaldehyde-binding/triple function, C-terminal (2);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.79375	0.4435	M	0.79805	2.47	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.80578	-0.1320	10	0.87932	D	0	.	20.2789	0.98501	0.0:1.0:0.0:0.0	.	628;1578;1599	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	Y	1599;1578;1244	ENSP00000351015:S1599Y;ENSP00000348498:S1578Y;ENSP00000389907:S1244Y	ENSP00000348498:S1578Y	S	+	2	0	NF1	26616444	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.266000	0.78452	2.788000	0.95919	0.650000	0.86243	TCC	.	.		0.313	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		A	29592318	C	A	29592318	3	1	140	1	0	0	0	0	1	0	0	0	10365	855	30	3	4999	3	NF1	17	29592318	Missense_Mutation	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10		29592318	51602892	31	21890										
ACACA	31	hgsc.bcm.edu	37	chr17	35580444	35580444	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	aatacttacctccagagctgCcatcctcactacttggttgc	6	14	1	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr17:35580444C>T	ENST00000394406.2	-	28	3632	c.3442G>A	c.(3442-3444)Gca>Aca	p.A1148T	ACACA_ENST00000360679.3_Missense_Mutation_p.A1090T|ACACA_ENST00000353139.5_Missense_Mutation_p.A1185T|ACACA_ENST00000335166.5_Missense_Mutation_p.A1070T	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1148					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TCCAGAGCTGCCATCCTCACT	0.403																																					p.A1185T	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.G3553A						.						200	179	186					17																	35580444		2203	4300	6503	SO:0001583	missense	31	exon28			GAGCTGCCATCCT	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.3442G>A	chr17.hg19:g.35580444C>T	ENSP00000377928:p.Ala1148Thr	76.0	0.0		84.0	4.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	hg19	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	C	34	5.404969	0.96051	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38	5.71	5.71	0.89125	Acetyl-CoA carboxylase, central domain (1);	0.049621	0.85682	D	0.000000	D	0.83746	0.5321	M	0.92507	3.315	0.80722	D	1	P;P;P	0.49358	0.923;0.798;0.759	P;P;P	0.55749	0.783;0.615;0.48	D	0.86718	0.1940	10	0.59425	D	0.04	-13.555	18.0482	0.89340	0.0:1.0:0.0:0.0	.	1185;1148;1090	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	T	1185;1090;1148;1172;1070	ENSP00000344789:A1185T;ENSP00000353898:A1090T;ENSP00000377928:A1148T;ENSP00000335323:A1070T	ENSP00000335323:A1070T	A	-	1	0	ACACA	32654557	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.709000	0.92574	0.655000	0.94253	GCA	.	.		0.403	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		T	35580444	C	T	35580444	3	4	140	1	0	0	0	0	1	0	0	0	106	739	26	3	3714	3	ACACA	17	35580444	Missense_Mutation	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10	5988126	35580444	45614766	32	21891										
NAGLU	4669	hgsc.bcm.edu	37	chr17	40689487	40689487	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	ggactgggcccgctgggagcGagagatagactggatggcgc	19	9	0	2	rs141018386		TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr17:40689487G>A	ENST00000225927.2	+	2	556	c.455G>A	c.(454-456)cGa>cAa	p.R152Q	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	152					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	CGCTGGGAGCGAGAGATAGAC	0.632																																					p.R152Q		Atlas-SNP	.											.	NAGLU	36	.	0			c.G455A						.	G	GLN/ARG	0,4406		0,0,2203	132	115	121		455	-5.5	0.4	17	dbSNP_134	121	1,8599	1.2+/-3.3	0,1,4299	no	missense	NAGLU	NM_000263.3	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	152/744	40689487	1,13005	2203	4300	6503	SO:0001583	missense	4669	exon2			GGGAGCGAGAGAT		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"Sanfilippo disease IIIB"	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.455G>A	chr17.hg19:g.40689487G>A	ENSP00000225927:p.Arg152Gln	70.0	0.0		84.0	10.0	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	hg19	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.587036	0.46110	0.0	1.16E-4	ENSG00000108784	ENST00000225927	D	0.98028	-4.67	4.3	-5.49	0.02584	Alpha-N-acetylglucosaminidase, tim-barrel domain (1);	0.744172	0.12823	N	0.436305	D	0.93363	0.7884	L	0.41356	1.27	0.09310	N	0.999996	P	0.35527	0.507	B	0.25614	0.062	T	0.82615	-0.0370	10	0.38643	T	0.18	-0.3759	15.2631	0.73640	0.3206:0.0:0.6794:0.0	.	152	P54802	ANAG_HUMAN	Q	152	ENSP00000225927:R152Q	ENSP00000225927:R152Q	R	+	2	0	NAGLU	37943013	0.000000	0.05858	0.438000	0.26821	0.987000	0.75469	0.127000	0.15790	-1.119000	0.02958	-0.291000	0.09656	CGA	.	G|1.000;A|0.000		0.632	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		A	40689487	G	A	40689487	3	1	140	1	0	0	0	0	1	0	0	0	10152	1058	37	1	461	1	NAGLU	17	40689487	Missense_Mutation	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10	5109043	40689487	40505723	33	21892										
PNPLA6	10908	hgsc.bcm.edu	37	chr19	7615936	7615936	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gtgcacgcggtgcgcgacacGgagctggccaagcttcccga	15	14	0	0			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr19:7615936G>A	ENST00000221249.6	+	20	2441	c.2010G>A	c.(2008-2010)acG>acA	p.T670T	PNPLA6_ENST00000600737.1_Silent_p.T709T|PNPLA6_ENST00000545201.2_Silent_p.T644T|PNPLA6_ENST00000414982.3_Silent_p.T718T|PNPLA6_ENST00000450331.3_Silent_p.T670T	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	709					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						TGCGCGACACGGAGCTGGCCA	0.706																																					p.T718T		Atlas-SNP	.											.	PNPLA6	163	.	0			c.G2154A						.						5	6	5					19																	7615936		2021	3905	5926	SO:0001819	synonymous_variant	10908	exon19			CGACACGGAGCTG	AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"Patatin-like phospholipase domain containing"	16268	protein-coding gene	gene with protein product	"neuropathy target esterase"	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.2010G>A	chr19.hg19:g.7615936G>A		47.0	0.0		62.0	7.0	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	ENST00000221249.6	hg19	CCDS32891.1																																																																																			.	.		0.706	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702		A	7615936	G	A	7615936	2	1	140	1	0	0	0	0	0	0	0	1	12178	1103	39	1		1	PNPLA6	19	7615936	Silent	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10		7615936	51513047	34	21893										
ZNF430	80264	hgsc.bcm.edu	37	chr19	21216304	21216304	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	tggccatagaattttctctgGaggagtggcaatgcctggac	13	8	1	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr19:21216304G>T	ENST00000261560.5	+	3	320	c.139G>T	c.(139-141)Gag>Tag	p.E47*	ZNF430_ENST00000599548.1_Nonsense_Mutation_p.E47*|ZNF430_ENST00000595401.1_Nonsense_Mutation_p.E47*	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	47	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						ATTTTCTCTGGAGGAGTGGCA	0.443																																					p.E47X		Atlas-SNP	.											.	ZNF430	59	.	0			c.G139T						.						115	119	118					19																	21216304		2203	4300	6503	SO:0001587	stop_gained	80264	exon3			TCTCTGGAGGAGT	AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"Zinc fingers, C2H2-type", "-"	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.139G>T	chr19.hg19:g.21216304G>T	ENSP00000261560:p.Glu47*	148.0	0.0		176.0	19.0	NM_025189	Q86V70	Nonsense_Mutation	SNP	ENST00000261560.5	hg19	CCDS32978.1	.	.	.	.	.	.	.	.	.	.	.	12.55	1.972866	0.34848	.	.	ENSG00000118620	ENST00000261560	.	.	.	0.916	0.916	0.19373	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	4.9698	0.14110	0.0:0.0:1.0:0.0	.	.	.	.	X	47	.	ENSP00000261560:E47X	E	+	1	0	ZNF430	21008144	0.782000	0.28689	0.090000	0.20809	0.093000	0.18481	0.998000	0.29744	0.300000	0.22699	0.305000	0.20034	GAG	.	.		0.443	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189		T	21216304	G	T	21216304	4	4	140	1	0	0	0	0	0	1	0	0	17919	1175	41	3	149	3	ZNF430	19	21216304	Nonsense_Mutation	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10	13600368	21216304	37912679	35	21894										
NPTXR	23467	hgsc.bcm.edu	37	chr22	39222683	39222683	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gcagagccttccgcacgcggGcgtacatgtagttgttacgg	14	11	0	1			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr22:39222683G>T	ENST00000333039.2	-	3	1043	c.920C>A	c.(919-921)gCc>gAc	p.A307D		NM_014293.3	NP_055108	O95502	NPTXR_HUMAN	neuronal pentraxin receptor	307	Pentaxin.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			central_nervous_system(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	Melanoma(58;0.04)					CCGCACGCGGGCGTACATGTA	0.632																																					p.A307D	Pancreas(139;2521 3281 36965)	Atlas-SNP	.											.	NPTXR	34	.	0			c.C920A						.						94	84	87					22																	39222683		2203	4300	6503	SO:0001583	missense	23467	exon3			ACGCGGGCGTACA	AF052163	CCDS33647.1	22q13.1	2007-01-25			ENSG00000221890	ENSG00000221890			7954	protein-coding gene	gene with protein product		609474				16497176	Standard	NM_014293		Approved		uc003awk.3	O95502	OTTHUMG00000150458	ENST00000333039.2:c.920C>A	chr22.hg19:g.39222683G>T	ENSP00000327545:p.Ala307Asp	68.0	0.0		88.0	13.0	NM_014293		Missense_Mutation	SNP	ENST00000333039.2	hg19	CCDS33647.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.872137	0.72180	.	.	ENSG00000221890	ENST00000333039	T	0.06528	3.29	4.64	2.48	0.30137	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.053901	0.64402	D	0.000001	T	0.29491	0.0735	M	0.88979	2.995	0.35904	D	0.830572	D	0.76494	0.999	D	0.72075	0.976	T	0.55068	-0.8198	9	0.72032	D	0.01	-39.9976	16.1083	0.81241	0.0:0.5096:0.4904:0.0	.	307	O95502	NPTXR_HUMAN	D	307	ENSP00000327545:A307D	ENSP00000327545:A307D	A	-	2	0	NPTXR	37552629	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.328000	0.33758	0.833000	0.34828	0.655000	0.94253	GCC	.	.		0.632	NPTXR-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318194.2	NM_014293		T	39222683	G	T	39222683	3	4	140	1	0	0	0	0	1	0	0	0	10613	1203	42	3	594	3	NPTXR	22	39222683	Missense_Mutation	SNP	G	TCGA-DD-A4NS-01A-11D-A30V-10		39222683	12081883	36	21895										
SYNGR1	9145	hgsc.bcm.edu	37	chr22	39746105	39746105	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	ccgcacaccatcctgcgcgtCgtgtcttgggtaaggacgga	13	13	1	0			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chr22:39746105C>A	ENST00000328933.5	+	1	105	c.90C>A	c.(88-90)gtC>gtA	p.V30V	SYNGR1_ENST00000216155.7_Silent_p.V30V|SYNGR1_ENST00000318801.4_Silent_p.V30V|SYNGR1_ENST00000406293.3_Silent_p.V30V	NM_004711.4	NP_004702.2	O43759	SNG1_HUMAN	synaptogyrin 1	30	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				protein targeting (GO:0006605)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle membrane (GO:0030672)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	7	Melanoma(58;0.04)					TCCTGCGCGTCGTGTCTTGGG	0.726																																					p.V30V		Atlas-SNP	.											.	SYNGR1	19	.	0			c.C90A						.						9	10	10					22																	39746105		2130	4203	6333	SO:0001819	synonymous_variant	9145	exon1			GCGCGTCGTGTCT	AJ002303	CCDS13989.1, CCDS13990.1, CCDS13991.1	22q13	2008-06-10			ENSG00000100321	ENSG00000100321			11498	protein-coding gene	gene with protein product		603925				9760194, 10595519	Standard	NM_004711		Approved			O43759	OTTHUMG00000030978	ENST00000328933.5:c.90C>A	chr22.hg19:g.39746105C>A		49.0	0.0		56.0	5.0	NM_145731	A6NP69|A8K0E2|O43757|O43758|Q53Y02|Q96J56|Q9UGZ4	Silent	SNP	ENST00000328933.5	hg19	CCDS13989.1																																																																																			.	.		0.726	SYNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075866.2	NM_004711		A	39746105	C	A	39746105	2	1	140	1	0	0	0	0	0	0	0	1	15463	871	31	1		1	SYNGR1	22	39746105	Silent	SNP	C	TCGA-DD-A4NS-01A-11D-A30V-10	523422	39746105	11558461	37	21896										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118250523	118250523	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0263157894736842	1	1	0.75046904315197	0	0.886917960088692	1	1	0	gatgttaatgttgctgctggAcaagctcagttctagcattt	10	7	2	0			TCGA-DD-A4NS-01A-11D-A30V-10	TCGA-DD-A4NS-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5abd0e3f-8431-4596-bc8a-f0a2a4b470b4	2c0ffc41-1663-4f25-8210-f48f55f1f30d	g.chrX:118250523A>G	ENST00000402510.2	-	4	585	c.586T>C	c.(586-588)Tcc>Ccc	p.S196P		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	196										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TTGCTGCTGGACAAGCTCAGT	0.453																																					p.S196P		Atlas-SNP	.											.	KIAA1210	171	.	0			c.T586C						.						189	165	173					X																	118250523		1965	4138	6103	SO:0001583	missense	57481	exon4			TGCTGGACAAGCT	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.586T>C	chrX.hg19:g.118250523A>G	ENSP00000384670:p.Ser196Pro	133.0	0.0		152.0	13.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	A	15.11	2.736729	0.49045	.	.	ENSG00000250423;ENSG00000241087	ENST00000402510;ENST00000420240	T	0.18810	2.19	5.14	3.98	0.46160	.	.	.	.	.	T	0.13798	0.0334	N	0.14661	0.345	0.09310	N	1	P	0.50710	0.938	P	0.44647	0.456	T	0.07790	-1.0754	9	0.44086	T	0.13	.	6.9514	0.24548	0.8942:0.0:0.1058:0.0	.	196	Q9ULL0	K1210_HUMAN	P	196;32	ENSP00000384670:S196P	ENSP00000396164:S32P	S	-	1	0	RP13-347D8.5;RP13-347D8.6	118134551	0.889000	0.30405	0.006000	0.13384	0.002000	0.02628	1.703000	0.37846	0.731000	0.32448	0.486000	0.48141	TCC	.	.		0.453	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		G	118250523	A	G	118250523	3	3	140	1	0	0	0	0	1	0	0	0	8223	275	10	2	4587	2	KIAA1210	23	118250523	Missense_Mutation	SNP	A	TCGA-DD-A4NS-01A-11D-A30V-10		118250523	37020037	38	21897										
SDF4	51150	hgsc.bcm.edu	37	chr1	1152909	1152909	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cgctcaaaactcctcgtgcaCgctgcgcgcgtagtccacca	9	17	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:1152909C>T	ENST00000360001.6	-	7	1334	c.1072G>A	c.(1072-1074)Gtg>Atg	p.V358M	SDF4_ENST00000263741.7_3'UTR			Q9BRK5	CAB45_HUMAN	stromal cell derived factor 4	358	Necessary for intracellular retention in Golgi apparatus lumen. {ECO:0000250}.				calcium ion-dependent exocytosis (GO:0017156)|cerebellum development (GO:0021549)|fat cell differentiation (GO:0045444)|response to ethanol (GO:0045471)|UV protection (GO:0009650)|zymogen granule exocytosis (GO:0070625)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|late endosome (GO:0005770)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;7.85e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.42e-21)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;4.83e-05)|Kidney(185;0.00252)|BRCA - Breast invasive adenocarcinoma(365;0.00263)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0368)|Lung(427;0.204)		TCCTCGTGCACGCTGCGCGCG	0.716																																					p.V358M		Atlas-SNP	.											.	SDF4	50	.	0			c.G1072A						.						49	51	51					1																	1152909		2203	4298	6501	SO:0001583	missense	51150	exon7			CGTGCACGCTGCG		CCDS12.1, CCDS30553.1	1p36.33	2013-01-10			ENSG00000078808	ENSG00000078808		"EF-hand domain containing"	24188	protein-coding gene	gene with protein product	"calcium binding protein"	614282				9254016, 8609160	Standard	NM_016176		Approved	Cab45	uc001adh.4	Q9BRK5	OTTHUMG00000001812	ENST00000360001.6:c.1072G>A	chr1.hg19:g.1152909C>T	ENSP00000353094:p.Val358Met	59.0	0.0		74.0	18.0	NM_016176	B1AME5|B1AME6|B2RDF1|B4DSM1|Q53G52|Q53HQ9|Q8NBQ3|Q96AA1|Q9NZP7|Q9UN53	Missense_Mutation	SNP	ENST00000360001.6	hg19	CCDS30553.1	.	.	.	.	.	.	.	.	.	.	c	24.8	4.571569	0.86542	.	.	ENSG00000078808	ENST00000360001	T	0.09255	3.0	4.9	4.9	0.64082	.	0.181870	0.47093	D	0.000244	T	0.27419	0.0673	L	0.51422	1.61	0.80722	D	1	D	0.76494	0.999	D	0.66979	0.948	T	0.00525	-1.1689	10	0.59425	D	0.04	-34.0199	17.2576	0.87062	0.0:1.0:0.0:0.0	.	358	Q9BRK5	CAB45_HUMAN	M	358	ENSP00000353094:V358M	ENSP00000353094:V358M	V	-	1	0	SDF4	1142772	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	7.313000	0.78978	2.546000	0.85860	0.550000	0.68814	GTG	.	.		0.716	SDF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005064.1	NM_016176		T	1152909	C	T	1152909	3	4	141	1	0	0	0	0	1	0	0	0	13977	536	19	1	20	1	SDF4	1	1152909	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10		1152909	248097712	1	21898										
RBP7	116362	hgsc.bcm.edu	37	chr1	10068317	10068317	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tggacccattggatcgaaggAgacaaactccacctggtatc	10	11	0	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:10068317A>C	ENST00000294435.7	+	3	382	c.339A>C	c.(337-339)ggA>ggC	p.G113G		NM_052960.2	NP_443192.1	Q96R05	RET7_HUMAN	retinol binding protein 7, cellular	113						cytoplasm (GO:0005737)	retinal binding (GO:0016918)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(1)	2		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|BRCA - Breast invasive adenocarcinoma(304;0.000302)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00856)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	GGATCGAAGGAGACAAACTCC	0.463																																					p.G113G		Atlas-SNP	.											.	RBP7	11	.	0			c.A339C						.						99	89	93					1																	10068317		2203	4300	6503	SO:0001819	synonymous_variant	116362	exon3			CGAAGGAGACAAA	AF399927	CCDS109.1	1p36.22	2013-03-01			ENSG00000162444	ENSG00000162444		"Fatty acid binding protein family"	30316	protein-coding gene	gene with protein product		608604				12177003	Standard	NM_052960		Approved	CRBPIV	uc001aqq.3	Q96R05	OTTHUMG00000001798	ENST00000294435.7:c.339A>C	chr1.hg19:g.10068317A>C		112.0	0.0		102.0	11.0	NM_052960	B2R517|Q5SWJ4	Silent	SNP	ENST00000294435.7	hg19	CCDS109.1																																																																																			.	.		0.463	RBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005027.2	NM_052960		C	10068317	A	C	10068317	2	2	141	1	0	0	0	0	0	0	0	1	13175	291	11	5		5	RBP7	1	10068317	Silent	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	8915408	10068317	239182304	2	21899										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42049187	42049187	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ggctgtcagcatggcggtccGctgtcctattcgcccacact	11	15	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:42049187G>T	ENST00000372583.1	-	4	2167	c.1282C>A	c.(1282-1284)Cgg>Agg	p.R428R	HIVEP3_ENST00000372584.1_Silent_p.R428R|HIVEP3_ENST00000247584.5_Silent_p.R428R|HIVEP3_ENST00000429157.2_Silent_p.R428R	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	428	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				ATGGCGGTCCGCTGTCCTATT	0.627																																					p.R428R		Atlas-SNP	.											HIVEP3,NS,adenocarcinoma,0,1	HIVEP3	235	.	0			c.C1282A						.						99	85	90					1																	42049187		2203	4300	6503	SO:0001819	synonymous_variant	59269	exon4			CGGTCCGCTGTCC	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.1282C>A	chr1.hg19:g.42049187G>T		36.0	0.0		38.0	3.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.		0.627	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	42049187	G	T	42049187	2	4	141	1	0	0	0	0	0	0	0	1	7197	1086	38	1		1	HIVEP3	1	42049187	Silent	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	31980870	42049187	207201434	3	21900										
USP1	7398	hgsc.bcm.edu	37	chr1	62914231	62914231	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	taggagaagataaatatttcTgtgaaaactgccatcattat	7	5	2	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:62914231T>C	ENST00000339950.4	+	8	2331	c.1516T>C	c.(1516-1518)Tgt>Cgt	p.C506R	USP1_ENST00000371146.1_Missense_Mutation_p.C506R	NM_003368.4	NP_003359.3	O94782	UBP1_HUMAN	ubiquitin specific peptidase 1	506	USP.				DNA repair (GO:0006281)|monoubiquitinated protein deubiquitination (GO:0035520)|protein deubiquitination (GO:0016579)|regulation of DNA repair (GO:0006282)|response to UV (GO:0009411)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	19		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		TAAATATTTCTGTGAAAACTG	0.363																																					p.C506R	Ovarian(122;1846 2315 3982 19504)	Atlas-SNP	.											USP1,NS,carcinoma,0,1	USP1	51	.	0			c.T1516C						.						104	111	108					1																	62914231		2203	4300	6503	SO:0001583	missense	7398	exon8			TATTTCTGTGAAA		CCDS621.1	1p31.3	2008-05-14	2005-08-08		ENSG00000162607	ENSG00000162607		"Ubiquitin-specific peptidases"	12607	protein-coding gene	gene with protein product		603478	"ubiquitin specific protease 1"			12838346	Standard	NM_003368		Approved		uc001dak.2	O94782	OTTHUMG00000008972	ENST00000339950.4:c.1516T>C	chr1.hg19:g.62914231T>C	ENSP00000343526:p.Cys506Arg	198.0	0.0		152.0	19.0	NM_001017415	A0PJ95|D3DQ57|Q05BX7|Q59H66|Q9UFR0|Q9UNJ3	Missense_Mutation	SNP	ENST00000339950.4	hg19	CCDS621.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.422471	0.83559	.	.	ENSG00000162607	ENST00000371146;ENST00000339950	D;D	0.81739	-1.53;-1.53	5.95	5.95	0.96441	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	D	0.91590	0.7343	M	0.90198	3.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92951	0.6380	10	0.66056	D	0.02	-11.9458	16.4237	0.83790	0.0:0.0:0.0:1.0	.	506	O94782	UBP1_HUMAN	R	506	ENSP00000360188:C506R;ENSP00000343526:C506R	ENSP00000343526:C506R	C	+	1	0	USP1	62686819	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.665000	0.83852	2.279000	0.76181	0.533000	0.62120	TGT	.	.		0.363	USP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024881.1	NM_001017415		C	62914231	T	C	62914231	3	2	141	1	0	0	0	0	1	0	0	0	17055	1580	55	2	1542	2	USP1	1	62914231	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	20865044	62914231	186336390	4	21901										
CAPZA1	829	hgsc.bcm.edu	37	chr1	113192072	113192072	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tacttaataatgacaatctcCtcagggaaggggcagcacag	10	9	2	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:113192072C>G	ENST00000263168.3	+	3	808	c.136C>G	c.(136-138)Ctc>Gtc	p.L46V	CAPZA1_ENST00000476936.1_3'UTR	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	46					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGACAATCTCCTCAGGGAAGG	0.368																																					p.L46V		Atlas-SNP	.											.	CAPZA1	16	.	0			c.C136G						.						108	104	106					1																	113192072		2203	4300	6503	SO:0001583	missense	829	exon3			AATCTCCTCAGGG	U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.136C>G	chr1.hg19:g.113192072C>G	ENSP00000263168:p.Leu46Val	132.0	0.0		105.0	25.0	NM_006135	Q53FQ6|Q6FHD5	Missense_Mutation	SNP	ENST00000263168.3	hg19	CCDS30805.1	.	.	.	.	.	.	.	.	.	.	C	32	5.132222	0.94473	.	.	ENSG00000116489	ENST00000263168	.	.	.	5.39	5.39	0.77823	.	0.076847	0.52532	D	0.000063	T	0.77505	0.4140	M	0.71296	2.17	0.80722	D	1	P	0.41673	0.759	P	0.60609	0.877	T	0.77264	-0.2652	9	0.52906	T	0.07	-10.7109	18.7748	0.91907	0.0:1.0:0.0:0.0	.	46	P52907	CAZA1_HUMAN	V	46	.	ENSP00000263168:L46V	L	+	1	0	CAPZA1	112993595	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.771000	0.85420	2.524000	0.85096	0.591000	0.81541	CTC	.	.		0.368	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135		G	113192072	C	G	113192072	3	3	141	1	0	0	0	0	1	0	0	0	2642	681	24	4	146	4	CAPZA1	1	113192072	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	50277841	113192072	136058549	5	21902										
OTUD7B	56957	hgsc.bcm.edu	37	chr1	149915759	149915759	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ttcagtgttccacccgttcaGaacctgtgcaccaggagctc	9	14	2	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:149915759G>A	ENST00000369135.4	-	12	2823	c.2529C>T	c.(2527-2529)ttC>ttT	p.F843F		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	843					mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CACCCGTTCAGAACCTGTGCA	0.512																																					p.F843F		Atlas-SNP	.											.	OTUD7B	76	.	0			c.C2529T						.						96	99	98					1																	149915759		1973	4144	6117	SO:0001819	synonymous_variant	56957	exon12			CGTTCAGAACCTG	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"OTU domain containing"	16683	protein-coding gene	gene with protein product		611748	"zinc finger, A20 domain containing 1", "OTU domain containing 7B"	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.2529C>T	chr1.hg19:g.149915759G>A		60.0	0.0		79.0	8.0	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Silent	SNP	ENST00000369135.4	hg19	CCDS41389.1																																																																																			.	.		0.512	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205		A	149915759	G	A	149915759	2	1	141	1	0	0	0	0	0	0	0	1	11328	933	33	3		3	OTUD7B	1	149915759	Silent	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	36723687	149915759	99334862	6	21903										
LASS2	29956	hgsc.bcm.edu	37	chr1	150939260	150939260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	caggatgaccagtcgggtgaTgataaaaacaatggcgaaga	13	6	0	4			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:150939260T>C	ENST00000271688.6	-	9	1206	c.820A>G	c.(820-822)Atc>Gtc	p.I274V	CERS2_ENST00000345896.4_5'UTR|RP11-316M1.12_ENST00000561111.1_RNA|RP11-316M1.12_ENST00000560481.1_RNA|CERS2_ENST00000368954.5_Missense_Mutation_p.I274V|CERS2_ENST00000561294.1_Missense_Mutation_p.I265V	NM_181746.3	NP_859530.1	Q96G23	CERS2_HUMAN	ceramide synthase 2	274	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AGTCGGGTGATGATAAAAACA	0.502																																					p.I274V		Atlas-SNP	.											.	.	.	.	0			c.A820G						.						159	129	140					1																	150939260		2203	4300	6503	SO:0001583	missense	29956	exon9			GGGTGATGATAAA	AF189062	CCDS973.1	1q21.3	2012-09-20	2011-07-08	2011-07-08	ENSG00000143418	ENSG00000143418		"Homeoboxes / CERS class"	14076	protein-coding gene	gene with protein product		606920	"longevity assurance (LAG1, S. cerevisiae) homolog 2", "LAG1 longevity assurance homolog 2 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 2"	LASS2		11543633	Standard	NM_181746		Approved	SP260, FLJ10243	uc001evz.3	Q96G23	OTTHUMG00000035064	ENST00000271688.6:c.820A>G	chr1.hg19:g.150939260T>C	ENSP00000271688:p.Ile274Val	90.0	0.0		114.0	7.0	NM_022075	D3DV06|Q5SZE5|Q9HD96|Q9NW79	Missense_Mutation	SNP	ENST00000271688.6	hg19	CCDS973.1	.	.	.	.	.	.	.	.	.	.	T	4.842	0.156616	0.09236	.	.	ENSG00000143418	ENST00000368954;ENST00000271688;ENST00000345896;ENST00000368949	D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83	5.86	4.74	0.60224	TRAM/LAG1/CLN8 homology domain (3);	0.143849	0.50627	D	0.000116	T	0.36663	0.0975	N	0.02142	-0.665	0.46044	D	0.998836	B	0.06786	0.001	B	0.16289	0.015	T	0.53718	-0.8399	10	0.02654	T	1	-27.2827	4.482	0.11771	0.1483:0.1468:0.0:0.7049	.	274	Q96G23	CERS2_HUMAN	V	274;274;124;294	ENSP00000357950:I274V;ENSP00000271688:I274V;ENSP00000337842:I124V;ENSP00000357945:I294V	ENSP00000271688:I274V	I	-	1	0	CERS2	149205884	0.977000	0.34250	1.000000	0.80357	0.967000	0.64934	0.094000	0.15107	2.232000	0.73038	0.533000	0.62120	ATC	.	.		0.502	CERS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084897.2	NM_022075		C	150939260	T	C	150939260	3	2	141	1	0	0	0	0	1	0	0	0	8648	1464	51	2	334	2	LASS2	1	150939260	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	1023501	150939260	98311361	7	21904										
SMG5	23381	hgsc.bcm.edu	37	chr1	156237933	156237933	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgggctgtaggaggctttgcAgatacataaagttcactagc	12	7	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:156237933A>G	ENST00000361813.5	-	9	1025	c.881T>C	c.(880-882)cTg>cCg	p.L294P	SMG5_ENST00000368267.5_Missense_Mutation_p.L294P|SMG5_ENST00000489907.2_5'Flank	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	294					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	48	Hepatocellular(266;0.158)					GAGGCTTTGCAGATACATAAA	0.458																																					p.L294P		Atlas-SNP	.											.	SMG5	98	.	0			c.T881C						.						164	147	153					1																	156237933		2203	4300	6503	SO:0001583	missense	23381	exon9			CTTTGCAGATACA	AB029012	CCDS1137.1	1q21	2013-07-02	2013-07-02		ENSG00000198952	ENSG00000198952			24644	protein-coding gene	gene with protein product	"EST1 telomerase component homolog B (S. cerevisiae)"	610962	"smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)"			12676087, 12699629	Standard	NM_015327		Approved	KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B	uc001foc.4	Q9UPR3	OTTHUMG00000017491	ENST00000361813.5:c.881T>C	chr1.hg19:g.156237933A>G	ENSP00000355261:p.Leu294Pro	171.0	0.0		154.0	11.0	NM_015327	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Missense_Mutation	SNP	ENST00000361813.5	hg19	CCDS1137.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.563934	0.86335	.	.	ENSG00000198952	ENST00000361813;ENST00000368267	T;T	0.49139	0.79;0.79	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.64371	0.2592	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70400	-0.4882	10	0.87932	D	0	-21.4449	14.5756	0.68243	1.0:0.0:0.0:0.0	.	294	Q9UPR3	SMG5_HUMAN	P	294	ENSP00000355261:L294P;ENSP00000357250:L294P	ENSP00000355261:L294P	L	-	2	0	SMG5	154504557	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	9.077000	0.94016	2.311000	0.77944	0.533000	0.62120	CTG	.	.		0.458	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327		G	156237933	A	G	156237933	3	3	141	1	0	0	0	0	1	0	0	0	14811	188	7	2	2225	2	SMG5	1	156237933	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	5298673	156237933	93012688	8	21905										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167095928	167095928	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	agggtgcgggaggatgatgaGgacagcgtgggctctgaggc	21	6	1	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:167095928G>T	ENST00000361200.2	+	6	1726	c.1560G>T	c.(1558-1560)gaG>gaT	p.E520D	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.E520D|DUSP27_ENST00000271385.5_Missense_Mutation_p.E520D			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	520					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						AGGATGATGAGGACAGCGTGG	0.562																																					p.E520D		Atlas-SNP	.											.	DUSP27	235	.	0			c.G1560T						.						78	72	74					1																	167095928		2203	4300	6503	SO:0001583	missense	92235	exon5			TGATGAGGACAGC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1560G>T	chr1.hg19:g.167095928G>T	ENSP00000354483:p.Glu520Asp	216.0	0.0		184.0	56.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	G	5.098	0.203777	0.09704	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03772	3.81;3.81;3.81	5.14	4.22	0.49857	.	0.429052	0.20866	N	0.084252	T	0.03305	0.0096	M	0.67953	2.075	0.29504	N	0.854695	P	0.43633	0.813	B	0.37047	0.24	T	0.10706	-1.0618	10	0.72032	D	0.01	-8.8605	15.6302	0.76904	0.0:0.1379:0.8621:0.0	.	520	Q5VZP5	DUS27_HUMAN	D	520	ENSP00000354483:E520D;ENSP00000271385:E520D;ENSP00000404874:E520D	ENSP00000271385:E520D	E	+	3	2	DUSP27	165362552	0.998000	0.40836	0.015000	0.15790	0.001000	0.01503	0.442000	0.21628	1.128000	0.42052	-0.189000	0.12847	GAG	.	.		0.562	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		T	167095928	G	T	167095928	3	4	141	1	0	0	0	0	1	0	0	0	4826	991	35	3	1578	3	DUSP27	1	167095928	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	10857995	167095928	82154693	9	21906										
TNN	63923	hgsc.bcm.edu	37	chr1	175052888	175052888	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ccgtcacccctgccctagacCttgctgtgcttggcactgcc	9	18	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:175052888C>G	ENST00000239462.4	+	5	1164	c.1051C>G	c.(1051-1053)Ctt>Gtt	p.L351V		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	351	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		TGCCCTAGACCTTGCTGTGCT	0.547																																					p.L351V		Atlas-SNP	.											.	TNN	297	.	0			c.C1051G						.						65	57	60					1																	175052888		2203	4300	6503	SO:0001583	missense	63923	exon5			CTAGACCTTGCTG	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1051C>G	chr1.hg19:g.175052888C>G	ENSP00000239462:p.Leu351Val	42.0	0.0		46.0	16.0	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	C	6.488	0.458310	0.12342	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.53423	0.62	5.52	2.41	0.29592	Fibronectin, type III (2);	0.670270	0.15048	N	0.283455	T	0.36908	0.0984	L	0.47190	1.495	0.09310	N	1	B;B	0.14805	0.011;0.002	B;B	0.15052	0.012;0.002	T	0.20940	-1.0260	10	0.13853	T	0.58	.	10.6207	0.45478	0.2013:0.5042:0.2945:0.0	.	351;351	B3KXB6;Q9UQP3	.;TENN_HUMAN	V	351	ENSP00000239462:L351V	ENSP00000239462:L351V	L	+	1	0	TNN	173319511	0.129000	0.22400	0.938000	0.37757	0.178000	0.23041	1.007000	0.29860	1.273000	0.44346	0.591000	0.81541	CTT	.	.		0.547	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		G	175052888	C	G	175052888	3	3	141	1	0	0	0	0	1	0	0	0	16338	681	24	4	1065	4	TNN	1	175052888	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	7956960	175052888	74197733	10	21907										
STX6	10228	hgsc.bcm.edu	37	chr1	180953892	180953892	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gtgctctccaattcgtgagaGaaatcttccaacatactaga	7	10	2	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:180953892G>C	ENST00000258301.5	-	7	849	c.612C>G	c.(610-612)ttC>ttG	p.F204L	STX6_ENST00000542060.1_Missense_Mutation_p.F103L|STX6_ENST00000469135.1_5'UTR	NM_005819.4	NP_005810.1	O43752	STX6_HUMAN	syntaxin 6	204	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				endosome organization (GO:0007032)|Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion (GO:0006906)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|trans-Golgi network membrane (GO:0032588)	SNAP receptor activity (GO:0005484)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	10						ATTCGTGAGAGAAATCTTCCA	0.473																																					p.F204L		Atlas-SNP	.											.	STX6	21	.	0			c.C612G						.						75	72	73					1																	180953892		2203	4300	6503	SO:0001583	missense	10228	exon7			GTGAGAGAAATCT	AJ002078	CCDS1341.1, CCDS65738.1	1q25.3	2008-02-05			ENSG00000135823	ENSG00000135823			11441	protein-coding gene	gene with protein product		603944				10080545	Standard	XM_005244824		Approved		uc021pfr.1	O43752	OTTHUMG00000035179	ENST00000258301.5:c.612C>G	chr1.hg19:g.180953892G>C	ENSP00000258301:p.Phe204Leu	61.0	0.0		50.0	4.0	NM_005819	B2R652|B4DR17|Q5VY08|Q6FH83	Missense_Mutation	SNP	ENST00000258301.5	hg19	CCDS1341.1	.	.	.	.	.	.	.	.	.	.	G	10.35	1.327195	0.24080	.	.	ENSG00000135823	ENST00000258301;ENST00000542060	.	.	.	5.7	2.85	0.33270	Syntaxin/epimorphin, conserved site (1);Target SNARE coiled-coil domain (3);	0.000000	0.85682	D	0.000000	T	0.23054	0.0557	N	0.05012	-0.13	0.54753	D	0.999981	B;B	0.20550	0.046;0.005	B;B	0.24269	0.028;0.052	T	0.23583	-1.0184	8	0.15499	T	0.54	-19.2894	8.6398	0.33970	0.3598:0.0:0.6402:0.0	.	103;204	B4DR17;O43752	.;STX6_HUMAN	L	204;103	.	ENSP00000258301:F204L	F	-	3	2	STX6	179220515	1.000000	0.71417	0.990000	0.47175	0.459000	0.32528	0.953000	0.29162	0.357000	0.24183	-0.768000	0.03414	TTC	.	.		0.473	STX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085143.1	NM_005819		C	180953892	G	C	180953892	3	2	141	1	0	0	0	0	1	0	0	0	15364	933	33	4	163	4	STX6	1	180953892	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	5901004	180953892	68296729	11	21908										
RRP15	51018	hgsc.bcm.edu	37	chr1	218475635	218475635	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ctttactctttggttctataGgaagctgtggatcggaaaag	11	6	2	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr1:218475635G>A	ENST00000366932.3	+	2	169		c.e2-1		RRP15_ENST00000491428.1_Splice_Site	NM_016052.3	NP_057136.2	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog (S. cerevisiae)							mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)			ACBD6/RRP15(2)	NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)		TGGTTCTATAGGAAGCTGTGG	0.463																																					.		Atlas-SNP	.											.	RRP15	33	.	0			c.140-1G>A						.						97	100	99					1																	218475635		2203	4300	6503	SO:0001630	splice_region_variant	51018	exon2			TCTATAGGAAGCT		CCDS1520.2	1q41	2008-02-05			ENSG00000067533	ENSG00000067533			24255	protein-coding gene	gene with protein product		611193	"KIAA0507"	KIAA0507		15769876	Standard	NM_016052		Approved	CGI-115	uc001hlj.3	Q9Y3B9	OTTHUMG00000039494	ENST00000366932.3:c.140-1G>A	chr1.hg19:g.218475635G>A		163.0	0.0		183.0	20.0	NM_016052		Splice_Site	SNP	ENST00000366932.3	hg19	CCDS1520.2	.	.	.	.	.	.	.	.	.	.	G	15.96	2.987556	0.53934	.	.	ENSG00000067533	ENST00000366932	.	.	.	5.87	2.94	0.34122	.	.	.	.	.	.	.	.	.	.	.	0.20196	N	0.999927	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.3529	0.11163	0.3228:0.0:0.5304:0.1468	.	.	.	.	.	-1	.	.	.	+	.	.	RRP15	216542258	0.985000	0.35326	0.012000	0.15200	0.873000	0.50193	1.527000	0.35975	0.369000	0.24510	0.650000	0.86243	.	.	.		0.463	RRP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095284.1	NM_016052	Intron	A	218475635	G	A	218475635	5	1	141	1	0	0	0	0	0	0	1	0	13702	1014	35	3	145	3	RRP15	1	218475635	Splice_Site	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	37521743	218475635	30774986	12	21909										
RAB1A	5861	hgsc.bcm.edu	37	chr2	65331882	65331882	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	acttactgcaaacctaagaaGaaggcaagactttccaaccc	6	12	0	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr2:65331882G>T	ENST00000409784.3	-	2	272	c.82C>A	c.(82-84)Ctt>Att	p.L28I	RAB1A_ENST00000409751.1_Missense_Mutation_p.L28I|RAB1A_ENST00000409892.1_Missense_Mutation_p.L28I|RAB1A_ENST00000356214.7_Missense_Mutation_p.L28I|RAB1A_ENST00000398529.3_Missense_Mutation_p.L28I|RAB1A_ENST00000494188.1_5'UTR|RAB1A_ENST00000260638.8_Missense_Mutation_p.L28I	NM_004161.4	NP_004152.1	P62820	RAB1A_HUMAN	RAB1A, member RAS oncogene family	28					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cargo loading into COPII-coated vesicle (GO:0090110)|cell migration (GO:0016477)|defense response to bacterium (GO:0042742)|endocytosis (GO:0006897)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|growth hormone secretion (GO:0030252)|GTP catabolic process (GO:0006184)|interleukin-8 secretion (GO:0072606)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|positive regulation of glycoprotein metabolic process (GO:1903020)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle transport along microtubule (GO:0047496)|vesicle-mediated transport (GO:0016192)|virion assembly (GO:0019068)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|melanosome (GO:0042470)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|kidney(1)|lung(3)|prostate(1)	6						AACCTAAGAAGAAGGCAAGAC	0.299																																					p.L28I		Atlas-SNP	.											.	RAB1A	15	.	0			c.C82A						.						37	34	35					2																	65331882		1855	4108	5963	SO:0001583	missense	5861	exon2			TAAGAAGAAGGCA	M28209	CCDS46305.1, CCDS46306.1	2p14	2008-02-05		2002-03-17	ENSG00000138069	ENSG00000138069		"RAB, member RAS oncogene"	9758	protein-coding gene	gene with protein product	"Rab GTPase YPT1 homolog (yeast)"	179508		RAB1		2501306	Standard	NM_004161		Approved	YPT1	uc002sdm.3	P62820	OTTHUMG00000152725	ENST00000409784.3:c.82C>A	chr2.hg19:g.65331882G>T	ENSP00000387286:p.Leu28Ile	728.0	1.0		597.0	148.0	NM_004161	P11476|Q6FIE7|Q96N61|Q9Y3T2	Missense_Mutation	SNP	ENST00000409784.3	hg19	CCDS46306.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923165	0.92319	.	.	ENSG00000138069	ENST00000409784;ENST00000409892;ENST00000409751;ENST00000398529;ENST00000260638;ENST00000356214	T;T;T;T;T;T	0.81330	-1.28;-1.48;-1.48;-1.28;-1.28;-1.28	5.81	5.81	0.92471	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85575	0.5728	L	0.31157	0.91	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;0.99;1.0;0.958	D;P;D;D	0.97110	1.0;0.859;0.999;0.94	D	0.86690	0.1922	10	0.87932	D	0	.	19.6699	0.95907	0.0:0.0:1.0:0.0	.	28;28;28;28	B7Z8M7;P62820-2;P62820-3;P62820	.;.;.;RAB1A_HUMAN	I	28	ENSP00000387286:L28I;ENSP00000386451:L28I;ENSP00000386672:L28I;ENSP00000381540:L28I;ENSP00000260638:L28I;ENSP00000348546:L28I	ENSP00000260638:L28I	L	-	1	0	RAB1A	65185386	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	9.000000	0.93564	2.759000	0.94783	0.591000	0.81541	CTT	.	.		0.299	RAB1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327572.1	NM_004161		T	65331882	G	T	65331882	3	4	141	1	0	0	0	0	1	0	0	0	12920	942	33	3	555	3	RAB1A	2	65331882	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10		65331882	177867491	13	21910										
RIF1	55183	hgsc.bcm.edu	37	chr2	152293757	152293757	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tttattcttccctttcagagCcattggaacatccgttaatc	5	11	2	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr2:152293757C>T	ENST00000243326.5	+	12	1858	c.1375C>T	c.(1375-1377)Cca>Tca	p.P459S	RIF1_ENST00000433166.2_3'UTR|RIF1_ENST00000453091.2_Missense_Mutation_p.P459S|RIF1_ENST00000430328.2_Missense_Mutation_p.P459S|RIF1_ENST00000428287.2_Missense_Mutation_p.P459S|RIF1_ENST00000444746.2_Missense_Mutation_p.P459S			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		CCTTTCAGAGCCATTGGAACA	0.323																																					p.P459S		Atlas-SNP	.											.	RIF1	244	.	0			c.C1375T						.						95	92	93					2																	152293757		2203	4300	6503	SO:0001583	missense	55183	exon13			TCAGAGCCATTGG	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.1375C>T	chr2.hg19:g.152293757C>T	ENSP00000243326:p.Pro459Ser	200.0	0.0		181.0	45.0	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	hg19	CCDS2194.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.28|14.28	2.487081|2.487081	0.44249|0.44249	.|.	.|.	ENSG00000080345|ENSG00000080345	ENST00000414861|ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	.|T;T;T;T;T	.|0.15139	.|2.46;2.45;2.45;2.46;2.45	5.58|5.58	2.73|2.73	0.32206|0.32206	.|.	.|0.101682	.|0.64402	.|D	.|0.000002	T|T	0.31451|0.31451	0.0797|0.0797	M|M	0.67953|0.67953	2.075|2.075	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.998;0.987	.|P;P	.|0.57468	.|0.821;0.799	T|T	0.02821|0.02821	-1.1106|-1.1106	5|10	.|0.66056	.|D	.|0.02	-2.3659|-2.3659	10.9002|10.9002	0.47047|0.47047	0.0:0.688:0.2447:0.0673|0.0:0.688:0.2447:0.0673	.|.	.|459;459	.|Q5UIP0;Q5UIP0-2	.|RIF1_HUMAN;.	V|S	450|459	.|ENSP00000390181:P459S;ENSP00000414615:P459S;ENSP00000415691:P459S;ENSP00000243326:P459S;ENSP00000416123:P459S	.|ENSP00000243326:P459S	A|P	+|+	2|1	0|0	RIF1|RIF1	152002003|152002003	1.000000|1.000000	0.71417|0.71417	0.725000|0.725000	0.30721|0.30721	0.018000|0.018000	0.09664|0.09664	3.656000|3.656000	0.54467|0.54467	0.368000|0.368000	0.24481|0.24481	-0.262000|-0.262000	0.10625|0.10625	GCC|CCA	.	.		0.323	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			T	152293757	C	T	152293757	3	4	141	1	0	0	0	0	1	0	0	0	13374	739	26	3	1421	3	RIF1	2	152293757	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	86961875	152293757	90905616	14	21911										
ZNF385B	151126	hgsc.bcm.edu	37	chr2	180348008	180348008	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gtgtcattgacctgatttgtCagagttgttgcctgtgattg	12	6	2	4			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr2:180348008C>A	ENST00000410066.1	-	6	1264	c.661G>T	c.(661-663)Gac>Tac	p.D221Y	ZNF385B_ENST00000409692.1_Missense_Mutation_p.D119Y|ZNF385B_ENST00000336917.5_Missense_Mutation_p.D119Y|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409343.1_Missense_Mutation_p.D145Y	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	221	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			CCTGATTTGTCAGAGTTGTTG	0.458																																					p.D221Y	Colon(155;204 2491 32774 51842)	Atlas-SNP	.											.	ZNF385B	68	.	0			c.G661T						.						284	230	249					2																	180348008		2203	4300	6503	SO:0001583	missense	151126	exon6			ATTTGTCAGAGTT	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.661G>T	chr2.hg19:g.180348008C>A	ENSP00000386845:p.Asp221Tyr	213.0	0.0		190.0	54.0	NM_152520	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Missense_Mutation	SNP	ENST00000410066.1	hg19	CCDS33339.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.804859	0.70682	.	.	ENSG00000144331	ENST00000410066;ENST00000336917;ENST00000409343;ENST00000409692;ENST00000457304	T;T;T;T;T	0.33216	1.42;1.43;1.42;1.43;1.43	5.93	5.93	0.95920	.	1.465370	0.03449	N	0.210371	T	0.59390	0.2190	L	0.56769	1.78	0.53688	D	0.999973	D;D	0.65815	0.991;0.995	P;D	0.64410	0.843;0.925	T	0.30822	-0.9965	10	0.59425	D	0.04	-11.8835	18.5086	0.90907	0.0:1.0:0.0:0.0	.	221;145	Q569K4;Q569K4-2	Z385B_HUMAN;.	Y	221;119;145;119;119	ENSP00000386845:D221Y;ENSP00000338225:D119Y;ENSP00000386379:D145Y;ENSP00000386507:D119Y;ENSP00000394038:D119Y	ENSP00000338225:D119Y	D	-	1	0	ZNF385B	180056253	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.889000	0.56212	2.802000	0.96397	0.561000	0.74099	GAC	.	.		0.458	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		A	180348008	C	A	180348008	3	1	141	1	0	0	0	0	1	0	0	0	17892	826	29	3	774	3	ZNF385B	2	180348008	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	28054251	180348008	62851365	15	21912										
SLC39A10	57181	hgsc.bcm.edu	37	chr2	196599744	196599744	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gccctctatgaagataaaatTgtgtttgacatccagttttg	8	7	1	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr2:196599744T>G	ENST00000409086.3	+	10	2750	c.2475T>G	c.(2473-2475)atT>atG	p.I825M	SLC39A10_ENST00000541054.1_Missense_Mutation_p.I375M|DNAH7_ENST00000484183.1_5'Flank|SLC39A10_ENST00000359634.5_Missense_Mutation_p.I825M	NM_001127257.1	NP_001120729.1	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter), member 10	825					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(16)|pancreas(1)|prostate(1)|skin(2)	34			OV - Ovarian serous cystadenocarcinoma(117;0.221)			AAGATAAAATTGTGTTTGACA	0.403																																					p.I825M		Atlas-SNP	.											.	SLC39A10	89	.	0			c.T2475G						.						215	201	206					2																	196599744		2203	4300	6503	SO:0001583	missense	57181	exon10			TAAAATTGTGTTT		CCDS33353.1	2q33.1	2013-05-22			ENSG00000196950	ENSG00000196950		"Solute carriers"	20861	protein-coding gene	gene with protein product		608733	"solute carrier family 39 (metal ion transporter), member 10"			12659941	Standard	NM_020342		Approved	KIAA1265, FLJ90515, DKFZp564L2123	uc002utg.4	Q9ULF5	OTTHUMG00000154380	ENST00000409086.3:c.2475T>G	chr2.hg19:g.196599744T>G	ENSP00000386766:p.Ile825Met	219.0	0.0		184.0	17.0	NM_020342	A8K5C6|B4DGU0|Q3MJA4|Q68CR5|Q6DKH6|Q9Y3Z1	Missense_Mutation	SNP	ENST00000409086.3	hg19	CCDS33353.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.706087	0.48412	.	.	ENSG00000196950	ENST00000409086;ENST00000359634;ENST00000541054	T;T;T	0.77229	-0.79;-0.79;-1.08	5.39	1.65	0.23941	.	0.000000	0.85682	D	0.000000	D	0.84924	0.5580	M	0.88704	2.975	0.49582	D	0.999806	D	0.54772	0.968	P	0.60541	0.876	T	0.81673	-0.0826	10	0.87932	D	0	.	4.4538	0.11633	0.2159:0.2185:0.0:0.5656	.	825	Q9ULF5	S39AA_HUMAN	M	825;825;375	ENSP00000386766:I825M;ENSP00000352655:I825M;ENSP00000437787:I375M	ENSP00000352655:I825M	I	+	3	3	SLC39A10	196307989	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	0.514000	0.22786	0.134000	0.18681	0.528000	0.53228	ATT	.	.		0.403	SLC39A10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335186.1	XM_047707		G	196599744	T	G	196599744	3	3	141	1	0	0	0	0	1	0	0	0	14628	1800	63	5	2509	5	SLC39A10	2	196599744	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	16251736	196599744	46599629	16	21913										
STK17B	9262	hgsc.bcm.edu	37	chr2	197008292	197008292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ggaaattcttacctaaatatTctggtgttcccatgatttcc	6	9	2	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr2:197008292T>C	ENST00000263955.4	-	5	885	c.599A>G	c.(598-600)gAa>gGa	p.E200G	STK17B_ENST00000409228.1_Missense_Mutation_p.E200G	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	200	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(10)	15			OV - Ovarian serous cystadenocarcinoma(117;0.141)			ACCTAAATATTCTGGTGTTCC	0.333																																					p.E200G		Atlas-SNP	.											.	STK17B	28	.	0			c.A599G						.						72	78	76					2																	197008292		2201	4300	6501	SO:0001583	missense	9262	exon5			AAATATTCTGGTG	AB011421	CCDS2315.1	2q33.1	2008-02-05	2007-02-12		ENSG00000081320	ENSG00000081320			11396	protein-coding gene	gene with protein product	"death-associated protein kinase-related 2"	604727	"serine/threonine kinase 17b (apoptosis-inducing)"			9786912	Standard	NM_004226		Approved	DRAK2	uc002utk.3	O94768	OTTHUMG00000132735	ENST00000263955.4:c.599A>G	chr2.hg19:g.197008292T>C	ENSP00000263955:p.Glu200Gly	173.0	0.0		119.0	9.0	NM_004226		Missense_Mutation	SNP	ENST00000263955.4	hg19	CCDS2315.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.849540	0.91277	.	.	ENSG00000081320	ENST00000263955;ENST00000409228	T;T	0.66995	-0.24;-0.24	5.29	5.29	0.74685	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.50627	D	0.000103	T	0.72301	0.3443	L	0.28608	0.87	0.80722	D	1	D	0.76494	0.999	D	0.67900	0.954	T	0.76107	-0.3080	10	0.87932	D	0	.	15.3814	0.74658	0.0:0.0:0.0:1.0	.	200	O94768	ST17B_HUMAN	G	200	ENSP00000263955:E200G;ENSP00000386853:E200G	ENSP00000263955:E200G	E	-	2	0	STK17B	196716537	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.843000	0.86859	2.216000	0.71823	0.533000	0.62120	GAA	.	.		0.333	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2			C	197008292	T	C	197008292	3	2	141	1	0	0	0	0	1	0	0	0	15306	1783	62	2	535	2	STK17B	2	197008292	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	408548	197008292	46191081	17	21914										
SERPINE2	5270	hgsc.bcm.edu	37	chr2	224866553	224866553	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cctcgagagacagaggattgAagtgggagcagatggaaggc	17	6	0	4			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr2:224866553A>G	ENST00000258405.4	-	2	307	c.65T>C	c.(64-66)tTc>tCc	p.F22S	SERPINE2_ENST00000409304.1_Missense_Mutation_p.F22S|SERPINE2_ENST00000447280.2_Missense_Mutation_p.F34S|SERPINE2_ENST00000409840.3_Missense_Mutation_p.F22S	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	22					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CAGAGGATTGAAGTGGGAGCA	0.527																																					p.F34S		Atlas-SNP	.											.	SERPINE2	103	.	0			c.T101C						.						109	118	115					2																	224866553		2203	4300	6503	SO:0001583	missense	5270	exon2			GGATTGAAGTGGG	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"Serine (or cysteine) peptidase inhibitors"	8951	protein-coding gene	gene with protein product	"glial-derived nexin 1"	177010	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.65T>C	chr2.hg19:g.224866553A>G	ENSP00000258405:p.Phe22Ser	67.0	0.0		53.0	6.0	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Missense_Mutation	SNP	ENST00000258405.4	hg19	CCDS2460.1	.	.	.	.	.	.	.	.	.	.	A	3.031	-0.199725	0.06219	.	.	ENSG00000135919	ENST00000409304;ENST00000258405;ENST00000409840;ENST00000447280;ENST00000432738;ENST00000454956;ENST00000423446	D;T;D;D;T;D	0.84298	-1.82;-0.76;-1.82;-1.83;-1.45;-1.57	5.17	3.99	0.46301	Serpin domain (1);	0.526968	0.21920	N	0.067161	T	0.67401	0.2889	N	0.08118	0	0.09310	N	1	B;B	0.15141	0.012;0.012	B;B	0.12837	0.008;0.008	T	0.53472	-0.8434	10	0.25106	T	0.35	.	6.8299	0.23905	0.7909:0.0:0.0736:0.1355	.	34;22	B4DIF2;P07093	.;GDN_HUMAN	S	22;22;22;34;22;22;22	ENSP00000386412:F22S;ENSP00000258405:F22S;ENSP00000386969:F22S;ENSP00000415786:F34S;ENSP00000408452:F22S;ENSP00000399655:F22S	ENSP00000258405:F22S	F	-	2	0	SERPINE2	224574797	0.987000	0.35691	0.246000	0.24233	0.156000	0.22039	2.471000	0.45127	0.875000	0.35847	0.533000	0.62120	TTC	.	.		0.527	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216		G	224866553	A	G	224866553	3	3	141	1	0	0	0	0	1	0	0	0	14127	246	9	2	1163	2	SERPINE2	2	224866553	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	27858261	224866553	18332820	18	21915										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227963489	227963494	+	In_Frame_Del	DEL	AGGGAA	AGGGAA	-													0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cctgtttctccatagcggccAgggaaccctgggtcccctgg							TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	AGGGAA	AGGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr2:227963489_227963494delAGGGAA	ENST00000396625.3	-	19	1327_1332	c.1120_1125delTTCCCT	c.(1120-1125)ttccctdel	p.FP374del	COL4A4_ENST00000329662.7_In_Frame_Del_p.FP374del	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	374	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CATAGCGGCCAGGGAACCCTGGGTCC	0.51																																					p.374_376del		Atlas-INDEL	.											.	COL4A4	215	.	0			c.1121_1126del						.																																			SO:0001651	inframe_deletion	1286	exon19			.		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.1120_1125delTTCCCT	chr2.hg19:g.227963489_227963494delAGGGAA	ENSP00000379866:p.Phe374_Pro375del	162.0	0.0		112.0	20.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	In_Frame_Del	DEL	ENST00000396625.3	hg19	CCDS42828.1																																																																																			.	.		0.51	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		-	227963494	AGGGAA	-	227963489	7	5	141	1	0	1	0	1	0	0	0	0	3695	175	7	0	4067	0	COL4A4	2	227963489	In_Frame_Del	DEL	AGGGAA	TCGA-DD-A4NV-01A-11D-A30V-10	3096936	227963489	15235884	19	21916	94	2								
COL4A4	1286	hgsc.bcm.edu	37	chr2	227963497	227963499	+	In_Frame_Del	DEL	CTG	CTG	-													0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tccatagcggccagggaaccCtgggtcccctggtgggcctg							TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr2:227963497_227963499delCTG	ENST00000396625.3	-	19	1322_1324	c.1115_1117delCAG	c.(1114-1119)ccaggg>cgg	p.372_373PG>R	COL4A4_ENST00000329662.7_In_Frame_Del_p.372_373PG>R	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	372	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CCAGGGAACCCTGGGTCCCCTGG	0.507																																					p.372_373del		Atlas-INDEL	.											.	COL4A4	215	.	0			c.1116_1118del						.																																			SO:0001651	inframe_deletion	1286	exon19			.		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.1115_1117delCAG	chr2.hg19:g.227963497_227963499delCTG	ENSP00000379866:p.Pro372_Gly373delinsArg	161.0	0.0		110.0	20.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	In_Frame_Del	DEL	ENST00000396625.3	hg19	CCDS42828.1																																																																																			.	.		0.507	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		-	227963499	CTG	-	227963497	7	5	141	1	0	1	0	1	0	0	0	0	3695	681	24	0	4075	0	COL4A4	2	227963497	In_Frame_Del	DEL	CTG	TCGA-DD-A4NV-01A-11D-A30V-10	8	227963497	15235876	20	21917	94	2								
ARMC9	80210	hgsc.bcm.edu	37	chr2	232079712	232079712	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgaagtactctgtggggagaCcggtgggtttacctggtgat	16	6	1	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr2:232079712C>T	ENST00000349938.4	+	4	540	c.346C>T	c.(346-348)Ccg>Tcg	p.P116S	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	116						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		TGTGGGGAGACCGGTGGGTTT	0.488																																					p.P116S		Atlas-SNP	.											.	ARMC9	129	.	0			c.C346T						.						90	92	92					2																	232079712		2203	4300	6503	SO:0001583	missense	80210	exon4			GGGAGACCGGTGG	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"Armadillo repeat containing"	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.346C>T	chr2.hg19:g.232079712C>T	ENSP00000258417:p.Pro116Ser	126.0	0.0		127.0	34.0	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	hg19	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.454981	0.43634	.	.	ENSG00000135931	ENST00000349938;ENST00000359743;ENST00000440107	T;T	0.42513	2.23;0.97	5.69	4.79	0.61399	.	0.534808	0.20762	N	0.086160	T	0.30008	0.0751	L	0.43152	1.355	0.80722	D	1	P	0.37276	0.589	B	0.33960	0.173	T	0.04029	-1.0983	10	0.09084	T	0.74	-17.1029	11.6365	0.51207	0.1389:0.7274:0.1337:0.0	.	116	Q7Z3E5	ARMC9_HUMAN	S	116	ENSP00000258417:P116S;ENSP00000387391:P116S	ENSP00000258417:P116S	P	+	1	0	ARMC9	231787956	0.996000	0.38824	0.994000	0.49952	0.714000	0.41099	3.835000	0.55805	2.666000	0.90696	0.650000	0.86243	CCG	.	.		0.488	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139		T	232079712	C	T	232079712	3	4	141	1	0	0	0	0	1	0	0	0	958	507	18	3	356	3	ARMC9	2	232079712	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	4116215	232079712	11119661	21	21918										
SEC13	6396	hgsc.bcm.edu	37	chr3	10347279	10347279	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ggttgtcacagccacctgatGcaaacctcttgatgtaattg	9	10	2	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr3:10347279G>A	ENST00000350697.3	-	6	673	c.548C>T	c.(547-549)gCa>gTa	p.A183V	SEC13_ENST00000397109.3_Missense_Mutation_p.A169V|SEC13_ENST00000492602.1_5'Flank|SEC13_ENST00000383801.2_Missense_Mutation_p.A229V|SEC13_ENST00000337354.4_Missense_Mutation_p.A186V|SEC13_ENST00000397117.1_Missense_Mutation_p.A169V	NM_183352.1	NP_899195.1	P55735	SEC13_HUMAN	SEC13 homolog (S. cerevisiae)	183					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	17						GCCACCTGATGCAAACCTCTT	0.527																																					p.A183V		Atlas-SNP	.											.	SEC13	35	.	0			c.C548T						.						187	161	170					3																	10347279		2203	4300	6503	SO:0001583	missense	6396	exon6			CCTGATGCAAACC		CCDS2599.1, CCDS46751.1, CCDS63540.1	3p25-p24	2013-01-10	2006-11-07	2006-11-07	ENSG00000157020	ENSG00000157020		"WD repeat domain containing"	10697	protein-coding gene	gene with protein product		600152	"SEC13 (S. cerevisiae)-like 1", "SEC13-like 1 (S. cerevisiae)"	D3S1231E, SEC13L1		7987303	Standard	NM_183352		Approved	SEC13R, npp-20	uc003bvn.3	P55735	OTTHUMG00000128671	ENST00000350697.3:c.548C>T	chr3.hg19:g.10347279G>A	ENSP00000312122:p.Ala183Val	89.0	0.0		108.0	17.0	NM_183352	A8MV37|B4DXJ1|Q5BJF0|Q9BRM6|Q9BUG7	Missense_Mutation	SNP	ENST00000350697.3	hg19	CCDS2599.1	.	.	.	.	.	.	.	.	.	.	G	8.715	0.913082	0.17907	.	.	ENSG00000157020	ENST00000397109;ENST00000337354;ENST00000350697;ENST00000397117;ENST00000383801	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.058088	0.64402	D	0.000001	T	0.25901	0.0631	N	0.00815	-1.16	0.49299	D	0.999777	B;B;B;B	0.13594	0.004;0.002;0.008;0.001	B;B;B;B	0.09377	0.003;0.004;0.003;0.002	T	0.41680	-0.9495	10	0.02654	T	1	.	10.6655	0.45728	0.0864:0.0:0.9136:0.0	.	183;169;229;183	E9PHR5;A8MXL6;B4DXJ1;P55735	.;.;.;SEC13_HUMAN	V	169;186;183;169;229	ENSP00000380298:A169V;ENSP00000336566:A186V;ENSP00000312122:A183V;ENSP00000380306:A169V;ENSP00000373312:A229V	ENSP00000336566:A186V	A	-	2	0	SEC13	10322279	1.000000	0.71417	0.957000	0.39632	0.991000	0.79684	7.355000	0.79434	2.676000	0.91093	0.655000	0.94253	GCA	.	.		0.527	SEC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250563.3			A	10347279	G	A	10347279	3	1	141	1	0	0	0	0	1	0	0	0	13995	1319	46	3	436	3	SEC13	3	10347279	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10		10347279	187675151	22	21919										
CLEC3B	7123	hgsc.bcm.edu	37	chr3	45077344	45077344	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgcgcggtcctgtcaggcgcGgccaacggcaagtggttcga	16	12	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr3:45077344G>A	ENST00000296130.4	+	3	717	c.537G>A	c.(535-537)gcG>gcA	p.A179A	CLEC3B_ENST00000490386.1_3'UTR|CLEC3B_ENST00000428034.1_Silent_p.A137A|RNU5B-3P_ENST00000516601.1_RNA	NM_003278.2	NP_003269.2	P05452	TETN_HUMAN	C-type lectin domain family 3, member B	179	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				bone mineralization (GO:0030282)|cellular response to organic substance (GO:0071310)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ossification (GO:0001503)|positive regulation of plasminogen activation (GO:0010756)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)|kringle domain binding (GO:0036143)			endometrium(1)|lung(3)	4				BRCA - Breast invasive adenocarcinoma(193;0.00863)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)	Tenecteplase(DB00031)	TGTCAGGCGCGGCCAACGGCA	0.677																																					p.A179A	GBM(139;1487 3263 30871)	Atlas-SNP	.											.	CLEC3B	15	.	0			c.G537A						.						32	33	33					3																	45077344		2201	4295	6496	SO:0001819	synonymous_variant	7123	exon3			AGGCGCGGCCAAC		CCDS2726.1	3p22-p21.3	2010-04-27	2005-02-09	2005-02-09	ENSG00000163815	ENSG00000163815		"C-type lectin domain containing"	11891	protein-coding gene	gene with protein product		187520	"tetranectin (plasminogen binding protein)"	TNA			Standard	NM_003278		Approved	TN	uc003cok.4	P05452	OTTHUMG00000133087	ENST00000296130.4:c.537G>A	chr3.hg19:g.45077344G>A		76.0	0.0		85.0	14.0	NM_003278	Q6FGX6	Silent	SNP	ENST00000296130.4	hg19	CCDS2726.1																																																																																			.	.		0.677	CLEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256745.1	NM_003278		A	45077344	G	A	45077344	2	1	141	1	0	0	0	0	0	0	0	1	3513	1103	39	1		1	CLEC3B	3	45077344	Silent	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	34730065	45077344	152945086	23	21920										
USP4	7375	hgsc.bcm.edu	37	chr3	49316327	49316327	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	attcagtttgttcttcgcatAtgcagtgtctgccaagtcaa	8	9	4	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr3:49316327A>G	ENST00000265560.4	-	21	2699	c.2653T>C	c.(2653-2655)Tat>Cat	p.Y885H	C3orf62_ENST00000343010.3_5'Flank|USP4_ENST00000351842.4_Missense_Mutation_p.Y838H	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	885	USP.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		TTCTTCGCATATGCAGTGTCT	0.413																																					p.Y885H		Atlas-SNP	.											.	USP4	72	.	0			c.T2653C						.						228	208	215					3																	49316327		2203	4300	6503	SO:0001583	missense	7375	exon21			TCGCATATGCAGT	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"Ubiquitin-specific peptidases"	12627	protein-coding gene	gene with protein product		603486	"ubiquitin specific protease 4 (proto-oncogene)"	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.2653T>C	chr3.hg19:g.49316327A>G	ENSP00000265560:p.Tyr885His	121.0	0.0		106.0	7.0	NM_003363	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Missense_Mutation	SNP	ENST00000265560.4	hg19	CCDS2793.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.463226	0.84425	.	.	ENSG00000114316	ENST00000351842;ENST00000265560	T;T	0.03580	3.88;3.88	5.45	5.45	0.79879	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.17023	0.0409	M	0.79614	2.46	0.80722	D	1	D;D	0.61697	0.99;0.987	D;D	0.66716	0.946;0.912	T	0.00395	-1.1766	10	0.41790	T	0.15	-18.2772	14.6366	0.68694	1.0:0.0:0.0:0.0	.	838;885	Q13107-2;Q13107	.;UBP4_HUMAN	H	838;885	ENSP00000341028:Y838H;ENSP00000265560:Y885H	ENSP00000265560:Y885H	Y	-	1	0	USP4	49291331	1.000000	0.71417	0.986000	0.45419	0.852000	0.48524	6.276000	0.72601	2.189000	0.69895	0.533000	0.62120	TAT	.	.		0.413	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		G	49316327	A	G	49316327	3	3	141	1	0	0	0	0	1	0	0	0	17086	449	16	2	246	2	USP4	3	49316327	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	4238983	49316327	148706103	24	21921										
ATP6V1A	523	hgsc.bcm.edu	37	chr3	113513944	113513952	+	In_Frame_Del	DEL	ATATCCAGC	ATATCCAGC	-													0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tttcatttttcagatagtggAtatccagcctatcttggtgc							TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	ATATCCAGC	ATATCCAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr3:113513944_113513952delATATCCAGC	ENST00000273398.3	+	10	1227_1235	c.1119_1127delATATCCAGC	c.(1117-1128)ggatatccagcc>ggc	p.YPA374del	ATP6V1A_ENST00000538620.1_In_Frame_Del_p.YPA341del	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	374					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	CAGATAGTGGATATCCAGCCTATCTTGGT	0.431																																					p.373_376del		Atlas-Indel,Pindel	.											.	ATP6V1A	71	.	0			c.1118_1126del						.																																			SO:0001651	inframe_deletion	523	exon10			.	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"ATPases / V-type"	851	protein-coding gene	gene with protein product		607027	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.1119_1127delATATCCAGC	chr3.hg19:g.113513944_113513952delATATCCAGC	ENSP00000273398:p.Tyr374_Ala376del	105.0	0.0		96.0	15.0	NM_001690	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	In_Frame_Del	DEL	ENST00000273398.3	hg19	CCDS2976.1																																																																																			.	.		0.431	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		-	113513952	ATATCCAGC	-	113513944	7	5	141	1	0	1	0	1	0	0	0	0	1177	320	12	0	1153	0	ATP6V1A	3	113513944	In_Frame_Del	DEL	ATATCCAGC	TCGA-DD-A4NV-01A-11D-A30V-10	64197617	113513944	84508486	25	21922										
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132175649	132175649	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gcttgtggcatccaaagctgGtttcctggctttcactcagc	10	12	2	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr3:132175649G>T	ENST00000260818.6	+	12	1570	c.1322G>T	c.(1321-1323)gGt>gTt	p.G441V	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	441					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TCCAAAGCTGGTTTCCTGGCT	0.428																																					p.G441V		Atlas-SNP	.											.	DNAJC13	253	.	0			c.G1322T						.						88	84	85					3																	132175649		2203	4300	6503	SO:0001583	missense	23317	exon12			AAGCTGGTTTCCT	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.1322G>T	chr3.hg19:g.132175649G>T	ENSP00000260818:p.Gly441Val	200.0	0.0		226.0	42.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	hg19	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.773652	0.90108	.	.	ENSG00000138246	ENST00000260818	T	0.30448	1.53	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.64159	0.2573	M	0.86651	2.83	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.68961	-0.5271	10	0.72032	D	0.01	.	19.8546	0.96752	0.0:0.0:1.0:0.0	.	441;108;441	A7E2Y5;Q8N7A5;O75165	.;.;DJC13_HUMAN	V	441	ENSP00000260818:G441V	ENSP00000260818:G441V	G	+	2	0	DNAJC13	133658339	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.593000	0.98250	2.697000	0.92050	0.655000	0.94253	GGT	.	.		0.428	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132175649	G	T	132175649	3	4	141	1	0	0	0	0	1	0	0	0	4634	1261	44	3	1364	3	DNAJC13	3	132175649	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	18661705	132175649	65846781	26	21923										
MFN1	55669	hgsc.bcm.edu	37	chr3	179096495	179096495	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tatgttcagattttcaagagGatattgtatttcctttttcc	6	6	2	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr3:179096495G>A	ENST00000471841.1	+	14	1681	c.1555G>A	c.(1555-1557)Gat>Aat	p.D519N	MFN1_ENST00000280653.7_Intron|MFN1_ENST00000263969.5_Missense_Mutation_p.D519N	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	519					mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			TTTTCAAGAGGATATTGTATT	0.388																																					p.D519N		Atlas-SNP	.											.	MFN1	72	.	0			c.G1555A						.						106	103	104					3																	179096495		2203	4300	6503	SO:0001583	missense	55669	exon14			CAAGAGGATATTG	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.1555G>A	chr3.hg19:g.179096495G>A	ENSP00000420617:p.Asp519Asn	262.0	0.0		199.0	28.0	NM_033540	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Missense_Mutation	SNP	ENST00000471841.1	hg19	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974223	0.53720	.	.	ENSG00000171109	ENST00000471841;ENST00000263969	T;T	0.61859	0.07;0.07	5.16	5.16	0.70880	.	0.088248	0.85682	D	0.000000	T	0.50854	0.1640	L	0.36672	1.1	0.80722	D	1	B;B	0.26318	0.146;0.146	B;B	0.21708	0.036;0.036	T	0.49881	-0.8892	10	0.51188	T	0.08	-21.1106	18.6527	0.91437	0.0:0.0:1.0:0.0	.	547;519	Q4AEJ4;Q8IWA4	.;MFN1_HUMAN	N	519	ENSP00000420617:D519N;ENSP00000263969:D519N	ENSP00000263969:D519N	D	+	1	0	MFN1	180579189	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.982000	0.63825	2.405000	0.81733	0.591000	0.81541	GAT	.	.		0.388	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		A	179096495	G	A	179096495	3	1	141	1	0	0	0	0	1	0	0	0	9532	1174	41	3	1605	3	MFN1	3	179096495	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	46920846	179096495	18925935	27	21924										
MFI2	4241	hgsc.bcm.edu	37	chr3	196744154	196744154	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gcctggccccaggagggaagCgtcttccctgggaagcagga	16	12	1	0	rs375237562		TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr3:196744154C>T	ENST00000296350.5	-	7	833	c.720G>A	c.(718-720)acG>acA	p.T240T		NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	240	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of plasminogen activation (GO:0010756)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ferric iron binding (GO:0008199)|iron ion binding (GO:0005506)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(1)	20	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		AGGAGGGAAGCGTCTTCCCTG	0.677																																					p.T240T		Atlas-SNP	.											.	MFI2	88	.	0			c.G720A						.	C		1,4363		0,1,2181	13	12	13		720	-7.1	0.4	3		13	0,8518		0,0,4259	no	coding-synonymous	MFI2	NM_005929.5		0,1,6440	TT,TC,CC		0.0,0.0229,0.0078		240/739	196744154	1,12881	2182	4259	6441	SO:0001819	synonymous_variant	4241	exon7			GGGAAGCGTCTTC		CCDS3325.1, CCDS3326.1	3q28-q29	2012-10-02			ENSG00000163975	ENSG00000163975		"CD molecules"	7037	protein-coding gene	gene with protein product	"melanotransferrin", "membrane-bound transferrin-like protein"	155750					Standard	NM_033316		Approved	CD228, FLJ38863, MAP97, MGC4856, MTF1	uc003fxk.4	P08582	OTTHUMG00000155518	ENST00000296350.5:c.720G>A	chr3.hg19:g.196744154C>T		123.0	0.0		104.0	27.0	NM_005929	Q9BQE2	Silent	SNP	ENST00000296350.5	hg19	CCDS3325.1																																																																																			.	.		0.677	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1			T	196744154	C	T	196744154	2	4	141	1	0	0	0	0	0	0	0	1	9531	755	27	1		1	MFI2	3	196744154	Silent	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	17647659	196744154	1278276	28	21925										
RNF212	285498	hgsc.bcm.edu	37	chr4	1107222	1107222	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cgtcctgtggggcggctggaAgcagcgattacagaacaccc	14	12	0	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr4:1107222A>T	ENST00000433731.2	-	1	92	c.31T>A	c.(31-33)Ttc>Atc	p.F11I	RNF212_ENST00000382968.5_Missense_Mutation_p.F11I|TMED11P_ENST00000502630.1_RNA|RNF212_ENST00000505730.1_5'UTR|RP11-20I20.2_ENST00000504969.1_RNA|RNF212_ENST00000333673.5_Missense_Mutation_p.F11I			Q495C1	RN212_HUMAN	ring finger protein 212	11					chiasma assembly (GO:0051026)|meiotic gene conversion (GO:0006311)|protein sumoylation (GO:0016925)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(23;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (64;0.151)		GGCGGCTGGAAGCAGCGATTA	0.687																																					p.F11I		Atlas-SNP	.											.	RNF212	69	.	0			c.T31A						.						48	38	41					4																	1107222		2194	4297	6491	SO:0001583	missense	285498	exon1			GCTGGAAGCAGCG	AK096160	CCDS3345.1, CCDS46996.1, CCDS54704.1	4p16.3	2013-02-27	2007-01-19	2007-01-19	ENSG00000178222	ENSG00000178222		"RING-type (C3HC4) zinc fingers"	27729	protein-coding gene	gene with protein product		612041	"hypothetical protein LOC285498"	LOC285498		23396135	Standard	NM_001131034		Approved	FLJ38841	uc003gcj.3	Q495C1	OTTHUMG00000118997	ENST00000433731.2:c.31T>A	chr4.hg19:g.1107222A>T	ENSP00000389709:p.Phe11Ile	107.0	0.0		100.0	28.0	NM_194439	C9J8N0|Q495C0|Q86W82|Q8IY99|Q8N8U7	Missense_Mutation	SNP	ENST00000433731.2	hg19	CCDS46996.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.594779	0.46318	.	.	ENSG00000178222	ENST00000382968;ENST00000433731;ENST00000333673	D;D;D	0.93488	-3.23;-3.23;-3.23	4.43	4.43	0.53597	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.090520	0.42172	U	0.000760	D	0.93710	0.7990	M	0.66378	2.025	0.36717	D	0.880991	P;P;P;P	0.50819	0.728;0.936;0.939;0.728	B;P;P;B	0.53912	0.297;0.737;0.503;0.277	D	0.94489	0.7700	10	0.52906	T	0.07	.	8.1528	0.31152	0.9022:0.0:0.0978:0.0	.	11;11;11;11	Q495C1-2;C9J8N0;Q495C1;Q495C1-5	.;.;RN212_HUMAN;.	I	11	ENSP00000372428:F11I;ENSP00000389709:F11I;ENSP00000327481:F11I	ENSP00000327481:F11I	F	-	1	0	RNF212	1097222	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	3.091000	0.50199	1.745000	0.51790	0.477000	0.44152	TTC	.	.		0.687	RNF212-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359124.2	NM_194439		T	1107222	A	T	1107222	3	4	141	1	0	0	0	0	1	0	0	0	13491	72	3	4	902	4	RNF212	4	1107222	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10		1107222	190047054	29	21926										
POLR2B	5431	hgsc.bcm.edu	37	chr4	57889912	57889912	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cttgtggtattcagtatagaCaagaggtaggtatctttgat	11	4	2	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr4:57889912C>T	ENST00000381227.1	+	21	3264	c.2851C>T	c.(2851-2853)Caa>Taa	p.Q951*	POLR2B_ENST00000441246.2_Nonsense_Mutation_p.Q944*|POLR2B_ENST00000431623.2_Nonsense_Mutation_p.Q876*|POLR2B_ENST00000314595.5_Nonsense_Mutation_p.Q951*			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	951					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					TCAGTATAGACAAGAGGTAGG	0.338																																					p.Q951X		Atlas-SNP	.											.	POLR2B	108	.	0			c.C2851T						.						84	82	82					4																	57889912		2203	4300	6503	SO:0001587	stop_gained	5431	exon20			TATAGACAAGAGG		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.2851C>T	chr4.hg19:g.57889912C>T	ENSP00000370625:p.Gln951*	204.0	0.0		175.0	16.0	NM_000938	A8K1A8|Q8IZ61	Nonsense_Mutation	SNP	ENST00000381227.1	hg19	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	C	42	9.519498	0.99193	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.3953	0.60849	0.0:0.9285:0.0:0.0715	.	.	.	.	X	951;876;944;951	.	ENSP00000312735:Q951X	Q	+	1	0	POLR2B	57584669	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.779000	0.85648	2.771000	0.95319	0.563000	0.77884	CAA	.	.		0.338	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		T	57889912	C	T	57889912	4	4	141	1	0	0	0	0	0	1	0	0	12224	479	17	3	2929	3	POLR2B	4	57889912	Nonsense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	56782690	57889912	133264364	30	21927										
ANK2	287	hgsc.bcm.edu	37	chr4	114279036	114279036	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	acaccactcctgctaggaccCcaactgaagaggggacccca	9	16	0	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr4:114279036C>G	ENST00000357077.4	+	38	9315	c.9262C>G	c.(9262-9264)Cca>Gca	p.P3088A	ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.P3055A	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3088					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TGCTAGGACCCCAACTGAAGA	0.463																																					p.P3088A		Atlas-SNP	.											.	ANK2	576	.	0			c.C9262G						.						56	57	57					4																	114279036		2203	4300	6503	SO:0001583	missense	287	exon38			AGGACCCCAACTG	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.9262C>G	chr4.hg19:g.114279036C>G	ENSP00000349588:p.Pro3088Ala	80.0	0.0		52.0	15.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.573287	0.65765	.	.	ENSG00000145362	ENST00000357077;ENST00000264366;ENST00000505342	D;D;D	0.99803	-3.37;-3.4;-6.82	5.78	5.78	0.91487	.	0.000000	0.56097	D	0.000025	D	0.99739	0.9897	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.936;0.997	D	0.98691	1.0696	10	0.36615	T	0.2	.	20.0139	0.97470	0.0:1.0:0.0:0.0	.	3055;3088	Q01484;Q01484-4	ANK2_HUMAN;.	A	3088;3055;98	ENSP00000349588:P3088A;ENSP00000264366:P3055A;ENSP00000422498:P98A	ENSP00000264366:P3055A	P	+	1	0	ANK2	114498485	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.999000	0.70665	2.724000	0.93272	0.563000	0.77884	CCA	.	.		0.463	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114279036	C	G	114279036	3	3	141	1	0	0	0	0	1	0	0	0	621	623	22	4	9477	4	ANK2	4	114279036	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	56389124	114279036	76875240	31	21928										
CLGN	1047	hgsc.bcm.edu	37	chr4	141313515	141313531	+	Splice_Site	DEL	TGTATCTTTATGTTTTT	TGTATCTTTATGTTTTT	-													0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	atgtcggtttttttatactcTgtatctttatgttttttctg					rs370853657		TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	TGTATCTTTATGTTTTT	TGTATCTTTATGTTTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr4:141313515_141313531delTGTATCTTTATGTTTTT	ENST00000325617.5	-	13	1933_1949	c.1493_1509delAAAAACATAAAGATACA	c.(1492-1509)aaaaaacataaagataca>a	p.KKHKDT498fs	CLGN_ENST00000537281.1_Splice_Site_p.KKHKDT498fs|CLGN_ENST00000414773.1_Splice_Site_p.KKHKDT498fs	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	498					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)	p.K499K(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					TTTTATACTCTGTATCTTTATGTTTTTTCTGTGGTAG	0.318																																					p.498_504del		Atlas-Indel,Pindel	.											.	CLGN	76	.	1	Substitution - coding silent(1)	endometrium(1)	c.1494_1510del						.																																			SO:0001630	splice_region_variant	1047	exon14			.	D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.1492-1AAAAACATAAAGATACA>-	chr4.hg19:g.141313515_141313531delTGTATCTTTATGTTTTT		117.0	0.0		84.0	17.0	NM_001130675	B3KS90|B4DXV8|D3DNY8	Frame_Shift_Del	DEL	ENST00000325617.5	hg19	CCDS3751.1																																																																																			.	.		0.318	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362	Frame_Shift_Del	-	141313531	TGTATCTTTATGTTTTT	-	141313515	8	5	141	1	0	1	0	1	0	0	1	0	3526	1567	55	0	335	0	CLGN	4	141313515	Splice_Site	DEL	TGTATCTTTATGTTTTT	TCGA-DD-A4NV-01A-11D-A30V-10	27034479	141313515	49840761	32	21929										
CCDC111	201973	hgsc.bcm.edu	37	chr4	185606652	185606652	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ataaagatggcattaaaggaGgtaaagttaatctcatcctt	8	5	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr4:185606652G>T	ENST00000314970.6	+	10	1619	c.1186G>T	c.(1186-1188)Gga>Tga	p.G396*	PRIMPOL_ENST00000515774.1_Splice_Site_p.G267*|PRIMPOL_ENST00000512834.1_Splice_Site_p.G395*|PRIMPOL_ENST00000503752.1_Splice_Site_p.G396*	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	396					mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)										CATTAAAGGAGGTAAAGTTAA	0.343																																					p.G396X		Atlas-SNP	.											.	CCDC111	43	.	0			c.G1186T						.						185	180	182					4																	185606652		2203	4300	6503	SO:0001630	splice_region_variant	201973	exon10			AAAGGAGGTAAAG	AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"coiled-coil domain containing 111"	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.1186+1G>T	chr4.hg19:g.185606652G>T		333.0	0.0		237.0	75.0	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Nonsense_Mutation	SNP	ENST00000314970.6	hg19	CCDS3837.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.182288	0.78677	.	.	ENSG00000164306	ENST00000314970;ENST00000515774;ENST00000503752;ENST00000512834;ENST00000508001	.	.	.	5.4	5.4	0.78164	.	0.055717	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-26.5288	12.6428	0.56718	0.0749:0.0:0.9251:0.0	.	.	.	.	X	396;267;396;395;70	.	ENSP00000313816:G396X	G	+	1	0	CCDC111	185843646	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	4.116000	0.57871	2.813000	0.96785	0.561000	0.74099	GGA	.	.		0.343	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683	Nonsense_Mutation	T	185606652	G	T	185606652	5	4	141	1	0	0	0	0	0	0	1	0	2750	1014	35	3	1216	3	CCDC111	4	185606652	Splice_Site	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	44293137	185606652	5547624	33	21930										
SLC6A18	348932	hgsc.bcm.edu	37	chr5	1245974	1245974	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gtcccgcaggagctgttcccCtcgcgtcaggagaagctcta	12	14	2	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:1245974C>G	ENST00000324642.3	+	12	1791	c.1668C>G	c.(1666-1668)ccC>ccG	p.P556P		NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	556					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			AGCTGTTCCCCTCGCGTCAGG	0.701																																					p.P556P		Atlas-SNP	.											.	SLC6A18	84	.	0			c.C1668G						.						20	22	21					5																	1245974		2200	4298	6498	SO:0001819	synonymous_variant	348932	exon12			GTTCCCCTCGCGT	AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"Solute carriers"	26441	protein-coding gene	gene with protein product		610300	"solute carrier family 6 (neurotransmitter transporter), member 18", "solute carrier family 6, member 18"			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.1668C>G	chr5.hg19:g.1245974C>G		85.0	0.0		101.0	20.0	NM_182632		Silent	SNP	ENST00000324642.3	hg19	CCDS3860.1																																																																																			.	.		0.701	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632		G	1245974	C	G	1245974	2	3	141	1	0	0	0	0	0	0	0	1	14696	668	24	4		4	SLC6A18	5	1245974	Silent	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10		1245974	179669286	34	21931										
DHX29	54505	hgsc.bcm.edu	37	chr5	54586093	54586096	+	Frame_Shift_Del	DEL	TTGT	TTGT	-													0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gagcctctttttggccttgcTtgtttttttctagtttaaag					rs150941078		TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	TTGT	TTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:54586093_54586096delTTGT	ENST00000251636.5	-	7	1005_1008	c.857_860delACAA	c.(856-861)aacaagfs	p.NK286fs	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	286						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				TTGGCCTTGCTTGTTTTTTTCTAG	0.328																																					p.286_287del		Atlas-Indel,Pindel	.											.	DHX29	116	.	0			c.858_861del						.																																			SO:0001589	frameshift_variant	54505	exon7			.	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"DEAH-boxes"	15815	protein-coding gene	gene with protein product		612720	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.857_860delACAA	chr5.hg19:g.54586093_54586096delTTGT	ENSP00000251636:p.Asn286fs	141.0	0.0		137.0	25.0	NM_019030	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Frame_Shift_Del	DEL	ENST00000251636.5	hg19	CCDS34158.1																																																																																			.	.		0.328	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030		-	54586096	TTGT	-	54586093	7	5	141	1	0	1	0	1	0	0	0	0	4505	1609	56	0	3333	0	DHX29	5	54586093	Frame_Shift_Del	DEL	TTGT	TCGA-DD-A4NV-01A-11D-A30V-10	53340119	54586093	126329167	35	21932										
OTP	23440	hgsc.bcm.edu	37	chr5	76932919	76932919	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gtggtgatgtcctccccgggCagcagagtggctccctccac	13	15	0	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:76932919C>A	ENST00000306422.3	-	2	1312	c.174G>T	c.(172-174)ctG>ctT	p.L58L	OTP_ENST00000515716.1_5'Flank	NM_032109.2	NP_115485.1	Q5XKR4	OTP_HUMAN	orthopedia homeobox	58					forebrain neuron differentiation (GO:0021879)|hypothalamus cell differentiation (GO:0021979)|neurohypophysis development (GO:0021985)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)	13		all_lung(232;0.00051)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;9.04e-51)|Epithelial(54;1.62e-45)|all cancers(79;4.4e-41)		CCTCCCCGGGCAGCAGAGTGG	0.726																																					p.L58L		Atlas-SNP	.											.	OTP	29	.	0			c.G174T						.						15	18	17					5																	76932919		2200	4295	6495	SO:0001819	synonymous_variant	23440	exon2			CCCGGGCAGCAGA		CCDS4039.1	5q14.1	2011-06-20	2007-02-15		ENSG00000171540	ENSG00000171540		"Homeoboxes / PRD class"	8518	protein-coding gene	gene with protein product		604529	"orthopedia homolog (Drosophila)"			10458915	Standard	NM_032109		Approved		uc003kfg.3	Q5XKR4	OTTHUMG00000102171	ENST00000306422.3:c.174G>T	chr5.hg19:g.76932919C>A		75.0	0.0		76.0	13.0	NM_032109		Silent	SNP	ENST00000306422.3	hg19	CCDS4039.1																																																																																			.	.		0.726	OTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220016.2			A	76932919	C	A	76932919	2	1	141	1	0	0	0	0	0	0	0	1	11319	697	25	3		3	OTP	5	76932919	Silent	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	22346826	76932919	103982341	36	21933										
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79733274	79733274	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	acaaagttccaaaatgtttcAtgccaaagacaagctacaac	5	10	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:79733274A>G	ENST00000338008.5	+	3	950	c.770A>G	c.(769-771)cAt>cGt	p.H257R	ZFYVE16_ENST00000505560.1_Missense_Mutation_p.H257R|ZFYVE16_ENST00000510158.1_Missense_Mutation_p.H257R	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	257					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		AAAATGTTTCATGCCAAAGAC	0.353																																					p.H257R	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.A770G						.						61	65	63					5																	79733274		2202	4299	6501	SO:0001583	missense	9765	exon4			TGTTTCATGCCAA	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"Zinc fingers, FYVE domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20756	protein-coding gene	gene with protein product	"endofin", "protein phosphatase 1, regulatory subunit 69"	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.770A>G	chr5.hg19:g.79733274A>G	ENSP00000337159:p.His257Arg	224.0	0.0		250.0	16.0	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Missense_Mutation	SNP	ENST00000338008.5	hg19	CCDS4050.1	.	.	.	.	.	.	.	.	.	.	A	8.051	0.765996	0.15983	.	.	ENSG00000039319	ENST00000338008;ENST00000510158;ENST00000505560	T;T;T	0.36878	1.23;1.23;1.23	5.09	5.09	0.68999	.	0.341252	0.25138	N	0.032844	T	0.20577	0.0495	N	0.14661	0.345	0.09310	N	1	B;B	0.14805	0.002;0.011	B;B	0.17433	0.018;0.008	T	0.12993	-1.0526	10	0.24483	T	0.36	-0.7872	8.8365	0.35115	0.9135:0.0:0.0865:0.0	.	257;257	Q7Z3T8-3;Q7Z3T8	.;ZFY16_HUMAN	R	257	ENSP00000337159:H257R;ENSP00000423663:H257R;ENSP00000426848:H257R	ENSP00000337159:H257R	H	+	2	0	ZFYVE16	79769030	0.940000	0.31905	0.783000	0.31826	0.422000	0.31414	1.322000	0.33689	2.044000	0.60594	0.383000	0.25322	CAT	.	.		0.353	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		G	79733274	A	G	79733274	3	3	141	1	0	0	0	0	1	0	0	0	17679	217	8	2	776	2	ZFYVE16	5	79733274	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	2800355	79733274	101181986	37	21934										
ATG10	83734	hgsc.bcm.edu	37	chr5	81474399	81474399	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gggaccatgggacactattaCgcaacaggttggagagtatt	13	7	0	1	rs548892230		TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:81474399C>T	ENST00000282185.3	+	5	740	c.446C>T	c.(445-447)aCg>aTg	p.T149M	ATG10_ENST00000514253.2_3'UTR|ATG10_ENST00000458350.3_Missense_Mutation_p.T149M|ATG10_ENST00000513634.1_Missense_Mutation_p.T149M	NM_031482.4	NP_113670.1	Q9H0Y0	ATG10_HUMAN	autophagy related 10	149					autophagy (GO:0006914)|autophagy in response to ER overload (GO:0034263)|positive regulation of protein modification process (GO:0031401)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	Atg12 ligase activity (GO:0019777)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(2)	9		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)		GACACTATTACGCAACAGGTT	0.433													C|||	1	0.000199681	0	0.0014	5008	,	,		19557	0		0	False		,,,				2504	0				p.T149M		Atlas-SNP	.											.	ATG10	23	.	0			c.C446T						.						180	156	164					5																	81474399		2203	4300	6503	SO:0001583	missense	83734	exon6			CTATTACGCAACA	AK024016	CCDS4057.1	5q14.1	2014-02-12	2012-06-06	2005-09-11	ENSG00000152348	ENSG00000152348			20315	protein-coding gene	gene with protein product		610800	"APG10 autophagy 10-like (S. cerevisiae)", "ATG10 autophagy related 10 homolog (S. cerevisiae)"	APG10L			Standard	NM_031482		Approved	DKFZP586I0418, FLJ13954	uc003khr.3	Q9H0Y0	OTTHUMG00000119041	ENST00000282185.3:c.446C>T	chr5.hg19:g.81474399C>T	ENSP00000282185:p.Thr149Met	126.0	0.0		161.0	11.0	NM_001131028	B2RE09|Q6PIX1|Q9H842	Missense_Mutation	SNP	ENST00000282185.3	hg19	CCDS4057.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.431692	0.43122	.	.	ENSG00000152348	ENST00000282185;ENST00000458350;ENST00000513634	T;T;T	0.55413	1.58;1.58;0.52	5.37	3.55	0.40652	Autophagy-related protein 3 (1);	0.159978	0.53938	D	0.000049	T	0.74481	0.3722	M	0.90145	3.09	0.42169	D	0.991636	D;D	0.89917	1.0;0.996	D;P	0.75484	0.986;0.863	T	0.77672	-0.2500	10	0.87932	D	0	-3.6582	10.2806	0.43537	0.0:0.7898:0.1361:0.0741	.	149;149	D6RDX3;Q9H0Y0	.;ATG10_HUMAN	M	149	ENSP00000282185:T149M;ENSP00000404938:T149M;ENSP00000425225:T149M	ENSP00000282185:T149M	T	+	2	0	ATG10	81510155	0.996000	0.38824	0.685000	0.30070	0.300000	0.27592	3.737000	0.55060	0.725000	0.32318	0.305000	0.20034	ACG	.	.		0.433	ATG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239252.2	NM_001131028		T	81474399	C	T	81474399	3	4	141	1	0	0	0	0	1	0	0	0	1089	536	19	1	460	1	ATG10	5	81474399	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	1741125	81474399	99440861	38	21935										
NUDT12	83594	hgsc.bcm.edu	37	chr5	102886634	102886634	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gctcggcttggtggcacaaaGaatgcctgctgcttcccttt	11	12	0	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:102886634G>A	ENST00000230792.2	-	7	1413	c.1317C>T	c.(1315-1317)ttC>ttT	p.F439F	NUDT12_ENST00000507423.1_Silent_p.F421F	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	439	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		GTGGCACAAAGAATGCCTGCT	0.358																																					p.F439F		Atlas-SNP	.											.	NUDT12	27	.	0			c.C1317T						.						108	108	108					5																	102886634		2203	4300	6503	SO:0001819	synonymous_variant	83594	exon7			CACAAAGAATGCC	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"Nudix motif containing", "Ankyrin repeat domain containing"	18826	protein-coding gene	gene with protein product	"nucleoside diphosphate linked moiety X-type motif 12"	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.1317C>T	chr5.hg19:g.102886634G>A		121.0	0.0		123.0	25.0	NM_031438	B3KUW2|Q8TAL7	Silent	SNP	ENST00000230792.2	hg19	CCDS4096.1																																																																																			.	.		0.358	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438		A	102886634	G	A	102886634	2	1	141	1	0	0	0	0	0	0	0	1	10737	933	33	3		3	NUDT12	5	102886634	Silent	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	21412235	102886634	78028626	39	21936										
CHSY3	337876	hgsc.bcm.edu	37	chr5	129520172	129520172	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gagcaaagaggaccagcagcTgggagtgataccttctttca	12	9	2	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:129520172T>A	ENST00000305031.4	+	3	1695	c.1337T>A	c.(1336-1338)cTg>cAg	p.L446Q	CHSY3_ENST00000507545.1_3'UTR	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	446					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		GACCAGCAGCTGGGAGTGATA	0.498																																					p.L446Q		Atlas-SNP	.											.	CHSY3	92	.	0			c.T1337A						.						56	52	53					5																	129520172		2203	4300	6503	SO:0001583	missense	337876	exon3			AGCAGCTGGGAGT	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.1337T>A	chr5.hg19:g.129520172T>A	ENSP00000302629:p.Leu446Gln	178.0	0.0		172.0	7.0	NM_175856	B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	hg19	CCDS34223.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.303751	0.81136	.	.	ENSG00000198108	ENST00000305031	T	0.21191	2.02	4.5	4.5	0.54988	.	0.000000	0.40302	N	0.001126	T	0.47930	0.1472	M	0.81942	2.565	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.51434	-0.8706	9	.	.	.	-2.2213	14.8652	0.70409	0.0:0.0:0.0:1.0	.	446	Q70JA7	CHSS3_HUMAN	Q	446	ENSP00000302629:L446Q	.	L	+	2	0	CHSY3	129548071	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.720000	0.84759	2.243000	0.73865	0.528000	0.53228	CTG	.	.		0.498	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856		A	129520172	T	A	129520172	3	1	141	1	0	0	0	0	1	0	0	0	3415	1580	55	4	1347	4	CHSY3	5	129520172	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	26633538	129520172	51395088	40	21937										
PCDH1	5097	hgsc.bcm.edu	37	chr5	141244054	141244054	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	actgagaagttgtagccactCagcataaatttggggtcatt	10	7	2	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:141244054C>G	ENST00000394536.3	-	3	1981	c.1842G>C	c.(1840-1842)ctG>ctC	p.L614L	PCDH1_ENST00000503492.1_Intron|PCDH1_ENST00000287008.3_Silent_p.L614L|PCDH1_ENST00000536585.1_Silent_p.L592L|PCDH1_ENST00000456271.1_Silent_p.L602L|PCDH1_ENST00000511044.1_5'UTR	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	614	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		TGTAGCCACTCAGCATAAATT	0.552																																					p.L614L	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.G1842C						.						82	76	78					5																	141244054		2203	4300	6503	SO:0001819	synonymous_variant	5097	exon3			GCCACTCAGCATA	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"Cadherins / Protocadherins : Non-clustered"	8655	protein-coding gene	gene with protein product		603626	"protocadherin 1 (cadherin-like 1)"			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.1842G>C	chr5.hg19:g.141244054C>G		64.0	0.0		55.0	8.0	NM_032420	Q8IUP2	Silent	SNP	ENST00000394536.3	hg19	CCDS43375.1																																																																																			.	.		0.552	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420		G	141244054	C	G	141244054	2	3	141	1	0	0	0	0	0	0	0	1	11515	813	29	4		4	PCDH1	5	141244054	Silent	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	11723882	141244054	39671206	41	21938										
ARHGEF37	389337	hgsc.bcm.edu	37	chr5	149003635	149003635	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tggtggaggacgcactgggcCggacgagtaaccagcttcgc	16	11	0	0	rs369747296		TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:149003635C>T	ENST00000333677.6	+	10	1559	c.1396C>T	c.(1396-1398)Cgg>Tgg	p.R466W		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	466						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						CGCACTGGGCCGGACGAGTAA	0.582																																					p.R466W		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.C1396T						.	C	TRP/ARG	1,4033		0,1,2016	87	95	93		1396	3.6	0.7	5		93	0,8354		0,0,4177	no	missense	ARHGEF37	NM_001001669.2	101	0,1,6193	TT,TC,CC		0.0,0.0248,0.0081	probably-damaging	466/676	149003635	1,12387	2017	4177	6194	SO:0001583	missense	389337	exon10			CTGGGCCGGACGA	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"Rho guanine nucleotide exchange factors"	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1396C>T	chr5.hg19:g.149003635C>T	ENSP00000328083:p.Arg466Trp	48.0	0.0		66.0	4.0	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	hg19	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	C	9.603	1.129342	0.21041	2.48E-4	0.0	ENSG00000183111	ENST00000333677	T	0.55588	0.51	5.61	3.63	0.41609	.	0.561907	0.20007	N	0.101214	T	0.30198	0.0757	N	0.08118	0	0.09310	N	1	P	0.43431	0.807	B	0.36989	0.238	T	0.16276	-1.0408	10	0.66056	D	0.02	-0.9871	11.243	0.48980	0.1489:0.7226:0.1285:0.0	.	466	A1IGU5	ARH37_HUMAN	W	466	ENSP00000328083:R466W	ENSP00000328083:R466W	R	+	1	2	ARHGEF37	148983828	0.518000	0.26234	0.689000	0.30133	0.028000	0.11728	2.172000	0.42463	1.350000	0.45770	-0.315000	0.08773	CGG	.	.		0.582	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669		T	149003635	C	T	149003635	3	4	141	1	0	0	0	0	1	0	0	0	906	643	23	1	1430	1	ARHGEF37	5	149003635	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	7759581	149003635	31911625	42	21939										
CAMK2A	815	hgsc.bcm.edu	37	chr5	149631366	149631366	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gcggtgctggtcctcatcccAgaacggggggtacccaacca	13	14	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:149631366A>G	ENST00000348628.6	-	9	1305	c.640T>C	c.(640-642)Tgg>Cgg	p.W214R	CAMK2A_ENST00000398376.3_Missense_Mutation_p.W214R	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	214	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCTCATCCCAGAACGGGGGG	0.602																																					p.W214R		Atlas-SNP	.											.	CAMK2A	42	.	0			c.T640C						.						25	32	30					5																	149631366		2097	4255	6352	SO:0001583	missense	815	exon9			CATCCCAGAACGG	AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"CaM-kinase II alpha chain", "calcium/calmodulin-dependent protein kinase II alpha-B subunit", "CaM kinase II alpha subunit", "CaMK-II alpha subunit", "calcium/calmodulin-dependent protein kinase type II alpha chain"	114078	"calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.640T>C	chr5.hg19:g.149631366A>G	ENSP00000261793:p.Trp214Arg	162.0	0.0		171.0	9.0	NM_171825	Q9UL21|Q9Y2H4|Q9Y352	Missense_Mutation	SNP	ENST00000348628.6	hg19	CCDS43386.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.797217	0.90538	.	.	ENSG00000070808	ENST00000348628;ENST00000398376	T;T	0.63417	-0.04;-0.04	5.67	5.67	0.87782	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.62938	0.2469	N	0.04686	-0.185	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.999;0.995	T	0.73000	-0.4120	10	0.87932	D	0	.	16.2045	0.82114	1.0:0.0:0.0:0.0	.	214;214;214	Q9UQM7-2;Q9UQM7;A8K161	.;KCC2A_HUMAN;.	R	214	ENSP00000261793:W214R;ENSP00000381412:W214R	ENSP00000261793:W214R	W	-	1	0	CAMK2A	149611559	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.238000	0.95380	2.288000	0.76882	0.533000	0.62120	TGG	.	.		0.602	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981		G	149631366	A	G	149631366	3	3	141	1	0	0	0	0	1	0	0	0	2601	188	7	2	873	2	CAMK2A	5	149631366	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	627731	149631366	31283894	43	21940										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167625964	167625964	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgccgtggaacagcttttacGccatggacaccctggtgatg	12	11	0	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:167625964G>A	ENST00000518659.1	+	16	3046	c.3007G>A	c.(3007-3009)Gcc>Acc	p.A1003T	TENM2_ENST00000519204.1_Missense_Mutation_p.A882T|TENM2_ENST00000520394.1_Missense_Mutation_p.A771T|TENM2_ENST00000545108.1_Missense_Mutation_p.A1003T|TENM2_ENST00000403607.2_Missense_Mutation_p.A827T	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1003					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										CAGCTTTTACGCCATGGACAC	0.567																																					p.A994T		Atlas-SNP	.											.	.	.	.	0			c.G2980A						.						76	81	79					5																	167625964		2103	4225	6328	SO:0001583	missense	57451	exon16			TTTTACGCCATGG	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.3007G>A	chr5.hg19:g.167625964G>A	ENSP00000429430:p.Ala1003Thr	96.0	0.0		112.0	21.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	G	33	5.211900	0.95069	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	T;T;T;T;T	0.12465	2.68;2.68;2.68;2.68;2.68	5.52	5.52	0.82312	Carboxypeptidase-like, regulatory domain (1);	0.096845	0.64402	D	0.000001	T	0.32585	0.0834	L	0.44542	1.39	0.58432	D	0.999999	D;D;D	0.89917	0.994;0.99;1.0	P;P;D	0.79108	0.806;0.645;0.992	T	0.01149	-1.1436	10	0.59425	D	0.04	.	19.4325	0.94776	0.0:0.0:1.0:0.0	.	1003;1003;771	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	T	1003;1003;882;771;827	ENSP00000429430:A1003T;ENSP00000438635:A1003T;ENSP00000428964:A882T;ENSP00000427874:A771T;ENSP00000384905:A827T	ENSP00000384905:A827T	A	+	1	0	ODZ2	167558542	1.000000	0.71417	0.961000	0.40146	0.831000	0.47069	9.869000	0.99810	2.593000	0.87608	0.563000	0.77884	GCC	.	.		0.567	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167625964	G	A	167625964	3	1	141	1	0	0	0	0	1	0	0	0	10844	1087	38	1	3042	1	ODZ2	5	167625964	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	17994598	167625964	13289296	44	21941										
NHP2	55651	hgsc.bcm.edu	37	chr5	177577899	177577899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgctccttaccgtcttagagGggatatagacatagggcaaa	11	8	1	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr5:177577899G>A	ENST00000274606.3	-	3	475	c.326C>T	c.(325-327)cCc>cTc	p.P109L	NHP2_ENST00000314397.4_Intron	NM_017838.3	NP_060308.1	Q9NX24	NHP2_HUMAN	NHP2 ribonucleoprotein	109					rRNA pseudouridine synthesis (GO:0031118)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			endometrium(1)|kidney(1)|ovary(2)	4						CGTCTTAGAGGGGATATAGAC	0.537																																					p.P109L		Atlas-SNP	.											.	NHP2	12	.	0			c.C326T						.						263	246	252					5																	177577899		2203	4300	6503	SO:0001583	missense	55651	exon3			TTAGAGGGGATAT	AF161404	CCDS4432.1, CCDS34308.1	5q35.3	2014-09-17	2012-12-10	2008-10-13	ENSG00000145912	ENSG00000145912			14377	protein-coding gene	gene with protein product		606470	"nucleolar protein family A, member 2 (H/ACA small nucleolar RNPs)", "NHP2 ribonucleoprotein homolog (yeast)"	NOLA2		11074001	Standard	NM_017838		Approved	FLJ20479	uc003mir.2	Q9NX24	OTTHUMG00000130886	ENST00000274606.3:c.326C>T	chr5.hg19:g.177577899G>A	ENSP00000274606:p.Pro109Leu	46.0	0.0		50.0	11.0	NM_017838	A6NKY8|Q9P095	Missense_Mutation	SNP	ENST00000274606.3	hg19	CCDS4432.1	.	.	.	.	.	.	.	.	.	.	g	19.81	3.896177	0.72639	.	.	ENSG00000145912	ENST00000274606;ENST00000502263;ENST00000514354;ENST00000511078	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	5.22	5.22	0.72569	Ribosomal protein L7Ae/L30e/S12e/Gadd45 (1);	0.000000	0.85682	D	0.000000	T	0.75722	0.3888	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80281	-0.1448	10	0.87932	D	0	-12.0937	16.2705	0.82616	0.0:0.0:1.0:0.0	.	109	Q9NX24	NHP2_HUMAN	L	109;62;109;109	ENSP00000274606:P109L;ENSP00000431126:P62L;ENSP00000423803:P109L;ENSP00000423849:P109L	ENSP00000274606:P109L	P	-	2	0	NHP2	177510505	1.000000	0.71417	1.000000	0.80357	0.304000	0.27724	9.283000	0.95860	2.419000	0.82065	0.563000	0.77884	CCC	.	.		0.537	NHP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253471.1	NM_017838		A	177577899	G	A	177577899	3	1	141	1	0	0	0	0	1	0	0	0	10418	1232	43	3	143	3	NHP2	5	177577899	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	9951935	177577899	3337361	45	21942										
ELOVL2	54898	hgsc.bcm.edu	37	chr6	10995354	10995354	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tttccgcaaaacgaagaaaaTtgtgtccaggaactctactg	8	9	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr6:10995354T>G	ENST00000354666.3	-	5	474	c.391A>C	c.(391-393)Att>Ctt	p.I131L		NM_017770.3	NP_060240.3	Q9NXB9	ELOV2_HUMAN	ELOVL fatty acid elongase 2	131					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	fatty acid elongase activity (GO:0009922)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(2)	14	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)			ACGAAGAAAATTGTGTCCAGG	0.388																																					p.I131L		Atlas-SNP	.											.	ELOVL2	40	.	0			c.A391C						.						112	107	109					6																	10995354		2203	4300	6503	SO:0001583	missense	54898	exon5			AGAAAATTGTGTC	AK000341	CCDS4518.1	6p24.1	2011-05-25	2011-05-25		ENSG00000197977	ENSG00000197977			14416	protein-coding gene	gene with protein product		611814	"elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2"			12371743, 16564093	Standard	NM_017770		Approved	Ssc2	uc003mzp.4	Q9NXB9	OTTHUMG00000014252	ENST00000354666.3:c.391A>C	chr6.hg19:g.10995354T>G	ENSP00000346693:p.Ile131Leu	247.0	0.0		172.0	51.0	NM_017770	Q6P9E1|Q86W94	Missense_Mutation	SNP	ENST00000354666.3	hg19	CCDS4518.1	.	.	.	.	.	.	.	.	.	.	T	13.32	2.201007	0.38905	.	.	ENSG00000197977	ENST00000354666	T	0.20881	2.04	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.08935	0.0221	L	0.31120	0.905	0.50813	D	0.999892	B	0.10296	0.003	B	0.15052	0.012	T	0.07849	-1.0751	10	0.33940	T	0.23	-2.1704	16.0707	0.80928	0.0:0.0:0.0:1.0	.	131	Q9NXB9	ELOV2_HUMAN	L	131	ENSP00000346693:I131L	ENSP00000346693:I131L	I	-	1	0	ELOVL2	11103340	1.000000	0.71417	0.907000	0.35723	0.860000	0.49131	4.140000	0.58031	2.194000	0.70268	0.533000	0.62120	ATT	.	.		0.388	ELOVL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039849.1			G	10995354	T	G	10995354	3	3	141	1	0	0	0	0	1	0	0	0	5076	1493	52	5	515	5	ELOVL2	6	10995354	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10		10995354	160119713	46	21943										
C6orf62	81688	hgsc.bcm.edu	37	chr6	24718827	24718828	+	Frame_Shift_Ins	INS	-	-	T													0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	aactggtcagctagagattcINSttttttctttctaagctgag							TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr6:24718827_24718828insT	ENST00000378119.4	-	1	2236_2237	c.69_70insA	c.(67-72)aaagaafs	p.E24fs	C6orf62_ENST00000540769.1_Intron|C6orf62_ENST00000378102.3_Intron	NM_030939.4	NP_112201.1	Q9GZU0	CF062_HUMAN	chromosome 6 open reading frame 62	24						intracellular (GO:0005622)				endometrium(2)|kidney(3)|large_intestine(2)|lung(3)	10						GCTAGAGATTCTTTTTTCTTTC	0.381																																					p.E24fs		Atlas-Indel,Pindel	.											.,1	C6orf62	18	.	0			c.70_71insA						.																																			SO:0001589	frameshift_variant	81688	exon1			.	AL136632	CCDS4559.1	6p22.1	2011-12-13			ENSG00000112308	ENSG00000112308			20998	protein-coding gene	gene with protein product	"HBV X-transactivated protein 12"					11230166	Standard	NM_030939		Approved	FLJ12619, DKFZP564G182, XTP12	uc003nel.3	Q9GZU0	OTTHUMG00000014361	ENST00000378119.4:c.70dupA	chr6.hg19:g.24718833_24718833dupT	ENSP00000367359:p.Glu24fs	173.0	0.0		133.0	16.0	NM_030939	Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2	Frame_Shift_Ins	INS	ENST00000378119.4	hg19	CCDS4559.1																																																																																			.	.		0.381	C6orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040017.1	NM_030939		T	24718828	-	T	24718827	7	5	141	1	0	1	1	0	0	0	0	0	2370	922	32	0	639	0	C6orf62	6	24718827	Frame_Shift_Ins	INS	-	TCGA-DD-A4NV-01A-11D-A30V-10	13723473	24718827	146396240	47	21944										
EGFL8	80864	hgsc.bcm.edu	37	chr6	32134918	32134918	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ctcgcaccattgttttaataCggcaggcagcttcacctgcg	9	13	1	0	rs370079247		TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr6:32134918C>A	ENST00000395512.1	+	6	590	c.485C>A	c.(484-486)aCg>aAg	p.T162K	PPT2-EGFL8_ENST00000422437.1_3'UTR|AGPAT1_ENST00000490711.1_5'Flank|EGFL8_ENST00000333845.6_Missense_Mutation_p.T162K			Q99944	EGFL8_HUMAN	EGF-like-domain, multiple 8	162	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	10						TGTTTTAATACGGCAGGCAGC	0.612																																					p.T162K		Atlas-SNP	.											.	EGFL8	15	.	0			c.C485A						.						111	125	120					6																	32134918		1507	2707	4214	SO:0001583	missense	80864	exon6			TTAATACGGCAGG	U89336	CCDS4743.1	6p21	2010-06-25	2003-05-21	2003-05-23	ENSG00000241404	ENSG00000241404			13944	protein-coding gene	gene with protein product		609897	"chromosome 6 open reading frame 8"	C6orf8			Standard	NM_030652		Approved	NG3		Q99944	OTTHUMG00000031222	ENST00000395512.1:c.485C>A	chr6.hg19:g.32134918C>A	ENSP00000378888:p.Thr162Lys	82.0	0.0		80.0	19.0	NM_030652	B0S884|G5E9Q0|Q5JP23|Q5SSX3|Q8IV30	Missense_Mutation	SNP	ENST00000395512.1	hg19	CCDS4743.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.123419	0.56613	.	.	ENSG00000241404	ENST00000333845;ENST00000395512	D;D	0.92495	-3.05;-3.05	5.35	4.49	0.54785	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.94348	0.8183	M	0.80028	2.48	0.53005	D	0.999962	D	0.89917	1.0	D	0.75484	0.986	D	0.94832	0.7997	9	0.87932	D	0	-10.1396	9.8427	0.41008	0.0:0.9078:0.0:0.0922	.	162	Q99944	EGFL8_HUMAN	K	162	ENSP00000333380:T162K;ENSP00000378888:T162K	ENSP00000333380:T162K	T	+	2	0	EGFL8	32242896	0.997000	0.39634	0.529000	0.27951	0.125000	0.20455	4.688000	0.61715	1.497000	0.48584	0.591000	0.81541	ACG	.	.		0.612	EGFL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076463.3	NM_030652		A	32134918	C	A	32134918	3	1	141	1	0	0	0	0	1	0	0	0	4967	536	19	1	503	1	EGFL8	6	32134918	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	7416091	32134918	138980149	48	21945										
ZNF76	7629	hgsc.bcm.edu	37	chr6	35255576	35255576	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ggcagcagaggatgatgaggGcttcagtgcagacgcagtgg	18	7	1	4			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr6:35255576G>T	ENST00000373953.3	+	5	652	c.386G>T	c.(385-387)gGc>gTc	p.G129V	ZNF76_ENST00000339411.5_Missense_Mutation_p.G129V|ZNF76_ENST00000440666.2_Missense_Mutation_p.G103V	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	129					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						GATGATGAGGGCTTCAGTGCA	0.617																																					p.G129V	Esophageal Squamous(52;92 1039 20612 23956 34676)	Atlas-SNP	.											.	ZNF76	37	.	0			c.G386T						.						99	87	91					6																	35255576		2203	4300	6503	SO:0001583	missense	7629	exon5			ATGAGGGCTTCAG	M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"Zinc fingers, C2H2-type"	13149	protein-coding gene	gene with protein product		194549	"zinc finger protein 76 (expressed in testis)"	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.386G>T	chr6.hg19:g.35255576G>T	ENSP00000363064:p.Gly129Val	64.0	0.0		48.0	13.0	NM_003427	Q9BQB2	Missense_Mutation	SNP	ENST00000373953.3	hg19	CCDS4801.1	.	.	.	.	.	.	.	.	.	.	G	9.776	1.174081	0.21704	.	.	ENSG00000065029	ENST00000469195;ENST00000448999;ENST00000373953;ENST00000417184;ENST00000440666;ENST00000339411	T;T;T;T	0.09630	2.98;2.96;2.96;2.98	5.04	4.14	0.48551	.	0.171412	0.28161	N	0.016370	T	0.10078	0.0247	N	0.14661	0.345	0.58432	D	0.999996	P;D;B;B	0.76494	0.804;0.999;0.137;0.1	B;D;B;B	0.73380	0.255;0.98;0.093;0.046	T	0.24977	-1.0145	10	0.42905	T	0.14	.	13.8538	0.63513	0.0:0.2034:0.7966:0.0	.	129;129;129;129	B7Z851;B7Z991;P36508-2;P36508	.;.;.;ZNF76_HUMAN	V	129;129;129;129;103;129	ENSP00000419106:G129V;ENSP00000363064:G129V;ENSP00000392243:G103V;ENSP00000344097:G129V	ENSP00000229405:G129V	G	+	2	0	ZNF76	35363554	1.000000	0.71417	1.000000	0.80357	0.012000	0.07955	2.355000	0.44107	2.615000	0.88500	0.563000	0.77884	GGC	.	.		0.617	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427		T	35255576	G	T	35255576	3	4	141	1	0	0	0	0	1	0	0	0	18150	1203	42	3	400	3	ZNF76	6	35255576	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	3120658	35255576	135859491	49	21946										
RFPL4B	442247	hgsc.bcm.edu	37	chr6	112671285	112671285	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgtaagaagatccaccacgaTctgacaaaagatcccaggct	8	11	1	4			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr6:112671285T>A	ENST00000441065.2	+	3	687	c.375T>A	c.(373-375)gaT>gaA	p.D125E	RP11-506B6.6_ENST00000590673.1_RNA|RP11-506B6.6_ENST00000587816.1_RNA|RP11-506B6.6_ENST00000585611.1_RNA	NM_001013734.2	NP_001013756.2	Q6ZWI9	RFPLB_HUMAN	ret finger protein-like 4B	125	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	14		all_cancers(87;9.44e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00265)|Colorectal(196;0.0209)		all cancers(137;0.0202)|OV - Ovarian serous cystadenocarcinoma(136;0.0477)|Epithelial(106;0.0646)|GBM - Glioblastoma multiforme(226;0.0866)|BRCA - Breast invasive adenocarcinoma(108;0.244)		TCCACCACGATCTGACAAAAG	0.537																																					p.D125E		Atlas-SNP	.											.	RFPL4B	36	.	0			c.T375A						.						72	75	74					6																	112671285		2203	4300	6503	SO:0001583	missense	442247	exon3			CCACGATCTGACA	AK122906	CCDS34515.1	6q21	2007-04-24			ENSG00000251258	ENSG00000251258		"RING-type (C3HC4) zinc fingers"	33264	protein-coding gene	gene with protein product							Standard	NM_001013734		Approved	RNF211	uc003pvx.1	Q6ZWI9	OTTHUMG00000015390	ENST00000441065.2:c.375T>A	chr6.hg19:g.112671285T>A	ENSP00000423391:p.Asp125Glu	66.0	0.0		54.0	5.0	NM_001013734	A2RU91	Missense_Mutation	SNP	ENST00000441065.2	hg19	CCDS34515.1	.	.	.	.	.	.	.	.	.	.	T	10.51	1.369974	0.24771	.	.	ENSG00000251258	ENST00000441065	T	0.61510	0.1	4.14	-0.604	0.11626	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	1.740060	0.03871	N	0.275586	T	0.22244	0.0536	L	0.45470	1.425	0.09310	N	1	B	0.20261	0.043	B	0.15870	0.014	T	0.03394	-1.1041	10	0.18710	T	0.47	.	3.6165	0.08079	0.3124:0.4484:0.0:0.2392	.	125	Q6ZWI9	RFPLB_HUMAN	E	125	ENSP00000423391:D125E	ENSP00000423391:D125E	D	+	3	2	RFPL4B	112777978	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.492000	0.06467	-0.117000	0.11872	-0.146000	0.13790	GAT	.	.		0.537	RFPL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041885.2	NM_001013734		A	112671285	T	A	112671285	3	1	141	1	0	0	0	0	1	0	0	0	13271	1432	50	4	377	4	RFPL4B	6	112671285	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	77415709	112671285	58443782	50	21947										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136582246	136582439	+	Stop_Codon_Del	DEL	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	-													0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ttgtaatcttacttcatattTattattcctaaaagagagag					rs376948280|rs537502804|rs562481221|rs527483217|rs62431283|rs112744301|rs62431282|rs370252607|rs570210520|rs111800140|rs193167212|rs375440569	byFrequency	TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr6:136582246_136582439delTGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	ENST00000531224.1	-	0	2973_3017				BCLAF1_ENST00000527759.1_Stop_Codon_Del|BCLAF1_ENST00000392348.2_Stop_Codon_Del|BCLAF1_ENST00000527536.1_Stop_Codon_Del|BCLAF1_ENST00000353331.4_Stop_Codon_Del|BCLAF1_ENST00000031135.9_Stop_Codon_Del|BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000530767.1_Stop_Codon_Del	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1						apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		ACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATTTTATACCTTTTCTTCCTTGCGTCTGTCCTTCTTTTCTTCATTATTTTCCATGG	0.315																																					p.920_921del	Colon(142;1534 1789 5427 7063 28491)	Pindel	.											.	BCLAF1	203	.	0			c.2758_3016del						.																																			SO:0001567	stop_retained_variant	9774	exon13			.	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	Exception_encountered	chr6.hg19:g.136582246_136582439delTGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	Exception_encountered	465.0	0.0		338.0	17.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Frame_Shift_Del	DEL	ENST00000531224.1	hg19	CCDS5177.1																																																																																			.	.		0.315	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		-	136582439	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	-	136582246	7	5	141	1	0	1	0	1	0	0	0	0	1383	1769	61	0	1	0	BCLAF1	6	136582246	Stop_Codon_Del	DEL	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TCGA-DD-A4NV-01A-11D-A30V-10	23910961	136582246	34532821	51	21948										
TIAM2	26230	hgsc.bcm.edu	37	chr6	155458347	155458347	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	agggcagtgactactttgacAgtcgctctgatggactgaat	12	8	1	4			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr6:155458347A>T	ENST00000461783.3	+	7	2504	c.1231A>T	c.(1231-1233)Agt>Tgt	p.S411C	TIAM2_ENST00000529824.2_Missense_Mutation_p.S411C|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000360366.4_Missense_Mutation_p.S411C|TIAM2_ENST00000318981.5_Missense_Mutation_p.S411C|TIAM2_ENST00000456144.1_Missense_Mutation_p.S411C			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	411					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		CTACTTTGACAGTCGCTCTGA	0.522																																					p.S411C		Atlas-SNP	.											.	TIAM2	161	.	0			c.A1231T						.						95	86	89					6																	155458347		2203	4300	6503	SO:0001583	missense	26230	exon4			TTTGACAGTCGCT		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.1231A>T	chr6.hg19:g.155458347A>T	ENSP00000437188:p.Ser411Cys	96.0	0.0		72.0	6.0	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	hg19	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.051869	0.55218	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000360366;ENST00000529824	T;T;T;T;T;T	0.11821	2.82;2.74;2.82;2.82;2.79;2.82	6.08	4.85	0.62838	.	0.085587	0.85682	D	0.000000	T	0.06325	0.0163	L	0.51914	1.62	0.80722	D	1	B	0.12013	0.005	B	0.14023	0.01	T	0.07214	-1.0784	10	0.87932	D	0	.	7.4374	0.27164	0.8027:0.0:0.0686:0.1288	.	411	Q8IVF5	TIAM2_HUMAN	C	411;657;411;411;411;411;411	ENSP00000437188:S411C;ENSP00000434901:S411C;ENSP00000407746:S411C;ENSP00000327315:S411C;ENSP00000353528:S411C;ENSP00000433348:S411C	ENSP00000327315:S411C	S	+	1	0	TIAM2	155500039	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.670000	0.68088	2.333000	0.79357	0.533000	0.62120	AGT	.	.		0.522	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155458347	A	T	155458347	3	4	141	1	0	0	0	0	1	0	0	0	15906	188	7	4	1237	4	TIAM2	6	155458347	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	18876101	155458347	15656720	52	21949										
CYP2W1	54905	hgsc.bcm.edu	37	chr7	1024648	1024648	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	agttcacggtgcgtgccctgCacagcctgggcgtgggccgg	17	13	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:1024648C>T	ENST00000308919.7	+	3	413	c.400C>T	c.(400-402)Cac>Tac	p.H134Y	CYP2W1_ENST00000340150.6_Missense_Mutation_p.H78Y	NM_017781.2	NP_060251.2	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W, polypeptide 1	134					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		GCGTGCCCTGCACAGCCTGGG	0.652																																					p.H134Y		Atlas-SNP	.											.	CYP2W1	28	.	0			c.C400T						.						30	37	35					7																	1024648		2200	4299	6499	SO:0001583	missense	54905	exon3			GCCCTGCACAGCC	AK000366	CCDS5319.2	7p22.3	2004-07-05			ENSG00000073067	ENSG00000073067		"Cytochrome P450s"	20243	protein-coding gene	gene with protein product		615967					Standard	XM_005249792		Approved	FLJ20359, MGC34287	uc003sjq.1	Q8TAV3	OTTHUMG00000074071	ENST00000308919.7:c.400C>T	chr7.hg19:g.1024648C>T	ENSP00000310149:p.His134Tyr	36.0	0.0		63.0	9.0	NM_017781		Missense_Mutation	SNP	ENST00000308919.7	hg19	CCDS5319.2	.	.	.	.	.	.	.	.	.	.	C	15.13	2.742044	0.49151	.	.	ENSG00000073067	ENST00000308919;ENST00000340150	T;T	0.79940	-1.32;-1.32	4.95	4.95	0.65309	.	0.152963	0.56097	D	0.000027	D	0.84593	0.5506	M	0.69823	2.125	0.27635	N	0.947918	P;P	0.51653	0.832;0.947	P;P	0.52454	0.699;0.699	T	0.80801	-0.1220	10	0.87932	D	0	.	13.1651	0.59567	0.1599:0.8401:0.0:0.0	.	78;134	A6NJ10;Q8TAV3	.;CP2W1_HUMAN	Y	134;78	ENSP00000310149:H134Y;ENSP00000344178:H78Y	ENSP00000310149:H134Y	H	+	1	0	CYP2W1	991174	1.000000	0.71417	0.648000	0.29521	0.043000	0.13939	1.956000	0.40382	2.290000	0.77057	0.491000	0.48974	CAC	.	.		0.652	CYP2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157249.1	NM_017781		T	1024648	C	T	1024648	3	4	141	1	0	0	0	0	1	0	0	0	4178	710	25	3	410	3	CYP2W1	7	1024648	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10		1024648	158114015	53	21950										
EEPD1	80820	hgsc.bcm.edu	37	chr7	36336619	36336619	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	caggagaaaaggatgtcattAtcttaggggattttggccaa	12	5	2	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:36336619A>G	ENST00000242108.4	+	7	2051	c.1333A>G	c.(1333-1335)Atc>Gtc	p.I445V	EEPD1_ENST00000534978.1_Missense_Mutation_p.I445V	NM_030636.2	NP_085139.2	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family domain containing 1	445					DNA repair (GO:0006281)		DNA binding (GO:0003677)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|skin(1)	18						GGATGTCATTATCTTAGGGGA	0.463																																					p.I445V		Atlas-SNP	.											.	EEPD1	47	.	0			c.A1333G						.						87	83	84					7																	36336619		2203	4300	6503	SO:0001583	missense	80820	exon7			GTCATTATCTTAG	AK027386	CCDS34619.1	7p14.2	2007-12-07	2007-12-07		ENSG00000122547	ENSG00000122547			22223	protein-coding gene	gene with protein product							Standard	NM_030636		Approved	KIAA1706	uc003tfa.3	Q7L9B9	OTTHUMG00000154904	ENST00000242108.4:c.1333A>G	chr7.hg19:g.36336619A>G	ENSP00000242108:p.Ile445Val	119.0	0.0		155.0	20.0	NM_030636	Q96K64|Q9C0F7	Missense_Mutation	SNP	ENST00000242108.4	hg19	CCDS34619.1	.	.	.	.	.	.	.	.	.	.	A	0.048	-1.259691	0.01445	.	.	ENSG00000122547	ENST00000242108;ENST00000534978	D;D	0.94931	-3.56;-3.56	5.1	0.158	0.14942	Endonuclease/exonuclease/phosphatase (2);	0.293466	0.37348	N	0.002140	T	0.81098	0.4752	N	0.03177	-0.4	0.19300	N	0.999979	B	0.02656	0.0	B	0.06405	0.002	T	0.70029	-0.4984	10	0.22706	T	0.39	-3.6303	4.57	0.12205	0.5198:0.1599:0.3203:0.0	.	445	Q7L9B9	EEPD1_HUMAN	V	445	ENSP00000242108:I445V;ENSP00000442692:I445V	ENSP00000242108:I445V	I	+	1	0	EEPD1	36303144	0.761000	0.28439	0.162000	0.22713	0.748000	0.42578	1.270000	0.33086	0.221000	0.20879	0.459000	0.35465	ATC	.	.		0.463	EEPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337602.1	NM_030636		G	36336619	A	G	36336619	3	3	141	1	0	0	0	0	1	0	0	0	4934	449	16	2	1355	2	EEPD1	7	36336619	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	35311971	36336619	122802044	54	21951										
TBL2	26608	hgsc.bcm.edu	37	chr7	72985569	72985569	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgcacagccgcggagtggccCtttagttcgaaggctcgcac	13	13	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:72985569C>A	ENST00000305632.5	-	6	1069	c.828G>T	c.(826-828)aaG>aaT	p.K276N	TBL2_ENST00000459913.1_5'UTR|TBL2_ENST00000432538.1_Missense_Mutation_p.K240N	NM_012453.2	NP_036585.1	Q9Y4P3	TBL2_HUMAN	transducin (beta)-like 2	276							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	19		Lung NSC(55;0.0659)|all_lung(88;0.152)				CGGAGTGGCCCTTTAGTTCGA	0.562																																					p.K276N		Atlas-SNP	.											.	TBL2	47	.	0			c.G828T						.						83	70	75					7																	72985569		2203	4300	6503	SO:0001583	missense	26608	exon6			GTGGCCCTTTAGT	AF056183	CCDS5551.1	7q11.23	2013-01-10			ENSG00000106638	ENSG00000106638		"WD repeat domain containing"	11586	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 13"	605842				9860302, 10575226	Standard	XM_006715923		Approved	WS-betaTRP, WBSCR13, DKFZP43N024	uc003tyh.3	Q9Y4P3	OTTHUMG00000023427	ENST00000305632.5:c.828G>T	chr7.hg19:g.72985569C>A	ENSP00000307260:p.Lys276Asn	135.0	0.0		144.0	27.0	NM_012453	Q9UQE2	Missense_Mutation	SNP	ENST00000305632.5	hg19	CCDS5551.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.866768	0.72065	.	.	ENSG00000106638	ENST00000305632;ENST00000541783;ENST00000432538	T;T	0.60920	0.15;0.15	5.31	4.43	0.53597	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.128449	0.64402	D	0.000002	T	0.63780	0.2540	L	0.28649	0.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.66114	-0.6004	10	0.59425	D	0.04	-30.5027	11.7691	0.51947	0.0:0.9151:0.0:0.0849	.	240;276	E9PF19;Q9Y4P3	.;TBL2_HUMAN	N	276;276;240	ENSP00000307260:K276N;ENSP00000413979:K240N	ENSP00000307260:K276N	K	-	3	2	TBL2	72623505	1.000000	0.71417	1.000000	0.80357	0.641000	0.38312	1.301000	0.33447	1.483000	0.48342	0.561000	0.74099	AAG	.	.		0.562	TBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252233.3	NM_012453		A	72985569	C	A	72985569	3	1	141	1	0	0	0	0	1	0	0	0	15657	680	24	3	523	3	TBL2	7	72985569	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	36648950	72985569	86153094	55	21952										
PCLO	27445	hgsc.bcm.edu	37	chr7	82764470	82764470	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	aactctgtgagggtttggcaGagtctgtttttagaggaggg	16	4	2	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:82764470G>C	ENST00000333891.9	-	3	2733	c.2396C>G	c.(2395-2397)tCt>tGt	p.S799C	PCLO_ENST00000423517.2_Missense_Mutation_p.S799C	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GGGTTTGGCAGAGTCTGTTTT	0.413																																					p.S799C		Atlas-SNP	.											.	PCLO	1506	.	0			c.C2396G						.						199	183	188					7																	82764470		1868	4104	5972	SO:0001583	missense	27445	exon3			TTGGCAGAGTCTG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.2396C>G	chr7.hg19:g.82764470G>C	ENSP00000334319:p.Ser799Cys	216.0	0.0		234.0	15.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	5.104	0.204815	0.09704	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17213	2.29;2.29	5.91	5.03	0.67393	.	.	.	.	.	T	0.19644	0.0472	L	0.27053	0.805	0.09310	N	1	P;P	0.51351	0.944;0.944	P;P	0.50192	0.634;0.634	T	0.07177	-1.0786	9	0.87932	D	0	.	11.3693	0.49690	0.1887:0.0:0.8113:0.0	.	799;799	Q9Y6V0-5;Q9Y6V0-6	.;.	C	745;799;799	ENSP00000334319:S799C;ENSP00000388393:S799C	ENSP00000334319:S799C	S	-	2	0	PCLO	82602406	0.486000	0.25980	0.896000	0.35187	0.857000	0.48899	0.956000	0.29202	1.510000	0.48803	0.650000	0.86243	TCT	.	.		0.413	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82764470	G	C	82764470	3	2	141	1	0	0	0	0	1	0	0	0	11592	942	33	4	13141	4	PCLO	7	82764470	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	9778901	82764470	76374193	56	21953										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83643565	83643565	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tagcgtgagtagcttttccaGagtgttctccatctattgca	9	9	2	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:83643565G>T	ENST00000265362.4	-	7	1084	c.770C>A	c.(769-771)tCt>tAt	p.S257Y	SEMA3A_ENST00000436949.1_Missense_Mutation_p.S257Y	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	257	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						AGCTTTTCCAGAGTGTTCTCC	0.388																																					p.S257Y		Atlas-SNP	.											.	SEMA3A	121	.	0			c.C770A						.						117	113	114					7																	83643565		2203	4300	6503	SO:0001583	missense	10371	exon7			TTTCCAGAGTGTT	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.770C>A	chr7.hg19:g.83643565G>T	ENSP00000265362:p.Ser257Tyr	93.0	0.0		106.0	13.0	NM_006080		Missense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.101745	0.56183	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.11495	2.77;2.77	5.6	5.6	0.85130	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.255154	0.43919	D	0.000502	T	0.06962	0.0177	N	0.05158	-0.105	0.39145	D	0.962115	B	0.29136	0.234	B	0.34779	0.189	T	0.12400	-1.0549	10	0.02654	T	1	.	19.615	0.95630	0.0:0.0:1.0:0.0	.	257	Q14563	SEM3A_HUMAN	Y	257	ENSP00000265362:S257Y;ENSP00000415260:S257Y	ENSP00000265362:S257Y	S	-	2	0	SEMA3A	83481501	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.293000	0.72731	2.630000	0.89119	0.655000	0.94253	TCT	.	.		0.388	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		T	83643565	G	T	83643565	3	4	141	1	0	0	0	0	1	0	0	0	14039	942	33	3	1589	3	SEMA3A	7	83643565	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	879095	83643565	75495098	57	21954										
DMTF1	9988	hgsc.bcm.edu	37	chr7	86824435	86824435	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gaagattcaaaggatgtcgaAgatttggtaaactgtcatta	10	4	2	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:86824435A>T	ENST00000394703.5	+	20	2825	c.2262A>T	c.(2260-2262)gaA>gaT	p.E754D	DMTF1_ENST00000432937.2_Missense_Mutation_p.E666D|DMTF1_ENST00000413276.2_Missense_Mutation_p.E684D|DMTF1_ENST00000331242.7_Missense_Mutation_p.E754D|DMTF1_ENST00000414194.2_Missense_Mutation_p.E488D|TMEM243_ENST00000481425.1_5'Flank	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	754	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Required for transcriptional activation. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					AGGATGTCGAAGATTTGGTAA	0.373																																					p.E754D		Atlas-SNP	.											.	DMTF1	48	.	0			c.A2262T						.						99	100	100					7																	86824435		2203	4299	6502	SO:0001583	missense	9988	exon18			TGTCGAAGATTTG	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.2262A>T	chr7.hg19:g.86824435A>T	ENSP00000378193:p.Glu754Asp	212.0	0.0		280.0	51.0	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Missense_Mutation	SNP	ENST00000394703.5	hg19	CCDS5601.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.88|19.88	3.909500|3.909500	0.72868|0.72868	.|.	.|.	ENSG00000135164|ENSG00000135164	ENST00000331242;ENST00000413276;ENST00000432937;ENST00000394703;ENST00000414194|ENST00000454008	T;T;T;T;T|.	0.60672|.	0.37;0.17;0.37;0.37;0.37|.	6.16|6.16	-0.765|-0.765	0.11023|0.11023	.|.	0.077540|.	0.53938|.	D|.	0.000041|.	T|.	0.37865|.	0.1019|.	L|L	0.27053|0.27053	0.805|0.805	0.35370|0.35370	D|D	0.788953|0.788953	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|.	0.37888|.	-0.9686|.	10|.	0.87932|.	D|.	0|.	-6.7269|-6.7269	6.5106|6.5106	0.22220|0.22220	0.4747:0.1254:0.3999:0.0|0.4747:0.1254:0.3999:0.0	.|.	754|.	Q9Y222|.	DMTF1_HUMAN|.	D|X	754;684;666;754;488|174	ENSP00000332171:E754D;ENSP00000402627:E684D;ENSP00000412532:E666D;ENSP00000378193:E754D;ENSP00000415910:E488D|.	ENSP00000332171:E754D|.	E|R	+|+	3|1	2|2	DMTF1|DMTF1	86662371|86662371	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.991000|0.991000	0.79684|0.79684	0.616000|0.616000	0.24344|0.24344	-0.042000|-0.042000	0.13535|0.13535	-0.248000|-0.248000	0.11899|0.11899	GAA|AGA	.	.		0.373	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145		T	86824435	A	T	86824435	3	4	141	1	0	0	0	0	1	0	0	0	4594	69	3	4	2324	4	DMTF1	7	86824435	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	3180870	86824435	72314228	58	21955										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88964910	88964910	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgaataaaagcaagagaaatCaagagtctttgggcagccct	10	7	2	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:88964910C>A	ENST00000333190.4	+	4	3223	c.2614C>A	c.(2614-2616)Caa>Aaa	p.Q872K		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	872							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			CAAGAGAAATCAAGAGTCTTT	0.423										HNSCC(36;0.09)																											p.Q872K		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C2614A						.						60	62	61					7																	88964910		2203	4299	6502	SO:0001583	missense	219578	exon4			AGAAATCAAGAGT	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2614C>A	chr7.hg19:g.88964910C>A	ENSP00000329638:p.Gln872Lys	193.0	0.0		273.0	35.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.733857	0.00687	.	.	ENSG00000182348	ENST00000333190	T	0.05382	3.45	4.95	3.13	0.36017	.	1.061480	0.07264	N	0.867883	T	0.04907	0.0132	L	0.32530	0.975	0.09310	N	1	B	0.18741	0.03	B	0.18561	0.022	T	0.45498	-0.9257	10	0.02654	T	1	0.2361	6.2299	0.20728	0.1174:0.5008:0.3094:0.0724	.	872	A4D1E1	Z804B_HUMAN	K	872	ENSP00000329638:Q872K	ENSP00000329638:Q872K	Q	+	1	0	ZNF804B	88802846	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-0.431000	0.06965	0.691000	0.31592	-0.122000	0.15005	CAA	.	.		0.423	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		A	88964910	C	A	88964910	3	1	141	1	0	0	0	0	1	0	0	0	18186	827	29	3	2628	3	ZNF804B	7	88964910	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	2140475	88964910	70173753	59	21956										
ANKIB1	54467	hgsc.bcm.edu	37	chr7	92027849	92027849	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	agaagtgatttctgtccctcAtctagtgatcctgactcagc	8	11	4	4	rs374467744		TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:92027849A>G	ENST00000265742.3	+	20	3232	c.2856A>G	c.(2854-2856)tcA>tcG	p.S952S		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	952							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TCTGTCCCTCATCTAGTGATC	0.493																																					p.S952S		Atlas-SNP	.											.	ANKIB1	92	.	0			c.A2856G						.	A		1,4091		0,1,2045	128	126	127		2856	-3.5	1	7		127	0,8366		0,0,4183	no	coding-synonymous	ANKIB1	NM_019004.1		0,1,6228	GG,GA,AA		0.0,0.0244,0.0080		952/1090	92027849	1,12457	2046	4183	6229	SO:0001819	synonymous_variant	54467	exon20			TCCCTCATCTAGT	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"Ankyrin repeat domain containing"	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.2856A>G	chr7.hg19:g.92027849A>G		97.0	0.0		121.0	15.0	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Silent	SNP	ENST00000265742.3	hg19	CCDS47639.1																																																																																			.	.		0.493	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			G	92027849	A	G	92027849	2	3	141	1	0	0	0	0	0	0	0	1	630	204	8	2		2	ANKIB1	7	92027849	Silent	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	3062939	92027849	67110814	60	21957										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98580989	98580989	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gcctgcacgacatgaagacgGtggtgaagacctggaggaac	15	9	0	4			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:98580989G>A	ENST00000359863.4	+	59	9117	c.8908G>A	c.(8908-8910)Gtg>Atg	p.V2970M	TRRAP_ENST00000355540.3_Missense_Mutation_p.V2952M|TRRAP_ENST00000446306.3_Missense_Mutation_p.V2952M	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2970	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			CATGAAGACGGTGGTGAAGAC	0.542																																					p.V2970M		Atlas-SNP	.											.	TRRAP	863	.	0			c.G8908A						.						188	138	155					7																	98580989		2203	4300	6503	SO:0001583	missense	8295	exon59			AAGACGGTGGTGA	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.8908G>A	chr7.hg19:g.98580989G>A	ENSP00000352925:p.Val2970Met	139.0	0.0		185.0	37.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564408	0.86335	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.69435	-0.4;-0.4	5.48	5.48	0.80851	PIK-related kinase (1);PIK-related kinase, FAT (1);	0.000000	0.85682	D	0.000000	T	0.79305	0.4423	L	0.56199	1.76	0.80722	D	1	D;D;D	0.67145	0.994;0.996;0.995	D;D;D	0.69142	0.937;0.95;0.962	T	0.80703	-0.1264	10	0.87932	D	0	.	19.3398	0.94336	0.0:0.0:1.0:0.0	.	2952;2691;2970	Q9Y4A5-2;Q59FH1;Q9Y4A5	.;.;TRRAP_HUMAN	M	2970;2952;2951	ENSP00000352925:V2970M;ENSP00000347733:V2952M	ENSP00000347733:V2952M	V	+	1	0	TRRAP	98418925	1.000000	0.71417	0.997000	0.53966	0.981000	0.71138	8.062000	0.89475	2.571000	0.86741	0.650000	0.86243	GTG	.	.		0.542	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		A	98580989	G	A	98580989	3	1	141	1	0	0	0	0	1	0	0	0	16616	1261	44	3	9080	3	TRRAP	7	98580989	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	6553140	98580989	60557674	61	21958										
C7orf51	222950	hgsc.bcm.edu	37	chr7	100086033	100086033	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ctttaggggaggaggacgaaGtggaggaggcctggctgggc	21	6	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:100086033G>C	ENST00000300179.2	+	4	848	c.689G>C	c.(688-690)aGt>aCt	p.S230T	NYAP1_ENST00000423930.1_Missense_Mutation_p.S230T|NYAP1_ENST00000454988.1_Missense_Mutation_p.S173T	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	230					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GGAGGACGAAGTGGAGGAGGC	0.647																																					p.S230T		Atlas-SNP	.											.	.	.	.	0			c.G689C						.						23	29	27					7																	100086033		2177	4262	6439	SO:0001583	missense	222950	exon4			GACGAAGTGGAGG	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.689G>C	chr7.hg19:g.100086033G>C	ENSP00000300179:p.Ser230Thr	81.0	0.0		105.0	20.0	NM_173564	Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	hg19	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.027215	0.35797	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.29142	1.58;1.58;1.58	5.14	4.24	0.50183	.	0.208186	0.34291	N	0.004094	T	0.19446	0.0467	N	0.19112	0.55	0.27520	N	0.951423	B;B	0.13145	0.007;0.007	B;B	0.18263	0.021;0.021	T	0.13899	-1.0492	10	0.27082	T	0.32	-0.3675	10.8102	0.46543	0.0:0.0:0.8105:0.1894	.	173;230	C9JS30;Q6ZVC0	.;CG051_HUMAN	T	230;230;173	ENSP00000300179:S230T;ENSP00000411861:S230T;ENSP00000394424:S173T	ENSP00000300179:S230T	S	+	2	0	C7orf51	99923969	0.998000	0.40836	0.997000	0.53966	0.972000	0.66771	1.155000	0.31700	1.124000	0.41980	0.407000	0.27541	AGT	.	.		0.647	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		C	100086033	G	C	100086033	3	2	141	1	0	0	0	0	1	0	0	0	2402	1029	36	4	699	4	C7orf51	7	100086033	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	1505044	100086033	59052630	62	21959										
NUP205	23165	hgsc.bcm.edu	37	chr7	135303347	135303347	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tattttacaagatgtgcatgAtaaggtgacgtacttcctaa	8	6	0	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:135303347A>C	ENST00000285968.6	+	28	3985	c.3959A>C	c.(3958-3960)gAt>gCt	p.D1320A		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1320					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						GATGTGCATGATAAGGTGACG	0.363																																					p.D1320A		Atlas-SNP	.											.	NUP205	198	.	0			c.A3959C						.						151	135	140					7																	135303347		2203	4300	6503	SO:0001583	missense	23165	exon28			TGCATGATAAGGT	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.3959A>C	chr7.hg19:g.135303347A>C	ENSP00000285968:p.Asp1320Ala	65.0	0.0		72.0	11.0	NM_015135	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	hg19	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.468936	0.43839	.	.	ENSG00000155561	ENST00000285968	T	0.28666	1.6	5.46	5.46	0.80206	.	0.045120	0.85682	D	0.000000	T	0.28566	0.0707	L	0.47716	1.5	0.80722	D	1	B	0.30146	0.27	B	0.34931	0.192	T	0.04593	-1.0940	10	0.06757	T	0.87	-35.4076	15.5256	0.75901	1.0:0.0:0.0:0.0	.	1320	Q92621	NU205_HUMAN	A	1320	ENSP00000285968:D1320A	ENSP00000285968:D1320A	D	+	2	0	NUP205	134953887	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.942000	0.92970	2.068000	0.61886	0.383000	0.25322	GAT	.	.		0.363	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			C	135303347	A	C	135303347	3	2	141	1	0	0	0	0	1	0	0	0	10768	333	12	5	4069	5	NUP205	7	135303347	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	35217314	135303347	23835316	63	21960										
ZNF212	7988	hgsc.bcm.edu	37	chr7	148949877	148949877	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	aagaggaaggtcctggtggtGcccacccaggtgagtggctc	16	10	0	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:148949877G>A	ENST00000335870.2	+	4	750	c.622G>A	c.(622-624)Gcc>Acc	p.A208T		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	208	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(4)|ovary(1)|prostate(1)	9	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)			TCCTGGTGGTGCCCACCCAGG	0.572																																					p.A208T		Atlas-SNP	.											.	ZNF212	28	.	0			c.G622A						.						127	109	115					7																	148949877		2203	4300	6503	SO:0001583	missense	7988	exon4			GGTGGTGCCCACC	U38864	CCDS5896.1	7q36.1	2013-01-08			ENSG00000170260	ENSG00000170260		"Zinc fingers, C2H2-type", "-"	13004	protein-coding gene	gene with protein product		602386				9169157	Standard	NM_012256		Approved	C2H2-150	uc003wfp.3	Q9UDV6	OTTHUMG00000158968	ENST00000335870.2:c.622G>A	chr7.hg19:g.148949877G>A	ENSP00000338572:p.Ala208Thr	57.0	0.0		87.0	7.0	NM_012256	B2RCF4|Q13396|Q8N664	Missense_Mutation	SNP	ENST00000335870.2	hg19	CCDS5896.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.62|12.62	1.991895|1.991895	0.35131|0.35131	.|.	.|.	ENSG00000170260|ENSG00000170260	ENST00000335870|ENST00000481584	T|.	0.06528|.	3.29|.	5.62|5.62	3.35|3.35	0.38373|0.38373	Krueppel-associated box (1);|.	0.618014|.	0.14384|.	N|.	0.322953|.	T|T	0.16557|0.16557	0.0398|0.0398	N|N	0.08118|0.08118	0|0	0.24072|0.24072	N|N	0.995976|0.995976	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.19031|0.19031	-1.0318|-1.0318	10|5	0.09843|.	T|.	0.71|.	-2.1678|-2.1678	4.8945|4.8945	0.13744|0.13744	0.1658:0.2599:0.5743:0.0|0.1658:0.2599:0.5743:0.0	.|.	208|.	Q9UDV6|.	ZN212_HUMAN|.	T|Y	208|121	ENSP00000338572:A208T|.	ENSP00000338572:A208T|.	A|C	+|+	1|2	0|0	ZNF212|ZNF212	148580810|148580810	0.497000|0.497000	0.26067|0.26067	0.805000|0.805000	0.32314|0.32314	0.990000|0.990000	0.78478|0.78478	1.395000|1.395000	0.34520|0.34520	1.033000|1.033000	0.39918|0.39918	0.655000|0.655000	0.94253|0.94253	GCC|TGC	.	.		0.572	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256		A	148949877	G	A	148949877	3	1	141	1	0	0	0	0	1	0	0	0	17783	1319	46	3	636	3	ZNF212	7	148949877	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	13646530	148949877	10188786	64	21961										
CHPF2	54480	hgsc.bcm.edu	37	chr7	150935740	150935740	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cagctggctatggctctcttTgagcaggagcaggccaatag	13	10	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:150935740T>A	ENST00000035307.2	+	4	3805	c.2292T>A	c.(2290-2292)ttT>ttA	p.F764L	CHPF2_ENST00000495645.1_Missense_Mutation_p.F756L|RP4-548D19.3_ENST00000607902.1_RNA|MIR671_ENST00000390183.1_RNA	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	764					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						TGGCTCTCTTTGAGCAGGAGC	0.617																																					p.F764L		Atlas-SNP	.											.	CHPF2	52	.	0			c.T2292A						.						14	14	14					7																	150935740		2200	4298	6498	SO:0001583	missense	54480	exon4			TCTCTTTGAGCAG	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.2292T>A	chr7.hg19:g.150935740T>A	ENSP00000035307:p.Phe764Leu	48.0	0.0		61.0	6.0	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	hg19	CCDS34779.1	.	.	.	.	.	.	.	.	.	.	T	18.04	3.534770	0.64972	.	.	ENSG00000033100	ENST00000495645;ENST00000035307	T;T	0.35236	1.32;1.34	4.51	-0.631	0.11526	.	0.000000	0.85682	D	0.000000	T	0.46870	0.1415	M	0.64997	1.995	0.58432	D	0.999998	D;D	0.67145	0.995;0.996	D;D	0.70935	0.963;0.971	T	0.44345	-0.9334	10	0.14656	T	0.56	-12.6072	10.0927	0.42456	0.0:0.188:0.0:0.812	.	764;756	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	L	756;764	ENSP00000418914:F756L;ENSP00000035307:F764L	ENSP00000035307:F764L	F	+	3	2	CHPF2	150566673	0.978000	0.34361	0.994000	0.49952	0.996000	0.88848	0.104000	0.15313	-0.187000	0.10516	0.533000	0.62120	TTT	.	.		0.617	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015		A	150935740	T	A	150935740	3	1	141	1	0	0	0	0	1	0	0	0	3371	1809	63	4	2306	4	CHPF2	7	150935740	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	1985863	150935740	8202923	65	21962										
DPP6	1804	hgsc.bcm.edu	37	chr7	153750014	153750014	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gccaggggcccgaggaggacGgcggcgcaggagccaagccc	19	14	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr7:153750014G>A	ENST00000377770.3	+	1	250	c.109G>A	c.(109-111)Ggc>Agc	p.G37S	AC006019.3_ENST00000425591.1_RNA|DPP6_ENST00000406326.1_Missense_Mutation_p.G37S|DPP6_ENST00000404039.1_Intron			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	37					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			CGAGGAGGACGGCGGCGCAGG	0.791																																					p.G37S	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.G109A						.						6	8	7					7																	153750014		680	1560	2240	SO:0001583	missense	1804	exon1			GAGGACGGCGGCG	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.109G>A	chr7.hg19:g.153750014G>A	ENSP00000367001:p.Gly37Ser	9.0	0.0		28.0	8.0	NM_130797		Missense_Mutation	SNP	ENST00000377770.3	hg19		.	.	.	.	.	.	.	.	.	.	G	3.393	-0.123880	0.06795	.	.	ENSG00000130226	ENST00000406326;ENST00000377770	T	0.16073	2.37	2.73	1.78	0.24846	.	.	.	.	.	T	0.07728	0.0194	.	.	.	0.22489	N	0.999058	B;B	0.34181	0.0;0.44	B;B	0.22753	0.001;0.041	T	0.29088	-1.0023	8	0.19147	T	0.46	.	7.7391	0.28831	0.1396:0.0:0.8604:0.0	.	37;37	P42658;Q8IYG9	DPP6_HUMAN;.	S	37	ENSP00000367001:G37S	ENSP00000367001:G37S	G	+	1	0	DPP6	153380947	0.983000	0.35010	0.465000	0.27155	0.023000	0.10783	2.289000	0.43523	1.225000	0.43566	0.549000	0.68633	GGC	.	.		0.791	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		A	153750014	G	A	153750014	3	1	141	1	0	0	0	0	1	0	0	0	4732	1116	39	1	166	1	DPP6	7	153750014	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	2814274	153750014	5388649	66	21963										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36666269	36666269	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ttttccaaactgctgtcaatAattctcagtacctggttcac	5	11	3	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr8:36666269A>C	ENST00000399881.3	+	7	727	c.690A>C	c.(688-690)atA>atC	p.I230I		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	230					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TGCTGTCAATAATTCTCAGTA	0.433																																					p.I230I		Atlas-SNP	.											.	KCNU1	359	.	0			c.A690C						.						138	132	134					8																	36666269		1897	4126	6023	SO:0001819	synonymous_variant	157855	exon7			GTCAATAATTCTC	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.690A>C	chr8.hg19:g.36666269A>C		154.0	0.0		94.0	12.0	NM_001031836		Silent	SNP	ENST00000399881.3	hg19	CCDS55220.1																																																																																			.	.		0.433	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		C	36666269	A	C	36666269	2	2	141	1	0	0	0	0	0	0	0	1	8102	352	13	5		5	KCNU1	8	36666269	Silent	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10		36666269	109697753	67	21964										
XKR4	114786	hgsc.bcm.edu	37	chr8	56015167	56015167	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	attggctccaggcttgccgtCggggtcgggagccgaggacg	18	11	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr8:56015167C>A	ENST00000327381.6	+	1	219	c.119C>A	c.(118-120)tCg>tAg	p.S40*		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	40						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GGCTTGCCGTCGGGGTCGGGA	0.721																																					p.S40X		Atlas-SNP	.											.	XKR4	104	.	0			c.C119A						.						15	17	16					8																	56015167		2200	4295	6495	SO:0001587	stop_gained	114786	exon1			TGCCGTCGGGGTC	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 4"				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.119C>A	chr8.hg19:g.56015167C>A	ENSP00000328326:p.Ser40*	76.0	0.0		84.0	22.0	NM_052898	Q96PZ8	Nonsense_Mutation	SNP	ENST00000327381.6	hg19	CCDS34893.1	.	.	.	.	.	.	.	.	.	.	C	38	6.888451	0.97912	.	.	ENSG00000206579	ENST00000327381;ENST00000543752	.	.	.	3.22	3.22	0.36961	.	3.456440	0.01806	N	0.033169	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-8.716	11.9643	0.53025	0.0:1.0:0.0:0.0	.	.	.	.	X	40	.	ENSP00000328326:S40X	S	+	2	0	XKR4	56177721	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.546000	0.36179	1.649000	0.50652	0.549000	0.68633	TCG	.	.		0.721	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		A	56015167	C	A	56015167	4	1	141	1	0	0	0	0	0	1	0	0	17448	893	31	1	121	1	XKR4	8	56015167	Nonsense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	19348898	56015167	90348855	68	21965										
RNF19A	25897	hgsc.bcm.edu	37	chr8	101271389	101271389	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	acttcgggtggcactgccatCatccacactactgcttccac	7	16	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr8:101271389C>A	ENST00000519449.1	-	11	2228	c.1912G>T	c.(1912-1914)Gat>Tat	p.D638Y	RNF19A_ENST00000341084.2_Missense_Mutation_p.D638Y|RNF19A_ENST00000523255.1_5'UTR	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	638					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			GCACTGCCATCATCCACACTA	0.483											OREG0018897	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D638Y		Atlas-SNP	.											.	RNF19A	67	.	0			c.G1912T						.						138	118	125					8																	101271389		2203	4300	6503	SO:0001583	missense	25897	exon11			TGCCATCATCCAC	AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.1912G>T	chr8.hg19:g.101271389C>A	ENSP00000428968:p.Asp638Tyr	39.0	0.0	1357	39.0	4.0	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	hg19	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.944196	0.92593	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.85955	-2.05;-2.05	5.74	5.74	0.90152	.	0.048021	0.85682	D	0.000000	D	0.86732	0.6003	L	0.56769	1.78	0.80722	D	1	P	0.48407	0.91	P	0.45946	0.498	D	0.88038	0.2779	10	0.87932	D	0	.	19.5387	0.95266	0.0:1.0:0.0:0.0	.	638	Q9NV58	RN19A_HUMAN	Y	638	ENSP00000428968:D638Y;ENSP00000342667:D638Y	ENSP00000342667:D638Y	D	-	1	0	RNF19A	101340565	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.708000	0.92522	0.585000	0.79938	GAT	.	.		0.483	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		A	101271389	C	A	101271389	3	1	141	1	0	0	0	0	1	0	0	0	13485	826	29	3	608	3	RNF19A	8	101271389	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	45256222	101271389	45092633	69	21966										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113519059	113519059	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	taaattgcctccacagggtgCtttaatttaaacaaacaaat	5	8	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr8:113519059C>A	ENST00000297405.5	-	29	5001		c.e29-1		CSMD3_ENST00000343508.3_Splice_Site|CSMD3_ENST00000455883.2_Splice_Site|CSMD3_ENST00000352409.3_Splice_Site	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CCACAGGGTGCTTTAATTTAA	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											.		Atlas-SNP	.											.	CSMD3	2325	.	0			c.4445-1G>T						.						56	56	56					8																	113519059		2203	4300	6503	SO:0001630	splice_region_variant	114788	exon29			AGGGTGCTTTAAT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4757-1G>T	chr8.hg19:g.113519059C>A		162.0	0.0		115.0	8.0	NM_052900	Q96PZ3	Splice_Site	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354384	0.82243	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4644	0.90750	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CSMD3	113588235	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.651000	0.83577	2.587000	0.87381	0.557000	0.71058	.	.	.		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	Intron	A	113519059	C	A	113519059	5	1	141	1	0	0	0	0	0	0	1	0	3948	811	28	3	6539	3	CSMD3	8	113519059	Splice_Site	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	12247670	113519059	32844963	70	21967										
NOV	4856	hgsc.bcm.edu	37	chr8	120430376	120430376	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tcagccaagctgcaaattccAgtgcacctgcagagatgggc	11	12	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr8:120430376A>G	ENST00000259526.3	+	3	616	c.389A>G	c.(388-390)cAg>cGg	p.Q130R	RP11-775B15.2_ENST00000519786.1_RNA	NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	0	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			TGCAAATTCCAGTGCACCTGC	0.527																																					p.Q130R		Atlas-SNP	.											.	NOV	51	.	0			c.A389G						.						91	92	92					8																	120430376		2203	4300	6503	SO:0001583	missense	4856	exon3			AATTCCAGTGCAC	X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"nephroblastoma overexpressed gene"			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.389A>G	chr8.hg19:g.120430376A>G	ENSP00000259526:p.Gln130Arg	95.0	0.0		95.0	28.0	NM_002514		Missense_Mutation	SNP	ENST00000259526.3	hg19	CCDS6328.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.800907	0.50315	.	.	ENSG00000136999	ENST00000259526	T	0.72282	-0.64	5.51	1.56	0.23342	von Willebrand factor, type C (4);	0.437543	0.27072	N	0.021070	T	0.62612	0.2442	L	0.48218	1.51	0.31879	N	0.618705	P	0.36354	0.549	B	0.37650	0.255	T	0.65747	-0.6093	10	0.54805	T	0.06	-5.1154	10.8333	0.46673	0.6409:0.0:0.0:0.3591	.	130	P48745	NOV_HUMAN	R	130	ENSP00000259526:Q130R	ENSP00000259526:Q130R	Q	+	2	0	NOV	120499557	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	3.551000	0.53698	0.101000	0.17610	0.459000	0.35465	CAG	.	.		0.527	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514		G	120430376	A	G	120430376	3	3	141	1	0	0	0	0	1	0	0	0	10562	188	7	2	399	2	NOV	8	120430376	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	6911317	120430376	25933646	71	21968										
DENND3	22898	hgsc.bcm.edu	37	chr8	142176419	142176419	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	acctgcaggacattgccatgCctgagctggcacccaggaac	11	14	0	1	rs556706834		TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr8:142176419C>A	ENST00000262585.2	+	12	1722	c.1444C>A	c.(1444-1446)Cct>Act	p.P482T	DENND3_ENST00000424248.1_Missense_Mutation_p.P430T|DENND3_ENST00000519811.1_Missense_Mutation_p.P562T	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	482					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			CATTGCCATGCCTGAGCTGGC	0.647													C|||	1	0.000199681	0	0.0014	5008	,	,		17462	0		0	False		,,,				2504	0				p.P482T		Atlas-SNP	.											.	DENND3	127	.	0			c.C1444A						.						86	89	88					8																	142176419		2203	4300	6503	SO:0001583	missense	22898	exon12			GCCATGCCTGAGC	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.1444C>A	chr8.hg19:g.142176419C>A	ENSP00000262585:p.Pro482Thr	45.0	0.0		43.0	17.0	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	hg19	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.226|5.226	0.227146|0.227146	0.09916|0.09916	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000518668|ENST00000262585;ENST00000424248;ENST00000519811	.|T;T;T	.|0.14893	.|2.93;2.47;2.92	4.74|4.74	3.86|3.86	0.44501|0.44501	.|.	.|0.603639	.|0.17555	.|N	.|0.170035	T|T	0.17195|0.17195	0.0413|0.0413	L|L	0.55481|0.55481	1.735|1.735	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.17465	.|0.013;0.022;0.013	.|B;B;B	.|0.15052	.|0.012;0.01;0.004	T|T	0.13098|0.13098	-1.0522|-1.0522	5|10	.|0.42905	.|T	.|0.14	-16.1658|-16.1658	9.6722|9.6722	0.40019|0.40019	0.1589:0.688:0.1532:0.0|0.1589:0.688:0.1532:0.0	.|.	.|562;430;482	.|E9PF32;A2RUS2-2;A2RUS2	.|.;.;DEND3_HUMAN	D|T	486|482;430;562	.|ENSP00000262585:P482T;ENSP00000410594:P430T;ENSP00000428714:P562T	.|ENSP00000262585:P482T	A|P	+|+	2|1	0|0	DENND3|DENND3	142245601|142245601	0.008000|0.008000	0.16893|0.16893	0.563000|0.563000	0.28383|0.28383	0.210000|0.210000	0.24377|0.24377	1.898000|1.898000	0.39809|0.39809	1.101000|1.101000	0.41535|0.41535	0.561000|0.561000	0.74099|0.74099	GCC|CCT	.	.		0.647	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		A	142176419	C	A	142176419	3	1	141	1	0	0	0	0	1	0	0	0	4434	739	26	3	1486	3	DENND3	8	142176419	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	21746043	142176419	4187603	72	21969										
OPLAH	26873	hgsc.bcm.edu	37	chr8	145113709	145113709	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgagcaccacagccaggctgCggatgcctcgagatagcagc	13	13	0	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr8:145113709C>T	ENST00000426825.1	-	5	635	c.554G>A	c.(553-555)cGc>cAc	p.R185H	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	185					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGCCAGGCTGCGGATGCCTCG	0.677																																					p.R185H		Atlas-SNP	.											.	OPLAH	78	.	0			c.G554A						.						21	27	25					8																	145113709		2094	4196	6290	SO:0001583	missense	26873	exon5			AGGCTGCGGATGC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.554G>A	chr8.hg19:g.145113709C>T	ENSP00000475943:p.Arg185His	66.0	0.0		49.0	14.0	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.51	2.855781	0.51376	.	.	ENSG00000178814	ENST00000426825	.	.	.	4.68	3.79	0.43588	Hydantoinaseoxoprolinase, N-terminal (1);	0.194195	0.43747	N	0.000535	T	0.40347	0.1113	.	.	.	0.34227	D	0.676085	B	0.09022	0.002	B	0.08055	0.003	T	0.48246	-0.9052	7	0.62326	D	0.03	.	6.6775	0.23102	0.0:0.7773:0.0:0.2227	.	185	O14841	OPLA_HUMAN	H	185	.	ENSP00000412071:R185H	R	-	2	0	OPLAH	145185697	0.987000	0.35691	0.999000	0.59377	0.944000	0.59088	0.567000	0.23608	0.948000	0.37687	0.561000	0.74099	CGC	.	.		0.677	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		T	145113709	C	T	145113709	3	4	141	1	0	0	0	0	1	0	0	0	10885	768	27	1	3406	1	OPLAH	8	145113709	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	2937290	145113709	1250313	73	21970										
OR13D1	286365	hgsc.bcm.edu	37	chr9	107457351	107457351	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cctgtgaaattttggcccttCtaaaacttgtttgttcagat	7	8	2	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr9:107457351C>T	ENST00000318763.5	+	1	692	c.649C>T	c.(649-651)Cta>Tta	p.L217L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						TTTGGCCCTTCTAAAACTTGT	0.368																																					p.L217L		Atlas-SNP	.											.	OR13D1	42	.	0			c.C649T						.						187	178	181					9																	107457351		2203	4300	6503	SO:0001819	synonymous_variant	286365	exon1			GCCCTTCTAAAAC		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"GPCR / Class A : Olfactory receptors"	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.649C>T	chr9.hg19:g.107457351C>T		178.0	0.0		151.0	35.0	NM_001004484	B9EIS1|Q6IFL1	Silent	SNP	ENST00000318763.5	hg19	CCDS35094.1																																																																																			.	.		0.368	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1			T	107457351	C	T	107457351	2	4	141	1	0	0	0	0	0	0	0	1	10949	912	32	3		3	OR13D1	9	107457351	Silent	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10		107457351	33756080	74	21971										
URM1	81605	hgsc.bcm.edu	37	chr9	131151593	131151593	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cgactgggagctactggtcaGtaccttgggggacatccctc	13	12	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr9:131151593G>T	ENST00000452446.1	+	4	304	c.242G>T	c.(241-243)aGt>aTt	p.S81I	URM1_ENST00000372850.1_3'UTR|RP11-339B21.11_ENST00000609303.1_lincRNA|URM1_ENST00000372853.4_Intron|URM1_ENST00000483206.1_3'UTR	NM_001135947.2	NP_001129419.1			ubiquitin related modifier 1											cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	5						CTACTGGTCAGTACCTTGGGG	0.587																																					p.S81I		Atlas-SNP	.											.	URM1	19	.	0			c.G242T						.						89	81	84					9																	131151593		2203	4300	6503	SO:0001583	missense	81605	exon4			TGGTCAGTACCTT	AK097029	CCDS6900.1, CCDS48035.1, CCDS59148.1	9q34.13	2010-06-24	2010-06-24	2006-11-28	ENSG00000167118	ENSG00000167118			28378	protein-coding gene	gene with protein product		612693	"chromosome 9 open reading frame 74", "ubiquitin related modifier 1 homolog (S. cerevisiae)"	C9orf74		16046629, 16864801	Standard	NM_030914		Approved	MGC2668	uc011may.2	Q9BTM9	OTTHUMG00000020742	ENST00000452446.1:c.242G>T	chr9.hg19:g.131151593G>T	ENSP00000412922:p.Ser81Ile	45.0	0.0		75.0	13.0	NM_001135947		Missense_Mutation	SNP	ENST00000452446.1	hg19	CCDS48035.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.306487	0.81247	.	.	ENSG00000167118	ENST00000452446	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	T	0.79534	0.4462	.	.	.	0.36006	D	0.837751	D	0.76494	0.999	D	0.72075	0.976	T	0.82010	-0.0669	6	.	.	.	.	19.1191	0.93355	0.0:0.0:1.0:0.0	.	81	Q9BTM9-2	.	I	81	.	.	S	+	2	0	URM1	130191414	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.960000	0.87893	2.837000	0.97791	0.655000	0.94253	AGT	.	.		0.587	URM1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_030914		T	131151593	G	T	131151593	3	4	141	1	0	0	0	0	1	0	0	0	17042	1029	36	3	256	3	URM1	9	131151593	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	23694242	131151593	10061838	75	21972										
C9orf9	11092	hgsc.bcm.edu	37	chr9	135763682	135763682	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cctgccgtcctgcagataccCtcatgatgtggtgaaccacc	9	15	1	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr9:135763682C>G	ENST00000372136.3	+	4	800	c.353C>G	c.(352-354)cCt>cGt	p.P118R	C9orf9_ENST00000356311.5_Missense_Mutation_p.P118R|C9orf9_ENST00000350499.6_Missense_Mutation_p.P118R			Q96E40	CI009_HUMAN	chromosome 9 open reading frame 9	118						cytoplasmic microtubule (GO:0005881)		p.?(1)		cervix(1)|large_intestine(1)|lung(1)|prostate(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|GBM - Glioblastoma multiforme(294;4.84e-07)|Epithelial(140;1.28e-06)		TGCAGATACCCTCATGATGTG	0.607																																					p.P118R		Atlas-SNP	.											.	C9orf9	10	.	1	Unknown(1)	bone(1)	c.C353G						.						89	75	80					9																	135763682		2203	4300	6503	SO:0001583	missense	11092	exon4			GATACCCTCATGA		CCDS6955.1	9q34.13	2012-03-06			ENSG00000165698	ENSG00000165698			1367	protein-coding gene	gene with protein product							Standard	NM_018956		Approved		uc004cby.1	Q96E40	OTTHUMG00000020847	ENST00000372136.3:c.353C>G	chr9.hg19:g.135763682C>G	ENSP00000361209:p.Pro118Arg	142.0	0.0		148.0	32.0	NM_018956	Q9UGQ0	Missense_Mutation	SNP	ENST00000372136.3	hg19		.	.	.	.	.	.	.	.	.	.	C	14.87	2.664676	0.47572	.	.	ENSG00000165698	ENST00000372136;ENST00000356311;ENST00000350499	T;T;T	0.66815	-0.23;-0.23;-0.23	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.81749	0.4888	M	0.73962	2.25	0.58432	D	0.999999	B;D	0.89917	0.202;1.0	B;D	0.97110	0.067;1.0	D	0.83929	0.0305	10	0.66056	D	0.02	-12.904	17.0347	0.86471	0.0:1.0:0.0:0.0	.	118;118	Q96E40-2;Q96E40	.;CI009_HUMAN	R	118	ENSP00000361209:P118R;ENSP00000348659:P118R;ENSP00000298546:P118R	ENSP00000298546:P118R	P	+	2	0	C9orf9	134753503	0.999000	0.42202	0.488000	0.27440	0.547000	0.35210	5.940000	0.70187	2.344000	0.79699	0.561000	0.74099	CCT	.	.		0.607	C9orf9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000054806.1	NM_018956		G	135763682	C	G	135763682	3	3	141	1	0	0	0	0	1	0	0	0	2506	681	24	4	363	4	C9orf9	9	135763682	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	4612089	135763682	5449749	76	21973										
USP6NL	9712	hgsc.bcm.edu	37	chr10	11505005	11505005	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tagggaagtgtttgggagagTttccgtggtaaacgggggga	19	3	0	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr10:11505005T>G	ENST00000609104.1	-	15	2316	c.1922A>C	c.(1921-1923)aAc>aCc	p.N641T	USP6NL_ENST00000277575.5_Missense_Mutation_p.N658T|USP6NL_ENST00000379237.2_Missense_Mutation_p.N664T	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	641					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						TTTGGGAGAGTTTCCGTGGTA	0.552																																					p.N658T		Atlas-SNP	.											.	USP6NL	57	.	0			c.A1973C						.						36	37	37					10																	11505005		1943	4127	6070	SO:0001583	missense	9712	exon14			GGAGAGTTTCCGT	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"related to the N terminus of tre"	605405	"USP6NL intronic transcript 1 (non-protein coding)"	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.1922A>C	chr10.hg19:g.11505005T>G	ENSP00000476462:p.Asn641Thr	43.0	0.0		48.0	6.0	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	hg19	CCDS53492.1	.	.	.	.	.	.	.	.	.	.	T	9.517	1.107347	0.20714	.	.	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.05996	3.36;3.38	6.04	-2.8	0.05823	.	0.246334	0.35124	N	0.003438	T	0.05960	0.0155	L	0.48642	1.525	0.09310	N	1	B;P	0.35575	0.376;0.51	B;B	0.32864	0.115;0.154	T	0.22556	-1.0213	10	0.62326	D	0.03	.	13.0109	0.58731	0.0:0.398:0.0:0.602	.	641;658	Q92738;Q92738-2	US6NL_HUMAN;.	T	641;658;641	ENSP00000277575:N658T;ENSP00000368539:N641T	ENSP00000277575:N658T	N	-	2	0	USP6NL	11545011	0.238000	0.23825	0.000000	0.03702	0.026000	0.11368	0.090000	0.15025	-0.355000	0.08199	0.460000	0.39030	AAC	.	.		0.552	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688		G	11505005	T	G	11505005	3	3	141	1	0	0	0	0	1	0	0	0	17102	1725	60	5	568	5	USP6NL	10	11505005	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10		11505005	124029742	77	21974										
MPP7	143098	hgsc.bcm.edu	37	chr10	28378706	28378706	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tactgatcactcttcttgcaTtcatacatggatttatttgt	5	8	4	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr10:28378706T>C	ENST00000375732.1	-	12	1276	c.1017A>G	c.(1015-1017)gaA>gaG	p.E339E	MPP7_ENST00000540098.1_Silent_p.E339E|MPP7_ENST00000337532.5_Silent_p.E339E|MPP7_ENST00000445954.2_Silent_p.E214E|MPP7_ENST00000375719.3_Silent_p.E339E			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	339					establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						TCTTCTTGCATTCATACATGG	0.333																																					p.E339E		Atlas-SNP	.											.	MPP7	60	.	0			c.A1017G						.						284	229	247					10																	28378706		2203	4300	6503	SO:0001819	synonymous_variant	143098	exon14			CTTGCATTCATAC	BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.1017A>G	chr10.hg19:g.28378706T>C		116.0	0.0		96.0	11.0	NM_173496	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Silent	SNP	ENST00000375732.1	hg19	CCDS7158.1																																																																																			.	.		0.333	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		C	28378706	T	C	28378706	2	2	141	1	0	0	0	0	0	0	0	1	9748	1490	52	2		2	MPP7	10	28378706	Silent	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	16873701	28378706	107156041	78	21975										
RET	5979	hgsc.bcm.edu	37	chr10	43598063	43598063	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ccccaacatcagcgtggcctAcaggctcctggagggtgagt	13	13	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr10:43598063A>G	ENST00000355710.3	+	3	843	c.611A>G	c.(610-612)tAc>tGc	p.Y204C	RET_ENST00000340058.5_Missense_Mutation_p.Y204C	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	204	Cadherin. {ECO:0000255|PROSITE- ProRule:PRU00043}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	AGCGTGGCCTACAGGCTCCTG	0.632		1	"T, Mis, N, F"	"H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"	"medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"	"medullary thyroid,  papillary thyroid, pheochromocytoma"	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												p.Y204C	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	.	RET	916	.	0			c.A611G						.						59	47	51					10																	43598063		2203	4300	6503	SO:0001583	missense	5979	exon3	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	TGGCCTACAGGCT	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"Cadherins / Cadherin-related"	9967	protein-coding gene	gene with protein product	"cadherin-related family member 16"	164761	"multiple endocrine neoplasia and medullary thyroid carcinoma 1", "Hirschsprung disease 1"	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.611A>G	chr10.hg19:g.43598063A>G	ENSP00000347942:p.Tyr204Cys	61.0	0.0		34.0	6.0	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	hg19	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	A	17.66	3.444954	0.63178	.	.	ENSG00000165731	ENST00000355710;ENST00000340058;ENST00000535749	D;D	0.88896	-2.44;-2.44	5.09	5.09	0.68999	Cadherin (4);Cadherin-like (1);	0.059166	0.64402	D	0.000001	D	0.91181	0.7222	L	0.38175	1.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.99	D	0.92236	0.5796	10	0.87932	D	0	.	13.8546	0.63519	1.0:0.0:0.0:0.0	.	204;204	P07949;P07949-2	RET_HUMAN;.	C	204	ENSP00000347942:Y204C;ENSP00000344798:Y204C	ENSP00000344798:Y204C	Y	+	2	0	RET	42918069	1.000000	0.71417	0.460000	0.27093	0.688000	0.40055	7.274000	0.78538	1.910000	0.55303	0.533000	0.62120	TAC	.	.		0.632	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		G	43598063	A	G	43598063	3	3	141	1	0	0	0	0	1	0	0	0	13250	391	14	2	621	2	RET	10	43598063	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	15219357	43598063	91936684	79	21976										
ARID5B	84159	hgsc.bcm.edu	37	chr10	63850753	63850753	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cagcgaagcccctggcatccAgagtagacccagagaaggac	12	13	0	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr10:63850753A>T	ENST00000279873.7	+	10	1941	c.1531A>T	c.(1531-1533)Aga>Tga	p.R511*	ARID5B_ENST00000309334.5_Nonsense_Mutation_p.R268*	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	511					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					CCTGGCATCCAGAGTAGACCC	0.517																																					p.R511X		Atlas-SNP	.											.	ARID5B	125	.	0			c.A1531T						.						99	92	94					10																	63850753		2203	4300	6503	SO:0001587	stop_gained	84159	exon10			GCATCCAGAGTAG	M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.1531A>T	chr10.hg19:g.63850753A>T	ENSP00000279873:p.Arg511*	168.0	0.0		150.0	16.0	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Nonsense_Mutation	SNP	ENST00000279873.7	hg19	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	A	35	5.450817	0.96205	.	.	ENSG00000150347	ENST00000279873;ENST00000309334	.	.	.	5.57	-3.6	0.04570	.	0.645108	0.17256	N	0.180952	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-3.4989	9.4476	0.38706	0.2485:0.5697:0.1818:0.0	.	.	.	.	X	511;268	.	ENSP00000279873:R511X	R	+	1	2	ARID5B	63520759	0.000000	0.05858	0.041000	0.18516	0.413000	0.31143	-0.516000	0.06282	-0.417000	0.07461	-0.250000	0.11733	AGA	.	.		0.517	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		T	63850753	A	T	63850753	4	4	141	1	0	0	0	0	0	1	0	0	922	180	7	4	1569	4	ARID5B	10	63850753	Nonsense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	20252690	63850753	71683994	80	21977										
SLIT1	6585	hgsc.bcm.edu	37	chr10	98762480	98762480	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cttgtggccatggcaggggcCgtcagcgggctggtcacagt	17	11	2	0	rs373006664		TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr10:98762480C>T	ENST00000266058.4	-	35	4380	c.4135G>A	c.(4135-4137)Ggc>Agc	p.G1379S	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Missense_Mutation_p.G1379S	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	1379	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TGGCAGGGGCCGTCAGCGGGC	0.667																																					p.G1379S		Atlas-SNP	.											.	SLIT1	154	.	0			c.G4135A						.	C	SER/GLY	0,4402		0,0,2201	16	19	18		4135	1.6	0.6	10		18	1,8577		0,1,4288	no	missense	SLIT1	NM_003061.2	56	0,1,6489	TT,TC,CC		0.0117,0.0,0.0077	benign	1379/1535	98762480	1,12979	2201	4289	6490	SO:0001583	missense	6585	exon35			AGGGGCCGTCAGC	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.4135G>A	chr10.hg19:g.98762480C>T	ENSP00000266058:p.Gly1379Ser	48.0	0.0		31.0	7.0	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	hg19	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	C	6.957	0.546543	0.13312	0.0	1.17E-4	ENSG00000187122	ENST00000266058;ENST00000371070	T;T	0.80214	-1.35;-1.32	4.75	1.64	0.23874	Epidermal growth factor-like, type 3 (1);	0.218174	0.45606	D	0.000354	T	0.54498	0.1862	N	0.11064	0.09	0.32073	N	0.594182	B	0.33073	0.396	B	0.19666	0.026	T	0.60515	-0.7248	10	0.59425	D	0.04	.	4.3557	0.11178	0.142:0.5864:0.1388:0.1327	.	1379	O75093	SLIT1_HUMAN	S	1379	ENSP00000266058:G1379S;ENSP00000360109:G1379S	ENSP00000266058:G1379S	G	-	1	0	SLIT1	98752470	0.858000	0.29795	0.562000	0.28370	0.006000	0.05464	1.503000	0.35715	1.157000	0.42530	0.561000	0.74099	GGC	.	.		0.667	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		T	98762480	C	T	98762480	3	4	141	1	0	0	0	0	1	0	0	0	14754	652	23	1	481	1	SLIT1	10	98762480	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	34911727	98762480	36772267	81	21978										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114912183	114912183	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gcaactgtaccccggctggtCcgcgcgggataactatgtag	13	12	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr10:114912183C>A	ENST00000355995.4	+	11	1760	c.1253C>A	c.(1252-1254)tCc>tAc	p.S418Y	TCF7L2_ENST00000542695.1_Missense_Mutation_p.S134Y|TCF7L2_ENST00000545257.1_Missense_Mutation_p.S418Y|TCF7L2_ENST00000352065.5_Missense_Mutation_p.S395Y|TCF7L2_ENST00000369389.1_Missense_Mutation_p.S129Y|TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000536810.1_Missense_Mutation_p.S418Y|TCF7L2_ENST00000543371.1_Missense_Mutation_p.S418Y|TCF7L2_ENST00000534894.1_Missense_Mutation_p.S418Y|TCF7L2_ENST00000369386.1_Missense_Mutation_p.S61Y|TCF7L2_ENST00000355717.4_Missense_Mutation_p.S442Y|TCF7L2_ENST00000538897.1_Missense_Mutation_p.S418Y|TCF7L2_ENST00000369397.4_Missense_Mutation_p.S395Y			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	418					blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CCCGGCTGGTCCGCGCGGGAT	0.537			T	VTI1A	colorectal																																p.S442Y		Atlas-SNP	.		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	.	TCF7L2	298	.	0			c.C1325A						.						116	123	120					10																	114912183		2203	4300	6503	SO:0001583	missense	6934	exon11			GCTGGTCCGCGCG	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1253C>A	chr10.hg19:g.114912183C>A	ENSP00000348274:p.Ser418Tyr	48.0	0.0		59.0	7.0	NM_001146283	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	hg19		.	.	.	.	.	.	.	.	.	.	c	29.3	4.996220	0.93167	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000355717;ENST00000538897;ENST00000534894;ENST00000369397;ENST00000352065;ENST00000542695;ENST00000369389;ENST00000277945;ENST00000369386	D;D;D;D;D;D;D;D;D;D;D;D	0.99394	-5.28;-5.29;-5.28;-5.29;-5.77;-5.81;-5.82;-5.3;-5.8;-5.22;-5.69;-5.73	5.66	5.66	0.87406	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (3);	0.053561	0.85682	D	0.000000	D	0.99527	0.9831	M	0.88105	2.93	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.991;0.999;1.0;1.0;0.999;1.0;1.0;1.0;1.0;0.999;1.0;1.0;0.999;1.0;1.0;0.992;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.983;0.996;0.962;0.999;0.999;0.999;0.998;0.998;1.0;0.998;0.997;0.981;0.999;0.999;0.997;0.999;0.998;0.953;1.0	D	0.98595	1.0656	10	0.87932	D	0	-23.4883	19.7439	0.96243	0.0:1.0:0.0:0.0	.	275;235;317;418;289;333;391;395;395;361;418;395;395;400;442;395;418;391;395	B4DJZ2;B7Z9Z6;B4DWD5;Q9NQB0;C6ZRK4;C6ZRJ6;C6ZRJ9;F8W742;B4DRJ8;C6ZRK2;B9X074;C6ZRJ8;C6ZRK1;C6ZRJ7;F8W7T5;C6ZRK5;Q9NQB0-7;Q9NQB0-10;Q6FHW4	.;.;.;TF7L2_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	Y	418;418;418;418;442;418;418;395;395;134;129;135;61	ENSP00000348274:S418Y;ENSP00000440547:S418Y;ENSP00000444972:S418Y;ENSP00000446238:S418Y;ENSP00000347949:S442Y;ENSP00000446172:S418Y;ENSP00000443626:S418Y;ENSP00000358404:S395Y;ENSP00000344823:S395Y;ENSP00000443883:S134Y;ENSP00000358396:S129Y;ENSP00000277945:S135Y	ENSP00000277945:S135Y	S	+	2	0	TCF7L2	114902173	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.814000	0.86154	2.669000	0.90835	0.655000	0.94253	TCC	.	.		0.537	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		A	114912183	C	A	114912183	3	1	141	1	0	0	0	0	1	0	0	0	15713	855	30	3	1440	3	TCF7L2	10	114912183	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	16149703	114912183	20622564	82	21979										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587564	55587564	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gtgggatcctatgcctggggAgtctcatgttccttggaact	13	9	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr11:55587564A>T	ENST00000333976.4	+	1	479	c.459A>T	c.(457-459)ggA>ggT	p.G153G		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				ATGCCTGGGGAGTCTCATGTT	0.473																																					p.G153G		Atlas-SNP	.											OR5D18,NS,carcinoma,+2,1	OR5D18	121	.	0			c.A459T						.						193	181	185					11																	55587564		2200	4296	6496	SO:0001819	synonymous_variant	219438	exon1			CTGGGGAGTCTCA	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.459A>T	chr11.hg19:g.55587564A>T		152.0	0.0		150.0	29.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Silent	SNP	ENST00000333976.4	hg19	CCDS31510.1																																																																																			.	.		0.473	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		T	55587564	A	T	55587564	2	4	141	1	0	0	0	0	0	0	0	1	11166	291	11	4		4	OR5D18	11	55587564	Silent	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10		55587564	79418952	83	21980										
OR8K1	390157	hgsc.bcm.edu	37	chr11	56113645	56113645	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cctcatcatatatctggtcaCagtgataggcaatctgggca	9	10	5	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr11:56113645C>A	ENST00000279783.2	+	1	225	c.131C>A	c.(130-132)aCa>aAa	p.T44K		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					TATCTGGTCACAGTGATAGGC	0.458										HNSCC(65;0.19)																											p.T44K		Atlas-SNP	.											.	OR8K1	93	.	0			c.C131A						.						152	134	140					11																	56113645		2201	4296	6497	SO:0001583	missense	390157	exon1			TGGTCACAGTGAT	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.131C>A	chr11.hg19:g.56113645C>A	ENSP00000279783:p.Thr44Lys	118.0	0.0		120.0	25.0	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	hg19	CCDS31528.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.190884	0.38707	.	.	ENSG00000150261	ENST00000279783	T	0.00509	6.91	5.09	4.18	0.49190	.	0.000000	0.52532	D	0.000075	T	0.01730	0.0055	M	0.92412	3.305	0.09310	N	1	D	0.62365	0.991	P	0.58210	0.835	T	0.15780	-1.0425	10	0.87932	D	0	-13.1605	9.3771	0.38290	0.0:0.8404:0.0:0.1596	.	44	Q8NGG5	OR8K1_HUMAN	K	44	ENSP00000279783:T44K	ENSP00000279783:T44K	T	+	2	0	OR8K1	55870221	0.012000	0.17670	0.007000	0.13788	0.159000	0.22180	1.706000	0.37878	2.344000	0.79699	0.549000	0.68633	ACA	.	.		0.458	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		A	56113645	C	A	56113645	3	1	141	1	0	0	0	0	1	0	0	0	11252	478	17	3	133	3	OR8K1	11	56113645	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	526081	56113645	78892871	84	21981										
MMP13	4322	hgsc.bcm.edu	37	chr11	102826222	102826222	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gtagtatgatctcaggtagcGctagaaaagacaccaaaatg	10	7	1	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr11:102826222G>A	ENST00000260302.3	-	2	149	c.121C>T	c.(121-123)Cgc>Tgc	p.R41C	MMP13_ENST00000340273.4_Splice_Site_p.R41C	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	41					bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	CTCAGGTAGCGCTAGAAAAGA	0.453																																					p.R41C		Atlas-SNP	.											MMP13,colon,carcinoma,+1,2	MMP13	75	.	0			c.C121T						.						154	148	150					11																	102826222		2202	4299	6501	SO:0001630	splice_region_variant	4322	exon2			GGTAGCGCTAGAA	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"Endogenous ligands"	7159	protein-coding gene	gene with protein product	"collagenase 3"	600108	"matrix metalloproteinase 13 (collagenase 3)"			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.121-1C>T	chr11.hg19:g.102826222G>A		70.0	0.0		73.0	19.0	NM_002427	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	hg19	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.560338	0.27827	.	.	ENSG00000137745	ENST00000260302;ENST00000546012;ENST00000340273	T;T	0.38722	1.12;1.12	5.67	2.22	0.28083	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	2.203110	0.01394	N	0.013347	T	0.59348	0.2187	L	0.52905	1.665	0.80722	D	1	P	0.43542	0.81	P	0.52386	0.697	T	0.47433	-0.9118	10	0.72032	D	0.01	.	15.4179	0.74987	0.0:0.0:0.5576:0.4424	.	41	P45452	MMP13_HUMAN	C	41	ENSP00000260302:R41C;ENSP00000339672:R41C	ENSP00000260302:R41C	R	-	1	0	MMP13	102331432	0.008000	0.16893	0.447000	0.26932	0.044000	0.14063	0.014000	0.13333	0.808000	0.34231	0.655000	0.94253	CGC	.	.		0.453	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427	Missense_Mutation	A	102826222	G	A	102826222	5	1	141	1	0	0	0	0	0	0	1	0	9661	1101	38	1	1330	1	MMP13	11	102826222	Splice_Site	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	46712577	102826222	32180294	85	21982										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103060527	103060527	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tatcttttagcaggatctatGgtacaagtgtatgaacaggt	10	5	2	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr11:103060527G>C	ENST00000375735.2	+	45	7563	c.7419G>C	c.(7417-7419)atG>atC	p.M2473I	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.M2473I|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2473	AAA 3. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CAGGATCTATGGTACAAGTGT	0.323																																					p.M2473I		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.G7419C						.						121	123	122					11																	103060527		1820	4069	5889	SO:0001583	missense	79659	exon45			ATCTATGGTACAA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.7419G>C	chr11.hg19:g.103060527G>C	ENSP00000364887:p.Met2473Ile	91.0	0.0		79.0	11.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267076	0.40095	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.39229	1.09;1.09	5.46	5.46	0.80206	.	.	.	.	.	T	0.44644	0.1303	L	0.55743	1.74	0.47183	D	0.999347	B;P	0.35383	0.201;0.498	B;B	0.36666	0.17;0.23	T	0.34229	-0.9837	9	0.40728	T	0.16	.	19.6629	0.95879	0.0:0.0:1.0:0.0	.	2473;2473	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	I	2473	ENSP00000364887:M2473I;ENSP00000381167:M2473I	ENSP00000364887:M2473I	M	+	3	0	DYNC2H1	102565737	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.791000	0.69045	2.726000	0.93360	0.655000	0.94253	ATG	.	.		0.323	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103060527	G	C	103060527	3	2	141	1	0	0	0	0	1	0	0	0	4848	1348	47	4	7597	4	DYNC2H1	11	103060527	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	234305	103060527	31945989	86	21983										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103229042	103229042	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tttgatagagaaatctggtcTaatgaactttctcctgtcct	7	8	3	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr11:103229042T>C	ENST00000375735.2	+	83	12255	c.12111T>C	c.(12109-12111)tcT>tcC	p.S4037S	DYNC2H1_ENST00000398093.3_Silent_p.S4044S|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4037					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AAATCTGGTCTAATGAACTTT	0.358																																					p.S4044S		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T12132C						.						80	70	73					11																	103229042		1835	4085	5920	SO:0001819	synonymous_variant	79659	exon84			CTGGTCTAATGAA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.12111T>C	chr11.hg19:g.103229042T>C		113.0	0.0		101.0	7.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.358	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103229042	T	C	103229042	2	2	141	1	0	0	0	0	0	0	0	1	4848	1509	53	2		2	DYNC2H1	11	103229042	Silent	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	168515	103229042	31777474	87	21984										
ATM	472	hgsc.bcm.edu	37	chr11	108114704	108114704	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gttctctgtgtacttcaggcTctatctgaaaccttcacaag	7	11	5	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr11:108114704T>G	ENST00000452508.2	+	7	710	c.521T>G	c.(520-522)cTc>cGc	p.L174R	ATM_ENST00000278616.4_Missense_Mutation_p.L174R			Q13315	ATM_HUMAN	ATM serine/threonine kinase	174					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TACTTCAGGCTCTATCTGAAA	0.284			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.L174R		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.T521G						.						67	60	62					11																	108114704		2200	4296	6496	SO:0001583	missense	472	exon6	Familial Cancer Database	AT, Louis-Bar syndrome	TCAGGCTCTATCT	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.521T>G	chr11.hg19:g.108114704T>G	ENSP00000388058:p.Leu174Arg	287.0	0.0		288.0	67.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.062147	0.76187	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000527891;ENST00000452508	T;T;T;T	0.29655	4.28;4.55;1.56;4.55	5.59	5.59	0.84812	.	0.171971	0.41823	D	0.000816	T	0.51312	0.1667	M	0.66939	2.045	0.22737	N	0.998795	D	0.65815	0.995	P	0.61070	0.883	T	0.50320	-0.8842	10	0.72032	D	0.01	.	15.7702	0.78162	0.0:0.0:0.0:1.0	.	174	Q13315	ATM_HUMAN	R	174;174;119;174	ENSP00000435747:L174R;ENSP00000278616:L174R;ENSP00000433955:L119R;ENSP00000388058:L174R	ENSP00000278616:L174R	L	+	2	0	ATM	107619914	0.952000	0.32445	0.108000	0.21378	0.904000	0.53231	5.404000	0.66344	2.135000	0.66039	0.533000	0.62120	CTC	.	.		0.284	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108114704	T	G	108114704	3	3	141	1	0	0	0	0	1	0	0	0	1109	1551	54	5	539	5	ATM	11	108114704	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	4885662	108114704	26891812	88	21985										
CCDC84	338657	hgsc.bcm.edu	37	chr11	118869172	118869172	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cgcaaggccatccgcgccgcTcaggtggagcgctatgtgcc	14	15	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr11:118869172T>G	ENST00000334418.1	+	2	209	c.153T>G	c.(151-153)gcT>gcG	p.A51A	RP11-110I1.12_ENST00000526453.1_lincRNA	NM_198489.1	NP_940891.1	Q86UT8	CCD84_HUMAN	coiled-coil domain containing 84	51										breast(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		TCCGCGCCGCTCAGGTGGAGC	0.667																																					p.A51A		Atlas-SNP	.											.	CCDC84	21	.	0			c.T153G						.						24	25	25					11																	118869172		2200	4295	6495	SO:0001819	synonymous_variant	338657	exon2			CGCCGCTCAGGTG	AB094093	CCDS8405.1	11q23.3	2006-03-13			ENSG00000186166	ENSG00000186166			30460	protein-coding gene	gene with protein product							Standard	NM_198489		Approved	DLNB14	uc001pul.3	Q86UT8	OTTHUMG00000166348	ENST00000334418.1:c.153T>G	chr11.hg19:g.118869172T>G		58.0	0.0		45.0	7.0	NM_198489		Silent	SNP	ENST00000334418.1	hg19	CCDS8405.1																																																																																			.	.		0.667	CCDC84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389315.1	NM_198489		G	118869172	T	G	118869172	2	3	141	1	0	0	0	0	0	0	0	1	2860	1538	54	5		5	CCDC84	11	118869172	Silent	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	10754468	118869172	16137344	89	21986										
IQSEC3	440073	hgsc.bcm.edu	37	chr12	274692	274692	+	Missense_Mutation	SNP	G	G	C													0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	atgcagttccagctctttgaGaacgagtgtaagtctttgac							TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr12:274692G>C	ENST00000538872.1	+	10	2920	c.2802G>C	c.(2800-2802)gaG>gaC	p.E934D	RP11-598F7.5_ENST00000540136.1_RNA|RP11-598F7.6_ENST00000537295.1_lincRNA|IQSEC3_ENST00000382841.2_Missense_Mutation_p.E631D|IQSEC3_ENST00000326261.4_Missense_Mutation_p.E934D			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	934	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		AGCTCTTTGAGAACGAGTGTA	0.498																																					p.E934D		Atlas-SNP	.											.	IQSEC3	154	.	0			c.G2802C						.						143	133	137					12																	274692		2203	4300	6503	SO:0001583	missense	440073	exon10			CTTTGAGAACGAG	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2802G>C	chr12.hg19:g.274692G>C	ENSP00000437554:p.Glu934Asp	89.0	0.0		80.0	6.0	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Missense_Mutation	SNP	ENST00000538872.1	hg19	CCDS53728.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.594755	0.66219	.	.	ENSG00000120645	ENST00000538872;ENST00000326261;ENST00000382841	T;T;T	0.52057	0.68;0.68;0.68	4.87	4.87	0.63330	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.50205	0.1602	M	0.69185	2.1	0.80722	D	1	B;B	0.16603	0.002;0.018	B;B	0.17098	0.012;0.017	T	0.49312	-0.8953	10	0.45353	T	0.12	.	18.5623	0.91105	0.0:0.0:1.0:0.0	.	934;631	Q9UPP2;Q9UPP2-2	IQEC3_HUMAN;.	D	934;934;631	ENSP00000437554:E934D;ENSP00000315662:E934D;ENSP00000372292:E631D	ENSP00000315662:E934D	E	+	3	2	IQSEC3	144953	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.377000	0.66184	2.684000	0.91462	0.650000	0.86243	GAG	.	.		0.498	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		C	274692	G	C	274692	3	2	141	1	0	0	0	0	1	0	0	0	7828	933	33	4	2840	4	IQSEC3	12	274692	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10		274692	133577203	90	21987	95	2								
IQSEC3	440073	hgsc.bcm.edu	37	chr12	274696	274696	+	Missense_Mutation	SNP	G	G	C													0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	agttccagctctttgagaacGagtgtaagtctttgacagcc					rs547194479	byFrequency	TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr12:274696G>C	ENST00000538872.1	+	10	2924	c.2806G>C	c.(2806-2808)Gag>Cag	p.E936Q	RP11-598F7.5_ENST00000540136.1_RNA|RP11-598F7.6_ENST00000537295.1_lincRNA|IQSEC3_ENST00000382841.2_Missense_Mutation_p.E633Q|IQSEC3_ENST00000326261.4_Missense_Mutation_p.E936Q			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	936	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		CTTTGAGAACGAGTGTAAGTC	0.502																																					p.E936Q		Atlas-SNP	.											.	IQSEC3	154	.	0			c.G2806C						.						135	126	129					12																	274696		2203	4300	6503	SO:0001583	missense	440073	exon10			GAGAACGAGTGTA	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2806G>C	chr12.hg19:g.274696G>C	ENSP00000437554:p.Glu936Gln	86.0	0.0		79.0	7.0	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Missense_Mutation	SNP	ENST00000538872.1	hg19	CCDS53728.1	.	.	.	.	.	.	.	.	.	.	G	14.86	2.661075	0.47572	.	.	ENSG00000120645	ENST00000538872;ENST00000326261;ENST00000382841	T;T;T	0.32515	1.45;1.45;1.45	4.87	4.87	0.63330	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.101640	0.64402	D	0.000003	T	0.32823	0.0842	L	0.52011	1.625	0.80722	D	1	B;B	0.31413	0.322;0.134	B;B	0.36608	0.229;0.191	T	0.06356	-1.0831	10	0.13470	T	0.59	.	18.5623	0.91105	0.0:0.0:1.0:0.0	.	936;633	Q9UPP2;Q9UPP2-2	IQEC3_HUMAN;.	Q	936;936;633	ENSP00000437554:E936Q;ENSP00000315662:E936Q;ENSP00000372292:E633Q	ENSP00000315662:E936Q	E	+	1	0	IQSEC3	144957	1.000000	0.71417	0.991000	0.47740	0.951000	0.60555	5.361000	0.66092	2.684000	0.91462	0.650000	0.86243	GAG	.	.		0.502	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		C	274696	G	C	274696	3	2	141	1	0	0	0	0	1	0	0	0	7828	1059	37	4	2844	4	IQSEC3	12	274696	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	4	274696	133577199	91	21988	95	2								
LETMD1	25875	hgsc.bcm.edu	37	chr12	51442826	51442826	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cttccttgtaggtcttcaaaGcttcacctttctccaaaggc	6	13	4	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr12:51442826G>T	ENST00000262055.4	+	2	171	c.132G>T	c.(130-132)aaG>aaT	p.K44N	LETMD1_ENST00000548516.1_3'UTR|LETMD1_ENST00000550929.1_5'UTR|LETMD1_ENST00000418425.2_Missense_Mutation_p.K44N|LETMD1_ENST00000552739.1_Intron|LETMD1_ENST00000380123.2_Missense_Mutation_p.K44N|LETMD1_ENST00000547008.1_Missense_Mutation_p.K44N	NM_015416.4	NP_056231.3	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1	44	Required and sufficient for mitochondrial import.					integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(3)	16						GGTCTTCAAAGCTTCACCTTT	0.448																																					p.K44N		Atlas-SNP	.											.	LETMD1	33	.	0			c.G132T						.						107	100	102					12																	51442826		2203	4300	6503	SO:0001583	missense	25875	exon2			TTCAAAGCTTCAC	AF195651	CCDS8806.1, CCDS58231.1, CCDS73469.1	12q13.13	2006-04-12				ENSG00000050426			24241	protein-coding gene	gene with protein product	"cervical cancer 1 protooncogene"					12879013, 12061725	Standard	NM_015416		Approved	HCCR1	uc009zlw.3	Q6P1Q0	OTTHUMG00000169538	ENST00000262055.4:c.132G>T	chr12.hg19:g.51442826G>T	ENSP00000262055:p.Lys44Asn	92.0	0.0		67.0	20.0	NM_001243689	A6NER7|B3KXK7|Q6X2E4|Q6X2E5|Q7L2G9|Q7L690|Q8WXW6|Q96PK7|Q9BY59|Q9Y3X3	Missense_Mutation	SNP	ENST00000262055.4	hg19	CCDS8806.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.853884	0.71719	.	.	ENSG00000050426	ENST00000551477;ENST00000262055;ENST00000550442;ENST00000549340;ENST00000548209;ENST00000548251;ENST00000380123;ENST00000548401;ENST00000418425;ENST00000448283;ENST00000547008	T;T;T;T;T;T;T;T;T;T	0.52057	0.75;0.75;0.76;0.72;0.68;0.72;0.75;0.81;0.76;0.74	4.86	4.86	0.63082	.	0.273309	0.26503	N	0.024003	T	0.45716	0.1356	N	0.24115	0.695	0.30737	N	0.7466	D;P;B;P;B;B	0.57571	0.98;0.904;0.18;0.904;0.275;0.361	P;B;B;P;B;B	0.57152	0.814;0.398;0.149;0.494;0.224;0.205	T	0.47509	-0.9112	10	0.51188	T	0.08	-4.302	9.288	0.37769	0.0958:0.0:0.9042:0.0	.	44;44;44;44;44;44	B7Z9A7;F8VVQ3;B3KXK7;F8W6J0;F8W1Z2;Q6P1Q0	.;.;.;.;.;LTMD1_HUMAN	N	11;44;44;44;44;44;44;51;44;44;44	ENSP00000446862:K11N;ENSP00000262055:K44N;ENSP00000448110:K44N;ENSP00000449896:K44N;ENSP00000450275:K44N;ENSP00000447166:K44N;ENSP00000369466:K44N;ENSP00000450082:K51N;ENSP00000389903:K44N;ENSP00000447419:K44N	ENSP00000262055:K44N	K	+	3	2	LETMD1	49729093	0.995000	0.38212	1.000000	0.80357	0.981000	0.71138	1.498000	0.35660	2.685000	0.91497	0.655000	0.94253	AAG	.	.		0.448	LETMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404710.1	NM_015416		T	51442826	G	T	51442826	3	4	141	1	0	0	0	0	1	0	0	0	8745	962	34	3	138	3	LETMD1	12	51442826	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	51168130	51442826	82409069	92	21989										
NXPH4	11247	hgsc.bcm.edu	37	chr12	57619424	57619424	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ctggctctgtgccaagccctTcaaagtcatctgtatcttcg	8	13	5	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr12:57619424T>C	ENST00000349394.5	+	2	996	c.821T>C	c.(820-822)tTc>tCc	p.F274S	Y_RNA_ENST00000365197.1_RNA	NM_007224.3	NP_009155.1	O95158	NXPH4_HUMAN	neurexophilin 4	274	V (Cys-rich).				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)	10						GCCAAGCCCTTCAAAGTCATC	0.577																																					p.F274S		Atlas-SNP	.											.	NXPH4	40	.	0			c.T821C						.						58	65	62					12																	57619424		2203	4300	6503	SO:0001583	missense	11247	exon2			AGCCCTTCAAAGT	AF043469	CCDS8933.1	12q13.3	2014-09-04			ENSG00000182379	ENSG00000182379			8078	protein-coding gene	gene with protein product		604637				9570794	Standard	NM_007224		Approved	NPH4	uc009zpj.4	O95158	OTTHUMG00000171241	ENST00000349394.5:c.821T>C	chr12.hg19:g.57619424T>C	ENSP00000333593:p.Phe274Ser	51.0	0.0		50.0	18.0	NM_007224	A8K4I4|Q7Z6L3|Q8N462	Missense_Mutation	SNP	ENST00000349394.5	hg19	CCDS8933.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.490594	0.64074	.	.	ENSG00000182379	ENST00000349394	.	.	.	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.69904	0.3163	L	0.54323	1.7	0.58432	D	0.999996	D	0.76494	0.999	D	0.83275	0.996	T	0.73164	-0.4069	9	0.87932	D	0	-19.2694	12.3172	0.54964	0.0:0.0:0.0:1.0	.	274	O95158	NXPH4_HUMAN	S	274	.	ENSP00000333593:F274S	F	+	2	0	NXPH4	55905691	1.000000	0.71417	1.000000	0.80357	0.428000	0.31595	7.635000	0.83286	1.744000	0.51775	0.460000	0.39030	TTC	.	.		0.577	NXPH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412474.1	NM_007224		C	57619424	T	C	57619424	3	2	141	1	0	0	0	0	1	0	0	0	10802	1783	62	2	827	2	NXPH4	12	57619424	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	6176598	57619424	76232471	93	21990										
FLT1	2321	hgsc.bcm.edu	37	chr13	28942739	28942739	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gatgatgatgatgatgacgaTgatgatgatgatgacaatgg	14	2	0	10	rs371573097|rs558386334	byFrequency	TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr13:28942739T>C	ENST00000282397.4	-	15	2368				FLT1_ENST00000541932.1_Silent_p.S726S	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1						blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	atgatgacgatgatgatgatg	0.343																																					p.S726S		Atlas-SNP	.											.	FLT1	393	.	0			c.A2178G						.						289	303	299					13																	28942739		692	1591	2283	SO:0001627	intron_variant	2321	exon15			TGACGATGATGAT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2117-10917A>G	chr13.hg19:g.28942739T>C		49.0	0.0		79.0	5.0	NM_001160030	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.		0.343	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	28942739	T	C	28942739	1	2	141	0	1	0	0	0	0	0	0	0	5949	1451	51	2		2	FLT1	13	28942739	Intron	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10		28942739	86227139	94	21991										
ATP7B	540	hgsc.bcm.edu	37	chr13	52542657	52542657	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	acccaggtcctggatgaactGagctatctcgaggggctgga	14	10	1	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr13:52542657G>C	ENST00000242839.4	-	4	1786	c.1630C>G	c.(1630-1632)Cag>Gag	p.Q544E	ATP7B_ENST00000542656.1_Intron|ATP7B_ENST00000400366.3_Missense_Mutation_p.Q433E|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000400370.3_Intron|ATP7B_ENST00000418097.2_Missense_Mutation_p.Q544E|ATP7B_ENST00000448424.2_Missense_Mutation_p.Q544E|ATP7B_ENST00000344297.5_Missense_Mutation_p.Q544E	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	544	HMA 5. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGGATGAACTGAGCTATCTCG	0.542									Wilson disease																												p.Q544E		Atlas-SNP	.											.	ATP7B	123	.	0			c.C1630G	GRCh37	CM970137	ATP7B	M		.						107	111	110					13																	52542657		2117	4225	6342	SO:0001583	missense	540	exon4	Familial Cancer Database		TGAACTGAGCTAT	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.1630C>G	chr13.hg19:g.52542657G>C	ENSP00000242839:p.Gln544Glu	106.0	0.0		98.0	10.0	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	hg19	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.559770	0.00910	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000448424;ENST00000418097	D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66	5.68	4.83	0.62350	Heavy metal-associated domain, HMA (3);Heavy metal-associated domain, copper ion-binding (1);	0.307970	0.40908	N	0.001000	T	0.54743	0.1877	N	0.00894	-1.105	0.80722	D	1	B;B;B;B;P;B	0.36027	0.135;0.005;0.054;0.168;0.533;0.002	B;B;B;B;B;B	0.32090	0.066;0.003;0.041;0.017;0.14;0.008	T	0.66634	-0.5874	10	0.02654	T	1	-5.6891	16.0307	0.80574	0.0:0.0:0.8645:0.1355	.	544;544;544;433;544;544	E7ET55;B7ZLR4;F5H748;P35670-3;P35670-2;P35670	.;.;.;.;.;ATP7B_HUMAN	E	544;433;544;544;544	ENSP00000242839:Q544E;ENSP00000383217:Q433E;ENSP00000342559:Q544E;ENSP00000416738:Q544E;ENSP00000393343:Q544E	ENSP00000242839:Q544E	Q	-	1	0	ATP7B	51440658	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	3.134000	0.50538	1.406000	0.46857	0.655000	0.94253	CAG	.	.		0.542	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		C	52542657	G	C	52542657	3	2	141	1	0	0	0	0	1	0	0	0	1191	1299	45	4	2839	4	ATP7B	13	52542657	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	23599918	52542657	62627221	95	21992										
IRS2	8660	hgsc.bcm.edu	37	chr13	110436226	110436226	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ggcgagctggccttgtagccGcccccgctcgccgggaatgt	15	15	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr13:110436226G>A	ENST00000375856.3	-	1	2689	c.2175C>T	c.(2173-2175)ggC>ggT	p.G725G		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	725					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			CCTTGTAGCCGCCCCCGCTCG	0.736																																					p.G725G	Melanoma(100;613 2409 40847)	Atlas-SNP	.											.	IRS2	44	.	0			c.C2175T						.						10	6	7					13																	110436226		1742	3572	5314	SO:0001819	synonymous_variant	8660	exon1			GTAGCCGCCCCCG	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"Pleckstrin homology (PH) domain containing"	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.2175C>T	chr13.hg19:g.110436226G>A		29.0	0.0		26.0	5.0	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Silent	SNP	ENST00000375856.3	hg19	CCDS9510.1																																																																																			.	.		0.736	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749		A	110436226	G	A	110436226	2	1	141	1	0	0	0	0	0	0	0	1	7850	1074	38	1		1	IRS2	13	110436226	Silent	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	57893569	110436226	4733652	96	21993										
OR4M1	441670	hgsc.bcm.edu	37	chr14	20248815	20248815	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	actttgttggggcttcggagAtgttcttgctcacagtgatg	13	7	2	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr14:20248815A>G	ENST00000315957.4	+	1	415	c.334A>G	c.(334-336)Atg>Gtg	p.M112V		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GGCTTCGGAGATGTTCTTGCT	0.478																																					p.M112V		Atlas-SNP	.											.	OR4M1	104	.	0			c.A334G						.						240	253	248					14																	20248815		2203	4300	6503	SO:0001583	missense	441670	exon1			TCGGAGATGTTCT		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"GPCR / Class A : Olfactory receptors"	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.334A>G	chr14.hg19:g.20248815A>G	ENSP00000319654:p.Met112Val	237.0	0.0		208.0	25.0	NM_001005500	B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	hg19	CCDS32021.1	.	.	.	.	.	.	.	.	.	.	.	2.302	-0.360033	0.05103	.	.	ENSG00000176299	ENST00000315957	T	0.00384	7.6	4.33	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000014	T	0.00210	0.0006	L	0.33093	0.98	0.25478	N	0.987765	B	0.34015	0.435	B	0.27608	0.081	T	0.40794	-0.9544	10	0.17832	T	0.49	-21.4932	8.1327	0.31037	0.7956:0.2044:0.0:0.0	.	112	Q8NGD0	OR4M1_HUMAN	V	112	ENSP00000319654:M112V	ENSP00000319654:M112V	M	+	1	0	OR4M1	19318655	0.001000	0.12720	1.000000	0.80357	0.945000	0.59286	0.100000	0.15231	1.949000	0.56562	0.414000	0.27820	ATG	.	.		0.478	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1			G	20248815	A	G	20248815	3	3	141	1	0	0	0	0	1	0	0	0	11084	333	12	2	336	2	OR4M1	14	20248815	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10		20248815	87100725	97	21994										
TMEM63C	57156	hgsc.bcm.edu	37	chr14	77705090	77705090	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	aaggacattgaagacccagaActcatcattaagcattttca	6	9	3	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr14:77705090A>T	ENST00000298351.4	+	10	849	c.705A>T	c.(703-705)gaA>gaT	p.E235D		NM_020431.2	NP_065164.2	Q9P1W3	CSC1_HUMAN	transmembrane protein 63C	235					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)	integral component of membrane (GO:0016021)	calcium activated cation channel activity (GO:0005227)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(1)	23			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		AAGACCCAGAACTCATCATTA	0.483																																					p.E235D		Atlas-SNP	.											.	TMEM63C	77	.	0			c.A705T						.						97	94	95					14																	77705090		1964	4141	6105	SO:0001583	missense	57156	exon10			CCCAGAACTCATC		CCDS45141.1	14q24.3	2014-05-30	2005-07-25	2005-07-25	ENSG00000165548	ENSG00000165548			23787	protein-coding gene	gene with protein product	"calcium permeable stress-gated cation channel 1 homolog (Arabidopsis)"		"chromosome 14 open reading frame 171"	C14orf171		24503647	Standard	NM_020431		Approved	DKFZp434P0111, CSC1, hsCSC1	uc001xtf.2	Q9P1W3	OTTHUMG00000171557	ENST00000298351.4:c.705A>T	chr14.hg19:g.77705090A>T	ENSP00000298351:p.Glu235Asp	150.0	0.0		113.0	24.0	NM_020431	B2RN22|B3KWJ5|Q86TS3|Q86TS4|Q9NSQ4|Q9P1W1	Missense_Mutation	SNP	ENST00000298351.4	hg19	CCDS45141.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.348893	0.41599	.	.	ENSG00000165548	ENST00000298351	T	0.20463	2.07	4.94	-4.97	0.03029	.	0.331422	0.32120	N	0.006553	T	0.13243	0.0321	L	0.50333	1.59	0.21147	N	0.99977	B	0.09022	0.002	B	0.10450	0.005	T	0.13710	-1.0499	10	0.34782	T	0.22	-8.5149	5.5631	0.17154	0.2506:0.112:0.527:0.1104	.	235	Q9P1W3	TM63C_HUMAN	D	235	ENSP00000298351:E235D	ENSP00000298351:E235D	E	+	3	2	TMEM63C	76774843	0.290000	0.24343	0.737000	0.30932	0.883000	0.51084	-0.363000	0.07593	-0.753000	0.04721	0.459000	0.35465	GAA	.	.		0.483	TMEM63C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414193.1			T	77705090	A	T	77705090	3	4	141	1	0	0	0	0	1	0	0	0	16207	40	2	4	735	4	TMEM63C	14	77705090	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	57456275	77705090	29644450	98	21995										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99641568	99641568	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tcctcctcctcctcctcctcCtcgtcctcctcctccggctc	3	25	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr14:99641568C>G	ENST00000357195.3	-	4	1614	c.1605G>C	c.(1603-1605)gaG>gaC	p.E535D	BCL11B_ENST00000345514.2_Missense_Mutation_p.E464D|BCL11B_ENST00000443726.2_Missense_Mutation_p.E341D	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	535	Glu-rich.				alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.E535_E536delEE(1)		NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		cctcctcctcctcgtcctcct	0.697			T	TLX3	T-ALL																																p.E535D		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	BCL11B,colon,carcinoma,0,1	BCL11B	108	.	1	Deletion - In frame(1)	prostate(1)	c.G1605C						.						5	5	5					14																	99641568		2084	4070	6154	SO:0001583	missense	64919	exon4			CTCCTCCTCGTCC	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.1605G>C	chr14.hg19:g.99641568C>G	ENSP00000349723:p.Glu535Asp	14.0	0.0		22.0	3.0	NM_138576	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	hg19	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.167616	0.38315	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.13657	2.57;2.6;2.57	3.81	0.863	0.19062	.	0.158674	0.40144	N	0.001176	T	0.07324	0.0185	N	0.22421	0.69	0.40982	D	0.984788	B;B	0.31413	0.322;0.185	B;B	0.31390	0.129;0.048	T	0.38394	-0.9663	10	0.30854	T	0.27	-8.4478	4.8239	0.13407	0.0:0.4986:0.1502:0.3512	.	464;535	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	D	535;464;341	ENSP00000349723:E535D;ENSP00000280435:E464D;ENSP00000387419:E341D	ENSP00000280435:E464D	E	-	3	2	BCL11B	98711321	0.591000	0.26824	0.998000	0.56505	0.990000	0.78478	-0.193000	0.09573	-0.059000	0.13154	0.561000	0.74099	GAG	.	.		0.697	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		G	99641568	C	G	99641568	3	3	141	1	0	0	0	0	1	0	0	0	1364	680	24	4	1083	4	BCL11B	14	99641568	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	21936478	99641568	7707972	99	21996										
MAPK6	5597	hgsc.bcm.edu	37	chr15	52356857	52356857	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ggactgttttttcataaatcAgttttgtgaggtaaggaagg	12	3	2	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr15:52356857A>G	ENST00000261845.5	+	6	2633	c.1826A>G	c.(1825-1827)cAg>cGg	p.Q609R	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	609					cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		TTCATAAATCAGTTTTGTGAG	0.403																																					p.Q609R		Atlas-SNP	.											.	MAPK6	70	.	0			c.A1826G						.						76	76	76					15																	52356857		2195	4293	6488	SO:0001583	missense	5597	exon6			TAAATCAGTTTTG	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"Mitogen-activated protein kinase cascade / Kinases"	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.1826A>G	chr15.hg19:g.52356857A>G	ENSP00000261845:p.Gln609Arg	381.0	0.0		379.0	22.0	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	hg19	CCDS10147.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.215528	0.39102	.	.	ENSG00000069956	ENST00000261845	T	0.72051	-0.62	5.27	5.27	0.74061	.	0.100405	0.64402	D	0.000001	T	0.62307	0.2417	L	0.32530	0.975	0.53688	D	0.999979	B	0.19200	0.034	B	0.14578	0.011	T	0.61574	-0.7035	10	0.87932	D	0	-7.1715	15.3381	0.74273	1.0:0.0:0.0:0.0	.	609	Q16659	MK06_HUMAN	R	609	ENSP00000261845:Q609R	ENSP00000261845:Q609R	Q	+	2	0	MAPK6	50144149	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.710000	0.91388	2.052000	0.61016	0.444000	0.29173	CAG	.	.		0.403	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748		G	52356857	A	G	52356857	3	3	141	1	0	0	0	0	1	0	0	0	9290	188	7	2	1844	2	MAPK6	15	52356857	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10		52356857	50174535	100	21997										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62146685	62146685	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	caattggggtctgagaagtcTcactgatgactgcttcatca	10	9	4	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr15:62146685T>G	ENST00000261517.5	-	85	11306	c.11233A>C	c.(11233-11235)Aga>Cga	p.R3745R	VPS13C_ENST00000249837.3_Silent_p.R3702R|RP11-16B9.1_ENST00000559251.1_RNA	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CTGAGAAGTCTCACTGATGAC	0.408																																					p.R3745R		Atlas-SNP	.											.	VPS13C	506	.	0			c.A11233C						.						216	192	200					15																	62146685		2203	4300	6503	SO:0001819	synonymous_variant	54832	exon85			GAAGTCTCACTGA	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.11233A>C	chr15.hg19:g.62146685T>G		93.0	0.0		100.0	28.0	NM_020821		Silent	SNP	ENST00000261517.5	hg19	CCDS32257.1																																																																																			.	.		0.408	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		G	62146685	T	G	62146685	2	3	141	1	0	0	0	0	0	0	0	1	17206	1559	54	5		5	VPS13C	15	62146685	Silent	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	9789828	62146685	40384707	101	21998										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86273887	86273887	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gagttctcttccgctccaacAcagaagaggctctcaaagga	9	12	2	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr15:86273887A>G	ENST00000394518.2	+	30	7326	c.7231A>G	c.(7231-7233)Aca>Gca	p.T2411A	AKAP13_ENST00000394510.2_Missense_Mutation_p.T656A|AKAP13_ENST00000361243.2_Missense_Mutation_p.T2415A|AKAP13_ENST00000560579.1_3'UTR	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2411	Interaction with ESR1.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CCGCTCCAACACAGAAGAGGC	0.488											OREG0023425	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T2415A	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.A7243G						.						113	106	108					15																	86273887		2202	4299	6501	SO:0001583	missense	11214	exon30			TCCAACACAGAAG	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.7231A>G	chr15.hg19:g.86273887A>G	ENSP00000378026:p.Thr2411Ala	75.0	0.0	1243	73.0	15.0	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	A	17.90	3.501353	0.64298	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	T;T;T	0.23950	2.88;2.91;1.88	5.82	5.82	0.92795	.	.	.	.	.	T	0.45716	0.1356	M	0.73962	2.25	0.38306	D	0.943126	D;D	0.65815	0.991;0.995	P;P	0.62435	0.8;0.902	T	0.50524	-0.8818	9	0.40728	T	0.16	.	10.585	0.45278	0.8564:0.0:0.0:0.1436	.	2411;2415	Q12802;Q12802-2	AKP13_HUMAN;.	A	2415;2411;2414;2390;656	ENSP00000354718:T2415A;ENSP00000378026:T2411A;ENSP00000378018:T656A	ENSP00000354718:T2415A	T	+	1	0	AKAP13	84074891	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.947000	0.40293	2.227000	0.72691	0.528000	0.53228	ACA	.	.		0.488	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		G	86273887	A	G	86273887	3	3	141	1	0	0	0	0	1	0	0	0	449	159	6	2	7415	2	AKAP13	15	86273887	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	24127202	86273887	16257505	102	21999										
MFGE8	4240	hgsc.bcm.edu	37	chr15	89443027	89443027	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gatgcctgtcacctccttcgAggagcccaggtccacctaca	9	16	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr15:89443027A>T	ENST00000566497.1	-	7	947	c.886T>A	c.(886-888)Tcg>Acg	p.S296T	MFGE8_ENST00000542878.1_Missense_Mutation_p.S252T|MFGE8_ENST00000539437.1_Missense_Mutation_p.S288T|MFGE8_ENST00000268150.8_Missense_Mutation_p.S296T|MFGE8_ENST00000268151.7_Intron			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	296	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					ACCTCCTTCGAGGAGCCCAGG	0.512																																					p.S296T		Atlas-SNP	.											.	MFGE8	60	.	0			c.T886A						.						56	48	51					15																	89443027		2200	4299	6499	SO:0001583	missense	4240	exon7			CCTTCGAGGAGCC	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"sperm surface protein hP47"	602281	"sperm associated antigen 10"	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.886T>A	chr15.hg19:g.89443027A>T	ENSP00000456281:p.Ser296Thr	79.0	0.0		93.0	20.0	NM_005928	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Missense_Mutation	SNP	ENST00000566497.1	hg19	CCDS10347.1	.	.	.	.	.	.	.	.	.	.	G	4.783	0.145606	0.09134	.	.	ENSG00000140545	ENST00000268150;ENST00000539437;ENST00000542878	D;D;D	0.98044	-4.68;-4.68;-4.68	5.03	1.97	0.26223	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.373344	0.29707	N	0.011406	D	0.86451	0.5936	N	0.00991	-1.07	0.09310	N	1	B;B;B;B	0.12013	0.0;0.005;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.79176	-0.1911	10	0.08599	T	0.76	-7.7452	4.9386	0.13954	0.0733:0.1292:0.5304:0.2671	.	288;252;288;296	B3KTQ2;F5GZN3;F5H7N9;Q08431	.;.;.;MFGM_HUMAN	T	296;288;252	ENSP00000268150:S296T;ENSP00000442386:S288T;ENSP00000444332:S252T	ENSP00000268150:S296T	S	-	1	0	MFGE8	87244031	0.083000	0.21467	0.000000	0.03702	0.100000	0.18952	1.776000	0.38594	-0.084000	0.12595	-0.330000	0.08379	TCG	.	.		0.512	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928		T	89443027	A	T	89443027	3	4	141	1	0	0	0	0	1	0	0	0	9529	304	11	4	285	4	MFGE8	15	89443027	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	3169140	89443027	13088365	103	22000										
BLM	641	hgsc.bcm.edu	37	chr15	91347543	91347543	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ctggggaaagtttttggtgtCcattacttcaatatttttaa	8	5	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr15:91347543C>A	ENST00000355112.3	+	19	3823	c.3705C>A	c.(3703-3705)gtC>gtA	p.V1235V	BLM_ENST00000560509.1_Intron|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1235	HRDC. {ECO:0000255|PROSITE- ProRule:PRU00328}.				alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TTTTTGGTGTCCATTACTTCA	0.398			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.V1235V		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	.	BLM	122	.	0			c.C3705A						.						105	109	108					15																	91347543		2198	4298	6496	SO:0001819	synonymous_variant	641	exon19	Familial Cancer Database		TGGTGTCCATTAC	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"Bloom syndrome"			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3705C>A	chr15.hg19:g.91347543C>A		173.0	0.0		188.0	41.0	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	hg19	CCDS10363.1																																																																																			.	.		0.398	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			A	91347543	C	A	91347543	2	1	141	1	0	0	0	0	0	0	0	1	1445	842	30	3		3	BLM	15	91347543	Silent	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	1904516	91347543	11183849	104	22001										
MAN2A2	4122	hgsc.bcm.edu	37	chr15	91448631	91448631	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgctgccctactacacggtcAatggctcctgggtggtgcca	12	13	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr15:91448631A>G	ENST00000559717.1	+	3	742	c.283A>G	c.(283-285)Aat>Gat	p.N95D	MAN2A2_ENST00000431652.2_5'Flank|MAN2A2_ENST00000360468.3_Missense_Mutation_p.N95D			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	95					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			CTACACGGTCAATGGCTCCTG	0.632																																					p.N95D		Atlas-SNP	.											.	MAN2A2	99	.	0			c.A283G						.						41	47	45					15																	91448631		2198	4298	6496	SO:0001583	missense	4122	exon2			ACGGTCAATGGCT	L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.283A>G	chr15.hg19:g.91448631A>G	ENSP00000452948:p.Asn95Asp	68.0	0.0		66.0	6.0	NM_006122	A6NH12|A8K1E8|Q13754	Missense_Mutation	SNP	ENST00000559717.1	hg19	CCDS32332.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.996855	0.54147	.	.	ENSG00000196547	ENST00000360468	T	0.77489	-1.1	6.0	6.0	0.97389	.	0.125481	0.64402	D	0.000001	T	0.79441	0.4446	L	0.43152	1.355	0.80722	D	1	D;P	0.54047	0.964;0.804	P;P	0.52881	0.712;0.519	T	0.77222	-0.2667	10	0.30854	T	0.27	-30.6061	16.2335	0.82360	1.0:0.0:0.0:0.0	.	95;95	P49641-1;P49641	.;MA2A2_HUMAN	D	95	ENSP00000353655:N95D	ENSP00000353655:N95D	N	+	1	0	MAN2A2	89249635	1.000000	0.71417	0.713000	0.30519	0.723000	0.41478	9.140000	0.94607	2.313000	0.78055	0.454000	0.30748	AAT	.	.		0.632	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122		G	91448631	A	G	91448631	3	3	141	1	0	0	0	0	1	0	0	0	9224	130	5	2	289	2	MAN2A2	15	91448631	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	101088	91448631	11082761	105	22002										
KIAA0430	9665	hgsc.bcm.edu	37	chr16	15727524	15727524	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cttgttttctttactgatgtCacatacacagatgaattctg	6	8	3	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr16:15727524C>T	ENST00000396368.3	-	5	1389	c.1183G>A	c.(1183-1185)Gac>Aac	p.D395N	KIAA0430_ENST00000602337.1_Missense_Mutation_p.D392N|KIAA0430_ENST00000540441.2_Missense_Mutation_p.D395N|KIAA0430_ENST00000548025.1_Missense_Mutation_p.D392N|KIAA0430_ENST00000344181.3_Missense_Mutation_p.D217N|KIAA0430_ENST00000551742.1_Missense_Mutation_p.D395N	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	395	NYN.				double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						TTACTGATGTCACATACACAG	0.378																																					p.D395N		Atlas-SNP	.											.	KIAA0430	154	.	0			c.G1183A						.						94	89	90					16																	15727524		1816	4081	5897	SO:0001583	missense	9665	exon5			TGATGTCACATAC	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29562	protein-coding gene	gene with protein product	"limkain b1", "protein phosphatase 1, regulatory subunit 34", "meiosis arrest female 1"	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.1183G>A	chr16.hg19:g.15727524C>T	ENSP00000379654:p.Asp395Asn	90.0	0.0		77.0	7.0	NM_014647	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Missense_Mutation	SNP	ENST00000396368.3	hg19	CCDS10562.2	.	.	.	.	.	.	.	.	.	.	C	34	5.404170	0.96051	.	.	ENSG00000166783	ENST00000396368;ENST00000540441;ENST00000321370;ENST00000344181;ENST00000548025;ENST00000551742;ENST00000551298	.	.	.	5.43	5.43	0.79202	Domain of unknown function DUF88 (1);	0.000000	0.85682	D	0.000000	D	0.84575	0.5502	M	0.85945	2.785	0.43793	D	0.996338	D;D;D;D	0.89917	0.986;1.0;1.0;0.989	D;D;D;D	0.91635	0.96;0.999;0.999;0.957	D	0.86455	0.1775	9	0.87932	D	0	.	19.5914	0.95514	0.0:1.0:0.0:0.0	.	394;392;391;394	Q9Y4F3-5;F8VV09;Q9Y4F3-4;Q9Y4F3	.;.;.;LKAP_HUMAN	N	395;395;394;217;392;395;395	.	ENSP00000315718:D394N	D	-	1	0	KIAA0430	15635025	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.210000	0.77924	2.720000	0.93068	0.591000	0.81541	GAC	.	.		0.378	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647		T	15727524	C	T	15727524	3	4	141	1	0	0	0	0	1	0	0	0	8186	826	29	3	4140	3	KIAA0430	16	15727524	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10		15727524	74627229	106	22003										
ALDOA	226	hgsc.bcm.edu	37	chr16	30080632	30080632	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tccctcgccctgcagaatggCattgtgcccatcgtggagcc	11	15	0	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr16:30080632C>T	ENST00000566897.1	+	9	1698	c.546C>T	c.(544-546)ggC>ggT	p.G182G	ALDOA_ENST00000569545.1_Silent_p.G182G|ALDOA_ENST00000395248.1_Silent_p.G236G|ALDOA_ENST00000412304.2_Silent_p.G182G|ALDOA_ENST00000395240.3_Silent_p.G186G|ALDOA_ENST00000564546.1_Silent_p.G182G|ALDOA_ENST00000338110.5_Silent_p.G182G|ALDOA_ENST00000564595.2_Silent_p.G236G|ALDOA_ENST00000563060.2_Silent_p.G182G|ALDOA_ENST00000569798.1_Silent_p.G182G			P04075	ALDOA_HUMAN	aldolase A, fructose-bisphosphate	182					actin filament organization (GO:0007015)|ATP biosynthetic process (GO:0006754)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homotetramerization (GO:0051289)|regulation of cell shape (GO:0008360)|small molecule metabolic process (GO:0044281)|striated muscle contraction (GO:0006941)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|membrane (GO:0016020)|nucleus (GO:0005634)|platelet alpha granule lumen (GO:0031093)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|fructose binding (GO:0070061)|fructose-bisphosphate aldolase activity (GO:0004332)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|tubulin binding (GO:0015631)			breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	17						TGCAGAATGGCATTGTGCCCA	0.567											OREG0023729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G236G		Atlas-SNP	.											.	ALDOA	33	.	0			c.C708T						.						105	91	96					16																	30080632		2197	4300	6497	SO:0001819	synonymous_variant	226	exon7			GAATGGCATTGTG	X05236	CCDS10668.1, CCDS58450.1	16p11.2	2008-03-06			ENSG00000149925	ENSG00000149925	4.1.2.13		414	protein-coding gene	gene with protein product		103850				3570299	Standard	NM_000034		Approved		uc010veg.2	P04075	OTTHUMG00000132107	ENST00000566897.1:c.546C>T	chr16.hg19:g.30080632C>T		96.0	0.0	814	60.0	18.0	NM_001243177	B4DXI7|Q6FH76|Q6FI10|Q96B15|Q9BWD9|Q9UCN2	Silent	SNP	ENST00000566897.1	hg19	CCDS10668.1																																																																																			.	.		0.567	ALDOA-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435360.1	NM_000034		T	30080632	C	T	30080632	2	4	141	1	0	0	0	0	0	0	0	1	507	697	25	3		3	ALDOA	16	30080632	Silent	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	14353108	30080632	60274121	107	22004										
CDH15	1013	hgsc.bcm.edu	37	chr16	89258218	89258218	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gcgccacggatgaggacctgCccccccacggggcccccttc	12	20	0	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr16:89258218C>T	ENST00000289746.2	+	10	1596	c.1531C>T	c.(1531-1533)Ccc>Tcc	p.P511S		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	511	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		TGAGGACCTGCCCCCCCACGG	0.731																																					p.P511S		Atlas-SNP	.											.	CDH15	54	.	0			c.C1531T						.						9	12	11					16																	89258218		2085	4090	6175	SO:0001583	missense	1013	exon10			GACCTGCCCCCCC	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"Cadherins / Major cadherins"	1754	protein-coding gene	gene with protein product		114019	"cadherin 15, M-cadherin (myotubule)"	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.1531C>T	chr16.hg19:g.89258218C>T	ENSP00000289746:p.Pro511Ser	49.0	0.0		47.0	10.0	NM_004933		Missense_Mutation	SNP	ENST00000289746.2	hg19	CCDS10976.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648098	0.47258	.	.	ENSG00000129910	ENST00000289746	T	0.61510	0.1	4.47	4.47	0.54385	Cadherin (1);Cadherin-like (1);	0.000000	0.52532	U	0.000078	T	0.55924	0.1951	L	0.56280	1.765	0.39533	D	0.968694	P	0.51147	0.942	P	0.46389	0.515	T	0.57388	-0.7820	10	0.30078	T	0.28	.	12.494	0.55916	0.0:0.8301:0.1699:0.0	.	511	P55291	CAD15_HUMAN	S	511	ENSP00000289746:P511S	ENSP00000289746:P511S	P	+	1	0	CDH15	87785719	0.618000	0.27051	1.000000	0.80357	0.935000	0.57460	0.444000	0.21661	2.047000	0.60756	0.289000	0.19496	CCC	.	.		0.731	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		T	89258218	C	T	89258218	3	4	141	1	0	0	0	0	1	0	0	0	3102	739	26	3	1569	3	CDH15	16	89258218	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	59177586	89258218	1096535	108	22005										
SMG6	23293	hgsc.bcm.edu	37	chr17	2200545	2200545	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	aaggtagcttactgtcttgcGtaatggcttgctgcgaatgg	13	7	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr17:2200545G>A	ENST00000263073.6	-	4	2193	c.2143C>T	c.(2143-2145)Cgc>Tgc	p.R715C	SMG6_ENST00000544865.1_Missense_Mutation_p.R684C	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	715					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						ACTGTCTTGCGTAATGGCTTG	0.393																																					p.R715C	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.C2143T						.						123	128	126					17																	2200545		2203	4300	6503	SO:0001583	missense	23293	exon4			TCTTGCGTAATGG	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"EST1 telomerase component homolog A (S. cerevisiae)"	610963	"chromosome 17 open reading frame 31", "smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.2143C>T	chr17.hg19:g.2200545G>A	ENSP00000263073:p.Arg715Cys	86.0	0.0		75.0	19.0	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	hg19	CCDS11016.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.033763	0.75504	.	.	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.17054	2.3;2.3	5.08	4.02	0.46733	Telomerase activating protein Est1 (1);	0.062472	0.64402	D	0.000004	T	0.34600	0.0903	M	0.72894	2.215	0.80722	D	1	D	0.71674	0.998	P	0.55871	0.786	T	0.22138	-1.0225	10	0.56958	D	0.05	-0.1579	15.8667	0.79071	0.0:0.0:0.7849:0.2151	.	715	Q86US8	EST1A_HUMAN	C	715;684	ENSP00000263073:R715C;ENSP00000443920:R684C	ENSP00000263073:R715C	R	-	1	0	SMG6	2147295	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.264000	0.58859	2.341000	0.79615	0.455000	0.32223	CGC	.	.		0.393	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			A	2200545	G	A	2200545	3	1	141	1	0	0	0	0	1	0	0	0	14812	1145	40	1	2180	1	SMG6	17	2200545	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10		2200545	78994665	109	22006										
SNX11	29916	hgsc.bcm.edu	37	chr17	46196421	46196421	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cggtgcctgagatagaagccTgtgtccagggccgaagtacc	14	11	0	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr17:46196421T>A	ENST00000393405.2	+	7	766	c.412T>A	c.(412-414)Tgt>Agt	p.C138S	SNX11_ENST00000582104.1_Missense_Mutation_p.C130S|SNX11_ENST00000439357.2_Missense_Mutation_p.C77S|SNX11_ENST00000580219.1_Missense_Mutation_p.C130S|SNX11_ENST00000452859.2_De_novo_Start_OutOfFrame|SNX11_ENST00000359238.2_Missense_Mutation_p.C138S	NM_152244.1	NP_689450.1	Q9Y5W9	SNX11_HUMAN	sorting nexin 11	138	Important for membrane trafficking.				intracellular protein transport (GO:0006886)|vesicle organization (GO:0016050)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol phosphate binding (GO:1901981)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	14						GATAGAAGCCTGTGTCCAGGG	0.537																																					p.C138S		Atlas-SNP	.											.	SNX11	20	.	0			c.T412A						.						152	122	133					17																	46196421		2203	4300	6503	SO:0001583	missense	29916	exon6			GAAGCCTGTGTCC	AF121861	CCDS11526.1	17q21.32	2011-05-03			ENSG00000002919	ENSG00000002919		"Sorting nexins"	14975	protein-coding gene	gene with protein product		614906					Standard	NM_013323		Approved		uc002ing.1	Q9Y5W9		ENST00000393405.2:c.412T>A	chr17.hg19:g.46196421T>A	ENSP00000377059:p.Cys138Ser	83.0	0.0		53.0	7.0	NM_013323	B3KRL6|B4DPY5|D3DTV0|Q53YC0|Q9H885	Missense_Mutation	SNP	ENST00000393405.2	hg19	CCDS11526.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.025526	0.93518	.	.	ENSG00000002919	ENST00000393405;ENST00000439357;ENST00000359238	T;T	0.66099	-0.19;-0.19	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.77651	0.4162	M	0.70595	2.14	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.994;0.994;0.994	T	0.79685	-0.1700	10	0.59425	D	0.04	-14.464	14.6096	0.68507	0.0:0.0:0.0:1.0	.	77;130;138	B4DKH7;B4DPY5;Q9Y5W9	.;.;SNX11_HUMAN	S	138;77;138	ENSP00000377059:C138S;ENSP00000352175:C138S	ENSP00000352175:C138S	C	+	1	0	SNX11	43551420	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.599000	0.82757	2.101000	0.63845	0.459000	0.35465	TGT	.	.		0.537	SNX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443423.1			A	46196421	T	A	46196421	3	1	141	1	0	0	0	0	1	0	0	0	14897	1580	55	4	430	4	SNX11	17	46196421	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	43995876	46196421	34998789	110	22007										
SUPT4H1	6827	hgsc.bcm.edu	37	chr17	56423671	56423671	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gacttttcagctcccgcacgAttcctgaagcaggaaaagaa	9	11	1	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr17:56423671A>T	ENST00000225504.3	-	5	356	c.290T>A	c.(289-291)aTc>aAc	p.I97N	BZRAP1-AS1_ENST00000578334.1_RNA|BZRAP1-AS1_ENST00000579527.1_RNA|BZRAP1-AS1_ENST00000582348.1_RNA|BZRAP1-AS1_ENST00000583826.1_RNA|SUPT4H1_ENST00000581540.1_Missense_Mutation_p.I88N|BZRAP1-AS1_ENST00000583841.1_RNA|SUPT4H1_ENST00000580947.1_Missense_Mutation_p.I97N|BZRAP1-AS1_ENST00000579859.1_RNA|BZRAP1-AS1_ENST00000580633.1_RNA|BZRAP1-AS1_ENST00000580022.1_RNA|SUPT4H1_ENST00000577396.1_Missense_Mutation_p.I56N|BZRAP1-AS1_ENST00000580515.1_RNA|BZRAP1-AS1_ENST00000578025.1_RNA|BZRAP1-AS1_ENST00000585236.1_RNA	NM_003168.1	NP_003159.1	P63272	SPT4H_HUMAN	suppressor of Ty 4 homolog 1 (S. cerevisiae)	97				QGIVRELKSRGVAYKSRDTAIKT -> HAKDSRSNVNKYEP RESSEGHDTCLASLFHSLRHSNSLFAL (in Ref. 3; BAC85230). {ECO:0000305}.	chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			large_intestine(2)|skin(2)	4	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTCCCGCACGATTCCTGAAGC	0.498																																					p.I97N	NSCLC(25;723 896 19867 29219 40028)	Atlas-SNP	.											.	SUPT4H1	11	.	0			c.T290A						.						111	99	103					17																	56423671		2203	4300	6503	SO:0001583	missense	6827	exon5			CGCACGATTCCTG	U38817	CCDS11606.1	17q22	2014-06-23	2001-11-28		ENSG00000213246	ENSG00000213246			11467	protein-coding gene	gene with protein product		603555	"suppressor of Ty (S.cerevisiae) 4 homolog 1"	SUPT4H		8786137	Standard	NM_003168		Approved	SPT4H	uc002iwe.2	P63272	OTTHUMG00000178926	ENST00000225504.3:c.290T>A	chr17.hg19:g.56423671A>T	ENSP00000225504:p.Ile97Asn	50.0	0.0		52.0	13.0	NM_003168	B2R4X8|D3DTZ4|Q16550|Q62387|Q6ZP89	Missense_Mutation	SNP	ENST00000225504.3	hg19	CCDS11606.1	.	.	.	.	.	.	.	.	.	.	A	12.08	1.830407	0.32329	.	.	ENSG00000213246	ENST00000225504	.	.	.	5.13	4.05	0.47172	.	0.072634	0.56097	U	0.000037	T	0.63450	0.2512	M	0.80982	2.52	0.58432	D	0.999999	P	0.42248	0.774	P	0.46275	0.51	T	0.65853	-0.6067	9	0.87932	D	0	-13.693	8.0717	0.30693	0.9073:0.0:0.0927:0.0	.	97	P63272	SPT4H_HUMAN	N	97	.	ENSP00000225504:I97N	I	-	2	0	SUPT4H1	53778670	1.000000	0.71417	0.933000	0.37362	0.857000	0.48899	8.102000	0.89548	0.907000	0.36646	-0.361000	0.07541	ATC	.	.		0.498	SUPT4H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444000.1	NM_003168		T	56423671	A	T	56423671	3	4	141	1	0	0	0	0	1	0	0	0	15413	333	12	4	67	4	SUPT4H1	17	56423671	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	10227250	56423671	24771539	111	22008										
AMZ2	51321	hgsc.bcm.edu	37	chr17	66252013	66252013	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cttcagcattgtagaaagatAcaaagtaagttggggggtgg	14	4	1	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr17:66252013A>G	ENST00000359904.3	+	6	2055	c.923A>G	c.(922-924)tAc>tGc	p.Y308C	AMZ2_ENST00000580753.1_Missense_Mutation_p.Y308C|AMZ2_ENST00000577273.1_Intron|AMZ2_ENST00000585050.1_Intron|AMZ2_ENST00000392720.2_Missense_Mutation_p.Y308C|AMZ2_ENST00000577985.1_Missense_Mutation_p.Y308C|AMZ2_ENST00000359783.4_Missense_Mutation_p.Y250C|AMZ2_ENST00000577866.1_Missense_Mutation_p.Y308C	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	308							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			GTAGAAAGATACAAAGTAAGT	0.443																																					p.Y308C		Atlas-SNP	.											.	AMZ2	15	.	0			c.A923G						.						40	41	40					17																	66252013		2203	4300	6503	SO:0001583	missense	51321	exon7			AAAGATACAAAGT	CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"archaemetzincin-2"	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.923A>G	chr17.hg19:g.66252013A>G	ENSP00000352976:p.Tyr308Cys	49.0	0.0		42.0	10.0	NM_001033572	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Missense_Mutation	SNP	ENST00000359904.3	hg19	CCDS11674.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.044477	0.55110	.	.	ENSG00000196704	ENST00000359904;ENST00000359783;ENST00000392720	T;T;T	0.45668	0.89;0.89;0.89	3.64	3.64	0.41730	.	0.198641	0.33457	N	0.004899	T	0.59266	0.2181	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.87578	0.819;0.998	T	0.61983	-0.6950	10	0.59425	D	0.04	-1.9359	10.8589	0.46815	1.0:0.0:0.0:0.0	.	250;308	A6NLD9;Q86W34	.;AMZ2_HUMAN	C	308;250;308	ENSP00000352976:Y308C;ENSP00000352831:Y250C;ENSP00000376481:Y308C	ENSP00000352831:Y250C	Y	+	2	0	AMZ2	63763608	1.000000	0.71417	0.997000	0.53966	0.677000	0.39632	5.851000	0.69481	1.873000	0.54277	0.383000	0.25322	TAC	.	.		0.443	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627		G	66252013	A	G	66252013	3	3	141	1	0	0	0	0	1	0	0	0	597	391	14	2	941	2	AMZ2	17	66252013	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	9828342	66252013	14943197	112	22009										
FASN	2194	hgsc.bcm.edu	37	chr17	80039092	80039092	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgcagtttccggagcgtgagTtgccgcacctcgcgcacgga	14	13	0	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr17:80039092T>C	ENST00000306749.2	-	38	6761	c.6543A>G	c.(6541-6543)caA>caG	p.Q2181Q	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2181					acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GGAGCGTGAGTTGCCGCACCT	0.697																																					p.Q2181Q	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.A6543G						.						26	23	24					17																	80039092		2190	4279	6469	SO:0001819	synonymous_variant	2194	exon38			CGTGAGTTGCCGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6543A>G	chr17.hg19:g.80039092T>C		63.0	0.0		75.0	16.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.697	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		C	80039092	T	C	80039092	2	2	141	1	0	0	0	0	0	0	0	1	5691	1722	60	2		2	FASN	17	80039092	Silent	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	13787079	80039092	1156118	113	22010										
ATP8B3	148229	hgsc.bcm.edu	37	chr19	1796715	1796715	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ggtgggtgggcgcacctgggCgctcacgggggctctcccgc	19	14	2	0	rs371318224		TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr19:1796715C>T	ENST00000310127.6	-	16	1986	c.1748G>A	c.(1747-1749)cGc>cAc	p.R583H	ATP8B3_ENST00000539485.1_Missense_Mutation_p.R583H|ATP8B3_ENST00000525591.1_Missense_Mutation_p.R536H	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	583					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGCACCTGGGCGCTCACGGGG	0.731																																					p.R583H		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G1748A						.	C	HIS/ARG,HIS/ARG	0,4026		0,0,2013	20	25	24		1607,1748	1.5	0	19		24	1,8287		0,1,4143	no	missense,missense	ATP8B3	NM_001178002.1,NM_138813.2	29,29	0,1,6156	TT,TC,CC		0.0121,0.0,0.0081	benign,benign	536/1264,583/1301	1796715	1,12313	2013	4144	6157	SO:0001583	missense	148229	exon16			CCTGGGCGCTCAC	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"ATPases / P-type"	13535	protein-coding gene	gene with protein product	"aminophospholipid translocase ATP8B3", "potential phospholipid-transporting ATPase IK"	605866	"ATPase, Class I, type 8B, member 3", "ATPase, class I, type 8B, member 3"			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.1748G>A	chr19.hg19:g.1796715C>T	ENSP00000311336:p.Arg583His	87.0	0.0		83.0	18.0	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	hg19	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.639464	0.29157	0.0	1.21E-4	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.63255	-0.03;-0.03;-0.03	3.63	1.46	0.22682	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	2.449250	0.02963	N	0.143364	T	0.41766	0.1173	N	0.04508	-0.205	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.30031	-0.9992	10	0.36615	T	0.2	.	8.057	0.30610	0.0:0.7922:0.0:0.2078	.	583;536	O60423;Q7Z485	AT8B3_HUMAN;.	H	583;583;536	ENSP00000311336:R583H;ENSP00000443574:R583H;ENSP00000437115:R536H	ENSP00000311336:R583H	R	-	2	0	ATP8B3	1747715	0.887000	0.30362	0.021000	0.16686	0.010000	0.07245	0.470000	0.22084	0.243000	0.21327	-0.291000	0.09656	CGC	.	.		0.731	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		T	1796715	C	T	1796715	3	4	141	1	0	0	0	0	1	0	0	0	1196	768	27	1	2240	1	ATP8B3	19	1796715	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10		1796715	57332268	114	22011										
ADAMTS10	81794	hgsc.bcm.edu	37	chr19	8651245	8651245	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	caccgcctgcacactgggccGagcacttggtccagggcgca	13	16	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr19:8651245G>C	ENST00000597188.1	-	21	2783	c.2513C>G	c.(2512-2514)tCg>tGg	p.S838W	ADAMTS10_ENST00000595838.1_Missense_Mutation_p.S325W|ADAMTS10_ENST00000270328.4_Missense_Mutation_p.S838W	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	838	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						ACACTGGGCCGAGCACTTGGT	0.692											OREG0025221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S838W		Atlas-SNP	.											.	ADAMTS10	132	.	0			c.C2513G						.						17	20	19					19																	8651245		2191	4286	6477	SO:0001583	missense	81794	exon21			TGGGCCGAGCACT	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"ADAM metallopeptidases with thrombospondin type 1 motif"	13201	protein-coding gene	gene with protein product		608990	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.2513C>G	chr19.hg19:g.8651245G>C	ENSP00000471851:p.Ser838Trp	122.0	0.0	81	144.0	39.0	NM_030957	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	hg19	CCDS12206.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239168	0.79800	.	.	ENSG00000142303	ENST00000270328;ENST00000393912	T	0.69926	-0.44	4.64	4.64	0.57946	.	0.000000	0.64402	U	0.000004	D	0.87865	0.6285	H	0.96633	3.855	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.996	D	0.92340	0.5881	10	0.87932	D	0	.	16.503	0.84262	0.0:0.0:1.0:0.0	.	592;838;325	Q59FE5;Q9H324;E9PCI6	.;ATS10_HUMAN;.	W	838;592	ENSP00000270328:S838W	ENSP00000270328:S838W	S	-	2	0	ADAMTS10	8557245	1.000000	0.71417	0.928000	0.36995	0.926000	0.56050	8.982000	0.93471	2.117000	0.64856	0.561000	0.74099	TCG	.	.		0.692	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957		C	8651245	G	C	8651245	3	2	141	1	0	0	0	0	1	0	0	0	256	1059	37	4	822	4	ADAMTS10	19	8651245	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	6854530	8651245	50477738	115	22012										
MAST3	23031	hgsc.bcm.edu	37	chr19	18255828	18255828	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgcagatgatggcagcggcgGccccctcatgagcccccttt	12	15	1	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr19:18255828G>C	ENST00000262811.6	+	23	2741	c.2741G>C	c.(2740-2742)gGc>gCc	p.G914A	AC007192.6_ENST00000600364.2_RNA	NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	914	Ser-rich.						ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						GGCAGCGGCGGCCCCCTCATG	0.687																																					p.G914A		Atlas-SNP	.											.	MAST3	83	.	0			c.G2741C						.						16	23	21					19																	18255828		1920	4113	6033	SO:0001583	missense	23031	exon23			GCGGCGGCCCCCT	AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.2741G>C	chr19.hg19:g.18255828G>C	ENSP00000262811:p.Gly914Ala	41.0	0.0		51.0	5.0	NM_015016	Q7LDZ8|Q9UPI0	Missense_Mutation	SNP	ENST00000262811.6	hg19	CCDS46014.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.584252	0.46110	.	.	ENSG00000099308	ENST00000262811	T	0.65732	-0.17	4.48	4.48	0.54585	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.69851	0.3157	M	0.67953	2.075	0.34127	D	0.664846	D	0.60160	0.987	P	0.54401	0.751	T	0.75698	-0.3227	10	0.21014	T	0.42	-33.24	16.1214	0.81359	0.0:0.0:1.0:0.0	.	914	O60307	MAST3_HUMAN	A	914	ENSP00000262811:G914A	ENSP00000262811:G914A	G	+	2	0	MAST3	18116828	1.000000	0.71417	0.997000	0.53966	0.559000	0.35586	4.891000	0.63185	2.060000	0.61445	0.313000	0.20887	GGC	.	.		0.687	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150		C	18255828	G	C	18255828	3	2	141	1	0	0	0	0	1	0	0	0	9335	1203	42	4	2831	4	MAST3	19	18255828	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	9604583	18255828	40873155	116	22013										
ZFP14	57677	hgsc.bcm.edu	37	chr19	36831783	36831783	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	acgaaggctttcccacattcCttacattcatagagcttttc	5	12	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr19:36831783C>T	ENST00000270001.7	-	5	1060	c.945G>A	c.(943-945)aaG>aaA	p.K315K		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					TCCCACATTCCTTACATTCAT	0.418																																					p.K315K		Atlas-SNP	.											.	ZFP14	68	.	0			c.G945A						.						97	99	99					19																	36831783		2203	4300	6503	SO:0001819	synonymous_variant	57677	exon5			ACATTCCTTACAT	AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"Zinc fingers, C2H2-type", "-"	29312	protein-coding gene	gene with protein product			"zinc finger protein 14 homolog (mouse)"			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.945G>A	chr19.hg19:g.36831783C>T		76.0	0.0		68.0	16.0	NM_020917	A7MD23	Silent	SNP	ENST00000270001.7	hg19	CCDS33002.1																																																																																			.	.		0.418	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		T	36831783	C	T	36831783	2	4	141	1	0	0	0	0	0	0	0	1	17654	680	24	3		3	ZFP14	19	36831783	Silent	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	18575955	36831783	22297200	117	22014										
BCL3	602	hgsc.bcm.edu	37	chr19	45260419	45260419	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ccgcagcccgacctgcctgcGagccctgctggacagcgcag	13	18	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr19:45260419G>A	ENST00000164227.5	+	4	909	c.665G>A	c.(664-666)cGa>cAa	p.R222Q		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	222					antimicrobial humoral response (GO:0019730)|cellular response to DNA damage stimulus (GO:0006974)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|protein import into nucleus, translocation (GO:0000060)|regulation of apoptotic process (GO:0042981)|regulation of DNA binding (GO:0051101)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to UV-C (GO:0010225)|response to virus (GO:0009615)|spleen development (GO:0048536)|T-helper 1 type immune response (GO:0042088)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	Bcl3-Bcl10 complex (GO:0032996)|Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)				ACCTGCCTGCGAGCCCTGCTG	0.701			T	IGH@	CLL																																p.R222Q		Atlas-SNP	.		Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	.	BCL3	28	.	0			c.G665A						.						9	8	8					19																	45260419		2159	4205	6364	SO:0001583	missense	602	exon4			GCCTGCGAGCCCT	M31732	CCDS12642.2	19q13.1-q13.2	2013-01-10			ENSG00000069399	ENSG00000069399		"Ankyrin repeat domain containing"	998	protein-coding gene	gene with protein product	"B-cell lymphoma 3-encoded protein", "B-cell leukemia/lymphoma 3", "chronic lymphatic leukemia protein"	109560		D19S37, BCL4		1501714, 2180580	Standard	NM_005178		Approved		uc010xxe.2	P20749	OTTHUMG00000151517	ENST00000164227.5:c.665G>A	chr19.hg19:g.45260419G>A	ENSP00000164227:p.Arg222Gln	39.0	0.0		49.0	5.0	NM_005178		Missense_Mutation	SNP	ENST00000164227.5	hg19	CCDS12642.2	.	.	.	.	.	.	.	.	.	.	G	14.51	2.557557	0.45590	.	.	ENSG00000069399	ENST00000403534;ENST00000164227	T	0.64991	-0.13	4.95	2.81	0.32909	Ankyrin repeat-containing domain (3);	0.198772	0.24980	N	0.034076	T	0.38719	0.1051	N	0.12182	0.205	0.25978	N	0.982419	B	0.21452	0.056	B	0.04013	0.001	T	0.25606	-1.0127	10	0.52906	T	0.07	0.0902	6.5726	0.22547	0.3004:0.0:0.6996:0.0	.	222	P20749	BCL3_HUMAN	Q	182;222	ENSP00000164227:R222Q	ENSP00000164227:R222Q	R	+	2	0	BCL3	49952259	0.995000	0.38212	1.000000	0.80357	0.802000	0.45316	1.953000	0.40352	0.481000	0.27557	0.305000	0.20034	CGA	.	.		0.701	BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1	NM_005178		A	45260419	G	A	45260419	3	1	141	1	0	0	0	0	1	0	0	0	1375	1058	37	1	679	1	BCL3	19	45260419	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	8428636	45260419	13868564	118	22015										
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48945414	48945414	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cgcccctccctagatgagatCgagatgctggagcggctgtg	14	12	0	3			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr19:48945414C>T	ENST00000263269.3	+	12	2536	c.2448C>T	c.(2446-2448)atC>atT	p.I816I		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	816					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.I816I(1)		autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TAGATGAGATCGAGATGCTGG	0.557																																					p.I816I		Atlas-SNP	.											GRIN2D,colon,carcinoma,0,1	GRIN2D	76	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2448T						.						106	105	105					19																	48945414		2203	4300	6503	SO:0001819	synonymous_variant	2906	exon12			TGAGATCGAGATG	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2448C>T	chr19.hg19:g.48945414C>T		58.0	0.0		46.0	9.0	NM_000836		Silent	SNP	ENST00000263269.3	hg19	CCDS12719.1																																																																																			.	.		0.557	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			T	48945414	C	T	48945414	2	4	141	1	0	0	0	0	0	0	0	1	6791	874	31	1		1	GRIN2D	19	48945414	Silent	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	3684995	48945414	10183569	119	22016										
MYBPC2	4606	hgsc.bcm.edu	37	chr19	50958840	50958840	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	accacactcaagtggaggccTccgaacaggatcggggcagg	14	12	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr19:50958840T>C	ENST00000357701.5	+	20	2328	c.2277T>C	c.(2275-2277)ccT>ccC	p.P759P		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	759	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		AGTGGAGGCCTCCGAACAGGA	0.592																																					p.P759P		Atlas-SNP	.											.	MYBPC2	103	.	0			c.T2277C						.						87	91	90					19																	50958840		2018	4186	6204	SO:0001819	synonymous_variant	4606	exon20			GAGGCCTCCGAAC		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7550	protein-coding gene	gene with protein product	"fast-type muscle myosin-binding-protein C"	160793	"myosin-binding protein C, fast-type"			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.2277T>C	chr19.hg19:g.50958840T>C		60.0	0.0		56.0	7.0	NM_004533	A1L4G9	Silent	SNP	ENST00000357701.5	hg19	CCDS46152.1																																																																																			.	.		0.592	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533		C	50958840	T	C	50958840	2	2	141	1	0	0	0	0	0	0	0	1	10021	1538	54	2		2	MYBPC2	19	50958840	Silent	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	2013426	50958840	8170143	120	22017										
VPS16	64601	hgsc.bcm.edu	37	chr20	2842263	2842265	+	Missense_Mutation	TNP	GCA	GCA	TTT													0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgtatatgctgctcacaggtGcagccgtcctcgtagcaagg							TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G|C|A	G|C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr20:2842263_2842265GCA>TTT	ENST00000380445.3	+	9	884_886	c.812_814GCA>TTT	c.(811-816)tGCAgc>tTTTgc	p.271_272CS>FC	VPS16_ENST00000380443.3_5'Flank|VPS16_ENST00000481812.2_3'UTR|VPS16_ENST00000380469.3_Missense_Mutation_p.271_272CS>FC|PTPRA_ENST00000380393.3_5'Flank	NM_022575.2	NP_072097.2	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 homolog (S. cerevisiae)	271					intracellular protein transport (GO:0006886)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|axon (GO:0030424)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	37						GCTCACAGGTGCAGCCGTCCTCG	0.591																																					p.C271F|p.C271C|p.S272C		Atlas-SNP	.											.	VPS16	76	.	0			c.G812T|c.C813T|c.A814T						.																																			SO:0001583	missense	64601	exon9			ACAGGTGCAGCCG|CAGGTGCAGCCGT|AGGTGCAGCCGTC	AF308801	CCDS13036.1, CCDS13037.1	20p13	2009-07-07	2009-07-07	2009-07-07	ENSG00000215305	ENSG00000215305			14584	protein-coding gene	gene with protein product		608550					Standard	NM_022575		Approved		uc002whe.3	Q9H269	OTTHUMG00000031714	ENST00000380445.3:c.812_814GCA>TTT	chr20.hg19:g.2842263GCA>TTT	ENSP00000369810:p.C271_S272delinsFC	36.0|37.0|37.0	0.0		23.0|22.0|25.0	7.0	NM_022575	Q5JUB1|Q8WU31|Q96EE7|Q96N92|Q9H1Q4|Q9H1Q5	Missense_Mutation|Silent|Missense_Mutation	SNP	ENST00000380445.3	hg19	CCDS13036.1																																																																																			.	.		0.591	VPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077658.2	NM_022575		TTT	2842265	GCA	TTT	2842263	3	4	141	1	0	0	0	0	1	0	0	0	17208	1319	46	3	846	3	VPS16	20	2842263	Missense_Mutation	TNP	GCA	TCGA-DD-A4NV-01A-11D-A30V-10		2842263	60183257	121	22018										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41459179	41459179	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	gtctttcatccatggagtagTcactgtcccactgaaggtca	9	11	4	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr21:41459179T>A	ENST00000400454.1	-	22	4363	c.3886A>T	c.(3886-3888)Act>Tct	p.T1296S		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1296	Ig-like C2-type 10.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CATGGAGTAGTCACTGTCCCA	0.488																																					p.T1296S	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.A3886T						.						150	145	147					21																	41459179		2004	4169	6173	SO:0001583	missense	1826	exon22			GAGTAGTCACTGT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.3886A>T	chr21.hg19:g.41459179T>A	ENSP00000383303:p.Thr1296Ser	82.0	0.0		90.0	14.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.074264	0.76415	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.28255	1.62;1.62	4.71	4.71	0.59529	Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.43411	0.1246	L	0.35854	1.095	0.36078	D	0.842614	D	0.76494	0.999	D	0.69654	0.965	T	0.50734	-0.8793	10	0.37606	T	0.19	.	14.5076	0.67762	0.0:0.0:0.0:1.0	.	1296	O60469	DSCAM_HUMAN	S	1296;1048	ENSP00000383303:T1296S;ENSP00000385342:T1048S	ENSP00000383303:T1296S	T	-	1	0	DSCAM	40381049	1.000000	0.71417	0.975000	0.42487	0.988000	0.76386	5.963000	0.70372	1.879000	0.54435	0.460000	0.39030	ACT	.	.		0.488	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41459179	T	A	41459179	3	1	141	1	0	0	0	0	1	0	0	0	4770	1667	58	4	2200	4	DSCAM	21	41459179	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10		41459179	6670716	122	22019										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41684133	41684133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	agctcgtgaagtcaatattgTcaatggtcaccccaaggctc	9	11	3	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr21:41684133T>C	ENST00000400454.1	-	9	2414	c.1937A>G	c.(1936-1938)gAc>gGc	p.D646G		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	646	Ig-like C2-type 7.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GTCAATATTGTCAATGGTCAC	0.552																																					p.D646G	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.A1937G						.						78	79	78					21																	41684133		1919	4145	6064	SO:0001583	missense	1826	exon9			ATATTGTCAATGG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.1937A>G	chr21.hg19:g.41684133T>C	ENSP00000383303:p.Asp646Gly	137.0	0.0		135.0	36.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.546234	0.86022	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.68025	-0.3;-0.3	5.55	5.55	0.83447	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.73760	0.3628	L	0.39020	1.185	0.58432	D	0.999995	D	0.76494	0.999	D	0.85130	0.997	T	0.70630	-0.4819	10	0.25751	T	0.34	.	15.6935	0.77473	0.0:0.0:0.0:1.0	.	646	O60469	DSCAM_HUMAN	G	646;398	ENSP00000383303:D646G;ENSP00000385342:D398G	ENSP00000383303:D646G	D	-	2	0	DSCAM	40606003	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.937000	0.87672	2.098000	0.63641	0.460000	0.39030	GAC	.	.		0.552	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		C	41684133	T	C	41684133	3	2	141	1	0	0	0	0	1	0	0	0	4770	1667	58	2	4201	2	DSCAM	21	41684133	Missense_Mutation	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	224954	41684133	6445762	123	22020										
SFI1	9814	hgsc.bcm.edu	37	chr22	32007130	32007130	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgacttggatctgccttaggCtgtctgcggacctggtttca	12	10	3	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr22:32007130C>T	ENST00000400288.2	+	23	2361	c.2256C>T	c.(2254-2256)ggC>ggT	p.G752G	SFI1_ENST00000540643.1_Splice_Site_p.G697G|SFI1_ENST00000432498.1_Splice_Site_p.G721G|SFI1_ENST00000400289.1_Splice_Site_p.G670G|SFI1_ENST00000443326.1_Splice_Site_p.G670G|SFI1_ENST00000443011.1_Splice_Site_p.G599G|SFI1_ENST00000414585.1_Splice_Site_p.G599G	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	752					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						CTGCCTTAGGCTGTCTGCGGA	0.577																																					p.G752G		Atlas-SNP	.											SFI1,colon,carcinoma,0,1	SFI1	78	.	0			c.C2256T						.						80	86	84					22																	32007130		2163	4273	6436	SO:0001630	splice_region_variant	9814	exon23			CTTAGGCTGTCTG	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.2255-1C>T	chr22.hg19:g.32007130C>T		92.0	0.0		63.0	14.0	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Silent	SNP	ENST00000400288.2	hg19	CCDS43004.1																																																																																			.	.		0.577	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	Silent	T	32007130	C	T	32007130	5	4	141	1	0	0	0	0	0	0	1	0	14171	811	28	3	2342	3	SFI1	22	32007130	Splice_Site	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10		32007130	19297436	124	22021										
GRAP2	9402	hgsc.bcm.edu	37	chr22	40366916	40366916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cttcccccaacagcgagtgcGgtgggcccgggcgctgtatg	15	14	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chr22:40366916G>A	ENST00000344138.4	+	8	1084	c.821G>A	c.(820-822)cGg>cAg	p.R274Q	GRAP2_ENST00000543252.1_Missense_Mutation_p.R234Q|GRAP2_ENST00000540310.1_Missense_Mutation_p.R208Q|GRAP2_ENST00000399090.2_Missense_Mutation_p.R161Q|GRAP2_ENST00000407075.3_Missense_Mutation_p.R274Q|GRAP2_ENST00000544756.1_Missense_Mutation_p.R202Q	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	274	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						CAGCGAGTGCGGTGGGCCCGG	0.642																																					p.R274Q		Atlas-SNP	.											.	GRAP2	29	.	0			c.G821A						.						40	42	41					22																	40366916		2203	4300	6503	SO:0001583	missense	9402	exon8			GAGTGCGGTGGGC	AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"SH2 domain containing"	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.821G>A	chr22.hg19:g.40366916G>A	ENSP00000339186:p.Arg274Gln	45.0	0.0		41.0	10.0	NM_004810	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	hg19	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.711173	0.68730	.	.	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000544006;ENST00000540310;ENST00000544756;ENST00000399090;ENST00000407075	T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55	5.38	5.38	0.77491	Src homology-3 domain (4);	0.744037	0.13093	N	0.414356	T	0.33235	0.0856	N	0.25426	0.745	0.29898	N	0.824618	P;D;D;D;D	0.71674	0.861;0.998;0.971;0.994;0.998	B;P;P;P;P	0.54140	0.073;0.743;0.725;0.557;0.743	T	0.04495	-1.0947	10	0.13853	T	0.58	-35.3168	14.9114	0.70761	0.0:0.0:0.8479:0.1521	.	161;274;208;248;274	B7Z8I3;Q6FI14;F5H548;B7Z8F8;O75791	.;.;.;.;GRAP2_HUMAN	Q	274;234;248;208;202;161;274	ENSP00000339186:R274Q;ENSP00000446350:R234Q;ENSP00000444734:R208Q;ENSP00000442195:R202Q;ENSP00000382040:R161Q;ENSP00000385607:R274Q	ENSP00000339186:R274Q	R	+	2	0	GRAP2	38696862	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	3.098000	0.50259	2.513000	0.84729	0.557000	0.71058	CGG	.	.		0.642	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810		A	40366916	G	A	40366916	3	1	141	1	0	0	0	0	1	0	0	0	6763	1116	39	1	847	1	GRAP2	22	40366916	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	8359786	40366916	10937650	125	22022										
AR	367	hgsc.bcm.edu	37	chrX	66766356	66766356	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	tgtggtggtggtgggggtggTggcggcggcggcggcggcgg	28	6	0	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chrX:66766356T>C	ENST00000374690.3	+	1	1892	c.1368T>C	c.(1366-1368)ggT>ggC	p.G456G	AR_ENST00000504326.1_Silent_p.G456G|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Silent_p.G456G	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	454	Modulating.|Poly-Gly.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	gtgggggtggtggcggcggcg	0.741									Androgen Insensitivity Syndrome																												p.G456G		Atlas-SNP	.											.	AR	249	.	0			c.T1368C						.						1	2	2					X																	66766356		861	1905	2766	SO:0001819	synonymous_variant	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GGGTGGTGGCGGC	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.1368T>C	chrX.hg19:g.66766356T>C		9.0	0.0		31.0	6.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.		0.741	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		C	66766356	T	C	66766356	2	2	141	1	0	0	0	0	0	0	0	1	836	1683	59	2		2	AR	23	66766356	Silent	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10		66766356	88504204	126	22023										
POU3F4	5456	hgsc.bcm.edu	37	chrX	82763684	82763684	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	ccaacgcctggggggccagcCcggcaccgaacccgtctatc	12	18	1	0			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chrX:82763684C>T	ENST00000373200.2	+	1	416	c.352C>T	c.(352-354)Ccg>Tcg	p.P118S	RP3-326L13.3_ENST00000607789.1_lincRNA|RP3-326L13.2_ENST00000607095.1_RNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	118					cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						GGGGGCCAGCCCGGCACCGAA	0.652																																					p.P118S		Atlas-SNP	.											.	POU3F4	136	.	0			c.C352T						.						34	33	33					X																	82763684		2198	4297	6495	SO:0001583	missense	5456	exon1			GCCAGCCCGGCAC	X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"Homeoboxes / POU class"	9217	protein-coding gene	gene with protein product	"brain-4"	300039	"POU domain class 3, transcription factor 4"	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.352C>T	chrX.hg19:g.82763684C>T	ENSP00000362296:p.Pro118Ser	102.0	0.0		151.0	8.0	NM_000307	B2RC71|Q5H9G9|Q99410	Missense_Mutation	SNP	ENST00000373200.2	hg19	CCDS14450.1	.	.	.	.	.	.	.	.	.	.	C	12.26	1.885601	0.33255	.	.	ENSG00000196767	ENST00000373200	D	0.84298	-1.83	5.01	5.01	0.66863	.	0.234157	0.34411	N	0.003984	T	0.71434	0.3339	N	0.08118	0	0.58432	D	0.999993	B	0.22211	0.066	B	0.20184	0.028	T	0.67432	-0.5672	10	0.23891	T	0.37	.	14.9378	0.70970	0.0:1.0:0.0:0.0	.	118	P49335	PO3F4_HUMAN	S	118	ENSP00000362296:P118S	ENSP00000362296:P118S	P	+	1	0	POU3F4	82650340	1.000000	0.71417	0.876000	0.34364	0.674000	0.39518	2.554000	0.45845	2.201000	0.70794	0.525000	0.51046	CCG	.	.		0.652	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		T	82763684	C	T	82763684	3	4	141	1	0	0	0	0	1	0	0	0	12286	623	22	3	354	3	POU3F4	23	82763684	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	15997328	82763684	72506876	127	22024										
DCAF12L1	139170	hgsc.bcm.edu	37	chrX	125685427	125685427	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cgaagaggactccagggtggCggaggctctttcctccagga	15	11	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chrX:125685427C>T	ENST00000371126.1	-	1	1407	c.1165G>A	c.(1165-1167)Gcc>Acc	p.A389T		NM_178470.4	NP_848565.2	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	389										breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(39)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68						TCCAGGGTGGCGGAGGCTCTT	0.582																																					p.A389T		Atlas-SNP	.											.	DCAF12L1	135	.	0			c.G1165A						.						51	53	52					X																	125685427		2203	4300	6503	SO:0001583	missense	139170	exon1			GGGTGGCGGAGGC	BC035674	CCDS14610.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198889	ENSG00000198889		"WD repeat domain containing"	29395	protein-coding gene	gene with protein product			"WD repeat domain 40B"	WDR40B		12477932	Standard	NM_178470		Approved	KIAA1892L	uc004eul.3	Q5VU92	OTTHUMG00000022353	ENST00000371126.1:c.1165G>A	chrX.hg19:g.125685427C>T	ENSP00000360167:p.Ala389Thr	73.0	0.0		94.0	8.0	NM_178470	Q8IYK3	Missense_Mutation	SNP	ENST00000371126.1	hg19	CCDS14610.1	.	.	.	.	.	.	.	.	.	.	C	1.497	-0.552961	0.03996	.	.	ENSG00000198889	ENST00000371126	T	0.17528	2.27	3.47	-2.03	0.07365	.	0.735039	0.11199	N	0.589062	T	0.08537	0.0212	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.39354	-0.9618	10	0.18276	T	0.48	.	3.5022	0.07677	0.1608:0.262:0.4679:0.1093	.	389	Q5VU92	DC121_HUMAN	T	389	ENSP00000360167:A389T	ENSP00000360167:A389T	A	-	1	0	DCAF12L1	125513108	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.532000	0.06164	-0.653000	0.05401	-1.656000	0.00753	GCC	.	.		0.582	DCAF12L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058186.1	NM_178470		T	125685427	C	T	125685427	3	4	141	1	0	0	0	0	1	0	0	0	4266	768	27	1	230	1	DCAF12L1	23	125685427	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	42921743	125685427	29585133	128	22025										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142717871	142717871	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	acttagtcccaaatctgaagGgtgtgttttgcagaagcaag	11	7	1	2			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chrX:142717871G>T	ENST00000381779.4	-	2	1279	c.1054C>A	c.(1054-1056)Cct>Act	p.P352T	SLITRK4_ENST00000338017.4_Missense_Mutation_p.P352T|SLITRK4_ENST00000356928.1_Missense_Mutation_p.P352T	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	352	LRRNT.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					AAATCTGAAGGGTGTGTTTTG	0.463																																					p.P352T		Atlas-SNP	.											.	SLITRK4	162	.	0			c.C1054A						.						117	104	109					X																	142717871		2203	4300	6503	SO:0001583	missense	139065	exon2			CTGAAGGGTGTGT	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.1054C>A	chrX.hg19:g.142717871G>T	ENSP00000371198:p.Pro352Thr	107.0	0.0		106.0	37.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	G	4.472	0.087565	0.08583	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.39997	1.05;1.05;1.05	5.57	5.57	0.84162	Leucine-rich repeat-containing N-terminal (1);	0.058314	0.64402	D	0.000001	T	0.37785	0.1016	L	0.47716	1.5	0.80722	D	1	P	0.37612	0.602	B	0.37239	0.244	T	0.12553	-1.0543	10	0.14252	T	0.57	-5.9646	17.1846	0.86863	0.0:0.0:1.0:0.0	.	352	Q8IW52	SLIK4_HUMAN	T	352	ENSP00000371198:P352T;ENSP00000349400:P352T;ENSP00000336627:P352T	ENSP00000336627:P352T	P	-	1	0	SLITRK4	142545537	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.004000	0.57068	2.466000	0.83321	0.594000	0.82650	CCT	.	.		0.463	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		T	142717871	G	T	142717871	3	4	141	1	0	0	0	0	1	0	0	0	14760	1232	43	3	1463	3	SLITRK4	23	142717871	Missense_Mutation	SNP	G	TCGA-DD-A4NV-01A-11D-A30V-10	17032444	142717871	12552689	129	22026										
PRRG3	79057	hgsc.bcm.edu	37	chrX	150869170	150869170	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cctatgctcagaaccggtacCtagccagtcgcgccgggcac	11	16	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chrX:150869170C>A	ENST00000370353.3	+	4	751	c.361C>A	c.(361-363)Cta>Ata	p.L121I	PRRG3_ENST00000538575.1_Missense_Mutation_p.L121I|PRRG3_ENST00000370354.1_3'UTR			Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	121						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(3)|prostate(2)|skin(3)	24	Acute lymphoblastic leukemia(192;6.56e-05)					GAACCGGTACCTAGCCAGTCG	0.632																																					p.L121I		Atlas-SNP	.											.	PRRG3	74	.	0			c.C361A						.						81	82	82					X																	150869170		2203	4300	6503	SO:0001583	missense	79057	exon4			CGGTACCTAGCCA	AK074574	CCDS14699.1	Xq28	2008-02-05			ENSG00000130032	ENSG00000130032			30798	protein-coding gene	gene with protein product		300685				11171957	Standard	NM_024082		Approved	TMG3	uc022cgt.1	Q9BZD7	OTTHUMG00000024170	ENST00000370353.3:c.361C>A	chrX.hg19:g.150869170C>A	ENSP00000359378:p.Leu121Ile	79.0	0.0		101.0	11.0	NM_024082	A1A523|A1A575|Q8N2N6	Missense_Mutation	SNP	ENST00000370353.3	hg19	CCDS14699.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.581062	0.65992	.	.	ENSG00000130032	ENST00000538575;ENST00000370353	D;D	0.98474	-4.95;-4.95	4.91	3.09	0.35607	.	0.000000	0.64402	D	0.000015	D	0.97529	0.9191	L	0.40543	1.245	0.37655	D	0.922546	D	0.76494	0.999	D	0.78314	0.991	D	0.96110	0.9076	10	0.23302	T	0.38	-9.5887	9.5138	0.39093	0.0:0.8048:0.0:0.1952	.	121	Q9BZD7	TMG3_HUMAN	I	121	ENSP00000440217:L121I;ENSP00000359378:L121I	ENSP00000359378:L121I	L	+	1	2	PRRG3	150619826	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	2.003000	0.40844	0.980000	0.38523	0.529000	0.55759	CTA	.	.		0.632	PRRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060880.1	NM_024082		A	150869170	C	A	150869170	3	1	141	1	0	0	0	0	1	0	0	0	12619	680	24	3	371	3	PRRG3	23	150869170	Missense_Mutation	SNP	C	TCGA-DD-A4NV-01A-11D-A30V-10	8151299	150869170	4401390	130	22027										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153133461	153133461	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cctaggacttacccaccaccAagagctgtgccctactctcc	6	18	1	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chrX:153133461A>G	ENST00000370060.1	-	15	2009	c.1820T>C	c.(1819-1821)tTg>tCg	p.L607S	L1CAM_ENST00000361981.3_Missense_Mutation_p.L602S|L1CAM_ENST00000370057.3_Missense_Mutation_p.L607S|L1CAM_ENST00000370055.1_Missense_Mutation_p.L602S|L1CAM_ENST00000361699.4_Missense_Mutation_p.L607S|L1CAM_ENST00000538883.1_Missense_Mutation_p.L609S|L1CAM_ENST00000543994.1_Missense_Mutation_p.L609S	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	607	Ig-like C2-type 6.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACCCACCACCAAGAGCTGTGC	0.637																																					p.L607S		Atlas-SNP	.											.	L1CAM	189	.	0			c.T1820C						.						75	65	68					X																	153133461		2203	4300	6503	SO:0001583	missense	3897	exon14			ACCACCAAGAGCT	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.1820T>C	chrX.hg19:g.153133461A>G	ENSP00000359077:p.Leu607Ser	35.0	0.0		43.0	8.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	hg19	CCDS14733.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.34|10.34	1.324014|1.324014	0.24080|0.24080	.|.	.|.	ENSG00000198910|ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699|ENST00000455590	T;T;T;T;T;T;T|.	0.65732|.	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17|.	5.53|5.53	5.53|5.53	0.82687|0.82687	Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.295217|.	0.23811|.	N|.	0.044334|.	T|T	0.40196|0.40196	0.1107|0.1107	N|N	0.21194|0.21194	0.64|0.64	0.33199|0.33199	D|D	0.55193|0.55193	B;P;B|.	0.35139|.	0.078;0.486;0.096|.	B;B;B|.	0.37239|.	0.031;0.244;0.052|.	T|T	0.52764|0.52764	-0.8532|-0.8532	10|5	0.37606|.	T|.	0.19|.	.|.	12.492|12.492	0.55905|0.55905	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	602;607;607|.	G3XAF4;P32004-2;P32004|.	.;.;L1CAM_HUMAN|.	S|R	607;609;607;609;602;602;607|65	ENSP00000359077:L607S;ENSP00000438430:L609S;ENSP00000359074:L607S;ENSP00000439645:L609S;ENSP00000354712:L602S;ENSP00000359072:L602S;ENSP00000355380:L607S|.	ENSP00000355380:L607S|.	L|W	-|-	2|1	0|0	L1CAM|L1CAM	152786655|152786655	0.010000|0.010000	0.17322|0.17322	0.937000|0.937000	0.37676|0.37676	0.874000|0.874000	0.50279|0.50279	0.728000|0.728000	0.26013|0.26013	1.856000|1.856000	0.53863|0.53863	0.430000|0.430000	0.28490|0.28490	TTG|TGG	.	.		0.637	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		G	153133461	A	G	153133461	3	3	141	1	0	0	0	0	1	0	0	0	8597	131	5	2	2013	2	L1CAM	23	153133461	Missense_Mutation	SNP	A	TCGA-DD-A4NV-01A-11D-A30V-10	2264291	153133461	2137099	131	22028										
F8	2157	hgsc.bcm.edu	37	chrX	154158630	154158630	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	8	1	1.30146341463415	2.32404181184669	0.903794037940379	1	1	0	cctaaggatactaattgcttTggactggggccttgcccaga	11	10	0	1			TCGA-DD-A4NV-01A-11D-A30V-10	TCGA-DD-A4NV-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3e5656c7-1284-4d60-92d5-12b88c3cb840	812b8551-4906-486e-84de-08451638352a	g.chrX:154158630T>C	ENST00000360256.4	-	14	3635	c.3435A>G	c.(3433-3435)ccA>ccG	p.P1145P		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1145	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CTAATTGCTTTGGACTGGGGC	0.413																																					p.P1145P		Atlas-SNP	.											.	F8	646	.	0			c.A3435G						.						65	69	67					X																	154158630		2201	4297	6498	SO:0001819	synonymous_variant	2157	exon14			TTGCTTTGGACTG	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3435A>G	chrX.hg19:g.154158630T>C		94.0	0.0		127.0	18.0	NM_000132	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	hg19	CCDS35457.1																																																																																			.	.		0.413	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			C	154158630	T	C	154158630	2	2	141	1	0	0	0	0	0	0	0	1	5352	1799	63	2		2	F8	23	154158630	Silent	SNP	T	TCGA-DD-A4NV-01A-11D-A30V-10	1025169	154158630	1111930	132	22029										
CELA3B	23436	hgsc.bcm.edu	37	chr1	22310306	22310306	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gacaccctgctacatcaccgGctggggccgtctctatagta	10	14	2	0	rs201377315		TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr1:22310306G>T	ENST00000337107.6	+	5	501	c.482G>T	c.(481-483)gGc>gTc	p.G161V		NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	161	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			breast(2)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						TACATCACCGGCTGGGGCCGT	0.617																																					p.G161V		Atlas-SNP	.											.	CELA3B	24	.	0			c.G482T						.						94	77	82					1																	22310306		2203	4300	6503	SO:0001583	missense	23436	exon5			TCACCGGCTGGGG	M18692	CCDS219.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000219073	ENSG00000219073	3.4.21.70		15945	protein-coding gene	gene with protein product	"proteinase E", "elastase 1", "cholesterol-binding pancreatic protease", "pancreatic endopeptidase E"		"elastase 3B, pancreatic"	ELA3B		2826474, 2460440	Standard	NM_007352		Approved	CBPP	uc001bfk.3	P08861	OTTHUMG00000002758	ENST00000337107.6:c.482G>T	chr1.hg19:g.22310306G>T	ENSP00000338369:p.Gly161Val	426.0	0.0		427.0	140.0	NM_007352	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	Missense_Mutation	SNP	ENST00000337107.6	hg19	CCDS219.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.332360	0.81801	.	.	ENSG00000219073	ENST00000337107;ENST00000400277	T;T	0.72615	-0.67;-0.67	4.56	4.56	0.56223	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.056662	0.64402	N	0.000001	D	0.90985	0.7165	H	0.99600	4.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94736	0.7914	10	0.87932	D	0	-57.6144	15.161	0.72785	0.0:0.0:1.0:0.0	.	161	P08861	CEL3B_HUMAN	V	161;64	ENSP00000338369:G161V;ENSP00000383135:G64V	ENSP00000338369:G161V	G	+	2	0	CELA3B	22182893	1.000000	0.71417	0.993000	0.49108	0.928000	0.56348	9.429000	0.97481	2.246000	0.74042	0.555000	0.69702	GGC	.	.		0.617	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007797.1	NM_007352		T	22310306	G	T	22310306	3	4	142	1	0	0	0	0	1	0	0	0	3216	1203	42	3	500	3	CELA3B	1	22310306	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10		22310306	226940315	1	22030										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35852656	35852656	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ttcagtagtgcccttgtctcAgggccaagtaattgtaagca	10	9	2	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr1:35852656A>G	ENST00000314607.6	+	12	1969	c.1889A>G	c.(1888-1890)cAg>cGg	p.Q630R	ZMYM4_ENST00000373297.2_Missense_Mutation_p.Q541R	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	630					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CCCTTGTCTCAGGGCCAAGTA	0.423																																					p.Q630R		Atlas-SNP	.											.	ZMYM4	143	.	0			c.A1889G						.						65	58	61					1																	35852656		2203	4300	6503	SO:0001583	missense	9202	exon12			TGTCTCAGGGCCA	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.1889A>G	chr1.hg19:g.35852656A>G	ENSP00000322915:p.Gln630Arg	78.0	0.0		59.0	21.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	hg19	CCDS389.1	.	.	.	.	.	.	.	.	.	.	A	15.68	2.906433	0.52333	.	.	ENSG00000146463	ENST00000314607;ENST00000373297	T;T	0.25250	1.81;1.89	5.81	5.81	0.92471	.	0.119831	0.56097	D	0.000025	T	0.29620	0.0739	M	0.73962	2.25	0.46654	D	0.999148	B	0.28880	0.226	B	0.19148	0.024	T	0.07065	-1.0792	10	0.21014	T	0.42	-7.431	16.1637	0.81739	1.0:0.0:0.0:0.0	.	630	Q5VZL5	ZMYM4_HUMAN	R	630;541	ENSP00000322915:Q630R;ENSP00000362394:Q541R	ENSP00000322915:Q630R	Q	+	2	0	ZMYM4	35625243	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.660000	0.74417	2.216000	0.71823	0.533000	0.62120	CAG	.	.		0.423	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		G	35852656	A	G	35852656	3	3	142	1	0	0	0	0	1	0	0	0	17717	188	7	2	1935	2	ZMYM4	1	35852656	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	13542350	35852656	213397965	2	22031										
GPR61	83873	hgsc.bcm.edu	37	chr1	110086824	110086824	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ggactggctgtccttctgagTcctgggtttcccgaccccta	11	14	1	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr1:110086824T>C	ENST00000527748.1	+	2	1863	c.1180T>C	c.(1180-1182)Tcc>Ccc	p.S394P	RP5-1160K1.8_ENST00000526411.1_RNA	NM_031936.4	NP_114142.3	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	394						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	23		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)		TCCTTCTGAGTCCTGGGTTTC	0.602																																					p.S394P		Atlas-SNP	.											.	GPR61	60	.	0			c.T1180C						.						37	41	39					1																	110086824		2203	4299	6502	SO:0001583	missense	83873	exon2			TCTGAGTCCTGGG	AF317652	CCDS801.1	1p13.3	2012-08-21			ENSG00000156097	ENSG00000156097		"GPCR / Class A : Orphans"	13300	protein-coding gene	gene with protein product		606916				11165367, 11690637	Standard	NM_031936		Approved	BALGR	uc001dxy.2	Q9BZJ8	OTTHUMG00000011633	ENST00000527748.1:c.1180T>C	chr1.hg19:g.110086824T>C	ENSP00000432456:p.Ser394Pro	66.0	0.0		92.0	26.0	NM_031936	A8K1W2|Q6NWS0|Q8TDV4|Q96PR4	Missense_Mutation	SNP	ENST00000527748.1	hg19	CCDS801.1	.	.	.	.	.	.	.	.	.	.	T	7.885	0.731059	0.15507	.	.	ENSG00000156097	ENST00000527748;ENST00000286603	T	0.70045	-0.45	5.2	2.84	0.33178	.	0.211592	0.41194	D	0.000924	T	0.13543	0.0328	N	0.01874	-0.695	0.31276	N	0.691132	B	0.02656	0.0	B	0.01281	0.0	T	0.05225	-1.0898	10	0.38643	T	0.18	-10.8095	0.1371	0.00080	0.2679:0.1814:0.1705:0.3801	.	394	Q9BZJ8	GPR61_HUMAN	P	394;522	ENSP00000432456:S394P	ENSP00000286603:S522P	S	+	1	0	GPR61	109888347	0.994000	0.37717	0.999000	0.59377	0.924000	0.55760	0.355000	0.20163	0.990000	0.38787	0.533000	0.62120	TCC	.	.		0.602	GPR61-005	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385575.1			C	110086824	T	C	110086824	3	2	142	1	0	0	0	0	1	0	0	0	6710	1667	58	2	1182	2	GPR61	1	110086824	Missense_Mutation	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	74234168	110086824	139163797	3	22032										
LAMC2	3918	hgsc.bcm.edu	37	chr1	183184629	183184629	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	acaactccggacggtgcagcTgtaaaccaggtgtgacagga	13	10	0	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr1:183184629T>A	ENST00000264144.4	+	3	375	c.310T>A	c.(310-312)Tgt>Agt	p.C104S	LAMC2_ENST00000493293.1_Missense_Mutation_p.C104S	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	104	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						ACGGTGCAGCTGTAAACCAGG	0.522																																					p.C104S		Atlas-SNP	.											.	LAMC2	113	.	0			c.T310A						.						113	100	105					1																	183184629		2203	4300	6503	SO:0001583	missense	3918	exon3			TGCAGCTGTAAAC	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.310T>A	chr1.hg19:g.183184629T>A	ENSP00000264144:p.Cys104Ser	97.0	0.0		62.0	34.0	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	hg19	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	T	33	5.287600	0.95517	.	.	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	D;D	0.94280	-3.39;-3.39	4.97	4.97	0.65823	EGF-like, laminin (4);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.98197	0.9404	H	0.99777	4.77	0.80722	D	1	D;P	0.58970	0.984;0.702	P;P	0.61275	0.886;0.544	D	0.99078	1.0836	10	0.59425	D	0.04	.	14.6551	0.68828	0.0:0.0:0.0:1.0	.	104;104	Q13753;Q13753-2	LAMC2_HUMAN;.	S	104	ENSP00000432063:C104S;ENSP00000264144:C104S	ENSP00000264144:C104S	C	+	1	0	LAMC2	181451252	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.173000	0.77612	1.881000	0.54492	0.533000	0.62120	TGT	.	.		0.522	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		A	183184629	T	A	183184629	3	1	142	1	0	0	0	0	1	0	0	0	8624	1580	55	4	320	4	LAMC2	1	183184629	Missense_Mutation	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	73097805	183184629	66065992	4	22033										
FAM129A	116496	hgsc.bcm.edu	37	chr1	184787922	184787922	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gccaggaatggctgcacactCtccaagcagcttttctccgc	9	15	2	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr1:184787922C>A	ENST00000367511.3	-	9	1216	c.1023G>T	c.(1021-1023)gaG>gaT	p.E341D	FAM129A_ENST00000487074.1_5'UTR|RNU7-13P_ENST00000516413.1_RNA	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	341					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						GCTGCACACTCTCCAAGCAGC	0.532																																					p.E341D		Atlas-SNP	.											.	FAM129A	98	.	0			c.G1023T						.						131	134	133					1																	184787922		2203	4300	6503	SO:0001583	missense	116496	exon9			CACACTCTCCAAG	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"cell growth inhibiting protein 39"		"chromosome 1 open reading frame 24"	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.1023G>T	chr1.hg19:g.184787922C>A	ENSP00000356481:p.Glu341Asp	104.0	0.0		69.0	35.0	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	hg19	CCDS1364.1	.	.	.	.	.	.	.	.	.	.	C	9.395	1.076604	0.20227	.	.	ENSG00000135842	ENST00000367511	T	0.13196	2.61	5.05	3.13	0.36017	.	0.050867	0.85682	N	0.000000	T	0.14527	0.0351	M	0.64997	1.995	0.40464	D	0.980277	B	0.24043	0.096	B	0.27796	0.083	T	0.04427	-1.0952	10	0.45353	T	0.12	-21.3025	6.6188	0.22792	0.0:0.6535:0.1377:0.2088	.	341	Q9BZQ8	NIBAN_HUMAN	D	341	ENSP00000356481:E341D	ENSP00000356481:E341D	E	-	3	2	FAM129A	183054545	0.627000	0.27129	0.988000	0.46212	0.041000	0.13682	-0.125000	0.10579	0.600000	0.29862	0.557000	0.71058	GAG	.	.		0.532	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			A	184787922	C	A	184787922	3	1	142	1	0	0	0	0	1	0	0	0	5441	912	32	3	1787	3	FAM129A	1	184787922	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	1603293	184787922	64462699	5	22034										
NEK2	4751	hgsc.bcm.edu	37	chr1	211840446	211840446	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ttgaccaagttgattctcatAcctggattacttgccagaga	8	9	1	3			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr1:211840446A>T	ENST00000366999.4	-	7	1250		c.e7+1		NEK2_ENST00000462283.1_Splice_Site|NEK2_ENST00000366998.3_Silent_p.G371G|NEK2_ENST00000540251.1_Splice_Site	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2						blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		TGATTCTCATACCTGGATTAC	0.438																																					p.G371G		Atlas-SNP	.											.	NEK2	49	.	0			c.T1113A						.						82	80	81					1																	211840446		2203	4300	6503	SO:0001630	splice_region_variant	4751	exon7			TCTCATACCTGGA	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"HsPK 21", "protein phosphatase 1, regulatory subunit 111"	604043	"NIMA (never in mitosis gene a)-related kinase 2"			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.1111+1T>A	chr1.hg19:g.211840446A>T		214.0	0.0		241.0	67.0	NM_001204183	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Silent	SNP	ENST00000366999.4	hg19	CCDS1500.1	.	.	.	.	.	.	.	.	.	.	A	18.97	3.735886	0.69189	.	.	ENSG00000117650	ENST00000366999;ENST00000540251	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8954	0.70642	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NEK2	209907069	1.000000	0.71417	0.999000	0.59377	0.841000	0.47740	5.321000	0.65846	2.054000	0.61138	0.528000	0.53228	.	.	.		0.438	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497	Intron	T	211840446	A	T	211840446	5	4	142	1	0	0	0	0	0	0	1	0	10333	405	14	4	232	4	NEK2	1	211840446	Splice_Site	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	27052524	211840446	37410175	6	22035										
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112914	248112914	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tgtagtaactttctactatgCaccttttgtctacacttatc	4	10	2	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr1:248112914C>T	ENST00000357191.3	+	1	755	c.755C>T	c.(754-756)gCa>gTa	p.A252V	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	252						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TTCTACTATGCACCTTTTGTC	0.478																																					p.A252V		Atlas-SNP	.											OR2L8,right_upper_lobe,carcinoma,0,1	OR2L8	92	.	0			c.C755T						.						143	103	116					1																	248112914		2203	4298	6501	SO:0001583	missense	391190	exon1			ACTATGCACCTTT	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.755C>T	chr1.hg19:g.248112914C>T	ENSP00000349719:p.Ala252Val	204.0	0.0		170.0	46.0	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	hg19	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	0.161	-1.081091	0.01888	.	.	ENSG00000196936	ENST00000357191	T	0.35421	1.31	1.8	-0.381	0.12485	GPCR, rhodopsin-like superfamily (1);	0.590255	0.12675	N	0.448469	T	0.12050	0.0293	N	0.01505	-0.83	0.09310	N	1	B	0.12013	0.005	B	0.19666	0.026	T	0.20538	-1.0272	10	0.51188	T	0.08	.	3.7754	0.08657	0.0:0.3475:0.3505:0.302	.	252	Q8NGY9	OR2L8_HUMAN	V	252	ENSP00000349719:A252V	ENSP00000349719:A252V	A	+	2	0	OR2L8	246179537	0.000000	0.05858	0.211000	0.23655	0.010000	0.07245	-0.477000	0.06583	-0.281000	0.09141	-0.443000	0.05667	GCA	.	.		0.478	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			T	248112914	C	T	248112914	3	4	142	1	0	0	0	0	1	0	0	0	11018	710	25	3	757	3	OR2L8	1	248112914	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	36272468	248112914	1137707	7	22036										
CPSF3	51692	hgsc.bcm.edu	37	chr2	9574031	9574031	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tggtgatttctcaagacaagAagataggcacttaatggcag	11	6	1	4			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr2:9574031A>G	ENST00000238112.3	+	6	757	c.551A>G	c.(550-552)gAa>gGa	p.E184G	CPSF3_ENST00000460593.1_Missense_Mutation_p.E147G	NM_016207.3	NP_057291.1	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3, 73kDa	184					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	5'-3' exonuclease activity (GO:0008409)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		TCAAGACAAGAAGATAGGCAC	0.308																																					p.E184G	Colon(194;1259 2048 3845 5218 19985)	Atlas-SNP	.											.	CPSF3	63	.	0			c.A551G						.						90	98	95					2																	9574031		2203	4299	6502	SO:0001583	missense	51692	exon6			GACAAGAAGATAG	AF171877	CCDS1664.1	2p25.1	2009-01-06	2002-08-29		ENSG00000119203	ENSG00000119203			2326	protein-coding gene	gene with protein product		606029	"cleavage and polyadenylation specific factor 3, 73kD subunit"			8929409	Standard	NM_016207		Approved	CPSF-73, CPSF73, YSH1	uc002qzo.2	Q9UKF6	OTTHUMG00000090415	ENST00000238112.3:c.551A>G	chr2.hg19:g.9574031A>G	ENSP00000238112:p.Glu184Gly	343.0	0.0		357.0	107.0	NM_016207	O14769|Q53RS2|Q96F36	Missense_Mutation	SNP	ENST00000238112.3	hg19	CCDS1664.1	.	.	.	.	.	.	.	.	.	.	A	32	5.114925	0.94339	.	.	ENSG00000119203	ENST00000238112;ENST00000427001;ENST00000460593	T;T	0.42131	0.98;0.98	5.72	5.72	0.89469	Beta-lactamase-like (2);	0.000000	0.85682	D	0.000000	T	0.59595	0.2205	L	0.58925	1.835	0.80722	D	1	D;P	0.69078	0.997;0.846	D;D	0.64776	0.916;0.929	T	0.60203	-0.7309	10	0.51188	T	0.08	-11.5964	15.9926	0.80217	1.0:0.0:0.0:0.0	.	184;184	E7ER23;Q9UKF6	.;CPSF3_HUMAN	G	184;184;147	ENSP00000238112:E184G;ENSP00000418957:E147G	ENSP00000238112:E184G	E	+	2	0	CPSF3	9491482	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.307000	0.96226	2.179000	0.69175	0.482000	0.46254	GAA	.	.		0.308	CPSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206843.1	NM_016207		G	9574031	A	G	9574031	3	3	142	1	0	0	0	0	1	0	0	0	3828	246	9	2	573	2	CPSF3	2	9574031	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10		9574031	233625342	8	22037										
THADA	63892	hgsc.bcm.edu	37	chr2	43801892	43801893	+	Frame_Shift_Ins	INS	-	-	AA													0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	agactctcagtcaattccacINSaaagaaaggatcagggacga							TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr2:43801892_43801893insAA	ENST00000405006.4	-	11	1662_1663	c.1311_1312insTT	c.(1309-1314)tttgtgfs	p.V438fs	THADA_ENST00000402360.2_Frame_Shift_Ins_p.V438fs|THADA_ENST00000404790.1_Frame_Shift_Ins_p.V438fs|THADA_ENST00000330266.7_Frame_Shift_Ins_p.V148fs|THADA_ENST00000415080.2_Frame_Shift_Ins_p.V148fs|THADA_ENST00000405975.2_Frame_Shift_Ins_p.V438fs|THADA_ENST00000403856.1_Frame_Shift_Ins_p.V438fs	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	438										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				GTCAATTCCACAAAGAAAGGAT	0.421																																					p.V438fs		Atlas-Indel,Pindel	.											.	THADA	131	.	0			c.1312_1313insTT						.																																			SO:0001589	frameshift_variant	63892	exon11			.	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.1310_1311dupTT	chr2.hg19:g.43801893_43801894dupAA	ENSP00000385995:p.Val438fs	104.0	0.0		96.0	32.0	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Frame_Shift_Ins	INS	ENST00000405006.4	hg19	CCDS46268.1																																																																																			.	.		0.421	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		AA	43801893	-	AA	43801892	7	5	142	1	0	1	1	0	0	0	0	0	15855	478	17	0	4661	0	THADA	2	43801892	Frame_Shift_Ins	INS	-	TCGA-DD-A73A-01A-12D-A32G-10	34227861	43801892	199397481	9	22038										
MGAT5	4249	hgsc.bcm.edu	37	chr2	135206375	135206375	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gagggtctgcccctgccgggActtcatcaagggccaggtgg	16	12	3	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr2:135206375A>T	ENST00000409645.1	+	17	2435	c.2183A>T	c.(2182-2184)gAc>gTc	p.D728V	MGAT5_ENST00000281923.2_Missense_Mutation_p.D728V			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	728					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|pancreas(1)|skin(3)	36				BRCA - Breast invasive adenocarcinoma(221;0.0964)		CCCTGCCGGGACTTCATCAAG	0.607																																					p.D728V		Atlas-SNP	.											.	MGAT5	84	.	0			c.A2183T						.						49	52	51					2																	135206375		2203	4300	6503	SO:0001583	missense	4249	exon16			GCCGGGACTTCAT	D17716	CCDS2171.1	2q21	2013-02-25			ENSG00000152127	ENSG00000152127	2.4.1.155	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7049	protein-coding gene	gene with protein product		601774				8292036	Standard	NM_002410		Approved	GNT-V	uc002ttw.4	Q09328	OTTHUMG00000131681	ENST00000409645.1:c.2183A>T	chr2.hg19:g.135206375A>T	ENSP00000386377:p.Asp728Val	130.0	0.0		126.0	33.0	NM_002410	D3DP70	Missense_Mutation	SNP	ENST00000409645.1	hg19	CCDS2171.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.647197	0.87958	.	.	ENSG00000152127	ENST00000409645;ENST00000281923	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.79293	0.4421	M	0.79475	2.455	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.82524	-0.0414	9	0.87932	D	0	-22.0629	15.088	0.72170	1.0:0.0:0.0:0.0	.	728	Q09328	MGT5A_HUMAN	V	728	.	ENSP00000281923:D728V	D	+	2	0	MGAT5	134922845	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.183000	0.94887	2.041000	0.60428	0.533000	0.62120	GAC	.	.		0.607	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410		T	135206375	A	T	135206375	3	4	142	1	0	0	0	0	1	0	0	0	9557	275	10	4	2245	4	MGAT5	2	135206375	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	91404483	135206375	107992998	10	22039										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189856233	189856233	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ggtgaaaatggtcttccaggCgaaaatggagctcctggacc	13	9	1	1	rs138569287		TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr2:189856233C>T	ENST00000304636.3	+	12	1043	c.873C>T	c.(871-873)ggC>ggT	p.G291G	COL3A1_ENST00000317840.5_Silent_p.G291G	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	291	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	GTCTTCCAGGCGAAAATGGAG	0.299																																					p.G291G		Atlas-SNP	.											COL3A1,NS,carcinoma,0,1	COL3A1	292	.	0			c.C873T						.	C		0,4406		0,0,2203	62	66	65		873	2	1	2	dbSNP_134	65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL3A1	NM_000090.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		291/1467	189856233	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1281	exon12			TCCAGGCGAAAAT	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.873C>T	chr2.hg19:g.189856233C>T		270.0	0.0		256.0	74.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	hg19	CCDS2297.1																																																																																			.	C|1.000;T|0.000		0.299	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		T	189856233	C	T	189856233	2	4	142	1	0	0	0	0	0	0	0	1	3690	755	27	1		1	COL3A1	2	189856233	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	54649858	189856233	53343140	11	22040										
SGOL2	151246	hgsc.bcm.edu	37	chr2	201399894	201399894	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	cgcctaaagctaaataacttGgtatgtaagctatattgttt	7	6	0	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr2:201399894G>C	ENST00000357799.4	+	3	407	c.309G>C	c.(307-309)ttG>ttC	p.L103F	SGOL2_ENST00000469840.1_3'UTR|SGOL2_ENST00000409203.3_Splice_Site_p.L103F	NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	103					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						TAAATAACTTGGTATGTAAGC	0.269																																					p.L103F		Atlas-SNP	.											.	SGOL2	126	.	0			c.G309C						.						72	66	68					2																	201399894		1791	4056	5847	SO:0001630	splice_region_variant	151246	exon3			TAACTTGGTATGT	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.309+1G>C	chr2.hg19:g.201399894G>C		364.0	0.0		335.0	71.0	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	hg19	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	G	19.06	3.753534	0.69648	.	.	ENSG00000163535	ENST00000357799;ENST00000409203	T;T	0.24151	1.87;1.87	5.46	5.46	0.80206	.	0.000000	0.42420	D	0.000708	T	0.51007	0.1649	M	0.66939	2.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	1.0;1.0;1.0;0.998	T	0.51332	-0.8719	10	0.72032	D	0.01	-4.64	17.0919	0.86624	0.0:0.0:1.0:0.0	.	103;103;103;103	B7Z7S9;Q562F6-2;Q562F6;Q562F6-3	.;.;SGOL2_HUMAN;.	F	103	ENSP00000350447:L103F;ENSP00000386249:L103F	ENSP00000350447:L103F	L	+	3	2	SGOL2	201108139	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	6.310000	0.72830	2.572000	0.86782	0.467000	0.42956	TTG	.	.		0.269	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	Missense_Mutation	C	201399894	G	C	201399894	5	2	142	1	0	0	0	0	0	0	1	0	14232	1362	47	4	315	4	SGOL2	2	201399894	Splice_Site	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	11543661	201399894	41799479	12	22041										
PLCD4	84812	hgsc.bcm.edu	37	chr2	219499332	219499332	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	aagcccatcagccctttcaaAgcccagactctcttaatcca	4	16	3	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr2:219499332A>C	ENST00000450993.2	+	13	2214	c.1875A>C	c.(1873-1875)aaA>aaC	p.K625N	PLCD4_ENST00000432688.1_Missense_Mutation_p.K657N|RP11-548H3.1_ENST00000607946.1_RNA|PLCD4_ENST00000417849.1_Missense_Mutation_p.K625N	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	625	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GCCCTTTCAAAGCCCAGACTC	0.507																																					p.K625N		Atlas-SNP	.											.	PLCD4	51	.	0			c.A1875C						.						182	170	174					2																	219499332		1895	4105	6000	SO:0001583	missense	84812	exon13			TTTCAAAGCCCAG	AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"EF-hand domain containing"	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.1875A>C	chr2.hg19:g.219499332A>C	ENSP00000388631:p.Lys625Asn	152.0	0.0		146.0	50.0	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	hg19	CCDS46516.1	.	.	.	.	.	.	.	.	.	.	A	9.967	1.224451	0.22457	.	.	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000417849;ENST00000432688	T;T;T	0.18502	2.24;2.24;2.21	5.19	-0.201	0.13212	C2 membrane targeting protein (1);PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);C2 calcium/lipid-binding domain, CaLB (1);	0.394774	0.28865	N	0.013891	T	0.08313	0.0207	N	0.13168	0.305	0.26698	N	0.971216	B	0.14012	0.009	B	0.12837	0.008	T	0.30534	-0.9975	10	0.27785	T	0.31	.	8.6332	0.33933	0.5598:0.0:0.4402:0.0	.	625	Q9BRC7	PLCD4_HUMAN	N	625;625;625;657	ENSP00000388631:K625N;ENSP00000396942:K625N;ENSP00000396185:K657N	ENSP00000251959:K625N	K	+	3	2	PLCD4	219207576	0.998000	0.40836	0.909000	0.35828	0.900000	0.52787	0.909000	0.28558	0.060000	0.16281	-0.230000	0.12252	AAA	.	.		0.507	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1			C	219499332	A	C	219499332	3	2	142	1	0	0	0	0	1	0	0	0	12042	69	3	5	1921	5	PLCD4	2	219499332	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	18099438	219499332	23700041	13	22042										
HDLBP	3069	hgsc.bcm.edu	37	chr2	242194526	242194526	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ttcttgccaatgatgaaacgGtgaagccaggaaggggcggc	15	8	1	3			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr2:242194526G>C	ENST00000391975.1	-	9	1355	c.1128C>G	c.(1126-1128)caC>caG	p.H376Q	HDLBP_ENST00000427183.2_Missense_Mutation_p.H343Q|HDLBP_ENST00000310931.4_Missense_Mutation_p.H376Q|HDLBP_ENST00000391976.2_Missense_Mutation_p.H376Q	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	376	KH 4. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		TGATGAAACGGTGAAGCCAGG	0.493																																					p.H376Q		Atlas-SNP	.											.	HDLBP	118	.	0			c.C1128G						.						186	200	195					2																	242194526		2203	4300	6503	SO:0001583	missense	3069	exon9			GAAACGGTGAAGC		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.1128C>G	chr2.hg19:g.242194526G>C	ENSP00000375836:p.His376Gln	75.0	0.0		73.0	21.0	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	hg19	CCDS2547.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	19.16|19.16|19.16	3.774071|3.774071|3.774071	0.69992|0.69992|0.69992	.|.|.	.|.|.	ENSG00000115677|ENSG00000115677|ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183|ENST00000373292|ENST00000453141	T;T;T;T|.|.	0.33654|.|.	1.4;1.4;1.4;1.4|.|.	5.93|5.93|5.93	3.17|3.17|3.17	0.36434|0.36434|0.36434	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.73946|0.73946|0.73946	0.3652|0.3652|0.3652	M|M|M	0.86651|0.86651|0.86651	2.83|2.83|2.83	0.80722|0.80722|0.80722	D|D|D	1|1|1	D;D;D|.|.	0.89917|.|.	1.0;1.0;1.0|.|.	D;D;D|.|.	0.97110|.|.	1.0;0.996;1.0|.|.	T|T|T	0.72070|0.72070|0.72070	-0.4401|-0.4401|-0.4401	10|5|5	0.66056|.|.	D|.|.	0.02|.|.	-42.5724|-42.5724|-42.5724	7.7771|7.7771|7.7771	0.29043|0.29043|0.29043	0.4322:0.0:0.5678:0.0|0.4322:0.0:0.5678:0.0|0.4322:0.0:0.5678:0.0	.|.|.	376;343;376|.|.	B2R5V9;E7EM71;Q00341|.|.	.;.;VIGLN_HUMAN|.|.	Q|A|S	376;376;376;343|185|254	ENSP00000375836:H376Q;ENSP00000375837:H376Q;ENSP00000312042:H376Q;ENSP00000399139:H343Q|.|.	ENSP00000312042:H376Q|.|.	H|P|T	-|-|-	3|1|2	2|0|0	HDLBP|HDLBP|HDLBP	241843199|241843199|241843199	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.994000|0.994000|0.994000	0.49952|0.49952|0.49952	0.920000|0.920000|0.920000	0.55202|0.55202|0.55202	0.936000|0.936000|0.936000	0.28938|0.28938|0.28938	0.413000|0.413000|0.413000	0.25759|0.25759|0.25759	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	CAC|CCG|ACC	.	.		0.493	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		C	242194526	G	C	242194526	3	2	142	1	0	0	0	0	1	0	0	0	7034	1252	44	4	2758	4	HDLBP	2	242194526	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	22695194	242194526	1004847	14	22043										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41274910	41274910	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ctgtctttggactctcaggaAtctttcagatgctgcaacta	8	10	4	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr3:41274910A>T	ENST00000349496.5	+	8	1440	c.1160A>T	c.(1159-1161)aAt>aTt	p.N387I	CTNNB1_ENST00000396183.3_Missense_Mutation_p.N387I|CTNNB1_ENST00000396185.3_Missense_Mutation_p.N387I|CTNNB1_ENST00000405570.1_Missense_Mutation_p.N387I|CTNNB1_ENST00000453024.1_Missense_Mutation_p.N380I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	387					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACTCTCAGGAATCTTTCAGAT	0.393		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.N387I	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	0			c.A1160T						.						102	93	96					3																	41274910		2203	4300	6503	SO:0001583	missense	1499	exon8	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TCAGGAATCTTTC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1160A>T	chr3.hg19:g.41274910A>T	ENSP00000344456:p.Asn387Ile	126.0	0.0		152.0	45.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.632816	0.87660	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79	5.72	5.72	0.89469	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.92430	0.7597	M	0.89478	3.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93767	0.7071	10	0.87932	D	0	-10.1444	15.9983	0.80268	1.0:0.0:0.0:0.0	.	315;387	B4DSW9;P35222	.;CTNB1_HUMAN	I	387;387;387;380;387	ENSP00000385604:N387I;ENSP00000379486:N387I;ENSP00000344456:N387I;ENSP00000411226:N380I;ENSP00000379488:N387I	ENSP00000344456:N387I	N	+	2	0	CTNNB1	41249914	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.339000	0.96797	2.171000	0.68590	0.533000	0.62120	AAT	.	.		0.393	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41274910	A	T	41274910	3	4	142	1	0	0	0	0	1	0	0	0	4018	101	4	4	1186	4	CTNNB1	3	41274910	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10		41274910	156747520	15	22044										
CCDC13	152206	hgsc.bcm.edu	37	chr3	42781149	42781149	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gagggcgtcgatgagctcgtCatcatgccggcccttctcca	12	14	3	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr3:42781149C>T	ENST00000310232.6	-	9	1224	c.1141G>A	c.(1141-1143)Gac>Aac	p.D381N	CCDC13-AS1_ENST00000446950.1_RNA|CCDC13-AS1_ENST00000418161.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	381										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						ATGAGCTCGTCATCATGCCGG	0.602																																					p.D381N		Atlas-SNP	.											.	CCDC13	71	.	0			c.G1141A						.						158	135	143					3																	42781149		2203	4300	6503	SO:0001583	missense	152206	exon9			GCTCGTCATCATG	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1141G>A	chr3.hg19:g.42781149C>T	ENSP00000309836:p.Asp381Asn	117.0	0.0		105.0	40.0	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055293	0.75960	.	.	ENSG00000244607	ENST00000310232	T	0.35973	1.28	5.27	5.27	0.74061	.	0.050358	0.85682	D	0.000000	T	0.33177	0.0854	L	0.38692	1.165	0.42629	D	0.993375	P	0.45474	0.859	P	0.46253	0.509	T	0.03443	-1.1036	10	0.29301	T	0.29	.	11.2031	0.48754	0.0:0.9139:0.0:0.0861	.	381	Q8IYE1	CCD13_HUMAN	N	381	ENSP00000309836:D381N	ENSP00000309836:D381N	D	-	1	0	CCDC13	42756153	0.998000	0.40836	0.999000	0.59377	0.952000	0.60782	3.962000	0.56766	2.472000	0.83506	0.561000	0.74099	GAC	.	.		0.602	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		T	42781149	C	T	42781149	3	4	142	1	0	0	0	0	1	0	0	0	2767	826	29	3	1038	3	CCDC13	3	42781149	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	1506239	42781149	155241281	16	22045										
TRAIP	10293	hgsc.bcm.edu	37	chr3	49866583	49866584	+	Frame_Shift_Del	DEL	CT	CT	-													0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ggcctggaagagagaaggcaCtgtcttcaccctcaccctct					rs35129566	byFrequency	TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr3:49866583_49866584delCT	ENST00000331456.2	-	15	1475_1476	c.1362_1363delAG	c.(1360-1365)acagtgfs	p.V455fs		NM_005879.2	NP_005870.2	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	455	Interaction with CYLD.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|receptor signaling protein activity (GO:0005057)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AGAGAAGGCACTGTCTTCACCC	0.54																																					p.455_455del		Atlas-Indel,Pindel	.											.	TRAIP	47	.	0			c.1363_1364del						.																																			SO:0001589	frameshift_variant	10293	exon15			.	BC019283	CCDS2806.1	3p21.31	2013-01-09			ENSG00000183763	ENSG00000183763		"RING-type (C3HC4) zinc fingers"	30764	protein-coding gene	gene with protein product	"ring finger protein 206"	605958				9104814	Standard	NM_005879		Approved	TRIP, RNF206	uc003cxs.1	Q9BWF2	OTTHUMG00000158269	ENST00000331456.2:c.1362_1363delAG	chr3.hg19:g.49866583_49866584delCT	ENSP00000328203:p.Val455fs	196.0	0.0		204.0	79.0	NM_005879	B5BU84|B5BUL3|O00467	Frame_Shift_Del	DEL	ENST00000331456.2	hg19	CCDS2806.1																																																																																			.	.		0.54	TRAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350518.1	NM_005879		-	49866584	CT	-	49866583	7	5	142	1	0	1	0	1	0	0	0	0	16463	565	20	0	50	0	TRAIP	3	49866583	Frame_Shift_Del	DEL	CT	TCGA-DD-A73A-01A-12D-A32G-10	7085434	49866583	148155847	17	22046										
RRP9	9136	hgsc.bcm.edu	37	chr3	51969471	51969471	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ctcaaggcatccagtgcagcCacagcgtcctggtgtccgaa	11	14	1	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr3:51969471C>T	ENST00000232888.6	-	10	931	c.858G>A	c.(856-858)gtG>gtA	p.V286V		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	286					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		CCAGTGCAGCCACAGCGTCCT	0.627																																					p.V286V		Atlas-SNP	.											.	RRP9	40	.	0			c.G858A						.						68	57	60					3																	51969471		2203	4300	6503	SO:0001819	synonymous_variant	9136	exon10			TGCAGCCACAGCG	AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"WD repeat domain containing"	16829	protein-coding gene	gene with protein product			"RNA, U3 small nucleolar interacting protein 2"	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.858G>A	chr3.hg19:g.51969471C>T		78.0	0.0		83.0	32.0	NM_004704	B2R996|Q8IZ30	Silent	SNP	ENST00000232888.6	hg19	CCDS2837.1																																																																																			.	.		0.627	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704		T	51969471	C	T	51969471	2	4	142	1	0	0	0	0	0	0	0	1	13706	581	21	3		3	RRP9	3	51969471	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	2102888	51969471	146052959	18	22047										
PDHB	5162	hgsc.bcm.edu	37	chr3	58419520	58419520	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gaaggggtctccgcaccaagCcagacaccgccgccatcttg	11	16	2	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr3:58419520C>T	ENST00000302746.6	-	1	59	c.17G>A	c.(16-18)gGc>gAc	p.G6D	PDHB_ENST00000485460.1_Missense_Mutation_p.G6D|PDHB_ENST00000474765.1_Missense_Mutation_p.G6D	NM_000925.3|NM_001173468.1	NP_000916.2|NP_001166939.1	P11177	ODPB_HUMAN	pyruvate dehydrogenase (lipoamide) beta	6					acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	9				BRCA - Breast invasive adenocarcinoma(55;0.000179)|Kidney(10;0.00231)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.187)	Pyruvic acid(DB00119)	CCGCACCAAGCCAGACACCGC	0.697																																					p.G6D		Atlas-SNP	.											.	PDHB	19	.	0			c.G17A						.						23	24	24					3																	58419520		2189	4283	6472	SO:0001583	missense	5162	exon1			ACCAAGCCAGACA		CCDS2890.1, CCDS54602.1	3p21.1-p14.2	1995-12-20			ENSG00000168291	ENSG00000168291	1.2.4.1		8808	protein-coding gene	gene with protein product		179060					Standard	NR_033384		Approved		uc003dkf.4	P11177	OTTHUMG00000159157	ENST00000302746.6:c.17G>A	chr3.hg19:g.58419520C>T	ENSP00000307241:p.Gly6Asp	104.0	0.0		140.0	29.0	NM_000925	B2R7L0|B4DDD7|Q6FH45|Q9BQ27|Q9UFK3	Missense_Mutation	SNP	ENST00000302746.6	hg19	CCDS2890.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.238260	0.39598	.	.	ENSG00000168291	ENST00000302746;ENST00000383714;ENST00000485460;ENST00000474765	D;D;D;D	0.97976	-4.07;-4.06;-4.64;-3.99	5.37	2.57	0.30868	.	0.508615	0.22001	N	0.066013	D	0.91630	0.7355	N	0.08118	0	0.09310	N	1	B;B;B;B	0.29085	0.01;0.232;0.062;0.01	B;B;B;B	0.30029	0.007;0.11;0.094;0.007	D	0.83412	0.0028	10	0.18710	T	0.47	-1.4522	10.2168	0.43173	0.1429:0.5812:0.2758:0.0	.	6;6;6;6	B4DDD7;C9J634;P11177-2;P11177	.;.;.;ODPB_HUMAN	D	6	ENSP00000307241:G6D;ENSP00000373220:G6D;ENSP00000417267:G6D;ENSP00000418448:G6D	ENSP00000307241:G6D	G	-	2	0	PDHB	58394560	0.000000	0.05858	0.001000	0.08648	0.690000	0.40134	-0.644000	0.05415	0.375000	0.24679	0.561000	0.74099	GGC	.	.		0.697	PDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353558.1			T	58419520	C	T	58419520	3	4	142	1	0	0	0	0	1	0	0	0	11675	739	26	3	1102	3	PDHB	3	58419520	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	6450049	58419520	139602910	19	22048										
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135825091	135825091	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	atgggcctgagccctcagacTgggaccggtttgccgctgag	15	12	1	3			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr3:135825091T>A	ENST00000264977.3	+	13	3873	c.3256T>A	c.(3256-3258)Tgg>Agg	p.W1086R	PPP2R3A_ENST00000334546.2_Missense_Mutation_p.W465R|PPP2R3A_ENST00000490467.1_Missense_Mutation_p.W350R|PPP2R3A_ENST00000469270.1_3'UTR	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	1086					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GCCCTCAGACTGGGACCGGTT	0.458																																					p.W1086R		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T3256A						.						71	72	72					3																	135825091		2203	4300	6503	SO:0001583	missense	5523	exon13			TCAGACTGGGACC	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.3256T>A	chr3.hg19:g.135825091T>A	ENSP00000264977:p.Trp1086Arg	82.0	0.0		107.0	25.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	hg19	CCDS3087.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.766989	0.90020	.	.	ENSG00000073711	ENST00000264977;ENST00000490467;ENST00000334546	T;T;T	0.39229	1.09;1.09;1.09	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.71476	0.3344	M	0.90145	3.09	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78011	-0.2371	10	0.87932	D	0	.	15.7305	0.77800	0.0:0.0:0.0:1.0	.	465;1086	Q06190-2;Q06190	.;P2R3A_HUMAN	R	1086;350;465	ENSP00000264977:W1086R;ENSP00000419344:W350R;ENSP00000334748:W465R	ENSP00000264977:W1086R	W	+	1	0	PPP2R3A	137307781	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.499000	0.81566	2.299000	0.77371	0.528000	0.53228	TGG	.	.		0.458	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		A	135825091	T	A	135825091	3	1	142	1	0	0	0	0	1	0	0	0	12400	1580	55	4	3438	4	PPP2R3A	3	135825091	Missense_Mutation	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	77405571	135825091	62197339	20	22049										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20525746	20525746	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	cccgttgcaccagcccccgcCgcctggcaaacaaaagaatt	8	17	0	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr4:20525746C>T	ENST00000504154.1	+	14	1636	c.1384C>T	c.(1384-1386)Cgc>Tgc	p.R462C	SLIT2_ENST00000503823.1_Missense_Mutation_p.R462C|SLIT2_ENST00000273739.5_Missense_Mutation_p.R466C|SLIT2_ENST00000503837.1_Missense_Mutation_p.R466C	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	462	LRRCT 2.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						CAGCCCCCGCCGCCTGGCAAA	0.483																																					p.R462C		Atlas-SNP	.											SLIT2,NS,lymphoid_neoplasm,0,1	SLIT2	290	.	0			c.C1384T						.						109	123	118					4																	20525746		2203	4300	6503	SO:0001583	missense	9353	exon14			CCCCGCCGCCTGG	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1384C>T	chr4.hg19:g.20525746C>T	ENSP00000422591:p.Arg462Cys	118.0	0.0		92.0	31.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	C	32	5.172718	0.94807	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	D;D;T;T	0.81579	-1.5;-1.51;-1.43;-1.48	5.93	5.93	0.95920	Cysteine-rich flanking region, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.91119	0.7204	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.977;1.0	D	0.91338	0.5095	10	0.87932	D	0	.	20.3368	0.98748	0.0:1.0:0.0:0.0	.	462;462	O94813-3;O94813	.;SLIT2_HUMAN	C	462;462;466;466;466	ENSP00000427548:R462C;ENSP00000422591:R462C;ENSP00000273739:R466C;ENSP00000422261:R466C	ENSP00000273739:R466C	R	+	1	0	SLIT2	20134844	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.770000	0.85390	2.805000	0.96524	0.655000	0.94253	CGC	.	.		0.483	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			T	20525746	C	T	20525746	3	4	142	1	0	0	0	0	1	0	0	0	14755	652	23	1	1438	1	SLIT2	4	20525746	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10		20525746	170628530	21	22050										
SCD5	79966	hgsc.bcm.edu	37	chr4	83626515	83626515	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	aggacctgtggctccacaagCgatgggcaccagctgtcaca	12	13	1	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr4:83626515C>T	ENST00000319540.4	-	2	603	c.284G>A	c.(283-285)cGc>cAc	p.R95H	SCD5_ENST00000273908.4_Missense_Mutation_p.R95H|SCD5_ENST00000282709.4_Missense_Mutation_p.R95H	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	95					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				GCTCCACAAGCGATGGGCACC	0.582																																					p.R95H		Atlas-SNP	.											.	SCD5	58	.	0			c.G284A						.						66	60	62					4																	83626515		2203	4300	6503	SO:0001583	missense	79966	exon2			CACAAGCGATGGG	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.284G>A	chr4.hg19:g.83626515C>T	ENSP00000316329:p.Arg95His	203.0	0.0		168.0	47.0	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	hg19	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.813311	0.90707	.	.	ENSG00000145284	ENST00000319540;ENST00000273908;ENST00000282709	T;T	0.00949	5.51;5.51	5.12	4.27	0.50696	Fatty acid desaturase, type 1 (1);	0.097978	0.64402	N	0.000003	T	0.13543	0.0328	H	0.99746	4.745	0.51482	D	0.999926	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.35847	-0.9772	10	0.87932	D	0	-6.1917	14.1484	0.65364	0.0:0.9258:0.0:0.0742	.	95;95;95	Q9BSN4;Q86SK9-2;Q86SK9	.;.;SCD5_HUMAN	H	95	ENSP00000316329:R95H;ENSP00000273908:R95H	ENSP00000273908:R95H	R	-	2	0	SCD5	83845539	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	5.706000	0.68362	1.496000	0.48567	0.491000	0.48974	CGC	.	.		0.582	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		T	83626515	C	T	83626515	3	4	142	1	0	0	0	0	1	0	0	0	13902	768	27	1	930	1	SCD5	4	83626515	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	63100769	83626515	107527761	22	22051										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90856220	90856220	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gtggaactaaggaatcacatTgtgaatgtaaggcaagaaat	11	4	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr4:90856220T>C	ENST00000394980.1	+	7	1708	c.1389T>C	c.(1387-1389)atT>atC	p.I463I	MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000508372.1_Silent_p.I205I|MMRN1_ENST00000264790.2_Silent_p.I463I			Q13201	MMRN1_HUMAN	multimerin 1	463					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		GGAATCACATTGTGAATGTAA	0.388																																					p.I463I		Atlas-SNP	.											.	MMRN1	174	.	0			c.T1389C						.						69	69	69					4																	90856220		2202	4299	6501	SO:0001819	synonymous_variant	22915	exon6			TCACATTGTGAAT	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.1389T>C	chr4.hg19:g.90856220T>C		264.0	0.0		269.0	97.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Silent	SNP	ENST00000394980.1	hg19	CCDS3635.1																																																																																			.	.		0.388	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		C	90856220	T	C	90856220	2	2	142	1	0	0	0	0	0	0	0	1	9679	1800	63	2		2	MMRN1	4	90856220	Silent	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	7229705	90856220	100298056	23	22052										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123097024	123097040	+	Frame_Shift_Del	DEL	ATTTTTCGGTGGTGGAA	ATTTTTCGGTGGTGGAA	-													0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ggattcaagatggattcatcAtttttcggtggtggaaaatg							TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	ATTTTTCGGTGGTGGAA	ATTTTTCGGTGGTGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr4:123097024_123097040delATTTTTCGGTGGTGGAA	ENST00000264501.4	+	6	686_702	c.313_329delATTTTTCGGTGGTGGAA	c.(313-330)atttttcggtggtggaaafs	p.IFRWWK105fs	KIAA1109_ENST00000455637.1_Frame_Shift_Del_p.IFRWWK105fs|KIAA1109_ENST00000388738.3_Frame_Shift_Del_p.IFRWWK105fs			Q2LD37	K1109_HUMAN	KIAA1109	105					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TGGATTCATCATTTTTCGGTGGTGGAAAATGTATAAC	0.272																																					p.104_110del		Atlas-Indel,Pindel	.											KIAA1109,colon,carcinoma,0,1	KIAA1109	424	.	0			c.312_328del						.																																			SO:0001589	frameshift_variant	84162	exon4			.	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.313_329delATTTTTCGGTGGTGGAA	chr4.hg19:g.123097024_123097040delATTTTTCGGTGGTGGAA	ENSP00000264501:p.Ile105fs	360.0	0.0		250.0	26.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Frame_Shift_Del	DEL	ENST00000264501.4	hg19	CCDS43267.1																																																																																			.	.		0.272	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		-	123097040	ATTTTTCGGTGGTGGAA	-	123097024	7	5	142	1	0	1	0	1	0	0	0	0	8217	217	8	0	327	0	KIAA1109	4	123097024	Frame_Shift_Del	DEL	ATTTTTCGGTGGTGGAA	TCGA-DD-A73A-01A-12D-A32G-10	32240804	123097024	68057252	24	22053										
PCDH10	57575	hgsc.bcm.edu	37	chr4	134072769	134072769	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tgagcgccaccgaccgggatGagggcgccaacgcccagctt	14	15	0	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr4:134072769G>C	ENST00000264360.5	+	1	2300	c.1474G>C	c.(1474-1476)Gag>Cag	p.E492Q	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	492	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		CGACCGGGATGAGGGCGCCAA	0.587																																					p.E492Q		Atlas-SNP	.											.	PCDH10	290	.	0			c.G1474C						.						60	61	61					4																	134072769		2203	4300	6503	SO:0001583	missense	57575	exon1			CGGGATGAGGGCG	AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.1474G>C	chr4.hg19:g.134072769G>C	ENSP00000264360:p.Glu492Gln	63.0	0.0		71.0	4.0	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	hg19	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	G	4.768	0.142716	0.09083	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.52057	0.68	4.51	4.51	0.55191	Cadherin (4);Cadherin-like (1);	0.000000	0.43579	D	0.000556	T	0.40719	0.1128	L	0.49455	1.56	0.34300	D	0.684218	B;B	0.06786	0.001;0.001	B;B	0.13407	0.004;0.009	T	0.48281	-0.9049	10	0.22109	T	0.4	.	12.6201	0.56597	0.0:0.1681:0.8319:0.0	.	492;492	Q9P2E7;Q96SF0	PCD10_HUMAN;.	Q	492	ENSP00000264360:E492Q	ENSP00000264360:E492Q	E	+	1	0	PCDH10	134292219	1.000000	0.71417	0.992000	0.48379	0.971000	0.66376	3.160000	0.50739	2.329000	0.79093	0.655000	0.94253	GAG	.	.		0.587	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		C	134072769	G	C	134072769	3	2	142	1	0	0	0	0	1	0	0	0	11516	1291	45	4	1476	4	PCDH10	4	134072769	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	10975745	134072769	57081507	25	22054										
POU4F2	5458	hgsc.bcm.edu	37	chr4	147561765	147561765	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ctcttcaatggcgcggagaaGaagcgcaagcgcacgtccat	12	12	2	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr4:147561765G>A	ENST00000281321.3	+	2	1283	c.1035G>A	c.(1033-1035)aaG>aaA	p.K345K	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	345					axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					GCGCGGAGAAGAAGCGCAAGC	0.612																																					p.K345K		Atlas-SNP	.											.	POU4F2	83	.	0			c.G1035A						.						87	91	90					4																	147561765		2203	4300	6503	SO:0001819	synonymous_variant	5458	exon2			GGAGAAGAAGCGC	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9219	protein-coding gene	gene with protein product		113725	"POU domain, class 4, transcription factor 2", "POU domain class 4, transcription factor 2"	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.1035G>A	chr4.hg19:g.147561765G>A		80.0	0.0		74.0	27.0	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	hg19	CCDS34074.1																																																																																			.	.		0.612	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		A	147561765	G	A	147561765	2	1	142	1	0	0	0	0	0	0	0	1	12288	933	33	3		3	POU4F2	4	147561765	Silent	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	13488996	147561765	43592511	26	22055										
FGA	2243	hgsc.bcm.edu	37	chr4	155507454	155507455	+	In_Frame_Ins	INS	-	-	CAG													0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	actaccagatacagagctctINScagaggtccagtgcccagca							TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr4:155507454_155507455insCAG	ENST00000302053.3	-	5	1204_1205	c.1126_1127insCTG	c.(1126-1128)gag>gCTGag	p.375_376insA	FGA_ENST00000403106.3_In_Frame_Ins_p.375_376insA	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	375					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)	p.E376K(1)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	TACAGAGCTCTCAGAGGTCCAG	0.55																																					p.E376delinsAE	NSCLC(143;340 1922 20892 22370 48145)	Atlas-Indel,Pindel	.											.	FGA	179	.	1	Substitution - Missense(1)	endometrium(1)	c.1127_1128insCTG						.																																			SO:0001652	inframe_insertion	2243	exon5			.		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1124_1126dupCTG	chr4.hg19:g.155507455_155507457dupCAG	ENSP00000306361:p.Ser375_Glu376insAla	98.0	0.0		88.0	22.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	In_Frame_Ins	INS	ENST00000302053.3	hg19	CCDS3787.1																																																																																			.	.		0.55	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		CAG	155507455	-	CAG	155507454	7	5	142	1	0	1	1	0	0	0	0	0	5838	1551	54	0	1525	0	FGA	4	155507454	In_Frame_Ins	INS	-	TCGA-DD-A73A-01A-12D-A32G-10	7945689	155507454	35646822	27	22056										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175897952	175897952	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gtgcaaaagatccctgctgtCtgtcaaattgcactctgact	8	11	3	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr4:175897952C>T	ENST00000359240.3	+	5	1946	c.1276C>T	c.(1276-1278)Ctg>Ttg	p.L426L	ADAM29_ENST00000445694.1_Silent_p.L426L|ADAM29_ENST00000404450.4_Silent_p.L426L|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Silent_p.L426L	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	426	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TCCCTGCTGTCTGTCAAATTG	0.448																																					p.L426L	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.C1276T						.						215	203	207					4																	175897952		2203	4300	6503	SO:0001819	synonymous_variant	11086	exon4			TGCTGTCTGTCAA	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.1276C>T	chr4.hg19:g.175897952C>T		120.0	0.0		101.0	38.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Silent	SNP	ENST00000359240.3	hg19	CCDS3823.1																																																																																			.	.		0.448	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				T	175897952	C	T	175897952	2	4	142	1	0	0	0	0	0	0	0	1	247	912	32	3		3	ADAM29	4	175897952	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	20390498	175897952	15256324	28	22057										
IRX1	79192	hgsc.bcm.edu	37	chr5	3600047	3600047	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	cagccacgagccccgacggtGcgcccaaggcttcgccacca	11	19	0	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:3600047G>A	ENST00000302006.3	+	2	1037	c.985G>A	c.(985-987)Gcg>Acg	p.A329T	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	329					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CCCCGACGGTGCGCCCAAGGC	0.776																																					p.A329T		Atlas-SNP	.											.	IRX1	106	.	0			c.G985A						.						3	4	3					5																	3600047		1708	3452	5160	SO:0001583	missense	79192	exon2			GACGGTGCGCCCA	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.985G>A	chr5.hg19:g.3600047G>A	ENSP00000305244:p.Ala329Thr	54.0	0.0		74.0	28.0	NM_024337	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	hg19	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	G	5.109	0.205786	0.09704	.	.	ENSG00000170549	ENST00000302006	T	0.59224	0.28	4.52	2.71	0.32032	.	0.390344	0.21896	N	0.067504	T	0.41119	0.1145	L	0.35414	1.06	0.42008	D	0.990924	B	0.09022	0.002	B	0.06405	0.002	T	0.16188	-1.0411	10	0.14656	T	0.56	.	9.8869	0.41266	0.1674:0.0:0.8326:0.0	.	329	P78414	IRX1_HUMAN	T	329	ENSP00000305244:A329T	ENSP00000305244:A329T	A	+	1	0	IRX1	3653047	0.975000	0.34042	0.982000	0.44146	0.012000	0.07955	2.352000	0.44080	0.863000	0.35553	-0.251000	0.11542	GCG	.	.		0.776	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		A	3600047	G	A	3600047	3	1	142	1	0	0	0	0	1	0	0	0	7852	1319	46	3	991	3	IRX1	5	3600047	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10		3600047	177315213	29	22058										
NIPBL	25836	hgsc.bcm.edu	37	chr5	37008169	37008169	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gtcagtgaactacagttgtgTgccattaagttagtcactgc	10	8	2	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:37008169T>C	ENST00000282516.8	+	19	4798	c.4299T>C	c.(4297-4299)tgT>tgC	p.C1433C	NIPBL_ENST00000448238.2_Silent_p.C1433C	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1433					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TACAGTTGTGTGCCATTAAGT	0.299																																					p.C1433C		Atlas-SNP	.											.	NIPBL	513	.	0			c.T4299C						.						100	95	97					5																	37008169		2202	4297	6499	SO:0001819	synonymous_variant	25836	exon19			GTTGTGTGCCATT	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.4299T>C	chr5.hg19:g.37008169T>C		248.0	0.0		241.0	77.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.		0.299	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		C	37008169	T	C	37008169	2	2	142	1	0	0	0	0	0	0	0	1	10437	1702	59	2		2	NIPBL	5	37008169	Silent	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	33408122	37008169	143907091	30	22059										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71493190	71493190	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	agtgctggtcacacaccttaCtatcaatctcctactgacga	6	13	3	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:71493190C>T	ENST00000296755.7	+	5	4306	c.4008C>T	c.(4006-4008)taC>taT	p.Y1336Y		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1336					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ACACACCTTACTATCAATCTC	0.458																																					p.Y1336Y	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.C4008T						.						67	65	66					5																	71493190		2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			ACCTTACTATCAA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4008C>T	chr5.hg19:g.71493190C>T		107.0	0.0		109.0	36.0	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	hg19	CCDS4012.1																																																																																			.	.		0.458	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71493190	C	T	71493190	2	4	142	1	0	0	0	0	0	0	0	1	9237	576	20	3		3	MAP1B	5	71493190	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	34485021	71493190	109422070	31	22060										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79026634	79026634	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tacatggtcctatcaggagaCgaggcctcagaaagtgggtg	14	8	2	2	rs539952978		TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:79026634C>T	ENST00000446378.2	+	2	2077	c.2046C>T	c.(2044-2046)gaC>gaT	p.D682D		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	682					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TATCAGGAGACGAGGCCTCAG	0.453													C|||	1	0.000199681	0	0.0014	5008	,	,		21643	0		0	False		,,,				2504	0				p.D682D		Atlas-SNP	.											.	CMYA5	643	.	0			c.C2046T						.						54	50	51					5																	79026634		1922	4126	6048	SO:0001819	synonymous_variant	202333	exon2			AGGAGACGAGGCC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.2046C>T	chr5.hg19:g.79026634C>T		106.0	0.0		148.0	6.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.		0.453	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79026634	C	T	79026634	2	4	142	1	0	0	0	0	0	0	0	1	3592	535	19	1		1	CMYA5	5	79026634	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	7533444	79026634	101888626	32	22061										
ACOT12	134526	hgsc.bcm.edu	37	chr5	80626218	80626218	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	attgaaagttgacctttaaaAtgtgcttacaaacccatcat	5	8	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:80626218A>C	ENST00000307624.3	-	15	1691	c.1663T>G	c.(1663-1665)Ttt>Gtt	p.F555V	ACOT12_ENST00000508234.1_5'UTR	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	555					acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		GACCTTTAAAATGTGCTTACA	0.398																																					p.F555V		Atlas-SNP	.											.	ACOT12	57	.	0			c.T1663G						.						68	70	69					5																	80626218		2203	4300	6503	SO:0001583	missense	134526	exon15			TTTAAAATGTGCT	AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	24436	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 15"	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.1663T>G	chr5.hg19:g.80626218A>C	ENSP00000303246:p.Phe555Val	109.0	0.0		139.0	76.0	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	hg19	CCDS4055.1	.	.	.	.	.	.	.	.	.	.	A	12.18	1.859962	0.32884	.	.	ENSG00000172497	ENST00000307624	T	0.13420	2.59	5.2	0.0617	0.14341	.	1.015390	0.07891	N	0.971204	T	0.08582	0.0213	N	0.22421	0.69	0.09310	N	1	B	0.15930	0.015	B	0.12156	0.007	T	0.38908	-0.9639	10	0.54805	T	0.06	-4.3237	3.2289	0.06741	0.5451:0.0:0.283:0.1719	.	555	Q8WYK0	ACO12_HUMAN	V	555	ENSP00000303246:F555V	ENSP00000303246:F555V	F	-	1	0	ACOT12	80661974	0.186000	0.23225	0.001000	0.08648	0.243000	0.25628	0.853000	0.27777	0.060000	0.16281	0.459000	0.35465	TTT	.	.		0.398	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767		C	80626218	A	C	80626218	3	2	142	1	0	0	0	0	1	0	0	0	150	101	4	5	8	5	ACOT12	5	80626218	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	1599584	80626218	100289042	33	22062										
GPR98	84059	hgsc.bcm.edu	37	chr5	89924641	89924641	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gaggtgcagaagtgagcgagCcagcggaggtataacccttg	16	8	0	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:89924641C>A	ENST00000405460.2	+	8	1597	c.1501C>A	c.(1501-1503)Cca>Aca	p.P501T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	501					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGTGAGCGAGCCAGCGGAGGT	0.403																																					p.P501T		Atlas-SNP	.											.	GPR98	605	.	0			c.C1501A						.						65	68	67					5																	89924641		1985	4152	6137	SO:0001583	missense	84059	exon8			AGCGAGCCAGCGG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.1501C>A	chr5.hg19:g.89924641C>A	ENSP00000384582:p.Pro501Thr	88.0	0.0		145.0	42.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.6|25.6	4.656972|4.656972	0.88154|0.88154	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000504142|ENST00000405460;ENST00000296619;ENST00000399043	.|T	.|0.42513	.|0.97	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.68403|0.68403	0.2997|0.2997	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	T|T	0.69942|0.69942	-0.5008|-0.5008	5|10	.|0.66056	.|D	.|0.02	.|.	20.0216|20.0216	0.97506|0.97506	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|501	.|Q8WXG9	.|GPR98_HUMAN	D|T	89|501	.|ENSP00000384582:P501T	.|ENSP00000296619:P501T	A|P	+|+	2|1	0|0	GPR98|GPR98	89960397|89960397	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.810000|0.810000	0.45777|0.45777	7.590000|7.590000	0.82653|0.82653	2.735000|2.735000	0.93741|0.93741	0.650000|0.650000	0.86243|0.86243	GCC|CCA	.	.		0.403	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	89924641	C	A	89924641	3	1	142	1	0	0	0	0	1	0	0	0	6730	739	26	3	1531	3	GPR98	5	89924641	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	9298423	89924641	90990619	34	22063										
PAM	5066	hgsc.bcm.edu	37	chr5	102360991	102360991	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tattccggtggttgtcctgcTggccattgccatatttattc	9	10	0	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:102360991T>A	ENST00000438793.3	+	23	3112	c.2642T>A	c.(2641-2643)cTg>cAg	p.L881Q	PAM_ENST00000346918.2_Intron|PAM_ENST00000379787.4_Missense_Mutation_p.L261Q|PAM_ENST00000348126.2_Missense_Mutation_p.L774Q|PAM_ENST00000274392.9_Missense_Mutation_p.L783Q|PAM_ENST00000304400.7_Missense_Mutation_p.L881Q|PAM_ENST00000455264.2_Intron	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	881					central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	GTTGTCCTGCTGGCCATTGCC	0.473																																					p.L881Q		Atlas-SNP	.											.	PAM	180	.	0			c.T2642A						.						100	112	108					5																	102360991		2203	4300	6503	SO:0001583	missense	5066	exon23			TCCTGCTGGCCAT	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.2642T>A	chr5.hg19:g.102360991T>A	ENSP00000396493:p.Leu881Gln	193.0	0.0		235.0	63.0	NM_001177306	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	hg19	CCDS54885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.4|24.4	4.531147|4.531147	0.85706|0.85706	.|.	.|.	ENSG00000145730|ENSG00000145730	ENST00000438793;ENST00000348126;ENST00000379787;ENST00000304400;ENST00000274392|ENST00000504691	T;T;T;T;T|.	0.67171|.	0.65;0.5;0.22;0.65;-0.25|.	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	0.363007|.	0.27311|.	N|.	0.019957|.	T|T	0.54791|0.54791	0.1880|0.1880	L|L	0.27053|0.27053	0.805|0.805	0.41240|0.41240	D|D	0.986637|0.986637	D;D;D;D;D|.	0.76494|.	0.998;0.999;0.997;0.986;0.998|.	D;D;D;P;D|.	0.70487|.	0.957;0.962;0.944;0.9;0.969|.	T|T	0.52426|0.52426	-0.8577|-0.8577	10|5	0.87932|.	D|.	0|.	.|.	16.0021|16.0021	0.80301|0.80301	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	783;261;881;881;774|.	F8WE90;A6NMH0;P19021;P19021-5;P19021-2|.	.;.;AMD_HUMAN;.;.|.	Q|R	881;774;261;881;783|176	ENSP00000396493:L881Q;ENSP00000314638:L774Q;ENSP00000369113:L261Q;ENSP00000306100:L881Q;ENSP00000274392:L783Q|.	ENSP00000274392:L783Q|.	L|W	+|+	2|1	0|0	PAM|PAM	102388890|102388890	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.343000|6.343000	0.72986|0.72986	2.184000|2.184000	0.69523|0.69523	0.529000|0.529000	0.55759|0.55759	CTG|TGG	.	.		0.473	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		A	102360991	T	A	102360991	3	1	142	1	0	0	0	0	1	0	0	0	11421	1580	55	4	2732	4	PAM	5	102360991	Missense_Mutation	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	12436350	102360991	78554269	35	22064										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140574371	140574371	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gggcgctgagaccctgtcccAgagctaccagtatgaggtgt	14	11	0	3			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:140574371A>T	ENST00000239446.4	+	1	2430	c.2246A>T	c.(2245-2247)cAg>cTg	p.Q749L		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	749					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACCCTGTCCCAGAGCTACCAG	0.622																																					p.Q749L		Atlas-SNP	.											.	PCDHB10	177	.	0			c.A2246T						.						76	85	82					5																	140574371		2203	4300	6503	SO:0001583	missense	56126	exon1			TGTCCCAGAGCTA	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.2246A>T	chr5.hg19:g.140574371A>T	ENSP00000239446:p.Gln749Leu	104.0	0.0		126.0	25.0	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	hg19	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	a	11.70	1.717153	0.30413	.	.	ENSG00000120324	ENST00000239446	T	0.53423	0.62	3.28	3.28	0.37604	.	.	.	.	.	T	0.53786	0.1818	M	0.85859	2.78	0.09310	N	1	P	0.42248	0.774	P	0.46026	0.501	T	0.56733	-0.7930	9	0.87932	D	0	.	2.8435	0.05536	0.6568:0.0:0.1218:0.2214	.	749	Q9UN67	PCDBA_HUMAN	L	749	ENSP00000239446:Q749L	ENSP00000239446:Q749L	Q	+	2	0	PCDHB10	140554555	0.000000	0.05858	0.981000	0.43875	0.324000	0.28378	0.251000	0.18257	1.508000	0.48769	0.248000	0.18094	CAG	.	.		0.622	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		T	140574371	A	T	140574371	3	4	142	1	0	0	0	0	1	0	0	0	11544	188	7	4	2248	4	PCDHB10	5	140574371	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	38213380	140574371	40340889	36	22065										
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140811741	140811741	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tcccagaggagtttccctcgTctctgtgaccgcccacgacc	9	17	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:140811741T>A	ENST00000252085.3	+	1	1557	c.1415T>A	c.(1414-1416)gTc>gAc	p.V472D	PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA9_ENST00000573521.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	472	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTTCCCTCGTCTCTGTGACC	0.572																																					p.V472D		Atlas-SNP	.											.	PCDHGA12	271	.	0			c.T1415A						.						71	74	73					5																	140811741		2203	4300	6503	SO:0001583	missense	26025	exon1			CCCTCGTCTCTGT	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1415T>A	chr5.hg19:g.140811741T>A	ENSP00000252085:p.Val472Asp	178.0	0.0		230.0	106.0	NM_032094	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	hg19	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	t	3.949	-0.012647	0.07727	.	.	ENSG00000253159	ENST00000252085	T	0.01705	4.68	5.23	2.73	0.32206	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.02929	0.0087	L	0.55990	1.75	0.09310	N	1	B;P	0.35456	0.274;0.502	B;B	0.41412	0.173;0.356	T	0.41770	-0.9490	9	0.62326	D	0.03	.	3.7857	0.08700	0.1288:0.0742:0.1342:0.6627	.	472;472	O60330-2;O60330	.;PCDGC_HUMAN	D	472	ENSP00000252085:V472D	ENSP00000252085:V472D	V	+	2	0	PCDHGA12	140791925	0.000000	0.05858	0.005000	0.12908	0.004000	0.04260	-0.210000	0.09345	0.842000	0.35045	0.459000	0.35465	GTC	.	.		0.572	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140811741	T	A	140811741	3	1	142	1	0	0	0	0	1	0	0	0	11562	1667	58	4	1417	4	PCDHGA12	5	140811741	Missense_Mutation	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	237370	140811741	40103519	37	22066										
FAT2	2196	hgsc.bcm.edu	37	chr5	150886868	150886868	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gagttcatttggaacagaggCcttgctgggttccggttggt	15	7	1	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:150886868C>A	ENST00000261800.5	-	22	12376	c.12364G>T	c.(12364-12366)Gcc>Tcc	p.A4122S	CTC-251D13.1_ENST00000606930.1_RNA	NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	4122					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K4121>?(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGAACAGAGGCCTTGCTGGGT	0.577																																					p.A4122S		Atlas-SNP	.											.,1	FAT2	465	.	1	Complex(1)	large_intestine(1)	c.G12364T						.						146	150	148					5																	150886868		2203	4300	6503	SO:0001583	missense	2196	exon22			CAGAGGCCTTGCT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.12364G>T	chr5.hg19:g.150886868C>A	ENSP00000261800:p.Ala4122Ser	151.0	0.0		185.0	32.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.864|1.864	-0.461973|-0.461973	0.04508|0.04508	.|.	.|.	ENSG00000086570|ENSG00000086570	ENST00000261800|ENST00000520200	T|.	0.68025|.	-0.3|.	4.63|4.63	-2.42|-2.42	0.06542|0.06542	.|.	0.531499|.	0.18493|.	N|.	0.139585|.	T|T	0.19087|0.19087	0.0458|0.0458	N|N	0.16368|0.16368	0.405|0.405	0.19945|0.19945	N|N	0.999944|0.999944	B;B|.	0.10296|.	0.0;0.003|.	B;B|.	0.06405|.	0.002;0.002|.	T|T	0.31138|0.31138	-0.9954|-0.9954	10|5	0.02654|.	T|.	1|.	.|.	6.362|6.362	0.21433|0.21433	0.0:0.446:0.2988:0.2552|0.0:0.446:0.2988:0.2552	.|.	4122;1227|.	Q9NYQ8;E9PDJ8|.	FAT2_HUMAN;.|.	S|V	4122|894	ENSP00000261800:A4122S|.	ENSP00000261800:A4122S|.	A|G	-|-	1|2	0|0	FAT2|FAT2	150867061|150867061	0.330000|0.330000	0.24705|0.24705	0.989000|0.989000	0.46669|0.46669	0.165000|0.165000	0.22458|0.22458	-0.228000|-0.228000	0.09114|0.09114	-0.235000|-0.235000	0.09767|0.09767	-1.077000|-1.077000	0.02231|0.02231	GCC|GGC	.	.		0.577	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150886868	C	A	150886868	3	1	142	1	0	0	0	0	1	0	0	0	5698	739	26	3	693	3	FAT2	5	150886868	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	10075127	150886868	30028392	38	22067										
LARP1	23367	hgsc.bcm.edu	37	chr5	154173763	154173763	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tactactttgacaatgtcagCagcaccgagctttacagtgt	8	10	1	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr5:154173763C>G	ENST00000336314.4	+	7	966	c.942C>G	c.(940-942)agC>agG	p.S314R		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	391					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			ACAATGTCAGCAGCACCGAGC	0.483																																					p.S314R		Atlas-SNP	.											.	LARP1	187	.	0			c.C942G						.						154	130	138					5																	154173763		2203	4300	6503	SO:0001583	missense	23367	exon7			TGTCAGCAGCACC	AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"La ribonucleoprotein domain containing"	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.942C>G	chr5.hg19:g.154173763C>G	ENSP00000336721:p.Ser314Arg	297.0	0.0		390.0	102.0	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	hg19	CCDS4328.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.6|24.6	4.547969|4.547969	0.86022|0.86022	.|.	.|.	ENSG00000155506|ENSG00000155506	ENST00000518194|ENST00000336314;ENST00000518297;ENST00000524248;ENST00000523163	.|T;T;T;T	.|0.46451	.|0.87;0.87;0.87;0.87	5.8|5.8	4.03|4.03	0.46877|0.46877	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.58623|0.58623	0.2135|0.2135	M|M	0.68952|0.68952	2.095|2.095	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D	.|0.65815	.|0.995;0.991	.|P;D	.|0.66979	.|0.858;0.948	T|T	0.56312|0.56312	-0.8000|-0.8000	5|10	.|0.38643	.|T	.|0.18	-17.3828|-17.3828	12.2596|12.2596	0.54642|0.54642	0.0:0.8635:0.0:0.1365|0.0:0.8635:0.0:0.1365	.|.	.|391;314	.|Q6PKG0;Q6PKG0-3	.|LARP1_HUMAN;.	E|R	127|314;391;186;99	.|ENSP00000336721:S314R;ENSP00000428589:S391R;ENSP00000429904:S186R;ENSP00000430438:S99R	.|ENSP00000336721:S314R	Q|S	+|+	1|3	0|2	LARP1|LARP1	154153956|154153956	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.991000|3.991000	0.56973|0.56973	0.794000|0.794000	0.33899|0.33899	0.655000|0.655000	0.94253|0.94253	CAG|AGC	.	.		0.483	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		G	154173763	C	G	154173763	3	3	142	1	0	0	0	0	1	0	0	0	8637	709	25	4	968	4	LARP1	5	154173763	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	3286895	154173763	26741497	39	22068										
WDR46	9277	hgsc.bcm.edu	37	chr6	33254618	33254618	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ccggaccccaccacgatgacAgagaatctttgccagtggct	10	14	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr6:33254618A>T	ENST00000374617.4	-	10	1425	c.1069T>A	c.(1069-1071)Tgt>Agt	p.C357S	PFDN6_ENST00000395131.1_5'Flank|WDR46_ENST00000477718.1_5'Flank|PFDN6_ENST00000374606.5_5'Flank|PFDN6_ENST00000463584.1_5'Flank|PFDN6_ENST00000374607.1_5'Flank|PFDN6_ENST00000374610.2_5'Flank	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	357							poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						CCACGATGACAGAGAATCTTT	0.507																																					p.C357S		Atlas-SNP	.											.	WDR46	43	.	0			c.T1069A						.						177	166	170					6																	33254618		2203	4300	6503	SO:0001583	missense	9277	exon10			GATGACAGAGAAT	Z97184	CCDS4772.1	6p21.3	2013-01-09	2005-05-31	2005-05-31	ENSG00000227057	ENSG00000227057		"WD repeat domain containing"	13923	protein-coding gene	gene with protein product		611440	"chromosome 6 open reading frame 11"	C6orf11		9545376, 9521053	Standard	NM_005452		Approved	BING4, UTP7	uc003ods.3	O15213	OTTHUMG00000031192	ENST00000374617.4:c.1069T>A	chr6.hg19:g.33254618A>T	ENSP00000363746:p.Cys357Ser	121.0	0.0		114.0	41.0	NM_005452	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Missense_Mutation	SNP	ENST00000374617.4	hg19	CCDS4772.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.295007	0.81025	.	.	ENSG00000227057	ENST00000374617;ENST00000444176	T;T	0.59083	0.29;0.29	4.94	4.94	0.65067	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.51075	0.1653	N	0.25144	0.715	0.80722	D	1	D;P	0.89917	1.0;0.875	D;P	0.75484	0.986;0.56	T	0.53823	-0.8384	10	0.34782	T	0.22	-10.4346	12.5989	0.56487	1.0:0.0:0.0:0.0	.	303;357	B4DP15;O15213	.;WDR46_HUMAN	S	357;284	ENSP00000363746:C357S;ENSP00000405568:C284S	ENSP00000363746:C357S	C	-	1	0	WDR46	33362596	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.025000	0.76449	2.067000	0.61834	0.448000	0.29417	TGT	.	.		0.507	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452		T	33254618	A	T	33254618	3	4	142	1	0	0	0	0	1	0	0	0	17314	188	7	4	787	4	WDR46	6	33254618	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10		33254618	137860449	40	22069										
KIAA1009	22832	hgsc.bcm.edu	37	chr6	84910598	84910598	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tcaagattgacctctgcaacAgagtctaatgaatcaagcag	8	9	4	4			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr6:84910598A>T	ENST00000403245.3	-	9	858	c.744T>A	c.(742-744)tcT>tcA	p.S248S	KIAA1009_ENST00000257766.4_Silent_p.S172S	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		CCTCTGCAACAGAGTCTAATG	0.338																																					p.S248S		Atlas-SNP	.											.	KIAA1009	119	.	0			c.T744A						.						138	133	135					6																	84910598		2203	4300	6503	SO:0001819	synonymous_variant	22832	exon9			TGCAACAGAGTCT																												ENST00000403245.3:c.744T>A	chr6.hg19:g.84910598A>T		106.0	0.0		113.0	41.0	NM_014895		Silent	SNP	ENST00000403245.3	hg19	CCDS34494.2																																																																																			.	.		0.338	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			T	84910598	A	T	84910598	2	4	142	1	0	0	0	0	0	0	0	1	8212	175	7	4		4	KIAA1009	6	84910598	Silent	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	51655980	84910598	86204469	41	22070										
SEC63	11231	hgsc.bcm.edu	37	chr6	108214765	108214765	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	caggtgtaggttttttttttAaaggtttctttttttttgat	8	2	1	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr6:108214765A>T	ENST00000369002.4	-	16	1774	c.1595T>A	c.(1594-1596)tTa>tAa	p.L532*		NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	532	SEC63 1.				liver development (GO:0001889)|multicellular organismal aging (GO:0010259)|nitrogen compound metabolic process (GO:0006807)|posttranslational protein targeting to membrane (GO:0006620)|posttranslational protein targeting to membrane, translocation (GO:0031204)|protein targeting to membrane (GO:0006612)|renal system development (GO:0072001)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.L532*(2)		endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		TTTTTTTTTTAAAGGTTTCTT	0.368																																					p.L532X		Atlas-SNP	.											SEC63,NS,carcinoma,0,2	SEC63	79	.	2	Substitution - Nonsense(2)	lung(1)|kidney(1)	c.T1595A						.						114	119	117					6																	108214765		2202	4300	6502	SO:0001587	stop_gained	11231	exon16			TTTTTTAAAGGTT	BC048287	CCDS5061.1	6q21	2011-09-05	2006-09-12		ENSG00000025796	ENSG00000025796		"Heat shock proteins / DNAJ (HSP40)"	21082	protein-coding gene	gene with protein product		608648	"SEC63-like (S. cerevisiae)"			10219736, 10543453	Standard	NM_007214		Approved	SEC63L, PRO2507, ERdj2, DNAJC23	uc003psc.4	Q9UGP8	OTTHUMG00000015316	ENST00000369002.4:c.1595T>A	chr6.hg19:g.108214765A>T	ENSP00000357998:p.Leu532*	82.0	1.0		82.0	4.0	NM_007214	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	Nonsense_Mutation	SNP	ENST00000369002.4	hg19	CCDS5061.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	37|37	6.342620|6.342620	0.97489|0.97489	.|.	.|.	ENSG00000025796|ENSG00000025796	ENST00000423697|ENST00000369002;ENST00000437345	.|.	.|.	.|.	5.38|5.38	3.01|3.01	0.34805|0.34805	.|.	.|0.323197	.|0.31989	.|N	.|0.006744	T|.	0.17450|.	0.0419|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.07673|.	-1.0760|.	4|.	0.10636|0.14656	T|T	0.68|0.56	-2.4355|-2.4355	7.8269|7.8269	0.29320|0.29320	0.7741:0.0:0.2259:0.0|0.7741:0.0:0.2259:0.0	.|.	.|.	.|.	.|.	L|X	391|532;183	.|.	ENSP00000394572:F391L|ENSP00000357998:L532X	F|L	-|-	3|2	2|0	SEC63|SEC63	108321458|108321458	0.977000|0.977000	0.34250|0.34250	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	2.787000|2.787000	0.47798|0.47798	0.991000|0.991000	0.38814|0.38814	0.460000|0.460000	0.39030|0.39030	TTT|TTA	.	.		0.368	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214		T	108214765	A	T	108214765	4	4	142	1	0	0	0	0	0	1	0	0	14020	372	13	4	711	4	SEC63	6	108214765	Nonsense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	23304167	108214765	62900302	42	22071										
SGK1	6446	hgsc.bcm.edu	37	chr6	134494621	134494621	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tttccaaaactgccctttccGatcactttcaagaagtgaaa	5	11	2	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr6:134494621G>A	ENST00000237305.7	-	4	400	c.312C>T	c.(310-312)atC>atT	p.I104I	SGK1_ENST00000475719.2_Silent_p.I104I|SGK1_ENST00000528577.1_Silent_p.I132I|SGK1_ENST00000367858.5_Silent_p.I199I|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000413996.3_Silent_p.I118I|SGK1_ENST00000367857.5_Silent_p.I94I	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	104	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TGCCCTTTCCGATCACTTTCA	0.393																																					p.I199I		Atlas-SNP	.											.	SGK1	387	.	0			c.C597T						.						64	69	67					6																	134494621		2203	4300	6503	SO:0001819	synonymous_variant	6446	exon6			CTTTCCGATCACT	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"serum/glucocorticoid regulated kinase"	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.312C>T	chr6.hg19:g.134494621G>A		158.0	0.0		157.0	36.0	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	hg19	CCDS5170.1																																																																																			.	.		0.393	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134494621	G	A	134494621	2	1	142	1	0	0	0	0	0	0	0	1	14222	1048	37	1		1	SGK1	6	134494621	Silent	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	26279856	134494621	36620446	43	22072										
KATNA1	11104	hgsc.bcm.edu	37	chr6	149916182	149916182	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	atgtgagaatttagcatgatCcaaactcaaatatccatttc	5	8	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr6:149916182C>G	ENST00000335647.5	-	10	1510	c.1466G>C	c.(1465-1467)gGa>gCa	p.G489A	KATNA1_ENST00000335643.8_3'UTR|RP1-12G14.7_ENST00000419134.1_RNA|KATNA1_ENST00000367411.2_Missense_Mutation_p.G489A|SNORA2_ENST00000365473.1_RNA|KATNA1_ENST00000494504.1_5'Flank					katanin p60 (ATPase containing) subunit A 1											endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	12		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		TTAGCATGATCCAAACTCAAA	0.333																																					p.G489A		Atlas-SNP	.											.	KATNA1	34	.	0			c.G1466C						.						99	95	96					6																	149916182		2203	4300	6503	SO:0001583	missense	11104	exon11			CATGATCCAAACT	AF056022	CCDS5217.1, CCDS56456.1	6q24.3	2011-01-25	2011-01-25		ENSG00000186625	ENSG00000186625		"ATPases / AAA-type"	6216	protein-coding gene	gene with protein product		606696	"katanin p60 (ATPase-containing) subunit A 1"			9658175	Standard	NM_007044		Approved		uc003qms.3	O75449	OTTHUMG00000015787	ENST00000335647.5:c.1466G>C	chr6.hg19:g.149916182C>G	ENSP00000335106:p.Gly489Ala	110.0	0.0		66.0	17.0	NM_007044		Missense_Mutation	SNP	ENST00000335647.5	hg19	CCDS5217.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.980479	0.92982	.	.	ENSG00000186625	ENST00000335647;ENST00000367411	D;D	0.99158	-5.5;-5.5	5.87	5.87	0.94306	Vps4 oligomerisation, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99612	0.9859	H	0.95679	3.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98225	1.0480	9	.	.	.	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	489	O75449	KTNA1_HUMAN	A	489	ENSP00000335106:G489A;ENSP00000356381:G489A	.	G	-	2	0	KATNA1	149957875	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.333	KATNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042641.2	NM_007044		G	149916182	C	G	149916182	3	3	142	1	0	0	0	0	1	0	0	0	7993	855	30	4	13	4	KATNA1	6	149916182	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	15421561	149916182	21198885	44	22073										
PARK2	5071	hgsc.bcm.edu	37	chr6	162206857	162206857	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	cgtgaacaaactgccgatcaTtgagtcttgtcacacagtat	8	10	3	2	rs373750972		TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr6:162206857T>C	ENST00000366898.1	-	7	920	c.818A>G	c.(817-819)aAt>aGt	p.N273S	PARK2_ENST00000366897.1_Missense_Mutation_p.N245S|PARK2_ENST00000366894.1_Missense_Mutation_p.N82S|PARK2_ENST00000366896.1_Missense_Mutation_p.N124S|PARK2_ENST00000338468.3_Missense_Mutation_p.N82S|PARK2_ENST00000366892.1_Missense_Mutation_p.N273S	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	273	SYT11 binding 2.				adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		CTGCCGATCATTGAGTCTTGT	0.478																																					p.N273S		Atlas-SNP	.											.	PARK2	96	.	0			c.A818G	GRCh37	CM080475	PARK2	M		.	T	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	106	90	96		818,734,371	5.8	0.9	6		96	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	PARK2	NM_004562.2,NM_013987.2,NM_013988.2	46,46,46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	273/466,245/438,124/317	162206857	1,13005	2203	4300	6503	SO:0001583	missense	5071	exon7			CGATCATTGAGTC		CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"Parkinson disease"	8607	protein-coding gene	gene with protein product	"E3 ubiquitin ligase"	602544	"Parkinson disease (autosomal recessive, juvenile) 2, parkin", "parkinson protein 2, E3 ubiquitin protein ligase (parkin)"			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.818A>G	chr6.hg19:g.162206857T>C	ENSP00000355865:p.Asn273Ser	156.0	0.0		156.0	46.0	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	hg19	CCDS5281.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.273185	0.80580	0.0	1.16E-4	ENSG00000185345	ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366894;ENST00000338468;ENST00000392134;ENST00000366892;ENST00000366895	D;D;D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57;-2.57;-2.57	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.91085	0.7194	M	0.78637	2.42	0.38863	D	0.956527	D;D;D;D;P	0.69078	0.989;0.997;0.993;0.993;0.911	P;D;P;P;P	0.70716	0.9;0.97;0.858;0.858;0.505	D	0.89755	0.3943	10	0.12103	T	0.63	.	14.2774	0.66189	0.0:0.0:0.0:1.0	.	273;124;245;273;82	O60260-5;Q5VVX3;Q5VVX4;O60260;Q8NI42	.;.;.;PRKN2_HUMAN;.	S	273;245;124;82;82;82;273;194	ENSP00000355865:N273S;ENSP00000355863:N245S;ENSP00000355862:N124S;ENSP00000355860:N82S;ENSP00000343589:N82S;ENSP00000355858:N273S	ENSP00000343589:N82S	N	-	2	0	PARK2	162126847	1.000000	0.71417	0.923000	0.36655	0.939000	0.58152	6.736000	0.74811	2.193000	0.70182	0.528000	0.53228	AAT	.	.		0.478	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			C	162206857	T	C	162206857	3	2	142	1	0	0	0	0	1	0	0	0	11458	1493	52	2	603	2	PARK2	6	162206857	Missense_Mutation	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	12290675	162206857	8908210	45	22074										
EGFR	1956	hgsc.bcm.edu	37	chr7	55225380	55225380	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tttgctgattcaggcttggcCtgaaaacaggacggacctcc	11	11	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr7:55225380C>G	ENST00000275493.2	+	11	1409	c.1232C>G	c.(1231-1233)cCt>cGt	p.P411R	EGFR_ENST00000344576.2_Missense_Mutation_p.P411R|EGFR_ENST00000455089.1_Missense_Mutation_p.P366R|EGFR_ENST00000454757.2_Missense_Mutation_p.P358R|EGFR_ENST00000442591.1_Missense_Mutation_p.P411R|EGFR_ENST00000342916.3_Missense_Mutation_p.P411R	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	411					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CAGGCTTGGCCTGAAAACAGG	0.463		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.P411R		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	.	EGFR	20426	.	0			c.C1232G						.						99	85	89					7																	55225380		2203	4300	6503	SO:0001583	missense	1956	exon11	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	CTTGGCCTGAAAA		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1232C>G	chr7.hg19:g.55225380C>G	ENSP00000275493:p.Pro411Arg	147.0	0.0		120.0	43.0	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	hg19	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.040735	0.93685	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.93	5.93	0.95920	EGF receptor, L domain (1);	0.000000	0.85682	D	0.000000	T	0.70439	0.3224	M	0.84511	2.7	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;1.0	T	0.73833	-0.3858	10	0.87932	D	0	.	18.9076	0.92469	0.0:1.0:0.0:0.0	.	366;411;411;411	Q504U8;P00533;P00533-3;P00533-4	.;EGFR_HUMAN;.;.	R	366;411;281;411;411;411;358;205	ENSP00000415559:P366R;ENSP00000342376:P411R;ENSP00000345973:P411R;ENSP00000275493:P411R;ENSP00000410031:P411R;ENSP00000395243:P358R	ENSP00000275493:P411R	P	+	2	0	EGFR	55192874	1.000000	0.71417	0.969000	0.41365	0.996000	0.88848	7.472000	0.80996	2.815000	0.96918	0.561000	0.74099	CCT	.	.		0.463	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55225380	C	G	55225380	3	3	142	1	0	0	0	0	1	0	0	0	4969	681	24	4	1285	4	EGFR	7	55225380	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10		55225380	103913283	46	22075										
XPO7	23039	hgsc.bcm.edu	37	chr8	21842213	21842213	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ggtccagcagcagttggaccAgctgtccaccattgggcgtt	13	12	0	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr8:21842213A>T	ENST00000252512.9	+	12	1434	c.1334A>T	c.(1333-1335)cAg>cTg	p.Q445L	XPO7_ENST00000433566.4_Missense_Mutation_p.Q446L|XPO7_ENST00000434536.1_Missense_Mutation_p.Q454L	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	445					mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		CAGTTGGACCAGCTGTCCACC	0.547																																					p.Q445L		Atlas-SNP	.											.	XPO7	79	.	0			c.A1334T						.						46	48	47					8																	21842213		1988	4155	6143	SO:0001583	missense	23039	exon12			TGGACCAGCTGTC	AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"Exportins"	14108	protein-coding gene	gene with protein product		606140	"RAN binding protein 16"	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.1334A>T	chr8.hg19:g.21842213A>T	ENSP00000252512:p.Gln445Leu	107.0	0.0		75.0	39.0	NM_015024	O94846|Q6PJK9|Q8NEK7	Missense_Mutation	SNP	ENST00000252512.9	hg19	CCDS47818.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.948887	0.92660	.	.	ENSG00000130227	ENST00000434536;ENST00000252512;ENST00000433566	T;T;T	0.61627	0.09;0.09;0.09	5.4	5.4	0.78164	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.79575	0.4469	M	0.91406	3.205	0.80722	D	1	D;B;B	0.89917	1.0;0.125;0.125	D;B;B	0.80764	0.994;0.119;0.082	T	0.80754	-0.1241	10	0.25751	T	0.34	-9.9419	15.0967	0.72242	1.0:0.0:0.0:0.0	.	446;454;445	E7ESC6;E9PEN8;Q9UIA9	.;.;XPO7_HUMAN	L	454;445;446	ENSP00000404853:Q454L;ENSP00000252512:Q445L;ENSP00000410249:Q446L	ENSP00000252512:Q445L	Q	+	2	0	XPO7	21898159	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.339000	0.96797	2.051000	0.60960	0.383000	0.25322	CAG	.	.		0.547	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024		T	21842213	A	T	21842213	3	4	142	1	0	0	0	0	1	0	0	0	17464	188	7	4	1432	4	XPO7	8	21842213	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10		21842213	124521809	47	22076										
ASPH	444	hgsc.bcm.edu	37	chr8	62593583	62593583	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	catcaccatcagcatcatagAttcctagttttcctataata	3	11	3	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr8:62593583A>G	ENST00000379454.4	-	3	453	c.266T>C	c.(265-267)aTc>aCc	p.I89T	ASPH_ENST00000517661.1_Missense_Mutation_p.I75T|ASPH_ENST00000389204.4_Missense_Mutation_p.I75T|ASPH_ENST00000522603.1_Missense_Mutation_p.I60T|ASPH_ENST00000445642.3_Missense_Mutation_p.I75T|ASPH_ENST00000517903.1_Missense_Mutation_p.I75T|ASPH_ENST00000379449.6_Missense_Mutation_p.I104T|ASPH_ENST00000517856.1_Missense_Mutation_p.I89T|ASPH_ENST00000522835.1_Missense_Mutation_p.I75T|ASPH_ENST00000541428.1_Missense_Mutation_p.I60T|ASPH_ENST00000518068.1_Missense_Mutation_p.I89T|ASPH_ENST00000517847.2_Missense_Mutation_p.I75T|ASPH_ENST00000356457.5_Missense_Mutation_p.I89T	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	89					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular response to calcium ion (GO:0071277)|detection of calcium ion (GO:0005513)|face morphogenesis (GO:0060325)|limb morphogenesis (GO:0035108)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|palate development (GO:0060021)|pattern specification process (GO:0007389)|peptidyl-aspartic acid hydroxylation (GO:0042264)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteolysis (GO:0045862)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|regulation of protein depolymerization (GO:1901879)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|response to ATP (GO:0033198)	calcium channel complex (GO:0034704)|cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|electron carrier activity (GO:0009055)|ion channel binding (GO:0044325)|peptide-aspartate beta-dioxygenase activity (GO:0004597)|structural constituent of muscle (GO:0008307)|structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(5)|large_intestine(5)|lung(16)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	AGCATCATAGATTCCTAGTTT	0.313																																					p.I104T		Atlas-SNP	.											.	ASPH	87	.	0			c.T311C						.						124	127	126					8																	62593583		2203	4295	6498	SO:0001583	missense	444	exon4			TCATAGATTCCTA	AF224468	CCDS34898.1, CCDS34899.1, CCDS34900.1, CCDS43742.1, CCDS47866.1, CCDS55234.1, CCDS55235.1, CCDS55236.1, CCDS55237.1, CCDS55238.1, CCDS75746.1	8q12.1	2008-02-05			ENSG00000198363	ENSG00000198363	1.14.11.16		757	protein-coding gene	gene with protein product	"junctin", "humbug", "junctate"	600582				7821814, 10974562	Standard	NM_004318		Approved	CASQ2BP1, BAH, JCTN, HAAH	uc003xuj.3	Q12797	OTTHUMG00000164375	ENST00000379454.4:c.266T>C	chr8.hg19:g.62593583A>G	ENSP00000368767:p.Ile89Thr	324.0	0.0		316.0	94.0	NM_001164756	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Missense_Mutation	SNP	ENST00000379454.4	hg19	CCDS34898.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.792445	0.50102	.	.	ENSG00000198363	ENST00000389213;ENST00000541428;ENST00000379454;ENST00000522349;ENST00000356457;ENST00000519234;ENST00000518068;ENST00000517903;ENST00000445642;ENST00000517847;ENST00000522835;ENST00000518306;ENST00000517856;ENST00000389204;ENST00000522603;ENST00000379449;ENST00000517661	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36	5.77	5.77	0.91146	Aspartyl beta-hydroxylase/Triadin domain (1);	0.616994	0.15683	N	0.249813	T	0.52175	0.1718	L	0.34521	1.04	0.35207	D	0.774787	B;B;P;B;B;B;B;B;P;B;B;B;B;B	0.45768	0.002;0.004;0.802;0.002;0.029;0.006;0.026;0.056;0.866;0.031;0.107;0.007;0.013;0.057	B;B;P;B;B;B;B;B;P;B;B;B;B;B	0.46796	0.005;0.017;0.527;0.026;0.039;0.039;0.037;0.141;0.507;0.028;0.069;0.014;0.026;0.062	T	0.64859	-0.6308	10	0.72032	D	0.01	-1.4402	16.068	0.80903	1.0:0.0:0.0:0.0	.	60;75;89;75;75;75;60;104;104;89;89;89;75;89	Q12797-4;Q12797-3;B8Y0L3;B4DIC9;B7ZM95;B7ZM96;F5H667;E5RG56;Q6NXR7;F8W7A9;Q8TB28;Q12797-2;Q9H291;Q12797	.;.;.;.;.;.;.;.;.;.;.;.;.;ASPH_HUMAN	T	89;60;89;60;89;104;89;75;75;75;75;60;89;75;60;104;75	ENSP00000437864:I60T;ENSP00000368767:I89T;ENSP00000429718:I60T;ENSP00000348841:I89T;ENSP00000427823:I104T;ENSP00000429286:I89T;ENSP00000430245:I75T;ENSP00000394013:I75T;ENSP00000429954:I75T;ENSP00000429160:I75T;ENSP00000427877:I60T;ENSP00000429743:I89T;ENSP00000373856:I75T;ENSP00000436188:I60T;ENSP00000368762:I104T;ENSP00000428060:I75T	ENSP00000348841:I89T	I	-	2	0	ASPH	62756137	1.000000	0.71417	0.856000	0.33681	0.968000	0.65278	6.965000	0.76067	2.326000	0.78906	0.533000	0.62120	ATC	.	.		0.313	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318		G	62593583	A	G	62593583	3	3	142	1	0	0	0	0	1	0	0	0	1053	333	12	2	2769	2	ASPH	8	62593583	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	40751370	62593583	83770439	48	22077										
LY96	23643	hgsc.bcm.edu	37	chr8	74917085	74917085	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	cccctgtatagaattgaaaaGatccaaaggattattgcaca	7	8	0	3			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr8:74917085G>T	ENST00000284818.2	+	2	258	c.167G>T	c.(166-168)aGa>aTa	p.R56I	LY96_ENST00000518893.1_Intron	NM_015364.4	NP_056179	Q9Y6Y9	LY96_HUMAN	lymphocyte antigen 96	56			R -> G (in dbSNP:rs6472812). {ECO:0000269|PubMed:10359581, ECO:0000269|PubMed:10891475, ECO:0000269|PubMed:11435474, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18810425}.		cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	endosome membrane (GO:0010008)|extracellular region (GO:0005576)|lipopolysaccharide receptor complex (GO:0046696)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|lipopolysaccharide receptor activity (GO:0001875)			endometrium(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5	Breast(64;0.0311)		Epithelial(68;0.0208)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0619)			GAATTGAAAAGATCCAAAGGA	0.269																																					p.R56I	GBM(131;1357 1748 34893 50149 52212)	Atlas-SNP	.											.	LY96	17	.	0			c.G167T						.						49	53	51					8																	74917085		2200	4284	6484	SO:0001583	missense	23643	exon2			TGAAAAGATCCAA	AB018549	CCDS6216.1, CCDS56540.1	8q13.3	2004-01-22			ENSG00000154589	ENSG00000154589			17156	protein-coding gene	gene with protein product		605243				10359581, 11466383	Standard	NM_015364		Approved	MD-2	uc003yad.3	Q9Y6Y9	OTTHUMG00000164504	ENST00000284818.2:c.167G>T	chr8.hg19:g.74917085G>T	ENSP00000284818:p.Arg56Ile	355.0	1.0		389.0	124.0	NM_015364	B3Y6A5|E5RJJ7	Missense_Mutation	SNP	ENST00000284818.2	hg19	CCDS6216.1	.	.	.	.	.	.	.	.	.	.	G	10.96	1.498429	0.26861	.	.	ENSG00000154589	ENST00000284818	T	0.44482	0.92	5.2	1.87	0.25490	MD-2-related lipid-recognition (2);Immunoglobulin E-set (1);	0.587686	0.16363	N	0.217688	T	0.19485	0.0468	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14254	-1.0479	10	0.66056	D	0.02	.	3.7764	0.08661	0.2529:0.1995:0.5477:0.0	.	56	Q9Y6Y9	LY96_HUMAN	I	56	ENSP00000284818:R56I	ENSP00000284818:R56I	R	+	2	0	LY96	75079639	0.046000	0.20272	0.019000	0.16419	0.003000	0.03518	1.150000	0.31639	0.583000	0.29574	0.650000	0.86243	AGA	.	.		0.269	LY96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379032.2	NM_015364		T	74917085	G	T	74917085	3	4	142	1	0	0	0	0	1	0	0	0	9111	942	33	3	173	3	LY96	8	74917085	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	12323502	74917085	71446937	49	22078										
OSR2	116039	hgsc.bcm.edu	37	chr8	99961205	99961205	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ggagcaaggctctgccagcgCccatcccgctccacccgtcg	11	19	1	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr8:99961205C>T	ENST00000297565.4	+	2	521	c.25C>T	c.(25-27)Ccc>Tcc	p.P9S	OSR2_ENST00000522510.1_Missense_Mutation_p.P9S|OSR2_ENST00000523368.1_Missense_Mutation_p.P9S|OSR2_ENST00000457907.2_Missense_Mutation_p.P130S|OSR2_ENST00000435298.2_Missense_Mutation_p.P9S	NM_001142462.1	NP_001135934.1	Q8N2R0	OSR2_HUMAN	odd-skipped related transciption factor 2	9					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|chondrocyte differentiation (GO:0002062)|embryo development (GO:0009790)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|embryonic skeletal system morphogenesis (GO:0048704)|eyelid development in camera-type eye (GO:0061029)|head development (GO:0060322)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|osteoblast proliferation (GO:0033687)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Breast(36;4.14e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.0136)			TCTGCCAGCGCCCATCCCGCT	0.662																																					p.P9S		Atlas-SNP	.											.	OSR2	56	.	0			c.C25T						.						45	50	48					8																	99961205		2038	4182	6220	SO:0001583	missense	116039	exon2			CCAGCGCCCATCC	AY038072	CCDS47901.1, CCDS47902.1, CCDS69520.1	8q22.2	2013-10-17	2013-10-17			ENSG00000164920		"Zinc fingers, C2H2-type"	15830	protein-coding gene	gene with protein product		611297	"odd-skipped related 2 (Drosophila)"				Standard	XM_005250779		Approved	FLJ90037	uc003yir.3	Q8N2R0		ENST00000297565.4:c.25C>T	chr8.hg19:g.99961205C>T	ENSP00000297565:p.Pro9Ser	72.0	0.0		102.0	21.0	NM_053001	A8K626|B4E3B7|Q96AM6|Q96LB6|Q96LB7	Missense_Mutation	SNP	ENST00000297565.4	hg19	CCDS47901.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.749979	0.89753	.	.	ENSG00000164920	ENST00000523368;ENST00000297565;ENST00000435298;ENST00000522510;ENST00000457907;ENST00000520951;ENST00000518199	T;T;T;T;T;T;T	0.19250	2.16;2.39;2.42;2.39;2.77;2.91;2.41	4.04	4.04	0.47022	.	0.000000	0.85682	D	0.000000	T	0.33147	0.0853	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;1.0;1.0	D;D;D;D	0.91635	0.997;0.937;0.96;0.999	T	0.06023	-1.0850	9	.	.	.	-20.3963	17.4991	0.87727	0.0:1.0:0.0:0.0	.	130;9;9;9	B4E3B7;E5RH04;Q8N2R0;Q8N2R0-2	.;.;OSR2_HUMAN;.	S	9;9;9;9;130;62;9	ENSP00000430041:P9S;ENSP00000297565:P9S;ENSP00000402862:P9S;ENSP00000430780:P9S;ENSP00000414657:P130S;ENSP00000430074:P62S;ENSP00000429910:P9S	.	P	+	1	0	OSR2	100030381	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.585000	0.82584	2.529000	0.85273	0.655000	0.94253	CCC	.	.		0.662	OSR2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000379505.1	NM_053001		T	99961205	C	T	99961205	3	4	142	1	0	0	0	0	1	0	0	0	11303	739	26	3	27	3	OSR2	8	99961205	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	25044120	99961205	46402817	50	22079										
KLF10	7071	hgsc.bcm.edu	37	chr8	103663550	103663550	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tgggagagagtctggtgccaTtcgggctcaccaccggaggc	16	11	2	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr8:103663550T>C	ENST00000285407.6	-	3	1310	c.1010A>G	c.(1009-1011)aAt>aGt	p.N337S	KLF10_ENST00000395884.3_Missense_Mutation_p.N326S	NM_005655.2	NP_005646.1	Q13118	KLF10_HUMAN	Kruppel-like factor 10	337					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular response to peptide (GO:1901653)|cellular response to starvation (GO:0009267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of circadian rhythm (GO:0042752)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(3)	18	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			TCTGGTGCCATTCGGGCTCAC	0.542																																					p.N337S	Esophageal Squamous(16;495 519 2144 16528 44005)	Atlas-SNP	.											.	KLF10	44	.	0			c.A1010G						.						82	92	89					8																	103663550		2203	4300	6503	SO:0001583	missense	7071	exon3			GTGCCATTCGGGC	U21847	CCDS6294.1, CCDS47905.1	8q22.3	2014-09-17	2004-11-29	2004-12-01	ENSG00000155090	ENSG00000155090		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11810	protein-coding gene	gene with protein product		601878	"TGFB inducible early growth response"	TIEG		8584037, 9721211	Standard	NM_001032282		Approved	EGRA, TIEG1	uc011lhk.1	Q13118	OTTHUMG00000164735	ENST00000285407.6:c.1010A>G	chr8.hg19:g.103663550T>C	ENSP00000285407:p.Asn337Ser	157.0	0.0		233.0	38.0	NM_005655	A8MVH0|B2R794|L0R4P6|L0R679|O75411|Q503B2	Missense_Mutation	SNP	ENST00000285407.6	hg19	CCDS6294.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.285864	0.23478	.	.	ENSG00000155090	ENST00000285407;ENST00000395884	T;T	0.12569	2.67;2.73	5.5	4.3	0.51218	.	0.328865	0.32970	N	0.005439	T	0.07413	0.0187	N	0.17082	0.46	0.30433	N	0.777012	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.28364	-1.0046	10	0.10636	T	0.68	.	9.1312	0.36846	0.0:0.1432:0.0:0.8568	.	337;326	Q13118;O75411	KLF10_HUMAN;.	S	337;326	ENSP00000285407:N337S;ENSP00000379222:N326S	ENSP00000285407:N337S	N	-	2	0	KLF10	103732726	1.000000	0.71417	0.708000	0.30435	0.992000	0.81027	3.229000	0.51278	0.974000	0.38366	0.533000	0.62120	AAT	.	.		0.542	KLF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379967.1			C	103663550	T	C	103663550	3	2	142	1	0	0	0	0	1	0	0	0	8347	1493	52	2	440	2	KLF10	8	103663550	Missense_Mutation	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	3702345	103663550	42700472	51	22080										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116632123	116632123	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gctatgttcctccttatgatTtagttctgcagcatcactct	6	11	3	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr8:116632123T>G	ENST00000220888.5	-	2	322	c.163A>C	c.(163-165)Aat>Cat	p.N55H	TRPS1_ENST00000519674.1_Missense_Mutation_p.N55H|TRPS1_ENST00000395715.3_Missense_Mutation_p.N68H|TRPS1_ENST00000520276.1_Missense_Mutation_p.N59H|TRPS1_ENST00000519076.1_Missense_Mutation_p.N55H			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	55					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			TCCTTATGATTTAGTTCTGCA	0.413									Langer-Giedion syndrome																												p.N68H		Atlas-SNP	.											.	TRPS1	516	.	0			c.A202C						.						118	106	110					8																	116632123		1922	4148	6070	SO:0001583	missense	7227	exon3	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	TATGATTTAGTTC	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.163A>C	chr8.hg19:g.116632123T>G	ENSP00000220888:p.Asn55His	117.0	0.0		212.0	130.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	T	13.92	2.379699	0.42207	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276;ENST00000519674;ENST00000395713;ENST00000519815	D;D;D;D;T	0.98717	-5.09;-5.06;-5.03;-5.06;0.74	5.55	5.55	0.83447	.	0.076780	0.53938	D	0.000047	D	0.95774	0.8625	N	0.12182	0.205	0.36102	D	0.844201	P;P;P	0.40794	0.729;0.61;0.729	B;B;B	0.41236	0.351;0.191;0.351	D	0.99421	1.0933	10	0.87932	D	0	-15.9627	14.2778	0.66191	0.0:0.0:0.0:1.0	.	59;55;68	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	H	68;55;55;59;55;68;68	ENSP00000379065:N68H;ENSP00000220888:N55H;ENSP00000428910:N55H;ENSP00000428680:N59H;ENSP00000429174:N55H	ENSP00000220888:N55H	N	-	1	0	TRPS1	116701298	0.993000	0.37304	0.996000	0.52242	0.870000	0.49936	2.300000	0.43620	2.104000	0.64026	0.528000	0.53228	AAT	.	.		0.413	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		G	116632123	T	G	116632123	3	3	142	1	0	0	0	0	1	0	0	0	16608	1841	64	5	3702	5	TRPS1	8	116632123	Missense_Mutation	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	12968573	116632123	29731899	52	22081										
CYP11B2	1585	hgsc.bcm.edu	37	chr8	143996179	143996179	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ttccacaccttggggctgatCcagcgagacaggctcctggg	13	13	0	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr8:143996179C>A	ENST00000323110.2	-	4	743	c.741G>T	c.(739-741)tgG>tgT	p.W247C		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	247					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	TGGGGCTGATCCAGCGAGACA	0.602									Familial Hyperaldosteronism type I																												p.W247C		Atlas-SNP	.											.	CYP11B2	107	.	0			c.G741T						.						56	50	52					8																	143996179		2202	4300	6502	SO:0001583	missense	1585	exon4	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	GCTGATCCAGCGA	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"Cytochrome P450s"	2592	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	124080	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.741G>T	chr8.hg19:g.143996179C>A	ENSP00000325822:p.Trp247Cys	341.0	0.0		457.0	103.0	NM_000498	B0ZBE4|Q16726	Missense_Mutation	SNP	ENST00000323110.2	hg19	CCDS6393.1	.	.	.	.	.	.	.	.	.	.	.	13.16	2.153309	0.38021	.	.	ENSG00000179142	ENST00000323110	T	0.68624	-0.34	3.79	2.88	0.33553	.	0.163582	0.26397	N	0.024616	T	0.77212	0.4097	M	0.80183	2.485	0.23956	N	0.996352	D	0.55800	0.973	P	0.61275	0.886	T	0.66192	-0.5985	10	0.54805	T	0.06	.	9.3243	0.37984	0.0:0.8878:0.0:0.1122	.	247	P19099	C11B2_HUMAN	C	247	ENSP00000325822:W247C	ENSP00000325822:W247C	W	-	3	0	CYP11B2	143993181	0.014000	0.17966	0.683000	0.30040	0.852000	0.48524	0.681000	0.25320	1.946000	0.56461	0.561000	0.74099	TGG	.	.		0.602	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1			A	143996179	C	A	143996179	3	1	142	1	0	0	0	0	1	0	0	0	4148	856	30	3	794	3	CYP11B2	8	143996179	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	27364056	143996179	2367843	53	22082										
DOCK8	81704	hgsc.bcm.edu	37	chr9	396809	396809	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	aaagcatggcccagcacgtaCataacatggacaaacgggac	10	11	0	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr9:396809C>G	ENST00000453981.1	+	25	3107	c.2995C>G	c.(2995-2997)Cat>Gat	p.H999D	DOCK8_ENST00000382331.1_Missense_Mutation_p.H301D|DOCK8_ENST00000382329.1_Missense_Mutation_p.H466D|DOCK8_ENST00000432829.2_Missense_Mutation_p.H931D|DOCK8_ENST00000469391.1_Missense_Mutation_p.H899D			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	999					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CCAGCACGTACATAACATGGA	0.473																																					p.H999D		Atlas-SNP	.											.	DOCK8	401	.	0			c.C2995G						.						192	179	183					9																	396809		2203	4300	6503	SO:0001583	missense	81704	exon25			CACGTACATAACA	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.2995C>G	chr9.hg19:g.396809C>G	ENSP00000408464:p.His999Asp	111.0	0.0		100.0	40.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	C	13.55	2.270212	0.40194	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382331;ENST00000382329	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	5.7	5.7	0.88788	.	0.194435	0.56097	D	0.000037	T	0.20495	0.0493	L	0.41236	1.265	0.46437	D	0.999043	B;B;B;B	0.12013	0.005;0.0;0.0;0.0	B;B;B;B	0.13407	0.009;0.002;0.001;0.001	T	0.01819	-1.1267	10	0.35671	T	0.21	.	16.1232	0.81375	0.0:0.8666:0.1334:0.0	.	301;899;466;999	A2A370;E9PH09;A2A369;Q8NF50	.;.;.;DOCK8_HUMAN	D	999;967;931;899;301;466	ENSP00000408464:H999D;ENSP00000394888:H931D;ENSP00000419438:H899D;ENSP00000371768:H301D;ENSP00000371766:H466D	ENSP00000287364:H967D	H	+	1	0	DOCK8	386809	0.587000	0.26791	0.921000	0.36526	0.992000	0.81027	1.804000	0.38873	2.683000	0.91414	0.655000	0.94253	CAT	.	.		0.473	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		G	396809	C	G	396809	3	3	142	1	0	0	0	0	1	0	0	0	4695	478	17	4	3093	4	DOCK8	9	396809	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10		396809	140816622	54	22083										
NACC2	138151	hgsc.bcm.edu	37	chr9	138903604	138903604	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	cacggcgtcagttctcagagCcacgatggtggcggcgtcgc	15	13	2	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr9:138903604C>A	ENST00000371753.1	-	5	1580	c.1522G>T	c.(1522-1524)Gct>Tct	p.A508S	NACC2_ENST00000277554.2_Missense_Mutation_p.A508S			Q96BF6	NACC2_HUMAN	NACC family member 2, BEN and BTB (POZ) domain containing	508					cellular protein complex localization (GO:0034629)|histone deacetylation (GO:0016575)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter (GO:1900477)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|posttranscriptional regulation of gene expression (GO:0010608)|protein homooligomerization (GO:0051260)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)			endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5						GTTCTCAGAGCCACGATGGTG	0.706																																					p.A508S		Atlas-SNP	.											.	NACC2	16	.	0			c.G1522T						.						8	8	8					9																	138903604		2158	4230	6388	SO:0001583	missense	138151	exon6			TCAGAGCCACGAT	BC015649	CCDS6993.1	9q34.3	2013-01-09	2008-10-03	2008-10-03	ENSG00000148411	ENSG00000148411		"BEN domain containing", "BTB/POZ domain containing"	23846	protein-coding gene	gene with protein product	"BEN domain containing 9"	615786	"BTB (POZ) domain containing 14A"	BTBD14A		12477932	Standard	NM_144653		Approved	MGC23427, BEND9, BTBD31	uc004cgv.4	Q96BF6	OTTHUMG00000020921	ENST00000371753.1:c.1522G>T	chr9.hg19:g.138903604C>A	ENSP00000360818:p.Ala508Ser	31.0	0.0		36.0	13.0	NM_144653		Missense_Mutation	SNP	ENST00000371753.1	hg19	CCDS6993.1	.	.	.	.	.	.	.	.	.	.	C	10.64	1.406841	0.25378	.	.	ENSG00000148411	ENST00000371753;ENST00000277554	T;T	0.69040	-0.37;-0.37	5.39	4.47	0.54385	.	0.399526	0.23302	N	0.049666	T	0.48484	0.1502	N	0.12182	0.205	0.35333	D	0.785763	B	0.17038	0.02	B	0.12156	0.007	T	0.54516	-0.8282	10	0.51188	T	0.08	.	12.1324	0.53950	0.3118:0.6882:0.0:0.0	.	508	Q96BF6	NACC2_HUMAN	S	508	ENSP00000360818:A508S;ENSP00000277554:A508S	ENSP00000277554:A508S	A	-	1	0	NACC2	138043425	0.570000	0.26651	0.968000	0.41197	0.046000	0.14306	1.646000	0.37249	1.204000	0.43247	0.491000	0.48974	GCT	.	.		0.706	NACC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055040.1	NM_144653		A	138903604	C	A	138903604	3	1	142	1	0	0	0	0	1	0	0	0	10145	739	26	3	245	3	NACC2	9	138903604	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	138506795	138903604	2309827	55	22084										
OR13A1	79290	hgsc.bcm.edu	37	chr10	45799015	45799015	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	agccaacttgctcttccctgCgctgtagccagagaccgggc	11	15	1	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr10:45799015C>T	ENST00000553795.1	-	4	1164	c.856G>A	c.(856-858)Gca>Aca	p.A286T	OR13A1_ENST00000374401.2_Missense_Mutation_p.A286T|OR13A1_ENST00000536058.1_Missense_Mutation_p.A286T	NM_001004297.2	NP_001004297.2	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A, member 1	286						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)|urinary_tract(1)	19						CTCTTCCCTGCGCTGTAGCCA	0.547																																					p.A286T		Atlas-SNP	.											.	OR13A1	49	.	0			c.G856A						.						68	63	65					10																	45799015		2203	4300	6503	SO:0001583	missense	79290	exon4			TCCCTGCGCTGTA	AB065728	CCDS31188.1	10q11.21	2012-10-03			ENSG00000256574	ENSG00000256574		"GPCR / Class A : Olfactory receptors"	14772	protein-coding gene	gene with protein product							Standard	NM_001004297		Approved		uc001jcc.1	Q8NGR1	OTTHUMG00000018080	ENST00000553795.1:c.856G>A	chr10.hg19:g.45799015C>T	ENSP00000451950:p.Ala286Thr	87.0	0.0		90.0	8.0	NM_001004297	Q2M3M4|Q5VV57|Q6IFH5|Q6ZMN6	Missense_Mutation	SNP	ENST00000553795.1	hg19	CCDS31188.1	.	.	.	.	.	.	.	.	.	.	c	5.954	0.359924	0.11296	.	.	ENSG00000256574	ENST00000553795;ENST00000536058;ENST00000374401	T;T;T	0.00107	8.72;8.72;8.72	5.68	0.323	0.15893	GPCR, rhodopsin-like superfamily (1);	0.940197	0.08767	N	0.896846	T	0.00073	0.0002	N	0.11560	0.145	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.01561	-1.1324	10	0.15952	T	0.53	-14.7853	3.0987	0.06318	0.359:0.2975:0.2628:0.0807	.	286	Q8NGR1	O13A1_HUMAN	T	286	ENSP00000451950:A286T;ENSP00000438657:A286T;ENSP00000363522:A286T	ENSP00000311379:A286T	A	-	1	0	OR13A1	45119021	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.120000	0.10660	0.315000	0.23110	-0.143000	0.13931	GCA	.	.		0.547	OR13A1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047779.2	NM_001004297		T	45799015	C	T	45799015	3	4	142	1	0	0	0	0	1	0	0	0	10942	768	27	1	134	1	OR13A1	10	45799015	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10		45799015	89735732	56	22085										
DDX50	79009	hgsc.bcm.edu	37	chr10	70661161	70661161	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	atgcctgggaaactcctctgGggggacattatggagctgga	15	8	1	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr10:70661161G>T	ENST00000373585.3	+	1	128	c.21G>T	c.(19-21)tgG>tgT	p.W7C		NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	7						membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						AACTCCTCTGGGGGGACATTA	0.642																																					p.W7C		Atlas-SNP	.											.	DDX50	65	.	0			c.G21T						.						22	20	20					10																	70661161		2191	4282	6473	SO:0001583	missense	79009	exon1			CCTCTGGGGGGAC	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.21G>T	chr10.hg19:g.70661161G>T	ENSP00000362687:p.Trp7Cys	204.0	0.0		196.0	73.0	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	hg19	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.212179	0.58452	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.19394	2.15	5.62	4.66	0.58398	.	0.693466	0.14873	N	0.293442	T	0.17408	0.0418	N	0.08118	0	0.52501	D	0.99995	D;D	0.64830	0.994;0.994	P;P	0.51415	0.669;0.669	T	0.02417	-1.1162	10	0.44086	T	0.13	-4.7945	12.0065	0.53261	0.0:0.1739:0.8261:0.0	.	7;7	Q9BQ39;B4DED6	DDX50_HUMAN;.	C	7	ENSP00000362687:W7C	ENSP00000362687:W7C	W	+	3	0	DDX50	70331167	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	2.584000	0.46102	2.818000	0.97014	0.655000	0.94253	TGG	.	.		0.642	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		T	70661161	G	T	70661161	3	4	142	1	0	0	0	0	1	0	0	0	4370	1241	43	3	23	3	DDX50	10	70661161	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	24862146	70661161	64873586	57	22086										
JAKMIP3	282973	hgsc.bcm.edu	37	chr10	133946888	133946888	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	taggggttcaagccgggcatGctcagagactgcagctccaa	13	11	2	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr10:133946888G>T	ENST00000298622.4	+	3	844	c.706G>T	c.(706-708)Gct>Tct	p.A236S		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	236						Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		AGCCGGGCATGCTCAGAGACT	0.547																																					p.A236S		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.G706T						.						39	43	42					10																	133946888		1965	4143	6108	SO:0001583	missense	282973	exon3			GGGCATGCTCAGA	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"neuroendocrine long coiled-coil 2"	611198	"chromosome 10 open reading frame 39", "chromosome 10 open reading frame 14"	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.706G>T	chr10.hg19:g.133946888G>T	ENSP00000298622:p.Ala236Ser	90.0	0.0		73.0	19.0	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	hg19	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.030658	0.54790	.	.	ENSG00000188385	ENST00000298622	T	0.09723	2.95	4.5	4.5	0.54988	.	0.000000	0.85682	D	0.000000	T	0.12390	0.0301	L	0.48642	1.525	0.25781	N	0.984725	P	0.48294	0.908	B	0.43916	0.436	T	0.26950	-1.0088	10	0.08599	T	0.76	-10.3014	17.3619	0.87353	0.0:0.0:1.0:0.0	.	236	Q5VZ66	JKIP3_HUMAN	S	236	ENSP00000298622:A236S	ENSP00000298622:A236S	A	+	1	0	JAKMIP3	133796878	0.536000	0.26378	0.998000	0.56505	0.995000	0.86356	1.088000	0.30877	2.328000	0.79073	0.563000	0.77884	GCT	.	.		0.547	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303		T	133946888	G	T	133946888	3	4	142	1	0	0	0	0	1	0	0	0	7951	1319	46	3	716	3	JAKMIP3	10	133946888	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	63285727	133946888	1587859	58	22087										
ST5	6764	hgsc.bcm.edu	37	chr11	8732433	8732433	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	aaagcgtctgctgccatcttCcccagtcagcatgaaagaaa	8	12	3	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr11:8732433C>G	ENST00000534127.1	-	14	2696	c.2311G>C	c.(2311-2313)Gaa>Caa	p.E771Q	ST5_ENST00000530991.1_Missense_Mutation_p.E243Q|RPL27A_ENST00000531102.1_Intron|ST5_ENST00000530438.1_Missense_Mutation_p.E351Q|ST5_ENST00000534278.1_5'Flank|ST5_ENST00000357665.1_Missense_Mutation_p.E771Q|ST5_ENST00000313726.6_Missense_Mutation_p.E771Q|ST5_ENST00000526099.1_Missense_Mutation_p.E284Q|ST5_ENST00000526757.1_Missense_Mutation_p.E351Q	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	771	UDENN.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		CTGCCATCTTCCCCAGTCAGC	0.572																																					p.E771Q		Atlas-SNP	.											.	ST5	85	.	0			c.G2311C						.						61	56	58					11																	8732433		2201	4296	6497	SO:0001583	missense	6764	exon14			CATCTTCCCCAGT	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"DENN/MADD domain containing"	11350	protein-coding gene	gene with protein product	"DENN/MADD domain containing 2B"	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.2311G>C	chr11.hg19:g.8732433C>G	ENSP00000433528:p.Glu771Gln	59.0	0.0		53.0	14.0	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	hg19	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	C	34	5.293435	0.95546	.	.	ENSG00000166444	ENST00000526757;ENST00000534127;ENST00000313726;ENST00000530991;ENST00000357665;ENST00000526099;ENST00000530438;ENST00000533020	T;T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.85	5.85	0.93711	uDENN (3);	0.000000	0.85682	D	0.000000	T	0.66858	0.2832	L	0.52905	1.665	0.80722	D	1	D;D;D	0.71674	0.996;0.991;0.998	D;D;D	0.73708	0.974;0.945;0.981	T	0.66984	-0.5785	10	0.87932	D	0	-13.027	20.1577	0.98120	0.0:1.0:0.0:0.0	.	284;351;771	B4DDL8;P78524-2;P78524	.;.;ST5_HUMAN	Q	351;771;771;243;771;284;351;243	ENSP00000435097:E351Q;ENSP00000433528:E771Q;ENSP00000319678:E771Q;ENSP00000432887:E243Q;ENSP00000350294:E771Q;ENSP00000436808:E284Q;ENSP00000436802:E351Q;ENSP00000433588:E243Q	ENSP00000319678:E771Q	E	-	1	0	ST5	8689009	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.761000	0.68801	2.767000	0.95098	0.655000	0.94253	GAA	.	.		0.572	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		G	8732433	C	G	8732433	3	3	142	1	0	0	0	0	1	0	0	0	15235	864	30	4	1142	4	ST5	11	8732433	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10		8732433	126274083	59	22088										
PATL1	219988	hgsc.bcm.edu	37	chr11	59416963	59416963	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tccaggcaatttcccccttaAgttgtcatacatgctacaaa	5	12	1	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr11:59416963A>C	ENST00000300146.9	-	14	1789	c.1705T>G	c.(1705-1707)Tta>Gta	p.L569V		NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	569	Involved in nuclear spleckles localization.|Region C.				cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						TTCCCCCTTAAGTTGTCATAC	0.423																																					p.L569V		Atlas-SNP	.											.	PATL1	92	.	0			c.T1705G						.						142	124	130					11																	59416963		1934	4140	6074	SO:0001583	missense	219988	exon14			CCCTTAAGTTGTC	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.1705T>G	chr11.hg19:g.59416963A>C	ENSP00000300146:p.Leu569Val	222.0	0.0		203.0	67.0	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Missense_Mutation	SNP	ENST00000300146.9	hg19	CCDS44613.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.155249	0.78114	.	.	ENSG00000166889	ENST00000300146;ENST00000428532	T	0.68765	-0.35	5.93	0.652	0.17823	.	0.000000	0.85682	D	0.000000	T	0.74951	0.3784	L	0.61218	1.895	0.51767	D	0.999932	D;D	0.67145	0.996;0.99	D;D	0.75484	0.986;0.978	T	0.73585	-0.3936	10	0.87932	D	0	-6.8567	9.1043	0.36687	0.4746:0.0:0.5254:0.0	.	539;569	Q86TB9-4;Q86TB9	.;PATL1_HUMAN	V	569;539	ENSP00000300146:L569V	ENSP00000300146:L569V	L	-	1	2	PATL1	59173539	1.000000	0.71417	0.959000	0.39883	0.975000	0.68041	1.577000	0.36515	0.175000	0.19841	0.533000	0.62120	TTA	.	.		0.423	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716		C	59416963	A	C	59416963	3	2	142	1	0	0	0	0	1	0	0	0	11484	69	3	5	631	5	PATL1	11	59416963	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	50684530	59416963	75589553	60	22089										
VWF	7450	hgsc.bcm.edu	37	chr12	6145595	6145601	+	Frame_Shift_Del	DEL	CTCCTTG	CTCCTTG	-													0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	actgtttctccaggggcataCtccttgccctgatggaagca							TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	CTCCTTG	CTCCTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr12:6145595_6145601delCTCCTTG	ENST00000261405.5	-	19	2753_2759	c.2499_2505delCAAGGAG	c.(2497-2505)ggcaaggagfs	p.GKE833fs		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	833	CX.|E1.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CAGGGGCATACTCCTTGCCCTGATGGA	0.585																																					p.834_836del		Atlas-Indel,Pindel	.											.	VWF	338	.	0			c.2500_2506del						.																																			SO:0001589	frameshift_variant	7450	exon19			.		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2499_2505delCAAGGAG	chr12.hg19:g.6145595_6145601delCTCCTTG	ENSP00000261405:p.Gly833fs	83.0	0.0		78.0	19.0	NM_000552	Q8TCE8|Q99806	Frame_Shift_Del	DEL	ENST00000261405.5	hg19	CCDS8539.1																																																																																			.	.		0.585	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		-	6145601	CTCCTTG	-	6145595	7	5	142	1	0	1	0	1	0	0	0	0	17261	564	20	0	6072	0	VWF	12	6145595	Frame_Shift_Del	DEL	CTCCTTG	TCGA-DD-A73A-01A-12D-A32G-10		6145595	127706300	61	22090										
C12orf11	55726	hgsc.bcm.edu	37	chr12	27066960	27066960	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	gaaataggtagaggatcattTtttctttccatatcaactaa	6	6	3	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr12:27066960T>G	ENST00000261191.7	-	13	2057	c.1521A>C	c.(1519-1521)aaA>aaC	p.K507N	ASUN_ENST00000539625.1_Missense_Mutation_p.K406N	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	507					centrosome localization (GO:0051642)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|protein localization to nuclear envelope (GO:0090435)|regulation of fertilization (GO:0080154)|regulation of mitotic cell cycle (GO:0007346)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GAGGATCATTTTTTCTTTCCA	0.318																																					p.K507N		Atlas-SNP	.											.	.	.	.	0			c.A1521C						.						91	94	93					12																	27066960		2203	4293	6496	SO:0001583	missense	55726	exon13			ATCATTTTTTCTT	AK001222	CCDS8708.1	12p12.3	2013-05-08	2013-05-08	2011-12-09	ENSG00000064102	ENSG00000064102			20174	protein-coding gene	gene with protein product	"spermatogenesis associated 30"	615079	"chromosome 12 open reading frame 11", "asunder, spermatogenesis regulator homolog (Drosphila)"	C12orf11		12414650, 19357193, 23097494	Standard	NM_018164		Approved	FLJ10637, NET48, Mat89Bb, SPATA30	uc001rhk.4	Q9NVM9	OTTHUMG00000169193	ENST00000261191.7:c.1521A>C	chr12.hg19:g.27066960T>G	ENSP00000261191:p.Lys507Asn	265.0	0.0		274.0	74.0	NM_018164	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Missense_Mutation	SNP	ENST00000261191.7	hg19	CCDS8708.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.2|20.2	3.942273|3.942273	0.73672|0.73672	.|.	.|.	ENSG00000064102|ENSG00000064102	ENST00000538155;ENST00000261191;ENST00000539625;ENST00000335745;ENST00000261190|ENST00000542392	T;T;T|T	0.48836|0.47869	0.8;0.8;0.8|0.83	5.37|5.37	0.0833|0.0833	0.14432|0.14432	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.55097|0.55097	0.1899|0.1899	M|M	0.66939|0.66939	2.045|2.045	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.61697|.	0.99;0.979|.	P;P|.	0.62491|.	0.903;0.871|.	T|T	0.57653|0.57653	-0.7774|-0.7774	10|8	0.72032|0.66056	D|D	0.01|0.02	-28.1458|-28.1458	10.9855|10.9855	0.47520|0.47520	0.0:0.4819:0.0:0.518|0.0:0.4819:0.0:0.518	.|.	507;406|.	Q9NVM9;B4DNK1|.	M89BB_HUMAN;.|.	N|Q	154;507;406;94;4|221	ENSP00000445645:K154N;ENSP00000261191:K507N;ENSP00000443724:K406N|ENSP00000448215:K221Q	ENSP00000261190:K4N|ENSP00000448215:K221Q	K|K	-|-	3|1	2|0	C12orf11|C12orf11	26958227|26958227	0.999000|0.999000	0.42202|0.42202	0.994000|0.994000	0.49952|0.49952	0.998000|0.998000	0.95712|0.95712	0.610000|0.610000	0.24253|0.24253	0.044000|0.044000	0.15775|0.15775	0.482000|0.482000	0.46254|0.46254	AAA|AAA	.	.		0.318	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164		G	27066960	T	G	27066960	3	3	142	1	0	0	0	0	1	0	0	0	1677	1838	64	5	619	5	C12orf11	12	27066960	Missense_Mutation	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	20921365	27066960	106784935	62	22091										
ANO6	196527	hgsc.bcm.edu	37	chr12	45803160	45803160	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ctggatcatgaatctaattgGgcgatttcacagagtttctg	10	7	4	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr12:45803160G>A	ENST00000320560.8	+	16	2103	c.1901G>A	c.(1900-1902)gGg>gAg	p.G634E	ANO6_ENST00000423947.3_Missense_Mutation_p.G655E|ANO6_ENST00000435642.1_Missense_Mutation_p.G634E|ANO6_ENST00000425752.2_Missense_Mutation_p.G634E|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000441606.2_Missense_Mutation_p.G616E	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	634					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						AATCTAATTGGGCGATTTCAC	0.373																																					p.G655E		Atlas-SNP	.											.	ANO6	163	.	0			c.G1964A						.						102	104	103					12																	45803160		2203	4300	6503	SO:0001583	missense	196527	exon17			TAATTGGGCGATT	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.1901G>A	chr12.hg19:g.45803160G>A	ENSP00000320087:p.Gly634Glu	83.0	0.0		77.0	23.0	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.157851	0.38119	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07	4.7	4.7	0.59300	.	0.419347	0.25900	N	0.027570	T	0.56046	0.1959	L	0.45051	1.395	0.41976	D	0.990772	B;B;P;B	0.36027	0.302;0.048;0.533;0.292	B;B;B;B	0.41374	0.219;0.158;0.355;0.166	T	0.58255	-0.7668	10	0.42905	T	0.14	.	16.7235	0.85416	0.0:0.0:1.0:0.0	.	616;655;634;634	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	E	634;655;634;634;616	ENSP00000391417:G634E;ENSP00000409126:G655E;ENSP00000413840:G634E;ENSP00000320087:G634E;ENSP00000413137:G616E	ENSP00000320087:G634E	G	+	2	0	ANO6	44089427	1.000000	0.71417	0.936000	0.37596	0.895000	0.52256	4.287000	0.59001	2.538000	0.85594	0.655000	0.94253	GGG	.	.		0.373	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743		A	45803160	G	A	45803160	3	1	142	1	0	0	0	0	1	0	0	0	701	1232	43	3	1983	3	ANO6	12	45803160	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	18736200	45803160	88048735	63	22092										
MAP3K12	7786	hgsc.bcm.edu	37	chr12	53875041	53875041	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	aattcagtgctgtcacagtcTgagtcctcagaattgggagg	12	8	4	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr12:53875041T>A	ENST00000267079.2	-	15	2730	c.2505A>T	c.(2503-2505)tcA>tcT	p.S835S	MAP3K12_ENST00000547035.1_Silent_p.S868S|MAP3K12_ENST00000547488.1_Silent_p.S868S	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	835					histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						TGTCACAGTCTGAGTCCTCAG	0.502																																					p.S868S		Atlas-SNP	.											.	MAP3K12	160	.	0			c.A2604T						.						67	59	62					12																	53875041		2203	4300	6503	SO:0001819	synonymous_variant	7786	exon14			ACAGTCTGAGTCC	U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.2505A>T	chr12.hg19:g.53875041T>A		91.0	0.0		117.0	54.0	NM_001193511	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Silent	SNP	ENST00000267079.2	hg19	CCDS8860.1																																																																																			.	.		0.502	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		A	53875041	T	A	53875041	2	1	142	1	0	0	0	0	0	0	0	1	9255	1567	55	4		4	MAP3K12	12	53875041	Silent	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10	8071881	53875041	79976854	64	22093										
R3HDM2	22864	hgsc.bcm.edu	37	chr12	57660557	57660557	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ggtggactgcagggagagggAgactgaggcatctggtactg	19	6	1	3			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr12:57660557A>T	ENST00000347140.3	-	19	2436	c.2046T>A	c.(2044-2046)tcT>tcA	p.S682S	R3HDM2_ENST00000403821.2_Silent_p.S716S|R3HDM2_ENST00000546843.1_5'UTR|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000402412.1_Silent_p.S696S|R3HDM2_ENST00000441731.2_Silent_p.S377S|R3HDM2_ENST00000358907.2_Silent_p.S682S|R3HDM2_ENST00000413953.2_Silent_p.S409S			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	682	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						AGGGAGAGGGAGACTGAGGCA	0.542																																					p.S682S		Atlas-SNP	.											.	R3HDM2	125	.	0			c.T2046A						.						99	77	85					12																	57660557		2203	4300	6503	SO:0001819	synonymous_variant	22864	exon17			AGAGGGAGACTGA	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.2046T>A	chr12.hg19:g.57660557A>T		53.0	0.0		52.0	15.0	NM_014925	Q2M1T9|Q3ZCT5	Silent	SNP	ENST00000347140.3	hg19	CCDS8937.2																																																																																			.	.		0.542	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		T	57660557	A	T	57660557	2	4	142	1	0	0	0	0	0	0	0	1	12903	291	11	4		4	R3HDM2	12	57660557	Silent	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	3785516	57660557	76191338	65	22094										
CNOT2	4848	hgsc.bcm.edu	37	chr12	70732260	70732260	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	caagacaacttcaagtacagAtggacccaaattccctggag	8	11	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr12:70732260A>G	ENST00000418359.3	+	11	1389	c.938A>G	c.(937-939)gAt>gGt	p.D313G	CNOT2_ENST00000551483.1_5'UTR|CNOT2_ENST00000229195.3_Missense_Mutation_p.D313G	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	313					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription corepressor binding (GO:0001226)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(2)|urinary_tract(1)	20	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			TCAAGTACAGATGGACCCAAA	0.338																																					p.D313G		Atlas-SNP	.											.	CNOT2	53	.	0			c.A938G						.						83	84	84					12																	70732260		2203	4300	6503	SO:0001583	missense	4848	exon11			GTACAGATGGACC	AF180473	CCDS31857.1	12q15	2008-05-14				ENSG00000111596			7878	protein-coding gene	gene with protein product		604909		NOT2		10637334	Standard	NM_014515		Approved	CDC36, NOT2H	uc001svv.3	Q9NZN8		ENST00000418359.3:c.938A>G	chr12.hg19:g.70732260A>G	ENSP00000412091:p.Asp313Gly	161.0	0.0		194.0	57.0	NM_001199302	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Missense_Mutation	SNP	ENST00000418359.3	hg19	CCDS31857.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.893083	0.33442	.	.	ENSG00000111596	ENST00000552231;ENST00000229195;ENST00000418359;ENST00000550160;ENST00000552915;ENST00000548159;ENST00000551043;ENST00000550155	T;T;T;T;T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.55033	0.1895	N	0.16743	0.435	0.80722	D	1	B;B	0.22211	0.066;0.031	B;B	0.20577	0.03;0.009	T	0.51545	-0.8692	10	0.19147	T	0.46	-7.0665	15.5405	0.76039	1.0:0.0:0.0:0.0	.	313;313	Q9NZN8-4;Q9NZN8	.;CNOT2_HUMAN	G	313;313;313;176;252;304;313;123	ENSP00000450318:D313G;ENSP00000229195:D313G;ENSP00000412091:D313G;ENSP00000448490:D176G;ENSP00000447497:D252G;ENSP00000449659:D304G;ENSP00000449260:D313G;ENSP00000448499:D123G	ENSP00000229195:D313G	D	+	2	0	CNOT2	69018527	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.070000	0.61991	0.482000	0.46254	GAT	.	.		0.338	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404260.1			G	70732260	A	G	70732260	3	3	142	1	0	0	0	0	1	0	0	0	3621	333	12	2	972	2	CNOT2	12	70732260	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	13071703	70732260	63119635	66	22095										
NOS1	4842	hgsc.bcm.edu	37	chr12	117698357	117698357	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tctgtggcatagaggatggtCgctttcaccctcttggccat	11	11	3	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr12:117698357C>G	ENST00000338101.4	-	13	2284	c.2280G>C	c.(2278-2280)gcG>gcC	p.A760A	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Silent_p.A760A			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		AGAGGATGGTCGCTTTCACCC	0.522																																					p.A760A	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.G2280C						.						100	100	100					12																	117698357		2000	4179	6179	SO:0001819	synonymous_variant	4842	exon14			GATGGTCGCTTTC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2280G>C	chr12.hg19:g.117698357C>G		110.0	0.0		99.0	31.0	NM_000620		Silent	SNP	ENST00000338101.4	hg19	CCDS55890.1																																																																																			.	.		0.522	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			G	117698357	C	G	117698357	2	3	142	1	0	0	0	0	0	0	0	1	10550	871	31	4		4	NOS1	12	117698357	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	46966097	117698357	16153538	67	22096										
CENPJ	55835	hgsc.bcm.edu	37	chr13	25467000	25467000	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	aaatctgctatttgctgtttTaaagtctctcaaaaaaaaaa	4	6	3	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr13:25467000T>C	ENST00000381884.4	-	10	3182	c.2997A>G	c.(2995-2997)ttA>ttG	p.L999L	CENPJ_ENST00000545981.1_Silent_p.L999L	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	999					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		TTTGCTGTTTTAAAGTCTCTC	0.333																																					p.L999L		Atlas-SNP	.											.	CENPJ	116	.	0			c.A2997G						.						97	94	95					13																	25467000		2203	4300	6503	SO:0001819	synonymous_variant	55835	exon10			CTGTTTTAAAGTC	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"centrosomal P4.1-associated protein"	609279	"microcephaly, primary autosomal recessive 6"	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.2997A>G	chr13.hg19:g.25467000T>C		144.0	0.0		161.0	54.0	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Silent	SNP	ENST00000381884.4	hg19	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	T	8.724	0.915074	0.17907	.	.	ENSG00000151849	ENST00000418179	.	.	.	5.22	3.09	0.35607	.	.	.	.	.	T	0.55049	0.1896	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46541	-0.9184	4	.	.	.	.	6.6852	0.23142	0.0:0.4675:0.0:0.5325	.	.	.	.	E	81	.	.	K	-	1	0	CENPJ	24365000	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.919000	0.40015	0.486000	0.27676	0.454000	0.30748	AAA	.	.		0.333	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		C	25467000	T	C	25467000	2	2	142	1	0	0	0	0	0	0	0	1	3236	1751	61	2		2	CENPJ	13	25467000	Silent	SNP	T	TCGA-DD-A73A-01A-12D-A32G-10		25467000	89702878	68	22097										
MTMR6	9107	hgsc.bcm.edu	37	chr13	25826056	25826056	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tgagattcggaactgtagagAggatttaagtacttcttttg	11	4	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr13:25826056A>T	ENST00000381801.5	-	12	2174	c.1413T>A	c.(1411-1413)ccT>ccA	p.P471P	MTMR6_ENST00000540661.1_Silent_p.P471P	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	471	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		AACTGTAGAGAGGATTTAAGT	0.338																																					p.P471P		Atlas-SNP	.											.	MTMR6	75	.	0			c.T1413A						.						115	130	125					13																	25826056		2203	4297	6500	SO:0001819	synonymous_variant	9107	exon12			GTAGAGAGGATTT	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.1413T>A	chr13.hg19:g.25826056A>T		83.0	0.0		104.0	33.0	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Silent	SNP	ENST00000381801.5	hg19	CCDS9313.1																																																																																			.	.		0.338	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		T	25826056	A	T	25826056	2	4	142	1	0	0	0	0	0	0	0	1	9956	291	11	4		4	MTMR6	13	25826056	Silent	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	359056	25826056	89343822	69	22098										
PCK2	5106	hgsc.bcm.edu	37	chr14	24567763	24567763	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	atcggggtgcagctcactgaCtcagcctatgtggtggcaag	14	10	2	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr14:24567763C>T	ENST00000216780.4	+	4	808	c.540C>T	c.(538-540)gaC>gaT	p.D180D	PCK2_ENST00000396973.4_Silent_p.D180D|PCK2_ENST00000561286.1_Silent_p.D46D|NRL_ENST00000561028.1_Intron|PCK2_ENST00000558096.1_Silent_p.D46D|PCK2_ENST00000545054.2_Silent_p.D46D|PCK2_ENST00000559250.1_Silent_p.D192D	NM_004563.2	NP_004554.2	Q16822	PCKGM_HUMAN	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	180					carbohydrate metabolic process (GO:0005975)|cellular response to glucose stimulus (GO:0071333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|NADH oxidation (GO:0006116)|oxaloacetate metabolic process (GO:0006107)|positive regulation of insulin secretion (GO:0032024)|pyruvate metabolic process (GO:0006090)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)|phosphoenolpyruvate carboxykinase activity (GO:0004611)			breast(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(265;0.0184)		AGCTCACTGACTCAGCCTATG	0.597																																					p.D180D		Atlas-SNP	.											.	PCK2	66	.	0			c.C540T						.						79	64	69					14																	24567763		2203	4300	6503	SO:0001819	synonymous_variant	5106	exon4			CACTGACTCAGCC	AK129934	CCDS9609.1, CCDS41928.1	14q12	2006-06-09			ENSG00000100889	ENSG00000100889	4.1.1.32		8725	protein-coding gene	gene with protein product		614095				8645161, 9657976	Standard	XM_005267726		Approved	PEPCK, PEPCK2	uc001wlt.3	Q16822	OTTHUMG00000028791	ENST00000216780.4:c.540C>T	chr14.hg19:g.24567763C>T		82.0	0.0		99.0	29.0	NM_001018073	O43253|Q86U01|Q9BV62	Silent	SNP	ENST00000216780.4	hg19	CCDS9609.1																																																																																			.	.		0.597	PCK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071900.3	NM_001018073		T	24567763	C	T	24567763	2	4	142	1	0	0	0	0	0	0	0	1	11591	564	20	3		3	PCK2	14	24567763	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10		24567763	82781777	70	22099										
SLC25A29	123096	hgsc.bcm.edu	37	chr14	100758804	100758804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	cccgtgtgaagacgcgccagCcctcggcgcggtagctctgg	15	15	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr14:100758804C>T	ENST00000359232.3	-	4	1028	c.728G>A	c.(727-729)gGc>gAc	p.G243D	AL157871.2_ENST00000553954.1_RNA|SLC25A29_ENST00000539621.1_Missense_Mutation_p.G177D|SLC25A29_ENST00000554912.1_Missense_Mutation_p.G177D|SLC25A29_ENST00000392908.3_3'UTR|SLC25A29_ENST00000556505.1_Missense_Mutation_p.G177D|RP11-638I2.6_ENST00000556458.1_lincRNA|SLC25A29_ENST00000555927.1_Missense_Mutation_p.G177D	NM_001039355.1	NP_001034444.1	Q8N8R3	MCATL_HUMAN	solute carrier family 25 (mitochondrial carnitine/acylcarnitine carrier), member 29	243						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	acyl carnitine transmembrane transporter activity (GO:0015227)			NS(1)|endometrium(1)|ovary(1)	3		Melanoma(154;0.152)			L-Carnitine(DB00583)	GACGCGCCAGCCCTCGGCGCG	0.726																																					p.G243D		Atlas-SNP	.											.	SLC25A29	14	.	0			c.G728A						.						10	13	12					14																	100758804		2135	4174	6309	SO:0001583	missense	123096	exon4			CGCCAGCCCTCGG	AK095532	CCDS32156.1	14q32.2	2013-05-22	2012-03-29	2004-01-21	ENSG00000197119	ENSG00000197119		"Solute carriers"	20116	protein-coding gene	gene with protein product		615064	"chromosome 14 open reading frame 69", "solute carrier family 25, member 29"	C14orf69			Standard	XM_005267343		Approved	FLJ38975	uc010twx.2	Q8N8R3	OTTHUMG00000171569	ENST00000359232.3:c.728G>A	chr14.hg19:g.100758804C>T	ENSP00000352167:p.Gly243Asp	13.0	0.0		30.0	9.0	NM_001039355	A3KMR5|Q541V0	Missense_Mutation	SNP	ENST00000359232.3	hg19	CCDS32156.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.624315	0.87560	.	.	ENSG00000197119	ENST00000359232;ENST00000554912;ENST00000539621;ENST00000556505;ENST00000555927	D;D;D;D;D	0.97665	-4.48;-4.48;-4.48;-4.48;-4.48	5.62	5.62	0.85841	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.99287	0.9751	H	0.99286	4.5	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98498	1.0613	10	0.87932	D	0	-32.0149	19.6706	0.95910	0.0:1.0:0.0:0.0	.	243	Q8N8R3	MCATL_HUMAN	D	243;177;177;177;177	ENSP00000352167:G243D;ENSP00000450913:G177D;ENSP00000442985:G177D;ENSP00000452446:G177D;ENSP00000452078:G177D	ENSP00000352167:G243D	G	-	2	0	SLC25A29	99828557	1.000000	0.71417	1.000000	0.80357	0.317000	0.28152	7.418000	0.80167	2.645000	0.89757	0.655000	0.94253	GGC	.	.		0.726	SLC25A29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072449.3			T	100758804	C	T	100758804	3	4	142	1	0	0	0	0	1	0	0	0	14507	739	26	3	187	3	SLC25A29	14	100758804	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	76191041	100758804	6590736	71	22100										
PAK6	56924	hgsc.bcm.edu	37	chr15	40564637	40564637	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tccccccgcacctggcacgcCcagatcagcaccagcaacct	7	21	1	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr15:40564637C>T	ENST00000542403.2	+	4	1182	c.1071C>T	c.(1069-1071)gcC>gcT	p.A357A	PAK6_ENST00000560346.1_Silent_p.A357A|PAK6_ENST00000455577.2_Silent_p.A357A|PAK6_ENST00000453867.1_Silent_p.A357A|PAK6_ENST00000441369.1_Silent_p.A357A|RP11-133K1.2_ENST00000558658.1_3'UTR|PAK6_ENST00000260404.4_Silent_p.A357A	NM_001276717.1	NP_001263646.1	Q9NQU5	PAK6_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 6	357	Linker.				apoptotic process (GO:0006915)|cytoskeleton organization (GO:0007010)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(2)	24		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)		CCTGGCACGCCCAGATCAGCA	0.667																																					p.A357A		Atlas-SNP	.											.	PAK6	49	.	0			c.C1071T						.						51	50	50					15																	40564637		2203	4300	6503	SO:0001819	synonymous_variant	56924	exon5			GCACGCCCAGATC	AF276893	CCDS10054.1, CCDS61590.1	15q14	2008-06-17	2008-06-17		ENSG00000137843	ENSG00000137843			16061	protein-coding gene	gene with protein product		608110	"p21(CDKN1A)-activated kinase 6"			11278661	Standard	NM_020168		Approved	PAK5	uc001zlb.3	Q9NQU5	OTTHUMG00000129921	ENST00000542403.2:c.1071C>T	chr15.hg19:g.40564637C>T		59.0	0.0		62.0	4.0	NM_001128629	A8K2G2|B3KYB0|G5E9R2	Silent	SNP	ENST00000542403.2	hg19	CCDS10054.1																																																																																			.	.		0.667	PAK6-004	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000418355.1			T	40564637	C	T	40564637	2	4	142	1	0	0	0	0	0	0	0	1	11413	610	22	3		3	PAK6	15	40564637	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10		40564637	61966755	72	22101										
SLCO3A1	28232	hgsc.bcm.edu	37	chr15	92459624	92459624	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ggcatcggtgctacccctgtGcagcccctgggcgtctccta	12	16	1	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr15:92459624G>T	ENST00000318445.6	+	2	796	c.582G>T	c.(580-582)gtG>gtT	p.V194V	SLCO3A1_ENST00000424469.2_Silent_p.V194V	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	194					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	CTACCCCTGTGCAGCCCCTGG	0.617																																					p.V194V		Atlas-SNP	.											.	SLCO3A1	84	.	0			c.G582T						.						22	23	23					15																	92459624		2198	4298	6496	SO:0001819	synonymous_variant	28232	exon2			CCCTGTGCAGCCC	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"Solute carriers"	10952	protein-coding gene	gene with protein product		612435	"solute carrier family 21 (organic anion transporter), member 11"	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.582G>T	chr15.hg19:g.92459624G>T		65.0	0.0		72.0	26.0	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Silent	SNP	ENST00000318445.6	hg19	CCDS10371.1																																																																																			.	.		0.617	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272		T	92459624	G	T	92459624	2	4	142	1	0	0	0	0	0	0	0	1	14743	1306	46	3		3	SLCO3A1	15	92459624	Silent	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	51894987	92459624	10071768	73	22102										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99459327	99459327	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ggcagcggcagcctcaggacGgctacctttaccggcacaat	12	14	1	0	rs143193096		TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr15:99459327G>A	ENST00000268035.6	+	9	2574	c.1963G>A	c.(1963-1965)Ggc>Agc	p.G655S	IGF1R_ENST00000558762.1_Missense_Mutation_p.G655S	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	655	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GCCTCAGGACGGCTACCTTTA	0.557																																					p.G655S		Atlas-SNP	.											.	IGF1R	147	.	0			c.G1963A						.	G	SER/GLY	0,4394		0,0,2197	67	63	64		1963	-1.1	1	15	dbSNP_134	64	1,8593	1.2+/-3.3	0,1,4296	yes	missense	IGF1R	NM_000875.3	56	0,1,6493	AA,AG,GG		0.0116,0.0,0.0077	benign	655/1368	99459327	1,12987	2197	4297	6494	SO:0001583	missense	3480	exon9			CAGGACGGCTACC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.1963G>A	chr15.hg19:g.99459327G>A	ENSP00000268035:p.Gly655Ser	183.0	0.0		170.0	53.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	G	7.286	0.610031	0.14066	0.0	1.16E-4	ENSG00000140443	ENST00000268035	T	0.67865	-0.29	4.83	-1.14	0.09741	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.360209	0.25964	N	0.027165	T	0.28566	0.0707	N	0.01529	-0.815	0.36790	D	0.8848	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.001	T	0.43228	-0.9404	10	0.02654	T	1	.	9.5461	0.39282	0.6952:0.0:0.3048:0.0	.	655;655	C9J5X1;P08069	.;IGF1R_HUMAN	S	655	ENSP00000268035:G655S	ENSP00000268035:G655S	G	+	1	0	IGF1R	97276850	0.993000	0.37304	0.980000	0.43619	0.994000	0.84299	0.406000	0.21032	-0.366000	0.08064	-0.218000	0.12543	GGC	.	G|1.000;A|0.000		0.557	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99459327	G	A	99459327	3	1	142	1	0	0	0	0	1	0	0	0	7580	1116	39	1	1997	1	IGF1R	15	99459327	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	6999703	99459327	3072065	74	22103										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24816121	24816121	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	agtgcactacctaaccaggcCcttggctccatagcagggct	10	14	0	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr16:24816121C>A	ENST00000395799.3	+	13	4062	c.3933C>A	c.(3931-3933)gcC>gcA	p.A1311A	TNRC6A_ENST00000315183.7_Intron|CTD-2515A14.1_ENST00000568895.1_RNA	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1311	Sufficient for interaction with AGO1 and AGO4.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		CTAACCAGGCCCTTGGCTCCA	0.433																																					p.A1311A		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C3933A						.						131	123	126					16																	24816121		2197	4300	6497	SO:0001819	synonymous_variant	27327	exon13			CCAGGCCCTTGGC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.3933C>A	chr16.hg19:g.24816121C>A		160.0	0.0		189.0	55.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	hg19	CCDS10624.2																																																																																			.	.		0.433	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24816121	C	A	24816121	2	1	142	1	0	0	0	0	0	0	0	1	16355	610	22	3		3	TNRC6A	16	24816121	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10		24816121	65538632	75	22104										
CDH11	1009	hgsc.bcm.edu	37	chr16	64984770	64984770	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ttgcaggagagcagtgccccGttcacgtcgcacccgcagac	12	15	1	2	rs563299959		TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr16:64984770G>A	ENST00000268603.4	-	12	2409	c.1794C>T	c.(1792-1794)aaC>aaT	p.N598N	CDH11_ENST00000394156.3_Silent_p.N598N|CDH11_ENST00000566827.1_Silent_p.N472N	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	598	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N598N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		GCAGTGCCCCGTTCACGTCGC	0.607			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			G|||	1	0.000199681	8e-04	0	5008	,	,		14798	0		0	False		,,,				2504	0				p.N598N		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	CDH11_ENST00000394156,NS,carcinoma,0,3	CDH11	260	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1794T						.						114	87	96					16																	64984770		2203	4300	6503	SO:0001819	synonymous_variant	1009	exon12			TGCCCCGTTCACG	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1794C>T	chr16.hg19:g.64984770G>A		74.0	0.0		62.0	22.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	hg19	CCDS10803.1																																																																																			.	.		0.607	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		A	64984770	G	A	64984770	2	1	142	1	0	0	0	0	0	0	0	1	3099	1136	40	1		1	CDH11	16	64984770	Silent	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	40168649	64984770	25369983	76	22105										
WWP2	11060	hgsc.bcm.edu	37	chr16	69973254	69973254	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tggatcacaggtagcaacggAccacagaagttttgcattga	11	8	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr16:69973254A>G	ENST00000359154.2	+	23	2552	c.2451A>G	c.(2449-2451)ggA>ggG	p.G817G	WWP2_ENST00000542271.1_Silent_p.G701G|WWP2_ENST00000568684.1_Silent_p.G378G|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000356003.2_Silent_p.G817G|WWP2_ENST00000448661.1_Silent_p.G817G	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	817	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GTAGCAACGGACCACAGAAGT	0.587																																					p.G817G		Atlas-SNP	.											.	WWP2	88	.	0			c.A2451G						.						94	85	88					16																	69973254		2198	4300	6498	SO:0001819	synonymous_variant	11060	exon23			CAACGGACCACAG	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.2451A>G	chr16.hg19:g.69973254A>G		97.0	0.0		81.0	28.0	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	hg19	CCDS10885.1																																																																																			.	.		0.587	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014		G	69973254	A	G	69973254	2	3	142	1	0	0	0	0	0	0	0	1	17431	262	10	2		2	WWP2	16	69973254	Silent	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	4988484	69973254	20381499	77	22106										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72991696	72991697	+	In_Frame_Ins	INS	-	-	GCCGCC													0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	aggagctactgatattggctINSgccgccgccgccgcagccac					rs576025667		TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr16:72991696_72991697insGCCGCC	ENST00000268489.5	-	2	3020_3021	c.2348_2349insGGCGGC	c.(2347-2349)gca>gcGGCGGCa	p.783_783A>AAA	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	783	Poly-Ala.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TGATATTGgctgccgccgccgc	0.649																																					p.A783delinsAAA		Atlas-INDEL	.											.	ZFHX3	404	.	0			c.2349_2350insGGCGGC						.																																			SO:0001652	inframe_insertion	463	exon2			.	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2343_2348dupGGCGGC	chr16.hg19:g.72991697_72991702dupGCCGCC	ENSP00000268489:p.AlaAla783dup	36.0	0.0		60.0	15.0	NM_006885	D3DWS8|O15101|Q13719	In_Frame_Ins	INS	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.649	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		GCCGCC	72991697	-	GCCGCC	72991696	7	5	142	1	0	1	1	0	0	0	0	0	17649	1567	55	0	8798	0	ZFHX3	16	72991696	In_Frame_Ins	INS	-	TCGA-DD-A73A-01A-12D-A32G-10	3018442	72991696	17363057	78	22107										
VAT1L	57687	hgsc.bcm.edu	37	chr16	77859321	77859321	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	agttgccaacctccgggaagGgatgtctgtgctcgtgcact	13	11	1	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr16:77859321G>A	ENST00000302536.2	+	3	695	c.542G>A	c.(541-543)gGg>gAg	p.G181E		NM_020927.1	NP_065978.1	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport 1-like	181							oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(10)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24						CTCCGGGAAGGGATGTCTGTG	0.527																																					p.G181E		Atlas-SNP	.											.	VAT1L	68	.	0			c.G542A						.						63	50	55					16																	77859321		2198	4300	6498	SO:0001583	missense	57687	exon3			GGGAAGGGATGTC	AB046796	CCDS32492.1	16q23.1	2014-09-09	2013-08-23		ENSG00000171724	ENSG00000171724			29315	protein-coding gene	gene with protein product			"vesicle amine transport protein 1 homolog (T. californica)-like"			10997877	Standard	NM_020927		Approved	KIAA1576	uc002ffg.1	Q9HCJ6	OTTHUMG00000176845	ENST00000302536.2:c.542G>A	chr16.hg19:g.77859321G>A	ENSP00000303129:p.Gly181Glu	146.0	0.0		108.0	34.0	NM_020927	Q8IYW8	Missense_Mutation	SNP	ENST00000302536.2	hg19	CCDS32492.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.936895	0.92458	.	.	ENSG00000171724	ENST00000302536	T	0.46451	0.87	6.03	6.03	0.97812	GroES-like (1);Quinone oxidoreductase/zeta-crystallin, conserved site (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.70842	0.3270	M	0.87617	2.895	0.80722	D	1	D	0.76494	0.999	D	0.68192	0.956	T	0.73754	-0.3883	10	0.66056	D	0.02	-4.1112	20.1519	0.98089	0.0:0.0:1.0:0.0	.	181	Q9HCJ6	VAT1L_HUMAN	E	181	ENSP00000303129:G181E	ENSP00000303129:G181E	G	+	2	0	VAT1L	76416822	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.861000	0.98227	0.655000	0.94253	GGG	.	.		0.527	VAT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434010.1	NM_020927		A	77859321	G	A	77859321	3	1	142	1	0	0	0	0	1	0	0	0	17145	1232	43	3	552	3	VAT1L	16	77859321	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	4867625	77859321	12495432	79	22108										
KLHDC4	54758	hgsc.bcm.edu	37	chr16	87788816	87788816	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ttacctggtgagcacagcgcCtcggaggtggactggggatg	17	9	0	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr16:87788816C>A	ENST00000270583.5	-	4	411	c.353G>T	c.(352-354)aGg>aTg	p.R118M	KLHDC4_ENST00000353170.5_Missense_Mutation_p.R61M|KLHDC4_ENST00000347925.5_Missense_Mutation_p.R118M	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	118										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		AGCACAGCGCCTCGGAGGTGG	0.517																																					p.R118M		Atlas-SNP	.											.	KLHDC4	45	.	0			c.G353T						.						195	177	183					16																	87788816		2198	4300	6498	SO:0001583	missense	54758	exon4			CAGCGCCTCGGAG	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.353G>T	chr16.hg19:g.87788816C>A	ENSP00000270583:p.Arg118Met	181.0	0.0		161.0	55.0	NM_001184856	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Missense_Mutation	SNP	ENST00000270583.5	hg19	CCDS10963.1	.	.	.	.	.	.	.	.	.	.	C	18.03	3.532243	0.64972	.	.	ENSG00000104731	ENST00000270583;ENST00000347925;ENST00000353170	T;T;T	0.66815	0.96;0.96;-0.23	5.22	5.22	0.72569	Kelch-type beta propeller (1);	0.048998	0.85682	D	0.000000	D	0.83078	0.5176	M	0.83012	2.62	0.51012	D	0.999905	D;D;D	0.89917	0.999;1.0;0.99	D;D;D	0.71414	0.973;0.957;0.957	D	0.85892	0.1429	10	0.87932	D	0	-13.0181	17.7584	0.88456	0.0:1.0:0.0:0.0	.	61;118;118	Q8TBB5-2;Q8TBB5-3;Q8TBB5	.;.;KLDC4_HUMAN	M	118;118;61	ENSP00000270583:R118M;ENSP00000325717:R118M;ENSP00000262530:R61M	ENSP00000270583:R118M	R	-	2	0	KLHDC4	86346317	1.000000	0.71417	0.956000	0.39512	0.638000	0.38207	5.094000	0.64523	2.432000	0.82394	0.561000	0.74099	AGG	.	.		0.517	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		A	87788816	C	A	87788816	3	1	142	1	0	0	0	0	1	0	0	0	8367	681	24	3	1241	3	KLHDC4	16	87788816	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	9929495	87788816	2565937	80	22109										
PELP1	27043	hgsc.bcm.edu	37	chr17	4575508	4575508	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tcctcaaactcttcttcctcCtcttcttcctcttcaaaata	0	16	7	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr17:4575508C>T	ENST00000574876.1	-	16	2795	c.2778G>A	c.(2776-2778)gaG>gaA	p.E926E	PELP1_ENST00000572293.1_Silent_p.E976E|PELP1_ENST00000269230.7_Silent_p.E836E|PELP1_ENST00000301396.4_Silent_p.E1070E|PELP1_ENST00000436683.2_Silent_p.E779E			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	926	Glu-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						cttcttcctcctcttcttcct	0.438																																					p.E926E		Atlas-SNP	.											.	PELP1	102	.	0			c.G2778A						.						43	43	43					17																	4575508		2049	4139	6188	SO:0001819	synonymous_variant	27043	exon16			TTCCTCCTCTTCT		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"proline, glutamic acid and leucine rich protein 1"			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2778G>A	chr17.hg19:g.4575508C>T		90.0	0.0		68.0	4.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	hg19	CCDS58503.1																																																																																			.	.		0.438	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		T	4575508	C	T	4575508	2	4	142	1	0	0	0	0	0	0	0	1	11734	680	24	3		3	PELP1	17	4575508	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10		4575508	76619702	81	22110										
ZNF18	7566	hgsc.bcm.edu	37	chr17	11881942	11881942	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tggctcatcctcagtgaagaAgcccctcaaggaagcctgag	11	12	3	3			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr17:11881942A>C	ENST00000322748.3	-	9	1586	c.982T>G	c.(982-984)Ttc>Gtc	p.F328V	RP11-1096G20.5_ENST00000580270.1_RNA|ZNF18_ENST00000454073.3_Missense_Mutation_p.F327V|ZNF18_ENST00000580306.2_Missense_Mutation_p.F328V	NM_144680.2	NP_653281.2	P17022	ZNF18_HUMAN	zinc finger protein 18	328					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	14				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		TCAGTGAAGAAGCCCCTCAAG	0.522																																					p.F328V		Atlas-SNP	.											ZNF18,caecum,carcinoma,0,1	ZNF18	42	.	0			c.T982G						.						133	141	139					17																	11881942		2203	4300	6503	SO:0001583	missense	7566	exon9			TGAAGAAGCCCCT	X52342	CCDS32568.1	17p12	2013-01-09	2006-05-10		ENSG00000154957	ENSG00000154957		"Zinc fingers, C2H2-type", "-", "-", "-"	12969	protein-coding gene	gene with protein product		194524	"zinc finger protein 18 (KOX 11)"			15702252	Standard	XM_005256786		Approved	ZKSCAN6, KOX11, HDSG1, Zfp535, ZNF535, ZSCAN38	uc002gng.1	P17022	OTTHUMG00000178307	ENST00000322748.3:c.982T>G	chr17.hg19:g.11881942A>C	ENSP00000315664:p.Phe328Val	73.0	0.0		79.0	22.0	NM_144680	Q5QHQ3|Q8IYC4|Q8NAH6	Missense_Mutation	SNP	ENST00000322748.3	hg19	CCDS32568.1	.	.	.	.	.	.	.	.	.	.	A	14.18	2.458195	0.43634	.	.	ENSG00000154957	ENST00000454073;ENST00000322748	T;T	0.05925	3.37;3.37	4.97	1.28	0.21552	.	0.482695	0.19494	N	0.112902	T	0.02380	0.0073	N	0.14661	0.345	0.09310	N	1	B;B	0.19200	0.034;0.02	B;B	0.22601	0.04;0.018	T	0.43163	-0.9408	10	0.05525	T	0.97	-1.8901	0.4195	0.00453	0.2646:0.2168:0.3053:0.2132	.	327;328	P17022-2;P17022	.;ZNF18_HUMAN	V	328	ENSP00000391376:F328V;ENSP00000315664:F328V	ENSP00000315664:F328V	F	-	1	0	ZNF18	11822667	0.022000	0.18835	0.504000	0.27639	0.872000	0.50106	0.718000	0.25866	0.508000	0.28173	0.455000	0.32223	TTC	.	.		0.522	ZNF18-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441450.2	XM_085596		C	11881942	A	C	11881942	3	2	142	1	0	0	0	0	1	0	0	0	17762	72	3	5	671	5	ZNF18	17	11881942	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	7306434	11881942	69313268	82	22111										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18025025	18025025	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ttctccagctcctgggccctGtgccatcccccaccctccag	7	21	1	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr17:18025025G>T	ENST00000205890.5	+	2	3249	c.2911G>T	c.(2911-2913)Gtg>Ttg	p.V971L		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	971					inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CCTGGGCCCTGTGCCATCCCC	0.662																																					p.V971L		Atlas-SNP	.											.	MYO15A	268	.	0			c.G2911T						.						15	17	17					17																	18025025		1915	4114	6029	SO:0001583	missense	51168	exon2			GGCCCTGTGCCAT	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.2911G>T	chr17.hg19:g.18025025G>T	ENSP00000205890:p.Val971Leu	147.0	0.0		143.0	54.0	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	g	5.999	0.368237	0.11352	.	.	ENSG00000091536	ENST00000205890	D	0.86497	-2.13	4.48	0.98	0.19750	.	.	.	.	.	T	0.71117	0.3302	N	0.08118	0	0.21256	N	0.999746	B	0.02656	0.0	B	0.04013	0.001	T	0.58381	-0.7646	9	0.37606	T	0.19	.	6.0525	0.19792	0.111:0.3672:0.5218:0.0	.	971	Q9UKN7	MYO15_HUMAN	L	971	ENSP00000205890:V971L	ENSP00000205890:V971L	V	+	1	0	MYO15A	17965750	0.000000	0.05858	0.508000	0.27688	0.164000	0.22412	0.131000	0.15870	0.280000	0.22209	0.455000	0.32223	GTG	.	.		0.662	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		T	18025025	G	T	18025025	3	4	142	1	0	0	0	0	1	0	0	0	10072	1377	48	3	2913	3	MYO15A	17	18025025	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	6143083	18025025	63170185	83	22112										
SLFN11	91607	hgsc.bcm.edu	37	chr17	33679758	33679758	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tttcttaattcgtaaggttcCctgaacaccctgggaccatt	7	11	1	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr17:33679758C>A	ENST00000394566.1	-	7	2595	c.2323G>T	c.(2323-2325)Gga>Tga	p.G775*	SLFN11_ENST00000308377.4_Nonsense_Mutation_p.G775*	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	775					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CGTAAGGTTCCCTGAACACCC	0.448																																					p.G775X		Atlas-SNP	.											.	SLFN11	112	.	0			c.G2323T						.						65	62	63					17																	33679758		2203	4300	6503	SO:0001587	stop_gained	91607	exon5			AGGTTCCCTGAAC	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.2323G>T	chr17.hg19:g.33679758C>A	ENSP00000378067:p.Gly775*	121.0	0.0		108.0	26.0	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Nonsense_Mutation	SNP	ENST00000394566.1	hg19	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	c	38	7.128658	0.98081	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	.	.	.	3.85	3.85	0.44370	.	0.275722	0.26016	N	0.026843	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	11.4779	0.50308	0.0:1.0:0.0:0.0	.	.	.	.	X	775	.	ENSP00000312402:G775X	G	-	1	0	SLFN11	30703871	0.306000	0.24490	0.005000	0.12908	0.018000	0.09664	2.947000	0.49058	2.144000	0.66660	0.655000	0.94253	GGA	.	.		0.448	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		A	33679758	C	A	33679758	4	1	142	1	0	0	0	0	0	1	0	0	14748	632	22	3	386	3	SLFN11	17	33679758	Nonsense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	15654733	33679758	47515452	84	22113										
CCL3	6348	hgsc.bcm.edu	37	chr17	34416065	34416065	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	atatttctggacccactcctCactggggtcagcacagacct	8	14	3	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr17:34416065C>T	ENST00000225245.5	-	3	314	c.232G>A	c.(232-234)Gag>Aag	p.E78K	AC069363.1_ENST00000592728.1_RNA|AC069363.1_ENST00000441575.1_RNA|AC069363.1_ENST00000590992.1_RNA	NM_002983.2	NP_002974.1	P10147	CCL3_HUMAN	chemokine (C-C motif) ligand 3	78			E -> D (in dbSNP:rs34171309).		astrocyte cell migration (GO:0043615)|behavior (GO:0007610)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|eosinophil degranulation (GO:0043308)|exocytosis (GO:0006887)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|MAPK cascade (GO:0000165)|monocyte chemotaxis (GO:0002548)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of bone mineralization (GO:0030502)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoclast differentiation (GO:0045671)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell migration (GO:0030335)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of tumor necrosis factor production (GO:0032760)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|response to toxic substance (GO:0009636)|signaling (GO:0023052)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular (GO:0005622)	calcium-dependent protein kinase C activity (GO:0004698)|CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|protein kinase activity (GO:0004672)			breast(2)|lung(3)|urinary_tract(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACCCACTCCTCACTGGGGTCA	0.617																																					p.E78K		Atlas-SNP	.											.	CCL3	8	.	0			c.G232A						.						126	124	125					17																	34416065		2203	4300	6503	SO:0001583	missense	6348	exon3			ACTCCTCACTGGG	M23178	CCDS11307.1	17q12	2014-05-06	2002-08-22	2002-08-23	ENSG00000006075	ENSG00000277632		"Chemokine ligands", "Endogenous ligands"	10627	protein-coding gene	gene with protein product		182283	"small inducible cytokine A3 (homologous to mouse Mip-1a)"	SCYA3			Standard	NM_002983		Approved	G0S19-1, LD78ALPHA, MIP-1-alpha	uc002hkv.3	P10147	OTTHUMG00000188413	ENST00000225245.5:c.232G>A	chr17.hg19:g.34416065C>T	ENSP00000225245:p.Glu78Lys	488.0	0.0		449.0	124.0	NM_002983		Missense_Mutation	SNP	ENST00000225245.5	hg19	CCDS11307.1	.	.	.	.	.	.	.	.	.	.	.	1.245	-0.620244	0.03636	.	.	ENSG00000006075	ENST00000225245	T	0.04809	3.55	5.82	1.52	0.23074	Chemokine interleukin-8-like domain (3);	0.150495	0.42548	D	0.000683	T	0.02533	0.0077	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.18263	0.021	T	0.48958	-0.8988	9	0.10902	T	0.67	.	7.5381	0.27723	0.0:0.5903:0.2578:0.1519	.	78	P10147	CCL3_HUMAN	K	78	ENSP00000225245:E78K	ENSP00000225245:E78K	E	-	1	0	CCL3	31440178	0.002000	0.14202	0.240000	0.24138	0.046000	0.14306	0.330000	0.19715	0.096000	0.17463	-1.869000	0.00555	GAG	.	.		0.617	CCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256581.1	NM_002983		T	34416065	C	T	34416065	3	4	142	1	0	0	0	0	1	0	0	0	2903	835	29	3	50	3	CCL3	17	34416065	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	736307	34416065	46779145	85	22114										
GNGT2	2793	hgsc.bcm.edu	37	chr17	47284155	47284155	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ccacctttctccttgaagggAttcttgtcctcagggatgcc	9	13	3	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr17:47284155A>G	ENST00000511277.1	-	4	353	c.174T>C	c.(172-174)aaT>aaC	p.N58N	GNGT2_ENST00000503070.1_Silent_p.N58N|GNGT2_ENST00000300406.2_Silent_p.N58N|GNGT2_ENST00000507680.1_Silent_p.N58N|GNGT2_ENST00000515635.1_Silent_p.N58N|GNGT2_ENST00000511673.1_Silent_p.N58N	NM_001198756.1	NP_001185685.1	O14610	GBGT2_HUMAN	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	58					G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|phototransduction (GO:0007602)|synaptic transmission (GO:0007268)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			endometrium(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			CCTTGAAGGGATTCTTGTCCT	0.532																																					p.N58N		Atlas-SNP	.											.	GNGT2	12	.	0			c.T174C						.						170	146	154					17																	47284155		2203	4300	6503	SO:0001819	synonymous_variant	2793	exon4			GAAGGGATTCTTG		CCDS11545.1	17q21	2003-12-17				ENSG00000167083			4412	protein-coding gene	gene with protein product		139391				9286705	Standard	NM_031498		Approved	GNG9	uc021tzq.1	O14610		ENST00000511277.1:c.174T>C	chr17.hg19:g.47284155A>G		167.0	0.0		166.0	59.0	NM_031498	B2R746|D3DTW5	Silent	SNP	ENST00000511277.1	hg19	CCDS11545.1																																																																																			.	.		0.532	GNGT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364482.1	NM_031498		G	47284155	A	G	47284155	2	3	142	1	0	0	0	0	0	0	0	1	6542	330	12	2		2	GNGT2	17	47284155	Silent	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	12868090	47284155	33911055	86	22115										
COG1	9382	hgsc.bcm.edu	37	chr17	71199899	71199899	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	atggttcaagtagtagctgcCtatgagaaactctccgaaga	10	8	2	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr17:71199899C>T	ENST00000299886.4	+	9	2429	c.2349C>T	c.(2347-2349)gcC>gcT	p.A783A		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	783					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			TAGTAGCTGCCTATGAGAAAC	0.393																																					p.A783A		Atlas-SNP	.											.	COG1	46	.	0			c.C2349T						.						121	121	121					17																	71199899		2203	4300	6503	SO:0001819	synonymous_variant	9382	exon9			AGCTGCCTATGAG		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"Components of oligomeric golgi complex"	6545	protein-coding gene	gene with protein product		606973	"low density lipoprotein receptor defect B complementing"	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.2349C>T	chr17.hg19:g.71199899C>T		157.0	0.0		173.0	59.0	NM_018714	Q9NPV9|Q9P2G6	Silent	SNP	ENST00000299886.4	hg19	CCDS11692.1																																																																																			.	.		0.393	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			T	71199899	C	T	71199899	2	4	142	1	0	0	0	0	0	0	0	1	3659	668	24	3		3	COG1	17	71199899	Silent	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	23915744	71199899	9995311	87	22116										
MEX3C	51320	hgsc.bcm.edu	37	chr18	48702858	48702858	+	5'Flank	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	aactagggcagcaataacctCattctcaaagcaaatcacac	5	12	3	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr18:48702858C>G	ENST00000591040.1	-	0	799							Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		GCAATAACCTCATTCTCAAAG	0.463																																					p.E615Q		Atlas-SNP	.											.	MEX3C	77	.	0			c.G1843C						.						247	216	226					18																	48702858		2203	4300	6503	SO:0001631	upstream_gene_variant	51320	exon2			TAACCTCATTCTC	BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	28040	protein-coding gene	gene with protein product		611005	"ring finger and KH domain containing 2", "mex-3 homolog C (C. elegans)"	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693		chr18.hg19:g.48702858C>G	Exception_encountered	162.0	0.0		185.0	70.0	NM_016626	A1L022|Q9NZE3	Missense_Mutation	SNP	ENST00000591040.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.79	2.938177	0.52972	.	.	ENSG00000176624	ENST00000406189	T	0.67523	-0.27	6.03	6.03	0.97812	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.099528	0.64402	D	0.000003	T	0.64505	0.2604	L	0.45137	1.4	0.45822	D	0.998696	P	0.34934	0.476	B	0.36378	0.223	T	0.65479	-0.6158	10	0.66056	D	0.02	-4.9696	19.3283	0.94273	0.0:1.0:0.0:0.0	.	615	Q5U5Q3	MEX3C_HUMAN	Q	615	ENSP00000385610:E615Q	ENSP00000385610:E615Q	E	-	1	0	MEX3C	46956856	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.365000	0.52335	2.861000	0.98227	0.655000	0.94253	GAG	.	.		0.463	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000449559.1	NM_016626		G	48702858	C	G	48702858	1	3	142	0	1	0	0	0	0	0	0	0	9520	835	29	4		4	MEX3C	18	48702858	5'Flank	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10		48702858	29374390	88	22117										
OR10H1	26539	hgsc.bcm.edu	37	chr19	15918464	15918464	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	agcacgttgtagcgcaggggGtggcagatggccacgtagcg	18	9	0	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr19:15918464G>T	ENST00000334920.2	-	1	472	c.384C>A	c.(382-384)caC>caA	p.H128Q		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						AGCGCAGGGGGTGGCAGATGG	0.647																																					p.H128Q		Atlas-SNP	.											.	OR10H1	59	.	0			c.C384A						.						61	50	54					19																	15918464		2203	4299	6502	SO:0001583	missense	26539	exon1			CAGGGGGTGGCAG	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"GPCR / Class A : Olfactory receptors"	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.384C>A	chr19.hg19:g.15918464G>T	ENSP00000335596:p.His128Gln	133.0	0.0		170.0	63.0	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	hg19	CCDS12335.1	.	.	.	.	.	.	.	.	.	.	.	11.16	1.556771	0.27827	.	.	ENSG00000186723	ENST00000334920	T	0.01335	5.0	4.71	-4.45	0.03546	GPCR, rhodopsin-like superfamily (1);	0.255144	0.27811	N	0.017755	T	0.01592	0.0051	L	0.41906	1.305	0.26712	N	0.970953	B	0.33748	0.423	B	0.41894	0.369	T	0.39502	-0.9611	10	0.49607	T	0.09	.	6.752	0.23491	0.4597:0.1201:0.4202:0.0	.	128	Q9Y4A9	O10H1_HUMAN	Q	128	ENSP00000335596:H128Q	ENSP00000335596:H128Q	H	-	3	2	OR10H1	15779464	0.964000	0.33143	0.667000	0.29798	0.133000	0.20885	0.033000	0.13754	-0.430000	0.07318	-0.835000	0.03068	CAC	.	.		0.647	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1			T	15918464	G	T	15918464	3	4	142	1	0	0	0	0	1	0	0	0	10914	1252	44	3	576	3	OR10H1	19	15918464	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10		15918464	43210519	89	22118										
MAP1S	55201	hgsc.bcm.edu	37	chr19	17835870	17835870	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tccctcagctccggaaccttCtgttggaccctgcctctcac	7	18	3	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr19:17835870C>G	ENST00000324096.4	+	4	467	c.316C>G	c.(316-318)Ctg>Gtg	p.L106V	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000544059.2_Missense_Mutation_p.L80V|MAP1S_ENST00000597681.1_Intron	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	106	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CCGGAACCTTCTGTTGGACCC	0.597																																					p.L106V		Atlas-SNP	.											.	MAP1S	74	.	0			c.C316G						.						111	109	110					19																	17835870		2203	4300	6503	SO:0001583	missense	55201	exon4			AACCTTCTGTTGG	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.316C>G	chr19.hg19:g.17835870C>G	ENSP00000325313:p.Leu106Val	176.0	0.0		160.0	55.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	hg19	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.436395	0.43224	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.02525	4.26;4.26	4.44	3.4	0.38934	.	0.000000	0.41605	D	0.000860	T	0.03695	0.0105	L	0.46157	1.445	0.30221	N	0.79681	B;B;P	0.35745	0.394;0.394;0.518	B;B;B	0.39465	0.3;0.3;0.147	T	0.19647	-1.0299	10	0.24483	T	0.36	-20.9382	8.362	0.32363	0.0:0.8876:0.0:0.1124	.	80;106;106	B4DH53;A8K940;Q66K74	.;.;MAP1S_HUMAN	V	106;80	ENSP00000325313:L106V;ENSP00000439243:L80V	ENSP00000325313:L106V	L	+	1	2	MAP1S	17696870	0.555000	0.26530	0.994000	0.49952	0.983000	0.72400	0.995000	0.29706	0.854000	0.35336	0.491000	0.48974	CTG	.	.		0.597	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		G	17835870	C	G	17835870	3	3	142	1	0	0	0	0	1	0	0	0	9243	912	32	4	330	4	MAP1S	19	17835870	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	1917406	17835870	41293113	90	22119										
ANKRD27	84079	hgsc.bcm.edu	37	chr19	33110252	33110252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ggaggactcttggctgatggAgtccacggagcgctgcgggg	19	9	1	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr19:33110252A>G	ENST00000306065.4	-	20	2079	c.1921T>C	c.(1921-1923)Tcc>Ccc	p.S641P		NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	641					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					TGGCTGATGGAGTCCACGGAG	0.607																																					p.S641P		Atlas-SNP	.											.	ANKRD27	86	.	0			c.T1921C						.						79	74	76					19																	33110252		2203	4300	6503	SO:0001583	missense	84079	exon20			TGATGGAGTCCAC	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"Ankyrin repeat domain containing"	25310	protein-coding gene	gene with protein product	"Vps9 domain and ankyrin-repeat-containing protein"					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.1921T>C	chr19.hg19:g.33110252A>G	ENSP00000304292:p.Ser641Pro	55.0	0.0		59.0	16.0	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	hg19	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	A	13.60	2.284941	0.40394	.	.	ENSG00000105186	ENST00000306065	T	0.64618	-0.11	5.57	5.57	0.84162	Ankyrin repeat-containing domain (2);	0.117017	0.38959	N	0.001520	T	0.57651	0.2068	M	0.61703	1.905	0.80722	D	1	P	0.45283	0.855	B	0.41571	0.36	T	0.59069	-0.7523	10	0.34782	T	0.22	-25.8552	9.0767	0.36527	0.7944:0.0:0.0:0.2056	.	641	Q96NW4	ANR27_HUMAN	P	641	ENSP00000304292:S641P	ENSP00000304292:S641P	S	-	1	0	ANKRD27	37802092	0.999000	0.42202	0.944000	0.38274	0.553000	0.35397	3.088000	0.50175	2.113000	0.64589	0.533000	0.62120	TCC	.	.		0.607	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		G	33110252	A	G	33110252	3	3	142	1	0	0	0	0	1	0	0	0	655	304	11	2	1271	2	ANKRD27	19	33110252	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	15274382	33110252	26018731	91	22120										
OPA3	7408	hgsc.bcm.edu	37	chr19	46032587	46032587	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	aggcagctgcaggcggtgatGaagatgatgccctcgcccag	15	11	0	4			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr19:46032587G>T	ENST00000245932.6	+	0	2305				OPA3_ENST00000323060.3_Missense_Mutation_p.F90L	NM_003370.3	NP_003361.1	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein						actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|neural tube closure (GO:0001843)|positive regulation of actin filament polymerization (GO:0030838)|protein homotetramerization (GO:0051289)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	profilin binding (GO:0005522)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)	18		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		AGGCGGTGATGAAGATGATGC	0.642																																					p.F90L		Atlas-SNP	.											.	OPA3	19	.	0			c.C270A						.						57	59	58					19																	46032587		2202	4300	6502	SO:0001628	intergenic_variant	80207	exon2			GGTGATGAAGATG		CCDS33051.1	19q13.32	2012-02-22			ENSG00000125753	ENSG00000125753			12652	protein-coding gene	gene with protein product		601703				8812448	Standard	XM_005259199		Approved		uc002pcg.3	P50552			chr19.hg19:g.46032587G>T		113.0	0.0		74.0	18.0	NM_001017989	B2RBT9|Q6PIZ1|Q93035	Missense_Mutation	SNP	ENST00000245932.6	hg19	CCDS33051.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.007076	0.35415	.	.	ENSG00000125741	ENST00000323060	D	0.84944	-1.92	3.67	0.0369	0.14194	.	0.000000	0.85682	D	0.000000	D	0.88934	0.6572	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.84925	0.0856	9	0.45353	T	0.12	-18.7637	6.7584	0.23526	0.376:0.0:0.624:0.0	.	90	Q9H6K4-2	.	L	90	ENSP00000319817:F90L	ENSP00000319817:F90L	F	-	3	2	OPA3	50724427	0.689000	0.27690	0.151000	0.22473	0.055000	0.15305	0.874000	0.28065	-0.019000	0.14055	-0.367000	0.07326	TTC	.	.		0.642	VASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459589.1			T	46032587	G	T	46032587	1	4	142	0	1	0	0	0	0	0	0	0	10881	1281	45	3		3	OPA3	19	46032587	IGR	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	12922335	46032587	13096396	92	22121										
ZNF552	79818	hgsc.bcm.edu	37	chr19	58319697	58319697	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tgtgaactctctggtgtgcaAtgaggtggtacttgtgccta	13	7	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr19:58319697A>G	ENST00000391701.1	-	3	1104	c.935T>C	c.(934-936)aTt>aCt	p.I312T	ZNF586_ENST00000598885.1_Intron|ZNF586_ENST00000599802.1_Intron	NM_024762.3	NP_079038.2	Q9H707	ZN552_HUMAN	zinc finger protein 552	312					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		CTGGTGTGCAATGAGGTGGTA	0.443																																					p.I312T		Atlas-SNP	.											.	ZNF552	32	.	0			c.T935C						.						89	81	83					19																	58319697		2203	4300	6503	SO:0001583	missense	79818	exon3			TGTGCAATGAGGT	AK097041	CCDS12963.1	19q13.43	2013-09-20			ENSG00000178935	ENSG00000178935		"Zinc fingers, C2H2-type", "-"	26135	protein-coding gene	gene with protein product							Standard	XM_005259267		Approved	FLJ21603	uc002qqg.3	Q9H707	OTTHUMG00000183478	ENST00000391701.1:c.935T>C	chr19.hg19:g.58319697A>G	ENSP00000375582:p.Ile312Thr	91.0	0.0		94.0	31.0	NM_024762	B3KUE9|Q6P5A6	Missense_Mutation	SNP	ENST00000391701.1	hg19	CCDS12963.1	.	.	.	.	.	.	.	.	.	.	A	9.960	1.222614	0.22457	.	.	ENSG00000178935	ENST00000391701	T	0.07114	3.22	1.73	0.668	0.17912	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03053	0.0090	N	0.02985	-0.445	0.09310	N	1	B;B	0.25850	0.005;0.136	B;B	0.32149	0.025;0.141	T	0.46470	-0.9189	9	0.23302	T	0.38	.	1.4669	0.02408	0.4715:0.0:0.2132:0.3153	.	308;312	B7Z1H1;Q9H707	.;ZN552_HUMAN	T	312	ENSP00000375582:I312T	ENSP00000375582:I312T	I	-	2	0	ZNF552	63011509	0.000000	0.05858	0.001000	0.08648	0.675000	0.39556	-0.664000	0.05292	0.777000	0.33496	0.164000	0.16699	ATT	.	.		0.443	ZNF552-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466829.1	NM_024762		G	58319697	A	G	58319697	3	3	142	1	0	0	0	0	1	0	0	0	17999	101	4	2	292	2	ZNF552	19	58319697	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10	12287110	58319697	809286	93	22122										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58449053	58449053	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	atgaagtttttggataaggtGatatagattttgttatgcag	11	1	0	3			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr20:58449053G>A	ENST00000357552.3	-	35	3638	c.3413C>T	c.(3412-3414)tCa>tTa	p.S1138L	SYCP2_ENST00000371001.2_Missense_Mutation_p.S1138L			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	1138					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			TGGATAAGGTGATATAGATTT	0.308																																					p.S1138L		Atlas-SNP	.											.	SYCP2	204	.	0			c.C3413T						.						131	120	123					20																	58449053		2202	4300	6502	SO:0001583	missense	10388	exon34			TAAGGTGATATAG	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.3413C>T	chr20.hg19:g.58449053G>A	ENSP00000350162:p.Ser1138Leu	161.0	0.0		127.0	36.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.083176	0.55861	.	.	ENSG00000196074	ENST00000371001;ENST00000357552	T;T	0.20069	2.1;2.1	4.88	3.85	0.44370	.	0.391238	0.22093	N	0.064722	T	0.35799	0.0944	L	0.56769	1.78	0.37687	D	0.92369	D	0.61697	0.99	P	0.59487	0.858	T	0.32481	-0.9905	10	0.72032	D	0.01	-3.7685	11.3204	0.49419	0.0:0.0:0.8185:0.1815	.	1138	Q9BX26	SYCP2_HUMAN	L	1138	ENSP00000360040:S1138L;ENSP00000350162:S1138L	ENSP00000350162:S1138L	S	-	2	0	SYCP2	57882448	0.999000	0.42202	0.856000	0.33681	0.490000	0.33462	2.841000	0.48223	2.433000	0.82419	0.563000	0.77884	TCA	.	.		0.308	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		A	58449053	G	A	58449053	3	1	142	1	0	0	0	0	1	0	0	0	15447	1294	45	3	1223	3	SYCP2	20	58449053	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10		58449053	4576467	94	22123										
C20orf151	140893	hgsc.bcm.edu	37	chr20	60989559	60989559	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	agagccggtccaccttcgggGagagcttcggggcctcatgg	16	12	1	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr20:60989559G>A	ENST00000252998.1	-	10	1004	c.848C>T	c.(847-849)tCc>tTc	p.S283F		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	283						extracellular space (GO:0005615)											CACCTTCGGGGAGAGCTTCGG	0.692																																					p.S283F		Atlas-SNP	.											.	.	.	.	0			c.C848T						.						4	5	5					20																	60989559		2042	4076	6118	SO:0001583	missense	140893	exon10			TTCGGGGAGAGCT	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"hypothetical protein LOC140893"		"chromosome 20 open reading frame 151"	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.848C>T	chr20.hg19:g.60989559G>A	ENSP00000252998:p.Ser283Phe	75.0	0.0		77.0	22.0	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	hg19	CCDS13498.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.119713	0.37436	.	.	ENSG00000130701	ENST00000252998	T	0.20738	2.05	5.11	4.15	0.48705	.	0.654623	0.14363	N	0.324301	T	0.30823	0.0777	L	0.48642	1.525	0.09310	N	1	D	0.56968	0.978	P	0.52267	0.694	T	0.09164	-1.0687	10	0.66056	D	0.02	-7.4802	13.581	0.61903	0.0:0.1563:0.8436:0.0	.	283	Q8NC74	CT151_HUMAN	F	283	ENSP00000252998:S283F	ENSP00000252998:S283F	S	-	2	0	C20orf151	60422954	0.003000	0.15002	0.073000	0.20177	0.006000	0.05464	1.224000	0.32539	1.140000	0.42260	0.491000	0.48974	TCC	.	.		0.692	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833		A	60989559	G	A	60989559	3	1	142	1	0	0	0	0	1	0	0	0	2093	1174	41	3	1166	3	C20orf151	20	60989559	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	2540506	60989559	2035961	95	22124										
TPTE	7179	hgsc.bcm.edu	37	chr21	10906954	10906954	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	aagtcattttctcgccaaaaAgtatctccacggcaaaatct	5	11	4	0			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr21:10906954A>T	ENST00000361285.4	-	24	1936	c.1607T>A	c.(1606-1608)cTt>cAt	p.L536H	TPTE_ENST00000298232.7_Missense_Mutation_p.L518H|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Missense_Mutation_p.L498H	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	536	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CTCGCCAAAAAGTATCTCCAC	0.378																																					p.L536H		Atlas-SNP	.											.	TPTE	513	.	0			c.T1607A						.						142	126	131					21																	10906954		2203	4300	6503	SO:0001583	missense	7179	exon24			CCAAAAAGTATCT	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1607T>A	chr21.hg19:g.10906954A>T	ENSP00000355208:p.Leu536His	344.0	0.0		350.0	44.0	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	1.633	-0.518468	0.04171	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.86230	-2.09;-2.09;-2.09	2.39	-0.354	0.12591	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	1.700170	0.03457	U	0.211538	T	0.76248	0.3961	N	0.17082	0.46	0.09310	N	1	B;B;B	0.29671	0.005;0.005;0.254	B;B;B	0.31686	0.018;0.023;0.134	T	0.62666	-0.6806	10	0.15952	T	0.53	-2.2927	5.9394	0.19184	0.4243:0.0:0.0:0.5757	.	498;518;536	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	H	518;536;498	ENSP00000298232:L518H;ENSP00000355208:L536H;ENSP00000344441:L498H	ENSP00000298232:L518H	L	-	2	0	TPTE	9928825	0.061000	0.20836	0.004000	0.12327	0.023000	0.10783	0.084000	0.14891	-0.076000	0.12775	0.155000	0.16302	CTT	.	.		0.378	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			T	10906954	A	T	10906954	3	4	142	1	0	0	0	0	1	0	0	0	16445	72	3	4	52	4	TPTE	21	10906954	Missense_Mutation	SNP	A	TCGA-DD-A73A-01A-12D-A32G-10		10906954	37222941	96	22125										
BAGE2	85319	hgsc.bcm.edu	37	chr21	11049587	11049587	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tgatctaagaggtctcccggGctgtcgcacactgcacagtt	11	12	2	2			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chr21:11049587G>A	ENST00000470054.1	-	0	521							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GGTCTCCCGGGCTGTCGCACA	0.393																																					p.A105V		Atlas-SNP	.											.	.	.	.	0			c.C314T						.						66	54	58					21																	11049587		692	1591	2283			85318	exon4			TCCCGGGCTGTCG	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"cancer/testis antigen family 2, member 2"					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		chr21.hg19:g.11049587G>A		473.0	0.0		564.0	31.0	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	hg19																																																																																				.	.		0.393	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		A	11049587	G	A	11049587	1	1	142	0	1	0	0	0	0	0	0	0	1292	1203	42	3		3	BAGE2	21	11049587	RNA	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10	142633	11049587	37080308	97	22126										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5810976	5810976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	tgtttggaatcatggtgatgGtgtttggcgtcataagtggg	16	3	2	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chrX:5810976G>A	ENST00000381095.3	-	6	2960	c.2333C>T	c.(2332-2334)aCc>aTc	p.T778I	NLGN4X_ENST00000381092.1_Missense_Mutation_p.T778I|NLGN4X_ENST00000275857.6_Missense_Mutation_p.T778I|NLGN4X_ENST00000381093.2_Missense_Mutation_p.T798I|NLGN4X_ENST00000538097.1_Missense_Mutation_p.T778I	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	778					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						CATGGTGATGGTGTTTGGCGT	0.542																																					p.T778I		Atlas-SNP	.											.	NLGN4X	191	.	0			c.C2333T						.						313	256	275					X																	5810976		2203	4300	6503	SO:0001583	missense	57502	exon6			GTGATGGTGTTTG	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.2333C>T	chrX.hg19:g.5810976G>A	ENSP00000370485:p.Thr778Ile	179.0	0.0		140.0	73.0	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486139	0.63962	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1	3.82	3.82	0.43975	.	0.000000	0.35838	N	0.002954	T	0.40595	0.1123	M	0.69823	2.125	0.46458	D	0.999051	P;P;D	0.55385	0.951;0.951;0.971	P;P;P	0.58721	0.703;0.703;0.844	T	0.44298	-0.9337	10	0.87932	D	0	.	14.222	0.65833	0.0:0.0:1.0:0.0	.	835;778;798	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	I	778;798;778;778;778	ENSP00000370485:T778I;ENSP00000370483:T798I;ENSP00000275857:T778I;ENSP00000370482:T778I;ENSP00000439203:T778I	ENSP00000275857:T778I	T	-	2	0	NLGN4X	5820976	1.000000	0.71417	0.993000	0.49108	0.906000	0.53458	6.565000	0.73974	1.508000	0.48769	0.513000	0.50165	ACC	.	.		0.542	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		A	5810976	G	A	5810976	3	1	142	1	0	0	0	0	1	0	0	0	10473	1261	44	3	121	3	NLGN4X	23	5810976	Missense_Mutation	SNP	G	TCGA-DD-A73A-01A-12D-A32G-10		5810976	149459584	98	22127										
MSL3	10943	hgsc.bcm.edu	37	chrX	11783626	11783626	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ccagtccgcctttgttgaatCcatccacgccacagtccaca	6	17	0	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chrX:11783626C>A	ENST00000312196.4	+	9	1054	c.949C>A	c.(949-951)Cca>Aca	p.P317T	MSL3_ENST00000361672.2_Missense_Mutation_p.P168T|MSL3_ENST00000398527.2_Missense_Mutation_p.P305T|MSL3_ENST00000380693.3_Missense_Mutation_p.P151T|MSL3_ENST00000337339.2_Missense_Mutation_p.P317T	NM_078629.3	NP_523353.2	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3 homolog (Drosophila)	317	MRG. {ECO:0000255|PROSITE- ProRule:PRU00972}.|Required for the histone acetyltransferase activity of the MSL complex.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|multicellular organismal development (GO:0007275)|transcription from RNA polymerase II promoter (GO:0006366)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	19						TTTGTTGAATCCATCCACGCC	0.572																																					p.P317T		Atlas-SNP	.											.	MSL3	88	.	0			c.C949A						.						114	104	108					X																	11783626		2203	4300	6503	SO:0001583	missense	10943	exon9			TTGAATCCATCCA	AF117065	CCDS14147.1, CCDS14148.1, CCDS14149.1, CCDS55369.1, CCDS65213.1	Xp22.3	2008-10-29	2008-10-29	2008-10-29	ENSG00000005302	ENSG00000005302			7370	protein-coding gene	gene with protein product		300609	"male-specific lethal-3 (Drosophila)-like 1", "male-specific lethal 3-like 1 (Drosophila)"	MSL3L1		10395802, 10908644	Standard	NM_078628		Approved		uc004cuw.3	Q8N5Y2	OTTHUMG00000021132	ENST00000312196.4:c.949C>A	chrX.hg19:g.11783626C>A	ENSP00000312244:p.Pro317Thr	87.0	0.0		77.0	58.0	NM_078628	A6NCU2|A6NHW8|A8K165|B4DUV8|B7Z227|Q9UG70|Q9Y5Z8	Missense_Mutation	SNP	ENST00000312196.4	hg19	CCDS14147.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.321924	0.81580	.	.	ENSG00000005302	ENST00000312196;ENST00000337339;ENST00000361672;ENST00000398527;ENST00000380693;ENST00000380692	T;T;T;T;T;T	0.13657	3.15;3.04;2.75;2.94;2.77;2.57	4.61	4.61	0.57282	.	0.109676	0.64402	D	0.000006	T	0.40247	0.1109	M	0.81942	2.565	0.52501	D	0.999955	D;D;D;D;D	0.89917	0.998;0.992;0.995;0.998;1.0	D;P;D;D;D	0.91635	0.966;0.883;0.919;0.966;0.999	T	0.32719	-0.9896	10	0.38643	T	0.18	.	17.0067	0.86395	0.0:1.0:0.0:0.0	.	305;168;258;317;317	B4DUV8;B7Z227;Q8N5Y2-2;Q8N5Y2;A6NHW8	.;.;.;MS3L1_HUMAN;.	T	317;317;168;305;151;151	ENSP00000312244:P317T;ENSP00000338078:P317T;ENSP00000354562:P168T;ENSP00000381538:P305T;ENSP00000370069:P151T;ENSP00000370068:P151T	ENSP00000312244:P317T	P	+	1	0	MSL3	11693547	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.436000	0.73417	2.021000	0.59480	0.600000	0.82982	CCA	.	.		0.572	MSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055757.1	NM_006800		A	11783626	C	A	11783626	3	1	142	1	0	0	0	0	1	0	0	0	9888	855	30	3	983	3	MSL3	23	11783626	Missense_Mutation	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	5972650	11783626	143486934	99	22128										
FANCB	2187	hgsc.bcm.edu	37	chrX	14876077	14876077	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.09	9	1	1.64348535678665	2.04190604934099	1.49739776951673	0.400323058285099	1	0	ttgcaatctgatggttcactCtaataaataaataaataaat	4	5	3	1			TCGA-DD-A73A-01A-12D-A32G-10	TCGA-DD-A73A-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9800ae3-b791-4398-8e47-b95090ce40c4	f9cccec6-b538-4d9d-a04a-c06ed1337e87	g.chrX:14876077C>T	ENST00000324138.3	-	4	1258		c.e4-1		FANCB_ENST00000398334.1_Splice_Site	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B						DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					ATGGTTCACTCTaataaataa	0.303								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												.		Atlas-SNP	.											.	FANCB	78	.	0			c.1105-1G>A						.						70	62	65					X																	14876077		2203	4300	6503	SO:0001630	splice_region_variant	2187	exon6	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TTCACTCTAATAA	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"Fanconi anemia, complementation groups"	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.1105-1G>A	chrX.hg19:g.14876077C>T		156.0	0.0		127.0	93.0	NM_001018113	B2RMZ4|Q7Z2U2|Q86XG1	Splice_Site	SNP	ENST00000324138.3	hg19	CCDS14161.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.138913	0.56936	.	.	ENSG00000181544	ENST00000324138;ENST00000398334;ENST00000452869	.	.	.	4.72	4.72	0.59763	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4792	0.67567	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FANCB	14785998	1.000000	0.71417	0.733000	0.30861	0.391000	0.30476	4.028000	0.57246	2.255000	0.74692	0.513000	0.50165	.	.	.		0.303	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633	Intron	T	14876077	C	T	14876077	5	4	142	1	0	0	0	0	0	0	1	0	5671	927	32	3	1499	3	FANCB	23	14876077	Splice_Site	SNP	C	TCGA-DD-A73A-01A-12D-A32G-10	3092451	14876077	140394483	100	22129										
FCGR2A	2212	hgsc.bcm.edu	37	chr1	161475295	161475295	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	aatgtctcagaatgtatgtcCcagaaacctgtggctgcttc	9	10	1	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr1:161475295C>T	ENST00000271450.6	+	1	76	c.38C>T	c.(37-39)cCc>cTc	p.P13L	FCGR2A_ENST00000367972.4_Missense_Mutation_p.P13L	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	13					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P13L(1)		autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AATGTATGTCCCAGAAACCTG	0.483																																					p.P13L		Atlas-SNP	.											FCGR2A,NS,carcinoma,0,1	FCGR2A	38	.	1	Substitution - Missense(1)	endometrium(1)	c.C38T						.						140	123	129					1																	161475295		2203	4300	6503	SO:0001583	missense	2212	exon1			TATGTCCCAGAAA	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3616	protein-coding gene	gene with protein product	"Immunoglobulin G Fc receptor II"	146790	"Fc fragment of IgG, low affinity IIa, receptor for (CD32)"	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.38C>T	chr1.hg19:g.161475295C>T	ENSP00000271450:p.Pro13Leu	60.0	0.0		90.0	33.0	NM_001136219	Q8WUN1|Q8WW64	Missense_Mutation	SNP	ENST00000271450.6	hg19	CCDS44264.1	.	.	.	.	.	.	.	.	.	.	C	18.17	3.563721	0.65651	.	.	ENSG00000143226	ENST00000367972;ENST00000271450	T;T	0.01871	4.64;4.59	2.96	1.01	0.19927	.	2.722680	0.01165	N	0.006739	T	0.00580	0.0019	N	0.08118	0	0.22489	N	0.999059	P;P	0.50819	0.9;0.939	B;B	0.42625	0.22;0.393	T	0.40813	-0.9543	9	0.44086	T	0.13	.	4.3353	0.11083	0.0:0.6295:0.2345:0.136	.	13;13	P12318;P12318-2	FCG2A_HUMAN;.	L	13	ENSP00000356949:P13L;ENSP00000271450:P13L	ENSP00000271450:P13L	P	+	2	0	FCGR2A	159741919	0.000000	0.05858	0.000000	0.03702	0.648000	0.38561	-0.004000	0.12878	0.270000	0.21984	0.655000	0.94253	CCC	.	.		0.483	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642		T	161475295	C	T	161475295	3	4	143	1	0	0	0	0	1	0	0	0	5789	623	22	3	40	3	FCGR2A	1	161475295	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10		161475295	87775326	1	22130										
FCGR3B	2214	hgsc.bcm.edu	37	chr1	161595991	161595991	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	catttttactcccaacaagcCccctgcagaagtaggagccg	8	14	0	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr1:161595991C>T	ENST00000540048.1	-	2	94				FCGR3B_ENST00000531221.1_Missense_Mutation_p.G210E|FCGR2B_ENST00000367962.4_Intron|FCGR3B_ENST00000367964.2_Missense_Mutation_p.G174E|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR2B_ENST00000403078.3_Intron|FCGR3B_ENST00000294800.3_Missense_Mutation_p.G174E			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CCCAACAAGCCCCCTGCAGAA	0.463																																					p.G210E		Atlas-SNP	.											.	FCGR3B	35	.	0			c.G629A						.						108	116	113					1																	161595991		2200	4300	6500	SO:0001627	intron_variant	2215	exon4			ACAAGCCCCCTGC	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3619	protein-coding gene	gene with protein product		146740	"Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+4166G>A	chr1.hg19:g.161595991C>T		133.0	0.0		184.0	100.0	NM_001244753	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	hg19		.	.	.	.	.	.	.	.	.	.	-	13.54	2.266680	0.40095	.	.	ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221	T;T;T	0.13778	2.56;2.56;2.56	2.47	0.106	0.14540	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.248184	0.28279	N	0.015925	T	0.20659	0.0497	M	0.84326	2.69	0.09310	N	0.999994	D	0.89917	1.0	D	0.85130	0.997	T	0.01956	-1.1240	10	0.87932	D	0	.	7.7203	0.28729	0.0:0.4785:0.5215:0.0	.	174	O75015	FCG3B_HUMAN	E	174;174;210	ENSP00000356941:G174E;ENSP00000294800:G174E;ENSP00000433642:G210E	ENSP00000294800:G174E	G	-	2	0	FCGR3B	159862615	0.025000	0.19082	0.376000	0.26042	0.058000	0.15608	0.792000	0.26929	0.352000	0.24053	0.393000	0.25936	GGG	.	.		0.463	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569		T	161595991	C	T	161595991	1	4	143	0	1	0	0	0	0	0	0	0	5793	623	22	3		3	FCGR3B	1	161595991	Intron	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	120696	161595991	87654630	2	22131										
ATP2B4	493	hgsc.bcm.edu	37	chr1	203683382	203683382	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	atgacgggcctgctctgaagAaagcggatgttggttttgcc	14	8	1	3			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr1:203683382A>C	ENST00000357681.5	+	15	3506	c.2383A>C	c.(2383-2385)Aaa>Caa	p.K795Q	ATP2B4_ENST00000341360.2_Missense_Mutation_p.K795Q|ATP2B4_ENST00000367218.3_Missense_Mutation_p.K795Q|ATP2B4_ENST00000367219.3_Missense_Mutation_p.K783Q|ATP2B4_ENST00000391954.2_Missense_Mutation_p.K795Q	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	795					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TGCTCTGAAGAAAGCGGATGT	0.547																																					p.K795Q		Atlas-SNP	.											.	ATP2B4	226	.	0			c.A2383C						.						211	172	186					1																	203683382		2203	4300	6503	SO:0001583	missense	493	exon15			CTGAAGAAAGCGG	M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"ATPases / P-type"	817	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 4"	108732	"matrix-remodelling associated 1"	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.2383A>C	chr1.hg19:g.203683382A>C	ENSP00000350310:p.Lys795Gln	42.0	0.0		60.0	28.0	NM_001001396	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Missense_Mutation	SNP	ENST00000357681.5	hg19	CCDS1440.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.029626	0.93518	.	.	ENSG00000058668	ENST00000357681;ENST00000367218;ENST00000367219;ENST00000391954;ENST00000341360	D;D;D;D;D	0.95821	-3.82;-3.82;-3.82;-3.82;-3.82	5.7	5.7	0.88788	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.64402	D	0.000016	D	0.96476	0.8850	L	0.43646	1.37	0.80722	D	1	D;D;D	0.89917	1.0;0.991;0.997	D;D;D	0.77004	0.989;0.955;0.953	D	0.97130	0.9817	10	0.72032	D	0.01	-24.7161	15.636	0.76953	1.0:0.0:0.0:0.0	.	795;795;795	P23634;P23634-6;B1APW5	AT2B4_HUMAN;.;.	Q	795;795;783;795;795	ENSP00000350310:K795Q;ENSP00000356187:K795Q;ENSP00000356188:K783Q;ENSP00000375816:K795Q;ENSP00000340930:K795Q	ENSP00000340930:K795Q	K	+	1	0	ATP2B4	201950005	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.518000	0.81795	2.168000	0.68352	0.533000	0.62120	AAA	.	.		0.547	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396		C	203683382	A	C	203683382	3	2	143	1	0	0	0	0	1	0	0	0	1142	247	9	5	2437	5	ATP2B4	1	203683382	Missense_Mutation	SNP	A	TCGA-DD-A73B-01A-12D-A32G-10	42087391	203683382	45567239	3	22132										
TLR5	7100	hgsc.bcm.edu	37	chr1	223284253	223284253	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tgtttgagcaaagcattctgCacccatgtgaagtctttgct	9	9	2	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr1:223284253C>A	ENST00000540964.1	-	4	2582	c.2121G>T	c.(2119-2121)gtG>gtT	p.V707V	TLR5_ENST00000342210.6_Silent_p.V707V			O60602	TLR5_HUMAN	toll-like receptor 5	707	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.		Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1). {ECO:0000269|PubMed:14623910}.		cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		AAGCATTCTGCACCCATGTGA	0.463																																					p.V707V		Atlas-SNP	.											.	TLR5	86	.	0			c.G2121T						.						65	62	63					1																	223284253		2203	4300	6503	SO:0001819	synonymous_variant	7100	exon6			ATTCTGCACCCAT		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"Toll/interleukin-1 receptor-like protein 3"	603031	"systemic lupus erythematosus susceptibility 1"	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.2121G>T	chr1.hg19:g.223284253C>A		123.0	0.0		106.0	5.0	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Silent	SNP	ENST00000540964.1	hg19	CCDS31033.1																																																																																			.	.		0.463	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		A	223284253	C	A	223284253	2	1	143	1	0	0	0	0	0	0	0	1	15969	697	25	3		3	TLR5	1	223284253	Silent	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	19600871	223284253	25966368	4	22133										
LYST	1130	hgsc.bcm.edu	37	chr1	235915327	235915327	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tgtgtcctcttgtttttgctAttttgaagatatccaagcat	7	7	1	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr1:235915327A>G	ENST00000389794.3	-	27	7779	c.7605T>C	c.(7603-7605)aaT>aaC	p.N2535N	LYST_ENST00000389793.2_Silent_p.N2535N			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2535					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TGTTTTTGCTATTTTGAAGAT	0.333																																					p.N2535N		Atlas-SNP	.											.	LYST	370	.	0			c.T7605C						.						72	64	67					1																	235915327		2202	4297	6499	SO:0001819	synonymous_variant	1130	exon27			TTTGCTATTTTGA	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.7605T>C	chr1.hg19:g.235915327A>G		86.0	0.0		89.0	50.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	A	9.547	1.115030	0.20795	.	.	ENSG00000143669	ENST00000487530	.	.	.	5.41	-4.15	0.03881	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3753	0.32440	0.2903:0.0:0.5226:0.1871	.	.	.	.	Q	49	.	.	X	-	1	0	LYST	233981950	0.990000	0.36364	0.992000	0.48379	0.997000	0.91878	0.198000	0.17217	-0.357000	0.08175	0.533000	0.62120	TAG	.	.		0.333	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			G	235915327	A	G	235915327	2	3	143	1	0	0	0	0	0	0	0	1	9137	446	16	2		2	LYST	1	235915327	Silent	SNP	A	TCGA-DD-A73B-01A-12D-A32G-10	12631074	235915327	13335294	5	22134										
SOS1	6654	hgsc.bcm.edu	37	chr2	39278406	39278406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gttcatgtatatctactatgCgactaaatatattttctaca	4	7	3	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr2:39278406C>T	ENST00000426016.1	-	7	829	c.743G>A	c.(742-744)cGc>cAc	p.R248H	SOS1_ENST00000428721.2_Missense_Mutation_p.R191H|SOS1_ENST00000402219.2_Missense_Mutation_p.R248H|SOS1_ENST00000395038.2_Missense_Mutation_p.R248H			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	248	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				ATCTACTATGCGACTAAATAT	0.343									Noonan syndrome																												p.R248H		Atlas-SNP	.											.	SOS1	134	.	0			c.G743A						.						109	112	111					2																	39278406		2203	4300	6503	SO:0001583	missense	6654	exon6	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	ACTATGCGACTAA	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.743G>A	chr2.hg19:g.39278406C>T	ENSP00000387784:p.Arg248His	99.0	0.0		91.0	85.0	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	hg19	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.525374	0.64747	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000395038;ENST00000263879;ENST00000428721	D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02	5.74	5.74	0.90152	Dbl homology (DH) domain (5);	0.300521	0.36628	N	0.002494	D	0.87281	0.6138	N	0.22421	0.69	0.45150	D	0.99816	P	0.45768	0.866	B	0.38106	0.265	D	0.89190	0.3550	10	0.87932	D	0	.	19.544	0.95284	0.0:1.0:0.0:0.0	.	248	Q07889	SOS1_HUMAN	H	248;248;248;248;191	ENSP00000387784:R248H;ENSP00000384675:R248H;ENSP00000378479:R248H;ENSP00000399992:R191H	ENSP00000263879:R248H	R	-	2	0	SOS1	39131910	0.769000	0.28531	1.000000	0.80357	0.994000	0.84299	1.182000	0.32029	2.717000	0.92951	0.563000	0.77884	CGC	.	.		0.343	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		T	39278406	C	T	39278406	3	4	143	1	0	0	0	0	1	0	0	0	14951	768	27	1	3330	1	SOS1	2	39278406	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10		39278406	203920967	6	22135										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73676478	73676478	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	cagctgtttctgtattggctGcccagaagactgggacacca	11	11	1	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr2:73676478G>A	ENST00000264448.6	+	8	2932	c.2821G>A	c.(2821-2823)Gcc>Acc	p.A941T	ALMS1_ENST00000377715.1_Missense_Mutation_p.A941T|ALMS1_ENST00000409009.1_Missense_Mutation_p.A899T	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	941	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TGTATTGGCTGCCCAGAAGAC	0.468																																					p.A941T		Atlas-SNP	.											.	ALMS1	384	.	0			c.G2821A						.						73	72	73					2																	73676478		1850	4105	5955	SO:0001583	missense	7840	exon8			TTGGCTGCCCAGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.2821G>A	chr2.hg19:g.73676478G>A	ENSP00000264448:p.Ala941Thr	185.0	0.0		254.0	93.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	8.670	0.902547	0.17760	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.14766	3.36;3.36;2.48	3.64	0.665	0.17896	.	.	.	.	.	T	0.07773	0.0195	N	0.22421	0.69	0.09310	N	1	B;B;B	0.22003	0.056;0.029;0.063	B;B;B	0.18263	0.021;0.01;0.006	T	0.34950	-0.9808	9	0.49607	T	0.09	.	2.5172	0.04671	0.1093:0.1846:0.5161:0.19	.	941;899;941	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	T	899;941;941	ENSP00000386627:A899T;ENSP00000264448:A941T;ENSP00000366944:A941T	ENSP00000264448:A941T	A	+	1	0	ALMS1	73529986	0.000000	0.05858	0.002000	0.10522	0.030000	0.12068	0.304000	0.19228	0.115000	0.18071	0.591000	0.81541	GCC	.	.		0.468	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73676478	G	A	73676478	3	1	143	1	0	0	0	0	1	0	0	0	535	1319	46	3	2851	3	ALMS1	2	73676478	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	34398072	73676478	169522895	7	22136										
TACR1	6869	hgsc.bcm.edu	37	chr2	75276831	75276831	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ggggcagcaccggaaggcatGcttgaagcccagacggaacc	15	12	0	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr2:75276831G>T	ENST00000305249.5	-	5	1717	c.952C>A	c.(952-954)Cat>Aat	p.H318N		NM_001058.3	NP_001049.1	P25103	NK1R_HUMAN	tachykinin receptor 1	318					acute inflammatory response (GO:0002526)|aggressive behavior (GO:0002118)|angiotensin-mediated drinking behavior (GO:0003051)|associative learning (GO:0008306)|behavioral response to pain (GO:0048266)|detection of abiotic stimulus (GO:0009582)|eating behavior (GO:0042755)|inflammatory response (GO:0006954)|long-term memory (GO:0007616)|operant conditioning (GO:0035106)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of action potential (GO:0045760)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of ossification (GO:0045778)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of saliva secretion (GO:0046878)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|positive regulation of vasoconstriction (GO:0045907)|regulation of smooth muscle cell migration (GO:0014910)|regulation of smooth muscle cell proliferation (GO:0048660)|response to auditory stimulus (GO:0010996)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to heat (GO:0009408)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to ozone (GO:0010193)|response to progesterone (GO:0032570)|smooth muscle contraction involved in micturition (GO:0060083)|sperm ejaculation (GO:0042713)|tachykinin receptor signaling pathway (GO:0007217)	cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance P receptor activity (GO:0016496)|tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(8)|ovary(1)|skin(1)	24					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)	CGGAAGGCATGCTTGAAGCCC	0.587																																					p.H318N	Pancreas(64;62 1268 3653 14826 43765)	Atlas-SNP	.											.	TACR1	62	.	0			c.C952A						.						34	32	33					2																	75276831		2203	4300	6503	SO:0001583	missense	6869	exon5			AGGCATGCTTGAA	M76675	CCDS1958.1, CCDS46345.1	2p13.1-p12	2012-08-08			ENSG00000115353	ENSG00000115353		"GPCR / Class A : Tachykinin receptors"	11526	protein-coding gene	gene with protein product		162323		TAC1R		1657150	Standard	NM_001058		Approved	SPR, NK1R, NKIR	uc002sng.2	P25103	OTTHUMG00000129973	ENST00000305249.5:c.952C>A	chr2.hg19:g.75276831G>T	ENSP00000303522:p.His318Asn	37.0	0.0		47.0	25.0	NM_001058	A8K150	Missense_Mutation	SNP	ENST00000305249.5	hg19	CCDS1958.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827426	0.50845	.	.	ENSG00000115353	ENST00000305249	T	0.36157	1.27	5.25	4.38	0.52667	.	0.047899	0.85682	D	0.000000	T	0.40067	0.1102	L	0.59436	1.845	0.80722	D	1	B	0.34399	0.452	B	0.42214	0.38	T	0.18398	-1.0338	10	0.27785	T	0.31	.	11.7451	0.51815	0.0848:0.0:0.9152:0.0	.	318	P25103	NK1R_HUMAN	N	318	ENSP00000303522:H318N	ENSP00000303522:H318N	H	-	1	0	TACR1	75130339	1.000000	0.71417	0.990000	0.47175	0.973000	0.67179	6.397000	0.73239	1.439000	0.47511	0.563000	0.77884	CAT	.	.		0.587	TACR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252239.3	NM_001058		T	75276831	G	T	75276831	3	4	143	1	0	0	0	0	1	0	0	0	15520	1319	46	3	275	3	TACR1	2	75276831	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	1600353	75276831	167922542	8	22137										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109380985	109380985	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	aaagaacccacaagtcatgaTaacaaggatatttgcaaatc	6	8	1	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr2:109380985T>C	ENST00000283195.6	+	20	4116	c.3990T>C	c.(3988-3990)gaT>gaC	p.D1330D		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1330					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CAAGTCATGATAACAAGGATA	0.403																																					p.D1330D		Atlas-SNP	.											.	RANBP2	488	.	0			c.T3990C						.						70	73	72					2																	109380985		2203	4299	6502	SO:0001819	synonymous_variant	5903	exon20			TCATGATAACAAG	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.3990T>C	chr2.hg19:g.109380985T>C		99.0	0.0		47.0	43.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	hg19	CCDS2079.1																																																																																			.	.		0.403	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109380985	T	C	109380985	2	2	143	1	0	0	0	0	0	0	0	1	13043	1403	49	2		2	RANBP2	2	109380985	Silent	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	34104154	109380985	133818388	9	22138										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166897863	166897863	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gtcaacaaatgggtccatcaCaaccaggttgacaacatgtt	8	10	2	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr2:166897863C>A	ENST00000303395.4	-	13	2292	c.2293G>T	c.(2293-2295)Gtg>Ttg	p.V765L	AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.V754L|SCN1A_ENST00000409050.1_Missense_Mutation_p.V737L|SCN1A_ENST00000423058.2_Missense_Mutation_p.V765L			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	765					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGGTCCATCACAACCAGGTTG	0.403																																					p.V765L		Atlas-SNP	.											.	SCN1A	641	.	0			c.G2293T						.						116	111	112					2																	166897863		2203	4300	6503	SO:0001583	missense	6323	exon13			CCATCACAACCAG	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2293G>T	chr2.hg19:g.166897863C>A	ENSP00000303540:p.Val765Leu	87.0	0.0		37.0	29.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.937153	0.92458	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97505	-4.41;-4.41;-4.37;-4.35	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000014	D	0.99105	0.9692	H	0.96691	3.865	0.80722	D	1	D;D;B	0.61697	0.99;0.984;0.217	D;D;B	0.75484	0.986;0.967;0.171	D	0.99072	1.0834	10	0.87932	D	0	.	19.8328	0.96642	0.0:1.0:0.0:0.0	.	754;737;765	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	L	765;765;754;737	ENSP00000407030:V765L;ENSP00000303540:V765L;ENSP00000364554:V754L;ENSP00000386312:V737L	ENSP00000303540:V765L	V	-	1	0	SCN1A	166606109	1.000000	0.71417	0.992000	0.48379	0.884000	0.51177	7.773000	0.85462	2.758000	0.94735	0.591000	0.81541	GTG	.	.		0.403	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		A	166897863	C	A	166897863	3	1	143	1	0	0	0	0	1	0	0	0	13929	478	17	3	3792	3	SCN1A	2	166897863	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	57516878	166897863	76301510	10	22139										
PRKAG3	53632	hgsc.bcm.edu	37	chr2	219688557	219688557	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	atgtcggagagggagaccacGcccaagagatgctgggtctc	15	10	1	3			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr2:219688557G>A	ENST00000529249.1	-	13	1713	c.1398C>T	c.(1396-1398)ggC>ggT	p.G466G	PRKAG3_ENST00000439262.2_Silent_p.G441G|PRKAG3_ENST00000545803.1_Silent_p.G282G			Q9UGI9	AAKG3_HUMAN	protein kinase, AMP-activated, gamma 3 non-catalytic subunit	466	CBS 4. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)	AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|protein kinase binding (GO:0019901)			large_intestine(7)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Acetylsalicylic acid(DB00945)	GGGAGACCACGCCCAAGAGAT	0.607																																					p.G466G		Atlas-SNP	.											.	PRKAG3	47	.	0			c.C1398T						.						131	105	114					2																	219688557		2203	4300	6503	SO:0001819	synonymous_variant	53632	exon13			GACCACGCCCAAG	AF214519	CCDS2424.1	2q35	2012-09-20			ENSG00000115592	ENSG00000115592			9387	protein-coding gene	gene with protein product		604976				10818001	Standard	NM_017431		Approved		uc002vjb.1	Q9UGI9	OTTHUMG00000133078	ENST00000529249.1:c.1398C>T	chr2.hg19:g.219688557G>A		34.0	0.0		13.0	8.0	NM_017431	Q4QQG8|Q4V779|Q9NRL1	Silent	SNP	ENST00000529249.1	hg19	CCDS2424.1																																																																																			.	.		0.607	PRKAG3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385992.1			A	219688557	G	A	219688557	2	1	143	1	0	0	0	0	0	0	0	1	12514	1074	38	1		1	PRKAG3	2	219688557	Silent	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	52790694	219688557	23510816	11	22140										
PASK	23178	hgsc.bcm.edu	37	chr2	242075390	242075390	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	agctggccaggtctgggagcTgtaatgagctgttgtacgca	15	8	1	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr2:242075390T>C	ENST00000405260.1	-	8	1900	c.1202A>G	c.(1201-1203)cAg>cGg	p.Q401R	PASK_ENST00000358649.4_Missense_Mutation_p.Q401R|PASK_ENST00000403638.3_Missense_Mutation_p.Q401R|PASK_ENST00000234040.4_Missense_Mutation_p.Q401R|PASK_ENST00000544142.1_Missense_Mutation_p.Q215R|PASK_ENST00000539818.1_Missense_Mutation_p.Q185R	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	401	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GTCTGGGAGCTGTAATGAGCT	0.557																																					p.Q401R		Atlas-SNP	.											.	PASK	230	.	0			c.A1202G						.						144	143	143					2																	242075390		2203	4300	6503	SO:0001583	missense	23178	exon8			GGGAGCTGTAATG	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.1202A>G	chr2.hg19:g.242075390T>C	ENSP00000384016:p.Gln401Arg	84.0	0.0		35.0	30.0	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	hg19	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	T	7.836	0.720824	0.15372	.	.	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.69435	-0.4;-0.38;-0.4;-0.35;-0.39;0.61	4.55	0.0993	0.14502	PAS (1);	0.265900	0.26404	N	0.024561	T	0.46908	0.1417	N	0.24115	0.695	0.09310	N	1	P;P;P;P;P	0.45827	0.791;0.867;0.867;0.867;0.791	B;P;B;B;B	0.47346	0.342;0.544;0.359;0.359;0.342	T	0.39251	-0.9623	10	0.21014	T	0.42	.	1.0119	0.01499	0.2122:0.1105:0.2689:0.4083	.	366;215;401;401;401	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	R	401;215;401;401;185;401	ENSP00000234040:Q401R;ENSP00000441374:Q215R;ENSP00000384016:Q401R;ENSP00000351475:Q401R;ENSP00000443083:Q185R;ENSP00000384438:Q401R	ENSP00000234040:Q401R	Q	-	2	0	PASK	241724063	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	0.063000	0.14410	-0.354000	0.08212	0.460000	0.39030	CAG	.	.		0.557	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		C	242075390	T	C	242075390	3	2	143	1	0	0	0	0	1	0	0	0	11481	1580	55	2	2813	2	PASK	2	242075390	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	22386833	242075390	1123983	12	22141										
TMEM42	131616	hgsc.bcm.edu	37	chr3	44906567	44906567	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gtgctgtatggagagtgccaGgaggtcttgtggtggggagg	21	4	1	1	rs376440839		TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr3:44906567G>A	ENST00000302392.4	+	3	431	c.375G>A	c.(373-375)caG>caA	p.Q125Q		NM_144638.1	NP_653239.1	Q69YG0	TMM42_HUMAN	transmembrane protein 42	125						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00839)|KIRC - Kidney renal clear cell carcinoma(197;0.0461)|Kidney(197;0.0576)		GAGAGTGCCAGGAGGTCTTGT	0.572																																					p.Q125Q		Atlas-SNP	.											.	TMEM42	15	.	0			c.G375A						.	G		1,4405	2.1+/-5.4	0,1,2202	206	160	176		375	2.6	1	3		176	0,8600		0,0,4300	no	coding-synonymous	TMEM42	NM_144638.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		125/160	44906567	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	131616	exon3			GTGCCAGGAGGTC	AL834253	CCDS2722.1	3p21.31	2005-01-19			ENSG00000169964	ENSG00000169964			28444	protein-coding gene	gene with protein product						12477932	Standard	NM_144638		Approved	MGC29956	uc003cnz.3	Q69YG0	OTTHUMG00000133092	ENST00000302392.4:c.375G>A	chr3.hg19:g.44906567G>A		155.0	0.0		135.0	64.0	NM_144638	Q8WUQ6	Silent	SNP	ENST00000302392.4	hg19	CCDS2722.1																																																																																			.	.		0.572	TMEM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256750.2	NM_144638		A	44906567	G	A	44906567	2	1	143	1	0	0	0	0	0	0	0	1	16181	991	35	3		3	TMEM42	3	44906567	Silent	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10		44906567	153115863	13	22142										
CCR2	729230	hgsc.bcm.edu	37	chr3	46399400	46399400	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	acatcggttattttggcggaAtcttcttcatcatcctcctg	7	11	4	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr3:46399400A>G	ENST00000400888.2	+	1	421	c.382A>G	c.(382-384)Atc>Gtc	p.I128V	CCR2_ENST00000292301.4_Missense_Mutation_p.I128V|CCR2_ENST00000465202.1_Intron|CCR2_ENST00000445132.2_Missense_Mutation_p.I128V			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	128					blood vessel remodeling (GO:0001974)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular homeostasis (GO:0019725)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JAK-STAT cascade (GO:0007259)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of angiogenesis (GO:0016525)|negative regulation of eosinophil degranulation (GO:0043310)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of astrocyte chemotaxis (GO:2000464)|positive regulation of CD8-positive, alpha-beta T cell extravasation (GO:2000451)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of monocyte extravasation (GO:2000439)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of vascular endothelial growth factor production (GO:0010574)|response to wounding (GO:0009611)|T-helper 17 cell chemotaxis (GO:0035705)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|CCR2 chemokine receptor binding (GO:0031727)|chemokine receptor activity (GO:0004950)|protein homodimerization activity (GO:0042803)			breast(3)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)	14				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)		TTTTGGCGGAATCTTCTTCAT	0.468																																					p.I128V		Atlas-SNP	.											.	CCR2	103	.	0			c.A382G						.						424	381	394					3																	46399400		1568	3582	5150	SO:0001583	missense	729230	exon2			GGCGGAATCTTCT		CCDS43078.1, CCDS46813.1	3p21	2012-08-08			ENSG00000121807	ENSG00000121807		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1603	protein-coding gene	gene with protein product		601267		CMKBR2		8146186	Standard	NM_001123041		Approved	CC-CKR-2, CKR2, MCP-1-R, CD192, FLJ78302	uc003cpn.4	P41597	OTTHUMG00000156466	ENST00000400888.2:c.382A>G	chr3.hg19:g.46399400A>G	ENSP00000383681:p.Ile128Val	178.0	0.0		180.0	82.0	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Missense_Mutation	SNP	ENST00000400888.2	hg19	CCDS43078.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.045269	0.36085	.	.	ENSG00000121807	ENST00000445132;ENST00000292301;ENST00000400888	T;T;T	0.73789	-0.78;-0.78;-0.78	4.57	2.15	0.27550	GPCR, rhodopsin-like superfamily (1);	0.453694	0.21544	N	0.072851	T	0.68458	0.3003	L	0.51422	1.61	0.40235	D	0.977895	B;B	0.23650	0.078;0.089	B;B	0.31869	0.1;0.137	T	0.66956	-0.5792	10	0.59425	D	0.04	.	9.1994	0.37249	0.8409:0.0:0.1591:0.0	.	128;128	P41597;Q4VBL2	CCR2_HUMAN;.	V	128	ENSP00000399285:I128V;ENSP00000292301:I128V;ENSP00000383681:I128V	ENSP00000292301:I128V	I	+	1	0	CCR2	46374404	0.700000	0.27796	0.323000	0.25347	0.931000	0.56810	3.603000	0.54074	0.726000	0.32339	0.528000	0.53228	ATC	.	.		0.468	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647		G	46399400	A	G	46399400	3	3	143	1	0	0	0	0	1	0	0	0	2943	101	4	2	384	2	CCR2	3	46399400	Missense_Mutation	SNP	A	TCGA-DD-A73B-01A-12D-A32G-10	1492833	46399400	151623030	14	22143										
BCL6	604	hgsc.bcm.edu	37	chr3	187447680	187447680	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ctgctctcacacccaggggcGctcctcagtggcaggttgtt	12	14	2	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr3:187447680G>A	ENST00000406870.2	-	5	879	c.513C>T	c.(511-513)agC>agT	p.S171S	RP11-211G3.3_ENST00000449623.1_Intron|BCL6_ENST00000232014.4_Silent_p.S171S|BCL6_ENST00000450123.2_Silent_p.S171S|RP11-211G3.3_ENST00000437407.1_Intron	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	171					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		ACCCAGGGGCGCTCCTCAGTG	0.602			"T, Mis"	"IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"	"NHL, CLL"																																p.S171S		Atlas-SNP	.		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	.	BCL6	107	.	0			c.C513T						.						74	73	73					3																	187447680		2203	4300	6503	SO:0001819	synonymous_variant	604	exon4			AGGGGCGCTCCTC		CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1001	protein-coding gene	gene with protein product		109565	"zinc finger protein 51"	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.513C>T	chr3.hg19:g.187447680G>A		72.0	0.0		36.0	34.0	NM_001134738	A7E241|B8PSA7|D3DNV5	Silent	SNP	ENST00000406870.2	hg19	CCDS3289.1																																																																																			.	.		0.602	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931		A	187447680	G	A	187447680	2	1	143	1	0	0	0	0	0	0	0	1	1376	1078	38	1		1	BCL6	3	187447680	Silent	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	141048280	187447680	10574750	15	22144										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158256937	158256937	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ccaaacattgtgggttcaagTacaagttgacaattgttggt	10	6	1	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr4:158256937T>A	ENST00000264426.9	+	10	1660	c.1381T>A	c.(1381-1383)Tac>Aac	p.Y461N	GRIA2_ENST00000393815.2_Missense_Mutation_p.Y414N|GRIA2_ENST00000296526.7_Missense_Mutation_p.Y461N|GRIA2_ENST00000507898.1_Missense_Mutation_p.Y414N|GRIA2_ENST00000449365.1_Missense_Mutation_p.Y414N	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	461					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TGGGTTCAAGTACAAGTTGAC	0.438																																					p.Y461N		Atlas-SNP	.											.	GRIA2	358	.	0			c.T1381A						.						193	166	175					4																	158256937		2203	4300	6503	SO:0001583	missense	2891	exon10			TTCAAGTACAAGT		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.1381T>A	chr4.hg19:g.158256937T>A	ENSP00000264426:p.Tyr461Asn	140.0	0.0		68.0	59.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.355744	0.82243	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	D;D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38;-2.38	5.86	5.86	0.93980	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.96932	0.8998	H	0.98351	4.21	0.80722	D	1	D;D;D	0.76494	0.998;0.99;0.999	D;P;D	0.83275	0.943;0.83;0.996	D	0.98498	1.0613	10	0.87932	D	0	.	16.5602	0.84551	0.0:0.0:0.0:1.0	.	461;461;414	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	N	414;414;461;461;414	ENSP00000426845:Y414N;ENSP00000377403:Y414N;ENSP00000296526:Y461N;ENSP00000264426:Y461N;ENSP00000389837:Y414N	ENSP00000264426:Y461N	Y	+	1	0	GRIA2	158476387	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.997000	0.88414	2.367000	0.80283	0.528000	0.53228	TAC	.	.		0.438	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			A	158256937	T	A	158256937	3	1	143	1	0	0	0	0	1	0	0	0	6777	1638	57	4	1419	4	GRIA2	4	158256937	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10		158256937	32897339	16	22145										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13913898	13913898	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gcccttcaattgtggaatctTgcaggactgaatacgtcttg	10	9	3	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr5:13913898T>C	ENST00000265104.4	-	11	1594	c.1490A>G	c.(1489-1491)cAa>cGa	p.Q497R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	497	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TGTGGAATCTTGCAGGACTGA	0.358									Kartagener syndrome																												p.Q497R		Atlas-SNP	.											.	DNAH5	868	.	0			c.A1490G						.						121	127	125					5																	13913898		2203	4300	6503	SO:0001583	missense	1767	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GAATCTTGCAGGA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.1490A>G	chr5.hg19:g.13913898T>C	ENSP00000265104:p.Gln497Arg	102.0	0.0		112.0	59.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	10.63	1.404535	0.25378	.	.	ENSG00000039139	ENST00000265104	T	0.55234	0.53	5.67	4.5	0.54988	Dynein heavy chain, domain-1 (1);	0.121891	0.56097	D	0.000026	T	0.48696	0.1514	M	0.68593	2.085	0.41474	D	0.988128	B	0.02656	0.0	B	0.10450	0.005	T	0.40757	-0.9546	10	0.18276	T	0.48	.	11.821	0.52238	0.0:0.0692:0.0:0.9308	.	497	Q8TE73	DYH5_HUMAN	R	497	ENSP00000265104:Q497R	ENSP00000265104:Q497R	Q	-	2	0	DNAH5	13966898	1.000000	0.71417	0.996000	0.52242	0.803000	0.45373	3.486000	0.53215	0.970000	0.38263	0.455000	0.32223	CAA	.	.		0.358	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13913898	T	C	13913898	3	2	143	1	0	0	0	0	1	0	0	0	4606	1812	63	2	12660	2	DNAH5	5	13913898	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10		13913898	167001362	17	22146										
C9	735	hgsc.bcm.edu	37	chr5	39308341	39308341	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gccacacttaccagctctacCctctcccctctttacacaat	2	19	3	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr5:39308341C>T	ENST00000263408.4	-	8	1326	c.1231G>A	c.(1231-1233)Ggt>Agt	p.G411S		NM_001737.3	NP_001728.1	P02748	CO9_HUMAN	complement component 9	411	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|hemolysis by symbiont of host erythrocytes (GO:0019836)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane attack complex (GO:0005579)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)			CCAGCTCTACCCTCTCCCCTC	0.428																																					p.G411S		Atlas-SNP	.											.	C9	116	.	0			c.G1231A						.						148	140	143					5																	39308341		2203	4300	6503	SO:0001583	missense	735	exon8			CTCTACCCTCTCC		CCDS3929.1	5p14-p12	2014-09-17			ENSG00000113600	ENSG00000113600		"Complement system"	1358	protein-coding gene	gene with protein product		120940					Standard	NM_001737		Approved		uc003jlv.4	P02748	OTTHUMG00000094767	ENST00000263408.4:c.1231G>A	chr5.hg19:g.39308341C>T	ENSP00000263408:p.Gly411Ser	324.0	0.0		287.0	120.0	NM_001737		Missense_Mutation	SNP	ENST00000263408.4	hg19	CCDS3929.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763873	0.31228	.	.	ENSG00000113600	ENST00000263408	D	0.83250	-1.7	4.73	-1.48	0.08745	Membrane attack complex component/perforin (MACPF) domain (3);	0.814956	0.11679	N	0.540023	T	0.72510	0.3469	L	0.54323	1.7	0.09310	N	1	B	0.30068	0.267	B	0.30495	0.116	T	0.56074	-0.8039	10	0.12766	T	0.61	-4.6242	5.2386	0.15460	0.0:0.2925:0.1646:0.5429	.	411	P02748	CO9_HUMAN	S	411	ENSP00000263408:G411S	ENSP00000263408:G411S	G	-	1	0	C9	39344098	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.392000	0.07314	-0.204000	0.10235	0.585000	0.79938	GGT	.	.		0.428	C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211576.3			T	39308341	C	T	39308341	3	4	143	1	0	0	0	0	1	0	0	0	2445	623	22	3	464	3	C9	5	39308341	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	25394443	39308341	141606919	18	22147										
C5orf34	375444	hgsc.bcm.edu	37	chr5	43492341	43492341	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	catatggttcagggtgttcaAtctgaattaactgctcttgt	9	7	4	1	rs145050535		TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr5:43492341A>G	ENST00000306862.2	-	10	1931	c.1556T>C	c.(1555-1557)aTt>aCt	p.I519T	RP11-159F24.3_ENST00000505645.1_RNA	NM_198566.2	NP_940968	Q96MH7	CE034_HUMAN	chromosome 5 open reading frame 34	519										breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|stomach(2)	21	Lung NSC(6;2.07e-05)					AGGGTGTTCAATCTGAATTAA	0.289																																					p.I519T		Atlas-SNP	.											C5orf34,NS,carcinoma,0,1	C5orf34	47	.	0			c.T1556C						.	A	THR/ILE	0,4406		0,0,2203	91	87	88		1556	2.3	0.9	5	dbSNP_134	88	1,8585	1.2+/-3.3	0,1,4292	no	missense	C5orf34	NM_198566.2	89	0,1,6495	GG,GA,AA		0.0116,0.0,0.0077	benign	519/639	43492341	1,12991	2203	4293	6496	SO:0001583	missense	375444	exon10			TGTTCAATCTGAA	AK056925	CCDS3946.1	5p12	2012-02-23			ENSG00000172244	ENSG00000172244			24738	protein-coding gene	gene with protein product						12477932	Standard	XM_006714473		Approved	FLJ32363	uc003jnz.2	Q96MH7	OTTHUMG00000131151	ENST00000306862.2:c.1556T>C	chr5.hg19:g.43492341A>G	ENSP00000303490:p.Ile519Thr	414.0	0.0		429.0	181.0	NM_198566		Missense_Mutation	SNP	ENST00000306862.2	hg19	CCDS3946.1	.	.	.	.	.	.	.	.	.	.	A	7.731	0.699214	0.15106	0.0	1.16E-4	ENSG00000172244	ENST00000306862	T	0.53206	0.63	5.98	2.33	0.28932	.	0.438058	0.24907	N	0.034648	T	0.29158	0.0725	N	0.22421	0.69	0.27320	N	0.95707	B	0.14805	0.011	B	0.13407	0.009	T	0.15694	-1.0428	10	0.26408	T	0.33	-1.963	7.6583	0.28388	0.7445:0.0:0.2555:0.0	.	519	Q96MH7	CE034_HUMAN	T	519	ENSP00000303490:I519T	ENSP00000303490:I519T	I	-	2	0	C5orf34	43528098	0.982000	0.34865	0.931000	0.37212	0.392000	0.30506	2.113000	0.41902	0.167000	0.19631	-0.263000	0.10527	ATT	.	A|1.000;G|0.000		0.289	C5orf34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253843.1	NM_198566		G	43492341	A	G	43492341	3	3	143	1	0	0	0	0	1	0	0	0	2295	101	4	2	376	2	C5orf34	5	43492341	Missense_Mutation	SNP	A	TCGA-DD-A73B-01A-12D-A32G-10	4184000	43492341	137422919	19	22148										
TMEM174	134288	hgsc.bcm.edu	37	chr5	72469597	72469597	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tggaggggcagcagccgccaTgtcaagtcctcctcaatact	11	13	2	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr5:72469597T>A	ENST00000296776.5	+	1	576	c.527T>A	c.(526-528)aTg>aAg	p.M176K	TMEM174_ENST00000511737.1_Intron	NM_153217.2	NP_694949.1	Q8WUU8	TM174_HUMAN	transmembrane protein 174	176						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-54)		GCAGCCGCCATGTCAAGTCCT	0.532																																					p.M176K		Atlas-SNP	.											.	TMEM174	22	.	0			c.T527A						.						84	84	84					5																	72469597		2203	4300	6503	SO:0001583	missense	134288	exon1			CCGCCATGTCAAG	BC019346	CCDS4018.1	5q13.2	2008-02-05			ENSG00000164325	ENSG00000164325			28187	protein-coding gene	gene with protein product		614909				12477932	Standard	NM_153217		Approved	MGC13034, FLJ31268	uc010izc.3	Q8WUU8	OTTHUMG00000131268	ENST00000296776.5:c.527T>A	chr5.hg19:g.72469597T>A	ENSP00000296776:p.Met176Lys	167.0	0.0		142.0	61.0	NM_153217	B2RDA0|Q96N81	Missense_Mutation	SNP	ENST00000296776.5	hg19	CCDS4018.1	.	.	.	.	.	.	.	.	.	.	T	10.75	1.438246	0.25900	.	.	ENSG00000164325	ENST00000296776	.	.	.	5.09	-6.92	0.01644	.	1.617020	0.02858	N	0.129920	T	0.40694	0.1127	L	0.44542	1.39	0.09310	N	1	B	0.22346	0.068	B	0.21546	0.035	T	0.30387	-0.9980	9	0.15952	T	0.53	-23.6664	17.3104	0.87208	0.0:0.746:0.1382:0.1158	.	176	Q8WUU8	TM174_HUMAN	K	176	.	ENSP00000296776:M176K	M	+	2	0	TMEM174	72505353	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.251000	0.02882	-1.255000	0.02481	-0.912000	0.02778	ATG	.	.		0.532	TMEM174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254036.1	NM_153217		A	72469597	T	A	72469597	3	1	143	1	0	0	0	0	1	0	0	0	16105	1464	51	4	529	4	TMEM174	5	72469597	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	28977256	72469597	108445663	20	22149										
ARSB	411	hgsc.bcm.edu	37	chr5	78280832	78280832	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gtgtagtagttgtccaggagCaccccgccggccgccagcgc	14	15	0	0	rs368338486		TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr5:78280832C>T	ENST00000264914.4	-	1	776	c.240G>A	c.(238-240)gtG>gtA	p.V80V	ARSB_ENST00000565165.1_Silent_p.V80V|ARSB_ENST00000396151.3_Silent_p.V80V	NM_000046.3	NP_000037.2	P15848	ARSB_HUMAN	arylsulfatase B	80					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|lysosomal transport (GO:0007041)|lysosome organization (GO:0007040)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|rough endoplasmic reticulum (GO:0005791)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		TGTCCAGGAGCACCCCGCCGG	0.726																																					p.V80V	Melanoma(169;563 1968 25780 26156 52266)	Atlas-SNP	.											.	ARSB	47	.	0			c.G240A						.	C	,	1,3863		0,1,1931	7	8	8		240,240	1.5	0.8	5		8	0,7822		0,0,3911	no	coding-synonymous,coding-synonymous	ARSB	NM_000046.3,NM_198709.2	,	0,1,5842	TT,TC,CC		0.0,0.0259,0.0086	,	80/534,80/414	78280832	1,11685	1932	3911	5843	SO:0001819	synonymous_variant	411	exon2			CAGGAGCACCCCG	M32373	CCDS4043.1, CCDS43334.1	5q14.1	2013-02-14			ENSG00000113273	ENSG00000113273	3.1.6.1	"Arylsulfatase family"	714	protein-coding gene	gene with protein product		611542				2303452	Standard	NM_000046		Approved		uc003kfq.3	P15848	OTTHUMG00000108129	ENST00000264914.4:c.240G>A	chr5.hg19:g.78280832C>T		7.0	0.0		29.0	10.0	NM_198709	B2RC20|Q8N322|Q9UDI9	Silent	SNP	ENST00000264914.4	hg19	CCDS4043.1																																																																																			.	.		0.726	ARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226932.2	NM_000046		T	78280832	C	T	78280832	2	4	143	1	0	0	0	0	0	0	0	1	988	697	25	3		3	ARSB	5	78280832	Silent	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	5811235	78280832	102634428	21	22150										
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109178033	109178033	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	atttttttaaatttaggaatAgaaggacagtctgtggaagt	10	2	1	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr5:109178033A>G	ENST00000261483.4	+	17	3623	c.2571A>G	c.(2569-2571)atA>atG	p.I857M		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	857					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		atttaGGAATAGAAGGACAGT	0.284																																					p.I857M		Atlas-SNP	.											.	MAN2A1	136	.	0			c.A2571G						.						22	23	23					5																	109178033		2181	4276	6457	SO:0001583	missense	4124	exon17			AGGAATAGAAGGA		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.2571A>G	chr5.hg19:g.109178033A>G	ENSP00000261483:p.Ile857Met	302.0	0.0		284.0	128.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	A	12.12	1.842010	0.32513	.	.	ENSG00000112893	ENST00000261483	T	0.78364	-1.17	5.49	5.49	0.81192	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.675464	0.15678	N	0.250069	T	0.75295	0.3830	M	0.72894	2.215	0.37422	D	0.91368	B	0.27264	0.173	B	0.33121	0.158	T	0.74337	-0.3698	10	0.34782	T	0.22	-10.1094	5.9458	0.19217	0.7696:0.0:0.0827:0.1477	.	857	Q16706	MA2A1_HUMAN	M	857	ENSP00000261483:I857M	ENSP00000261483:I857M	I	+	3	3	MAN2A1	109205932	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.210000	0.42816	2.205000	0.71048	0.528000	0.53228	ATA	.	.		0.284	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			G	109178033	A	G	109178033	3	3	143	1	0	0	0	0	1	0	0	0	9223	410	15	2	2637	2	MAN2A1	5	109178033	Missense_Mutation	SNP	A	TCGA-DD-A73B-01A-12D-A32G-10	30897201	109178033	71737227	22	22151										
SPINK6	404203	hgsc.bcm.edu	37	chr5	147593575	147593575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	atggcaataaatgtgccttcTgtaaggccatagtgtaagta	10	6	1	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr5:147593575T>C	ENST00000325630.2	+	3	440	c.184T>C	c.(184-186)Tgt>Cgt	p.C62R		NM_001195290.1|NM_205841.3	NP_001182219.1|NP_995313.2	Q6UWN8	ISK6_HUMAN	serine peptidase inhibitor, Kazal type 6	62	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGTGCCTTCTGTAAGGCCAT	0.423																																					p.C62R		Atlas-SNP	.											.	SPINK6	8	.	0			c.T184C						.						93	77	82					5																	147593575		2203	4300	6503	SO:0001583	missense	404203	exon3			GCCTTCTGTAAGG	AY358716	CCDS34268.1	5q32	2011-08-31	2005-08-17		ENSG00000178172	ENSG00000178172		"Serine peptidase inhibitors, Kazal type"	29486	protein-coding gene	gene with protein product	"protease inhibitor H"	615868	"serine protease inhibitor, Kazal type 6"			15060002	Standard	NM_205841		Approved	MGC21394, UNQ844, BUSI2	uc021yff.1	Q6UWN8	OTTHUMG00000163425	ENST00000325630.2:c.184T>C	chr5.hg19:g.147593575T>C	ENSP00000324870:p.Cys62Arg	58.0	0.0		70.0	30.0	NM_205841	E0X656|Q8N5P0	Missense_Mutation	SNP	ENST00000325630.2	hg19	CCDS34268.1	.	.	.	.	.	.	.	.	.	.	T	18.96	3.733542	0.69189	.	.	ENSG00000178172	ENST00000325630	D	0.91996	-2.95	5.75	5.75	0.90469	Proteinase inhibitor I1, Kazal (3);	0.000000	0.85682	D	0.000000	D	0.95535	0.8549	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.95314	0.8414	8	.	.	.	-19.7628	12.7479	0.57291	0.0:0.0:0.0:1.0	.	62	Q6UWN8	ISK6_HUMAN	R	62	ENSP00000324870:C62R	.	C	+	1	0	SPINK6	147573768	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.529000	0.60588	2.326000	0.78906	0.533000	0.62120	TGT	.	.		0.423	SPINK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373332.1	NM_205841		C	147593575	T	C	147593575	3	2	143	1	0	0	0	0	1	0	0	0	15078	1580	55	2	194	2	SPINK6	5	147593575	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	38415542	147593575	33321685	23	22152										
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12120242	12120242	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ccccactgagaaatcctcttCaggcaaaacataaacaaaat	4	12	2	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr6:12120242C>T	ENST00000379388.2	+	4	546	c.214C>T	c.(214-216)Cag>Tag	p.Q72*		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	72					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				AAATCCTCTTCAGGCAAAACA	0.378																																					p.Q72X		Atlas-SNP	.											.	HIVEP1	242	.	0			c.C214T						.						119	113	115					6																	12120242		1825	4084	5909	SO:0001587	stop_gained	3096	exon4			CCTCTTCAGGCAA	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.214C>T	chr6.hg19:g.12120242C>T	ENSP00000368698:p.Gln72*	110.0	0.0		102.0	5.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Nonsense_Mutation	SNP	ENST00000379388.2	hg19	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.577809	0.65878	.	.	ENSG00000095951	ENST00000491710;ENST00000487103;ENST00000379388;ENST00000478545	.	.	.	5.79	5.79	0.91817	.	0.000000	0.34245	N	0.004123	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-19.3296	11.5308	0.50610	0.1302:0.728:0.1417:0.0	.	.	.	.	X	72	.	ENSP00000368698:Q72X	Q	+	1	0	HIVEP1	12228228	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	2.851000	0.48302	2.733000	0.93635	0.655000	0.94253	CAG	.	.		0.378	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		T	12120242	C	T	12120242	4	4	143	1	0	0	0	0	0	1	0	0	7195	827	29	3	224	3	HIVEP1	6	12120242	Nonsense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10		12120242	158994825	24	22153										
E2F3	1871	hgsc.bcm.edu	37	chr6	20481488	20481488	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tgatacgtctcttggtctgcTcaccaagaagttcattcagc	8	11	5	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr6:20481488T>G	ENST00000346618.3	+	3	623	c.557T>G	c.(556-558)cTc>cGc	p.L186R	E2F3_ENST00000535432.1_Missense_Mutation_p.L55R	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	186					mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			CTTGGTCTGCTCACCAAGAAG	0.458																																					p.L186R		Atlas-SNP	.											.	E2F3	30	.	0			c.T557G						.						97	99	98					6																	20481488		2203	4300	6503	SO:0001583	missense	1871	exon3			GTCTGCTCACCAA	Y10479	CCDS4545.1, CCDS58999.1	6p22	2008-08-29			ENSG00000112242	ENSG00000112242			3115	protein-coding gene	gene with protein product		600427				8246996	Standard	NM_001949		Approved		uc003nda.2	O00716	OTTHUMG00000016389	ENST00000346618.3:c.557T>G	chr6.hg19:g.20481488T>G	ENSP00000262904:p.Leu186Arg	69.0	0.0		57.0	25.0	NM_001949	Q15000|Q68DT0|Q9BZ44	Missense_Mutation	SNP	ENST00000346618.3	hg19	CCDS4545.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.861905	0.91433	.	.	ENSG00000112242	ENST00000378646;ENST00000346618;ENST00000535432	T;T	0.28255	1.62;1.96	5.98	5.98	0.97165	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.65133	0.2662	H	0.96943	3.91	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78147	-0.2317	10	0.66056	D	0.02	.	16.4622	0.84064	0.0:0.0:0.0:1.0	.	186;55	O00716;Q68DT0	E2F3_HUMAN;.	R	65;186;55	ENSP00000262904:L186R;ENSP00000443418:L55R	ENSP00000262904:L186R	L	+	2	0	E2F3	20589467	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.289000	0.77006	0.533000	0.62120	CTC	.	.		0.458	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1			G	20481488	T	G	20481488	3	3	143	1	0	0	0	0	1	0	0	0	4870	1551	54	5	567	5	E2F3	6	20481488	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	8361246	20481488	150633579	25	22154										
INHBA	3624	hgsc.bcm.edu	37	chr7	41729922	41729922	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tttttcagagagcaacagttCactcctctccccctttaagc	5	14	3	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr7:41729922C>A	ENST00000242208.4	-	3	853	c.607G>T	c.(607-609)Gaa>Taa	p.E203*	INHBA_ENST00000442711.1_Nonsense_Mutation_p.E203*|AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	203					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						AGCAACAGTTCACTCCTCTCC	0.582										TSP Lung(11;0.080)																											p.E203X		Atlas-SNP	.											.	INHBA	118	.	0			c.G607T						.						83	74	77					7																	41729922		2203	4300	6503	SO:0001587	stop_gained	3624	exon3			ACAGTTCACTCCT		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.607G>T	chr7.hg19:g.41729922C>A	ENSP00000242208:p.Glu203*	118.0	0.0		104.0	30.0	NM_002192	Q14599	Nonsense_Mutation	SNP	ENST00000242208.4	hg19	CCDS5464.1	.	.	.	.	.	.	.	.	.	.	.	39	7.379859	0.98248	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	.	.	.	6.06	6.06	0.98353	.	0.319905	0.37348	N	0.002124	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06757	T	0.87	-15.3359	20.6208	0.99490	0.0:1.0:0.0:0.0	.	.	.	.	X	203	.	ENSP00000242208:E203X	E	-	1	0	INHBA	41696447	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.763000	0.62257	2.882000	0.98803	0.655000	0.94253	GAA	.	.		0.582	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			A	41729922	C	A	41729922	4	1	143	1	0	0	0	0	0	1	0	0	7750	835	29	3	677	3	INHBA	7	41729922	Nonsense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10		41729922	117408741	26	22155										
CCDC146	57639	hgsc.bcm.edu	37	chr7	76796998	76796998	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	cgtgaaaaatggaagacagtAgcacagacacagaaaaagaa	10	6	0	5			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr7:76796998A>G	ENST00000285871.4	+	2	140	c.13A>G	c.(13-15)Agc>Ggc	p.S5G	CCDC146_ENST00000431197.1_5'UTR|RP11-467H10.2_ENST00000459742.1_RNA	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	5										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				GGAAGACAGTAGCACAGACAC	0.328																																					p.S5G		Atlas-SNP	.											.	CCDC146	87	.	0			c.A13G						.						36	37	37					7																	76796998		2203	4298	6501	SO:0001583	missense	57639	exon2			GACAGTAGCACAG	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.13A>G	chr7.hg19:g.76796998A>G	ENSP00000285871:p.Ser5Gly	492.0	0.0		486.0	155.0	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	hg19	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	A	12.12	1.841273	0.32513	.	.	ENSG00000135205	ENST00000415750;ENST00000285871	D;D	0.85411	-1.98;-1.98	4.07	-1.77	0.07982	.	1.474430	0.04140	N	0.319323	T	0.66177	0.2763	N	0.03608	-0.345	0.22639	N	0.998905	B;B	0.21606	0.03;0.058	B;B	0.22601	0.025;0.04	T	0.57201	-0.7852	10	0.56958	D	0.05	0.0615	2.373	0.04335	0.4119:0.0:0.2209:0.3672	.	5;5	Q8IYE0;C9JRR4	CC146_HUMAN;.	G	5	ENSP00000388649:S5G;ENSP00000285871:S5G	ENSP00000285871:S5G	S	+	1	0	AC007000.1	76634934	0.001000	0.12720	0.368000	0.25939	0.963000	0.63663	-0.411000	0.07142	-0.062000	0.13088	0.372000	0.22366	AGC	.	.		0.328	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		G	76796998	A	G	76796998	3	3	143	1	0	0	0	0	1	0	0	0	2782	420	15	2	15	2	CCDC146	7	76796998	Missense_Mutation	SNP	A	TCGA-DD-A73B-01A-12D-A32G-10	35067076	76796998	82341665	27	22156										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83035265	83035265	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	acctaaaaacatttacctaaTtcatcaaaatatgtgtcaat	2	8	3	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr7:83035265T>C	ENST00000307792.3	-	8	1391	c.924A>G	c.(922-924)gaA>gaG	p.E308E	SEMA3E_ENST00000427262.1_Silent_p.E248E	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	308	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				ATTTACCTAATTCATCAAAAT	0.348																																					p.E308E		Atlas-SNP	.											.	SEMA3E	125	.	0			c.A924G						.						125	115	119					7																	83035265		2203	4300	6503	SO:0001819	synonymous_variant	9723	exon8			ACCTAATTCATCA	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.924A>G	chr7.hg19:g.83035265T>C		71.0	0.0		84.0	37.0	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	hg19	CCDS34674.1																																																																																			.	.		0.348	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		C	83035265	T	C	83035265	2	2	143	1	0	0	0	0	0	0	0	1	14043	1490	52	2		2	SEMA3E	7	83035265	Silent	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	6238267	83035265	76103398	28	22157										
SRRT	51593	hgsc.bcm.edu	37	chr7	100478943	100478943	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gtgagcgccgtagtcggggtGaatatcgggactatgaccgg	17	8	0	3			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr7:100478943G>T	ENST00000347433.4	+	3	318	c.160G>T	c.(160-162)Gaa>Taa	p.E54*	SRRT_ENST00000457580.2_Nonsense_Mutation_p.E54*|SRRT_ENST00000432932.1_Nonsense_Mutation_p.E54*|SRRT_ENST00000388793.4_Nonsense_Mutation_p.E54*			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	54	Arg-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						TAGTCGGGGTGAATATCGGGA	0.577																																					p.E54X		Atlas-SNP	.											.	SRRT	108	.	0			c.G160T						.						97	87	91					7																	100478943		2203	4300	6503	SO:0001587	stop_gained	51593	exon3			CGGGGTGAATATC		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.160G>T	chr7.hg19:g.100478943G>T	ENSP00000314491:p.Glu54*	46.0	0.0		77.0	29.0	NM_001128853	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Nonsense_Mutation	SNP	ENST00000347433.4	hg19	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	G	36	5.732789	0.96856	.	.	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000432932;ENST00000347433;ENST00000431645	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	15.9856	0.80151	0.0:0.0:1.0:0.0	.	.	.	.	X	54;54;54;54;61	.	ENSP00000314491:E54X	E	+	1	0	SRRT	100316879	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	8.979000	0.93455	2.360000	0.80028	0.650000	0.86243	GAA	.	.		0.577	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		T	100478943	G	T	100478943	4	4	143	1	0	0	0	0	0	1	0	0	15187	1291	45	3	166	3	SRRT	7	100478943	Nonsense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	17443678	100478943	58659720	29	22158										
RELN	5649	hgsc.bcm.edu	37	chr7	103202066	103202066	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tacacttcaggccaaaggtcAggatgtaaattcccattgaa	8	9	2	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr7:103202066A>G	ENST00000428762.1	-	36	5601	c.5442T>C	c.(5440-5442)ccT>ccC	p.P1814P	RELN_ENST00000343529.5_Silent_p.P1814P|RELN_ENST00000424685.2_Silent_p.P1814P	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1814					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GCCAAAGGTCAGGATGTAAAT	0.443																																					p.P1814P	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T5442C						.						108	107	107					7																	103202066		2203	4300	6503	SO:0001819	synonymous_variant	5649	exon36			AAGGTCAGGATGT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.5442T>C	chr7.hg19:g.103202066A>G		71.0	0.0		81.0	37.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	hg19	CCDS47680.1																																																																																			.	.		0.443	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		G	103202066	A	G	103202066	2	3	143	1	0	0	0	0	0	0	0	1	13235	175	7	2		2	RELN	7	103202066	Silent	SNP	A	TCGA-DD-A73B-01A-12D-A32G-10	2723123	103202066	55936597	30	22159										
DOCK4	9732	hgsc.bcm.edu	37	chr7	111449457	111449457	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gtaaaagtaggaatcccagaTctaaaacaagaacaagatat	7	6	1	3			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr7:111449457T>C	ENST00000437633.1	-	29	3263	c.3007A>G	c.(3007-3009)Atc>Gtc	p.I1003V	DOCK4-AS1_ENST00000452714.1_RNA|DOCK4_ENST00000428084.1_Splice_Site_p.I1003V	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1003					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				GAATCCCAGATCTAAAACAAG	0.363																																					p.I1003V		Atlas-SNP	.											.	DOCK4	365	.	0			c.A3007G						.						49	44	45					7																	111449457		1855	4090	5945	SO:0001630	splice_region_variant	9732	exon29			CCCAGATCTAAAA		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.3007-1A>G	chr7.hg19:g.111449457T>C		70.0	0.0		50.0	30.0	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	T	7.010	0.556665	0.13436	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	T;T	0.38560	1.13;1.13	5.27	5.27	0.74061	.	0.051771	0.85682	D	0.000000	T	0.13030	0.0316	N	0.00280	-1.71	0.80722	D	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.08055	0.002;0.002;0.003	T	0.21314	-1.0249	10	0.16896	T	0.51	.	15.0222	0.71637	0.0:0.0:0.0:1.0	.	1039;1003;1003	Q149N5;Q8N1I0;Q8N1I0-2	.;DOCK4_HUMAN;.	V	991;1003;1003;991;1002	ENSP00000410746:I1003V;ENSP00000404179:I1003V	ENSP00000345432:I991V	I	-	1	0	DOCK4	111236693	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.072000	0.57563	2.200000	0.70718	0.455000	0.32223	ATC	.	.		0.363	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	Missense_Mutation	C	111449457	T	C	111449457	5	2	143	1	0	0	0	0	0	0	1	0	4691	1449	50	2	2989	2	DOCK4	7	111449457	Splice_Site	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	8247391	111449457	47689206	31	22160										
DPP6	1804	hgsc.bcm.edu	37	chr7	154645526	154645526	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ggtgacggtgcacaacacaaCagataagaaaagtaagtgct	11	7	0	3			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr7:154645526C>G	ENST00000377770.3	+	17	1844	c.1703C>G	c.(1702-1704)aCa>aGa	p.T568R	DPP6_ENST00000404039.1_Missense_Mutation_p.T504R|DPP6_ENST00000427557.1_Missense_Mutation_p.T461R|DPP6_ENST00000332007.3_Missense_Mutation_p.T506R|RP11-476H24.1_ENST00000448767.1_RNA			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	568					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			CACAACACAACAGATAAGAAA	0.433																																					p.T568R	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.C1703G						.						177	157	163					7																	154645526		1880	4112	5992	SO:0001583	missense	1804	exon17			ACACAACAGATAA	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.1703C>G	chr7.hg19:g.154645526C>G	ENSP00000367001:p.Thr568Arg	113.0	0.0		103.0	35.0	NM_130797		Missense_Mutation	SNP	ENST00000377770.3	hg19		.	.	.	.	.	.	.	.	.	.	C	0.356	-0.941924	0.02322	.	.	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	4.47	3.58	0.41010	.	0.695408	0.14661	N	0.305954	T	0.22282	0.0537	L	0.40543	1.245	0.38510	D	0.948454	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.05750	-1.0866	10	0.11485	T	0.65	-0.0057	9.5442	0.39271	0.0:0.8986:0.0:0.1014	.	461;506;568;504	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	R	504;568;506;461	ENSP00000385578:T504R;ENSP00000367001:T568R;ENSP00000328226:T506R;ENSP00000397303:T461R	ENSP00000328226:T506R	T	+	2	0	DPP6	154276459	0.107000	0.21998	0.711000	0.30485	0.126000	0.20510	1.933000	0.40153	0.968000	0.38212	0.655000	0.94253	ACA	.	.		0.433	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		G	154645526	C	G	154645526	3	3	143	1	0	0	0	0	1	0	0	0	4732	478	17	4	1885	4	DPP6	7	154645526	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	43196069	154645526	4493137	32	22161										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114124389	114124389	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tgctgtctggctccatagtaGctaaagactcaattaggagc	10	9	2	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr9:114124389G>A	ENST00000338205.5	-	49	5660	c.5441C>T	c.(5440-5442)gCt>gTt	p.A1814V	KIAA0368_ENST00000374378.3_Intron|KIAA0368_ENST00000259335.4_Missense_Mutation_p.A1992V			Q5VYK3	ECM29_HUMAN	KIAA0368	1820					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						CTCCATAGTAGCTAAAGACTC	0.358																																					p.A1992V		Atlas-SNP	.											.	KIAA0368	144	.	0			c.C5975T						.						100	102	102					9																	114124389		1905	4129	6034	SO:0001583	missense	23392	exon51			ATAGTAGCTAAAG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.5441C>T	chr9.hg19:g.114124389G>A	ENSP00000339889:p.Ala1814Val	148.0	0.0		130.0	69.0	NM_001080398	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	hg19		.	.	.	.	.	.	.	.	.	.	G	15.32	2.799749	0.50208	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	T	0.66638	-0.22	5.93	5.03	0.67393	.	0.352438	0.32970	N	0.005427	T	0.56717	0.2004	L	0.34521	1.04	0.80722	D	1	B	0.28713	0.22	B	0.25140	0.058	T	0.52343	-0.8588	10	0.29301	T	0.29	-7.9857	17.1759	0.86841	0.0:0.1263:0.8737:0.0	.	1289	B3KXF2	.	V	1814;1992;1289	ENSP00000259335:A1992V	ENSP00000259335:A1992V	A	-	2	0	KIAA0368	113164210	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	4.717000	0.61923	1.489000	0.48450	0.655000	0.94253	GCT	.	.		0.358	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		A	114124389	G	A	114124389	3	1	143	1	0	0	0	0	1	0	0	0	8180	971	34	3	82	3	KIAA0368	9	114124389	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10		114124389	27089042	33	22162										
OLFML2A	169611	hgsc.bcm.edu	37	chr9	127563879	127563879	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gcgccctggcccagcagcagGctgtgatccggggcttcacc	14	16	1	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr9:127563879G>T	ENST00000373580.3	+	5	856	c.856G>T	c.(856-858)Gct>Tct	p.A286S	OLFML2A_ENST00000288815.5_Missense_Mutation_p.A72S	NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	286					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						CCAGCAGCAGGCTGTGATCCG	0.642																																					p.A286S		Atlas-SNP	.											.	OLFML2A	61	.	0			c.G856T						.						33	34	33					9																	127563879		2203	4300	6503	SO:0001583	missense	169611	exon5			CAGCAGGCTGTGA	AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.856G>T	chr9.hg19:g.127563879G>T	ENSP00000362682:p.Ala286Ser	130.0	0.0		132.0	59.0	NM_182487	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Missense_Mutation	SNP	ENST00000373580.3	hg19	CCDS6857.2	.	.	.	.	.	.	.	.	.	.	G	19.41	3.821743	0.71028	.	.	ENSG00000185585	ENST00000331715;ENST00000425732;ENST00000373580;ENST00000288815	T;T;D	0.89343	0.87;0.87;-2.5	6.07	5.17	0.71159	.	0.175449	0.50627	D	0.000120	D	0.85137	0.5628	L	0.47716	1.5	0.31939	N	0.611165	P;P;P	0.43826	0.818;0.649;0.583	B;B;B	0.42343	0.384;0.23;0.156	D	0.85457	0.1164	10	0.30078	T	0.28	.	11.1077	0.48212	0.149:0.0:0.851:0.0	.	250;72;286	Q5JTM7;Q68BL7-3;Q68BL7	.;.;OLM2A_HUMAN	S	250;250;286;72	ENSP00000336425:A250S;ENSP00000362682:A286S;ENSP00000288815:A72S	ENSP00000288815:A72S	A	+	1	0	OLFML2A	126603700	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	4.150000	0.58098	1.567000	0.49668	0.655000	0.94253	GCT	.	.		0.642	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487		T	127563879	G	T	127563879	3	4	143	1	0	0	0	0	1	0	0	0	10866	1203	42	3	874	3	OLFML2A	9	127563879	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	13439490	127563879	13649552	34	22163										
RABEPK	10244	hgsc.bcm.edu	37	chr9	127996064	127996064	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ccatggccagtgacgtgtgcTtctgagaaagaagattccaa	11	9	1	4			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr9:127996064T>C	ENST00000373538.3	+	8	1234	c.924T>C	c.(922-924)gcT>gcC	p.A308A	RABEPK_ENST00000394124.4_3'UTR|RABEPK_ENST00000259460.8_Silent_p.A257A|RABEPK_ENST00000394125.4_Silent_p.A308A	NM_005833.3	NP_005824.2	Q7Z6M1	RABEK_HUMAN	Rab9 effector protein with kelch motifs	308					receptor-mediated endocytosis (GO:0006898)|vesicle docking involved in exocytosis (GO:0006904)	endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15						TGACGTGTGCTTCTGAGAAAG	0.458																																					p.A308A		Atlas-SNP	.											.	RABEPK	46	.	0			c.T924C						.						186	158	168					9																	127996064		2203	4300	6503	SO:0001819	synonymous_variant	10244	exon8			GTGTGCTTCTGAG	BC000503	CCDS6862.1, CCDS55341.1	9q33.1-q33.3	2010-04-19			ENSG00000136933	ENSG00000136933			16896	protein-coding gene	gene with protein product		605962				9230071	Standard	NM_005833		Approved	RAB9P40, bA65N13.1	uc004bpi.3	Q7Z6M1	OTTHUMG00000020674	ENST00000373538.3:c.924T>C	chr9.hg19:g.127996064T>C		122.0	0.0		126.0	56.0	NM_005833	A8K403|O00568|Q69YR2|Q6FHA4|Q6IBG7|Q6P092|Q86Y76|Q9BWB1	Silent	SNP	ENST00000373538.3	hg19	CCDS6862.1																																																																																			.	.		0.458	RABEPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054064.1	NM_005833		C	127996064	T	C	127996064	2	2	143	1	0	0	0	0	0	0	0	1	12978	1596	56	2		2	RABEPK	9	127996064	Silent	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	432185	127996064	13217367	35	22164										
URM1	81605	hgsc.bcm.edu	37	chr9	131152007	131152007	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ttcatctccactctgcacggCggctgagggcccttctctgg	11	15	4	1	rs374697837		TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr9:131152007C>T	ENST00000372853.4	+	5	362	c.300C>T	c.(298-300)ggC>ggT	p.G100G	RP11-339B21.11_ENST00000609303.1_lincRNA|URM1_ENST00000483206.1_3'UTR|URM1_ENST00000372850.1_3'UTR|URM1_ENST00000452446.1_3'UTR|MIR219-2_ENST00000385220.1_lincRNA	NM_001265582.1|NM_030914.3	NP_001252511.1|NP_112176.1			ubiquitin related modifier 1											cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	5						CTCTGCACGGCGGCTGAGGGC	0.647																																					p.G100G		Atlas-SNP	.											.	URM1	19	.	0			c.C300T						.	C	,	0,4406		0,0,2203	54	47	49		,300	-9.3	0.6	9		49	1,8599	1.2+/-3.3	0,1,4299	no	utr-3,coding-synonymous	URM1	NM_001135947.1,NM_030914.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	,100/102	131152007	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	81605	exon5			GCACGGCGGCTGA	AK097029	CCDS6900.1, CCDS48035.1, CCDS59148.1	9q34.13	2010-06-24	2010-06-24	2006-11-28	ENSG00000167118	ENSG00000167118			28378	protein-coding gene	gene with protein product		612693	"chromosome 9 open reading frame 74", "ubiquitin related modifier 1 homolog (S. cerevisiae)"	C9orf74		16046629, 16864801	Standard	NM_030914		Approved	MGC2668	uc011may.2	Q9BTM9	OTTHUMG00000020742	ENST00000372853.4:c.300C>T	chr9.hg19:g.131152007C>T		101.0	0.0		94.0	39.0	NM_030914		Silent	SNP	ENST00000372853.4	hg19	CCDS6900.1																																																																																			.	.		0.647	URM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054422.1	NM_030914		T	131152007	C	T	131152007	2	4	143	1	0	0	0	0	0	0	0	1	17042	755	27	1		1	URM1	9	131152007	Silent	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	3155943	131152007	10061424	36	22165										
NPFFR1	64106	hgsc.bcm.edu	37	chr10	72015152	72015152	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gcagcagcagcgcccagagcGgcagccaggacagcgtgaag	16	13	0	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr10:72015152G>A	ENST00000277942.6	-	4	853	c.854C>T	c.(853-855)cCg>cTg	p.P285L		NM_022146.4	NP_071429.1	Q9GZQ6	NPFF1_HUMAN	neuropeptide FF receptor 1	285					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			endometrium(2)|lung(1)	3						CGCCCAGAGCGGCAGCCAGGA	0.706																																					p.P285L		Atlas-SNP	.											.	NPFFR1	21	.	0			c.C854T						.						6	11	9					10																	72015152		2110	4153	6263	SO:0001583	missense	64106	exon4			CAGAGCGGCAGCC	AB040104	CCDS53539.1	10q21-q22	2012-08-10	2006-02-15	2006-02-15	ENSG00000148734	ENSG00000148734		"GPCR / Class A :  Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors"	17425	protein-coding gene	gene with protein product	"neuropeptide FF 1"	607448	"G protein-coupled receptor 147"	GPR147		11024015	Standard	NM_022146		Approved	OT7T022, NPFF1R1	uc021psj.1	Q9GZQ6	OTTHUMG00000018404	ENST00000277942.6:c.854C>T	chr10.hg19:g.72015152G>A	ENSP00000277942:p.Pro285Leu	21.0	0.0		18.0	9.0	NM_022146	A2RRF0|Q8NGR0|Q96RN3	Missense_Mutation	SNP	ENST00000277942.6	hg19	CCDS53539.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.751744	0.89753	.	.	ENSG00000148734	ENST00000449957;ENST00000277942	T;T	0.79845	-1.31;-1.31	4.73	4.73	0.59995	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.93374	0.7887	H	0.97465	4.01	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95811	0.8841	10	0.87932	D	0	.	16.2923	0.82757	0.0:0.0:1.0:0.0	.	285	Q9GZQ6	NPFF1_HUMAN	L	283;285	ENSP00000401171:P283L;ENSP00000277942:P285L	ENSP00000277942:P285L	P	-	2	0	NPFFR1	71685158	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.422000	0.97458	2.169000	0.68431	0.462000	0.41574	CCG	.	.		0.706	NPFFR1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048504.2	NM_022146		A	72015152	G	A	72015152	3	1	143	1	0	0	0	0	1	0	0	0	10586	1116	39	1	441	1	NPFFR1	10	72015152	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10		72015152	63519595	37	22166										
ACSL5	51703	hgsc.bcm.edu	37	chr10	114168208	114168208	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ctccgaattggcttgttacaCgtactctatggtagctgtac	9	10	1	0	rs140011392		TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr10:114168208C>G	ENST00000393081.1	+	6	768	c.461C>G	c.(460-462)aCg>aGg	p.T154R	RP11-324O2.3_ENST00000594870.2_RNA|ACSL5_ENST00000479936.1_3'UTR|ACSL5_ENST00000356116.1_Missense_Mutation_p.T210R|ACSL5_ENST00000369410.3_5'Flank|RP11-324O2.3_ENST00000598447.1_RNA|RP11-324O2.3_ENST00000449782.2_RNA|ACSL5_ENST00000354655.4_Missense_Mutation_p.T154R|ACSL5_ENST00000354273.4_Missense_Mutation_p.T154R|ACSL5_ENST00000433418.1_Missense_Mutation_p.T154R	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	154					cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		GCTTGTTACACGTACTCTATG	0.438																																					p.T210R		Atlas-SNP	.											.	ACSL5	51	.	0			c.C629G						.						298	228	252					10																	114168208		2203	4300	6503	SO:0001583	missense	51703	exon6			GTTACACGTACTC	AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142		"Acyl-CoA synthetase family"	16526	protein-coding gene	gene with protein product	"FACL5 for fatty acid coenzyme A ligase 5", "long-chain acyl-CoA synthetase 5", "long-chain fatty acid coenzyme A ligase 5", "fatty-acid-Coenzyme A ligase, long-chain 5"	605677	"fatty-acid-Coenzyme A ligase, long-chain 5"	FACL5		11127823	Standard	NM_016234		Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.461C>G	chr10.hg19:g.114168208C>G	ENSP00000376796:p.Thr154Arg	156.0	0.0		153.0	68.0	NM_016234	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Missense_Mutation	SNP	ENST00000393081.1	hg19	CCDS7573.1	.	.	.	.	.	.	.	.	.	.	C	18.96	3.733313	0.69189	.	.	ENSG00000197142	ENST00000354655;ENST00000393081;ENST00000356116;ENST00000433418;ENST00000354273	T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2	5.92	5.92	0.95590	AMP-dependent synthetase/ligase (1);	0.046435	0.85682	D	0.000000	T	0.48040	0.1478	L	0.50993	1.605	0.80722	D	1	D;B;B	0.58620	0.983;0.086;0.298	P;B;B	0.54706	0.759;0.095;0.154	T	0.11494	-1.0585	10	0.21014	T	0.42	-12.0121	19.0814	0.93185	0.0:1.0:0.0:0.0	.	154;210;154	A6GV77;Q9ULC5-3;Q9ULC5	.;.;ACSL5_HUMAN	R	154;154;210;154;154	ENSP00000346680:T154R;ENSP00000376796:T154R;ENSP00000348429:T210R;ENSP00000403647:T154R;ENSP00000346223:T154R	ENSP00000346223:T154R	T	+	2	0	ACSL5	114158198	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	7.481000	0.81124	2.798000	0.96311	0.643000	0.83706	ACG	.	C|1.000;T|0.000		0.438	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1	NM_016234		G	114168208	C	G	114168208	3	3	143	1	0	0	0	0	1	0	0	0	180	536	19	4	651	4	ACSL5	10	114168208	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	42153056	114168208	21366539	38	22167										
KCNK18	338567	hgsc.bcm.edu	37	chr10	118969678	118969678	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	aacttcttcctgttcttctcCatttatatcatcgttggaat	4	10	4	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr10:118969678C>G	ENST00000334549.1	+	3	1023	c.1023C>G	c.(1021-1023)tcC>tcG	p.S341S		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	341					cellular response to pH (GO:0071467)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41		Colorectal(252;0.19)		all cancers(201;0.0211)		TGTTCTTCTCCATTTATATCA	0.383																																					p.S341S		Atlas-SNP	.											.	KCNK18	70	.	0			c.C1023G						.						278	246	257					10																	118969678		2203	4300	6503	SO:0001819	synonymous_variant	338567	exon3			CTTCTCCATTTAT	AB087138	CCDS7598.1	10q26.11	2012-03-07			ENSG00000186795	ENSG00000186795		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	19439	protein-coding gene	gene with protein product	"TWIK related spinal cord K+ channel"	613655				16382106	Standard	NM_181840		Approved	K2p18.1, TRESK-2, TRESK2, TRESK, TRIK	uc010qsr.2	Q7Z418	OTTHUMG00000019120	ENST00000334549.1:c.1023C>G	chr10.hg19:g.118969678C>G		102.0	0.0		94.0	42.0	NM_181840	Q5SQQ8	Silent	SNP	ENST00000334549.1	hg19	CCDS7598.1																																																																																			.	.		0.383	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840		G	118969678	C	G	118969678	2	3	143	1	0	0	0	0	0	0	0	1	8074	581	21	4		4	KCNK18	10	118969678	Silent	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	4801470	118969678	16565069	39	22168										
PRLHR	2834	hgsc.bcm.edu	37	chr10	120354363	120354363	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gaagaccaggtggcacaggcCgccgccgaacacccagccgc	13	17	0	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr10:120354363C>T	ENST00000369169.1	-	1	393	c.394G>A	c.(394-396)Ggc>Agc	p.G132S	PRLHR_ENST00000239032.2_Missense_Mutation_p.G132S			P49683	PRLHR_HUMAN	prolactin releasing hormone receptor	132					feeding behavior (GO:0007631)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|hormone metabolic process (GO:0042445)|neuropeptide signaling pathway (GO:0007218)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)|neuropeptide Y receptor activity (GO:0004983)			large_intestine(2)|lung(8)|ovary(1)|skin(1)	12		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)		TGGCACAGGCCGCCGCCGAAC	0.657																																					p.G132S		Atlas-SNP	.											.	PRLHR	41	.	0			c.G394A						.						40	36	37					10																	120354363		2202	4299	6501	SO:0001583	missense	2834	exon2			ACAGGCCGCCGCC	AB048946	CCDS7606.1	10q25.3-q26	2014-02-21	2005-11-24	2005-11-24	ENSG00000119973	ENSG00000119973		"GPCR / Class A : RF amide peptide receptors"	4464	protein-coding gene	gene with protein product		600895	"G protein-coupled receptor 10"	GPR10		8666380, 15885496	Standard	NM_004248		Approved	PrRPR	uc001ldp.1	P49683	OTTHUMG00000019136	ENST00000369169.1:c.394G>A	chr10.hg19:g.120354363C>T	ENSP00000358167:p.Gly132Ser	28.0	0.0		36.0	17.0	NM_004248	O75194|Q502U8|Q5VXR9	Missense_Mutation	SNP	ENST00000369169.1	hg19	CCDS7606.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.727068	0.30593	.	.	ENSG00000119973	ENST00000239032;ENST00000369169	T;T	0.71698	-0.59;-0.59	4.66	2.65	0.31530	GPCR, rhodopsin-like superfamily (1);	0.334028	0.30969	N	0.008515	T	0.41050	0.1142	N	0.05414	-0.055	0.31884	N	0.618122	B	0.10296	0.003	B	0.06405	0.002	T	0.23904	-1.0175	10	0.16896	T	0.51	.	2.9845	0.05964	0.3475:0.3804:0.0:0.2721	.	132	P49683	PRLHR_HUMAN	S	132	ENSP00000239032:G132S;ENSP00000358167:G132S	ENSP00000239032:G132S	G	-	1	0	PRLHR	120344353	0.956000	0.32656	0.949000	0.38748	0.968000	0.65278	1.312000	0.33574	1.188000	0.43014	0.655000	0.94253	GGC	.	.		0.657	PRLHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050610.1	NM_004248		T	120354363	C	T	120354363	3	4	143	1	0	0	0	0	1	0	0	0	12542	652	23	1	722	1	PRLHR	10	120354363	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	1384685	120354363	15180384	40	22169										
C11orf40	143501	hgsc.bcm.edu	37	chr11	4592676	4592676	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gggcagggacttcaagtagtTcacatccacatgaagtagaa	11	8	2	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr11:4592676T>C	ENST00000307616.1	-	4	630	c.631A>G	c.(631-633)Aac>Gac	p.N211D		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	211										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		ttcaagtagttcacatccaca	0.403																																					p.N211D		Atlas-SNP	.											.	C11orf40	37	.	0			c.A631G						.						85	75	78					11																	4592676		2021	3886	5907	SO:0001583	missense	143501	exon4			AGTAGTTCACATC		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.631A>G	chr11.hg19:g.4592676T>C	ENSP00000302918:p.Asn211Asp	72.0	0.0		73.0	15.0	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	hg19	CCDS31354.1	.	.	.	.	.	.	.	.	.	.	T	4.332	0.061047	0.08339	.	.	ENSG00000171987	ENST00000307616	T	0.52295	0.67	0.56	-1.09	0.09904	.	.	.	.	.	T	0.22627	0.0546	N	0.08118	0	0.09310	N	1	P	0.49961	0.93	B	0.40444	0.329	T	0.14615	-1.0466	8	0.87932	D	0	.	.	.	.	.	211	Q8WZ69	CK040_HUMAN	D	211	ENSP00000302918:N211D	ENSP00000302918:N211D	N	-	1	0	C11orf40	4549252	0.000000	0.05858	0.001000	0.08648	0.037000	0.13140	-0.115000	0.10741	-0.501000	0.06605	0.155000	0.16302	AAC	.	.		0.403	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663		C	4592676	T	C	4592676	3	2	143	1	0	0	0	0	1	0	0	0	1641	1783	62	2	25	2	C11orf40	11	4592676	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10		4592676	130413840	41	22170										
OR51F1	256892	hgsc.bcm.edu	37	chr11	4790712	4790712	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tgtaatcatcagaagacccaTttgaatgattctggaattag	8	6	3	4			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr11:4790712T>C	ENST00000380383.1	-	1	456	c.457A>G	c.(457-459)Atg>Gtg	p.M153V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.M146V			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)		AGAAGACCCATTTGAATGATT	0.438																																					p.M146V		Atlas-SNP	.											.	OR51F1	60	.	0			c.A436G						.						93	95	94					11																	4790712		2201	4298	6499	SO:0001583	missense	256892	exon1			GACCCATTTGAAT	BK004771	CCDS31359.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188069	ENSG00000188069		"GPCR / Class A : Olfactory receptors"	15196	protein-coding gene	gene with protein product				OR51F1P			Standard	NM_001004752		Approved		uc010qyl.2	A6NGY5	OTTHUMG00000066503	ENST00000380383.1:c.457A>G	chr11.hg19:g.4790712T>C	ENSP00000369744:p.Met153Val	63.0	0.0		76.0	34.0	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.860	-0.735567	0.03111	.	.	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.35789	1.29;1.29	5.03	-0.876	0.10624	GPCR, rhodopsin-like superfamily (1);	0.474452	0.19550	N	0.111582	T	0.20414	0.0491	L	0.38531	1.155	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.10109	-1.0644	10	0.39692	T	0.17	.	1.9592	0.03382	0.2756:0.0842:0.1283:0.5118	.	153	A6NGY5	O51F1_HUMAN	V	146;153	ENSP00000345163:M146V;ENSP00000369744:M153V	ENSP00000345163:M146V	M	-	1	0	OR51F1	4747288	0.000000	0.05858	0.008000	0.14137	0.003000	0.03518	-0.027000	0.12371	0.015000	0.14971	0.533000	0.62120	ATG	.	.		0.438	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752		C	4790712	T	C	4790712	3	2	143	1	0	0	0	0	1	0	0	0	11105	1493	52	2	505	2	OR51F1	11	4790712	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	198036	4790712	130215804	42	22171										
CYP2R1	120227	hgsc.bcm.edu	37	chr11	14902228	14902228	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gattttagattcaaaagactTttggccatatccaaaatatc	5	7	1	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr11:14902228T>G	ENST00000334636.5	-	3	500	c.454A>C	c.(454-456)Aag>Cag	p.K152Q	CYP2R1_ENST00000532378.1_Intron|CYP2R1_ENST00000526489.1_5'UTR	NM_024514.4	NP_078790.2	Q6VVX0	CP2R1_HUMAN	cytochrome P450, family 2, subfamily R, polypeptide 1	152					small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14					Cholecalciferol(DB00169)|Ergocalciferol(DB00153)	TCAAAAGACTTTTGGCCATAT	0.328																																					p.K152Q	NSCLC(173;1584 2058 26117 29365 41534)	Atlas-SNP	.											.	CYP2R1	41	.	0			c.A454C						.						47	49	48					11																	14902228		2196	4293	6489	SO:0001583	missense	120227	exon3			AAGACTTTTGGCC	AY323817	CCDS7818.1	11p15.2	2008-02-05			ENSG00000186104	ENSG00000186104		"Cytochrome P450s"	20580	protein-coding gene	gene with protein product		608713				12464240, 12867411	Standard	XM_005252788		Approved		uc001mlr.3	Q6VVX0	OTTHUMG00000165900	ENST00000334636.5:c.454A>C	chr11.hg19:g.14902228T>G	ENSP00000334592:p.Lys152Gln	121.0	0.0		141.0	60.0	NM_024514	Q2M3H3|Q5RT65	Missense_Mutation	SNP	ENST00000334636.5	hg19	CCDS7818.1	.	.	.	.	.	.	.	.	.	.	T	15.63	2.890731	0.52014	.	.	ENSG00000186104	ENST00000334636	T	0.68765	-0.35	5.9	5.9	0.94986	.	0.133325	0.64402	D	0.000003	T	0.61035	0.2315	L	0.42008	1.315	0.40586	D	0.981449	P;B	0.45212	0.853;0.064	B;B	0.39562	0.303;0.059	T	0.67063	-0.5765	10	0.59425	D	0.04	.	16.3196	0.82941	0.0:0.0:0.0:1.0	.	37;152	E9PS56;Q6VVX0	.;CP2R1_HUMAN	Q	152	ENSP00000334592:K152Q	ENSP00000334592:K152Q	K	-	1	0	CYP2R1	14858804	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.254000	0.51477	2.248000	0.74166	0.459000	0.35465	AAG	.	.		0.328	CYP2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386985.1	NM_024514		G	14902228	T	G	14902228	3	3	143	1	0	0	0	0	1	0	0	0	4175	1850	64	5	1063	5	CYP2R1	11	14902228	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	10111516	14902228	120104288	43	22172										
OR8I2	120586	hgsc.bcm.edu	37	chr11	55861688	55861688	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tgtgaaaaatgctcttctgaGagtcatacatagaaaacttt	7	6	3	3			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr11:55861688G>A	ENST00000302124.2	+	1	936	c.905G>A	c.(904-906)aGa>aAa	p.R302K		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R302K(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					GCTCTTCTGAGAGTCATACAT	0.383																																					p.R302K		Atlas-SNP	.											OR8I2,scalp,carcinoma,0,1	OR8I2	119	.	1	Substitution - Missense(1)	skin(1)	c.G905A						.						24	24	24					11																	55861688		2200	4276	6476	SO:0001583	missense	120586	exon1			TTCTGAGAGTCAT	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.905G>A	chr11.hg19:g.55861688G>A	ENSP00000303864:p.Arg302Lys	39.0	0.0		29.0	13.0	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	hg19	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	G	0.864	-0.734183	0.03111	.	.	ENSG00000172154	ENST00000302124	T	0.35973	1.28	4.0	3.08	0.35506	.	0.240490	0.21555	U	0.072671	T	0.19846	0.0477	L	0.31845	0.965	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.31971	-0.9924	10	0.02654	T	1	-0.9653	6.2384	0.20776	0.3165:0.0:0.6835:0.0	.	302	Q8N0Y5	OR8I2_HUMAN	K	302	ENSP00000303864:R302K	ENSP00000303864:R302K	R	+	2	0	OR8I2	55618264	0.378000	0.25114	0.002000	0.10522	0.167000	0.22549	1.382000	0.34374	0.798000	0.33994	0.447000	0.29281	AGA	.	.		0.383	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		A	55861688	G	A	55861688	3	1	143	1	0	0	0	0	1	0	0	0	11249	942	33	3	907	3	OR8I2	11	55861688	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	40959460	55861688	79144828	44	22173										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65359477	65359477	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	aacgtccgctcagcagcaccGagagcagctcctactggagg	12	14	1	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr11:65359477G>T	ENST00000309295.4	+	18	4653	c.4388G>T	c.(4387-4389)cGa>cTa	p.R1463L	EHBP1L1_ENST00000533364.1_Missense_Mutation_p.R68L|AP001362.1_ENST00000597463.1_Silent_p.R115R|EHBP1L1_ENST00000529596.1_Intron	NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	1463						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CAGCAGCACCGAGAGCAGCTC	0.662																																					p.R1463L		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G4388T						.						49	57	54					11																	65359477		2043	4177	6220	SO:0001583	missense	254102	exon18			AGCACCGAGAGCA	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.4388G>T	chr11.hg19:g.65359477G>T	ENSP00000312671:p.Arg1463Leu	57.0	0.0		56.0	25.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.847694	0.91277	.	.	ENSG00000173442	ENST00000309295;ENST00000533364	T;T	0.48201	0.82;0.82	3.66	3.66	0.41972	Domain of unknown function DUF3585 (1);	0.190274	0.28958	N	0.013589	T	0.69620	0.3131	M	0.87971	2.92	0.46279	D	0.99896	D	0.89917	1.0	D	0.91635	0.999	T	0.74691	-0.3580	10	0.72032	D	0.01	.	10.7148	0.46006	0.0:0.0:1.0:0.0	.	1463	Q8N3D4	EH1L1_HUMAN	L	1463;68	ENSP00000312671:R1463L;ENSP00000435843:R68L	ENSP00000312671:R1463L	R	+	2	0	EHBP1L1	65116053	1.000000	0.71417	0.989000	0.46669	0.820000	0.46376	5.106000	0.64597	1.881000	0.54492	0.313000	0.20887	CGA	.	.		0.662	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		T	65359477	G	T	65359477	3	4	143	1	0	0	0	0	1	0	0	0	4978	1058	37	1	4458	1	EHBP1L1	11	65359477	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	9497789	65359477	69647039	45	22174										
ADRBK1	156	hgsc.bcm.edu	37	chr11	67046702	67046702	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ttccgagacttctgcctgaaCcacctggaggaggccaggcc	12	14	1	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr11:67046702C>A	ENST00000308595.5	+	3	512	c.222C>A	c.(220-222)aaC>aaA	p.N74K	ADRBK1_ENST00000526285.1_Missense_Mutation_p.N74K	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	74	N-terminal.|RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	TCTGCCTGAACCACCTGGAGG	0.597																																					p.N74K		Atlas-SNP	.											.	ADRBK1	51	.	0			c.C222A						.						89	83	85					11																	67046702		2200	4295	6495	SO:0001583	missense	156	exon3			CCTGAACCACCTG	X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"Pleckstrin homology (PH) domain containing"	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.222C>A	chr11.hg19:g.67046702C>A	ENSP00000312262:p.Asn74Lys	100.0	0.0		96.0	37.0	NM_001619	B0ZBE1|Q13837|Q6GTT3	Missense_Mutation	SNP	ENST00000308595.5	hg19	CCDS8156.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.241494	0.39598	.	.	ENSG00000173020	ENST00000308595;ENST00000526285	T;T	0.02216	4.39;4.39	4.5	1.87	0.25490	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.101746	0.42172	N	0.000744	T	0.02767	0.0083	L	0.45285	1.41	0.48762	D	0.999707	P;P	0.45044	0.849;0.739	B;B	0.43990	0.438;0.371	T	0.62282	-0.6887	10	0.28530	T	0.3	-14.2184	8.3066	0.32047	0.1769:0.5592:0.264:0.0	.	74;74	P25098;E9PRV7	ARBK1_HUMAN;.	K	74	ENSP00000312262:N74K;ENSP00000434126:N74K	ENSP00000312262:N74K	N	+	3	2	ADRBK1	66803278	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.611000	0.24268	0.302000	0.22762	0.655000	0.94253	AAC	.	.		0.597	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619		A	67046702	C	A	67046702	3	1	143	1	0	0	0	0	1	0	0	0	343	506	18	3	232	3	ADRBK1	11	67046702	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	1687225	67046702	67959814	46	22175										
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94318670	94318670	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	cttctataatccttcagagcCaatggaaattccccagcaca	5	13	2	1	rs574384867		TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr11:94318670C>A	ENST00000299001.6	+	6	906	c.695C>A	c.(694-696)cCa>cAa	p.P232Q	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	232					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CCTTCAGAGCCAATGGAAATT	0.313																																					p.P232Q		Atlas-SNP	.											.	PIWIL4	70	.	0			c.C695A						.						118	124	122					11																	94318670		2201	4298	6499	SO:0001583	missense	143689	exon6			CAGAGCCAATGGA	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.695C>A	chr11.hg19:g.94318670C>A	ENSP00000299001:p.Pro232Gln	116.0	0.0		77.0	63.0	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	hg19	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745275	0.49151	.	.	ENSG00000134627	ENST00000299001	T	0.09723	2.95	4.87	3.95	0.45737	Argonaute/Dicer protein, PAZ (1);	0.095085	0.44483	N	0.000447	T	0.16685	0.0401	M	0.70595	2.14	0.80722	D	1	P	0.51933	0.949	P	0.44946	0.465	T	0.05468	-1.0883	10	0.30854	T	0.27	-5.4269	13.4329	0.61066	0.1586:0.8414:0.0:0.0	.	232	Q7Z3Z4	PIWL4_HUMAN	Q	232	ENSP00000299001:P232Q	ENSP00000299001:P232Q	P	+	2	0	PIWIL4	93958318	0.985000	0.35326	0.882000	0.34594	0.962000	0.63368	4.516000	0.60496	1.253000	0.44018	0.561000	0.74099	CCA	.	.		0.313	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		A	94318670	C	A	94318670	3	1	143	1	0	0	0	0	1	0	0	0	11969	594	21	3	717	3	PIWIL4	11	94318670	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	27271968	94318670	40687846	47	22176										
CD9	928	hgsc.bcm.edu	37	chr12	6342629	6342629	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ttgaaatagctgcggccatcTggggatattcccacaaggat	11	9	1	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr12:6342629T>G	ENST00000382518.1	+	5	761	c.325T>G	c.(325-327)Tgg>Ggg	p.W109G	Y_RNA_ENST00000365448.1_RNA|CD9_ENST00000382515.2_Missense_Mutation_p.W40G|CD9_ENST00000481267.1_3'UTR|CD9_ENST00000009180.4_Missense_Mutation_p.W109G			P21926	CD9_HUMAN	CD9 molecule	109					blood coagulation (GO:0007596)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|oligodendrocyte development (GO:0014003)|paranodal junction assembly (GO:0030913)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|response to water deprivation (GO:0009414)|single fertilization (GO:0007338)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|vesicle (GO:0031982)				endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	8						TGCGGCCATCTGGGGATATTC	0.562																																					p.W109G		Atlas-SNP	.											.	CD9	24	.	0			c.T325G						.						125	112	117					12																	6342629		2203	4300	6503	SO:0001583	missense	928	exon4			GCCATCTGGGGAT	M38690	CCDS8540.1	12p13	2013-02-14	2006-03-28		ENSG00000010278	ENSG00000010278		"CD molecules", "Tetraspanins"	1709	protein-coding gene	gene with protein product	"motility related protein-1"	143030	"CD9 antigen (p24)"	MIC3		6198179	Standard	NM_001769		Approved	BA2, P24, TSPAN29, MRP-1	uc001qnq.2	P21926	OTTHUMG00000044400	ENST00000382518.1:c.325T>G	chr12.hg19:g.6342629T>G	ENSP00000371958:p.Trp109Gly	93.0	0.0		83.0	41.0	NM_001769	D3DUQ9|Q5J7W6|Q96ES4	Missense_Mutation	SNP	ENST00000382518.1	hg19	CCDS8540.1	.	.	.	.	.	.	.	.	.	.	T	16.24	3.066123	0.55539	.	.	ENSG00000010278	ENST00000382518;ENST00000536586;ENST00000382519;ENST00000425469;ENST00000543424;ENST00000009180;ENST00000382515	T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26	5.87	5.87	0.94306	.	0.049531	0.85682	D	0.000000	D	0.90188	0.6933	M	0.91354	3.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92157	0.5733	10	0.87932	D	0	.	14.2221	0.65833	0.0:0.0:0.0:1.0	.	109;109	B4DK09;P21926	.;CD9_HUMAN	G	109;109;132;109;22;109;40	ENSP00000371958:W109G;ENSP00000440985:W109G;ENSP00000371959:W132G;ENSP00000009180:W109G;ENSP00000371955:W40G	ENSP00000009180:W109G	W	+	1	0	CD9	6212890	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	7.121000	0.77160	2.248000	0.74166	0.533000	0.62120	TGG	.	.		0.562	CD9-004	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103348.1			G	6342629	T	G	6342629	3	3	143	1	0	0	0	0	1	0	0	0	3048	1580	55	5	339	5	CD9	12	6342629	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10		6342629	127509266	48	22177										
ARID2	196528	hgsc.bcm.edu	37	chr12	46246151	46246151	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ggtgatcaactagaaagaatTtctaatggacctgtattaac	8	6	2	3			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr12:46246151T>G	ENST00000334344.6	+	15	4417	c.4245T>G	c.(4243-4245)atT>atG	p.I1415M	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_Missense_Mutation_p.I23M|ARID2_ENST00000422737.1_Missense_Mutation_p.I1266M|ARID2_ENST00000444670.1_Missense_Mutation_p.I1025M	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1415					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TAGAAAGAATTTCTAATGGAC	0.408			"N, S, F"		hepatocellular carcinoma																																p.I1415M		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.T4245G						.						79	80	80					12																	46246151		2203	4299	6502	SO:0001583	missense	196528	exon15			AAGAATTTCTAAT		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4245T>G	chr12.hg19:g.46246151T>G	ENSP00000335044:p.Ile1415Met	163.0	0.0		155.0	63.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	T	9.550	1.115563	0.20795	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670;ENST00000457135	T	0.34472	1.36	6.07	6.07	0.98685	.	0.215200	0.49305	D	0.000154	T	0.30792	0.0776	N	0.19112	0.55	0.30985	N	0.722054	B;B;B	0.32526	0.374;0.374;0.087	B;B;B	0.36186	0.219;0.219;0.033	T	0.40384	-0.9566	10	0.72032	D	0.01	-3.99	16.6288	0.85011	0.0:0.0:0.0:1.0	.	1415;1025;1415	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	M	1415;532;532;1266;1025;23	ENSP00000335044:I1415M	ENSP00000335044:I1415M	I	+	3	3	ARID2	44532418	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.569000	0.45973	2.326000	0.78906	0.533000	0.62120	ATT	.	.		0.408	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		G	46246151	T	G	46246151	3	3	143	1	0	0	0	0	1	0	0	0	915	1829	64	5	4303	5	ARID2	12	46246151	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	39903522	46246151	87605744	49	22178										
CALCOCO1	57658	hgsc.bcm.edu	37	chr12	54118936	54118936	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gggaagggtgtagtgacattCcaccttggtgttggggatgt	17	5	0	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr12:54118936C>A	ENST00000550804.1	-	2	151	c.91G>T	c.(91-93)Gaa>Taa	p.E31*	CALCOCO1_ENST00000548263.1_Nonsense_Mutation_p.E31*|CALCOCO1_ENST00000547885.1_5'UTR|CALCOCO1_ENST00000430117.2_Nonsense_Mutation_p.E31*|CALCOCO1_ENST00000262059.4_Nonsense_Mutation_p.E31*			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	31	N-terminal AD (CTNNB1 binding site). {ECO:0000250}.				intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						TAGTGACATTCCACCTTGGTG	0.542																																					p.E31X		Atlas-SNP	.											.	CALCOCO1	50	.	0			c.G91T						.						208	163	178					12																	54118936		2203	4300	6503	SO:0001587	stop_gained	57658	exon2			GACATTCCACCTT	AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"coiled-coil leucine zipper coactivator 1", "inorganic pyrophosphatase activator"					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.91G>T	chr12.hg19:g.54118936C>A	ENSP00000449960:p.Glu31*	117.0	0.0		135.0	58.0	NM_020898	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Nonsense_Mutation	SNP	ENST00000550804.1	hg19	CCDS8864.1	.	.	.	.	.	.	.	.	.	.	C	39	7.299316	0.98196	.	.	ENSG00000012822	ENST00000430117;ENST00000262059;ENST00000413257;ENST00000548263;ENST00000550804;ENST00000549935;ENST00000551900;ENST00000546619;ENST00000547949;ENST00000553154;ENST00000549784;ENST00000549173;ENST00000548177;ENST00000552623;ENST00000549349;ENST00000549688;ENST00000547885;ENST00000548431	.	.	.	4.86	3.97	0.46021	.	0.000000	0.46758	D	0.000280	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-11.3184	12.6432	0.56720	0.0:0.9181:0.0:0.0819	.	.	.	.	X	31	.	ENSP00000262059:E31X	E	-	1	0	CALCOCO1	52405203	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.098000	0.71458	1.428000	0.47296	0.655000	0.94253	GAA	.	.		0.542	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898		A	54118936	C	A	54118936	4	1	143	1	0	0	0	0	0	1	0	0	2579	864	30	3	2040	3	CALCOCO1	12	54118936	Nonsense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	7872785	54118936	79732959	50	22179										
CHST11	50515	hgsc.bcm.edu	37	chr12	105151023	105151023	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ctgaagaccctgaaccagtaCagcatcccagaaatcaacca	6	14	1	4			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr12:105151023C>A	ENST00000303694.5	+	3	940	c.501C>A	c.(499-501)taC>taA	p.Y167*	CHST11_ENST00000549260.1_Nonsense_Mutation_p.Y162*	NM_018413.5	NP_060883.1	Q9NPF2	CHSTB_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 11	167					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondrocyte development (GO:0002063)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|developmental growth (GO:0048589)|embryonic digit morphogenesis (GO:0042733)|embryonic viscerocranium morphogenesis (GO:0048703)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|polysaccharide localization (GO:0033037)|post-anal tail morphogenesis (GO:0036342)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)	18						TGAACCAGTACAGCATCCCAG	0.572																																					p.Y167X		Atlas-SNP	.											.	CHST11	54	.	0			c.C501A						.						73	68	70					12																	105151023		2203	4300	6503	SO:0001587	stop_gained	50515	exon3			CCAGTACAGCATC	AB042326	CCDS9099.1, CCDS55878.1	12q23.3	2008-02-05				ENSG00000171310	2.8.2.5	"Sulfotransferases, membrane-bound"	17422	protein-coding gene	gene with protein product		610128				10781601	Standard	NM_018413		Approved	C4ST1, C4St-1, C4ST, HSA269537	uc001tkz.3	Q9NPF2	OTTHUMG00000169803	ENST00000303694.5:c.501C>A	chr12.hg19:g.105151023C>A	ENSP00000305725:p.Tyr167*	65.0	0.0		71.0	31.0	NM_018413	A8K4F8|Q9NXY6|Q9NY36	Nonsense_Mutation	SNP	ENST00000303694.5	hg19	CCDS9099.1	.	.	.	.	.	.	.	.	.	.	C	37	6.197700	0.97367	.	.	ENSG00000171310	ENST00000549260;ENST00000303694;ENST00000549016	.	.	.	5.42	3.58	0.41010	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.9522	12.4791	0.55831	0.0:0.8619:0.0:0.1381	.	.	.	.	X	162;167;127	.	ENSP00000305725:Y167X	Y	+	3	2	CHST11	103675153	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.980000	0.63812	1.312000	0.45043	-0.123000	0.14984	TAC	.	.		0.572	CHST11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405960.2	NM_018413		A	105151023	C	A	105151023	4	1	143	1	0	0	0	0	0	1	0	0	3401	489	17	3	511	3	CHST11	12	105151023	Nonsense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	51032087	105151023	28700872	51	22180										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77656079	77656079	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	aatgtgatgaaagacgttgcTctgatgaaggaactggtgat	13	4	1	6			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr13:77656079T>C	ENST00000544440.2	-	64	10989	c.10972A>G	c.(10972-10974)Agc>Ggc	p.S3658G	MYCBP2_ENST00000407578.2_Missense_Mutation_p.S3696G|MYCBP2-AS1_ENST00000450627.2_RNA|MYCBP2-AS1_ENST00000448470.2_RNA|MYCBP2-AS1_ENST00000422231.2_RNA|MYCBP2_ENST00000357337.6_Missense_Mutation_p.S3658G|MYCBP2-AS2_ENST00000428716.2_RNA|MYCBP2-AS1_ENST00000593933.1_RNA					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		AAGACGTTGCTCTGATGAAGG	0.363																																					p.S3696G		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A11086G						.						103	95	98					13																	77656079		2203	4300	6503	SO:0001583	missense	23077	exon64			CGTTGCTCTGATG	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.10972A>G	chr13.hg19:g.77656079T>C	ENSP00000444596:p.Ser3658Gly	82.0	0.0		124.0	56.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.3|24.3	4.512218|4.512218	0.85389|0.85389	.|.	.|.	ENSG00000005810|ENSG00000005810	ENST00000429715|ENST00000357337;ENST00000407578;ENST00000544440	.|T;T;T	.|0.67865	.|-0.29;-0.29;-0.29	5.17|5.17	5.17|5.17	0.71159|0.71159	.|Galactose-binding domain-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.79233|0.79233	0.4411|0.4411	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	.|P	.|0.49447	.|0.924	.|P	.|0.60682	.|0.878	T|T	0.81775|0.81775	-0.0778|-0.0778	5|10	.|0.72032	.|D	.|0.01	.|.	15.2956|15.2956	0.73906|0.73906	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|3658	.|O75592	.|MYCB2_HUMAN	G|G	81|3658;3696;3658	.|ENSP00000349892:S3658G;ENSP00000384288:S3696G;ENSP00000444596:S3658G	.|ENSP00000349892:S3658G	E|S	-|-	2|1	0|0	MYCBP2|MYCBP2	76554080|76554080	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	7.997000|7.997000	0.88414|0.88414	2.063000|2.063000	0.61619|0.61619	0.533000|0.533000	0.62120|0.62120	GAG|AGC	.	.		0.363	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77656079	T	C	77656079	3	2	143	1	0	0	0	0	1	0	0	0	10027	1551	54	2	3030	2	MYCBP2	13	77656079	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10		77656079	37513799	52	22181										
MYO16	23026	hgsc.bcm.edu	37	chr13	109793226	109793226	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	agtaccccgtgcagccggagGggtcgagcccgctgtccccg	15	16	0	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr13:109793226G>A	ENST00000357550.2	+	31	4641	c.4600G>A	c.(4600-4602)Ggg>Agg	p.G1534R	MYO16_ENST00000356711.2_Missense_Mutation_p.G1534R	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			GCAGCCGGAGGGGTCGAGCCC	0.706																																					p.G1556R		Atlas-SNP	.											.	MYO16	285	.	0			c.G4666A						.						17	21	20					13																	109793226		2193	4286	6479	SO:0001583	missense	23026	exon32			CCGGAGGGGTCGA		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4600G>A	chr13.hg19:g.109793226G>A	ENSP00000350160:p.Gly1534Arg	70.0	0.0		150.0	44.0	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	hg19	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	G	11.16	1.555911	0.27827	.	.	ENSG00000041515	ENST00000356711;ENST00000357550	T;T	0.46063	0.88;0.88	4.8	3.05	0.35203	.	0.370184	0.19093	U	0.122920	T	0.42494	0.1205	L	0.54323	1.7	0.19575	N	0.999968	P	0.46706	0.883	P	0.47402	0.546	T	0.20009	-1.0288	9	.	.	.	.	8.6125	0.33811	0.2262:0.0:0.7738:0.0	.	1534	Q9Y6X6	MYO16_HUMAN	R	1534	ENSP00000349145:G1534R;ENSP00000350160:G1534R	.	G	+	1	0	MYO16	108591227	0.768000	0.28519	0.002000	0.10522	0.007000	0.05969	1.842000	0.39250	0.452000	0.26830	0.467000	0.42956	GGG	.	.		0.706	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		A	109793226	G	A	109793226	3	1	143	1	0	0	0	0	1	0	0	0	10073	1232	43	3	4722	3	MYO16	13	109793226	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	32137147	109793226	5376652	53	22182										
CHURC1	91612	hgsc.bcm.edu	37	chr14	65398946	65398946	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gacaaatgactctcttattcTaaggatccttctacagatct	5	10	4	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr14:65398946T>C	ENST00000549115.1	+	4	472	c.418T>C	c.(418-420)Taa>Caa	p.*140Q	CHURC1_ENST00000548752.2_3'UTR|CHURC1-FNTB_ENST00000549987.1_Intron|CHURC1_ENST00000607599.1_Nonstop_Mutation_p.*141Q|FNTB_ENST00000542227.1_Intron|CHURC1_ENST00000359118.2_Nonstop_Mutation_p.*114Q|FNTB_ENST00000447296.2_Intron|CHURC1_ENST00000552002.2_Nonstop_Mutation_p.*113Q			Q8WUH1	CHUR_HUMAN	churchill domain containing 1	0					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)		zinc ion binding (GO:0008270)			breast(1)|pancreas(1)	2				all cancers(60;0.00119)|OV - Ovarian serous cystadenocarcinoma(108;0.0056)|BRCA - Breast invasive adenocarcinoma(234;0.00976)		TCTCTTATTCTAAGGATCCTT	0.388																																					p.X141Q		Atlas-SNP	.											.	CHURC1	6	.	0			c.T421C						.						106	99	101					14																	65398946		2203	4300	6503	SO:0001578	stop_lost	91612	exon4			TTATTCTAAGGAT	AF060510	CCDS32101.1, CCDS32101.2, CCDS55921.1, CCDS55922.1	14q23.3	2011-09-28	2004-05-05	2004-05-07	ENSG00000258289	ENSG00000258289			20099	protein-coding gene	gene with protein product		608577		C14orf52			Standard	NM_145165		Approved	My015, FLJ33064		Q8WUH1	OTTHUMG00000170218	ENST00000549115.1:c.418T>C	chr14.hg19:g.65398946T>C	ENSP00000448050:p.*140Glnext*20	109.0	0.0		131.0	31.0	NM_145165	B3KQ81|G3V1X3|G3V214|Q9H3K7	Missense_Mutation	SNP	ENST00000549115.1	hg19	CCDS55921.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.263736	0.80358	.	.	ENSG00000258289	ENST00000552002;ENST00000549115;ENST00000359118	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8268	0.63354	0.0:0.0:0.0:1.0	.	.	.	.	Q	141;140;114	.	.	X	+	1	0	CHURC1	64468699	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	7.215000	0.77966	2.251000	0.74343	0.533000	0.62120	TAA	.	.		0.388	CHURC1-002	KNOWN	NAGNAG_splice_site|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408062.1	NM_145165		C	65398946	T	C	65398946	4	2	143	1	0	0	0	0	0	0	0	0	3419	1535	53	2	354	2	CHURC1	14	65398946	Nonstop_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10		65398946	41950594	54	22183										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48056407	48056407	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gtctgtgcatttagcatggaTgacattgaaaaagtattcaa	9	5	2	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr15:48056407T>A	ENST00000316364.5	+	11	1441	c.1002T>A	c.(1000-1002)gaT>gaA	p.D334E	SEMA6D_ENST00000537942.1_Missense_Mutation_p.D334E|SEMA6D_ENST00000355997.3_Missense_Mutation_p.D334E|SEMA6D_ENST00000358066.4_Missense_Mutation_p.D334E|SEMA6D_ENST00000389425.3_Missense_Mutation_p.D334E|SEMA6D_ENST00000354744.4_Missense_Mutation_p.D334E|SEMA6D_ENST00000389428.3_Missense_Mutation_p.D334E|SEMA6D_ENST00000558816.1_Missense_Mutation_p.D334E|SEMA6D_ENST00000558014.1_Missense_Mutation_p.D334E|SEMA6D_ENST00000536845.2_Missense_Mutation_p.D334E|SEMA6D_ENST00000389433.2_Missense_Mutation_p.D334E|SEMA6D_ENST00000389432.2_Missense_Mutation_p.D334E	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	334	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TTAGCATGGATGACATTGAAA	0.448																																					p.D334E		Atlas-SNP	.											.	SEMA6D	322	.	0			c.T1002A						.						121	111	115					15																	48056407		2198	4297	6495	SO:0001583	missense	80031	exon11			CATGGATGACATT	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1002T>A	chr15.hg19:g.48056407T>A	ENSP00000324857:p.Asp334Glu	186.0	0.0		104.0	84.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	T	15.17	2.753056	0.49362	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98	6.08	3.75	0.43078	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.136166	0.64402	D	0.000003	T	0.26521	0.0648	L	0.39020	1.185	0.46749	D	0.999186	D;D;D;B;D	0.59357	0.982;0.985;0.982;0.002;0.982	D;D;P;B;D	0.68765	0.934;0.96;0.88;0.029;0.934	T	0.22382	-1.0218	10	0.18710	T	0.47	.	4.086	0.09947	0.1269:0.0692:0.1327:0.6711	.	334;334;334;334;334	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	E	334	ENSP00000442040:D334E;ENSP00000446152:D334E;ENSP00000324857:D334E;ENSP00000374084:D334E;ENSP00000374083:D334E;ENSP00000346786:D334E;ENSP00000350770:D334E;ENSP00000374079:D334E;ENSP00000348276:D334E;ENSP00000374076:D334E	ENSP00000324857:D334E	D	+	3	2	SEMA6D	45843699	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.617000	0.24359	0.527000	0.28560	0.533000	0.62120	GAT	.	.		0.448	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48056407	T	A	48056407	3	1	143	1	0	0	0	0	1	0	0	0	14057	1461	51	4	1040	4	SEMA6D	15	48056407	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10		48056407	54474985	55	22184										
ACAN	176	hgsc.bcm.edu	37	chr15	89400397	89400397	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ggagtagaggacctcagcagGctcccttctggagaagaagt	14	9	2	3			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr15:89400397G>A	ENST00000561243.1	+	11	4581	c.4581G>A	c.(4579-4581)agG>agA	p.R1527R	ACAN_ENST00000352105.7_Silent_p.R1527R|ACAN_ENST00000559004.1_Silent_p.R1527R|ACAN_ENST00000439576.2_Silent_p.R1527R			P16112	PGCA_HUMAN	aggrecan	1536	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			ACCTCAGCAGGCTCCCTTCTG	0.507																																					p.R1527R		Atlas-SNP	.											.	ACAN	220	.	0			c.G4581A						.						53	54	54					15																	89400397		1841	4084	5925	SO:0001819	synonymous_variant	176	exon12			CAGCAGGCTCCCT	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.4581G>A	chr15.hg19:g.89400397G>A		64.0	0.0		42.0	38.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.507	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		A	89400397	G	A	89400397	2	1	143	1	0	0	0	0	0	0	0	1	117	1194	42	3		3	ACAN	15	89400397	Silent	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	41343990	89400397	13130995	56	22185										
ZNF764	92595	hgsc.bcm.edu	37	chr16	30569410	30569410	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ctcccggcagaagtacacggCcacgtccgcgaagctcacag	11	16	1	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr16:30569410C>A	ENST00000252797.2	-	1	174	c.94G>T	c.(94-96)Gcc>Tcc	p.A32S	ZNF764_ENST00000395091.2_Missense_Mutation_p.A32S|AC002310.13_ENST00000568114.1_Missense_Mutation_p.A32S	NM_001172679.1|NM_033410.3	NP_001166150.1|NP_219363.2	Q96H86	ZN764_HUMAN	zinc finger protein 764	32	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7						AAGTACACGGCCACGTCCGCG	0.716																																					p.A32S		Atlas-SNP	.											.	ZNF764	20	.	0			c.G94T						.						18	21	20					16																	30569410		2194	4297	6491	SO:0001583	missense	92595	exon1			ACACGGCCACGTC	BC008821	CCDS10683.1, CCDS54001.1	16p11.2	2013-01-08			ENSG00000169951	ENSG00000169951		"Zinc fingers, C2H2-type", "-"	28200	protein-coding gene	gene with protein product						12477932	Standard	NM_033410		Approved	MGC13138	uc002dyq.3	Q96H86	OTTHUMG00000132406	ENST00000252797.2:c.94G>T	chr16.hg19:g.30569410C>A	ENSP00000252797:p.Ala32Ser	31.0	0.0		18.0	9.0	NM_001172679	A8MZF4|B3KSN2|H9KV99|Q9BWS1	Missense_Mutation	SNP	ENST00000252797.2	hg19	CCDS10683.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.322411	0.81580	.	.	ENSG00000169951	ENST00000252797;ENST00000395091	T;T	0.03181	4.02;4.02	4.27	3.3	0.37823	Krueppel-associated box (4);	0.000000	0.35936	N	0.002896	T	0.14313	0.0346	M	0.76727	2.345	0.28520	N	0.913117	D;D	0.76494	0.999;0.997	D;D	0.85130	0.997;0.994	T	0.01062	-1.1464	10	0.56958	D	0.05	-19.3155	8.5193	0.33266	0.0:0.891:0.0:0.109	.	32;32	B3KSN2;Q96H86	.;ZN764_HUMAN	S	32	ENSP00000252797:A32S;ENSP00000378526:A32S	ENSP00000252797:A32S	A	-	1	0	ZNF764	30476911	0.986000	0.35501	1.000000	0.80357	0.775000	0.43874	2.305000	0.43664	1.128000	0.42052	0.462000	0.41574	GCC	.	.		0.716	ZNF764-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255541.1	NM_033410		A	30569410	C	A	30569410	3	1	143	1	0	0	0	0	1	0	0	0	18153	739	26	3	1144	3	ZNF764	16	30569410	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10		30569410	59785343	57	22186										
NAGS	162417	hgsc.bcm.edu	37	chr17	42083959	42083959	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tgcaacgccgagtgggtgagCacaaaagaacggcagcagat	14	9	0	3			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr17:42083959C>T	ENST00000293404.3	+	4	1096	c.978C>T	c.(976-978)agC>agT	p.S326S	PYY_ENST00000360085.2_5'Flank	NM_153006.2	NP_694551.1	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	326	Amino-acid kinase domain (AAK).				arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial matrix (GO:0005759)	acetyl-CoA:L-glutamate N-acetyltransferase activity (GO:0004042)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		AGTGGGTGAGCACAAAAGAAC	0.662																																					p.S326S		Atlas-SNP	.											.	NAGS	25	.	0			c.C978T						.						39	29	33					17																	42083959		2201	4299	6500	SO:0001819	synonymous_variant	162417	exon4			GGTGAGCACAAAA	AY116537	CCDS11473.1	17q21.31	2008-02-05				ENSG00000161653			17996	protein-coding gene	gene with protein product		608300				15050968, 12459178	Standard	NM_153006		Approved	AGAS, ARGA, NAT7	uc002ies.3	Q8N159		ENST00000293404.3:c.978C>T	chr17.hg19:g.42083959C>T		60.0	0.0		61.0	25.0	NM_153006	B2RAZ9|Q8IWR4	Silent	SNP	ENST00000293404.3	hg19	CCDS11473.1																																																																																			.	.		0.662	NAGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457660.1	NM_153006		T	42083959	C	T	42083959	2	4	143	1	0	0	0	0	0	0	0	1	10154	709	25	3		3	NAGS	17	42083959	Silent	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10		42083959	39111251	58	22187										
ITGA3	3675	hgsc.bcm.edu	37	chr17	48156884	48156884	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gggccccccacctgtcactcTggctgctgccaaaaaagcca	9	17	2	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr17:48156884T>C	ENST00000320031.8	+	21	2999	c.2669T>C	c.(2668-2670)cTg>cCg	p.L890P	ITGA3_ENST00000007722.7_Missense_Mutation_p.L890P	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	890					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						CCTGTCACTCTGGCTGCTGCC	0.647																																					p.L890P		Atlas-SNP	.											.	ITGA3	128	.	0			c.T2669C						.						31	32	31					17																	48156884		2203	4300	6503	SO:0001583	missense	3675	exon21			TCACTCTGGCTGC	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"CD molecules", "Integrins"	6139	protein-coding gene	gene with protein product		605025	"antigen identified by monoclonal antibody J143"	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.2669T>C	chr17.hg19:g.48156884T>C	ENSP00000315190:p.Leu890Pro	62.0	0.0		68.0	31.0	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	hg19	CCDS11558.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.161772	0.78226	.	.	ENSG00000005884	ENST00000007722;ENST00000538917;ENST00000320031	T;T	0.46063	0.88;0.88	4.79	4.79	0.61399	Integrin alpha-2 (1);	0.536026	0.18682	N	0.134128	T	0.64011	0.2560	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.63269	-0.6675	10	0.34782	T	0.22	.	11.9399	0.52894	0.0:0.0:0.0:1.0	.	890;890	P26006-1;P26006	.;ITA3_HUMAN	P	890;876;890	ENSP00000007722:L890P;ENSP00000315190:L890P	ENSP00000007722:L890P	L	+	2	0	ITGA3	45511883	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	4.404000	0.59735	2.012000	0.59069	0.260000	0.18958	CTG	.	.		0.647	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		C	48156884	T	C	48156884	3	2	143	1	0	0	0	0	1	0	0	0	7886	1580	55	2	2751	2	ITGA3	17	48156884	Missense_Mutation	SNP	T	TCGA-DD-A73B-01A-12D-A32G-10	6072925	48156884	33038326	59	22188										
ZACN	353174	hgsc.bcm.edu	37	chr17	74075584	74075584	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gaaagcatccagatcccgaaCaatgggagtgcgcccctgct	11	13	0	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr17:74075584C>A	ENST00000334586.5	+	2	245	c.162C>A	c.(160-162)aaC>aaA	p.N54K	ZACN_ENST00000392503.2_Missense_Mutation_p.N54K|EXOC7_ENST00000591724.1_5'Flank	NM_180990.3	NP_851321.2	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel	54					ion transmembrane transport (GO:0034220)|response to zinc ion (GO:0010043)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)|ligand-gated ion channel activity (GO:0015276)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	11						AGATCCCGAACAATGGGAGTG	0.542																																					p.N54K		Atlas-SNP	.											.	ZACN	29	.	0			c.C162A						.						164	140	148					17																	74075584		2203	4300	6503	SO:0001583	missense	353174	exon2			CCCGAACAATGGG	AK122638	CCDS11740.2	17q25.3	2012-01-18	2008-04-17	2008-04-17	ENSG00000186919	ENSG00000186919		"Ligand-gated ion channels / Zinc activated channels"	29504	protein-coding gene	gene with protein product		610935	"ligand-gated ion channel, zinc activated 1"	LGICZ1		12381728, 16083862	Standard	NM_180990		Approved	LGICZ, L2, ZAC, ZAC1	uc002jqn.2	Q401N2	OTTHUMG00000157186	ENST00000334586.5:c.162C>A	chr17.hg19:g.74075584C>A	ENSP00000334854:p.Asn54Lys	153.0	0.0		164.0	79.0	NM_180990	Q2TB29|Q6ZWK3|Q86YW4	Missense_Mutation	SNP	ENST00000334586.5	hg19	CCDS11740.2	.	.	.	.	.	.	.	.	.	.	C	7.967	0.748165	0.15710	.	.	ENSG00000186919	ENST00000334586;ENST00000392503	T	0.77620	-1.11	3.66	-0.0571	0.13803	Neurotransmitter-gated ion-channel ligand-binding (3);	0.810482	0.11207	N	0.588107	T	0.57504	0.2058	L	0.38838	1.175	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.39210	-0.9625	10	0.06365	T	0.9	-6.723	1.8195	0.03107	0.2027:0.3037:0.3649:0.1286	.	54	Q401N2	ZACN_HUMAN	K	54	ENSP00000334854:N54K	ENSP00000334854:N54K	N	+	3	2	ZACN	71587179	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-1.604000	0.02076	0.176000	0.19873	0.462000	0.41574	AAC	.	.		0.542	ZACN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347827.2	NM_180990		A	74075584	C	A	74075584	3	1	143	1	0	0	0	0	1	0	0	0	17525	477	17	3	168	3	ZACN	17	74075584	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	25918700	74075584	7119626	60	22189										
CHMP6	79643	hgsc.bcm.edu	37	chr17	78968447	78968447	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tcgcccagcagctggagcgcGagcgcgccctggcccggcag	16	17	0	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr17:78968447G>T	ENST00000325167.5	+	2	208	c.130G>T	c.(130-132)Gag>Tag	p.E44*		NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	44					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein N-terminus binding (GO:0047485)			lung(2)|ovary(1)	3	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0175)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GCTGGAGCGCGAGCGCGCCCT	0.716																																					p.E44X		Atlas-SNP	.											CHMP6,right_upper_lobe,carcinoma,0,1	CHMP6	16	.	0			c.G130T						.						16	13	14					17																	78968447		2159	4266	6425	SO:0001587	stop_gained	79643	exon2			GAGCGCGAGCGCG	BC010108	CCDS11774.1	17q25.3	2014-08-13	2011-09-21		ENSG00000176108	ENSG00000176108		"Charged multivesicular body proteins"	25675	protein-coding gene	gene with protein product		610901	"chromatin modifying protein 6"			11559748, 15511219	Standard	NM_024591		Approved	FLJ11749, VPS20	uc002jyw.4	Q96FZ7	OTTHUMG00000177645	ENST00000325167.5:c.130G>T	chr17.hg19:g.78968447G>T	ENSP00000317468:p.Glu44*	63.0	0.0		79.0	33.0	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Nonsense_Mutation	SNP	ENST00000325167.5	hg19	CCDS11774.1	.	.	.	.	.	.	.	.	.	.	.	38	6.806771	0.97853	.	.	ENSG00000176108	ENST00000325167	.	.	.	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-1.9258	14.78	0.69760	0.0:0.0:1.0:0.0	.	.	.	.	X	44	.	ENSP00000317468:E44X	E	+	1	0	CHMP6	76583042	1.000000	0.71417	0.951000	0.38953	0.886000	0.51366	7.035000	0.76517	1.987000	0.57996	0.511000	0.50034	GAG	.	.		0.716	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591		T	78968447	G	T	78968447	4	4	143	1	0	0	0	0	0	1	0	0	3362	1059	37	1	136	1	CHMP6	17	78968447	Nonsense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	4892863	78968447	2226763	61	22190										
FASN	2194	hgsc.bcm.edu	37	chr17	80045029	80045029	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tccaggatgggcacctgctgCtcctgctgccgccgcggggc	15	16	0	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr17:80045029C>T	ENST00000306749.2	-	21	3542	c.3324G>A	c.(3322-3324)gaG>gaA	p.E1108E		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1108					acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GCACCTGCTGCTCCTGCTGCC	0.667																																					p.E1108E	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G3324A						.						21	22	22					17																	80045029		2187	4287	6474	SO:0001819	synonymous_variant	2194	exon21			CTGCTGCTCCTGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.3324G>A	chr17.hg19:g.80045029C>T		68.0	0.0		58.0	30.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.667	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80045029	C	T	80045029	2	4	143	1	0	0	0	0	0	0	0	1	5691	796	28	3		3	FASN	17	80045029	Silent	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	1076582	80045029	1150181	62	22191										
EMILIN2	84034	hgsc.bcm.edu	37	chr18	2909794	2909794	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	caaagtgctggtgaacgacgGggatgtttacaaccccagca	12	10	0	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr18:2909794G>T	ENST00000254528.3	+	7	2960	c.2801G>T	c.(2800-2802)gGg>gTg	p.G934V	EMILIN2_ENST00000308080.5_3'UTR	NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	934	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		GTGAACGACGGGGATGTTTAC	0.587																																					p.G934V		Atlas-SNP	.											.	EMILIN2	97	.	0			c.G2801T						.						121	106	111					18																	2909794		2203	4300	6503	SO:0001583	missense	84034	exon7			ACGACGGGGATGT	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.2801G>T	chr18.hg19:g.2909794G>T	ENSP00000254528:p.Gly934Val	104.0	0.0		104.0	40.0	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	hg19	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.722790	0.68959	.	.	ENSG00000132205	ENST00000254528;ENST00000308080	T	0.04917	3.53	5.8	5.8	0.92144	Tumour necrosis factor-like (2);Complement C1q protein (2);	0.000000	0.85682	D	0.000000	T	0.35248	0.0925	M	0.90595	3.13	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.28170	-1.0052	10	0.87932	D	0	-35.1375	20.063	0.97692	0.0:0.0:1.0:0.0	.	934	Q9BXX0	EMIL2_HUMAN	V	934;211	ENSP00000254528:G934V	ENSP00000254528:G934V	G	+	2	0	EMILIN2	2899794	1.000000	0.71417	0.629000	0.29254	0.249000	0.25844	8.901000	0.92560	2.735000	0.93741	0.655000	0.94253	GGG	.	.		0.587	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2909794	G	T	2909794	3	4	143	1	0	0	0	0	1	0	0	0	5096	1232	43	3	2827	3	EMILIN2	18	2909794	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10		2909794	75167454	63	22192										
DOT1L	84444	hgsc.bcm.edu	37	chr19	2217014	2217014	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	cccagcgtgcctggcagcatGaagctgagccctcaggaccc	12	16	1	2	rs562099241		TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr19:2217014G>T	ENST00000398665.3	+	21	2505	c.2469G>T	c.(2467-2469)atG>atT	p.M823I	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	823					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGGCAGCATGAAGCTGAGCC	0.672													G|||	1	0.000199681	0	0	5008	,	,		18920	0.001		0	False		,,,				2504	0				p.M823I		Atlas-SNP	.											.	DOT1L	205	.	0			c.G2469T						.						36	39	38					19																	2217014		2070	4198	6268	SO:0001583	missense	84444	exon21			CAGCATGAAGCTG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.2469G>T	chr19.hg19:g.2217014G>T	ENSP00000381657:p.Met823Ile	68.0	0.0		49.0	21.0	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.019|0.019	-1.466184|-1.466184	0.01053|0.01053	.|.	.|.	ENSG00000104885|ENSG00000104885	ENST00000398665;ENST00000221482|ENST00000440640	T|.	0.20598|.	2.06|.	5.15|5.15	1.32|1.32	0.21799|0.21799	.|.	0.858231|.	0.10496|.	N|.	0.667812|.	T|.	0.11580|.	0.0282|.	N|N	0.01352|0.01352	-0.895|-0.895	0.21652|0.21652	N|N	0.999602|0.999602	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.0;0.001|.	T|.	0.27673|.	-1.0067|.	10|.	0.87932|.	D|.	0|.	-11.9448|-11.9448	10.0247|10.0247	0.42063|0.42063	0.1323:0.6922:0.1755:0.0|0.1323:0.6922:0.1755:0.0	.|.	823;823|.	Q8TEK3;Q8TEK3-2|.	DOT1L_HUMAN;.|.	I|L	823|610	ENSP00000381657:M823I|.	ENSP00000221482:M823I|.	M|X	+|+	3|2	0|2	DOT1L|DOT1L	2168014|2168014	0.994000|0.994000	0.37717|0.37717	0.754000|0.754000	0.31244|0.31244	0.251000|0.251000	0.25915|0.25915	0.233000|0.233000	0.17911|0.17911	0.409000|0.409000	0.25649|0.25649	0.655000|0.655000	0.94253|0.94253	ATG|TGA	.	.		0.672	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2217014	G	T	2217014	3	4	143	1	0	0	0	0	1	0	0	0	4711	1290	45	3	2551	3	DOT1L	19	2217014	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10		2217014	56911969	64	22193										
C3	718	hgsc.bcm.edu	37	chr19	6714382	6714382	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	cttgacgagttccggaatgtCccaagacaagggcaagacgc	12	11	0	3			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr19:6714382C>T	ENST00000245907.6	-	5	672	c.580G>A	c.(580-582)Gac>Aac	p.D194N		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	194					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TCCGGAATGTCCCAAGACAAG	0.607																																					p.D194N		Atlas-SNP	.											.	C3	192	.	0			c.G580A						.						73	67	69					19																	6714382		2203	4300	6503	SO:0001583	missense	718	exon5			GAATGTCCCAAGA	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.580G>A	chr19.hg19:g.6714382C>T	ENSP00000245907:p.Asp194Asn	79.0	0.0		101.0	56.0	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	c	0.011	-1.729245	0.00687	.	.	ENSG00000125730	ENST00000245907	T	0.73469	-0.75	5.04	-0.986	0.10252	Alpha-2-macroglobulin, N-terminal (1);	1.017600	0.07807	N	0.957490	T	0.40423	0.1116	N	0.02192	-0.645	0.09310	N	0.999995	B	0.02656	0.0	B	0.09377	0.004	T	0.21690	-1.0238	10	0.10902	T	0.67	.	1.567	0.02606	0.1595:0.3682:0.1641:0.3082	.	194	P01024	CO3_HUMAN	N	194	ENSP00000245907:D194N	ENSP00000245907:D194N	D	-	1	0	C3	6665382	0.781000	0.28676	0.532000	0.27989	0.082000	0.17680	-0.530000	0.06179	-0.318000	0.08665	-0.482000	0.04802	GAC	.	.		0.607	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		T	6714382	C	T	6714382	3	4	143	1	0	0	0	0	1	0	0	0	2206	855	30	3	4559	3	C3	19	6714382	Missense_Mutation	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10	4497368	6714382	52414601	65	22194										
MYO9B	4650	hgsc.bcm.edu	37	chr19	17291744	17291744	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ccctcccctcagcgatttgcAtaaccaaatgatcaagagca	6	14	2	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr19:17291744A>T	ENST00000594824.1	+	15	2375	c.2228A>T	c.(2227-2229)cAt>cTt	p.H743L	CTD-3032J10.4_ENST00000594678.1_RNA|MYO9B_ENST00000595618.1_Missense_Mutation_p.H743L|MYO9B_ENST00000397274.2_Missense_Mutation_p.H743L			Q13459	MYO9B_HUMAN	myosin IXB	743	Myosin motor.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						AGCGATTTGCATAACCAAATG	0.607																																					p.H743L		Atlas-SNP	.											.	MYO9B	264	.	0			c.A2228T						.						63	71	69					19																	17291744		1949	4128	6077	SO:0001583	missense	4650	exon15			ATTTGCATAACCA		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"Myosins / Myosin superfamily : Class IX"	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.2228A>T	chr19.hg19:g.17291744A>T	ENSP00000471367:p.His743Leu	79.0	0.0		93.0	37.0	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.86	3.492678	0.64074	.	.	ENSG00000099331	ENST00000397274	D	0.84589	-1.87	4.77	4.77	0.60923	Myosin head, motor domain (2);	0.143577	0.31134	N	0.008181	D	0.87362	0.6158	L	0.34521	1.04	0.46542	D	0.999092	D;D;D	0.76494	0.987;0.987;0.999	D;D;D	0.77004	0.91;0.91;0.989	D	0.88254	0.2918	10	0.66056	D	0.02	.	11.9558	0.52981	1.0:0.0:0.0:0.0	.	743;743;749	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	L	743	ENSP00000380444:H743L	ENSP00000380444:H743L	H	+	2	0	MYO9B	17152744	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.883000	0.87264	1.922000	0.55676	0.402000	0.26972	CAT	.	.		0.607	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			T	17291744	A	T	17291744	3	4	143	1	0	0	0	0	1	0	0	0	10094	217	8	4	2282	4	MYO9B	19	17291744	Missense_Mutation	SNP	A	TCGA-DD-A73B-01A-12D-A32G-10	10577362	17291744	41837239	66	22195										
GPI	2821	hgsc.bcm.edu	37	chr19	34890537	34890537	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	catgcttggagccttggtcgGtgagtgagtaggggaaaggt	18	5	0	2			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr19:34890537G>T	ENST00000356487.5	+	16	1715		c.e16+1		GPI_ENST00000415930.3_Splice_Site|RP11-618P17.4_ENST00000606020.1_5'Flank|GPI_ENST00000586425.1_Intron	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase						aldehyde catabolic process (GO:0046185)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|hemostasis (GO:0007599)|humoral immune response (GO:0006959)|learning or memory (GO:0007611)|methylglyoxal biosynthetic process (GO:0019242)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucose-6-phosphate isomerase activity (GO:0004347)|intramolecular transferase activity (GO:0016866)|monosaccharide binding (GO:0048029)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	25	Esophageal squamous(110;0.162)					GCCTTGGTCGGTGAGTGAGTA	0.522																																					.		Atlas-SNP	.											.	GPI	63	.	0			c.1507+1G>T						.						147	147	147					19																	34890537		2203	4300	6503	SO:0001630	splice_region_variant	2821	exon16			TGGTCGGTGAGTG	M61214	CCDS12437.1, CCDS54246.1	19q13.1	2012-10-02	2010-05-11			ENSG00000105220	5.3.1.9		4458	protein-coding gene	gene with protein product		172400	"glucose phosphate isomerase"			2387591, 8575767	Standard	NM_001184722		Approved	AMF, NLK	uc002nvg.2	P06744		ENST00000356487.5:c.1474+1G>T	chr19.hg19:g.34890537G>T		150.0	0.0		156.0	59.0	NM_001184722	B4DG39|Q9BRD3|Q9BSK5|Q9UHE6	Splice_Site	SNP	ENST00000356487.5	hg19	CCDS12437.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.697727	0.88830	.	.	ENSG00000105220	ENST00000415930;ENST00000356487	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8557	0.96758	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPI	39582377	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	9.780000	0.99024	2.707000	0.92482	0.655000	0.94253	.	.	.		0.522	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451693.3		Intron	T	34890537	G	T	34890537	5	4	143	1	0	0	0	0	0	0	1	0	6619	1275	44	3	1658	3	GPI	19	34890537	Splice_Site	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	17598793	34890537	24238446	67	22196										
DMKN	93099	hgsc.bcm.edu	37	chr19	35992755	35992755	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ctcccctgggtccaggccagGcccagcaggagcaggagcag	15	15	0	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr19:35992755G>A	ENST00000339686.3	-	11	1416				DMKN_ENST00000472252.2_Intron|DMKN_ENST00000492341.2_Intron|DMKN_ENST00000480502.1_Intron|DMKN_ENST00000467637.1_Intron|DMKN_ENST00000408915.2_Silent_p.G17G|DMKN_ENST00000402589.2_Intron|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000414866.2_Intron|DMKN_ENST00000443640.1_Intron|DMKN_ENST00000462126.1_Intron|DMKN_ENST00000436012.1_Intron|DMKN_ENST00000602781.1_Intron	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine							extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TCCAGGCCAGGCCCAGCAGGA	0.657																																					p.G17G		Atlas-SNP	.											.	DMKN	116	.	0			c.C51T						.						22	29	26					19																	35992755		2112	4232	6344	SO:0001627	intron_variant	93099	exon1			GGCCAGGCCCAGC	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.1239+282C>T	chr19.hg19:g.35992755G>A		42.0	0.0		30.0	8.0	NM_001035516	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	hg19	CCDS12463.1																																																																																			.	.		0.657	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		A	35992755	G	A	35992755	1	1	143	0	1	0	0	0	0	0	0	0	4584	1190	42	3		3	DMKN	19	35992755	Intron	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	1102218	35992755	23136228	68	22197										
ZNF221	7638	hgsc.bcm.edu	37	chr19	44471018	44471018	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gccatataactgtgaggagtGtggtaaggactataaaagga	13	4	0	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr19:44471018G>A	ENST00000251269.5	+	6	1692	c.1364G>A	c.(1363-1365)tGt>tAt	p.C455Y	ZNF221_ENST00000587682.1_Missense_Mutation_p.C455Y|ZNF221_ENST00000592350.1_Missense_Mutation_p.C455Y	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	455					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				TGTGAGGAGTGTGGTAAGGAC	0.438																																					p.C455Y		Atlas-SNP	.											.	ZNF221	59	.	0			c.G1364A						.						70	67	68					19																	44471018		2203	4300	6503	SO:0001583	missense	7638	exon6			AGGAGTGTGGTAA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1364G>A	chr19.hg19:g.44471018G>A	ENSP00000251269:p.Cys455Tyr	64.0	0.0		71.0	39.0	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	hg19	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	g	25.1	4.601654	0.87055	.	.	ENSG00000159905	ENST00000251269	D	0.85861	-2.04	2.63	2.63	0.31362	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94108	0.8111	H	0.96175	3.78	0.36439	D	0.865365	D	0.89917	1.0	D	0.97110	1.0	D	0.96344	0.9253	9	0.66056	D	0.02	.	12.3732	0.55265	0.0:0.0:1.0:0.0	.	455	Q9UK13	ZN221_HUMAN	Y	455	ENSP00000251269:C455Y	ENSP00000251269:C455Y	C	+	2	0	ZNF221	49162858	1.000000	0.71417	0.497000	0.27552	0.862000	0.49288	7.342000	0.79310	1.460000	0.47911	0.313000	0.20887	TGT	.	.		0.438	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			A	44471018	G	A	44471018	3	1	143	1	0	0	0	0	1	0	0	0	17790	1377	48	3	1378	3	ZNF221	19	44471018	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	8478263	44471018	14657965	69	22198										
CENPB	1059	hgsc.bcm.edu	37	chr20	3765895	3765895	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	tcttcctcctcctcttcttcCtcctcctcctcctcttcctc	0	23	4	0	rs545901224	byFrequency	TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr20:3765895C>T	ENST00000379751.4	-	1	1442	c.1236G>A	c.(1234-1236)gaG>gaA	p.E412E	CDC25B_ENST00000379598.5_5'Flank|CDC25B_ENST00000344256.6_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	412	Glu-rich (acidic).				regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)	centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|satellite DNA binding (GO:0003696)|sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(2)|lung(4)|skin(1)	8						cctcttcttcctcctcctcct	0.597																																					p.E412E		Atlas-SNP	.											CENPB,NS,carcinoma,0,1	CENPB	24	.	0			c.G1236A						.						72	59	63					20																	3765895		2201	4298	6499	SO:0001819	synonymous_variant	1059	exon1			TTCTTCCTCCTCC	X05299	CCDS13064.1	20p13	2013-11-05	2002-08-29		ENSG00000125817	ENSG00000125817			1852	protein-coding gene	gene with protein product		117140	"centromere protein B (80kD)"			8406460, 11884609	Standard	NM_001810		Approved		uc002wjk.3	P07199	OTTHUMG00000031761	ENST00000379751.4:c.1236G>A	chr20.hg19:g.3765895C>T		45.0	0.0		51.0	3.0	NM_001810	Q96EI4	Silent	SNP	ENST00000379751.4	hg19	CCDS13064.1																																																																																			.	.		0.597	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810		T	3765895	C	T	3765895	2	4	143	1	0	0	0	0	0	0	0	1	3229	680	24	3		3	CENPB	20	3765895	Silent	SNP	C	TCGA-DD-A73B-01A-12D-A32G-10		3765895	59259625	70	22199										
KIF16B	55614	hgsc.bcm.edu	37	chr20	16387061	16387061	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gcggcttcctttggatggttAaagcgaaacatattggttct	11	7	1	0			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr20:16387061A>G	ENST00000354981.2	-	16	1810	c.1653T>C	c.(1651-1653)ttT>ttC	p.F551F	KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Silent_p.F551F|KIF16B_ENST00000408042.1_Silent_p.F551F	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	551					ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						TTGGATGGTTAAAGCGAAACA	0.473																																					p.F551F		Atlas-SNP	.											.	KIF16B	305	.	0			c.T1653C						.						221	200	207					20																	16387061		2203	4300	6503	SO:0001819	synonymous_variant	55614	exon16			ATGGTTAAAGCGA	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.1653T>C	chr20.hg19:g.16387061A>G		98.0	0.0		122.0	62.0	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	hg19	CCDS13122.1																																																																																			.	.		0.473	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		G	16387061	A	G	16387061	2	3	143	1	0	0	0	0	0	0	0	1	8287	359	13	2		2	KIF16B	20	16387061	Silent	SNP	A	TCGA-DD-A73B-01A-12D-A32G-10	12621166	16387061	46638459	71	22200										
EDEM2	55741	hgsc.bcm.edu	37	chr20	33703635	33703635	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gtggacccattgttgtggatGaagttggttgggtcaaacag	15	5	1	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr20:33703635G>C	ENST00000374492.3	-	11	1443	c.1338C>G	c.(1336-1338)ttC>ttG	p.F446L	EDEM2_ENST00000541621.1_Missense_Mutation_p.F225L|EDEM2_ENST00000374491.3_Missense_Mutation_p.F409L|SNORD56_ENST00000364281.1_RNA|EDEM2_ENST00000542871.1_Missense_Mutation_p.F170L	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	446					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			TGTTGTGGATGAAGTTGGTTG	0.552																																					p.F446L	Esophageal Squamous(51;906 1021 24535 36410 39145)	Atlas-SNP	.											EDEM2,NS,carcinoma,0,1	EDEM2	46	.	0			c.C1338G						.						70	63	66					20																	33703635		2203	4300	6503	SO:0001583	missense	55741	exon11			GTGGATGAAGTTG	AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"chromosome 20 open reading frame 31"	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.1338C>G	chr20.hg19:g.33703635G>C	ENSP00000363616:p.Phe446Leu	149.0	0.0		150.0	65.0	NM_018217	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Missense_Mutation	SNP	ENST00000374492.3	hg19	CCDS13247.1	.	.	.	.	.	.	.	.	.	.	G	11.22	1.573908	0.28092	.	.	ENSG00000088298	ENST00000374491;ENST00000374492;ENST00000541621;ENST00000542871	T;T;T;T	0.38887	1.11;1.11;1.11;1.11	5.51	1.49	0.22878	.	0.043308	0.85682	D	0.000000	T	0.44222	0.1283	L	0.32530	0.975	0.80722	D	1	D;P;D	0.65815	0.994;0.909;0.995	D;P;D	0.66847	0.947;0.701;0.942	T	0.16689	-1.0394	10	0.20046	T	0.44	-23.8926	8.6765	0.34183	0.3519:0.0:0.6481:0.0	.	225;409;446	G3V1Q0;Q9BV94-2;Q9BV94	.;.;EDEM2_HUMAN	L	409;446;225;170	ENSP00000363615:F409L;ENSP00000363616:F446L;ENSP00000443528:F225L;ENSP00000441642:F170L	ENSP00000363615:F409L	F	-	3	2	EDEM2	33167296	1.000000	0.71417	0.999000	0.59377	0.921000	0.55340	2.880000	0.48530	0.159000	0.19401	0.561000	0.74099	TTC	.	.		0.552	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217		C	33703635	G	C	33703635	3	2	143	1	0	0	0	0	1	0	0	0	4914	1281	45	4	402	4	EDEM2	20	33703635	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	17316574	33703635	29321885	72	22201										
SCAND1	51282	hgsc.bcm.edu	37	chr20	34541998	34541998	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	cgagaggcagctccagggccGcggaggccgcagctcggggc	19	14	0	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr20:34541998G>A	ENST00000373991.3	-	3	1279	c.209C>T	c.(208-210)gCg>gTg	p.A70V	SCAND1_ENST00000305978.2_Missense_Mutation_p.A70V			P57086	SCND1_HUMAN	SCAN domain containing 1	70					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)					Breast(12;0.00631)|all_lung(11;0.0233)					CTCCAGGGCCGCGGAGGCCGC	0.731																																					p.A133V		Atlas-SNP	.											.	SCAND1	2	.	0			c.C398T						.						3	4	4					20																	34541998		1880	3657	5537	SO:0001583	missense	51282	exon2			AGGGCCGCGGAGG	AF204271	CCDS13269.1	20q11.1-q11.23	2013-01-08	2002-01-14		ENSG00000171222	ENSG00000171222		"-"	10566	protein-coding gene	gene with protein product		610416	"SCAN domain-containing 1"			10777584, 10747874, 12444922	Standard	NM_016558		Approved	SDP1, RAZ1	uc002xen.2	P57086	OTTHUMG00000032370	ENST00000373991.3:c.209C>T	chr20.hg19:g.34541998G>A	ENSP00000363103:p.Ala70Val	26.0	0.0		23.0	12.0	NM_033630	Q6IAG7	Missense_Mutation	SNP	ENST00000373991.3	hg19	CCDS13269.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.207306	0.79240	.	.	ENSG00000171222	ENST00000305978;ENST00000373991	T;T	0.09163	3.01;3.01	4.39	3.37	0.38596	.	.	.	.	.	T	0.15609	0.0376	N	0.24115	0.695	0.09310	N	1	D	0.89917	1.0	D	0.64506	0.926	T	0.12041	-1.0563	9	0.39692	T	0.17	.	8.1089	0.30903	0.0:0.1683:0.6594:0.1723	.	70	P57086	SCND1_HUMAN	V	70	ENSP00000301995:A70V;ENSP00000363103:A70V	ENSP00000301995:A70V	A	-	2	0	SCAND1	34005412	0.000000	0.05858	0.078000	0.20375	0.003000	0.03518	0.291000	0.18994	2.157000	0.67596	0.655000	0.94253	GCG	.	.		0.731	SCAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078958.2	NM_016558		A	34541998	G	A	34541998	3	1	143	1	0	0	0	0	1	0	0	0	13890	1087	38	1	334	1	SCAND1	20	34541998	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	838363	34541998	28483522	73	22202										
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62076074	62076074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	gcctccccgccggtccatgcGgatcatccgcagaatctgca	10	17	2	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chr20:62076074G>A	ENST00000359125.2	-	4	802	c.628C>T	c.(628-630)Cgc>Tgc	p.R210C	KCNQ2_ENST00000370224.1_Missense_Mutation_p.R210C|KCNQ2_ENST00000359689.1_Missense_Mutation_p.R210C|KCNQ2_ENST00000360480.3_Missense_Mutation_p.R210C|KCNQ2_ENST00000344425.5_Missense_Mutation_p.R210C|KCNQ2_ENST00000357249.2_Missense_Mutation_p.R210C|KCNQ2_ENST00000344462.4_Missense_Mutation_p.R210C|KCNQ2_ENST00000354587.3_Missense_Mutation_p.R210C	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	210					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CGGTCCATGCGGATCATCCGC	0.677																																					p.R210C		Atlas-SNP	.											.	KCNQ2	201	.	0			c.C628T						.						21	22	21					20																	62076074		2200	4288	6488	SO:0001583	missense	3785	exon4			CCATGCGGATCAT	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.628C>T	chr20.hg19:g.62076074G>A	ENSP00000352035:p.Arg210Cys	56.0	0.0		57.0	25.0	NM_172106	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	hg19	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.654063	0.88056	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222;ENST00000370221;ENST00000344425	D;D;D;D;D;D;D;D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98	4.05	4.05	0.47172	Ion transport (1);	0.082781	0.48767	D	0.000171	D	0.99152	0.9707	M	0.92367	3.3	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.99;0.998;0.997;0.997;0.997;0.998	D	0.99218	1.0878	10	0.87932	D	0	-4.058	16.5766	0.84681	0.0:0.0:1.0:0.0	.	210;210;210;210;210;210	B4DEP4;Q53Y30;O43526-3;O43526-2;O43526-4;O43526	.;.;.;.;.;KCNQ2_HUMAN	C	210	ENSP00000349789:R210C;ENSP00000352035:R210C;ENSP00000359246:R210C;ENSP00000346601:R210C;ENSP00000352718:R210C;ENSP00000399612:R210C;ENSP00000353668:R210C;ENSP00000339611:R210C;ENSP00000359244:R210C;ENSP00000359242:R210C;ENSP00000359241:R210C;ENSP00000345523:R210C	ENSP00000345523:R210C	R	-	1	0	KCNQ2	61546518	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	9.598000	0.98277	1.978000	0.57642	0.484000	0.47621	CGC	.	.		0.677	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		A	62076074	G	A	62076074	3	1	143	1	0	0	0	0	1	0	0	0	8092	1116	39	1	2110	1	KCNQ2	20	62076074	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	27534076	62076074	949446	74	22203										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34962716	34962716	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	ttgacggtctttatggaccaAttgcctttaaggatttcatt	8	7	2	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chrX:34962716A>T	ENST00000329357.5	+	1	1804	c.1768A>T	c.(1768-1770)Att>Ttt	p.I590F		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	590								p.I590F(1)		breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						TTATGGACCAATTGCCTTTAA	0.448																																					p.I590F		Atlas-SNP	.											.	FAM47B	209	.	1	Substitution - Missense(1)	endometrium(1)	c.A1768T						.						146	138	140					X																	34962716		2202	4300	6502	SO:0001583	missense	170062	exon1			GGACCAATTGCCT	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.1768A>T	chrX.hg19:g.34962716A>T	ENSP00000328307:p.Ile590Phe	186.0	0.0		217.0	49.0	NM_152631	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	hg19	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	A	16.09	3.023069	0.54683	.	.	ENSG00000189132	ENST00000329357	T	0.16743	2.32	0.843	0.843	0.18935	.	.	.	.	.	T	0.39627	0.1085	M	0.81341	2.54	0.22745	N	0.998784	D	0.89917	1.0	D	0.83275	0.996	T	0.08889	-1.0700	8	0.87932	D	0	.	.	.	.	.	590	Q8NA70	FA47B_HUMAN	F	590	ENSP00000328307:I590F	ENSP00000328307:I590F	I	+	1	0	FAM47B	34872637	0.901000	0.30685	0.464000	0.27143	0.673000	0.39480	0.347000	0.20014	0.575000	0.29434	0.242000	0.17961	ATT	.	.		0.448	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		T	34962716	A	T	34962716	3	4	143	1	0	0	0	0	1	0	0	0	5578	101	4	4	1770	4	FAM47B	23	34962716	Missense_Mutation	SNP	A	TCGA-DD-A73B-01A-12D-A32G-10		34962716	120307844	75	22204										
USP26	83844	hgsc.bcm.edu	37	chrX	132161219	132161219	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.714932126696833	1.78733031674208	0.549947789766794	1	1	0	atctttaaaaaaaagtagccGtgccaagcacatggtaagag	9	7	1	1			TCGA-DD-A73B-01A-12D-A32G-10	TCGA-DD-A73B-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9df4d-9dd6-46d9-a147-8b26ebd05af3	1669b7ec-5ff8-4578-afe1-3e5d3094b3bf	g.chrX:132161219G>A	ENST00000511190.1	-	6	1499	c.1030C>T	c.(1030-1032)Cgg>Tgg	p.R344W	USP26_ENST00000370832.1_Missense_Mutation_p.R344W|USP26_ENST00000406273.1_Missense_Mutation_p.R344W	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	344	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					AAAAGTAGCCGTGCCAAGCAC	0.378																																					p.R344W	NSCLC(104;342 1621 36940 47097 52632)	Atlas-SNP	.											.	USP26	135	.	0			c.C1030T						.						34	36	35					X																	132161219		2197	4288	6485	SO:0001583	missense	83844	exon1			GTAGCCGTGCCAA	AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"Ubiquitin-specific peptidases"	13485	protein-coding gene	gene with protein product		300309	"ubiquitin specific protease 26"			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.1030C>T	chrX.hg19:g.132161219G>A	ENSP00000423390:p.Arg344Trp	268.0	0.0		264.0	133.0	NM_031907	B9WRT6|Q5H9H4	Missense_Mutation	SNP	ENST00000511190.1	hg19	CCDS14635.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.166360	0.38217	.	.	ENSG00000134588	ENST00000370832;ENST00000511190;ENST00000406273	T;T;T	0.32023	1.47;1.47;1.47	3.71	2.85	0.33270	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.532585	0.13822	N	0.360341	T	0.37972	0.1023	L	0.38175	1.15	0.09310	N	1	D	0.61697	0.99	P	0.59595	0.86	T	0.09975	-1.0650	10	0.62326	D	0.03	-1.6362	8.7988	0.34896	0.1175:0.0:0.8825:0.0	.	344	Q9BXU7	UBP26_HUMAN	W	344	ENSP00000359869:R344W;ENSP00000423390:R344W;ENSP00000384360:R344W	ENSP00000359869:R344W	R	-	1	2	USP26	131988885	0.719000	0.27986	0.002000	0.10522	0.010000	0.07245	1.903000	0.39858	0.948000	0.37687	-0.381000	0.06696	CGG	.	.		0.378	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907		A	132161219	G	A	132161219	3	1	143	1	0	0	0	0	1	0	0	0	17072	1144	40	1	1714	1	USP26	23	132161219	Missense_Mutation	SNP	G	TCGA-DD-A73B-01A-12D-A32G-10	97198503	132161219	23109341	76	22205										
TPRG1L	127262	hgsc.bcm.edu	37	chr1	3544159	3544159	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gtctaccaacgtgccctatgCcactttcacagaacacccga	6	16	2	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr1:3544159C>G	ENST00000378344.2	+	4	637	c.566C>G	c.(565-567)gCc>gGc	p.A189G	RP11-46F15.2_ENST00000435049.1_RNA|TPRG1L_ENST00000344579.5_Missense_Mutation_p.A130G	NM_182752.3	NP_877429.2	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	189						cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(1)	8	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)		GTGCCCTATGCCACTTTCACA	0.517																																					p.A189G		Atlas-SNP	.											.	TPRG1L	24	.	0			c.C566G						.						155	154	155					1																	3544159		2203	4300	6503	SO:0001583	missense	127262	exon4			CCTATGCCACTTT	BC019034	CCDS47.1	1p36.32	2008-02-05	2008-01-16	2008-01-16	ENSG00000158109	ENSG00000158109			27007	protein-coding gene	gene with protein product		611460	"family with sequence similarity 79, member A"	FAM79A		12477932	Standard	NM_182752		Approved	RP11-46F15.3, FLJ21811	uc001akm.3	Q5T0D9	OTTHUMG00000000609	ENST00000378344.2:c.566C>G	chr1.hg19:g.3544159C>G	ENSP00000367595:p.Ala189Gly	99.0	0.0		75.0	25.0	NM_182752	A8K1K4|Q8WV04	Missense_Mutation	SNP	ENST00000378344.2	hg19	CCDS47.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.693960	0.68386	.	.	ENSG00000158109	ENST00000378344;ENST00000456805;ENST00000344579	.	.	.	4.93	4.93	0.64822	.	0.210172	0.48767	D	0.000171	T	0.60170	0.2248	M	0.74258	2.255	0.58432	D	0.999997	P;B	0.41848	0.763;0.321	B;B	0.41510	0.359;0.056	T	0.67612	-0.5626	9	0.87932	D	0	9.2791	12.5961	0.56470	0.0:0.9169:0.0:0.0831	.	130;189	Q5T0D9-2;Q5T0D9	.;TPRGL_HUMAN	G	189;146;130	.	ENSP00000339714:A130G	A	+	2	0	TPRG1L	3534019	0.980000	0.34600	0.846000	0.33378	0.885000	0.51271	4.567000	0.60850	2.282000	0.76494	0.563000	0.77884	GCC	.	.		0.517	TPRG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001466.1	NM_182752		G	3544159	C	G	3544159	3	3	144	1	0	0	0	0	1	0	0	0	16434	739	26	4	580	4	TPRG1L	1	3544159	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10		3544159	245706462	1	22206										
UBR4	23352	hgsc.bcm.edu	37	chr1	19525340	19525340	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gcagcttggcggatttcatcAttgctgtaaatgtgataatt	10	6	2	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr1:19525340A>T	ENST00000375254.3	-	4	488	c.461T>A	c.(460-462)aTg>aAg	p.M154K	UBR4_ENST00000375267.2_Missense_Mutation_p.M154K|UBR4_ENST00000375226.2_Missense_Mutation_p.M154K|UBR4_ENST00000375217.2_Missense_Mutation_p.M154K	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	154					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GGATTTCATCATTGCTGTAAA	0.448																																					p.M154K		Atlas-SNP	.											.	UBR4	415	.	0			c.T461A						.						142	139	140					1																	19525340		2203	4300	6503	SO:0001583	missense	23352	exon4			TTCATCATTGCTG	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.461T>A	chr1.hg19:g.19525340A>T	ENSP00000364403:p.Met154Lys	158.0	0.0		128.0	42.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	A	18.11	3.550609	0.65311	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.24538	1.86;1.86;1.86;1.85	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.24774	0.0601	N	0.12182	0.205	0.80722	D	1	P	0.40431	0.717	P	0.49047	0.599	T	0.11299	-1.0593	10	0.56958	D	0.05	.	14.2818	0.66219	1.0:0.0:0.0:0.0	.	154	Q5T4S7	UBR4_HUMAN	K	154	ENSP00000364403:M154K;ENSP00000364416:M154K;ENSP00000364365:M154K;ENSP00000364374:M154K	ENSP00000364365:M154K	M	-	2	0	UBR4	19397927	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.281000	0.95811	2.053000	0.61076	0.460000	0.39030	ATG	.	.		0.448	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19525340	A	T	19525340	3	4	144	1	0	0	0	0	1	0	0	0	16919	217	8	4	15502	4	UBR4	1	19525340	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	15981181	19525340	229725281	2	22207										
INSRR	3645	hgsc.bcm.edu	37	chr1	156815015	156815015	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ctcacggggcaccttgtcctCctggatctcgaaatccgagc	10	15	2	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr1:156815015C>T	ENST00000368195.3	-	12	2686	c.2290G>A	c.(2290-2292)Gag>Aag	p.E764K	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	764					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACCTTGTCCTCCTGGATCTCG	0.687																																					p.E764K		Atlas-SNP	.											.	INSRR	309	.	0			c.G2290A						.						22	20	21					1																	156815015		2201	4299	6500	SO:0001583	missense	3645	exon12			TGTCCTCCTGGAT	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2290G>A	chr1.hg19:g.156815015C>T	ENSP00000357178:p.Glu764Lys	67.0	0.0		87.0	23.0	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.579539	0.46006	.	.	ENSG00000027644	ENST00000368195	T	0.78126	-1.15	3.39	3.39	0.38822	Fibronectin, type III (2);	0.000000	0.40064	N	0.001187	T	0.47135	0.1429	.	.	.	0.32675	N	0.516305	B	0.15141	0.012	B	0.12837	0.008	T	0.36504	-0.9745	9	0.29301	T	0.29	.	8.5071	0.33195	0.0:0.8877:0.0:0.1123	.	764	P14616	INSRR_HUMAN	K	764	ENSP00000357178:E764K	ENSP00000357178:E764K	E	-	1	0	INSRR	155081639	0.983000	0.35010	0.993000	0.49108	0.986000	0.74619	2.526000	0.45607	2.193000	0.70182	0.561000	0.74099	GAG	.	.		0.687	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		T	156815015	C	T	156815015	3	4	144	1	0	0	0	0	1	0	0	0	7783	864	30	3	1646	3	INSRR	1	156815015	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	137289675	156815015	92435606	3	22208										
FCRL1	115350	hgsc.bcm.edu	37	chr1	157771365	157771365	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	attgcttctggccccagtagGcactagagggagagacctgt	13	10	1	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr1:157771365G>A	ENST00000368176.3	-	6	956	c.889C>T	c.(889-891)Cct>Tct	p.P297S	FCRL1_ENST00000358292.3_Intron|FCRL1_ENST00000489998.1_Intron|FCRL1_ENST00000491942.1_Missense_Mutation_p.P297S	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	297						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GCCCCAGTAGGCACTAGAGGG	0.557																																					p.P297S	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.C889T						.						68	69	69					1																	157771365		2203	4300	6503	SO:0001583	missense	115350	exon6			CAGTAGGCACTAG	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.889C>T	chr1.hg19:g.157771365G>A	ENSP00000357158:p.Pro297Ser	128.0	0.0		132.0	52.0	NM_001159398	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Missense_Mutation	SNP	ENST00000368176.3	hg19	CCDS1170.1	.	.	.	.	.	.	.	.	.	.	G	11.93	1.785102	0.31593	.	.	ENSG00000163534	ENST00000368176;ENST00000491942	T;T	0.49139	0.79;0.79	5.25	4.33	0.51752	Immunoglobulin-like fold (1);	0.957579	0.08730	N	0.902182	T	0.49355	0.1552	M	0.65975	2.015	0.34465	D	0.702158	D;D	0.56968	0.972;0.978	P;P	0.57846	0.828;0.539	T	0.44174	-0.9345	10	0.45353	T	0.12	.	9.8543	0.41077	0.0926:0.0:0.9074:0.0	.	297;297	Q96LA6-2;Q96LA6	.;FCRL1_HUMAN	S	297	ENSP00000357158:P297S;ENSP00000418130:P297S	ENSP00000357158:P297S	P	-	1	0	FCRL1	156037989	1.000000	0.71417	0.992000	0.48379	0.044000	0.14063	2.449000	0.44935	1.580000	0.49851	0.655000	0.94253	CCT	.	.		0.557	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938		A	157771365	G	A	157771365	3	1	144	1	0	0	0	0	1	0	0	0	5802	1203	42	3	490	3	FCRL1	1	157771365	Missense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	956350	157771365	91479256	4	22209										
TIPRL	261726	hgsc.bcm.edu	37	chr1	168165787	168165787	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ctttttttttttttccagagAgtaatgccttctagcttttt	5	7	1	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr1:168165787A>C	ENST00000367833.2	+	5	664	c.519A>C	c.(517-519)agA>agC	p.R173S		NM_152902.3	NP_690866.1	O75663	TIPRL_HUMAN	TOR signaling pathway regulator	173	Interaction with PPP2CA.				DNA damage checkpoint (GO:0000077)|negative regulation of protein phosphatase type 2A activity (GO:0034048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|kidney(1)|large_intestine(1)|ovary(2)|skin(1)	6	all_hematologic(923;0.215)					TTTTCCAGAGAGTAATGCCTT	0.284																																					p.R173S		Atlas-SNP	.											.	TIPRL	16	.	0			c.A519C						.						86	85	85					1																	168165787		2203	4300	6503	SO:0001583	missense	261726	exon5			CCAGAGAGTAATG	AB097034	CCDS1270.1, CCDS30935.1	1q23.2	2014-03-07	2014-03-07		ENSG00000143155	ENSG00000143155			30231	protein-coding gene	gene with protein product		611807	"TIP41, TOR signaling pathway regulator-like (S. cerevisiae)"			12761501	Standard	NM_001031800		Approved	MGC3794, dJ69E11.3, TIP41	uc001gfg.3	O75663	OTTHUMG00000034646	ENST00000367833.2:c.519A>C	chr1.hg19:g.168165787A>C	ENSP00000356807:p.Arg173Ser	44.0	0.0		25.0	10.0	NM_152902	B2R8V3|Q5HYB2|Q8IZ86	Missense_Mutation	SNP	ENST00000367833.2	hg19	CCDS1270.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.216046	0.79352	.	.	ENSG00000143155	ENST00000367833	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.83431	0.5253	M	0.93328	3.405	0.46279	D	0.998965	D	0.89917	1.0	D	0.91635	0.999	D	0.88415	0.3024	8	0.87932	D	0	-15.878	14.0998	0.65046	1.0:0.0:0.0:0.0	.	173	O75663	TIPRL_HUMAN	S	173	.	ENSP00000356807:R173S	R	+	3	2	TIPRL	166432411	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.542000	0.53625	2.145000	0.66743	0.533000	0.62120	AGA	.	.		0.284	TIPRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083822.1	NM_152902		C	168165787	A	C	168165787	3	2	144	1	0	0	0	0	1	0	0	0	15941	301	11	5	562	5	TIPRL	1	168165787	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	10394422	168165787	81084834	5	22210										
CEP350	9857	hgsc.bcm.edu	37	chr1	180080224	180080224	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ctagccgacgggatctttgaGaccctgatcaaagatactat	9	10	2	3	rs201090590		TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr1:180080224G>T	ENST00000367607.3	+	38	9700	c.9282G>T	c.(9280-9282)gaG>gaT	p.E3094D	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	3094					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						GGATCTTTGAGACCCTGATCA	0.453																																					p.E3094D		Atlas-SNP	.											.	CEP350	418	.	0			c.G9282T						.						129	110	116					1																	180080224		2203	4300	6503	SO:0001583	missense	9857	exon38			CTTTGAGACCCTG	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.9282G>T	chr1.hg19:g.180080224G>T	ENSP00000356579:p.Glu3094Asp	108.0	0.0		71.0	19.0	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.768|9.768	1.171906|1.171906	0.21704|0.21704	.|.	.|.	ENSG00000135837|ENSG00000135837	ENST00000429851|ENST00000367607;ENST00000417046	.|T	.|0.55760	.|0.5	6.05|6.05	3.18|3.18	0.36537|0.36537	.|.	.|0.000000	.|0.49305	.|D	.|0.000146	T|T	0.37461|0.37461	0.1004|0.1004	L|L	0.41236|0.41236	1.265|1.265	0.43145|0.43145	D|D	0.9949|0.9949	.|B;P	.|0.39116	.|0.355;0.66	.|B;B	.|0.30716	.|0.057;0.119	T|T	0.10132|0.10132	-1.0643|-1.0643	5|9	.|.	.|.	.|.	.|.	11.5353|11.5353	0.50634|0.50634	0.1936:0.0:0.8064:0.0|0.1936:0.0:0.8064:0.0	.|.	.|3094;3094	.|E7EU22;Q5VT06	.|.;CE350_HUMAN	Y|D	1269|3094;558	.|ENSP00000356579:E3094D	.|.	D|E	+|+	1|3	0|2	CEP350|CEP350	178346847|178346847	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.879000|0.879000	0.50718|0.50718	0.804000|0.804000	0.27098|0.27098	0.446000|0.446000	0.26666|0.26666	0.650000|0.650000	0.86243|0.86243	GAC|GAG	.	G|1.000;C|0.000		0.453	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	180080224	G	T	180080224	3	4	144	1	0	0	0	0	1	0	0	0	3256	933	33	3	9428	3	CEP350	1	180080224	Missense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	11914437	180080224	69170397	6	22211										
NT5C1B	93034	hgsc.bcm.edu	37	chr2	18765784	18765784	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	cggcgggctggctcaccggcCaggggcgcgagcagctcggg	20	14	1	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr2:18765784C>T	ENST00000359846.2	-	5	976	c.899G>A	c.(898-900)tGg>tAg	p.W300*	NT5C1B-RDH14_ENST00000532967.1_Nonsense_Mutation_p.W300*|NT5C1B_ENST00000304081.4_Nonsense_Mutation_p.W240*|RNU6-1215P_ENST00000384441.1_RNA|NT5C1B_ENST00000460052.1_5'Flank|NT5C1B_ENST00000600945.1_Nonsense_Mutation_p.W300*	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	300					nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				GCTCACCGGCCAGGGGCGCGA	0.697																																					p.W317X		Atlas-SNP	.											.	NT5C1B	72	.	0			c.G950A						.						8	9	9					2																	18765784		2151	4216	6367	SO:0001587	stop_gained	93034	exon5			ACCGGCCAGGGGC	AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.899G>A	chr2.hg19:g.18765784C>T	ENSP00000352904:p.Trp300*	40.0	0.0		57.0	13.0	NM_001199087	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Nonsense_Mutation	SNP	ENST00000359846.2	hg19	CCDS33150.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.884710	0.72410	.	.	ENSG00000250741;ENSG00000250741;ENSG00000185013;ENSG00000185013	ENST00000532967;ENST00000444297;ENST00000304081;ENST00000359846	.	.	.	4.59	3.71	0.42584	.	0.177705	0.47852	D	0.000215	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-1.5138	4.4181	0.11466	0.1537:0.6075:0.1497:0.0891	.	.	.	.	X	300;242;240;300	.	ENSP00000305979:W240X	W	-	2	0	NT5C1B-RDH14;NT5C1B	18629265	0.851000	0.29673	0.957000	0.39632	0.296000	0.27459	0.781000	0.26774	1.241000	0.43820	0.462000	0.41574	TGG	.	.		0.697	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1			T	18765784	C	T	18765784	4	4	144	1	0	0	0	0	0	1	0	0	10695	595	21	3	957	3	NT5C1B	2	18765784	Nonsense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10		18765784	224433589	7	22212										
DHX57	90957	hgsc.bcm.edu	37	chr2	39041005	39041005	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gcagcacacagcattgctgaTatcagcttggggttctcagc	11	11	2	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr2:39041005T>C	ENST00000295373.6	-	21	3765	c.3639A>G	c.(3637-3639)atA>atG	p.I1213M		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1213							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				GCATTGCTGATATCAGCTTGG	0.353																																					p.I1213M	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											DHX57,NS,chondrosarcoma,0,1	DHX57	127	.	0			c.A3639G						.						132	125	127					2																	39041005		2203	4300	6503	SO:0001583	missense	90957	exon21			TGCTGATATCAGC	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3639A>G	chr2.hg19:g.39041005T>C	ENSP00000295373:p.Ile1213Met	288.0	0.0		215.0	11.0	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	hg19	CCDS1800.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.63|12.63	1.995640|1.995640	0.35226|0.35226	.|.	.|.	ENSG00000163214|ENSG00000163214	ENST00000295373|ENST00000452978	T|T	0.02944|0.03889	4.1|3.77	5.65|5.65	4.46|4.46	0.54185|0.54185	Domain of unknown function DUF1605 (1);|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000009|0.000009	T|T	0.04182|0.04182	0.0116|0.0116	L|L	0.28054|0.28054	0.825|0.825	0.39016|0.39016	D|D	0.959652|0.959652	B;P|.	0.36837|.	0.277;0.571|.	B;B|.	0.42163|.	0.145;0.378|.	T|T	0.47812|0.47812	-0.9088|-0.9088	10|8	0.51188|0.09843	T|T	0.08|0.71	.|.	7.466|7.466	0.27322|0.27322	0.134:0.0:0.1586:0.7074|0.134:0.0:0.1586:0.7074	.|.	1213;605|.	Q6P158;Q59G60|.	DHX57_HUMAN;.|.	M|V	1213|537	ENSP00000295373:I1213M|ENSP00000397841:I537V	ENSP00000295373:I1213M|ENSP00000397841:I537V	I|I	-|-	3|1	3|0	DHX57|DHX57	38894509|38894509	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	3.543000|3.543000	0.53633|0.53633	0.924000|0.924000	0.37069|0.37069	0.383000|0.383000	0.25322|0.25322	ATA|ATC	.	.		0.353	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		C	39041005	T	C	39041005	3	2	144	1	0	0	0	0	1	0	0	0	4515	1396	49	2	537	2	DHX57	2	39041005	Missense_Mutation	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	20275221	39041005	204158368	8	22213										
CDCA7	83879	hgsc.bcm.edu	37	chr2	174224163	174224163	+	Intron	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tggccggtatttttcatgccGactctgacgatgaatcattt	9	9	3	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr2:174224163G>T	ENST00000347703.3	+	2	291				CDCA7_ENST00000306721.3_Missense_Mutation_p.D110Y|CDCA7_ENST00000410019.3_Intron|CDCA7_ENST00000392567.2_Intron|CDCA7_ENST00000410101.3_Missense_Mutation_p.D66Y	NM_145810.2	NP_665809.1	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7						apoptotic process (GO:0006915)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.116)			TTTTCATGCCGACTCTGACGA	0.403																																					p.D110Y		Atlas-SNP	.											.	CDCA7	48	.	0			c.G328T						.						105	102	103					2																	174224163		2203	4300	6503	SO:0001627	intron_variant	83879	exon3			CATGCCGACTCTG	BG354580	CCDS2252.1, CCDS2253.1	2q31.1	2008-02-05			ENSG00000144354	ENSG00000144354			14628	protein-coding gene	gene with protein product		609937				11598121, 12188893	Standard	NM_145810		Approved	FLJ14736, JPO1	uc002uic.1	Q9BWT1	OTTHUMG00000132296	ENST00000347703.3:c.147+598G>T	chr2.hg19:g.174224163G>T		129.0	0.0		106.0	38.0	NM_031942	B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	Missense_Mutation	SNP	ENST00000347703.3	hg19	CCDS2253.1	.	.	.	.	.	.	.	.	.	.	G	17.12	3.307892	0.60305	.	.	ENSG00000144354	ENST00000306721;ENST00000410101	T;T	0.55588	0.51;0.74	5.87	4.98	0.66077	.	0.145934	0.47093	D	0.000255	T	0.66557	0.2801	L	0.61218	1.895	0.80722	D	1	D;D	0.67145	0.992;0.996	P;P	0.62491	0.73;0.903	T	0.70339	-0.4899	10	0.87932	D	0	-22.5441	13.3614	0.60659	0.0745:0.0:0.9255:0.0	.	66;110	B4DV66;Q9BWT1-2	.;.	Y	110;66	ENSP00000306968:D110Y;ENSP00000386656:D66Y	ENSP00000306968:D110Y	D	+	1	0	CDCA7	173932409	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.129000	0.50500	1.456000	0.47831	0.650000	0.86243	GAC	.	.		0.403	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255400.1	NM_031942		T	174224163	G	T	174224163	1	4	144	0	1	0	0	0	0	0	0	0	3092	1058	37	1		1	CDCA7	2	174224163	Intron	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	135183158	174224163	68975210	9	22214										
TTN	7273	hgsc.bcm.edu	37	chr2	179435859	179435859	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	catgggtcacgagccacataAcattctgatactttactcgg	8	11	2	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr2:179435859A>G	ENST00000591111.1	-	276	70301	c.70077T>C	c.(70075-70077)tgT>tgC	p.C23359C	TTN_ENST00000342175.6_Silent_p.C16127C|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.C16060C|TTN_ENST00000460472.2_Silent_p.C15935C|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Silent_p.C22432C|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Silent_p.C25000C|TTN-AS1_ENST00000592689.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23359	Fibronectin type-III 69. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAGCCACATAACATTCTGATA	0.463																																					p.C25000C		Atlas-SNP	.											.	TTN	18412	.	0			c.T75000C						.						119	121	121					2																	179435859		1991	4169	6160	SO:0001819	synonymous_variant	7273	exon326			CACATAACATTCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.70077T>C	chr2.hg19:g.179435859A>G		49.0	0.0		41.0	16.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179435859	A	G	179435859	2	3	144	1	0	0	0	0	0	0	0	1	16750	41	2	2		2	TTN	2	179435859	Silent	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	5211696	179435859	63763514	10	22215										
CPS1	1373	hgsc.bcm.edu	37	chr2	211512674	211512674	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	agaatggtgtcaagatcatgGgcacaagccccctgcagatc	11	11	2	3			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr2:211512674G>C	ENST00000233072.5	+	26	3425	c.3229G>C	c.(3229-3231)Ggc>Cgc	p.G1077R	CPS1_ENST00000430249.2_Missense_Mutation_p.G1083R|CPS1_ENST00000451903.2_Missense_Mutation_p.G626R	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1077					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	CAAGATCATGGGCACAAGCCC	0.512																																					p.G1083R		Atlas-SNP	.											.	CPS1	485	.	0			c.G3247C						.						113	105	108					2																	211512674		2203	4300	6503	SO:0001583	missense	1373	exon27			ATCATGGGCACAA	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3229G>C	chr2.hg19:g.211512674G>C	ENSP00000233072:p.Gly1077Arg	245.0	0.0		219.0	56.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.926450	0.92319	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.99685	-6.4;-6.4;-6.4	5.99	5.99	0.97316	PreATP-grasp-like fold (1);Carbamoyl-phosphate synthase, large subunit, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99900	0.9952	H	0.99825	4.815	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96165	0.9118	10	0.87932	D	0	-8.9006	20.4777	0.99188	0.0:0.0:1.0:0.0	.	1087;1077	Q59HF8;P31327	.;CPSM_HUMAN	R	1083;1085;1077;626	ENSP00000402608:G1083R;ENSP00000233072:G1077R;ENSP00000406136:G626R	ENSP00000233072:G1077R	G	+	1	0	CPS1	211220919	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.476000	0.97823	2.840000	0.97914	0.655000	0.94253	GGC	.	.		0.512	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			C	211512674	G	C	211512674	3	2	144	1	0	0	0	0	1	0	0	0	3825	1232	43	4	3353	4	CPS1	2	211512674	Missense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	32076815	211512674	31686699	11	22216										
MARCH4	57574	hgsc.bcm.edu	37	chr2	217124227	217124227	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gtgcctgcggtctcctcttcCgaggaggggatattggcctg	15	11	2	0	rs139359941	byFrequency	TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr2:217124227C>T	ENST00000273067.4	-	4	2807	c.1041G>A	c.(1039-1041)tcG>tcA	p.S347S	AC012513.6_ENST00000417481.1_RNA	NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	347						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		TCTCCTCTTCCGAGGAGGGGA	0.622													C|||	4	0.000798722	0	0	5008	,	,		18850	0		0	False		,,,				2504	0.0041				p.S347S		Atlas-SNP	.											.	MARCH4	50	.	0			c.G1041A						.	C		0,4406		0,0,2203	55	55	55		1041	-11.2	0	2	dbSNP_134	55	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MARCH4	NM_020814.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		347/411	217124227	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57574	exon4			CTCTTCCGAGGAG	AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	29269	protein-coding gene	gene with protein product		608208	"membrane-associated ring finger (C3HC4) 4"			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.1041G>A	chr2.hg19:g.217124227C>T		118.0	0.0		88.0	32.0	NM_020814	Q4KMN7|Q86WR8	Silent	SNP	ENST00000273067.4	hg19	CCDS33376.1																																																																																			.	C|1.000;T|0.000		0.622	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814		T	217124227	C	T	217124227	2	4	144	1	0	0	0	0	0	0	0	1	9312	639	23	1		1	MARCH4	2	217124227	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	5611553	217124227	26075146	12	22217										
LRRN1	57633	hgsc.bcm.edu	37	chr3	3887625	3887625	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ctcacgacagcttcccaaatCgtttaaacgtggatatcggc	8	12	1	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr3:3887625C>T	ENST00000319331.3	+	2	2061	c.1300C>T	c.(1300-1302)Cgt>Tgt	p.R434C	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	434	Ig-like C2-type.					integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		CTTCCCAAATCGTTTAAACGT	0.478																																					p.R434C		Atlas-SNP	.											.	LRRN1	82	.	0			c.C1300T						.						90	92	91					3																	3887625		2203	4300	6503	SO:0001583	missense	57633	exon2			CCAAATCGTTTAA	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"Immunoglobulin superfamily / I-set domain containing"	20980	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 3"					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.1300C>T	chr3.hg19:g.3887625C>T	ENSP00000314901:p.Arg434Cys	150.0	0.0		109.0	10.0	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Missense_Mutation	SNP	ENST00000319331.3	hg19	CCDS33685.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.063475	0.36373	.	.	ENSG00000175928	ENST00000319331	T	0.68331	-0.32	5.65	5.65	0.86999	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.138414	0.64402	D	0.000003	T	0.68842	0.3045	L	0.47716	1.5	0.45747	D	0.998646	P	0.49253	0.921	P	0.46975	0.533	T	0.70934	-0.4737	10	0.56958	D	0.05	.	19.7243	0.96157	0.0:1.0:0.0:0.0	.	434	Q6UXK5	LRRN1_HUMAN	C	434	ENSP00000314901:R434C	ENSP00000314901:R434C	R	+	1	0	LRRN1	3862625	1.000000	0.71417	0.077000	0.20336	0.864000	0.49448	6.030000	0.70903	2.665000	0.90641	0.650000	0.86243	CGT	.	.		0.478	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873		T	3887625	C	T	3887625	3	4	144	1	0	0	0	0	1	0	0	0	9043	884	31	1	1302	1	LRRN1	3	3887625	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10		3887625	194134805	13	22218										
CNOT10	25904	hgsc.bcm.edu	37	chr3	32801028	32801028	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gctttgaatcatgcagataaActtcttcagcagcccaagct	7	11	3	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr3:32801028A>C	ENST00000328834.5	+	14	1990	c.1674A>C	c.(1672-1674)aaA>aaC	p.K558N	CNOT10_ENST00000331889.6_Missense_Mutation_p.K531N|CNOT10_ENST00000454516.2_Missense_Mutation_p.K618N|CNOT10_ENST00000538368.1_Missense_Mutation_p.K330N	NM_015442.2	NP_056257.1	Q9H9A5	CNO10_HUMAN	CCR4-NOT transcription complex, subunit 10	558					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(3)	23						ATGCAGATAAACTTCTTCAGC	0.473																																					p.K618N		Atlas-SNP	.											.	CNOT10	57	.	0			c.A1854C						.						362	349	353					3																	32801028		2203	4300	6503	SO:0001583	missense	25904	exon14			AGATAAACTTCTT	BC002928	CCDS2655.1, CCDS58821.1, CCDS58822.1	3p23	2013-01-10			ENSG00000182973	ENSG00000182973		"Tetratricopeptide (TTC) repeat domain containing"	23817	protein-coding gene	gene with protein product							Standard	NR_046352		Approved	FLJ12890, FLJ13165	uc011axj.2	Q9H9A5	OTTHUMG00000130748	ENST00000328834.5:c.1674A>C	chr3.hg19:g.32801028A>C	ENSP00000330060:p.Lys558Asn	87.0	0.0		71.0	9.0	NM_001256742	B7Z7L1|F8WAF2|Q9BU30|Q9H5J7|Q9H8X1|Q9H9W0|Q9HAH3|Q9UFJ2	Missense_Mutation	SNP	ENST00000328834.5	hg19	CCDS2655.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.611047	0.28712	.	.	ENSG00000182973	ENST00000331889;ENST00000328834;ENST00000538368;ENST00000454516;ENST00000430408	T;T;T;T;T	0.43294	1.25;1.25;0.95;1.25;0.95	5.81	3.45	0.39498	Tetratricopeptide-like helical (1);	0.042023	0.85682	D	0.000000	T	0.24661	0.0598	N	0.17082	0.46	0.58432	D	0.99999	B;B;B;B	0.20459	0.001;0.045;0.005;0.001	B;B;B;B	0.21360	0.004;0.034;0.004;0.001	T	0.04347	-1.0958	10	0.21540	T	0.41	-16.9714	9.4295	0.38601	0.7896:0.0:0.2104:0.0	.	618;531;557;558	F8WAF2;Q9H9A5-3;Q9H9A5-2;Q9H9A5	.;.;.;CNOTA_HUMAN	N	531;558;330;618;105	ENSP00000329376:K531N;ENSP00000330060:K558N;ENSP00000442552:K330N;ENSP00000399862:K618N;ENSP00000395385:K105N	ENSP00000330060:K558N	K	+	3	2	CNOT10	32776032	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.591000	0.36665	0.477000	0.27464	0.482000	0.46254	AAA	.	.		0.473	CNOT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253248.2	NM_015442		C	32801028	A	C	32801028	3	2	144	1	0	0	0	0	1	0	0	0	3620	40	2	5	1728	5	CNOT10	3	32801028	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	28913403	32801028	165221402	14	22219										
OXSR1	9943	hgsc.bcm.edu	37	chr3	38263170	38263170	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gttggatggcacctgaagttAtggaacaggtaccgtgtctt	13	7	1	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr3:38263170A>G	ENST00000446845.1	+	6	964	c.592A>G	c.(592-594)Atg>Gtg	p.M198V	OXSR1_ENST00000311806.3_Missense_Mutation_p.M198V					oxidative stress responsive 1											skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		ACCTGAAGTTATGGAACAGGT	0.398																																					p.M198V		Atlas-SNP	.											.	OXSR1	74	.	0			c.A592G						.						171	170	170					3																	38263170		2203	4300	6503	SO:0001583	missense	9943	exon6			GAAGTTATGGAAC	AB017642	CCDS2675.1	3p22.2	2013-05-17	2013-05-17	2004-11-26	ENSG00000172939	ENSG00000172939			8508	protein-coding gene	gene with protein product		604046	"oxidative-stress responsive 1"	OSR1		10083736	Standard	XM_005265638		Approved	KIAA1101	uc003chy.3	O95747	OTTHUMG00000131084	ENST00000446845.1:c.592A>G	chr3.hg19:g.38263170A>G	ENSP00000415851:p.Met198Val	102.0	0.0		91.0	7.0	NM_005109		Missense_Mutation	SNP	ENST00000446845.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.9	4.222953	0.79464	.	.	ENSG00000172939	ENST00000446845;ENST00000311806	T;T	0.63255	-0.03;-0.03	5.26	5.26	0.73747	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.63082	0.2481	N	0.11892	0.195	0.80722	D	1	D;D	0.62365	0.991;0.991	D;D	0.67382	0.934;0.951	T	0.69487	-0.5132	10	0.59425	D	0.04	-19.2781	14.6683	0.68924	1.0:0.0:0.0:0.0	.	198;198	C9JIG9;O95747	.;OXSR1_HUMAN	V	198	ENSP00000415851:M198V;ENSP00000311713:M198V	ENSP00000311713:M198V	M	+	1	0	OXSR1	38238174	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.240000	0.95396	2.134000	0.65973	0.460000	0.39030	ATG	.	.		0.398	OXSR1-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000342708.1	NM_005109		G	38263170	A	G	38263170	3	3	144	1	0	0	0	0	1	0	0	0	11345	449	16	2	614	2	OXSR1	3	38263170	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	5462142	38263170	159759260	15	22220										
SETD2	29072	hgsc.bcm.edu	37	chr3	47163059	47163059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ttctggggcatgaccactacTgtcacactttaatgcataag	8	10	2	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr3:47163059T>C	ENST00000409792.3	-	3	3109	c.3067A>G	c.(3067-3069)Agt>Ggt	p.S1023G		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1023					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGACCACTACTGTCACACTTT	0.363			"N, F, S, Mis"		clear cell renal carcinoma																																p.S1023G		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.A3067G						.						86	83	84					3																	47163059		2203	4300	6503	SO:0001583	missense	29072	exon3			CACTACTGTCACA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.3067A>G	chr3.hg19:g.47163059T>C	ENSP00000386759:p.Ser1023Gly	206.0	0.0		172.0	57.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	17.70	3.455384	0.63401	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792;ENST00000412450	D;T	0.91894	-2.93;0.75	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000003	D	0.92195	0.7525	N	0.24115	0.695	0.36064	D	0.841632	D;D	0.63880	0.993;0.993	D;D	0.68192	0.956;0.956	D	0.94846	0.8009	10	0.72032	D	0.01	.	13.5012	0.61457	0.0:0.0:0.0:1.0	.	1023;1023	F2Z317;Q9BYW2	.;SETD2_HUMAN	G	1023;1023;1023;979	ENSP00000386759:S1023G;ENSP00000416401:S979G	ENSP00000386759:S1023G	S	-	1	0	SETD2	47138063	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	3.315000	0.51951	2.115000	0.64714	0.528000	0.53228	AGT	.	.		0.363	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		C	47163059	T	C	47163059	3	2	144	1	0	0	0	0	1	0	0	0	14146	1580	55	2	4703	2	SETD2	3	47163059	Missense_Mutation	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	8899889	47163059	150859371	16	22221										
RNF123	63891	hgsc.bcm.edu	37	chr3	49749928	49749930	+	In_Frame_Del	DEL	TCT	TCT	-													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gcaggagaagatgctggacaTctactggctgctgcgcgtct							TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr3:49749928_49749930delTCT	ENST00000327697.6	+	27	2657_2659	c.2513_2515delTCT	c.(2512-2517)atctac>aac	p.838_839IY>N	RNF123_ENST00000432042.1_In_Frame_Del_p.692_693IY>N|RNF123_ENST00000433785.1_5'Flank	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	838					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		ATGCTGGACATCTACTGGCTGCT	0.621																																					p.838_838del		Atlas-Indel,Pindel	.											.	RNF123	100	.	0			c.2512_2514del						.																																			SO:0001651	inframe_deletion	63891	exon27			.	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.2513_2515delTCT	chr3.hg19:g.49749928_49749930delTCT	ENSP00000328287:p.Ile838_Tyr839delinsAsn	55.0	0.0		48.0	12.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	In_Frame_Del	DEL	ENST00000327697.6	hg19	CCDS33758.1																																																																																			.	.		0.621	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		-	49749930	TCT	-	49749928	7	5	144	1	0	1	0	1	0	0	0	0	13448	1435	50	0	2615	0	RNF123	3	49749928	In_Frame_Del	DEL	TCT	TCGA-DD-A73C-01A-12D-A33K-10	2586869	49749928	148272502	17	22222										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121410667	121410667	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ttctcaagcctcgtatttctTctttaagcttattattctct	3	10	4	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr3:121410667T>A	ENST00000340645.5	-	14	7654	c.7529A>T	c.(7528-7530)gAa>gTa	p.E2510V	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E2515V	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2510					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TCGTATTTCTTCTTTAAGCTT	0.418																																					p.E2515V		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A7544T						.						159	166	163					3																	121410667		2203	4300	6503	SO:0001583	missense	2804	exon14			ATTTCTTCTTTAA	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.7529A>T	chr3.hg19:g.121410667T>A	ENSP00000341848:p.Glu2510Val	67.0	0.0		59.0	11.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.586347	0.46110	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.18960	2.18;2.18	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000005	T	0.46698	0.1406	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.997	T	0.47209	-0.9135	10	0.62326	D	0.03	.	13.648	0.62292	0.0:0.0:0.0:1.0	.	2515;2515;2510	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	V	2510;2515	ENSP00000341848:E2510V;ENSP00000377275:E2515V	ENSP00000341848:E2510V	E	-	2	0	GOLGB1	122893357	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.065000	0.64344	2.102000	0.63906	0.460000	0.39030	GAA	.	.		0.418	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121410667	T	A	121410667	3	1	144	1	0	0	0	0	1	0	0	0	6573	1783	62	4	2286	4	GOLGB1	3	121410667	Missense_Mutation	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	71660739	121410667	76611763	18	22223										
SLC9A9	285195	hgsc.bcm.edu	37	chr3	143271227	143271227	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tttagttcttattttggaatCcgaagacagattgttgtagg	10	4	1	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr3:143271227C>A	ENST00000316549.6	-	9	1274	c.1066G>T	c.(1066-1068)Gat>Tat	p.D356Y		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	356					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)			breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						ATTTTGGAATCCGAAGACAGA	0.348																																					p.D356Y		Atlas-SNP	.											.	SLC9A9	117	.	0			c.G1066T						.						114	107	109					3																	143271227		2203	4300	6503	SO:0001583	missense	285195	exon9			TGGAATCCGAAGA	AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"Solute carriers"	20653	protein-coding gene	gene with protein product		608396	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 9", "solute carrier family 9 (sodium/hydrogen exchanger), member 9"			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.1066G>T	chr3.hg19:g.143271227C>A	ENSP00000320246:p.Asp356Tyr	75.0	0.0		43.0	19.0	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Missense_Mutation	SNP	ENST00000316549.6	hg19	CCDS33872.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374759	0.82573	.	.	ENSG00000181804	ENST00000316549;ENST00000450105	T	0.15952	2.38	5.6	5.6	0.85130	Cation/H+ exchanger (1);	0.146970	0.47455	D	0.000240	T	0.24470	0.0593	N	0.20685	0.6	0.58432	D	0.999998	P	0.47484	0.896	P	0.53450	0.726	T	0.01512	-1.1336	10	0.87932	D	0	.	19.9801	0.97322	0.0:1.0:0.0:0.0	.	356	Q8IVB4	SL9A9_HUMAN	Y	356;239	ENSP00000320246:D356Y	ENSP00000320246:D356Y	D	-	1	0	SLC9A9	144753917	1.000000	0.71417	0.956000	0.39512	0.903000	0.53119	6.861000	0.75478	2.808000	0.96608	0.650000	0.86243	GAT	.	.		0.348	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653		A	143271227	C	A	143271227	3	1	144	1	0	0	0	0	1	0	0	0	14736	855	30	3	903	3	SLC9A9	3	143271227	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	21860560	143271227	54751203	19	22224										
SKIL	6498	hgsc.bcm.edu	37	chr3	170110171	170110171	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gataaaagagctaaagctgcAaattctgaaatcatcaaaga	7	6	3	3			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr3:170110171A>T	ENST00000458537.3	+	6	2730	c.2021A>T	c.(2020-2022)cAa>cTa	p.Q674L	SKIL_ENST00000426052.2_Missense_Mutation_p.Q654L|SKIL_ENST00000259119.4_Missense_Mutation_p.Q674L|SKIL_ENST00000413427.2_Missense_Mutation_p.Q628L	NM_001145097.2|NM_001248008.1|NM_005414.4	NP_001138569.1|NP_001234937.1|NP_005405.2	P12757	SKIL_HUMAN	SKI-like proto-oncogene	674					blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			CTAAAGCTGCAAATTCTGAAA	0.388																																					p.Q674L		Atlas-SNP	.											.	SKIL	67	.	0			c.A2021T						.						94	103	100					3																	170110171		2203	4300	6503	SO:0001583	missense	6498	exon6			AGCTGCAAATTCT	X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603		"SKI transcriptional corepressors"	10897	protein-coding gene	gene with protein product		165340	"SKI-like oncogene"			2762147	Standard	NM_005414		Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000458537.3:c.2021A>T	chr3.hg19:g.170110171A>T	ENSP00000415243:p.Gln674Leu	260.0	0.0		239.0	78.0	NM_001248008	A6NGT1|B4DT50|O00464|P12756|Q07501	Missense_Mutation	SNP	ENST00000458537.3	hg19	CCDS33890.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.418393	0.83559	.	.	ENSG00000136603	ENST00000259119;ENST00000426052;ENST00000413427;ENST00000458537	D;D;D;D	0.95853	-3.83;-3.8;-3.81;-3.83	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.97182	0.9079	M	0.62723	1.935	0.45580	D	0.99852	D;D	0.89917	0.997;1.0	D;D	0.83275	0.993;0.996	D	0.97388	0.9987	10	0.54805	T	0.06	-16.4945	16.6438	0.85155	1.0:0.0:0.0:0.0	.	628;674	P12757-3;P12757	.;SKIL_HUMAN	L	674;654;628;674	ENSP00000259119:Q674L;ENSP00000406520:Q654L;ENSP00000400193:Q628L;ENSP00000415243:Q674L	ENSP00000259119:Q674L	Q	+	2	0	SKIL	171592865	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.754000	0.74909	2.333000	0.79357	0.533000	0.62120	CAA	.	.		0.388	SKIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352351.4	NM_005414		T	170110171	A	T	170110171	3	4	144	1	0	0	0	0	1	0	0	0	14373	130	5	4	2043	4	SKIL	3	170110171	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	26838944	170110171	27912259	20	22225										
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15516353	15516353	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gaggaagaactgcttaatggTgatgatgccgaggacttcct	13	7	0	3			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr4:15516353T>A	ENST00000503292.1	+	10	921	c.741T>A	c.(739-741)ggT>ggA	p.G247G	CC2D2A_ENST00000413206.1_Silent_p.G247G|CC2D2A_ENST00000389652.5_Silent_p.G198G|CC2D2A_ENST00000424120.1_Silent_p.G247G|CC2D2A_ENST00000513811.1_3'UTR	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	247					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						TGCTTAATGGTGATGATGCCG	0.388																																					p.G247G		Atlas-SNP	.											.	CC2D2A	158	.	0			c.T741A						.						115	112	113					4																	15516353		1953	4155	6108	SO:0001819	synonymous_variant	57545	exon10			TAATGGTGATGAT	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.741T>A	chr4.hg19:g.15516353T>A		58.0	0.0		51.0	19.0	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	hg19	CCDS47026.1																																																																																			.	.		0.388	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		A	15516353	T	A	15516353	2	1	144	1	0	0	0	0	0	0	0	1	2730	1683	59	4		4	CC2D2A	4	15516353	Silent	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10		15516353	175637923	21	22226										
SPATA18	132671	hgsc.bcm.edu	37	chr4	52938154	52938154	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gaggagctcagagaataggcGgtcagagccttggagcttgg	17	7	2	2	rs376481625		TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr4:52938154G>T	ENST00000295213.4	+	6	964	c.590G>T	c.(589-591)cGg>cTg	p.R197L	SPATA18_ENST00000506829.1_3'UTR|SPATA18_ENST00000419395.2_Missense_Mutation_p.R165L	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	197					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			GAGAATAGGCGGTCAGAGCCT	0.527																																					p.R197L		Atlas-SNP	.											.	SPATA18	222	.	0			c.G590T						.						73	68	70					4																	52938154		2203	4300	6503	SO:0001583	missense	132671	exon6			ATAGGCGGTCAGA	BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"spermatogenesis associated 18 homolog (rat)"			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.590G>T	chr4.hg19:g.52938154G>T	ENSP00000295213:p.Arg197Leu	115.0	0.0		106.0	25.0	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	hg19	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	G	5.932	0.355943	0.11239	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	D;D	0.87491	-2.25;-2.26	2.68	0.739	0.18324	.	2.273110	0.01545	N	0.019384	T	0.81754	0.4889	L	0.34521	1.04	0.09310	N	1	B;B;B	0.28400	0.034;0.034;0.21	B;B;B	0.26094	0.031;0.019;0.066	T	0.65952	-0.6043	10	0.34782	T	0.22	-0.001	9.0017	0.36085	0.0:0.5765:0.4235:0.0	.	165;197;197	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	L	197;165	ENSP00000295213:R197L;ENSP00000415309:R165L	ENSP00000295213:R197L	R	+	2	0	SPATA18	52632911	.	.	0.000000	0.03702	0.001000	0.01503	.	.	0.119000	0.18210	-0.156000	0.13503	CGG	.	.		0.527	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263		T	52938154	G	T	52938154	3	4	144	1	0	0	0	0	1	0	0	0	15018	1116	39	1	612	1	SPATA18	4	52938154	Missense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	37421801	52938154	138216122	22	22227										
ARL9	132946	hgsc.bcm.edu	37	chr4	57384922	57384922	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gctgatctttgtggtggattCagcagatcacagccgattac	11	9	3	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr4:57384922C>A	ENST00000360096.2	+	3	409	c.95C>A	c.(94-96)tCa>tAa	p.S32*		NM_206919.1	NP_996802.1	Q6T311	ARL9_HUMAN	ADP-ribosylation factor-like 9	96					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			lung(2)	2	Glioma(25;0.08)|all_neural(26;0.101)					GTGGTGGATTCAGCAGATCAC	0.448																																					p.S32X		Atlas-SNP	.											.	ARL9	10	.	0			c.C95A						.						172	157	162					4																	57384922		1908	4153	6061	SO:0001587	stop_gained	132946	exon3			TGGATTCAGCAGA	AY439003	CCDS59474.1	4q12	2014-05-09				ENSG00000196503		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	23592	protein-coding gene	gene with protein product		612405					Standard	NM_206919		Approved		uc003hby.1	Q6T311		ENST00000360096.2:c.95C>A	chr4.hg19:g.57384922C>A	ENSP00000353210:p.Ser32*	130.0	0.0		91.0	27.0	NM_206919		Nonsense_Mutation	SNP	ENST00000360096.2	hg19	CCDS59474.1	.	.	.	.	.	.	.	.	.	.	C	38	6.696940	0.97772	.	.	ENSG00000196503	ENST00000360096	.	.	.	5.3	5.3	0.74995	.	0.193072	0.46442	D	0.000284	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.7391	16.462	0.84059	0.0:1.0:0.0:0.0	.	.	.	.	X	96	.	ENSP00000353210:S96X	S	+	2	0	ARL9	57079679	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.008000	0.76341	2.483000	0.83821	0.462000	0.41574	TCA	.	.		0.448	ARL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467724.1	NM_206919		A	57384922	C	A	57384922	4	1	144	1	0	0	0	0	0	1	0	0	948	838	29	3	101	3	ARL9	4	57384922	Nonsense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	4446768	57384922	133769354	23	22228										
C4orf35	85438	hgsc.bcm.edu	37	chr4	71201468	71201468	+	Frame_Shift_Del	DEL	A	A	-													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	taactgcccttgaagaagagAaaataaccgaaattgaccta							TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr4:71201468delA	ENST00000273936.5	+	1	786	c.712delA	c.(712-714)aaafs	p.K238fs		NM_033122.3	NP_149113.3	Q96KC9	CABS1_HUMAN	calcium-binding protein, spermatid-specific 1	238					spermatogenesis (GO:0007283)	mitochondrial inner membrane (GO:0005743)|motile cilium (GO:0031514)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(4)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TGAAGAAGAGAAAATAACCGA	0.423																																					p.E237fs		Atlas-Indel,Pindel	.											CABS1,colon,carcinoma,0,1	CABS1	75	.	0			c.711delG						.						104	104	104					4																	71201468		2203	4300	6503	SO:0001589	frameshift_variant	85438	exon1			.	AF380838	CCDS3539.1	4q13.3	2013-10-11	2011-01-25	2011-01-25	ENSG00000145309	ENSG00000145309			30710	protein-coding gene	gene with protein product	"casein-like phosphoprotein"		"chromosome 4 open reading frame 35"	C4orf35		19208547, 19271754	Standard	NM_033122		Approved	NYD-SP26, FLJ32897, CLPH	uc003hff.3	Q96KC9	OTTHUMG00000129405	ENST00000273936.5:c.712delA	chr4.hg19:g.71201468delA	ENSP00000273936:p.Lys238fs	74.0	0.0		67.0	26.0	NM_033122	B2RCB5|Q86UE0|Q96M17	Frame_Shift_Del	DEL	ENST00000273936.5	hg19	CCDS3539.1																																																																																			.	.		0.423	CABS1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251561.3	NM_033122		-	71201468	A	-	71201468	7	5	144	1	0	1	0	1	0	0	0	0	2267	247	9	0	714	0	C4orf35	4	71201468	Frame_Shift_Del	DEL	A	TCGA-DD-A73C-01A-12D-A33K-10	13816546	71201468	119952808	24	22229										
MFSD8	256471	hgsc.bcm.edu	37	chr4	128851953	128851953	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	agtccaggcatacatatccaTtgttaatggagtaatgatgc	9	7	0	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr4:128851953T>C	ENST00000296468.3	-	10	1010	c.883A>G	c.(883-885)Atg>Gtg	p.M295V	MFSD8_ENST00000541133.1_3'UTR|MFSD8_ENST00000515130.1_5'UTR|MFSD8_ENST00000513559.1_Missense_Mutation_p.M250V	NM_152778.2	NP_689991.1	Q8NHS3	MFSD8_HUMAN	major facilitator superfamily domain containing 8	295					cell death (GO:0008219)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)				cervix(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)	23						TACATATCCATTGTTAATGGA	0.303																																					p.M295V		Atlas-SNP	.											.	MFSD8	46	.	0			c.A883G						.						92	96	95					4																	128851953		2203	4298	6501	SO:0001583	missense	256471	exon10			TATCCATTGTTAA	AK074564	CCDS3736.1	4q28.2	2014-09-17			ENSG00000164073	ENSG00000164073			28486	protein-coding gene	gene with protein product		611124	"ceroid-lipofuscinosis, neuronal 7, late infantile, variant"	CLN7		17564970	Standard	NM_152778		Approved	MGC33302	uc003ifp.3	Q8NHS3	OTTHUMG00000133303	ENST00000296468.3:c.883A>G	chr4.hg19:g.128851953T>C	ENSP00000296468:p.Met295Val	293.0	0.0		233.0	13.0	NM_152778	B2RDM1|B7Z205|Q8N2P3	Missense_Mutation	SNP	ENST00000296468.3	hg19	CCDS3736.1	.	.	.	.	.	.	.	.	.	.	T	11.61	1.690288	0.29962	.	.	ENSG00000164073	ENST00000296468;ENST00000513559	T;T	0.79845	-1.31;-1.31	4.65	3.44	0.39384	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.086307	0.85682	D	0.000000	T	0.81955	0.4932	M	0.79123	2.44	0.80722	D	1	P;P	0.36483	0.518;0.555	B;B	0.43508	0.08;0.422	T	0.77512	-0.2560	10	0.25751	T	0.34	-19.7122	11.6783	0.51442	0.0:0.0:0.1479:0.8521	.	257;295	B7Z280;Q8NHS3	.;MFSD8_HUMAN	V	295;250	ENSP00000296468:M295V;ENSP00000425000:M250V	ENSP00000296468:M295V	M	-	1	0	MFSD8	129071403	1.000000	0.71417	0.979000	0.43373	0.089000	0.18198	5.160000	0.64929	0.780000	0.33566	0.383000	0.25322	ATG	.	.		0.303	MFSD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257097.1	NM_152778		C	128851953	T	C	128851953	3	2	144	1	0	0	0	0	1	0	0	0	9547	1493	52	2	689	2	MFSD8	4	128851953	Missense_Mutation	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	57650485	128851953	62302323	25	22230										
WWC2	80014	hgsc.bcm.edu	37	chr4	184182412	184182412	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ccccgaagtctgtggcctccCtgtcctcgaggtcctccctt	9	18	1	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr4:184182412C>G	ENST00000403733.3	+	11	1835	c.1636C>G	c.(1636-1638)Ctg>Gtg	p.L546V	WWC2_ENST00000448232.2_Missense_Mutation_p.L546V|WWC2_ENST00000504005.1_Missense_Mutation_p.L228V|WWC2_ENST00000378925.3_Missense_Mutation_p.L448V|WWC2_ENST00000513834.1_Missense_Mutation_p.L546V	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	546					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TGTGGCCTCCCTGTCCTCGAG	0.602																																					p.L546V		Atlas-SNP	.											.	WWC2	78	.	0			c.C1636G						.						89	68	75					4																	184182412		2203	4300	6503	SO:0001583	missense	80014	exon11			GCCTCCCTGTCCT	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.1636C>G	chr4.hg19:g.184182412C>G	ENSP00000384222:p.Leu546Val	47.0	0.0		48.0	18.0	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	hg19	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393906	0.62066	.	.	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232;ENST00000504005	T;T;T;T;T	0.28666	2.38;1.6;2.46;2.2;2.18	4.97	4.14	0.48551	.	0.105348	0.41500	D	0.000878	T	0.56485	0.1988	M	0.86268	2.805	0.47214	D	0.999358	D;D	0.89917	0.999;1.0	D;D	0.83275	0.918;0.996	T	0.58819	-0.7569	10	0.23891	T	0.37	-9.4531	13.3408	0.60542	0.0:0.9244:0.0:0.0756	.	546;546	Q6AWC2;Q6AWC2-4	WWC2_HUMAN;.	V	546;448;546;546;228	ENSP00000384222:L546V;ENSP00000368205:L448V;ENSP00000425054:L546V;ENSP00000398577:L546V;ENSP00000427569:L228V	ENSP00000368205:L448V	L	+	1	2	WWC2	184419406	0.998000	0.40836	1.000000	0.80357	0.946000	0.59487	3.571000	0.53841	1.336000	0.45506	-0.225000	0.12378	CTG	.	.		0.602	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		G	184182412	C	G	184182412	3	3	144	1	0	0	0	0	1	0	0	0	17427	680	24	4	1678	4	WWC2	4	184182412	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	55330459	184182412	6971864	26	22231										
FAT1	2195	hgsc.bcm.edu	37	chr4	187557324	187557324	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	agggacggtttgggcttggaGatccattcaatatggagtct	14	6	2	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr4:187557324G>T	ENST00000441802.2	-	6	4247	c.4038C>A	c.(4036-4038)atC>atA	p.I1346I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1346	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TGGGCTTGGAGATCCATTCAA	0.438										HNSCC(5;0.00058)																											p.I1346I	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C4038A						.						81	79	80					4																	187557324		1926	4138	6064	SO:0001819	synonymous_variant	2195	exon6			CTTGGAGATCCAT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.4038C>A	chr4.hg19:g.187557324G>T		86.0	0.0		87.0	28.0	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.438	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187557324	G	T	187557324	2	4	144	1	0	0	0	0	0	0	0	1	5697	932	33	3		3	FAT1	4	187557324	Silent	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	3374912	187557324	3596952	27	22232										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13830842	13830842	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gcaggtccagcaggggctccCcccatgctcattcccagagc	11	17	1	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr5:13830842C>T	ENST00000265104.4	-	36	6029	c.5925G>A	c.(5923-5925)ggG>ggA	p.G1975G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1975	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.G1975G(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CAGGGGCTCCCCCCATGCTCA	0.517									Kartagener syndrome																												p.G1975G		Atlas-SNP	.											.	DNAH5	868	.	1	Substitution - coding silent(1)	lung(1)	c.G5925A						.						115	111	112					5																	13830842		2203	4300	6503	SO:0001819	synonymous_variant	1767	exon36	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGCTCCCCCCATG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.5925G>A	chr5.hg19:g.13830842C>T		50.0	0.0		56.0	19.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	hg19	CCDS3882.1																																																																																			.	.		0.517	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13830842	C	T	13830842	2	4	144	1	0	0	0	0	0	0	0	1	4606	610	22	3		3	DNAH5	5	13830842	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10		13830842	167084418	28	22233										
FYB	2533	hgsc.bcm.edu	37	chr5	39137761	39137761	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ctctttctgttcctttttctCcagctctaacctcttctttt	2	14	6	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr5:39137761C>A	ENST00000351578.6	-	7	1646	c.1456G>T	c.(1456-1458)Gag>Tag	p.E486*	FYB_ENST00000512982.1_Nonsense_Mutation_p.E486*|FYB_ENST00000505428.1_Nonsense_Mutation_p.E486*|FYB_ENST00000515010.1_Nonsense_Mutation_p.E486*|FYB_ENST00000540520.1_Nonsense_Mutation_p.E496*	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	486					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			tcctttttctccagctctaac	0.338																																					p.E496X		Atlas-SNP	.											.	FYB	354	.	0			c.G1486T						.						267	219	234					5																	39137761		934	2082	3016	SO:0001587	stop_gained	2533	exon7			TTTTCTCCAGCTC	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1456G>T	chr5.hg19:g.39137761C>A	ENSP00000316460:p.Glu486*	124.0	0.0		90.0	37.0	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Nonsense_Mutation	SNP	ENST00000351578.6	hg19	CCDS47200.1	.	.	.	.	.	.	.	.	.	.	C	37	6.248166	0.97412	.	.	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542	.	.	.	4.48	4.48	0.54585	.	0.314836	0.30538	N	0.009409	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-11.5646	12.9708	0.58511	0.0:1.0:0.0:0.0	.	.	.	.	X	486;486;486;486;496;486	.	ENSP00000316460:E486X	E	-	1	0	FYB	39173518	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.758000	0.47565	2.776000	0.95493	0.655000	0.94253	GAG	.	.		0.338	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		A	39137761	C	A	39137761	4	1	144	1	0	0	0	0	0	1	0	0	6132	864	30	3	1085	3	FYB	5	39137761	Nonsense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	25306919	39137761	141777499	29	22234										
LHFPL2	10184	hgsc.bcm.edu	37	chr5	77805629	77805629	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gcaattccttgcaacagcccAcagacattgaagatgctttt	7	11	0	3			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr5:77805629A>G	ENST00000515007.2	-	2	718	c.408T>C	c.(406-408)tgT>tgC	p.C136C	LHFPL2_ENST00000380345.2_Silent_p.C136C			Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2	136						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	6		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)		GCAACAGCCCACAGACATTGA	0.547																																					p.C136C		Atlas-SNP	.											.	LHFPL2	9	.	0			c.T408C						.						111	115	113					5																	77805629		2203	4300	6503	SO:0001819	synonymous_variant	10184	exon4			CAGCCCACAGACA	D86961	CCDS4042.1	5q13	2008-02-05			ENSG00000145685	ENSG00000145685			6588	protein-coding gene	gene with protein product		609718				10329012	Standard	NM_005779		Approved	KIAA0206	uc003kfo.3	Q6ZUX7	OTTHUMG00000107579	ENST00000515007.2:c.408T>C	chr5.hg19:g.77805629A>G		57.0	0.0		45.0	18.0	NM_005779	B2RMQ6|Q7Z5P0|Q92605	Silent	SNP	ENST00000515007.2	hg19	CCDS4042.1																																																																																			.	.		0.547	LHFPL2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369098.2	NM_005779		G	77805629	A	G	77805629	2	3	144	1	0	0	0	0	0	0	0	1	8774	157	6	2		2	LHFPL2	5	77805629	Silent	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	38667868	77805629	103109631	30	22235										
PCDHB2	56133	hgsc.bcm.edu	37	chr5	140475012	140475012	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gcagcctgagatcaggttaaCcctcacagcgctagatggcg	12	12	2	2	rs376693798		TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr5:140475012C>A	ENST00000194155.4	+	1	786	c.638C>A	c.(637-639)aCc>aAc	p.T213N		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	213	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATCAGGTTAACCCTCACAGCG	0.522																																					p.T213N		Atlas-SNP	.											.	PCDHB2	163	.	0			c.C638A						.						41	43	43					5																	140475012		2203	4300	6503	SO:0001583	missense	56133	exon1			GGTTAACCCTCAC	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"Cadherins / Protocadherins : Clustered"	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.638C>A	chr5.hg19:g.140475012C>A	ENSP00000194155:p.Thr213Asn	64.0	0.0		46.0	15.0	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	hg19	CCDS4244.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.848603	0.51164	.	.	ENSG00000112852	ENST00000194155	T	0.55052	0.54	5.42	0.512	0.16994	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.66742	0.2820	M	0.75085	2.285	0.09310	N	1	D	0.58970	0.984	D	0.63283	0.913	T	0.57888	-0.7733	9	0.87932	D	0	.	10.0225	0.42053	0.0:0.4781:0.0:0.5219	.	213	Q9Y5E7	PCDB2_HUMAN	N	213	ENSP00000194155:T213N	ENSP00000194155:T213N	T	+	2	0	PCDHB2	140455196	0.000000	0.05858	0.787000	0.31911	0.959000	0.62525	-0.903000	0.04084	-0.127000	0.11661	0.655000	0.94253	ACC	.	.		0.522	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		A	140475012	C	A	140475012	3	1	144	1	0	0	0	0	1	0	0	0	11551	507	18	3	640	3	PCDHB2	5	140475012	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	62669383	140475012	40440248	31	22236										
WWC1	23286	hgsc.bcm.edu	37	chr5	167857166	167857182	+	Frame_Shift_Del	DEL	TGCAATATTAATCATCC	TGCAATATTAATCATCC	-													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gatgagaagaataagcaattTgcaatattaatcatccagct					rs149629970		TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	TGCAATATTAATCATCC	TGCAATATTAATCATCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr5:167857166_167857182delTGCAATATTAATCATCC	ENST00000265293.4	+	14	2527_2543	c.2025_2041delTGCAATATTAATCATCC	c.(2023-2043)tttgcaatattaatcatccagfs	p.FAILIIQ675fs	WWC1_ENST00000521089.1_Frame_Shift_Del_p.FAILIIQ675fs	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	675	C2.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		ATAAGCAATTTGCAATATTAATCATCCAGCTGAGTAA	0.401																																					p.675_680del		Atlas-INDEL	.											.	WWC1	98	.	0			c.2024_2040del						.																																			SO:0001589	frameshift_variant	23286	exon14			.	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2025_2041delTGCAATATTAATCATCC	chr5.hg19:g.167857166_167857182delTGCAATATTAATCATCC	ENSP00000265293:p.Phe675fs	60.0	0.0		42.0	10.0	NM_001161662	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Frame_Shift_Del	DEL	ENST00000265293.4	hg19	CCDS4366.1																																																																																			.	.		0.401	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		-	167857182	TGCAATATTAATCATCC	-	167857166	7	5	144	1	0	1	0	1	0	0	0	0	17426	1809	63	0	2079	0	WWC1	5	167857166	Frame_Shift_Del	DEL	TGCAATATTAATCATCC	TCGA-DD-A73C-01A-12D-A33K-10	27382154	167857166	13058094	32	22237										
TRIM41	90933	hgsc.bcm.edu	37	chr5	180661549	180661549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gtggtgcgtgggcaccaacgGcaaacgctatcaggcccaga	14	12	1	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr5:180661549G>A	ENST00000315073.5	+	6	2377	c.1667G>A	c.(1666-1668)gGc>gAc	p.G556D	TRIM41_ENST00000510072.1_3'UTR|TRIM41_ENST00000351937.5_Intron	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	556	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCACCAACGGCAAACGCTAT	0.657																																					p.G556D		Atlas-SNP	.											.	TRIM41	96	.	0			c.G1667A						.						72	75	74					5																	180661549		2203	4300	6503	SO:0001583	missense	90933	exon6			CCAACGGCAAACG	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19013	protein-coding gene	gene with protein product	"RING-finger protein that interacts with C kinase"	610530	"tripartite motif-containing 41"			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.1667G>A	chr5.hg19:g.180661549G>A	ENSP00000320869:p.Gly556Asp	137.0	0.0		113.0	45.0	NM_033549	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	hg19	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.626993	0.28978	.	.	ENSG00000146063	ENST00000315073;ENST00000438174	T	0.61158	0.13	4.87	4.0	0.46444	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	D	0.000013	T	0.47469	0.1447	L	0.31804	0.96	0.38827	D	0.95576	B	0.33883	0.43	B	0.39771	0.309	T	0.51980	-0.8636	10	0.49607	T	0.09	.	9.1647	0.37043	0.0996:0.0:0.9004:0.0	.	556	Q8WV44	TRI41_HUMAN	D	556;241	ENSP00000320869:G556D	ENSP00000320869:G556D	G	+	2	0	TRIM41	180594155	1.000000	0.71417	0.970000	0.41538	0.014000	0.08584	4.931000	0.63469	1.410000	0.46936	0.455000	0.32223	GGC	.	.		0.657	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		A	180661549	G	A	180661549	3	1	144	1	0	0	0	0	1	0	0	0	16531	1203	42	3	1689	3	TRIM41	5	180661549	Missense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	12804383	180661549	253711	33	22238										
EHMT2	10919	hgsc.bcm.edu	37	chr6	31860513	31860513	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ttcctccttttggccagatcTggaagaagagagagaatggt	12	7	1	4			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr6:31860513T>A	ENST00000375537.4	-	6	674		c.e6-2		EHMT2_ENST00000375530.4_Splice_Site|EHMT2_ENST00000395728.3_Splice_Site|EHMT2_ENST00000480912.1_Splice_Site|EHMT2_ENST00000375528.4_Splice_Site	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2						DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						TGGCCAGATCTGGAAGAAGAG	0.597																																					.		Atlas-SNP	.											.	EHMT2	45	.	0			c.668-2A>T						.						83	93	90					6																	31860513		1507	2708	4215	SO:0001630	splice_region_variant	10919	exon7			CAGATCTGGAAGA	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.668-2A>T	chr6.hg19:g.31860513T>A		99.0	0.0		66.0	13.0	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Splice_Site	SNP	ENST00000375537.4	hg19	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	T	11.65	1.701718	0.30142	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537;ENST00000442298	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.1741	0.48588	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EHMT2	31968492	1.000000	0.71417	0.990000	0.47175	0.226000	0.24999	2.258000	0.43249	2.202000	0.70862	0.533000	0.62120	.	.	.		0.597	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709	Intron	A	31860513	T	A	31860513	5	1	144	1	0	0	0	0	0	0	1	0	4986	1594	55	4	3058	4	EHMT2	6	31860513	Splice_Site	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10		31860513	139254554	34	22239										
SMPD2	6610	hgsc.bcm.edu	37	chr6	109762571	109762571	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	cttccttaggggcattccgtActtgagcaagcaccgggccg	12	13	0	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr6:109762571A>T	ENST00000258052.3	+	2	421	c.62A>T	c.(61-63)tAc>tTc	p.Y21F	PPIL6_ENST00000440797.2_5'Flank|PPIL6_ENST00000521072.2_5'Flank|PPIL6_ENST00000424445.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	21					apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		GGCATTCCGTACTTGAGCAAG	0.627																																					p.Y21F		Atlas-SNP	.											.	SMPD2	25	.	0			c.A62T						.						53	61	58					6																	109762571		2203	4300	6503	SO:0001583	missense	6610	exon2			TTCCGTACTTGAG	AJ222801	CCDS5075.1	6q21	2009-10-23			ENSG00000135587	ENSG00000135587	3.1.4.12		11121	protein-coding gene	gene with protein product		603498				9520418	Standard	XM_005267109		Approved	nSMase, ISC1	uc003pti.3	O60906	OTTHUMG00000015348	ENST00000258052.3:c.62A>T	chr6.hg19:g.109762571A>T	ENSP00000258052:p.Tyr21Phe	68.0	0.0		52.0	20.0	NM_003080	Q5TED1|Q9BWR3	Missense_Mutation	SNP	ENST00000258052.3	hg19	CCDS5075.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.710207	0.48517	.	.	ENSG00000135587	ENST00000258052	T	0.29917	1.55	5.76	5.76	0.90799	Endonuclease/exonuclease/phosphatase (2);	0.057454	0.64402	D	0.000001	T	0.22975	0.0555	N	0.16743	0.435	0.52099	D	0.999945	B;D	0.76494	0.001;0.999	B;D	0.85130	0.013;0.997	T	0.11446	-1.0587	10	0.14656	T	0.56	-17.0373	12.4555	0.55702	1.0:0.0:0.0:0.0	.	21;21	B2R8U8;O60906	.;NSMA_HUMAN	F	21	ENSP00000258052:Y21F	ENSP00000258052:Y21F	Y	+	2	0	SMPD2	109869264	0.992000	0.36948	0.959000	0.39883	0.373000	0.29922	1.815000	0.38981	2.197000	0.70478	0.533000	0.62120	TAC	.	.		0.627	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1			T	109762571	A	T	109762571	3	4	144	1	0	0	0	0	1	0	0	0	14820	391	14	4	68	4	SMPD2	6	109762571	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	77902058	109762571	61352496	35	22240										
TAAR2	9287	hgsc.bcm.edu	37	chr6	132938436	132938436	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	catgtggagttaaaatagccAaaccatgtcaaggcatcaaa	8	8	2	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr6:132938436A>G	ENST00000367931.1	-	2	908	c.909T>C	c.(907-909)ttT>ttC	p.F303F	TAAR2_ENST00000537809.1_Silent_p.F258F|TAAR2_ENST00000275191.2_Silent_p.F258F			Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2	303					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)	23	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		TAAAATAGCCAAACCATGTCA	0.348																																					p.F303F		Atlas-SNP	.											.	TAAR2	45	.	0			c.T909C						.						67	61	63					6																	132938436		2203	4300	6503	SO:0001819	synonymous_variant	9287	exon2			ATAGCCAAACCAT	AF112460	CCDS34541.1, CCDS5157.1	6q24	2012-08-08	2005-02-23	2005-02-24	ENSG00000146378	ENSG00000146378		"GPCR / Class A : Trace amine associated receptors"	4514	protein-coding gene	gene with protein product		604849	"G protein-coupled receptor 58"	GPR58		10684976, 15718104	Standard	NM_014626		Approved		uc003qdl.1	Q9P1P5	OTTHUMG00000015585	ENST00000367931.1:c.909T>C	chr6.hg19:g.132938436A>G		203.0	0.0		136.0	46.0	NM_001033080	Q5QD02|Q6NWS1|Q6NWS2|Q6NWS3	Silent	SNP	ENST00000367931.1	hg19	CCDS34541.1																																																																																			.	.		0.348	TAAR2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390735.1	NM_014626		G	132938436	A	G	132938436	2	3	144	1	0	0	0	0	0	0	0	1	15505	127	5	2		2	TAAR2	6	132938436	Silent	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	23175865	132938436	38176631	36	22241										
OPRM1	4988	hgsc.bcm.edu	37	chr6	154360707	154360708	+	Missense_Mutation	DNP	GC	GC	TT													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gcagcgctgcccccacgaacGccagcaattgcactgatgcc							TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr6:154360707_154360708GC>TT	ENST00000330432.7	+	1	265_266	c.28_29GC>TT	c.(28-30)GCc>TTc	p.A10F	OPRM1_ENST00000428397.2_Missense_Mutation_p.A10F|OPRM1_ENST00000435918.2_Missense_Mutation_p.A10F|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000452687.2_Missense_Mutation_p.A10F|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000414028.2_Missense_Mutation_p.A10F|OPRM1_ENST00000419506.2_Missense_Mutation_p.A10F|OPRM1_ENST00000337049.4_Missense_Mutation_p.A10F|OPRM1_ENST00000434900.2_Missense_Mutation_p.A103F|OPRM1_ENST00000523520.1_3'UTR|OPRM1_ENST00000360422.4_Missense_Mutation_p.A10F|OPRM1_ENST00000229768.5_Missense_Mutation_p.A10F|OPRM1_ENST00000524163.1_Missense_Mutation_p.A10F	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1	10					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CCCCACGAACGCCAGCAATTGC	0.634																																					p.A103S|p.A103V		Atlas-SNP	.											.	OPRM1	241	.	0			c.G307T|c.C308T						.																																			SO:0001583	missense	4988	exon3			ACGAACGCCAGCA|CGAACGCCAGCAA	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	Exception_encountered	chr6.hg19:g.154360707_154360708delinsTT	ENSP00000328264:p.Ala10Phe	83.0	0.0		103.0	38.0|40.0	NM_001145279	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	hg19	CCDS55070.1																																																																																			.	.		0.634	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		TT	154360708	GC	TT	154360707	3	4	144	1	0	0	0	0	1	0	0	0	10896	1087	38	1	364	1	OPRM1	6	154360707	Missense_Mutation	DNP	GC	TCGA-DD-A73C-01A-12D-A33K-10	21422271	154360707	16754360	37	22242										
TMEM184A	202915	hgsc.bcm.edu	37	chr7	1589783	1589783	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ttacagaagcgcaggaacccGatggagtaggtcatgccccg	13	11	1	1	rs139449337	byFrequency	TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr7:1589783G>T	ENST00000297477.5	-	5	844	c.528C>A	c.(526-528)atC>atA	p.I176I		NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	176					germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)		p.I176I(1)		endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		GCAGGAACCCGATGGAGTAGG	0.721																																					p.I176I		Atlas-SNP	.											.	TMEM184A	35	.	1	Substitution - coding silent(1)	lung(1)	c.C528A						.						12	15	14					7																	1589783		2098	4238	6336	SO:0001819	synonymous_variant	202915	exon5			GAACCCGATGGAG		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.528C>A	chr7.hg19:g.1589783G>T		38.0	0.0		29.0	12.0	NM_001097620	Q8TBQ6	Silent	SNP	ENST00000297477.5	hg19	CCDS43537.1																																																																																			.	G|0.997;A|0.003		0.721	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689		T	1589783	G	T	1589783	2	4	144	1	0	0	0	0	0	0	0	1	16119	1048	37	1		1	TMEM184A	7	1589783	Silent	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10		1589783	157548880	38	22243										
C7orf10	79783	hgsc.bcm.edu	37	chr7	40535937	40535937	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ctttttgaaggcagtggagtCccgtatggcccaatcaacaa	10	10	1	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr7:40535937C>A	ENST00000335693.4	+	12	1085	c.1062C>A	c.(1060-1062)gtC>gtA	p.V354V	C7orf10_ENST00000309930.5_Silent_p.V354V|C7orf10_ENST00000401647.2_Silent_p.V306V	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		354					metabolic process (GO:0008152)	mitochondrion (GO:0005739)	succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369)			endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)	18						GCAGTGGAGTCCCGTATGGCC	0.378																																					p.V354V		Atlas-SNP	.											.	C7orf10	99	.	0			c.C1062A						.						113	108	110					7																	40535937		1860	4105	5965	SO:0001819	synonymous_variant	79783	exon12			TGGAGTCCCGTAT																												ENST00000335693.4:c.1062C>A	chr7.hg19:g.40535937C>A		78.0	0.0		76.0	24.0	NM_001193313	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	Silent	SNP	ENST00000335693.4	hg19	CCDS55105.1	.	.	.	.	.	.	.	.	.	.	C	5.016	0.188720	0.09547	.	.	ENSG00000175600	ENST00000416370	.	.	.	5.42	1.31	0.21738	.	.	.	.	.	T	0.41396	0.1157	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25363	-1.0134	4	.	.	.	-5.3029	0.3937	0.00415	0.185:0.2925:0.1825:0.3399	.	.	.	.	Y	349	.	.	S	+	2	0	C7orf10	40502462	0.904000	0.30761	0.176000	0.23000	0.620000	0.37586	-0.217000	0.09253	0.183000	0.20059	-0.175000	0.13238	TCC	.	.		0.378	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338388.1			A	40535937	C	A	40535937	2	1	144	1	0	0	0	0	0	0	0	1	2378	842	30	3		3	C7orf10	7	40535937	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	38946154	40535937	118602726	39	22244										
PDK4	5166	hgsc.bcm.edu	37	chr7	95216812	95216812	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	agaggcggtcaataattctcAggggaacaccacctcctctg	10	12	3	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr7:95216812A>C	ENST00000005178.5	-	9	1096	c.899T>G	c.(898-900)cTg>cGg	p.L300R		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	300	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			AATAATTCTCAGGGGAACACC	0.388																																					p.L300R		Atlas-SNP	.											.	PDK4	42	.	0			c.T899G						.						77	79	78					7																	95216812		2203	4300	6503	SO:0001583	missense	5166	exon9			ATTCTCAGGGGAA	U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"pyruvate dehydrogenase kinase, isoenzyme 4"			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.899T>G	chr7.hg19:g.95216812A>C	ENSP00000005178:p.Leu300Arg	117.0	0.0		126.0	32.0	NM_002612		Missense_Mutation	SNP	ENST00000005178.5	hg19	CCDS5643.1	.	.	.	.	.	.	.	.	.	.	A	15.48	2.847315	0.51164	.	.	ENSG00000004799	ENST00000005178;ENST00000542888	T	0.54279	0.58	5.61	5.61	0.85477	Signal transduction histidine kinase, core (1);ATPase-like, ATP-binding domain (4);	0.066915	0.64402	D	0.000010	T	0.28366	0.0701	N	0.02225	-0.63	0.80722	D	1	B	0.12630	0.006	B	0.17979	0.02	T	0.19321	-1.0309	10	0.13470	T	0.59	.	16.1127	0.81273	1.0:0.0:0.0:0.0	.	300	Q16654	PDK4_HUMAN	R	300;264	ENSP00000005178:L300R	ENSP00000005178:L300R	L	-	2	0	PDK4	95054748	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.332000	0.96446	2.270000	0.75569	0.482000	0.46254	CTG	.	.		0.388	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612		C	95216812	A	C	95216812	3	2	144	1	0	0	0	0	1	0	0	0	11687	188	7	5	348	5	PDK4	7	95216812	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	54680875	95216812	63921851	40	22245										
MLL5	55904	hgsc.bcm.edu	37	chr7	104753453	104753453	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	catcaaggacctccacttttTccttcgagtgctcatccaac	5	15	2	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr7:104753453T>G	ENST00000311117.3	+	27	5795	c.5250T>G	c.(5248-5250)ttT>ttG	p.F1750L	KMT2E_ENST00000334877.4_Missense_Mutation_p.F1708L|SRPK2_ENST00000493638.1_Intron|KMT2E_ENST00000257745.4_Missense_Mutation_p.F1750L	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1750	Pro-rich. {ECO:0000255}.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										CTCCACTTTTTCCTTCGAGTG	0.562																																					p.F1750L		Atlas-SNP	.											.	MLL5	173	.	0			c.T5250G						.						277	217	237					7																	104753453		2203	4300	6503	SO:0001583	missense	55904	exon26			ACTTTTTCCTTCG	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.5250T>G	chr7.hg19:g.104753453T>G	ENSP00000312379:p.Phe1750Leu	229.0	0.0		264.0	72.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	10.31|10.31	1.315469|1.315469	0.23908|0.23908	.|.	.|.	ENSG00000005483|ENSG00000005483	ENST00000393656|ENST00000311117;ENST00000334877;ENST00000351043;ENST00000257745	.|D;D;D	.|0.94046	.|-3.34;-3.32;-3.34	3.94|3.94	-3.09|-3.09	0.05331|0.05331	.|.	0.000000|0.000000	0.45126|0.45126	D|D	0.000398|0.000398	D|D	0.90407|0.90407	0.6997|0.6997	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|D;P	.|0.67145	.|0.996;0.956	.|D;D	.|0.70935	.|0.971;0.931	D|D	0.85509|0.85509	0.1196|0.1196	7|10	0.87932|0.12103	D|T	0|0.63	.|.	11.913|11.913	0.52749|0.52749	0.0:0.5905:0.0:0.4095|0.0:0.5905:0.0:0.4095	.|.	.|1670;1750	.|F8W6H1;Q8IZD2	.|.;MLL5_HUMAN	C|L	1533|1750;1708;1670;1750	.|ENSP00000312379:F1750L;ENSP00000335599:F1708L;ENSP00000257745:F1750L	ENSP00000377266:F1533C|ENSP00000257745:F1750L	F|F	+|+	2|3	0|2	MLL5|MLL5	104540689|104540689	0.388000|0.388000	0.25197|0.25197	0.779000|0.779000	0.31741|0.31741	0.695000|0.695000	0.40330|0.40330	-0.688000|-0.688000	0.05150|0.05150	-0.551000|-0.551000	0.06175|0.06175	0.373000|0.373000	0.22412|0.22412	TTC|TTT	.	.		0.562	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			G	104753453	T	G	104753453	3	3	144	1	0	0	0	0	1	0	0	0	9633	1780	62	5	5348	5	MLL5	7	104753453	Missense_Mutation	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	9536641	104753453	54385210	41	22246										
TRPV6	55503	hgsc.bcm.edu	37	chr7	142574898	142574899	+	Frame_Shift_Del	DEL	AG	AG	-													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	cccagccctgctctcaccaaAgtagatgaggttgcagggac					rs200244204	byFrequency	TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr7:142574898_142574899delAG	ENST00000359396.3	-	4	728_729	c.483_484delCT	c.(481-486)tactttfs	p.F162fs	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	162					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					ctctCACCAAAGTAGATGAGGT	0.624																																					p.162_162del		Atlas-Indel,Pindel	.											.	TRPV6	108	.	0			c.484_485del						.																																			SO:0001589	frameshift_variant	55503	exon4			.	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.483_484delCT	chr7.hg19:g.142574898_142574899delAG	ENSP00000352358:p.Phe162fs	78.0	0.0		75.0	39.0	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Frame_Shift_Del	DEL	ENST00000359396.3	hg19	CCDS5874.1																																																																																			.	.		0.624	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		-	142574899	AG	-	142574898	7	5	144	1	0	1	0	1	0	0	0	0	16615	72	3	0	1741	0	TRPV6	7	142574898	Frame_Shift_Del	DEL	AG	TCGA-DD-A73C-01A-12D-A33K-10	37821445	142574898	16563765	42	22247										
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24254788	24254788	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ctctatatctcccagaggatActtcacacatcatcaccaaa	3	14	5	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr8:24254788A>G	ENST00000256412.4	+	6	666	c.446A>G	c.(445-447)tAc>tGc	p.Y149C	ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.Y70C|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.Y70C|RP11-624C23.1_ENST00000519689.1_RNA	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	149					immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		CCCAGAGGATACTTCACACAT	0.423																																					p.Y149C	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.A446G						.						95	94	94					8																	24254788		2203	4300	6503	SO:0001583	missense	27299	exon6			GAGGATACTTCAC	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.446A>G	chr8.hg19:g.24254788A>G	ENSP00000256412:p.Tyr149Cys	87.0	0.0		38.0	22.0	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	hg19	CCDS6044.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.451912	0.43531	.	.	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.06068	3.35;3.35;3.35	5.56	2.83	0.33086	Peptidase M12B, propeptide (1);	0.467917	0.20238	N	0.096339	T	0.20618	0.0496	M	0.77616	2.38	0.28169	N	0.928638	D	0.71674	0.998	D	0.67231	0.95	T	0.01829	-1.1265	10	0.87932	D	0	-12.8218	8.698	0.34307	0.6808:0.0:0.0:0.3192	.	149	O15204	ADEC1_HUMAN	C	149;70;70	ENSP00000256412:Y149C;ENSP00000442592:Y70C;ENSP00000428993:Y70C	ENSP00000256412:Y149C	Y	+	2	0	ADAMDEC1	24310733	0.771000	0.28555	0.996000	0.52242	0.524000	0.34500	1.056000	0.30480	0.907000	0.36646	0.455000	0.32223	TAC	.	.		0.423	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		G	24254788	A	G	24254788	3	3	144	1	0	0	0	0	1	0	0	0	254	391	14	2	468	2	ADAMDEC1	8	24254788	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10		24254788	122109234	43	22248										
RAD54B	25788	hgsc.bcm.edu	37	chr8	95404076	95404077	+	Frame_Shift_Del	DEL	CA	CA	-													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tcttctaaggataaagagtcCagtgaggcaagtaagttcag							TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr8:95404076_95404077delCA	ENST00000336148.5	-	10	1693_1694	c.1569_1570delTG	c.(1567-1572)actggafs	p.G524fs		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	524					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			ATAAAGAGTCCAGTGAGGCAAG	0.361								Direct reversal of damage;Homologous recombination																													p.524_524del		Atlas-Indel,Pindel	.											.	RAD54B	88	.	0			c.1570_1571del						.																																			SO:0001589	frameshift_variant	25788	exon10			.	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.1569_1570delTG	chr8.hg19:g.95404076_95404077delCA	ENSP00000336606:p.Gly524fs	72.0	0.0		47.0	19.0	NM_012415	F6WBS8	Frame_Shift_Del	DEL	ENST00000336148.5	hg19	CCDS6262.1																																																																																			.	.		0.361	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		-	95404077	CA	-	95404076	7	5	144	1	0	1	0	1	0	0	0	0	13007	603	21	0	1186	0	RAD54B	8	95404076	Frame_Shift_Del	DEL	CA	TCGA-DD-A73C-01A-12D-A33K-10	71149288	95404076	50959946	44	22249										
IFNE	338376	hgsc.bcm.edu	37	chr9	21481103	21481103	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	aactctgtagtaagctcttgCttcatgtcgttcaagggtct	9	9	5	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr9:21481103C>T	ENST00000448696.3	-	1	1209	c.591G>A	c.(589-591)aaG>aaA	p.K197K	MIR31HG_ENST00000304425.3_RNA	NM_176891.4	NP_795372.1	Q86WN2	IFNE_HUMAN	interferon, epsilon	197					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(2)|lung(1)|skin(1)	4						TAAGCTCTTGCTTCATGTCGT	0.438																																					p.K197K		Atlas-SNP	.											.	IFNE	16	.	0			c.G591A						.						105	107	107					9																	21481103		2203	4300	6503	SO:0001819	synonymous_variant	338376	exon1			CTCTTGCTTCATG	AY190045	CCDS34997.1	9p21.1	2008-12-12			ENSG00000184995	ENSG00000184995			18163	protein-coding gene	gene with protein product		615223				15546383, 17287131	Standard	NM_176891		Approved	IFNE1	uc003zpg.3	Q86WN2	OTTHUMG00000019672	ENST00000448696.3:c.591G>A	chr9.hg19:g.21481103C>T		110.0	0.0		77.0	25.0	NM_176891		Silent	SNP	ENST00000448696.3	hg19	CCDS34997.1																																																																																			.	.		0.438	IFNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051901.2	NM_176891		T	21481103	C	T	21481103	2	4	144	1	0	0	0	0	0	0	0	1	7556	796	28	3		3	IFNE	9	21481103	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10		21481103	119732328	45	22250										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32543942	32543942	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tgttcacaggaccactaggtGaatacacagaagcatttcgt	9	9	1	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr9:32543942G>C	ENST00000360538.2	-	3	697	c.581C>G	c.(580-582)tCa>tGa	p.S194*	TOPORS_ENST00000379858.1_Nonsense_Mutation_p.S129*	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	194	E3 ubiquitin-protein ligase activity.|Required for DNA-binding.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		ACCACTAGGTGAATACACAGA	0.438																																					p.S194X		Atlas-SNP	.											.	TOPORS	127	.	0			c.C581G						.						124	109	114					9																	32543942		2203	4300	6503	SO:0001587	stop_gained	10210	exon3			CTAGGTGAATACA	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.581C>G	chr9.hg19:g.32543942G>C	ENSP00000353735:p.Ser194*	102.0	0.0		106.0	32.0	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Nonsense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.628081	0.46944	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	.	.	.	5.6	3.65	0.41850	.	0.364657	0.20326	N	0.094535	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-1.2053	10.3422	0.43884	0.0753:0.1356:0.789:0.0	.	.	.	.	X	194;129	.	ENSP00000353735:S194X	S	-	2	0	TOPORS	32533942	0.965000	0.33210	0.999000	0.59377	0.015000	0.08874	4.413000	0.59795	1.515000	0.48885	-0.140000	0.14226	TCA	.	.		0.438	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		C	32543942	G	C	32543942	4	2	144	1	0	0	0	0	0	1	0	0	16385	1294	45	4	2560	4	TOPORS	9	32543942	Nonsense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	11062839	32543942	108669489	46	22251										
C9orf84	158401	hgsc.bcm.edu	37	chr9	114469021	114469021	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tatgtacaactacacaggaaCttgtactaaagacaaaagag	7	7	0	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr9:114469021C>G	ENST00000318737.4	-	18	2500	c.2372G>C	c.(2371-2373)aGt>aCt	p.S791T	C9orf84_ENST00000394777.4_Missense_Mutation_p.S717T|C9orf84_ENST00000374287.3_Missense_Mutation_p.S791T|C9orf84_ENST00000394779.3_Missense_Mutation_p.S752T	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	791										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TACACAGGAACTTGTACTAAA	0.348																																					p.S791T		Atlas-SNP	.											.	C9orf84	207	.	0			c.G2372C						.						98	109	105					9																	114469021		2203	4299	6502	SO:0001583	missense	158401	exon18			CAGGAACTTGTAC	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.2372G>C	chr9.hg19:g.114469021C>G	ENSP00000322108:p.Ser791Thr	52.0	0.0		39.0	11.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	hg19	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	C	11.75	1.732339	0.30684	.	.	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.04502	3.61;3.61;3.61;3.61	4.84	1.9	0.25705	.	0.462533	0.20560	N	0.089936	T	0.03827	0.0108	L	0.27053	0.805	0.09310	N	0.999998	B;P;P	0.41848	0.358;0.763;0.557	B;B;B	0.42282	0.152;0.382;0.366	T	0.38929	-0.9638	10	0.40728	T	0.16	0.0914	4.3985	0.11374	0.1508:0.5227:0.0:0.3265	.	717;791;752	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	T	752;717;405;791;791	ENSP00000378259:S752T;ENSP00000378257:S717T;ENSP00000363405:S791T;ENSP00000322108:S791T	ENSP00000322108:S791T	S	-	2	0	C9orf84	113508842	0.968000	0.33430	0.231000	0.23993	0.883000	0.51084	0.719000	0.25881	0.093000	0.17368	-0.518000	0.04402	AGT	.	.		0.348	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		G	114469021	C	G	114469021	3	3	144	1	0	0	0	0	1	0	0	0	2502	565	20	4	1998	4	C9orf84	9	114469021	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	81925079	114469021	26744410	47	22252										
MCM10	55388	hgsc.bcm.edu	37	chr10	13234349	13234349	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	aacttaaaacaacatttagcCaaagccacagcttcaggtac	5	11	1	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr10:13234349C>G	ENST00000484800.2	+	12	1717	c.1614C>G	c.(1612-1614)gcC>gcG	p.A538A	MCM10_ENST00000378694.1_Silent_p.A537A|MCM10_ENST00000378714.3_Silent_p.A537A			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	538					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						AACATTTAGCCAAAGCCACAG	0.552																																					p.A538A		Atlas-SNP	.											.	MCM10	76	.	0			c.C1614G						.						147	116	127					10																	13234349		2203	4300	6503	SO:0001819	synonymous_variant	55388	exon12			TTTAGCCAAAGCC	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.1614C>G	chr10.hg19:g.13234349C>G		75.0	0.0		77.0	24.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Silent	SNP	ENST00000484800.2	hg19	CCDS7096.1																																																																																			.	.		0.552	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		G	13234349	C	G	13234349	2	3	144	1	0	0	0	0	0	0	0	1	9394	581	21	4		4	MCM10	10	13234349	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10		13234349	122300398	48	22253										
AP3M1	26985	hgsc.bcm.edu	37	chr10	75896531	75896531	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tatgaccacattatccttaaTtgcagcctctgaacactcac	4	13	2	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr10:75896531T>C	ENST00000355264.4	-	3	615	c.304A>G	c.(304-306)Att>Gtt	p.I102V	AP3M1_ENST00000372745.1_Missense_Mutation_p.I102V|AP3M1_ENST00000487653.1_5'Flank	NM_012095.4	NP_036227.1	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit	102					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|protein targeting to lysosome (GO:0006622)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	Rab GTPase binding (GO:0017137)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	13	Prostate(51;0.0112)					TTATCCTTAATTGCAGCCTCT	0.348																																					p.I102V		Atlas-SNP	.											.	AP3M1	28	.	0			c.A304G						.						105	97	100					10																	75896531		2203	4300	6503	SO:0001583	missense	26985	exon4			CCTTAATTGCAGC	AF092092	CCDS7342.1	10q22.1-q22.3	2008-07-07			ENSG00000185009	ENSG00000185009			569	protein-coding gene	gene with protein product		610366				10024875	Standard	NM_207012		Approved		uc001jwh.3	Q9Y2T2	OTTHUMG00000018497	ENST00000355264.4:c.304A>G	chr10.hg19:g.75896531T>C	ENSP00000347408:p.Ile102Val	118.0	0.0		108.0	39.0	NM_207012	Q5JQ12|Q9H5L2	Missense_Mutation	SNP	ENST00000355264.4	hg19	CCDS7342.1	.	.	.	.	.	.	.	.	.	.	T	16.48	3.134462	0.56828	.	.	ENSG00000185009	ENST00000355264;ENST00000372745	D;D	0.81739	-1.53;-1.53	5.88	4.75	0.60458	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	T	0.77611	0.4156	L	0.52823	1.66	0.58432	D	0.999999	B	0.20550	0.046	B	0.30495	0.116	T	0.71859	-0.4465	10	0.36615	T	0.2	.	11.7276	0.51718	0.0:0.0685:0.0:0.9315	.	102	Q9Y2T2	AP3M1_HUMAN	V	102	ENSP00000347408:I102V;ENSP00000361831:I102V	ENSP00000347408:I102V	I	-	1	0	AP3M1	75566537	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.755000	0.62198	1.060000	0.40578	0.533000	0.62120	ATT	.	.		0.348	AP3M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048747.1			C	75896531	T	C	75896531	3	2	144	1	0	0	0	0	1	0	0	0	747	1493	52	2	980	2	AP3M1	10	75896531	Missense_Mutation	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	62662182	75896531	59638216	49	22254										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124352076	124352076	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tggctggctctcccacaactGtggccatcatgaagatgctg	11	12	2	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr10:124352076G>C	ENST00000338354.3	+	20	2571	c.2465G>C	c.(2464-2466)tGt>tCt	p.C822S	DMBT1_ENST00000344338.3_Missense_Mutation_p.C812S|DMBT1_ENST00000368955.3_Missense_Mutation_p.C812S|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000368909.3_Missense_Mutation_p.C822S			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	822	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TCCCACAACTGTGGCCATCAT	0.567																																					p.C822S	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G2465C						.						109	80	89					10																	124352076		1957	4088	6045	SO:0001583	missense	1755	exon20			ACAACTGTGGCCA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.2465G>C	chr10.hg19:g.124352076G>C	ENSP00000342210:p.Cys822Ser	57.0	0.0		61.0	21.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	G	11.54	1.669804	0.29693	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	3.49	3.49	0.39957	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.81307	0.4795	H	0.99347	4.525	0.80722	D	1	D;P;D;D	0.89917	1.0;0.907;1.0;1.0	D;B;D;D	0.91635	0.999;0.395;0.999;0.999	D	0.89689	0.3896	9	0.66056	D	0.02	.	15.3348	0.74244	0.0:0.0:1.0:0.0	.	583;822;812;822	Q9UGM3-4;Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	S	822;822;822;822;822;822;812;822;812	ENSP00000342210:C822S;ENSP00000343175:C812S;ENSP00000357905:C822S;ENSP00000357951:C812S	ENSP00000342210:C822S	C	+	2	0	DMBT1	124342066	1.000000	0.71417	0.764000	0.31436	0.012000	0.07955	7.487000	0.81328	1.660000	0.50760	0.655000	0.94253	TGT	.	.		0.567	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		C	124352076	G	C	124352076	3	2	144	1	0	0	0	0	1	0	0	0	4579	1377	48	4	2543	4	DMBT1	10	124352076	Missense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	48455545	124352076	11182671	50	22255										
SYT9	143425	hgsc.bcm.edu	37	chr11	7335070	7335070	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tacgactttgacaggttctcTcgtcatgacttaatcggcca	8	11	2	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr11:7335070T>C	ENST00000318881.6	+	3	1179	c.942T>C	c.(940-942)tcT>tcC	p.S314S	SYT9_ENST00000396716.2_Silent_p.S282S	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	314	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		ACAGGTTCTCTCGTCATGACT	0.463																																					p.S314S		Atlas-SNP	.											.	SYT9	91	.	0			c.T942C						.						190	189	189					11																	7335070		2201	4296	6497	SO:0001819	synonymous_variant	143425	exon3			GTTCTCTCGTCAT	AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.942T>C	chr11.hg19:g.7335070T>C		84.0	0.0		77.0	30.0	NM_175733		Silent	SNP	ENST00000318881.6	hg19	CCDS7778.1																																																																																			.	.		0.463	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		C	7335070	T	C	7335070	2	2	144	1	0	0	0	0	0	0	0	1	15496	1538	54	2		2	SYT9	11	7335070	Silent	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10		7335070	127671446	51	22256										
GYLTL1B	120071	hgsc.bcm.edu	37	chr11	45948990	45948990	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	cctcaccagtgcttgctgccCggcaggacgtggcctaccat	11	16	1	0	rs148997856		TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr11:45948990C>T	ENST00000531526.1	+	11	1561	c.1450C>T	c.(1450-1452)Cgg>Tgg	p.R484W	GYLTL1B_ENST00000401752.1_Missense_Mutation_p.R484W|GYLTL1B_ENST00000389968.3_Missense_Mutation_p.R211W|GYLTL1B_ENST00000529052.1_Missense_Mutation_p.R453W|GYLTL1B_ENST00000325468.5_Missense_Mutation_p.R484W|GYLTL1B_ENST00000536139.1_Missense_Mutation_p.R453W	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	484					muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		GCTTGCTGCCCGGCAGGACGT	0.637																																					p.R484W		Atlas-SNP	.											.	GYLTL1B	45	.	0			c.C1450T						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	101	87	92		1450	4.8	1	11	dbSNP_134	92	0,8598		0,0,4299	no	missense	GYLTL1B	NM_152312.3	101	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	484/722	45948990	1,13003	2203	4299	6502	SO:0001583	missense	120071	exon11			GCTGCCCGGCAGG		CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"Glycosyltransferase family 8 domain containing"	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.1450C>T	chr11.hg19:g.45948990C>T	ENSP00000432869:p.Arg484Trp	105.0	0.0		102.0	6.0	NM_152312	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Missense_Mutation	SNP	ENST00000531526.1	hg19	CCDS31473.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888973	0.91814	2.27E-4	0.0	ENSG00000165905	ENST00000529052;ENST00000531526;ENST00000401752;ENST00000389968;ENST00000325468;ENST00000536139	T;T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71;1.71	5.76	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.59280	0.2182	M	0.90814	3.15	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.998	T	0.70059	-0.4976	10	0.87932	D	0	-35.7757	15.7478	0.77958	0.1415:0.8585:0.0:0.0	.	453;453;484	B3KP69;E9PIZ2;Q8N3Y3	.;.;LARG2_HUMAN	W	453;484;484;211;484;453	ENSP00000431932:R453W;ENSP00000432869:R484W;ENSP00000385235:R484W;ENSP00000374618:R211W;ENSP00000324570:R484W;ENSP00000445044:R453W	ENSP00000324570:R484W	R	+	1	2	GYLTL1B	45905566	1.000000	0.71417	0.984000	0.44739	0.918000	0.54935	4.574000	0.60900	1.378000	0.46305	0.563000	0.77884	CGG	.	C|1.000;T|0.000		0.637	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312		T	45948990	C	T	45948990	3	4	144	1	0	0	0	0	1	0	0	0	6916	643	23	1	1488	1	GYLTL1B	11	45948990	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	38613920	45948990	89057526	52	22257										
LRP4	4038	hgsc.bcm.edu	37	chr11	46880821	46880821	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	agacaggaggcagattccctCtacgatcttgatcttctcct	8	12	4	3			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr11:46880821C>A	ENST00000378623.1	-	38	5673	c.5431G>T	c.(5431-5433)Gag>Tag	p.E1811*	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1811					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		CAGATTCCCTCTACGATCTTG	0.547																																					p.E1811X		Atlas-SNP	.											.	LRP4	160	.	0			c.G5431T						.						152	142	145					11																	46880821		2201	4299	6500	SO:0001587	stop_gained	4038	exon38			TTCCCTCTACGAT	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.5431G>T	chr11.hg19:g.46880821C>A	ENSP00000367888:p.Glu1811*	88.0	0.0		82.0	25.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Nonsense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	C	47	13.226188	0.99728	.	.	ENSG00000134569	ENST00000378623	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.0953	0.97838	0.0:1.0:0.0:0.0	.	.	.	.	X	1811	.	ENSP00000367888:E1811X	E	-	1	0	LRP4	46837397	1.000000	0.71417	0.994000	0.49952	0.862000	0.49288	7.461000	0.80834	2.767000	0.95098	0.655000	0.94253	GAG	.	.		0.547	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		A	46880821	C	A	46880821	4	1	144	1	0	0	0	0	0	1	0	0	8968	922	32	3	290	3	LRP4	11	46880821	Nonsense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	931831	46880821	88125695	53	22258										
NRXN2	9379	hgsc.bcm.edu	37	chr11	64434903	64434903	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ctgtggctgccagctccaccCccagcccgccggccctggct	11	21	0	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr11:64434903C>T	ENST00000377551.1	-	8	1828	c.1617G>A	c.(1615-1617)ggG>ggA	p.G539G	NRXN2_ENST00000377559.3_Silent_p.G508G|NRXN2_ENST00000409571.1_Silent_p.G532G|NRXN2_ENST00000265459.6_Silent_p.G539G			Q9P2S2	NRX2A_HUMAN	neurexin 2	539	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						CAGCTCCACCCCCAGCCCGCC	0.652																																					p.G539G		Atlas-SNP	.											.	NRXN2	247	.	0			c.G1617A						.						47	51	50					11																	64434903		2201	4297	6498	SO:0001819	synonymous_variant	9379	exon9			TCCACCCCCAGCC		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"neurexin II"	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.1617G>A	chr11.hg19:g.64434903C>T		71.0	0.0		70.0	6.0	NM_015080	A7E2C1|Q9Y2D6	Silent	SNP	ENST00000377551.1	hg19	CCDS8077.1																																																																																			.	.		0.652	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		T	64434903	C	T	64434903	2	4	144	1	0	0	0	0	0	0	0	1	10675	610	22	3		3	NRXN2	11	64434903	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	17554082	64434903	70571613	54	22259										
RELA	5970	hgsc.bcm.edu	37	chr11	65423177	65423177	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	acctggcttggggacagaagCtgagctgcgggaaggcacag	17	9	0	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr11:65423177C>T	ENST00000406246.3	-	10	1276	c.1015G>A	c.(1015-1017)Gct>Act	p.A339T	RELA_ENST00000525693.1_Missense_Mutation_p.A339T|RELA_ENST00000308639.9_Missense_Mutation_p.A336T	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	339					acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						GGGACAGAAGCTGAGCTGCGG	0.607																																					p.A339T		Atlas-SNP	.											.	RELA	44	.	0			c.G1015A						.						80	76	77					11																	65423177		2201	4297	6498	SO:0001583	missense	5970	exon10			CAGAAGCTGAGCT	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1015G>A	chr11.hg19:g.65423177C>T	ENSP00000384273:p.Ala339Thr	55.0	0.0		42.0	14.0	NM_021975	Q6GTV1|Q6SLK1	Missense_Mutation	SNP	ENST00000406246.3	hg19	CCDS31609.1	.	.	.	.	.	.	.	.	.	.	C	1.246	-0.619830	0.03636	.	.	ENSG00000173039	ENST00000406246;ENST00000525693;ENST00000308639;ENST00000545816;ENST00000532999	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	4.46	-8.92	0.00774	.	1.628790	0.03553	N	0.225728	T	0.25457	0.0619	L	0.29908	0.895	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001;0.0	T	0.18935	-1.0321	10	0.10111	T	0.7	1.385	10.8329	0.46671	0.0:0.6324:0.2313:0.1363	.	329;326;336;339;350;339	Q04206-3;Q04206-2;Q04206-4;Q04206;B4E082;Q2TAM5	.;.;.;TF65_HUMAN;.;.	T	339;339;336;350;350	ENSP00000384273:A339T;ENSP00000432537:A339T;ENSP00000311508:A336T;ENSP00000433526:A350T	ENSP00000311508:A336T	A	-	1	0	RELA	65179753	0.000000	0.05858	0.001000	0.08648	0.248000	0.25809	-5.225000	0.00140	-2.123000	0.00823	-0.378000	0.06908	GCT	.	.		0.607	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		T	65423177	C	T	65423177	3	4	144	1	0	0	0	0	1	0	0	0	13231	797	28	3	648	3	RELA	11	65423177	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	988274	65423177	69583339	55	22260										
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94533439	94533439	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gtgagaacagatgtggccgtCctgcggtaccagccaccccc	12	15	0	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr11:94533439C>T	ENST00000433060.2	+	3	1224	c.1083C>T	c.(1081-1083)gtC>gtT	p.V361V	AMOTL1_ENST00000317837.9_Silent_p.V361V|AMOTL1_ENST00000317829.8_Silent_p.V311V	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	361					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				ATGTGGCCGTCCTGCGGTACC	0.527																																					p.V361V		Atlas-SNP	.											.	AMOTL1	95	.	0			c.C1083T						.						89	91	90					11																	94533439		1985	4150	6135	SO:0001819	synonymous_variant	154810	exon3			GGCCGTCCTGCGG	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"junction-enriched and associated protein"	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.1083C>T	chr11.hg19:g.94533439C>T		63.0	0.0		51.0	13.0	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Silent	SNP	ENST00000433060.2	hg19	CCDS44712.1																																																																																			.	.		0.527	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		T	94533439	C	T	94533439	2	4	144	1	0	0	0	0	0	0	0	1	583	842	30	3		3	AMOTL1	11	94533439	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	29110262	94533439	40473077	56	22261										
CUL5	8065	hgsc.bcm.edu	37	chr11	107923507	107923507	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	cttttgattctcagctggttAttggagtaagagaatcctat	9	6	1	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr11:107923507A>G	ENST00000393094.2	+	5	1148	c.532A>G	c.(532-534)Att>Gtt	p.I178V		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	178					calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		TCAGCTGGTTATTGGAGTAAG	0.343																																					p.I178V		Atlas-SNP	.											.	CUL5	71	.	0			c.A532G						.						107	104	105					11																	107923507		2201	4298	6499	SO:0001583	missense	8065	exon5			CTGGTTATTGGAG	X81882	CCDS31668.1	11q22.3	2011-05-24			ENSG00000166266	ENSG00000166266			2556	protein-coding gene	gene with protein product		601741				8681378, 9037604	Standard	XM_005271682		Approved	VACM-1	uc001pjv.3	Q93034	OTTHUMG00000166369	ENST00000393094.2:c.532A>G	chr11.hg19:g.107923507A>G	ENSP00000376808:p.Ile178Val	74.0	0.0		53.0	20.0	NM_003478	A8K960|O14766|Q9BZC6	Missense_Mutation	SNP	ENST00000393094.2	hg19	CCDS31668.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.13|14.13	2.444077|2.444077	0.43429|0.43429	.|.	.|.	ENSG00000166266|ENSG00000166266	ENST00000393094|ENST00000532782	T|.	0.29397|.	1.57|.	5.76|5.76	5.76|5.76	0.90799|0.90799	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);|.	0.093539|.	0.64402|.	D|.	0.000001|.	T|T	0.60521|0.60521	0.2275|0.2275	L|L	0.39397|0.39397	1.21|1.21	0.80722|0.80722	D|D	1|1	B|.	0.22683|.	0.073|.	B|.	0.24269|.	0.052|.	T|T	0.56823|0.56823	-0.7915|-0.7915	10|5	0.02654|.	T|.	1|.	-15.8856|-15.8856	16.0653|16.0653	0.80867|0.80867	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	178|.	Q93034|.	CUL5_HUMAN|.	V|C	178|74	ENSP00000376808:I178V|.	ENSP00000376808:I178V|.	I|Y	+|+	1|2	0|0	CUL5|CUL5	107428717|107428717	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	9.300000|9.300000	0.96151|0.96151	2.196000|2.196000	0.70406|0.70406	0.523000|0.523000	0.50628|0.50628	ATT|TAT	.	.		0.343	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1			G	107923507	A	G	107923507	3	3	144	1	0	0	0	0	1	0	0	0	4061	449	16	2	550	2	CUL5	11	107923507	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	13390068	107923507	27083009	57	22262										
CADM1	23705	hgsc.bcm.edu	37	chr11	115111039	115111039	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ctgcctgttgggattcagtaGctgaatcacagagtcgtcac	11	10	3	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr11:115111039G>A	ENST00000452722.3	-	2	246	c.226C>T	c.(226-228)Cta>Tta	p.L76L	CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000331581.6_Silent_p.L76L|CADM1_ENST00000536727.1_Silent_p.L76L|CADM1_ENST00000542447.2_Silent_p.L76L|CADM1_ENST00000537058.1_Silent_p.L76L	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		GGATTCAGTAGCTGAATCACA	0.443																																					p.L76L		Atlas-SNP	.											.	CADM1	74	.	0			c.C226T						.						98	90	93					11																	115111039		2201	4296	6497	SO:0001819	synonymous_variant	23705	exon2			TCAGTAGCTGAAT	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5951	protein-coding gene	gene with protein product	"nectin-like 2"	605686	"tumor suppressor in lung cancer 1", "immunoglobulin superfamily, member 4"	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.226C>T	chr11.hg19:g.115111039G>A		119.0	0.0		88.0	20.0	NM_014333		Silent	SNP	ENST00000452722.3	hg19	CCDS8373.1	.	.	.	.	.	.	.	.	.	.	G	9.794	1.178632	0.21787	.	.	ENSG00000182985	ENST00000545380	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	T	0.77018	0.4069	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73936	-0.3825	4	.	.	.	.	20.4238	0.99064	0.0:0.0:1.0:0.0	.	.	.	.	V	74	.	.	A	-	2	0	CADM1	114616249	1.000000	0.71417	0.807000	0.32361	0.993000	0.82548	7.650000	0.83521	2.834000	0.97654	0.650000	0.86243	GCT	.	.		0.443	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		A	115111039	G	A	115111039	2	1	144	1	0	0	0	0	0	0	0	1	2568	962	34	3		3	CADM1	11	115111039	Silent	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	7187532	115111039	19895477	58	22263										
ITGA7	3679	hgsc.bcm.edu	37	chr12	56081838	56081841	+	Frame_Shift_Del	DEL	CTGC	CTGC	-													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gacccaccagggcactccttCtgccaccacagccatggggt							TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	CTGC	CTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr12:56081838_56081841delCTGC	ENST00000555728.1	-	25	3257_3260	c.3229_3232delGCAG	c.(3229-3234)gcagaafs	p.AE1077fs	ITGA7_ENST00000394229.2_Frame_Shift_Del_p.AE1033fs|ITGA7_ENST00000257879.6_Frame_Shift_Del_p.AE1033fs|ITGA7_ENST00000553804.1_Frame_Shift_Del_p.AE1037fs|ITGA7_ENST00000394230.2_Frame_Shift_Del_p.AE1037fs|ITGA7_ENST00000452168.2_Frame_Shift_Del_p.AE940fs|ITGA7_ENST00000347027.6_Frame_Shift_Del_p.AE1027fs|ITGA7_ENST00000257880.7_Frame_Shift_Del_p.AE1077fs			Q13683	ITA7_HUMAN	integrin, alpha 7	1077					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GGCACTCCTTCTGCCACCACAGCC	0.593																																					p.1037_1038del		Atlas-Indel,Pindel	.											.	ITGA7	194	.	0			c.3110_3113del						.																																			SO:0001589	frameshift_variant	3679	exon24			.		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.3229_3232delGCAG	chr12.hg19:g.56081838_56081841delCTGC	ENSP00000452387:p.Ala1077fs	136.0	0.0		96.0	26.0	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Frame_Shift_Del	DEL	ENST00000555728.1	hg19																																																																																				.	.		0.593	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		-	56081841	CTGC	-	56081838	7	5	144	1	0	1	0	1	0	0	0	0	7890	922	32	0	321	0	ITGA7	12	56081838	Frame_Shift_Del	DEL	CTGC	TCGA-DD-A73C-01A-12D-A33K-10		56081838	77770057	59	22264										
ORMDL2	29095	hgsc.bcm.edu	37	chr12	56214115	56214116	+	Frame_Shift_Del	DEL	GT	GT	-													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	caacacagcctcattgctaaGtgtactgctgccgaagttgc							TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr12:56214115_56214116delGT	ENST00000243045.5	+	4	593_594	c.398_399delGT	c.(397-399)agtfs	p.S133fs	SARNP_ENST00000336133.3_5'Flank|ORMDL2_ENST00000550836.1_Frame_Shift_Del_p.S45fs|ORMDL2_ENST00000548974.1_Frame_Shift_Del_p.S133fs|RP11-762I7.5_ENST00000546837.1_Intron|RP11-762I7.5_ENST00000552719.1_Intron|ORMDL2_ENST00000552672.1_Frame_Shift_Del_p.S99fs|SARNP_ENST00000444631.2_5'Flank|SARNP_ENST00000552080.1_5'Flank	NM_014182.4	NP_054901.1	Q53FV1	ORML2_HUMAN	ORMDL sphingolipid biosynthesis regulator 2	133					ceramide metabolic process (GO:0006672)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|lung(3)	4						TCATTGCTAAGTGTACTGCTGC	0.505																																					p.133_133del		Atlas-Indel,Pindel	.											.	ORMDL2	8	.	0			c.397_398del						.																																			SO:0001589	frameshift_variant	29095	exon4			.	AF395707	CCDS8893.1	12q13.2	2014-06-16	2014-06-16			ENSG00000123353			16037	protein-coding gene	gene with protein product		610074	"ORM1 (S. cerevisiae)-like 2", "ORM1-like 2 (S. cerevisiae)"			12093374, 23066021	Standard	NM_014182		Approved	HSPC160, adoplin-2, MST095, MSTP095	uc001shw.1	Q53FV1		ENST00000243045.5:c.398_399delGT	chr12.hg19:g.56214117_56214118delGT	ENSP00000243045:p.Ser133fs	177.0	0.0		142.0	36.0	NM_014182	B2RA58|Q7Z4E5|Q8NFX0|Q9P004	Frame_Shift_Del	DEL	ENST00000243045.5	hg19	CCDS8893.1																																																																																			.	.		0.505	ORMDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407934.1	NM_014182		-	56214116	GT	-	56214115	7	5	144	1	0	1	0	1	0	0	0	0	11279	1029	36	0	408	0	ORMDL2	12	56214115	Frame_Shift_Del	DEL	GT	TCGA-DD-A73C-01A-12D-A33K-10	132277	56214115	77637780	60	22265										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121416899	121416899	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tggtggagacccttctgcagTaaggagccctgccccgtccc	12	15	1	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr12:121416899T>A	ENST00000257555.6	+	1	552		c.e1+2		HNF1A_ENST00000402929.1_Splice_Site|HNF1A_ENST00000400024.2_Splice_Site|HNF1A_ENST00000541395.1_Splice_Site|HNF1A-AS1_ENST00000537361.1_RNA|HNF1A-AS1_ENST00000535301.1_RNA|HNF1A_ENST00000543427.1_Splice_Site|HNF1A_ENST00000538626.1_Intron|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A_ENST00000544413.1_Splice_Site			P20823	HNF1A_HUMAN	HNF1 homeobox A						glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.?(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCTTCTGCAGTAAGGAGCCCT	0.642									Hepatic Adenoma, Familial Clustering of																												.		Atlas-SNP	.											.,1	HNF1A	302	.	1	Unknown(1)	liver(1)	c.326+2T>A						.						23	30	28					12																	121416899		2180	4255	6435	SO:0001630	splice_region_variant	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CTGCAGTAAGGAG	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.326+2T>A	chr12.hg19:g.121416899T>A		66.0	0.0		68.0	13.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Splice_Site	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	T	17.68	3.449297	0.63178	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543027;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	.	.	.	4.52	4.52	0.55395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0315	0.58845	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNF1A	119901282	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	6.952000	0.75989	1.674000	0.50907	0.482000	0.46254	.	.	.		0.642	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	Intron	A	121416899	T	A	121416899	5	1	144	1	0	0	0	0	0	0	1	0	7260	1652	57	4	330	4	HNF1A	12	121416899	Splice_Site	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	65202784	121416899	12434996	61	22266										
ATP12A	479	hgsc.bcm.edu	37	chr13	25284610	25284610	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	attaacagacaaggtaccagAgggaatacctagaatggacg	11	7	0	3			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr13:25284610A>G	ENST00000381946.3	+	20	2943	c.2776A>G	c.(2776-2778)Agg>Ggg	p.R926G	ATP12A_ENST00000218548.6_Missense_Mutation_p.R932G			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	926					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		AAGGTACCAGAGGGAATACCT	0.453																																					p.R932G	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.A2794G						.						91	89	89					13																	25284610		2203	4300	6503	SO:0001583	missense	479	exon20			TACCAGAGGGAAT	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2776A>G	chr13.hg19:g.25284610A>G	ENSP00000371372:p.Arg926Gly	162.0	0.0		153.0	45.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.025129	0.35701	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.89343	-2.5;-2.5	5.19	-0.836	0.10770	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.95245	0.8458	H	0.94771	3.58	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.95409	0.8496	10	0.87932	D	0	.	14.2889	0.66263	0.3179:0.6821:0.0:0.0	.	932;926	P54707-2;P54707	.;AT12A_HUMAN	G	932;926	ENSP00000218548:R932G;ENSP00000371372:R926G	ENSP00000218548:R932G	R	+	1	2	ATP12A	24182610	0.997000	0.39634	0.971000	0.41717	0.029000	0.11900	0.614000	0.24314	0.027000	0.15297	-0.316000	0.08728	AGG	.	.		0.453	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		G	25284610	A	G	25284610	3	3	144	1	0	0	0	0	1	0	0	0	1122	295	11	2	2872	2	ATP12A	13	25284610	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10		25284610	89885268	62	22267										
HEATR4	399671	hgsc.bcm.edu	37	chr14	73964942	73964942	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ccttgaagtttcagggctagGatgctacggcaagcttccag	12	10	1	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr14:73964942G>T	ENST00000553558.1	-	14	2784	c.2463C>A	c.(2461-2463)atC>atA	p.I821I	HEATR4_ENST00000334988.2_Silent_p.I821I|HEATR4_ENST00000560393.1_Silent_p.I774I	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	821										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		TCAGGGCTAGGATGCTACGGC	0.537																																					p.I821I		Atlas-SNP	.											HEATR4_ENST00000553558,bladder,carcinoma,0,2	HEATR4	126	.	0			c.C2463A						.						119	98	105					14																	73964942		2203	4300	6503	SO:0001819	synonymous_variant	399671	exon13			GGCTAGGATGCTA	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2463C>A	chr14.hg19:g.73964942G>T		102.0	0.0		102.0	41.0	NM_203309	B7Z7V9|E9KL41	Silent	SNP	ENST00000553558.1	hg19	CCDS9815.2																																																																																			.	.		0.537	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		T	73964942	G	T	73964942	2	4	144	1	0	0	0	0	0	0	0	1	7039	1164	41	3		3	HEATR4	14	73964942	Silent	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10		73964942	33384598	63	22268										
SNW1	22938	hgsc.bcm.edu	37	chr14	78184553	78184553	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	cttgtccaaaccaaaaggatCttcctcaaactgcactggtc	6	13	2	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr14:78184553C>A	ENST00000261531.7	-	14	1551	c.1489G>T	c.(1489-1491)Gat>Tat	p.D497Y	SLIRP_ENST00000557623.1_Intron|SNW1_ENST00000555761.1_Missense_Mutation_p.K523N|SNW1_ENST00000554775.1_Missense_Mutation_p.D335Y|SLIRP_ENST00000557431.1_Intron	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	497					cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)			NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CCAAAAGGATCTTCCTCAAAC	0.473																																					p.D497Y		Atlas-SNP	.											.	SNW1	44	.	0			c.G1489T						.						171	178	176					14																	78184553		2203	4300	6503	SO:0001583	missense	22938	exon14			AAGGATCTTCCTC	AF045184	CCDS9867.1	14q22.1-q22.3	2005-09-13	2005-09-13	2005-09-13		ENSG00000100603			16696	protein-coding gene	gene with protein product		603055	"SKI interacting protein"	SKIIP		8973337, 9632709	Standard	NM_012245		Approved	NCoA-62, SKIP, Prp45, PRPF45, Bx42	uc001xuf.3	Q13573		ENST00000261531.7:c.1489G>T	chr14.hg19:g.78184553C>A	ENSP00000261531:p.Asp497Tyr	134.0	0.0		108.0	35.0	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Missense_Mutation	SNP	ENST00000261531.7	hg19	CCDS9867.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.1|23.1	4.379096|4.379096	0.82682|0.82682	.|.	.|.	ENSG00000100603|ENSG00000100603	ENST00000261531;ENST00000554775|ENST00000555761	.|.	.|.	.|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80281|0.80281	0.4594|0.4594	M|M	0.92169|0.92169	3.28|3.28	0.40444|0.40444	D|D	0.980071|0.980071	D|B	0.76494|0.19817	0.999|0.039	D|B	0.79784|0.26517	0.993|0.07	T|T	0.78298|0.78298	-0.2258|-0.2258	9|7	0.87932|.	D|.	0|.	.|.	19.7701|19.7701	0.96359|0.96359	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	497|523	Q13573|G3V3A4	SNW1_HUMAN|.	Y|N	497;335|523	.|.	ENSP00000261531:D497Y|.	D|K	-|-	1|3	0|2	SNW1|SNW1	77254306|77254306	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	7.228000|7.228000	0.78079|0.78079	2.690000|2.690000	0.91761|0.91761	0.460000|0.460000	0.39030|0.39030	GAT|AAG	.	.		0.473	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245		A	78184553	C	A	78184553	3	1	144	1	0	0	0	0	1	0	0	0	14894	913	32	3	125	3	SNW1	14	78184553	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	4219611	78184553	29164987	64	22269										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96779439	96779439	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tttatccaatgcaacgctacTggaaacactgaatgtttcca	6	10	0	1	rs529500826		TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr14:96779439T>G	ENST00000359933.4	-	25	4698	c.3805A>C	c.(3805-3807)Agt>Cgt	p.S1269R	ATG2B_ENST00000261834.5_5'Flank	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1269					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		GCAACGCTACTGGAAACACTG	0.383													T|||	1	0.000199681	0	0	5008	,	,		16900	0.001		0	False		,,,				2504	0				p.S1269R		Atlas-SNP	.											.	ATG2B	169	.	0			c.A3805C						.						116	113	114					14																	96779439		2203	4300	6503	SO:0001583	missense	55102	exon25			CGCTACTGGAAAC	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.3805A>C	chr14.hg19:g.96779439T>G	ENSP00000353010:p.Ser1269Arg	71.0	0.0		67.0	11.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	T	19.51	3.840463	0.71488	.	.	ENSG00000066739	ENST00000359933	T	0.34472	1.36	6.01	6.01	0.97437	.	0.122489	0.85682	N	0.000000	T	0.53094	0.1775	M	0.75615	2.305	0.80722	D	1	D	0.54397	0.966	P	0.52109	0.69	T	0.58555	-0.7616	10	0.87932	D	0	.	16.5237	0.84324	0.0:0.0:0.0:1.0	.	1269	Q96BY7	ATG2B_HUMAN	R	1269	ENSP00000353010:S1269R	ENSP00000353010:S1269R	S	-	1	0	ATG2B	95849192	1.000000	0.71417	0.977000	0.42913	0.110000	0.19582	5.595000	0.67563	2.306000	0.77630	0.533000	0.62120	AGT	.	.		0.383	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96779439	T	G	96779439	3	3	144	1	0	0	0	0	1	0	0	0	1094	1580	55	5	2503	5	ATG2B	14	96779439	Missense_Mutation	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	18594886	96779439	10570101	65	22270										
CILP	8483	hgsc.bcm.edu	37	chr15	65489133	65489133	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	aggccaccactccaccctggCgctggccacccctgctcgct	9	21	0	0	rs377269093		TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr15:65489133C>A	ENST00000261883.4	-	9	3657	c.3491G>T	c.(3490-3492)cGc>cTc	p.R1164L		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	1164					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						TCCACCCTGGCGCTGGCCACC	0.592																																					p.R1164L		Atlas-SNP	.											.	CILP	124	.	0			c.G3491T						.						39	39	39					15																	65489133		2202	4299	6501	SO:0001583	missense	8483	exon9			CCCTGGCGCTGGC	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.3491G>T	chr15.hg19:g.65489133C>A	ENSP00000261883:p.Arg1164Leu	65.0	0.0		51.0	18.0	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	hg19	CCDS10203.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.772308	0.31411	.	.	ENSG00000138615	ENST00000261883	T	0.38887	1.11	5.44	4.51	0.55191	.	0.306943	0.29355	N	0.012392	T	0.32882	0.0844	L	0.46157	1.445	0.09310	N	1	B	0.28082	0.2	B	0.25987	0.065	T	0.24083	-1.0170	10	0.54805	T	0.06	-0.7745	6.7476	0.23470	0.0:0.6988:0.1519:0.1492	.	1164	O75339	CILP1_HUMAN	L	1164	ENSP00000261883:R1164L	ENSP00000261883:R1164L	R	-	2	0	CILP	63276186	0.000000	0.05858	0.795000	0.32087	0.170000	0.22686	0.762000	0.26503	2.541000	0.85698	0.561000	0.74099	CGC	.	.		0.592	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		A	65489133	C	A	65489133	3	1	144	1	0	0	0	0	1	0	0	0	3431	768	27	1	67	1	CILP	15	65489133	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10		65489133	37042259	66	22271										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9862753	9862753	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ggccggtcggagcacacgccCgtgaaacagaagcgcagctt	14	13	0	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr16:9862753C>T	ENST00000396573.2	-	13	2859	c.2550G>A	c.(2548-2550)acG>acA	p.T850T	GRIN2A_ENST00000535259.1_Silent_p.T693T|GRIN2A_ENST00000562109.1_Silent_p.T850T|GRIN2A_ENST00000396575.2_Silent_p.T850T|GRIN2A_ENST00000404927.2_Silent_p.T850T|GRIN2A_ENST00000330684.3_Silent_p.T850T	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	850					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.T850T(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AGCACACGCCCGTGAAACAGA	0.577																																					p.T850T		Atlas-SNP	.											GRIN2A,NS,carcinoma,0,1	GRIN2A	366	.	1	Substitution - coding silent(1)	prostate(1)	c.G2550A						.						86	85	86					16																	9862753		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon13			CACGCCCGTGAAA		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.2550G>A	chr16.hg19:g.9862753C>T		44.0	0.0		39.0	13.0	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	hg19	CCDS10539.1																																																																																			.	.		0.577	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	9862753	C	T	9862753	2	4	144	1	0	0	0	0	0	0	0	1	6788	639	23	1		1	GRIN2A	16	9862753	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10		9862753	80492000	67	22272										
WDR59	79726	hgsc.bcm.edu	37	chr16	74919609	74919609	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ttcaacacttcagctcgcttCtctctcagaccccaacggta	5	16	4	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr16:74919609C>T	ENST00000262144.6	-	25	2761	c.2631G>A	c.(2629-2631)gaG>gaA	p.E877E		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	877										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						CAGCTCGCTTCTCTCTCAGAC	0.463																																					p.E877E		Atlas-SNP	.											.	WDR59	66	.	0			c.G2631A						.						118	106	110					16																	74919609		2198	4300	6498	SO:0001819	synonymous_variant	79726	exon25			TCGCTTCTCTCTC	AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"WD repeat domain containing"	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.2631G>A	chr16.hg19:g.74919609C>T		99.0	0.0		113.0	39.0	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Silent	SNP	ENST00000262144.6	hg19	CCDS32488.1																																																																																			.	.		0.463	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581		T	74919609	C	T	74919609	2	4	144	1	0	0	0	0	0	0	0	1	17323	912	32	3		3	WDR59	16	74919609	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	65056856	74919609	15435144	68	22273										
OR1G1	8390	hgsc.bcm.edu	37	chr17	3030650	3030650	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gcaggcatctgcaagggagaGgttggctagaaagaagtaca	15	6	1	3			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr17:3030650G>A	ENST00000328890.2	-	1	225	c.196C>T	c.(196-198)Ctc>Ttc	p.L66F		NM_003555.1	NP_003546.1	P47890	OR1G1_HUMAN	olfactory receptor, family 1, subfamily G, member 1	66					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(3)|skin(3)	11						GCAAGGGAGAGGTTGGCTAGA	0.498																																					p.L66F	Colon(127;1481 1654 8243 19426 50557)	Atlas-SNP	.											.	OR1G1	29	.	0			c.C196T						.						106	93	97					17																	3030650		2203	4300	6503	SO:0001583	missense	8390	exon1			GGGAGAGGTTGGC	U04689	CCDS11020.1	17p13.3	2012-08-09			ENSG00000183024	ENSG00000183024		"GPCR / Class A : Olfactory receptors"	8204	protein-coding gene	gene with protein product				OR1G2		8004088, 9500546	Standard	NM_003555		Approved	OR17-209	uc002fvc.1	P47890	OTTHUMG00000090618	ENST00000328890.2:c.196C>T	chr17.hg19:g.3030650G>A	ENSP00000331545:p.Leu66Phe	81.0	0.0		71.0	20.0	NM_003555	Q4VBM1|Q6IFL9|Q9UM76	Missense_Mutation	SNP	ENST00000328890.2	hg19	CCDS11020.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.647856	0.47258	.	.	ENSG00000183024	ENST00000328890	T	0.00354	7.93	4.4	2.29	0.28610	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00580	0.0019	M	0.73598	2.24	0.09310	N	0.999995	D	0.69078	0.997	D	0.66196	0.942	T	0.50906	-0.8772	9	0.87932	D	0	.	5.5367	0.17016	0.1792:0.0:0.6642:0.1565	.	66	P47890	OR1G1_HUMAN	F	66	ENSP00000331545:L66F	ENSP00000331545:L66F	L	-	1	0	OR1G1	2977400	0.011000	0.17503	0.295000	0.24960	0.948000	0.59901	-0.157000	0.10085	1.062000	0.40625	0.530000	0.56133	CTC	.	.		0.498	OR1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207206.2			A	3030650	G	A	3030650	3	1	144	1	0	0	0	0	1	0	0	0	10966	1000	35	3	749	3	OR1G1	17	3030650	Missense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10		3030650	78164560	69	22274										
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4442761	4442761	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ttcttcttggccccactctgAagcaggctgggactcctgat	10	13	3	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr17:4442761A>C	ENST00000254718.4	-	26	4242	c.3936T>G	c.(3934-3936)ctT>ctG	p.L1312L	MYBBP1A_ENST00000381556.2_Silent_p.L1312L			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	1312	Required for nuclear and nucleolar localization. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						CCCCACTCTGAAGCAGGCTGG	0.607																																					p.L1312L		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.T3936G						.						128	133	131					17																	4442761		2203	4300	6503	SO:0001819	synonymous_variant	10514	exon26			ACTCTGAAGCAGG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"p53-activated protein-2"	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.3936T>G	chr17.hg19:g.4442761A>C		65.0	0.0		68.0	24.0	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	hg19	CCDS11046.1																																																																																			.	.		0.607	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		C	4442761	A	C	4442761	2	2	144	1	0	0	0	0	0	0	0	1	10017	233	9	5		5	MYBBP1A	17	4442761	Silent	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	1412111	4442761	76752449	70	22275										
PTRF	284119	hgsc.bcm.edu	37	chr17	40556905	40556905	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gccctcgcggatcttcttgaCgtggaaggtgaagggtggca	16	9	2	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr17:40556905C>T	ENST00000357037.5	-	2	1392	c.973G>A	c.(973-975)Gtc>Atc	p.V325I		NM_012232.5	NP_036364.2			polymerase I and transcript release factor											breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		ATCTTCTTGACGTGGAAGGTG	0.672																																					p.V325I		Atlas-SNP	.											.	PTRF	48	.	0			c.G973A						.						86	76	79					17																	40556905		2203	4300	6503	SO:0001583	missense	284119	exon2			TCTTGACGTGGAA	AF000421	CCDS11425.1	17q21.31	2011-04-20				ENSG00000177469			9688	protein-coding gene	gene with protein product		603198				9582279	Standard	NM_012232		Approved	cavin-1, CAVIN1	uc002hzo.3	Q6NZI2		ENST00000357037.5:c.973G>A	chr17.hg19:g.40556905C>T	ENSP00000349541:p.Val325Ile	107.0	0.0		101.0	35.0	NM_012232		Missense_Mutation	SNP	ENST00000357037.5	hg19	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.592674	0.86953	.	.	ENSG00000177469	ENST00000357037;ENST00000357684	T	0.61742	0.08	4.73	4.73	0.59995	.	0.000000	0.64402	D	0.000001	T	0.65933	0.2739	L	0.38531	1.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.59215	-0.7496	10	0.15952	T	0.53	-38.3733	17.8979	0.88895	0.0:1.0:0.0:0.0	.	307;325	B4DNU9;Q6NZI2	.;PTRF_HUMAN	I	325;280	ENSP00000349541:V325I	ENSP00000349541:V325I	V	-	1	0	PTRF	37810431	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.604000	0.82830	2.445000	0.82738	0.557000	0.71058	GTC	.	.		0.672	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232		T	40556905	C	T	40556905	3	4	144	1	0	0	0	0	1	0	0	0	12830	536	19	1	203	1	PTRF	17	40556905	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	36114144	40556905	40638305	71	22276										
EZH1	2145	hgsc.bcm.edu	37	chr17	40872423	40872423	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	attcagggcatcgaccaactCcagaaaaacagcatcactaa	6	12	2	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr17:40872423C>G	ENST00000428826.2	-	7	653	c.532G>C	c.(532-534)Gag>Cag	p.E178Q	EZH1_ENST00000592743.1_Missense_Mutation_p.E178Q|EZH1_ENST00000435174.1_Missense_Mutation_p.E39Q|EZH1_ENST00000585893.1_Missense_Mutation_p.E138Q|EZH1_ENST00000415827.2_Missense_Mutation_p.E169Q|EZH1_ENST00000590078.1_Missense_Mutation_p.E108Q			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	178					anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)			breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		TCGACCAACTCCAGAAAAACA	0.468																																					p.E178Q		Atlas-SNP	.											.	EZH1	62	.	0			c.G532C						.						159	125	136					17																	40872423		2203	4300	6503	SO:0001583	missense	2145	exon7			CCAACTCCAGAAA		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.532G>C	chr17.hg19:g.40872423C>G	ENSP00000404658:p.Glu178Gln	84.0	0.0		81.0	28.0	NM_001991	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Missense_Mutation	SNP	ENST00000428826.2	hg19	CCDS32659.1	.	.	.	.	.	.	.	.	.	.	C	32	5.106427	0.94292	.	.	ENSG00000108799	ENST00000264646;ENST00000428826;ENST00000415827;ENST00000435174	D;D	0.95377	-2.08;-3.69	5.32	5.32	0.75619	SANT domain, DNA binding (1);	0.042919	0.85682	D	0.000000	D	0.96673	0.8914	L	0.59912	1.85	0.80722	D	1	D;D;D;D	0.62365	0.97;0.987;0.987;0.991	P;P;P;P	0.59487	0.721;0.858;0.858;0.725	D	0.96651	0.9481	10	0.56958	D	0.05	.	18.9557	0.92658	0.0:1.0:0.0:0.0	.	39;138;184;178	Q92800-5;Q92800-3;Q92800-2;Q92800	.;.;.;EZH1_HUMAN	Q	181;178;138;39	ENSP00000404658:E178Q;ENSP00000404071:E39Q	ENSP00000264646:E181Q	E	-	1	0	EZH1	38125949	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.163000	0.77524	2.667000	0.90743	0.561000	0.74099	GAG	.	.		0.468	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		G	40872423	C	G	40872423	3	3	144	1	0	0	0	0	1	0	0	0	5335	864	30	4	1771	4	EZH1	17	40872423	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	315518	40872423	40322787	72	22277										
C17orf57	124989	hgsc.bcm.edu	37	chr17	45421602	45421602	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tctttatgcaagttgccgaaTcagtacagcgttcacaagac	8	10	3	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr17:45421602T>A	ENST00000331493.2	+	7	789	c.378T>A	c.(376-378)aaT>aaA	p.N126K	ITGB3_ENST00000435993.2_3'UTR|ITGB3_ENST00000560629.1_3'UTR|EFCAB13_ENST00000517484.1_Missense_Mutation_p.N126K	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	126						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										AGTTGCCGAATCAGTACAGCG	0.383																																					p.N126K		Atlas-SNP	.											.	.	.	.	0			c.T378A						.						222	205	211					17																	45421602		2203	4300	6503	SO:0001583	missense	124989	exon7			GCCGAATCAGTAC	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.378T>A	chr17.hg19:g.45421602T>A	ENSP00000332111:p.Asn126Lys	99.0	0.0		89.0	20.0	NM_152347	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	hg19	CCDS11512.1	.	.	.	.	.	.	.	.	.	.	T	0.776	-0.763931	0.02996	.	.	ENSG00000178852	ENST00000331493;ENST00000517484;ENST00000344176	T;T	0.64085	0.41;-0.08	3.19	3.19	0.36642	.	1.650740	0.03078	N	0.158121	T	0.58708	0.2141	L	0.44542	1.39	0.09310	N	1	P;P;P	0.46512	0.782;0.763;0.879	B;B;B	0.42030	0.189;0.205;0.373	T	0.53542	-0.8424	10	0.87932	D	0	-0.2434	8.1554	0.31165	0.0:0.0:0.0:1.0	.	126;126;126	Q8N7U2;Q8IY85;G3V128	.;CQ057_HUMAN;.	K	126	ENSP00000332111:N126K;ENSP00000430048:N126K	ENSP00000332111:N126K	N	+	3	2	C17orf57	42776601	0.001000	0.12720	0.027000	0.17364	0.003000	0.03518	0.050000	0.14120	1.694000	0.51137	0.477000	0.44152	AAT	.	.		0.383	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		A	45421602	T	A	45421602	3	1	144	1	0	0	0	0	1	0	0	0	1867	1432	50	4	392	4	C17orf57	17	45421602	Missense_Mutation	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	4549179	45421602	35773608	73	22278										
KATNAL2	83473	hgsc.bcm.edu	37	chr18	44593424	44593424	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	cataatccaaacataaagtgGaatgacattattggacttga	7	6	0	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr18:44593424G>T	ENST00000245121.5	+	8	737	c.543G>T	c.(541-543)tgG>tgT	p.W181C	KATNAL2_ENST00000356157.7_Missense_Mutation_p.W253C|KATNAL2_ENST00000592005.1_Intron	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						ACATAAAGTGGAATGACATTA	0.388																																					p.W181C		Atlas-SNP	.											.	KATNAL2	64	.	0			c.G543T						.						106	96	100					18																	44593424		2203	4300	6503	SO:0001583	missense	83473	exon8			AAAGTGGAATGAC	BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"ATPases / AAA-type"	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.543G>T	chr18.hg19:g.44593424G>T	ENSP00000245121:p.Trp181Cys	69.0	0.0		58.0	19.0	NM_031303		Missense_Mutation	SNP	ENST00000245121.5	hg19	CCDS32828.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.192716	0.78902	.	.	ENSG00000167216	ENST00000356157;ENST00000245121;ENST00000454462	D;D	0.95001	-3.58;-3.58	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.98391	0.9465	H	0.96269	3.795	0.80722	D	1	.	.	.	.	.	.	D	0.98826	1.0749	8	0.87932	D	0	-1.4157	20.3539	0.98825	0.0:0.0:1.0:0.0	.	.	.	.	C	253;181;21	ENSP00000348478:W253C;ENSP00000245121:W181C	ENSP00000245121:W181C	W	+	3	0	KATNAL2	42847422	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	9.014000	0.93635	2.826000	0.97356	0.655000	0.94253	TGG	.	.		0.388	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303		T	44593424	G	T	44593424	3	4	144	1	0	0	0	0	1	0	0	0	7995	1183	41	3	569	3	KATNAL2	18	44593424	Missense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10		44593424	33483824	74	22279										
PTBP1	5725	hgsc.bcm.edu	37	chr19	804341	804341	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tgccaacaccatggtgaactActacacctcggtgacccctg	8	15	0	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr19:804341A>G	ENST00000349038.4	+	5	411	c.338A>G	c.(337-339)tAc>tGc	p.Y113C	PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000394601.4_Missense_Mutation_p.Y113C|PTBP1_ENST00000356948.6_Missense_Mutation_p.Y113C|MIR4745_ENST00000577608.1_RNA	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	113	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGGTGAACTACTACACCTCG	0.627																																					p.Y113C		Atlas-SNP	.											.	PTBP1	43	.	0			c.A338G						.						85	72	76					19																	804341		2203	4300	6503	SO:0001583	missense	5725	exon5			TGAACTACTACAC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"RNA binding motif (RRM) containing"	9583	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein I"	600693	"polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.338A>G	chr19.hg19:g.804341A>G	ENSP00000014112:p.Tyr113Cys	36.0	0.0		44.0	15.0	NM_031990	Q9BUQ0	Missense_Mutation	SNP	ENST00000349038.4	hg19	CCDS32859.1	.	.	.	.	.	.	.	.	.	.	A	12.69	2.014178	0.35511	.	.	ENSG00000011304	ENST00000356948;ENST00000394601;ENST00000349038	T;T;T	0.53640	0.61;0.61;0.92	4.57	3.55	0.40652	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.216549	0.41001	D	0.000971	T	0.68229	0.2978	M	0.87269	2.87	0.80722	D	1	B;B;D	0.71674	0.229;0.102;0.998	B;B;D	0.73708	0.213;0.18;0.981	T	0.68273	-0.5452	10	0.48119	T	0.1	-57.0102	9.2933	0.37800	0.9142:0.0:0.0858:0.0	.	113;113;113	P26599;P26599-2;Q9BUQ0	PTBP1_HUMAN;.;.	C	113	ENSP00000349428:Y113C;ENSP00000408096:Y113C;ENSP00000014112:Y113C	ENSP00000014112:Y113C	Y	+	2	0	PTBP1	755341	1.000000	0.71417	0.995000	0.50966	0.774000	0.43823	7.175000	0.77632	0.625000	0.30304	0.533000	0.62120	TAC	.	.		0.627	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1			G	804341	A	G	804341	3	3	144	1	0	0	0	0	1	0	0	0	12737	391	14	2	356	2	PTBP1	19	804341	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10		804341	58324642	75	22280										
ARID3A	1820	hgsc.bcm.edu	37	chr19	966608	966608	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ccccatcacagtccctggccGcctgcctgtgtccctggcgg	11	19	1	0	rs368267576		TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr19:966608G>T	ENST00000263620.3	+	7	1562	c.1235G>T	c.(1234-1236)cGc>cTc	p.R412L		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	412						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCCCTGGCCGCCTGCCTGTG	0.667																																					p.R412L	Pancreas(29;54 1022 32760 50921)	Atlas-SNP	.											.	ARID3A	35	.	0			c.G1235T						.						21	22	22					19																	966608		2176	4257	6433	SO:0001583	missense	1820	exon7			CTGGCCGCCTGCC	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"-"	3031	protein-coding gene	gene with protein product		603265	"dead ringer-like 1 (Drosophila)", "AT rich interactive domain 3A (BRIGHT- like)"	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.1235G>T	chr19.hg19:g.966608G>T	ENSP00000263620:p.Arg412Leu	113.0	0.0		82.0	11.0	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Missense_Mutation	SNP	ENST00000263620.3	hg19	CCDS12050.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.849668	0.91277	.	.	ENSG00000116017	ENST00000263620	T	0.44083	0.93	4.99	4.99	0.66335	.	0.248604	0.32416	N	0.006128	T	0.64983	0.2648	M	0.80746	2.51	0.80722	D	1	D	0.61697	0.99	D	0.64506	0.926	T	0.67488	-0.5658	10	0.44086	T	0.13	-6.5768	16.8584	0.86011	0.0:0.0:1.0:0.0	.	412	Q99856	ARI3A_HUMAN	L	412	ENSP00000263620:R412L	ENSP00000263620:R412L	R	+	2	0	ARID3A	917608	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	3.559000	0.53756	2.321000	0.78463	0.609000	0.83330	CGC	.	.		0.667	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224		T	966608	G	T	966608	3	4	144	1	0	0	0	0	1	0	0	0	916	1087	38	1	1257	1	ARID3A	19	966608	Missense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	162267	966608	58162375	76	22281										
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35501096	35501096	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	aacatcttccgctgggagacCacggtgagcccgcagcgggg	15	13	1	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr19:35501096C>G	ENST00000317991.5	+	5	618	c.426C>G	c.(424-426)acC>acG	p.T142T	GRAMD1A_ENST00000599564.1_Silent_p.T229T|GRAMD1A_ENST00000598073.1_3'UTR|GRAMD1A_ENST00000424536.2_Silent_p.T142T|GRAMD1A_ENST00000411896.2_Silent_p.T135T|GRAMD1A_ENST00000504615.2_5'UTR	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	142	GRAM.					integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GCTGGGAGACCACGGTGAGCC	0.647																																					p.T142T		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.C426G						.						68	71	70					19																	35501096		1928	4128	6056	SO:0001819	synonymous_variant	57655	exon5			GGAGACCACGGTG	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"KIAA1533"	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.426C>G	chr19.hg19:g.35501096C>G		84.0	0.0		53.0	19.0	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Silent	SNP	ENST00000317991.5	hg19	CCDS42546.1																																																																																			.	.		0.647	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		G	35501096	C	G	35501096	2	3	144	1	0	0	0	0	0	0	0	1	6756	581	21	4		4	GRAMD1A	19	35501096	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	34534488	35501096	23627887	77	22282										
KPTN	11133	hgsc.bcm.edu	37	chr19	47984228	47984228	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	acctcacctccttgtagagaTgaatggccgggtcgttccca	10	13	1	2			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr19:47984228T>C	ENST00000338134.3	-	5	619	c.512A>G	c.(511-513)cAt>cGt	p.H171R	KPTN_ENST00000536339.1_5'UTR|KPTN_ENST00000595484.1_5'UTR	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	171					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		CTTGTAGAGATGAATGGCCGG	0.567																																					p.H171R		Atlas-SNP	.											.	KPTN	34	.	0			c.A512G						.						41	43	43					19																	47984228		1963	4153	6116	SO:0001583	missense	11133	exon5			TAGAGATGAATGG	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"kaptin (actin-binding protein)"			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.512A>G	chr19.hg19:g.47984228T>C	ENSP00000337850:p.His171Arg	81.0	0.0		90.0	21.0	NM_007059	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	hg19	CCDS42583.1	.	.	.	.	.	.	.	.	.	.	T	19.97	3.924398	0.73213	.	.	ENSG00000118162	ENST00000338134	T	0.42900	0.96	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.68439	0.3001	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74386	-0.3682	10	0.87932	D	0	.	14.8738	0.70481	0.0:0.0:0.0:1.0	.	171	Q9Y664	KPTN_HUMAN	R	171	ENSP00000337850:H171R	ENSP00000337850:H171R	H	-	2	0	KPTN	52676040	1.000000	0.71417	1.000000	0.80357	0.428000	0.31595	6.512000	0.73737	2.153000	0.67306	0.374000	0.22700	CAT	.	.		0.567	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2			C	47984228	T	C	47984228	3	2	144	1	0	0	0	0	1	0	0	0	8446	1464	51	2	830	2	KPTN	19	47984228	Missense_Mutation	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	12483132	47984228	11144755	78	22283										
IRF3	3661	hgsc.bcm.edu	37	chr19	50167999	50167999	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	cttccaagggatgcggaagcGcgtgcggctcttgttcaccc	13	13	2	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr19:50167999G>A	ENST00000597198.1	-	2	478	c.97C>T	c.(97-99)Cgc>Tgc	p.R33C	IRF3_ENST00000309877.7_Missense_Mutation_p.R33C|IRF3_ENST00000600911.1_Missense_Mutation_p.R33C|IRF3_ENST00000377139.3_Missense_Mutation_p.R33C|BCL2L12_ENST00000246785.3_5'Flank|IRF3_ENST00000601291.1_Missense_Mutation_p.R33C|IRF3_ENST00000442265.2_Missense_Mutation_p.R33C|IRF3_ENST00000596765.1_Intron|IRF3_ENST00000593922.1_Intron|BCL2L12_ENST00000441864.2_5'Flank|IRF3_ENST00000377135.4_Missense_Mutation_p.R33C|IRF3_ENST00000598808.1_Intron|IRF3_ENST00000599223.1_Missense_Mutation_p.R33C|IRF3_ENST00000599144.1_Intron|IRF3_ENST00000600022.1_Intron|IRF3_ENST00000596822.1_Intron|BCL2L12_ENST00000246784.3_5'Flank			Q14653	IRF3_HUMAN	interferon regulatory factor 3	33					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dsRNA (GO:0071359)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage apoptotic process (GO:0071888)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of interferon-beta biosynthetic process (GO:0045358)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|programmed necrotic cell death (GO:0097300)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(2)|lung(4)|ovary(2)|stomach(1)	10		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.02)		ATGCGGAAGCGCGTGCGGCTC	0.647																																					p.R33C		Atlas-SNP	.											.	IRF3	27	.	0			c.C97T						.						98	91	93					19																	50167999		2203	4300	6503	SO:0001583	missense	3661	exon2			GGAAGCGCGTGCG		CCDS12775.1, CCDS56099.1, CCDS59407.1, CCDS59408.1, CCDS59409.1	19q13.3-q13.4	2008-07-16				ENSG00000126456			6118	protein-coding gene	gene with protein product		603734				8524823	Standard	NM_001571		Approved		uc002pow.3	Q14653		ENST00000597198.1:c.97C>T	chr19.hg19:g.50167999G>A	ENSP00000469113:p.Arg33Cys	67.0	0.0		63.0	12.0	NM_001197122	A8K7L2|B2RAZ3|Q5FBY1|Q5FBY2|Q5FBY4|Q7Z5G6	Missense_Mutation	SNP	ENST00000597198.1	hg19	CCDS12775.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028032	0.75390	.	.	ENSG00000126456	ENST00000377139;ENST00000309877;ENST00000377135;ENST00000442265	D;D;D;D	0.97752	-4.52;-4.52;-4.52;-4.52	4.63	3.56	0.40772	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.238872	0.30109	U	0.010399	D	0.97742	0.9259	L	0.52905	1.665	0.49798	D	0.999825	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;P;D	0.76575	0.972;0.93;0.966;0.966;0.803;0.988	D	0.97222	0.9878	10	0.62326	D	0.03	-8.6232	9.6869	0.40105	0.0:0.0:0.6083:0.3917	.	33;33;33;33;33;33	Q5FBY4;B2RAZ3;Q96GL3;Q7Z5G6;Q14653;Q5FBY1	.;.;.;.;IRF3_HUMAN;.	C	33	ENSP00000366344:R33C;ENSP00000310127:R33C;ENSP00000366339:R33C;ENSP00000400378:R33C	ENSP00000310127:R33C	R	-	1	0	IRF3	54859811	0.834000	0.29399	0.850000	0.33497	0.972000	0.66771	1.515000	0.35845	0.866000	0.35629	0.591000	0.81541	CGC	.	.		0.647	IRF3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465962.1	NM_001571		A	50167999	G	A	50167999	3	1	144	1	0	0	0	0	1	0	0	0	7840	1087	38	1	1214	1	IRF3	19	50167999	Missense_Mutation	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	2183771	50167999	8960984	79	22284										
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42159524	42159524	+	Missense_Mutation	SNP	A	A	T													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	agcacctgtttgtgagccagAgccacgtgagtgcccctgag							TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr20:42159524A>T	ENST00000427442.2	+	11	1372	c.1213A>T	c.(1213-1215)Agc>Tgc	p.S405C	L3MBTL1_ENST00000373135.3_Missense_Mutation_p.S337C|L3MBTL1_ENST00000418998.1_Missense_Mutation_p.S405C|L3MBTL1_ENST00000444063.1_Missense_Mutation_p.S337C|L3MBTL1_ENST00000373134.1_Missense_Mutation_p.S337C			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	337					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						TGTGAGCCAGAGCCACGTGAG	0.592																																					p.S405C		Atlas-SNP	.											.	L3MBTL1	105	.	0			c.A1213T						.						60	51	54					20																	42159524		2203	4300	6503	SO:0001583	missense	26013	exon11			AGCCAGAGCCACG	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.1213A>T	chr20.hg19:g.42159524A>T	ENSP00000402107:p.Ser405Cys	155.0	0.0		124.0	38.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Missense_Mutation	SNP	ENST00000427442.2	hg19	CCDS46602.2	.	.	.	.	.	.	.	.	.	.	A	19.15	3.771998	0.69992	.	.	ENSG00000185513	ENST00000427442;ENST00000418998;ENST00000373135;ENST00000444063;ENST00000373134;ENST00000422861	D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	5.06	5.06	0.68205	.	0.291907	0.43747	D	0.000536	D	0.86661	0.5986	M	0.69523	2.12	0.27485	N	0.952468	D;D;D	0.65815	0.995;0.985;0.989	P;B;P	0.50617	0.646;0.441;0.646	T	0.82721	-0.0317	10	0.72032	D	0.01	.	9.2855	0.37755	0.9141:0.0:0.0859:0.0	.	405;337;337	Q9Y468-5;Q9Y468-2;Q9Y468-1	.;.;.	C	405;405;337;337;337;123	ENSP00000402107:S405C;ENSP00000398516:S405C;ENSP00000362227:S337C;ENSP00000403316:S337C;ENSP00000362226:S337C;ENSP00000410139:S123C	ENSP00000362226:S337C	S	+	1	0	L3MBTL1	41592938	0.581000	0.26741	1.000000	0.80357	0.999000	0.98932	3.107000	0.50329	2.042000	0.60477	0.533000	0.62120	AGC	.	.		0.592	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		T	42159524	A	T	42159524	3	4	144	1	0	0	0	0	1	0	0	0	8600	304	11	4	1039	4	L3MBTL	20	42159524	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10		42159524	20865996	80	22285	96	2								
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42159526	42159526	+	Silent	SNP	C	C	T													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	cacctgtttgtgagccagagCcacgtgagtgcccctgagtg							TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr20:42159526C>T	ENST00000427442.2	+	11	1374	c.1215C>T	c.(1213-1215)agC>agT	p.S405S	L3MBTL1_ENST00000373135.3_Silent_p.S337S|L3MBTL1_ENST00000418998.1_Silent_p.S405S|L3MBTL1_ENST00000444063.1_Silent_p.S337S|L3MBTL1_ENST00000373134.1_Silent_p.S337S			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	337					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						TGAGCCAGAGCCACGTGAGTG	0.592																																					p.S405S		Atlas-SNP	.											.	L3MBTL1	105	.	0			c.C1215T						.						60	50	54					20																	42159526		2203	4300	6503	SO:0001819	synonymous_variant	26013	exon11			CCAGAGCCACGTG	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.1215C>T	chr20.hg19:g.42159526C>T		150.0	0.0		120.0	37.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Silent	SNP	ENST00000427442.2	hg19	CCDS46602.2																																																																																			.	.		0.592	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		T	42159526	C	T	42159526	2	4	144	1	0	0	0	0	0	0	0	1	8600	738	26	3		3	L3MBTL	20	42159526	Silent	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10	2	42159526	20865994	81	22286	96	2								
CRYZL1	9946	hgsc.bcm.edu	37	chr21	35003837	35003837	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tcttcatctgtggaactctgTtggaaatataagcctttcat	7	8	5	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chr21:35003837T>C	ENST00000381554.3	-	2	106	c.21A>G	c.(19-21)caA>caG	p.Q7Q	CRYZL1_ENST00000290244.5_Silent_p.Q7Q|CRYZL1_ENST00000381540.3_Silent_p.Q7Q|CRYZL1_ENST00000413017.2_Silent_p.Q7Q|CRYZL1_ENST00000445393.1_Silent_p.Q7Q|CRYZL1_ENST00000361534.2_Silent_p.Q31Q|AP000304.12_ENST00000429238.1_Intron	NM_145858.2	NP_665857.2	O95825	QORL1_HUMAN	crystallin, zeta (quinone reductase)-like 1	7					quinone metabolic process (GO:1901661)	cytosol (GO:0005829)	NADP binding (GO:0050661)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			lung(1)|prostate(1)|urinary_tract(1)	3						TGGAACTCTGTTGGAAATATA	0.244																																					p.Q7Q		Atlas-SNP	.											.	CRYZL1	16	.	0			c.A21G						.						46	51	49					21																	35003837		2189	4268	6457	SO:0001819	synonymous_variant	9946	exon2			ACTCTGTTGGAAA	AF029689	CCDS13633.2	21q22.1	2008-07-31			ENSG00000205758	ENSG00000205758			2420	protein-coding gene	gene with protein product	"quinone reductase-like 1"	603920				10191096	Standard	NM_145858		Approved	QOH-1, 4P11	uc021wio.1	O95825	OTTHUMG00000065954	ENST00000381554.3:c.21A>G	chr21.hg19:g.35003837T>C		318.0	0.0		257.0	92.0	NM_145858	B2RDX1|B3KQ77|Q96DY0|Q9NVY7	Silent	SNP	ENST00000381554.3	hg19	CCDS13633.2																																																																																			.	.		0.244	CRYZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141282.2	NM_145858		C	35003837	T	C	35003837	2	2	144	1	0	0	0	0	0	0	0	1	3925	1722	60	2		2	CRYZL1	21	35003837	Silent	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10		35003837	13126058	82	22287										
NHS	4810	hgsc.bcm.edu	37	chrX	17746802	17746802	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tgatgactccatcatttcacCacttagtgaagactcccaag	6	12	2	4			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chrX:17746802C>T	ENST00000380060.3	+	7	4531	c.4193C>T	c.(4192-4194)cCa>cTa	p.P1398L	NHS_ENST00000398097.3_Missense_Mutation_p.P1242L	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1419					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					ATCATTTCACCACTTAGTGAA	0.438																																					p.P1398L		Atlas-SNP	.											.	NHS	302	.	0			c.C4193T						.						105	95	99					X																	17746802		2203	4300	6503	SO:0001583	missense	4810	exon7			TTTCACCACTTAG		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.4193C>T	chrX.hg19:g.17746802C>T	ENSP00000369400:p.Pro1398Leu	233.0	0.0		243.0	96.0	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	hg19	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.654102	0.88056	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.48522	0.81;0.81	6.06	6.06	0.98353	.	0.052914	0.85682	D	0.000000	T	0.61949	0.2388	L	0.54323	1.7	0.80722	D	1	P;P;P;P	0.51933	0.859;0.859;0.859;0.949	B;B;B;P	0.56278	0.435;0.435;0.435;0.795	T	0.60306	-0.7289	10	0.52906	T	0.07	-14.6648	19.5104	0.95139	0.0:1.0:0.0:0.0	.	1419;1240;1242;1398	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	L	1398;1242;1240	ENSP00000369400:P1398L;ENSP00000381170:P1242L	ENSP00000369397:P1240L	P	+	2	0	NHS	17656723	0.998000	0.40836	0.997000	0.53966	0.991000	0.79684	5.288000	0.65651	2.562000	0.86427	0.600000	0.82982	CCA	.	.		0.438	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		T	17746802	C	T	17746802	3	4	144	1	0	0	0	0	1	0	0	0	10420	594	21	3	4324	3	NHS	23	17746802	Missense_Mutation	SNP	C	TCGA-DD-A73C-01A-12D-A33K-10		17746802	137523758	83	22288										
WDR45	11152	hgsc.bcm.edu	37	chrX	48933031	48933031	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	gggggtactcacgcggagcgGcggttgaggcgggtatcctt	19	9	1	1			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chrX:48933031G>A	ENST00000376372.3	-	9	1000	c.819C>T	c.(817-819)cgC>cgT	p.R273R	WDR45_ENST00000485908.1_Silent_p.R238R|AF196779.12_ENST00000376358.3_Silent_p.R171R|WDR45_ENST00000465431.1_5'Flank|WDR45_ENST00000322995.8_Silent_p.R284R|WDR45_ENST00000376368.2_Silent_p.R274R|WDR45_ENST00000356463.3_Silent_p.R274R|PRAF2_ENST00000491199.1_5'Flank|WDR45_ENST00000396681.4_Silent_p.R259R|WDR45_ENST00000473974.1_Intron|PRAF2_ENST00000376390.4_5'Flank|PRAF2_ENST00000376386.3_5'Flank|WDR45_ENST00000553851.1_Silent_p.R171R	NM_001029896.1	NP_001025067.1	Q9Y484	WIPI4_HUMAN	WD repeat domain 45	273					autophagy (GO:0006914)|cell death (GO:0008219)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	19						ACGCGGAGCGGCGGTTGAGGC	0.592																																					p.R274R		Atlas-SNP	.											.	WDR45	40	.	0			c.C822T						.						22	22	22					X																	48933031		2203	4296	6499	SO:0001819	synonymous_variant	11152	exon10			GGAGCGGCGGTTG	BC003037	CCDS14318.1, CCDS35250.1	Xp11.23	2013-06-06	2004-09-02	2004-09-03	ENSG00000196998	ENSG00000196998		"WD repeat domain containing"	28912	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 5"	300526	"WD repeat domain, X-linked 1"	WDRX1		12477932	Standard	NM_007075		Approved	JM5, WIPI4, NBIA5	uc004dmk.1	Q9Y484	OTTHUMG00000034500	ENST00000376372.3:c.819C>T	chrX.hg19:g.48933031G>A		146.0	0.0		118.0	35.0	NM_007075	A6NGH5|B7WPI2|Q5MNZ5|Q6IBS7|Q6NT94|Q96H03	Silent	SNP	ENST00000376372.3	hg19	CCDS35250.1	.	.	.	.	.	.	.	.	.	.	G	10.34	1.323237	0.24080	.	.	ENSG00000196998	ENST00000367375	.	.	.	4.09	-0.028	0.13924	.	.	.	.	.	T	0.43233	0.1238	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21314	-1.0249	4	.	.	.	-12.4629	3.2163	0.06700	0.287:0.0:0.3869:0.3262	.	.	.	.	S	200	.	.	P	-	1	0	WDR45	48819975	0.817000	0.29147	0.999000	0.59377	0.937000	0.57800	-0.281000	0.08456	-0.036000	0.13669	-0.578000	0.04140	CCG	.	.		0.592	WDR45-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083418.2	NM_007075		A	48933031	G	A	48933031	2	1	144	1	0	0	0	0	0	0	0	1	17312	1190	42	3		3	WDR45	23	48933031	Silent	SNP	G	TCGA-DD-A73C-01A-12D-A33K-10	31186229	48933031	106337529	84	22289										
FAM46D	169966	hgsc.bcm.edu	37	chrX	79698133	79698133	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tccaattcatggaaaggggaAtttccccacaatggaggtaa	10	8	1	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chrX:79698133A>T	ENST00000308293.5	+	3	334	c.95A>T	c.(94-96)aAt>aTt	p.N32I	FAM46D_ENST00000538312.1_Missense_Mutation_p.N32I	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	32										kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						GGAAAGGGGAATTTCCCCACA	0.368																																					p.N32I		Atlas-SNP	.											.	FAM46D	69	.	0			c.A95T						.						98	83	88					X																	79698133		2203	4299	6502	SO:0001583	missense	169966	exon5			AGGGGAATTTCCC	BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"cancer/testis antigen 112"					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.95A>T	chrX.hg19:g.79698133A>T	ENSP00000308575:p.Asn32Ile	191.0	0.0		135.0	52.0	NM_001170574	B2R9Q6|Q7Z3F6|Q8NHU1	Missense_Mutation	SNP	ENST00000308293.5	hg19	CCDS14446.1	.	.	.	.	.	.	.	.	.	.	A	16.40	3.113279	0.56398	.	.	ENSG00000174016	ENST00000538312;ENST00000308293	T;T	0.26660	1.72;1.72	4.41	4.41	0.53225	Domain of unknown function DUF1693 (1);	0.000000	0.85682	D	0.000000	T	0.55289	0.1911	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63844	-0.6545	10	0.87932	D	0	-13.5436	11.6886	0.51501	1.0:0.0:0.0:0.0	.	32	Q8NEK8	FA46D_HUMAN	I	32	ENSP00000443410:N32I;ENSP00000308575:N32I	ENSP00000308575:N32I	N	+	2	0	FAM46D	79584789	1.000000	0.71417	0.996000	0.52242	0.807000	0.45602	8.363000	0.90103	1.632000	0.50472	0.345000	0.21793	AAT	.	.		0.368	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630		T	79698133	A	T	79698133	3	4	144	1	0	0	0	0	1	0	0	0	5576	101	4	4	97	4	FAM46D	23	79698133	Missense_Mutation	SNP	A	TCGA-DD-A73C-01A-12D-A33K-10	30765102	79698133	75572427	85	22290										
STAG2	10735	hgsc.bcm.edu	37	chrX	123176443	123176451	+	In_Frame_Del	DEL	GACATATGC	GACATATGC	-													0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	tgtcacagcagaaatgtttaGacatatgcagaactctgaga							TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	GACATATGC	GACATATGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chrX:123176443_123176451delGACATATGC	ENST00000371160.1	+	7	700_708	c.410_418delGACATATGC	c.(409-420)agacatatgcag>aag	p.137_140RHMQ>K	STAG2_ENST00000371144.3_In_Frame_Del_p.137_140RHMQ>K|STAG2_ENST00000371157.3_In_Frame_Del_p.137_140RHMQ>K|STAG2_ENST00000371145.3_In_Frame_Del_p.137_140RHMQ>K|STAG2_ENST00000354548.5_In_Frame_Del_p.68_71RHMQ>K|STAG2_ENST00000218089.9_In_Frame_Del_p.137_140RHMQ>K|STAG2_ENST00000469481.1_Intron	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	137					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.R137I(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GAAATGTTTAGACATATGCAGAACTCTGA	0.306																																					p.137_139del		Atlas-Indel,Pindel	.											.	STAG2	309	.	1	Substitution - Missense(1)	large_intestine(1)	c.409_417del						.																																			SO:0001651	inframe_deletion	10735	exon7			.	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.410_418delGACATATGC	chrX.hg19:g.123176443_123176451delGACATATGC	ENSP00000360202:p.Arg137_Gln140delinsLys	447.0	0.0		338.0	79.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	In_Frame_Del	DEL	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.		0.306	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		-	123176451	GACATATGC	-	123176443	7	5	144	1	0	1	0	1	0	0	0	0	15258	942	33	0	428	0	STAG2	23	123176443	In_Frame_Del	DEL	GACATATGC	TCGA-DD-A73C-01A-12D-A33K-10	43478310	123176443	32094117	86	22291										
GPC3	2719	hgsc.bcm.edu	37	chrX	132887923	132887923	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	2	1	0.480349344978166	0.773896166909267	0.34825327510917	1	1	0	ttggggaaattcccaaatacTttcaggtcacgtcttgctcc	8	11	3	0			TCGA-DD-A73C-01A-12D-A33K-10	TCGA-DD-A73C-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffe9f06b-c676-4f9f-8bc5-cd6a3db3f2ca	27060b4f-ef3b-4437-90c3-99ef91ddbc47	g.chrX:132887923T>G	ENST00000370818.3	-	3	1063	c.618A>C	c.(616-618)aaA>aaC	p.K206N	GPC3_ENST00000543339.1_Missense_Mutation_p.K152N|GPC3_ENST00000394299.2_Missense_Mutation_p.K206N	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	206					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|body morphogenesis (GO:0010171)|bone mineralization (GO:0030282)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cell proliferation involved in metanephros development (GO:0072203)|chondroitin sulfate metabolic process (GO:0030204)|coronary vasculature development (GO:0060976)|embryonic hindlimb morphogenesis (GO:0035116)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lung development (GO:0030324)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesonephric duct morphogenesis (GO:0072180)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of growth (GO:0045926)|negative regulation of smoothened signaling pathway (GO:0045879)|osteoclast differentiation (GO:0030316)|phototransduction, visible light (GO:0007603)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endocytosis (GO:0045807)|positive regulation of glucose import (GO:0046326)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	peptidyl-dipeptidase inhibitor activity (GO:0060422)			breast(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|prostate(1)|skin(2)	36	Acute lymphoblastic leukemia(192;0.000127)					TCCCAAATACTTTCAGGTCAC	0.478			"T, D, Mis, N, F, S"			Wilms tumour			Simpson-Golabi-Behmel syndrome																												p.K206N		Atlas-SNP	.	yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	.	GPC3	88	.	0			c.A618C						.						381	287	319					X																	132887923		2203	4300	6503	SO:0001583	missense	2719	exon3	Familial Cancer Database	SGBS	AAATACTTTCAGG	L47125	CCDS14638.1, CCDS55496.1	Xq26	2014-09-17			ENSG00000147257	ENSG00000147257		"Proteoglycans / Cell Surface : Glypicans"	4451	protein-coding gene	gene with protein product	"glypican proteoglycan 3"	300037		SDYS		8589713, 9787072	Standard	NM_004484		Approved	OCI-5, SGBS, SGBS1, SGB, DGSX	uc010nrn.2	P51654	OTTHUMG00000022448	ENST00000370818.3:c.618A>C	chrX.hg19:g.132887923T>G	ENSP00000359854:p.Lys206Asn	199.0	0.0		199.0	11.0	NM_001164617	C9JLE3|G3V1R0|Q2L880|Q2L882	Missense_Mutation	SNP	ENST00000370818.3	hg19	CCDS14638.1	.	.	.	.	.	.	.	.	.	.	T	5.641	0.302961	0.10678	.	.	ENSG00000147257	ENST00000370818;ENST00000394299;ENST00000543339	T;T;T	0.54479	0.57;0.57;0.57	5.48	5.48	0.80851	.	0.344031	0.34853	N	0.003623	T	0.33644	0.0870	N	0.21545	0.675	0.32844	D	0.505762	B;B;B;B	0.18310	0.027;0.022;0.013;0.027	B;B;B;B	0.22152	0.038;0.01;0.038;0.038	T	0.39482	-0.9612	10	0.19590	T	0.45	.	5.3954	0.16266	0.1575:0.0853:0.0:0.7572	.	190;152;206;206	B4DTD8;G3V1R0;C9JLE3;P51654	.;.;.;GPC3_HUMAN	N	206;206;152	ENSP00000359854:K206N;ENSP00000377836:K206N;ENSP00000444222:K152N	ENSP00000359854:K206N	K	-	3	2	GPC3	132715589	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.542000	0.23222	1.829000	0.53265	0.481000	0.45027	AAA	.	.		0.478	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484		G	132887923	T	G	132887923	3	3	144	1	0	0	0	0	1	0	0	0	6607	1606	56	5	1221	5	GPC3	23	132887923	Missense_Mutation	SNP	T	TCGA-DD-A73C-01A-12D-A33K-10	9711480	132887923	22382637	87	22292										
FAAH	2166	hgsc.bcm.edu	37	chr1	46867761	46867761	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gatccgagtttgttccccacAgaacccagacctggactcag	9	14	1	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr1:46867761A>G	ENST00000243167.8	+	2	279		c.e2-1		FAAH_ENST00000493735.1_Splice_Site	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase						fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	TGTTCCCCACAGAACCCAGAC	0.627																																					.		Atlas-SNP	.											.	FAAH	36	.	0			c.196-2A>G						.						37	33	34					1																	46867761		2202	4300	6502	SO:0001630	splice_region_variant	2166	exon2			CCCCACAGAACCC	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.196-1A>G	chr1.hg19:g.46867761A>G		66.0	0.0		72.0	27.0	NM_001441	D3DQ19|Q52M86|Q5TDF8	Splice_Site	SNP	ENST00000243167.8	hg19	CCDS535.1	.	.	.	.	.	.	.	.	.	.	A	17.83	3.485490	0.63962	.	.	ENSG00000117480	ENST00000243167	.	.	.	4.32	4.32	0.51571	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2997	0.60317	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAAH	46640348	1.000000	0.71417	0.997000	0.53966	0.906000	0.53458	7.064000	0.76721	1.808000	0.52836	0.450000	0.29827	.	.	.		0.627	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	Intron	G	46867761	A	G	46867761	5	3	145	1	0	0	0	0	0	0	1	0	5358	202	7	2	200	2	FAAH	1	46867761	Splice_Site	SNP	A	TCGA-DD-A73D-01A-12D-A32G-10		46867761	202382860	1	22293										
LDLRAD1	388633	hgsc.bcm.edu	37	chr1	54477846	54477846	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ctcatcctcgtcctcgccgtGggtacaggtgcgaacgccat	11	15	1	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr1:54477846G>A	ENST00000371360.1	-	4	327	c.310C>T	c.(310-312)Cac>Tac	p.H104Y	LDLRAD1_ENST00000545928.1_Missense_Mutation_p.H61Y|LDLRAD1_ENST00000420619.1_Missense_Mutation_p.H65Y|LDLRAD1_ENST00000371362.3_Intron	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1	104	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						TCCTCGCCGTGGGTACAGGTG	0.592																																					p.H104Y		Atlas-SNP	.											.	LDLRAD1	22	.	0			c.C310T						.						126	96	106					1																	54477846		2203	4300	6503	SO:0001583	missense	388633	exon4			CGCCGTGGGTACA		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"low density lipoprotein receptor A domain containing 1"				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.310C>T	chr1.hg19:g.54477846G>A	ENSP00000360411:p.His104Tyr	27.0	0.0		22.0	13.0	NM_001010978	A0PJY0|B7ZME3|Q5T6Z9	Missense_Mutation	SNP	ENST00000371360.1	hg19	CCDS30725.1	.	.	.	.	.	.	.	.	.	.	G	5.287	0.238307	0.10023	.	.	ENSG00000203985	ENST00000371360;ENST00000545928;ENST00000420619	D;D;D	0.95588	-3.75;-3.71;-3.71	3.97	3.05	0.35203	.	0.238406	0.29059	N	0.013275	D	0.92338	0.7569	M	0.64997	1.995	0.09310	N	1	B;B	0.14438	0.003;0.01	B;B	0.11329	0.004;0.006	D	0.86249	0.1648	10	0.87932	D	0	-9.9624	5.0431	0.14469	0.109:0.0:0.6855:0.2055	.	61;104	B7ZME3;Q5T700	.;LRAD1_HUMAN	Y	104;61;65	ENSP00000360411:H104Y;ENSP00000445871:H61Y;ENSP00000411017:H65Y	ENSP00000360411:H104Y	H	-	1	0	LDLRAD1	54250434	0.047000	0.20315	0.208000	0.23602	0.101000	0.19017	1.327000	0.33746	1.012000	0.39366	0.655000	0.94253	CAC	.	.		0.592	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978		A	54477846	G	A	54477846	3	1	145	1	0	0	0	0	1	0	0	0	8714	1348	47	3	319	3	LDLRAD1	1	54477846	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	7610085	54477846	194772775	2	22294										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144868027	144868027	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	cacttgccactgctgcccagGtacccaggctctaggattct	9	15	2	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr1:144868027G>T	ENST00000369354.3	-	33	5601	c.5412C>A	c.(5410-5412)taC>taA	p.Y1804*	PDE4DIP_ENST00000369359.4_Nonsense_Mutation_p.Y1940*|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Nonsense_Mutation_p.Y1889*|PDE4DIP_ENST00000313382.9_Nonsense_Mutation_p.Y1698*|PDE4DIP_ENST00000369356.4_Nonsense_Mutation_p.Y1804*			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1804					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGCTGCCCAGGTACCCAGGCT	0.552			T	PDGFRB	MPD																																p.Y1804X		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C5412A						.						226	230	229					1																	144868027		2203	4296	6499	SO:0001587	stop_gained	9659	exon33			GCCCAGGTACCCA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.5412C>A	chr1.hg19:g.144868027G>T	ENSP00000358360:p.Tyr1804*	159.0	0.0		223.0	79.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Nonsense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	48	14.479251	0.99797	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	.	.	.	5.23	4.28	0.50868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.1445	0.59452	0.0:0.0:0.8404:0.1595	.	.	.	.	X	1698;1804;1804;1889;1940	.	ENSP00000327209:Y1698X	Y	-	3	2	PDE4DIP	143579384	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	1.484000	0.35508	2.724000	0.93272	0.650000	0.86243	TAC	.	.		0.552	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144868027	G	T	144868027	4	4	145	1	0	0	0	0	0	1	0	0	11652	1256	44	3	1676	3	PDE4DIP	1	144868027	Nonsense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	90390181	144868027	104382594	3	22295										
SEMA6C	10500	hgsc.bcm.edu	37	chr1	151105186	151105186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gggcagggggggcccggtggCcggagaaaggcaacctccgg	21	11	0	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr1:151105186C>T	ENST00000341697.3	-	19	4258	c.2567G>A	c.(2566-2568)gGc>gAc	p.G856D	RP11-68I18.10_ENST00000563624.1_RNA|SEMA6C_ENST00000479820.1_Intron			Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	856					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GGCCCGGTGGCCGGAGAAAGG	0.786																																					p.G888D		Atlas-SNP	.											.	SEMA6C	70	.	0			c.G2663A						.						2	2	2					1																	151105186		1393	2881	4274	SO:0001583	missense	10500	exon20			CGGTGGCCGGAGA	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"Semaphorins"	10740	protein-coding gene	gene with protein product	"m-Sema Y2"	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.2567G>A	chr1.hg19:g.151105186C>T	ENSP00000344148:p.Gly856Asp	52.0	0.0		108.0	27.0	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	hg19	CCDS984.1	.	.	.	.	.	.	.	.	.	.	C	2.082	-0.410535	0.04799	.	.	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697	T;T;T;T	0.18502	2.23;2.4;2.21;2.23	3.44	1.51	0.23008	.	0.852975	0.09933	N	0.736934	T	0.02267	0.0070	N	0.08118	0	0.09310	N	1	B;B;B	0.22211	0.002;0.066;0.02	B;B;B	0.18561	0.001;0.022;0.01	T	0.45920	-0.9228	10	0.40728	T	0.16	.	4.5733	0.12221	0.135:0.2453:0.6196:0.0	.	848;888;856	Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;SEM6C_HUMAN	D	856;848;888;856	ENSP00000357910:G856D;ENSP00000357908:G848D;ENSP00000357909:G888D;ENSP00000344148:G856D	ENSP00000344148:G856D	G	-	2	0	SEMA6C	149371810	0.001000	0.12720	0.000000	0.03702	0.058000	0.15608	0.500000	0.22562	0.166000	0.19597	-0.519000	0.04390	GGC	.	.		0.786	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		T	151105186	C	T	151105186	3	4	145	1	0	0	0	0	1	0	0	0	14056	739	26	3	229	3	SEMA6C	1	151105186	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	6237159	151105186	98145435	4	22296										
OR6Y1	391112	hgsc.bcm.edu	37	chr1	158517298	158517298	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gaagaagtccaccatctcagCctgtgaggcatcctcacagg	10	13	2	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr1:158517298C>A	ENST00000302617.3	-	1	597	c.598G>T	c.(598-600)Gct>Tct	p.A200S		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					ACCATCTCAGCCTGTGAGGCA	0.478																																					p.A200S		Atlas-SNP	.											.	OR6Y1	73	.	0			c.G598T						.						87	77	80					1																	158517298		2202	4300	6502	SO:0001583	missense	391112	exon1			TCTCAGCCTGTGA	BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"GPCR / Class A : Olfactory receptors"	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.598G>T	chr1.hg19:g.158517298C>A	ENSP00000304807:p.Ala200Ser	61.0	0.0		130.0	67.0	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	hg19	CCDS30899.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.816663	0.50633	.	.	ENSG00000197532	ENST00000302617	T	0.80214	-1.35	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41938	D	0.000800	T	0.72977	0.3528	N	0.20881	0.62	0.26968	N	0.965653	D	0.69078	0.997	D	0.66196	0.942	T	0.65405	-0.6176	10	0.26408	T	0.33	.	13.2112	0.59825	0.1599:0.8401:0.0:0.0	.	200	Q8NGX8	OR6Y1_HUMAN	S	200	ENSP00000304807:A200S	ENSP00000304807:A200S	A	-	1	0	OR6Y1	156783922	0.000000	0.05858	0.995000	0.50966	0.979000	0.70002	0.135000	0.15952	2.763000	0.94921	0.655000	0.94253	GCT	.	.		0.478	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		A	158517298	C	A	158517298	3	1	145	1	0	0	0	0	1	0	0	0	11222	739	26	3	381	3	OR6Y1	1	158517298	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	7412112	158517298	90733323	5	22297										
LHX9	56956	hgsc.bcm.edu	37	chr1	197896793	197896793	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	accctcgcagaagaccaagcGcatgcgaacctctttcaagc	8	15	2	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr1:197896793G>A	ENST00000367387.4	+	4	1231	c.806G>A	c.(805-807)cGc>cAc	p.R269H	LHX9_ENST00000337020.2_Missense_Mutation_p.R269H|LHX9_ENST00000367390.3_Missense_Mutation_p.R260H|LHX9_ENST00000367391.1_Missense_Mutation_p.R260H|LHX9_ENST00000561173.1_Missense_Mutation_p.R275H	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	269					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						AAGACCAAGCGCATGCGAACC	0.527																																					p.R269H		Atlas-SNP	.											.	LHX9	144	.	0			c.G806A						.						256	250	252					1																	197896793		2203	4300	6503	SO:0001583	missense	56956	exon4			CCAAGCGCATGCG	AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"Homeoboxes / LIM class"	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367387.4:c.806G>A	chr1.hg19:g.197896793G>A	ENSP00000356357:p.Arg269His	93.0	0.0		215.0	114.0	NM_020204	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Missense_Mutation	SNP	ENST00000367387.4	hg19	CCDS1393.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.707531	0.89018	.	.	ENSG00000143355	ENST00000367391;ENST00000367390;ENST00000337020;ENST00000367387	D;D;D;D	0.97138	-4.26;-4.26;-4.26;-4.26	5.88	5.88	0.94601	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98960	0.9646	M	0.93763	3.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99215	1.0877	10	0.72032	D	0.01	.	20.2441	0.98394	0.0:0.0:1.0:0.0	.	269;260;260	Q9NQ69;Q9NQ69-3;Q9NQ69-2	LHX9_HUMAN;.;.	H	260;260;269;269	ENSP00000356361:R260H;ENSP00000356360:R260H;ENSP00000337969:R269H;ENSP00000356357:R269H	ENSP00000337969:R269H	R	+	2	0	LHX9	196163416	1.000000	0.71417	1.000000	0.80357	0.414000	0.31173	9.476000	0.97823	2.774000	0.95407	0.655000	0.94253	CGC	.	.		0.527	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086547.2	NM_020204		A	197896793	G	A	197896793	3	1	145	1	0	0	0	0	1	0	0	0	8786	1087	38	1	852	1	LHX9	1	197896793	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	39379495	197896793	51353828	6	22298										
MARK1	4139	hgsc.bcm.edu	37	chr1	220791830	220791830	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	agtggatgtgtggagtctggGcgtcattctctatacattag	13	6	3	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr1:220791830G>T	ENST00000366917.4	+	8	997	c.731G>T	c.(730-732)gGc>gTc	p.G244V	MARK1_ENST00000366918.4_Missense_Mutation_p.G222V|MARK1_ENST00000402574.1_Missense_Mutation_p.G109V					MAP/microtubule affinity-regulating kinase 1											central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		TGGAGTCTGGGCGTCATTCTC	0.433																																					p.G244V		Atlas-SNP	.											.	MARK1	161	.	0			c.G731T						.						90	92	91					1																	220791830		2203	4300	6503	SO:0001583	missense	4139	exon8			GTCTGGGCGTCAT	AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.731G>T	chr1.hg19:g.220791830G>T	ENSP00000355884:p.Gly244Val	104.0	0.0		163.0	36.0	NM_018650		Missense_Mutation	SNP	ENST00000366917.4	hg19	CCDS31029.2	.	.	.	.	.	.	.	.	.	.	G	22.7	4.324094	0.81580	.	.	ENSG00000116141	ENST00000402574;ENST00000366918;ENST00000366917	T;T;T	0.72725	-0.68;-0.68;-0.68	5.74	5.74	0.90152	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91469	0.7307	H	0.98849	4.35	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;0.996;1.0;0.999	D	0.94440	0.7657	10	0.87932	D	0	.	19.9145	0.97053	0.0:0.0:1.0:0.0	.	244;109;244;222	B4DIB3;Q9P0L2-2;Q9P0L2;Q9P0L2-3	.;.;MARK1_HUMAN;.	V	109;222;244	ENSP00000386017:G109V;ENSP00000355885:G222V;ENSP00000355884:G244V	ENSP00000355884:G244V	G	+	2	0	MARK1	218858453	1.000000	0.71417	0.799000	0.32177	0.522000	0.34438	9.807000	0.99171	2.709000	0.92574	0.655000	0.94253	GGC	.	.		0.433	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			T	220791830	G	T	220791830	3	4	145	1	0	0	0	0	1	0	0	0	9321	1203	42	3	761	3	MARK1	1	220791830	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	22895037	220791830	28458791	7	22299										
TP53BP2	7159	hgsc.bcm.edu	37	chr1	224009040	224009040	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	acttctgtgaagtgctgctcAttgttactgagatacacggt	10	8	2	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr1:224009040A>C	ENST00000343537.7	-	2	348	c.57T>G	c.(55-57)aaT>aaG	p.N19K	TP53BP2_ENST00000391878.2_5'UTR	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	13					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		AGTGCTGCTCATTGTTACTGA	0.423																																					p.N19K		Atlas-SNP	.											.	TP53BP2	144	.	0			c.T57G						.						214	218	217					1																	224009040		2001	4189	6190	SO:0001583	missense	7159	exon2			CTGCTCATTGTTA	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.57T>G	chr1.hg19:g.224009040A>C	ENSP00000341957:p.Asn19Lys	70.0	0.0		135.0	65.0	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	hg19	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.464737	0.63513	.	.	ENSG00000143514	ENST00000343537	D	0.83673	-1.75	5.75	-5.15	0.02866	.	0.189267	0.53938	D	0.000042	T	0.76535	0.4001	L	0.54323	1.7	0.80722	D	1	B	0.24258	0.1	B	0.24541	0.054	T	0.59451	-0.7452	10	0.72032	D	0.01	.	15.6636	0.77209	0.4471:0.0:0.5529:0.0	.	19	B4DG66	.	K	19	ENSP00000341957:N19K	ENSP00000341957:N19K	N	-	3	2	TP53BP2	222075663	0.004000	0.15560	0.741000	0.31004	0.997000	0.91878	-0.898000	0.04105	-1.004000	0.03421	0.482000	0.46254	AAT	.	.		0.423	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		C	224009040	A	C	224009040	3	2	145	1	0	0	0	0	1	0	0	0	16399	214	8	5	3415	5	TP53BP2	1	224009040	Missense_Mutation	SNP	A	TCGA-DD-A73D-01A-12D-A32G-10	3217210	224009040	25241581	8	22300										
FH	2271	hgsc.bcm.edu	37	chr1	241667442	241667442	+	Missense_Mutation	SNP	C	C	T													0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	cgaatatcatttgctatcttCatcagactgcaggcagtagt							TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr1:241667442C>T	ENST00000366560.3	-	7	1046	c.1008G>A	c.(1006-1008)atG>atA	p.M336I		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	336					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		TTGCTATCTTCATCAGACTGC	0.473			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												p.M336I	Melanoma(148;1573 2486 7381 46575)	Atlas-SNP	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	.	FH	64	.	0			c.G1008A						.						103	86	92					1																	241667442		2203	4300	6503	SO:0001583	missense	2271	exon7	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	TATCTTCATCAGA	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.1008G>A	chr1.hg19:g.241667442C>T	ENSP00000355518:p.Met336Ile	98.0	0.0		213.0	109.0	NM_000143	B1ANK7	Missense_Mutation	SNP	ENST00000366560.3	hg19	CCDS1617.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.852960	0.91355	.	.	ENSG00000091483	ENST00000366560	D	0.99298	-5.71	5.73	5.73	0.89815	Lyase 1, N-terminal (1);L-Aspartase-like (1);	0.159969	0.64402	D	0.000001	D	0.99152	0.9707	M	0.62016	1.91	0.80722	D	1	D	0.54047	0.964	P	0.61201	0.885	D	0.99723	1.1010	10	0.72032	D	0.01	-35.535	17.3941	0.87440	0.0:1.0:0.0:0.0	.	336	P07954	FUMH_HUMAN	I	336	ENSP00000355518:M336I	ENSP00000355518:M336I	M	-	3	0	FH	239734065	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.293000	0.78740	2.709000	0.92574	0.655000	0.94253	ATG	.	.		0.473	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		T	241667442	C	T	241667442	3	4	145	1	0	0	0	0	1	0	0	0	5883	826	29	3	540	3	FH	1	241667442	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	17658402	241667442	7583179	9	22301	97	2								
FH	2271	hgsc.bcm.edu	37	chr1	241667444	241667444	+	Missense_Mutation	SNP	T	T	G													0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	aatatcatttgctatcttcaTcagactgcaggcagtagtgt							TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr1:241667444T>G	ENST00000366560.3	-	7	1044	c.1006A>C	c.(1006-1008)Atg>Ctg	p.M336L		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	336					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		GCTATCTTCATCAGACTGCAG	0.473			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												p.M336L	Melanoma(148;1573 2486 7381 46575)	Atlas-SNP	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	.	FH	64	.	0			c.A1006C						.						103	85	91					1																	241667444		2203	4300	6503	SO:0001583	missense	2271	exon7	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	TCTTCATCAGACT	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.1006A>C	chr1.hg19:g.241667444T>G	ENSP00000355518:p.Met336Leu	94.0	0.0		215.0	110.0	NM_000143	B1ANK7	Missense_Mutation	SNP	ENST00000366560.3	hg19	CCDS1617.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.765506	0.69878	.	.	ENSG00000091483	ENST00000366560	D	0.99319	-5.74	5.73	5.73	0.89815	Lyase 1, N-terminal (1);L-Aspartase-like (1);	0.159969	0.64402	D	0.000001	D	0.98692	0.9561	M	0.77103	2.36	0.80722	D	1	B	0.26195	0.144	B	0.34590	0.186	D	0.98543	1.0633	10	0.59425	D	0.04	-35.535	13.9704	0.64237	0.0:0.0:0.0:1.0	.	336	P07954	FUMH_HUMAN	L	336	ENSP00000355518:M336L	ENSP00000355518:M336L	M	-	1	0	FH	239734067	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.498000	0.81546	2.187000	0.69744	0.533000	0.62120	ATG	.	.		0.473	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		G	241667444	T	G	241667444	3	3	145	1	0	0	0	0	1	0	0	0	5883	1435	50	5	542	5	FH	1	241667444	Missense_Mutation	SNP	T	TCGA-DD-A73D-01A-12D-A32G-10	2	241667444	7583177	10	22302	97	2								
DPP10	57628	hgsc.bcm.edu	37	chr2	116503668	116503668	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	tcattttctcaaaggcaggtCaagtgaacccaacaataaaa	6	9	3	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr2:116503668C>G	ENST00000410059.1	+	10	1339	c.859C>G	c.(859-861)Caa>Gaa	p.Q287E	DPP10_ENST00000393147.2_Missense_Mutation_p.Q291E|DPP10_ENST00000310323.8_Missense_Mutation_p.Q280E|DPP10_ENST00000409163.1_Missense_Mutation_p.Q237E	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	287						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						AAAGGCAGGTCAAGTGAACCC	0.333																																					p.Q291E		Atlas-SNP	.											.	DPP10	415	.	0			c.C871G						.						84	78	80					2																	116503668		2203	4300	6503	SO:0001583	missense	57628	exon10			GCAGGTCAAGTGA	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.859C>G	chr2.hg19:g.116503668C>G	ENSP00000386565:p.Gln287Glu	74.0	0.0		106.0	61.0	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.888090	0.33348	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.21	5.21	0.72293	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.18923	0.0454	N	0.13168	0.305	0.58432	D	0.999998	B;B;B;B	0.10296	0.002;0.003;0.002;0.002	B;B;B;B	0.15484	0.008;0.007;0.013;0.013	T	0.06534	-1.0821	10	0.07175	T	0.84	-9.865	17.9186	0.88959	0.0:1.0:0.0:0.0	.	280;291;283;287	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	E	287;237;291;280;237	ENSP00000386565:Q287E;ENSP00000387038:Q237E;ENSP00000376855:Q291E;ENSP00000309066:Q280E	ENSP00000309066:Q280E	Q	+	1	0	DPP10	116220138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.233000	0.58651	2.718000	0.92993	0.585000	0.79938	CAA	.	.		0.333	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		G	116503668	C	G	116503668	3	3	145	1	0	0	0	0	1	0	0	0	4729	827	29	4	1068	4	DPP10	2	116503668	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10		116503668	126695705	11	22303										
SP3	6670	hgsc.bcm.edu	37	chr2	174820570	174820570	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ctgtggtatgagattctggaTgttagcagaaggtgttccag	14	5	1	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr2:174820570T>C	ENST00000310015.6	-	4	1200	c.670A>G	c.(670-672)Atc>Gtc	p.I224V	SP3_ENST00000455789.2_Missense_Mutation_p.I171V|SP3_ENST00000483084.1_5'Flank|SP3_ENST00000418194.2_Missense_Mutation_p.I156V	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	224	Transactivation domain (Gln-rich).				B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			AGATTCTGGATGTTAGCAGAA	0.438																																					p.I224V		Atlas-SNP	.											.	SP3	82	.	0			c.A670G						.						151	155	154					2																	174820570		2203	4300	6503	SO:0001583	missense	6670	exon4			TCTGGATGTTAGC	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.670A>G	chr2.hg19:g.174820570T>C	ENSP00000310301:p.Ile224Val	62.0	0.0		103.0	68.0	NM_003111	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Missense_Mutation	SNP	ENST00000310015.6	hg19	CCDS2254.1	.	.	.	.	.	.	.	.	.	.	T	12.15	1.851429	0.32699	.	.	ENSG00000172845	ENST00000310015;ENST00000455789;ENST00000418194	T;T;T	0.06068	3.37;3.35;3.35	5.95	5.95	0.96441	.	0.096173	0.64402	D	0.000001	T	0.08313	0.0207	L	0.47190	1.495	0.32573	N	0.529519	B;B;B	0.19706	0.022;0.022;0.038	B;B;B	0.21708	0.016;0.016;0.036	T	0.03739	-1.1008	10	0.39692	T	0.17	.	12.8669	0.57944	0.0:0.0:0.1357:0.8643	.	221;224;171	B7ZLN9;Q02447;Q02447-6	.;SP3_HUMAN;.	V	224;171;156	ENSP00000310301:I224V;ENSP00000388903:I171V;ENSP00000406140:I156V	ENSP00000310301:I224V	I	-	1	0	SP3	174528816	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.752000	0.62176	2.272000	0.75746	0.460000	0.39030	ATC	.	.		0.438	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111		C	174820570	T	C	174820570	3	2	145	1	0	0	0	0	1	0	0	0	14980	1464	51	2	1691	2	SP3	2	174820570	Missense_Mutation	SNP	T	TCGA-DD-A73D-01A-12D-A32G-10	58316902	174820570	68378803	12	22304										
TTN	7273	hgsc.bcm.edu	37	chr2	179560965	179560965	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gtcattatttttacttcttcAgctttagaggatacatcaat	5	7	4	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr2:179560965A>G	ENST00000591111.1	-	112	30107	c.29883T>C	c.(29881-29883)gcT>gcC	p.A9961A	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Silent_p.A10278A|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.A9034A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTACTTCTTCAGCTTTAGAGG	0.328																																					p.A10278A		Atlas-SNP	.											.	TTN	18412	.	0			c.T30834C						.						34	28	30					2																	179560965		1790	4034	5824	SO:0001819	synonymous_variant	7273	exon114			TTCTTCAGCTTTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.29883T>C	chr2.hg19:g.179560965A>G		71.0	0.0		82.0	49.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.328	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179560965	A	G	179560965	2	3	145	1	0	0	0	0	0	0	0	1	16750	175	7	2		2	TTN	2	179560965	Silent	SNP	A	TCGA-DD-A73D-01A-12D-A32G-10	4740395	179560965	63638408	13	22305										
STRADB	55437	hgsc.bcm.edu	37	chr2	202344886	202344886	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	cctgatgaaaaagactcataCtgggaattctagggctgcca	10	9	2	3	rs146098224		TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr2:202344886C>T	ENST00000194530.3	+	12	1610	c.1245C>T	c.(1243-1245)taC>taT	p.Y415Y	STRADB_ENST00000392249.2_3'UTR	NM_001206864.1|NM_018571.5	NP_001193793.1|NP_061041.2	Q9C0K7	STRAB_HUMAN	STE20-related kinase adaptor beta	415					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cell morphogenesis (GO:0000902)|insulin receptor signaling pathway (GO:0008286)|JNK cascade (GO:0007254)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|lung(5)|prostate(1)|skin(3)|stomach(1)	13						AAGACTCATACTGGGAATTCT	0.393																																					p.Y415Y		Atlas-SNP	.											.	STRADB	33	.	0			c.C1245T						.						134	136	135					2																	202344886		2203	4300	6503	SO:0001819	synonymous_variant	55437	exon12			CTCATACTGGGAA	AB038950	CCDS2348.1, CCDS56161.1	2q33.1	2010-09-30	2008-09-15	2008-09-15	ENSG00000082146	ENSG00000082146			13205	protein-coding gene	gene with protein product		607333	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2"	ALS2CR2		11161814, 14511394	Standard	NM_018571		Approved	CALS-21, PAPK, ILPIPA, ILPIP	uc002uyd.4	Q9C0K7	OTTHUMG00000132831	ENST00000194530.3:c.1245C>T	chr2.hg19:g.202344886C>T		50.0	0.0		131.0	7.0	NM_018571	Q5BKY7|Q9P1L0	Silent	SNP	ENST00000194530.3	hg19	CCDS2348.1																																																																																			.	.		0.393	STRADB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256297.1	NM_018571		T	202344886	C	T	202344886	2	4	145	1	0	0	0	0	0	0	0	1	15340	576	20	3		3	STRADB	2	202344886	Silent	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	22783921	202344886	40854487	14	22306										
PSMD1	5707	hgsc.bcm.edu	37	chr2	231931711	231931711	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	attgaccagagattggaaggCatcgtaaataaaatgttcca	9	6	0	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr2:231931711C>T	ENST00000308696.6	+	5	558	c.396C>T	c.(394-396)ggC>ggT	p.G132G	PSMD1_ENST00000373635.4_Silent_p.G132G|PSMD1_ENST00000409643.1_Silent_p.G132G	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	132					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	GATTGGAAGGCATCGTAAATA	0.403																																					p.G132G		Atlas-SNP	.											.	PSMD1	77	.	0			c.C396T						.						92	80	84					2																	231931711		2203	4300	6503	SO:0001819	synonymous_variant	5707	exon5			GGAAGGCATCGTA	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.396C>T	chr2.hg19:g.231931711C>T		85.0	0.0		112.0	14.0	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Silent	SNP	ENST00000308696.6	hg19	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	C	9.125	1.009968	0.19277	.	.	ENSG00000173692	ENST00000444007	.	.	.	5.5	2.64	0.31445	.	.	.	.	.	T	0.56381	0.1981	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49854	-0.8895	4	.	.	.	-19.4227	8.226	0.31568	0.0:0.5538:0.2694:0.1768	.	.	.	.	Y	32	.	.	H	+	1	0	PSMD1	231639955	0.993000	0.37304	1.000000	0.80357	0.934000	0.57294	0.288000	0.18939	0.678000	0.31325	0.591000	0.81541	CAT	.	.		0.403	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			T	231931711	C	T	231931711	2	4	145	1	0	0	0	0	0	0	0	1	12704	697	25	3		3	PSMD1	2	231931711	Silent	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	29586825	231931711	11267662	15	22307										
GALNTL2	117248	hgsc.bcm.edu	37	chr3	16217085	16217085	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gggctgatgaggacggggagGtgtctgaagaagaggagttg	21	3	1	5			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr3:16217085G>A	ENST00000339732.5	+	1	930	c.427G>A	c.(427-429)Gtg>Atg	p.V143M	GALNT15_ENST00000470031.1_3'UTR|GALNT15_ENST00000437509.1_Missense_Mutation_p.V143M	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	143					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										GGACGGGGAGGTGTCTGAAGA	0.647																																					p.V143M		Atlas-SNP	.											.	.	.	.	0			c.G427A						.						36	30	32					3																	16217085		2203	4299	6502	SO:0001583	missense	117248	exon1			GGGGAGGTGTCTG	AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"Glycosyltransferase family 2 domain containing"	21531	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 15"	615131	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.427G>A	chr3.hg19:g.16217085G>A	ENSP00000344260:p.Val143Met	41.0	0.0		31.0	18.0	NM_054110	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	hg19	CCDS33711.1	.	.	.	.	.	.	.	.	.	.	G	3.814	-0.039093	0.07497	.	.	ENSG00000131386	ENST00000339732;ENST00000437509	T;T	0.57595	0.61;0.39	3.43	1.58	0.23477	.	2.240140	0.02772	U	0.119801	T	0.34716	0.0907	N	0.08118	0	0.09310	N	1	B	0.22480	0.07	B	0.24541	0.054	T	0.29701	-1.0003	10	0.42905	T	0.14	.	6.6406	0.22906	0.3242:0.0:0.6758:0.0	.	143	Q8N3T1	GLTL2_HUMAN	M	143	ENSP00000344260:V143M;ENSP00000395873:V143M	ENSP00000344260:V143M	V	+	1	0	GALNTL2	16192089	0.159000	0.22864	0.056000	0.19401	0.275000	0.26752	3.323000	0.52014	0.802000	0.34089	0.442000	0.29010	GTG	.	.		0.647	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110		A	16217085	G	A	16217085	3	1	145	1	0	0	0	0	1	0	0	0	6230	1261	44	3	429	3	GALNTL2	3	16217085	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10		16217085	181805345	16	22308										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr3:41266098A>G	ENST00000349496.5	+	3	375	c.95A>G	c.(94-96)gAc>gGc	p.D32G	CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95G						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>G	chr3.hg19:g.41266098A>G	ENSP00000344456:p.Asp32Gly	106.0	0.0		145.0	82.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308122	0.81247	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69788	0.3150	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.74137	-0.3762	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	G	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25G;ENSP00000385604:D32G;ENSP00000412219:D32G;ENSP00000379486:D32G;ENSP00000344456:D32G;ENSP00000411226:D25G;ENSP00000379488:D32G;ENSP00000409302:D32G;ENSP00000401599:D32G	ENSP00000344456:D32G	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266098	A	G	41266098	3	3	145	1	0	0	0	0	1	0	0	0	4018	275	10	2	101	2	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-DD-A73D-01A-12D-A32G-10	25049013	41266098	156756332	17	22309										
MAPKAPK3	7867	hgsc.bcm.edu	37	chr3	50677796	50677796	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	tctatgtgcacccacctacaGctcctgtatgacagccccaa	6	16	1	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr3:50677796G>A	ENST00000446044.1	+	5	815		c.e5-1		MAPKAPK3_ENST00000357955.2_Splice_Site	NM_001243926.1	NP_001230855.1	Q16644	MAPK3_HUMAN	mitogen-activated protein kinase-activated protein kinase 3						activation of MAPK activity (GO:0000187)|innate immune response (GO:0045087)|macropinocytosis (GO:0044351)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|Ras protein signal transduction (GO:0007265)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.0188)|Kidney(197;0.0223)		CCCACCTACAGCTCCTGTATG	0.542																																					.		Atlas-SNP	.											.	MAPKAPK3	32	.	0			c.220-1G>A						.						109	116	113					3																	50677796		2203	4300	6503	SO:0001630	splice_region_variant	7867	exon5			CCTACAGCTCCTG	U43784	CCDS2832.1	3p21.3	2004-03-10			ENSG00000114738	ENSG00000114738			6888	protein-coding gene	gene with protein product		602130				8626550, 8622688	Standard	NM_004635		Approved	3pK, MAPKAP3, 3PK	uc003dba.2	Q16644	OTTHUMG00000156850	ENST00000446044.1:c.220-1G>A	chr3.hg19:g.50677796G>A		78.0	0.0		79.0	36.0	NM_001243926	B5BU67	Splice_Site	SNP	ENST00000446044.1	hg19	CCDS2832.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.973063	0.53614	.	.	ENSG00000114738	ENST00000446044;ENST00000430409;ENST00000357955;ENST00000457064	.	.	.	5.58	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4652	0.75394	0.0:0.0:0.86:0.14	.	.	.	.	.	-1	.	.	.	+	.	.	MAPKAPK3	50652800	1.000000	0.71417	0.977000	0.42913	0.407000	0.30961	9.835000	0.99442	1.324000	0.45282	0.655000	0.94253	.	.	.		0.542	MAPKAPK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346237.1	NM_004635	Intron	A	50677796	G	A	50677796	5	1	145	1	0	0	0	0	0	0	1	0	9299	985	34	3	225	3	MAPKAPK3	3	50677796	Splice_Site	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	9411698	50677796	147344634	18	22310										
OR5H6	79295	hgsc.bcm.edu	37	chr3	97983496	97983496	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	atttttttcccttgtaaccaCtgtaaccacagaatgttttc	4	10	0	1	rs398062605|rs74203917|rs145155372	byFrequency	TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr3:97983496C>T	ENST00000383696.2	+	1	409	c.368C>T	c.(367-369)aCt>aTt	p.T123I	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						CTTGTAACCACTGTAACCACA	0.383																																					p.T123I		Atlas-SNP	.											.	OR5H6	89	.	0			c.C368T						.						94	59	70					3																	97983496		2193	4234	6427	SO:0001583	missense	79295	exon1			TAACCACTGTAAC	BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"GPCR / Class A : Olfactory receptors"	14767	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily H, member 6"				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.368C>T	chr3.hg19:g.97983496C>T	ENSP00000373196:p.Thr123Ile	53.0	0.0		79.0	7.0	NM_001005479	Q6IF88	Missense_Mutation	SNP	ENST00000383696.2	hg19	CCDS33800.1	.	.	.	.	.	.	.	.	.	.	-	2.074	-0.412329	0.04799	.	.	ENSG00000230301	ENST00000383696	T	0.00469	7.21	2.19	-0.203	0.13204	GPCR, rhodopsin-like superfamily (1);	0.914442	0.09287	N	0.822835	T	0.00241	0.0007	N	0.11560	0.145	0.09310	N	1	B	0.23591	0.088	B	0.23275	0.045	T	0.37776	-0.9691	10	0.72032	D	0.01	.	4.9951	0.14235	0.0:0.4399:0.3432:0.217	.	123	Q8NGV6	OR5H6_HUMAN	I	123	ENSP00000373196:T123I	ENSP00000373196:T123I	T	+	2	0	OR5H6	99466186	0.000000	0.05858	0.076000	0.20297	0.003000	0.03518	0.098000	0.15189	0.251000	0.21505	-1.188000	0.01700	ACT	.	.		0.383	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2			T	97983496	C	T	97983496	3	4	145	1	0	0	0	0	1	0	0	0	11172	565	20	3	370	3	OR5H6	3	97983496	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	47305700	97983496	100038934	19	22311										
VEPH1	79674	hgsc.bcm.edu	37	chr3	157098983	157098983	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gtattttccagttgtcgggtAaggagtttagcaatggcggt	14	5	0	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr3:157098983A>C	ENST00000362010.2	-	7	1396	c.1089T>G	c.(1087-1089)ctT>ctG	p.L363L	VEPH1_ENST00000392833.2_Silent_p.L363L|VEPH1_ENST00000543418.1_Silent_p.L363L|RP11-550I24.2_ENST00000487238.1_RNA|VEPH1_ENST00000392832.2_Silent_p.L363L	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	363						plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			GTTGTCGGGTAAGGAGTTTAG	0.522																																					p.L363L		Atlas-SNP	.											.	VEPH1	129	.	0			c.T1089G						.						190	175	180					3																	157098983		2203	4300	6503	SO:0001819	synonymous_variant	79674	exon7			TCGGGTAAGGAGT	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"Pleckstrin homology (PH) domain containing"	25735	protein-coding gene	gene with protein product		609594	"ventricular zone expressed PH domain homolog 1 (zebrafish)"			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.1089T>G	chr3.hg19:g.157098983A>C		85.0	0.0		104.0	43.0	NM_001167911	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Silent	SNP	ENST00000362010.2	hg19	CCDS3179.1																																																																																			.	.		0.522	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621		C	157098983	A	C	157098983	2	2	145	1	0	0	0	0	0	0	0	1	17169	349	13	5		5	VEPH1	3	157098983	Silent	SNP	A	TCGA-DD-A73D-01A-12D-A32G-10	59115487	157098983	40923447	20	22312										
CPEB2	132864	hgsc.bcm.edu	37	chr4	15067830	15067830	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	atgtgtgatgaatgccagggCgcacgctgtggtggaaaatt	15	6	0	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr4:15067830C>T	ENST00000507071.1	+	11	1683	c.1596C>T	c.(1594-1596)ggC>ggT	p.G532G	CPEB2_ENST00000259997.5_Silent_p.G540G|CPEB2_ENST00000345451.3_Silent_p.G502G|CPEB2_ENST00000538197.1_Silent_p.G977G|CPEB2_ENST00000382395.3_Silent_p.G510G|RP11-665G4.1_ENST00000513384.1_RNA|CPEB2_ENST00000442003.2_Silent_p.G950G|CPEB2_ENST00000382401.3_Silent_p.G505G|RP11-665G4.1_ENST00000502344.1_RNA|CPEB2_ENST00000541112.1_Silent_p.G969G			Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding protein 2	532					cellular response to arsenic-containing substance (GO:0071243)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to oxidative stress (GO:0034599)|negative regulation of cytoplasmic translation (GO:2000766)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of GTPase activity (GO:0034260)	cytoplasm (GO:0005737)|messenger ribonucleoprotein complex (GO:1990124)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|ribosome binding (GO:0043022)|translation repressor activity, nucleic acid binding (GO:0000900)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(3)	14						AATGCCAGGGCGCACGCTGTG	0.438																																					p.G977G		Atlas-SNP	.											CPEB2_ENST00000538197,caecum,carcinoma,0,2	CPEB2	77	.	0			c.C2931T						.						271	253	259					4																	15067830		2203	4300	6503	SO:0001819	synonymous_variant	132864	exon12			CCAGGGCGCACGC	AY247744	CCDS56325.1, CCDS56326.1	4p15.33	2013-02-12			ENSG00000137449	ENSG00000137449		"RNA binding motif (RRM) containing"	21745	protein-coding gene	gene with protein product		610605				12672660	Standard	NM_182485		Approved		uc003gnk.2	Q7Z5Q1	OTTHUMG00000090669	ENST00000507071.1:c.1596C>T	chr4.hg19:g.15067830C>T		113.0	0.0		119.0	42.0	NM_001177382	E7EPM3|F5H160|Q3B8N6|Q3MI89|Q3MI90|Q3MI92|Q7Z5Q0	Silent	SNP	ENST00000507071.1	hg19																																																																																				.	.		0.438	CPEB2-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000207349.2	XM_059607		T	15067830	C	T	15067830	2	4	145	1	0	0	0	0	0	0	0	1	3803	755	27	1		1	CPEB2	4	15067830	Silent	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10		15067830	176086446	21	22313										
KIT	3815	hgsc.bcm.edu	37	chr4	55604594	55604594	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ctatgggcttgttttctccaGatttactccaacttagcaaa	6	10	1	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr4:55604594G>T	ENST00000288135.5	+	21	2899		c.e21-1			NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog						actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GTTTTCTCCAGATTTACTCCA	0.483		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												.		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT	7396	.	0			c.2803-1G>T						.						182	172	175					4																	55604594		2203	4300	6503	SO:0001630	splice_region_variant	3815	exon21	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	TCTCCAGATTTAC	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2803-1G>T	chr4.hg19:g.55604594G>T		87.0	0.0		69.0	31.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Splice_Site	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475945	0.63737	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4545	0.87603	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIT	55299351	1.000000	0.71417	1.000000	0.80357	0.567000	0.35839	8.058000	0.89460	2.649000	0.89929	0.561000	0.74099	.	.	.		0.483	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		Intron	T	55604594	G	T	55604594	5	4	145	1	0	0	0	0	0	0	1	0	8338	956	33	3	2884	3	KIT	4	55604594	Splice_Site	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	40536764	55604594	135549682	22	22314										
SOX30	11063	hgsc.bcm.edu	37	chr5	157065387	157065387	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gaagcctgggggattggagcActtctgggacaaggggaaac	17	7	1	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr5:157065387A>T	ENST00000265007.6	-	4	2072	c.1731T>A	c.(1729-1731)agT>agA	p.S577R	SOX30_ENST00000519442.1_Missense_Mutation_p.S272R|SOX30_ENST00000311371.5_Intron	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	577	Pro-rich.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGATTGGAGCACTTCTGGGAC	0.547																																					p.S577R	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.T1731A						.						97	94	95					5																	157065387		2203	4300	6503	SO:0001583	missense	11063	exon4			TGGAGCACTTCTG	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"SRY (sex determining region Y)-boxes"	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.1731T>A	chr5.hg19:g.157065387A>T	ENSP00000265007:p.Ser577Arg	60.0	0.0		87.0	38.0	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	hg19	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.908333	0.52333	.	.	ENSG00000039600	ENST00000265007;ENST00000519442	D;D	0.98044	-4.47;-4.68	5.61	1.44	0.22558	.	0.128095	0.53938	D	0.000047	D	0.93841	0.8030	N	0.24115	0.695	0.27152	N	0.961391	P;D	0.54397	0.664;0.966	B;P	0.44860	0.235;0.462	D	0.89330	0.3646	10	0.87932	D	0	.	8.8124	0.34976	0.637:0.0:0.363:0.0	.	272;577	B4DXW7;O94993	.;SOX30_HUMAN	R	577;272	ENSP00000265007:S577R;ENSP00000427984:S272R	ENSP00000265007:S577R	S	-	3	2	SOX30	156997965	0.994000	0.37717	0.992000	0.48379	0.970000	0.65996	0.524000	0.22940	0.010000	0.14839	0.528000	0.53228	AGT	.	.		0.547	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		T	157065387	A	T	157065387	3	4	145	1	0	0	0	0	1	0	0	0	14967	156	6	4	538	4	SOX30	5	157065387	Missense_Mutation	SNP	A	TCGA-DD-A73D-01A-12D-A32G-10		157065387	23849873	23	22315										
RNF39	80352	hgsc.bcm.edu	37	chr6	30043421	30043421	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ccgtgaccgccttcgagcgcGcagatggcgggccgcccctg	15	17	0	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr6:30043421G>A	ENST00000244360.6	-	1	243	c.146C>T	c.(145-147)gCg>gTg	p.A49V	RNF39_ENST00000376751.3_Missense_Mutation_p.A49V	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	49						cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										CTTCGAGCGCGCAGATGGCGG	0.672																																					p.A49V	NSCLC(8;188 360 1520 20207 31481)	Atlas-SNP	.											.	RNF39	27	.	0			c.C146T						.						25	27	26					6																	30043421		2201	4296	6497	SO:0001583	missense	80352	exon1			GAGCGCGCAGATG	AF238315	CCDS4673.1, CCDS4674.1	6p21.3	2013-01-09			ENSG00000204618	ENSG00000204618		"RING-type (C3HC4) zinc fingers"	18064	protein-coding gene	gene with protein product		607524				11130983, 11716498	Standard	NM_170769		Approved	HZFw1, LIRF	uc003npe.3	Q9H2S5	OTTHUMG00000031288	ENST00000244360.6:c.146C>T	chr6.hg19:g.30043421G>A	ENSP00000244360:p.Ala49Val	69.0	0.0		151.0	8.0	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Missense_Mutation	SNP	ENST00000244360.6	hg19	CCDS4673.1	.	.	.	.	.	.	.	.	.	.	g	18.49	3.635272	0.67130	.	.	ENSG00000204618	ENST00000376751;ENST00000244360;ENST00000376746	T;T	0.71103	-0.06;-0.54	3.79	0.627	0.17675	.	.	.	.	.	T	0.21427	0.0516	N	0.08118	0	0.09310	N	1	B;B	0.31318	0.013;0.319	B;B	0.18561	0.005;0.022	T	0.07616	-1.0763	9	0.35671	T	0.21	-2.6255	5.6728	0.17731	0.1038:0.0:0.454:0.4422	.	49;49	Q9H2S5;Q9H2S5-2	RNF39_HUMAN;.	V	49	ENSP00000365942:A49V;ENSP00000244360:A49V	ENSP00000244360:A49V	A	-	2	0	RNF39	30151400	0.003000	0.15002	0.014000	0.15608	0.861000	0.49209	0.783000	0.26802	0.216000	0.20781	0.436000	0.28706	GCG	.	.		0.672	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769		A	30043421	G	A	30043421	3	1	145	1	0	0	0	0	1	0	0	0	13506	1087	38	1	1132	1	RNF39	6	30043421	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10		30043421	141071646	24	22316										
IER3	8870	hgsc.bcm.edu	37	chr6	30712289	30712289	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	cgggtggcagctgcgagagtGacacatggtgagccgagcgg	19	9	0	3			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr6:30712289G>A	ENST00000259874.5	-	1	42	c.7C>T	c.(7-9)Cac>Tac	p.H3Y	XXbac-BPG252P9.10_ENST00000607333.1_RNA|FLOT1_ENST00000456573.2_5'Flank|FLOT1_ENST00000470643.1_5'Flank|IER3_ENST00000376377.2_Missense_Mutation_p.H3Y|FLOT1_ENST00000376389.3_5'Flank	NM_003897.3	NP_003888.2	P46695	IEX1_HUMAN	immediate early response 3	3					anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glycolytic process (GO:0045820)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|negative regulation of systemic arterial blood pressure (GO:0003085)|positive regulation of protein catabolic process (GO:0045732)|regulation of DNA repair (GO:0006282)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of response to DNA damage stimulus (GO:2001020)|response to protozoan (GO:0001562)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)	1						CTGCGAGAGTGACACATGGTG	0.642																																					p.H3Y		Atlas-SNP	.											.	IER3	5	.	0			c.C7T						.						5	4	4					6																	30712289		1325	2403	3728	SO:0001583	missense	8870	exon1			GAGAGTGACACAT	AF083421	CCDS4689.1	6p21.3	2010-02-17			ENSG00000137331	ENSG00000137331			5392	protein-coding gene	gene with protein product		602996				8603392, 9703517	Standard	NM_003897		Approved	IEX-1, DIF-2, PRG1, IEX-1L	uc003nrn.3	P46695	OTTHUMG00000031265	ENST00000259874.5:c.7C>T	chr6.hg19:g.30712289G>A	ENSP00000259874:p.His3Tyr	71.0	0.0		135.0	105.0	NM_003897	Q5SU30|Q92691|Q93044	Missense_Mutation	SNP	ENST00000259874.5	hg19	CCDS4689.1	.	.	.	.	.	.	.	.	.	.	G	18.93	3.727072	0.69074	.	.	ENSG00000137331	ENST00000259874;ENST00000376377;ENST00000376382	T	0.48522	0.81	4.9	3.97	0.46021	.	0.704428	0.13527	N	0.381256	T	0.32763	0.0840	L	0.57536	1.79	0.28407	N	0.918345	P	0.46912	0.886	B	0.44133	0.442	T	0.17379	-1.0371	10	0.87932	D	0	.	9.7288	0.40348	0.0:0.0:0.7938:0.2062	.	3	P46695	IEX1_HUMAN	Y	3	ENSP00000259874:H3Y	ENSP00000259874:H3Y	H	-	1	0	IER3	30820268	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	1.999000	0.40806	2.265000	0.75225	0.549000	0.68633	CAC	.	.		0.642	IER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076578.2			A	30712289	G	A	30712289	3	1	145	1	0	0	0	0	1	0	0	0	7515	1290	45	3	471	3	IER3	6	30712289	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	668868	30712289	140402778	25	22317										
TREML2	79865	hgsc.bcm.edu	37	chr6	41166123	41166123	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ctgcacagacagagtctcccCttcaaggagcctcacttttg	8	14	3	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr6:41166123C>T	ENST00000483722.1	-	2	285	c.100G>A	c.(100-102)Ggg>Agg	p.G34R		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	34	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					AGAGTCTCCCCTTCAAGGAGC	0.493																																					p.G34R		Atlas-SNP	.											.	TREML2	41	.	0			c.G100A						.						127	130	129					6																	41166123		2203	4300	6503	SO:0001583	missense	79865	exon2			TCTCCCCTTCAAG	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"Immunoglobulin superfamily / V-set domain containing"	21092	protein-coding gene	gene with protein product	"TREM-like transcript 2"	609715	"chromosome 6 open reading frame 76"	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.100G>A	chr6.hg19:g.41166123C>T	ENSP00000418767:p.Gly34Arg	38.0	0.0		67.0	6.0	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	hg19	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	14.59	2.581804	0.46006	.	.	ENSG00000112195	ENST00000483722	D	0.81499	-1.5	4.75	4.75	0.60458	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000044	D	0.86623	0.5977	M	0.75085	2.285	0.40423	D	0.979861	D	0.89917	1.0	D	0.97110	1.0	D	0.88269	0.2928	10	0.72032	D	0.01	-23.1011	13.6225	0.62144	0.0:1.0:0.0:0.0	.	34	Q5T2D2	TRML2_HUMAN	R	34	ENSP00000418767:G34R	ENSP00000418767:G34R	G	-	1	0	TREML2	41274101	1.000000	0.71417	0.998000	0.56505	0.028000	0.11728	3.388000	0.52509	2.344000	0.79699	0.563000	0.77884	GGG	.	.		0.493	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807		T	41166123	C	T	41166123	3	4	145	1	0	0	0	0	1	0	0	0	16488	681	24	3	881	3	TREML2	6	41166123	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	10453834	41166123	129948944	26	22318										
CNR1	1268	hgsc.bcm.edu	37	chr6	88854115	88854115	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ttccagagaatatacatgtaCgcatacacgatgaacagaag	8	8	0	3	rs35057475		TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr6:88854115C>T	ENST00000537554.1	-	2	4441	c.879G>A	c.(877-879)gcG>gcA	p.A293A	CNR1_ENST00000369499.2_Silent_p.A293A|CNR1_ENST00000535130.1_Silent_p.A293A|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000549716.1_Silent_p.A232A|CNR1_ENST00000468898.1_Silent_p.A260A|CNR1_ENST00000549890.1_Silent_p.A293A|CNR1_ENST00000428600.2_Silent_p.A293A|CNR1_ENST00000369501.2_Silent_p.A293A	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	293					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	TATACATGTACGCATACACGA	0.507																																					p.A293A		Atlas-SNP	.											.	CNR1	91	.	0			c.G879A						.						81	72	75					6																	88854115		2203	4300	6503	SO:0001819	synonymous_variant	1268	exon4			CATGTACGCATAC	AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"GPCR / Class A : Cannabinoid receptors"	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.879G>A	chr6.hg19:g.88854115C>T		45.0	0.0		47.0	20.0	NM_001160258	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Silent	SNP	ENST00000537554.1	hg19	CCDS5015.1																																																																																			.	C|0.987;T|0.013		0.507	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2			T	88854115	C	T	88854115	2	4	145	1	0	0	0	0	0	0	0	1	3633	523	19	1		1	CNR1	6	88854115	Silent	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	47687992	88854115	82260952	27	22319										
FAM164A	51101	hgsc.bcm.edu	37	chr8	79598709	79598709	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	tatttatttatagccagaacCaccaaagaaaccatctaatt	3	9	1	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr8:79598709C>A	ENST00000263849.4	+	4	320	c.218C>A	c.(217-219)cCa>cAa	p.P73Q	ZC2HC1A_ENST00000521176.1_3'UTR	NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	73							metal ion binding (GO:0046872)										tAGCCAGAACCACCAAAGAAA	0.303																																					p.P73Q		Atlas-SNP	.											.	.	.	.	0			c.C218A						.						41	36	38					8																	79598709		2201	4300	6501	SO:0001583	missense	51101	exon4			CAGAACCACCAAA		CCDS6223.1	8q21.11	2013-01-10	2012-02-03	2012-02-03	ENSG00000104427	ENSG00000104427		"Zinc fingers, C2HC-type containing"	24277	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 70", "family with sequence similarity 164, member A"	C8orf70, FAM164A		10810093	Standard	NM_016010		Approved	CGI-62	uc003ybd.3	Q96GY0	OTTHUMG00000164619	ENST00000263849.4:c.218C>A	chr8.hg19:g.79598709C>A	ENSP00000263849:p.Pro73Gln	154.0	0.0		276.0	81.0	NM_016010	Q9Y372	Missense_Mutation	SNP	ENST00000263849.4	hg19	CCDS6223.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.977151	0.74360	.	.	ENSG00000104427	ENST00000263849	T	0.46819	0.86	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.70587	0.3241	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.71126	-0.4683	9	.	.	.	-13.5331	19.429	0.94756	0.0:1.0:0.0:0.0	.	73	Q96GY0	F164A_HUMAN	Q	73	ENSP00000263849:P73Q	.	P	+	2	0	FAM164A	79761264	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.216000	0.77974	2.667000	0.90743	0.585000	0.79938	CCA	.	.		0.303	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010		A	79598709	C	A	79598709	3	1	145	1	0	0	0	0	1	0	0	0	5483	594	21	3	232	3	FAM164A	8	79598709	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10		79598709	66765313	28	22320										
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126044596	126044596	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	agcagtcccaggacaagtggTggccaatcaaccgggtcggt	14	11	1	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr8:126044596T>A	ENST00000318410.7	-	27	3571	c.3222A>T	c.(3220-3222)ccA>ccT	p.P1074P	KIAA0196_ENST00000517845.1_Silent_p.P926P	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	1074					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			GGACAAGTGGTGGCCAATCAA	0.527																																					p.P1074P		Atlas-SNP	.											.	KIAA0196	90	.	0			c.A3222T						.						113	105	108					8																	126044596		2203	4300	6503	SO:0001819	synonymous_variant	9897	exon27			AAGTGGTGGCCAA		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.3222A>T	chr8.hg19:g.126044596T>A		82.0	0.0		89.0	30.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	hg19	CCDS6355.1																																																																																			.	.		0.527	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		A	126044596	T	A	126044596	2	1	145	1	0	0	0	0	0	0	0	1	8170	1683	59	4		4	KIAA0196	8	126044596	Silent	SNP	T	TCGA-DD-A73D-01A-12D-A32G-10	46445887	126044596	20319426	29	22321										
KCNK9	51305	hgsc.bcm.edu	37	chr8	140631270	140631270	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ggaacatgaccagtgtcagcGggatgcccagcacggcgtag	15	11	1	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr8:140631270G>T	ENST00000520439.1	-	2	419	c.356C>A	c.(355-357)cCg>cAg	p.P119Q	KCNK9_ENST00000523477.1_5'Flank|KCNK9_ENST00000303015.1_Missense_Mutation_p.P119Q	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	119					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	CAGTGTCAGCGGGATGCCCAG	0.592																																					p.P119Q		Atlas-SNP	.											.	KCNK9	100	.	0			c.C356A						.						80	65	70					8																	140631270		2203	4300	6503	SO:0001583	missense	51305	exon2			GTCAGCGGGATGC	AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.356C>A	chr8.hg19:g.140631270G>T	ENSP00000430676:p.Pro119Gln	59.0	0.0		90.0	30.0	NM_016601	Q2M290|Q540F2	Missense_Mutation	SNP	ENST00000520439.1	hg19	CCDS6377.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.896193	0.72639	.	.	ENSG00000169427	ENST00000522317;ENST00000303015;ENST00000520439	T;T;T	0.34275	1.37;1.37;1.37	5.73	5.73	0.89815	Ion transport 2 (1);	0.059114	0.64402	D	0.000001	T	0.76821	0.4041	H	0.98407	4.225	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.85951	0.1464	10	0.87932	D	0	.	18.8824	0.92362	0.0:0.0:1.0:0.0	.	119	Q9NPC2	KCNK9_HUMAN	Q	119	ENSP00000429847:P119Q;ENSP00000302166:P119Q;ENSP00000430676:P119Q	ENSP00000302166:P119Q	P	-	2	0	KCNK9	140700452	1.000000	0.71417	0.992000	0.48379	0.492000	0.33523	9.606000	0.98325	2.692000	0.91855	0.655000	0.94253	CCG	.	.		0.592	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601		T	140631270	G	T	140631270	3	4	145	1	0	0	0	0	1	0	0	0	8081	1116	39	1	772	1	KCNK9	8	140631270	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	14586674	140631270	5732752	30	22322										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131339464	131339464	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ggagcagttaatggcctctgAtgattttggccgagacctgg	14	8	1	3			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr9:131339464A>G	ENST00000372731.4	+	7	952	c.842A>G	c.(841-843)gAt>gGt	p.D281G	SPTAN1_ENST00000358161.5_Missense_Mutation_p.D281G|SPTAN1_ENST00000372739.3_Missense_Mutation_p.D281G	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	281					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						ATGGCCTCTGATGATTTTGGC	0.483																																					p.D281G	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.A842G						.						154	159	157					9																	131339464		2203	4300	6503	SO:0001583	missense	6709	exon7			CCTCTGATGATTT	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.842A>G	chr9.hg19:g.131339464A>G	ENSP00000361816:p.Asp281Gly	64.0	0.0		67.0	33.0	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.922003	0.92319	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.51325	0.71;0.71;0.71	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.65657	0.2712	L	0.58302	1.8	0.80722	D	1	D;D;D;B;D	0.76494	0.998;0.997;0.999;0.179;0.969	P;D;D;P;P	0.79108	0.908;0.992;0.986;0.472;0.898	T	0.65187	-0.6229	10	0.49607	T	0.09	.	16.0034	0.80327	1.0:0.0:0.0:0.0	.	281;281;281;281;281	A6NG51;B4DTV8;Q13813-3;Q13813-2;Q13813	.;.;.;.;SPTA2_HUMAN	G	281	ENSP00000350882:D281G;ENSP00000361816:D281G;ENSP00000361824:D281G	ENSP00000350882:D281G	D	+	2	0	SPTAN1	130379285	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	8.962000	0.93254	2.371000	0.80710	0.533000	0.62120	GAT	.	.		0.483	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		G	131339464	A	G	131339464	3	3	145	1	0	0	0	0	1	0	0	0	15132	333	12	2	864	2	SPTAN1	9	131339464	Missense_Mutation	SNP	A	TCGA-DD-A73D-01A-12D-A32G-10		131339464	9873967	31	22323										
COMMD3	23412	hgsc.bcm.edu	37	chr10	22607754	22607754	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gaccaatcaacttcataggaTgtacagacctgcatatttgg	8	9	2	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr10:22607754T>G	ENST00000376836.3	+	6	875	c.431T>G	c.(430-432)aTg>aGg	p.M144R	BMI1_ENST00000376663.3_5'Flank|COMMD3-BMI1_ENST00000602390.1_Intron|COMMD3_ENST00000483684.1_3'UTR|COMMD3-BMI1_ENST00000463409.2_3'UTR	NM_012071.3	NP_036203.1	Q9UBI1	COMD3_HUMAN	COMM domain containing 3	144	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.									kidney(2)|lung(2)|ovary(1)	5						CTTCATAGGATGTACAGACCT	0.328																																					p.M144R		Atlas-SNP	.											.	COMMD3	13	.	0			c.T431G						.						184	195	191					10																	22607754		2203	4300	6503	SO:0001583	missense	23412	exon6			ATAGGATGTACAG	AY542159	CCDS7137.1	10p12.2	2012-09-20	2004-02-13	2004-02-18	ENSG00000148444	ENSG00000148444			23332	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 8"	C10orf8		11042152, 15799966	Standard	NM_012071		Approved	BUP		Q9UBI1	OTTHUMG00000017806	ENST00000376836.3:c.431T>G	chr10.hg19:g.22607754T>G	ENSP00000366032:p.Met144Arg	157.0	0.0		315.0	60.0	NM_012071	D3DRU7|Q5T8Y9	Missense_Mutation	SNP	ENST00000376836.3	hg19	CCDS7137.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	11.93|11.93|11.93	1.786458|1.786458|1.786458	0.31593|0.31593|0.31593	.|.|.	.|.|.	ENSG00000148444|ENSG00000148444|ENSG00000148444	ENST00000448361|ENST00000456711|ENST00000376836;ENST00000376787	.|.|T	.|.|0.09911	.|.|2.93	5.22|5.22|5.22	4.08|4.08|4.08	0.47627|0.47627|0.47627	.|.|COMM domain (1);	.|.|0.359901	.|.|0.32719	.|.|N	.|.|0.005740	T|T|T	0.06962|0.06962|0.06962	0.0177|0.0177|0.0177	L|L|L	0.34521|0.34521|0.34521	1.04|1.04|1.04	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|B	.|.|0.30973	.|.|0.302	.|.|B	.|.|0.28011	.|.|0.085	T|T|T	0.36553|0.36553|0.36553	-0.9743|-0.9743|-0.9743	5|5|10	.|.|0.32370	.|.|T	.|.|0.25	-17.4337|-17.4337|-17.4337	3.3919|3.3919|3.3919	0.07291|0.07291|0.07291	0.2727:0.1607:0.0:0.5666|0.2727:0.1607:0.0:0.5666|0.2727:0.1607:0.0:0.5666	.|.|.	.|.|144	.|.|Q9UBI1	.|.|COMD3_HUMAN	G|E|R	98|111|144;111	.|.|ENSP00000366032:M144R	.|.|ENSP00000365983:M111R	C|D|M	+|+|+	1|3|2	0|2|0	COMMD3|COMMD3|COMMD3	22647760|22647760|22647760	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.987000|0.987000|0.987000	0.75469|0.75469|0.75469	2.974000|2.974000|2.974000	0.49272|0.49272|0.49272	0.929000|0.929000|0.929000	0.37192|0.37192|0.37192	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	TGT|GAT|ATG	.	.		0.328	COMMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047159.1	NM_012071		G	22607754	T	G	22607754	3	3	145	1	0	0	0	0	1	0	0	0	3719	1464	51	5	453	5	COMMD3	10	22607754	Missense_Mutation	SNP	T	TCGA-DD-A73D-01A-12D-A32G-10		22607754	112926993	32	22324										
FAM24A	118670	hgsc.bcm.edu	37	chr10	124672364	124672364	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gaacagccaggccaaagccaCcaccatggagtcttgtccat	9	14	1	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr10:124672364C>G	ENST00000368894.1	+	3	333	c.212C>G	c.(211-213)aCc>aGc	p.T71S		NM_001029888.1	NP_001025059.1	A6NFZ4	FA24A_HUMAN	family with sequence similarity 24, member A	71						extracellular region (GO:0005576)				large_intestine(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	9		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.124)|COAD - Colon adenocarcinoma(40;0.141)		GCCAAAGCCACCACCATGGAG	0.502																																					p.T71S		Atlas-SNP	.											.	FAM24A	16	.	0			c.C212G						.						165	122	136					10																	124672364		2203	4300	6503	SO:0001583	missense	118670	exon3			AAGCCACCACCAT		CCDS31304.1	10q26.13	2008-08-27			ENSG00000203795	ENSG00000203795			23470	protein-coding gene	gene with protein product							Standard	NM_001029888		Approved	AC073585.4	uc001lgv.3	A6NFZ4	OTTHUMG00000019193	ENST00000368894.1:c.212C>G	chr10.hg19:g.124672364C>G	ENSP00000357889:p.Thr71Ser	76.0	0.0		96.0	44.0	NM_001029888		Missense_Mutation	SNP	ENST00000368894.1	hg19	CCDS31304.1	.	.	.	.	.	.	.	.	.	.	C	9.160	1.018506	0.19355	.	.	ENSG00000203795	ENST00000368894	.	.	.	3.3	-6.6	0.01824	.	0.512553	0.14559	U	0.312155	T	0.12732	0.0309	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.07214	-1.0784	9	0.41790	T	0.15	.	4.4073	0.11416	0.2991:0.4328:0.0:0.2682	.	71	A6NFZ4	FA24A_HUMAN	S	71	.	ENSP00000357889:T71S	T	+	2	0	FAM24A	124662354	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.968000	0.01507	-1.416000	0.02019	-1.355000	0.01225	ACC	.	.		0.502	FAM24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050824.1	XM_058332		G	124672364	C	G	124672364	3	3	145	1	0	0	0	0	1	0	0	0	5552	507	18	4	218	4	FAM24A	10	124672364	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	102064610	124672364	10862383	33	22325										
CHRM4	1132	hgsc.bcm.edu	37	chr11	46407538	46407538	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	aaggtcactgctgggttggaCaggaactggatgaagcactg	15	7	1	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr11:46407538C>G	ENST00000433765.2	-	1	569	c.570G>C	c.(568-570)ctG>ctC	p.L190L		NM_000741.2	NP_000732.2	P08173	ACM4_HUMAN	cholinergic receptor, muscarinic 4	190					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|regulation of locomotion (GO:0040012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			breast(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	20				GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CTGGGTTGGACAGGAACTGGA	0.582																																					p.L190L	Esophageal Squamous(171;1020 1936 4566 30205 42542)	Atlas-SNP	.											.	CHRM4	47	.	0			c.G570C						.						36	40	39					11																	46407538		2187	4288	6475	SO:0001819	synonymous_variant	1132	exon1			GTTGGACAGGAAC	M16405	CCDS44581.1	11p12-p11.2	2012-08-08			ENSG00000180720	ENSG00000180720		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1953	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 4"	118495				1577490	Standard	NM_000741		Approved		uc001nct.1	P08173	OTTHUMG00000154371	ENST00000433765.2:c.570G>C	chr11.hg19:g.46407538C>G		67.0	0.0		80.0	38.0	NM_000741	B2RPP4|Q0VD60|Q4VBK7	Silent	SNP	ENST00000433765.2	hg19	CCDS44581.1																																																																																			.	.		0.582	CHRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334985.1	NM_000741		G	46407538	C	G	46407538	2	3	145	1	0	0	0	0	0	0	0	1	3381	465	17	4		4	CHRM4	11	46407538	Silent	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10		46407538	88598978	34	22326										
OR9G4	283189	hgsc.bcm.edu	37	chr11	56510613	56510613	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gaaatcaggatagcaagaatGctggagagtactgtgaagcc	13	6	1	3			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr11:56510613G>T	ENST00000302957.3	-	1	674	c.675C>A	c.(673-675)agC>agA	p.S225R		NM_001005284.1	NP_001005284.1	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G, member 4	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						TAGCAAGAATGCTGGAGAGTA	0.478																																					p.S225R		Atlas-SNP	.											.	OR9G4	73	.	0			c.C675A						.						106	96	99					11																	56510613		2201	4296	6497	SO:0001583	missense	283189	exon1			AAGAATGCTGGAG	BK004400	CCDS31537.1	11q11	2012-08-09			ENSG00000172457	ENSG00000172457		"GPCR / Class A : Olfactory receptors"	15322	protein-coding gene	gene with protein product							Standard	NM_001005284		Approved		uc010rjo.2	Q8NGQ1	OTTHUMG00000166932	ENST00000302957.3:c.675C>A	chr11.hg19:g.56510613G>T	ENSP00000307515:p.Ser225Arg	54.0	0.0		50.0	25.0	NM_001005284	Q6IF62|Q96RA9	Missense_Mutation	SNP	ENST00000302957.3	hg19	CCDS31537.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.606903	0.46527	.	.	ENSG00000172457	ENST00000302957	T	0.38240	1.15	5.07	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.147954	0.31290	N	0.007906	T	0.48187	0.1486	M	0.93678	3.445	0.09310	N	1	P	0.46784	0.884	B	0.44224	0.444	T	0.54682	-0.8257	10	0.87932	D	0	-9.9661	5.5382	0.17023	0.0788:0.1403:0.6361:0.1448	.	225	Q8NGQ1	OR9G4_HUMAN	R	225	ENSP00000307515:S225R	ENSP00000307515:S225R	S	-	3	2	OR9G4	56267189	0.000000	0.05858	0.593000	0.28771	0.818000	0.46254	-0.504000	0.06375	0.724000	0.32296	0.643000	0.83706	AGC	.	.		0.478	OR9G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391945.1	NM_001005284		T	56510613	G	T	56510613	3	4	145	1	0	0	0	0	1	0	0	0	11260	1310	46	3	311	3	OR9G4	11	56510613	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	10103075	56510613	78495903	35	22327										
EML3	256364	hgsc.bcm.edu	37	chr11	62373664	62373664	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gaaccttcatgagcgtgagcCtgggccacaatcccataggt	11	12	1	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr11:62373664C>T	ENST00000394773.2	-	13	1834	c.1527G>A	c.(1525-1527)caG>caA	p.Q509Q	EML3_ENST00000494176.2_Silent_p.Q481Q|EML3_ENST00000278845.4_Silent_p.Q510Q|RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000531557.1_Silent_p.Q292Q|EML3_ENST00000529309.1_Silent_p.Q509Q|EML3_ENST00000438258.1_5'UTR	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	509						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GAGCGTGAGCCTGGGCCACAA	0.612																																					p.Q509Q		Atlas-SNP	.											.	EML3	61	.	0			c.G1527A						.						46	41	43					11																	62373664		2202	4299	6501	SO:0001819	synonymous_variant	256364	exon13			GTGAGCCTGGGCC	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"WD repeat domain containing"	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.1527G>A	chr11.hg19:g.62373664C>T		66.0	0.0		66.0	23.0	NM_153265	Q6ZQW7|Q8NA55	Silent	SNP	ENST00000394773.2	hg19	CCDS8023.2	.	.	.	.	.	.	.	.	.	.	C	12.87	2.067978	0.36470	.	.	ENSG00000149499	ENST00000394776	.	.	.	5.25	3.38	0.38709	.	.	.	.	.	T	0.54303	0.1850	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46911	-0.9157	4	.	.	.	-19.5325	5.5567	0.17121	0.0:0.6587:0.1633:0.178	.	.	.	.	S	504	.	.	G	-	1	0	EML3	62130240	1.000000	0.71417	0.996000	0.52242	0.805000	0.45488	1.944000	0.40263	0.600000	0.29862	0.467000	0.42956	GGC	.	.		0.612	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265		T	62373664	C	T	62373664	2	4	145	1	0	0	0	0	0	0	0	1	5100	680	24	3		3	EML3	11	62373664	Silent	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	5863051	62373664	72632852	36	22328										
IL10RA	3587	hgsc.bcm.edu	37	chr11	117864027	117864027	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	tcgggaagattcagctacccAggcccaagatggcccccgca	11	15	1	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr11:117864027A>T	ENST00000227752.3	+	4	559	c.439A>T	c.(439-441)Agg>Tgg	p.R147W	IL10RA_ENST00000545409.1_De_novo_Start_InFrame|IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000541785.1_Missense_Mutation_p.R127W	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	147					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		TCAGCTACCCAGGCCCAAGAT	0.517																																					p.R147W		Atlas-SNP	.											.	IL10RA	46	.	0			c.A439T						.						91	82	85					11																	117864027		2200	4296	6496	SO:0001583	missense	3587	exon4			CTACCCAGGCCCA	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"Interleukins and interleukin receptors", "CD molecules"	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.439A>T	chr11.hg19:g.117864027A>T	ENSP00000227752:p.Arg147Trp	48.0	0.0		65.0	26.0	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	hg19	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	A	16.49	3.136760	0.56936	.	.	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000536858	T;T	0.55413	0.52;0.52	5.73	3.23	0.37069	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.345700	0.26143	N	0.026095	T	0.67192	0.2867	M	0.71581	2.175	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.974	T	0.68198	-0.5472	10	0.66056	D	0.02	-28.2915	9.4332	0.38624	0.6505:0.3495:0.0:0.0	.	127;147	F5GYV8;Q13651	.;I10R1_HUMAN	W	147;127;127	ENSP00000227752:R147W;ENSP00000441397:R127W	ENSP00000227752:R147W	R	+	1	2	IL10RA	117369237	1.000000	0.71417	1.000000	0.80357	0.281000	0.26958	2.605000	0.46283	0.961000	0.38030	0.533000	0.62120	AGG	.	.		0.517	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117864027	A	T	117864027	3	4	145	1	0	0	0	0	1	0	0	0	7629	179	7	4	453	4	IL10RA	11	117864027	Missense_Mutation	SNP	A	TCGA-DD-A73D-01A-12D-A32G-10	55490363	117864027	17142489	37	22329										
TRIM29	23650	hgsc.bcm.edu	37	chr11	120008342	120008342	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ccgtgggcttccgggactccGagaaaatggacttgcgcagc	14	12	0	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr11:120008342G>A	ENST00000341846.5	-	1	819	c.398C>T	c.(397-399)tCg>tTg	p.S133L		NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	133					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		CCGGGACTCCGAGAAAATGGA	0.647																																					p.S133L		Atlas-SNP	.											.	TRIM29	78	.	0			c.C398T						.						91	104	100					11																	120008342		2203	4300	6503	SO:0001583	missense	23650	exon1			GACTCCGAGAAAA	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"Tripartite motif containing / Tripartite motif containing"	17274	protein-coding gene	gene with protein product	"tripartite motif protein TRIM29", "ataxia-telangiectasia group D-associated protein"	610658	"tripartite motif-containing 29"			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.398C>T	chr11.hg19:g.120008342G>A	ENSP00000343129:p.Ser133Leu	43.0	0.0		29.0	10.0	NM_012101	Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	hg19	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.654592	0.47467	.	.	ENSG00000137699	ENST00000341846	T	0.39592	1.07	5.19	4.28	0.50868	.	0.295747	0.26369	N	0.024768	T	0.35098	0.0920	L	0.32530	0.975	0.80722	D	1	D	0.62365	0.991	P	0.48270	0.572	T	0.06303	-1.0834	9	.	.	.	.	8.0019	0.30301	0.0807:0.0:0.7619:0.1574	.	133	Q14134	TRI29_HUMAN	L	133	ENSP00000343129:S133L	.	S	-	2	0	TRIM29	119513552	0.868000	0.29978	0.972000	0.41901	0.021000	0.10359	3.101000	0.50283	1.197000	0.43143	-0.253000	0.11424	TCG	.	.		0.647	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101		A	120008342	G	A	120008342	3	1	145	1	0	0	0	0	1	0	0	0	16518	1059	37	1	1404	1	TRIM29	11	120008342	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	2144315	120008342	14998174	38	22330										
OR8A1	390275	hgsc.bcm.edu	37	chr11	124440804	124440804	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	atgtacttaaaaccctccacAatcagttccttgacccagga	5	13	1	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr11:124440804A>C	ENST00000284287.3	+	1	912	c.840A>C	c.(838-840)acA>acC	p.T280T		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	280					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		AACCCTCCACAATCAGTTCCT	0.498																																					p.T280T		Atlas-SNP	.											.	OR8A1	61	.	0			c.A840C						.						89	77	81					11																	124440804		2201	4299	6500	SO:0001819	synonymous_variant	390275	exon1			CTCCACAATCAGT	BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"GPCR / Class A : Olfactory receptors"	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.840A>C	chr11.hg19:g.124440804A>C		74.0	0.0		86.0	39.0	NM_001005194	Q6IEW7|Q96RC6	Silent	SNP	ENST00000284287.3	hg19	CCDS31712.1																																																																																			.	.		0.498	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194		C	124440804	A	C	124440804	2	2	145	1	0	0	0	0	0	0	0	1	11234	117	5	5		5	OR8A1	11	124440804	Silent	SNP	A	TCGA-DD-A73D-01A-12D-A32G-10	4432462	124440804	10565712	39	22331										
ARID2	196528	hgsc.bcm.edu	37	chr12	46215247	46215247	+	Frame_Shift_Del	DEL	A	A	-													0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ttggagaagaatggaaagagAagactgatagagacttcgtt							TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr12:46215247delA	ENST00000334344.6	+	6	854	c.682delA	c.(682-684)aagfs	p.K228fs	ARID2_ENST00000422737.1_Frame_Shift_Del_p.K79fs	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	228					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		ATGGAAAGAGAAGACTGATAG	0.289			"N, S, F"		hepatocellular carcinoma																																p.E227fs		Atlas-Indel,Pindel	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.681delG						.						70	76	74					12																	46215247		2203	4291	6494	SO:0001589	frameshift_variant	196528	exon6			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.682delA	chr12.hg19:g.46215247delA	ENSP00000335044:p.Lys228fs	385.0	0.0		415.0	184.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.289	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		-	46215247	A	-	46215247	7	5	145	1	0	1	0	1	0	0	0	0	915	247	9	0	704	0	ARID2	12	46215247	Frame_Shift_Del	DEL	A	TCGA-DD-A73D-01A-12D-A32G-10		46215247	87636648	40	22332										
CAND1	55832	hgsc.bcm.edu	37	chr12	67701255	67701255	+	Frame_Shift_Del	DEL	T	T	-													0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	tccacaacctattgatccacTgttaaagaactgcataggta							TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr12:67701255delT	ENST00000545606.1	+	11	3445	c.3008delT	c.(3007-3009)ctgfs	p.L1004fs		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	1004					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		ATTGATCCACTGTTAAAGAAC	0.348																																					p.L1003fs		Atlas-Indel,Pindel	.											.	CAND1	100	.	0			c.3007delC						.						46	43	44					12																	67701255		2203	4298	6501	SO:0001589	frameshift_variant	55832	exon11			.		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.3008delT	chr12.hg19:g.67701255delT	ENSP00000442318:p.Leu1004fs	93.0	0.0		86.0	46.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Frame_Shift_Del	DEL	ENST00000545606.1	hg19	CCDS8977.1																																																																																			.	.		0.348	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		-	67701255	T	-	67701255	7	5	145	1	0	1	0	1	0	0	0	0	2617	1580	55	0	3050	0	CAND1	12	67701255	Frame_Shift_Del	DEL	T	TCGA-DD-A73D-01A-12D-A32G-10	21486008	67701255	66150640	41	22333										
LRRC43	254050	hgsc.bcm.edu	37	chr12	122687883	122687883	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	aaagccgaaagccgtgattcCgatctacgaaggcgattacc	10	11	1	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr12:122687883C>T	ENST00000339777.4	+	12	1893	c.1865C>T	c.(1864-1866)cCg>cTg	p.P622L	B3GNT4_ENST00000324189.4_5'Flank|B3GNT4_ENST00000546192.1_5'Flank|LRRC43_ENST00000425921.1_Missense_Mutation_p.P437L|B3GNT4_ENST00000535274.1_5'Flank	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	622										NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		GCCGTGATTCCGATCTACGAA	0.602																																					p.P622L		Atlas-SNP	.											.	LRRC43	105	.	0			c.C1865T						.						91	100	97					12																	122687883		1959	4145	6104	SO:0001583	missense	254050	exon12			TGATTCCGATCTA	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.1865C>T	chr12.hg19:g.122687883C>T	ENSP00000344233:p.Pro622Leu	26.0	0.0		22.0	9.0	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	hg19	CCDS45001.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.526503	0.27299	.	.	ENSG00000158113	ENST00000339777;ENST00000289014;ENST00000425921	T;T	0.55052	0.54;0.96	4.71	-1.91	0.07641	.	2.303270	0.01732	N	0.028908	T	0.42517	0.1206	L	0.45581	1.43	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.12319	-1.0552	10	0.35671	T	0.21	-2.7639	2.8934	0.05684	0.3279:0.2928:0.0:0.3794	.	622	Q8N309	LRC43_HUMAN	L	622;493;437	ENSP00000344233:P622L;ENSP00000416628:P437L	ENSP00000289014:P493L	P	+	2	0	LRRC43	121253836	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.068000	0.03447	-0.062000	0.13088	-0.314000	0.08810	CCG	.	.		0.602	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		T	122687883	C	T	122687883	3	4	145	1	0	0	0	0	1	0	0	0	9010	652	23	1	1911	1	LRRC43	12	122687883	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	54986628	122687883	11164012	42	22334										
F10	2159	hgsc.bcm.edu	37	chr13	113803570	113803570	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ttcatcatcacccagaacatGttctgtgccggctacgacac	7	14	4	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr13:113803570G>A	ENST00000375559.3	+	8	1244	c.1206G>A	c.(1204-1206)atG>atA	p.M402I	F10_ENST00000409306.1_3'UTR|F10_ENST00000375551.3_3'UTR	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	402	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(4)|lung(10)|pancreas(1)|stomach(1)	18	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Antihemophilic Factor(DB00025)|Apixaban(DB06605)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Menadione(DB00170)|Rivaroxaban(DB06228)	CCCAGAACATGTTCTGTGCCG	0.622																																					p.M402I		Atlas-SNP	.											.	F10	53	.	0			c.G1206A						.						60	66	64					13																	113803570		2203	4300	6503	SO:0001583	missense	2159	exon8			GAACATGTTCTGT		CCDS9530.1	13q34	2012-10-02			ENSG00000126218	ENSG00000126218	3.4.21.6		3528	protein-coding gene	gene with protein product		613872					Standard	XM_005268298		Approved		uc001vsx.3	P00742	OTTHUMG00000017374	ENST00000375559.3:c.1206G>A	chr13.hg19:g.113803570G>A	ENSP00000364709:p.Met402Ile	71.0	0.0		69.0	34.0	NM_000504	Q14340	Missense_Mutation	SNP	ENST00000375559.3	hg19	CCDS9530.1	.	.	.	.	.	.	.	.	.	.	G	32	5.105458	0.94245	.	.	ENSG00000126218	ENST00000375559	D	0.94000	-3.33	5.37	5.37	0.77165	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.97328	0.9126	M	0.89214	3.015	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97952	1.0332	10	0.87932	D	0	.	19.132	0.93412	0.0:0.0:1.0:0.0	.	402	P00742	FA10_HUMAN	I	402	ENSP00000364709:M402I	ENSP00000364709:M402I	M	+	3	0	F10	112851571	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	9.658000	0.98594	2.510000	0.84645	0.650000	0.86243	ATG	.	.		0.622	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3			A	113803570	G	A	113803570	3	1	145	1	0	0	0	0	1	0	0	0	5338	1377	48	3	1236	3	F10	13	113803570	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10		113803570	1366308	43	22335										
IRF9	10379	hgsc.bcm.edu	37	chr14	24631525	24631526	+	Missense_Mutation	DNP	TT	TT	GC													0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gggaggaccaggatgctgccTtcttcaaggtgaaagggcct							TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr14:24631525_24631526TT>GC	ENST00000396864.3	+	2	459_460	c.172_173TT>GC	c.(172-174)TTc>GCc	p.F58A	IRF9_ENST00000557894.1_Intron|RP11-468E2.4_ENST00000558468.1_3'UTR	NM_006084.4	NP_006075.3	Q00978	IRF9_HUMAN	interferon regulatory factor 9	58					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(265;0.00853)		GGATGCTGCCTTCTTCAAGGTG	0.545																																					p.F58V|p.F58S		Atlas-SNP	.											.	IRF9	33	.	0			c.T172G|c.T173C						.																																			SO:0001583	missense	10379	exon2			GCTGCCTTCTTCA|CTGCCTTCTTCAA	M87503	CCDS9615.1	14q11.2	2007-07-06	2007-07-06	2007-07-06	ENSG00000213928	ENSG00000213928			6131	protein-coding gene	gene with protein product		147574	"interferon-stimulated transcription factor 3, gamma (48kD)", "interferon-stimulated transcription factor 3, gamma 48kDa"	ISGF3G		1630447, 10199920	Standard	NM_006084		Approved		uc001wmq.3	Q00978	OTTHUMG00000028799	Exception_encountered	chr14.hg19:g.24631525_24631526delinsGC	ENSP00000380073:p.Phe58Ala	65.0|64.0	0.0		52.0	17.0	NM_006084	D3DS61	Missense_Mutation	SNP	ENST00000396864.3	hg19	CCDS9615.1																																																																																			.	.		0.545	IRF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071927.2			GC	24631526	TT	GC	24631525	3	3	145	1	0	0	0	0	1	0	0	0	7846	1609	56	5	174	5	IRF9	14	24631525	Missense_Mutation	DNP	TT	TCGA-DD-A73D-01A-12D-A32G-10		24631525	82718015	44	22336										
FRMD6	122786	hgsc.bcm.edu	37	chr14	52186983	52187007	+	Frame_Shift_Del	DEL	ACTCCAGCAGTGCCATCCACCGCAA	ACTCCAGCAGTGCCATCCACCGCAA	-													0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	cacggggccagaagacagctActccagcagtgccatccacc					rs369688308|rs200768573|rs372877962|rs549602598		TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	ACTCCAGCAGTGCCATCCACCGCAA	ACTCCAGCAGTGCCATCCACCGCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr14:52186983_52187007delACTCCAGCAGTGCCATCCACCGCAA	ENST00000344768.5	+	11	1431_1455	c.1235_1259delACTCCAGCAGTGCCATCCACCGCAA	c.(1234-1260)tactccagcagtgccatccaccgcaagfs	p.YSSSAIHRK412fs	FRMD6_ENST00000553556.1_Frame_Shift_Del_p.YSSSAIHRK54fs|FRMD6_ENST00000395718.2_Frame_Shift_Del_p.YSSSAIHRK404fs|FRMD6_ENST00000356218.4_Frame_Shift_Del_p.YSSSAIHRK404fs|FRMD6_ENST00000554167.1_Frame_Shift_Del_p.YSSSAIHRK335fs			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	412					apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					GAAGACAGCTACTCCAGCAGTGCCATCCACCGCAAGCTGAAAACC	0.613																																					p.412_420del		Atlas-Indel,Pindel	.											.	FRMD6	100	.	0			c.1234_1258del						.																																			SO:0001589	frameshift_variant	122786	exon11			.	BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"expanded homolog"	614555	"chromosome 14 open reading frame 31"	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.1235_1259delACTCCAGCAGTGCCATCCACCGCAA	chr14.hg19:g.52186983_52187007delACTCCAGCAGTGCCATCCACCGCAA	ENSP00000343899:p.Tyr412fs	67.0	0.0		56.0	11.0	NM_001267046	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Frame_Shift_Del	DEL	ENST00000344768.5	hg19	CCDS58318.1																																																																																			.	.		0.613	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330		-	52187007	ACTCCAGCAGTGCCATCCACCGCAA	-	52186983	7	5	145	1	0	1	0	1	0	0	0	0	6062	391	14	0	1249	0	FRMD6	14	52186983	Frame_Shift_Del	DEL	ACTCCAGCAGTGCCATCCACCGCAA	TCGA-DD-A73D-01A-12D-A32G-10	27555458	52186983	55162557	45	22337										
TEX9	374618	hgsc.bcm.edu	37	chr15	56683606	56683606	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ttttctggtgttagtaatgaCattggaacaggtagattttc	10	4	1	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr15:56683606C>T	ENST00000352903.2	+	7	585	c.561C>T	c.(559-561)gaC>gaT	p.D187D	RP11-48G14.2_ENST00000564401.1_lincRNA|TEX9_ENST00000558083.2_Silent_p.D112D|TEX9_ENST00000561221.2_Silent_p.D187D|TEX9_ENST00000537232.1_Silent_p.D112D	NM_198524.1	NP_940926.1	Q8N6V9	TEX9_HUMAN	testis expressed 9	187										cervix(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	14				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		TTAGTAATGACATTGGAACAG	0.303																																					p.D187D		Atlas-SNP	.											.	TEX9	29	.	0			c.C561T						.						91	92	92					15																	56683606		2192	4292	6484	SO:0001819	synonymous_variant	374618	exon7			TAATGACATTGGA	BC028119	CCDS10157.1, CCDS66776.1	15q21.3	2007-03-13	2007-03-13		ENSG00000151575	ENSG00000151575			29585	protein-coding gene	gene with protein product			"testis expressed sequence 9"				Standard	XM_005254361		Approved		uc002adp.3	Q8N6V9	OTTHUMG00000132035	ENST00000352903.2:c.561C>T	chr15.hg19:g.56683606C>T		138.0	0.0		144.0	69.0	NM_198524	B4DH73	Silent	SNP	ENST00000352903.2	hg19	CCDS10157.1																																																																																			.	.		0.303	TEX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255048.2	NM_198524		T	56683606	C	T	56683606	2	4	145	1	0	0	0	0	0	0	0	1	15799	477	17	3		3	TEX9	15	56683606	Silent	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10		56683606	45847786	46	22338										
COX5A	9377	hgsc.bcm.edu	37	chr15	75221554	75221554	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	tcctgtgacccatgggaataGcagcgaactgactggatagc	12	10	0	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr15:75221554G>C	ENST00000322347.6	-	2	273	c.120C>G	c.(118-120)tgC>tgG	p.C40W	COX5A_ENST00000564811.1_Missense_Mutation_p.C40W|COX5A_ENST00000568517.1_5'UTR|COX5A_ENST00000562233.1_Missense_Mutation_p.C40W|COX5A_ENST00000568783.1_Missense_Mutation_p.C40W|COX5A_ENST00000567270.1_Intron	NM_004255.3	NP_004246.2	P20674	COX5A_HUMAN	cytochrome c oxidase subunit Va	40					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|pancreas(1)	3						CATGGGAATAGCAGCGAACTG	0.388																																					p.C40W		Atlas-SNP	.											.	COX5A	9	.	0			c.C120G						.						132	121	125					15																	75221554		2197	4295	6492	SO:0001583	missense	9377	exon2			GGAATAGCAGCGA	M22760	CCDS10273.1	15q25	2011-07-04			ENSG00000178741	ENSG00000178741	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2267	protein-coding gene	gene with protein product		603773				10072584, 2853101	Standard	NM_004255		Approved		uc002azi.4	P20674	OTTHUMG00000142825	ENST00000322347.6:c.120C>G	chr15.hg19:g.75221554G>C	ENSP00000317780:p.Cys40Trp	70.0	0.0		82.0	37.0	NM_004255	P30045|Q8TB65	Missense_Mutation	SNP	ENST00000322347.6	hg19	CCDS10273.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.867897	0.32977	.	.	ENSG00000178741	ENST00000322347	.	.	.	5.58	5.58	0.84498	.	0.142736	0.64402	D	0.000004	T	0.49029	0.1533	N	0.19112	0.55	0.80722	D	1	D	0.58620	0.983	P	0.54759	0.76	T	0.44205	-0.9343	9	0.38643	T	0.18	-13.3356	11.6708	0.51399	0.0812:0.0:0.9188:0.0	.	40	P20674	COX5A_HUMAN	W	40	.	ENSP00000317780:C40W	C	-	3	2	COX5A	73008607	1.000000	0.71417	1.000000	0.80357	0.071000	0.16799	2.365000	0.44196	2.656000	0.90262	0.644000	0.83932	TGC	.	.		0.388	COX5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286417.1	NM_004255		C	75221554	G	C	75221554	3	2	145	1	0	0	0	0	1	0	0	0	3774	963	34	4	344	4	COX5A	15	75221554	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	18537948	75221554	27309838	47	22339										
GNPTG	84572	hgsc.bcm.edu	37	chr16	1412312	1412312	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ccctcgtctgccacccccacGccttgctaggtaggggtgcg	12	17	1	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr16:1412312G>A	ENST00000204679.4	+	7	560	c.517G>A	c.(517-519)Gcc>Acc	p.A173T	LA16c-316G12.2_ENST00000569831.1_RNA	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit	173					carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				CCACCCCCACGCCTTGCTAGG	0.687																																					p.A173T		Atlas-SNP	.											.	GNPTG	18	.	0			c.G517A						.						29	29	29					16																	1412312		2198	4298	6496	SO:0001583	missense	84572	exon7			CCCCACGCCTTGC	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"GlcNAc-phosphotransferase gamma-subunit"	607838	"N-acetylglucosamine-1-phosphotransferase, gamma subunit", "chromosome 16 open reading frame 27"	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835	ENST00000204679.4:c.517G>A	chr16.hg19:g.1412312G>A	ENSP00000204679:p.Ala173Thr	36.0	0.0		31.0	12.0	NM_032520	B2R556|Q6XYD7|Q96L13	Missense_Mutation	SNP	ENST00000204679.4	hg19	CCDS10436.1	.	.	.	.	.	.	.	.	.	.	G	11.64	1.699783	0.30142	.	.	ENSG00000090581	ENST00000204679	D	0.82433	-1.61	5.29	0.164	0.14990	.	0.362761	0.32120	N	0.006552	T	0.75391	0.3843	L	0.55481	1.735	0.22081	N	0.999376	P	0.40180	0.705	B	0.38264	0.269	T	0.65323	-0.6196	10	0.41790	T	0.15	-21.3775	8.8578	0.35238	0.1039:0.0:0.5257:0.3705	.	173	Q9UJJ9	GNPTG_HUMAN	T	173	ENSP00000204679:A173T	ENSP00000204679:A173T	A	+	1	0	GNPTG	1352313	0.996000	0.38824	0.640000	0.29408	0.891000	0.51852	1.731000	0.38135	-0.272000	0.09259	-0.266000	0.10368	GCC	.	.		0.687	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520		A	1412312	G	A	1412312	3	1	145	1	0	0	0	0	1	0	0	0	6554	1087	38	1	543	1	GNPTG	16	1412312	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10		1412312	88942441	48	22340										
ITGAL	3683	hgsc.bcm.edu	37	chr16	30507788	30507788	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gacccaagtgctctcaggaaTtcagtggtttggacgctcca	11	11	2	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr16:30507788T>C	ENST00000356798.6	+	15	1913	c.1733T>C	c.(1732-1734)aTt>aCt	p.I578T	RP11-297C4.1_ENST00000563751.1_RNA|ITGAL_ENST00000358164.5_Missense_Mutation_p.I495T|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	578					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	CTCTCAGGAATTCAGTGGTTT	0.562																																					p.I578T	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.T1733C						.						148	133	138					16																	30507788		2197	4300	6497	SO:0001583	missense	3683	exon15			CAGGAATTCAGTG		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1733T>C	chr16.hg19:g.30507788T>C	ENSP00000349252:p.Ile578Thr	105.0	0.0		104.0	49.0	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	hg19	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.161694	0.78226	.	.	ENSG00000005844	ENST00000356798;ENST00000358164	T;T	0.56941	0.43;0.43	5.94	5.94	0.96194	.	0.330476	0.26275	N	0.025315	T	0.55970	0.1954	M	0.65320	2	0.80722	D	1	P;P	0.45594	0.862;0.773	P;P	0.44477	0.451;0.451	T	0.61879	-0.6972	10	0.87932	D	0	.	13.9183	0.63914	0.0:0.0:0.0:1.0	.	495;578	Q96HB1;P20701	.;ITAL_HUMAN	T	578;495	ENSP00000349252:I578T;ENSP00000350886:I495T	ENSP00000349252:I578T	I	+	2	0	ITGAL	30415289	0.901000	0.30685	0.944000	0.38274	0.913000	0.54294	2.736000	0.47385	2.272000	0.75746	0.460000	0.39030	ATT	.	.		0.562	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			C	30507788	T	C	30507788	3	2	145	1	0	0	0	0	1	0	0	0	7895	1493	52	2	1791	2	ITGAL	16	30507788	Missense_Mutation	SNP	T	TCGA-DD-A73D-01A-12D-A32G-10	29095476	30507788	59846965	49	22341										
ERN1	2081	hgsc.bcm.edu	37	chr17	62133223	62133223	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	caggtgggtggaagggcagcTgctgctgctgctgctgcagg	19	9	0	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr17:62133223T>A	ENST00000433197.3	-	13	1579	c.1484A>T	c.(1483-1485)cAg>cTg	p.Q495L		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						GAAGGGCAgctgctgctgctg	0.632																																					p.Q495L		Atlas-SNP	.											.	ERN1	102	.	0			c.A1484T						.						5	6	6					17																	62133223		2017	4062	6079	SO:0001583	missense	2081	exon13			GGCAGCTGCTGCT	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"inositol-requiring enzyme 1"	604033	"ER to nucleus signalling 1"			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.1484A>T	chr17.hg19:g.62133223T>A	ENSP00000401445:p.Gln495Leu	27.0	0.0		77.0	5.0	NM_001433		Missense_Mutation	SNP	ENST00000433197.3	hg19	CCDS45762.1	.	.	.	.	.	.	.	.	.	.	T	3.711	-0.059492	0.07317	.	.	ENSG00000178607	ENST00000433197	T	0.16457	2.34	0.14	0.14	0.14804	.	.	.	.	.	T	0.13157	0.0319	L	0.48642	1.525	0.24475	N	0.994376	B	0.22003	0.063	B	0.15052	0.012	T	0.27905	-1.0060	8	0.33141	T	0.24	-15.5741	.	.	.	.	495	O75460	ERN1_HUMAN	L	495	ENSP00000401445:Q495L	ENSP00000401445:Q495L	Q	-	2	0	ERN1	59486955	0.994000	0.37717	0.998000	0.56505	0.867000	0.49689	-0.604000	0.05667	0.157000	0.19338	0.155000	0.16302	CAG	.	.		0.632	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		A	62133223	T	A	62133223	3	1	145	1	0	0	0	0	1	0	0	0	5239	1580	55	4	1489	4	ERN1	17	62133223	Missense_Mutation	SNP	T	TCGA-DD-A73D-01A-12D-A32G-10		62133223	19061987	50	22342										
C3	718	hgsc.bcm.edu	37	chr19	6697550	6697550	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ctgcagaaggctggattgtgGagtagttccaccctcacctg	12	11	1	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr19:6697550G>A	ENST00000245907.6	-	21	2693	c.2601C>T	c.(2599-2601)ctC>ctT	p.L867L		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	867					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CTGGATTGTGGAGTAGTTCCA	0.597																																					p.L867L		Atlas-SNP	.											.	C3	192	.	0			c.C2601T						.						89	71	77					19																	6697550		2203	4300	6503	SO:0001819	synonymous_variant	718	exon21			ATTGTGGAGTAGT	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.2601C>T	chr19.hg19:g.6697550G>A		50.0	0.0		50.0	24.0	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	hg19	CCDS32883.1																																																																																			.	.		0.597	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		A	6697550	G	A	6697550	2	1	145	1	0	0	0	0	0	0	0	1	2206	1161	41	3		3	C3	19	6697550	Silent	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10		6697550	52431433	51	22343										
ANGPTL6	83854	hgsc.bcm.edu	37	chr19	10204121	10204121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	accatggtactggccaagccGcaggcggtagtggtcgctct	14	12	1	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr19:10204121G>A	ENST00000253109.4	-	5	1364	c.1126C>T	c.(1126-1128)Cgg>Tgg	p.R376W	ANGPTL6_ENST00000592641.1_Missense_Mutation_p.R376W|ANGPTL6_ENST00000589181.1_Missense_Mutation_p.R336W	NM_031917.2	NP_114123.2	Q8NI99	ANGL6_HUMAN	angiopoietin-like 6	376	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)	12			OV - Ovarian serous cystadenocarcinoma(20;3.58e-08)|Epithelial(33;2.5e-05)|all cancers(31;5.96e-05)			TGGCCAAGCCGCAGGCGGTAG	0.597																																					p.R376W		Atlas-SNP	.											.	ANGPTL6	28	.	0			c.C1126T						.						66	59	61					19																	10204121		2203	4300	6503	SO:0001583	missense	83854	exon5			CAAGCCGCAGGCG	AB054064	CCDS12224.1	19p13.2	2013-02-06				ENSG00000130812		"Fibrinogen C domain containing"	23140	protein-coding gene	gene with protein product	"angiopoietin-related protein 5"	609336				12871997	Standard	NM_031917		Approved	ARP5, AGF	uc002mmy.1	Q8NI99		ENST00000253109.4:c.1126C>T	chr19.hg19:g.10204121G>A	ENSP00000253109:p.Arg376Trp	66.0	0.0		95.0	39.0	NM_031917	A5PKV7|Q9BZZ0	Missense_Mutation	SNP	ENST00000253109.4	hg19	CCDS12224.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.331110	0.60853	.	.	ENSG00000130812	ENST00000253109	T	0.77750	-1.12	4.47	2.15	0.27550	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.64402	D	0.000002	D	0.86748	0.6007	M	0.81179	2.53	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	D	0.87522	0.2447	10	0.52906	T	0.07	.	12.9306	0.58284	0.0:0.0:0.6971:0.3029	.	376	Q8NI99	ANGL6_HUMAN	W	376	ENSP00000253109:R376W	ENSP00000253109:R376W	R	-	1	2	ANGPTL6	10065121	0.998000	0.40836	1.000000	0.80357	0.950000	0.60333	1.322000	0.33689	1.106000	0.41623	-0.515000	0.04445	CGG	.	.		0.597	ANGPTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451142.1	NM_031917		A	10204121	G	A	10204121	3	1	145	1	0	0	0	0	1	0	0	0	618	1086	38	1	294	1	ANGPTL6	19	10204121	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	3506571	10204121	48924862	52	22344										
CALR	811	hgsc.bcm.edu	37	chr19	13054718	13054718	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gtccccggccaggccaaggaCgagctgtagagaggcctgcc	15	14	0	1	rs148604761	byFrequency	TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr19:13054718C>G	ENST00000316448.5	+	9	1318	c.1245C>G	c.(1243-1245)gaC>gaG	p.D415E	RAD23A_ENST00000586534.1_5'Flank|RAD23A_ENST00000541222.1_5'Flank|CTC-425F1.4_ENST00000589120.1_RNA|RAD23A_ENST00000316856.3_5'Flank|RAD23A_ENST00000592268.1_5'Flank	NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	415	C-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	AGGCCAAGGACGAGCTGTAGA	0.587																																					p.D415E		Atlas-SNP	.											.	CALR	31	.	0			c.C1245G						.						165	132	143					19																	13054718		2203	4299	6502	SO:0001583	missense	811	exon9			CAAGGACGAGCTG	M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"Sicca syndrome antigen A (autoantigen Ro; calreticulin)", "autoantigen Ro"	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.1245C>G	chr19.hg19:g.13054718C>G	ENSP00000320866:p.Asp415Glu	95.0	0.0		97.0	44.0	NM_004343	Q6IAT4|Q9UDG2	Missense_Mutation	SNP	ENST00000316448.5	hg19	CCDS12288.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.364361	0.41902	.	.	ENSG00000179218	ENST00000316448;ENST00000539083	T	0.51325	0.71	5.59	-8.66	0.00866	.	0.000000	0.64402	D	0.000001	T	0.28067	0.0692	N	0.19112	0.55	0.41172	D	0.986179	B	0.13145	0.007	B	0.12837	0.008	T	0.03148	-1.1067	10	0.87932	D	0	-34.4168	17.0204	0.86432	0.0:0.1445:0.0:0.8555	.	415	P27797	CALR_HUMAN	E	415;294	ENSP00000320866:D415E	ENSP00000320866:D415E	D	+	3	2	CALR	12915718	0.007000	0.16637	0.758000	0.31321	0.660000	0.38997	-1.013000	0.03645	-1.360000	0.02172	-1.013000	0.02462	GAC	.	C|1.000;T|0.000		0.587	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343		G	13054718	C	G	13054718	3	3	145	1	0	0	0	0	1	0	0	0	2594	535	19	4	1279	4	CALR	19	13054718	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	2850597	13054718	46074265	53	22345										
CD97	976	hgsc.bcm.edu	37	chr19	14516639	14516639	+	Frame_Shift_Del	DEL	T	T	-													0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	gctgtgcatcctcactttccTgctggtgcggcccatccagg							TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr19:14516639delT	ENST00000242786.5	+	14	1789	c.1709delT	c.(1708-1710)ctgfs	p.L571fs	CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000357355.3_Frame_Shift_Del_p.L522fs|CD97_ENST00000358600.3_Frame_Shift_Del_p.L478fs	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	571					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTCACTTTCCTGCTGGTGCGG	0.627																																					p.L570fs		Atlas-Indel,Pindel	.											.	CD97	86	.	0			c.1708delC						.						161	121	135					19																	14516639		2203	4300	6503	SO:0001589	frameshift_variant	976	exon14			.		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.1709delT	chr19.hg19:g.14516639delT	ENSP00000242786:p.Leu571fs	44.0	0.0		43.0	21.0	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Frame_Shift_Del	DEL	ENST00000242786.5	hg19	CCDS32929.1																																																																																			.	.		0.627	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		-	14516639	T	-	14516639	7	5	145	1	0	1	0	1	0	0	0	0	3051	1580	55	0	1763	0	CD97	19	14516639	Frame_Shift_Del	DEL	T	TCGA-DD-A73D-01A-12D-A32G-10	1461921	14516639	44612344	54	22346										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40408468	40408468	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	aggagcccacagaactcctcCttctgatacttcttctccag	6	15	3	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr19:40408468C>T	ENST00000221347.6	-	8	4378	c.4371G>A	c.(4369-4371)aaG>aaA	p.K1457K		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1457	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGAACTCCTCCTTCTGATACT	0.622																																					p.K1457K		Atlas-SNP	.											.	FCGBP	416	.	0			c.G4371A						.						42	46	45					19																	40408468		2203	4300	6503	SO:0001819	synonymous_variant	8857	exon8			CTCCTCCTTCTGA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4371G>A	chr19.hg19:g.40408468C>T		242.0	0.0		213.0	67.0	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.		0.622	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40408468	C	T	40408468	2	4	145	1	0	0	0	0	0	0	0	1	5786	680	24	3		3	FCGBP	19	40408468	Silent	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	25891829	40408468	18720515	55	22347										
PRX	57716	hgsc.bcm.edu	37	chr19	40903727	40903727	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ggcaggggcagccgggacagGacccttgacagcctcggctt	16	13	0	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr19:40903727G>T	ENST00000324001.7	-	7	802	c.532C>A	c.(532-534)Cct>Act	p.P178T	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	178	Arg/Lys-rich (basic).				axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCCGGGACAGGACCCTTGACA	0.711																																					p.P178T		Atlas-SNP	.											.	PRX	151	.	0			c.C532A						.						8	10	9					19																	40903727		2179	4260	6439	SO:0001583	missense	57716	exon7			GGACAGGACCCTT	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.532C>A	chr19.hg19:g.40903727G>T	ENSP00000326018:p.Pro178Thr	29.0	0.0		21.0	12.0	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	hg19	CCDS33028.1	.	.	.	.	.	.	.	.	.	.	G	16.46	3.129647	0.56721	.	.	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.01981	4.52	4.71	4.71	0.59529	.	0.272829	0.26411	N	0.024530	T	0.06781	0.0173	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.57100	-0.7869	10	0.19147	T	0.46	-3.4696	14.6881	0.69065	0.0:0.0:1.0:0.0	.	178	Q9BXM0	PRAX_HUMAN	T	178	ENSP00000326018:P178T	ENSP00000326018:P178T	P	-	1	0	PRX	45595567	1.000000	0.71417	0.998000	0.56505	0.708000	0.40852	4.177000	0.58276	2.437000	0.82529	0.591000	0.81541	CCT	.	.		0.711	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956		T	40903727	G	T	40903727	3	4	145	1	0	0	0	0	1	0	0	0	12654	1174	41	3	3857	3	PRX	19	40903727	Missense_Mutation	SNP	G	TCGA-DD-A73D-01A-12D-A32G-10	495259	40903727	18225256	56	22348										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44739094	44739097	+	Frame_Shift_Del	DEL	TTTT	TTTT	-													0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ttgaaaatcaagagtttccaTtttggagaacccagcattct					rs370304805		TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	TTTT	TTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr19:44739094_44739097delTTTT	ENST00000313040.7	+	6	716_719	c.511_514delTTTT	c.(511-516)ttttggfs	p.FW171fs	ZNF227_ENST00000391961.2_Frame_Shift_Del_p.FW120fs|ZNF227_ENST00000589005.1_Frame_Shift_Del_p.FW120fs	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				AGAGTTTCCATTTTGGAGAACCCA	0.348																																					p.170_171del		Atlas-Indel,Pindel	.											.	ZNF227	62	.	0			c.510_513del						.																																			SO:0001589	frameshift_variant	7770	exon6			.	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.511_514delTTTT	chr19.hg19:g.44739094_44739097delTTTT	ENSP00000321049:p.Phe171fs	128.0	0.0		127.0	47.0	NM_182490	B3KRU7|B7Z5P9	Frame_Shift_Del	DEL	ENST00000313040.7	hg19	CCDS12636.1																																																																																			.	.		0.348	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		-	44739097	TTTT	-	44739094	7	5	145	1	0	1	0	1	0	0	0	0	17796	1493	52	0	525	0	ZNF227	19	44739094	Frame_Shift_Del	DEL	TTTT	TCGA-DD-A73D-01A-12D-A32G-10	3835367	44739094	14389889	57	22349										
LMTK3	114783	hgsc.bcm.edu	37	chr19	49002759	49002759	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	ggcgctgatgacaggcagcaCgctgggcgtggacagcgcct	17	12	0	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr19:49002759C>A	ENST00000600059.1	-	11	1794	c.1567G>T	c.(1567-1569)Gtg>Ttg	p.V523L	LMTK3_ENST00000270238.3_Missense_Mutation_p.V552L			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	523	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		ACAGGCAGCACGCTGGGCGTG	0.721																																					p.V552L		Atlas-SNP	.											.	LMTK3	125	.	0			c.G1654T						.						2	2	2					19																	49002759		1321	2812	4133	SO:0001583	missense	114783	exon12			GCAGCACGCTGGG	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 101"						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.1567G>T	chr19.hg19:g.49002759C>A	ENSP00000472020:p.Val523Leu	51.0	0.0		49.0	23.0	NM_001080434	Q4G0U1	Missense_Mutation	SNP	ENST00000600059.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.88	3.496970	0.64186	.	.	ENSG00000142235	ENST00000270238	T	0.81163	-1.46	3.55	3.55	0.40652	.	0.190349	0.31156	U	0.008156	D	0.83266	0.5217	L	0.47716	1.5	0.44927	D	0.997945	D	0.76494	0.999	P	0.59595	0.86	D	0.85212	0.1021	10	0.72032	D	0.01	.	13.0352	0.58867	0.0:1.0:0.0:0.0	.	523	Q96Q04	LMTK3_HUMAN	L	552	ENSP00000270238:V552L	ENSP00000270238:V552L	V	-	1	0	LMTK3	53694571	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.491000	0.66887	2.020000	0.59435	0.386000	0.25728	GTG	.	.		0.721	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895		A	49002759	C	A	49002759	3	1	145	1	0	0	0	0	1	0	0	0	8869	536	19	1	2835	1	LMTK3	19	49002759	Missense_Mutation	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	4263665	49002759	10126224	58	22350										
SIGLEC8	27181	hgsc.bcm.edu	37	chr19	51960896	51960896	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	caggagatcatggggggtgtCccctgcttacaggcccaggg	16	11	1	1			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr19:51960896C>A	ENST00000321424.3	-	2	618	c.552G>T	c.(550-552)ggG>ggT	p.G184G	SIGLEC8_ENST00000340550.5_Intron|SIGLEC8_ENST00000430817.1_Intron|SIGLEC8_ENST00000597352.1_5'UTR	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	184	Ig-like C2-type 1.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TGGGGGGTGTCCCCTGCTTAC	0.647																																					p.G184G		Atlas-SNP	.											.	SIGLEC8	130	.	0			c.G552T						.						71	77	75					19																	51960896		2203	4300	6503	SO:0001819	synonymous_variant	27181	exon2			GGGTGTCCCCTGC	AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.552G>T	chr19.hg19:g.51960896C>A		34.0	0.0		40.0	17.0	NM_014442	Q7Z728	Silent	SNP	ENST00000321424.3	hg19	CCDS33086.1																																																																																			.	.		0.647	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442		A	51960896	C	A	51960896	2	1	145	1	0	0	0	0	0	0	0	1	14329	842	30	3		3	SIGLEC8	19	51960896	Silent	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10	2958137	51960896	7168087	59	22351										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44664102	44664102	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	agtggcctggccaactacacCaacctgccccagggaagtag	11	14	0	0			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chr20:44664102C>A	ENST00000454036.2	+	3	325	c.276C>A	c.(274-276)acC>acA	p.T92T	SLC12A5_ENST00000608944.1_Silent_p.T18T|SLC12A5_ENST00000243964.3_Silent_p.T69T|SLC12A5_ENST00000372315.1_Silent_p.T69T	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	92					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)	p.T69T(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCAACTACACCAACCTGCCCC	0.577																																					p.T92T		Atlas-SNP	.											SLC12A5,colon,carcinoma,0,1	SLC12A5	181	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C276A						.						94	101	98					20																	44664102		2203	4300	6503	SO:0001819	synonymous_variant	57468	exon3			CTACACCAACCTG	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.276C>A	chr20.hg19:g.44664102C>A		91.0	0.0		76.0	30.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	hg19	CCDS46610.1																																																																																			.	.		0.577	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			A	44664102	C	A	44664102	2	1	145	1	0	0	0	0	0	0	0	1	14401	581	21	3		3	SLC12A5	20	44664102	Silent	SNP	C	TCGA-DD-A73D-01A-12D-A32G-10		44664102	18361418	60	22352										
RLIM	51132	hgsc.bcm.edu	37	chrX	73812012	73812012	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	2	1	0.651629072681704	1.7593984962406	0.399863294600137	1	1	0	aatgggaattctgatggtacTgacataggttctcacacctg	10	8	2	2			TCGA-DD-A73D-01A-12D-A32G-10	TCGA-DD-A73D-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6ace15b-9da3-4260-86f4-4e0cfb35e204	4d8c018d-9b4f-4288-ac78-501085f38978	g.chrX:73812012T>A	ENST00000332687.6	-	4	1356	c.1138A>T	c.(1138-1140)Agt>Tgt	p.S380C	RLIM_ENST00000349225.2_Missense_Mutation_p.S380C	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	380					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CTGATGGTACTGACATAGGTT	0.423																																					p.S380C	Esophageal Squamous(169;1899 1923 14997 18818 32118)	Atlas-SNP	.											.	RLIM	90	.	0			c.A1138T						.						115	103	108					X																	73812012		2203	4300	6503	SO:0001583	missense	51132	exon5			TGGTACTGACATA	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1138A>T	chrX.hg19:g.73812012T>A	ENSP00000328059:p.Ser380Cys	94.0	0.0		108.0	57.0	NM_183353	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	hg19	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.628996	0.46944	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.16457	2.34;2.34	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.44477	0.1295	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.46205	-0.9208	10	0.87932	D	0	-19.3282	14.9929	0.71401	0.0:0.0:0.0:1.0	.	380	Q9NVW2	RNF12_HUMAN	C	380	ENSP00000328059:S380C;ENSP00000253571:S380C	ENSP00000328059:S380C	S	-	1	0	RLIM	73728737	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.695000	0.84257	1.923000	0.55706	0.486000	0.48141	AGT	.	.		0.423	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		A	73812012	T	A	73812012	3	1	145	1	0	0	0	0	1	0	0	0	13405	1580	55	4	740	4	RLIM	23	73812012	Missense_Mutation	SNP	T	TCGA-DD-A73D-01A-12D-A32G-10		73812012	81458548	61	22353										
CROCC	9696	hgsc.bcm.edu	37	chr1	17248518	17248518	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ccacagcctcccccccatgaGcttggggctggcgagggcac	13	17	0	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:17248518G>A	ENST00000375541.5	+	1	74	c.5G>A	c.(4-6)aGc>aAc	p.S2N		NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CCCCCCATGAGCTTGGGGCTG	0.672																																					p.S2N		Atlas-SNP	.											.	CROCC	185	.	0			c.G5A						.						8	8	8					1																	17248518		2127	4132	6259	SO:0001583	missense	9696	exon1			CCATGAGCTTGGG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.5G>A	chr1.hg19:g.17248518G>A	ENSP00000364691:p.Ser2Asn	215.0	0.0		224.0	45.0	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	9.949	1.219570	0.22373	.	.	ENSG00000058453	ENST00000375541	T	0.10477	2.87	4.53	-2.28	0.06826	.	.	.	.	.	T	0.07143	0.0181	L	0.29908	0.895	0.21861	N	0.999502	B	0.02656	0.0	B	0.06405	0.002	T	0.34700	-0.9818	9	0.66056	D	0.02	.	5.2082	0.15302	0.4783:0.15:0.3717:0.0	.	2	Q5TZA2	CROCC_HUMAN	N	2	ENSP00000364691:S2N	ENSP00000364691:S2N	S	+	2	0	CROCC	17121105	0.841000	0.29509	0.916000	0.36221	0.707000	0.40811	-0.126000	0.10563	-0.699000	0.05077	-0.218000	0.12543	AGC	.	.		0.672	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		A	17248518	G	A	17248518	3	1	146	1	0	0	0	0	1	0	0	0	3895	971	34	3	7	3	CROCC	1	17248518	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10		17248518	232002103	1	22354										
PLA2G2F	64600	hgsc.bcm.edu	37	chr1	20466020	20466020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	cacgcttcggggcctcctgtCcttcaagaacctccaggtag	10	15	1	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:20466020C>T	ENST00000375102.3	+	1	202	c.100C>T	c.(100-102)Cct>Tct	p.P34S		NM_022819.3	NP_073730.3	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	0					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		GGCCTCCTGTCCTTCAAGAAC	0.592																																					p.P34S		Atlas-SNP	.											.	PLA2G2F	28	.	0			c.C100T						.						30	35	33					1																	20466020		1874	4090	5964	SO:0001583	missense	64600	exon1			TCCTGTCCTTCAA	AL158172	CCDS204.2	1p35	2008-09-19			ENSG00000158786	ENSG00000158786	3.1.1.4		30040	protein-coding gene	gene with protein product						11112443	Standard	NM_022819		Approved		uc009vpp.1	Q9BZM2	OTTHUMG00000002704	ENST00000375102.3:c.100C>T	chr1.hg19:g.20466020C>T	ENSP00000364243:p.Pro34Ser	65.0	0.0		70.0	36.0	NM_022819	Q5R385|Q8N217|Q9H506	Missense_Mutation	SNP	ENST00000375102.3	hg19	CCDS204.2	.	.	.	.	.	.	.	.	.	.	C	2.272	-0.366780	0.05069	.	.	ENSG00000158786	ENST00000375102	T	0.26810	1.71	4.92	-1.83	0.07833	.	1.532860	0.03995	N	0.295562	T	0.18425	0.0442	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.35549	-0.9784	9	0.87932	D	0	0.0063	4.3185	0.11005	0.1691:0.3491:0.0:0.4818	.	34	Q9BZM2-2	.	S	34	ENSP00000364243:P34S	ENSP00000364243:P34S	P	+	1	0	PLA2G2F	20338607	0.000000	0.05858	0.000000	0.03702	0.159000	0.22180	-0.972000	0.03802	-0.305000	0.08831	-0.136000	0.14681	CCT	.	.		0.592	PLA2G2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007687.1	NM_022819		T	20466020	C	T	20466020	3	4	146	1	0	0	0	0	1	0	0	0	12008	855	30	3	102	3	PLA2G2F	1	20466020	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	3217502	20466020	228784601	2	22355										
NIPAL3	57185	hgsc.bcm.edu	37	chr1	24768656	24768656	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tgggcgagctgggtgtgttcGcctcctacgccttcgcgccg	15	14	0	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:24768656G>T	ENST00000374399.4	+	4	642	c.274G>T	c.(274-276)Gcc>Tcc	p.A92S	NIPAL3_ENST00000339255.2_Missense_Mutation_p.A92S|NIPAL3_ENST00000358028.4_Missense_Mutation_p.A92S|NIPAL3_ENST00000003912.3_Missense_Mutation_p.A10S|NIPAL3_ENST00000428131.1_Missense_Mutation_p.A92S	NM_020448.4	NP_065181.1	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3	92						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(1)	14						GGGTGTGTTCGCCTCCTACGC	0.637																																					p.A92S		Atlas-SNP	.											.	NIPAL3	36	.	0			c.G274T						.						131	117	122					1																	24768656		2203	4300	6503	SO:0001583	missense	57185	exon4			GTGTTCGCCTCCT	BX640883	CCDS30631.1	1p36.12-p35.1	2009-03-24		2009-03-24	ENSG00000001461	ENSG00000001461			25233	protein-coding gene	gene with protein product				NPAL3		8619474, 9110174	Standard	NM_020448		Approved	DJ462O23.2	uc001bjh.3	Q6P499	OTTHUMG00000003299	ENST00000374399.4:c.274G>T	chr1.hg19:g.24768656G>T	ENSP00000363520:p.Ala92Ser	58.0	0.0		67.0	4.0	NM_020448	A2A298|Q6MZT9|Q9BVE6	Missense_Mutation	SNP	ENST00000374399.4	hg19	CCDS30631.1	.	.	.	.	.	.	.	.	.	.	g	12.76	2.034773	0.35893	.	.	ENSG00000001461	ENST00000374399;ENST00000003912;ENST00000358028;ENST00000339255;ENST00000428131	D;D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08;-3.08	5.22	1.81	0.25067	.	0.273628	0.42420	D	0.000716	T	0.80412	0.4618	N	0.12746	0.255	0.32286	N	0.56696	B;B;B	0.20550	0.024;0.002;0.046	B;B;B	0.26614	0.02;0.021;0.071	T	0.71899	-0.4453	10	0.30854	T	0.27	-17.2805	3.3689	0.07213	0.0896:0.1102:0.4421:0.3581	.	92;92;92	Q6P499-3;Q6P499;A6NN97	.;NPAL3_HUMAN;.	S	92;10;92;92;92	ENSP00000363520:A92S;ENSP00000003912:A10S;ENSP00000350722:A92S;ENSP00000343549:A92S;ENSP00000406509:A92S	ENSP00000003912:A10S	A	+	1	0	NIPAL3	24641243	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.494000	0.53273	0.691000	0.31592	-0.119000	0.15052	GCC	.	.		0.637	NIPAL3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276996.1	NM_020448		T	24768656	G	T	24768656	3	4	146	1	0	0	0	0	1	0	0	0	10435	1087	38	1	284	1	NIPAL3	1	24768656	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	4302636	24768656	224481965	3	22356										
C1orf87	127795	hgsc.bcm.edu	37	chr1	60520924	60520924	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gcccctgttagtagtttctgGttgttttctgatttctggtt	10	7	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:60520924G>A	ENST00000371201.3	-	3	401	c.294C>T	c.(292-294)aaC>aaT	p.N98N	C1orf87_ENST00000450089.2_Silent_p.N98N	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	98							calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						GTAGTTTCTGGTTGTTTTCTG	0.388																																					p.N98N	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.C294T						.						342	322	329					1																	60520924		2203	4300	6503	SO:0001819	synonymous_variant	127795	exon3			TTTCTGGTTGTTT	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"carcinoma-related EF-hand protein"					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.294C>T	chr1.hg19:g.60520924G>A		228.0	0.0		233.0	104.0	NM_152377	Q6ZU07|Q8IVS0	Silent	SNP	ENST00000371201.3	hg19	CCDS614.1																																																																																			.	.		0.388	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377		A	60520924	G	A	60520924	2	1	146	1	0	0	0	0	0	0	0	1	2066	1252	44	3		3	C1orf87	1	60520924	Silent	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	35752268	60520924	188729697	4	22357										
WDR63	126820	hgsc.bcm.edu	37	chr1	85561679	85561679	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ccgagtgatcctaatatcatTgctggaggctgtatcaatgg	11	8	2	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:85561679T>A	ENST00000294664.6	+	11	1419	c.1239T>A	c.(1237-1239)atT>atA	p.I413I	WDR63_ENST00000326813.8_Silent_p.I374I|WDR63_ENST00000370596.1_Silent_p.I374I	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	413										NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		CTAATATCATTGCTGGAGGCT	0.388																																					p.I413I		Atlas-SNP	.											.	WDR63	91	.	0			c.T1239A						.						155	149	151					1																	85561679		2203	4300	6503	SO:0001819	synonymous_variant	126820	exon11			TATCATTGCTGGA		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"WD repeat domain containing"	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.1239T>A	chr1.hg19:g.85561679T>A		136.0	0.0		152.0	53.0	NM_145172	A8K988|Q96L72|Q96NU4	Silent	SNP	ENST00000294664.6	hg19	CCDS702.1																																																																																			.	.		0.388	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172		A	85561679	T	A	85561679	2	1	146	1	0	0	0	0	0	0	0	1	17329	1800	63	4		4	WDR63	1	85561679	Silent	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	25040755	85561679	163688942	5	22358										
NBPF14	25832	hgsc.bcm.edu	37	chr1	148004618	148004618	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ccgtcaaagtaaaaaacctaTtgtccacgtaaagggcgaag	9	9	1	0	rs143743039	byFrequency	TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:148004618T>C	ENST00000369219.1	-	22	2712	c.2696A>G	c.(2695-2697)aAt>aGt	p.N899S				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	899	NBPF 10. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					AAAAAACCTATTGTCCACGTA	0.448													-|||	2	0.000399361	8e-04	0	5008	,	,		29882	0		0.001	False		,,,				2504	0				p.N899S		Atlas-SNP	.											.	NBPF14	107	.	0			c.A2696G						.	T	SER/ASN	0,3962		0,0,1981	61	98	86		2696	-1	0	1	dbSNP_134	86	2,8300		0,2,4149	no	missense	NBPF14	NM_015383.1	46	0,2,6130	CC,CT,TT		0.0241,0.0,0.0163	benign	899/922	148004618	2,12262	1981	4151	6132	SO:0001583	missense	25832	exon22			AACCTATTGTCCA	AK092351		1q21.1	2013-01-17			ENSG00000122497			"neuroblastoma breakpoint family"	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.2696A>G	chr1.hg19:g.148004618T>C	ENSP00000358221:p.Asn899Ser	410.0	0.0		453.0	265.0	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	0.010|0.010	-1.756989|-1.756989	0.00657|0.00657	0.0|0.0	2.41E-4|2.41E-4	ENSG00000122497|ENSG00000122497	ENST00000310701|ENST00000369219;ENST00000369368	.|T	.|0.05319	.|3.46	0.512|0.512	-1.02|-1.02	0.10135|0.10135	.|DUF1220 (1);	.|.	.|.	.|.	.|.	T|T	0.00875|0.00875	0.0029|0.0029	N|N	0.17082|0.17082	0.46|0.46	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.15473	.|0.0;0.013;0.007	.|B;B;B	.|0.17433	.|0.0;0.007;0.018	T|T	0.48103|0.48103	-0.9064|-0.9064	4|8	.|0.22109	.|T	.|0.4	.|.	.|.	.|.	.|.	.|.	.|247;880;899	.|F8WEX8;B4DH59;Q5TI25	.|.;.;NBPFE_HUMAN	V|S	905|899;247	.|ENSP00000358221:N899S	.|ENSP00000358221:N899S	I|N	-|-	1|2	0|0	NBPF14|NBPF14	146471242|146471242	0.671000|0.671000	0.27521|0.27521	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.784000|-0.784000	0.04633|0.04633	-1.010000|-1.010000	0.03396|0.03396	-0.571000|-0.571000	0.04153|0.04153	ATA|AAT	.	T|1.000;C|0.000		0.448	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383		C	148004618	T	C	148004618	3	2	146	1	0	0	0	0	1	0	0	0	10203	1493	52	2	73	2	NBPF14	1	148004618	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	62442939	148004618	101246003	6	22359										
THBS3	7059	hgsc.bcm.edu	37	chr1	155172876	155172876	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ctcccctgctctcccactcaCcgcacacctgacactccata	3	22	2	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:155172876C>A	ENST00000368378.3	-	7	829		c.e7+1		RP11-263K19.4_ENST00000422665.1_RNA|RP11-263K19.4_ENST00000454348.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000457183.2_Splice_Site|THBS3_ENST00000486260.1_Intron|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|THBS3_ENST00000541990.1_Splice_Site|THBS3_ENST00000541576.1_5'Flank|RP11-263K19.4_ENST00000453136.1_RNA	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3						bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CTCCCACTCACCGCACACCTG	0.562																																					.		Atlas-SNP	.											.	THBS3	70	.	0			c.808+1G>T						.						114	97	103					1																	155172876		2203	4300	6503	SO:0001630	splice_region_variant	7059	exon8			CACTCACCGCACA	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.808+1G>T	chr1.hg19:g.155172876C>A		103.0	0.0		143.0	58.0	NM_007112	B1AVR8|B4DQ20|Q8WV34	Splice_Site	SNP	ENST00000368378.3	hg19	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.212999	0.79352	.	.	ENSG00000169231	ENST00000368378;ENST00000457183	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7058	0.85371	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	THBS3	153439500	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.234000	0.78134	2.884000	0.98904	0.655000	0.94253	.	.	.		0.562	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112	Intron	A	155172876	C	A	155172876	5	1	146	1	0	0	0	0	0	0	1	0	15870	521	18	3	2129	3	THBS3	1	155172876	Splice_Site	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	7168258	155172876	94077745	7	22360										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155448114	155448114	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	catcctttccaaatctatagCgcttcaaagattccaggaca	5	12	2	1	rs370694359		TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:155448114C>G	ENST00000368346.3	-	3	5186	c.4547G>C	c.(4546-4548)cGc>cCc	p.R1516P	ASH1L_ENST00000392403.3_Missense_Mutation_p.R1516P			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1516					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AAATCTATAGCGCTTCAAAGA	0.473																																					p.R1516P		Atlas-SNP	.											ASH1L,colon,carcinoma,0,1	ASH1L	279	.	0			c.G4547C						.						116	110	112					1																	155448114		2203	4300	6503	SO:0001583	missense	55870	exon3			CTATAGCGCTTCA	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.4547G>C	chr1.hg19:g.155448114C>G	ENSP00000357330:p.Arg1516Pro	115.0	0.0		137.0	50.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	C	19.77	3.889713	0.72524	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.90004	-2.6;-2.6	5.44	5.44	0.79542	.	0.059137	0.64402	D	0.000004	D	0.87900	0.6294	N	0.14661	0.345	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.68943	0.916;0.961	D	0.89763	0.3948	10	0.59425	D	0.04	.	19.0495	0.93038	0.0:1.0:0.0:0.0	.	1516;1516	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	P	1516	ENSP00000357330:R1516P;ENSP00000376204:R1516P	ENSP00000357330:R1516P	R	-	2	0	ASH1L	153714738	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.155000	0.58131	2.832000	0.97577	0.655000	0.94253	CGC	.	.		0.473	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		G	155448114	C	G	155448114	3	3	146	1	0	0	0	0	1	0	0	0	1041	768	27	4	4451	4	ASH1L	1	155448114	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	275238	155448114	93802507	8	22361										
FMO1	2326	hgsc.bcm.edu	37	chr1	171251220	171251220	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aagaggtaaaggaaaactctGtcatatttaacaatacttca	6	6	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:171251220G>T	ENST00000354841.4	+	6	1062	c.931G>T	c.(931-933)Gtc>Ttc	p.V311F	FMO1_ENST00000402921.2_Missense_Mutation_p.V248F|FMO1_ENST00000367750.3_Missense_Mutation_p.V311F|FMO1_ENST00000469112.1_3'UTR	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	311					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	GGAAAACTCTGTCATATTTAA	0.413																																					p.V311F		Atlas-SNP	.											.	FMO1	79	.	0			c.G931T						.						116	109	111					1																	171251220		2203	4300	6503	SO:0001583	missense	2326	exon7			AACTCTGTCATAT	M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.931G>T	chr1.hg19:g.171251220G>T	ENSP00000346901:p.Val311Phe	69.0	0.0		86.0	11.0	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Missense_Mutation	SNP	ENST00000354841.4	hg19	CCDS1294.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.275737	0.59649	.	.	ENSG00000010932	ENST00000367750;ENST00000402921;ENST00000354841	T;T;T	0.55588	0.51;0.51;0.51	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.75547	0.3864	M	0.88241	2.94	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.989;0.999;0.98	T	0.78735	-0.2088	10	0.87932	D	0	-13.1637	19.3467	0.94365	0.0:0.0:1.0:0.0	.	248;311;311	B7Z3P4;B2RCG5;Q01740	.;.;FMO1_HUMAN	F	311;248;311	ENSP00000356724:V311F;ENSP00000385543:V248F;ENSP00000346901:V311F	ENSP00000346901:V311F	V	+	1	0	FMO1	169517844	1.000000	0.71417	0.196000	0.23383	0.051000	0.14879	9.428000	0.97476	2.868000	0.98415	0.557000	0.71058	GTC	.	.		0.413	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021		T	171251220	G	T	171251220	3	4	146	1	0	0	0	0	1	0	0	0	5962	1377	48	3	953	3	FMO1	1	171251220	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	15803106	171251220	77999401	9	22362										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179604969	179604969	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	cctagtcaattctacatccgGatctatagcagggattcgtc	8	11	3	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:179604969G>C	ENST00000367614.1	+	9	1826	c.1467G>C	c.(1465-1467)cgG>cgC	p.R489R	TDRD5_ENST00000294848.8_Silent_p.R489R|TDRD5_ENST00000444136.1_Silent_p.R489R	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	489					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)		p.R489R(1)		NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						TCTACATCCGGATCTATAGCA	0.418																																					p.R489R		Atlas-SNP	.											TDRD5,NS,carcinoma,0,1	TDRD5	149	.	1	Substitution - coding silent(1)	lung(1)	c.G1467C						.						106	102	103					1																	179604969		2203	4300	6503	SO:0001819	synonymous_variant	163589	exon9			CATCCGGATCTAT	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1467G>C	chr1.hg19:g.179604969G>C		97.0	0.0		89.0	36.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.		0.418	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		C	179604969	G	C	179604969	2	2	146	1	0	0	0	0	0	0	0	1	15748	1161	41	4		4	TDRD5	1	179604969	Silent	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	8353749	179604969	69645652	10	22363										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181693632	181693632	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tactgaatgtgttcttggctAtcgctgtggataatctcgcc	10	9	2	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:181693632A>G	ENST00000367573.2	+	17	2101	c.2101A>G	c.(2101-2103)Atc>Gtc	p.I701V	CACNA1E_ENST00000367570.1_Missense_Mutation_p.I701V|CACNA1E_ENST00000367567.4_Missense_Mutation_p.I308V|CACNA1E_ENST00000526775.1_Missense_Mutation_p.I701V|CACNA1E_ENST00000358338.5_Missense_Mutation_p.I652V|CACNA1E_ENST00000357570.5_Missense_Mutation_p.I652V|CACNA1E_ENST00000360108.3_Missense_Mutation_p.I701V	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	701					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GTTCTTGGCTATCGCTGTGGA	0.478																																					p.I701V		Atlas-SNP	.											.	CACNA1E	778	.	0			c.A2101G						.						144	134	137					1																	181693632		1984	4175	6159	SO:0001583	missense	777	exon17			TTGGCTATCGCTG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2101A>G	chr1.hg19:g.181693632A>G	ENSP00000356545:p.Ile701Val	78.0	0.0		113.0	50.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	13.34	2.206634	0.39003	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.97870	-4.58;-4.58;-4.58;-4.58;-4.58;-4.58;-4.58	4.86	4.86	0.63082	.	0.095951	0.64402	N	0.000001	D	0.97729	0.9255	L	0.48362	1.52	0.51012	D	0.999903	P;P	0.46327	0.876;0.876	D;D	0.64595	0.927;0.927	D	0.97408	1.0000	10	0.34782	T	0.22	.	14.4131	0.67128	1.0:0.0:0.0:0.0	.	701;701	Q15878-2;Q15878-3	.;.	V	701;701;652;652;308;701;701	ENSP00000356542:I701V;ENSP00000434814:I701V;ENSP00000350183:I652V;ENSP00000351101:I652V;ENSP00000356539:I308V;ENSP00000353222:I701V;ENSP00000356545:I701V	ENSP00000350183:I652V	I	+	1	0	CACNA1E	179960255	1.000000	0.71417	0.998000	0.56505	0.454000	0.32378	9.157000	0.94714	1.936000	0.56123	0.379000	0.24179	ATC	.	.		0.478	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		G	181693632	A	G	181693632	3	3	146	1	0	0	0	0	1	0	0	0	2544	449	16	2	2167	2	CACNA1E	1	181693632	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	2088663	181693632	67556989	11	22364										
CRB1	23418	hgsc.bcm.edu	37	chr1	197407733	197407733	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gaagacaaatctcacttgctAcaatggaggcaactgcacag	9	10	1	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:197407733A>G	ENST00000367400.3	+	10	3941	c.3806A>G	c.(3805-3807)tAc>tGc	p.Y1269C	CRB1_ENST00000367399.2_Missense_Mutation_p.Y1157C|CRB1_ENST00000535699.1_Missense_Mutation_p.Y1245C|CRB1_ENST00000544212.1_Missense_Mutation_p.Y750C|CRB1_ENST00000367397.1_Missense_Mutation_p.Y650C|CRB1_ENST00000538660.1_Missense_Mutation_p.Y733C|RP11-75C23.1_ENST00000422250.1_RNA	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	1269	EGF-like 18. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CTCACTTGCTACAATGGAGGC	0.443																																					p.Y1269C		Atlas-SNP	.											.	CRB1	284	.	0			c.A3806G						.						104	101	102					1																	197407733		2203	4300	6503	SO:0001583	missense	23418	exon10			CTTGCTACAATGG		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.3806A>G	chr1.hg19:g.197407733A>G	ENSP00000356370:p.Tyr1269Cys	88.0	0.0		114.0	42.0	NM_201253	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	hg19	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	A	18.70	3.679698	0.68042	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	T;D;T;D;D;D	0.91894	1.24;-2.93;1.24;-2.93;-2.93;-2.07	6.17	6.17	0.99709	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.95683	0.8596	M	0.81682	2.555	0.52501	D	0.999953	D;D;D;D;P	0.89917	0.998;1.0;1.0;0.999;0.618	P;D;D;D;B	0.91635	0.87;0.999;0.998;0.939;0.188	D	0.95029	0.8167	9	0.39692	T	0.17	.	12.9656	0.58481	0.879:0.0:0.0:0.121	.	733;1245;1157;918;1269	B7Z5T2;F5H0L2;P82279-3;P82279-4;P82279	.;.;.;.;CRUM1_HUMAN	C	1245;733;1269;1157;750;650;918	ENSP00000438786:Y1245C;ENSP00000438091:Y733C;ENSP00000356370:Y1269C;ENSP00000356369:Y1157C;ENSP00000444556:Y750C;ENSP00000356367:Y650C	ENSP00000356367:Y650C	Y	+	2	0	CRB1	195674356	1.000000	0.71417	0.985000	0.45067	0.951000	0.60555	2.974000	0.49272	2.371000	0.80710	0.533000	0.62120	TAC	.	.		0.443	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		G	197407733	A	G	197407733	3	3	146	1	0	0	0	0	1	0	0	0	3850	391	14	2	3844	2	CRB1	1	197407733	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	15714101	197407733	51842888	12	22365										
IARS2	55699	hgsc.bcm.edu	37	chr1	220276901	220276901	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ttgagactatttcaacacttTcaggtgaagatttttagata	7	5	2	4			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:220276901T>A	ENST00000302637.5	+	8	1167	c.1063T>A	c.(1063-1065)Tca>Aca	p.S355T	IARS2_ENST00000366922.1_Missense_Mutation_p.S283T	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	355					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	TTCAACACTTTCAGGTGAAGA	0.363																																					p.S355T		Atlas-SNP	.											.	IARS2	106	.	0			c.T1063A						.						82	83	82					1																	220276901		2203	4300	6503	SO:0001583	missense	55699	exon8			ACACTTTCAGGTG	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.1063T>A	chr1.hg19:g.220276901T>A	ENSP00000303279:p.Ser355Thr	58.0	0.0		82.0	20.0	NM_018060	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Missense_Mutation	SNP	ENST00000302637.5	hg19	CCDS1523.1	.	.	.	.	.	.	.	.	.	.	T	10.92	1.488146	0.26686	.	.	ENSG00000067704	ENST00000366922;ENST00000302637	T;T	0.35236	1.32;1.32	5.38	0.163	0.14986	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.602172	0.17646	N	0.166847	T	0.15998	0.0385	N	0.13352	0.335	0.45183	D	0.998194	B	0.10296	0.003	B	0.15052	0.012	T	0.10965	-1.0607	10	0.49607	T	0.09	-14.5012	0.5971	0.00738	0.2461:0.2539:0.1158:0.3843	.	355	Q9NSE4	SYIM_HUMAN	T	283;355	ENSP00000355889:S283T;ENSP00000303279:S355T	ENSP00000303279:S355T	S	+	1	0	IARS2	218343524	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	0.641000	0.24720	0.049000	0.15920	0.533000	0.62120	TCA	.	.		0.363	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		A	220276901	T	A	220276901	3	1	146	1	0	0	0	0	1	0	0	0	7483	1783	62	4	1093	4	IARS2	1	220276901	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	22869168	220276901	28973720	13	22366										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228467595	228467595	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	cagtcagtggtcctgtcctgCgacttccggccagcccccaa	10	17	1	0	rs553927346		TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:228467595C>T	ENST00000422127.1	+	28	7514	c.7470C>T	c.(7468-7470)tgC>tgT	p.C2490C	OBSCN_ENST00000359599.6_Silent_p.C1337C|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.C2919C|OBSCN_ENST00000284548.11_Silent_p.C2490C	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2490	Ig-like 24.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TCCTGTCCTGCGACTTCCGGC	0.627																																					p.C2919C		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C8757T						.						22	28	26					1																	228467595		2128	4231	6359	SO:0001819	synonymous_variant	84033	exon33			GTCCTGCGACTTC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.7470C>T	chr1.hg19:g.228467595C>T		80.0	0.0		155.0	51.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228467595	C	T	228467595	2	4	146	1	0	0	0	0	0	0	0	1	10821	776	27	1		1	OBSCN	1	228467595	Silent	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	8190694	228467595	20783026	14	22367										
AGT	183	hgsc.bcm.edu	37	chr1	230846423	230846423	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gggtctttgggcttcccggcAttggcctttgccagctgctc	13	13	1	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:230846423A>G	ENST00000366667.4	-	2	388	c.174T>C	c.(172-174)aaT>aaC	p.N58N	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	58				N -> D (in Ref. 7; AA sequence). {ECO:0000305}.	activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GCTTCCCGGCATTGGCCTTTG	0.587																																					p.N58N		Atlas-SNP	.											.	AGT	62	.	0			c.T174C						.						88	89	89					1																	230846423		2203	4300	6503	SO:0001819	synonymous_variant	183	exon2			CCCGGCATTGGCC	K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"Serine (or cysteine) peptidase inhibitors", "Endogenous ligands"	333	protein-coding gene	gene with protein product	"alpha-1 antiproteinase, antitrypsin"	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.174T>C	chr1.hg19:g.230846423A>G		93.0	0.0		161.0	43.0	NM_000029	Q16358|Q16359|Q96F91	Silent	SNP	ENST00000366667.4	hg19	CCDS1585.1																																																																																			.	.		0.587	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		G	230846423	A	G	230846423	2	3	146	1	0	0	0	0	0	0	0	1	399	214	8	2		2	AGT	1	230846423	Silent	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	2378828	230846423	18404198	15	22368										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247024551	247024551	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	cagtttccactggaactgcaCattttttaggtgtagtaaat	8	7	0	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr1:247024551C>A	ENST00000391829.2	-	29	3905	c.3782G>T	c.(3781-3783)tGt>tTt	p.C1261F	AHCTF1_ENST00000366508.1_Missense_Mutation_p.C1296F|AHCTF1_ENST00000326225.3_Missense_Mutation_p.C1270F|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1261	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TGGAACTGCACATTTTTTAGG	0.363																																					p.C1270F	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.G3809T						.						29	29	29					1																	247024551		2203	4294	6497	SO:0001583	missense	25909	exon29			ACTGCACATTTTT		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.3782G>T	chr1.hg19:g.247024551C>A	ENSP00000375705:p.Cys1261Phe	246.0	0.0		426.0	120.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	hg19		.	.	.	.	.	.	.	.	.	.	C	1.149	-0.647290	0.03506	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.32272	1.46;1.47;1.47	5.8	3.81	0.43845	.	0.085601	0.51477	D	0.000091	T	0.16300	0.0392	L	0.42245	1.32	0.21473	N	0.999677	P;B;B	0.37122	0.583;0.023;0.003	B;B;B	0.32090	0.14;0.015;0.003	T	0.08932	-1.0698	10	0.09338	T	0.73	-11.0283	2.1624	0.03828	0.1609:0.513:0.1553:0.1708	.	122;1296;1261	B3KTD2;Q8WYP5-2;Q8WYP5	.;.;ELYS_HUMAN	F	1296;1270;1261	ENSP00000355464:C1296F;ENSP00000355465:C1270F;ENSP00000375705:C1261F	ENSP00000355465:C1270F	C	-	2	0	AHCTF1	245091174	0.002000	0.14202	0.566000	0.28421	0.008000	0.06430	-0.462000	0.06704	1.586000	0.49944	0.603000	0.83216	TGT	.	.		0.363	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		A	247024551	C	A	247024551	3	1	146	1	0	0	0	0	1	0	0	0	408	478	17	3	3050	3	AHCTF1	1	247024551	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	16178128	247024551	2226070	16	22369										
TPO	7173	hgsc.bcm.edu	37	chr2	1488375	1488375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	cctatctgcacagatcatcaCcctgagggattacatcccca	6	15	3	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr2:1488375C>T	ENST00000345913.4	+	9	1437	c.1346C>T	c.(1345-1347)aCc>aTc	p.T449I	TPO_ENST00000349624.3_Missense_Mutation_p.T276I|TPO_ENST00000329066.4_Missense_Mutation_p.T449I|TPO_ENST00000346956.3_Missense_Mutation_p.T449I|TPO_ENST00000382201.3_Missense_Mutation_p.T449I|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000337415.3_Missense_Mutation_p.T449I|TPO_ENST00000382198.1_Missense_Mutation_p.T276I	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	449					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CAGATCATCACCCTGAGGGAT	0.582																																					p.T449I		Atlas-SNP	.											.	TPO	224	.	0			c.C1346T						.						55	51	52					2																	1488375		2203	4300	6503	SO:0001583	missense	7173	exon9			TCATCACCCTGAG		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.1346C>T	chr2.hg19:g.1488375C>T	ENSP00000318820:p.Thr449Ile	149.0	0.0		239.0	83.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275390	0.59649	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.85048	0.5608	M	0.77712	2.385	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.91635	0.992;0.999;0.982;0.996	D	0.86662	0.1905	10	0.72032	D	0.01	-56.2999	18.9749	0.92731	0.0:1.0:0.0:0.0	.	449;276;449;449	P07202-4;P07202-5;P07202-2;P07202	.;.;.;PERT_HUMAN	I	449;449;449;276;449;449;276;378	ENSP00000337263:T449I;ENSP00000318820:T449I;ENSP00000263886:T449I;ENSP00000332044:T276I;ENSP00000329869:T449I;ENSP00000371636:T449I;ENSP00000371633:T276I;ENSP00000405788:T378I	ENSP00000329869:T449I	T	+	2	0	TPO	1467382	1.000000	0.71417	0.962000	0.40283	0.031000	0.12232	4.551000	0.60740	2.473000	0.83533	0.561000	0.74099	ACC	.	.		0.582	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1488375	C	T	1488375	3	4	146	1	0	0	0	0	1	0	0	0	16425	507	18	3	1376	3	TPO	2	1488375	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10		1488375	241710998	17	22370										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1915791	1915791	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	agtgacccacgcgtggcttaCcttcggtgggagttcctgtt	13	11	0	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr2:1915791C>A	ENST00000399161.2	-	12	2457		c.e12+1		MYT1L_ENST00000428368.2_Splice_Site	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like						cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GCGTGGCTTACCTTCGGTGGG	0.632																																					.		Atlas-SNP	.											.	MYT1L	241	.	0			c.1703+1G>T						.						37	41	40					2																	1915791		2062	4212	6274	SO:0001630	splice_region_variant	23040	exon13			GGCTTACCTTCGG	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.1709+1G>T	chr2.hg19:g.1915791C>A		40.0	0.0		95.0	26.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Splice_Site	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	C	16.98	3.271077	0.59540	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1783	0.93612	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYT1L	1894798	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	7.677000	0.84024	2.595000	0.87683	0.561000	0.74099	.	.	.		0.632	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	Intron	A	1915791	C	A	1915791	5	1	146	1	0	0	0	0	0	0	1	0	10116	521	18	3	1906	3	MYT1L	2	1915791	Splice_Site	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	427416	1915791	241283582	18	22371										
DOK1	1796	hgsc.bcm.edu	37	chr2	74783058	74783058	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	acggtgcagaggactgaggcCgccgagcgctgtggcctgca	17	12	0	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr2:74783058C>T	ENST00000233668.5	+	4	1161	c.492C>T	c.(490-492)gcC>gcT	p.A164A	DOK1_ENST00000340004.6_Intron|DOK1_ENST00000409429.1_Silent_p.A25A|DOK1_ENST00000480318.1_3'UTR|LOXL3_ENST00000409549.1_5'Flank|M1AP_ENST00000464686.1_5'Flank|LOXL3_ENST00000264094.3_5'Flank|LOXL3_ENST00000409986.1_5'Flank|LOXL3_ENST00000393937.2_5'Flank	NM_001381.3	NP_001372.1	Q99704	DOK1_HUMAN	docking protein 1, 62kDa (downstream of tyrosine kinase 1)	164	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				cell surface receptor signaling pathway (GO:0007166)|insulin receptor signaling pathway (GO:0008286)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor signaling protein activity (GO:0005057)			endometrium(3)|large_intestine(2)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						GGACTGAGGCCGCCGAGCGCT	0.637																																					p.A164A	Esophageal Squamous(36;520 860 12502 33616 51270)	Atlas-SNP	.											.	DOK1	39	.	0			c.C492T						.						49	48	48					2																	74783058		2203	4299	6502	SO:0001819	synonymous_variant	1796	exon4			TGAGGCCGCCGAG	U70987	CCDS1954.1, CCDS56125.1	2p13	2008-05-21	2002-08-29		ENSG00000115325	ENSG00000115325			2990	protein-coding gene	gene with protein product		602919	"docking protein 1, 62kD (downstream of tyrosine kinase 1)"			9008160, 9790776, 15546884	Standard	NM_001381		Approved	p62dok	uc002sms.3	Q99704	OTTHUMG00000129956	ENST00000233668.5:c.492C>T	chr2.hg19:g.74783058C>T		60.0	0.0		112.0	36.0	NM_001381	O43204|Q53TY2|Q9UHG6	Silent	SNP	ENST00000233668.5	hg19	CCDS1954.1																																																																																			.	.		0.637	DOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252218.3	NM_001381		T	74783058	C	T	74783058	2	4	146	1	0	0	0	0	0	0	0	1	4698	639	23	1		1	DOK1	2	74783058	Silent	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	72867267	74783058	168416315	19	22372										
LYG2	254773	hgsc.bcm.edu	37	chr2	99861785	99861785	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tcttgcaggacagatccgccAtggctttccctggagatgat	11	11	1	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr2:99861785A>G	ENST00000409238.1	-	3	341	c.321T>C	c.(319-321)caT>caC	p.H107H	LYG2_ENST00000423800.1_Silent_p.H107H|LYG2_ENST00000333017.2_Silent_p.H107H|LYG2_ENST00000409679.1_Silent_p.H107H			Q86SG7	LYG2_HUMAN	lysozyme G-like 2	107					cell wall macromolecule catabolic process (GO:0016998)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)|stomach(1)	12						CAGATCCGCCATGGCTTTCCC	0.522																																					p.H107H		Atlas-SNP	.											.	LYG2	26	.	0			c.T321C						.						112	102	106					2																	99861785		2203	4300	6503	SO:0001819	synonymous_variant	254773	exon4			TCCGCCATGGCTT	AF323919	CCDS2042.1	2q11.2	2008-02-05			ENSG00000185674	ENSG00000185674			29615	protein-coding gene	gene with protein product						8889548, 12574869	Standard	NM_175735		Approved	LYGH	uc002szw.1	Q86SG7	OTTHUMG00000130643	ENST00000409238.1:c.321T>C	chr2.hg19:g.99861785A>G		52.0	0.0		71.0	38.0	NM_175735	Q496G2|Q53RW0	Silent	SNP	ENST00000409238.1	hg19	CCDS2042.1																																																																																			.	.		0.522	LYG2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330307.1	NM_175735		G	99861785	A	G	99861785	2	3	146	1	0	0	0	0	0	0	0	1	9114	214	8	2		2	LYG2	2	99861785	Silent	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	25078727	99861785	143337588	20	22373										
ZRANB3	84083	hgsc.bcm.edu	37	chr2	135976732	135976732	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ccagaggaatgaaattacagCtcatctgttttccatcctga	7	10	2	3	rs373108921		TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr2:135976732C>T	ENST00000264159.6	-	16	2383	c.2267G>A	c.(2266-2268)aGc>aAc	p.S756N	ZRANB3_ENST00000401392.1_Missense_Mutation_p.S754N|ZRANB3_ENST00000536680.1_Missense_Mutation_p.S754N|ZRANB3_ENST00000412849.1_5'UTR	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	756					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		GAAATTACAGCTCATCTGTTT	0.313																																					p.S756N		Atlas-SNP	.											.	ZRANB3	109	.	0			c.G2267A						.						40	38	38					2																	135976732		1796	4055	5851	SO:0001583	missense	84083	exon16			TTACAGCTCATCT	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"Zinc fingers, RAN-binding domain containing"	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.2267G>A	chr2.hg19:g.135976732C>T	ENSP00000264159:p.Ser756Asn	215.0	0.0		287.0	86.0	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	hg19	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	C	3.359	-0.130935	0.06753	.	.	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	D;D;D	0.90324	-2.65;-2.65;-2.64	6.07	3.76	0.43208	.	0.196582	0.52532	N	0.000072	T	0.59542	0.2201	N	0.00088	-2.19	0.25032	N	0.991263	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.60762	-0.7199	10	0.02654	T	1	-19.2355	9.3422	0.38087	0.0:0.1476:0.0:0.8524	.	756;754	Q5FWF4;Q5FWF4-3	ZRAB3_HUMAN;.	N	219;219;754;756;754	ENSP00000383979:S754N;ENSP00000264159:S756N;ENSP00000441320:S754N	ENSP00000264159:S756N	S	-	2	0	ZRANB3	135693202	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.004000	0.29822	1.127000	0.42034	-0.302000	0.09304	AGC	.	.		0.313	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		T	135976732	C	T	135976732	3	4	146	1	0	0	0	0	1	0	0	0	18239	797	28	3	996	3	ZRANB3	2	135976732	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	36114947	135976732	107222641	21	22374										
CACNB4	785	hgsc.bcm.edu	37	chr2	152729009	152729009	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	agaatttccacttgatttccTaggatatagaaaaggaacta	7	6	0	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr2:152729009T>C	ENST00000539935.1	-	6	589		c.e6-2		CACNB4_ENST00000534999.1_Splice_Site|CACNB4_ENST00000427385.1_Splice_Site|CACNB4_ENST00000397327.2_Splice_Site|CACNB4_ENST00000201943.5_Splice_Site|CACNB4_ENST00000360283.6_Splice_Site	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit						adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CTTGATTTCCTAGGATATAGA	0.388																																					.		Atlas-SNP	.											.	CACNB4	108	.	0			c.522-2A>G						.						92	89	90					2																	152729009		1817	4081	5898	SO:0001630	splice_region_variant	785	exon7			ATTTCCTAGGATA	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"Calcium channel subunits"	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.522-2A>G	chr2.hg19:g.152729009T>C		71.0	0.0		91.0	41.0	NM_000726	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Splice_Site	SNP	ENST00000539935.1	hg19	CCDS46426.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.654605	0.88056	.	.	ENSG00000182389	ENST00000539935;ENST00000360283;ENST00000543269;ENST00000439467;ENST00000534999;ENST00000397327;ENST00000427385;ENST00000201943;ENST00000339254	.	.	.	5.98	5.98	0.97165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4781	0.84144	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CACNB4	152437255	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	7.625000	0.83145	2.288000	0.76882	0.528000	0.53228	.	.	.		0.388	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3	Intron	C	152729009	T	C	152729009	5	2	146	1	0	0	0	0	0	0	1	0	2557	1536	53	2	1078	2	CACNB4	2	152729009	Splice_Site	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	16752277	152729009	90470364	22	22375										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166245504	166245504	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ttcttaatagtggacctccaGactgtgaccctgacaaagat	8	10	1	4			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr2:166245504G>T	ENST00000375437.2	+	27	5478	c.5188G>T	c.(5188-5190)Gac>Tac	p.D1730Y	SCN2A_ENST00000357398.3_Missense_Mutation_p.D1730Y|SCN2A_ENST00000375427.2_Missense_Mutation_p.D1730Y|SCN2A_ENST00000283256.6_Missense_Mutation_p.D1730Y	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1730					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGGACCTCCAGACTGTGACCC	0.453																																					p.D1730Y		Atlas-SNP	.											.	SCN2A	589	.	0			c.G5188T						.						193	192	192					2																	166245504		2203	4300	6503	SO:0001583	missense	6326	exon26			CCTCCAGACTGTG	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.5188G>T	chr2.hg19:g.166245504G>T	ENSP00000364586:p.Asp1730Tyr	225.0	0.0		318.0	56.0	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	hg19	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.505875	0.44558	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.97404	-4.37;-4.37;-4.37;-4.37	5.72	5.72	0.89469	Ion transport (1);	0.000000	0.64402	D	0.000001	D	0.97598	0.9213	L	0.43598	1.365	0.80722	D	1	P;D	0.89917	0.699;1.0	P;D	0.97110	0.565;1.0	D	0.96247	0.9180	10	0.26408	T	0.33	.	20.3082	0.98638	0.0:0.0:1.0:0.0	.	1730;1730	Q99250-2;Q99250	.;SCN2A_HUMAN	Y	1730	ENSP00000364586:D1730Y;ENSP00000349973:D1730Y;ENSP00000283256:D1730Y;ENSP00000364576:D1730Y	ENSP00000283256:D1730Y	D	+	1	0	SCN2A	165953750	1.000000	0.71417	0.986000	0.45419	0.937000	0.57800	9.742000	0.98846	2.875000	0.98604	0.644000	0.83932	GAC	.	.		0.453	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166245504	G	T	166245504	3	4	146	1	0	0	0	0	1	0	0	0	13931	942	33	3	5386	3	SCN2A	2	166245504	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	13516495	166245504	76953869	23	22376										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166898866	166898866	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tgcctttgggaaggatcttcTagaaagtccatggaaacgtg	12	7	2	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr2:166898866T>C	ENST00000303395.4	-	12	2111	c.2112A>G	c.(2110-2112)ctA>ctG	p.L704L	AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Silent_p.L676L|SCN1A_ENST00000423058.2_Silent_p.L704L|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Silent_p.L693L			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	704					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAGGATCTTCTAGAAAGTCCA	0.348																																					p.L704L		Atlas-SNP	.											.	SCN1A	641	.	0			c.A2112G						.						151	144	146					2																	166898866		2203	4300	6503	SO:0001819	synonymous_variant	6323	exon12			ATCTTCTAGAAAG	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2112A>G	chr2.hg19:g.166898866T>C		108.0	0.0		150.0	63.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.348	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		C	166898866	T	C	166898866	2	2	146	1	0	0	0	0	0	0	0	1	13929	1509	53	2		2	SCN1A	2	166898866	Silent	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	653362	166898866	76300507	24	22377										
TTN	7273	hgsc.bcm.edu	37	chr2	179590676	179590676	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ttgtctttgtaccataccacCtcaaacggtggtgttcccga	8	12	2	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr2:179590676C>G	ENST00000591111.1	-	68	19646	c.19422G>C	c.(19420-19422)gaG>gaC	p.E6474D	TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.E6791D|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E5547D|TTN_ENST00000342175.6_Intron|RP11-171I2.1_ENST00000590024.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12075	Ig-like 46.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACCATACCACCTCAAACGGTG	0.428																																					p.E6791D		Atlas-SNP	.											.	TTN	18412	.	0			c.G20373C						.						95	91	92					2																	179590676		1908	4137	6045	SO:0001583	missense	7273	exon70			TACCACCTCAAAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.19422G>C	chr2.hg19:g.179590676C>G	ENSP00000465570:p.Glu6474Asp	169.0	0.0		234.0	128.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.85	1.467413	0.26335	.	.	ENSG00000155657	ENST00000342992	T	0.68181	-0.31	5.87	2.08	0.27032	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.54854	0.1884	L	0.58510	1.815	0.80722	D	1	B	0.15141	0.012	B	0.12156	0.007	T	0.56318	-0.7999	9	0.87932	D	0	.	0.5624	0.00681	0.1872:0.3153:0.2277:0.2699	.	6474	Q8WZ42	TITIN_HUMAN	D	5547	ENSP00000343764:E5547D	ENSP00000343764:E5547D	E	-	3	2	TTN	179298921	0.134000	0.22483	1.000000	0.80357	0.919000	0.55068	-0.499000	0.06413	0.486000	0.27676	-0.150000	0.13652	GAG	.	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179590676	C	G	179590676	3	3	146	1	0	0	0	0	1	0	0	0	16750	680	24	4	84328	4	TTN	2	179590676	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	12691810	179590676	63608697	25	22378										
TNS1	7145	hgsc.bcm.edu	37	chr2	218700829	218700829	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	agcgaaccccagggctacgaGgggatgtggcttctggagac	16	10	1	1	rs141836163	byFrequency	TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr2:218700829G>T	ENST00000171887.4	-	18	3190	c.2738C>A	c.(2737-2739)cCt>cAt	p.P913H	TNS1_ENST00000430930.1_Missense_Mutation_p.P913H|TNS1_ENST00000419504.1_Missense_Mutation_p.P913H	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	913					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		AGGGCTACGAGGGGATGTGGC	0.647																																					p.P913H		Atlas-SNP	.											.	TNS1	251	.	0			c.C2738A						.						81	79	80					2																	218700829		2203	4300	6503	SO:0001583	missense	7145	exon18			CTACGAGGGGATG	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.2738C>A	chr2.hg19:g.218700829G>T	ENSP00000171887:p.Pro913His	88.0	0.0		128.0	69.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.199551	0.58126	.	.	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;T;D;D	0.91740	-2.9;2.06;-2.86;-2.9	5.38	5.38	0.77491	.	0.180261	0.49305	D	0.000147	D	0.92335	0.7568	N	0.19112	0.55	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.66196	0.942;0.942;0.897	D	0.92534	0.6036	10	0.46703	T	0.11	.	18.0736	0.89421	0.0:0.0:1.0:0.0	.	913;913;913	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	H	913;72;913;913	ENSP00000171887:P913H;ENSP00000394171:P72H;ENSP00000408724:P913H;ENSP00000406016:P913H	ENSP00000171887:P913H	P	-	2	0	TNS1	218409074	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.122000	0.50446	2.793000	0.96121	0.655000	0.94253	CCT	.	G|0.999;A|0.001		0.647	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		T	218700829	G	T	218700829	3	4	146	1	0	0	0	0	1	0	0	0	16358	1000	35	3	2533	3	TNS1	2	218700829	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	39110153	218700829	24498544	26	22379										
RBMS3	27303	hgsc.bcm.edu	37	chr3	29977613	29977613	+	Missense_Mutation	SNP	T	T	C													0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	caaccatggaccatcccatgTcaatgcagccagccaacatg							TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr3:29977613T>C	ENST00000383767.2	+	11	1312	c.976T>C	c.(976-978)Tca>Cca	p.S326P	RBMS3_ENST00000473799.1_3'UTR|RBMS3_ENST00000383766.2_Missense_Mutation_p.S308P|RBMS3_ENST00000273139.9_Missense_Mutation_p.S326P|RBMS3_ENST00000456853.1_Missense_Mutation_p.S339P|RBMS3_ENST00000434693.2_Missense_Mutation_p.S325P|RBMS3_ENST00000396583.3_Missense_Mutation_p.S339P|RBMS3_ENST00000452462.1_Missense_Mutation_p.S326P|RBMS3-AS1_ENST00000414547.1_RNA			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	326					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				CCATCCCATGTCAATGCAGCC	0.438																																					p.S339P		Atlas-SNP	.											.	RBMS3	62	.	0			c.T1015C						.						116	96	103					3																	29977613		2203	4300	6503	SO:0001583	missense	27303	exon12			CCCATGTCAATGC	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"RNA binding motif (RRM) containing"	13427	protein-coding gene	gene with protein product	"RNA-binding protein"	605786	"RNA binding motif, single stranded interacting protein"			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.976T>C	chr3.hg19:g.29977613T>C	ENSP00000373277:p.Ser326Pro	198.0	0.0		298.0	161.0	NM_001177712	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Missense_Mutation	SNP	ENST00000383767.2	hg19	CCDS33724.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.853255	0.91355	.	.	ENSG00000144642	ENST00000434693;ENST00000396583;ENST00000383767;ENST00000273139;ENST00000383766;ENST00000452462;ENST00000456853	T;T;T;T;T;T;T	0.29397	1.58;1.72;1.57;1.65;1.75;1.63;1.74	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.59838	0.2223	M	0.83852	2.665	0.80722	D	1	D;D;D;D	0.65815	0.991;0.991;0.995;0.991	D;D;D;D	0.71870	0.962;0.953;0.975;0.944	T	0.62835	-0.6770	9	.	.	.	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	326;339;308;326	G5E9J9;Q6XE24-2;Q6XE24-3;Q6XE24	.;.;.;RBMS3_HUMAN	P	325;339;326;326;308;326;339	ENSP00000395592:S325P;ENSP00000379828:S339P;ENSP00000373277:S326P;ENSP00000273139:S326P;ENSP00000373276:S308P;ENSP00000397926:S326P;ENSP00000400519:S339P	.	S	+	1	0	RBMS3	29952617	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.980000	0.88113	2.371000	0.80710	0.533000	0.62120	TCA	.	.		0.438	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792		C	29977613	T	C	29977613	3	2	146	1	0	0	0	0	1	0	0	0	13165	1667	58	2	1061	2	RBMS3	3	29977613	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10		29977613	168044817	27	22380	98	2								
RBMS3	27303	hgsc.bcm.edu	37	chr3	29977619	29977619	+	Missense_Mutation	SNP	C	C	A													0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tggaccatcccatgtcaatgCagccagccaacatgatgggc							TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr3:29977619C>A	ENST00000383767.2	+	11	1318	c.982C>A	c.(982-984)Cag>Aag	p.Q328K	RBMS3_ENST00000473799.1_3'UTR|RBMS3_ENST00000383766.2_Missense_Mutation_p.Q310K|RBMS3_ENST00000273139.9_Missense_Mutation_p.Q328K|RBMS3_ENST00000456853.1_Missense_Mutation_p.Q341K|RBMS3_ENST00000434693.2_Missense_Mutation_p.Q327K|RBMS3_ENST00000396583.3_Missense_Mutation_p.Q341K|RBMS3_ENST00000452462.1_Missense_Mutation_p.Q328K|RBMS3-AS1_ENST00000414547.1_RNA			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	328					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				CATGTCAATGCAGCCAGCCAA	0.443																																					p.Q341K		Atlas-SNP	.											.	RBMS3	62	.	0			c.C1021A						.						118	98	104					3																	29977619		2203	4300	6503	SO:0001583	missense	27303	exon12			TCAATGCAGCCAG	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"RNA binding motif (RRM) containing"	13427	protein-coding gene	gene with protein product	"RNA-binding protein"	605786	"RNA binding motif, single stranded interacting protein"			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.982C>A	chr3.hg19:g.29977619C>A	ENSP00000373277:p.Gln328Lys	204.0	0.0		294.0	161.0	NM_001177712	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Missense_Mutation	SNP	ENST00000383767.2	hg19	CCDS33724.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640196	0.87859	.	.	ENSG00000144642	ENST00000434693;ENST00000396583;ENST00000383767;ENST00000273139;ENST00000383766;ENST00000452462;ENST00000456853	T;T;T;T;T;T;T	0.30182	1.67;1.57;1.68;1.63;1.68;1.65;1.54	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.54565	0.1866	M	0.85099	2.735	0.80722	D	1	P;P;P;P	0.44659	0.57;0.523;0.84;0.588	B;B;P;B	0.50405	0.363;0.273;0.64;0.359	T	0.53229	-0.8468	9	.	.	.	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	328;341;310;328	G5E9J9;Q6XE24-2;Q6XE24-3;Q6XE24	.;.;.;RBMS3_HUMAN	K	327;341;328;328;310;328;341	ENSP00000395592:Q327K;ENSP00000379828:Q341K;ENSP00000373277:Q328K;ENSP00000273139:Q328K;ENSP00000373276:Q310K;ENSP00000397926:Q328K;ENSP00000400519:Q341K	.	Q	+	1	0	RBMS3	29952623	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.760000	0.85248	2.941000	0.99782	0.655000	0.94253	CAG	.	.		0.443	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792		A	29977619	C	A	29977619	3	1	146	1	0	0	0	0	1	0	0	0	13165	711	25	3	1067	3	RBMS3	3	29977619	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	6	29977619	168044811	28	22381	98	2								
OXSR1	9943	hgsc.bcm.edu	37	chr3	38292941	38292941	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tcatttctgctggcctggtcGacggaagggatttagtaata	12	7	2	0	rs145431865	byFrequency	TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr3:38292941G>T	ENST00000311806.3	+	16	1795	c.1423G>T	c.(1423-1425)Gac>Tac	p.D475Y		NM_005109.2	NP_005100.1			oxidative stress responsive 1											skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TGGCCTGGTCGACGGAAGGGA	0.448																																					p.D475Y		Atlas-SNP	.											.	OXSR1	74	.	0			c.G1423T						.						305	276	286					3																	38292941		2203	4300	6503	SO:0001583	missense	9943	exon16			CTGGTCGACGGAA	AB017642	CCDS2675.1	3p22.2	2013-05-17	2013-05-17	2004-11-26	ENSG00000172939	ENSG00000172939			8508	protein-coding gene	gene with protein product		604046	"oxidative-stress responsive 1"	OSR1		10083736	Standard	XM_005265638		Approved	KIAA1101	uc003chy.3	O95747	OTTHUMG00000131084	ENST00000311806.3:c.1423G>T	chr3.hg19:g.38292941G>T	ENSP00000311713:p.Asp475Tyr	144.0	0.0		164.0	84.0	NM_005109		Missense_Mutation	SNP	ENST00000311806.3	hg19	CCDS2675.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782855	0.90282	.	.	ENSG00000172939	ENST00000311806	T	0.78003	-1.14	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.88123	0.6352	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	D	0.88930	0.3372	10	0.87932	D	0	-20.8632	17.1648	0.86812	0.0:0.0:1.0:0.0	.	475	O95747	OXSR1_HUMAN	Y	475	ENSP00000311713:D475Y	ENSP00000311713:D475Y	D	+	1	0	OXSR1	38267945	1.000000	0.71417	0.644000	0.29465	0.993000	0.82548	8.284000	0.89912	2.801000	0.96364	0.650000	0.86243	GAC	.	G|0.999;A|0.001		0.448	OXSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253744.1	NM_005109		T	38292941	G	T	38292941	3	4	146	1	0	0	0	0	1	0	0	0	11345	1058	37	1	1485	1	OXSR1	3	38292941	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	8315322	38292941	159729489	29	22382										
SCN11A	11280	hgsc.bcm.edu	37	chr3	38921513	38921513	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aatccgaaggctacccatttTagtaccatctccaggataaa	6	11	1	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr3:38921513T>C	ENST00000302328.3	-	19	3519	c.3321A>G	c.(3319-3321)ctA>ctG	p.L1107L	SCN11A_ENST00000456224.3_Silent_p.L1069L|SCN11A_ENST00000444237.2_Silent_p.L1107L|SCN11A_ENST00000450244.1_Silent_p.L1107L	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1107					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTACCCATTTTAGTACCATCT	0.373																																					p.L1107L		Atlas-SNP	.											.	SCN11A	296	.	0			c.A3321G						.						71	70	70					3																	38921513		2203	4300	6503	SO:0001819	synonymous_variant	11280	exon19			CCATTTTAGTACC	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.3321A>G	chr3.hg19:g.38921513T>C		93.0	0.0		107.0	38.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.		0.373	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		C	38921513	T	C	38921513	2	2	146	1	0	0	0	0	0	0	0	1	13928	1741	61	2		2	SCN11A	3	38921513	Silent	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	628572	38921513	159100917	30	22383										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr3:41266098A>T	ENST00000349496.5	+	3	375	c.95A>T	c.(94-96)gAc>gTc	p.D32V	CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32V|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32V|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32V	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95T						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>T	chr3.hg19:g.41266098A>T	ENSP00000344456:p.Asp32Val	175.0	1.0		222.0	84.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184569	0.78677	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70037	0.3178	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.74325	-0.3702	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	V	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25V;ENSP00000385604:D32V;ENSP00000412219:D32V;ENSP00000379486:D32V;ENSP00000344456:D32V;ENSP00000411226:D25V;ENSP00000379488:D32V;ENSP00000409302:D32V;ENSP00000401599:D32V	ENSP00000344456:D32V	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266098	A	T	41266098	3	4	146	1	0	0	0	0	1	0	0	0	4018	275	10	4	101	4	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	2344585	41266098	156756332	31	22384										
ITIH4	3700	hgsc.bcm.edu	37	chr3	52860642	52860642	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tctccagaaagctgatgcccTggggctcgaagatgtgaatg	13	9	1	4			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr3:52860642T>C	ENST00000266041.4	-	5	641	c.545A>G	c.(544-546)cAg>cGg	p.Q182R	ITIH4_ENST00000485816.1_Missense_Mutation_p.Q182R|ITIH4_ENST00000434759.3_Missense_Mutation_p.Q94R|ITIH4-AS1_ENST00000478366.1_RNA|ITIH4_ENST00000467462.1_5'Flank|ITIH4_ENST00000406595.1_Missense_Mutation_p.Q182R|ITIH4_ENST00000346281.5_Missense_Mutation_p.Q182R|RP5-966M1.6_ENST00000468472.1_3'UTR	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	182					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GCTGATGCCCTGGGGCTCGAA	0.592																																					p.Q182R		Atlas-SNP	.											.	ITIH4	74	.	0			c.A545G						.						89	82	84					3																	52860642		2203	4300	6503	SO:0001583	missense	3700	exon5			ATGCCCTGGGGCT	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"plasma Kallikrein-sensitive glycoprotein"	600564	"inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.545A>G	chr3.hg19:g.52860642T>C	ENSP00000266041:p.Gln182Arg	48.0	0.0		53.0	32.0	NM_001166449	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Missense_Mutation	SNP	ENST00000266041.4	hg19	CCDS2865.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.210740	0.79240	.	.	ENSG00000055955	ENST00000266041;ENST00000346281;ENST00000485816;ENST00000406595;ENST00000538421;ENST00000434759	T;T;T;T;T	0.03094	4.81;4.79;4.83;4.86;4.05	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000006	T	0.13713	0.0332	M	0.65677	2.01	0.80722	D	1	P;D;D;P	0.62365	0.864;0.991;0.991;0.559	B;P;P;P	0.58970	0.327;0.849;0.804;0.533	T	0.00234	-1.1893	10	0.72032	D	0.01	-24.8528	14.8606	0.70379	0.0:0.0:0.0:1.0	.	182;182;182;182	E9PGN5;B7ZKJ8;Q14624;Q14624-2	.;.;ITIH4_HUMAN;.	R	182;182;182;182;170;94	ENSP00000266041:Q182R;ENSP00000340520:Q182R;ENSP00000417824:Q182R;ENSP00000384425:Q182R;ENSP00000440036:Q94R	ENSP00000266041:Q182R	Q	-	2	0	ITIH4	52835682	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.394000	0.52551	1.997000	0.58415	0.533000	0.62120	CAG	.	.		0.592	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218		C	52860642	T	C	52860642	3	2	146	1	0	0	0	0	1	0	0	0	7915	1580	55	2	2327	2	ITIH4	3	52860642	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	11594544	52860642	145161788	32	22385										
TRIM59	286827	hgsc.bcm.edu	37	chr3	160156300	160156300	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tgctctcgtatttccttcatTctttcaatttgtggagtata	6	8	4	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr3:160156300T>A	ENST00000309784.4	-	3	857	c.672A>T	c.(670-672)agA>agT	p.R224S	RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.R224S|TRIM59_ENST00000543469.1_Missense_Mutation_p.R224S	NM_173084.2	NP_775107.1	Q8IWR1	TRI59_HUMAN	tripartite motif containing 59	224					innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral entry into host cell (GO:0046597)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(3)	15			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TTTCCTTCATTCTTTCAATTT	0.328																																					p.R224S		Atlas-SNP	.											.	TRIM59	42	.	0			c.A672T						.						88	93	92					3																	160156300		2203	4300	6503	SO:0001583	missense	286827	exon3			CTTCATTCTTTCA	AY159379	CCDS3190.1	3q26	2013-01-09	2011-01-25		ENSG00000213186	ENSG00000213186		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	30834	protein-coding gene	gene with protein product			"tripartite motif-containing 57", "tripartite motif-containing 59"	TRIM57		12095697	Standard	NM_173084		Approved	TSBF1, Mrf1, RNF104	uc003fdm.3	Q8IWR1	OTTHUMG00000159034	ENST00000309784.4:c.672A>T	chr3.hg19:g.160156300T>A	ENSP00000311219:p.Arg224Ser	119.0	0.0		209.0	64.0	NM_173084	A8K5G9|D3DNL9	Missense_Mutation	SNP	ENST00000309784.4	hg19	CCDS3190.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.418725	0.62622	.	.	ENSG00000213186	ENST00000543469;ENST00000309784	T;T	0.23950	2.07;1.88	5.77	0.644	0.17776	.	0.227039	0.45606	D	0.000353	T	0.15565	0.0375	L	0.42245	1.32	0.21762	N	0.999554	B	0.27625	0.183	B	0.22386	0.039	T	0.14337	-1.0476	9	.	.	.	-4.4696	3.9254	0.09261	0.172:0.413:0.0:0.4149	.	224	Q8IWR1	TRI59_HUMAN	S	224	ENSP00000444313:R224S;ENSP00000311219:R224S	.	R	-	3	2	TRIM59	161638994	0.001000	0.12720	0.924000	0.36721	0.982000	0.71751	-0.473000	0.06615	0.090000	0.17273	0.459000	0.35465	AGA	.	.		0.328	TRIM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352963.1	NM_173084		A	160156300	T	A	160156300	3	1	146	1	0	0	0	0	1	0	0	0	16547	1780	62	4	543	4	TRIM59	3	160156300	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	107295658	160156300	37866130	33	22386										
AP2M1	1173	hgsc.bcm.edu	37	chr3	183899820	183899820	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aactttaaaccctcactgctGgctcagaagatcgaggtgag	10	10	2	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr3:183899820G>T	ENST00000292807.5	+	9	1096	c.948G>T	c.(946-948)ctG>ctT	p.L316L	AP2M1_ENST00000382456.3_Silent_p.L314L|AP2M1_ENST00000439647.1_Silent_p.L314L|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000461733.1_3'UTR|AP2M1_ENST00000411763.2_Silent_p.L341L	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	316	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CCTCACTGCTGGCTCAGAAGA	0.537																																					p.L314L		Atlas-SNP	.											.	AP2M1	35	.	0			c.G942T						.						46	47	47					3																	183899820		2011	4178	6189	SO:0001819	synonymous_variant	1173	exon8			ACTGCTGGCTCAG	U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"clathrin-associated/assembly/adaptor protein, medium 1", "plasma membrane adaptor AP-2 50kDA protein", "clathrin coat adaptor protein AP50", "clathrin adaptor complex AP2, mu subunit", "HA2 50 kDA subunit", "clathrin assembly protein complex 2 medium chain", "AP-2 mu 2 chain"	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.948G>T	chr3.hg19:g.183899820G>T		67.0	0.0		91.0	4.0	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Silent	SNP	ENST00000292807.5	hg19	CCDS43177.1																																																																																			.	.		0.537	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068		T	183899820	G	T	183899820	2	4	146	1	0	0	0	0	0	0	0	1	742	1335	47	3		3	AP2M1	3	183899820	Silent	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	23743520	183899820	14122610	34	22387										
CCKAR	886	hgsc.bcm.edu	37	chr4	26491839	26491839	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ttttcgagcccgagttcacaGggaggagtgatgttgcttcc	13	9	1	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr4:26491839G>A	ENST00000295589.3	-	1	245	c.51C>T	c.(49-51)ccC>ccT	p.P17P		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	17					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)			NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	CGAGTTCACAGGGAGGAGTGA	0.488																																					p.P17P		Atlas-SNP	.											.	CCKAR	74	.	0			c.C51T						.						127	104	112					4																	26491839		2203	4300	6503	SO:0001819	synonymous_variant	886	exon1			TTCACAGGGAGGA	L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"GPCR / Class A : Cholecystokinin receptors"	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.51C>T	chr4.hg19:g.26491839G>A		101.0	0.0		99.0	41.0	NM_000730	B2R9Z5	Silent	SNP	ENST00000295589.3	hg19	CCDS3438.1																																																																																			.	.		0.488	CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2			A	26491839	G	A	26491839	2	1	146	1	0	0	0	0	0	0	0	1	2882	987	35	3		3	CCKAR	4	26491839	Silent	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10		26491839	164662437	35	22388										
GABRB1	2560	hgsc.bcm.edu	37	chr4	47427952	47427952	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ccgacttgactgatgtgaatTccatagacaagtggtcccga	10	10	0	4			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr4:47427952T>C	ENST00000295454.3	+	9	1634	c.1342T>C	c.(1342-1344)Tcc>Ccc	p.S448P	GABRB1_ENST00000538619.1_Missense_Mutation_p.S378P	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	448					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGATGTGAATTCCATAGACAA	0.527																																					p.S448P		Atlas-SNP	.											.	GABRB1	107	.	0			c.T1342C						.						106	103	104					4																	47427952		2203	4300	6503	SO:0001583	missense	2560	exon9			GTGAATTCCATAG		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4081	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 1"	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.1342T>C	chr4.hg19:g.47427952T>C	ENSP00000295454:p.Ser448Pro	175.0	0.0		140.0	60.0	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Missense_Mutation	SNP	ENST00000295454.3	hg19	CCDS3474.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.388430	0.42308	.	.	ENSG00000163288	ENST00000295454;ENST00000538619	D;D	0.85773	-2.03;-2.03	5.34	5.34	0.76211	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.225184	0.39020	N	0.001491	T	0.75982	0.3924	L	0.29908	0.895	0.36066	D	0.84177	B;P	0.35821	0.282;0.523	B;B	0.37144	0.242;0.21	T	0.78894	-0.2024	10	0.40728	T	0.16	-20.1064	7.4507	0.27237	0.0:0.0737:0.1434:0.7829	.	378;448	F5GXV5;P18505	.;GBRB1_HUMAN	P	448;378	ENSP00000295454:S448P;ENSP00000440330:S378P	ENSP00000295454:S448P	S	+	1	0	GABRB1	47122709	0.993000	0.37304	0.969000	0.41365	0.990000	0.78478	2.157000	0.42320	2.244000	0.73946	0.528000	0.53228	TCC	.	.		0.527	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1			C	47427952	T	C	47427952	3	2	146	1	0	0	0	0	1	0	0	0	6174	1783	62	2	1376	2	GABRB1	4	47427952	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	20936113	47427952	143726324	36	22389										
USP53	54532	hgsc.bcm.edu	37	chr4	120182988	120182988	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tcacaccaaaagttccaaatGggtattttttgatgatgcaa	7	7	1	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr4:120182988G>T	ENST00000274030.6	+	12	2120	c.941G>T	c.(940-942)tGg>tTg	p.W314L	USP53_ENST00000450251.1_Missense_Mutation_p.W314L	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						AGTTCCAAATGGGTATTTTTT	0.308																																					p.W314L		Atlas-SNP	.											.	USP53	69	.	0			c.G941T						.						98	90	92					4																	120182988		1829	4084	5913	SO:0001583	missense	54532	exon11			CCAAATGGGTATT	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"Ubiquitin-specific peptidases"	29255	protein-coding gene	gene with protein product			"ubiquitin specific protease 53"			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.941G>T	chr4.hg19:g.120182988G>T	ENSP00000274030:p.Trp314Leu	91.0	0.0		112.0	56.0	NM_019050		Missense_Mutation	SNP	ENST00000274030.6	hg19	CCDS43265.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.876206	0.91664	.	.	ENSG00000145390	ENST00000274030;ENST00000450251	T;T	0.33216	1.42;1.42	5.81	5.81	0.92471	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.64394	0.2594	M	0.87971	2.92	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.69018	-0.5256	10	0.87932	D	0	-10.4211	20.089	0.97809	0.0:0.0:1.0:0.0	.	314	Q70EK8	UBP53_HUMAN	L	314	ENSP00000274030:W314L;ENSP00000409906:W314L	ENSP00000274030:W314L	W	+	2	0	USP53	120402436	1.000000	0.71417	0.999000	0.59377	0.925000	0.55904	9.292000	0.96076	2.752000	0.94435	0.557000	0.71058	TGG	.	.		0.308	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597		T	120182988	G	T	120182988	3	4	146	1	0	0	0	0	1	0	0	0	17099	1357	47	3	971	3	USP53	4	120182988	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	72755036	120182988	70971288	37	22390										
C4orf51	646603	hgsc.bcm.edu	37	chr4	146648100	146648100	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	accaggccctttaaaaagtcAtttgatgtcaagcatggagt	9	8	2	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr4:146648100A>G	ENST00000438731.1	+	3	345	c.345A>G	c.(343-345)tcA>tcG	p.S115S		NM_001080531.1	NP_001074000.1	C9J302	CD051_HUMAN	chromosome 4 open reading frame 51	115										haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)	6						TTAAAAAGTCATTTGATGTCA	0.353																																					p.S115S		Atlas-SNP	.											.	C4orf51	18	.	0			c.A345G						.						142	133	135					4																	146648100		1855	4110	5965	SO:0001819	synonymous_variant	646603	exon3			AAAGTCATTTGAT		CCDS47140.1	4q31.21	2009-09-09			ENSG00000237136	ENSG00000237136			37264	protein-coding gene	gene with protein product							Standard	NM_001080531		Approved		uc003ikk.3	C9J302	OTTHUMG00000161367	ENST00000438731.1:c.345A>G	chr4.hg19:g.146648100A>G		260.0	0.0		510.0	139.0	NM_001080531		Silent	SNP	ENST00000438731.1	hg19	CCDS47140.1	.	.	.	.	.	.	.	.	.	.	A	10.95	1.495628	0.26774	.	.	ENSG00000237136	ENST00000511965	.	.	.	5.25	2.75	0.32379	.	.	.	.	.	T	0.25344	0.0616	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.18650	-1.0330	4	.	.	.	.	4.081	0.09925	0.7218:0.0:0.0963:0.1819	.	.	.	.	R	75	.	.	H	+	2	0	C4orf51	146867550	0.001000	0.12720	0.018000	0.16275	0.738000	0.42128	0.754000	0.26390	0.898000	0.36418	0.383000	0.25322	CAT	.	.		0.353	C4orf51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080531		G	146648100	A	G	146648100	2	3	146	1	0	0	0	0	0	0	0	1	2279	204	8	2		2	C4orf51	4	146648100	Silent	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	26465112	146648100	44506176	38	22391										
FSTL5	56884	hgsc.bcm.edu	37	chr4	162307497	162307497	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gtgtatatgccaatgactgaGgaacgcacttatagtccttc	9	9	0	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr4:162307497G>A	ENST00000306100.5	-	16	2382	c.1946C>T	c.(1945-1947)cCt>cTt	p.P649L	FSTL5_ENST00000427802.2_Missense_Mutation_p.P639L|FSTL5_ENST00000379164.4_Missense_Mutation_p.P648L|RP11-234O6.2_ENST00000508189.1_RNA|FSTL5_ENST00000536695.1_Missense_Mutation_p.P648L	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	649						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.P649L(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		CAATGACTGAGGAACGCACTT	0.428																																					p.P649L		Atlas-SNP	.											FSTL5,NS,carcinoma,0,1	FSTL5	207	.	1	Substitution - Missense(1)	endometrium(1)	c.C1946T						.						92	84	86					4																	162307497		2203	4300	6503	SO:0001583	missense	56884	exon16			GACTGAGGAACGC	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.1946C>T	chr4.hg19:g.162307497G>A	ENSP00000305334:p.Pro649Leu	99.0	1.0		180.0	40.0	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	hg19	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.195721	0.58126	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.53	5.53	0.82687	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.61413	0.2345	M	0.83223	2.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.66221	-0.5978	10	0.87932	D	0	.	18.4642	0.90749	0.0:0.0:1.0:0.0	.	639;648;649	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	L	649;648;639;648	ENSP00000305334:P649L;ENSP00000368462:P648L;ENSP00000389270:P639L;ENSP00000440409:P648L	ENSP00000305334:P649L	P	-	2	0	FSTL5	162526947	1.000000	0.71417	0.080000	0.20451	0.362000	0.29581	9.315000	0.96313	2.616000	0.88540	0.563000	0.77884	CCT	.	.		0.428	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		A	162307497	G	A	162307497	3	1	146	1	0	0	0	0	1	0	0	0	6088	1000	35	3	601	3	FSTL5	4	162307497	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	15659397	162307497	28846779	39	22392										
IRX4	50805	hgsc.bcm.edu	37	chr5	1878852	1878852	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gcggctctgcttccagcgggTcgaagtcgtccaagtcacta	12	13	2	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:1878852T>C	ENST00000505790.1	-	6	1247	c.791A>G	c.(790-792)gAc>gGc	p.D264G	IRX4_ENST00000505938.1_5'Flank|IRX4_ENST00000513692.1_Missense_Mutation_p.D264G|IRX4_ENST00000231357.2_Missense_Mutation_p.D264G	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	264					establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		TTCCAGCGGGTCGAAGTCGTC	0.687																																					p.D264G		Atlas-SNP	.											.	IRX4	45	.	0			c.A791G						.						30	32	31					5																	1878852		2203	4300	6503	SO:0001583	missense	50805	exon5			AGCGGGTCGAAGT	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"Homeoboxes / TALE class"	6129	protein-coding gene	gene with protein product		606199	"iroquois homeobox protein 4"			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.791A>G	chr5.hg19:g.1878852T>C	ENSP00000423161:p.Asp264Gly	170.0	0.0		193.0	80.0	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Missense_Mutation	SNP	ENST00000505790.1	hg19	CCDS3867.1	.	.	.	.	.	.	.	.	.	.	t	15.82	2.946878	0.53186	.	.	ENSG00000113430	ENST00000231357;ENST00000505790;ENST00000513692	T;T;T	0.69175	-0.38;-0.38;-0.38	3.75	3.75	0.43078	.	0.198676	0.41605	U	0.000858	T	0.60327	0.2260	L	0.61218	1.895	0.58432	D	0.99999	P	0.46987	0.888	B	0.39465	0.3	T	0.61676	-0.7014	10	0.30854	T	0.27	-33.5842	12.3115	0.54931	0.0:0.0:0.0:1.0	.	264	P78413	IRX4_HUMAN	G	264	ENSP00000231357:D264G;ENSP00000423161:D264G;ENSP00000424235:D264G	ENSP00000231357:D264G	D	-	2	0	IRX4	1931852	1.000000	0.71417	0.886000	0.34754	0.138000	0.21146	4.084000	0.57650	1.563000	0.49615	0.370000	0.22315	GAC	.	.		0.687	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358		C	1878852	T	C	1878852	3	2	146	1	0	0	0	0	1	0	0	0	7855	1667	58	2	772	2	IRX4	5	1878852	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10		1878852	179036408	40	22393										
CDH6	1004	hgsc.bcm.edu	37	chr5	31323299	31323299	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tggcggattccctgagctcgCtggagtcagtgaccacggat	14	11	1	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:31323299C>T	ENST00000265071.2	+	12	2522	c.2257C>T	c.(2257-2259)Ctg>Ttg	p.L753L		NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	753					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CCTGAGCTCGCTGGAGTCAGT	0.532																																					p.L753L		Atlas-SNP	.											.	CDH6	175	.	0			c.C2257T						.						56	52	53					5																	31323299		2203	4300	6503	SO:0001819	synonymous_variant	1004	exon12			AGCTCGCTGGAGT	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"Cadherins / Major cadherins"	1765	protein-coding gene	gene with protein product	"K-Cadherin"	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.2257C>T	chr5.hg19:g.31323299C>T		146.0	0.0		165.0	73.0	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	hg19	CCDS3894.1																																																																																			.	.		0.532	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		T	31323299	C	T	31323299	2	4	146	1	0	0	0	0	0	0	0	1	3116	796	28	3		3	CDH6	5	31323299	Silent	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	29444447	31323299	149591961	41	22394										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32089802	32089802	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	caacataatggccagcgatcGcctcgaaagaacaaaccagc	8	13	0	1	rs202221834		TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:32089802G>T	ENST00000438447.1	+	20	6636	c.6248G>T	c.(6247-6249)cGc>cTc	p.R2083L	PDZD2_ENST00000282493.3_Missense_Mutation_p.R2083L			O15018	PDZD2_HUMAN	PDZ domain containing 2	2083					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GCCAGCGATCGCCTCGAAAGA	0.552																																					p.R2083L		Atlas-SNP	.											PDZD2,colon,carcinoma,0,1	PDZD2	306	.	0			c.G6248T						.						70	69	69					5																	32089802		2203	4300	6503	SO:0001583	missense	23037	exon19			GCGATCGCCTCGA	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.6248G>T	chr5.hg19:g.32089802G>T	ENSP00000402033:p.Arg2083Leu	44.0	0.0		64.0	3.0	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.593866	0.28445	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.05717	3.4;3.4	5.59	3.82	0.43975	.	0.510432	0.18335	N	0.144345	T	0.03651	0.0104	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38329	-0.9666	10	0.66056	D	0.02	.	7.6913	0.28569	0.0:0.7373:0.1735:0.0892	.	2083	O15018	PDZD2_HUMAN	L	2083;1884;2083	ENSP00000402033:R2083L;ENSP00000282493:R2083L	ENSP00000282493:R2083L	R	+	2	0	PDZD2	32125559	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.089000	0.15002	0.732000	0.32470	-0.867000	0.03001	CGC	.	G|1.000;A|0.000		0.552	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32089802	G	T	32089802	3	4	146	1	0	0	0	0	1	0	0	0	11710	1087	38	1	6322	1	PDZD2	5	32089802	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	766503	32089802	148825458	42	22395										
TARS	6897	hgsc.bcm.edu	37	chr5	33448802	33448802	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	caggttgatgcggaatcttgGaaaactacaccatatcaaat	8	8	2	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:33448802G>A	ENST00000265112.3	+	3	605	c.294G>A	c.(292-294)tgG>tgA	p.W98*	TARS_ENST00000541634.1_Intron|TARS_ENST00000502553.1_Nonsense_Mutation_p.W98*|TARS_ENST00000455217.2_Nonsense_Mutation_p.W98*|TARS_ENST00000414361.2_Missense_Mutation_p.G31E	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	98					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)			NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	CGGAATCTTGGAAAACTACAC	0.383																																					p.W98X		Atlas-SNP	.											.	TARS	66	.	0			c.G294A						.						137	126	130					5																	33448802		2203	4300	6503	SO:0001587	stop_gained	6897	exon3			ATCTTGGAAAACT	AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	11572	protein-coding gene	gene with protein product	"threonine tRNA ligase 1, cytoplasmic"	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.294G>A	chr5.hg19:g.33448802G>A	ENSP00000265112:p.Trp98*	112.0	0.0		136.0	62.0	NM_152295	A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Nonsense_Mutation	SNP	ENST00000265112.3	hg19	CCDS3899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.4|24.4	4.524973|4.524973	0.85600|0.85600	.|.	.|.	ENSG00000113407|ENSG00000113407	ENST00000414361|ENST00000502553;ENST00000514259;ENST00000265112;ENST00000455217;ENST00000506040	.|.	.|.	.|.	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.49932|.	0.1586|.	.|.	.|.	.|.	0.47374|0.47374	D|D	0.999405|0.999405	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|.	0.37888|.	-0.9686|.	7|.	0.02654|0.02654	T|T	1|1	-7.9176|-7.9176	20.6242|20.6242	0.99512|0.99512	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	31|.	E7ERI3|.	.|.	E|X	31|98;98;98;98;39	.|.	ENSP00000394291:G31E|ENSP00000265112:W98X	G|W	+|+	2|3	0|0	TARS|TARS	33484559|33484559	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.826000|0.826000	0.46750|0.46750	9.562000|9.562000	0.98145|0.98145	2.880000|2.880000	0.98712|0.98712	0.650000|0.650000	0.86243|0.86243	GGA|TGG	.	.		0.383	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295		A	33448802	G	A	33448802	4	1	146	1	0	0	0	0	0	1	0	0	15574	1183	41	3	304	3	TARS	5	33448802	Nonsense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	1359000	33448802	147466458	43	22396										
HOMER1	9456	hgsc.bcm.edu	37	chr5	78734957	78734957	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tgttaaaggagactgaagatCcccgcctgcggattccttta	10	10	0	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:78734957C>A	ENST00000334082.6	-	5	1845	c.403G>T	c.(403-405)Gat>Tat	p.D135Y	HOMER1_ENST00000508576.1_Missense_Mutation_p.D135Y|HOMER1_ENST00000535690.1_Intron|HOMER1_ENST00000282260.6_Intron	NM_004272.3	NP_004263.1	Q86YM7	HOME1_HUMAN	homer homolog 1 (Drosophila)	135					behavioral response to cocaine (GO:0048148)|chemical homeostasis within a tissue (GO:0048875)|circadian rhythm (GO:0007623)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of signal transduction (GO:0009967)|protein localization to synapse (GO:0035418)|regulation of calcium ion import (GO:0090279)|regulation of cation channel activity (GO:2001257)|regulation of store-operated calcium entry (GO:2001256)|response to calcium ion (GO:0051592)|response to nicotine (GO:0035094)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell junction (GO:0030054)|costamere (GO:0043034)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|signaling adaptor activity (GO:0035591)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|skin(1)	14		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)		GACTGAAGATCCCCGCCTGCG	0.423																																					p.W135W		Atlas-SNP	.											.	HOMER1	37	.	0			c.T403T						.						113	107	109					5																	78734957		1839	4092	5931	SO:0001583	missense	9456	exon5			GAAGATCCCCGCC	BC015502	CCDS43335.1, CCDS64188.1, CCDS64189.1	5q14.2	2008-02-05			ENSG00000152413	ENSG00000152413			17512	protein-coding gene	gene with protein product		604798				9808459, 9808458	Standard	NM_004272		Approved	Ves-1, SYN47, HOMER-1B	uc003kfy.4	Q86YM7	OTTHUMG00000134278	ENST00000334082.6:c.403G>T	chr5.hg19:g.78734957C>A	ENSP00000334382:p.Asp135Tyr	94.0	0.0		116.0	57.0	NM_004272	B2R688|O96003|Q86YM5	Silent	SNP	ENST00000334082.6	hg19	CCDS43335.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.148204	0.57151	.	.	ENSG00000152413	ENST00000334082;ENST00000508576	T;T	0.47177	2.17;0.85	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.39091	0.1065	L	0.38175	1.15	0.80722	D	1	B;P	0.49253	0.113;0.921	B;B	0.35727	0.056;0.209	T	0.44421	-0.9329	10	0.59425	D	0.04	-8.716	19.3022	0.94148	0.0:1.0:0.0:0.0	.	135;135	Q86YM7-3;Q86YM7	.;HOME1_HUMAN	Y	135	ENSP00000334382:D135Y;ENSP00000426651:D135Y	ENSP00000334382:D135Y	D	-	1	0	HOMER1	78770713	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.114000	0.77103	2.552000	0.86080	0.585000	0.79938	GAT	.	.		0.423	HOMER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258856.1	NM_004272		A	78734957	C	A	78734957	3	1	146	1	0	0	0	0	1	0	0	0	7287	855	30	3	681	3	HOMER1	5	78734957	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	45286155	78734957	102180303	44	22397										
FBN2	2201	hgsc.bcm.edu	37	chr5	127626533	127626533	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aaagctttgggtacagaacaCtttccattttcaaaatttgt	6	7	1	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:127626533C>A	ENST00000508053.1	-	56	7310	c.6336G>T	c.(6334-6336)aaG>aaT	p.K2112N	FBN2_ENST00000262464.4_Missense_Mutation_p.K2112N			P35556	FBN2_HUMAN	fibrillin 2	2112	TB 8.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GTACAGAACACTTTCCATTTT	0.433																																					p.K2112N		Atlas-SNP	.											.	FBN2	858	.	0			c.G6336T						.						102	98	99					5																	127626533		2203	4300	6503	SO:0001583	missense	2201	exon50			AGAACACTTTCCA	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.6336G>T	chr5.hg19:g.127626533C>A	ENSP00000424571:p.Lys2112Asn	145.0	0.0		152.0	59.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696964	0.68386	.	.	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.92911	-3.13;-3.13	5.01	2.26	0.28386	Matrix fibril-associated (3);TGF-beta binding (1);	0.091133	0.47455	D	0.000225	D	0.90424	0.7002	L	0.38531	1.155	0.34494	D	0.705247	D	0.59767	0.986	P	0.56563	0.801	D	0.89862	0.4017	10	0.38643	T	0.18	.	8.8514	0.35201	0.0:0.7095:0.0:0.2905	.	2112	P35556	FBN2_HUMAN	N	2112	ENSP00000262464:K2112N;ENSP00000424571:K2112N	ENSP00000262464:K2112N	K	-	3	2	FBN2	127654432	0.040000	0.19996	1.000000	0.80357	0.996000	0.88848	-0.531000	0.06171	0.391000	0.25143	0.655000	0.94253	AAG	.	.		0.433	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127626533	C	A	127626533	3	1	146	1	0	0	0	0	1	0	0	0	5711	564	20	3	2466	3	FBN2	5	127626533	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	48891576	127626533	53288727	45	22398										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140208380	140208380	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gctggtcacagtgctggatgTgaatgataatgctcccactt	11	9	1	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:140208380T>C	ENST00000529310.1	+	1	818	c.704T>C	c.(703-705)gTg>gCg	p.V235A	PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Missense_Mutation_p.V235A|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	235	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGCTGGATGTGAATGATAAT	0.463																																					p.V235A		Atlas-SNP	.											.	PCDHA6	442	.	0			c.T704C						.						65	63	64					5																	140208380		2203	4297	6500	SO:0001583	missense	56142	exon1			TGGATGTGAATGA	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.704T>C	chr5.hg19:g.140208380T>C	ENSP00000433378:p.Val235Ala	148.0	0.0		170.0	84.0	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	hg19	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.846988	0.00568	.	.	ENSG00000081842	ENST00000529310;ENST00000527624	T;T	0.02032	4.49;4.49	3.7	2.56	0.30785	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.257775	0.19837	U	0.104955	T	0.01353	0.0044	N	0.21324	0.655	0.09310	N	1	B;B;B	0.19706	0.038;0.006;0.004	B;B;B	0.20955	0.032;0.007;0.005	T	0.49418	-0.8942	10	0.02654	T	1	.	5.0187	0.14350	0.0:0.2349:0.0:0.7651	.	235;235;235	Q9UN73-3;Q9UN73;Q9UN73-2	.;PCDA6_HUMAN;.	A	235	ENSP00000433378:V235A;ENSP00000434113:V235A	ENSP00000434113:V235A	V	+	2	0	PCDHA6	140188564	0.000000	0.05858	0.994000	0.49952	0.709000	0.40893	-0.589000	0.05767	1.669000	0.50854	0.260000	0.18958	GTG	.	.		0.463	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		C	140208380	T	C	140208380	3	2	146	1	0	0	0	0	1	0	0	0	11537	1696	59	2	706	2	PCDHA6	5	140208380	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	12581847	140208380	40706880	46	22399										
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140347864	140347864	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aaaaggagaatgcagaggtgAcctactcccttctggagagg	13	8	1	4			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:140347864A>G	ENST00000289269.5	+	1	2045	c.1513A>G	c.(1513-1515)Acc>Gcc	p.T505A	PCDHA13_ENST00000409494.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	505	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCAGAGGTGACCTACTCCCT	0.498																																					p.T505A	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.A1513G						.						107	101	103					5																	140347864		2203	4300	6503	SO:0001583	missense	56134	exon1			GAGGTGACCTACT	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"Cadherins / Protocadherins : Clustered"	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1513A>G	chr5.hg19:g.140347864A>G	ENSP00000289269:p.Thr505Ala	126.0	0.0		156.0	66.0	NM_031883	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	hg19	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	A	12.03	1.814777	0.32053	.	.	ENSG00000243232	ENST00000289269	T	0.51574	0.7	6.02	6.02	0.97574	Cadherin (4);Cadherin-like (1);	0.000000	0.43260	D	0.000582	T	0.51787	0.1695	L	0.56280	1.765	0.44937	D	0.997953	P;P	0.43231	0.566;0.801	B;P	0.48770	0.198;0.589	T	0.55560	-0.8122	10	0.66056	D	0.02	.	9.9761	0.41783	0.7503:0.0:0.0:0.2497	.	505;505	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	A	505	ENSP00000289269:T505A	ENSP00000289269:T505A	T	+	1	0	PCDHAC2	140328048	0.002000	0.14202	1.000000	0.80357	0.993000	0.82548	0.715000	0.25822	2.311000	0.77944	0.533000	0.62120	ACC	.	.		0.498	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		G	140347864	A	G	140347864	3	3	146	1	0	0	0	0	1	0	0	0	11542	275	10	2	1515	2	PCDHAC2	5	140347864	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	139484	140347864	40567396	47	22400										
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140481966	140481966	+	Frame_Shift_Del	DEL	G	G	-													0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ctgcaccgagctggtgccccGggcggctgagccgggctacc					rs541148618	byFrequency	TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:140481966delG	ENST00000231130.2	+	1	1733	c.1733delG	c.(1732-1734)cggfs	p.R578fs	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	578	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGGTGCCCCGGGCGGCTGAG	0.706																																					p.R578fs		Atlas-INDEL	.											.	PCDHB3	208	.	0			c.1732delC						.						17	22	20					5																	140481966		2170	4201	6371	SO:0001589	frameshift_variant	56132	exon1			.	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1733delG	chr5.hg19:g.140481966delG	ENSP00000231130:p.Arg578fs	28.0	0.0		47.0	11.0	NM_018937	B2R8P2	Frame_Shift_Del	DEL	ENST00000231130.2	hg19	CCDS4245.1																																																																																			.	.		0.706	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		-	140481966	G	-	140481966	7	5	146	1	0	1	0	1	0	0	0	0	11552	1116	39	0	1735	0	PCDHB3	5	140481966	Frame_Shift_Del	DEL	G	TCGA-DD-A73E-01A-12D-A32G-10	134102	140481966	40433294	48	22401										
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140773532	140773532	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aagaatggtcaagttgtctgTtacacacgtgataatttacc	8	7	2	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:140773532T>C	ENST00000398604.2	+	1	1152	c.1152T>C	c.(1150-1152)tgT>tgC	p.C384C	PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	384	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGTTGTCTGTTACACACGTG	0.358																																					p.C384C		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.T1152C						.						46	44	45					5																	140773532		1843	4090	5933	SO:0001819	synonymous_variant	9708	exon1			TGTCTGTTACACA	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.1152T>C	chr5.hg19:g.140773532T>C		117.0	0.0		125.0	55.0	NM_014004	A7MCZ4|O15039	Silent	SNP	ENST00000398604.2	hg19	CCDS47291.1																																																																																			.	.		0.358	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		C	140773532	T	C	140773532	2	2	146	1	0	0	0	0	0	0	0	1	11569	1731	60	2		2	PCDHGA8	5	140773532	Silent	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	291566	140773532	40141728	49	22402										
HDAC3	8841	hgsc.bcm.edu	37	chr5	141008783	141008783	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ccgtatttgtggaaggacacCgtcatgacccggtcagtgag	13	10	2	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:141008783C>T	ENST00000305264.3	-	7	646	c.567G>A	c.(565-567)acG>acA	p.T189T	AC008781.7_ENST00000422040.2_RNA	NM_003883.3	NP_003874.2	O15379	HDAC3_HUMAN	histone deacetylase 3	189	Histone deacetylase.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|protein deacetylation (GO:0006476)|regulation of mitotic cell cycle (GO:0007346)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|cyclin binding (GO:0030332)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Vorinostat(DB02546)	GGAAGGACACCGTCATGACCC	0.498																																					p.T189T		Atlas-SNP	.											HDAC3,bladder,carcinoma,0,1	HDAC3	42	.	0			c.G567A						.						125	107	113					5																	141008783		2203	4300	6503	SO:0001819	synonymous_variant	8841	exon7			GGACACCGTCATG	AF059650	CCDS4264.1	5q31.1-q31.2	2008-07-18			ENSG00000171720	ENSG00000171720	3.5.1.98		4854	protein-coding gene	gene with protein product		605166				9501169, 9464271	Standard	NM_003883		Approved	RPD3, HD3, RPD3-2	uc003llf.2	O15379	OTTHUMG00000129629	ENST00000305264.3:c.567G>A	chr5.hg19:g.141008783C>T		109.0	0.0		115.0	52.0	NM_003883	D3DQE1|O43268|Q9UEI5|Q9UEV0	Silent	SNP	ENST00000305264.3	hg19	CCDS4264.1																																																																																			.	.		0.498	HDAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251824.2	NM_003883		T	141008783	C	T	141008783	2	4	146	1	0	0	0	0	0	0	0	1	7017	639	23	1		1	HDAC3	5	141008783	Silent	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	235251	141008783	39906477	50	22403										
RANBP17	64901	hgsc.bcm.edu	37	chr5	170598268	170598268	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	taatttcaaggactcttcagTtcctaaatgacctttctgtt	5	9	4	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:170598268T>G	ENST00000523189.1	+	16	2007	c.1843T>G	c.(1843-1845)Ttc>Gtc	p.F615V	RANBP17_ENST00000521759.1_Intron	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	615					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GACTCTTCAGTTCCTAAATGA	0.318			T	TRD@	ALL																																p.F615V		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.T1843G						.						138	133	135					5																	170598268		2203	4296	6499	SO:0001583	missense	64901	exon16			CTTCAGTTCCTAA	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.1843T>G	chr5.hg19:g.170598268T>G	ENSP00000427975:p.Phe615Val	153.0	0.0		163.0	71.0	NM_022897	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	hg19	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	T	16.26	3.073825	0.55646	.	.	ENSG00000204764	ENST00000523189;ENST00000534916	T	0.67523	-0.27	6.08	6.08	0.98989	Armadillo-type fold (1);	0.093422	0.47093	D	0.000252	T	0.56848	0.2013	L	0.38175	1.15	0.38926	D	0.957846	B	0.18610	0.029	B	0.20184	0.028	T	0.57711	-0.7764	10	0.56958	D	0.05	-16.6915	10.6336	0.45551	0.0:0.0717:0.0:0.9283	.	615	Q9H2T7	RBP17_HUMAN	V	615;45	ENSP00000427975:F615V	ENSP00000427975:F615V	F	+	1	0	RANBP17	170530873	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.925000	0.56484	2.333000	0.79357	0.482000	0.46254	TTC	.	.		0.318	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		G	170598268	T	G	170598268	3	3	146	1	0	0	0	0	1	0	0	0	13042	1725	60	5	1905	5	RANBP17	5	170598268	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	29589485	170598268	10316992	51	22404										
CPEB4	80315	hgsc.bcm.edu	37	chr5	173316743	173316743	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	cctaaagataataaatggggGattacgggtttggagtgcta	13	4	0	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr5:173316743G>T	ENST00000265085.5	+	1	1461	c.7G>T	c.(7-9)Gat>Tat	p.D3Y	CPEB4_ENST00000334035.5_Missense_Mutation_p.D3Y|CPEB4_ENST00000519835.1_Missense_Mutation_p.D3Y|CPEB4_ENST00000520867.1_Missense_Mutation_p.D3Y	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	3					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			ATAAATGGGGGATTACGGGTT	0.408																																					p.D3Y		Atlas-SNP	.											.	CPEB4	54	.	0			c.G7T						.						88	97	94					5																	173316743		2203	4300	6503	SO:0001583	missense	80315	exon1			ATGGGGGATTACG	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.7G>T	chr5.hg19:g.173316743G>T	ENSP00000265085:p.Asp3Tyr	220.0	0.0		228.0	91.0	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Missense_Mutation	SNP	ENST00000265085.5	hg19	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.472129	0.63737	.	.	ENSG00000113742	ENST00000265085;ENST00000520867;ENST00000334035;ENST00000519835	T;T;T;T	0.58797	0.46;0.34;0.42;0.31	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.67767	0.2928	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.85130	0.993;0.997;0.993;0.995	T	0.71076	-0.4697	10	0.87932	D	0	-20.9008	19.6772	0.95941	0.0:0.0:1.0:0.0	.	3;3;3;3	B7ZLQ8;Q17RY0-2;E5RJM0;Q17RY0	.;.;.;CPEB4_HUMAN	Y	3	ENSP00000265085:D3Y;ENSP00000429092:D3Y;ENSP00000334533:D3Y;ENSP00000429048:D3Y	ENSP00000265085:D3Y	D	+	1	0	CPEB4	173249349	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.434000	0.97515	2.656000	0.90262	0.655000	0.94253	GAT	.	.		0.408	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		T	173316743	G	T	173316743	3	4	146	1	0	0	0	0	1	0	0	0	3805	1174	41	3	9	3	CPEB4	5	173316743	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	2718475	173316743	7598517	52	22405										
MAK	4117	hgsc.bcm.edu	37	chr6	10784806	10784806	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	agggtactggctctggaagcCttgaaagccaatgaaaggta	13	7	1	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr6:10784806C>A	ENST00000313243.2	-	11	1699		c.e11-1		MAK_ENST00000474039.1_Splice_Site|RP11-637O19.3_ENST00000480294.1_Intron|MAK_ENST00000538030.1_Splice_Site|MAK_ENST00000354489.2_Splice_Site|SYCP2L_ENST00000543878.1_Intron			P20794	MAK_HUMAN	male germ cell-associated kinase						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				CTCTGGAAGCCTTGAAAGCCA	0.512																																					.		Atlas-SNP	.											.	MAK	47	.	0			c.1317-1G>T						.						105	97	100					6																	10784806		2203	4300	6503	SO:0001630	splice_region_variant	4117	exon12			GGAAGCCTTGAAA		CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1317-1G>T	chr6.hg19:g.10784806C>A		80.0	0.0		191.0	67.0	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Splice_Site	SNP	ENST00000313243.2	hg19	CCDS4516.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.673631	0.47781	.	.	ENSG00000111837	ENST00000313243;ENST00000354489	.	.	.	5.27	3.28	0.37604	.	.	.	.	.	.	.	.	.	.	.	0.21290	N	0.99974	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4613	0.55733	0.2652:0.7348:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MAK	10892792	1.000000	0.71417	0.815000	0.32552	0.439000	0.31926	4.233000	0.58651	2.472000	0.83506	0.563000	0.77884	.	.	.		0.512	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906	Intron	A	10784806	C	A	10784806	5	1	146	1	0	0	0	0	0	0	1	0	9206	695	24	3	571	3	MAK	6	10784806	Splice_Site	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10		10784806	160330261	53	22406										
PPT2	9374	hgsc.bcm.edu	37	chr6	32122457	32122457	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gctgctgctgcttgcagcccCcgcgccccaccgcgcgtcct	11	21	0	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr6:32122457C>T	ENST00000324816.6	+	2	654	c.86C>T	c.(85-87)cCc>cTc	p.P29L	PPT2_ENST00000437001.2_5'UTR|PRRT1_ENST00000375150.2_5'Flank|PPT2_ENST00000361568.2_Missense_Mutation_p.P35L|PRRT1_ENST00000375152.2_5'Flank|PPT2_ENST00000395523.1_Missense_Mutation_p.P29L|PPT2_ENST00000493548.1_3'UTR|PPT2-EGFL8_ENST00000422437.1_Missense_Mutation_p.P29L|PPT2_ENST00000445576.2_Missense_Mutation_p.P29L|PRRT1_ENST00000211413.5_5'Flank|PPT2-EGFL8_ENST00000453656.2_3'UTR|PPT2_ENST00000375143.2_Missense_Mutation_p.P29L|PPT2_ENST00000375137.2_Missense_Mutation_p.P29L			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	29					cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						CTTGCAGCCCCCGCGCCCCAC	0.662																																					p.P35L		Atlas-SNP	.											.	PPT2	19	.	0			c.C104T						.						57	66	63					6																	32122457		1507	2705	4212	SO:0001583	missense	9374	exon2			CAGCCCCCGCGCC	AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	3.1.2.22		9326	protein-coding gene	gene with protein product		603298				9341199, 10051407	Standard	NM_138717		Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.86C>T	chr6.hg19:g.32122457C>T	ENSP00000320528:p.Pro29Leu	63.0	0.0		127.0	39.0	NM_138717	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	Missense_Mutation	SNP	ENST00000324816.6	hg19	CCDS4742.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.845631	0.51164	.	.	ENSG00000221988	ENST00000414204;ENST00000361568;ENST00000395523;ENST00000445576;ENST00000324816;ENST00000375137;ENST00000375143;ENST00000424499;ENST00000436118;ENST00000453656	T;D;D;D;D;D;D;T;T	0.91407	1.59;-2.82;-2.81;-2.84;-2.81;-2.81;-2.81;-1.47;1.55	4.63	4.63	0.57726	.	0.367119	0.27691	N	0.018243	T	0.77896	0.4199	N	0.08118	0	0.80722	D	1	D;P;P	0.57571	0.98;0.906;0.906	P;B;B	0.52957	0.714;0.346;0.346	T	0.78919	-0.2014	10	0.07175	T	0.84	-4.6008	15.0206	0.71627	0.0:1.0:0.0:0.0	.	29;29;35	Q9UMR5-2;Q9UMR5;B0S872	.;PPT2_HUMAN;.	L	29;35;29;29;29;29;29;29;29;29	ENSP00000398847:P29L;ENSP00000354608:P35L;ENSP00000378894:P29L;ENSP00000412381:P29L;ENSP00000320528:P29L;ENSP00000364279:P29L;ENSP00000364285:P29L;ENSP00000409877:P29L;ENSP00000395456:P29L	ENSP00000320528:P29L	P	+	2	0	PPT2	32230435	0.437000	0.25593	0.703000	0.30354	0.321000	0.28281	2.579000	0.46059	2.384000	0.81235	0.484000	0.47621	CCC	.	.		0.662	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076552.4	NM_138717		T	32122457	C	T	32122457	3	4	146	1	0	0	0	0	1	0	0	0	12424	623	22	3	110	3	PPT2	6	32122457	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	21337651	32122457	138992610	54	22407										
KCTD20	222658	hgsc.bcm.edu	37	chr6	36442832	36442832	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ctgctcatccggataccatgCtgggaaggtaactgatgata	11	9	1	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr6:36442832C>G	ENST00000373731.2	+	3	818	c.427C>G	c.(427-429)Ctg>Gtg	p.L143V	KCTD20_ENST00000544295.1_Intron|KCTD20_ENST00000449081.2_Intron|KCTD20_ENST00000536244.1_Intron|KCTD20_ENST00000474988.1_Intron	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	143	BTB.				protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						GGATACCATGCTGGGAAGGTA	0.368																																					p.L143V		Atlas-SNP	.											.	KCTD20	37	.	0			c.C427G						.						103	100	101					6																	36442832		2203	4300	6503	SO:0001583	missense	222658	exon3			ACCATGCTGGGAA	BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"chromosome 6 open reading frame 69", "potassium channel tetramerisation domain containing 20"	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.427C>G	chr6.hg19:g.36442832C>G	ENSP00000362836:p.Leu143Val	112.0	0.0		231.0	74.0	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	hg19	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.562852	0.65538	.	.	ENSG00000112078	ENST00000373731	D	0.86497	-2.13	5.16	-0.292	0.12839	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.53938	D	0.000044	D	0.92008	0.7468	M	0.92555	3.32	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.91501	0.5219	10	0.87932	D	0	-11.0887	10.1399	0.42730	0.0:0.3762:0.0:0.6238	.	143	Q7Z5Y7	KCD20_HUMAN	V	143	ENSP00000362836:L143V	ENSP00000362836:L143V	L	+	1	2	KCTD20	36550810	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	1.002000	0.29796	-0.129000	0.11620	-0.290000	0.09829	CTG	.	.		0.368	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562		G	36442832	C	G	36442832	3	3	146	1	0	0	0	0	1	0	0	0	8117	796	28	4	433	4	KCTD20	6	36442832	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	4320375	36442832	134672235	55	22408										
TREML2	79865	hgsc.bcm.edu	37	chr6	41166123	41166123	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ctgcacagacagagtctcccCttcaaggagcctcacttttg	8	14	3	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr6:41166123C>T	ENST00000483722.1	-	2	285	c.100G>A	c.(100-102)Ggg>Agg	p.G34R		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	34	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					AGAGTCTCCCCTTCAAGGAGC	0.493																																					p.G34R		Atlas-SNP	.											.	TREML2	41	.	0			c.G100A						.						127	130	129					6																	41166123		2203	4300	6503	SO:0001583	missense	79865	exon2			TCTCCCCTTCAAG	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"Immunoglobulin superfamily / V-set domain containing"	21092	protein-coding gene	gene with protein product	"TREM-like transcript 2"	609715	"chromosome 6 open reading frame 76"	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.100G>A	chr6.hg19:g.41166123C>T	ENSP00000418767:p.Gly34Arg	52.0	0.0		107.0	8.0	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	hg19	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	14.59	2.581804	0.46006	.	.	ENSG00000112195	ENST00000483722	D	0.81499	-1.5	4.75	4.75	0.60458	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000044	D	0.86623	0.5977	M	0.75085	2.285	0.40423	D	0.979861	D	0.89917	1.0	D	0.97110	1.0	D	0.88269	0.2928	10	0.72032	D	0.01	-23.1011	13.6225	0.62144	0.0:1.0:0.0:0.0	.	34	Q5T2D2	TRML2_HUMAN	R	34	ENSP00000418767:G34R	ENSP00000418767:G34R	G	-	1	0	TREML2	41274101	1.000000	0.71417	0.998000	0.56505	0.028000	0.11728	3.388000	0.52509	2.344000	0.79699	0.563000	0.77884	GGG	.	.		0.493	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807		T	41166123	C	T	41166123	3	4	146	1	0	0	0	0	1	0	0	0	16488	681	24	3	881	3	TREML2	6	41166123	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	4723291	41166123	129948944	56	22409										
TDRD6	221400	hgsc.bcm.edu	37	chr6	46660441	46660441	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aaatgataagagcttatgccActgtgatagatggacctgag	11	6	0	5			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr6:46660441A>G	ENST00000316081.6	+	1	4576	c.4576A>G	c.(4576-4578)Act>Gct	p.T1526A	TDRD6_ENST00000544460.1_Missense_Mutation_p.T1526A	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1526					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			AGCTTATGCCACTGTGATAGA	0.378																																					p.T1526A		Atlas-SNP	.											.	TDRD6	205	.	0			c.A4576G						.						118	117	117					6																	46660441		2203	4300	6503	SO:0001583	missense	221400	exon1			TATGCCACTGTGA	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.4576A>G	chr6.hg19:g.46660441A>G	ENSP00000346065:p.Thr1526Ala	126.0	0.0		284.0	88.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	hg19	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	A	15.83	2.948829	0.53186	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.12361	2.69;2.69	6.07	3.68	0.42216	Maternal tudor protein (1);	0.413900	0.25648	N	0.029232	T	0.12390	0.0301	M	0.83223	2.63	0.22541	N	0.999001	P;P	0.49358	0.906;0.923	P;P	0.51415	0.539;0.669	T	0.14504	-1.0470	10	0.28530	T	0.3	-10.7704	7.5322	0.27689	0.7937:0.0:0.0683:0.1379	.	1526;1526	F5H5M3;O60522	.;TDRD6_HUMAN	A	1526	ENSP00000443299:T1526A;ENSP00000346065:T1526A	ENSP00000346065:T1526A	T	+	1	0	TDRD6	46768400	0.058000	0.20735	0.957000	0.39632	0.991000	0.79684	1.423000	0.34837	0.526000	0.28541	0.533000	0.62120	ACT	.	.		0.378	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		G	46660441	A	G	46660441	3	3	146	1	0	0	0	0	1	0	0	0	15749	159	6	2	4578	2	TDRD6	6	46660441	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	5494318	46660441	124454626	57	22410										
IBTK	25998	hgsc.bcm.edu	37	chr6	82912269	82912269	+	Frame_Shift_Del	DEL	T	T	-													0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	cttcaagtaaagctgccataTtcaatcctataaactgtaaa							TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr6:82912269delT	ENST00000306270.7	-	18	3254	c.2705delA	c.(2704-2706)aatfs	p.N902fs	IBTK_ENST00000503631.1_Frame_Shift_Del_p.N701fs|IBTK_ENST00000510291.1_Frame_Shift_Del_p.N902fs	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	902					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		AGCTGCCATATTCAATCCTAT	0.338																																					p.N902fs		Atlas-Indel,Pindel	.											.	IBTK	128	.	0			c.2706delT						.						133	137	135					6																	82912269		2203	4300	6503	SO:0001589	frameshift_variant	25998	exon18			.	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.2705delA	chr6.hg19:g.82912269delT	ENSP00000305721:p.Asn902fs	204.0	0.0		126.0	107.0	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Frame_Shift_Del	DEL	ENST00000306270.7	hg19	CCDS34490.1																																																																																			.	.		0.338	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		-	82912269	T	-	82912269	7	5	146	1	0	1	0	1	0	0	0	0	7485	1493	52	0	1404	0	IBTK	6	82912269	Frame_Shift_Del	DEL	T	TCGA-DD-A73E-01A-12D-A32G-10	36251828	82912269	88202798	58	22411										
SMOC2	64094	hgsc.bcm.edu	37	chr6	168927046	168927046	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	acgtgtccaggtgtgtggccGaaaggaagtatacccaggag	15	8	0	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr6:168927046G>A	ENST00000356284.2	+	3	497	c.277G>A	c.(277-279)Gaa>Aaa	p.E93K	SMOC2_ENST00000354536.5_Missense_Mutation_p.E93K	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	93	Thyroglobulin type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		GTGTGTGGCCGAAAGGAAGTA	0.502																																					p.E93K		Atlas-SNP	.											.	SMOC2	57	.	0			c.G277A						.						129	104	113					6																	168927046		2203	4300	6503	SO:0001583	missense	64094	exon3			GTGGCCGAAAGGA	AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"EF-hand domain containing"	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.277G>A	chr6.hg19:g.168927046G>A	ENSP00000348630:p.Glu93Lys	108.0	0.0		71.0	55.0	NM_022138	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Missense_Mutation	SNP	ENST00000356284.2	hg19	CCDS55076.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.959648	0.92791	.	.	ENSG00000112562	ENST00000356284;ENST00000354536;ENST00000366793	T;T	0.63913	-0.07;-0.07	4.86	4.86	0.63082	Thyroglobulin type-1 (3);	0.000000	0.85682	D	0.000000	T	0.71281	0.3321	M	0.71296	2.17	0.43471	D	0.995689	D;D	0.89917	0.999;1.0	D;D	0.67231	0.95;0.943	T	0.74047	-0.3790	10	0.52906	T	0.07	-1.7924	15.2225	0.73324	0.0:0.0:1.0:0.0	.	93;93	Q9H3U7;Q9H3U7-2	SMOC2_HUMAN;.	K	93	ENSP00000348630:E93K;ENSP00000346537:E93K	ENSP00000346537:E93K	E	+	1	0	SMOC2	168669895	1.000000	0.71417	0.998000	0.56505	0.881000	0.50899	8.019000	0.88732	2.241000	0.73720	0.650000	0.86243	GAA	.	.		0.502	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043201.1			A	168927046	G	A	168927046	3	1	146	1	0	0	0	0	1	0	0	0	14817	1059	37	1	287	1	SMOC2	6	168927046	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	86014777	168927046	2188021	59	22412										
FLNC	2318	hgsc.bcm.edu	37	chr7	128486943	128486943	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gacgtcaacatcaccttcggGgggcggcccatcccaggtgt	13	14	2	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr7:128486943G>C	ENST00000325888.8	+	24	4533	c.4272G>C	c.(4270-4272)ggG>ggC	p.G1424G	FLNC_ENST00000346177.6_Silent_p.G1424G	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1424					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TCACCTTCGGGGGGCGGCCCA	0.592																																					p.G1424G		Atlas-SNP	.											.	FLNC	339	.	0			c.G4272C						.						63	65	65					7																	128486943		1984	4168	6152	SO:0001819	synonymous_variant	2318	exon24			CTTCGGGGGGCGG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.4272G>C	chr7.hg19:g.128486943G>C		64.0	0.0		121.0	87.0	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.592	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			C	128486943	G	C	128486943	2	2	146	1	0	0	0	0	0	0	0	1	5943	1219	43	4		4	FLNC	7	128486943	Silent	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10		128486943	30651720	60	22413										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	146536896	146536896	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gatcagtgccattgcaacccAaggaaggtatagcagctcag	11	10	2	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr7:146536896A>T	ENST00000361727.3	+	3	818	c.302A>T	c.(301-303)cAa>cTa	p.Q101L		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	101	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			ATTGCAACCCAAGGAAGGTAT	0.502										HNSCC(39;0.1)																											p.Q101L		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.A302T						.						102	89	94					7																	146536896		2203	4300	6503	SO:0001583	missense	26047	exon3			CAACCCAAGGAAG	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.302A>T	chr7.hg19:g.146536896A>T	ENSP00000354778:p.Gln101Leu	123.0	0.0		176.0	106.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	hg19	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.729716	0.89390	.	.	ENSG00000174469	ENST00000361727	D	0.97924	-4.61	5.83	5.83	0.93111	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.000000	0.53938	D	0.000050	D	0.99299	0.9755	H	0.98951	4.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98750	1.0720	10	0.52906	T	0.07	.	15.0243	0.71656	1.0:0.0:0.0:0.0	.	101	Q9UHC6	CNTP2_HUMAN	L	101	ENSP00000354778:Q101L	ENSP00000354778:Q101L	Q	+	2	0	CNTNAP2	146167829	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.339000	0.96797	2.227000	0.72691	0.528000	0.53228	CAA	.	.		0.502	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			T	146536896	A	T	146536896	3	4	146	1	0	0	0	0	1	0	0	0	3649	130	5	4	312	4	CNTNAP2	7	146536896	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	18049953	146536896	12601767	61	22414										
PENK	5179	hgsc.bcm.edu	37	chr8	57353832	57353832	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ccactagtgggaaaagatatTaaaatctcataaatcctccg	6	9	1	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr8:57353832T>C	ENST00000314922.3	-	2	879	c.803A>G	c.(802-804)tAa>tGa	p.*268*	PENK_ENST00000523274.1_5'Flank|PENK_ENST00000451791.2_Silent_p.*268*	NM_006211.3	NP_006202.1	P01210	PENK_HUMAN	proenkephalin	0					aggressive behavior (GO:0002118)|behavioral fear response (GO:0001662)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|startle response (GO:0001964)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	21		all_lung(136;0.229)	Epithelial(17;0.000873)|all cancers(17;0.0069)			GAAAAGATATTAAAATCTCAT	0.478																																					p.X268X		Atlas-SNP	.											.	PENK	59	.	0			c.A803G						.						77	87	84					8																	57353832		2203	4300	6503	SO:0001819	synonymous_variant	5179	exon4			AGATATTAAAATC		CCDS6168.1	8q23-q24	2013-02-26				ENSG00000181195		"Endogenous ligands"	8831	protein-coding gene	gene with protein product	"preproenkephalin"	131330				6281660	Standard	NM_006211		Approved		uc003xsz.2	P01210		ENST00000314922.3:c.803A>G	chr8.hg19:g.57353832T>C		78.0	0.0		46.0	40.0	NM_001135690	B2RC23|Q6FHC6|Q6FHE6	Silent	SNP	ENST00000314922.3	hg19	CCDS6168.1																																																																																			.	.		0.478	PENK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378645.1			C	57353832	T	C	57353832	2	2	146	1	0	0	0	0	0	0	0	1	11736	1761	61	2		2	PENK	8	57353832	Silent	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10		57353832	89010190	62	22415										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113585851	113585851	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gatgcaccagtaaaagcaccTagtagatgagtcgttttatc	9	8	0	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr8:113585851T>A	ENST00000297405.5	-	24	4165	c.3921A>T	c.(3919-3921)ctA>ctT	p.L1307L	CSMD3_ENST00000352409.3_Silent_p.L1307L|CSMD3_ENST00000343508.3_Silent_p.L1267L|CSMD3_ENST00000455883.2_Silent_p.L1203L	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1307	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TAAAAGCACCTAGTAGATGAG	0.333										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.L1307L		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A3921T						.						113	112	112					8																	113585851		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon24			AGCACCTAGTAGA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3921A>T	chr8.hg19:g.113585851T>A		88.0	0.0		82.0	18.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.333	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113585851	T	A	113585851	2	1	146	1	0	0	0	0	0	0	0	1	3948	1509	53	4		4	CSMD3	8	113585851	Silent	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	56232019	113585851	32778171	63	22416										
SLC24A2	25769	hgsc.bcm.edu	37	chr9	19786089	19786089	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tttcccaccacatgatgacaTtatccaggaaaaatatgatc	5	10	0	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr9:19786089T>C	ENST00000341998.2	-	1	837	c.776A>G	c.(775-777)aAt>aGt	p.N259S	SLC24A2_ENST00000286344.3_Missense_Mutation_p.N259S	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	259					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		CATGATGACATTATCCAGGAA	0.378																																					p.N259S		Atlas-SNP	.											.	SLC24A2	93	.	0			c.A776G						.						111	104	106					9																	19786089		2203	4300	6503	SO:0001583	missense	25769	exon1			ATGACATTATCCA	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"Solute carriers"	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.776A>G	chr9.hg19:g.19786089T>C	ENSP00000344801:p.Asn259Ser	102.0	0.0		137.0	32.0	NM_001193288	B7ZLL8|Q9NTN5|Q9NZQ4	Missense_Mutation	SNP	ENST00000341998.2	hg19	CCDS6493.1	.	.	.	.	.	.	.	.	.	.	T	12.39	1.922815	0.33908	.	.	ENSG00000155886	ENST00000341998;ENST00000286344	T;T	0.63255	-0.03;-0.03	5.91	4.78	0.61160	Sodium/calcium exchanger membrane region (1);	0.041428	0.85682	D	0.000000	T	0.58694	0.2140	N	0.21508	0.67	0.80722	D	1	B;D	0.55605	0.357;0.972	B;P	0.54706	0.155;0.759	T	0.55835	-0.8078	9	.	.	.	.	11.8686	0.52507	0.0:0.0679:0.0:0.9321	.	259;259	Q9UI40-2;Q9UI40	.;NCKX2_HUMAN	S	259	ENSP00000344801:N259S;ENSP00000286344:N259S	.	N	-	2	0	SLC24A2	19776089	1.000000	0.71417	0.888000	0.34837	0.983000	0.72400	8.036000	0.88901	1.066000	0.40716	0.533000	0.62120	AAT	.	.		0.378	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344		C	19786089	T	C	19786089	3	2	146	1	0	0	0	0	1	0	0	0	14481	1493	52	2	1249	2	SLC24A2	9	19786089	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10		19786089	121427342	64	22417										
MOBKL2B	79817	hgsc.bcm.edu	37	chr9	27330605	27330605	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ttagtgacacatcctgctcgTcatttctttctggaaagcaa	7	10	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr9:27330605T>C	ENST00000262244.5	-	4	1055	c.631A>G	c.(631-633)Acg>Gcg	p.T211A		NM_024761.4	NP_079037.3	Q86TA1	MOB3B_HUMAN	MOB kinase activator 3B	211							metal ion binding (GO:0046872)										ATCCTGCTCGTCATTTCTTTC	0.502																																					p.T211A		Atlas-SNP	.											.	.	.	.	0			c.A631G						.						113	96	102					9																	27330605		2203	4300	6503	SO:0001583	missense	79817	exon4			TGCTCGTCATTTC	AK023266	CCDS6520.1	9p21.1	2012-07-05	2011-09-28	2011-09-28	ENSG00000120162	ENSG00000120162		"MOB kinase activators"	23825	protein-coding gene	gene with protein product	"monopolar spindle 1 binding, MOB1, domain containing"		"MOB1, Mps One Binder kinase activator-like 2B (yeast)", "chromosome 9 open reading frame 35"	MOBKL2B, C9orf35		12477932	Standard	NM_024761		Approved	MOB1D, FLJ13204	uc003zqn.3	Q86TA1	OTTHUMG00000019717	ENST00000262244.5:c.631A>G	chr9.hg19:g.27330605T>C	ENSP00000262244:p.Thr211Ala	113.0	0.0		112.0	54.0	NM_024761	Q8NEB4|Q9H8V4	Missense_Mutation	SNP	ENST00000262244.5	hg19	CCDS6520.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.573057	0.45902	.	.	ENSG00000120162	ENST00000262244	.	.	.	5.45	5.45	0.79879	.	0.393532	0.23120	N	0.051709	T	0.54046	0.1834	L	0.45285	1.41	0.46586	D	0.999111	B	0.14438	0.01	B	0.12156	0.007	T	0.51426	-0.8707	9	0.42905	T	0.14	-5.7892	11.912	0.52745	0.0:0.0:0.0:1.0	.	211	Q86TA1	MOB3B_HUMAN	A	211	.	ENSP00000262244:T211A	T	-	1	0	MOBKL2B	27320605	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.198000	0.58419	2.062000	0.61559	0.533000	0.62120	ACG	.	.		0.502	MOB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051974.2	NM_024761		C	27330605	T	C	27330605	3	2	146	1	0	0	0	0	1	0	0	0	9694	1667	58	2	23	2	MOBKL2B	9	27330605	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	7544516	27330605	113882826	65	22418										
DBC1	1620	hgsc.bcm.edu	37	chr9	122011265	122011265	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tgtggctgagatgagcaggtGggtgccgtactttttgatga	16	5	0	4			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr9:122011265G>C	ENST00000265922.3	-	3	843	c.382C>G	c.(382-384)Cac>Gac	p.H128D	BRINP1_ENST00000373964.2_Missense_Mutation_p.H128D	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	128	MACPF.				cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											ATGAGCAGGTGGGTGCCGTAC	0.557																																					p.H128D		Atlas-SNP	.											.	DBC1	194	.	0			c.C382G						.						132	92	105					9																	122011265		2203	4300	6503	SO:0001583	missense	1620	exon3			GCAGGTGGGTGCC	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.382C>G	chr9.hg19:g.122011265G>C	ENSP00000265922:p.His128Asp	68.0	0.0		70.0	16.0	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	hg19	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868665	0.72065	.	.	ENSG00000078725	ENST00000373969;ENST00000265922;ENST00000373964	D;D	0.95238	-3.65;-3.65	5.66	5.66	0.87406	Membrane attack complex component/perforin (MACPF) domain (2);	0.042512	0.85682	D	0.000000	D	0.96191	0.8758	L	0.45137	1.4	0.80722	D	1	D;D	0.62365	0.989;0.991	D;D	0.76071	0.978;0.987	D	0.95953	0.8956	10	0.56958	D	0.05	-33.0796	20.1076	0.97898	0.0:0.0:1.0:0.0	.	128;128	O60477-2;O60477	.;DBC1_HUMAN	D	128	ENSP00000265922:H128D;ENSP00000363075:H128D	ENSP00000265922:H128D	H	-	1	0	DBC1	121051086	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.823000	0.97156	0.650000	0.86243	CAC	.	.		0.557	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		C	122011265	G	C	122011265	3	2	146	1	0	0	0	0	1	0	0	0	4249	1348	47	4	1927	4	DBC1	9	122011265	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	94680660	122011265	19202166	66	22419										
FCN1	2219	hgsc.bcm.edu	37	chr9	137801655	137801655	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ctggcccgtctaggcgggccGcaccttcatctctgacacct	10	17	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr9:137801655G>A	ENST00000371806.3	-	9	1061	c.970C>T	c.(970-972)Cgg>Tgg	p.R324W		NM_002003.3	NP_001994.2	O00602	FCN1_HUMAN	ficolin (collagen/fibrinogen domain containing) 1	324	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.|P domain.				cell surface pattern recognition receptor signaling pathway (GO:0002752)|complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of interleukin-8 secretion (GO:2000484)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extrinsic component of external side of plasma membrane (GO:0031232)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|G-protein coupled receptor binding (GO:0001664)|signaling pattern recognition receptor activity (GO:0008329)			endometrium(3)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	37		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		TAGGCGGGCCGCACCTTCATC	0.592																																					p.R324W		Atlas-SNP	.											.	FCN1	62	.	0			c.C970T						.						71	70	70					9																	137801655		2203	4300	6503	SO:0001583	missense	2219	exon9			CGGGCCGCACCTT	D83920	CCDS6985.1	9q34	2013-02-06	2002-01-14		ENSG00000085265	ENSG00000085265		"Fibrinogen C domain containing"	3623	protein-coding gene	gene with protein product		601252	"ficolin (collagen/fibrinogen domain-containing) 1"			8573080, 8884275	Standard	NM_002003		Approved	FCNM	uc004cfi.3	O00602	OTTHUMG00000020895	ENST00000371806.3:c.970C>T	chr9.hg19:g.137801655G>A	ENSP00000360871:p.Arg324Trp	47.0	0.0		68.0	27.0	NM_002003	Q5VYV5|Q92596	Missense_Mutation	SNP	ENST00000371806.3	hg19	CCDS6985.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032366	0.54790	.	.	ENSG00000085265	ENST00000371806	T	0.81078	-1.45	3.2	2.17	0.27698	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);	.	.	.	.	D	0.93167	0.7824	H	0.99454	4.575	0.54753	D	0.999987	D	0.89917	1.0	D	0.97110	1.0	D	0.93121	0.6525	9	0.87932	D	0	.	9.2672	0.37647	0.0:0.0:0.7852:0.2148	.	324	O00602	FCN1_HUMAN	W	324	ENSP00000360871:R324W	ENSP00000360871:R324W	R	-	1	2	FCN1	136941476	0.960000	0.32886	0.985000	0.45067	0.516000	0.34256	1.843000	0.39259	1.771000	0.52183	0.643000	0.83706	CGG	.	.		0.592	FCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054963.1	NM_002003		A	137801655	G	A	137801655	3	1	146	1	0	0	0	0	1	0	0	0	5799	1086	38	1	14	1	FCN1	9	137801655	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	15790390	137801655	3411776	67	22420										
SPAG6	9576	hgsc.bcm.edu	37	chr10	22676816	22676816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ggatctggcagaaatggttgTtgaagcagagatttttccag	13	5	1	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr10:22676816T>C	ENST00000376624.3	+	6	885	c.743T>C	c.(742-744)gTt>gCt	p.V248A	RP11-301N24.3_ENST00000422675.1_RNA|SPAG6_ENST00000538630.1_Missense_Mutation_p.V223A|SPAG6_ENST00000376601.1_Intron|SPAG6_ENST00000313311.6_Missense_Mutation_p.V248A|SPAG6_ENST00000376603.2_Missense_Mutation_p.V324A	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	248					cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						GAAATGGTTGTTGAAGCAGAG	0.373																																					p.V248A		Atlas-SNP	.											.	SPAG6	90	.	0			c.T743C						.						96	96	96					10																	22676816		2203	4300	6503	SO:0001583	missense	9576	exon6			TGGTTGTTGAAGC	AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"Armadillo repeat containing"	11215	protein-coding gene	gene with protein product	"axoneme central apparatus protein"	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.743T>C	chr10.hg19:g.22676816T>C	ENSP00000365811:p.Val248Ala	90.0	0.0		103.0	45.0	NM_172242	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Missense_Mutation	SNP	ENST00000376624.3	hg19	CCDS7139.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.313061	0.81358	.	.	ENSG00000077327	ENST00000376624;ENST00000376603;ENST00000538630;ENST00000313311	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	5.64	4.51	0.55191	Armadillo-like helical (1);Armadillo-type fold (1);	0.296544	0.36628	N	0.002484	T	0.75635	0.3876	M	0.92026	3.265	0.58432	D	0.99999	B;B;P;P	0.45768	0.329;0.294;0.638;0.866	B;P;P;P	0.49853	0.292;0.624;0.486;0.521	T	0.79671	-0.1706	10	0.72032	D	0.01	-20.0336	11.5016	0.50441	0.0:0.0701:0.0:0.9299	.	223;324;248;248	B4DXZ4;O75602-3;O75602-2;O75602	.;.;.;SPAG6_HUMAN	A	248;324;223;248	ENSP00000365811:V248A;ENSP00000365788:V324A;ENSP00000441325:V223A;ENSP00000323599:V248A	ENSP00000323599:V248A	V	+	2	0	SPAG6	22716822	1.000000	0.71417	0.982000	0.44146	0.997000	0.91878	5.005000	0.63972	0.969000	0.38237	0.533000	0.62120	GTT	.	.		0.373	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1			C	22676816	T	C	22676816	3	2	146	1	0	0	0	0	1	0	0	0	14997	1725	60	2	765	2	SPAG6	10	22676816	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10		22676816	112857931	68	22421										
RASGEF1A	221002	hgsc.bcm.edu	37	chr10	43694401	43694401	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ctccaagacatcaaacttggCtgtcttgaccttggaccaag	8	12	2	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr10:43694401C>A	ENST00000395809.1	-	9	3518	c.1012G>T	c.(1012-1014)Gcc>Tcc	p.A338S	RASGEF1A_ENST00000472864.1_5'Flank|RASGEF1A_ENST00000374459.1_Missense_Mutation_p.A346S|RASGEF1A_ENST00000395810.1_Missense_Mutation_p.A338S			Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A	338	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cell migration (GO:0016477)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)	11						TCAAACTTGGCTGTCTTGACC	0.617																																					p.A338S		Atlas-SNP	.											.	RASGEF1A	66	.	0			c.G1012T						.						139	133	135					10																	43694401		2203	4300	6503	SO:0001583	missense	221002	exon9			ACTTGGCTGTCTT	AK095136	CCDS7202.2, CCDS60517.1	10q11.21	2006-01-11			ENSG00000198915	ENSG00000198915			24246	protein-coding gene	gene with protein product		614531				12477932	Standard	XM_005271808		Approved	CG4853, FLJ37817	uc001jap.1	Q8N9B8	OTTHUMG00000018025	ENST00000395809.1:c.1012G>T	chr10.hg19:g.43694401C>A	ENSP00000379154:p.Ala338Ser	58.0	0.0		69.0	25.0	NM_145313	Q8TBF1	Missense_Mutation	SNP	ENST00000395809.1	hg19	CCDS7202.2	.	.	.	.	.	.	.	.	.	.	C	32	5.120339	0.94385	.	.	ENSG00000198915	ENST00000374459;ENST00000395810;ENST00000395809	T;T;T	0.30182	1.54;1.54;1.54	5.39	5.39	0.77823	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.64402	D	0.000001	T	0.42449	0.1203	L	0.47716	1.5	0.80722	D	1	B;P	0.36183	0.41;0.542	P;P	0.46718	0.45;0.525	T	0.22068	-1.0227	10	0.49607	T	0.09	.	19.143	0.93452	0.0:1.0:0.0:0.0	.	338;346	Q8N9B8;Q8N9B8-2	RGF1A_HUMAN;.	S	346;338;338	ENSP00000363583:A346S;ENSP00000379155:A338S;ENSP00000379154:A338S	ENSP00000363583:A346S	A	-	1	0	RASGEF1A	43014407	1.000000	0.71417	0.990000	0.47175	0.981000	0.71138	7.342000	0.79310	2.509000	0.84616	0.561000	0.74099	GCC	.	.		0.617	RASGEF1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313989.1	NM_145313		A	43694401	C	A	43694401	3	1	146	1	0	0	0	0	1	0	0	0	13084	797	28	3	453	3	RASGEF1A	10	43694401	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	21017585	43694401	91840346	69	22422										
SLC25A16	8034	hgsc.bcm.edu	37	chr10	70243246	70243246	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gttgtaaaagccactgcttgAgagggaatacagcgaatgta	12	6	0	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr10:70243246A>T	ENST00000609923.1	-	9	1040	c.942T>A	c.(940-942)tcT>tcA	p.S314S	SLC25A16_ENST00000265870.3_5'UTR|SLC25A16_ENST00000539557.1_Silent_p.S216S	NM_152707.3	NP_689920.1	P16260	GDC_HUMAN	solute carrier family 25 (mitochondrial carrier), member 16	314					coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	antiporter activity (GO:0015297)			endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	7						CCACTGCTTGAGAGGGAATAC	0.368																																					p.S314S		Atlas-SNP	.											.	SLC25A16	16	.	0			c.T942A						.						131	126	128					10																	70243246		2203	4300	6503	SO:0001819	synonymous_variant	8034	exon9			TGCTTGAGAGGGA	M31659	CCDS7280.1	10q21.3-q22.1	2014-06-17	2014-06-17		ENSG00000122912	ENSG00000122912		"Solute carriers"	10986	protein-coding gene	gene with protein product	"Graves disease autoantigen"	139080				8444471, 2575220	Standard	NM_152707		Approved	GDA, D10S105E, HGT.1, ML7	uc001joi.3	P16260	OTTHUMG00000018354	ENST00000609923.1:c.942T>A	chr10.hg19:g.70243246A>T		45.0	0.0		42.0	9.0	NM_152707	Q8N2U1	Silent	SNP	ENST00000609923.1	hg19	CCDS7280.1																																																																																			.	.		0.368	SLC25A16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048347.2			T	70243246	A	T	70243246	2	4	146	1	0	0	0	0	0	0	0	1	14493	291	11	4		4	SLC25A16	10	70243246	Silent	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	26548845	70243246	65291501	70	22423										
TYSND1	219743	hgsc.bcm.edu	37	chr10	71899886	71899886	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	attattgtcccgggtgttgcTggtgattatgcctgttgagg	14	6	0	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr10:71899886T>A	ENST00000287078.6	-	4	1494	c.1495A>T	c.(1495-1497)Agc>Tgc	p.S499C	TYSND1_ENST00000494143.1_5'UTR|TYSND1_ENST00000335494.5_Missense_Mutation_p.Q393L	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	499	Serine protease.				protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						CGGGTGTTGCTGGTGATTATG	0.597																																					p.S499C		Atlas-SNP	.											.	TYSND1	20	.	0			c.A1495T						.						111	86	94					10																	71899886		2203	4300	6503	SO:0001583	missense	219743	exon4			TGTTGCTGGTGAT	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.1495A>T	chr10.hg19:g.71899886T>A	ENSP00000287078:p.Ser499Cys	141.0	0.0		168.0	76.0	NM_173555	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	Missense_Mutation	SNP	ENST00000287078.6	hg19	CCDS31213.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.5|22.5	4.296577|4.296577	0.81025|0.81025	.|.	.|.	ENSG00000156521|ENSG00000156521	ENST00000335494|ENST00000287078	T|D	0.42513|0.88818	0.97|-2.43	5.85|5.85	5.85|5.85	0.93711|0.93711	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94434|0.94434	0.8209|0.8209	.|.	.|.	.|.	0.38745|0.38745	D|D	0.953983|0.953983	D|D	0.76494|0.89917	0.999|1.0	D|D	0.68943|0.87578	0.961|0.998	D|D	0.95717|0.95717	0.8763|0.8763	8|9	0.18276|0.72032	T|D	0.48|0.01	-41.7766|-41.7766	15.0531|15.0531	0.71891|0.71891	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	393|499	Q2T9J0-2|Q2T9J0	.|TYSD1_HUMAN	L|C	393|499	ENSP00000335673:Q393L|ENSP00000287078:S499C	ENSP00000335673:Q393L|ENSP00000287078:S499C	Q|S	-|-	2|1	0|0	TYSND1|TYSND1	71569892|71569892	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.663000|0.663000	0.39108|0.39108	7.825000|7.825000	0.86693|0.86693	2.238000|2.238000	0.73509|0.73509	0.528000|0.528000	0.53228|0.53228	CAG|AGC	.	.		0.597	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555		A	71899886	T	A	71899886	3	1	146	1	0	0	0	0	1	0	0	0	16832	1580	55	4	209	4	TYSND1	10	71899886	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	1656640	71899886	63634861	71	22424										
CDH23	64072	hgsc.bcm.edu	37	chr10	73453964	73453964	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gtctgaatacatcctcatcgTtcgcgcagtggacgggggtg	14	10	2	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr10:73453964T>G	ENST00000224721.6	+	20	2257	c.2252T>G	c.(2251-2253)gTt>gGt	p.V751G	CDH23_ENST00000299366.7_Missense_Mutation_p.V791G	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	746	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ATCCTCATCGTTCGCGCAGTG	0.632																																					p.V746G		Atlas-SNP	.											.	CDH23	365	.	0			c.T2237G						.						70	87	82					10																	73453964		2080	4194	6274	SO:0001583	missense	64072	exon20			TCATCGTTCGCGC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.2252T>G	chr10.hg19:g.73453964T>G	ENSP00000224721:p.Val751Gly	56.0	0.0		59.0	25.0	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	T	19.66	3.868662	0.72065	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000299366;ENST00000224721;ENST00000442677	.	.	.	5.55	5.55	0.83447	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000003	D	0.88317	0.6404	H	0.97291	3.975	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.925;0.994	D	0.92445	0.5965	9	0.87932	D	0	.	15.7083	0.77602	0.0:0.0:0.0:1.0	.	746;749;746	Q6P152;G3XCN8;Q9H251	.;.;CAD23_HUMAN	G	751;746;746;749;749;263	.	ENSP00000224721:V751G	V	+	2	0	CDH23	73123970	1.000000	0.71417	0.718000	0.30602	0.224000	0.24922	8.008000	0.88588	2.119000	0.64992	0.523000	0.50628	GTT	.	.		0.632	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		G	73453964	T	G	73453964	3	3	146	1	0	0	0	0	1	0	0	0	3110	1725	60	5	2542	5	CDH23	10	73453964	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	1554078	73453964	62080783	72	22425										
OR52N1	79473	hgsc.bcm.edu	37	chr11	5809718	5809718	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gcaccccagactccatccctGtgaaggtgtgcacaaagaac	9	14	0	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr11:5809718G>A	ENST00000317078.1	-	1	328	c.329C>T	c.(328-330)aCa>aTa	p.T110I	TRIM5_ENST00000380027.1_Intron	NM_001001913.1	NP_001001913.1	Q8NH53	O52N1_HUMAN	olfactory receptor, family 52, subfamily N, member 1	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(15)|prostate(2)|skin(3)	31		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		CTCCATCCCTGTGAAGGTGTG	0.502																																					p.T110I		Atlas-SNP	.											.	OR52N1	70	.	0			c.C329T						.						156	140	145					11																	5809718		2201	4296	6497	SO:0001583	missense	79473	exon1			ATCCCTGTGAAGG	AB065538	CCDS31398.1	11p15.4	2012-08-09			ENSG00000181001	ENSG00000181001		"GPCR / Class A : Olfactory receptors"	14853	protein-coding gene	gene with protein product							Standard	NM_001001913		Approved		uc010qzo.2	Q8NH53	OTTHUMG00000168800	ENST00000317078.1:c.329C>T	chr11.hg19:g.5809718G>A	ENSP00000322823:p.Thr110Ile	45.0	0.0		68.0	37.0	NM_001001913	Q6IFF6	Missense_Mutation	SNP	ENST00000317078.1	hg19	CCDS31398.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.536171	0.64972	.	.	ENSG00000181001	ENST00000317078	T	0.19938	2.11	4.59	4.59	0.56863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000096	T	0.40196	0.1107	L	0.60455	1.87	0.28687	N	0.904773	D	0.63046	0.992	D	0.65010	0.931	T	0.17349	-1.0372	10	0.59425	D	0.04	.	14.6035	0.68460	0.0:0.0:1.0:0.0	.	110	Q8NH53	O52N1_HUMAN	I	110	ENSP00000322823:T110I	ENSP00000322823:T110I	T	-	2	0	OR52N1	5766294	0.001000	0.12720	1.000000	0.80357	0.998000	0.95712	1.010000	0.29898	2.528000	0.85240	0.609000	0.83330	ACA	.	.		0.502	OR52N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401142.1	NM_001001913		A	5809718	G	A	5809718	3	1	146	1	0	0	0	0	1	0	0	0	11136	1377	48	3	636	3	OR52N1	11	5809718	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10		5809718	129196798	73	22426										
KCNA4	3739	hgsc.bcm.edu	37	chr11	30032269	30032269	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	caggtggaaaaagattcacaCatcagtctccacagcctttg	8	11	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr11:30032269C>A	ENST00000328224.6	-	2	3190	c.1957G>T	c.(1957-1959)Gtg>Ttg	p.V653L	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	653					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	AAGATTCACACATCAGTCTCC	0.433																																					p.V653L		Atlas-SNP	.											.	KCNA4	158	.	0			c.G1957T						.						75	81	79					11																	30032269		1974	4148	6122	SO:0001583	missense	3739	exon2			TTCACACATCAGT	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1957G>T	chr11.hg19:g.30032269C>A	ENSP00000328511:p.Val653Leu	94.0	0.0		120.0	50.0	NM_002233		Missense_Mutation	SNP	ENST00000328224.6	hg19	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.283161	0.80803	.	.	ENSG00000182255	ENST00000328224	D	0.97731	-4.51	5.7	5.7	0.88788	.	0.484707	0.21100	N	0.080165	D	0.96185	0.8756	L	0.42529	1.33	0.80722	D	1	B	0.15719	0.014	B	0.12837	0.008	D	0.92603	0.6093	10	0.87932	D	0	.	19.8411	0.96685	0.0:1.0:0.0:0.0	.	653	P22459	KCNA4_HUMAN	L	653	ENSP00000328511:V653L	ENSP00000328511:V653L	V	-	1	0	KCNA4	29988845	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.818000	0.86416	2.683000	0.91414	0.655000	0.94253	GTG	.	.		0.433	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		A	30032269	C	A	30032269	3	1	146	1	0	0	0	0	1	0	0	0	8014	478	17	3	8	3	KCNA4	11	30032269	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	24222551	30032269	104974247	74	22427										
LRP4	4038	hgsc.bcm.edu	37	chr11	46912023	46912023	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ctcaatacggggggtgttgcCccagtctgtccagtaaatgg	13	10	2	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr11:46912023C>T	ENST00000378623.1	-	14	1962	c.1720G>A	c.(1720-1722)Ggc>Agc	p.G574S		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	574					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GGGGTGTTGCCCCAGTCTGTC	0.527											OREG0020948	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G574S		Atlas-SNP	.											.	LRP4	160	.	0			c.G1720A						.						34	34	34					11																	46912023		2201	4299	6500	SO:0001583	missense	4038	exon14			TGTTGCCCCAGTC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.1720G>A	chr11.hg19:g.46912023C>T	ENSP00000367888:p.Gly574Ser	67.0	0.0	942	62.0	33.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	C	35	5.536369	0.96460	.	.	ENSG00000134569	ENST00000378623	D	0.95103	-3.61	5.73	5.73	0.89815	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.97005	0.9022	M	0.67569	2.06	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96677	0.9501	10	0.59425	D	0.04	.	20.2602	0.98440	0.0:1.0:0.0:0.0	.	574	O75096	LRP4_HUMAN	S	574	ENSP00000367888:G574S	ENSP00000367888:G574S	G	-	1	0	LRP4	46868599	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.861000	0.98227	0.655000	0.94253	GGC	.	.		0.527	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		T	46912023	C	T	46912023	3	4	146	1	0	0	0	0	1	0	0	0	8968	623	22	3	4097	3	LRP4	11	46912023	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	16879754	46912023	88094493	75	22428										
OR10Q1	219960	hgsc.bcm.edu	37	chr11	57995924	57995924	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	catctgcgtgcacagctcgcGggtcatgatgagggtgtagt	15	9	2	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr11:57995924G>A	ENST00000316770.2	-	1	466	c.424C>T	c.(424-426)Cgc>Tgc	p.R142C		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				CACAGCTCGCGGGTCATGATG	0.627																																					p.R142C		Atlas-SNP	.											OR10Q1,colon,carcinoma,0,1	OR10Q1	79	.	0			c.C424T						.						64	55	58					11																	57995924		2201	4295	6496	SO:0001583	missense	219960	exon1			GCTCGCGGGTCAT	AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475		"GPCR / Class A : Olfactory receptors"	15134	protein-coding gene	gene with protein product							Standard	NM_001004471		Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.424C>T	chr11.hg19:g.57995924G>A	ENSP00000314324:p.Arg142Cys	61.0	0.0		46.0	23.0	NM_001004471	Q6IFG4	Missense_Mutation	SNP	ENST00000316770.2	hg19	CCDS31547.1	.	.	.	.	.	.	.	.	.	.	G	1.984	-0.433489	0.04669	.	.	ENSG00000180475	ENST00000316770	T	0.01388	4.95	4.54	2.64	0.31445	GPCR, rhodopsin-like superfamily (1);	0.916466	0.09003	N	0.862742	T	0.02494	0.0076	M	0.64997	1.995	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.39187	-0.9626	10	0.59425	D	0.04	.	8.4661	0.32958	0.0:0.1499:0.5405:0.3095	.	142	Q8NGQ4	O10Q1_HUMAN	C	142	ENSP00000314324:R142C	ENSP00000314324:R142C	R	-	1	0	OR10Q1	57752500	0.000000	0.05858	0.247000	0.24249	0.003000	0.03518	-0.667000	0.05274	0.526000	0.28541	-0.224000	0.12420	CGC	.	.		0.627	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471		A	57995924	G	A	57995924	3	1	146	1	0	0	0	0	1	0	0	0	10925	1116	39	1	539	1	OR10Q1	11	57995924	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	11083901	57995924	77010592	76	22429										
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64603631	64603631	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tcctccagctgggagctcagGgcccgggtctggctagctgt	15	13	2	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr11:64603631G>A	ENST00000342711.5	-	13	1625	c.1626C>T	c.(1624-1626)gcC>gcT	p.A542A		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						GGGAGCTCAGGGCCCGGGTCT	0.697											OREG0004017	type=REGULATORY REGION|Gene=CDC42BPG|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.A542A		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.C1626T						.						13	15	15					11																	64603631		2185	4278	6463	SO:0001819	synonymous_variant	55561	exon13			GCTCAGGGCCCGG	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"Pleckstrin homology (PH) domain containing"	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.1626C>T	chr11.hg19:g.64603631G>A		48.0	0.0	1077	51.0	18.0	NM_017525		Silent	SNP	ENST00000342711.5	hg19	CCDS31601.1																																																																																			.	.		0.697	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		A	64603631	G	A	64603631	2	1	146	1	0	0	0	0	0	0	0	1	3076	1219	43	3		3	CDC42BPG	11	64603631	Silent	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	6607707	64603631	70402885	77	22430										
DHCR7	1717	hgsc.bcm.edu	37	chr11	71146469	71146469	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ggcactgcggcggtgtagcgCtcccagtcccggccgtactt	14	15	0	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr11:71146469C>T	ENST00000355527.3	-	9	1656	c.1380G>A	c.(1378-1380)gaG>gaA	p.E460E	DHCR7_ENST00000407721.2_Silent_p.E460E	NM_001163817.1|NM_001360.2	NP_001157289.1|NP_001351.2	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	460					blood vessel development (GO:0001568)|cell differentiation (GO:0030154)|cholesterol biosynthetic process (GO:0006695)|lung development (GO:0030324)|multicellular organism growth (GO:0035264)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|regulation of cholesterol biosynthetic process (GO:0045540)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear outer membrane (GO:0005640)	7-dehydrocholesterol reductase activity (GO:0047598)			endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(1)|skin(1)	19						CGGTGTAGCGCTCCCAGTCCC	0.637									Smith-Lemli-Opitz syndrome																												p.E460E		Atlas-SNP	.											.	DHCR7	98	.	0			c.G1380A						.						42	46	44					11																	71146469		2196	4289	6485	SO:0001819	synonymous_variant	1717	exon9	Familial Cancer Database	SLOS type I & II	GTAGCGCTCCCAG	AF034544	CCDS8200.1	11q13.4	2014-09-17	2004-02-13				1.3.1.21		2860	protein-coding gene	gene with protein product		602858	"Smith-Lemli-Opitz syndrome"	SLOS		9465114, 9634533	Standard	NM_001360		Approved		uc001oql.3	Q9UBM7		ENST00000355527.3:c.1380G>A	chr11.hg19:g.71146469C>T		37.0	0.0		77.0	19.0	NM_001163817	B2R6Z2|O60492|O60717	Silent	SNP	ENST00000355527.3	hg19	CCDS8200.1																																																																																			.	.		0.637	DHCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394243.1	NM_001360		T	71146469	C	T	71146469	2	4	146	1	0	0	0	0	0	0	0	1	4479	796	28	3		3	DHCR7	11	71146469	Silent	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	6542838	71146469	63860047	78	22431										
CNTN5	53942	hgsc.bcm.edu	37	chr11	99690405	99690405	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	agcccttcattaggaacactGagtgcttcttcacccagctg	8	13	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr11:99690405G>T	ENST00000524871.1	+	4	476	c.186G>T	c.(184-186)ctG>ctT	p.L62L	CNTN5_ENST00000279463.3_Silent_p.L62L|CNTN5_ENST00000527185.1_Silent_p.L62L|CNTN5_ENST00000418526.2_Intron|CNTN5_ENST00000528682.1_Silent_p.L62L	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	62					cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TAGGAACACTGAGTGCTTCTT	0.428																																					p.L62L		Atlas-SNP	.											.	CNTN5	324	.	0			c.G186T						.						97	97	97					11																	99690405		1918	4129	6047	SO:0001819	synonymous_variant	53942	exon3			AACACTGAGTGCT	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.186G>T	chr11.hg19:g.99690405G>T		196.0	0.0		213.0	42.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Silent	SNP	ENST00000524871.1	hg19	CCDS53696.1																																																																																			.	.		0.428	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		T	99690405	G	T	99690405	2	4	146	1	0	0	0	0	0	0	0	1	3646	1277	45	3		3	CNTN5	11	99690405	Silent	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	28543936	99690405	35316111	79	22432										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103175403	103175403	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	caatggagactggctctgttTgaagaacttacatcttgtgg	11	7	2	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr11:103175403T>G	ENST00000375735.2	+	77	11480	c.11336T>G	c.(11335-11337)tTg>tGg	p.L3779W	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.L3786W|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3779	AAA 6. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGGCTCTGTTTGAAGAACTTA	0.373																																					p.L3786W		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T11357G						.						95	95	95					11																	103175403		1877	4107	5984	SO:0001583	missense	79659	exon78			TCTGTTTGAAGAA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.11336T>G	chr11.hg19:g.103175403T>G	ENSP00000364887:p.Leu3779Trp	88.0	0.0		90.0	37.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450012	0.84101	.	.	ENSG00000187240	ENST00000375735;ENST00000398093;ENST00000540621	T;T	0.32023	1.47;1.47	5.37	5.37	0.77165	Dynein heavy chain (1);	0.000000	0.64402	D	0.000002	T	0.64616	0.2614	M	0.92169	3.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.74225	-0.3734	10	0.87932	D	0	.	14.242	0.65963	0.0:0.0:0.0:1.0	.	3779;3786	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	W	3779;3786;25	ENSP00000364887:L3779W;ENSP00000381167:L3786W	ENSP00000364887:L3779W	L	+	2	0	DYNC2H1	102680613	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.772000	0.85439	2.170000	0.68504	0.533000	0.62120	TTG	.	.		0.373	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103175403	T	G	103175403	3	3	146	1	0	0	0	0	1	0	0	0	4848	1821	63	5	11667	5	DYNC2H1	11	103175403	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	3484998	103175403	31831113	80	22433										
CCT2	10576	hgsc.bcm.edu	37	chr12	69986800	69986800	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gactctacagcaaaggttgcAgaaatagaacatgcggaaaa	10	7	1	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr12:69986800A>G	ENST00000299300.6	+	9	983	c.795A>G	c.(793-795)gcA>gcG	p.A265A	CCT2_ENST00000543146.2_Silent_p.A218A|CCT2_ENST00000544368.2_Silent_p.A265A	NM_006431.2	NP_006422.1	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2 (beta)	265					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(1)	24	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			CAAAGGTTGCAGAAATAGAAC	0.343																																					p.A265A		Atlas-SNP	.											.	CCT2	49	.	0			c.A795G						.						85	86	86					12																	69986800		2203	4300	6503	SO:0001819	synonymous_variant	10576	exon9			GGTTGCAGAAATA	AF026293	CCDS8991.1, CCDS55843.1	12q14	2011-09-02						"Heat Shock Proteins / Chaperonins"	1615	protein-coding gene	gene with protein product		605139				9819444	Standard	NM_001198842		Approved	Cctb	uc001svb.1	P78371	OTTHUMG00000169383	ENST00000299300.6:c.795A>G	chr12.hg19:g.69986800A>G		55.0	0.0		81.0	26.0	NM_006431	A8K402|B5BTY7|B7Z243|B7Z7K4|B7ZAT2|Q14D36|Q6IAT3	Silent	SNP	ENST00000299300.6	hg19	CCDS8991.1																																																																																			.	.		0.343	CCT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403818.1	NM_006431		G	69986800	A	G	69986800	2	3	146	1	0	0	0	0	0	0	0	1	2955	175	7	2		2	CCT2	12	69986800	Silent	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10		69986800	63865095	81	22434										
RASAL1	8437	hgsc.bcm.edu	37	chr12	113553809	113553809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	agcactgggagggcaggacgCggtcctcaatcaggcgtacc	15	12	2	0	rs150792397		TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr12:113553809C>T	ENST00000261729.5	-	10	1094	c.779G>A	c.(778-780)cGc>cAc	p.R260H	RASAL1_ENST00000446861.3_Missense_Mutation_p.R260H|RASAL1_ENST00000546530.1_Missense_Mutation_p.R260H|RASAL1_ENST00000548055.1_Missense_Mutation_p.R260H|RASAL1_ENST00000418411.2_5'UTR			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	260					intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						GGGCAGGACGCGGTCCTCAAT	0.582																																					p.R260H		Atlas-SNP	.											.	RASAL1	89	.	0			c.G779A						.	C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	80	76	78		779,779,779	4.1	0.8	12	dbSNP_134	78	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	RASAL1	NM_001193520.1,NM_001193521.1,NM_004658.2	29,29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign	260/807,260/777,260/805	113553809	2,13004	2203	4300	6503	SO:0001583	missense	8437	exon10			AGGACGCGGTCCT	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"Pleckstrin homology (PH) domain containing"	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.779G>A	chr12.hg19:g.113553809C>T	ENSP00000261729:p.Arg260His	107.0	0.0		131.0	61.0	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	hg19	CCDS9165.1	.	.	.	.	.	.	.	.	.	.	C	5.562	0.288508	0.10513	0.0	2.33E-4	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.67698	-0.28;-0.21;-0.18;-0.28	4.98	4.08	0.47627	Ras GTPase-activating protein (1);	0.532365	0.19108	N	0.122512	T	0.50633	0.1627	N	0.21508	0.67	0.35045	D	0.760136	B;B;B;B;B;B;B	0.20164	0.025;0.006;0.042;0.025;0.011;0.006;0.042	B;B;B;B;B;B;B	0.18561	0.01;0.004;0.022;0.004;0.013;0.006;0.022	T	0.52457	-0.8573	10	0.11794	T	0.64	.	14.5788	0.68271	0.0:0.8524:0.1476:0.0	.	260;260;260;272;260;260;260	B7ZKM4;B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;.;RASL1_HUMAN;.	H	260	ENSP00000450244:R260H;ENSP00000261729:R260H;ENSP00000395920:R260H;ENSP00000448510:R260H	ENSP00000261729:R260H	R	-	2	0	RASAL1	112038192	0.547000	0.26465	0.767000	0.31495	0.543000	0.35085	1.157000	0.31724	1.204000	0.43247	0.484000	0.47621	CGC	.	C|1.000;T|0.000		0.582	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658		T	113553809	C	T	113553809	3	4	146	1	0	0	0	0	1	0	0	0	13078	768	27	1	1687	1	RASAL1	12	113553809	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	43567009	113553809	20298086	82	22435										
OGFOD2	79676	hgsc.bcm.edu	37	chr12	123461262	123461262	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gtcagcagctaggaaagcccTcatcgcgagttcctaccacc	9	15	2	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr12:123461262T>G	ENST00000228922.7	+	3	283	c.251T>G	c.(250-252)cTc>cGc	p.L84R	OGFOD2_ENST00000545317.1_5'UTR|OGFOD2_ENST00000454694.2_5'UTR|OGFOD2_ENST00000538755.1_5'UTR|OGFOD2_ENST00000542117.1_3'UTR|OGFOD2_ENST00000545612.1_5'UTR|ABCB9_ENST00000542678.1_Intron|RP11-197N18.2_ENST00000540866.2_RNA|ABCB9_ENST00000442028.2_5'Flank|OGFOD2_ENST00000397389.2_Missense_Mutation_p.L24R|OGFOD2_ENST00000538628.1_5'UTR|OGFOD2_ENST00000536150.1_5'UTR|ABCB9_ENST00000392439.3_5'Flank			Q6N063	OGFD2_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 2	84							iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			breast(1)|endometrium(2)|lung(4)|pancreas(1)	8	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.11e-05)|Epithelial(86;0.000127)|BRCA - Breast invasive adenocarcinoma(302;0.107)	Vitamin C(DB00126)	AGGAAAGCCCTCATCGCGAGT	0.642																																					p.L24R		Atlas-SNP	.											.	OGFOD2	18	.	0			c.T71G						.						41	52	48					12																	123461262		2200	4291	6491	SO:0001583	missense	79676	exon4			AAGCCCTCATCGC	AK094820	CCDS41855.1	12q24.31	2010-11-23			ENSG00000111325	ENSG00000111325			25823	protein-coding gene	gene with protein product						12477932	Standard	NM_024623		Approved	FLJ13491, FLJ37501	uc001udz.1	Q6N063		ENST00000228922.7:c.251T>G	chr12.hg19:g.123461262T>G	ENSP00000228922:p.Leu84Arg	60.0	0.0		90.0	44.0	NM_024623	B3KT24|Q4KN13|Q6N023|Q9H8K6	Missense_Mutation	SNP	ENST00000228922.7	hg19		.	.	.	.	.	.	.	.	.	.	T	18.49	3.634402	0.67130	.	.	ENSG00000111325	ENST00000397389;ENST00000228922;ENST00000537966	D;D	0.85955	-2.05;-2.02	5.67	4.51	0.55191	.	0.391203	0.30020	N	0.010617	D	0.82282	0.5003	L	0.34521	1.04	0.35682	D	0.814179	D;B;B	0.59767	0.986;0.001;0.178	P;B;B	0.57152	0.814;0.003;0.086	T	0.81457	-0.0924	10	0.21014	T	0.42	-31.7487	6.8534	0.24028	0.1327:0.0729:0.0:0.7944	.	65;84;24	B4DZU3;Q6N063;Q6N063-2	.;OGFD2_HUMAN;.	R	24;84;157	ENSP00000380544:L24R;ENSP00000228922:L84R	ENSP00000228922:L84R	L	+	2	0	OGFOD2	122027215	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	2.093000	0.41710	2.153000	0.67306	0.528000	0.53228	CTC	.	.		0.642	OGFOD2-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000400984.1	NM_024623		G	123461262	T	G	123461262	3	3	146	1	0	0	0	0	1	0	0	0	10851	1551	54	5	77	5	OGFOD2	12	123461262	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	9907453	123461262	10390633	83	22436										
F10	2159	hgsc.bcm.edu	37	chr13	113793724	113793724	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	accagggcaaatgtaaagacGgcctcggggaatacacctgc	12	11	0	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr13:113793724G>T	ENST00000375559.3	+	4	348	c.310G>T	c.(310-312)Ggc>Tgc	p.G104C	F10_ENST00000375551.3_Missense_Mutation_p.G104C|F10_ENST00000409306.1_Missense_Mutation_p.G104C	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	104	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(4)|lung(10)|pancreas(1)|stomach(1)	18	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Antihemophilic Factor(DB00025)|Apixaban(DB06605)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Menadione(DB00170)|Rivaroxaban(DB06228)	ATGTAAAGACGGCCTCGGGGA	0.498																																					p.G104C		Atlas-SNP	.											.	F10	53	.	0			c.G310T						.						117	104	108					13																	113793724		2203	4300	6503	SO:0001583	missense	2159	exon4			AAAGACGGCCTCG		CCDS9530.1	13q34	2012-10-02			ENSG00000126218	ENSG00000126218	3.4.21.6		3528	protein-coding gene	gene with protein product		613872					Standard	XM_005268298		Approved		uc001vsx.3	P00742	OTTHUMG00000017374	ENST00000375559.3:c.310G>T	chr13.hg19:g.113793724G>T	ENSP00000364709:p.Gly104Cys	66.0	0.0		100.0	31.0	NM_000504	Q14340	Missense_Mutation	SNP	ENST00000375559.3	hg19	CCDS9530.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.129585	0.37630	.	.	ENSG00000126218	ENST00000409306;ENST00000375551;ENST00000375559	D;D;D	0.99769	-6.7;-6.7;-6.7	5.63	4.79	0.61399	Gamma-carboxyglutamic acid-rich (GLA) domain (1);EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.112416	0.64402	D	0.000012	D	0.99832	0.9924	H	0.94306	3.52	0.42482	D	0.992868	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.96735	0.9542	10	0.87932	D	0	.	14.3883	0.66961	0.0714:0.0:0.9286:0.0	.	104;104;104	B7ZBK1;Q5JVE8;P00742	.;.;FA10_HUMAN	C	104	ENSP00000387092:G104C;ENSP00000364701:G104C;ENSP00000364709:G104C	ENSP00000364701:G104C	G	+	1	0	F10	112841725	0.786000	0.28738	0.049000	0.19019	0.012000	0.07955	1.767000	0.38501	1.381000	0.46364	0.655000	0.94253	GGC	.	.		0.498	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3			T	113793724	G	T	113793724	3	4	146	1	0	0	0	0	1	0	0	0	5338	1116	39	1	324	1	F10	13	113793724	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10		113793724	1376154	84	22437										
MNAT1	4331	hgsc.bcm.edu	37	chr14	61275080	61275080	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aatgtggatttggacaacacCaaaaagaaaatggagatata	9	4	0	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr14:61275080C>T	ENST00000261245.4	+	4	455	c.354C>T	c.(352-354)acC>acT	p.T118T	MNAT1_ENST00000539616.2_Silent_p.T118T	NM_002431.3	NP_002422.1	P51948	MAT1_HUMAN	MNAT CDK-activating kinase assembly factor 1	118					7-methylguanosine mRNA capping (GO:0006370)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to calcium ion (GO:0051592)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|ventricular system development (GO:0021591)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	11				OV - Ovarian serous cystadenocarcinoma(108;0.0174)		TGGACAACACCAAAAAGAAAA	0.289								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																													p.T118T		Atlas-SNP	.											.	MNAT1	24	.	0			c.C354T						.						52	50	51					14																	61275080		2203	4297	6500	SO:0001819	synonymous_variant	4331	exon4			CAACACCAAAAAG	X87843	CCDS9750.1, CCDS53899.1	14q23	2013-07-31	2013-07-31		ENSG00000020426	ENSG00000020426		"RING-type (C3HC4) zinc fingers", "General transcription factor IIH complex subunits"	7181	protein-coding gene	gene with protein product	"CDK-activating kinase assembly factor"	602659	"menage a trois 1 (CAK assembly factor)", "menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis)"			9465303	Standard	NM_002431		Approved	MAT1, RNF66	uc001xfd.3	P51948	OTTHUMG00000152340	ENST00000261245.4:c.354C>T	chr14.hg19:g.61275080C>T		442.0	1.0		475.0	231.0	NM_001177963	G3V1U8|Q15817|Q6ICQ7	Silent	SNP	ENST00000261245.4	hg19	CCDS9750.1																																																																																			.	.		0.289	MNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276956.1	NM_002431		T	61275080	C	T	61275080	2	4	146	1	0	0	0	0	0	0	0	1	9683	581	21	3		3	MNAT1	14	61275080	Silent	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10		61275080	46074460	85	22438										
APH1B	83464	hgsc.bcm.edu	37	chr15	63571457	63571457	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	atggaccaacacagaaatatCtgctgatctttggagcgttt	9	8	2	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr15:63571457C>T	ENST00000261879.5	+	2	281	c.211C>T	c.(211-213)Ctg>Ttg	p.L71L	APH1B_ENST00000380343.4_Silent_p.L71L	NM_001145646.1|NM_031301.3	NP_001139118.1|NP_112591.2	Q8WW43	APH1B_HUMAN	APH1B gamma secretase subunit	71					apoptotic signaling pathway (GO:0097190)|membrane protein intracellular domain proteolysis (GO:0031293)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	peptidase activity (GO:0008233)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	12						ACAGAAATATCTGCTGATCTT	0.378																																					p.L71L		Atlas-SNP	.											.	APH1B	27	.	0			c.C211T						.						167	159	162					15																	63571457		2203	4300	6503	SO:0001819	synonymous_variant	83464	exon2			AAATATCTGCTGA	AY358698	CCDS10184.1, CCDS45276.1	15q22.2	2013-05-01	2013-05-01		ENSG00000138613	ENSG00000138613			24080	protein-coding gene	gene with protein product		607630	"anterior pharynx defective 1 homolog B (C. elegans)"			12110170, 11230166	Standard	NM_031301		Approved	PSFL, APH-1B, DKFZp564D0372	uc002ama.3	Q8WW43	OTTHUMG00000132863	ENST00000261879.5:c.211C>T	chr15.hg19:g.63571457C>T		126.0	0.0		156.0	14.0	NM_001145646	A8K589|Q564N3|Q6UWQ1|Q9H0S0	Silent	SNP	ENST00000261879.5	hg19	CCDS10184.1																																																																																			.	.		0.378	APH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256337.1	NM_031301		T	63571457	C	T	63571457	2	4	146	1	0	0	0	0	0	0	0	1	772	912	32	3		3	APH1B	15	63571457	Silent	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10		63571457	38959935	86	22439										
SLCO3A1	28232	hgsc.bcm.edu	37	chr15	92397220	92397220	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	acgaggcgcagaggaacaagAaaaagaaaaagaaggtgtcc	13	6	0	4			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr15:92397220A>G	ENST00000318445.6	+	1	296	c.82A>G	c.(82-84)Aaa>Gaa	p.K28E	SLCO3A1_ENST00000424469.2_Missense_Mutation_p.K28E	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	28					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	GAGGAACAAGAAAAAGAAAAA	0.657																																					p.K28E		Atlas-SNP	.											.	SLCO3A1	84	.	0			c.A82G						.						17	18	18					15																	92397220		2194	4296	6490	SO:0001583	missense	28232	exon1			AACAAGAAAAAGA	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"Solute carriers"	10952	protein-coding gene	gene with protein product		612435	"solute carrier family 21 (organic anion transporter), member 11"	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.82A>G	chr15.hg19:g.92397220A>G	ENSP00000320634:p.Lys28Glu	113.0	0.0		100.0	38.0	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Missense_Mutation	SNP	ENST00000318445.6	hg19	CCDS10371.1	.	.	.	.	.	.	.	.	.	.	A	12.43	1.935329	0.34189	.	.	ENSG00000176463	ENST00000318445;ENST00000424469	T;T	0.37411	1.2;1.2	3.49	3.49	0.39957	Major facilitator superfamily domain, general substrate transporter (1);	0.431079	0.23036	N	0.052666	T	0.15652	0.0377	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.10451	-1.0629	10	0.02654	T	1	.	11.1339	0.48362	1.0:0.0:0.0:0.0	.	28;28	Q9UIG8-2;Q9UIG8	.;SO3A1_HUMAN	E	28	ENSP00000320634:K28E;ENSP00000387846:K28E	ENSP00000320634:K28E	K	+	1	0	SLCO3A1	90198224	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.798000	0.69095	1.380000	0.46344	0.397000	0.26171	AAA	.	.		0.657	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272		G	92397220	A	G	92397220	3	3	146	1	0	0	0	0	1	0	0	0	14743	247	9	2	84	2	SLCO3A1	15	92397220	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	28825763	92397220	10134172	87	22440										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72828036	72828036	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gttatctgcgttgccctcgtCtccagttgtggtatctgtga	11	10	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr16:72828036C>G	ENST00000268489.5	-	9	9217	c.8545G>C	c.(8545-8547)Gac>Cac	p.D2849H	ZFHX3_ENST00000397992.5_Missense_Mutation_p.D1935H|RP5-991G20.4_ENST00000569195.1_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2849					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TTGCCCTCGTCTCCAGTTGTG	0.493																																					p.D2849H		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G8545C						.						260	213	229					16																	72828036		2198	4300	6498	SO:0001583	missense	463	exon9			CCTCGTCTCCAGT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.8545G>C	chr16.hg19:g.72828036C>G	ENSP00000268489:p.Asp2849His	72.0	0.0		88.0	44.0	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	hg19	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.841602	0.32513	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.77750	-1.12;-1.08	5.96	5.96	0.96718	.	0.000000	0.52532	D	0.000075	D	0.87676	0.6237	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87367	0.2348	10	0.72032	D	0.01	.	20.4043	0.99006	0.0:1.0:0.0:0.0	.	2849	Q15911	ZFHX3_HUMAN	H	2849;1935	ENSP00000268489:D2849H;ENSP00000438926:D1935H	ENSP00000268489:D2849H	D	-	1	0	ZFHX3	71385537	1.000000	0.71417	0.904000	0.35570	0.963000	0.63663	7.818000	0.86416	2.823000	0.97156	0.650000	0.86243	GAC	.	.		0.493	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		G	72828036	C	G	72828036	3	3	146	1	0	0	0	0	1	0	0	0	17649	913	32	4	2574	4	ZFHX3	16	72828036	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10		72828036	17526717	88	22441										
LDHD	84937	hgsc.bcm.edu	37	chr16	75147448	75147448	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ctcaccttgcagcctggccgCgtggccagggctgcgtacca	13	16	1	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr16:75147448C>A	ENST00000335325.4	+	0	4620				LDHD_ENST00000450168.2_Silent_p.T357T|RP11-252E2.1_ENST00000499110.1_RNA|LDHD_ENST00000300051.4_Silent_p.T380T	NM_032268.4	NP_115644.1	Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase						proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)	1						AGCCTGGCCGCGTGGCCAGGG	0.652																																					p.T380T		Atlas-SNP	.											.	LDHD	34	.	0			c.G1140T						.						17	20	19					16																	75147448		2188	4274	6462	SO:0001628	intergenic_variant	197257	exon8			TGGCCGCGTGGCC	AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187		"RING-type (C3HC4) zinc fingers"	18452	protein-coding gene	gene with protein product		612060	"zinc and ring finger 1"				Standard	NM_032268		Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606		chr16.hg19:g.75147448C>A		53.0	0.0		61.0	31.0	NM_153486	D3DUJ9|Q9H083	Silent	SNP	ENST00000335325.4	hg19	CCDS10912.1																																																																																			.	.		0.652	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2			A	75147448	C	A	75147448	1	1	146	0	1	0	0	0	0	0	0	0	8712	755	27	1		1	LDHD	16	75147448	IGR	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	2319412	75147448	15207305	89	22442										
MYH13	8735	hgsc.bcm.edu	37	chr17	10223741	10223741	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ttcctgggacattttcagatCtccttccagcttcctcttcg	6	14	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr17:10223741C>T	ENST00000418404.3	-	24	3347	c.3184G>A	c.(3184-3186)Gat>Aat	p.D1062N	RP11-401O9.3_ENST00000577743.1_RNA|RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Missense_Mutation_p.D1062N			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1062					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						ATTTTCAGATCTCCTTCCAGC	0.423																																					p.D1062N		Atlas-SNP	.											.	MYH13	533	.	0			c.G3184A						.						81	79	79					17																	10223741		1882	4099	5981	SO:0001583	missense	8735	exon25			TCAGATCTCCTTC	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3184G>A	chr17.hg19:g.10223741C>T	ENSP00000404570:p.Asp1062Asn	90.0	0.0		81.0	69.0	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	hg19	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.796779	0.90453	.	.	ENSG00000006788	ENST00000252172	D	0.93019	-3.15	3.78	3.78	0.43462	.	.	.	.	.	D	0.97420	0.9156	M	0.93594	3.435	0.46478	D	0.999066	D	0.76494	0.999	D	0.97110	1.0	D	0.98400	1.0567	9	0.62326	D	0.03	.	16.1667	0.81768	0.0:1.0:0.0:0.0	.	1062	Q9UKX3	MYH13_HUMAN	N	1062	ENSP00000252172:D1062N	ENSP00000252172:D1062N	D	-	1	0	MYH13	10164466	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.495000	0.81514	2.102000	0.63906	0.655000	0.94253	GAT	.	.		0.423	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		T	10223741	C	T	10223741	3	4	146	1	0	0	0	0	1	0	0	0	10041	913	32	3	2700	3	MYH13	17	10223741	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10		10223741	70971469	90	22443										
MYH3	4621	hgsc.bcm.edu	37	chr17	10549294	10549294	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tctatgctggccaccaggatCtccccctggctaatgaacgg	10	14	2	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr17:10549294C>T	ENST00000583535.1	-	11	1041	c.954G>A	c.(952-954)gaG>gaA	p.E318E	MYH3_ENST00000226209.7_Silent_p.E318E	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	318	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						CCACCAGGATCTCCCCCTGGC	0.517											OREG0024181	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E318E		Atlas-SNP	.											.	MYH3	227	.	0			c.G954A						.						133	123	126					17																	10549294		2203	4300	6503	SO:0001819	synonymous_variant	4621	exon11			CAGGATCTCCCCC		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.954G>A	chr17.hg19:g.10549294C>T		211.0	0.0	665	189.0	11.0	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	hg19	CCDS11157.1																																																																																			.	.		0.517	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		T	10549294	C	T	10549294	2	4	146	1	0	0	0	0	0	0	0	1	10045	912	32	3		3	MYH3	17	10549294	Silent	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	325553	10549294	70645916	91	22444										
SARM1	113235	hgsc.bcm.edu	37	chr17	26723269	26723269	+	3'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tcatctgcaggctctgacacCagtttggagggtgctgcacc	12	12	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr17:26723269C>T	ENST00000440501.1	-	0	4878				SLC46A1_ENST00000584729.1_5'UTR|SARM1_ENST00000457710.3_Silent_p.T679T|SARM1_ENST00000379061.4_3'UTR|SLC46A1_ENST00000321666.5_3'UTR	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1						cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	GCTCTGACACCAGTTTGGAGG	0.592																																					p.T712T		Atlas-SNP	.											.	SARM1	40	.	0			c.C2136T						.						87	87	87					17																	26723269		2203	4300	6503	SO:0001624	3_prime_UTR_variant	23098	exon10			TGACACCAGTTTG	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"Solute carriers"	30521	protein-coding gene	gene with protein product	"heme carrier protein 1", "proton-coupled folate transporter"	611672	"solute carrier family 46, member 1"			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.*3403G>A	chr17.hg19:g.26723269C>T		70.0	0.0		103.0	59.0	NM_015077	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Silent	SNP	ENST00000440501.1	hg19																																																																																				.	.		0.592	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		T	26723269	C	T	26723269	1	4	146	0	1	0	0	0	0	0	0	0	13857	581	21	3		3	SARM1	17	26723269	3'UTR	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	16173975	26723269	54471941	92	22445										
AP2B1	163	hgsc.bcm.edu	37	chr17	33935332	33935332	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gcgtggcaaaactccatgatAtcaatgcccaaatggtggaa	10	9	1	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr17:33935332A>G	ENST00000262325.7	+	5	1004	c.451A>G	c.(451-453)Atc>Gtc	p.I151V	AP2B1_ENST00000589344.1_Missense_Mutation_p.I151V|AP2B1_ENST00000537622.2_Missense_Mutation_p.I151V|AP2B1_ENST00000592545.1_Missense_Mutation_p.I113V|AP2B1_ENST00000538556.1_Missense_Mutation_p.I94V|AP2B1_ENST00000312678.8_Missense_Mutation_p.I151V	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	151					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		ACTCCATGATATCAATGCCCA	0.438																																					p.I151V		Atlas-SNP	.											.	AP2B1	70	.	0			c.A451G						.						105	107	106					17																	33935332		2203	4300	6503	SO:0001583	missense	163	exon5			CATGATATCAATG	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.451A>G	chr17.hg19:g.33935332A>G	ENSP00000262325:p.Ile151Val	103.0	0.0		180.0	110.0	NM_001282	A6NJP3|P21851|Q7Z451|Q96J19	Missense_Mutation	SNP	ENST00000262325.7	hg19	CCDS32622.1	.	.	.	.	.	.	.	.	.	.	A	16.69	3.192840	0.58017	.	.	ENSG00000006125	ENST00000262325;ENST00000312678;ENST00000538556;ENST00000537622	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	5.41	5.41	0.78517	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.093693	0.64402	D	0.000001	T	0.26159	0.0638	L	0.46567	1.45	0.80722	D	1	B;B;B	0.25441	0.126;0.0;0.0	B;B;B	0.26517	0.07;0.002;0.0	T	0.03051	-1.1078	10	0.44086	T	0.13	-1.0476	14.6718	0.68951	1.0:0.0:0.0:0.0	.	113;151;151	B4DWG4;P63010;P63010-2	.;AP2B1_HUMAN;.	V	151;151;94;151	ENSP00000262325:I151V;ENSP00000314414:I151V;ENSP00000440563:I94V;ENSP00000437413:I151V	ENSP00000262325:I151V	I	+	1	0	AP2B1	30959445	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.239000	0.95389	2.060000	0.61445	0.529000	0.55759	ATC	.	.		0.438	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1			G	33935332	A	G	33935332	3	3	146	1	0	0	0	0	1	0	0	0	741	449	16	2	465	2	AP2B1	17	33935332	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	7212063	33935332	47259878	93	22446										
MRC2	9902	hgsc.bcm.edu	37	chr17	60767109	60767109	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	acgccgctctggattgggctGgctggcgaggaggtgggctc	19	10	1	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr17:60767109G>A	ENST00000303375.5	+	24	3963	c.3561G>A	c.(3559-3561)ctG>ctA	p.L1187L	MRC2_ENST00000446119.2_Intron|MRC2_ENST00000580916.1_Intron	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1187	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						GGATTGGGCTGGCTGGCGAGG	0.706																																					p.L1187L		Atlas-SNP	.											.	MRC2	126	.	0			c.G3561A						.						8	8	8					17																	60767109		2179	4277	6456	SO:0001819	synonymous_variant	9902	exon24			TGGGCTGGCTGGC	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3561G>A	chr17.hg19:g.60767109G>A		27.0	0.0		28.0	17.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	hg19	CCDS11634.1																																																																																			.	.		0.706	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			A	60767109	G	A	60767109	2	1	146	1	0	0	0	0	0	0	0	1	9767	1335	47	3		3	MRC2	17	60767109	Silent	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	26831777	60767109	20428101	94	22447										
OTOP2	92736	hgsc.bcm.edu	37	chr17	72921033	72921033	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gcgcacgctggccccatctgGctccgaggtgccaggggagg	17	14	1	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr17:72921033G>T	ENST00000580223.1	+	1	336	c.306G>T	c.(304-306)tgG>tgT	p.W102C	USH1G_ENST00000319642.1_5'Flank|OTOP2_ENST00000331427.4_Missense_Mutation_p.W102C			Q7RTS6	OTOP2_HUMAN	otopetrin 2	102						integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|prostate(4)|skin(1)|urinary_tract(2)	39	all_lung(278;0.172)|Lung NSC(278;0.207)					GCCCCATCTGGCTCCGAGGTG	0.657																																					p.W102C		Atlas-SNP	.											.	OTOP2	81	.	0			c.G306T						.						14	10	11					17																	72921033		2187	4269	6456	SO:0001583	missense	92736	exon2			CATCTGGCTCCGA	BK000567	CCDS11708.1	17q25.3	2006-09-20				ENSG00000183034			19657	protein-coding gene	gene with protein product		607827				12651873	Standard	NM_178160		Approved		uc010wrp.2	Q7RTS6		ENST00000580223.1:c.306G>T	chr17.hg19:g.72921033G>T	ENSP00000463837:p.Trp102Cys	40.0	0.0		62.0	22.0	NM_178160		Missense_Mutation	SNP	ENST00000580223.1	hg19	CCDS11708.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.223018	0.79464	.	.	ENSG00000183034	ENST00000331427	T	0.22134	1.97	4.12	4.12	0.48240	.	0.000000	0.85682	D	0.000000	T	0.46347	0.1388	M	0.74647	2.275	0.80722	D	1	D	0.71674	0.998	D	0.68943	0.961	T	0.54063	-0.8349	10	0.87932	D	0	-4.6811	16.5517	0.84474	0.0:0.0:1.0:0.0	.	102	Q7RTS6	OTOP2_HUMAN	C	102	ENSP00000332528:W102C	ENSP00000332528:W102C	W	+	3	0	OTOP2	70432628	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.056000	0.93881	2.122000	0.65172	0.555000	0.69702	TGG	.	.		0.657	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160		T	72921033	G	T	72921033	3	4	146	1	0	0	0	0	1	0	0	0	11315	1212	42	3	308	3	OTOP2	17	72921033	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	12153924	72921033	8274177	95	22448										
RNF213	57674	hgsc.bcm.edu	37	chr17	78327327	78327327	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tgcagtgggcttggaacaccGggcggaagacggccatgagg	18	9	0	2	rs113011315		TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr17:78327327G>T	ENST00000582970.1	+	34	10582	c.10439G>T	c.(10438-10440)cGg>cTg	p.R3480L	CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.R1553L|RNF213_ENST00000508628.2_Missense_Mutation_p.R3529L|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3480					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TTGGAACACCGGGCGGAAGAC	0.602																																					p.R3480L		Atlas-SNP	.											.	RNF213	766	.	0			c.G10439T						.						66	56	59					17																	78327327		2203	4300	6503	SO:0001583	missense	57674	exon34			AACACCGGGCGGA	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.10439G>T	chr17.hg19:g.78327327G>T	ENSP00000464087:p.Arg3480Leu	66.0	0.0		96.0	4.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	7.380	0.628618	0.14257	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.23552	1.9	2.84	-3.39	0.04868	.	3.082280	0.01522	N	0.018397	T	0.16300	0.0392	L	0.43152	1.355	0.09310	N	1	B	0.18610	0.029	B	0.14578	0.011	T	0.09707	-1.0662	10	0.09590	T	0.72	.	0.5608	0.00679	0.3503:0.1729:0.3009:0.1759	.	1553	Q63HN8	RN213_HUMAN	L	3480;3529;1553	ENSP00000338218:R1553L	ENSP00000338218:R1553L	R	+	2	0	RNF213	75941922	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.120000	0.15647	-0.731000	0.04862	0.561000	0.74099	CGG	.	G|0.500;A|0.500		0.602	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78327327	G	T	78327327	3	4	146	1	0	0	0	0	1	0	0	0	13492	1116	39	1	10888	1	RNF213	17	78327327	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	5406294	78327327	2867883	96	22449										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31319755	31319755	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tgccaaacctctgggagagaAccttacctcccagcagaaga	9	13	1	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr18:31319755A>T	ENST00000269197.5	+	11	2387	c.2387A>T	c.(2386-2388)aAc>aTc	p.N796I		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	796					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						CTGGGAGAGAACCTTACCTCC	0.478																																					p.N796I		Atlas-SNP	.											.	ASXL3	405	.	0			c.A2387T						.						35	35	35					18																	31319755		1901	4127	6028	SO:0001583	missense	80816	exon11			GAGAGAACCTTAC	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.2387A>T	chr18.hg19:g.31319755A>T	ENSP00000269197:p.Asn796Ile	65.0	0.0		58.0	17.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	A	9.442	1.088313	0.20390	.	.	ENSG00000141431	ENST00000269197	T	0.15487	2.42	6.04	0.701	0.18104	.	0.826812	0.11358	N	0.572259	T	0.10680	0.0261	N	0.14661	0.345	0.23396	N	0.997763	B	0.34103	0.437	B	0.32289	0.143	T	0.21965	-1.0230	10	0.51188	T	0.08	.	12.3714	0.55256	0.3687:0.0:0.6313:0.0	.	796	Q9C0F0	ASXL3_HUMAN	I	796	ENSP00000269197:N796I	ENSP00000269197:N796I	N	+	2	0	ASXL3	29573753	0.989000	0.36119	0.025000	0.17156	0.543000	0.35085	1.020000	0.30027	-0.151000	0.11176	0.460000	0.39030	AAC	.	.		0.478	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			T	31319755	A	T	31319755	3	4	146	1	0	0	0	0	1	0	0	0	1068	43	2	4	2429	4	ASXL3	18	31319755	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10		31319755	46757493	97	22450										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34289345	34289345	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aggacaagctctccagggacAggacaactggtaaatgaagc	12	9	1	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr18:34289345A>T	ENST00000359247.4	+	14	1948	c.1948A>T	c.(1948-1950)Agg>Tgg	p.R650W	FHOD3_ENST00000587493.1_3'UTR|FHOD3_ENST00000591635.1_Intron|FHOD3_ENST00000445677.1_Missense_Mutation_p.R629W|FHOD3_ENST00000590592.1_Missense_Mutation_p.R842W|FHOD3_ENST00000257209.4_Missense_Mutation_p.R667W	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	650					actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CTCCAGGGACAGGACAACTGG	0.607																																					p.R667W		Atlas-SNP	.											.	FHOD3	210	.	0			c.A1999T						.						51	37	42					18																	34289345		2202	4299	6501	SO:0001583	missense	80206	exon15			AGGGACAGGACAA	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.1948A>T	chr18.hg19:g.34289345A>T	ENSP00000352186:p.Arg650Trp	131.0	0.0		100.0	65.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	hg19		.	.	.	.	.	.	.	.	.	.	A	17.23	3.337895	0.60963	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.32988	1.43;1.89;1.98	5.65	3.34	0.38264	.	0.798245	0.12292	N	0.481973	T	0.39118	0.1066	L	0.36672	1.1	0.28827	N	0.897373	P;D;P;P	0.69078	0.891;0.997;0.692;0.89	P;P;P;P	0.61477	0.46;0.889;0.46;0.502	T	0.19778	-1.0295	10	0.66056	D	0.02	.	7.5693	0.27898	0.7647:0.1594:0.076:0.0	.	629;650;667;842	Q2V2M9-2;Q2V2M9;Q2V2M9-3;E5F5Q0	.;FHOD3_HUMAN;.;.	W	667;650;629	ENSP00000257209:R667W;ENSP00000352186:R650W;ENSP00000411430:R629W	ENSP00000257209:R667W	R	+	1	2	FHOD3	32543343	1.000000	0.71417	0.940000	0.37924	0.358000	0.29455	5.655000	0.67981	0.592000	0.29728	0.533000	0.62120	AGG	.	.		0.607	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		T	34289345	A	T	34289345	3	4	146	1	0	0	0	0	1	0	0	0	5891	179	7	4	2057	4	FHOD3	18	34289345	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	2969590	34289345	43787903	98	22451										
WDR7	23335	hgsc.bcm.edu	37	chr18	54358525	54358525	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	catggaccgggggggactttGtctcatcagataaagtcatc	12	9	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr18:54358525G>A	ENST00000254442.3	+	8	1007	c.796G>A	c.(796-798)Gtc>Atc	p.V266I	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Missense_Mutation_p.V266I	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	266					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		GGGGGACTTTGTCTCATCAGA	0.423																																					p.V266I		Atlas-SNP	.											.	WDR7	166	.	0			c.G796A						.						88	96	93					18																	54358525		2203	4300	6503	SO:0001583	missense	23335	exon8			GACTTTGTCTCAT	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"WD repeat domain containing"	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.796G>A	chr18.hg19:g.54358525G>A	ENSP00000254442:p.Val266Ile	77.0	0.0		66.0	16.0	NM_052834	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Missense_Mutation	SNP	ENST00000254442.3	hg19	CCDS11962.1	.	.	.	.	.	.	.	.	.	.	G	7.350	0.622634	0.14193	.	.	ENSG00000091157	ENST00000254442;ENST00000357574;ENST00000398311	T;T	0.46819	0.86;0.86	5.45	4.57	0.56435	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.181053	0.48767	D	0.000180	T	0.22205	0.0535	N	0.03253	-0.375	0.40458	D	0.980212	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.13229	-1.0517	10	0.14656	T	0.56	.	11.1937	0.48700	0.147:0.0:0.853:0.0	.	266;266	Q9Y4E6-2;Q9Y4E6	.;WDR7_HUMAN	I	266	ENSP00000254442:V266I;ENSP00000350187:V266I	ENSP00000254442:V266I	V	+	1	0	WDR7	52509523	1.000000	0.71417	0.999000	0.59377	0.834000	0.47266	2.591000	0.46163	2.729000	0.93468	0.460000	0.39030	GTC	.	.		0.423	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			A	54358525	G	A	54358525	3	1	146	1	0	0	0	0	1	0	0	0	17335	1377	48	3	822	3	WDR7	18	54358525	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	20069180	54358525	23718723	99	22452										
TRMT1	55621	hgsc.bcm.edu	37	chr19	13220610	13220610	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	cgttgcccacagtgttcacaCtcgggggtcacagggggacc	14	13	2	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr19:13220610C>T	ENST00000592062.1	-	11	1719	c.1149G>A	c.(1147-1149)gaG>gaA	p.E383E	TRMT1_ENST00000437766.1_Silent_p.E383E|TRMT1_ENST00000221504.8_Silent_p.E354E|TRMT1_ENST00000357720.4_Silent_p.E383E			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	383	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		AGTGTTCACACTCGGGGGTCA	0.612																																					p.E383E		Atlas-SNP	.											.	TRMT1	31	.	0			c.G1149A						.						74	75	75					19																	13220610		2203	4300	6503	SO:0001819	synonymous_variant	55621	exon10			TTCACACTCGGGG	AF196479	CCDS12293.1, CCDS45997.1	19p13.13	2012-06-12	2012-06-12						25980	protein-coding gene	gene with protein product		611669				10982862	Standard	NM_001142554		Approved	FLJ20244, TRM1	uc002mwl.3	Q9NXH9		ENST00000592062.1:c.1149G>A	chr19.hg19:g.13220610C>T		41.0	0.0		61.0	20.0	NM_001136035	O76103|Q548Y5|Q8WVA6	Silent	SNP	ENST00000592062.1	hg19	CCDS12293.1																																																																																			.	.		0.612	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722		T	13220610	C	T	13220610	2	4	146	1	0	0	0	0	0	0	0	1	16576	564	20	3		3	TRMT1	19	13220610	Silent	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10		13220610	45908373	100	22453										
EMR3	84658	hgsc.bcm.edu	37	chr19	14740911	14740911	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ccttggaggctgttgatgatGgtgaagaggtaggccatgac	16	6	0	5			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr19:14740911G>T	ENST00000253673.5	-	14	1852	c.1752C>A	c.(1750-1752)acC>acA	p.T584T	EMR3_ENST00000344373.4_Silent_p.T532T|EMR3_ENST00000443157.2_Silent_p.T458T|EMR3_ENST00000599900.1_Silent_p.T369T	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	584					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						TGTTGATGATGGTGAAGAGGT	0.502																																					p.T584T		Atlas-SNP	.											.	EMR3	99	.	0			c.C1752A						.						119	101	107					19																	14740911		2203	4300	6503	SO:0001819	synonymous_variant	84658	exon14			GATGATGGTGAAG	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"-", "GPCR / Class B : Orphans"	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.1752C>A	chr19.hg19:g.14740911G>T		56.0	0.0		76.0	34.0	NM_032571		Silent	SNP	ENST00000253673.5	hg19	CCDS12315.1																																																																																			.	.		0.502	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571		T	14740911	G	T	14740911	2	4	146	1	0	0	0	0	0	0	0	1	5108	1335	47	3		3	EMR3	19	14740911	Silent	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	1520301	14740911	44388072	101	22454										
ILVBL	10994	hgsc.bcm.edu	37	chr19	15233713	15233713	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ctccacctacctggggtgccCgactgggcggcagccatcgc	13	17	0	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr19:15233713C>A	ENST00000263383.3	-	5	733	c.594G>T	c.(592-594)tcG>tcT	p.S198S	AC003956.1_ENST00000598450.1_RNA|ILVBL_ENST00000534378.1_Silent_p.S91S|ILVBL_ENST00000531635.1_5'UTR	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	198						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						CTGGGGTGCCCGACTGGGCGG	0.642																																					p.S198S		Atlas-SNP	.											.	ILVBL	54	.	0			c.G594T						.						57	59	58					19																	15233713		2203	4300	6503	SO:0001819	synonymous_variant	10994	exon5			GGTGCCCGACTGG	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"acetolactate synthase homolog"	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.594G>T	chr19.hg19:g.15233713C>A		31.0	0.0		43.0	16.0	NM_006844	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Silent	SNP	ENST00000263383.3	hg19	CCDS12325.1																																																																																			.	.		0.642	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844		A	15233713	C	A	15233713	2	1	146	1	0	0	0	0	0	0	0	1	7724	639	23	1		1	ILVBL	19	15233713	Silent	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	492802	15233713	43895270	102	22455										
LSR	51599	hgsc.bcm.edu	37	chr19	35740010	35740010	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	acgcggtcgtcttcgtgtggCttctgcttagcacctggtgc	13	12	2	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr19:35740010C>T	ENST00000361790.3	+	1	388	c.229C>T	c.(229-231)Ctt>Ttt	p.L77F	LSR_ENST00000602122.1_Missense_Mutation_p.L77F|LSR_ENST00000347609.4_Intron|LSR_ENST00000597933.1_Intron|LSR_ENST00000360798.3_Missense_Mutation_p.L77F|LSR_ENST00000354900.3_Missense_Mutation_p.L77F|AC002128.5_ENST00000604161.1_RNA|LSR_ENST00000427250.1_Missense_Mutation_p.L29F	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	77					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CTTCGTGTGGCTTCTGCTTAG	0.716																																					p.L77F		Atlas-SNP	.											.	LSR	60	.	0			c.C229T						.						3	4	3					19																	35740010		1895	3662	5557	SO:0001583	missense	51599	exon1			GTGTGGCTTCTGC	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.229C>T	chr19.hg19:g.35740010C>T	ENSP00000354575:p.Leu77Phe	72.0	0.0		90.0	31.0	NM_205834	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Missense_Mutation	SNP	ENST00000361790.3	hg19	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.425959	0.83667	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000360798;ENST00000427250	T;T;T;T	0.69175	0.17;0.26;-0.11;-0.38	3.39	3.39	0.38822	.	0.334023	0.27289	N	0.020043	T	0.65719	0.2718	L	0.54323	1.7	0.24268	N	0.995256	P;P;P;P;D	0.61697	0.938;0.925;0.892;0.877;0.99	P;P;P;B;P	0.49528	0.614;0.571;0.447;0.368;0.614	T	0.60052	-0.7338	10	0.52906	T	0.07	-24.1551	10.5643	0.45163	0.0:1.0:0.0:0.0	.	34;77;77;77;77	Q9BT33;Q86X29-3;A6NDW3;E9PHD4;Q86X29	.;.;.;.;LSR_HUMAN	F	77;77;77;29	ENSP00000354575:L77F;ENSP00000346976:L77F;ENSP00000354034:L77F;ENSP00000394479:L29F	ENSP00000346976:L77F	L	+	1	0	LSR	40431850	0.975000	0.34042	0.862000	0.33874	0.180000	0.23129	1.152000	0.31663	2.200000	0.70718	0.491000	0.48974	CTT	.	.		0.716	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		T	35740010	C	T	35740010	3	4	146	1	0	0	0	0	1	0	0	0	9073	797	28	3	231	3	LSR	19	35740010	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	20506297	35740010	23388973	103	22456										
MLL4	9757	hgsc.bcm.edu	37	chr19	36221665	36221665	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aggcgctgctggtatcggtgCcgaattctggagtatcggcc	15	10	1	0			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr19:36221665C>A	ENST00000222270.7	+	26	5334	c.5334C>A	c.(5332-5334)tgC>tgA	p.C1778*	KMT2B_ENST00000420124.1_Nonsense_Mutation_p.C1778*|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1778	FYR N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00875}.				chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GGTATCGGTGCCGAATTCTGG	0.607																																					p.C1778X		Atlas-SNP	.											.	MLL4	229	.	0			c.C5334A						.						45	51	49					19																	36221665		2038	4195	6233	SO:0001587	stop_gained	8085	exon26			TCGGTGCCGAATT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5334C>A	chr19.hg19:g.36221665C>A	ENSP00000222270:p.Cys1778*	66.0	0.0		85.0	32.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Nonsense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	44	11.157437	0.99524	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	.	.	.	5.97	3.8	0.43715	.	0.000000	0.49305	D	0.000157	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7366	0.40392	0.0:0.7683:0.0:0.2317	.	.	.	.	X	1778	.	ENSP00000222270:C1778X	C	+	3	2	AD000671.1	40913505	0.999000	0.42202	0.977000	0.42913	0.999000	0.98932	0.952000	0.29149	0.807000	0.34208	0.655000	0.94253	TGC	.	.		0.607	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		A	36221665	C	A	36221665	4	1	146	1	0	0	0	0	0	1	0	0	9632	747	26	3	5436	3	MLL4	19	36221665	Nonsense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	481655	36221665	22907318	104	22457										
KCNK6	9424	hgsc.bcm.edu	37	chr19	38818018	38818018	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	actctctgccagctcccacaCcgactacgcttccatcccca	4	21	1	0	rs371433357		TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr19:38818018C>T	ENST00000263372.3	+	3	1024	c.917C>T	c.(916-918)aCc>aTc	p.T306I		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	306					negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	AGCTCCCACACCGACTACGCT	0.662																																					p.T306I		Atlas-SNP	.											.	KCNK6	37	.	0			c.C917T						.	C	ILE/THR	0,4406		0,0,2203	44	44	44		917	2	0	19		44	1,8599	1.2+/-3.3	0,1,4299	no	missense	KCNK6	NM_004823.1	89	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	306/314	38818018	1,13005	2203	4300	6503	SO:0001583	missense	9424	exon3			CCCACACCGACTA	AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.917C>T	chr19.hg19:g.38818018C>T	ENSP00000263372:p.Thr306Ile	41.0	0.0		40.0	21.0	NM_004823	Q9HB47	Missense_Mutation	SNP	ENST00000263372.3	hg19	CCDS12513.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.546587	0.45383	0.0	1.16E-4	ENSG00000099337	ENST00000263372	T	0.23348	1.91	5.36	1.99	0.26369	.	1.362410	0.04438	N	0.370303	T	0.24470	0.0593	L	0.40543	1.245	0.09310	N	1	B	0.26845	0.161	B	0.29176	0.099	T	0.33007	-0.9885	10	0.62326	D	0.03	.	6.2581	0.20885	0.1493:0.6874:0.0:0.1634	.	306	Q9Y257	KCNK6_HUMAN	I	306	ENSP00000263372:T306I	ENSP00000263372:T306I	T	+	2	0	KCNK6	43509858	0.000000	0.05858	0.000000	0.03702	0.203000	0.24098	0.485000	0.22324	0.238000	0.21222	0.561000	0.74099	ACC	.	.		0.662	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823		T	38818018	C	T	38818018	3	4	146	1	0	0	0	0	1	0	0	0	8079	507	18	3	927	3	KCNK6	19	38818018	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	2596353	38818018	20310965	105	22458										
ZNF320	162967	hgsc.bcm.edu	37	chr19	53384284	53384284	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	agacgtgaatcactccggaaAgccttgtcacaaaccttaca	7	12	2	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr19:53384284A>C	ENST00000595635.1	-	8	1596	c.1095T>G	c.(1093-1095)gcT>gcG	p.A365A	ZNF320_ENST00000391781.2_Silent_p.A365A|ZNF320_ENST00000597909.1_Intron|ZNF320_ENST00000600930.1_Intron	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	365					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		CACTCCGGAAAGCCTTGTCAC	0.403																																					p.A365A		Atlas-SNP	.											.	ZNF320	67	.	0			c.T1095G						.						128	122	124					19																	53384284		2203	4300	6503	SO:0001819	synonymous_variant	162967	exon4			CCGGAAAGCCTTG	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"Zinc fingers, C2H2-type", "-"	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.1095T>G	chr19.hg19:g.53384284A>C		60.0	0.0		97.0	41.0	NM_207333	Q8NDR6	Silent	SNP	ENST00000595635.1	hg19	CCDS33095.1																																																																																			.	.		0.403	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333		C	53384284	A	C	53384284	2	2	146	1	0	0	0	0	0	0	0	1	17854	59	3	5		5	ZNF320	19	53384284	Silent	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	14566266	53384284	5744699	106	22459										
JAG1	182	hgsc.bcm.edu	37	chr20	10654131	10654131	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	gcacagagcagggcgagcagGaggcttagggggcgcccgga	20	10	0	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr20:10654131G>T	ENST00000254958.5	-	1	563	c.48C>A	c.(46-48)ctC>ctA	p.L16L	RP11-103J8.1_ENST00000605292.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	16					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						GGGCGAGCAGGAGGCTTAGGG	0.771									Alagille Syndrome																												p.L16L		Atlas-SNP	.											.	JAG1	213	.	0			c.C48A						.						9	10	10					20																	10654131		1687	3222	4909	SO:0001819	synonymous_variant	182	exon1	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GAGCAGGAGGCTT	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"CD molecules"	6188	protein-coding gene	gene with protein product		601920	"Alagille syndrome"	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.48C>A	chr20.hg19:g.10654131G>T		48.0	0.0		73.0	26.0	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	hg19	CCDS13112.1																																																																																			.	.		0.771	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		T	10654131	G	T	10654131	2	4	146	1	0	0	0	0	0	0	0	1	7943	1161	41	3		3	JAG1	20	10654131	Silent	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10		10654131	52371389	107	22460										
C20orf111	51526	hgsc.bcm.edu	37	chr20	42826241	42826248	+	Frame_Shift_Del	DEL	GCTTTTGT	GCTTTTGT	-													0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	ccatcaggtgagtcagtctgGcttttgtgcttgagttgact					rs142485619		TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	GCTTTTGT	GCTTTTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr20:42826241_42826248delGCTTTTGT	ENST00000372970.2	-	6	503_510	c.323_330delACAAAAGC	c.(322-330)cacaaaagcfs	p.HKS108fs	OSER1_ENST00000255174.2_Frame_Shift_Del_p.HKS108fs			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	108					cellular response to hydrogen peroxide (GO:0070301)												AGTCAGTCTGGCTTTTGTGCTTGAGTTG	0.476																																					p.108_111del		Atlas-Indel,Pindel	.											.	C20orf111	28	.	0			c.324_331del						.																																			SO:0001589	frameshift_variant	51526	exon4			.	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"peroxide-inducible transcript 1", "oxidative stress-responsive 1"		"chromosome 20 open reading frame 111"	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.323_330delACAAAAGC	chr20.hg19:g.42826241_42826248delGCTTTTGT	ENSP00000362061:p.His108fs	87.0	0.0		109.0	37.0	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Frame_Shift_Del	DEL	ENST00000372970.2	hg19	CCDS13327.1																																																																																			.	.		0.476	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470		-	42826248	GCTTTTGT	-	42826241	7	5	146	1	0	1	0	1	0	0	0	0	2082	1194	42	0	552	0	C20orf111	20	42826241	Frame_Shift_Del	DEL	GCTTTTGT	TCGA-DD-A73E-01A-12D-A32G-10	32172110	42826241	20199279	108	22461										
HNF4A	3172	hgsc.bcm.edu	37	chr20	43036067	43036067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	aagacaagaggaaccagtgcCgctactgcaggctcaagaaa	11	10	1	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr20:43036067C>T	ENST00000316099.4	+	3	426	c.337C>T	c.(337-339)Cgc>Tgc	p.R113C	HNF4A_ENST00000316673.4_Missense_Mutation_p.R91C|MIR3646_ENST00000578301.1_RNA|HNF4A_ENST00000457232.1_Missense_Mutation_p.R91C|HNF4A_ENST00000415691.2_Missense_Mutation_p.R113C|HNF4A_ENST00000609795.1_Missense_Mutation_p.R91C|HNF4A_ENST00000443598.2_Missense_Mutation_p.R113C	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	113					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			GAACCAGTGCCGCTACTGCAG	0.597																																					p.R113C	Colon(79;2 1269 8820 14841 52347)	Atlas-SNP	.											Q8N8C9_HUMAN,NS,carcinoma,0,3	HNF4A	150	.	0			c.C337T						.						77	64	68					20																	43036067		2203	4300	6503	SO:0001583	missense	3172	exon3			CAGTGCCGCTACT	X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"Nuclear hormone receptors"	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.337C>T	chr20.hg19:g.43036067C>T	ENSP00000312987:p.Arg113Cys	75.0	0.0		76.0	31.0	NM_178849	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316099.4	hg19	CCDS13330.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.848147	0.71603	.	.	ENSG00000101076	ENST00000316673;ENST00000457232;ENST00000316099;ENST00000443598;ENST00000338692;ENST00000415691	D;D;D;D;D	0.96967	-4.19;-4.19;-4.19;-4.19;-4.19	5.69	2.7	0.31948	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.152113	0.64402	N	0.000012	D	0.97999	0.9341	M	0.93678	3.445	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.999;1.0;1.0;1.0	D	0.96230	0.9167	10	0.87932	D	0	.	4.812	0.13347	0.1246:0.6224:0.1204:0.1326	.	106;113;113;113;91;91;91	Q5QPB7;P41235;F1D8S2;P41235-3;F1D8T0;P41235-6;P41235-7	.;HNF4A_HUMAN;.;.;.;.;.	C	91;91;113;113;143;113	ENSP00000315180:R91C;ENSP00000396216:R91C;ENSP00000312987:R113C;ENSP00000410911:R113C;ENSP00000412111:R113C	ENSP00000312987:R113C	R	+	1	0	HNF4A	42469481	0.981000	0.34729	0.987000	0.45799	0.984000	0.73092	1.393000	0.34497	0.336000	0.23639	-0.163000	0.13421	CGC	.	.		0.597	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			T	43036067	C	T	43036067	3	4	146	1	0	0	0	0	1	0	0	0	7262	652	23	1	400	1	HNF4A	20	43036067	Missense_Mutation	SNP	C	TCGA-DD-A73E-01A-12D-A32G-10	209826	43036067	19989453	109	22462										
ZNFX1	57169	hgsc.bcm.edu	37	chr20	47865291	47865291	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	cttgactagcagaccaccatAcaggaggccttccacatgac	8	14	0	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr20:47865291A>G	ENST00000396105.1	-	14	4516	c.4270T>C	c.(4270-4272)Tat>Cat	p.Y1424H	ZNFX1_ENST00000371752.1_Missense_Mutation_p.Y1424H|ZNFX1_ENST00000371754.4_Intron	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1424							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			AGACCACCATACAGGAGGCCT	0.527																																					p.Y1424H		Atlas-SNP	.											.	ZNFX1	194	.	0			c.T4270C						.						87	85	85					20																	47865291		2203	4300	6503	SO:0001583	missense	57169	exon14			CACCATACAGGAG	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.4270T>C	chr20.hg19:g.47865291A>G	ENSP00000379412:p.Tyr1424His	48.0	0.0		53.0	28.0	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	hg19	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.536997	0.00942	.	.	ENSG00000124201	ENST00000371752;ENST00000396105	D;D	0.85861	-2.04;-2.04	6.06	2.63	0.31362	.	0.324362	0.29126	N	0.013075	T	0.71995	0.3406	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.53556	-0.8422	10	0.16896	T	0.51	-8.242	8.2977	0.31995	0.7708:0.0:0.2292:0.0	.	1424	Q9P2E3	ZNFX1_HUMAN	H	1424	ENSP00000360817:Y1424H;ENSP00000379412:Y1424H	ENSP00000360817:Y1424H	Y	-	1	0	ZNFX1	47298698	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.695000	0.25527	0.526000	0.28541	0.528000	0.53228	TAT	.	.		0.527	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		G	47865291	A	G	47865291	3	3	146	1	0	0	0	0	1	0	0	0	18220	391	14	2	1490	2	ZNFX1	20	47865291	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	4829224	47865291	15160229	110	22463										
SALL4	57167	hgsc.bcm.edu	37	chr20	50407317	50407317	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	taagactcggtggcaaatgaGacattcgttgggatcagtgg	14	6	1	2			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr20:50407317G>A	ENST00000217086.4	-	2	1816	c.1705C>T	c.(1705-1707)Ctc>Ttc	p.L569F	SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron|SALL4_ENST00000483130.1_5'Flank	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	569					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGGCAAATGAGACATTCGTTG	0.552																																					p.L569F		Atlas-SNP	.											.	SALL4	168	.	0			c.C1705T						.						134	114	121					20																	50407317		2203	4300	6503	SO:0001583	missense	57167	exon2			AAATGAGACATTC	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1705C>T	chr20.hg19:g.50407317G>A	ENSP00000217086:p.Leu569Phe	72.0	0.0		119.0	58.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	hg19	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.818592	0.32145	.	.	ENSG00000101115	ENST00000217086	T	0.07444	3.19	5.59	0.862	0.19056	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.370925	0.19948	N	0.102487	T	0.12135	0.0295	M	0.79475	2.455	0.80722	D	1	P	0.46706	0.883	P	0.46659	0.523	T	0.06516	-1.0822	10	0.54805	T	0.06	-37.1761	2.4308	0.04470	0.173:0.2437:0.4368:0.1465	.	569	Q9UJQ4	SALL4_HUMAN	F	569	ENSP00000217086:L569F	ENSP00000217086:L569F	L	-	1	0	SALL4	49840724	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.405000	0.34635	0.651000	0.30788	0.650000	0.86243	CTC	.	.		0.552	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			A	50407317	G	A	50407317	3	1	146	1	0	0	0	0	1	0	0	0	13828	942	33	3	1468	3	SALL4	20	50407317	Missense_Mutation	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10	2542026	50407317	12618203	111	22464										
SLC5A1	6523	hgsc.bcm.edu	37	chr22	32487698	32487698	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	cctcttcaccatggacatctAcgccaaggtccgcaagagag	9	14	3	1			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr22:32487698A>G	ENST00000266088.4	+	11	1479	c.1229A>G	c.(1228-1230)tAc>tGc	p.Y410C	SLC5A1_ENST00000543737.1_Missense_Mutation_p.Y283C	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	410					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	ATGGACATCTACGCCAAGGTC	0.542																																					p.Y410C		Atlas-SNP	.											.	SLC5A1	80	.	0			c.A1229G						.						130	109	116					22																	32487698		2203	4300	6503	SO:0001583	missense	6523	exon11			ACATCTACGCCAA		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"Solute carriers"	11036	protein-coding gene	gene with protein product	"sodium/glucose cotransporter 1"	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.1229A>G	chr22.hg19:g.32487698A>G	ENSP00000266088:p.Tyr410Cys	68.0	0.0		91.0	42.0	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Missense_Mutation	SNP	ENST00000266088.4	hg19	CCDS13902.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.524912	0.85600	.	.	ENSG00000100170	ENST00000266088;ENST00000543737	D;D	0.96232	-3.95;-3.95	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	D	0.98707	0.9566	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99709	1.1006	10	0.87932	D	0	.	15.5887	0.76506	1.0:0.0:0.0:0.0	.	410	P13866	SC5A1_HUMAN	C	410;283	ENSP00000266088:Y410C;ENSP00000444898:Y283C	ENSP00000266088:Y410C	Y	+	2	0	SLC5A1	30817698	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	6.118000	0.71583	2.275000	0.75901	0.528000	0.53228	TAC	.	.		0.542	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343		G	32487698	A	G	32487698	3	3	146	1	0	0	0	0	1	0	0	0	14676	391	14	2	1271	2	SLC5A1	22	32487698	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10		32487698	18816868	112	22465										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38119757	38119757	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tctcccaacagaaccactcaAcgagagaattccagaacatc	5	14	2	3	rs71322688|rs67890459|rs199535040|rs55745992	byFrequency	TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr22:38119757A>T	ENST00000406386.3	+	7	1449	c.1194A>T	c.(1192-1194)caA>caT	p.Q398H		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	398					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GAACCACTCAACGAGAGAATT	0.547																																					p.Q398H		Atlas-SNP	.											.	TRIOBP	262	.	0			c.A1194T						.						118	99	106					22																	38119757		1848	3567	5415	SO:0001583	missense	11078	exon7			CACTCAACGAGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1194A>T	chr22.hg19:g.38119757A>T	ENSP00000384312:p.Gln398His	0.0	0.0		28.0	13.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.346788	0.41599	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.34275	1.37	2.47	-1.65	0.08291	.	.	.	.	.	T	0.42177	0.1191	L	0.44542	1.39	0.09310	N	0.999998	D	0.54964	0.969	P	0.62382	0.901	T	0.32402	-0.9908	9	0.49607	T	0.09	.	6.5071	0.22202	0.6093:0.0:0.3907:0.0	.	398	Q9H2D6	TARA_HUMAN	H	398	ENSP00000384312:Q398H	ENSP00000384312:Q398H	Q	+	3	2	TRIOBP	36449703	.	.	0.034000	0.17996	0.078000	0.17371	.	.	-0.503000	0.06586	0.113000	0.15668	CAA	.	.		0.547	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			T	38119757	A	T	38119757	3	4	146	1	0	0	0	0	1	0	0	0	16568	40	2	4	1212	4	TRIOBP	22	38119757	Missense_Mutation	SNP	A	TCGA-DD-A73E-01A-12D-A32G-10	5632059	38119757	13184809	113	22466										
CSNK1E	1454	hgsc.bcm.edu	37	chr22	38690173	38690173	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	tgaggtctgaggaggagacgTtggcgggcgcacccctgtgc	18	10	1	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chr22:38690173T>C	ENST00000396832.1	-	9	1420	c.1160A>G	c.(1159-1161)aAc>aGc	p.N387S	CSNK1E_ENST00000403904.1_Missense_Mutation_p.N387S|CSNK1E_ENST00000400206.2_Missense_Mutation_p.N387S|CSNK1E_ENST00000359867.3_Missense_Mutation_p.N387S|CSNK1E_ENST00000498529.1_5'Flank	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	387					cellular protein localization (GO:0034613)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Melanoma(58;0.045)					GGAGGAGACGTTGGCGGGCGC	0.647																																					p.N387S	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)	Atlas-SNP	.											.	CSNK1E	143	.	0			c.A1160G						.						35	36	35					22																	38690173		2202	4300	6502	SO:0001583	missense	1454	exon9			GAGACGTTGGCGG		CCDS13970.1	22q13.1	2013-01-17			ENSG00000213923	ENSG00000213923			2453	protein-coding gene	gene with protein product		600863				7797465, 10535959	Standard	NM_001894		Approved	HCKIE, CKIE, CKIepsilon	uc003avk.3	P49674	OTTHUMG00000151135	ENST00000396832.1:c.1160A>G	chr22.hg19:g.38690173T>C	ENSP00000380044:p.Asn387Ser	43.0	0.0		51.0	25.0	NM_001894		Missense_Mutation	SNP	ENST00000396832.1	hg19	CCDS13970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.87|19.87	3.906593|3.906593	0.72868|0.72868	.|.	.|.	ENSG00000213923|ENSG00000213923	ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904|ENST00000366216	T;T;T;T|.	0.54675|.	0.56;0.56;0.56;0.56|.	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	0.083044|.	0.85682|.	D|.	0.000000|.	T|T	0.54759|0.54759	0.1878|0.1878	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	P|.	0.42203|.	0.773|.	B|.	0.35931|.	0.214|.	T|T	0.51560|0.51560	-0.8690|-0.8690	10|5	0.07644|.	T|.	0.81|.	.|.	15.942|15.942	0.79763|0.79763	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	387|.	P49674|.	KC1E_HUMAN|.	S|A	387|90	ENSP00000352929:N387S;ENSP00000380044:N387S;ENSP00000383067:N387S;ENSP00000384074:N387S|.	ENSP00000352929:N387S|.	N|T	-|-	2|1	0|0	CSNK1E|CSNK1E	37020119|37020119	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.198000|0.198000	0.23893|0.23893	7.685000|7.685000	0.84117|0.84117	2.162000|2.162000	0.67917|0.67917	0.533000|0.533000	0.62120|0.62120	AAC|ACG	.	.		0.647	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894		C	38690173	T	C	38690173	3	2	146	1	0	0	0	0	1	0	0	0	3955	1725	60	2	98	2	CSNK1E	22	38690173	Missense_Mutation	SNP	T	TCGA-DD-A73E-01A-12D-A32G-10	570416	38690173	12614393	114	22467										
GLRA2	2742	hgsc.bcm.edu	37	chrX	14550361	14550361	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.043859649122807	5	1	0.898443519802743	0.94336569579288	0.887873596040358	0.265734265734266	0.917767417767419	0	agagttaatgatgtgtttagGacggctttctgcaaagacca	11	6	1	3			TCGA-DD-A73E-01A-12D-A32G-10	TCGA-DD-A73E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7c7b2ed-0c9e-4c8e-a7f0-fb7d0f0b11ea	004c3f02-8bf1-4c76-9fb6-8a3c75687ce2	g.chrX:14550361G>C	ENST00000218075.4	+	2	599	c.69G>C	c.(67-69)agG>agC	p.R23S	GLRA2_ENST00000355020.4_Splice_Site_p.R23S|GLRA2_ENST00000443437.2_5'UTR	NM_002063.3	NP_002054.1	P23416	GLRA2_HUMAN	glycine receptor, alpha 2	23					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)|synapse assembly (GO:0007416)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(22)|ovary(1)|prostate(1)|skin(2)	37	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)|Lindane(DB00431)	ATGTGTTTAGGACGGCTTTCT	0.393																																					p.R23S		Atlas-SNP	.											.	GLRA2	140	.	0			c.G69C						.						133	115	121					X																	14550361		2203	4300	6503	SO:0001630	splice_region_variant	2742	exon3			GTTTAGGACGGCT		CCDS14160.1, CCDS48085.1, CCDS55371.1	Xp22.2	2012-02-07			ENSG00000101958	ENSG00000101958		"Ligand-gated ion channels / Glycine receptors"	4327	protein-coding gene	gene with protein product		305990		GLR			Standard	NM_002063		Approved		uc010nep.3	P23416	OTTHUMG00000021166	ENST00000218075.4:c.69-1G>C	chrX.hg19:g.14550361G>C		175.0	1.0		193.0	171.0	NM_001118885	A8K0J6|B2R6I8|B7Z4F5|J3KQ59|Q53YX7|Q6ICQ0|Q99862	Missense_Mutation	SNP	ENST00000218075.4	hg19	CCDS14160.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.20|12.20	1.865642|1.865642	0.32977|0.32977	.|.	.|.	ENSG00000101958|ENSG00000101958	ENST00000415367|ENST00000218075;ENST00000355020	T|T;T	0.54071|0.79454	0.59|-1.27;-1.27	4.87|4.87	4.87|4.87	0.63330|0.63330	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.58878|0.58878	0.2153|0.2153	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B|B;B	0.12630|0.25048	0.006|0.117;0.035	B|B;B	0.17722|0.16722	0.019|0.005;0.016	T|T	0.56703|0.56703	-0.7935|-0.7935	8|9	.|.	.|.	.|.	.|.	16.3031|16.3031	0.82832|0.82832	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	7|23;23	B7Z4E9|P23416;P23416-2	.|GLRA2_HUMAN;.	I|S	7|23	ENSP00000391606:M7I|ENSP00000218075:R23S;ENSP00000347123:R23S	.|.	M|R	+|+	3|3	0|2	GLRA2|GLRA2	14460282|14460282	1.000000|1.000000	0.71417|0.71417	0.916000|0.916000	0.36221|0.36221	0.653000|0.653000	0.38743|0.38743	5.348000|5.348000	0.66004|0.66004	2.134000|2.134000	0.65973|0.65973	0.594000|0.594000	0.82650|0.82650	ATG|AGG	.	.		0.393	GLRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055829.1		Missense_Mutation	C	14550361	G	C	14550361	5	2	146	1	0	0	0	0	0	0	1	0	6463	1188	41	4	75	4	GLRA2	23	14550361	Splice_Site	SNP	G	TCGA-DD-A73E-01A-12D-A32G-10		14550361	140720199	115	22468										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7723459	7723459	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tgtaacagcgccaaacaccgCatcatctcgcccaaggtgga	9	14	2	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr1:7723459C>T	ENST00000303635.7	+	9	1059	c.852C>T	c.(850-852)cgC>cgT	p.R284R	CAMTA1_ENST00000439411.2_Silent_p.R284R	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	284					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CCAAACACCGCATCATCTCGC	0.627			T	WWTR1	epitheliod hemangioendothelioma																																p.R284R		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.C852T						.						128	126	127					1																	7723459		2203	4300	6503	SO:0001819	synonymous_variant	23261	exon9			ACACCGCATCATC	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.852C>T	chr1.hg19:g.7723459C>T		126.0	0.0		135.0	44.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	hg19	CCDS30576.1																																																																																			.	.		0.627	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		T	7723459	C	T	7723459	2	4	147	1	0	0	0	0	0	0	0	1	2615	697	25	3		3	CAMTA1	1	7723459	Silent	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10		7723459	241527162	1	22469										
AADACL3	126767	hgsc.bcm.edu	37	chr1	12785194	12785194	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ttgattcctttttagttaccGcaagttacctaagcataagt	6	8	0	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr1:12785194G>A	ENST00000359318.5	+	4	489	c.284G>A	c.(283-285)cGc>cAc	p.R95H	AADACL3_ENST00000332530.3_Missense_Mutation_p.R25H	NM_001103170.1	NP_001096640.1	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3	95							hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	15	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TTTAGTTACCGCAAGTTACCT	0.463																																					p.R95H		Atlas-SNP	.											AADACL3_ENST00000359318,colon,carcinoma,0,2	AADACL3	84	.	0			c.G284A						.						109	113	112					1																	12785194		1966	4154	6120	SO:0001583	missense	126767	exon4			GTTACCGCAAGTT		CCDS41253.1	1p36.21	2014-07-17			ENSG00000188984	ENSG00000188984			32037	protein-coding gene	gene with protein product							Standard	XM_006710337		Approved	OTTHUMG00000001887	uc009vnn.1	Q5VUY0	OTTHUMG00000001887	ENST00000359318.5:c.284G>A	chr1.hg19:g.12785194G>A	ENSP00000352268:p.Arg95His	114.0	0.0		136.0	36.0	NM_001103170	B3KXR9|Q5VUY1	Missense_Mutation	SNP	ENST00000359318.5	hg19	CCDS41253.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.484947	0.63962	.	.	ENSG00000188984	ENST00000332530;ENST00000359318	T;T	0.22539	1.95;1.95	5.31	2.36	0.29203	Alpha/beta hydrolase fold-3 (1);	0.053408	0.64402	N	0.000001	T	0.58878	0.2153	H	0.99130	4.44	0.48571	D	0.999671	D;D	0.76494	0.999;0.999	D;P	0.66602	0.945;0.867	T	0.65100	-0.6250	10	0.72032	D	0.01	-15.1905	8.3834	0.32486	0.1432:0.1274:0.7294:0.0	.	95;25	Q5VUY0;Q5VUY0-2	ADCL3_HUMAN;.	H	25;95	ENSP00000333352:R25H;ENSP00000352268:R95H	ENSP00000333352:R25H	R	+	2	0	AADACL3	12707781	0.999000	0.42202	0.003000	0.11579	0.021000	0.10359	3.128000	0.50492	0.225000	0.20959	0.484000	0.47621	CGC	.	.		0.463	AADACL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005324.2	NM_001103170		A	12785194	G	A	12785194	3	1	147	1	0	0	0	0	1	0	0	0	12	1087	38	1	302	1	AADACL3	1	12785194	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	5061735	12785194	236465427	2	22470										
CAMK2N1	55450	hgsc.bcm.edu	37	chr1	20811831	20811831	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	acgtcgccgccgtcgccgtaGgggctcagcttctcgtcgcc	13	17	2	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr1:20811831G>T	ENST00000375078.3	-	1	882	c.42C>A	c.(40-42)ccC>ccA	p.P14P	CAMK2N1_ENST00000489020.1_5'Flank	NM_018584.5	NP_061054.2	Q7Z7J9	CK2N1_HUMAN	calcium/calmodulin-dependent protein kinase II inhibitor 1	14						cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	calcium-dependent protein kinase inhibitor activity (GO:0008427)			lung(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.0013)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000132)|Kidney(64;0.00016)|GBM - Glioblastoma multiforme(114;0.00116)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.195)		CGTCGCCGTAGGGGCTCAGCT	0.741																																					p.P14P		Atlas-SNP	.											.	CAMK2N1	7	.	0			c.C42A						.						12	14	13					1																	20811831		2178	4272	6450	SO:0001819	synonymous_variant	55450	exon1			GCCGTAGGGGCTC	AY204901	CCDS207.1	1p36.12	2008-02-05			ENSG00000162545	ENSG00000162545			24190	protein-coding gene	gene with protein product		614986				12477932	Standard	NM_018584		Approved	CaMKIINalpha	uc001bdh.3	Q7Z7J9	OTTHUMG00000002837	ENST00000375078.3:c.42C>A	chr1.hg19:g.20811831G>T		42.0	0.0		43.0	14.0	NM_018584		Silent	SNP	ENST00000375078.3	hg19	CCDS207.1																																																																																			.	.		0.741	CAMK2N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007949.1	NM_018584		T	20811831	G	T	20811831	2	4	147	1	0	0	0	0	0	0	0	1	2605	987	35	3		3	CAMK2N1	1	20811831	Silent	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	8026637	20811831	228438790	3	22471										
USP1	7398	hgsc.bcm.edu	37	chr1	62916161	62916161	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	accaaatgtgtgaaataggtAagccagaaccattgaatgag	10	6	0	4			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr1:62916161A>C	ENST00000339950.4	+	9	2682	c.1867A>C	c.(1867-1869)Aag>Cag	p.K623Q	USP1_ENST00000371146.1_Missense_Mutation_p.K623Q	NM_003368.4	NP_003359.3	O94782	UBP1_HUMAN	ubiquitin specific peptidase 1	623	USP.				DNA repair (GO:0006281)|monoubiquitinated protein deubiquitination (GO:0035520)|protein deubiquitination (GO:0016579)|regulation of DNA repair (GO:0006282)|response to UV (GO:0009411)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	19		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		TGAAATAGGTAAGCCAGAACC	0.383																																					p.K623Q	Ovarian(122;1846 2315 3982 19504)	Atlas-SNP	.											.	USP1	51	.	0			c.A1867C						.						77	71	73					1																	62916161		2203	4300	6503	SO:0001583	missense	7398	exon9			ATAGGTAAGCCAG		CCDS621.1	1p31.3	2008-05-14	2005-08-08		ENSG00000162607	ENSG00000162607		"Ubiquitin-specific peptidases"	12607	protein-coding gene	gene with protein product		603478	"ubiquitin specific protease 1"			12838346	Standard	NM_003368		Approved		uc001dak.2	O94782	OTTHUMG00000008972	ENST00000339950.4:c.1867A>C	chr1.hg19:g.62916161A>C	ENSP00000343526:p.Lys623Gln	114.0	0.0		113.0	38.0	NM_001017415	A0PJ95|D3DQ57|Q05BX7|Q59H66|Q9UFR0|Q9UNJ3	Missense_Mutation	SNP	ENST00000339950.4	hg19	CCDS621.1	.	.	.	.	.	.	.	.	.	.	A	7.066	0.567283	0.13560	.	.	ENSG00000162607	ENST00000371146;ENST00000339950	T;T	0.20069	2.1;2.1	5.64	5.64	0.86602	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (1);	0.298608	0.39615	N	0.001309	T	0.12008	0.0292	N	0.19112	0.55	0.29623	N	0.846055	P	0.34934	0.476	B	0.29267	0.1	T	0.13388	-1.0511	10	0.19147	T	0.46	-16.413	11.7424	0.51801	0.8682:0.0:0.0:0.1318	.	623	O94782	UBP1_HUMAN	Q	623	ENSP00000360188:K623Q;ENSP00000343526:K623Q	ENSP00000343526:K623Q	K	+	1	0	USP1	62688749	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	2.977000	0.49297	2.367000	0.80283	0.528000	0.53228	AAG	.	.		0.383	USP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024881.1	NM_001017415		C	62916161	A	C	62916161	3	2	147	1	0	0	0	0	1	0	0	0	17055	363	13	5	1897	5	USP1	1	62916161	Missense_Mutation	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10	42104330	62916161	186334460	4	22472										
RPE65	6121	hgsc.bcm.edu	37	chr1	68897225	68897225	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cactgcacagaattgcagtgGcagttgtattggggagcgtg	15	7	0	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr1:68897225G>A	ENST00000262340.5	-	11	1225	c.1172C>T	c.(1171-1173)gCc>gTc	p.A391V		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	391					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						AATTGCAGTGGCAGTTGTATT	0.473																																					p.A391V		Atlas-SNP	.											.	RPE65	87	.	0			c.C1172T						.						59	63	61					1																	68897225		2203	4300	6503	SO:0001583	missense	6121	exon11			GCAGTGGCAGTTG	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.1172C>T	chr1.hg19:g.68897225G>A	ENSP00000262340:p.Ala391Val	80.0	0.0		89.0	29.0	NM_000329	A8K1L0|Q5T9U3	Missense_Mutation	SNP	ENST00000262340.5	hg19	CCDS643.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.225860	0.58668	.	.	ENSG00000116745	ENST00000262340	D	0.95788	-3.81	5.14	4.21	0.49690	.	0.093292	0.64402	D	0.000001	D	0.97455	0.9167	M	0.91300	3.195	0.80722	D	1	D	0.76494	0.999	D	0.65874	0.939	D	0.97214	0.9873	10	0.45353	T	0.12	1.2949	14.8555	0.70332	0.0:0.0:0.8552:0.1448	.	391	Q16518	RPE65_HUMAN	V	391	ENSP00000262340:A391V	ENSP00000262340:A391V	A	-	2	0	RPE65	68669813	1.000000	0.71417	1.000000	0.80357	0.521000	0.34408	9.300000	0.96151	1.138000	0.42230	0.561000	0.74099	GCC	.	.		0.473	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		A	68897225	G	A	68897225	3	1	147	1	0	0	0	0	1	0	0	0	13560	1203	42	3	445	3	RPE65	1	68897225	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	5981064	68897225	180353396	5	22473										
GJA8	2703	hgsc.bcm.edu	37	chr1	147380859	147380859	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cactccattgctgtctcctcCatccagaaagccaagggcta	7	15	1	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr1:147380859C>T	ENST00000369235.1	+	1	777	c.777C>T	c.(775-777)tcC>tcT	p.S259S	GJA8_ENST00000240986.4_Silent_p.S259S			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	259					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					CTGTCTCCTCCATCCAGAAAG	0.562																																					p.S259S	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											.	GJA8	108	.	0			c.C777T						.						50	52	52					1																	147380859		2203	4300	6503	SO:0001819	synonymous_variant	2703	exon2			CTCCTCCATCCAG	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.777C>T	chr1.hg19:g.147380859C>T		72.0	0.0		110.0	39.0	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Silent	SNP	ENST00000369235.1	hg19	CCDS30834.1																																																																																			.	.		0.562	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		T	147380859	C	T	147380859	2	4	147	1	0	0	0	0	0	0	0	1	6413	581	21	3		3	GJA8	1	147380859	Silent	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	78483634	147380859	101869762	6	22474										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204394000	204394000	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tcacaaggtgccatgacttcGagatcccagggcgaaccagc	11	13	1	2	rs376434764		TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr1:204394000G>A	ENST00000367187.3	-	34	5441	c.4885C>T	c.(4885-4887)Cga>Tga	p.R1629*	RP11-739N20.2_ENST00000443515.1_RNA|PIK3C2B_ENST00000424712.2_Nonsense_Mutation_p.R1601*	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1629					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CCATGACTTCGAGATCCCAGG	0.637																																					p.R1629X		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C4885T						.	G	stop/ARG	0,4406		0,0,2203	60	56	57		4885	4.6	1	1		57	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	PIK3C2B	NM_002646.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		1629/1635	204394000	1,13005	2203	4300	6503	SO:0001587	stop_gained	5287	exon34			GACTTCGAGATCC	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4885C>T	chr1.hg19:g.204394000G>A	ENSP00000356155:p.Arg1629*	106.0	0.0		117.0	50.0	NM_002646	O95666|Q5SW99	Nonsense_Mutation	SNP	ENST00000367187.3	hg19	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	G	47	13.369480	0.99738	0.0	1.16E-4	ENSG00000133056	ENST00000367187;ENST00000424712	.	.	.	5.46	4.55	0.56014	.	0.278501	0.32563	N	0.005934	.	.	.	.	.	.	0.38154	D	0.938836	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	9.7339	0.40376	0.074:0.0:0.7862:0.1398	.	.	.	.	X	1629;1601	.	ENSP00000356155:R1629X	R	-	1	2	PIK3C2B	202660623	1.000000	0.71417	0.963000	0.40424	0.531000	0.34715	2.863000	0.48396	1.315000	0.45114	0.655000	0.94253	CGA	.	.		0.637	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		A	204394000	G	A	204394000	4	1	147	1	0	0	0	0	0	1	0	0	11919	1066	37	1	23	1	PIK3C2B	1	204394000	Nonsense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	57013141	204394000	44856621	7	22475										
OR14A16	284532	hgsc.bcm.edu	37	chr1	247978151	247978151	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	acatccccagagccacctttAtggccttgtttctcaaactg	6	14	1	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr1:247978151A>G	ENST00000357627.1	-	1	880	c.881T>C	c.(880-882)aTa>aCa	p.I294T		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	294						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(32)|skin(2)|stomach(1)	45						AGCCACCTTTATGGCCTTGTT	0.373																																					p.I294T	Ovarian(112;180 1586 15073 21914 33526)	Atlas-SNP	.											.	OR14A16	90	.	0			c.T881C						.						61	59	60					1																	247978151		2203	4300	6503	SO:0001583	missense	284532	exon1			ACCTTTATGGCCT	BK004366	CCDS31097.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000196772	ENSG00000196772		"GPCR / Class A : Olfactory receptors"	15022	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily AT, member 1"	OR5AT1			Standard	NM_001001966		Approved		uc001idm.1	Q8NHC5	OTTHUMG00000040199	ENST00000357627.1:c.881T>C	chr1.hg19:g.247978151A>G	ENSP00000350248:p.Ile294Thr	139.0	0.0		150.0	31.0	NM_001001966	Q6IF96	Missense_Mutation	SNP	ENST00000357627.1	hg19	CCDS31097.1	.	.	.	.	.	.	.	.	.	.	A	10.63	1.405587	0.25378	.	.	ENSG00000196772	ENST00000357627	T	0.39406	1.08	3.69	3.69	0.42338	.	0.526499	0.16954	U	0.192742	T	0.48732	0.1516	M	0.87971	2.92	0.25068	N	0.991012	P	0.34587	0.458	B	0.32677	0.15	T	0.53457	-0.8436	10	0.87932	D	0	.	12.3272	0.55018	1.0:0.0:0.0:0.0	.	294	Q8NHC5	O14AG_HUMAN	T	294	ENSP00000350248:I294T	ENSP00000350248:I294T	I	-	2	0	OR14A16	246044774	0.271000	0.24162	0.135000	0.22099	0.303000	0.27691	5.962000	0.70364	1.570000	0.49709	0.486000	0.48141	ATA	.	.		0.373	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1	NM_001001966		G	247978151	A	G	247978151	3	3	147	1	0	0	0	0	1	0	0	0	10954	449	16	2	52	2	OR14A16	1	247978151	Missense_Mutation	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10	43584151	247978151	1272470	8	22476										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1926429	1926429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ccgagtagtttctgtccggcGtccttccggggaagtcctct	12	13	2	0	rs573013583		TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr2:1926429G>A	ENST00000399161.2	-	10	1859	c.1112C>T	c.(1111-1113)aCg>aTg	p.T371M	MYT1L_ENST00000428368.2_Missense_Mutation_p.T371M	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	371					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TCTGTCCGGCGTCCTTCCGGG	0.602													G|||	1	0.000199681	0	0	5008	,	,		19981	0		0.001	False		,,,				2504	0				p.T371M		Atlas-SNP	.											.	MYT1L	241	.	0			c.C1112T						.						35	39	37					2																	1926429		2097	4221	6318	SO:0001583	missense	23040	exon10			TCCGGCGTCCTTC	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.1112C>T	chr2.hg19:g.1926429G>A	ENSP00000382114:p.Thr371Met	84.0	0.0		98.0	35.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	G	14.97	2.694323	0.48202	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.48522	0.81;0.81	5.86	5.86	0.93980	.	0.120915	0.53938	D	0.000051	T	0.34861	0.0912	L	0.27053	0.805	0.48185	D	0.999605	P;P	0.39480	0.546;0.675	B;B	0.25140	0.026;0.058	T	0.29882	-0.9997	10	0.56958	D	0.05	-36.759	20.1802	0.98196	0.0:0.0:1.0:0.0	.	371;371	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	M	371;319;371	ENSP00000382114:T371M;ENSP00000396103:T371M	ENSP00000295067:T319M	T	-	2	0	MYT1L	1905436	1.000000	0.71417	0.572000	0.28498	0.945000	0.59286	5.870000	0.69620	2.777000	0.95525	0.655000	0.94253	ACG	.	.		0.602	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1926429	G	A	1926429	3	1	147	1	0	0	0	0	1	0	0	0	10116	1145	40	1	2506	1	MYT1L	2	1926429	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10		1926429	241272944	9	22477										
MAP4K3	8491	hgsc.bcm.edu	37	chr2	39481600	39481600	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	aatttacttacctcattagaTctaaaacttctaccttgcat	2	10	3	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr2:39481600T>A	ENST00000263881.3	-	32	2856	c.2532A>T	c.(2530-2532)agA>agT	p.R844S	MAP4K3_ENST00000437545.1_Missense_Mutation_p.R760S|MAP4K3_ENST00000341681.5_Missense_Mutation_p.R823S|MAP4K3_ENST00000536018.1_Missense_Mutation_p.R397S	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	844	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				CCTCATTAGATCTAAAACTTC	0.358																																					p.R844S		Atlas-SNP	.											.	MAP4K3	109	.	0			c.A2532T						.						181	167	172					2																	39481600		2203	4300	6503	SO:0001583	missense	8491	exon32			ATTAGATCTAAAA	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.2532A>T	chr2.hg19:g.39481600T>A	ENSP00000263881:p.Arg844Ser	90.0	0.0		88.0	33.0	NM_003618	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	hg19	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.331919	0.41297	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681;ENST00000542094;ENST00000536018	T;T;T;T	0.04654	3.58;3.58;3.58;3.58	4.63	2.25	0.28309	Citron-like (3);	0.045134	0.85682	D	0.000000	T	0.04815	0.0130	L	0.42245	1.32	0.48975	D	0.999732	B;B	0.32893	0.115;0.389	B;B	0.32980	0.043;0.156	T	0.48514	-0.9029	10	0.33940	T	0.23	.	7.9665	0.30102	0.0:0.2407:0.0:0.7593	.	823;844	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	S	844;760;823;140;397	ENSP00000263881:R844S;ENSP00000416958:R760S;ENSP00000345434:R823S;ENSP00000440580:R397S	ENSP00000263881:R844S	R	-	3	2	MAP4K3	39335104	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.132000	0.31418	0.314000	0.23086	0.455000	0.32223	AGA	.	.		0.358	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618		A	39481600	T	A	39481600	3	1	147	1	0	0	0	0	1	0	0	0	9270	1432	50	4	164	4	MAP4K3	2	39481600	Missense_Mutation	SNP	T	TCGA-DD-A73F-01A-11D-A32G-10	37555171	39481600	203717773	10	22478										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73799982	73799982	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	atagcagaggggaacgaagtGtgaaggaatggagtggtaga	18	2	0	3			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr2:73799982G>A	ENST00000264448.6	+	16	11086	c.10975G>A	c.(10975-10977)Gtg>Atg	p.V3659M	ALMS1_ENST00000409009.1_Missense_Mutation_p.V3617M	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3659					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GGAACGAAGTGTGAAGGAATG	0.418																																					p.V3659M		Atlas-SNP	.											.	ALMS1	384	.	0			c.G10975A						.						137	132	133					2																	73799982		1897	4117	6014	SO:0001583	missense	7840	exon16			CGAAGTGTGAAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.10975G>A	chr2.hg19:g.73799982G>A	ENSP00000264448:p.Val3659Met	98.0	0.0		150.0	37.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	2.290	-0.362760	0.05103	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.06218	3.33;3.33	4.75	-5.2	0.02823	.	2.240310	0.01860	N	0.036529	T	0.04497	0.0123	L	0.29908	0.895	0.09310	N	1	B;B;B	0.22146	0.026;0.065;0.012	B;B;B	0.19148	0.022;0.022;0.024	T	0.32666	-0.9898	10	0.49607	T	0.09	.	0.9696	0.01413	0.3828:0.1133:0.282:0.2218	.	3659;3617;3659	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	M	3617;3659	ENSP00000386627:V3617M;ENSP00000264448:V3659M	ENSP00000264448:V3659M	V	+	1	0	ALMS1	73653490	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.039000	0.12124	-1.332000	0.02249	-0.137000	0.14449	GTG	.	.		0.418	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73799982	G	A	73799982	3	1	147	1	0	0	0	0	1	0	0	0	535	1377	48	3	11037	3	ALMS1	2	73799982	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	34318382	73799982	169399391	11	22479										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160840493	160840493	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	aattctcttcctcaatatggGcaaagcttgcaagatgagct	8	9	2	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr2:160840493G>T	ENST00000283243.7	-	13	2335	c.2129C>A	c.(2128-2130)gCc>gAc	p.A710D	PLA2R1_ENST00000392771.1_Missense_Mutation_p.A710D	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	710	C-type lectin 4. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CTCAATATGGGCAAAGCTTGC	0.313																																					p.A710D		Atlas-SNP	.											.	PLA2R1	153	.	0			c.C2129A						.						58	61	60					2																	160840493		2202	4300	6502	SO:0001583	missense	22925	exon13			ATATGGGCAAAGC	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.2129C>A	chr2.hg19:g.160840493G>T	ENSP00000283243:p.Ala710Asp	195.0	0.0		205.0	69.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	hg19	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.609786	0.66558	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.15487	2.42;2.42	5.68	3.83	0.44106	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.216367	0.44097	D	0.000495	T	0.13756	0.0333	N	0.08118	0	0.35759	D	0.820054	P;P;P	0.52061	0.578;0.95;0.916	P;P;P	0.51701	0.491;0.653;0.677	T	0.14254	-1.0479	10	0.11794	T	0.64	.	15.5049	0.75731	0.0:0.2619:0.7381:0.0	.	710;710;710	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	D	710	ENSP00000283243:A710D;ENSP00000376524:A710D	ENSP00000283243:A710D	A	-	2	0	PLA2R1	160548739	0.991000	0.36638	0.995000	0.50966	0.990000	0.78478	1.540000	0.36115	0.825000	0.34637	0.650000	0.86243	GCC	.	.		0.313	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			T	160840493	G	T	160840493	3	4	147	1	0	0	0	0	1	0	0	0	12019	1203	42	3	2342	3	PLA2R1	2	160840493	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	87040511	160840493	82358880	12	22480										
CEP70	80321	hgsc.bcm.edu	37	chr3	138289885	138289885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cattttctcacctaagctgtTgattagtttctataagctcc	5	10	2	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr3:138289885T>C	ENST00000264982.3	-	5	541	c.275A>G	c.(274-276)cAa>cGa	p.Q92R	CEP70_ENST00000484888.1_Missense_Mutation_p.Q92R|CEP70_ENST00000542237.1_Missense_Mutation_p.Q72R|CEP70_ENST00000464035.1_Missense_Mutation_p.Q92R|CEP70_ENST00000489254.1_Intron|CEP70_ENST00000478673.1_5'UTR|CEP70_ENST00000481834.1_Missense_Mutation_p.Q92R	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	92					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						CCTAAGCTGTTGATTAGTTTC	0.318																																					p.Q92R		Atlas-SNP	.											.	CEP70	51	.	0			c.A275G						.						89	89	89					3																	138289885		2202	4296	6498	SO:0001583	missense	80321	exon5			AGCTGTTGATTAG	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.275A>G	chr3.hg19:g.138289885T>C	ENSP00000264982:p.Gln92Arg	182.0	0.0		210.0	61.0	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	hg19	CCDS3102.1	.	.	.	.	.	.	.	.	.	.	T	4.858	0.159569	0.09287	.	.	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000484888;ENST00000474781;ENST00000481834;ENST00000468900;ENST00000462419;ENST00000464035;ENST00000470159	T;T;T;T;T;T;T;T	0.42513	1.58;1.58;1.58;1.58;1.57;0.99;0.99;0.97	5.06	5.06	0.68205	.	0.278002	0.34603	N	0.003835	T	0.31979	0.0814	L	0.40543	1.245	0.27915	N	0.938477	B;B;B	0.27416	0.078;0.002;0.178	B;B;B	0.28011	0.037;0.007;0.085	T	0.17440	-1.0369	10	0.14656	T	0.56	-2.1262	11.1119	0.48237	0.0:0.0:0.0:1.0	.	72;92;92	F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;CEP70_HUMAN	R	92;72;92;74;92;71;72;92;92	ENSP00000264982:Q92R;ENSP00000444128:Q72R;ENSP00000419231:Q92R;ENSP00000419833:Q74R;ENSP00000417465:Q92R;ENSP00000418131:Q71R;ENSP00000417819:Q72R;ENSP00000419743:Q92R	ENSP00000264982:Q92R	Q	-	2	0	CEP70	139772575	0.973000	0.33851	0.972000	0.41901	0.253000	0.25986	1.946000	0.40283	2.114000	0.64651	0.533000	0.62120	CAA	.	.		0.318	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491		C	138289885	T	C	138289885	3	2	147	1	0	0	0	0	1	0	0	0	3261	1812	63	2	1574	2	CEP70	3	138289885	Missense_Mutation	SNP	T	TCGA-DD-A73F-01A-11D-A32G-10		138289885	59732545	13	22481										
C3orf72	401089	hgsc.bcm.edu	37	chr3	138669208	138669208	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	gctgctctgaggcaggcagcGcttcgctagaaccactcagc	12	14	2	2	rs530645680		TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr3:138669208G>A	ENST00000383165.3	+	3	453	c.322G>A	c.(322-324)Gct>Act	p.A108T		NM_001040061.2	NP_001035150.1	Q6ZUU3	FOXNB_HUMAN		108										large_intestine(1)|lung(3)	4						GGCAGGCAGCGCTTCGCTAGA	0.706													G|||	1	0.000199681	0	0	5008	,	,		12866	0		0	False		,,,				2504	0.001				p.A108T		Atlas-SNP	.											.	C3orf72	13	.	0			c.G322A						.						12	17	16					3																	138669208		1820	4050	5870	SO:0001583	missense	401089	exon3			GGCAGCGCTTCGC																												ENST00000383165.3:c.322G>A	chr3.hg19:g.138669208G>A	ENSP00000372651:p.Ala108Thr	51.0	0.0		76.0	26.0	NM_001040061	A6NGX0	Missense_Mutation	SNP	ENST00000383165.3	hg19	CCDS43155.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.856431	0.51376	.	.	ENSG00000206262	ENST00000383165	.	.	.	2.91	0.903	0.19296	.	.	.	.	.	T	0.24392	0.0591	N	0.19112	0.55	0.09310	N	1	D	0.61080	0.989	P	0.50825	0.651	T	0.11494	-1.0585	8	0.87932	D	0	.	5.0631	0.14568	0.0:0.2371:0.5195:0.2434	.	108	Q6ZUU3	CC072_HUMAN	T	108	.	ENSP00000372651:A108T	A	+	1	0	C3orf72	140151898	0.000000	0.05858	0.000000	0.03702	0.440000	0.31957	0.500000	0.22562	0.210000	0.20664	0.555000	0.69702	GCT	.	.		0.706	C3orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357986.1			A	138669208	G	A	138669208	3	1	147	1	0	0	0	0	1	0	0	0	2246	1087	38	1	332	1	C3orf72	3	138669208	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	379323	138669208	59353222	14	22482										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87701601	87701601	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	caaagaggtctgctgtttcaGctccaaagtcaaccaaaggc	9	11	3	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr4:87701601G>A	ENST00000411767.2	+	36	6001	c.5938G>A	c.(5938-5940)Gct>Act	p.A1980T	PTPN13_ENST00000511467.1_Missense_Mutation_p.A1985T|PTPN13_ENST00000316707.6_Missense_Mutation_p.A1789T|PTPN13_ENST00000436978.1_Missense_Mutation_p.A1985T|PTPN13_ENST00000427191.2_Missense_Mutation_p.A1961T			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1980					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TGCTGTTTCAGCTCCAAAGTC	0.403																																					p.A1985T		Atlas-SNP	.											.	PTPN13	203	.	0			c.G5953A						.						70	69	69					4																	87701601		1889	4113	6002	SO:0001583	missense	5783	exon36			GTTTCAGCTCCAA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.5938G>A	chr4.hg19:g.87701601G>A	ENSP00000407249:p.Ala1980Thr	74.0	0.0		84.0	34.0	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	5.117	0.207209	0.09704	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.51071	0.72;0.75;0.82;0.72;0.75	5.16	-0.0944	0.13645	.	1.282590	0.05795	N	0.611054	T	0.26159	0.0638	N	0.19112	0.55	0.18873	N	0.999985	B;B;B;B	0.06786	0.0;0.001;0.0;0.001	B;B;B;B	0.09377	0.001;0.004;0.002;0.004	T	0.14839	-1.0458	10	0.07813	T	0.8	.	3.3326	0.07089	0.5:0.0:0.3255:0.1746	.	1789;1961;1980;1985	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	T	1961;1985;1789;1980;1985;1929	ENSP00000408368:A1961T;ENSP00000394794:A1985T;ENSP00000322675:A1789T;ENSP00000407249:A1980T;ENSP00000426626:A1985T	ENSP00000322675:A1789T	A	+	1	0	PTPN13	87920625	0.513000	0.26194	0.073000	0.20177	0.842000	0.47809	0.544000	0.23253	-0.242000	0.09667	-0.482000	0.04802	GCT	.	.		0.403	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87701601	G	A	87701601	3	1	147	1	0	0	0	0	1	0	0	0	12795	971	34	3	6091	3	PTPN13	4	87701601	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10		87701601	103452675	15	22483										
NDST4	64579	hgsc.bcm.edu	37	chr4	115773896	115773896	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tttacctgttttttgtggacCaattactagaaattttggta	7	5	0	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr4:115773896C>G	ENST00000264363.2	-	8	2479	c.1801G>C	c.(1801-1803)Ggt>Cgt	p.G601R		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	601	Heparan sulfate N-sulfotransferase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		TTTTGTGGACCAATTACTAGA	0.308																																					p.G601R		Atlas-SNP	.											.	NDST4	193	.	0			c.G1801C						.						134	130	132					4																	115773896		2203	4299	6502	SO:0001583	missense	64579	exon8			GTGGACCAATTAC	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.1801G>C	chr4.hg19:g.115773896C>G	ENSP00000264363:p.Gly601Arg	132.0	0.0		133.0	40.0	NM_022569	Q2KHM8	Missense_Mutation	SNP	ENST00000264363.2	hg19	CCDS3706.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.770039	0.90020	.	.	ENSG00000138653	ENST00000264363	T	0.80909	-1.43	5.58	5.58	0.84498	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.93719	0.7993	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95404	0.8492	10	0.87932	D	0	.	19.5672	0.95398	0.0:1.0:0.0:0.0	.	601	Q9H3R1	NDST4_HUMAN	R	601	ENSP00000264363:G601R	ENSP00000264363:G601R	G	-	1	0	NDST4	115993345	1.000000	0.71417	0.992000	0.48379	0.979000	0.70002	7.476000	0.81055	2.616000	0.88540	0.655000	0.94253	GGT	.	.		0.308	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		G	115773896	C	G	115773896	3	3	147	1	0	0	0	0	1	0	0	0	10267	594	21	4	845	4	NDST4	4	115773896	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	28072295	115773896	75380380	16	22484										
IRX1	79192	hgsc.bcm.edu	37	chr5	3599546	3599546	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ccaccaagggcgagaagatcAtgctggccatcatcaccaag	10	13	3	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr5:3599546A>G	ENST00000302006.3	+	2	536	c.484A>G	c.(484-486)Atg>Gtg	p.M162V	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	162					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CGAGAAGATCATGCTGGCCAT	0.637																																					p.M162V		Atlas-SNP	.											.	IRX1	106	.	0			c.A484G						.						166	129	141					5																	3599546		2203	4300	6503	SO:0001583	missense	79192	exon2			AAGATCATGCTGG	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.484A>G	chr5.hg19:g.3599546A>G	ENSP00000305244:p.Met162Val	123.0	0.0		117.0	43.0	NM_024337	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	hg19	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	A	19.71	3.879169	0.72294	.	.	ENSG00000170549	ENST00000302006	D	0.91237	-2.81	4.81	4.81	0.61882	Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1);	0.080102	0.85682	D	0.000000	D	0.92482	0.7613	L	0.43757	1.38	0.80722	D	1	D	0.59357	0.985	D	0.64506	0.926	D	0.93328	0.6698	10	0.87932	D	0	.	14.0584	0.64784	1.0:0.0:0.0:0.0	.	162	P78414	IRX1_HUMAN	V	162	ENSP00000305244:M162V	ENSP00000305244:M162V	M	+	1	0	IRX1	3652546	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.018000	0.93657	1.765000	0.52091	0.533000	0.62120	ATG	.	.		0.637	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		G	3599546	A	G	3599546	3	3	147	1	0	0	0	0	1	0	0	0	7852	217	8	2	490	2	IRX1	5	3599546	Missense_Mutation	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10		3599546	177315714	17	22485										
RANBP3L	202151	hgsc.bcm.edu	37	chr5	36253830	36253830	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ttgtggtttgctctttgaatCttcatttgggcccagagttt	10	7	3	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr5:36253830C>A	ENST00000296604.3	-	12	1571	c.1086G>T	c.(1084-1086)aaG>aaT	p.K362N	RANBP3L_ENST00000502994.1_Missense_Mutation_p.K387N	NM_145000.3	NP_659437.3	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like	362	RanBD1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				intracellular transport (GO:0046907)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	16	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			CTCTTTGAATCTTCATTTGGG	0.383																																					p.K387N		Atlas-SNP	.											.	RANBP3L	41	.	0			c.G1161T						.						182	166	172					5																	36253830		2203	4299	6502	SO:0001583	missense	202151	exon13			TTGAATCTTCATT	BC047660	CCDS3918.1, CCDS54843.1	5p13.2	2008-02-05			ENSG00000164188	ENSG00000164188			26353	protein-coding gene	gene with protein product						12477932	Standard	NM_145000		Approved	FLJ25422	uc011cow.2	Q86VV4	OTTHUMG00000131110	ENST00000296604.3:c.1086G>T	chr5.hg19:g.36253830C>A	ENSP00000296604:p.Lys362Asn	109.0	0.0		137.0	37.0	NM_001161429	B7Z866|E9PGP9|Q96LK2	Missense_Mutation	SNP	ENST00000296604.3	hg19	CCDS3918.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.471389	0.43942	.	.	ENSG00000164188	ENST00000296604;ENST00000502994	T;T	0.45668	0.89;0.89	5.18	3.35	0.38373	Pleckstrin homology-type (1);Ran binding protein 1 (3);	0.452234	0.22560	N	0.058474	T	0.34454	0.0898	L	0.54323	1.7	0.80722	D	1	B;P	0.35226	0.105;0.491	B;B	0.37780	0.117;0.258	T	0.05500	-1.0881	10	0.19590	T	0.45	-0.0595	5.8693	0.18795	0.0:0.5323:0.3023:0.1654	.	387;362	E9PGP9;Q86VV4	.;RNB3L_HUMAN	N	362;387	ENSP00000296604:K362N;ENSP00000421853:K387N	ENSP00000296604:K362N	K	-	3	2	RANBP3L	36289587	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	0.842000	0.27627	0.660000	0.30964	0.557000	0.71058	AAG	.	.		0.383	RANBP3L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253773.2	NM_145000		A	36253830	C	A	36253830	3	1	147	1	0	0	0	0	1	0	0	0	13045	912	32	3	323	3	RANBP3L	5	36253830	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	32654284	36253830	144661430	18	22486										
LNPEP	4012	hgsc.bcm.edu	37	chr5	96350727	96350727	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	actgcacccatcaccgaagcCctgtttcagacagacctcat	6	16	3	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr5:96350727C>T	ENST00000231368.5	+	13	2996	c.2304C>T	c.(2302-2304)gcC>gcT	p.A768A	LNPEP_ENST00000395770.3_Silent_p.A754A	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	768					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		TCACCGAAGCCCTGTTTCAGA	0.443																																					p.A768A		Atlas-SNP	.											LNPEP,NS,carcinoma,0,1	LNPEP	80	.	0			c.C2304T						.						123	115	118					5																	96350727		2203	4300	6503	SO:0001819	synonymous_variant	4012	exon13			CGAAGCCCTGTTT	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"cystinyl aminopeptidase", "placental leucine aminopeptidase"	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.2304C>T	chr5.hg19:g.96350727C>T		114.0	0.0		152.0	13.0	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Silent	SNP	ENST00000231368.5	hg19	CCDS4087.1																																																																																			.	.		0.443	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		T	96350727	C	T	96350727	2	4	147	1	0	0	0	0	0	0	0	1	8873	610	22	3		3	LNPEP	5	96350727	Silent	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	60096897	96350727	84564533	19	22487										
PHAX	51808	hgsc.bcm.edu	37	chr5	125944167	125944167	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	gttgaacaaaatggtggtctCtttataatggtaagactgct	10	5	1	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr5:125944167C>A	ENST00000297540.4	+	3	1517	c.822C>A	c.(820-822)ctC>ctA	p.L274L		NM_032177.3	NP_115553.2	Q9H814	PHAX_HUMAN	phosphorylated adaptor for RNA export	274	Necessary for interaction with CBP80. {ECO:0000250}.|Sufficient for poly U RNA-binding.				gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein transport (GO:0015031)|RNA metabolic process (GO:0016070)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA binding (GO:0003723)|toxic substance binding (GO:0015643)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	8						ATGGTGGTCTCTTTATAATGG	0.348																																					p.L274L		Atlas-SNP	.											.	PHAX	20	.	0			c.C822A						.						144	152	149					5																	125944167		2203	4300	6503	SO:0001819	synonymous_variant	51808	exon3			TGGTCTCTTTATA	AK023255	CCDS4138.1	5q23.2	2011-05-24	2008-10-01	2008-10-01	ENSG00000164902	ENSG00000164902			10241	protein-coding gene	gene with protein product		604924	"RNA U, small nuclear RNA export adaptor (phosphorylation regulated)"	RNUXA		10786834	Standard	NM_032177		Approved	FLJ13193	uc003kua.2	Q9H814	OTTHUMG00000163273	ENST00000297540.4:c.822C>A	chr5.hg19:g.125944167C>A		56.0	0.0		79.0	20.0	NM_032177	Q9H8W1	Silent	SNP	ENST00000297540.4	hg19	CCDS4138.1																																																																																			.	.		0.348	PHAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250924.1	NM_032177		A	125944167	C	A	125944167	2	1	147	1	0	0	0	0	0	0	0	1	11822	900	32	3		3	PHAX	5	125944167	Silent	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	29593440	125944167	54971093	20	22488										
SLC27A6	28965	hgsc.bcm.edu	37	chr5	128364118	128364118	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	catacaggaagcaaacgtctAtggtgtggctatatcaggta	11	7	2	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr5:128364118A>T	ENST00000262462.4	+	8	2545	c.1535A>T	c.(1534-1536)tAt>tTt	p.Y512F	SLC27A6_ENST00000395266.1_Missense_Mutation_p.Y512F|SLC27A6_ENST00000506176.1_Missense_Mutation_p.Y512F			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	512					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		GCAAACGTCTATGGTGTGGCT	0.338																																					p.Y512F		Atlas-SNP	.											.	SLC27A6	112	.	0			c.A1535T						.						83	81	81					5																	128364118		2203	4300	6503	SO:0001583	missense	28965	exon8			ACGTCTATGGTGT	AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"Acyl-CoA synthetase family", "Solute carriers"	11000	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 2"	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.1535A>T	chr5.hg19:g.128364118A>T	ENSP00000262462:p.Tyr512Phe	67.0	0.0		70.0	17.0	NM_001017372	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	hg19	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	A	18.74	3.688646	0.68271	.	.	ENSG00000113396	ENST00000262462;ENST00000395266;ENST00000506176	T;T;T	0.58358	0.34;0.34;0.34	4.55	3.39	0.38822	.	0.000000	0.85682	D	0.000000	T	0.73892	0.3645	M	0.89414	3.03	0.43342	D	0.995399	D	0.89917	1.0	D	0.97110	1.0	T	0.77264	-0.2652	9	.	.	.	0.5469	10.8411	0.46715	0.9243:0.0:0.0757:0.0	.	512	Q9Y2P4	S27A6_HUMAN	F	512	ENSP00000262462:Y512F;ENSP00000378684:Y512F;ENSP00000421024:Y512F	.	Y	+	2	0	SLC27A6	128392017	1.000000	0.71417	0.626000	0.29213	0.788000	0.44548	6.898000	0.75676	1.063000	0.40649	0.455000	0.32223	TAT	.	.		0.338	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031		T	128364118	A	T	128364118	3	4	147	1	0	0	0	0	1	0	0	0	14545	449	16	4	1565	4	SLC27A6	5	128364118	Missense_Mutation	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10	2419951	128364118	52551142	21	22489										
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140255085	140255085	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ttatcggaccaagaggcccgGgatcccagcgtctgctgctc	12	14	1	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr5:140255085G>C	ENST00000398631.2	+	1	28	c.28G>C	c.(28-30)Gga>Cga	p.G10R	PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	10					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGAGGCCCGGGATCCCAGCG	0.567																																					p.G10R	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.G28C						.						34	39	38					5																	140255085		2194	4294	6488	SO:0001583	missense	56137	exon1			GGCCCGGGATCCC	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.28G>C	chr5.hg19:g.140255085G>C	ENSP00000381628:p.Gly10Arg	49.0	0.0		92.0	33.0	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	hg19	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	7.643	0.681376	0.14907	.	.	ENSG00000251664	ENST00000398631	T	0.49432	0.78	5.28	1.98	0.26296	.	.	.	.	.	T	0.26557	0.0649	N	0.10837	0.055	0.09310	N	1	B;B	0.19445	0.036;0.024	B;B	0.22880	0.042;0.027	T	0.24835	-1.0149	9	0.20046	T	0.44	.	9.0754	0.36517	0.3377:0.0:0.6623:0.0	.	10;10	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	R	10	ENSP00000381628:G10R	ENSP00000381628:G10R	G	+	1	0	PCDHA12	140235269	0.098000	0.21812	0.000000	0.03702	0.008000	0.06430	1.044000	0.30329	0.065000	0.16485	-0.345000	0.07892	GGA	.	.		0.567	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		C	140255085	G	C	140255085	3	2	147	1	0	0	0	0	1	0	0	0	11531	1233	43	4	30	4	PCDHA12	5	140255085	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	11890967	140255085	40660175	22	22490										
EBF1	1879	hgsc.bcm.edu	37	chr5	158158157	158158157	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	accataatcgatggtgggttCgttgagcgctgcaataaaga	12	7	0	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr5:158158157C>G	ENST00000313708.6	-	11	1327	c.1045G>C	c.(1045-1047)Gaa>Caa	p.E349Q	EBF1_ENST00000517373.1_Missense_Mutation_p.E341Q|EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000380654.4_Missense_Mutation_p.E318Q	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	349					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATGGTGGGTTCGTTGAGCGCT	0.448			T	HMGA2	lipoma																																p.E349Q		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	.	EBF1	110	.	0			c.G1045C						.						60	62	61					5																	158158157		2203	4300	6503	SO:0001583	missense	1879	exon11			TGGGTTCGTTGAG	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"early B-cell factor"	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1045G>C	chr5.hg19:g.158158157C>G	ENSP00000322898:p.Glu349Gln	53.0	0.0		84.0	30.0	NM_024007	Q8IW11	Missense_Mutation	SNP	ENST00000313708.6	hg19	CCDS4343.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708625	0.89018	.	.	ENSG00000164330	ENST00000318060;ENST00000313708;ENST00000380654;ENST00000517373	T;T;T	0.47177	0.85;0.85;0.85	5.51	5.51	0.81932	Helix-loop-helix DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.71970	0.3403	M	0.85630	2.765	0.80722	D	1	D;D;D;D	0.76494	0.997;0.986;0.999;0.969	P;P;D;P	0.64321	0.846;0.89;0.924;0.684	T	0.74728	-0.3567	10	0.54805	T	0.06	-5.0504	19.7818	0.96418	0.0:1.0:0.0:0.0	.	349;336;349;318	A8K0Z7;B4E2U8;Q9UH73;Q9UH73-2	.;.;COE1_HUMAN;.	Q	349;349;318;341	ENSP00000322898:E349Q;ENSP00000370029:E318Q;ENSP00000428020:E341Q	ENSP00000322898:E349Q	E	-	1	0	EBF1	158090735	1.000000	0.71417	0.960000	0.40013	0.806000	0.45545	7.445000	0.80570	2.736000	0.93811	0.655000	0.94253	GAA	.	.		0.448	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		G	158158157	C	G	158158157	3	3	147	1	0	0	0	0	1	0	0	0	4882	893	31	4	754	4	EBF1	5	158158157	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	17903072	158158157	22757103	23	22491										
PRRT1	80863	hgsc.bcm.edu	37	chr6	32117487	32117487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tcctgttccccccggggtccCgcctgcatatggctgtggaa	12	15	0	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr6:32117487C>T	ENST00000211413.5	-	3	695	c.571G>A	c.(571-573)Ggg>Agg	p.G191R	PRRT1_ENST00000375152.2_Missense_Mutation_p.G110R|PRRT1_ENST00000467780.1_5'UTR|PRRT1_ENST00000375150.2_Missense_Mutation_p.G110R	NM_030651.3	NP_085154.3	Q99946	PRRT1_HUMAN	proline-rich transmembrane protein 1	191					response to biotic stimulus (GO:0009607)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						CCCGGGGTCCCGCCTGCATAT	0.667																																					p.G191R		Atlas-SNP	.											.	PRRT1	14	.	0			c.G571A						.						10	13	12					6																	32117487		1491	2686	4177	SO:0001583	missense	80863	exon3			GGGTCCCGCCTGC	AK054885	CCDS4739.1	6p21.32	2011-10-10	2005-07-24	2005-07-24		ENSG00000204314		"Proline-rich transmembrane proteins"	13943	protein-coding gene	gene with protein product	"interferon induced transmembrane protein domain containing 7"		"chromosome 6 open reading frame 31"	C6orf31			Standard	XM_006715221		Approved	NG5, IFITMD7	uc003nzt.3	Q99946		ENST00000211413.5:c.571G>A	chr6.hg19:g.32117487C>T	ENSP00000211413:p.Gly191Arg	28.0	0.0		33.0	12.0	NM_030651	A6ND08|A6ND40|B0S869|Q5SSW4|Q5SSX7|Q5STI1|Q96DW3|Q96NQ8	Missense_Mutation	SNP	ENST00000211413.5	hg19	CCDS4739.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.365899	0.41902	.	.	ENSG00000204314	ENST00000211413;ENST00000375150;ENST00000375152	D;D;D	0.90620	-2.67;-2.7;-2.7	4.8	4.8	0.61643	.	.	.	.	.	D	0.86548	0.5959	N	0.14661	0.345	0.37152	D	0.902203	D;D	0.89917	1.0;1.0	D;D	0.74348	0.926;0.983	D	0.86295	0.1676	9	0.27082	T	0.32	-0.0271	13.3504	0.60599	0.0:1.0:0.0:0.0	.	191;110	Q99946;Q99946-2	PRRT1_HUMAN;.	R	191;110;110	ENSP00000211413:G191R;ENSP00000364292:G110R;ENSP00000364294:G110R	ENSP00000211413:G191R	G	-	1	0	PRRT1	32225465	0.995000	0.38212	1.000000	0.80357	0.789000	0.44602	2.351000	0.44071	2.225000	0.72522	0.557000	0.71058	GGG	.	.		0.667	PRRT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076255.2	NM_030651		T	32117487	C	T	32117487	3	4	147	1	0	0	0	0	1	0	0	0	12621	652	23	1	357	1	PRRT1	6	32117487	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10		32117487	138997580	24	22492										
SLC29A1	2030	hgsc.bcm.edu	37	chr6	44197695	44197695	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ctggtggccatcctgctggtGtttctgatcactgccatcct	10	13	2	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr6:44197695G>T	ENST00000393841.1	+	6	857	c.366G>T	c.(364-366)gtG>gtT	p.V122V	SLC29A1_ENST00000371724.1_Silent_p.V122V|SLC29A1_ENST00000371740.5_Silent_p.V122V|SLC29A1_ENST00000313248.7_Silent_p.V201V|SLC29A1_ENST00000472176.1_3'UTR|SLC29A1_ENST00000371731.1_Silent_p.V122V|SLC29A1_ENST00000371708.1_Silent_p.V122V|SLC29A1_ENST00000427851.2_Silent_p.V122V|SLC29A1_ENST00000371755.3_Silent_p.V122V|SLC29A1_ENST00000371713.1_Silent_p.V122V|SLC29A1_ENST00000393844.1_Silent_p.V122V	NM_001078177.1	NP_001071645.1	Q99808	S29A1_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 1	122					cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|lactation (GO:0007595)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sleep (GO:0030431)|transmembrane transport (GO:0055085)|uridine transport (GO:0015862)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	17	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Cytarabine(DB00987)|Didanosine(DB00900)|Fludarabine(DB01073)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Pemetrexed(DB00642)|Ribavirin(DB00811)|Zalcitabine(DB00943)	TCCTGCTGGTGTTTCTGATCA	0.582																																					p.V122V		Atlas-SNP	.											.	SLC29A1	45	.	0			c.G366T						.						64	54	58					6																	44197695		2203	4300	6503	SO:0001819	synonymous_variant	2030	exon5			GCTGGTGTTTCTG	U81375	CCDS4908.1	6p21.1	2013-07-17	2013-07-17		ENSG00000112759	ENSG00000112759		"Solute carriers"	11003	protein-coding gene	gene with protein product		602193	"solute carrier family 29 (nucleoside transporters), member 1"	ENT1		8986748, 9344680	Standard	NM_004955		Approved		uc003owy.2	Q99808	OTTHUMG00000014759	ENST00000393841.1:c.366G>T	chr6.hg19:g.44197695G>T		57.0	0.0		68.0	23.0	NM_004955	B3KQV7|B3KQY5|Q5T9W9|Q9UJY2	Silent	SNP	ENST00000393841.1	hg19	CCDS4908.1																																																																																			.	.		0.582	SLC29A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040721.1			T	44197695	G	T	44197695	2	4	147	1	0	0	0	0	0	0	0	1	14549	1364	48	3		3	SLC29A1	6	44197695	Silent	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	12080208	44197695	126917372	25	22493										
EYS	346007	hgsc.bcm.edu	37	chr6	65301374	65301374	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	atatcctcttgagcccccctAgagacaactggagttgcact	8	13	1	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr6:65301374A>G	ENST00000370621.3	-	26	4912	c.4386T>C	c.(4384-4386)tcT>tcC	p.S1462S	EYS_ENST00000503581.1_Silent_p.S1462S|EYS_ENST00000370616.2_Silent_p.S1462S			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1462					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GAGCCCCCCTAGAGACAACTG	0.463																																					p.S1462S		Atlas-SNP	.											.	EYS	527	.	0			c.T4386C						.						57	56	57					6																	65301374		692	1591	2283	SO:0001819	synonymous_variant	346007	exon26			CCCCCTAGAGACA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4386T>C	chr6.hg19:g.65301374A>G		79.0	0.0		79.0	22.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	hg19																																																																																				.	.		0.463	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	65301374	A	G	65301374	2	3	147	1	0	0	0	0	0	0	0	1	5334	407	15	2		2	EYS	6	65301374	Silent	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10	21103679	65301374	105813693	26	22494										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76124503	76124503	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	gtttttcgttcacattctccAgatgtttttaggtgtcgttt	8	7	2	1	rs554060815		TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr6:76124503A>T	ENST00000237172.7	-	2	516	c.186T>A	c.(184-186)tcT>tcA	p.S62S	FILIP1_ENST00000393004.2_Silent_p.S62S	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	62										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						CACATTCTCCAGATGTTTTTA	0.398																																					p.S62S		Atlas-SNP	.											.	FILIP1	173	.	0			c.T186A						.						234	229	231					6																	76124503		2203	4300	6503	SO:0001819	synonymous_variant	27145	exon2			TTCTCCAGATGTT	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.186T>A	chr6.hg19:g.76124503A>T		219.0	0.0		244.0	67.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Silent	SNP	ENST00000237172.7	hg19	CCDS4984.1																																																																																			.	.		0.398	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		T	76124503	A	T	76124503	2	4	147	1	0	0	0	0	0	0	0	1	5902	175	7	4		4	FILIP1	6	76124503	Silent	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10	10823129	76124503	94990564	27	22495										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136582246	136582439	+	Stop_Codon_Del	DEL	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	-													0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ttgtaatcttacttcatattTattattcctaaaagagagag					rs376948280|rs537502804|rs562481221|rs527483217|rs62431283|rs112744301|rs62431282|rs370252607|rs570210520|rs111800140|rs193167212|rs375440569	byFrequency	TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr6:136582246_136582439delTGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	ENST00000531224.1	-	0	2973_3017				BCLAF1_ENST00000031135.9_Stop_Codon_Del|BCLAF1_ENST00000530767.1_Stop_Codon_Del|BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000527759.1_Stop_Codon_Del|BCLAF1_ENST00000527536.1_Stop_Codon_Del|BCLAF1_ENST00000392348.2_Stop_Codon_Del|BCLAF1_ENST00000353331.4_Stop_Codon_Del	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1						apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		ACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATTTTATACCTTTTCTTCCTTGCGTCTGTCCTTCTTTTCTTCATTATTTTCCATGG	0.315																																					p.920_921del	Colon(142;1534 1789 5427 7063 28491)	Pindel	.											.	BCLAF1	203	.	0			c.2758_3016del						.																																			SO:0001567	stop_retained_variant	9774	exon13			.	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	Exception_encountered	chr6.hg19:g.136582246_136582439delTGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	Exception_encountered	320.0	0.0		273.0	11.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Frame_Shift_Del	DEL	ENST00000531224.1	hg19	CCDS5177.1																																																																																			.	.		0.315	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		-	136582439	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	-	136582246	7	5	147	1	0	1	0	1	0	0	0	0	1383	1769	61	0	1	0	BCLAF1	6	136582246	Stop_Codon_Del	DEL	TGGTGGGTGCAAGTTCTGCTCTGTTGTAATCTTACTTCATATTTATTATTCCTAAAAGAGAGAGAAAAAATTAAAGATTAACAAAAGATGCGGAGAGTGAAAAGGAACCATATTAATAATTGTTCCTAAAAATGAAATAATTCACCCACCAAACCTATATCAAAAAAAATCTGTCAGAATCACAAGTTGAAATT	TCGA-DD-A73F-01A-11D-A32G-10	60457743	136582246	34532821	28	22496										
GET4	51608	hgsc.bcm.edu	37	chr7	930603	930603	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cgaggtatcattttctgcacTcagcggacggggagggctgt	15	9	3	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr7:930603T>G	ENST00000265857.3	+	5	599	c.505T>G	c.(505-507)Tca>Gca	p.S169A	GET4_ENST00000407192.1_Missense_Mutation_p.S116A	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	169					tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)				breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TTTTCTGCACTCAGCGGACGG	0.498																																					p.S169A		Atlas-SNP	.											.	GET4	17	.	0			c.T505G						.						130	121	124					7																	930603		2203	4300	6503	SO:0001583	missense	51608	exon5			CTGCACTCAGCGG	AK023560	CCDS5317.1	7p22.3	2010-08-05	2010-03-24	2010-03-24	ENSG00000239857	ENSG00000239857			21690	protein-coding gene	gene with protein product	"CGI-20 protein", "conserved edge protein", "transmembrane domain recognition complex, 35kDa"	612056	"chromosome 7 open reading frame 20"	C7orf20		10810093, 20106980, 20676083	Standard	NM_015949		Approved	CGI-20, H_NH1244M04.5, CEE, TRC35	uc003sjl.1	Q7L5D6	OTTHUMG00000112459	ENST00000265857.3:c.505T>G	chr7.hg19:g.930603T>G	ENSP00000265857:p.Ser169Ala	148.0	0.0		186.0	56.0	NM_015949	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	Missense_Mutation	SNP	ENST00000265857.3	hg19	CCDS5317.1	.	.	.	.	.	.	.	.	.	.	t	13.65	2.299715	0.40694	.	.	ENSG00000239857	ENST00000265857;ENST00000412734;ENST00000407192;ENST00000426056	.	.	.	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.66944	0.2841	L	0.60957	1.885	0.54753	D	0.999982	D	0.57257	0.979	P	0.59487	0.858	T	0.63207	-0.6689	9	0.18276	T	0.48	-22.1134	14.8892	0.70594	0.0:0.0:0.0:1.0	.	169	Q7L5D6	GET4_HUMAN	A	169;123;116;130	.	ENSP00000265857:S169A	S	+	1	0	GET4	897129	1.000000	0.71417	0.993000	0.49108	0.026000	0.11368	5.859000	0.69539	1.940000	0.56252	0.398000	0.26397	TCA	.	.		0.498	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000231930.1	NM_015949		G	930603	T	G	930603	3	3	147	1	0	0	0	0	1	0	0	0	6344	1551	54	5	523	5	GET4	7	930603	Missense_Mutation	SNP	T	TCGA-DD-A73F-01A-11D-A32G-10		930603	158208060	29	22497										
SCIN	85477	hgsc.bcm.edu	37	chr7	12610490	12610490	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	caggtctggaggattgagaaGctggagctggtgcccgtgcc	17	9	1	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr7:12610490G>A	ENST00000297029.5	+	1	179	c.78G>A	c.(76-78)aaG>aaA	p.K26K	AC005281.2_ENST00000433040.1_RNA	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	26	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		GGATTGAGAAGCTGGAGCTGG	0.672																																					p.K26K		Atlas-SNP	.											.	SCIN	105	.	0			c.G78A						.						28	43	38					7																	12610490		692	1591	2283	SO:0001819	synonymous_variant	85477	exon1			TGAGAAGCTGGAG	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.78G>A	chr7.hg19:g.12610490G>A		87.0	0.0		69.0	15.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Silent	SNP	ENST00000297029.5	hg19	CCDS47545.1																																																																																			.	.		0.672	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		A	12610490	G	A	12610490	2	1	147	1	0	0	0	0	0	0	0	1	13920	962	34	3		3	SCIN	7	12610490	Silent	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	11679887	12610490	146528173	30	22498										
SP4	6671	hgsc.bcm.edu	37	chr7	21521737	21521737	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cagagacatagaagaacccaTacaggttagttgattttagg	10	6	0	4			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr7:21521737T>C	ENST00000222584.3	+	5	2321	c.2103T>C	c.(2101-2103)caT>caC	p.H701H		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	701					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						GAAGAACCCATACAGGTTAGT	0.348																																					p.H701H		Atlas-SNP	.											.	SP4	91	.	0			c.T2103C						.						108	105	106					7																	21521737		2203	4300	6503	SO:0001819	synonymous_variant	6671	exon5			AACCCATACAGGT		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.2103T>C	chr7.hg19:g.21521737T>C		135.0	0.0		156.0	53.0	NM_003112	O60402|Q32M52	Silent	SNP	ENST00000222584.3	hg19	CCDS5373.1																																																																																			.	.		0.348	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		C	21521737	T	C	21521737	2	2	147	1	0	0	0	0	0	0	0	1	14981	1403	49	2		2	SP4	7	21521737	Silent	SNP	T	TCGA-DD-A73F-01A-11D-A32G-10	8911247	21521737	137616926	31	22499										
CROT	54677	hgsc.bcm.edu	37	chr7	86986879	86986879	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cagatgctaagagagggttcTtggatctcacgcgggaagga	15	7	2	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr7:86986879T>C	ENST00000331536.3	+	4	300				CROT_ENST00000419147.2_Silent_p.L58L|CROT_ENST00000442291.1_Intron|CROT_ENST00000412227.2_Intron	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase						carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	gagagggttcttggatctcac	0.483																																					p.L58L		Atlas-SNP	.											.	CROT	81	.	0			c.T172C						.						117	100	105					7																	86986879		692	1591	2283	SO:0001627	intron_variant	54677	exon4			GGGTTCTTGGATC		CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.116-1643T>C	chr7.hg19:g.86986879T>C		28.0	0.0		32.0	9.0	NM_001143935	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Silent	SNP	ENST00000331536.3	hg19	CCDS5604.1																																																																																			.	.		0.483	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		C	86986879	T	C	86986879	1	2	147	0	1	0	0	0	0	0	0	0	3896	1606	56	2		2	CROT	7	86986879	Intron	SNP	T	TCGA-DD-A73F-01A-11D-A32G-10	65465142	86986879	72151784	32	22500										
C7orf43	55262	hgsc.bcm.edu	37	chr7	99754128	99754128	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	gaacaggggacttacaagaaGcggtcatcacaaaacacggg	12	9	2	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr7:99754128G>T	ENST00000316937.3	-	8	1306	c.1121C>A	c.(1120-1122)gCt>gAt	p.A374D	C7orf43_ENST00000457641.1_Missense_Mutation_p.A105D|MIR4658_ENST00000584344.1_RNA|C7orf43_ENST00000419841.1_Missense_Mutation_p.A142D|C7orf43_ENST00000498638.1_5'UTR|C7orf43_ENST00000394035.2_5'Flank	NM_018275.3	NP_060745.3	Q8WVR3	CG043_HUMAN	chromosome 7 open reading frame 43	374										breast(1)|endometrium(3)|large_intestine(3)|lung(2)|prostate(1)	10	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTTACAAGAAGCGGTCATCAC	0.567																																					p.A374D		Atlas-SNP	.											.	C7orf43	28	.	0			c.C1121A						.						85	81	82					7																	99754128		2203	4300	6503	SO:0001583	missense	55262	exon8			CAAGAAGCGGTCA		CCDS5687.1	7q22.1	2011-11-25			ENSG00000146826	ENSG00000146826			25604	protein-coding gene	gene with protein product						12477932	Standard	NM_018275		Approved	FLJ10925	uc003utr.3	Q8WVR3	OTTHUMG00000154862	ENST00000316937.3:c.1121C>A	chr7.hg19:g.99754128G>T	ENSP00000324741:p.Ala374Asp	81.0	0.0		118.0	5.0	NM_018275	A4D2A9|D6W5U4|Q9BQJ1|Q9BUB6|Q9NV47	Missense_Mutation	SNP	ENST00000316937.3	hg19	CCDS5687.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.658333	0.88154	.	.	ENSG00000146826	ENST00000457641;ENST00000316937;ENST00000419841	T;T;T	0.60171	0.28;0.21;0.25	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.65749	0.2721	N	0.24115	0.695	0.58432	D	0.999997	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.69363	-0.5165	10	0.87932	D	0	-10.0996	17.3306	0.87262	0.0:0.0:1.0:0.0	.	142;374	E9PFF9;Q8WVR3	.;CG043_HUMAN	D	105;374;142	ENSP00000396432:A105D;ENSP00000324741:A374D;ENSP00000406326:A142D	ENSP00000324741:A374D	A	-	2	0	C7orf43	99592064	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	8.650000	0.91073	2.702000	0.92279	0.561000	0.74099	GCT	.	.		0.567	C7orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337395.2	NM_018275		T	99754128	G	T	99754128	3	4	147	1	0	0	0	0	1	0	0	0	2395	971	34	3	637	3	C7orf43	7	99754128	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	12767249	99754128	59384535	33	22501										
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138761070	138761070	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cagtagcctttctcgatcgtCtccatgtgctcaaagtccgt	8	13	3	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr7:138761070C>T	ENST00000242351.5	-	6	1975	c.1659G>A	c.(1657-1659)gaG>gaA	p.E553E	ZC3HAV1_ENST00000464606.1_Silent_p.E675E|ZC3HAV1_ENST00000471652.1_Silent_p.E553E	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	553					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						TCTCGATCGTCTCCATGTGCT	0.478																																					p.E553E		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.G1659A						.						166	148	154					7																	138761070		2203	4300	6503	SO:0001819	synonymous_variant	56829	exon6			GATCGTCTCCATG	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.1659G>A	chr7.hg19:g.138761070C>T		90.0	0.0		95.0	34.0	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Silent	SNP	ENST00000242351.5	hg19	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	C	0.046	-1.265320	0.01433	.	.	ENSG00000105939	ENST00000460845	.	.	.	5.14	1.38	0.22167	.	.	.	.	.	T	0.45736	0.1357	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	T	0.22730	-1.0208	4	.	.	.	.	3.8432	0.08923	0.1594:0.4972:0.0:0.3434	.	.	.	.	N	118	.	.	D	-	1	0	ZC3HAV1	138411610	0.478000	0.25917	0.156000	0.22583	0.007000	0.05969	0.894000	0.28350	0.078000	0.16900	-0.150000	0.13652	GAC	.	.		0.478	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		T	138761070	C	T	138761070	2	4	147	1	0	0	0	0	0	0	0	1	17590	912	32	3		3	ZC3HAV1	7	138761070	Silent	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	39006942	138761070	20377593	34	22502										
STAR	6770	hgsc.bcm.edu	37	chr8	38002821	38002821	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tgaagcaccatgcaagtgggAccgtgctccgccctggcaaa	12	13	0	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr8:38002821A>G	ENST00000276449.4	-	6	1109	c.663T>C	c.(661-663)ggT>ggC	p.G221G		NM_000349.2	NP_000340.2	P49675	STAR_HUMAN	steroidogenic acute regulatory protein	221	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				bile acid biosynthetic process (GO:0006699)|biphenyl metabolic process (GO:0018879)|brain development (GO:0007420)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth hormone stimulus (GO:0071378)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-alpha (GO:0035457)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to luteinizing hormone stimulus (GO:0071373)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cholesterol metabolic process (GO:0008203)|circadian sleep/wake cycle, REM sleep (GO:0042747)|dibenzo-p-dioxin metabolic process (GO:0018894)|diterpenoid metabolic process (GO:0016101)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|glucocorticoid metabolic process (GO:0008211)|insecticide metabolic process (GO:0017143)|intracellular cholesterol transport (GO:0032367)|male gonad development (GO:0008584)|negative regulation of neuron apoptotic process (GO:0043524)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of gene expression (GO:0010628)|positive regulation of neurogenesis (GO:0050769)|progesterone biosynthetic process (GO:0006701)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of steroid biosynthetic process (GO:0050810)|response to activity (GO:0014823)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to hydrogen peroxide (GO:0042542)|response to ionizing radiation (GO:0010212)|response to lead ion (GO:0010288)|response to leptin (GO:0044321)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytosol (GO:0005829)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	cholesterol binding (GO:0015485)			breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11	Colorectal(12;0.000442)	all_lung(54;0.0151)|Lung NSC(58;0.0295)		READ - Rectum adenocarcinoma(644;0.188)		TGCAAGTGGGACCGTGCTCCG	0.542																																					p.G221G		Atlas-SNP	.											STAR,NS,lymphoid_neoplasm,0,1	STAR	29	.	0			c.T663C						.						114	90	98					8																	38002821		2203	4300	6503	SO:0001819	synonymous_variant	6770	exon6			AGTGGGACCGTGC	BC010550	CCDS6102.1	8p11.2	2011-09-13	2007-05-15		ENSG00000147465	ENSG00000147465		"StAR-related lipid transfer (START) domain containing"	11359	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 1"	600617	"steroidogenic acute regulator"			7761400	Standard	NM_000349		Approved	StAR, STARD1	uc003xkv.1	P49675	OTTHUMG00000164058	ENST00000276449.4:c.663T>C	chr8.hg19:g.38002821A>G		33.0	0.0		31.0	3.0	NM_000349	Q16396	Silent	SNP	ENST00000276449.4	hg19	CCDS6102.1																																																																																			.	.		0.542	STAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376990.2	NM_000349		G	38002821	A	G	38002821	2	3	147	1	0	0	0	0	0	0	0	1	15269	262	10	2		2	STAR	8	38002821	Silent	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10		38002821	108361201	35	22503										
ST18	9705	hgsc.bcm.edu	37	chr8	53084937	53084937	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	aaagcactcgtctgcttcatCgctctctgcttttaaagact	6	12	3	1	rs147121734		TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr8:53084937C>A	ENST00000276480.7	-	10	1167	c.484G>T	c.(484-486)Gat>Tat	p.D162Y		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	162					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TCTGCTTCATCGCTCTCTGCT	0.388																																					p.D162Y		Atlas-SNP	.											.	ST18	212	.	0			c.G484T						.						113	104	107					8																	53084937		2203	4300	6503	SO:0001583	missense	9705	exon10			CTTCATCGCTCTC	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.484G>T	chr8.hg19:g.53084937C>A	ENSP00000276480:p.Asp162Tyr	117.0	0.0		150.0	42.0	NM_014682	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	hg19	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638969	0.47153	.	.	ENSG00000147488	ENST00000276480;ENST00000517580	T;T	0.51574	0.71;0.7	5.63	5.63	0.86233	.	0.470314	0.25704	N	0.028843	T	0.59252	0.2180	M	0.64997	1.995	0.41628	D	0.989001	D	0.54964	0.969	P	0.54924	0.764	T	0.63042	-0.6725	10	0.87932	D	0	-8.5407	13.9144	0.63887	0.0:0.9273:0.0:0.0727	.	162	O60284	ST18_HUMAN	Y	162	ENSP00000276480:D162Y;ENSP00000428521:D162Y	ENSP00000276480:D162Y	D	-	1	0	ST18	53247490	0.970000	0.33590	0.222000	0.23844	0.261000	0.26267	3.474000	0.53129	2.650000	0.89964	0.655000	0.94253	GAT	.	C|1.000;T|0.000		0.388	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			A	53084937	C	A	53084937	3	1	147	1	0	0	0	0	1	0	0	0	15227	884	31	1	2727	1	ST18	8	53084937	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	15082116	53084937	93279085	36	22504										
POU5F1B	5462	hgsc.bcm.edu	37	chr8	128428642	128428642	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ctgggggttctatttgggaaGgtgttcagccaaaagaccat	13	7	2	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr8:128428642G>A	ENST00000465342.2	+	2	1688	c.531G>A	c.(529-531)aaG>aaA	p.K177K	CASC8_ENST00000501396.1_RNA|CASC8_ENST00000523825.1_RNA|CASC8_ENST00000502082.1_RNA|POU5F1B_ENST00000391675.1_Silent_p.K177K			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	177	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|prostate(1)|urinary_tract(1)	3						TATTTGGGAAGGTGTTCAGCC	0.532																																					p.K177K		Atlas-SNP	.											.	POU5F1B	32	.	0			c.G531A						.						77	89	86					8																	128428642		692	1591	2283	SO:0001819	synonymous_variant	5462	exon1			TGGGAAGGTGTTC	AF268615	CCDS55274.1	8q24.21	2011-06-20	2009-04-15	2009-04-15	ENSG00000212993	ENSG00000212993		"Homeoboxes / POU class"	9223	protein-coding gene	gene with protein product		615739	"POU domain class 5, transcription factor 1 pseudogene 1", "POU class 5 homeobox 1 pseudogene 1"	OTF3P1, POU5F1P1		1408763	Standard	NM_001159542		Approved	OTF3C	uc003ysf.3	Q06416	OTTHUMG00000157807	ENST00000465342.2:c.531G>A	chr8.hg19:g.128428642G>A		60.0	0.0		71.0	21.0	NM_001159542	D5K9S4|D5K9S9|D5K9T0|D5K9T1|D5K9T3|D5K9U3|D5K9U6|D5K9V4|D5K9V6|D5K9W0|D5K9W2|D5K9W7|D5K9X2|D5K9X3|D5K9X5|D5K9X8|D5K9X9|E9LRB1|E9LRB2|E9LRH5|E9LRH6|E9LRH7|E9LRK4|E9LRK5|E9LRK7|E9LRK8|E9LRM7|E9LRM9|E9LRN2|E9LRN4|E9LRN5|E9LRP8|E9LRQ0|E9LRQ2|E9LRQ3|E9LRQ4|E9LRQ5|E9LRS3|Q2VIK6|Q9BZV7|Q9BZV9	Silent	SNP	ENST00000465342.2	hg19	CCDS55274.1																																																																																			.	.		0.532	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542		A	128428642	G	A	128428642	2	1	147	1	0	0	0	0	0	0	0	1	12291	991	35	3		3	POU5F1B	8	128428642	Silent	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	75343705	128428642	17935380	37	22505										
ZER1	10444	hgsc.bcm.edu	37	chr9	131515868	131515868	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tcgcagttagtcaggtacagCtccaccaggtcctgggagtg	13	11	1	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr9:131515868C>T	ENST00000291900.2	-	4	727	c.321G>A	c.(319-321)gaG>gaA	p.E107E	ZER1_ENST00000494461.1_5'UTR	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	107					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						TCAGGTACAGCTCCACCAGGT	0.612																																					p.E107E		Atlas-SNP	.											.	ZER1	49	.	0			c.G321A						.						41	42	41					9																	131515868		2203	4300	6503	SO:0001819	synonymous_variant	10444	exon4			GTACAGCTCCACC	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"ZYG11 cell cycle regulator family"	30960	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 60", "zyg-11 homolog B (C. elegans)-like", "zer-1 homolog (C. elegans)"	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.321G>A	chr9.hg19:g.131515868C>T		40.0	0.0		36.0	10.0	NM_006336	O00156|Q5T272|Q5T273	Silent	SNP	ENST00000291900.2	hg19	CCDS6910.1																																																																																			.	.		0.612	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336		T	131515868	C	T	131515868	2	4	147	1	0	0	0	0	0	0	0	1	17640	796	28	3		3	ZER1	9	131515868	Silent	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10		131515868	9697563	38	22506										
GDF10	2662	hgsc.bcm.edu	37	chr10	48428812	48428812	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	gctttctgcatcgtcttctcGtcaaagtccagcacctgcga	8	14	4	0	rs374890077		TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr10:48428812G>A	ENST00000224605.2	-	2	1339	c.1074C>T	c.(1072-1074)gaC>gaT	p.D358D		NM_004962.3	NP_004953.1	P55107	BMP3B_HUMAN	growth differentiation factor 10	358					fat cell differentiation (GO:0045444)|growth (GO:0040007)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(20)|skin(1)	31						TCGTCTTCTCGTCAAAGTCCA	0.637																																					p.D358D		Atlas-SNP	.											.	GDF10	79	.	0			c.C1074T						.	G		0,4406		0,0,2203	85	73	77		1074	-8.3	0.4	10		77	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GDF10	NM_004962.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		358/479	48428812	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	2662	exon2			CTTCTCGTCAAAG	L42113	CCDS73117.1	10q11.22	2014-04-10			ENSG00000107623	ENSG00000266524		"Endogenous ligands"	4215	protein-coding gene	gene with protein product		601361				8679252	Standard	NM_004962		Approved	BMP-3b	uc001jfb.3	P55107	OTTHUMG00000188319	ENST00000224605.2:c.1074C>T	chr10.hg19:g.48428812G>A		122.0	0.0		160.0	49.0	NM_004962	Q5VSQ8|Q9UCX6	Silent	SNP	ENST00000224605.2	hg19	CCDS7220.1																																																																																			.	.		0.637	GDF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047884.1	NM_004962		A	48428812	G	A	48428812	2	1	147	1	0	0	0	0	0	0	0	1	6319	1136	40	1		1	GDF10	10	48428812	Silent	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10		48428812	87105935	39	22507										
TM9SF3	56889	hgsc.bcm.edu	37	chr10	98325145	98325145	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tgcatctctcttttctttatCtaaatcaatttcacagtaag	3	9	6	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr10:98325145C>A	ENST00000371142.4	-	3	553	c.337G>T	c.(337-339)Gat>Tat	p.D113Y		NM_020123.3	NP_064508.3	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3	113						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)	15		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		TTTTCTTTATCTAAATCAATT	0.303																																					p.D113Y		Atlas-SNP	.											.	TM9SF3	45	.	0			c.G337T						.						138	135	136					10																	98325145		2203	4300	6503	SO:0001583	missense	56889	exon3			CTTTATCTAAATC	AF160213, AF269150	CCDS7450.1	10q24.2	2006-04-12			ENSG00000077147	ENSG00000077147			21529	protein-coding gene	gene with protein product						11530251, 11595169	Standard	NM_020123		Approved	SMBP	uc001kmm.4	Q9HD45	OTTHUMG00000018834	ENST00000371142.4:c.337G>T	chr10.hg19:g.98325145C>A	ENSP00000360184:p.Asp113Tyr	61.0	0.0		90.0	26.0	NM_020123	Q5TB57|Q6UWE7|Q9NWL8|Q9P0G9|Q9UHW8	Missense_Mutation	SNP	ENST00000371142.4	hg19	CCDS7450.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380609	0.82792	.	.	ENSG00000077147	ENST00000371142;ENST00000443638	T;T	0.46063	0.88;0.88	5.79	5.79	0.91817	.	0.142109	0.64402	D	0.000007	T	0.49338	0.1551	M	0.79475	2.455	0.80722	D	1	P	0.39480	0.675	B	0.41894	0.369	T	0.55522	-0.8128	10	0.87932	D	0	-19.1802	12.3436	0.55107	0.0:0.9234:0.0:0.0766	.	113	Q9HD45	TM9S3_HUMAN	Y	113;69	ENSP00000360184:D113Y;ENSP00000401152:D69Y	ENSP00000360184:D113Y	D	-	1	0	TM9SF3	98315135	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.660000	0.61511	2.727000	0.93392	0.563000	0.77884	GAT	.	.		0.303	TM9SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049610.2	NM_020123		A	98325145	C	A	98325145	3	1	147	1	0	0	0	0	1	0	0	0	15994	913	32	3	1484	3	TM9SF3	10	98325145	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	49896333	98325145	37209602	40	22508										
TDRD1	56165	hgsc.bcm.edu	37	chr10	115985937	115985937	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	accaatcacctctagccaccTggcgcttcctttccaaatta	4	16	2	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr10:115985937T>C	ENST00000369280.1	+	22	3597	c.3137T>C	c.(3136-3138)cTg>cCg	p.L1046P	TDRD1_ENST00000251864.2_Missense_Mutation_p.L1046P|TDRD1_ENST00000369282.1_Missense_Mutation_p.L1046P|TDRD1_ENST00000422662.1_Missense_Mutation_p.L650P|TDRD1_ENST00000369281.2_Missense_Mutation_p.L932P			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	1046	Tudor 4. {ECO:0000255|PROSITE- ProRule:PRU00211}.				DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TCTAGCCACCTGGCGCTTCCT	0.423																																					p.L1046P		Atlas-SNP	.											.	TDRD1	126	.	0			c.T3137C						.						89	83	85					10																	115985937		2203	4300	6503	SO:0001583	missense	56165	exon22			GCCACCTGGCGCT	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.3137T>C	chr10.hg19:g.115985937T>C	ENSP00000358286:p.Leu1046Pro	87.0	0.0		100.0	38.0	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.93	3.917587	0.73098	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000422662;ENST00000369280	T;T;T;T;T	0.10668	2.85;2.85;2.85;2.85;2.85	6.01	6.01	0.97437	Tudor subgroup (1);Maternal tudor protein (1);Tudor domain (1);	0.215770	0.36703	N	0.002459	T	0.43897	0.1268	M	0.93150	3.385	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;0.999	T	0.53683	-0.8404	10	0.44086	T	0.13	-10.0464	15.0995	0.72262	0.0:0.0:0.0:1.0	.	650;1046;932;1046;932	Q9BXT4-4;Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2	.;TDRD1_HUMAN;.;.;.	P	1046;1046;932;650;1046	ENSP00000358288:L1046P;ENSP00000251864:L1046P;ENSP00000358287:L932P;ENSP00000402794:L650P;ENSP00000358286:L1046P	ENSP00000251864:L1046P	L	+	2	0	TDRD1	115975927	1.000000	0.71417	0.998000	0.56505	0.789000	0.44602	6.328000	0.72915	2.307000	0.77673	0.528000	0.53228	CTG	.	.		0.423	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			C	115985937	T	C	115985937	3	2	147	1	0	0	0	0	1	0	0	0	15745	1580	55	2	3219	2	TDRD1	10	115985937	Missense_Mutation	SNP	T	TCGA-DD-A73F-01A-11D-A32G-10	17660792	115985937	19548810	41	22509										
DPF2	5977	hgsc.bcm.edu	37	chr11	65116351	65116351	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tcttctgtgatgactgcgatCgtggctaccacatgtactgt	10	10	2	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr11:65116351C>G	ENST00000528416.1	+	10	1181	c.1048C>G	c.(1048-1050)Cgt>Ggt	p.R350G	DPF2_ENST00000415073.2_Missense_Mutation_p.R166G|DPF2_ENST00000252268.4_Missense_Mutation_p.R364G	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	350					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						TGACTGCGATCGTGGCTACCA	0.488																																					p.R350G		Atlas-SNP	.											DPF2,NS,carcinoma,0,1	DPF2	54	.	0			c.C1048G						.						222	178	193					11																	65116351		2201	4297	6498	SO:0001583	missense	5977	exon10			TGCGATCGTGGCT	U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"Zinc fingers, PHD-type"	9964	protein-coding gene	gene with protein product		601671	"requiem, apoptosis response zinc finger gene"	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.1048C>G	chr11.hg19:g.65116351C>G	ENSP00000436901:p.Arg350Gly	139.0	0.0		158.0	9.0	NM_006268	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	hg19	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.455040	0.84209	.	.	ENSG00000133884	ENST00000528416;ENST00000415073;ENST00000252268;ENST00000531989	D;T;D;T	0.85171	-1.95;0.43;-1.95;0.43	5.7	5.7	0.88788	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.38381	N	0.001704	D	0.92322	0.7564	M	0.77712	2.385	0.58432	D	0.999992	D;P	0.64830	0.994;0.946	D;P	0.74023	0.982;0.827	D	0.92837	0.6285	10	0.87932	D	0	-16.1324	17.3282	0.87255	0.0:1.0:0.0:0.0	.	166;350	B4DT58;Q92785	.;REQU_HUMAN	G	350;166;364;75	ENSP00000436901:R350G;ENSP00000399714:R166G;ENSP00000252268:R364G;ENSP00000435887:R75G	ENSP00000252268:R364G	R	+	1	0	DPF2	64872927	0.997000	0.39634	1.000000	0.80357	0.997000	0.91878	3.725000	0.54970	2.696000	0.92011	0.561000	0.74099	CGT	.	.		0.488	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		G	65116351	C	G	65116351	3	3	147	1	0	0	0	0	1	0	0	0	4719	884	31	4	1086	4	DPF2	11	65116351	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10		65116351	69890165	42	22510										
SPCS2	9789	hgsc.bcm.edu	37	chr11	74660392	74660392	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cggaggctgtagtggggctgGtggtgcttccaactgcggga	19	8	0	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr11:74660392G>A	ENST00000263672.6	+	1	101	c.62G>A	c.(61-63)gGt>gAt	p.G21D	XRRA1_ENST00000527087.1_5'Flank|XRRA1_ENST00000321448.8_5'Flank|SPCS2_ENST00000528265.1_Splice_Site|XRRA1_ENST00000533598.1_5'Flank|SPCS2_ENST00000530257.1_Missense_Mutation_p.G21D|XRRA1_ENST00000340360.6_5'Flank|SPCS2_ENST00000526361.1_5'UTR	NM_014752.2	NP_055567.2	Q15005	SPCS2_HUMAN	signal peptidase complex subunit 2 homolog (S. cerevisiae)	21					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)			breast(1)	1						AGTGGGGCTGGTGGTGCTTCC	0.632																																					p.G21D		Atlas-SNP	.											.	SPCS2	17	.	0			c.G62A						.						94	133	121					11																	74660392		692	1591	2283	SO:0001583	missense	9789	exon1			GGGCTGGTGGTGC	D14658	CCDS44681.1	11q13.4	2008-02-05			ENSG00000118363	ENSG00000118363			28962	protein-coding gene	gene with protein product						7788527	Standard	NM_014752		Approved	KIAA0102	uc001ovu.2	Q15005	OTTHUMG00000165517	ENST00000263672.6:c.62G>A	chr11.hg19:g.74660392G>A	ENSP00000263672:p.Gly21Asp	43.0	0.0		66.0	25.0	NM_014752	Q15507|Q3KQT0|Q641R4|Q6FG65|Q6IRX0|Q6P1P4|Q96HU9	Missense_Mutation	SNP	ENST00000263672.6	hg19	CCDS44681.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.595104	0.28445	.	.	ENSG00000118363	ENST00000263672;ENST00000530257;ENST00000532972	.	.	.	4.95	3.97	0.46021	.	0.423912	0.23129	N	0.051608	T	0.28200	0.0696	N	0.22421	0.69	0.26976	N	0.965477	B	0.18968	0.032	B	0.17098	0.017	T	0.12553	-1.0543	9	0.51188	T	0.08	-7.0932	10.0684	0.42317	0.0:0.0:0.7999:0.2001	.	21	Q15005	SPCS2_HUMAN	D	21	.	ENSP00000263672:G21D	G	+	2	0	SPCS2	74338040	0.923000	0.31300	0.995000	0.50966	0.322000	0.28314	2.437000	0.44828	2.730000	0.93505	0.655000	0.94253	GGT	.	.		0.632	SPCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384587.1	NM_014752		A	74660392	G	A	74660392	3	1	147	1	0	0	0	0	1	0	0	0	15039	1261	44	3	64	3	SPCS2	11	74660392	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	9544041	74660392	60346124	43	22511										
PTPRB	5787	hgsc.bcm.edu	37	chr12	71003577	71003577	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	gtgatccacaaggccaacccGgctccatggctcagcattgc	10	15	1	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr12:71003577G>A	ENST00000261266.5	-	1	47	c.18C>T	c.(16-18)gcC>gcT	p.A6A	PTPRB_ENST00000551525.1_Intron|PTPRB_ENST00000334414.6_Intron|PTPRB_ENST00000550857.1_Silent_p.A6A|PTPRB_ENST00000550358.1_Intron|PTPRB_ENST00000538174.2_Intron|PTPRB_ENST00000451516.2_Silent_p.A6A|PTPRB_ENST00000538708.1_Silent_p.A6A	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	6					angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			AGGCCAACCCGGCTCCATGGC	0.647																																					p.A6A		Atlas-SNP	.											.	PTPRB	676	.	0			c.C18T						.						18	21	20					12																	71003577		2040	4216	6256	SO:0001819	synonymous_variant	5787	exon1			CAACCCGGCTCCA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.18C>T	chr12.hg19:g.71003577G>A		74.0	0.0		93.0	27.0	NM_001206972	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.647	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			A	71003577	G	A	71003577	2	1	147	1	0	0	0	0	0	0	0	1	12811	1103	39	1		1	PTPRB	12	71003577	Silent	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10		71003577	62848318	44	22512										
ACACB	32	hgsc.bcm.edu	37	chr12	109677646	109677646	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ctttggcaggaagcctccttCgaatacctgcagaacgaggg	12	11	0	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr12:109677646C>A	ENST00000338432.7	+	35	4793	c.4674C>A	c.(4672-4674)ttC>ttA	p.F1558L	ACACB_ENST00000377848.3_Missense_Mutation_p.F1558L|ACACB_ENST00000377854.5_Missense_Mutation_p.F1488L|ACACB_ENST00000543201.1_Missense_Mutation_p.F224L			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1558					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	AAGCCTCCTTCGAATACCTGC	0.622																																					p.F1558L		Atlas-SNP	.											.	ACACB	330	.	0			c.C4674A						.						48	40	43					12																	109677646		2203	4300	6503	SO:0001583	missense	32	exon34			CTCCTTCGAATAC	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.4674C>A	chr12.hg19:g.109677646C>A	ENSP00000341044:p.Phe1558Leu	50.0	0.0		66.0	12.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.728023	0.30593	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027;ENST00000543201	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	4.01	2.07	0.26955	Acetyl-CoA carboxylase, central domain (1);	0.000000	0.85682	D	0.000000	T	0.55114	0.1900	M	0.67953	2.075	0.48040	D	0.999573	D	0.89917	1.0	D	0.91635	0.999	T	0.49224	-0.8962	10	0.25106	T	0.35	.	8.2716	0.31846	0.0:0.5642:0.0:0.4358	.	1558	O00763	ACACB_HUMAN	L	1558;1558;1488;789;224	ENSP00000341044:F1558L;ENSP00000367079:F1558L;ENSP00000367085:F1488L;ENSP00000444075:F224L	ENSP00000341044:F1558L	F	+	3	2	ACACB	108162029	0.695000	0.27747	1.000000	0.80357	0.989000	0.77384	-0.146000	0.10250	0.385000	0.24970	0.561000	0.74099	TTC	.	.		0.622	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		A	109677646	C	A	109677646	3	1	147	1	0	0	0	0	1	0	0	0	107	883	31	1	4808	1	ACACB	12	109677646	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	38674069	109677646	24174249	45	22513										
RPH3A	22895	hgsc.bcm.edu	37	chr12	113303242	113303242	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cctggtggaccgcctagaaaAcatgaggaagaacgtggctg	14	9	0	3			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr12:113303242A>T	ENST00000389385.4	+	6	751	c.254A>T	c.(253-255)aAc>aTc	p.N85I	RPH3A_ENST00000447659.2_Missense_Mutation_p.N36I|RPH3A_ENST00000415485.3_Missense_Mutation_p.N85I|RPH3A_ENST00000551052.1_Missense_Mutation_p.N81I|RPH3A_ENST00000548866.1_Missense_Mutation_p.N36I|RPH3A_ENST00000420983.2_Missense_Mutation_p.N85I|RPH3A_ENST00000543106.2_Missense_Mutation_p.N85I	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	85	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		CGCCTAGAAAACATGAGGAAG	0.542																																					p.N85I		Atlas-SNP	.											.	RPH3A	98	.	0			c.A254T						.						202	181	188					12																	113303242		2203	4300	6503	SO:0001583	missense	22895	exon6			TAGAAAACATGAG	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.254A>T	chr12.hg19:g.113303242A>T	ENSP00000374036:p.Asn85Ile	90.0	0.0		88.0	18.0	NM_001143854	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	hg19	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	A	18.64	3.667363	0.67814	.	.	ENSG00000089169	ENST00000548197;ENST00000547686;ENST00000543106;ENST00000551593;ENST00000551748;ENST00000547840;ENST00000547728;ENST00000549769;ENST00000552667;ENST00000389385;ENST00000447659;ENST00000550901;ENST00000551198;ENST00000551052;ENST00000415485;ENST00000553114;ENST00000548866;ENST00000420983	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	5.61	0.195	0.15151	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Rabphilin-3A effector, zinc-binding (1);Zinc finger, FYVE/PHD-type (1);	0.293525	0.29185	N	0.012882	T	0.76321	0.3971	M	0.66297	2.02	0.31698	N	0.641007	P;P;P;P	0.39624	0.631;0.681;0.681;0.631	B;B;B;B	0.41619	0.165;0.361;0.255;0.165	T	0.78658	-0.2118	10	0.87932	D	0	.	14.0515	0.64739	0.4779:0.5221:0.0:0.0	.	36;85;85;81	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	I	85;85;85;85;85;85;85;85;85;85;36;18;85;81;85;85;36;85	ENSP00000446570:N85I;ENSP00000449705:N85I;ENSP00000440384:N85I;ENSP00000446780:N85I;ENSP00000447306:N85I;ENSP00000450382:N85I;ENSP00000449613:N85I;ENSP00000447505:N85I;ENSP00000449650:N85I;ENSP00000374036:N85I;ENSP00000413254:N36I;ENSP00000448100:N18I;ENSP00000447083:N85I;ENSP00000448297:N81I;ENSP00000405357:N85I;ENSP00000450216:N85I;ENSP00000450347:N36I;ENSP00000408889:N85I	ENSP00000374036:N85I	N	+	2	0	RPH3A	111787625	1.000000	0.71417	0.996000	0.52242	0.909000	0.53808	3.100000	0.50275	-0.194000	0.10399	-1.236000	0.01555	AAC	.	.		0.542	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		T	113303242	A	T	113303242	3	4	147	1	0	0	0	0	1	0	0	0	13566	43	2	4	268	4	RPH3A	12	113303242	Missense_Mutation	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10	3625596	113303242	20548653	46	22514										
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84454719	84454719	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cagttgcctgggatctttgtAcctccgtttggagcagaccc	11	12	1	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr13:84454719A>T	ENST00000377084.2	-	1	1809	c.924T>A	c.(922-924)ggT>ggA	p.G308G		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	308					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		GGATCTTTGTACCTCCGTTTG	0.537																																					p.G308G		Atlas-SNP	.											.	SLITRK1	196	.	0			c.T924A						.						76	75	75					13																	84454719		2203	4300	6503	SO:0001819	synonymous_variant	114798	exon1			CTTTGTACCTCCG	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.924T>A	chr13.hg19:g.84454719A>T		125.0	0.0		83.0	42.0	NM_052910	Q5U5I6|Q96SF9	Silent	SNP	ENST00000377084.2	hg19	CCDS9464.1																																																																																			.	.		0.537	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		T	84454719	A	T	84454719	2	4	147	1	0	0	0	0	0	0	0	1	14757	378	14	4		4	SLITRK1	13	84454719	Silent	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10		84454719	30715159	47	22515										
F10	2159	hgsc.bcm.edu	37	chr13	113795287	113795287	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ctgtgaccagttctgccacgAggaacagaactctgtggtgt	12	10	2	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr13:113795287A>T	ENST00000375559.3	+	5	463	c.425A>T	c.(424-426)gAg>gTg	p.E142V	F10_ENST00000375551.3_Missense_Mutation_p.E142V|F10_ENST00000409306.1_Missense_Mutation_p.E142V	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	142	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.		E -> K (in FA10D; uncertain pathological significance; detected in patients carrying K-54 or P-374; slightly reduced activity; dbSNP:rs61753266). {ECO:0000269|PubMed:1973167, ECO:0000269|PubMed:7669671}.		blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(4)|lung(10)|pancreas(1)|stomach(1)	18	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Antihemophilic Factor(DB00025)|Apixaban(DB06605)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Menadione(DB00170)|Rivaroxaban(DB06228)	TTCTGCCACGAGGAACAGAAC	0.617																																					p.E142V		Atlas-SNP	.											.	F10	53	.	0			c.A425T						.						112	95	101					13																	113795287		2203	4300	6503	SO:0001583	missense	2159	exon5			GCCACGAGGAACA		CCDS9530.1	13q34	2012-10-02			ENSG00000126218	ENSG00000126218	3.4.21.6		3528	protein-coding gene	gene with protein product		613872					Standard	XM_005268298		Approved		uc001vsx.3	P00742	OTTHUMG00000017374	ENST00000375559.3:c.425A>T	chr13.hg19:g.113795287A>T	ENSP00000364709:p.Glu142Val	91.0	0.0		117.0	27.0	NM_000504	Q14340	Missense_Mutation	SNP	ENST00000375559.3	hg19	CCDS9530.1	.	.	.	.	.	.	.	.	.	.	A	6.286	0.420841	0.11928	.	.	ENSG00000126218	ENST00000409306;ENST00000375551;ENST00000375559	D;D;D	0.96491	-4.03;-4.03;-4.03	4.68	3.4	0.38934	Epidermal growth factor-like (1);	0.301259	0.31257	N	0.007962	D	0.91078	0.7192	L	0.38649	1.16	0.09310	N	1	P;P;B	0.39480	0.675;0.553;0.011	B;B;B	0.31442	0.13;0.13;0.028	D	0.85347	0.1099	10	0.40728	T	0.16	.	9.9877	0.41852	0.8305:0.1695:0.0:0.0	.	142;142;142	B7ZBK1;Q5JVE8;P00742	.;.;FA10_HUMAN	V	142	ENSP00000387092:E142V;ENSP00000364701:E142V;ENSP00000364709:E142V	ENSP00000364701:E142V	E	+	2	0	F10	112843288	0.003000	0.15002	0.057000	0.19452	0.514000	0.34195	0.792000	0.26929	1.870000	0.54199	0.379000	0.24179	GAG	.	.		0.617	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3			T	113795287	A	T	113795287	3	4	147	1	0	0	0	0	1	0	0	0	5338	304	11	4	443	4	F10	13	113795287	Missense_Mutation	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10	29340568	113795287	1374591	48	22516										
INO80	54617	hgsc.bcm.edu	37	chr15	41388013	41388013	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	acattccagaactgcctgctCcagaagtttcaccaagcaat	6	13	1	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr15:41388013C>A	ENST00000361937.3	-	3	681	c.257G>T	c.(256-258)gGa>gTa	p.G86V	INO80_ENST00000401393.3_Missense_Mutation_p.G86V			Q9ULG1	INO80_HUMAN	INO80 complex subunit	86	Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						ACTGCCTGCTCCAGAAGTTTC	0.443																																					p.G86V		Atlas-SNP	.											.	INO80	122	.	0			c.G257T						.						70	73	72					15																	41388013		2203	4300	6503	SO:0001583	missense	54617	exon3			CCTGCTCCAGAAG	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.257G>T	chr15.hg19:g.41388013C>A	ENSP00000355205:p.Gly86Val	93.0	0.0		101.0	33.0	NM_017553	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	hg19	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.317110	0.60524	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.90504	-2.68;-2.68	6.08	4.11	0.48088	.	0.268091	0.38663	N	0.001611	D	0.84906	0.5576	L	0.43152	1.355	0.80722	D	1	P	0.37781	0.608	B	0.36534	0.227	T	0.81322	-0.0985	10	0.16896	T	0.51	.	11.6218	0.51121	0.0:0.8083:0.1249:0.0667	.	86	Q9ULG1	INO80_HUMAN	V	86	ENSP00000355205:G86V;ENSP00000384686:G86V	ENSP00000355205:G86V	G	-	2	0	INO80	39175305	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.794000	0.47853	1.580000	0.49851	0.591000	0.81541	GGA	.	.		0.443	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		A	41388013	C	A	41388013	3	1	147	1	0	0	0	0	1	0	0	0	7755	855	30	3	4549	3	INO80	15	41388013	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10		41388013	61143379	49	22517										
MGA	23269	hgsc.bcm.edu	37	chr15	42028493	42028493	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	gatcatctcagactgcaactGggaggaagatcggaacaaga	12	8	2	3			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr15:42028493G>A	ENST00000570161.1	+	12	4031	c.4031G>A	c.(4030-4032)tGg>tAg	p.W1344*	MGA_ENST00000566586.1_Nonsense_Mutation_p.W1344*|MGA_ENST00000545763.1_Nonsense_Mutation_p.W1344*|MGA_ENST00000389936.4_Nonsense_Mutation_p.W1344*|MGA_ENST00000219905.7_Nonsense_Mutation_p.W1344*			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GACTGCAACTGGGAGGAAGAT	0.453																																					p.W1344X		Atlas-SNP	.											.	MGA	264	.	0			c.G4031A						.						142	131	135					15																	42028493		1945	4158	6103	SO:0001587	stop_gained	23269	exon13			GCAACTGGGAGGA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.4031G>A	chr15.hg19:g.42028493G>A	ENSP00000457035:p.Trp1344*	83.0	0.0		96.0	33.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Nonsense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.565420	0.86439	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	.	.	.	5.82	5.82	0.92795	.	0.431614	0.21057	N	0.080882	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.3562	0.83236	0.0:0.0:0.8676:0.1324	.	.	.	.	X	1344	.	ENSP00000219905:W1344X	W	+	2	0	MGA	39815785	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.063000	0.64332	2.757000	0.94681	0.585000	0.79938	TGG	.	.		0.453	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42028493	G	A	42028493	4	1	147	1	0	0	0	0	0	1	0	0	9549	1357	47	3	4077	3	MGA	15	42028493	Nonsense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	640480	42028493	60502899	50	22518										
PIGB	9488	hgsc.bcm.edu	37	chr15	55647553	55647553	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tcttccacactcacttgccaGagggtcgaattggaagtcac	9	12	3	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr15:55647553G>A	ENST00000164305.5	+	12	1879	c.1588G>A	c.(1588-1590)Gag>Aag	p.E530K	PIGB_ENST00000539642.1_Missense_Mutation_p.E335K|CCPG1_ENST00000442196.3_3'UTR|CCPG1_ENST00000310958.6_3'UTR|DYX1C1-CCPG1_ENST00000565113.1_RNA	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	530					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		TCACTTGCCAGAGGGTCGAAT	0.318																																					p.E530K		Atlas-SNP	.											.	PIGB	36	.	0			c.G1588A						.						84	83	83					15																	55647553		1822	4074	5896	SO:0001583	missense	9488	exon12			TTGCCAGAGGGTC	D42138	CCDS61641.1	15q21.3	2013-02-26	2006-06-28		ENSG00000069943	ENSG00000069943		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	8959	protein-coding gene	gene with protein product	"GPI mannosyltransferase 3", "dol-P-Man dependent GPI mannosyltransferase"	604122	"phosphatidylinositol glycan, class B"			8861954	Standard	NM_004855		Approved		uc002act.3	Q92521	OTTHUMG00000172654	ENST00000164305.5:c.1588G>A	chr15.hg19:g.55647553G>A	ENSP00000164305:p.Glu530Lys	147.0	0.0		181.0	13.0	NM_004855	Q53FF9|Q8WVN7	Missense_Mutation	SNP	ENST00000164305.5	hg19		.	.	.	.	.	.	.	.	.	.	G	18.96	3.734651	0.69189	.	.	ENSG00000069943	ENST00000164305;ENST00000539642	T;T	0.59502	0.58;0.26	6.08	5.17	0.71159	.	0.049207	0.85682	D	0.000000	T	0.68063	0.2960	M	0.80183	2.485	0.80722	D	1	D	0.54772	0.968	P	0.54664	0.758	T	0.67677	-0.5609	10	0.22706	T	0.39	-8.206	10.9909	0.47549	0.0718:0.1379:0.7903:0.0	.	530	Q92521	PIGB_HUMAN	K	530;335	ENSP00000164305:E530K;ENSP00000438963:E335K	ENSP00000164305:E530K	E	+	1	0	PIGB	53434845	1.000000	0.71417	0.896000	0.35187	0.990000	0.78478	4.093000	0.57714	1.586000	0.49944	0.591000	0.81541	GAG	.	.		0.318	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855		A	55647553	G	A	55647553	3	1	147	1	0	0	0	0	1	0	0	0	11894	943	33	3	1634	3	PIGB	15	55647553	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	13619060	55647553	46883839	51	22519										
SLTM	79811	hgsc.bcm.edu	37	chr15	59192012	59192012	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	accgagatgttgtcatcctcAgcttctttcacagtcgtatg	8	11	4	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr15:59192012A>G	ENST00000380516.2	-	7	801	c.714T>C	c.(712-714)gcT>gcC	p.A238A	SLTM_ENST00000536328.1_Intron|SLTM_ENST00000557950.1_5'Flank	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	238	Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TGTCATCCTCAGCTTCTTTCA	0.443																																					p.A238A		Atlas-SNP	.											.	SLTM	90	.	0			c.T714C						.						166	141	150					15																	59192012		2192	4292	6484	SO:0001819	synonymous_variant	79811	exon7			ATCCTCAGCTTCT	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"RNA binding motif (RRM) containing"	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.714T>C	chr15.hg19:g.59192012A>G		106.0	0.0		124.0	43.0	NM_024755	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000380516.2	hg19	CCDS10168.2																																																																																			.	.		0.443	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755		G	59192012	A	G	59192012	2	3	147	1	0	0	0	0	0	0	0	1	14769	175	7	2		2	SLTM	15	59192012	Silent	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10	3544459	59192012	43339380	52	22520										
IGDCC3	9543	hgsc.bcm.edu	37	chr15	65622666	65622666	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ctcccctcaaagacacaaagCggactgtggcattgccatct	8	14	2	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr15:65622666C>T	ENST00000327987.4	-	11	2074	c.1823G>A	c.(1822-1824)cGc>cAc	p.R608H	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	608	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AGACACAAAGCGGACTGTGGC	0.592																																					p.R608H		Atlas-SNP	.											.	IGDCC3	82	.	0			c.G1823A						.						197	160	172					15																	65622666		2201	4299	6500	SO:0001583	missense	9543	exon11			ACAAAGCGGACTG	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9700	protein-coding gene	gene with protein product		604184	"putative neuronal cell adhesion molecule"	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.1823G>A	chr15.hg19:g.65622666C>T	ENSP00000332773:p.Arg608His	97.0	0.0		107.0	40.0	NM_004884	O95215	Missense_Mutation	SNP	ENST00000327987.4	hg19	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.631091	0.67015	.	.	ENSG00000174498	ENST00000327987;ENST00000443278	T	0.66638	-0.22	5.26	4.35	0.52113	Fibronectin, type III (1);	0.126644	0.53938	D	0.000051	T	0.79125	0.4393	M	0.71581	2.175	0.53688	D	0.999978	D	0.89917	1.0	D	0.69479	0.964	T	0.80513	-0.1349	10	0.54805	T	0.06	-32.1962	13.5931	0.61971	0.0:0.9255:0.0:0.0745	.	608	Q8IVU1	IGDC3_HUMAN	H	608;471	ENSP00000332773:R608H	ENSP00000332773:R608H	R	-	2	0	IGDCC3	63409719	1.000000	0.71417	0.923000	0.36655	0.285000	0.27093	7.466000	0.80914	1.218000	0.43458	0.655000	0.94253	CGC	.	.		0.592	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884		T	65622666	C	T	65622666	3	4	147	1	0	0	0	0	1	0	0	0	7577	768	27	1	637	1	IGDCC3	15	65622666	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	6430654	65622666	36908726	53	22521										
SLC5A11	115584	hgsc.bcm.edu	37	chr16	24920370	24920370	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tgtccacggtcaccctcatcActgtctccaccgtgagctgg	9	16	4	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr16:24920370A>C	ENST00000347898.3	+	14	2225	c.1603A>C	c.(1603-1605)Act>Cct	p.T535P	SLC5A11_ENST00000539472.1_Missense_Mutation_p.T471P|SLC5A11_ENST00000569071.1_Missense_Mutation_p.T379P|SLC5A11_ENST00000567758.1_Missense_Mutation_p.T500P|SLC5A11_ENST00000568579.1_Missense_Mutation_p.T465P|SLC5A11_ENST00000424767.2_Missense_Mutation_p.T500P|SLC5A11_ENST00000545376.1_Missense_Mutation_p.T465P|SLC5A11_ENST00000565769.1_Missense_Mutation_p.T471P|SLC5A11_ENST00000449109.2_Missense_Mutation_p.T379P	NM_052944.3	NP_443176.2			solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		CACCCTCATCACTGTCTCCAC	0.552																																					p.T535P		Atlas-SNP	.											.	SLC5A11	97	.	0			c.A1603C						.						132	100	111					16																	24920370		2197	4300	6497	SO:0001583	missense	115584	exon14			CTCATCACTGTCT	AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"Solute carriers"	23091	protein-coding gene	gene with protein product		610238	"solute carrier family 5 (sodium/glucose cotransporter), member 11"			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000347898.3:c.1603A>C	chr16.hg19:g.24920370A>C	ENSP00000289932:p.Thr535Pro	102.0	0.0		109.0	10.0	NM_052944		Missense_Mutation	SNP	ENST00000347898.3	hg19	CCDS10625.1	.	.	.	.	.	.	.	.	.	.	A	15.79	2.936599	0.52972	.	.	ENSG00000158865	ENST00000347898;ENST00000449109;ENST00000424767;ENST00000545376;ENST00000539472	T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0	6.08	4.98	0.66077	.	0.465232	0.26279	N	0.025297	T	0.70780	0.3263	M	0.66939	2.045	0.09310	N	1	D;D;D;D	0.65815	0.991;0.995;0.966;0.974	P;P;P;P	0.59703	0.642;0.862;0.543;0.497	T	0.64761	-0.6331	10	0.87932	D	0	.	7.3192	0.26517	0.8247:0.0:0.1753:0.0	.	465;500;535;379	B7Z329;Q8WWX8-2;Q8WWX8;Q05BF1	.;.;SC5AB_HUMAN;.	P	535;379;500;465;471	ENSP00000289932:T535P;ENSP00000389606:T379P;ENSP00000416782:T500P;ENSP00000441384:T465P;ENSP00000441018:T471P	ENSP00000289932:T535P	T	+	1	0	SLC5A11	24827871	0.006000	0.16342	0.010000	0.14722	0.655000	0.38815	1.476000	0.35420	1.099000	0.41499	0.482000	0.46254	ACT	.	.		0.552	SLC5A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214091.3	NM_052944		C	24920370	A	C	24920370	3	2	147	1	0	0	0	0	1	0	0	0	14678	159	6	5	1653	5	SLC5A11	16	24920370	Missense_Mutation	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10		24920370	65434383	54	22522										
ADCY7	113	hgsc.bcm.edu	37	chr16	50339757	50339757	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ctggagaagggctttgagcgCgaggtgagggcccccagcag	18	10	0	3			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr16:50339757C>T	ENST00000394697.2	+	14	2089	c.1749C>T	c.(1747-1749)cgC>cgT	p.R583R	ADCY7_ENST00000538642.1_Silent_p.R583R|ADCY7_ENST00000254235.3_Silent_p.R583R|ADCY7_ENST00000537579.1_3'UTR|ADCY7_ENST00000566433.2_Silent_p.R583R			P51828	ADCY7_HUMAN	adenylate cyclase 7	583					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		GCTTTGAGCGCGAGGTGAGGG	0.672																																					p.R583R		Atlas-SNP	.											ADCY7,colon,carcinoma,0,1	ADCY7	90	.	0			c.C1749T						.						43	42	42					16																	50339757		2198	4300	6498	SO:0001819	synonymous_variant	113	exon13			TGAGCGCGAGGTG	D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"Adenylate cyclases"	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.1749C>T	chr16.hg19:g.50339757C>T		106.0	0.0		113.0	41.0	NM_001114	A0AVA6	Silent	SNP	ENST00000394697.2	hg19	CCDS10741.1																																																																																			.	.		0.672	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3			T	50339757	C	T	50339757	2	4	147	1	0	0	0	0	0	0	0	1	299	755	27	1		1	ADCY7	16	50339757	Silent	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	25419387	50339757	40014996	55	22523										
MINK1	50488	hgsc.bcm.edu	37	chr17	4789860	4789860	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cgggaccagcccacggagcgGcaggtccgcatccagcttaa	13	15	0	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr17:4789860G>A	ENST00000355280.6	+	10	1084	c.888G>A	c.(886-888)cgG>cgA	p.R296R	MINK1_ENST00000347992.7_Silent_p.R296R|MINK1_ENST00000453408.3_Silent_p.R296R	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						CCACGGAGCGGCAGGTCCGCA	0.587																																					p.R296R		Atlas-SNP	.											.	MINK1	110	.	0			c.G888A						.						57	61	60					17																	4789860		1958	4132	6090	SO:0001819	synonymous_variant	50488	exon10			GGAGCGGCAGGTC	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"misshapen/NIK-related kinase"	609426	"misshapen-like kinase 1 (zebrafish)"			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.888G>A	chr17.hg19:g.4789860G>A		55.0	0.0		65.0	20.0	NM_170663		Silent	SNP	ENST00000355280.6	hg19	CCDS45588.1																																																																																			.	.		0.587	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		A	4789860	G	A	4789860	2	1	147	1	0	0	0	0	0	0	0	1	9596	1190	42	3		3	MINK1	17	4789860	Silent	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10		4789860	76405350	56	22524										
SLC16A3	9123	hgsc.bcm.edu	37	chr17	80195333	80195333	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ttccgggaccgcggctttgtGctttacgccgtggccgcctc	13	15	0	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr17:80195333G>T	ENST00000581287.1	+	3	3009	c.687G>T	c.(685-687)gtG>gtT	p.V229V	SLC16A3_ENST00000392341.1_Silent_p.V229V|SLC16A3_ENST00000582743.1_Silent_p.V229V|SLC16A3_ENST00000392339.1_Silent_p.V229V	NM_001206951.1|NM_001206952.1	NP_001193880.1|NP_001193881.1	O15427	MOT4_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 3	229					blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|leukocyte migration (GO:0050900)|monocarboxylic acid transport (GO:0015718)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|poly(A) RNA binding (GO:0044822)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	Breast(20;0.00285)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0149)		Gamma Hydroxybutyric Acid(DB01440)|Niacin(DB00627)|Pyruvic acid(DB00119)	GCGGCTTTGTGCTTTACGCCG	0.711																																					p.V229V	Pancreas(52;652 1135 19190 37282 52456)	Atlas-SNP	.											.	SLC16A3	19	.	0			c.G687T						.						16	18	17					17																	80195333		2187	4290	6477	SO:0001819	synonymous_variant	9123	exon4			CTTTGTGCTTTAC	U81800	CCDS11804.1	17q25.3	2013-07-18	2013-07-18		ENSG00000141526	ENSG00000141526		"Solute carriers"	10924	protein-coding gene	gene with protein product		603877	"solute carrier family 16 (monocarboxylic acid transporters), member 3", "solute carrier family 16, member 3 (monocarboxylic acid transporter 4)"			9425115	Standard	NM_004207		Approved	MCT3, MCT4	uc021ufm.1	O15427	OTTHUMG00000178832	ENST00000581287.1:c.687G>T	chr17.hg19:g.80195333G>T		32.0	0.0		83.0	5.0	NM_001206950	B3KXG8|Q2M1P8	Silent	SNP	ENST00000581287.1	hg19	CCDS11804.1																																																																																			.	.		0.711	SLC16A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443498.1	NM_004207		T	80195333	G	T	80195333	2	4	147	1	0	0	0	0	0	0	0	1	14424	1306	46	3		3	SLC16A3	17	80195333	Silent	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	75405473	80195333	999877	57	22525										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8784213	8784213	+	De_novo_Start_OutOfFrame	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	gctgctgtccaacatccagcGctgcgacctggcagcccacc	10	18	0	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr18:8784213G>A	ENST00000306285.7	+	0	1245				SOGA2_ENST00000400050.3_Missense_Mutation_p.R368H|SOGA2_ENST00000517570.1_Missense_Mutation_p.R368H|SOGA2_ENST00000306329.11_Missense_Mutation_p.R728H|SOGA2_ENST00000359865.3_Missense_Mutation_p.R368H																							AACATCCAGCGCTGCGACCTG	0.652																																					p.R368H		Atlas-SNP	.											CCDC165,NS,carcinoma,0,1	.	.	.	0			c.G1103A						.						30	34	33					18																	8784213		2203	4298	6501			23255	exon6			TCCAGCGCTGCGA																												ENST00000306285.7:c.-953G>A	chr18.hg19:g.8784213G>A		34.0	0.0		58.0	14.0	NM_015210		Missense_Mutation	SNP	ENST00000306285.7	hg19		.	.	.	.	.	.	.	.	.	.	G	15.09	2.730837	0.48939	.	.	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050	T;T;T	0.27720	1.65;1.75;1.65	5.15	5.15	0.70609	.	0.000000	0.47093	D	0.000243	T	0.62258	0.2413	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.69300	-0.5181	10	0.87932	D	0	-26.832	18.629	0.91352	0.0:0.0:1.0:0.0	.	389;368	A8MQ54;Q9Y4B5-3	.;.	H	389;368;368;368	ENSP00000429556:R368H;ENSP00000352927:R368H;ENSP00000382924:R368H	ENSP00000305027:R389H	R	+	2	0	CCDC165	8774213	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.468000	0.97676	2.413000	0.81919	0.650000	0.86243	CGC	.	.		0.652	SOGA2-201	KNOWN	basic	protein_coding	protein_coding				A	8784213	G	A	8784213	1	1	147	1	0	1	0	0	0	0	0	0	8203	1087	38	1		1	KIAA0802	18	8784213	De_novo_Start_OutOfFrame	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10		8784213	69293035	58	22526										
MUC16	94025	hgsc.bcm.edu	37	chr19	9074914	9074914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ggagggactgtgcccttgtgAtgtcaacaaaatattggaag	13	6	1	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr19:9074914A>G	ENST00000397910.4	-	3	12735	c.12532T>C	c.(12532-12534)Tca>Cca	p.S4178P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4180	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGCCCTTGTGATGTCAACAAA	0.512																																					p.S4178P		Atlas-SNP	.											.	MUC16	4315	.	0			c.T12532C						.						153	143	146					19																	9074914		1987	4159	6146	SO:0001583	missense	94025	exon3			CTTGTGATGTCAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.12532T>C	chr19.hg19:g.9074914A>G	ENSP00000381008:p.Ser4178Pro	128.0	0.0		181.0	64.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	4.943	0.175156	0.09391	.	.	ENSG00000181143	ENST00000397910	T	0.22134	1.97	1.12	-1.27	0.09347	.	.	.	.	.	T	0.11024	0.0269	N	0.19112	0.55	.	.	.	D	0.58268	0.982	B	0.41332	0.354	T	0.19778	-1.0295	8	0.87932	D	0	.	4.3322	0.11069	0.5028:0.0:0.4972:0.0	.	4178	B5ME49	.	P	4178	ENSP00000381008:S4178P	ENSP00000381008:S4178P	S	-	1	0	MUC16	8935914	0.000000	0.05858	0.001000	0.08648	0.363000	0.29612	-0.616000	0.05591	-0.553000	0.06158	0.260000	0.18958	TCA	.	.		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9074914	A	G	9074914	3	3	147	1	0	0	0	0	1	0	0	0	9982	333	12	2	31319	2	MUC16	19	9074914	Missense_Mutation	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10		9074914	50054069	59	22527										
AP1M1	8907	hgsc.bcm.edu	37	chr19	16338431	16338431	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	gcggctatcacgcttcgagaAtgaccgcaccatctccttca	8	15	3	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr19:16338431A>G	ENST00000291439.3	+	7	1195	c.746A>G	c.(745-747)aAt>aGt	p.N249S	AP1M1_ENST00000541844.1_Missense_Mutation_p.N177S|AP1M1_ENST00000444449.2_Missense_Mutation_p.N261S|AP1M1_ENST00000590756.1_Missense_Mutation_p.N177S|AP1M1_ENST00000429941.2_Missense_Mutation_p.N249S	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	249	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						CGCTTCGAGAATGACCGCACC	0.607																																					p.N261S		Atlas-SNP	.											.	AP1M1	48	.	0			c.A782G						.						283	231	249					19																	16338431		2203	4300	6503	SO:0001583	missense	8907	exon8			TCGAGAATGACCG		CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.746A>G	chr19.hg19:g.16338431A>G	ENSP00000291439:p.Asn249Ser	95.0	0.0		93.0	11.0	NM_001130524	Q4TTY5	Missense_Mutation	SNP	ENST00000291439.3	hg19	CCDS12342.1	.	.	.	.	.	.	.	.	.	.	A	11.75	1.731170	0.30684	.	.	ENSG00000072958	ENST00000444449;ENST00000291439;ENST00000541844;ENST00000429941	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	4.26	3.2	0.36748	Clathrin adaptor, mu subunit, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.12902	0.0313	L	0.33792	1.035	0.53005	D	0.999961	B;B;B	0.20368	0.005;0.044;0.025	B;B;B	0.27887	0.01;0.084;0.084	T	0.10314	-1.0635	10	0.19147	T	0.46	-40.2913	9.9444	0.41600	0.8286:0.1714:0.0:0.0	.	249;261;249	E7ENJ6;Q4TTY5;Q9BXS5	.;.;AP1M1_HUMAN	S	261;249;177;249	ENSP00000388996:N261S;ENSP00000291439:N249S;ENSP00000445682:N177S;ENSP00000411498:N249S	ENSP00000291439:N249S	N	+	2	0	AP1M1	16199431	1.000000	0.71417	0.589000	0.28718	0.929000	0.56500	5.837000	0.69381	0.646000	0.30693	0.459000	0.35465	AAT	.	.		0.607	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493		G	16338431	A	G	16338431	3	3	147	1	0	0	0	0	1	0	0	0	734	101	4	2	812	2	AP1M1	19	16338431	Missense_Mutation	SNP	A	TCGA-DD-A73F-01A-11D-A32G-10	7263517	16338431	42790552	60	22528										
ZNF607	84775	hgsc.bcm.edu	37	chr19	38189778	38189778	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tccttacatttgtagggtttCtcaccggtatgaatattttg	8	7	1	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr19:38189778C>T	ENST00000355202.4	-	5	1849	c.1254G>A	c.(1252-1254)gaG>gaA	p.E418E	ZNF607_ENST00000395835.3_Silent_p.E417E|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	418					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			TGTAGGGTTTCTCACCGGTAT	0.393																																					p.E418E		Atlas-SNP	.											.	ZNF607	82	.	0			c.G1254A						.						95	97	97					19																	38189778		2203	4300	6503	SO:0001819	synonymous_variant	84775	exon5			GGGTTTCTCACCG	AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.1254G>A	chr19.hg19:g.38189778C>T		67.0	0.0		70.0	26.0	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Silent	SNP	ENST00000355202.4	hg19	CCDS33006.1																																																																																			.	.		0.393	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		T	38189778	C	T	38189778	2	4	147	1	0	0	0	0	0	0	0	1	18048	912	32	3		3	ZNF607	19	38189778	Silent	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	21851347	38189778	20939205	61	22529										
KCNN4	3783	hgsc.bcm.edu	37	chr19	44278585	44278585	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cagggacagcagcgcttcccCttggcccaggaatcccggcc	12	17	0	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr19:44278585C>G	ENST00000262888.3	-	3	837	c.442G>C	c.(442-444)Ggg>Cgg	p.G148R		NM_002250.2	NP_002241.1	O15554	KCNN4_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	148					calcium ion transport (GO:0006816)|cell volume homeostasis (GO:0006884)|defense response (GO:0006952)|immune system process (GO:0002376)|phospholipid translocation (GO:0045332)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell receptor signaling pathway (GO:0050862)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|saliva secretion (GO:0046541)|stabilization of membrane potential (GO:0030322)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|Intermediate conductance calcium-activated potassium channel activity (GO:0022894)|protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0352)			Clotrimazole(DB00257)|Enflurane(DB00228)|Halothane(DB01159)|Miconazole(DB01110)|Procaine(DB00721)|Quinine(DB00468)	AGCGCTTCCCCTTGGCCCAGG	0.731											OREG0025535	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G148R		Atlas-SNP	.											.	KCNN4	37	.	0			c.G442C						.						10	11	11					19																	44278585		2175	4278	6453	SO:0001583	missense	3783	exon3			CTTCCCCTTGGCC	AF022797	CCDS12630.1	19q13.2	2012-07-05				ENSG00000104783		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6293	protein-coding gene	gene with protein product		602754				9380751, 9407042, 16382103	Standard	NM_002250		Approved	KCa3.1, hSK4, hKCa4, hIKCa1	uc002oxl.3	O15554		ENST00000262888.3:c.442G>C	chr19.hg19:g.44278585C>G	ENSP00000262888:p.Gly148Arg	62.0	0.0	922	47.0	18.0	NM_002250	Q53XR4	Missense_Mutation	SNP	ENST00000262888.3	hg19	CCDS12630.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.616355	0.28801	.	.	ENSG00000104783	ENST00000262888	D	0.99853	-7.18	3.61	2.44	0.29823	.	0.953602	0.08751	N	0.899144	D	0.98510	0.9503	N	0.08118	0	0.25606	N	0.986544	P;P	0.37015	0.578;0.454	B;B	0.31337	0.128;0.034	D	0.99987	1.3511	10	0.48119	T	0.1	-8.8391	9.8535	0.41070	0.205:0.795:0.0:0.0	.	42;148	D1MQ10;O15554	.;KCNN4_HUMAN	R	148	ENSP00000262888:G148R	ENSP00000262888:G148R	G	-	1	0	KCNN4	48970425	0.993000	0.37304	0.576000	0.28549	0.910000	0.53928	1.372000	0.34261	1.985000	0.57927	0.549000	0.68633	GGG	.	.		0.731	KCNN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463598.1	NM_002250		G	44278585	C	G	44278585	3	3	147	1	0	0	0	0	1	0	0	0	8090	681	24	4	865	4	KCNN4	19	44278585	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	6088807	44278585	14850398	62	22530										
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48602999	48602999	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	gtaattctcagacctcgctgCttggatggttttctgtaggc	11	9	2	1	rs574891473		TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr19:48602999C>G	ENST00000599921.1	-	5	733	c.376G>C	c.(376-378)Gca>Cca	p.A126P	PLA2G4C_ENST00000413144.2_Missense_Mutation_p.A126P|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.A126P|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.A136P			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	126	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		GACCTCGCTGCTTGGATGGTT	0.512																																					p.A136P		Atlas-SNP	.											PLA2G4C,NS,carcinoma,0,1	PLA2G4C	76	.	0			c.G406C						.						195	175	182					19																	48602999		2203	4300	6503	SO:0001583	missense	8605	exon5			TCGCTGCTTGGAT	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.376G>C	chr19.hg19:g.48602999C>G	ENSP00000469473:p.Ala126Pro	92.0	0.0		96.0	27.0	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	hg19	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.844889	0.51164	.	.	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.24151	1.87;1.87	3.17	-1.14	0.09741	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	2.133970	0.02758	U	0.118260	T	0.49830	0.1580	M	0.79123	2.44	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.993;0.995	T	0.42949	-0.9421	10	0.27082	T	0.32	-2.4518	8.6279	0.33901	0.5925:0.4075:0.0:0.0	.	136;126;126	B4DI40;Q8WWC5;Q9UP65	.;.;PA24C_HUMAN	P	126	ENSP00000346228:A126P;ENSP00000400036:A126P	ENSP00000346228:A126P	A	-	1	0	PLA2G4C	53294811	0.162000	0.22906	0.000000	0.03702	0.300000	0.27592	0.471000	0.22100	-0.423000	0.07394	0.411000	0.27672	GCA	.	.		0.512	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			G	48602999	C	G	48602999	3	3	147	1	0	0	0	0	1	0	0	0	12012	797	28	4	1305	4	PLA2G4C	19	48602999	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	4324414	48602999	10525984	63	22531										
NLRP4	147945	hgsc.bcm.edu	37	chr19	56369797	56369797	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	atcccgctcctctgctggatCctgtgtaccagtctgaagca	9	14	2	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr19:56369797C>T	ENST00000301295.6	+	3	1460	c.1038C>T	c.(1036-1038)atC>atT	p.I346I	NLRP4_ENST00000346986.5_Silent_p.I346I|NLRP4_ENST00000587891.1_Silent_p.I271I	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	346	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TCTGCTGGATCCTGTGTACCA	0.478																																					p.I346I		Atlas-SNP	.											.	NLRP4	331	.	0			c.C1038T						.						52	51	51					19																	56369797		2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			CTGGATCCTGTGT	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1038C>T	chr19.hg19:g.56369797C>T		49.0	0.0		74.0	32.0	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	hg19	CCDS12936.1																																																																																			.	.		0.478	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56369797	C	T	56369797	2	4	147	1	0	0	0	0	0	0	0	1	10488	845	30	3		3	NLRP4	19	56369797	Silent	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	7766798	56369797	2759186	64	22532										
MC3R	4159	hgsc.bcm.edu	37	chr20	54824818	54824818	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ctttccggagcctggaattgCgcaacacctttagggagatt	11	10	0	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr20:54824818C>T	ENST00000243911.2	+	1	1031	c.919C>T	c.(919-921)Cgc>Tgc	p.R307C		NM_019888.3	NP_063941.3	P41968	MC3R_HUMAN	melanocortin 3 receptor	307					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|homoiothermy (GO:0042309)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of blood pressure (GO:0008217)|regulation of heart rate (GO:0002027)|sodium ion homeostasis (GO:0055078)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)	p.R344C(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(3)|skin(1)	26			Colorectal(105;0.202)			CCTGGAATTGCGCAACACCTT	0.517																																					p.R307C		Atlas-SNP	.											MC3R,colon,carcinoma,-1,2	MC3R	83	.	1	Substitution - Missense(1)	breast(1)	c.C919T						.						171	162	165					20																	54824818		2203	4300	6503	SO:0001583	missense	4159	exon1			GAATTGCGCAACA		CCDS13449.2	20q13.2-q13.3	2012-08-10			ENSG00000124089	ENSG00000124089		"GPCR / Class A : Melanocortin receptors"	6931	protein-coding gene	gene with protein product		155540				8463333	Standard	NM_019888		Approved	MC3	uc002xxb.2	P41968	OTTHUMG00000032785	ENST00000243911.2:c.919C>T	chr20.hg19:g.54824818C>T	ENSP00000243911:p.Arg307Cys	131.0	0.0		203.0	53.0	NM_019888	Q4KN27|Q9H517	Missense_Mutation	SNP	ENST00000243911.2	hg19	CCDS13449.2	.	.	.	.	.	.	.	.	.	.	C	12.54	1.967174	0.34754	.	.	ENSG00000124089	ENST00000243911	T	0.58358	0.34	5.09	3.06	0.35304	.	0.000000	0.64402	D	0.000014	T	0.80989	0.4730	H	0.97440	4.005	0.54753	D	0.999986	D	0.89917	1.0	D	0.83275	0.996	D	0.85842	0.1398	10	0.87932	D	0	.	13.1951	0.59734	0.4134:0.5866:0.0:0.0	.	344	P41968	MC3R_HUMAN	C	307	ENSP00000243911:R307C	ENSP00000243911:R307C	R	+	1	0	MC3R	54258225	1.000000	0.71417	0.993000	0.49108	0.191000	0.23601	2.103000	0.41806	0.477000	0.27464	0.555000	0.69702	CGC	.	.		0.517	MC3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079786.2			T	54824818	C	T	54824818	3	4	147	1	0	0	0	0	1	0	0	0	9374	768	27	1	921	1	MC3R	20	54824818	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10		54824818	8200702	65	22533										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61981053	61981053	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tggtctgcaatgtactggacGccctccaccgcccgggtcag	12	15	2	0			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr20:61981053G>A	ENST00000370263.4	-	5	1931	c.1710C>T	c.(1708-1710)ggC>ggT	p.G570G	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	570					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	TGTACTGGACGCCCTCCACCG	0.687																																					p.G570G		Atlas-SNP	.											.	CHRNA4	98	.	0			c.C1710T						.						45	53	51					20																	61981053		2201	4300	6501	SO:0001819	synonymous_variant	1137	exon5			CTGGACGCCCTCC		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1710C>T	chr20.hg19:g.61981053G>A		82.0	0.0		127.0	61.0	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Silent	SNP	ENST00000370263.4	hg19	CCDS13517.1																																																																																			.	.		0.687	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			A	61981053	G	A	61981053	2	1	147	1	0	0	0	0	0	0	0	1	3387	1074	38	1		1	CHRNA4	20	61981053	Silent	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	7156235	61981053	1044467	66	22534										
TPTE	7179	hgsc.bcm.edu	37	chr21	10971325	10971325	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cgagctcaatgatgactcccGccaggtcagtcggatcagga	12	12	3	2	rs139096194	byFrequency	TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr21:10971325G>T	ENST00000361285.4	-	5	361	c.32C>A	c.(31-33)gCg>gAg	p.A11E	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Missense_Mutation_p.A11E|TPTE_ENST00000298232.7_Missense_Mutation_p.A11E	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	11					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.A11V(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GATGACTCCCGCCAGGTCAGT	0.448																																					p.A11E		Atlas-SNP	.											TPTE_ENST00000361285,NS,carcinoma,+1,3	TPTE	513	.	1	Substitution - Missense(1)	large_intestine(1)	c.C32A						.						121	97	105					21																	10971325		2203	4300	6503	SO:0001583	missense	7179	exon5			ACTCCCGCCAGGT	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.32C>A	chr21.hg19:g.10971325G>T	ENSP00000355208:p.Ala11Glu	51.0	0.0		101.0	21.0	NM_199259	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	g	0.012	-1.680387	0.00745	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420;ENST00000328758	D;D;D	0.95342	-3.52;-3.61;-3.68	0.728	-1.46	0.08800	.	.	.	.	.	D	0.82875	0.5132	N	0.08118	0	0.09310	N	1	B;B;B	0.29936	0.001;0.262;0.0	B;B;B	0.29663	0.001;0.105;0.0	T	0.61501	-0.7050	9	0.29301	T	0.29	.	0.8066	0.01085	0.1897:0.1806:0.3753:0.2543	.	11;11;11	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	E	11	ENSP00000298232:A11E;ENSP00000355208:A11E;ENSP00000344441:A11E	ENSP00000298232:A11E	A	-	2	0	TPTE	9993196	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.248000	0.02890	-3.986000	0.00084	-2.931000	0.00088	GCG	.	G|1.000;A|0.000		0.448	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			T	10971325	G	T	10971325	3	4	147	1	0	0	0	0	1	0	0	0	16445	1087	38	1	1703	1	TPTE	21	10971325	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10		10971325	37158570	67	22535										
KRTAP13-2	337959	hgsc.bcm.edu	37	chr21	31744148	31744148	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cagcttccataacccagggaTctgacaccactggacccaca	7	16	1	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr21:31744148T>C	ENST00000399889.2	-	1	409	c.384A>G	c.(382-384)agA>agG	p.R128R		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	128						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						AACCCAGGGATCTGACACCAC	0.577																																					p.R128R		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.A384G						.						68	64	66					21																	31744148		2203	4300	6503	SO:0001819	synonymous_variant	337959	exon1			CAGGGATCTGACA	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"Keratin associated proteins"	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.384A>G	chr21.hg19:g.31744148T>C		86.0	0.0		91.0	31.0	NM_181621		Silent	SNP	ENST00000399889.2	hg19	CCDS13589.1																																																																																			.	.		0.577	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1			C	31744148	T	C	31744148	2	2	147	1	0	0	0	0	0	0	0	1	8532	1432	50	2		2	KRTAP13-2	21	31744148	Silent	SNP	T	TCGA-DD-A73F-01A-11D-A32G-10	20772823	31744148	16385747	68	22536										
ELFN2	114794	hgsc.bcm.edu	37	chr22	37769399	37769399	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	cttgaggaaggacacgcgctGgctcaggctgtcggcaccct	14	13	1	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr22:37769399G>T	ENST00000402918.2	-	3	2961	c.2176C>A	c.(2176-2178)Cag>Aag	p.Q726K	RP1-63G5.5_ENST00000430883.1_RNA|RP1-63G5.8_ENST00000609322.1_RNA|ELFN2_ENST00000435824.1_5'Flank	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	726					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					GACACGCGCTGGCTCAGGCTG	0.652																																					p.Q726K		Atlas-SNP	.											.	ELFN2	89	.	0			c.C2176A						.						43	41	41					22																	37769399		2202	4300	6502	SO:0001583	missense	114794	exon3			CGCGCTGGCTCAG	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing"	29396	protein-coding gene	gene with protein product			"leucine rich repeat containing 62", "extracellular leucine-rich repeat and fibronectin type III containing 2", "extracellular leucine-rich repeat and fibronectin type III domain containing 2", "protein phosphatase 1, regulatory subunit 29"	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.2176C>A	chr22.hg19:g.37769399G>T	ENSP00000385277:p.Gln726Lys	41.0	0.0		107.0	5.0	NM_052906	Q96PY3	Missense_Mutation	SNP	ENST00000402918.2	hg19	CCDS33642.1	.	.	.	.	.	.	.	.	.	.	G	16.02	3.002811	0.54254	.	.	ENSG00000166897	ENST00000349653;ENST00000402918	T;T	0.51574	0.7;0.7	4.93	4.93	0.64822	.	0.138847	0.51477	D	0.000091	T	0.39911	0.1096	L	0.34521	1.04	0.80722	D	1	B	0.28233	0.204	B	0.21360	0.034	T	0.33394	-0.9870	10	0.56958	D	0.05	-23.9469	18.1427	0.89644	0.0:0.0:1.0:0.0	.	726	Q5R3F8	PPR29_HUMAN	K	726	ENSP00000300147:Q726K;ENSP00000385277:Q726K	ENSP00000300147:Q726K	Q	-	1	0	ELFN2	36099345	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.526000	0.81920	2.265000	0.75225	0.561000	0.74099	CAG	.	.		0.652	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906		T	37769399	G	T	37769399	3	4	147	1	0	0	0	0	1	0	0	0	5060	1357	47	3	290	3	ELFN2	22	37769399	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10		37769399	13535167	69	22537										
CARD10	29775	hgsc.bcm.edu	37	chr22	37893159	37893159	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ctgggccccctggggggctcCggccagacacccgaatagcc	14	17	0	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr22:37893159C>T	ENST00000403299.1	-	13	2030	c.1814G>A	c.(1813-1815)cGg>cAg	p.R605Q	CARD10_ENST00000251973.5_Missense_Mutation_p.R605Q|CARD10_ENST00000406271.3_Missense_Mutation_p.R319Q			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	605					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					TGGGGGGCTCCGGCCAGACAC	0.567																																					p.R605Q		Atlas-SNP	.											.	CARD10	55	.	0			c.G1814A						.						55	64	61					22																	37893159		2203	4300	6503	SO:0001583	missense	29775	exon12			GGGCTCCGGCCAG	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1814G>A	chr22.hg19:g.37893159C>T	ENSP00000384570:p.Arg605Gln	84.0	0.0		149.0	80.0	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	hg19	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	C	14.55	2.567962	0.45798	.	.	ENSG00000100065	ENST00000403299;ENST00000406271;ENST00000251973;ENST00000437756;ENST00000433485	T;T;T;T	0.40225	1.04;2.74;1.04;1.49	5.52	3.2	0.36748	.	1.067200	0.07216	N	0.860036	T	0.28134	0.0694	L	0.40543	1.245	0.25159	N	0.990365	B;P	0.45283	0.397;0.855	B;B	0.34536	0.042;0.185	T	0.13980	-1.0489	10	0.33940	T	0.23	-3.5096	4.8979	0.13760	0.2134:0.6774:0.0:0.1091	.	605;319	Q9BWT7;Q8NC81	CAR10_HUMAN;.	Q	605;319;605;246;77	ENSP00000384570:R605Q;ENSP00000385799:R319Q;ENSP00000251973:R605Q;ENSP00000416239:R246Q	ENSP00000251973:R605Q	R	-	2	0	CARD10	36223105	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	1.679000	0.37597	2.586000	0.87340	0.655000	0.94253	CGG	.	.		0.567	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		T	37893159	C	T	37893159	3	4	147	1	0	0	0	0	1	0	0	0	2646	652	23	1	1320	1	CARD10	22	37893159	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	123760	37893159	13411407	70	22538										
ACO2	50	hgsc.bcm.edu	37	chr22	41895734	41895734	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	atgtttcttcttgcagaaagCtctgggtgtgcggcagtacc	12	9	3	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr22:41895734C>G	ENST00000216254.4	+	2	63	c.41C>G	c.(40-42)gCt>gGt	p.A14G	ACO2_ENST00000396512.3_Missense_Mutation_p.A14G	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	14					cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						TTGCAGAAAGCTCTGGGTGTG	0.522																																					p.A14G		Atlas-SNP	.											.	ACO2	58	.	0			c.C41G						.						198	195	196					22																	41895734		2203	4300	6503	SO:0001583	missense	50	exon2			AGAAAGCTCTGGG	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"aconitate hydratase, mitochondrial"	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.41C>G	chr22.hg19:g.41895734C>G	ENSP00000216254:p.Ala14Gly	19.0	0.0		27.0	10.0	NM_001098	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Missense_Mutation	SNP	ENST00000216254.4	hg19	CCDS14017.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.029533	0.54790	.	.	ENSG00000100412	ENST00000544234;ENST00000216254;ENST00000396512	T;T	0.46063	0.88;0.88	5.01	3.97	0.46021	.	0.207502	0.49916	D	0.000140	T	0.37812	0.1017	L	0.53249	1.67	0.58432	D	0.999993	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.18555	-1.0333	10	0.26408	T	0.33	.	14.2913	0.66281	0.0:0.9242:0.0:0.0758	.	14;14	A2A274;Q99798	.;ACON_HUMAN	G	14	ENSP00000216254:A14G;ENSP00000379769:A14G	ENSP00000216254:A14G	A	+	2	0	ACO2	40225680	0.409000	0.25368	1.000000	0.80357	0.967000	0.64934	0.721000	0.25911	2.483000	0.83821	0.585000	0.79938	GCT	.	.		0.522	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098		G	41895734	C	G	41895734	3	3	147	1	0	0	0	0	1	0	0	0	147	797	28	4	47	4	ACO2	22	41895734	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	4002575	41895734	9408832	71	22539										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46657638	46657638	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ctcagcttccaaaaaatgccGaaaagcaaaagcttttatag	6	9	1	0	rs369645000		TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chr22:46657638G>T	ENST00000253255.5	-	1	1581	c.1582C>A	c.(1582-1584)Cgg>Agg	p.R528R		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	528	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		R -> Q (in dbSNP:rs6008394).		acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.R528W(1)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		AAAAAATGCCGAAAAGCAAAA	0.408																																					p.R528R		Atlas-SNP	.											PKDREJ,NS,carcinoma,0,1	PKDREJ	195	.	1	Substitution - Missense(1)	cervix(1)	c.C1582A						.						101	113	109					22																	46657638		2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			AATGCCGAAAAGC	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.1582C>A	chr22.hg19:g.46657638G>T		93.0	0.0		96.0	4.0	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	hg19	CCDS14073.1																																																																																			.	.		0.408	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		T	46657638	G	T	46657638	2	4	147	1	0	0	0	0	0	0	0	1	11979	1057	37	1		1	PKDREJ	22	46657638	Silent	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	4761904	46657638	4646928	72	22540										
CXorf38	159013	hgsc.bcm.edu	37	chrX	40498275	40498275	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	tcttacctctgtgactttctTtcgatcaaccacgaagtgat	6	11	4	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chrX:40498275T>G	ENST00000327877.5	-	3	483	c.457A>C	c.(457-459)Aag>Cag	p.K153Q	CXorf38_ENST00000440784.2_Intron|CXorf38_ENST00000378421.1_Missense_Mutation_p.K34Q|CXorf38_ENST00000378426.1_Missense_Mutation_p.K34Q	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	153										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						GTGACTTTCTTTCGATCAACC	0.483																																					p.K153Q		Atlas-SNP	.											.	CXorf38	29	.	0			c.A457C						.						156	108	124					X																	40498275		2203	4300	6503	SO:0001583	missense	159013	exon3			CTTTCTTTCGATC	AL832829	CCDS14253.1	Xp11	2008-02-05			ENSG00000185753	ENSG00000185753			28589	protein-coding gene	gene with protein product							Standard	NM_144970		Approved	MGC39350	uc004dew.3	Q8TB03	OTTHUMG00000024104	ENST00000327877.5:c.457A>C	chrX.hg19:g.40498275T>G	ENSP00000330488:p.Lys153Gln	86.0	0.0		109.0	39.0	NM_144970	B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	hg19	CCDS14253.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.057045	0.36277	.	.	ENSG00000185753	ENST00000378426;ENST00000327877;ENST00000378421	T;T;T	0.47869	0.83;0.83;0.83	4.25	4.25	0.50352	.	0.374635	0.25663	N	0.029125	T	0.42607	0.1210	L	0.60455	1.87	0.80722	D	1	P	0.44429	0.835	B	0.41088	0.347	T	0.43491	-0.9388	10	0.56958	D	0.05	-8.1426	7.5894	0.28012	0.1927:0.0:0.0:0.8073	.	153	Q8TB03	CX038_HUMAN	Q	34;153;34	ENSP00000367683:K34Q;ENSP00000330488:K153Q;ENSP00000367677:K34Q	ENSP00000330488:K153Q	K	-	1	0	CXorf38	40383219	1.000000	0.71417	0.998000	0.56505	0.800000	0.45204	2.422000	0.44696	1.691000	0.51100	0.483000	0.47432	AAG	.	.		0.483	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3	NM_144970		G	40498275	T	G	40498275	3	3	147	1	0	0	0	0	1	0	0	0	4109	1850	64	5	518	5	CXorf38	23	40498275	Missense_Mutation	SNP	T	TCGA-DD-A73F-01A-11D-A32G-10		40498275	114772285	73	22541										
CXorf36	79742	hgsc.bcm.edu	37	chrX	45011086	45011086	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	actggggaggggaacctcccCtggagaagtcgaggcagcaa	16	10	0	1			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chrX:45011086C>T	ENST00000398000.2	-	5	1187	c.1113G>A	c.(1111-1113)caG>caA	p.Q371Q	CXorf36_ENST00000477281.1_5'UTR	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	371						extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						GGAACCTCCCCTGGAGAAGTC	0.617																																					p.Q371Q		Atlas-SNP	.											.	CXorf36	53	.	0			c.G1113A						.						35	32	33					X																	45011086		1568	3582	5150	SO:0001819	synonymous_variant	79742	exon5			CCTCCCCTGGAGA	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.1113G>A	chrX.hg19:g.45011086C>T		153.0	0.0		149.0	53.0	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Silent	SNP	ENST00000398000.2	hg19	CCDS48096.1																																																																																			.	.		0.617	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689		T	45011086	C	T	45011086	2	4	147	1	0	0	0	0	0	0	0	1	4108	680	24	3		3	CXorf36	23	45011086	Silent	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	4512811	45011086	110259474	74	22542										
FAM46D	169966	hgsc.bcm.edu	37	chrX	79698375	79698375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	actgtctacttgactttttaCcaaaagatgtaaagaaggaa	7	6	1	3			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chrX:79698375C>T	ENST00000308293.5	+	3	576	c.337C>T	c.(337-339)Cca>Tca	p.P113S	FAM46D_ENST00000538312.1_Missense_Mutation_p.P113S	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	113										kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						TGACTTTTTACCAAAAGATGT	0.393																																					p.P113S		Atlas-SNP	.											.	FAM46D	69	.	0			c.C337T						.						91	87	88					X																	79698375		2203	4299	6502	SO:0001583	missense	169966	exon5			TTTTTACCAAAAG	BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"cancer/testis antigen 112"					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.337C>T	chrX.hg19:g.79698375C>T	ENSP00000308575:p.Pro113Ser	154.0	0.0		158.0	52.0	NM_001170574	B2R9Q6|Q7Z3F6|Q8NHU1	Missense_Mutation	SNP	ENST00000308293.5	hg19	CCDS14446.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.409143	0.42715	.	.	ENSG00000174016	ENST00000538312;ENST00000308293	T;T	0.47177	0.85;0.85	4.27	4.27	0.50696	Domain of unknown function DUF1693 (1);	0.000000	0.85682	D	0.000000	T	0.72358	0.3450	M	0.88842	2.985	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78168	-0.2309	10	0.54805	T	0.06	-7.9	14.5078	0.67764	0.0:1.0:0.0:0.0	.	113	Q8NEK8	FA46D_HUMAN	S	113	ENSP00000443410:P113S;ENSP00000308575:P113S	ENSP00000308575:P113S	P	+	1	0	FAM46D	79585031	1.000000	0.71417	0.994000	0.49952	0.223000	0.24884	7.323000	0.79105	1.965000	0.57142	0.538000	0.68166	CCA	.	.		0.393	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630		T	79698375	C	T	79698375	3	4	147	1	0	0	0	0	1	0	0	0	5576	507	18	3	339	3	FAM46D	23	79698375	Missense_Mutation	SNP	C	TCGA-DD-A73F-01A-11D-A32G-10	34687289	79698375	75572185	75	22543										
GPR101	83550	hgsc.bcm.edu	37	chrX	136113472	136113472	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0394736842105263	3	1	0.621951219512195	0	0.762391817466562	0.181818181818182	0.751940625889747	0	ccactgacaccacgacaatgGtgttgacgctggcgaaggcg	13	12	0	2			TCGA-DD-A73F-01A-11D-A32G-10	TCGA-DD-A73F-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	26191956-5876-4a9c-94ba-68e53766fb9b	58d96a98-3030-4b89-b405-adb2c0cd8f7a	g.chrX:136113472G>T	ENST00000298110.1	-	1	361	c.362C>A	c.(361-363)aCc>aAc	p.T121N		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					CACGACAATGGTGTTGACGCT	0.607																																					p.T121N		Atlas-SNP	.											.	GPR101	96	.	0			c.C362A						.						88	63	71					X																	136113472		2203	4300	6503	SO:0001583	missense	83550	exon1			ACAATGGTGTTGA	AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.362C>A	chrX.hg19:g.136113472G>T	ENSP00000298110:p.Thr121Asn	39.0	0.0		73.0	36.0	NM_054021	Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	hg19	CCDS14662.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.712548	0.48517	.	.	ENSG00000165370	ENST00000298110	T	0.19806	2.12	5.04	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.235140	0.22147	N	0.063967	T	0.27559	0.0677	N	0.21617	0.685	0.54753	D	0.99998	D	0.89917	1.0	D	0.91635	0.999	T	0.02009	-1.1230	10	0.02654	T	1	-30.3191	14.8214	0.70077	0.0:0.0:1.0:0.0	.	121	Q96P66	GP101_HUMAN	N	121	ENSP00000298110:T121N	ENSP00000298110:T121N	T	-	2	0	GPR101	135941138	1.000000	0.71417	0.994000	0.49952	0.382000	0.30200	3.009000	0.49552	2.081000	0.62600	0.600000	0.82982	ACC	.	.		0.607	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			T	136113472	G	T	136113472	3	4	147	1	0	0	0	0	1	0	0	0	6630	1261	44	3	1167	3	GPR101	23	136113472	Missense_Mutation	SNP	G	TCGA-DD-A73F-01A-11D-A32G-10	56415097	136113472	19157088	76	22544										
FBLIM1	54751	hgsc.bcm.edu	37	chr1	16096974	16096974	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gaggccatgaagaggcagtaCcatgcccagtgcttcacgtg	13	11	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:16096974C>G	ENST00000375766.3	+	6	1252	c.612C>G	c.(610-612)taC>taG	p.Y204*	FBLIM1_ENST00000375771.1_Nonsense_Mutation_p.Y204*|FBLIM1_ENST00000441801.2_Nonsense_Mutation_p.Y204*|FBLIM1_ENST00000332305.5_Nonsense_Mutation_p.Y107*|FBLIM1_ENST00000400773.1_Nonsense_Mutation_p.Y107*	NM_017556.2	NP_060026.2	Q8WUP2	FBLI1_HUMAN	filamin binding LIM protein 1	204	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell junction assembly (GO:0034329)|regulation of cell shape (GO:0008360)|regulation of integrin activation (GO:0033623)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|stress fiber (GO:0001725)	filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	16		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|READ - Rectum adenocarcinoma(331;0.0649)|STAD - Stomach adenocarcinoma(313;0.138)		AGAGGCAGTACCATGCCCAGT	0.642																																					p.Y204X		Atlas-SNP	.											.	FBLIM1	46	.	0			c.C612G						.						65	61	62					1																	16096974		2203	4300	6503	SO:0001587	stop_gained	54751	exon5			GCAGTACCATGCC		CCDS163.1, CCDS30609.1, CCDS44064.1	1p36.13	2014-04-07			ENSG00000162458	ENSG00000162458			24686	protein-coding gene	gene with protein product		607747				12679033, 12496242	Standard	XM_005245900		Approved	FBLP-1, CAL, migfilin	uc001axe.1	Q8WUP2	OTTHUMG00000003079	ENST00000375766.3:c.612C>G	chr1.hg19:g.16096974C>G	ENSP00000364921:p.Tyr204*	48.0	0.0		41.0	11.0	NM_001024215	B3KNY0|Q5VVE0|Q5VVE1|Q8IX23|Q96T00|Q9UFD6	Nonsense_Mutation	SNP	ENST00000375766.3	hg19	CCDS163.1	.	.	.	.	.	.	.	.	.	.	C	38	6.692953	0.97768	.	.	ENSG00000162458	ENST00000375771;ENST00000375766;ENST00000400773;ENST00000502739;ENST00000441801;ENST00000332305	.	.	.	5.24	5.24	0.73138	.	0.207190	0.43110	D	0.000609	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.2082	0.89861	0.0:1.0:0.0:0.0	.	.	.	.	X	204;204;107;107;204;107	.	ENSP00000364920:Y107X	Y	+	3	2	FBLIM1	15969561	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.499000	0.53310	2.618000	0.88619	0.591000	0.81541	TAC	.	.		0.642	FBLIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008511.3	NM_001024215		G	16096974	C	G	16096974	4	3	148	1	0	0	0	0	0	1	0	0	5705	518	18	4	626	4	FBLIM1	1	16096974	Nonsense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10		16096974	233153647	1	22545										
USP24	23358	hgsc.bcm.edu	37	chr1	55549487	55549488	+	Frame_Shift_Ins	INS	-	-	A													0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ggaaaaagtactgagcacagINStttttacaattttctgggac							TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:55549487_55549488insA	ENST00000294383.6	-	57	6838_6839	c.6839_6840insT	c.(6838-6840)aacfs	p.N2280fs	USP24_ENST00000407756.1_Frame_Shift_Ins_p.N2120fs	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	2280					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						ACTGAGCACAGTTTTTACAATT	0.312																																					p.N2280fs		Atlas-Indel,Pindel	.											.	USP24	323	.	0			c.6840_6841insT						.																																			SO:0001589	frameshift_variant	23358	exon57			.	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.6839_6840insT	chr1.hg19:g.55549487_55549488insA	ENSP00000294383:p.Asn2280fs	372.0	0.0		314.0	163.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Frame_Shift_Ins	INS	ENST00000294383.6	hg19	CCDS44154.2																																																																																			.	.		0.312	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			A	55549488	-	A	55549487	7	5	148	1	0	1	1	0	0	0	0	0	17070	1020	36	0	1070	0	USP24	1	55549487	Frame_Shift_Ins	INS	-	TCGA-DD-A73G-01A-22D-A32G-10	39452513	55549487	193701134	2	22546										
EFCAB7	84455	hgsc.bcm.edu	37	chr1	64038167	64038167	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aagaatggatatattattgtAtatattctcttatttcttaa	4	3	2	1	rs371640057		TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:64038167A>G	ENST00000371088.4	+	14	2116	c.1870A>G	c.(1870-1872)Ata>Gta	p.I624V	EFCAB7_ENST00000461039.1_3'UTR	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	624							calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						ATATTATTGTATATATTCTCT	0.239																																					p.I624V		Atlas-SNP	.											.	EFCAB7	45	.	0			c.A1870G						.	A	VAL/ILE	0,4330		0,0,2165	23	27	26		1870	3.9	1	1		26	1,8489		0,1,4244	no	missense	EFCAB7	NM_032437.2	29	0,1,6409	GG,GA,AA		0.0118,0.0,0.0078	benign	624/630	64038167	1,12819	2165	4245	6410	SO:0001583	missense	84455	exon14			TATTGTATATATT	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"EF-hand domain containing"	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.1870A>G	chr1.hg19:g.64038167A>G	ENSP00000360129:p.Ile624Val	447.0	0.0		487.0	81.0	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	hg19	CCDS30737.1	.	.	.	.	.	.	.	.	.	.	A	0.022	-1.413913	0.01145	0.0	1.18E-4	ENSG00000203965	ENST00000371088	T	0.54675	0.56	4.83	3.9	0.45041	.	0.283861	0.34531	N	0.003900	T	0.03959	0.0111	N	0.00119	-2.075	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44997	-0.9291	10	0.02654	T	1	-3.2702	10.1473	0.42771	0.1668:0.0:0.8332:0.0	.	624	A8K855	EFCB7_HUMAN	V	624	ENSP00000360129:I624V	ENSP00000360129:I624V	I	+	1	0	EFCAB7	63810755	1.000000	0.71417	0.994000	0.49952	0.530000	0.34684	2.304000	0.43655	1.120000	0.41904	-0.479000	0.04858	ATA	.	.		0.239	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437		G	64038167	A	G	64038167	3	3	148	1	0	0	0	0	1	0	0	0	4942	449	16	2	1920	2	EFCAB7	1	64038167	Missense_Mutation	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10	8488680	64038167	185212454	3	22547										
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150529206	150529206	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cgatataaccgtcctcccagGgaggagggcaaaggggagag	16	9	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:150529206G>A	ENST00000369038.2	+	8	1887	c.1686G>A	c.(1684-1686)agG>agA	p.R562R	ADAMTSL4_ENST00000369041.5_Silent_p.R562R|ADAMTSL4_ENST00000369039.5_Silent_p.R585R|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Silent_p.R562R			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	562					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GTCCTCCCAGGGAGGAGGGCA	0.652																																					p.R562R		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.G1686A						.						100	117	112					1																	150529206		2203	4300	6503	SO:0001819	synonymous_variant	54507	exon10			TCCCAGGGAGGAG	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.1686G>A	chr1.hg19:g.150529206G>A		57.0	0.0		84.0	7.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Silent	SNP	ENST00000369038.2	hg19	CCDS955.1																																																																																			.	.		0.652	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		A	150529206	G	A	150529206	2	1	148	1	0	0	0	0	0	0	0	1	277	1223	43	3		3	ADAMTSL4	1	150529206	Silent	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	86491039	150529206	98721415	4	22548										
SPRR3	6707	hgsc.bcm.edu	37	chr1	152975594	152975594	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gcctccacctcaggaaatatTtgttcccacaaccaaggagc	7	14	1	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:152975594T>G	ENST00000295367.4	+	2	140	c.98T>G	c.(97-99)tTt>tGt	p.F33C	SPRR3_ENST00000331860.3_Missense_Mutation_p.F33C|SPRR3_ENST00000542696.1_Missense_Mutation_p.F33C	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	33					epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAGGAAATATTTGTTCCCACA	0.527																																					p.F33C		Atlas-SNP	.											.	SPRR3	45	.	0			c.T98G						.						80	74	76					1																	152975594		2203	4300	6503	SO:0001583	missense	6707	exon2			AAATATTTGTTCC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.98T>G	chr1.hg19:g.152975594T>G	ENSP00000295367:p.Phe33Cys	144.0	0.0		172.0	58.0	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Missense_Mutation	SNP	ENST00000295367.4	hg19	CCDS1033.1	.	.	.	.	.	.	.	.	.	.	T	7.187	0.590721	0.13812	.	.	ENSG00000163209	ENST00000331860;ENST00000443178;ENST00000295367;ENST00000542696	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	3.78	1.39	0.22231	.	.	.	.	.	T	0.02888	0.0086	N	0.16743	0.435	0.09310	N	0.999997	B;B	0.32324	0.314;0.364	B;B	0.38616	0.182;0.277	T	0.45469	-0.9259	9	0.35671	T	0.21	.	5.2229	0.15377	0.0:0.1019:0.1813:0.7168	.	33;33	F5GZ12;Q9UBC9	.;SPRR3_HUMAN	C	33	ENSP00000330391:F33C;ENSP00000402016:F33C;ENSP00000295367:F33C;ENSP00000441477:F33C	ENSP00000295367:F33C	F	+	2	0	SPRR3	151242218	0.000000	0.05858	0.503000	0.27626	0.705000	0.40729	-1.661000	0.01972	0.267000	0.21916	0.460000	0.39030	TTT	.	.		0.527	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416		G	152975594	T	G	152975594	3	3	148	1	0	0	0	0	1	0	0	0	15118	1841	64	5	100	5	SPRR3	1	152975594	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	2446388	152975594	96275027	5	22549										
OR10K2	391107	hgsc.bcm.edu	37	chr1	158390017	158390017	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gtgaacataggacaccaagaTcaacaataaggggatagcca	10	8	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:158390017T>A	ENST00000314902.2	-	1	639	c.640A>T	c.(640-642)Atc>Ttc	p.I214F		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					GACACCAAGATCAACAATAAG	0.448																																					p.I214F		Atlas-SNP	.											.	OR10K2	69	.	0			c.A640T						.						147	136	140					1																	158390017		2203	4300	6503	SO:0001583	missense	391107	exon1			CCAAGATCAACAA	AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"GPCR / Class A : Olfactory receptors"	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.640A>T	chr1.hg19:g.158390017T>A	ENSP00000324251:p.Ile214Phe	70.0	0.0		126.0	20.0	NM_001004476		Missense_Mutation	SNP	ENST00000314902.2	hg19	CCDS30896.1	.	.	.	.	.	.	.	.	.	.	t	12.62	1.993357	0.35131	.	.	ENSG00000180708	ENST00000314902	T	0.00333	8.07	4.13	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000207	T	0.00666	0.0022	H	0.94925	3.6	0.39901	D	0.973894	D	0.89917	1.0	D	0.91635	0.999	T	0.47195	-0.9136	10	0.87932	D	0	.	12.5328	0.56126	0.0:0.0:0.0:1.0	.	214	Q6IF99	O10K2_HUMAN	F	214	ENSP00000324251:I214F	ENSP00000324251:I214F	I	-	1	0	OR10K2	156656641	0.013000	0.17824	0.371000	0.25978	0.068000	0.16541	1.284000	0.33249	1.852000	0.53769	0.378000	0.23410	ATC	.	.		0.448	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476		A	158390017	T	A	158390017	3	1	148	1	0	0	0	0	1	0	0	0	10923	1435	50	4	300	4	OR10K2	1	158390017	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	5414423	158390017	90860604	6	22550										
DNM3	26052	hgsc.bcm.edu	37	chr1	172356431	172356431	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cttgggataattggggacatCagcacagccaccgtgtccac	11	12	1	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:172356431C>T	ENST00000355305.5	+	19	2392	c.2235C>T	c.(2233-2235)atC>atT	p.I745I	DNM3_ENST00000367731.1_Silent_p.I735I|DNM3_ENST00000358155.4_Silent_p.I739I			Q9UQ16	DYN3_HUMAN	dynamin 3	745	GED. {ECO:0000255|PROSITE- ProRule:PRU00720}.				endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TTGGGGACATCAGCACAGCCA	0.587																																					p.I739I		Atlas-SNP	.											.	DNM3	85	.	0			c.C2217T						.						43	47	45					1																	172356431		2065	4199	6264	SO:0001819	synonymous_variant	26052	exon19			GGACATCAGCACA	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.2235C>T	chr1.hg19:g.172356431C>T		75.0	0.0		111.0	9.0	NM_015569	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Silent	SNP	ENST00000355305.5	hg19																																																																																				.	.		0.587	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		T	172356431	C	T	172356431	2	4	148	1	0	0	0	0	0	0	0	1	4675	816	29	3		3	DNM3	1	172356431	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	13966414	172356431	76894190	7	22551										
C4BPA	722	hgsc.bcm.edu	37	chr1	207288822	207288822	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gtagagattaagacagatttAtcttttggatcacaaataga	8	4	2	4			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:207288822A>G	ENST00000367070.3	+	4	584	c.390A>G	c.(388-390)ttA>ttG	p.L130L		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	130	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						AGACAGATTTATCTTTTGGAT	0.338																																					p.L130L		Atlas-SNP	.											.	C4BPA	70	.	0			c.A390G						.						93	93	93					1																	207288822		2203	4300	6503	SO:0001819	synonymous_variant	722	exon4			AGATTTATCTTTT	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.390A>G	chr1.hg19:g.207288822A>G		79.0	0.0		108.0	26.0	NM_000715	Q5VVQ8	Silent	SNP	ENST00000367070.3	hg19	CCDS1477.1																																																																																			.	.		0.338	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			G	207288822	A	G	207288822	2	3	148	1	0	0	0	0	0	0	0	1	2251	446	16	2		2	C4BPA	1	207288822	Silent	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10	34932391	207288822	41961799	8	22552										
CR1L	1379	hgsc.bcm.edu	37	chr1	207871016	207871016	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ctggagccctgcagcccccaGatgtgaaggtgactagactc	12	13	0	4	rs532505670		TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:207871016G>C	ENST00000508064.2	+	6	1091	c.1031G>C	c.(1030-1032)aGa>aCa	p.R344T	CR1L_ENST00000530905.1_Intron	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	344	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GCAGCCCCCAGATGTGAAGGT	0.493													.|||	1	0.000199681	0	0.0014	5008	,	,		20118	0		0	False		,,,				2504	0				p.R344T		Atlas-SNP	.											CR1L_ENST00000508064,colon,carcinoma,0,2	CR1L	97	.	0			c.G1031C						.						170	170	170					1																	207871016		1893	4118	6011	SO:0001583	missense	1379	exon6			CCCCCAGATGTGA	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"Complement system"	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1031G>C	chr1.hg19:g.207871016G>C	ENSP00000421736:p.Arg344Thr	303.0	0.0		471.0	67.0	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	hg19	CCDS44310.1	.	.	.	.	.	.	.	.	.	.	.	0.020	-1.448032	0.01080	.	.	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.63096	-0.02	2.53	0.428	0.16499	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.33789	0.0875	N	0.11000	0.08	0.21445	N	0.999686	B	0.11235	0.004	B	0.08055	0.003	T	0.18366	-1.0339	9	0.13470	T	0.59	.	3.7628	0.08610	0.1908:0.4411:0.3681:0.0	.	344	Q2VPA4	CR1L_HUMAN	T	344	ENSP00000421736:R344T	ENSP00000434864:R288T	R	+	2	0	CR1L	205937639	0.000000	0.05858	0.933000	0.37362	0.156000	0.22039	-0.921000	0.04008	0.321000	0.23259	0.298000	0.19748	AGA	.	.		0.493	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735		C	207871016	G	C	207871016	3	2	148	1	0	0	0	0	1	0	0	0	3843	942	33	4	1053	4	CR1L	1	207871016	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	582194	207871016	41379605	9	22553										
USH2A	7399	hgsc.bcm.edu	37	chr1	216363610	216363610	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cgaagcactggtcacacaacCaactgaattgcagagagtaa	9	10	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:216363610C>A	ENST00000307340.3	-	20	4737	c.4351G>T	c.(4351-4353)Ggt>Tgt	p.G1451C	USH2A_ENST00000366942.3_Missense_Mutation_p.G1451C|USH2A_ENST00000366943.2_Missense_Mutation_p.G1451C	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1451	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GTCACACAACCAACTGAATTG	0.383										HNSCC(13;0.011)																											p.G1451C		Atlas-SNP	.											.	USH2A	1168	.	0			c.G4351T						.						112	108	109					1																	216363610		2203	4300	6503	SO:0001583	missense	7399	exon20			CACAACCAACTGA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.4351G>T	chr1.hg19:g.216363610C>A	ENSP00000305941:p.Gly1451Cys	60.0	0.0		94.0	19.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393908	0.62066	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.65178	-0.14;-0.14;-0.14	5.51	4.59	0.56863	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.153474	0.29892	U	0.010933	T	0.81470	0.4829	M	0.85299	2.745	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.85389	0.1124	10	0.87932	D	0	.	16.6133	0.84900	0.0:0.8696:0.1304:0.0	.	1451;1451	O75445-2;O75445	.;USH2A_HUMAN	C	1451	ENSP00000305941:G1451C;ENSP00000355910:G1451C;ENSP00000355909:G1451C	ENSP00000305941:G1451C	G	-	1	0	USH2A	214430233	1.000000	0.71417	0.204000	0.23530	0.549000	0.35272	6.774000	0.75012	1.441000	0.47550	0.655000	0.94253	GGT	.	.		0.383	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216363610	C	A	216363610	3	1	148	1	0	0	0	0	1	0	0	0	17051	594	21	3	11483	3	USH2A	1	216363610	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	8492594	216363610	32887011	10	22554										
ITPKB	3707	hgsc.bcm.edu	37	chr1	226829808	226829808	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttcttccgggccttcgtgagCtcctcctccaggtaggtcct	10	15	1	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:226829808C>T	ENST00000272117.3	-	4	2264	c.2265G>A	c.(2263-2265)gaG>gaA	p.E755E	ITPKB_ENST00000429204.1_Silent_p.E755E			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	755					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				CCTTCGTGAGCTCCTCCTCCA	0.637																																					p.E755E	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.G2265A						.						100	103	102					1																	226829808		2203	4300	6503	SO:0001819	synonymous_variant	3707	exon5			CGTGAGCTCCTCC	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"inositol 1,4,5-trisphosphate 3-kinase B"			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.2265G>A	chr1.hg19:g.226829808C>T		40.0	0.0		68.0	8.0	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	hg19	CCDS1555.1																																																																																			.	.		0.637	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		T	226829808	C	T	226829808	2	4	148	1	0	0	0	0	0	0	0	1	7927	796	28	3		3	ITPKB	1	226829808	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	10466198	226829808	22420813	11	22555										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232607246	232607246	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ggaagacgatggtgacgatgTcatttcctatgtgccttttc	11	8	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:232607246T>A	ENST00000366630.1	-	7	2472	c.2114A>T	c.(2113-2115)gAc>gTc	p.D705V	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.D705V			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	705	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GGTGACGATGTCATTTCCTAT	0.388																																					p.D705V		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.A2114T						.						129	134	133					1																	232607246		2121	4275	6396	SO:0001583	missense	57568	exon6			ACGATGTCATTTC	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.2114A>T	chr1.hg19:g.232607246T>A	ENSP00000355589:p.Asp705Val	102.0	0.0		99.0	20.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.924592	0.92319	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	D;D	0.97138	-4.26;-4.26	5.99	5.99	0.97316	Rap/ran-GAP (2);	0.000000	0.85682	D	0.000000	D	0.99202	0.9723	H	0.98786	4.33	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98802	1.0740	10	0.87932	D	0	-44.4057	16.4892	0.84195	0.0:0.0:0.0:1.0	.	705	Q9P2F8	SI1L2_HUMAN	V	705	ENSP00000355589:D705V;ENSP00000262861:D705V	ENSP00000262861:D705V	D	-	2	0	SIPA1L2	230673869	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.296000	0.77279	0.533000	0.62120	GAC	.	.		0.388	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232607246	T	A	232607246	3	1	148	1	0	0	0	0	1	0	0	0	14345	1667	58	4	3118	4	SIPA1L2	1	232607246	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	5777438	232607246	16643375	12	22556										
SMYD3	64754	hgsc.bcm.edu	37	chr1	246021833	246021833	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gtccgagtaccatagaacaaGgcttcctccaacaggccgag	10	13	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr1:246021833G>A	ENST00000388985.4	-	10	1040	c.1041C>T	c.(1039-1041)gcC>gcT	p.A347A	SMYD3_ENST00000490107.1_Silent_p.A288A|SMYD3_ENST00000366517.1_5'UTR|SMYD3_ENST00000541742.1_Silent_p.A288A			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	347					cellular response to dexamethasone stimulus (GO:0071549)|establishment of protein localization (GO:0045184)|myotube cell development (GO:0014904)|negative regulation of protein kinase activity (GO:0006469)|nucleosome assembly (GO:0006334)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)			breast(3)|large_intestine(5)|lung(8)|skin(1)	17	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		CATAGAACAAGGCTTCCTCCA	0.552																																					p.A347A		Atlas-SNP	.											.	SMYD3	77	.	0			c.C1041T						.						118	97	104					1																	246021833		2203	4300	6503	SO:0001819	synonymous_variant	64754	exon10			GAACAAGGCTTCC	AK023594	CCDS31083.1	1q44	2011-07-01	2003-05-14	2003-05-16	ENSG00000185420	ENSG00000185420		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	15513	protein-coding gene	gene with protein product		608783	"zinc finger, MYND domain containing 1"	ZNFN3A1, ZMYND1			Standard	NM_022743		Approved	KMT3E	uc001ibl.3	Q9H7B4	OTTHUMG00000040508	ENST00000388985.4:c.1041C>T	chr1.hg19:g.246021833G>A		95.0	0.0		121.0	12.0	NM_001167740	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Silent	SNP	ENST00000388985.4	hg19	CCDS53486.1																																																																																			.	.		0.552	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743		A	246021833	G	A	246021833	2	1	148	1	0	0	0	0	0	0	0	1	14838	987	35	3		3	SMYD3	1	246021833	Silent	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	13414587	246021833	3228788	13	22557										
SOX11	6664	hgsc.bcm.edu	37	chr2	5834087	5834087	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gcagcctgggctcccacttcGagttccccgactactgcacg	10	17	0	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:5834087G>T	ENST00000322002.3	+	1	1289	c.1234G>T	c.(1234-1236)Gag>Tag	p.E412*	AC108025.2_ENST00000420221.1_RNA|AC107057.2_ENST00000458264.1_RNA|AC108025.2_ENST00000453678.1_RNA|AC010729.1_ENST00000455579.2_RNA	NM_003108.3	NP_003099.1	P35716	SOX11_HUMAN	SRY (sex determining region Y)-box 11	412					cardiac ventricle formation (GO:0003211)|closure of optic fissure (GO:0061386)|cornea development in camera-type eye (GO:0061303)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|eyelid development in camera-type eye (GO:0061029)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|hard palate development (GO:0060022)|kidney development (GO:0001822)|lens morphogenesis in camera-type eye (GO:0002089)|limb bud formation (GO:0060174)|lung morphogenesis (GO:0060425)|negative regulation of cell death (GO:0060548)|negative regulation of gene expression (GO:0010629)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural crest cell development (GO:0014032)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|neuron differentiation (GO:0030182)|noradrenergic neuron differentiation (GO:0003357)|oligodendrocyte development (GO:0014003)|outflow tract morphogenesis (GO:0003151)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of hippo signaling (GO:0035332)|positive regulation of hormone secretion (GO:0046887)|positive regulation of lens epithelial cell proliferation (GO:2001111)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|signal transduction involved in cell cycle checkpoint (GO:0072395)|skeletal muscle cell differentiation (GO:0035914)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)|somite development (GO:0061053)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|translation (GO:0006412)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|translation factor activity, nucleic acid binding (GO:0008135)	p.E412*(1)		central_nervous_system(5)|cervix(1)|endometrium(1)|liver(1)|lung(4)|stomach(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)		CTCCCACTTCGAGTTCCCCGA	0.647																																					p.E412X		Atlas-SNP	.											SOX11,colon,carcinoma,0,3	SOX11	69	.	1	Substitution - Nonsense(1)	central_nervous_system(1)	c.G1234T						.						12	9	10					2																	5834087		2000	3826	5826	SO:0001587	stop_gained	6664	exon1			CACTTCGAGTTCC		CCDS1654.1	2p25	2008-05-21			ENSG00000176887	ENSG00000176887		"SRY (sex determining region Y)-boxes"	11191	protein-coding gene	gene with protein product	"SRY-related HMG-box gene 11"	600898				8666406, 12637543	Standard	NM_003108		Approved		uc002qyj.3	P35716	OTTHUMG00000090333	ENST00000322002.3:c.1234G>T	chr2.hg19:g.5834087G>T	ENSP00000322568:p.Glu412*	59.0	1.0		70.0	19.0	NM_003108	Q4ZFV8	Nonsense_Mutation	SNP	ENST00000322002.3	hg19	CCDS1654.1	.	.	.	.	.	.	.	.	.	.	G	38	6.952028	0.97960	.	.	ENSG00000176887	ENST00000322002	.	.	.	5.15	5.15	0.70609	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.6079	0.91273	0.0:0.0:1.0:0.0	.	.	.	.	X	412	.	ENSP00000322568:E412X	E	+	1	0	SOX11	5751538	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.514000	0.98013	2.393000	0.81446	0.561000	0.74099	GAG	.	.		0.647	SOX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206698.1	NM_003108		T	5834087	G	T	5834087	4	4	148	1	0	0	0	0	0	1	0	0	14957	1059	37	1	1236	1	SOX11	2	5834087	Nonsense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10		5834087	237365286	14	22558										
PUM2	23369	hgsc.bcm.edu	37	chr2	20454712	20454712	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttcaggtcgaccgtgttccaGtacatgctgaataacataat	8	9	1	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:20454712G>A	ENST00000361078.2	-	18	2810	c.2788C>T	c.(2788-2790)Ctg>Ttg	p.L930L	PUM2_ENST00000338086.5_Silent_p.L928L|PUM2_ENST00000536417.1_Silent_p.L872L|PUM2_ENST00000319801.5_Silent_p.L851L|PUM2_ENST00000403432.1_Silent_p.L928L			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	930	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCGTGTTCCAGTACATGCTGA	0.358																																					p.L928L		Atlas-SNP	.											.	PUM2	91	.	0			c.C2782T						.						105	102	103					2																	20454712		2203	4300	6503	SO:0001819	synonymous_variant	23369	exon18			GTTCCAGTACATG	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"pumilio (Drosphila) homolog 2", "pumilio homolog 2 (Drosophila)"			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.2788C>T	chr2.hg19:g.20454712G>A		227.0	0.0		204.0	45.0	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Silent	SNP	ENST00000361078.2	hg19																																																																																				.	.		0.358	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		A	20454712	G	A	20454712	2	1	148	1	0	0	0	0	0	0	0	1	12841	1020	36	3		3	PUM2	2	20454712	Silent	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	14620625	20454712	222744661	15	22559										
GTF3C2	2976	hgsc.bcm.edu	37	chr2	27559284	27559284	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gctctggatgtgctgtgatcGagctaaatctagagaaaaat	11	6	2	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:27559284G>A	ENST00000359541.2	-	8	1565	c.1136C>T	c.(1135-1137)tCg>tTg	p.S379L	AC109828.1_ENST00000587586.1_RNA|GTF3C2_ENST00000264720.3_Missense_Mutation_p.S379L|AC109828.1_ENST00000592265.1_RNA|AC109828.1_ENST00000590754.1_RNA|AC109828.1_ENST00000608473.1_RNA|AC109828.1_ENST00000585645.1_RNA|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000585326.1_RNA|AC109828.1_ENST00000416453.2_RNA|AC109828.1_ENST00000589853.1_RNA|AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000588707.1_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	379					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTGTGATCGAGCTAAATCT	0.542																																					p.S379F		Atlas-SNP	.											.	GTF3C2	73	.	0			c.C1136T						.						34	37	36					2																	27559284		2202	4300	6502	SO:0001583	missense	2976	exon9			GTGATCGAGCTAA	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.1136C>T	chr2.hg19:g.27559284G>A	ENSP00000352536:p.Ser379Leu	86.0	0.0		62.0	9.0	NM_001521	D6W557|Q16632|Q9BWI7	Missense_Mutation	SNP	ENST00000359541.2	hg19	CCDS1749.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.420123	0.83559	.	.	ENSG00000115207	ENST00000359541;ENST00000264720	T;T	0.75477	-0.94;-0.94	5.7	5.7	0.88788	.	0.067277	0.64402	D	0.000008	T	0.79482	0.4453	L	0.32530	0.975	0.58432	D	0.999998	D;D;D	0.76494	0.999;0.998;0.998	D;P;P	0.66084	0.941;0.773;0.884	T	0.78324	-0.2248	10	0.41790	T	0.15	-9.7855	17.3276	0.87253	0.0:0.0:1.0:0.0	.	379;379;379	Q8WUA4-2;Q8WUA4;Q53QN0	.;TF3C2_HUMAN;.	L	379	ENSP00000352536:S379L;ENSP00000264720:S379L	ENSP00000264720:S379L	S	-	2	0	GTF3C2	27412788	1.000000	0.71417	0.959000	0.39883	0.457000	0.32468	8.388000	0.90170	2.706000	0.92434	0.557000	0.71058	TCG	.	.		0.542	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			A	27559284	G	A	27559284	3	1	148	1	0	0	0	0	1	0	0	0	6882	1059	37	1	1647	1	GTF3C2	2	27559284	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	7104572	27559284	215640089	16	22560										
ZFP36L2	678	hgsc.bcm.edu	37	chr2	43451848	43451848	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aggctgctgagctccggaccGaaggcgaaggcgttgttggc	17	10	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:43451848G>A	ENST00000282388.3	-	2	1388	c.1095C>T	c.(1093-1095)ttC>ttT	p.F365F	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	365					cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				GCTCCGGACCGAAGGCGAAGG	0.726																																					p.F365F		Atlas-SNP	.											.	ZFP36L2	56	.	0			c.C1095T						.						10	12	11					2																	43451848		2128	4207	6335	SO:0001819	synonymous_variant	678	exon2			CGGACCGAAGGCG	X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"RING-type (C3HC4) zinc fingers"	1108	protein-coding gene	gene with protein product		612053	"zinc finger protein 36, C3H type-like 1", "zinc finger protein 36, C3H type-like 2"	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.1095C>T	chr2.hg19:g.43451848G>A		9.0	0.0		26.0	8.0	NM_006887	Q53TB4|Q9BSJ3	Silent	SNP	ENST00000282388.3	hg19	CCDS1811.1																																																																																			.	.		0.726	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887		A	43451848	G	A	43451848	2	1	148	1	0	0	0	0	0	0	0	1	17662	1049	37	1		1	ZFP36L2	2	43451848	Silent	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	15892564	43451848	199747525	17	22561										
FER1L5	81562	hgsc.bcm.edu	37	chr2	97370374	97370374	+	IGR	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tgagtggaaactccacccagGacccacaaatcacctgagtg	9	13	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:97370374G>T	ENST00000264963.4	-	0	2397				FER1L5_ENST00000457909.1_RNA	NM_030805.3	NP_110432.1	Q9H0V9	LMA2L_HUMAN	lectin, mannose-binding 2-like						ER to Golgi vesicle-mediated transport (GO:0006888)|protein folding (GO:0006457)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|lung(2)|skin(1)|urinary_tract(1)	7						CTCCACCCAGGACCCACAAAT	0.507																																					p.G2076V		Atlas-SNP	.											.	FER1L5	113	.	0			c.G6227T						.						92	91	91					2																	97370374		1877	4100	5977	SO:0001628	intergenic_variant	90342	exon52			ACCCAGGACCCAC	AL136617	CCDS2023.1, CCDS46365.1	2q11.1	2008-02-05			ENSG00000114988	ENSG00000114988			19263	protein-coding gene	gene with protein product		609552				12609988	Standard	NM_001142292		Approved	DKFZp564L2423, VIPL	uc002swv.3	Q9H0V9	OTTHUMG00000130453		chr2.hg19:g.97370374G>T		151.0	0.0		135.0	27.0	NM_001113382	B4DSH3|D3DXH6|Q53GV3|Q53S67|Q63HN6|Q8NBQ6|Q9BQ14	Missense_Mutation	SNP	ENST00000264963.4	hg19	CCDS2023.1	.	.	.	.	.	.	.	.	.	.	G	3.179	-0.168393	0.06461	.	.	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	4.43	-0.00959	0.14000	.	.	.	.	.	T	0.23249	0.0562	N	0.19112	0.55	.	.	.	B;B;B	0.16802	0.011;0.003;0.019	B;B;B	0.17433	0.008;0.003;0.018	T	0.24119	-1.0169	7	0.66056	D	0.02	-1.6009	2.1665	0.03838	0.1013:0.1707:0.3785:0.3495	.	784;2076;785	B7ZLI3;A0AVI2;A0AVI2-2	.;FR1L5_HUMAN;.	V	2076;2080;785	.	ENSP00000442027:G785V	G	+	2	0	FER1L5	96734101	0.000000	0.05858	0.011000	0.14972	0.004000	0.04260	-1.059000	0.03479	0.157000	0.19338	-0.169000	0.13324	GGA	.	.		0.507	LMAN2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252844.1	NM_030805		T	97370374	G	T	97370374	1	4	148	0	1	0	0	0	0	0	0	0	5822	1174	41	3		3	FER1L5	2	97370374	IGR	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	53918526	97370374	145828999	18	22562										
BIN1	274	hgsc.bcm.edu	37	chr2	127806198	127806198	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ctctccttcacgcccatgagCcagccttcatcctgaggggc	9	17	3	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:127806198C>T	ENST00000316724.5	-	19	2097	c.1686G>A	c.(1684-1686)tgG>tgA	p.W562*	BIN1_ENST00000466111.1_5'Flank|BIN1_ENST00000348750.4_Nonsense_Mutation_p.W378*|BIN1_ENST00000393040.3_Nonsense_Mutation_p.W451*|BIN1_ENST00000351659.3_Nonsense_Mutation_p.W475*|BIN1_ENST00000409400.1_Nonsense_Mutation_p.W408*|BIN1_ENST00000376113.2_Nonsense_Mutation_p.W393*|BIN1_ENST00000346226.3_Nonsense_Mutation_p.W487*|BIN1_ENST00000357970.3_Nonsense_Mutation_p.W519*|BIN1_ENST00000393041.3_Nonsense_Mutation_p.W444*|BIN1_ENST00000352848.3_Nonsense_Mutation_p.W423*|BIN1_ENST00000259238.4_Nonsense_Mutation_p.W466*	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	562	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CGCCCATGAGCCAGCCTTCAT	0.632																																					p.W562X		Atlas-SNP	.											.	BIN1	85	.	0			c.G1686A						.						74	67	70					2																	127806198		2203	4300	6503	SO:0001587	stop_gained	274	exon19			CATGAGCCAGCCT	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"amphiphysin II"	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.1686G>A	chr2.hg19:g.127806198C>T	ENSP00000316779:p.Trp562*	101.0	0.0		89.0	22.0	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Nonsense_Mutation	SNP	ENST00000316724.5	hg19	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	C	41	8.676158	0.98910	.	.	ENSG00000136717	ENST00000376113;ENST00000357970;ENST00000393040;ENST00000348750;ENST00000259238;ENST00000346226;ENST00000393041;ENST00000351659;ENST00000352848;ENST00000316724;ENST00000409400	.	.	.	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.0032	15.6379	0.76970	0.0:1.0:0.0:0.0	.	.	.	.	X	393;519;451;378;466;487;444;475;423;562;408	.	ENSP00000259238:W466X	W	-	3	0	BIN1	127522668	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.071000	0.71229	2.565000	0.86533	0.555000	0.69702	TGG	.	.		0.632	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		T	127806198	C	T	127806198	4	4	148	1	0	0	0	0	0	1	0	0	1432	740	26	3	99	3	BIN1	2	127806198	Nonsense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	30435824	127806198	115393175	19	22563										
IWS1	55677	hgsc.bcm.edu	37	chr2	128262855	128262855	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tcctcactttcagaatcactCattcgaggtttgggaggctc	9	11	4	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:128262855C>A	ENST00000295321.4	-	3	883	c.624G>T	c.(622-624)atG>atT	p.M208I	IWS1_ENST00000486662.1_5'UTR|IWS1_ENST00000455721.2_Missense_Mutation_p.M215I|AC010976.2_ENST00000599001.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	208	Glu-rich.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		CAGAATCACTCATTCGAGGTT	0.502																																					p.M208I		Atlas-SNP	.											.	IWS1	61	.	0			c.G624T						.						141	145	143					2																	128262855		2203	4300	6503	SO:0001583	missense	55677	exon3			ATCACTCATTCGA	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.624G>T	chr2.hg19:g.128262855C>A	ENSP00000295321:p.Met208Ile	159.0	0.0		149.0	31.0	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	hg19	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	C	4.183	0.032672	0.08101	.	.	ENSG00000163166	ENST00000295321;ENST00000433551;ENST00000455721;ENST00000409725	T;T	0.28454	1.64;1.61	5.7	-0.873	0.10635	.	0.898347	0.09753	N	0.760319	T	0.08133	0.0203	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28933	-1.0028	10	0.33940	T	0.23	0.3917	4.3121	0.10976	0.0838:0.1425:0.4913:0.2823	.	208	Q96ST2	IWS1_HUMAN	I	208;161;215;213	ENSP00000295321:M208I;ENSP00000399245:M215I	ENSP00000295321:M208I	M	-	3	0	IWS1	127979325	0.000000	0.05858	0.012000	0.15200	0.642000	0.38348	-3.011000	0.00647	-0.543000	0.06240	-0.218000	0.12543	ATG	.	.		0.502	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		A	128262855	C	A	128262855	3	1	148	1	0	0	0	0	1	0	0	0	7940	826	29	3	1883	3	IWS1	2	128262855	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	456657	128262855	114936518	20	22564										
EVX2	344191	hgsc.bcm.edu	37	chr2	176945497	176945497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gtaggtgtagaagctggggtCggctgggtgcggccaggaca	20	7	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:176945497C>T	ENST00000308618.4	-	3	905	c.769G>A	c.(769-771)Gac>Aac	p.D257N		NM_001080458.1	NP_001073927.1	Q03828	EVX2_HUMAN	even-skipped homeobox 2	257					limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(3)	16			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	READ - Rectum adenocarcinoma(9;0.0678)|Colorectal(32;0.115)		AAGCTGGGGTCGGCTGGGTGC	0.677																																					p.D257N		Atlas-SNP	.											.	EVX2	51	.	0			c.G769A						.						28	35	33					2																	176945497		2180	4241	6421	SO:0001583	missense	344191	exon3			TGGGGTCGGCTGG		CCDS33333.1	2q31.1	2012-03-09	2007-02-15		ENSG00000174279	ENSG00000174279		"Homeoboxes / ANTP class : HOXL subclass"	3507	protein-coding gene	gene with protein product		142991	"eve, even-skipped homeobox homolog 2 (Drosophila)"			1675198	Standard	NM_001080458		Approved		uc010zeu.2	Q03828	OTTHUMG00000154173	ENST00000308618.4:c.769G>A	chr2.hg19:g.176945497C>T	ENSP00000312385:p.Asp257Asn	32.0	0.0		17.0	8.0	NM_001080458		Missense_Mutation	SNP	ENST00000308618.4	hg19	CCDS33333.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.265013	0.80358	.	.	ENSG00000174279	ENST00000308618	D	0.91740	-2.9	4.51	4.51	0.55191	Homeodomain-like (1);	0.098661	0.64402	D	0.000003	D	0.89480	0.6727	M	0.66939	2.045	0.80722	D	1	P	0.41475	0.751	B	0.32724	0.151	D	0.89669	0.3882	10	0.35671	T	0.21	-31.2504	17.0219	0.86436	0.0:1.0:0.0:0.0	.	257	Q03828	EVX2_HUMAN	N	257	ENSP00000312385:D257N	ENSP00000312385:D257N	D	-	1	0	EVX2	176653743	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	7.490000	0.81461	2.355000	0.79922	0.462000	0.41574	GAC	.	.		0.677	EVX2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359252.1			T	176945497	C	T	176945497	3	4	148	1	0	0	0	0	1	0	0	0	5297	884	31	1	663	1	EVX2	2	176945497	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	48682642	176945497	66253876	21	22565										
TTN	7273	hgsc.bcm.edu	37	chr2	179410949	179410949	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	acatgcttaccaagcactttGaccatgacagacacggcctt	7	13	0	3			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:179410949G>A	ENST00000591111.1	-	292	90410	c.90186C>T	c.(90184-90186)gtC>gtT	p.V30062V	TTN_ENST00000342992.6_Silent_p.V29135V|TTN_ENST00000589042.1_Silent_p.V31703V|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Silent_p.V22830V|TTN_ENST00000359218.5_Silent_p.V22763V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Silent_p.V22638V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590932.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30062					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAAGCACTTTGACCATGACAG	0.428																																					p.V31703V		Atlas-SNP	.											.	TTN	18412	.	0			c.C95109T						.						235	229	231					2																	179410949		1962	4148	6110	SO:0001819	synonymous_variant	7273	exon342			CACTTTGACCATG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.90186C>T	chr2.hg19:g.179410949G>A		55.0	0.0		70.0	11.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179410949	G	A	179410949	2	1	148	1	0	0	0	0	0	0	0	1	16750	1277	45	3		3	TTN	2	179410949	Silent	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	2465452	179410949	63788424	22	22566										
TTN	7273	hgsc.bcm.edu	37	chr2	179431181	179431181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gagggcacagactcgtatttTatactcttggtgttcagtga	11	7	2	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:179431181T>C	ENST00000591111.1	-	276	74979	c.74755A>G	c.(74755-74757)Aaa>Gaa	p.K24919E	TTN_ENST00000342992.6_Missense_Mutation_p.K23992E|TTN_ENST00000589042.1_Missense_Mutation_p.K26560E|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K17687E|TTN_ENST00000359218.5_Missense_Mutation_p.K17620E|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.K17495E|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24919	Fibronectin type-III 81. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K17620E(1)|p.K17687E(1)|p.K23990E(1)|p.K17495E(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTCGTATTTTATACTCTTGG	0.413																																					p.K26560E		Atlas-SNP	.											TTN_ENST00000359218,trunk,malignant_melanoma,0,4	TTN	18412	.	4	Substitution - Missense(4)	skin(4)	c.A79678G						.						140	141	141					2																	179431181		1895	4119	6014	SO:0001583	missense	7273	exon326			GTATTTTATACTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.74755A>G	chr2.hg19:g.179431181T>C	ENSP00000465570:p.Lys24919Glu	80.0	0.0		47.0	10.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.85	2.061070	0.36373	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55052	0.54;0.54;0.54;0.54	5.92	5.92	0.95590	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.45518	0.1346	N	0.25485	0.75	0.46298	D	0.998977	P;P;P;P	0.46859	0.885;0.885;0.885;0.885	P;P;P;P	0.45538	0.484;0.484;0.484;0.484	T	0.50448	-0.8827	9	0.87932	D	0	.	12.2414	0.54544	0.0:0.0:0.1417:0.8583	.	17495;17620;17687;24919	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	23992;17495;17687;17620;17493	ENSP00000343764:K23992E;ENSP00000434586:K17495E;ENSP00000340554:K17687E;ENSP00000352154:K17620E	ENSP00000340554:K17687E	K	-	1	0	TTN	179139427	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.147000	0.71783	2.270000	0.75569	0.459000	0.35465	AAA	.	.		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179431181	T	C	179431181	3	2	148	1	0	0	0	0	1	0	0	0	16750	1763	61	2	28449	2	TTN	2	179431181	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	20232	179431181	63768192	23	22567										
ZNF385B	151126	hgsc.bcm.edu	37	chr2	180308145	180308145	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gctgcgagaggtgaggacagGaaggctggggccaaaggctt	19	7	0	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:180308145G>C	ENST00000410066.1	-	10	1851	c.1248C>G	c.(1246-1248)ttC>ttG	p.F416L	ZNF385B_ENST00000409343.1_Missense_Mutation_p.F340L|ZNF385B_ENST00000336917.5_Missense_Mutation_p.F314L|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409692.1_Missense_Mutation_p.F314L	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	416	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			GTGAGGACAGGAAGGCTGGGG	0.577																																					p.F416L	Colon(155;204 2491 32774 51842)	Atlas-SNP	.											.	ZNF385B	68	.	0			c.C1248G						.						33	41	39					2																	180308145		2200	4299	6499	SO:0001583	missense	151126	exon10			GGACAGGAAGGCT	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.1248C>G	chr2.hg19:g.180308145G>C	ENSP00000386845:p.Phe416Leu	45.0	0.0		19.0	5.0	NM_152520	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Missense_Mutation	SNP	ENST00000410066.1	hg19	CCDS33339.1	.	.	.	.	.	.	.	.	.	.	G	2.043	-0.419653	0.04734	.	.	ENSG00000144331	ENST00000410066;ENST00000336917;ENST00000409343;ENST00000409692	T;T;T;T	0.28666	1.6;1.63;1.61;1.63	5.49	4.61	0.57282	.	0.207022	0.51477	D	0.000100	T	0.18130	0.0435	N	0.21324	0.655	0.54753	D	0.99998	B;B	0.17667	0.023;0.009	B;B	0.17979	0.016;0.02	T	0.05599	-1.0875	10	0.09843	T	0.71	-27.7032	9.8606	0.41112	0.2148:0.0:0.7852:0.0	.	416;340	Q569K4;Q569K4-2	Z385B_HUMAN;.	L	416;314;340;314	ENSP00000386845:F416L;ENSP00000338225:F314L;ENSP00000386379:F340L;ENSP00000386507:F314L	ENSP00000338225:F314L	F	-	3	2	ZNF385B	180016390	1.000000	0.71417	0.998000	0.56505	0.912000	0.54170	1.825000	0.39081	1.307000	0.44944	0.561000	0.74099	TTC	.	.		0.577	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		C	180308145	G	C	180308145	3	2	148	1	0	0	0	0	1	0	0	0	17892	1165	41	4	171	4	ZNF385B	2	180308145	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	876964	180308145	62891228	24	22568										
STAT4	6775	hgsc.bcm.edu	37	chr2	192011406	192011406	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttttctctttggaaacacgaCctaactgttcatccagttgt	6	10	2	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:192011406C>A	ENST00000392320.2	-	3	520	c.206G>T	c.(205-207)gGt>gTt	p.G69V	STAT4_ENST00000409995.1_Missense_Mutation_p.G69V|STAT4_ENST00000358470.4_Missense_Mutation_p.G69V	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	69					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			GGAAACACGACCTAACTGTTC	0.338																																					p.G69V		Atlas-SNP	.											.	STAT4	85	.	0			c.G206T						.						85	82	83					2																	192011406		2203	4297	6500	SO:0001583	missense	6775	exon3			ACACGACCTAACT		CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"SH2 domain containing"	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.206G>T	chr2.hg19:g.192011406C>A	ENSP00000376134:p.Gly69Val	98.0	0.0		108.0	15.0	NM_001243835	Q96NZ6	Missense_Mutation	SNP	ENST00000392320.2	hg19	CCDS2310.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.952549	0.53293	.	.	ENSG00000138378	ENST00000358470;ENST00000392320;ENST00000413064;ENST00000409995;ENST00000450994	T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58	5.55	5.55	0.83447	STAT transcription factor, protein interaction (4);	0.378286	0.27294	N	0.020030	T	0.46560	0.1399	N	0.19112	0.55	0.53005	D	0.999963	P;D;D	0.56287	0.915;0.975;0.975	P;P;P	0.54026	0.601;0.74;0.654	T	0.48736	-0.9009	10	0.87932	D	0	-15.749	6.7041	0.23240	0.0:0.8015:0.0:0.1985	.	69;69;69	B4DSY7;B4DV04;Q14765	.;.;STAT4_HUMAN	V	69;69;42;69;69	ENSP00000351255:G69V;ENSP00000376134:G69V;ENSP00000403238:G42V;ENSP00000386288:G69V;ENSP00000412397:G69V	ENSP00000351255:G69V	G	-	2	0	STAT4	191719651	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.725000	0.47294	2.885000	0.99019	0.655000	0.94253	GGT	.	.		0.338	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151		A	192011406	C	A	192011406	3	1	148	1	0	0	0	0	1	0	0	0	15282	507	18	3	2128	3	STAT4	2	192011406	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	11703261	192011406	51187967	25	22569										
SLC11A1	6556	hgsc.bcm.edu	37	chr2	219254739	219254739	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	caggccttctaccagaaaacCaaccaggctgcggtgagaca	10	13	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr2:219254739C>T	ENST00000233202.6	+	9	1282	c.942C>T	c.(940-942)acC>acT	p.T314T	SLC11A1_ENST00000539932.1_Silent_p.T196T	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	314					activation of protein kinase activity (GO:0032147)|antigen processing and presentation of peptide antigen (GO:0048002)|cadmium ion transmembrane transport (GO:0070574)|cellular cadmium ion homeostasis (GO:0006876)|cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|divalent metal ion export (GO:0070839)|inflammatory response (GO:0006954)|interaction with host (GO:0051701)|interleukin-2 production (GO:0032623)|interleukin-3 production (GO:0032632)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|L-arginine import (GO:0043091)|macrophage activation (GO:0042116)|manganese ion transport (GO:0006828)|MHC class II biosynthetic process (GO:0045342)|mRNA stabilization (GO:0048255)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cytokine production (GO:0001818)|nitrite transport (GO:0015707)|phagocytosis (GO:0006909)|phagosome maturation (GO:0090382)|positive regulation of cytokine production (GO:0001819)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of gene expression (GO:0010628)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus, translocation (GO:0000060)|respiratory burst (GO:0045730)|response to bacterium (GO:0009617)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|T cell cytokine production (GO:0002369)|T cell proliferation involved in immune response (GO:0002309)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|wound healing (GO:0042060)	cell outer membrane (GO:0009279)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|tertiary granule membrane (GO:0070821)	manganese ion transmembrane transporter activity (GO:0005384)|metal ion:proton antiporter activity (GO:0051139)|protein homodimerization activity (GO:0042803)|transition metal ion transmembrane transporter activity (GO:0046915)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACCAGAAAACCAACCAGGCTG	0.552																																					p.T314T		Atlas-SNP	.											.	SLC11A1	41	.	0			c.C942T						.						148	118	128					2																	219254739		2203	4300	6503	SO:0001819	synonymous_variant	6556	exon9			GAAAACCAACCAG	D38171	CCDS2415.1	2q35	2013-07-18	2013-07-18		ENSG00000018280	ENSG00000018280		"Solute carriers"	10907	protein-coding gene	gene with protein product	"natural resistance-associated macrophage protein 1"	600266		LSH, NRAMP, NRAMP1		7964458, 7980580	Standard	NM_000578		Approved		uc002vhv.3	P49279	OTTHUMG00000086747	ENST00000233202.6:c.942C>T	chr2.hg19:g.219254739C>T		79.0	0.0		75.0	20.0	NM_000578	C0H5Y3	Silent	SNP	ENST00000233202.6	hg19	CCDS2415.1																																																																																			.	.		0.552	SLC11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195076.2	NM_000578		T	219254739	C	T	219254739	2	4	148	1	0	0	0	0	0	0	0	1	14395	581	21	3		3	SLC11A1	2	219254739	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	27243333	219254739	23944634	26	22570										
FYCO1	79443	hgsc.bcm.edu	37	chr3	46006599	46006599	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aagctggcccctgaggctctTgcactcttcaccagcattct	8	15	4	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr3:46006599T>C	ENST00000296137.2	-	9	3281	c.3076A>G	c.(3076-3078)Aag>Gag	p.K1026E	FYCO1_ENST00000535325.1_Missense_Mutation_p.K1026E	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1026					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CTGAGGCTCTTGCACTCTTCA	0.552																																					p.K1026E		Atlas-SNP	.											.	FYCO1	115	.	0			c.A3076G						.						49	49	49					3																	46006599		2203	4300	6503	SO:0001583	missense	79443	exon9			GGCTCTTGCACTC	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.3076A>G	chr3.hg19:g.46006599T>C	ENSP00000296137:p.Lys1026Glu	24.0	0.0		27.0	6.0	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	T	2.802	-0.248873	0.05867	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.79554	-1.28;-1.28	5.79	-0.342	0.12635	.	1.274560	0.04713	N	0.417928	T	0.61223	0.2330	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.49762	-0.8905	10	0.05959	T	0.93	-3.5581	6.577	0.22573	0.0:0.4614:0.1465:0.3921	.	1026;1026	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	E	1026	ENSP00000296137:K1026E;ENSP00000441178:K1026E	ENSP00000296137:K1026E	K	-	1	0	FYCO1	45981603	0.208000	0.23494	0.043000	0.18650	0.179000	0.23085	0.460000	0.21924	0.015000	0.14971	0.533000	0.62120	AAG	.	.		0.552	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		C	46006599	T	C	46006599	3	2	148	1	0	0	0	0	1	0	0	0	6133	1821	63	2	1400	2	FYCO1	3	46006599	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10		46006599	152015831	27	22571										
BAP1	8314	hgsc.bcm.edu	37	chr3	52441263	52441263	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ataggcacatagctgacaaaGtggaacgcctccatggtccg	11	11	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr3:52441263G>C	ENST00000460680.1	-	7	978	c.507C>G	c.(505-507)caC>caG	p.H169Q	BAP1_ENST00000296288.5_Missense_Mutation_p.H169Q	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0	Interaction with HIP2.				anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.H169Q(2)|p.E166fs*13(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		AGCTGACAAAGTGGAACGCCT	0.572			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.H169Q	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	BAP1,uveal_tract,malignant_melanoma,0,2	BAP1	371	.	3	Substitution - Missense(2)|Deletion - Frameshift(1)	eye(3)	c.C507G						.						83	81	82					3																	52441263		2203	4300	6503	SO:0001583	missense	8314	exon7			GACAAAGTGGAAC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.507C>G	chr3.hg19:g.52441263G>C	ENSP00000417132:p.His169Gln	85.0	0.0		55.0	32.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	18.26	3.584163	0.65992	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000470173	D;D;D	0.82526	-1.62;-1.62;-1.62	5.95	4.16	0.48862	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	D	0.93432	0.7905	H	0.97158	3.95	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93788	0.7090	10	0.87932	D	0	-7.8942	11.0249	0.47739	0.217:0.0:0.783:0.0	.	169	Q92560	BAP1_HUMAN	Q	169;169;90	ENSP00000417132:H169Q;ENSP00000296288:H169Q;ENSP00000417776:H90Q	ENSP00000296288:H169Q	H	-	3	2	BAP1	52416303	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.356000	0.20181	0.847000	0.35167	-0.136000	0.14681	CAC	.	.		0.572	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			C	52441263	G	C	52441263	3	2	148	1	0	0	0	0	1	0	0	0	1311	1020	36	4	1726	4	BAP1	3	52441263	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	6434664	52441263	145581167	28	22572										
GPR128	84873	hgsc.bcm.edu	37	chr3	100328724	100328724	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gcttcctgccgtgcctggaaCcttagggtgctggtggctgt	15	11	0	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr3:100328724C>A	ENST00000273352.3	+	1	292	c.24C>A	c.(22-24)aaC>aaA	p.N8K		NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	8					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						GTGCCTGGAACCTTAGGGTGC	0.478																																					p.N8K	Pancreas(87;185 1975 7223 18722)	Atlas-SNP	.											.	GPR128	126	.	0			c.C24A						.						174	147	156					3																	100328724		2203	4300	6503	SO:0001583	missense	84873	exon1			CTGGAACCTTAGG	AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"-", "GPCR / Class B : Orphans"	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.24C>A	chr3.hg19:g.100328724C>A	ENSP00000273352:p.Asn8Lys	195.0	0.0		158.0	24.0	NM_032787	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	hg19	CCDS2938.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.076128	0.36662	.	.	ENSG00000144820	ENST00000273352	T	0.38077	1.16	5.69	4.81	0.61882	.	1.017810	0.07833	N	0.961614	T	0.31420	0.0796	L	0.44542	1.39	0.27520	N	0.951425	P	0.38922	0.651	B	0.32805	0.153	T	0.23904	-1.0175	10	0.66056	D	0.02	.	9.7137	0.40260	0.0:0.9036:0.0:0.0964	.	8	Q96K78	GP128_HUMAN	K	8	ENSP00000273352:N8K	ENSP00000273352:N8K	N	+	3	2	GPR128	101811414	0.015000	0.18098	0.007000	0.13788	0.017000	0.09413	1.277000	0.33167	1.375000	0.46248	0.563000	0.77884	AAC	.	.		0.478	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1			A	100328724	C	A	100328724	3	1	148	1	0	0	0	0	1	0	0	0	6649	506	18	3	26	3	GPR128	3	100328724	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	47887461	100328724	97693706	29	22573										
FAM55C	91775	hgsc.bcm.edu	37	chr3	101540508	101540508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tccggcggctcaggaacatcCgtcgagcagtggttcggctc	14	13	1	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr3:101540508C>T	ENST00000491511.2	+	8	2346	c.1390C>T	c.(1390-1392)Cgt>Tgt	p.R464C	NXPE3_ENST00000477909.1_Missense_Mutation_p.R464C|RP11-49I4.3_ENST00000490324.2_RNA|NXPE3_ENST00000422132.1_Missense_Mutation_p.R464C|NXPE3_ENST00000273347.5_Missense_Mutation_p.R464C	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	464						extracellular region (GO:0005576)											CAGGAACATCCGTCGAGCAGT	0.572																																					p.R464C		Atlas-SNP	.											.	.	.	.	0			c.C1390T						.						99	95	97					3																	101540508		2203	4300	6503	SO:0001583	missense	91775	exon8			AACATCCGTCGAG	AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"family with sequence similarity 55, member C"	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.1390C>T	chr3.hg19:g.101540508C>T	ENSP00000417485:p.Arg464Cys	76.0	0.0		55.0	12.0	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Missense_Mutation	SNP	ENST00000491511.2	hg19	CCDS2945.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.320856	0.81469	.	.	ENSG00000144815	ENST00000273347;ENST00000491511;ENST00000477909;ENST00000422132	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	6.03	5.13	0.70059	.	0.150449	0.64402	N	0.000016	T	0.51958	0.1705	M	0.85299	2.745	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.61377	-0.7075	10	0.87932	D	0	-17.1789	16.2691	0.82606	0.1373:0.8627:0.0:0.0	.	464	Q969Y0	FA55C_HUMAN	C	464	ENSP00000273347:R464C;ENSP00000417485:R464C;ENSP00000418369:R464C;ENSP00000396421:R464C	ENSP00000273347:R464C	R	+	1	0	FAM55C	103023198	1.000000	0.71417	0.988000	0.46212	0.889000	0.51656	3.880000	0.56145	1.495000	0.48549	0.655000	0.94253	CGT	.	.		0.572	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037		T	101540508	C	T	101540508	3	4	148	1	0	0	0	0	1	0	0	0	5594	652	23	1	1408	1	FAM55C	3	101540508	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	1211784	101540508	96481922	30	22574										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	120959330	120959330	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttggaaccttggagcacaaaCatatccagaaattattatta	6	7	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr3:120959330C>G	ENST00000273666.6	+	14	1647	c.1376C>G	c.(1375-1377)aCa>aGa	p.T459R	STXBP5L_ENST00000492541.1_Missense_Mutation_p.T459R|STXBP5L_ENST00000472879.1_Missense_Mutation_p.T459R|STXBP5L_ENST00000497029.1_Missense_Mutation_p.T459R|STXBP5L_ENST00000471454.1_Missense_Mutation_p.T459R	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	459					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		GGAGCACAAACATATCCAGAA	0.323																																					p.T459R		Atlas-SNP	.											.	STXBP5L	159	.	0			c.C1376G						.						85	84	84					3																	120959330		1828	4084	5912	SO:0001583	missense	9515	exon14			CACAAACATATCC	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.1376C>G	chr3.hg19:g.120959330C>G	ENSP00000273666:p.Thr459Arg	38.0	0.0		34.0	6.0	NM_014980	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	hg19	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.956356	0.53293	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54	5.21	5.21	0.72293	WD40 repeat-like-containing domain (2);	0.049594	0.85682	D	0.000000	T	0.51669	0.1688	L	0.59436	1.845	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.69654	0.965;0.965	T	0.34477	-0.9827	10	0.31617	T	0.26	-34.4949	18.9528	0.92646	0.0:1.0:0.0:0.0	.	459;459	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	R	459	ENSP00000273666:T459R;ENSP00000420019:T459R;ENSP00000419627:T459R;ENSP00000420287:T459R;ENSP00000420666:T459R;ENSP00000420167:T459R	ENSP00000273666:T459R	T	+	2	0	STXBP5L	122442020	0.980000	0.34600	1.000000	0.80357	0.893000	0.52053	1.863000	0.39459	2.716000	0.92895	0.561000	0.74099	ACA	.	.		0.323	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			G	120959330	C	G	120959330	3	3	148	1	0	0	0	0	1	0	0	0	15372	478	17	4	1426	4	STXBP5L	3	120959330	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	19418822	120959330	77063100	31	22575										
PTTG2	23216	hgsc.bcm.edu	37	chr4	37962607	37962607	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ctgtttgcagtctccttcaaGcattctgtcgaccctggatg	9	12	3	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr4:37962607G>T	ENST00000261439.4	+	3	772				PTTG2_ENST00000504686.1_Missense_Mutation_p.K184N|TBC1D1_ENST00000508802.1_Intron	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1						membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						TCTCCTTCAAGCATTCTGTCG	0.438																																					p.K184N		Atlas-SNP	.											.	PTTG2	15	.	0			c.G552T						.						192	194	194					4																	37962607		2203	4300	6503	SO:0001627	intron_variant	10744	exon1			CTTCAAGCATTCT	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.418-53523G>T	chr4.hg19:g.37962607G>T		68.0	0.0		63.0	14.0	NM_006607	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	hg19	CCDS33972.1	.	.	.	.	.	.	.	.	.	.	G	9.939	1.216924	0.22373	.	.	ENSG00000250254	ENST00000504686	T	0.48836	0.8	1.4	0.483	0.16820	.	.	.	.	.	T	0.30541	0.0768	.	.	.	0.09310	N	1	P	0.51147	0.942	B	0.39217	0.294	T	0.14227	-1.0480	8	0.40728	T	0.16	.	4.7285	0.12952	0.0:0.0:0.6347:0.3653	.	184	Q9NZH5-2	.	N	184	ENSP00000424261:K184N	ENSP00000424261:K184N	K	+	3	2	PTTG2	37639002	0.016000	0.18221	0.017000	0.16124	0.013000	0.08279	0.029000	0.13666	0.140000	0.18849	0.563000	0.77884	AAG	.	.		0.438	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173		T	37962607	G	T	37962607	1	4	148	0	1	0	0	0	0	0	0	0	12836	962	34	3		3	PTTG2	4	37962607	Intron	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10		37962607	153191669	32	22576										
PARM1	25849	hgsc.bcm.edu	37	chr4	75971416	75971416	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tggacgaccatgactacgggTcctggggaaactacaacaac	11	11	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr4:75971416T>C	ENST00000307428.7	+	4	1104	c.892T>C	c.(892-894)Tcc>Ccc	p.S298P	PARM1_ENST00000513238.1_Missense_Mutation_p.S56P	NM_015393.3	NP_056208.2	Q6UWI2	PARM1_HUMAN	prostate androgen-regulated mucin-like protein 1	298					positive regulation of telomerase activity (GO:0051973)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|lung(4)|ovary(1)	8						TGACTACGGGTCCTGGGGAAA	0.453																																					p.S298P		Atlas-SNP	.											.	PARM1	52	.	0			c.T892C						.						114	116	115					4																	75971416		2106	4251	6357	SO:0001583	missense	25849	exon4			TACGGGTCCTGGG	AK022311	CCDS47077.1	4q13.3-q21.3	2010-02-17	2009-09-28		ENSG00000169116	ENSG00000169116			24536	protein-coding gene	gene with protein product	"Prostatic androgen-repressed message 1", "Castration-induced prostatic apoptosis-related protein 1", "WSC4, cell wall integrity and stress response component 4 homolog (S. cerevisiae)"					10499539, 12772192, 18027867	Standard	NM_015393		Approved	DKFZP564O0823, Cipar1, WSC4	uc003hih.2	Q6UWI2	OTTHUMG00000160827	ENST00000307428.7:c.892T>C	chr4.hg19:g.75971416T>C	ENSP00000370224:p.Ser298Pro	140.0	0.0		109.0	35.0	NM_015393	B3KMQ9|Q96DV8|Q9Y4S1	Missense_Mutation	SNP	ENST00000307428.7	hg19	CCDS47077.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.421259	0.83559	.	.	ENSG00000169116	ENST00000513238;ENST00000307428	T;T	0.26957	1.7;1.7	5.36	5.36	0.76844	.	0.000000	0.53938	D	0.000051	T	0.36744	0.0978	N	0.24115	0.695	0.43218	D	0.995094	D	0.89917	1.0	D	0.91635	0.999	T	0.24190	-1.0167	10	0.87932	D	0	-24.7374	13.3503	0.60597	0.0:0.0:0.0:1.0	.	298	Q6UWI2	PARM1_HUMAN	P	56;298	ENSP00000424276:S56P;ENSP00000370224:S298P	ENSP00000370224:S298P	S	+	1	0	PARM1	76190440	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.965000	0.63708	2.257000	0.74773	0.459000	0.35465	TCC	.	.		0.453	PARM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362494.1	NM_015393		C	75971416	T	C	75971416	3	2	148	1	0	0	0	0	1	0	0	0	11461	1667	58	2	906	2	PARM1	4	75971416	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	38008809	75971416	115182860	33	22577										
DSPP	1834	hgsc.bcm.edu	37	chr4	88534393	88534393	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gaagctcaaccatagagaaaGcaaacgcgtagaaaatagaa	9	7	1	3			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr4:88534393G>T	ENST00000282478.7	+	3	1088	c.1055G>T	c.(1054-1056)aGc>aTc	p.S352I	DSPP_ENST00000399271.1_Missense_Mutation_p.S352I|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	352					biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		CATAGAGAAAGCAAACGCGTA	0.433																																					p.S352I		Atlas-SNP	.											.	DSPP	174	.	0			c.G1055T						.						38	38	38					4																	88534393		1886	4110	5996	SO:0001583	missense	1834	exon4			GAGAAAGCAAACG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.1055G>T	chr4.hg19:g.88534393G>T	ENSP00000282478:p.Ser352Ile	151.0	0.0		125.0	31.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.810345	0.32053	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87491	-2.26;-2.26	4.68	-2.03	0.07365	.	.	.	.	.	T	0.77811	0.4186	L	0.44542	1.39	0.09310	N	1	B	0.24823	0.112	B	0.23574	0.047	T	0.65676	-0.6110	9	0.66056	D	0.02	-0.0042	1.606	0.02684	0.1794:0.1202:0.4345:0.2658	.	352	Q9NZW4	DSPP_HUMAN	I	352	ENSP00000382213:S352I;ENSP00000282478:S352I	ENSP00000282478:S352I	S	+	2	0	DSPP	88753417	0.000000	0.05858	0.004000	0.12327	0.059000	0.15707	-1.538000	0.02204	-0.218000	0.10018	0.557000	0.71058	AGC	.	.		0.433	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88534393	G	T	88534393	3	4	148	1	0	0	0	0	1	0	0	0	4784	971	34	3	1065	3	DSPP	4	88534393	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	12562977	88534393	102619883	34	22578										
SLC39A8	64116	hgsc.bcm.edu	37	chr4	103225548	103225548	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gacagcaggatttgcatagcAtgtcacaccattgatggcag	11	9	1	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr4:103225548A>T	ENST00000394833.2	-	5	1242	c.766T>A	c.(766-768)Tgc>Agc	p.C256S	SLC39A8_ENST00000424970.2_Missense_Mutation_p.C256S|SLC39A8_ENST00000510255.1_5'Flank|SLC39A8_ENST00000356736.4_Missense_Mutation_p.C256S	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	256					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		TTTGCATAGCATGTCACACCA	0.378																																					p.C256S		Atlas-SNP	.											.	SLC39A8	24	.	0			c.T766A						.						165	144	151					4																	103225548		2203	4300	6503	SO:0001583	missense	64116	exon5			CATAGCATGTCAC		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"Solute carriers"	20862	protein-coding gene	gene with protein product		608732	"solute carrier family 39 (metal ion transporter), member 8"			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.766T>A	chr4.hg19:g.103225548A>T	ENSP00000378310:p.Cys256Ser	104.0	0.0		111.0	26.0	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Missense_Mutation	SNP	ENST00000394833.2	hg19	CCDS3656.1	.	.	.	.	.	.	.	.	.	.	A	11.02	1.515357	0.27123	.	.	ENSG00000138821	ENST00000424970;ENST00000356736;ENST00000394833	T;T;T	0.69926	-0.3;-0.44;-0.44	4.81	4.81	0.61882	.	4.723360	0.00166	N	0.000003	T	0.49098	0.1537	N	0.12637	0.245	0.42748	D	0.993769	B;B;B	0.25206	0.12;0.002;0.002	B;B;B	0.18561	0.022;0.017;0.007	T	0.37641	-0.9697	10	0.07813	T	0.8	-25.4895	9.2864	0.37760	0.8395:0.0:0.0:0.1605	.	256;256;189	B4E2H3;Q9C0K1;Q9C0K1-2	.;S39A8_HUMAN;.	S	256	ENSP00000394548:C256S;ENSP00000349174:C256S;ENSP00000378310:C256S	ENSP00000349174:C256S	C	-	1	0	SLC39A8	103444571	1.000000	0.71417	0.996000	0.52242	0.933000	0.57130	5.719000	0.68462	1.930000	0.55929	0.528000	0.53228	TGC	.	.		0.378	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154		T	103225548	A	T	103225548	3	4	148	1	0	0	0	0	1	0	0	0	14639	217	8	4	709	4	SLC39A8	4	103225548	Missense_Mutation	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10	14691155	103225548	87928728	35	22579										
SLC9A3	6550	hgsc.bcm.edu	37	chr5	481731	481731	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cggatatgtcctcgatggccGagaggatgtggtcgaaagcc	15	9	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr5:481731G>C	ENST00000264938.3	-	9	1475	c.1466C>G	c.(1465-1467)tCg>tGg	p.S489W	CTD-2228K2.7_ENST00000607286.1_RNA|SLC9A3_ENST00000514375.1_Missense_Mutation_p.S480W|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	489					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CTCGATGGCCGAGAGGATGTG	0.617																																					p.S489W		Atlas-SNP	.											.	SLC9A3	89	.	0			c.C1466G						.						167	170	169					5																	481731		2203	4300	6503	SO:0001583	missense	6550	exon9			ATGGCCGAGAGGA		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.1466C>G	chr5.hg19:g.481731G>C	ENSP00000264938:p.Ser489Trp	50.0	0.0		90.0	4.0	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	hg19	CCDS3855.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.876066	0.51695	.	.	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.57436	0.81;0.4	3.98	3.98	0.46160	.	0.223994	0.38837	N	0.001551	T	0.71213	0.3313	M	0.72894	2.215	0.49130	D	0.999756	D;D	0.89917	1.0;1.0	D;D	0.85130	0.98;0.997	T	0.76656	-0.2879	10	0.87932	D	0	.	16.0321	0.80585	0.0:0.0:1.0:0.0	.	480;489	E9PF67;P48764	.;SL9A3_HUMAN	W	489;480	ENSP00000264938:S489W;ENSP00000422983:S480W	ENSP00000264938:S489W	S	-	2	0	SLC9A3	534731	0.979000	0.34478	0.991000	0.47740	0.745000	0.42441	3.650000	0.54424	1.938000	0.56188	0.561000	0.74099	TCG	.	.		0.617	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		C	481731	G	C	481731	3	2	148	1	0	0	0	0	1	0	0	0	14728	1059	37	4	1074	4	SLC9A3	5	481731	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10		481731	180433529	36	22580										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13866359	13866359	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ataagcctgtcactggcttcCtggggcttcaagccgctagc	11	13	2	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr5:13866359C>T	ENST00000265104.4	-	26	4190	c.4086G>A	c.(4084-4086)caG>caA	p.Q1362Q	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1362	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CACTGGCTTCCTGGGGCTTCA	0.338									Kartagener syndrome																												p.Q1362Q		Atlas-SNP	.											.	DNAH5	868	.	0			c.G4086A						.						26	31	29					5																	13866359		2202	4299	6501	SO:0001819	synonymous_variant	1767	exon26	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGCTTCCTGGGGC	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.4086G>A	chr5.hg19:g.13866359C>T		198.0	0.0		271.0	34.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	hg19	CCDS3882.1																																																																																			.	.		0.338	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13866359	C	T	13866359	2	4	148	1	0	0	0	0	0	0	0	1	4606	680	24	3		3	DNAH5	5	13866359	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	13384628	13866359	167048901	37	22581										
CDH9	1007	hgsc.bcm.edu	37	chr5	26881302	26881302	+	Frame_Shift_Del	DEL	C	C	-													0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gcaagttttttgaaacgaggCccccagtcactgaggtaatc							TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr5:26881302delC	ENST00000231021.4	-	12	2485	c.2313delG	c.(2311-2313)gggfs	p.G771fs		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	771					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TGAAACGAGGCCCCCAGTCAC	0.413																																					p.P772fs	Melanoma(8;187 585 15745 40864 52829)	Atlas-Indel,Pindel	.											CDH9,NS,carcinoma,0,2	CDH9	305	.	0			c.2314delC						.						127	123	124					5																	26881302		2203	4299	6502	SO:0001589	frameshift_variant	1007	exon12			.	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.2313delG	chr5.hg19:g.26881302delC	ENSP00000231021:p.Gly771fs	117.0	0.0		79.0	19.0	NM_016279	Q3B7I5	Frame_Shift_Del	DEL	ENST00000231021.4	hg19	CCDS3893.1																																																																																			.	.		0.413	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		-	26881302	C	-	26881302	7	5	148	1	0	1	0	1	0	0	0	0	3119	726	26	0	60	0	CDH9	5	26881302	Frame_Shift_Del	DEL	C	TCGA-DD-A73G-01A-22D-A32G-10	13014943	26881302	154033958	38	22582										
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79734325	79734325	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aaacaaaatacaatagaaaaTggcctttctttaggagaaaa	6	5	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr5:79734325T>C	ENST00000338008.5	+	3	2001	c.1821T>C	c.(1819-1821)aaT>aaC	p.N607N	ZFYVE16_ENST00000510158.1_Silent_p.N607N|ZFYVE16_ENST00000505560.1_Silent_p.N607N	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	607					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		CAATAGAAAATGGCCTTTCTT	0.313																																					p.N607N	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.T1821C						.						71	81	78					5																	79734325		2203	4298	6501	SO:0001819	synonymous_variant	9765	exon4			AGAAAATGGCCTT	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"Zinc fingers, FYVE domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20756	protein-coding gene	gene with protein product	"endofin", "protein phosphatase 1, regulatory subunit 69"	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.1821T>C	chr5.hg19:g.79734325T>C		190.0	0.0		210.0	24.0	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Silent	SNP	ENST00000338008.5	hg19	CCDS4050.1																																																																																			.	.		0.313	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		C	79734325	T	C	79734325	2	2	148	1	0	0	0	0	0	0	0	1	17679	1461	51	2		2	ZFYVE16	5	79734325	Silent	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	52853023	79734325	101180935	39	22583										
RPS23	6228	hgsc.bcm.edu	37	chr5	81573513	81573514	+	Splice_Site	INS	-	-	T													0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cgggagcaatggacttacacINStttttccagcacgattcctt							TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr5:81573513_81573514insT	ENST00000296674.8	-	2	415_416	c.162_163insA	c.(160-165)aaagta>aaaAgta	p.V55fs	RPS23_ENST00000512493.1_Splice_Site_p.V55fs|RPS23_ENST00000510019.1_Splice_Site_p.V55fs|RPS23_ENST00000503605.1_5'UTR|ATP6AP1L_ENST00000380167.4_5'Flank|RPS23_ENST00000510210.1_Splice_Site_p.V55fs|RPS23_ENST00000511844.1_Frame_Shift_Ins_p.V55fs|RPS23_ENST00000507980.1_Splice_Site_p.V55fs	NM_001025.4	NP_001016.1	P62266	RS23_HUMAN	ribosomal protein S23	55					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			prostate(1)	1		Lung NSC(167;0.0025)|all_lung(232;0.00278)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-42)|Epithelial(54;8.38e-37)|all cancers(79;1.42e-31)		TGGACTTACACTTTTTCCAGCA	0.396																																					p.V55fs		Atlas-Indel,Pindel	.											.	RPS23	11	.	0			c.163_164insA						.																																			SO:0001630	splice_region_variant	6228	exon2			.	AB007158	CCDS47241.1	5q14.2	2013-05-09			ENSG00000186468	ENSG00000186468		"S ribosomal proteins"	10410	protein-coding gene	gene with protein product		603683				9582194	Standard	NM_001025		Approved	S23	uc003khu.3	P62266	OTTHUMG00000162557	ENST00000296674.8:c.164+1->A	chr5.hg19:g.81573518_81573518dupT		99.0	0.0		103.0	19.0	NM_001025	P39028|Q6IB08	Frame_Shift_Ins	INS	ENST00000296674.8	hg19	CCDS47241.1																																																																																			.	.		0.396	RPS23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369546.2	NM_001025	Frame_Shift_Ins	T	81573514	-	T	81573513	8	5	148	1	0	1	1	0	0	0	1	0	13649	579	20	0	280	0	RPS23	5	81573513	Splice_Site	INS	-	TCGA-DD-A73G-01A-22D-A32G-10	1839188	81573513	99341747	40	22584										
TCF7	6932	hgsc.bcm.edu	37	chr5	133473769	133473769	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gcacaaggccaatcagccccCccacggtgtcccccaactct	7	20	2	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr5:133473769C>A	ENST00000321584.4	+	4	657	c.461C>A	c.(460-462)cCc>cAc	p.P154H	TCF7_ENST00000378564.1_Missense_Mutation_p.P154H|TCF7_ENST00000342854.5_Missense_Mutation_p.P154H|TCF7_ENST00000518915.1_Missense_Mutation_p.P39H|TCF7_ENST00000432532.2_Missense_Mutation_p.P39H|TCF7_ENST00000520958.1_Missense_Mutation_p.P39H|TCF7_ENST00000378560.4_Missense_Mutation_p.P39H|TCF7_ENST00000395023.1_Missense_Mutation_p.P39H|TCF7_ENST00000321603.6_Missense_Mutation_p.P154H|TCF7_ENST00000395029.1_Missense_Mutation_p.P154H			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)	154					alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AATCAGCCCCCCCACGGTGTC	0.577																																					p.P154H		Atlas-SNP	.											.	TCF7	81	.	0			c.C461A						.						113	110	111					5																	133473769		2203	4300	6503	SO:0001583	missense	6932	exon4			AGCCCCCCCACGG	Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.461C>A	chr5.hg19:g.133473769C>A	ENSP00000326540:p.Pro154His	162.0	0.0		194.0	38.0	NM_003202	B3KSH3|Q86WR9|Q9UKI4	Missense_Mutation	SNP	ENST00000321584.4	hg19		.	.	.	.	.	.	.	.	.	.	C	14.15	2.448261	0.43429	.	.	ENSG00000081059	ENST00000342854;ENST00000361590;ENST00000321603;ENST00000321584;ENST00000378564;ENST00000395029;ENST00000518887;ENST00000517851;ENST00000521639;ENST00000522375;ENST00000378560;ENST00000432532;ENST00000520958;ENST00000518915;ENST00000395023;ENST00000519037	D;D;D;D;D;D;D;D;D;D;T	0.99201	-5.49;-5.54;-5.54;-5.55;-5.54;-5.48;-5.49;-5.49;-5.47;-5.49;0.95	4.95	2.08	0.27032	CTNNB1 binding, N-teminal (1);	0.381500	0.29884	N	0.010959	D	0.97926	0.9318	L	0.43152	1.355	0.09310	N	1	B;D;P;B	0.56287	0.073;0.975;0.954;0.0	B;P;P;B	0.55011	0.115;0.766;0.69;0.001	D	0.94600	0.7795	10	0.56958	D	0.05	.	8.3219	0.32134	0.3151:0.5325:0.1523:0.0	.	154;154;154;154	P36402-9;B7WNT5;P36402;P36402-5	.;.;TCF7_HUMAN;.	H	154;154;154;154;154;154;39;39;39;39;39;39;39;39;39;14	ENSP00000340347:P154H;ENSP00000326654:P154H;ENSP00000326540:P154H;ENSP00000367827:P154H;ENSP00000378472:P154H;ENSP00000367822:P39H;ENSP00000397946:P39H;ENSP00000429547:P39H;ENSP00000430179:P39H;ENSP00000378469:P39H;ENSP00000429696:P14H	ENSP00000326540:P154H	P	+	2	0	TCF7	133501668	0.022000	0.18835	0.001000	0.08648	0.893000	0.52053	2.933000	0.48948	0.232000	0.21100	0.557000	0.71058	CCC	.	.		0.577	TCF7-201	KNOWN	basic	protein_coding	protein_coding		NM_201634		A	133473769	C	A	133473769	3	1	148	1	0	0	0	0	1	0	0	0	15711	623	22	3	475	3	TCF7	5	133473769	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	51900256	133473769	47441491	41	22585										
REEP2	51308	hgsc.bcm.edu	37	chr5	137780127	137780127	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ccccttctactttgaactgaAgatcgccttcgtgatatggc	8	12	1	4			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr5:137780127A>C	ENST00000254901.5	+	4	328	c.206A>C	c.(205-207)aAg>aCg	p.K69T	REEP2_ENST00000378339.2_Missense_Mutation_p.K69T|REEP2_ENST00000506158.1_Missense_Mutation_p.K31T	NM_016606.2	NP_057690.2	Q9BRK0	REEP2_HUMAN	receptor accessory protein 2	69					cell death (GO:0008219)|endoplasmic reticulum tubular network organization (GO:0071786)|protein transport into membrane raft (GO:0032596)|regulation of intracellular transport (GO:0032386)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			TTTGAACTGAAGATCGCCTTC	0.587																																					p.K69T		Atlas-SNP	.											.	REEP2	21	.	0			c.A206C						.						159	127	138					5																	137780127		2203	4300	6503	SO:0001583	missense	51308	exon4			AACTGAAGATCGC	AK056193	CCDS4205.1, CCDS64259.1	5q31	2014-03-12	2006-02-07	2006-02-07	ENSG00000132563	ENSG00000132563		"Receptor accessory proteins"	17975	protein-coding gene	gene with protein product		609347	"chromosome 5 open reading frame 19"	C5orf19		16271481, 15550249, 24388663	Standard	NM_016606		Approved	SGC32445, SPG72	uc003lda.4	Q9BRK0	OTTHUMG00000129205	ENST00000254901.5:c.206A>C	chr5.hg19:g.137780127A>C	ENSP00000254901:p.Lys69Thr	45.0	0.0		65.0	11.0	NM_016606	Q53EM8|Q9NYF2	Missense_Mutation	SNP	ENST00000254901.5	hg19	CCDS4205.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.902600	0.92035	.	.	ENSG00000132563	ENST00000378339;ENST00000254901;ENST00000506158	D;D;D	0.96802	-4.13;-4.13;-4.13	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.98883	0.9622	H	0.98351	4.21	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99297	1.0900	10	0.87932	D	0	-4.7393	14.0341	0.64634	1.0:0.0:0.0:0.0	.	69;69	A8K3D2;Q9BRK0	.;REEP2_HUMAN	T	69;69;31	ENSP00000367590:K69T;ENSP00000254901:K69T;ENSP00000422530:K31T	ENSP00000254901:K69T	K	+	2	0	REEP2	137808026	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.017000	0.93651	2.159000	0.67721	0.533000	0.62120	AAG	.	.		0.587	REEP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251284.1	NM_016606		C	137780127	A	C	137780127	3	2	148	1	0	0	0	0	1	0	0	0	13220	72	3	5	220	5	REEP2	5	137780127	Missense_Mutation	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10	4306358	137780127	43135133	42	22586										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140221574	140221574	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tgggggcaaacctgagctcaCaggcactgttcagctgctgg	14	11	2	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr5:140221574C>A	ENST00000531613.1	+	1	668	c.668C>A	c.(667-669)aCa>aAa	p.T223K	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.T223K|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	223	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGAGCTCACAGGCACTGTT	0.483																																					p.T223K		Atlas-SNP	.											.	PCDHA8	366	.	0			c.C668A						.						50	51	51					5																	140221574		2203	4298	6501	SO:0001583	missense	56140	exon1			AGCTCACAGGCAC	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.668C>A	chr5.hg19:g.140221574C>A	ENSP00000434655:p.Thr223Lys	127.0	0.0		138.0	9.0	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	hg19	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630599	0.67015	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.02890	4.12;4.12	3.73	2.83	0.33086	Cadherin (4);Cadherin-like (1);	0.000000	0.37715	U	0.001966	T	0.11281	0.0275	M	0.93106	3.38	0.09310	N	1	P;P	0.44578	0.806;0.838	P;B	0.46940	0.532;0.397	T	0.06679	-1.0813	10	0.87932	D	0	.	12.0049	0.53252	0.0:0.6636:0.3364:0.0	.	223;223	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	K	223	ENSP00000434655:T223K;ENSP00000367363:T223K	ENSP00000367363:T223K	T	+	2	0	PCDHA8	140201758	0.019000	0.18553	0.008000	0.14137	0.634000	0.38068	2.118000	0.41949	0.644000	0.30656	0.558000	0.71614	ACA	.	.		0.483	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		A	140221574	C	A	140221574	3	1	148	1	0	0	0	0	1	0	0	0	11539	478	17	3	670	3	PCDHA8	5	140221574	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	2441447	140221574	40693686	43	22587										
ABCF1	23	hgsc.bcm.edu	37	chr6	30557649	30557649	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aggagacgcccactgagtacCtgcagcggggcttcaacctg	13	13	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr6:30557649C>T	ENST00000326195.8	+	22	2243	c.2131C>T	c.(2131-2133)Ctg>Ttg	p.L711L	ABCF1_ENST00000376545.3_Silent_p.L673L|ABCF1_ENST00000396515.4_Intron	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	711	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						CACTGAGTACCTGCAGCGGGG	0.597																																					p.L711L		Atlas-SNP	.											.	ABCF1	61	.	0			c.C2131T						.						106	117	113					6																	30557649		1511	2709	4220	SO:0001819	synonymous_variant	23	exon22			GAGTACCTGCAGC	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"ATP binding cassette transporters / subfamily F"	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.2131C>T	chr6.hg19:g.30557649C>T		68.0	0.0		93.0	16.0	NM_001025091	A2BF75|O14897|Q69YP6	Silent	SNP	ENST00000326195.8	hg19	CCDS34380.1																																																																																			.	.		0.597	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			T	30557649	C	T	30557649	2	4	148	1	0	0	0	0	0	0	0	1	65	680	24	3		3	ABCF1	6	30557649	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10		30557649	140557418	44	22588										
KCNK16	83795	hgsc.bcm.edu	37	chr6	39286882	39286882	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	agagttgcctttggggttcaCacctttcacccaggcttcca	9	13	2	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr6:39286882C>T	ENST00000373229.5	-	2	254	c.241G>A	c.(241-243)Gtg>Atg	p.V81M	KCNK16_ENST00000373227.4_Missense_Mutation_p.V81M|KCNK16_ENST00000507712.1_Missense_Mutation_p.V16M|KCNK16_ENST00000437525.2_Missense_Mutation_p.V81M|KCNK16_ENST00000425054.2_Missense_Mutation_p.V81M	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	81					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						TTGGGGTTCACACCTTTCACC	0.542																																					p.V81M		Atlas-SNP	.											.	KCNK16	59	.	0			c.G241A						.						112	109	110					6																	39286882		2203	4300	6503	SO:0001583	missense	83795	exon2			GGTTCACACCTTT	AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.241G>A	chr6.hg19:g.39286882C>T	ENSP00000362326:p.Val81Met	41.0	0.0		34.0	5.0	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Missense_Mutation	SNP	ENST00000373229.5	hg19	CCDS4843.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.445880	0.63178	.	.	ENSG00000095981	ENST00000373229;ENST00000425054;ENST00000507712;ENST00000373227;ENST00000437525	T;T;T;T;T	0.20463	2.33;2.32;2.36;2.94;2.07	5.33	4.45	0.53987	.	0.144829	0.46758	D	0.000275	T	0.24084	0.0583	L	0.55481	1.735	0.42219	D	0.991847	D;D;D;D	0.67145	0.988;0.996;0.993;0.969	P;D;P;D	0.67548	0.9;0.952;0.864;0.944	T	0.05305	-1.0893	10	0.87932	D	0	.	7.11	0.25384	0.0:0.7034:0.142:0.1546	.	81;81;81;81	B5TJL9;Q96T55-5;Q96T55-4;Q96T55	.;.;.;KCNKG_HUMAN	M	81;81;16;81;81	ENSP00000362326:V81M;ENSP00000391498:V81M;ENSP00000423842:V16M;ENSP00000362324:V81M;ENSP00000415375:V81M	ENSP00000362324:V81M	V	-	1	0	KCNK16	39394860	0.959000	0.32827	0.998000	0.56505	0.994000	0.84299	2.137000	0.42130	1.208000	0.43306	0.561000	0.74099	GTG	.	.		0.542	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115		T	39286882	C	T	39286882	3	4	148	1	0	0	0	0	1	0	0	0	8072	478	17	3	1093	3	KCNK16	6	39286882	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	8729233	39286882	131828185	45	22589										
DST	667	hgsc.bcm.edu	37	chr6	56341127	56341127	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tgctgatgttgctttgcccaGgccagcacctgtcagagaaa	11	11	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr6:56341127G>A	ENST00000361203.3	-	87	20731	c.20724C>T	c.(20722-20724)gcC>gcT	p.A6908A	DST_ENST00000370769.4_Silent_p.A7019A|DST_ENST00000312431.6_3'UTR|DST_ENST00000370754.5_Silent_p.A7197A|DST_ENST00000446842.2_Silent_p.A6693A|DST_ENST00000370788.2_Silent_p.A4822A|DST_ENST00000421834.2_Silent_p.A4931A|DST_ENST00000244364.6_Silent_p.A4605A			Q03001	DYST_HUMAN	dystonin	6908					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GCTTTGCCCAGGCCAGCACCT	0.398																																					p.A4605A		Atlas-SNP	.											.	DST	1427	.	0			c.C13815T						.						33	31	32					6																	56341127		1878	4103	5981	SO:0001819	synonymous_variant	667	exon73			TGCCCAGGCCAGC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.20724C>T	chr6.hg19:g.56341127G>A		65.0	0.0		64.0	15.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.398	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56341127	G	A	56341127	2	1	148	1	0	0	0	0	0	0	0	1	4785	987	35	3		3	DST	6	56341127	Silent	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	17054245	56341127	114773940	46	22590										
CD109	135228	hgsc.bcm.edu	37	chr6	74502505	74502505	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	agataatttgaaagaaaaagCtctttcatttatgaggcaag	8	4	2	4			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr6:74502505C>G	ENST00000287097.5	+	23	2970	c.2858C>G	c.(2857-2859)gCt>gGt	p.A953G	CD109_ENST00000437994.2_Missense_Mutation_p.A953G|CD109_ENST00000422508.2_Missense_Mutation_p.A876G|CD109_ENST00000474094.1_3'UTR			Q6YHK3	CD109_HUMAN	CD109 molecule	953					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AAAGAAAAAGCTCTTTCATTT	0.313																																					p.A953G		Atlas-SNP	.											.	CD109	170	.	0			c.C2858G						.						47	49	48					6																	74502505		2203	4298	6501	SO:0001583	missense	135228	exon23			AAAAAGCTCTTTC	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2858C>G	chr6.hg19:g.74502505C>G	ENSP00000287097:p.Ala953Gly	23.0	0.0		29.0	6.0	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	hg19	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	C	19.72	3.880009	0.72294	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.46063	0.88;0.88;0.88	5.87	5.0	0.66597	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.114074	0.64402	D	0.000014	T	0.61375	0.2342	M	0.91300	3.195	0.42286	D	0.992114	D;D;P	0.89917	1.0;0.997;0.883	D;D;P	0.70227	0.968;0.913;0.652	T	0.71427	-0.4596	10	0.72032	D	0.01	.	10.8014	0.46491	0.0:0.8005:0.1318:0.0677	.	876;953;953	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	G	953;876;953	ENSP00000388062:A953G;ENSP00000404475:A876G;ENSP00000287097:A953G	ENSP00000287097:A953G	A	+	2	0	CD109	74559226	0.999000	0.42202	0.993000	0.49108	0.967000	0.64934	4.239000	0.58694	1.616000	0.50265	0.655000	0.94253	GCT	.	.		0.313	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		G	74502505	C	G	74502505	3	3	148	1	0	0	0	0	1	0	0	0	2965	797	28	4	2948	4	CD109	6	74502505	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	18161378	74502505	96612562	47	22591										
RNGTT	8732	hgsc.bcm.edu	37	chr6	89554193	89554193	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ggacttataatttctcgttcTatacactgcagacgaacatt	6	9	2	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr6:89554193T>C	ENST00000369485.4	-	11	1338	c.1152A>G	c.(1150-1152)atA>atG	p.I384M	RNGTT_ENST00000265607.6_Missense_Mutation_p.I384M|RNGTT_ENST00000538899.1_Missense_Mutation_p.I324M|RNGTT_ENST00000369475.3_Missense_Mutation_p.I384M	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	384	GTase.|Interaction with POLR2A. {ECO:0000250}.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA processing (GO:0006396)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|mRNA guanylyltransferase activity (GO:0004484)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA guanylyltransferase activity (GO:0008192)|triphosphatase activity (GO:0050355)			endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	21		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		TTTCTCGTTCTATACACTGCA	0.348																																					p.I384M		Atlas-SNP	.											.	RNGTT	52	.	0			c.A1152G						.						145	147	146					6																	89554193		2203	4300	6503	SO:0001583	missense	8732	exon11			TCGTTCTATACAC	AF025654	CCDS5017.1	6q16	2011-06-09			ENSG00000111880	ENSG00000111880	2.7.7.50	"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	10073	protein-coding gene	gene with protein product		603512				9828141, 9512541	Standard	NM_001286428		Approved	HCE, HCE1, hCAP	uc003pmr.2	O60942	OTTHUMG00000015190	ENST00000369485.4:c.1152A>G	chr6.hg19:g.89554193T>C	ENSP00000358497:p.Ile384Met	84.0	0.0		46.0	13.0	NM_003800	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	Missense_Mutation	SNP	ENST00000369485.4	hg19	CCDS5017.1	.	.	.	.	.	.	.	.	.	.	T	17.29	3.351332	0.61183	.	.	ENSG00000111880	ENST00000369485;ENST00000265607;ENST00000538899;ENST00000536746;ENST00000369475	D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89	5.49	2.87	0.33458	mRNA capping enzyme (1);	0.039036	0.85682	D	0.000000	D	0.90150	0.6922	M	0.91249	3.19	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.997;0.998;0.995;0.997	D	0.89042	0.3449	10	0.49607	T	0.09	.	6.9231	0.24399	0.3539:0.0:0.1174:0.5287	.	324;384;384;384	B4DSJ8;Q5TCW7;O60942-2;O60942	.;.;.;MCE1_HUMAN	M	384;384;324;355;384	ENSP00000358497:I384M;ENSP00000265607:I384M;ENSP00000442609:I324M;ENSP00000358487:I384M	ENSP00000265607:I384M	I	-	3	3	RNGTT	89610912	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.134000	0.31442	0.985000	0.38656	0.460000	0.39030	ATA	.	.		0.348	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041469.1			C	89554193	T	C	89554193	3	2	148	1	0	0	0	0	1	0	0	0	13518	1512	53	2	665	2	RNGTT	6	89554193	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	15051688	89554193	81560874	48	22592										
UTRN	7402	hgsc.bcm.edu	37	chr6	144875994	144875994	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	atattcttcagcaagcccgaCgggatccactcaccaaacaa	6	14	3	0	rs375508056		TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr6:144875994C>A	ENST00000367545.3	+	48	7099	c.7099C>A	c.(7099-7101)Cgg>Agg	p.R2367R		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2367					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GCAAGCCCGACGGGATCCACT	0.383																																					p.R2367R		Atlas-SNP	.											.	UTRN	327	.	0			c.C7099A						.						61	62	61					6																	144875994		2203	4300	6503	SO:0001819	synonymous_variant	7402	exon48			GCCCGACGGGATC	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.7099C>A	chr6.hg19:g.144875994C>A		111.0	0.0		88.0	20.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	hg19	CCDS34547.1																																																																																			.	.		0.383	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			A	144875994	C	A	144875994	2	1	148	1	0	0	0	0	0	0	0	1	17118	527	19	1		1	UTRN	6	144875994	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	55321801	144875994	26239073	49	22593										
USP42	84132	hgsc.bcm.edu	37	chr7	6187455	6187455	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cccgccccgtcatcagtcagCgggttgtcaccaacaaacag	9	16	4	0	rs377573018		TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr7:6187455C>T	ENST00000306177.5	+	12	1476	c.1318C>T	c.(1318-1320)Cgg>Tgg	p.R440W		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	440					cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		CATCAGTCAGCGGGTTGTCAC	0.517																																					p.R440W		Atlas-SNP	.											.	USP42	138	.	0			c.C1318T						.	C	TRP/ARG	0,3918		0,0,1959	92	95	94		1318	5.4	1	7		94	1,8307		0,1,4153	no	missense	USP42	NM_032172.2	101	0,1,6112	TT,TC,CC		0.012,0.0,0.0082	probably-damaging	440/1317	6187455	1,12225	1959	4154	6113	SO:0001583	missense	84132	exon12			AGTCAGCGGGTTG	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"Ubiquitin-specific peptidases"	20068	protein-coding gene	gene with protein product			"ubiquitin specific protease 42"			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.1318C>T	chr7.hg19:g.6187455C>T	ENSP00000301962:p.Arg440Trp	63.0	0.0		62.0	4.0	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Missense_Mutation	SNP	ENST00000306177.5	hg19	CCDS47535.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.214241	0.79352	0.0	1.2E-4	ENSG00000106346	ENST00000306177;ENST00000465073;ENST00000426246	T;T;T	0.18016	2.24;2.98;2.66	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000016	T	0.41236	0.1150	M	0.69823	2.125	0.38106	D	0.937408	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.976;0.996;0.991;0.991	T	0.41805	-0.9488	10	0.87932	D	0	.	13.887	0.63714	0.1516:0.8484:0.0:0.0	.	403;440;440;440	A4D2N7;Q9H9J4-2;Q9H9J4;A4D2N6	.;.;UBP42_HUMAN;.	W	440;373;286	ENSP00000301962:R440W;ENSP00000430568:R373W;ENSP00000408217:R286W	ENSP00000301962:R440W	R	+	1	2	USP42	6153981	1.000000	0.71417	0.999000	0.59377	0.888000	0.51559	3.867000	0.56047	2.531000	0.85337	0.563000	0.77884	CGG	.	.		0.517	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526		T	6187455	C	T	6187455	3	4	148	1	0	0	0	0	1	0	0	0	17088	759	27	1	1360	1	USP42	7	6187455	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10		6187455	152951208	50	22594										
CPSF4	10898	hgsc.bcm.edu	37	chr7	99045802	99045802	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	acagttgtgtgcaaacactgGctgcgtggcctatgcaagaa	12	9	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr7:99045802G>T	ENST00000292476.5	+	3	223	c.213G>T	c.(211-213)tgG>tgT	p.W71C	CPSF4_ENST00000451876.1_Missense_Mutation_p.W71C|ATP5J2-PTCD1_ENST00000413834.1_Intron|PTCD1_ENST00000555673.1_Intron|ATP5J2_ENST00000466753.1_5'Flank|ATP5J2-PTCD1_ENST00000437572.1_5'UTR|CPSF4_ENST00000471455.1_3'UTR|CPSF4_ENST00000441580.1_Missense_Mutation_p.W18C|CPSF4_ENST00000436336.2_Missense_Mutation_p.W71C			O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4, 30kDa	71					modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA processing (GO:0006397)|viral life cycle (GO:0019058)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(5)	14	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					GCAAACACTGGCTGCGTGGCC	0.552																																					p.W71C		Atlas-SNP	.											.	CPSF4	24	.	0			c.G213T						.						165	122	136					7																	99045802		2203	4300	6503	SO:0001583	missense	10898	exon3			ACACTGGCTGCGT		CCDS5664.1, CCDS47652.1	7q22	2007-10-18	2002-08-29		ENSG00000160917	ENSG00000160917			2327	protein-coding gene	gene with protein product		603052	"cleavage and polyadenylation specific factor 4, 30kD subunit"			9651582, 9224719	Standard	NM_006693		Approved	NAR, CPSF30	uc003uqj.3	O95639	OTTHUMG00000154599	ENST00000292476.5:c.213G>T	chr7.hg19:g.99045802G>T	ENSP00000292476:p.Trp71Cys	121.0	0.0		118.0	43.0	NM_001081559	D6W5S8|Q6FGE6|Q86TF8|Q9BTW6	Missense_Mutation	SNP	ENST00000292476.5	hg19	CCDS5664.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.766144	0.90020	.	.	ENSG00000160917	ENST00000436336;ENST00000451876;ENST00000292476;ENST00000441580;ENST00000412686;ENST00000452047	T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85	5.96	5.96	0.96718	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.81178	0.4768	H	0.97077	3.935	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.86486	0.1794	10	0.87932	D	0	-15.1016	20.4084	0.99013	0.0:0.0:1.0:0.0	.	18;71;71;71	B7Z7B0;O95639-3;O95639;O95639-2	.;.;CPSF4_HUMAN;.	C	71;71;71;18;18;38	ENSP00000395311:W71C;ENSP00000396060:W71C;ENSP00000292476:W71C;ENSP00000402224:W18C;ENSP00000401150:W18C;ENSP00000392584:W38C	ENSP00000292476:W71C	W	+	3	0	CPSF4	98883738	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.476000	0.97823	2.833000	0.97629	0.650000	0.86243	TGG	.	.		0.552	CPSF4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336254.1			T	99045802	G	T	99045802	3	4	148	1	0	0	0	0	1	0	0	0	3830	1212	42	3	223	3	CPSF4	7	99045802	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	92858347	99045802	60092861	51	22595										
MLL5	55904	hgsc.bcm.edu	37	chr7	104742001	104742001	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aagttaaaactgaatgtaaaGatacacagattgtcagtgat	8	4	1	4			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr7:104742001G>C	ENST00000311117.3	+	16	2397	c.1852G>C	c.(1852-1854)Gat>Cat	p.D618H	KMT2E_ENST00000334877.4_Missense_Mutation_p.D618H|KMT2E_ENST00000334914.7_5'UTR|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000257745.4_Missense_Mutation_p.D618H	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	618					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										TGAATGTAAAGATACACAGAT	0.323																																					p.D618H		Atlas-SNP	.											.	MLL5	173	.	0			c.G1852C						.						92	89	90					7																	104742001		2203	4300	6503	SO:0001583	missense	55904	exon15			TGTAAAGATACAC	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.1852G>C	chr7.hg19:g.104742001G>C	ENSP00000312379:p.Asp618His	46.0	0.0		41.0	6.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.145315	0.57044	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745	D;D;D	0.92495	-3.05;-2.63;-3.05	5.53	5.53	0.82687	.	0.427481	0.26062	N	0.026575	D	0.90988	0.7166	L	0.40543	1.245	0.80722	D	1	P	0.49696	0.927	P	0.45946	0.498	D	0.91732	0.5397	10	0.62326	D	0.03	.	19.4728	0.94969	0.0:0.0:1.0:0.0	.	618	Q8IZD2	MLL5_HUMAN	H	618;618;618;538;618	ENSP00000312379:D618H;ENSP00000335599:D618H;ENSP00000257745:D618H	ENSP00000257745:D618H	D	+	1	0	MLL5	104529237	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	4.521000	0.60532	2.608000	0.88229	0.561000	0.74099	GAT	.	.		0.323	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			C	104742001	G	C	104742001	3	2	148	1	0	0	0	0	1	0	0	0	9633	942	33	4	1906	4	MLL5	7	104742001	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	5696199	104742001	54396662	52	22596										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142562074	142562074	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tcctcctcctcctcctcctcCtcttcttcctctgcagcgtg	4	21	3	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr7:142562074C>T	ENST00000392957.2	+	7	1303	c.516C>T	c.(514-516)tcC>tcT	p.S172S	EPHB6_ENST00000411471.2_Intron|EPHB6_ENST00000442129.1_Silent_p.S172S	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	172	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.|Poly-Ser.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					cctcctcctcctcttcttcct	0.622																																					p.S172S		Atlas-SNP	.											.	EPHB6	168	.	0			c.C516T						.						83	98	93					7																	142562074		2200	4299	6499	SO:0001819	synonymous_variant	2051	exon7			CTCCTCCTCTTCT	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.516C>T	chr7.hg19:g.142562074C>T		53.0	0.0		124.0	9.0	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	hg19	CCDS5873.2																																																																																			.	.		0.622	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142562074	C	T	142562074	2	4	148	1	0	0	0	0	0	0	0	1	5180	668	24	3		3	EPHB6	7	142562074	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	37820073	142562074	16576589	53	22597										
MLL3	58508	hgsc.bcm.edu	37	chr7	151849960	151849960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aacccatggatgggacatctGgagcactgctaacctcatag	10	11	2	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr7:151849960G>A	ENST00000262189.6	-	49	12574	c.12356C>T	c.(12355-12357)cCa>cTa	p.P4119L	KMT2C_ENST00000355193.2_Missense_Mutation_p.P4176L|KMT2C_ENST00000485241.1_5'Flank	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4119					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TGGGACATCTGGAGCACTGCT	0.498																																					p.P4119L		Atlas-SNP	.											.	MLL3	1564	.	0			c.C12356T						.						123	120	121					7																	151849960		2203	4300	6503	SO:0001583	missense	58508	exon49			ACATCTGGAGCAC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.12356C>T	chr7.hg19:g.151849960G>A	ENSP00000262189:p.Pro4119Leu	139.0	0.0		139.0	27.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.867707	0.51588	.	.	ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877	D;D;D	0.91011	-2.1;-2.04;-2.77	5.84	5.84	0.93424	.	0.000000	0.44483	U	0.000452	D	0.94125	0.8116	M	0.73962	2.25	0.80722	D	1	P;D;D	0.63046	0.651;0.992;0.992	B;P;P	0.59357	0.15;0.856;0.856	D	0.94383	0.7606	10	0.87932	D	0	.	15.6008	0.76623	0.0:0.1369:0.8631:0.0	.	4119;3237;4176	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	MLL3_HUMAN;.;.	L	4119;4176;736	ENSP00000262189:P4119L;ENSP00000347325:P4176L;ENSP00000410411:P736L	ENSP00000262189:P4119L	P	-	2	0	MLL3	151480893	.	.	1.000000	0.80357	0.990000	0.78478	.	.	2.764000	0.94973	0.655000	0.94253	CCA	.	.		0.498	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151849960	G	A	151849960	3	1	148	1	0	0	0	0	1	0	0	0	9631	1348	47	3	2423	3	MLL3	7	151849960	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	9287886	151849960	7288703	54	22598										
TEX15	56154	hgsc.bcm.edu	37	chr8	30702749	30702749	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	atataagtacgtcagttttcGcctttgtgtgacctatgcaa	8	8	1	1	rs115550830		TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr8:30702749G>A	ENST00000256246.2	-	1	3859	c.3785C>T	c.(3784-3786)gCg>gTg	p.A1262V		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1262					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		GTCAGTTTTCGCCTTTGTGTG	0.313																																					p.A1262V		Atlas-SNP	.											.	TEX15	350	.	0			c.C3785T						.						99	94	96					8																	30702749		2203	4299	6502	SO:0001583	missense	56154	exon1			GTTTTCGCCTTTG	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.3785C>T	chr8.hg19:g.30702749G>A	ENSP00000256246:p.Ala1262Val	101.0	0.0		45.0	17.0	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.829462	0.00584	.	.	ENSG00000133863	ENST00000256246	T	0.24538	1.85	5.96	-0.991	0.10235	.	0.700000	0.13040	N	0.418590	T	0.07593	0.0191	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25047	-1.0143	10	0.87932	D	0	.	1.4564	0.02386	0.4456:0.2626:0.1637:0.1281	.	1262	Q9BXT5	TEX15_HUMAN	V	1262	ENSP00000256246:A1262V	ENSP00000256246:A1262V	A	-	2	0	TEX15	30822291	0.000000	0.05858	0.009000	0.14445	0.071000	0.16799	0.117000	0.15583	0.159000	0.19401	-0.238000	0.12139	GCG	.	G|0.999;C|0.001		0.313	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30702749	G	A	30702749	3	1	148	1	0	0	0	0	1	0	0	0	15794	1087	38	1	4600	1	TEX15	8	30702749	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10		30702749	115661273	55	22599										
ZHX1	11244	hgsc.bcm.edu	37	chr8	124266184	124266185	+	Frame_Shift_Ins	INS	-	-	T													0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	catgtgcagctgctcaggtgINStttttttacatatcttgcct							TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr8:124266184_124266185insT	ENST00000522655.1	-	3	2542_2543	c.2002_2003insA	c.(2002-2004)acafs	p.T668fs	ZHX1_ENST00000395571.3_Frame_Shift_Ins_p.T668fs|ZHX1_ENST00000297857.2_Frame_Shift_Ins_p.T668fs|ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000522595.1_5'Flank			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	668					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			CTGCTCAGGTGTTTTTTTACAT	0.465																																					p.T668fs		Atlas-Indel,Pindel	.											.	ZHX1	89	.	0			c.2003_2004insA						.																																			SO:0001589	frameshift_variant	11244	exon3			.	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	12871	protein-coding gene	gene with protein product		604764	"zinc-fingers and homeoboxes 1"			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.2003dupA	chr8.hg19:g.124266191_124266191dupT	ENSP00000428821:p.Thr668fs	133.0	0.0		175.0	21.0	NM_001017926	Q8IWD8	Frame_Shift_Ins	INS	ENST00000522655.1	hg19	CCDS6342.1																																																																																			.	.		0.465	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1			T	124266185	-	T	124266184	7	5	148	1	0	1	1	0	0	0	0	0	17690	1377	48	0	622	0	ZHX1	8	124266184	Frame_Shift_Ins	INS	-	TCGA-DD-A73G-01A-22D-A32G-10	93563435	124266184	22097838	56	22600										
IL33	90865	hgsc.bcm.edu	37	chr9	6241766	6241766	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aagaacacagcaagcaaagcCttgtgtttcaagctgggaag	11	8	1	1	rs557833104		TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr9:6241766C>T	ENST00000381434.3	+	1	85	c.72C>T	c.(70-72)gcC>gcT	p.A24A	IL33_ENST00000417746.2_Silent_p.A24A|IL33_ENST00000463336.1_3'UTR|IL33_ENST00000456383.2_Silent_p.A24A	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	24	Homeodomain-like HTH domain.				extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)			breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		CAAGCAAAGCCTTGTGTTTCA	0.313																																					p.A24A		Atlas-SNP	.											.	IL33	27	.	0			c.C72T						.						93	91	92					9																	6241766		2203	4300	6503	SO:0001819	synonymous_variant	90865	exon2			CAAAGCCTTGTGT	AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"Interleukins and interleukin receptors"	16028	protein-coding gene	gene with protein product	"DVS27-related protein", "nuclear factor for high endothelial venules", "interleukin-1 family, member 11"	608678	"chromosome 9 open reading frame 26 (NF-HEV)"	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.72C>T	chr9.hg19:g.6241766C>T		131.0	0.0		110.0	51.0	NM_001199640	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Silent	SNP	ENST00000381434.3	hg19	CCDS6468.1																																																																																			.	.		0.313	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1	NM_033439		T	6241766	C	T	6241766	2	4	148	1	0	0	0	0	0	0	0	1	7702	668	24	3		3	IL33	9	6241766	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10		6241766	134971665	57	22601										
C5	727	hgsc.bcm.edu	37	chr9	123768307	123768307	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gaagacatctttgaacacctTtgccttgacagtatcagcaa	7	10	2	3			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr9:123768307T>A	ENST00000223642.1	-	20	2481	c.2452A>T	c.(2452-2454)Aag>Tag	p.K818*	C5_ENST00000466280.1_5'UTR	NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	818					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	TTGAACACCTTTGCCTTGACA	0.348																																					p.K818X		Atlas-SNP	.											.	C5	124	.	0			c.A2452T						.						115	105	108					9																	123768307		2203	4300	6503	SO:0001587	stop_gained	727	exon20			ACACCTTTGCCTT	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.2452A>T	chr9.hg19:g.123768307T>A	ENSP00000223642:p.Lys818*	93.0	0.0		96.0	18.0	NM_001735	Q14CJ0|Q27I61	Nonsense_Mutation	SNP	ENST00000223642.1	hg19	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.781991	0.90282	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	.	.	.	5.54	0.0134	0.14096	.	0.939082	0.09034	N	0.858344	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.2216	0.31545	0.0:0.0792:0.5177:0.4031	.	.	.	.	X	818;889	.	ENSP00000223642:K818X	K	-	1	0	C5	122808128	0.142000	0.22610	0.000000	0.03702	0.099000	0.18886	1.572000	0.36461	0.109000	0.17891	-0.321000	0.08615	AAG	.	.		0.348	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		A	123768307	T	A	123768307	4	1	148	1	0	0	0	0	0	1	0	0	2282	1850	64	4	2666	4	C5	9	123768307	Nonsense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	117526541	123768307	17445124	58	22602										
OR1J2	26740	hgsc.bcm.edu	37	chr9	125273953	125273953	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttgaacccctttatctacagCcttaggaacagggacatgaa	8	10	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr9:125273953C>G	ENST00000335302.5	+	1	873	c.873C>G	c.(871-873)agC>agG	p.S291R		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	291						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						TTATCTACAGCCTTAGGAACA	0.423																																					p.S291R		Atlas-SNP	.											.	OR1J2	64	.	0			c.C873G						.						96	95	95					9																	125273953		2203	4300	6503	SO:0001583	missense	26740	exon1			CTACAGCCTTAGG		CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"GPCR / Class A : Olfactory receptors"	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.873C>G	chr9.hg19:g.125273953C>G	ENSP00000335575:p.Ser291Arg	134.0	0.0		120.0	29.0	NM_054107	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Missense_Mutation	SNP	ENST00000335302.5	hg19	CCDS35121.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.847608	0.51164	.	.	ENSG00000197233	ENST00000335302	T	0.39229	1.09	5.14	0.466	0.16716	.	0.000000	0.47455	U	0.000238	T	0.68265	0.2982	H	0.97131	3.945	0.09310	N	0.999999	D	0.57899	0.981	P	0.61592	0.891	T	0.62029	-0.6940	10	0.87932	D	0	.	8.828	0.35067	0.0:0.461:0.0:0.539	.	291	Q8NGS2	OR1J2_HUMAN	R	291	ENSP00000335575:S291R	ENSP00000335575:S291R	S	+	3	2	OR1J2	124313774	0.000000	0.05858	0.697000	0.30258	0.991000	0.79684	-1.448000	0.02394	0.181000	0.19994	0.632000	0.83419	AGC	.	.		0.423	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1			G	125273953	C	G	125273953	3	3	148	1	0	0	0	0	1	0	0	0	10969	738	26	4	875	4	OR1J2	9	125273953	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	1505646	125273953	15939478	59	22603										
OR1N2	138882	hgsc.bcm.edu	37	chr9	125315781	125315781	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cagagtcagatcatctcgtaTtctgggtgtcttgcacagct	10	10	5	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr9:125315781T>C	ENST00000373688.2	+	1	391	c.333T>C	c.(331-333)taT>taC	p.Y111Y		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						TCATCTCGTATTCTGGGTGTC	0.493																																					p.Y111Y		Atlas-SNP	.											.	OR1N2	51	.	0			c.T333C						.						231	226	227					9																	125315781		2203	4300	6503	SO:0001819	synonymous_variant	138882	exon1			CTCGTATTCTGGG		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"GPCR / Class A : Olfactory receptors"	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.333T>C	chr9.hg19:g.125315781T>C		59.0	0.0		59.0	19.0	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Silent	SNP	ENST00000373688.2	hg19	CCDS35123.1																																																																																			.	.		0.493	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2			C	125315781	T	C	125315781	2	2	148	1	0	0	0	0	0	0	0	1	10979	1500	52	2		2	OR1N2	9	125315781	Silent	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	41828	125315781	15897650	60	22604										
WDR37	22884	hgsc.bcm.edu	37	chr10	1149723	1149723	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tgtgactgcctcctgggaccGgacggcaaacctgtacgacg	13	13	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr10:1149723G>T	ENST00000358220.1	+	10	1052	c.908G>T	c.(907-909)cGg>cTg	p.R303L	WDR37_ENST00000263150.4_Missense_Mutation_p.R303L			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37	303										breast(2)|endometrium(2)|kidney(1)|lung(9)|prostate(2)|skin(1)	17		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)		TCCTGGGACCGGACGGCAAAC	0.632																																					p.R303L		Atlas-SNP	.											WDR37,NS,NS,0,10	WDR37	52	.	0			c.G908T						.						62	55	57					10																	1149723		2203	4300	6503	SO:0001583	missense	22884	exon10			GGGACCGGACGGC	AB023199	CCDS7057.1	10p15.3	2013-01-09			ENSG00000047056	ENSG00000047056		"WD repeat domain containing"	31406	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_014023		Approved	KIAA0982	uc001igf.1	Q9Y2I8	OTTHUMG00000017540	ENST00000358220.1:c.908G>T	chr10.hg19:g.1149723G>T	ENSP00000350954:p.Arg303Leu	40.0	0.0		55.0	11.0	NM_014023	A8K976|D3DRQ7|Q5SW03|Q8WVG2|Q9NTJ6	Missense_Mutation	SNP	ENST00000358220.1	hg19	CCDS7057.1	.	.	.	.	.	.	.	.	.	.	G	35	5.522038	0.96416	.	.	ENSG00000047056	ENST00000358220;ENST00000263150	T;T	0.61627	0.09;0.09	5.72	5.72	0.89469	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83760	0.5324	H	0.94698	3.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87270	0.2285	10	0.62326	D	0.03	.	19.8834	0.96906	0.0:0.0:1.0:0.0	.	304;303	A8K976;Q9Y2I8	.;WDR37_HUMAN	L	303	ENSP00000350954:R303L;ENSP00000263150:R303L	ENSP00000263150:R303L	R	+	2	0	WDR37	1139723	1.000000	0.71417	0.382000	0.26119	0.910000	0.53928	9.480000	0.97931	2.694000	0.91930	0.655000	0.94253	CGG	.	.		0.632	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	NM_014023		T	1149723	G	T	1149723	3	4	148	1	0	0	0	0	1	0	0	0	17306	1116	39	1	942	1	WDR37	10	1149723	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10		1149723	134385024	61	22605										
AKR1C3	8644	hgsc.bcm.edu	37	chr10	5139644	5139644	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	agctttggtccacttttcatCgaccagagttggtccgacca	9	12	1	1	rs118150330	byFrequency	TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr10:5139644C>A	ENST00000380554.3	+	3	923	c.271C>A	c.(271-273)Cga>Aga	p.R91R	AKR1C3_ENST00000470862.2_3'UTR|AKR1C3_ENST00000605149.1_Silent_p.R68R|AKR1C3_ENST00000439082.2_5'UTR	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	91					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	CACTTTTCATCGACCAGAGTT	0.393																																					p.R91R		Atlas-SNP	.											.	AKR1C3	21	.	0			c.C271A						.						132	127	129					10																	5139644		2203	4300	6503	SO:0001819	synonymous_variant	8644	exon3			TTTCATCGACCAG	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"Aldo-keto reductases"	386	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase X", "prostaglandin F synthase", "3-alpha hydroxysteroid dehydrogenase, type II"	603966	"hydroxysteroid (17-beta) dehydrogenase 5", "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.271C>A	chr10.hg19:g.5139644C>A		159.0	0.0		155.0	27.0	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Silent	SNP	ENST00000380554.3	hg19	CCDS7063.1																																																																																			.	C|0.999;T|0.001		0.393	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		A	5139644	C	A	5139644	2	1	148	1	0	0	0	0	0	0	0	1	471	876	31	1		1	AKR1C3	10	5139644	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	3989921	5139644	130395103	62	22606										
ARL5B	221079	hgsc.bcm.edu	37	chr10	18957556	18957556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttcttatgtgggatattggtGgtcaggagtctctgcgatca	13	6	4	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr10:18957556G>A	ENST00000377275.3	+	3	438	c.205G>A	c.(205-207)Ggt>Agt	p.G69S		NM_178815.3	NP_848930.1	Q96KC2	ARL5B_HUMAN	ADP-ribosylation factor-like 5B	69					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			lung(1)|ovary(1)	2						GGATATTGGTGGTCAGGAGTC	0.373																																					p.G69S		Atlas-SNP	.											.	ARL5B	12	.	0			c.G205A						.						149	142	144					10																	18957556		2203	4300	6503	SO:0001583	missense	221079	exon3			ATTGGTGGTCAGG	AF494061	CCDS7131.1	10p13	2014-05-09	2005-11-03	2005-11-03	ENSG00000165997	ENSG00000165997		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	23052	protein-coding gene	gene with protein product		608909	"ADP-ribosylation factor-like 8"	ARL8		12853149	Standard	XM_005252400		Approved		uc001iqd.1	Q96KC2	OTTHUMG00000017765	ENST00000377275.3:c.205G>A	chr10.hg19:g.18957556G>A	ENSP00000366487:p.Gly69Ser	91.0	0.0		79.0	18.0	NM_178815		Missense_Mutation	SNP	ENST00000377275.3	hg19	CCDS7131.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.029595	0.93518	.	.	ENSG00000165997	ENST00000377275	D	0.99186	-5.53	5.83	5.83	0.93111	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.99648	0.9870	H	0.98664	4.295	0.80722	D	1	D	0.71674	0.998	D	0.74674	0.984	D	0.97607	1.0127	10	0.87932	D	0	-13.4351	20.1162	0.97934	0.0:0.0:1.0:0.0	.	69	Q96KC2	ARL5B_HUMAN	S	69	ENSP00000366487:G69S	ENSP00000366487:G69S	G	+	1	0	ARL5B	18997562	1.000000	0.71417	1.000000	0.80357	0.534000	0.34807	9.864000	0.99589	2.756000	0.94617	0.655000	0.94253	GGT	.	.		0.373	ARL5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047078.1	NM_178815		A	18957556	G	A	18957556	3	1	148	1	0	0	0	0	1	0	0	0	940	1348	47	3	215	3	ARL5B	10	18957556	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	13817912	18957556	116577191	63	22607										
TACR2	6865	hgsc.bcm.edu	37	chr10	71166949	71166949	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cttgtggcagtagatgtcctCctggaagctgcccaggatga	13	10	0	2	rs200848530		TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr10:71166949C>G	ENST00000373306.4	-	4	1372	c.829G>C	c.(829-831)Gag>Cag	p.E277Q	TACR2_ENST00000373307.1_Missense_Mutation_p.E65Q	NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	277					excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						TAGATGTCCTCCTGGAAGCTG	0.532																																					p.E277Q		Atlas-SNP	.											.	TACR2	37	.	0			c.G829C						.						223	183	197					10																	71166949		2203	4300	6503	SO:0001583	missense	6865	exon4			TGTCCTCCTGGAA		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"GPCR / Class A : Tachykinin receptors"	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.829G>C	chr10.hg19:g.71166949C>G	ENSP00000362403:p.Glu277Gln	74.0	0.0		115.0	35.0	NM_001057	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Missense_Mutation	SNP	ENST00000373306.4	hg19	CCDS7293.1	.	.	.	.	.	.	.	.	.	.	C	6.070	0.381138	0.11466	.	.	ENSG00000075073	ENST00000373307;ENST00000373306	T;T	0.37235	1.21;1.21	5.11	0.863	0.19062	GPCR, rhodopsin-like superfamily (1);	0.567000	0.17722	N	0.164200	T	0.18882	0.0453	N	0.19112	0.55	0.09310	N	0.999996	B	0.16802	0.019	B	0.19666	0.026	T	0.24977	-1.0145	10	0.14252	T	0.57	.	7.457	0.27272	0.0:0.5866:0.1267:0.2867	.	277	P21452	NK2R_HUMAN	Q	65;277	ENSP00000362404:E65Q;ENSP00000362403:E277Q	ENSP00000362403:E277Q	E	-	1	0	TACR2	70836955	0.000000	0.05858	0.991000	0.47740	0.602000	0.36980	-0.287000	0.08388	0.555000	0.29079	-0.300000	0.09419	GAG	.	.		0.532	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1			G	71166949	C	G	71166949	3	3	148	1	0	0	0	0	1	0	0	0	15521	864	30	4	375	4	TACR2	10	71166949	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	52209393	71166949	64367798	64	22608										
CYP2C9	1559	hgsc.bcm.edu	37	chr10	96709012	96709012	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tgaacaaccctcaggactttAttgattgcttcctgatgaaa	7	9	1	4			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr10:96709012A>G	ENST00000260682.6	+	5	802	c.790A>G	c.(790-792)Att>Gtt	p.I264V		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	264					arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TCAGGACTTTATTGATTGCTT	0.313																																					p.I264V	Ovarian(54;1266 1406 16072 35076)	Atlas-SNP	.											.	CYP2C9	82	.	0			c.A790G						.						84	85	85					10																	96709012		2203	4300	6503	SO:0001583	missense	1559	exon5			GACTTTATTGATT	M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"Cytochrome P450s"	2623	protein-coding gene	gene with protein product		601130	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.790A>G	chr10.hg19:g.96709012A>G	ENSP00000260682:p.Ile264Val	250.0	0.0		268.0	55.0	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	hg19	CCDS7437.1	.	.	.	.	.	.	.	.	.	.	.	15.98	2.991462	0.54041	.	.	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.71222	-0.55	3.29	3.29	0.37713	.	0.000000	0.64402	U	0.000001	T	0.68016	0.2955	L	0.55834	1.745	0.36862	D	0.88847	P;P	0.39094	0.659;0.659	B;B	0.43838	0.433;0.433	T	0.74788	-0.3546	10	0.59425	D	0.04	.	9.8769	0.41209	1.0:0.0:0.0:0.0	.	264;264	Q5VX92;P11712	.;CP2C9_HUMAN	V	264	ENSP00000260682:I264V	ENSP00000260682:I264V	I	+	1	0	CYP2C9	96699002	1.000000	0.71417	0.999000	0.59377	0.832000	0.47134	7.109000	0.77062	1.501000	0.48654	0.402000	0.26972	ATT	.	.		0.313	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771		G	96709012	A	G	96709012	3	3	148	1	0	0	0	0	1	0	0	0	4170	449	16	2	808	2	CYP2C9	10	96709012	Missense_Mutation	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10	25542063	96709012	38825735	65	22609										
CALY	50632	hgsc.bcm.edu	37	chr10	135140487	135140487	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gcgaaggcgatcatccgtgcGgtgggcagctggcaggaggg	20	9	1	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr10:135140487G>T	ENST00000252939.4	-	4	348	c.255C>A	c.(253-255)acC>acA	p.T85T	CALY_ENST00000467611.1_5'Flank|CALY_ENST00000368556.2_Silent_p.T85T|ZNF511_ENST00000368554.4_Intron|RP11-122K13.14_ENST00000605518.1_lincRNA|CALY_ENST00000368558.1_Silent_p.T85T	NM_015722.3	NP_056537.1	Q9NYX4	CALY_HUMAN	calcyon neuron-specific vesicular protein	85					clathrin coat assembly (GO:0048268)|dopamine receptor signaling pathway (GO:0007212)|endocytosis (GO:0006897)|positive regulation of endocytosis (GO:0045807)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)	clathrin light chain binding (GO:0032051)			kidney(1)|lung(2)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;6.94e-06)|OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)	Apomorphine(DB00714)|Clozapine(DB00363)|Trifluoperazine(DB00831)	TCATCCGTGCGGTGGGCAGCT	0.667																																					p.T85T		Atlas-SNP	.											.	CALY	19	.	0			c.C255A						.						44	36	39					10																	135140487		2200	4292	6492	SO:0001819	synonymous_variant	50632	exon4			CCGTGCGGTGGGC	AF225903	CCDS7678.1	10q26.3	2008-07-02	2008-01-16	2008-01-16	ENSG00000130643	ENSG00000130643			17938	protein-coding gene	gene with protein product		604647	"dopamine receptor D1 interacting protein"	DRD1IP		10698743, 17623072	Standard	NM_015722		Approved	CALCYON, NSG3	uc001lmo.2	Q9NYX4	OTTHUMG00000019310	ENST00000252939.4:c.255C>A	chr10.hg19:g.135140487G>T		83.0	0.0		101.0	37.0	NM_015722	Q5VWX3|Q5VWY5|Q5VWY6	Silent	SNP	ENST00000252939.4	hg19	CCDS7678.1																																																																																			.	.		0.667	CALY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051122.1	NM_015722		T	135140487	G	T	135140487	2	4	148	1	0	0	0	0	0	0	0	1	2597	1103	39	1		1	CALY	10	135140487	Silent	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	38431475	135140487	394260	66	22610										
ATHL1	80162	hgsc.bcm.edu	37	chr11	290808	290808	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aggctaggacgtgggacttcCtgacagcagtgggcggcagc	17	10	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr11:290808C>G	ENST00000409548.2	+	4	716	c.601C>G	c.(601-603)Ctg>Gtg	p.L201V	RP11-326C3.2_ENST00000533924.1_RNA|RP11-326C3.2_ENST00000525217.1_RNA|RP11-326C3.2_ENST00000534742.1_RNA|ATHL1_ENST00000409655.1_Missense_Mutation_p.L24V|ATHL1_ENST00000409479.1_Missense_Mutation_p.L201V	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	201					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		GTGGGACTTCCTGACAGCAGT	0.667																																					p.L201V		Atlas-SNP	.											.	ATHL1	88	.	0			c.C601G						.						51	50	50					11																	290808		2203	4300	6503	SO:0001583	missense	80162	exon4			GACTTCCTGACAG	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.601C>G	chr11.hg19:g.290808C>G	ENSP00000387185:p.Leu201Val	31.0	0.0		31.0	6.0	NM_025092	Q658X8|Q8TEG9|Q9H635	Missense_Mutation	SNP	ENST00000409548.2	hg19	CCDS31322.2	.	.	.	.	.	.	.	.	.	.	C	6.510	0.462331	0.12342	.	.	ENSG00000142102	ENST00000409548;ENST00000409655;ENST00000409479	.	.	.	4.06	-1.78	0.07957	.	0.178793	0.37178	N	0.002214	T	0.36358	0.0964	L	0.45581	1.43	0.37722	D	0.924966	B;B;B	0.21225	0.009;0.038;0.053	B;B;B	0.18263	0.021;0.02;0.019	T	0.39981	-0.9587	9	0.02654	T	1	.	5.6093	0.17396	0.0:0.4993:0.2639:0.2367	.	201;201;24	Q32M88;E7EMA9;B8ZZ60	ATHL1_HUMAN;.;.	V	201;24;201	.	ENSP00000387099:L201V	L	+	1	2	ATHL1	280808	0.999000	0.42202	0.454000	0.27019	0.031000	0.12232	1.005000	0.29834	-0.287000	0.09064	0.448000	0.29417	CTG	.	.		0.667	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092		G	290808	C	G	290808	3	3	148	1	0	0	0	0	1	0	0	0	1104	680	24	4	611	4	ATHL1	11	290808	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10		290808	134715708	67	22611										
PHRF1	57661	hgsc.bcm.edu	37	chr11	606503	606503	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aggagccagtgcctgacctgCtgggcagcatcctgtcgggc	15	13	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr11:606503C>T	ENST00000264555.5	+	13	1644	c.1516C>T	c.(1516-1518)Ctg>Ttg	p.L506L	PHRF1_ENST00000413872.2_Silent_p.L504L|PHRF1_ENST00000533464.1_Silent_p.L502L|PHRF1_ENST00000416188.2_Silent_p.L505L	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	506					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GCCTGACCTGCTGGGCAGCAT	0.682																																					p.L505L		Atlas-SNP	.											.	PHRF1	188	.	0			c.C1513T						.						18	23	21					11																	606503		2085	4201	6286	SO:0001819	synonymous_variant	57661	exon13			GACCTGCTGGGCA	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.1516C>T	chr11.hg19:g.606503C>T		26.0	0.0		33.0	19.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	hg19																																																																																				.	.		0.682	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		T	606503	C	T	606503	2	4	148	1	0	0	0	0	0	0	0	1	11870	796	28	3		3	PHRF1	11	606503	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	315695	606503	134400013	68	22612										
EIF4G2	1982	hgsc.bcm.edu	37	chr11	10824597	10824597	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttttactgcatcttgacgaaTttgattgatcgtctttggtc	8	7	2	3			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr11:10824597T>C	ENST00000526148.1	-	11	1486	c.976A>G	c.(976-978)Att>Gtt	p.I326V	SNORD97_ENST00000459187.1_RNA|EIF4G2_ENST00000525995.1_5'Flank|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000525681.1_Missense_Mutation_p.I326V|EIF4G2_ENST00000396525.2_Missense_Mutation_p.I326V|EIF4G2_ENST00000339995.5_Missense_Mutation_p.I326V	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TCTTGACGAATTTGATTGATC	0.393																																					p.I326V		Atlas-SNP	.											.	EIF4G2	89	.	0			c.A976G						.						80	75	77					11																	10824597		2201	4294	6495	SO:0001583	missense	1982	exon11			GACGAATTTGATT	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.976A>G	chr11.hg19:g.10824597T>C	ENSP00000433664:p.Ile326Val	65.0	0.0		62.0	4.0	NM_001172705		Missense_Mutation	SNP	ENST00000526148.1	hg19	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.074621	0.55646	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000531416	T;T;T;T;T	0.42131	1.25;1.25;1.25;1.22;0.98	6.07	6.07	0.98685	.	0.044346	0.85682	D	0.000000	T	0.35799	0.0944	L	0.33245	0.995	0.46564	D	0.999108	B;B;B	0.17465	0.009;0.005;0.022	B;B;B	0.15052	0.012;0.005;0.005	T	0.30880	-0.9963	9	0.37606	T	0.19	-6.4612	16.6407	0.85098	0.0:0.0:0.0:1.0	.	326;326;399	P78344-2;P78344;B4DZF2	.;IF4G2_HUMAN;.	V	326;326;326;326;399;326	ENSP00000433664:I326V;ENSP00000433371:I326V;ENSP00000340281:I326V;ENSP00000379778:I326V;ENSP00000431583:I326V	ENSP00000340281:I326V	I	-	1	0	EIF4G2	10781173	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.045000	0.71020	2.326000	0.78906	0.533000	0.62120	ATT	.	.		0.393	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418		C	10824597	T	C	10824597	3	2	148	1	0	0	0	0	1	0	0	0	5039	1493	52	2	1795	2	EIF4G2	11	10824597	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	10218094	10824597	124181919	69	22613										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17191175	17191175	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tccttttgcagttttgctaaAgcctctgcttccatctgtaa	6	11	2	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr11:17191175A>G	ENST00000265970.7	-	1	113	c.114T>C	c.(112-114)gcT>gcC	p.A38A	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	38	Interaction with clathrin; sufficient to induce clathrin assemby.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						GTTTTGCTAAAGCCTCTGCTT	0.423																																					p.A38A		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T114C						.						222	213	216					11																	17191175		2200	4293	6493	SO:0001819	synonymous_variant	5286	exon1			TGCTAAAGCCTCT	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.114T>C	chr11.hg19:g.17191175A>G		64.0	0.0		92.0	17.0	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Silent	SNP	ENST00000265970.7	hg19	CCDS7824.1																																																																																			.	.		0.423	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17191175	A	G	17191175	2	3	148	1	0	0	0	0	0	0	0	1	11918	59	3	2		2	PIK3C2A	11	17191175	Silent	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10	6366578	17191175	117815341	70	22614										
MYBPC3	4607	hgsc.bcm.edu	37	chr11	47364195	47364195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tgcatagtgccccgcgtcctCcagcatggcctcgttgatga	11	14	0	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr11:47364195C>T	ENST00000545968.1	-	17	1612	c.1558G>A	c.(1558-1560)Gag>Aag	p.E520K	MYBPC3_ENST00000256993.4_Missense_Mutation_p.E519K|MYBPC3_ENST00000399249.2_Missense_Mutation_p.E520K	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	520	Ig-like C2-type 3.				cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		CCCGCGTCCTCCAGCATGGCC	0.627																																					p.E520K		Atlas-SNP	.											.	MYBPC3	102	.	0			c.G1558A						.						122	122	122					11																	47364195		2162	4263	6425	SO:0001583	missense	4607	exon16			CGTCCTCCAGCAT	X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7551	protein-coding gene	gene with protein product		600958	"myosin-binding protein C, cardiac"	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.1558G>A	chr11.hg19:g.47364195C>T	ENSP00000442795:p.Glu520Lys	124.0	0.0		105.0	25.0	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	hg19	CCDS53621.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.588465	0.46110	.	.	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.78924	-1.22;-1.22;-1.22	4.63	4.63	0.57726	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.81465	0.4828	L	0.60957	1.885	0.58432	D	0.999997	P	0.41569	0.755	P	0.48873	0.593	T	0.82977	-0.0189	9	0.52906	T	0.07	.	17.6444	0.88145	0.0:1.0:0.0:0.0	.	519	Q14896	MYPC3_HUMAN	K	520;520;519	ENSP00000442795:E520K;ENSP00000382193:E520K;ENSP00000256993:E519K	ENSP00000256993:E519K	E	-	1	0	MYBPC3	47320771	1.000000	0.71417	1.000000	0.80357	0.105000	0.19272	7.234000	0.78134	2.395000	0.81488	0.462000	0.41574	GAG	.	.		0.627	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3			T	47364195	C	T	47364195	3	4	148	1	0	0	0	0	1	0	0	0	10022	864	30	3	2338	3	MYBPC3	11	47364195	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	30173020	47364195	87642321	71	22615										
MS4A3	932	hgsc.bcm.edu	37	chr11	59837694	59837694	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	taggaaatttcctcacctccCaattctgtgtaatcaagaat	5	10	3	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr11:59837694C>T	ENST00000278865.3	+	7	706	c.633C>T	c.(631-633)ccC>ccT	p.P211P	MS4A3_ENST00000395032.2_Silent_p.P88P|MS4A3_ENST00000534744.1_Silent_p.P165P|MS4A3_ENST00000358152.2_Silent_p.P165P	NM_006138.4	NP_006129.4	Q96HJ5	MS4A3_HUMAN	membrane-spanning 4-domains, subfamily A, member 3 (hematopoietic cell-specific)	211						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(4)|kidney(2)|lung(9)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		all_epithelial(135;0.245)				CCTCACCTCCCAATTCTGTGT	0.388																																					p.P211P		Atlas-SNP	.											.	MS4A3	47	.	0			c.C633T						.						188	166	174					11																	59837694		2201	4294	6495	SO:0001819	synonymous_variant	932	exon7			ACCTCCCAATTCT	L35848	CCDS31567.1, CCDS31568.1, CCDS41651.1	11q12-q13.1	2008-03-25				ENSG00000149516			7317	protein-coding gene	gene with protein product		606498		CD20L		7524084	Standard	NM_006138		Approved	HTM4	uc001nom.3	Q96HJ5		ENST00000278865.3:c.633C>T	chr11.hg19:g.59837694C>T		74.0	0.0		61.0	12.0	NM_006138	A8MTP8|Q8NHW2	Silent	SNP	ENST00000278865.3	hg19	CCDS31567.1																																																																																			.	.		0.388	MS4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394417.1			T	59837694	C	T	59837694	2	4	148	1	0	0	0	0	0	0	0	1	9870	581	21	3		3	MS4A3	11	59837694	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	12473499	59837694	75168822	72	22616										
KIAA1826	84437	hgsc.bcm.edu	37	chr11	105881627	105881627	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ctaaaattgcttttccttttTcttttcaactgcttcatttt	2	9	3	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr11:105881627T>A	ENST00000301919.4	-	2	1433	c.18A>T	c.(16-18)agA>agT	p.R6S	MSANTD4_ENST00000529805.1_5'Flank	NM_032424.1	NP_115800.1	Q8NCY6	MSD4_HUMAN	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	6	Myb-like.					nucleus (GO:0005634)											TTTTCCTTTTTCTTTTCAACT	0.323																																					p.R6S		Atlas-SNP	.											.	.	.	.	0			c.A18T						.						37	38	38					11																	105881627		2201	4298	6499	SO:0001583	missense	84437	exon2			CCTTTTTCTTTTC	AB058729	CCDS31663.1	11q22	2012-03-13	2012-03-13	2012-03-13	ENSG00000170903	ENSG00000170903			29383	protein-coding gene	gene with protein product			"KIAA1826"	KIAA1826			Standard	XM_005271697		Approved		uc001piz.3	Q8NCY6	OTTHUMG00000166240	ENST00000301919.4:c.18A>T	chr11.hg19:g.105881627T>A	ENSP00000304713:p.Arg6Ser	89.0	0.0		89.0	10.0	NM_032424	Q96JK1|Q96JZ3|Q9H2N4	Missense_Mutation	SNP	ENST00000301919.4	hg19	CCDS31663.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.581617	0.65992	.	.	ENSG00000170903	ENST00000301919;ENST00000530788;ENST00000534458;ENST00000530108	.	.	.	5.79	-0.993	0.10228	.	0.000000	0.85682	D	0.000000	T	0.49115	0.1538	N	0.12182	0.205	0.45899	D	0.998749	P	0.51653	0.947	D	0.67231	0.95	T	0.50988	-0.8762	9	0.87932	D	0	-13.5711	11.4882	0.50367	0.0:0.4549:0.0:0.5451	.	6	Q8NCY6	K1826_HUMAN	S	6	.	ENSP00000304713:R6S	R	-	3	2	KIAA1826	105386837	0.994000	0.37717	0.997000	0.53966	0.995000	0.86356	0.206000	0.17375	-0.176000	0.10707	0.533000	0.62120	AGA	.	.		0.323	MSANTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388619.1	NM_032424		A	105881627	T	A	105881627	3	1	148	1	0	0	0	0	1	0	0	0	8269	1780	62	4	1027	4	KIAA1826	11	105881627	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	46043933	105881627	29124889	73	22617										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43837682	43837682	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ggaatctttacaacaacattAtaacctgcaatataatttta	3	7	1	0	rs370946000		TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr12:43837682A>G	ENST00000389420.3	-	16	2201	c.2202T>C	c.(2200-2202)taT>taC	p.Y734Y	ADAMTS20_ENST00000553158.1_Silent_p.Y734Y	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	734	Spacer.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		CAACAACATTATAACCTGCAA	0.363																																					p.Y734Y		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T2202C						.	A		0,4406		0,0,2203	127	130	129		2202	2.7	1	12		129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADAMTS20	NM_025003.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		734/1911	43837682	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	80070	exon16			AACATTATAACCT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2202T>C	chr12.hg19:g.43837682A>G		75.0	0.0		81.0	14.0	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.		0.363	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43837682	A	G	43837682	2	3	148	1	0	0	0	0	0	0	0	1	266	456	16	2		2	ADAMTS20	12	43837682	Silent	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10		43837682	90014213	74	22618										
LRP1	4035	hgsc.bcm.edu	37	chr12	57573867	57573867	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	atggtgacaacatcagcatgGccaacatggatggcagcaat	11	9	1	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr12:57573867G>A	ENST00000243077.3	+	31	5645	c.5179G>A	c.(5179-5181)Gcc>Acc	p.A1727T		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1727					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CATCAGCATGGCCAACATGGA	0.622																																					p.A1727T		Atlas-SNP	.											.	LRP1	428	.	0			c.G5179A						.						173	170	171					12																	57573867		2203	4300	6503	SO:0001583	missense	4035	exon31			AGCATGGCCAACA	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.5179G>A	chr12.hg19:g.57573867G>A	ENSP00000243077:p.Ala1727Thr	40.0	0.0		62.0	10.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411556	0.83340	.	.	ENSG00000123384	ENST00000243077	D	0.91464	-2.85	4.87	4.87	0.63330	Six-bladed beta-propeller, TolB-like (1);	0.075813	0.50627	D	0.000104	D	0.95217	0.8449	M	0.88031	2.925	0.80722	D	1	D	0.61080	0.989	P	0.58331	0.837	D	0.96053	0.9033	10	0.87932	D	0	.	16.9423	0.86221	0.0:0.0:1.0:0.0	.	1727	Q07954	LRP1_HUMAN	T	1727	ENSP00000243077:A1727T	ENSP00000243077:A1727T	A	+	1	0	LRP1	55860134	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.780000	0.85658	2.518000	0.84900	0.655000	0.94253	GCC	.	.		0.622	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57573867	G	A	57573867	3	1	148	1	0	0	0	0	1	0	0	0	8960	1203	42	3	5301	3	LRP1	12	57573867	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	13736185	57573867	76278028	75	22619										
UNG	7374	hgsc.bcm.edu	37	chr12	109535499	109535499	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tccaggatgatcggccagaaGacgctctactcctttttctc	8	13	2	3			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr12:109535499G>A	ENST00000242576.2	+	1	121	c.15G>A	c.(13-15)aaG>aaA	p.K5K	UNG_ENST00000336865.2_5'Flank	NM_080911.2	NP_550433.1			uracil-DNA glycosylase											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						TCGGCCAGAAGACGCTCTACT	0.706								Base excision repair (BER), DNA glycosylases	Immune Deficiency with Hyper-IgM																												p.K5K		Atlas-SNP	.											.	UNG	30	.	0			c.G15A						.						14	14	14					12																	109535499		2199	4288	6487	SO:0001819	synonymous_variant	7374	exon1	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	CCAGAAGACGCTC	A64377	CCDS9124.1, CCDS9125.1	12q23-q24.1	2014-09-17			ENSG00000076248	ENSG00000076248	3.2.2.27		12572	protein-coding gene	gene with protein product	"uracil-DNA glycosylase 1, uracil-DNA glycosylase 2"	191525		DGU		1923798, 17101234	Standard	NM_080911		Approved	UDG, UNG1, UNG2, HIGM4	uc001tnz.2	P13051	OTTHUMG00000169247	ENST00000242576.2:c.15G>A	chr12.hg19:g.109535499G>A		162.0	0.0		223.0	46.0	NM_080911		Silent	SNP	ENST00000242576.2	hg19	CCDS9124.1																																																																																			.	.		0.706	UNG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403067.1	NM_080911		A	109535499	G	A	109535499	2	1	148	1	0	0	0	0	0	0	0	1	17014	933	33	3		3	UNG	12	109535499	Silent	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	51961632	109535499	24316396	76	22620										
OAS2	4939	hgsc.bcm.edu	37	chr12	113444239	113444239	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tcagctgagttctggctccaCacccagccccgaggtttatg	10	14	2	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr12:113444239C>A	ENST00000342315.4	+	8	1704	c.1490C>A	c.(1489-1491)aCa>aAa	p.T497K	OAS2_ENST00000392583.2_Missense_Mutation_p.T497K|RP1-71H24.1_ENST00000552784.1_RNA	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	497	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						TCTGGCTCCACACCCAGCCCC	0.468																																					p.T497K	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.C1490A						.						66	65	65					12																	113444239		2203	4300	6503	SO:0001583	missense	4939	exon8			GCTCCACACCCAG	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"2'-5'-oligoadenylate synthetase 2 (69-71 kD)"			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.1490C>A	chr12.hg19:g.113444239C>A	ENSP00000342278:p.Thr497Lys	49.0	0.0		64.0	12.0	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	hg19	CCDS31906.1	.	.	.	.	.	.	.	.	.	.	.	0.059	-1.228514	0.01518	.	.	ENSG00000111335	ENST00000342315;ENST00000392583	T;T	0.07114	3.22;3.22	4.51	-1.23	0.09465	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	1.183370	0.06544	U	0.743700	T	0.03434	0.0099	N	0.01446	-0.86	0.09310	N	1	P;B	0.47484	0.896;0.052	P;B	0.51550	0.673;0.022	T	0.22906	-1.0203	10	0.02654	T	1	-18.8292	2.2114	0.03949	0.3389:0.2753:0.2888:0.097	.	497;497	P29728;P29728-2	OAS2_HUMAN;.	K	497	ENSP00000342278:T497K;ENSP00000376362:T497K	ENSP00000342278:T497K	T	+	2	0	OAS2	111928622	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	-1.061000	0.03472	0.094000	0.17404	-0.140000	0.14226	ACA	.	.		0.468	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1			A	113444239	C	A	113444239	3	1	148	1	0	0	0	0	1	0	0	0	10809	478	17	3	1591	3	OAS2	12	113444239	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	3908740	113444239	20407656	77	22621										
DACH1	1602	hgsc.bcm.edu	37	chr13	72049304	72049304	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ctttcagcatctgttctgccGccactgcggtcagcctctat	8	15	5	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr13:72049304G>A	ENST00000359684.2	-	11	2213	c.2214C>T	c.(2212-2214)ggC>ggT	p.G738G	DACH1_ENST00000354591.4_Silent_p.G484G|DACH1_ENST00000305425.4_Silent_p.G686G|DACH1_ENST00000313174.7_Silent_p.G538G			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	738					cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		CTGTTCTGCCGCCACTGCGGT	0.408																																					p.G686G		Atlas-SNP	.											DACH1,right_upper_lobe,carcinoma,0,1	DACH1	123	.	0			c.C2058T						.						82	83	83					13																	72049304		1863	4107	5970	SO:0001819	synonymous_variant	1602	exon10			TCTGCCGCCACTG	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.2214C>T	chr13.hg19:g.72049304G>A		68.0	0.0		60.0	9.0	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Silent	SNP	ENST00000359684.2	hg19																																																																																				.	.		0.408	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		A	72049304	G	A	72049304	2	1	148	1	0	0	0	0	0	0	0	1	4222	1074	38	1		1	DACH1	13	72049304	Silent	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10		72049304	43120574	78	22622										
LMO7	4008	hgsc.bcm.edu	37	chr13	76397962	76397962	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gtcttgatttaatgtctgaaTctggagaaggggaaatctcc	11	6	4	3	rs200869696		TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr13:76397962T>G	ENST00000321797.8	+	13	2924	c.2203T>G	c.(2203-2205)Tct>Gct	p.S735A	LMO7_ENST00000357063.3_Missense_Mutation_p.S1020A|LMO7_ENST00000526202.1_Missense_Mutation_p.S585A|LMO7_ENST00000377534.3_Missense_Mutation_p.S1020A|LMO7_ENST00000341547.4_Missense_Mutation_p.S686A|LMO7_ENST00000465261.2_Missense_Mutation_p.S735A			Q8WWI1	LMO7_HUMAN	LIM domain 7	1020					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AATGTCTGAATCTGGAGAAGG	0.453																																					p.S735A		Atlas-SNP	.											.	LMO7	334	.	0			c.T2203G						.						73	66	69					13																	76397962		2203	4300	6503	SO:0001583	missense	4008	exon12			TCTGAATCTGGAG	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"F-box only protein 20"	604362	"LIM domain only 7"	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.2203T>G	chr13.hg19:g.76397962T>G	ENSP00000317802:p.Ser735Ala	148.0	0.0		83.0	21.0	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	12.90|12.90|12.90	2.075814|2.075814|2.075814	0.36662|0.36662|0.36662	.|.|.	.|.|.	ENSG00000136153|ENSG00000136153|ENSG00000136153	ENST00000447038|ENST00000524651|ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261	.|.|T;T;T;T;T;T;T	.|.|0.42900	.|.|1.56;1.55;1.55;0.97;0.98;0.96;0.97	5.98|5.98|5.98	3.66|3.66|3.66	0.41972|0.41972|0.41972	.|.|PDZ/DHR/GLGF (1);	.|.|0.866859	.|.|0.10480	.|.|N	.|.|0.669664	T|T|T	0.33585|0.33585|0.33585	0.0868|0.0868|0.0868	L|L|L	0.43923|0.43923|0.43923	1.385|1.385|1.385	0.09310|0.09310|0.09310	N|N|N	0.999998|0.999998|0.999998	.|.|B;B;B;B;B	.|.|0.29988	.|.|0.104;0.264;0.039;0.104;0.058	.|.|B;B;B;B;B	.|.|0.28011	.|.|0.039;0.085;0.016;0.079;0.075	T|T|T	0.22591|0.22591|0.22591	-1.0212|-1.0212|-1.0212	5|5|10	.|.|0.33141	.|.|T	.|.|0.24	4.066|4.066|4.066	7.2531|7.2531|7.2531	0.26160|0.26160|0.26160	0.0:0.1867:0.0:0.8133|0.0:0.1867:0.0:0.8133|0.0:0.1867:0.0:0.8133	.|.|.	.|.|585;686;1020;735;968	.|.|E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5	.|.|.;.;LMO7_HUMAN;.;.	S|K|A	643|39|686;1020;1020;634;735;585;735	.|.|ENSP00000342112:S686A;ENSP00000349571:S1020A;ENSP00000366757:S1020A;ENSP00000366719:S634A;ENSP00000317802:S735A;ENSP00000431129:S585A;ENSP00000433352:S735A	.|.|ENSP00000317802:S735A	I|N|S	+|+|+	2|3|1	0|2|0	LMO7|LMO7|LMO7	75295963|75295963|75295963	0.842000|0.842000|0.842000	0.29525|0.29525|0.29525	0.125000|0.125000|0.125000	0.21846|0.21846|0.21846	0.617000|0.617000|0.617000	0.37484|0.37484|0.37484	1.232000|1.232000|1.232000	0.32636|0.32636|0.32636	0.548000|0.548000|0.548000	0.28955|0.28955|0.28955	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	ATC|AAT|TCT	.	T|0.999;C|0.001		0.453	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		G	76397962	T	G	76397962	3	3	148	1	0	0	0	0	1	0	0	0	8864	1435	50	5	3120	5	LMO7	13	76397962	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	4348658	76397962	38771916	79	22623										
SOX21	11166	hgsc.bcm.edu	37	chr13	95363656	95363656	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gtgtgccccccggcggcggcGgccgccgctgcagccgccgc	17	20	0	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr13:95363656G>A	ENST00000376945.2	-	1	733	c.648C>T	c.(646-648)gcC>gcT	p.A216A	SOX21-AS1_ENST00000438290.2_lincRNA	NM_007084.2	NP_009015.1	Q9Y651	SOX21_HUMAN	SRY (sex determining region Y)-box 21	216					hair follicle development (GO:0001942)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6	all_neural(89;0.0646)|Medulloblastoma(90;0.163)					CGGCGGCGGCGgccgccgctg	0.796																																					p.A216A		Atlas-SNP	.											SOX21,NS,carcinoma,0,1	SOX21	21	.	0			c.C648T						.						1	1	1					13																	95363656		283	817	1100	SO:0001819	synonymous_variant	11166	exon1			GGCGGCGGCCGCC	AF107044	CCDS9473.1	13q31-q32	2008-07-18			ENSG00000125285	ENSG00000125285		"SRY (sex determining region Y)-boxes"	11197	protein-coding gene	gene with protein product	"SRY-box 21"	604974				10441749	Standard	NM_007084		Approved	SOX25	uc001vma.3	Q9Y651	OTTHUMG00000017209	ENST00000376945.2:c.648C>T	chr13.hg19:g.95363656G>A		8.0	0.0		20.0	2.0	NM_007084	P35715|Q15504|Q5TBS1	Silent	SNP	ENST00000376945.2	hg19	CCDS9473.1																																																																																			.	.		0.796	SOX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045467.4	NM_007084		A	95363656	G	A	95363656	2	1	148	1	0	0	0	0	0	0	0	1	14965	1103	39	1		1	SOX21	13	95363656	Silent	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	18965694	95363656	19806222	80	22624										
DNAJC3	5611	hgsc.bcm.edu	37	chr13	96409903	96409903	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttattttccttatagctcaaAtctaatccaagtgaaaatga	4	7	2	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr13:96409903A>G	ENST00000602402.1	+	5	516	c.399A>G	c.(397-399)aaA>aaG	p.K133K	DNAJC3_ENST00000376795.6_Intron	NM_006260.4	NP_006251.1	Q13217	DNJC3_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 3	133					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of protein kinase activity (GO:0006469)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum Sec complex (GO:0031205)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|vesicle (GO:0031982)	protein kinase inhibitor activity (GO:0004860)			NS(1)|breast(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.126)			TATAGCTCAAATCTAATCCAA	0.323																																					p.K133K		Atlas-SNP	.											.	DNAJC3	38	.	0			c.A399G						.						50	51	51					13																	96409903		2203	4300	6503	SO:0001819	synonymous_variant	5611	exon5			GCTCAAATCTAAT	U28424	CCDS9479.1	13q32	2013-01-10			ENSG00000102580	ENSG00000102580		"Heat shock proteins / DNAJ (HSP40)", "Tetratricopeptide (TTC) repeat domain containing"	9439	protein-coding gene	gene with protein product		601184		PRKRI		7511204, 8824806	Standard	NM_006260		Approved	P58, P58IPK, HP58	uc001vmq.3	Q13217	OTTHUMG00000017227	ENST00000602402.1:c.399A>G	chr13.hg19:g.96409903A>G		47.0	0.0		36.0	8.0	NM_006260	Q86WT9|Q8N4N2	Silent	SNP	ENST00000602402.1	hg19	CCDS9479.1																																																																																			.	.		0.323	DNAJC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045504.3			G	96409903	A	G	96409903	2	3	148	1	0	0	0	0	0	0	0	1	4649	98	4	2		2	DNAJC3	13	96409903	Silent	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10	1046247	96409903	18759975	81	22625										
IL25	64806	hgsc.bcm.edu	37	chr14	23842468	23842468	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cccagcaaagggcaggacacCtctgaggagctgctgaggtg	15	11	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr14:23842468C>T	ENST00000329715.2	+	1	399	c.141C>T	c.(139-141)acC>acT	p.T47T	IL25_ENST00000397242.2_Silent_p.T31T	NM_022789.3	NP_073626.1	Q9H293	IL25_HUMAN	interleukin 25	47					eosinophil differentiation (GO:0030222)|inflammatory response to antigenic stimulus (GO:0002437)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to fungus (GO:0009620)|response to nematode (GO:0009624)	extracellular space (GO:0005615)	interleukin-17E receptor binding (GO:0030380)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9	all_cancers(95;2e-05)			GBM - Glioblastoma multiforme(265;0.00665)|READ - Rectum adenocarcinoma(4;0.0276)|Colorectal(4;0.0396)		GGCAGGACACCTCTGAGGAGC	0.602																																					p.T47T		Atlas-SNP	.											.	IL25	21	.	0			c.C141T						.						85	73	77					14																	23842468		2203	4300	6503	SO:0001819	synonymous_variant	64806	exon1			GGACACCTCTGAG	AF305200	CCDS9597.1, CCDS45086.1	14q11.2	2008-01-07	2006-05-17	2006-05-17	ENSG00000166090	ENSG00000166090		"Interleukins and interleukin receptors"	13765	protein-coding gene	gene with protein product		605658	"interleukin 17E"	IL17E		11058597, 11754819	Standard	NM_172314		Approved	IL-25, IL-17E	uc001wjq.3	Q9H293	OTTHUMG00000028749	ENST00000329715.2:c.141C>T	chr14.hg19:g.23842468C>T		39.0	0.0		39.0	11.0	NM_022789	Q2M3F0|Q8IZV3|Q8WXB0	Silent	SNP	ENST00000329715.2	hg19	CCDS9597.1																																																																																			.	.		0.602	IL25-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071789.2			T	23842468	C	T	23842468	2	4	148	1	0	0	0	0	0	0	0	1	7687	668	24	3		3	IL25	14	23842468	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10		23842468	83507072	82	22626										
CPNE6	9362	hgsc.bcm.edu	37	chr14	24545726	24545726	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ccctcacaggtgtcccatgaCtttgctatcaactttgaccc	6	15	2	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr14:24545726C>G	ENST00000397016.2	+	14	1436	c.1125C>G	c.(1123-1125)gaC>gaG	p.D375E	CPNE6_ENST00000537691.1_Missense_Mutation_p.D430E|CPNE6_ENST00000216775.2_Missense_Mutation_p.D375E	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	375	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		TGTCCCATGACTTTGCTATCA	0.567																																					p.D375E		Atlas-SNP	.											.	CPNE6	40	.	0			c.C1125G						.						108	111	110					14																	24545726		2203	4300	6503	SO:0001583	missense	9362	exon13			CCATGACTTTGCT	AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.1125C>G	chr14.hg19:g.24545726C>G	ENSP00000380211:p.Asp375Glu	47.0	0.0		51.0	13.0	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Missense_Mutation	SNP	ENST00000397016.2	hg19	CCDS9607.1	.	.	.	.	.	.	.	.	.	.	C	5.033	0.191840	0.09547	.	.	ENSG00000100884	ENST00000537691;ENST00000397016;ENST00000216775	T;T;T	0.26223	1.75;1.75;1.75	4.82	1.94	0.25998	von Willebrand factor, type A (2);Copine (1);	0.221420	0.31834	N	0.006991	T	0.15219	0.0367	N	0.16016	0.355	0.34117	D	0.663636	P;B	0.45126	0.851;0.094	P;B	0.49829	0.623;0.085	T	0.21621	-1.0240	10	0.02654	T	1	-27.8941	6.9845	0.24721	0.0:0.7031:0.0:0.2969	.	430;375	F5GXN1;O95741	.;CPNE6_HUMAN	E	430;375;375	ENSP00000440077:D430E;ENSP00000380211:D375E;ENSP00000216775:D375E	ENSP00000216775:D375E	D	+	3	2	CPNE6	23615566	0.047000	0.20315	1.000000	0.80357	0.646000	0.38490	-0.600000	0.05693	0.635000	0.30488	-0.251000	0.11542	GAC	.	.		0.567	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5			G	24545726	C	G	24545726	3	3	148	1	0	0	0	0	1	0	0	0	3818	564	20	4	1171	4	CPNE6	14	24545726	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	703258	24545726	82803814	83	22627										
HEATR5A	25938	hgsc.bcm.edu	37	chr14	31819906	31819906	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gctttatactgtccaaaagcTgttccaatataagaagccta	6	9	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr14:31819906T>C	ENST00000389961.3	-	16	2410	c.2411A>G	c.(2410-2412)cAg>cGg	p.Q804R	HEATR5A_ENST00000404677.3_Missense_Mutation_p.Q810R|HEATR5A_ENST00000543095.2_Missense_Mutation_p.Q810R|HEATR5A_ENST00000439348.1_Missense_Mutation_p.Q804R|HEATR5A_ENST00000439727.1_Missense_Mutation_p.Q517R			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	804										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		GTCCAAAAGCTGTTCCAATAT	0.328																																					p.Q810R		Atlas-SNP	.											.	HEATR5A	181	.	0			c.A2429G						.						59	57	58					14																	31819906		1821	4071	5892	SO:0001583	missense	25938	exon17			AAAAGCTGTTCCA	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 125"	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.2411A>G	chr14.hg19:g.31819906T>C	ENSP00000374611:p.Gln804Arg	45.0	0.0		28.0	8.0	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.51|19.51	3.840919|3.840919	0.71488|0.71488	.|.	.|.	ENSG00000129493|ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095;ENST00000404677|ENST00000538864	T;T;T;T;T|.	0.05319|.	3.46;3.46;3.46;3.46;3.46|.	5.61|5.61	4.41|4.41	0.53225|0.53225	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.060604|.	0.64402|.	D|.	0.000002|.	T|T	0.64405|0.64405	0.2595|0.2595	M|M	0.63428|0.63428	1.95|1.95	0.49213|0.49213	D|D	0.99976|0.99976	P;P;B|.	0.49253|.	0.921;0.696;0.409|.	P;B;B|.	0.52710|.	0.707;0.433;0.438|.	T|T	0.63808|0.63808	-0.6553|-0.6553	10|5	0.72032|.	D|.	0.01|.	.|.	11.316|11.316	0.49392|0.49392	0.1357:0.0:0.0:0.8643|0.1357:0.0:0.0:0.8643	.|.	810;804;804|.	B5MC49;Q86XA9-2;Q86XA9|.	.;.;HTR5A_HUMAN|.	R|G	804;804;517;810;810|438	ENSP00000374611:Q804R;ENSP00000405407:Q804R;ENSP00000408681:Q517R;ENSP00000437968:Q810R;ENSP00000384646:Q810R|.	ENSP00000374611:Q804R|.	Q|S	-|-	2|1	0|0	HEATR5A|HEATR5A	30889657|30889657	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	5.774000|5.774000	0.68906|0.68906	2.137000|2.137000	0.66172|0.66172	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.328	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		C	31819906	T	C	31819906	3	2	148	1	0	0	0	0	1	0	0	0	7040	1580	55	2	3791	2	HEATR5A	14	31819906	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	7274180	31819906	75529634	84	22628										
PLEKHG3	26030	hgsc.bcm.edu	37	chr14	65208636	65208637	+	Missense_Mutation	DNP	CC	CC	GT													0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aggcagtcaaaggggacccaCctcccatctcagatgctgag							TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr14:65208636_65208637CC>GT	ENST00000394691.1	+	16	2548_2549	c.2401_2402CC>GT	c.(2401-2403)CCt>GTt	p.P801V	PLEKHG3_ENST00000484731.2_Missense_Mutation_p.P306V|PLEKHG3_ENST00000247226.7_Missense_Mutation_p.P745V|PLEKHG3_ENST00000471182.2_Missense_Mutation_p.P334V|PLEKHG3_ENST00000492928.1_Intron			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	801							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		AGGGGACCCACCTCCCATCTCA	0.614																																					p.P745A|p.P745L		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.C2233G|c.C2234T						.																																			SO:0001583	missense	26030	exon14			GACCCACCTCCCA|ACCCACCTCCCAT	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20364	protein-coding gene	gene with protein product			"KIAA0599"	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	Exception_encountered	chr14.hg19:g.65208636_65208637delinsGT	ENSP00000378183:p.Pro801Val	59.0	0.0		46.0	9.0	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Missense_Mutation	SNP	ENST00000394691.1	hg19																																																																																				.	.		0.614	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549		GT	65208637	CC	GT	65208636	3	3	148	1	0	0	0	0	1	0	0	0	12079	507	18	4	2283	4	PLEKHG3	14	65208636	Missense_Mutation	DNP	CC	TCGA-DD-A73G-01A-22D-A32G-10	33388730	65208636	42140904	85	22629										
PAPOLA	10914	hgsc.bcm.edu	37	chr14	96986492	96986492	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cccccaaggagactgactgcGtacttacacagaaactaatt	7	12	0	3			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr14:96986492G>A	ENST00000216277.8	+	2	329	c.109G>A	c.(109-111)Gta>Ata	p.V37I	PAPOLA_ENST00000554130.1_3'UTR|PAPOLA_ENST00000392990.2_Missense_Mutation_p.V37I|PAPOLA_ENST00000557320.1_Missense_Mutation_p.V37I|PAPOLA_ENST00000557471.1_Missense_Mutation_p.V37I	NM_032632.4	NP_116021.2	P51003	PAPOA_HUMAN	poly(A) polymerase alpha	37					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|RNA polyadenylation (GO:0043631)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		GACTGACTGCGTACTTACACA	0.423																																					p.V37I	NSCLC(19;254 734 11908 35501 39234)	Atlas-SNP	.											.	PAPOLA	58	.	0			c.G109A						.						119	105	110					14																	96986492		2203	4300	6503	SO:0001583	missense	10914	exon2			GACTGCGTACTTA	X76770	CCDS9946.1, CCDS58334.1, CCDS58335.1	14q32.1-q32.2	2008-02-08				ENSG00000090060	2.7.7.19		14981	protein-coding gene	gene with protein product		605553				8302877, 10429366	Standard	NM_032632		Approved	PAP	uc001yfq.3	P51003		ENST00000216277.8:c.109G>A	chr14.hg19:g.96986492G>A	ENSP00000216277:p.Val37Ile	60.0	0.0		34.0	10.0	NM_001252006	Q86SX4|Q86TV0|Q8IYF5|Q9BVU2	Missense_Mutation	SNP	ENST00000216277.8	hg19	CCDS9946.1	.	.	.	.	.	.	.	.	.	.	G	1.512	-0.549241	0.04024	.	.	ENSG00000090060	ENST00000216277;ENST00000557320;ENST00000546064;ENST00000557471;ENST00000556619;ENST00000392990	.	.	.	4.94	-1.68	0.08212	Poly(A) polymerase, central domain (1);	1.325060	0.05095	N	0.486031	T	0.18467	0.0443	N	0.05441	-0.05	0.09310	N	1	B;B;B;B;B	0.11235	0.001;0.001;0.004;0.001;0.001	B;B;B;B;B	0.10450	0.001;0.002;0.005;0.001;0.005	T	0.21008	-1.0258	9	0.31617	T	0.26	.	6.2973	0.21093	0.4795:0.2948:0.2257:0.0	.	53;53;37;37;53	F5H5I8;B4DYF4;P51003;P51003-2;B4DHB8	.;.;PAPOA_HUMAN;.;.	I	37;37;53;37;37;37	.	ENSP00000216277:V37I	V	+	1	0	PAPOLA	96056245	0.004000	0.15560	0.045000	0.18777	0.805000	0.45488	-0.082000	0.11304	-0.476000	0.06842	-0.247000	0.11927	GTA	.	.		0.423	PAPOLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413411.2			A	96986492	G	A	96986492	3	1	148	1	0	0	0	0	1	0	0	0	11438	1145	40	1	115	1	PAPOLA	14	96986492	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	31777856	96986492	10363048	86	22630										
WDR20	91833	hgsc.bcm.edu	37	chr14	102676045	102676045	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	taaaactctgggaacgccccTgtgtcctcgaatggaagatg	11	10	1	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr14:102676045T>C	ENST00000342702.3	+	3	1569	c.1538T>C	c.(1537-1539)cTg>cCg	p.L513P	WDR20_ENST00000424963.2_Missense_Mutation_p.L389P|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000499851.2_Missense_Mutation_p.L256P|WDR20_ENST00000335263.5_Missense_Mutation_p.L513P|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000545563.1_Missense_Mutation_p.L340P|WDR20_ENST00000556807.1_Missense_Mutation_p.L452P|WDR20_ENST00000556511.2_Missense_Mutation_p.L452P|WDR20_ENST00000454394.2_Missense_Mutation_p.L544P	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	513										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						GGAACGCCCCTGTGTCCTCGA	0.423											OREG0022939	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L544P		Atlas-SNP	.											.	WDR20	35	.	0			c.T1631C						.						96	92	94					14																	102676045		2203	4300	6503	SO:0001583	missense	91833	exon4			CGCCCCTGTGTCC	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.1538T>C	chr14.hg19:g.102676045T>C	ENSP00000341037:p.Leu513Pro	111.0	0.0	1368	72.0	16.0	NM_001242417	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Missense_Mutation	SNP	ENST00000342702.3	hg19	CCDS9969.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.720593	0.48728	.	.	ENSG00000140153	ENST00000335263;ENST00000299135;ENST00000424963;ENST00000342702;ENST00000556807;ENST00000499851;ENST00000454394;ENST00000401892;ENST00000545563	D;D;D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62;-1.62;-1.62	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.85031	0.5604	L	0.31926	0.97	0.80722	D	1	P;P;D;D;D;D;P	0.55800	0.955;0.943;0.958;0.966;0.973;0.966;0.904	P;P;P;P;P;P;P	0.58873	0.786;0.548;0.804;0.648;0.847;0.543;0.707	D	0.85688	0.1305	10	0.49607	T	0.09	.	16.2159	0.82217	0.0:0.0:0.0:1.0	.	544;525;452;513;452;389;513	E7EUY8;Q5JPH5;G3V2F8;Q8TBZ3-2;F8W9S4;B3KR43;Q8TBZ3	.;.;.;.;.;.;WDR20_HUMAN	P	513;452;389;513;452;256;544;443;340	ENSP00000335434:L513P;ENSP00000395793:L389P;ENSP00000341037:L513P;ENSP00000450636:L452P;ENSP00000443641:L256P;ENSP00000406084:L544P;ENSP00000437927:L340P	ENSP00000299135:L452P	L	+	2	0	WDR20	101745798	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.691000	0.84191	2.243000	0.73865	0.533000	0.62120	CTG	.	.		0.423	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		C	102676045	T	C	102676045	3	2	148	1	0	0	0	0	1	0	0	0	17295	1580	55	2	1565	2	WDR20	14	102676045	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	5689553	102676045	4673495	87	22631										
CHAC1	79094	hgsc.bcm.edu	37	chr15	41247820	41247820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tggcctgccggggcttctccGgccacaaccttgaatacttg	11	14	1	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr15:41247820G>A	ENST00000446533.3	+	3	952	c.643G>A	c.(643-645)Ggc>Agc	p.G215S	CHAC1_ENST00000444189.2_Missense_Mutation_p.G170S|CHAC1_ENST00000487220.1_5'UTR	NM_001142776.1|NM_024111.3	NP_001136248.1|NP_077016.2	Q9BUX1	CHAC1_HUMAN	ChaC, cation transport regulator homolog 1 (E. coli)	215					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein processing (GO:0010955)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|trans-Golgi network (GO:0005802)	Notch binding (GO:0005112)			endometrium(1)|large_intestine(1)|skin(1)	3		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.66e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.163)		GGGCTTCTCCGGCCACAACCT	0.642																																					p.G215S		Atlas-SNP	.											.	CHAC1	25	.	0			c.G643A						.						72	74	73					15																	41247820		2203	4300	6503	SO:0001583	missense	79094	exon3			TTCTCCGGCCACA	BC019625	CCDS10070.2, CCDS45233.1	15q15.1	2013-09-12	2006-09-12		ENSG00000128965	ENSG00000128965			28680	protein-coding gene	gene with protein product	"gamma-GCT acting on glutathione homolog 1"	614587	"ChaC, cation transport regulator-like 1 (E. coli)"			23070364	Standard	NM_024111		Approved	MGC4504	uc001znh.2	Q9BUX1	OTTHUMG00000130208	ENST00000446533.3:c.643G>A	chr15.hg19:g.41247820G>A	ENSP00000398105:p.Gly215Ser	26.0	0.0		32.0	16.0	NM_024111	Q0VIA0	Missense_Mutation	SNP	ENST00000446533.3	hg19	CCDS10070.2	.	.	.	.	.	.	.	.	.	.	G	23.6	4.430288	0.83776	.	.	ENSG00000128965	ENST00000446533;ENST00000444189	T	0.77877	-1.13	5.66	5.66	0.87406	Butirosin biosynthesis, BtrG-like (1);	0.000000	0.85682	D	0.000000	D	0.93180	0.7828	H	0.97874	4.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95175	0.8294	10	0.72032	D	0.01	-26.755	19.7464	0.96253	0.0:0.0:1.0:0.0	.	170;215	Q9BUX1-2;Q9BUX1	.;CHAC1_HUMAN	S	215;170	ENSP00000398105:G215S	ENSP00000395466:G170S	G	+	1	0	CHAC1	39035112	1.000000	0.71417	0.971000	0.41717	0.109000	0.19521	9.781000	0.99029	2.660000	0.90430	0.462000	0.41574	GGC	.	.		0.642	CHAC1-001	KNOWN	downstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252526.3	NM_024111		A	41247820	G	A	41247820	3	1	148	1	0	0	0	0	1	0	0	0	3310	1116	39	1	653	1	CHAC1	15	41247820	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10		41247820	61283572	88	22632										
DUOX2	50506	hgsc.bcm.edu	37	chr15	45400255	45400257	+	In_Frame_Del	DEL	TGT	TGT	-													0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	caagccttacccattcctggTgttctcaaaccagtagcggt							TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr15:45400255_45400257delTGT	ENST00000603300.1	-	13	1764_1766	c.1562_1564delACA	c.(1561-1566)aacacc>acc	p.N521del	DUOX2_ENST00000389039.6_In_Frame_Del_p.N521del	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	521	Peroxidase-like; mediates peroxidase activity. {ECO:0000250}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CCATTCCTGGTGTTCTCAAACCA	0.611																																					p.521_522del		Atlas-Indel,Pindel	.											.	DUOX2	137	.	0			c.1563_1565del						.																																			SO:0001651	inframe_deletion	50506	exon13			.	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"EF-hand domain containing"	13273	protein-coding gene	gene with protein product	"dual oxidase-like domains 2", "nicotinamide adenine dinucleotide phosphate oxidase", "flavoprotein NADPH oxidase", "NADPH thyroid oxidase 2", "NADH/NADPH thyroid oxidase p138-tox", "NADPH oxidase/peroxidase DUOX2"	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.1562_1564delACA	chr15.hg19:g.45400255_45400257delTGT	ENSP00000475084:p.Asn521del	54.0	0.0		66.0	22.0	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	In_Frame_Del	DEL	ENST00000603300.1	hg19	CCDS10117.1																																																																																			.	.		0.611	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		-	45400257	TGT	-	45400255	7	5	148	1	0	1	0	1	0	0	0	0	4803	1696	59	0	3170	0	DUOX2	15	45400255	In_Frame_Del	DEL	TGT	TCGA-DD-A73G-01A-22D-A32G-10	4152435	45400255	57131137	89	22633										
TRPM7	54822	hgsc.bcm.edu	37	chr15	50884667	50884667	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttatgaactttgctagcttcCgacgctttctgggcagtgag	11	9	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr15:50884667C>T	ENST00000313478.7	-	26	4046	c.3765G>A	c.(3763-3765)tcG>tcA	p.S1255S	TRPM7_ENST00000560955.1_Silent_p.S1255S	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1255					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		TGCTAGCTTCCGACGCTTTCT	0.393																																					p.S1255S		Atlas-SNP	.											.	TRPM7	145	.	0			c.G3765A						.						228	205	212					15																	50884667		1885	4117	6002	SO:0001819	synonymous_variant	54822	exon26			AGCTTCCGACGCT	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.3765G>A	chr15.hg19:g.50884667C>T		96.0	0.0		102.0	22.0	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Silent	SNP	ENST00000313478.7	hg19	CCDS42035.1																																																																																			.	.		0.393	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		T	50884667	C	T	50884667	2	4	148	1	0	0	0	0	0	0	0	1	16606	639	23	1		1	TRPM7	15	50884667	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	5484412	50884667	51646725	90	22634										
AP3B2	8120	hgsc.bcm.edu	37	chr15	83328618	83328618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tgtactcatcagatgtcccaCaaggaacacgacccaggttg	9	12	2	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr15:83328618C>T	ENST00000261722.3	-	25	3284	c.3077G>A	c.(3076-3078)tGt>tAt	p.C1026Y	AP3B2_ENST00000535348.1_Missense_Mutation_p.C994Y|AP3B2_ENST00000535359.1_Missense_Mutation_p.C1045Y|RP11-752G15.3_ENST00000560650.1_RNA	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	1026					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			AGATGTCCCACAAGGAACACG	0.547																																					p.C1026Y		Atlas-SNP	.											.	AP3B2	103	.	0			c.G3077A						.						104	96	99					15																	83328618		2055	4196	6251	SO:0001583	missense	8120	exon25			GTCCCACAAGGAA	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.3077G>A	chr15.hg19:g.83328618C>T	ENSP00000261722:p.Cys1026Tyr	74.0	0.0		77.0	18.0	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Missense_Mutation	SNP	ENST00000261722.3	hg19	CCDS45331.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.685673	0.68157	.	.	ENSG00000103723	ENST00000261722;ENST00000535348;ENST00000535359	T;T;T	0.55413	0.52;0.52;0.53	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.70570	0.3239	M	0.65975	2.015	0.80722	D	1	D;P;P	0.71674	0.998;0.91;0.91	D;B;B	0.72982	0.979;0.332;0.332	T	0.69569	-0.5110	10	0.36615	T	0.2	-8.7608	18.2494	0.89997	0.0:1.0:0.0:0.0	.	994;1045;1026	B7ZKR7;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	Y	1026;994;1045	ENSP00000261722:C1026Y;ENSP00000438721:C994Y;ENSP00000440984:C1045Y	ENSP00000261722:C1026Y	C	-	2	0	AP3B2	81125673	1.000000	0.71417	0.809000	0.32408	0.876000	0.50452	5.828000	0.69307	2.320000	0.78422	0.462000	0.41574	TGT	.	.		0.547	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			T	83328618	C	T	83328618	3	4	148	1	0	0	0	0	1	0	0	0	745	478	17	3	179	3	AP3B2	15	83328618	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	32443951	83328618	19202774	91	22635										
UNC45A	55898	hgsc.bcm.edu	37	chr15	91478859	91478859	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cgccctggcggcctacactcAggccctgggtctggacgcga	14	16	2	0	rs34963697		TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr15:91478859A>C	ENST00000418476.2	+	2	177	c.137A>C	c.(136-138)cAg>cCg	p.Q46P	UNC45A_ENST00000553671.2_3'UTR|AC068831.3_ENST00000448987.1_RNA|UNC45A_ENST00000394275.2_Missense_Mutation_p.Q31P|AC068831.3_ENST00000438890.1_RNA	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	46					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GCCTACACTCAGGCCCTGGGT	0.667																																					p.Q46P		Atlas-SNP	.											.	UNC45A	57	.	0			c.A137C						.						38	48	44					15																	91478859		2194	4297	6491	SO:0001583	missense	55898	exon2			ACACTCAGGCCCT		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"smooth muscle cell associated protein-1"	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.137A>C	chr15.hg19:g.91478859A>C	ENSP00000407487:p.Gln46Pro	76.0	0.0		69.0	12.0	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	hg19	CCDS10367.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.944662	0.53079	.	.	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.62105	0.05;0.05	5.17	1.19	0.21007	Elongated TPR repeat-containing domain (1);Tetratricopeptide repeat-containing (1);	1.081060	0.06936	N	0.811985	T	0.68100	0.2964	M	0.81614	2.55	0.31266	N	0.692296	P;P;B;B	0.45428	0.685;0.858;0.177;0.177	B;P;B;B	0.48982	0.407;0.597;0.239;0.161	T	0.65524	-0.6147	10	0.59425	D	0.04	-16.0786	3.5096	0.07703	0.539:0.0:0.2132:0.2478	rs34963697	46;31;46;31	B4DZL0;B4DLE6;Q9H3U1;A8K6F7	.;.;UN45A_HUMAN;.	P	31;46	ENSP00000377816:Q31P;ENSP00000407487:Q46P	ENSP00000377816:Q31P	Q	+	2	0	UNC45A	89279863	0.846000	0.29590	0.975000	0.42487	0.774000	0.43823	1.300000	0.33436	0.826000	0.34661	0.454000	0.30748	CAG	.	A|0.982;C|0.018		0.667	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671		C	91478859	A	C	91478859	3	2	148	1	0	0	0	0	1	0	0	0	17003	188	7	5	143	5	UNC45A	15	91478859	Missense_Mutation	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10	8150241	91478859	11052533	92	22636										
ST8SIA2	8128	hgsc.bcm.edu	37	chr15	92981799	92981799	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tcgggggtcttgctgaacagCggctgtgggcaggagattga	18	7	1	3			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr15:92981799C>A	ENST00000268164.3	+	4	744	c.507C>A	c.(505-507)agC>agA	p.S169R	ST8SIA2_ENST00000539113.1_Missense_Mutation_p.S148R	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	169					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			TGCTGAACAGCGGCTGTGGGC	0.607																																					p.S169R		Atlas-SNP	.											.	ST8SIA2	41	.	0			c.C507A						.						53	46	49					15																	92981799		2198	4298	6496	SO:0001583	missense	8128	exon4			GAACAGCGGCTGT	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.507C>A	chr15.hg19:g.92981799C>A	ENSP00000268164:p.Ser169Arg	51.0	0.0		65.0	22.0	NM_006011	Q4VAZ0|Q92470|Q92746	Missense_Mutation	SNP	ENST00000268164.3	hg19	CCDS10372.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.817165	0.70912	.	.	ENSG00000140557	ENST00000268164;ENST00000539113;ENST00000555434	T;T;T	0.40225	1.04;1.04;1.04	5.03	-3.0	0.05480	.	0.078649	0.85682	D	0.000000	T	0.65396	0.2687	M	0.91920	3.255	0.58432	D	0.999991	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.70890	-0.4749	10	0.87932	D	0	-25.3223	11.7529	0.51859	0.0:0.462:0.0:0.538	.	148;169	C6G488;Q92186	.;SIA8B_HUMAN	R	169;148;126	ENSP00000268164:S169R;ENSP00000437382:S148R;ENSP00000450851:S126R	ENSP00000268164:S169R	S	+	3	2	ST8SIA2	90782803	0.462000	0.25791	0.989000	0.46669	0.975000	0.68041	-0.250000	0.08830	-0.420000	0.07427	0.563000	0.77884	AGC	.	.		0.607	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		A	92981799	C	A	92981799	3	1	148	1	0	0	0	0	1	0	0	0	15247	767	27	1	521	1	ST8SIA2	15	92981799	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	1502940	92981799	9549593	93	22637										
LRRC28	123355	hgsc.bcm.edu	37	chr15	99828120	99828120	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tgagagctttacgtcatcttCgattagctaataaccaactg	7	9	2	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr15:99828120C>T	ENST00000301981.3	+	5	589	c.349C>T	c.(349-351)Cga>Tga	p.R117*	LRRC28_ENST00000331450.5_Intron|LRRC28_ENST00000558879.1_Intron|LRRC28_ENST00000422500.2_Nonsense_Mutation_p.R117*|LRRC28_ENST00000442993.2_Nonsense_Mutation_p.R117*|LRRC28_ENST00000447360.2_Nonsense_Mutation_p.R117*|LRRC28_ENST00000559399.1_3'UTR	NM_144598.2	NP_653199.2	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	117										endometrium(2)|large_intestine(3)|lung(6)|prostate(1)	12	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			ACGTCATCTTCGATTAGCTAA	0.373																																					p.R117X		Atlas-SNP	.											.	LRRC28	38	.	0			c.C349T						.						157	151	153					15																	99828120		2197	4297	6494	SO:0001587	stop_gained	123355	exon5			CATCTTCGATTAG	AK091588	CCDS10380.1, CCDS66873.1	15q26.3	2004-06-29			ENSG00000168904	ENSG00000168904			28355	protein-coding gene	gene with protein product						12975309	Standard	XM_005254861		Approved	MGC24976, FLJ34269, FLJ45242	uc002bva.1	Q86X40	OTTHUMG00000149854	ENST00000301981.3:c.349C>T	chr15.hg19:g.99828120C>T	ENSP00000304923:p.Arg117*	101.0	0.0		118.0	19.0	NM_144598	A8KA22|Q6UY49|Q6ZSS6	Nonsense_Mutation	SNP	ENST00000301981.3	hg19	CCDS10380.1	.	.	.	.	.	.	.	.	.	.	C	38	6.774367	0.97829	.	.	ENSG00000168904	ENST00000301981;ENST00000447360;ENST00000422500;ENST00000442993	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	.	18.6355	0.91376	0.0:1.0:0.0:0.0	.	.	.	.	X	117	.	ENSP00000304923:R117X	R	+	1	2	LRRC28	97645643	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.170000	0.58229	2.741000	0.93983	0.585000	0.79938	CGA	.	.		0.373	LRRC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313546.1	NM_144598		T	99828120	C	T	99828120	4	4	148	1	0	0	0	0	0	1	0	0	8991	876	31	1	363	1	LRRC28	15	99828120	Nonsense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	6846321	99828120	2703272	94	22638										
IFT140	9742	hgsc.bcm.edu	37	chr16	1575967	1575967	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ggtgctgcgcaggtgcacgcGatcgtggtgctcggctacct	16	12	0	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr16:1575967G>T	ENST00000426508.2	-	21	3052	c.2689C>A	c.(2689-2691)Cgc>Agc	p.R897S	TMEM204_ENST00000253934.5_5'Flank|IFT140_ENST00000361339.5_Missense_Mutation_p.R91S	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	897					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				AGGTGCACGCGATCGTGGTGC	0.687																																					p.R897S		Atlas-SNP	.											IFT140,NS,carcinoma,0,1	IFT140	128	.	0			c.C2689A						.						35	32	33					16																	1575967		2183	4291	6474	SO:0001583	missense	9742	exon21			GCACGCGATCGTG	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"Intraflagellar transport homologs", "WD repeat domain containing"	29077	protein-coding gene	gene with protein product		614620	"WD and tetratricopeptide repeats 2", "intraflagellar transport 140 homolog (Chlamydomonas)"	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.2689C>A	chr16.hg19:g.1575967G>T	ENSP00000406012:p.Arg897Ser	37.0	0.0		42.0	11.0	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	hg19	CCDS10439.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.929706	0.73327	.	.	ENSG00000187535	ENST00000397417;ENST00000361339;ENST00000426508	T;T	0.55588	0.51;0.51	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.76300	0.3968	M	0.92219	3.285	0.80722	D	1	D;D	0.69078	0.996;0.997	P;P	0.61874	0.788;0.895	T	0.79391	-0.1823	10	0.33940	T	0.23	.	16.8983	0.86106	0.0:0.0:1.0:0.0	.	897;584	Q96RY7;B4DR58	IF140_HUMAN;.	S	897;91;897	ENSP00000354895:R91S;ENSP00000406012:R897S	ENSP00000354895:R91S	R	-	1	0	IFT140	1515968	1.000000	0.71417	0.981000	0.43875	0.028000	0.11728	7.733000	0.84916	2.514000	0.84764	0.561000	0.74099	CGC	.	.		0.687	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		T	1575967	G	T	1575967	3	4	148	1	0	0	0	0	1	0	0	0	7565	1058	37	1	1743	1	IFT140	16	1575967	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10		1575967	88778786	95	22639										
ZC3H7A	29066	hgsc.bcm.edu	37	chr16	11846585	11846585	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gccagcagtactggtcgtccTcggtgtggaaaaccttctct	11	12	1	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr16:11846585T>G	ENST00000396516.2	-	21	2863	c.2666A>C	c.(2665-2667)gAg>gCg	p.E889A	ZC3H7A_ENST00000355758.4_Missense_Mutation_p.E889A|ZC3H7A_ENST00000575984.1_Missense_Mutation_p.E85A			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	889						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						CTGGTCGTCCTCGGTGTGGAA	0.483																																					p.E889A		Atlas-SNP	.											.	ZC3H7A	72	.	0			c.A2666C						.						169	130	143					16																	11846585		2197	4300	6497	SO:0001583	missense	29066	exon22			TCGTCCTCGGTGT	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30959	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 7", "zinc finger CCCH-type containing 7"	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.2666A>C	chr16.hg19:g.11846585T>G	ENSP00000379773:p.Glu889Ala	69.0	0.0		54.0	12.0	NM_014153	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	hg19	CCDS10550.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.217741	0.79352	.	.	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.11604	2.76;2.76	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.31199	0.0789	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	T	0.01464	-1.1348	10	0.59425	D	0.04	.	15.165	0.72818	0.0:0.0:0.0:1.0	.	889	Q8IWR0	Z3H7A_HUMAN	A	889	ENSP00000347999:E889A;ENSP00000379773:E889A	ENSP00000347999:E889A	E	-	2	0	ZC3H7A	11754086	1.000000	0.71417	0.442000	0.26870	0.990000	0.78478	8.040000	0.89188	2.171000	0.68590	0.482000	0.46254	GAG	.	.		0.483	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153		G	11846585	T	G	11846585	3	3	148	1	0	0	0	0	1	0	0	0	17587	1551	54	5	257	5	ZC3H7A	16	11846585	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	10270618	11846585	78508168	96	22640										
MYH11	4629	hgsc.bcm.edu	37	chr16	15857692	15857692	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	cgcctggtctgtgtttctttCcttcttgaagacgatatttc	8	10	3	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr16:15857692C>T	ENST00000300036.5	-	10	1199	c.1090G>A	c.(1090-1092)Gaa>Aaa	p.E364K	MYH11_ENST00000396324.3_Missense_Mutation_p.E371K|MYH11_ENST00000452625.2_Missense_Mutation_p.E371K|MYH11_ENST00000576790.2_Missense_Mutation_p.E364K	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	364	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GTGTTTCTTTCCTTCTTGAAG	0.517			T	CBFB	AML																																p.E371K		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.G1111A						.						205	176	186					16																	15857692		2197	4300	6497	SO:0001583	missense	4629	exon11			TTCTTTCCTTCTT	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.1090G>A	chr16.hg19:g.15857692C>T	ENSP00000300036:p.Glu364Lys	93.0	0.0		68.0	32.0	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	hg19	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	c	34	5.396011	0.96009	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	5.31	5.31	0.75309	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.87857	0.6283	L	0.53671	1.685	0.80722	D	1	P;P;P;P;P;P	0.44877	0.486;0.845;0.845;0.845;0.845;0.845	P;P;P;P;P;P	0.52189	0.692;0.692;0.692;0.692;0.692;0.692	D	0.83983	0.0333	10	0.02654	T	1	.	17.9753	0.89126	0.0:1.0:0.0:0.0	.	371;364;364;371;364;371	B1PS43;D2JYH7;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;.;MYH11_HUMAN;.;.;.	K	364;364;371;371;371	ENSP00000300036:E364K;ENSP00000345136:E364K;ENSP00000379616:E371K;ENSP00000407821:E371K	ENSP00000300036:E364K	E	-	1	0	MYH11	15765193	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.773000	0.85462	2.482000	0.83794	0.556000	0.70494	GAA	.	.		0.517	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15857692	C	T	15857692	3	4	148	1	0	0	0	0	1	0	0	0	10040	864	30	3	4991	3	MYH11	16	15857692	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	4011107	15857692	74497061	97	22641										
ESRP2	80004	hgsc.bcm.edu	37	chr16	68266322	68266322	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttgtgtctctgcagcgctagGtcccgctgctcgctgtccac	11	15	1	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr16:68266322G>T	ENST00000565858.1	-	8	1022	c.936C>A	c.(934-936)gaC>gaA	p.D312E	ESRP2_ENST00000473183.2_Missense_Mutation_p.D302E	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	312	RRM 1.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						GCAGCGCTAGGTCCCGCTGCT	0.632																																					p.D302E		Atlas-SNP	.											.	ESRP2	118	.	0			c.C906A						.						66	66	66					16																	68266322		2198	4300	6498	SO:0001583	missense	80004	exon8			CGCTAGGTCCCGC	AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"RNA binding motif (RRM) containing"	26152	protein-coding gene	gene with protein product		612960	"RNA binding motif protein 35B"	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.936C>A	chr16.hg19:g.68266322G>T	ENSP00000454554:p.Asp312Glu	62.0	0.0		83.0	17.0	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Missense_Mutation	SNP	ENST00000565858.1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.69	3.875066	0.72180	.	.	ENSG00000103067	ENST00000473183	T	0.07216	3.21	5.65	4.7	0.59300	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.10294	0.0252	N	0.11427	0.14	0.80722	D	1	D;P	0.63880	0.993;0.823	P;P	0.59948	0.866;0.615	T	0.42949	-0.9421	10	0.25751	T	0.34	-21.4757	12.379	0.55295	0.1397:0.0:0.8603:0.0	.	312;302	Q9H6T0;Q9H6T0-2	ESRP2_HUMAN;.	E	302	ENSP00000418748:D302E	ENSP00000418748:D302E	D	-	3	2	ESRP2	66823823	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.308000	0.51896	1.396000	0.46663	0.561000	0.74099	GAC	.	.		0.632	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939		T	68266322	G	T	68266322	3	4	148	1	0	0	0	0	1	0	0	0	5261	1252	44	3	1279	3	ESRP2	16	68266322	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	52408630	68266322	22088431	98	22642										
FANCA	2175	hgsc.bcm.edu	37	chr16	89831471	89831471	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	caatctgaacatgaggaactGaaactgaaacagagagtgac	10	7	1	6			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr16:89831471G>C	ENST00000389301.3	-	28	2635	c.2605C>G	c.(2605-2607)Cag>Gag	p.Q869E	FANCA_ENST00000568369.1_Missense_Mutation_p.Q869E	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	869			Q -> P (in FA). {ECO:0000269|PubMed:17924555}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		ATGAGGAACTGAAACTGAAAC	0.522			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.Q869E		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.C2605G						.						70	66	67					16																	89831471		2198	4300	6498	SO:0001583	missense	2175	exon28	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGAACTGAAACTG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"Fanconi anemia, complementation groups"	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.2605C>G	chr16.hg19:g.89831471G>C	ENSP00000373952:p.Gln869Glu	45.0	0.0		41.0	4.0	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	hg19	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990896	0.54041	.	.	ENSG00000187741	ENST00000389301	D	0.85339	-1.97	5.21	5.21	0.72293	.	0.000000	0.53938	D	0.000058	D	0.90174	0.6929	M	0.76574	2.34	0.80722	D	1	D;D	0.67145	0.996;0.996	P;P	0.58266	0.836;0.836	D	0.91227	0.5011	10	0.72032	D	0.01	-25.0849	14.3113	0.66416	0.0:0.0:1.0:0.0	.	869;869	B4DRI7;O15360	.;FANCA_HUMAN	E	869	ENSP00000373952:Q869E	ENSP00000373952:Q869E	Q	-	1	0	FANCA	88358972	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	5.135000	0.64777	2.440000	0.82611	0.650000	0.86243	CAG	.	.		0.522	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			C	89831471	G	C	89831471	3	2	148	1	0	0	0	0	1	0	0	0	5670	1299	45	4	1826	4	FANCA	16	89831471	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	21565149	89831471	523282	99	22643										
KRT26	353288	hgsc.bcm.edu	37	chr17	38922867	38922867	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tcagtgaaaggagattgccaAtttgatccagttcctcaacc	8	10	2	3			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr17:38922867A>G	ENST00000335552.4	-	8	1355	c.1307T>C	c.(1306-1308)aTt>aCt	p.I436T		NM_181539.4	NP_853517.2			keratin 26											central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				GAGATTGCCAATTTGATCCAG	0.338																																					p.I436T		Atlas-SNP	.											.	KRT26	49	.	0			c.T1307C						.						168	164	165					17																	38922867		2203	4300	6503	SO:0001583	missense	353288	exon8			TTGCCAATTTGAT	AJ564205	CCDS11374.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000186393	ENSG00000186393		"-", "Intermediate filaments type I, keratins (acidic)"	30840	protein-coding gene	gene with protein product			"keratin 25B"	KRT25B		16831889	Standard	NM_181539		Approved		uc002hvf.3	Q7Z3Y9	OTTHUMG00000133370	ENST00000335552.4:c.1307T>C	chr17.hg19:g.38922867A>G	ENSP00000334798:p.Ile436Thr	65.0	0.0		58.0	4.0	NM_181539		Missense_Mutation	SNP	ENST00000335552.4	hg19	CCDS11374.1	.	.	.	.	.	.	.	.	.	.	A	1.340	-0.594385	0.03771	.	.	ENSG00000186393	ENST00000335552	T	0.80994	-1.44	5.49	1.8	0.24995	.	1.038830	0.07615	N	0.925995	T	0.64768	0.2628	N	0.22421	0.69	0.09310	N	1	B	0.19200	0.034	B	0.17722	0.019	T	0.49615	-0.8921	10	0.13470	T	0.59	.	5.1308	0.14909	0.4816:0.3345:0.0:0.1839	.	436	Q7Z3Y9	K1C26_HUMAN	T	436	ENSP00000334798:I436T	ENSP00000334798:I436T	I	-	2	0	KRT26	36176393	0.461000	0.25783	0.116000	0.21606	0.041000	0.13682	1.136000	0.31467	0.872000	0.35775	0.533000	0.62120	ATT	.	.		0.338	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539		G	38922867	A	G	38922867	3	3	148	1	0	0	0	0	1	0	0	0	8472	101	4	2	103	2	KRT26	17	38922867	Missense_Mutation	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10		38922867	42272343	100	22644										
SCRN2	90507	hgsc.bcm.edu	37	chr17	45916030	45916030	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	accactctccttgtctctgaGgatgcccatcatcacctctg	6	16	5	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr17:45916030G>C	ENST00000290216.9	-	6	930	c.805C>G	c.(805-807)Ctc>Gtc	p.L269V	SCRN2_ENST00000584123.1_Missense_Mutation_p.L277V|SCRN2_ENST00000407215.3_Missense_Mutation_p.L269V	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	269						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						TTGTCTCTGAGGATGCCCATC	0.637																																					p.L269V		Atlas-SNP	.											.	SCRN2	35	.	0			c.C805G						.						93	72	79					17																	45916030		2203	4300	6503	SO:0001583	missense	90507	exon6			CTCTGAGGATGCC	BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.805C>G	chr17.hg19:g.45916030G>C	ENSP00000290216:p.Leu269Val	67.0	0.0		49.0	13.0	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	hg19	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	G	18.93	3.728715	0.69074	.	.	ENSG00000141295	ENST00000290216;ENST00000407215	T;T	0.13657	2.61;2.57	5.52	5.52	0.82312	.	0.125936	0.56097	D	0.000039	T	0.40222	0.1108	M	0.89353	3.025	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.997	D;D;D	0.78314	0.991;0.991;0.991	T	0.39961	-0.9588	10	0.87932	D	0	-28.511	8.5536	0.33467	0.1648:0.0:0.8352:0.0	.	269;269;269	E9PBV5;Q96FV2;B7Z8S7	.;SCRN2_HUMAN;.	V	269	ENSP00000290216:L269V;ENSP00000383935:L269V	ENSP00000290216:L269V	L	-	1	0	SCRN2	43271029	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.102000	0.57776	2.588000	0.87417	0.655000	0.94253	CTC	.	.		0.637	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		C	45916030	G	C	45916030	3	2	148	1	0	0	0	0	1	0	0	0	13954	1000	35	4	502	4	SCRN2	17	45916030	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	6993163	45916030	35279180	101	22645										
ZNF407	55628	hgsc.bcm.edu	37	chr18	72775252	72775252	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gcagcaggaggccagcgccgCcccctgagcaggtgcagcag	16	15	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr18:72775252C>T	ENST00000299687.5	+	8	5575	c.5575C>T	c.(5575-5577)Ccc>Tcc	p.P1859S		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1859					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GCCAGCGCCGCCCCCTGAGCA	0.677																																					p.P1859S		Atlas-SNP	.											.	ZNF407	231	.	0			c.C5575T						.																																			SO:0001583	missense	55628	exon8			GCGCCGCCCCCTG	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.5575C>T	chr18.hg19:g.72775252C>T	ENSP00000299687:p.Pro1859Ser	89.0	0.0		49.0	12.0	NM_017757	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	C	1.485	-0.556210	0.03967	.	.	ENSG00000215421	ENST00000299687	T	0.08458	3.09	4.96	-5.09	0.02920	.	.	.	.	.	T	0.03263	0.0095	N	0.04508	-0.205	0.27643	N	0.947669	B	0.09022	0.002	B	0.04013	0.001	T	0.52540	-0.8562	9	0.14252	T	0.57	.	12.5036	0.55970	0.0:0.6397:0.1204:0.2399	.	1859	Q9C0G0	ZN407_HUMAN	S	1859	ENSP00000299687:P1859S	ENSP00000299687:P1859S	P	+	1	0	ZNF407	70904240	0.000000	0.05858	0.007000	0.13788	0.017000	0.09413	-0.147000	0.10234	2.293000	0.77203	0.650000	0.86243	CCC	.	.		0.677	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72775252	C	T	72775252	3	4	148	1	0	0	0	0	1	0	0	0	17902	739	26	3	5735	3	ZNF407	18	72775252	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10		72775252	5301996	102	22646										
ZNF236	7776	hgsc.bcm.edu	37	chr18	74622651	74622651	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	atacgtaccatcagcagcctCagtttccacctgtccaacag	6	15	2	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr18:74622651C>G	ENST00000253159.8	+	16	2881	c.2683C>G	c.(2683-2685)Cag>Gag	p.Q895E	ZNF236_ENST00000320610.9_Missense_Mutation_p.Q897E	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	895					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		TCAGCAGCCTCAGTTTCCACC	0.433																																					p.Q895E		Atlas-SNP	.											.	ZNF236	325	.	0			c.C2683G						.						79	77	78					18																	74622651		1968	4159	6127	SO:0001583	missense	7776	exon16			CAGCCTCAGTTTC	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"Zinc fingers, C2H2-type"	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.2683C>G	chr18.hg19:g.74622651C>G	ENSP00000253159:p.Gln895Glu	72.0	0.0		52.0	4.0	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	hg19	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	C	2.064	-0.414778	0.04766	.	.	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T;T	0.11604	2.8;2.93;2.76	4.78	0.697	0.18081	.	0.852017	0.10422	N	0.676534	T	0.08714	0.0216	L	0.47716	1.5	0.24198	N	0.995526	B	0.02656	0.0	B	0.04013	0.001	T	0.45920	-0.9228	10	0.02654	T	1	.	10.18	0.42961	0.0:0.5396:0.3874:0.073	.	895	Q9UL36	ZN236_HUMAN	E	895	ENSP00000253159:Q895E;ENSP00000444524:Q895E;ENSP00000322361:Q895E	ENSP00000253159:Q895E	Q	+	1	0	ZNF236	72751639	0.036000	0.19791	0.003000	0.11579	0.995000	0.86356	2.422000	0.44696	-0.104000	0.12154	0.467000	0.42956	CAG	.	.		0.433	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			G	74622651	C	G	74622651	3	3	148	1	0	0	0	0	1	0	0	0	17804	827	29	4	2745	4	ZNF236	18	74622651	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	1847399	74622651	3454597	103	22647										
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2399148	2399148	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	aggctgcgggagcacggcatCtccctggctgcctatggcac	14	14	1	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr19:2399148C>T	ENST00000332578.3	+	3	369	c.369C>T	c.(367-369)atC>atT	p.I123I		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	123					plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCACGGCATCTCCCTGGCTG	0.647																																					p.I123I		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C369T						.						44	38	40					19																	2399148		2203	4300	6503	SO:0001819	synonymous_variant	360200	exon3			CGGCATCTCCCTG	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"Serine peptidases / Transmembrane"	30079	protein-coding gene	gene with protein product	"polyserase 1"	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.369C>T	chr19.hg19:g.2399148C>T		72.0	0.0		54.0	5.0	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	hg19	CCDS12088.1																																																																																			.	.		0.647	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		T	2399148	C	T	2399148	2	4	148	1	0	0	0	0	0	0	0	1	16268	903	32	3		3	TMPRSS9	19	2399148	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10		2399148	56729835	104	22648										
PLVAP	83483	hgsc.bcm.edu	37	chr19	17476642	17476642	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gttgctccttggccagctggCgctcttggtgctgcagctcc	13	14	1	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr19:17476642C>T	ENST00000252590.4	-	3	693	c.632G>A	c.(631-633)cGc>cAc	p.R211H		NM_031310.1	NP_112600.1	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	211					MAPK cascade (GO:0000165)|positive regulation of cellular extravasation (GO:0002693)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GGCCAGCTGGCGCTCTTGGTG	0.562																																					p.R211H		Atlas-SNP	.											.	PLVAP	64	.	0			c.G632A						.						79	72	74					19																	17476642		2203	4300	6503	SO:0001583	missense	83483	exon3			AGCTGGCGCTCTT	AF326591	CCDS32952.1	19p13.2	2008-07-17				ENSG00000130300			13635	protein-coding gene	gene with protein product	"fenestrated-endothelial linked structure protein; PV-1 protein"	607647				11401446	Standard	NM_031310		Approved	gp68, PV-1, PV1, FELS	uc002ngk.1	Q9BX97		ENST00000252590.4:c.632G>A	chr19.hg19:g.17476642C>T	ENSP00000252590:p.Arg211His	45.0	0.0		54.0	11.0	NM_031310	Q86VP0|Q8N8Y0|Q8ND68|Q8TER8|Q9BZD5	Missense_Mutation	SNP	ENST00000252590.4	hg19	CCDS32952.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.224342	0.58668	.	.	ENSG00000130300	ENST00000252590	.	.	.	4.86	-3.53	0.04667	.	1.476590	0.04187	N	0.327502	T	0.25938	0.0632	L	0.27053	0.805	0.09310	N	1	D	0.59767	0.986	P	0.52598	0.703	T	0.19128	-1.0315	9	0.40728	T	0.16	-5.6057	1.5906	0.02653	0.1382:0.3449:0.1367:0.3803	.	211	Q9BX97	PLVAP_HUMAN	H	211	.	ENSP00000252590:R211H	R	-	2	0	PLVAP	17337642	0.000000	0.05858	0.000000	0.03702	0.157000	0.22087	-0.542000	0.06091	-0.388000	0.07797	0.305000	0.20034	CGC	.	.		0.562	PLVAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463655.1	NM_031310		T	17476642	C	T	17476642	3	4	148	1	0	0	0	0	1	0	0	0	12125	768	27	1	712	1	PLVAP	19	17476642	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	15077494	17476642	41652341	105	22649										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36352846	36352846	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	catttcggggacccaggagtCtgactttagcaggagcttta	12	9	1	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr19:36352846C>A	ENST00000360202.5	+	11	1628	c.1430C>A	c.(1429-1431)tCt>tAt	p.S477Y	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Missense_Mutation_p.S477Y|KIRREL2_ENST00000347900.6_Missense_Mutation_p.S427Y|KIRREL2_ENST00000262625.7_Missense_Mutation_p.S477Y	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	477	Ig-like C2-type 5.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ACCCAGGAGTCTGACTTTAGC	0.657																																					p.S477Y		Atlas-SNP	.											.	KIRREL2	170	.	0			c.C1430A						.						38	41	40					19																	36352846		2203	4300	6503	SO:0001583	missense	84063	exon11			AGGAGTCTGACTT	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.1430C>A	chr19.hg19:g.36352846C>A	ENSP00000353331:p.Ser477Tyr	91.0	0.0		126.0	16.0	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	hg19	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.845370	0.32606	.	.	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.15834	2.39;2.39;2.39	4.95	2.77	0.32553	Immunoglobulin-like (1);	0.160614	0.29838	N	0.011069	T	0.28001	0.0690	L	0.49126	1.545	0.09310	N	1	D;D;D;D;D	0.71674	0.989;0.998;0.996;0.998;0.998	P;D;P;D;D	0.64877	0.726;0.93;0.853;0.93;0.93	T	0.02491	-1.1151	10	0.38643	T	0.18	-17.2205	8.0251	0.30431	0.0:0.8012:0.0:0.1988	.	477;457;477;427;477	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	Y	477;427;477;457	ENSP00000262625:S477Y;ENSP00000345067:S427Y;ENSP00000353331:S477Y	ENSP00000262625:S477Y	S	+	2	0	KIRREL2	41044686	0.001000	0.12720	0.334000	0.25495	0.119000	0.20118	0.887000	0.28254	1.088000	0.41272	0.555000	0.69702	TCT	.	.		0.657	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		A	36352846	C	A	36352846	3	1	148	1	0	0	0	0	1	0	0	0	8334	913	32	3	1472	3	KIRREL2	19	36352846	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	18876204	36352846	22776137	106	22650										
EML2	24139	hgsc.bcm.edu	37	chr19	46136177	46136177	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	acacccccaagcccagcacgTgtaaggtggagagggaaact	12	12	0	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr19:46136177T>G	ENST00000245925.3	-	6	502	c.452A>C	c.(451-453)cAc>cCc	p.H151P	EML2_ENST00000536630.1_Missense_Mutation_p.H298P|EML2_ENST00000586902.1_5'Flank|EML2_ENST00000587152.1_Missense_Mutation_p.H352P|EML2_ENST00000589876.1_Missense_Mutation_p.H151P	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	151	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.H151R(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		GCCCAGCACGTGTAAGGTGGA	0.622																																					p.H352P		Atlas-SNP	.											EML2,NS,carcinoma,0,1	EML2	64	.	1	Substitution - Missense(1)	kidney(1)	c.A1055C						.						108	91	97					19																	46136177		2203	4300	6503	SO:0001583	missense	24139	exon9			AGCACGTGTAAGG	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"WD repeat domain containing"	18035	protein-coding gene	gene with protein product	"echinoderm MT-associated protein (EMAP)-like protein 70", "microtubule-associated protein like echinoderm EMAP"					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.452A>C	chr19.hg19:g.46136177T>G	ENSP00000245925:p.His151Pro	81.0	0.0		137.0	19.0	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	hg19	CCDS12670.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.565171	0.86439	.	.	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055;ENST00000399594	T;T;T	0.40225	1.04;1.04;4.99	4.97	4.97	0.65823	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.64724	0.2624	M	0.80982	2.52	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.993;0.994;0.997;0.993	T	0.67688	-0.5606	10	0.49607	T	0.09	-30.8838	12.649	0.56751	0.0:0.0:0.0:1.0	.	151;317;298;309;151	B7Z918;B7Z3Q9;B7Z3I2;B7Z872;O95834	.;.;.;.;EMAL2_HUMAN	P	298;151;352;309	ENSP00000442365:H298P;ENSP00000245925:H151P;ENSP00000382503:H309P	ENSP00000245925:H151P	H	-	2	0	EML2	50828017	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.416000	0.80143	2.075000	0.62263	0.460000	0.39030	CAC	.	.		0.622	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155		G	46136177	T	G	46136177	3	3	148	1	0	0	0	0	1	0	0	0	5099	1696	59	5	1553	5	EML2	19	46136177	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	9783331	46136177	12992806	107	22651										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35431376	35431376	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ttgcgctcactgatctgcagCtgccgagtcagctccatgac	10	14	3	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr20:35431376C>T	ENST00000357779.3	-	11	2834	c.2508G>A	c.(2506-2508)caG>caA	p.Q836Q	SOGA1_ENST00000456801.2_Silent_p.Q677Q|SOGA1_ENST00000279034.6_Silent_p.Q836Q|SOGA1_ENST00000237536.4_Silent_p.Q1074Q			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	836					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						TGATCTGCAGCTGCCGAGTCA	0.642																																					p.Q1074Q		Atlas-SNP	.											.	SOGA1	136	.	0			c.G3222A						.																																			SO:0001819	synonymous_variant	140710	exon11			CTGCAGCTGCCGA	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.2508G>A	chr20.hg19:g.35431376C>T		46.0	0.0		67.0	15.0	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Silent	SNP	ENST00000357779.3	hg19																																																																																				.	.		0.642	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		T	35431376	C	T	35431376	2	4	148	1	0	0	0	0	0	0	0	1	2085	796	28	3		3	C20orf117	20	35431376	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10		35431376	27594144	108	22652										
KCNK15	140730	hgsc.bcm.edu	37	chr20	43378872	43378872	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ggtcactttccagagcctggGcgaacggctgaacgcggtgg	16	11	1	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr20:43378872G>A	ENST00000372851.3	-	0	5203				KCNK15_ENST00000372861.3_Missense_Mutation_p.G129D	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4						exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				CAGAGCCTGGGCGAACGGCTG	0.687																																					p.G129D		Atlas-SNP	.											.	KCNK15	19	.	0			c.G386A						.						32	29	30					20																	43378872		2203	4300	6503	SO:0001628	intergenic_variant	60598	exon2			GCCTGGGCGAACG		CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"chromosome 20 open reading frame 190"	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546		chr20.hg19:g.43378872G>A		47.0	0.0		41.0	7.0	NM_022358	A4FU94|E1P613|Q3MI44|Q5JWT7	Missense_Mutation	SNP	ENST00000372851.3	hg19	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.417197	0.83449	.	.	ENSG00000124249	ENST00000372861	T	0.35048	1.33	4.08	4.08	0.47627	Ion transport 2 (1);	0.138661	0.47093	U	0.000257	T	0.74966	0.3786	H	0.98559	4.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86492	0.1798	10	0.87932	D	0	.	16.4786	0.84151	0.0:0.0:1.0:0.0	.	129	Q9H427	KCNKF_HUMAN	D	129	ENSP00000361952:G129D	ENSP00000361952:G129D	G	+	2	0	KCNK15	42812286	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.552000	0.82192	2.095000	0.63458	0.655000	0.94253	GGC	.	.		0.687	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970		A	43378872	G	A	43378872	1	1	148	0	1	0	0	0	0	0	0	0	8071	1203	42	3		3	KCNK15	20	43378872	IGR	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	7947496	43378872	19646648	109	22653										
ZFP64	55734	hgsc.bcm.edu	37	chr20	50782459	50782459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gtgttgtgggctttttggtgCgtgacttggcagggagagag	19	4	0	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr20:50782459C>T	ENST00000216923.4	-	3	741	c.392G>A	c.(391-393)cGc>cAc	p.R131H	ZFP64_ENST00000361387.2_Missense_Mutation_p.R131H|ZFP64_ENST00000371518.2_Missense_Mutation_p.R131H|ZFP64_ENST00000346617.4_Intron|ZFP64_ENST00000371515.4_Missense_Mutation_p.R129H|ZFP64_ENST00000477786.1_5'UTR	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	131					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R131H(3)		breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CTTTTTGGTGCGTGACTTGGC	0.458																																					p.R131H		Atlas-SNP	.											ZFP64_ENST00000361387,NS,carcinoma,0,3	ZFP64	240	.	3	Substitution - Missense(3)	endometrium(3)	c.G392A						.						272	224	240					20																	50782459		2203	4300	6503	SO:0001583	missense	55734	exon3			TTGGTGCGTGACT	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.392G>A	chr20.hg19:g.50782459C>T	ENSP00000216923:p.Arg131His	133.0	0.0		122.0	11.0	NM_018197	Q9NTS7|Q9NVH4	Missense_Mutation	SNP	ENST00000216923.4	hg19	CCDS13440.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380341	0.82682	.	.	ENSG00000020256	ENST00000371518;ENST00000361387;ENST00000216923;ENST00000371515;ENST00000371516	T;T;T;T	0.08634	3.16;3.15;3.07;3.08	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000015	T	0.27349	0.0671	M	0.61703	1.905	0.39584	D	0.969476	D;D;D	0.89917	1.0;1.0;0.964	D;D;B	0.85130	0.997;0.997;0.354	T	0.00325	-1.1816	10	0.32370	T	0.25	-21.8346	18.1401	0.89637	0.0:1.0:0.0:0.0	.	129;131;131	Q5JWM1;Q9NPA5;Q9NTW7	.;ZF64A_HUMAN;ZF64B_HUMAN	H	131;131;131;129;131	ENSP00000360573:R131H;ENSP00000355179:R131H;ENSP00000216923:R131H;ENSP00000360570:R129H	ENSP00000216923:R131H	R	-	2	0	ZFP64	50215866	0.995000	0.38212	0.983000	0.44433	0.918000	0.54935	3.755000	0.55197	2.726000	0.93360	0.655000	0.94253	CGC	.	.		0.458	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197		T	50782459	C	T	50782459	3	4	148	1	0	0	0	0	1	0	0	0	17667	768	27	1	2860	1	ZFP64	20	50782459	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	7403587	50782459	12243061	110	22654										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47666686	47666686	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gtacacgtcctcctctgccaTgtcctcactcttcattttgg	6	15	4	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr21:47666686T>A	ENST00000397708.1	-	22	4659	c.4405A>T	c.(4405-4407)Atg>Ttg	p.M1469L	MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.M1469L			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1469					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					TCCTCTGCCATGTCCTCACTC	0.587																																					p.M1469L		Atlas-SNP	.											.	MCM3AP	146	.	0			c.A4405T						.						173	167	169					21																	47666686		2203	4300	6503	SO:0001583	missense	8888	exon21			CTGCCATGTCCTC	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.4405A>T	chr21.hg19:g.47666686T>A	ENSP00000380820:p.Met1469Leu	137.0	0.0		111.0	31.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	t	5.229	0.227731	0.09916	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.03035	4.07;4.07	5.68	-8.33	0.00992	.	2.169910	0.01461	N	0.015882	T	0.01765	0.0056	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43458	-0.9390	10	0.20046	T	0.44	0.1722	4.5933	0.12317	0.0788:0.3015:0.1553:0.4643	.	1469	O60318	MCM3A_HUMAN	L	1469	ENSP00000380820:M1469L;ENSP00000291688:M1469L	ENSP00000291688:M1469L	M	-	1	0	MCM3AP	46491114	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-3.127000	0.00592	-1.597000	0.01609	-0.722000	0.03604	ATG	.	.		0.587	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		A	47666686	T	A	47666686	3	1	148	1	0	0	0	0	1	0	0	0	9397	1464	51	4	1569	4	MCM3AP	21	47666686	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10		47666686	463209	111	22655										
PI4KA	5297	hgsc.bcm.edu	37	chr22	21066826	21066826	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	actggcgtgtgaagtagtcgTacatgccgaagtctgtctgg	14	8	2	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr22:21066826T>C	ENST00000572273.1	-	50	5806	c.5576A>G	c.(5575-5577)tAc>tGc	p.Y1859C	PI4KA_ENST00000414196.3_Missense_Mutation_p.Y669C|PI4KA_ENST00000255882.6_Missense_Mutation_p.Y1917C			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1859	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			GAAGTAGTCGTACATGCCGAA	0.652																																					p.Y1917C	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.A5750G						.						33	32	32					22																	21066826		2187	4266	6453	SO:0001583	missense	5297	exon50			TAGTCGTACATGC	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.5576A>G	chr22.hg19:g.21066826T>C	ENSP00000458238:p.Tyr1859Cys	300.0	0.0		302.0	72.0	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	hg19		.	.	.	.	.	.	.	.	.	.	T	22.8	4.333044	0.81801	.	.	ENSG00000241973	ENST00000255882;ENST00000414196;ENST00000399213	T;T	0.76839	-1.05;-1.05	4.49	4.49	0.54785	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.116625	0.64402	D	0.000011	D	0.89083	0.6614	M	0.88570	2.965	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.77557	0.967;0.99	D	0.91163	0.4962	10	0.72032	D	0.01	-15.5712	13.9524	0.64126	0.0:0.0:0.0:1.0	.	252;1859	A8MTF1;P42356	.;PI4KA_HUMAN	C	1859;669;252	ENSP00000402981:Y669C;ENSP00000382162:Y252C	ENSP00000255882:Y1859C	Y	-	2	0	PI4KA	19396826	1.000000	0.71417	0.969000	0.41365	0.986000	0.74619	7.817000	0.86213	1.894000	0.54839	0.519000	0.50382	TAC	.	.		0.652	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		C	21066826	T	C	21066826	3	2	148	1	0	0	0	0	1	0	0	0	11882	1638	57	2	582	2	PI4KA	22	21066826	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10		21066826	30237740	112	22656										
ZNF280A	129025	hgsc.bcm.edu	37	chr22	22869868	22869868	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ccaacatagatcagatctggAtcttcatcatcctcctccct	4	15	5	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr22:22869868A>G	ENST00000302097.3	-	2	339	c.87T>C	c.(85-87)gaT>gaC	p.D29D	snoU13_ENST00000459485.1_RNA	NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	29					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TCAGATCTGGATCTTCATCAT	0.368																																					p.D29D		Atlas-SNP	.											.	ZNF280A	67	.	0			c.T87C						.						146	126	133					22																	22869868		2203	4300	6503	SO:0001819	synonymous_variant	129025	exon2			ATCTGGATCTTCA	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"zinc finger protein 280", "suppressor of hairy wing homolog 1 (Drosophila)"	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.87T>C	chr22.hg19:g.22869868A>G		109.0	0.0		104.0	16.0	NM_080740		Silent	SNP	ENST00000302097.3	hg19	CCDS13800.1																																																																																			.	.		0.368	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740		G	22869868	A	G	22869868	2	3	148	1	0	0	0	0	0	0	0	1	17829	330	12	2		2	ZNF280A	22	22869868	Silent	SNP	A	TCGA-DD-A73G-01A-22D-A32G-10	1803042	22869868	28434698	113	22657										
CRYBA4	1413	hgsc.bcm.edu	37	chr22	27026303	27026303	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tctgccttttctcttttccaGctgggtttgctcccagtttc	7	13	2	0			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr22:27026303G>A	ENST00000354760.3	+	6	478		c.e6-1		CRYBA4_ENST00000466315.1_Splice_Site	NM_001886.2	NP_001877.1	P53673	CRBA4_HUMAN	crystallin, beta A4						camera-type eye development (GO:0043010)|visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(6)|liver(1)|lung(6)|skin(3)|urinary_tract(2)	18						CTCTTTTCCAGCTGGGTTTGC	0.512																																					.		Atlas-SNP	.											.	CRYBA4	33	.	0			c.444-1G>A						.						146	107	120					22																	27026303		2203	4300	6503	SO:0001630	splice_region_variant	1413	exon6			TTTCCAGCTGGGT		CCDS13841.1	22q12.1	2008-06-10			ENSG00000196431	ENSG00000196431			2396	protein-coding gene	gene with protein product		123631				8999933, 960806	Standard	NM_001886		Approved		uc003acz.4	P53673	OTTHUMG00000150983	ENST00000354760.3:c.444-1G>A	chr22.hg19:g.27026303G>A		56.0	0.0		55.0	8.0	NM_001886	Q4VB22|Q6ICE4	Splice_Site	SNP	ENST00000354760.3	hg19	CCDS13841.1	.	.	.	.	.	.	.	.	.	.	G	8.394	0.840363	0.16891	.	.	ENSG00000196431	ENST00000354760	.	.	.	4.42	3.4	0.38934	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2798	0.43532	0.0971:0.0:0.9029:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CRYBA4	25356303	1.000000	0.71417	0.549000	0.28204	0.017000	0.09413	8.263000	0.89864	1.087000	0.41251	-0.300000	0.09419	.	.	.		0.512	CRYBA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320793.1	NM_001886	Intron	A	27026303	G	A	27026303	5	1	148	1	0	0	0	0	0	0	1	0	3911	985	34	3	461	3	CRYBA4	22	27026303	Splice_Site	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	4156435	27026303	24278263	114	22658										
SBF1	6305	hgsc.bcm.edu	37	chr22	50905841	50905841	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ctccaggcacacattcaggcCctccacgtggatggcataga	10	14	1	1			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chr22:50905841C>T	ENST00000390679.3	-	5	659	c.475G>A	c.(475-477)Ggc>Agc	p.G159S	SBF1_ENST00000380817.3_Missense_Mutation_p.G159S|SBF1_ENST00000348911.6_Missense_Mutation_p.G160S			O95248	MTMR5_HUMAN	SET binding factor 1	159	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		ACATTCAGGCCCTCCACGTGG	0.617																																					p.G159S		Atlas-SNP	.											.	SBF1	211	.	0			c.G475A						.						95	104	101					22																	50905841		2156	4245	6401	SO:0001583	missense	6305	exon5			TCAGGCCCTCCAC	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.475G>A	chr22.hg19:g.50905841C>T	ENSP00000375097:p.Gly159Ser	219.0	0.0		202.0	25.0	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	C	8.360	0.832829	0.16820	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000356279;ENST00000337034;ENST00000390679	T;T;T	0.10382	2.88;2.88;2.88	4.75	4.75	0.60458	.	1.634860	0.03868	N	0.275222	T	0.07728	0.0194	N	0.04373	-0.215	0.49798	D	0.999823	B;B	0.33694	0.421;0.421	B;B	0.40199	0.322;0.322	T	0.25847	-1.0120	10	0.02654	T	1	.	12.3763	0.55281	0.0:0.9154:0.0:0.0846	.	160;159	G5E933;O95248-4	.;.	S	159;160;170;169;159	ENSP00000370196:G159S;ENSP00000252027:G160S;ENSP00000375097:G159S	ENSP00000336522:G169S	G	-	1	0	SBF1	49252707	0.858000	0.29795	1.000000	0.80357	0.982000	0.71751	1.751000	0.38339	2.467000	0.83353	0.561000	0.74099	GGC	.	.		0.617	SBF1-201	KNOWN	basic	protein_coding	protein_coding				T	50905841	C	T	50905841	3	4	148	1	0	0	0	0	1	0	0	0	13873	623	22	3	5354	3	SBF1	22	50905841	Missense_Mutation	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	23879538	50905841	398725	115	22659										
WWC3	55841	hgsc.bcm.edu	37	chrX	10085608	10085608	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	gacagactgcgggcacacgcCtcggctatgggggacgaaga	16	11	0	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chrX:10085608C>T	ENST00000380861.4	+	11	1900	c.1509C>T	c.(1507-1509)gcC>gcT	p.A503A	WWC3_ENST00000454666.1_Silent_p.A503A	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	503					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						GGGCACACGCCTCGGCTATGG	0.721																																					p.A503A		Atlas-SNP	.											.	WWC3	142	.	0			c.C1509T						.						6	7	7					X																	10085608		2138	4194	6332	SO:0001819	synonymous_variant	55841	exon11			ACACGCCTCGGCT	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1509C>T	chrX.hg19:g.10085608C>T		72.0	0.0		84.0	15.0	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	hg19	CCDS14136.1																																																																																			.	.		0.721	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		T	10085608	C	T	10085608	2	4	148	1	0	0	0	0	0	0	0	1	17428	668	24	3		3	WWC3	23	10085608	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10		10085608	145184952	116	22660										
TLR8	51311	hgsc.bcm.edu	37	chrX	12937742	12937742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	agaaaactaacatagaagatGgagtatttgaaacgctgaca	9	5	0	5			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chrX:12937742G>A	ENST00000218032.6	+	2	670	c.583G>A	c.(583-585)Gga>Aga	p.G195R	TLR8_ENST00000311912.5_Missense_Mutation_p.G213R	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	195					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CATAGAAGATGGAGTATTTGA	0.373																																					p.G195R		Atlas-SNP	.											.	TLR8	134	.	0			c.G583A						.						65	70	68					X																	12937742		2203	4299	6502	SO:0001583	missense	51311	exon2			GAAGATGGAGTAT	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.583G>A	chrX.hg19:g.12937742G>A	ENSP00000218032:p.Gly195Arg	218.0	0.0		237.0	36.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210039	0.39003	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.01059	5.39;5.39	4.93	4.93	0.64822	.	0.000000	0.40222	N	0.001143	T	0.02807	0.0084	N	0.25992	0.78	0.31765	N	0.632822	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.35943	-0.9768	10	0.59425	D	0.04	.	8.6708	0.34149	0.1584:0.0:0.8416:0.0	.	195;213	Q9NR97;D1CS70	TLR8_HUMAN;.	R	195;213	ENSP00000218032:G195R;ENSP00000312082:G213R	ENSP00000218032:G195R	G	+	1	0	TLR8	12847663	0.861000	0.29849	0.026000	0.17262	0.046000	0.14306	2.645000	0.46621	2.048000	0.60808	0.523000	0.50628	GGA	.	.		0.373	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		A	12937742	G	A	12937742	3	1	148	1	0	0	0	0	1	0	0	0	15972	1349	47	3	589	3	TLR8	23	12937742	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	2852134	12937742	142332818	117	22661										
GLOD5	392465	hgsc.bcm.edu	37	chrX	48631828	48631828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	ccgacagaaatctgattgagGtgtccaactacatctcctcg	8	12	2	3			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chrX:48631828G>A	ENST00000303227.6	+	4	501	c.460G>A	c.(460-462)Gtg>Atg	p.V154M	GLOD5_ENST00000470676.1_3'UTR	NM_001080489.2	NP_001073958.2	A6NK44	GLOD5_HUMAN	glyoxalase domain containing 5	154										endometrium(1)|lung(2)	3						TCTGATTGAGGTGTCCAACTA	0.562																																					p.V154M		Atlas-SNP	.											.	GLOD5	9	.	0			c.G460A						.						95	87	90					X																	48631828		1931	4123	6054	SO:0001583	missense	392465	exon4			ATTGAGGTGTCCA		CCDS55410.1	Xp11.23	2008-02-05			ENSG00000171433	ENSG00000171433			33358	protein-coding gene	gene with protein product							Standard	NM_001080489		Approved		uc011mmh.2	A6NK44	OTTHUMG00000024125	ENST00000303227.6:c.460G>A	chrX.hg19:g.48631828G>A	ENSP00000302552:p.Val154Met	40.0	0.0		59.0	6.0	NM_001080489		Missense_Mutation	SNP	ENST00000303227.6	hg19	CCDS55410.1	.	.	.	.	.	.	.	.	.	.	g	19.46	3.832094	0.71258	.	.	ENSG00000171433	ENST00000303227	.	.	.	5.05	4.19	0.49359	.	0.057487	0.64402	D	0.000002	T	0.75140	0.3809	M	0.70595	2.14	0.45690	D	0.998604	D	0.76494	0.999	D	0.71870	0.975	T	0.76623	-0.2891	9	0.72032	D	0.01	.	10.6748	0.45778	0.0971:0.0:0.9029:0.0	.	142	A6NK44	GLOD5_HUMAN	M	154	.	ENSP00000302552:V154M	V	+	1	0	GLOD5	48516772	1.000000	0.71417	0.998000	0.56505	0.904000	0.53231	3.707000	0.54838	1.031000	0.39867	0.597000	0.82753	GTG	.	.		0.562	GLOD5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080489		A	48631828	G	A	48631828	3	1	148	1	0	0	0	0	1	0	0	0	6459	1261	44	3	474	3	GLOD5	23	48631828	Missense_Mutation	SNP	G	TCGA-DD-A73G-01A-22D-A32G-10	35694086	48631828	106638732	118	22662										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123680738	123680738	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	atgtacctgctgtcaaatgaCacctcaggaggaatgacatg	10	9	2	2			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chrX:123680738C>T	ENST00000371130.3	-	15	2700	c.2637G>A	c.(2635-2637)gtG>gtA	p.V879V	TENM1_ENST00000422452.2_Silent_p.V879V	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	879					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TGTCAAATGACACCTCAGGAG	0.378																																					p.V879V		Atlas-SNP	.											.	.	.	.	0			c.G2637A						.						105	98	101					X																	123680738		2203	4300	6503	SO:0001819	synonymous_variant	10178	exon15			AAATGACACCTCA	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.2637G>A	chrX.hg19:g.123680738C>T		142.0	0.0		91.0	12.0	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	hg19	CCDS14609.1																																																																																			.	.		0.378	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123680738	C	T	123680738	2	4	148	1	0	0	0	0	0	0	0	1	10843	465	17	3		3	ODZ1	23	123680738	Silent	SNP	C	TCGA-DD-A73G-01A-22D-A32G-10	75048910	123680738	31589822	119	22663										
MAGEA11	4110	hgsc.bcm.edu	37	chrX	148798396	148798396	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	8	1	0.941084818385432	1.97627811860941	0.61758691206544	1	1	0	tcccacttcttacccatcccTgtatgaagatgctttgagag	7	12	1	3			TCGA-DD-A73G-01A-22D-A32G-10	TCGA-DD-A73G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	635235fc-77f3-49c0-96fa-9af89c5094c2	f14048d4-6611-479c-8cc0-9fe14f2b1618	g.chrX:148798396T>A	ENST00000355220.5	+	5	1352	c.1250T>A	c.(1249-1251)cTg>cAg	p.L417Q	MAGEA11_ENST00000333104.4_Missense_Mutation_p.L388Q	NM_005366.4	NP_005357.2	P43364	MAGAB_HUMAN	melanoma antigen family A, 11	417	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	9	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					TACCCATCCCTGTATGAAGAT	0.552																																					p.L417Q		Atlas-SNP	.											.	MAGEA11	86	.	0			c.T1250A						.						122	95	104					X																	148798396		2203	4300	6503	SO:0001583	missense	4110	exon5			CATCCCTGTATGA		CCDS48180.1	Xq28	2009-03-13			ENSG00000185247	ENSG00000185247			6798	protein-coding gene	gene with protein product	"MAGE-11 antigen", "melanoma-associated antigen 11", "cancer/testis antigen family 1, member 11"	300344		MAGE11		8575766	Standard	NM_001011544		Approved	MAGE-11, MAGEA-11, MGC10511, CT1.11	uc004fdq.3	P43364	OTTHUMG00000022633	ENST00000355220.5:c.1250T>A	chrX.hg19:g.148798396T>A	ENSP00000347358:p.Leu417Gln	123.0	0.0		147.0	22.0	NM_005366	Q5ETU4|Q6ZRZ5	Missense_Mutation	SNP	ENST00000355220.5	hg19	CCDS48180.1	.	.	.	.	.	.	.	.	.	.	N	1.088	-0.664898	0.03428	.	.	ENSG00000185247	ENST00000333104;ENST00000355220	T;T	0.01584	4.77;4.75	0.976	-1.95	0.07548	.	.	.	.	.	T	0.00875	0.0029	N	0.11154	0.105	0.09310	N	1	P;B	0.34955	0.477;0.346	B;B	0.32090	0.14;0.066	T	0.44817	-0.9303	8	.	.	.	.	1.4184	0.02306	0.3263:0.2663:0.0:0.4074	.	388;417	G5E962;P43364	.;MAGAB_HUMAN	Q	388;417	ENSP00000328177:L388Q;ENSP00000347358:L417Q	.	L	+	2	0	MAGEA11	148576009	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.501000	0.02281	-0.911000	0.03843	0.350000	0.21858	CTG	.	.		0.552	MAGEA11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058725.4	NM_005366		A	148798396	T	A	148798396	3	1	148	1	0	0	0	0	1	0	0	0	9174	1580	55	4	1277	4	MAGEA11	23	148798396	Missense_Mutation	SNP	T	TCGA-DD-A73G-01A-22D-A32G-10	25117658	148798396	6472164	120	22664										
SYNC	81493	hgsc.bcm.edu	37	chr1	33160953	33160953	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	aggccacacattcctttgtcActttgaaaagcttctgcttg	7	11	2	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr1:33160953A>G	ENST00000409190.3	-	2	1204	c.746T>C	c.(745-747)gTg>gCg	p.V249A	SYNC_ENST00000373484.3_Missense_Mutation_p.V249A	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein	249	Coil 1b.				intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TTCCTTTGTCACTTTGAAAAG	0.557																																					p.V249A		Atlas-SNP	.											.	SYNC	36	.	0			c.T746C						.						33	28	30					1																	33160953		692	1591	2283	SO:0001583	missense	81493	exon2			TTTGTCACTTTGA	AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"Intermediate filaments type III"	28897	protein-coding gene	gene with protein product		611750	"syncoilin, intermediate filament 1"	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.746T>C	chr1.hg19:g.33160953A>G	ENSP00000386439:p.Val249Ala	67.0	0.0		71.0	35.0	NM_001161708	B4DNK8|B4DY58|C9IY41	Missense_Mutation	SNP	ENST00000409190.3	hg19	CCDS367.2	.	.	.	.	.	.	.	.	.	.	A	15.51	2.854954	0.51376	.	.	ENSG00000162520	ENST00000373484;ENST00000409190	D;D	0.88201	-2.35;-2.35	4.57	4.57	0.56435	Filament (1);	.	.	.	.	D	0.88800	0.6535	N	0.14661	0.345	0.30562	N	0.764398	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.994	D	0.85621	0.1264	9	0.37606	T	0.19	-10.6603	13.45	0.61165	1.0:0.0:0.0:0.0	.	249;249	Q9H7C4-2;Q9H7C4	.;SYNCI_HUMAN	A	249	ENSP00000362583:V249A;ENSP00000386439:V249A	ENSP00000362583:V249A	V	-	2	0	SYNC	32933540	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	4.376000	0.59556	1.853000	0.53794	0.459000	0.35465	GTG	.	.		0.557	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786		G	33160953	A	G	33160953	3	3	149	1	0	0	0	0	1	0	0	0	15458	159	6	2	780	2	SYNC	1	33160953	Missense_Mutation	SNP	A	TCGA-DD-AA3A-01A-11D-A36X-10		33160953	216089668	1	22665										
RBM15	64783	hgsc.bcm.edu	37	chr1	110882218	110882218	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ctcccgtggtggtgaggactCgacttcccgcggtgagcgga	16	12	0	2			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr1:110882218C>G	ENST00000369784.3	+	1	1091	c.191C>G	c.(190-192)tCg>tGg	p.S64W	RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000602849.1_Missense_Mutation_p.S64W|RBM15_ENST00000487146.2_Missense_Mutation_p.S64W	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	64	Gly/Ser-rich.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		GGTGAGGACTCGACTTCCCGC	0.637			T	MKL1	acute megakaryocytic leukemia																																p.S64W		Atlas-SNP	.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	RBM15	93	.	0			c.C191G						.						40	41	40					1																	110882218		2203	4300	6503	SO:0001583	missense	64783	exon1			AGGACTCGACTTC	AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"RNA binding motif (RRM) containing"	14959	protein-coding gene	gene with protein product	"one twenty-two"	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.191C>G	chr1.hg19:g.110882218C>G	ENSP00000358799:p.Ser64Trp	240.0	0.0		280.0	112.0	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	hg19	CCDS822.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.042262	0.75732	.	.	ENSG00000162775	ENST00000369784	T	0.20069	2.1	5.31	5.31	0.75309	.	0.000000	0.39909	N	0.001222	T	0.23926	0.0579	N	0.19112	0.55	0.58432	D	0.999999	D;D	0.61080	0.989;0.981	D;P	0.65684	0.937;0.867	T	0.07233	-1.0783	10	0.72032	D	0.01	-6.0825	18.7537	0.91825	0.0:1.0:0.0:0.0	.	64;64	Q96T37-3;Q96T37	.;RBM15_HUMAN	W	64	ENSP00000358799:S64W	ENSP00000358799:S64W	S	+	2	0	RBM15	110683741	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.911000	0.48774	2.763000	0.94921	0.655000	0.94253	TCG	.	.		0.637	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		G	110882218	C	G	110882218	3	3	149	1	0	0	0	0	1	0	0	0	13131	893	31	4	193	4	RBM15	1	110882218	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	77721265	110882218	138368403	2	22666										
NUP210L	91181	hgsc.bcm.edu	37	chr1	154062058	154062058	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	acctggatgatttccaattcGgaatgtgagaacctttaagg	10	7	0	2			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr1:154062058G>A	ENST00000368559.3	-	16	2271	c.2200C>T	c.(2200-2202)Cga>Tga	p.R734*	NUP210L_ENST00000271854.3_Nonsense_Mutation_p.R734*	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	734					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			TTTCCAATTCGGAATGTGAGA	0.423																																					p.R734X		Atlas-SNP	.											.	NUP210L	181	.	0			c.C2200T						.						74	75	75					1																	154062058		1891	4124	6015	SO:0001587	stop_gained	91181	exon16			CAATTCGGAATGT	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2200C>T	chr1.hg19:g.154062058G>A	ENSP00000357547:p.Arg734*	123.0	0.0		282.0	58.0	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Nonsense_Mutation	SNP	ENST00000368559.3	hg19	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	G	39	7.522494	0.98335	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	.	.	.	4.57	4.57	0.56435	.	0.150747	0.30752	N	0.008943	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-27.8864	15.3044	0.73982	0.0:0.0:1.0:0.0	.	.	.	.	X	734	.	ENSP00000271854:R734X	R	-	1	2	NUP210L	152328682	0.996000	0.38824	0.954000	0.39281	0.941000	0.58515	4.027000	0.57239	2.363000	0.80096	0.467000	0.42956	CGA	.	.		0.423	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		A	154062058	G	A	154062058	4	1	149	1	0	0	0	0	0	1	0	0	10770	1124	39	1	3566	1	NUP210L	1	154062058	Nonsense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	43179840	154062058	95188563	3	22667										
C1orf14	81626	hgsc.bcm.edu	37	chr1	182922018	182922018	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	cctccgccgccgccgccgccGcctctcccgtgtcctcggcc	10	25	1	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr1:182922018G>T	ENST00000367547.3	-	1	487	c.251C>A	c.(250-252)gCg>gAg	p.A84E	SHCBP1L_ENST00000423786.1_5'Flank|SHCBP1L_ENST00000488956.1_5'UTR	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	156										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						cgccgccgccgccTCTCCCGT	0.751																																					p.A84E		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.C251A						.						3	5	4					1																	182922018		1575	3339	4914	SO:0001583	missense	81626	exon1			GCCGCCGCCTCTC	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.251C>A	chr1.hg19:g.182922018G>T	ENSP00000356518:p.Ala84Glu	97.0	0.0		226.0	12.0	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	hg19	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	G	2.175	-0.388855	0.04932	.	.	ENSG00000157060	ENST00000367547;ENST00000287709	T	0.49720	0.77	3.09	-0.43	0.12299	.	1.097780	0.07237	N	0.863539	T	0.20536	0.0494	N	0.03608	-0.345	0.20074	N	0.999933	B	0.02656	0.0	B	0.06405	0.002	T	0.17167	-1.0378	10	0.25106	T	0.35	.	3.5265	0.07761	0.0:0.3945:0.3188:0.2868	.	84	Q9BZQ2-3	.	E	84;153	ENSP00000356518:A84E	ENSP00000287709:A153E	A	-	2	0	SHCBP1L	181188641	0.000000	0.05858	0.012000	0.15200	0.187000	0.23431	-0.880000	0.04183	-0.078000	0.12730	0.205000	0.17691	GCG	.	.		0.751	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		T	182922018	G	T	182922018	3	4	149	1	0	0	0	0	1	0	0	0	2002	1087	38	1	1750	1	C1orf14	1	182922018	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	28859960	182922018	66328603	4	22668										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38103672	38103672	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	tgctgtaggcatctccctacCtggatgttcaaaactgacat	8	11	2	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:38103672C>A	ENST00000308059.6	+	4	707	c.686C>A	c.(685-687)cCt>cAt	p.P229H	DLEC1_ENST00000452631.2_Missense_Mutation_p.P229H|DLEC1_ENST00000346219.3_Missense_Mutation_p.P229H					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		ATCTCCCTACCTGGATGTTCA	0.453																																					p.P229H		Atlas-SNP	.											.	DLEC1	278	.	0			c.C686A						.						106	94	98					3																	38103672		1970	4157	6127	SO:0001583	missense	9940	exon4			CCCTACCTGGATG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.686C>A	chr3.hg19:g.38103672C>A	ENSP00000308597:p.Pro229His	79.0	0.0		86.0	34.0	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	13.77	2.336703	0.41398	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.07327	3.23;3.2;3.45	3.92	3.03	0.35002	.	0.163073	0.41194	D	0.000937	T	0.23965	0.0580	M	0.75777	2.31	0.19300	N	0.999979	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.992;0.992	T	0.01549	-1.1327	10	0.87932	D	0	-8.3179	8.0406	0.30519	0.0:0.8863:0.0:0.1137	.	229;229;229	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	H	229	ENSP00000308597:P229H;ENSP00000315914:P229H;ENSP00000410427:P229H	ENSP00000308597:P229H	P	+	2	0	DLEC1	38078676	0.078000	0.21339	0.109000	0.21407	0.016000	0.09150	1.634000	0.37123	1.193000	0.43086	0.655000	0.94253	CCT	.	.		0.453	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		A	38103672	C	A	38103672	3	1	149	1	0	0	0	0	1	0	0	0	4554	681	24	3	700	3	DLEC1	3	38103672	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10		38103672	159918758	5	22669										
BAP1	8314	hgsc.bcm.edu	37	chr3	52437901	52437901	+	Frame_Shift_Del	DEL	C	C	-													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	cctggcttccctgttcccttCcccttatacctgtggggccc							TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:52437901delC	ENST00000460680.1	-	13	1731	c.1260delG	c.(1258-1260)gggfs	p.G420fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.G402fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K421fs*11(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CTGTTCCCTTCCCCTTATACC	0.562			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.K421fs	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	1	Insertion - Frameshift(1)	kidney(1)	c.1261delA						.						76	80	78					3																	52437901		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon13			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1260delG	chr3.hg19:g.52437901delC	ENSP00000417132:p.Gly420fs	54.0	0.0		24.0	16.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.562	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52437901	C	-	52437901	7	5	149	1	0	1	0	1	0	0	0	0	1311	842	30	0	949	0	BAP1	3	52437901	Frame_Shift_Del	DEL	C	TCGA-DD-AA3A-01A-11D-A36X-10	14334229	52437901	145584529	6	22670										
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113755465	113755465	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	tccctcccacctgcttatgtCtcatctccatggtaagacga	6	15	2	1	rs529892538		TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:113755465C>T	ENST00000295878.3	-	5	730	c.584G>A	c.(583-585)aGa>aAa	p.R195K	KIAA1407_ENST00000545063.1_Missense_Mutation_p.R26K	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	195										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						CTGCTTATGTCTCATCTCCAT	0.373													C|||	1	0.000199681	0	0	5008	,	,		14349	0		0.001	False		,,,				2504	0				p.R195K		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G584A						.						243	227	232					3																	113755465		2203	4300	6503	SO:0001583	missense	57577	exon5			TTATGTCTCATCT	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.584G>A	chr3.hg19:g.113755465C>T	ENSP00000295878:p.Arg195Lys	137.0	0.0		195.0	74.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.750109	0.89753	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000;ENST00000483766	T;T;T	0.78003	-0.82;-1.14;-0.19	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.87669	0.6235	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.83275	0.996;0.99;0.996	D	0.86626	0.1882	10	0.44086	T	0.13	.	19.1032	0.93282	0.0:1.0:0.0:0.0	.	182;71;195	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	K	195;26;182;159	ENSP00000295878:R195K;ENSP00000446381:R26K;ENSP00000418099:R182K	ENSP00000295878:R195K	R	-	2	0	KIAA1407	115238155	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.748000	0.68697	2.734000	0.93682	0.650000	0.86243	AGA	.	.		0.373	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		T	113755465	C	T	113755465	3	4	149	1	0	0	0	0	1	0	0	0	8238	913	32	3	2278	3	KIAA1407	3	113755465	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	61317564	113755465	84266965	7	22671			1	24		5	4	86	N	C	6.495191e-13
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113755521	113755521	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ttcttgtcttggttttccttCcttccaagatcttccatcat	4	12	4	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:113755521C>T	ENST00000295878.3	-	5	674	c.528G>A	c.(526-528)agG>agA	p.R176R	KIAA1407_ENST00000545063.1_Silent_p.R7R	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	176										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						GGTTTTCCTTCCTTCCAAGAT	0.398																																					p.R176R		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G528A						.						242	220	227					3																	113755521		2203	4300	6503	SO:0001819	synonymous_variant	57577	exon5			TTCCTTCCTTCCA	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.528G>A	chr3.hg19:g.113755521C>T		150.0	0.0		207.0	81.0	NM_020817	B4DYL1|Q9P2E0	Silent	SNP	ENST00000295878.3	hg19	CCDS2977.1																																																																																			.	.		0.398	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		T	113755521	C	T	113755521	2	4	149	1	0	0	0	0	0	0	0	1	8238	854	30	3		3	KIAA1407	3	113755521	Silent	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	56	113755521	84266909	8	22672			1	24		5	4	86	N	C	6.495191e-13
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113755536	113755536	+	Missense_Mutation	SNP	C	C	T													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	tccttccttccaagatcttcCatcattgcagaatctaccac							TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:113755536C>T	ENST00000295878.3	-	5	659	c.513G>A	c.(511-513)atG>atA	p.M171I	KIAA1407_ENST00000545063.1_Missense_Mutation_p.M2I	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	171										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						CAAGATCTTCCATCATTGCAG	0.413																																					p.M171I		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G513A						.						211	191	197					3																	113755536		2203	4300	6503	SO:0001583	missense	57577	exon5			ATCTTCCATCATT	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.513G>A	chr3.hg19:g.113755536C>T	ENSP00000295878:p.Met171Ile	148.0	0.0		208.0	83.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.449946	0.43531	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000;ENST00000483766	T;T;T	0.47869	1.53;0.83;0.96	5.28	5.28	0.74379	.	0.308811	0.33040	N	0.005341	T	0.31009	0.0783	N	0.14661	0.345	0.80722	D	1	B;B;B	0.15719	0.002;0.014;0.003	B;B;B	0.12837	0.005;0.008;0.005	T	0.07654	-1.0761	10	0.36615	T	0.2	.	12.4291	0.55563	0.0:0.9237:0.0:0.0763	.	158;47;171	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	I	171;2;158;135	ENSP00000295878:M171I;ENSP00000446381:M2I;ENSP00000418099:M158I	ENSP00000295878:M171I	M	-	3	0	KIAA1407	115238226	0.998000	0.40836	0.998000	0.56505	0.987000	0.75469	1.375000	0.34295	2.734000	0.93682	0.650000	0.86243	ATG	.	.		0.413	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		T	113755536	C	T	113755536	3	4	149	1	0	0	0	0	1	0	0	0	8238	594	21	3	2349	3	KIAA1407	3	113755536	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	15	113755536	84266894	9	22673	99	2	1	24		5	4	86	N	C	6.495191e-13
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113755539	113755539	+	Missense_Mutation	SNP	C	C	T													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ttccttccaagatcttccatCattgcagaatctaccacatt							TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:113755539C>T	ENST00000295878.3	-	5	656	c.510G>A	c.(508-510)atG>atA	p.M170I	KIAA1407_ENST00000545063.1_Start_Codon_SNP_p.M1I	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	170										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						GATCTTCCATCATTGCAGAAT	0.428																																					p.M170I		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G510A						.						201	182	188					3																	113755539		2203	4300	6503	SO:0001583	missense	57577	exon5			TTCCATCATTGCA	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.510G>A	chr3.hg19:g.113755539C>T	ENSP00000295878:p.Met170Ile	151.0	0.0		204.0	81.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	5.721	0.317595	0.10845	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000;ENST00000483766	T;T;T	0.55413	1.68;0.52;1.1	5.28	-0.347	0.12617	.	0.411620	0.29087	N	0.013190	T	0.24586	0.0596	N	0.19112	0.55	0.31370	N	0.680314	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.31251	-0.9950	10	0.02654	T	1	.	4.2143	0.10526	0.1732:0.2622:0.0:0.5646	.	157;46;170	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	I	170;1;157;134	ENSP00000295878:M170I;ENSP00000446381:M1I;ENSP00000418099:M157I	ENSP00000295878:M170I	M	-	3	0	KIAA1407	115238229	0.144000	0.22641	0.261000	0.24466	0.969000	0.65631	0.371000	0.20450	0.028000	0.15324	0.650000	0.86243	ATG	.	.		0.428	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		T	113755539	C	T	113755539	3	4	149	1	0	0	0	0	1	0	0	0	8238	826	29	3	2352	3	KIAA1407	3	113755539	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	3	113755539	84266891	10	22674	99	2	1	24		5	4	86	N	C	6.495191e-13
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113755550	113755550	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	atcttccatcattgcagaatCtaccacatttttatggagca	5	10	3	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:113755550C>T	ENST00000295878.3	-	5	645	c.499G>A	c.(499-501)Gat>Aat	p.D167N	KIAA1407_ENST00000545063.1_5'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	167										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						ATTGCAGAATCTACCACATTT	0.428																																					p.D167N		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G499A						.						174	158	164					3																	113755550		2203	4300	6503	SO:0001583	missense	57577	exon5			CAGAATCTACCAC	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.499G>A	chr3.hg19:g.113755550C>T	ENSP00000295878:p.Asp167Asn	156.0	0.0		204.0	75.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.737220	0.49045	.	.	ENSG00000163617	ENST00000295878;ENST00000491000;ENST00000483766	T;T	0.49139	1.38;0.79	5.28	4.41	0.53225	.	0.313039	0.33382	N	0.004973	T	0.48892	0.1525	L	0.43152	1.355	0.80722	D	1	B;D;B	0.61080	0.084;0.989;0.084	B;P;B	0.55923	0.037;0.787;0.037	T	0.39099	-0.9630	10	0.24483	T	0.36	.	8.5385	0.33377	0.0:0.7835:0.0:0.2165	.	154;43;167	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	N	167;154;131	ENSP00000295878:D167N;ENSP00000418099:D154N	ENSP00000295878:D167N	D	-	1	0	KIAA1407	115238240	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.821000	0.39041	1.443000	0.47586	0.650000	0.86243	GAT	.	.		0.428	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		T	113755550	C	T	113755550	3	4	149	1	0	0	0	0	1	0	0	0	8238	913	32	3	2363	3	KIAA1407	3	113755550	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	11	113755550	84266880	11	22675			1	24		5	4	86	N	C	6.495191e-13
XRN1	54464	hgsc.bcm.edu	37	chr3	142030539	142030542	+	Frame_Shift_Del	DEL	ACTT	ACTT	-													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gctgatgagctctcccgtggActtactttgacaatgttgga							TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	ACTT	ACTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:142030539_142030542delACTT	ENST00000264951.4	-	42	5049_5052	c.4932_4935delAAGT	c.(4930-4935)gtaagtfs	p.VS1644fs	XRN1_ENST00000392981.2_Frame_Shift_Del_p.VS1632fs	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1644					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TCTCCCGTGGACTTACTTTGACAA	0.451																																					p.1645_1646del		Atlas-Indel,Pindel	.											.	XRN1	138	.	0			c.4933_4936del						.																																			SO:0001589	frameshift_variant	54464	exon42			.	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.4932_4935delAAGT	chr3.hg19:g.142030543_142030546delACTT	ENSP00000264951:p.Val1644fs	205.0	0.0		192.0	146.0	NM_019001	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Frame_Shift_Del	DEL	ENST00000264951.4	hg19	CCDS3123.1																																																																																			.	.		0.451	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		-	142030542	ACTT	-	142030539	7	5	149	1	0	1	0	1	0	0	0	0	17474	272	10	0	189	0	XRN1	3	142030539	Frame_Shift_Del	DEL	ACTT	TCGA-DD-AA3A-01A-11D-A36X-10	28274989	142030539	55991891	12	22676										
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73169792	73169792	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	atggcctgtagcctggttctTaatagctaaagggagaaaaa	11	6	1	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr4:73169792T>G	ENST00000286657.4	-	17	2302	c.2266A>C	c.(2266-2268)Aag>Cag	p.K756Q		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	756	Spacer.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GCCTGGTTCTTAATAGCTAAA	0.373																																					p.K756Q	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											.	ADAMTS3	164	.	0			c.A2266C						.						113	119	117					4																	73169792		2203	4300	6503	SO:0001583	missense	9508	exon17			GGTTCTTAATAGC	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.2266A>C	chr4.hg19:g.73169792T>G	ENSP00000286657:p.Lys756Gln	102.0	0.0		112.0	49.0	NM_014243	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	hg19	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.402314	0.83230	.	.	ENSG00000156140	ENST00000286657	T	0.59083	0.29	5.57	5.57	0.84162	ADAM-TS Spacer 1 (1);	0.000000	0.85682	D	0.000000	T	0.77445	0.4131	M	0.82056	2.57	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.80656	-0.1285	10	0.66056	D	0.02	.	15.7409	0.77894	0.0:0.0:0.0:1.0	.	756	O15072	ATS3_HUMAN	Q	756	ENSP00000286657:K756Q	ENSP00000286657:K756Q	K	-	1	0	ADAMTS3	73388656	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	7.950000	0.87804	2.120000	0.65058	0.533000	0.62120	AAG	.	.		0.373	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			G	73169792	T	G	73169792	3	3	149	1	0	0	0	0	1	0	0	0	267	1763	61	5	1375	5	ADAMTS3	4	73169792	Missense_Mutation	SNP	T	TCGA-DD-AA3A-01A-11D-A36X-10		73169792	117984484	13	22677										
DSPP	1834	hgsc.bcm.edu	37	chr4	88536436	88536436	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	agcgatagcagtgacagcagCaacagcagtgacagcagtga	13	9	0	3			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr4:88536436C>T	ENST00000282478.7	+	4	2655	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	DSPP_ENST00000399271.1_Silent_p.S874S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	874	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagcaacagcagtg	0.502																																					p.S874S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2622T						.						70	85	79					4																	88536436		1641	2936	4577	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCAACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2622C>T	chr4.hg19:g.88536436C>T		265.0	0.0		348.0	28.0	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.502	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88536436	C	T	88536436	2	4	149	1	0	0	0	0	0	0	0	1	4784	709	25	3		3	DSPP	4	88536436	Silent	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	15366644	88536436	102617840	14	22678										
FSTL5	56884	hgsc.bcm.edu	37	chr4	162421233	162421233	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ttcacattctatgggttgtaTcactttgattccatcttcat	5	9	5	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr4:162421233T>C	ENST00000306100.5	-	12	1829	c.1393A>G	c.(1393-1395)Ata>Gta	p.I465V	FSTL5_ENST00000427802.2_Missense_Mutation_p.I455V|FSTL5_ENST00000379164.4_Missense_Mutation_p.I464V|FSTL5_ENST00000536695.1_Missense_Mutation_p.I464V	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	465						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		ATGGGTTGTATCACTTTGATT	0.323																																					p.I465V		Atlas-SNP	.											.	FSTL5	207	.	0			c.A1393G						.						104	98	100					4																	162421233		2203	4299	6502	SO:0001583	missense	56884	exon12			GTTGTATCACTTT	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.1393A>G	chr4.hg19:g.162421233T>C	ENSP00000305334:p.Ile465Val	123.0	0.0		182.0	18.0	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	hg19	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.416852	0.42918	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.72505	-0.62;-0.6;-0.66;-0.6	5.29	4.11	0.48088	.	0.041760	0.85682	N	0.000000	T	0.66636	0.2809	M	0.62723	1.935	0.53005	D	0.999968	B;B;B	0.31077	0.083;0.307;0.172	B;B;B	0.33620	0.037;0.167;0.058	T	0.63278	-0.6673	10	0.38643	T	0.18	.	10.1207	0.42618	0.0:0.0799:0.0:0.9201	.	455;464;465	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	V	465;464;455;464	ENSP00000305334:I465V;ENSP00000368462:I464V;ENSP00000389270:I455V;ENSP00000440409:I464V	ENSP00000305334:I465V	I	-	1	0	FSTL5	162640683	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.761000	0.62243	0.961000	0.38030	0.460000	0.39030	ATA	.	.		0.323	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		C	162421233	T	C	162421233	3	2	149	1	0	0	0	0	1	0	0	0	6088	1435	50	2	1170	2	FSTL5	4	162421233	Missense_Mutation	SNP	T	TCGA-DD-AA3A-01A-11D-A36X-10	73884797	162421233	28733043	15	22679										
TCERG1	10915	hgsc.bcm.edu	37	chr5	145847914	145847914	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	cattttacaggtgtagcaatGatgcaaatagtcagctgccc	9	9	1	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr5:145847914G>T	ENST00000296702.5	+	6	1184	c.1146G>T	c.(1144-1146)atG>atT	p.M382I	TCERG1_ENST00000394421.2_Intron	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	382					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTGTAGCAATGATGCAAATAG	0.413																																					p.M382I		Atlas-SNP	.											.	TCERG1	148	.	0			c.G1146T						.						120	103	109					5																	145847914		2203	4300	6503	SO:0001583	missense	10915	exon6			AGCAATGATGCAA	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.1146G>T	chr5.hg19:g.145847914G>T	ENSP00000296702:p.Met382Ile	125.0	0.0		209.0	10.0	NM_006706	Q2NKN2|Q59EA1	Missense_Mutation	SNP	ENST00000296702.5	hg19	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.036131	0.54896	.	.	ENSG00000113649	ENST00000296702	T	0.25414	1.8	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.24084	0.0583	N	0.19112	0.55	0.80722	D	1	P	0.35872	0.525	B	0.42214	0.38	T	0.03473	-1.1033	10	0.20519	T	0.43	-12.432	19.3205	0.94236	0.0:0.0:1.0:0.0	.	382	O14776	TCRG1_HUMAN	I	382	ENSP00000296702:M382I	ENSP00000296702:M382I	M	+	3	0	TCERG1	145828107	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.567000	0.86603	0.563000	0.77884	ATG	.	.		0.413	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		T	145847914	G	T	145847914	3	4	149	1	0	0	0	0	1	0	0	0	15700	1290	45	3	1168	3	TCERG1	5	145847914	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10		145847914	35067346	16	22680										
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156941	26156941	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gtcgggttccttcaaactcaAcaagaaggcggcctctgggg	13	11	3	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr6:26156941A>C	ENST00000304218.3	+	1	383	c.323A>C	c.(322-324)aAc>aCc	p.N108T	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	108	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						TTCAAACTCAACAAGAAGGCG	0.612																																					p.N108T		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.A323C						.						34	40	38					6																	26156941		2203	4300	6503	SO:0001583	missense	3008	exon1			AACTCAACAAGAA	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"Histones / Replication-dependent"	4718	protein-coding gene	gene with protein product		142220	"H1 histone family, member 4", "histone 1, H1e"	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.323A>C	chr6.hg19:g.26156941A>C	ENSP00000307705:p.Asn108Thr	202.0	0.0		239.0	95.0	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	hg19	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	17.47	3.397487	0.62177	.	.	ENSG00000168298	ENST00000304218	T	0.09723	2.95	5.35	5.35	0.76521	Histone H1/H5 (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.153236	0.56097	D	0.000029	T	0.20901	0.0503	M	0.77103	2.36	0.58432	D	0.99999	D	0.60160	0.987	D	0.69142	0.962	T	0.01294	-1.1393	10	0.72032	D	0.01	-12.771	9.2621	0.37619	0.9099:0.0:0.0901:0.0	.	108	P10412	H14_HUMAN	T	108	ENSP00000307705:N108T	ENSP00000307705:N108T	N	+	2	0	HIST1H1E	26264920	0.848000	0.29623	1.000000	0.80357	0.940000	0.58332	0.218000	0.17622	2.146000	0.66826	0.459000	0.35465	AAC	.	.		0.612	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		C	26156941	A	C	26156941	3	2	149	1	0	0	0	0	1	0	0	0	7135	43	2	5	325	5	HIST1H1E	6	26156941	Missense_Mutation	SNP	A	TCGA-DD-AA3A-01A-11D-A36X-10		26156941	144958126	17	22681										
CALCR	799	hgsc.bcm.edu	37	chr7	93073038	93073038	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	agttgcaggccatcatgtacTggtggaaaaaatgcaaaatc	10	7	1	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr7:93073038T>A	ENST00000394441.1	-	8	995	c.680A>T	c.(679-681)cAg>cTg	p.Q227L	CALCR_ENST00000426151.1_Missense_Mutation_p.Q227L|CALCR_ENST00000359558.2_Missense_Mutation_p.Q261L|CALCR_ENST00000360249.4_Missense_Mutation_p.Q243L|CALCR_ENST00000421592.1_Missense_Mutation_p.Q243L	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	261					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CATCATGTACTGGTGGAAAAA	0.453																																					p.Q261L		Atlas-SNP	.											.	CALCR	200	.	0			c.A782T						.						119	112	114					7																	93073038		2203	4300	6503	SO:0001583	missense	799	exon11			ATGTACTGGTGGA	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"GPCR / Class B : Calcitonin receptors"	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.680A>T	chr7.hg19:g.93073038T>A	ENSP00000377959:p.Gln227Leu	135.0	0.0		186.0	67.0	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	hg19	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	T	6.496	0.459721	0.12342	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85	4.94	4.94	0.65067	.	.	.	.	.	T	0.32882	0.0844	N	0.24115	0.695	0.47123	D	0.999323	B;B	0.26195	0.144;0.023	B;B	0.31547	0.132;0.09	T	0.11155	-1.0599	9	0.02654	T	1	.	15.0839	0.72135	0.0:0.0:0.0:1.0	.	261;227	F5H605;A4D1G6	.;.	L	261;243;243;227;227	ENSP00000352561:Q261L;ENSP00000353385:Q243L;ENSP00000399552:Q243L;ENSP00000377959:Q227L;ENSP00000389295:Q227L	ENSP00000352561:Q261L	Q	-	2	0	CALCR	92910974	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.051000	0.57412	2.223000	0.72356	0.455000	0.32223	CAG	.	.		0.453	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		A	93073038	T	A	93073038	3	1	149	1	0	0	0	0	1	0	0	0	2581	1580	55	4	768	4	CALCR	7	93073038	Missense_Mutation	SNP	T	TCGA-DD-AA3A-01A-11D-A36X-10		93073038	66065625	18	22682										
SULF1	23213	hgsc.bcm.edu	37	chr8	70551053	70551053	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gagctcagaagctgtcaaggAtataagcagtgcaacccaag	11	9	2	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr8:70551053A>G	ENST00000260128.4	+	21	3228	c.2511A>G	c.(2509-2511)ggA>ggG	p.G837G	SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000402687.4_Silent_p.G837G|SULF1_ENST00000458141.2_Silent_p.G837G|SULF1_ENST00000419716.3_Silent_p.G837G	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	837					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			GCTGTCAAGGATATAAGCAGT	0.393																																					p.G837G		Atlas-SNP	.											.	SULF1	153	.	0			c.A2511G						.						93	81	85					8																	70551053		2203	4300	6503	SO:0001819	synonymous_variant	23213	exon21			TCAAGGATATAAG	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2511A>G	chr8.hg19:g.70551053A>G		297.0	0.0		401.0	27.0	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Silent	SNP	ENST00000260128.4	hg19	CCDS6204.1																																																																																			.	.		0.393	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		G	70551053	A	G	70551053	2	3	149	1	0	0	0	0	0	0	0	1	15385	320	12	2		2	SULF1	8	70551053	Silent	SNP	A	TCGA-DD-AA3A-01A-11D-A36X-10		70551053	75812969	19	22683										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77768190	77768190	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	accaaaccagagtgtaccctCtgcggggtgaagtactctgc	11	12	2	2			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr8:77768190C>T	ENST00000521891.2	+	10	9481	c.9033C>T	c.(9031-9033)ctC>ctT	p.L3011L	ZFHX4_ENST00000455469.2_Silent_p.L2966L|ZFHX4_ENST00000050961.6_Silent_p.L2966L|ZFHX4_ENST00000518282.1_Silent_p.L2985L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2966					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AGTGTACCCTCTGCGGGGTGA	0.463										HNSCC(33;0.089)																											p.L3011L		Atlas-SNP	.											.	ZFHX4	878	.	0			c.C9033T						.						48	47	48					8																	77768190		1928	4134	6062	SO:0001819	synonymous_variant	79776	exon10			TACCCTCTGCGGG		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.9033C>T	chr8.hg19:g.77768190C>T		162.0	0.0		215.0	83.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.463	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77768190	C	T	77768190	2	4	149	1	0	0	0	0	0	0	0	1	17650	900	32	3		3	ZFHX4	8	77768190	Silent	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	7217137	77768190	68595832	20	22684										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113301744	113301744	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	caggactgcattaggaggaaCgccagggtgtccacagtcaa	13	10	1	0	rs2193430	byFrequency	TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr8:113301744C>T	ENST00000297405.5	-	57	9242	c.8998G>A	c.(8998-9000)Gtt>Att	p.V3000I	CSMD3_ENST00000352409.3_Missense_Mutation_p.V2930I|CSMD3_ENST00000455883.2_Missense_Mutation_p.V2831I|CSMD3_ENST00000343508.3_Missense_Mutation_p.V2960I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3000	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.		V -> L (in dbSNP:rs2193430).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTAGGAGGAACGCCAGGGTGT	0.393										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.V3000I		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G8998A						.						60	51	54					8																	113301744		2203	4300	6503	SO:0001583	missense	114788	exon57			GAGGAACGCCAGG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8998G>A	chr8.hg19:g.113301744C>T	ENSP00000297405:p.Val3000Ile	45.0	0.0		59.0	19.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.568966	0.28003	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12	6.01	3.23	0.37069	Complement control module (2);Sushi/SCR/CCP (3);	0.456519	0.21299	N	0.076830	T	0.50103	0.1596	L	0.41710	1.295	0.22446	N	0.999095	B;B;B	0.15141	0.005;0.001;0.012	B;B;B	0.12837	0.002;0.004;0.008	T	0.36841	-0.9731	10	0.33940	T	0.23	.	9.7625	0.40541	0.0:0.7215:0.0:0.2785	.	2831;3000;2960	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	I	2960;3000;2270;2831;2930	ENSP00000345799:V2960I;ENSP00000297405:V3000I;ENSP00000341558:V2270I;ENSP00000412263:V2831I;ENSP00000343124:V2930I	ENSP00000297405:V3000I	V	-	1	0	CSMD3	113370920	0.142000	0.22610	0.502000	0.27614	0.912000	0.54170	0.333000	0.19768	0.415000	0.25817	-0.150000	0.13652	GTT	.	C|0.991;G|0.009		0.393	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113301744	C	T	113301744	3	4	149	1	0	0	0	0	1	0	0	0	3948	536	19	1	2185	1	CSMD3	8	113301744	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	35533554	113301744	33062278	21	22685										
ACO1	48	hgsc.bcm.edu	37	chr9	32434613	32434613	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gcctatgtgctgctaaatttGggagattcggtaacaactga	11	7	0	2			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr9:32434613G>T	ENST00000309951.6	+	17	2151	c.2013G>T	c.(2011-2013)ttG>ttT	p.L671F	ACO1_ENST00000379923.1_Missense_Mutation_p.L671F|ACO1_ENST00000541043.1_Missense_Mutation_p.L572F	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	671					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		TGCTAAATTTGGGAGATTCGG	0.438																																					p.L671F		Atlas-SNP	.											.	ACO1	149	.	0			c.G2013T						.						215	209	211					9																	32434613		2203	4300	6503	SO:0001583	missense	48	exon17			AAATTTGGGAGAT	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.2013G>T	chr9.hg19:g.32434613G>T	ENSP00000309477:p.Leu671Phe	130.0	0.0		114.0	5.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	hg19	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.268171	0.23136	.	.	ENSG00000122729	ENST00000432017;ENST00000309951;ENST00000379923;ENST00000541043	T;T;T	0.45668	0.89;0.89;1.92	5.78	3.93	0.45458	Aconitase/3-isopropylmalate dehydratase, swivel (2);	0.067179	0.64402	D	0.000010	T	0.35624	0.0938	L	0.52206	1.635	0.58432	D	0.999999	P;B	0.50369	0.934;0.153	P;B	0.45660	0.489;0.064	T	0.12863	-1.0531	10	0.16420	T	0.52	-11.8682	6.6508	0.22961	0.1578:0.0:0.6978:0.1444	.	707;671	Q59FI0;P21399	.;ACOC_HUMAN	F	707;671;671;572	ENSP00000309477:L671F;ENSP00000369255:L671F;ENSP00000438733:L572F	ENSP00000309477:L671F	L	+	3	2	ACO1	32424613	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	0.971000	0.29396	0.787000	0.33731	0.655000	0.94253	TTG	.	.		0.438	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		T	32434613	G	T	32434613	3	4	149	1	0	0	0	0	1	0	0	0	146	1339	47	3	2075	3	ACO1	9	32434613	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10		32434613	108778818	22	22686										
TLR4	7099	hgsc.bcm.edu	37	chr9	120476829	120476829	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	cctggggcggcacatcttctGgagacgactcagaaaagccc	12	13	3	2			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr9:120476829G>T	ENST00000355622.6	+	3	2524	c.2423G>T	c.(2422-2424)tGg>tTg	p.W808L	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.W768L	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	808	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.W808F(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	CACATCTTCTGGAGACGACTC	0.537																																					p.W808L		Atlas-SNP	.											.,1	TLR4	220	.	1	Substitution - Missense(1)	lung(1)	c.G2423T						.						95	98	97					9																	120476829		2203	4300	6503	SO:0001583	missense	7099	exon3			TCTTCTGGAGACG	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"CD molecules"	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.2423G>T	chr9.hg19:g.120476829G>T	ENSP00000363089:p.Trp808Leu	96.0	0.0		90.0	66.0	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	hg19	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.464376	0.84425	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.16073	2.37;2.37	6.03	6.03	0.97812	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.64402	D	0.000004	T	0.41949	0.1181	M	0.80982	2.52	0.58432	D	0.999999	D	0.69078	0.997	D	0.63381	0.914	T	0.20605	-1.0270	10	0.56958	D	0.05	.	14.4478	0.67364	0.0:0.0:0.8533:0.1467	.	808	O00206	TLR4_HUMAN	L	768;808	ENSP00000377997:W768L;ENSP00000363089:W808L	ENSP00000363089:W808L	W	+	2	0	TLR4	119516650	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.199000	0.77831	2.861000	0.98227	0.655000	0.94253	TGG	.	.		0.537	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		T	120476829	G	T	120476829	3	4	149	1	0	0	0	0	1	0	0	0	15968	1357	47	3	2433	3	TLR4	9	120476829	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	88042216	120476829	20736602	23	22687										
GPR158	57512	hgsc.bcm.edu	37	chr10	25887038	25887038	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	tgaccacgtgagagaccaaaCggaagagtccagtagcctac	11	11	0	4	rs143609365		TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr10:25887038C>T	ENST00000376351.3	+	11	2842	c.2483C>T	c.(2482-2484)aCg>aTg	p.T828M	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	828					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						AGAGACCAAACGGAAGAGTCC	0.468																																					p.T828M		Atlas-SNP	.											.	GPR158	255	.	0			c.C2483T						.						119	130	126					10																	25887038		2203	4300	6503	SO:0001583	missense	57512	exon11			ACCAAACGGAAGA	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.2483C>T	chr10.hg19:g.25887038C>T	ENSP00000365529:p.Thr828Met	367.0	0.0		440.0	168.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.105543	0.77096	.	.	ENSG00000151025	ENST00000376351	T	0.61158	0.13	5.88	5.88	0.94601	.	0.548889	0.17149	N	0.185152	T	0.46502	0.1396	N	0.22421	0.69	0.09310	N	1	D	0.53151	0.958	B	0.41619	0.361	T	0.48536	-0.9027	10	0.49607	T	0.09	.	15.6895	0.77439	0.0:0.8638:0.1362:0.0	.	828	Q5T848	GP158_HUMAN	M	828	ENSP00000365529:T828M	ENSP00000365529:T828M	T	+	2	0	GPR158	25927044	0.003000	0.15002	0.007000	0.13788	0.831000	0.47069	1.575000	0.36493	2.779000	0.95612	0.650000	0.86243	ACG	.	C|1.000;G|0.000		0.468	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		T	25887038	C	T	25887038	3	4	149	1	0	0	0	0	1	0	0	0	6671	536	19	1	2525	1	GPR158	10	25887038	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10		25887038	109647709	24	22688										
P4HA1	5033	hgsc.bcm.edu	37	chr10	74810844	74810844	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	tccccacggcacagcatttcGtacttctgtctctctggcag	8	15	3	0	rs200368222		TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr10:74810844G>T	ENST00000307116.2	-	7	983	c.867C>A	c.(865-867)taC>taA	p.Y289*	P4HA1_ENST00000412021.2_Nonsense_Mutation_p.Y289*|P4HA1_ENST00000440381.1_Nonsense_Mutation_p.Y289*|P4HA1_ENST00000373008.2_Nonsense_Mutation_p.Y289*|P4HA1_ENST00000394890.2_Nonsense_Mutation_p.Y289*|P4HA1_ENST00000263556.3_Nonsense_Mutation_p.Y289*			P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha polypeptide I	289					collagen fibril organization (GO:0030199)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|procollagen-proline 4-dioxygenase complex (GO:0016222)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	ACAGCATTTCGTACTTCTGTC	0.423																																					p.Y289X	Colon(147;367 2405 2662 52127)	Atlas-SNP	.											P4HA1_ENST00000412021,NS,carcinoma,0,3	P4HA1	86	.	0			c.C867A						.						300	283	289					10																	74810844		2203	4300	6503	SO:0001587	stop_gained	5033	exon7			CATTTCGTACTTC		CCDS7320.1, CCDS41537.1, CCDS44432.1	10q21.3-q23.1	2008-12-09	2008-12-09		ENSG00000122884	ENSG00000122884	1.14.11.2		8546	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(I)"	176710	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I"	P4HA		2556027	Standard	NM_001017962		Approved	C-P4Halpha(I)	uc001jtg.3	P13674	OTTHUMG00000018449	ENST00000307116.2:c.867C>A	chr10.hg19:g.74810844G>T	ENSP00000307318:p.Tyr289*	102.0	0.0		124.0	5.0	NM_001142596	C9JL12|Q15082|Q15083|Q5VSQ5	Nonsense_Mutation	SNP	ENST00000307116.2	hg19		.	.	.	.	.	.	.	.	.	.	G	37	6.359858	0.97502	.	.	ENSG00000122884	ENST00000307116;ENST00000373008;ENST00000412021;ENST00000394890;ENST00000263556;ENST00000440381	.	.	.	5.67	0.0145	0.14100	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.1147	6.1825	0.20480	0.4442:0.1275:0.4283:0.0	.	.	.	.	X	289	.	ENSP00000263556:Y289X	Y	-	3	2	P4HA1	74480850	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.176000	0.31957	0.187000	0.20147	0.557000	0.71058	TAC	.	.		0.423	P4HA1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000048601.1	NM_000917		T	74810844	G	T	74810844	4	4	149	1	0	0	0	0	0	1	0	0	11365	1140	40	1	848	1	P4HA1	10	74810844	Nonsense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	48923806	74810844	60723903	25	22689										
PRLHR	2834	hgsc.bcm.edu	37	chr10	120354129	120354142	+	Frame_Shift_Del	DEL	GGCGCACGTCGTGC	GGCGCACGTCGTGC	-													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gccccagaactcctcgcagaGgcgcacgtcgtgcggcttga					rs34269354|rs143477537|rs369106208	byFrequency	TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	GGCGCACGTCGTGC	GGCGCACGTCGTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr10:120354129_120354142delGGCGCACGTCGTGC	ENST00000369169.1	-	1	614_627	c.615_628delGCACGACGTGCGCC	c.(613-630)ccgcacgacgtgcgcctcfs	p.HDVRL206fs	PRLHR_ENST00000239032.2_Frame_Shift_Del_p.HDVRL206fs			P49683	PRLHR_HUMAN	prolactin releasing hormone receptor	206					feeding behavior (GO:0007631)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|hormone metabolic process (GO:0042445)|neuropeptide signaling pathway (GO:0007218)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)|neuropeptide Y receptor activity (GO:0004983)			large_intestine(2)|lung(8)|ovary(1)|skin(1)	12		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)		TCCTCGCAGAGGCGCACGTCGTGCGGCTTGAGCT	0.701																																					p.206_210del		Atlas-Indel,Pindel	.											.	PRLHR	41	.	0			c.616_629del						.																																			SO:0001589	frameshift_variant	2834	exon2			.	AB048946	CCDS7606.1	10q25.3-q26	2014-02-21	2005-11-24	2005-11-24	ENSG00000119973	ENSG00000119973		"GPCR / Class A : RF amide peptide receptors"	4464	protein-coding gene	gene with protein product		600895	"G protein-coupled receptor 10"	GPR10		8666380, 15885496	Standard	NM_004248		Approved	PrRPR	uc001ldp.1	P49683	OTTHUMG00000019136	ENST00000369169.1:c.615_628delGCACGACGTGCGCC	chr10.hg19:g.120354129_120354142delGGCGCACGTCGTGC	ENSP00000358167:p.His206fs	68.0	0.0		72.0	16.0	NM_004248	O75194|Q502U8|Q5VXR9	Frame_Shift_Del	DEL	ENST00000369169.1	hg19	CCDS7606.1																																																																																			.	.		0.701	PRLHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050610.1	NM_004248		-	120354142	GGCGCACGTCGTGC	-	120354129	7	5	149	1	0	1	0	1	0	0	0	0	12542	1000	35	0	488	0	PRLHR	10	120354129	Frame_Shift_Del	DEL	GGCGCACGTCGTGC	TCGA-DD-AA3A-01A-11D-A36X-10	45543285	120354129	15180618	26	22690										
CHID1	66005	hgsc.bcm.edu	37	chr11	870164	870179	+	Splice_Site	DEL	CTGCAAGACAAAGGGA	CTGCAAGACAAAGGGA	-													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	cgtgcctcccactgcggctcCtgcaagacaaagggactgtc							TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	CTGCAAGACAAAGGGA	CTGCAAGACAAAGGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:870164_870179delCTGCAAGACAAAGGGA	ENST00000449825.1	-	12	1397		c.e12-1		CHID1_ENST00000436108.2_Splice_Site|CHID1_ENST00000323578.8_Splice_Site|CHID1_ENST00000526714.1_5'Flank|CHID1_ENST00000528581.1_Splice_Site|CHID1_ENST00000454838.2_Splice_Site|CHID1_ENST00000429789.2_Splice_Site|CHID1_ENST00000336845.5_Splice_Site|CHID1_ENST00000323541.7_Splice_Site	NM_001142675.1	NP_001136147.1	Q9BWS9	CHID1_HUMAN	chitinase domain containing 1						carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|innate immune response (GO:0045087)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	chitinase activity (GO:0004568)|oligosaccharide binding (GO:0070492)			endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	13		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.48e-25)|Epithelial(43;3.75e-24)|BRCA - Breast invasive adenocarcinoma(625;4.65e-05)|Lung(200;0.0624)|LUSC - Lung squamous cell carcinoma(625;0.0735)		ACTGCGGCTCCTGCAAGACAAAGGGACTGTCAGCCC	0.667																																					p.372_372del	Pancreas(117;992 2327 5172 41921)	Atlas-Indel,Pindel	.											.	CHID1	29	.	0			c.1116_1116del						.																																			SO:0001630	splice_region_variant	66005	exon13			.	AK124697	CCDS7722.1, CCDS44510.1, CCDS44511.1	11p15.5	2005-10-27			ENSG00000177830	ENSG00000177830			28474	protein-coding gene	gene with protein product		615692					Standard	NM_023947		Approved	MGC3234, FLJ42707	uc001lsm.3	Q9BWS9	OTTHUMG00000133314	ENST00000449825.1:c.1041-1TCCCTTTGTCTTGCAG>-	chr11.hg19:g.870164_870179delCTGCAAGACAAAGGGA		115.0	0.0		125.0	17.0	NM_001142676	B3KWB0|Q8NBM9|Q96CZ3|Q96S93|Q96SK0|Q9BY52	Frame_Shift_Del	DEL	ENST00000449825.1	hg19	CCDS7722.1																																																																																			.	.		0.667	CHID1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257112.1	NM_023947	Intron	-	870179	CTGCAAGACAAAGGGA	-	870164	8	5	149	1	0	1	0	1	0	0	1	0	3347	695	24	0	149	0	CHID1	11	870164	Splice_Site	DEL	CTGCAAGACAAAGGGA	TCGA-DD-AA3A-01A-11D-A36X-10		870164	134136352	27	22691										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66472298	66472298	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	cacctcgggcgtgcggctcaGtgtggggggcagggctgctg	20	11	1	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:66472298G>A	ENST00000533211.1	-	15	2780	c.2449C>T	c.(2449-2451)Ctg>Ttg	p.L817L	SPTBN2_ENST00000529997.1_Silent_p.L817L|SPTBN2_ENST00000309996.2_Silent_p.L817L			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	817					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GTGCGGCTCAGTGTGGGGGGC	0.721																																					p.L817L		Atlas-SNP	.											.	SPTBN2	188	.	0			c.C2449T						.						19	20	20					11																	66472298		2200	4292	6492	SO:0001819	synonymous_variant	6712	exon14			GGCTCAGTGTGGG	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.2449C>T	chr11.hg19:g.66472298G>A		51.0	0.0		53.0	22.0	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	hg19	CCDS8150.1																																																																																			.	.		0.721	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		A	66472298	G	A	66472298	2	1	149	1	0	0	0	0	0	0	0	1	15135	1020	36	3		3	SPTBN2	11	66472298	Silent	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	65602134	66472298	68534218	28	22692										
SUV420H1	51111	hgsc.bcm.edu	37	chr11	67926442	67926442	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ttttgctccagccgcttgcaAtgatttctcaattttatctt	5	10	2	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:67926442A>G	ENST00000304363.4	-	11	1724	c.1371T>C	c.(1369-1371)caT>caC	p.H457H		NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	457					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						GCCGCTTGCAATGATTTCTCA	0.358																																					p.H457H		Atlas-SNP	.											.	SUV420H1	125	.	0			c.T1371C						.						77	81	80					11																	67926442		2200	4294	6494	SO:0001819	synonymous_variant	51111	exon11			CTTGCAATGATTT	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.1371T>C	chr11.hg19:g.67926442A>G		110.0	0.0		134.0	61.0	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Silent	SNP	ENST00000304363.4	hg19	CCDS31623.1																																																																																			.	.		0.358	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		G	67926442	A	G	67926442	2	3	149	1	0	0	0	0	0	0	0	1	15429	98	4	2		2	SUV420H1	11	67926442	Silent	SNP	A	TCGA-DD-AA3A-01A-11D-A36X-10	1454144	67926442	67080074	29	22693										
MMP7	4316	hgsc.bcm.edu	37	chr11	102395766	102395766	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	atgagccagcgtgtttcctgGcccatcaaatgggtaggagt	13	9	1	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:102395766G>A	ENST00000260227.4	-	4	566	c.514C>T	c.(514-516)Cca>Tca	p.P172S		NM_002423.3	NP_002414.1	P09237	MMP7_HUMAN	matrix metallopeptidase 7 (matrilysin, uterine)	172					antibacterial peptide secretion (GO:0002779)|collagen catabolic process (GO:0030574)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_cancers(8;2.04e-05)|all_epithelial(12;0.00053)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0105)|all cancers(10;0.0496)|Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0147)	Marimastat(DB00786)	GTGTTTCCTGGCCCATCAAAT	0.473																																					p.P172S		Atlas-SNP	.											.	MMP7	27	.	0			c.C514T						.						90	76	81					11																	102395766		2203	4299	6502	SO:0001583	missense	4316	exon4			TTCCTGGCCCATC	Z11887	CCDS8317.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000137673	ENSG00000137673	3.4.24.23		7174	protein-coding gene	gene with protein product		178990	"matrix metalloproteinase 7 (matrilysin, uterine)"	MPSL1		8978768	Standard	NM_002423		Approved	PUMP-1	uc001phb.3	P09237	OTTHUMG00000048193	ENST00000260227.4:c.514C>T	chr11.hg19:g.102395766G>A	ENSP00000260227:p.Pro172Ser	135.0	0.0		149.0	52.0	NM_002423	Q9BTK9	Missense_Mutation	SNP	ENST00000260227.4	hg19	CCDS8317.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.208178	0.58343	.	.	ENSG00000137673	ENST00000260227	T	0.20738	2.05	5.12	5.12	0.69794	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.123708	0.34133	N	0.004235	T	0.41903	0.1179	M	0.79011	2.435	0.09310	N	0.999999	D;D	0.65815	0.995;0.995	P;P	0.59487	0.858;0.746	T	0.36744	-0.9735	10	0.72032	D	0.01	-23.0146	11.6743	0.51422	0.0:0.1318:0.732:0.1362	.	172;172	Q53GF1;P09237	.;MMP7_HUMAN	S	172	ENSP00000260227:P172S	ENSP00000260227:P172S	P	-	1	0	MMP7	101900976	0.646000	0.27295	0.995000	0.50966	0.745000	0.42441	2.377000	0.44300	2.399000	0.81585	0.655000	0.94253	CCA	.	.		0.473	MMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109633.2			A	102395766	G	A	102395766	3	1	149	1	0	0	0	0	1	0	0	0	9676	1203	42	3	301	3	MMP7	11	102395766	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	34469324	102395766	32610750	30	22694										
PCSK7	9159	hgsc.bcm.edu	37	chr11	117097882	117097882	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gcacaagttacctgcgatgcGgctcccgtaggccacgccca	11	16	0	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:117097882G>A	ENST00000320934.3	-	5	1390	c.760C>T	c.(760-762)Cgc>Tgc	p.R254C	PCSK7_ENST00000540028.1_5'Flank	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	254	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CCTGCGATGCGGCTCCCGTAG	0.582			T	IGH@	MLCLS						OREG0021371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R254C		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.C760T						.						80	65	70					11																	117097882		2201	4296	6497	SO:0001583	missense	9159	exon5			CGATGCGGCTCCC	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.760C>T	chr11.hg19:g.117097882G>A	ENSP00000325917:p.Arg254Cys	57.0	0.0	1478	70.0	20.0	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	hg19	CCDS8382.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.234474	0.79800	.	.	ENSG00000160613	ENST00000320934;ENST00000543900;ENST00000525027	D;T	0.82081	-1.57;0.85	5.61	4.61	0.57282	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.170822	0.48767	D	0.000170	D	0.90034	0.6888	M	0.82056	2.57	0.80722	D	1	D	0.76494	0.999	P	0.60886	0.88	D	0.91478	0.5202	10	0.87932	D	0	-27.6348	16.3613	0.83269	0.0:0.0:0.8594:0.1406	.	254	Q16549	PCSK7_HUMAN	C	254	ENSP00000325917:R254C;ENSP00000431181:R254C	ENSP00000325917:R254C	R	-	1	0	PCSK7	116603092	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.071000	0.57556	2.633000	0.89246	0.655000	0.94253	CGC	.	.		0.582	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		A	117097882	G	A	117097882	3	1	149	1	0	0	0	0	1	0	0	0	11614	1116	39	1	1649	1	PCSK7	11	117097882	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	14702116	117097882	17908634	31	22695										
GLB1L3	112937	hgsc.bcm.edu	37	chr11	134179570	134179570	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	aatatgagatctccttcaatGtatatatgttccatggtgga	8	6	2	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:134179570G>A	ENST00000431683.2	+	11	1012	c.1012G>A	c.(1012-1014)Gta>Ata	p.V338I		NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	338					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		CTCCTTCAATGTATATATGTT	0.438																																					p.V338I		Atlas-SNP	.											.	GLB1L3	102	.	0			c.G1012A						.						89	84	86					11																	134179570		1889	4097	5986	SO:0001583	missense	112937	exon11			TTCAATGTATATA		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.1012G>A	chr11.hg19:g.134179570G>A	ENSP00000396615:p.Val338Ile	102.0	0.0		109.0	47.0	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Missense_Mutation	SNP	ENST00000431683.2	hg19	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.977369	0.34848	.	.	ENSG00000166105	ENST00000431683	D	0.97850	-4.57	4.76	-2.19	0.07015	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.	.	.	.	D	0.91012	0.7173	N	0.13098	0.295	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.82725	-0.0315	9	0.37606	T	0.19	.	1.0589	0.01596	0.3603:0.1474:0.3414:0.1509	.	338	Q8NCI6	GLBL3_HUMAN	I	338	ENSP00000396615:V338I	ENSP00000396615:V338I	V	+	1	0	GLB1L3	133684780	0.000000	0.05858	0.000000	0.03702	0.908000	0.53690	-0.110000	0.10824	-0.171000	0.10797	0.455000	0.32223	GTA	.	.		0.438	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416		A	134179570	G	A	134179570	3	1	149	1	0	0	0	0	1	0	0	0	6438	1377	48	3	1054	3	GLB1L3	11	134179570	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	17081688	134179570	826946	32	22696										
GALNT8	26290	hgsc.bcm.edu	37	chr12	4829970	4829970	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	tgtttacgggtggtctccacAgggagcttcctttacatctg	11	10	2	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:4829970A>T	ENST00000252318.2	+	1	464	c.127A>T	c.(127-129)Agg>Tgg	p.R43W	RP11-234B24.2_ENST00000527518.1_lincRNA|RP11-234B24.6_ENST00000544741.2_Intron	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	43					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						TGGTCTCCACAGGGAGCTTCC	0.473																																					p.R43W	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											.	GALNT8	89	.	0			c.A127T						.						100	102	101					12																	4829970		2203	4300	6503	SO:0001583	missense	26290	exon1			CTCCACAGGGAGC	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4130	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 8"	606250	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.127A>T	chr12.hg19:g.4829970A>T	ENSP00000252318:p.Arg43Trp	156.0	0.0		227.0	91.0	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	hg19	CCDS8533.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.471916	0.43942	.	.	ENSG00000130035	ENST00000252318	T	0.55052	0.54	3.74	0.084	0.14436	.	119.586000	0.00166	N	0.000000	T	0.30572	0.0769	N	0.08118	0	0.09310	N	1	P	0.38788	0.647	B	0.32289	0.143	T	0.31943	-0.9925	10	0.66056	D	0.02	.	5.7037	0.17897	0.6194:0.0:0.3806:0.0	.	43	Q9NY28	GALT8_HUMAN	W	43	ENSP00000252318:R43W	ENSP00000252318:R43W	R	+	1	2	GALNT8	4700231	0.000000	0.05858	0.001000	0.08648	0.474000	0.32979	-0.094000	0.11094	0.147000	0.19030	0.374000	0.22700	AGG	.	.		0.473	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417		T	4829970	A	T	4829970	3	4	149	1	0	0	0	0	1	0	0	0	6227	179	7	4	129	4	GALNT8	12	4829970	Missense_Mutation	SNP	A	TCGA-DD-AA3A-01A-11D-A36X-10		4829970	129021925	33	22697										
PRB3	5544	hgsc.bcm.edu	37	chr12	11421025	11421025	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gtccttctggctttcctggaGgaggtggggtacgttggggc	18	8	1	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:11421025G>C	ENST00000279573.7	-	3	293	c.158C>G	c.(157-159)cCt>cGt	p.P53R	PRB3_ENST00000381842.3_Missense_Mutation_p.P53R|PRB3_ENST00000538488.1_Missense_Mutation_p.P53R|PRB3_ENST00000440870.3_5'UTR			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	53	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.		P -> C (in Gl-8; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:2171329}.	PQRTPPP -> SQGPPPR (in Ref. 1; CAA30728). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			CTTTCCTGGAGGAGGTGGGGT	0.607																																					p.P53R		Atlas-SNP	.											PRB3_ENST00000538488,NS,malignant_melanoma,0,4	PRB3	84	.	0			c.C158G						.						156	164	161					12																	11421025		2195	4297	6492	SO:0001583	missense	5544	exon3			CCTGGAGGAGGTG			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.158C>G	chr12.hg19:g.11421025G>C	ENSP00000279573:p.Pro53Arg	69.0	2.0		100.0	6.0	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	hg19		.	.	.	.	.	.	.	.	.	.	.	0.001	-3.726183	0.00005	.	.	ENSG00000197870	ENST00000381842;ENST00000538488	T;T	0.09630	2.96;2.96	0.522	-1.04	0.10068	.	0.000000	0.35677	U	0.003053	T	0.02455	0.0075	.	.	.	0.09310	N	1	P	0.41748	0.761	B	0.31869	0.137	T	0.50759	-0.8790	8	0.05959	T	0.93	.	.	.	.	.	53	Q04118	PRB3_HUMAN	R	53	ENSP00000371264:P53R;ENSP00000442626:P53R	ENSP00000279573:P53R	P	-	2	0	PRB3	11312292	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-2.740000	0.00799	-3.021000	0.00269	-4.297000	0.00007	CCT	.	.		0.607	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249		C	11421025	G	C	11421025	3	2	149	1	0	0	0	0	1	0	0	0	12456	1000	35	4	779	4	PRB3	12	11421025	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	6591055	11421025	122430870	34	22698										
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50190546	50190546	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	acttagacagctgtgggggcGcctggtctggggaggatgac	18	8	1	2	rs369718554		TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:50190546G>A	ENST00000335999.6	-	8	1298	c.1097C>T	c.(1096-1098)gCg>gTg	p.A366V		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	362	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CTGTGGGGGCGCCTGGTCTGG	0.657																																					p.A366V		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.C1097T						.	G	VAL/ALA	1,3805		0,1,1902	25	30	28		1097	2.7	0.9	12		28	0,8186		0,0,4093	no	missense	NCKAP5L	NM_001037806.3	64	0,1,5995	AA,AG,GG		0.0,0.0263,0.0083	benign	366/1335	50190546	1,11991	1903	4093	5996	SO:0001583	missense	57701	exon8			GGGGGCGCCTGGT	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.1097C>T	chr12.hg19:g.50190546G>A	ENSP00000337998:p.Ala366Val	84.0	0.0		87.0	26.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Missense_Mutation	SNP	ENST00000335999.6	hg19	CCDS41781.2	.	.	.	.	.	.	.	.	.	.	G	18.52	3.642759	0.67244	2.63E-4	0.0	ENSG00000167566	ENST00000335999;ENST00000354423	T	0.44881	0.91	3.6	2.71	0.32032	.	0.202420	0.24864	N	0.034983	T	0.22742	0.0549	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.16837	-1.0389	10	0.32370	T	0.25	-7.3521	12.1469	0.54028	0.0:0.8229:0.1771:0.0	.	362	E2QRB5	.	V	366;362	ENSP00000337998:A366V	ENSP00000337998:A366V	A	-	2	0	NCKAP5L	48476813	0.000000	0.05858	0.897000	0.35233	0.927000	0.56198	0.510000	0.22723	0.875000	0.35847	-0.384000	0.06662	GCG	.	.		0.657	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		A	50190546	G	A	50190546	3	1	149	1	0	0	0	0	1	0	0	0	10233	1087	38	1	2931	1	NCKAP5L	12	50190546	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	38769521	50190546	83661349	35	22699										
KRT2	3849	hgsc.bcm.edu	37	chr12	53045631	53045632	+	In_Frame_Ins	INS	-	-	CGCCTCCAAAGCCGCTGC													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gccacctccaaagctgctgcINScgcctccaaaaccacctcct							TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:53045631_53045632insCGCCTCCAAAGCCGCTGC	ENST00000309680.3	-	1	316_317	c.295_296insGCAGCGGCTTTGGAGGCG	c.(295-297)ggc>gGCAGCGGCTTTGGAGGCGgc	p.99_99G>GSGFGGG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	99	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		aaagctgctgccgcctccaaaa	0.619																																					p.G99delinsGSGFGGG		Atlas-INDEL	.											.	KRT2	94	.	0			c.296_297insGCAGCGGCTTTGGAGGCG						.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.295_296insGCAGCGGCTTTGGAGGCG	chr12.hg19:g.53045631_53045632insCGCCTCCAAAGCCGCTGC	Exception_encountered	165.0	0.0		196.0	43.0	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.619	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		CGCCTCCAAAGCCGCTGC	53045632	-	CGCCTCCAAAGCCGCTGC	53045631	7	5	149	1	0	1	1	0	0	0	0	0	8466	739	26	0	1659	0	KRT2	12	53045631	In_Frame_Ins	INS	-	TCGA-DD-AA3A-01A-11D-A36X-10	2855085	53045631	80806264	36	22700										
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56566407	56566407	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ttttgtgtacatgtctgtgcGcagcccaaagttttgcatgt	10	8	1	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:56566407G>A	ENST00000267064.4	-	18	1818	c.1732C>T	c.(1732-1734)Cgc>Tgc	p.R578C	SMARCC2_ENST00000394023.3_Missense_Mutation_p.R609C|SMARCC2_ENST00000550164.1_Missense_Mutation_p.R609C|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000347471.4_Missense_Mutation_p.R609C	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	578					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			ATGTCTGTGCGCAGCCCAAAG	0.498																																					p.R609C		Atlas-SNP	.											.	SMARCC2	212	.	0			c.C1825T						.						212	190	198					12																	56566407		2203	4300	6503	SO:0001583	missense	6601	exon19			CTGTGCGCAGCCC	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.1732C>T	chr12.hg19:g.56566407G>A	ENSP00000267064:p.Arg578Cys	104.0	0.0		133.0	23.0	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.568502	0.65651	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T	0.51574	0.76;0.79;0.7	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.73353	0.3576	M	0.88906	2.99	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.80764	0.985;0.994;0.985;0.985;0.994	T	0.74893	-0.3509	10	0.35671	T	0.21	-9.4038	17.8293	0.88676	0.0:0.0:1.0:0.0	.	498;609;613;578;609	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	C	609;609;609;578	ENSP00000449396:R609C;ENSP00000302919:R609C;ENSP00000267064:R578C	ENSP00000267064:R578C	R	-	1	0	SMARCC2	54852674	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.496000	0.66918	2.575000	0.86900	0.462000	0.41574	CGC	.	.		0.498	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			A	56566407	G	A	56566407	3	1	149	1	0	0	0	0	1	0	0	0	14791	1087	38	1	1956	1	SMARCC2	12	56566407	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	3520776	56566407	77285488	37	22701										
LTA4H	4048	hgsc.bcm.edu	37	chr12	96394788	96394788	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	taatccacttttaagtctttCcccaccagcattgcagtcac	4	14	2	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:96394788C>T	ENST00000228740.2	-	19	1956	c.1815G>A	c.(1813-1815)ggG>ggA	p.G605G	LTA4H_ENST00000413268.2_3'UTR|LTA4H_ENST00000552789.1_Silent_p.G581G|RP11-256L6.3_ENST00000551849.1_RNA	NM_000895.2	NP_000886.1	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase	605					arachidonic acid metabolic process (GO:0019369)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|peptide catabolic process (GO:0043171)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|leukotriene-A4 hydrolase activity (GO:0004463)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(3)|lung(4)|skin(2)|stomach(1)	12					Captopril(DB01197)	TTAAGTCTTTCCCCACCAGCA	0.408																																					p.G605G		Atlas-SNP	.											.	LTA4H	38	.	0			c.G1815A						.						130	120	123					12																	96394788		2203	4300	6503	SO:0001819	synonymous_variant	4048	exon19			GTCTTTCCCCACC	BC032528	CCDS9059.1, CCDS58266.1, CCDS58267.1	12q22	2005-10-06				ENSG00000111144	3.3.2.6		6710	protein-coding gene	gene with protein product		151570				7628486	Standard	NM_000895		Approved		uc001ten.2	P09960	OTTHUMG00000170355	ENST00000228740.2:c.1815G>A	chr12.hg19:g.96394788C>T		86.0	0.0		124.0	11.0	NM_000895	B4DNQ9|F8VV40|Q6IAT6|Q9UCT7	Silent	SNP	ENST00000228740.2	hg19	CCDS9059.1																																																																																			.	.		0.408	LTA4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408655.1	NM_000895		T	96394788	C	T	96394788	2	4	149	1	0	0	0	0	0	0	0	1	9078	842	30	3		3	LTA4H	12	96394788	Silent	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	39828381	96394788	37457107	38	22702										
DAO	1610	hgsc.bcm.edu	37	chr12	109288134	109288134	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ctgcagccaggccgggggcaGatcatgaaggtgagtgtgag	18	8	1	4			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:109288134G>T	ENST00000228476.3	+	7	807	c.603G>T	c.(601-603)caG>caT	p.Q201H	DAO_ENST00000551281.1_Missense_Mutation_p.Q135H	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	201					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	GCCGGGGGCAGATCATGAAGG	0.537																																					p.Q201H		Atlas-SNP	.											.	DAO	58	.	0			c.G603T						.						50	40	43					12																	109288134		2203	4300	6503	SO:0001583	missense	1610	exon7			GGGGCAGATCATG	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.603G>T	chr12.hg19:g.109288134G>T	ENSP00000228476:p.Gln201His	126.0	0.0		129.0	55.0	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	hg19	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.740582	0.89573	.	.	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547768	D;D;D	0.82433	-1.61;-1.61;-1.61	5.51	5.51	0.81932	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.92619	0.7655	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.93376	0.6739	10	0.62326	D	0.03	-14.4171	18.047	0.89335	0.0:0.0:1.0:0.0	.	201;184	P14920;Q7Z312	OXDA_HUMAN;.	H	135;201;78	ENSP00000446853:Q135H;ENSP00000228476:Q201H;ENSP00000449967:Q78H	ENSP00000228476:Q201H	Q	+	3	2	DAO	107812263	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.747000	0.47475	2.609000	0.88269	0.499000	0.49734	CAG	.	.		0.537	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			T	109288134	G	T	109288134	3	4	149	1	0	0	0	0	1	0	0	0	4233	933	33	3	625	3	DAO	12	109288134	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	12893346	109288134	24563761	39	22703										
SBNO1	55206	hgsc.bcm.edu	37	chr12	123789129	123789129	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	atgtacaaatgaaaaaatacCttcttatatttcttttttag	3	5	2	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:123789129C>G	ENST00000602398.1	-	29	3895	c.3768G>C	c.(3766-3768)aaG>aaC	p.K1256N	SBNO1_ENST00000602750.1_Splice_Site_p.K1255N|SBNO1_ENST00000267176.4_Splice_Site_p.K1255N|SBNO1_ENST00000420886.2_Splice_Site_p.K1256N			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1256					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		GAAAAAATACCTTCTTATATT	0.348																																					p.K1256N		Atlas-SNP	.											.	SBNO1	138	.	0			c.G3768C						.						25	27	26					12																	123789129		2194	4292	6486	SO:0001630	splice_region_variant	55206	exon28			AAATACCTTCTTA	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.3768+1G>C	chr12.hg19:g.123789129C>G		342.0	1.0		427.0	153.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	hg19	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.541803	0.85917	.	.	ENSG00000139697	ENST00000420886;ENST00000267176	D;D	0.83163	-1.69;-1.69	6.17	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.90724	0.7089	M	0.84219	2.685	0.80722	D	1	P;P;D	0.67145	0.455;0.59;0.996	B;B;D	0.64595	0.111;0.223;0.927	D	0.90685	0.4608	9	.	.	.	-21.7595	15.9972	0.80260	0.0:0.935:0.0:0.065	.	1256;1255;367	A3KN83;A3KN83-2;B3KUC1	SBNO1_HUMAN;.;.	N	1256;1255	ENSP00000387361:K1256N;ENSP00000267176:K1255N	.	K	-	3	2	SBNO1	122355082	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	5.704000	0.68347	2.941000	0.99782	0.655000	0.94253	AAG	.	.		0.348	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	Missense_Mutation	G	123789129	C	G	123789129	5	3	149	1	0	0	0	0	0	0	1	0	13877	695	24	4	429	4	SBNO1	12	123789129	Splice_Site	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	14500995	123789129	10062766	40	22704										
INO80	54617	hgsc.bcm.edu	37	chr15	41313209	41313209	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ccagtctgcagccagttcagGggccccattcaacaaacact	8	15	3	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr15:41313209G>C	ENST00000361937.3	-	26	3587	c.3163C>G	c.(3163-3165)Cct>Gct	p.P1055A	INO80_ENST00000401393.3_Missense_Mutation_p.P1055A|RP11-540O11.4_ENST00000558967.1_RNA			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1055	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GCCAGTTCAGGGGCCCCATTC	0.507																																					p.P1055A		Atlas-SNP	.											INOC1,NS,malignant_melanoma,0,2	INO80	122	.	0			c.C3163G						.						81	74	76					15																	41313209		2203	4300	6503	SO:0001583	missense	54617	exon26			GTTCAGGGGCCCC	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.3163C>G	chr15.hg19:g.41313209G>C	ENSP00000355205:p.Pro1055Ala	86.0	0.0		83.0	36.0	NM_017553	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	hg19	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137486	0.77775	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.91407	-2.84;-2.84	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.93628	0.7965	L	0.49126	1.545	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.91614	0.5305	10	0.28530	T	0.3	.	19.0427	0.93008	0.0:0.0:1.0:0.0	.	1055	Q9ULG1	INO80_HUMAN	A	1055	ENSP00000355205:P1055A;ENSP00000384686:P1055A	ENSP00000355205:P1055A	P	-	1	0	INO80	39100501	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.669000	0.91163	2.722000	0.93159	0.655000	0.94253	CCT	.	.		0.507	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		C	41313209	G	C	41313209	3	2	149	1	0	0	0	0	1	0	0	0	7755	1232	43	4	1551	4	INO80	15	41313209	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10		41313209	61218183	41	22705										
ADAM10	102	hgsc.bcm.edu	37	chr15	58891888	58891888	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ccagccattagcatgatcagAgcaattcccataagtaatac	6	11	1	2			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr15:58891888A>C	ENST00000260408.3	-	15	2504	c.2061T>G	c.(2059-2061)gcT>gcG	p.A687A	ADAM10_ENST00000402627.1_Intron|ADAM10_ENST00000396140.2_Silent_p.A386A|ADAM10_ENST00000561288.1_Intron|snoU13_ENST00000458913.1_RNA	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	687					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		GCATGATCAGAGCAATTCCCA	0.338																																					p.A687A		Atlas-SNP	.											.	ADAM10	59	.	0			c.T2061G						.						125	122	123					15																	58891888		2192	4292	6484	SO:0001819	synonymous_variant	102	exon15			GATCAGAGCAATT	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"ADAM metallopeptidase domain containing", "CD molecules"	188	protein-coding gene	gene with protein product		602192	"a disintegrin and metalloproteinase domain 10"			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.2061T>G	chr15.hg19:g.58891888A>C		127.0	0.0		144.0	56.0	NM_001110	B4DU28|Q10742|Q92650	Silent	SNP	ENST00000260408.3	hg19	CCDS10167.1																																																																																			.	.		0.338	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110		C	58891888	A	C	58891888	2	2	149	1	0	0	0	0	0	0	0	1	234	291	11	5		5	ADAM10	15	58891888	Silent	SNP	A	TCGA-DD-AA3A-01A-11D-A36X-10	17578679	58891888	43639504	42	22706										
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11214572	11214670	+	Splice_Site	DEL	TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	-													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	cagatgagtttggtggagccTgatgtgtccaggcttggctg					rs3217121|rs200560039|rs201962167|rs555596086|rs374910952|rs201061352|rs199864914|rs397699050|rs58648897|rs56282757|rs12925474|rs113276201|rs201455904|rs544295262|rs201350159|rs557770599|rs112965500|rs369310040|rs199582436|rs200624127|rs201460026	byFrequency	TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr16:11214572_11214670delTGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	ENST00000409790.1	+	20	2447_2498	c.2217_2268delTGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	c.(2215-2268)cctgatgtgtccaggcttggctggggagtggtcaagtttgcaggcctattgcag>cc	p.PDVSRLGWGVVKFAGLLQ739del	CLEC16A_ENST00000409552.3_Splice_Site_p.PDVSRLGWGVVKFAGLLQ721del|CLEC16A_ENST00000465491.1_3'UTR	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TGGTGGAGCCTGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTacaaacacacacacac	0.462																																					p.739_756del		Pindel	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.2216_2268del						.																																			SO:0001630	splice_region_variant	23274	exon19			.	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2268+1TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC>-	chr16.hg19:g.11214572_11214670delTGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC		42.0	0.0		48.0	10.0	NM_015226		Frame_Shift_Del	DEL	ENST00000409790.1	hg19	CCDS45409.1																																																																																			.	.		0.462	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	In_Frame_Del	-	11214670	TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	-	11214572	8	5	149	1	0	1	0	1	0	0	1	0	3502	1567	55	0	2291	0	CLEC16A	16	11214572	Splice_Site	DEL	TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	TCGA-DD-AA3A-01A-11D-A36X-10		11214572	79140181	43	22707										
SNN	8303	hgsc.bcm.edu	37	chr16	11770176	11770176	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	cccaacggcccggaagtccaCggctgagccaggatgcaagg	14	14	0	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr16:11770176C>T	ENST00000329565.5	+	2	473	c.261C>T	c.(259-261)caC>caT	p.H87H	TXNDC11_ENST00000570917.1_5'Flank	NM_003498.5	NP_003489.1	O75324	SNN_HUMAN	stannin	87					response to abiotic stimulus (GO:0009628)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				endometrium(1)	1						CGGAAGTCCACGGCTGAGCCA	0.622																																					p.H87H		Atlas-SNP	.											.	SNN	7	.	0			c.C261T						.						58	39	46					16																	11770176		2197	4300	6497	SO:0001819	synonymous_variant	8303	exon2			AGTCCACGGCTGA	AF030196	CCDS10549.1	16p13	2008-02-05			ENSG00000184602	ENSG00000184602			11149	protein-coding gene	gene with protein product		603032				9657854	Standard	NM_003498		Approved		uc002dbf.3	O75324	OTTHUMG00000090535	ENST00000329565.5:c.261C>T	chr16.hg19:g.11770176C>T		133.0	0.0		154.0	60.0	NM_003498	D3DUG4|Q6FGI0	Silent	SNP	ENST00000329565.5	hg19	CCDS10549.1																																																																																			.	.		0.622	SNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207059.1	NM_003498		T	11770176	C	T	11770176	2	4	149	1	0	0	0	0	0	0	0	1	14864	535	19	1		1	SNN	16	11770176	Silent	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	555604	11770176	78584577	44	22708										
KRT33A	3883	hgsc.bcm.edu	37	chr17	39506775	39506775	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ggatgaggttctccagctccGcgttgtcccgctccagctga	12	14	1	2			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr17:39506775G>A	ENST00000007735.3	-	1	289	c.245C>T	c.(244-246)gCg>gTg	p.A82V		NM_004138.3	NP_004129.2	O76009	KT33A_HUMAN	keratin 33A	82	Coil 1A.|Rod.			A -> T (in Ref. 3; BAG36784). {ECO:0000305}.		extracellular space (GO:0005615)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	21		Breast(137;0.000496)				CTCCAGCTCCGCGTTGTCCCG	0.607																																					p.A82V		Atlas-SNP	.											.	KRT33A	53	.	0			c.C245T						.						91	84	86					17																	39506775		2203	4300	6503	SO:0001583	missense	3883	exon1			AGCTCCGCGTTGT	Y16788	CCDS11388.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000006059	ENSG00000006059		"-", "Intermediate filaments type I, keratins (acidic)"	6450	protein-coding gene	gene with protein product	"hard keratin type I 3I"	602761	"keratin, hair, acidic, 3A"	KRTHA3A		7565656, 16831889	Standard	NM_004138		Approved	Ha-3I, Krt1-3	uc002hwk.2	O76009	OTTHUMG00000133432	ENST00000007735.3:c.245C>T	chr17.hg19:g.39506775G>A	ENSP00000007735:p.Ala82Val	148.0	0.0		212.0	81.0	NM_004138	B2RA87|Q6NTB9|Q6ZZB9	Missense_Mutation	SNP	ENST00000007735.3	hg19	CCDS11388.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.422370	0.62622	.	.	ENSG00000006059	ENST00000007735	D	0.89415	-2.51	5.22	4.24	0.50183	Filament (1);	0.000000	0.64402	D	0.000004	D	0.89904	0.6850	M	0.84082	2.675	0.23959	N	0.99635	P	0.37176	0.586	B	0.39152	0.292	D	0.84981	0.0888	10	0.66056	D	0.02	.	13.8543	0.63517	0.0:0.2917:0.7083:0.0	.	82	O76009	KT33A_HUMAN	V	82	ENSP00000007735:A82V	ENSP00000007735:A82V	A	-	2	0	KRT33A	36760301	0.068000	0.21057	0.973000	0.42090	0.981000	0.71138	2.440000	0.44855	1.554000	0.49487	0.650000	0.86243	GCG	.	.		0.607	KRT33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257295.1	NM_004138		A	39506775	G	A	39506775	3	1	149	1	0	0	0	0	1	0	0	0	8478	1087	38	1	997	1	KRT33A	17	39506775	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10		39506775	41688435	45	22709										
ENOSF1	55556	hgsc.bcm.edu	37	chr18	712566	712566	+	Frame_Shift_Del	DEL	G	G	-													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	cacgtcccggaccgagagccGggagatcctgccgcgcacca							TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr18:712566delG	ENST00000251101.7	-	1	110	c.22delC	c.(22-24)cggfs	p.R8fs	ENOSF1_ENST00000383578.3_5'UTR|ENOSF1_ENST00000340116.7_5'Flank|ENOSF1_ENST00000539164.1_Frame_Shift_Del_p.R8fs|ENOSF1_ENST00000580982.1_Frame_Shift_Del_p.R8fs	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	8					cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						ACCGAGAGCCGGGAGATCCTG	0.761																																					p.R8fs		Atlas-Indel,Pindel	.											.	ENOSF1	44	.	0			c.23delG						.						5	5	5					18																	712566		1632	3121	4753	SO:0001589	frameshift_variant	55556	exon1			.	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.22delC	chr18.hg19:g.712566delG	ENSP00000251101:p.Arg8fs	153.0	0.0		197.0	71.0	NM_017512	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Frame_Shift_Del	DEL	ENST00000251101.7	hg19	CCDS11822.1																																																																																			.	.		0.761	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512		-	712566	G	-	712566	7	5	149	1	0	1	0	1	0	0	0	0	5127	1115	39	0	1517	0	ENOSF1	18	712566	Frame_Shift_Del	DEL	G	TCGA-DD-AA3A-01A-11D-A36X-10		712566	77364682	46	22710										
DSG3	1830	hgsc.bcm.edu	37	chr18	29039050	29039050	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	atgtagagaaaccacttataCtaacggttaaaattttggat	7	5	0	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr18:29039050C>T	ENST00000257189.4	+	5	510	c.427C>T	c.(427-429)Cta>Tta	p.L143L		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	143	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACCACTTATACTAACGGTTAA	0.353																																					p.L143L		Atlas-SNP	.											.	DSG3	172	.	0			c.C427T						.						78	79	78					18																	29039050		2203	4300	6503	SO:0001819	synonymous_variant	1830	exon5			CTTATACTAACGG	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.427C>T	chr18.hg19:g.29039050C>T		317.0	1.0		429.0	156.0	NM_001944	A8K2V2	Silent	SNP	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.353	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		T	29039050	C	T	29039050	2	4	149	1	0	0	0	0	0	0	0	1	4780	564	20	3		3	DSG3	18	29039050	Silent	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	28326484	29039050	49038198	47	22711										
ZBTB7C	201501	hgsc.bcm.edu	37	chr18	45567333	45567333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	tgcaggcagccaggacggagCggtgggtccgatactcctgc	16	12	0	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr18:45567333C>T	ENST00000588982.1	-	3	647	c.146G>A	c.(145-147)cGc>cAc	p.R49H	ZBTB7C_ENST00000535628.2_Missense_Mutation_p.R49H|ZBTB7C_ENST00000332053.2_Missense_Mutation_p.R49H|ZBTB7C_ENST00000590800.1_Missense_Mutation_p.R49H|ZBTB7C_ENST00000586438.1_Missense_Mutation_p.R49H			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	49	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						CAGGACGGAGCGGTGGGTCCG	0.597																																					p.R49H		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.G146A						.						80	74	76					18																	45567333		2203	4300	6503	SO:0001583	missense	201501	exon2			ACGGAGCGGTGGG	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	31700	protein-coding gene	gene with protein product			"zinc finger and BTB domain containing 36"	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.146G>A	chr18.hg19:g.45567333C>T	ENSP00000468782:p.Arg49His	77.0	0.0		81.0	28.0	NM_001039360	O73453	Missense_Mutation	SNP	ENST00000588982.1	hg19	CCDS32830.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.098628	0.76870	.	.	ENSG00000184828	ENST00000535628;ENST00000332053	T;T	0.75367	-0.93;-0.93	5.04	5.04	0.67666	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.90988	0.7166	H	0.98351	4.21	0.54753	D	0.999984	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.99;0.945;0.945	D	0.93689	0.7005	10	0.87932	D	0	.	12.7794	0.57469	0.0:0.9201:0.0:0.0799	.	49;49;49	B4DKU0;B2RG49;A1YPR0	.;.;ZBT7C_HUMAN	H	49	ENSP00000439781:R49H;ENSP00000328732:R49H	ENSP00000328732:R49H	R	-	2	0	ZBTB7C	43821331	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.083000	0.71326	2.332000	0.79248	0.561000	0.74099	CGC	.	.		0.597	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360		T	45567333	C	T	45567333	3	4	149	1	0	0	0	0	1	0	0	0	17570	768	27	1	1721	1	ZBTB7C	18	45567333	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	16528283	45567333	32509915	48	22712										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17100489	17100489	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ggtggctgcagctgcaggtaGcactggctgggggagtacca	18	9	0	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr19:17100489G>T	ENST00000443236.1	-	13	1531	c.1500C>A	c.(1498-1500)tgC>tgA	p.C500*	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	453						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GCTGCAGGTAGCACTGGCTGG	0.607																																					p.C500X		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C1500A						.						39	47	45					19																	17100489		1959	4136	6095	SO:0001587	stop_gained	27151	exon13			CAGGTAGCACTGG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1500C>A	chr19.hg19:g.17100489G>T	ENSP00000402505:p.Cys500*	131.0	0.0		137.0	71.0	NM_015692	Q8NC09|Q9ULD7	Nonsense_Mutation	SNP	ENST00000443236.1	hg19	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.185569|6.185569	0.97357|0.97357	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440	.|.	.|.	.|.	2.91|2.91	2.91|2.91	0.33838|0.33838	.|.	.|0.000000	.|0.64402	.|U	.|0.000001	T|.	0.55401|.	0.1918|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.49799|.	-0.8901|.	4|.	.|0.25106	.|T	.|0.35	.|.	10.1768|10.1768	0.42943|0.42943	0.1068:0.0:0.8932:0.0|0.1068:0.0:0.8932:0.0	.|.	.|.	.|.	.|.	D|X	511|500	.|.	.|ENSP00000291440:C500X	A|C	-|-	2|3	0|2	CPAMD8|CPAMD8	16961489|16961489	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.927000|0.927000	0.56198|0.56198	1.798000|1.798000	0.38814|0.38814	1.366000|1.366000	0.46076|0.46076	0.561000|0.561000	0.74099|0.74099	GCT|TGC	.	.		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17100489	G	T	17100489	4	4	149	1	0	0	0	0	0	1	0	0	3797	963	34	3	4418	3	CPAMD8	19	17100489	Nonsense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10		17100489	42028494	49	22713										
PAK4	10298	hgsc.bcm.edu	37	chr19	39663569	39663569	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ggaccccagaccatcgtgcgGggcagcaaaggtgccaaaga	14	12	0	2			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr19:39663569G>T	ENST00000593690.1	+	5	643	c.216G>T	c.(214-216)cgG>cgT	p.R72R	PAK4_ENST00000321944.4_Silent_p.R72R|PAK4_ENST00000360442.3_Silent_p.R72R|PAK4_ENST00000599470.1_Intron|PAK4_ENST00000435673.2_Silent_p.R72R|PAK4_ENST00000358301.3_Silent_p.R72R|PAK4_ENST00000599386.1_Intron	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	72	Linker.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			CCATCGTGCGGGGCAGCAAAG	0.647																																					p.R72R		Atlas-SNP	.											.	PAK4	40	.	0			c.G216T						.						17	17	17					19																	39663569		2069	3996	6065	SO:0001819	synonymous_variant	10298	exon3			CGTGCGGGGCAGC	AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"p21(CDKN1A)-activated kinase 4"			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.216G>T	chr19.hg19:g.39663569G>T		129.0	0.0		202.0	82.0	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Silent	SNP	ENST00000593690.1	hg19	CCDS12528.1																																																																																			.	.		0.647	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			T	39663569	G	T	39663569	2	4	149	1	0	0	0	0	0	0	0	1	11412	1219	43	3		3	PAK4	19	39663569	Silent	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	22563080	39663569	19465414	50	22714										
LRFN1	57622	hgsc.bcm.edu	37	chr19	39805727	39805727	+	Missense_Mutation	SNP	C	C	G													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gctggtcatgttggcgaagtCtcggcggcgcacggcggcga							TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr19:39805727C>G	ENST00000248668.4	-	1	249	c.250G>C	c.(250-252)Gac>Cac	p.D84H	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	84						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			TTGGCGAAGTCTCGGCGGCGC	0.697																																					p.D84H		Atlas-SNP	.											.	LRFN1	59	.	0			c.G250C						.						10	13	12					19																	39805727		2167	4251	6418	SO:0001583	missense	57622	exon1			CGAAGTCTCGGCG	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.250G>C	chr19.hg19:g.39805727C>G	ENSP00000248668:p.Asp84His	56.0	0.0		58.0	18.0	NM_020862	Q8TBS9	Missense_Mutation	SNP	ENST00000248668.4	hg19	CCDS46071.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.177334	0.78564	.	.	ENSG00000128011	ENST00000248668	T	0.56941	0.43	4.43	4.43	0.53597	.	0.000000	0.41823	D	0.000801	T	0.77343	0.4116	M	0.91663	3.23	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82890	-0.0233	10	0.66056	D	0.02	.	14.5711	0.68210	0.0:1.0:0.0:0.0	.	84	Q9P244	LRFN1_HUMAN	H	84	ENSP00000248668:D84H	ENSP00000248668:D84H	D	-	1	0	LRFN1	44497567	1.000000	0.71417	0.991000	0.47740	0.994000	0.84299	7.541000	0.82084	2.288000	0.76882	0.557000	0.71058	GAC	.	.		0.697	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862		G	39805727	C	G	39805727	3	3	149	1	0	0	0	0	1	0	0	0	8946	913	32	4	2073	4	LRFN1	19	39805727	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	142158	39805727	19323256	51	22715	100	2								
LRFN1	57622	hgsc.bcm.edu	37	chr19	39805729	39805729	+	Frame_Shift_Del	DEL	C	C	-													0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	tggtcatgttggcgaagtctCggcggcgcacggcggcgatg							TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr19:39805729delC	ENST00000248668.4	-	1	247	c.248delG	c.(247-249)cgafs	p.R83fs	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	83						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GGCGAAGTCTCGGCGGCGCAC	0.692																																					p.R83fs		Atlas-INDEL	.											.	LRFN1	59	.	0			c.249delA						.						10	13	12					19																	39805729		2160	4246	6406	SO:0001589	frameshift_variant	57622	exon1			.	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.248delG	chr19.hg19:g.39805729delC	ENSP00000248668:p.Arg83fs	55.0	0.0		58.0	18.0	NM_020862	Q8TBS9	Frame_Shift_Del	DEL	ENST00000248668.4	hg19	CCDS46071.1																																																																																			.	.		0.692	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862		-	39805729	C	-	39805729	7	5	149	1	0	1	0	1	0	0	0	0	8946	884	31	0	2075	0	LRFN1	19	39805729	Frame_Shift_Del	DEL	C	TCGA-DD-AA3A-01A-11D-A36X-10	2	39805729	19323254	52	22716	100	2								
SNAP25	6616	hgsc.bcm.edu	37	chr20	10273637	10273637	+	Intron	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gctgtggccttttcatatgtCcttgtaacaagtaggtactg	10	8	1	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr20:10273637C>G	ENST00000254976.2	+	5	374				SNAP25-AS1_ENST00000421143.2_RNA|SNAP25_ENST00000304886.2_Missense_Mutation_p.P91A|SNAP25-AS1_ENST00000453544.1_RNA	NM_130811.2	NP_570824.1	P60880	SNP25_HUMAN	synaptosomal-associated protein, 25kDa						energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long-term synaptic potentiation (GO:0060291)|neurotransmitter secretion (GO:0007269)|neurotransmitter uptake (GO:0001504)|regulation of establishment of protein localization (GO:0070201)|regulation of insulin secretion (GO:0050796)|regulation of neuron projection development (GO:0010975)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|SNARE complex (GO:0031201)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|trans-Golgi network (GO:0005802)	calcium-dependent protein binding (GO:0048306)			endometrium(1)|large_intestine(2)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	18					Botulinum Toxin Type A(DB00083)	TTTCATATGTCCTTGTAACAA	0.378																																					p.P91A		Atlas-SNP	.											.	SNAP25	79	.	0			c.C271G						.						100	99	100					20																	10273637		2203	4300	6503	SO:0001627	intron_variant	6616	exon5			ATATGTCCTTGTA		CCDS13109.1, CCDS13110.1	20p12-p11.2	2008-08-01	2002-08-29		ENSG00000132639	ENSG00000132639			11132	protein-coding gene	gene with protein product	"resistance to inhibitors of cholinesterase 4 homolog"	600322	"synaptosomal-associated protein, 25kD"	SNAP		8661740, 10692432	Standard	NM_003081		Approved	SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2	uc002wnr.2	P60880	OTTHUMG00000031863	ENST00000254976.2:c.164-172C>G	chr20.hg19:g.10273637C>G		137.0	0.0		149.0	31.0	NM_003081	B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45	Missense_Mutation	SNP	ENST00000254976.2	hg19	CCDS13110.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646403	0.67358	.	.	ENSG00000132639	ENST00000304886	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	T	0.64821	0.2633	.	.	.	0.80722	D	1	B	0.21452	0.056	B	0.25140	0.058	T	0.57106	-0.7868	7	0.44086	T	0.13	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	91	P60880-2	.	A	91	.	ENSP00000307341:P91A	P	+	1	0	SNAP25	10221637	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	CCT	.	.		0.378	SNAP25-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077976.3	NM_130811		G	10273637	C	G	10273637	1	3	149	0	1	0	0	0	0	0	0	0	14845	855	30	4		4	SNAP25	20	10273637	Intron	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10		10273637	52751883	53	22717										
SNAP25	6616	hgsc.bcm.edu	37	chr20	10273846	10273846	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gaggaagggatggaccaaatCaataaggacatgaaagaagc	13	5	1	2			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr20:10273846C>G	ENST00000254976.2	+	5	412	c.201C>G	c.(199-201)atC>atG	p.I67M	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25_ENST00000304886.2_Intron|SNAP25-AS1_ENST00000453544.1_RNA	NM_130811.2	NP_570824.1	P60880	SNP25_HUMAN	synaptosomal-associated protein, 25kDa	67	Interaction with CENPF. {ECO:0000250}.|t-SNARE coiled-coil homology 1. {ECO:0000255|PROSITE-ProRule:PRU00202}.				energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long-term synaptic potentiation (GO:0060291)|neurotransmitter secretion (GO:0007269)|neurotransmitter uptake (GO:0001504)|regulation of establishment of protein localization (GO:0070201)|regulation of insulin secretion (GO:0050796)|regulation of neuron projection development (GO:0010975)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|SNARE complex (GO:0031201)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|trans-Golgi network (GO:0005802)	calcium-dependent protein binding (GO:0048306)			endometrium(1)|large_intestine(2)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	18					Botulinum Toxin Type A(DB00083)	TGGACCAAATCAATAAGGACA	0.428																																					p.I67M		Atlas-SNP	.											.	SNAP25	79	.	0			c.C201G						.						150	160	157					20																	10273846		2203	4300	6503	SO:0001583	missense	6616	exon5			CCAAATCAATAAG		CCDS13109.1, CCDS13110.1	20p12-p11.2	2008-08-01	2002-08-29		ENSG00000132639	ENSG00000132639			11132	protein-coding gene	gene with protein product	"resistance to inhibitors of cholinesterase 4 homolog"	600322	"synaptosomal-associated protein, 25kD"	SNAP		8661740, 10692432	Standard	NM_003081		Approved	SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2	uc002wnr.2	P60880	OTTHUMG00000031863	ENST00000254976.2:c.201C>G	chr20.hg19:g.10273846C>G	ENSP00000254976:p.Ile67Met	212.0	0.0		236.0	88.0	NM_130811	B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45	Missense_Mutation	SNP	ENST00000254976.2	hg19	CCDS13110.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.400937	0.62177	.	.	ENSG00000132639	ENST00000254976;ENST00000430336	.	.	.	5.9	5.9	0.94986	Target SNARE coiled-coil domain (2);	0.000000	0.85682	D	0.000000	T	0.76385	0.3980	M	0.83312	2.635	0.80722	D	1	D	0.55605	0.972	P	0.53006	0.715	T	0.74746	-0.3561	9	0.33141	T	0.24	-7.9478	20.2789	0.98501	0.0:1.0:0.0:0.0	.	67	P60880	SNP25_HUMAN	M	67	.	ENSP00000254976:I67M	I	+	3	3	SNAP25	10221846	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.788000	0.95919	0.650000	0.86243	ATC	.	.		0.428	SNAP25-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077976.3	NM_130811		G	10273846	C	G	10273846	3	3	149	1	0	0	0	0	1	0	0	0	14845	816	29	4	337	4	SNAP25	20	10273846	Missense_Mutation	SNP	C	TCGA-DD-AA3A-01A-11D-A36X-10	209	10273846	52751674	54	22718										
SPAG4	6676	hgsc.bcm.edu	37	chr20	34204001	34204001	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	actttttcagcgagaacagcTcaatgagcatcacctcggag	9	11	3	2			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr20:34204001T>G	ENST00000374273.3	+	1	188	c.76T>G	c.(76-78)Tca>Gca	p.S26A		NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	26					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			CGAGAACAGCTCAATGAGCAT	0.682																																					p.S26A		Atlas-SNP	.											.	SPAG4	36	.	0			c.T76G						.						22	24	23					20																	34204001		2201	4295	6496	SO:0001583	missense	6676	exon1			AACAGCTCAATGA	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"acrosomal protein ACR55", "Sad1 and UNC84 domain containing 4", "cancer/testis antigen 127"	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.76T>G	chr20.hg19:g.34204001T>G	ENSP00000363391:p.Ser26Ala	131.0	0.0		151.0	34.0	NM_003116	O43648	Missense_Mutation	SNP	ENST00000374273.3	hg19	CCDS13259.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.643051	0.87859	.	.	ENSG00000061656	ENST00000374273	T	0.15017	2.46	4.72	4.72	0.59763	.	0.105204	0.40385	N	0.001110	T	0.27559	0.0677	L	0.34521	1.04	0.31538	N	0.660258	D	0.58268	0.982	D	0.67548	0.952	T	0.14035	-1.0487	10	0.72032	D	0.01	-17.5121	10.5157	0.44887	0.0:0.0:0.0:1.0	.	26	Q9NPE6	SPAG4_HUMAN	A	26	ENSP00000363391:S26A	ENSP00000363391:S26A	S	+	1	0	SPAG4	33667415	0.993000	0.37304	0.938000	0.37757	0.927000	0.56198	1.365000	0.34182	1.991000	0.58162	0.459000	0.35465	TCA	.	.		0.682	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116		G	34204001	T	G	34204001	3	3	149	1	0	0	0	0	1	0	0	0	14995	1551	54	5	78	5	SPAG4	20	34204001	Missense_Mutation	SNP	T	TCGA-DD-AA3A-01A-11D-A36X-10	23930155	34204001	28821519	55	22719										
COL20A1	57642	hgsc.bcm.edu	37	chr20	61943320	61943320	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	tcagacgtgagccacgacgcGgcacgagtgttctgggaggg	17	10	2	2	rs374496650		TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr20:61943320G>A	ENST00000358894.6	+	14	1816	c.1716G>A	c.(1714-1716)gcG>gcA	p.A572A	COL20A1_ENST00000435874.1_Silent_p.A579A|COL20A1_ENST00000422202.1_Silent_p.A579A|COL20A1_ENST00000326996.6_Silent_p.A572A	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	572	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GCCACGACGCGGCACGAGTGT	0.677																																					p.A572A		Atlas-SNP	.											.	COL20A1	137	.	0			c.G1716A						.	G		0,4030		0,0,2015	20	24	23		1716	-7.2	0	20		23	6,8320		0,6,4157	no	coding-synonymous	COL20A1	NM_020882.2		0,6,6172	AA,AG,GG		0.0721,0.0,0.0486		572/1285	61943320	6,12350	2015	4163	6178	SO:0001819	synonymous_variant	57642	exon14			CGACGCGGCACGA	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.1716G>A	chr20.hg19:g.61943320G>A		85.0	0.0		100.0	35.0	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Silent	SNP	ENST00000358894.6	hg19	CCDS46628.1																																																																																			.	.		0.677	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		A	61943320	G	A	61943320	2	1	149	1	0	0	0	0	0	0	0	1	3681	1103	39	1		1	COL20A1	20	61943320	Silent	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	27739319	61943320	1082200	56	22720										
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38845103	38845103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ttcacatcagtacagtgaccGtcgccagccaaacataagtg	8	12	2	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr21:38845103G>A	ENST00000398960.2	+	2	203	c.128G>A	c.(127-129)cGt>cAt	p.R43H	DYRK1A_ENST00000398956.2_Missense_Mutation_p.R43H|DYRK1A_ENST00000339659.4_Missense_Mutation_p.R43H|DYRK1A_ENST00000462274.1_3'UTR|DYRK1A_ENST00000338785.3_Missense_Mutation_p.R43H|DYRK1A_ENST00000321219.8_Missense_Mutation_p.R43H|DYRK1A_ENST00000451934.1_Missense_Mutation_p.R43H	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	43					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TACAGTGACCGTCGCCAGCCA	0.473																																					p.R43H	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.G128A						.						151	129	137					21																	38845103		2203	4300	6503	SO:0001583	missense	1859	exon2			GTGACCGTCGCCA	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.128G>A	chr21.hg19:g.38845103G>A	ENSP00000381932:p.Arg43His	103.0	0.0		58.0	42.0	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	hg19	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	G	36	5.933585	0.97122	.	.	ENSG00000157540	ENST00000338785;ENST00000455097;ENST00000426672;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956	T;T;T;T;T;T;T	0.57273	0.46;0.77;0.41;0.47;0.46;0.43;0.47	6.16	6.16	0.99307	.	0.050757	0.85682	D	0.000000	T	0.42698	0.1214	N	0.14661	0.345	0.80722	D	1	D;D;P;D;D	0.60575	0.979;0.979;0.955;0.988;0.979	B;P;B;P;P	0.45474	0.361;0.482;0.212;0.482;0.482	T	0.18871	-1.0323	10	0.17832	T	0.49	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	43;43;43;43;43	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	H	43	ENSP00000342690:R43H;ENSP00000412269:R43H;ENSP00000340373:R43H;ENSP00000319032:R43H;ENSP00000416089:R43H;ENSP00000381932:R43H;ENSP00000381929:R43H	ENSP00000319032:R43H	R	+	2	0	DYRK1A	37766973	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.937000	0.99478	0.650000	0.86243	CGT	.	.		0.473	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		A	38845103	G	A	38845103	3	1	149	1	0	0	0	0	1	0	0	0	4856	1145	40	1	134	1	DYRK1A	21	38845103	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10		38845103	9284792	57	22721										
NOL12	79159	hgsc.bcm.edu	37	chr22	38083917	38083917	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	tgccggcttccttcctgtagGgagtacctgacaggcttcca	11	13	0	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr22:38083917G>T	ENST00000359114.4	+	2	154	c.84G>T	c.(82-84)cgG>cgT	p.R28R	NOL12_ENST00000493862.1_3'UTR	NM_024313.2	NP_077289.1	Q9UGY1	NOL12_HUMAN	nucleolar protein 12	28						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	8	Melanoma(58;0.0574)					CTTCCTGTAGGGAGTACCTGA	0.537																																					p.R28R		Atlas-SNP	.											.	NOL12	22	.	0			c.G84T						.						23	21	22					22																	38083917		2195	4285	6480	SO:0001630	splice_region_variant	79159	exon2			CTGTAGGGAGTAC	Z83844	CCDS13955.1	22q13.1	2012-05-02			ENSG00000256872	ENSG00000273899			28585	protein-coding gene	gene with protein product						12477932	Standard	NM_024313		Approved	MGC3731, Nop25, RRP17	uc003atp.3	Q9UGY1	OTTHUMG00000150660	ENST00000359114.4:c.84-1G>T	chr22.hg19:g.38083917G>T		295.0	0.0		325.0	22.0	NM_024313		Silent	SNP	ENST00000359114.4	hg19	CCDS13955.1																																																																																			.	.		0.537	NOL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319476.1	NM_024313	Silent	T	38083917	G	T	38083917	5	4	149	1	0	0	0	0	0	0	1	0	10531	1246	43	3	90	3	NOL12	22	38083917	Splice_Site	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10		38083917	13220649	58	22722										
WDR45	11152	hgsc.bcm.edu	37	chrX	48934306	48934306	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	ggtcctcctcaggctcacttGtcatggcgcatgcgcacaga	11	14	3	1			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chrX:48934306G>A	ENST00000376372.3	-	5	520	c.339C>T	c.(337-339)gaC>gaT	p.D113D	WDR45_ENST00000376368.2_Silent_p.D114D|WDR45_ENST00000473974.1_Silent_p.D113D|WDR45_ENST00000553851.1_Intron|WDR45_ENST00000485908.1_Silent_p.D78D|WDR45_ENST00000465431.1_5'Flank|WDR45_ENST00000322995.8_Silent_p.D113D|WDR45_ENST00000396681.4_Silent_p.D113D|PRAF2_ENST00000491199.1_5'Flank|PRAF2_ENST00000376386.3_5'Flank|AF196779.12_ENST00000376358.3_Intron|WDR45_ENST00000356463.3_Silent_p.D114D|PRAF2_ENST00000376390.4_5'Flank	NM_001029896.1	NP_001025067.1	Q9Y484	WIPI4_HUMAN	WD repeat domain 45	113					autophagy (GO:0006914)|cell death (GO:0008219)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	19						AGGCTCACTTGTCATGGCGCA	0.622																																					p.D114D		Atlas-SNP	.											.	WDR45	40	.	0			c.C342T						.						69	54	59					X																	48934306		2203	4300	6503	SO:0001819	synonymous_variant	11152	exon6			TCACTTGTCATGG	BC003037	CCDS14318.1, CCDS35250.1	Xp11.23	2013-06-06	2004-09-02	2004-09-03	ENSG00000196998	ENSG00000196998		"WD repeat domain containing"	28912	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 5"	300526	"WD repeat domain, X-linked 1"	WDRX1		12477932	Standard	NM_007075		Approved	JM5, WIPI4, NBIA5	uc004dmk.1	Q9Y484	OTTHUMG00000034500	ENST00000376372.3:c.339C>T	chrX.hg19:g.48934306G>A		214.0	0.0		271.0	120.0	NM_007075	A6NGH5|B7WPI2|Q5MNZ5|Q6IBS7|Q6NT94|Q96H03	Silent	SNP	ENST00000376372.3	hg19	CCDS35250.1	.	.	.	.	.	.	.	.	.	.	G	13.25	2.179685	0.38511	.	.	ENSG00000196998	ENST00000367375	.	.	.	3.87	3.87	0.44632	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.6696	14.6194	0.68574	0.0:0.0:1.0:0.0	.	.	.	.	X	70	.	.	Q	-	1	0	WDR45	48821250	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.994000	0.70623	2.182000	0.69389	0.529000	0.55759	CAA	.	.		0.622	WDR45-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083418.2	NM_007075		A	48934306	G	A	48934306	2	1	149	1	0	0	0	0	0	0	0	1	17312	1368	48	3		3	WDR45	23	48934306	Silent	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10		48934306	106336254	59	22723										
MAGIX	79917	hgsc.bcm.edu	37	chrX	49020204	49020204	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.18755256518082	1.22996515679443	1.17405764966741	0.545454545454546	1	0	gccccctggcggcgcgagctGcggtcgacgtggcagcgctg	18	15	0	0			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chrX:49020204G>C	ENST00000412696.2	+	2	133	c.133G>C	c.(133-135)Gcg>Ccg	p.A45P	MAGIX_ENST00000376339.1_5'UTR|MAGIX_ENST00000425661.2_Missense_Mutation_p.A45P|MAGIX_ENST00000376338.3_5'Flank	NM_024859.2	NP_079135.3	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked	45																	GGCGCGAGCTGCGGTCGACGT	0.781																																					p.A45P		Atlas-SNP	.											.	MAGIX	25	.	0			c.G133C						.						1	1	1					X																	49020204		736	1642	2378	SO:0001583	missense	79917	exon2			CGAGCTGCGGTCG	AK025340	CCDS48106.1, CCDS48107.1, CCDS75976.1	Xp11.23	2014-05-06			ENSG00000017621	ENSG00000269313			30006	protein-coding gene	gene with protein product							Standard	XM_005278065		Approved	PDZX, JM10, FLJ21687	uc010nin.1	Q9H6Y5	OTTHUMG00000188218	ENST00000412696.2:c.133G>C	chrX.hg19:g.49020204G>C	ENSP00000387928:p.Ala45Pro	62.0	0.0		105.0	55.0	NM_001099681	A6XND4|A8MSX9|B7WP26|Q14C81	Missense_Mutation	SNP	ENST00000412696.2	hg19	CCDS48106.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	13.23|13.23	2.175406|2.175406	0.38413|0.38413	.|.	.|.	ENSG00000017621|ENSG00000017621	ENST00000425661;ENST00000412696|ENST00000458388	T;T|.	0.26957|.	1.92;1.7|.	3.37|3.37	2.5|2.5	0.30297|0.30297	.|.	.|.	.|.	.|.	.|.	T|T	0.30823|0.30823	0.0777|0.0777	L|L	0.29908|0.29908	0.895|0.895	0.26836|0.26836	N|N	0.96847|0.96847	D;D|.	0.67145|.	0.996;0.994|.	P;P|.	0.61132|.	0.884;0.854|.	T|T	0.20438|0.20438	-1.0275|-1.0275	9|5	0.37606|.	T|.	0.19|.	-5.4914|-5.4914	6.1176|6.1176	0.20136|0.20136	0.1442:0.0:0.8558:0.0|0.1442:0.0:0.8558:0.0	.|.	45;45|.	F8WCY7;Q9H6Y5|.	.;MAGIX_HUMAN|.	P|S	45|50	ENSP00000403515:A45P;ENSP00000387928:A45P|.	ENSP00000387928:A45P|.	A|C	+|+	1|2	0|0	MAGIX|MAGIX	48907148|48907148	0.347000|0.347000	0.24853|0.24853	0.430000|0.430000	0.26722|0.26722	0.009000|0.009000	0.06853|0.06853	1.088000|1.088000	0.30877|0.30877	0.822000|0.822000	0.34565|0.34565	0.284000|0.284000	0.19432|0.19432	GCG|TGC	.	.		0.781	MAGIX-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378832.1	NM_024859		C	49020204	G	C	49020204	3	2	149	1	0	0	0	0	1	0	0	0	9202	1319	46	4	139	4	MAGIX	23	49020204	Missense_Mutation	SNP	G	TCGA-DD-AA3A-01A-11D-A36X-10	85898	49020204	106250356	60	22724										
TNFRSF25	8718	hgsc.bcm.edu	37	chr1	6524732	6524732	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccagcctggcttacagccacAgcgggtgtcggccactgctg	13	15	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:6524732A>T	ENST00000356876.3	-	4	430	c.343T>A	c.(343-345)Tgt>Agt	p.C115S	TNFRSF25_ENST00000461703.2_5'UTR|TNFRSF25_ENST00000348333.3_Missense_Mutation_p.C70S|TNFRSF25_ENST00000377782.3_Missense_Mutation_p.C115S|TNFRSF25_ENST00000351748.3_Intron|TNFRSF25_ENST00000351959.5_Missense_Mutation_p.C115S	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	115					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|central_nervous_system(2)|endometrium(1)|lung(4)|prostate(1)|stomach(1)	10	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		TTACAGCCACAGCGGGTGTCG	0.617																																					p.C115S		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.T343A						.						46	48	47					1																	6524732		2203	4300	6503	SO:0001583	missense	8718	exon4			AGCCACAGCGGGT	U72763	CCDS71.1, CCDS72.1, CCDS73.1, CCDS74.1, CCDS75.1	1p36.2	2008-02-05	2002-12-20	2002-12-20	ENSG00000215788	ENSG00000215788		"Tumor necrosis factor receptor superfamily"	11910	protein-coding gene	gene with protein product		603366	"tumor necrosis factor receptor superfamily, member 12 (translocating chain-association membrane protein)"	TNFRSF12		9052839, 8934525	Standard	NM_003790		Approved	DR3, TRAMP, WSL-1, LARD, WSL-LR, DDR3, TR3, APO-3	uc001anh.3	Q93038	OTTHUMG00000000831	ENST00000356876.3:c.343T>A	chr1.hg19:g.6524732A>T	ENSP00000349341:p.Cys115Ser	94.0	0.0		69.0	21.0	NM_148966	B1ALX2|B1ALX3|B7ZLL7|O00275|O00276|O00277|O00278|O00279|O00280|O14865|O14866|P78507|P78515|Q17RU4|Q92983|Q93036|Q93037|Q99722|Q99830|Q99831|Q9BY86|Q9UME0|Q9UME1|Q9UME5	Missense_Mutation	SNP	ENST00000356876.3	hg19	CCDS71.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.575606	0.86645	.	.	ENSG00000215788	ENST00000356876;ENST00000377782;ENST00000351959;ENST00000348333	D;D;D;D	0.97066	-4.23;-4.23;-4.23;-4.23	5.5	5.5	0.81552	TNFR/CD27/30/40/95 cysteine-rich region (3);	0.350783	0.20537	U	0.090386	D	0.98620	0.9538	M	0.91140	3.18	0.53688	D	0.999976	P;D;P;D	0.89917	0.952;1.0;0.892;1.0	P;D;P;D	0.91635	0.789;0.999;0.851;0.998	D	0.99160	1.0861	10	0.49607	T	0.09	0.8167	12.9857	0.58590	1.0:0.0:0.0:0.0	.	115;70;115;115	Q93038-11;Q93038-9;Q93038-10;Q93038	.;.;.;TNR25_HUMAN	S	115;115;115;70	ENSP00000349341:C115S;ENSP00000367013:C115S;ENSP00000337713:C115S;ENSP00000314451:C70S	ENSP00000314451:C70S	C	-	1	0	TNFRSF25	6447319	0.980000	0.34600	0.996000	0.52242	0.682000	0.39822	5.651000	0.67951	2.065000	0.61736	0.519000	0.50382	TGT	.	.		0.617	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965		T	6524732	A	T	6524732	3	4	150	1	0	0	0	0	1	0	0	0	16311	188	7	4	969	4	TNFRSF25	1	6524732	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		6524732	242725889	1	22725										
TNFRSF8	943	hgsc.bcm.edu	37	chr1	12183820	12183820	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gactcccaggccagtaagacGctgcccatcccaaccagcgc	9	18	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:12183820G>A	ENST00000263932.2	+	10	1311	c.1089G>A	c.(1087-1089)acG>acA	p.T363T	TNFRSF8_ENST00000417814.2_Silent_p.T252T|TNFRSF8_ENST00000413146.2_5'Flank	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	363	Pro/Ser/Thr-rich.				cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	CCAGTAAGACGCTGCCCATCC	0.632																																					p.T363T		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.G1089A						.						37	29	32					1																	12183820		2200	4295	6495	SO:0001819	synonymous_variant	943	exon10			TAAGACGCTGCCC	M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"Tumor necrosis factor receptor superfamily", "CD molecules"	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.1089G>A	chr1.hg19:g.12183820G>A		114.0	0.0		77.0	31.0	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Silent	SNP	ENST00000263932.2	hg19	CCDS144.1																																																																																			.	.		0.632	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1			A	12183820	G	A	12183820	2	1	150	1	0	0	0	0	0	0	0	1	16314	1074	38	1		1	TNFRSF8	1	12183820	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	5659088	12183820	237066801	2	22726										
CLCNKA	1187	hgsc.bcm.edu	37	chr1	16358337	16358337	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tatcccctggtggagagcacAggtgcccagctggaagggag	16	10	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:16358337A>T	ENST00000331433.4	+	16	1774	c.1755A>T	c.(1753-1755)acA>acT	p.T585T	CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000375692.1_Splice_Site_p.T585T|CLCNKA_ENST00000420078.1_Splice_Site_p.T585T|CLCNKA_ENST00000439316.2_Splice_Site_p.T542T			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	585	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	TGGAGAGCACAGGTGCCCAGC	0.612																																					p.T585T		Atlas-SNP	.											.	CLCNKA	56	.	0			c.A1755T						.						90	68	75					1																	16358337		2202	4300	6502	SO:0001630	splice_region_variant	1187	exon16			GAGCACAGGTGCC		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"Ion channels / Chloride channels : Voltage-sensitive"	2026	protein-coding gene	gene with protein product		602024	"chloride channel Ka"			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.1756+1A>T	chr1.hg19:g.16358337A>T		129.0	0.0		84.0	63.0	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Silent	SNP	ENST00000331433.4	hg19	CCDS167.1																																																																																			.	.		0.612	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		Silent	T	16358337	A	T	16358337	5	4	150	1	0	0	0	0	0	0	1	0	3471	202	7	4	1813	4	CLCNKA	1	16358337	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	4174517	16358337	232892284	3	22727										
LAPTM5	7805	hgsc.bcm.edu	37	chr1	31210494	31210494	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggcgatggaaaagatgatcAtcatcttgatgaactggtta	11	5	3	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:31210494A>T	ENST00000294507.3	-	6	637	c.563T>A	c.(562-564)aTg>aAg	p.M188K	MIR4420_ENST00000583944.1_RNA	NM_006762.2	NP_006753.1	Q13571	LAPM5_HUMAN	lysosomal protein transmembrane 5	188					transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)				large_intestine(2)|lung(7)|skin(1)	10		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)		AAAGATGATCATCATCTTGAT	0.517																																					p.M188K		Atlas-SNP	.											.	LAPTM5	30	.	0			c.T563A						.						216	187	197					1																	31210494		2203	4300	6503	SO:0001583	missense	7805	exon6			ATGATCATCATCT	U51240	CCDS337.1	1p34	2009-07-20	2009-07-20		ENSG00000162511	ENSG00000162511			29612	protein-coding gene	gene with protein product		601476	"lysosomal multispanning membrane protein 5"			8661146, 12527926	Standard	NM_006762		Approved		uc001bsc.2	Q13571	OTTHUMG00000003707	ENST00000294507.3:c.563T>A	chr1.hg19:g.31210494A>T	ENSP00000294507:p.Met188Lys	86.0	0.0		46.0	21.0	NM_006762	Q13240|Q14698|Q3KP54	Missense_Mutation	SNP	ENST00000294507.3	hg19	CCDS337.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.071777	0.76301	.	.	ENSG00000162511	ENST00000294507;ENST00000424259	T	0.50277	0.75	5.52	5.52	0.82312	.	0.060246	0.64402	D	0.000002	T	0.65322	0.2680	M	0.67953	2.075	0.39571	D	0.969277	D	0.76494	0.999	D	0.75484	0.986	T	0.70193	-0.4939	10	0.72032	D	0.01	-47.5065	12.049	0.53495	1.0:0.0:0.0:0.0	.	188	Q13571	LAPM5_HUMAN	K	188	ENSP00000294507:M188K	ENSP00000294507:M188K	M	-	2	0	LAPTM5	30983081	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	3.545000	0.53648	2.091000	0.63221	0.460000	0.39030	ATG	.	.		0.517	LAPTM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010463.1	NM_006762		T	31210494	A	T	31210494	3	4	150	1	0	0	0	0	1	0	0	0	8635	217	8	4	237	4	LAPTM5	1	31210494	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	14852157	31210494	218040127	4	22728										
MACF1	23499	hgsc.bcm.edu	37	chr1	39823516	39823516	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agaaattggaaacttagtaaAggacaagttgaaggatgcaa	11	3	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:39823516A>T	ENST00000372915.3	+	44	11996	c.11909A>T	c.(11908-11910)aAg>aTg	p.K3970M	MACF1_ENST00000361689.2_Missense_Mutation_p.K1903M|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000545844.1_Missense_Mutation_p.K1903M|MACF1_ENST00000564288.1_Missense_Mutation_p.K3965M|MACF1_ENST00000317713.7_Missense_Mutation_p.K1903M|MACF1_ENST00000567887.1_Missense_Mutation_p.K4002M|MACF1_ENST00000289893.4_Missense_Mutation_p.K2405M|MACF1_ENST00000539005.1_Missense_Mutation_p.K1903M			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3970					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AACTTAGTAAAGGACAAGTTG	0.433																																					p.K1903M		Atlas-SNP	.											.	MACF1	909	.	0			c.A5708T						.						72	68	70					1																	39823516		2203	4300	6503	SO:0001583	missense	23499	exon41			TAGTAAAGGACAA	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.11909A>T	chr1.hg19:g.39823516A>T	ENSP00000362006:p.Lys3970Met	66.0	0.0		46.0	18.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.82|19.82	3.897807|3.897807	0.72639|0.72639	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.36157|.	1.27;1.27;1.27;1.27;1.27;1.27|.	6.07|6.07	3.63|3.63	0.41609|0.41609	.|.	0.190103|0.190103	0.37012|0.37012	N|N	0.002284|0.002284	T|T	0.58495|0.58495	0.2126|0.2126	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	P;P;P;P|.	0.47545|.	0.897;0.738;0.725;0.878|.	P;P;P;P|.	0.61003|.	0.707;0.69;0.601;0.882|.	T|T	0.54997|0.54997	-0.8209|-0.8209	10|6	0.72032|.	D|.	0.01|.	.|.	10.2536|10.2536	0.43383|0.43383	0.758:0.176:0.066:0.0|0.758:0.176:0.066:0.0	.|.	3970;1903;1903;1868|.	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	MACF1_HUMAN;.;.;.|.	M|N	1903;3970;1903;1903;1903;2405|1036	ENSP00000439537:K1903M;ENSP00000362006:K3970M;ENSP00000354573:K1903M;ENSP00000313438:K1903M;ENSP00000444364:K1903M;ENSP00000289893:K2405M|.	ENSP00000289893:K2405M|.	K|K	+|+	2|3	0|2	MACF1|MACF1	39596103|39596103	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	3.066000|3.066000	0.50002|0.50002	1.112000|1.112000	0.41740|0.41740	-0.274000|-0.274000	0.10170|0.10170	AAG|AAA	.	.		0.433	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39823516	A	T	39823516	3	4	150	1	0	0	0	0	1	0	0	0	9153	72	3	4	12017	4	MACF1	1	39823516	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	8613022	39823516	209427105	5	22729										
NASP	4678	hgsc.bcm.edu	37	chr1	46078848	46078855	+	Frame_Shift_Del	DEL	AGGCTCAG	AGGCTCAG	-													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tttttacttgtagaaactgaAggctcagaagaggatgataa					rs2230658|rs534850061	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	AGGCTCAG	AGGCTCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:46078848_46078855delAGGCTCAG	ENST00000350030.3	+	7	1521_1528	c.1434_1441delAGGCTCAG	c.(1432-1443)gaaggctcagaafs	p.EGSE478fs	NASP_ENST00000537798.1_Frame_Shift_Del_p.EGSE414fs|NASP_ENST00000402363.3_Frame_Shift_Del_p.EGSE480fs|NASP_ENST00000372052.4_Frame_Shift_Del_p.EGSE112fs|NASP_ENST00000530073.1_3'UTR|NASP_ENST00000351223.3_Frame_Shift_Del_p.EGSE139fs	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	478	Glu-rich (acidic).|Histone-binding.				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					TAGAAACTGAAGGCTCAGAAGAGGATGA	0.365																																					p.478_480del		Atlas-Indel,Pindel	.											.	NASP	77	.	0			c.1433_1440del						.																																			SO:0001589	frameshift_variant	4678	exon7			.	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"Tetratricopeptide (TTC) repeat domain containing"	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.1434_1441delAGGCTCAG	chr1.hg19:g.46078848_46078855delAGGCTCAG	ENSP00000255120:p.Glu478fs	75.0	0.0		23.0	17.0	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Frame_Shift_Del	DEL	ENST00000350030.3	hg19	CCDS524.1																																																																																			.	.		0.365	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		-	46078855	AGGCTCAG	-	46078848	7	5	150	1	0	1	0	1	0	0	0	0	10181	69	3	0	1537	0	NASP	1	46078848	Frame_Shift_Del	DEL	AGGCTCAG	TCGA-DD-AAC8-01A-11D-A40R-10	6255332	46078848	203171773	6	22730										
GLIS1	148979	hgsc.bcm.edu	37	chr1	53995547	53995547	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acccgggtgctggcacaggtAcggcttctcgcccgtgtggc	15	14	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:53995547A>T	ENST00000312233.2	-	4	1440	c.874T>A	c.(874-876)Tac>Aac	p.Y292N		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						TGGCACAGGTACGGCTTCTCG	0.637																																					p.Y292N		Atlas-SNP	.											.	GLIS1	52	.	0			c.T874A						.						71	74	73					1																	53995547		2203	4300	6503	SO:0001583	missense	148979	exon4			ACAGGTACGGCTT	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"Zinc fingers, C2H2-type"	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.874T>A	chr1.hg19:g.53995547A>T	ENSP00000309653:p.Tyr292Asn	50.0	0.0		36.0	17.0	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	hg19	CCDS582.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.486978	0.84854	.	.	ENSG00000174332	ENST00000312233	T	0.69306	-0.39	4.58	4.58	0.56647	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43579	D	0.000544	T	0.76357	0.3976	L	0.46819	1.47	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79225	-0.1891	10	0.87932	D	0	.	14.2651	0.66113	1.0:0.0:0.0:0.0	.	292	Q8NBF1	GLIS1_HUMAN	N	292	ENSP00000309653:Y292N	ENSP00000309653:Y292N	Y	-	1	0	GLIS1	53768135	1.000000	0.71417	0.909000	0.35828	0.870000	0.49936	9.287000	0.95975	1.842000	0.53543	0.402000	0.26972	TAC	.	.		0.637	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193		T	53995547	A	T	53995547	3	4	150	1	0	0	0	0	1	0	0	0	6453	391	14	4	1016	4	GLIS1	1	53995547	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	7916699	53995547	195255074	7	22731										
C8B	732	hgsc.bcm.edu	37	chr1	57411614	57411614	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atctctgtattccccgtagcTgtactccaggggcagccgct	10	14	1	0	rs373750492		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:57411614T>A	ENST00000371237.4	-	7	1051	c.985A>T	c.(985-987)Agc>Tgc	p.S329C	C8B_ENST00000535057.1_Missense_Mutation_p.S267C|C8B_ENST00000543257.1_Missense_Mutation_p.S277C	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	329	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						TCCCCGTAGCTGTACTCCAGG	0.493																																					p.S329C		Atlas-SNP	.											.	C8B	107	.	0			c.A985T						.						86	83	84					1																	57411614		2203	4300	6503	SO:0001583	missense	732	exon7			CGTAGCTGTACTC	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"Complement system"	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.985A>T	chr1.hg19:g.57411614T>A	ENSP00000360281:p.Ser329Cys	162.0	0.0		96.0	28.0	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	hg19	CCDS30730.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.847163	0.51164	.	.	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	D;D;D	0.84800	-1.9;-1.9;-1.9	4.71	-0.517	0.11947	Membrane attack complex component/perforin (MACPF) domain (3);	0.491866	0.25561	N	0.029821	D	0.87732	0.6251	M	0.75447	2.3	0.37609	D	0.920877	P;P;D	0.54207	0.911;0.911;0.965	P;P;P	0.56398	0.518;0.518;0.797	D	0.86666	0.1907	10	0.72032	D	0.01	-6.7146	9.3374	0.38058	0.0:0.4023:0.0:0.5977	.	277;267;329	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	C	329;277;267	ENSP00000360281:S329C;ENSP00000442548:S277C;ENSP00000440113:S267C	ENSP00000360281:S329C	S	-	1	0	C8B	57184202	0.933000	0.31639	0.807000	0.32361	0.816000	0.46133	0.733000	0.26087	-0.263000	0.09378	-1.054000	0.02325	AGC	.	.		0.493	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2			A	57411614	T	A	57411614	3	1	150	1	0	0	0	0	1	0	0	0	2419	1580	55	4	814	4	C8B	1	57411614	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3416067	57411614	191839007	8	22732										
UBE2U	148581	hgsc.bcm.edu	37	chr1	64676461	64676461	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcagccctgtatagacttttTggacaaccctgagaagtgga	10	9	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:64676461T>A	ENST00000371076.3	+	4	522	c.278T>A	c.(277-279)tTg>tAg	p.L93*		NM_152489.1	NP_689702.1	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)	93					protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			large_intestine(3)|lung(2)|skin(1)	6						ATAGACTTTTTGGACAACCCT	0.308																																					p.L93X		Atlas-SNP	.											.	UBE2U	16	.	0			c.T278A						.						85	80	82					1																	64676461		2203	4300	6503	SO:0001587	stop_gained	148581	exon4			ACTTTTTGGACAA	BC029895	CCDS627.1	1p31.3	2008-02-05			ENSG00000177414	ENSG00000177414		"Ubiquitin-conjugating enzymes E2"	28559	protein-coding gene	gene with protein product						12477932	Standard	NM_152489		Approved	MGC35130	uc001dbn.1	Q5VVX9	OTTHUMG00000009023	ENST00000371076.3:c.278T>A	chr1.hg19:g.64676461T>A	ENSP00000360116:p.Leu93*	414.0	0.0		264.0	97.0	NM_152489	Q8N1D4	Nonsense_Mutation	SNP	ENST00000371076.3	hg19	CCDS627.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.734771	0.89482	.	.	ENSG00000177414	ENST00000371077;ENST00000371076	.	.	.	5.5	5.5	0.81552	.	0.000000	0.43579	D	0.000547	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.989	0.53163	0.0:0.0:0.0:1.0	.	.	.	.	X	93	.	ENSP00000360116:L93X	L	+	2	0	UBE2U	64449049	1.000000	0.71417	1.000000	0.80357	0.087000	0.18053	4.425000	0.59875	2.082000	0.62665	0.459000	0.35465	TTG	.	.		0.308	UBE2U-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025005.1	NM_152489		A	64676461	T	A	64676461	4	1	150	1	0	0	0	0	0	1	0	0	16889	1821	63	4	292	4	UBE2U	1	64676461	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	7264847	64676461	184574160	9	22733										
C1orf173	127254	hgsc.bcm.edu	37	chr1	75038865	75038865	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cttctgaccccttctgcttcTgctgctccctctgcccccct	5	21	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:75038865T>A	ENST00000326665.5	-	14	2747	c.2529A>T	c.(2527-2529)gcA>gcT	p.A843A	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		843	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CTTCTGCTTCTGCTGCTCCCT	0.557																																					p.A843A		Atlas-SNP	.											.	C1orf173	380	.	0			c.A2529T						.						114	107	109					1																	75038865		2203	4300	6503	SO:0001819	synonymous_variant	127254	exon14			TGCTTCTGCTGCT																												ENST00000326665.5:c.2529A>T	chr1.hg19:g.75038865T>A		81.0	0.0		40.0	22.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	hg19	CCDS30755.1																																																																																			.	.		0.557	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75038865	T	A	75038865	2	1	150	1	0	0	0	0	0	0	0	1	2016	1567	55	4		4	C1orf173	1	75038865	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	10362404	75038865	174211756	10	22734										
ZZZ3	26009	hgsc.bcm.edu	37	chr1	78098739	78098739	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccttctctcacaattttctaTagcctgcctttctatgttat	3	12	4	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:78098739T>A	ENST00000370801.3	-	5	776	c.301A>T	c.(301-303)Ata>Tta	p.I101L	ZZZ3_ENST00000476275.1_5'Flank|ZZZ3_ENST00000370798.1_Intron	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	101					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						CAATTTTCTATAGCCTGCCTT	0.388																																					p.I101L		Atlas-SNP	.											.	ZZZ3	80	.	0			c.A301T						.						240	247	245					1																	78098739		2203	4300	6503	SO:0001583	missense	26009	exon5			TTTCTATAGCCTG	AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"Zinc fingers, ZZ-type"	24523	protein-coding gene	gene with protein product	"ATAC component 1 homolog (Drosophila)"					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.301A>T	chr1.hg19:g.78098739T>A	ENSP00000359837:p.Ile101Leu	77.0	0.0		53.0	16.0	NM_015534	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Missense_Mutation	SNP	ENST00000370801.3	hg19	CCDS677.1	.	.	.	.	.	.	.	.	.	.	T	6.675	0.493206	0.12702	.	.	ENSG00000036549	ENST00000370801	.	.	.	5.55	0.304	0.15796	.	0.834054	0.11063	N	0.603772	T	0.05456	0.0144	N	0.01352	-0.895	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38972	-0.9636	8	.	.	.	.	6.0723	0.19895	0.0:0.4928:0.2351:0.2721	.	101;101;101	Q8IYH5-4;Q8IYH5;Q8IYH5-2	.;ZZZ3_HUMAN;.	L	101	.	.	I	-	1	0	ZZZ3	77871327	0.900000	0.30661	0.984000	0.44739	0.987000	0.75469	-0.109000	0.10840	-0.123000	0.11745	-0.248000	0.11899	ATA	.	.		0.388	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1	NM_015534		A	78098739	T	A	78098739	3	1	150	1	0	0	0	0	1	0	0	0	18271	1406	49	4	2454	4	ZZZ3	1	78098739	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3059874	78098739	171151882	11	22735										
PTGFR	5737	hgsc.bcm.edu	37	chr1	78958823	78958823	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggcagtgtgatggccattgAgcggtgtattggagtcacaa	15	6	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:78958823A>T	ENST00000370757.3	+	2	632	c.395A>T	c.(394-396)gAg>gTg	p.E132V	PTGFR_ENST00000370758.1_Missense_Mutation_p.E132V|PTGFR_ENST00000370756.3_Missense_Mutation_p.E132V	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	132					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)			breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	ATGGCCATTGAGCGGTGTATT	0.403																																					p.E132V		Atlas-SNP	.											.	PTGFR	121	.	0			c.A395T						.						157	146	150					1																	78958823		2203	4300	6503	SO:0001583	missense	5737	exon2			CCATTGAGCGGTG	AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"GPCR / Class A : Prostanoid receptors"	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.395A>T	chr1.hg19:g.78958823A>T	ENSP00000359793:p.Glu132Val	137.0	0.0		89.0	29.0	NM_000959	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Missense_Mutation	SNP	ENST00000370757.3	hg19	CCDS686.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.327374	0.81690	.	.	ENSG00000122420	ENST00000370758;ENST00000370757;ENST00000370756	T;T;T	0.74737	-0.87;-0.87;-0.87	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.84261	0.5433	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.86441	0.1767	10	0.87932	D	0	-16.2877	16.5479	0.84454	1.0:0.0:0.0:0.0	.	132;132	P43088;P43088-2	PF2R_HUMAN;.	V	132	ENSP00000359794:E132V;ENSP00000359793:E132V;ENSP00000359792:E132V	ENSP00000359792:E132V	E	+	2	0	PTGFR	78731411	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.403	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		T	78958823	A	T	78958823	3	4	150	1	0	0	0	0	1	0	0	0	12762	304	11	4	397	4	PTGFR	1	78958823	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	860084	78958823	170291798	12	22736										
ABCA4	24	hgsc.bcm.edu	37	chr1	94508911	94508911	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctgataggtcctgagcctcTtcattccgcttgtggtggag	12	11	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:94508911T>A	ENST00000370225.3	-	21	3257	c.3171A>T	c.(3169-3171)gaA>gaT	p.E1057D		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1057	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CCTGAGCCTCTTCATTCCGCT	0.592																																					p.E1057D		Atlas-SNP	.											.	ABCA4	275	.	0			c.A3171T						.						100	87	92					1																	94508911		2203	4300	6503	SO:0001583	missense	24	exon21			AGCCTCTTCATTC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.3171A>T	chr1.hg19:g.94508911T>A	ENSP00000359245:p.Glu1057Asp	66.0	0.0		49.0	24.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	T	11.80	1.747941	0.30955	.	.	ENSG00000198691	ENST00000370225	D	0.93659	-3.26	5.83	0.92	0.19397	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.149319	0.64402	D	0.000013	T	0.71745	0.3376	N	0.16790	0.44	0.80722	D	1	B	0.06786	0.001	B	0.14023	0.01	T	0.59332	-0.7474	10	0.21014	T	0.42	.	4.7768	0.13184	0.1288:0.296:0.0:0.5752	.	1057	P78363	ABCA4_HUMAN	D	1057	ENSP00000359245:E1057D	ENSP00000359245:E1057D	E	-	3	2	ABCA4	94281499	0.614000	0.27017	0.989000	0.46669	0.956000	0.61745	-0.019000	0.12546	-0.080000	0.12685	-0.326000	0.08463	GAA	.	.		0.592	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94508911	T	A	94508911	3	1	150	1	0	0	0	0	1	0	0	0	34	1606	56	4	3770	4	ABCA4	1	94508911	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	15550088	94508911	154741710	13	22737										
ABCA4	24	hgsc.bcm.edu	37	chr1	94577058	94577058	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggtggggctttgaaaacaggGattgttcacattgcagaaga	14	5	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:94577058G>T	ENST00000370225.3	-	3	324	c.238C>A	c.(238-240)Ccc>Acc	p.P80T	ABCA4_ENST00000535735.1_Missense_Mutation_p.P80T	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	80					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TGAAAACAGGGATTGTTCACA	0.493																																					p.P80T		Atlas-SNP	.											.	ABCA4	275	.	0			c.C238A						.						71	69	70					1																	94577058		2203	4300	6503	SO:0001583	missense	24	exon3			AACAGGGATTGTT	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.238C>A	chr1.hg19:g.94577058G>T	ENSP00000359245:p.Pro80Thr	156.0	0.0		75.0	31.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155031	0.78114	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.99287	-5.69;-5.69	5.62	5.62	0.85841	.	0.056575	0.64402	D	0.000001	D	0.99217	0.9728	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;0.985	D;P	0.97110	1.0;0.845	D	0.99813	1.1042	10	0.32370	T	0.25	.	18.4977	0.90870	0.0:0.0:1.0:0.0	.	80;80	F5H6E5;P78363	.;ABCA4_HUMAN	T	80	ENSP00000359245:P80T;ENSP00000437682:P80T	ENSP00000359245:P80T	P	-	1	0	ABCA4	94349646	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	9.423000	0.97461	2.671000	0.90904	0.644000	0.83932	CCC	.	.		0.493	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		T	94577058	G	T	94577058	3	4	150	1	0	0	0	0	1	0	0	0	34	1174	41	3	6775	3	ABCA4	1	94577058	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	68147	94577058	154673563	14	22738										
KCNA2	3737	hgsc.bcm.edu	37	chr1	111146551	111146551	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tggccagtgacatggcctgcTggccttgctgagcgtcctct	13	13	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:111146551T>A	ENST00000485317.1	-	3	1527	c.854A>T	c.(853-855)cAg>cTg	p.Q285L	KCNA2_ENST00000525120.1_5'Flank|KCNA2_ENST00000316361.4_Missense_Mutation_p.Q285L|KCNA2_ENST00000440270.1_Missense_Mutation_p.Q285L|KCNA2_ENST00000369770.3_Missense_Mutation_p.Q285L			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	285					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	CATGGCCTGCTGGCCTTGCTG	0.512																																					p.Q285L	Pancreas(18;568 735 10587 23710 36357)	Atlas-SNP	.											.	KCNA2	61	.	0			c.A854T						.						105	105	105					1																	111146551		2203	4300	6503	SO:0001583	missense	3737	exon3			GCCTGCTGGCCTT	L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.854A>T	chr1.hg19:g.111146551T>A	ENSP00000433109:p.Gln285Leu	95.0	0.0		71.0	30.0	NM_001204269	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	hg19	CCDS827.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.711369	0.68730	.	.	ENSG00000177301	ENST00000369770;ENST00000485317;ENST00000440270;ENST00000316361	D;D;D;D	0.97430	-4.38;-4.14;-4.14;-4.14	5.87	5.87	0.94306	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.96543	0.8872	L	0.37850	1.14	0.80722	D	1	D;P	0.60575	0.988;0.695	D;B	0.63793	0.918;0.345	D	0.96946	0.9691	10	0.48119	T	0.1	.	16.2806	0.82678	0.0:0.0:0.0:1.0	.	285;285	Q86XG6;P16389	.;KCNA2_HUMAN	L	285	ENSP00000358785:Q285L;ENSP00000433109:Q285L;ENSP00000415257:Q285L;ENSP00000314520:Q285L	ENSP00000314520:Q285L	Q	-	2	0	KCNA2	110948074	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.991000	0.88244	2.248000	0.74166	0.533000	0.62120	CAG	.	.		0.512	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		A	111146551	T	A	111146551	3	1	150	1	0	0	0	0	1	0	0	0	8012	1580	55	4	649	4	KCNA2	1	111146551	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	16569493	111146551	138104070	15	22739										
CD101	9398	hgsc.bcm.edu	37	chr1	117556032	117556032	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgcttttgtttcccagtgaaAgattttcaagtcaacattac	6	8	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:117556032A>T	ENST00000256652.4	+	4	904	c.846A>T	c.(844-846)aaA>aaT	p.K282N	CD101_ENST00000369470.1_Missense_Mutation_p.K282N	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	282	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TCCCAGTGAAAGATTTTCAAG	0.483																																					p.K282N		Atlas-SNP	.											.	CD101	95	.	0			c.A846T						.						126	134	132					1																	117556032		2203	4300	6503	SO:0001583	missense	9398	exon4			AGTGAAAGATTTT	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5949	protein-coding gene	gene with protein product		604516	"immunoglobulin superfamily, member 2"	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.846A>T	chr1.hg19:g.117556032A>T	ENSP00000256652:p.Lys282Asn	73.0	0.0		52.0	21.0	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	hg19	CCDS891.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.683324	0.47991	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.03524	3.9;3.9	6.06	3.78	0.43462	Immunoglobulin-like (1);	0.711521	0.13188	N	0.406983	T	0.00875	0.0029	N	0.17082	0.46	0.25613	N	0.986485	B	0.06786	0.001	B	0.06405	0.002	T	0.48340	-0.9044	10	0.39692	T	0.17	-2.9633	6.8982	0.24267	0.8265:0.0:0.1735:0.0	.	282	Q93033	IGSF2_HUMAN	N	282	ENSP00000256652:K282N;ENSP00000358482:K282N	ENSP00000256652:K282N	K	+	3	2	CD101	117357555	0.077000	0.21312	0.975000	0.42487	0.995000	0.86356	0.280000	0.18790	1.121000	0.41925	0.533000	0.62120	AAA	.	.		0.483	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		T	117556032	A	T	117556032	3	4	150	1	0	0	0	0	1	0	0	0	2964	69	3	4	860	4	CD101	1	117556032	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	6409481	117556032	131694589	16	22740										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144868114	144868114	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgaggtagtaggaagagtcGgcttccaagtcgttgctcag	14	7	1	2	rs376826439		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:144868114G>T	ENST00000369354.3	-	33	5514	c.5325C>A	c.(5323-5325)gcC>gcA	p.A1775A	PDE4DIP_ENST00000369359.4_Silent_p.A1911A|PDE4DIP_ENST00000369356.4_Silent_p.A1775A|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Silent_p.A1669A|PDE4DIP_ENST00000530740.1_Silent_p.A1860A|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1775					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.A1775A(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGGAAGAGTCGGCTTCCAAGT	0.537			T	PDGFRB	MPD																																p.A1775A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP,pharynx,carcinoma,0,1	PDE4DIP	817	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C5325A						.						134	140	138					1																	144868114		2203	4296	6499	SO:0001819	synonymous_variant	9659	exon33			AGAGTCGGCTTCC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.5325C>A	chr1.hg19:g.144868114G>T		154.0	0.0		194.0	18.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	hg19	CCDS30824.1																																																																																			.	.		0.537	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144868114	G	T	144868114	2	4	150	1	0	0	0	0	0	0	0	1	11652	1103	39	1		1	PDE4DIP	1	144868114	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	27312082	144868114	104382507	17	22741										
ANKRD35	148741	hgsc.bcm.edu	37	chr1	145555806	145555806	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccgacccaccaagcttgacTcgaatggccagtccccgtaa	8	17	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:145555806T>A	ENST00000355594.4	+	2	241	c.154T>A	c.(154-156)Tcg>Acg	p.S52T	ANKRD35_ENST00000544626.1_Missense_Mutation_p.S52T	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	52										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CAAGCTTGACTCGAATGGCCA	0.592																																					p.S52T	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.T154A						.						59	64	62					1																	145555806		2203	4300	6503	SO:0001583	missense	148741	exon2			CTTGACTCGAATG	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.154T>A	chr1.hg19:g.145555806T>A	ENSP00000347802:p.Ser52Thr	143.0	0.0		263.0	68.0	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	hg19	CCDS919.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.449333	0.43531	.	.	ENSG00000198483	ENST00000355594;ENST00000544626	T;T	0.53857	0.6;1.35	5.62	0.27	0.15635	Ankyrin repeat-containing domain (4);	0.327512	0.22221	N	0.062947	T	0.16811	0.0404	L	0.35288	1.05	0.23454	N	0.997641	P	0.36354	0.549	B	0.37550	0.253	T	0.21895	-1.0232	10	0.22109	T	0.4	-1.1405	6.7434	0.23449	0.0:0.0856:0.4757:0.4386	.	52	Q8N283	ANR35_HUMAN	T	52	ENSP00000347802:S52T;ENSP00000442671:S52T	ENSP00000347802:S52T	S	+	1	0	ANKRD35	144267163	0.921000	0.31238	0.798000	0.32154	0.565000	0.35776	0.509000	0.22707	0.069000	0.16605	0.533000	0.62120	TCG	.	.		0.592	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		A	145555806	T	A	145555806	3	1	150	1	0	0	0	0	1	0	0	0	664	1551	54	4	160	4	ANKRD35	1	145555806	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	687692	145555806	103694815	18	22742										
GJA5	2702	hgsc.bcm.edu	37	chr1	147231300	147231300	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgcctaccacggtcgagtgcTtgtgtacttcctccaggaaa	10	12	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:147231300T>A	ENST00000271348.2	-	2	208	c.47A>T	c.(46-48)aAg>aTg	p.K16M	GJA5_ENST00000369237.1_Missense_Mutation_p.K16M|RP11-433J22.2_ENST00000428911.1_RNA	NM_005266.5	NP_005257.2	P36382	CXA5_HUMAN	gap junction protein, alpha 5, 40kDa	16					angiogenesis (GO:0001525)|artery morphogenesis (GO:0048844)|atrial cardiac muscle cell action potential (GO:0086014)|atrial septum development (GO:0003283)|AV node cell to bundle of His cell communication by electrical coupling (GO:0086053)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|gap junction assembly (GO:0016264)|mitral valve development (GO:0003174)|outflow tract morphogenesis (GO:0003151)|pulmonary valve formation (GO:0003193)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|transmembrane transport (GO:0055085)|ventricular septum development (GO:0003281)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)	gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling (GO:0086077)|gap junction channel activity involved in cardiac conduction electrical coupling (GO:0086075)|gap junction hemi-channel activity (GO:0055077)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	20	all_hematologic(923;0.0276)		LUSC - Lung squamous cell carcinoma(543;0.202)			GGTCGAGTGCTTGTGTACTTC	0.542																																					p.K16M		Atlas-SNP	.											.	GJA5	64	.	0			c.A47T						.						92	99	96					1																	147231300		2203	4300	6503	SO:0001583	missense	2702	exon2			GAGTGCTTGTGTA		CCDS929.1	1q21.1	2008-02-05	2007-01-16		ENSG00000143140	ENSG00000265107		"Ion channels / Gap junction proteins (connexins)"	4279	protein-coding gene	gene with protein product	"connexin 40"	121013	"gap junction protein, alpha 5, 40kD (connexin 40)", "gap junction protein, alpha 5, 40kDa (connexin 40)"				Standard	NM_005266		Approved	CX40	uc001eps.1	P36382	OTTHUMG00000014020	ENST00000271348.2:c.47A>T	chr1.hg19:g.147231300T>A	ENSP00000271348:p.Lys16Met	73.0	0.0		113.0	13.0	NM_005266	Q5T3B6|Q5U0N6	Missense_Mutation	SNP	ENST00000271348.2	hg19	CCDS929.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561812	0.65538	.	.	ENSG00000143140	ENST00000271348;ENST00000369237;ENST00000430508	D;D;D	0.99186	-5.53;-5.53;-5.53	4.97	4.97	0.65823	Connexin, N-terminal (1);	0.051337	0.85682	D	0.000000	D	0.99171	0.9713	M	0.83223	2.63	0.53005	D	0.999965	D	0.69078	0.997	D	0.70227	0.968	D	0.99537	1.0962	10	0.87932	D	0	.	14.8539	0.70319	0.0:0.0:0.0:1.0	.	16	P36382	CXA5_HUMAN	M	16	ENSP00000271348:K16M;ENSP00000358240:K16M;ENSP00000407645:K16M	ENSP00000271348:K16M	K	-	2	0	GJA5	145697924	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	6.017000	0.70805	2.090000	0.63153	0.460000	0.39030	AAG	.	.		0.542	GJA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039422.2	NM_181703		A	147231300	T	A	147231300	3	1	150	1	0	0	0	0	1	0	0	0	6412	1609	56	4	1033	4	GJA5	1	147231300	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1675494	147231300	102019321	19	22743										
PLEKHO1	51177	hgsc.bcm.edu	37	chr1	150123217	150123217	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaaccgctatgtggtgctgaAaggggaccagctctacatct	11	10	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:150123217A>T	ENST00000369124.4	+	2	424	c.146A>T	c.(145-147)aAa>aTa	p.K49I	PLEKHO1_ENST00000479194.1_3'UTR|PLEKHO1_ENST00000025469.6_Missense_Mutation_p.K49I|PLEKHO1_ENST00000369126.1_De_novo_Start_OutOfFrame	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	49	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GTGGTGCTGAAAGGGGACCAG	0.562																																					p.K49I		Atlas-SNP	.											.	PLEKHO1	37	.	0			c.A146T						.						127	132	130					1																	150123217		2203	4300	6503	SO:0001583	missense	51177	exon2			TGCTGAAAGGGGA	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.146A>T	chr1.hg19:g.150123217A>T	ENSP00000358120:p.Lys49Ile	244.0	0.0		444.0	45.0	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Missense_Mutation	SNP	ENST00000369124.4	hg19	CCDS945.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.000021	0.74818	.	.	ENSG00000023902	ENST00000025469;ENST00000369124	T;T	0.17854	2.25;2.25	3.46	2.34	0.29019	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.231148	0.42420	D	0.000706	T	0.17023	0.0409	M	0.65975	2.015	0.44275	D	0.997131	D	0.53462	0.96	P	0.57776	0.827	T	0.01725	-1.1287	10	0.45353	T	0.12	-6.9587	6.1411	0.20261	0.791:0.0:0.209:0.0	.	49	Q53GL0	PKHO1_HUMAN	I	49	ENSP00000025469:K49I;ENSP00000358120:K49I	ENSP00000025469:K49I	K	+	2	0	PLEKHO1	148389841	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	1.615000	0.36922	0.718000	0.32166	0.459000	0.35465	AAA	.	.		0.562	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		T	150123217	A	T	150123217	3	4	150	1	0	0	0	0	1	0	0	0	12093	14	1	4	152	4	PLEKHO1	1	150123217	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2891917	150123217	99127404	20	22744										
HORMAD1	84072	hgsc.bcm.edu	37	chr1	150686584	150686584	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttttttctgtaaagcatcatAacatcctagcatcctaaaaa	3	9	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:150686584A>T	ENST00000361824.2	-	5	361	c.256T>A	c.(256-258)Tat>Aat	p.Y86N	HORMAD1_ENST00000368993.2_Missense_Mutation_p.Y86N|HORMAD1_ENST00000368995.4_Missense_Mutation_p.Y15N|HORMAD1_ENST00000476530.1_5'UTR|HORMAD1_ENST00000322343.7_Missense_Mutation_p.Y86N	NM_032132.4	NP_115508.2	Q86X24	HORM1_HUMAN	HORMA domain containing 1	86	HORMA. {ECO:0000255|PROSITE- ProRule:PRU00109}.				blastocyst development (GO:0001824)|meiotic DNA double-strand break formation (GO:0042138)|meiotic nuclear division (GO:0007126)|meiotic recombination checkpoint (GO:0051598)|meiotic sister chromatid cohesion (GO:0051177)|oogenesis (GO:0048477)|regulation of homologous chromosome segregation (GO:0060629)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(3)	16	all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			AAAGCATCATAACATCCTAGC	0.264																																					p.Y86N		Atlas-SNP	.											.	HORMAD1	59	.	0			c.T256A						.						52	60	58					1																	150686584		2194	4271	6465	SO:0001583	missense	84072	exon5			CATCATAACATCC	AL136755	CCDS967.1, CCDS55633.1	1q21.2	2009-03-09			ENSG00000143452	ENSG00000143452			25245	protein-coding gene	gene with protein product	"cancer/testis antigen 46"	609824				11230166, 15999985	Standard	NM_032132		Approved	DKFZP434A1315, CT46	uc001evk.2	Q86X24	OTTHUMG00000035005	ENST00000361824.2:c.256T>A	chr1.hg19:g.150686584A>T	ENSP00000355167:p.Tyr86Asn	531.0	0.0		905.0	222.0	NM_001199829	A6NMK2|B3KUK1|Q4G114|Q5T5I3|Q5T5I4|Q5T5I5|Q6FIC1|Q9H0K8	Missense_Mutation	SNP	ENST00000361824.2	hg19	CCDS967.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308364	0.81247	.	.	ENSG00000143452	ENST00000368995;ENST00000368993;ENST00000368992;ENST00000540570;ENST00000322343;ENST00000361824;ENST00000368987;ENST00000442853	T;T;T;T	0.55588	0.51;1.42;1.39;1.42	5.52	5.52	0.82312	DNA-binding HORMA (4);	0.050252	0.85682	D	0.000000	T	0.63873	0.2548	M	0.66297	2.02	0.51482	D	0.999929	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.99	T	0.68047	-0.5512	10	0.59425	D	0.04	-14.7869	14.4815	0.67587	1.0:0.0:0.0:0.0	.	15;86;86	Q86X24-4;Q86X24-2;Q86X24	.;.;HORM1_HUMAN	N	15;86;15;15;86;86;15;15	ENSP00000357991:Y15N;ENSP00000357989:Y86N;ENSP00000326489:Y86N;ENSP00000355167:Y86N	ENSP00000326489:Y86N	Y	-	1	0	HORMAD1	148953208	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.672000	0.91181	2.100000	0.63781	0.383000	0.25322	TAT	.	.		0.264	HORMAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084722.1	NM_032132		T	150686584	A	T	150686584	3	4	150	1	0	0	0	0	1	0	0	0	7295	362	13	4	972	4	HORMAD1	1	150686584	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	563367	150686584	98564037	21	22745										
ANXA9	8416	hgsc.bcm.edu	37	chr1	150956826	150956826	+	Frame_Shift_Del	DEL	C	C	-													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgtgatggctctgctgcagCccacagcccagtttgacgcc							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:150956826delC	ENST00000368947.4	+	6	813	c.337delC	c.(337-339)cccfs	p.P113fs	ANXA9_ENST00000474997.1_3'UTR	NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	113					single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCTGCTGCAGCCCACAGCCCA	0.567																																					p.Q112fs		Atlas-INDEL	.											.	ANXA9	28	.	0			c.336delG						.						107	102	104					1																	150956826		2203	4300	6503	SO:0001589	frameshift_variant	8416	exon6			.	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"Annexins"	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.337delC	chr1.hg19:g.150956826delC	ENSP00000357943:p.Pro113fs	109.0	0.0		177.0	23.0	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Frame_Shift_Del	DEL	ENST00000368947.4	hg19	CCDS975.2																																																																																			.	.		0.567	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568		-	150956826	C	-	150956826	7	5	150	1	0	1	0	1	0	0	0	0	725	739	26	0	351	0	ANXA9	1	150956826	Frame_Shift_Del	DEL	C	TCGA-DD-AAC8-01A-11D-A40R-10	270242	150956826	98293795	22	22746	101	3								
ANXA9	8416	hgsc.bcm.edu	37	chr1	150956828	150956829	+	Frame_Shift_Del	DEL	CA	CA	-													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtgatggctctgctgcagccCacagcccagtttgacgccca					rs7536645	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:150956828_150956829delCA	ENST00000368947.4	+	6	815_816	c.339_340delCA	c.(337-342)cccacafs	p.T114fs	ANXA9_ENST00000474997.1_3'UTR	NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	114			T -> A (in dbSNP:rs7536645).		single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TGCTGCAGCCCACAGCCCAGTT	0.569																																					p.113_113del		Pindel	.											.	ANXA9	28	.	0			c.338_339del						.																																			SO:0001589	frameshift_variant	8416	exon6			.	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"Annexins"	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.339_340delCA	chr1.hg19:g.150956830_150956831delCA	ENSP00000357943:p.Thr114fs	108.0	0.0		175.0	19.0	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Frame_Shift_Del	DEL	ENST00000368947.4	hg19	CCDS975.2																																																																																			.	.		0.569	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568		-	150956829	CA	-	150956828	7	5	150	1	0	1	0	1	0	0	0	0	725	581	21	0	353	0	ANXA9	1	150956828	Frame_Shift_Del	DEL	CA	TCGA-DD-AAC8-01A-11D-A40R-10	2	150956828	98293793	23	22747	101	3								
ANXA9	8416	hgsc.bcm.edu	37	chr1	150956829	150956829	+	Missense_Mutation	SNP	A	A	T													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgatggctctgctgcagcccAcagcccagtttgacgcccag					rs7536645	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:150956829A>T	ENST00000368947.4	+	6	816	c.340A>T	c.(340-342)Aca>Tca	p.T114S	ANXA9_ENST00000474997.1_3'UTR	NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	114			T -> A (in dbSNP:rs7536645).		single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GCTGCAGCCCACAGCCCAGTT	0.567																																					p.T114S		Atlas-SNP	.											.	ANXA9	28	.	0			c.A340T						.						106	101	102					1																	150956829		2203	4300	6503	SO:0001583	missense	8416	exon6			CAGCCCACAGCCC	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"Annexins"	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.340A>T	chr1.hg19:g.150956829A>T	ENSP00000357943:p.Thr114Ser	106.0	0.0		174.0	24.0	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Missense_Mutation	SNP	ENST00000368947.4	hg19	CCDS975.2	.	.	.	.	.	.	.	.	.	.	A	8.392	0.839917	0.16891	.	.	ENSG00000143412	ENST00000368947	T	0.04758	3.56	5.0	-2.45	0.06481	.	0.635660	0.16333	N	0.219039	T	0.00724	0.0024	N	0.17764	0.52	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.46541	-0.9184	10	0.32370	T	0.25	.	1.102	0.01686	0.4177:0.153:0.2735:0.1558	.	114	O76027	ANXA9_HUMAN	S	114	ENSP00000357943:T114S	ENSP00000357943:T114S	T	+	1	0	ANXA9	149223453	0.000000	0.05858	0.073000	0.20177	0.047000	0.14425	-0.205000	0.09411	-0.277000	0.09193	-1.177000	0.01723	ACA	.	A|0.978;G|0.022		0.567	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568		T	150956829	A	T	150956829	3	4	150	1	0	0	0	0	1	0	0	0	725	159	6	4	354	4	ANXA9	1	150956829	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1	150956829	98293792	24	22748	101	3								
ANXA9	8416	hgsc.bcm.edu	37	chr1	150957133	150957133	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccaccccagctgcaggagtgCctggcagtctacaaacacag	10	15	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:150957133C>G	ENST00000368947.4	+	7	929	c.453C>G	c.(451-453)tgC>tgG	p.C151W		NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	151					single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TGCAGGAGTGCCTGGCAGTCT	0.542																																					p.C151W		Atlas-SNP	.											.	ANXA9	28	.	0			c.C453G						.						46	44	45					1																	150957133		2203	4300	6503	SO:0001583	missense	8416	exon7			GGAGTGCCTGGCA	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"Annexins"	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.453C>G	chr1.hg19:g.150957133C>G	ENSP00000357943:p.Cys151Trp	47.0	0.0		103.0	15.0	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Missense_Mutation	SNP	ENST00000368947.4	hg19	CCDS975.2	.	.	.	.	.	.	.	.	.	.	C	12.95	2.091772	0.36952	.	.	ENSG00000143412	ENST00000368947	T	0.03272	3.99	5.25	3.35	0.38373	.	0.142017	0.49916	D	0.000138	T	0.06645	0.0170	L	0.56769	1.78	0.58432	D	0.999998	D	0.76494	0.999	D	0.73380	0.98	T	0.05037	-1.0910	10	0.87932	D	0	.	8.3046	0.32034	0.0:0.8078:0.0:0.1921	.	151	O76027	ANXA9_HUMAN	W	151	ENSP00000357943:C151W	ENSP00000357943:C151W	C	+	3	2	ANXA9	149223757	1.000000	0.71417	1.000000	0.80357	0.254000	0.26022	0.657000	0.24963	1.336000	0.45506	0.655000	0.94253	TGC	.	.		0.542	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568		G	150957133	C	G	150957133	3	3	150	1	0	0	0	0	1	0	0	0	725	747	26	4	471	4	ANXA9	1	150957133	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	304	150957133	98293488	25	22749										
PRUNE	58497	hgsc.bcm.edu	37	chr1	151006513	151006513	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aagtggacaaggaattggacAgggcaagtaactccctgatt	12	7	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:151006513A>T	ENST00000271620.3	+	8	1321	c.1165A>T	c.(1165-1167)Agg>Tgg	p.R389W	PRUNE_ENST00000368937.1_Missense_Mutation_p.R154W|BNIPL_ENST00000368931.3_5'Flank|PRUNE_ENST00000368934.1_Missense_Mutation_p.R154W|BNIPL_ENST00000295294.7_5'Flank|PRUNE_ENST00000271619.8_Missense_Mutation_p.R177W|PRUNE_ENST00000368936.1_Missense_Mutation_p.R207W|PRUNE_ENST00000368935.1_Missense_Mutation_p.R104W	NM_021222.1	NP_067045.1	Q86TP1	PRUNE_HUMAN	prune exopolyphosphatase	389						cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GGAATTGGACAGGGCAAGTAA	0.552																																					p.R389W		Atlas-SNP	.											.	PRUNE	40	.	0			c.A1165T						.						103	91	95					1																	151006513		2203	4300	6503	SO:0001583	missense	58497	exon8			TTGGACAGGGCAA	U67085	CCDS977.1	1q21.2	2013-04-29	2013-04-29		ENSG00000143363	ENSG00000143363	3.6.1.11		13420	protein-coding gene	gene with protein product			"prune homolog (Drosophila)"			10602478, 11687967, 18700747	Standard	NM_021222		Approved	DRES-17, HTCD37	uc001ewh.1	Q86TP1	OTTHUMG00000035062	ENST00000271620.3:c.1165A>T	chr1.hg19:g.151006513A>T	ENSP00000271620:p.Arg389Trp	171.0	0.0		258.0	27.0	NM_021222	B2RCH8|B4DFL7|Q5SZF9|Q659E5|Q6P4E0|Q8N654|Q96JU5|Q9C071|Q9C072|Q9UIV0	Missense_Mutation	SNP	ENST00000271620.3	hg19	CCDS977.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.823762	0.71143	.	.	ENSG00000143363	ENST00000271620;ENST00000302413;ENST00000271619;ENST00000368937;ENST00000431193;ENST00000368936;ENST00000368935;ENST00000368934	T;T;T;T;T;T;T	0.34667	1.4;1.35;1.35;1.38;1.35;1.37;1.35	5.35	2.96	0.34315	.	0.264276	0.33515	N	0.004834	T	0.13286	0.0322	N	0.08118	0	0.25591	N	0.986696	D;P	0.56968	0.978;0.953	P;P	0.57371	0.819;0.715	T	0.08249	-1.0731	9	.	.	.	.	6.8309	0.23909	0.7678:0.1519:0.0803:0.0	.	177;389	E9PCU1;Q86TP1	.;PRUNE_HUMAN	W	389;322;177;154;154;207;104;154	ENSP00000271620:R389W;ENSP00000271619:R177W;ENSP00000357933:R154W;ENSP00000392632:R154W;ENSP00000357932:R207W;ENSP00000357931:R104W;ENSP00000357930:R154W	.	R	+	1	2	PRUNE	149273137	0.992000	0.36948	0.998000	0.56505	0.956000	0.61745	2.665000	0.46791	0.527000	0.28560	0.533000	0.62120	AGG	.	.		0.552	PRUNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084885.1	NM_021222		T	151006513	A	T	151006513	3	4	150	1	0	0	0	0	1	0	0	0	12652	179	7	4	1195	4	PRUNE	1	151006513	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	49380	151006513	98244108	26	22750										
PI4KB	5298	hgsc.bcm.edu	37	chr1	151278812	151278812	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtcaaagttttcacattcaaGgacttccacataaatcaggt	6	9	4	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:151278812G>A	ENST00000368873.1	-	5	1378	c.1210C>T	c.(1210-1212)Ctt>Ttt	p.L404F	PI4KB_ENST00000368875.2_Missense_Mutation_p.L416F|PI4KB_ENST00000368872.1_Missense_Mutation_p.L389F|PI4KB_ENST00000368874.4_Missense_Mutation_p.L389F|PI4KB_ENST00000271657.5_Missense_Mutation_p.L416F|PI4KB_ENST00000529142.1_Missense_Mutation_p.L72F			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta	404					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TCACATTCAAGGACTTCCACA	0.493																																					p.L416F	Colon(154;765 1838 9854 28443 37492)	Atlas-SNP	.											.	PI4KB	76	.	0			c.C1246T						.						54	52	53					1																	151278812		2203	4300	6503	SO:0001583	missense	5298	exon6			ATTCAAGGACTTC	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348	ENST00000368873.1:c.1210C>T	chr1.hg19:g.151278812G>A	ENSP00000357867:p.Leu404Phe	113.0	0.0		252.0	35.0	NM_002651	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	Missense_Mutation	SNP	ENST00000368873.1	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.366319	0.95900	.	.	ENSG00000143393	ENST00000368874;ENST00000368875;ENST00000271657;ENST00000368873;ENST00000529142;ENST00000368872;ENST00000430800;ENST00000489223	D;D;D;D;D;D;T;T	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5;-1.5;1.89;1.89	5.88	5.88	0.94601	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.89897	0.6848	M	0.84683	2.71	0.80722	D	1	P;D;D	0.76494	0.781;0.999;0.997	B;D;D	0.74023	0.358;0.982;0.954	D	0.90408	0.4407	10	0.72032	D	0.01	-11.117	18.8019	0.92022	0.0:0.0:1.0:0.0	.	404;389;72	Q9UBF8;Q9UBF8-2;Q9UBF8-3	PI4KB_HUMAN;.;.	F	389;416;416;404;72;389;72;72	ENSP00000357868:L389F;ENSP00000357869:L416F;ENSP00000271657:L416F;ENSP00000357867:L404F;ENSP00000433149:L72F;ENSP00000357866:L389F;ENSP00000413599:L72F;ENSP00000431501:L72F	ENSP00000271657:L416F	L	-	1	0	PI4KB	149545436	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.119000	0.94362	2.779000	0.95612	0.650000	0.86243	CTT	.	.		0.493	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651		A	151278812	G	A	151278812	3	1	150	1	0	0	0	0	1	0	0	0	11883	1000	35	3	1272	3	PI4KB	1	151278812	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	272299	151278812	97971809	27	22751										
HRNR	388697	hgsc.bcm.edu	37	chr1	152191860	152191860	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgctgaccatagctggaagAcaaacctgagctagatccgt	10	10	0	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:152191860A>T	ENST00000368801.2	-	3	2320	c.2245T>A	c.(2245-2247)Tct>Act	p.S749T	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	749					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TAGCTGGAAGACAAACCTGAG	0.567																																					p.S749T		Atlas-SNP	.											.	HRNR	403	.	0			c.T2245A						.						173	170	171					1																	152191860		2203	4300	6503	SO:0001583	missense	388697	exon3			TGGAAGACAAACC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.2245T>A	chr1.hg19:g.152191860A>T	ENSP00000357791:p.Ser749Thr	79.0	0.0		166.0	19.0	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	hg19	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	5.261	0.233680	0.09969	.	.	ENSG00000197915	ENST00000368801	T	0.02974	4.09	2.65	-0.0682	0.13757	.	.	.	.	.	T	0.00608	0.0020	L	0.36672	1.1	0.09310	N	1	B	0.27951	0.195	B	0.23018	0.043	T	0.47368	-0.9123	9	0.17832	T	0.49	.	2.4479	0.04510	0.6202:0.0:0.1459:0.2339	.	749	Q86YZ3	HORN_HUMAN	T	749	ENSP00000357791:S749T	ENSP00000357791:S749T	S	-	1	0	HRNR	150458484	0.016000	0.18221	0.000000	0.03702	0.004000	0.04260	0.229000	0.17833	-0.145000	0.11294	-0.451000	0.05528	TCT	.	.		0.567	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		T	152191860	A	T	152191860	3	4	150	1	0	0	0	0	1	0	0	0	7368	275	10	4	6311	4	HRNR	1	152191860	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	913048	152191860	97058761	28	22752										
FLG	2312	hgsc.bcm.edu	37	chr1	152283807	152283807	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctgagtgtccagatctatcTaccgattgctcatggtggga	11	10	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:152283807T>A	ENST00000368799.1	-	3	3590	c.3555A>T	c.(3553-3555)gtA>gtT	p.V1185V	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1185	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAGATCTATCTACCGATTGCT	0.592									Ichthyosis																												p.V1185V		Atlas-SNP	.											.	FLG	900	.	0			c.A3555T						.						347	352	350					1																	152283807		2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCTATCTACCGAT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.3555A>T	chr1.hg19:g.152283807T>A		123.0	0.0		195.0	21.0	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152283807	T	A	152283807	2	1	150	1	0	0	0	0	0	0	0	1	5930	1509	53	4		4	FLG	1	152283807	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	91947	152283807	96966814	29	22753										
FLG	2312	hgsc.bcm.edu	37	chr1	152285144	152285144	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctgactaccactggaccctcGgtgtccactgtctctgactg	9	15	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:152285144G>C	ENST00000368799.1	-	3	2253	c.2218C>G	c.(2218-2220)Cga>Gga	p.R740G	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	740	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGGACCCTCGGTGTCCACTG	0.572									Ichthyosis																												p.R740G		Atlas-SNP	.											.	FLG	900	.	0			c.C2218G						.						357	373	367					1																	152285144		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ACCCTCGGTGTCC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2218C>G	chr1.hg19:g.152285144G>C	ENSP00000357789:p.Arg740Gly	86.0	0.0		124.0	14.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	6.492	0.458958	0.12342	.	.	ENSG00000143631	ENST00000368799	T	0.01725	4.67	4.17	-4.32	0.03688	.	.	.	.	.	T	0.00580	0.0019	L	0.56769	1.78	0.09310	N	1	P	0.39665	0.682	B	0.33799	0.17	T	0.43750	-0.9372	9	0.33141	T	0.24	-6.6813	4.0775	0.09911	0.0855:0.1226:0.2438:0.548	.	740	P20930	FILA_HUMAN	G	740	ENSP00000357789:R740G	ENSP00000357789:R740G	R	-	1	2	FLG	150551768	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.683000	0.00835	-0.570000	0.06022	-0.462000	0.05337	CGA	.	.		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152285144	G	C	152285144	3	2	150	1	0	0	0	0	1	0	0	0	5930	1124	39	4	9971	4	FLG	1	152285144	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	1337	152285144	96965477	30	22754										
S100A3	6274	hgsc.bcm.edu	37	chr1	153520241	153520241	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcaggcaagtgagcgcacatActccacaaagtccacctcgc	9	15	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:153520241A>T	ENST00000368713.3	-	3	419	c.223T>A	c.(223-225)Tat>Aat	p.Y75N	S100A4_ENST00000368714.1_Intron|S100A4_ENST00000368716.4_5'Flank|S100A4_ENST00000368715.1_5'Flank|S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000481009.1_5'Flank|S100A3_ENST00000368712.1_Missense_Mutation_p.Y75N	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	75	EF-hand 2.					cytoplasm (GO:0005737)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|liver(1)|lung(1)	3	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAGCGCACATACTCCACAAAG	0.552																																					p.Y75N		Atlas-SNP	.											.	S100A3	7	.	0			c.T223A						.						240	204	216					1																	153520241		2203	4300	6503	SO:0001583	missense	6274	exon3			GCACATACTCCAC	BC012893	CCDS1043.1	1q21	2008-02-05	2001-11-28		ENSG00000188015	ENSG00000188015		"S100 calcium binding proteins"	10493	protein-coding gene	gene with protein product		176992	"S100 calcium-binding protein A3"	S100E		8341667	Standard	NM_002960		Approved		uc001fca.1	P33764	OTTHUMG00000013550	ENST00000368713.3:c.223T>A	chr1.hg19:g.153520241A>T	ENSP00000357702:p.Tyr75Asn	131.0	0.0		225.0	39.0	NM_002960	D3DV51|Q6FGE4	Missense_Mutation	SNP	ENST00000368713.3	hg19	CCDS1043.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.713123	0.68730	.	.	ENSG00000188015	ENST00000368713;ENST00000368712	T;T	0.16597	2.33;2.33	4.85	4.85	0.62838	S100/Calbindin-D9k, conserved site (1);EF-hand-like domain (1);	0.155014	0.44483	D	0.000441	T	0.27134	0.0665	M	0.84511	2.7	0.58432	D	0.999994	D	0.61080	0.989	P	0.55011	0.766	T	0.14924	-1.0455	10	0.87932	D	0	.	11.1049	0.48197	1.0:0.0:0.0:0.0	.	75	P33764	S10A3_HUMAN	N	75	ENSP00000357702:Y75N;ENSP00000357701:Y75N	ENSP00000357701:Y75N	Y	-	1	0	S100A3	151786865	1.000000	0.71417	0.894000	0.35097	0.686000	0.39977	5.494000	0.66905	1.926000	0.55796	0.533000	0.62120	TAT	.	.		0.552	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960		T	153520241	A	T	153520241	3	4	150	1	0	0	0	0	1	0	0	0	13794	391	14	4	86	4	S100A3	1	153520241	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1235097	153520241	95730380	31	22755										
TPM3	91181	hgsc.bcm.edu	37	chr1	154130187	154130187	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggtgctcctctttggtgcaTttcagtttatctaatggggg	12	7	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:154130187T>C	ENST00000368559.3	-	0	0				NUP210L_ENST00000271854.3_5'Flank|TPM3_ENST00000341372.3_Silent_p.K200K|TPM3_ENST00000341485.5_Silent_p.K209K|TPM3_ENST00000271850.7_Silent_p.K262K|TPM3_ENST00000368533.3_Silent_p.K225K|TPM3_ENST00000328159.4_3'UTR|TPM3_ENST00000330188.9_Silent_p.K225K|TPM3_ENST00000469717.1_5'UTR|TPM3_ENST00000302206.5_Silent_p.K135K	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like						Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CTTTGGTGCATTTCAGTTTAT	0.483																																					p.K225K		Atlas-SNP	.											.	TPM3	46	.	0			c.A675G						.						98	103	101					1																	154130187		2203	4300	6503	SO:0001631	upstream_gene_variant	7170	exon8			GGTGCATTTCAGT	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852		chr1.hg19:g.154130187T>C	Exception_encountered	44.0	0.0		58.0	14.0	NM_153649	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Silent	SNP	ENST00000368559.3	hg19	CCDS41399.1																																																																																			.	.		0.483	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		C	154130187	T	C	154130187	1	2	150	0	1	0	0	0	0	0	0	0	16422	1490	52	2		2	TPM3	1	154130187	5'Flank	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	609946	154130187	95120434	32	22756										
UBAP2L	9898	hgsc.bcm.edu	37	chr1	154226401	154226401	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	catcctctacaatttcatctAaccagagtcaggagtctggt	7	11	5	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:154226401A>T	ENST00000361546.2	+	14	1732	c.1690A>T	c.(1690-1692)Aac>Tac	p.N564Y	AL590431.1_ENST00000517008.1_RNA|UBAP2L_ENST00000271877.7_Missense_Mutation_p.N575Y|UBAP2L_ENST00000428931.1_Missense_Mutation_p.N564Y|UBAP2L_ENST00000343815.6_Missense_Mutation_p.N564Y			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	564					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AATTTCATCTAACCAGAGTCA	0.418																																					p.N564Y		Atlas-SNP	.											.	UBAP2L	197	.	0			c.A1690T						.						82	78	79					1																	154226401		2203	4300	6503	SO:0001583	missense	9898	exon15			TCATCTAACCAGA	BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.1690A>T	chr1.hg19:g.154226401A>T	ENSP00000355343:p.Asn564Tyr	101.0	0.0		183.0	46.0	NM_001127320	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	hg19	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.112221	0.77210	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000456955;ENST00000433006;ENST00000271877;ENST00000361546	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	4.84	4.84	0.62591	.	0.392298	0.26883	N	0.022006	T	0.11239	0.0274	N	0.24115	0.695	0.43226	D	0.995117	P;D;P;P;P	0.64830	0.86;0.994;0.856;0.856;0.91	B;P;P;P;B	0.56865	0.446;0.808;0.648;0.648;0.446	T	0.05517	-1.0880	10	0.54805	T	0.06	-2.6009	13.7512	0.62908	1.0:0.0:0.0:0.0	.	478;575;557;564;564	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	Y	564;564;60;60;575;564	ENSP00000345308:N564Y;ENSP00000389445:N564Y;ENSP00000271877:N575Y;ENSP00000355343:N564Y	ENSP00000271877:N575Y	N	+	1	0	UBAP2L	152493025	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.348000	0.73009	2.032000	0.59987	0.533000	0.62120	AAC	.	.		0.418	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		T	154226401	A	T	154226401	3	4	150	1	0	0	0	0	1	0	0	0	16853	362	13	4	1744	4	UBAP2L	1	154226401	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	96214	154226401	95024220	33	22757										
TDRD10	126668	hgsc.bcm.edu	37	chr1	154517399	154517399	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cttctggaccatcccaccccTgactcagccattcatgctgg	7	17	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:154517399T>A	ENST00000368480.3	+	11	1011	c.926T>A	c.(925-927)cTg>cAg	p.L309Q	TDRD10_ENST00000479937.1_3'UTR|TDRD10_ENST00000368482.4_Missense_Mutation_p.L309Q			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	309	Tudor.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			ATCCCACCCCTGACTCAGCCA	0.537																																					p.L309Q		Atlas-SNP	.											.	TDRD10	48	.	0			c.T926A						.						139	122	128					1																	154517399		2203	4300	6503	SO:0001583	missense	126668	exon11			CACCCCTGACTCA	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"Tudor domain containing", "RNA binding motif (RRM) containing"	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.926T>A	chr1.hg19:g.154517399T>A	ENSP00000357465:p.Leu309Gln	80.0	0.0		119.0	14.0	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Missense_Mutation	SNP	ENST00000368480.3	hg19	CCDS41406.1	.	.	.	.	.	.	.	.	.	.	T	15.25	2.778374	0.49786	.	.	ENSG00000163239	ENST00000368482;ENST00000368480	T;T	0.08896	3.04;3.04	3.63	2.44	0.29823	Maternal tudor protein (1);	0.000000	0.40222	N	0.001159	T	0.05410	0.0143	L	0.32530	0.975	0.24931	N	0.991912	D;D	0.89917	1.0;0.999	D;D	0.74674	0.984;0.973	T	0.29458	-1.0011	10	0.23891	T	0.37	-7.4813	5.7039	0.17897	0.0:0.1304:0.0:0.8696	.	309;309	Q5VZ19;Q5VZ19-2	TDR10_HUMAN;.	Q	309	ENSP00000357467:L309Q;ENSP00000357465:L309Q	ENSP00000357465:L309Q	L	+	2	0	TDRD10	152784023	0.190000	0.23276	0.239000	0.24122	0.778000	0.44026	0.769000	0.26604	0.435000	0.26365	0.528000	0.53228	CTG	.	.		0.537	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499		A	154517399	T	A	154517399	3	1	150	1	0	0	0	0	1	0	0	0	15746	1580	55	4	964	4	TDRD10	1	154517399	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	290998	154517399	94733222	34	22758										
ADAR	103	hgsc.bcm.edu	37	chr1	154561139	154561139	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gttgtatttcattaactcacTgtagagaaacctacaaaaag	6	7	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:154561139T>A	ENST00000368474.4	-	10	2972	c.2773A>T	c.(2773-2775)Agt>Tgt	p.S925C	ADAR_ENST00000292205.5_Missense_Mutation_p.S968C|ADAR_ENST00000368471.3_Missense_Mutation_p.S630C	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	925	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		ATTAACTCACTGTAGAGAAAC	0.388																																					p.S925C		Atlas-SNP	.											.	ADAR	113	.	0			c.A2773T						.						95	94	94					1																	154561139		2203	4300	6503	SO:0001583	missense	103	exon10			ACTCACTGTAGAG	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.2773A>T	chr1.hg19:g.154561139T>A	ENSP00000357459:p.Ser925Cys	94.0	0.0		154.0	20.0	NM_001111	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	hg19	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.660738	0.67700	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168	D;D;D;D	0.94457	-3.43;-3.43;-3.43;-3.43	5.19	4.05	0.47172	Adenosine deaminase/editase (3);	0.280867	0.43260	D	0.000591	D	0.95996	0.8696	M	0.79805	2.47	0.58432	D	0.999998	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.936;0.965;0.998	D	0.95956	0.8958	10	0.87932	D	0	-16.9448	8.4381	0.32799	0.0:0.0763:0.1432:0.7805	.	880;899;925	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	C	968;925;630;894	ENSP00000292205:S968C;ENSP00000357459:S925C;ENSP00000357456:S630C;ENSP00000431794:S894C	ENSP00000292205:S968C	S	-	1	0	ADAR	152827763	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.896000	0.56266	2.176000	0.68965	0.455000	0.32223	AGT	.	.		0.388	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		A	154561139	T	A	154561139	3	1	150	1	0	0	0	0	1	0	0	0	281	1580	55	4	931	4	ADAR	1	154561139	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	43740	154561139	94689482	35	22759										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155450303	155450303	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aagagagcaagagatggagcTgtggatttgctcaactttgg	14	5	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:155450303T>A	ENST00000368346.3	-	3	2997	c.2358A>T	c.(2356-2358)acA>acT	p.T786T	ASH1L_ENST00000392403.3_Silent_p.T786T			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	786					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			GAGATGGAGCTGTGGATTTGC	0.413																																					p.T786T		Atlas-SNP	.											.	ASH1L	279	.	0			c.A2358T						.						153	151	151					1																	155450303		2203	4298	6501	SO:0001819	synonymous_variant	55870	exon3			TGGAGCTGTGGAT	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.2358A>T	chr1.hg19:g.155450303T>A		208.0	0.0		327.0	35.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.		0.413	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155450303	T	A	155450303	2	1	150	1	0	0	0	0	0	0	0	1	1041	1567	55	4		4	ASH1L	1	155450303	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	889164	155450303	93800318	36	22760										
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156517962	156517962	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cacggaggcgggcctggagcTggataacaaagccgacgttg	16	10	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:156517962T>A	ENST00000361170.2	-	19	2217	c.2207A>T	c.(2206-2208)cAg>cTg	p.Q736L		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	736	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.				activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGCCTGGAGCTGGATAACAAA	0.577																																					p.Q736L		Atlas-SNP	.											.	IQGAP3	146	.	0			c.A2207T						.						43	43	43					1																	156517962		2203	4300	6503	SO:0001583	missense	128239	exon19			TGGAGCTGGATAA	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.2207A>T	chr1.hg19:g.156517962T>A	ENSP00000354451:p.Gln736Leu	92.0	0.0		188.0	33.0	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	hg19	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	T	10.02	1.235563	0.22626	.	.	ENSG00000183856	ENST00000361170	T	0.69435	-0.4	4.32	-0.566	0.11767	.	0.604741	0.16984	N	0.191599	T	0.30039	0.0752	L	0.31476	0.935	0.26785	N	0.969529	B	0.23185	0.081	B	0.21917	0.037	T	0.25467	-1.0131	10	0.46703	T	0.11	-0.8431	9.2591	0.37601	0.0:0.4856:0.0:0.5144	.	736	Q86VI3	IQGA3_HUMAN	L	736	ENSP00000354451:Q736L	ENSP00000354451:Q736L	Q	-	2	0	IQGAP3	154784586	0.007000	0.16637	0.173000	0.22940	0.578000	0.36192	-0.782000	0.04643	-0.286000	0.09076	0.459000	0.35465	CAG	.	.		0.577	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		A	156517962	T	A	156517962	3	1	150	1	0	0	0	0	1	0	0	0	7825	1580	55	4	2768	4	IQGAP3	1	156517962	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1067659	156517962	92732659	37	22761										
BCAN	63827	hgsc.bcm.edu	37	chr1	156617431	156617431	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgccgcctaccttgggggcTatgagcaatgtgatgctggc	14	10	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:156617431T>A	ENST00000329117.5	+	4	934	c.598T>A	c.(598-600)Tat>Aat	p.Y200N	RP11-284F21.10_ENST00000605886.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.Y200N|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	200	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCTTGGGGGCTATGAGCAATG	0.642																																					p.Y200N		Atlas-SNP	.											.	BCAN	174	.	0			c.T598A						.						78	81	80					1																	156617431		2203	4300	6503	SO:0001583	missense	63827	exon4			GGGGGCTATGAGC	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.598T>A	chr1.hg19:g.156617431T>A	ENSP00000331210:p.Tyr200Asn	28.0	0.0		51.0	6.0	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.112124	0.77210	.	.	ENSG00000132692	ENST00000329117;ENST00000457777;ENST00000424639;ENST00000361588	T;T;T;T	0.09073	3.02;3.02;3.02;3.02	4.28	4.28	0.50868	C-type lectin fold (1);Link (5);C-type lectin-like (1);	0.000000	0.53938	D	0.000047	T	0.21227	0.0511	M	0.82517	2.595	0.52099	D	0.999949	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.01914	-1.1248	10	0.87932	D	0	-2.1451	12.3748	0.55273	0.0:0.0:0.0:1.0	.	200;200	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	N	200;200;98;200	ENSP00000331210:Y200N;ENSP00000389898:Y200N;ENSP00000401709:Y98N;ENSP00000354925:Y200N	ENSP00000331210:Y200N	Y	+	1	0	BCAN	154884055	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.058000	0.71126	1.782000	0.52362	0.374000	0.22700	TAT	.	.		0.642	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		A	156617431	T	A	156617431	3	1	150	1	0	0	0	0	1	0	0	0	1345	1522	53	4	608	4	BCAN	1	156617431	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	99469	156617431	92633190	38	22762										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156939079	156939079	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctgctgggactcacctcacTgagggaaggaaagcgttctg	13	11	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:156939079T>A	ENST00000361409.2	-	9	1442	c.700A>T	c.(700-702)Agt>Tgt	p.S234C	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.S274C	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	234					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTCACCTCACTGAGGGAAGGA	0.567																																					p.S274C		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.A820T						.						45	36	39					1																	156939079		2203	4299	6502	SO:0001583	missense	9826	exon10			CCTCACTGAGGGA	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.700A>T	chr1.hg19:g.156939079T>A	ENSP00000354644:p.Ser234Cys	105.0	0.0		179.0	18.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	hg19	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	T	15.78	2.934432	0.52866	.	.	ENSG00000132694	ENST00000368194;ENST00000361409	T;T	0.69561	-0.41;-0.41	4.89	-0.0762	0.13723	.	0.093451	0.46758	D	0.000272	T	0.36468	0.0968	L	0.29908	0.895	0.80722	D	1	B;P	0.37914	0.251;0.611	B;B	0.36289	0.038;0.221	T	0.35525	-0.9785	10	0.72032	D	0.01	-2.1015	12.3396	0.55087	0.0:0.0845:0.0:0.9155	.	234;274	O15085;O15085-2	ARHGB_HUMAN;.	C	274;234	ENSP00000357177:S274C;ENSP00000354644:S234C	ENSP00000354644:S234C	S	-	1	0	ARHGEF11	155205703	0.988000	0.35896	0.648000	0.29521	0.981000	0.71138	0.802000	0.27069	-0.102000	0.12197	0.533000	0.62120	AGT	.	.		0.567	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		A	156939079	T	A	156939079	3	1	150	1	0	0	0	0	1	0	0	0	896	1580	55	4	3996	4	ARHGEF11	1	156939079	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	321648	156939079	92311542	39	22763										
CD5L	922	hgsc.bcm.edu	37	chr1	157804379	157804379	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtacagccctcccacatcccAgctgccggcacaccaccttt	6	20	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:157804379A>T	ENST00000368174.4	-	4	632	c.536T>A	c.(535-537)cTg>cAg	p.L179Q	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	179	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CCCACATCCCAGCTGCCGGCA	0.582																																					p.L179Q		Atlas-SNP	.											.	CD5L	112	.	0			c.T536A						.						90	84	86					1																	157804379		2203	4300	6503	SO:0001583	missense	922	exon4			CATCCCAGCTGCC	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.536T>A	chr1.hg19:g.157804379A>T	ENSP00000357156:p.Leu179Gln	47.0	0.0		121.0	42.0	NM_005894	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	hg19	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.949902	0.73787	.	.	ENSG00000073754	ENST00000368174	T	0.58060	0.36	5.13	5.13	0.70059	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.207580	0.24191	N	0.040713	T	0.78000	0.4215	H	0.97340	3.985	0.39200	D	0.963129	D	0.89917	1.0	D	0.81914	0.995	D	0.85848	0.1402	10	0.87932	D	0	.	12.9409	0.58342	1.0:0.0:0.0:0.0	.	179	O43866	CD5L_HUMAN	Q	179	ENSP00000357156:L179Q	ENSP00000357156:L179Q	L	-	2	0	CD5L	156071003	1.000000	0.71417	1.000000	0.80357	0.503000	0.33858	8.554000	0.90689	2.150000	0.67090	0.533000	0.62120	CTG	.	.		0.582	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		T	157804379	A	T	157804379	3	4	150	1	0	0	0	0	1	0	0	0	3029	188	7	4	519	4	CD5L	1	157804379	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	865300	157804379	91446242	40	22764										
FCRLB	127943	hgsc.bcm.edu	37	chr1	161693276	161693276	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcctggagctccagcccatcAgcactctctggtatttgggc	10	14	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:161693276A>T	ENST00000367948.2	+	5	387	c.172A>T	c.(172-174)Agc>Tgc	p.S58C	FCRLB_ENST00000367944.3_Missense_Mutation_p.S51C|FCRLB_ENST00000367946.3_Missense_Mutation_p.S58C|FCRLB_ENST00000392158.1_Missense_Mutation_p.S58C|FCRLB_ENST00000367945.1_Missense_Mutation_p.S51C|FCRLB_ENST00000336830.5_Missense_Mutation_p.S58C			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	58	Ig-like C2-type 1.				negative regulation of immune response (GO:0050777)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|skin(1)	17	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			CCAGCCCATCAGCACTCTCTG	0.547																																					p.S58C		Atlas-SNP	.											.	FCRLB	35	.	0			c.A172T						.						133	126	129					1																	161693276		2203	4300	6503	SO:0001583	missense	127943	exon3			CCCATCAGCACTC	AY670683	CCDS30927.1, CCDS72962.1, CCDS72963.1, CCDS72964.1, CCDS72965.1	1q23.3	2013-01-11	2006-09-26	2006-09-26	ENSG00000162746	ENSG00000162746		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26431	protein-coding gene	gene with protein product		609251	"Fc receptor-like and mucin-like 2"	FCRLM2		15676285	Standard	NM_001288829		Approved	FLJ31052, FCRL2, FREB-2, FCRLY	uc001gbi.3	Q6BAA4	OTTHUMG00000133629	ENST00000367948.2:c.172A>T	chr1.hg19:g.161693276A>T	ENSP00000356925:p.Ser58Cys	153.0	0.0		283.0	40.0	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Missense_Mutation	SNP	ENST00000367948.2	hg19	CCDS30927.1	.	.	.	.	.	.	.	.	.	.	A	19.23	3.786991	0.70337	.	.	ENSG00000162746	ENST00000367948;ENST00000367946;ENST00000367945;ENST00000336830;ENST00000367944;ENST00000392158	T;T;T;T;T;T	0.13901	2.55;2.55;2.55;2.55;2.55;2.55	5.76	4.61	0.57282	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.647571	0.14906	N	0.291553	T	0.19886	0.0478	M	0.75447	2.3	0.28651	N	0.906669	D;D;D;D;D	0.76494	0.999;0.993;0.996;0.993;0.975	D;P;P;P;P	0.63192	0.912;0.8;0.855;0.8;0.739	T	0.10847	-1.0612	10	0.87932	D	0	.	9.874	0.41191	0.8282:0.1718:0.0:0.0	.	51;51;58;58;58	Q6BAA4-3;Q6BAA4-5;Q6BAA4-2;Q6BAA4-4;Q6BAA4	.;.;.;.;FCRLB_HUMAN	C	58;58;51;58;51;58	ENSP00000356925:S58C;ENSP00000356923:S58C;ENSP00000356922:S51C;ENSP00000338598:S58C;ENSP00000356921:S51C;ENSP00000375999:S58C	ENSP00000338598:S58C	S	+	1	0	FCRLB	159959900	0.984000	0.35163	0.902000	0.35471	0.974000	0.67602	1.834000	0.39171	0.964000	0.38108	0.533000	0.62120	AGC	.	.		0.547	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378		T	161693276	A	T	161693276	3	4	150	1	0	0	0	0	1	0	0	0	5809	188	7	4	182	4	FCRLB	1	161693276	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3888897	161693276	87557345	41	22765										
ILDR2	387597	hgsc.bcm.edu	37	chr1	166927035	166927035	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcgtgatctctctgcccctgTagaaatctcccagggtgaca	9	13	3	3	rs138041277		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:166927035T>A	ENST00000271417.3	-	2	405	c.350A>T	c.(349-351)tAc>tTc	p.Y117F	ILDR2_ENST00000529387.1_Missense_Mutation_p.Y117F|ILDR2_ENST00000469934.2_Missense_Mutation_p.Y117F|ILDR2_ENST00000528703.1_Missense_Mutation_p.Y117F|ILDR2_ENST00000529071.1_Missense_Mutation_p.Y117F|ILDR2_ENST00000526687.1_Missense_Mutation_p.Y117F|ILDR2_ENST00000525740.1_Missense_Mutation_p.Y117F	NM_199351.2	NP_955383.1	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor 2	117	Ig-like V-type.				cell differentiation (GO:0030154)|homeostasis of number of cells within a tissue (GO:0048873)|insulin secretion (GO:0030073)|pancreas development (GO:0031016)|response to glucose (GO:0009749)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(3)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	22						TCTGCCCCTGTAGAAATCTCC	0.473																																					p.Y117F		Atlas-SNP	.											.	ILDR2	79	.	0			c.A350T						.						67	68	68					1																	166927035		2203	4300	6503	SO:0001583	missense	387597	exon2			CCCCTGTAGAAAT	AF503509	CCDS1256.1	1q24.1	2008-12-18	2008-12-18	2008-12-18	ENSG00000143195	ENSG00000143195			18131	protein-coding gene	gene with protein product	"LISCH-like"		"chromosome 1 open reading frame 32"	C1orf32			Standard	NM_199351		Approved		uc001gdx.2	Q71H61	OTTHUMG00000034320	ENST00000271417.3:c.350A>T	chr1.hg19:g.166927035T>A	ENSP00000271417:p.Tyr117Phe	101.0	0.0		172.0	24.0	NM_199351		Missense_Mutation	SNP	ENST00000271417.3	hg19	CCDS1256.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.484617	0.84854	.	.	ENSG00000143195	ENST00000271417;ENST00000525740;ENST00000529387;ENST00000469934;ENST00000529071;ENST00000526687;ENST00000528703	T;T;T;T;T;T;T	0.01505	4.82;4.82;4.82;4.82;4.82;4.82;4.82	6.03	6.03	0.97812	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.06917	0.0176	M	0.77486	2.375	0.58432	D	0.999999	D	0.76494	0.999	D	0.78314	0.991	T	0.02781	-1.1111	10	0.87932	D	0	.	16.5655	0.84588	0.0:0.0:0.0:1.0	.	117	Q71H61	ILDR2_HUMAN	F	117	ENSP00000271417:Y117F;ENSP00000436120:Y117F;ENSP00000431316:Y117F;ENSP00000437008:Y117F;ENSP00000436882:Y117F;ENSP00000434273:Y117F;ENSP00000432750:Y117F	ENSP00000271417:Y117F	Y	-	2	0	ILDR2	165193659	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.033000	0.88852	2.302000	0.77476	0.533000	0.62120	TAC	.	T|1.000;C|0.000		0.473	ILDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082880.2	NM_199351		A	166927035	T	A	166927035	3	1	150	1	0	0	0	0	1	0	0	0	7719	1638	57	4	1605	4	ILDR2	1	166927035	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	5233759	166927035	82323586	42	22766										
NME7	29922	hgsc.bcm.edu	37	chr1	169200018	169200018	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	attattctgttgaatctccaTtgctacacaagggccagaat	7	9	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:169200018T>C	ENST00000367811.3	-	10	1184	c.928A>G	c.(928-930)Atg>Gtg	p.M310V	NME7_ENST00000472647.1_Missense_Mutation_p.M274V	NM_013330.3	NP_037462.1	Q9Y5B8	NDK7_HUMAN	NME/NM23 family member 7	310					brain development (GO:0007420)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|CTP biosynthetic process (GO:0006241)|determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(8)|skin(1)	16	all_hematologic(923;0.208)					TGAATCTCCATTGCTACACAA	0.313																																					p.M310V		Atlas-SNP	.											.	NME7	34	.	0			c.A928G						.						88	82	84					1																	169200018		2203	4299	6502	SO:0001583	missense	29922	exon10			TCTCCATTGCTAC	AF153191	CCDS1277.1, CCDS44274.1	1q24.2	2014-07-31	2012-05-18		ENSG00000143156	ENSG00000143156			20461	protein-coding gene	gene with protein product	"cilia and flagella associated protein 67"	613465	"non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)"			19852809	Standard	NM_197972		Approved	FLJ37194, NM23-H7, CFAP67	uc001gfu.3	Q9Y5B8	OTTHUMG00000034586	ENST00000367811.3:c.928A>G	chr1.hg19:g.169200018T>C	ENSP00000356785:p.Met310Val	455.0	0.0		949.0	117.0	NM_013330	A8K3T6|A8MY09|B3KSW9|Q5TGZ4	Missense_Mutation	SNP	ENST00000367811.3	hg19	CCDS1277.1	.	.	.	.	.	.	.	.	.	.	T	12.14	1.849787	0.32699	.	.	ENSG00000143156	ENST00000472647;ENST00000367811	T;T	0.55760	0.5;0.5	5.65	-11.3	0.00108	.	0.646940	0.16510	N	0.211261	T	0.20414	0.0491	L	0.56769	1.78	0.32853	D	0.506970	B	0.02656	0.0	B	0.24155	0.051	T	0.02925	-1.1093	9	0.49607	T	0.09	-0.7583	9.0524	0.36385	0.2051:0.0684:0.6032:0.1233	.	310	Q9Y5B8	NDK7_HUMAN	V	274;310	ENSP00000433341:M274V;ENSP00000356785:M310V	ENSP00000356785:M310V	M	-	1	0	NME7	167466642	0.821000	0.29204	0.089000	0.20774	0.933000	0.57130	-0.063000	0.11655	-2.106000	0.00841	-1.341000	0.01249	ATG	.	.		0.313	NME7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083688.1	NM_013330		C	169200018	T	C	169200018	3	2	150	1	0	0	0	0	1	0	0	0	10505	1493	52	2	214	2	NME7	1	169200018	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2272983	169200018	80050603	43	22767										
C1orf129	80133	hgsc.bcm.edu	37	chr1	170916672	170916672	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccttctttctggctagagagTagtctccagattctgcaaga	9	10	4	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:170916672T>A	ENST00000367758.3	+	3	129	c.30T>A	c.(28-30)agT>agA	p.S10R	MROH9_ENST00000367759.4_Missense_Mutation_p.S10R	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	10																	GGCTAGAGAGTAGTCTCCAGA	0.383																																					p.S10R		Atlas-SNP	.											.	.	.	.	0			c.T30A						.						140	129	132					1																	170916672		1870	4109	5979	SO:0001583	missense	80133	exon3			AGAGAGTAGTCTC	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"maestro heat-like repeat containing"	26287	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 129"	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.30T>A	chr1.hg19:g.170916672T>A	ENSP00000356732:p.Ser10Arg	104.0	0.0		190.0	35.0	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	hg19	CCDS41436.1	.	.	.	.	.	.	.	.	.	.	T	10.43	1.347508	0.24426	.	.	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.17691	3.9;2.26	2.82	-2.36	0.06663	.	3.192640	0.02365	U	0.077284	T	0.02119	0.0066	N	0.08118	0	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.12156	0.007;0.007	T	0.38329	-0.9666	10	0.66056	D	0.02	0.0083	0.2964	0.00266	0.2036:0.2705:0.2079:0.3179	.	10;10	F5GWX6;Q5TGP6	.;CA129_HUMAN	R	10	ENSP00000356733:S10R;ENSP00000356732:S10R	ENSP00000356732:S10R	S	+	3	2	C1orf129	169183296	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.884000	0.01622	-0.548000	0.06199	-0.349000	0.07799	AGT	.	.		0.383	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		A	170916672	T	A	170916672	3	1	150	1	0	0	0	0	1	0	0	0	1998	1635	57	4	36	4	C1orf129	1	170916672	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1716654	170916672	78333949	44	22768										
PIGC	5279	hgsc.bcm.edu	37	chr1	172411330	172411330	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggcatagatggtgtcagtgcTgacagactctgtaagggtct	14	7	3	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:172411330T>A	ENST00000367728.1	-	1	1896	c.433A>T	c.(433-435)Agc>Tgc	p.S145C	PIGC_ENST00000484368.1_Intron|PIGC_ENST00000344529.4_Missense_Mutation_p.S145C|C1orf105_ENST00000367727.4_Intron|PIGC_ENST00000258324.1_Missense_Mutation_p.S145C			Q92535	PIGC_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class C	145					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			breast(1)|endometrium(1)|kidney(1)|lung(1)	4						GTGTCAGTGCTGACAGACTCT	0.488																																					p.S145C		Atlas-SNP	.											.	PIGC	24	.	0			c.A433T						.						59	54	56					1																	172411330		2203	4300	6503	SO:0001583	missense	5279	exon2			CAGTGCTGACAGA	BC006539	CCDS1302.1	1q23-q25	2013-02-26	2006-06-28		ENSG00000135845	ENSG00000135845	2.4.1.198	"Phosphatidylinositol glycan anchor biosynthesis"	8960	protein-coding gene	gene with protein product	"phosphatidylinositol N-acetylglucosaminyltransferase"	601730	"phosphatidylinositol glycan, class C"			8806613, 9325057	Standard	NM_153747		Approved		uc001gio.3	Q92535	OTTHUMG00000034751	ENST00000367728.1:c.433A>T	chr1.hg19:g.172411330T>A	ENSP00000356702:p.Ser145Cys	153.0	0.0		252.0	38.0	NM_153747	O14491	Missense_Mutation	SNP	ENST00000367728.1	hg19	CCDS1302.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.196441	0.78902	.	.	ENSG00000135845	ENST00000344529;ENST00000367728;ENST00000258324	T;T;T	0.61627	0.09;0.09;0.09	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.75376	0.3841	M	0.89785	3.06	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81865	-0.0736	10	0.87932	D	0	0.0372	13.6827	0.62496	0.0:0.0:0.0:1.0	.	145	Q92535	PIGC_HUMAN	C	145	ENSP00000356701:S145C;ENSP00000356702:S145C;ENSP00000258324:S145C	ENSP00000258324:S145C	S	-	1	0	PIGC	170677953	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.528000	0.81941	1.917000	0.55516	0.528000	0.53228	AGC	.	.		0.488	PIGC-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084068.1	NM_153747		A	172411330	T	A	172411330	3	1	150	1	0	0	0	0	1	0	0	0	11895	1580	55	4	464	4	PIGC	1	172411330	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1494658	172411330	76839291	45	22769										
RC3H1	149041	hgsc.bcm.edu	37	chr1	173934198	173934198	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggcaggcccacctcattaagTtgacccaaagaggcactcaa	9	13	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:173934198T>A	ENST00000367696.2	-	10	1746	c.1395A>T	c.(1393-1395)caA>caT	p.Q465H	RC3H1_ENST00000258349.4_Missense_Mutation_p.Q465H|RC3H1_ENST00000367694.2_Missense_Mutation_p.Q465H			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	465					B cell homeostasis (GO:0001782)|cytoplasmic mRNA processing body assembly (GO:0033962)|lymph node development (GO:0048535)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of germinal center formation (GO:0002635)|negative regulation of T-helper cell differentiation (GO:0045623)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|posttranscriptional regulation of gene expression (GO:0010608)|protein ubiquitination (GO:0016567)|regulation of germinal center formation (GO:0002634)|regulation of mRNA stability (GO:0043488)|regulation of T cell receptor signaling pathway (GO:0050856)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	50						CCTCATTAAGTTGACCCAAAG	0.438																																					p.Q465H		Atlas-SNP	.											.	RC3H1	110	.	0			c.A1395T						.						86	81	83					1																	173934198		2203	4300	6503	SO:0001583	missense	149041	exon9			ATTAAGTTGACCC	AK093501	CCDS30940.1, CCDS72987.1	1q25.1	2013-01-18	2010-09-15		ENSG00000135870	ENSG00000135870		"RING-type (C3HC4) zinc fingers", "Zinc fingers, CCCH-type domain containing"	29434	protein-coding gene	gene with protein product	"KIAA2025 protein"	609424	"ring finger and CCCH-type zinc finger domains 1"			15917799	Standard	XM_005244918		Approved	KIAA2025, roquin, RP5-1198E17.5, RNF198	uc001gju.4	Q5TC82	OTTHUMG00000037275	ENST00000367696.2:c.1395A>T	chr1.hg19:g.173934198T>A	ENSP00000356669:p.Gln465His	111.0	0.0		230.0	27.0	NM_172071	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	Missense_Mutation	SNP	ENST00000367696.2	hg19	CCDS30940.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.737968	0.69304	.	.	ENSG00000135870	ENST00000367696;ENST00000258349;ENST00000367694	T;T;T	0.45668	0.89;0.89;0.89	5.8	-8.88	0.00789	.	0.075071	0.56097	N	0.000030	T	0.42245	0.1194	L	0.44542	1.39	0.47778	D	0.999518	D;D;D;D	0.71674	0.996;0.996;0.998;0.996	D;D;D;D	0.75484	0.953;0.986;0.979;0.93	T	0.66881	-0.5811	10	0.22706	T	0.39	-6.2429	10.0172	0.42022	0.096:0.3044:0.0:0.5996	.	465;465;465;465	B9EGU6;B7ZMB3;Q5TC82-2;Q5TC82	.;.;.;RC3H1_HUMAN	H	465	ENSP00000356669:Q465H;ENSP00000258349:Q465H;ENSP00000356667:Q465H	ENSP00000258349:Q465H	Q	-	3	2	RC3H1	172200821	0.891000	0.30450	0.601000	0.28877	0.985000	0.73830	0.002000	0.13061	-2.058000	0.00895	-0.899000	0.02877	CAA	.	.		0.438	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090733.2	NM_172071		A	173934198	T	A	173934198	3	1	150	1	0	0	0	0	1	0	0	0	13181	1722	60	4	2050	4	RC3H1	1	173934198	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1522868	173934198	75316423	46	22770										
NPHS2	7827	hgsc.bcm.edu	37	chr1	179530443	179530443	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccagggcctttggctcttccAggaagcagatgtcccagtcg	12	13	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:179530443A>T	ENST00000367615.4	-	3	500	c.432T>A	c.(430-432)ccT>ccA	p.P144P	NPHS2_ENST00000367616.4_Silent_p.P144P	NM_014625.2	NP_055440.1	Q9NP85	PODO_HUMAN	nephrosis 2, idiopathic, steroid-resistant (podocin)	144					actin cytoskeleton reorganization (GO:0031532)|excretion (GO:0007588)|metanephric glomerular visceral epithelial cell development (GO:0072249)	cell-cell junction (GO:0005911)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)				NS(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	20						TGGCTCTTCCAGGAAGCAGAT	0.373																																					p.P144P		Atlas-SNP	.											.	NPHS2	46	.	0			c.T432A						.						141	159	153					1																	179530443		2203	4300	6503	SO:0001819	synonymous_variant	7827	exon3			TCTTCCAGGAAGC	AJ279254	CCDS1331.1, CCDS72988.1	1q25-q31	2014-06-27			ENSG00000116218	ENSG00000116218			13394	protein-coding gene	gene with protein product		604766				8589695, 10742096	Standard	XM_005245483		Approved	SRN1, PDCN	uc001gmq.4	Q9NP85	OTTHUMG00000035252	ENST00000367615.4:c.432T>A	chr1.hg19:g.179530443A>T		245.0	0.0		489.0	74.0	NM_014625	B1AM32|B1AM33|Q8N6Q5	Silent	SNP	ENST00000367615.4	hg19	CCDS1331.1																																																																																			.	.		0.373	NPHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085283.1			T	179530443	A	T	179530443	2	4	150	1	0	0	0	0	0	0	0	1	10592	175	7	4		4	NPHS2	1	179530443	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5596245	179530443	69720178	47	22771										
DHX9	1660	hgsc.bcm.edu	37	chr1	182836162	182836162	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgtaattgtagatgaaatacAtgaaagagatattaatgtaa	8	1	0	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:182836162A>T	ENST00000367549.3	+	14	1651	c.1541A>T	c.(1540-1542)cAt>cTt	p.H514L		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	514	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						GATGAAATACATGAAAGAGAT	0.323																																					p.H514L	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.A1541T						.						150	136	140					1																	182836162		1829	4080	5909	SO:0001583	missense	1660	exon14			AAATACATGAAAG	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.1541A>T	chr1.hg19:g.182836162A>T	ENSP00000356520:p.His514Leu	68.0	0.0		169.0	23.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.509870	0.85282	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	T	0.62364	0.03	5.36	5.36	0.76844	DEAD-like helicase (2);DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.88647	0.6493	H	0.99740	4.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93532	0.6870	10	0.72032	D	0.01	.	15.0124	0.71560	1.0:0.0:0.0:0.0	.	514	Q08211	DHX9_HUMAN	L	514	ENSP00000356520:H514L	ENSP00000356520:H514L	H	+	2	0	DHX9	181102785	1.000000	0.71417	0.982000	0.44146	0.989000	0.77384	8.421000	0.90259	2.033000	0.60031	0.482000	0.46254	CAT	.	.		0.323	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		T	182836162	A	T	182836162	3	4	150	1	0	0	0	0	1	0	0	0	4518	217	8	4	1591	4	DHX9	1	182836162	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3305719	182836162	66414459	48	22772										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186034407	186034407	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	attacatggcacaaagatggGcagcccctccaagaagatga	10	10	0	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:186034407G>T	ENST00000271588.4	+	49	7780	c.7551G>T	c.(7549-7551)ggG>ggT	p.G2517G	HMCN1_ENST00000367492.2_Silent_p.G2517G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2517	Ig-like C2-type 23.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ACAAAGATGGGCAGCCCCTCC	0.398																																					p.G2517G		Atlas-SNP	.											.	HMCN1	797	.	0			c.G7551T						.						64	62	62					1																	186034407		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon49			AGATGGGCAGCCC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7551G>T	chr1.hg19:g.186034407G>T		60.0	0.0		131.0	24.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.398	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186034407	G	T	186034407	2	4	150	1	0	0	0	0	0	0	0	1	7229	1190	42	3		3	HMCN1	1	186034407	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	3198245	186034407	63216214	49	22773										
PRG4	10216	hgsc.bcm.edu	37	chr1	186275482	186275482	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agaagaacagaactaaaaagAaacctacccccaaaccacca	4	13	0	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:186275482A>C	ENST00000445192.2	+	7	676	c.631A>C	c.(631-633)Aaa>Caa	p.K211Q	PRG4_ENST00000367484.3_Missense_Mutation_p.K170Q|PRG4_ENST00000367486.3_Missense_Mutation_p.K168Q|PRG4_ENST00000367483.4_Missense_Mutation_p.K170Q|PRG4_ENST00000367485.4_Missense_Mutation_p.K118Q	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	211					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						AACTAAAAAGAAACCTACCCC	0.358																																					p.K211Q		Atlas-SNP	.											.	PRG4	259	.	0			c.A631C						.						133	138	136					1																	186275482		2203	4300	6503	SO:0001583	missense	10216	exon7			AAAAAGAAACCTA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.631A>C	chr1.hg19:g.186275482A>C	ENSP00000399679:p.Lys211Gln	142.0	0.0		245.0	32.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	hg19	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	A	1.708	-0.499759	0.04291	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000533951;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T;T	0.52295	2.91;3.53;0.67;3.47;3.35;3.53	4.07	1.43	0.22495	.	0.142736	0.31438	U	0.007649	T	0.44477	0.1295	M	0.61703	1.905	0.09310	N	1	P;P;P;P	0.42518	0.782;0.782;0.675;0.782	P;P;B;B	0.46172	0.506;0.506;0.246;0.428	T	0.27434	-1.0074	10	0.25106	T	0.35	-0.6262	5.8859	0.18882	0.7841:0.0:0.2159:0.0	.	77;118;211;170	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	Q	168;170;120;77;170;118;211	ENSP00000356456:K168Q;ENSP00000356454:K170Q;ENSP00000431330:K120Q;ENSP00000356453:K170Q;ENSP00000356455:K118Q;ENSP00000399679:K211Q	ENSP00000356452:K77Q	K	+	1	0	PRG4	184542105	0.037000	0.19845	0.457000	0.27056	0.100000	0.18952	0.993000	0.29680	0.045000	0.15804	0.383000	0.25322	AAA	.	.		0.358	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		C	186275482	A	C	186275482	3	2	150	1	0	0	0	0	1	0	0	0	12493	247	9	5	653	5	PRG4	1	186275482	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	241075	186275482	62975139	50	22774										
PTGS2	5743	hgsc.bcm.edu	37	chr1	186644523	186644523	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggtggaacattcctaccaccAgcaacctgtggaaagtaaaa	9	10	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:186644523A>T	ENST00000367468.5	-	9	1399	c.1263T>A	c.(1261-1263)gcT>gcA	p.A421A	PTGS2_ENST00000490885.2_5'UTR	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	421					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	TCCTACCACCAGCAACCTGTG	0.393																																					p.A421A		Atlas-SNP	.											.	PTGS2	144	.	0			c.T1263A						.						77	75	76					1																	186644523		2203	4300	6503	SO:0001819	synonymous_variant	5743	exon9			ACCACCAGCAACC	D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.1263T>A	chr1.hg19:g.186644523A>T		115.0	0.0		280.0	34.0	NM_000963	A8K802|Q16876	Silent	SNP	ENST00000367468.5	hg19	CCDS1371.1																																																																																			.	.		0.393	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963		T	186644523	A	T	186644523	2	4	150	1	0	0	0	0	0	0	0	1	12769	175	7	4		4	PTGS2	1	186644523	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	369041	186644523	62606098	51	22775										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190068155	190068155	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gaacgcggtgcagaccacctGgtcattcggacacgtgcacg	13	13	1	1	rs560983384		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:190068155G>T	ENST00000367462.3	-	8	1525	c.1294C>A	c.(1294-1296)Cag>Aag	p.Q432K	BRINP3_ENST00000534846.1_Missense_Mutation_p.Q330K	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	432					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											CAGACCACCTGGTCATTCGGA	0.597													G|||	1	0.000199681	8e-04	0	5008	,	,		17138	0		0	False		,,,				2504	0				p.Q432K		Atlas-SNP	.											.	FAM5C	343	.	0			c.C1294A						.						56	44	48					1																	190068155		2203	4300	6503	SO:0001583	missense	339479	exon8			CCACCTGGTCATT	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1294C>A	chr1.hg19:g.190068155G>T	ENSP00000356432:p.Gln432Lys	180.0	0.0		257.0	37.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.483590	0.63962	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	D;D	0.87334	-2.24;-2.24	5.65	5.65	0.86999	.	0.056763	0.64402	D	0.000001	D	0.84365	0.5456	L	0.47716	1.5	0.49130	D	0.99975	B;B	0.27732	0.187;0.055	B;B	0.27500	0.08;0.015	T	0.81342	-0.0976	10	0.42905	T	0.14	.	17.2216	0.86959	0.0:0.0:1.0:0.0	.	330;432	B7Z260;Q76B58	.;FAM5C_HUMAN	K	432;330	ENSP00000356432:Q432K;ENSP00000438022:Q330K	ENSP00000356432:Q432K	Q	-	1	0	FAM5C	188334778	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.353000	0.97080	2.656000	0.90262	0.591000	0.81541	CAG	.	.		0.597	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190068155	G	T	190068155	3	4	150	1	0	0	0	0	1	0	0	0	5602	1357	47	3	1010	3	FAM5C	1	190068155	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	3423632	190068155	59182466	52	22776										
RGS2	5997	hgsc.bcm.edu	37	chr1	192778220	192778220	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	taatgcaaagtgctatgttcTtggctgttcaacacgactgc	9	9	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:192778220T>A	ENST00000235382.5	+	1	50	c.19T>A	c.(19-21)Ttg>Atg	p.L7M	RGS2_ENST00000483295.1_3'UTR	NM_002923.3	NP_002914.1	P41220	RGS2_HUMAN	regulator of G-protein signaling 2	7					brown fat cell differentiation (GO:0050873)|cell cycle (GO:0007049)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phospholipase activity (GO:0010519)|positive regulation of cardiac muscle contraction (GO:0060452)|positive regulation of microtubule polymerization (GO:0031116)|regulation of adrenergic receptor signaling pathway (GO:0071877)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of translation (GO:0006417)|relaxation of cardiac muscle (GO:0055119)|relaxation of vascular smooth muscle (GO:0060087)|spermatogenesis (GO:0007283)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			large_intestine(3)|lung(1)|urinary_tract(1)	5						TGCTATGTTCTTGGCTGTTCA	0.587																																					p.L7M	Pancreas(71;51 2183 4981)	Atlas-SNP	.											.	RGS2	19	.	0			c.T19A						.						167	148	155					1																	192778220		2203	4300	6503	SO:0001583	missense	5997	exon1			ATGTTCTTGGCTG	L13463	CCDS1377.1	1q31	2014-06-19	2014-06-19		ENSG00000116741	ENSG00000116741		"Regulators of G-protein signaling", "Endogenous ligands"	9998	protein-coding gene	gene with protein product		600861	"regulator of G-protein signalling 2, 24kD", "regulator of G-protein signalling 2, 24kDa", "regulator of G-protein signaling 2, 24kDa"	G0S8		8179820	Standard	NM_002923		Approved		uc001gsl.3	P41220	OTTHUMG00000035600	ENST00000235382.5:c.19T>A	chr1.hg19:g.192778220T>A	ENSP00000235382:p.Leu7Met	430.0	0.0		798.0	117.0	NM_002923	Q6I9U5	Missense_Mutation	SNP	ENST00000235382.5	hg19	CCDS1377.1	.	.	.	.	.	.	.	.	.	.	T	11.65	1.702766	0.30232	.	.	ENSG00000116741	ENST00000235382	T	0.73681	-0.77	4.44	0.0971	0.14493	.	0.346810	0.22981	N	0.053308	T	0.55273	0.1910	N	0.24115	0.695	0.28770	N	0.900439	B	0.15473	0.013	B	0.12837	0.008	T	0.43718	-0.9374	10	0.36615	T	0.2	.	7.988	0.30224	0.0:0.5996:0.0:0.4004	.	7	P41220	RGS2_HUMAN	M	7	ENSP00000235382:L7M	ENSP00000235382:L7M	L	+	1	2	RGS2	191044843	0.041000	0.20044	0.998000	0.56505	0.577000	0.36160	-1.541000	0.02198	-0.068000	0.12953	-0.462000	0.05337	TTG	.	.		0.587	RGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086396.1	NM_002923		A	192778220	T	A	192778220	3	1	150	1	0	0	0	0	1	0	0	0	13317	1606	56	4	21	4	RGS2	1	192778220	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2710065	192778220	56472401	53	22777										
ZBTB41	360023	hgsc.bcm.edu	37	chr1	197169358	197169358	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcacaaaaagatggttgcttCtgcctatcatcatttaaata	5	8	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:197169358C>A	ENST00000367405.4	-	1	314	c.246G>T	c.(244-246)caG>caT	p.Q82H	CRB1_ENST00000535699.1_5'Flank|ZBTB41_ENST00000467322.1_5'UTR	NM_194314.2	NP_919290.2	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	82					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(11)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	40						ATGGTTGCTTCTGCCTATCAT	0.353																																					p.Q82H		Atlas-SNP	.											.	ZBTB41	116	.	0			c.G246T						.						61	63	62					1																	197169358		2203	4300	6503	SO:0001583	missense	360023	exon1			TTGCTTCTGCCTA		CCDS30960.1	1q31.3	2013-01-08			ENSG00000177888	ENSG00000177888		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	24819	protein-coding gene	gene with protein product							Standard	NM_194314		Approved	FRBZ1, FLJ36199, DKFZp686C06120, ZNF924	uc001gtx.1	Q5SVQ8	OTTHUMG00000036275	ENST00000367405.4:c.246G>T	chr1.hg19:g.197169358C>A	ENSP00000356375:p.Gln82His	68.0	0.0		150.0	14.0	NM_194314	A2RUA8|Q6MZT8|Q6ZR25|Q7Z4T1|Q8IZ99	Missense_Mutation	SNP	ENST00000367405.4	hg19	CCDS30960.1	.	.	.	.	.	.	.	.	.	.	C	11.91	1.780718	0.31502	.	.	ENSG00000177888	ENST00000367405	T	0.68624	-0.34	4.96	4.96	0.65561	BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.41605	D	0.000849	T	0.54532	0.1864	N	0.16656	0.425	0.38528	D	0.948905	B	0.15141	0.012	B	0.23150	0.044	T	0.53592	-0.8417	10	0.40728	T	0.16	.	18.2007	0.89836	0.0:1.0:0.0:0.0	.	82	Q5SVQ8	ZBT41_HUMAN	H	82	ENSP00000356375:Q82H	ENSP00000356375:Q82H	Q	-	3	2	ZBTB41	195435981	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.931000	0.40134	2.265000	0.75225	0.305000	0.20034	CAG	.	.		0.353	ZBTB41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088249.2	NM_194314		A	197169358	C	A	197169358	3	1	150	1	0	0	0	0	1	0	0	0	17558	912	32	3	2523	3	ZBTB41	1	197169358	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	4391138	197169358	52081263	54	22778										
CRB1	23418	hgsc.bcm.edu	37	chr1	197403940	197403940	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcacatttggtttcagaacaAgggatgcaaatgtaataata	8	5	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:197403940A>T	ENST00000367400.3	+	9	3082	c.2947A>T	c.(2947-2949)Agg>Tgg	p.R983W	CRB1_ENST00000538660.1_Intron|CRB1_ENST00000367399.2_Missense_Mutation_p.R871W|CRB1_ENST00000535699.1_Missense_Mutation_p.R959W|CRB1_ENST00000544212.1_Missense_Mutation_p.R464W|CRB1_ENST00000367397.1_Missense_Mutation_p.R364W	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	983	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TTTCAGAACAAGGGATGCAAA	0.333																																					p.R983W		Atlas-SNP	.											.	CRB1	284	.	0			c.A2947T						.						75	79	78					1																	197403940		2203	4300	6503	SO:0001583	missense	23418	exon9			AGAACAAGGGATG		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2947A>T	chr1.hg19:g.197403940A>T	ENSP00000356370:p.Arg983Trp	195.0	0.0		329.0	56.0	NM_201253	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	hg19	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.044633	0.36085	.	.	ENSG00000134376	ENST00000535699;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26	5.34	1.49	0.22878	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.87079	0.6088	M	0.81341	2.54	0.09310	N	0.999998	D;D;D;D	0.76494	0.998;0.996;0.994;0.999	P;D;D;D	0.66716	0.891;0.928;0.946;0.934	T	0.79771	-0.1663	9	0.42905	T	0.14	.	15.4999	0.75691	0.3525:0.6475:0.0:0.0	.	959;871;632;983	F5H0L2;P82279-3;P82279-4;P82279	.;.;.;CRUM1_HUMAN	W	959;983;871;464;364;632	ENSP00000438786:R959W;ENSP00000356370:R983W;ENSP00000356369:R871W;ENSP00000444556:R464W;ENSP00000356367:R364W	ENSP00000356367:R364W	R	+	1	2	CRB1	195670563	0.872000	0.30054	0.138000	0.22173	0.301000	0.27625	2.036000	0.41165	-0.008000	0.14320	0.533000	0.62120	AGG	.	.		0.333	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		T	197403940	A	T	197403940	3	4	150	1	0	0	0	0	1	0	0	0	3850	63	3	4	2981	4	CRB1	1	197403940	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	234582	197403940	51846681	55	22779										
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200818090	200818090	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gttgcttgggcacaaattccAgaagaaacagggcttccaca	10	10	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:200818090A>T	ENST00000236925.4	+	12	2275	c.2226A>T	c.(2224-2226)ccA>ccT	p.P742P	CAMSAP2_ENST00000413307.2_Silent_p.P715P|CAMSAP2_ENST00000358823.2_Silent_p.P731P			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	742					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										CACAAATTCCAGAAGAAACAG	0.453																																					p.P731P		Atlas-SNP	.											.	.	.	.	0			c.A2193T						.						72	79	76					1																	200818090		2203	4300	6503	SO:0001819	synonymous_variant	23271	exon11			AATTCCAGAAGAA	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.2226A>T	chr1.hg19:g.200818090A>T		190.0	0.0		370.0	57.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Silent	SNP	ENST00000236925.4	hg19																																																																																				.	.		0.453	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		T	200818090	A	T	200818090	2	4	150	1	0	0	0	0	0	0	0	1	2614	175	7	4		4	CAMSAP1L1	1	200818090	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3414150	200818090	48432531	56	22780										
NFASC	23114	hgsc.bcm.edu	37	chr1	204945893	204945893	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccagcaccgagctagaccaaGacctggccaaggcctacctc	9	17	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:204945893G>T	ENST00000401399.1	+	15	2000	c.1801G>T	c.(1801-1803)Gac>Tac	p.D601Y	NFASC_ENST00000539706.1_Missense_Mutation_p.D612Y|NFASC_ENST00000404907.1_Missense_Mutation_p.D612Y|NFASC_ENST00000367170.4_Missense_Mutation_p.D601Y|NFASC_ENST00000339876.6_Missense_Mutation_p.D601Y|NFASC_ENST00000367169.4_Missense_Mutation_p.D601Y|NFASC_ENST00000360049.4_Missense_Mutation_p.D612Y|NFASC_ENST00000338586.6_Missense_Mutation_p.D601Y|NFASC_ENST00000367171.4_Missense_Mutation_p.D601Y|NFASC_ENST00000403080.1_Missense_Mutation_p.D601Y|NFASC_ENST00000338515.6_Missense_Mutation_p.D601Y|NFASC_ENST00000367172.4_Missense_Mutation_p.D601Y|NFASC_ENST00000513543.1_Missense_Mutation_p.D612Y|NFASC_ENST00000404076.1_Missense_Mutation_p.D595Y			O94856	NFASC_HUMAN	neurofascin	601	Ig-like C2-type 6.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GCTAGACCAAGACCTGGCCAA	0.622																																					p.D612Y		Atlas-SNP	.											NFASC_ENST00000403080,caecum,carcinoma,0,3	NFASC	396	.	0			c.G1834T						.						191	156	168					1																	204945893		2203	4300	6503	SO:0001583	missense	23114	exon16			GACCAAGACCTGG	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.1801G>T	chr1.hg19:g.204945893G>T	ENSP00000385637:p.Asp601Tyr	99.0	0.0		194.0	35.0	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	hg19	CCDS53460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.2|23.2	4.391065|4.391065	0.82902|0.82902	.|.	.|.	ENSG00000163531|ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393|ENST00000367173	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.68479|.	-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33|.	5.19|5.19	4.27|4.27	0.50696|0.50696	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.107759|.	0.40640|.	N|.	0.001054|.	T|T	0.76485|0.76485	0.3994|0.3994	M|M	0.83692|0.83692	2.655|2.655	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.76494|.	0.998;0.983;0.986;0.997;0.999;0.994;0.984|.	D;D;D;D;P;D;P|.	0.73380|.	0.98;0.94;0.917;0.95;0.854;0.917;0.894|.	T|T	0.78807|0.78807	-0.2059|-0.2059	10|5	0.66056|.	D|.	0.02|.	.|.	13.7779|13.7779	0.63066|0.63066	0.0766:0.0:0.9234:0.0|0.0766:0.0:0.9234:0.0	.|.	601;612;612;601;601;612;601|.	O94856;O94856-11;O94856-8;F8W791;O94856-9;O94856-3;O94856-2|.	NFASC_HUMAN;.;.;.;.;.;.|.	Y|N	601;601;601;601;601;601;612;612;612;601;601;595;601;612;612;588|570	ENSP00000356140:D601Y;ENSP00000356139:D601Y;ENSP00000356138:D601Y;ENSP00000342128:D601Y;ENSP00000344786:D601Y;ENSP00000343509:D601Y;ENSP00000438614:D612Y;ENSP00000353154:D612Y;ENSP00000356137:D601Y;ENSP00000384875:D601Y;ENSP00000385676:D595Y;ENSP00000385637:D601Y;ENSP00000384061:D612Y;ENSP00000425908:D612Y;ENSP00000415031:D588Y|.	ENSP00000295776:D612Y|.	D|K	+|+	1|3	0|2	NFASC|NFASC	203212516|203212516	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.958000|0.958000	0.62258|0.62258	6.590000|6.590000	0.74085|0.74085	2.433000|2.433000	0.82419|0.82419	0.561000|0.561000	0.74099|0.74099	GAC|AAG	.	.		0.622	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		T	204945893	G	T	204945893	3	4	150	1	0	0	0	0	1	0	0	0	10368	942	33	3	1910	3	NFASC	1	204945893	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	4127803	204945893	44304728	57	22781										
SLC26A9	115019	hgsc.bcm.edu	37	chr1	205898402	205898402	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cattgagctccttcaccagcAccaggaaggcaccgctgatg	10	14	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:205898402A>T	ENST00000367135.3	-	7	913	c.800T>A	c.(799-801)gTg>gAg	p.V267E	SLC26A9_ENST00000367134.2_Missense_Mutation_p.V267E|SLC26A9_ENST00000340781.4_Missense_Mutation_p.V267E	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	267					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			CTTCACCAGCACCAGGAAGGC	0.522																																					p.V267E		Atlas-SNP	.											.	SLC26A9	176	.	0			c.T800A						.						191	177	182					1																	205898402		2203	4300	6503	SO:0001583	missense	115019	exon7			ACCAGCACCAGGA	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"Solute carriers"	14469	protein-coding gene	gene with protein product	"anion transporter/exchanger-9"	608481	"solute carrier family 26, member 9"			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.800T>A	chr1.hg19:g.205898402A>T	ENSP00000356103:p.Val267Glu	134.0	0.0		222.0	130.0	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	hg19	CCDS30990.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.960497	0.53400	.	.	ENSG00000174502	ENST00000340781;ENST00000367135;ENST00000367134	D;D;D	0.93247	-3.19;-3.19;-3.19	5.6	4.45	0.53987	Sulphate transporter (1);	0.157726	0.38605	N	0.001634	D	0.92773	0.7702	M	0.69823	2.125	0.38878	D	0.956832	P;P	0.43542	0.627;0.81	B;B	0.44224	0.327;0.444	D	0.92227	0.5789	10	0.59425	D	0.04	.	11.3861	0.49787	0.9275:0.0:0.0725:0.0	.	267;267	Q7LBE3;B1AVM8	S26A9_HUMAN;.	E	267	ENSP00000341682:V267E;ENSP00000356103:V267E;ENSP00000356102:V267E	ENSP00000341682:V267E	V	-	2	0	SLC26A9	204165025	1.000000	0.71417	0.994000	0.49952	0.525000	0.34531	6.072000	0.71238	0.914000	0.36822	0.459000	0.35465	GTG	.	.		0.522	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934		T	205898402	A	T	205898402	3	4	150	1	0	0	0	0	1	0	0	0	14539	159	6	4	1931	4	SLC26A9	1	205898402	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	952509	205898402	43352219	58	22782										
CR1	1378	hgsc.bcm.edu	37	chr1	207753643	207753643	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	accccaagccatcaggacaaCttttcacctgggcaggaagt	9	13	2	0	rs141954836	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:207753643C>G	ENST00000367049.4	+	30	4995	c.4995C>G	c.(4993-4995)aaC>aaG	p.N1665K	CR1_ENST00000400960.2_Missense_Mutation_p.N1215K|CR1_ENST00000367051.1_Missense_Mutation_p.N1215K|CR1_ENST00000367052.1_Missense_Mutation_p.N1215K|CR1_ENST00000367053.1_Missense_Mutation_p.N1215K|RP11-78B10.2_ENST00000596003.1_RNA|RP11-78B10.2_ENST00000597497.1_RNA	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1215	Sushi 26. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ATCAGGACAACTTTTCACCTG	0.562																																					p.N1665K		Atlas-SNP	.											.	CR1	354	.	0			c.C4995G						.						128	130	129					1																	207753643		1975	4168	6143	SO:0001583	missense	1378	exon30			GGACAACTTTTCA	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.4995C>G	chr1.hg19:g.207753643C>G	ENSP00000356016:p.Asn1665Lys	152.0	0.0		268.0	36.0	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	hg19	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	C	2.842	-0.240298	0.05944	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	4.34	-2.85	0.05734	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.35480	0.0933	L	0.28014	0.82	0.09310	N	1	B;B;B	0.15141	0.012;0.0;0.001	B;B;B	0.19946	0.027;0.001;0.003	T	0.28902	-1.0029	9	0.07175	T	0.84	.	0.6283	0.00789	0.2643:0.3355:0.1299:0.2703	.	1215;1215;1665	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	K	1215;1215;1215;1215;765;1665	ENSP00000356019:N1215K;ENSP00000356018:N1215K;ENSP00000356020:N1215K;ENSP00000383744:N1215K;ENSP00000436139:N765K;ENSP00000356016:N1665K	ENSP00000356016:N1665K	N	+	3	2	CR1	205820266	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	-0.014000	0.12656	-0.504000	0.06577	-2.454000	0.00207	AAC	.	C|0.999;A|0.001		0.562	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		G	207753643	C	G	207753643	3	3	150	1	0	0	0	0	1	0	0	0	3842	564	20	4	5113	4	CR1	1	207753643	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	1855241	207753643	41496978	59	22783										
VASH2	79805	hgsc.bcm.edu	37	chr1	213146157	213146157	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatacctgcacacagtcaagAaggtcaagattgggctgtac	10	9	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:213146157A>G	ENST00000517399.1	+	5	733	c.733A>G	c.(733-735)Aag>Gag	p.K245E	VASH2_ENST00000366967.2_Missense_Mutation_p.K141E|VASH2_ENST00000366965.2_Missense_Mutation_p.K201E|VASH2_ENST00000271776.4_3'UTR|VASH2_ENST00000366966.2_Missense_Mutation_p.K180E|VASH2_ENST00000366968.4_Missense_Mutation_p.K180E|VASH2_ENST00000366964.3_Missense_Mutation_p.K103E			Q86V25	VASH2_HUMAN	vasohibin 2	245					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)	cytoplasm (GO:0005737)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)		CACAGTCAAGAAGGTCAAGAT	0.507																																					p.K201E		Atlas-SNP	.											.	VASH2	55	.	0			c.A601G						.						119	105	110					1																	213146157		2203	4300	6503	SO:0001583	missense	79805	exon4			GTCAAGAAGGTCA	AK022567	CCDS1511.1, CCDS44315.1, CCDS44316.1, CCDS73026.1	1q23	2008-02-05			ENSG00000143494	ENSG00000143494			25723	protein-coding gene	gene with protein product		610471				16528006	Standard	XR_247041		Approved	FLJ12505	uc001hjw.3	Q86V25	OTTHUMG00000036925	ENST00000517399.1:c.733A>G	chr1.hg19:g.213146157A>G	ENSP00000428324:p.Lys245Glu	99.0	0.0		142.0	10.0	NM_024749	B4DYZ5|Q2VT46|Q5VTE7|Q5VTE9|Q7Z6E3|Q8IZ24|Q9H9W5	Missense_Mutation	SNP	ENST00000517399.1	hg19	CCDS1511.1	.	.	.	.	.	.	.	.	.	.	A	16.40	3.112809	0.56398	.	.	ENSG00000143494	ENST00000366966;ENST00000366964;ENST00000366968;ENST00000366965;ENST00000366967;ENST00000517399	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.73481	0.3592	L	0.58583	1.82	0.52501	D	0.999956	B;D	0.64830	0.031;0.994	B;P	0.61397	0.028;0.888	T	0.75479	-0.3303	9	0.54805	T	0.06	-14.3872	15.4812	0.75528	1.0:0.0:0.0:0.0	.	245;201	Q86V25;Q86V25-5	VASH2_HUMAN;.	E	180;103;180;201;141;245	.	ENSP00000355931:K103E	K	+	1	0	VASH2	211212780	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.893000	0.75649	2.118000	0.64928	0.533000	0.62120	AAG	.	.		0.507	VASH2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381686.1	NM_024749		G	213146157	A	G	213146157	3	3	150	1	0	0	0	0	1	0	0	0	17141	247	9	2	751	2	VASH2	1	213146157	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5392514	213146157	36104464	60	22784										
KCNK2	3776	hgsc.bcm.edu	37	chr1	215408460	215408460	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gccacactgtgctggtgaagAgattgctgtgattgagaaca	13	7	0	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:215408460A>G	ENST00000444842.2	+	7	1403	c.1253A>G	c.(1252-1254)gAg>gGg	p.E418G	KCNK2_ENST00000391895.2_Missense_Mutation_p.E414G|KCNK2_ENST00000391894.2_Missense_Mutation_p.E403G	NM_001017425.2|NM_014217.3	NP_001017425.2|NP_055032.1	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2	418	Essential for chloroform and halothane sensitivity. {ECO:0000250}.|Required for basal channel activity. {ECO:0000250}.				G-protein coupled receptor signaling pathway (GO:0007186)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|potassium ion leak channel activity (GO:0022841)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)|Dronedarone(DB04855)	GCTGGTGAAGAGATTGCTGTG	0.458																																					p.E418G		Atlas-SNP	.											.	KCNK2	135	.	0			c.A1253G						.						147	143	144					1																	215408460		2203	4300	6503	SO:0001583	missense	3776	exon7			GTGAAGAGATTGC	AF004711	CCDS31024.1, CCDS41466.1, CCDS41467.1	1q41	2012-03-07			ENSG00000082482	ENSG00000082482		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6277	protein-coding gene	gene with protein product		603219				9721223, 16382106	Standard	NM_001017424		Approved	K2p2.1, TREK-1	uc001hkr.4	O95069	OTTHUMG00000037017	ENST00000444842.2:c.1253A>G	chr1.hg19:g.215408460A>G	ENSP00000394033:p.Glu418Gly	42.0	0.0		76.0	6.0	NM_001017425	A1Z1V3|A8K618|B2RCS4|B7ZL56|D3DTA5|Q5DP47|Q5DP48|Q9NRT2|Q9UNE3	Missense_Mutation	SNP	ENST00000444842.2	hg19	CCDS41467.1	.	.	.	.	.	.	.	.	.	.	A	17.06	3.293107	0.60086	.	.	ENSG00000082482	ENST00000391895;ENST00000391894;ENST00000444842	T;T;T	0.25250	1.81;1.83;1.81	5.63	5.63	0.86233	.	0.567905	0.19602	N	0.110374	T	0.18718	0.0449	N	0.24115	0.695	0.58432	D	0.999998	B;P;B	0.37525	0.447;0.598;0.447	B;B;B	0.30646	0.118;0.099;0.118	T	0.04946	-1.0916	10	0.87932	D	0	.	15.8309	0.78749	1.0:0.0:0.0:0.0	.	403;418;414	O95069-2;O95069;O95069-3	.;KCNK2_HUMAN;.	G	414;403;418	ENSP00000375765:E414G;ENSP00000375764:E403G;ENSP00000394033:E418G	ENSP00000375764:E403G	E	+	2	0	KCNK2	213475083	1.000000	0.71417	0.986000	0.45419	0.989000	0.77384	8.901000	0.92560	2.149000	0.67028	0.402000	0.26972	GAG	.	.		0.458	KCNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089856.2	NM_014217		G	215408460	A	G	215408460	3	3	150	1	0	0	0	0	1	0	0	0	8075	304	11	2	1322	2	KCNK2	1	215408460	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2262303	215408460	33842161	61	22785										
BPNT1	10380	hgsc.bcm.edu	37	chr1	220253130	220253130	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgactatcattcctgcctttTgagcaatagaatatgcggag	9	8	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:220253130T>A	ENST00000469520.2	-	3	508	c.59A>T	c.(58-60)cAa>cTa	p.Q20L	BPNT1_ENST00000482136.1_Intron|BPNT1_ENST00000354807.3_Missense_Mutation_p.Q20L|BPNT1_ENST00000414869.2_Missense_Mutation_p.Q20L|BPNT1_ENST00000322067.7_Missense_Mutation_p.Q20L|BPNT1_ENST00000544404.1_Intron			O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1	20					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|dephosphorylation (GO:0016311)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|magnesium ion binding (GO:0000287)			breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)|skin(1)	14				GBM - Glioblastoma multiforme(131;0.0558)		TCCTGCCTTTTGAGCAATAGA	0.403																																					p.Q20L		Atlas-SNP	.											.	BPNT1	29	.	0			c.A59T						.						131	118	122					1																	220253130		1929	4129	6058	SO:0001583	missense	10380	exon2			GCCTTTTGAGCAA	AF125042	CCDS41469.1, CCDS65787.1, CCDS65788.1	1q42	2008-02-05			ENSG00000162813	ENSG00000162813	3.1.3.7		1096	protein-coding gene	gene with protein product		604053				10224133	Standard	XM_005272998		Approved		uc001hma.3	O95861	OTTHUMG00000037435	ENST00000469520.2:c.59A>T	chr1.hg19:g.220253130T>A	ENSP00000446828:p.Gln20Leu	132.0	0.0		240.0	21.0	NM_006085	A8K7C8|B4DPS5|B4DUS9|D3DTA9|Q8WVL5|Q9UGJ3	Missense_Mutation	SNP	ENST00000469520.2	hg19	CCDS41469.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.020929	0.54576	.	.	ENSG00000162813	ENST00000322067;ENST00000469520;ENST00000354807;ENST00000302686;ENST00000414869;ENST00000463953;ENST00000498791;ENST00000498237	T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.51	5.51	0.81932	.	0.155025	0.53938	D	0.000044	T	0.34048	0.0884	N	0.25647	0.755	0.80722	D	1	B;P;B	0.35944	0.021;0.529;0.078	B;B;B	0.29524	0.103;0.069;0.089	T	0.22103	-1.0226	10	0.48119	T	0.1	.	14.6341	0.68676	0.0:0.0:0.0:1.0	.	20;20;20	B4DUS9;A6NF51;O95861	.;.;BPNT1_HUMAN	L	20	ENSP00000318852:Q20L;ENSP00000446828:Q20L;ENSP00000346862:Q20L;ENSP00000410348:Q20L;ENSP00000446953:Q20L;ENSP00000446850:Q20L;ENSP00000449883:Q20L	ENSP00000307087:Q20L	Q	-	2	0	BPNT1	218319753	0.988000	0.35896	0.990000	0.47175	0.994000	0.84299	3.449000	0.52950	2.112000	0.64535	0.472000	0.43445	CAA	.	.		0.403	BPNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091137.2	NM_006085		A	220253130	T	A	220253130	3	1	150	1	0	0	0	0	1	0	0	0	1496	1812	63	4	899	4	BPNT1	1	220253130	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4844670	220253130	28997491	62	22786										
MIA3	375056	hgsc.bcm.edu	37	chr1	222801852	222801852	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaacaggggaaaccacagtcAgcaacagattatagtgaccc	9	10	1	2	rs375042330		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:222801852A>T	ENST00000344922.5	+	4	1315	c.1290A>T	c.(1288-1290)tcA>tcT	p.S430S	MIA3_ENST00000344441.6_Silent_p.S430S|MIA3_ENST00000470521.1_3'UTR|MIA3_ENST00000344507.1_Silent_p.S430S	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	430					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		AACCACAGTCAGCAACAGATT	0.378																																					p.S430S		Atlas-SNP	.											.	MIA3	167	.	0			c.A1290T						.						122	117	119					1																	222801852		1927	4129	6056	SO:0001819	synonymous_variant	375056	exon4			ACAGTCAGCAACA		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.1290A>T	chr1.hg19:g.222801852A>T		298.0	0.0		578.0	78.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Silent	SNP	ENST00000344922.5	hg19	CCDS41470.1	.	.	.	.	.	.	.	.	.	.	A	11.15	1.555053	0.27739	.	.	ENSG00000154305	ENST00000354906	T	0.20069	2.1	4.52	2.07	0.26955	.	.	.	.	.	T	0.26340	0.0643	.	.	.	0.36132	D	0.846227	.	.	.	.	.	.	T	0.17167	-1.0378	6	0.51188	T	0.08	.	6.6651	0.23037	0.7613:0.1548:0.0839:0.0	.	.	.	.	C	13	ENSP00000355062:S13C	ENSP00000355062:S13C	S	+	1	0	MIA3	220868475	0.000000	0.05858	0.005000	0.12908	0.649000	0.38597	0.735000	0.26115	0.292000	0.22492	0.254000	0.18369	AGC	.	.		0.378	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		T	222801852	A	T	222801852	2	4	150	1	0	0	0	0	0	0	0	1	9574	175	7	4		4	MIA3	1	222801852	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2548722	222801852	26448769	63	22787										
WNT3A	89780	hgsc.bcm.edu	37	chr1	228246857	228246857	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gagaagcaccgggagtcccgCggctgggtggagaccctgcg	18	12	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:228246857C>T	ENST00000284523.1	+	4	828	c.750C>T	c.(748-750)cgC>cgT	p.R250R	WNT3A_ENST00000366753.2_Silent_p.R250R	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	250					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				GGGAGTCCCGCGGCTGGGTGG	0.657																																					p.R250R		Atlas-SNP	.											.	WNT3A	40	.	0			c.C750T						.						47	50	49					1																	228246857		2203	4300	6503	SO:0001819	synonymous_variant	89780	exon4			GTCCCGCGGCTGG	AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"Wingless-type MMTV integration sites", "Endogenous ligands"	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.750C>T	chr1.hg19:g.228246857C>T		117.0	0.0		187.0	17.0	NM_033131	Q3SY79|Q3SY80|Q969P2	Silent	SNP	ENST00000284523.1	hg19	CCDS1564.1																																																																																			.	.		0.657	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131		T	228246857	C	T	228246857	2	4	150	1	0	0	0	0	0	0	0	1	17404	755	27	1		1	WNT3A	1	228246857	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	5445005	228246857	21003764	64	22788										
GJC2	57165	hgsc.bcm.edu	37	chr1	228345591	228345591	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctgacggctgtgggcggcgaGgccatctactcggacgagca	16	12	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:228345591G>C	ENST00000366714.2	+	2	307	c.132G>C	c.(130-132)gaG>gaC	p.E44D		NM_020435.3	NP_065168.2	Q5T442	CXG2_HUMAN	gap junction protein, gamma 2, 47kDa	44					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|response to toxic substance (GO:0009636)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)	gap junction channel activity (GO:0005243)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7		Prostate(94;0.0405)				TGGGCGGCGAGGCCATCTACT	0.647																																					p.E44D		Atlas-SNP	.											.	GJC2	20	.	0			c.G132C						.						69	49	56					1																	228345591		2203	4300	6503	SO:0001583	missense	57165	exon2			CGGCGAGGCCATC	AF014643	CCDS1569.1	1q41-q42	2009-01-02	2007-12-14	2007-11-06	ENSG00000198835	ENSG00000198835		"Ion channels / Gap junction proteins (connexins)"	17494	protein-coding gene	gene with protein product	"connexin 47"	608803	"gap junction protein, alpha 12, 47kDa"	GJA12		19056803	Standard	NM_020435		Approved	CX47, CX46.6, SPG44	uc001hsk.3	Q5T442	OTTHUMG00000039771	ENST00000366714.2:c.132G>C	chr1.hg19:g.228345591G>C	ENSP00000355675:p.Glu44Asp	255.0	0.0		434.0	53.0	NM_020435	O43440|Q7Z7J2|Q8IWJ9	Missense_Mutation	SNP	ENST00000366714.2	hg19	CCDS1569.1	.	.	.	.	.	.	.	.	.	.	G	13.64	2.297074	0.40694	.	.	ENSG00000198835	ENST00000366714	D	0.99239	-5.61	4.06	3.14	0.36123	Connexin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99017	0.9664	L	0.61387	1.9	0.48511	D	0.999663	D	0.71674	0.998	D	0.76575	0.988	D	0.99257	1.0889	10	0.72032	D	0.01	.	10.1024	0.42513	0.1715:0.0:0.8285:0.0	.	44	Q5T442	CXG2_HUMAN	D	44	ENSP00000355675:E44D	ENSP00000355675:E44D	E	+	3	2	GJC2	226412214	1.000000	0.71417	0.995000	0.50966	0.623000	0.37688	3.757000	0.55212	0.929000	0.37192	0.313000	0.20887	GAG	.	.		0.647	GJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095985.1	NM_020435		C	228345591	G	C	228345591	3	2	150	1	0	0	0	0	1	0	0	0	6423	991	35	4	134	4	GJC2	1	228345591	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	98734	228345591	20905030	65	22789										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228521428	228521428	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctctggccagtatgcagcctAtatcagcaatgccatgggtg	11	11	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:228521428A>T	ENST00000422127.1	+	59	16045	c.16001A>T	c.(16000-16002)tAt>tTt	p.Y5334F	OBSCN_ENST00000366707.4_Missense_Mutation_p.Y2968F|OBSCN_ENST00000570156.2_Missense_Mutation_p.Y6291F|OBSCN_ENST00000284548.11_Missense_Mutation_p.Y5334F|OBSCN_ENST00000366709.4_Missense_Mutation_p.Y2453F	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5334	Ig-like 50.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TATGCAGCCTATATCAGCAAT	0.617																																					p.Y6291F		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A18872T						.						39	43	42					1																	228521428		2038	4195	6233	SO:0001583	missense	84033	exon70			CAGCCTATATCAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.16001A>T	chr1.hg19:g.228521428A>T	ENSP00000409493:p.Tyr5334Phe	89.0	0.0		127.0	17.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	12.86	2.065667	0.36470	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.62	3.26	0.37387	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.081740	0.50627	D	0.000101	T	0.39911	0.1096	N	0.08118	0	0.30604	N	0.760253	B;B	0.25048	0.117;0.096	B;B	0.29524	0.103;0.062	T	0.33599	-0.9862	10	0.11182	T	0.66	.	5.9489	0.19234	0.6156:0.0:0.0736:0.3107	.	5334;5334	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	F	5334;5334;2968;2453	ENSP00000284548:Y5334F;ENSP00000409493:Y5334F;ENSP00000355668:Y2968F;ENSP00000355670:Y2453F	ENSP00000284548:Y5334F	Y	+	2	0	OBSCN	226588051	1.000000	0.71417	0.844000	0.33320	0.004000	0.04260	4.646000	0.61411	0.395000	0.25257	-0.250000	0.11733	TAT	.	.		0.617	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228521428	A	T	228521428	3	4	150	1	0	0	0	0	1	0	0	0	10821	449	16	4	16231	4	OBSCN	1	228521428	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	175837	228521428	20729193	66	22790										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228552712	228552712	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gagggtgccacagcccctccTccacgaaggcccagagcagg	13	16	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:228552712T>A	ENST00000422127.1	+	81	18916	c.18872T>A	c.(18871-18873)cTc>cAc	p.L6291H	OBSCN_ENST00000366707.4_Missense_Mutation_p.L3925H|OBSCN_ENST00000570156.2_Missense_Mutation_p.L7248H	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6291					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CAGCCCCTCCTCCACGAAGGC	0.662																																					p.L7248H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T21743A						.						15	22	20					1																	228552712		2064	4185	6249	SO:0001583	missense	84033	exon92			CCCTCCTCCACGA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18872T>A	chr1.hg19:g.228552712T>A	ENSP00000409493:p.Leu6291His	321.0	0.0		574.0	70.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	T	13.22	2.170768	0.38315	.	.	ENSG00000154358	ENST00000422127;ENST00000366707	T;T	0.61392	0.11;0.12	3.51	0.168	0.15012	.	.	.	.	.	T	0.28167	0.0695	N	0.08118	0	0.09310	N	1	P	0.42785	0.79	B	0.37550	0.253	T	0.10776	-1.0615	9	0.27082	T	0.32	.	3.1674	0.06540	0.0:0.4915:0.2269:0.2816	.	6291	Q5VST9	OBSCN_HUMAN	H	6291;3925	ENSP00000409493:L6291H;ENSP00000355668:L3925H	ENSP00000355668:L3925H	L	+	2	0	OBSCN	226619335	0.000000	0.05858	0.003000	0.11579	0.053000	0.15095	0.606000	0.24194	0.287000	0.22375	-0.415000	0.06103	CTC	.	.		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228552712	T	A	228552712	3	1	150	1	0	0	0	0	1	0	0	0	10821	1551	54	4	20400	4	OBSCN	1	228552712	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	31284	228552712	20697909	67	22791										
TRIM67	440730	hgsc.bcm.edu	37	chr1	231299389	231299389	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcagccacgctctgcgagcAgtgcgacgtcctctactgct	11	15	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:231299389A>T	ENST00000366653.5	+	1	674	c.674A>T	c.(673-675)cAg>cTg	p.Q225L	TRIM67_ENST00000366652.2_Missense_Mutation_p.Q225L|TRIM67_ENST00000444294.3_Missense_Mutation_p.Q225L|TRIM67_ENST00000449018.3_Missense_Mutation_p.Q185L			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	225					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				CTCTGCGAGCAGTGCGACGTC	0.741																																					p.Q225L		Atlas-SNP	.											.	TRIM67	160	.	0			c.A674T						.						5	7	7					1																	231299389		1571	2918	4489	SO:0001583	missense	440730	exon1			GCGAGCAGTGCGA	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.674A>T	chr1.hg19:g.231299389A>T	ENSP00000355613:p.Gln225Leu	39.0	0.0		68.0	10.0	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	hg19	CCDS44333.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.198485	0.79015	.	.	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000449018;ENST00000366653	T;T;T;T	0.73152	-0.72;-0.63;-0.57;-0.72	4.37	4.37	0.52481	Zinc finger, B-box (2);	0.201896	0.43579	N	0.000543	D	0.82291	0.5005	M	0.70842	2.15	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.84604	0.0674	10	0.72032	D	0.01	.	13.7092	0.62659	1.0:0.0:0.0:0.0	.	225	Q6ZTA4	TRI67_HUMAN	L	225;225;185;225	ENSP00000412124:Q225L;ENSP00000355612:Q225L;ENSP00000400163:Q185L;ENSP00000355613:Q225L	ENSP00000355612:Q225L	Q	+	2	0	TRIM67	229366012	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.613000	0.74192	1.824000	0.53156	0.402000	0.26972	CAG	.	.		0.741	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		T	231299389	A	T	231299389	3	4	150	1	0	0	0	0	1	0	0	0	16555	188	7	4	676	4	TRIM67	1	231299389	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2746677	231299389	17951232	68	22792										
RYR2	6262	hgsc.bcm.edu	37	chr1	237551411	237551411	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tctcattggtggtgatgtccTcaggttgctgcatggacaca	12	9	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:237551411T>A	ENST00000366574.2	+	10	1018	c.701T>A	c.(700-702)cTc>cAc	p.L234H	RYR2_ENST00000542537.1_Missense_Mutation_p.L218H|RYR2_ENST00000360064.6_Missense_Mutation_p.L232H	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	234	MIR 3. {ECO:0000255|PROSITE- ProRule:PRU00131}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GGTGATGTCCTCAGGTTGCTG	0.488																																					p.L234H		Atlas-SNP	.											.	RYR2	1273	.	0			c.T701A						.						123	119	120					1																	237551411		2035	4194	6229	SO:0001583	missense	6262	exon10			ATGTCCTCAGGTT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.701T>A	chr1.hg19:g.237551411T>A	ENSP00000355533:p.Leu234His	80.0	0.0		153.0	18.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	17.36	3.370754	0.61624	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.92446	-3.04;-3.04;-3.04	5.33	5.33	0.75918	MIR motif (2);MIR (2);	0.000000	0.52532	D	0.000065	D	0.95714	0.8606	M	0.83483	2.645	0.80722	D	1	D	0.67145	0.996	D	0.68192	0.956	D	0.96151	0.9108	10	0.87932	D	0	.	12.8175	0.57673	0.0:0.0:0.0:1.0	.	234	Q92736	RYR2_HUMAN	H	234;232;218	ENSP00000355533:L234H;ENSP00000353174:L232H;ENSP00000443798:L218H	ENSP00000353174:L232H	L	+	2	0	RYR2	235618034	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.860000	0.75473	2.021000	0.59480	0.528000	0.53228	CTC	.	.		0.488	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237551411	T	A	237551411	3	1	150	1	0	0	0	0	1	0	0	0	13784	1551	54	4	739	4	RYR2	1	237551411	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	6252022	237551411	11699210	69	22793										
RYR2	6262	hgsc.bcm.edu	37	chr1	237823356	237823356	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagccattaatgaagccataTaagctattgtctgaaaaggt	8	7	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:237823356T>A	ENST00000366574.2	+	55	8597	c.8280T>A	c.(8278-8280)taT>taA	p.Y2760*	RYR2_ENST00000542537.1_Nonsense_Mutation_p.Y2744*|RYR2_ENST00000360064.6_Nonsense_Mutation_p.Y2758*	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2760	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGAAGCCATATAAGCTATTGT	0.254																																					p.Y2760X		Atlas-SNP	.											.	RYR2	1273	.	0			c.T8280A						.						51	48	49					1																	237823356		1792	4057	5849	SO:0001587	stop_gained	6262	exon55			GCCATATAAGCTA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.8280T>A	chr1.hg19:g.237823356T>A	ENSP00000355533:p.Tyr2760*	90.0	0.0		173.0	21.0	NM_001035	Q15411|Q546N8|Q5T3P2	Nonsense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	49	14.973841	0.99817	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	.	.	.	5.09	2.77	0.32553	.	0.000000	0.53938	U	0.000043	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.8315	0.29344	0.0:0.2278:0.0:0.7722	.	.	.	.	X	2760;2758;2744	.	ENSP00000353174:Y2758X	Y	+	3	2	RYR2	235889979	1.000000	0.71417	0.998000	0.56505	0.575000	0.36095	0.699000	0.25586	0.893000	0.36288	-0.541000	0.04245	TAT	.	.		0.254	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237823356	T	A	237823356	4	1	150	1	0	0	0	0	0	1	0	0	13784	1413	49	4	8498	4	RYR2	1	237823356	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	271945	237823356	11427265	70	22794										
WDR64	128025	hgsc.bcm.edu	37	chr1	241904820	241904820	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttcttacttctgttccaggaTctagtgttatggacatgtat	8	7	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:241904820T>A	ENST00000366552.2	+	11	1501	c.1294T>A	c.(1294-1296)Tct>Act	p.S432T	WDR64_ENST00000437684.2_Missense_Mutation_p.S432T	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	432										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			TGTTCCAGGATCTAGTGTTAT	0.373																																					p.S432T		Atlas-SNP	.											.	WDR64	234	.	0			c.T1294A						.						111	103	105					1																	241904820		2203	4300	6503	SO:0001583	missense	128025	exon11			CCAGGATCTAGTG	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1294T>A	chr1.hg19:g.241904820T>A	ENSP00000355510:p.Ser432Thr	66.0	0.0		120.0	26.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	hg19		.	.	.	.	.	.	.	.	.	.	T	14.80	2.643106	0.47153	.	.	ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635	T;T;T	0.51574	1.25;0.7;0.76	5.49	5.49	0.81192	.	0.398691	0.24445	N	0.038466	T	0.56848	0.2013	L	0.35644	1.08	0.35442	D	0.794979	D	0.63880	0.993	D	0.70935	0.971	T	0.64132	-0.6479	10	0.36615	T	0.2	-6.6	13.1105	0.59270	0.0:0.0:0.0:1.0	.	152	D1MPS4	.	T	432;432;203	ENSP00000355510:S432T;ENSP00000402446:S432T;ENSP00000406656:S203T	ENSP00000355510:S432T	S	+	1	0	WDR64	239971443	1.000000	0.71417	0.999000	0.59377	0.623000	0.37688	4.795000	0.62489	2.089000	0.63090	0.533000	0.62120	TCT	.	.		0.373	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		A	241904820	T	A	241904820	3	1	150	1	0	0	0	0	1	0	0	0	17330	1435	50	4	1336	4	WDR64	1	241904820	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4081464	241904820	7345801	71	22795										
OR2L2	26246	hgsc.bcm.edu	37	chr1	248202345	248202345	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	accctttgcttatacctatgTacgtccaagatccctgcgat	6	13	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:248202345T>A	ENST00000366479.2	+	1	872	c.776T>A	c.(775-777)gTa>gAa	p.V259E	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	259			V -> L (in dbSNP:rs6658141).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TATACCTATGTACGTCCAAGA	0.502																																					p.V259E		Atlas-SNP	.											.	OR2L2	115	.	0			c.T776A						.						156	140	145					1																	248202345		2203	4300	6503	SO:0001583	missense	26246	exon1			CCTATGTACGTCC	X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"GPCR / Class A : Olfactory receptors"	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.776T>A	chr1.hg19:g.248202345T>A	ENSP00000355435:p.Val259Glu	90.0	0.0		187.0	25.0	NM_001004686	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	hg19	CCDS31103.1	.	.	.	.	.	.	.	.	.	.	.	9.741	1.164794	0.21538	.	.	ENSG00000203663	ENST00000366479	T	0.39056	1.1	1.9	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	0.000000	0.26055	U	0.026610	T	0.57154	0.2034	H	0.94808	3.585	0.09310	N	1	B	0.24258	0.1	B	0.36092	0.217	T	0.59418	-0.7458	10	0.87932	D	0	.	9.0367	0.36291	0.0:0.0:0.0:1.0	.	259	Q8NH16	OR2L2_HUMAN	E	259	ENSP00000355435:V259E	ENSP00000355435:V259E	V	+	2	0	OR2L2	246268968	0.000000	0.05858	0.006000	0.13384	0.132000	0.20833	0.119000	0.15626	0.746000	0.32786	0.163000	0.16589	GTA	.	.		0.502	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686		A	248202345	T	A	248202345	3	1	150	1	0	0	0	0	1	0	0	0	11016	1638	57	4	778	4	OR2L2	1	248202345	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	6297525	248202345	1048276	72	22796										
OR2M7	391196	hgsc.bcm.edu	37	chr1	248487043	248487043	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggagtgacgatggtgtagaaTacagacaccatcttgtcctg	12	8	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:248487043T>C	ENST00000317965.2	-	1	856	c.828A>G	c.(826-828)gtA>gtG	p.V276V		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	276						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGGTGTAGAATACAGACACCA	0.458																																					p.V276V		Atlas-SNP	.											.	OR2M7	84	.	0			c.A828G						.						126	115	119					1																	248487043		2203	4300	6503	SO:0001819	synonymous_variant	391196	exon1			GTAGAATACAGAC	BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"GPCR / Class A : Olfactory receptors"	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.828A>G	chr1.hg19:g.248487043T>C		147.0	0.0		267.0	35.0	NM_001004691	B2RNL0|Q6IEX6	Silent	SNP	ENST00000317965.2	hg19	CCDS31111.1																																																																																			.	.		0.458	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691		C	248487043	T	C	248487043	2	2	150	1	0	0	0	0	0	0	0	1	11023	1393	49	2		2	OR2M7	1	248487043	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	284698	248487043	763578	73	22797										
OR14I1	401994	hgsc.bcm.edu	37	chr1	248845007	248845007	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccagaaccaagcatgagctcAgggccagggtcaaaaactct	10	12	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr1:248845007A>T	ENST00000342623.3	-	1	622	c.599T>A	c.(598-600)cTg>cAg	p.L200Q		NM_001004734.1	NP_001004734.1	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I, member 1	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(4)|large_intestine(2)|lung(24)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	35						GCATGAGCTCAGGGCCAGGGT	0.483																																					p.L200Q		Atlas-SNP	.											.	OR14I1	64	.	0			c.T599A						.						79	86	84					1																	248845007		2203	4300	6503	SO:0001583	missense	401994	exon1			GAGCTCAGGGCCA		CCDS31125.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000189181	ENSG00000189181		"GPCR / Class A : Olfactory receptors"	19575	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily BU, member 1"	OR5BU1P, OR5BU1			Standard	NM_001004734		Approved		uc001ieu.1	A6ND48	OTTHUMG00000040378	ENST00000342623.3:c.599T>A	chr1.hg19:g.248845007A>T	ENSP00000339726:p.Leu200Gln	158.0	0.0		274.0	31.0	NM_001004734		Missense_Mutation	SNP	ENST00000342623.3	hg19	CCDS31125.1	.	.	.	.	.	.	.	.	.	.	.	17.36	3.368898	0.61624	.	.	ENSG00000189181	ENST00000342623	T	0.00198	8.57	3.3	3.3	0.37823	GPCR, rhodopsin-like superfamily (1);	0.862603	0.09406	N	0.806538	T	0.00552	0.0018	M	0.84219	2.685	0.09310	N	1	D	0.54964	0.969	D	0.66497	0.944	T	0.52064	-0.8625	10	0.54805	T	0.06	.	9.6218	0.39725	1.0:0.0:0.0:0.0	.	200	A6ND48	O14I1_HUMAN	Q	200	ENSP00000339726:L200Q	ENSP00000339726:L200Q	L	-	2	0	OR14I1	246911630	0.000000	0.05858	0.001000	0.08648	0.791000	0.44710	0.700000	0.25601	1.337000	0.45525	0.443000	0.29094	CTG	.	.		0.483	OR14I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097128.1	NM_001004734		T	248845007	A	T	248845007	3	4	150	1	0	0	0	0	1	0	0	0	10956	188	7	4	340	4	OR14I1	1	248845007	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	357964	248845007	405614	74	22798										
TSSC1	7260	hgsc.bcm.edu	37	chr2	3358335	3358335	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agttacctgattatcatattTaagagactgcgtcccaacca	6	10	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:3358335T>A	ENST00000382125.4	-	2	304	c.112A>T	c.(112-114)Aaa>Taa	p.K38*	TSSC1_ENST00000398659.4_Nonsense_Mutation_p.K38*|TSSC1_ENST00000443925.2_Nonsense_Mutation_p.K38*	NM_003310.2	NP_003301.1	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	38										breast(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		TTATCATATTTAAGAGACTGC	0.373																																					p.K38X	Colon(140;1261 1762 4183 34270 49743)	Atlas-SNP	.											.	TSSC1	39	.	0			c.A112T						.						78	77	78					2																	3358335		2203	4300	6503	SO:0001587	stop_gained	7260	exon2			CATATTTAAGAGA	AF019952	CCDS1651.1	2p25.3	2013-01-10			ENSG00000032389	ENSG00000032389		"WD repeat domain containing"	12383	protein-coding gene	gene with protein product		608998				9403053, 9925925	Standard	NM_003310		Approved		uc002qxj.2	Q53HC9	OTTHUMG00000090329	ENST00000382125.4:c.112A>T	chr2.hg19:g.3358335T>A	ENSP00000371559:p.Lys38*	273.0	0.0		209.0	59.0	NM_003310	D6W4Y1|O43179|Q53S19|Q53SG2	Nonsense_Mutation	SNP	ENST00000382125.4	hg19	CCDS1651.1	.	.	.	.	.	.	.	.	.	.	t	37	6.320514	0.97471	.	.	ENSG00000032389	ENST00000382125;ENST00000398659;ENST00000443925;ENST00000444776	.	.	.	4.33	4.33	0.51752	.	0.103470	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.8001	11.8125	0.52192	0.0:0.0:0.0:1.0	.	.	.	.	X	38	.	ENSP00000371559:K38X	K	-	1	0	TSSC1	3337342	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.304000	0.72800	1.957000	0.56846	0.456000	0.33151	AAA	.	.		0.373	TSSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206694.2	NM_003310		A	3358335	T	A	3358335	4	1	150	1	0	0	0	0	0	1	0	0	16681	1763	61	4	1083	4	TSSC1	2	3358335	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10		3358335	239841038	75	22799										
MATN3	4148	hgsc.bcm.edu	37	chr2	20212202	20212202	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cgcggccaggctcgctggtcCcggaagcgggcgcgccgtcg	18	16	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:20212202C>T	ENST00000407540.3	-	1	253	c.191G>A	c.(190-192)gGg>gAg	p.G64E	MATN3_ENST00000421259.2_Missense_Mutation_p.G64E	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	64					extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCGCTGGTCCCGGAAGCGGG	0.771																																					p.G64E		Atlas-SNP	.											.	MATN3	28	.	0			c.G191A						.						1	1	1					2																	20212202		305	662	967	SO:0001583	missense	4148	exon1			CTGGTCCCGGAAG	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.191G>A	chr2.hg19:g.20212202C>T	ENSP00000383894:p.Gly64Glu	227.0	0.0		176.0	116.0	NM_002381	B2CPU0|Q4ZG02	Missense_Mutation	SNP	ENST00000407540.3	hg19	CCDS46226.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.888132	0.52014	.	.	ENSG00000132031	ENST00000407540;ENST00000421259	T;T	0.77750	-0.8;-1.12	4.04	3.15	0.36227	.	0.448843	0.21207	N	0.078377	T	0.69691	0.3139	L	0.57536	1.79	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.002	T	0.56884	-0.7905	10	0.30078	T	0.28	-11.5057	7.7961	0.29148	0.0:0.8827:0.0:0.1173	.	64;64	B2CPU0;O15232	.;MATN3_HUMAN	E	64	ENSP00000383894:G64E;ENSP00000398753:G64E	ENSP00000383894:G64E	G	-	2	0	MATN3	20075683	0.000000	0.05858	0.038000	0.18304	0.007000	0.05969	0.511000	0.22739	1.028000	0.39785	-0.145000	0.13849	GGG	.	.		0.771	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381		T	20212202	C	T	20212202	3	4	150	1	0	0	0	0	1	0	0	0	9344	623	22	3	1301	3	MATN3	2	20212202	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	16853867	20212202	222987171	76	22800										
RHOB	388	hgsc.bcm.edu	37	chr2	20647467	20647467	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acccggacaccgacgtcattCtcatgtgcttctcggtggac	10	14	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:20647467C>T	ENST00000272233.4	+	1	633	c.241C>T	c.(241-243)Ctc>Ttc	p.L81F		NM_004040.2	NP_004031.1	P62745	RHOB_HUMAN	ras homolog family member B	81					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|GTP catabolic process (GO:0006184)|negative regulation of cell cycle (GO:0045786)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|transformed cell apoptotic process (GO:0006927)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|kidney(1)|lung(2)|ovary(1)|urinary_tract(2)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)	all_epithelial(98;4.19e-09)|Lung NSC(108;0.00452)|Ovarian(717;0.0164)		OV - Ovarian serous cystadenocarcinoma(76;1.14e-22)|Epithelial(75;7.84e-19)	Botulinum Toxin Type A(DB00083)	CGACGTCATTCTCATGTGCTT	0.647																																					p.L81F		Atlas-SNP	.											.	RHOB	18	.	0			c.C241T						.						86	99	94					2																	20647467		2203	4300	6503	SO:0001583	missense	388	exon1			GTCATTCTCATGT		CCDS1699.1	2p24	2012-02-27	2012-02-27	2004-03-24	ENSG00000143878	ENSG00000143878			668	protein-coding gene	gene with protein product	"oncogene RHO H6"	165370	"ras homolog gene family, member B"	ARH6, ARHB		3283705, 16278215	Standard	NM_004040		Approved	RhoB, RHOH6, MST081	uc002rdv.3	P62745	OTTHUMG00000090755	ENST00000272233.4:c.241C>T	chr2.hg19:g.20647467C>T	ENSP00000272233:p.Leu81Phe	166.0	0.0		151.0	36.0	NM_004040	B2R692|P01121|Q5U0H6|Q7RTN5|Q7RTR9|Q9CUV7	Missense_Mutation	SNP	ENST00000272233.4	hg19	CCDS1699.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.822364	0.50739	.	.	ENSG00000143878	ENST00000272233	D	0.82711	-1.64	5.06	4.18	0.49190	Small GTP-binding protein domain (1);	0.000000	0.64402	U	0.000002	D	0.89375	0.6697	M	0.69248	2.105	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.90352	0.4367	10	0.87932	D	0	-15.1028	13.778	0.63066	0.0:0.9259:0.0:0.0741	.	81	P62745	RHOB_HUMAN	F	81	ENSP00000272233:L81F	ENSP00000272233:L81F	L	+	1	0	RHOB	20510948	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	7.668000	0.83897	1.281000	0.44480	-0.251000	0.11542	CTC	.	.		0.647	RHOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207500.1	NM_004040		T	20647467	C	T	20647467	3	4	150	1	0	0	0	0	1	0	0	0	13347	913	32	3	243	3	RHOB	2	20647467	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	435265	20647467	222551906	77	22801										
C2orf28	51374	hgsc.bcm.edu	37	chr2	27438566	27438566	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatactatcacctcttatatAgacaaccaaatctgtcaagg	4	10	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:27438566A>T	ENST00000606999.1	+	5	490	c.432A>T	c.(430-432)atA>atT	p.I144I	ATRAID_ENST00000405489.3_Silent_p.I86I|CAD_ENST00000264705.4_5'Flank|ATRAID_ENST00000380171.3_Silent_p.I199I|CAD_ENST00000403525.1_5'Flank	NM_001170795.1	NP_001164266.1	Q6UW56	ARAID_HUMAN	all-trans retinoic acid-induced differentiation factor	144					cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)											CCTCTTATATAGACAACCAAA	0.423																																					p.I199I		Atlas-SNP	.											.	.	.	.	0			c.A597T						.						115	114	114					2																	27438566		2203	4300	6503	SO:0001819	synonymous_variant	51374	exon5			TTATATAGACAAC	BC021237	CCDS1741.1, CCDS46243.1, CCDS62877.1	2p23.3	2012-08-01	2012-07-30	2012-07-30	ENSG00000138085	ENSG00000138085			24090	protein-coding gene	gene with protein product	"apoptosis-related protein 3"		"chromosome 2 open reading frame 28"	C2orf28		17524364, 21723284	Standard	NM_016085		Approved	HSPC013, p18, APR3	uc002rjf.3	Q6UW56	OTTHUMG00000128405	ENST00000606999.1:c.432A>T	chr2.hg19:g.27438566A>T		172.0	0.0		138.0	42.0	NM_080592	A8C1S2|A8K779|Q96FF6|Q96RT2|Q9Y2R7|Q9Y5L7	Silent	SNP	ENST00000606999.1	hg19																																																																																				.	.		0.423	ATRAID-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470709.1	NM_016085		T	27438566	A	T	27438566	2	4	150	1	0	0	0	0	0	0	0	1	2162	410	15	4		4	C2orf28	2	27438566	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	6791099	27438566	215760807	78	22802										
CAPN13	92291	hgsc.bcm.edu	37	chr2	30966407	30966407	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctttggacagtgtttctgaaCgaggaaaaaaacacgggtgg	13	6	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:30966407C>T	ENST00000295055.8	-	13	1463	c.1287G>A	c.(1285-1287)tcG>tcA	p.S429S	CAPN13_ENST00000534090.2_Silent_p.S429S	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	429					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					TGTTTCTGAACGAGGAAAAAA	0.473																																					p.S429S		Atlas-SNP	.											.	CAPN13	70	.	0			c.G1287A						.						147	139	142					2																	30966407		1847	4088	5935	SO:0001819	synonymous_variant	92291	exon13			TCTGAACGAGGAA		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.1287G>A	chr2.hg19:g.30966407C>T		99.0	0.0		91.0	25.0	NM_144575	Q17RF0|Q580X1|Q8TE80	Silent	SNP	ENST00000295055.8	hg19	CCDS46252.1																																																																																			.	.		0.473	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		T	30966407	C	T	30966407	2	4	150	1	0	0	0	0	0	0	0	1	2628	523	19	1		1	CAPN13	2	30966407	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	3527841	30966407	212232966	79	22803										
XDH	7498	hgsc.bcm.edu	37	chr2	31606664	31606664	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttcagctcagggatccaggcTgggcagacaatcataggaaa	12	9	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:31606664T>A	ENST00000379416.3	-	10	891	c.843A>T	c.(841-843)ccA>ccT	p.P281P	XDH_ENST00000491727.1_5'UTR	NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	281	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GGATCCAGGCTGGGCAGACAA	0.493																																					p.P281P	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.A843T						.						124	107	113					2																	31606664		2203	4300	6503	SO:0001819	synonymous_variant	7498	exon10			CCAGGCTGGGCAG	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.843A>T	chr2.hg19:g.31606664T>A		98.0	0.0		85.0	32.0	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	hg19	CCDS1775.1																																																																																			.	.		0.493	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		A	31606664	T	A	31606664	2	1	150	1	0	0	0	0	0	0	0	1	17441	1567	55	4		4	XDH	2	31606664	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	640257	31606664	211592709	80	22804										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32661167	32661167	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gatcataaagaagacattctAtgtgggccagtatggcttgc	11	7	2	2	rs188040071		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:32661167A>T	ENST00000421745.2	+	15	3680	c.3546A>T	c.(3544-3546)ctA>ctT	p.L1182L		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1182					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AAGACATTCTATGTGGGCCAG	0.333																																					p.L1182L	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A3546T						.						46	43	44					2																	32661167		2187	4284	6471	SO:0001819	synonymous_variant	57448	exon15			CATTCTATGTGGG	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.3546A>T	chr2.hg19:g.32661167A>T		82.0	0.0		82.0	25.0	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	A|1.000;G|0.000		0.333	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32661167	A	T	32661167	2	4	150	1	0	0	0	0	0	0	0	1	1438	436	16	4		4	BIRC6	2	32661167	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1054503	32661167	210538206	81	22805										
TTC27	55622	hgsc.bcm.edu	37	chr2	32858993	32858993	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagtttgcaactttttgttcAgagcaactggacggggcccc	11	11	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:32858993A>T	ENST00000317907.4	+	3	548	c.317A>T	c.(316-318)cAg>cTg	p.Q106L	MIR4765_ENST00000585007.1_RNA	NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	106										breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						CTTTTTGTTCAGAGCAACTGG	0.388																																					p.Q106L		Atlas-SNP	.											.	TTC27	71	.	0			c.A317T						.						138	136	136					2																	32858993		2203	4300	6503	SO:0001583	missense	55622	exon3			TTGTTCAGAGCAA	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.317A>T	chr2.hg19:g.32858993A>T	ENSP00000313953:p.Gln106Leu	97.0	0.0		71.0	17.0	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	hg19	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492283	0.84962	.	.	ENSG00000018699	ENST00000448773;ENST00000317907	T	0.74947	-0.89	5.59	5.59	0.84812	.	0.270269	0.36854	N	0.002373	D	0.86356	0.5913	M	0.81497	2.545	0.58432	D	0.999997	D	0.76494	0.999	D	0.81914	0.995	D	0.88288	0.2941	10	0.87932	D	0	-13.6704	14.7692	0.69662	1.0:0.0:0.0:0.0	.	106	Q6P3X3	TTC27_HUMAN	L	56;106	ENSP00000313953:Q106L	ENSP00000313953:Q106L	Q	+	2	0	TTC27	32712497	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.666000	0.74446	2.120000	0.65058	0.460000	0.39030	CAG	.	.		0.388	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		T	32858993	A	T	32858993	3	4	150	1	0	0	0	0	1	0	0	0	16710	188	7	4	327	4	TTC27	2	32858993	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	197826	32858993	210340380	82	22806										
KCNG3	170850	hgsc.bcm.edu	37	chr2	42720359	42720359	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccagtagatcatctcgttgtAgaaggagagctcgcacatcc	10	11	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:42720359A>T	ENST00000306078.1	-	1	878	c.283T>A	c.(283-285)Tac>Aac	p.Y95N	KCNG3_ENST00000394973.4_Missense_Mutation_p.Y95N|MTA3_ENST00000405592.1_5'Flank	NM_133329.5|NM_172344.2	NP_579875.1|NP_758847.1	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G, member 3	95					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	6						ATCTCGTTGTAGAAGGAGAGC	0.647																																					p.Y95N		Atlas-SNP	.											.	KCNG3	19	.	0			c.T283A						.						22	25	24					2																	42720359		2200	4298	6498	SO:0001583	missense	170850	exon1			CGTTGTAGAAGGA	AB070604	CCDS1809.1, CCDS42674.1	2p21	2011-07-05			ENSG00000171126	ENSG00000171126		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18306	protein-coding gene	gene with protein product		606767				11852086, 16382104	Standard	NM_133329		Approved	Kv6.3	uc002rsn.3	Q8TAE7	OTTHUMG00000128604	ENST00000306078.1:c.283T>A	chr2.hg19:g.42720359A>T	ENSP00000304127:p.Tyr95Asn	82.0	0.0		45.0	13.0	NM_172344	Q53SC1	Missense_Mutation	SNP	ENST00000306078.1	hg19	CCDS1809.1	.	.	.	.	.	.	.	.	.	.	A	18.31	3.596142	0.66332	.	.	ENSG00000171126	ENST00000306078;ENST00000394973	T;T	0.43688	0.94;0.94	3.54	3.54	0.40534	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.160550	0.44285	D	0.000475	T	0.55641	0.1933	L	0.56199	1.76	0.50813	D	0.999891	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.996	T	0.51725	-0.8669	10	0.28530	T	0.3	.	12.2655	0.54676	1.0:0.0:0.0:0.0	.	95;95	Q8TAE7;Q8TAE7-2	KCNG3_HUMAN;.	N	95	ENSP00000304127:Y95N;ENSP00000378424:Y95N	ENSP00000304127:Y95N	Y	-	1	0	KCNG3	42573863	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.758000	0.55220	1.483000	0.48342	0.374000	0.22700	TAC	.	.		0.647	KCNG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250464.2	NM_172344		T	42720359	A	T	42720359	3	4	150	1	0	0	0	0	1	0	0	0	8038	420	15	4	1035	4	KCNG3	2	42720359	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	9861366	42720359	200479014	83	22807										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54891657	54891657	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acaaaggacgagctctaaagAgtccagccccatcccctccc	7	17	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:54891657A>T	ENST00000356805.4	+	33	6769	c.6488A>T	c.(6487-6489)gAg>gTg	p.E2163V	AC093110.3_ENST00000456363.1_RNA	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	2163	Mediates interaction with CAMSAP1.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			AGCTCTAAAGAGTCCAGCCCC	0.582																																					p.E2163V		Atlas-SNP	.											.	SPTBN1	378	.	0			c.A6488T						.						167	151	156					2																	54891657		2203	4300	6503	SO:0001583	missense	6711	exon33			CTAAAGAGTCCAG		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.6488A>T	chr2.hg19:g.54891657A>T	ENSP00000349259:p.Glu2163Val	123.0	0.0		135.0	39.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.951980	0.53293	.	.	ENSG00000115306	ENST00000356805	T	0.70282	-0.47	5.93	5.93	0.95920	.	0.194126	0.44902	D	0.000407	T	0.53222	0.1783	N	0.14661	0.345	0.80722	D	1	P;B	0.45902	0.868;0.437	B;B	0.37239	0.244;0.045	T	0.57189	-0.7854	10	0.32370	T	0.25	.	16.3943	0.83563	1.0:0.0:0.0:0.0	.	153;2163	B4DIF8;Q01082	.;SPTB2_HUMAN	V	2163	ENSP00000349259:E2163V	ENSP00000349259:E2163V	E	+	2	0	SPTBN1	54745161	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.281000	0.95811	2.281000	0.76405	0.533000	0.62120	GAG	.	.		0.582	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54891657	A	T	54891657	3	4	150	1	0	0	0	0	1	0	0	0	15134	304	11	4	6814	4	SPTBN1	2	54891657	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	12171298	54891657	188307716	84	22808										
GFPT1	2673	hgsc.bcm.edu	37	chr2	69585596	69585596	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aagtcatagcctttgctttcCtgtaagtagaaagaaaaaaa	7	6	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:69585596C>T	ENST00000357308.4	-	6	587		c.e6-1		GFPT1_ENST00000361060.5_Splice_Site	NM_001244710.1	NP_001231639.1	Q06210	GFPT1_HUMAN	glutamine--fructose-6-phosphate transaminase 1						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|circadian regulation of gene expression (GO:0032922)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glucosamine biosynthetic process (GO:0006042)|glutamine metabolic process (GO:0006541)|negative regulation of glycogen biosynthetic process (GO:0045719)|post-translational protein modification (GO:0043687)|protein homotetramerization (GO:0051289)|protein N-linked glycosylation via asparagine (GO:0018279)|response to sucrose (GO:0009744)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			endometrium(1)|large_intestine(3)|lung(5)|skin(3)	12						CTTTGCTTTCCTGTAAGTAGA	0.323																																					.		Atlas-SNP	.											.	GFPT1	38	.	0			c.409-1G>A						.						96	82	87					2																	69585596		2202	4300	6502	SO:0001630	splice_region_variant	2673	exon7			GCTTTCCTGTAAG		CCDS33216.1, CCDS58713.1	2p13	2014-09-17	2010-05-11		ENSG00000198380	ENSG00000198380	2.6.1.16		4241	protein-coding gene	gene with protein product		138292	"glutamine-fructose-6-phosphate transaminase 1"	GFPT		1460020	Standard	NM_002056		Approved	GFAT, GFA, GFAT1	uc002sfi.2	Q06210	OTTHUMG00000152666	ENST00000357308.4:c.409-1G>A	chr2.hg19:g.69585596C>T		56.0	0.0		30.0	9.0	NM_002056	Q53QE6|Q9BXF8	Splice_Site	SNP	ENST00000357308.4	hg19	CCDS58713.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.281235	0.80692	.	.	ENSG00000198380	ENST00000357308;ENST00000361060	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9235	0.86169	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GFPT1	69439100	1.000000	0.71417	0.996000	0.52242	0.971000	0.66376	5.556000	0.67307	2.564000	0.86499	0.561000	0.74099	.	.	.		0.323	GFPT1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			Intron	T	69585596	C	T	69585596	5	4	150	1	0	0	0	0	0	0	1	0	6353	695	24	3	1693	3	GFPT1	2	69585596	Splice_Site	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	14693939	69585596	173613777	85	22809										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71661921	71661921	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggagcagaatgaggctgaagAaagaagctctaggtgattgg	16	4	1	6			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:71661921A>T	ENST00000409544.1	+	28	6551	c.5921A>T	c.(5920-5922)gAa>gTa	p.E1974V	ZNF638_ENST00000264447.4_Missense_Mutation_p.E1974V|ZNF638_ENST00000409407.1_Missense_Mutation_p.E914V|ZNF638_ENST00000355812.3_3'UTR	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1974					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GAGGCTGAAGAAAGAAGCTCT	0.318																																					p.E1974V		Atlas-SNP	.											.	ZNF638	179	.	0			c.A5921T						.						72	85	81					2																	71661921		2203	4300	6503	SO:0001583	missense	27332	exon28			CTGAAGAAAGAAG	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5921A>T	chr2.hg19:g.71661921A>T	ENSP00000386433:p.Glu1974Val	473.0	0.0		373.0	91.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.137337	0.77775	.	.	ENSG00000075292	ENST00000264447;ENST00000409544;ENST00000409407	T;T;T	0.45668	0.89;0.89;1.23	6.08	4.93	0.64822	.	0.000000	0.64402	D	0.000018	T	0.50939	0.1645	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.991	T	0.48833	-0.9000	10	0.46703	T	0.11	-21.3726	9.0298	0.36252	0.9176:0.0:0.0824:0.0	.	1953;1974	Q14966-3;Q14966	.;ZN638_HUMAN	V	1974;1974;914	ENSP00000264447:E1974V;ENSP00000386433:E1974V;ENSP00000386813:E914V	ENSP00000264447:E1974V	E	+	2	0	ZNF638	71515429	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.738000	0.47401	1.129000	0.42072	0.482000	0.46254	GAA	.	.		0.318	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		T	71661921	A	T	71661921	3	4	150	1	0	0	0	0	1	0	0	0	18070	246	9	4	6027	4	ZNF638	2	71661921	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2076325	71661921	171537452	86	22810										
C2orf65	130951	hgsc.bcm.edu	37	chr2	74867347	74867347	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgagaagccgtggaggttgcTggtcaatctgagtgtgagta	16	5	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:74867347T>A	ENST00000290536.5	-	2	172	c.56A>T	c.(55-57)cAg>cTg	p.Q19L	M1AP_ENST00000358434.2_5'UTR|M1AP_ENST00000536235.1_Missense_Mutation_p.Q19L|M1AP_ENST00000409585.1_Missense_Mutation_p.Q19L	NM_001281296.1|NM_138804.3	NP_001268225.1|NP_620159.2	Q8TC57	M1AP_HUMAN	meiosis 1 associated protein	19					cell differentiation (GO:0030154)|chromatin assembly (GO:0031497)|female gamete generation (GO:0007292)|male meiosis chromosome separation (GO:0051308)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											TGGAGGTTGCTGGTCAATCTG	0.542																																					p.Q19L		Atlas-SNP	.											.	.	.	.	0			c.A56T						.						124	115	118					2																	74867347		2203	4300	6503	SO:0001583	missense	130951	exon2			GGTTGCTGGTCAA		CCDS33229.1, CCDS62941.1	2p13.1	2013-02-05	2013-02-05	2013-01-16	ENSG00000159374	ENSG00000159374			25183	protein-coding gene	gene with protein product	"meiosis 1 arresting protein", "spermatogenesis associated 37"		"chromosome 2 open reading frame 65"	C2orf65		16881047, 23269666	Standard	NM_138804		Approved	D6Mm5e, SPATA37	uc002smy.3	Q8TC57	OTTHUMG00000152918	ENST00000290536.5:c.56A>T	chr2.hg19:g.74867347T>A	ENSP00000290536:p.Gln19Leu	167.0	0.0		110.0	23.0	NM_138804	B7Z6E7|E9PGG8|Q6ZP30|Q96L07	Missense_Mutation	SNP	ENST00000290536.5	hg19	CCDS33229.1	.	.	.	.	.	.	.	.	.	.	T	15.69	2.907377	0.52333	.	.	ENSG00000159374	ENST00000290536;ENST00000409585;ENST00000536235;ENST00000421985	T;T;T;T	0.33216	1.42;1.42;1.42;1.42	5.65	3.34	0.38264	.	0.289402	0.34268	N	0.004116	T	0.24431	0.0592	L	0.51422	1.61	0.80722	D	1	B;B;B	0.34015	0.403;0.435;0.403	B;B;B	0.33042	0.157;0.08;0.157	T	0.05468	-1.0883	10	0.41790	T	0.15	-5.0862	6.8682	0.24104	0.0:0.1548:0.0:0.8452	.	19;19;19	E9PGG8;Q8TC57-2;Q8TC57	.;.;CB065_HUMAN	L	19	ENSP00000290536:Q19L;ENSP00000386793:Q19L;ENSP00000445662:Q19L;ENSP00000414882:Q19L	ENSP00000290536:Q19L	Q	-	2	0	C2orf65	74720855	0.999000	0.42202	0.997000	0.53966	0.877000	0.50540	0.935000	0.28924	2.155000	0.67459	0.533000	0.62120	CAG	.	.		0.542	M1AP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328569.1	NM_138804		A	74867347	T	A	74867347	3	1	150	1	0	0	0	0	1	0	0	0	2186	1580	55	4	1576	4	C2orf65	2	74867347	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3205426	74867347	168332026	87	22811										
POLR1A	25885	hgsc.bcm.edu	37	chr2	86305011	86305011	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tccaatttcgttggtgttgaTgtacatgtctgggcagatga	12	6	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:86305011T>A	ENST00000263857.6	-	11	1729	c.1351A>T	c.(1351-1353)Atc>Ttc	p.I451F	POLR1A_ENST00000409681.1_Missense_Mutation_p.I451F			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	451					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						TTGGTGTTGATGTACATGTCT	0.517																																					p.I451F		Atlas-SNP	.											.	POLR1A	137	.	0			c.A1351T						.						141	144	143					2																	86305011		2018	4162	6180	SO:0001583	missense	25885	exon11			TGTTGATGTACAT	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1351A>T	chr2.hg19:g.86305011T>A	ENSP00000263857:p.Ile451Phe	52.0	0.0		37.0	7.0	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.291690	0.80914	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.70749	-0.51;-0.51	5.62	5.62	0.85841	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.093744	0.64402	D	0.000001	T	0.79958	0.4536	M	0.91818	3.245	0.80722	D	1	P	0.41673	0.759	B	0.42692	0.395	D	0.84382	0.0550	10	0.62326	D	0.03	-21.3433	15.7908	0.78364	0.0:0.0:0.0:1.0	.	451	O95602	RPA1_HUMAN	F	451	ENSP00000263857:I451F;ENSP00000386300:I451F	ENSP00000263857:I451F	I	-	1	0	POLR1A	86158522	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.541000	0.82084	2.270000	0.75569	0.459000	0.35465	ATC	.	.		0.517	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		A	86305011	T	A	86305011	3	1	150	1	0	0	0	0	1	0	0	0	12218	1464	51	4	3907	4	POLR1A	2	86305011	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	11437664	86305011	156894362	88	22812										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99006230	99006230	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tctataactggtatctgcttAtttgcaggtaagcgacaggg	11	7	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:99006230A>C	ENST00000272602.2	+	5	598	c.559A>C	c.(559-561)Att>Ctt	p.I187L	CNGA3_ENST00000393504.1_Missense_Mutation_p.I187L|CNGA3_ENST00000409937.1_Missense_Mutation_p.I191L|CNGA3_ENST00000436404.2_Missense_Mutation_p.I169L			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	187					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						GTATCTGCTTATTTGCAGGTA	0.597																																					p.I187L		Atlas-SNP	.											.	CNGA3	118	.	0			c.A559C						.						89	78	82					2																	99006230		2203	4300	6503	SO:0001583	missense	1261	exon6			CTGCTTATTTGCA	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.559A>C	chr2.hg19:g.99006230A>C	ENSP00000272602:p.Ile187Leu	78.0	0.0		51.0	14.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.760814	0.31137	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.97505	-4.41;-4.41;-4.41;-4.41	4.85	3.04	0.35103	.	0.133223	0.50627	D	0.000119	D	0.94525	0.8237	M	0.64404	1.975	0.36508	D	0.869395	B;B;B	0.16802	0.019;0.006;0.014	B;B;B	0.20384	0.014;0.014;0.029	D	0.90805	0.4697	10	0.19147	T	0.46	.	9.5874	0.39526	0.1785:0.0:0.8215:0.0	.	191;169;187	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	L	187;169;187;191	ENSP00000377140:I187L;ENSP00000410070:I169L;ENSP00000272602:I187L;ENSP00000386761:I191L	ENSP00000272602:I187L	I	+	1	0	CNGA3	98372662	0.986000	0.35501	0.017000	0.16124	0.174000	0.22865	1.931000	0.40134	0.630000	0.30394	-0.475000	0.04921	ATT	.	.		0.597	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		C	99006230	A	C	99006230	3	2	150	1	0	0	0	0	1	0	0	0	3600	449	16	5	577	5	CNGA3	2	99006230	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	12701219	99006230	144193143	89	22813										
IL18RAP	8807	hgsc.bcm.edu	37	chr2	103061692	103061692	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaatcattgagcgtaatatcAtcttggaaaaagtcactcag	7	7	5	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:103061692A>T	ENST00000264260.2	+	9	1553	c.964A>T	c.(964-966)Atc>Ttc	p.I322F	IL18RAP_ENST00000409369.1_Missense_Mutation_p.I180F	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	322	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						GCGTAATATCATCTTGGAAAA	0.388																																					p.I322F		Atlas-SNP	.											.	IL18RAP	102	.	0			c.A964T						.						103	95	98					2																	103061692		2203	4300	6503	SO:0001583	missense	8807	exon9			AATATCATCTTGG	AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.964A>T	chr2.hg19:g.103061692A>T	ENSP00000264260:p.Ile322Phe	119.0	0.0		112.0	26.0	NM_003853	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Missense_Mutation	SNP	ENST00000264260.2	hg19	CCDS2061.1	.	.	.	.	.	.	.	.	.	.	A	6.713	0.500318	0.12762	.	.	ENSG00000115607	ENST00000264260;ENST00000409369	T;T	0.14266	2.52;2.52	5.63	-7.12	0.01537	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.831060	0.02424	N	0.082889	T	0.06462	0.0166	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.33240	-0.9876	10	0.09843	T	0.71	.	6.1748	0.20437	0.4096:0.3805:0.0:0.2099	.	322	O95256	I18RA_HUMAN	F	322;180	ENSP00000264260:I322F;ENSP00000387201:I180F	ENSP00000264260:I322F	I	+	1	0	IL18RAP	102428124	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.791000	0.04599	-0.838000	0.04218	0.533000	0.62120	ATC	.	.		0.388	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853		T	103061692	A	T	103061692	3	4	150	1	0	0	0	0	1	0	0	0	7657	217	8	4	990	4	IL18RAP	2	103061692	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	4055462	103061692	140137681	90	22814										
SLC9A4	389015	hgsc.bcm.edu	37	chr2	103148873	103148873	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acttcagaagcaagaggcacAagaaataataccaatgaaga	8	7	1	5			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:103148873A>T	ENST00000295269.4	+	12	2580	c.2123A>T	c.(2122-2124)cAa>cTa	p.Q708L		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	708					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CAAGAGGCACAAGAAATAATA	0.463																																					p.Q708L		Atlas-SNP	.											.	SLC9A4	115	.	0			c.A2123T						.						92	88	90					2																	103148873		2203	4300	6503	SO:0001583	missense	389015	exon12			AGGCACAAGAAAT		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"Solute carriers"	11077	protein-coding gene	gene with protein product		600531	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 4", "solute carrier family 9 (sodium/hydrogen exchanger), member 4"			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.2123A>T	chr2.hg19:g.103148873A>T	ENSP00000295269:p.Gln708Leu	118.0	0.0		86.0	20.0	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	hg19	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.780422	0.31502	.	.	ENSG00000180251	ENST00000295269	T	0.50813	0.73	4.76	0.618	0.17624	.	1.605070	0.03266	N	0.183960	T	0.34629	0.0904	L	0.27053	0.805	0.09310	N	1	B	0.26400	0.148	B	0.19391	0.025	T	0.20538	-1.0272	10	0.37606	T	0.19	.	6.5998	0.22695	0.5172:0.3914:0.0914:0.0	.	708	Q6AI14	SL9A4_HUMAN	L	708	ENSP00000295269:Q708L	ENSP00000295269:Q708L	Q	+	2	0	SLC9A4	102515305	0.001000	0.12720	0.001000	0.08648	0.010000	0.07245	0.316000	0.19469	0.256000	0.21614	0.533000	0.62120	CAA	.	.		0.463	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		T	103148873	A	T	103148873	3	4	150	1	0	0	0	0	1	0	0	0	14731	130	5	4	2169	4	SLC9A4	2	103148873	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	87181	103148873	140050500	91	22815										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109347864	109347864	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatgatgttactgatggaagAgcaaaatactggcttgaaag	11	4	0	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:109347864A>T	ENST00000283195.6	+	4	465	c.339A>T	c.(337-339)agA>agT	p.R113S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	113					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CTGATGGAAGAGCAAAATACT	0.338																																					p.R113S		Atlas-SNP	.											.	RANBP2	488	.	0			c.A339T						.						143	158	153					2																	109347864		2203	4299	6502	SO:0001583	missense	5903	exon4			TGGAAGAGCAAAA	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.339A>T	chr2.hg19:g.109347864A>T	ENSP00000283195:p.Arg113Ser	909.0	0.0		764.0	185.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	A	19.77	3.888653	0.72524	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.37584	1.19	4.97	4.97	0.65823	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.	.	.	.	T	0.48187	0.1486	M	0.70275	2.135	0.37186	D	0.903711	D	0.62365	0.991	P	0.49799	0.622	T	0.62863	-0.6764	9	0.87932	D	0	-29.3377	14.939	0.70978	1.0:0.0:0.0:0.0	.	113	P49792	RBP2_HUMAN	S	113	ENSP00000283195:R113S	ENSP00000283195:R113S	R	+	3	2	RANBP2	108714296	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.627000	0.61276	2.004000	0.58718	0.467000	0.42956	AGA	.	.		0.338	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		T	109347864	A	T	109347864	3	4	150	1	0	0	0	0	1	0	0	0	13043	301	11	4	353	4	RANBP2	2	109347864	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	6198991	109347864	133851509	92	22816										
SH3RF3	344558	hgsc.bcm.edu	37	chr2	109964388	109964388	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acaaagaccaagacaaggacTgtctgaccttcaccaaggta	8	11	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:109964388T>A	ENST00000309415.6	+	2	832	c.832T>A	c.(832-834)Tgt>Agt	p.C278S		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	278	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.						zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						AGACAAGGACTGTCTGACCTT	0.592																																					p.C278S		Atlas-SNP	.											.	SH3RF3	62	.	0			c.T832A						.						26	29	28					2																	109964388		1971	4153	6124	SO:0001583	missense	344558	exon2			AAGGACTGTCTGA	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.832T>A	chr2.hg19:g.109964388T>A	ENSP00000309186:p.Cys278Ser	100.0	0.0		68.0	12.0	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	hg19		.	.	.	.	.	.	.	.	.	.	T	23.4	4.414082	0.83449	.	.	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.28069	1.63;1.63	5.16	5.16	0.70880	Src homology-3 domain (4);	.	.	.	.	T	0.53610	0.1807	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.52290	-0.8595	8	0.34782	T	0.22	.	15.0095	0.71539	0.0:0.0:0.0:1.0	.	278	Q8TEJ3	SH3R3_HUMAN	S	278	ENSP00000414997:C278S;ENSP00000309186:C278S	ENSP00000309186:C278S	C	+	1	0	SH3RF3	109330820	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.948000	0.87774	1.938000	0.56188	0.454000	0.30748	TGT	.	.		0.592	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		A	109964388	T	A	109964388	3	1	150	1	0	0	0	0	1	0	0	0	14275	1580	55	4	838	4	SH3RF3	2	109964388	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	616524	109964388	133234985	93	22817										
PAX8	7849	hgsc.bcm.edu	37	chr2	114004421	114004421	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctggtgggccaggtctacgAtgcgctggcggaccacttcc	14	14	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:114004421A>T	ENST00000429538.3	-	3	295	c.101T>A	c.(100-102)aTc>aAc	p.I34N	AC016683.6_ENST00000451179.1_RNA|AC016683.6_ENST00000422956.2_RNA|AC016683.6_ENST00000436293.2_RNA|AC016683.6_ENST00000445745.1_RNA|PAX8_ENST00000263334.5_Missense_Mutation_p.I34N|AC016683.6_ENST00000556070.1_RNA|AC016683.6_ENST00000553869.2_RNA|PAX8_ENST00000397647.3_Missense_Mutation_p.I34N|PAX8_ENST00000263335.7_Missense_Mutation_p.I34N|AC016683.6_ENST00000333145.5_RNA|PAX8_ENST00000348715.5_Missense_Mutation_p.I34N	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	34	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				anatomical structure morphogenesis (GO:0009653)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular response to gonadotropin stimulus (GO:0071371)|central nervous system development (GO:0007417)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesonephros development (GO:0001823)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric nephron tubule formation (GO:0072289)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|otic vesicle development (GO:0071599)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|regulation of apoptotic process (GO:0042981)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of thyroid-stimulating hormone secretion (GO:2000612)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone signaling pathway (GO:0038194)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid-stimulating hormone receptor activity (GO:0004996)|transcription regulatory region DNA binding (GO:0044212)		PAX8/PPARG(117)	breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|skin(1)	20						CAGGTCTACGATGCGCTGGCG	0.617			T	PPARG	follicular thyroid		Thyroid dysgenesis																														p.I34N	Ovarian(188;7 2067 9084 29802 29892)	Atlas-SNP	.		Dom	yes		2	2q12-q14	7849	paired box gene 8	yes	E	.	PAX8	42	.	0			c.T101A	GRCh37	CM065371	PAX8	M		.						44	51	48					2																	114004421		2135	4283	6418	SO:0001583	missense	7849	exon3			TCTACGATGCGCT	X69699	CCDS42735.1, CCDS42736.1, CCDS46398.1, CCDS46399.1	2q13	2011-06-20	2007-07-12		ENSG00000125618	ENSG00000125618		"Paired boxes", "Homeoboxes / PRD class"	8622	protein-coding gene	gene with protein product		167415	"paired box gene 8"			8431641, 7981748	Standard	NM_003466		Approved		uc010yxt.2	Q06710	OTTHUMG00000128529	ENST00000429538.3:c.101T>A	chr2.hg19:g.114004421A>T	ENSP00000395498:p.Ile34Asn	139.0	0.0		126.0	29.0	NM_013952	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Missense_Mutation	SNP	ENST00000429538.3	hg19	CCDS46398.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.352789	0.82132	.	.	ENSG00000125618	ENST00000263335;ENST00000397647;ENST00000348715;ENST00000429538;ENST00000263334	D;D;D;D;D	0.99674	-6.36;-6.36;-6.36;-6.36;-6.36	5.1	5.1	0.69264	Paired box protein, N-terminal (4);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99819	0.9920	H	0.97540	4.025	0.80722	D	1	D;D;D;D;D	0.89917	0.994;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.991;1.0;0.999;1.0;1.0	D	0.96869	0.9638	10	0.87932	D	0	.	12.8594	0.57906	1.0:0.0:0.0:0.0	.	34;34;34;34;34	Q06710-2;Q06710-3;Q06710;Q06710-5;Q06710-4	.;.;PAX8_HUMAN;.;.	N	34	ENSP00000263335:I34N;ENSP00000380768:I34N;ENSP00000314750:I34N;ENSP00000395498:I34N;ENSP00000263334:I34N	ENSP00000263334:I34N	I	-	2	0	PAX8	113720891	1.000000	0.71417	0.997000	0.53966	0.741000	0.42261	9.271000	0.95698	1.931000	0.55961	0.533000	0.62120	ATC	.	.		0.617	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5			T	114004421	A	T	114004421	3	4	150	1	0	0	0	0	1	0	0	0	11494	333	12	4	1166	4	PAX8	2	114004421	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	4040033	114004421	129194952	94	22818										
IWS1	55677	hgsc.bcm.edu	37	chr2	128249661	128249661	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggtctcctggctcacactagGcagctggggaacataaacac	11	12	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:128249661G>A	ENST00000295321.4	-	10	2192	c.1933C>T	c.(1933-1935)Cct>Tct	p.P645S	AC010976.2_ENST00000454503.2_RNA|AC010976.2_ENST00000595561.1_RNA|IWS1_ENST00000455721.2_3'UTR|AC010976.2_ENST00000599001.1_RNA|AC010976.2_ENST00000598065.1_RNA|AC010976.2_ENST00000596439.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	645	Interaction with SUPT6H and ALYREF.|TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		CTCACACTAGGCAGCTGGGGA	0.473																																					p.P645S		Atlas-SNP	.											.	IWS1	61	.	0			c.C1933T						.						81	70	74					2																	128249661		2203	4300	6503	SO:0001583	missense	55677	exon10			CACTAGGCAGCTG	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.1933C>T	chr2.hg19:g.128249661G>A	ENSP00000295321:p.Pro645Ser	102.0	0.0		97.0	24.0	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	hg19	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.926055	0.92319	.	.	ENSG00000163166	ENST00000295321;ENST00000433551	T	0.51325	0.71	5.2	5.2	0.72013	Transcription factor IIS, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.60612	0.2282	M	0.76170	2.325	0.80722	D	1	P	0.37781	0.608	P	0.45406	0.479	T	0.65952	-0.6043	10	0.87932	D	0	-18.0837	18.8155	0.92075	0.0:0.0:1.0:0.0	.	645	Q96ST2	IWS1_HUMAN	S	645;598	ENSP00000295321:P645S	ENSP00000295321:P645S	P	-	1	0	IWS1	127966131	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.802000	0.99131	2.431000	0.82371	0.558000	0.71614	CCT	.	.		0.473	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		A	128249661	G	A	128249661	3	1	150	1	0	0	0	0	1	0	0	0	7940	1203	42	3	546	3	IWS1	2	128249661	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	14245240	128249661	114949712	95	22819										
SAP130	79595	hgsc.bcm.edu	37	chr2	128747139	128747139	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgcaaaaatttaaaattaccTgaagtctttccttcaggctg	6	8	2	1	rs372682996		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:128747139T>A	ENST00000259235.3	-	13	1986	c.1857A>T	c.(1855-1857)tcA>tcT	p.S619S	SAP130_ENST00000259234.6_Splice_Site_p.S593S|SAP130_ENST00000357702.5_Splice_Site_p.S619S	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	619					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		TAAAATTACCTGAAGTCTTTC	0.428																																					p.S619S		Atlas-SNP	.											.	SAP130	169	.	0			c.A1857T						.						59	60	59					2																	128747139		2203	4300	6503	SO:0001630	splice_region_variant	79595	exon13			ATTACCTGAAGTC	BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"sin3A-associated protein, 130kDa"			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.1858+1A>T	chr2.hg19:g.128747139T>A		134.0	0.0		101.0	33.0	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Silent	SNP	ENST00000259235.3	hg19	CCDS2153.1																																																																																			.	.		0.428	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545	Silent	A	128747139	T	A	128747139	5	1	150	1	0	0	0	0	0	0	1	0	13846	1594	55	4	1430	4	SAP130	2	128747139	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	497478	128747139	114452234	96	22820										
MCM6	4175	hgsc.bcm.edu	37	chr2	136609093	136609093	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	catctctctggcggagatgtTtatattgctccacaatgaag	9	9	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:136609093T>A	ENST00000264156.2	-	13	1856	c.1796A>T	c.(1795-1797)aAa>aTa	p.K599I	MCM6_ENST00000492091.1_5'UTR	NM_005915.5	NP_005906.2	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	599					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(15)|prostate(2)|skin(1)	29				BRCA - Breast invasive adenocarcinoma(221;0.166)		GCGGAGATGTTTATATTGCTC	0.428																																					p.K599I	Ovarian(196;141 2104 8848 24991 25939)	Atlas-SNP	.											.	MCM6	64	.	0			c.A1796T						.						106	90	95					2																	136609093		2203	4300	6503	SO:0001583	missense	4175	exon13			AGATGTTTATATT		CCDS2179.1	2q14-q21	2008-02-05	2007-04-04		ENSG00000076003	ENSG00000076003			6949	protein-coding gene	gene with protein product	"MIS5 homolog (S.pombe)"	601806	"minichromosome maintenance deficient (mis5, S. pombe) 6", "MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, S. pombe) (S. cerevisiae)", "minichromosome maintenance deficient 6 homolog (S. cerevisiae)"				Standard	NM_005915		Approved	Mis5	uc002tuw.4	Q14566	OTTHUMG00000131739	ENST00000264156.2:c.1796A>T	chr2.hg19:g.136609093T>A	ENSP00000264156:p.Lys599Ile	61.0	0.0		42.0	10.0	NM_005915	B2R6H2|Q13504|Q99859	Missense_Mutation	SNP	ENST00000264156.2	hg19	CCDS2179.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.864644	0.91511	.	.	ENSG00000076003	ENST00000264156	T	0.06528	3.29	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.14056	0.0340	L	0.31420	0.93	0.80722	D	1	P	0.49447	0.924	P	0.61201	0.885	T	0.08106	-1.0738	10	0.34782	T	0.22	-23.1599	15.8555	0.78975	0.0:0.0:0.0:1.0	.	599	Q14566	MCM6_HUMAN	I	599	ENSP00000264156:K599I	ENSP00000264156:K599I	K	-	2	0	MCM6	136325563	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	6.226000	0.72277	2.140000	0.66376	0.374000	0.22700	AAA	.	.		0.428	MCM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254658.1	NM_005915		A	136609093	T	A	136609093	3	1	150	1	0	0	0	0	1	0	0	0	9400	1841	64	4	689	4	MCM6	2	136609093	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	7861954	136609093	106590280	97	22821										
NOSTRIN	115677	hgsc.bcm.edu	37	chr2	169688005	169688005	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gacaatgaagttgaaaagacAgcaaatcttgtcattagcaa	8	6	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:169688005A>T	ENST00000317647.7	+	6	595	c.366A>T	c.(364-366)acA>acT	p.T122T	NOSTRIN_ENST00000397206.2_Silent_p.T44T|NOSTRIN_ENST00000397209.2_Silent_p.T94T|NOSTRIN_ENST00000444448.2_Silent_p.T122T|NOSTRIN_ENST00000458381.2_Silent_p.T122T|NOSTRIN_ENST00000445023.2_Silent_p.T44T|NOSTRIN_ENST00000421711.2_Silent_p.T94T	NM_001039724.3	NP_001034813.2	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficking	122					endocytosis (GO:0006897)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoskeleton (GO:0005856)|endocytic vesicle membrane (GO:0030666)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						TTGAAAAGACAGCAAATCTTG	0.333																																					p.T122T		Atlas-SNP	.											.	NOSTRIN	68	.	0			c.A366T						.						93	84	87					2																	169688005		1853	4106	5959	SO:0001819	synonymous_variant	115677	exon6			AAAGACAGCAAAT	AJ532842	CCDS42771.1, CCDS42772.1, CCDS54415.1, CCDS54416.1	2q31.1	2013-08-05	2013-08-05		ENSG00000163072	ENSG00000163072			20203	protein-coding gene	gene with protein product		607496	"nitric oxide synthase trafficker"			12446846	Standard	NM_001171631		Approved	MGC20702	uc002ueg.3	Q8IVI9	OTTHUMG00000153990	ENST00000317647.7:c.366A>T	chr2.hg19:g.169688005A>T		253.0	0.0		238.0	53.0	NM_001039724	A8K2I9|B3KSF5|E7EPT9|Q27HG3|Q53S62|Q96CJ9	Silent	SNP	ENST00000317647.7	hg19	CCDS42771.1																																																																																			.	.		0.333	NOSTRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333356.4	NM_052946		T	169688005	A	T	169688005	2	4	150	1	0	0	0	0	0	0	0	1	10555	175	7	4		4	NOSTRIN	2	169688005	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	33078912	169688005	73511368	98	22822										
BBS5	129880	hgsc.bcm.edu	37	chr2	170355994	170355994	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tttattattttttctcttgtAgagtggtggatatgttcttg	9	3	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:170355994A>T	ENST00000295240.3	+	9	1057		c.e9-1		RP11-724O16.1_ENST00000513963.1_Splice_Site|BBS5_ENST00000392663.2_Splice_Site|BBS5_ENST00000554017.1_Splice_Site	NM_152384.2	NP_689597.1	Q8N3I7	BBS5_HUMAN	Bardet-Biedl syndrome 5						cilium assembly (GO:0042384)|heart looping (GO:0001947)|melanosome transport (GO:0032402)|motile cilium assembly (GO:0044458)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphate binding (GO:0032266)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TTTCTCTTGTAGAGTGGTGGA	0.299									Bardet-Biedl syndrome																												.		Atlas-SNP	.											.	BBS5	27	.	0			c.682-2A>T						.						53	55	55					2																	170355994		2203	4298	6501	SO:0001630	splice_region_variant	129880	exon9	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TCTTGTAGAGTGG	AY604003	CCDS2233.1	2q31	2011-08-02			ENSG00000163093	ENSG00000163093			970	protein-coding gene	gene with protein product		603650				9888993, 10053027	Standard	NM_152384		Approved	DKFZp762I194		Q8N3I7	OTTHUMG00000132207	ENST00000295240.3:c.682-1A>T	chr2.hg19:g.170355994A>T		214.0	0.0		186.0	59.0	NM_152384	D3DPC3|Q6PKN0	Splice_Site	SNP	ENST00000295240.3	hg19	CCDS2233.1	.	.	.	.	.	.	.	.	.	.	A	16.09	3.024720	0.54683	.	.	ENSG00000163093;ENSG00000163093;ENSG00000163093;ENSG00000251569	ENST00000295240;ENST00000554017;ENST00000392663;ENST00000513963	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0271	0.80551	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BBS5;RP11-724O16.1	170064240	1.000000	0.71417	0.925000	0.36789	0.558000	0.35554	9.267000	0.95665	2.188000	0.69820	0.482000	0.46254	.	.	.		0.299	BBS5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255265.2	NM_152384	Intron	T	170355994	A	T	170355994	5	4	150	1	0	0	0	0	0	0	1	0	1340	434	15	4	714	4	BBS5	2	170355994	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	667989	170355994	72843379	99	22823										
DCAF17	80067	hgsc.bcm.edu	37	chr2	172300031	172300031	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atttatttttcttttttcccAgtgttgcatctgagccaaga	6	8	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:172300031A>T	ENST00000375255.3	+	3	557		c.e3-1		DCAF17_ENST00000539783.1_Splice_Site|DCAF17_ENST00000468592.1_Splice_Site	NM_025000.3	NP_079276.2	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17						protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)	17						CTTTTTTCCCAGTGTTGCATC	0.323																																					.		Atlas-SNP	.											.	DCAF17	41	.	0			c.231-2A>T						.						85	78	80					2																	172300031		1791	4069	5860	SO:0001630	splice_region_variant	80067	exon3			TTTCCCAGTGTTG	AK023158	CCDS2243.2, CCDS54419.1	2q31.1	2014-01-28	2009-07-17	2009-07-17	ENSG00000115827	ENSG00000115827		"DDB1 and CUL4 associated factors"	25784	protein-coding gene	gene with protein product	"Woodhouse-Sakati syndrome"	612515	"chromosome 2 open reading frame 37"	C2orf37			Standard	NM_001164821		Approved	FLJ13096	uc002ugx.3	Q5H9S7	OTTHUMG00000132259	ENST00000375255.3:c.231-1A>T	chr2.hg19:g.172300031A>T		41.0	0.0		41.0	12.0	NM_025000	B2RTW5|Q53TN3|Q9H908	Splice_Site	SNP	ENST00000375255.3	hg19	CCDS2243.2	.	.	.	.	.	.	.	.	.	.	A	15.23	2.770789	0.49680	.	.	ENSG00000115827	ENST00000375255;ENST00000539783	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2196	0.73299	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DCAF17	172008277	1.000000	0.71417	0.923000	0.36655	0.634000	0.38068	6.614000	0.74197	2.073000	0.62155	0.472000	0.43445	.	.	.		0.323	DCAF17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255342.2	NM_025000	Intron	T	172300031	A	T	172300031	5	4	150	1	0	0	0	0	0	0	1	0	4271	202	7	4	239	4	DCAF17	2	172300031	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1944037	172300031	70899342	100	22824										
WIPF1	7456	hgsc.bcm.edu	37	chr2	175432711	175432711	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtccactcctgggactgtctActccactcctggatggcaac	9	15	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:175432711A>T	ENST00000392547.2	-	6	1319	c.1220T>A	c.(1219-1221)gTa>gAa	p.V407E	WIPF1_ENST00000272746.5_Missense_Mutation_p.V407E|WIPF1_ENST00000409891.1_Missense_Mutation_p.V407E|WIPF1_ENST00000467149.1_5'UTR|WIPF1_ENST00000359761.3_Missense_Mutation_p.V407E|WIPF1_ENST00000392546.2_Missense_Mutation_p.V407E|AC018890.6_ENST00000412835.1_RNA|AC018890.6_ENST00000442996.1_RNA	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	407	Pro-rich.				actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)			NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						GGGACTGTCTACTCCACTCCT	0.612																																					p.V407E		Atlas-SNP	.											.	WIPF1	88	.	0			c.T1220A						.						55	55	55					2																	175432711		2203	4300	6503	SO:0001583	missense	7456	exon6			CTGTCTACTCCAC	AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"Wiskott-Aldrich syndrome protein interacting protein"	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.1220T>A	chr2.hg19:g.175432711A>T	ENSP00000376330:p.Val407Glu	101.0	0.0		64.0	20.0	NM_003387	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Missense_Mutation	SNP	ENST00000392547.2	hg19	CCDS2260.1	.	.	.	.	.	.	.	.	.	.	A	13.48	2.249736	0.39797	.	.	ENSG00000115935	ENST00000392547;ENST00000392548;ENST00000272746;ENST00000359761;ENST00000392546;ENST00000409891	T;T;T;T;T	0.46819	1.55;1.55;1.55;1.55;0.86	5.49	3.03	0.35002	.	0.815711	0.11106	N	0.599157	T	0.34716	0.0907	N	0.19112	0.55	0.22996	N	0.998457	B;B;B	0.26258	0.145;0.145;0.09	B;B;B	0.34779	0.189;0.189;0.057	T	0.37430	-0.9706	10	0.22706	T	0.39	.	8.5897	0.33679	0.8024:0.1299:0.0677:0.0	.	407;407;407	O43516-3;O43516-2;O43516	.;.;WIPF1_HUMAN	E	407;263;407;407;407;407	ENSP00000376330:V407E;ENSP00000272746:V407E;ENSP00000352802:V407E;ENSP00000376329:V407E;ENSP00000386431:V407E	ENSP00000272746:V407E	V	-	2	0	WIPF1	175140957	0.990000	0.36364	0.014000	0.15608	0.884000	0.51177	3.261000	0.51530	0.428000	0.26173	0.533000	0.62120	GTA	.	.		0.612	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387		T	175432711	A	T	175432711	3	4	150	1	0	0	0	0	1	0	0	0	17382	391	14	4	303	4	WIPF1	2	175432711	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3132680	175432711	67766662	101	22825										
ATF2	1386	hgsc.bcm.edu	37	chr2	175939359	175939359	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aacttcctgagggctgtgacTgggaggaaggagccataacg	15	8	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:175939359T>A	ENST00000264110.2	-	14	1794	c.1496A>T	c.(1495-1497)cAg>cTg	p.Q499L	ATF2_ENST00000409437.1_Missense_Mutation_p.Q383L|ATF2_ENST00000538946.1_3'UTR|ATF2_ENST00000409499.1_Missense_Mutation_p.Q138L|ATF2_ENST00000409635.1_Missense_Mutation_p.Q441L|ATF2_ENST00000426833.3_Missense_Mutation_p.Q481L|ATF2_ENST00000487334.2_3'UTR|ATF2_ENST00000345739.5_Missense_Mutation_p.Q441L|ATF2_ENST00000392544.1_Missense_Mutation_p.Q499L|ATF2_ENST00000392543.2_Missense_Mutation_p.Q120L	NM_001256090.1|NM_001256091.1|NM_001880.3	NP_001243019.1|NP_001243020.1|NP_001871.2	P15336	ATF2_HUMAN	activating transcription factor 2	499					adipose tissue development (GO:0060612)|cellular response to DNA damage stimulus (GO:0006974)|chromatin organization (GO:0006325)|fat cell differentiation (GO:0045444)|histone acetylation (GO:0016573)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|outflow tract morphogenesis (GO:0003151)|positive regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902110)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta2 production (GO:0032915)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	cAMP response element binding (GO:0035497)|cAMP response element binding protein binding (GO:0008140)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.125)		Pseudoephedrine(DB00852)	GGGCTGTGACTGGGAGGAAGG	0.473																																					p.Q499L	Pancreas(17;87 705 4534 15538 30988)	Atlas-SNP	.											.	ATF2	52	.	0			c.A1496T						.						46	43	44					2																	175939359		2203	4300	6503	SO:0001583	missense	1386	exon14			TGTGACTGGGAGG	X15875	CCDS2262.1, CCDS58737.1, CCDS58738.1, CCDS58739.1	2q32	2013-01-10			ENSG00000115966	ENSG00000115966		"basic leucine zipper proteins"	784	protein-coding gene	gene with protein product		123811	"cAMP responsive element binding protein 2"	CREB2		1833307, 1838349	Standard	NM_001880		Approved	TREB7, CRE-BP1, HB16	uc002ujl.4	P15336	OTTHUMG00000132424	ENST00000264110.2:c.1496A>T	chr2.hg19:g.175939359T>A	ENSP00000264110:p.Gln499Leu	102.0	0.0		112.0	29.0	NM_001880	A1L3Z2|A4D7U4|A4D7U5|A4D7V1|D3DPE9|G8JLM5|Q13000|Q3B7B7|Q4ZFU9|Q53RY2|Q8TAR1|Q96JT8	Missense_Mutation	SNP	ENST00000264110.2	hg19	CCDS2262.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.081896	0.36758	.	.	ENSG00000115966	ENST00000264110;ENST00000345739;ENST00000542046;ENST00000409437;ENST00000409635;ENST00000392544;ENST00000409499;ENST00000426833;ENST00000392543	D;T;T;T;D;D	0.81821	-1.54;0.02;-0.7;0.02;-1.54;-1.5	5.91	5.91	0.95273	.	0.125508	0.56097	D	0.000033	D	0.83289	0.5222	N	0.24115	0.695	0.80722	D	1	B;D;B;B	0.53745	0.231;0.962;0.413;0.231	B;D;B;B	0.66716	0.05;0.946;0.066;0.05	D	0.85783	0.1362	10	0.87932	D	0	-48.7905	16.3472	0.83146	0.0:0.0:0.0:1.0	.	481;138;441;499	A4D7U4;Q96JT8;Q3B7B7;P15336	.;.;.;ATF2_HUMAN	L	499;441;476;383;441;499;138;481;120	ENSP00000264110:Q499L;ENSP00000340576:Q441L;ENSP00000386326:Q383L;ENSP00000387093:Q441L;ENSP00000376327:Q499L;ENSP00000407911:Q481L	ENSP00000264110:Q499L	Q	-	2	0	ATF2	175647605	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.785000	0.55424	2.266000	0.75297	0.454000	0.30748	CAG	.	.		0.473	ATF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255562.1	NM_001880		A	175939359	T	A	175939359	3	1	150	1	0	0	0	0	1	0	0	0	1080	1580	55	4	25	4	ATF2	2	175939359	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	506648	175939359	67260014	102	22826										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098800	178098800	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctggctgaattgggagaaatTcacctgtctcttcatctagt	9	9	4	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:178098800T>C	ENST00000397062.3	-	2	799	c.245A>G	c.(244-246)gAa>gGa	p.E82G	NFE2L2_ENST00000446151.2_Missense_Mutation_p.E66G|NFE2L2_ENST00000464747.1_Missense_Mutation_p.E66G|NFE2L2_ENST00000397063.4_Missense_Mutation_p.E66G|NFE2L2_ENST00000423513.1_Missense_Mutation_p.E66G	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	82					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E82G(3)|p.G81_F83delGEF(1)|p.E82V(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			TGGGAGAAATTCACCTGTCTC	0.433			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.E82G		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,+1,7	NFE2L2	225	.	5	Substitution - Missense(4)|Deletion - In frame(1)	liver(3)|lung(1)|oesophagus(1)	c.A245G						.						137	137	137					2																	178098800		1900	4105	6005	SO:0001583	missense	4780	exon2			AGAAATTCACCTG		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.245A>G	chr2.hg19:g.178098800T>C	ENSP00000380252:p.Glu82Gly	67.0	0.0		56.0	28.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.048793	0.93740	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T	0.38077	1.57;1.57;1.57;1.16;1.16;1.57	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.66287	0.2774	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.87578	0.997;0.994;0.998;0.997	T	0.72959	-0.4133	10	0.87932	D	0	.	16.098	0.81144	0.0:0.0:0.0:1.0	.	66;66;66;82	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	G	66;82;66;66;66;66	ENSP00000380253:E66G;ENSP00000380252:E82G;ENSP00000411575:E66G;ENSP00000400073:E66G;ENSP00000412191:E66G;ENSP00000410015:E66G	ENSP00000380252:E82G	E	-	2	0	NFE2L2	177807046	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.503000	0.81632	2.210000	0.71456	0.460000	0.39030	GAA	.	.		0.433	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		C	178098800	T	C	178098800	3	2	150	1	0	0	0	0	1	0	0	0	10377	1783	62	2	1588	2	NFE2L2	2	178098800	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2159441	178098800	65100573	103	22827										
TTN	7273	hgsc.bcm.edu	37	chr2	179417476	179417476	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atcaaagtcaggtttggtccAgctgaggatgacagatgtct	12	7	3	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:179417476A>T	ENST00000591111.1	-	285	85452	c.85228T>A	c.(85228-85230)Tgg>Agg	p.W28410R	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.W21178R|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.W27483R|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.W21111R|TTN_ENST00000460472.2_Missense_Mutation_p.W20986R|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.W30051R|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28410	Fibronectin type-III 107. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTTTGGTCCAGCTGAGGATG	0.463																																					p.W30051R		Atlas-SNP	.											.	TTN	18412	.	0			c.T90151A						.						110	99	102					2																	179417476		1996	4176	6172	SO:0001583	missense	7273	exon335			TGGTCCAGCTGAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.85228T>A	chr2.hg19:g.179417476A>T	ENSP00000465570:p.Trp28410Arg	130.0	0.0		119.0	39.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.27	3.076478	0.55753	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82	5.76	5.76	0.90799	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.95837	0.8645	H	0.98849	4.35	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.97693	1.0180	9	0.87932	D	0	.	16.3634	0.83296	1.0:0.0:0.0:0.0	.	20986;21111;21178;28410	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	R	27483;20986;21178;21111;20983	ENSP00000343764:W27483R;ENSP00000434586:W20986R;ENSP00000340554:W21178R;ENSP00000352154:W21111R	ENSP00000340554:W21178R	W	-	1	0	TTN	179125722	1.000000	0.71417	0.986000	0.45419	0.998000	0.95712	9.339000	0.96797	2.324000	0.78689	0.533000	0.62120	TGG	.	.		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179417476	A	T	179417476	3	4	150	1	0	0	0	0	1	0	0	0	16750	188	7	4	17940	4	TTN	2	179417476	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1318676	179417476	63781897	104	22828										
TTN	7273	hgsc.bcm.edu	37	chr2	179439715	179439715	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gaatggtgatgacatcaccaAcctctcctacaatgttcctt	6	12	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:179439715A>T	ENST00000591111.1	-	276	66445	c.66221T>A	c.(66220-66222)gTt>gAt	p.V22074D	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V14842D|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V21147D|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V14775D|TTN_ENST00000460472.2_Missense_Mutation_p.V14650D|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V23715D|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000456053.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	22074	Ig-like 115.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GACATCACCAACCTCTCCTAC	0.413																																					p.V23715D		Atlas-SNP	.											.	TTN	18412	.	0			c.T71144A						.						78	72	74					2																	179439715		1924	4135	6059	SO:0001583	missense	7273	exon326			TCACCAACCTCTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.66221T>A	chr2.hg19:g.179439715A>T	ENSP00000465570:p.Val22074Asp	90.0	0.0		108.0	39.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	11.32	1.602884	0.28534	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.69	4.5	0.54988	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67813	0.2933	N	0.20986	0.625	0.80722	D	1	D;D;D;D	0.58620	0.983;0.971;0.983;0.971	P;P;P;P	0.62298	0.9;0.9;0.9;0.867	T	0.70753	-0.4786	9	0.87932	D	0	.	11.8911	0.52630	0.9309:0.0:0.0691:0.0	.	14650;14775;14842;22074	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	21147;14650;14842;14775;14648	ENSP00000343764:V21147D;ENSP00000434586:V14650D;ENSP00000340554:V14842D;ENSP00000352154:V14775D	ENSP00000340554:V14842D	V	-	2	0	TTN	179147961	1.000000	0.71417	0.986000	0.45419	0.911000	0.54048	9.281000	0.95811	0.948000	0.37687	0.528000	0.53228	GTT	.	.		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179439715	A	T	179439715	3	4	150	1	0	0	0	0	1	0	0	0	16750	43	2	4	36983	4	TTN	2	179439715	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	22239	179439715	63759658	105	22829										
TTN	7273	hgsc.bcm.edu	37	chr2	179575489	179575489	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcgctgttttccagataactAatctggtactttccgccact	7	12	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:179575489A>T	ENST00000591111.1	-	96	27608	c.27384T>A	c.(27382-27384)atT>atA	p.I9128I	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342992.6_Silent_p.I8201I|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.I9445I|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13259	Ig-like 74.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCAGATAACTAATCTGGTACT	0.473																																					p.I9445I		Atlas-SNP	.											.	TTN	18412	.	0			c.T28335A						.						158	151	153					2																	179575489		1966	4158	6124	SO:0001819	synonymous_variant	7273	exon98			ATAACTAATCTGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.27384T>A	chr2.hg19:g.179575489A>T		97.0	0.0		90.0	24.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179575489	A	T	179575489	2	4	150	1	0	0	0	0	0	0	0	1	16750	358	13	4		4	TTN	2	179575489	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	135774	179575489	63623884	106	22830										
TTN	7273	hgsc.bcm.edu	37	chr2	179612800	179612800	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cttccatttcaccaacccctAaaggcttttcctcacttgct	3	16	2	0	rs142132973	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:179612800A>T	ENST00000591111.1	-	45	10585				TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000360870.5_Nonsense_Mutation_p.L4776*			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACCAACCCCTAAAGGCTTTTC	0.423																																					p.L4776X		Atlas-SNP	.											TTN_ENST00000360870,NS,lymphoid_neoplasm,0,1	TTN	18412	.	0			c.T14327A						.																																			SO:0001627	intron_variant	7273	exon46			ACCCCTAAAGGCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+5050T>A	chr2.hg19:g.179612800A>T		77.0	0.0		82.0	23.0	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	54	23.311441	0.99954	.	.	ENSG00000155657	ENST00000360870;ENST00000306136	.	.	.	6.05	-0.358	0.12575	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.3174	0.43745	0.553:0.0:0.447:0.0	.	.	.	.	X	4776;90	.	ENSP00000304714:L90X	L	-	2	0	TTN	179321045	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	0.062000	0.14389	-0.267000	0.09325	-0.263000	0.10527	TTA	.	A|0.999;G|0.001		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179612800	A	T	179612800	1	4	150	0	1	0	0	0	0	0	0	0	16750	372	13	4		4	TTN	2	179612800	Intron	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	37311	179612800	63586573	107	22831										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187605125	187605125	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aattaggacttagtttaactAttattgcttacaaagatggc	7	5	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:187605125A>G	ENST00000304698.5	+	2	612	c.409A>G	c.(409-411)Att>Gtt	p.I137V		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	137						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						TAGTTTAACTATTATTGCTTA	0.363																																					p.I137V		Atlas-SNP	.											.	FAM171B	146	.	0			c.A409G						.						117	109	112					2																	187605125		2203	4300	6503	SO:0001583	missense	165215	exon2			TTAACTATTATTG	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.409A>G	chr2.hg19:g.187605125A>G	ENSP00000304108:p.Ile137Val	179.0	0.0		159.0	35.0	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	A	3.871	-0.027915	0.07589	.	.	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.24538	1.85	5.98	4.82	0.62117	.	0.128720	0.53938	D	0.000055	T	0.12902	0.0313	N	0.13235	0.315	0.36456	D	0.866387	B;B	0.34329	0.449;0.449	B;B	0.34873	0.191;0.191	T	0.10800	-1.0614	10	0.05351	T	0.99	-18.9574	10.8533	0.46782	0.9289:0.0:0.0711:0.0	.	137;138	Q6P995;A8K122	F171B_HUMAN;.	V	137	ENSP00000304108:I137V	ENSP00000272804:I137V	I	+	1	0	FAM171B	187313370	1.000000	0.71417	0.959000	0.39883	0.978000	0.69477	2.806000	0.47947	1.077000	0.40990	0.528000	0.53228	ATT	.	.		0.363	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		G	187605125	A	G	187605125	3	3	150	1	0	0	0	0	1	0	0	0	5496	449	16	2	415	2	FAM171B	2	187605125	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	7992325	187605125	55594248	108	22832										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189870090	189870090	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atacagggtgaaagtgggaaAccaggagctaacggtctcag	14	7	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:189870090A>T	ENST00000304636.3	+	41	3116	c.2946A>T	c.(2944-2946)aaA>aaT	p.K982N	COL3A1_ENST00000317840.5_Intron	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	982	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	AAAGTGGGAAACCAGGAGCTA	0.433																																					p.K982N		Atlas-SNP	.											.	COL3A1	292	.	0			c.A2946T						.						110	114	112					2																	189870090		2203	4300	6503	SO:0001583	missense	1281	exon41			TGGGAAACCAGGA	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.2946A>T	chr2.hg19:g.189870090A>T	ENSP00000304408:p.Lys982Asn	117.0	0.0		105.0	24.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	hg19	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	A	19.65	3.866632	0.72065	.	.	ENSG00000168542	ENST00000304636	D	0.94232	-3.38	5.5	-2.67	0.06059	.	0.000000	0.53938	D	0.000041	D	0.92090	0.7493	L	0.28556	0.865	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.87381	0.2357	10	0.25106	T	0.35	.	11.7586	0.51890	0.574:0.0:0.426:0.0	.	982	P02461	CO3A1_HUMAN	N	982	ENSP00000304408:K982N	ENSP00000304408:K982N	K	+	3	2	COL3A1	189578335	0.960000	0.32886	0.725000	0.30721	0.873000	0.50193	0.230000	0.17852	-0.746000	0.04766	0.528000	0.53228	AAA	.	.		0.433	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		T	189870090	A	T	189870090	3	4	150	1	0	0	0	0	1	0	0	0	3690	40	2	4	3108	4	COL3A1	2	189870090	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2264965	189870090	53329283	109	22833										
FZD7	8324	hgsc.bcm.edu	37	chr2	202900427	202900427	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcggcatggccagctccatcTggtgggtcattctgtctctc	11	13	4	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:202900427T>A	ENST00000286201.1	+	1	1118	c.1057T>A	c.(1057-1059)Tgg>Agg	p.W353R	RP11-107N15.1_ENST00000608741.1_lincRNA	NM_003507.1	NP_003498.1	O75084	FZD7_HUMAN	frizzled class receptor 7	353					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of ectodermal cell fate specification (GO:0042666)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of catenin import into nucleus (GO:0035412)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|stem cell maintenance (GO:0019827)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|endometrium(6)|large_intestine(6)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	31						CAGCTCCATCTGGTGGGTCAT	0.627											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W353R		Atlas-SNP	.											.	FZD7	70	.	0			c.T1057A						.						79	78	78					2																	202900427		2203	4300	6503	SO:0001583	missense	8324	exon1			TCCATCTGGTGGG	AB010881	CCDS2351.1	2q33	2014-01-29	2014-01-29		ENSG00000155760	ENSG00000155760		"GPCR / Class F : Frizzled receptors"	4045	protein-coding gene	gene with protein product		603410	"frizzled (Drosophila) homolog 7", "frizzled homolog 7 (Drosophila)", "frizzled 7, seven transmembrane spanning receptor", "frizzled family receptor 7"			9707618, 9813155	Standard	NM_003507		Approved	FzE3	uc002uyw.1	O75084	OTTHUMG00000132841	ENST00000286201.1:c.1057T>A	chr2.hg19:g.202900427T>A	ENSP00000286201:p.Trp353Arg	84.0	0.0	2133	98.0	26.0	NM_003507	O94816|Q53S59|Q96B74	Missense_Mutation	SNP	ENST00000286201.1	hg19	CCDS2351.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.083506	0.76642	.	.	ENSG00000155760	ENST00000286201	D	0.91351	-2.83	5.41	5.41	0.78517	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	D	0.96996	0.9019	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98370	1.0553	10	0.87932	D	0	.	15.4377	0.75160	0.0:0.0:0.0:1.0	.	353	O75084	FZD7_HUMAN	R	353	ENSP00000286201:W353R	ENSP00000286201:W353R	W	+	1	0	FZD7	202608672	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.035000	0.88872	2.061000	0.61500	0.379000	0.24179	TGG	.	.		0.627	FZD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256314.1	NM_003507		A	202900427	T	A	202900427	3	1	150	1	0	0	0	0	1	0	0	0	6143	1580	55	4	1059	4	FZD7	2	202900427	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	13030337	202900427	40298946	110	22834										
FZD7	8324	hgsc.bcm.edu	37	chr2	202900508	202900508	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccatcgaggccaactcgcagTacttccacctggccgcgtgg	11	16	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:202900508T>A	ENST00000286201.1	+	1	1199	c.1138T>A	c.(1138-1140)Tac>Aac	p.Y380N	RP11-107N15.1_ENST00000608741.1_lincRNA	NM_003507.1	NP_003498.1	O75084	FZD7_HUMAN	frizzled class receptor 7	380					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of ectodermal cell fate specification (GO:0042666)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of catenin import into nucleus (GO:0035412)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|stem cell maintenance (GO:0019827)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|endometrium(6)|large_intestine(6)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	31						CAACTCGCAGTACTTCCACCT	0.652											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y380N		Atlas-SNP	.											.	FZD7	70	.	0			c.T1138A						.						59	61	60					2																	202900508		2203	4300	6503	SO:0001583	missense	8324	exon1			TCGCAGTACTTCC	AB010881	CCDS2351.1	2q33	2014-01-29	2014-01-29		ENSG00000155760	ENSG00000155760		"GPCR / Class F : Frizzled receptors"	4045	protein-coding gene	gene with protein product		603410	"frizzled (Drosophila) homolog 7", "frizzled homolog 7 (Drosophila)", "frizzled 7, seven transmembrane spanning receptor", "frizzled family receptor 7"			9707618, 9813155	Standard	NM_003507		Approved	FzE3	uc002uyw.1	O75084	OTTHUMG00000132841	ENST00000286201.1:c.1138T>A	chr2.hg19:g.202900508T>A	ENSP00000286201:p.Tyr380Asn	85.0	0.0	2133	70.0	12.0	NM_003507	O94816|Q53S59|Q96B74	Missense_Mutation	SNP	ENST00000286201.1	hg19	CCDS2351.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.062275	0.76187	.	.	ENSG00000155760	ENST00000286201	D	0.86366	-2.11	5.41	5.41	0.78517	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	D	0.94938	0.8363	M	0.93016	3.37	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96069	0.9044	10	0.87932	D	0	.	15.4377	0.75160	0.0:0.0:0.0:1.0	.	380	O75084	FZD7_HUMAN	N	380	ENSP00000286201:Y380N	ENSP00000286201:Y380N	Y	+	1	0	FZD7	202608753	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.035000	0.88872	2.061000	0.61500	0.379000	0.24179	TAC	.	.		0.652	FZD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256314.1	NM_003507		A	202900508	T	A	202900508	3	1	150	1	0	0	0	0	1	0	0	0	6143	1638	57	4	1140	4	FZD7	2	202900508	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	81	202900508	40298865	111	22835										
ICOS	29851	hgsc.bcm.edu	37	chr2	204820588	204820588	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aacagtgtctctttttttctAtacaacttggaccattctca	4	10	3	0	rs372256111		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:204820588A>G	ENST00000316386.6	+	2	355	c.288A>G	c.(286-288)ctA>ctG	p.L96L	ICOS_ENST00000435193.1_Silent_p.L96L	NM_012092.3	NP_036224.1	Q9Y6W8	ICOS_HUMAN	inducible T-cell co-stimulator	96	Ig-like V-type.				immune response (GO:0006955)|single organismal cell-cell adhesion (GO:0016337)|T cell costimulation (GO:0031295)|T cell tolerance induction (GO:0002517)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(4)	6						CTTTTTTTCTATACAACTTGG	0.373																																					p.L96L		Atlas-SNP	.											.	ICOS	20	.	0			c.A288G						.	A		0,4406		0,0,2203	140	133	136		288	-4.8	0	2		136	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ICOS	NM_012092.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		96/200	204820588	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	29851	exon2			TTTTCTATACAAC	AB023135	CCDS2363.1	2q33	2014-09-17			ENSG00000163600	ENSG00000163600		"CD molecules"	5351	protein-coding gene	gene with protein product	"activation-inducible lymphocyte immunomediatory molecule"	604558				9930702, 10617205	Standard	NM_012092		Approved	AILIM, CD278	uc002vam.3	Q9Y6W8	OTTHUMG00000132880	ENST00000316386.6:c.288A>G	chr2.hg19:g.204820588A>G		171.0	0.0		168.0	48.0	NM_012092	Q8N6W8	Silent	SNP	ENST00000316386.6	hg19	CCDS2363.1																																																																																			.	.		0.373	ICOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256369.1	NM_012092		G	204820588	A	G	204820588	2	3	150	1	0	0	0	0	0	0	0	1	7495	436	16	2		2	ICOS	2	204820588	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1920080	204820588	38378785	112	22836										
ADAM23	8745	hgsc.bcm.edu	37	chr2	207436449	207436449	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcacgtgaagtgttttctctAggaatgctatggattatgct	10	6	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:207436449A>T	ENST00000264377.3	+	17	1894		c.e17-1		ADAM23_ENST00000374416.1_Splice_Site|ADAM23_ENST00000374415.3_Splice_Site	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23						cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		TGTTTTCTCTAGGAATGCTAT	0.453																																					.	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											.	ADAM23	239	.	0			c.1567-2A>T						.						98	88	91					2																	207436449		2203	4300	6503	SO:0001630	splice_region_variant	8745	exon17			TTCTCTAGGAATG	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"ADAM metallopeptidase domain containing"	202	protein-coding gene	gene with protein product		603710	"a disintegrin and metalloproteinase domain 23"			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.1567-1A>T	chr2.hg19:g.207436449A>T		86.0	0.0		55.0	17.0	NM_003812	A2RU59	Splice_Site	SNP	ENST00000264377.3	hg19	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.622871	0.46840	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7887	0.78332	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADAM23	207144694	1.000000	0.71417	0.983000	0.44433	0.143000	0.21401	7.524000	0.81866	2.367000	0.80283	0.528000	0.53228	.	.	.		0.453	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812	Intron	T	207436449	A	T	207436449	5	4	150	1	0	0	0	0	0	0	1	0	245	434	15	4	1631	4	ADAM23	2	207436449	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2615861	207436449	35762924	113	22837										
MAP2	4133	hgsc.bcm.edu	37	chr2	210559831	210559831	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcaaaagaacatgccaagaaAactgaagaggctggtgatga	11	6	1	6			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:210559831A>T	ENST00000360351.4	+	7	3443	c.2937A>T	c.(2935-2937)aaA>aaT	p.K979N	MAP2_ENST00000199940.6_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.K975N|MAP2_ENST00000392194.1_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	979					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	ATGCCAAGAAAACTGAAGAGG	0.393																																					p.K979N	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.A2937T						.						73	71	72					2																	210559831		2203	4300	6503	SO:0001583	missense	4133	exon7			CAAGAAAACTGAA		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.2937A>T	chr2.hg19:g.210559831A>T	ENSP00000353508:p.Lys979Asn	335.0	0.0		305.0	82.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	hg19	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	A	7.139	0.581399	0.13686	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.18502	2.21;2.21	5.79	4.68	0.58851	MAP2/Tau projection (1);	0.669186	0.14360	N	0.324524	T	0.07593	0.0191	N	0.11427	0.14	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.30297	-0.9983	10	0.29301	T	0.29	-0.4207	1.6616	0.02793	0.5386:0.1397:0.0938:0.2279	.	975;979	P11137-3;P11137	.;MAP2_HUMAN	N	979;975	ENSP00000353508:K979N;ENSP00000392164:K975N	ENSP00000353508:K979N	K	+	3	2	MAP2	210268076	0.001000	0.12720	0.007000	0.13788	0.790000	0.44656	0.621000	0.24418	1.087000	0.41251	0.528000	0.53228	AAA	.	.		0.393	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		T	210559831	A	T	210559831	3	4	150	1	0	0	0	0	1	0	0	0	9244	11	1	4	2951	4	MAP2	2	210559831	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3123382	210559831	32639542	114	22838										
VWC2L	402117	hgsc.bcm.edu	37	chr2	215440464	215440464	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgaaagtggacgaatgtaacAtctgtcattgtcacaacggg	11	7	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:215440464A>T	ENST00000312504.5	+	4	1391	c.589A>T	c.(589-591)Atc>Ttc	p.I197F	AC107218.3_ENST00000437883.1_RNA|AC107218.3_ENST00000412896.1_RNA|VWC2L_ENST00000427124.1_3'UTR	NM_001080500.2	NP_001073969.1	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain containing protein 2-like	197					negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				breast(1)|endometrium(1)|large_intestine(3)|lung(10)|prostate(1)	16						CGAATGTAACATCTGTCATTG	0.458																																					p.I197F		Atlas-SNP	.											.	VWC2L	40	.	0			c.A589T						.						233	226	229					2																	215440464		2018	4206	6224	SO:0001583	missense	402117	exon4			TGTAACATCTGTC	AB374231	CCDS46509.1	2q34-q35	2011-01-25	2011-01-25		ENSG00000174453	ENSG00000174453			37203	protein-coding gene	gene with protein product			"von Willebrand factor C domain-containing protein 2-like"				Standard	NM_001080500		Approved		uc002vet.2	B2RUY7	OTTHUMG00000154811	ENST00000312504.5:c.589A>T	chr2.hg19:g.215440464A>T	ENSP00000308976:p.Ile197Phe	122.0	0.0		97.0	31.0	NM_001080500	A6NC69|B2RUW7|B7X8X1	Missense_Mutation	SNP	ENST00000312504.5	hg19	CCDS46509.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.503260	0.85176	.	.	ENSG00000174453	ENST00000312504	T	0.44083	0.93	5.58	5.58	0.84498	.	.	.	.	.	T	0.54822	0.1882	L	0.42245	1.32	0.80722	D	1	D	0.71674	0.998	P	0.62649	0.905	T	0.55692	-0.8101	9	0.54805	T	0.06	-1.7923	15.759	0.78063	1.0:0.0:0.0:0.0	.	197	B2RUY7	VWC2L_HUMAN	F	197	ENSP00000308976:I197F	ENSP00000308976:I197F	I	+	1	0	VWC2L	215148709	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.121000	0.65114	0.533000	0.62120	ATC	.	.		0.458	VWC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337175.1	NM_001080500		T	215440464	A	T	215440464	3	4	150	1	0	0	0	0	1	0	0	0	17259	217	8	4	599	4	VWC2L	2	215440464	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	4880633	215440464	27758909	115	22839										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230638852	230638852	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgtggatagtgactggtatAtccttccctcctttcttcag	8	10	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:230638852A>G	ENST00000283943.5	-	37	5608	c.5430T>C	c.(5428-5430)gaT>gaC	p.D1810D	TRIP12_ENST00000389044.4_Silent_p.D1858D|TRIP12_ENST00000389045.3_Silent_p.D1540D	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1810					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TGACTGGTATATCCTTCCCTC	0.448																																					p.D1810D		Atlas-SNP	.											.	TRIP12	207	.	0			c.T5430C						.						187	168	174					2																	230638852		2203	4300	6503	SO:0001819	synonymous_variant	9320	exon37			TGGTATATCCTTC	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.5430T>C	chr2.hg19:g.230638852A>G		86.0	0.0		87.0	26.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.		0.448	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		G	230638852	A	G	230638852	2	3	150	1	0	0	0	0	0	0	0	1	16571	446	16	2		2	TRIP12	2	230638852	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	15198388	230638852	12560521	116	22840										
ALPP	250	hgsc.bcm.edu	37	chr2	233244624	233244624	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccaggacatcgctacgcagcTcatctccaacatggacattg	8	14	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr2:233244624T>A	ENST00000392027.2	+	5	904	c.635T>A	c.(634-636)cTc>cAc	p.L212H	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	212					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GCTACGCAGCTCATCTCCAAC	0.667																																					p.L212H		Atlas-SNP	.											.	ALPP	53	.	0			c.T635A						.						69	70	70					2																	233244624		2203	4300	6503	SO:0001583	missense	250	exon5			CGCAGCTCATCTC	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"Regan isozyme"	171800	"alkaline phosphatase, placental (Regan isozyme)"			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.635T>A	chr2.hg19:g.233244624T>A	ENSP00000375881:p.Leu212His	249.0	0.0		180.0	50.0	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	hg19	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	.	14.13	2.444826	0.43429	.	.	ENSG00000163283	ENST00000392027	D	0.97529	-4.42	2.31	2.31	0.28768	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.072538	0.56097	D	0.000021	D	0.98998	0.9658	H	0.99169	4.455	0.58432	D	0.999992	D	0.89917	1.0	D	0.91635	0.999	D	0.98132	1.0431	10	0.87932	D	0	.	10.365	0.44017	0.0:0.0:0.0:1.0	.	212	P05187	PPB1_HUMAN	H	212	ENSP00000375881:L212H	ENSP00000375881:L212H	L	+	2	0	ALPP	232952868	1.000000	0.71417	0.683000	0.30040	0.075000	0.17131	4.433000	0.59929	1.061000	0.40601	0.248000	0.18094	CTC	.	.		0.667	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632		A	233244624	T	A	233244624	3	1	150	1	0	0	0	0	1	0	0	0	548	1551	54	4	653	4	ALPP	2	233244624	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2605772	233244624	9954749	117	22841										
PDCD6IP	10015	hgsc.bcm.edu	37	chr3	33840379	33840379	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcaagctgcgccgcgccgcAgtcggtcgtccgctggacaa	14	15	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:33840379A>T	ENST00000307296.3	+	1	536	c.159A>T	c.(157-159)gcA>gcT	p.A53A	RP11-10C24.1_ENST00000605513.1_lincRNA|RP11-10C24.3_ENST00000604982.1_lincRNA|PDCD6IP_ENST00000457054.2_Silent_p.A53A			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	53	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						GCCGCGCCGCAGTCGGTCGTC	0.701																																					p.A53A		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.A159T						.						7	9	8					3																	33840379		2061	4031	6092	SO:0001819	synonymous_variant	10015	exon1			CGCCGCAGTCGGT	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.159A>T	chr3.hg19:g.33840379A>T		144.0	0.0		135.0	40.0	NM_013374	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Silent	SNP	ENST00000307296.3	hg19	CCDS2660.1																																																																																			.	.		0.701	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			T	33840379	A	T	33840379	2	4	150	1	0	0	0	0	0	0	0	1	11633	175	7	4		4	PDCD6IP	3	33840379	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		33840379	164182051	118	22842										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266103	41266103	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aacagtcttacctggactctGgaatccattctggtgccact	8	12	3	0	rs121913399|rs121913416		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:41266103G>C	ENST00000349496.5	+	3	380	c.100G>C	c.(100-102)Gga>Cga	p.G34R	CTNNB1_ENST00000453024.1_Missense_Mutation_p.G27R|CTNNB1_ENST00000396185.3_Missense_Mutation_p.G34R|CTNNB1_ENST00000396183.3_Missense_Mutation_p.G34R|CTNNB1_ENST00000405570.1_Missense_Mutation_p.G34R	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	34			G -> E (in PTR). {ECO:0000269|PubMed:10192393}.|G -> R (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|G -> V (in hepatoblastoma; dbSNP:rs28931589). {ECO:0000269|PubMed:9927029}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.G34R(87)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.S33_G34insGTS(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.GIHS34?(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.S33_G34insGI(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CCTGGACTCTGGAATCCATTC	0.488		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.G34R	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	220	Deletion - In frame(105)|Substitution - Missense(87)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Insertion - In frame(2)	liver(126)|large_intestine(21)|central_nervous_system(19)|pancreas(15)|endometrium(11)|stomach(10)|skin(4)|pituitary(4)|soft_tissue(2)|small_intestine(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)|lung(1)|ovary(1)|kidney(1)	c.G100C						.						92	77	82					3																	41266103		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GACTCTGGAATCC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.100G>C	chr3.hg19:g.41266103G>C	ENSP00000344456:p.Gly34Arg	151.0	0.0		126.0	42.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.625128	0.87560	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66;0.66;0.66;0.66;0.66	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-31.2232	19.9596	0.97236	0.0:0.0:1.0:0.0	.	34	P35222	CTNB1_HUMAN	R	27;34;34;34;34;27;34;34;34	ENSP00000400508:G27R;ENSP00000385604:G34R;ENSP00000412219:G34R;ENSP00000379486:G34R;ENSP00000344456:G34R;ENSP00000411226:G27R;ENSP00000379488:G34R;ENSP00000409302:G34R;ENSP00000401599:G34R	ENSP00000344456:G34R	G	+	1	0	CTNNB1	41241107	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GGA	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266103	G	C	41266103	3	2	150	1	0	0	0	0	1	0	0	0	4018	1349	47	4	106	4	CTNNB1	3	41266103	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	7425724	41266103	156756327	119	22843										
HHATL	57467	hgsc.bcm.edu	37	chr3	42735312	42735312	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatgtggttatacacatatcTgcaggaaagatgggagaagg	13	4	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:42735312T>A	ENST00000441594.1	-	10	1308		c.e10-2		HHATL_ENST00000310417.5_Splice_Site	NM_020707.3	NP_065758.3	Q9HCP6	HHATL_HUMAN	hedgehog acyltransferase-like						negative regulation of N-terminal protein palmitoylation (GO:0060262)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(3)	19				KIRC - Kidney renal clear cell carcinoma(284;0.215)		TACACATATCTGCAGGAAAGA	0.572																																					.		Atlas-SNP	.											.	HHATL	49	.	0			c.1047-2A>T						.						56	45	49					3																	42735312		2203	4300	6503	SO:0001630	splice_region_variant	57467	exon11			CATATCTGCAGGA	AB042554	CCDS2704.1	3p22	2009-10-06	2007-02-06	2007-02-06	ENSG00000010282	ENSG00000010282			13242	protein-coding gene	gene with protein product	"membrane bound O-acyltransferase domain containing 3"	608116	"chromosome 3 open reading frame 3", "GUP1, glycerol uptake/transporter homolog (yeast)"	C3orf3, GUP1		11374908	Standard	NM_020707		Approved	KIAA1173, OACT3, MSTP002, MBOAT3	uc003clx.3	Q9HCP6	OTTHUMG00000133043	ENST00000441594.1:c.1047-2A>T	chr3.hg19:g.42735312T>A		76.0	0.0		76.0	23.0	NM_020707	Q8TBG3|Q9ULP7	Splice_Site	SNP	ENST00000441594.1	hg19	CCDS2704.1	.	.	.	.	.	.	.	.	.	.	t	11.45	1.641621	0.29157	.	.	ENSG00000010282	ENST00000310417;ENST00000441594	.	.	.	4.09	4.09	0.47781	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1086	0.59261	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HHATL	42710316	1.000000	0.71417	0.845000	0.33349	0.220000	0.24768	7.936000	0.87665	1.476000	0.48215	0.370000	0.22315	.	.	.		0.572	HHATL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343627.1	NM_020707	Intron	A	42735312	T	A	42735312	5	1	150	1	0	0	0	0	0	0	1	0	7099	1594	55	4	481	4	HHATL	3	42735312	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1469209	42735312	155287118	120	22844										
CCDC13	152206	hgsc.bcm.edu	37	chr3	42751273	42751273	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccggttgggttgtgcctgtTgttagaggtgggcagacctg	17	8	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:42751273T>A	ENST00000310232.6	-	15	1974	c.1891A>T	c.(1891-1893)Aac>Tac	p.N631Y		NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	631										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TTGTGCCTGTTGTTAGAGGTG	0.597																																					p.N631Y		Atlas-SNP	.											.	CCDC13	71	.	0			c.A1891T						.						198	170	179					3																	42751273		2203	4300	6503	SO:0001583	missense	152206	exon15			GCCTGTTGTTAGA	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1891A>T	chr3.hg19:g.42751273T>A	ENSP00000309836:p.Asn631Tyr	94.0	0.0		88.0	23.0	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	T	11.31	1.601972	0.28534	.	.	ENSG00000244607	ENST00000310232	T	0.10860	2.83	4.82	-4.66	0.03329	.	0.789022	0.11530	N	0.554791	T	0.03348	0.0097	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.38672	-0.9650	10	0.30854	T	0.27	.	0.3845	0.00400	0.2552:0.2347:0.1315:0.3786	.	631	Q8IYE1	CCD13_HUMAN	Y	631	ENSP00000309836:N631Y	ENSP00000309836:N631Y	N	-	1	0	CCDC13	42726277	0.000000	0.05858	0.020000	0.16555	0.008000	0.06430	-1.541000	0.02198	-0.553000	0.06158	-1.219000	0.01604	AAC	.	.		0.597	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		A	42751273	T	A	42751273	3	1	150	1	0	0	0	0	1	0	0	0	2767	1812	63	4	264	4	CCDC13	3	42751273	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	15961	42751273	155271157	121	22845										
ZNF197	10168	hgsc.bcm.edu	37	chr3	44685446	44685446	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtaggaaatcctttacttctAagaggaatttagttggccac	9	7	1	1	rs543730571		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:44685446A>T	ENST00000396058.1	+	5	2991	c.2824A>T	c.(2824-2826)Aag>Tag	p.K942*	ZNF197_ENST00000383745.2_Intron|ZNF197_ENST00000344387.4_Nonsense_Mutation_p.K942*|RP11-944L7.4_ENST00000457331.1_RNA|ZNF197_ENST00000383744.4_Intron			O14709	ZN197_HUMAN	zinc finger protein 197	942					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		CTTTACTTCTAAGAGGAATTT	0.373																																					p.K942X		Atlas-SNP	.											.	ZNF197	81	.	0			c.A2824T						.						71	78	76					3																	44685446		2203	4300	6503	SO:0001587	stop_gained	10168	exon6			ACTTCTAAGAGGA	AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"Zinc fingers, C2H2-type", "-", "-", "-"	12988	protein-coding gene	gene with protein product			"zinc finger protein 166"	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.2824A>T	chr3.hg19:g.44685446A>T	ENSP00000379370:p.Lys942*	208.0	0.0		190.0	52.0	NM_006991	B2RAH8|Q86VG0	Nonsense_Mutation	SNP	ENST00000396058.1	hg19	CCDS2717.1	.	.	.	.	.	.	.	.	.	.	A	37	6.587061	0.97684	.	.	ENSG00000186448	ENST00000344387;ENST00000396058	.	.	.	4.07	4.07	0.47477	.	0.000000	0.34025	U	0.004335	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.3905	0.26907	0.8988:0.0:0.1012:0.0	.	.	.	.	X	942	.	ENSP00000345809:K942X	K	+	1	0	ZNF197	44660450	0.000000	0.05858	1.000000	0.80357	0.991000	0.79684	1.491000	0.35583	1.828000	0.53243	0.455000	0.32223	AAG	.	.		0.373	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991		T	44685446	A	T	44685446	4	4	150	1	0	0	0	0	0	1	0	0	17774	363	13	4	2842	4	ZNF197	3	44685446	Nonsense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1934173	44685446	153336984	122	22846										
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48455080	48455080	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cacatctggctgcacccaccTgtacatgaggacaatgatga	9	12	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:48455080T>A	ENST00000358536.4	-	23	4803	c.4534A>T	c.(4534-4536)Agg>Tgg	p.R1512W	PLXNB1_ENST00000465117.1_5'Flank|PLXNB1_ENST00000296440.6_Splice_Site_p.R1512W|PLXNB1_ENST00000448774.2_Splice_Site_p.R123W|PLXNB1_ENST00000358459.4_Splice_Site_p.R1329W|PLXNB1_ENST00000456774.1_Splice_Site_p.R1329W	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1512					axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TGCACCCACCTGTACATGAGG	0.622																																					p.R1512W		Atlas-SNP	.											.	PLXNB1	150	.	0			c.A4534T						.						30	33	32					3																	48455080		2203	4300	6503	SO:0001630	splice_region_variant	5364	exon23			CCCACCTGTACAT	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.4535+1A>T	chr3.hg19:g.48455080T>A		100.0	0.0		89.0	28.0	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	hg19	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	T	18.57	3.652585	0.67472	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000448774;ENST00000456774	T;T;T;T;T	0.14516	3.65;3.69;3.65;2.5;3.69	5.29	5.29	0.74685	.	0.102139	0.64402	D	0.000004	T	0.37237	0.0996	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.975;0.997	T	0.10042	-1.0647	10	0.42905	T	0.14	.	14.4032	0.67063	0.0:0.0:0.0:1.0	.	1512;1329	O43157;O43157-2	PLXB1_HUMAN;.	W	1512;1329;1512;123;1329	ENSP00000296440:R1512W;ENSP00000351242:R1329W;ENSP00000351338:R1512W;ENSP00000389320:R123W;ENSP00000414199:R1329W	ENSP00000296440:R1512W	R	-	1	2	PLXNB1	48430084	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.927000	0.87577	1.984000	0.57885	0.460000	0.39030	AGG	.	.		0.622	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	Missense_Mutation	A	48455080	T	A	48455080	5	1	150	1	0	0	0	0	0	0	1	0	12132	1594	55	4	1937	4	PLXNB1	3	48455080	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3769634	48455080	149567350	123	22847										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48685300	48685300	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atggggatggccgtggggacTgggaaggcagcagcacatgg	20	7	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:48685300T>A	ENST00000164024.4	-	20	7383	c.7103A>T	c.(7102-7104)cAg>cTg	p.Q2368L	CELSR3_ENST00000544264.1_Missense_Mutation_p.Q2373L	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	2368					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CCGTGGGGACTGGGAAGGCAG	0.632																																					p.Q2368L		Atlas-SNP	.											.	CELSR3	237	.	0			c.A7103T						.						85	94	91					3																	48685300		2203	4299	6502	SO:0001583	missense	1951	exon20			GGGGACTGGGAAG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.7103A>T	chr3.hg19:g.48685300T>A	ENSP00000164024:p.Gln2368Leu	34.0	0.0		38.0	9.0	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.499384	0.26861	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.09723	2.95;2.95	4.22	2.96	0.34315	Domain of unknown function DUF3497 (1);	.	.	.	.	T	0.04770	0.0129	N	0.03608	-0.345	0.27686	N	0.946268	B;B	0.06786	0.001;0.001	B;B	0.14023	0.01;0.007	T	0.34004	-0.9846	9	0.21540	T	0.41	.	9.4711	0.38842	0.0:0.0:0.4095:0.5905	.	2368;2438	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	L	2368;2373	ENSP00000164024:Q2368L;ENSP00000445694:Q2373L	ENSP00000164024:Q2368L	Q	-	2	0	CELSR3	48660304	1.000000	0.71417	0.979000	0.43373	0.899000	0.52679	3.783000	0.55409	1.906000	0.55180	0.379000	0.24179	CAG	.	.		0.632	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48685300	T	A	48685300	3	1	150	1	0	0	0	0	1	0	0	0	3225	1580	55	4	2899	4	CELSR3	3	48685300	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	230220	48685300	149337130	124	22848										
ARIH2	10425	hgsc.bcm.edu	37	chr3	49006053	49006053	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccaatgaagaattgagagagAaatacaggcgctacctcttc	9	9	1	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:49006053A>C	ENST00000356401.4	+	7	964	c.625A>C	c.(625-627)Aaa>Caa	p.K209Q	ARIH2_ENST00000449376.1_Missense_Mutation_p.K209Q|ARIH2_ENST00000490095.1_3'UTR	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	209					developmental cell growth (GO:0048588)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organismal development (GO:0007275)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		ATTGAGAGAGAAATACAGGCG	0.507																																					p.K209Q		Atlas-SNP	.											.	ARIH2	32	.	0			c.A625C						.						171	167	168					3																	49006053		2203	4300	6503	SO:0001583	missense	10425	exon7			AGAGAGAAATACA	AF099149	CCDS2780.1	3p21	2013-10-03	2013-10-03		ENSG00000177479	ENSG00000177479			690	protein-coding gene	gene with protein product	"all-trans retinoic acid inducible RING finger"	605615	"ariadne (Drosophila) homolog 2", "ariadne homolog 2 (Drosophila)"			10422847, 24058416	Standard	XM_005264798		Approved	TRIAD1	uc003cvb.3	O95376	OTTHUMG00000133547	ENST00000356401.4:c.625A>C	chr3.hg19:g.49006053A>C	ENSP00000348769:p.Lys209Gln	67.0	0.0		51.0	12.0	NM_006321	Q9HBZ6|Q9UEM9	Missense_Mutation	SNP	ENST00000356401.4	hg19	CCDS2780.1	.	.	.	.	.	.	.	.	.	.	A	33	5.277347	0.95459	.	.	ENSG00000177479	ENST00000356401;ENST00000449376;ENST00000444790;ENST00000395481	T;T	0.67698	-0.28;-0.28	5.95	5.95	0.96441	Zinc finger, C6HC-type (2);	0.000000	0.85682	D	0.000000	D	0.85120	0.5624	M	0.89904	3.07	0.80722	D	1	D;D;D	0.89917	0.997;0.991;1.0	D;D;D	0.78314	0.939;0.991;0.991	D	0.87905	0.2693	10	0.66056	D	0.02	.	16.4237	0.83790	1.0:0.0:0.0:0.0	.	216;209;209	B3KMG5;Q53ET9;O95376	.;.;ARI2_HUMAN	Q	209;209;208;33	ENSP00000348769:K209Q;ENSP00000403222:K209Q	ENSP00000348769:K209Q	K	+	1	0	ARIH2	48981057	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.932000	0.92897	2.279000	0.76181	0.533000	0.62120	AAA	.	.		0.507	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257525.1	NM_006321		C	49006053	A	C	49006053	3	2	150	1	0	0	0	0	1	0	0	0	924	247	9	5	643	5	ARIH2	3	49006053	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	320753	49006053	149016377	125	22849										
QRICH1	54870	hgsc.bcm.edu	37	chr3	49070097	49070097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tccaagggccttcaagtaccGgatactcgtgcttttatcct	8	12	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:49070097G>A	ENST00000395443.2	-	8	2477	c.2005C>T	c.(2005-2007)Cgg>Tgg	p.R669W	QRICH1_ENST00000357496.2_Missense_Mutation_p.R669W|QRICH1_ENST00000424300.1_Missense_Mutation_p.R669W|QRICH1_ENST00000479449.1_5'Flank|RP13-131K19.6_ENST00000607245.1_RNA	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	669						nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		TTCAAGTACCGGATACTCGTG	0.517																																					p.R669W		Atlas-SNP	.											.	QRICH1	48	.	0			c.C2005T						.						128	115	119					3																	49070097		2203	4300	6503	SO:0001583	missense	54870	exon8			AGTACCGGATACT		CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.2005C>T	chr3.hg19:g.49070097G>A	ENSP00000378830:p.Arg669Trp	79.0	0.0		73.0	5.0	NM_198880	Q4G0F7|Q7L621|Q8TEA5	Missense_Mutation	SNP	ENST00000395443.2	hg19	CCDS2787.1	.	.	.	.	.	.	.	.	.	.	G	32	5.153115	0.94645	.	.	ENSG00000198218	ENST00000395443;ENST00000357496;ENST00000424300	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.83622	0.5294	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85425	0.1145	9	0.87932	D	0	-11.435	19.4646	0.94932	0.0:0.0:1.0:0.0	.	669	Q2TAL8	QRIC1_HUMAN	W	669	.	ENSP00000350094:R669W	R	-	1	2	QRICH1	49045101	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.403000	0.66338	2.606000	0.88127	0.650000	0.86243	CGG	.	.		0.517	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		A	49070097	G	A	49070097	3	1	150	1	0	0	0	0	1	0	0	0	12894	1115	39	1	337	1	QRICH1	3	49070097	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	64044	49070097	148952333	126	22850										
DAG1	1605	hgsc.bcm.edu	37	chr3	49570032	49570032	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctgccttctccaacgccctAgagcctgactttaaggccac	7	17	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:49570032A>T	ENST00000539901.1	+	3	2646	c.2088A>T	c.(2086-2088)ctA>ctT	p.L696L	DAG1_ENST00000538711.1_Silent_p.L696L|DAG1_ENST00000308775.2_Silent_p.L696L|DAG1_ENST00000545947.1_Silent_p.L696L|DAG1_ENST00000541308.1_Silent_p.L696L|DAG1_ENST00000515359.2_Silent_p.L696L	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	696	Peptidase S72.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CCAACGCCCTAGAGCCTGACT	0.607																																					p.L696L		Atlas-SNP	.											.	DAG1	60	.	0			c.A2088T						.						67	64	65					3																	49570032		2203	4300	6503	SO:0001819	synonymous_variant	1605	exon4			CGCCCTAGAGCCT	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.2088A>T	chr3.hg19:g.49570032A>T		86.0	0.0		94.0	23.0	NM_001177642	A8K6M7|Q969J9	Silent	SNP	ENST00000539901.1	hg19	CCDS2799.1																																																																																			.	.		0.607	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			T	49570032	A	T	49570032	2	4	150	1	0	0	0	0	0	0	0	1	4227	407	15	4		4	DAG1	3	49570032	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	499935	49570032	148452398	127	22851										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51264732	51264732	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggattgcatcagcttgggtTcaggagagccaaataggagt	14	6	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:51264732T>A	ENST00000266037.9	+	16	1419	c.1396T>A	c.(1396-1398)Tca>Aca	p.S466T		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	466	DHR-1.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		CAGCTTGGGTTCAGGAGAGCC	0.438																																					p.S466T		Atlas-SNP	.											.	DOCK3	397	.	0			c.T1396A						.						169	161	163					3																	51264732		1867	4101	5968	SO:0001583	missense	1795	exon16			TTGGGTTCAGGAG	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.1396T>A	chr3.hg19:g.51264732T>A	ENSP00000266037:p.Ser466Thr	80.0	0.0		55.0	18.0	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.672392	0.47781	.	.	ENSG00000088538	ENST00000266037	T	0.14766	2.48	6.05	6.05	0.98169	.	0.331275	0.32503	N	0.006012	T	0.16981	0.0408	L	0.53671	1.685	0.43852	D	0.996449	B	0.30889	0.299	B	0.34824	0.19	T	0.02294	-1.1181	10	0.44086	T	0.13	.	11.6453	0.51257	0.1324:0.0:0.0:0.8676	.	466	Q8IZD9	DOCK3_HUMAN	T	466	ENSP00000266037:S466T	ENSP00000266037:S466T	S	+	1	0	DOCK3	51239772	0.109000	0.22037	1.000000	0.80357	0.998000	0.95712	1.625000	0.37029	2.320000	0.78422	0.528000	0.53228	TCA	.	.		0.438	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		A	51264732	T	A	51264732	3	1	150	1	0	0	0	0	1	0	0	0	4690	1783	62	4	1458	4	DOCK3	3	51264732	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1694700	51264732	146757698	128	22852										
TKT	7086	hgsc.bcm.edu	37	chr3	53263101	53263101	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aagacagttgatgtggggacTgaccgaaacatagccagatc	12	8	0	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:53263101T>A	ENST00000462138.1	-	10	1405	c.1317A>T	c.(1315-1317)tcA>tcT	p.S439S	TKT_ENST00000423525.2_Silent_p.S439S|TKT_ENST00000296289.6_Silent_p.S392S|TKT_ENST00000423516.1_Silent_p.S447S|TKT_ENST00000461139.1_5'UTR			P29401	TKT_HUMAN	transketolase	439					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		ATGTGGGGACTGACCGAAACA	0.537																																					p.S447S	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.A1341T						.						160	157	158					3																	53263101		2203	4300	6503	SO:0001819	synonymous_variant	7086	exon11			GGGGACTGACCGA		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"Wernicke-Korsakoff syndrome"	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.1317A>T	chr3.hg19:g.53263101T>A		115.0	0.0		95.0	20.0	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Silent	SNP	ENST00000462138.1	hg19	CCDS2871.1																																																																																			.	.		0.537	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1			A	53263101	T	A	53263101	2	1	150	1	0	0	0	0	0	0	0	1	15949	1567	55	4		4	TKT	3	53263101	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1998369	53263101	144759329	129	22853										
FLNB	2317	hgsc.bcm.edu	37	chr3	58112352	58112352	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cgcaggaattggtgggcttgGcataactgttgagggaccat	15	7	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:58112352G>T	ENST00000295956.4	+	24	4250	c.4085G>T	c.(4084-4086)gGc>gTc	p.G1362V	FLNB_ENST00000358537.3_Missense_Mutation_p.G1362V|FLNB_ENST00000493452.1_Missense_Mutation_p.G1193V|FLNB_ENST00000357272.4_Missense_Mutation_p.G1362V|FLNB_ENST00000419752.2_Missense_Mutation_p.G1193V|FLNB_ENST00000490882.1_Missense_Mutation_p.G1362V|FLNB_ENST00000348383.5_Missense_Mutation_p.G1362V|FLNB_ENST00000429972.2_Missense_Mutation_p.G1362V	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1362	Interaction with FBLP1.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GGTGGGCTTGGCATAACTGTT	0.458																																					p.G1362V		Atlas-SNP	.											.	FLNB	430	.	0			c.G4085T						.						111	109	110					3																	58112352		2203	4300	6503	SO:0001583	missense	2317	exon24			GGCTTGGCATAAC	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.4085G>T	chr3.hg19:g.58112352G>T	ENSP00000295956:p.Gly1362Val	182.0	0.0		170.0	89.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.692024	0.88735	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92	5.95	5.95	0.96441	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92948	0.7756	M	0.79123	2.44	0.80722	D	1	D;D;D;D;D;D	0.89917	0.992;1.0;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.97110	0.892;0.999;1.0;1.0;1.0;1.0	D	0.92845	0.6292	10	0.87932	D	0	.	20.3931	0.98965	0.0:0.0:1.0:0.0	.	1362;1362;1193;1193;1362;1362	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	V	1362;1362;1362;1362;1362;1362;1193;1193	ENSP00000295956:G1362V;ENSP00000420213:G1362V;ENSP00000351339:G1362V;ENSP00000415599:G1362V;ENSP00000232447:G1362V;ENSP00000349819:G1362V;ENSP00000418510:G1193V;ENSP00000414532:G1193V	ENSP00000295956:G1362V	G	+	2	0	FLNB	58087392	1.000000	0.71417	1.000000	0.80357	0.686000	0.39977	9.869000	0.99810	2.824000	0.97209	0.655000	0.94253	GGC	.	.		0.458	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		T	58112352	G	T	58112352	3	4	150	1	0	0	0	0	1	0	0	0	5942	1203	42	3	4179	3	FLNB	3	58112352	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	4849251	58112352	139910078	130	22854										
ATXN7	6314	hgsc.bcm.edu	37	chr3	63973873	63973873	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcaaccaccgcagcctctcAgggacccgcatcccgcccct	8	21	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:63973873A>T	ENST00000295900.6	+	9	1784	c.1234A>T	c.(1234-1236)Agg>Tgg	p.R412W	ATXN7_ENST00000484332.1_Missense_Mutation_p.R267W|ATXN7_ENST00000538065.1_Missense_Mutation_p.R412W|ATXN7_ENST00000398590.3_Missense_Mutation_p.R412W|ATXN7_ENST00000487717.1_Missense_Mutation_p.R412W	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	412	Pro-rich.				cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		GCAGCCTCTCAGGGACCCGCA	0.507																																					p.R412W		Atlas-SNP	.											.	ATXN7	126	.	0			c.A1234T						.						115	131	126					3																	63973873		1956	4146	6102	SO:0001583	missense	6314	exon9			CCTCTCAGGGACC	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"Ataxins"	10560	protein-coding gene	gene with protein product		607640	"spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.1234A>T	chr3.hg19:g.63973873A>T	ENSP00000295900:p.Arg412Trp	177.0	0.0		145.0	39.0	NM_000333	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	ENST00000295900.6	hg19	CCDS43102.1	.	.	.	.	.	.	.	.	.	.	A	35	5.547343	0.96488	.	.	ENSG00000163635	ENST00000398590;ENST00000295900;ENST00000487717;ENST00000538065;ENST00000484332	T;T;T;T;T	0.18338	2.22;2.23;2.23;2.22;2.22	5.95	5.95	0.96441	.	0.131887	0.64402	D	0.000002	T	0.44414	0.1292	M	0.75264	2.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.995	T	0.40440	-0.9563	10	0.87932	D	0	-15.7601	16.4237	0.83790	1.0:0.0:0.0:0.0	.	267;412;412	E9PHP9;O15265-2;O15265	.;.;ATX7_HUMAN	W	412;412;412;412;267	ENSP00000381590:R412W;ENSP00000295900:R412W;ENSP00000420234:R412W;ENSP00000439585:R412W;ENSP00000428277:R267W	ENSP00000295900:R412W	R	+	1	2	ATXN7	63948913	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.279000	0.95777	2.279000	0.76181	0.533000	0.62120	AGG	.	.		0.507	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333		T	63973873	A	T	63973873	3	4	150	1	0	0	0	0	1	0	0	0	1215	179	7	4	1328	4	ATXN7	3	63973873	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5861521	63973873	134048557	131	22855										
MINA	84864	hgsc.bcm.edu	37	chr3	97686360	97686360	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaagctgaaggccccccagcTgcttctaacttcatctgctt	7	14	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:97686360T>A	ENST00000333396.7	-	2	660	c.78A>T	c.(76-78)gcA>gcT	p.A26A	MINA_ENST00000330299.2_Silent_p.A26A|MINA_ENST00000394198.2_Silent_p.A26A|MINA_ENST00000360258.4_Silent_p.A26A	NM_001042533.2|NM_032778.5	NP_001035998.1|NP_116167.3			MYC induced nuclear antigen											breast(2)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)	13						GCCCCCCAGCTGCTTCTAACT	0.478																																					p.A26A		Atlas-SNP	.											.	MINA	39	.	0			c.A78T						.						48	49	48					3																	97686360		2203	4300	6503	SO:0001819	synonymous_variant	84864	exon2			CCCAGCTGCTTCT	AB083189	CCDS2929.1, CCDS43114.1	3q22.1	2005-07-22			ENSG00000170854	ENSG00000170854			19441	protein-coding gene	gene with protein product		612049				12091391	Standard	NM_001042533		Approved	MINA53, FLJ14393, mdig	uc003dsb.1	Q8IUF8	OTTHUMG00000160107	ENST00000333396.7:c.78A>T	chr3.hg19:g.97686360T>A		58.0	0.0		67.0	13.0	NM_001261829		Silent	SNP	ENST00000333396.7	hg19	CCDS43114.1																																																																																			.	.		0.478	MINA-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359244.3	NM_032778		A	97686360	T	A	97686360	2	1	150	1	0	0	0	0	0	0	0	1	9595	1567	55	4		4	MINA	3	97686360	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	33712487	97686360	100336070	132	22856										
OR5K2	402135	hgsc.bcm.edu	37	chr3	98216964	98216964	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctgcattcagatgaccacagGcgccttcatagctggaaatc	9	12	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:98216964G>A	ENST00000427338.1	+	1	517	c.440G>A	c.(439-441)gGc>gAc	p.G147D	CLDND1_ENST00000502288.1_3'UTR	NM_001004737.1	NP_001004737.1	Q8NHB8	OR5K2_HUMAN	olfactory receptor, family 5, subfamily K, member 2	147						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ATGACCACAGGCGCCTTCATA	0.458																																					p.G147D		Atlas-SNP	.											.	OR5K2	56	.	0			c.G440A						.						147	149	149					3																	98216964		2203	4300	6503	SO:0001583	missense	402135	exon1			CCACAGGCGCCTT	AC021660	CCDS33804.1	3q11.2	2013-09-23			ENSG00000231861	ENSG00000231861		"GPCR / Class A : Olfactory receptors"	14774	protein-coding gene	gene with protein product							Standard	NM_001004737		Approved		uc011bgx.2	Q8NHB8	OTTHUMG00000160049	ENST00000427338.1:c.440G>A	chr3.hg19:g.98216964G>A	ENSP00000393889:p.Gly147Asp	124.0	0.0		126.0	37.0	NM_001004737	B2RN70|Q6IF47	Missense_Mutation	SNP	ENST00000427338.1	hg19	CCDS33804.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.102826	0.37145	.	.	ENSG00000231861	ENST00000427338	T	0.39787	1.06	2.87	2.87	0.33458	GPCR, rhodopsin-like superfamily (1);	0.172228	0.27807	N	0.017775	T	0.67646	0.2915	M	0.93283	3.4	0.34987	D	0.754642	D	0.67145	0.996	D	0.72075	0.976	T	0.78125	-0.2326	10	0.66056	D	0.02	-7.634	8.0572	0.30612	0.0:0.2519:0.7481:0.0	.	147	Q8NHB8	OR5K2_HUMAN	D	147	ENSP00000393889:G147D	ENSP00000393889:G147D	G	+	2	0	OR5K2	99699654	0.014000	0.17966	0.553000	0.28255	0.603000	0.37013	-0.232000	0.09055	1.918000	0.55548	0.298000	0.19748	GGC	.	.		0.458	OR5K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359020.2			A	98216964	G	A	98216964	3	1	150	1	0	0	0	0	1	0	0	0	11176	1203	42	3	442	3	OR5K2	3	98216964	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	530604	98216964	99805466	133	22857										
ALCAM	214	hgsc.bcm.edu	37	chr3	105266289	105266289	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccagtggactatctaaaacAataatctgccatgtggaagg	9	9	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:105266289A>T	ENST00000306107.5	+	11	1796	c.1296A>T	c.(1294-1296)acA>acT	p.T432T	ALCAM_ENST00000486979.2_Silent_p.T381T|ALCAM_ENST00000389927.4_Silent_p.T154T|ALCAM_ENST00000472644.2_Silent_p.T432T	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	432	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TATCTAAAACAATAATCTGCC	0.348																																					p.T432T		Atlas-SNP	.											.	ALCAM	71	.	0			c.A1296T						.						73	69	71					3																	105266289		2203	4297	6500	SO:0001819	synonymous_variant	214	exon11			TAAAACAATAATC	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	400	protein-coding gene	gene with protein product		601662	"activated leucocyte cell adhesion molecule"			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1296A>T	chr3.hg19:g.105266289A>T		339.0	0.0		302.0	80.0	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Silent	SNP	ENST00000306107.5	hg19	CCDS33810.1	.	.	.	.	.	.	.	.	.	.	A	7.080	0.570033	0.13560	.	.	ENSG00000170017	ENST00000465413	.	.	.	5.76	-1.82	0.07857	.	.	.	.	.	T	0.53530	0.1802	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49103	-0.8974	4	.	.	.	-16.0416	8.5618	0.33516	0.3412:0.4366:0.0:0.2222	.	.	.	.	Y	193	.	.	N	+	1	0	ALCAM	106748979	0.883000	0.30277	0.993000	0.49108	0.638000	0.38207	-0.133000	0.10451	-0.177000	0.10690	0.477000	0.44152	AAT	.	.		0.348	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627		T	105266289	A	T	105266289	2	4	150	1	0	0	0	0	0	0	0	1	487	117	5	4		4	ALCAM	3	105266289	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	7049325	105266289	92756141	134	22858										
ATG3	64422	hgsc.bcm.edu	37	chr3	112262916	112262916	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	accagtaccttattttccagTgtgatctctttaacggcttc	6	11	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:112262916T>A	ENST00000283290.5	-	6	815	c.381A>T	c.(379-381)acA>acT	p.T127T	ATG3_ENST00000495756.1_5'UTR|ATG3_ENST00000402314.2_Silent_p.T127T	NM_022488.3	NP_071933.2	Q9NT62	ATG3_HUMAN	autophagy related 3	127					autophagic vacuole assembly (GO:0000045)|cellular protein modification process (GO:0006464)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)|protein targeting to membrane (GO:0006612)|protein ubiquitination (GO:0016567)|regulation of cilium assembly (GO:1902017)	cytoplasmic ubiquitin ligase complex (GO:0000153)|cytosol (GO:0005829)	Atg12 ligase activity (GO:0019777)|Atg8 ligase activity (GO:0019776)|enzyme binding (GO:0019899)|small conjugating protein ligase activity (GO:0019787)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(3)	9						TATTTTCCAGTGTGATCTCTT	0.279																																					p.T127T		Atlas-SNP	.											.	ATG3	23	.	0			c.A381T						.						37	43	41					3																	112262916		2200	4279	6479	SO:0001819	synonymous_variant	64422	exon6			TTCCAGTGTGATC		CCDS2966.1, CCDS63721.1	3q13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000144848	ENSG00000144848			20962	protein-coding gene	gene with protein product		609606	"APG3 autophagy 3-like (S. cerevisiae)", "ATG3 autophagy related 3 homolog (S. cerevisiae)"	APG3L		11825910	Standard	NM_022488		Approved	PC3-96, FLJ22125, MGC15201, DKFZp564M1178	uc003dzd.3	Q9NT62	OTTHUMG00000159260	ENST00000283290.5:c.381A>T	chr3.hg19:g.112262916T>A		449.0	1.0		400.0	114.0	NM_022488	Q6PKC5|Q9H6L9	Silent	SNP	ENST00000283290.5	hg19	CCDS2966.1																																																																																			.	.		0.279	ATG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354147.1	NM_022488		A	112262916	T	A	112262916	2	1	150	1	0	0	0	0	0	0	0	1	1095	1683	59	4		4	ATG3	3	112262916	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	6996627	112262916	85759514	135	22859										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112357260	112357260	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cattactaagaattttgtccTgggccttctttttgggaggt	10	7	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:112357260T>A	ENST00000206423.3	-	2	2446	c.1493A>T	c.(1492-1494)cAg>cTg	p.Q498L	CCDC80_ENST00000475181.1_5'Flank|CCDC80_ENST00000439685.2_Missense_Mutation_p.Q498L	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	498	Lys-rich.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						AATTTTGTCCTGGGCCTTCTT	0.552																																					p.Q498L		Atlas-SNP	.											.	CCDC80	100	.	0			c.A1493T						.						82	86	85					3																	112357260		2203	4300	6503	SO:0001583	missense	151887	exon2			TTGTCCTGGGCCT	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.1493A>T	chr3.hg19:g.112357260T>A	ENSP00000206423:p.Gln498Leu	90.0	0.0		73.0	21.0	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	hg19	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.741267	0.49151	.	.	ENSG00000091986	ENST00000206423;ENST00000439685;ENST00000444594	T;T	0.44482	0.92;0.92	4.98	0.879	0.19155	.	0.190911	0.47093	D	0.000259	T	0.20333	0.0489	N	0.24115	0.695	0.09310	N	1	B;B;B	0.26809	0.16;0.099;0.043	B;B;B	0.22601	0.037;0.04;0.011	T	0.06481	-1.0824	10	0.29301	T	0.29	-11.1986	1.9084	0.03282	0.1308:0.1486:0.1356:0.5851	.	509;498;498	Q76M96-2;A3KC71;Q76M96	.;.;CCD80_HUMAN	L	498;498;126	ENSP00000206423:Q498L;ENSP00000411814:Q498L	ENSP00000206423:Q498L	Q	-	2	0	CCDC80	113839950	0.791000	0.28800	0.904000	0.35570	0.944000	0.59088	1.381000	0.34362	0.323000	0.23307	0.454000	0.30748	CAG	.	.		0.552	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		A	112357260	T	A	112357260	3	1	150	1	0	0	0	0	1	0	0	0	2856	1580	55	4	1387	4	CCDC80	3	112357260	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	94344	112357260	85665170	136	22860										
POLQ	10721	hgsc.bcm.edu	37	chr3	121186434	121186434	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctctgtctgcagctctctccTccatctgtgcctggcatcta	7	16	5	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:121186434T>A	ENST00000264233.5	-	24	7027	c.6899A>T	c.(6898-6900)gAg>gTg	p.E2300V		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2300					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		AGCTCTCTCCTCCATCTGTGC	0.453								DNA polymerases (catalytic subunits)																													p.E2300V	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A6899T						.						187	171	176					3																	121186434		2203	4300	6503	SO:0001583	missense	10721	exon24			CTCTCCTCCATCT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.6899A>T	chr3.hg19:g.121186434T>A	ENSP00000264233:p.Glu2300Val	110.0	0.0		95.0	34.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.952134	0.73787	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.52526	0.66	5.58	-4.36	0.03645	.	0.397058	0.24708	N	0.036244	T	0.32406	0.0828	L	0.60455	1.87	0.09310	N	1	B;P	0.51933	0.011;0.949	B;B	0.43052	0.008;0.406	T	0.26121	-1.0112	10	0.40728	T	0.16	.	1.2713	0.02022	0.2011:0.2144:0.1128:0.4717	.	2300;1472	O75417;O75417-2	DPOLQ_HUMAN;.	V	1923;2300;2436	ENSP00000264233:E2300V	ENSP00000264233:E2300V	E	-	2	0	POLQ	122669124	0.099000	0.21834	0.000000	0.03702	0.908000	0.53690	0.306000	0.19279	-0.464000	0.06963	0.482000	0.46254	GAG	.	.		0.453	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121186434	T	A	121186434	3	1	150	1	0	0	0	0	1	0	0	0	12217	1551	54	4	901	4	POLQ	3	121186434	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	8829174	121186434	76835996	137	22861										
POLQ	10721	hgsc.bcm.edu	37	chr3	121256056	121256056	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttcatccacaaccaccattcCtaaaaagattttccagatac	2	13	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:121256056C>G	ENST00000264233.5	-	5	760		c.e5-1			NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta						ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		ACCACCATTCCTAAAAAGATT	0.353								DNA polymerases (catalytic subunits)																													.	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.632-1G>C						.						82	79	80					3																	121256056		2203	4300	6503	SO:0001630	splice_region_variant	10721	exon6			CCATTCCTAAAAA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.632-1G>C	chr3.hg19:g.121256056C>G		222.0	0.0		195.0	99.0	NM_199420	O95160|Q6VMB5	Splice_Site	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.100266	0.76983	.	.	ENSG00000051341	ENST00000264233;ENST00000393672	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.882	0.88843	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	POLQ	122738746	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.203000	0.77864	2.202000	0.70862	0.462000	0.41574	.	.	.		0.353	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	Intron	G	121256056	C	G	121256056	5	3	150	1	0	0	0	0	0	0	1	0	12217	695	24	4	7245	4	POLQ	3	121256056	Splice_Site	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	69622	121256056	76766374	138	22862										
CASR	846	hgsc.bcm.edu	37	chr3	121981126	121981126	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	catagattacacgcatttacGgatatcctacaatgtgtact	6	9	0	1	rs193922421		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:121981126G>A	ENST00000490131.1	+	4	1616	c.1244G>A	c.(1243-1245)cGg>cAg	p.R415Q	CASR_ENST00000498619.1_Missense_Mutation_p.R415Q|CASR_ENST00000296154.5_Missense_Mutation_p.R415Q	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	415					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	ACGCATTTACGGATATCCTAC	0.498																																					p.R415Q		Atlas-SNP	.											.	CASR	190	.	0			c.G1244A						.						131	121	124					3																	121981126		2203	4300	6503	SO:0001583	missense	846	exon4			ATTTACGGATATC	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.1244G>A	chr3.hg19:g.121981126G>A	ENSP00000418685:p.Arg415Gln	72.0	0.0		74.0	13.0	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	hg19	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	G	33	5.237354	0.95240	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.83419	-1.72;-1.72;-1.72	5.93	5.93	0.95920	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.90964	0.7159	M	0.70108	2.13	0.80722	D	1	D;D	0.76494	0.999;0.998	D;P	0.80764	0.994;0.877	D	0.90967	0.4817	10	0.72032	D	0.01	.	19.3193	0.94231	0.0:0.0:1.0:0.0	.	415;415	E7ENE0;P41180	.;CASR_HUMAN	Q	415	ENSP00000418685:R415Q;ENSP00000420194:R415Q;ENSP00000296154:R415Q	ENSP00000296154:R415Q	R	+	2	0	CASR	123463816	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	9.869000	0.99810	2.797000	0.96272	0.655000	0.94253	CGG	.	.		0.498	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		A	121981126	G	A	121981126	3	1	150	1	0	0	0	0	1	0	0	0	2684	1116	39	1	1254	1	CASR	3	121981126	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	725070	121981126	76041304	139	22863										
TPRA1	131601	hgsc.bcm.edu	37	chr3	127295719	127295719	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atggccagcaggaagaagcgGgtgatctcccacaggatctg	14	10	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:127295719G>A	ENST00000355552.3	-	5	739	c.363C>T	c.(361-363)acC>acT	p.T121T	TPRA1_ENST00000465915.1_5'Flank|TPRA1_ENST00000489960.1_Silent_p.T121T|TPRA1_ENST00000296210.7_Silent_p.T121T|TPRA1_ENST00000450633.2_Silent_p.T121T	NM_001136053.1	NP_001129525.1	Q86W33	TPRA1_HUMAN	transmembrane protein, adipocyte asscociated 1	121					aging (GO:0007568)|G-protein coupled receptor signaling pathway (GO:0007186)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	9						GGAAGAAGCGGGTGATCTCCC	0.657																																					p.T121T		Atlas-SNP	.											.	TPRA1	21	.	0			c.C363T						.						77	75	76					3																	127295719		2203	4300	6503	SO:0001819	synonymous_variant	131601	exon5			GAAGCGGGTGATC	AK056759	CCDS3042.1, CCDS46899.1	3q21.2	2012-08-22	2009-07-08	2009-07-08	ENSG00000163870	ENSG00000163870		"GPCR / Unclassified : 7TM orphan receptors"	30413	protein-coding gene	gene with protein product	"transmembrane protein 227"	608336	"G protein-coupled receptor 175"	GPR175		10342878	Standard	NM_001136053		Approved	TPRA40, FLJ32197, TMEM227	uc003ejn.3	Q86W33	OTTHUMG00000159639	ENST00000355552.3:c.363C>T	chr3.hg19:g.127295719G>A		245.0	0.0		191.0	41.0	NM_001142646	A8MVB8|D3DNA9|Q8WZ24|Q96AJ6|Q9P2R4	Silent	SNP	ENST00000355552.3	hg19	CCDS3042.1																																																																																			.	.		0.657	TPRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356624.1	NM_016372		A	127295719	G	A	127295719	2	1	150	1	0	0	0	0	0	0	0	1	16432	1219	43	3		3	TPRA1	3	127295719	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	5314593	127295719	70726711	140	22864										
KBTBD12	166348	hgsc.bcm.edu	37	chr3	127703119	127703119	+	Nonstop_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tggaagaaggcaatgagcacTaaggtgaccttgctggagga	15	6	0	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:127703119T>A	ENST00000405109.1	+	6	2337	c.1870T>A	c.(1870-1872)Taa>Aaa	p.*624K	KBTBD12_ENST00000343941.4_Nonstop_Mutation_p.*199K|KBTBD12_ENST00000405256.1_Nonstop_Mutation_p.*624K|KBTBD12_ENST00000492025.1_3'UTR|KBTBD12_ENST00000407609.3_Nonstop_Mutation_p.*231K			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	0										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						CAATGAGCACTAAGGTGACCT	0.547																																					p.X624K		Atlas-SNP	.											.	KBTBD12	41	.	0			c.T1870A						.						78	72	74					3																	127703119		2203	4300	6503	SO:0001578	stop_lost	166348	exon5			GAGCACTAAGGTG		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.1870T>A	chr3.hg19:g.127703119T>A	ENSP00000385957:p.*624Lysext*35	107.0	0.0		86.0	24.0	NM_207335	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	hg19	CCDS33848.2	.	.	.	.	.	.	.	.	.	.	T	18.13	3.555638	0.65425	.	.	ENSG00000187715	ENST00000405109;ENST00000407609;ENST00000405256;ENST00000343941	.	.	.	5.96	2.09	0.27110	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.4744	0.04572	0.1466:0.079:0.285:0.4894	.	.	.	.	K	624;231;624;199	.	.	X	+	1	0	KBTBD12	129185809	0.010000	0.17322	0.185000	0.23176	0.957000	0.61999	0.019000	0.13444	0.112000	0.17975	0.482000	0.46254	TAA	.	.		0.547	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		A	127703119	T	A	127703119	4	1	150	1	0	0	0	0	0	0	0	0	8000	1535	53	4	1888	4	KBTBD12	3	127703119	Nonstop_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	407400	127703119	70319311	141	22865										
KIAA1257	57501	hgsc.bcm.edu	37	chr3	128696958	128696958	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgttcctggttcgactcttcTctgacaatgttggtattctc	8	10	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:128696958T>A	ENST00000265068.5	-	5	905	c.738A>T	c.(736-738)agA>agT	p.R246S	KIAA1257_ENST00000515659.1_Missense_Mutation_p.R134S|KIAA1257_ENST00000511438.1_Missense_Mutation_p.R246S|KIAA1257_ENST00000510149.1_5'UTR	NM_020741.2	NP_065792.1	Q9ULG3	K1257_HUMAN	KIAA1257	246										breast(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(2)	14						TCGACTCTTCTCTGACAATGT	0.413																																					p.R246S		Atlas-SNP	.											.	KIAA1257	33	.	0			c.A738T						.						176	170	172					3																	128696958		1928	4125	6053	SO:0001583	missense	57501	exon5			CTCTTCTCTGACA	AB033083	CCDS46905.1	3q21.3	2011-11-07			ENSG00000114656	ENSG00000114656			29231	protein-coding gene	gene with protein product						10574462	Standard	NM_020741		Approved		uc003elj.4	Q9ULG3	OTTHUMG00000159946	ENST00000265068.5:c.738A>T	chr3.hg19:g.128696958T>A	ENSP00000265068:p.Arg246Ser	104.0	0.0		105.0	28.0	NM_020741	Q8IXY7|Q8N5T4	Missense_Mutation	SNP	ENST00000265068.5	hg19	CCDS46905.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.495122	0.26774	.	.	ENSG00000114656	ENST00000511438;ENST00000265068;ENST00000515659	.	.	.	3.78	-1.71	0.08133	.	2.846150	0.01307	N	0.010489	T	0.18341	0.0440	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.05582	-1.0876	9	0.08837	T	0.75	0.0411	0.4002	0.00425	0.1817:0.2241:0.1872:0.407	.	246;246	Q9ULG3;D6RH05	K1257_HUMAN;.	S	246;246;134	.	ENSP00000265068:R246S	R	-	3	2	KIAA1257	130179648	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.028000	0.12350	-0.409000	0.07553	0.383000	0.25322	AGA	.	.		0.413	KIAA1257-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000358430.1	NM_020741		A	128696958	T	A	128696958	3	1	150	1	0	0	0	0	1	0	0	0	8227	1548	54	4	507	4	KIAA1257	3	128696958	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	993839	128696958	69325472	142	22866										
TMCC1	23023	hgsc.bcm.edu	37	chr3	129373861	129373861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atacgcgattttttcttccaTgcttgccagttcctgcttca	6	12	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:129373861T>C	ENST00000393238.3	-	5	1937	c.1597A>G	c.(1597-1599)Atg>Gtg	p.M533V	TMCC1_ENST00000426664.2_Missense_Mutation_p.M419V|TMCC1_ENST00000329333.5_Missense_Mutation_p.M354V|TMCC1_ENST00000432054.2_Missense_Mutation_p.M209V	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	533						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						TTTTCTTCCATGCTTGCCAGT	0.418																																					p.M533V		Atlas-SNP	.											.	TMCC1	105	.	0			c.A1597G						.						149	146	147					3																	129373861		2203	4300	6503	SO:0001583	missense	23023	exon5			CTTCCATGCTTGC	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.1597A>G	chr3.hg19:g.129373861T>C	ENSP00000376930:p.Met533Val	116.0	0.0		97.0	30.0	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Missense_Mutation	SNP	ENST00000393238.3	hg19	CCDS33855.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470431	0.63625	.	.	ENSG00000172765	ENST00000432054;ENST00000393238;ENST00000426664;ENST00000329333;ENST00000510323	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.61148	0.2324	M	0.71206	2.165	0.80722	D	1	P;P	0.47191	0.891;0.843	P;D	0.64506	0.826;0.926	T	0.56013	-0.8049	10	0.13470	T	0.59	-17.0852	16.4221	0.83766	0.0:0.0:0.0:1.0	.	354;533	B4DE04;O94876	.;TMCC1_HUMAN	V	209;533;419;354;1	ENSP00000404711:M209V;ENSP00000376930:M533V;ENSP00000389892:M419V;ENSP00000327349:M354V;ENSP00000426180:M1V	ENSP00000327349:M354V	M	-	1	0	TMCC1	130856551	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.035000	0.88872	2.283000	0.76528	0.477000	0.44152	ATG	.	.		0.418	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		C	129373861	T	C	129373861	3	2	150	1	0	0	0	0	1	0	0	0	16007	1464	51	2	372	2	TMCC1	3	129373861	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	676903	129373861	68648569	143	22867										
ARMC8	25852	hgsc.bcm.edu	37	chr3	138007891	138007891	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tctttttctgtattaataggGccattcacatgttaaactgc	6	8	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:138007891G>T	ENST00000469044.1	+	20	2094	c.1823G>T	c.(1822-1824)gGc>gTc	p.G608V	NME9_ENST00000383180.2_Intron|NME9_ENST00000341790.5_Intron|ARMC8_ENST00000481646.1_Splice_Site_p.G594V|ARMC8_ENST00000393058.3_Splice_Site_p.G598V|NME9_ENST00000317876.4_Intron|NME9_ENST00000536478.1_Intron|ARMC8_ENST00000461822.1_Splice_Site_p.G541V|ARMC8_ENST00000491704.1_Splice_Site_p.G566V|ARMC8_ENST00000485396.1_Splice_Site_p.G535V|NME9_ENST00000484930.1_Intron|ARMC8_ENST00000538260.1_Splice_Site_p.G577V	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	608										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						TATTAATAGGGCCATTCACAT	0.338																																					p.G594V		Atlas-SNP	.											.	ARMC8	79	.	0			c.G1781T						.						65	58	61					3																	138007891		1817	4076	5893	SO:0001630	splice_region_variant	25852	exon21			AATAGGGCCATTC		CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"Armadillo repeat containing"	24999	protein-coding gene	gene with protein product	"GID complex subunit 5, VID28 homolog (S. cerevisiae)"					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.1822-1G>T	chr3.hg19:g.138007891G>T		255.0	0.0		265.0	145.0	NM_015396	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Missense_Mutation	SNP	ENST00000469044.1	hg19		.	.	.	.	.	.	.	.	.	.	g	11.09	1.535444	0.27475	.	.	ENSG00000114098	ENST00000481646;ENST00000469044;ENST00000491704;ENST00000461822;ENST00000485396;ENST00000538260;ENST00000393058;ENST00000539459	T;T;T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;0.75;0.75;0.75;-0.1	5.39	5.39	0.77823	Armadillo-like helical (1);Armadillo-type fold (1);	0.049311	0.85682	D	0.000000	T	0.47040	0.1424	N	0.17474	0.49	0.80722	D	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.001;0.001	T	0.34976	-0.9807	10	0.22706	T	0.39	-47.7555	16.7171	0.85399	0.0:0.0:1.0:0.0	.	535;541;577;608;594	B7Z637;B7Z441;F5GWK4;Q8IUR7;Q8IUR7-2	.;.;.;ARMC8_HUMAN;.	V	594;608;566;541;535;577;598;465	ENSP00000420333:G594V;ENSP00000419413:G608V;ENSP00000417304:G566V;ENSP00000420706:G541V;ENSP00000417049:G535V;ENSP00000441592:G577V;ENSP00000376778:G598V	ENSP00000376778:G598V	G	+	2	0	ARMC8	139490581	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	9.153000	0.94687	2.526000	0.85167	0.585000	0.79938	GGC	.	.		0.338	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396	Missense_Mutation	T	138007891	G	T	138007891	5	4	150	1	0	0	0	0	0	0	1	0	957	1217	42	3	1925	3	ARMC8	3	138007891	Splice_Site	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	8634030	138007891	60014539	144	22868										
ESYT3	83850	hgsc.bcm.edu	37	chr3	138180931	138180931	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcctgccttgtgtccagtgaTgtgtcagacagcttactgga	11	10	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:138180931T>A	ENST00000389567.4	+	8	984	c.798T>A	c.(796-798)gaT>gaA	p.D266E	ESYT3_ENST00000289135.4_Missense_Mutation_p.D266E	NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	266	Glycerophospholipid-binding barrel-like domain. {ECO:0000250}.				lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|organelle membrane contact site (GO:0044232)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	25						TGTCCAGTGATGTGTCAGACA	0.607																																					p.D266E		Atlas-SNP	.											.	ESYT3	64	.	0			c.T798A						.						181	137	152					3																	138180931		2203	4300	6503	SO:0001583	missense	83850	exon8			CAGTGATGTGTCA	AJ303366	CCDS3101.2	3q22.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000158220	ENSG00000158220		"Synaptotagmins"	24295	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member C"	FAM62C		11543631, 17672888	Standard	NM_031913		Approved	CHR3SYT	uc003esk.3	A0FGR9	OTTHUMG00000147354	ENST00000389567.4:c.798T>A	chr3.hg19:g.138180931T>A	ENSP00000374218:p.Asp266Glu	63.0	0.0		43.0	11.0	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Missense_Mutation	SNP	ENST00000389567.4	hg19	CCDS3101.2	.	.	.	.	.	.	.	.	.	.	T	4.919	0.170757	0.09391	.	.	ENSG00000158220	ENST00000389567;ENST00000289135	T;T	0.23552	1.9;1.9	4.65	-0.406	0.12389	.	0.450748	0.25971	N	0.027137	T	0.09202	0.0227	N	0.16266	0.395	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20505	-1.0273	10	0.09590	T	0.72	-22.9442	0.9789	0.01432	0.1705:0.2746:0.2716:0.2833	.	266	A0FGR9	ESYT3_HUMAN	E	266	ENSP00000374218:D266E;ENSP00000289135:D266E	ENSP00000289135:D266E	D	+	3	2	ESYT3	139663621	0.006000	0.16342	0.174000	0.22961	0.620000	0.37586	-0.089000	0.11180	0.227000	0.20999	-0.973000	0.02599	GAT	.	.		0.607	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913		A	138180931	T	A	138180931	3	1	150	1	0	0	0	0	1	0	0	0	5268	1461	51	4	828	4	ESYT3	3	138180931	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	173040	138180931	59841499	145	22869										
SPSB4	92369	hgsc.bcm.edu	37	chr3	140785482	140785482	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gctgcccgactcgctgctcgTggtgctggacatggatgagg	16	11	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:140785482T>A	ENST00000310546.2	+	2	1280	c.536T>A	c.(535-537)gTg>gAg	p.V179E		NM_080862.1	NP_543138.1	Q96A44	SPSB4_HUMAN	splA/ryanodine receptor domain and SOCS box containing 4	179	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				biliary_tract(1)|large_intestine(1)|lung(1)|pancreas(1)	4						TCGCTGCTCGTGGTGCTGGAC	0.662																																					p.V179E		Atlas-SNP	.											.	SPSB4	19	.	0			c.T536A						.						39	35	37					3																	140785482		2203	4300	6503	SO:0001583	missense	92369	exon2			TGCTCGTGGTGCT		CCDS3115.1	3q23	2008-02-05			ENSG00000175093	ENSG00000175093			30630	protein-coding gene	gene with protein product		611660				12076535	Standard	NM_080862		Approved	SSB-4	uc003ett.3	Q96A44	OTTHUMG00000160223	ENST00000310546.2:c.536T>A	chr3.hg19:g.140785482T>A	ENSP00000311609:p.Val179Glu	137.0	0.0		98.0	17.0	NM_080862		Missense_Mutation	SNP	ENST00000310546.2	hg19	CCDS3115.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.184819	0.78677	.	.	ENSG00000175093	ENST00000310546	T	0.74842	-0.88	5.03	5.03	0.67393	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	D	0.89392	0.6702	H	0.95504	3.68	0.80722	D	1	D	0.67145	0.996	D	0.72982	0.979	D	0.92079	0.5671	10	0.87932	D	0	-37.919	12.7037	0.57049	0.0:0.0:0.0:1.0	.	179	Q96A44	SPSB4_HUMAN	E	179	ENSP00000311609:V179E	ENSP00000311609:V179E	V	+	2	0	SPSB4	142268172	1.000000	0.71417	0.851000	0.33527	0.941000	0.58515	8.040000	0.89188	1.881000	0.54492	0.460000	0.39030	GTG	.	.		0.662	SPSB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359727.1	NM_080862		A	140785482	T	A	140785482	3	1	150	1	0	0	0	0	1	0	0	0	15130	1696	59	4	538	4	SPSB4	3	140785482	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2604551	140785482	57236948	146	22870										
ATR	545	hgsc.bcm.edu	37	chr3	142188239	142188239	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	taggctagaaatactttggcTattatttccatcaagacaac	6	8	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:142188239T>A	ENST00000350721.4	-	38	6613	c.6492A>T	c.(6490-6492)atA>atT	p.I2164I	RP11-383G6.3_ENST00000460977.1_RNA|ATR_ENST00000383101.3_Silent_p.I2100I	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2164	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						ATACTTTGGCTATTATTTCCA	0.333								Other conserved DNA damage response genes																													p.I2164I		Atlas-SNP	.											.	ATR	285	.	0			c.A6492T						.						105	108	107					3																	142188239		2203	4300	6503	SO:0001819	synonymous_variant	545	exon38			TTTGGCTATTATT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.6492A>T	chr3.hg19:g.142188239T>A		225.0	0.0		194.0	50.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	T	10.36	1.328115	0.24080	.	.	ENSG00000175054	ENST00000513291	.	.	.	5.15	3.93	0.45458	.	.	.	.	.	T	0.48021	0.1477	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45454	-0.9260	4	.	.	.	-17.2193	4.1392	0.10186	0.3148:0.1051:0.0:0.5801	.	.	.	.	C	11	.	.	S	-	1	0	ATR	143670929	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.603000	0.36794	1.926000	0.55796	0.482000	0.46254	AGC	.	.		0.333	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142188239	T	A	142188239	2	1	150	1	0	0	0	0	0	0	0	1	1204	1512	53	4		4	ATR	3	142188239	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1402757	142188239	55834191	147	22871										
ATR	545	hgsc.bcm.edu	37	chr3	142278251	142278251	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcactacagaaggtttcttcTtggatttatgttgacagtcc	8	8	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:142278251T>A	ENST00000350721.4	-	7	1695	c.1574A>T	c.(1573-1575)aAg>aTg	p.K525M	ATR_ENST00000383101.3_Missense_Mutation_p.K461M	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	525					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						AGGTTTCTTCTTGGATTTATG	0.323								Other conserved DNA damage response genes																													p.K525M		Atlas-SNP	.											.	ATR	285	.	0			c.A1574T						.						85	82	83					3																	142278251		2203	4300	6503	SO:0001583	missense	545	exon7			TTCTTCTTGGATT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.1574A>T	chr3.hg19:g.142278251T>A	ENSP00000343741:p.Lys525Met	155.0	0.0		117.0	31.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.690611	0.48097	.	.	ENSG00000175054	ENST00000350721;ENST00000383101;ENST00000515149	T;T	0.03889	3.9;3.77	5.6	5.6	0.85130	Armadillo-type fold (1);	0.518940	0.20332	N	0.094420	T	0.04998	0.0134	L	0.27053	0.805	0.35962	D	0.834641	B	0.16802	0.019	B	0.09377	0.004	T	0.30297	-0.9983	10	0.51188	T	0.08	-8.453	13.1662	0.59573	0.0:0.0:0.0:1.0	.	525	Q13535	ATR_HUMAN	M	525;461;142	ENSP00000343741:K525M;ENSP00000372581:K461M	ENSP00000343741:K525M	K	-	2	0	ATR	143760941	0.921000	0.31238	0.996000	0.52242	0.191000	0.23601	1.841000	0.39240	2.123000	0.65237	0.533000	0.62120	AAG	.	.		0.323	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142278251	T	A	142278251	3	1	150	1	0	0	0	0	1	0	0	0	1204	1609	56	4	6524	4	ATR	3	142278251	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	90012	142278251	55744179	148	22872										
CLRN1	7401	hgsc.bcm.edu	37	chr3	150690482	150690482	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgcaaaaaatgattttcttcTgttggcttggcatgatgaga	10	5	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:150690482T>A	ENST00000327047.1	-	1	304	c.14A>T	c.(13-15)cAg>cTg	p.Q5L	CLRN1-AS1_ENST00000465576.1_RNA|CLRN1-AS1_ENST00000476886.1_RNA|CLRN1_ENST00000328863.4_Missense_Mutation_p.Q5L|RP11-166N6.2_ENST00000469268.1_RNA	NM_174878.2	NP_777367.1	P58418	CLRN1_HUMAN	clarin 1	5					actin filament organization (GO:0007015)|auditory receptor cell stereocilium organization (GO:0060088)|cell motility (GO:0048870)|equilibrioception (GO:0050957)|photoreceptor cell maintenance (GO:0045494)|positive regulation of lamellipodium assembly (GO:0010592)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)	14			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GATTTTCTTCTGTTGGCTTGG	0.488																																					p.Q5L		Atlas-SNP	.											.	CLRN1	44	.	0			c.A14T						.						72	70	71					3																	150690482		2203	4300	6503	SO:0001583	missense	7401	exon1			TTCTTCTGTTGGC	AF388366	CCDS3153.1, CCDS35492.1, CCDS56285.1	3q25.1	2014-09-17	2006-11-23	2006-11-23	ENSG00000163646	ENSG00000163646			12605	protein-coding gene	gene with protein product		606397	"Usher syndrome 3A"	USH3, USH3A, RP61		7711740, 8975700	Standard	NM_052995		Approved		uc021xfr.1	P58418	OTTHUMG00000140368	ENST00000327047.1:c.14A>T	chr3.hg19:g.150690482T>A	ENSP00000322280:p.Gln5Leu	82.0	0.0		81.0	21.0	NM_001256819	D3DNJ3|E1ACU9|Q8N6A9	Missense_Mutation	SNP	ENST00000327047.1	hg19	CCDS3153.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.192623	0.38707	.	.	ENSG00000163646	ENST00000327047;ENST00000328863	T;T	0.75367	-0.93;-0.93	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.80358	0.4608	M	0.70595	2.14	0.80722	D	1	D	0.63880	0.993	P	0.55923	0.787	T	0.77408	-0.2599	10	0.10636	T	0.68	2.2764	15.7075	0.77594	0.0:0.0:0.0:1.0	.	5	P58418	CLRN1_HUMAN	L	5	ENSP00000322280:Q5L;ENSP00000329158:Q5L	ENSP00000322280:Q5L	Q	-	2	0	CLRN1	152173172	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.461000	0.80834	2.117000	0.64856	0.533000	0.62120	CAG	.	.		0.488	CLRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277060.1			A	150690482	T	A	150690482	3	1	150	1	0	0	0	0	1	0	0	0	3559	1580	55	4	750	4	CLRN1	3	150690482	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	8412231	150690482	47331948	149	22873										
OTOL1	131149	hgsc.bcm.edu	37	chr3	161221107	161221107	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaaaaggtagcaaaggagacAgtggaatggaaggcaaaagc	14	4	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:161221107A>T	ENST00000327928.4	+	4	811	c.811A>T	c.(811-813)Agt>Tgt	p.S271C		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	271						collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						CAAAGGAGACAGTGGAATGGA	0.532																																					p.S271C		Atlas-SNP	.											.	OTOL1	63	.	0			c.A811T						.						11	12	12					3																	161221107		1964	4146	6110	SO:0001583	missense	131149	exon4			GGAGACAGTGGAA		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"C1q and tumor necrosis factor related protein 15"		"otolin 1 homolog (zebrafish)"			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.811A>T	chr3.hg19:g.161221107A>T	ENSP00000330808:p.Ser271Cys	331.0	0.0		299.0	81.0	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	hg19	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	A	11.16	1.557296	0.27827	.	.	ENSG00000182447	ENST00000327928	D	0.93604	-3.25	4.49	-8.99	0.00751	.	2.248860	0.01739	N	0.029308	D	0.91459	0.7304	L	0.55481	1.735	0.09310	N	1	P	0.34757	0.467	B	0.42386	0.386	D	0.85851	0.1404	10	0.54805	T	0.06	.	8.8546	0.35221	0.2721:0.5098:0.2181:0.0	.	271	A6NHN0	OTOL1_HUMAN	C	271	ENSP00000330808:S271C	ENSP00000330808:S271C	S	+	1	0	OTOL1	162703801	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.394000	0.07296	-1.926000	0.01061	-1.272000	0.01410	AGT	.	.		0.532	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440		T	161221107	A	T	161221107	3	4	150	1	0	0	0	0	1	0	0	0	11313	188	7	4	825	4	OTOL1	3	161221107	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	10530625	161221107	36801323	150	22874										
MECOM	2122	hgsc.bcm.edu	37	chr3	168834399	168834399	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acaaaacctcctgtgtttatTtaaggaagacgtagtgctga	9	7	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:168834399T>A	ENST00000464456.1	-	7	1897	c.697A>T	c.(697-699)Aat>Tat	p.N233Y	MECOM_ENST00000433243.2_Missense_Mutation_p.N234Y|MECOM_ENST00000264674.3_Missense_Mutation_p.N298Y|MECOM_ENST00000468789.1_Missense_Mutation_p.N233Y|MECOM_ENST00000460814.1_Missense_Mutation_p.N233Y|MECOM_ENST00000392736.3_Missense_Mutation_p.N233Y|MECOM_ENST00000494292.1_Missense_Mutation_p.N421Y|MECOM_ENST00000472280.1_Missense_Mutation_p.N234Y	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CTGTGTTTATTTAAGGAAGAC	0.448																																					p.N421Y		Atlas-SNP	.											.	MECOM	216	.	0			c.A1261T						.						440	371	394					3																	168834399		2203	4300	6503	SO:0001583	missense	2122	exon8			GTTTATTTAAGGA	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.697A>T	chr3.hg19:g.168834399T>A	ENSP00000419770:p.Asn233Tyr	140.0	0.0		117.0	41.0	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	hg19	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.372102	0.61624	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243	T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.88	5.88	0.94601	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.64402	D	0.000001	T	0.64649	0.2617	L	0.52266	1.64	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.994;0.999	T	0.66929	-0.5799	10	0.87932	D	0	-22.2034	16.3015	0.82820	0.0:0.0:0.0:1.0	.	421;234;421;298;233	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	Y	298;233;233;234;421;233;233;234	ENSP00000264674:N298Y;ENSP00000376493:N233Y;ENSP00000419770:N233Y;ENSP00000420048:N234Y;ENSP00000417899:N421Y;ENSP00000419995:N233Y;ENSP00000420466:N233Y;ENSP00000394302:N234Y	ENSP00000264674:N298Y	N	-	1	0	MECOM	170317093	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.239000	0.73571	0.533000	0.62120	AAT	.	.		0.448	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		A	168834399	T	A	168834399	3	1	150	1	0	0	0	0	1	0	0	0	9431	1841	64	4	2498	4	MECOM	3	168834399	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	7613292	168834399	29188031	151	22875										
PLD1	5337	hgsc.bcm.edu	37	chr3	171443814	171443814	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttattgcaacttacatgcccTttggtcccaaatcatggatg	7	10	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:171443814T>A	ENST00000351298.4	-	7	785	c.659A>T	c.(658-660)aAg>aTg	p.K220M	PLD1_ENST00000340989.4_Missense_Mutation_p.K220M|PLD1_ENST00000342215.6_Missense_Mutation_p.K220M|PLD1_ENST00000356327.5_Missense_Mutation_p.K220M	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	220	PH.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	TTACATGCCCTTTGGTCCCAA	0.378																																					p.K220M	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.A659T						.						144	133	136					3																	171443814		2203	4300	6503	SO:0001583	missense	5337	exon7			ATGCCCTTTGGTC	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"Pleckstrin homology (PH) domain containing"	9067	protein-coding gene	gene with protein product	"choline phosphatase 1"	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.659A>T	chr3.hg19:g.171443814T>A	ENSP00000342793:p.Lys220Met	82.0	0.0		84.0	21.0	NM_002662		Missense_Mutation	SNP	ENST00000351298.4	hg19	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.360259	0.82353	.	.	ENSG00000075651	ENST00000356327;ENST00000351298;ENST00000342215;ENST00000340989	T;T;T;T	0.39787	2.99;2.97;1.06;2.83	5.38	5.38	0.77491	Pleckstrin homology domain (1);	0.097920	0.64402	D	0.000001	T	0.66157	0.2761	M	0.84948	2.725	0.80722	D	1	D;D	0.69078	0.997;0.988	D;P	0.64687	0.928;0.77	T	0.72161	-0.4374	10	0.62326	D	0.03	-23.0449	14.3768	0.66884	0.0:0.0:0.0:1.0	.	243;220	Q59EA4;Q13393	.;PLD1_HUMAN	M	220	ENSP00000348681:K220M;ENSP00000342793:K220M;ENSP00000339936:K220M;ENSP00000340326:K220M	ENSP00000340326:K220M	K	-	2	0	PLD1	172926508	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.324000	0.72896	2.035000	0.60131	0.528000	0.53228	AAG	.	.		0.378	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		A	171443814	T	A	171443814	3	1	150	1	0	0	0	0	1	0	0	0	12054	1609	56	4	2649	4	PLD1	3	171443814	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2609415	171443814	26578616	152	22876										
EPHB3	2049	hgsc.bcm.edu	37	chr3	184290454	184290454	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcaagttcactgtgcgtgacTgcaacagcatccccaacatc	7	14	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:184290454T>A	ENST00000330394.2	+	3	798	c.346T>A	c.(346-348)Tgc>Agc	p.C116S	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	116	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)	p.C116R(1)		breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TGTGCGTGACTGCAACAGCAT	0.602																																					p.C116S		Atlas-SNP	.											EPHB3,NS,carcinoma,0,1	EPHB3	114	.	1	Substitution - Missense(1)	ovary(1)	c.T346A						.						72	66	68					3																	184290454		2202	4300	6502	SO:0001583	missense	2049	exon3			CGTGACTGCAACA	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3394	protein-coding gene	gene with protein product		601839	"EphB3"	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.346T>A	chr3.hg19:g.184290454T>A	ENSP00000332118:p.Cys116Ser	107.0	0.0		98.0	28.0	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.719374	0.89205	.	.	ENSG00000182580	ENST00000330394	T	0.64991	-0.13	5.53	5.53	0.82687	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.84615	0.5511	H	0.96048	3.76	0.80722	D	1	D	0.69078	0.997	D	0.65573	0.936	D	0.89621	0.3848	10	0.87932	D	0	.	14.8554	0.70332	0.0:0.0:0.0:1.0	.	116	P54753	EPHB3_HUMAN	S	116	ENSP00000332118:C116S	ENSP00000332118:C116S	C	+	1	0	EPHB3	185773148	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.004000	0.88535	2.095000	0.63458	0.533000	0.62120	TGC	.	.		0.602	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		A	184290454	T	A	184290454	3	1	150	1	0	0	0	0	1	0	0	0	5178	1580	55	4	356	4	EPHB3	3	184290454	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	12846640	184290454	13731976	153	22877										
IGF2BP2	10644	hgsc.bcm.edu	37	chr3	185390424	185390424	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgaaaagatgccaagtgcgcTgaggttcaaccctgggatca	12	9	2	3	rs368787882		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:185390424T>A	ENST00000382199.2	-	10	1200	c.1105A>T	c.(1105-1107)Agc>Tgc	p.S369C	IGF2BP2_ENST00000494906.1_Intron|IGF2BP2_ENST00000457616.2_Missense_Mutation_p.S375C|IGF2BP2_ENST00000346192.3_Intron|IGF2BP2_ENST00000421047.2_Missense_Mutation_p.S312C	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	369					anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			CCAAGTGCGCTGAGGTTCAAC	0.582																																					p.S369C		Atlas-SNP	.											.	IGF2BP2	69	.	0			c.A1105T						.						75	66	69					3																	185390424		2203	4300	6503	SO:0001583	missense	10644	exon10			GTGCGCTGAGGTT	BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792		"RNA binding motif (RRM) containing"	28867	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 2"	608289				10190901, 9891060	Standard	NM_001007225		Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.1105A>T	chr3.hg19:g.185390424T>A	ENSP00000371634:p.Ser369Cys	520.0	0.0		429.0	111.0	NM_006548	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Missense_Mutation	SNP	ENST00000382199.2	hg19	CCDS3273.2	.	.	.	.	.	.	.	.	.	.	T	26.7	4.763467	0.89932	.	.	ENSG00000073792	ENST00000382199;ENST00000421047;ENST00000457616	T;T;T	0.49139	2.12;0.79;2.39	5.48	5.48	0.80851	.	0.080944	0.85682	D	0.000000	T	0.54127	0.1839	L	0.40543	1.245	0.53005	D	0.999965	P;D;D;P	0.61697	0.94;0.99;0.983;0.836	P;P;P;P	0.58013	0.753;0.753;0.831;0.571	T	0.54091	-0.8345	10	0.48119	T	0.1	-17.1355	13.3761	0.60739	0.0:0.0:0.0:1.0	.	306;312;375;369	Q9Y6M1-3;Q9Y6M1-4;F8W930;Q9Y6M1	.;.;.;IF2B2_HUMAN	C	369;312;375	ENSP00000371634:S369C;ENSP00000413787:S312C;ENSP00000410242:S375C	ENSP00000371634:S369C	S	-	1	0	IGF2BP2	186873118	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.508000	0.81686	2.210000	0.71456	0.533000	0.62120	AGC	.	.		0.582	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548		A	185390424	T	A	185390424	3	1	150	1	0	0	0	0	1	0	0	0	7583	1580	55	4	722	4	IGF2BP2	3	185390424	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1099970	185390424	12632006	154	22878										
ETV5	2119	hgsc.bcm.edu	37	chr3	185797835	185797835	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	attctgatgggtgggtgagaGgggggttgtaggaggggtta	22	1	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:185797835G>C	ENST00000306376.5	-	7	667	c.421C>G	c.(421-423)Ctc>Gtc	p.L141V	ETV5_ENST00000537818.1_Missense_Mutation_p.L183V|ETV5_ENST00000434744.1_Missense_Mutation_p.L141V|ETV5-AS1_ENST00000453370.1_RNA	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	141					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			GTGGGTGAGAGGGGGGTTGTA	0.547			T	"TMPRSS2, SCL45A3"	Prostate																																p.L141V		Atlas-SNP	.		Dom	yes		3	3q28	2119	ets variant gene 5		E	.	ETV5	106	.	0			c.C421G						.						19	24	22					3																	185797835		2124	4237	6361	SO:0001583	missense	2119	exon7			GTGAGAGGGGGGT	BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"ets-related molecule"	601600	"ets variant gene 5 (ets-related molecule)"			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.421C>G	chr3.hg19:g.185797835G>C	ENSP00000306894:p.Leu141Val	68.0	0.0		91.0	31.0	NM_004454	A6NH46|B7Z7D7|Q6IBN5	Missense_Mutation	SNP	ENST00000306376.5	hg19	CCDS33906.1	.	.	.	.	.	.	.	.	.	.	G	0.213	-1.034972	0.02029	.	.	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818;ENST00000440773	T;T;T;T	0.20881	2.04;2.04;2.04;2.04	5.31	-0.0789	0.13713	PEA3-type ETS-domain transcription factor, N-terminal (1);	1.102340	0.06653	N	0.763155	T	0.07098	0.0180	N	0.03948	-0.315	0.28907	N	0.892938	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.38908	-0.9639	10	0.02654	T	1	.	5.1111	0.14809	0.3394:0.208:0.4527:0.0	.	141;183	P41161;B7Z7D7	ETV5_HUMAN;.	V	141;141;183;141	ENSP00000306894:L141V;ENSP00000413755:L141V;ENSP00000441737:L183V;ENSP00000389707:L141V	ENSP00000306894:L141V	L	-	1	0	ETV5	187280529	0.421000	0.25465	0.994000	0.49952	0.879000	0.50718	0.791000	0.26915	0.218000	0.20820	0.557000	0.71058	CTC	.	.		0.547	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454		C	185797835	G	C	185797835	3	2	150	1	0	0	0	0	1	0	0	0	5284	1000	35	4	1139	4	ETV5	3	185797835	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	407411	185797835	12224595	155	22879										
KNG1	3827	hgsc.bcm.edu	37	chr3	186459911	186459911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgcaactatgatgcctcctAtatcaccagctcccatacag	5	14	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:186459911A>G	ENST00000265023.4	+	10	1938	c.1726A>G	c.(1726-1728)Ata>Gta	p.I576V	RP11-573D15.8_ENST00000609652.1_RNA|RP11-573D15.8_ENST00000609726.1_RNA|RP11-573D15.8_ENST00000596632.1_RNA|KNG1_ENST00000287611.2_Intron|RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000596329.1_RNA|RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000447445.1_Intron	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	576					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		GATGCCTCCTATATCACCAGC	0.458																																					p.I576V		Atlas-SNP	.											.	KNG1	129	.	0			c.A1726G						.						148	140	143					3																	186459911		1979	4153	6132	SO:0001583	missense	3827	exon10			CCTCCTATATCAC		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"Endogenous ligands"	6383	protein-coding gene	gene with protein product	"alpha-2-thiol proteinase inhibitor", "bradykinin"	612358	"kininogen"	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.1726A>G	chr3.hg19:g.186459911A>G	ENSP00000265023:p.Ile576Val	156.0	0.0		118.0	27.0	NM_001102416	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	hg19	CCDS43183.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.646795	0.00111	.	.	ENSG00000113889	ENST00000265023	T	0.12879	2.64	5.42	3.05	0.35203	.	0.983616	0.08274	N	0.970886	T	0.12263	0.0298	L	0.43152	1.355	0.09310	N	0.999999	B	0.06786	0.001	B	0.08055	0.003	T	0.32693	-0.9897	9	.	.	.	-0.004	6.5616	0.22489	0.8145:0.0:0.1855:0.0	.	576	P01042	KNG1_HUMAN	V	576	ENSP00000265023:I576V	.	I	+	1	0	KNG1	187942605	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.201000	0.17276	1.008000	0.39264	0.533000	0.62120	ATA	.	.		0.458	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416		G	186459911	A	G	186459911	3	3	150	1	0	0	0	0	1	0	0	0	8436	449	16	2	1764	2	KNG1	3	186459911	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	662076	186459911	11562519	156	22880										
C3orf21	152002	hgsc.bcm.edu	37	chr3	194877312	194877312	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgaatgatctgcaggatctcTgcgggaaagagaaaaggaca	13	6	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr3:194877312T>A	ENST00000310380.6	-	3	761		c.e3-2		XXYLT1_ENST00000429994.1_Splice_Site|XXYLT1_ENST00000437101.1_Splice_Site|XXYLT1_ENST00000355729.4_Splice_Site	NM_152531.4	NP_689744.3	Q8NBI6	XXLT1_HUMAN	xyloside xylosyltransferase 1							endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring pentosyl groups (GO:0016763)										GCAGGATCTCTGCGGGAAAGA	0.517																																					.		Atlas-SNP	.											.	.	.	.	0			c.653-2A>T						.						77	79	78					3																	194877312		1945	4154	6099	SO:0001630	splice_region_variant	152002	exon4			GATCTCTGCGGGA	AK075551	CCDS43188.1	3q29	2013-02-22	2011-10-19	2011-10-19	ENSG00000173950	ENSG00000173950		"Glycosyltransferase family 8 domain containing"	26639	protein-coding gene	gene with protein product		614552	"chromosome 3 open reading frame 21"	C3orf21		22117070	Standard	NM_152531		Approved	FLJ35155	uc003fum.4	Q8NBI6	OTTHUMG00000155915	ENST00000310380.6:c.653-2A>T	chr3.hg19:g.194877312T>A		83.0	0.0		46.0	11.0	NM_152531	D3DNW5|Q8NAL3|Q8WV03|Q96ME0	Splice_Site	SNP	ENST00000310380.6	hg19	CCDS43188.1	.	.	.	.	.	.	.	.	.	.	T	18.35	3.604786	0.66445	.	.	ENSG00000173950	ENST00000310380;ENST00000437101;ENST00000355729;ENST00000429994;ENST00000458652	.	.	.	5.69	5.69	0.88448	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9022	0.63812	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	C3orf21	196358601	1.000000	0.71417	0.998000	0.56505	0.648000	0.38561	7.450000	0.80656	2.167000	0.68274	0.460000	0.39030	.	.	.		0.517	XXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342290.1	NM_152531	Intron	A	194877312	T	A	194877312	5	1	150	1	0	0	0	0	0	0	1	0	2216	1594	55	4	538	4	C3orf21	3	194877312	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	8417401	194877312	3145118	157	22881										
RGS12	6002	hgsc.bcm.edu	37	chr4	3424630	3424630	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttctggtctctctgttcctcAgcctctggtgctgcaccaag	9	14	5	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:3424630A>T	ENST00000344733.5	+	12	3937		c.e12-1		RGS12_ENST00000508158.1_Splice_Site|RGS12_ENST00000336727.3_Splice_Site|RGS12_ENST00000306648.7_Splice_Site|RGS12_ENST00000382788.3_Splice_Site|RGS12_ENST00000338806.4_Splice_Site|RGS12_ENST00000538395.1_Splice_Site	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12						positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TCTGTTCCTCAGCCTCTGGTG	0.572																																					.		Atlas-SNP	.											.	RGS12	128	.	0			c.3034-2A>T						.						99	90	93					4																	3424630		2203	4300	6503	SO:0001630	splice_region_variant	6002	exon12			TTCCTCAGCCTCT	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"Regulators of G-protein signaling"	9994	protein-coding gene	gene with protein product		602512	"regulator of G-protein signalling 12"			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.3034-1A>T	chr4.hg19:g.3424630A>T		51.0	0.0		24.0	11.0	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Splice_Site	SNP	ENST00000344733.5	hg19	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	A	13.23	2.174218	0.38413	.	.	ENSG00000159788	ENST00000344733;ENST00000336727;ENST00000382788;ENST00000306648;ENST00000338806;ENST00000538395	.	.	.	4.6	3.41	0.39046	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2512	0.37555	0.9131:0.0:0.0869:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RGS12	3394428	1.000000	0.71417	0.355000	0.25773	0.629000	0.37895	8.441000	0.90313	0.622000	0.30249	0.334000	0.21626	.	.	.		0.572	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926	Intron	T	3424630	A	T	3424630	5	4	150	1	0	0	0	0	0	0	1	0	13310	202	7	4	3132	4	RGS12	4	3424630	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		3424630	187729646	158	22882										
STK32B	55351	hgsc.bcm.edu	37	chr4	5500757	5500757	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccaaagcaagctccaggacGggtgcaacaacaacctcctc	8	16	0	0	rs558465928		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:5500757G>C	ENST00000282908.5	+	12	1614	c.1192G>C	c.(1192-1194)Ggg>Cgg	p.G398R	STK32B_ENST00000510398.1_Missense_Mutation_p.G351R|STK32B_ENST00000512636.1_Missense_Mutation_p.G321R|STK32B_ENST00000508728.1_3'UTR	NM_018401.1	NP_060871.1			serine/threonine kinase 32B									p.G398R(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						GCTCCAGGACGGGTGCAACAA	0.632													G|||	1	0.000199681	0	0	5008	,	,		18403	0		0	False		,,,				2504	0.001				p.G398R		Atlas-SNP	.											STK32B,mouth,carcinoma,0,1	STK32B	87	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G1192C						.						167	124	138					4																	5500757		2203	4300	6503	SO:0001583	missense	55351	exon12			CAGGACGGGTGCA	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.1192G>C	chr4.hg19:g.5500757G>C	ENSP00000282908:p.Gly398Arg	301.0	1.0		191.0	67.0	NM_018401		Missense_Mutation	SNP	ENST00000282908.5	hg19	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.826182	0.50739	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.69685	-0.35;-0.07;-0.42	4.97	4.97	0.65823	.	0.000000	0.40818	U	0.001010	T	0.68915	0.3053	M	0.65498	2.005	0.35393	D	0.790908	P	0.50272	0.933	P	0.46718	0.525	T	0.77778	-0.2460	10	0.40728	T	0.16	.	13.7115	0.62672	0.0:0.0:1.0:0.0	.	398	Q9NY57	ST32B_HUMAN	R	398;321;351	ENSP00000282908:G398R;ENSP00000423209:G321R;ENSP00000420984:G351R	ENSP00000282908:G398R	G	+	1	0	STK32B	5551658	0.988000	0.35896	0.815000	0.32552	0.045000	0.14185	4.377000	0.59562	2.293000	0.77203	0.561000	0.74099	GGG	.	.		0.632	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		C	5500757	G	C	5500757	3	2	150	1	0	0	0	0	1	0	0	0	15313	1116	39	4	1238	4	STK32B	4	5500757	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	2076127	5500757	185653519	159	22883										
TBC1D14	57533	hgsc.bcm.edu	37	chr4	6925360	6925360	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acccggagcctgtaccctgcAgcgcggtccacgtgaggagg	15	14	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:6925360A>T	ENST00000409757.4	+	2	368	c.244A>T	c.(244-246)Agc>Tgc	p.S82C	TBC1D14_ENST00000448507.1_Missense_Mutation_p.S82C	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	82					negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						TGTACCCTGCAGCGCGGTCCA	0.657																																					p.S82C		Atlas-SNP	.											.	TBC1D14	110	.	0			c.A244T						.						48	53	51					4																	6925360		2203	4300	6503	SO:0001583	missense	57533	exon2			CCCTGCAGCGCGG	AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405			29246	protein-coding gene	gene with protein product		614855				10718198	Standard	NM_020773		Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.244A>T	chr4.hg19:g.6925360A>T	ENSP00000386921:p.Ser82Cys	171.0	0.0		82.0	39.0	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	hg19	CCDS3394.2	.	.	.	.	.	.	.	.	.	.	A	15.09	2.729911	0.48833	.	.	ENSG00000132405	ENST00000444368;ENST00000448507;ENST00000409757	T;T;T	0.54279	0.58;3.32;3.32	4.83	3.66	0.41972	.	0.306951	0.30244	N	0.010077	T	0.41373	0.1156	L	0.27053	0.805	0.80722	D	1	D	0.57257	0.979	P	0.46975	0.533	T	0.20638	-1.0269	10	0.42905	T	0.14	-11.5914	8.0332	0.30478	0.9092:0.0:0.0908:0.0	.	82	Q9P2M4	TBC14_HUMAN	C	82	ENSP00000414951:S82C;ENSP00000404041:S82C;ENSP00000386921:S82C	ENSP00000386921:S82C	S	+	1	0	TBC1D14	6976261	1.000000	0.71417	0.981000	0.43875	0.180000	0.23129	2.763000	0.47605	0.902000	0.36520	0.533000	0.62120	AGC	.	.		0.657	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773		T	6925360	A	T	6925360	3	4	150	1	0	0	0	0	1	0	0	0	15618	188	7	4	246	4	TBC1D14	4	6925360	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1424603	6925360	184228916	160	22884										
LRRC66	339977	hgsc.bcm.edu	37	chr4	52860981	52860981	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgcccctgagctctcgtccTgcagggactcctcatcaggc	10	16	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:52860981T>A	ENST00000343457.3	-	4	2213	c.2207A>T	c.(2206-2208)cAg>cTg	p.Q736L		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	736						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(8)|lung(34)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	58						GCTCTCGTCCTGCAGGGACTC	0.498																																					p.Q736L		Atlas-SNP	.											.	LRRC66	128	.	0			c.A2207T						.						119	117	118					4																	52860981		2031	4196	6227	SO:0001583	missense	339977	exon4			TCGTCCTGCAGGG	BC040414	CCDS43229.1	4q12	2008-08-08			ENSG00000188993	ENSG00000188993			34299	protein-coding gene	gene with protein product							Standard	XM_005265739		Approved		uc003gzi.3	Q68CR7	OTTHUMG00000160623	ENST00000343457.3:c.2207A>T	chr4.hg19:g.52860981T>A	ENSP00000341944:p.Gln736Leu	77.0	0.0		63.0	23.0	NM_001024611		Missense_Mutation	SNP	ENST00000343457.3	hg19	CCDS43229.1	.	.	.	.	.	.	.	.	.	.	T	12.63	1.996286	0.35226	.	.	ENSG00000188993	ENST00000343457	T	0.28069	1.63	4.21	0.217	0.15264	.	0.950663	0.08711	N	0.904982	T	0.13713	0.0332	N	0.08118	0	0.09310	N	1	P	0.39480	0.675	B	0.36504	0.226	T	0.14282	-1.0478	10	0.56958	D	0.05	-0.677	3.5626	0.07888	0.0:0.2362:0.2099:0.5539	.	736	Q68CR7	LRC66_HUMAN	L	736	ENSP00000341944:Q736L	ENSP00000341944:Q736L	Q	-	2	0	LRRC66	52555738	0.000000	0.05858	0.001000	0.08648	0.329000	0.28539	0.072000	0.14617	-0.029000	0.13827	0.496000	0.49642	CAG	.	.		0.498	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		A	52860981	T	A	52860981	3	1	150	1	0	0	0	0	1	0	0	0	9027	1580	55	4	439	4	LRRC66	4	52860981	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	45935621	52860981	138293295	161	22885										
CENPC1	1060	hgsc.bcm.edu	37	chr4	68357970	68357970	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggatctccaagaggtatacCtagatttaccattaagttag	8	7	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:68357970C>G	ENST00000273853.6	-	16	2693	c.2443G>C	c.(2443-2445)Ggt>Cgt	p.G815R		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	815					chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										AGAGGTATACCTAGATTTACC	0.348																																					p.G815R		Atlas-SNP	.											.	CENPC1	66	.	0			c.G2443C						.						74	63	67					4																	68357970		1820	4076	5896	SO:0001583	missense	1060	exon16			GTATACCTAGATT	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"centromere protein C 1"	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.2443G>C	chr4.hg19:g.68357970C>G	ENSP00000273853:p.Gly815Arg	81.0	0.0		46.0	23.0	NM_001812	Q8IW27|Q9P0M5	Missense_Mutation	SNP	ENST00000273853.6	hg19	CCDS47063.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.673093	0.29693	.	.	ENSG00000145241	ENST00000273853	.	.	.	5.34	2.05	0.26809	Cupin, RmlC-type (1);	0.552784	0.17801	N	0.161570	T	0.11879	0.0289	N	0.08118	0	0.22880	N	0.998615	P	0.34462	0.454	B	0.24006	0.05	T	0.13818	-1.0495	9	0.45353	T	0.12	-9.2474	6.0144	0.19594	0.0:0.3764:0.0:0.6236	.	815	Q03188	CENPC_HUMAN	R	815	.	ENSP00000273853:G815R	G	-	1	0	CENPC1	68040565	0.569000	0.26643	0.679000	0.29978	0.684000	0.39900	0.193000	0.17116	0.566000	0.29273	0.563000	0.77884	GGT	.	.		0.348	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2			G	68357970	C	G	68357970	3	3	150	1	0	0	0	0	1	0	0	0	3231	681	24	4	404	4	CENPC1	4	68357970	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	15496989	68357970	122796306	162	22886										
NPFFR2	10886	hgsc.bcm.edu	37	chr4	72994540	72994540	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgaggaacaaacatatgcacAcagtcactaatctcttcatc	5	11	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:72994540A>G	ENST00000308744.6	+	2	636	c.538A>G	c.(538-540)Aca>Gca	p.T180A	NPFFR2_ENST00000358749.3_Missense_Mutation_p.T78A|NPFFR2_ENST00000344413.5_Intron|NPFFR2_ENST00000395999.1_Missense_Mutation_p.T81A	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	180					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			ACATATGCACACAGTCACTAA	0.368																																					p.T180A		Atlas-SNP	.											.	NPFFR2	98	.	0			c.A538G						.						192	179	184					4																	72994540		2203	4300	6503	SO:0001583	missense	10886	exon2			ATGCACACAGTCA	AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"GPCR / Class A :  Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors"	4525	protein-coding gene	gene with protein product	"neuropeptide FF 2"	607449	"G protein-coupled receptor 74"	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.538A>G	chr4.hg19:g.72994540A>G	ENSP00000307822:p.Thr180Ala	132.0	0.0		47.0	18.0	NM_004885	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	hg19	CCDS3551.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.674499	0.88445	.	.	ENSG00000056291	ENST00000308744;ENST00000395999;ENST00000358749	T;T;T	0.45668	0.89;0.89;0.89	5.9	5.9	0.94986	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000052	T	0.76579	0.4007	H	0.96576	3.845	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.77557	0.975;0.99	D	0.85000	0.0899	10	0.87932	D	0	.	15.9936	0.80225	1.0:0.0:0.0:0.0	.	81;180	Q9Y5X5-3;Q9Y5X5	.;NPFF2_HUMAN	A	180;81;78	ENSP00000307822:T180A;ENSP00000379321:T81A;ENSP00000351599:T78A	ENSP00000307822:T180A	T	+	1	0	NPFFR2	73213404	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.163000	0.94750	2.251000	0.74343	0.528000	0.53228	ACA	.	.		0.368	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		G	72994540	A	G	72994540	3	3	150	1	0	0	0	0	1	0	0	0	10587	159	6	2	550	2	NPFFR2	4	72994540	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	4636570	72994540	118159736	163	22887										
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73181644	73181644	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttacaaaagtagggattatcAggatggctacaccacagctg	10	8	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:73181644A>T	ENST00000286657.4	-	11	1566	c.1530T>A	c.(1528-1530)ccT>ccA	p.P510P		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	510	Disintegrin.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGGGATTATCAGGATGGCTAC	0.403																																					p.P510P	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											.	ADAMTS3	164	.	0			c.T1530A						.						100	95	96					4																	73181644		2203	4300	6503	SO:0001819	synonymous_variant	9508	exon11			ATTATCAGGATGG	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.1530T>A	chr4.hg19:g.73181644A>T		153.0	0.0		88.0	30.0	NM_014243	A1L3U9|Q9BXZ8	Silent	SNP	ENST00000286657.4	hg19	CCDS3553.1																																																																																			.	.		0.403	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			T	73181644	A	T	73181644	2	4	150	1	0	0	0	0	0	0	0	1	267	175	7	4		4	ADAMTS3	4	73181644	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	187104	73181644	117972632	164	22888										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79366793	79366793	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgaaagcattgagccaacccAtgatatttttagtttttatg	7	6	0	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:79366793A>G	ENST00000325942.6	+	42	6223	c.5783A>G	c.(5782-5784)cAt>cGt	p.H1928R	FRAS1_ENST00000264895.6_Missense_Mutation_p.H1928R	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1928					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GAGCCAACCCATGATATTTTT	0.388																																					p.H1928R		Atlas-SNP	.											.	FRAS1	779	.	0			c.A5783G						.						219	217	218					4																	79366793		1881	4109	5990	SO:0001583	missense	80144	exon42			CAACCCATGATAT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.5783A>G	chr4.hg19:g.79366793A>G	ENSP00000326330:p.His1928Arg	103.0	0.0		52.0	20.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.320684	0.41096	.	.	ENSG00000138759	ENST00000325942;ENST00000264895	T;T	0.28255	1.62;1.62	5.96	4.59	0.56863	.	0.442701	0.26746	N	0.022703	T	0.20820	0.0501	L	0.51422	1.61	0.80722	D	1	P;B	0.36086	0.536;0.384	B;B	0.30401	0.115;0.096	T	0.08617	-1.0713	10	0.33940	T	0.23	.	3.3313	0.07085	0.6348:0.0:0.1739:0.1913	.	1928;1928	E9PHH6;A2RRR8	.;.	R	1928	ENSP00000326330:H1928R;ENSP00000264895:H1928R	ENSP00000264895:H1928R	H	+	2	0	FRAS1	79585817	0.896000	0.30565	0.999000	0.59377	0.992000	0.81027	2.664000	0.46783	2.283000	0.76528	0.477000	0.44152	CAT	.	.		0.388	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			G	79366793	A	G	79366793	3	3	150	1	0	0	0	0	1	0	0	0	6050	217	8	2	5949	2	FRAS1	4	79366793	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	6185149	79366793	111787483	165	22889										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79455718	79455718	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgttcctaatggatcccaatAcatctgatatgtcactagca	6	10	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:79455718A>T	ENST00000264895.6	+	71	11481	c.11041A>T	c.(11041-11043)Aca>Tca	p.T3681S		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3677					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GGATCCCAATACATCTGATAT	0.448																																					p.T3681S		Atlas-SNP	.											.	FRAS1	779	.	0			c.A11041T						.						123	110	114					4																	79455718		1893	4119	6012	SO:0001583	missense	80144	exon71			CCCAATACATCTG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11041A>T	chr4.hg19:g.79455718A>T	ENSP00000264895:p.Thr3681Ser	75.0	0.0		42.0	17.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.998|6.998	0.554236|0.554236	0.13374|0.13374	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000264895|ENST00000512123	T|.	0.11063|.	2.81|.	5.05|5.05	3.84|3.84	0.44239|0.44239	.|.	0.217790|.	0.37955|.	N|.	0.001868|.	T|T	0.46852|0.46852	0.1414|0.1414	N|N	0.19112|0.19112	0.55|0.55	0.58432|0.58432	D|D	0.999999|0.999999	P|.	0.46064|.	0.872|.	B|.	0.37731|.	0.257|.	T|T	0.27536|0.27536	-1.0071|-1.0071	10|5	0.22706|.	T|.	0.39|.	.|.	11.9167|11.9167	0.52769|0.52769	0.8541:0.1459:0.0:0.0|0.8541:0.1459:0.0:0.0	.|.	3681|.	E9PHH6|.	.|.	S|F	3681|1909	ENSP00000264895:T3681S|.	ENSP00000264895:T3681S|.	T|Y	+|+	1|2	0|0	FRAS1|FRAS1	79674742|79674742	1.000000|1.000000	0.71417|0.71417	0.879000|0.879000	0.34478|0.34478	0.648000|0.648000	0.38561|0.38561	3.893000|3.893000	0.56243|0.56243	0.741000|0.741000	0.32674|0.32674	0.482000|0.482000	0.46254|0.46254	ACA|TAC	.	.		0.448	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79455718	A	T	79455718	3	4	150	1	0	0	0	0	1	0	0	0	6050	391	14	4	11398	4	FRAS1	4	79455718	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	88925	79455718	111698558	166	22890										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87638220	87638220	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggtttgaatccagcagtggTctcccaggggtagatgaaac	13	8	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:87638220T>A	ENST00000411767.2	+	9	1398	c.1335T>A	c.(1333-1335)ggT>ggA	p.G445G	PTPN13_ENST00000427191.2_Silent_p.G445G|PTPN13_ENST00000316707.6_Silent_p.G445G|PTPN13_ENST00000511467.1_Silent_p.G445G|PTPN13_ENST00000436978.1_Silent_p.G445G			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	445					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CCAGCAGTGGTCTCCCAGGGG	0.403																																					p.G445G		Atlas-SNP	.											.	PTPN13	203	.	0			c.T1335A						.						68	68	68					4																	87638220		1849	4102	5951	SO:0001819	synonymous_variant	5783	exon9			CAGTGGTCTCCCA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.1335T>A	chr4.hg19:g.87638220T>A		78.0	0.0		48.0	22.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	hg19	CCDS47094.1																																																																																			.	.		0.403	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87638220	T	A	87638220	2	1	150	1	0	0	0	0	0	0	0	1	12795	1654	58	4		4	PTPN13	4	87638220	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	8182502	87638220	103516056	167	22891										
FAM190A	401145	hgsc.bcm.edu	37	chr4	92519745	92519745	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tacatatcgaaatcgaattgTgagccaaaatctcagcacaa	6	9	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:92519745T>A	ENST00000509176.1	+	11	2528	c.2240T>A	c.(2239-2241)gTg>gAg	p.V747E	CCSER1_ENST00000333691.8_Missense_Mutation_p.V747E	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	747																	AATCGAATTGTGAGCCAAAAT	0.398																																					p.V747E		Atlas-SNP	.											.	.	.	.	0			c.T2240A						.						46	40	42					4																	92519745		692	1591	2283	SO:0001583	missense	401145	exon11			GAATTGTGAGCCA		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.2240T>A	chr4.hg19:g.92519745T>A	ENSP00000425040:p.Val747Glu	175.0	0.0		118.0	48.0	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	hg19	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	T	15.63	2.889566	0.52014	.	.	ENSG00000184305	ENST00000509176;ENST00000333691	T;T	0.35236	1.32;1.32	5.77	4.59	0.56863	.	.	.	.	.	T	0.24122	0.0584	N	0.08118	0	0.26559	N	0.973771	D	0.55385	0.971	P	0.46917	0.531	T	0.04165	-1.0972	9	0.56958	D	0.05	-2.186	8.4929	0.33110	0.0:0.1502:0.0:0.8498	.	747	Q9C0I3	F190A_HUMAN	E	747	ENSP00000425040:V747E;ENSP00000329482:V747E	ENSP00000329482:V747E	V	+	2	0	FAM190A	92738768	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.797000	0.26999	1.126000	0.42016	0.528000	0.53228	GTG	.	.		0.398	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		A	92519745	T	A	92519745	3	1	150	1	0	0	0	0	1	0	0	0	5526	1696	59	4	2306	4	FAM190A	4	92519745	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4881525	92519745	98634531	168	22892										
CENPE	1062	hgsc.bcm.edu	37	chr4	104061192	104061192	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgactcatattgacatcttcTttcactctaagcagttgaag	6	9	5	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:104061192T>A	ENST00000265148.3	-	38	6047	c.5958A>T	c.(5956-5958)aaA>aaT	p.K1986N	CENPE_ENST00000380026.3_Intron	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1986					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TGACATCTTCTTTCACTCTAA	0.323																																					p.K1986N		Atlas-SNP	.											.	CENPE	253	.	0			c.A5958T						.						101	76	85					4																	104061192		2203	4299	6502	SO:0001583	missense	1062	exon38			ATCTTCTTTCACT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.5958A>T	chr4.hg19:g.104061192T>A	ENSP00000265148:p.Lys1986Asn	94.0	0.0		59.0	22.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	T	10.32	1.317374	0.23908	.	.	ENSG00000138778	ENST00000265148;ENST00000394771	T	0.71461	-0.57	4.92	-0.369	0.12534	.	.	.	.	.	T	0.74596	0.3737	M	0.62723	1.935	0.09310	N	1	D	0.76494	0.999	D	0.64144	0.922	T	0.61317	-0.7087	9	0.44086	T	0.13	.	3.7279	0.08481	0.1531:0.2574:0.0:0.5895	.	1986	Q02224	CENPE_HUMAN	N	1986	ENSP00000265148:K1986N	ENSP00000265148:K1986N	K	-	3	2	CENPE	104280641	0.001000	0.12720	0.001000	0.08648	0.017000	0.09413	0.050000	0.14120	-0.294000	0.08973	0.523000	0.50628	AAA	.	.		0.323	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104061192	T	A	104061192	3	1	150	1	0	0	0	0	1	0	0	0	3232	1606	56	4	2195	4	CENPE	4	104061192	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	11541447	104061192	87093084	169	22893										
TACR3	6870	hgsc.bcm.edu	37	chr4	104511135	104511135	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acaccagcgaaatgctctctTgaagccagctcgaaatctga	8	12	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:104511135T>A	ENST00000304883.2	-	5	1242	c.1102A>T	c.(1102-1104)Aag>Tag	p.K368*	RP11-297P16.3_ENST00000502936.1_RNA|RP11-297P16.3_ENST00000512401.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	368					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		AATGCTCTCTTGAAGCCAGCT	0.428																																					p.K368X		Atlas-SNP	.											TACR3,rectum,carcinoma,+1,1	TACR3	102	.	0			c.A1102T						.						65	64	64					4																	104511135		2203	4300	6503	SO:0001587	stop_gained	6870	exon5			CTCTCTTGAAGCC	M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"GPCR / Class A : Tachykinin receptors"	11528	protein-coding gene	gene with protein product	"neurokinin beta receptor"	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.1102A>T	chr4.hg19:g.104511135T>A	ENSP00000303325:p.Lys368*	109.0	0.0		72.0	29.0	NM_001059	Q0P510	Nonsense_Mutation	SNP	ENST00000304883.2	hg19	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	T	39	7.694338	0.98438	.	.	ENSG00000169836	ENST00000304883	.	.	.	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3584	0.74448	0.0:0.0:0.0:1.0	.	.	.	.	X	368	.	ENSP00000303325:K368X	K	-	1	0	TACR3	104730584	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.565000	0.82337	2.217000	0.71921	0.482000	0.46254	AAG	.	.		0.428	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		A	104511135	T	A	104511135	4	1	150	1	0	0	0	0	0	1	0	0	15522	1821	63	4	299	4	TACR3	4	104511135	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	449943	104511135	86643141	170	22894										
EGF	1950	hgsc.bcm.edu	37	chr4	110915949	110915949	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctattccgtaagaaatagtgActctgaatgtcccctgtccc	7	12	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:110915949A>C	ENST00000265171.5	+	20	3363	c.2918A>C	c.(2917-2919)gAc>gCc	p.D973A	RNU6-35P_ENST00000384530.1_RNA|EGF_ENST00000509793.1_Missense_Mutation_p.D931A|EGF_ENST00000503392.1_Missense_Mutation_p.D932A	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	973	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.				activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	AGAAATAGTGACTCTGAATGT	0.443																																					p.D973A		Atlas-SNP	.											.	EGF	113	.	0			c.A2918C						.						167	143	151					4																	110915949		2203	4300	6503	SO:0001583	missense	1950	exon20			ATAGTGACTCTGA	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.2918A>C	chr4.hg19:g.110915949A>C	ENSP00000265171:p.Asp973Ala	70.0	0.0		54.0	16.0	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	hg19	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	A	6.701	0.497961	0.12762	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.87571	-2.27;-2.18;-2.19	5.35	-3.14	0.05250	Epidermal growth factor-like, type 3 (1);	1.123320	0.06488	N	0.734176	T	0.74869	0.3773	L	0.27053	0.805	0.09310	N	1	B;B;B	0.15141	0.012;0.003;0.012	B;B;B	0.10450	0.002;0.005;0.002	T	0.57539	-0.7794	10	0.16896	T	0.51	.	6.0503	0.19783	0.3294:0.2157:0.0:0.4549	.	932;931;973	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	A	931;973;932	ENSP00000424316:D931A;ENSP00000265171:D973A;ENSP00000421384:D932A	ENSP00000265171:D973A	D	+	2	0	EGF	111135398	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.733000	0.04898	-0.012000	0.14223	0.533000	0.62120	GAC	.	.		0.443	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			C	110915949	A	C	110915949	3	2	150	1	0	0	0	0	1	0	0	0	4964	275	10	5	2996	5	EGF	4	110915949	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	6404814	110915949	80238327	171	22895										
PDE5A	8654	hgsc.bcm.edu	37	chr4	120463621	120463621	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaacttcacccacctccaatGtgaccatttgcttggccatg	6	14	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:120463621G>T	ENST00000354960.3	-	10	1884	c.1565C>A	c.(1564-1566)aCa>aAa	p.T522K	PDE5A_ENST00000264805.5_Missense_Mutation_p.T480K|PDE5A_ENST00000394439.1_Missense_Mutation_p.T470K|RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000512739.1_5'UTR	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	522					blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	CACCTCCAATGTGACCATTTG	0.478																																					p.T522K		Atlas-SNP	.											.	PDE5A	83	.	0			c.C1565A						.						133	118	123					4																	120463621		2203	4300	6503	SO:0001583	missense	8654	exon10			TCCAATGTGACCA	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1565C>A	chr4.hg19:g.120463621G>T	ENSP00000347046:p.Thr522Lys	145.0	0.0		87.0	29.0	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	hg19	CCDS3713.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.796566	0.90453	.	.	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	T;T;T	0.54675	0.56;0.56;0.56	5.11	5.11	0.69529	.	0.172780	0.53938	D	0.000060	T	0.71341	0.3328	M	0.78049	2.395	0.80722	D	1	D;D	0.54601	0.967;0.967	P;P	0.59115	0.852;0.799	T	0.75528	-0.3286	10	0.72032	D	0.01	.	18.8992	0.92435	0.0:0.0:1.0:0.0	.	522;480	O76074;O76074-2	PDE5A_HUMAN;.	K	522;470;480	ENSP00000347046:T522K;ENSP00000377957:T470K;ENSP00000264805:T480K	ENSP00000264805:T480K	T	-	2	0	PDE5A	120683069	1.000000	0.71417	0.942000	0.38095	0.899000	0.52679	9.789000	0.99068	2.549000	0.85964	0.650000	0.86243	ACA	.	.		0.478	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		T	120463621	G	T	120463621	3	4	150	1	0	0	0	0	1	0	0	0	11653	1377	48	3	1110	3	PDE5A	4	120463621	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	9547672	120463621	70690655	172	22896										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123246433	123246433	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccagaaatccgtgtggatgcAgcatctcctggacctagagt	11	11	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:123246433A>T	ENST00000264501.4	+	65	11326	c.10953A>T	c.(10951-10953)gcA>gcT	p.A3651A	KIAA1109_ENST00000455637.1_Silent_p.A3651A|KIAA1109_ENST00000388738.3_Silent_p.A3651A			Q2LD37	K1109_HUMAN	KIAA1109	3651					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GTGTGGATGCAGCATCTCCTG	0.323																																					p.A3651A		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A10953T						.						76	78	78					4																	123246433		1813	4073	5886	SO:0001819	synonymous_variant	84162	exon63			GGATGCAGCATCT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.10953A>T	chr4.hg19:g.123246433A>T		377.0	1.0		255.0	102.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.27|11.27	1.590646|1.590646	0.28357|0.28357	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000306802|ENST00000419325	.|.	.|.	.|.	5.93|5.93	3.4|3.4	0.38934|0.38934	.|.	.|.	.|.	.|.	.|.	T|T	0.55721|0.55721	0.1938|0.1938	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.47446|0.47446	-0.9117|-0.9117	4|4	.|.	.|.	.|.	.|.	7.1251|7.1251	0.25467|0.25467	0.5173:0.1176:0.0:0.3651|0.5173:0.1176:0.0:0.3651	.|.	.|.	.|.	.|.	L|C	41|1609	.|.	.|.	Q|S	+|+	2|1	0|0	KIAA1109|KIAA1109	123465883|123465883	0.993000|0.993000	0.37304|0.37304	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	0.380000|0.380000	0.20602|0.20602	0.440000|0.440000	0.26502|0.26502	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.323	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123246433	A	T	123246433	2	4	150	1	0	0	0	0	0	0	0	1	8217	175	7	4		4	KIAA1109	4	123246433	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2782812	123246433	67907843	173	22897										
FAT4	79633	hgsc.bcm.edu	37	chr4	126370737	126370737	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	attctgggtggactgtaagtAcagatgtcacaatatttgtg	11	5	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:126370737A>T	ENST00000394329.3	+	9	8579	c.8566A>T	c.(8566-8568)Aca>Tca	p.T2856S	FAT4_ENST00000335110.5_Missense_Mutation_p.T1154S	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2856	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GACTGTAAGTACAGATGTCAC	0.408																																					p.T2856S		Atlas-SNP	.											.	FAT4	1752	.	0			c.A8566T						.						85	82	83					4																	126370737		2203	4300	6503	SO:0001583	missense	79633	exon9			GTAAGTACAGATG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.8566A>T	chr4.hg19:g.126370737A>T	ENSP00000377862:p.Thr2856Ser	106.0	0.0		75.0	25.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	20.6	4.009869	0.75046	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01685	4.69;4.69	5.51	5.51	0.81932	Cadherin (4);Cadherin-like (1);	0.000000	0.35235	U	0.003348	T	0.06962	0.0177	L	0.41492	1.28	0.58432	D	0.999999	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.87578	0.987;0.998;0.994	T	0.31779	-0.9931	10	0.59425	D	0.04	.	15.924	0.79597	1.0:0.0:0.0:0.0	.	1154;2856;2856	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	S	2856;1154	ENSP00000377862:T2856S;ENSP00000335169:T1154S	ENSP00000335169:T1154S	T	+	1	0	FAT4	126590187	1.000000	0.71417	0.997000	0.53966	0.861000	0.49209	9.097000	0.94193	2.217000	0.71921	0.533000	0.62120	ACA	.	.		0.408	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126370737	A	T	126370737	3	4	150	1	0	0	0	0	1	0	0	0	5700	391	14	4	8600	4	FAT4	4	126370737	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3124304	126370737	64783539	174	22898										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155156250	155156250	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctctctcttctgaactgtcTggggtaacacattattttga	7	10	4	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:155156250T>A	ENST00000357232.4	-	25	8188	c.8189A>T	c.(8188-8190)cAg>cTg	p.Q2730L		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2730					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CTGAACTGTCTGGGGTAACAC	0.483																																					p.Q2730L		Atlas-SNP	.											.	DCHS2	594	.	0			c.A8189T						.						78	63	68					4																	155156250		2203	4300	6503	SO:0001583	missense	54798	exon25			ACTGTCTGGGGTA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.8189A>T	chr4.hg19:g.155156250T>A	ENSP00000349768:p.Gln2730Leu	94.0	0.0		64.0	28.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.492591	0.64074	.	.	ENSG00000197410	ENST00000357232	T	0.54675	0.56	5.94	-1.1	0.09872	.	0.396151	0.23844	N	0.044018	T	0.26738	0.0654	N	0.20766	0.605	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.17077	-1.0381	10	0.11182	T	0.66	.	4.9814	0.14166	0.1087:0.0601:0.3403:0.491	.	2730	Q6V1P9	PCD23_HUMAN	L	2730	ENSP00000349768:Q2730L	ENSP00000349768:Q2730L	Q	-	2	0	DCHS2	155375700	0.006000	0.16342	0.000000	0.03702	0.419000	0.31324	0.630000	0.24553	-0.363000	0.08101	-0.385000	0.06624	CAG	.	.		0.483	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155156250	T	A	155156250	3	1	150	1	0	0	0	0	1	0	0	0	4290	1580	55	4	565	4	DCHS2	4	155156250	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	28785513	155156250	35998026	175	22899										
ETFDH	2110	hgsc.bcm.edu	37	chr4	159603531	159603531	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctctcaggggcttgccttgaTccaggtgcttttaaagaact	10	10	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:159603531T>G	ENST00000511912.1	+	3	692	c.360T>G	c.(358-360)gaT>gaG	p.D120E	ETFDH_ENST00000307738.5_Missense_Mutation_p.D73E	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	120					cellular metabolic process (GO:0044237)|electron transport chain (GO:0022900)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, oxidizing metal ions with flavin as acceptor (GO:0043783)|quinone binding (GO:0048038)|ubiquinone binding (GO:0048039)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|prostate(1)|skin(3)	28	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		CTTGCCTTGATCCAGGTGCTT	0.413																																					p.D120E		Atlas-SNP	.											.	ETFDH	57	.	0			c.T360G						.						101	108	106					4																	159603531		2203	4300	6503	SO:0001583	missense	2110	exon3			CCTTGATCCAGGT	S69232	CCDS3800.1, CCDS64090.1	4q32-q35	2008-08-26			ENSG00000171503	ENSG00000171503			3483	protein-coding gene	gene with protein product		231675					Standard	NM_004453		Approved	ETFQO	uc003iqb.3	Q16134	OTTHUMG00000161684	ENST00000511912.1:c.360T>G	chr4.hg19:g.159603531T>G	ENSP00000426638:p.Asp120Glu	80.0	0.0		56.0	16.0	NM_004453	B4E3R9|J3KND9|Q7Z347	Missense_Mutation	SNP	ENST00000511912.1	hg19	CCDS3800.1	.	.	.	.	.	.	.	.	.	.	T	9.899	1.206361	0.22205	.	.	ENSG00000171503	ENST00000511912;ENST00000307738	D;D	0.95482	-3.72;-3.72	5.78	-11.0	0.00169	.	0.093945	0.64402	N	0.000001	T	0.78947	0.4364	N	0.05330	-0.07	0.41941	D	0.990614	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.003	T	0.70066	-0.4974	10	0.02654	T	1	0.2788	5.1954	0.15233	0.2346:0.4952:0.135:0.1352	.	73;59;120	B4E3R9;B4DEQ0;Q16134	.;.;ETFD_HUMAN	E	120;73	ENSP00000426638:D120E;ENSP00000303552:D73E	ENSP00000303552:D73E	D	+	3	2	ETFDH	159822981	1.000000	0.71417	0.010000	0.14722	0.794000	0.44872	0.659000	0.24994	-1.503000	0.01812	0.460000	0.39030	GAT	.	.		0.413	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2			G	159603531	T	G	159603531	3	3	150	1	0	0	0	0	1	0	0	0	5273	1432	50	5	370	5	ETFDH	4	159603531	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4447281	159603531	31550745	176	22900										
TRIM60	166655	hgsc.bcm.edu	37	chr4	165962511	165962511	+	Frame_Shift_Del	DEL	T	T	-													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgggtgatctttccttttaTaatatgaatgataggtctat							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:165962511delT	ENST00000512596.1	+	3	1503	c.1287delT	c.(1285-1287)tatfs	p.Y429fs	TRIM60_ENST00000341062.5_Frame_Shift_Del_p.Y429fs|TRIM60_ENST00000508504.1_Frame_Shift_Del_p.Y429fs	NM_152620.2	NP_689833.1	Q495X7	TRI60_HUMAN	tripartite motif containing 60	429	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	29	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0844)		TTTCCTTTTATAATATGAATG	0.368																																					p.Y429fs		Atlas-Indel,Pindel	.											.	TRIM60	73	.	0			c.1286delA						.						74	81	78					4																	165962511		2203	4300	6503	SO:0001589	frameshift_variant	166655	exon3			.	AK093201	CCDS3808.1	4q32.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000176979	ENSG00000176979		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21162	protein-coding gene	gene with protein product			"ring finger protein 129", "tripartite motif-containing 60"	RNF129, RNF33			Standard	NM_152620		Approved	FLJ35882	uc003iqy.1	Q495X7	OTTHUMG00000161262	ENST00000512596.1:c.1287delT	chr4.hg19:g.165962511delT	ENSP00000421142:p.Tyr429fs	97.0	0.0		71.0	30.0	NM_152620	Q8NA35	Frame_Shift_Del	DEL	ENST00000512596.1	hg19	CCDS3808.1																																																																																			.	.		0.368	TRIM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364325.1	NM_152620		-	165962511	T	-	165962511	7	5	150	1	0	1	0	1	0	0	0	0	16550	1413	49	0	1289	0	TRIM60	4	165962511	Frame_Shift_Del	DEL	T	TCGA-DD-AAC8-01A-11D-A40R-10	6358980	165962511	25191765	177	22901										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169369824	169369824	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	attcatagtagaaggctataTtctttaacaattgctcatca	5	7	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr4:169369824T>C	ENST00000511577.1	-	9	1350	c.1103A>G	c.(1102-1104)aAt>aGt	p.N368S	DDX60L_ENST00000260184.7_Missense_Mutation_p.N368S|DDX60L_ENST00000505890.1_Missense_Mutation_p.N368S			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	368							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		GAAGGCTATATTCTTTAACAA	0.279																																					p.N368S		Atlas-SNP	.											.	DDX60L	116	.	0			c.A1103G						.						49	46	47					4																	169369824		1819	4074	5893	SO:0001583	missense	91351	exon9			GCTATATTCTTTA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.1103A>G	chr4.hg19:g.169369824T>C	ENSP00000422423:p.Asn368Ser	361.0	0.0		228.0	82.0	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	hg19		.	.	.	.	.	.	.	.	.	.	T	9.678	1.148510	0.21288	.	.	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.25912	1.77;1.77;1.79;2.44	2.55	2.55	0.30701	.	0.187799	0.24856	U	0.035060	T	0.32406	0.0828	L	0.55481	1.735	0.09310	N	1	D;D;D	0.69078	0.995;0.997;0.995	P;P;P	0.55965	0.788;0.788;0.788	T	0.07009	-1.0795	10	0.26408	T	0.33	.	8.0632	0.30646	0.0:0.0:0.0:1.0	.	368;368;368	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	S	368;368;368;96	ENSP00000260184:N368S;ENSP00000422423:N368S;ENSP00000422202:N368S;ENSP00000421026:N96S	ENSP00000260184:N368S	N	-	2	0	DDX60L	169606399	1.000000	0.71417	0.085000	0.20634	0.176000	0.22953	3.581000	0.53914	1.147000	0.42369	0.383000	0.25322	AAT	.	.		0.279	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		C	169369824	T	C	169369824	3	2	150	1	0	0	0	0	1	0	0	0	4381	1493	52	2	4137	2	DDX60L	4	169369824	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3407313	169369824	21784452	178	22902										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13920675	13920675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgctagagtcaagtagtccgTaggttcctttagggttttca	11	7	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:13920675T>C	ENST00000265104.4	-	6	816	c.712A>G	c.(712-714)Acg>Gcg	p.T238A		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	238	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AAGTAGTCCGTAGGTTCCTTT	0.348									Kartagener syndrome																												p.T238A		Atlas-SNP	.											.	DNAH5	868	.	0			c.A712G						.						163	158	160					5																	13920675		2203	4300	6503	SO:0001583	missense	1767	exon6	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGTCCGTAGGTTC	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.712A>G	chr5.hg19:g.13920675T>C	ENSP00000265104:p.Thr238Ala	130.0	0.0		149.0	37.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	.	0.015	-1.552610	0.00918	.	.	ENSG00000039139	ENST00000265104	T	0.21543	2.0	6.07	-3.1	0.05315	.	1.385200	0.03796	N	0.263676	T	0.09468	0.0233	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31336	-0.9947	10	0.08837	T	0.75	.	8.1826	0.31319	0.1835:0.4598:0.0:0.3567	.	238	Q8TE73	DYH5_HUMAN	A	238	ENSP00000265104:T238A	ENSP00000265104:T238A	T	-	1	0	DNAH5	13973675	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-0.199000	0.09491	-0.269000	0.09298	-0.899000	0.02877	ACG	.	.		0.348	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13920675	T	C	13920675	3	2	150	1	0	0	0	0	1	0	0	0	4606	1638	57	2	13458	2	DNAH5	5	13920675	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10		13920675	166994585	179	22903										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13928204	13928204	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcacatcaaattcagataccTgtttctgcttcctccacatc	3	14	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:13928204T>A	ENST00000265104.4	-	3	380	c.276A>T	c.(274-276)acA>acT	p.T92T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	92	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TTCAGATACCTGTTTCTGCTT	0.388									Kartagener syndrome																												p.T92T		Atlas-SNP	.											.	DNAH5	868	.	0			c.A276T						.						107	105	106					5																	13928204		2203	4300	6503	SO:0001630	splice_region_variant	1767	exon3	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GATACCTGTTTCT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.277+1A>T	chr5.hg19:g.13928204T>A		71.0	0.0		104.0	25.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	hg19	CCDS3882.1																																																																																			.	.		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	Silent	A	13928204	T	A	13928204	5	1	150	1	0	0	0	0	0	0	1	0	4606	1594	55	4	13906	4	DNAH5	5	13928204	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	7529	13928204	166987056	180	22904										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13931352	13931352	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccttctctcccttcagtcttTgctaaaagaaaagaataaaa	4	10	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:13931352T>A	ENST00000265104.4	-	2	163	c.59A>T	c.(58-60)cAa>cTa	p.Q20L		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	20	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTTCAGTCTTTGCTAAAAGAA	0.373									Kartagener syndrome																												p.Q20L		Atlas-SNP	.											.	DNAH5	868	.	0			c.A59T						.						73	75	74					5																	13931352		2203	4300	6503	SO:0001630	splice_region_variant	1767	exon2	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGTCTTTGCTAAA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.58-1A>T	chr5.hg19:g.13931352T>A		95.0	0.0		94.0	21.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.496828	0.64186	.	.	ENSG00000039139	ENST00000265104	T	0.24723	1.84	5.6	5.6	0.85130	.	0.053610	0.85682	D	0.000000	T	0.32912	0.0845	M	0.76574	2.34	0.80722	D	1	P	0.34546	0.456	B	0.33521	0.165	T	0.13469	-1.0508	10	0.49607	T	0.09	.	15.7445	0.77929	0.0:0.0:0.0:1.0	.	20	Q8TE73	DYH5_HUMAN	L	20	ENSP00000265104:Q20L	ENSP00000265104:Q20L	Q	-	2	0	DNAH5	13984352	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.021000	0.76425	2.257000	0.74773	0.528000	0.53228	CAA	.	.		0.373	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	Missense_Mutation	A	13931352	T	A	13931352	5	1	150	1	0	0	0	0	0	0	1	0	4606	1826	63	4	14127	4	DNAH5	5	13931352	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3148	13931352	166983908	181	22905										
FBXL7	23194	hgsc.bcm.edu	37	chr5	15936796	15936796	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggtgatctactgcgcctccaTcaaggagctgagcgtcagcg	13	12	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:15936796T>A	ENST00000504595.1	+	4	1458	c.977T>A	c.(976-978)aTc>aAc	p.I326N	FBXL7_ENST00000329673.7_Missense_Mutation_p.I314N|FBXL7_ENST00000510662.1_Missense_Mutation_p.I279N|MIR887_ENST00000401258.1_RNA	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	326					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						TGCGCCTCCATCAAGGAGCTG	0.672																																					p.I326N		Atlas-SNP	.											.	FBXL7	138	.	0			c.T977A						.						27	30	29					5																	15936796		2185	4272	6457	SO:0001583	missense	23194	exon4			CCTCCATCAAGGA	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.977T>A	chr5.hg19:g.15936796T>A	ENSP00000423630:p.Ile326Asn	49.0	0.0		59.0	10.0	NM_012304	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	hg19	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.862352	0.71949	.	.	ENSG00000183580	ENST00000504595;ENST00000510662;ENST00000329673	T;T;T	0.56611	0.45;0.45;0.45	5.37	5.37	0.77165	.	0.098474	0.64402	D	0.000001	T	0.53834	0.1821	M	0.67569	2.06	0.58432	D	0.999997	P	0.49559	0.925	B	0.41666	0.363	T	0.63051	-0.6723	10	0.87932	D	0	.	15.3717	0.74570	0.0:0.0:0.0:1.0	.	326	Q9UJT9	FBXL7_HUMAN	N	326;279;314	ENSP00000423630:I326N;ENSP00000425184:I279N;ENSP00000329632:I314N	ENSP00000329632:I314N	I	+	2	0	FBXL7	15989796	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.040000	0.89188	2.042000	0.60477	0.533000	0.62120	ATC	.	.		0.672	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		A	15936796	T	A	15936796	3	1	150	1	0	0	0	0	1	0	0	0	5732	1435	50	4	991	4	FBXL7	5	15936796	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2005444	15936796	164978464	182	22906										
IL7R	3575	hgsc.bcm.edu	37	chr5	35874564	35874564	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tttccaggggagatggatccTatcttactaaccatcagcat	8	10	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:35874564T>A	ENST00000303115.3	+	6	849	c.720T>A	c.(718-720)ccT>ccA	p.P240P	IL7R_ENST00000343305.4_Intron|IL7R_ENST00000506850.1_Intron	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	240					B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)	p.E237_L242>ASWC(2)|p.M238_L243>PCK(2)|p.P240_T244>RFCPH(1)|p.P240_L242>QSPSC(1)|p.I241_L242>CRPH(1)|p.P240_I241insCS(1)|p.P240_S246>LKC(1)|p.P240_S246>LQSC(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			AGATGGATCCTATCTTACTAA	0.428			"Mis, O"		"ALL, ETP ALL"		Severe combined immune deficiency																														p.P240P		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	.,1	IL7R	200	.	10	Complex - deletion inframe(6)|Complex - insertion inframe(2)|Insertion - In frame(1)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(10)	c.T720A						.						242	210	221					5																	35874564		2203	4300	6503	SO:0001819	synonymous_variant	3575	exon6			GGATCCTATCTTA	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.720T>A	chr5.hg19:g.35874564T>A		115.0	0.0		142.0	46.0	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Silent	SNP	ENST00000303115.3	hg19	CCDS3911.1																																																																																			.	.		0.428	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2			A	35874564	T	A	35874564	2	1	150	1	0	0	0	0	0	0	0	1	7714	1509	53	4		4	IL7R	5	35874564	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	19937768	35874564	145040696	183	22907										
FYB	2533	hgsc.bcm.edu	37	chr5	39130702	39130702	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgtggcttacctccacttccActctgactgtggctagaaaa	8	12	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:39130702A>T	ENST00000351578.6	-	10	2020	c.1830T>A	c.(1828-1830)agT>agA	p.S610R	FYB_ENST00000505428.1_Missense_Mutation_p.S610R|FYB_ENST00000540520.1_Missense_Mutation_p.S620R|FYB_ENST00000515010.1_Missense_Mutation_p.S610R|FYB_ENST00000512982.1_Missense_Mutation_p.S610R	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	610					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			CTCCACTTCCACTCTGACTGT	0.333																																					p.S620R		Atlas-SNP	.											.	FYB	354	.	0			c.T1860A						.						74	69	70					5																	39130702		1889	4117	6006	SO:0001583	missense	2533	exon10			ACTTCCACTCTGA	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1830T>A	chr5.hg19:g.39130702A>T	ENSP00000316460:p.Ser610Arg	107.0	0.0		125.0	29.0	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	hg19	CCDS47200.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.061175	0.76187	.	.	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542	T;T;T;T;T	0.25579	1.79;1.79;1.85;1.85;1.85	5.94	2.23	0.28157	.	0.261548	0.35407	N	0.003232	T	0.43743	0.1261	M	0.73962	2.25	0.27661	N	0.947068	D;D	0.76494	0.999;0.997	D;D	0.80764	0.994;0.916	T	0.20538	-1.0272	10	0.36615	T	0.2	-9.2975	7.11	0.25384	0.7451:0.0:0.2549:0.0	.	620;610	B4DLN2;O15117	.;FYB_HUMAN	R	610;610;610;610;620;610	ENSP00000316460:S610R;ENSP00000426346:S610R;ENSP00000425845:S610R;ENSP00000427114:S610R;ENSP00000442840:S620R	ENSP00000316460:S610R	S	-	3	2	FYB	39166459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.882000	0.28186	0.470000	0.27294	0.528000	0.53228	AGT	.	.		0.333	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		T	39130702	A	T	39130702	3	4	150	1	0	0	0	0	1	0	0	0	6132	156	6	4	699	4	FYB	5	39130702	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3256138	39130702	141784558	184	22908										
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41048467	41048467	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	caggtaaacgtgttttccatAggtctaccaattttgggtga	10	7	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:41048467A>T	ENST00000399564.4	-	16	2093	c.1643T>A	c.(1642-1644)cTa>cAa	p.L548Q	MROH2B_ENST00000506092.2_Missense_Mutation_p.L103Q	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	548																	TGTTTTCCATAGGTCTACCAA	0.468																																					p.L548Q		Atlas-SNP	.											.	.	.	.	0			c.T1643A						.						144	136	138					5																	41048467		1892	4118	6010	SO:0001583	missense	133558	exon16			TTCCATAGGTCTA		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.1643T>A	chr5.hg19:g.41048467A>T	ENSP00000382476:p.Leu548Gln	128.0	0.0		131.0	28.0	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	hg19	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	A	15.83	2.950400	0.53186	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.07216	3.21;3.21	4.87	4.87	0.63330	Armadillo-type fold (1);	0.174107	0.28257	N	0.016019	T	0.17365	0.0417	L	0.50333	1.59	0.25720	N	0.985388	D	0.57899	0.981	P	0.58873	0.847	T	0.04203	-1.0969	10	0.36615	T	0.2	.	11.0524	0.47898	1.0:0.0:0.0:0.0	.	548	Q7Z745	HTRB2_HUMAN	Q	103;252;548	ENSP00000441504:L103Q;ENSP00000382476:L548Q	ENSP00000296803:L252Q	L	-	2	0	HEATR7B2	41084224	0.143000	0.22626	0.622000	0.29159	0.968000	0.65278	3.953000	0.56699	2.168000	0.68352	0.533000	0.62120	CTA	.	.		0.468	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		T	41048467	A	T	41048467	3	4	150	1	0	0	0	0	1	0	0	0	7044	420	15	4	3222	4	HEATR7B2	5	41048467	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1917765	41048467	139866793	185	22909										
CDC20B	166979	hgsc.bcm.edu	37	chr5	54429246	54429246	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaatgataacttacagtagtCatttcgaagaccagtaatat	6	6	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:54429246C>G	ENST00000381375.2	-	6	836	c.691G>C	c.(691-693)Gac>Cac	p.D231H	CDC20B_ENST00000296733.1_Missense_Mutation_p.D231H|CDC20B_ENST00000322374.6_Missense_Mutation_p.D231H|CDC20B_ENST00000334206.5_Missense_Mutation_p.D231H			Q86Y33	CD20B_HUMAN	cell division cycle 20B	231										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TTACAGTAGTCATTTCGAAGA	0.353																																					p.D231H		Atlas-SNP	.											.	CDC20B	61	.	0			c.G691C						.						99	100	100					5																	54429246		2203	4300	6503	SO:0001583	missense	166979	exon6			AGTAGTCATTTCG	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"WD repeat domain containing"	24222	protein-coding gene	gene with protein product			"CDC20 cell division cycle 20 homolog B (S. cerevisiae)", "cell division cycle 20 homolog B (S. cerevisiae)"				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.691G>C	chr5.hg19:g.54429246C>G	ENSP00000370781:p.Asp231His	77.0	0.0		97.0	16.0	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	hg19	CCDS54852.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.782502	0.70222	.	.	ENSG00000164287	ENST00000334206;ENST00000296733;ENST00000381375;ENST00000322374	T;T;T;T	0.10099	2.91;2.91;2.91;2.91	4.97	4.1	0.47936	WD40 repeat-like-containing domain (1);	0.000000	0.49305	D	0.000156	T	0.42086	0.1187	M	0.93328	3.405	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;1.0	D;D;P;D	0.80764	0.994;0.944;0.879;0.983	T	0.56792	-0.7920	10	0.87932	D	0	-6.0811	13.2244	0.59907	0.0:0.9223:0.0:0.0777	.	231;231;231;231	Q86Y33-4;Q86Y33-3;Q86Y33;Q86Y33-2	.;.;CD20B_HUMAN;.	H	231	ENSP00000335664:D231H;ENSP00000296733:D231H;ENSP00000370781:D231H;ENSP00000315720:D231H	ENSP00000296733:D231H	D	-	1	0	CDC20B	54465003	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.180000	0.65048	1.303000	0.44873	0.650000	0.86243	GAC	.	.		0.353	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623		G	54429246	C	G	54429246	3	3	150	1	0	0	0	0	1	0	0	0	3062	826	29	4	896	4	CDC20B	5	54429246	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	13380779	54429246	126486014	186	22910										
CDC20B	166979	hgsc.bcm.edu	37	chr5	54429259	54429259	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagtagtcatttcgaagaccAgtaatatgaatcttcacctc	6	10	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:54429259A>T	ENST00000381375.2	-	6	823	c.678T>A	c.(676-678)acT>acA	p.T226T	CDC20B_ENST00000296733.1_Silent_p.T226T|CDC20B_ENST00000322374.6_Silent_p.T226T|CDC20B_ENST00000334206.5_Silent_p.T226T			Q86Y33	CD20B_HUMAN	cell division cycle 20B	226										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TTCGAAGACCAGTAATATGAA	0.353																																					p.T226T		Atlas-SNP	.											.	CDC20B	61	.	0			c.T678A						.						113	114	114					5																	54429259		2203	4300	6503	SO:0001819	synonymous_variant	166979	exon6			AAGACCAGTAATA	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"WD repeat domain containing"	24222	protein-coding gene	gene with protein product			"CDC20 cell division cycle 20 homolog B (S. cerevisiae)", "cell division cycle 20 homolog B (S. cerevisiae)"				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.678T>A	chr5.hg19:g.54429259A>T		83.0	0.0		108.0	19.0	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Silent	SNP	ENST00000381375.2	hg19	CCDS54852.1																																																																																			.	.		0.353	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623		T	54429259	A	T	54429259	2	4	150	1	0	0	0	0	0	0	0	1	3062	175	7	4		4	CDC20B	5	54429259	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	13	54429259	126486001	187	22911										
DEPDC1B	55789	hgsc.bcm.edu	37	chr5	59899387	59899387	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agatgcaacgggaaaatgtcTgaaccatctaaaaaaagagc	9	7	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:59899387T>A	ENST00000265036.5	-	9	1140	c.1073A>T	c.(1072-1074)cAg>cTg	p.Q358L	DEPDC1B_ENST00000453022.2_Missense_Mutation_p.Q358L|DEPDC1B_ENST00000545085.1_Missense_Mutation_p.Q331L|DEPDC1B_ENST00000509006.1_5'Flank	NM_018369.2	NP_060839.2	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B	358	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(2)|skin(2)	17		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				GGAAAATGTCTGAACCATCTA	0.408																																					p.Q358L		Atlas-SNP	.											.	DEPDC1B	56	.	0			c.A1073T						.						62	66	65					5																	59899387		2203	4300	6503	SO:0001583	missense	55789	exon9			AATGTCTGAACCA	AF303178	CCDS3977.1, CCDS47214.1	5q12	2008-02-05			ENSG00000035499	ENSG00000035499			24902	protein-coding gene	gene with protein product	"breast cancer cell 3"					12477932	Standard	NM_001145208		Approved	XTP1, BRCC3	uc003jsh.3	Q8WUY9	OTTHUMG00000097083	ENST00000265036.5:c.1073A>T	chr5.hg19:g.59899387T>A	ENSP00000265036:p.Gln358Leu	47.0	0.0		57.0	14.0	NM_001145208	A8K3R9|B4DUT4|Q86WJ3|Q8IZY6|Q9NUN3|Q9NW57	Missense_Mutation	SNP	ENST00000265036.5	hg19	CCDS3977.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.557662	0.45590	.	.	ENSG00000035499	ENST00000265036;ENST00000453022;ENST00000545085	T;T;T	0.32272	1.46;1.46;1.46	5.27	4.12	0.48240	Rho GTPase-activating protein domain (2);Rho GTPase activation protein (1);	0.159640	0.56097	D	0.000022	T	0.34424	0.0897	M	0.76838	2.35	0.58432	D	0.999999	B;B	0.33345	0.27;0.409	B;B	0.33690	0.168;0.118	T	0.11060	-1.0603	9	.	.	.	-19.1281	10.8395	0.46706	0.0:0.0734:0.0:0.9266	.	358;358	B4DUT4;Q8WUY9	.;DEP1B_HUMAN	L	358;358;331	ENSP00000265036:Q358L;ENSP00000389101:Q358L;ENSP00000438320:Q331L	.	Q	-	2	0	DEPDC1B	59935144	1.000000	0.71417	1.000000	0.80357	0.572000	0.35998	7.269000	0.78482	1.025000	0.39708	0.482000	0.46254	CAG	.	.		0.408	DEPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214207.1	NM_018369		A	59899387	T	A	59899387	3	1	150	1	0	0	0	0	1	0	0	0	4442	1580	55	4	528	4	DEPDC1B	5	59899387	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	5470128	59899387	121015873	188	22912										
MARVELD2	153562	hgsc.bcm.edu	37	chr5	68715848	68715848	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggtgtctttgcttgtgtcacAgcttacattcacaaggacag	10	9	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:68715848A>T	ENST00000325631.5	+	2	710	c.636A>T	c.(634-636)acA>acT	p.T212T	MARVELD2_ENST00000413223.2_Silent_p.T212T	NM_001038603.2|NM_001244734.1	NP_001033692.2|NP_001231663.1	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	212	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cell-cell junction organization (GO:0045216)|establishment of endothelial barrier (GO:0061028)|sensory perception of sound (GO:0007605)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(4)|skin(1)|urinary_tract(1)	15		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		CTTGTGTCACAGCTTACATTC	0.512																																					p.T212T		Atlas-SNP	.											.	MARVELD2	49	.	0			c.A636T						.						214	199	204					5																	68715848		2203	4300	6503	SO:0001819	synonymous_variant	153562	exon2			TGTCACAGCTTAC	AK055094	CCDS34175.1, CCDS58956.1	5q13.1	2007-05-01	2004-07-12	2004-07-14	ENSG00000152939	ENSG00000152939			26401	protein-coding gene	gene with protein product	"tricellulin"	610572	"MARVEL (membrane-associating) domain containing 2", "deafness, autosomal recessive 49"	MRVLDC2, DFNB49		17186462	Standard	NM_001038603		Approved	FLJ30532, TRIC	uc003jwq.3	Q8N4S9	OTTHUMG00000162512	ENST00000325631.5:c.636A>T	chr5.hg19:g.68715848A>T		171.0	0.0		170.0	36.0	NM_001244734	A1BQX0|A1BQX1|A8KA97|Q96NM9	Silent	SNP	ENST00000325631.5	hg19	CCDS34175.1																																																																																			.	.		0.512	MARVELD2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369583.1	NM_144724		T	68715848	A	T	68715848	2	4	150	1	0	0	0	0	0	0	0	1	9327	175	7	4		4	MARVELD2	5	68715848	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	8816461	68715848	112199412	189	22913										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71411599	71411599	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aactttttgtatctcgacacTctgcaagattctctcctgaa	5	11	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:71411599T>A	ENST00000296755.7	+	2	557	c.259T>A	c.(259-261)Tct>Act	p.S87T	MAP1B_ENST00000504183.1_3'UTR	NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	87					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ATCTCGACACTCTGCAAGATT	0.463																																					p.S87T	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T259A						.						136	124	128					5																	71411599		2203	4300	6503	SO:0001583	missense	4131	exon2			CGACACTCTGCAA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.259T>A	chr5.hg19:g.71411599T>A	ENSP00000296755:p.Ser87Thr	59.0	0.0		53.0	10.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.391208	0.82902	.	.	ENSG00000131711	ENST00000512974;ENST00000296755;ENST00000511641	T;T	0.17528	2.27;2.27	5.75	5.75	0.90469	.	0.000000	0.53938	D	0.000042	T	0.37758	0.1015	L	0.59436	1.845	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.03259	-1.1055	10	0.32370	T	0.25	-16.5086	16.0623	0.80847	0.0:0.0:0.0:1.0	.	87	P46821	MAP1B_HUMAN	T	87	ENSP00000296755:S87T;ENSP00000423444:S87T	ENSP00000296755:S87T	S	+	1	0	MAP1B	71447355	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.431000	0.80335	2.195000	0.70347	0.533000	0.62120	TCT	.	.		0.463	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71411599	T	A	71411599	3	1	150	1	0	0	0	0	1	0	0	0	9237	1551	54	4	265	4	MAP1B	5	71411599	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2695751	71411599	109503661	190	22914										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71491824	71491824	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcctacgtcatccagaaggAgagagaagtcaccaaaggtc	11	10	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:71491824A>T	ENST00000296755.7	+	5	2940	c.2642A>T	c.(2641-2643)gAg>gTg	p.E881V		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	881					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ATCCAGAAGGAGAGAGAAGTC	0.532																																					p.E881V	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A2642T						.						118	119	119					5																	71491824		2203	4300	6503	SO:0001583	missense	4131	exon5			AGAAGGAGAGAGA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.2642A>T	chr5.hg19:g.71491824A>T	ENSP00000296755:p.Glu881Val	102.0	0.0		136.0	32.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	18.19	3.569611	0.65765	.	.	ENSG00000131711	ENST00000296755	T	0.03524	3.9	5.17	4.02	0.46733	.	0.307900	0.28119	N	0.016530	T	0.04272	0.0118	L	0.39898	1.24	0.53005	D	0.999962	P;P	0.37955	0.612;0.612	B;B	0.37943	0.261;0.261	T	0.50676	-0.8800	10	0.42905	T	0.14	-9.8103	10.3101	0.43704	0.9226:0.0:0.0774:0.0	.	755;881	A2BDK6;P46821	.;MAP1B_HUMAN	V	881	ENSP00000296755:E881V	ENSP00000296755:E881V	E	+	2	0	MAP1B	71527580	1.000000	0.71417	0.999000	0.59377	0.808000	0.45660	7.498000	0.81546	1.950000	0.56595	0.482000	0.46254	GAG	.	.		0.532	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71491824	A	T	71491824	3	4	150	1	0	0	0	0	1	0	0	0	9237	304	11	4	2660	4	MAP1B	5	71491824	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	80225	71491824	109423436	191	22915										
FAM169A	26049	hgsc.bcm.edu	37	chr5	74101006	74101006	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	attttaagtgcttctctttgTaatgctctggtgactggtat	9	6	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:74101006T>A	ENST00000389156.4	-	7	864	c.774A>T	c.(772-774)ttA>ttT	p.L258F	FAM169A_ENST00000380515.3_3'UTR|FAM169A_ENST00000510496.1_Missense_Mutation_p.L198F	NM_015566.2	NP_056381.1	Q9Y6X4	F169A_HUMAN	family with sequence similarity 169, member A	258						membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	27						CTTCTCTTTGTAATGCTCTGG	0.413																																					p.L258F		Atlas-SNP	.											.	FAM169A	61	.	0			c.A774T						.						119	116	117					5																	74101006		1855	4088	5943	SO:0001583	missense	26049	exon7			TCTTTGTAATGCT		CCDS43330.1	5q13.3	2008-08-08			ENSG00000198780	ENSG00000198780			29138	protein-coding gene	gene with protein product		615769				10048485	Standard	NM_015566		Approved	KIAA0888	uc003kdm.4	Q9Y6X4	OTTHUMG00000162930	ENST00000389156.4:c.774A>T	chr5.hg19:g.74101006T>A	ENSP00000373808:p.Leu258Phe	68.0	0.0		82.0	12.0	NM_015566	A8K1T9|Q6MZT0|Q9H989	Missense_Mutation	SNP	ENST00000389156.4	hg19	CCDS43330.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.132928	0.56828	.	.	ENSG00000198780	ENST00000389156;ENST00000510496	T	0.57595	0.39	5.45	-2.97	0.05530	.	0.184844	0.26496	N	0.024052	T	0.33876	0.0878	L	0.39397	1.21	0.80722	D	1	P;P	0.46277	0.875;0.644	B;B	0.37198	0.243;0.192	T	0.14448	-1.0472	10	0.44086	T	0.13	-3.0567	9.5262	0.39165	0.1156:0.5465:0.0:0.3379	.	198;258	D6RB01;Q9Y6X4	.;F169A_HUMAN	F	258;198	ENSP00000373808:L258F	ENSP00000373808:L258F	L	-	3	2	FAM169A	74136762	0.331000	0.24713	0.985000	0.45067	0.986000	0.74619	-0.799000	0.04560	-0.461000	0.06993	0.477000	0.44152	TTA	.	.		0.413	FAM169A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371092.2			A	74101006	T	A	74101006	3	1	150	1	0	0	0	0	1	0	0	0	5492	1635	57	4	1266	4	FAM169A	5	74101006	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2609182	74101006	106814254	192	22916										
MCTP1	79772	hgsc.bcm.edu	37	chr5	94230454	94230454	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgctgtcagagtgaccagcAgcaccaggtgtccctcaccc	10	15	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:94230454A>T	ENST00000515393.1	-	11	1738	c.1739T>A	c.(1738-1740)cTg>cAg	p.L580Q	MCTP1_ENST00000505208.1_Missense_Mutation_p.L359Q|MCTP1_ENST00000505078.1_Missense_Mutation_p.L96Q|MCTP1_ENST00000429576.2_Missense_Mutation_p.L313Q|MCTP1_ENST00000312216.8_Missense_Mutation_p.L359Q	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	580					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		AGTGACCAGCAGCACCAGGTG	0.537																																					p.L580Q		Atlas-SNP	.											.	MCTP1	110	.	0			c.T1739A						.						91	74	80					5																	94230454		2203	4300	6503	SO:0001583	missense	79772	exon11			ACCAGCAGCACCA		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.1739T>A	chr5.hg19:g.94230454A>T	ENSP00000424126:p.Leu580Gln	62.0	0.0		92.0	17.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Missense_Mutation	SNP	ENST00000515393.1	hg19	CCDS34203.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.291736	0.80914	.	.	ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000505078;ENST00000312216;ENST00000508509;ENST00000512425;ENST00000505208;ENST00000506568	T;T;T;T;T;T;T;T	0.80653	-1.36;-1.08;-0.36;-1.27;-1.06;-1.26;-1.4;-1.04	5.38	5.38	0.77491	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000002	D	0.89146	0.6632	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.78314	0.949;0.991;0.989	D	0.90488	0.4465	10	0.87932	D	0	-7.3821	15.6821	0.77376	1.0:0.0:0.0:0.0	.	580;313;359	Q6DN14;Q6DN14-3;Q6DN14-2	MCTP1_HUMAN;.;.	Q	580;313;96;359;300;241;359;181	ENSP00000424126:L580Q;ENSP00000391639:L313Q;ENSP00000426417:L96Q;ENSP00000308957:L359Q;ENSP00000423410:L300Q;ENSP00000431075:L241Q;ENSP00000426438:L359Q;ENSP00000426294:L181Q	ENSP00000308957:L359Q	L	-	2	0	MCTP1	94256210	1.000000	0.71417	0.998000	0.56505	0.866000	0.49608	8.910000	0.92685	2.165000	0.68154	0.482000	0.46254	CTG	.	.		0.537	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		T	94230454	A	T	94230454	3	4	150	1	0	0	0	0	1	0	0	0	9409	188	7	4	1312	4	MCTP1	5	94230454	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	20129448	94230454	86684806	193	22917										
MCTP1	79772	hgsc.bcm.edu	37	chr5	94353130	94353130	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgtaatgtccagctggtacAttccgggatcagccaagggg	13	9	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:94353130A>T	ENST00000515393.1	-	2	778	c.779T>A	c.(778-780)aTg>aAg	p.M260K	MCTP1_ENST00000505208.1_Missense_Mutation_p.M39K|MCTP1_ENST00000429576.2_Missense_Mutation_p.M39K|MCTP1_ENST00000312216.8_Missense_Mutation_p.M39K	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	260	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		CAGCTGGTACATTCCGGGATC	0.378																																					p.M260K		Atlas-SNP	.											.	MCTP1	110	.	0			c.T779A						.						137	129	131					5																	94353130		2203	4300	6503	SO:0001583	missense	79772	exon2			TGGTACATTCCGG		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.779T>A	chr5.hg19:g.94353130A>T	ENSP00000424126:p.Met260Lys	60.0	0.0		81.0	16.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Missense_Mutation	SNP	ENST00000515393.1	hg19	CCDS34203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.16|18.16	3.562006|3.562006	0.65538|0.65538	.|.	.|.	ENSG00000175471|ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000312216;ENST00000508509;ENST00000505208;ENST00000415885;ENST00000507214;ENST00000514780;ENST00000510732;ENST00000505465|ENST00000503301	T;T;T;T;T;T;T;T;T|.	0.66280|.	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;1.15;3.0|.	5.79|5.79	5.79|5.79	0.91817|0.91817	C2 calcium/lipid-binding domain, CaLB (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.51568|0.51568	0.1682|0.1682	N|N	0.25060|0.25060	0.705|0.705	0.58432|0.58432	D|D	0.999999|0.999999	D;D;P|.	0.65815|.	0.995;0.981;0.956|.	P;P;P|.	0.53593|.	0.718;0.73;0.583|.	T|T	0.49163|0.49163	-0.8968|-0.8968	10|5	0.62326|.	D|.	0.03|.	-20.8458|-20.8458	13.651|13.651	0.62310|0.62310	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	260;39;39|.	Q6DN14;Q6DN14-3;Q6DN14-2|.	MCTP1_HUMAN;.;.|.	K|K	260;39;39;39;39;1;21;20;54;39|68	ENSP00000424126:M260K;ENSP00000391639:M39K;ENSP00000308957:M39K;ENSP00000423410:M39K;ENSP00000426438:M39K;ENSP00000424936:M21K;ENSP00000421543:M20K;ENSP00000422219:M54K;ENSP00000422317:M39K|.	ENSP00000308957:M39K|.	M|N	-|-	2|3	0|2	MCTP1|MCTP1	94378886|94378886	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	5.185000|5.185000	0.65076|0.65076	2.213000|2.213000	0.71641|0.71641	0.533000|0.533000	0.62120|0.62120	ATG|AAT	.	.		0.378	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		T	94353130	A	T	94353130	3	4	150	1	0	0	0	0	1	0	0	0	9409	217	8	4	2308	4	MCTP1	5	94353130	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	122676	94353130	86562130	194	22918										
SLC25A46	91137	hgsc.bcm.edu	37	chr5	110081977	110081977	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atcttttttacaggttaattAccatgctcagcattaccatc	4	10	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:110081977A>T	ENST00000355943.3	+	4	518	c.392A>T	c.(391-393)tAc>tTc	p.Y131F	SLC25A46_ENST00000504098.1_5'UTR|SLC25A46_ENST00000509442.2_Missense_Mutation_p.Y40F|SLC25A46_ENST00000447245.2_Missense_Mutation_p.Y131F|SLC25A46_ENST00000513807.1_5'UTR	NM_138773.1	NP_620128.1	Q96AG3	S2546_HUMAN	solute carrier family 25, member 46	131					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10		all_cancers(142;0.00203)|all_epithelial(76;4.52e-05)|Prostate(80;0.0115)|Colorectal(57;0.0676)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;2.58e-09)|Epithelial(69;7.29e-08)|all cancers(49;9.35e-06)|COAD - Colon adenocarcinoma(37;0.211)		CAGGTTAATTACCATGCTCAG	0.303																																					p.Y131F		Atlas-SNP	.											.	SLC25A46	33	.	0			c.A392T						.						81	88	85					5																	110081977		2201	4294	6495	SO:0001583	missense	91137	exon4			TTAATTACCATGC	BC017169	CCDS4100.1	5q22.1	2013-05-22			ENSG00000164209	ENSG00000164209		"Solute carriers"	25198	protein-coding gene	gene with protein product		610826				1651562, 1651563, 16949250	Standard	NM_138773		Approved		uc003koz.3	Q96AG3	OTTHUMG00000128794	ENST00000355943.3:c.392A>T	chr5.hg19:g.110081977A>T	ENSP00000348211:p.Tyr131Phe	335.0	0.0		315.0	115.0	NM_138773	A8K2F2|B3KRE6|B4DTA3|D3DSZ6|D6R9W7|Q04197	Missense_Mutation	SNP	ENST00000355943.3	hg19	CCDS4100.1	.	.	.	.	.	.	.	.	.	.	A	10.26	1.302411	0.23736	.	.	ENSG00000164209	ENST00000509442;ENST00000355943;ENST00000447245	T;T;T	0.77750	-1.12;-1.12;-1.12	5.5	5.5	0.81552	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.77343	0.4116	L	0.55103	1.725	0.58432	D	0.999994	D;D	0.63880	0.993;0.985	P;P	0.49999	0.628;0.622	T	0.74169	-0.3752	10	0.10377	T	0.69	-8.2498	15.2619	0.73631	1.0:0.0:0.0:0.0	.	40;131	B4DY98;Q96AG3	.;S2546_HUMAN	F	40;131;131	ENSP00000424136:Y40F;ENSP00000348211:Y131F;ENSP00000399717:Y131F	ENSP00000348211:Y131F	Y	+	2	0	SLC25A46	110109876	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	8.229000	0.89791	2.084000	0.62774	0.528000	0.53228	TAC	.	.		0.303	SLC25A46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250721.5	NM_138773		T	110081977	A	T	110081977	3	4	150	1	0	0	0	0	1	0	0	0	14526	391	14	4	406	4	SLC25A46	5	110081977	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	15728847	110081977	70833283	195	22919										
ACSL6	23305	hgsc.bcm.edu	37	chr5	131323886	131323886	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctagcagaagcacagccttcTgaggtttgtccacaatcacg	9	12	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:131323886T>A	ENST00000379240.1	-	7	764	c.611A>T	c.(610-612)cAg>cTg	p.Q204L	ACSL6_ENST00000544770.1_Missense_Mutation_p.Q113L|ACSL6_ENST00000543479.1_Missense_Mutation_p.Q204L|ACSL6_ENST00000431707.1_Missense_Mutation_p.Q184L|ACSL6_ENST00000379249.3_Missense_Mutation_p.Q204L|ACSL6_ENST00000379255.1_Missense_Mutation_p.Q169L|ACSL6_ENST00000379246.1_Missense_Mutation_p.Q215L|ACSL6_ENST00000379244.1_Missense_Mutation_p.Q204L|ACSL6_ENST00000379264.2_Missense_Mutation_p.Q229L|ACSL6_ENST00000357096.1_Missense_Mutation_p.Q169L|ACSL6_ENST00000379272.2_Missense_Mutation_p.Q219L|ACSL6_ENST00000296869.4_Missense_Mutation_p.Q229L			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	204					acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CACAGCCTTCTGAGGTTTGTC	0.567																																					p.Q229L		Atlas-SNP	.											.	ACSL6	169	.	0			c.A686T						.						266	249	255					5																	131323886		2203	4300	6503	SO:0001583	missense	23305	exon7			GCCTTCTGAGGTT	AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"Acyl-CoA synthetase family"	16496	protein-coding gene	gene with protein product		604443	"fatty-acid-Coenzyme A ligase, long-chain 6"	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.611A>T	chr5.hg19:g.131323886T>A	ENSP00000368542:p.Gln204Leu	61.0	0.0		79.0	16.0	NM_001009185	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Missense_Mutation	SNP	ENST00000379240.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.19	2.460391	0.43736	.	.	ENSG00000164398	ENST00000379249;ENST00000379264;ENST00000379272;ENST00000357096;ENST00000379255;ENST00000296869;ENST00000379246;ENST00000379244;ENST00000544770;ENST00000379240;ENST00000431707;ENST00000543479;ENST00000434099;ENST00000430403	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.08720	3.06;3.06;3.06;3.06;3.06;3.06;3.06;3.06;3.06;3.06;3.06;3.06;3.06;3.06	5.92	3.47	0.39725	AMP-dependent synthetase/ligase (1);	0.439517	0.27595	N	0.018672	T	0.05547	0.0146	N	0.13098	0.295	0.29883	N	0.825873	B;B;B;B;B;B;B	0.26041	0.115;0.031;0.019;0.14;0.031;0.031;0.031	B;B;B;B;B;B;B	0.31337	0.078;0.062;0.063;0.128;0.038;0.038;0.038	T	0.27331	-1.0077	10	0.30078	T	0.28	.	8.6304	0.33915	0.0:0.0668:0.1304:0.8029	.	204;219;194;204;169;229;229	Q9UKU0-3;Q9UKU0-6;B4DFW3;Q9UKU0;Q9UKU0-7;Q9UKU0-1;Q9UKU0-8	.;.;.;ACSL6_HUMAN;.;.;.	L	204;229;219;169;169;229;215;204;113;204;184;204;169;204	ENSP00000368551:Q204L;ENSP00000368566:Q229L;ENSP00000368574:Q219L;ENSP00000349608:Q169L;ENSP00000368557:Q169L;ENSP00000296869:Q229L;ENSP00000368548:Q215L;ENSP00000368546:Q204L;ENSP00000445154:Q113L;ENSP00000368542:Q204L;ENSP00000413329:Q184L;ENSP00000442124:Q204L;ENSP00000397507:Q169L;ENSP00000398423:Q204L	ENSP00000296869:Q229L	Q	-	2	0	ACSL6	131351785	1.000000	0.71417	0.970000	0.41538	0.399000	0.30720	4.060000	0.57477	0.470000	0.27294	0.454000	0.30748	CAG	.	.		0.567	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256		A	131323886	T	A	131323886	3	1	150	1	0	0	0	0	1	0	0	0	181	1580	55	4	1624	4	ACSL6	5	131323886	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	21241909	131323886	49591374	196	22920										
CATSPER3	347732	hgsc.bcm.edu	37	chr5	134332053	134332053	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	actactggaagaacggctacAacctgctggatgtgatcatt	10	9	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:134332053A>T	ENST00000282611.6	+	3	429	c.343A>T	c.(343-345)Aac>Tac	p.N115Y		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	115					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GAACGGCTACAACCTGCTGGA	0.473																																					p.N115Y		Atlas-SNP	.											.	CATSPER3	38	.	0			c.A343T						.						258	203	222					5																	134332053		2203	4300	6503	SO:0001583	missense	347732	exon3			GGCTACAACCTGC	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"Voltage-gated ion channels / Cation channels, sperm associated"	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.343A>T	chr5.hg19:g.134332053A>T	ENSP00000282611:p.Asn115Tyr	53.0	0.0		64.0	9.0	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	hg19	CCDS4181.1	.	.	.	.	.	.	.	.	.	.	A	13.75	2.329246	0.41197	.	.	ENSG00000152705	ENST00000282611	D	0.99259	-5.64	4.14	4.14	0.48551	Ion transport (1);	0.105491	0.42172	D	0.000744	D	0.99281	0.9749	M	0.87827	2.91	0.36895	D	0.890081	D	0.63046	0.992	D	0.66847	0.947	D	0.99912	1.1208	10	0.87932	D	0	-32.1956	9.8501	0.41051	1.0:0.0:0.0:0.0	.	115	Q86XQ3	CTSR3_HUMAN	Y	115	ENSP00000282611:N115Y	ENSP00000282611:N115Y	N	+	1	0	CATSPER3	134359952	1.000000	0.71417	0.998000	0.56505	0.138000	0.21146	2.495000	0.45337	2.092000	0.63282	0.459000	0.35465	AAC	.	.		0.473	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019		T	134332053	A	T	134332053	3	4	150	1	0	0	0	0	1	0	0	0	2691	130	5	4	353	4	CATSPER3	5	134332053	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3008167	134332053	46583207	197	22921										
HBEGF	1839	hgsc.bcm.edu	37	chr5	139725617	139725617	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gggttgctggttccagcagcTagccctctccgaagccgctc	12	15	1	0	rs375401691		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:139725617T>A	ENST00000230990.6	-	2	401	c.99A>T	c.(97-99)ctA>ctT	p.L33L	CTC-329D1.3_ENST00000520443.1_RNA|HBEGF_ENST00000507104.1_Silent_p.L33L	NM_001945.2	NP_001936.1	Q99075	HBEGF_HUMAN	heparin-binding EGF-like growth factor	33					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|muscle organ development (GO:0007517)|negative regulation of elastin biosynthetic process (GO:0051545)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of wound healing (GO:0090303)|regulation of heart contraction (GO:0008016)|signal transduction (GO:0007165)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)	7			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCAGCAGCTAGCCCTCTCC	0.667											OREG0016844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L33L		Atlas-SNP	.											.	HBEGF	12	.	0			c.A99T						.	T		0,4406		0,0,2203	30	35	34		99	2.6	0.4	5		34	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	HBEGF	NM_001945.2		0,1,6502	AA,AT,TT		0.0116,0.0,0.0077		33/209	139725617	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1839	exon2			AGCAGCTAGCCCT		CCDS4223.1	5q23	2012-10-02	2005-01-14	2005-01-14	ENSG00000113070	ENSG00000113070			3059	protein-coding gene	gene with protein product	"Diphtheria toxin receptor (heparin-binding EGF-like growth factor)", "heparin-binding epidermal growth factor"	126150	"diphtheria toxin receptor (heparin-binding epidermal growth factor-like growth factor)"	HEGFL, DTS, DTR		7590736, 12163414	Standard	NM_001945		Approved		uc003lfi.3	Q99075	OTTHUMG00000129496	ENST00000230990.6:c.99A>T	chr5.hg19:g.139725617T>A		105.0	0.0	1651	103.0	20.0	NM_001945	B2R821	Silent	SNP	ENST00000230990.6	hg19	CCDS4223.1																																																																																			.	.		0.667	HBEGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251665.2	NM_001945		A	139725617	T	A	139725617	2	1	150	1	0	0	0	0	0	0	0	1	6990	1509	53	4		4	HBEGF	5	139725617	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	5393564	139725617	41189643	198	22922										
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140481325	140481325	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gagaactcgggagagactgtActggctgttttcagtgtttc	13	7	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:140481325A>T	ENST00000231130.2	+	1	1092	c.1092A>T	c.(1090-1092)gtA>gtT	p.V364V	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	364	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAGAGACTGTACTGGCTGTTT	0.473																																					p.V364V		Atlas-SNP	.											.	PCDHB3	208	.	0			c.A1092T						.						85	82	83					5																	140481325		2203	4300	6503	SO:0001819	synonymous_variant	56132	exon1			GACTGTACTGGCT	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1092A>T	chr5.hg19:g.140481325A>T		53.0	0.0		62.0	16.0	NM_018937	B2R8P2	Silent	SNP	ENST00000231130.2	hg19	CCDS4245.1																																																																																			.	.		0.473	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		T	140481325	A	T	140481325	2	4	150	1	0	0	0	0	0	0	0	1	11552	378	14	4		4	PCDHB3	5	140481325	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	755708	140481325	40433935	199	22923										
PCDHB6	56130	hgsc.bcm.edu	37	chr5	140531957	140531957	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcttttcggtgctcctgttcGtggcggtgcggctgtgcagg	16	10	1	0	rs540523095		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:140531957G>T	ENST00000231136.1	+	1	2119	c.2119G>T	c.(2119-2121)Gtg>Ttg	p.V707L	PCDHB6_ENST00000543635.1_Missense_Mutation_p.V571L	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	707					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCTCCTGTTCGTGGCGGTGCG	0.687																																					p.V707L		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G2119T						.						80	93	89					5																	140531957		2199	4269	6468	SO:0001583	missense	56130	exon1			CTGTTCGTGGCGG	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.2119G>T	chr5.hg19:g.140531957G>T	ENSP00000231136:p.Val707Leu	69.0	0.0		66.0	10.0	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	hg19	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.932948	0.34096	.	.	ENSG00000113211	ENST00000543635;ENST00000231136	T;T	0.13901	2.55;2.55	4.55	-0.0228	0.13946	.	.	.	.	.	T	0.14527	0.0351	L	0.51914	1.62	0.09310	N	1	B	0.18310	0.027	B	0.25405	0.06	T	0.31806	-0.9930	9	0.72032	D	0.01	.	10.3991	0.44218	0.3439:0.0:0.6561:0.0	.	707	Q9Y5E3	PCDB6_HUMAN	L	571;707	ENSP00000438466:V571L;ENSP00000231136:V707L	ENSP00000231136:V707L	V	+	1	0	PCDHB6	140512141	0.000000	0.05858	0.284000	0.24805	0.974000	0.67602	-0.315000	0.08081	0.116000	0.18110	0.556000	0.70494	GTG	.	.		0.687	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		T	140531957	G	T	140531957	3	4	150	1	0	0	0	0	1	0	0	0	11555	1145	40	1	2121	1	PCDHB6	5	140531957	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	50632	140531957	40383303	200	22924										
PCDHB7	56129	hgsc.bcm.edu	37	chr5	140552882	140552882	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gggcggcatttctcctagagAgtgcacaggattcagatgtt	13	8	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:140552882A>T	ENST00000231137.3	+	1	640	c.466A>T	c.(466-468)Agt>Tgt	p.S156C		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	156	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCTCCTAGAGAGTGCACAGGA	0.458																																					p.S156C		Atlas-SNP	.											.	PCDHB7	231	.	0			c.A466T						.						53	56	55					5																	140552882		2203	4300	6503	SO:0001583	missense	56129	exon1			CTAGAGAGTGCAC	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.466A>T	chr5.hg19:g.140552882A>T	ENSP00000231137:p.Ser156Cys	105.0	0.0		132.0	24.0	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	hg19	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	A	10.03	1.237785	0.22711	.	.	ENSG00000113212	ENST00000231137	T	0.53640	0.61	4.61	2.09	0.27110	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.56124	0.1964	H	0.94886	3.595	0.09310	N	1	B	0.18863	0.031	B	0.27262	0.078	T	0.58346	-0.7652	9	0.54805	T	0.06	.	3.1162	0.06375	0.4211:0.3683:0.0808:0.1298	.	156	Q9Y5E2	PCDB7_HUMAN	C	156	ENSP00000231137:S156C	ENSP00000231137:S156C	S	+	1	0	PCDHB7	140533066	0.000000	0.05858	0.906000	0.35671	0.908000	0.53690	-0.160000	0.10041	0.202000	0.20498	0.533000	0.62120	AGT	.	.		0.458	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		T	140552882	A	T	140552882	3	4	150	1	0	0	0	0	1	0	0	0	11556	304	11	4	468	4	PCDHB7	5	140552882	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	20925	140552882	40362378	201	22925										
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140559337	140559337	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatggctccgcgccctgcacCgagctggtgccccgggcggc	15	17	0	0	rs374710779		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:140559337C>T	ENST00000239444.2	+	1	1967	c.1722C>T	c.(1720-1722)acC>acT	p.T574T	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	574	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCCCTGCACCGAGCTGGTGC	0.701																																					p.T574T		Atlas-SNP	.											PCDHB8,NS,carcinoma,0,1	PCDHB8	199	.	0			c.C1722T						.						9	18	15					5																	140559337		2148	4213	6361	SO:0001819	synonymous_variant	56128	exon1			CTGCACCGAGCTG	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.1722C>T	chr5.hg19:g.140559337C>T		68.0	0.0		86.0	4.0	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	hg19	CCDS4250.1																																																																																			.	.		0.701	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		T	140559337	C	T	140559337	2	4	150	1	0	0	0	0	0	0	0	1	11557	639	23	1		1	PCDHB8	5	140559337	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	6455	140559337	40355923	202	22926										
PCDHB11	56125	hgsc.bcm.edu	37	chr5	140581442	140581442	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tggcgttggcctcggtgtctTcgctcttcctcttctcggtg	12	13	4	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:140581442T>A	ENST00000354757.3	+	1	2095	c.2095T>A	c.(2095-2097)Tcg>Acg	p.S699T	PCDHB11_ENST00000536699.1_Missense_Mutation_p.S334T	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	699					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCGGTGTCTTCGCTCTTCCT	0.687																																					p.S699T		Atlas-SNP	.											PCDHB11,right_upper_lobe,carcinoma,0,1	PCDHB11	162	.	0			c.T2095A						.						92	93	93					5																	140581442		2202	4295	6497	SO:0001583	missense	56125	exon1			GTGTCTTCGCTCT	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"Cadherins / Protocadherins : Clustered"	8682	other	protocadherin	"cadherin ME2"	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.2095T>A	chr5.hg19:g.140581442T>A	ENSP00000346802:p.Ser699Thr	91.0	0.0		99.0	25.0	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	hg19	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	t	9.122	1.009275	0.19277	.	.	ENSG00000197479	ENST00000536699;ENST00000354757	T;T	0.13538	2.58;2.58	2.64	2.64	0.31445	.	.	.	.	.	T	0.23094	0.0558	M	0.86343	2.81	0.09310	N	1	B	0.31077	0.307	B	0.34093	0.175	T	0.10382	-1.0632	9	0.41790	T	0.15	.	10.6444	0.45610	0.0:0.0:0.0:1.0	.	699	Q9Y5F2	PCDBB_HUMAN	T	334;699	ENSP00000440344:S334T;ENSP00000346802:S699T	ENSP00000346802:S699T	S	+	1	0	PCDHB11	140561626	0.000000	0.05858	0.536000	0.28039	0.692000	0.40212	0.004000	0.13106	1.215000	0.43411	0.369000	0.22263	TCG	.	.		0.687	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931		A	140581442	T	A	140581442	3	1	150	1	0	0	0	0	1	0	0	0	11545	1783	62	4	2097	4	PCDHB11	5	140581442	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	22105	140581442	40333818	203	22927										
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140726047	140726047	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gagtttatttatttctttgaTtattaagaacaaatatgaga	6	2	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:140726047T>C	ENST00000253812.6	+	1	2424				PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATTTCTTTGATTATTAAGAAC	0.323																																					p.I816T		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.T2447C						.						34	38	36					5																	140726047		2096	4239	6335	SO:0001627	intron_variant	56112	exon1			CTTTGATTATTAA	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.2424+23T>C	chr5.hg19:g.140726047T>C		294.0	0.0		344.0	67.0	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	hg19	CCDS47290.1																																																																																			.	.		0.323	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		C	140726047	T	C	140726047	1	2	150	0	1	0	0	0	0	0	0	0	11564	1493	52	2		2	PCDHGA3	5	140726047	Intron	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	144605	140726047	40189213	204	22928										
PCDHGC4	56098	hgsc.bcm.edu	37	chr5	140865877	140865877	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agtgtgcaggatccagactcAgggtcaaacggagatgtgag	15	7	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:140865877A>T	ENST00000306593.1	+	1	1137	c.1137A>T	c.(1135-1137)tcA>tcT	p.S379S	PCDHGB6_ENST00000520790.1_Intron|PCDHGC5_ENST00000252087.1_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	379	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCCAGACTCAGGGTCAAACG	0.562																																					p.S379S		Atlas-SNP	.											.	PCDHGC4	91	.	0			c.A1137T						.						117	97	104					5																	140865877		2203	4300	6503	SO:0001819	synonymous_variant	56098	exon1			AGACTCAGGGTCA	AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"Cadherins / Protocadherins : Clustered"	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.1137A>T	chr5.hg19:g.140865877A>T		115.0	0.0		146.0	32.0	NM_018928	Q495T2|Q9Y5C3	Silent	SNP	ENST00000306593.1	hg19	CCDS4262.1																																																																																			.	.		0.562	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928		T	140865877	A	T	140865877	2	4	150	1	0	0	0	0	0	0	0	1	11579	175	7	4		4	PCDHGC4	5	140865877	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	139830	140865877	40049383	205	22929										
ARSI	340075	hgsc.bcm.edu	37	chr5	149676796	149676796	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atcagatccgttgggacattAgcctggtgttgagtttacgg	13	7	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:149676796A>T	ENST00000328668.7	-	2	2270	c.1691T>A	c.(1690-1692)cTa>cAa	p.L564Q		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	564					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTGGGACATTAGCCTGGTGTT	0.527																																					p.L564Q		Atlas-SNP	.											.	ARSI	65	.	0			c.T1691A						.						105	99	101					5																	149676796		2203	4300	6503	SO:0001583	missense	340075	exon2			GACATTAGCCTGG	AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"Arylsulfatase family"	32521	protein-coding gene	gene with protein product		610009	"arylsulfatase I"			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.1691T>A	chr5.hg19:g.149676796A>T	ENSP00000333395:p.Leu564Gln	167.0	0.0		199.0	45.0	NM_001012301	A1L3B0|B3KV22|B7XD03	Missense_Mutation	SNP	ENST00000328668.7	hg19	CCDS34275.1	.	.	.	.	.	.	.	.	.	.	A	8.481	0.859725	0.17178	.	.	ENSG00000183876	ENST00000328668;ENST00000515301	D;D	0.97710	-4.5;-3.61	4.56	4.56	0.56223	.	0.077544	0.50627	D	0.000110	D	0.95557	0.8556	L	0.50333	1.59	0.44030	D	0.996751	P	0.45348	0.856	B	0.38803	0.282	D	0.95850	0.8874	10	0.87932	D	0	.	14.0867	0.64962	1.0:0.0:0.0:0.0	.	564	Q5FYB1	ARSI_HUMAN	Q	564;421	ENSP00000333395:L564Q;ENSP00000426879:L421Q	ENSP00000333395:L564Q	L	-	2	0	ARSI	149656989	1.000000	0.71417	0.996000	0.52242	0.138000	0.21146	7.107000	0.77047	1.909000	0.55274	0.523000	0.50628	CTA	.	.		0.527	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301		T	149676796	A	T	149676796	3	4	150	1	0	0	0	0	1	0	0	0	994	420	15	4	22	4	ARSI	5	149676796	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	8810919	149676796	31238464	206	22930										
FAT2	2196	hgsc.bcm.edu	37	chr5	150933925	150933925	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttccttctgtctgctcaccgTtaggatgttgtactctccag	8	12	4	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:150933925T>A	ENST00000261800.5	-	4	3955	c.3943A>T	c.(3943-3945)Acg>Tcg	p.T1315S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1315	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGCTCACCGTTAGGATGTTG	0.537																																					p.T1315S		Atlas-SNP	.											.	FAT2	465	.	0			c.A3943T						.						69	63	65					5																	150933925		2203	4300	6503	SO:0001583	missense	2196	exon4			TCACCGTTAGGAT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3943A>T	chr5.hg19:g.150933925T>A	ENSP00000261800:p.Thr1315Ser	109.0	0.0		114.0	18.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.879833	0.51801	.	.	ENSG00000086570	ENST00000261800	T	0.02345	4.33	5.46	5.46	0.80206	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000005	T	0.05547	0.0146	L	0.58810	1.83	0.51767	D	0.999931	P	0.44946	0.846	P	0.48189	0.57	T	0.50759	-0.8790	10	0.11794	T	0.64	.	10.2894	0.43586	0.1471:0.0:0.0:0.8529	.	1315	Q9NYQ8	FAT2_HUMAN	S	1315	ENSP00000261800:T1315S	ENSP00000261800:T1315S	T	-	1	0	FAT2	150914118	1.000000	0.71417	0.913000	0.36048	0.665000	0.39181	4.721000	0.61951	2.191000	0.70037	0.533000	0.62120	ACG	.	.		0.537	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150933925	T	A	150933925	3	1	150	1	0	0	0	0	1	0	0	0	5698	1725	60	4	9186	4	FAT2	5	150933925	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1257129	150933925	29981335	207	22931										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153085377	153085377	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttaaaaaaccacagaaatccAagccgggtgtcttctccttc	6	12	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:153085377A>T	ENST00000285900.5	+	11	1916	c.1573A>T	c.(1573-1575)Aag>Tag	p.K525*	GRIA1_ENST00000448073.4_Nonsense_Mutation_p.K535*|GRIA1_ENST00000518783.1_Nonsense_Mutation_p.K535*|GRIA1_ENST00000521843.2_Nonsense_Mutation_p.K456*|GRIA1_ENST00000340592.5_Nonsense_Mutation_p.K525*|GRIA1_ENST00000518142.1_Nonsense_Mutation_p.K445*	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	525					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	ACAGAAATCCAAGCCGGGTGT	0.423																																					p.K535X		Atlas-SNP	.											.	GRIA1	321	.	0			c.A1603T						.						165	162	163					5																	153085377		2203	4300	6503	SO:0001587	stop_gained	2890	exon11			AAATCCAAGCCGG		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.1573A>T	chr5.hg19:g.153085377A>T	ENSP00000285900:p.Lys525*	132.0	0.0		157.0	34.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Nonsense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	A	38	6.805579	0.97853	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	.	.	.	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.2848	0.66240	1.0:0.0:0.0:0.0	.	.	.	.	X	525;525;445;479;525;456;456;535;535	.	ENSP00000285900:K525X	K	+	1	0	GRIA1	153065570	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	9.072000	0.93986	2.020000	0.59435	0.533000	0.62120	AAG	.	.		0.423	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			T	153085377	A	T	153085377	4	4	150	1	0	0	0	0	0	1	0	0	6776	131	5	4	1615	4	GRIA1	5	153085377	Nonsense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2151452	153085377	27829883	208	22932										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160071197	160071197	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtgtttctgatggtgcagccTcgaagcagaagactctcaca	11	10	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:160071197T>A	ENST00000327245.5	-	9	1662	c.816A>T	c.(814-816)cgA>cgT	p.R272R		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	272					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGGTGCAGCCTCGAAGCAGAA	0.498																																					p.R272R		Atlas-SNP	.											.	ATP10B	201	.	0			c.A816T						.						119	121	120					5																	160071197		2011	4183	6194	SO:0001819	synonymous_variant	23120	exon9			GCAGCCTCGAAGC	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.816A>T	chr5.hg19:g.160071197T>A		122.0	0.0		116.0	25.0	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	hg19	CCDS43394.1																																																																																			.	.		0.498	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		A	160071197	T	A	160071197	2	1	150	1	0	0	0	0	0	0	0	1	1117	1538	54	4		4	ATP10B	5	160071197	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	6985820	160071197	20844063	209	22933										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169174411	169174411	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgtttcaggctttatgaagGcaaagaacagatggagtttg	12	4	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:169174411G>A	ENST00000256935.8	+	23	2359	c.2279G>A	c.(2278-2280)gGc>gAc	p.G760D	DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000520908.1_Missense_Mutation_p.G252D	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	760					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTTTATGAAGGCAAAGAACAG	0.353																																					p.G760D		Atlas-SNP	.											.	DOCK2	389	.	0			c.G2279A						.						78	75	76					5																	169174411		2203	4300	6503	SO:0001583	missense	1794	exon23			ATGAAGGCAAAGA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2279G>A	chr5.hg19:g.169174411G>A	ENSP00000256935:p.Gly760Asp	119.0	0.0		99.0	23.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	13.03	2.116645	0.37339	.	.	ENSG00000134516	ENST00000256935;ENST00000520908	T;T	0.37235	1.21;1.21	5.57	5.57	0.84162	.	0.047995	0.85682	D	0.000000	T	0.49029	0.1533	L	0.35793	1.09	0.80722	D	1	D;D	0.76494	0.999;0.994	P;P	0.62089	0.879;0.898	T	0.36432	-0.9748	10	0.42905	T	0.14	.	18.3118	0.90203	0.0:0.0:1.0:0.0	.	252;760	E7ERW7;Q92608	.;DOCK2_HUMAN	D	760;252	ENSP00000256935:G760D;ENSP00000429283:G252D	ENSP00000256935:G760D	G	+	2	0	DOCK2	169106989	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.921000	0.87530	2.623000	0.88846	0.561000	0.74099	GGC	.	.		0.353	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169174411	G	A	169174411	3	1	150	1	0	0	0	0	1	0	0	0	4689	1203	42	3	2369	3	DOCK2	5	169174411	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	9103214	169174411	11740849	210	22934										
STC2	8614	hgsc.bcm.edu	37	chr5	172744922	172744922	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccggaaggtccctgagccccAaggcccccgactctgcctcg	11	19	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:172744922A>T	ENST00000265087.4	-	4	2146	c.837T>A	c.(835-837)ctT>ctA	p.L279L	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	279					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CCTGAGCCCCAAGGCCCCCGA	0.602																																					p.L279L		Atlas-SNP	.											.	STC2	59	.	0			c.T837A						.						76	81	79					5																	172744922		2203	4300	6503	SO:0001819	synonymous_variant	8614	exon4			AGCCCCAAGGCCC	AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.837T>A	chr5.hg19:g.172744922A>T		82.0	0.0		92.0	24.0	NM_003714		Silent	SNP	ENST00000265087.4	hg19	CCDS4388.1																																																																																			.	.		0.602	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	NM_003714		T	172744922	A	T	172744922	2	4	150	1	0	0	0	0	0	0	0	1	15291	117	5	4		4	STC2	5	172744922	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3570511	172744922	8170338	211	22935										
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178541069	178541069	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtggcattggtgctggaggcAttgagagggacctccagggg	19	7	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:178541069A>T	ENST00000251582.7	-	22	3536	c.3435T>A	c.(3433-3435)aaT>aaA	p.N1145K		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	1145					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		TGCTGGAGGCATTGAGAGGGA	0.567																																					p.N1145K		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.T3435A						.						204	190	195					5																	178541069		2203	4300	6503	SO:0001583	missense	9509	exon22			GGAGGCATTGAGA	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.3435T>A	chr5.hg19:g.178541069A>T	ENSP00000251582:p.Asn1145Lys	175.0	0.0		198.0	34.0	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	hg19	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	A	6.399	0.441796	0.12164	.	.	ENSG00000087116	ENST00000251582	T	0.58797	0.31	5.05	-1.47	0.08772	.	0.373259	0.22207	N	0.063151	T	0.36166	0.0957	L	0.27053	0.805	0.09310	N	1	B	0.26318	0.146	B	0.24974	0.057	T	0.28839	-1.0031	10	0.10902	T	0.67	.	11.0286	0.47759	0.5528:0.0:0.4472:0.0	.	1145	O95450	ATS2_HUMAN	K	1145	ENSP00000251582:N1145K	ENSP00000251582:N1145K	N	-	3	2	ADAMTS2	178473675	0.000000	0.05858	0.369000	0.25952	0.161000	0.22273	-0.197000	0.09518	-0.277000	0.09193	-0.441000	0.05720	AAT	.	.		0.567	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		T	178541069	A	T	178541069	3	4	150	1	0	0	0	0	1	0	0	0	265	214	8	4	204	4	ADAMTS2	5	178541069	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5796147	178541069	2374191	212	22936										
RUFY1	80230	hgsc.bcm.edu	37	chr5	179016569	179016569	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttcagctgcaacagaccgaaTttgctcacttcaagaagaac	7	11	3	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:179016569T>C	ENST00000319449.4	+	9	1061	c.1049T>C	c.(1048-1050)aTt>aCt	p.I350T	RUFY1_ENST00000393438.2_Missense_Mutation_p.I242T|RUFY1_ENST00000377001.2_Silent_p.N398N|RUFY1_ENST00000437570.2_Missense_Mutation_p.I242T	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	350					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACAGACCGAATTTGCTCACTT	0.313										HNSCC(44;0.11)																											p.I350T		Atlas-SNP	.											.	RUFY1	101	.	0			c.T1049C						.						96	96	96					5																	179016569		2203	4300	6503	SO:0001583	missense	80230	exon9			ACCGAATTTGCTC	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"Zinc fingers, FYVE domain containing"	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.1049T>C	chr5.hg19:g.179016569T>C	ENSP00000325594:p.Ile350Thr	374.0	0.0		477.0	116.0	NM_025158	Q59FF3|Q71S93|Q9H6I3	Missense_Mutation	SNP	ENST00000319449.4	hg19	CCDS4445.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.5|20.5	4.005708|4.005708	0.74932|0.74932	.|.	.|.	ENSG00000176783|ENSG00000176783	ENST00000508609|ENST00000319449;ENST00000437570;ENST00000393438	.|T;T;T	.|0.80123	.|-1.34;-1.34;-1.34	5.09|5.09	5.09|5.09	0.68999|0.68999	.|.	.|0.093541	.|0.64402	.|D	.|0.000001	D|D	0.87148|0.87148	0.6105|0.6105	M|M	0.78049|0.78049	2.395|2.395	0.80722|0.80722	D|D	1|1	.|D	.|0.62365	.|0.991	.|P	.|0.57468	.|0.821	D|D	0.87581|0.87581	0.2484|0.2484	5|10	.|0.44086	.|T	.|0.13	-15.9482|-15.9482	15.0943|15.0943	0.72220|0.72220	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|350	.|Q96T51	.|RUFY1_HUMAN	L|T	139|350;242;242	.|ENSP00000325594:I350T;ENSP00000390025:I242T;ENSP00000377087:I242T	.|ENSP00000325594:I350T	F|I	+|+	1|2	0|0	RUFY1|RUFY1	178949175|178949175	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	6.998000|6.998000	0.76277|0.76277	2.148000|2.148000	0.66965|0.66965	0.449000|0.449000	0.29647|0.29647	TTT|ATT	.	.		0.313	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451		C	179016569	T	C	179016569	3	2	150	1	0	0	0	0	1	0	0	0	13753	1493	52	2	1083	2	RUFY1	5	179016569	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	475500	179016569	1898691	213	22937										
MGAT1	4245	hgsc.bcm.edu	37	chr5	180219134	180219134	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggcctttggccacttgggctCcagctcagcccagagctcgg	13	15	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr5:180219134C>G	ENST00000446023.2	-	3	1588	c.838G>C	c.(838-840)Gag>Cag	p.E280Q	MGAT1_ENST00000307826.4_Missense_Mutation_p.E280Q|MGAT1_ENST00000427865.2_Missense_Mutation_p.E280Q|MGAT1_ENST00000393340.3_Missense_Mutation_p.E280Q|MGAT1_ENST00000333055.3_Missense_Mutation_p.E280Q	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	280					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CACTTGGGCTCCAGCTCAGCC	0.662																																					p.E280Q		Atlas-SNP	.											.	MGAT1	48	.	0			c.G838C						.						27	28	28					5																	180219134		2203	4298	6501	SO:0001583	missense	4245	exon3			TGGGCTCCAGCTC	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.838G>C	chr5.hg19:g.180219134C>G	ENSP00000404718:p.Glu280Gln	77.0	0.0		86.0	21.0	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	hg19	CCDS4458.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.367841	0.82463	.	.	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865	D;D;D;D;D	0.84873	-1.91;-1.91;-1.91;-1.91;-1.91	5.41	5.41	0.78517	.	0.055037	0.64402	D	0.000001	D	0.91730	0.7385	M	0.77486	2.375	0.80722	D	1	D	0.71674	0.998	D	0.68765	0.96	D	0.90626	0.4563	10	0.37606	T	0.19	-31.8305	17.0589	0.86541	0.0:1.0:0.0:0.0	.	280	P26572	MGAT1_HUMAN	Q	280;280;280;280;137;280	ENSP00000332073:E280Q;ENSP00000311888:E280Q;ENSP00000404718:E280Q;ENSP00000377010:E280Q;ENSP00000402838:E280Q	ENSP00000311888:E280Q	E	-	1	0	MGAT1	180151740	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	7.111000	0.77077	2.696000	0.92011	0.655000	0.94253	GAG	.	.		0.662	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618		G	180219134	C	G	180219134	3	3	150	1	0	0	0	0	1	0	0	0	9551	864	30	4	503	4	MGAT1	5	180219134	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	1202565	180219134	696126	214	22938										
SCAND3	114821	hgsc.bcm.edu	37	chr6	28540129	28540129	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aacaaatttgtaagatgttcActgataacttttcgcagatg	7	6	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:28540129A>T	ENST00000452236.2	-	4	4154	c.3537T>A	c.(3535-3537)agT>agA	p.S1179R		NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						taagatgttcactgataactt	0.289																																					p.S1179R		Atlas-SNP	.											.	SCAND3	156	.	0			c.T3537A						.						34	33	33					6																	28540129		2197	4290	6487	SO:0001583	missense	114821	exon4			ATGTTCACTGATA																												ENST00000452236.2:c.3537T>A	chr6.hg19:g.28540129A>T	ENSP00000395259:p.Ser1179Arg	191.0	0.0		293.0	205.0	NM_052923		Missense_Mutation	SNP	ENST00000452236.2	hg19	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	A	1.434	-0.569409	0.03910	.	.	ENSG00000232040	ENST00000452236	T	0.20738	2.05	2.53	-1.59	0.08453	Ribonuclease H-like (1);	1.115970	0.07146	U	0.848318	T	0.03695	0.0105	L	0.34521	1.04	0.18873	N	0.999988	B	0.15719	0.014	B	0.14023	0.01	T	0.43621	-0.9380	10	0.16896	T	0.51	.	3.93	0.09281	0.4294:0.4327:0.1379:0.0	.	1179	Q6R2W3	SCND3_HUMAN	R	1179	ENSP00000395259:S1179R	ENSP00000395259:S1179R	S	-	3	2	SCAND3	28648108	0.335000	0.24748	0.329000	0.25429	0.941000	0.58515	-0.110000	0.10824	-0.343000	0.08351	0.533000	0.62120	AGT	.	.		0.289	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			T	28540129	A	T	28540129	3	4	150	1	0	0	0	0	1	0	0	0	13891	156	6	4	444	4	SCAND3	6	28540129	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		28540129	142574938	215	22939										
HLA-G	3135	hgsc.bcm.edu	37	chr6	29797324	29797324	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggatggggaggaccagacccAggacgtggagctcgtggaga	19	8	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:29797324A>T	ENST00000360323.6	+	4	773	c.749A>T	c.(748-750)cAg>cTg	p.Q250L	HLA-G_ENST00000428701.1_Missense_Mutation_p.Q250L|HLA-G_ENST00000376818.3_Missense_Mutation_p.Q158L|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376828.2_Missense_Mutation_p.Q255L			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	250	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						GACCAGACCCAGGACGTGGAG	0.622																																					p.Q250L		Atlas-SNP	.											.	HLA-G	90	.	0			c.A749T						.						79	73	75					6																	29797324		2203	4300	6503	SO:0001583	missense	3135	exon5			AGACCCAGGACGT		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4964	protein-coding gene	gene with protein product	"b2 microglobulin"	142871	"HLA-G histocompatibility antigen, class I, G"				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.749A>T	chr6.hg19:g.29797324A>T	ENSP00000353472:p.Gln250Leu	120.0	0.0		156.0	104.0	NM_002127		Missense_Mutation	SNP	ENST00000360323.6	hg19	CCDS4668.1	.	.	.	.	.	.	.	.	.	.	.	10.54	1.379690	0.24944	.	.	ENSG00000204632	ENST00000376828;ENST00000428701;ENST00000360323;ENST00000376818	T;T;T;T	0.03035	4.07;4.07;4.07;4.07	1.72	1.72	0.24424	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.38272	U	0.001742	T	0.09555	0.0235	M	0.89904	3.07	0.25782	N	0.984716	D;P;D	0.57899	0.978;0.891;0.981	D;B;D	0.75484	0.986;0.391;0.97	T	0.02743	-1.1116	10	0.87932	D	0	.	7.1442	0.25573	1.0:0.0:0.0:0.0	.	255;158;250	Q5RJ85;Q31611;P17693	.;.;HLAG_HUMAN	L	255;250;250;158	ENSP00000366024:Q255L;ENSP00000412927:Q250L;ENSP00000353472:Q250L;ENSP00000366014:Q158L	ENSP00000353472:Q250L	Q	+	2	0	HLA-G	29905303	0.993000	0.37304	0.497000	0.27552	0.016000	0.09150	4.430000	0.59907	0.791000	0.33826	0.248000	0.18094	CAG	.	.		0.622	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		T	29797324	A	T	29797324	3	4	150	1	0	0	0	0	1	0	0	0	7221	188	7	4	763	4	HLA-G	6	29797324	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1257195	29797324	141317743	216	22940										
CDSN	170679	hgsc.bcm.edu	37	chr6	31084505	31084505	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggagccacccaccacctcgTagccaccataggatttgtct	8	15	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:31084505T>A	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Missense_Mutation_p.Y296F|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						CACCACCTCGTAGCCACCATA	0.552																																					p.Y296F		Atlas-SNP	.											.	CDSN	48	.	0			c.A887T						.						34	33	34					6																	31084505		1920	3825	5745	SO:0001627	intron_variant	1041	exon2			ACCTCGTAGCCAC	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"chromosome 6 open reading frame 16"	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1837T>A	chr6.hg19:g.31084505T>A		37.0	0.0		67.0	50.0	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	hg19	CCDS34390.1	.	.	.	.	.	.	.	.	.	.	T	19.69	3.875591	0.72180	.	.	ENSG00000204539	ENST00000376288	T	0.12984	2.63	4.76	4.76	0.60689	.	0.000000	0.46145	D	0.000305	T	0.14399	0.0348	L	0.36672	1.1	0.28094	N	0.931694	D	0.67145	0.996	D	0.77557	0.99	T	0.02966	-1.1088	10	0.66056	D	0.02	-14.1856	10.6432	0.45604	0.0:0.0:0.0:1.0	.	296	Q15517	CDSN_HUMAN	F	296	ENSP00000365465:Y296F	ENSP00000365465:Y296F	Y	-	2	0	CDSN	31192484	0.988000	0.35896	0.998000	0.56505	0.977000	0.68977	2.242000	0.43106	1.778000	0.52293	0.448000	0.29417	TAC	.	.		0.552	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		A	31084505	T	A	31084505	1	1	150	0	1	0	0	0	0	0	0	0	3181	1638	57	4		4	CDSN	6	31084505	Intron	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1287181	31084505	140030562	217	22941										
XPO5	57510	hgsc.bcm.edu	37	chr6	43526298	43526298	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaaccgagaatattcacagcTagggctgtctgttttagaag	10	7	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:43526298T>A	ENST00000265351.7	-	12	1462	c.1252A>T	c.(1252-1254)Agc>Tgc	p.S418C	XPO5_ENST00000424378.2_5'UTR	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	418					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			TATTCACAGCTAGGGCTGTCT	0.423																																					p.S418C		Atlas-SNP	.											.	XPO5	79	.	0			c.A1252T						.						70	65	66					6																	43526298		1848	4083	5931	SO:0001583	missense	57510	exon12			CACAGCTAGGGCT	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.1252A>T	chr6.hg19:g.43526298T>A	ENSP00000265351:p.Ser418Cys	111.0	0.0		160.0	118.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Missense_Mutation	SNP	ENST00000265351.7	hg19	CCDS47430.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582744	0.86748	.	.	ENSG00000124571	ENST00000265351;ENST00000436943;ENST00000439465	D	0.89485	-2.52	6.06	6.06	0.98353	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.91774	0.7398	L	0.60455	1.87	0.58432	D	0.999999	D	0.89917	1.0	D	0.67231	0.95	D	0.92460	0.5977	10	0.62326	D	0.03	-18.4017	16.6093	0.84858	0.0:0.0:0.0:1.0	.	418	Q9HAV4	XPO5_HUMAN	C	418;123;46	ENSP00000265351:S418C	ENSP00000265351:S418C	S	-	1	0	XPO5	43634276	1.000000	0.71417	0.960000	0.40013	0.955000	0.61496	4.748000	0.62148	2.324000	0.78689	0.533000	0.62120	AGC	.	.		0.423	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		A	43526298	T	A	43526298	3	1	150	1	0	0	0	0	1	0	0	0	17462	1522	53	4	2446	4	XPO5	6	43526298	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	12441793	43526298	127588769	218	22942										
TMEM63B	55362	hgsc.bcm.edu	37	chr6	44116248	44116248	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	taaccagtgcccatctttctAgcatcctgaaggacttcaac	6	13	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:44116248A>T	ENST00000259746.9	+	14	1304		c.e14-1		TMEM63B_ENST00000323267.6_Splice_Site			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B						ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			CCATCTTTCTAGCATCCTGAA	0.622																																					.		Atlas-SNP	.											.	TMEM63B	77	.	0			c.1122-2A>T						.						105	95	99					6																	44116248		2203	4300	6503	SO:0001630	splice_region_variant	55362	exon14			CTTTCTAGCATCC	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 110"	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1122-1A>T	chr6.hg19:g.44116248A>T		63.0	0.0		78.0	14.0	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Splice_Site	SNP	ENST00000259746.9	hg19	CCDS34461.1	.	.	.	.	.	.	.	.	.	.	A	15.77	2.931602	0.52866	.	.	ENSG00000137216	ENST00000259746;ENST00000323267;ENST00000371893	.	.	.	4.38	4.38	0.52667	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9603	0.58453	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM63B	44224226	1.000000	0.71417	0.991000	0.47740	0.645000	0.38454	7.106000	0.77039	1.851000	0.53745	0.460000	0.39030	.	.	.		0.622	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	Intron	T	44116248	A	T	44116248	5	4	150	1	0	0	0	0	0	0	1	0	16206	434	15	4	1170	4	TMEM63B	6	44116248	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	589950	44116248	126998819	219	22943										
TNFRSF21	27242	hgsc.bcm.edu	37	chr6	47202430	47202430	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggtaataaaggaaccgttccTgctcagcgcggaggagccgc	14	11	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:47202430T>A	ENST00000296861.2	-	5	2107	c.1714A>T	c.(1714-1716)Agg>Tgg	p.R572W		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	572					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			GAACCGTTCCTGCTCAGCGCG	0.597																																					p.R572W		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.A1714T						.						45	43	44					6																	47202430		2203	4300	6503	SO:0001583	missense	27242	exon5			CGTTCCTGCTCAG	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"Tumor necrosis factor receptor superfamily", "CD molecules"	13469	protein-coding gene	gene with protein product	"death receptor 6"	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1714A>T	chr6.hg19:g.47202430T>A	ENSP00000296861:p.Arg572Trp	51.0	0.0		104.0	13.0	NM_014452	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	hg19	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.144082	0.77888	.	.	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.76186	-1.0	5.26	2.61	0.31194	.	0.080591	0.85682	D	0.000000	T	0.69717	0.3142	L	0.29908	0.895	0.52501	D	0.999957	D	0.71674	0.998	D	0.69307	0.963	T	0.74765	-0.3554	10	0.87932	D	0	.	12.562	0.56286	0.0:0.0:0.3803:0.6197	.	572	O75509	TNR21_HUMAN	W	572;261	ENSP00000296861:R572W	ENSP00000296861:R572W	R	-	1	2	TNFRSF21	47310389	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	2.173000	0.42472	0.917000	0.36895	0.529000	0.55759	AGG	.	.		0.597	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		A	47202430	T	A	47202430	3	1	150	1	0	0	0	0	1	0	0	0	16310	1579	55	4	261	4	TNFRSF21	6	47202430	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3086182	47202430	123912637	220	22944										
GPR111	222611	hgsc.bcm.edu	37	chr6	47650129	47650129	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tggccttcgtgatcccagctTtggccatcgtggtagtaaac	11	11	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:47650129T>A	ENST00000296862.1	+	6	1834	c.1834T>A	c.(1834-1836)Ttg>Atg	p.L612M	GPR111_ENST00000398742.2_Missense_Mutation_p.L544M|GPR111_ENST00000507065.1_Missense_Mutation_p.L544M			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	612					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						GATCCCAGCTTTGGCCATCGT	0.532																																					p.L544M		Atlas-SNP	.											.	GPR111	123	.	0			c.T1630A						.						57	58	57					6																	47650129		2051	4204	6255	SO:0001583	missense	222611	exon7			CCAGCTTTGGCCA	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"-", "GPCR / Class B : Orphans"	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.1834T>A	chr6.hg19:g.47650129T>A	ENSP00000296862:p.Leu612Met	97.0	0.0		138.0	26.0	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.60	3.429870	0.62844	.	.	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.42513	0.97;0.97;0.97	5.64	3.82	0.43975	GPCR, family 2-like (1);	0.000000	0.49305	D	0.000150	T	0.54791	0.1880	M	0.85542	2.76	0.34655	D	0.722014	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.64339	-0.6431	10	0.72032	D	0.01	.	9.9031	0.41359	0.0:0.7834:0.1396:0.077	.	544;612	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	M	544;612;544	ENSP00000422934:L544M;ENSP00000296862:L612M;ENSP00000381727:L544M	ENSP00000296862:L612M	L	+	1	2	GPR111	47758088	0.590000	0.26815	0.993000	0.49108	0.852000	0.48524	1.292000	0.33342	0.699000	0.31761	-0.242000	0.12053	TTG	.	.		0.532	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839		A	47650129	T	A	47650129	3	1	150	1	0	0	0	0	1	0	0	0	6636	1838	64	4	1648	4	GPR111	6	47650129	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	447699	47650129	123464938	221	22945										
CD109	135228	hgsc.bcm.edu	37	chr6	74502490	74502490	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaagaaacaactgacagataAtttgaaagaaaaagctcttt	6	5	1	5			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:74502490A>C	ENST00000287097.5	+	23	2955	c.2843A>C	c.(2842-2844)aAt>aCt	p.N948T	CD109_ENST00000474094.1_3'UTR|CD109_ENST00000437994.2_Missense_Mutation_p.N948T|CD109_ENST00000422508.2_Missense_Mutation_p.N871T			Q6YHK3	CD109_HUMAN	CD109 molecule	948					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CTGACAGATAATTTGAAAGAA	0.318																																					p.N948T		Atlas-SNP	.											.	CD109	170	.	0			c.A2843C						.						50	52	52					6																	74502490		2203	4298	6501	SO:0001583	missense	135228	exon23			CAGATAATTTGAA	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2843A>C	chr6.hg19:g.74502490A>C	ENSP00000287097:p.Asn948Thr	57.0	0.0		54.0	17.0	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	hg19	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	A	12.61	1.988810	0.35131	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.37915	1.17;1.17;1.17	5.87	-2.46	0.06461	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.507932	0.23521	N	0.047297	T	0.08447	0.0210	L	0.28649	0.875	0.09310	N	1	B;B;B	0.19331	0.035;0.027;0.014	B;B;B	0.26693	0.029;0.072;0.011	T	0.32666	-0.9898	10	0.35671	T	0.21	.	6.3715	0.21483	0.5443:0.2134:0.2424:0.0	.	871;948;948	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	T	948;871;948	ENSP00000388062:N948T;ENSP00000404475:N871T;ENSP00000287097:N948T	ENSP00000287097:N948T	N	+	2	0	CD109	74559211	0.032000	0.19561	0.001000	0.08648	0.928000	0.56348	1.471000	0.35365	-0.287000	0.09064	-0.316000	0.08728	AAT	.	.		0.318	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		C	74502490	A	C	74502490	3	2	150	1	0	0	0	0	1	0	0	0	2965	101	4	5	2933	5	CD109	6	74502490	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	26852361	74502490	96612577	222	22946										
IBTK	25998	hgsc.bcm.edu	37	chr6	82921267	82921267	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctttccatccactgatttcaTggtcacgtcacacagaaatg	6	12	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:82921267T>A	ENST00000306270.7	-	14	2863	c.2314A>T	c.(2314-2316)Atg>Ttg	p.M772L	IBTK_ENST00000510291.1_Missense_Mutation_p.M772L|RNU6-130P_ENST00000411112.1_RNA|IBTK_ENST00000503631.1_Missense_Mutation_p.M571L	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	772	BTB 2. {ECO:0000255|PROSITE- ProRule:PRU00037}.				negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		ACTGATTTCATGGTCACGTCA	0.343																																					p.M772L		Atlas-SNP	.											.	IBTK	128	.	0			c.A2314T						.						77	73	74					6																	82921267		2203	4300	6503	SO:0001583	missense	25998	exon14			ATTTCATGGTCAC	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.2314A>T	chr6.hg19:g.82921267T>A	ENSP00000305721:p.Met772Leu	479.0	0.0		292.0	104.0	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	hg19	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	T	12.41	1.930562	0.34096	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.59906	0.23;0.23;0.23	5.74	5.74	0.90152	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.091238	0.85682	D	0.000000	T	0.09774	0.0240	N	0.00329	-1.635	0.37649	D	0.922343	B;B;B;B	0.21071	0.051;0.005;0.004;0.005	B;B;B;B	0.20184	0.028;0.01;0.006;0.01	T	0.12041	-1.0563	10	0.30078	T	0.28	-18.8857	8.9326	0.35680	0.1238:0.0:0.1294:0.7468	.	571;772;772;772	E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0	.;.;.;IBTK_HUMAN	L	772;571;772	ENSP00000305721:M772L;ENSP00000422762:M571L;ENSP00000426405:M772L	ENSP00000305721:M772L	M	-	1	0	IBTK	82977986	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.395000	0.52558	2.190000	0.69967	0.477000	0.44152	ATG	.	.		0.343	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		A	82921267	T	A	82921267	3	1	150	1	0	0	0	0	1	0	0	0	7485	1464	51	4	1811	4	IBTK	6	82921267	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	8418777	82921267	88193800	223	22947										
ORC3L	23595	hgsc.bcm.edu	37	chr6	88375515	88375515	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgctgaaaaaatggatgcaaAttctgcaacctcagaagaaa	8	7	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:88375515A>C	ENST00000392844.3	+	19	2042	c.1994A>C	c.(1993-1995)aAt>aCt	p.N665T	ORC3_ENST00000546266.1_Missense_Mutation_p.N522T|ORC3_ENST00000257789.4_Missense_Mutation_p.N666T	NM_012381.3|NM_181837.2	NP_036513.2|NP_862820.1	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3	665					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|neural precursor cell proliferation (GO:0061351)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|origin recognition complex (GO:0000808)	DNA replication origin binding (GO:0003688)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	28						ATGGATGCAAATTCTGCAACC	0.313																																					p.N666T		Atlas-SNP	.											.	ORC3	51	.	0			c.A1997C						.						54	56	55					6																	88375515		2203	4299	6502	SO:0001583	missense	23595	exon19			ATGCAAATTCTGC	AF093535	CCDS5012.1, CCDS43486.1, CCDS56440.1	6q	2010-10-12	2010-10-12	2010-10-12	ENSG00000135336	ENSG00000135336			8489	protein-coding gene	gene with protein product		604972	"origin recognition complex, subunit 3 (yeast homolog)-like", "origin recognition complex, subunit 3-like (yeast)", "origin recognition complex, subunit 3 honolog (yeast)"	ORC3L		9829972, 10402192	Standard	NM_181837		Approved	IMAGE50150, LATHEO	uc003pmg.3	Q9UBD5	OTTHUMG00000015179	ENST00000392844.3:c.1994A>C	chr6.hg19:g.88375515A>C	ENSP00000376586:p.Asn665Thr	105.0	0.0		51.0	21.0	NM_181837	A2A2T5|B4E025|Q13565|Q53GY6|Q5T159|Q6IUY7|Q86TN5|Q9UG44|Q9UNT6	Missense_Mutation	SNP	ENST00000392844.3	hg19	CCDS43486.1	.	.	.	.	.	.	.	.	.	.	A	13.15	2.150056	0.37923	.	.	ENSG00000135336	ENST00000392844;ENST00000257789;ENST00000546266	T;T;T	0.12569	3.01;3.02;2.67	5.85	2.85	0.33270	.	0.428631	0.27522	N	0.018983	T	0.04363	0.0120	L	0.43152	1.355	0.09310	N	0.999998	B;B;B	0.29037	0.002;0.121;0.231	B;B;B	0.32980	0.003;0.034;0.156	T	0.40869	-0.9540	10	0.16896	T	0.51	-1.2314	12.0699	0.53609	0.9156:0.0:0.0844:0.0	.	603;665;666	B4E014;Q9UBD5;Q9UBD5-2	.;ORC3_HUMAN;.	T	665;666;522	ENSP00000376586:N665T;ENSP00000257789:N666T;ENSP00000444695:N522T	ENSP00000257789:N666T	N	+	2	0	ORC3	88432234	1.000000	0.71417	0.142000	0.22268	0.996000	0.88848	2.230000	0.42999	0.419000	0.25927	0.533000	0.62120	AAT	.	.		0.313	ORC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041452.2			C	88375515	A	C	88375515	3	2	150	1	0	0	0	0	1	0	0	0	11272	101	4	5	2071	5	ORC3L	6	88375515	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5454248	88375515	82739552	224	22948										
TRDN	10345	hgsc.bcm.edu	37	chr6	123851680	123851680	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtattttcctttcaggtttcTcttgtttttcagtcttatct	5	8	5	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:123851680T>A	ENST00000398178.3	-	5	476	c.455A>T	c.(454-456)gAg>gTg	p.E152V	TRDN_ENST00000334268.4_Missense_Mutation_p.E152V|TRDN_ENST00000542443.1_Missense_Mutation_p.E152V|TRDN_ENST00000546248.1_Missense_Mutation_p.E152V	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	152					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		TTCAGGTTTCTCTTGTTTTTC	0.234																																					p.E152V		Atlas-SNP	.											.	TRDN	88	.	0			c.A455T						.						47	41	43					6																	123851680		1070	2430	3500	SO:0001583	missense	10345	exon5			GGTTTCTCTTGTT	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.455A>T	chr6.hg19:g.123851680T>A	ENSP00000381240:p.Glu152Val	214.0	0.0		120.0	45.0	NM_001256022	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	hg19	CCDS55053.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.84|13.84	2.358081|2.358081	0.41801|0.41801	.|.	.|.	ENSG00000186439|ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268;ENST00000542014;ENST00000543022;ENST00000546248;ENST00000333613;ENST00000542443;ENST00000265491|ENST00000359698;ENST00000422596	T;T;T;T|.	0.70045|.	1.26;1.26;0.91;-0.45|.	5.33|5.33	5.33|5.33	0.75918|0.75918	Aspartyl beta-hydroxylase/Triadin domain (1);|.	0.062472|.	0.64402|.	D|.	0.000010|.	T|.	0.48003|.	0.1476|.	M|M	0.76574|0.76574	2.34|2.34	0.29689|0.29689	N|N	0.841055|0.841055	D;P;D;D;D|.	0.89917|.	0.996;0.885;1.0;1.0;1.0|.	D;P;D;D;D|.	0.77557|.	0.99;0.487;0.979;0.979;0.99|.	T|.	0.49934|.	-0.8886|.	10|.	0.87932|.	D|.	0|.	-17.1943|-17.1943	12.9569|12.9569	0.58432|0.58432	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	152;152;152;152;152|.	F5H6E3;F5H2W7;Q5SWK9;Q8IVK2;Q13061|.	.;.;.;.;TRDN_HUMAN|.	V|X	152;152;152;152;152;152;57;152;57|11	ENSP00000381240:E152V;ENSP00000333984:E152V;ENSP00000439281:E152V;ENSP00000437684:E152V|.	ENSP00000265491:E57V|.	E|R	-|-	2|1	0|2	TRDN|TRDN	123893379|123893379	0.758000|0.758000	0.28405|0.28405	0.819000|0.819000	0.32651|0.32651	0.808000|0.808000	0.45660|0.45660	2.246000|2.246000	0.43142|0.43142	2.155000|2.155000	0.67459|0.67459	0.460000|0.460000	0.39030|0.39030	GAG|AGA	.	.		0.234	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	123851680	T	A	123851680	3	1	150	1	0	0	0	0	1	0	0	0	16483	1551	54	4	1882	4	TRDN	6	123851680	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	35476165	123851680	47263387	225	22949										
C6orf174	387104	hgsc.bcm.edu	37	chr6	127837602	127837602	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gggaccgggtggccgcgattGtctgtcgcagcgaactgtcc	16	12	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:127837602G>T	ENST00000525778.1	-	2	903	c.158C>A	c.(157-159)aCa>aAa	p.T53K	SOGA3_ENST00000556132.1_Missense_Mutation_p.T53K|SOGA3_ENST00000465909.2_Missense_Mutation_p.T53K|SOGA3_ENST00000481848.2_Missense_Mutation_p.T53K|SOGA3_ENST00000368268.2_Missense_Mutation_p.T53K			Q5TF21	SOGA3_HUMAN	SOGA family member 3	53					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GGCCGCGATTGTCTGTCGCAG	0.642																																					p.T53K		Atlas-SNP	.											.	.	.	.	0			c.C158A						.						28	32	31					6																	127837602		1981	4163	6144	SO:0001583	missense	387104	exon2			GCGATTGTCTGTC	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.158C>A	chr6.hg19:g.127837602G>T	ENSP00000434570:p.Thr53Lys	25.0	0.0		16.0	7.0	NM_001012279		Missense_Mutation	SNP	ENST00000525778.1	hg19	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.271568	0.40194	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.79	5.79	0.91817	.	0.573888	0.16839	N	0.197421	T	0.09730	0.0239	N	0.08118	0	0.35030	D	0.758737	B	0.17667	0.023	B	0.28139	0.086	T	0.16041	-1.0416	10	0.13853	T	0.58	-1.9333	18.7926	0.91980	0.0:0.0:1.0:0.0	.	53	Q5TF21	CF174_HUMAN	K	53	ENSP00000451768:T53K;ENSP00000357251:T53K;ENSP00000434570:T53K;ENSP00000435559:T53K	ENSP00000435559:T53K	T	-	2	0	C6orf174	127879295	0.444000	0.25649	0.858000	0.33744	0.061000	0.15899	2.114000	0.41911	2.735000	0.93741	0.561000	0.74099	ACA	.	.		0.642	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		T	127837602	G	T	127837602	3	4	150	1	0	0	0	0	1	0	0	0	2347	1377	48	3	2709	3	C6orf174	6	127837602	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	3985922	127837602	43277465	226	22950										
AHI1	54806	hgsc.bcm.edu	37	chr6	135644338	135644338	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tagctggaaaataaccttccTgtccctttcctatgctgcca	6	13	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:135644338T>A	ENST00000367800.4	-	23	3506	c.3290A>T	c.(3289-3291)cAg>cTg	p.Q1097L	AHI1_ENST00000457866.2_Missense_Mutation_p.Q1097L|AHI1_ENST00000417892.2_Missense_Mutation_p.Q451L	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	1097	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		ATAACCTTCCTGTCCCTTTCC	0.403																																					p.Q1097L		Atlas-SNP	.											.	AHI1	81	.	0			c.A3290T						.						110	104	105					6																	135644338		1896	4098	5994	SO:0001583	missense	54806	exon24			CCTTCCTGTCCCT	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.3290A>T	chr6.hg19:g.135644338T>A	ENSP00000356774:p.Gln1097Leu	108.0	0.0		69.0	25.0	NM_017651	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Missense_Mutation	SNP	ENST00000367800.4	hg19	CCDS47483.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.17|18.17	3.564872|3.564872	0.65651|0.65651	.|.	.|.	ENSG00000135541|ENSG00000135541	ENST00000367800;ENST00000457866;ENST00000417892;ENST00000265602|ENST00000367799	T;T;T;T|.	0.53857|.	0.6;0.6;0.6;0.6|.	6.06|6.06	6.06|6.06	0.98353|0.98353	Src homology-3 domain (5);|.	0.119062|.	0.56097|.	D|.	0.000022|.	T|T	0.63745|0.63745	0.2537|0.2537	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	D|D	1|1	P;P|.	0.47034|.	0.889;0.659|.	P;B|.	0.49799|.	0.622;0.424|.	T|T	0.62840|0.62840	-0.6769|-0.6769	10|5	0.62326|.	D|.	0.03|.	-13.0256|-13.0256	16.6093|16.6093	0.84858|0.84858	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1097;1097|.	Q8N157;Q4FD35|.	AHI1_HUMAN;.|.	L|W	1097;1097;451;1097|597	ENSP00000356774:Q1097L;ENSP00000388650:Q1097L;ENSP00000416867:Q451L;ENSP00000265602:Q1097L|.	ENSP00000265602:Q1097L|.	Q|R	-|-	2|1	0|2	AHI1|AHI1	135686031|135686031	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.835000|3.835000	0.55805|0.55805	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	CAG|AGG	.	.		0.403	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		A	135644338	T	A	135644338	3	1	150	1	0	0	0	0	1	0	0	0	413	1580	55	4	320	4	AHI1	6	135644338	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	7806736	135644338	35470729	227	22951										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152651184	152651184	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tctgcaccattcggctctcaCattctgtcaccgtctcacca	5	17	5	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:152651184C>A	ENST00000367255.5	-	78	15237	c.14636G>T	c.(14635-14637)tGt>tTt	p.C4879F	SYNE1_ENST00000341594.5_Missense_Mutation_p.C4626F|SYNE1_ENST00000265368.4_Missense_Mutation_p.C4879F|SYNE1_ENST00000423061.1_Missense_Mutation_p.C4808F|SYNE1_ENST00000448038.1_Missense_Mutation_p.C4808F	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4879					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCGGCTCTCACATTCTGTCAC	0.537										HNSCC(10;0.0054)																											p.C4879F		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G14636T						.						89	85	86					6																	152651184		2203	4300	6503	SO:0001583	missense	23345	exon78			CTCTCACATTCTG	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.14636G>T	chr6.hg19:g.152651184C>A	ENSP00000356224:p.Cys4879Phe	69.0	0.0		65.0	18.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	15.44	2.833807	0.50951	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000002	T	0.60715	0.2290	L	0.54323	1.7	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.998;0.999	D;D;D;D	0.76071	0.987;0.923;0.923;0.965	T	0.59584	-0.7427	10	0.56958	D	0.05	.	20.0109	0.97448	0.0:1.0:0.0:0.0	.	4879;4879;4879;4808	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	F	4879;4808;4879;4808;4626	ENSP00000356224:C4879F;ENSP00000396024:C4808F;ENSP00000265368:C4879F;ENSP00000390975:C4808F;ENSP00000341887:C4626F	ENSP00000265368:C4879F	C	-	2	0	SYNE1	152692877	1.000000	0.71417	0.995000	0.50966	0.942000	0.58702	7.818000	0.86416	2.738000	0.93877	0.591000	0.81541	TGT	.	.		0.537	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152651184	C	A	152651184	3	1	150	1	0	0	0	0	1	0	0	0	15460	478	17	3	12106	3	SYNE1	6	152651184	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	17006846	152651184	18463883	228	22952										
TIAM2	26230	hgsc.bcm.edu	37	chr6	155458554	155458554	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctgagaacatagaaacatctAcagaaaccgccgagtccagc	8	12	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr6:155458554A>T	ENST00000461783.3	+	7	2711	c.1438A>T	c.(1438-1440)Aca>Tca	p.T480S	TIAM2_ENST00000318981.5_Missense_Mutation_p.T480S|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000529824.2_Missense_Mutation_p.T480S|TIAM2_ENST00000360366.4_Missense_Mutation_p.T480S|TIAM2_ENST00000456144.1_Missense_Mutation_p.T480S			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	480					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		AGAAACATCTACAGAAACCGC	0.532																																					p.T480S		Atlas-SNP	.											.	TIAM2	161	.	0			c.A1438T						.						85	94	91					6																	155458554		2203	4300	6503	SO:0001583	missense	26230	exon4			ACATCTACAGAAA		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.1438A>T	chr6.hg19:g.155458554A>T	ENSP00000437188:p.Thr480Ser	116.0	0.0		106.0	37.0	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	hg19	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	A	4.757	0.140758	0.09083	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000360366;ENST00000529824	T;T;T;T;T;T	0.05319	3.58;3.46;3.53;3.58;3.59;3.53	6.08	4.88	0.63580	.	0.111618	0.64402	N	0.000010	T	0.02047	0.0064	L	0.43701	1.375	0.80722	D	1	B;B	0.21147	0.052;0.031	B;B	0.21151	0.033;0.015	T	0.40979	-0.9534	10	0.25751	T	0.34	.	5.8384	0.18619	0.653:0.0:0.0701:0.2769	.	480;480	Q8IVF5-2;Q8IVF5	.;TIAM2_HUMAN	S	480;726;480;480;480;480;480	ENSP00000437188:T480S;ENSP00000434901:T480S;ENSP00000407746:T480S;ENSP00000327315:T480S;ENSP00000353528:T480S;ENSP00000433348:T480S	ENSP00000327315:T480S	T	+	1	0	TIAM2	155500246	0.973000	0.33851	0.011000	0.14972	0.009000	0.06853	3.158000	0.50723	1.066000	0.40716	0.533000	0.62120	ACA	.	.		0.532	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155458554	A	T	155458554	3	4	150	1	0	0	0	0	1	0	0	0	15906	391	14	4	1444	4	TIAM2	6	155458554	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2807370	155458554	15656513	229	22953										
LFNG	3955	hgsc.bcm.edu	37	chr7	2552910	2552910	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gatggatggatggatggatgAgtggagcccaacaccagctc	15	8	0	1	rs199517402		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:2552910A>G	ENST00000402506.1	+	2	293	c.167A>G	c.(166-168)gAg>gGg	p.E56G		NM_001166355.1	NP_001159827.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		tggatggatgagtggaGCCCA	0.547																																					p.E56G		Atlas-SNP	.											.	LFNG	57	.	0			c.A167G						.						101	98	99					7																	2552910		1568	3582	5150	SO:0001583	missense	3955	exon2			TGGATGAGTGGAG	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"Beta 3-glycosyltransferases"	6560	protein-coding gene	gene with protein product		602576	"lunatic fringe (Drosophila) homolog", "lunatic fringe homolog (Drosophila)"			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000402506.1:c.167A>G	chr7.hg19:g.2552910A>G	ENSP00000385764:p.Glu56Gly	68.0	0.0		57.0	4.0	NM_001166355	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Missense_Mutation	SNP	ENST00000402506.1	hg19	CCDS55081.1	.	.	.	.	.	.	.	.	.	.	a	2.466	-0.323062	0.05350	.	.	ENSG00000106003	ENST00000402506	T	0.44083	0.93	1.61	-1.65	0.08291	.	.	.	.	.	T	0.21590	0.0520	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.24368	-1.0162	7	0.87932	D	0	.	5.1731	0.15120	0.5881:0.0:0.4119:0.0	.	.	.	.	G	56	ENSP00000385764:E56G	ENSP00000385764:E56G	E	+	2	0	LFNG	2519436	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.608000	0.05641	-0.582000	0.05929	-1.528000	0.00924	GAG	.	.		0.547	LFNG-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000325023.1	NM_002304		G	2552910	A	G	2552910	3	3	150	1	0	0	0	0	1	0	0	0	8746	304	11	2	173	2	LFNG	7	2552910	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		2552910	156585753	230	22954										
MMD2	221938	hgsc.bcm.edu	37	chr7	4959927	4959927	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcgtccgacaggaagtagagGttggagctgcccaggatgct	15	9	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:4959927G>T	ENST00000404774.3	-	3	359	c.165C>A	c.(163-165)aaC>aaA	p.N55K	MMD2_ENST00000406755.1_Missense_Mutation_p.N55K|MMD2_ENST00000401401.3_Missense_Mutation_p.N55K	NM_001100600.1	NP_001094070.1	Q8IY49	PAQRA_HUMAN	monocyte to macrophage differentiation-associated 2	55						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(11)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		GGAAGTAGAGGTTGGAGCTGC	0.627																																					p.N55K		Atlas-SNP	.											.	MMD2	63	.	0			c.C165A						.						47	54	52					7																	4959927		2118	4231	6349	SO:0001583	missense	221938	exon3			GTAGAGGTTGGAG	BC037881	CCDS47529.1, CCDS47530.1, CCDS59047.1	7p22	2004-06-23			ENSG00000136297	ENSG00000136297			30133	protein-coding gene	gene with protein product		614581				12477932	Standard	NM_198403		Approved	PAQR10	uc003sno.4	Q8IY49	OTTHUMG00000151844	ENST00000404774.3:c.165C>A	chr7.hg19:g.4959927G>T	ENSP00000384690:p.Asn55Lys	102.0	0.0		78.0	24.0	NM_198403	B5MBW4|Q6NVU5|Q6TCH0	Missense_Mutation	SNP	ENST00000404774.3	hg19	CCDS47529.1	.	.	.	.	.	.	.	.	.	.	G	10.98	1.505364	0.26949	.	.	ENSG00000136297	ENST00000404774;ENST00000406755;ENST00000401401	T;T;T	0.28895	1.59;1.59;1.59	4.44	3.56	0.40772	.	0.443567	0.24438	N	0.038538	T	0.19366	0.0465	N	0.14661	0.345	0.31007	N	0.719678	B;B;B	0.30634	0.288;0.013;0.003	B;B;B	0.38156	0.266;0.038;0.007	T	0.18209	-1.0344	10	0.26408	T	0.33	-27.1991	7.5037	0.27532	0.0897:0.1672:0.7431:0.0	.	55;55;55	B5MBW4;Q8IY49;Q8IY49-2	.;PAQRA_HUMAN;.	K	55	ENSP00000384690:N55K;ENSP00000385963:N55K;ENSP00000384141:N55K	ENSP00000384141:N55K	N	-	3	2	MMD2	4926453	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.415000	0.44635	1.083000	0.41159	0.561000	0.74099	AAC	.	.		0.627	MMD2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324136.1	NM_198403		T	4959927	G	T	4959927	3	4	150	1	0	0	0	0	1	0	0	0	9653	1252	44	3	667	3	MMD2	7	4959927	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	2407017	4959927	154178736	231	22955										
ZNF12	7559	hgsc.bcm.edu	37	chr7	6737036	6737036	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttctccttgctccaacttgcTgataacatccggtttgataa	6	11	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:6737036T>A	ENST00000405858.1	-	4	713	c.172A>T	c.(172-174)Agc>Tgc	p.S58C	ZNF12_ENST00000342651.5_Missense_Mutation_p.S58C|ZNF12_ENST00000404360.1_Missense_Mutation_p.S22C|AC073343.13_ENST00000366167.2_RNA	NM_006956.2|NM_016265.3	NP_008887.2|NP_057349.2	P17014	ZNF12_HUMAN	zinc finger protein 12	58	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(3)	16		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)		TCCAACTTGCTGATAACATCC	0.468																																					p.S58C		Atlas-SNP	.											.	ZNF12	53	.	0			c.A172T						.						85	85	85					7																	6737036		2064	4232	6296	SO:0001583	missense	7559	exon4			ACTTGCTGATAAC	X52334, AB021643	CCDS47538.1, CCDS47539.1	7p21.1	2013-01-08	2005-06-09		ENSG00000164631	ENSG00000164631		"Zinc fingers, C2H2-type", "-"	12902	protein-coding gene	gene with protein product		194536	"zinc finger protein 325"	ZNF325			Standard	NM_016265		Approved	KOX3, GIOT-3	uc003sqt.1	P17014	OTTHUMG00000151910	ENST00000405858.1:c.172A>T	chr7.hg19:g.6737036T>A	ENSP00000385939:p.Ser58Cys	105.0	0.0		77.0	23.0	NM_016265	A8MYC4|A8WFQ8|B2RNQ7|B4DF45|Q6N016|Q8NHZ0|Q9H9P0|Q9ULZ6	Missense_Mutation	SNP	ENST00000405858.1	hg19	CCDS47538.1	.	.	.	.	.	.	.	.	.	.	.	13.66	2.302258	0.40694	.	.	ENSG00000164631	ENST00000404360;ENST00000405858;ENST00000342651;ENST00000399476;ENST00000330442	T;T;T	0.42900	5.54;0.96;0.96	4.13	0.247	0.15521	Krueppel-associated box (3);	0.583037	0.14374	N	0.323611	T	0.39545	0.1082	M	0.86502	2.82	0.19775	N	0.999951	B;B	0.31859	0.343;0.047	B;B	0.29716	0.106;0.009	T	0.37454	-0.9705	10	0.37606	T	0.19	.	1.7189	0.02908	0.1653:0.0958:0.3411:0.3978	.	58;58	P17014;P17014-5	ZNF12_HUMAN;.	C	22;58;58;116;22	ENSP00000384405:S22C;ENSP00000385939:S58C;ENSP00000344745:S58C	ENSP00000331039:S22C	S	-	1	0	ZNF12	6703561	0.921000	0.31238	0.835000	0.33067	0.958000	0.62258	0.653000	0.24902	0.043000	0.15746	0.482000	0.46254	AGC	.	.		0.468	ZNF12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324373.2	NM_016265		A	6737036	T	A	6737036	3	1	150	1	0	0	0	0	1	0	0	0	17733	1580	55	4	1929	4	ZNF12	7	6737036	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1777109	6737036	152401627	232	22956										
PHF14	9678	hgsc.bcm.edu	37	chr7	11080358	11080358	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agaaaaccaagtaaaaaagaAggaggcacacaaaagacatc	8	7	0	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:11080358A>T	ENST00000403050.3	+	12	2588	c.2136A>T	c.(2134-2136)gaA>gaT	p.E712D	PHF14_ENST00000445996.2_Missense_Mutation_p.E427D	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	712					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		GTAAAAAAGAAGGAGGCACAC	0.303																																					p.E712D		Atlas-SNP	.											.	PHF14	90	.	0			c.A2136T						.						52	52	52					7																	11080358		1813	4074	5887	SO:0001583	missense	9678	exon12			AAAAGAAGGAGGC	AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"Zinc fingers, PHD-type"	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.2136A>T	chr7.hg19:g.11080358A>T	ENSP00000385795:p.Glu712Asp	469.0	1.0		435.0	115.0	NM_014660	A7MCZ3|B4DI82	Missense_Mutation	SNP	ENST00000403050.3	hg19	CCDS47542.1	.	.	.	.	.	.	.	.	.	.	A	18.00	3.526226	0.64860	.	.	ENSG00000106443	ENST00000403050;ENST00000445996	T;T	0.71103	-0.19;-0.54	5.36	5.36	0.76844	Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.72763	0.3501	N	0.24115	0.695	0.53005	D	0.999968	D;P;D;D	0.58970	0.974;0.956;0.984;0.963	D;P;D;P	0.68192	0.953;0.899;0.956;0.543	T	0.69292	-0.5183	10	0.21014	T	0.42	.	15.5304	0.75956	1.0:0.0:0.0:0.0	.	427;427;712;712	O94880-2;B4DG57;A8MSQ1;O94880	.;.;.;PHF14_HUMAN	D	712;427	ENSP00000385795:E712D;ENSP00000403907:E427D	ENSP00000385795:E712D	E	+	3	2	PHF14	11046883	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.275000	0.58927	2.246000	0.74042	0.533000	0.62120	GAA	.	.		0.303	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		T	11080358	A	T	11080358	3	4	150	1	0	0	0	0	1	0	0	0	11834	69	3	4	2182	4	PHF14	7	11080358	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	4343322	11080358	148058305	233	22957										
AGR2	10551	hgsc.bcm.edu	37	chr7	16832566	16832566	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcagcaacttgagagctttcTtcatgttgtcaagcactaat	7	9	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:16832566T>C	ENST00000419304.2	-	8	646	c.494A>G	c.(493-495)aAg>aGg	p.K165R	AGR2_ENST00000419572.2_Missense_Mutation_p.K185R	NM_006408.3	NP_006399.1	O95994	AGR2_HUMAN	anterior gradient 2	165					lung goblet cell differentiation (GO:0060480)|mucus secretion (GO:0070254)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	dystroglycan binding (GO:0002162)			endometrium(2)|lung(1)|prostate(1)|skin(2)	6	Lung NSC(10;0.0376)|all_lung(11;0.0855)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		GAGAGCTTTCTTCATGTTGTC	0.413																																					p.K165R		Atlas-SNP	.											.	AGR2	14	.	0			c.A494G						.						103	95	98					7																	16832566		2203	4300	6503	SO:0001583	missense	10551	exon8			GCTTTCTTCATGT	AF038451	CCDS5364.1	7p21.3	2013-07-31	2013-07-31		ENSG00000106541	ENSG00000106541		"Protein disulfide isomerases"	328	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 17"	606358	"anterior gradient 2 homolog (Xenopus laevis)"			9790916	Standard	NM_006408		Approved	XAG-2, HAG-2, AG2, PDIA17	uc003str.3	O95994	OTTHUMG00000023446	ENST00000419304.2:c.494A>G	chr7.hg19:g.16832566T>C	ENSP00000391490:p.Lys165Arg	64.0	0.0		50.0	10.0	NM_006408		Missense_Mutation	SNP	ENST00000419304.2	hg19	CCDS5364.1	.	.	.	.	.	.	.	.	.	.	T	15.72	2.915379	0.52546	.	.	ENSG00000106541	ENST00000419304;ENST00000419572	.	.	.	5.86	3.49	0.39957	.	0.202835	0.52532	N	0.000080	T	0.47414	0.1444	L	0.39245	1.2	0.39685	D	0.970955	B	0.10296	0.003	B	0.16289	0.015	T	0.43410	-0.9393	9	0.62326	D	0.03	.	10.435	0.44430	0.0:0.1332:0.0:0.8668	.	165	O95994	AGR2_HUMAN	R	165;185	.	ENSP00000391490:K165R	K	-	2	0	AGR2	16799091	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.068000	0.41471	0.563000	0.29222	0.528000	0.53228	AAG	.	.		0.413	AGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207594.2	NM_006408		C	16832566	T	C	16832566	3	2	150	1	0	0	0	0	1	0	0	0	395	1609	56	2	37	2	AGR2	7	16832566	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	5752208	16832566	142306097	234	22958										
MACC1	346389	hgsc.bcm.edu	37	chr7	20198999	20198999	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gacttggatggtgtctttatAaatgtagcagttgcttaaaa	10	4	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:20198999A>T	ENST00000400331.5	-	5	1293	c.985T>A	c.(985-987)Tat>Aat	p.Y329N	MACC1_ENST00000589011.1_Missense_Mutation_p.Y329N|MACC1_ENST00000332878.4_Missense_Mutation_p.Y329N	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	329					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						GTGTCTTTATAAATGTAGCAG	0.423																																					p.Y329N		Atlas-SNP	.											.	MACC1	99	.	0			c.T985A						.						54	52	53					7																	20198999		2203	4300	6503	SO:0001583	missense	346389	exon5			CTTTATAAATGTA		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.985T>A	chr7.hg19:g.20198999A>T	ENSP00000383185:p.Tyr329Asn	93.0	0.0		81.0	25.0	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	hg19	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	A	10.58	1.389053	0.25118	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.17854	2.25;2.25	5.47	5.47	0.80525	.	0.221502	0.48767	D	0.000169	T	0.41259	0.1151	M	0.78637	2.42	0.53688	D	0.999976	D	0.63880	0.993	P	0.61397	0.888	T	0.38866	-0.9641	10	0.72032	D	0.01	-9.7349	15.5516	0.76158	1.0:0.0:0.0:0.0	.	329	Q6ZN28	MACC1_HUMAN	N	329	ENSP00000383185:Y329N;ENSP00000328410:Y329N	ENSP00000328410:Y329N	Y	-	1	0	MACC1	20165524	1.000000	0.71417	0.981000	0.43875	0.011000	0.07611	4.315000	0.59172	2.078000	0.62432	0.477000	0.44152	TAT	.	.		0.423	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		T	20198999	A	T	20198999	3	4	150	1	0	0	0	0	1	0	0	0	9152	362	13	4	1585	4	MACC1	7	20198999	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3366433	20198999	138939664	235	22959										
TXNDC3	51314	hgsc.bcm.edu	37	chr7	37936559	37936559	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccaacagacccagaagaagcAaaattactttcccctgactc	5	14	0	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:37936559A>T	ENST00000199447.4	+	17	2004	c.1632A>T	c.(1630-1632)gcA>gcT	p.A544A	NME8_ENST00000440017.1_Silent_p.A544A|EPDR1_ENST00000476620.1_Intron	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	544	NDK 3.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										CAGAAGAAGCAAAATTACTTT	0.458																																					p.A544A		Atlas-SNP	.											.	.	.	.	0			c.A1632T						.						104	99	101					7																	37936559		2203	4300	6503	SO:0001819	synonymous_variant	51314	exon17			AGAAGCAAAATTA	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 2"	607421	"thioredoxin domain containing 3 (spermatozoa)"	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.1632A>T	chr7.hg19:g.37936559A>T		153.0	0.0		155.0	34.0	NM_016616	Q9NZH1	Silent	SNP	ENST00000199447.4	hg19	CCDS5452.1																																																																																			.	.		0.458	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616		T	37936559	A	T	37936559	2	4	150	1	0	0	0	0	0	0	0	1	16813	117	5	4		4	TXNDC3	7	37936559	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	17737560	37936559	121202104	236	22960										
ADCY1	107	hgsc.bcm.edu	37	chr7	45614683	45614683	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgccttgctgcccgtgcgcAgcctgctggccataggcttt	12	14	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:45614683A>T	ENST00000297323.7	+	1	563	c.541A>T	c.(541-543)Agc>Tgc	p.S181C	ADCY1_ENST00000432715.1_5'UTR	NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	181					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GCCCGTGCGCAGCCTGCTGGC	0.677																																					p.S181C		Atlas-SNP	.											.	ADCY1	187	.	0			c.A541T						.						21	18	19					7																	45614683		2190	4280	6470	SO:0001583	missense	107	exon1			GTGCGCAGCCTGC	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.541A>T	chr7.hg19:g.45614683A>T	ENSP00000297323:p.Ser181Cys	82.0	0.0		85.0	24.0	NM_021116	A4D2L8|Q75MI1	Missense_Mutation	SNP	ENST00000297323.7	hg19	CCDS34631.1	.	.	.	.	.	.	.	.	.	.	A	17.25	3.341774	0.61073	.	.	ENSG00000164742	ENST00000297323;ENST00000545300	T	0.79454	-1.27	3.7	3.7	0.42460	.	0.060259	0.64402	D	0.000006	T	0.73210	0.3558	L	0.29908	0.895	0.39195	D	0.963038	P	0.49185	0.92	P	0.51229	0.663	T	0.76526	-0.2927	10	0.59425	D	0.04	.	10.3691	0.44042	1.0:0.0:0.0:0.0	.	181	Q08828	ADCY1_HUMAN	C	181	ENSP00000297323:S181C	ENSP00000297323:S181C	S	+	1	0	ADCY1	45581208	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	8.108000	0.89559	1.531000	0.49152	0.172000	0.16884	AGC	.	.		0.677	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		T	45614683	A	T	45614683	3	4	150	1	0	0	0	0	1	0	0	0	292	188	7	4	543	4	ADCY1	7	45614683	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	7678124	45614683	113523980	237	22961										
ZPBP	11055	hgsc.bcm.edu	37	chr7	50132767	50132767	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cgccgcctgccccgccgcgcTgggccaagggcgaaggcctc	15	19	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:50132767T>A	ENST00000046087.2	-	1	93	c.24A>T	c.(22-24)ccA>ccT	p.P8P	ZPBP_ENST00000419417.1_Silent_p.P8P|C7orf72_ENST00000297001.6_5'Flank	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	8					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					cccgccgcgcTGGGCCAAGGG	0.731																																					p.P8P		Atlas-SNP	.											.	ZPBP	65	.	0			c.A24T						.						2	4	3					7																	50132767		1524	3135	4659	SO:0001819	synonymous_variant	11055	exon1			CCGCGCTGGGCCA	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.24A>T	chr7.hg19:g.50132767T>A		67.0	0.0		42.0	15.0	NM_007009	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Silent	SNP	ENST00000046087.2	hg19	CCDS5509.1																																																																																			.	.		0.731	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009		A	50132767	T	A	50132767	2	1	150	1	0	0	0	0	0	0	0	1	18234	1567	55	4		4	ZPBP	7	50132767	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4518084	50132767	109005896	238	22962										
EGFR	1956	hgsc.bcm.edu	37	chr7	55273271	55273271	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gctgaaaatgcagaatacctAagggtcgcgccacaaagcag	11	10	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:55273271A>T	ENST00000275493.2	+	28	3771	c.3594A>T	c.(3592-3594)ctA>ctT	p.L1198L	EGFR_ENST00000454757.2_Silent_p.L1145L|EGFR_ENST00000442591.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	1198					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CAGAATACCTAAGGGTCGCGC	0.493		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.L1198L		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	.	EGFR	20426	.	0			c.A3594T						.						63	60	61					7																	55273271		2203	4300	6503	SO:0001819	synonymous_variant	1956	exon28	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	ATACCTAAGGGTC		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.3594A>T	chr7.hg19:g.55273271A>T		153.0	0.0		152.0	31.0	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	hg19	CCDS5514.1																																																																																			.	.		0.493	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55273271	A	T	55273271	2	4	150	1	0	0	0	0	0	0	0	1	4969	349	13	4		4	EGFR	7	55273271	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5140504	55273271	103865392	239	22963										
FKBP6	8468	hgsc.bcm.edu	37	chr7	72745693	72745693	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatttccacttcagaaggtcCtgaaagtggcagctacggaa	10	9	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:72745693C>A	ENST00000252037.4	+	5	571	c.502C>A	c.(502-504)Ctg>Atg	p.L168M	FKBP6_ENST00000431982.2_Missense_Mutation_p.L163M|FKBP6_ENST00000413573.2_Missense_Mutation_p.L138M	NM_003602.3	NP_003593.3	O75344	FKBP6_HUMAN	FK506 binding protein 6, 36kDa	168					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|piRNA metabolic process (GO:0034587)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|synaptonemal complex (GO:0000795)	FK506 binding (GO:0005528)|Hsp90 protein binding (GO:0051879)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	16		Lung NSC(55;0.0908)|all_lung(88;0.198)				TCAGAAGGTCCTGAAAGTGGC	0.453																																					p.L168M		Atlas-SNP	.											.	FKBP6	35	.	0			c.C502A						.						92	89	90					7																	72745693		1889	4113	6002	SO:0001583	missense	8468	exon5			AAGGTCCTGAAAG	AF038847	CCDS43595.1, CCDS47604.1, CCDS64670.1	7q11.23	2009-01-05	2002-08-29		ENSG00000077800	ENSG00000077800			3722	protein-coding gene	gene with protein product	"FK506 binding protein 6 (36kD)", "peptidylprolyl cis-trans isomerase", "rotamase", "immunophilin FKBP36"	604839	"FK506-binding protein 6 (36kD)"			9782077, 19001379	Standard	NM_003602		Approved	PPIase, FKBP36	uc003tya.2	O75344	OTTHUMG00000150520	ENST00000252037.4:c.502C>A	chr7.hg19:g.72745693C>A	ENSP00000252037:p.Leu168Met	88.0	0.0		82.0	39.0	NM_003602	B4DXT7|G3V0I2|Q7Z4T4|Q9UDS0	Missense_Mutation	SNP	ENST00000252037.4	hg19	CCDS43595.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.854967	0.51376	.	.	ENSG00000077800	ENST00000431982;ENST00000413573;ENST00000252037	T;T;T	0.74421	-0.84;-0.84;-0.84	5.2	5.2	0.72013	.	0.072350	0.56097	D	0.000025	T	0.80037	0.4550	L	0.60455	1.87	0.51767	D	0.999933	D;P;D	0.89917	1.0;0.899;0.994	D;B;P	0.79784	0.993;0.421;0.591	T	0.78119	-0.2328	10	0.33940	T	0.23	-10.5982	6.3705	0.21479	0.1842:0.7199:0.0:0.0959	.	163;168;138	O75344-2;O75344;Q7Z4T4	.;FKBP6_HUMAN;.	M	163;138;168	ENSP00000416277:L163M;ENSP00000394952:L138M;ENSP00000252037:L168M	ENSP00000252037:L168M	L	+	1	2	FKBP6	72383629	1.000000	0.71417	0.998000	0.56505	0.830000	0.47004	0.952000	0.29149	2.442000	0.82660	0.591000	0.81541	CTG	.	.		0.453	FKBP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318723.1	NM_003602		A	72745693	C	A	72745693	3	1	150	1	0	0	0	0	1	0	0	0	5920	680	24	3	566	3	FKBP6	7	72745693	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	17472422	72745693	86392970	240	22964										
UPK3B	80761	hgsc.bcm.edu	37	chr7	76143358	76143358	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcttctctggccggcctcctActcttggccttcttggcagc	9	16	4	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:76143358A>C	ENST00000257632.5	+	3	849	c.721A>C	c.(721-723)Act>Cct	p.T241P	UPK3B_ENST00000334348.3_Silent_p.L212L|UPK3B_ENST00000419923.2_Missense_Mutation_p.T241P|UPK3B_ENST00000394849.1_Missense_Mutation_p.T186P|UPK3B_ENST00000448265.3_Missense_Mutation_p.T241P|UPK3B_ENST00000443097.2_Silent_p.L212L			Q9BT76	UPK3B_HUMAN	uroplakin 3B	241					negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				CCGGCCTCCTACTCTTGGCCT	0.622																																					p.T241P		Atlas-SNP	.											.	UPK3B	15	.	0			c.A721C						.						168	121	137					7																	76143358		2203	4300	6503	SO:0001583	missense	80761	exon3			CCTCCTACTCTTG	BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566			21444	protein-coding gene	gene with protein product	"uroplakin IIIb"	611887				12446744	Standard	XM_005250612		Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000257632.5:c.721A>C	chr7.hg19:g.76143358A>C	ENSP00000257632:p.Thr241Pro	102.0	0.0		100.0	36.0	NM_030570	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Missense_Mutation	SNP	ENST00000257632.5	hg19	CCDS5588.1	.	.	.	.	.	.	.	.	.	.	.	12.76	2.033122	0.35893	.	.	ENSG00000243566	ENST00000419923;ENST00000448265;ENST00000257632;ENST00000394849	T;T;T;T	0.35789	1.29;1.29;1.29;1.34	5.22	1.08	0.20341	.	1.778480	0.02936	N	0.139844	T	0.18882	0.0453	N	0.03608	-0.345	0.80722	D	1	B;B	0.16166	0.016;0.016	B;B	0.20384	0.029;0.018	T	0.28073	-1.0055	10	0.48119	T	0.1	-30.3739	4.8266	0.13419	0.2535:0.0:0.5981:0.1483	.	186;241	Q9BT76-2;Q9BT76	.;UPK3B_HUMAN	P	241;241;241;186	ENSP00000441602:T241P;ENSP00000441284:T241P;ENSP00000257632:T241P;ENSP00000378319:T186P	ENSP00000257632:T241P	T	+	1	0	UPK3B	75981294	0.998000	0.40836	1.000000	0.80357	0.567000	0.35839	0.155000	0.16362	0.617000	0.30160	-0.344000	0.07964	ACT	.	.		0.622	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570		C	76143358	A	C	76143358	3	2	150	1	0	0	0	0	1	0	0	0	17026	391	14	5	815	5	UPK3B	7	76143358	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3397665	76143358	82995305	241	22965										
PCLO	27445	hgsc.bcm.edu	37	chr7	82544071	82544071	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtcacggtcatagcctcgagTccgtgattcttccctcatgt	9	13	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:82544071T>C	ENST00000333891.9	-	7	13568	c.13231A>G	c.(13231-13233)Act>Gct	p.T4411A	PCLO_ENST00000423517.2_Missense_Mutation_p.T4411A|PCLO_ENST00000437081.1_Missense_Mutation_p.T1131A	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TAGCCTCGAGTCCGTGATTCT	0.493																																					p.T4411A		Atlas-SNP	.											.	PCLO	1506	.	0			c.A13231G						.						90	89	89					7																	82544071		2068	4196	6264	SO:0001583	missense	27445	exon7			CTCGAGTCCGTGA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.13231A>G	chr7.hg19:g.82544071T>C	ENSP00000334319:p.Thr4411Ala	103.0	0.0		85.0	17.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	8.844	0.942904	0.18281	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.17854	2.25;2.26	5.75	5.75	0.90469	.	.	.	.	.	T	0.21761	0.0524	L	0.54323	1.7	0.48571	D	0.99967	B;P;P	0.41450	0.058;0.75;0.75	B;B;B	0.43274	0.017;0.414;0.414	T	0.01245	-1.1407	9	0.87932	D	0	.	11.147	0.48436	0.0:0.0711:0.0:0.9289	.	4342;4411;4411	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	A	4411;4411;1131	ENSP00000334319:T4411A;ENSP00000388393:T4411A	ENSP00000334319:T4411A	T	-	1	0	PCLO	82382007	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	2.574000	0.46016	2.201000	0.70794	0.533000	0.62120	ACT	.	.		0.493	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82544071	T	C	82544071	3	2	150	1	0	0	0	0	1	0	0	0	11592	1667	58	2	2290	2	PCLO	7	82544071	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	6400713	82544071	76594592	242	22966										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83689783	83689783	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgattgttgactacgcacctAttaaaagggatgctgtcagc	10	8	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:83689783A>G	ENST00000265362.4	-	5	859	c.545T>C	c.(544-546)aTa>aCa	p.I182T	SEMA3A_ENST00000436949.1_Missense_Mutation_p.I182T	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	182	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CTACGCACCTATTAAAAGGGA	0.348																																					p.I182T		Atlas-SNP	.											.	SEMA3A	121	.	0			c.T545C						.						106	110	109					7																	83689783		2203	4300	6503	SO:0001583	missense	10371	exon5			GCACCTATTAAAA	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.545T>C	chr7.hg19:g.83689783A>G	ENSP00000265362:p.Ile182Thr	205.0	0.0		173.0	40.0	NM_006080		Missense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.569453	0.45798	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.22539	1.95;1.95	5.65	5.65	0.86999	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.121250	0.64402	D	0.000001	T	0.22666	0.0547	L	0.33710	1.025	0.58432	D	0.999995	B	0.17038	0.02	B	0.33392	0.163	T	0.04386	-1.0955	10	0.36615	T	0.2	.	16.1718	0.81822	1.0:0.0:0.0:0.0	.	182	Q14563	SEM3A_HUMAN	T	182	ENSP00000265362:I182T;ENSP00000415260:I182T	ENSP00000265362:I182T	I	-	2	0	SEMA3A	83527719	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.649000	0.83500	2.267000	0.75376	0.528000	0.53228	ATA	.	.		0.348	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		G	83689783	A	G	83689783	3	3	150	1	0	0	0	0	1	0	0	0	14039	449	16	2	1822	2	SEMA3A	7	83689783	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1145712	83689783	75448880	243	22967										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84649627	84649627	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgctgacaactttgaggacAgttccaatgtctgaaaaaat	8	7	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:84649627A>T	ENST00000284136.6	-	12	1468	c.1425T>A	c.(1423-1425)acT>acA	p.T475T	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	475	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CTTTGAGGACAGTTCCAATGT	0.413																																					p.T475T	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.T1425A						.						94	82	86					7																	84649627		2203	4300	6503	SO:0001819	synonymous_variant	223117	exon12			GAGGACAGTTCCA	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1425T>A	chr7.hg19:g.84649627A>T		79.0	0.0		70.0	18.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Silent	SNP	ENST00000284136.6	hg19	CCDS34676.1																																																																																			.	.		0.413	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		T	84649627	A	T	84649627	2	4	150	1	0	0	0	0	0	0	0	1	14042	175	7	4		4	SEMA3D	7	84649627	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	959844	84649627	74489036	244	22968										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94055788	94055788	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccggtgaaaaggggcccagAggtcttcctggcttaaaggg	15	10	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:94055788A>T	ENST00000297268.6	+	46	3522	c.3051A>T	c.(3049-3051)agA>agT	p.R1017S		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1017					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	AGGGGCCCAGAGGTCTTCCTG	0.478										HNSCC(75;0.22)																											p.R1017S		Atlas-SNP	.											.	COL1A2	240	.	0			c.A3051T						.						69	54	59					7																	94055788		2203	4300	6503	SO:0001583	missense	1278	exon46			GCCCAGAGGTCTT	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3051A>T	chr7.hg19:g.94055788A>T	ENSP00000297268:p.Arg1017Ser	130.0	0.0		103.0	27.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	A	17.67	3.446562	0.63178	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.94092	-3.35	5.85	3.43	0.39272	.	0.000000	0.85682	D	0.000000	D	0.93822	0.8024	L	0.38531	1.155	0.58432	D	0.999995	D	0.71674	0.998	D	0.79784	0.993	D	0.92957	0.6385	10	0.87932	D	0	.	10.5471	0.45066	0.8683:0.0:0.1317:0.0	.	1017	P08123	CO1A2_HUMAN	S	1017;1018	ENSP00000297268:R1017S	ENSP00000297268:R1017S	R	+	3	2	COL1A2	93893724	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.498000	0.60373	0.539000	0.28788	0.533000	0.62120	AGA	.	.		0.478	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		T	94055788	A	T	94055788	3	4	150	1	0	0	0	0	1	0	0	0	3680	301	11	4	3233	4	COL1A2	7	94055788	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	9406161	94055788	65082875	245	22969										
MUC17	140453	hgsc.bcm.edu	37	chr7	100677847	100677847	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttaacacgtatgcctgtcagCaccacaatggtggccagttc	9	12	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:100677847C>T	ENST00000306151.4	+	3	3214	c.3150C>T	c.(3148-3150)agC>agT	p.S1050S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1050	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TGCCTGTCAGCACCACAATGG	0.502																																					p.S1050S		Atlas-SNP	.											.	MUC17	804	.	0			c.C3150T						.						512	393	433					7																	100677847		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TGTCAGCACCACA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3150C>T	chr7.hg19:g.100677847C>T		129.0	0.0		183.0	45.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100677847	C	T	100677847	2	4	150	1	0	0	0	0	0	0	0	1	9983	709	25	3		3	MUC17	7	100677847	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	6622059	100677847	58460816	246	22970										
LRRC17	10234	hgsc.bcm.edu	37	chr7	102574534	102574534	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctcccgtgtgacgtgtacacAtatctccatgagaaatactt	7	11	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:102574534A>T	ENST00000339431.4	+	2	469	c.174A>T	c.(172-174)acA>acT	p.T58T	FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000313221.4_Intron|LRRC17_ENST00000249377.4_Silent_p.T58T	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	58					bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						ACGTGTACACATATCTCCATG	0.522																																					p.T58T		Atlas-SNP	.											.	LRRC17	45	.	0			c.A174T						.						56	51	52					7																	102574534		2203	4300	6503	SO:0001819	synonymous_variant	10234	exon2			GTACACATATCTC	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.174A>T	chr7.hg19:g.102574534A>T		114.0	0.0		97.0	28.0	NM_005824	Q13288|Q6UWA7|Q75MG5	Silent	SNP	ENST00000339431.4	hg19	CCDS34721.1																																																																																			.	.		0.522	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824		T	102574534	A	T	102574534	2	4	150	1	0	0	0	0	0	0	0	1	8982	204	8	4		4	LRRC17	7	102574534	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1896687	102574534	56564129	247	22971										
FOXP2	93986	hgsc.bcm.edu	37	chr7	114299675	114299675	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	taacacttaatgaaatttacAgctggtttacacggacattt	6	7	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:114299675A>T	ENST00000393494.2	+	13	1873	c.1594A>T	c.(1594-1596)Agc>Tgc	p.S532C	FOXP2_ENST00000393491.3_Missense_Mutation_p.S347C|FOXP2_ENST00000408937.3_Missense_Mutation_p.S557C|FOXP2_ENST00000350908.4_Missense_Mutation_p.S532C|FOXP2_ENST00000393500.3_3'UTR|FOXP2_ENST00000403559.4_Missense_Mutation_p.S549C|FOXP2_ENST00000393498.2_Missense_Mutation_p.S511C|FOXP2_ENST00000393489.3_Missense_Mutation_p.S440C			O15409	FOXP2_HUMAN	forkhead box P2	532					camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						TGAAATTTACAGCTGGTTTAC	0.383																																					p.S557C		Atlas-SNP	.											.	FOXP2	133	.	0			c.A1669T						.						157	147	151					7																	114299675		2203	4300	6503	SO:0001583	missense	93986	exon14			ATTTACAGCTGGT	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"Forkhead boxes"	13875	protein-coding gene	gene with protein product	"trinucleotide repeat containing 10", "forkhead/winged-helix transcription factor", "speech and language disorder 1", "CAG repeat protein 44"	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.1594A>T	chr7.hg19:g.114299675A>T	ENSP00000377132:p.Ser532Cys	157.0	0.0		133.0	30.0	NM_148898	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	hg19	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	A	13.31	2.197852	0.38806	.	.	ENSG00000128573	ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489;ENST00000393491	D;D;D;D;D;D	0.95853	-3.83;-3.83;-3.83;-3.83;-3.83;-3.83	6.06	6.06	0.98353	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	D	0.000000	D	0.96839	0.8968	L	0.51914	1.62	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.995;0.999;0.998	D;D;D;D;D	0.76575	0.978;0.986;0.988;0.978;0.975	D	0.97470	1.0040	10	0.87932	D	0	.	16.6127	0.84892	1.0:0.0:0.0:0.0	.	531;549;347;532;557	B7ZLK5;B4DLD9;Q0PRL4;O15409;O15409-4	.;.;.;FOXP2_HUMAN;.	C	532;557;549;532;509;440;347	ENSP00000377132:S532C;ENSP00000386200:S557C;ENSP00000385069:S549C;ENSP00000265436:S532C;ENSP00000377129:S440C;ENSP00000377130:S347C	ENSP00000265436:S532C	S	+	1	0	FOXP2	114086911	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.322000	0.78497	0.528000	0.53228	AGC	.	.		0.383	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		T	114299675	A	T	114299675	3	4	150	1	0	0	0	0	1	0	0	0	6035	188	7	4	1807	4	FOXP2	7	114299675	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	11725141	114299675	44838988	248	22972										
ASZ1	136991	hgsc.bcm.edu	37	chr7	117060261	117060261	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tttcttgaaagtagtagttcTacacacttcaagatctgttc	6	8	4	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:117060261T>C	ENST00000284629.2	-	4	458	c.396A>G	c.(394-396)gtA>gtG	p.V132V		NM_130768.2	NP_570124.1			ankyrin repeat, SAM and basic leucine zipper domain containing 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(3)|skin(1)	24	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)			GTAGTAGTTCTACACACTTCA	0.343																																					p.V132V		Atlas-SNP	.											.	ASZ1	56	.	0			c.A396G						.						106	104	104					7																	117060261		2203	4300	6503	SO:0001819	synonymous_variant	136991	exon4			TAGTTCTACACAC	AF461259	CCDS5772.1	7q31.2	2013-01-10	2005-03-15	2004-07-16	ENSG00000154438	ENSG00000154438		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	1350	protein-coding gene	gene with protein product		605797	"ankyrin-like 1"	C7orf7, ANKL1		12040005, 11279520	Standard	NM_130768		Approved	Orf3, GASZ, ALP1, CT1.19	uc003vjb.2	Q8WWH4	OTTHUMG00000064565	ENST00000284629.2:c.396A>G	chr7.hg19:g.117060261T>C		45.0	0.0		40.0	11.0	NM_130768		Silent	SNP	ENST00000284629.2	hg19	CCDS5772.1																																																																																			.	.		0.343	ASZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000138907.7	NM_130768		C	117060261	T	C	117060261	2	2	150	1	0	0	0	0	0	0	0	1	1069	1509	53	2		2	ASZ1	7	117060261	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2760586	117060261	42078402	249	22973										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	132192611	132192611	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgtcctccttgcaaagcctcAcgagcttggatgtatacacc	8	13	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:132192611A>T	ENST00000359827.3	-	2	1804	c.842T>A	c.(841-843)gTg>gAg	p.V281E	PLXNA4_ENST00000321063.4_Missense_Mutation_p.V281E|PLXNA4_ENST00000423507.2_Missense_Mutation_p.V281E|PLXNA4_ENST00000378539.5_Missense_Mutation_p.V281E			Q9HCM2	PLXA4_HUMAN	plexin A4	281	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						GCAAAGCCTCACGAGCTTGGA	0.552																																					p.V281E		Atlas-SNP	.											.	PLXNA4	873	.	0			c.T842A						.						69	52	58					7																	132192611		2203	4300	6503	SO:0001583	missense	91584	exon2			AGCCTCACGAGCT	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.842T>A	chr7.hg19:g.132192611A>T	ENSP00000352882:p.Val281Glu	71.0	0.0		88.0	32.0	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	A	14.74	2.626336	0.46840	.	.	ENSG00000221866	ENST00000321063;ENST00000359827;ENST00000423507;ENST00000378539	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	5.84	5.84	0.93424	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.56097	U	0.000031	T	0.45617	0.1351	M	0.88105	2.93	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.53387	-0.8446	10	0.66056	D	0.02	.	16.2159	0.82217	1.0:0.0:0.0:0.0	.	281;281;281	Q9HCM2-2;A4D1N6;Q9HCM2	.;.;PLXA4_HUMAN	E	281	ENSP00000323194:V281E;ENSP00000352882:V281E;ENSP00000392772:V281E;ENSP00000367800:V281E	ENSP00000323194:V281E	V	-	2	0	PLXNA4	131843151	1.000000	0.71417	0.998000	0.56505	0.028000	0.11728	9.339000	0.96797	2.243000	0.73865	0.533000	0.62120	GTG	.	.		0.552	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	132192611	A	T	132192611	3	4	150	1	0	0	0	0	1	0	0	0	12131	159	6	4	5280	4	PLXNA4	7	132192611	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	15132350	132192611	26946052	250	22974										
MKRN1	23608	hgsc.bcm.edu	37	chr7	140171777	140171777	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtcatgcgagtagcgacagtTgtctccttccttacaaaccc	8	13	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:140171777T>A	ENST00000255977.2	-	2	444	c.220A>T	c.(220-222)Aac>Tac	p.N74Y	MKRN1_ENST00000481705.1_5'UTR|MKRN1_ENST00000443720.2_Missense_Mutation_p.N74Y|MKRN1_ENST00000474576.1_Missense_Mutation_p.N10Y|MKRN1_ENST00000437223.2_5'UTR|MKRN1_ENST00000480552.1_Missense_Mutation_p.N10Y	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	74					protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					TAGCGACAGTTGTCTCCTTCC	0.408																																					p.N74Y		Atlas-SNP	.											.	MKRN1	35	.	0			c.A220T						.						82	77	78					7																	140171777		2203	4300	6503	SO:0001583	missense	23608	exon2			GACAGTTGTCTCC	AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606		"RING-type (C3HC4) zinc fingers"	7112	protein-coding gene	gene with protein product		607754				10843807	Standard	NM_013446		Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.220A>T	chr7.hg19:g.140171777T>A	ENSP00000255977:p.Asn74Tyr	84.0	0.0		80.0	16.0	NM_013446	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Missense_Mutation	SNP	ENST00000255977.2	hg19	CCDS5860.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.534557	0.85812	.	.	ENSG00000133606	ENST00000255977;ENST00000539898;ENST00000474576;ENST00000480552;ENST00000443720;ENST00000471104;ENST00000467513;ENST00000494939;ENST00000473444;ENST00000481705	T;T;T;T;T;T;T	0.47528	0.93;2.18;0.93;1.81;1.79;1.8;0.84	5.88	4.75	0.60458	Zinc finger, CCCH-type (3);	0.094910	0.64402	D	0.000001	T	0.65688	0.2715	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.66512	-0.5905	10	0.45353	T	0.12	.	11.1264	0.48322	0.0:0.0722:0.0:0.9278	.	74	Q9UHC7	MKRN1_HUMAN	Y	74;10;10;10;74;10;10;10;25;74	ENSP00000255977:N74Y;ENSP00000417863:N10Y;ENSP00000416369:N74Y;ENSP00000418864:N10Y;ENSP00000418588:N10Y;ENSP00000419843:N10Y;ENSP00000418620:N25Y	ENSP00000255977:N74Y	N	-	1	0	MKRN1	139818246	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.858000	0.69532	2.246000	0.74042	0.533000	0.62120	AAC	.	.		0.408	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446		A	140171777	T	A	140171777	3	1	150	1	0	0	0	0	1	0	0	0	9615	1812	63	4	1260	4	MKRN1	7	140171777	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	7979166	140171777	18966886	251	22975										
PRSS1	5644	hgsc.bcm.edu	37	chr7	142459633	142459633	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctgcccatcagccgcatccAggtgagactgggagagcaca	12	14	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:142459633A>T	ENST00000311737.7	+	3	215	c.209A>T	c.(208-210)cAg>cTg	p.Q70L	PRSS1_ENST00000486171.1_Missense_Mutation_p.Q84L	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	70	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	AGCCGCATCCAGGTGAGACTG	0.577																																					p.Q70L		Atlas-SNP	.											.	PRSS1	68	.	0			c.A209T						.						144	140	141					7																	142459633		2203	4300	6503	SO:0001583	missense	5644	exon3			GCATCCAGGTGAG	M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"Serine peptidases / Serine peptidases"	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.209A>T	chr7.hg19:g.142459633A>T	ENSP00000308720:p.Gln70Leu	148.0	0.0		137.0	20.0	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Missense_Mutation	SNP	ENST00000311737.7	hg19	CCDS5872.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.779097	0.31502	.	.	ENSG00000204983	ENST00000486171;ENST00000311737;ENST00000529243;ENST00000492062	D;D;D	0.89343	-2.5;-2.5;-2.5	3.28	3.28	0.37604	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	T	0.81716	0.4881	N	0.21545	0.675	0.42457	D	0.992772	B;B	0.29612	0.251;0.159	B;B	0.32624	0.149;0.149	T	0.81616	-0.0852	10	0.72032	D	0.01	.	11.1704	0.48569	1.0:0.0:0.0:0.0	.	84;70	E7EQ64;P07477	.;TRY1_HUMAN	L	84;70;70;20	ENSP00000417854:Q84L;ENSP00000308720:Q70L;ENSP00000419912:Q20L	ENSP00000308720:Q70L	Q	+	2	0	PRSS1	142139207	1.000000	0.71417	0.999000	0.59377	0.529000	0.34654	7.162000	0.77515	1.459000	0.47892	0.327000	0.21459	CAG	.	.		0.577	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2			T	142459633	A	T	142459633	3	4	150	1	0	0	0	0	1	0	0	0	12626	188	7	4	219	4	PRSS1	7	142459633	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2287856	142459633	16679030	252	22976										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142562074	142562074	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcctcctcctcctcctcctcCtcttcttcctctgcagcgtg	4	21	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:142562074C>T	ENST00000392957.2	+	7	1303	c.516C>T	c.(514-516)tcC>tcT	p.S172S	EPHB6_ENST00000442129.1_Silent_p.S172S|EPHB6_ENST00000411471.2_Intron	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	172	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.|Poly-Ser.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					cctcctcctcctcttcttcct	0.622																																					p.S172S		Atlas-SNP	.											.	EPHB6	168	.	0			c.C516T						.						83	98	93					7																	142562074		2200	4299	6499	SO:0001819	synonymous_variant	2051	exon7			CTCCTCCTCTTCT	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.516C>T	chr7.hg19:g.142562074C>T		94.0	0.0		81.0	7.0	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	hg19	CCDS5873.2																																																																																			.	.		0.622	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142562074	C	T	142562074	2	4	150	1	0	0	0	0	0	0	0	1	5180	668	24	3		3	EPHB6	7	142562074	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	102441	142562074	16576589	253	22977										
TRPV5	56302	hgsc.bcm.edu	37	chr7	142609803	142609803	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	caagtccacgtcgtagttggCaggtgcatcaataacagtga	11	9	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:142609803C>A	ENST00000265310.1	-	13	1981	c.1633G>T	c.(1633-1635)Gcc>Tcc	p.A545S		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	545					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					TCGTAGTTGGCAGGTGCATCA	0.493																																					p.A545S		Atlas-SNP	.											.	TRPV5	164	.	0			c.G1633T						.						212	177	188					7																	142609803		2203	4300	6503	SO:0001583	missense	56302	exon13			AGTTGGCAGGTGC	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1633G>T	chr7.hg19:g.142609803C>A	ENSP00000265310:p.Ala545Ser	208.0	0.0		177.0	105.0	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	hg19	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.366477	0.61513	.	.	ENSG00000127412	ENST00000265310;ENST00000439304	D;D	0.85171	-1.95;-1.95	5.79	5.79	0.91817	Ion transport (1);	0.059359	0.64402	D	0.000002	D	0.89976	0.6871	M	0.73753	2.245	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.85701	0.1313	10	0.08837	T	0.75	-18.0362	12.6801	0.56916	0.0:0.9249:0.0:0.0751	.	545	Q9NQA5	TRPV5_HUMAN	S	545;490	ENSP00000265310:A545S;ENSP00000406361:A490S	ENSP00000265310:A545S	A	-	1	0	TRPV5	142319925	1.000000	0.71417	0.973000	0.42090	0.130000	0.20726	4.951000	0.63610	2.899000	0.99337	0.655000	0.94253	GCC	.	.		0.493	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		A	142609803	C	A	142609803	3	1	150	1	0	0	0	0	1	0	0	0	16614	710	25	3	568	3	TRPV5	7	142609803	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	47729	142609803	16528860	254	22978										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	146825821	146825821	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tccctttctctggcaagcccAgctccagcagtagaaagaat	8	13	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:146825821A>T	ENST00000361727.3	+	7	1492	c.976A>T	c.(976-978)Agc>Tgc	p.S326C		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	326	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TGGCAAGCCCAGCTCCAGCAG	0.398										HNSCC(39;0.1)																											p.S326C		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.A976T						.						96	99	98					7																	146825821		2203	4300	6503	SO:0001583	missense	26047	exon7			AAGCCCAGCTCCA	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.976A>T	chr7.hg19:g.146825821A>T	ENSP00000354778:p.Ser326Cys	172.0	0.0		168.0	40.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	hg19	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.534399	0.45073	.	.	ENSG00000174469	ENST00000361727	T	0.79653	-1.29	5.84	5.84	0.93424	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.262784	0.32147	N	0.006501	D	0.85665	0.5749	L	0.56280	1.765	0.80722	D	1	P	0.52170	0.951	P	0.59288	0.855	D	0.86612	0.1873	10	0.62326	D	0.03	.	15.0509	0.71867	1.0:0.0:0.0:0.0	.	326	Q9UHC6	CNTP2_HUMAN	C	326	ENSP00000354778:S326C	ENSP00000354778:S326C	S	+	1	0	CNTNAP2	146456754	0.996000	0.38824	0.998000	0.56505	0.103000	0.19146	3.239000	0.51360	2.243000	0.73865	0.533000	0.62120	AGC	.	.		0.398	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			T	146825821	A	T	146825821	3	4	150	1	0	0	0	0	1	0	0	0	3649	188	7	4	1002	4	CNTNAP2	7	146825821	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	4216018	146825821	12312842	255	22979										
KCNH2	3757	hgsc.bcm.edu	37	chr7	150643965	150643965	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gaagcagggctggagcttacCtgagaaagcgagtccaaggt	15	8	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:150643965C>A	ENST00000262186.5	-	14	3731	c.3330G>T	c.(3328-3330)caG>caT	p.Q1110H	KCNH2_ENST00000330883.4_Splice_Site_p.Q770H|KCNH2_ENST00000392968.2_Splice_Site_p.Q1014H	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	1110					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	TGGAGCTTACCTGAGAAAGCG	0.637																																					p.Q1110H	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.G3330T						.						63	54	57					7																	150643965		2203	4300	6503	SO:0001630	splice_region_variant	3757	exon14			GCTTACCTGAGAA	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.3330+1G>T	chr7.hg19:g.150643965C>A		92.0	0.0		48.0	16.0	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	hg19	CCDS5910.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	3.996132|3.996132	0.74703|0.74703	.|.	.|.	ENSG00000055118|ENSG00000055118	ENST00000350328|ENST00000330883;ENST00000392968;ENST00000262186	.|D;D;D	.|0.98777	.|-4.86;-4.92;-5.13	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	.|0.317543	.|0.27956	.|N	.|0.017165	D|D	0.97707|0.97707	0.9248|0.9248	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.64830	.|0.989;0.989;0.994	.|P;P;P	.|0.56865	.|0.648;0.648;0.808	D|D	0.97273|0.97273	0.9912|0.9912	5|9	.|.	.|.	.|.	.|.	15.9235|15.9235	0.79592|0.79592	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1014;1110;770	.|C4PFH9;Q12809;Q12809-2	.|.;KCNH2_HUMAN;.	C|H	387|770;1014;1110	.|ENSP00000328531:Q770H;ENSP00000376695:Q1014H;ENSP00000262186:Q1110H	.|.	G|Q	-|-	1|3	0|2	KCNH2|KCNH2	150274898|150274898	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.683000|0.683000	0.39861|0.39861	4.485000|4.485000	0.60279|0.60279	2.426000|2.426000	0.82243|0.82243	0.484000|0.484000	0.47621|0.47621	GGT|CAG	.	.		0.637	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	Missense_Mutation	A	150643965	C	A	150643965	5	1	150	1	0	0	0	0	0	0	1	0	8041	695	24	3	157	3	KCNH2	7	150643965	Splice_Site	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	3818144	150643965	8494698	256	22980										
DNAJB6	10049	hgsc.bcm.edu	37	chr7	157174947	157174947	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgtttgattttagaagacccTtttgaggacttctttgggaa	10	5	1	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr7:157174947T>C	ENST00000262177.4	+	6	559	c.354T>C	c.(352-354)ccT>ccC	p.P118P	DNAJB6_ENST00000429029.2_Silent_p.P118P|DNAJB6_ENST00000443280.1_Intron|DNAJB6_ENST00000452797.2_Silent_p.P69P	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	118	Gly/Phe-rich.|Interaction with HSP70.				intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		TAGAAGACCCTTTTGAGGACT	0.413																																					p.P118P	Esophageal Squamous(46;195 967 1350 20350 43814)	Atlas-SNP	.											.	DNAJB6	39	.	0			c.T354C						.						77	81	80					7																	157174947		2203	4300	6503	SO:0001819	synonymous_variant	10049	exon6			AGACCCTTTTGAG	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"Heat shock proteins / DNAJ (HSP40)"	14888	protein-coding gene	gene with protein product		611332	"limb girdle muscular dystrophy 1D (autosomal dominant)"	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.354T>C	chr7.hg19:g.157174947T>C		75.0	0.0		55.0	4.0	NM_058246	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Silent	SNP	ENST00000262177.4	hg19	CCDS5946.1																																																																																			.	.		0.413	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2			C	157174947	T	C	157174947	2	2	150	1	0	0	0	0	0	0	0	1	4626	1596	56	2		2	DNAJB6	7	157174947	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	6530982	157174947	1963716	257	22981										
XKR5	389610	hgsc.bcm.edu	37	chr8	6690291	6690291	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	catcatcaaggagcaatgccCtggatgcccgtctgctcgga	11	13	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:6690291C>T	ENST00000518724.1	-	0	340				GS1-24F4.2_ENST00000500823.2_lincRNA			Q6UX68	XKR5_HUMAN	XK, Kell blood group complex subunit-related family, member 5							integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)	3			STAD - Stomach adenocarcinoma(24;0.0984)	READ - Rectum adenocarcinoma(644;0.137)|COAD - Colon adenocarcinoma(149;0.166)		GAGCAATGCCCTGGATGCCCG	0.592																																					p.G64R		Atlas-SNP	.											.	XKR5	20	.	0			c.G190A						.						92	102	99					8																	6690291		2079	4210	6289			389610	exon2			AATGCCCTGGATG	AY358489		8p23.1	2006-01-12	2006-01-12		ENSG00000186530	ENSG00000275591			20782	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 5"				Standard	NM_207411		Approved		uc022aqv.1	Q6UX68	OTTHUMG00000153652		chr8.hg19:g.6690291C>T		100.0	0.0		122.0	21.0	NM_207411	Q5GH74	Missense_Mutation	SNP	ENST00000518724.1	hg19																																																																																				.	.		0.592	XKR5-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000331969.2	NM_207411		T	6690291	C	T	6690291	1	4	150	0	1	0	0	0	0	0	0	0	17449	681	24	3		3	XKR5	8	6690291	RNA	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10		6690291	139673731	258	22982										
MTMR9	66036	hgsc.bcm.edu	37	chr8	11177226	11177226	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aagctacagcagaagacgatGtctttgtggtcctgggttaa	12	7	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:11177226G>A	ENST00000221086.3	+	9	1838	c.1365G>A	c.(1363-1365)atG>atA	p.M455I	AF131216.6_ENST00000498997.2_RNA|MTMR9_ENST00000526292.1_Missense_Mutation_p.M370I	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	455	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		AGAAGACGATGTCTTTGTGGT	0.428																																					p.M455I		Atlas-SNP	.											.	MTMR9	58	.	0			c.G1365A						.						137	126	130					8																	11177226		2203	4300	6503	SO:0001583	missense	66036	exon9			GACGATGTCTTTG	AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	14596	protein-coding gene	gene with protein product		606260	"myotubularin related protein 8"	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.1365G>A	chr8.hg19:g.11177226G>A	ENSP00000221086:p.Met455Ile	79.0	0.0		83.0	15.0	NM_015458	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Missense_Mutation	SNP	ENST00000221086.3	hg19	CCDS5979.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.978543	0.34942	.	.	ENSG00000104643	ENST00000221086;ENST00000526292	D;D	0.89552	-2.53;-2.53	4.43	4.43	0.53597	Myotubularin phosphatase domain (1);	0.205047	0.56097	D	0.000037	T	0.74711	0.3752	N	0.02539	-0.55	0.46113	D	0.998874	B	0.06786	0.001	B	0.01281	0.0	T	0.69800	-0.5047	10	0.23891	T;T	0.37;0.37	.	16.5541	0.84481	0.0:0.0:1.0:0.0	.	455	Q96QG7	MTMR9_HUMAN	I	455;370	ENSP00000221086:M455I;ENSP00000433239:M370I	ENSP00000221086:M455I;ENSP00000221086:M455I	M	+	3	0	MTMR9	11214636	1.000000	0.71417	1.000000	0.80357	0.695000	0.40330	6.197000	0.72100	2.441000	0.82636	0.563000	0.77884	ATG	.	.		0.428	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458		A	11177226	G	A	11177226	3	1	150	1	0	0	0	0	1	0	0	0	9959	1377	48	3	1399	3	MTMR9	8	11177226	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	4486935	11177226	135186796	259	22983										
ATP6V1B2	526	hgsc.bcm.edu	37	chr8	20068078	20068078	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctgtcttcttactgatttctAggtcgggtattcaatggatc	9	8	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:20068078A>T	ENST00000276390.2	+	5	425		c.e5-1			NM_001693.3	NP_001684.2	P21281	VATB2_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2						ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|ruffle (GO:0001726)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			endometrium(1)|kidney(2)|lung(5)|prostate(1)	9				Colorectal(74;0.0535)|COAD - Colon adenocarcinoma(73;0.211)	Gallium nitrate(DB05260)	ACTGATTTCTAGGTCGGGTAT	0.388																																					.	Pancreas(119;1230 1726 3901 4036 31644)	Atlas-SNP	.											.	ATP6V1B2	34	.	0			c.386-2A>T						.						160	156	157					8																	20068078		2203	4300	6503	SO:0001630	splice_region_variant	526	exon5			ATTTCTAGGTCGG	L35249	CCDS6014.1	8p21.3	2010-04-21	2006-01-13	2002-05-10	ENSG00000147416	ENSG00000147416	3.6.3.14	"ATPases / V-type"	854	protein-coding gene	gene with protein product		606939	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), beta polypeptide, 56/58kD, isoform 2", "ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B, isoform 2"	VPP3, ATP6B2		2145275, 14580332	Standard	NM_001693		Approved	VATB, Vma2, HO57	uc003wzp.3	P21281	OTTHUMG00000131073	ENST00000276390.2:c.386-1A>T	chr8.hg19:g.20068078A>T		144.0	0.0		165.0	36.0	NM_001693	B2R5Z3|D3DSQ5|Q14544|Q15859|Q96IR0	Splice_Site	SNP	ENST00000276390.2	hg19	CCDS6014.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.979219	0.74360	.	.	ENSG00000147416	ENST00000276390;ENST00000542368;ENST00000519667	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4514	0.61174	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP6V1B2	20112358	1.000000	0.71417	0.966000	0.40874	0.757000	0.42996	7.342000	0.79310	2.252000	0.74401	0.519000	0.50382	.	.	.		0.388	ATP6V1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253732.1	NM_001693	Intron	T	20068078	A	T	20068078	5	4	150	1	0	0	0	0	0	0	1	0	1179	434	15	4	402	4	ATP6V1B2	8	20068078	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	8890852	20068078	126295944	260	22984										
PRKDC	5591	hgsc.bcm.edu	37	chr8	48746959	48746959	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcaaatgagcttcttccatcTgtgacatgcaatcagagagg	9	9	4	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:48746959T>A	ENST00000523565.1	-	59	8007		c.e59-2		PRKDC_ENST00000314191.2_Splice_Site|PRKDC_ENST00000338368.3_Splice_Site			P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide						B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	TTCTTCCATCTGTGACATGCA	0.592								Non-homologous end-joining																													.	Esophageal Squamous(79;1091 1253 12329 31680 40677)	Atlas-SNP	.											.	PRKDC	394	.	0			c.7951-2A>T						.						73	81	78					8																	48746959		2179	4277	6456	SO:0001630	splice_region_variant	5591	exon60			TCCATCTGTGACA		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000523565.1:c.5502-2A>T	chr8.hg19:g.48746959T>A		53.0	0.0		61.0	16.0	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Splice_Site	SNP	ENST00000523565.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.50	3.140375	0.56936	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4107	0.67113	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRKDC	48909512	1.000000	0.71417	0.994000	0.49952	0.493000	0.33554	6.158000	0.71851	1.800000	0.52685	0.460000	0.39030	.	.	.		0.592	PRKDC-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000377896.1	NM_001081640	Intron	A	48746959	T	A	48746959	5	1	150	1	0	0	0	0	0	0	1	0	12533	1594	55	4	4548	4	PRKDC	8	48746959	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	28678881	48746959	97617063	261	22985										
OPRK1	4986	hgsc.bcm.edu	37	chr8	54142248	54142248	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gccggacgctcttgagacgcAggatcatcagggtgtagcag	15	10	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:54142248A>T	ENST00000265572.3	-	4	1049	c.752T>A	c.(751-753)cTg>cAg	p.L251Q	OPRK1_ENST00000524278.1_Missense_Mutation_p.L162Q|OPRK1_ENST00000520287.1_Missense_Mutation_p.L251Q|RP11-162D9.3_ENST00000524425.1_RNA	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	251					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)			NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CTTGAGACGCAGGATCATCAG	0.552																																					p.L251Q		Atlas-SNP	.											.	OPRK1	90	.	0			c.T752A						.						87	93	91					8																	54142248		2203	4300	6503	SO:0001583	missense	4986	exon4			AGACGCAGGATCA		CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"GPCR / Class A : Opioid receptors"	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.752T>A	chr8.hg19:g.54142248A>T	ENSP00000265572:p.Leu251Gln	165.0	0.0		203.0	30.0	NM_000912	E5RHC9|Q499G4	Missense_Mutation	SNP	ENST00000265572.3	hg19	CCDS6152.1	.	.	.	.	.	.	.	.	.	.	A	18.50	3.637284	0.67130	.	.	ENSG00000082556	ENST00000265572;ENST00000524278;ENST00000520287;ENST00000396798	T;T;T	0.38560	1.13;1.13;1.13	5.64	5.64	0.86602	GPCR, rhodopsin-like superfamily (1);	0.132704	0.52532	D	0.000074	T	0.59252	0.2180	L	0.55213	1.73	0.80722	D	1	D	0.60575	0.988	D	0.69654	0.965	T	0.58375	-0.7647	10	0.45353	T	0.12	.	15.8659	0.79063	1.0:0.0:0.0:0.0	.	251	P41145	OPRK_HUMAN	Q	251;162;251;237	ENSP00000265572:L251Q;ENSP00000430923:L162Q;ENSP00000429706:L251Q	ENSP00000265572:L251Q	L	-	2	0	OPRK1	54304801	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	7.369000	0.79578	2.152000	0.67230	0.528000	0.53228	CTG	.	.		0.552	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1			T	54142248	A	T	54142248	3	4	150	1	0	0	0	0	1	0	0	0	10894	188	7	4	394	4	OPRK1	8	54142248	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5395289	54142248	92221774	262	22986										
CYP7B1	9420	hgsc.bcm.edu	37	chr8	65528610	65528610	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acagctggggttcaaaaactTgttttagattctgcatcatg	9	7	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:65528610T>A	ENST00000310193.3	-	3	661	c.488A>T	c.(487-489)cAa>cTa	p.Q163L	CYP7B1_ENST00000523954.1_5'Flank	NM_004820.3	NP_004811.1	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B, polypeptide 1	163					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|cholesterol metabolic process (GO:0008203)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|positive regulation of epithelial cell proliferation (GO:0050679)|prostate gland epithelium morphogenesis (GO:0060740)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	25-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				TTCAAAAACTTGTTTTAGATT	0.368																																					p.Q163L		Atlas-SNP	.											.	CYP7B1	94	.	0			c.A488T						.						66	65	65					8																	65528610		2203	4300	6503	SO:0001583	missense	9420	exon3			AAAACTTGTTTTA	AF029403	CCDS6180.1	8q21.3	2008-07-04	2003-01-14		ENSG00000172817	ENSG00000172817		"Cytochrome P450s"	2652	protein-coding gene	gene with protein product		603711	"cytochrome P450, subfamily VIIB (oxysterol 7 alpha-hydroxylase), polypeptide 1", "spastic paraplegia 5A (autosomal recessive)"	SPG5A		9802883, 18252231	Standard	NM_004820		Approved		uc003xvj.2	O75881	OTTHUMG00000164387	ENST00000310193.3:c.488A>T	chr8.hg19:g.65528610T>A	ENSP00000310721:p.Gln163Leu	75.0	0.0		90.0	20.0	NM_004820	B2RN07|Q9UNF5	Missense_Mutation	SNP	ENST00000310193.3	hg19	CCDS6180.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.808131	0.00606	.	.	ENSG00000172817	ENST00000310193	T	0.68903	-0.36	5.17	4.01	0.46588	.	0.685395	0.15989	N	0.234924	T	0.48750	0.1517	N	0.25485	0.75	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.21930	-1.0231	9	.	.	.	-7.7898	7.1398	0.25550	0.0:0.2249:0.0:0.7751	.	163	O75881	CP7B1_HUMAN	L	163	ENSP00000310721:Q163L	.	Q	-	2	0	CYP7B1	65691164	0.031000	0.19500	0.050000	0.19076	0.458000	0.32498	1.639000	0.37176	2.069000	0.61940	0.533000	0.62120	CAA	.	.		0.368	CYP7B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378550.1			A	65528610	T	A	65528610	3	1	150	1	0	0	0	0	1	0	0	0	4199	1812	63	4	1048	4	CYP7B1	8	65528610	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	11386362	65528610	80835412	263	22987										
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68211585	68211585	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtcaagtgcccataagcaatAagtttctaaaatggagaaag	9	6	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:68211585A>C	ENST00000262215.3	-	4	707	c.318T>G	c.(316-318)ctT>ctG	p.L106L		NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	106	DCB; DCB:DCB domain and DCB:HUS domain interaction.				endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			CATAAGCAATAAGTTTCTAAA	0.303																																					p.L106L		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.T318G						.						57	56	56					8																	68211585		2203	4300	6503	SO:0001819	synonymous_variant	10565	exon4			AGCAATAAGTTTC	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.318T>G	chr8.hg19:g.68211585A>C		135.0	0.0		157.0	90.0	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Silent	SNP	ENST00000262215.3	hg19	CCDS6199.1																																																																																			.	.		0.303	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		C	68211585	A	C	68211585	2	2	150	1	0	0	0	0	0	0	0	1	852	349	13	5		5	ARFGEF1	8	68211585	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2682975	68211585	78152437	264	22988										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77617787	77617787	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cttgatgacgaggaagtattAggtgaactcaccgatagtat	11	6	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:77617787A>C	ENST00000521891.2	+	2	1912	c.1464A>C	c.(1462-1464)ttA>ttC	p.L488F	ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000050961.6_Missense_Mutation_p.L488F|ZFHX4_ENST00000518282.1_Missense_Mutation_p.L488F|ZFHX4_ENST00000455469.2_Missense_Mutation_p.L488F	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	488					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AGGAAGTATTAGGTGAACTCA	0.423										HNSCC(33;0.089)																											p.L488F		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A1464C						.						59	60	59					8																	77617787		2000	4167	6167	SO:0001583	missense	79776	exon2			AGTATTAGGTGAA		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.1464A>C	chr8.hg19:g.77617787A>C	ENSP00000430497:p.Leu488Phe	142.0	0.0		233.0	39.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	13.10	2.135719	0.37728	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.51071	0.72;0.78;0.74;0.74	5.41	5.41	0.78517	.	0.000000	0.34314	U	0.004073	T	0.46983	0.1421	N	0.19112	0.55	0.53688	D	0.999974	D;D;D;P	0.59767	0.976;0.986;0.986;0.868	P;P;P;B	0.54174	0.559;0.656;0.744;0.397	T	0.49224	-0.8962	10	0.51188	T	0.08	.	15.612	0.76733	1.0:0.0:0.0:0.0	.	488;488;488;488	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	F	488	ENSP00000430497:L488F;ENSP00000399605:L488F;ENSP00000050961:L488F;ENSP00000430848:L488F	ENSP00000050961:L488F	L	+	3	2	ZFHX4	77780342	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	4.553000	0.60753	2.281000	0.76405	0.533000	0.62120	TTA	.	.		0.423	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77617787	A	C	77617787	3	2	150	1	0	0	0	0	1	0	0	0	17650	417	15	5	1466	5	ZFHX4	8	77617787	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	9406202	77617787	68746235	265	22989										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77766437	77766437	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccttctcaaggcaccaaacCagccctgccattagcatcga	6	17	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:77766437C>T	ENST00000521891.2	+	10	7728	c.7280C>T	c.(7279-7281)cCa>cTa	p.P2427L	ZFHX4_ENST00000050961.6_Missense_Mutation_p.P2382L|ZFHX4_ENST00000518282.1_Missense_Mutation_p.P2401L|ZFHX4_ENST00000455469.2_Missense_Mutation_p.P2382L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2382	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GGCACCAAACCAGCCCTGCCA	0.552										HNSCC(33;0.089)																											p.P2427L		Atlas-SNP	.											.	ZFHX4	878	.	0			c.C7280T						.						46	76	66					8																	77766437		2036	4154	6190	SO:0001583	missense	79776	exon10			CCAAACCAGCCCT		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.7280C>T	chr8.hg19:g.77766437C>T	ENSP00000430497:p.Pro2427Leu	132.0	0.0		157.0	32.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	3.378	-0.126986	0.06795	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.50813	0.73;0.79;0.76;0.75	5.23	4.35	0.52113	.	0.353337	0.20228	U	0.096546	T	0.32224	0.0822	L	0.36672	1.1	0.32514	N	0.537226	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.32955	-0.9887	10	0.08179	T	0.78	.	8.9085	0.35539	0.1499:0.7763:0.0:0.0739	.	2382;2382;2427	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	L	2427;2411;2382;2382;2401	ENSP00000430497:P2427L;ENSP00000399605:P2382L;ENSP00000050961:P2382L;ENSP00000430848:P2401L	ENSP00000050961:P2382L	P	+	2	0	ZFHX4	77928992	0.995000	0.38212	0.538000	0.28064	0.046000	0.14306	3.825000	0.55730	1.427000	0.47276	-0.175000	0.13238	CCA	.	.		0.552	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77766437	C	T	77766437	3	4	150	1	0	0	0	0	1	0	0	0	17650	594	21	3	7314	3	ZFHX4	8	77766437	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	148650	77766437	68597585	266	22990										
CDH17	1015	hgsc.bcm.edu	37	chr8	95174341	95174341	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttttcaaagatggggatctgAtcattgatatcaataacgtt	8	5	4	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:95174341A>G	ENST00000027335.3	-	11	1456	c.1332T>C	c.(1330-1332)gaT>gaC	p.D444D	CDH17_ENST00000450165.2_Silent_p.D444D|CDH17_ENST00000441892.2_Silent_p.D230D	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	444	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			TGGGGATCTGATCATTGATAT	0.318																																					p.D444D		Atlas-SNP	.											.	CDH17	119	.	0			c.T1332C						.						105	103	103					8																	95174341		2203	4300	6503	SO:0001819	synonymous_variant	1015	exon11			GATCTGATCATTG	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1332T>C	chr8.hg19:g.95174341A>G		213.0	0.0		353.0	257.0	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	hg19	CCDS6260.1																																																																																			.	.		0.318	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		G	95174341	A	G	95174341	2	3	150	1	0	0	0	0	0	0	0	1	3104	330	12	2		2	CDH17	8	95174341	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	17407904	95174341	51189681	267	22991										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95539091	95539091	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgctagtgaggacactaattTggtcccagctttgagctgtc	11	9	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:95539091T>A	ENST00000297591.5	-	8	1456	c.1381A>T	c.(1381-1383)Aaa>Taa	p.K461*	KIAA1429_ENST00000437199.1_Nonsense_Mutation_p.K461*|KIAA1429_ENST00000421249.2_Nonsense_Mutation_p.K461*	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	461					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			GACACTAATTTGGTCCCAGCT	0.463																																					p.K461X		Atlas-SNP	.											.	KIAA1429	176	.	0			c.A1381T						.						113	108	109					8																	95539091		2203	4300	6503	SO:0001587	stop_gained	25962	exon8			CTAATTTGGTCCC	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.1381A>T	chr8.hg19:g.95539091T>A	ENSP00000297591:p.Lys461*	70.0	0.0		113.0	49.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Nonsense_Mutation	SNP	ENST00000297591.5	hg19	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	T	39	7.512537	0.98329	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.7314	16.2285	0.82315	0.0:0.0:0.0:1.0	.	.	.	.	X	461	.	ENSP00000297591:K461X	K	-	1	0	KIAA1429	95608267	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	2.235000	0.73313	0.460000	0.39030	AAA	.	.		0.463	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		A	95539091	T	A	95539091	4	1	150	1	0	0	0	0	0	1	0	0	8240	1821	63	4	4179	4	KIAA1429	8	95539091	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	364750	95539091	50824931	268	22992										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113599330	113599330	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgtgctaaatgaaatgttcTggctgaaatattgattccct	8	6	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:113599330T>A	ENST00000297405.5	-	23	4094	c.3850A>T	c.(3850-3852)Aga>Tga	p.R1284*	CSMD3_ENST00000352409.3_Nonsense_Mutation_p.R1284*|CSMD3_ENST00000343508.3_Nonsense_Mutation_p.R1244*|CSMD3_ENST00000455883.2_Nonsense_Mutation_p.R1180*	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1284	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TGAAATGTTCTGGCTGAAATA	0.318										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.R1284X		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A3850T						.						126	115	119					8																	113599330		2203	4299	6502	SO:0001587	stop_gained	114788	exon23			ATGTTCTGGCTGA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3850A>T	chr8.hg19:g.113599330T>A	ENSP00000297405:p.Arg1284*	99.0	0.0		157.0	30.0	NM_198123	Q96PZ3	Nonsense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	44	11.122374	0.99518	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	.	.	.	4.08	4.08	0.47627	.	0.167593	0.46145	D	0.000315	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4972	0.61432	0.0:0.0:0.0:1.0	.	.	.	.	X	1244;1284;624;1180;1284	.	ENSP00000297405:R1284X	R	-	1	2	CSMD3	113668506	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.061000	0.41403	1.839000	0.53478	0.482000	0.46254	AGA	.	.		0.318	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113599330	T	A	113599330	4	1	150	1	0	0	0	0	0	1	0	0	3948	1588	55	4	7469	4	CSMD3	8	113599330	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	18060239	113599330	32764692	269	22993										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125103790	125103790	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagataggaaaccaagtcttTtctggaaaaactatcttcac	6	9	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:125103790T>C	ENST00000522917.1	+	34	4724	c.4518T>C	c.(4516-4518)ttT>ttC	p.F1506F	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6_ENST00000399018.1_Silent_p.F1506F	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1506						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			ACCAAGTCTTTTCTGGAAAAA	0.428																																					p.F1506F		Atlas-SNP	.											.	FER1L6	268	.	0			c.T4518C						.						111	103	106					8																	125103790		1859	4087	5946	SO:0001819	synonymous_variant	654463	exon34			AGTCTTTTCTGGA	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.4518T>C	chr8.hg19:g.125103790T>C		150.0	0.0		196.0	101.0	NM_001039112		Silent	SNP	ENST00000522917.1	hg19	CCDS43767.1																																																																																			.	.		0.428	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		C	125103790	T	C	125103790	2	2	150	1	0	0	0	0	0	0	0	1	5823	1838	64	2		2	FER1L6	8	125103790	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	11504460	125103790	21260232	270	22994										
TG	7038	hgsc.bcm.edu	37	chr8	133899402	133899402	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gaagatgtggcaagagatttAggtgatgtgatggaaacggt	16	2	0	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:133899402A>T	ENST00000220616.4	+	9	1825	c.1785A>T	c.(1783-1785)ttA>ttT	p.L595F	TG_ENST00000377869.1_Missense_Mutation_p.L595F	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	595					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CAAGAGATTTAGGTGATGTGA	0.473																																					p.L595F		Atlas-SNP	.											.	TG	416	.	0			c.A1785T						.						132	122	125					8																	133899402		2203	4300	6503	SO:0001583	missense	7038	exon9			AGATTTAGGTGAT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1785A>T	chr8.hg19:g.133899402A>T	ENSP00000220616:p.Leu595Phe	173.0	0.0		239.0	36.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.104002	0.37145	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.67865	-0.29;-0.29	5.03	0.0604	0.14336	.	0.132698	0.32244	N	0.006375	T	0.79240	0.4412	M	0.89414	3.03	0.29969	N	0.818738	D	0.58268	0.982	P	0.62740	0.906	T	0.75619	-0.3255	10	0.87932	D	0	.	8.7505	0.34613	0.5974:0.0:0.4026:0.0	.	595	P01266	THYG_HUMAN	F	595	ENSP00000367100:L595F;ENSP00000220616:L595F	ENSP00000220616:L595F	L	+	3	2	TG	133968584	0.987000	0.35691	0.859000	0.33776	0.209000	0.24338	0.495000	0.22483	-0.122000	0.11766	0.533000	0.62120	TTA	.	.		0.473	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133899402	A	T	133899402	3	4	150	1	0	0	0	0	1	0	0	0	15828	417	15	4	1819	4	TG	8	133899402	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	8795612	133899402	12464620	271	22995										
TG	7038	hgsc.bcm.edu	37	chr8	133913655	133913655	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctccaggagagtcagcccagGctatgtcccagcctgcaggg	13	14	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:133913655G>T	ENST00000220616.4	+	16	3531	c.3491G>T	c.(3490-3492)gGc>gTc	p.G1164V	TG_ENST00000377869.1_Missense_Mutation_p.G1164V	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1164	Thyroglobulin type-1 10. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GTCAGCCCAGGCTATGTCCCA	0.607																																					p.G1164V		Atlas-SNP	.											.	TG	416	.	0			c.G3491T						.						74	74	74					8																	133913655		2203	4300	6503	SO:0001583	missense	7038	exon16			GCCCAGGCTATGT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.3491G>T	chr8.hg19:g.133913655G>T	ENSP00000220616:p.Gly1164Val	121.0	0.0		163.0	28.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.609296	0.28623	.	.	ENSG00000042832	ENST00000377869;ENST00000220616	T;T	0.61742	0.08;0.08	5.12	5.12	0.69794	Thyroglobulin type-1 (4);	0.436747	0.21424	N	0.074773	T	0.64193	0.2576	L	0.29908	0.895	0.50171	D	0.999858	D	0.89917	1.0	D	0.81914	0.995	T	0.66452	-0.5920	10	0.72032	D	0.01	.	11.8975	0.52663	0.0:0.176:0.824:0.0	.	1164	P01266	THYG_HUMAN	V	1164	ENSP00000367100:G1164V;ENSP00000220616:G1164V	ENSP00000220616:G1164V	G	+	2	0	TG	133982837	1.000000	0.71417	0.798000	0.32154	0.015000	0.08874	4.083000	0.57643	2.377000	0.81083	0.655000	0.94253	GGC	.	.		0.607	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133913655	G	T	133913655	3	4	150	1	0	0	0	0	1	0	0	0	15828	1203	42	3	3553	3	TG	8	133913655	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	14253	133913655	12450367	272	22996										
CYP11B1	1584	hgsc.bcm.edu	37	chr8	143961039	143961039	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tctggtgtacttccaggtgcAggtcctcataaccctgctcc	9	14	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:143961039A>T	ENST00000292427.4	-	1	223	c.191T>A	c.(190-192)cTg>cAg	p.L64Q	CYP11B1_ENST00000517471.1_Missense_Mutation_p.L64Q|CYP11B1_ENST00000377675.3_Missense_Mutation_p.L64Q	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	64					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	TTCCAGGTGCAGGTCCTCATA	0.622									Familial Hyperaldosteronism type I																												p.L64Q		Atlas-SNP	.											.	CYP11B1	128	.	0			c.T191A						.						81	73	75					8																	143961039		2203	4300	6503	SO:0001583	missense	1584	exon1	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	AGGTGCAGGTCCT	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"Cytochrome P450s"	2591	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	610613	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.191T>A	chr8.hg19:g.143961039A>T	ENSP00000292427:p.Leu64Gln	137.0	0.0		187.0	47.0	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	ENST00000292427.4	hg19	CCDS6392.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.234987	0.39498	.	.	ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675	T;T;T	0.80123	-0.53;-0.53;-1.34	2.96	1.69	0.24217	.	1.218420	0.06447	N	0.727002	D	0.87505	0.6194	M	0.75615	2.305	0.09310	N	1	D;D;D	0.64830	0.986;0.989;0.994	D;D;D	0.71870	0.938;0.975;0.954	T	0.69057	-0.5246	10	0.41790	T	0.15	.	6.267	0.20932	0.7428:0.2572:0.0:0.0	.	64;64;64	Q4VAR0;Q4VAQ9;P15538	.;.;C11B1_HUMAN	Q	64	ENSP00000292427:L64Q;ENSP00000428043:L64Q;ENSP00000366903:L64Q	ENSP00000292427:L64Q	L	-	2	0	CYP11B1	143958041	0.174000	0.23070	0.002000	0.10522	0.695000	0.40330	5.531000	0.67148	0.273000	0.22049	0.254000	0.18369	CTG	.	.		0.622	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			T	143961039	A	T	143961039	3	4	150	1	0	0	0	0	1	0	0	0	4147	188	7	4	1356	4	CYP11B1	8	143961039	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	10047384	143961039	2402983	273	22997										
RECQL4	113655	hgsc.bcm.edu	37	chr8	145738779	145738779	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccaccacccggcaactggccCtgcatgaaggctcgctgtac	10	17	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr8:145738779C>T	ENST00000301327.4	+	0	1548				RECQL4_ENST00000428558.2_Silent_p.Q762Q|CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000532237.1_5'UTR	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GCAACTGGCCCTGCATGAAGG	0.682																																					p.Q762Q		Atlas-SNP	.											.	RECQL4	75	.	0			c.G2286A						.						16	21	20					8																	145738779		2090	4203	6293	SO:0001628	intergenic_variant	9401	exon14			CTGGCCCTGCATG		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		chr8.hg19:g.145738779C>T		106.0	0.0		121.0	12.0	NM_004260		Silent	SNP	ENST00000301327.4	hg19	CCDS6431.1																																																																																			.	.		0.682	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		T	145738779	C	T	145738779	1	4	150	0	1	0	0	0	0	0	0	0	13217	680	24	3		3	RECQL4	8	145738779	IGR	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	1777740	145738779	625243	274	22998										
DOCK8	81704	hgsc.bcm.edu	37	chr9	336700	336700	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaaacctccactctgagcgtTagcagctttttcaagcaggt	8	11	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:336700T>A	ENST00000453981.1	+	12	1516	c.1404T>A	c.(1402-1404)gtT>gtA	p.V468V	DOCK8_ENST00000432829.2_Silent_p.V400V|DOCK8_ENST00000469391.1_Silent_p.V400V			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	468					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CTCTGAGCGTTAGCAGCTTTT	0.488																																					p.V468V		Atlas-SNP	.											.	DOCK8	401	.	0			c.T1404A						.						96	92	93					9																	336700		2203	4300	6503	SO:0001819	synonymous_variant	81704	exon12			GAGCGTTAGCAGC	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.1404T>A	chr9.hg19:g.336700T>A		109.0	0.0		99.0	32.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	hg19	CCDS6440.2																																																																																			.	.		0.488	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		A	336700	T	A	336700	2	1	150	1	0	0	0	0	0	0	0	1	4695	1741	61	4		4	DOCK8	9	336700	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10		336700	140876731	275	22999										
GLDC	2731	hgsc.bcm.edu	37	chr9	6592892	6592892	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaaattgatctgccgctgagCggccctgcccaagacctcct	9	15	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:6592892C>A	ENST00000321612.6	-	10	1510	c.1360G>T	c.(1360-1362)Gct>Tct	p.A454S		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	454					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	TGCCGCTGAGCGGCCCTGCCC	0.443																																					p.A454S		Atlas-SNP	.											.	GLDC	118	.	0			c.G1360T						.						68	67	67					9																	6592892		2203	4298	6501	SO:0001583	missense	2731	exon10			GCTGAGCGGCCCT	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"glycine cleavage system protein P", "glycine decarboxylase"	238300	"glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.1360G>T	chr9.hg19:g.6592892C>A	ENSP00000370737:p.Ala454Ser	341.0	1.0		303.0	173.0	NM_000170	Q2M2F8	Missense_Mutation	SNP	ENST00000321612.6	hg19	CCDS34987.1	.	.	.	.	.	.	.	.	.	.	C	9.251	1.040684	0.19669	.	.	ENSG00000178445	ENST00000321612	D	0.95853	-3.83	5.74	3.86	0.44501	Glycine cleavage system P-protein, N-terminal (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.199645	0.53938	D	0.000056	D	0.92476	0.7611	L	0.58810	1.83	0.46927	D	0.999254	B	0.20550	0.046	B	0.21917	0.037	D	0.86649	0.1897	10	0.11794	T	0.64	-5.6063	11.7802	0.52010	0.0:0.8542:0.0:0.1458	.	454	P23378	GCSP_HUMAN	S	454	ENSP00000370737:A454S	ENSP00000370737:A454S	A	-	1	0	GLDC	6582892	0.016000	0.18221	0.654000	0.29608	0.941000	0.58515	0.785000	0.26830	0.738000	0.32606	0.563000	0.77884	GCT	.	.		0.443	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170		A	6592892	C	A	6592892	3	1	150	1	0	0	0	0	1	0	0	0	6441	768	27	1	1766	1	GLDC	9	6592892	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	6256192	6592892	134620539	276	23000										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8341889	8341889	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gggctctcattaaagttacaTggccataaatatctacagtt	7	8	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:8341889T>A	ENST00000381196.4	-	37	5294	c.4751A>T	c.(4750-4752)cAt>cTt	p.H1584L	PTPRD_ENST00000358503.5_Missense_Mutation_p.H1562L|PTPRD_ENST00000355233.5_Missense_Mutation_p.H1178L|PTPRD_ENST00000486161.1_Missense_Mutation_p.H1177L|PTPRD_ENST00000360074.4_Missense_Mutation_p.H1571L|PTPRD_ENST00000540109.1_Missense_Mutation_p.H1584L|PTPRD_ENST00000397617.3_Missense_Mutation_p.H1177L|PTPRD_ENST00000356435.5_Missense_Mutation_p.H1584L|PTPRD_ENST00000397611.3_Missense_Mutation_p.H1174L|PTPRD_ENST00000397606.3_Missense_Mutation_p.H1177L|PTPRD_ENST00000537002.1_Missense_Mutation_p.H1174L	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1584	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TAAAGTTACATGGCCATAAAT	0.398										TSP Lung(15;0.13)																											p.H1584L		Atlas-SNP	.											.	PTPRD	1348	.	0			c.A4751T						.						162	160	161					9																	8341889		2203	4300	6503	SO:0001583	missense	5789	exon40			GTTACATGGCCAT	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.4751A>T	chr9.hg19:g.8341889T>A	ENSP00000370593:p.His1584Leu	109.0	0.0		68.0	14.0	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	hg19	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.310861	0.81358	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7	6.07	6.07	0.98685	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.31420	0.0796	N	0.08118	0	0.80722	D	1	D;D;D;D;P;D;D;D;P	0.89917	0.99;0.99;0.99;0.99;0.862;0.988;0.976;1.0;0.948	P;P;P;P;B;P;P;D;P	0.91635	0.743;0.743;0.743;0.743;0.386;0.626;0.679;0.999;0.737	T	0.32375	-0.9909	9	.	.	.	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	1177;1168;1177;1178;1174;1174;1571;1584;1584	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	L	1584;1584;1571;1562;1178;1177;1174;1174;1055;1584;1177;1177	ENSP00000370593:H1584L;ENSP00000348812:H1584L;ENSP00000353187:H1571L;ENSP00000351293:H1562L;ENSP00000347373:H1178L;ENSP00000380741:H1177L;ENSP00000380735:H1174L;ENSP00000440515:H1174L;ENSP00000438164:H1584L;ENSP00000417093:H1177L;ENSP00000380731:H1177L	.	H	-	2	0	PTPRD	8331889	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.326000	0.78906	0.533000	0.62120	CAT	.	.		0.398	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			A	8341889	T	A	8341889	3	1	150	1	0	0	0	0	1	0	0	0	12814	1464	51	4	1015	4	PTPRD	9	8341889	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1748997	8341889	132871542	277	23001										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8636718	8636718	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctcaaatctctgattgctgActttctttccttttttgttc	4	11	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:8636718A>C	ENST00000381196.4	-	10	734	c.191T>G	c.(190-192)gTc>gGc	p.V64G	PTPRD_ENST00000360074.4_Missense_Mutation_p.V64G|PTPRD_ENST00000358503.5_Missense_Mutation_p.V64G|PTPRD_ENST00000355233.5_Missense_Mutation_p.V64G|PTPRD_ENST00000486161.1_Missense_Mutation_p.V64G|PTPRD_ENST00000463477.1_Missense_Mutation_p.V64G|PTPRD_ENST00000540109.1_Missense_Mutation_p.V64G|PTPRD_ENST00000397617.3_Missense_Mutation_p.V64G|PTPRD_ENST00000356435.5_Missense_Mutation_p.V64G|PTPRD_ENST00000397611.3_Missense_Mutation_p.V64G|PTPRD_ENST00000397606.3_Missense_Mutation_p.V64G|PTPRD_ENST00000537002.1_Missense_Mutation_p.V64G	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	64	Ig-like C2-type 1.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CTGATTGCTGACTTTCTTTCC	0.443										TSP Lung(15;0.13)																											p.V64G		Atlas-SNP	.											.	PTPRD	1348	.	0			c.T191G						.						141	129	133					9																	8636718		2203	4300	6503	SO:0001583	missense	5789	exon2			TTGCTGACTTTCT	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.191T>G	chr9.hg19:g.8636718A>C	ENSP00000370593:p.Val64Gly	147.0	0.0		105.0	6.0	NM_001040712	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	hg19	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.212532	0.79240	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606;ENST00000463477;ENST00000481079	T;T;T;T;T;T;T;T;T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41	5.57	5.57	0.84162	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.78175	0.4242	L	0.54863	1.705	0.80722	D	1	D;D;D;D;D;P;D;D;D;D	0.89917	1.0;0.996;0.999;1.0;1.0;0.942;0.999;0.999;1.0;0.998	D;D;D;D;D;P;D;D;D;D	0.91635	0.999;0.977;0.995;0.997;0.997;0.614;0.995;0.983;0.999;0.985	T	0.77416	-0.2596	9	.	.	.	.	15.7282	0.77780	1.0:0.0:0.0:0.0	.	64;64;64;64;64;64;64;64;64;64	C9J8S8;Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;.;PTPRD_HUMAN	G	64	ENSP00000370593:V64G;ENSP00000348812:V64G;ENSP00000353187:V64G;ENSP00000351293:V64G;ENSP00000347373:V64G;ENSP00000380741:V64G;ENSP00000380735:V64G;ENSP00000440515:V64G;ENSP00000438164:V64G;ENSP00000417093:V64G;ENSP00000380731:V64G;ENSP00000417661:V64G;ENSP00000417890:V64G	.	V	-	2	0	PTPRD	8626718	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.288000	0.96055	2.113000	0.64589	0.455000	0.32223	GTC	.	.		0.443	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			C	8636718	A	C	8636718	3	2	150	1	0	0	0	0	1	0	0	0	12814	275	10	5	5751	5	PTPRD	9	8636718	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	294829	8636718	132576713	278	23002										
BNC2	54796	hgsc.bcm.edu	37	chr9	16418994	16418994	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtccattctgagactaatctActgaagtgaagggaatgttt	10	6	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:16418994A>T	ENST00000380672.4	-	7	3350	c.3293T>A	c.(3292-3294)gTa>gAa	p.V1098E	BNC2_ENST00000380667.2_Missense_Mutation_p.V1031E|BNC2_ENST00000545497.1_Missense_Mutation_p.V1003E	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		AGACTAATCTACTGAAGTGAA	0.463																																					p.V1098E		Atlas-SNP	.											.	BNC2	166	.	0			c.T3293A						.						126	122	123					9																	16418994		2203	4300	6503	SO:0001583	missense	54796	exon7			TAATCTACTGAAG	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.3293T>A	chr9.hg19:g.16418994A>T	ENSP00000370047:p.Val1098Glu	68.0	0.0		67.0	13.0	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	hg19	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	A	13.95	2.390904	0.42410	.	.	ENSG00000173068	ENST00000380672;ENST00000380667;ENST00000545497	T;T;T	0.36157	1.27;1.3;1.29	6.08	6.08	0.98989	.	0.170192	0.51477	D	0.000092	T	0.24431	0.0592	N	0.08118	0	0.80722	D	1	B;B;B	0.25105	0.118;0.072;0.072	B;B;B	0.25291	0.059;0.059;0.059	T	0.08932	-1.0698	10	0.72032	D	0.01	-7.2811	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1003;1098;863	F5H586;Q6ZN30;D3DRJ1	.;BNC2_HUMAN;.	E	1098;1031;1003	ENSP00000370047:V1098E;ENSP00000370042:V1031E;ENSP00000444640:V1003E	ENSP00000370042:V1031E	V	-	2	0	BNC2	16408994	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.964000	0.70379	2.333000	0.79357	0.482000	0.46254	GTA	.	.		0.463	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		T	16418994	A	T	16418994	3	4	150	1	0	0	0	0	1	0	0	0	1475	391	14	4	10	4	BNC2	9	16418994	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	7782276	16418994	124794437	279	23003										
IFNA7	3444	hgsc.bcm.edu	37	chr9	21202098	21202098	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggtctgaggcagatcacagcCcagagagcagatggatttgt	14	8	2	4	rs112551811		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:21202098C>T	ENST00000239347.3	-	1	106	c.67G>A	c.(67-69)Ggc>Agc	p.G23S		NM_021057.2	NP_066401.2	P01567	IFNA7_HUMAN	interferon, alpha 7	23					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(6)	12				GBM - Glioblastoma multiforme(5;4.75e-197)|Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		AGATCACAGCCCAGAGAGCAG	0.507																																					p.G23S		Atlas-SNP	.											.	IFNA7	24	.	0			c.G67A						.						87	86	86					9																	21202098		2203	4300	6503	SO:0001583	missense	3444	exon1			CACAGCCCAGAGA		CCDS34995.1	9p22	2010-12-10			ENSG00000214042	ENSG00000214042		"Interferons"	5428	protein-coding gene	gene with protein product		147567				1385305	Standard	NM_021057		Approved	IFNA-J, IFN-alphaJ	uc003zop.1	P01567	OTTHUMG00000019662	ENST00000239347.3:c.67G>A	chr9.hg19:g.21202098C>T	ENSP00000239347:p.Gly23Ser	134.0	0.0		144.0	33.0	NM_021057	Q14607|Q5VV14	Missense_Mutation	SNP	ENST00000239347.3	hg19	CCDS34995.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.531452	0.45073	.	.	ENSG00000214042	ENST00000239347	T	0.03035	4.07	3.56	1.61	0.23674	Four-helical cytokine-like, core (1);	0.590041	0.16895	N	0.195148	T	0.05318	0.0141	M	0.72118	2.19	0.09310	N	1	P	0.45474	0.859	B	0.38921	0.285	T	0.28650	-1.0037	10	0.72032	D	0.01	.	7.6473	0.28327	0.0:0.7663:0.0:0.2337	.	23	P01567	IFNA7_HUMAN	S	23	ENSP00000239347:G23S	ENSP00000239347:G23S	G	-	1	0	IFNA7	21192098	0.004000	0.15560	0.016000	0.15963	0.308000	0.27856	0.998000	0.29744	0.611000	0.30052	-0.225000	0.12378	GGC	.	C|0.500;T|0.500		0.507	IFNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051891.1	NM_021057		T	21202098	C	T	21202098	3	4	150	1	0	0	0	0	1	0	0	0	7551	623	22	3	506	3	IFNA7	9	21202098	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	4783104	21202098	120011333	280	23004										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32632698	32632699	+	Missense_Mutation	DNP	GG	GG	TT													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggagacacttgcccttcatGgcagcaatgaaggcccttgt							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:32632698_32632699GG>TT	ENST00000242310.4	-	1	2968_2969	c.2879_2880CC>AA	c.(2878-2880)gCC>gAA	p.A960E	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	960					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TGCCCTTCATGGCAGCAATGAA	0.475																																					p.A960A|p.A960D		Atlas-SNP	.											.	TAF1L	382	.	0			c.C2880A|c.C2879A						.																																			SO:0001583	missense	138474	exon1			CTTCATGGCAGCA|TTCATGGCAGCAA	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.2879_2880delinsTT	chr9.hg19:g.32632698_32632699delinsTT	ENSP00000418379:p.Ala960Glu	222.0|220.0	0.0		197.0|198.0	55.0	NM_153809	Q0VG57	Silent|Missense_Mutation	SNP	ENST00000242310.4	hg19	CCDS35003.1																																																																																			.	.		0.475	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			TT	32632699	GG	TT	32632698	3	4	150	1	0	0	0	0	1	0	0	0	15538	1335	47	3	2604	3	TAF1L	9	32632698	Missense_Mutation	DNP	GG	TCGA-DD-AAC8-01A-11D-A40R-10	11430600	32632698	108580733	281	23005										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35403468	35403468	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatgacctcaagtggcagacAgcgggtatgttccggccttt	12	10	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:35403468A>T	ENST00000378495.3	+	38	4584	c.4362A>T	c.(4360-4362)acA>acT	p.T1454T	UNC13B_ENST00000396787.1_Silent_p.T1485T|UNC13B_ENST00000378496.4_Silent_p.T1473T	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1454	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			AGTGGCAGACAGCGGGTATGT	0.527																																					p.T1454T		Atlas-SNP	.											.	UNC13B	153	.	0			c.A4362T						.						61	60	61					9																	35403468		2203	4300	6503	SO:0001819	synonymous_variant	10497	exon38			GCAGACAGCGGGT	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.4362A>T	chr9.hg19:g.35403468A>T		172.0	0.0		120.0	36.0	NM_006377	Q5VYM8	Silent	SNP	ENST00000378495.3	hg19	CCDS6579.1																																																																																			.	.		0.527	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		T	35403468	A	T	35403468	2	4	150	1	0	0	0	0	0	0	0	1	17000	175	7	4		4	UNC13B	9	35403468	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2770770	35403468	105809963	282	23006										
CA9	768	hgsc.bcm.edu	37	chr9	35675916	35675916	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagaactgcgcctgcgcaacAatggccacagtggtgagggg	15	11	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:35675916A>T	ENST00000378357.4	+	3	696	c.592A>T	c.(592-594)Aat>Tat	p.N198Y		NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	198	Catalytic.				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	CCTGCGCAACAATGGCCACAG	0.726																																					p.N198Y		Atlas-SNP	.											.	CA9	48	.	0			c.A592T						.						19	21	21					9																	35675916		1749	3612	5361	SO:0001583	missense	768	exon3			CGCAACAATGGCC	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"Carbonic anhydrases"	1383	protein-coding gene	gene with protein product	"carbonic dehydratase", "RCC-associated protein G250"	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.592A>T	chr9.hg19:g.35675916A>T	ENSP00000367608:p.Asn198Tyr	74.0	0.0		52.0	12.0	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	hg19	CCDS6585.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.224089	0.79576	.	.	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.57752	0.38	4.68	4.68	0.58851	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.64402	D	0.000001	T	0.77322	0.4113	M	0.93375	3.41	0.45541	D	0.99849	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.993	T	0.82416	-0.0468	10	0.87932	D	0	.	10.6845	0.45835	1.0:0.0:0.0:0.0	.	198;198	F5H404;Q16790	.;CAH9_HUMAN	Y	198	ENSP00000367608:N198Y	ENSP00000367608:N198Y	N	+	1	0	CA9	35665916	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.563000	0.60823	2.088000	0.63022	0.459000	0.35465	AAT	.	.		0.726	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216		T	35675916	A	T	35675916	3	4	150	1	0	0	0	0	1	0	0	0	2526	130	5	4	602	4	CA9	9	35675916	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	272448	35675916	105537515	283	23007										
TLN1	7094	hgsc.bcm.edu	37	chr9	35707454	35707454	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgctgctcggcactgggcaCggttctcctctgtgaaggcc	13	13	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:35707454C>A	ENST00000314888.9	-	36	5017	c.4664G>T	c.(4663-4665)cGt>cTt	p.R1555L	TLN1_ENST00000540444.1_Missense_Mutation_p.R1555L|TLN1_ENST00000464379.1_Intron	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1555	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCACTGGGCACGGTTCTCCTC	0.577																																					p.R1555L		Atlas-SNP	.											.	TLN1	185	.	0			c.G4664T						.						47	44	45					9																	35707454		2203	4300	6503	SO:0001583	missense	7094	exon36			TGGGCACGGTTCT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.4664G>T	chr9.hg19:g.35707454C>A	ENSP00000316029:p.Arg1555Leu	78.0	0.0		51.0	25.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	33	5.197261	0.94960	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.31769	1.48;1.48	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.55752	0.1940	M	0.84433	2.695	0.80722	D	1	D	0.63046	0.992	P	0.53861	0.736	T	0.61148	-0.7121	10	0.62326	D	0.03	-11.0069	20.1386	0.98045	0.0:1.0:0.0:0.0	.	1555	Q9Y490	TLN1_HUMAN	L	1555	ENSP00000316029:R1555L;ENSP00000442981:R1555L	ENSP00000316029:R1555L	R	-	2	0	TLN1	35697454	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.794000	0.85869	2.767000	0.95098	0.561000	0.74099	CGT	.	.		0.577	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35707454	C	A	35707454	3	1	150	1	0	0	0	0	1	0	0	0	15962	536	19	1	3049	1	TLN1	9	35707454	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	31538	35707454	105505977	284	23008										
DAPK1	1612	hgsc.bcm.edu	37	chr9	90296521	90296521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagcaggttcccaccttcacCcctggcttctaagcccacag	7	18	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:90296521C>T	ENST00000408954.3	+	20	2539	c.2204C>T	c.(2203-2205)cCc>cTc	p.P735L	DAPK1_ENST00000472284.1_Missense_Mutation_p.P735L|DAPK1_ENST00000358077.5_Missense_Mutation_p.P735L|DAPK1_ENST00000491893.1_Missense_Mutation_p.P735L|DAPK1_ENST00000469640.2_Missense_Mutation_p.P735L	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	735					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						CCACCTTCACCCCTGGCTTCT	0.577									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.P735L		Atlas-SNP	.											.	DAPK1	329	.	0			c.C2204T						.						32	34	33					9																	90296521		1923	4110	6033	SO:0001583	missense	1612	exon20	Familial Cancer Database	Familial CLL	CTTCACCCCTGGC	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.2204C>T	chr9.hg19:g.90296521C>T	ENSP00000386135:p.Pro735Leu	55.0	0.0		54.0	16.0	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	hg19	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.050506	0.55218	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.69306	-0.28;-0.28;-0.26;-0.28;-0.39	5.17	4.27	0.50696	.	0.000000	0.49916	D	0.000124	T	0.76955	0.4060	L	0.54323	1.7	0.80722	D	1	B;D;B	0.89917	0.001;1.0;0.001	B;D;B	0.91635	0.002;0.999;0.002	T	0.77619	-0.2520	10	0.49607	T	0.09	.	13.3899	0.60818	0.0:0.9239:0.0:0.0761	.	735;289;735	B7ZLE7;P53355-2;P53355	.;.;DAPK1_HUMAN	L	735	ENSP00000350785:P735L;ENSP00000417076:P735L;ENSP00000418885:P735L;ENSP00000386135:P735L;ENSP00000419026:P735L	ENSP00000350785:P735L	P	+	2	0	DAPK1	89486341	1.000000	0.71417	0.975000	0.42487	0.253000	0.25986	7.576000	0.82467	1.437000	0.47472	0.556000	0.70494	CCC	.	.		0.577	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		T	90296521	C	T	90296521	3	4	150	1	0	0	0	0	1	0	0	0	4237	623	22	3	2278	3	DAPK1	9	90296521	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	54589067	90296521	50916910	285	23009										
SEMA4D	10507	hgsc.bcm.edu	37	chr9	91994239	91994239	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgtctgaacaactgacaaggTgggggccactacgggctttg	14	9	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:91994239T>A	ENST00000450295.1	-	16	2745	c.1969A>T	c.(1969-1971)Acc>Tcc	p.T657S	SEMA4D_ENST00000356444.2_Missense_Mutation_p.T657S|SEMA4D_ENST00000422704.2_Missense_Mutation_p.T657S|SEMA4D_ENST00000343780.4_Intron|SEMA4D_ENST00000438547.2_Missense_Mutation_p.T657S|SEMA4D_ENST00000339861.4_Intron|SEMA4D_ENST00000420987.1_Intron|SEMA4D_ENST00000455551.2_Intron			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	657					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						ACTGACAAGGTGGGGGCCACT	0.567																																					p.T657S		Atlas-SNP	.											.	SEMA4D	81	.	0			c.A1969T						.						124	132	129					9																	91994239		2203	4300	6503	SO:0001583	missense	10507	exon18			ACAAGGTGGGGGC	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"Semaphorins", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10732	protein-coding gene	gene with protein product	"M-sema G"	601866	"chromosome 9 open reading frame 164"	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.1969A>T	chr9.hg19:g.91994239T>A	ENSP00000416523:p.Thr657Ser	101.0	0.0		57.0	14.0	NM_006378	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	hg19	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	T	4.704	0.130851	0.08981	.	.	ENSG00000187764	ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	3.92	1.55	0.23275	.	1.722020	0.02641	N	0.105346	T	0.15003	0.0362	L	0.29908	0.895	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.22208	-1.0223	10	0.32370	T	0.25	.	1.5817	0.02636	0.1461:0.1549:0.1506:0.5484	.	657	Q92854	SEM4D_HUMAN	S	657	ENSP00000416523:T657S;ENSP00000405102:T657S;ENSP00000348822:T657S;ENSP00000388768:T657S	ENSP00000348822:T657S	T	-	1	0	SEMA4D	91184059	0.808000	0.29022	0.005000	0.12908	0.101000	0.19017	0.043000	0.13971	0.656000	0.30886	0.459000	0.35465	ACC	.	.		0.567	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378		A	91994239	T	A	91994239	3	1	150	1	0	0	0	0	1	0	0	0	14049	1696	59	4	1193	4	SEMA4D	9	91994239	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1697718	91994239	49219192	286	23010										
FGD3	89846	hgsc.bcm.edu	37	chr9	95772649	95772649	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gctcccgcaggacgccccagAccggaaggatgcggagagtg	16	13	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:95772649A>T	ENST00000375482.3	+	7	1455	c.959A>T	c.(958-960)gAc>gTc	p.D320V	FGD3_ENST00000416701.2_Missense_Mutation_p.D320V|FGD3_ENST00000337352.6_Missense_Mutation_p.D320V	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	320	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						GACGCCCCAGACCGGAAGGAT	0.662																																					p.D320V		Atlas-SNP	.											.	FGD3	116	.	0			c.A959T						.						19	22	21					9																	95772649		1994	4183	6177	SO:0001583	missense	89846	exon7			CCCCAGACCGGAA	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16027	protein-coding gene	gene with protein product			"FGD1 family, member 3"			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.959A>T	chr9.hg19:g.95772649A>T	ENSP00000364631:p.Asp320Val	126.0	0.0		92.0	31.0	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Missense_Mutation	SNP	ENST00000375482.3	hg19	CCDS43849.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.664810	0.47572	.	.	ENSG00000127084	ENST00000375482;ENST00000416701;ENST00000337352	T;T;T	0.41758	0.99;0.99;0.99	4.29	4.29	0.51040	Dbl homology (DH) domain (5);	0.000000	0.40385	N	0.001110	T	0.76807	0.4039	H	0.98525	4.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.997;1.0	D	0.85554	0.1223	10	0.87932	D	0	.	12.9694	0.58503	1.0:0.0:0.0:0.0	.	320;320;320	Q5JSP0-2;F8W7P2;Q5JSP0	.;.;FGD3_HUMAN	V	320	ENSP00000364631:D320V;ENSP00000413833:D320V;ENSP00000336914:D320V	ENSP00000336914:D320V	D	+	2	0	FGD3	94812470	1.000000	0.71417	0.289000	0.24876	0.029000	0.11900	8.835000	0.92100	1.891000	0.54761	0.459000	0.35465	GAC	.	.		0.662	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086		T	95772649	A	T	95772649	3	4	150	1	0	0	0	0	1	0	0	0	5842	275	10	4	977	4	FGD3	9	95772649	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3778410	95772649	45440782	287	23011										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100116932	100116932	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gagaaggaagctgcccggatAgagttggttgaaagtgtcat	15	5	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:100116932A>T	ENST00000357054.1	+	34	4064	c.3129A>T	c.(3127-3129)atA>atT	p.I1043I	RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000375202.2_Silent_p.I1072I|CCDC180_ENST00000529487.1_Silent_p.I1072I			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1043						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CTGCCCGGATAGAGTTGGTTG	0.493																																					p.I1072I		Atlas-SNP	.											.	.	.	.	0			c.A3216T						.						76	76	76					9																	100116932		2203	4300	6503	SO:0001819	synonymous_variant	0	exon23			CCGGATAGAGTTG	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.3129A>T	chr9.hg19:g.100116932A>T		205.0	0.0		173.0	35.0	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	hg19																																																																																				.	.		0.493	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		T	100116932	A	T	100116932	2	4	150	1	0	0	0	0	0	0	0	1	8249	410	15	4		4	KIAA1529	9	100116932	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	4344283	100116932	41096499	288	23012										
ZNF462	58499	hgsc.bcm.edu	37	chr9	109765689	109765689	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acaaggaagaagaaatgaacAgcaaggctgaagacagaggt	13	5	0	6			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:109765689A>T	ENST00000277225.5	+	11	7460	c.7171A>T	c.(7171-7173)Agc>Tgc	p.S2391C	RP11-508N12.2_ENST00000439901.1_RNA|ZNF462_ENST00000441147.2_Missense_Mutation_p.S1297C|ZNF462_ENST00000542028.1_Missense_Mutation_p.S348C|ZNF462_ENST00000457913.1_Missense_Mutation_p.S2451C			Q96JM2	ZN462_HUMAN	zinc finger protein 462	2391					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						AGAAATGAACAGCAAGGCTGA	0.512																																					p.S2391C		Atlas-SNP	.											.	ZNF462	322	.	0			c.A7171T						.						121	98	106					9																	109765689		2203	4300	6503	SO:0001583	missense	58499	exon11			ATGAACAGCAAGG	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.7171A>T	chr9.hg19:g.109765689A>T	ENSP00000277225:p.Ser2391Cys	73.0	0.0		65.0	18.0	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	hg19	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	A	14.63	2.592024	0.46214	.	.	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147;ENST00000542028	T;T;T;T;T	0.15603	3.4;3.87;3.97;3.98;2.41	5.13	3.99	0.46301	.	0.371919	0.28176	N	0.016313	T	0.14227	0.0344	L	0.46157	1.445	0.33130	D	0.54301	P;B	0.39862	0.692;0.0	B;B	0.38712	0.28;0.001	T	0.17745	-1.0359	10	0.38643	T	0.18	.	5.9486	0.19234	0.69:0.221:0.089:0.0	.	2451;2391	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	C	2391;2451;1334;1297;348	ENSP00000277225:S2391C;ENSP00000414570:S2451C;ENSP00000363818:S1334C;ENSP00000397306:S1297C;ENSP00000439771:S348C	ENSP00000277225:S2391C	S	+	1	0	ZNF462	108805510	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.093000	0.41710	0.973000	0.38340	0.383000	0.25322	AGC	.	.		0.512	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		T	109765689	A	T	109765689	3	4	150	1	0	0	0	0	1	0	0	0	17941	188	7	4	7209	4	ZNF462	9	109765689	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	9648757	109765689	31447742	289	23013										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113169638	113169638	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	taagtcagagcctgctagaaTgtgtccaggtttacagctat	10	8	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:113169638T>A	ENST00000401783.2	-	38	8578	c.8242A>T	c.(8242-8244)Att>Ttt	p.I2748F	SVEP1_ENST00000374469.1_Missense_Mutation_p.I2725F|SVEP1_ENST00000297826.5_Missense_Mutation_p.I674F	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2748	Sushi 22. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CCTGCTAGAATGTGTCCAGGT	0.453																																					p.I2748F		Atlas-SNP	.											.	SVEP1	326	.	0			c.A8242T						.						79	82	81					9																	113169638		1989	4159	6148	SO:0001583	missense	79987	exon38			CTAGAATGTGTCC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8242A>T	chr9.hg19:g.113169638T>A	ENSP00000384917:p.Ile2748Phe	107.0	0.0		92.0	15.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	6.503	0.461092	0.12342	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	T;T;T	0.63913	-0.07;-0.07;-0.07	5.87	-9.8	0.00490	Complement control module (2);Sushi/SCR/CCP (3);	1.031550	0.07601	N	0.923634	T	0.46034	0.1372	L	0.36672	1.1	0.09310	N	1	B	0.25904	0.137	B	0.24974	0.057	T	0.43065	-0.9414	10	0.49607	T	0.09	.	11.8495	0.52403	0.0:0.5033:0.1748:0.3219	.	2748	Q4LDE5	SVEP1_HUMAN	F	2748;2725;674;420	ENSP00000384917:I2748F;ENSP00000363593:I2725F;ENSP00000297826:I674F	ENSP00000297826:I674F	I	-	1	0	SVEP1	112209459	0.410000	0.25376	0.001000	0.08648	0.080000	0.17528	-0.165000	0.09968	-1.798000	0.01250	-0.334000	0.08254	ATT	.	.		0.453	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113169638	T	A	113169638	3	1	150	1	0	0	0	0	1	0	0	0	15435	1464	51	4	2517	4	SVEP1	9	113169638	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3403949	113169638	28043793	290	23014										
ZNF618	114991	hgsc.bcm.edu	37	chr9	116798646	116798646	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	caacctgttggagcacatgcAgtcccatgcaggtaagtagg	12	10	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:116798646A>T	ENST00000374126.5	+	13	1334	c.1235A>T	c.(1234-1236)cAg>cTg	p.Q412L	ZNF618_ENST00000288466.7_Missense_Mutation_p.Q319L|ZNF618_ENST00000470105.1_3'UTR			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						GAGCACATGCAGTCCCATGCA	0.572																																					p.Q319L		Atlas-SNP	.											.	ZNF618	184	.	0			c.A956T						.						63	67	66					9																	116798646		1943	4142	6085	SO:0001583	missense	114991	exon12			ACATGCAGTCCCA	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"Zinc fingers, C2H2-type"	29416	protein-coding gene	gene with protein product	"neural precursor cell expressed, developmentally down-regulated 10"					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.1235A>T	chr9.hg19:g.116798646A>T	ENSP00000363241:p.Gln412Leu	117.0	0.0		106.0	24.0	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Missense_Mutation	SNP	ENST00000374126.5	hg19		.	.	.	.	.	.	.	.	.	.	A	19.67	3.870248	0.72065	.	.	ENSG00000157657	ENST00000374126;ENST00000288466	T;T	0.33654	1.4;1.4	4.88	4.88	0.63580	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.60534	0.2276	.	.	.	0.80722	D	1	D;D;B	0.71674	0.969;0.998;0.216	D;D;P	0.85130	0.968;0.997;0.502	T	0.65557	-0.6139	9	0.66056	D	0.02	-21.1973	13.6156	0.62105	1.0:0.0:0.0:0.0	.	379;412;319	B9EG82;Q5T7W0;Q5T7W0-2	.;ZN618_HUMAN;.	L	412;319	ENSP00000363241:Q412L;ENSP00000288466:Q319L	ENSP00000288466:Q319L	Q	+	2	0	ZNF618	115838467	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	8.555000	0.90693	1.962000	0.57031	0.459000	0.35465	CAG	.	.		0.572	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983		T	116798646	A	T	116798646	3	4	150	1	0	0	0	0	1	0	0	0	18057	188	7	4	1002	4	ZNF618	9	116798646	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3629008	116798646	24414785	291	23015										
PTGS1	5742	hgsc.bcm.edu	37	chr9	125148941	125148941	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctacgagcagttcttgttcaAcacctccatgttggtggact	9	11	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:125148941A>T	ENST00000362012.2	+	9	1231	c.1226A>T	c.(1225-1227)aAc>aTc	p.N409I	AL162424.1_ENST00000600713.1_5'Flank|PTGS1_ENST00000540753.1_Intron|PTGS1_ENST00000373698.5_Missense_Mutation_p.N300I|PTGS1_ENST00000223423.4_Intron	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)	409					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|prostaglandin biosynthetic process (GO:0001516)|regulation of blood pressure (GO:0008217)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	dioxygenase activity (GO:0051213)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			large_intestine(3)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	8					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TTCTTGTTCAACACCTCCATG	0.577																																					p.N409I		Atlas-SNP	.											.	PTGS1	84	.	0			c.A1226T						.						140	117	125					9																	125148941		2203	4300	6503	SO:0001583	missense	5742	exon9			TGTTCAACACCTC	M59979	CCDS6842.1, CCDS6843.1, CCDS59520.1, CCDS59521.1, CCDS75895.1	9q32-q33.3	2008-02-05			ENSG00000095303	ENSG00000095303	1.14.99.1		9604	protein-coding gene	gene with protein product		176805				2512924, 1907252	Standard	NM_000962		Approved	COX1, PGHS-1, PTGHS	uc004bmg.2	P23219	OTTHUMG00000020605	ENST00000362012.2:c.1226A>T	chr9.hg19:g.125148941A>T	ENSP00000354612:p.Asn409Ile	111.0	0.0		78.0	18.0	NM_000962	A8K1V7|B4DHQ2|B4E2S5|Q15122|Q3HY28|Q3HY29|Q5T7T6|Q5T7T7|Q5T7T8	Missense_Mutation	SNP	ENST00000362012.2	hg19	CCDS6842.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.681052	0.88542	.	.	ENSG00000095303	ENST00000362012;ENST00000373698	T;T	0.12569	2.67;2.67	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.46756	0.1409	M	0.92738	3.34	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.60042	-0.7340	10	0.87932	D	0	-29.4922	14.2194	0.65815	1.0:0.0:0.0:0.0	.	409	P23219	PGH1_HUMAN	I	409;300	ENSP00000354612:N409I;ENSP00000362802:N300I	ENSP00000354612:N409I	N	+	2	0	PTGS1	124188762	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	1.948000	0.56530	0.533000	0.62120	AAC	.	.		0.577	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1			T	125148941	A	T	125148941	3	4	150	1	0	0	0	0	1	0	0	0	12768	43	2	4	1260	4	PTGS1	9	125148941	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	8350295	125148941	16064490	292	23016										
PKN3	29941	hgsc.bcm.edu	37	chr9	131469505	131469505	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gttgtcccctctgcaggcccAggcccagctacaggagtcct	11	16	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:131469505A>T	ENST00000291906.4	+	6	1049	c.656A>T	c.(655-657)cAg>cTg	p.Q219L	RN7SL560P_ENST00000577943.1_RNA	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	219					epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						CTGCAGGCCCAGGCCCAGCTA	0.637																																					p.Q219L		Atlas-SNP	.											.	PKN3	62	.	0			c.A656T						.						24	26	26					9																	131469505		2203	4300	6503	SO:0001583	missense	29941	exon6			AGGCCCAGGCCCA	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.656A>T	chr9.hg19:g.131469505A>T	ENSP00000291906:p.Gln219Leu	73.0	0.0		55.0	12.0	NM_013355	Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	hg19	CCDS6908.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.144538	0.77888	.	.	ENSG00000160447	ENST00000291906	T	0.20200	2.09	5.37	5.37	0.77165	.	.	.	.	.	T	0.46288	0.1385	M	0.77406	2.37	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.80764	0.994;0.988	T	0.42050	-0.9474	9	0.40728	T	0.16	.	13.3212	0.60434	1.0:0.0:0.0:0.0	.	219;219	Q05BU1;Q6P5Z2	.;PKN3_HUMAN	L	219	ENSP00000291906:Q219L	ENSP00000291906:Q219L	Q	+	2	0	PKN3	130509326	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	8.274000	0.89889	2.033000	0.60031	0.459000	0.35465	CAG	.	.		0.637	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		T	131469505	A	T	131469505	3	4	150	1	0	0	0	0	1	0	0	0	11990	188	7	4	678	4	PKN3	9	131469505	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	6320564	131469505	9743926	293	23017										
C9orf171	389799	hgsc.bcm.edu	37	chr9	135374923	135374923	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tccgcatcagtgaccaggatGaccggcgcatgaagaaagag	13	10	1	5			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:135374923G>A	ENST00000343036.2	+	4	616	c.568G>A	c.(568-570)Gac>Aac	p.D190N	C9orf171_ENST00000393215.3_Missense_Mutation_p.D154N|C9orf171_ENST00000393216.2_Missense_Mutation_p.D154N	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	190										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						TGACCAGGATGACCGGCGCAT	0.602																																					p.D190N		Atlas-SNP	.											.	C9orf171	53	.	0			c.G568A						.						82	83	83					9																	135374923		2203	4300	6503	SO:0001583	missense	389799	exon4			CAGGATGACCGGC	AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.568G>A	chr9.hg19:g.135374923G>A	ENSP00000343290:p.Asp190Asn	180.0	0.0		149.0	38.0	NM_207417	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	hg19	CCDS6949.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910071	0.52439	.	.	ENSG00000188523	ENST00000393215;ENST00000343036;ENST00000393216	T;T;T	0.20463	2.07;2.07;2.07	5.15	3.31	0.37934	.	0.599767	0.17593	N	0.168692	T	0.11324	0.0276	N	0.24115	0.695	0.27478	N	0.952671	B;B	0.27140	0.014;0.169	B;B	0.20955	0.004;0.032	T	0.21280	-1.0250	10	0.27785	T	0.31	.	5.0277	0.14393	0.1778:0.0:0.6558:0.1665	.	154;190	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	N	154;190;154	ENSP00000376908:D154N;ENSP00000343290:D190N;ENSP00000376909:D154N	ENSP00000343290:D190N	D	+	1	0	C9orf171	134364744	0.927000	0.31430	0.860000	0.33809	0.940000	0.58332	2.093000	0.41710	0.672000	0.31204	0.561000	0.74099	GAC	.	.		0.602	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417		A	135374923	G	A	135374923	3	1	150	1	0	0	0	0	1	0	0	0	2472	1290	45	3	582	3	C9orf171	9	135374923	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	3905418	135374923	5838508	294	23018										
BRD3	8019	hgsc.bcm.edu	37	chr9	136905393	136905393	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gctcgtgcacggccttcagcTggaaaagagcgggcggctga	16	11	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:136905393T>A	ENST00000303407.7	-	9	1593		c.e9-2		BRD3_ENST00000473349.1_Intron|BRD3_ENST00000357885.2_Splice_Site|BRD3_ENST00000371834.2_Splice_Site	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3						chromatin modification (GO:0016568)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)		BRD3/C15orf55(3)	kidney(1)|skin(1)|stomach(4)	6				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)		GGCCTTCAGCTGGAAAAGAGC	0.622			T	C15orf55	lethal midline carcinoma of young people																																.		Atlas-SNP	.		Dom	yes		9	9q34	8019	bromodomain containing 3		E	.	BRD3	82	.	0			c.1408-2A>T						.						11	11	11					9																	136905393		2190	4291	6481	SO:0001630	splice_region_variant	8019	exon10			TTCAGCTGGAAAA		CCDS6980.1	9q34	2010-12-23	2002-01-14		ENSG00000169925	ENSG00000169925			1104	protein-coding gene	gene with protein product	"RING3-like"	601541	"bromodomain-containing 3"			7584044, 8781126	Standard	NM_007371		Approved	RING3L, ORFX, KIAA0043	uc004cew.3	Q15059	OTTHUMG00000021004	ENST00000303407.7:c.1408-2A>T	chr9.hg19:g.136905393T>A		19.0	0.0		31.0	5.0	NM_007371	B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645	Splice_Site	SNP	ENST00000303407.7	hg19	CCDS6980.1	.	.	.	.	.	.	.	.	.	.	T	15.97	2.989215	0.53934	.	.	ENSG00000169925	ENST00000303407;ENST00000540795;ENST00000371834;ENST00000357885	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8032	0.63214	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	BRD3	135895214	1.000000	0.71417	0.908000	0.35775	0.520000	0.34377	7.659000	0.83766	1.913000	0.55393	0.459000	0.35465	.	.	.		0.622	BRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055390.4	NM_007371	Intron	A	136905393	T	A	136905393	5	1	150	1	0	0	0	0	0	0	1	0	1505	1594	55	4	790	4	BRD3	9	136905393	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1530470	136905393	4308038	295	23019										
WDR5	11091	hgsc.bcm.edu	37	chr9	137023031	137023031	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcagatgtcgtgatctcaacAgcttgtcacccaacagaaaa	7	11	3	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:137023031A>T	ENST00000358625.3	+	14	1092	c.921A>T	c.(919-921)acA>acT	p.T307T	WDR5_ENST00000425041.1_Silent_p.T307T	NM_017588.2	NP_060058.1	P61964	WDR5_HUMAN	WD repeat domain 5	307					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|histone H3-K4 methylation (GO:0051568)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|positive regulation of gluconeogenesis (GO:0045722)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|histone acetyltransferase complex (GO:0000123)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)				endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123)		Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154)		TGATCTCAACAGCTTGTCACC	0.507																																					p.T307T		Atlas-SNP	.											.	WDR5	29	.	0			c.A921T						.						154	128	137					9																	137023031		2203	4300	6503	SO:0001819	synonymous_variant	11091	exon13			CTCAACAGCTTGT	AJ011376	CCDS6981.1	9q34	2014-09-03			ENSG00000196363	ENSG00000196363		"WD repeat domain containing"	12757	protein-coding gene	gene with protein product	"SWD3, Set1c WD40 repeat protein, homolog (S. cerevisiae)", "cilia and flagella associated protein 89"	609012				11551928	Standard	XM_005272163		Approved	SWD3, CFAP89	uc004cey.3	P61964	OTTHUMG00000131707	ENST00000358625.3:c.921A>T	chr9.hg19:g.137023031A>T		82.0	0.0		62.0	19.0	NM_052821	Q91VA5|Q9NWX7|Q9UGP9	Silent	SNP	ENST00000358625.3	hg19	CCDS6981.1																																																																																			.	.		0.507	WDR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254621.1	NM_052821		T	137023031	A	T	137023031	2	4	150	1	0	0	0	0	0	0	0	1	17318	175	7	4		4	WDR5	9	137023031	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	117638	137023031	4190400	296	23020										
COBRA1	25920	hgsc.bcm.edu	37	chr9	140166672	140166672	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttcttcctcaccgcctctccAaggtaggcctgctgggtacc	9	16	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr9:140166672A>T	ENST00000343053.4	+	11	1822	c.1485A>T	c.(1483-1485)ccA>ccT	p.P495P		NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B	495					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CCGCCTCTCCAAGGTAGGCCT	0.637																																					p.P495P		Atlas-SNP	.											.	.	.	.	0			c.A1485T						.						78	72	74					9																	140166672		2203	4300	6503	SO:0001819	synonymous_variant	25920	exon11			CTCTCCAAGGTAG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"cofactor of BRCA1"	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778	ENST00000343053.4:c.1485A>T	chr9.hg19:g.140166672A>T		55.0	0.0		60.0	21.0	NM_015456	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Silent	SNP	ENST00000343053.4	hg19	CCDS7040.1																																																																																			.	.		0.637	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456		T	140166672	A	T	140166672	2	4	150	1	0	0	0	0	0	0	0	1	3657	117	5	4		4	COBRA1	9	140166672	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3143641	140166672	1046759	297	23021										
MCM10	55388	hgsc.bcm.edu	37	chr10	13214750	13214750	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agagggtggctcgaacaccaAaggcttcacctccaggtgta	12	11	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:13214750A>G	ENST00000484800.2	+	5	683	c.580A>G	c.(580-582)Aag>Gag	p.K194E	MCM10_ENST00000378714.3_Missense_Mutation_p.K193E|MCM10_ENST00000378694.1_Missense_Mutation_p.K193E			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	194					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						TCGAACACCAAAGGCTTCACC	0.498																																					p.K194E		Atlas-SNP	.											.	MCM10	76	.	0			c.A580G						.						91	78	82					10																	13214750		2203	4300	6503	SO:0001583	missense	55388	exon5			ACACCAAAGGCTT	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.580A>G	chr10.hg19:g.13214750A>G	ENSP00000418268:p.Lys194Glu	112.0	0.0		92.0	23.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	hg19	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.820830	0.50633	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.16196	2.36;2.37;2.36	5.23	5.23	0.72850	.	0.165528	0.51477	D	0.000089	T	0.20333	0.0489	M	0.63428	1.95	0.45477	D	0.99844	P;P;P	0.45348	0.856;0.787;0.682	B;B;B	0.41510	0.355;0.359;0.197	T	0.02691	-1.1123	10	0.26408	T	0.33	-13.1271	13.4958	0.61426	1.0:0.0:0.0:0.0	.	193;193;194	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	E	193;194;194;193	ENSP00000367986:K193E;ENSP00000418268:K194E;ENSP00000367966:K193E	ENSP00000354945:K194E	K	+	1	0	MCM10	13254756	0.996000	0.38824	0.052000	0.19188	0.023000	0.10783	3.639000	0.54339	2.197000	0.70478	0.533000	0.62120	AAG	.	.		0.498	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		G	13214750	A	G	13214750	3	3	150	1	0	0	0	0	1	0	0	0	9394	15	1	2	594	2	MCM10	10	13214750	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		13214750	122319997	298	23022										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24722117	24722117	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtctattatgaattaaatgaTgtaaggtaagttgtgacatc	9	3	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:24722117T>C	ENST00000376454.3	+	4	777	c.747T>C	c.(745-747)gaT>gaC	p.D249D	KIAA1217_ENST00000430453.2_Silent_p.D170D|KIAA1217_ENST00000376462.1_Silent_p.D169D|KIAA1217_ENST00000458595.1_Silent_p.D249D|KIAA1217_ENST00000376452.3_Silent_p.D249D	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	249					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AATTAAATGATGTAAGGTAAG	0.358																																					p.D249D		Atlas-SNP	.											.	KIAA1217	235	.	0			c.T747C						.						74	70	71					10																	24722117		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon4			AAATGATGTAAGG	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.747T>C	chr10.hg19:g.24722117T>C		34.0	0.0		38.0	11.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	hg19	CCDS31165.1																																																																																			.	.		0.358	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		C	24722117	T	C	24722117	2	2	150	1	0	0	0	0	0	0	0	1	8225	1461	51	2		2	KIAA1217	10	24722117	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	11507367	24722117	110812630	299	23023										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26385344	26385344	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttcatattttttactacattTatgctggtttggctgaaaag	7	5	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:26385344T>A	ENST00000265944.5	+	16	1763	c.1597T>A	c.(1597-1599)Tat>Aat	p.Y533N	MYO3A_ENST00000543632.1_Missense_Mutation_p.Y533N	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	533	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TTACTACATTTATGCTGGTTT	0.323																																					p.Y533N		Atlas-SNP	.											.	MYO3A	371	.	0			c.T1597A						.						47	51	49					10																	26385344		2200	4297	6497	SO:0001583	missense	53904	exon16			TACATTTATGCTG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1597T>A	chr10.hg19:g.26385344T>A	ENSP00000265944:p.Tyr533Asn	339.0	0.0		373.0	91.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.335813	0.81801	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	D;D	0.87571	-2.27;-2.27	5.13	5.13	0.70059	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.94062	0.8097	M	0.86953	2.85	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.998	D	0.95073	0.8206	10	0.87932	D	0	.	15.2533	0.73564	0.0:0.0:0.0:1.0	.	533;533;533	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	N	533	ENSP00000265944:Y533N;ENSP00000445909:Y533N	ENSP00000265944:Y533N	Y	+	1	0	MYO3A	26425350	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.655000	0.83696	2.069000	0.61940	0.533000	0.62120	TAT	.	.		0.323	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26385344	T	A	26385344	3	1	150	1	0	0	0	0	1	0	0	0	10085	1754	61	4	1651	4	MYO3A	10	26385344	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1663227	26385344	109149403	300	23024										
GAD2	2572	hgsc.bcm.edu	37	chr10	26518688	26518688	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gctgctcttcccaggctcatTgccttcacgtctgaacatgt	8	14	4	1	rs375159804		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:26518688T>C	ENST00000376261.3	+	7	1325	c.822T>C	c.(820-822)atT>atC	p.I274I	GAD2_ENST00000259271.3_Silent_p.I274I	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	274					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CCAGGCTCATTGCCTTCACGT	0.438																																					p.I274I		Atlas-SNP	.											.	GAD2	116	.	0			c.T822C						.						227	181	197					10																	26518688		2203	4300	6503	SO:0001819	synonymous_variant	2572	exon7			GCTCATTGCCTTC	AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.822T>C	chr10.hg19:g.26518688T>C		76.0	0.0		52.0	8.0	NM_000818	Q9UD87	Silent	SNP	ENST00000376261.3	hg19	CCDS7149.1																																																																																			.	.		0.438	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818		C	26518688	T	C	26518688	2	2	150	1	0	0	0	0	0	0	0	1	6188	1800	63	2		2	GAD2	10	26518688	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	133344	26518688	109016059	301	23025										
GDF10	2662	hgsc.bcm.edu	37	chr10	48429198	48429198	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccggggcacccccgggtcccTctcctcagaatccagctggg	12	18	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:48429198T>A	ENST00000224605.2	-	2	953	c.688A>T	c.(688-690)Agg>Tgg	p.R230W		NM_004962.3	NP_004953.1	P55107	BMP3B_HUMAN	growth differentiation factor 10	230					fat cell differentiation (GO:0045444)|growth (GO:0040007)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(20)|skin(1)	31						CCCGGGTCCCTCTCCTCAGAA	0.682																																					p.R230W		Atlas-SNP	.											.	GDF10	79	.	0			c.A688T						.						10	15	13					10																	48429198		2171	4282	6453	SO:0001583	missense	2662	exon2			GGTCCCTCTCCTC	L42113	CCDS73117.1	10q11.22	2014-04-10			ENSG00000107623	ENSG00000266524		"Endogenous ligands"	4215	protein-coding gene	gene with protein product		601361				8679252	Standard	NM_004962		Approved	BMP-3b	uc001jfb.3	P55107	OTTHUMG00000188319	ENST00000224605.2:c.688A>T	chr10.hg19:g.48429198T>A	ENSP00000224605:p.Arg230Trp	92.0	0.0		87.0	22.0	NM_004962	Q5VSQ8|Q9UCX6	Missense_Mutation	SNP	ENST00000224605.2	hg19	CCDS7220.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.386047	0.42308	.	.	ENSG00000107623	ENST00000374247;ENST00000224605	T	0.76060	-0.99	5.44	0.276	0.15663	.	0.382872	0.30011	N	0.010634	T	0.68393	0.2996	N	0.19112	0.55	0.23120	N	0.998261	P;D	0.58620	0.89;0.983	P;P	0.61722	0.476;0.893	T	0.60005	-0.7347	10	0.52906	T	0.07	.	6.0154	0.19601	0.0:0.2071:0.1262:0.6667	.	40;230	Q8N6T2;P55107	.;BMP3B_HUMAN	W	40;230	ENSP00000224605:R230W	ENSP00000224605:R230W	R	-	1	2	GDF10	48049204	0.021000	0.18746	0.050000	0.19076	0.061000	0.15899	0.223000	0.17719	-0.188000	0.10499	-0.501000	0.04562	AGG	.	.		0.682	GDF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047884.1	NM_004962		A	48429198	T	A	48429198	3	1	150	1	0	0	0	0	1	0	0	0	6319	1550	54	4	756	4	GDF10	10	48429198	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	21910510	48429198	87105549	302	23026										
C10orf71	118461	hgsc.bcm.edu	37	chr10	50531471	50531471	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gctggagagaaaggacacagCtggaaccgtcccagaaagca	13	10	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:50531471C>A	ENST00000374144.3	+	3	1169	c.881C>A	c.(880-882)gCt>gAt	p.A294D	C10orf71_ENST00000323868.4_Missense_Mutation_p.A294D			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	294										endometrium(1)	1						AAGGACACAGCTGGAACCGTC	0.542																																					p.A294D		Atlas-SNP	.											.	C10orf71	179	.	0			c.C881A						.						69	81	77					10																	50531471		2031	4190	6221	SO:0001583	missense	118461	exon3			ACACAGCTGGAAC	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.881C>A	chr10.hg19:g.50531471C>A	ENSP00000363259:p.Ala294Asp	135.0	0.0		103.0	31.0	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	hg19	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	C	7.397	0.632030	0.14322	.	.	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.15017	2.46;3.6	5.4	3.31	0.37934	.	0.783434	0.11097	N	0.600073	T	0.12518	0.0304	L	0.33485	1.01	0.09310	N	1	B	0.17667	0.023	B	0.17433	0.018	T	0.24657	-1.0154	10	0.30854	T	0.27	.	6.1116	0.20104	0.1483:0.6378:0.1283:0.0856	.	294	Q711Q0-3	.	D	294	ENSP00000318713:A294D;ENSP00000363259:A294D	ENSP00000318713:A294D	A	+	2	0	C10orf71	50201477	0.026000	0.19158	0.002000	0.10522	0.005000	0.04900	2.679000	0.46909	1.259000	0.44117	0.561000	0.74099	GCT	.	.		0.542	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		A	50531471	C	A	50531471	3	1	150	1	0	0	0	0	1	0	0	0	1616	797	28	3	883	3	C10orf71	10	50531471	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	2102273	50531471	85003276	303	23027										
TMEM26	219623	hgsc.bcm.edu	37	chr10	63212811	63212811	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggaacagcaaccgagtggccAgggcgttaaggaagaccagt	15	9	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:63212811A>G	ENST00000399298.3	-	1	397	c.29T>C	c.(28-30)cTg>cCg	p.L10P	TMEM26_ENST00000399293.1_Missense_Mutation_p.L10P|RP11-809M12.1_ENST00000389640.4_RNA	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	10						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					CCGAGTGGCCAGGGCGTTAAG	0.677																																					p.L10P		Atlas-SNP	.											.	TMEM26	47	.	0			c.T29C						.						59	70	66					10																	63212811		2105	4229	6334	SO:0001583	missense	219623	exon1			GTGGCCAGGGCGT	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.29T>C	chr10.hg19:g.63212811A>G	ENSP00000382237:p.Leu10Pro	97.0	0.0		88.0	26.0	NM_178505	Q6ZVM0|Q8IVN9	Missense_Mutation	SNP	ENST00000399298.3	hg19	CCDS41530.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.808152	0.50421	.	.	ENSG00000196932	ENST00000399298;ENST00000399293	.	.	.	5.23	4.07	0.47477	.	0.256767	0.32802	N	0.005625	T	0.76271	0.3964	M	0.71036	2.16	0.58432	D	0.999999	D	0.89917	1.0	D	0.76071	0.987	T	0.78219	-0.2289	9	0.87932	D	0	-29.0541	12.1911	0.54273	0.8571:0.1429:0.0:0.0	.	10	Q6ZUK4	TMM26_HUMAN	P	10	.	ENSP00000382232:L10P	L	-	2	0	TMEM26	62882817	1.000000	0.71417	1.000000	0.80357	0.149000	0.21700	5.779000	0.68948	0.973000	0.38340	0.533000	0.62120	CTG	.	.		0.677	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505		G	63212811	A	G	63212811	3	3	150	1	0	0	0	0	1	0	0	0	16166	188	7	2	1101	2	TMEM26	10	63212811	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	12681340	63212811	72321936	304	23028										
GRID1	2894	hgsc.bcm.edu	37	chr10	87379775	87379775	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cacatcccacaggaaggcgtAgttccccttctttgcctgaa	8	14	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:87379775A>C	ENST00000327946.7	-	14	2294	c.2209T>G	c.(2209-2211)Tac>Gac	p.Y737D	GRID1_ENST00000536331.1_Missense_Mutation_p.Y308D	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	737					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						AGGAAGGCGTAGTTCCCCTTC	0.532										Multiple Myeloma(13;0.14)																											p.Y737D		Atlas-SNP	.											.	GRID1	204	.	0			c.T2209G						.						109	79	89					10																	87379775		2203	4300	6503	SO:0001583	missense	2894	exon14			AGGCGTAGTTCCC	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.2209T>G	chr10.hg19:g.87379775A>C	ENSP00000330148:p.Tyr737Asp	153.0	0.0		71.0	26.0	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	hg19	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.395647	0.83011	.	.	ENSG00000182771	ENST00000327946;ENST00000536331	T;T	0.27557	1.66;1.66	5.28	5.28	0.74379	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.56992	0.2023	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.62746	-0.6789	10	0.87932	D	0	.	14.3972	0.67020	1.0:0.0:0.0:0.0	.	737	Q9ULK0	GRID1_HUMAN	D	737;308	ENSP00000330148:Y737D;ENSP00000444455:Y308D	ENSP00000330148:Y737D	Y	-	1	0	GRID1	87369755	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.297000	0.96120	1.987000	0.57996	0.459000	0.35465	TAC	.	.		0.532	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		C	87379775	A	C	87379775	3	2	150	1	0	0	0	0	1	0	0	0	6780	420	15	5	832	5	GRID1	10	87379775	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	24166964	87379775	48154972	305	23029										
ANKRD1	27063	hgsc.bcm.edu	37	chr10	92678913	92678913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tttcaggttctggttcctttAcaactggaactttagttttc	7	8	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:92678913A>G	ENST00000371697.3	-	3	568	c.320T>C	c.(319-321)gTa>gCa	p.V107A		NM_014391.2	NP_055206.2	Q15327	ANKR1_HUMAN	ankyrin repeat domain 1 (cardiac muscle)	107					cardiac muscle tissue morphogenesis (GO:0055008)|cellular lipid metabolic process (GO:0044255)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|skeletal muscle cell differentiation (GO:0035914)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I band (GO:0031674)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|p53 binding (GO:0002039)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|titin binding (GO:0031432)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|prostate(3)|skin(1)	27		Colorectal(252;0.0475)				TGGTTCCTTTACAACTGGAAC	0.353																																					p.V107A		Atlas-SNP	.											.	ANKRD1	50	.	0			c.T320C						.						103	101	102					10																	92678913		2203	4300	6503	SO:0001583	missense	27063	exon3			TCCTTTACAACTG	X83703	CCDS7412.1	10q23.33	2014-09-17			ENSG00000148677	ENSG00000148677		"Ankyrin repeat domain containing"	15819	protein-coding gene	gene with protein product		609599				7730328	Standard	NM_014391		Approved	C-193, ALRP, CARP, CVARP, MCARP	uc001khe.1	Q15327	OTTHUMG00000018734	ENST00000371697.3:c.320T>C	chr10.hg19:g.92678913A>G	ENSP00000360762:p.Val107Ala	64.0	0.0		60.0	20.0	NM_014391	Q96LE7	Missense_Mutation	SNP	ENST00000371697.3	hg19	CCDS7412.1	.	.	.	.	.	.	.	.	.	.	A	0.061	-1.224621	0.01530	.	.	ENSG00000148677	ENST00000371697	T	0.66280	-0.2	5.49	0.366	0.16136	.	0.541157	0.18123	N	0.150986	T	0.32615	0.0835	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25363	-1.0134	10	0.02654	T	1	.	5.1086	0.14796	0.6616:0.0:0.2165:0.1219	.	107	Q15327	ANKR1_HUMAN	A	107	ENSP00000360762:V107A	ENSP00000360762:V107A	V	-	2	0	ANKRD1	92668893	0.219000	0.23619	0.004000	0.12327	0.086000	0.17979	2.191000	0.42640	-0.114000	0.11936	-0.274000	0.10170	GTA	.	.		0.353	ANKRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049357.1	NM_014391		G	92678913	A	G	92678913	3	3	150	1	0	0	0	0	1	0	0	0	637	391	14	2	667	2	ANKRD1	10	92678913	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5299138	92678913	42855834	306	23030										
MYOF	26509	hgsc.bcm.edu	37	chr10	95072901	95072901	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctttgaggtccggaatcatgTccaatctgcatttctctggt	9	10	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:95072901T>A	ENST00000359263.4	-	51	5764	c.5765A>T	c.(5764-5766)gAc>gTc	p.D1922V	MYOF_ENST00000358334.5_Missense_Mutation_p.D1909V|MYOF_ENST00000371502.4_Missense_Mutation_p.D1912V|MYOF_ENST00000371501.4_Missense_Mutation_p.D1922V	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1922					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						CGGAATCATGTCCAATCTGCA	0.483																																					p.D1922V		Atlas-SNP	.											.	MYOF	177	.	0			c.A5765T						.						229	222	224					10																	95072901		1985	4171	6156	SO:0001583	missense	26509	exon51			ATCATGTCCAATC	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.5765A>T	chr10.hg19:g.95072901T>A	ENSP00000352208:p.Asp1922Val	100.0	0.0		75.0	20.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.644831	0.67358	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.7	5.42	5.42	0.78866	C2 calcium/lipid-binding domain, CaLB (1);	0.485741	0.26638	N	0.023273	D	0.84710	0.5532	M	0.73962	2.25	0.58432	D	0.999999	B;B	0.19331	0.035;0.023	B;B	0.30716	0.119;0.031	T	0.83050	-0.0153	10	0.62326	D	0.03	-18.6733	15.621	0.76805	0.0:0.0:0.0:1.0	.	1909;1922	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	V	1909;1922;1922;1912	ENSP00000351094:D1909V;ENSP00000352208:D1922V;ENSP00000360556:D1922V;ENSP00000360557:D1912V	ENSP00000351094:D1909V	D	-	2	0	MYOF	95062891	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	4.957000	0.63652	2.270000	0.75569	0.523000	0.50628	GAC	.	.		0.483	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		A	95072901	T	A	95072901	3	1	150	1	0	0	0	0	1	0	0	0	10098	1667	58	4	436	4	MYOF	10	95072901	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2393988	95072901	40461846	307	23031										
PIK3AP1	118788	hgsc.bcm.edu	37	chr10	98369550	98369550	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatgacacttttcctggggcCactctcatagactccaaact	6	13	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:98369550C>A	ENST00000339364.5	-	14	2208	c.2089G>T	c.(2089-2091)Ggc>Tgc	p.G697C	PIK3AP1_ENST00000371109.3_Missense_Mutation_p.G296C|PIK3AP1_ENST00000371110.2_Missense_Mutation_p.G519C	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	697					negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		TTCCTGGGGCCACTCTCATAG	0.552																																					p.G697C		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.G2089T						.						225	232	230					10																	98369550		2203	4300	6503	SO:0001583	missense	118788	exon14			TGGGGCCACTCTC	AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.2089G>T	chr10.hg19:g.98369550C>A	ENSP00000339826:p.Gly697Cys	137.0	0.0		103.0	54.0	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Missense_Mutation	SNP	ENST00000339364.5	hg19	CCDS31259.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.350716	0.82132	.	.	ENSG00000155629	ENST00000339364;ENST00000371110;ENST00000371109	T;T;T	0.47528	0.84;0.84;0.84	5.69	5.69	0.88448	.	0.317119	0.34507	N	0.003916	T	0.59824	0.2222	L	0.47716	1.5	0.44825	D	0.997837	D;D	0.71674	0.988;0.998	P;P	0.61592	0.73;0.891	T	0.55661	-0.8106	10	0.44086	T	0.13	-25.2151	16.8983	0.86106	0.0:1.0:0.0:0.0	.	697;296	Q6ZUJ8;Q6ZUJ8-3	BCAP_HUMAN;.	C	697;519;296	ENSP00000339826:G697C;ENSP00000360151:G519C;ENSP00000360150:G296C	ENSP00000339826:G697C	G	-	1	0	PIK3AP1	98359540	0.870000	0.30015	0.994000	0.49952	0.960000	0.62799	1.361000	0.34136	2.840000	0.97914	0.655000	0.94253	GGC	.	.		0.552	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309		A	98369550	C	A	98369550	3	1	150	1	0	0	0	0	1	0	0	0	11917	594	21	3	344	3	PIK3AP1	10	98369550	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	3296649	98369550	37165197	308	23032										
ARHGAP19	84986	hgsc.bcm.edu	37	chr10	99025682	99025682	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggccagccccgccaggcaacTtaaggtccacttcccccatc	8	19	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:99025682T>A	ENST00000358531.4	-	2	285	c.257A>T	c.(256-258)aAg>aTg	p.K86M	ARHGAP19_ENST00000355366.5_Missense_Mutation_p.K77M|ARHGAP19-SLIT1_ENST00000316676.8_Missense_Mutation_p.K86M|ARHGAP19-SLIT1_ENST00000358308.3_Missense_Mutation_p.K86M|ARHGAP19-SLIT1_ENST00000453547.2_Missense_Mutation_p.K86M|ARHGAP19_ENST00000371027.1_Missense_Mutation_p.K77M	NM_001204300.1|NM_032900.5	NP_001191229.1|NP_116289.4	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	86					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|urinary_tract(1)	13		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		GCCAGGCAACTTAAGGTCCAC	0.527																																					p.K86M		Atlas-SNP	.											.	ARHGAP19	72	.	0			c.A257T						.						86	81	83					10																	99025682		2203	4300	6503	SO:0001583	missense	84986	exon2			GGCAACTTAAGGT	AK074122	CCDS7454.2, CCDS58092.1, CCDS73175.1	10q24.2	2011-06-29			ENSG00000213390	ENSG00000213390		"Rho GTPase activating proteins"	23724	protein-coding gene	gene with protein product		611587					Standard	NM_032900		Approved	FLJ00194, MGC14258	uc001knb.3	Q14CB8	OTTHUMG00000018845	ENST00000358531.4:c.257A>T	chr10.hg19:g.99025682T>A	ENSP00000351333:p.Lys86Met	132.0	0.0		112.0	38.0	NM_001204300	A1XCP1|B4DZR1|Q14CF2|Q5J8M2|Q5T460|Q5T462|Q68DG6|Q8N9X1|Q8NF34|Q8TEK1	Missense_Mutation	SNP	ENST00000358531.4	hg19	CCDS7454.2	.	.	.	.	.	.	.	.	.	.	T	21.7	4.195050	0.78902	.	.	ENSG00000213390	ENST00000453547;ENST00000316676;ENST00000355366;ENST00000358531;ENST00000371027;ENST00000358308	T;T;T;T;T;T	0.12465	2.68;2.71;2.72;2.71;2.72;2.68	5.94	4.78	0.61160	.	0.000000	0.85682	U	0.000000	T	0.24353	0.0590	L	0.29908	0.895	0.41772	D	0.989775	D;D;D	0.76494	0.999;0.999;0.999	D;P;D	0.68039	0.955;0.906;0.946	T	0.01617	-1.1311	10	0.87932	D	0	-15.8445	13.1382	0.59421	0.0:0.0:0.1336:0.8664	.	86;86;77	Q14CB8-6;Q14CB8;Q14CB8-3	.;RHG19_HUMAN;.	M	86;86;77;86;77;86	ENSP00000414774:K86M;ENSP00000324468:K86M;ENSP00000347526:K77M;ENSP00000351333:K86M;ENSP00000360066:K77M;ENSP00000351058:K86M	ENSP00000324468:K86M	K	-	2	0	ARHGAP19	99015672	1.000000	0.71417	0.997000	0.53966	0.910000	0.53928	3.469000	0.53093	1.021000	0.39600	0.455000	0.32223	AAG	.	.		0.527	ARHGAP19-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049647.2	NM_032900		A	99025682	T	A	99025682	3	1	150	1	0	0	0	0	1	0	0	0	869	1609	56	4	1271	4	ARHGAP19	10	99025682	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	656132	99025682	36509065	309	23033										
LDB1	8861	hgsc.bcm.edu	37	chr10	103870894	103870894	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agtttggttgccatatggtgTgtgcctcctggaggaagtga	15	6	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:103870894T>A	ENST00000425280.1	-	4	523	c.181A>T	c.(181-183)Aca>Tca	p.T61S	LDB1_ENST00000361198.5_Missense_Mutation_p.T25S|LDB1_ENST00000490751.1_5'UTR	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	61					anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		CCATATGGTGTGTGCCTCCTG	0.557																																					p.T61S		Atlas-SNP	.											.	LDB1	61	.	0			c.A181T						.						144	144	144					10																	103870894		2203	4300	6503	SO:0001583	missense	8861	exon4			ATGGTGTGTGCCT	AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"carboxy terminal LIM domain protein 2"	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.181A>T	chr10.hg19:g.103870894T>A	ENSP00000392466:p.Thr61Ser	53.0	0.0		49.0	14.0	NM_001113407	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Missense_Mutation	SNP	ENST00000425280.1	hg19	CCDS44472.1	.	.	.	.	.	.	.	.	.	.	T	18.22	3.576407	0.65878	.	.	ENSG00000198728	ENST00000361198;ENST00000425280	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.67429	0.2892	L	0.54323	1.7	0.58432	D	0.999999	P;B	0.52842	0.956;0.03	P;B	0.62184	0.899;0.03	T	0.62167	-0.6911	9	0.13108	T	0.6	-13.3938	15.6898	0.77442	0.0:0.0:0.0:1.0	.	61;25	Q86U70;Q86U70-3	LDB1_HUMAN;.	S	25;61	.	ENSP00000354616:T25S	T	-	1	0	LDB1	103860884	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.771000	0.68881	2.199000	0.70637	0.459000	0.35465	ACA	.	.		0.557	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407		A	103870894	T	A	103870894	3	1	150	1	0	0	0	0	1	0	0	0	8704	1696	59	4	1086	4	LDB1	10	103870894	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4845212	103870894	31663853	310	23034										
CALHM1	255022	hgsc.bcm.edu	37	chr10	105215321	105215321	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggcctcgaagaactgctggaTgcagaccttggcaaaggctt	13	10	0	2	rs536458604	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:105215321T>A	ENST00000329905.5	-	2	875	c.739A>T	c.(739-741)Atc>Ttc	p.I247F	RP11-225H22.4_ENST00000411906.1_RNA|CALHM2_ENST00000393235.1_5'Flank	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	247					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						AACTGCTGGATGCAGACCTTG	0.612																																					p.I247F		Atlas-SNP	.											.	CALHM1	33	.	0			c.A739T						.						88	68	75					10																	105215321		2203	4300	6503	SO:0001583	missense	255022	exon2			GCTGGATGCAGAC	BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"family with sequence similarity 26, member C"	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.739A>T	chr10.hg19:g.105215321T>A	ENSP00000329926:p.Ile247Phe	96.0	0.0		83.0	17.0	NM_001001412	Q5W091	Missense_Mutation	SNP	ENST00000329905.5	hg19	CCDS7550.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.039512	0.93630	.	.	ENSG00000185933	ENST00000329905	T	0.24723	1.84	5.26	5.26	0.73747	.	0.104705	0.64402	D	0.000004	T	0.50888	0.1642	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.54768	-0.8244	10	0.72032	D	0.01	-41.1511	15.161	0.72785	0.0:0.0:0.0:1.0	.	247	Q8IU99	CAHM1_HUMAN	F	247	ENSP00000329926:I247F	ENSP00000329926:I247F	I	-	1	0	CALHM1	105205311	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	5.830000	0.69324	1.989000	0.58080	0.379000	0.24179	ATC	.	.		0.612	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412		A	105215321	T	A	105215321	3	1	150	1	0	0	0	0	1	0	0	0	2584	1464	51	4	305	4	CALHM1	10	105215321	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1344427	105215321	30319426	311	23035										
ADD3	120	hgsc.bcm.edu	37	chr10	111879082	111879082	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gaacaggaggagagaattcaActgcagaaggttctgggacc	14	7	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:111879082A>T	ENST00000356080.4	+	7	1198	c.831A>T	c.(829-831)caA>caT	p.Q277H	ADD3_ENST00000277900.8_Missense_Mutation_p.Q277H|ADD3_ENST00000360162.3_Missense_Mutation_p.Q277H	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	277						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		AGAGAATTCAACTGCAGAAGG	0.423																																					p.Q277H		Atlas-SNP	.											.	ADD3	89	.	0			c.A831T						.						94	95	94					10																	111879082		2203	4300	6503	SO:0001583	missense	120	exon7			AATTCAACTGCAG	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.831A>T	chr10.hg19:g.111879082A>T	ENSP00000348381:p.Gln277His	171.0	0.0		154.0	42.0	NM_001121	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Missense_Mutation	SNP	ENST00000356080.4	hg19	CCDS7561.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.638071	0.47153	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	T;T;T	0.22336	1.96;1.96;1.96	6.17	-0.229	0.13094	Class II aldolase/adducin, N-terminal (3);	0.095691	0.64402	D	0.000001	T	0.19248	0.0462	N	0.16656	0.425	0.37856	D	0.929568	B;P	0.35982	0.431;0.531	P;B	0.46419	0.516;0.382	T	0.11717	-1.0576	10	0.59425	D	0.04	-8.7629	13.5282	0.61607	0.6468:0.0:0.3532:0.0	.	277;277	Q9UEY8;Q9UEY8-2	ADDG_HUMAN;.	H	277	ENSP00000353286:Q277H;ENSP00000348381:Q277H;ENSP00000277900:Q277H	ENSP00000277900:Q277H	Q	+	3	2	ADD3	111869072	1.000000	0.71417	0.993000	0.49108	0.962000	0.63368	1.199000	0.32235	-0.253000	0.09514	-1.139000	0.01908	CAA	.	.		0.423	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903		T	111879082	A	T	111879082	3	4	150	1	0	0	0	0	1	0	0	0	306	40	2	4	853	4	ADD3	10	111879082	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	6663761	111879082	23655665	312	23036										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117059542	117059542	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccccttttcctgttgtttacAgaaagtatcaccttgggtag	8	10	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:117059542A>G	ENST00000355044.3	+	16	2541		c.e16-1		ATRNL1_ENST00000423111.2_5'Flank|ATRNL1_ENST00000303745.7_5'Flank	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1						G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TGTTGTTTACAGAAAGTATCA	0.353																																					.		Atlas-SNP	.											.	ATRNL1	219	.	0			c.2416-2A>G						.						86	83	84					10																	117059542		2203	4300	6503	SO:0001630	splice_region_variant	26033	exon16			GTTTACAGAAAGT	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2416-1A>G	chr10.hg19:g.117059542A>G		83.0	0.0		68.0	15.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Splice_Site	SNP	ENST00000355044.3	hg19	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.625411	0.66901	.	.	ENSG00000107518	ENST00000355044	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3786	0.83431	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATRNL1	117049532	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.256000	0.78350	2.323000	0.78572	0.528000	0.53228	.	.	.		0.353	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	Intron	G	117059542	A	G	117059542	5	3	150	1	0	0	0	0	0	0	1	0	1207	202	7	2	2476	2	ATRNL1	10	117059542	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5180460	117059542	18475205	313	23037										
TACC2	10579	hgsc.bcm.edu	37	chr10	123970404	123970404	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccagtgaaggagacgcaacAggagccagatgaagagagcc	14	10	0	5			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:123970404A>T	ENST00000369005.1	+	9	6804	c.6464A>T	c.(6463-6465)cAg>cTg	p.Q2155L	TACC2_ENST00000369001.1_De_novo_Start_OutOfFrame|TACC2_ENST00000358010.1_Missense_Mutation_p.Q301L|TACC2_ENST00000360561.3_Missense_Mutation_p.Q233L|TACC2_ENST00000515273.1_Missense_Mutation_p.Q2159L|TACC2_ENST00000453444.2_Missense_Mutation_p.Q2159L|TACC2_ENST00000369000.1_De_novo_Start_OutOfFrame|TACC2_ENST00000260733.3_Missense_Mutation_p.Q233L|TACC2_ENST00000369004.3_Missense_Mutation_p.Q233L|TACC2_ENST00000515603.1_Missense_Mutation_p.Q2110L|TACC2_ENST00000334433.3_Missense_Mutation_p.Q2155L|TACC2_ENST00000368999.1_Missense_Mutation_p.Q233L|TACC2_ENST00000513429.1_Missense_Mutation_p.Q301L	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2155					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GAGACGCAACAGGAGCCAGAT	0.517																																					p.Q2155L		Atlas-SNP	.											.	TACC2	271	.	0			c.A6464T						.						102	115	111					10																	123970404		2203	4300	6503	SO:0001583	missense	10579	exon9			CGCAACAGGAGCC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.6464A>T	chr10.hg19:g.123970404A>T	ENSP00000358001:p.Gln2155Leu	65.0	0.0		42.0	8.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	hg19	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	A	0.105	-1.146426	0.01714	.	.	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000514539	T;T;T;T;T;T;T;T;T;T;T;T	0.08896	3.98;3.56;4.01;4.0;3.98;3.56;4.01;3.44;3.4;3.4;3.45;3.04	5.54	-0.0152	0.13977	.	0.247890	0.21274	N	0.077276	T	0.11452	0.0279	M	0.63428	1.95	0.09310	N	1	P;B;B;B;B;P;B;P;B	0.40834	0.73;0.258;0.258;0.258;0.258;0.515;0.374;0.604;0.258	B;B;B;B;B;B;B;B;B	0.39531	0.302;0.103;0.103;0.196;0.103;0.135;0.208;0.208;0.196	T	0.15752	-1.0426	10	0.31617	T	0.26	-0.4321	17.5354	0.87829	0.2934:0.7065:0.0:0.0	.	250;2159;233;2110;2159;233;233;301;2155	E9PGB3;E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	L	2155;301;2159;2110;2155;301;2159;2145;233;233;233;233;250	ENSP00000358001:Q2155L;ENSP00000425062:Q301L;ENSP00000424467:Q2159L;ENSP00000427618:Q2110L;ENSP00000334280:Q2155L;ENSP00000350701:Q301L;ENSP00000395048:Q2159L;ENSP00000353763:Q233L;ENSP00000357995:Q233L;ENSP00000422815:Q233L;ENSP00000260733:Q233L;ENSP00000420967:Q250L	ENSP00000260733:Q233L	Q	+	2	0	TACC2	123960394	0.142000	0.22610	0.008000	0.14137	0.137000	0.21094	0.450000	0.21762	0.039000	0.15632	0.533000	0.62120	CAG	.	.		0.517	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123970404	A	T	123970404	3	4	150	1	0	0	0	0	1	0	0	0	15517	188	7	4	6566	4	TACC2	10	123970404	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	6910862	123970404	11564343	314	23038										
FAM24A	118670	hgsc.bcm.edu	37	chr10	124672386	124672386	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	accatggagtcttgtccatcTctccagtgctgtgaaggttg	11	10	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:124672386T>A	ENST00000368894.1	+	3	355	c.234T>A	c.(232-234)tcT>tcA	p.S78S		NM_001029888.1	NP_001025059.1	A6NFZ4	FA24A_HUMAN	family with sequence similarity 24, member A	78						extracellular region (GO:0005576)				large_intestine(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	9		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.124)|COAD - Colon adenocarcinoma(40;0.141)		CTTGTCCATCTCTCCAGTGCT	0.527																																					p.S78S		Atlas-SNP	.											.	FAM24A	16	.	0			c.T234A						.						173	124	141					10																	124672386		2203	4300	6503	SO:0001819	synonymous_variant	118670	exon3			TCCATCTCTCCAG		CCDS31304.1	10q26.13	2008-08-27			ENSG00000203795	ENSG00000203795			23470	protein-coding gene	gene with protein product							Standard	NM_001029888		Approved	AC073585.4	uc001lgv.3	A6NFZ4	OTTHUMG00000019193	ENST00000368894.1:c.234T>A	chr10.hg19:g.124672386T>A		127.0	0.0		116.0	40.0	NM_001029888		Silent	SNP	ENST00000368894.1	hg19	CCDS31304.1																																																																																			.	.		0.527	FAM24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050824.1	XM_058332		A	124672386	T	A	124672386	2	1	150	1	0	0	0	0	0	0	0	1	5552	1538	54	4		4	FAM24A	10	124672386	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	701982	124672386	10862361	315	23039										
VENTX	27287	hgsc.bcm.edu	37	chr10	135053795	135053795	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctgtgtgctatgccacagacGggggatgcattttgaggagg	16	7	0	2	rs376398632|rs528996055		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr10:135053795G>A	ENST00000325980.9	+	3	1273	c.762G>A	c.(760-762)acG>acA	p.T254T		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	254					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(1)	14		all_cancers(35;4.15e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)|all cancers(32;1.19e-05)		TGCCACAGACGGGGGATGCAT	0.657																																					p.T254T		Atlas-SNP	.											VENTX,right_upper_lobe,carcinoma,0,1	VENTX	24	.	0			c.G762A						.						16	18	17					10																	135053795		2026	4029	6055	SO:0001819	synonymous_variant	27287	exon3			ACAGACGGGGGAT	AF068006	CCDS7675.1	10q26.3	2011-06-20	2011-06-01	2005-09-27	ENSG00000151650	ENSG00000151650		"Homeoboxes / ANTP class : NKL subclass"	13639	protein-coding gene	gene with protein product		607158	"VENT-like homeobox 2", "VENT homeobox homolog (Xenopus laevis)"	VENTX2		10790436	Standard	NM_014468		Approved	HPX42B	uc010quy.1	O95231	OTTHUMG00000019307	ENST00000325980.9:c.762G>A	chr10.hg19:g.135053795G>A		50.0	0.0		52.0	17.0	NM_014468	Q32MZ3	Silent	SNP	ENST00000325980.9	hg19	CCDS7675.1																																																																																			.	.		0.657	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468		A	135053795	G	A	135053795	2	1	150	1	0	0	0	0	0	0	0	1	17168	1103	39	1		1	VENTX	10	135053795	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	10381409	135053795	480952	316	23040										
PKP3	11187	hgsc.bcm.edu	37	chr11	399156	399156	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atcttcgagctgctgcggacActgcgggagcaggatgatga	15	9	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:399156A>G	ENST00000331563.2	+	5	1309	c.1233A>G	c.(1231-1233)acA>acG	p.T411T		NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	411					desmosome assembly (GO:0002159)|establishment of protein localization to plasma membrane (GO:0090002)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|desmosome (GO:0030057)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)			breast(1)|central_nervous_system(1)|endometrium(3)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGCTGCGGACACTGCGGGAGC	0.612																																					p.T411T		Atlas-SNP	.											.	PKP3	36	.	0			c.A1233G						.						123	104	110					11																	399156		2187	4290	6477	SO:0001819	synonymous_variant	11187	exon5			GCGGACACTGCGG	Z98265	CCDS7695.1	11p15	2013-02-14			ENSG00000184363	ENSG00000184363		"Armadillo repeat containing"	9025	protein-coding gene	gene with protein product		605561				10374265	Standard	XM_005252760		Approved		uc001lpc.3	Q9Y446	OTTHUMG00000119068	ENST00000331563.2:c.1233A>G	chr11.hg19:g.399156A>G		106.0	0.0		74.0	18.0	NM_007183	F8J390|Q53EX8	Silent	SNP	ENST00000331563.2	hg19	CCDS7695.1																																																																																			.	.		0.612	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183		G	399156	A	G	399156	2	3	150	1	0	0	0	0	0	0	0	1	11995	146	6	2		2	PKP3	11	399156	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		399156	134607360	317	23041										
KRTAP5-6	440023	hgsc.bcm.edu	37	chr11	1718756	1718756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtgcagttgctgcaagccctGctactgttcctcaggctgtg	12	12	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:1718756G>A	ENST00000382160.1	+	1	332	c.281G>A	c.(280-282)tGc>tAc	p.C94Y		NM_001012416.1	NP_001012416.1	Q6L8G9	KRA56_HUMAN	keratin associated protein 5-6	94	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(6)|skin(1)	10		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		TGCAAGCCCTGCTACTGTTCC	0.637																																					p.C94Y		Atlas-SNP	.											.	KRTAP5-6	18	.	0			c.G281A						.						93	111	105					11																	1718756		2202	4299	6501	SO:0001583	missense	440023	exon1			AGCCCTGCTACTG	AB126075	CCDS31332.1	11p15.5	2008-02-05			ENSG00000205864	ENSG00000205864		"Keratin associated proteins"	23600	protein-coding gene	gene with protein product						15144888	Standard	NM_001012416		Approved	KRTAP5.6	uc001lua.3	Q6L8G9	OTTHUMG00000043932	ENST00000382160.1:c.281G>A	chr11.hg19:g.1718756G>A	ENSP00000371595:p.Cys94Tyr	119.0	0.0		90.0	29.0	NM_001012416	A1L452	Missense_Mutation	SNP	ENST00000382160.1	hg19	CCDS31332.1	.	.	.	.	.	.	.	.	.	.	g	0.177	-1.065766	0.01934	.	.	ENSG00000205864	ENST00000382160	T	0.08984	3.03	3.75	1.59	0.23543	.	.	.	.	.	T	0.11196	0.0273	M	0.74467	2.265	0.21579	N	0.999635	P	0.36249	0.545	B	0.35607	0.206	T	0.17077	-1.0381	9	0.72032	D	0.01	.	6.1755	0.20441	0.0:0.207:0.5802:0.2128	.	94	Q6L8G9	KRA56_HUMAN	Y	94	ENSP00000371595:C94Y	ENSP00000371595:C94Y	C	+	2	0	KRTAP5-6	1675332	0.992000	0.36948	0.010000	0.14722	0.040000	0.13550	5.348000	0.66004	0.507000	0.28148	0.399000	0.26434	TGC	.	.		0.637	KRTAP5-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102339.2			A	1718756	G	A	1718756	3	1	150	1	0	0	0	0	1	0	0	0	8574	1319	46	3	283	3	KRTAP5-6	11	1718756	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	1319600	1718756	133287760	318	23042										
OR51L1	119682	hgsc.bcm.edu	37	chr11	5020231	5020231	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctatgggagactggaataacAgtgatgctgtggagcccata	13	7	0	2	rs61910724		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:5020231A>G	ENST00000321543.1	+	1	19	c.19A>G	c.(19-21)Agt>Ggt	p.S7G		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	7						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTGGAATAACAGTGATGCTGT	0.433																																					p.S7G		Atlas-SNP	.											.	OR51L1	60	.	0			c.A19G						.						168	164	165					11																	5020231		2201	4298	6499	SO:0001583	missense	119682	exon1			AATAACAGTGATG	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"GPCR / Class A : Olfactory receptors"	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.19A>G	chr11.hg19:g.5020231A>G	ENSP00000322156:p.Ser7Gly	118.0	0.0		106.0	65.0	NM_001004755	Q6IFE5	Missense_Mutation	SNP	ENST00000321543.1	hg19	CCDS31369.1	.	.	.	.	.	.	.	.	.	.	A	14.38	2.519298	0.44866	.	.	ENSG00000176798	ENST00000321543	T	0.54071	0.59	5.58	5.58	0.84498	.	0.281465	0.25660	N	0.029150	T	0.56659	0.2000	M	0.89658	3.05	0.23198	N	0.998133	P	0.41393	0.748	B	0.31390	0.129	T	0.65894	-0.6057	10	0.72032	D	0.01	.	13.241	0.59997	1.0:0.0:0.0:0.0	.	7	Q8NGJ5	O51L1_HUMAN	G	7	ENSP00000322156:S7G	ENSP00000322156:S7G	S	+	1	0	OR51L1	4976807	0.874000	0.30092	0.903000	0.35520	0.969000	0.65631	5.312000	0.65792	2.343000	0.79666	0.533000	0.62120	AGT	.	A|0.987;C|0.013		0.433	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755		G	5020231	A	G	5020231	3	3	150	1	0	0	0	0	1	0	0	0	11111	188	7	2	21	2	OR51L1	11	5020231	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3301475	5020231	129986285	319	23043										
OR52E2	119678	hgsc.bcm.edu	37	chr11	5080160	5080160	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgagggacttgagtcgggctTcatgagtaggaagacggaaa	16	5	1	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:5080160T>A	ENST00000321522.2	-	1	697	c.698A>T	c.(697-699)gAa>gTa	p.E233V		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(13)|ovary(2)|skin(3)	20		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.03e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.191)		GAGTCGGGCTTCATGAGTAGG	0.433																																					p.E233V		Atlas-SNP	.											.	OR52E2	63	.	0			c.A698T						.						82	76	78					11																	5080160		2201	4298	6499	SO:0001583	missense	119678	exon1			CGGGCTTCATGAG	AB065800	CCDS31371.1	11p15.4	2012-08-09			ENSG00000176787	ENSG00000176787		"GPCR / Class A : Olfactory receptors"	14769	protein-coding gene	gene with protein product							Standard	NM_001005164		Approved		uc010qyw.2	Q8NGJ4	OTTHUMG00000066608	ENST00000321522.2:c.698A>T	chr11.hg19:g.5080160T>A	ENSP00000322088:p.Glu233Val	184.0	0.0		155.0	35.0	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	hg19	CCDS31371.1	.	.	.	.	.	.	.	.	.	.	T	11.74	1.727419	0.30593	.	.	ENSG00000176787	ENST00000321522	T	0.00220	8.52	3.76	3.76	0.43208	GPCR, rhodopsin-like superfamily (1);	0.942816	0.08847	N	0.885004	T	0.00524	0.0017	M	0.92026	3.265	0.09310	N	1	P	0.45986	0.87	P	0.49012	0.598	T	0.47058	-0.9146	10	0.87932	D	0	.	12.3384	0.55081	0.0:0.0:0.0:1.0	.	233	Q8NGJ4	O52E2_HUMAN	V	233	ENSP00000322088:E233V	ENSP00000322088:E233V	E	-	2	0	OR52E2	5036736	0.000000	0.05858	0.745000	0.31077	0.378000	0.30076	0.024000	0.13555	1.963000	0.57068	0.524000	0.50904	GAA	.	.		0.433	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164		A	5080160	T	A	5080160	3	1	150	1	0	0	0	0	1	0	0	0	11124	1783	62	4	282	4	OR52E2	11	5080160	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	59929	5080160	129926356	320	23044										
OR51B6	390058	hgsc.bcm.edu	37	chr11	5373112	5373112	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gactgtttcattaccatccgCagccccttaagatatacctc	5	14	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:5373112C>T	ENST00000380219.1	+	1	375	c.375C>T	c.(373-375)cgC>cgT	p.R125R	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	125			R -> H (in dbSNP:rs7479477).	TIRS -> AIHN (in Ref. 1; AAG41682). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTACCATCCGCAGCCCCTTAA	0.468																																					p.R125R		Atlas-SNP	.											.	OR51B6	53	.	0			c.C375T						.						126	116	119					11																	5373112		2201	4297	6498	SO:0001819	synonymous_variant	390058	exon1			CATCCGCAGCCCC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"GPCR / Class A : Olfactory receptors"	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.375C>T	chr11.hg19:g.5373112C>T		107.0	0.0		105.0	55.0	NM_001004750		Silent	SNP	ENST00000380219.1	hg19	CCDS31379.1																																																																																			.	.		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750		T	5373112	C	T	5373112	2	4	150	1	0	0	0	0	0	0	0	1	11101	697	25	3		3	OR51B6	11	5373112	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	292952	5373112	129633404	321	23045										
OR52B6	340980	hgsc.bcm.edu	37	chr11	5602597	5602597	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	caaggtcattgggaagatcgTcactgccgccctgagccaca	11	13	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:5602597T>C	ENST00000345043.2	+	1	491	c.491T>C	c.(490-492)gTc>gCc	p.V164A	HBG2_ENST00000380259.2_Intron|AC015691.13_ENST00000394793.2_RNA	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	164						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGAAGATCGTCACTGCCGCC	0.507																																					p.V164A		Atlas-SNP	.											.	OR52B6	37	.	0			c.T491C						.						190	198	195					11																	5602597		2201	4297	6498	SO:0001583	missense	340980	exon1			AGATCGTCACTGC	AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"GPCR / Class A : Olfactory receptors"	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.491T>C	chr11.hg19:g.5602597T>C	ENSP00000341581:p.Val164Ala	48.0	0.0		45.0	11.0	NM_001005162	Q6IFI7	Missense_Mutation	SNP	ENST00000345043.2	hg19	CCDS41611.1	.	.	.	.	.	.	.	.	.	.	T	1.402	-0.577869	0.03854	.	.	ENSG00000187747	ENST00000345043	T	0.39056	1.1	5.15	-4.92	0.03075	GPCR, rhodopsin-like superfamily (1);	1.912130	0.03822	N	0.267676	T	0.19327	0.0464	N	0.03209	-0.39	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.19160	-1.0314	10	0.23302	T	0.38	.	9.9	0.41342	0.0:0.4874:0.0977:0.4149	.	164	Q8NGF0	O52B6_HUMAN	A	164	ENSP00000341581:V164A	ENSP00000341581:V164A	V	+	2	0	OR52B6	5559173	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.627000	0.00206	-0.690000	0.05142	-0.137000	0.14449	GTC	.	.		0.507	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162		C	5602597	T	C	5602597	3	2	150	1	0	0	0	0	1	0	0	0	11122	1667	58	2	493	2	OR52B6	11	5602597	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	229485	5602597	129403919	322	23046										
OR56A4	120793	hgsc.bcm.edu	37	chr11	6024147	6024147	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagagacaaccagtgctgccAgctctggaagttggggaagc	14	10	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:6024147A>T	ENST00000330728.4	-	1	277	c.232T>A	c.(232-234)Tgg>Agg	p.W78R		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	26						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAGTGCTGCCAGCTCTGGAAG	0.557																																					p.W78R		Atlas-SNP	.											.	OR56A4	66	.	0			c.T232A						.						86	81	83					11																	6024147		2201	4296	6497	SO:0001583	missense	120793	exon1			GCTGCCAGCTCTG	BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"GPCR / Class A : Olfactory receptors"	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.232T>A	chr11.hg19:g.6024147A>T	ENSP00000328215:p.Trp78Arg	169.0	0.0		148.0	34.0	NM_001005179	B9EH17	Missense_Mutation	SNP	ENST00000330728.4	hg19	CCDS31404.1	.	.	.	.	.	.	.	.	.	.	A	15.06	2.720776	0.48728	.	.	ENSG00000183389	ENST00000330728	T	0.00231	8.49	3.62	3.62	0.41486	.	0.910037	0.08857	U	0.883572	T	0.00271	0.0008	L	0.60845	1.875	0.26470	N	0.975298	P	0.48640	0.913	P	0.47891	0.56	T	0.54497	-0.8285	10	0.41790	T	0.15	.	8.6004	0.33740	0.8064:0.1936:0.0:0.0	.	26	Q8NGH8	O56A4_HUMAN	R	78	ENSP00000328215:W78R	ENSP00000328215:W78R	W	-	1	0	OR56A4	5980723	0.000000	0.05858	0.937000	0.37676	0.918000	0.54935	0.238000	0.18004	1.629000	0.50426	0.454000	0.30748	TGG	.	.		0.557	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179		T	6024147	A	T	6024147	3	4	150	1	0	0	0	0	1	0	0	0	11144	188	7	4	867	4	OR56A4	11	6024147	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	421550	6024147	128982369	323	23047										
SBF2	81846	hgsc.bcm.edu	37	chr11	9868576	9868576	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggttctgcattgtaatcttcTtctccttggtgatggaggca	11	8	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:9868576T>A	ENST00000256190.8	-	23	2998	c.2861A>T	c.(2860-2862)aAg>aTg	p.K954M	RP11-1H15.2_ENST00000533659.1_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	954	GRAM.				cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		TGTAATCTTCTTCTCCTTGGT	0.438																																					p.K954M		Atlas-SNP	.											.	SBF2	146	.	0			c.A2861T						.						215	183	194					11																	9868576		2201	4294	6495	SO:0001583	missense	81846	exon23			ATCTTCTTCTCCT	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.2861A>T	chr11.hg19:g.9868576T>A	ENSP00000256190:p.Lys954Met	129.0	0.0		97.0	20.0	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	ENST00000256190.8	hg19	CCDS31427.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.038572	0.93630	.	.	ENSG00000133812	ENST00000256190	D	0.88509	-2.39	6.03	6.03	0.97812	GRAM (2);	0.000000	0.85682	D	0.000000	D	0.95220	0.8450	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.95780	0.8816	10	0.87932	D	0	.	16.5582	0.84512	0.0:0.0:0.0:1.0	.	954	Q86WG5	MTMRD_HUMAN	M	954	ENSP00000256190:K954M	ENSP00000256190:K954M	K	-	2	0	SBF2	9825152	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.308000	0.77769	0.533000	0.62120	AAG	.	.		0.438	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		A	9868576	T	A	9868576	3	1	150	1	0	0	0	0	1	0	0	0	13874	1609	56	4	2760	4	SBF2	11	9868576	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3844429	9868576	125137940	324	23048										
DKK3	27122	hgsc.bcm.edu	37	chr11	11987363	11987363	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tagggggcctcacctgtgggGctggcagaggaggccactgg	19	10	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:11987363G>A	ENST00000396505.2	-	7	1061	c.823C>T	c.(823-825)Ccc>Tcc	p.P275S	DKK3_ENST00000326932.4_Missense_Mutation_p.P275S|DKK3_ENST00000525493.1_Missense_Mutation_p.P275S|DKK3_ENST00000527132.1_Intron|DKK3_ENST00000450094.2_Missense_Mutation_p.P247S	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	275	DKK-type Cys-2.				adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		CACCTGTGGGGCTGGCAGAGG	0.657																																					p.P275S		Atlas-SNP	.											.	DKK3	35	.	0			c.C823T						.						51	50	50					11																	11987363		2201	4294	6495	SO:0001583	missense	27122	exon6			TGTGGGGCTGGCA	AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"regulated in glioma"	605416	"dickkopf (Xenopus laevis) homolog 3", "dickkopf 3 homolog (Xenopus laevis)"			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.823C>T	chr11.hg19:g.11987363G>A	ENSP00000379762:p.Pro275Ser	35.0	0.0		39.0	9.0	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Missense_Mutation	SNP	ENST00000396505.2	hg19	CCDS7808.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.710210	0.89018	.	.	ENSG00000050165	ENST00000396505;ENST00000326932;ENST00000366345;ENST00000525493;ENST00000450094;ENST00000326914	T;T;T;T	0.30448	2.26;2.26;2.18;1.53	5.65	5.65	0.86999	.	0.157444	0.64402	D	0.000019	T	0.51295	0.1666	L	0.61218	1.895	0.47183	D	0.999344	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.71870	0.975;0.915;0.915	T	0.40117	-0.9580	10	0.37606	T	0.19	-13.224	15.0107	0.71547	0.0:0.0:0.857:0.143	.	275;247;275	F6SYF8;E7EUD0;Q9UBP4	.;.;DKK3_HUMAN	S	275;275;218;275;247;119	ENSP00000379762:P275S;ENSP00000314910:P275S;ENSP00000433112:P275S;ENSP00000398365:P247S	ENSP00000314730:P119S	P	-	1	0	DKK3	11943939	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.576000	0.53878	2.655000	0.90218	0.655000	0.94253	CCC	.	.		0.657	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253		A	11987363	G	A	11987363	3	1	150	1	0	0	0	0	1	0	0	0	4548	1203	42	3	237	3	DKK3	11	11987363	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	2118787	11987363	123019153	325	23049										
CYP2R1	120227	hgsc.bcm.edu	37	chr11	14902118	14902118	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgatcagattggttatgttTgaaacagcattcgttattaa	8	4	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:14902118T>G	ENST00000334636.5	-	3	610	c.564A>C	c.(562-564)tcA>tcC	p.S188S	CYP2R1_ENST00000526489.1_5'UTR|CYP2R1_ENST00000532378.1_Intron	NM_024514.4	NP_078790.2	Q6VVX0	CP2R1_HUMAN	cytochrome P450, family 2, subfamily R, polypeptide 1	188					small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14					Cholecalciferol(DB00169)|Ergocalciferol(DB00153)	TGGTTATGTTTGAAACAGCAT	0.318																																					p.S188S	NSCLC(173;1584 2058 26117 29365 41534)	Atlas-SNP	.											.	CYP2R1	41	.	0			c.A564C						.						99	92	94					11																	14902118		2200	4293	6493	SO:0001819	synonymous_variant	120227	exon3			TATGTTTGAAACA	AY323817	CCDS7818.1	11p15.2	2008-02-05			ENSG00000186104	ENSG00000186104		"Cytochrome P450s"	20580	protein-coding gene	gene with protein product		608713				12464240, 12867411	Standard	XM_005252788		Approved		uc001mlr.3	Q6VVX0	OTTHUMG00000165900	ENST00000334636.5:c.564A>C	chr11.hg19:g.14902118T>G		92.0	0.0		90.0	22.0	NM_024514	Q2M3H3|Q5RT65	Silent	SNP	ENST00000334636.5	hg19	CCDS7818.1																																																																																			.	.		0.318	CYP2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386985.1	NM_024514		G	14902118	T	G	14902118	2	3	150	1	0	0	0	0	0	0	0	1	4175	1799	63	5		5	CYP2R1	11	14902118	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2914755	14902118	120104398	326	23050										
ELP4	26610	hgsc.bcm.edu	37	chr11	31669364	31669364	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatcatttattggttctgagAgagaaactaacccattgtat	7	6	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:31669364A>T	ENST00000350638.5	+	8	1038	c.1003A>T	c.(1003-1005)Aga>Tga	p.R335*	ELP4_ENST00000395934.2_Nonsense_Mutation_p.R335*|Z83001.1_ENST00000429821.1_RNA|ELP4_ENST00000379163.5_Nonsense_Mutation_p.R336*	NM_019040.3	NP_061913.3	Q96EB1	ELP4_HUMAN	elongator acetyltransferase complex subunit 4	335					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)			breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)	20	Lung SC(675;0.225)					TGGTTCTGAGAGAGAAACTAA	0.403																																					p.R335X		Atlas-SNP	.											.	ELP4	78	.	0			c.A1003T						.						180	165	170					11																	31669364		1857	4101	5958	SO:0001587	stop_gained	26610	exon8			TCTGAGAGAGAAA	AJ276005	CCDS7875.2, CCDS73271.1, CCDS73272.1	11p13	2012-08-14	2012-08-08	2002-05-24	ENSG00000109911	ENSG00000109911		"Elongator acetyltransferase complex subunits"	1171	protein-coding gene	gene with protein product		606985	"chromosome 11 open reading frame 19", "elongation protein 4 homolog (S. cerevisiae)"	C11orf19		11889558, 11435442	Standard	XM_005252865		Approved	PAXNEB	uc001mtb.3	Q96EB1	OTTHUMG00000142919	ENST00000350638.5:c.1003A>T	chr11.hg19:g.31669364A>T	ENSP00000298937:p.Arg335*	116.0	0.0		144.0	47.0	NM_019040	B4E3W0|E7EPZ6|Q9H4E8|Q9NX11	Nonsense_Mutation	SNP	ENST00000350638.5	hg19	CCDS7875.2	.	.	.	.	.	.	.	.	.	.	A	29.2	4.989003	0.93106	.	.	ENSG00000109911	ENST00000350638;ENST00000379163;ENST00000395934	.	.	.	5.92	5.92	0.95590	.	0.195426	0.53938	D	0.000053	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	-11.9345	16.3604	0.83263	1.0:0.0:0.0:0.0	.	.	.	.	X	335;336;335	.	ENSP00000298937:R335X	R	+	1	2	ELP4	31625940	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	7.781000	0.85668	2.260000	0.74910	0.528000	0.53228	AGA	.	.		0.403	ELP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286640.1	NM_019040		T	31669364	A	T	31669364	4	4	150	1	0	0	0	0	0	1	0	0	5084	296	11	4	1033	4	ELP4	11	31669364	Nonsense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	16767246	31669364	103337152	327	23051										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33566763	33566763	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	actgacagtcacggccgcgcTgacatccattacagcctcag	9	15	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:33566763T>A	ENST00000321505.4	+	2	2513	c.2333T>A	c.(2332-2334)cTg>cAg	p.L778Q	KIAA1549L_ENST00000265654.5_Missense_Mutation_p.L784Q|KIAA1549L_ENST00000389726.3_Missense_Mutation_p.L784Q			Q6ZVL6	K154L_HUMAN	KIAA1549-like	778						integral component of membrane (GO:0016021)											ACGGCCGCGCTGACATCCATT	0.612																																					p.L778Q		Atlas-SNP	.											.	.	.	.	0			c.T2333A						.						81	98	92					11																	33566763		2184	4283	6467	SO:0001583	missense	25758	exon2			CCGCGCTGACATC	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.2333T>A	chr11.hg19:g.33566763T>A	ENSP00000315295:p.Leu778Gln	127.0	0.0		108.0	34.0	NM_012194	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	hg19	CCDS44565.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.29|14.29	2.492117|2.492117	0.44352|0.44352	.|.	.|.	ENSG00000110427|ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000265654;ENST00000536568|ENST00000526400	.|.	.|.	.|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.000000|.	0.56097|.	D|.	0.000023|.	T|.	0.62986|.	0.2473|.	M|M	0.64997|0.64997	1.995|1.995	0.33158|0.33158	D|D	0.546609|0.546609	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.986;0.999|.	T|.	0.72327|.	-0.4327|.	9|.	0.20519|.	T|.	0.43|.	-13.5133|-13.5133	14.7306|14.7306	0.69379|0.69379	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	784;784|.	E9PAT2;Q6ZVL6-2|.	.;.|.	Q|R	778;784;784;617|176	.|.	ENSP00000265654:L784Q|.	L|X	+|+	2|1	0|0	C11orf41|C11orf41	33523339|33523339	0.998000|0.998000	0.40836|0.40836	0.087000|0.087000	0.20705|0.20705	0.107000|0.107000	0.19398|0.19398	3.548000|3.548000	0.53670|0.53670	2.220000|2.220000	0.72140|0.72140	0.459000|0.459000	0.35465|0.35465	CTG|TGA	.	.		0.612	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33566763	T	A	33566763	3	1	150	1	0	0	0	0	1	0	0	0	1642	1580	55	4	2357	4	C11orf41	11	33566763	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1897399	33566763	101439753	328	23052										
CD44	960	hgsc.bcm.edu	37	chr11	35226078	35226078	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtccaggcaactcctagtagTacaacggaagaaacagctac	9	11	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:35226078T>A	ENST00000428726.2	+	10	1296	c.1173T>A	c.(1171-1173)agT>agA	p.S391R	CD44_ENST00000263398.6_Intron|CD44_ENST00000433892.2_Intron|CD44_ENST00000415148.2_Missense_Mutation_p.S348R|CD44_ENST00000526669.2_Intron|CD44_ENST00000278386.6_Intron|CD44_ENST00000449691.2_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000437706.2_Missense_Mutation_p.S391R|CD44_ENST00000360158.4_Intron|CD44_ENST00000434472.2_Intron|CD44_ENST00000433354.2_Missense_Mutation_p.S392R	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	391	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	CTCCTAGTAGTACAACGGAAG	0.438																																					p.S391R		Atlas-SNP	.											.	CD44	48	.	0			c.T1173A						.						149	126	134					11																	35226078		2202	4298	6500	SO:0001583	missense	960	exon10			TAGTAGTACAACG	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"CD molecules", "Blood group antigens", "Proteoglycans / Cell surface : Other"	1681	protein-coding gene	gene with protein product	"hematopoietic cell E- and L-selectin ligand", "chondroitin sulfate proteoglycan 8"	107269	"CD44 antigen (homing function and Indian blood group system)"	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.1173T>A	chr11.hg19:g.35226078T>A	ENSP00000398632:p.Ser391Arg	86.0	0.0		83.0	23.0	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Missense_Mutation	SNP	ENST00000428726.2	hg19	CCDS7897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.334|7.334	0.619466|0.619466	0.14129|0.14129	.|.	.|.	ENSG00000026508|ENSG00000026508	ENST00000415148;ENST00000433354;ENST00000437706;ENST00000428726;ENST00000531110;ENST00000528672|ENST00000526553	T;T;T;T;T;T|.	0.25912|.	1.77;1.77;1.77;1.77;1.77;1.77|.	4.39|4.39	-6.13|-6.13	0.02118|0.02118	.|.	0.466636|.	0.20449|.	N|.	0.092132|.	T|T	0.21761|0.21761	0.0524|0.0524	L|L	0.37561|0.37561	1.115|1.115	0.09310|0.09310	N|N	1|1	B;B|.	0.12013|.	0.002;0.005|.	B;B|.	0.09377|.	0.004;0.004|.	T|T	0.28522|0.28522	-1.0041|-1.0041	10|5	0.36615|.	T|.	0.2|.	-22.2004|-22.2004	2.1465|2.1465	0.03789|0.03789	0.1314:0.3617:0.2687:0.2381|0.1314:0.3617:0.2687:0.2381	.|.	348;391|.	P16070-4;P16070|.	.;CD44_HUMAN|.	R|N	348;392;391;391;103;43|45	ENSP00000389830:S348R;ENSP00000414567:S392R;ENSP00000403990:S391R;ENSP00000398632:S391R;ENSP00000436549:S103R;ENSP00000431860:S43R|.	ENSP00000389830:S348R|.	S|Y	+|+	3|1	2|0	CD44|CD44	35182654|35182654	0.012000|0.012000	0.17670|0.17670	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.424000|-0.424000	0.07025|0.07025	-1.249000|-1.249000	0.02500|0.02500	-1.155000|-1.155000	0.01812|0.01812	AGT|TAC	.	.		0.438	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610		A	35226078	T	A	35226078	3	1	150	1	0	0	0	0	1	0	0	0	3019	1635	57	4	1211	4	CD44	11	35226078	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1659315	35226078	99780438	329	23053										
LDLRAD3	143458	hgsc.bcm.edu	37	chr11	36250861	36250861	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcctgagcgtggaagacaccAgccacagcccggggcagcct	13	15	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:36250861A>T	ENST00000315571.5	+	6	973	c.952A>T	c.(952-954)Agc>Tgc	p.S318C	LDLRAD3_ENST00000528989.1_Missense_Mutation_p.S269C|LDLRAD3_ENST00000524419.1_Missense_Mutation_p.S308C	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	318					receptor-mediated endocytosis (GO:0006898)|regulation of protein processing (GO:0070613)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(7)|skin(1)	28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				GGAAGACACCAGCCACAGCCC	0.662																																					p.S318C		Atlas-SNP	.											.	LDLRAD3	52	.	0			c.A952T						.						56	67	63					11																	36250861		2201	4292	6493	SO:0001583	missense	143458	exon6			GACACCAGCCACA	AK075546	CCDS31462.1	11p13	2014-06-05			ENSG00000179241	ENSG00000179241			27046	protein-coding gene	gene with protein product						21795536	Standard	NM_174902		Approved	LRAD3	uc001mwk.1	Q86YD5	OTTHUMG00000166313	ENST00000315571.5:c.952A>T	chr11.hg19:g.36250861A>T	ENSP00000318607:p.Ser318Cys	195.0	0.0		190.0	46.0	NM_174902	B7Z1U3|B9EG81|Q8NBJ0	Missense_Mutation	SNP	ENST00000315571.5	hg19	CCDS31462.1	.	.	.	.	.	.	.	.	.	.	A	3.800	-0.041806	0.07452	.	.	ENSG00000179241	ENST00000528989;ENST00000524419;ENST00000315571	D;D;D	0.94576	-3.46;-3.31;-3.21	5.12	-10.2	0.00374	.	1.204760	0.05640	N	0.583225	D	0.84669	0.5523	N	0.08118	0	0.09310	N	1	B;B;B	0.28512	0.001;0.214;0.07	B;B;B	0.27170	0.002;0.077;0.077	T	0.78537	-0.2166	10	0.59425	D	0.04	.	10.2419	0.43316	0.6743:0.1099:0.1507:0.0651	.	308;269;318	E9PR86;B7Z1U3;Q86YD5	.;.;LRAD3_HUMAN	C	269;308;318	ENSP00000433954:S269C;ENSP00000434313:S308C;ENSP00000318607:S318C	ENSP00000318607:S318C	S	+	1	0	LDLRAD3	36207437	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-1.570000	0.02140	-2.955000	0.00292	-2.346000	0.00244	AGC	.	.		0.662	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902		T	36250861	A	T	36250861	3	4	150	1	0	0	0	0	1	0	0	0	8716	188	7	4	974	4	LDLRAD3	11	36250861	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1024783	36250861	98755655	330	23054										
RAG2	5897	hgsc.bcm.edu	37	chr11	36614484	36614484	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgtaatccagtagcctgtcTcagactcatcttcttcatca	5	12	6	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:36614484T>A	ENST00000311485.3	-	2	1396	c.1235A>T	c.(1234-1236)gAg>gTg	p.E412V	C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000334307.5_5'Flank|RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000347206.4_5'Flank|C11orf74_ENST00000446510.2_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	412					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				GTAGCCTGTCTCAGACTCATC	0.403									Familial Hemophagocytic Lymphohistiocytosis																												p.E412V		Atlas-SNP	.											.	RAG2	92	.	0			c.A1235T						.						147	139	141					11																	36614484		2202	4298	6500	SO:0001583	missense	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CCTGTCTCAGACT	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.1235A>T	chr11.hg19:g.36614484T>A	ENSP00000308620:p.Glu412Val	72.0	0.0		55.0	13.0	NM_001243785	A8K9E9|Q8TBL4	Missense_Mutation	SNP	ENST00000311485.3	hg19	CCDS7903.1	.	.	.	.	.	.	.	.	.	.	T	0.620	-0.821701	0.02755	.	.	ENSG00000175097	ENST00000311485	D	0.96300	-3.97	5.45	3.07	0.35406	.	0.174480	0.49916	N	0.000131	D	0.92509	0.7621	L	0.42487	1.325	0.40961	D	0.984626	B	0.02656	0.0	B	0.01281	0.0	D	0.86340	0.1704	10	0.24483	T	0.36	-1.7618	10.3425	0.43887	0.3088:0.0:0.0:0.6912	.	412	P55895	RAG2_HUMAN	V	412	ENSP00000308620:E412V	ENSP00000308620:E412V	E	-	2	0	RAG2	36571060	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	3.310000	0.51911	0.415000	0.25817	0.528000	0.53228	GAG	.	.		0.403	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536		A	36614484	T	A	36614484	3	1	150	1	0	0	0	0	1	0	0	0	13020	1551	54	4	352	4	RAG2	11	36614484	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	363623	36614484	98392032	331	23055										
API5	8539	hgsc.bcm.edu	37	chr11	43350345	43350346	+	Frame_Shift_Ins	INS	-	-	TA													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agctacagttcagttatgtgINSgaatgtttgttgtacagttt							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:43350345_43350346insTA	ENST00000531273.1	+	9	1168_1169	c.1029_1030insTA	c.(1030-1032)gaafs	p.E344fs	API5_ENST00000420461.2_Frame_Shift_Ins_p.E290fs|API5_ENST00000378852.3_Frame_Shift_Ins_p.E344fs|API5_ENST00000534600.1_Frame_Shift_Ins_p.E344fs|RP11-484D2.2_ENST00000526220.1_RNA|API5_ENST00000534695.1_Intron|API5_ENST00000455725.2_Frame_Shift_Ins_p.E333fs|Y_RNA_ENST00000516843.1_RNA			Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5	344	ARM-like and Heat-like helical repeats.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fibroblast apoptotic process (GO:2000270)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	fibroblast growth factor binding (GO:0017134)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20						TCAGTTATGTGGAATGTTTGTT	0.406																																					p.V343fs	Pancreas(1;98 122 5625 20895 49453)	Atlas-Indel,Pindel	.											.	API5	91	.	0			c.1029_1030insTA						.																																			SO:0001589	frameshift_variant	8539	exon9			.	U83857	CCDS31465.1, CCDS44572.1, CCDS44573.1	11p12	2010-09-30			ENSG00000166181	ENSG00000166181			594	protein-coding gene	gene with protein product	"API5-like 1", "fibroblast growth factor 2-interacting factor 2", "migration-inducing protein MIG8"	609774				9307294	Standard	NR_024625		Approved	AAC-11, API5L1, AAC11	uc010rfh.1	Q9BZZ5	OTTHUMG00000166395	Exception_encountered	chr11.hg19:g.43350345_43350346insTA	ENSP00000431391:p.Glu344fs	278.0	0.0		217.0	53.0	NM_006595	B4DGR0|B4DRJ2|D3DR21|O15441|Q9Y4J7	Frame_Shift_Ins	INS	ENST00000531273.1	hg19	CCDS44572.1																																																																																			.	.		0.406	API5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389545.1	NM_006595		TA	43350346	-	TA	43350345	7	5	150	1	0	1	1	0	0	0	0	0	773	1335	47	0	1063	0	API5	11	43350345	Frame_Shift_Ins	INS	-	TCGA-DD-AAC8-01A-11D-A40R-10	6735861	43350345	91656171	332	23056										
EXT2	2132	hgsc.bcm.edu	37	chr11	44253901	44253901	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gttattatgtgtctgtccttAggtctggcgggaatttcctg	12	7	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:44253901A>T	ENST00000343631.3	+	11	1791		c.e11-1		EXT2_ENST00000358681.4_Splice_Site|EXT2_ENST00000395673.3_Splice_Site|EXT2_ENST00000533608.1_Splice_Site			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2						carbohydrate metabolic process (GO:0005975)|cell differentiation (GO:0030154)|cellular polysaccharide biosynthetic process (GO:0033692)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm formation (GO:0001707)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|lung(17)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	32						GTCTGTCCTTAGGTCTGGCGG	0.478			"Mis, N, F, S"			"exostoses, osteosarcoma"			Hereditary Multiple Exostoses																												.		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	.	EXT2	129	.	0			c.1663-2A>T						.						128	113	118					11																	44253901		2203	4299	6502	SO:0001630	splice_region_variant	2132	exon11	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	GTCCTTAGGTCTG		CCDS7908.1, CCDS53618.1, CCDS53619.1	11p12-p11	2014-09-17	2013-03-01		ENSG00000151348	ENSG00000151348	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3513	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608210	"exostoses (multiple) 2", "exostosin 2"			8162019, 9576285	Standard	NM_000401		Approved	SOTV	uc001mya.3	Q93063	OTTHUMG00000166498	ENST00000343631.3:c.1663-1A>T	chr11.hg19:g.44253901A>T		122.0	0.0		80.0	22.0	NM_207122	B2R5Z6|C9JU51|J3KPT2|O15288	Splice_Site	SNP	ENST00000343631.3	hg19	CCDS7908.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.055462	0.75960	.	.	ENSG00000151348	ENST00000533608;ENST00000358681;ENST00000395673;ENST00000343631	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8211	0.70074	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EXT2	44210477	1.000000	0.71417	0.971000	0.41717	0.950000	0.60333	7.465000	0.80898	1.913000	0.55393	0.482000	0.46254	.	.	.		0.478	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401	Intron	T	44253901	A	T	44253901	5	4	150	1	0	0	0	0	0	0	1	0	5326	434	15	4	1899	4	EXT2	11	44253901	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	903556	44253901	90752615	333	23057										
CREB3L1	90993	hgsc.bcm.edu	37	chr11	46329400	46329400	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcatgggcgctgggacacaAactgtgctccatcatggtga	13	10	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:46329400A>T	ENST00000529193.1	+	3	816	c.365A>T	c.(364-366)aAa>aTa	p.K122I	CREB3L1_ENST00000288400.3_Missense_Mutation_p.K122I			Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like 1	122					regulation of bone mineralization (GO:0030500)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)		FUS/CREB3L1(6)	NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3)	12				GBM - Glioblastoma multiforme(35;0.0285)		CTGGGACACAAACTGTGCTCC	0.682			T	FUS	myxofibrosarcoma																																p.K122I	Pancreas(3;159 194 19597 26278 47995)	Atlas-SNP	.		Dom	yes		11	11p11.2	90993	cAMP responsive element binding protein 3-like 1		M	.	CREB3L1	30	.	0			c.A365T						.						10	13	12					11																	46329400		2040	4177	6217	SO:0001583	missense	90993	exon3			GACACAAACTGTG		CCDS53620.1	11q11	2013-01-10				ENSG00000157613		"basic leucine zipper proteins"	18856	protein-coding gene	gene with protein product	"BBF-2 homolog (drosophila)"						Standard	NM_052854		Approved	OASIS	uc021qil.1	Q96BA8		ENST00000529193.1:c.365A>T	chr11.hg19:g.46329400A>T	ENSP00000434939:p.Lys122Ile	200.0	0.0		153.0	46.0	NM_052854	Q8N2D5|Q96CP0	Missense_Mutation	SNP	ENST00000529193.1	hg19	CCDS53620.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.277516	0.80580	.	.	ENSG00000157613	ENST00000529193;ENST00000288400;ENST00000534787	T;T;T	0.38240	2.43;2.43;1.15	4.68	2.23	0.28157	.	0.288076	0.33813	N	0.004522	T	0.43366	0.1244	L	0.44542	1.39	0.29740	N	0.837183	D	0.64830	0.994	P	0.59288	0.855	T	0.39722	-0.9600	10	0.49607	T	0.09	-17.056	10.4158	0.44320	0.684:0.316:0.0:0.0	.	122	Q96BA8	CR3L1_HUMAN	I	122;122;76	ENSP00000434939:K122I;ENSP00000288400:K122I;ENSP00000431677:K76I	ENSP00000288400:K122I	K	+	2	0	CREB3L1	46285976	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	2.449000	0.44935	0.216000	0.20781	0.454000	0.30748	AAA	.	.		0.682	CREB3L1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389702.1	NM_052854		T	46329400	A	T	46329400	3	4	150	1	0	0	0	0	1	0	0	0	3858	14	1	4	375	4	CREB3L1	11	46329400	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2075499	46329400	88677116	334	23058										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587486	55587486	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tatgaccgcttcgtggccatTtgcaaccctctgctctacac	7	15	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:55587486T>A	ENST00000333976.4	+	1	401	c.381T>A	c.(379-381)atT>atA	p.I127I		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	127						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				TCGTGGCCATTTGCAACCCTC	0.463																																					p.I127I		Atlas-SNP	.											.	OR5D18	121	.	0			c.T381A						.						180	168	172					11																	55587486		2200	4296	6496	SO:0001819	synonymous_variant	219438	exon1			GGCCATTTGCAAC	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.381T>A	chr11.hg19:g.55587486T>A		138.0	0.0		109.0	23.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Silent	SNP	ENST00000333976.4	hg19	CCDS31510.1																																																																																			.	.		0.463	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		A	55587486	T	A	55587486	2	1	150	1	0	0	0	0	0	0	0	1	11166	1829	64	4		4	OR5D18	11	55587486	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	9258086	55587486	79419030	335	23059										
OR5F1	338674	hgsc.bcm.edu	37	chr11	55761572	55761572	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtgggggactgtcacagaagAagtgatggatgacattggag	17	4	1	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:55761572A>T	ENST00000278409.1	-	1	529	c.530T>A	c.(529-531)tTc>tAc	p.F177Y		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	177					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					GTCACAGAAGAAGTGATGGAT	0.468																																					p.F177Y		Atlas-SNP	.											.	OR5F1	116	.	0			c.T530A						.						93	88	90					11																	55761572		2201	4296	6497	SO:0001583	missense	338674	exon1			CAGAAGAAGTGAT	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"GPCR / Class A : Olfactory receptors"	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.530T>A	chr11.hg19:g.55761572A>T	ENSP00000278409:p.Phe177Tyr	169.0	0.0		127.0	33.0	NM_003697	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	hg19	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	A	14.23	2.472907	0.43942	.	.	ENSG00000149133	ENST00000278409	T	0.00318	8.12	3.03	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00496	0.0016	M	0.66560	2.04	0.09310	N	1	D	0.76494	0.999	D	0.73380	0.98	T	0.52881	-0.8516	9	0.51188	T	0.08	.	6.4031	0.21650	0.7809:0.0:0.0:0.2191	.	177	O95221	OR5F1_HUMAN	Y	177	ENSP00000278409:F177Y	ENSP00000278409:F177Y	F	-	2	0	OR5F1	55518148	0.111000	0.22076	0.902000	0.35471	0.694000	0.40290	2.486000	0.45259	1.167000	0.42706	0.247000	0.18012	TTC	.	.		0.468	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697		T	55761572	A	T	55761572	3	4	150	1	0	0	0	0	1	0	0	0	11167	246	9	4	417	4	OR5F1	11	55761572	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	174086	55761572	79244944	336	23060										
MPEG1	219972	hgsc.bcm.edu	37	chr11	58978713	58978713	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaatctctggatatagcaggAtctaccagggggttcccaac	10	10	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:58978713A>C	ENST00000361050.3	-	1	1711	c.1626T>G	c.(1624-1626)gaT>gaG	p.D542E		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	542						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				ATATAGCAGGATCTACCAGGG	0.552																																					p.D542E		Atlas-SNP	.											.	MPEG1	72	.	0			c.T1626G						.						39	42	41					11																	58978713		1836	4082	5918	SO:0001583	missense	219972	exon1			AGCAGGATCTACC	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"macrophage expressed gene 1"	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.1626T>G	chr11.hg19:g.58978713A>C	ENSP00000354335:p.Asp542Glu	93.0	0.0		63.0	12.0	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	hg19	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	A	4.735	0.136761	0.09032	.	.	ENSG00000197629	ENST00000361050	T	0.21543	2.0	5.93	-2.81	0.05805	.	0.776296	0.11828	N	0.525479	T	0.15696	0.0378	L	0.44542	1.39	0.09310	N	1	B	0.20887	0.049	B	0.19666	0.026	T	0.25641	-1.0126	10	0.42905	T	0.14	-3.8218	8.6342	0.33936	0.2424:0.1586:0.599:0.0	.	542	Q2M385	MPEG1_HUMAN	E	542	ENSP00000354335:D542E	ENSP00000354335:D542E	D	-	3	2	MPEG1	58735289	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.068000	0.14531	-0.406000	0.07588	-0.250000	0.11733	GAT	.	.		0.552	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		C	58978713	A	C	58978713	3	2	150	1	0	0	0	0	1	0	0	0	9732	330	12	5	528	5	MPEG1	11	58978713	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3217141	58978713	76027803	337	23061										
DAGLA	747	hgsc.bcm.edu	37	chr11	61511593	61511593	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccgagttcatcgacagcctcTtcaacctggacagcaagagc	9	14	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:61511593T>A	ENST00000257215.5	+	20	2877	c.2761T>A	c.(2761-2763)Ttc>Atc	p.F921I	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	921					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		CGACAGCCTCTTCAACCTGGA	0.662																																					p.F921I		Atlas-SNP	.											.	DAGLA	109	.	0			c.T2761A						.						68	59	62					11																	61511593		2202	4298	6500	SO:0001583	missense	747	exon20			AGCCTCTTCAACC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"neural stem cell-derived dendrite regulator"	614015	"chromosome 11 open reading frame 11"	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.2761T>A	chr11.hg19:g.61511593T>A	ENSP00000257215:p.Phe921Ile	113.0	0.0		97.0	34.0	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	hg19	CCDS31578.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.584025	0.86748	.	.	ENSG00000134780	ENST00000257215	T	0.38887	1.11	3.97	3.97	0.46021	.	0.000000	0.85682	D	0.000000	T	0.48995	0.1531	L	0.27053	0.805	0.58432	D	0.999999	D	0.57899	0.981	D	0.67231	0.95	T	0.53578	-0.8419	10	0.72032	D	0.01	-33.3698	13.1654	0.59569	0.0:0.0:0.0:1.0	.	921	Q9Y4D2	DGLA_HUMAN	I	921	ENSP00000257215:F921I	ENSP00000257215:F921I	F	+	1	0	DAGLA	61268169	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.518000	0.81795	1.581000	0.49865	0.379000	0.24179	TTC	.	.		0.662	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		A	61511593	T	A	61511593	3	1	150	1	0	0	0	0	1	0	0	0	4228	1609	56	4	2835	4	DAGLA	11	61511593	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2532880	61511593	73494923	338	23062										
SLC22A12	116085	hgsc.bcm.edu	37	chr11	64359422	64359422	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcatcttcacctccacaatcGtggccaaggtagggcctccc	9	16	2	0	rs547191924		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:64359422G>C	ENST00000377574.1	+	1	1141	c.394G>C	c.(394-396)Gtg>Ctg	p.V132L	SLC22A12_ENST00000336464.7_Missense_Mutation_p.V132L|SLC22A12_ENST00000377567.2_Missense_Mutation_p.V132L|SLC22A12_ENST00000473690.1_5'UTR|SLC22A12_ENST00000377572.1_Missense_Mutation_p.V132L	NM_144585.2	NP_653186.2	Q96S37	S22AC_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 12	132					cellular homeostasis (GO:0019725)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|urate transmembrane transporter activity (GO:0015143)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27					Losartan(DB00678)|Probenecid(DB01032)	CTCCACAATCGTGGCCAAGGT	0.627																																					p.V132L		Atlas-SNP	.											.	SLC22A12	68	.	0			c.G394C						.						26	28	27					11																	64359422		2201	4297	6498	SO:0001583	missense	116085	exon1			ACAATCGTGGCCA	AB071863	CCDS8075.1, CCDS60835.1, CCDS60836.1	11q13.1	2013-05-22	2008-01-11		ENSG00000197891	ENSG00000197891		"Solute carriers"	17989	protein-coding gene	gene with protein product		607096	"solute carrier family 22 (organic anion/cation transporter), member 12"			12024214	Standard	NM_144585		Approved	OAT4L, RST, URAT1	uc009yps.2	Q96S37	OTTHUMG00000045213	ENST00000377574.1:c.394G>C	chr11.hg19:g.64359422G>C	ENSP00000366797:p.Val132Leu	32.0	0.0		26.0	9.0	NM_144585	B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2	Missense_Mutation	SNP	ENST00000377574.1	hg19	CCDS8075.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.928963	0.73327	.	.	ENSG00000197891	ENST00000377567;ENST00000377574;ENST00000377572;ENST00000336464	D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52	4.4	4.4	0.53042	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.067890	0.56097	D	0.000022	D	0.88070	0.6338	M	0.88241	2.94	0.24856	N	0.992377	P;P;D;P	0.59767	0.685;0.903;0.986;0.903	P;P;P;P	0.54210	0.447;0.525;0.745;0.525	T	0.83269	-0.0044	10	0.72032	D	0.01	.	14.481	0.67582	0.0:0.0:1.0:0.0	.	132;132;132;132	B5ME56;B3KV05;Q96S37-2;Q96S37	.;.;.;S22AC_HUMAN	L	132	ENSP00000366790:V132L;ENSP00000366797:V132L;ENSP00000366795:V132L;ENSP00000336836:V132L	ENSP00000336836:V132L	V	+	1	0	SLC22A12	64115998	0.996000	0.38824	0.079000	0.20413	0.958000	0.62258	2.543000	0.45752	1.988000	0.58038	0.484000	0.47621	GTG	.	.		0.627	SLC22A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104966.2	NM_144585		C	64359422	G	C	64359422	3	2	150	1	0	0	0	0	1	0	0	0	14458	1145	40	4	396	4	SLC22A12	11	64359422	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	2847829	64359422	70647094	339	23063										
SIPA1	6494	hgsc.bcm.edu	37	chr11	65417088	65417111	+	In_Frame_Del	DEL	CCACCACAGCCAAGCCATCAGTAC	CCACCACAGCCAAGCCATCAGTAC	-													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	caccccggacctcctcctggCcaccacagccaagccatcag							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	CCACCACAGCCAAGCCATCAGTAC	CCACCACAGCCAAGCCATCAGTAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:65417088_65417111delCCACCACAGCCAAGCCATCAGTAC	ENST00000394224.3	+	11	2878_2901	c.2582_2605delCCACCACAGCCAAGCCATCAGTAC	c.(2581-2607)gccaccacagccaagccatcagtaccc>gcc	p.TTAKPSVP862del	MIR4489_ENST00000578869.1_RNA|SIPA1_ENST00000394227.3_In_Frame_Del_p.TTAKPSVP760del|SIPA1_ENST00000534313.1_In_Frame_Del_p.TTAKPSVP862del|SIPA1_ENST00000527525.1_In_Frame_Del_p.TTAKPSVP760del	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	862					cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582)			cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	10						CTCCTCCTGGCCACCACAGCCAAGCCATCAGTACCCAGTGCTGA	0.612																																					p.861_868del		Atlas-Indel,Pindel	.											.	SIPA1	45	.	0			c.2581_2604del						.																																			SO:0001651	inframe_deletion	6494	exon11			.	AH006363, BC010492, BM677738	CCDS8108.1	11q13.3	2008-09-12	2008-09-12		ENSG00000213445	ENSG00000213445			10885	protein-coding gene	gene with protein product		602180				9027487	Standard	NM_006747		Approved	SPA1	uc001ofb.2	Q96FS4	OTTHUMG00000166541	ENST00000394224.3:c.2582_2605delCCACCACAGCCAAGCCATCAGTAC	chr11.hg19:g.65417088_65417111delCCACCACAGCCAAGCCATCAGTAC	ENSP00000377771:p.Thr862_Pro869del	65.0	0.0		36.0	10.0	NM_006747	O14518|O60484|O60618|Q2YD83	In_Frame_Del	DEL	ENST00000394224.3	hg19	CCDS8108.1																																																																																			.	.		0.612	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747		-	65417111	CCACCACAGCCAAGCCATCAGTAC	-	65417088	7	5	150	1	0	1	0	1	0	0	0	0	14343	739	26	0	2620	0	SIPA1	11	65417088	In_Frame_Del	DEL	CCACCACAGCCAAGCCATCAGTAC	TCGA-DD-AAC8-01A-11D-A40R-10	1057666	65417088	69589428	340	23064										
CATSPER1	117144	hgsc.bcm.edu	37	chr11	65787819	65787819	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctttctcaaggcctttgaacAgcgccgtctggaagctatcc	9	13	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:65787819A>T	ENST00000312106.5	-	8	2170	c.2033T>A	c.(2032-2034)cTg>cAg	p.L678Q		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	678					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						GCCTTTGAACAGCGCCGTCTG	0.642																																					p.L678Q		Atlas-SNP	.											.	CATSPER1	101	.	0			c.T2033A						.						122	117	119					11																	65787819		2201	4296	6497	SO:0001583	missense	117144	exon8			TTGAACAGCGCCG	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"Voltage-gated ion channels / Cation channels, sperm associated"	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.2033T>A	chr11.hg19:g.65787819A>T	ENSP00000309052:p.Leu678Gln	95.0	0.0		88.0	28.0	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	hg19	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	A	12.55	1.973085	0.34848	.	.	ENSG00000175294	ENST00000312106	D	0.97114	-4.25	5.14	3.97	0.46021	.	0.000000	0.26571	U	0.023637	D	0.96030	0.8707	L	0.34521	1.04	0.27518	N	0.951494	D	0.69078	0.997	D	0.64410	0.925	D	0.90432	0.4425	10	0.23302	T	0.38	-9.4742	8.7857	0.34818	0.8088:0.1911:0.0:0.0	.	678	Q8NEC5	CTSR1_HUMAN	Q	678	ENSP00000309052:L678Q	ENSP00000309052:L678Q	L	-	2	0	CATSPER1	65544395	0.995000	0.38212	0.812000	0.32479	0.069000	0.16628	3.908000	0.56355	0.758000	0.33059	0.402000	0.26972	CTG	.	.		0.642	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		T	65787819	A	T	65787819	3	4	150	1	0	0	0	0	1	0	0	0	2689	188	7	4	329	4	CATSPER1	11	65787819	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	370731	65787819	69218697	341	23065										
CCDC87	55231	hgsc.bcm.edu	37	chr11	66360350	66360350	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcttcgccagagggaaggacTgcagaatccggccctcctgc	13	14	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:66360350T>A	ENST00000333861.3	-	1	204	c.137A>T	c.(136-138)cAg>cTg	p.Q46L	CCS_ENST00000310190.4_5'Flank|CCS_ENST00000533244.1_5'UTR	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	46					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						AGGGAAGGACTGCAGAATCCG	0.687											OREG0021111	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q46L		Atlas-SNP	.											.	CCDC87	83	.	0			c.A137T						.						21	24	23					11																	66360350		2154	4218	6372	SO:0001583	missense	55231	exon1			AAGGACTGCAGAA	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.137A>T	chr11.hg19:g.66360350T>A	ENSP00000328487:p.Gln46Leu	78.0	0.0	1091	68.0	23.0	NM_018219	Q8NE76	Missense_Mutation	SNP	ENST00000333861.3	hg19	CCDS8145.1	.	.	.	.	.	.	.	.	.	.	T	8.470	0.857287	0.17106	.	.	ENSG00000182791	ENST00000333861	T	0.30981	1.51	5.39	-0.16	0.13375	.	0.918974	0.08933	N	0.872707	T	0.13372	0.0324	N	0.04355	-0.22	0.09310	N	0.999994	B	0.09022	0.002	B	0.06405	0.002	T	0.27806	-1.0063	10	0.36615	T	0.2	-4.0533	6.655	0.22982	0.1651:0.0:0.4743:0.3606	.	46	Q9NVE4	CCD87_HUMAN	L	46	ENSP00000328487:Q46L	ENSP00000328487:Q46L	Q	-	2	0	CCDC87	66116926	0.000000	0.05858	0.003000	0.11579	0.073000	0.16967	0.670000	0.25157	0.095000	0.17434	0.533000	0.62120	CAG	.	.		0.687	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		A	66360350	T	A	66360350	3	1	150	1	0	0	0	0	1	0	0	0	2864	1580	55	4	2416	4	CCDC87	11	66360350	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	572531	66360350	68646166	342	23066										
MTL5	9633	hgsc.bcm.edu	37	chr11	68517742	68517742	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gccgggctgcggtgcgcgggTagcagcgaggacaggaagtg	21	9	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:68517742T>A	ENST00000255087.5	-	2	570	c.387A>T	c.(385-387)ctA>ctT	p.L129L	MTL5_ENST00000443940.2_Silent_p.L129L|MTL5_ENST00000544963.1_Silent_p.L129L|MTL5_ENST00000540869.1_5'Flank	NM_004923.3	NP_004914.2	Q9Y4I5	MTL5_HUMAN	metallothionein-like 5, testis-specific (tesmin)	129					cell differentiation (GO:0030154)|cellular metal ion homeostasis (GO:0006875)|multicellular organismal development (GO:0007275)|response to metal ion (GO:0010038)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	15	Esophageal squamous(3;4.37e-12)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.185)			GGTGCGCGGGTAGCAGCGAGG	0.721																																					p.L129L		Atlas-SNP	.											.	MTL5	37	.	0			c.A387T						.						8	10	9					11																	68517742		2164	4233	6397	SO:0001819	synonymous_variant	9633	exon2			CGCGGGTAGCAGC	U86074	CCDS8184.1, CCDS44661.1	11q13.2-q13.3	2007-01-03			ENSG00000132749	ENSG00000132749			7446	protein-coding gene	gene with protein product	"CXC domain containing 2"	604374				1091092	Standard	XR_428932		Approved	CXCDC2	uc001ooc.3	Q9Y4I5	OTTHUMG00000167891	ENST00000255087.5:c.387A>T	chr11.hg19:g.68517742T>A		91.0	0.0		92.0	29.0	NM_001039656	A8K8J3|Q4G182|Q6P2E2|Q8NCC8	Silent	SNP	ENST00000255087.5	hg19	CCDS8184.1																																																																																			.	.		0.721	MTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396844.1	NM_004923		A	68517742	T	A	68517742	2	1	150	1	0	0	0	0	0	0	0	1	9945	1625	57	4		4	MTL5	11	68517742	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2157392	68517742	66488774	343	23067										
RSF1	51773	hgsc.bcm.edu	37	chr11	77413496	77413496	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agaacggttttctaaatccaTaggctgctcctcacttttca	6	11	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:77413496T>C	ENST00000308488.6	-	6	1080	c.778A>G	c.(778-780)Atg>Gtg	p.M260V	RSF1_ENST00000480887.1_Missense_Mutation_p.M8V|RSF1_ENST00000360355.2_Missense_Mutation_p.M229V			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	260	Glu-rich.				CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			TCTAAATCCATAGGCTGCTCC	0.333																																					p.M260V		Atlas-SNP	.											.	RSF1	105	.	0			c.A778G						.						51	57	55					11																	77413496		2161	4119	6280	SO:0001583	missense	51773	exon6			AATCCATAGGCTG	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"Zinc fingers, PHD-type"	18118	protein-coding gene	gene with protein product		608522	"hepatitis B virus x associated protein"	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.778A>G	chr11.hg19:g.77413496T>C	ENSP00000311513:p.Met260Val	69.0	0.0		49.0	14.0	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	hg19	CCDS8253.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.965152	0.00049	.	.	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000526324;ENST00000528095	D;D;D;D;T	0.84298	-1.79;-1.83;-1.78;-1.83;1.67	5.28	-8.16	0.01061	.	1.479250	0.04013	N	0.298577	T	0.68613	0.3020	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.65849	-0.6068	10	0.02654	T	1	1.121	19.1506	0.93487	0.0:0.2187:0.0:0.7813	.	260	Q96T23	RSF1_HUMAN	V	260;8;229;61;259	ENSP00000311513:M260V;ENSP00000434509:M8V;ENSP00000353511:M229V;ENSP00000432022:M61V;ENSP00000436408:M259V	ENSP00000311513:M260V	M	-	1	0	RSF1	77091144	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.669000	0.05262	-1.669000	0.01470	-0.408000	0.06270	ATG	.	.		0.333	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		C	77413496	T	C	77413496	3	2	150	1	0	0	0	0	1	0	0	0	13714	1406	49	2	3591	2	RSF1	11	77413496	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	8895754	77413496	57593020	344	23068										
TRPC6	7225	hgsc.bcm.edu	37	chr11	101323689	101323689	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctaaggaagtcttcgcattaTctattggtttcctcttgatt	7	8	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:101323689T>A	ENST00000344327.3	-	13	3217	c.2793A>T	c.(2791-2793)agA>agT	p.R931S	TRPC6_ENST00000360497.4_Missense_Mutation_p.R876S|TRPC6_ENST00000348423.4_Missense_Mutation_p.R815S|TRPC6_ENST00000532133.1_Missense_Mutation_p.R853S	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	931					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		CTTCGCATTATCTATTGGTTT	0.338																																					p.R931S	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											.	TRPC6	132	.	0			c.A2793T						.						175	177	176					11																	101323689		2202	4300	6502	SO:0001583	missense	7225	exon13			GCATTATCTATTG	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.2793A>T	chr11.hg19:g.101323689T>A	ENSP00000340913:p.Arg931Ser	107.0	0.0		83.0	17.0	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	hg19	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.901635	0.33535	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.80123	-1.19;-1.27;-1.07;-1.34	5.55	5.55	0.83447	.	0.237633	0.43747	D	0.000526	T	0.79263	0.4416	N	0.08118	0	0.32409	N	0.550908	B;D	0.54601	0.009;0.967	B;D	0.63597	0.009;0.916	D	0.85010	0.0905	10	0.87932	D	0	.	15.7429	0.77914	0.0:0.0:0.0:1.0	.	815;931	Q9Y210-2;Q9Y210	.;TRPC6_HUMAN	S	931;853;815;876	ENSP00000340913:R931S;ENSP00000435574:R853S;ENSP00000343672:R815S;ENSP00000353687:R876S	ENSP00000340913:R931S	R	-	3	2	TRPC6	100828899	1.000000	0.71417	0.992000	0.48379	0.174000	0.22865	2.510000	0.45468	2.119000	0.64992	0.529000	0.55759	AGA	.	.		0.338	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		A	101323689	T	A	101323689	3	1	150	1	0	0	0	0	1	0	0	0	16598	1432	50	4	6	4	TRPC6	11	101323689	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	23910193	101323689	33682827	345	23069										
TRPC6	7225	hgsc.bcm.edu	37	chr11	101375297	101375297	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cactgccaactgtagggcatTctggcccatgtaatccacac	8	14	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:101375297T>A	ENST00000344327.3	-	2	827	c.403A>T	c.(403-405)Aat>Tat	p.N135Y	TRPC6_ENST00000360497.4_Missense_Mutation_p.N135Y|TRPC6_ENST00000526713.1_5'Flank|TRPC6_ENST00000348423.4_Missense_Mutation_p.N135Y|TRPC6_ENST00000532133.1_Missense_Mutation_p.N135Y	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	135					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		TGTAGGGCATTCTGGCCCATG	0.458																																					p.N135Y	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											.	TRPC6	132	.	0			c.A403T						.						119	102	108					11																	101375297		2203	4299	6502	SO:0001583	missense	7225	exon2			GGGCATTCTGGCC	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.403A>T	chr11.hg19:g.101375297T>A	ENSP00000340913:p.Asn135Tyr	88.0	0.0		93.0	27.0	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	hg19	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.325259	0.81580	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55	5.96	5.96	0.96718	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.80088	0.4559	L	0.43646	1.37	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.81588	-0.0864	10	0.72032	D	0.01	-13.0051	16.4484	0.83959	0.0:0.0:0.0:1.0	.	135;135;135	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	Y	135	ENSP00000340913:N135Y;ENSP00000435574:N135Y;ENSP00000343672:N135Y;ENSP00000353687:N135Y	ENSP00000340913:N135Y	N	-	1	0	TRPC6	100880507	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.040000	0.89188	2.285000	0.76669	0.533000	0.62120	AAT	.	.		0.458	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		A	101375297	T	A	101375297	3	1	150	1	0	0	0	0	1	0	0	0	16598	1783	62	4	2440	4	TRPC6	11	101375297	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	51608	101375297	33631219	346	23070										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117314605	117314605	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcctcaggcttctcaccctTgccagcaggctcgatggtca	10	15	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:117314605T>A	ENST00000321322.6	-	21	4040	c.4039A>T	c.(4039-4041)Aag>Tag	p.K1347*	DSCAML1_ENST00000527706.1_Nonsense_Mutation_p.K1077*	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1287	Ig-like C2-type 10.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		TTCTCACCCTTGCCAGCAGGC	0.622																																					p.K1347X		Atlas-SNP	.											.	DSCAML1	286	.	0			c.A4039T						.						50	50	50					11																	117314605		2201	4296	6497	SO:0001587	stop_gained	57453	exon21			CACCCTTGCCAGC		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.4039A>T	chr11.hg19:g.117314605T>A	ENSP00000315465:p.Lys1347*	33.0	0.0		33.0	11.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Nonsense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	T	42	9.301018	0.99130	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	.	.	.	4.59	4.59	0.56863	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.1423	0.65327	0.0:0.0:0.0:1.0	.	.	.	.	X	1077;1347;1054	.	ENSP00000315465:K1347X	K	-	1	0	DSCAML1	116819815	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.747000	0.85070	1.916000	0.55485	0.260000	0.18958	AAG	.	.		0.622	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		A	117314605	T	A	117314605	4	1	150	1	0	0	0	0	0	1	0	0	4771	1821	63	4	2354	4	DSCAML1	11	117314605	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	15939308	117314605	17691911	347	23071										
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117789473	117789473	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggagatgcctgggctggagaTgcccggcctggaggtgtccc	18	11	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:117789473T>G	ENST00000430170.2	-	2	189	c.102A>C	c.(100-102)gcA>gcC	p.A34A	TMPRSS13_ENST00000524993.1_Silent_p.A34A|TMPRSS13_ENST00000528626.1_Silent_p.A34A|TMPRSS13_ENST00000526090.1_Silent_p.A34A|TMPRSS13_ENST00000445164.2_Silent_p.A34A	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	34	13 X 5 AA repeats of A-S-P-A-[GLQR].|4 X 5 AA repeats of T-P-P-G-R.|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		GGGCTGGAGATGCCCGGCCTG	0.627																																					p.A34A		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.A102C						.						46	53	51					11																	117789473		1924	4133	6057	SO:0001819	synonymous_variant	84000	exon2			TGGAGATGCCCGG	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"Serine peptidases / Transmembrane"	29808	protein-coding gene	gene with protein product		610050	"transmembrane protease, serine 11"	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.102A>C	chr11.hg19:g.117789473T>G		68.0	0.0		72.0	19.0	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000430170.2	hg19	CCDS58185.1																																																																																			.	.		0.627	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		G	117789473	T	G	117789473	2	3	150	1	0	0	0	0	0	0	0	1	16260	1451	51	5		5	TMPRSS13	11	117789473	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	474868	117789473	17217043	348	23072										
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118502989	118502989	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aagctggtggccttggagacAggcatccagaaggagaggga	17	7	0	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:118502989A>T	ENST00000361417.2	+	10	2766	c.2355A>T	c.(2353-2355)acA>acT	p.T785T	PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000356063.5_Silent_p.T785T	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	785										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CCTTGGAGACAGGCATCCAGA	0.612																																					p.T785T		Atlas-SNP	.											.	PHLDB1	103	.	0			c.A2355T						.						89	76	80					11																	118502989		2200	4295	6495	SO:0001819	synonymous_variant	23187	exon9			GGAGACAGGCATC		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.2355A>T	chr11.hg19:g.118502989A>T		173.0	0.0		144.0	43.0	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Silent	SNP	ENST00000361417.2	hg19	CCDS8401.1																																																																																			.	.		0.612	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		T	118502989	A	T	118502989	2	4	150	1	0	0	0	0	0	0	0	1	11860	175	7	4		4	PHLDB1	11	118502989	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	713516	118502989	16503527	349	23073										
ASAM	79827	hgsc.bcm.edu	37	chr11	122945480	122945480	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcggattagcagccacaccaAgaggaaaatcagcagggctc	11	11	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:122945480A>T	ENST00000448775.2	-	6	1091	c.751T>A	c.(751-753)Ttg>Atg	p.L251M	CLMP_ENST00000530371.1_5'UTR	NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein	251					digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						AGCCACACCAAGAGGAAAATC	0.458																																					p.L251M		Atlas-SNP	.											.	CLMP	39	.	0			c.T751A						.						118	112	114					11																	122945480		2202	4299	6501	SO:0001583	missense	79827	exon6			ACACCAAGAGGAA	BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24039	protein-coding gene	gene with protein product	"adipocyte-specific adhesion molecule", "coxsackie- and adenovirus receptor-like membrane protein", "adipocyte adhesion molecule"	611693				12851705, 14573622	Standard	NM_024769		Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.751T>A	chr11.hg19:g.122945480A>T	ENSP00000405577:p.Leu251Met	83.0	0.0		62.0	13.0	NM_024769		Missense_Mutation	SNP	ENST00000448775.2	hg19	CCDS8441.1	.	.	.	.	.	.	.	.	.	.	A	19.10	3.761582	0.69763	.	.	ENSG00000166250	ENST00000448775	T	0.77750	-1.12	5.33	-3.36	0.04913	.	0.233552	0.42172	D	0.000750	T	0.75642	0.3877	M	0.81341	2.54	0.30662	N	0.754314	P	0.50617	0.937	P	0.49276	0.605	T	0.71912	-0.4449	10	0.44086	T	0.13	.	4.9316	0.13919	0.2889:0.1401:0.4711:0.0999	.	251	Q9H6B4	CLMP_HUMAN	M	251	ENSP00000405577:L251M	ENSP00000405577:L251M	L	-	1	2	CLMP	122450690	0.126000	0.22350	0.986000	0.45419	0.990000	0.78478	-0.430000	0.06973	-0.419000	0.07439	-0.256000	0.11100	TTG	.	.		0.458	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387542.1	NM_024769		T	122945480	A	T	122945480	3	4	150	1	0	0	0	0	1	0	0	0	1009	69	3	4	378	4	ASAM	11	122945480	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	4442491	122945480	12061036	350	23074										
C11orf61	79684	hgsc.bcm.edu	37	chr11	124637132	124637132	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggcactcaactaaagagccTgcggaaagaaaatccctctc	8	12	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr11:124637132T>A	ENST00000374979.3	-	4	1628	c.1620A>T	c.(1618-1620)gcA>gcT	p.A540A	MSANTD2_ENST00000526629.1_Silent_p.A310A|MSANTD2_ENST00000239614.4_Silent_p.A488A|RP11-677M14.3_ENST00000532579.1_RNA|RP11-677M14.3_ENST00000504932.2_RNA			Q6P1R3	MSD2_HUMAN	Myb/SANT-like DNA-binding domain containing 2	540																	CTAAAGAGCCTGCGGAAAGAA	0.413																																					p.A488A		Atlas-SNP	.											.	MSANTD2	7	.	0			c.A1464T						.						70	80	77					11																	124637132		2201	4299	6500	SO:0001819	synonymous_variant	79684	exon4			AGAGCCTGCGGAA	AK026995	CCDS8454.1, CCDS73408.1	11q24.2	2012-03-02	2012-03-02	2012-03-02	ENSG00000120458	ENSG00000120458			26266	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 61"	C11orf61			Standard	NM_024631		Approved	FLJ23342	uc001qaz.1	Q6P1R3	OTTHUMG00000165931	ENST00000374979.3:c.1620A>T	chr11.hg19:g.124637132T>A		153.0	0.0		119.0	32.0	NM_024631	B3KRY6|Q9H042|Q9H5K8	Silent	SNP	ENST00000374979.3	hg19																																																																																				.	.		0.413	MSANTD2-002	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000387084.1	NM_024631		A	124637132	T	A	124637132	2	1	150	1	0	0	0	0	0	0	0	1	1655	1567	55	4		4	C11orf61	11	124637132	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1691652	124637132	10369384	351	23075										
SLC6A13	6540	hgsc.bcm.edu	37	chr12	333252	333252	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcttgcggaacacgtgagggTacatgtccaccagcgctgtc	12	12	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:333252T>A	ENST00000343164.4	-	11	1269	c.1217A>T	c.(1216-1218)tAc>tTc	p.Y406F	SLC6A13_ENST00000539668.1_5'UTR|SLC6A13_ENST00000445055.2_Missense_Mutation_p.Y314F	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	406					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			CACGTGAGGGTACATGTCCAC	0.557																																					p.Y406F		Atlas-SNP	.											.	SLC6A13	62	.	0			c.A1217T						.						119	99	106					12																	333252		2203	4300	6503	SO:0001583	missense	6540	exon11			TGAGGGTACATGT	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1217A>T	chr12.hg19:g.333252T>A	ENSP00000339260:p.Tyr406Phe	114.0	0.0		75.0	17.0	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	hg19	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	T	5.679	0.309845	0.10733	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.72394	-0.65;-0.65	5.5	5.5	0.81552	.	0.112740	0.64402	D	0.000007	T	0.48333	0.1494	N	0.05280	-0.08	0.47009	D	0.999282	B;B;B	0.11235	0.004;0.001;0.0	B;B;B	0.23574	0.047;0.046;0.017	T	0.49322	-0.8952	10	0.02654	T	1	.	15.5878	0.76499	0.0:0.0:0.0:1.0	.	314;385;406	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	F	314;385;406	ENSP00000407104:Y314F;ENSP00000339260:Y406F	ENSP00000318097:Y385F	Y	-	2	0	SLC6A13	203513	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	3.813000	0.55636	2.098000	0.63641	0.402000	0.26972	TAC	.	.		0.557	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		A	333252	T	A	333252	3	1	150	1	0	0	0	0	1	0	0	0	14691	1638	57	4	611	4	SLC6A13	12	333252	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10		333252	133518643	352	23076										
C12orf4	57102	hgsc.bcm.edu	37	chr12	4645227	4645227	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgtgcagcagcatcagacgtCcatgcaaatgactggcattc	10	11	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:4645227C>A	ENST00000261250.3	-	2	221	c.134G>T	c.(133-135)gGa>gTa	p.G45V	RAD51AP1_ENST00000228843.9_5'Flank|RAD51AP1_ENST00000544927.1_5'Flank|RAD51AP1_ENST00000321524.7_5'Flank|RAD51AP1_ENST00000352618.4_5'Flank|RAD51AP1_ENST00000543041.1_5'Flank|C12orf4_ENST00000545746.1_Missense_Mutation_p.G45V	NM_020374.2	NP_065107.1	Q9NQ89	CL004_HUMAN	chromosome 12 open reading frame 4	45										NS(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)		CATCAGACGTCCATGCAAATG	0.368																																					p.G45V		Atlas-SNP	.											.	C12orf4	58	.	0			c.G134T						.						120	114	116					12																	4645227		2203	4300	6503	SO:0001583	missense	57102	exon2			AGACGTCCATGCA	AJ272205	CCDS8528.1	12p13.3	2012-08-10			ENSG00000047621	ENSG00000047621			1184	protein-coding gene	gene with protein product							Standard	NM_020374		Approved		uc001qms.3	Q9NQ89	OTTHUMG00000168258	ENST00000261250.3:c.134G>T	chr12.hg19:g.4645227C>A	ENSP00000261250:p.Gly45Val	228.0	0.0		201.0	52.0	NM_020374	D3DUQ8|Q6MZH5	Missense_Mutation	SNP	ENST00000261250.3	hg19	CCDS8528.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.440987	0.63067	.	.	ENSG00000047621	ENST00000261250;ENST00000545746	.	.	.	6.17	5.24	0.73138	.	0.053164	0.85682	D	0.000000	T	0.70850	0.3271	L	0.57536	1.79	0.80722	D	1	D	0.54601	0.967	P	0.58013	0.831	T	0.63404	-0.6645	9	0.18710	T	0.47	.	17.0967	0.86637	0.0:0.8736:0.1264:0.0	.	45	Q9NQ89	CL004_HUMAN	V	45	.	ENSP00000261250:G45V	G	-	2	0	C12orf4	4515488	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.644000	0.67902	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.368	C12orf4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398992.1	NM_020374		A	4645227	C	A	4645227	3	1	150	1	0	0	0	0	1	0	0	0	1687	855	30	3	1576	3	C12orf4	12	4645227	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	4311975	4645227	129206668	353	23077										
KLRK1	22914	hgsc.bcm.edu	37	chr12	10532337	10532337	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tccatattgttaccataataAtgaaacggattcccatggct	6	9	0	1	rs377167821		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:10532337A>T	ENST00000240618.6	-	4	343	c.203T>A	c.(202-204)aTt>aAt	p.I68N	RP11-277P12.20_ENST00000500682.1_RNA|KLRC4-KLRK1_ENST00000539300.1_3'UTR|KLRK1_ENST00000540818.1_Missense_Mutation_p.I68N	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	68					cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						TACCATAATAATGAAACGGAT	0.348																																					p.I68N		Atlas-SNP	.											.	.	.	.	0			c.T203A						.	A	ASN/ILE,ASN/ILE	0,4406		0,0,2203	71	65	67		203,203	4.5	0.1	12		67	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	KLRK1,KLRC4-KLRK1	NM_001199805.1,NM_007360.3	149,149	0,2,6501	TT,TA,AA		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	68/217,68/217	10532337	2,13004	2203	4300	6503	SO:0001583	missense	0	exon9			ATAATAATGAAAC	AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"Killer cell lectin-like receptors", "CD molecules"	18788	protein-coding gene	gene with protein product		611817	"DNA segment on chromosome 12 (unique) 2489 expressed sequence"	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.203T>A	chr12.hg19:g.10532337A>T	ENSP00000240618:p.Ile68Asn	182.0	0.0		135.0	37.0	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Missense_Mutation	SNP	ENST00000240618.6	hg19	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	A	11.87	1.768931	0.31320	0.0	2.33E-4	ENSG00000213809	ENST00000240618;ENST00000540818	T;T	0.01560	4.77;4.77	5.64	4.51	0.55191	.	0.619766	0.15348	N	0.267083	T	0.05823	0.0152	L	0.52573	1.65	0.09310	N	1	D;D;P	0.64830	0.962;0.994;0.949	P;D;P	0.64321	0.717;0.924;0.621	T	0.30208	-0.9986	10	0.87932	D	0	.	7.622	0.28191	0.9024:0.0:0.0976:0.0	.	68;49;68	Q8WZ67;Q1HEA1;P26718	.;.;NKG2D_HUMAN	N	68	ENSP00000240618:I68N;ENSP00000446003:I68N	ENSP00000240618:I68N	I	-	2	0	KLRK1	10423604	0.032000	0.19561	0.096000	0.21009	0.060000	0.15804	2.415000	0.44635	0.990000	0.38787	0.528000	0.53228	ATT	.	.		0.348	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		T	10532337	A	T	10532337	3	4	150	1	0	0	0	0	1	0	0	0	8432	101	4	4	467	4	KLRK1	12	10532337	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5887110	10532337	123319558	354	23078										
BICD1	636	hgsc.bcm.edu	37	chr12	32369351	32369351	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtggtcactaatgtacaggcAgaaaacgagaggctcaccgc	12	10	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:32369351A>T	ENST00000281474.5	+	2	487	c.384A>T	c.(382-384)gcA>gcT	p.A128A	BICD1_ENST00000548411.1_Silent_p.A128A	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	128					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			ATGTACAGGCAGAAAACGAGA	0.478																																					p.A128A		Atlas-SNP	.											.	BICD1	89	.	0			c.A384T						.						92	84	87					12																	32369351		2203	4300	6503	SO:0001819	synonymous_variant	636	exon2			ACAGGCAGAAAAC	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.384A>T	chr12.hg19:g.32369351A>T		121.0	0.0		115.0	25.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	hg19	CCDS8726.1																																																																																			.	.		0.478	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		T	32369351	A	T	32369351	2	4	150	1	0	0	0	0	0	0	0	1	1428	175	7	4		4	BICD1	12	32369351	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	21837014	32369351	101482544	355	23079										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40761452	40761452	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttttctttttctagagatacAatcttgcttgaccgtttggg	8	7	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:40761452A>T	ENST00000298910.7	+	51	7527	c.7469A>T	c.(7468-7470)cAa>cTa	p.Q2490L		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2490					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CTAGAGATACAATCTTGCTTG	0.299																																					p.Q2490L		Atlas-SNP	.											.	LRRK2	763	.	0			c.A7469T						.						46	49	48					12																	40761452		2202	4297	6499	SO:0001583	missense	120892	exon51			AGATACAATCTTG	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.7469A>T	chr12.hg19:g.40761452A>T	ENSP00000298910:p.Gln2490Leu	255.0	0.0		225.0	66.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.003590	0.54254	.	.	ENSG00000188906	ENST00000298910	T	0.35605	1.3	5.3	5.3	0.74995	WD40 repeat-like-containing domain (1);	0.172705	0.51477	D	0.000086	T	0.37433	0.1003	L	0.54323	1.7	0.40611	D	0.981679	B;B	0.28552	0.215;0.215	B;B	0.29524	0.103;0.103	T	0.30504	-0.9976	10	0.56958	D	0.05	.	15.2534	0.73564	1.0:0.0:0.0:0.0	.	2490;2490	Q17RV3;Q5S007	.;LRRK2_HUMAN	L	2490	ENSP00000298910:Q2490L	ENSP00000298910:Q2490L	Q	+	2	0	LRRK2	39047719	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.657000	0.74402	2.007000	0.58848	0.459000	0.35465	CAA	.	.		0.299	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40761452	A	T	40761452	3	4	150	1	0	0	0	0	1	0	0	0	9042	130	5	4	7671	4	LRRK2	12	40761452	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	8392101	40761452	93090443	356	23080										
ARID2	196528	hgsc.bcm.edu	37	chr12	46205216	46205216	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttcagttacctagaaaagtaCgagaaagttcatcattttgg	8	6	3	2	rs567746850	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:46205216C>G	ENST00000334344.6	+	4	472	c.300C>G	c.(298-300)taC>taG	p.Y100*	ARID2_ENST00000422737.1_5'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	100	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TAGAAAAGTACGAGAAAGTTC	0.358			"N, S, F"		hepatocellular carcinoma																																p.Y100X		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.C300G						.						108	98	102					12																	46205216		2203	4300	6503	SO:0001587	stop_gained	196528	exon4			AAAGTACGAGAAA		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.300C>G	chr12.hg19:g.46205216C>G	ENSP00000335044:p.Tyr100*	99.0	0.0		79.0	43.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Nonsense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	C	35	5.476042	0.96291	.	.	ENSG00000189079	ENST00000334344	.	.	.	5.87	2.98	0.34508	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.8581	7.6302	0.28234	0.0:0.5194:0.0:0.4806	.	.	.	.	X	100	.	ENSP00000335044:Y100X	Y	+	3	2	ARID2	44491483	0.993000	0.37304	1.000000	0.80357	0.973000	0.67179	0.268000	0.18571	0.353000	0.24079	-0.162000	0.13425	TAC	.	.		0.358	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		G	46205216	C	G	46205216	4	3	150	1	0	0	0	0	0	1	0	0	915	547	19	4	314	4	ARID2	12	46205216	Nonsense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	5443764	46205216	87646679	357	23081										
RACGAP1	29127	hgsc.bcm.edu	37	chr12	50388025	50388025	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atggatatcatccactttgcTgaggaggggtacagttttca	11	7	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:50388025T>A	ENST00000427314.2	-	14	1451	c.1228A>T	c.(1228-1230)Agc>Tgc	p.S410C	RACGAP1_ENST00000454520.2_Missense_Mutation_p.S410C|RACGAP1_ENST00000547905.1_Missense_Mutation_p.S410C|RACGAP1_ENST00000312377.5_Missense_Mutation_p.S410C|RACGAP1_ENST00000548961.1_5'Flank|RACGAP1_ENST00000551016.1_Missense_Mutation_p.S410C|RACGAP1_ENST00000434422.1_Missense_Mutation_p.S410C|RACGAP1_ENST00000547061.1_5'Flank	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						TCCACTTTGCTGAGGAGGGGT	0.428																																					p.S410C		Atlas-SNP	.											.	RACGAP1	36	.	0			c.A1228T						.						130	131	131					12																	50388025		2203	4300	6503	SO:0001583	missense	29127	exon14			CTTTGCTGAGGAG		CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000427314.2:c.1228A>T	chr12.hg19:g.50388025T>A	ENSP00000404190:p.Ser410Cys	100.0	0.0		83.0	24.0	NM_013277		Missense_Mutation	SNP	ENST00000427314.2	hg19	CCDS8795.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.203846	0.79127	.	.	ENSG00000161800	ENST00000427314;ENST00000312377;ENST00000434422;ENST00000454520;ENST00000551016;ENST00000547905;ENST00000549342	T;T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79;1.79	5.35	5.35	0.76521	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.071913	0.85682	D	0.000000	T	0.54095	0.1837	M	0.88570	2.965	0.80722	D	1	D	0.67145	0.996	P	0.59948	0.866	T	0.64676	-0.6351	10	0.72032	D	0.01	-14.0885	15.3371	0.74266	0.0:0.0:0.0:1.0	.	410	Q9H0H5	RGAP1_HUMAN	C	410;410;410;410;410;410;146	ENSP00000404190:S410C;ENSP00000309871:S410C;ENSP00000413241:S410C;ENSP00000404808:S410C;ENSP00000449374:S410C;ENSP00000449370:S410C;ENSP00000449565:S146C	ENSP00000309871:S410C	S	-	1	0	RACGAP1	48674292	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.077000	0.64419	2.014000	0.59158	0.454000	0.30748	AGC	.	.		0.428	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277		A	50388025	T	A	50388025	3	1	150	1	0	0	0	0	1	0	0	0	12992	1580	55	4	694	4	RACGAP1	12	50388025	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4182809	50388025	83463870	358	23082										
ESPL1	9700	hgsc.bcm.edu	37	chr12	53684151	53684151	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cttcatctgcgttcagtcctGaatgagtttgatgccatcca	8	11	3	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:53684151G>T	ENST00000257934.4	+	24	5353	c.5262G>T	c.(5260-5262)ctG>ctT	p.L1754L	ESPL1_ENST00000552462.1_Silent_p.L1754L	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1754					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						GTTCAGTCCTGAATGAGTTTG	0.542																																					p.L1754L	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.G5262T						.						120	104	109					12																	53684151		2203	4300	6503	SO:0001819	synonymous_variant	9700	exon24			AGTCCTGAATGAG	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"separin", "separase", "separin, cysteine protease"	604143	"extra spindle poles like 1 (S. cerevisiae)"			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.5262G>T	chr12.hg19:g.53684151G>T		55.0	0.0		37.0	16.0	NM_012291		Silent	SNP	ENST00000257934.4	hg19	CCDS8852.1																																																																																			.	.		0.542	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		T	53684151	G	T	53684151	2	4	150	1	0	0	0	0	0	0	0	1	5255	1277	45	3		3	ESPL1	12	53684151	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	3296126	53684151	80167744	359	23083										
KIAA0748	9840	hgsc.bcm.edu	37	chr12	55356690	55356690	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gccccaaatcagagtcttgcTggaggaactgcttctcttct	9	12	4	1	rs61733026	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:55356690T>A	ENST00000449076.1	-	9	1124	c.992A>T	c.(991-993)cAg>cTg	p.Q331L	TESPA1_ENST00000524959.1_5'Flank|TESPA1_ENST00000532804.1_Missense_Mutation_p.Q193L|TESPA1_ENST00000316577.8_Missense_Mutation_p.Q331L|TESPA1_ENST00000524622.1_Missense_Mutation_p.Q193L|TESPA1_ENST00000531122.1_Missense_Mutation_p.Q193L	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	331					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)											AGAGTCTTGCTGGAGGAACTG	0.517																																					p.Q331L		Atlas-SNP	.											.	.	.	.	0			c.A992T						.						70	73	72					12																	55356690		1956	4151	6107	SO:0001583	missense	9840	exon9			TCTTGCTGGAGGA	AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"KIAA0748"	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.992A>T	chr12.hg19:g.55356690T>A	ENSP00000400892:p.Gln331Leu	93.0	0.0		71.0	16.0	NM_001098815	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Missense_Mutation	SNP	ENST00000449076.1	hg19	CCDS44913.1	.	.	.	.	.	.	.	.	.	.	T	18.40	3.615536	0.66672	.	.	ENSG00000135426	ENST00000524622;ENST00000532804;ENST00000449076;ENST00000316577;ENST00000531122	T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01	4.96	4.96	0.65561	.	0.378758	0.22809	N	0.055364	T	0.49474	0.1559	L	0.34521	1.04	0.29542	N	0.851962	P	0.36535	0.557	B	0.33890	0.172	T	0.57802	-0.7748	10	0.72032	D	0.01	-0.5228	11.2201	0.48848	0.0:0.0:0.0:1.0	.	331	A2RU30	K0748_HUMAN	L	193;193;331;331;193	ENSP00000435622:Q193L;ENSP00000432030:Q193L;ENSP00000400892:Q331L;ENSP00000312679:Q331L;ENSP00000433098:Q193L	ENSP00000312679:Q331L	Q	-	2	0	KIAA0748	53642957	.	.	0.327000	0.25402	0.631000	0.37964	.	.	2.213000	0.71641	0.533000	0.62120	CAG	.	T|0.992;C|0.008		0.517	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815		A	55356690	T	A	55356690	3	1	150	1	0	0	0	0	1	0	0	0	8199	1580	55	4	581	4	KIAA0748	12	55356690	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1672539	55356690	78495205	360	23084										
KIAA0748	9840	hgsc.bcm.edu	37	chr12	55357002	55357002	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggcatcagcagtgacagccAgtgtttgcacctgcttaaac	10	11	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:55357002A>G	ENST00000449076.1	-	9	812	c.680T>C	c.(679-681)cTg>cCg	p.L227P	TESPA1_ENST00000524959.1_5'UTR|TESPA1_ENST00000532804.1_Missense_Mutation_p.L89P|TESPA1_ENST00000316577.8_Missense_Mutation_p.L227P|TESPA1_ENST00000524622.1_Missense_Mutation_p.L89P|TESPA1_ENST00000531122.1_Missense_Mutation_p.L89P	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	227					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)											AGTGACAGCCAGTGTTTGCAC	0.463																																					p.L227P		Atlas-SNP	.											.	.	.	.	0			c.T680C						.						67	71	69					12																	55357002		1986	4174	6160	SO:0001583	missense	9840	exon9			ACAGCCAGTGTTT	AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"KIAA0748"	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.680T>C	chr12.hg19:g.55357002A>G	ENSP00000400892:p.Leu227Pro	55.0	0.0		51.0	8.0	NM_001098815	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Missense_Mutation	SNP	ENST00000449076.1	hg19	CCDS44913.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.164183	0.78339	.	.	ENSG00000135426	ENST00000524622;ENST00000532804;ENST00000449076;ENST00000316577;ENST00000531122	T;T;T;T;T	0.76060	-0.73;-0.73;-0.99;-0.99;-0.73	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000002	D	0.82462	0.5042	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84048	0.0368	10	0.87932	D	0	-23.7939	12.2763	0.54737	1.0:0.0:0.0:0.0	.	227	A2RU30	K0748_HUMAN	P	89;89;227;227;89	ENSP00000435622:L89P;ENSP00000432030:L89P;ENSP00000400892:L227P;ENSP00000312679:L227P;ENSP00000433098:L89P	ENSP00000312679:L227P	L	-	2	0	KIAA0748	53643269	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.754000	0.85163	2.213000	0.71641	0.533000	0.62120	CTG	.	.		0.463	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815		G	55357002	A	G	55357002	3	3	150	1	0	0	0	0	1	0	0	0	8199	188	7	2	893	2	KIAA0748	12	55357002	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	312	55357002	78494893	361	23085										
OR6C68	403284	hgsc.bcm.edu	37	chr12	55886887	55886887	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttttctacctgttcttcacaTattactgtggtttccatcac	4	11	4	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:55886887T>C	ENST00000548615.1	+	1	726	c.726T>C	c.(724-726)caT>caC	p.H242H	RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|OR6C68_ENST00000379662.1_Silent_p.H247H	NM_001005519.2	NP_001005519.2	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C, member 68	242						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15						GTTCTTCACATATTACTGTGG	0.348																																					p.H242H		Atlas-SNP	.											.	OR6C68	36	.	0			c.T726C						.						86	85	86					12																	55886887		2203	4300	6503	SO:0001819	synonymous_variant	403284	exon1			TTCACATATTACT		CCDS31826.1, CCDS31826.2	12q13.2	2013-09-23			ENSG00000205327	ENSG00000205327		"GPCR / Class A : Olfactory receptors"	31297	protein-coding gene	gene with protein product							Standard	NM_001005519		Approved		uc031qhq.1	A6NDL8	OTTHUMG00000169958	ENST00000548615.1:c.726T>C	chr12.hg19:g.55886887T>C		90.0	0.0		62.0	30.0	NM_001005519		Silent	SNP	ENST00000548615.1	hg19	CCDS31826.2																																																																																			.	.		0.348	OR6C68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406677.1			C	55886887	T	C	55886887	2	2	150	1	0	0	0	0	0	0	0	1	11205	1403	49	2		2	OR6C68	12	55886887	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	529885	55886887	77965008	362	23086										
WIF1	11197	hgsc.bcm.edu	37	chr12	65514841	65514841	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tacctatgagtactcttgccTggtgagcatcgatccatagg	10	10	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:65514841T>A	ENST00000286574.4	-	1	505	c.131A>T	c.(130-132)cAg>cTg	p.Q44L		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	44	WIF. {ECO:0000255|PROSITE- ProRule:PRU00222}.				multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		TACTCTTGCCTGGTGAGCATC	0.622			T	HMGA2	pleomorphic salivary gland adenoma																																p.Q44L	Esophageal Squamous(148;1595 1816 48559 49439 49664)	Atlas-SNP	.		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	WIF1	96	.	0			c.A131T						.						26	24	25					12																	65514841		2071	4035	6106	SO:0001583	missense	11197	exon1			CTTGCCTGGTGAG	AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.131A>T	chr12.hg19:g.65514841T>A	ENSP00000286574:p.Gln44Leu	147.0	0.0		129.0	29.0	NM_007191	Q6UXI1|Q8WVG4	Missense_Mutation	SNP	ENST00000286574.4	hg19	CCDS8971.1	.	.	.	.	.	.	.	.	.	.	T	11.47	1.647258	0.29246	.	.	ENSG00000156076	ENST00000286574	T	0.50548	0.74	3.7	3.7	0.42460	WIF domain (3);	0.133760	0.50627	D	0.000109	T	0.60104	0.2243	L	0.55990	1.75	0.58432	D	0.999996	D	0.59357	0.985	D	0.69654	0.965	T	0.59511	-0.7441	9	.	.	.	.	12.5732	0.56349	0.0:0.0:0.0:1.0	.	44	Q9Y5W5	WIF1_HUMAN	L	44	ENSP00000286574:Q44L	.	Q	-	2	0	WIF1	63801108	1.000000	0.71417	1.000000	0.80357	0.156000	0.22039	5.328000	0.65887	1.932000	0.55993	0.402000	0.26972	CAG	.	.		0.622	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2			A	65514841	T	A	65514841	3	1	150	1	0	0	0	0	1	0	0	0	17381	1580	55	4	1048	4	WIF1	12	65514841	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	9627954	65514841	68337054	363	23087										
MDM1	56890	hgsc.bcm.edu	37	chr12	68715351	68715352	+	Frame_Shift_Ins	INS	-	-	T													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcttccttttaggctggtgINStaagtcttttaattccatct					rs148344415		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:68715351_68715352insT	ENST00000303145.7	-	6	944_945	c.858_859insA	c.(856-861)ttacacfs	p.H287fs	MDM1_ENST00000540418.1_Frame_Shift_Ins_p.H7fs|MDM1_ENST00000411698.2_Frame_Shift_Ins_p.H242fs	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	287					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		TTAGGCTGGTGTAAGTCTTTTA	0.307																																					p.H287fs		Atlas-Indel,Pindel	.											.	MDM1	74	.	0			c.859_860insA						.																																			SO:0001589	frameshift_variant	56890	exon6			.	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.859dupA	chr12.hg19:g.68715352_68715352dupT	ENSP00000302537:p.His287fs	108.0	0.0		93.0	23.0	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Frame_Shift_Ins	INS	ENST00000303145.7	hg19	CCDS8983.1																																																																																			.	.		0.307	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		T	68715352	-	T	68715351	7	5	150	1	0	1	1	0	0	0	0	0	9421	1377	48	0	1321	0	MDM1	12	68715351	Frame_Shift_Ins	INS	-	TCGA-DD-AAC8-01A-11D-A40R-10	3200510	68715351	65136544	364	23088										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70983958	70983958	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gggggcgaccagctcactacAagagacctcatcctgccatt	10	14	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:70983958A>T	ENST00000261266.5	-	6	1211	c.1182T>A	c.(1180-1182)ctT>ctA	p.L394L	PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000538708.1_Silent_p.L394L|PTPRB_ENST00000334414.6_Silent_p.L612L|PTPRB_ENST00000551525.1_Silent_p.L611L|PTPRB_ENST00000451516.2_Intron|PTPRB_ENST00000550857.1_Intron|PTPRB_ENST00000550358.1_Silent_p.L612L	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	394	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			AGCTCACTACAAGAGACCTCA	0.468											OREG0021990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L612L		Atlas-SNP	.											.	PTPRB	676	.	0			c.T1836A						.						106	108	108					12																	70983958		1952	4162	6114	SO:0001819	synonymous_variant	5787	exon8			CACTACAAGAGAC	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1182T>A	chr12.hg19:g.70983958A>T		114.0	0.0	1126	110.0	32.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.468	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70983958	A	T	70983958	2	4	150	1	0	0	0	0	0	0	0	1	12811	117	5	4		4	PTPRB	12	70983958	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2268607	70983958	62867937	365	23089										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80655748	80655748	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcattgtctttgctttctaGttctccatcaggcatgatag	8	9	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:80655748G>C	ENST00000547103.1	+	18	1868		c.e18-1		OTOGL_ENST00000458043.2_Splice_Site			Q3ZCN5	OTOGL_HUMAN	otogelin-like						L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TTGCTTTCTAGTTCTCCATCA	0.378																																					.		Atlas-SNP	.											.	OTOGL	235	.	0			c.1863-1G>C						.						119	118	118					12																	80655748		1931	4124	6055	SO:0001630	splice_region_variant	283310	exon18			TTTCTAGTTCTCC	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.1863-1G>C	chr12.hg19:g.80655748G>C		65.0	0.0		72.0	16.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Splice_Site	SNP	ENST00000547103.1	hg19		.	.	.	.	.	.	.	.	.	.	G	22.4	4.287785	0.80803	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8686	0.92303	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	OTOGL	79179879	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.069000	0.93967	2.770000	0.95276	0.655000	0.94253	.	.	.		0.378	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	Intron	C	80655748	G	C	80655748	5	2	150	1	0	0	0	0	0	0	1	0	1709	1043	36	4	1932	4	C12orf64	12	80655748	Splice_Site	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	9671790	80655748	53196147	366	23090										
SLC5A8	160728	hgsc.bcm.edu	37	chr12	101560282	101560282	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aattcaatacctttgaacatTgtatatttgaaaaacactag	4	6	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:101560282T>A	ENST00000536262.2	-	12	2074	c.1516A>T	c.(1516-1518)Aat>Tat	p.N506Y		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTTTGAACATTGTATATTTGA	0.323																																					p.N506Y	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.A1516T						.						82	81	81					12																	101560282		2203	4300	6503	SO:0001583	missense	160728	exon12			GAACATTGTATAT	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1516A>T	chr12.hg19:g.101560282T>A	ENSP00000445340:p.Asn506Tyr	99.0	0.0		47.0	17.0	NM_145913		Missense_Mutation	SNP	ENST00000536262.2	hg19	CCDS9080.1	.	.	.	.	.	.	.	.	.	.	T	9.221	1.033262	0.19590	.	.	ENSG00000256870	ENST00000536262	T	0.63744	-0.06	5.39	2.98	0.34508	.	0.727114	0.13642	N	0.372866	T	0.52108	0.1714	L	0.47190	1.495	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.46303	-0.9201	10	0.54805	T	0.06	.	7.0512	0.25073	0.0:0.2636:0.0:0.7364	.	506	Q8N695	SC5A8_HUMAN	Y	506	ENSP00000445340:N506Y	ENSP00000445340:N506Y	N	-	1	0	SLC5A8	100084413	0.000000	0.05858	0.001000	0.08648	0.028000	0.11728	0.041000	0.13927	0.341000	0.23771	0.533000	0.62120	AAT	.	.		0.323	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		A	101560282	T	A	101560282	3	1	150	1	0	0	0	0	1	0	0	0	14686	1812	63	4	332	4	SLC5A8	12	101560282	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	20904534	101560282	32291613	367	23091										
STAB2	55576	hgsc.bcm.edu	37	chr12	104071229	104071229	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gctttttcttttcctcctgcAggcagaatgcatcaaaactg	7	11	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:104071229A>T	ENST00000388887.2	+	25	2850		c.e25-1			NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TTCCTCCTGCAGGCAGAATGC	0.493																																					.		Atlas-SNP	.											.	STAB2	370	.	0			c.2647-2A>T						.						87	90	89					12																	104071229		2203	4300	6503	SO:0001630	splice_region_variant	55576	exon25			TCCTGCAGGCAGA	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.2647-1A>T	chr12.hg19:g.104071229A>T		61.0	0.0		39.0	13.0	NM_017564		Splice_Site	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	A	13.00	2.106841	0.37145	.	.	ENSG00000136011	ENST00000388887	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.903	0.70696	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	STAB2	102595359	1.000000	0.71417	0.990000	0.47175	0.072000	0.16883	8.312000	0.89976	2.174000	0.68829	0.533000	0.62120	.	.	.		0.493	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		Intron	T	104071229	A	T	104071229	5	4	150	1	0	0	0	0	0	0	1	0	15253	202	7	4	2743	4	STAB2	12	104071229	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2510947	104071229	29780666	368	23092										
CHST11	50515	hgsc.bcm.edu	37	chr12	105151144	105151144	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccagaagtacaacatctccTtccacaagcggtacggcacc	7	16	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:105151144T>A	ENST00000303694.5	+	3	1061	c.622T>A	c.(622-624)Ttc>Atc	p.F208I	CHST11_ENST00000549260.1_Missense_Mutation_p.F203I	NM_018413.5	NP_060883.1	Q9NPF2	CHSTB_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 11	208					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondrocyte development (GO:0002063)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|developmental growth (GO:0048589)|embryonic digit morphogenesis (GO:0042733)|embryonic viscerocranium morphogenesis (GO:0048703)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|polysaccharide localization (GO:0033037)|post-anal tail morphogenesis (GO:0036342)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)	18						CAACATCTCCTTCCACAAGCG	0.547																																					p.F208I		Atlas-SNP	.											.	CHST11	54	.	0			c.T622A						.						111	97	102					12																	105151144		2203	4300	6503	SO:0001583	missense	50515	exon3			ATCTCCTTCCACA	AB042326	CCDS9099.1, CCDS55878.1	12q23.3	2008-02-05				ENSG00000171310	2.8.2.5	"Sulfotransferases, membrane-bound"	17422	protein-coding gene	gene with protein product		610128				10781601	Standard	NM_018413		Approved	C4ST1, C4St-1, C4ST, HSA269537	uc001tkz.3	Q9NPF2	OTTHUMG00000169803	ENST00000303694.5:c.622T>A	chr12.hg19:g.105151144T>A	ENSP00000305725:p.Phe208Ile	159.0	0.0		90.0	31.0	NM_018413	A8K4F8|Q9NXY6|Q9NY36	Missense_Mutation	SNP	ENST00000303694.5	hg19	CCDS9099.1	.	.	.	.	.	.	.	.	.	.	T	31	5.070691	0.93950	.	.	ENSG00000171310	ENST00000549260;ENST00000303694	T;T	0.74632	-0.86;-0.86	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.89476	0.6726	M	0.93720	3.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.91761	0.5420	10	0.56958	D	0.05	-24.1475	15.4615	0.75359	0.0:0.0:0.0:1.0	.	203;208	Q9NPF2-2;Q9NPF2	.;CHSTB_HUMAN	I	203;208	ENSP00000450004:F203I;ENSP00000305725:F208I	ENSP00000305725:F208I	F	+	1	0	CHST11	103675274	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.065000	0.61736	0.533000	0.62120	TTC	.	.		0.547	CHST11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405960.2	NM_018413		A	105151144	T	A	105151144	3	1	150	1	0	0	0	0	1	0	0	0	3401	1609	56	4	632	4	CHST11	12	105151144	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1079915	105151144	28700751	369	23093										
MYO1H	283446	hgsc.bcm.edu	37	chr12	109876380	109876380	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctggcgtggggccctggctcGgaaggcaatccaaaggagaa	16	10	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:109876380G>A	ENST00000431443.2	+	22	2231	c.2231G>A	c.(2230-2232)cGg>cAg	p.R744Q	MYO1H_ENST00000310903.5_Missense_Mutation_p.R734Q	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	744	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						GCCCTGGCTCGGAAGGCAATC	0.512																																					p.R734Q		Atlas-SNP	.											.	MYO1H	98	.	0			c.G2201A						.						36	36	36					12																	109876380		1912	4118	6030	SO:0001583	missense	283446	exon22			TGGCTCGGAAGGC		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.2231G>A	chr12.hg19:g.109876380G>A	ENSP00000444076:p.Arg744Gln	70.0	0.0		45.0	14.0	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	hg19		.	.	.	.	.	.	.	.	.	.	G	14.50	2.553794	0.45487	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	T;T	0.76968	-1.06;-1.06	5.13	4.24	0.50183	.	.	.	.	.	T	0.58892	0.2154	N	0.08118	0	0.38082	D	0.93669	B	0.31209	0.313	B	0.32090	0.14	T	0.58934	-0.7548	9	0.29301	T	0.29	.	11.6434	0.51246	0.0878:0.0:0.9122:0.0	.	734	F5H3C6	.	Q	734;744	ENSP00000439182:R734Q;ENSP00000444076:R744Q	ENSP00000439182:R734Q	R	+	2	0	MYO1H	108360763	1.000000	0.71417	0.962000	0.40283	0.563000	0.35712	5.343000	0.65976	1.147000	0.42369	0.655000	0.94253	CGG	.	.		0.512	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		A	109876380	G	A	109876380	3	1	150	1	0	0	0	0	1	0	0	0	10084	1116	39	1	2287	1	MYO1H	12	109876380	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	4725236	109876380	23975515	370	23094										
UBE3B	89910	hgsc.bcm.edu	37	chr12	109921745	109921745	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tttgtattttcaagattgccAggaaactgctgttcctattc	7	8	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:109921745A>T	ENST00000342494.3	+	4	836	c.241A>T	c.(241-243)Agg>Tgg	p.R81W	UBE3B_ENST00000340074.5_Missense_Mutation_p.R81W|UBE3B_ENST00000540230.1_Missense_Mutation_p.R81W|UBE3B_ENST00000280774.5_Missense_Mutation_p.R81W|UBE3B_ENST00000537063.1_Missense_Mutation_p.R81W|UBE3B_ENST00000434735.2_Missense_Mutation_p.R81W|UBE3B_ENST00000536398.1_Missense_Mutation_p.R81W	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	81					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						CAAGATTGCCAGGAAACTGCT	0.328																																					p.R81W		Atlas-SNP	.											.	UBE3B	116	.	0			c.A241T						.						110	112	111					12																	109921745		2203	4300	6503	SO:0001583	missense	89910	exon4			ATTGCCAGGAAAC	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.241A>T	chr12.hg19:g.109921745A>T	ENSP00000340596:p.Arg81Trp	118.0	0.0		74.0	29.0	NM_001270451	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	ENST00000342494.3	hg19	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.519914	0.64634	.	.	ENSG00000151148	ENST00000434735;ENST00000280774;ENST00000536398;ENST00000539599;ENST00000342494;ENST00000340074;ENST00000540230;ENST00000537063	T;T;T;T;T;T;T;T	0.68624	1.9;1.9;-0.34;1.9;1.9;-0.34;-0.34;1.9	5.35	2.92	0.33932	.	0.000000	0.85682	D	0.000000	T	0.77336	0.4115	M	0.61703	1.905	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	P;D;D	0.78314	0.864;0.991;0.991	T	0.79310	-0.1856	10	0.87932	D	0	-0.0163	12.1142	0.53856	0.5304:0.4696:0.0:0.0	.	81;81;81	Q7Z3V4;Q7Z3V4-3;F5H6D6	UBE3B_HUMAN;.;.	W	81	ENSP00000391529:R81W;ENSP00000280774:R81W;ENSP00000440585:R81W;ENSP00000443131:R81W;ENSP00000340596:R81W;ENSP00000342614:R81W;ENSP00000443565:R81W;ENSP00000437694:R81W	ENSP00000280774:R81W	R	+	1	2	UBE3B	108406128	0.979000	0.34478	1.000000	0.80357	0.678000	0.39670	0.556000	0.23438	1.075000	0.40932	0.528000	0.53228	AGG	.	.		0.328	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		T	109921745	A	T	109921745	3	4	150	1	0	0	0	0	1	0	0	0	16895	179	7	4	247	4	UBE3B	12	109921745	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	45365	109921745	23930150	371	23095										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124298165	124298165	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtcagcaaaagaggagctctAtaatctccatgaagagatgg	11	7	3	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:124298165A>T	ENST00000409039.3	+	19	3270	c.3245A>T	c.(3244-3246)tAt>tTt	p.Y1082F		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1082	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GAGGAGCTCTATAATCTCCAT	0.433																																					p.Y1082F		Atlas-SNP	.											.	DNAH10	888	.	0			c.A3245T						.						58	53	54					12																	124298165		2203	4300	6503	SO:0001583	missense	196385	exon19			AGCTCTATAATCT	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.3245A>T	chr12.hg19:g.124298165A>T	ENSP00000386770:p.Tyr1082Phe	117.0	0.0		74.0	30.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	15.53	2.859731	0.51376	.	.	ENSG00000197653	ENST00000409039	T	0.20881	2.04	5.77	0.0859	0.14443	.	2.497630	0.01623	N	0.023112	T	0.11110	0.0271	N	0.03177	-0.4	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.0	T	0.27806	-1.0063	10	0.46703	T	0.11	.	7.4994	0.27509	0.5406:0.0:0.0706:0.3887	.	1082;957;1082	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	F	1082	ENSP00000386770:Y1082F	ENSP00000386770:Y1082F	Y	+	2	0	DNAH10	122864118	0.000000	0.05858	0.000000	0.03702	0.780000	0.44128	0.552000	0.23376	0.084000	0.17077	0.460000	0.39030	TAT	.	.		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124298165	A	T	124298165	3	4	150	1	0	0	0	0	1	0	0	0	4600	449	16	4	3319	4	DNAH10	12	124298165	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	14376420	124298165	9553730	372	23096										
EP400	57634	hgsc.bcm.edu	37	chr12	132464277	132464277	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcctggtagcaggggccggAagcacagtagagacggacct	16	10	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:132464277A>T	ENST00000333577.4	+	4	1591	c.1482A>T	c.(1480-1482)ggA>ggT	p.G494G	EP400_ENST00000330386.6_Silent_p.G458G|EP400_ENST00000389561.2_Silent_p.G458G|EP400_ENST00000332482.4_Silent_p.G457G|EP400_ENST00000389562.2_Silent_p.G457G			Q96L91	EP400_HUMAN	E1A binding protein p400	494					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CAGGGGCCGGAAGCACAGTAG	0.552																																					p.G458G		Atlas-SNP	.											.	EP400	370	.	0			c.A1374T						.						55	54	54					12																	132464277		2203	4300	6503	SO:0001819	synonymous_variant	57634	exon3			GGCCGGAAGCACA	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.1482A>T	chr12.hg19:g.132464277A>T		295.0	0.0		177.0	66.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.		0.552	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		T	132464277	A	T	132464277	2	4	150	1	0	0	0	0	0	0	0	1	5151	233	9	4		4	EP400	12	132464277	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	8166112	132464277	1387618	373	23097										
POLE	5426	hgsc.bcm.edu	37	chr12	133219131	133219131	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcgacaggcaggtgtccaggTtgaggtagtgacggatcatg	17	7	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr12:133219131T>A	ENST00000320574.5	-	37	4956	c.4913A>T	c.(4912-4914)aAc>aTc	p.N1638I	POLE_ENST00000535270.1_Missense_Mutation_p.N1611I|POLE_ENST00000434528.3_5'Flank	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1638					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GGTGTCCAGGTTGAGGTAGTG	0.612								DNA polymerases (catalytic subunits)																													p.N1638I		Atlas-SNP	.											.	POLE	416	.	0			c.A4913T						.						53	50	51					12																	133219131		2203	4300	6503	SO:0001583	missense	5426	exon37			TCCAGGTTGAGGT		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.4913A>T	chr12.hg19:g.133219131T>A	ENSP00000322570:p.Asn1638Ile	71.0	0.0		41.0	13.0	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	hg19	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.661957	0.88251	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270	T;T;T	0.23754	1.89;1.89;1.89	5.51	5.51	0.81932	DNA polymerase epsilon, catalytic subunit A, C-terminal (1);	0.167222	0.64402	D	0.000004	T	0.45895	0.1365	M	0.72894	2.215	0.80722	D	1	B	0.32526	0.374	P	0.48921	0.595	T	0.42207	-0.9465	10	0.51188	T	0.08	.	15.6353	0.76946	0.0:0.0:0.0:1.0	.	1638	Q07864	DPOE1_HUMAN	I	1638;1649;1611	ENSP00000322570:N1638I;ENSP00000406383:N1649I;ENSP00000445753:N1611I	ENSP00000322570:N1638I	N	-	2	0	POLE	131729204	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.929000	0.56514	2.101000	0.63845	0.533000	0.62120	AAC	.	.		0.612	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		A	133219131	T	A	133219131	3	1	150	1	0	0	0	0	1	0	0	0	12205	1725	60	4	1999	4	POLE	12	133219131	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	754854	133219131	632764	374	23098										
TUBA3C	7278	hgsc.bcm.edu	37	chr13	19752513	19752513	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctgggtggaagagctgcctaTaggttcctgtgcgcacttca	13	10	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr13:19752513T>G	ENST00000400113.3	-	3	352	c.248A>C	c.(247-249)tAt>tCt	p.Y83S		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	83					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		GAGCTGCCTATAGGTTCCTGT	0.498																																					p.Y83S		Atlas-SNP	.											.	TUBA3C	166	.	0			c.A248C						.						119	104	109					13																	19752513		2203	4300	6503	SO:0001583	missense	7278	exon3			TGCCTATAGGTTC	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"Tubulins"	12408	protein-coding gene	gene with protein product		602528	"tubulin, alpha 2"	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.248A>C	chr13.hg19:g.19752513T>G	ENSP00000382982:p.Tyr83Ser	131.0	0.0		69.0	26.0	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000400113.3	hg19	CCDS9284.1	.	.	.	.	.	.	.	.	.	.	t	13.09	2.133510	0.37630	.	.	ENSG00000198033	ENST00000400113;ENST00000360801	T	0.68903	-0.36	1.53	1.53	0.23141	.	0.000000	0.44483	U	0.000443	T	0.69672	0.3137	.	.	.	0.42739	D	0.993739	.	.	.	.	.	.	T	0.70839	-0.4763	7	0.87932	D	0	.	7.129	0.25488	0.0:0.0:0.0:1.0	.	.	.	.	S	83	ENSP00000382982:Y83S	ENSP00000354037:Y83S	Y	-	2	0	TUBA3C	18650513	1.000000	0.71417	0.997000	0.53966	0.943000	0.58893	6.510000	0.73729	0.958000	0.37956	0.347000	0.21830	TAT	.	.		0.498	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001		G	19752513	T	G	19752513	3	3	150	1	0	0	0	0	1	0	0	0	16761	1406	49	5	1116	5	TUBA3C	13	19752513	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10		19752513	95417365	375	23099										
SKA3	221150	hgsc.bcm.edu	37	chr13	21734117	21734117	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtaccaaaggagagttggtaTattcggcatctaaaagacac	10	7	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr13:21734117T>A	ENST00000314759.5	-	6	963	c.839A>T	c.(838-840)tAt>tTt	p.Y280F	SKA3_ENST00000400018.3_Missense_Mutation_p.Y280F	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	280					chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AGAGTTGGTATATTCGGCATC	0.318																																					p.Y280F		Atlas-SNP	.											.	SKA3	76	.	0			c.A839T						.						127	136	133					13																	21734117		2203	4300	6503	SO:0001583	missense	221150	exon6			TTGGTATATTCGG	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 3"	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.839A>T	chr13.hg19:g.21734117T>A	ENSP00000319417:p.Tyr280Phe	101.0	0.0		43.0	20.0	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	hg19	CCDS31946.1	.	.	.	.	.	.	.	.	.	.	T	3.711	-0.059582	0.07317	.	.	ENSG00000165480	ENST00000314759;ENST00000400018	T;T	0.22743	1.94;1.94	5.52	-1.24	0.09435	.	0.860123	0.10544	N	0.662370	T	0.12263	0.0298	L	0.44542	1.39	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.14023	0.01;0.01	T	0.39210	-0.9625	10	0.12766	T	0.61	-1.5826	1.1999	0.01883	0.1452:0.2935:0.1506:0.4106	.	280;280	Q8IX90-3;Q8IX90	.;SKA3_HUMAN	F	280	ENSP00000319417:Y280F;ENSP00000382896:Y280F	ENSP00000319417:Y280F	Y	-	2	0	SKA3	20632117	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.998000	0.03701	-0.107000	0.12088	-0.301000	0.09380	TAT	.	.		0.318	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061		A	21734117	T	A	21734117	3	1	150	1	0	0	0	0	1	0	0	0	14369	1406	49	4	462	4	SKA3	13	21734117	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1981604	21734117	93435761	376	23100										
ATP12A	479	hgsc.bcm.edu	37	chr13	25283840	25283840	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggcctcatgcaagccctgggAgctttccttgtgtatttcac	10	12	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr13:25283840A>T	ENST00000381946.3	+	19	2804	c.2637A>T	c.(2635-2637)ggA>ggT	p.G879G	ATP12A_ENST00000218548.6_Silent_p.G885G			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	879					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		AAGCCCTGGGAGCTTTCCTTG	0.517																																					p.G885G	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.A2655T						.						160	162	161					13																	25283840		2203	4300	6503	SO:0001819	synonymous_variant	479	exon19			CCTGGGAGCTTTC	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2637A>T	chr13.hg19:g.25283840A>T		104.0	0.0		52.0	19.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	hg19	CCDS31948.1																																																																																			.	.		0.517	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25283840	A	T	25283840	2	4	150	1	0	0	0	0	0	0	0	1	1122	291	11	4		4	ATP12A	13	25283840	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3549723	25283840	89886038	377	23101										
GPR12	2835	hgsc.bcm.edu	37	chr13	27333221	27333221	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atagccagggtggagaccccTttccgggtggtcacatagtg	14	10	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr13:27333221T>A	ENST00000381436.2	-	1	1206	c.744A>T	c.(742-744)aaA>aaT	p.K248N	GPR12_ENST00000405846.3_Missense_Mutation_p.K248N			P47775	GPR12_HUMAN	G protein-coupled receptor 12	248					cellular calcium ion homeostasis (GO:0006874)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			endometrium(7)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		TGGAGACCCCTTTCCGGGTGG	0.547																																					p.K248N		Atlas-SNP	.											.	GPR12	67	.	0			c.A744T						.						66	65	65					13																	27333221		2203	4300	6503	SO:0001583	missense	2835	exon2			GACCCCTTTCCGG	U18548	CCDS9319.1	13q12	2014-06-12			ENSG00000132975	ENSG00000132975		"GPCR / Class A : Orphans"	4466	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 84"	600752				8262253, 8530049	Standard	NM_005288		Approved	GPCR21, PPP1R84	uc010aal.3	P47775	OTTHUMG00000016620	ENST00000381436.2:c.744A>T	chr13.hg19:g.27333221T>A	ENSP00000370844:p.Lys248Asn	89.0	0.0		72.0	30.0	NM_005288	Q5T8P3	Missense_Mutation	SNP	ENST00000381436.2	hg19	CCDS9319.1	.	.	.	.	.	.	.	.	.	.	T	17.51	3.406464	0.62399	.	.	ENSG00000132975	ENST00000405846;ENST00000381436	T;T	0.42900	0.96;0.96	5.42	-2.85	0.05734	GPCR, rhodopsin-like superfamily (1);	0.045487	0.85682	D	0.000000	T	0.63954	0.2555	M	0.89904	3.07	0.48830	D	0.99971	D	0.89917	1.0	D	0.79108	0.992	T	0.68010	-0.5522	10	0.66056	D	0.02	.	11.2008	0.48741	0.0:0.3554:0.0:0.6446	.	248	P47775	GPR12_HUMAN	N	248	ENSP00000384932:K248N;ENSP00000370844:K248N	ENSP00000370844:K248N	K	-	3	2	GPR12	26231221	1.000000	0.71417	0.957000	0.39632	0.814000	0.46013	0.830000	0.27462	-0.465000	0.06953	-0.441000	0.05720	AAA	.	.		0.547	GPR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044257.2			A	27333221	T	A	27333221	3	1	150	1	0	0	0	0	1	0	0	0	6643	1606	56	4	264	4	GPR12	13	27333221	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2049381	27333221	87836657	378	23102										
CDX2	1045	hgsc.bcm.edu	37	chr13	28542904	28542904	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gccgcggcgcctccgggcgcGtagccattccagtcctcccg	13	19	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr13:28542904G>A	ENST00000381020.7	-	1	2372	c.240C>T	c.(238-240)taC>taT	p.Y80Y	CDX2_ENST00000548877.1_5'Flank	NM_001265.4	NP_001256.3	Q99626	CDX2_HUMAN	caudal type homeobox 2	80					anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|endosome to lysosome transport (GO:0008333)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|labyrinthine layer development (GO:0060711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|large_intestine(1)|lung(6)	9	all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155)	Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199)		ctccgggcgcgTAGCCATTCC	0.746			T	ETV6	AML																																p.Y80Y		Atlas-SNP	.		Dom	yes		13	13q12.3	1045	caudal type homeo box transcription factor 2		L	.	CDX2	30	.	0			c.C240T						.						7	12	11					13																	28542904		1851	3617	5468	SO:0001819	synonymous_variant	1045	exon1			GGGCGCGTAGCCA	Y13709	CCDS9328.1	13q12.2	2012-03-09	2007-07-09		ENSG00000165556	ENSG00000165556		"Homeoboxes / ANTP class : HOXL subclass"	1806	protein-coding gene	gene with protein product		600297	"caudal type homeo box transcription factor 2"	CDX3		7698771	Standard	NM_001265		Approved		uc001urv.4	Q99626	OTTHUMG00000016640	ENST00000381020.7:c.240C>T	chr13.hg19:g.28542904G>A		54.0	0.0		43.0	22.0	NM_001265	O00503|Q5VTU7|Q969L8|Q9UD92	Silent	SNP	ENST00000381020.7	hg19	CCDS9328.1																																																																																			.	.		0.746	CDX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044312.5			A	28542904	G	A	28542904	2	1	150	1	0	0	0	0	0	0	0	1	3185	1140	40	1		1	CDX2	13	28542904	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	1209683	28542904	86626974	379	23103										
PDS5B	23047	hgsc.bcm.edu	37	chr13	33320210	33320210	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgaaatcatcacattagaacAatatcagctatgtgcattag	6	7	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr13:33320210A>T	ENST00000315596.10	+	24	2894	c.2708A>T	c.(2707-2709)cAa>cTa	p.Q903L		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	903					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		ACATTAGAACAATATCAGCTA	0.403																																					p.Q903L		Atlas-SNP	.											.	PDS5B	141	.	0			c.A2708T						.						133	127	129					13																	33320210		1948	4154	6102	SO:0001583	missense	23047	exon24			TAGAACAATATCA	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"androgen-induced proliferation inhibitor"	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.2708A>T	chr13.hg19:g.33320210A>T	ENSP00000313851:p.Gln903Leu	76.0	0.0		47.0	15.0	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	hg19	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.918925	0.92249	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	5.92	5.92	0.95590	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77558	0.4148	M	0.74881	2.28	0.80722	D	1	D	0.65815	0.995	D	0.71414	0.973	T	0.74765	-0.3554	9	0.23891	T	0.37	-12.8905	16.3604	0.83263	1.0:0.0:0.0:0.0	.	903	Q9NTI5	PDS5B_HUMAN	L	903	.	ENSP00000313851:Q903L	Q	+	2	0	PDS5B	32218210	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	9.233000	0.95337	2.260000	0.74910	0.528000	0.53228	CAA	.	.		0.403	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		T	33320210	A	T	33320210	3	4	150	1	0	0	0	0	1	0	0	0	11701	130	5	4	2798	4	PDS5B	13	33320210	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	4777306	33320210	81849668	380	23104										
C13orf30	144809	hgsc.bcm.edu	37	chr13	43360937	43360937	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagcgctacttttacagcatTatgaggatttacaactccag	7	10	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr13:43360937T>A	ENST00000537894.1	+	3	261	c.138T>A	c.(136-138)atT>atA	p.I46I	FAM216B_ENST00000313851.1_Silent_p.I46I	NM_182508.2	NP_872314.1	Q8N7L0	F216B_HUMAN	family with sequence similarity 216, member B	46																	TTTACAGCATTATGAGGATTT	0.493																																					p.I46I		Atlas-SNP	.											.	.	.	.	0			c.T138A						.						139	136	137					13																	43360937		2203	4300	6503	SO:0001819	synonymous_variant	144809	exon3			CAGCATTATGAGG	AK098238	CCDS9386.1	13q14.11	2012-02-07	2012-02-07	2012-02-07	ENSG00000179813	ENSG00000179813			26883	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 30"	C13orf30			Standard	NM_182508		Approved	FLJ40919	uc010tfk.2	Q8N7L0	OTTHUMG00000016809	ENST00000537894.1:c.138T>A	chr13.hg19:g.43360937T>A		103.0	0.0		49.0	15.0	NM_182508	B1ALI3	Silent	SNP	ENST00000537894.1	hg19	CCDS9386.1																																																																																			.	.		0.493	FAM216B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044705.2	NM_182508		A	43360937	T	A	43360937	2	1	150	1	0	0	0	0	0	0	0	1	1727	1742	61	4		4	C13orf30	13	43360937	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	10040727	43360937	71808941	381	23105										
TSC22D1	8848	hgsc.bcm.edu	37	chr13	45148297	45148297	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acatggcctggggccatctgTgtagaaaccattggttgctg	13	9	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr13:45148297T>A	ENST00000458659.2	-	1	2404	c.1914A>T	c.(1912-1914)acA>acT	p.T638T	TSC22D1_ENST00000501704.2_Intron|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	638	Gln-rich.				negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		GGGCCATCTGTGTAGAAACCA	0.507																																					p.T638T		Atlas-SNP	.											.	TSC22D1	88	.	0			c.A1914T						.						118	114	115					13																	45148297		2203	4300	6503	SO:0001819	synonymous_variant	8848	exon1			CATCTGTGTAGAA	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"transforming growth factor beta 1 induced transcript 4"	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.1914A>T	chr13.hg19:g.45148297T>A		52.0	0.0		44.0	10.0	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Silent	SNP	ENST00000458659.2	hg19	CCDS31966.1																																																																																			.	.		0.507	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		A	45148297	T	A	45148297	2	1	150	1	0	0	0	0	0	0	0	1	16622	1683	59	4		4	TSC22D1	13	45148297	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1787360	45148297	70021581	382	23106										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77755971	77755971	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcaatcgggaagatggaagtCagcttaacagacgtgtgaca	13	7	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr13:77755971C>A	ENST00000544440.2	-	33	4709	c.4692G>T	c.(4690-4692)ctG>ctT	p.L1564L	MYCBP2_ENST00000407578.2_Silent_p.L1602L|MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Silent_p.L1564L					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		AGATGGAAGTCAGCTTAACAG	0.398																																					p.L1602L		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.G4806T						.						132	115	121					13																	77755971		2203	4300	6503	SO:0001819	synonymous_variant	23077	exon33			GGAAGTCAGCTTA	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.4692G>T	chr13.hg19:g.77755971C>A		88.0	0.0		78.0	55.0	NM_015057		Silent	SNP	ENST00000544440.2	hg19																																																																																				.	.		0.398	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		A	77755971	C	A	77755971	2	1	150	1	0	0	0	0	0	0	0	1	10027	813	29	3		3	MYCBP2	13	77755971	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	32607674	77755971	37413907	383	23107										
MYO16	23026	hgsc.bcm.edu	37	chr13	109535531	109535531	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcggcctcagtgtttcatccTcaggtgagtcctcctcaacc	9	15	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr13:109535531T>A	ENST00000357550.2	+	12	1525	c.1484T>A	c.(1483-1485)cTc>cAc	p.L495H	MYO16_ENST00000251041.5_Missense_Mutation_p.L495H|MYO16_ENST00000356711.2_Missense_Mutation_p.L495H|MYO16_ENST00000457511.2_5'Flank	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TGTTTCATCCTCAGGTGAGTC	0.522																																					p.L517H		Atlas-SNP	.											.	MYO16	285	.	0			c.T1550A						.						125	117	120					13																	109535531		2203	4300	6503	SO:0001583	missense	23026	exon13			TCATCCTCAGGTG		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.1484T>A	chr13.hg19:g.109535531T>A	ENSP00000350160:p.Leu495His	55.0	0.0		39.0	13.0	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	hg19	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	T	19.61	3.859725	0.71834	.	.	ENSG00000041515	ENST00000356711;ENST00000397258;ENST00000357550;ENST00000251041;ENST00000375857	D;D;D	0.96365	-3.99;-3.99;-3.99	5.43	5.43	0.79202	Myosin head, motor domain (3);	0.000000	0.34025	U	0.004324	D	0.97766	0.9267	M	0.80982	2.52	0.80722	D	1	P;D	0.89917	0.892;1.0	P;D	0.77004	0.577;0.989	D	0.97922	1.0315	9	.	.	.	.	12.2147	0.54400	0.0:0.0:0.0:1.0	.	495;495	Q9Y6X6-2;Q9Y6X6	.;MYO16_HUMAN	H	495;495;495;495;283	ENSP00000349145:L495H;ENSP00000350160:L495H;ENSP00000251041:L495H	.	L	+	2	0	MYO16	108333532	1.000000	0.71417	0.997000	0.53966	0.744000	0.42396	6.358000	0.73055	2.195000	0.70347	0.529000	0.55759	CTC	.	.		0.522	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		A	109535531	T	A	109535531	3	1	150	1	0	0	0	0	1	0	0	0	10073	1551	54	4	1530	4	MYO16	13	109535531	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	31779560	109535531	5634347	384	23108										
OR5AU1	390445	hgsc.bcm.edu	37	chr14	21624103	21624103	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgaacacctggggctctgacTgggtttaattctgcctaagg	12	9	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:21624103T>A	ENST00000304418.3	-	1	119	c.82A>T	c.(82-84)Agt>Tgt	p.S28C		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(12)|pancreas(1)	21	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		GGGCTCTGACTGGGTTTAATT	0.478																																					p.S28C		Atlas-SNP	.											.	OR5AU1	46	.	0			c.A82T						.						143	138	140					14																	21624103		2203	4300	6503	SO:0001583	missense	390445	exon1			TCTGACTGGGTTT	AL157687	CCDS32042.1	14q11.2	2013-09-23			ENSG00000169327	ENSG00000169327		"GPCR / Class A : Olfactory receptors"	15362	protein-coding gene	gene with protein product							Standard	NM_001004731		Approved		uc010tlp.2	Q8NGC0	OTTHUMG00000170753	ENST00000304418.3:c.82A>T	chr14.hg19:g.21624103T>A	ENSP00000302057:p.Ser28Cys	113.0	0.0		112.0	27.0	NM_001004731	B2RP78|Q6IEU2|Q96R10	Missense_Mutation	SNP	ENST00000304418.3	hg19	CCDS32042.1	.	.	.	.	.	.	.	.	.	.	T	9.787	1.176908	0.21787	.	.	ENSG00000169327	ENST00000304418	T	0.00958	5.5	3.81	1.27	0.21489	.	.	.	.	.	T	0.00552	0.0018	N	0.08118	0	0.09310	N	1	P	0.47034	0.889	B	0.37550	0.253	T	0.53365	-0.8449	9	0.37606	T	0.19	.	4.6629	0.12652	0.0:0.1062:0.3958:0.498	.	28	Q8NGC0	O5AU1_HUMAN	C	28	ENSP00000302057:S28C	ENSP00000302057:S28C	S	-	1	0	OR5AU1	20693943	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.738000	0.04871	0.137000	0.18759	-0.619000	0.04042	AGT	.	.		0.478	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1			A	21624103	T	A	21624103	3	1	150	1	0	0	0	0	1	0	0	0	11156	1580	55	4	1009	4	OR5AU1	14	21624103	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10		21624103	85725437	385	23109										
MMP14	4323	hgsc.bcm.edu	37	chr14	23315040	23315040	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctgcccatcgggaggccggcCggatgaggggactgaggagg	20	10	0	2	rs202185020		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:23315040C>T	ENST00000311852.6	+	10	1802	c.1541C>T	c.(1540-1542)cCg>cTg	p.P514L	MMP14_ENST00000548162.1_Intron	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	514					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	GGAGGCCGGCCGGATGAGGGG	0.632																																					p.P514L		Atlas-SNP	.											.	MMP14	40	.	0			c.C1541T						.						59	69	65					14																	23315040		2203	4300	6503	SO:0001583	missense	4323	exon10			GCCGGCCGGATGA		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"membrane type 1 metalloprotease"	600754	"matrix metalloproteinase 14 (membrane-inserted)"			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.1541C>T	chr14.hg19:g.23315040C>T	ENSP00000308208:p.Pro514Leu	144.0	0.0		97.0	51.0	NM_004995	A8K5L0|Q6GSF3|Q92678	Missense_Mutation	SNP	ENST00000311852.6	hg19	CCDS9577.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427408	0.62733	.	.	ENSG00000157227	ENST00000311852	T	0.30714	1.52	4.52	4.52	0.55395	Peptidase M10A, matrix metallopeptidase, C-terminal (1);	0.724607	0.13465	N	0.385817	T	0.36276	0.0961	L	0.59436	1.845	0.51482	D	0.999928	P	0.49559	0.925	P	0.44623	0.455	T	0.16837	-1.0389	10	0.35671	T	0.21	.	15.0866	0.72158	0.0:1.0:0.0:0.0	.	514	P50281	MMP14_HUMAN	L	514	ENSP00000308208:P514L	ENSP00000308208:P514L	P	+	2	0	MMP14	22384880	.	.	0.892000	0.35008	0.878000	0.50629	.	.	2.226000	0.72624	0.305000	0.20034	CCG	.	.		0.632	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995		T	23315040	C	T	23315040	3	4	150	1	0	0	0	0	1	0	0	0	9662	652	23	1	1579	1	MMP14	14	23315040	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	1690937	23315040	84034500	386	23110										
SLC22A17	51310	hgsc.bcm.edu	37	chr14	23821009	23821009	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agccggaggcaaagcccaagAtgaagaggatctgctccagg	14	10	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:23821009A>T	ENST00000206544.8	-	2	659	c.323T>A	c.(322-324)aTc>aAc	p.I108N	SLC22A17_ENST00000474057.1_Intron|SLC22A17_ENST00000397267.1_Missense_Mutation_p.I108N|SLC22A17_ENST00000397260.3_Intron|SLC22A17_ENST00000354772.3_Missense_Mutation_p.I108N	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	108					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|vacuole (GO:0005773)	transmembrane signaling receptor activity (GO:0004888)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)		AAAGCCCAAGATGAAGAGGAT	0.642																																					p.I108N		Atlas-SNP	.											.	SLC22A17	32	.	0			c.T323A						.						76	63	68					14																	23821009		2203	4300	6503	SO:0001583	missense	51310	exon3			CCCAAGATGAAGA	AJ243653	CCDS9593.1, CCDS9594.2	14q11.2	2013-05-22	2008-01-11		ENSG00000092096	ENSG00000092096		"Solute carriers"	23095	protein-coding gene	gene with protein product	"neutrophil gelatinase-associated lipocalin receptor"	611461				16377569	Standard	NM_016609		Approved	BOCT, BOIT, NGALR	uc001wjl.3	Q8WUG5	OTTHUMG00000028740	ENST00000206544.8:c.323T>A	chr14.hg19:g.23821009A>T	ENSP00000206544:p.Ile108Asn	298.0	0.0		259.0	81.0	NM_016609	A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	Missense_Mutation	SNP	ENST00000206544.8	hg19	CCDS9593.1	.	.	.	.	.	.	.	.	.	.	A	19.78	3.891716	0.72524	.	.	ENSG00000092096	ENST00000354772;ENST00000206544;ENST00000397267	T;T;T	0.55588	0.51;0.51;0.51	3.67	3.67	0.42095	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.084250	0.45126	U	0.000385	T	0.42743	0.1216	N	0.04203	-0.255	0.47037	D	0.999295	D;D;P	0.64830	0.994;0.969;0.92	P;P;B	0.59889	0.865;0.558;0.304	T	0.34950	-0.9808	10	0.24483	T	0.36	-11.8441	11.428	0.50022	1.0:0.0:0.0:0.0	.	108;108;108	Q8WUG5-3;Q8WUG5-2;Q8WUG5	.;.;S22AH_HUMAN	N	108	ENSP00000346824:I108N;ENSP00000206544:I108N;ENSP00000380437:I108N	ENSP00000206544:I108N	I	-	2	0	SLC22A17	22890849	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.417000	0.80156	1.522000	0.49001	0.379000	0.24179	ATC	.	.		0.642	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157223.3	NM_020372		T	23821009	A	T	23821009	3	4	150	1	0	0	0	0	1	0	0	0	14463	333	12	4	1325	4	SLC22A17	14	23821009	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	505969	23821009	83528531	387	23111										
RNF31	55072	hgsc.bcm.edu	37	chr14	24620416	24620416	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gggcactgaggtgcctctgcAgtggttgcgctcagaactgc	15	11	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:24620416A>T	ENST00000324103.6	+	9	1885	c.1565A>T	c.(1564-1566)cAg>cTg	p.Q522L	RNF31_ENST00000559275.1_Missense_Mutation_p.Q371L|RNF31_ENST00000382687.3_Missense_Mutation_p.Q371L|RP11-468E2.4_ENST00000558468.1_5'Flank	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	522					CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		GTGCCTCTGCAGTGGTTGCGC	0.637																																					p.Q522L		Atlas-SNP	.											.	RNF31	95	.	0			c.A1565T						.						61	66	64					14																	24620416		2105	4228	6333	SO:0001583	missense	55072	exon9			CTCTGCAGTGGTT	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"RING-type (C3HC4) zinc fingers"	16031	protein-coding gene	gene with protein product	"HOIL-1-interacting protein"	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.1565A>T	chr14.hg19:g.24620416A>T	ENSP00000315112:p.Gln522Leu	28.0	0.0		28.0	13.0	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	hg19	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	A	10.60	1.394396	0.25205	.	.	ENSG00000092098	ENST00000324103;ENST00000382687	T;T	0.47177	0.86;0.85	5.16	4.02	0.46733	.	0.479529	0.22057	N	0.065222	T	0.34366	0.0895	L	0.44542	1.39	0.30922	N	0.727933	B;B	0.32467	0.255;0.372	B;B	0.30316	0.037;0.114	T	0.41963	-0.9479	10	0.52906	T	0.07	-6.0182	4.2939	0.10892	0.6536:0.1724:0.1739:0.0	.	522;371	Q96EP0;Q96EP0-3	RNF31_HUMAN;.	L	522;371	ENSP00000315112:Q522L;ENSP00000372134:Q371L	ENSP00000315112:Q522L	Q	+	2	0	RNF31	23690256	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.884000	0.48562	0.986000	0.38683	0.533000	0.62120	CAG	.	.		0.637	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		T	24620416	A	T	24620416	3	4	150	1	0	0	0	0	1	0	0	0	13502	188	7	4	1599	4	RNF31	14	24620416	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	799407	24620416	82729124	388	23112										
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24884806	24884806	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctgctgggggagaaccgccTgctcacccccgcggcctcca	12	19	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:24884806T>A	ENST00000382554.3	+	9	4169	c.3851T>A	c.(3850-3852)cTg>cAg	p.L1284Q		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1284					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GAGAACCGCCTGCTCACCCCC	0.612																																					p.L1284Q		Atlas-SNP	.											.	NYNRIN	120	.	0			c.T3851A						.						65	71	69					14																	24884806		2025	4160	6185	SO:0001583	missense	57523	exon9			ACCGCCTGCTCAC	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.3851T>A	chr14.hg19:g.24884806T>A	ENSP00000371994:p.Leu1284Gln	71.0	0.0		50.0	11.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	T	13.88	2.369276	0.42003	.	.	ENSG00000205978	ENST00000382554	T	0.12147	2.71	4.93	4.93	0.64822	.	.	.	.	.	T	0.19248	0.0462	N	0.24115	0.695	0.30264	N	0.792919	D	0.58620	0.983	P	0.56474	0.799	T	0.03043	-1.1079	9	0.87932	D	0	.	12.5824	0.56397	0.0:0.0:0.0:1.0	.	1284	Q9P2P1	NYNRI_HUMAN	Q	1284	ENSP00000371994:L1284Q	ENSP00000371994:L1284Q	L	+	2	0	NYNRIN	23954646	0.607000	0.26958	0.915000	0.36163	0.289000	0.27227	2.726000	0.47302	2.063000	0.61619	0.533000	0.62120	CTG	.	.		0.612	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			A	24884806	T	A	24884806	3	1	150	1	0	0	0	0	1	0	0	0	10805	1580	55	4	3881	4	NYNRIN	14	24884806	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	264390	24884806	82464734	389	23113										
SIX4	51804	hgsc.bcm.edu	37	chr14	61186827	61186827	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atggatataccattgctcacAatgtttgatgacatttttgg	8	6	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:61186827A>T	ENST00000216513.4	-	2	1259	c.1200T>A	c.(1198-1200)atT>atA	p.I400I		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	400					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		CATTGCTCACAATGTTTGATG	0.433																																					p.I400I		Atlas-SNP	.											.	SIX4	69	.	0			c.T1200A						.						128	102	111					14																	61186827		2203	4300	6503	SO:0001819	synonymous_variant	51804	exon2			GCTCACAATGTTT	AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"Homeoboxes / SINE class"	10890	protein-coding gene	gene with protein product		606342	"sine oculis homeobox (Drosophila) homolog 4", "sine oculis homeobox homolog 4 (Drosophila)"			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.1200T>A	chr14.hg19:g.61186827A>T		128.0	0.0		110.0	36.0	NM_017420	Q4QQH5|Q4V764	Silent	SNP	ENST00000216513.4	hg19	CCDS9749.2																																																																																			.	.		0.433	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			T	61186827	A	T	61186827	2	4	150	1	0	0	0	0	0	0	0	1	14364	126	5	4		4	SIX4	14	61186827	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	36302021	61186827	46162713	390	23114										
HIF1A	3091	hgsc.bcm.edu	37	chr14	62200973	62200973	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	caccaagaattctcaaccacAgtgcattgtatgtgtgaatt	7	9	1	2	rs367767967		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:62200973A>T	ENST00000337138.4	+	8	1263	c.998A>T	c.(997-999)cAg>cTg	p.Q333L	HIF1A_ENST00000394997.1_Missense_Mutation_p.Q334L|HIF1A_ENST00000323441.6_Missense_Mutation_p.Q333L|HIF1A_ENST00000539097.1_Missense_Mutation_p.Q357L|RP11-618G20.1_ENST00000555937.1_RNA|HIF1A_ENST00000557538.1_Missense_Mutation_p.Q274L|HIF1A-AS2_ENST00000554254.1_lincRNA	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	333	Interaction with TSGA10. {ECO:0000250}.|PAC.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	TCTCAACCACAGTGCATTGTA	0.373																																					p.Q357L		Atlas-SNP	.											.	HIF1A	120	.	0			c.A1070T						.						117	103	108					14																	62200973		2203	4300	6503	SO:0001583	missense	3091	exon8			AACCACAGTGCAT	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.998A>T	chr14.hg19:g.62200973A>T	ENSP00000338018:p.Gln333Leu	129.0	0.0		107.0	32.0	NM_001243084	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Missense_Mutation	SNP	ENST00000337138.4	hg19	CCDS9753.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.873165	0.91664	.	.	ENSG00000100644	ENST00000539494;ENST00000394988;ENST00000337138;ENST00000394997;ENST00000323441;ENST00000557538;ENST00000539097	T;T;T;T;T	0.19394	2.15;2.15;2.15;2.15;2.15	5.44	5.44	0.79542	PAS fold-3 (1);	0.000000	0.85682	D	0.000000	T	0.46092	0.1375	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.45323	-0.9269	10	0.87932	D	0	.	15.7835	0.78281	1.0:0.0:0.0:0.0	.	334;333;333	A8MYV6;D0VY79;Q16665	.;.;HIF1A_HUMAN	L	84;274;333;334;333;274;357	ENSP00000338018:Q333L;ENSP00000378446:Q334L;ENSP00000323326:Q333L;ENSP00000451696:Q274L;ENSP00000437955:Q357L	ENSP00000323326:Q333L	Q	+	2	0	HIF1A	61270726	1.000000	0.71417	0.928000	0.36995	0.989000	0.77384	9.287000	0.95975	2.185000	0.69588	0.455000	0.32223	CAG	.	.		0.373	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		T	62200973	A	T	62200973	3	4	150	1	0	0	0	0	1	0	0	0	7112	188	7	4	1028	4	HIF1A	14	62200973	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1014146	62200973	45148567	391	23115										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64408641	64408641	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aataccttccagtgtagaatCaatatagaacatgccttgac	6	9	1	3	rs575263745	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:64408641C>T	ENST00000344113.4	+	5	488	c.276C>T	c.(274-276)atC>atT	p.I92I	SYNE2_ENST00000358025.3_Silent_p.I92I|SYNE2_ENST00000356081.3_Silent_p.I92I|SYNE2_ENST00000341472.5_Silent_p.I92I|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.I92I	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	92	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGTGTAGAATCAATATAGAAC	0.318													C|||	2	0.000399361	0	0	5008	,	,		18319	0		0	False		,,,				2504	0.002				p.I92I		Atlas-SNP	.											.	SYNE2	577	.	0			c.C276T						.						86	82	83					14																	64408641		1804	4072	5876	SO:0001819	synonymous_variant	23224	exon5			TAGAATCAATATA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.276C>T	chr14.hg19:g.64408641C>T		77.0	0.0		45.0	16.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.318	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64408641	C	T	64408641	2	4	150	1	0	0	0	0	0	0	0	1	15461	816	29	3		3	SYNE2	14	64408641	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	2207668	64408641	42940899	392	23116										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64408680	64408680	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acattcctaagaaaccgatcAgtaagtataaatttttctta	4	7	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:64408680A>T	ENST00000344113.4	+	5	527	c.315A>T	c.(313-315)tcA>tcT	p.S105S	SYNE2_ENST00000358025.3_Splice_Site_p.S105S|SYNE2_ENST00000356081.3_Splice_Site_p.S105S|SYNE2_ENST00000341472.5_Splice_Site_p.S105S|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Splice_Site_p.S105S	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	105	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GAAACCGATCAGTAAGTATAA	0.333																																					p.S105S		Atlas-SNP	.											.	SYNE2	577	.	0			c.A315T						.						70	66	67					14																	64408680		1791	4061	5852	SO:0001630	splice_region_variant	23224	exon5			CCGATCAGTAAGT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.315+1A>T	chr14.hg19:g.64408680A>T		65.0	0.0		46.0	19.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.333	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	Silent	T	64408680	A	T	64408680	5	4	150	1	0	0	0	0	0	0	1	0	15461	202	7	4	329	4	SYNE2	14	64408680	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	39	64408680	42940860	393	23117										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68233158	68233158	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggcaatgcacaaggaggcgcTgggggcctggccggggtgga	21	9	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:68233158T>A	ENST00000347230.4	-	32	5935	c.5797A>T	c.(5797-5799)Agc>Tgc	p.S1933C	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.S1933C	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1933					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		AAGGAGGCGCTGGGGGCCTGG	0.602																																					p.S1933C		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A5797T						.						42	46	45					14																	68233158		2203	4300	6503	SO:0001583	missense	23503	exon32			AGGCGCTGGGGGC	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.5797A>T	chr14.hg19:g.68233158T>A	ENSP00000251119:p.Ser1933Cys	191.0	0.0		121.0	39.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.805897	0.90623	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.45276	1.08;0.9	5.71	5.71	0.89125	.	0.039141	0.85682	D	0.000000	T	0.65015	0.2651	M	0.76838	2.35	0.80722	D	1	D;D	0.76494	0.999;0.995	D;P	0.66497	0.944;0.816	T	0.69859	-0.5031	10	0.87932	D	0	-5.125	15.9832	0.80127	0.0:0.0:0.0:1.0	.	1933;1933	G3V2D8;Q68DK2	.;ZFY26_HUMAN	C	1933;1912;1933	ENSP00000251119:S1933C;ENSP00000450603:S1933C	ENSP00000251119:S1933C	S	-	1	0	ZFYVE26	67302911	1.000000	0.71417	0.980000	0.43619	0.945000	0.59286	7.992000	0.88273	2.184000	0.69523	0.454000	0.30748	AGC	.	.		0.602	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68233158	T	A	68233158	3	1	150	1	0	0	0	0	1	0	0	0	17683	1580	55	4	1866	4	ZFYVE26	14	68233158	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3824478	68233158	39116382	394	23118										
POMT2	29954	hgsc.bcm.edu	37	chr14	77767555	77767555	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	accagcaagactaacgccagTcaggctgagccagaaccacc	9	15	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:77767555T>A	ENST00000261534.4	-	6	896	c.694A>T	c.(694-696)Act>Tct	p.T232S	POMT2_ENST00000556880.1_5'Flank	NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	232						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		CTAACGCCAGTCAGGCTGAGC	0.522											OREG0022837	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T232S		Atlas-SNP	.											.	POMT2	47	.	0			c.A694T						.						90	83	86					14																	77767555		2203	4300	6503	SO:0001583	missense	29954	exon6			CGCCAGTCAGGCT	AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.694A>T	chr14.hg19:g.77767555T>A	ENSP00000261534:p.Thr232Ser	154.0	0.0	1178	91.0	29.0	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	hg19	CCDS9857.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.494906	0.85069	.	.	ENSG00000009830	ENST00000261534	D	0.87491	-2.26	5.75	5.75	0.90469	Glycosyl transferase, family 39 (1);	0.000000	0.85682	D	0.000000	D	0.91442	0.7299	M	0.68317	2.08	0.80722	D	1	P	0.52061	0.95	P	0.58266	0.836	D	0.91659	0.5341	10	0.52906	T	0.07	-14.1461	16.0509	0.80763	0.0:0.0:0.0:1.0	.	232	Q9UKY4	POMT2_HUMAN	S	232	ENSP00000261534:T232S	ENSP00000261534:T232S	T	-	1	0	POMT2	76837308	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.989000	0.70587	2.187000	0.69744	0.533000	0.62120	ACT	.	.		0.522	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382		A	77767555	T	A	77767555	3	1	150	1	0	0	0	0	1	0	0	0	12255	1667	58	4	1622	4	POMT2	14	77767555	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	9534397	77767555	29581985	395	23119										
SMEK1	55671	hgsc.bcm.edu	37	chr14	91942204	91942204	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcttacttacatcatcattcTgttgtgcctcctgcatgaca	5	12	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:91942204T>A	ENST00000554943.1	-	7	1332	c.1217A>T	c.(1216-1218)cAg>cTg	p.Q406L	SMEK1_ENST00000555462.1_Missense_Mutation_p.Q167L|SMEK1_ENST00000554684.1_Missense_Mutation_p.Q406L|SMEK1_ENST00000428424.2_Missense_Mutation_p.Q167L|SMEK1_ENST00000337238.4_Missense_Mutation_p.Q406L			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	406					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		ATCATCATTCTGTTGTGCCTC	0.348																																					p.Q406L		Atlas-SNP	.											.	SMEK1	94	.	0			c.A1217T						.						117	104	109					14																	91942204		2203	4300	6503	SO:0001583	missense	55671	exon8			TCATTCTGTTGTG	AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"KIAA2010"	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.1217A>T	chr14.hg19:g.91942204T>A	ENSP00000450883:p.Gln406Leu	123.0	0.0		95.0	30.0	NM_032560	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Missense_Mutation	SNP	ENST00000554943.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.51	3.639496	0.67244	.	.	ENSG00000100796	ENST00000554684;ENST00000337238;ENST00000428424;ENST00000554943;ENST00000555462;ENST00000554390;ENST00000555029;ENST00000417249	T;T;T;T;T;T;T	0.42131	1.01;1.01;0.98;0.98;0.98;1.01;0.98	5.31	5.31	0.75309	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.54902	0.1887	L	0.50333	1.59	0.80722	D	1	P;B;B;B	0.48294	0.908;0.114;0.315;0.442	P;B;B;B	0.61397	0.888;0.032;0.067;0.142	T	0.47873	-0.9083	10	0.23891	T	0.37	-1.8984	15.2588	0.73606	0.0:0.0:0.0:1.0	.	167;406;406;406	Q6IN85-4;G3V5Z3;Q6IN85;Q6IN85-2	.;.;P4R3A_HUMAN;.	L	406;406;167;406;167;406;167;196	ENSP00000450864:Q406L;ENSP00000337125:Q406L;ENSP00000392704:Q167L;ENSP00000450883:Q406L;ENSP00000450891:Q167L;ENSP00000452596:Q406L;ENSP00000452257:Q167L	ENSP00000337125:Q406L	Q	-	2	0	SMEK1	91011957	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.993000	0.88291	2.018000	0.59344	0.482000	0.46254	CAG	.	.		0.348	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560		A	91942204	T	A	91942204	3	1	150	1	0	0	0	0	1	0	0	0	14808	1580	55	4	1281	4	SMEK1	14	91942204	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	14174649	91942204	15407336	396	23120										
CATSPERB	79820	hgsc.bcm.edu	37	chr14	92091187	92091187	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtgaatcaagagtgagtttaTagacatttccagctttatta	8	5	1	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:92091187T>A	ENST00000256343.3	-	18	2063	c.1907A>T	c.(1906-1908)tAt>tTt	p.Y636F		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	636					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				AGTGAGTTTATAGACATTTCC	0.323																																					p.Y636F		Atlas-SNP	.											.	CATSPERB	114	.	0			c.A1907T						.						68	71	70					14																	92091187		2202	4298	6500	SO:0001583	missense	79820	exon18			AGTTTATAGACAT	AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.1907A>T	chr14.hg19:g.92091187T>A	ENSP00000256343:p.Tyr636Phe	137.0	0.0		82.0	37.0	NM_024764	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	hg19	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.054841	0.36277	.	.	ENSG00000133962	ENST00000256343	T	0.45668	0.89	4.98	2.35	0.29111	.	0.292557	0.24681	N	0.036470	T	0.26593	0.0650	L	0.38531	1.155	0.09310	N	1	B	0.27910	0.193	B	0.24701	0.055	T	0.14476	-1.0471	10	0.15066	T	0.55	-8.7241	7.3613	0.26748	0.3501:0.0:0.0:0.6499	.	636	Q9H7T0	CTSRB_HUMAN	F	636	ENSP00000256343:Y636F	ENSP00000256343:Y636F	Y	-	2	0	CATSPERB	91160940	0.531000	0.26338	0.790000	0.31976	0.675000	0.39556	1.136000	0.31467	0.808000	0.34231	0.254000	0.18369	TAT	.	.		0.323	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		A	92091187	T	A	92091187	3	1	150	1	0	0	0	0	1	0	0	0	2693	1406	49	4	1483	4	CATSPERB	14	92091187	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	148983	92091187	15258353	397	23121										
RIN3	79890	hgsc.bcm.edu	37	chr14	93118727	93118727	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgaaagccagcgatcctcacAgcatgccagagctgcccagg	11	14	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:93118727A>T	ENST00000216487.7	+	6	1492	c.1333A>T	c.(1333-1335)Agc>Tgc	p.S445C	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	445	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				CGATCCTCACAGCATGCCAGA	0.647																																					p.S445C		Atlas-SNP	.											.	RIN3	81	.	0			c.A1333T						.						98	115	109					14																	93118727		2203	4300	6503	SO:0001583	missense	79890	exon6			CCTCACAGCATGC	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.1333A>T	chr14.hg19:g.93118727A>T	ENSP00000216487:p.Ser445Cys	279.0	0.0		152.0	57.0	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	hg19	CCDS32144.1	.	.	.	.	.	.	.	.	.	.	A	11.74	1.729629	0.30684	.	.	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.07688	3.17	4.22	1.61	0.23674	.	1.806560	0.02482	N	0.088605	T	0.20129	0.0484	L	0.60455	1.87	0.09310	N	0.999998	D;B;B;D	0.76494	0.999;0.005;0.005;0.999	D;B;B;P	0.64595	0.927;0.005;0.005;0.846	T	0.10177	-1.0641	10	0.54805	T	0.06	-3.4238	0.1083	0.00054	0.2781:0.2539:0.2099:0.2581	.	445;491;370;445	Q8TB24-4;Q86U22;Q6ZRC2;Q8TB24	.;.;.;RIN3_HUMAN	C	445;369	ENSP00000216487:S445C	ENSP00000216487:S445C	S	+	1	0	RIN3	92188480	0.000000	0.05858	0.010000	0.14722	0.056000	0.15407	0.358000	0.20216	0.502000	0.28037	0.260000	0.18958	AGC	.	.		0.647	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			T	93118727	A	T	93118727	3	4	150	1	0	0	0	0	1	0	0	0	13388	188	7	4	1355	4	RIN3	14	93118727	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1027540	93118727	14230813	398	23122										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99642349	99642349	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aattcatgagcggggactgcGccacggcctccggcccgagc	14	15	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:99642349G>A	ENST00000357195.3	-	4	833	c.824C>T	c.(823-825)gCg>gTg	p.A275V	BCL11B_ENST00000345514.2_Missense_Mutation_p.A204V|BCL11B_ENST00000443726.2_Missense_Mutation_p.A81V	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	275					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		CGGGGACTGCGCCACGGCCTC	0.721			T	TLX3	T-ALL																																p.A275V		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	.	BCL11B	108	.	0			c.C824T						.						7	9	8					14																	99642349		2141	4151	6292	SO:0001583	missense	64919	exon4			GACTGCGCCACGG	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.824C>T	chr14.hg19:g.99642349G>A	ENSP00000349723:p.Ala275Val	167.0	0.0		129.0	39.0	NM_138576	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	hg19	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.621279	0.46736	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.46063	0.88;0.88;0.88	4.68	3.78	0.43462	.	0.191220	0.33553	N	0.004794	T	0.45677	0.1354	L	0.40543	1.245	0.44555	D	0.997517	D;D	0.64830	0.994;0.989	P;P	0.52710	0.682;0.707	T	0.39313	-0.9620	10	0.42905	T	0.14	-16.1376	14.3543	0.66727	0.0:0.0:0.8504:0.1496	.	204;275	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	V	275;204;81	ENSP00000349723:A275V;ENSP00000280435:A204V;ENSP00000387419:A81V	ENSP00000280435:A204V	A	-	2	0	BCL11B	98712102	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.664000	0.98607	1.084000	0.41184	-0.181000	0.13052	GCG	.	.		0.721	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		A	99642349	G	A	99642349	3	1	150	1	0	0	0	0	1	0	0	0	1364	1087	38	1	1864	1	BCL11B	14	99642349	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	6523622	99642349	7707191	399	23123										
CDC42BPB	9578	hgsc.bcm.edu	37	chr14	103442078	103442078	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tagctttttgatttctttatCtcggtttgaattgctgaggg	10	5	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:103442078C>T	ENST00000361246.2	-	11	1738	c.1450G>A	c.(1450-1452)Gat>Aat	p.D484N		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		ATTTCTTTATCTCGGTTTGAA	0.468																																					p.D484N		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.G1450A						.						154	157	156					14																	103442078		2203	4300	6503	SO:0001583	missense	9578	exon11			CTTTATCTCGGTT	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"CDC42-binding protein kinase beta (DMPK-like)"			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.1450G>A	chr14.hg19:g.103442078C>T	ENSP00000355237:p.Asp484Asn	91.0	0.0		59.0	41.0	NM_006035		Missense_Mutation	SNP	ENST00000361246.2	hg19	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	C	19.28	3.797686	0.70567	.	.	ENSG00000198752	ENST00000361246	T	0.65178	-0.14	5.34	5.34	0.76211	.	0.088809	0.85682	D	0.000000	T	0.66066	0.2752	M	0.76002	2.32	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.64149	-0.6475	10	0.51188	T	0.08	.	19.0682	0.93122	0.0:1.0:0.0:0.0	.	484	Q9Y5S2	MRCKB_HUMAN	N	484	ENSP00000355237:D484N	ENSP00000355237:D484N	D	-	1	0	CDC42BPB	102511831	1.000000	0.71417	0.332000	0.25469	0.967000	0.64934	7.212000	0.77941	2.489000	0.83994	0.650000	0.86243	GAT	.	.		0.468	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		T	103442078	C	T	103442078	3	4	150	1	0	0	0	0	1	0	0	0	3075	913	32	3	3793	3	CDC42BPB	14	103442078	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	3799729	103442078	3907462	400	23124										
TDRD9	122402	hgsc.bcm.edu	37	chr14	104433111	104433111	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgacaactggagtcctgctTcagaaaatagttagtgccaa	9	8	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:104433111T>A	ENST00000409874.4	+	5	756	c.708T>A	c.(706-708)ctT>ctA	p.L236L	TDRD9_ENST00000339063.5_Silent_p.L236L|TDRD9_ENST00000554571.1_3'UTR	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	236	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				GAGTCCTGCTTCAGAAAATAG	0.363																																					p.L236L		Atlas-SNP	.											.	TDRD9	175	.	0			c.T708A						.						216	186	195					14																	104433111		692	1591	2283	SO:0001819	synonymous_variant	122402	exon5			CCTGCTTCAGAAA	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.708T>A	chr14.hg19:g.104433111T>A		68.0	0.0		84.0	30.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	hg19	CCDS9987.2																																																																																			.	.		0.363	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		A	104433111	T	A	104433111	2	1	150	1	0	0	0	0	0	0	0	1	15751	1770	62	4		4	TDRD9	14	104433111	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	991033	104433111	2916429	401	23125										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105419689	105419689	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctccaccttcggcgcagacAcatccaccgaggcctccatg	8	19	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr14:105419689A>T	ENST00000333244.5	-	7	2218	c.2099T>A	c.(2098-2100)gTg>gAg	p.V700E	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	700						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CGGCGCAGACACATCCACCGA	0.607																																					p.V700E		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T2099A						.						150	160	157					14																	105419689		1962	4152	6114	SO:0001583	missense	113146	exon7			GCAGACACATCCA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.2099T>A	chr14.hg19:g.105419689A>T	ENSP00000353114:p.Val700Glu	182.0	0.0		127.0	39.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	a	12.06	1.824061	0.32237	.	.	ENSG00000185567	ENST00000333244	T	0.01804	4.63	2.91	-0.0568	0.13803	.	.	.	.	.	T	0.09069	0.0224	M	0.89414	3.03	0.09310	N	1	D	0.76494	0.999	D	0.80764	0.994	T	0.13019	-1.0525	9	0.72032	D	0.01	-2.3935	4.2928	0.10886	0.4683:0.3184:0.2134:0.0	.	700	Q8IVF2	AHNK2_HUMAN	E	700	ENSP00000353114:V700E	ENSP00000353114:V700E	V	-	2	0	AHNAK2	104490734	0.000000	0.05858	0.005000	0.12908	0.006000	0.05464	1.139000	0.31504	0.982000	0.38575	0.454000	0.30748	GTG	.	.		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105419689	A	T	105419689	3	4	150	1	0	0	0	0	1	0	0	0	415	159	6	4	15292	4	AHNAK2	14	105419689	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	986578	105419689	1929851	402	23126										
GABRG3	2567	hgsc.bcm.edu	37	chr15	27222169	27222169	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtccagaaaggtggaagaggAtgaatatgaagattcatcat	12	4	2	5			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:27222169A>G	ENST00000333743.6	+	2	328	c.74A>G	c.(73-75)gAt>gGt	p.D25G	GABRG3_ENST00000555083.1_Missense_Mutation_p.D25G	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	25					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GTGGAAGAGGATGAATATGAA	0.423																																					p.D25G	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.A74G						.						85	83	84					15																	27222169		1870	4100	5970	SO:0001583	missense	2567	exon2			AAGAGGATGAATA		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4088	protein-coding gene	gene with protein product	"GABA(G) receptor, gamma 3"	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.74A>G	chr15.hg19:g.27222169A>G	ENSP00000331912:p.Asp25Gly	101.0	0.0		75.0	26.0	NM_001270873	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	hg19	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	A	17.78	3.474161	0.63737	.	.	ENSG00000182256	ENST00000333743;ENST00000555083	T;T	0.81330	-1.48;0.6	5.28	5.28	0.74379	.	.	.	.	.	T	0.76471	0.3992	L	0.59436	1.845	0.49051	D	0.999742	B;P	0.44521	0.354;0.837	B;B	0.38755	0.101;0.281	T	0.76879	-0.2796	9	0.33940	T	0.23	.	14.6626	0.68882	1.0:0.0:0.0:0.0	.	25;25	Q99928;G3V594	GBRG3_HUMAN;.	G	25	ENSP00000331912:D25G;ENSP00000452244:D25G	ENSP00000331912:D25G	D	+	2	0	GABRG3	24804915	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	6.461000	0.73522	2.115000	0.64714	0.455000	0.32223	GAT	.	.		0.423	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			G	27222169	A	G	27222169	3	3	150	1	0	0	0	0	1	0	0	0	6181	333	12	2	80	2	GABRG3	15	27222169	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		27222169	75309223	403	23127										
THBS1	7057	hgsc.bcm.edu	37	chr15	39885868	39885868	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cacaggaaacacccctggccAggtaagaagcaaagccctgg	11	13	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:39885868A>T	ENST00000260356.5	+	19	3431	c.3266A>T	c.(3265-3267)cAg>cTg	p.Q1089L	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1089	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		ACCCCTGGCCAGGTAAGAAGC	0.567																																					p.Q1089L		Atlas-SNP	.											.	THBS1	106	.	0			c.A3266T						.						76	82	80					15																	39885868		2200	4297	6497	SO:0001630	splice_region_variant	7057	exon19			CTGGCCAGGTAAG		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.3267+1A>T	chr15.hg19:g.39885868A>T		110.0	0.0		58.0	24.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.947593	0.92593	.	.	ENSG00000137801	ENST00000260356	D	0.96073	-3.9	5.78	5.78	0.91487	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.34268	N	0.004111	D	0.97907	0.9312	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.989;0.994	D	0.98805	1.0741	10	0.87932	D	0	-16.612	16.0881	0.81073	1.0:0.0:0.0:0.0	.	1004;1089	B4E3J7;P07996	.;TSP1_HUMAN	L	1089	ENSP00000260356:Q1089L	ENSP00000260356:Q1089L	Q	+	2	0	THBS1	37673160	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	CAG	.	.		0.567	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	Missense_Mutation	T	39885868	A	T	39885868	5	4	150	1	0	0	0	0	0	0	1	0	15868	202	7	4	3336	4	THBS1	15	39885868	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	12663699	39885868	62645524	404	23128										
MYEF2	50804	hgsc.bcm.edu	37	chr15	48443350	48443350	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atcctattcttcctgcaaacCctccaatcattgcactgcct	3	16	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:48443350C>T	ENST00000324324.7	-	14	1604	c.1325G>A	c.(1324-1326)gGg>gAg	p.G442E	MYEF2_ENST00000267836.6_Intron	NM_016132.3	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2	442	Gly-rich.				myotube differentiation (GO:0014902)|neuron differentiation (GO:0030182)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		TCCTGCAAACCCTCCAATCAT	0.318																																					p.G442E		Atlas-SNP	.											.	MYEF2	67	.	0			c.G1325A						.						84	85	85					15																	48443350		2198	4295	6493	SO:0001583	missense	50804	exon14			GCAAACCCTCCAA	AB037762	CCDS32230.1, CCDS73722.1	15q15.1	2013-07-16				ENSG00000104177		"RNA binding motif (RRM) containing"	17940	protein-coding gene	gene with protein product						10718198, 2601707	Standard	XM_005254422		Approved	MEF-2, FLJ11213, KIAA1341, HsT18564	uc001zwi.4	Q9P2K5		ENST00000324324.7:c.1325G>A	chr15.hg19:g.48443350C>T	ENSP00000316950:p.Gly442Glu	337.0	1.0		239.0	84.0	NM_016132	A7MCZ9|C9J921|C9K0J4|Q6NUM5|Q7L388|Q7Z4B7|Q9H922|Q9NUQ1	Missense_Mutation	SNP	ENST00000324324.7	hg19	CCDS32230.1	.	.	.	.	.	.	.	.	.	.	C	3.004	-0.205423	0.06180	.	.	ENSG00000104177	ENST00000324324	T	0.35973	1.28	5.3	5.3	0.74995	.	0.163439	0.53938	D	0.000048	T	0.32376	0.0827	L	0.48642	1.525	0.80722	D	1	P	0.48162	0.906	P	0.46585	0.521	T	0.04607	-1.0939	10	0.07813	T	0.8	-0.56	10.5818	0.45259	0.1471:0.7108:0.1421:0.0	.	442	Q9P2K5	MYEF2_HUMAN	E	442	ENSP00000316950:G442E	ENSP00000316950:G442E	G	-	2	0	MYEF2	46230642	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.022000	0.57203	2.753000	0.94483	0.655000	0.94253	GGG	.	.		0.318	MYEF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416909.2	NM_016132		T	48443350	C	T	48443350	3	4	150	1	0	0	0	0	1	0	0	0	10033	623	22	3	493	3	MYEF2	15	48443350	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	8557482	48443350	54088042	405	23129										
PRTG	283659	hgsc.bcm.edu	37	chr15	55967845	55967845	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	taatataatgagttgtgtcaTttccgatgactacttgatac	7	6	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:55967845T>C	ENST00000389286.4	-	9	1465	c.1418A>G	c.(1417-1419)aAt>aGt	p.N473S		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		AGTTGTGTCATTTCCGATGAC	0.318																																					p.N473S		Atlas-SNP	.											.	PRTG	110	.	0			c.A1418G						.						64	61	62					15																	55967845		1835	4081	5916	SO:0001583	missense	283659	exon9			GTGTCATTTCCGA	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.1418A>G	chr15.hg19:g.55967845T>C	ENSP00000373937:p.Asn473Ser	78.0	0.0		53.0	18.0	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	hg19	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.229447	0.79688	.	.	ENSG00000166450	ENST00000389286	T	0.56776	0.44	4.99	4.99	0.66335	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.217493	0.47852	D	0.000217	T	0.67915	0.2944	M	0.64260	1.97	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65788	-0.6083	10	0.30078	T	0.28	-25.0674	14.176	0.65542	0.0:0.0:0.0:1.0	.	473	Q2VWP7	PRTG_HUMAN	S	473	ENSP00000373937:N473S	ENSP00000373937:N473S	N	-	2	0	PRTG	53755137	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.802000	0.85969	2.001000	0.58596	0.460000	0.39030	AAT	.	.		0.318	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		C	55967845	T	C	55967845	3	2	150	1	0	0	0	0	1	0	0	0	12650	1493	52	2	2082	2	PRTG	15	55967845	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	7524495	55967845	46563547	406	23130										
TMEM202	338949	hgsc.bcm.edu	37	chr15	72700152	72700152	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggtgactacagtatcacctgCtaaagatgaagggccaaggt	12	8	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:72700152C>A	ENST00000341689.3	+	5	794	c.740C>A	c.(739-741)gCt>gAt	p.A247D	TMEM202_ENST00000567679.1_3'UTR	NM_001080462.1	NP_001073931.1	A6NGA9	TM202_HUMAN	transmembrane protein 202	247						integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	18						GTATCACCTGCTAAAGATGAA	0.453																																					p.A247D		Atlas-SNP	.											.	TMEM202	40	.	0			c.C740A						.						87	81	83					15																	72700152		2199	4297	6496	SO:0001583	missense	338949	exon5			CACCTGCTAAAGA		CCDS32287.1	15q24.1	2007-12-18				ENSG00000187806			33733	protein-coding gene	gene with protein product							Standard	NM_001080462		Approved	FLJ27523	uc002auq.3	A6NGA9		ENST00000341689.3:c.740C>A	chr15.hg19:g.72700152C>A	ENSP00000340212:p.Ala247Asp	65.0	0.0		45.0	17.0	NM_001080462		Missense_Mutation	SNP	ENST00000341689.3	hg19	CCDS32287.1	.	.	.	.	.	.	.	.	.	.	C	13.93	2.382854	0.42207	.	.	ENSG00000187806	ENST00000341689	T	0.56103	0.48	4.29	0.0693	0.14373	.	0.895616	0.09376	N	0.810686	T	0.36524	0.0970	L	0.37630	1.12	0.09310	N	1	B	0.16802	0.019	B	0.15870	0.014	T	0.24225	-1.0166	10	0.33141	T	0.24	-4.7749	3.2966	0.06968	0.3598:0.438:0.0:0.2021	.	247	A6NGA9	TM202_HUMAN	D	247	ENSP00000340212:A247D	ENSP00000340212:A247D	A	+	2	0	TMEM202	70487206	0.000000	0.05858	0.000000	0.03702	0.193000	0.23685	-0.506000	0.06359	-0.061000	0.13110	0.561000	0.74099	GCT	.	.		0.453	TMEM202-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435756.1	NM_001080462		A	72700152	C	A	72700152	3	1	150	1	0	0	0	0	1	0	0	0	16142	797	28	3	758	3	TMEM202	15	72700152	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	16732307	72700152	29831240	407	23131										
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79291113	79291113	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cgttcaagacacgattggtgGctgctctgcggatcacaaac	11	11	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:79291113G>T	ENST00000419573.3	-	19	3123	c.2849C>A	c.(2848-2850)gCc>gAc	p.A950D	RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000558480.2_Missense_Mutation_p.A934D|RASGRF1_ENST00000394745.3_Missense_Mutation_p.A166D	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	950					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ACGATTGGTGGCTGCTCTGCG	0.617																																					p.A950D		Atlas-SNP	.											.	RASGRF1	168	.	0			c.C2849A						.						119	109	112					15																	79291113		2196	4293	6489	SO:0001583	missense	5923	exon19			TTGGTGGCTGCTC	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.2849C>A	chr15.hg19:g.79291113G>T	ENSP00000405963:p.Ala950Asp	58.0	0.0		43.0	13.0	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.976398	0.53720	.	.	ENSG00000058335	ENST00000419573;ENST00000394741;ENST00000394745	T;T	0.31247	1.5;1.5	4.74	3.81	0.43845	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (1);	0.062116	0.64402	D	0.000005	T	0.40570	0.1122	M	0.80422	2.495	0.80722	D	1	P;B;B;B	0.46621	0.881;0.076;0.185;0.074	P;B;B;B	0.44518	0.452;0.071;0.144;0.104	T	0.49457	-0.8938	10	0.87932	D	0	.	12.1452	0.54020	0.0:0.0:0.828:0.1719	.	346;934;952;934	B7Z6Z6;Q8IUU5;Q13972;F8VPA5	.;.;RGRF1_HUMAN;.	D	950;934;166	ENSP00000405963:A950D;ENSP00000378228:A166D	ENSP00000378224:A934D	A	-	2	0	RASGRF1	77078168	1.000000	0.71417	0.993000	0.49108	0.968000	0.65278	6.129000	0.71657	1.166000	0.42689	0.591000	0.81541	GCC	.	.		0.617	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		T	79291113	G	T	79291113	3	4	150	1	0	0	0	0	1	0	0	0	13087	1203	42	3	1012	3	RASGRF1	15	79291113	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	6590961	79291113	23240279	408	23132										
HDGFRP3	50810	hgsc.bcm.edu	37	chr15	83826759	83826759	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaacttgtctttgtactcctTatatggaaaaaggtctttgg	8	6	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:83826759T>C	ENST00000299633.4	-	3	799	c.196A>G	c.(196-198)Aag>Gag	p.K66E		NM_016073.3	NP_057157.1	Q9Y3E1	HDGR3_HUMAN		66	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						TTGTACTCCTTATATGGAAAA	0.348																																					p.K66E		Atlas-SNP	.											.	HDGFRP3	17	.	0			c.A196G						.						106	95	99					15																	83826759		2203	4300	6503	SO:0001583	missense	0	exon3			ACTCCTTATATGG																												ENST00000299633.4:c.196A>G	chr15.hg19:g.83826759T>C	ENSP00000299633:p.Lys66Glu	83.0	0.0		49.0	21.0	NM_016073		Missense_Mutation	SNP	ENST00000299633.4	hg19	CCDS32314.1	.	.	.	.	.	.	.	.	.	.	T	3.674	-0.066865	0.07273	.	.	ENSG00000166503	ENST00000299633	T	0.69175	-0.38	5.28	5.28	0.74379	PWWP (3);	0.101757	0.64402	D	0.000005	T	0.32496	0.0831	N	0.00621	-1.32	0.32425	N	0.548797	B	0.18013	0.025	B	0.20577	0.03	T	0.35624	-0.9781	10	0.02654	T	1	.	15.5016	0.75703	0.0:0.0:0.0:1.0	.	66	Q9Y3E1	HDGR3_HUMAN	E	66	ENSP00000299633:K66E	ENSP00000299633:K66E	K	-	1	0	AC024270.1	81617763	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.606000	0.46291	2.124000	0.65301	0.460000	0.39030	AAG	.	.		0.348	HDGFRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419898.1			C	83826759	T	C	83826759	3	2	150	1	0	0	0	0	1	0	0	0	7030	1763	61	2	431	2	HDGFRP3	15	83826759	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4535646	83826759	18704633	409	23133										
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84694127	84694127	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcatgtgcccctaaagaccGgcctctgggaagaaaaccat	10	12	1	2	rs143304781		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:84694127G>T	ENST00000286744.5	+	27	4819	c.4595G>T	c.(4594-4596)cGg>cTg	p.R1532L	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R1532L	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1532	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			CCTAAAGACCGGCCTCTGGGA	0.522																																					p.R1532L		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.G4595T						.						120	108	112					15																	84694127		2203	4299	6502	SO:0001583	missense	57188	exon27			AAGACCGGCCTCT	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.4595G>T	chr15.hg19:g.84694127G>T	ENSP00000286744:p.Arg1532Leu	230.0	0.0		156.0	59.0	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	hg19	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.907580	0.52333	.	.	ENSG00000156218	ENST00000286744	T	0.61040	0.14	5.15	4.23	0.50019	.	1.071190	0.07455	N	0.899666	T	0.77565	0.4149	M	0.83774	2.66	0.26696	N	0.97126	D;B	0.61080	0.989;0.285	D;B	0.67382	0.951;0.06	T	0.61023	-0.7146	10	0.72032	D	0.01	.	11.0758	0.48030	0.0849:0.0:0.9151:0.0	.	1532;1532	P82987-2;P82987	.;ATL3_HUMAN	L	1532	ENSP00000286744:R1532L	ENSP00000286744:R1532L	R	+	2	0	ADAMTSL3	82485131	0.014000	0.17966	0.723000	0.30687	0.592000	0.36648	0.703000	0.25646	1.381000	0.46364	0.655000	0.94253	CGG	.	G|1.000;A|0.000		0.522	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		T	84694127	G	T	84694127	3	4	150	1	0	0	0	0	1	0	0	0	276	1116	39	1	4697	1	ADAMTSL3	15	84694127	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	867368	84694127	17837265	410	23134										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91038004	91038004	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	caaaaagatttctctgaaatAtacagcagcaagactacatg	6	8	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:91038004A>G	ENST00000268182.5	+	36	4812	c.4688A>G	c.(4687-4689)tAt>tGt	p.Y1563C	IQGAP1_ENST00000560738.1_Missense_Mutation_p.Y991C	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1563	C2.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TCTCTGAAATATACAGCAGCA	0.338																																					p.Y1563C		Atlas-SNP	.											.	IQGAP1	140	.	0			c.A4688G						.						142	147	145					15																	91038004		2198	4298	6496	SO:0001583	missense	8826	exon36			TGAAATATACAGC	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.4688A>G	chr15.hg19:g.91038004A>G	ENSP00000268182:p.Tyr1563Cys	267.0	1.0		182.0	69.0	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	hg19	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.577768	0.86645	.	.	ENSG00000140575	ENST00000268182	T	0.53206	0.63	5.77	5.77	0.91146	RasGAP protein, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71409	0.3336	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	0.992;1.0	D;D	0.97110	0.984;1.0	T	0.75167	-0.3413	10	0.59425	D	0.04	-17.4566	15.5623	0.76258	1.0:0.0:0.0:0.0	.	184;1563	B4DNP4;P46940	.;IQGA1_HUMAN	C	1563	ENSP00000268182:Y1563C	ENSP00000268182:Y1563C	Y	+	2	0	IQGAP1	88839008	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.210000	0.95106	2.330000	0.79161	0.528000	0.53228	TAT	.	.		0.338	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		G	91038004	A	G	91038004	3	3	150	1	0	0	0	0	1	0	0	0	7823	449	16	2	4830	2	IQGAP1	15	91038004	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	6343877	91038004	11493388	411	23135										
CHD2	1106	hgsc.bcm.edu	37	chr15	93552536	93552536	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcctactcagatcaggagcaCatcaaactctggaggaggta	11	10	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:93552536C>T	ENST00000394196.4	+	35	5643	c.4575C>T	c.(4573-4575)caC>caT	p.H1525H	CHD2_ENST00000557381.1_Silent_p.H1525H	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1525					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			ATCAGGAGCACATCAAACTCT	0.498																																					p.H1525H		Atlas-SNP	.											.	CHD2	280	.	0			c.C4575T						.						75	65	68					15																	93552536		2197	4298	6495	SO:0001819	synonymous_variant	1106	exon35			GGAGCACATCAAA	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4575C>T	chr15.hg19:g.93552536C>T		92.0	0.0		63.0	30.0	NM_001271	C6G482|Q96IP5	Silent	SNP	ENST00000394196.4	hg19	CCDS10374.2																																																																																			.	.		0.498	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		T	93552536	C	T	93552536	2	4	150	1	0	0	0	0	0	0	0	1	3327	477	17	3		3	CHD2	15	93552536	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	2514532	93552536	8978856	412	23136										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99251163	99251163	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctgttacctctccactgtggActggtccctgatcctggatg	10	13	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr15:99251163A>T	ENST00000268035.6	+	2	1078	c.467A>T	c.(466-468)gAc>gTc	p.D156V	IGF1R_ENST00000558762.1_Missense_Mutation_p.D156V	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	156					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	TCCACTGTGGACTGGTCCCTG	0.512																																					p.D156V		Atlas-SNP	.											.	IGF1R	147	.	0			c.A467T						.						98	88	92					15																	99251163		2197	4297	6494	SO:0001583	missense	3480	exon2			CTGTGGACTGGTC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.467A>T	chr15.hg19:g.99251163A>T	ENSP00000268035:p.Asp156Val	164.0	0.0		91.0	42.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.351834	0.82132	.	.	ENSG00000140443	ENST00000268035	D	0.84146	-1.81	5.36	5.36	0.76844	EGF receptor, L domain (1);	0.000000	0.56097	D	0.000024	D	0.93716	0.7992	M	0.91510	3.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94986	0.8130	10	0.87932	D	0	.	14.824	0.70097	1.0:0.0:0.0:0.0	.	156;156	C9J5X1;P08069	.;IGF1R_HUMAN	V	156	ENSP00000268035:D156V	ENSP00000268035:D156V	D	+	2	0	IGF1R	97068686	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.150000	0.94667	2.148000	0.66965	0.460000	0.39030	GAC	.	.		0.512	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		T	99251163	A	T	99251163	3	4	150	1	0	0	0	0	1	0	0	0	7580	275	10	4	473	4	IGF1R	15	99251163	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5698627	99251163	3280229	413	23137										
ABAT	18	hgsc.bcm.edu	37	chr16	8860122	8860122	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agctggagacgtgcatgattAaccaggtgagtgcagctggg	16	7	0	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:8860122A>T	ENST00000396600.2	+	9	1536	c.598A>T	c.(598-600)Aac>Tac	p.N200Y	ABAT_ENST00000567812.1_Missense_Mutation_p.N215Y|ABAT_ENST00000569156.1_Missense_Mutation_p.N200Y|ABAT_ENST00000425191.2_Missense_Mutation_p.N200Y|ABAT_ENST00000268251.8_Missense_Mutation_p.N200Y	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	200					behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	GTGCATGATTAACCAGGTGAG	0.557																																					p.N200Y		Atlas-SNP	.											.	ABAT	46	.	0			c.A598T						.						63	60	61					16																	8860122		2197	4300	6497	SO:0001583	missense	18	exon9			ATGATTAACCAGG	L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	2.6.1.19		23	protein-coding gene	gene with protein product	"4-aminobutyrate transaminase"	137150				7721088	Standard	NM_020686		Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000396600.2:c.598A>T	chr16.hg19:g.8860122A>T	ENSP00000379845:p.Asn200Tyr	85.0	0.0		73.0	42.0	NM_001127448	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	Missense_Mutation	SNP	ENST00000396600.2	hg19	CCDS10534.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.520426	0.85495	.	.	ENSG00000183044	ENST00000268251;ENST00000396600;ENST00000425191	T;T;T	0.77750	-1.12;-1.12;-1.12	5.0	5.0	0.66597	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.91734	0.7386	H	0.96633	3.855	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94220	0.7466	10	0.87932	D	0	-16.2983	13.9442	0.64075	1.0:0.0:0.0:0.0	.	200	P80404	GABT_HUMAN	Y	200	ENSP00000268251:N200Y;ENSP00000379845:N200Y;ENSP00000411916:N200Y	ENSP00000268251:N200Y	N	+	1	0	ABAT	8767623	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.432000	0.90288	1.892000	0.54788	0.454000	0.30748	AAC	.	.		0.557	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2	NM_020686		T	8860122	A	T	8860122	3	4	150	1	0	0	0	0	1	0	0	0	27	362	13	4	628	4	ABAT	16	8860122	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		8860122	81494631	414	23138										
TMC5	79838	hgsc.bcm.edu	37	chr16	19468227	19468227	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aaaggaatgaccaaaagggtAaccaggtgctgcggttttca	12	7	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:19468227A>C	ENST00000396229.2	+	6	1797				TMC5_ENST00000561503.1_Intron|TMC5_ENST00000541464.1_Intron|TMC5_ENST00000542583.2_Intron|TMC5_ENST00000219821.5_Missense_Mutation_p.N67H|TMC5_ENST00000564959.1_Intron|TMC5_ENST00000381414.4_Intron	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5						ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CCAAAAGGGTAACCAGGTGCT	0.438																																					p.N67H		Atlas-SNP	.											.	TMC5	169	.	0			c.A199C						.						124	109	114					16																	19468227		2197	4300	6497	SO:0001627	intron_variant	79838	exon1			AAGGGTAACCAGG	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.1049-3330A>C	chr16.hg19:g.19468227A>C		92.0	0.0		71.0	24.0	NM_024780	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	hg19	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	A	8.665	0.901466	0.17760	.	.	ENSG00000103534	ENST00000219821	T	0.69561	-0.41	4.07	-1.33	0.09172	.	.	.	.	.	T	0.47488	0.1448	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.28073	-1.0055	9	0.14252	T	0.57	.	11.7366	0.51769	0.3399:0.6601:0.0:0.0	.	67;67	Q6UXY8-3;B3KUQ8	.;.	H	67	ENSP00000219821:N67H	ENSP00000219821:N67H	N	+	1	0	TMC5	19375728	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.419000	0.21247	-0.254000	0.09500	0.533000	0.62120	AAC	.	.		0.438	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		C	19468227	A	C	19468227	1	2	150	0	1	0	0	0	0	0	0	0	16003	362	13	5		5	TMC5	16	19468227	Intron	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	10608105	19468227	70886526	415	23139										
PDILT	204474	hgsc.bcm.edu	37	chr16	20396093	20396093	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cactttgccaaagccgatccCattcttgcctttgcccatga	6	15	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:20396093C>T	ENST00000302451.4	-	3	531	c.283G>A	c.(283-285)Ggg>Agg	p.G95R	RP11-429K17.1_ENST00000577173.1_RNA	NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	95					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						AAGCCGATCCCATTCTTGCCT	0.493																																					p.G95R		Atlas-SNP	.											.	PDILT	120	.	0			c.G283A						.						332	322	326					16																	20396093		2203	4300	6503	SO:0001583	missense	204474	exon3			CGATCCCATTCTT		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.283G>A	chr16.hg19:g.20396093C>T	ENSP00000305465:p.Gly95Arg	95.0	0.0		75.0	44.0	NM_174924	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	hg19	CCDS10584.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.401177	0.62288	.	.	ENSG00000169340	ENST00000302451	T	0.03152	4.03	5.43	5.43	0.79202	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.170044	0.40728	N	0.001033	T	0.04272	0.0118	L	0.34521	1.04	0.32825	D	0.503202	P	0.39535	0.677	B	0.39419	0.299	T	0.41197	-0.9522	10	0.20519	T	0.43	.	14.599	0.68427	0.0:1.0:0.0:0.0	.	95	Q8N807	PDILT_HUMAN	R	95	ENSP00000305465:G95R	ENSP00000305465:G95R	G	-	1	0	PDILT	20303594	0.477000	0.25909	0.677000	0.29947	0.735000	0.41995	3.347000	0.52200	2.825000	0.97269	0.655000	0.94253	GGG	.	.		0.493	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		T	20396093	C	T	20396093	3	4	150	1	0	0	0	0	1	0	0	0	11683	594	21	3	1511	3	PDILT	16	20396093	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	927866	20396093	69958660	416	23140										
SCNN1G	6340	hgsc.bcm.edu	37	chr16	23208731	23208731	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgagacagcaatggtcaccTctataggaatgcacctggta	10	9	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:23208731T>A	ENST00000300061.2	+	6	1203	c.1060T>A	c.(1060-1062)Tct>Act	p.S354T	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	354					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	AATGGTCACCTCTATAGGAAT	0.463																																					p.S354T		Atlas-SNP	.											.	SCNN1G	82	.	0			c.T1060A						.						113	107	109					16																	23208731		2197	4300	6497	SO:0001583	missense	6340	exon6			GTCACCTCTATAG	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.1060T>A	chr16.hg19:g.23208731T>A	ENSP00000300061:p.Ser354Thr	114.0	0.0		80.0	14.0	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Missense_Mutation	SNP	ENST00000300061.2	hg19	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.952158	0.73787	.	.	ENSG00000166828	ENST00000300061	T	0.64618	-0.11	5.62	4.48	0.54585	.	0.000000	0.64402	D	0.000001	T	0.72676	0.3490	L	0.53729	1.69	0.37235	D	0.905846	D	0.76494	0.999	D	0.83275	0.996	T	0.75462	-0.3309	10	0.40728	T	0.16	-36.3791	12.1782	0.54198	0.0:0.0:0.1421:0.8579	.	354	P51170	SCNNG_HUMAN	T	354	ENSP00000300061:S354T	ENSP00000300061:S354T	S	+	1	0	SCNN1G	23116232	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.920000	0.56446	2.151000	0.67156	0.533000	0.62120	TCT	.	.		0.463	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		A	23208731	T	A	23208731	3	1	150	1	0	0	0	0	1	0	0	0	13945	1551	54	4	1078	4	SCNN1G	16	23208731	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2812638	23208731	67146022	417	23141										
MVP	9961	hgsc.bcm.edu	37	chr16	29847023	29847023	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttaccctccactcttggcccAggggaagaatggctggtcac	11	13	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:29847023A>T	ENST00000357402.5	+	6	715		c.e6-1		MVP_ENST00000395353.1_Splice_Site|MVP_ENST00000452209.2_Intron	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein						cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						CTCTTGGCCCAGGGGAAGAAT	0.592																																					.		Atlas-SNP	.											.	MVP	80	.	0			c.578-2A>T						.						69	61	63					16																	29847023		2197	4300	6497	SO:0001630	splice_region_variant	9961	exon6			TGGCCCAGGGGAA	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"lung resistance-related protein"	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.578-1A>T	chr16.hg19:g.29847023A>T		135.0	0.0		102.0	25.0	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Splice_Site	SNP	ENST00000357402.5	hg19	CCDS10656.1	.	.	.	.	.	.	.	.	.	.	a	16.83	3.230276	0.58777	.	.	ENSG00000013364	ENST00000357402;ENST00000395353	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1238	0.59342	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MVP	29754524	1.000000	0.71417	0.921000	0.36526	0.619000	0.37552	6.832000	0.75329	2.067000	0.61834	0.375000	0.23000	.	.	.		0.592	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115	Intron	T	29847023	A	T	29847023	5	4	150	1	0	0	0	0	0	0	1	0	10005	202	7	4	594	4	MVP	16	29847023	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	6638292	29847023	60507730	418	23142										
CD2BP2	10421	hgsc.bcm.edu	37	chr16	30364546	30364546	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccatacagctcggcatcccCcgtgttctcccacttatatt	5	17	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:30364546C>A	ENST00000305596.3	-	6	1046	c.871G>T	c.(871-873)Ggg>Tgg	p.G291W	CD2BP2_ENST00000569466.1_Missense_Mutation_p.G291W|RP11-347C12.10_ENST00000563252.1_lincRNA	NM_006110.2	NP_006101.1	O95400	CD2B2_HUMAN	CD2 (cytoplasmic tail) binding protein 2	291	GYF. {ECO:0000255|PROSITE- ProRule:PRU00101}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of phosphatase activity (GO:0010923)|RNA splicing (GO:0008380)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	ribonucleoprotein complex binding (GO:0043021)			breast(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	15						TCGGCATCCCCCGTGTTCTCC	0.567																																					p.G291W		Atlas-SNP	.											.	CD2BP2	30	.	0			c.G871T						.						138	119	126					16																	30364546		2197	4300	6497	SO:0001583	missense	10421	exon6			CATCCCCCGTGTT	AF104222	CCDS10675.1	16p11.2	2012-04-17	2006-03-28		ENSG00000169217	ENSG00000169217		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 59"	604470	"CD2 antigen (cytoplasmic tail)-binding protein 2"			9843987	Standard	NM_006110		Approved	LIN1, Snu40, PPP1R59	uc002dxs.3	O95400	OTTHUMG00000132397	ENST00000305596.3:c.871G>T	chr16.hg19:g.30364546C>A	ENSP00000304903:p.Gly291Trp	126.0	0.0		113.0	26.0	NM_006110	B2RDX2|Q9ULP2	Missense_Mutation	SNP	ENST00000305596.3	hg19	CCDS10675.1	.	.	.	.	.	.	.	.	.	.	c	15.69	2.907567	0.52333	.	.	ENSG00000169217	ENST00000305596	T	0.32272	1.46	4.81	1.2	0.21068	GYF (4);	0.365474	0.31020	N	0.008410	T	0.21307	0.0513	L	0.27053	0.805	0.40983	D	0.984794	P	0.51537	0.946	P	0.46543	0.52	T	0.04128	-1.0975	10	0.66056	D	0.02	0.0014	4.8133	0.13354	0.0:0.551:0.1752:0.2739	.	291	O95400	CD2B2_HUMAN	W	291	ENSP00000304903:G291W	ENSP00000304903:G291W	G	-	1	0	CD2BP2	30272047	0.581000	0.26741	0.991000	0.47740	0.923000	0.55619	1.912000	0.39946	0.541000	0.28827	-0.140000	0.14226	GGG	.	.		0.567	CD2BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255528.1	NM_006110		A	30364546	C	A	30364546	3	1	150	1	0	0	0	0	1	0	0	0	2997	623	22	3	162	3	CD2BP2	16	30364546	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	517523	30364546	59990207	419	23143										
TGFB1I1	7041	hgsc.bcm.edu	37	chr16	31484780	31484780	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agatgccctgctctctgaccTggagactaccacctcgcaca	8	16	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:31484780T>C	ENST00000394863.3	+	2	162	c.32T>C	c.(31-33)cTg>cCg	p.L11P	TGFB1I1_ENST00000567607.1_5'UTR|TGFB1I1_ENST00000361773.3_5'UTR|TGFB1I1_ENST00000394858.2_5'UTR	NM_001042454.2	NP_001035919.1	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced transcript 1	11	Interaction with PTK2B/PYK2.|Transcription activation. {ECO:0000250}.				androgen receptor signaling pathway (GO:0030521)|cell adhesion (GO:0007155)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|response to heat (GO:0009408)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|I-SMAD binding (GO:0070411)|Roundabout binding (GO:0048495)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(8)|upper_aerodigestive_tract(1)	9						CTCTCTGACCTGGAGACTACC	0.602																																					p.L11P		Atlas-SNP	.											.	TGFB1I1	60	.	0			c.T32C						.						48	52	50					16																	31484780		2197	4300	6497	SO:0001583	missense	7041	exon2			CTGACCTGGAGAC	AB007836	CCDS10713.1, CCDS42156.1	16p11	2008-02-05			ENSG00000140682	ENSG00000140682			11767	protein-coding gene	gene with protein product		602353				9422762, 10075738	Standard	NM_015927		Approved	Hic-5, TSC-5, ARA55, HIC-5	uc002ecd.2	O43294	OTTHUMG00000132467	ENST00000394863.3:c.32T>C	chr16.hg19:g.31484780T>C	ENSP00000378332:p.Leu11Pro	42.0	0.0		30.0	8.0	NM_001042454	B2R8D5|Q9BPW3|Q9Y2V5	Missense_Mutation	SNP	ENST00000394863.3	hg19	CCDS42156.1	.	.	.	.	.	.	.	.	.	.	T	15.62	2.887572	0.52014	.	.	ENSG00000140682	ENST00000394863	T	0.65549	-0.16	4.8	4.8	0.61643	.	2.348640	0.03424	U	0.206806	T	0.72938	0.3523	L	0.28115	0.83	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58429	-0.7638	10	0.87932	D	0	.	12.3524	0.55155	0.0:0.0:0.0:1.0	.	11	O43294	TGFI1_HUMAN	P	11	ENSP00000378332:L11P	ENSP00000378332:L11P	L	+	2	0	TGFB1I1	31392281	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.005000	0.76323	2.007000	0.58848	0.454000	0.30748	CTG	.	.		0.602	TGFB1I1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255630.3			C	31484780	T	C	31484780	3	2	150	1	0	0	0	0	1	0	0	0	15832	1580	55	2	38	2	TGFB1I1	16	31484780	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1120234	31484780	58869973	420	23144										
ABCC12	94160	hgsc.bcm.edu	37	chr16	48158122	48158122	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagcactcatcacacagcttAcctgtcctaggagagctgca	8	14	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:48158122A>T	ENST00000311303.3	-	10	1933		c.e10+1		ABCC12_ENST00000416054.1_Splice_Site|ABCC12_ENST00000448542.1_Splice_Site	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12							integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				CACACAGCTTACCTGTCCTAG	0.527																																					.		Atlas-SNP	.											.	ABCC12	190	.	0			c.1587+2T>A						.						242	226	231					16																	48158122		2201	4300	6501	SO:0001630	splice_region_variant	94160	exon11			CAGCTTACCTGTC	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.1587+1T>A	chr16.hg19:g.48158122A>T		89.0	0.0		53.0	39.0	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Splice_Site	SNP	ENST00000311303.3	hg19	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.748898	0.89753	.	.	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939;ENST00000416054	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1108	0.72355	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCC12	46715623	1.000000	0.71417	0.994000	0.49952	0.967000	0.64934	8.468000	0.90393	2.206000	0.71126	0.528000	0.53228	.	.	.		0.527	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	Intron	T	48158122	A	T	48158122	5	4	150	1	0	0	0	0	0	0	1	0	52	405	14	4	2570	4	ABCC12	16	48158122	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	16673342	48158122	42196631	421	23145										
MT1M	4499	hgsc.bcm.edu	37	chr16	56667700	56667700	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccgtgggctgtgccaagtgTgcccacggctgtgtctgcaa	14	13	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:56667700T>A	ENST00000379818.3	+	3	631	c.132T>A	c.(130-132)tgT>tgA	p.C44*	MT1JP_ENST00000564564.1_RNA|AC026461.1_ENST00000600389.1_5'Flank	NM_176870.2	NP_789846.1	Q8N339	MT1M_HUMAN	metallothionein 1M	44	Alpha.				cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	5						GTGCCAAGTGTGCCCACGGCT	0.592																																					p.C44X		Atlas-SNP	.											.	MT1M	13	.	0			c.T132A						.						126	129	128					16																	56667700		2198	4300	6498	SO:0001587	stop_gained	4499	exon3			CAAGTGTGCCCAC	AF136177	CCDS42166.1	16q13	2008-02-05				ENSG00000205364		"Metallothioneins"	14296	protein-coding gene	gene with protein product		156357	"metallothionein 1K"	MT1, MT1K		2286373, 8049263	Standard	NM_176870		Approved		uc002ejn.3	Q8N339		ENST00000379818.3:c.132T>A	chr16.hg19:g.56667700T>A	ENSP00000369146:p.Cys44*	41.0	0.0		26.0	8.0	NM_176870	Q8TDN3	Nonsense_Mutation	SNP	ENST00000379818.3	hg19	CCDS42166.1	.	.	.	.	.	.	.	.	.	.	T	37	6.513523	0.97629	.	.	ENSG00000205364	ENST00000379818	.	.	.	2.41	2.41	0.29592	.	0.000000	0.64402	U	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.9971	0.30275	0.0:0.0:0.0:1.0	.	.	.	.	X	44	.	ENSP00000369146:C44X	C	+	3	2	MT1M	55225201	1.000000	0.71417	0.996000	0.52242	0.831000	0.47069	0.857000	0.27831	1.100000	0.41517	0.378000	0.23410	TGT	.	.		0.592	MT1M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434359.1	NM_176870		A	56667700	T	A	56667700	4	1	150	1	0	0	0	0	0	1	0	0	9912	1702	59	4	142	4	MT1M	16	56667700	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	8509578	56667700	33687053	422	23146										
CDH11	1009	hgsc.bcm.edu	37	chr16	64981610	64981610	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atagtccaagtctgaatctgTggtggccgactctagggagc	13	9	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:64981610T>A	ENST00000268603.4	-	13	2902	c.2287A>T	c.(2287-2289)Aca>Tca	p.T763S	CDH11_ENST00000566827.1_Missense_Mutation_p.T637S|CDH11_ENST00000394156.3_3'UTR	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	763					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TCTGAATCTGTGGTGGCCGAC	0.488			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.T763S		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	.	CDH11	260	.	0			c.A2287T						.						77	81	80					16																	64981610		2203	4300	6503	SO:0001583	missense	1009	exon13			AATCTGTGGTGGC	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.2287A>T	chr16.hg19:g.64981610T>A	ENSP00000268603:p.Thr763Ser	172.0	0.0		141.0	36.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	hg19	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	T	1.292	-0.607250	0.03717	.	.	ENSG00000140937	ENST00000268603;ENST00000538390	T	0.76060	-0.99	6.17	5.07	0.68467	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.53158	0.1779	N	0.11000	0.08	0.58432	D	0.999993	B	0.16166	0.016	B	0.20184	0.028	T	0.47471	-0.9115	10	0.07030	T	0.85	.	12.9702	0.58508	0.0:0.0:0.1352:0.8648	.	763	P55287	CAD11_HUMAN	S	763;746	ENSP00000268603:T763S	ENSP00000268603:T763S	T	-	1	0	CDH11	63539111	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	6.002000	0.70693	1.134000	0.42165	-0.313000	0.08912	ACA	.	.		0.488	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		A	64981610	T	A	64981610	3	1	150	1	0	0	0	0	1	0	0	0	3099	1696	59	4	107	4	CDH11	16	64981610	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	8313910	64981610	25373143	423	23147										
CMTM4	146223	hgsc.bcm.edu	37	chr16	66656097	66656097	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccaggaatgtgttcactgcaTatgccgcagtcgccaagaag	11	11	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:66656097T>A	ENST00000330687.4	-	4	672	c.491A>T	c.(490-492)tAt>tTt	p.Y164F	CMTM4_ENST00000394106.2_Missense_Mutation_p.Y164F|CMTM4_ENST00000563952.1_Missense_Mutation_p.Y135F	NM_178818.2|NM_181521.2	NP_848933.1|NP_852662.1	Q8IZR5	CKLF4_HUMAN	CKLF-like MARVEL transmembrane domain containing 4	164	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		GTTCACTGCATATGCCGCAGT	0.567																																					p.Y164F		Atlas-SNP	.											.	CMTM4	19	.	0			c.A491T						.						53	47	49					16																	66656097		2201	4300	6501	SO:0001583	missense	146223	exon4			ACTGCATATGCCG	AF479814	CCDS10817.1, CCDS42170.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000183723	ENSG00000183723			19175	protein-coding gene	gene with protein product		607887	"chemokine-like factor super family 4", "chemokine-like factor superfamily 4"	CKLFSF4		12782130	Standard	NM_178818		Approved		uc002epz.3	Q8IZR5	OTTHUMG00000137500	ENST00000330687.4:c.491A>T	chr16.hg19:g.66656097T>A	ENSP00000333833:p.Tyr164Phe	70.0	0.0		45.0	29.0	NM_178818	Q52M40|Q8IZR4|Q8IZV1	Missense_Mutation	SNP	ENST00000330687.4	hg19	CCDS10817.1	.	.	.	.	.	.	.	.	.	.	T	8.561	0.877747	0.17395	.	.	ENSG00000183723	ENST00000330687;ENST00000394106	T;T	0.20738	2.05;2.05	6.11	6.11	0.99139	Marvel (1);MARVEL-like domain (1);	0.000000	0.85682	D	0.000000	T	0.27098	0.0664	L	0.28054	0.825	0.80722	D	1	D	0.54397	0.966	P	0.56163	0.793	T	0.02713	-1.1120	10	0.17832	T	0.49	-18.3614	16.3636	0.83296	0.0:0.0:0.0:1.0	.	164	Q8IZR5	CKLF4_HUMAN	F	164	ENSP00000333833:Y164F;ENSP00000377666:Y164F	ENSP00000333833:Y164F	Y	-	2	0	CMTM4	65213598	1.000000	0.71417	0.255000	0.24374	0.059000	0.15707	6.592000	0.74095	2.343000	0.79666	0.533000	0.62120	TAT	.	.		0.567	CMTM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268807.1			A	66656097	T	A	66656097	3	1	150	1	0	0	0	0	1	0	0	0	3587	1406	49	4	225	4	CMTM4	16	66656097	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1674487	66656097	23698656	424	23148										
FHOD1	29109	hgsc.bcm.edu	37	chr16	67264347	67264347	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcagcgtgtggcagaactgcAtgatgcgcacttcacgggcc	14	12	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:67264347A>G	ENST00000258201.4	-	19	3168	c.2921T>C	c.(2920-2922)aTg>aCg	p.M974T		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	974	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		GCAGAACTGCATGATGCGCAC	0.607																																					p.M974T		Atlas-SNP	.											.	FHOD1	86	.	0			c.T2921C						.						95	91	92					16																	67264347		2198	4300	6498	SO:0001583	missense	29109	exon19			AACTGCATGATGC	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.2921T>C	chr16.hg19:g.67264347A>G	ENSP00000258201:p.Met974Thr	86.0	0.0		109.0	29.0	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Missense_Mutation	SNP	ENST00000258201.4	hg19	CCDS10834.1	.	.	.	.	.	.	.	.	.	.	G	0.047	-1.262606	0.01445	.	.	ENSG00000135723	ENST00000258201	T	0.16073	2.37	5.76	1.16	0.20824	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.136267	0.64402	N	0.000003	T	0.07324	0.0185	N	0.03608	-0.345	0.27623	N	0.948275	B	0.15141	0.012	B	0.24701	0.055	T	0.34675	-0.9819	10	0.25751	T	0.34	.	10.054	0.42233	0.6208:0.0:0.3791:0.0	.	974	Q9Y613	FHOD1_HUMAN	T	974	ENSP00000258201:M974T	ENSP00000258201:M974T	M	-	2	0	FHOD1	65821848	0.713000	0.27926	0.997000	0.53966	0.073000	0.16967	1.109000	0.31135	-0.073000	0.12842	-1.163000	0.01768	ATG	.	.		0.607	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2			G	67264347	A	G	67264347	3	3	150	1	0	0	0	0	1	0	0	0	5890	217	8	2	589	2	FHOD1	16	67264347	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	608250	67264347	23090406	425	23149										
PLEKHG4	25894	hgsc.bcm.edu	37	chr16	67319047	67319047	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgccgcagaccagaggctggAggaggtgccctgccccaggc	16	14	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:67319047A>T	ENST00000360461.5	+	12	4659	c.2124A>T	c.(2122-2124)ggA>ggT	p.G708G	PLEKHG4_ENST00000450733.1_Silent_p.G627G|PLEKHG4_ENST00000379344.3_Silent_p.G708G|PLEKHG4_ENST00000427155.2_Silent_p.G708G	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	708							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CAGAGGCTGGAGGAGGTGCCC	0.652																																					p.G708G		Atlas-SNP	.											PLEKHG4,NS,carcinoma,0,1	PLEKHG4	94	.	0			c.A2124T						.						21	23	22					16																	67319047		2191	4279	6470	SO:0001819	synonymous_variant	25894	exon13			GGCTGGAGGAGGT	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24501	protein-coding gene	gene with protein product	"puratrophin-1"	609526	"spinocerebellar ataxia 4"	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.2124A>T	chr16.hg19:g.67319047A>T		86.0	0.0		55.0	31.0	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Silent	SNP	ENST00000360461.5	hg19	CCDS32466.1																																																																																			.	.		0.652	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432		T	67319047	A	T	67319047	2	4	150	1	0	0	0	0	0	0	0	1	12080	291	11	4		4	PLEKHG4	16	67319047	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	54700	67319047	23035706	426	23150										
SLC7A6OS	84138	hgsc.bcm.edu	37	chr16	68344261	68344261	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcaggagcctgcagaggcggCttcaggttctccctcctcgt	13	14	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr16:68344261C>T	ENST00000263997.6	-	2	466	c.448G>A	c.(448-450)Gcc>Acc	p.A150T	snoU13_ENST00000458872.1_RNA|PRMT7_ENST00000441236.1_5'Flank|PRMT7_ENST00000339507.5_5'Flank|PRMT7_ENST00000449359.3_5'Flank|PRMT7_ENST00000348497.4_5'Flank	NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	150					hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		GCAGAGGCGGCTTCAGGTTCT	0.612																																					p.A150T		Atlas-SNP	.											.	SLC7A6OS	22	.	0			c.G448A						.						24	25	25					16																	68344261		2198	4300	6498	SO:0001583	missense	84138	exon2			AGGCGGCTTCAGG		CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061			25807	protein-coding gene	gene with protein product							Standard	NM_032178		Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558	ENST00000263997.6:c.448G>A	chr16.hg19:g.68344261C>T	ENSP00000263997:p.Ala150Thr	145.0	0.0		134.0	33.0	NM_032178	Q8TCZ3|Q9H8R8	Missense_Mutation	SNP	ENST00000263997.6	hg19	CCDS10865.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.386061	0.42308	.	.	ENSG00000103061	ENST00000263997	T	0.17054	2.3	4.25	2.31	0.28768	.	0.944258	0.09045	N	0.856764	T	0.24314	0.0589	L	0.51422	1.61	0.09310	N	1	D	0.54964	0.969	P	0.55824	0.785	T	0.16100	-1.0414	10	0.13853	T	0.58	-20.3953	6.8433	0.23975	0.0:0.7924:0.0:0.2076	.	150	Q96CW6	S7A6O_HUMAN	T	150	ENSP00000263997:A150T	ENSP00000263997:A150T	A	-	1	0	SLC7A6OS	66901762	0.010000	0.17322	0.017000	0.16124	0.159000	0.22180	0.505000	0.22642	0.755000	0.32990	-0.261000	0.10672	GCC	.	.		0.612	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178		T	68344261	C	T	68344261	3	4	150	1	0	0	0	0	1	0	0	0	14717	797	28	3	497	3	SLC7A6OS	16	68344261	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	1025214	68344261	22010492	427	23151										
OR1A2	26189	hgsc.bcm.edu	37	chr17	3101071	3101071	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggtgctggccaaccatctcTtggggagcaagttcatctcc	11	12	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:3101071T>A	ENST00000381951.1	+	1	259	c.259T>A	c.(259-261)Ttg>Atg	p.L87M		NM_012352.1	NP_036484.1	Q9Y585	OR1A2_HUMAN	olfactory receptor, family 1, subfamily A, member 2	87					positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(4)|stomach(2)	18						CAACCATCTCTTGGGGAGCAA	0.493																																					p.L87M		Atlas-SNP	.											.	OR1A2	52	.	0			c.T259A						.						171	146	154					17																	3101071		2203	4300	6503	SO:0001583	missense	26189	exon1			CATCTCTTGGGGA	AF155225	CCDS11021.1	17p13.3	2012-08-09			ENSG00000172150	ENSG00000172150		"GPCR / Class A : Olfactory receptors"	8180	protein-coding gene	gene with protein product						10673334	Standard	NM_012352		Approved	OR17-6	uc002fvd.1	Q9Y585	OTTHUMG00000090638	ENST00000381951.1:c.259T>A	chr17.hg19:g.3101071T>A	ENSP00000371377:p.Leu87Met	149.0	0.0		85.0	30.0	NM_012352	Q3KPH3|Q6IFM0|Q6NTD8|Q96R86	Missense_Mutation	SNP	ENST00000381951.1	hg19	CCDS11021.1	.	.	.	.	.	.	.	.	.	.	T	4.222	0.040113	0.08148	.	.	ENSG00000172150	ENST00000381951	D	0.82081	-1.57	3.86	-1.45	0.08828	GPCR, rhodopsin-like superfamily (1);	0.391535	0.18836	N	0.129817	T	0.68677	0.3027	L	0.31845	0.965	0.09310	N	1	B	0.26602	0.154	B	0.29077	0.098	T	0.58239	-0.7671	10	0.54805	T	0.06	.	3.279	0.06908	0.29:0.192:0.0:0.518	.	87	Q9Y585	OR1A2_HUMAN	M	87	ENSP00000371377:L87M	ENSP00000371377:L87M	L	+	1	2	OR1A2	3047821	0.000000	0.05858	0.022000	0.16811	0.120000	0.20174	-4.041000	0.00307	-0.073000	0.12842	0.491000	0.48974	TTG	.	.		0.493	OR1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207293.1	NM_012352		A	3101071	T	A	3101071	3	1	150	1	0	0	0	0	1	0	0	0	10959	1606	56	4	261	4	OR1A2	17	3101071	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10		3101071	78094139	428	23152										
ZNF594	84622	hgsc.bcm.edu	37	chr17	5086891	5086891	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gacaaggtttgagcttccctTaaaagccttcccacactctt	6	13	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:5086891T>A	ENST00000399604.4	-	1	801	c.661A>T	c.(661-663)Aag>Tag	p.K221*	ZNF594_ENST00000575779.1_Nonsense_Mutation_p.K221*			Q96JF6	ZN594_HUMAN	zinc finger protein 594	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GAGCTTCCCTTAAAAGCCTTC	0.448																																					p.K221X		Atlas-SNP	.											.	ZNF594	89	.	0			c.A661T						.						109	111	110					17																	5086891		2038	4204	6242	SO:0001587	stop_gained	84622	exon2			TTCCCTTAAAAGC	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"Zinc fingers, C2H2-type"	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.661A>T	chr17.hg19:g.5086891T>A	ENSP00000382513:p.Lys221*	97.0	0.0		77.0	20.0	NM_032530	Q6RFS0	Nonsense_Mutation	SNP	ENST00000399604.4	hg19	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.121990	0.37436	.	.	ENSG00000180626	ENST00000399604	.	.	.	2.63	2.63	0.31362	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	5.0116	0.14315	0.2674:0.0:0.0:0.7326	.	.	.	.	X	221	.	ENSP00000382513:K221X	K	-	1	0	ZNF594	5027615	0.000000	0.05858	0.957000	0.39632	0.075000	0.17131	-0.169000	0.09911	1.217000	0.43442	0.460000	0.39030	AAG	.	.		0.448	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		A	5086891	T	A	5086891	4	1	150	1	0	0	0	0	0	1	0	0	18039	1763	61	4	1766	4	ZNF594	17	5086891	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1985820	5086891	76108319	429	23153										
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6373607	6373607	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggatgaaggccaccacgtcTgtggactcccagtaactggc	12	12	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:6373607T>A	ENST00000262483.8	-	13	1833	c.1746A>T	c.(1744-1746)acA>acT	p.T582T	PITPNM3_ENST00000421306.3_Silent_p.T546T|PITPNM3_ENST00000576664.1_5'UTR	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	582	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		CCACCACGTCTGTGGACTCCC	0.652																																					p.T582T		Atlas-SNP	.											.	PITPNM3	91	.	0			c.A1746T						.						92	65	74					17																	6373607		2203	4300	6503	SO:0001819	synonymous_variant	83394	exon13			CACGTCTGTGGAC	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.1746A>T	chr17.hg19:g.6373607T>A		54.0	0.0		43.0	13.0	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	hg19	CCDS11076.1																																																																																			.	.		0.652	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		A	6373607	T	A	6373607	2	1	150	1	0	0	0	0	0	0	0	1	11961	1567	55	4		4	PITPNM3	17	6373607	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1286716	6373607	74821603	430	23154										
TXNDC17	84817	hgsc.bcm.edu	37	chr17	6546320	6546320	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcaggccaacctggtggaaaTgttgttctctgaagattaag	11	7	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:6546320T>G	ENST00000250101.5	+	4	678	c.353T>G	c.(352-354)aTg>aGg	p.M118R	TXNDC17_ENST00000570330.1_Missense_Mutation_p.M93R|TXNDC17_ENST00000577146.1_3'UTR|TXNDC17_ENST00000574838.1_3'UTR|KIAA0753_ENST00000572370.1_5'Flank|KIAA0753_ENST00000361413.3_5'Flank	NM_032731.3	NP_116120.1	Q9BRA2	TXD17_HUMAN	thioredoxin domain containing 17	118	Thioredoxin.				oxidation-reduction process (GO:0055114)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|peroxidase activity (GO:0004601)|protein-disulfide reductase activity (GO:0047134)			endometrium(1)|kidney(1)|ovary(1)	3						CTGGTGGAAATGTTGTTCTCT	0.348																																					p.M118R		Atlas-SNP	.											.	TXNDC17	10	.	0			c.T353G						.						152	134	140					17																	6546320		2203	4300	6503	SO:0001583	missense	84817	exon4			TGGAAATGTTGTT	BC006405	CCDS11077.1	17p13.2	2007-08-16	2007-08-16	2007-08-16	ENSG00000129235	ENSG00000129235			28218	protein-coding gene	gene with protein product	"thioredoxin (Trx)-related protein, 14 kDa"		"thioredoxin-like 5"	TXNL5		14607844, 14607843	Standard	NM_032731		Approved	MGC14353, TRP14	uc002gdf.4	Q9BRA2	OTTHUMG00000102053	ENST00000250101.5:c.353T>G	chr17.hg19:g.6546320T>G	ENSP00000250101:p.Met118Arg	95.0	0.0		81.0	9.0	NM_032731	A8K7E8	Missense_Mutation	SNP	ENST00000250101.5	hg19	CCDS11077.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.498223	0.64186	.	.	ENSG00000129235	ENST00000250101	.	.	.	5.85	5.85	0.93711	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.72078	0.3416	M	0.80982	2.52	0.80722	D	1	P	0.52316	0.952	P	0.54590	0.756	T	0.70132	-0.4956	9	0.13853	T	0.58	-27.5886	12.9295	0.58278	0.0:0.0:0.0:1.0	.	118	Q9BRA2	TXD17_HUMAN	R	118	.	ENSP00000250101:M118R	M	+	2	0	TXNDC17	6487044	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.756000	0.74919	2.371000	0.80710	0.533000	0.62120	ATG	.	.		0.348	TXNDC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219854.2	NM_032731		G	6546320	T	G	6546320	3	3	150	1	0	0	0	0	1	0	0	0	16811	1464	51	5	367	5	TXNDC17	17	6546320	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	172713	6546320	74648890	431	23155										
TEKT1	83659	hgsc.bcm.edu	37	chr17	6718508	6718508	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcaatcctcacggcgttctcAgaatatctgatgtttggtga	9	9	4	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:6718508A>T	ENST00000338694.2	-	5	732	c.603T>A	c.(601-603)tcT>tcA	p.S201S	TEKT1_ENST00000535086.1_Silent_p.S55S	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	201						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				CGGCGTTCTCAGAATATCTGA	0.502																																					p.S201S		Atlas-SNP	.											.	TEKT1	49	.	0			c.T603A						.						206	185	193					17																	6718508		2203	4300	6503	SO:0001819	synonymous_variant	83659	exon5			GTTCTCAGAATAT		CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.603T>A	chr17.hg19:g.6718508A>T		127.0	0.0		97.0	29.0	NM_053285	D3DTM7	Silent	SNP	ENST00000338694.2	hg19	CCDS11083.1																																																																																			.	.		0.502	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285		T	6718508	A	T	6718508	2	4	150	1	0	0	0	0	0	0	0	1	15767	175	7	4		4	TEKT1	17	6718508	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	172188	6718508	74476702	432	23156										
NEURL4	84461	hgsc.bcm.edu	37	chr17	7227004	7227004	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	accagcggtccaccatcttcTgaatgacaatttcaaacagc	6	13	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:7227004T>A	ENST00000399464.2	-	13	2315	c.2300A>T	c.(2299-2301)cAg>cTg	p.Q767L	NEURL4_ENST00000315614.7_Missense_Mutation_p.Q767L|NEURL4_ENST00000570460.1_Missense_Mutation_p.Q745L	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	767	NHR 4. {ECO:0000255|PROSITE- ProRule:PRU00400}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CACCATCTTCTGAATGACAAT	0.592																																					p.Q767L		Atlas-SNP	.											.	NEURL4	192	.	0			c.A2300T						.						53	60	58					17																	7227004		2070	4192	6262	SO:0001583	missense	84461	exon13			ATCTTCTGAATGA		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"neuralized homolog 4 (Drosophila)"			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.2300A>T	chr17.hg19:g.7227004T>A	ENSP00000382390:p.Gln767Leu	96.0	0.0		84.0	20.0	NM_001005408	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	hg19	CCDS42251.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.107027	0.77096	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.72615	1.49;-0.67	5.8	5.8	0.92144	NEUZ (3);	0.000000	0.85682	D	0.000000	T	0.61223	0.2330	N	0.01705	-0.755	0.50467	D	0.999872	D;D	0.69078	0.997;0.993	P;P	0.59221	0.854;0.824	T	0.72750	-0.4199	10	0.46703	T	0.11	-17.5541	15.1328	0.72539	0.0:0.0:0.0:1.0	.	767;767	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	L	767	ENSP00000319826:Q767L;ENSP00000382390:Q767L	ENSP00000319826:Q767L	Q	-	2	0	NEURL4	7167728	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.614000	0.67695	2.224000	0.72417	0.533000	0.62120	CAG	.	.		0.592	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442		A	7227004	T	A	7227004	3	1	150	1	0	0	0	0	1	0	0	0	10356	1580	55	4	2456	4	NEURL4	17	7227004	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	508496	7227004	73968206	433	23157										
GUCY2D	3000	hgsc.bcm.edu	37	chr17	7912843	7912843	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gggagacagggtttggctgaAgaaattcccaggggatcagc	16	7	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:7912843A>T	ENST00000254854.4	+	8	1838	c.1688A>T	c.(1687-1689)aAg>aTg	p.K563M		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	563	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				GTTTGGCTGAAGAAATTCCCA	0.572																																					p.K563M		Atlas-SNP	.											.	GUCY2D	82	.	0			c.A1688T						.						130	126	127					17																	7912843		2203	4300	6503	SO:0001583	missense	3000	exon8			GGCTGAAGAAATT	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.1688A>T	chr17.hg19:g.7912843A>T	ENSP00000254854:p.Lys563Met	125.0	0.0		86.0	26.0	NM_000180	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	hg19	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172466	0.78452	.	.	ENSG00000132518	ENST00000254854	D	0.86432	-2.12	4.67	4.67	0.58626	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000057	D	0.95162	0.8432	H	0.96518	3.835	0.44825	D	0.997833	D	0.89917	1.0	D	0.97110	1.0	D	0.95977	0.8974	10	0.72032	D	0.01	.	12.0094	0.53278	1.0:0.0:0.0:0.0	.	563	Q02846	GUC2D_HUMAN	M	563	ENSP00000254854:K563M	ENSP00000254854:K563M	K	+	2	0	GUCY2D	7853568	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.402000	0.90205	2.094000	0.63399	0.459000	0.35465	AAG	.	.		0.572	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			T	7912843	A	T	7912843	3	4	150	1	0	0	0	0	1	0	0	0	6906	72	3	4	1714	4	GUCY2D	17	7912843	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	685839	7912843	73282367	434	23158										
MYH4	4622	hgsc.bcm.edu	37	chr17	10357033	10357033	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggtcatcaatgtctttcttgAgctctgaacattcatcctcc	6	12	6	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:10357033A>T	ENST00000255381.2	-	23	2971	c.2861T>A	c.(2860-2862)cTc>cAc	p.L954H	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	954					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						GTCTTTCTTGAGCTCTGAACA	0.433																																					p.L954H		Atlas-SNP	.											.	MYH4	349	.	0			c.T2861A						.						351	323	333					17																	10357033		2203	4300	6503	SO:0001583	missense	4622	exon23			TTCTTGAGCTCTG		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.2861T>A	chr17.hg19:g.10357033A>T	ENSP00000255381:p.Leu954His	146.0	0.0		141.0	30.0	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.101679	0.76983	.	.	ENSG00000141048	ENST00000255381	D	0.95412	-3.7	5.57	5.57	0.84162	.	0.000000	0.32314	U	0.006268	D	0.98735	0.9575	H	0.98525	4.255	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.99701	1.1004	10	0.87932	D	0	.	16.0284	0.80558	1.0:0.0:0.0:0.0	.	954	Q9Y623	MYH4_HUMAN	H	954	ENSP00000255381:L954H	ENSP00000255381:L954H	L	-	2	0	MYH4	10297758	1.000000	0.71417	0.921000	0.36526	0.989000	0.77384	9.182000	0.94881	2.253000	0.74438	0.533000	0.62120	CTC	.	.		0.433	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10357033	A	T	10357033	3	4	150	1	0	0	0	0	1	0	0	0	10046	304	11	4	3030	4	MYH4	17	10357033	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2444190	10357033	70838177	435	23159										
MYH4	4622	hgsc.bcm.edu	37	chr17	10357189	10357189	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atctttcctctgcatcagccAaggcatctgcttcctaaagg	7	13	4	0	rs138202203		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:10357189A>T	ENST00000255381.2	-	23	2815	c.2705T>A	c.(2704-2706)tTg>tAg	p.L902*	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	902					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						TGCATCAGCCAAGGCATCTGC	0.373																																					p.L902X		Atlas-SNP	.											.	MYH4	349	.	0			c.T2705A						.						206	197	200					17																	10357189		2203	4300	6503	SO:0001587	stop_gained	4622	exon23			TCAGCCAAGGCAT		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.2705T>A	chr17.hg19:g.10357189A>T	ENSP00000255381:p.Leu902*	126.0	0.0		92.0	22.0	NM_017533		Nonsense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	A	38	6.655714	0.97739	.	.	ENSG00000141048	ENST00000255381	.	.	.	5.43	5.43	0.79202	.	0.000000	0.30620	U	0.009232	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7669	0.78135	1.0:0.0:0.0:0.0	.	.	.	.	X	902	.	ENSP00000255381:L902X	L	-	2	0	MYH4	10297914	1.000000	0.71417	0.998000	0.56505	0.378000	0.30076	9.150000	0.94667	2.180000	0.69256	0.533000	0.62120	TTG	.	A|1.000;G|0.000		0.373	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10357189	A	T	10357189	4	4	150	1	0	0	0	0	0	1	0	0	10046	131	5	4	3186	4	MYH4	17	10357189	Nonsense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	156	10357189	70838021	436	23160										
MYH1	4619	hgsc.bcm.edu	37	chr17	10409339	10409339	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatgtcttaccaggagttttAgtttcattggggatgatgca	11	5	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:10409339A>T	ENST00000226207.5	-	18	2140	c.2046T>A	c.(2044-2046)acT>acA	p.T682T	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	682	Myosin motor.				muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CAGGAGTTTTAGTTTCATTGG	0.448																																					p.T682T		Atlas-SNP	.											.	MYH1	403	.	0			c.T2046A						.						134	135	135					17																	10409339		2203	4297	6500	SO:0001819	synonymous_variant	4619	exon18			AGTTTTAGTTTCA		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2046T>A	chr17.hg19:g.10409339A>T		204.0	0.0		208.0	49.0	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	hg19	CCDS11155.1																																																																																			.	.		0.448	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10409339	A	T	10409339	2	4	150	1	0	0	0	0	0	0	0	1	10038	407	15	4		4	MYH1	17	10409339	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	52150	10409339	70785871	437	23161										
BLMH	642	hgsc.bcm.edu	37	chr17	28616480	28616480	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aagcctcataacattcagacAagaaaagatccagcatcgcc	6	12	2	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:28616480A>T	ENST00000261714.6	-	3	406	c.232T>A	c.(232-234)Tgt>Agt	p.C78S	RNU6-1267P_ENST00000410747.1_RNA|BLMH_ENST00000394819.3_Intron	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	78					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	ACATTCAGACAAGAAAAGATC	0.388																																					p.C78S	Pancreas(127;628 1772 12912 33293 36203)	Atlas-SNP	.											.	BLMH	42	.	0			c.T232A						.						58	56	56					17																	28616480		2203	4300	6503	SO:0001583	missense	642	exon3			TCAGACAAGAAAA	X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.232T>A	chr17.hg19:g.28616480A>T	ENSP00000261714:p.Cys78Ser	193.0	0.0		181.0	60.0	NM_000386	B2R796|Q53F86|Q9UER9	Missense_Mutation	SNP	ENST00000261714.6	hg19	CCDS32604.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.163106	0.78226	.	.	ENSG00000108578	ENST00000261714	T	0.40476	1.03	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.44159	0.1280	N	0.12637	0.245	0.80722	D	1	D	0.54397	0.966	D	0.70016	0.967	T	0.36939	-0.9727	10	0.18710	T	0.47	-11.3298	14.897	0.70651	1.0:0.0:0.0:0.0	.	78	Q13867	BLMH_HUMAN	S	78	ENSP00000261714:C78S	ENSP00000261714:C78S	C	-	1	0	BLMH	25640606	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.432000	0.90288	2.100000	0.63781	0.528000	0.53228	TGT	.	.		0.388	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386		T	28616480	A	T	28616480	3	4	150	1	0	0	0	0	1	0	0	0	1446	130	5	4	1175	4	BLMH	17	28616480	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	18207141	28616480	52578730	438	23162										
SLFN12	55106	hgsc.bcm.edu	37	chr17	33738498	33738498	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tttaaggctttaaaaagggcTttcagcaagtatttccttct	7	7	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:33738498T>A	ENST00000394562.1	-	6	2119	c.1596A>T	c.(1594-1596)aaA>aaT	p.K532N	RP11-686D22.8_ENST00000587012.1_RNA|SLFN12_ENST00000460530.1_5'UTR|SLFN12_ENST00000452764.3_Missense_Mutation_p.K532N|SLFN12_ENST00000304905.5_Missense_Mutation_p.K532N			Q8IYM2	SLN12_HUMAN	schlafen family member 12	532							ATP binding (GO:0005524)			breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TAAAAAGGGCTTTCAGCAAGT	0.388																																					p.K532N		Atlas-SNP	.											.	SLFN12	56	.	0			c.A1596T						.						58	59	59					17																	33738498		2203	4299	6502	SO:0001583	missense	55106	exon4			AAGGGCTTTCAGC	AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.1596A>T	chr17.hg19:g.33738498T>A	ENSP00000378063:p.Lys532Asn	134.0	0.0		162.0	30.0	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	hg19	CCDS11295.1	.	.	.	.	.	.	.	.	.	.	T	10.77	1.442890	0.25987	.	.	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764	T;T;T	0.03982	3.74;3.74;3.74	2.74	-2.12	0.07165	.	.	.	.	.	T	0.06371	0.0164	L	0.36672	1.1	0.09310	N	1	P	0.52061	0.95	P	0.50314	0.637	T	0.32079	-0.9920	9	0.72032	D	0.01	.	6.3654	0.21451	0.0:0.3992:0.0:0.6008	.	532	Q8IYM2	SLN12_HUMAN	N	532	ENSP00000378063:K532N;ENSP00000302077:K532N;ENSP00000394903:K532N	ENSP00000302077:K532N	K	-	3	2	SLFN12	30762611	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.536000	0.00940	-0.276000	0.09206	-0.437000	0.05841	AAA	.	.		0.388	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042		A	33738498	T	A	33738498	3	1	150	1	0	0	0	0	1	0	0	0	14749	1606	56	4	144	4	SLFN12	17	33738498	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	5122018	33738498	47456712	439	23163										
MYO19	80179	hgsc.bcm.edu	37	chr17	34859822	34859822	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccagcagcactgatatggatGgtctccacgaggccacaggc	12	13	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:34859822G>T	ENST00000431794.3	-	20	2466	c.1944C>A	c.(1942-1944)acC>acA	p.T648T	MYO19_ENST00000268852.9_Silent_p.T448T	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	648	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TGATATGGATGGTCTCCACGA	0.637																																					p.T648T		Atlas-SNP	.											.	MYO19	130	.	0			c.C1944A						.						20	23	22					17																	34859822		2065	4202	6267	SO:0001819	synonymous_variant	80179	exon21			ATGGATGGTCTCC	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"Myosins / Myosin superfamily : Class XIX"	26234	protein-coding gene	gene with protein product			"myosin head domain containing 1"	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.1944C>A	chr17.hg19:g.34859822G>T		32.0	0.0		29.0	10.0	NM_001163735	Q59GS4|Q9H5X2	Silent	SNP	ENST00000431794.3	hg19	CCDS54112.1																																																																																			.	.		0.637	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109		T	34859822	G	T	34859822	2	4	150	1	0	0	0	0	0	0	0	1	10076	1335	47	3		3	MYO19	17	34859822	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	1121324	34859822	46335388	440	23164										
KRTAP9-3	83900	hgsc.bcm.edu	37	chr17	39388765	39388765	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctgacaccatgacccactgTtgctccccttgctgtcagcc	7	18	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:39388765T>A	ENST00000411528.2	+	1	51	c.12T>A	c.(10-12)tgT>tgA	p.C4*		NM_031962.2	NP_114168.1	Q9BYQ3	KRA93_HUMAN	keratin associated protein 9-3	4						keratin filament (GO:0045095)				breast(1)|endometrium(3)|lung(2)|ovary(1)|prostate(1)	8		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			TGACCCACTGTTGCTCCCCTT	0.572																																					p.C4X		Atlas-SNP	.											.	KRTAP9-3	11	.	0			c.T12A						.						124	141	135					17																	39388765		2105	4300	6405	SO:0001587	stop_gained	83900	exon1			CCACTGTTGCTCC	AJ406947	CCDS11385.1	17q21.2	2013-06-25			ENSG00000204873	ENSG00000204873		"Keratin associated proteins"	16927	protein-coding gene	gene with protein product						11279113	Standard	NM_031962		Approved	KAP9.3	uc021txg.1	Q9BYQ3	OTTHUMG00000133427	ENST00000411528.2:c.12T>A	chr17.hg19:g.39388765T>A	ENSP00000392189:p.Cys4*	191.0	0.0		248.0	35.0	NM_031962		Nonsense_Mutation	SNP	ENST00000411528.2	hg19	CCDS11385.1	.	.	.	.	.	.	.	.	.	.	.	19.22	3.786166	0.70337	.	.	ENSG00000204873	ENST00000411528	.	.	.	2.93	0.784	0.18578	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.9316	0.24444	0.0:0.736:0.0:0.264	.	.	.	.	X	4	.	ENSP00000392189:C4X	C	+	3	2	KRTAP9-3	36642291	0.902000	0.30710	0.962000	0.40283	0.292000	0.27327	0.505000	0.22642	0.089000	0.17243	-0.548000	0.04221	TGT	.	.		0.572	KRTAP9-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257290.1			A	39388765	T	A	39388765	4	1	150	1	0	0	0	0	0	1	0	0	8583	1731	60	4	14	4	KRTAP9-3	17	39388765	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4528943	39388765	41806445	441	23165										
KRT35	3886	hgsc.bcm.edu	37	chr17	39635249	39635249	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcgcagtgagttcacttccTatagcacagaccaggatgag	11	10	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:39635249T>A	ENST00000393989.1	-	4	754		c.e4-2		KRT35_ENST00000246639.2_Splice_Site	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35						anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				GTTCACTTCCTATAGCACAGA	0.562																																					.		Atlas-SNP	.											.	KRT35	58	.	0			c.712-2A>T						.						48	52	50					17																	39635249		2200	4300	6500	SO:0001630	splice_region_variant	3886	exon5			ACTTCCTATAGCA	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"-", "Intermediate filaments type I, keratins (acidic)"	6453	protein-coding gene	gene with protein product	"hard keratin type I 5"	602764	"keratin, hair, acidic, 5"	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.712-2A>T	chr17.hg19:g.39635249T>A		73.0	0.0		81.0	7.0	NM_002280	O76012|Q92651	Splice_Site	SNP	ENST00000393989.1	hg19	CCDS11394.2	.	.	.	.	.	.	.	.	.	.	T	17.92	3.507391	0.64410	.	.	ENSG00000197079	ENST00000246639;ENST00000393989	.	.	.	4.7	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7876	0.63119	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KRT35	36888775	1.000000	0.71417	0.918000	0.36340	0.708000	0.40852	7.360000	0.79487	2.095000	0.63458	0.533000	0.62120	.	.	.		0.562	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280	Intron	A	39635249	T	A	39635249	5	1	150	1	0	0	0	0	0	0	1	0	8481	1536	53	4	673	4	KRT35	17	39635249	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	246484	39635249	41559961	442	23166										
CRHR1	1394	hgsc.bcm.edu	37	chr17	43893924	43893924	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggccctgccctgcctttttcTatggtgtccgctacaatacc	8	15	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:43893924T>A	ENST00000398285.3	+	3	217	c.217T>A	c.(217-219)Tat>Aat	p.Y73N	RP11-105N13.4_ENST00000587305.1_RNA|CRHR1_ENST00000293493.7_De_novo_Start_OutOfFrame|CRHR1_ENST00000577353.1_Missense_Mutation_p.Y73N|CRHR1_ENST00000352855.5_Intron|CRHR1_ENST00000339069.5_De_novo_Start_InFrame|CRHR1_ENST00000314537.5_Missense_Mutation_p.Y73N	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	73					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		TGCCTTTTTCTATGGTGTCCG	0.617																																					p.Y73N	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.T217A						.						48	50	49					17																	43893924		1952	4132	6084	SO:0001583	missense	1394	exon3			TTTTTCTATGGTG	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"GPCR / Class B : Corticotropin-releasing factor receptors"	2357	protein-coding gene	gene with protein product	"corticotropin-releasing factor receptor"	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.217T>A	chr17.hg19:g.43893924T>A	ENSP00000381333:p.Tyr73Asn	54.0	0.0		77.0	19.0	NM_001145148	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Missense_Mutation	SNP	ENST00000398285.3	hg19	CCDS45712.1	.	.	.	.	.	.	.	.	.	.	T	11.31	1.601725	0.28534	.	.	ENSG00000120088	ENST00000398285;ENST00000314537;ENST00000347197	T;T;T	0.52754	0.65;0.65;0.65	5.04	5.04	0.67666	GPCR, family 2, extracellular hormone receptor domain (3);	0.282495	0.35646	N	0.003074	T	0.21062	0.0507	N	0.01576	-0.805	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.08166	-1.0735	10	0.35671	T	0.21	.	11.109	0.48221	0.0:0.0:0.0:1.0	.	73;73;73	P34998-4;P34998;P34998-2	.;CRFR1_HUMAN;.	N	73	ENSP00000381333:Y73N;ENSP00000326060:Y73N;ENSP00000239167:Y73N	ENSP00000326060:Y73N	Y	+	1	0	CRHR1	41249705	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	2.026000	0.41069	2.126000	0.65437	0.533000	0.62120	TAT	.	.		0.617	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3			A	43893924	T	A	43893924	3	1	150	1	0	0	0	0	1	0	0	0	3873	1522	53	4	227	4	CRHR1	17	43893924	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4258675	43893924	37301286	443	23167										
OSBPL7	114881	hgsc.bcm.edu	37	chr17	45888020	45888020	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccagggatttgccccagaacTtgttcttccacttcatatct	6	13	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:45888020T>A	ENST00000007414.3	-	18	2011	c.1820A>T	c.(1819-1821)aAg>aTg	p.K607M	OSBPL7_ENST00000392507.3_Missense_Mutation_p.K607M	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	607					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						GCCCCAGAACTTGTTCTTCCA	0.562																																					p.K607M		Atlas-SNP	.											.	OSBPL7	65	.	0			c.A1820T						.						64	59	61					17																	45888020		2203	4300	6503	SO:0001583	missense	114881	exon18			CAGAACTTGTTCT	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.1820A>T	chr17.hg19:g.45888020T>A	ENSP00000007414:p.Lys607Met	110.0	0.0		125.0	28.0	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	hg19	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.317630	0.81469	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.38887	1.11;1.11	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	T	0.74458	0.3719	H	0.96748	3.875	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.82892	-0.0232	10	0.87932	D	0	-29.8689	12.4486	0.55666	0.0:0.0:0.0:1.0	.	607	Q9BZF2	OSBL7_HUMAN	M	607	ENSP00000007414:K607M;ENSP00000376295:K607M	ENSP00000007414:K607M	K	-	2	0	OSBPL7	43243019	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.944000	0.87722	1.588000	0.49971	0.402000	0.26972	AAG	.	.		0.562	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		A	45888020	T	A	45888020	3	1	150	1	0	0	0	0	1	0	0	0	11291	1609	56	4	732	4	OSBPL7	17	45888020	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1994096	45888020	35307190	444	23168										
HOXB8	3218	hgsc.bcm.edu	37	chr17	46691811	46691811	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttgcagcgggtcgtagccgtAgaaattgccggggtccccgt	15	11	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:46691811A>T	ENST00000239144.4	-	1	490	c.256T>A	c.(256-258)Tac>Aac	p.Y86N	HOXB7_ENST00000567101.2_Intron|HOXB8_ENST00000576562.1_Missense_Mutation_p.Y86N	NM_024016.3	NP_076921.1	P17481	HXB8_HUMAN	homeobox B8	86					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|dorsal spinal cord development (GO:0021516)|embryonic skeletal system morphogenesis (GO:0048704)|grooming behavior (GO:0007625)|negative regulation of myeloid cell differentiation (GO:0045638)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(8)|urinary_tract(2)	11						TCGTAGCCGTAGAAATTGCCG	0.667																																					p.Y86N		Atlas-SNP	.											.	HOXB8	26	.	0			c.T256A						.						49	49	49					17																	46691811		2203	4298	6501	SO:0001583	missense	3218	exon1			AGCCGTAGAAATT		CCDS11533.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120068	ENSG00000120068		"Homeoboxes / ANTP class : HOXL subclass"	5119	protein-coding gene	gene with protein product		142963	"homeo box B8"	HOX2, HOX2D		1973146, 1358459	Standard	XM_005257286		Approved		uc002inw.3	P17481	OTTHUMG00000159904	ENST00000239144.4:c.256T>A	chr17.hg19:g.46691811A>T	ENSP00000239144:p.Tyr86Asn	106.0	0.0		113.0	24.0	NM_024016	Q9H1I2	Missense_Mutation	SNP	ENST00000239144.4	hg19	CCDS11533.1	.	.	.	.	.	.	.	.	.	.	a	16.03	3.007494	0.54361	.	.	ENSG00000120068	ENST00000239144	T	0.44482	0.92	2.97	1.87	0.25490	.	0.000000	0.53938	U	0.000052	T	0.62816	0.2459	M	0.86740	2.835	0.53005	D	0.999963	D	0.71674	0.998	D	0.75484	0.986	T	0.61422	-0.7066	10	0.49607	T	0.09	.	7.8125	0.29239	0.895:0.0:0.105:0.0	.	86	P17481	HXB8_HUMAN	N	86	ENSP00000239144:Y86N	ENSP00000239144:Y86N	Y	-	1	0	HOXB8	44046810	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	6.872000	0.75536	0.377000	0.24735	0.241000	0.17934	TAC	.	.		0.667	HOXB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358092.3			T	46691811	A	T	46691811	3	4	150	1	0	0	0	0	1	0	0	0	7316	420	15	4	483	4	HOXB8	17	46691811	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	803791	46691811	34503399	445	23169										
WFIKKN2	124857	hgsc.bcm.edu	37	chr17	48917022	48917022	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcagggctctgagtgtgacAtctgggatggccagcccgtg	16	10	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:48917022A>T	ENST00000311378.4	+	2	901	c.373A>T	c.(373-375)Atc>Ttc	p.I125F	WFIKKN2_ENST00000426127.1_Missense_Mutation_p.I32F|RP11-506D12.5_ENST00000572491.2_RNA	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	125					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			TGAGTGTGACATCTGGGATGG	0.587																																					p.I125F		Atlas-SNP	.											.	WFIKKN2	69	.	0			c.A373T						.						85	78	80					17																	48917022		2203	4300	6503	SO:0001583	missense	124857	exon2			TGTGACATCTGGG	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"Immunoglobulin superfamily / I-set domain containing", "WAP four-disulfide core domain containing"	30916	protein-coding gene	gene with protein product	"WAP four-disulfide core domain 20B"	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.373A>T	chr17.hg19:g.48917022A>T	ENSP00000311184:p.Ile125Phe	179.0	0.0		144.0	44.0	NM_175575	Q6UXZ9	Missense_Mutation	SNP	ENST00000311378.4	hg19	CCDS11575.1	.	.	.	.	.	.	.	.	.	.	A	17.81	3.481595	0.63849	.	.	ENSG00000173714	ENST00000426127;ENST00000311378;ENST00000393226	D;D	0.82433	-1.55;-1.61	5.24	4.15	0.48705	.	0.058387	0.64402	D	0.000001	D	0.88051	0.6333	M	0.66939	2.045	0.58432	D	0.999998	D	0.69078	0.997	D	0.63488	0.915	D	0.87880	0.2677	10	0.87932	D	0	.	10.8307	0.46659	0.9253:0.0:0.0747:0.0	.	125	Q8TEU8	WFKN2_HUMAN	F	32;125;32	ENSP00000405889:I32F;ENSP00000311184:I125F	ENSP00000311184:I125F	I	+	1	0	WFIKKN2	46272021	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.313000	0.65798	0.825000	0.34637	0.524000	0.50904	ATC	.	.		0.587	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575		T	48917022	A	T	48917022	3	4	150	1	0	0	0	0	1	0	0	0	17374	217	8	4	379	4	WFIKKN2	17	48917022	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2225211	48917022	32278188	446	23170										
TRIM25	7706	hgsc.bcm.edu	37	chr17	54981763	54981763	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcctcttcctttatcttcctTgtcgaggtggtctctgaggc	9	12	3	1	rs200224902		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:54981763T>A	ENST00000316881.4	-	3	829	c.780A>T	c.(778-780)acA>acT	p.T260T	TRIM25_ENST00000537230.1_Silent_p.T260T	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	260	Interaction with influenza A virus NS1.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)|response to estrogen (GO:0043627)|response to vitamin D (GO:0033280)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Breast(9;6.15e-08)					TTATCTTCCTTGTCGAGGTGG	0.478																																					p.T260T		Atlas-SNP	.											.	TRIM25	52	.	0			c.A780T						.						215	195	202					17																	54981763		2203	4300	6503	SO:0001819	synonymous_variant	7706	exon3			CTTCCTTGTCGAG	D21205	CCDS11591.1	17q23.1	2013-01-09	2011-01-25	2004-03-30				"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	12932	protein-coding gene	gene with protein product		600453	"zinc finger protein 147 (estrogen-responsive finger protein)", "tripartite motif-containing 25"	ZNF147		7789997	Standard	NM_005082		Approved	EFP, RNF147	uc002iut.3	Q14258		ENST00000316881.4:c.780A>T	chr17.hg19:g.54981763T>A		101.0	0.0		125.0	32.0	NM_005082		Silent	SNP	ENST00000316881.4	hg19	CCDS11591.1																																																																																			.	T|1.000;C|0.000		0.478	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082		A	54981763	T	A	54981763	2	1	150	1	0	0	0	0	0	0	0	1	16514	1799	63	4		4	TRIM25	17	54981763	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	6064741	54981763	26213447	447	23171										
CCDC46	201134	hgsc.bcm.edu	37	chr17	64059102	64059102	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tttttttcccagtcattattTagagattccgtactttgttc	5	8	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:64059102T>A	ENST00000392769.2	-	11	1271	c.1053A>T	c.(1051-1053)ctA>ctT	p.L351L	CEP112_ENST00000541355.1_5'UTR|CEP112_ENST00000537949.1_Silent_p.L309L|CEP112_ENST00000535342.2_Silent_p.L351L	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	351					receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						AGTCATTATTTAGAGATTCCG	0.313																																					p.L351L		Atlas-SNP	.											.	CEP112	192	.	0			c.A1053T						.						124	115	118					17																	64059102		2201	4297	6498	SO:0001819	synonymous_variant	201134	exon11			ATTATTTAGAGAT	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"coiled-coil domain containing 46"	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.1053A>T	chr17.hg19:g.64059102T>A		67.0	0.0		68.0	6.0	NM_001199165	Q6PIB5|Q8NCR4|Q8NFR4	Silent	SNP	ENST00000392769.2	hg19	CCDS32710.1																																																																																			.	.		0.313	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036		A	64059102	T	A	64059102	2	1	150	1	0	0	0	0	0	0	0	1	2819	1741	61	4		4	CCDC46	17	64059102	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	9077339	64059102	17136108	448	23172										
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76047470	76047470	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	caacaccacacacagggtcgAgacgccgcccccgcaccagg	10	19	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:76047470A>T	ENST00000588061.1	+	5	3054	c.2327A>T	c.(2326-2328)gAg>gTg	p.E776V	TNRC6C_ENST00000335749.4_Missense_Mutation_p.E776V|TNRC6C_ENST00000544502.1_Missense_Mutation_p.E776V|TNRC6C_ENST00000588847.1_Missense_Mutation_p.E776V|TNRC6C_ENST00000301624.4_Missense_Mutation_p.E776V|TNRC6C_ENST00000541771.1_Missense_Mutation_p.E776V			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	776	Sufficient for interaction with argonaute family proteins.|Thr-rich.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CACAGGGTCGAGACGCCGCCC	0.517																																					p.E776V		Atlas-SNP	.											.	TNRC6C	173	.	0			c.A2327T						.						15	14	14					17																	76047470		1660	3290	4950	SO:0001583	missense	57690	exon4			GGGTCGAGACGCC	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.2327A>T	chr17.hg19:g.76047470A>T	ENSP00000468647:p.Glu776Val	88.0	0.0		101.0	21.0	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.894739	0.33442	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.15372	2.43;2.46;2.46;2.43	6.08	3.88	0.44766	.	1.325240	0.04396	N	0.363338	T	0.15998	0.0385	L	0.27053	0.805	0.09310	N	0.999998	B;B;B	0.22983	0.078;0.034;0.0	B;B;B	0.21708	0.036;0.036;0.001	T	0.36407	-0.9749	10	0.37606	T	0.19	-7.0007	10.3965	0.44203	0.8695:0.0:0.1305:0.0	.	776;776;776	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	V	776	ENSP00000336783:E776V;ENSP00000301624:E776V;ENSP00000440310:E776V;ENSP00000442421:E776V	ENSP00000301624:E776V	E	+	2	0	TNRC6C	73559065	1.000000	0.71417	0.101000	0.21167	0.026000	0.11368	2.512000	0.45485	0.547000	0.28938	0.533000	0.62120	GAG	.	.		0.517	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		T	76047470	A	T	76047470	3	4	150	1	0	0	0	0	1	0	0	0	16357	304	11	4	2329	4	TNRC6C	17	76047470	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	11988368	76047470	5147740	449	23173										
CYTH1	9267	hgsc.bcm.edu	37	chr17	76677126	76677126	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttccacggggctccttatccTacagaacagttgaagagagg	11	10	0	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:76677126T>A	ENST00000446868.3	-	12	962		c.e12-2		CYTH1_ENST00000361101.4_Splice_Site|CYTH1_ENST00000585509.1_Splice_Site|CYTH1_ENST00000591455.1_Splice_Site|CYTH1_ENST00000589297.1_Splice_Site|CYTH1_ENST00000589296.1_Intron|CYTH1_ENST00000586175.1_Splice_Site			Q15438	CYH1_HUMAN	cytohesin 1						establishment of epithelial cell polarity (GO:0090162)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	19						CTCCTTATCCTACAGAACAGT	0.453																																					.		Atlas-SNP	.											.	CYTH1	36	.	0			c.892-2A>T						.						83	86	85					17																	76677126		2203	4300	6503	SO:0001630	splice_region_variant	9267	exon12			TTATCCTACAGAA	M85169	CCDS32754.1, CCDS42392.2	17q25	2014-05-02	2008-08-14	2008-08-14	ENSG00000108669	ENSG00000108669		"Pleckstrin homology (PH) domain containing"	9501	protein-coding gene	gene with protein product		182115	"pleckstrin homology, Sec7 and coiled-coil domains 1"	PSCD1		1511013, 8449036, 21628335, 20018626	Standard	XM_006722180		Approved	B2-1, D17S811E, cytohesin-1	uc002jvw.3	Q15438	OTTHUMG00000150253	ENST00000446868.3:c.892-2A>T	chr17.hg19:g.76677126T>A		86.0	0.0		133.0	27.0	NM_004762	A6NFW7|B7Z1T4|Q9P123|Q9P124	Splice_Site	SNP	ENST00000446868.3	hg19		.	.	.	.	.	.	.	.	.	.	T	24.7	4.563340	0.86335	.	.	ENSG00000108669	ENST00000446868;ENST00000361101;ENST00000539525;ENST00000537048;ENST00000262763;ENST00000392453	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2049	0.65728	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CYTH1	74188721	1.000000	0.71417	0.895000	0.35142	0.956000	0.61745	7.865000	0.87049	1.836000	0.53414	0.383000	0.25322	.	.	.		0.453	CYTH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317099.1	NM_004762	Intron	A	76677126	T	A	76677126	5	1	150	1	0	0	0	0	0	0	1	0	4205	1536	53	4	318	4	CYTH1	17	76677126	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	629656	76677126	4518084	450	23174										
SLC38A10	124565	hgsc.bcm.edu	37	chr17	79256084	79256084	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	caggctgagcgggagcacgaTgcacagcgacacggcgaaca	15	12	0	1	rs146598954	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:79256084T>A	ENST00000374759.3	-	5	789	c.406A>T	c.(406-408)Atc>Ttc	p.I136F	SLC38A10_ENST00000288439.5_Missense_Mutation_p.I136F|SLC38A10_ENST00000546352.1_5'Flank	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	136					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GGGAGCACGATGCACAGCGAC	0.652																																					p.I136F		Atlas-SNP	.											.	SLC38A10	133	.	0			c.A406T						.						93	70	78					17																	79256084		2202	4300	6502	SO:0001583	missense	124565	exon5			GCACGATGCACAG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.406A>T	chr17.hg19:g.79256084T>A	ENSP00000363891:p.Ile136Phe	196.0	0.0		243.0	46.0	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Missense_Mutation	SNP	ENST00000374759.3	hg19	CCDS42397.1	.	.	.	.	.	.	.	.	.	.	T	17.36	3.369220	0.61624	.	.	ENSG00000157637	ENST00000374759;ENST00000288439;ENST00000539748	T;T;T	0.03152	4.03;4.03;4.03	5.19	4.07	0.47477	.	0.228496	0.43579	D	0.000542	T	0.10680	0.0261	M	0.66939	2.045	0.58432	D	0.999998	P;P	0.43607	0.812;0.58	P;P	0.53360	0.481;0.724	T	0.01283	-1.1396	10	0.46703	T	0.11	-9.8895	10.1012	0.42507	0.0:0.0849:0.0:0.9151	.	136;136	Q9HBR0-2;Q9HBR0	.;S38AA_HUMAN	F	136;136;88	ENSP00000363891:I136F;ENSP00000288439:I136F;ENSP00000439115:I88F	ENSP00000288439:I136F	I	-	1	0	SLC38A10	76870679	1.000000	0.71417	0.994000	0.49952	0.093000	0.18481	3.136000	0.50554	0.766000	0.33244	-0.408000	0.06270	ATC	.	T|0.995;C|0.005		0.652	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		A	79256084	T	A	79256084	3	1	150	1	0	0	0	0	1	0	0	0	14617	1464	51	4	3279	4	SLC38A10	17	79256084	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2578958	79256084	1939126	451	23175										
ARHGDIA	396	hgsc.bcm.edu	37	chr17	79826836	79826836	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcgtctgtgaagcgggacttGatgctgtagctgccccgggc	15	11	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr17:79826836G>C	ENST00000269321.7	-	6	666	c.531C>G	c.(529-531)atC>atG	p.I177M	ARHGDIA_ENST00000582520.1_5'Flank|RP11-498C9.3_ENST00000576554.1_RNA|ARHGDIA_ENST00000580685.1_Missense_Mutation_p.I177M|ARHGDIA_ENST00000541078.2_Missense_Mutation_p.I177M|RP11-498C9.3_ENST00000576021.1_RNA|ARHGDIA_ENST00000400721.4_Intron|ARHGDIA_ENST00000581876.1_Missense_Mutation_p.I102M|ARHGDIA_ENST00000584461.1_Intron	NM_001185078.1|NM_004309.4	NP_001172007.1|NP_004300.1	P52565	GDIR1_HUMAN	Rho GDP dissociation inhibitor (GDI) alpha	177					cellular component movement (GO:0006928)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of axonogenesis (GO:0050772)|regulation of axonogenesis (GO:0050770)|regulation of protein localization (GO:0032880)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|semaphorin-plexin signaling pathway (GO:0071526)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)	GTPase activator activity (GO:0005096)|Rho GDP-dissociation inhibitor activity (GO:0005094)			endometrium(1)|lung(1)|prostate(1)	3	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			AGCGGGACTTGATGCTGTAGC	0.627																																					p.I177M		Atlas-SNP	.											.	ARHGDIA	14	.	0			c.C531G						.						101	87	92					17																	79826836		2203	4300	6503	SO:0001583	missense	396	exon6			GGACTTGATGCTG	BC028333	CCDS11788.1, CCDS58609.1	17q25.3	2005-12-20				ENSG00000141522			678	protein-coding gene	gene with protein product		601925		GDIA1		9186513	Standard	NM_001185077		Approved	RHOGDI	uc002kbq.3	P52565		ENST00000269321.7:c.531C>G	chr17.hg19:g.79826836G>C	ENSP00000269321:p.Ile177Met	80.0	0.0		87.0	9.0	NM_004309	A8MXW0|B2R5X1|B4DDD3|B4DUV9|Q6IBM5	Missense_Mutation	SNP	ENST00000269321.7	hg19	CCDS11788.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.592605	0.46214	.	.	ENSG00000141522	ENST00000269321;ENST00000541078;ENST00000400721	.	.	.	4.44	3.47	0.39725	Immunoglobulin E-set (1);	0.115737	0.56097	D	0.000025	T	0.74520	0.3727	M	0.78637	2.42	0.51767	D	0.999931	P	0.41929	0.765	P	0.61003	0.882	T	0.74532	-0.3634	9	0.62326	D	0.03	-27.2918	7.3657	0.26772	0.0855:0.0:0.7478:0.1666	.	177	P52565	GDIR1_HUMAN	M	177;177;151	.	ENSP00000269321:I177M	I	-	3	3	ARHGDIA	77420125	1.000000	0.71417	1.000000	0.80357	0.122000	0.20287	4.899000	0.63245	1.070000	0.40811	0.563000	0.77884	ATC	.	.		0.627	ARHGDIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441679.2	NM_004309		C	79826836	G	C	79826836	3	2	150	1	0	0	0	0	1	0	0	0	890	1280	45	4	87	4	ARHGDIA	17	79826836	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	570752	79826836	1368374	452	23176										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3067424	3067424	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggtgctcacgccgttgatggTgaagtacgcggtcctcccag	14	12	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr18:3067424T>A	ENST00000356443.4	-	38	5227	c.4894A>T	c.(4894-4896)Acc>Tcc	p.T1632S	MYOM1_ENST00000400569.3_Missense_Mutation_p.T1632S|MYOM1_ENST00000261606.7_Missense_Mutation_p.T1536S	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1632	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CCGTTGATGGTGAAGTACGCG	0.592																																					p.T1632S		Atlas-SNP	.											.	MYOM1	192	.	0			c.A4894T						.						75	78	77					18																	3067424		2203	4300	6503	SO:0001583	missense	8736	exon38			TGATGGTGAAGTA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4894A>T	chr18.hg19:g.3067424T>A	ENSP00000348821:p.Thr1632Ser	144.0	0.0		65.0	27.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	16.96	3.265427	0.59431	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.69435	-0.4;-0.4;-0.4	5.79	4.62	0.57501	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.199476	0.52532	D	0.000080	T	0.65770	0.2723	M	0.73319	2.225	0.42002	D	0.990894	B;P	0.38110	0.04;0.618	B;B	0.42163	0.044;0.378	T	0.61008	-0.7149	10	0.13470	T	0.59	.	11.3034	0.49320	0.2418:0.0:0.0:0.7581	.	1536;1632	P52179-2;P52179	.;MYOM1_HUMAN	S	1632;1632;1536	ENSP00000348821:T1632S;ENSP00000383413:T1632S;ENSP00000261606:T1536S	ENSP00000261606:T1536S	T	-	1	0	MYOM1	3057424	1.000000	0.71417	0.999000	0.59377	0.261000	0.26267	5.142000	0.64820	0.999000	0.39023	0.533000	0.62120	ACC	.	.		0.592	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		A	3067424	T	A	3067424	3	1	150	1	0	0	0	0	1	0	0	0	10100	1696	59	4	167	4	MYOM1	18	3067424	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10		3067424	75009824	453	23177										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3086130	3086130	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgtaccacacaatatgagtcTccttcttaatatttgccacc	4	12	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr18:3086130T>A	ENST00000356443.4	-	30	4490	c.4157A>T	c.(4156-4158)gAg>gTg	p.E1386V	MYOM1_ENST00000400569.3_Missense_Mutation_p.E1386V|MYOM1_ENST00000261606.7_Missense_Mutation_p.E1290V	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1386	Ig-like C2-type 4.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AATATGAGTCTCCTTCTTAAT	0.358																																					p.E1386V		Atlas-SNP	.											.	MYOM1	192	.	0			c.A4157T						.						139	121	127					18																	3086130		1839	4089	5928	SO:0001583	missense	8736	exon30			TGAGTCTCCTTCT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4157A>T	chr18.hg19:g.3086130T>A	ENSP00000348821:p.Glu1386Val	63.0	0.0		52.0	16.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.396982	0.62177	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.70986	-0.53;-0.53;-0.53	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.160187	0.56097	D	0.000029	T	0.82038	0.4950	M	0.75085	2.285	0.80722	D	1	P;D	0.56521	0.942;0.976	P;P	0.60949	0.697;0.881	T	0.82864	-0.0246	10	0.48119	T	0.1	.	16.0953	0.81117	0.0:0.0:0.0:1.0	.	1290;1386	P52179-2;P52179	.;MYOM1_HUMAN	V	1386;1386;1290	ENSP00000348821:E1386V;ENSP00000383413:E1386V;ENSP00000261606:E1290V	ENSP00000261606:E1290V	E	-	2	0	MYOM1	3076130	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	7.993000	0.88291	2.204000	0.70986	0.383000	0.25322	GAG	.	.		0.358	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		A	3086130	T	A	3086130	3	1	150	1	0	0	0	0	1	0	0	0	10100	1551	54	4	936	4	MYOM1	18	3086130	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	18706	3086130	74991118	454	23178										
DLGAP1	9229	hgsc.bcm.edu	37	chr18	3880047	3880047	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gaccccgtggtgatggctgcGgctgcctgatagccctttca	13	13	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr18:3880047G>A	ENST00000315677.3	-	4	617	c.22C>T	c.(22-24)Cgc>Tgc	p.R8C	DLGAP1_ENST00000515196.2_Missense_Mutation_p.R8C|DLGAP1_ENST00000584874.1_Missense_Mutation_p.R8C|DLGAP1_ENST00000581527.1_Missense_Mutation_p.R8C|DLGAP1-AS3_ENST00000577649.1_RNA	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	8					synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				TGATGGCTGCGGCTGCCTGAT	0.672																																					p.R8C		Atlas-SNP	.											.	DLGAP1	201	.	0			c.C22T						.																																			SO:0001583	missense	9229	exon4			GGCTGCGGCTGCC	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"discs, large (Drosophila) homolog-associated protein 1"			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.22C>T	chr18.hg19:g.3880047G>A	ENSP00000316377:p.Arg8Cys	23.0	0.0		11.0	5.0	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	hg19	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.361662	0.82353	.	.	ENSG00000170579	ENST00000315677;ENST00000515196	T;T	0.18338	2.23;2.22	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.50205	0.1602	M	0.86028	2.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.925;0.998;1.0	T	0.53989	-0.8360	10	0.87932	D	0	-24.0757	20.0706	0.97721	0.0:0.0:1.0:0.0	.	8;8;8	B7Z9Y4;Q6IS01;O14490	.;.;DLGP1_HUMAN	C	8	ENSP00000316377:R8C;ENSP00000445973:R8C	ENSP00000316377:R8C	R	-	1	0	DLGAP1	3870047	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.020000	0.88740	2.744000	0.94065	0.655000	0.94253	CGC	.	.		0.672	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4			A	3880047	G	A	3880047	3	1	150	1	0	0	0	0	1	0	0	0	4561	1116	39	1	3006	1	DLGAP1	18	3880047	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	793917	3880047	74197201	455	23179										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5423442	5423442	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gttcaaagtaaggtgctgggCgatctatcaacgcactggct	12	9	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr18:5423442C>T	ENST00000341928.2	-	11	1614	c.1274G>A	c.(1273-1275)cGc>cAc	p.R425H	EPB41L3_ENST00000540638.2_Missense_Mutation_p.R425H|EPB41L3_ENST00000544123.1_Missense_Mutation_p.R425H|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000400111.3_Missense_Mutation_p.R425H|EPB41L3_ENST00000342933.3_Missense_Mutation_p.R425H	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	425	Hydrophilic.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						AGGTGCTGGGCGATCTATCAA	0.493																																					p.R425H		Atlas-SNP	.											EPB41L3,colon,carcinoma,0,2	EPB41L3	222	.	0			c.G1274A						.						202	153	169					18																	5423442		2203	4300	6503	SO:0001583	missense	23136	exon11			GCTGGGCGATCTA	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.1274G>A	chr18.hg19:g.5423442C>T	ENSP00000343158:p.Arg425His	166.0	0.0		118.0	33.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	C	36	5.705110	0.96812	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	D;D;D;D	0.91521	-2.86;-2.86;-2.86;-2.86	6.08	6.08	0.98989	FERM adjacent (FA) (1);	0.000000	0.85682	D	0.000000	D	0.96430	0.8835	M	0.88181	2.935	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.978	D;D;D;D	0.91635	0.997;0.999;0.998;0.948	D	0.96191	0.9138	10	0.87932	D	0	.	20.6721	0.99693	0.0:1.0:0.0:0.0	.	425;316;425;425	F5GX05;A8K968;Q9Y2J2-2;Q9Y2J2	.;.;.;E41L3_HUMAN	H	425;316;425;316;425;425	ENSP00000343158:R425H;ENSP00000441174:R425H;ENSP00000341138:R425H;ENSP00000382981:R425H	ENSP00000343158:R425H	R	-	2	0	EPB41L3	5413442	1.000000	0.71417	0.991000	0.47740	0.930000	0.56654	7.788000	0.85771	2.894000	0.99253	0.591000	0.81541	CGC	.	.		0.493	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		T	5423442	C	T	5423442	3	4	150	1	0	0	0	0	1	0	0	0	5156	768	27	1	2037	1	EPB41L3	18	5423442	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	1543395	5423442	72653806	456	23180										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9258388	9258388	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtcaactcaaccagaaatgcAtaaatatggtcagttagtta	7	7	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr18:9258388A>T	ENST00000262126.4	+	9	5363	c.5123A>T	c.(5122-5124)cAt>cTt	p.H1708L	ANKRD12_ENST00000383440.2_Missense_Mutation_p.H1685L|RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Missense_Mutation_p.H1685L	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1708						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CCAGAAATGCATAAATATGGT	0.338																																					p.H1708L		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A5123T						.						51	50	50					18																	9258388		2203	4300	6503	SO:0001583	missense	23253	exon9			AAATGCATAAATA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5123A>T	chr18.hg19:g.9258388A>T	ENSP00000262126:p.His1708Leu	111.0	0.0		57.0	22.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.730754	0.48939	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.50277	0.75;0.75	5.33	5.33	0.75918	.	0.138696	0.49916	D	0.000135	T	0.40196	0.1107	L	0.29908	0.895	0.40159	D	0.977044	B;B	0.30361	0.277;0.181	B;B	0.35607	0.206;0.1	T	0.26744	-1.0094	10	0.22706	T	0.39	-10.5776	15.5958	0.76578	1.0:0.0:0.0:0.0	.	1685;1708	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	L	1685;1708	ENSP00000372932:H1685L;ENSP00000262126:H1708L	ENSP00000262126:H1708L	H	+	2	0	ANKRD12	9248388	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	3.039000	0.49791	2.141000	0.66446	0.533000	0.62120	CAT	.	.		0.338	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		T	9258388	A	T	9258388	3	4	150	1	0	0	0	0	1	0	0	0	640	217	8	4	5153	4	ANKRD12	18	9258388	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3834946	9258388	68818860	457	23181										
IMPACT	55364	hgsc.bcm.edu	37	chr18	22017984	22017984	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aagagatgttcttatacaaaAatctcagatgacagaaccag	7	7	2	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr18:22017984A>G	ENST00000284202.4	+	5	488	c.347A>G	c.(346-348)aAa>aGa	p.K116R	RP11-178F10.1_ENST00000579049.1_RNA	NM_018439.3	NP_060909	Q9P2X3	IMPCT_HUMAN	impact RWD domain protein	116	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				negative regulation of protein phosphorylation (GO:0001933)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(2)	16	all_cancers(21;0.00018)|all_epithelial(16;1.5e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)					CTTATACAAAAATCTCAGATG	0.279																																					p.K116R		Atlas-SNP	.											.	IMPACT	37	.	0			c.A347G						.						44	50	48					18																	22017984		2199	4279	6478	SO:0001583	missense	55364	exon5			TACAAAAATCTCA	AB026264	CCDS11886.1	18q11.2-q12.1	2012-12-07	2012-12-07		ENSG00000154059	ENSG00000154059			20387	protein-coding gene	gene with protein product	"RWD domain containing 5"	615319	"Impact homolog (mouse)"			11116084	Standard	NM_018439		Approved	RWDD5	uc002kvh.4	Q9P2X3	OTTHUMG00000131943	ENST00000284202.4:c.347A>G	chr18.hg19:g.22017984A>G	ENSP00000284202:p.Lys116Arg	522.0	0.0		298.0	108.0	NM_018439	A8MXG0|Q49AM0|Q9H2X4	Missense_Mutation	SNP	ENST00000284202.4	hg19	CCDS11886.1	.	.	.	.	.	.	.	.	.	.	A	12.60	1.986429	0.35036	.	.	ENSG00000154059	ENST00000284202	T	0.32023	1.47	5.48	5.48	0.80851	RWD domain (2);	0.092424	0.64402	D	0.000001	T	0.31513	0.0799	M	0.63428	1.95	0.43342	D	0.99539	B	0.06786	0.001	B	0.09377	0.004	T	0.09729	-1.0661	10	0.18710	T	0.47	.	14.5246	0.67878	1.0:0.0:0.0:0.0	.	116	Q9P2X3	IMPCT_HUMAN	R	116	ENSP00000284202:K116R	ENSP00000284202:K116R	K	+	2	0	IMPACT	20271982	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.456000	0.53000	2.060000	0.61445	0.533000	0.62120	AAA	.	.		0.279	IMPACT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254901.1	NM_018439		G	22017984	A	G	22017984	3	3	150	1	0	0	0	0	1	0	0	0	7733	14	1	2	365	2	IMPACT	18	22017984	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	12759596	22017984	56059264	458	23182										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30913332	30913332	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aagatgccattgtaattctaTaacatcactcaaataggcct	5	9	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr18:30913332T>A	ENST00000383096.3	-	10	867	c.685A>T	c.(685-687)Ata>Tta	p.I229L	CCDC178_ENST00000583930.1_Missense_Mutation_p.I229L|CCDC178_ENST00000406524.2_Missense_Mutation_p.I229L|CCDC178_ENST00000402325.1_Missense_Mutation_p.I229L|CCDC178_ENST00000403303.1_Missense_Mutation_p.I229L|CCDC178_ENST00000579947.1_Missense_Mutation_p.I229L|CCDC178_ENST00000300227.8_Missense_Mutation_p.I229L|CCDC178_ENST00000579916.1_Intron			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	229																	TGTAATTCTATAACATCACTC	0.289																																					p.I229L		Atlas-SNP	.											.	.	.	.	0			c.A685T						.						127	114	118					18																	30913332		2202	4300	6502	SO:0001583	missense	374864	exon9			ATTCTATAACATC	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.685A>T	chr18.hg19:g.30913332T>A	ENSP00000372576:p.Ile229Leu	53.0	0.0		26.0	8.0	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	hg19	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	T	10.53	1.374859	0.24857	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	T;T;T;T;T;T	0.39997	2.66;2.66;2.65;2.64;2.65;1.05	5.17	-0.6	0.11642	.	.	.	.	.	T	0.26593	0.0650	L	0.38838	1.175	0.09310	N	0.999999	B;B;B;B	0.20550	0.046;0.015;0.015;0.015	B;B;B;B	0.15484	0.013;0.01;0.01;0.01	T	0.19844	-1.0293	9	0.27082	T	0.32	-3.6271	4.5065	0.11891	0.0:0.3432:0.1697:0.4871	.	229;229;229;229	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	L	229	ENSP00000385591:I229L;ENSP00000372576:I229L;ENSP00000300227:I229L;ENSP00000385867:I229L;ENSP00000385234:I229L;ENSP00000382130:I229L	ENSP00000300227:I229L	I	-	1	0	C18orf34	29167330	0.005000	0.15991	0.120000	0.21714	0.010000	0.07245	-0.440000	0.06888	-0.260000	0.09418	0.455000	0.32223	ATA	.	.		0.289	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		A	30913332	T	A	30913332	3	1	150	1	0	0	0	0	1	0	0	0	1904	1406	49	4	1974	4	C18orf34	18	30913332	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	8895348	30913332	47163916	459	23183										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30926215	30926215	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agttcttgaagtttccagacTgaccaagagtcaattttcat	7	8	3	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr18:30926215T>A	ENST00000383096.3	-	9	800	c.618A>T	c.(616-618)tcA>tcT	p.S206S	CCDC178_ENST00000583930.1_Silent_p.S206S|CCDC178_ENST00000406524.2_Silent_p.S206S|CCDC178_ENST00000402325.1_Silent_p.S206S|CCDC178_ENST00000403303.1_Silent_p.S206S|CCDC178_ENST00000579947.1_Silent_p.S206S|CCDC178_ENST00000300227.8_Silent_p.S206S|CCDC178_ENST00000579916.1_Intron			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	206																	GTTTCCAGACTGACCAAGAGT	0.358																																					p.S206S		Atlas-SNP	.											.	.	.	.	0			c.A618T						.						116	116	116					18																	30926215		2203	4300	6503	SO:0001819	synonymous_variant	374864	exon8			CCAGACTGACCAA	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.618A>T	chr18.hg19:g.30926215T>A		132.0	0.0		66.0	25.0	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Silent	SNP	ENST00000383096.3	hg19	CCDS42424.1																																																																																			.	.		0.358	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		A	30926215	T	A	30926215	2	1	150	1	0	0	0	0	0	0	0	1	1904	1567	55	4		4	C18orf34	18	30926215	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	12883	30926215	47151033	460	23184										
NOL4	8715	hgsc.bcm.edu	37	chr18	31523123	31523123	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctgcaactgctgaagtaaggTgggaaggaataggtcgagac	15	6	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr18:31523123T>A	ENST00000261592.5	-	9	1745	c.1448A>T	c.(1447-1449)cAc>cTc	p.H483L	NOL4_ENST00000589544.1_Intron|NOL4_ENST00000535384.1_Missense_Mutation_p.H198L|NOL4_ENST00000269185.4_Intron|NOL4_ENST00000538587.1_Missense_Mutation_p.H409L|NOL4_ENST00000535475.1_Missense_Mutation_p.H264L	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	483						nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						TGAAGTAAGGTGGGAAGGAAT	0.418																																					p.H483L		Atlas-SNP	.											.	NOL4	139	.	0			c.A1448T						.						81	75	77					18																	31523123		2203	4300	6503	SO:0001583	missense	8715	exon9			GTAAGGTGGGAAG	AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.1448A>T	chr18.hg19:g.31523123T>A	ENSP00000261592:p.His483Leu	72.0	0.0		34.0	11.0	NM_003787	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Missense_Mutation	SNP	ENST00000261592.5	hg19	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	T	23.0	4.364716	0.82463	.	.	ENSG00000101746	ENST00000261592;ENST00000399171;ENST00000535384;ENST00000535475;ENST00000538587	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.68842	0.3045	M	0.70595	2.14	0.24898	N	0.992128	D;D;D;D;D;D	0.89917	0.999;1.0;0.994;0.993;1.0;1.0	D;D;D;D;D;D	0.91635	0.994;0.998;0.924;0.986;0.998;0.999	T	0.65389	-0.6180	9	0.87932	D	0	-19.293	16.3863	0.83505	0.0:0.0:0.0:1.0	.	168;198;409;483;198;264	F8W825;B7Z3Z7;B4DSQ0;O94818;F5H1E3;B3KRF4	.;.;.;NOL4_HUMAN;.;.	L	483;168;198;264;409	.	ENSP00000261592:H483L	H	-	2	0	NOL4	29777121	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.022000	0.76431	2.264000	0.75181	0.528000	0.53228	CAC	.	.		0.418	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		A	31523123	T	A	31523123	3	1	150	1	0	0	0	0	1	0	0	0	10533	1696	59	4	480	4	NOL4	18	31523123	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	596908	31523123	46554125	461	23185										
BSG	682	hgsc.bcm.edu	37	chr19	579507	579507	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccgggccttgcagccggcacAgtcttcactaccgtagaaga	11	14	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:579507A>T	ENST00000333511.3	+	3	493	c.423A>T	c.(421-423)acA>acT	p.T141T	BSG_ENST00000545507.2_5'UTR|BSG_ENST00000346916.4_Intron|BSG_ENST00000353555.4_Silent_p.T25T|BSG_ENST00000574970.1_3'UTR	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	141	Ig-like C2-type.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCCGGCACAGTCTTCACTA	0.662																																					p.T141T		Atlas-SNP	.											.	BSG	48	.	0			c.A423T						.						39	36	37					19																	579507		2200	4295	6495	SO:0001819	synonymous_variant	682	exon3			CGGCACAGTCTTC	L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1116	protein-coding gene	gene with protein product	"Ok blood group"	109480	"basigin"	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.423A>T	chr19.hg19:g.579507A>T		82.0	0.0		69.0	18.0	NM_001728	A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Silent	SNP	ENST00000333511.3	hg19	CCDS12033.1																																																																																			.	.		0.662	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728		T	579507	A	T	579507	2	4	150	1	0	0	0	0	0	0	0	1	1531	175	7	4		4	BSG	19	579507	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		579507	58549476	462	23186										
PRSSL1	400668	hgsc.bcm.edu	37	chr19	691985	691985	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cgtgggcgcccagcaccaccAggccagtgcggaggtctctg	15	15	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:691985A>T	ENST00000329267.7	-	3	283	c.254T>A	c.(253-255)cTg>cAg	p.L85Q		NM_214710.3	NP_999875	Q6UWY2	PRS57_HUMAN	protease, serine, 57	85	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|lung(5)	6						CAGCACCACCAGGCCAGTGCG	0.662																																					p.L85Q		Atlas-SNP	.											.	PRSS57	18	.	0			c.T254A						.						46	29	35					19																	691985		2201	4300	6501	SO:0001583	missense	400668	exon3			ACCACCAGGCCAG	AY358594	CCDS12041.1	19p13.3	2012-03-26	2011-03-07	2011-03-07		ENSG00000185198		"Serine peptidases / Serine peptidases"	31397	protein-coding gene	gene with protein product			"protease, serine-like 1"	PRSSL1		12975309	Standard	NM_214710		Approved	UNQ782	uc002lpl.1	Q6UWY2		ENST00000329267.7:c.254T>A	chr19.hg19:g.691985A>T	ENSP00000327386:p.Leu85Gln	95.0	0.0		74.0	24.0	NM_214710	B2RNW8	Missense_Mutation	SNP	ENST00000329267.7	hg19	CCDS12041.1	.	.	.	.	.	.	.	.	.	.	A	3.087	-0.187659	0.06299	.	.	ENSG00000185198	ENST00000329267	D	0.92965	-3.14	4.28	0.422	0.16457	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.264352	0.20046	N	0.100411	T	0.72614	0.3482	N	0.01668	-0.77	0.32055	N	0.596455	B;B	0.18310	0.027;0.027	B;B	0.17098	0.017;0.017	T	0.65138	-0.6241	10	0.12766	T	0.61	.	5.8809	0.18854	0.3859:0.4561:0.0:0.1579	.	84;85	B7ZMF6;Q6UWY2	.;PRS57_HUMAN	Q	85	ENSP00000327386:L85Q	ENSP00000327386:L85Q	L	-	2	0	PRSS57	642985	0.100000	0.21855	0.738000	0.30950	0.087000	0.18053	0.121000	0.15667	0.115000	0.18071	0.260000	0.18958	CTG	.	.		0.662	PRSS57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452480.2	NM_214710		T	691985	A	T	691985	3	4	150	1	0	0	0	0	1	0	0	0	12648	188	7	4	609	4	PRSSL1	19	691985	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	112478	691985	58436998	463	23187										
ZFR2	23217	hgsc.bcm.edu	37	chr19	3823272	3823272	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	catattccgggcccaccggcTgcgcatcagagcagcccgcg	12	17	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:3823272T>A	ENST00000262961.4	-	8	1353	c.1343A>T	c.(1342-1344)cAg>cTg	p.Q448L		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	448							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		GCCCACCGGCTGCGCATCAGA	0.617																																					p.Q448L		Atlas-SNP	.											.	ZFR2	63	.	0			c.A1343T						.						89	95	93					19																	3823272		1893	4108	6001	SO:0001583	missense	23217	exon8			ACCGGCTGCGCAT	AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"KIAA1086"	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.1343A>T	chr19.hg19:g.3823272T>A	ENSP00000262961:p.Gln448Leu	66.0	0.0		41.0	11.0	NM_015174		Missense_Mutation	SNP	ENST00000262961.4	hg19	CCDS45921.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.009415	0.54361	.	.	ENSG00000105278	ENST00000262961	T	0.39056	1.1	3.4	2.35	0.29111	.	0.000000	0.64402	U	0.000006	T	0.41673	0.1169	M	0.81802	2.56	0.80722	D	1	P	0.42010	0.768	B	0.39379	0.298	T	0.31558	-0.9939	10	0.56958	D	0.05	-9.9101	6.643	0.22919	0.0:0.0:0.243:0.757	.	448	Q9UPR6	ZFR2_HUMAN	L	448	ENSP00000262961:Q448L	ENSP00000262961:Q448L	Q	-	2	0	ZFR2	3774272	1.000000	0.71417	0.017000	0.16124	0.008000	0.06430	1.731000	0.38135	0.378000	0.24764	0.459000	0.35465	CAG	.	.		0.617	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174		A	3823272	T	A	3823272	3	1	150	1	0	0	0	0	1	0	0	0	17675	1580	55	4	1524	4	ZFR2	19	3823272	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3131287	3823272	55305711	464	23188										
FUT5	2527	hgsc.bcm.edu	37	chr19	5867550	5867550	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cgccatgctgtcctggcagcGggacccattgggagccccgg	15	15	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:5867550G>A	ENST00000588525.1	-	2	274	c.187C>T	c.(187-189)Cgc>Tgc	p.R63C	FUT5_ENST00000252675.5_Missense_Mutation_p.R63C	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	63					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						TCCTGGCAGCGGGACCCATTG	0.632																																					p.R63C		Atlas-SNP	.											FUT5,NS,adenocarcinoma,0,1	FUT5	29	.	0			c.C187T						.						37	37	37					19																	5867550		2203	4300	6503	SO:0001583	missense	2527	exon2			GGCAGCGGGACCC		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"Fucosyltransferases"	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.187C>T	chr19.hg19:g.5867550G>A	ENSP00000466880:p.Arg63Cys	99.0	1.0		116.0	33.0	NM_002034	A8K4X2	Missense_Mutation	SNP	ENST00000588525.1	hg19	CCDS12154.1	.	.	.	.	.	.	.	.	.	.	G	6.407	0.443183	0.12164	.	.	ENSG00000130383	ENST00000252675	T	0.32272	1.46	1.55	1.55	0.23275	.	.	.	.	.	T	0.27349	0.0671	L	0.52573	1.65	0.09310	N	1	P	0.50272	0.933	B	0.43916	0.436	T	0.10730	-1.0617	9	0.38643	T	0.18	.	6.5424	0.22387	0.0:0.0:1.0:0.0	.	63	Q11128	FUT5_HUMAN	C	63	ENSP00000252675:R63C	ENSP00000252675:R63C	R	-	1	0	FUT5	5818550	0.000000	0.05858	0.002000	0.10522	0.025000	0.11179	-1.990000	0.01479	1.175000	0.42826	0.407000	0.27541	CGC	.	.		0.632	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034		A	5867550	G	A	5867550	3	1	150	1	0	0	0	0	1	0	0	0	6115	1116	39	1	941	1	FUT5	19	5867550	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	2044278	5867550	53261433	465	23189										
CLPP	8192	hgsc.bcm.edu	37	chr19	6366366	6366366	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcacaccaaacagagcctgcAggtgatcggtaagcaccctc	10	14	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:6366366A>T	ENST00000245816.4	+	5	776	c.653A>T	c.(652-654)cAg>cTg	p.Q218L	CLPP_ENST00000596149.1_Missense_Mutation_p.Q131L|CLPP_ENST00000596605.1_3'UTR	NM_006012.2	NP_006003.1	Q16740	CLPP_HUMAN	caseinolytic mitochondrial matrix peptidase proteolytic subunit	218					protein homooligomerization (GO:0051260)|proteolysis involved in cellular protein catabolic process (GO:0051603)	endopeptidase Clp complex (GO:0009368)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|ovary(2)	6						CAGAGCCTGCAGGTGATCGGT	0.562																																					p.Q218L		Atlas-SNP	.											.	CLPP	15	.	0			c.A653T						.						165	126	139					19																	6366366		2202	4300	6502	SO:0001583	missense	8192	exon5			GCCTGCAGGTGAT	Z50853	CCDS12162.1	19p13.3	2013-09-12	2013-09-12		ENSG00000125656	ENSG00000125656		"ATPases / AAA-type"	2084	protein-coding gene	gene with protein product	"ATP-dependent protease ClpAP (E. coli), proteolytic subunit, human"	601119	"ClpP (caseinolytic protease, ATP-dependent, proteolytic subunit, E. coli) homolog", "ClpP caseinolytic protease, ATP-dependent, proteolytic subunit homolog (E. coli)", "ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)"			8543061, 23360988	Standard	NM_006012		Approved		uc002mem.1	Q16740	OTTHUMG00000180779	ENST00000245816.4:c.653A>T	chr19.hg19:g.6366366A>T	ENSP00000245816:p.Gln218Leu	88.0	0.0		46.0	12.0	NM_006012	B2R4W5	Missense_Mutation	SNP	ENST00000245816.4	hg19	CCDS12162.1	.	.	.	.	.	.	.	.	.	.	A	15.12	2.739334	0.49045	.	.	ENSG00000125656	ENST00000245816	.	.	.	5.5	4.48	0.54585	.	0.644172	0.15430	N	0.262752	T	0.43055	0.1230	L	0.27053	0.805	0.39660	D	0.97059	B	0.19445	0.036	B	0.20184	0.028	T	0.40175	-0.9577	9	0.87932	D	0	-20.004	6.7289	0.23373	0.7675:0.1535:0.079:0.0	.	218	Q16740	CLPP_HUMAN	L	218	.	ENSP00000245816:Q218L	Q	+	2	0	CLPP	6317366	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.881000	0.48538	1.050000	0.40346	0.529000	0.55759	CAG	.	.		0.562	CLPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452984.1	NM_006012		T	6366366	A	T	6366366	3	4	150	1	0	0	0	0	1	0	0	0	3554	188	7	4	671	4	CLPP	19	6366366	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	498816	6366366	52762617	466	23190										
PNPLA6	10908	hgsc.bcm.edu	37	chr19	7625969	7625969	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cccggattgagccccccacgAgctatgtctctgatggctgt	11	14	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:7625969A>T	ENST00000221249.6	+	33	4203	c.3772A>T	c.(3772-3774)Agc>Tgc	p.S1258C	PNPLA6_ENST00000450331.3_Missense_Mutation_p.S1258C|PNPLA6_ENST00000600737.1_Missense_Mutation_p.S1296C|PNPLA6_ENST00000414982.3_Missense_Mutation_p.S1306C|PNPLA6_ENST00000545201.2_Missense_Mutation_p.S1231C	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	1297					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						GCCCCCCACGAGCTATGTCTC	0.632																																					p.S1306C		Atlas-SNP	.											.	PNPLA6	163	.	0			c.A3916T						.						32	31	31					19																	7625969		2203	4300	6503	SO:0001583	missense	10908	exon32			CCCACGAGCTATG	AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"Patatin-like phospholipase domain containing"	16268	protein-coding gene	gene with protein product	"neuropathy target esterase"	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.3772A>T	chr19.hg19:g.7625969A>T	ENSP00000221249:p.Ser1258Cys	56.0	0.0		50.0	26.0	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Missense_Mutation	SNP	ENST00000221249.6	hg19	CCDS32891.1	.	.	.	.	.	.	.	.	.	.	a	16.27	3.076128	0.55646	.	.	ENSG00000032444	ENST00000221249;ENST00000545201;ENST00000414982;ENST00000450331	T;T;T;T	0.04360	3.65;3.66;3.64;3.65	4.33	4.33	0.51752	.	.	.	.	.	T	0.11623	0.0283	L	0.53249	1.67	0.35271	D	0.780502	D;D;D;D	0.65815	0.991;0.99;0.995;0.967	P;P;P;P	0.57324	0.662;0.818;0.818;0.818	T	0.15178	-1.0446	9	0.39692	T	0.17	-22.9894	9.8073	0.40801	1.0:0.0:0.0:0.0	.	1297;1231;1296;1258	Q8IY17;F5H5K9;Q8IY17-3;Q8IY17-2	PLPL6_HUMAN;.;.;.	C	1258;1231;1306;1258	ENSP00000221249:S1258C;ENSP00000443323:S1231C;ENSP00000407509:S1306C;ENSP00000394348:S1258C	ENSP00000221249:S1258C	S	+	1	0	PNPLA6	7531969	0.992000	0.36948	0.869000	0.34112	0.414000	0.31173	3.136000	0.50554	1.814000	0.52955	0.379000	0.24179	AGC	.	.		0.632	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702		T	7625969	A	T	7625969	3	4	150	1	0	0	0	0	1	0	0	0	12178	304	11	4	4038	4	PNPLA6	19	7625969	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1259603	7625969	51503014	467	23191										
PRAM1	84106	hgsc.bcm.edu	37	chr19	8563756	8563756	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttggagagcgctttgaattcGgccggccgcggcctcttggg	16	11	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:8563756G>A	ENST00000423345.4	-	2	1456	c.936C>T	c.(934-936)gcC>gcT	p.A312A	PRAM1_ENST00000255612.3_Silent_p.A312A			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	360	Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						CTTTGAATTCGGCCGGCCGCG	0.657																																					p.A312A		Atlas-SNP	.											.	PRAM1	53	.	0			c.C936T						.																																			SO:0001819	synonymous_variant	84106	exon2			GAATTCGGCCGGC	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.936C>T	chr19.hg19:g.8563756G>A		79.0	0.0		105.0	35.0	NM_032152	Q8N6W7	Silent	SNP	ENST00000423345.4	hg19	CCDS45954.2																																																																																			.	.		0.657	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152		A	8563756	G	A	8563756	2	1	150	1	0	0	0	0	0	0	0	1	12435	1103	39	1		1	PRAM1	19	8563756	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	937787	8563756	50565227	468	23192										
MUC16	94025	hgsc.bcm.edu	37	chr19	9061256	9061256	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gtagcaccagtgggcattccAgaaagagaagcacttctctc	10	11	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:9061256A>T	ENST00000397910.4	-	3	26393	c.26190T>A	c.(26188-26190)tcT>tcA	p.S8730S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8732	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGGCATTCCAGAAAGAGAAG	0.502																																					p.S8730S		Atlas-SNP	.											.	MUC16	4315	.	0			c.T26190A						.						109	99	102					19																	9061256		1942	4145	6087	SO:0001819	synonymous_variant	94025	exon3			CATTCCAGAAAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.26190T>A	chr19.hg19:g.9061256A>T		121.0	0.0		99.0	35.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9061256	A	T	9061256	2	4	150	1	0	0	0	0	0	0	0	1	9982	175	7	4		4	MUC16	19	9061256	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	497500	9061256	50067727	469	23193										
TNPO2	30000	hgsc.bcm.edu	37	chr19	12821577	12821577	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggacgtccagtgcagccgcTgagcacttccctggggaagg	15	12	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:12821577T>A	ENST00000592287.1	-	12	1236	c.1128A>T	c.(1126-1128)tcA>tcT	p.S376S	TNPO2_ENST00000441499.1_Silent_p.S376S|TNPO2_ENST00000588216.1_Silent_p.S376S|TNPO2_ENST00000450764.2_Silent_p.S376S|TNPO2_ENST00000425528.1_Silent_p.S376S|TNPO2_ENST00000589956.1_5'UTR|TNPO2_ENST00000356861.5_Silent_p.S376S	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	376					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GTGCAGCCGCTGAGCACTTCC	0.642																																					p.S376S		Atlas-SNP	.											.	TNPO2	108	.	0			c.A1128T						.						24	28	27					19																	12821577		1997	4150	6147	SO:0001819	synonymous_variant	30000	exon12			AGCCGCTGAGCAC	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"Importins"	19998	protein-coding gene	gene with protein product	"importin 3", "karyopherin beta 2b"	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.1128A>T	chr19.hg19:g.12821577T>A		66.0	0.0		82.0	21.0	NM_013433	O14655|Q6IN77	Silent	SNP	ENST00000592287.1	hg19	CCDS45991.1																																																																																			.	.		0.642	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433		A	12821577	T	A	12821577	2	1	150	1	0	0	0	0	0	0	0	1	16351	1567	55	4		4	TNPO2	19	12821577	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3760321	12821577	46307406	470	23194										
NDUFB7	4713	hgsc.bcm.edu	37	chr19	14677729	14677729	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgcgcgtccatcatctcctgCtgtgtggccaccatctctgc	9	16	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:14677729C>A	ENST00000215565.2	-	2	190	c.129G>T	c.(127-129)caG>caT	p.Q43H		NM_004146.5	NP_004137.2	P17568	NDUB7_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa	43					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						TCATCTCCTGCTGTGTGGCCA	0.662																																					p.Q43H		Atlas-SNP	.											.	NDUFB7	14	.	0			c.G129T						.						38	31	33					19																	14677729		2196	4295	6491	SO:0001583	missense	4713	exon2			CTCCTGCTGTGTG		CCDS12314.1	19p13.12	2011-07-04	2002-08-29		ENSG00000099795	ENSG00000099795		"Mitochondrial respiratory chain complex / Complex I"	7702	protein-coding gene	gene with protein product	"NADH-ubiquinone oxidoreductase B18 subunit", "complex I B18 subunit"	603842	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7 (18kD, B18)"			9763677, 10830904	Standard	NM_004146		Approved	B18, CI-B18, MGC2480	uc002mzg.3	P17568		ENST00000215565.2:c.129G>T	chr19.hg19:g.14677729C>A	ENSP00000215565:p.Gln43His	31.0	0.0		27.0	10.0	NM_004146	Q6ICN9|Q9UI16	Missense_Mutation	SNP	ENST00000215565.2	hg19	CCDS12314.1	.	.	.	.	.	.	.	.	.	.	C	18.60	3.659702	0.67586	.	.	ENSG00000099795	ENST00000215565	T	0.50548	0.74	4.76	2.58	0.30949	.	0.058089	0.64402	D	0.000001	T	0.63402	0.2508	M	0.73962	2.25	0.58432	D	0.999999	D	0.76494	0.999	D	0.70227	0.968	T	0.63431	-0.6639	10	0.59425	D	0.04	-5.3708	9.4077	0.38471	0.0:0.821:0.0:0.179	.	43	P17568	NDUB7_HUMAN	H	43	ENSP00000215565:Q43H	ENSP00000215565:Q43H	Q	-	3	2	NDUFB7	14538729	1.000000	0.71417	0.999000	0.59377	0.906000	0.53458	3.287000	0.51732	0.600000	0.29862	0.585000	0.79938	CAG	.	.		0.662	NDUFB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466025.1	NM_004146		A	14677729	C	A	14677729	3	1	150	1	0	0	0	0	1	0	0	0	10295	796	28	3	292	3	NDUFB7	19	14677729	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	1856152	14677729	44451254	471	23195										
OR7A17	26333	hgsc.bcm.edu	37	chr19	14991448	14991448	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	actgagaggtgtgatgcacaGgtggaaaatgccttgtactt	13	6	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:14991448G>T	ENST00000327462.2	-	1	816	c.720C>A	c.(718-720)acC>acA	p.T240T		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					GTGATGCACAGGTGGAAAATG	0.483																																					p.T240T		Atlas-SNP	.											.	OR7A17	37	.	0			c.C720A						.						110	96	101					19																	14991448		2203	4300	6503	SO:0001819	synonymous_variant	26333	exon1			TGCACAGGTGGAA	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"GPCR / Class A : Olfactory receptors"	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.720C>A	chr19.hg19:g.14991448G>T		111.0	0.0		84.0	22.0	NM_030901	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	hg19	CCDS12319.1																																																																																			.	.		0.483	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901		T	14991448	G	T	14991448	2	4	150	1	0	0	0	0	0	0	0	1	11224	987	35	3		3	OR7A17	19	14991448	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	313719	14991448	44137535	472	23196										
MYO9B	4650	hgsc.bcm.edu	37	chr19	17256246	17256246	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagcccacaacaacaactccAgccggtttgggaaattcatc	7	14	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:17256246A>T	ENST00000594824.1	+	3	1027	c.880A>T	c.(880-882)Agc>Tgc	p.S294C	MYO9B_ENST00000595618.1_Missense_Mutation_p.S294C|MYO9B_ENST00000397274.2_Missense_Mutation_p.S294C			Q13459	MYO9B_HUMAN	myosin IXB	294	Myosin motor.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						CAACAACTCCAGCCGGTTTGG	0.512																																					p.S294C		Atlas-SNP	.											.	MYO9B	264	.	0			c.A880T						.						103	103	103					19																	17256246		1962	4144	6106	SO:0001583	missense	4650	exon3			AACTCCAGCCGGT		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"Myosins / Myosin superfamily : Class IX"	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.880A>T	chr19.hg19:g.17256246A>T	ENSP00000471367:p.Ser294Cys	120.0	0.0		104.0	32.0	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	hg19		.	.	.	.	.	.	.	.	.	.	A	23.8	4.460150	0.84317	.	.	ENSG00000099331	ENST00000397274	D	0.83837	-1.77	4.77	4.77	0.60923	Myosin head, motor domain (3);	0.000000	0.64402	D	0.000014	D	0.94594	0.8258	H	0.98883	4.36	0.47778	D	0.999513	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.96219	0.9159	10	0.87932	D	0	.	13.1108	0.59273	1.0:0.0:0.0:0.0	.	294;294;300	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	C	294	ENSP00000380444:S294C	ENSP00000380444:S294C	S	+	1	0	MYO9B	17117246	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	6.979000	0.76154	1.796000	0.52611	0.459000	0.35465	AGC	.	.		0.512	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			T	17256246	A	T	17256246	3	4	150	1	0	0	0	0	1	0	0	0	10094	188	7	4	886	4	MYO9B	19	17256246	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2264798	17256246	41872737	473	23197										
RPL18A	6142	hgsc.bcm.edu	37	chr19	17973829	17973829	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccgccggccggctgtcaagcAgttccacgtgagtgccctgg	14	15	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:17973829A>T	ENST00000222247.5	+	4	512	c.431A>T	c.(430-432)cAg>cTg	p.Q144L	RPL18A_ENST00000600147.1_Intron|SNORA68_ENST00000384437.1_RNA|RPL18A_ENST00000599870.1_Missense_Mutation_p.Q115L|RPL18A_ENST00000599898.1_Missense_Mutation_p.Q105L	NM_000980.3	NP_000971.1	Q02543	RL18A_HUMAN	ribosomal protein L18a	144					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(1)	5						GCTGTCAAGCAGTTCCACGTG	0.677																																					p.Q144L		Atlas-SNP	.											.	RPL18A	15	.	0			c.A431T						.						21	24	23					19																	17973829		2202	4299	6501	SO:0001583	missense	6142	exon4			TCAAGCAGTTCCA	AB007175	CCDS12367.1	19p13.11	2011-04-06			ENSG00000105640	ENSG00000105640		"L ribosomal proteins"	10311	protein-coding gene	gene with protein product	"60S ribosomal protein L18a", "ribosomal protein L18a-like protein"	604178				9582194	Standard	NM_000980		Approved	L18A	uc002nhp.3	Q02543		ENST00000222247.5:c.431A>T	chr19.hg19:g.17973829A>T	ENSP00000222247:p.Gln144Leu	90.0	0.0		95.0	35.0	NM_000980		Missense_Mutation	SNP	ENST00000222247.5	hg19	CCDS12367.1	.	.	.	.	.	.	.	.	.	.	A	18.12	3.552562	0.65425	.	.	ENSG00000105640	ENST00000222247	.	.	.	4.71	4.71	0.59529	.	0.060094	0.64402	D	0.000002	T	0.78502	0.4293	M	0.94063	3.49	0.80722	D	1	D	0.65815	0.995	P	0.53266	0.722	D	0.84616	0.0681	8	.	.	.	.	12.4351	0.55595	1.0:0.0:0.0:0.0	.	144	Q02543	RL18A_HUMAN	L	144	.	.	Q	+	2	0	RPL18A	17834829	1.000000	0.71417	1.000000	0.80357	0.248000	0.25809	9.179000	0.94861	1.894000	0.54839	0.377000	0.23210	CAG	.	.		0.677	RPL18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466679.1	NM_000980		T	17973829	A	T	17973829	3	4	150	1	0	0	0	0	1	0	0	0	13580	188	7	4	445	4	RPL18A	19	17973829	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	717583	17973829	41155154	474	23198										
SLC5A5	6528	hgsc.bcm.edu	37	chr19	17988625	17988625	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgtatggcgtgaaccaggcGcaggtgcagcgctacgtggc	16	10	0	1	rs148887708		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:17988625G>T	ENST00000222248.3	+	6	1139	c.792G>T	c.(790-792)gcG>gcT	p.A264A		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	264					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						TGAACCAGGCGCAGGTGCAGC	0.607																																					p.A264A	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											SLC5A5,colon,carcinoma,0,2	SLC5A5	67	.	0			c.G792T						.	G		1,4405	2.1+/-5.4	0,1,2202	151	125	134		792	-10.6	0.4	19	dbSNP_134	134	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	SLC5A5	NM_000453.2		0,4,6499	TT,TG,GG		0.0349,0.0227,0.0308		264/644	17988625	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	6528	exon6			CCAGGCGCAGGTG		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"Solute carriers"	11040	protein-coding gene	gene with protein product		601843	"solute carrier family 5 (sodium iodide symporter), member 5"			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.792G>T	chr19.hg19:g.17988625G>T		76.0	1.0		88.0	30.0	NM_000453	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	hg19	CCDS12368.1																																																																																			.	G|1.000;T|0.000		0.607	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			T	17988625	G	T	17988625	2	4	150	1	0	0	0	0	0	0	0	1	14683	1074	38	1		1	SLC5A5	19	17988625	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	14796	17988625	41140358	475	23199										
COMP	1311	hgsc.bcm.edu	37	chr19	18899478	18899478	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gctgggcgagccgtcggggcAgaagcgctgtgcgcgccgct	19	13	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:18899478A>T	ENST00000222271.2	-	7	729	c.685T>A	c.(685-687)Tgc>Agc	p.C229S	COMP_ENST00000542601.2_Missense_Mutation_p.C196S|COMP_ENST00000425807.1_Missense_Mutation_p.C176S	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	229	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CCGTCGGGGCAGAAGCGCTGT	0.746																																					p.C229S		Atlas-SNP	.											.	COMP	62	.	0			c.T685A						.						5	6	5					19																	18899478		1813	3424	5237	SO:0001583	missense	1311	exon7			CGGGGCAGAAGCG	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"thrombospondin-5"	600310	"cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.685T>A	chr19.hg19:g.18899478A>T	ENSP00000222271:p.Cys229Ser	52.0	0.0		39.0	13.0	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	ENST00000222271.2	hg19	CCDS12385.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.823619	0.71143	.	.	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.92805	-3.11;-3.11;-2.99	4.2	3.18	0.36537	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.96688	0.8919	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.95706	0.8753	10	0.87932	D	0	-26.4467	6.6301	0.22851	0.8857:0.0:0.1143:0.0	.	176;229	B4DKJ3;P49747	.;COMP_HUMAN	S	196;229;176;216	ENSP00000439156:C196S;ENSP00000222271:C229S;ENSP00000403792:C176S	ENSP00000222271:C229S	C	-	1	0	COMP	18760478	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	4.665000	0.61547	1.553000	0.49476	0.397000	0.26171	TGC	.	.		0.746	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095		T	18899478	A	T	18899478	3	4	150	1	0	0	0	0	1	0	0	0	3726	188	7	4	1640	4	COMP	19	18899478	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	910853	18899478	40229505	476	23200										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22156559	22156559	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctttgccacattcttcacatTtgtagggtttctctccagta	6	11	3	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:22156559T>A	ENST00000397126.4	-	4	1425	c.1277A>T	c.(1276-1278)aAa>aTa	p.K426I	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	426					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTCTTCACATTTGTAGGGTTT	0.398																																					p.K426I		Atlas-SNP	.											.	ZNF208	817	.	0			c.A1277T						.						50	59	56					19																	22156559		2039	4225	6264	SO:0001583	missense	7757	exon4			TCACATTTGTAGG	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1277A>T	chr19.hg19:g.22156559T>A	ENSP00000380315:p.Lys426Ile	93.0	0.0		77.0	21.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	12.42	1.931844	0.34096	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.20881	2.04	2.65	-2.17	0.07059	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32645	0.0836	.	.	.	0.09310	N	1	D	0.69078	0.997	D	0.91635	0.999	T	0.24728	-1.0152	8	0.59425	D	0.04	.	0.6615	0.00843	0.31:0.118:0.1588:0.4132	.	426	O43345	ZN208_HUMAN	I	426	ENSP00000380315:K426I	ENSP00000380315:K426I	K	-	2	0	ZNF208	21948399	0.000000	0.05858	0.008000	0.14137	0.046000	0.14306	-2.240000	0.01197	-0.030000	0.13804	0.254000	0.18369	AAA	.	.		0.398	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		A	22156559	T	A	22156559	3	1	150	1	0	0	0	0	1	0	0	0	17781	1841	64	4	2569	4	ZNF208	19	22156559	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3257081	22156559	36972424	477	23201										
RYR1	6261	hgsc.bcm.edu	37	chr19	38964354	38964354	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcaggcggggggagaggcgcAgcccgccagggcggagaatg	22	10	0	2	rs185821937		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:38964354A>T	ENST00000359596.3	+	28	4103	c.4103A>T	c.(4102-4104)cAg>cTg	p.Q1368L	RYR1_ENST00000355481.4_Missense_Mutation_p.Q1368L|RYR1_ENST00000360985.3_Missense_Mutation_p.Q1368L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1368	6 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.			GEAQ -> RGA (in Ref. 1; AA sequence). {ECO:0000305}.	calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGAGAGGCGCAGCCCGCCAGG	0.697																																					p.Q1368L		Atlas-SNP	.											.	RYR1	708	.	0			c.A4103T						.						3	3	3					19																	38964354		1583	3156	4739	SO:0001583	missense	6261	exon28			AGGCGCAGCCCGC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.4103A>T	chr19.hg19:g.38964354A>T	ENSP00000352608:p.Gln1368Leu	284.0	0.0		250.0	73.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	A	3.557	-0.090394	0.07053	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96651	-4.08;-4.08;-4.08	4.32	1.97	0.26223	B30.2/SPRY domain (1);	.	.	.	.	D	0.88358	0.6415	N	0.08118	0	0.31181	N	0.702024	P;B	0.44816	0.844;0.08	B;B	0.39738	0.308;0.075	D	0.85948	0.1462	9	0.34782	T	0.22	.	5.5868	0.17279	0.6541:0.1759:0.0:0.17	.	1368;1368	P21817-2;P21817	.;RYR1_HUMAN	L	1368	ENSP00000352608:Q1368L;ENSP00000347667:Q1368L;ENSP00000354254:Q1368L	ENSP00000347667:Q1368L	Q	+	2	0	RYR1	43656194	1.000000	0.71417	0.995000	0.50966	0.005000	0.04900	1.866000	0.39489	0.747000	0.32809	-0.686000	0.03744	CAG	.	A|1.000;C|0.000		0.697	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38964354	A	T	38964354	3	4	150	1	0	0	0	0	1	0	0	0	13783	188	7	4	4213	4	RYR1	19	38964354	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	16807795	38964354	20164629	478	23202										
CEACAM5	1048	hgsc.bcm.edu	37	chr19	42223902	42223902	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	actccaaacccgtggaggacAaggatgctgtggccttcacc	11	13	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:42223902A>T	ENST00000221992.6	+	7	1660	c.1546A>T	c.(1546-1548)Aag>Tag	p.K516*	CEACAM5_ENST00000405816.1_Nonsense_Mutation_p.K516*|CEA_ENST00000598976.1_Intron|CEACAM5_ENST00000398599.4_Nonsense_Mutation_p.K515*	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	516	Ig-like 6.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CGTGGAGGACAAGGATGCTGT	0.552																																					p.K516X		Atlas-SNP	.											.	CEACAM5	84	.	0			c.A1546T						.						135	120	125					19																	42223902		2203	4300	6503	SO:0001587	stop_gained	1048	exon7			GAGGACAAGGATG	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1546A>T	chr19.hg19:g.42223902A>T	ENSP00000221992:p.Lys516*	109.0	0.0		72.0	18.0	NM_004363	H9KVA7	Nonsense_Mutation	SNP	ENST00000221992.6	hg19	CCDS12584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.35|14.35	2.509474|2.509474	0.44660|0.44660	.|.	.|.	ENSG00000105388|ENSG00000105388	ENST00000221992;ENST00000405816;ENST00000378181|ENST00000398599	.|.	.|.	.|.	2.43|2.43	-4.86|-4.86	0.03132|0.03132	.|.	.|.	.|.	.|.	.|.	.|T	.|0.15998	.|0.0385	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.09662	.|-1.0664	.|3	0.02654|.	T|.	1|.	.|.	0.2625|0.2625	0.00220|0.00220	0.1982:0.2409:0.226:0.3348|0.1982:0.2409:0.226:0.3348	.|.	.|.	.|.	.|.	X|L	516;516;234|511	.|.	ENSP00000221992:K516X|.	K|Q	+|+	1|2	0|0	CEACAM5|CEACAM5	46915742|46915742	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-2.711000|-2.711000	0.00817|0.00817	-3.198000|-3.198000	0.00218|0.00218	0.332000|0.332000	0.21555|0.21555	AAG|CAA	.	.		0.552	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363		T	42223902	A	T	42223902	4	4	150	1	0	0	0	0	0	1	0	0	3197	131	5	4	1572	4	CEACAM5	19	42223902	Nonsense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	3259548	42223902	16905081	479	23203										
CEACAM3	1084	hgsc.bcm.edu	37	chr19	42312947	42312947	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggccgcgctggtgtgtttccTgctccttgccaaaactggaa	12	12	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:42312947T>A	ENST00000357396.3	+	3	762	c.521T>A	c.(520-522)cTg>cAg	p.L174Q	CEACAM3_ENST00000221999.4_Missense_Mutation_p.L174Q|CEACAM3_ENST00000344550.4_Missense_Mutation_p.L174Q|CEACAM3_ENST00000595255.1_3'UTR	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	174						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						GTGTGTTTCCTGCTCCTTGCC	0.602																																					p.L174Q		Atlas-SNP	.											.	CEACAM3	37	.	0			c.T521A						.						159	150	153					19																	42312947		2203	4300	6503	SO:0001583	missense	1084	exon3			GTTTCCTGCTCCT	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.521T>A	chr19.hg19:g.42312947T>A	ENSP00000349971:p.Leu174Gln	109.0	0.0		83.0	14.0	NM_001815	G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	hg19	CCDS12586.2	.	.	.	.	.	.	.	.	.	.	T	13.87	2.365804	0.41902	.	.	ENSG00000170956	ENST00000357396;ENST00000221999;ENST00000344550	T;T;T	0.02763	4.52;4.17;4.17	2.87	2.87	0.33458	.	.	.	.	.	T	0.09247	0.0228	L	0.50847	1.595	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.974	T	0.15009	-1.0452	9	0.56958	D	0.05	.	7.8178	0.29269	0.0:0.0:0.0:1.0	.	174;174	G5E978;P40198	.;CEAM3_HUMAN	Q	174	ENSP00000349971:L174Q;ENSP00000221999:L174Q;ENSP00000341725:L174Q	ENSP00000221999:L174Q	L	+	2	0	CEACAM3	47004787	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.340000	0.19892	1.264000	0.44198	0.421000	0.28195	CTG	.	.		0.602	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815		A	42312947	T	A	42312947	3	1	150	1	0	0	0	0	1	0	0	0	3195	1580	55	4	531	4	CEACAM3	19	42312947	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	89045	42312947	16816036	480	23204										
CEACAM1	634	hgsc.bcm.edu	37	chr19	43026217	43026217	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ggacagctgcagcctgggacTgaccgggaggctctgattgt	16	10	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:43026217T>A	ENST00000161559.6	-	3	696	c.562A>T	c.(562-564)Agt>Tgt	p.S188C	CEACAM1_ENST00000403461.1_Missense_Mutation_p.S188C|CEACAM1_ENST00000599389.1_Missense_Mutation_p.S188C|CEACAM1_ENST00000358394.3_Missense_Mutation_p.S188C|CEACAM1_ENST00000403444.3_Missense_Mutation_p.S188C|CEACAM1_ENST00000308072.4_Missense_Mutation_p.S148C|LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000352591.5_Missense_Mutation_p.S188C|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000351134.3_Intron|LIPE-AS1_ENST00000457234.2_RNA	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	188	Ig-like C2-type 1.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	AGCCTGGGACTGACCGGGAGG	0.532																																					p.S188C		Atlas-SNP	.											.	CEACAM1	43	.	0			c.A562T						.						212	191	198					19																	43026217		2203	4300	6503	SO:0001583	missense	634	exon3			TGGGACTGACCGG	M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.562A>T	chr19.hg19:g.43026217T>A	ENSP00000161559:p.Ser188Cys	112.0	0.0		86.0	25.0	NM_001184816	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	hg19	CCDS12609.1	.	.	.	.	.	.	.	.	.	.	t	15.30	2.792910	0.50102	.	.	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000446434;ENST00000378065;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000308072;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T	0.03330	3.97;3.97;3.97;3.97;3.97;3.97	4.56	1.1	0.20463	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19805	0.0476	M	0.94142	3.5	0.09310	N	1	P;D;P;P;P;P;P;P;P	0.89917	0.89;1.0;0.821;0.951;0.821;0.865;0.876;0.922;0.859	D;D;P;P;P;P;P;D;P	0.97110	0.927;1.0;0.823;0.876;0.823;0.74;0.678;0.932;0.884	T	0.08249	-1.0731	9	0.72032	D	0.01	.	2.8958	0.05690	0.0:0.3336:0.2541:0.4123	.	188;188;188;188;188;188;188;188;188	P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;CEAM1_HUMAN	C	188;188;215;148;188;188;188;148;188;188;188	ENSP00000161559:S188C;ENSP00000351165:S188C;ENSP00000244291:S188C;ENSP00000384709:S188C;ENSP00000384083:S188C;ENSP00000312184:S148C	ENSP00000161559:S188C	S	-	1	0	CEACAM1	47718057	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.769000	0.26604	0.851000	0.35264	0.379000	0.24179	AGT	.	.		0.532	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712		A	43026217	T	A	43026217	3	1	150	1	0	0	0	0	1	0	0	0	3189	1580	55	4	1143	4	CEACAM1	19	43026217	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	713270	43026217	16102766	481	23205										
PSG6	5675	hgsc.bcm.edu	37	chr19	43414973	43414973	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tccatgacctccctggggttTaagttgctgctggagatgga	13	9	0	2	rs1058674		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:43414973T>A	ENST00000292125.2	-	3	509	c.465A>T	c.(463-465)ttA>ttT	p.L155F	PSG6_ENST00000187910.2_Missense_Mutation_p.L155F|PSG6_ENST00000402603.4_Missense_Mutation_p.L155F	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	155	Ig-like C2-type 1.		L -> F (in dbSNP:rs1058674).		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				CCCTGGGGTTTAAGTTGCTGC	0.522																																					p.L155F		Atlas-SNP	.											.	PSG6	89	.	0			c.A465T						.						165	166	165					19																	43414973		2201	4299	6500	SO:0001583	missense	5675	exon3			GGGGTTTAAGTTG		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.465A>T	chr19.hg19:g.43414973T>A	ENSP00000292125:p.Leu155Phe	100.0	0.0		59.0	16.0	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	hg19	CCDS12613.1	.	.	.	.	.	.	.	.	.	.	N	1.537	-0.542825	0.04053	.	.	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.00717	5.79;5.79;5.79	1.64	-3.28	0.05033	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00906	0.0030	L	0.41492	1.28	0.09310	N	1	P;B;P	0.37207	0.587;0.052;0.529	B;B;B	0.44163	0.268;0.073;0.443	T	0.30416	-0.9979	9	0.25751	T	0.34	.	3.8961	0.09139	0.1639:0.0:0.4765:0.3597	.	155;155;155	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	F	155	ENSP00000187910:L155F;ENSP00000385736:L155F;ENSP00000292125:L155F	ENSP00000187910:L155F	L	-	3	2	PSG6	48106813	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.180000	0.16860	-2.167000	0.00779	-1.241000	0.01538	TTA	.	T|1.000;|0.000		0.522	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782		A	43414973	T	A	43414973	3	1	150	1	0	0	0	0	1	0	0	0	12671	1751	61	4	897	4	PSG6	19	43414973	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	388756	43414973	15714010	482	23206										
PSG2	5670	hgsc.bcm.edu	37	chr19	43576010	43576010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	taattgtccaagaatactgtGccggtgggttagagttcgcg	13	7	0	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:43576010G>A	ENST00000406487.1	-	4	904	c.806C>T	c.(805-807)gCa>gTa	p.A269V		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	269	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				AGAATACTGTGCCGGTGGGTT	0.453																																					p.A269V		Atlas-SNP	.											.	PSG2	84	.	0			c.C806T						.						181	191	187					19																	43576010		2202	4299	6501	SO:0001583	missense	5670	exon4			TACTGTGCCGGTG		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9519	protein-coding gene	gene with protein product	"pregnancy-specific beta-1 glycoprotein", "pregnancy-specific beta-1-glycoprotein 7", "carcinoembryonic antigen SG8"	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.806C>T	chr19.hg19:g.43576010G>A	ENSP00000385706:p.Ala269Val	136.0	0.0		135.0	40.0	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	hg19	CCDS12616.1	.	.	.	.	.	.	.	.	.	.	g	9.591	1.126263	0.20959	.	.	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.72505	-0.66	1.26	1.26	0.21427	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.76047	0.3933	M	0.78916	2.43	0.09310	N	1	P;B	0.36162	0.54;0.174	P;P	0.51487	0.671;0.45	T	0.63247	-0.6680	9	0.21014	T	0.42	.	5.8601	0.18743	0.0:0.0:1.0:0.0	.	269;269	B5MCM8;P11465	.;PSG2_HUMAN	V	269	ENSP00000385706:A269V	ENSP00000332984:A269V	A	-	2	0	PSG2	48267850	0.418000	0.25440	0.044000	0.18714	0.033000	0.12548	2.483000	0.45233	0.659000	0.30945	0.398000	0.26397	GCA	.	.		0.453	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246		A	43576010	G	A	43576010	3	1	150	1	0	0	0	0	1	0	0	0	12667	1319	46	3	209	3	PSG2	19	43576010	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	161037	43576010	15552973	483	23207										
MARK4	57787	hgsc.bcm.edu	37	chr19	45790824	45790824	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcagcaccgcggggagtgggAgtcgagggctgcccccctcc	17	15	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:45790824A>T	ENST00000262891.4	+	13	1727	c.1396A>T	c.(1396-1398)Agt>Tgt	p.S466C	MARK4_ENST00000300843.4_Missense_Mutation_p.S466C	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	466					microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)			NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GGGGAGTGGGAGTCGAGGGCT	0.711																																					p.S466C		Atlas-SNP	.											.	MARK4	132	.	0			c.A1396T						.						27	32	30					19																	45790824		2185	4295	6480	SO:0001583	missense	57787	exon13			AGTGGGAGTCGAG	AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"MAP/microtubule affinity-regulating kinase like 1"	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.1396A>T	chr19.hg19:g.45790824A>T	ENSP00000262891:p.Ser466Cys	359.0	0.0		300.0	93.0	NM_001199867	Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Missense_Mutation	SNP	ENST00000262891.4	hg19	CCDS56097.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.20|17.20	3.328829|3.328829	0.60743|0.60743	.|.	.|.	ENSG00000007047|ENSG00000007047	ENST00000262893|ENST00000262891;ENST00000300843	.|T;T	.|0.37584	.|1.19;1.19	5.06|5.06	4.05|4.05	0.47172|0.47172	.|.	.|0.000000	.|0.48767	.|D	.|0.000170	T|T	0.48150|0.48150	0.1484|0.1484	L|L	0.43923|0.43923	1.385|1.385	0.51767|0.51767	D|D	0.999939|0.999939	.|D;D;D	.|0.76494	.|0.999;0.999;0.979	.|P;D;P	.|0.80764	.|0.894;0.994;0.723	T|T	0.45308|0.45308	-0.9270|-0.9270	6|10	0.28530|0.72032	T|D	0.3|0.01	.|.	8.8674|8.8674	0.35294|0.35294	0.9116:0.0:0.0884:0.0|0.9116:0.0:0.0884:0.0	.|.	.|332;466;466	.|Q8N2N5;Q96L34;Q96L34-2	.|.;MARK4_HUMAN;.	V|C	430|466	.|ENSP00000262891:S466C;ENSP00000300843:S466C	ENSP00000262893:E430V|ENSP00000262891:S466C	E|S	+|+	2|1	0|0	MARK4|MARK4	50482664|50482664	1.000000|1.000000	0.71417|0.71417	0.264000|0.264000	0.24511|0.24511	0.499000|0.499000	0.33736|0.33736	7.733000|7.733000	0.84916|0.84916	0.970000|0.970000	0.38263|0.38263	0.482000|0.482000	0.46254|0.46254	GAG|AGT	.	.		0.711	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417		T	45790824	A	T	45790824	3	4	150	1	0	0	0	0	1	0	0	0	9324	304	11	4	1446	4	MARK4	19	45790824	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	2214814	45790824	13338159	484	23208										
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48182982	48182983	+	Missense_Mutation	DNP	GG	GG	TT													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	caggccctggtgccgccccaGgacgtggtcaacaaggccct							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:48182982_48182983GG>TT	ENST00000396720.3	+	6	749_750	c.555_556GG>TT	c.(553-558)caGGac>caTTac	p.185_186QD>HY	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	185										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		TGCCGCCCCAGGACGTGGTCAA	0.703																																					p.Q185H|p.D186Y		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G555T|c.G556T						.																																			SO:0001583	missense	29998	exon6			GCCCCAGGACGTG|CCCCAGGACGTGG	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		Exception_encountered	chr19.hg19:g.48182982_48182983delinsTT	ENSP00000379946:p.Q185_D186delinsHY	62.0	0.0		49.0|48.0	9.0|8.0	NM_015711	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	hg19	CCDS46134.1																																																																																			.	.		0.703	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		TT	48182983	GG	TT	48182982	3	4	150	1	0	0	0	0	1	0	0	0	6482	991	35	3	569	3	GLTSCR1	19	48182982	Missense_Mutation	DNP	GG	TCGA-DD-AAC8-01A-11D-A40R-10	2392158	48182982	10946001	485	23209										
SCAF1	58506	hgsc.bcm.edu	37	chr19	50156008	50156008	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	acagggacagagatagggacAgggacaggtcatccaagaag	15	7	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:50156008A>T	ENST00000360565.3	+	7	2486	c.2362A>T	c.(2362-2364)Agg>Tgg	p.R788W		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	788	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		agatagggacagggacagGTC	0.687																																					p.R788W		Atlas-SNP	.											.	SCAF1	78	.	0			c.A2362T						.						31	39	36					19																	50156008		2198	4297	6495	SO:0001583	missense	58506	exon7			AGGGACAGGGACA	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.2362A>T	chr19.hg19:g.50156008A>T	ENSP00000353769:p.Arg788Trp	116.0	0.0		114.0	28.0	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	hg19	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	14.07	2.425491	0.43020	.	.	ENSG00000126461	ENST00000360565	T	0.36520	1.25	3.73	1.36	0.22044	.	0.000000	0.37955	U	0.001865	T	0.40145	0.1105	L	0.27053	0.805	0.37725	D	0.925059	D	0.76494	0.999	D	0.71870	0.975	T	0.23797	-1.0178	9	.	.	.	-25.5875	10.2437	0.43328	0.5465:0.4535:0.0:0.0	.	788	Q9H7N4	SFR19_HUMAN	W	788	ENSP00000353769:R788W	.	R	+	1	2	SCAF1	54847820	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.005000	0.40864	0.472000	0.27344	0.459000	0.35465	AGG	.	.		0.687	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		T	50156008	A	T	50156008	3	4	150	1	0	0	0	0	1	0	0	0	13883	179	7	4	2384	4	SCAF1	19	50156008	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1973026	50156008	8972975	486	23210										
SIGLEC11	114132	hgsc.bcm.edu	37	chr19	50453402	50453402	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgagggaggcatagtggagcTcctgctcttcccccttcccc	11	15	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:50453402T>A	ENST00000447370.2	-	11	2012	c.1922A>T	c.(1921-1923)gAg>gTg	p.E641V	SIGLEC11_ENST00000426971.2_Missense_Mutation_p.E545V|CTC-326K19.6_ENST00000451973.1_Intron|U3_ENST00000408198.1_RNA	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	641					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		ATAGTGGAGCTCCTGCTCTTC	0.652																																					p.E641V		Atlas-SNP	.											.	SIGLEC11	70	.	0			c.A1922T						.						32	32	32					19																	50453402		2202	4300	6502	SO:0001583	missense	114132	exon11			TGGAGCTCCTGCT	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.1922A>T	chr19.hg19:g.50453402T>A	ENSP00000412361:p.Glu641Val	68.0	0.0		64.0	21.0	NM_052884		Missense_Mutation	SNP	ENST00000447370.2	hg19	CCDS12790.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.95|10.95	1.496744|1.496744	0.26861|0.26861	.|.	.|.	ENSG00000161640|ENSG00000161640	ENST00000447370;ENST00000458019|ENST00000426971	T|.	0.10192|.	2.9|.	3.97|3.97	1.66|1.66	0.24008|0.24008	.|.	0.160723|.	0.29501|.	N|.	0.011975|.	T|T	0.55130|0.55130	0.1901|0.1901	M|M	0.83312|0.83312	2.635|2.635	0.09310|0.09310	N|N	1|1	D;B|.	0.56521|.	0.976;0.005|.	P;B|.	0.54140|.	0.743;0.006|.	T|T	0.50092|0.50092	-0.8868|-0.8868	10|5	0.87932|.	D|.	0|.	.|.	4.6719|4.6719	0.12692|0.12692	0.1901:0.0:0.1971:0.6128|0.1901:0.0:0.1971:0.6128	.|.	545;641|.	Q96RL6-2;Q96RL6|.	.;SIG11_HUMAN|.	V|C	641;545|535	ENSP00000412361:E641V|.	ENSP00000412361:E641V|.	E|S	-|-	2|1	0|0	SIGLEC11|SIGLEC11	55145214|55145214	0.016000|0.016000	0.18221|0.18221	0.001000|0.001000	0.08648|0.08648	0.124000|0.124000	0.20399|0.20399	0.256000|0.256000	0.18351|0.18351	0.123000|0.123000	0.18342|0.18342	0.533000|0.533000	0.62120|0.62120	GAG|AGC	.	.		0.652	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		A	50453402	T	A	50453402	3	1	150	1	0	0	0	0	1	0	0	0	14322	1551	54	4	178	4	SIGLEC11	19	50453402	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	297394	50453402	8675581	487	23211										
C19orf41	126123	hgsc.bcm.edu	37	chr19	50662761	50662761	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tatgctgcaccttttaattcAtatgaaattaaaactttctt	3	7	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:50662761A>T	ENST00000293405.3	-	3	384	c.384T>A	c.(382-384)taT>taA	p.Y128*		NM_152358.2	NP_689571.2	Q6UXV1	IZUM2_HUMAN	IZUMO family member 2	128						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						CTTTTAATTCATATGAAATTA	0.448																																					p.Y128X		Atlas-SNP	.											.	IZUMO2	26	.	0			c.T384A						.						72	74	73					19																	50662761		1871	4106	5977	SO:0001587	stop_gained	126123	exon3			TAATTCATATGAA	AY358196	CCDS12792.2	19q13.33	2014-02-17	2010-07-29	2010-07-29	ENSG00000161652	ENSG00000161652		"-"	28518	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 41"	C19orf41		19658160, 22957301	Standard	XM_006723007		Approved	MGC33947, SCRL	uc002prp.1	Q6UXV1	OTTHUMG00000074063	ENST00000293405.3:c.384T>A	chr19.hg19:g.50662761A>T	ENSP00000293405:p.Tyr128*	217.0	0.0		193.0	63.0	NM_152358	Q5GRG3|Q5GRG4|Q6ZNM5|Q8NHR8	Nonsense_Mutation	SNP	ENST00000293405.3	hg19	CCDS12792.2	.	.	.	.	.	.	.	.	.	.	A	14.06	2.423179	0.43020	.	.	ENSG00000161652	ENST00000293405;ENST00000377000	.	.	.	4.22	-2.77	0.05877	.	0.179764	0.27327	N	0.019870	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.8665	0.46858	0.4051:0.0:0.5949:0.0	.	.	.	.	X	128	.	ENSP00000293405:Y128X	Y	-	3	2	IZUMO2	55354573	0.971000	0.33674	0.002000	0.10522	0.038000	0.13279	0.144000	0.16135	-0.735000	0.04837	0.459000	0.35465	TAT	.	.		0.448	IZUMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157232.1	NM_152358		T	50662761	A	T	50662761	4	4	150	1	0	0	0	0	0	1	0	0	1926	224	8	4	301	4	C19orf41	19	50662761	Nonsense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	209359	50662761	8466222	488	23212										
KLK10	5655	hgsc.bcm.edu	37	chr19	51520376	51520376	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctcctcctacttgtttccgcAgtgcgcggccgtcagcaccc	9	18	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:51520376A>T	ENST00000309958.3	-	3	477	c.259T>A	c.(259-261)Tgc>Agc	p.C87S	KLK10_ENST00000391805.1_Missense_Mutation_p.C87S|KLK10_ENST00000358789.3_Missense_Mutation_p.C87S|CTC-518B2.12_ENST00000596286.1_RNA	NM_002776.4	NP_002767.2	O43240	KLK10_HUMAN	kallikrein-related peptidase 10	87	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		TTGTTTCCGCAGTGCGCGGCC	0.697											OREG0025646	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C87S		Atlas-SNP	.											.	KLK10	32	.	0			c.T259A						.						20	21	21					19																	51520376		2202	4294	6496	SO:0001583	missense	5655	exon3			TTCCGCAGTGCGC	AF024605	CCDS12817.1	19q13	2011-03-07	2006-10-27			ENSG00000129451		"Kallikreins"	6358	protein-coding gene	gene with protein product		602673	"kallikrein 10"	PRSSL1		8764136, 9533035, 16800724, 16800723, 10675891	Standard	NM_145888		Approved	NES1	uc002pva.3	O43240		ENST00000309958.3:c.259T>A	chr19.hg19:g.51520376A>T	ENSP00000311746:p.Cys87Ser	126.0	0.0	978	138.0	36.0	NM_145888	A6NC12|Q53YL3|Q99920|Q9GZW9	Missense_Mutation	SNP	ENST00000309958.3	hg19	CCDS12817.1	.	.	.	.	.	.	.	.	.	.	a	23.8	4.457661	0.84317	.	.	ENSG00000129451	ENST00000391805;ENST00000309958;ENST00000358789	D;D;D	0.98044	-4.68;-4.68;-4.68	4.43	4.43	0.53597	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.37761	N	0.001958	D	0.99102	0.9691	H	0.98238	4.18	0.42367	D	0.992435	D	0.89917	1.0	D	0.81914	0.995	D	0.99107	1.0845	10	0.87932	D	0	.	10.3503	0.43931	1.0:0.0:0.0:0.0	.	87	O43240	KLK10_HUMAN	S	87	ENSP00000375681:C87S;ENSP00000311746:C87S;ENSP00000351640:C87S	ENSP00000311746:C87S	C	-	1	0	KLK10	56212188	1.000000	0.71417	0.996000	0.52242	0.964000	0.63967	4.552000	0.60747	1.758000	0.51981	0.402000	0.26972	TGC	.	.		0.697	KLK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464337.2	NM_002776		T	51520376	A	T	51520376	3	4	150	1	0	0	0	0	1	0	0	0	8407	188	7	4	587	4	KLK10	19	51520376	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	857615	51520376	7608607	489	23213										
ZNF615	284370	hgsc.bcm.edu	37	chr19	52497458	52497458	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gaaggctttcccacattggcTacatgtgtaaggtttccctc	9	11	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:52497458T>A	ENST00000602063.1	-	6	1220	c.871A>T	c.(871-873)Agc>Tgc	p.S291C	ZNF615_ENST00000598071.1_Missense_Mutation_p.S302C|ZNF615_ENST00000376716.5_Missense_Mutation_p.S291C|ZNF615_ENST00000594083.1_Missense_Mutation_p.S302C|ZNF615_ENST00000391795.3_Missense_Mutation_p.S296C			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		CCACATTGGCTACATGTGTAA	0.423																																					p.S302C		Atlas-SNP	.											.	ZNF615	111	.	0			c.A904T						.						178	162	168					19																	52497458		2203	4300	6503	SO:0001583	missense	284370	exon7			ATTGGCTACATGT	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.871A>T	chr19.hg19:g.52497458T>A	ENSP00000473089:p.Ser291Cys	67.0	0.0		52.0	16.0	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	hg19	CCDS12846.1	.	.	.	.	.	.	.	.	.	.	T	12.23	1.875090	0.33162	.	.	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.08008	3.14;3.14	3.09	3.09	0.35607	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15565	0.0375	M	0.75777	2.31	0.09310	N	1	P;P;P;P	0.51449	0.945;0.932;0.932;0.945	P;P;P;P	0.51415	0.669;0.54;0.54;0.669	T	0.22243	-1.0222	9	0.72032	D	0.01	.	2.6581	0.05018	0.2287:0.1276:0.0:0.6437	.	296;298;302;291	B4DH87;Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;.;ZN615_HUMAN	C	291;301;296;301	ENSP00000365906:S291C;ENSP00000375672:S296C	ENSP00000347019:S301C	S	-	1	0	ZNF615	57189270	0.000000	0.05858	0.118000	0.21660	0.739000	0.42172	-0.873000	0.04214	1.402000	0.46780	0.454000	0.30748	AGC	.	.		0.423	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		A	52497458	T	A	52497458	3	1	150	1	0	0	0	0	1	0	0	0	18055	1522	53	4	1328	4	ZNF615	19	52497458	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	977082	52497458	6631525	490	23214										
ZNF415	55786	hgsc.bcm.edu	37	chr19	53611940	53611940	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cctgatgggtagttaagttcGaatgcacactaaaggctttc	10	8	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:53611940G>T	ENST00000500065.4	-	4	1691	c.1358C>A	c.(1357-1359)tCg>tAg	p.S453*	ZNF415_ENST00000440291.1_Nonsense_Mutation_p.S440*|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000448501.1_Nonsense_Mutation_p.S501*|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000601493.1_Nonsense_Mutation_p.S223*|ZNF415_ENST00000243643.4_Nonsense_Mutation_p.S453*|ZNF415_ENST00000421033.1_Nonsense_Mutation_p.S465*|ZNF415_ENST00000455735.2_Nonsense_Mutation_p.S501*	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	501					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		AGTTAAGTTCGAATGCACACT	0.428																																					p.S453X		Atlas-SNP	.											.	ZNF415	68	.	0			c.C1358A						.						198	176	183					19																	53611940		2203	4300	6503	SO:0001587	stop_gained	55786	exon4			AAGTTCGAATGCA	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.1358C>A	chr19.hg19:g.53611940G>T	ENSP00000439435:p.Ser453*	91.0	0.0		100.0	21.0	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Nonsense_Mutation	SNP	ENST00000500065.4	hg19	CCDS54313.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.492457	0.84962	.	.	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	.	.	.	2.51	1.44	0.22558	.	.	.	.	.	.	.	.	.	.	.	0.49687	D	0.999816	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.1407	0.31082	0.1313:0.0:0.8687:0.0	.	.	.	.	X	453;453;501;465;501;440	.	ENSP00000243643:S453X	S	-	2	0	ZNF415	58303752	0.000000	0.05858	0.000000	0.03702	0.109000	0.19521	-0.228000	0.09114	0.395000	0.25257	0.313000	0.20887	TCG	.	.		0.428	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		T	53611940	G	T	53611940	4	4	150	1	0	0	0	0	0	1	0	0	17907	1059	37	1	313	1	ZNF415	19	53611940	Nonsense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	1114482	53611940	5517043	491	23215										
ZNF665	79788	hgsc.bcm.edu	37	chr19	53668306	53668306	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	taaggtttctctccagaatgAattccccgatgacttgcaag	8	10	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:53668306A>T	ENST00000600412.1	-	2	1357	c.1242T>A	c.(1240-1242)atT>atA	p.I414I	ZNF665_ENST00000396424.3_Silent_p.I479I|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		CTCCAGAATGAATTCCCCGAT	0.418																																					p.I479I		Atlas-SNP	.											.	ZNF665	136	.	0			c.T1437A						.						87	90	89					19																	53668306		2203	4300	6503	SO:0001819	synonymous_variant	79788	exon4			AGAATGAATTCCC		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1242T>A	chr19.hg19:g.53668306A>T		79.0	0.0		63.0	21.0	NM_024733	A8K5T8	Silent	SNP	ENST00000600412.1	hg19																																																																																				.	.		0.418	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		T	53668306	A	T	53668306	2	4	150	1	0	0	0	0	0	0	0	1	18088	242	9	4		4	ZNF665	19	53668306	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	56366	53668306	5460677	492	23216										
PRKCG	5582	hgsc.bcm.edu	37	chr19	54401692	54401692	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccttttggaactgtgcgcatAggtgatgctggccgagcgca	14	10	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:54401692A>T	ENST00000263431.3	+	11	1374		c.e11-1		PRKCG_ENST00000536044.1_Splice_Site|PRKCG_ENST00000540413.1_Splice_Site|PRKCG_ENST00000542049.1_Splice_Site	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma						activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	CTGTGCGCATAGGTGATGCTG	0.592																																					.		Atlas-SNP	.											.	PRKCG	246	.	0			c.1093-2A>T						.						55	50	52					19																	54401692		2203	4300	6503	SO:0001630	splice_region_variant	5582	exon11			GCGCATAGGTGAT	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.1093-1A>T	chr19.hg19:g.54401692A>T		163.0	0.0		151.0	46.0	NM_002739	B7Z8Q0	Splice_Site	SNP	ENST00000263431.3	hg19	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.357590	0.82243	.	.	ENSG00000126583	ENST00000540413;ENST00000263431;ENST00000542049	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0909	0.59166	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRKCG	59093504	1.000000	0.71417	0.988000	0.46212	0.844000	0.47949	9.169000	0.94788	2.044000	0.60594	0.459000	0.35465	.	.	.		0.592	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739	Intron	T	54401692	A	T	54401692	5	4	150	1	0	0	0	0	0	0	1	0	12524	434	15	4	1133	4	PRKCG	19	54401692	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	733386	54401692	4727291	493	23217										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55512159	55512159	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atgactttaatgatgaactcAataagctgctggaagaaata	8	5	1	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr19:55512159A>T	ENST00000543010.1	+	13	3225	c.3082A>T	c.(3082-3084)Aat>Tat	p.N1028Y	NLRP2_ENST00000448584.2_Missense_Mutation_p.N1028Y|NLRP2_ENST00000263437.6_Missense_Mutation_p.N1025Y|NLRP2_ENST00000427260.2_Missense_Mutation_p.N1005Y|NLRP2_ENST00000339757.7_Missense_Mutation_p.N1006Y|NLRP2_ENST00000391721.4_Missense_Mutation_p.N1004Y|NLRP2_ENST00000538819.1_Missense_Mutation_p.N1004Y|NLRP2_ENST00000537859.1_Missense_Mutation_p.N1006Y	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	1028					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TGATGAACTCAATAAGCTGCT	0.388																																					p.N1028Y		Atlas-SNP	.											.	NLRP2	161	.	0			c.A3082T						.						89	86	87					19																	55512159		2203	4300	6503	SO:0001583	missense	55655	exon13			GAACTCAATAAGC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.3082A>T	chr19.hg19:g.55512159A>T	ENSP00000445135:p.Asn1028Tyr	92.0	0.0		88.0	19.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	A	8.280	0.815264	0.16607	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	3.24	-2.68	0.06041	.	.	.	.	.	T	0.26593	0.0650	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B	0.29909	0.17;0.261;0.17;0.261;0.17	B;B;B;B;B	0.27076	0.035;0.047;0.035;0.076;0.035	T	0.31696	-0.9934	9	0.02654	T	1	.	6.4428	0.21859	0.5213:0.3113:0.1675:0.0	.	1005;1006;1025;1004;1028	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	Y	1028;1004;1006;1028;1006;1005;1004;1025	ENSP00000445135:N1028Y;ENSP00000375601:N1004Y;ENSP00000344074:N1006Y;ENSP00000409370:N1028Y;ENSP00000440601:N1006Y;ENSP00000402474:N1005Y;ENSP00000441133:N1004Y;ENSP00000263437:N1025Y	ENSP00000263437:N1025Y	N	+	1	0	NLRP2	60203971	0.009000	0.17119	0.000000	0.03702	0.000000	0.00434	-0.284000	0.08422	-0.263000	0.09378	-1.621000	0.00791	AAT	.	.		0.388	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		T	55512159	A	T	55512159	3	4	150	1	0	0	0	0	1	0	0	0	10486	130	5	4	3128	4	NLRP2	19	55512159	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1110467	55512159	3616824	494	23218										
NRSN2	80023	hgsc.bcm.edu	37	chr20	333979	333979	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctggtgttggatcagcgggcAgccgactacaaccaggccct	13	13	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:333979A>T	ENST00000382291.3	+	4	555	c.315A>T	c.(313-315)gcA>gcT	p.A105A	NRSN2_ENST00000608736.1_Intron|NRSN2_ENST00000382285.2_Silent_p.A105A|NRSN2_ENST00000492242.1_3'UTR	NM_024958.2	NP_079234.1	Q9GZP1	NRSN2_HUMAN	neurensin 2	105						integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				endometrium(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8		all_cancers(10;0.0834)				ATCAGCGGGCAGCCGACTACA	0.642																																					p.A105A		Atlas-SNP	.											.	NRSN2	20	.	0			c.A315T						.						71	66	67					20																	333979		2203	4300	6503	SO:0001819	synonymous_variant	80023	exon4			GCGGGCAGCCGAC	AL136915	CCDS12996.1	20p13	2008-02-04	2006-07-04	2006-07-04	ENSG00000125841	ENSG00000125841			16229	protein-coding gene	gene with protein product		610666	"chromosome 20 open reading frame 98"	C20orf98		16527258	Standard	NM_024958		Approved	dJ1103G7.6	uc002wdi.4	Q9GZP1	OTTHUMG00000031628	ENST00000382291.3:c.315A>T	chr20.hg19:g.333979A>T		79.0	0.0		97.0	18.0	NM_024958	A8K3B2|Q6FII5|Q9NUD3	Silent	SNP	ENST00000382291.3	hg19	CCDS12996.1																																																																																			.	.		0.642	NRSN2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077446.1	NM_024958		T	333979	A	T	333979	2	4	150	1	0	0	0	0	0	0	0	1	10672	175	7	4		4	NRSN2	20	333979	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		333979	62691541	495	23219										
ANKRD5	63926	hgsc.bcm.edu	37	chr20	10033917	10033917	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gaaggccctgaaattaagaaAgaagaggtaagaaaaatggt	12	3	0	5	rs199615882		TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:10033917A>G	ENST00000378380.3	+	8	2357	c.2028A>G	c.(2026-2028)aaA>aaG	p.K676K	SNAP25-AS1_ENST00000421143.2_RNA|ANKEF1_ENST00000378392.1_Silent_p.K676K|ANKEF1_ENST00000488991.1_3'UTR|SNAP25-AS1_ENST00000603542.1_RNA	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	676							calcium ion binding (GO:0005509)										AAATTAAGAAAGAAGAGGTAA	0.358																																					p.K676K		Atlas-SNP	.											.	.	.	.	0			c.A2028G						.						91	92	92					20																	10033917		2203	4299	6502	SO:0001819	synonymous_variant	63926	exon8			TAAGAAAGAAGAG	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.2028A>G	chr20.hg19:g.10033917A>G		126.0	0.0		165.0	68.0	NM_198798	B3KUQ0|Q9H6Y9	Silent	SNP	ENST00000378380.3	hg19	CCDS13108.1																																																																																			.	A|0.999;G|0.001		0.358	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		G	10033917	A	G	10033917	2	3	150	1	0	0	0	0	0	0	0	1	676	69	3	2		2	ANKRD5	20	10033917	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	9699938	10033917	52991603	496	23220										
PDRG1	81572	hgsc.bcm.edu	37	chr20	30539689	30539689	+	Frame_Shift_Del	DEL	C	C	-													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcctctcacctgccgcttgtCcgccagcacctcctcggcga							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:30539689delC	ENST00000202017.4	-	1	206	c.76delG	c.(76-78)gacfs	p.D26fs		NM_030815.2	NP_110442.1	Q9NUG6	PDRG1_HUMAN	p53 and DNA-damage regulated 1	26					protein folding (GO:0006457)	cytoplasm (GO:0005737)|prefoldin complex (GO:0016272)				endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|stomach(1)	8			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			TGCCGCTTGTCCGCCAGCACC	0.701											OREG0025859	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D26fs		Atlas-Indel,Pindel	.											.	PDRG1	17	.	0			c.77delA						.						20	18	19					20																	30539689		2199	4289	6488	SO:0001589	frameshift_variant	81572	exon1			.	AL031658	CCDS13194.1	20q11.21	2009-06-12	2009-06-12	2004-10-07	ENSG00000088356	ENSG00000088356			16119	protein-coding gene	gene with protein product		610789	"chromosome 20 open reading frame 126"	C20orf126		14562055	Standard	NM_030815		Approved	dJ310O13.3	uc002wxd.3	Q9NUG6	OTTHUMG00000032196	ENST00000202017.4:c.76delG	chr20.hg19:g.30539689delC	ENSP00000202017:p.Asp26fs	150.0	0.0	102	159.0	36.0	NM_030815	B2R511|Q96GP3|Q9BUW8	Frame_Shift_Del	DEL	ENST00000202017.4	hg19	CCDS13194.1																																																																																			.	.		0.701	PDRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078593.2	NM_030815		-	30539689	C	-	30539689	7	5	150	1	0	1	0	1	0	0	0	0	11699	855	30	0	345	0	PDRG1	20	30539689	Frame_Shift_Del	DEL	C	TCGA-DD-AAC8-01A-11D-A40R-10	20505772	30539689	32485831	497	23221										
SUN5	140732	hgsc.bcm.edu	37	chr20	31572988	31572988	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctccttgggggagccctccaTgccctgtggaaccagaacca	11	15	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:31572988T>A	ENST00000356173.3	-	12	993	c.901A>T	c.(901-903)Atg>Ttg	p.M301L	SUN5_ENST00000375523.3_Missense_Mutation_p.M276L	NM_080675.3	NP_542406.2	Q8TC36	SUN5_HUMAN	Sad1 and UNC84 domain containing 5	301	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	25						GAGCCCTCCATGCCCTGTGGA	0.577																																					p.M301L		Atlas-SNP	.											.	SUN5	63	.	0			c.A901T						.						76	75	75					20																	31572988		2203	4300	6503	SO:0001583	missense	140732	exon12			CCTCCATGCCCTG	AL121756	CCDS13209.1	20q11.21	2010-01-27	2010-01-27	2010-01-27	ENSG00000167098	ENSG00000167098			16252	protein-coding gene	gene with protein product	"testis and spermatogenesis related gene 4"	613942	"sperm associated antigen 4-like"	SPAG4L		9691178, 10373309	Standard	NM_080675		Approved	dJ726C3.1, TSARG4	uc002wyi.3	Q8TC36	OTTHUMG00000032239	ENST00000356173.3:c.901A>T	chr20.hg19:g.31572988T>A	ENSP00000348496:p.Met301Leu	109.0	0.0		106.0	18.0	NM_080675	A6NJ82|Q5T9R0	Missense_Mutation	SNP	ENST00000356173.3	hg19	CCDS13209.1	.	.	.	.	.	.	.	.	.	.	T	2.808	-0.247585	0.05867	.	.	ENSG00000167098	ENST00000356173;ENST00000375523	T;T	0.79845	-1.31;-1.31	5.67	0.672	0.17935	Sad1/UNC-like, C-terminal (2);	0.490007	0.23189	N	0.050921	T	0.34424	0.0897	N	0.00193	-1.875	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.45026	-0.9289	10	0.02654	T	1	-18.4525	2.9582	0.05883	0.3095:0.1708:0.0:0.5197	.	301	Q8TC36	SUN5_HUMAN	L	301;276	ENSP00000348496:M301L;ENSP00000364673:M276L	ENSP00000348496:M301L	M	-	1	0	SUN5	31036649	0.998000	0.40836	0.999000	0.59377	0.812000	0.45895	0.104000	0.15313	0.050000	0.15949	0.459000	0.35465	ATG	.	.		0.577	SUN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078659.1	NM_080675		A	31572988	T	A	31572988	3	1	150	1	0	0	0	0	1	0	0	0	15409	1464	51	4	246	4	SUN5	20	31572988	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1033299	31572988	31452532	498	23222										
PLUNC	51297	hgsc.bcm.edu	37	chr20	31829908	31829908	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cagaggcttggacatcacccTggtgcatgacattgttagta	11	9	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:31829908T>A	ENST00000354297.4	+	7	784	c.713T>A	c.(712-714)cTg>cAg	p.L238Q	BPIFA1_ENST00000375422.2_Missense_Mutation_p.L238Q|BPIFA1_ENST00000375413.4_Missense_Mutation_p.L238Q	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	238					antibacterial humoral response (GO:0019731)|innate immune response (GO:0045087)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|regulation of liquid surface tension (GO:0050828)|regulation of sodium ion transmembrane transport (GO:1902305)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)										GACATCACCCTGGTGCATGAC	0.557																																					p.L238Q		Atlas-SNP	.											.	.	.	.	0			c.T713A						.						132	95	107					20																	31829908		2203	4300	6503	SO:0001583	missense	51297	exon7			TCACCCTGGTGCA	AB024937	CCDS13217.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000198183	ENSG00000198183		"BPI fold containing"	15749	protein-coding gene	gene with protein product		607412	"palate, lung and nasal epithelium carcinoma associated", "palate, lung and nasal epithelium associated"	PLUNC		11018263, 11251963, 21787333	Standard	NM_130852		Approved	LUNX, bA49G10.5, SPLUNC1	uc002wyv.3	Q9NP55	OTTHUMG00000032243	ENST00000354297.4:c.713T>A	chr20.hg19:g.31829908T>A	ENSP00000346251:p.Leu238Gln	85.0	0.0		69.0	9.0	NM_016583	A8K9R3|E1P5M9|Q9NZT0	Missense_Mutation	SNP	ENST00000354297.4	hg19	CCDS13217.1	.	.	.	.	.	.	.	.	.	.	t	14.82	2.649171	0.47362	.	.	ENSG00000198183	ENST00000375422;ENST00000354297;ENST00000375413;ENST00000544328	T;T;T	0.05717	3.4;3.4;3.4	5.31	5.31	0.75309	.	0.277700	0.25625	N	0.029383	T	0.21761	0.0524	M	0.67953	2.075	0.30949	N	0.725008	D	0.89917	1.0	D	0.83275	0.996	T	0.03761	-1.1006	10	0.72032	D	0.01	-4.6099	11.6146	0.51080	0.0:0.0:0.0:1.0	.	238	Q9NP55	BPIA1_HUMAN	Q	238;238;238;224	ENSP00000364571:L238Q;ENSP00000346251:L238Q;ENSP00000364562:L238Q	ENSP00000346251:L238Q	L	+	2	0	BPIFA1	31293569	0.978000	0.34361	0.672000	0.29872	0.299000	0.27559	3.429000	0.52800	2.237000	0.73441	0.473000	0.43528	CTG	.	.		0.557	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		A	31829908	T	A	31829908	3	1	150	1	0	0	0	0	1	0	0	0	12124	1580	55	4	735	4	PLUNC	20	31829908	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	256920	31829908	31195612	499	23223										
EMILIN3	90187	hgsc.bcm.edu	37	chr20	39993757	39993757	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctccgctccctcctgtaggaTgcaggtcacattcctgtgca	9	15	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:39993757T>G	ENST00000332312.3	-	2	400	c.208A>C	c.(208-210)Atc>Ctc	p.I70L		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	70	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				TCCTGTAGGATGCAGGTCACA	0.592																																					p.I70L		Atlas-SNP	.											.	EMILIN3	63	.	0			c.A208C						.						192	146	162					20																	39993757		2203	4300	6503	SO:0001583	missense	90187	exon2			GTAGGATGCAGGT	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"EMI domain containing"	16123	protein-coding gene	gene with protein product	"chromosome 20 open reading frame 130"	608929	"elastin microfibril interfacer 5"	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.208A>C	chr20.hg19:g.39993757T>G	ENSP00000332806:p.Ile70Leu	75.0	0.0		68.0	12.0	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Missense_Mutation	SNP	ENST00000332312.3	hg19	CCDS13316.1	.	.	.	.	.	.	.	.	.	.	T	16.13	3.036510	0.54896	.	.	ENSG00000183798	ENST00000332312	T	0.40476	1.03	4.48	-4.09	0.03951	EMI domain (2);	0.751776	0.13062	N	0.416849	T	0.26629	0.0651	L	0.29908	0.895	0.24495	N	0.994282	B	0.20052	0.041	B	0.18263	0.021	T	0.22417	-1.0217	9	.	.	.	-7.1765	13.1667	0.59575	0.0:0.278:0.0:0.722	.	70	Q9NT22	EMIL3_HUMAN	L	70	ENSP00000332806:I70L	.	I	-	1	0	EMILIN3	39427171	0.000000	0.05858	0.710000	0.30468	0.976000	0.68499	-1.565000	0.02150	-0.607000	0.05738	-0.177000	0.13119	ATC	.	.		0.592	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741		G	39993757	T	G	39993757	3	3	150	1	0	0	0	0	1	0	0	0	5097	1464	51	5	2104	5	EMILIN3	20	39993757	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	8163849	39993757	23031763	500	23224										
CHD6	84181	hgsc.bcm.edu	37	chr20	40127977	40127977	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggatcttctcaatgatgttTgcatcatcttctggaggctc	9	9	5	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:40127977T>A	ENST00000373233.3	-	6	1050	c.873A>T	c.(871-873)gcA>gcT	p.A291A	CHD6_ENST00000373222.3_Silent_p.A326A|CHD6_ENST00000309279.7_Silent_p.A291A	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	291	Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CAATGATGTTTGCATCATCTT	0.378																																					p.A291A		Atlas-SNP	.											.	CHD6	312	.	0			c.A873T						.						67	56	59					20																	40127977		2203	4300	6503	SO:0001819	synonymous_variant	84181	exon6			GATGTTTGCATCA	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.873A>T	chr20.hg19:g.40127977T>A		41.0	0.0		62.0	8.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	hg19	CCDS13317.1																																																																																			.	.		0.378	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40127977	T	A	40127977	2	1	150	1	0	0	0	0	0	0	0	1	3331	1799	63	4		4	CHD6	20	40127977	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	134220	40127977	22897543	501	23225										
BCAS1	8537	hgsc.bcm.edu	37	chr20	52601945	52601945	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccccgatgggttgcatccttTggaattcttgccagcccctt	9	14	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:52601945T>A	ENST00000395961.3	-	7	1187	c.1021A>T	c.(1021-1023)Aaa>Taa	p.K341*	BCAS1_ENST00000371435.2_Nonsense_Mutation_p.K341*|BCAS1_ENST00000371440.3_Nonsense_Mutation_p.K386*|BCAS1_ENST00000434986.2_Nonsense_Mutation_p.K99*	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	341						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			TTGCATCCTTTGGAATTCTTG	0.542																																					p.K341X		Atlas-SNP	.											.	BCAS1	77	.	0			c.A1021T						.						233	211	219					20																	52601945		2203	4300	6503	SO:0001587	stop_gained	8537	exon7			ATCCTTTGGAATT	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.1021A>T	chr20.hg19:g.52601945T>A	ENSP00000379290:p.Lys341*	159.0	0.0		218.0	56.0	NM_003657	A0AVG5|Q68CZ3	Nonsense_Mutation	SNP	ENST00000395961.3	hg19	CCDS13444.1	.	.	.	.	.	.	.	.	.	.	T	33	5.238486	0.95240	.	.	ENSG00000064787	ENST00000448484;ENST00000371440;ENST00000448710;ENST00000395961;ENST00000371435;ENST00000434986	.	.	.	6.03	4.9	0.64082	.	0.066950	0.56097	D	0.000021	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.7819	10.1586	0.42838	0.0:0.0:0.1675:0.8325	.	.	.	.	X	248;386;219;341;341;99	.	ENSP00000360490:K341X	K	-	1	0	BCAS1	52035352	0.981000	0.34729	0.082000	0.20525	0.008000	0.06430	0.860000	0.27871	1.052000	0.40392	0.533000	0.62120	AAA	.	.		0.542	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657		A	52601945	T	A	52601945	4	1	150	1	0	0	0	0	0	1	0	0	1350	1821	63	4	757	4	BCAS1	20	52601945	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	12473968	52601945	10423575	502	23226										
ZBP1	81030	hgsc.bcm.edu	37	chr20	56188317	56188317	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tccagctgttgggtccattcTggcagatcatgttgattgga	12	8	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:56188317T>A	ENST00000371173.3	-	5	749	c.572A>T	c.(571-573)cAg>cTg	p.Q191L	ZBP1_ENST00000538947.1_5'Flank|ZBP1_ENST00000340462.4_Missense_Mutation_p.Q168L|ZBP1_ENST00000541799.1_Missense_Mutation_p.Q191L|ZBP1_ENST00000343535.4_Missense_Mutation_p.Q191L|ZBP1_ENST00000395822.3_Missense_Mutation_p.Q116L	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	191					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			GGGTCCATTCTGGCAGATCAT	0.443																																					p.Q191L		Atlas-SNP	.											.	ZBP1	65	.	0			c.A572T						.						217	188	198					20																	56188317		2203	4300	6503	SO:0001583	missense	81030	exon5			CCATTCTGGCAGA	AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"DNA-dependent activator of IRFs"	606750	"chromosome 20 open reading frame 183"	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.572A>T	chr20.hg19:g.56188317T>A	ENSP00000360215:p.Gln191Leu	71.0	0.0		82.0	17.0	NM_001160419	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Missense_Mutation	SNP	ENST00000371173.3	hg19	CCDS13461.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.872716	0.51695	.	.	ENSG00000124256	ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535;ENST00000541799	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	3.36	3.36	0.38483	.	0.000000	0.41097	D	0.000953	T	0.54679	0.1873	L	0.54323	1.7	0.09310	N	0.999999	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.87578	0.996;0.998;0.998;0.998	T	0.38134	-0.9675	10	0.87932	D	0	-24.968	8.4548	0.32893	0.0:0.0:0.0:1.0	.	191;191;116;191	F5GYT1;A2RRL9;A2A2F7;Q9H171	.;.;.;ZBP1_HUMAN	L	191;116;168;191;191;191	ENSP00000360215:Q191L;ENSP00000379167:Q116L;ENSP00000344954:Q168L;ENSP00000340584:Q191L;ENSP00000440552:Q191L	ENSP00000344954:Q168L	Q	-	2	0	ZBP1	55621723	0.845000	0.29573	0.142000	0.22268	0.011000	0.07611	1.637000	0.37155	1.781000	0.52344	0.379000	0.24179	CAG	.	.		0.443	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776		A	56188317	T	A	56188317	3	1	150	1	0	0	0	0	1	0	0	0	17536	1580	55	4	810	4	ZBP1	20	56188317	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3586372	56188317	6837203	503	23227										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60909582	60909582	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gggaaggggtacccactcgcTgcaggtggggccctgggtgt	19	10	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:60909582T>A	ENST00000252999.3	-	21	2644	c.2578A>T	c.(2578-2580)Agc>Tgc	p.S860C	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	860	Domain IV 1 (domain IV B).				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			ACCCACTCGCTGCAGGTGGGG	0.706																																					p.S860C		Atlas-SNP	.											.	LAMA5	268	.	0			c.A2578T						.						4	4	4					20																	60909582		1807	3504	5311	SO:0001583	missense	3911	exon21			ACTCGCTGCAGGT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.2578A>T	chr20.hg19:g.60909582T>A	ENSP00000252999:p.Ser860Cys	117.0	0.0		115.0	25.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	t	17.60	3.429944	0.62844	.	.	ENSG00000130702	ENST00000252999	T	0.62232	0.04	4.79	2.45	0.29901	EGF-like, laminin (3);	0.172078	0.53938	D	0.000044	T	0.75715	0.3887	M	0.82132	2.575	0.80722	D	1	D	0.76494	0.999	D	0.68192	0.956	T	0.74671	-0.3587	10	0.72032	D	0.01	.	9.2157	0.37346	0.0:0.153:0.0:0.847	.	860	O15230	LAMA5_HUMAN	C	860	ENSP00000252999:S860C	ENSP00000252999:S860C	S	-	1	0	LAMA5	60342977	1.000000	0.71417	0.990000	0.47175	0.616000	0.37450	1.974000	0.40559	0.180000	0.19960	0.454000	0.30748	AGC	.	.		0.706	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60909582	T	A	60909582	3	1	150	1	0	0	0	0	1	0	0	0	8618	1580	55	4	8749	4	LAMA5	20	60909582	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	4721265	60909582	2115938	504	23228										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61537425	61537425	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tttttctggagctggtctctTgtgcacagaagagattttaa	10	6	2	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr20:61537425T>A	ENST00000266070.4	-	6	1727	c.1402A>T	c.(1402-1404)Aag>Tag	p.K468*	DIDO1_ENST00000370368.1_Nonsense_Mutation_p.K468*|DIDO1_ENST00000395343.1_Nonsense_Mutation_p.K468*|DIDO1_ENST00000395340.1_Nonsense_Mutation_p.K468*|DIDO1_ENST00000354665.4_Nonsense_Mutation_p.K468*|DIDO1_ENST00000370366.1_Nonsense_Mutation_p.K468*|DIDO1_ENST00000266071.5_Nonsense_Mutation_p.K468*|DIDO1_ENST00000395335.2_Nonsense_Mutation_p.K468*|DIDO1_ENST00000370371.4_Nonsense_Mutation_p.K468*	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	468					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GCTGGTCTCTTGTGCACAGAA	0.448																																					p.K468X	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.A1402T						.						85	94	91					20																	61537425		2203	4300	6503	SO:0001587	stop_gained	11083	exon6			GTCTCTTGTGCAC	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.1402A>T	chr20.hg19:g.61537425T>A	ENSP00000266070:p.Lys468*	41.0	0.0		29.0	6.0	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Nonsense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	T	40	8.089264	0.98648	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335;ENST00000370371;ENST00000370368;ENST00000354665;ENST00000370366;ENST00000266071	.	.	.	5.82	5.82	0.92795	.	0.000000	0.41712	U	0.000823	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-58.5818	16.1778	0.81874	0.0:0.0:0.0:1.0	.	.	.	.	X	468	.	ENSP00000266070:K468X	K	-	1	0	DIDO1	61007870	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.015000	0.64035	2.225000	0.72522	0.459000	0.35465	AAG	.	.		0.448	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		A	61537425	T	A	61537425	4	1	150	1	0	0	0	0	0	1	0	0	4524	1821	63	4	5494	4	DIDO1	20	61537425	Nonsense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	627843	61537425	1488095	505	23229										
JAM2	58494	hgsc.bcm.edu	37	chr21	27062287	27062287	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tatcaacagactcttcaaggTaagcagctgtaggcttgaag	10	8	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr21:27062287T>C	ENST00000480456.1	+	3	791		c.e3+2		JAM2_ENST00000425221.2_Intron|JAM2_ENST00000400532.1_Splice_Site|JAM2_ENST00000312957.5_Splice_Site	NM_001270407.1|NM_021219.3	NP_001257336.1|NP_067042.1	P57087	JAM2_HUMAN	junctional adhesion molecule 2						blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|stomach(1)|urinary_tract(1)	19						CTCTTCAAGGTAAGCAGCTGT	0.443																																					.		Atlas-SNP	.											.	JAM2	33	.	0			c.241+2T>C						.						98	100	99					21																	27062287		1889	4108	5997	SO:0001630	splice_region_variant	58494	exon3			TCAAGGTAAGCAG	AF255910	CCDS42911.1, CCDS58787.1, CCDS58788.1	21q21.2	2013-01-11			ENSG00000154721	ENSG00000154721		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing"	14686	protein-coding gene	gene with protein product		606870		C21orf43		10779521, 10945976	Standard	NM_021219		Approved	VE-JAM, JAM-B, JAMB, CD322	uc031rvc.1	P57087	OTTHUMG00000078441	ENST00000480456.1:c.241+2T>C	chr21.hg19:g.27062287T>C		70.0	0.0		32.0	9.0	NM_021219	B2R6T9|B4DGT9|Q6UXG6|Q6YNC1	Splice_Site	SNP	ENST00000480456.1	hg19	CCDS42911.1	.	.	.	.	.	.	.	.	.	.	T	15.64	2.892368	0.52121	.	.	ENSG00000154721	ENST00000480456;ENST00000400533;ENST00000400532;ENST00000400537;ENST00000312957	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4919	0.50385	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	JAM2	25984158	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	3.827000	0.55745	2.279000	0.76181	0.528000	0.53228	.	.	.		0.443	JAM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171347.1		Intron	C	27062287	T	C	27062287	5	2	150	1	0	0	0	0	0	0	1	0	7952	1652	57	2	253	2	JAM2	21	27062287	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10		27062287	21067608	506	23230										
APP	351	hgsc.bcm.edu	37	chr21	27269958	27269958	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcttcacttcagagatctccTccgtcttgatatttgtcaac	5	12	6	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr21:27269958T>A	ENST00000346798.3	-	16	2024	c.1991A>T	c.(1990-1992)gAg>gTg	p.E664V	APP_ENST00000359726.3_Missense_Mutation_p.E608V|APP_ENST00000357903.3_Missense_Mutation_p.E645V|APP_ENST00000440126.3_Missense_Mutation_p.E640V|APP_ENST00000439274.2_Missense_Mutation_p.E608V|APP_ENST00000348990.5_Missense_Mutation_p.E589V|APP_ENST00000358918.3_Missense_Mutation_p.E646V|APP_ENST00000448388.2_Missense_Mutation_p.E554V|APP_ENST00000354192.3_Missense_Mutation_p.E533V	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	664					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				AGAGATCTCCTCCGTCTTGAT	0.343																																					p.E664V		Atlas-SNP	.											.	APP	90	.	0			c.A1991T						.						174	166	169					21																	27269958		2203	4300	6503	SO:0001583	missense	351	exon16			ATCTCCTCCGTCT	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1991A>T	chr21.hg19:g.27269958T>A	ENSP00000284981:p.Glu664Val	104.0	0.0		45.0	12.0	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	hg19	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	T	15.67	2.901836	0.52227	.	.	ENSG00000142192	ENST00000346798;ENST00000354192;ENST00000348990;ENST00000357903;ENST00000358918;ENST00000359726;ENST00000448388;ENST00000440126;ENST00000439274;ENST00000456209	D;D;D;D;D;D;D;D;D;D	0.96774	-2.16;-4.12;-4.11;-2.17;-1.91;-4.11;-4.11;-2.17;-2.16;-3.23	5.5	5.5	0.81552	.	0.057723	0.64402	D	0.000001	D	0.96390	0.8822	L	0.46157	1.445	0.80722	D	1	D;D;P;D;P;P;D	0.57899	0.968;0.973;0.816;0.981;0.884;0.884;0.973	P;P;B;P;B;B;P	0.57101	0.655;0.786;0.186;0.813;0.344;0.344;0.786	D	0.96232	0.9169	10	0.48119	T	0.1	-23.0203	15.4312	0.75102	0.0:0.0:0.0:1.0	.	554;608;640;533;589;645;664	E9PEV0;E9PG40;B4DII8;P05067-10;P05067-4;P05067-8;P05067	.;.;.;.;.;.;A4_HUMAN	V	664;533;589;645;646;608;554;640;608;233	ENSP00000284981:E664V;ENSP00000346129:E533V;ENSP00000345463:E589V;ENSP00000350578:E645V;ENSP00000351796:E646V;ENSP00000352760:E608V;ENSP00000388538:E554V;ENSP00000387483:E640V;ENSP00000398879:E608V;ENSP00000397795:E233V	ENSP00000284981:E664V	E	-	2	0	APP	26191829	1.000000	0.71417	0.972000	0.41901	0.908000	0.53690	5.046000	0.64226	2.310000	0.77875	0.450000	0.29827	GAG	.	.		0.343	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		A	27269958	T	A	27269958	3	1	150	1	0	0	0	0	1	0	0	0	815	1551	54	4	333	4	APP	21	27269958	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	207671	27269958	20859937	507	23231										
PDE9A	5152	hgsc.bcm.edu	37	chr21	44192597	44192597	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctggggccaccgagaagtccAgagagagaagcagagatgtg	16	8	0	4			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr21:44192597A>T	ENST00000291539.6	+	19	1795	c.1735A>T	c.(1735-1737)Aga>Tga	p.R579*	PDE9A_ENST00000398227.3_Nonsense_Mutation_p.R419*|PDE9A_ENST00000380328.2_Nonsense_Mutation_p.R526*|PDE9A_ENST00000328862.6_Nonsense_Mutation_p.R553*|PDE9A_ENST00000398225.3_Nonsense_Mutation_p.R538*|PDE9A_ENST00000398224.3_Nonsense_Mutation_p.R452*|PDE9A_ENST00000398232.3_Nonsense_Mutation_p.R512*|PDE9A_ENST00000349112.3_Nonsense_Mutation_p.R451*|PDE9A_ENST00000398236.3_Nonsense_Mutation_p.R493*|PDE9A_ENST00000539837.1_Nonsense_Mutation_p.R451*|PDE9A_ENST00000398234.3_Nonsense_Mutation_p.R478*|PDE9A_ENST00000398229.3_Nonsense_Mutation_p.R445*|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000335512.4_Nonsense_Mutation_p.R519*|PDE9A_ENST00000335440.6_Nonsense_Mutation_p.R477*	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	579					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	CGAGAAGTCCAGAGAGAGAAG	0.498																																					p.R579X		Atlas-SNP	.											.	PDE9A	69	.	0			c.A1735T						.						76	61	66					21																	44192597		2202	4300	6502	SO:0001587	stop_gained	5152	exon19			AAGTCCAGAGAGA	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"Phosphodiesterases"	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.1735A>T	chr21.hg19:g.44192597A>T	ENSP00000291539:p.Arg579*	94.0	0.0		56.0	25.0	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Nonsense_Mutation	SNP	ENST00000291539.6	hg19	CCDS13690.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.431880	0.83776	.	.	ENSG00000160191	ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000328862;ENST00000335440;ENST00000398225;ENST00000398229;ENST00000398227;ENST00000349112;ENST00000398224	.	.	.	3.4	0.951	0.19579	.	148.372000	0.00166	N	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	3.2296	0.06744	0.5568:0.2142:0.229:0.0	.	.	.	.	X	519;451;579;526;512;478;493;553;477;538;445;419;451;452	.	ENSP00000291539:R579X	R	+	1	2	PDE9A	43065666	0.024000	0.19004	0.022000	0.16811	0.111000	0.19643	0.487000	0.22356	0.189000	0.20188	0.454000	0.30748	AGA	.	.		0.498	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			T	44192597	A	T	44192597	4	4	150	1	0	0	0	0	0	1	0	0	11664	180	7	4	1889	4	PDE9A	21	44192597	Nonsense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	16922639	44192597	3937298	508	23232										
CDC45	8318	hgsc.bcm.edu	37	chr22	19495303	19495303	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttccagtcttcccctgaagcAggtgaagcagaagttccagg	11	11	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr22:19495303A>T	ENST00000407835.1	+	13	1227	c.971A>T	c.(970-972)cAg>cTg	p.Q324L	CDC45_ENST00000404724.3_Missense_Mutation_p.Q278L|CDC45_ENST00000263201.1_Missense_Mutation_p.Q324L|CDC45_ENST00000437685.2_Missense_Mutation_p.Q356L			O75419	CDC45_HUMAN	cell division cycle 45	324					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						CCCCTGAAGCAGGTGAAGCAG	0.483																																					p.Q356L		Atlas-SNP	.											.	CDC45	48	.	0			c.A1067T						.						100	96	98					22																	19495303		2203	4300	6503	SO:0001583	missense	8318	exon13			TGAAGCAGGTGAA	AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"human CDC45"	603465	"CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like", "CDC45 cell division cycle 45-like (S. cerevisiae)", "cell division cycle 45 homolog (S. cerevisiae)"	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.971A>T	chr22.hg19:g.19495303A>T	ENSP00000385240:p.Gln324Leu	100.0	0.0		63.0	26.0	NM_001178010	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Missense_Mutation	SNP	ENST00000407835.1	hg19	CCDS13762.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.951828	0.92660	.	.	ENSG00000093009	ENST00000407835;ENST00000437685;ENST00000263201;ENST00000404724	T;T;T;T	0.25579	1.79;1.79;1.79;1.79	5.26	5.26	0.73747	.	0.050750	0.85682	D	0.000000	T	0.54663	0.1872	M	0.86420	2.815	0.80722	D	1	P;D;D;P;P	0.60575	0.931;0.963;0.988;0.931;0.931	P;D;P;P;P	0.64321	0.816;0.924;0.903;0.816;0.751	T	0.63773	-0.6561	10	0.87932	D	0	-25.5348	15.3365	0.74260	1.0:0.0:0.0:0.0	.	356;319;278;356;324	E9PDH7;B4E092;B4DDB4;B4DDU3;O75419	.;.;.;.;CDC45_HUMAN	L	324;356;324;278	ENSP00000385240:Q324L;ENSP00000405726:Q356L;ENSP00000263201:Q324L;ENSP00000384978:Q278L	ENSP00000263201:Q324L	Q	+	2	0	CDC45	17875303	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.761000	0.91691	2.208000	0.71279	0.459000	0.35465	CAG	.	.		0.483	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504		T	19495303	A	T	19495303	3	4	150	1	0	0	0	0	1	0	0	0	3083	188	7	4	1117	4	CDC45	22	19495303	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10		19495303	31809263	509	23233										
GGT5	2687	hgsc.bcm.edu	37	chr22	24629895	24629895	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctccgcccaggcccatgctcTgagggttgacgacgctggtg	14	14	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr22:24629895T>A	ENST00000327365.4	-	2	667	c.251A>T	c.(250-252)cAg>cTg	p.Q84L	GGT5_ENST00000263112.7_Missense_Mutation_p.Q84L|GGT5_ENST00000418439.2_Intron|GGT5_ENST00000398292.3_Missense_Mutation_p.Q84L	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	84					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						GCCCATGCTCTGAGGGTTGAC	0.612																																					p.Q84L		Atlas-SNP	.											.	GGT5	61	.	0			c.A251T						.						111	90	97					22																	24629895		2203	4300	6503	SO:0001583	missense	2687	exon2			ATGCTCTGAGGGT	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"Gamma-glutamyltransferases"	4260	protein-coding gene	gene with protein product		137168	"gamma-glutamyltransferase-like activity 1"	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.251A>T	chr22.hg19:g.24629895T>A	ENSP00000330080:p.Gln84Leu	120.0	0.0		67.0	28.0	NM_001099782	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Missense_Mutation	SNP	ENST00000327365.4	hg19	CCDS13825.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.398051	0.83120	.	.	ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000398292	T;T;T	0.07021	3.23;3.23;3.23	4.87	4.87	0.63330	.	0.062767	0.64402	D	0.000004	T	0.35711	0.0941	M	0.91920	3.255	0.80722	D	1	P;D;P;D	0.89917	0.908;1.0;0.943;1.0	P;D;P;D	0.87578	0.847;0.998;0.857;0.998	T	0.41324	-0.9515	10	0.72032	D	0.01	-49.8574	12.755	0.57331	0.0:0.0:0.0:1.0	.	84;84;84;84	P36269-2;Q53XM9;Q6GMP0;P36269	.;.;.;GGT5_HUMAN	L	84	ENSP00000330080:Q84L;ENSP00000263112:Q84L;ENSP00000381340:Q84L	ENSP00000263112:Q84L	Q	-	2	0	GGT5	22959895	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	7.515000	0.81761	1.983000	0.57843	0.254000	0.18369	CAG	.	.		0.612	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121		A	24629895	T	A	24629895	3	1	150	1	0	0	0	0	1	0	0	0	6370	1580	55	4	1556	4	GGT5	22	24629895	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	5134592	24629895	26674671	510	23234										
PLA2G3	50487	hgsc.bcm.edu	37	chr22	31536135	31536135	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	catcctcccagctacatgacTgcagcctcctatgcgcatcc	6	18	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr22:31536135T>A	ENST00000215885.3	-	1	458	c.206A>T	c.(205-207)cAg>cTg	p.Q69L		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	69					acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						GCTACATGACTGCAGCCTCCT	0.647																																					p.Q69L		Atlas-SNP	.											.,2	PLA2G3	85	.	0			c.A206T						.						67	70	69					22																	31536135		2203	4300	6503	SO:0001583	missense	50487	exon1			CATGACTGCAGCC	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.206A>T	chr22.hg19:g.31536135T>A	ENSP00000215885:p.Gln69Leu	43.0	0.0		34.0	14.0	NM_015715	O95768	Missense_Mutation	SNP	ENST00000215885.3	hg19	CCDS13889.1	.	.	.	.	.	.	.	.	.	.	T	2.916	-0.224345	0.06061	.	.	ENSG00000100078	ENST00000215885	T	0.09723	2.95	5.69	2.31	0.28768	.	0.500789	0.20316	N	0.094725	T	0.05731	0.0150	L	0.36672	1.1	0.30895	N	0.729934	B	0.18610	0.029	B	0.15052	0.012	T	0.38693	-0.9649	10	0.02654	T	1	-3.1582	2.9736	0.05930	0.2278:0.2007:0.0:0.5715	.	69	Q9NZ20	PA2G3_HUMAN	L	69	ENSP00000215885:Q69L	ENSP00000215885:Q69L	Q	-	2	0	PLA2G3	29866135	0.676000	0.27567	0.334000	0.25495	0.645000	0.38454	0.489000	0.22387	0.455000	0.26910	0.533000	0.62120	CAG	.	.		0.647	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715		A	31536135	T	A	31536135	3	1	150	1	0	0	0	0	1	0	0	0	12009	1580	55	4	1351	4	PLA2G3	22	31536135	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	6906240	31536135	19768431	511	23235										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32293526	32293526	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cttgttagtcccagttttggAggggccttttgcactgccca	11	11	0	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr22:32293526A>T	ENST00000382112.3	+	39	4305	c.4235A>T	c.(4234-4236)gAg>gTg	p.E1412V	DEPDC5_ENST00000400249.2_Missense_Mutation_p.E1390V|DEPDC5_ENST00000535622.1_Missense_Mutation_p.E1321V|DEPDC5_ENST00000382111.2_Missense_Mutation_p.E1421V|DEPDC5_ENST00000400246.1_Missense_Mutation_p.E1421V|DEPDC5_ENST00000539165.1_Missense_Mutation_p.E238V|DEPDC5_ENST00000400248.2_Missense_Mutation_p.E1390V|DEPDC5_ENST00000382105.2_3'UTR|DEPDC5_ENST00000266091.3_Missense_Mutation_p.E1399V	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1421					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CCAGTTTTGGAGGGGCCTTTT	0.537																																					p.E1421V		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A4262T						.						118	116	117					22																	32293526		1929	4123	6052	SO:0001583	missense	9681	exon40			TTTTGGAGGGGCC	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.4235A>T	chr22.hg19:g.32293526A>T	ENSP00000371546:p.Glu1412Val	110.0	0.0		65.0	22.0	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	a	22.6	4.314148	0.81358	.	.	ENSG00000100150	ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382112;ENST00000382111;ENST00000400248;ENST00000539165	T;T;T;T;T;T;T	0.35605	1.3;1.72;1.73;1.72;1.73;1.72;1.73	5.61	5.61	0.85477	.	0.052668	0.64402	D	0.000001	T	0.45816	0.1361	L	0.31664	0.95	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999;0.999	D;D;D;D;D;D	0.91635	0.994;0.996;0.999;0.996;0.991;0.991	T	0.25293	-1.0136	10	0.15066	T	0.55	.	14.9748	0.71264	1.0:0.0:0.0:0.0	.	1421;1321;807;1399;1412;1390	B9EGN9;B4DH93;O75140-7;O75140-4;A8MPX9;O75140	.;.;.;.;.;DEPD5_HUMAN	V	1321;1399;1390;1321;1421;1412;1421;1390;238	ENSP00000440210:E1321V;ENSP00000266091:E1399V;ENSP00000383108:E1390V;ENSP00000383105:E1421V;ENSP00000371546:E1412V;ENSP00000371545:E1421V;ENSP00000383107:E1390V	ENSP00000266091:E1399V	E	+	2	0	DEPDC5	30623526	1.000000	0.71417	0.714000	0.30535	0.883000	0.51084	8.948000	0.93006	2.139000	0.66308	0.454000	0.30748	GAG	.	.		0.537	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		T	32293526	A	T	32293526	3	4	150	1	0	0	0	0	1	0	0	0	4444	304	11	4	4407	4	DEPDC5	22	32293526	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	757391	32293526	19011040	512	23236										
CSF2RB	1439	hgsc.bcm.edu	37	chr22	37318309	37318309	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gccctgtgctgggagcgcagCctggcaggggcagaaggtga	19	10	0	2	rs200588212	byFrequency	TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr22:37318309C>T	ENST00000403662.3	+	2	282	c.60C>T	c.(58-60)agC>agT	p.S20S	CSF2RB_ENST00000262825.5_Silent_p.S20S|CSF2RB_ENST00000406230.1_Silent_p.S20S|CSF2RB_ENST00000536485.1_5'Flank			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	20					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GGGAGCGCAGCCTGGCAGGGG	0.682																																					p.S20S		Atlas-SNP	.											.	CSF2RB	104	.	0			c.C60T						.						21	19	20					22																	37318309		2200	4291	6491	SO:0001819	synonymous_variant	1439	exon2			GCGCAGCCTGGCA	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"CD molecules", "Fibronectin type III domain containing"	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.60C>T	chr22.hg19:g.37318309C>T		108.0	0.0		77.0	28.0	NM_000395	Q5JZI1|Q6ICE0	Silent	SNP	ENST00000403662.3	hg19	CCDS13936.1																																																																																			.	C|0.999;A|0.001		0.682	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395		T	37318309	C	T	37318309	2	4	150	1	0	0	0	0	0	0	0	1	3937	738	26	3		3	CSF2RB	22	37318309	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	5024783	37318309	13986257	513	23237										
PICK1	9463	hgsc.bcm.edu	37	chr22	38461007	38461007	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cactctccttatgcacccacAggtatttgacaacaccccag	5	16	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr22:38461007A>C	ENST00000404072.3	+	4	500		c.e4-1		PICK1_ENST00000356976.3_Splice_Site|RP5-1039K5.13_ENST00000445483.1_RNA|PICK1_ENST00000468288.1_Splice_Site	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1						ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					ATGCACCCACAGGTATTTGAC	0.552																																					.		Atlas-SNP	.											.	PICK1	30	.	0			c.154-2A>C						.						137	114	122					22																	38461007		2203	4300	6503	SO:0001630	splice_region_variant	9463	exon4			ACCCACAGGTATT	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"protein kinase C, alpha binding protein", "protein interacting with PRKCA"	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.154-1A>C	chr22.hg19:g.38461007A>C		135.0	0.0		66.0	23.0	NM_012407	B3KS52|O95906	Splice_Site	SNP	ENST00000404072.3	hg19	CCDS13965.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.913455	0.72983	.	.	ENSG00000100151	ENST00000404072;ENST00000424694;ENST00000437453;ENST00000356976;ENST00000435166	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2435	0.73488	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PICK1	36790953	1.000000	0.71417	0.992000	0.48379	0.903000	0.53119	9.030000	0.93725	2.071000	0.62044	0.460000	0.39030	.	.	.		0.552	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407	Intron	C	38461007	A	C	38461007	5	2	150	1	0	0	0	0	0	0	1	0	11890	202	7	5	162	5	PICK1	22	38461007	Splice_Site	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1142698	38461007	12843559	514	23238										
PARVB	29780	hgsc.bcm.edu	37	chr22	44547368	44547368	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ttttattcttggcagtctctCatcacttttgtgaacaagca	6	9	4	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr22:44547368C>A	ENST00000338758.7	+	10	843	c.780C>A	c.(778-780)ctC>ctA	p.L260L	PARVB_ENST00000406477.3_Silent_p.L293L|PARVB_ENST00000404989.1_Silent_p.L223L	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	260	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				GGCAGTCTCTCATCACTTTTG	0.522																																					p.L293L		Atlas-SNP	.											.	PARVB	44	.	0			c.C879A						.						124	104	111					22																	44547368		2203	4300	6503	SO:0001819	synonymous_variant	29780	exon11			GTCTCTCATCACT	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"Parvins"	14653	protein-coding gene	gene with protein product	"affixin"	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.780C>A	chr22.hg19:g.44547368C>A		92.0	0.0		38.0	15.0	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Silent	SNP	ENST00000338758.7	hg19	CCDS14056.1																																																																																			.	.		0.522	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828		A	44547368	C	A	44547368	2	1	150	1	0	0	0	0	0	0	0	1	11478	813	29	3		3	PARVB	22	44547368	Silent	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	6086361	44547368	6757198	515	23239										
IL17REL	400935	hgsc.bcm.edu	37	chr22	50439576	50439576	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cgtcagaggggacacactgcAtggcagtggaggacgtcagg	17	9	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chr22:50439576A>T	ENST00000389983.2	-	4	308	c.44T>A	c.(43-45)aTg>aAg	p.M15K	IL17REL_ENST00000341280.5_Missense_Mutation_p.M15K	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	15										endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GACACACTGCATGGCAGTGGA	0.632																																					p.M15K		Atlas-SNP	.											.	IL17REL	21	.	0			c.T44A						.						43	35	38					22																	50439576		2196	4294	6490	SO:0001583	missense	400935	exon4			CACTGCATGGCAG	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.44T>A	chr22.hg19:g.50439576A>T	ENSP00000374633:p.Met15Lys	153.0	0.0		103.0	41.0	NM_001001694	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	hg19	CCDS33679.1	.	.	.	.	.	.	.	.	.	.	a	14.89	2.671916	0.47781	.	.	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.27402	1.67;1.67	3.16	2.06	0.26882	.	0.282230	0.31897	U	0.006891	T	0.37705	0.1013	L	0.47716	1.5	0.09310	N	1	D	0.69078	0.997	P	0.62184	0.899	T	0.05435	-1.0885	10	0.66056	D	0.02	.	5.1524	0.15017	0.8518:0.0:0.1482:0.0	.	15	Q6ZVW7	I17EL_HUMAN	K	15	ENSP00000374633:M15K;ENSP00000342520:M15K	ENSP00000342520:M15K	M	-	2	0	IL17REL	48781703	0.724000	0.28038	0.031000	0.17742	0.003000	0.03518	1.722000	0.38042	1.303000	0.44873	0.529000	0.55759	ATG	.	.		0.632	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694		T	50439576	A	T	50439576	3	4	150	1	0	0	0	0	1	0	0	0	7653	217	8	4	1010	4	IL17REL	22	50439576	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5892208	50439576	864990	516	23240										
ASMTL	8623	hgsc.bcm.edu	37	chrX	1531641	1531641	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tcacctggcttgcagctctcGgcgaccctgctgagtaactt	10	14	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:1531641G>A	ENST00000381317.3	-	12	1661	c.1629C>T	c.(1627-1629)gcC>gcT	p.A543A	ASMTL-AS1_ENST00000602357.1_RNA|ASMTL_ENST00000534940.1_Silent_p.A485A|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL_ENST00000416733.2_Silent_p.A467A|ASMTL_ENST00000381333.4_Silent_p.A527A|ASMTL-AS1_ENST00000425740.2_RNA|ASMTL-AS1_ENST00000419737.2_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	543	ASMT-like.					cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGCAGCTCTCGGCGACCCTGC	0.562																																					p.A543A		Atlas-SNP	.											.	ASMTL	56	.	0			c.C1629T						.						189	204	199					X																	1531641		2052	4199	6251	SO:0001819	synonymous_variant	8623	exon12			GCTCTCGGCGACC	Y15521	CCDS43917.1, CCDS55362.1, CCDS55363.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000169093	ENSG00000169093		"Pseudoautosomal regions / PAR1"	751	protein-coding gene	gene with protein product		300162, 400011				9736779	Standard	NM_004192		Approved		uc004cpx.2	O95671	OTTHUMG00000021057	ENST00000381317.3:c.1629C>T	chrX.hg19:g.1531641G>A		715.0	1.0		501.0	96.0	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Silent	SNP	ENST00000381317.3	hg19	CCDS43917.1																																																																																			.	.		0.562	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192		A	1531641	G	A	1531641	2	1	150	1	0	0	0	0	0	0	0	1	1046	1103	39	1		1	ASMTL	23	1531641	Silent	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10		1531641	153738919	517	23241										
ARHGAP6	395	hgsc.bcm.edu	37	chrX	11204488	11204488	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agcaggcaaggaaagttgtaAagcttctagtagtcgagact	12	6	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:11204488A>T	ENST00000337414.4	-	5	2013	c.1141T>A	c.(1141-1143)Tta>Ata	p.L381I	ARHGAP6_ENST00000303025.6_Missense_Mutation_p.L178I|ARHGAP6_ENST00000534860.1_Missense_Mutation_p.L206I|ARHGAP6_ENST00000413512.3_Missense_Mutation_p.L190I|ARHGAP6_ENST00000380736.1_Missense_Mutation_p.L178I|ARHGAP6_ENST00000380718.1_Missense_Mutation_p.L381I|ARHGAP6_ENST00000380732.3_Missense_Mutation_p.L413I	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	381					actin filament polymerization (GO:0030041)|activation of phospholipase C activity (GO:0007202)|focal adhesion assembly (GO:0048041)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of signal transduction (GO:0009967)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						GAAAGTTGTAAAGCTTCTAGT	0.443																																					p.L381I		Atlas-SNP	.											.	ARHGAP6	130	.	0			c.T1141A						.						155	140	145					X																	11204488		2203	4300	6503	SO:0001583	missense	395	exon5			GTTGTAAAGCTTC	AF012272	CCDS14140.1, CCDS14141.1, CCDS14142.1	Xp22.3	2008-02-05			ENSG00000047648	ENSG00000047648		"Rho GTPase activating proteins"	676	protein-coding gene	gene with protein product		300118				9417914	Standard	XM_005274507		Approved	rhoGAPX-1	uc004cup.1	O43182	OTTHUMG00000021134	ENST00000337414.4:c.1141T>A	chrX.hg19:g.11204488A>T	ENSP00000338967:p.Leu381Ile	67.0	0.0		62.0	31.0	NM_006125	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	hg19	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.446378	0.84101	.	.	ENSG00000047648	ENST00000534860;ENST00000380736;ENST00000303025;ENST00000337414;ENST00000380717;ENST00000380718;ENST00000413512;ENST00000380732	T;T;T;T;T;T;T;T	0.31769	1.51;1.56;1.56;1.49;1.52;1.48;1.6;1.7	5.51	1.92	0.25849	.	0.000000	0.38217	N	0.001764	T	0.45498	0.1345	M	0.62723	1.935	0.58432	D	0.999999	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.994;1.0;0.998;0.997;0.997	T	0.32025	-0.9922	10	0.51188	T	0.08	.	6.3189	0.21206	0.5005:0.0:0.4995:0.0	.	190;178;381;381;381	B7Z8H7;O43182-5;O43182-2;O43182;A8KAL3	.;.;.;RHG06_HUMAN;.	I	206;178;178;381;217;381;190;413	ENSP00000438135:L206I;ENSP00000370112:L178I;ENSP00000302312:L178I;ENSP00000338967:L381I;ENSP00000370093:L217I;ENSP00000370094:L381I;ENSP00000389394:L190I;ENSP00000370108:L413I	ENSP00000302312:L178I	L	-	1	2	ARHGAP6	11114409	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	3.246000	0.51414	0.736000	0.32559	0.486000	0.48141	TTA	.	.		0.443	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427		T	11204488	A	T	11204488	3	4	150	1	0	0	0	0	1	0	0	0	887	11	1	4	1941	4	ARHGAP6	23	11204488	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	9672847	11204488	144066072	518	23242										
TLR7	51284	hgsc.bcm.edu	37	chrX	12906214	12906214	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tgatgacagcaagtcacctcTatttctgggatgtgtggtat	11	7	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:12906214T>A	ENST00000380659.3	+	3	2726	c.2587T>A	c.(2587-2589)Tat>Aat	p.Y863N		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	863					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	AAGTCACCTCTATTTCTGGGA	0.398																																					p.Y863N		Atlas-SNP	.											.	TLR7	125	.	0			c.T2587A						.						213	186	195					X																	12906214		2203	4300	6503	SO:0001583	missense	51284	exon3			CACCTCTATTTCT	AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.2587T>A	chrX.hg19:g.12906214T>A	ENSP00000370034:p.Tyr863Asn	62.0	0.0		94.0	52.0	NM_016562	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	hg19	CCDS14151.1	.	.	.	.	.	.	.	.	.	.	T	16.82	3.229808	0.58777	.	.	ENSG00000196664	ENST00000380659	T	0.36157	1.27	5.62	5.62	0.85841	.	0.135968	0.50627	D	0.000105	T	0.47967	0.1474	M	0.61703	1.905	0.44129	D	0.996912	P	0.46621	0.881	P	0.49597	0.616	T	0.51553	-0.8691	10	0.87932	D	0	.	14.8622	0.70389	0.0:0.0:0.0:1.0	.	863	Q9NYK1	TLR7_HUMAN	N	863	ENSP00000370034:Y863N	ENSP00000370034:Y863N	Y	+	1	0	TLR7	12816135	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.994000	0.88315	1.891000	0.54761	0.430000	0.28490	TAT	.	.		0.398	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		A	12906214	T	A	12906214	3	1	150	1	0	0	0	0	1	0	0	0	15971	1522	53	4	2593	4	TLR7	23	12906214	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1701726	12906214	142364346	519	23243										
BEND2	139105	hgsc.bcm.edu	37	chrX	18183181	18183181	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctggctttgactcctgctccAgctctggaggggtcactgct	12	13	2	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:18183181A>T	ENST00000380033.4	-	14	2480	c.2348T>A	c.(2347-2349)cTg>cAg	p.L783Q		NM_153346.4	NP_699177.2	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	783										NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(11)|liver(1)|lung(21)|ovary(3)|prostate(1)	49						CTCCTGCTCCAGCTCTGGAGG	0.512																																					p.L783Q		Atlas-SNP	.											.	BEND2	108	.	0			c.T2348A						.						131	124	127					X																	18183181		2203	4300	6503	SO:0001583	missense	139105	exon14			TGCTCCAGCTCTG	AK128155	CCDS14184.1, CCDS55375.1	Xp22.22	2012-11-22	2008-10-03	2008-10-03	ENSG00000177324	ENSG00000177324		"BEN domain containing"	28509	protein-coding gene	gene with protein product			"chromosome X open reading frame 20"	CXorf20		12477932	Standard	NM_153346		Approved	MGC33653	uc004cyj.4	Q8NDZ0	OTTHUMG00000021211	ENST00000380033.4:c.2348T>A	chrX.hg19:g.18183181A>T	ENSP00000369372:p.Leu783Gln	39.0	0.0		46.0	20.0	NM_153346	E9PFY2|Q4V9S2|Q5JXE5	Missense_Mutation	SNP	ENST00000380033.4	hg19	CCDS14184.1	.	.	.	.	.	.	.	.	.	.	a	0.017	-1.506811	0.00992	.	.	ENSG00000177324	ENST00000380033	T	0.34667	1.35	0.217	-0.433	0.12287	.	18.757500	0.00166	N	0.000000	T	0.18425	0.0442	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11203	-1.0597	9	0.39692	T	0.17	.	.	.	.	.	783	Q8NDZ0	BEND2_HUMAN	Q	783	ENSP00000369372:L783Q	ENSP00000369372:L783Q	L	-	2	0	BEND2	18093102	0.007000	0.16637	0.001000	0.08648	0.001000	0.01503	-0.075000	0.11431	-2.468000	0.00531	-2.476000	0.00200	CTG	.	.		0.512	BEND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055940.1	NM_153346		T	18183181	A	T	18183181	3	4	150	1	0	0	0	0	1	0	0	0	1398	188	7	4	55	4	BEND2	23	18183181	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5276967	18183181	137087379	520	23244										
MAP3K15	389840	hgsc.bcm.edu	37	chrX	19418698	19418698	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atcgtccatgactcacctccAaggtgtctccatcggtctct	7	15	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:19418698A>T	ENST00000338883.4	-	14	1927	c.1928T>A	c.(1927-1929)tTg>tAg	p.L643*	MAP3K15_ENST00000518578.1_5'UTR|MAP3K15_ENST00000469203.2_Nonsense_Mutation_p.L475*|MAP3K15_ENST00000359173.3_Nonsense_Mutation_p.L78*	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	643							ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					ACTCACCTCCAAGGTGTCTCC	0.428																																					p.L643X		Atlas-SNP	.											.	MAP3K15	108	.	0			c.T1928A						.						372	320	338					X																	19418698		2203	4300	6503	SO:0001587	stop_gained	389840	exon14			ACCTCCAAGGTGT	AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.1928T>A	chrX.hg19:g.19418698A>T	ENSP00000345629:p.Leu643*	19.0	0.0		25.0	6.0	NM_001001671	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Nonsense_Mutation	SNP	ENST00000338883.4	hg19		.	.	.	.	.	.	.	.	.	.	A	39	7.349449	0.98228	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	.	.	.	5.28	5.28	0.74379	.	0.072738	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3447	0.66651	1.0:0.0:0.0:0.0	.	.	.	.	X	643;78;475	.	ENSP00000345629:L643X	L	-	2	0	MAP3K15	19328619	1.000000	0.71417	0.969000	0.41365	0.961000	0.63080	8.465000	0.90383	1.766000	0.52107	0.483000	0.47432	TTG	.	.		0.428	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671		T	19418698	A	T	19418698	4	4	150	1	0	0	0	0	0	1	0	0	9258	131	5	4	2077	4	MAP3K15	23	19418698	Nonsense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1235517	19418698	135851862	521	23245										
POLA1	5422	hgsc.bcm.edu	37	chrX	24757522	24757522	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gatttggtgaaagaaatgctAcctgtggtcgaatgatctgt	12	5	1	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:24757522A>T	ENST00000379059.3	+	20	2068	c.2053A>T	c.(2053-2055)Acc>Tcc	p.T685S	POLA1_ENST00000379068.3_Missense_Mutation_p.T691S	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	685	DNA-binding region. {ECO:0000255}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	AAGAAATGCTACCTGTGGTCG	0.393																																					p.T685S		Atlas-SNP	.											.	POLA1	117	.	0			c.A2053T						.						140	125	130					X																	24757522		2203	4300	6503	SO:0001583	missense	5422	exon20			AATGCTACCTGTG		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.2053A>T	chrX.hg19:g.24757522A>T	ENSP00000368349:p.Thr685Ser	126.0	0.0		134.0	54.0	NM_016937	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	hg19	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	A	12.68	2.010841	0.35511	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.43294	0.95;0.95	5.19	2.82	0.32997	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.156412	0.64402	D	0.000017	T	0.41994	0.1183	M	0.74881	2.28	0.48288	D	0.999625	B	0.33448	0.412	B	0.37731	0.257	T	0.31052	-0.9957	10	0.46703	T	0.11	-7.6036	5.8972	0.18945	0.6205:0.0:0.3795:0.0	.	685	P09884	DPOLA_HUMAN	S	691;685	ENSP00000368358:T691S;ENSP00000368349:T685S	ENSP00000368349:T685S	T	+	1	0	POLA1	24667443	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.681000	0.46926	0.803000	0.34113	0.345000	0.21793	ACC	.	.		0.393	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		T	24757522	A	T	24757522	3	4	150	1	0	0	0	0	1	0	0	0	12196	391	14	4	2131	4	POLA1	23	24757522	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	5338824	24757522	130513038	522	23246										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50377203	50377203	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggactttctgggggctcctGggtctcttccactggctcct	12	13	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:50377203G>T	ENST00000289292.7	-	4	2153	c.1870C>A	c.(1870-1872)Cag>Aag	p.Q624K	SHROOM4_ENST00000376020.2_Missense_Mutation_p.Q624K|SHROOM4_ENST00000460112.3_Missense_Mutation_p.Q508K			Q9ULL8	SHRM4_HUMAN	shroom family member 4	624					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					GGGGGCTCCTGGGTCTCTTCC	0.502																																					p.Q624K		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C1870A						.						54	56	55					X																	50377203		2203	4300	6503	SO:0001583	missense	57477	exon4			GCTCCTGGGTCTC	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.1870C>A	chrX.hg19:g.50377203G>T	ENSP00000289292:p.Gln624Lys	79.0	0.0		75.0	68.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	7.983	0.751686	0.15778	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	D;D;D	0.87650	-2.28;-2.28;-2.28	6.06	5.2	0.72013	.	0.294296	0.32608	N	0.005871	T	0.78767	0.4335	N	0.22421	0.69	0.35502	D	0.799852	B	0.17038	0.02	B	0.16722	0.016	T	0.76310	-0.3006	10	0.23891	T	0.37	.	13.0471	0.58933	0.0:0.7525:0.2475:0.0	.	624	Q9ULL8	SHRM4_HUMAN	K	624;624;508	ENSP00000289292:Q624K;ENSP00000365188:Q624K;ENSP00000421450:Q508K	ENSP00000289292:Q624K	Q	-	1	0	SHROOM4	50393943	0.972000	0.33761	0.904000	0.35570	0.546000	0.35178	2.742000	0.47434	1.316000	0.45131	0.600000	0.82982	CAG	.	.		0.502	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		T	50377203	G	T	50377203	3	4	150	1	0	0	0	0	1	0	0	0	14311	1357	47	3	2635	3	SHROOM4	23	50377203	Missense_Mutation	SNP	G	TCGA-DD-AAC8-01A-11D-A40R-10	25619681	50377203	104893357	523	23247										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53674399	53674399	+	Missense_Mutation	SNP	T	T	C													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccaagagaagcattttcagtTgctctctttctggcctatca							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:53674399T>C	ENST00000342160.3	-	5	720	c.263A>G	c.(262-264)cAa>cGa	p.Q88R	HUWE1_ENST00000262854.6_Missense_Mutation_p.Q88R|HUWE1_ENST00000218328.8_Missense_Mutation_p.Q88R			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	88					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CATTTTCAGTTGCTCTCTTTC	0.488																																					p.Q88R		Atlas-SNP	.											.	HUWE1	724	.	0			c.A263G						.						169	137	148					X																	53674399		2203	4300	6503	SO:0001583	missense	10075	exon6			TTCAGTTGCTCTC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.263A>G	chrX.hg19:g.53674399T>C	ENSP00000340648:p.Gln88Arg	132.0	0.0		126.0	106.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	T	17.03	3.284937	0.59867	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328;ENST00000432528;ENST00000446750	T;T;T	0.43688	1.25;1.25;0.94	5.6	5.6	0.85130	.	0.071005	0.56097	D	0.000028	T	0.36138	0.0956	L	0.47716	1.5	0.54753	D	0.999989	B	0.16166	0.016	B	0.12837	0.008	T	0.14559	-1.0468	10	0.18710	T	0.47	.	13.7065	0.62644	0.0:0.0:0.0:1.0	.	88	Q7Z6Z7	HUWE1_HUMAN	R	88	ENSP00000340648:Q88R;ENSP00000262854:Q88R;ENSP00000218328:Q88R	ENSP00000218328:Q88R	Q	-	2	0	HUWE1	53691124	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	4.841000	0.62824	1.881000	0.54492	0.486000	0.48141	CAA	.	.		0.488	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		C	53674399	T	C	53674399	3	2	150	1	0	0	0	0	1	0	0	0	7470	1812	63	2	13177	2	HUWE1	23	53674399	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3297196	53674399	101596161	524	23248	102	3								
HUWE1	10075	hgsc.bcm.edu	37	chrX	53674402	53674402	+	Missense_Mutation	SNP	T	T	C													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agagaagcattttcagttgcTctctttctggcctatcacat							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:53674402T>C	ENST00000342160.3	-	5	717	c.260A>G	c.(259-261)gAg>gGg	p.E87G	HUWE1_ENST00000262854.6_Missense_Mutation_p.E87G|HUWE1_ENST00000218328.8_Missense_Mutation_p.E87G			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	87					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TTTCAGTTGCTCTCTTTCTGG	0.493																																					p.E87G		Atlas-SNP	.											.	HUWE1	724	.	0			c.A260G						.						175	142	153					X																	53674402		2203	4300	6503	SO:0001583	missense	10075	exon6			AGTTGCTCTCTTT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.260A>G	chrX.hg19:g.53674402T>C	ENSP00000340648:p.Glu87Gly	132.0	0.0		124.0	103.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.376915	0.42105	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328;ENST00000432528;ENST00000446750	T;T;T	0.49432	1.08;1.08;0.78	5.6	5.6	0.85130	.	0.064924	0.64402	D	0.000010	T	0.24928	0.0605	N	0.02539	-0.55	0.38004	D	0.934338	B	0.12630	0.006	B	0.09377	0.004	T	0.13629	-1.0502	10	0.42905	T	0.14	.	13.7065	0.62644	0.0:0.0:0.0:1.0	.	87	Q7Z6Z7	HUWE1_HUMAN	G	87	ENSP00000340648:E87G;ENSP00000262854:E87G;ENSP00000218328:E87G	ENSP00000218328:E87G	E	-	2	0	HUWE1	53691127	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	4.369000	0.59511	1.881000	0.54492	0.486000	0.48141	GAG	.	.		0.493	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		C	53674402	T	C	53674402	3	2	150	1	0	0	0	0	1	0	0	0	7470	1551	54	2	13180	2	HUWE1	23	53674402	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	3	53674402	101596158	525	23249	102	3								
HUWE1	10075	hgsc.bcm.edu	37	chrX	53674404	53674404	+	Silent	SNP	T	T	C													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agaagcattttcagttgctcTctttctggcctatcacatac							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:53674404T>C	ENST00000342160.3	-	5	715	c.258A>G	c.(256-258)agA>agG	p.R86R	HUWE1_ENST00000262854.6_Silent_p.R86R|HUWE1_ENST00000218328.8_Silent_p.R86R			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	86					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TCAGTTGCTCTCTTTCTGGCC	0.493																																					p.R86R		Atlas-SNP	.											.	HUWE1	724	.	0			c.A258G						.						177	144	155					X																	53674404		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon6			TTGCTCTCTTTCT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.258A>G	chrX.hg19:g.53674404T>C		133.0	0.0		125.0	104.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1																																																																																			.	.		0.493	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		C	53674404	T	C	53674404	2	2	150	1	0	0	0	0	0	0	0	1	7470	1548	54	2		2	HUWE1	23	53674404	Silent	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2	53674404	101596156	526	23250	102	3								
TEX11	56159	hgsc.bcm.edu	37	chrX	70072999	70072999	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	atttgacgtataattgctccAgactctggaaaataaaccca	6	9	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:70072999A>T	ENST00000395889.2	-	8	610	c.455T>A	c.(454-456)cTg>cAg	p.L152Q	TEX11_ENST00000374333.2_Missense_Mutation_p.L137Q|TEX11_ENST00000344304.3_Missense_Mutation_p.L152Q	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	152					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					TAATTGCTCCAGACTCTGGAA	0.398																																					p.L152Q		Atlas-SNP	.											.	TEX11	132	.	0			c.T455A						.						72	60	64					X																	70072999		2203	4300	6503	SO:0001583	missense	56159	exon8			TGCTCCAGACTCT	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.455T>A	chrX.hg19:g.70072999A>T	ENSP00000379226:p.Leu152Gln	60.0	0.0		82.0	25.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	hg19	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.031672	0.35797	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000344304	T;T;T	0.38077	1.16;1.18;1.18	4.56	4.56	0.56223	Tetratricopeptide-like helical (1);	0.197085	0.33980	N	0.004373	T	0.50599	0.1625	L	0.49778	1.585	0.33362	D	0.572498	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.982	T	0.61705	-0.7008	9	.	.	.	-3.7026	11.0541	0.47907	1.0:0.0:0.0:0.0	.	137;152	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	Q	137;152;152	ENSP00000363453:L137Q;ENSP00000379226:L152Q;ENSP00000340995:L152Q	.	L	-	2	0	TEX11	69989724	1.000000	0.71417	0.937000	0.37676	0.044000	0.14063	4.476000	0.60216	1.810000	0.52873	0.432000	0.28606	CTG	.	.		0.398	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			T	70072999	A	T	70072999	3	4	150	1	0	0	0	0	1	0	0	0	15789	188	7	4	2463	4	TEX11	23	70072999	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	16398595	70072999	85197561	527	23251										
ATRX	546	hgsc.bcm.edu	37	chrX	76872153	76872153	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	tctcacagctaacacatattCgtgttttggaggcaagaatt	8	8	1	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:76872153C>G	ENST00000373344.5	-	22	5708	c.5494G>C	c.(5494-5496)Gaa>Caa	p.E1832Q	ATRX_ENST00000395603.3_Missense_Mutation_p.E1794Q|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1832					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						AACACATATTCGTGTTTTGGA	0.313			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.E1832Q		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.G5494C						.						134	119	124					X																	76872153		2202	4291	6493	SO:0001583	missense	546	exon22			CATATTCGTGTTT	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.5494G>C	chrX.hg19:g.76872153C>G	ENSP00000362441:p.Glu1832Gln	101.0	0.0		139.0	121.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	hg19	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.761852	0.89932	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	D;D	0.93906	-3.31;-3.31	5.77	5.77	0.91146	SNF2-related (1);	0.000000	0.85682	U	0.000000	D	0.97648	0.9229	M	0.92219	3.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98411	1.0572	10	0.87932	D	0	-12.4853	18.9785	0.92747	0.0:1.0:0.0:0.0	.	1794;1832	P46100-4;P46100	.;ATRX_HUMAN	Q	1832;1794	ENSP00000362441:E1832Q;ENSP00000378967:E1794Q	ENSP00000362441:E1832Q	E	-	1	0	ATRX	76758809	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.463000	0.80869	2.430000	0.82344	0.544000	0.68410	GAA	.	.		0.313	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		G	76872153	C	G	76872153	3	3	150	1	0	0	0	0	1	0	0	0	1208	893	31	4	2040	4	ATRX	23	76872153	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	6799154	76872153	78398407	528	23252										
CENPI	2491	hgsc.bcm.edu	37	chrX	100402946	100402947	+	Missense_Mutation	DNP	CA	CA	TC													0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cattagacaaaatcagagttCaatttcagcagcaagactta							TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:100402946_100402947CA>TC	ENST00000372927.1	+	19	2167_2168	c.1890_1891CA>TC	c.(1888-1893)ttCAat>ttTCat	p.N631H	CENPI_ENST00000218507.5_Missense_Mutation_p.N631H|CENPI_ENST00000423383.1_Missense_Mutation_p.N631H	NM_006733.2	NP_006724.2	Q92674	CENPI_HUMAN	centromere protein I	631					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|sex differentiation (GO:0007548)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(19)|prostate(1)|skin(2)	30						AATCAGAGTTCAATTTCAGCAG	0.351																																					p.F630F|p.N631H		Atlas-SNP	.											.	CENPI	70	.	0			c.C1890T|c.A1891C						.																																			SO:0001583	missense	2491	exon19			AGAGTTCAATTTC|GAGTTCAATTTCA	X97249	CCDS14479.1	Xq22.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000102384	ENSG00000102384			3968	protein-coding gene	gene with protein product		300065	"FSH primary response (LRPR1, rat) homolog 1", "FSH primary response (LRPR1 homolog, rat) 1"	FSHPRH1		16622420	Standard	NM_006733		Approved	LRPR1, CENP-I, Mis6	uc004egx.3	Q92674	OTTHUMG00000022018	Exception_encountered	chrX.hg19:g.100402946_100402947delinsTC	ENSP00000362018:p.Asn631His	144.0|146.0	0.0		149.0	67.0|66.0	NM_006733	Q5JWZ9|Q96ED0	Silent|Missense_Mutation	SNP	ENST00000372927.1	hg19	CCDS14479.1																																																																																			.	.		0.351	CENPI-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057519.1	NM_006733		TC	100402947	CA	TC	100402946	3	4	150	1	0	0	0	0	1	0	0	0	3235	825	29	3	1960	3	CENPI	23	100402946	Missense_Mutation	DNP	CA	TCGA-DD-AAC8-01A-11D-A40R-10	23530793	100402946	54867614	529	23253										
NXF3	56000	hgsc.bcm.edu	37	chrX	102338424	102338424	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gctggcatgcatgttttcatAgtgaaactatagggagagtt	12	5	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:102338424A>T	ENST00000395065.3	-	5	543	c.442T>A	c.(442-444)Tat>Aat	p.Y148N	NXF3_ENST00000425644.1_5'UTR|NXF3_ENST00000425463.2_Missense_Mutation_p.Y59N	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	148	RRM.				mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)			NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						ATGTTTTCATAGTGAAACTAT	0.468																																					p.Y148N		Atlas-SNP	.											.	NXF3	81	.	0			c.T442A						.						98	86	90					X																	102338424		2203	4300	6503	SO:0001583	missense	56000	exon5			TTTCATAGTGAAA	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.442T>A	chrX.hg19:g.102338424A>T	ENSP00000378504:p.Tyr148Asn	69.0	0.0		78.0	37.0	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Missense_Mutation	SNP	ENST00000395065.3	hg19	CCDS14503.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.30|12.30	1.896354|1.896354	0.33442|0.33442	.|.	.|.	ENSG00000147206|ENSG00000147206	ENST00000427570|ENST00000395065;ENST00000425463	.|T;T	.|0.48522	.|0.81;0.81	3.64|3.64	3.64|3.64	0.41730|0.41730	.|Nuclear RNA export factor Tap, RNA-binding domain (2);Nucleotide-binding, alpha-beta plait (1);	.|0.353536	.|0.27932	.|N	.|0.017276	T|T	0.64757|0.64757	0.2627|0.2627	M|M	0.81802|0.81802	2.56|2.56	0.29047|0.29047	N|N	0.884745|0.884745	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.83275	.|0.996;0.996	T|T	0.59053|0.59053	-0.7526|-0.7526	5|10	.|0.37606	.|T	.|0.19	-2.3404|-2.3404	7.9073|7.9073	0.29769|0.29769	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|148;148	.|B4DYI1;Q9H4D5	.|.;NXF3_HUMAN	Q|N	24|148;59	.|ENSP00000378504:Y148N;ENSP00000404347:Y59N	.|ENSP00000378504:Y148N	L|Y	-|-	2|1	0|0	NXF3|NXF3	102225080|102225080	0.999000|0.999000	0.42202|0.42202	0.947000|0.947000	0.38551|0.38551	0.381000|0.381000	0.30169|0.30169	2.024000|2.024000	0.41049|0.41049	1.681000|1.681000	0.50988|0.50988	0.430000|0.430000	0.28490|0.28490	CTA|TAT	.	.		0.468	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		T	102338424	A	T	102338424	3	4	150	1	0	0	0	0	1	0	0	0	10794	420	15	4	1213	4	NXF3	23	102338424	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1935478	102338424	52932136	530	23254										
ESX1	80712	hgsc.bcm.edu	37	chrX	103499021	103499021	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gcggctcctcctgctcttgcTtcagctcgagcaggggcggc	14	15	2	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:103499021T>A	ENST00000372588.4	-	2	403	c.320A>T	c.(319-321)aAg>aTg	p.K107M		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	107					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						CTGCTCTTGCTTCAGCTCGAG	0.711																																					p.K107M	Pancreas(200;1705 2227 25194 28471 45274)	Atlas-SNP	.											.	ESX1	57	.	0			c.A320T						.						32	38	36					X																	103499021		2195	4280	6475	SO:0001583	missense	80712	exon2			TCTTGCTTCAGCT	AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"Homeoboxes / PRD class"	14865	protein-coding gene	gene with protein product		300154	"extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.320A>T	chrX.hg19:g.103499021T>A	ENSP00000361669:p.Lys107Met	70.0	0.0		69.0	28.0	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	hg19	CCDS14516.1	.	.	.	.	.	.	.	.	.	.	t	15.95	2.985050	0.53934	.	.	ENSG00000123576	ENST00000372588	D	0.91521	-2.86	4.11	-8.23	0.01033	.	.	.	.	.	D	0.82967	0.5152	N	0.08118	0	0.09310	N	1	D	0.67145	0.996	D	0.64506	0.926	T	0.74278	-0.3717	9	0.51188	T	0.08	.	0.6407	0.00810	0.1896:0.2354:0.2632:0.3118	.	107	Q8N693	ESX1_HUMAN	M	107	ENSP00000361669:K107M	ENSP00000361669:K107M	K	-	2	0	ESX1	103385677	0.000000	0.05858	0.000000	0.03702	0.268000	0.26511	-1.475000	0.02335	-2.262000	0.00690	0.144000	0.16011	AAG	.	.		0.711	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448		A	103499021	T	A	103499021	3	1	150	1	0	0	0	0	1	0	0	0	5265	1609	56	4	912	4	ESX1	23	103499021	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	1160597	103499021	51771539	531	23255										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	105011036	105011036	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	actccagactatattctcagAcggggatggagtattttcga	10	8	1	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:105011036A>T	ENST00000372582.1	+	11	2199	c.1443A>T	c.(1441-1443)agA>agT	p.R481S	IL1RAPL2_ENST00000344799.4_Missense_Mutation_p.R481S	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	481	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						ATATTCTCAGACGGGGATGGA	0.383																																					p.R481S		Atlas-SNP	.											.	IL1RAPL2	105	.	0			c.A1443T						.						91	84	86					X																	105011036		2203	4300	6503	SO:0001583	missense	26280	exon11			TCTCAGACGGGGA	AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1443A>T	chrX.hg19:g.105011036A>T	ENSP00000361663:p.Arg481Ser	198.0	0.0		234.0	104.0	NM_017416	Q2M3U3|Q9NZN0	Missense_Mutation	SNP	ENST00000372582.1	hg19	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	A	15.90	2.968206	0.53614	.	.	ENSG00000189108	ENST00000372582;ENST00000344799;ENST00000538500	T;T;T	0.04156	3.69;3.69;3.69	5.39	4.26	0.50523	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.082759	0.52532	D	0.000076	T	0.05593	0.0147	L	0.35854	1.095	0.58432	D	0.999993	D	0.59357	0.985	P	0.52646	0.705	T	0.51164	-0.8740	10	0.11182	T	0.66	.	3.1573	0.06509	0.6055:0.0:0.3945:0.0	.	481	Q9NP60	IRPL2_HUMAN	S	481;481;86	ENSP00000361663:R481S;ENSP00000344976:R481S;ENSP00000445576:R86S	ENSP00000344976:R481S	R	+	3	2	IL1RAPL2	104897692	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.195000	0.58400	1.790000	0.52503	0.486000	0.48141	AGA	.	.		0.383	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		T	105011036	A	T	105011036	3	4	150	1	0	0	0	0	1	0	0	0	7671	272	10	4	1481	4	IL1RAPL2	23	105011036	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	1512015	105011036	50259524	532	23256										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107823970	107823970	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aggagagccaggcaaaagagTaagtgatgtaactgctaata	12	5	0	3			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:107823970T>A	ENST00000361603.2	+	15	1135		c.e15+2		COL4A5_ENST00000328300.6_Splice_Site	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5						axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GGCAAAAGAGTAAGTGATGTA	0.378									Alport syndrome with Diffuse Leiomyomatosis																												.		Atlas-SNP	.											.	COL4A5	262	.	0			c.891+2T>A						.						152	151	151					X																	107823970		2203	4300	6503	SO:0001630	splice_region_variant	1287	exon15	Familial Cancer Database		AAAGAGTAAGTGA	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.891+2T>A	chrX.hg19:g.107823970T>A		273.0	0.0		300.0	130.0	NM_033380	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Splice_Site	SNP	ENST00000361603.2	hg19	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.372040	0.82573	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6067	0.68483	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL4A5	107710626	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	6.732000	0.74790	1.829000	0.53265	0.486000	0.48141	.	.	.		0.378	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2		Intron	A	107823970	T	A	107823970	5	1	150	1	0	0	0	0	0	0	1	0	3696	1652	57	4	951	4	COL4A5	23	107823970	Splice_Site	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	2812934	107823970	47446590	533	23257										
GUCY2F	2986	hgsc.bcm.edu	37	chrX	108631785	108631785	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	cgcatcttgaaagtgcccacAgagctcaggatatctaagga	10	10	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:108631785A>T	ENST00000218006.2	-	15	3180	c.2889T>A	c.(2887-2889)tcT>tcA	p.S963S		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	963	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						AAGTGCCCACAGAGCTCAGGA	0.488																																					p.S963S		Atlas-SNP	.											.	GUCY2F	178	.	0			c.T2889A						.						174	154	161					X																	108631785		2203	4300	6503	SO:0001819	synonymous_variant	2986	exon15			GCCCACAGAGCTC	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.2889T>A	chrX.hg19:g.108631785A>T		96.0	0.0		127.0	50.0	NM_001522	Q9UJF1	Silent	SNP	ENST00000218006.2	hg19	CCDS14545.1																																																																																			.	.		0.488	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		T	108631785	A	T	108631785	2	4	150	1	0	0	0	0	0	0	0	1	6907	175	7	4		4	GUCY2F	23	108631785	Silent	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	807815	108631785	46638775	534	23258										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118230582	118230582	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	aatgggcagctgggtgctacTggtagaggcaagtgtggcaa	17	6	0	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:118230582T>A	ENST00000402510.2	-	8	1140	c.1141A>T	c.(1141-1143)Agt>Tgt	p.S381C		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	381										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TGGGTGCTACTGGTAGAGGCA	0.522																																					p.S381C		Atlas-SNP	.											.	KIAA1210	171	.	0			c.A1141T						.						83	84	84					X																	118230582		2066	4188	6254	SO:0001583	missense	57481	exon8			TGCTACTGGTAGA	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.1141A>T	chrX.hg19:g.118230582T>A	ENSP00000384670:p.Ser381Cys	100.0	0.0		121.0	61.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.412454	0.42817	.	.	ENSG00000250423;ENSG00000241087	ENST00000402510;ENST00000420240	T	0.16743	2.32	4.28	-2.12	0.07165	.	.	.	.	.	T	0.19685	0.0473	N	0.14661	0.345	0.09310	N	1	D	0.76494	0.999	D	0.68483	0.958	T	0.26258	-1.0108	9	0.59425	D	0.04	.	9.0514	0.36378	0.0:0.5937:0.0:0.4062	.	381	Q9ULL0	K1210_HUMAN	C	381;217	ENSP00000384670:S381C	ENSP00000396164:S217C	S	-	1	0	RP13-347D8.5;RP13-347D8.6	118114610	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.068000	0.14531	-0.427000	0.07350	-0.368000	0.07277	AGT	.	.		0.522	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		A	118230582	T	A	118230582	3	1	150	1	0	0	0	0	1	0	0	0	8223	1580	55	4	4016	4	KIAA1210	23	118230582	Missense_Mutation	SNP	T	TCGA-DD-AAC8-01A-11D-A40R-10	9598797	118230582	37039978	535	23259										
GPR112	139378	hgsc.bcm.edu	37	chrX	135431162	135431162	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ccatacttccttcaatattcAggtttccccatctctgacta	3	14	3	1			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:135431162A>T	ENST00000394143.1	+	6	5588	c.5297A>T	c.(5296-5298)cAg>cTg	p.Q1766L	GPR112_ENST00000287534.4_Missense_Mutation_p.Q1703L|GPR112_ENST00000394141.1_Missense_Mutation_p.Q1561L|GPR112_ENST00000370652.1_Missense_Mutation_p.Q1766L|GPR112_ENST00000412101.1_Missense_Mutation_p.Q1561L	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1766					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TTCAATATTCAGGTTTCCCCA	0.388																																					p.Q1766L		Atlas-SNP	.											.	GPR112	459	.	0			c.A5297T						.						167	154	158					X																	135431162		2203	4300	6503	SO:0001583	missense	139378	exon6			ATATTCAGGTTTC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5297A>T	chrX.hg19:g.135431162A>T	ENSP00000377699:p.Gln1766Leu	94.0	0.0		118.0	53.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	a	11.98	1.800414	0.31869	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.38401	1.18;1.18;1.14;1.25;1.14	3.57	2.25	0.28309	.	.	.	.	.	T	0.23451	0.0567	L	0.32530	0.975	0.09310	N	1	B;P;P	0.44816	0.408;0.844;0.759	B;B;B	0.38616	0.086;0.277;0.143	T	0.10268	-1.0637	9	0.48119	T	0.1	.	5.0965	0.14737	0.734:0.0:0.0:0.266	.	1703;1561;1766	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	L	1766;1766;1561;1703;1561	ENSP00000377699:Q1766L;ENSP00000359686:Q1766L;ENSP00000416526:Q1561L;ENSP00000287534:Q1703L;ENSP00000377697:Q1561L	ENSP00000287534:Q1703L	Q	+	2	0	GPR112	135258828	0.170000	0.23016	0.007000	0.13788	0.176000	0.22953	4.467000	0.60155	1.252000	0.44001	0.372000	0.22366	CAG	.	.		0.388	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			T	135431162	A	T	135431162	3	4	150	1	0	0	0	0	1	0	0	0	6637	188	7	4	5307	4	GPR112	23	135431162	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	17200580	135431162	19839398	536	23260										
GPR101	83550	hgsc.bcm.edu	37	chrX	136113821	136113821	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	ctcgcgcgtgctgttggtgcAggtggacgtcatggcaacag	16	10	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:136113821A>T	ENST00000298110.1	-	1	12	c.13T>A	c.(13-15)Tgc>Agc	p.C5S		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	5						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					CTGTTGGTGCAGGTGGACGTC	0.637																																					p.C5S		Atlas-SNP	.											.	GPR101	96	.	0			c.T13A						.						86	47	60					X																	136113821		2203	4300	6503	SO:0001583	missense	83550	exon1			TGGTGCAGGTGGA	AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.13T>A	chrX.hg19:g.136113821A>T	ENSP00000298110:p.Cys5Ser	23.0	0.0		20.0	9.0	NM_054021	Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	hg19	CCDS14662.1	.	.	.	.	.	.	.	.	.	.	A	13.12	2.140917	0.37825	.	.	ENSG00000165370	ENST00000298110	T	0.64438	-0.1	4.64	2.14	0.27477	.	.	.	.	.	T	0.37100	0.0991	N	0.24115	0.695	0.22531	N	0.999019	B	0.34015	0.435	B	0.32393	0.145	T	0.15896	-1.0421	9	0.14656	T	0.56	-16.5905	0.7547	0.00996	0.475:0.2054:0.1185:0.2011	.	5	Q96P66	GP101_HUMAN	S	5	ENSP00000298110:C5S	ENSP00000298110:C5S	C	-	1	0	GPR101	135941487	0.007000	0.16637	0.539000	0.28077	0.583000	0.36354	0.233000	0.17911	1.627000	0.50400	0.441000	0.28932	TGC	.	.		0.637	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			T	136113821	A	T	136113821	3	4	150	1	0	0	0	0	1	0	0	0	6630	188	7	4	1516	4	GPR101	23	136113821	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	682659	136113821	19156739	537	23261										
ATP2B3	492	hgsc.bcm.edu	37	chrX	152845550	152845550	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	agtttctgatcaatgactacAcccacaacatcccgctcatt	4	14	3	2			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:152845550A>T	ENST00000349466.2	+	21	3783	c.3457A>T	c.(3457-3459)Acc>Tcc	p.T1153S	ATP2B3_ENST00000359149.3_3'UTR|ATP2B3_ENST00000263519.4_Missense_Mutation_p.T1153S|ATP2B3_ENST00000370181.2_3'UTR|ATP2B3_ENST00000370186.1_3'UTR			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	1153					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAATGACTACACCCACAACAT	0.587																																					p.T1153S		Atlas-SNP	.											.	ATP2B3	552	.	0			c.A3457T						.						171	152	158					X																	152845550		2203	4300	6503	SO:0001583	missense	492	exon20			GACTACACCCACA	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"ATPases / P-type"	816	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 3", "cilia and flagella associated protein 39"	300014	"spinocerebellar ataxia, X-linked 1", "cerebellar ataxia 2 (X-linked)"	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.3457A>T	chrX.hg19:g.152845550A>T	ENSP00000343886:p.Thr1153Ser	119.0	0.0		140.0	59.0	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Missense_Mutation	SNP	ENST00000349466.2	hg19	CCDS35440.1	.	.	.	.	.	.	.	.	.	.	a	11.83	1.756566	0.31137	.	.	ENSG00000067842	ENST00000349466;ENST00000263519	T;T	0.75938	-0.98;-0.98	5.02	5.02	0.67125	.	0.129231	0.50627	D	0.000107	T	0.62792	0.2457	L	0.36672	1.1	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.56914	-0.7900	10	0.12766	T	0.61	-44.2003	12.7904	0.57530	1.0:0.0:0.0:0.0	.	1139;1153	Q16720-4;Q16720	.;AT2B3_HUMAN	S	1153	ENSP00000343886:T1153S;ENSP00000263519:T1153S	ENSP00000263519:T1153S	T	+	1	0	ATP2B3	152498744	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	1.959000	0.40412	1.658000	0.50742	0.427000	0.28365	ACC	.	.		0.587	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		T	152845550	A	T	152845550	3	4	150	1	0	0	0	0	1	0	0	0	1141	159	6	4	3693	4	ATP2B3	23	152845550	Missense_Mutation	SNP	A	TCGA-DD-AAC8-01A-11D-A40R-10	16731729	152845550	2425010	538	23262										
DNASE1L1	1774	hgsc.bcm.edu	37	chrX	153631374	153631374	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.011214953271028	6	1	0.677789797786469	0.861357868020305	0.612521150592217	0.635117204776648	1	0	gctccccgtgcagcacgacgCggtcataggtgcagtgggtg	16	12	1	0			TCGA-DD-AAC8-01A-11D-A40R-10	TCGA-DD-AAC8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7b3c3428-4aba-4f50-ab9e-852dbd0e4141	b7eb2f91-437b-4009-bda9-315bd19c65e2	g.chrX:153631374C>T	ENST00000393638.1	-	7	969	c.683G>A	c.(682-684)cGc>cAc	p.R228H	DNASE1L1_ENST00000369809.1_Missense_Mutation_p.R228H|SNORA70_ENST00000384436.1_RNA	NM_001009934.1	NP_001009934.1	P49184	DNSL1_HUMAN	deoxyribonuclease I-like 1	228					DNA metabolic process (GO:0006259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			lung(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CAGCACGACGCGGTCATAGGT	0.652																																					p.R228H		Atlas-SNP	.											.	DNASE1L1	20	.	0			c.G683A						.						53	50	51					X																	153631374		2203	4299	6502	SO:0001583	missense	1774	exon7			ACGACGCGGTCAT	L40817	CCDS14747.1	Xq28	2008-02-05			ENSG00000013563	ENSG00000013563			2957	protein-coding gene	gene with protein product	"DNase X"	300081		DNL1L		8541839, 8654957	Standard	XM_005277829		Approved	DNAS1L1, XIB, DNASEX	uc004fkw.1	P49184	OTTHUMG00000033188	ENST00000393638.1:c.683G>A	chrX.hg19:g.153631374C>T	ENSP00000377255:p.Arg228His	47.0	0.0		53.0	47.0	NM_006730	D3DWW7|Q5HY41	Missense_Mutation	SNP	ENST00000393638.1	hg19	CCDS14747.1	.	.	.	.	.	.	.	.	.	.	C	16.73	3.203667	0.58234	.	.	ENSG00000013563	ENST00000369809;ENST00000393638;ENST00000014935;ENST00000369808;ENST00000369807;ENST00000309585	T;T;T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38;-1.38;-1.38	4.71	3.84	0.44239	Endonuclease/exonuclease/phosphatase (2);	0.054374	0.64402	N	0.000001	D	0.89487	0.6729	M	0.86805	2.84	0.39922	D	0.974161	D	0.89917	1.0	D	0.91635	0.999	D	0.90171	0.4235	10	0.87932	D	0	-0.0766	9.9673	0.41732	0.0:0.896:0.0:0.104	.	228	P49184	DNSL1_HUMAN	H	228	ENSP00000358824:R228H;ENSP00000377255:R228H;ENSP00000014935:R228H;ENSP00000358823:R228H;ENSP00000358822:R228H;ENSP00000309168:R228H	ENSP00000014935:R228H	R	-	2	0	DNASE1L1	153284568	1.000000	0.71417	0.428000	0.26697	0.088000	0.18126	4.515000	0.60489	0.898000	0.36418	0.597000	0.82753	CGC	.	.		0.652	DNASE1L1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080928.2			T	153631374	C	T	153631374	3	4	150	1	0	0	0	0	1	0	0	0	4663	768	27	1	233	1	DNASE1L1	23	153631374	Missense_Mutation	SNP	C	TCGA-DD-AAC8-01A-11D-A40R-10	785824	153631374	1639186	539	23263										
KCNA3	3738	hgsc.bcm.edu	37	chr1	111217151	111217151	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	agtcctgctcgcccgcggccGgcagtgagggcggcagcggc	18	15	0	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:111217151G>T	ENST00000369769.2	-	1	504	c.281C>A	c.(280-282)cCg>cAg	p.P94Q		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	94					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	GCCCGCGGCCGGCAGTGAGGG	0.726																																					p.P94Q		Atlas-SNP	.											.	KCNA3	91	.	0			c.C281A						.						9	11	10					1																	111217151		2126	4234	6360	SO:0001583	missense	3738	exon1			GCGGCCGGCAGTG	L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.281C>A	chr1.hg19:g.111217151G>T	ENSP00000358784:p.Pro94Gln	103.0	0.0		99.0	4.0	NM_002232	Q5VWN2	Missense_Mutation	SNP	ENST00000369769.2	hg19	CCDS828.2	.	.	.	.	.	.	.	.	.	.	G	5.372	0.253877	0.10185	.	.	ENSG00000177272	ENST00000369769	D	0.96885	-4.16	3.71	1.45	0.22620	.	.	.	.	.	D	0.82935	0.5145	N	0.14661	0.345	0.26823	N	0.968758	B	0.16802	0.019	B	0.09377	0.004	T	0.73867	-0.3847	9	0.17369	T	0.5	.	10.6977	0.45909	0.0:0.3182:0.6818:0.0	.	94	P22001	KCNA3_HUMAN	Q	94	ENSP00000358784:P94Q	ENSP00000358784:P94Q	P	-	2	0	KCNA3	111018674	0.667000	0.27484	0.999000	0.59377	0.212000	0.24457	0.082000	0.14847	1.613000	0.50231	0.462000	0.41574	CCG	.	.		0.726	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		T	111217151	G	T	111217151	3	4	151	1	0	0	0	0	1	0	0	0	8013	1116	39	1	1450	1	KCNA3	1	111217151	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		111217151	138033470	1	23264										
TCHH	7062	hgsc.bcm.edu	37	chr1	152084323	152084323	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tctcctcctcgcgcttcagcCaatcgcgcctctcctcctgc	6	21	3	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:152084323C>A	ENST00000368804.1	-	2	1369	c.1370G>T	c.(1369-1371)tGg>tTg	p.W457L		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	457	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			gcgcttcagccaatcgcgcct	0.672																																					p.W457L		Atlas-SNP	.											.	TCHH	275	.	0			c.G1370T						.						49	55	53					1																	152084323		2111	4227	6338	SO:0001583	missense	7062	exon3			TTCAGCCAATCGC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1370G>T	chr1.hg19:g.152084323C>A	ENSP00000357794:p.Trp457Leu	44.0	0.0		56.0	10.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	c	3.094	-0.186236	0.06340	.	.	ENSG00000159450	ENST00000368804	T	0.05081	3.5	1.75	-3.51	0.04696	.	.	.	.	.	T	0.00637	0.0021	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47573	-0.9107	9	0.14252	T	0.57	.	2.9757	0.05936	0.2017:0.4955:0.0:0.3028	.	457	Q07283	TRHY_HUMAN	L	457	ENSP00000357794:W457L	ENSP00000357794:W457L	W	-	2	0	TCHH	150350947	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	-0.019000	0.12546	-1.042000	0.03262	-1.149000	0.01842	TGG	.	.		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		A	152084323	C	A	152084323	3	1	151	1	0	0	0	0	1	0	0	0	15715	595	21	3	4465	3	TCHH	1	152084323	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	40867172	152084323	97166298	2	23265										
DCST1	149095	hgsc.bcm.edu	37	chr1	155011941	155011941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gtgccagcctcctactagtaCccaagatgctgggcaaggaa	11	12	0	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:155011941C>T	ENST00000295542.1	+	5	421	c.325C>T	c.(325-327)Ccc>Tcc	p.P109S	DCST1_ENST00000423025.2_Missense_Mutation_p.P84S|DCST1_ENST00000392480.1_Missense_Mutation_p.P109S|DCST1_ENST00000368419.2_Missense_Mutation_p.P109S	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	109						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			CCTACTAGTACCCAAGATGCT	0.602																																					p.P109S		Atlas-SNP	.											.	DCST1	69	.	0			c.C325T						.						120	112	115					1																	155011941		2203	4300	6503	SO:0001583	missense	149095	exon5			CTAGTACCCAAGA	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.325C>T	chr1.hg19:g.155011941C>T	ENSP00000295542:p.Pro109Ser	70.0	0.0		111.0	6.0	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	hg19	CCDS1083.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475054	0.84640	.	.	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.26	5.26	0.73747	.	0.276731	0.34156	N	0.004212	T	0.65069	0.2656	M	0.72894	2.215	0.46396	D	0.999024	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.983;0.989	T	0.69000	-0.5261	10	0.72032	D	0.01	-28.1907	14.3669	0.66812	0.0:1.0:0.0:0.0	.	84;134;109	E9PHV3;E9PJX3;Q5T197	.;.;DCST1_HUMAN	S	109;109;84;109	ENSP00000295542:P109S;ENSP00000376271:P109S;ENSP00000387369:P84S;ENSP00000357404:P109S	ENSP00000295542:P109S	P	+	1	0	DCST1	153278565	0.998000	0.40836	0.928000	0.36995	0.984000	0.73092	5.030000	0.64128	2.472000	0.83506	0.585000	0.79938	CCC	.	.		0.602	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494		T	155011941	C	T	155011941	3	4	151	1	0	0	0	0	1	0	0	0	4304	507	18	3	339	3	DCST1	1	155011941	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	2927618	155011941	94238680	3	23266										
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161018501	161018501	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tgatcttcctgggccccttgCtctaggtcccttccagcttc	8	16	2	1	rs377370667		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:161018501C>T	ENST00000368013.3	-	12	2630	c.2310G>A	c.(2308-2310)gaG>gaA	p.E770E	USF1_ENST00000368021.3_5'Flank|ARHGAP30_ENST00000368016.3_Intron|ARHGAP30_ENST00000368015.1_Silent_p.E593E|USF1_ENST00000435396.1_5'Flank	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	770	Glu-rich.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GGGCCCCTTGCTCTAGGTCCC	0.488																																					p.E770E		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.G2310A						.						207	206	207					1																	161018501		2203	4300	6503	SO:0001819	synonymous_variant	257106	exon12			CCCTTGCTCTAGG	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"Rho GTPase activating proteins"	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.2310G>A	chr1.hg19:g.161018501C>T		122.0	0.0		189.0	135.0	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Silent	SNP	ENST00000368013.3	hg19	CCDS30918.1																																																																																			.	.		0.488	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		T	161018501	C	T	161018501	2	4	151	1	0	0	0	0	0	0	0	1	879	796	28	3		3	ARHGAP30	1	161018501	Silent	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	6006560	161018501	88232120	4	23267										
SLC30A1	7779	hgsc.bcm.edu	37	chr1	211751728	211751728	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gagcccccattacctcggctCggatccagccgaacgtgttc	10	16	0	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:211751728C>A	ENST00000367001.4	-	1	356	c.227G>T	c.(226-228)cGa>cTa	p.R76L		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	76					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)	p.R76L(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		TACCTCGGCTCGGATCCAGCC	0.662																																					p.R76L		Atlas-SNP	.											SLC30A1,NS,carcinoma,0,1	SLC30A1	27	.	1	Substitution - Missense(1)	ovary(1)	c.G227T						.						36	45	42					1																	211751728		2203	4300	6503	SO:0001583	missense	7779	exon1			TCGGCTCGGATCC	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.227G>T	chr1.hg19:g.211751728C>A	ENSP00000355968:p.Arg76Leu	167.0	0.0		212.0	148.0	NM_021194	Q0VAK9|Q9BZF6	Missense_Mutation	SNP	ENST00000367001.4	hg19	CCDS1499.1	.	.	.	.	.	.	.	.	.	.	C	31	5.070240	0.93950	.	.	ENSG00000170385	ENST00000367001	T	0.73789	-0.78	3.68	3.68	0.42216	.	0.000000	0.85682	D	0.000000	D	0.91327	0.7265	H	0.98446	4.235	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.94905	0.8060	10	0.87932	D	0	-8.1932	15.5717	0.76345	0.0:1.0:0.0:0.0	.	76	Q9Y6M5	ZNT1_HUMAN	L	76	ENSP00000355968:R76L	ENSP00000355968:R76L	R	-	2	0	SLC30A1	209818351	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	6.787000	0.75099	1.881000	0.54492	0.400000	0.26472	CGA	.	.		0.662	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			A	211751728	C	A	211751728	3	1	151	1	0	0	0	0	1	0	0	0	14568	884	31	1	1304	1	SLC30A1	1	211751728	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	50733227	211751728	37498893	5	23268										
USH2A	7399	hgsc.bcm.edu	37	chr1	216595468	216595469	+	In_Frame_Ins	INS	-	-	AGA													0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tgaatactttcagcagcagcINSagagctgtgacaaaaagtgc							TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:216595468_216595469insAGA	ENST00000307340.3	-	2	596_597	c.210_211insTCT	c.(208-213)tctgct>tctTCTgct	p.70_71insS	USH2A_ENST00000366942.3_In_Frame_Ins_p.70_71insS|USH2A_ENST00000366943.2_In_Frame_Ins_p.70_71insS	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	70					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCAGCAGCAGCAGAGCTGTGAC	0.5										HNSCC(13;0.011)																											p.A71delinsSA		Atlas-Indel,Pindel	.											.	USH2A	1168	.	0			c.211_212insTCT						.																																			SO:0001652	inframe_insertion	7399	exon2			.	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.208_210dupTCT	chr1.hg19:g.216595469_216595471dupAGA	ENSP00000305941:p.Ser70_Ser70dup	142.0	0.0		244.0	109.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	In_Frame_Ins	INS	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.5	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		AGA	216595469	-	AGA	216595468	7	5	151	1	0	1	1	0	0	0	0	0	17051	710	25	0	15695	0	USH2A	1	216595468	In_Frame_Ins	INS	-	TCGA-DD-AAC9-01A-11D-A40R-10	4843740	216595468	32655153	6	23269										
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220340743	220340743	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	taggctaaatgcagtaagtcTgaaagtcagaagaaagcagt	11	5	2	3			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:220340743T>C	ENST00000358951.2	-	26	3097		c.e26-2			NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)						establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		GCAGTAAGTCTGAAAGTCAGA	0.388																																					.		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.2981-2A>G						.						121	115	117					1																	220340743		2203	4300	6503	SO:0001630	splice_region_variant	25782	exon27			TAAGTCTGAAAGT	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.2981-2A>G	chr1.hg19:g.220340743T>C		183.0	1.0		267.0	183.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Splice_Site	SNP	ENST00000358951.2	hg19	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.111694	0.56398	.	.	ENSG00000118873	ENST00000358951	.	.	.	6.02	6.02	0.97574	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5446	0.84426	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RAB3GAP2	218407366	1.000000	0.71417	0.988000	0.46212	0.322000	0.28314	8.040000	0.89188	2.311000	0.77944	0.533000	0.62120	.	.	.		0.388	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414	Intron	C	220340743	T	C	220340743	5	2	151	1	0	0	0	0	0	0	1	0	12951	1594	55	2	1242	2	RAB3GAP2	1	220340743	Splice_Site	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	3745275	220340743	28909878	7	23270										
HIST3H2A	92815	hgsc.bcm.edu	37	chr1	228645397	228645397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cgccggcgcccacgcgctccGaatagttgcccttgcggagc	13	17	0	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:228645397G>A	ENST00000366695.2	-	1	163	c.122C>T	c.(121-123)tCg>tTg	p.S41L	HIST3H2BB_ENST00000369160.2_5'Flank	NM_033445.2	NP_254280.1	Q7L7L0	H2A3_HUMAN	histone cluster 3, H2a	41					nucleosome disassembly (GO:0006337)|UV-damage excision repair (GO:0070914)	extracellular vesicular exosome (GO:0070062)|nuclear nucleosome (GO:0000788)	DNA binding (GO:0003677)			endometrium(1)|lung(3)|ovary(1)	5		Prostate(94;0.183)				CACGCGCTCCGAATAGTTGCC	0.716																																					p.S41L		Atlas-SNP	.											.	HIST3H2A	13	.	0			c.C122T						.						16	20	19					1																	228645397		2196	4295	6491	SO:0001583	missense	92815	exon1			CGCTCCGAATAGT	AY131974	CCDS1573.1	1q42.13	2011-01-27	2006-10-11		ENSG00000181218	ENSG00000181218		"Histones / Replication-dependent"	20507	protein-coding gene	gene with protein product		615015	"histone 3, H2a"			12408966	Standard	NM_033445		Approved	MGC3165	uc001hsy.3	Q7L7L0	OTTHUMG00000040046	ENST00000366695.2:c.122C>T	chr1.hg19:g.228645397G>A	ENSP00000355656:p.Ser41Leu	175.0	0.0		324.0	18.0	NM_033445	B2R4S4	Missense_Mutation	SNP	ENST00000366695.2	hg19	CCDS1573.1	.	.	.	.	.	.	.	.	.	.	.	13.21	2.169766	0.38315	.	.	ENSG00000181218	ENST00000366695	T	0.69040	-0.37	4.07	3.13	0.36017	Histone-fold (2);Histone core (1);Histone H2A (1);	0.176181	0.27500	N	0.019083	T	0.74928	0.3781	M	0.80746	2.51	0.22591	N	0.998952	D	0.56746	0.977	P	0.52793	0.709	T	0.68957	-0.5272	10	0.87932	D	0	.	11.8956	0.52654	0.0:0.1781:0.8219:0.0	.	41	Q7L7L0	H2A3_HUMAN	L	41	ENSP00000355656:S41L	ENSP00000355656:S41L	S	-	2	0	HIST3H2A	226712020	1.000000	0.71417	0.028000	0.17463	0.132000	0.20833	5.869000	0.69613	1.253000	0.44018	0.655000	0.94253	TCG	.	.		0.716	HIST3H2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096598.1	NM_033445		A	228645397	G	A	228645397	3	1	151	1	0	0	0	0	1	0	0	0	7191	1059	37	1	274	1	HIST3H2A	1	228645397	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	8304654	228645397	20605224	8	23271										
CEP170	9859	hgsc.bcm.edu	37	chr1	243354614	243354614	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	agcatgccctgcacctgttaTatgggaacttggcgtgtctt	11	10	1	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:243354614T>A	ENST00000366542.1	-	8	865	c.814A>T	c.(814-816)Ata>Tta	p.I272L	CEP170_ENST00000366544.1_Missense_Mutation_p.I272L|CEP170_ENST00000366543.1_Missense_Mutation_p.I272L	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	272						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GCACCTGTTATATGGGAACTT	0.383																																					p.I272L		Atlas-SNP	.											.	CEP170	153	.	0			c.A814T						.						94	83	86					1																	243354614		1863	4091	5954	SO:0001583	missense	9859	exon8			CTGTTATATGGGA	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.814A>T	chr1.hg19:g.243354614T>A	ENSP00000355500:p.Ile272Leu	117.0	0.0		167.0	108.0	NM_001042405	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	hg19	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.150789	0.37923	.	.	ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000424081	T;T;T	0.28666	1.6;1.6;1.6	4.71	3.58	0.41010	.	0.419377	0.24388	N	0.038957	T	0.12433	0.0302	N	0.03608	-0.345	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.13407	0.007;0.009;0.003	T	0.07424	-1.0773	10	0.34782	T	0.22	-5.953	6.5992	0.22691	0.0:0.2795:0.0:0.7205	.	272;272;272	Q5SW79-3;Q5SW79-2;Q5SW79	.;.;CE170_HUMAN	L	272;272;272;170	ENSP00000355500:I272L;ENSP00000355502:I272L;ENSP00000355501:I272L	ENSP00000355500:I272L	I	-	1	0	CEP170	241421237	0.988000	0.35896	0.987000	0.45799	0.984000	0.73092	0.914000	0.28624	1.767000	0.52121	0.374000	0.22700	ATA	.	.		0.383	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		A	243354614	T	A	243354614	3	1	151	1	0	0	0	0	1	0	0	0	3252	1406	49	4	4022	4	CEP170	1	243354614	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	14709217	243354614	5896007	9	23272										
RPS27A	6233	hgsc.bcm.edu	37	chr2	55460543	55460543	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	aatgtaaaggccaagatccaGgataaggaaggcaagtagta	12	5	0	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:55460543G>A	ENST00000272317.6	+	3	417	c.93G>A	c.(91-93)caG>caA	p.Q31Q	RPS27A_ENST00000404735.1_Silent_p.Q31Q|CLHC1_ENST00000406437.2_5'Flank|CLHC1_ENST00000406076.1_5'Flank|CLHC1_ENST00000407122.1_5'Flank|CLHC1_ENST00000401408.1_5'Flank|CLHC1_ENST00000494539.1_5'Flank|RPS27A_ENST00000402285.3_Silent_p.Q31Q	NM_002954.5	NP_002945.1	P62979	RS27A_HUMAN	ribosomal protein S27a	31	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|viral transcription (GO:0019083)|virion assembly (GO:0019068)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|small ribosomal subunit (GO:0015935)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			cervix(1)|ovary(1)|urinary_tract(1)	3						CCAAGATCCAGGATAAGGAAG	0.433																																					p.Q31Q		Atlas-SNP	.											.	RPS27A	12	.	0			c.G93A						.						84	79	81					2																	55460543		2203	4300	6503	SO:0001819	synonymous_variant	6233	exon3			GATCCAGGATAAG	AB007163	CCDS33202.1	2p16	2011-04-06			ENSG00000143947	ENSG00000143947		"S ribosomal proteins"	10417	protein-coding gene	gene with protein product	"ubiquitin carboxyl extension protein 80"	191343				9582194	Standard	NM_001135592		Approved	UBCEP80, Uba80, S27A	uc010yow.2	P62979	OTTHUMG00000151919	ENST00000272317.6:c.93G>A	chr2.hg19:g.55460543G>A		99.0	0.0		92.0	4.0	NM_001135592	P02248|P02249|P02250|P14798|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BQ77|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000272317.6	hg19	CCDS33202.1																																																																																			.	.		0.433	RPS27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324423.15			A	55460543	G	A	55460543	2	1	151	1	0	0	0	0	0	0	0	1	13654	991	35	3		3	RPS27A	2	55460543	Silent	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		55460543	187738830	10	23273										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	catggccgggcgagctggagGaggaggaggaggaggaggag	24	5	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						.						3	4	4					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	186.0	0.0		263.0	19.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73613036	G	C	73613036	3	2	151	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	18152493	73613036	169586337	11	23274										
SLC9A2	6549	hgsc.bcm.edu	37	chr2	103236548	103236548	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	attacccccacgtgcagatcCccttcgagatcaccctttgg	7	16	1	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:103236548C>A	ENST00000233969.2	+	1	383	c.241C>A	c.(241-243)Ccc>Acc	p.P81T		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	81					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						CGTGCAGATCCCCTTCGAGAT	0.642																																					p.P81T		Atlas-SNP	.											.	SLC9A2	112	.	0			c.C241A						.						59	51	54					2																	103236548		2203	4300	6503	SO:0001583	missense	6549	exon1			CAGATCCCCTTCG		CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"Solute carriers"	11072	protein-coding gene	gene with protein product		600530	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 2"	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.241C>A	chr2.hg19:g.103236548C>A	ENSP00000233969:p.Pro81Thr	196.0	0.0		211.0	67.0	NM_003048	B2RMS2	Missense_Mutation	SNP	ENST00000233969.2	hg19	CCDS2062.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.677163	0.88445	.	.	ENSG00000115616	ENST00000233969	D	0.83837	-1.77	5.15	5.15	0.70609	.	0.058224	0.64402	D	0.000001	T	0.76744	0.4030	L	0.29908	0.895	0.80722	D	1	P	0.45126	0.851	B	0.40165	0.321	T	0.81123	-0.1076	10	0.72032	D	0.01	.	17.3902	0.87428	0.0:1.0:0.0:0.0	.	81	Q9UBY0	SL9A2_HUMAN	T	81	ENSP00000233969:P81T	ENSP00000233969:P81T	P	+	1	0	SLC9A2	102602980	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	6.700000	0.74619	2.401000	0.81631	0.555000	0.69702	CCC	.	.		0.642	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2			A	103236548	C	A	103236548	3	1	151	1	0	0	0	0	1	0	0	0	14727	623	22	3	243	3	SLC9A2	2	103236548	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	29623512	103236548	139962825	12	23275										
PSD4	23550	hgsc.bcm.edu	37	chr2	113940649	113940649	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cgggcctgcactccagcccaCctgagaatgaagactcaggg	12	14	1	3			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:113940649C>T	ENST00000245796.6	+	2	811	c.616C>T	c.(616-618)Cct>Tct	p.P206S	PSD4_ENST00000441564.3_Missense_Mutation_p.P206S	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	206					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTCCAGCCCACCTGAGAATGA	0.647																																					p.P206S		Atlas-SNP	.											.	PSD4	74	.	0			c.C616T						.						58	62	61					2																	113940649		2203	4300	6503	SO:0001583	missense	23550	exon2			AGCCCACCTGAGA	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"Pleckstrin homology (PH) domain containing"	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.616C>T	chr2.hg19:g.113940649C>T	ENSP00000245796:p.Pro206Ser	78.0	0.0		72.0	5.0	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	hg19	CCDS33276.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.386696	0.42308	.	.	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.12255	2.7;2.73	5.59	3.74	0.42951	.	2.786630	0.00871	N	0.002024	T	0.20170	0.0485	L	0.29908	0.895	0.09310	N	0.99999	D;P	0.53462	0.96;0.933	P;P	0.52217	0.693;0.497	T	0.15093	-1.0449	9	.	.	.	.	8.038	0.30504	0.0:0.7535:0.159:0.0875	.	206;206	Q8NDX1-2;Q8NDX1	.;PSD4_HUMAN	S	206	ENSP00000245796:P206S;ENSP00000413997:P206S	.	P	+	1	0	PSD4	113657120	0.000000	0.05858	0.032000	0.17829	0.009000	0.06853	0.573000	0.23699	1.321000	0.45227	0.561000	0.74099	CCT	.	.		0.647	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455		T	113940649	C	T	113940649	3	4	151	1	0	0	0	0	1	0	0	0	12661	507	18	3	618	3	PSD4	2	113940649	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	10704101	113940649	129258724	13	23276										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227919329	227919329	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cctttggcccctctcagtccCcggtctccaggaaggccaga	10	17	2	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:227919329C>A	ENST00000396625.3	-	31	3048	c.2841G>T	c.(2839-2841)cgG>cgT	p.R947R	COL4A4_ENST00000329662.7_Silent_p.R947R	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	947	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CTCTCAGTCCCCGGTCTCCAG	0.483																																					p.R947R		Atlas-SNP	.											.	COL4A4	215	.	0			c.G2841T						.						104	110	108					2																	227919329		1910	4121	6031	SO:0001819	synonymous_variant	1286	exon31			CAGTCCCCGGTCT		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.2841G>T	chr2.hg19:g.227919329C>A		123.0	0.0		152.0	9.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	hg19	CCDS42828.1																																																																																			.	.		0.483	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		A	227919329	C	A	227919329	2	1	151	1	0	0	0	0	0	0	0	1	3695	610	22	3		3	COL4A4	2	227919329	Silent	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	113978680	227919329	15280044	14	23277										
NEU2	4759	hgsc.bcm.edu	37	chr2	233897434	233897434	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cgtgttccagtcgggagcccAtgcctacagaatccctgccc	10	16	0	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:233897434A>T	ENST00000233840.3	+	1	53	c.53A>T	c.(52-54)cAt>cTt	p.H18L		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	18					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	TCGGGAGCCCATGCCTACAGA	0.627																																					p.H18L		Atlas-SNP	.											.	NEU2	42	.	0			c.A53T						.						131	111	118					2																	233897434		2203	4300	6503	SO:0001583	missense	4759	exon1			GAGCCCATGCCTA	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"N-acetyl-alpha-neuraminidase 2"	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.53A>T	chr2.hg19:g.233897434A>T	ENSP00000233840:p.His18Leu	128.0	0.0		125.0	30.0	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	hg19	CCDS2501.1	.	.	.	.	.	.	.	.	.	.	A	10.93	1.490103	0.26686	.	.	ENSG00000115488	ENST00000233840	T	0.08807	3.05	5.48	3.17	0.36434	Neuraminidase (2);	1.082620	0.07117	N	0.843272	T	0.07683	0.0193	L	0.46157	1.445	0.09310	N	1	B	0.22480	0.07	B	0.15484	0.013	T	0.46428	-0.9192	10	0.10111	T	0.7	-8.6775	5.4599	0.16612	0.7188:0.0:0.2812:0.0	.	18	Q9Y3R4	NEUR2_HUMAN	L	18	ENSP00000233840:H18L	ENSP00000233840:H18L	H	+	2	0	NEU2	233605678	0.000000	0.05858	0.008000	0.14137	0.651000	0.38670	1.141000	0.31528	0.918000	0.36919	0.533000	0.62120	CAT	.	.		0.627	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383		T	233897434	A	T	233897434	3	4	151	1	0	0	0	0	1	0	0	0	10351	217	8	4	55	4	NEU2	2	233897434	Missense_Mutation	SNP	A	TCGA-DD-AAC9-01A-11D-A40R-10	5978105	233897434	9301939	15	23278										
RPP14	11102	hgsc.bcm.edu	37	chr3	58303188	58303189	+	Frame_Shift_Del	DEL	TT	TT	-													0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tttctccatttcttcttgcaTtatctggtaatagtagggaa							TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr3:58303188_58303189delTT	ENST00000445193.3	+	6	751_752	c.340_341delTT	c.(340-342)ttafs	p.L114fs	RPP14_ENST00000466547.1_Frame_Shift_Del_p.L114fs|RPP14_ENST00000295959.5_Frame_Shift_Del_p.L114fs|RPP14_ENST00000477305.1_3'UTR|RPP14_ENST00000528153.1_5'Flank	NM_001098783.2	NP_001092253.1	O95059	RPP14_HUMAN	ribonuclease P/MRP 14kDa subunit	114					tRNA processing (GO:0008033)	nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)|RNA binding (GO:0003723)			large_intestine(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.000187)|KIRC - Kidney renal clear cell carcinoma(10;0.0102)|Kidney(10;0.0118)|OV - Ovarian serous cystadenocarcinoma(275;0.191)		TCTTCTTGCATTATCTGGTAAT	0.391																																					p.113_114del		Atlas-Indel,Pindel	.											.	RPP14	6	.	0			c.339_340del						.																																			SO:0001589	frameshift_variant	11102	exon6			.	AF001175	CCDS2888.1	3p21.2	2012-05-21	2007-06-26		ENSG00000163684	ENSG00000163684			30327	protein-coding gene	gene with protein product		606112	"ribonuclease P 14kDa subunit"			10024167, 11929972	Standard	NM_001098783		Approved	P14	uc031sah.1	O95059	OTTHUMG00000159152	ENST00000445193.3:c.340_341delTT	chr3.hg19:g.58303188_58303189delTT	ENSP00000412894:p.Leu114fs	57.0	0.0		89.0	20.0	NM_007042	Q53X97	Frame_Shift_Del	DEL	ENST00000445193.3	hg19	CCDS2888.1																																																																																			.	.		0.391	RPP14-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353527.2	NM_007042		-	58303189	TT	-	58303188	7	5	151	1	0	1	0	1	0	0	0	0	13624	1490	52	0	358	0	RPP14	3	58303188	Frame_Shift_Del	DEL	TT	TCGA-DD-AAC9-01A-11D-A40R-10		58303188	139719242	16	23279										
MYH15	22989	hgsc.bcm.edu	37	chr3	108179187	108179187	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tttggaatgaagctcctttcTttcgtttcttctccccaaat	5	11	3	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr3:108179187T>A	ENST00000273353.3	-	18	2008	c.1952A>T	c.(1951-1953)aAg>aTg	p.K651M	MYH15_ENST00000495753.2_5'UTR	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	651	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						AGCTCCTTTCTTTCGTTTCTT	0.313																																					p.K651M		Atlas-SNP	.											.	MYH15	223	.	0			c.A1952T						.						59	57	57					3																	108179187		1821	4067	5888	SO:0001583	missense	22989	exon18			CCTTTCTTTCGTT	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1952A>T	chr3.hg19:g.108179187T>A	ENSP00000273353:p.Lys651Met	269.0	0.0		283.0	20.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.823054	0.50739	.	.	ENSG00000144821	ENST00000273353	D	0.88046	-2.33	4.39	1.94	0.25998	Myosin head, motor domain (2);	.	.	.	.	D	0.93569	0.7947	M	0.93763	3.455	0.44728	D	0.997722	D	0.76494	0.999	D	0.80764	0.994	D	0.91559	0.5263	9	0.87932	D	0	.	6.6819	0.23125	0.1369:0.0761:0.0:0.7871	.	651	Q9Y2K3	MYH15_HUMAN	M	651	ENSP00000273353:K651M	ENSP00000273353:K651M	K	-	2	0	MYH15	109661877	1.000000	0.71417	0.642000	0.29436	0.480000	0.33159	3.373000	0.52394	0.424000	0.26061	0.459000	0.35465	AAG	.	.		0.313	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		A	108179187	T	A	108179187	3	1	151	1	0	0	0	0	1	0	0	0	10043	1609	56	4	3988	4	MYH15	3	108179187	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	49875999	108179187	89843243	17	23280										
ACOX3	8310	hgsc.bcm.edu	37	chr4	8418225	8418225	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tctgggagcagagctgtgtcGcctccttccacagtggatgc	13	12	1	1	rs146635266		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr4:8418225G>A	ENST00000356406.5	-	2	101	c.24C>T	c.(22-24)ggC>ggT	p.G8G	ACOX3_ENST00000413009.2_Silent_p.G8G|ACOX3_ENST00000503233.1_Silent_p.G8G	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	8					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						GAGCTGTGTCGCCTCCTTCCA	0.582													G|||	1	0.000199681	8e-04	0	5008	,	,		16330	0		0	False		,,,				2504	0				p.G8G		Atlas-SNP	.											.	ACOX3	70	.	0			c.C24T						.	G	,	1,4405	2.1+/-5.4	0,1,2202	65	64	64		24,24	-5.3	0	4	dbSNP_134	64	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ACOX3	NM_001101667.1,NM_003501.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	8/625,8/701	8418225	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8310	exon2			TGTGTCGCCTCCT	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.24C>T	chr4.hg19:g.8418225G>A		80.0	0.0		112.0	32.0	NM_001101667	Q96AJ8	Silent	SNP	ENST00000356406.5	hg19	CCDS3401.1																																																																																			.	G|1.000;A|0.000		0.582	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			A	8418225	G	A	8418225	2	1	151	1	0	0	0	0	0	0	0	1	160	1074	38	1		1	ACOX3	4	8418225	Silent	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		8418225	182736051	18	23281										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90856570	90856570	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gattaacaatctcaccgtctCtttggagatggagaaagagt	10	7	2	3			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr4:90856570C>A	ENST00000394980.1	+	7	2058	c.1739C>A	c.(1738-1740)tCt>tAt	p.S580Y	MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000264790.2_Missense_Mutation_p.S580Y|MMRN1_ENST00000508372.1_Missense_Mutation_p.S322Y			Q13201	MMRN1_HUMAN	multimerin 1	580					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		CTCACCGTCTCTTTGGAGATG	0.343																																					p.S580Y		Atlas-SNP	.											.	MMRN1	174	.	0			c.C1739A						.						56	58	57					4																	90856570		2203	4297	6500	SO:0001583	missense	22915	exon6			CCGTCTCTTTGGA	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.1739C>A	chr4.hg19:g.90856570C>A	ENSP00000378431:p.Ser580Tyr	215.0	0.0		193.0	45.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	hg19	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	C	3.869	-0.028322	0.07589	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.65732	0.18;0.18;-0.17	5.12	0.973	0.19710	.	1.347860	0.04935	N	0.457576	T	0.31638	0.0803	N	0.08118	0	0.09310	N	1	P	0.48162	0.906	B	0.35413	0.202	T	0.20240	-1.0281	10	0.09084	T	0.74	.	3.8393	0.08908	0.1212:0.5764:0.1482:0.1542	.	580	Q13201	MMRN1_HUMAN	Y	580;580;322	ENSP00000378431:S580Y;ENSP00000264790:S580Y;ENSP00000426461:S322Y	ENSP00000264790:S580Y	S	+	2	0	MMRN1	91075593	0.003000	0.15002	0.075000	0.20258	0.071000	0.16799	-0.020000	0.12525	0.325000	0.23359	0.591000	0.81541	TCT	.	.		0.343	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		A	90856570	C	A	90856570	3	1	151	1	0	0	0	0	1	0	0	0	9679	913	32	3	1761	3	MMRN1	4	90856570	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	82438345	90856570	100297706	19	23282										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123260512	123260512	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	agactttatcccctggaggtAatgctactcagagtggaaca	10	9	1	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr4:123260512A>G	ENST00000264501.4	+	72	12674	c.12301A>G	c.(12301-12303)Aat>Gat	p.N4101D	KIAA1109_ENST00000388738.3_Missense_Mutation_p.N4101D			Q2LD37	K1109_HUMAN	KIAA1109	4101					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CCCTGGAGGTAATGCTACTCA	0.403																																					p.N4101D		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A12301G						.						88	80	82					4																	123260512		1826	4082	5908	SO:0001583	missense	84162	exon70			GGAGGTAATGCTA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.12301A>G	chr4.hg19:g.123260512A>G	ENSP00000264501:p.Asn4101Asp	157.0	0.0		162.0	46.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	A	11.80	1.747415	0.30955	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707	T;T;T	0.29917	2.5;2.5;1.55	5.68	-0.0957	0.13640	.	1.143810	0.06229	N	0.688359	T	0.14141	0.0342	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.25082	-1.0142	10	0.36615	T	0.2	.	2.6803	0.05091	0.5475:0.2039:0.1452:0.1033	.	4100;4101	Q2LD37-4;Q2LD37	.;K1109_HUMAN	D	4101;4101;770	ENSP00000264501:N4101D;ENSP00000373390:N4101D;ENSP00000410874:N770D	ENSP00000264501:N4101D	N	+	1	0	KIAA1109	123479962	0.009000	0.17119	0.005000	0.12908	0.997000	0.91878	0.908000	0.28545	0.089000	0.17243	0.460000	0.39030	AAT	.	.		0.403	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123260512	A	G	123260512	3	3	151	1	0	0	0	0	1	0	0	0	8217	362	13	2	12579	2	KIAA1109	4	123260512	Missense_Mutation	SNP	A	TCGA-DD-AAC9-01A-11D-A40R-10	32403942	123260512	67893764	20	23283										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148743969	148743969	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gtgacagatgatgaacgatgCataggtaattaaacatgata	10	4	0	5			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr4:148743969C>G	ENST00000336498.3	+	2	485	c.246C>G	c.(244-246)tgC>tgG	p.C82W		NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		ATGAACGATGCATAGGTAATT	0.398																																					p.C82W		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.C246G						.						179	167	171					4																	148743969		2203	4300	6503	SO:0001583	missense	79658	exon2			ACGATGCATAGGT	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.246C>G	chr4.hg19:g.148743969C>G	ENSP00000336923:p.Cys82Trp	156.0	0.0		203.0	38.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	C	10.79	1.448903	0.26074	.	.	ENSG00000071205	ENST00000336498	T	0.29142	1.58	5.95	2.66	0.31614	IRSp53/MIM homology domain (IMD) (1);	0.043983	0.85682	D	0.000000	T	0.29817	0.0745	M	0.68317	2.08	0.80722	D	1	P	0.49358	0.923	B	0.40702	0.338	T	0.05053	-1.0909	10	0.38643	T	0.18	.	10.1317	0.42682	0.0:0.6328:0.0:0.3672	.	82	A1A4S6	RHG10_HUMAN	W	82	ENSP00000336923:C82W	ENSP00000336923:C82W	C	+	3	2	ARHGAP10	148963419	0.999000	0.42202	0.995000	0.50966	0.076000	0.17211	0.548000	0.23314	0.370000	0.24538	-0.142000	0.14014	TGC	.	.		0.398	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		G	148743969	C	G	148743969	3	3	151	1	0	0	0	0	1	0	0	0	862	718	25	4	252	4	ARHGAP10	4	148743969	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	25483457	148743969	42410307	21	23284										
MAST4	375449	hgsc.bcm.edu	37	chr5	66460639	66460639	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tgctggagccttggttcctgCcccccagccgaggtctccag	12	16	1	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:66460639C>T	ENST00000403625.2	+	29	5927	c.5632C>T	c.(5632-5634)Ccc>Tcc	p.P1878S	MAST4_ENST00000403666.1_Missense_Mutation_p.P1689S|MAST4_ENST00000404260.3_Missense_Mutation_p.P1881S|MAST4_ENST00000261569.7_Missense_Mutation_p.P1684S|MAST4_ENST00000405643.1_Missense_Mutation_p.P1699S	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1881						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.S1883fs*59(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TTGGTTCCTGCCCCCCAGCCG	0.547																																					p.P1878S		Atlas-SNP	.											.,1	MAST4	218	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.C5632T						.						47	52	50					5																	66460639		1901	4108	6009	SO:0001583	missense	375449	exon29			TTCCTGCCCCCCA	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.5632C>T	chr5.hg19:g.66460639C>T	ENSP00000385727:p.Pro1878Ser	86.0	0.0		103.0	19.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.994|7.994	0.753982|0.753982	0.15778|0.15778	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000443808|ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569	.|T;T;T;T;T	.|0.65916	.|-0.16;-0.16;-0.18;-0.18;-0.15	4.66|4.66	3.78|3.78	0.43462|0.43462	.|.	.|0.422637	.|0.20823	.|N	.|0.085036	T|T	0.43144|0.43144	0.1234|0.1234	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|B;B	.|0.32829	.|0.267;0.386	.|B;B	.|0.31101	.|0.058;0.124	T|T	0.18461|0.18461	-1.0336|-1.0336	5|10	.|0.16896	.|T	.|0.51	-13.0751|-13.0751	5.6869|5.6869	0.17807|0.17807	0.1963:0.7057:0.0:0.0981|0.1963:0.7057:0.0:0.0981	.|.	.|1881;1689	.|O15021;O15021-3	.|MAST4_HUMAN;.	V|S	934|1881;1878;1689;1699;1699;1684	.|ENSP00000385048:P1881S;ENSP00000385727:P1878S;ENSP00000384313:P1689S;ENSP00000384099:P1699S;ENSP00000261569:P1684S	.|ENSP00000261569:P1684S	A|P	+|+	2|1	0|0	MAST4|MAST4	66496395|66496395	0.024000|0.024000	0.19004|0.19004	0.741000|0.741000	0.31004|0.31004	0.227000|0.227000	0.25037|0.25037	1.647000|1.647000	0.37260|0.37260	1.135000|1.135000	0.42183|0.42183	-0.309000|-0.309000	0.09137|0.09137	GCC|CCC	.	.		0.547	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			T	66460639	C	T	66460639	3	4	151	1	0	0	0	0	1	0	0	0	9336	739	26	3	5876	3	MAST4	5	66460639	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10		66460639	114454621	22	23285										
AQPEP	206338	hgsc.bcm.edu	37	chr5	115327845	115327845	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	attgccttgcctagttttgaCaaccatgcaatggaaaactg	8	9	0	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:115327845C>A	ENST00000357872.4	+	5	1255	c.1131C>A	c.(1129-1131)gaC>gaA	p.D377E	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		377						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CTAGTTTTGACAACCATGCAA	0.318																																					p.D377E		Atlas-SNP	.											.	.	.	.	0			c.C1131A						.						112	118	116					5																	115327845		2202	4300	6502	SO:0001583	missense	0	exon5			TTTTGACAACCAT																												ENST00000357872.4:c.1131C>A	chr5.hg19:g.115327845C>A	ENSP00000350541:p.Asp377Glu	109.0	0.0		114.0	23.0	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	hg19	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.325778	0.41197	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.02395	4.31	5.81	2.94	0.34122	Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	0.472937	0.21269	N	0.077347	T	0.02380	0.0073	L	0.31207	0.915	0.23076	N	0.998339	B	0.23249	0.082	B	0.26864	0.074	T	0.43130	-0.9410	10	0.41790	T	0.15	.	3.5656	0.07899	0.1673:0.5103:0.0:0.3224	.	377	Q6Q4G3	AMPQ_HUMAN	E	377;366	ENSP00000350541:D377E	ENSP00000350541:D377E	D	+	3	2	AC010282.1	115355744	0.712000	0.27916	0.637000	0.29366	0.951000	0.60555	0.108000	0.15396	0.805000	0.34159	0.655000	0.94253	GAC	.	.		0.318	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			A	115327845	C	A	115327845	3	1	151	1	0	0	0	0	1	0	0	0	834	477	17	3	1149	3	AQPEP	5	115327845	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	48867206	115327845	65587415	23	23286										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130797637	130797637	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gtcggttcaatattacgaaaCaaatcaaagtccctcattga	6	9	3	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:130797637C>T	ENST00000509018.1	-	19	2830	c.2625G>A	c.(2623-2625)ttG>ttA	p.L875L	RAPGEF6_ENST00000307984.5_Silent_p.L880L|RAPGEF6_ENST00000512052.1_Silent_p.L590L|RAPGEF6_ENST00000507093.1_Silent_p.L875L|CTC-432M15.3_ENST00000514667.1_Silent_p.L925L|RAPGEF6_ENST00000296859.6_Silent_p.L875L|RAPGEF6_ENST00000308008.6_Silent_p.L875L	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	875	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TATTACGAAACAAATCAAAGT	0.408																																					p.L880L	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.G2640A						.						102	99	100					5																	130797637		2203	4300	6503	SO:0001819	synonymous_variant	51735	exon20			ACGAAACAAATCA	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.2625G>A	chr5.hg19:g.130797637C>T		124.0	0.0		146.0	46.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Silent	SNP	ENST00000509018.1	hg19	CCDS34225.1																																																																																			.	.		0.408	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		T	130797637	C	T	130797637	2	4	151	1	0	0	0	0	0	0	0	1	13063	477	17	3		3	RAPGEF6	5	130797637	Silent	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	15469792	130797637	50117623	24	23287										
AFF4	27125	hgsc.bcm.edu	37	chr5	132216770	132216771	+	Frame_Shift_Ins	INS	-	-	C													0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tcaagatatcaacttggcatINScctggcgaagccagtgcagt							TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:132216770_132216771insC	ENST00000265343.5	-	21	3851_3852	c.3472_3473insG	c.(3472-3474)gatfs	p.D1158fs		NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	1158					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAACTTGGCATCCTGGCGAAGC	0.46																																					p.D1158fs	Ovarian(126;889 1733 2942 10745 11605)	Atlas-Indel,Pindel	.											.	AFF4	120	.	0			c.3473_3474insG						.																																			SO:0001589	frameshift_variant	27125	exon21			.	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.3473dupG	chr5.hg19:g.132216772_132216772dupC	ENSP00000265343:p.Asp1158fs	190.0	0.0		212.0	47.0	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Frame_Shift_Ins	INS	ENST00000265343.5	hg19	CCDS4164.1																																																																																			.	.		0.46	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		C	132216771	-	C	132216770	7	5	151	1	0	1	1	0	0	0	0	0	359	1435	50	0	22	0	AFF4	5	132216770	Frame_Shift_Ins	INS	-	TCGA-DD-AAC9-01A-11D-A40R-10	1419133	132216770	48698490	25	23288										
KLHL3	26249	hgsc.bcm.edu	37	chr5	136974747	136974747	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ggcaatggacgtccactggtCcttcacgccgtcatacacat	9	14	2	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:136974747C>G	ENST00000309755.4	-	10	1557	c.1114G>C	c.(1114-1116)Gac>Cac	p.D372H	KLHL3_ENST00000541417.1_Intron|KLHL3_ENST00000506491.1_Missense_Mutation_p.D290H|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000508657.1_Missense_Mutation_p.D340H	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	372					distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		GTCCACTGGTCCTTCACGCCG	0.607																																					p.D372H		Atlas-SNP	.											.	KLHL3	54	.	0			c.G1114C						.						99	72	82					5																	136974747		2203	4300	6503	SO:0001583	missense	26249	exon10			ACTGGTCCTTCAC	AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"Kelch-like", "BTB/POZ domain containing"	6354	protein-coding gene	gene with protein product		605775	"kelch (Drosophila)-like 3", "kelch-like 3 (Drosophila)"			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.1114G>C	chr5.hg19:g.136974747C>G	ENSP00000312397:p.Asp372His	77.0	0.0		87.0	7.0	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Missense_Mutation	SNP	ENST00000309755.4	hg19	CCDS4192.1	.	.	.	.	.	.	.	.	.	.	C	31	5.086053	0.94100	.	.	ENSG00000146021	ENST00000506491;ENST00000508657;ENST00000309755;ENST00000505853	T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25	4.69	4.69	0.59074	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.90089	0.6904	M	0.90309	3.105	0.80722	D	1	D;D;D;D	0.76494	0.999;0.996;0.998;0.999	D;P;P;D	0.72075	0.976;0.906;0.894;0.959	D	0.91941	0.5563	10	0.66056	D	0.02	.	18.1398	0.89636	0.0:1.0:0.0:0.0	.	141;332;340;372	B7Z6E2;D6RH21;Q9UH77-2;Q9UH77	.;.;.;KLHL3_HUMAN	H	290;340;372;332	ENSP00000424828:D290H;ENSP00000422099:D340H;ENSP00000312397:D372H;ENSP00000426173:D332H	ENSP00000312397:D372H	D	-	1	0	KLHL3	137002646	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.869000	0.69613	2.581000	0.87130	0.561000	0.74099	GAC	.	.		0.607	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2			G	136974747	C	G	136974747	3	3	151	1	0	0	0	0	1	0	0	0	8392	855	30	4	673	4	KLHL3	5	136974747	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	4757977	136974747	43940513	26	23289										
HBEGF	1839	hgsc.bcm.edu	37	chr5	139714267	139714267	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	agcacaagtctctctcagtgGgaattagtcatgcccaactt	8	11	3	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:139714267G>A	ENST00000230990.6	-	5	923	c.621C>T	c.(619-621)tcC>tcT	p.S207S	HBEGF_ENST00000507104.1_Silent_p.S207S	NM_001945.2	NP_001936.1	Q99075	HBEGF_HUMAN	heparin-binding EGF-like growth factor	207					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|muscle organ development (GO:0007517)|negative regulation of elastin biosynthetic process (GO:0051545)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of wound healing (GO:0090303)|regulation of heart contraction (GO:0008016)|signal transduction (GO:0007165)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)	7			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCTCAGTGGGAATTAGTCA	0.468																																					p.S207S		Atlas-SNP	.											.	HBEGF	12	.	0			c.C621T						.						346	300	316					5																	139714267		2203	4300	6503	SO:0001819	synonymous_variant	1839	exon5			TCAGTGGGAATTA		CCDS4223.1	5q23	2012-10-02	2005-01-14	2005-01-14	ENSG00000113070	ENSG00000113070			3059	protein-coding gene	gene with protein product	"Diphtheria toxin receptor (heparin-binding EGF-like growth factor)", "heparin-binding epidermal growth factor"	126150	"diphtheria toxin receptor (heparin-binding epidermal growth factor-like growth factor)"	HEGFL, DTS, DTR		7590736, 12163414	Standard	NM_001945		Approved		uc003lfi.3	Q99075	OTTHUMG00000129496	ENST00000230990.6:c.621C>T	chr5.hg19:g.139714267G>A		99.0	0.0		108.0	5.0	NM_001945	B2R821	Silent	SNP	ENST00000230990.6	hg19	CCDS4223.1																																																																																			.	.		0.468	HBEGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251665.2	NM_001945		A	139714267	G	A	139714267	2	1	151	1	0	0	0	0	0	0	0	1	6990	1219	43	3		3	HBEGF	5	139714267	Silent	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	2739520	139714267	41200993	27	23290										
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140603901	140603910	+	Frame_Shift_Del	DEL	GAAAAATATC	GAAAAATATC	-													0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tctggatgcaggaaactatgGaaaaatatcttacacatttt							TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	GAAAAATATC	GAAAAATATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:140603901_140603910delGAAAAATATC	ENST00000239449.4	+	1	824_833	c.824_833delGAAAAATATC	c.(823-834)ggaaaaatatctfs	p.GKIS275fs	PCDHB14_ENST00000515856.2_Frame_Shift_Del_p.GKIS122fs	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	275	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGAAACTATGGAAAAATATCTTACACATTT	0.414																																					p.275_278del	Ovarian(141;50 1831 27899 33809 37648)	Atlas-Indel,Pindel	.											.	PCDHB14	132	.	0			c.823_832del						.																																			SO:0001589	frameshift_variant	56122	exon1			.	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"Cadherins / Protocadherins : Clustered"	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.824_833delGAAAAATATC	chr5.hg19:g.140603901_140603910delGAAAAATATC	ENSP00000239449:p.Gly275fs	102.0	0.0		87.0	17.0	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Frame_Shift_Del	DEL	ENST00000239449.4	hg19	CCDS4256.1																																																																																			.	.		0.414	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		-	140603910	GAAAAATATC	-	140603901	7	5	151	1	0	1	0	1	0	0	0	0	11548	1174	41	0	826	0	PCDHB14	5	140603901	Frame_Shift_Del	DEL	GAAAAATATC	TCGA-DD-AAC9-01A-11D-A40R-10	889634	140603901	40311359	28	23291										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141034964	141034964	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ggtcctccggttgtgtagtcGccgctggacacaggtggggt	17	10	0	0	rs372420144		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:141034964G>A	ENST00000239440.4	-	32	4179	c.4114C>T	c.(4114-4116)Cga>Tga	p.R1372*	ARAP3_ENST00000513878.1_Intron|ARAP3_ENST00000508305.1_Nonsense_Mutation_p.R1203*|ARAP3_ENST00000512390.1_5'UTR	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1372					cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						TTGTGTAGTCGCCGCTGGACA	0.567																																					p.R1372X		Atlas-SNP	.											.	ARAP3	139	.	0			c.C4114T						.	G	stop/ARG	1,4393		0,1,2196	61	48	52		4114	5.1	1	5		52	1,8595		0,1,4297	no	stop-gained	ARAP3	NM_022481.5		0,2,6493	AA,AG,GG		0.0116,0.0228,0.0154		1372/1545	141034964	2,12988	2197	4298	6495	SO:0001587	stop_gained	64411	exon32			GTAGTCGCCGCTG	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.4114C>T	chr5.hg19:g.141034964G>A	ENSP00000239440:p.Arg1372*	172.0	0.0		197.0	55.0	NM_022481	B4DIT1|D3DQE3	Nonsense_Mutation	SNP	ENST00000239440.4	hg19	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	G	41	8.589286	0.98875	2.28E-4	1.16E-4	ENSG00000120318	ENST00000508305;ENST00000239440	.	.	.	5.12	5.12	0.69794	.	0.253727	0.34879	N	0.003616	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.3501	0.90336	0.0:0.0:1.0:0.0	.	.	.	.	X	1203;1372	.	ENSP00000239440:R1372X	R	-	1	2	ARAP3	141015148	1.000000	0.71417	1.000000	0.80357	0.482000	0.33219	6.059000	0.71133	2.662000	0.90505	0.655000	0.94253	CGA	.	.		0.567	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		A	141034964	G	A	141034964	4	1	151	1	0	0	0	0	0	1	0	0	840	1095	38	1	528	1	ARAP3	5	141034964	Nonsense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	431063	141034964	39880296	29	23292										
PTTG1	9232	hgsc.bcm.edu	37	chr5	159855662	159855662	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ccctggatgttgaattgccaCctgtttgctgtgacatagat	10	9	0	3			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:159855662C>A	ENST00000393964.1	+	5	986	c.583C>A	c.(583-585)Cct>Act	p.P195T	PTTG1_ENST00000519287.1_3'UTR|PTTG1_ENST00000520452.1_Missense_Mutation_p.P195T|PTTG1_ENST00000352433.5_Missense_Mutation_p.P195T	NM_001282382.1	NP_001269311.1	O95997	PTTG1_HUMAN	pituitary tumor-transforming 1	195					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|DNA repair (GO:0006281)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of endopeptidase activity (GO:0010951)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(1)|lung(4)	6	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.00219)|Epithelial(171;0.00348)|all cancers(165;0.0104)		TGAATTGCCACCTGTTTGCTG	0.348																																					p.P195T		Atlas-SNP	.											.	PTTG1	15	.	0			c.C583A						.						220	215	217					5																	159855662		2203	4300	6503	SO:0001583	missense	9232	exon6			TTGCCACCTGTTT	AF062649	CCDS4353.1	5q35.1	2014-08-04			ENSG00000164611	ENSG00000164611			9690	protein-coding gene	gene with protein product	"ESP1-associated protein 1", "tumor-transforming protein 1"	604147		TUTR1		9811450, 9892021	Standard	NM_004219		Approved	PTTG, HPTTG, EAP1, securin	uc003lyj.3	O95997	OTTHUMG00000130328	ENST00000393964.1:c.583C>A	chr5.hg19:g.159855662C>A	ENSP00000377536:p.Pro195Thr	66.0	0.0		75.0	10.0	NM_004219		Missense_Mutation	SNP	ENST00000393964.1	hg19	CCDS4353.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.054733	0.75960	.	.	ENSG00000164611	ENST00000352433;ENST00000520452;ENST00000393964	T;T;T	0.60920	0.15;0.15;0.15	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.68229	0.2978	M	0.77616	2.38	0.47659	D	0.999483	P	0.52463	0.953	P	0.51170	0.661	T	0.70702	-0.4799	9	.	.	.	-16.6492	14.9156	0.70795	0.0:1.0:0.0:0.0	.	195	O95997	PTTG1_HUMAN	T	195	ENSP00000344936:P195T;ENSP00000430642:P195T;ENSP00000377536:P195T	.	P	+	1	0	PTTG1	159788240	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.946000	0.56644	2.589000	0.87451	0.561000	0.74099	CCT	.	.		0.348	PTTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252677.1	NM_004219		A	159855662	C	A	159855662	3	1	151	1	0	0	0	0	1	0	0	0	12834	507	18	3	601	3	PTTG1	5	159855662	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	18820698	159855662	21059598	30	23293										
FARS2	10667	hgsc.bcm.edu	37	chr6	5369227	5369227	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	accccagcaggaagaaggggGacaactattacctgaatcgg	12	10	0	2	rs145555213		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr6:5369227G>A	ENST00000324331.6	+	2	760	c.424G>A	c.(424-426)Gac>Aac	p.D142N	FARS2_ENST00000274680.4_Missense_Mutation_p.D142N			O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2, mitochondrial	142					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)|stomach(2)	15	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	GAAGAAGGGGGACAACTATTA	0.572																																					p.D142N		Atlas-SNP	.											.	FARS2	33	.	0			c.G424A						.	G	ASN/ASP	0,4406		0,0,2203	99	88	92		424	4.5	1	6	dbSNP_134	92	1,8599	1.2+/-3.3	0,1,4299	no	missense	FARS2	NM_006567.3	23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	142/452	5369227	1,13005	2203	4300	6503	SO:0001583	missense	10667	exon2			AAGGGGGACAACT	AF097441	CCDS4494.1	6p25.1	2011-07-01	2007-02-23	2004-12-03	ENSG00000145982	ENSG00000145982	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	21062	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 2, mitochondrial"	611592	"phenylalanine-tRNA synthetase 1 (mitochondrial)"	FARS1		10329163	Standard	NM_006567		Approved	dJ236A3.1	uc003mwr.2	O95363	OTTHUMG00000014178	ENST00000324331.6:c.424G>A	chr6.hg19:g.5369227G>A	ENSP00000316335:p.Asp142Asn	752.0	1.0		763.0	183.0	NM_006567	B2R664|Q53F66|Q5TCS3|Q6FG29|Q9NPY7|Q9P062	Missense_Mutation	SNP	ENST00000324331.6	hg19	CCDS4494.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.806963	0.90623	0.0	1.16E-4	ENSG00000145982	ENST00000274680;ENST00000324331	T;T	0.73469	-0.75;-0.75	5.38	4.49	0.54785	Phenylalanyl-tRNA synthetase (1);	0.096626	0.64402	D	0.000001	D	0.88706	0.6509	H	0.97103	3.94	0.58432	D	0.999995	D	0.89917	1.0	D	0.70487	0.969	D	0.92698	0.6172	10	0.87932	D	0	-8.6428	15.2621	0.73631	0.0:0.1409:0.8591:0.0	.	142	O95363	SYFM_HUMAN	N	142	ENSP00000274680:D142N;ENSP00000316335:D142N	ENSP00000274680:D142N	D	+	1	0	FARS2	5314226	1.000000	0.71417	0.993000	0.49108	0.999000	0.98932	9.489000	0.97949	1.329000	0.45376	0.655000	0.94253	GAC	.	G|1.000;A|0.000		0.572	FARS2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467790.1	NM_006567		A	5369227	G	A	5369227	3	1	151	1	0	0	0	0	1	0	0	0	5686	1174	41	3	426	3	FARS2	6	5369227	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		5369227	165745840	31	23294										
HSD17B8	7923	hgsc.bcm.edu	37	chr6	33172866	33172866	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gctgacgtgtctgaggccagGgccgccaggtgcctgctgga	17	12	1	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr6:33172866G>T	ENST00000374662.3	+	2	267	c.240G>T	c.(238-240)agG>agT	p.R80S	HSD17B8_ENST00000469186.1_3'UTR|MIR219-1_ENST00000362166.1_RNA	NM_014234.4	NP_055049.1	Q92506	DHB8_HUMAN	hydroxysteroid (17-beta) dehydrogenase 8	80					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|fatty acid biosynthetic process (GO:0006633)	mitochondrial envelope (GO:0005740)|mitochondrial matrix (GO:0005759)|plasma membrane (GO:0005886)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	9						CTGAGGCCAGGGCCGCCAGGT	0.662																																					p.R80S		Atlas-SNP	.											.	HSD17B8	20	.	0			c.G240T						.						15	17	16					6																	33172866		1508	2709	4217	SO:0001583	missense	7923	exon2			GGCCAGGGCCGCC	D82061	CCDS4769.1	6p21.3	2011-09-14	2002-02-19	2002-02-22	ENSG00000204228	ENSG00000204228	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	3554	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 30C, member 1"	601417	"FabG (beta-ketoacyl-[acyl-carrier-protein] reductase, E coli) like (E. coli)"	FABGL		8812499, 19027726	Standard	NM_014234		Approved	HKE6, D6S2245E, RING2, KE6, H2-KE6, SDR30C1	uc003odi.2	Q92506	OTTHUMG00000031117	ENST00000374662.3:c.240G>T	chr6.hg19:g.33172866G>T	ENSP00000363794:p.Arg80Ser	57.0	0.0		68.0	20.0	NM_014234	A6NLX7|Q5STP7|Q9UIQ1	Missense_Mutation	SNP	ENST00000374662.3	hg19	CCDS4769.1	.	.	.	.	.	.	.	.	.	.	G	0.274	-0.990706	0.02162	.	.	ENSG00000204228	ENST00000374662	T	0.20463	2.07	4.39	0.26	0.15588	NAD(P)-binding domain (1);	0.590685	0.16822	N	0.198124	T	0.01387	0.0045	N	0.00783	-1.19	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45352	-0.9267	10	0.34782	T	0.22	.	3.1484	0.06479	0.1816:0.1419:0.5401:0.1363	.	80	Q92506	DHB8_HUMAN	S	80	ENSP00000363794:R80S	ENSP00000363794:R80S	R	+	3	2	HSD17B8	33280844	0.149000	0.22717	0.017000	0.16124	0.256000	0.26092	0.168000	0.16622	-0.092000	0.12417	-2.830000	0.00107	AGG	.	.		0.662	HSD17B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076196.1	NM_014234		T	33172866	G	T	33172866	3	4	151	1	0	0	0	0	1	0	0	0	7398	1223	43	3	246	3	HSD17B8	6	33172866	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	27803639	33172866	137942201	32	23295										
C6orf81	221481	hgsc.bcm.edu	37	chr6	35715163	35715163	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	catccacagctgcgacgggtGatgcctgccttgatggagat	13	11	0	3			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr6:35715163G>T	ENST00000373866.3	+	4	592	c.570G>T	c.(568-570)gtG>gtT	p.V190V	ARMC12_ENST00000373869.3_Silent_p.V190V|ARMC12_ENST00000288065.2_Silent_p.V217V			Q5T9G4	ARM12_HUMAN	armadillo repeat containing 12	190						nucleus (GO:0005634)											TGCGACGGGTGATGCCTGCCT	0.592																																					p.V217V		Atlas-SNP	.											.	.	.	.	0			c.G651T						.						105	93	97					6																	35715163		2203	4300	6503	SO:0001819	synonymous_variant	221481	exon4			ACGGGTGATGCCT	AK058119	CCDS4809.1, CCDS69093.1, CCDS69094.1	6p21.31	2013-02-14	2011-12-14	2011-12-14	ENSG00000157343	ENSG00000157343		"Armadillo repeat containing"	21099	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 81"	C6orf81			Standard	XM_005248920		Approved	FLJ25390	uc003ola.3	Q5T9G4	OTTHUMG00000014577	ENST00000373866.3:c.570G>T	chr6.hg19:g.35715163G>T		72.0	0.0		87.0	25.0	NM_145028	Q8NEB2|Q96LL8	Silent	SNP	ENST00000373866.3	hg19																																																																																				.	.		0.592	ARMC12-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040311.2	NM_145028		T	35715163	G	T	35715163	2	4	151	1	0	0	0	0	0	0	0	1	2374	1277	45	3		3	C6orf81	6	35715163	Silent	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	2542297	35715163	135399904	33	23296										
SENP6	26054	hgsc.bcm.edu	37	chr6	76344460	76344460	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cgtcattatgttctggaactGtagttcatggtagacgtttt	10	6	3	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr6:76344460G>T	ENST00000447266.2	+	5	869	c.391G>T	c.(391-393)Gta>Tta	p.V131L	SENP6_ENST00000370010.2_Missense_Mutation_p.V131L|SENP6_ENST00000327284.8_Missense_Mutation_p.V131L|SENP6_ENST00000370014.3_Missense_Mutation_p.V131L	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	131					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				TTCTGGAACTGTAGTTCATGG	0.318																																					p.V131L		Atlas-SNP	.											.	SENP6	189	.	0			c.G391T						.						115	105	108					6																	76344460		1870	4112	5982	SO:0001583	missense	26054	exon5			GGAACTGTAGTTC		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.391G>T	chr6.hg19:g.76344460G>T	ENSP00000402527:p.Val131Leu	84.0	0.0		122.0	29.0	NM_001100409	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	hg19	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.991363	0.54041	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000538088;ENST00000327284;ENST00000447266;ENST00000483859;ENST00000424947	T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73	5.83	0.511	0.16989	.	0.284063	0.33753	N	0.004597	T	0.28532	0.0706	M	0.62723	1.935	0.80722	D	1	B;B;B	0.26744	0.158;0.098;0.158	B;B;B	0.30029	0.11;0.051;0.11	T	0.28073	-1.0055	10	0.72032	D	0.01	-7.9296	10.8136	0.46562	0.4266:0.0:0.5734:0.0	.	131;131;131	Q9GZR1-2;Q9GZR1;F8W6D9	.;SENP6_HUMAN;.	L	131;131;131;131;131;22;21	ENSP00000359027:V131L;ENSP00000359031:V131L;ENSP00000321820:V131L;ENSP00000402527:V131L;ENSP00000426480:V22L;ENSP00000391426:V21L	ENSP00000321820:V131L	V	+	1	0	SENP6	76401180	0.986000	0.35501	0.997000	0.53966	0.945000	0.59286	0.637000	0.24659	0.130000	0.18549	-0.237000	0.12165	GTA	.	.		0.318	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		T	76344460	G	T	76344460	3	4	151	1	0	0	0	0	1	0	0	0	14065	1377	48	3	409	3	SENP6	6	76344460	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	40629297	76344460	94770607	34	23297										
MDN1	23195	hgsc.bcm.edu	37	chr6	90460121	90460121	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gtcagacgtgtaacaaccaaTgtactcctgaatatccgtgt	8	10	1	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr6:90460121T>C	ENST00000369393.3	-	24	3473	c.3358A>G	c.(3358-3360)Att>Gtt	p.I1120V	MDN1_ENST00000428876.1_Missense_Mutation_p.I1120V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1120					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TAACAACCAATGTACTCCTGA	0.443																																					p.I1120V		Atlas-SNP	.											.	MDN1	478	.	0			c.A3358G						.						233	199	211					6																	90460121		2203	4300	6503	SO:0001583	missense	23195	exon24			AACCAATGTACTC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.3358A>G	chr6.hg19:g.90460121T>C	ENSP00000358400:p.Ile1120Val	121.0	0.0		122.0	39.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.549947	0.45383	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.42131	0.98;0.98;0.98	5.59	5.59	0.84812	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.104322	0.64402	D	0.000005	T	0.26195	0.0639	N	0.26130	0.795	0.52501	D	0.999955	P	0.37207	0.587	B	0.44224	0.444	T	0.08722	-1.0708	10	0.34782	T	0.22	.	15.7669	0.78135	0.0:0.0:0.0:1.0	.	1120	Q9NU22	MDN1_HUMAN	V	1120;1120;1047	ENSP00000358400:I1120V;ENSP00000413970:I1120V;ENSP00000409664:I1047V	ENSP00000358400:I1120V	I	-	1	0	MDN1	90516842	1.000000	0.71417	0.997000	0.53966	0.362000	0.29581	7.364000	0.79526	2.130000	0.65690	0.402000	0.26972	ATT	.	.		0.443	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90460121	T	C	90460121	3	2	151	1	0	0	0	0	1	0	0	0	9424	1464	51	2	13748	2	MDN1	6	90460121	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	14115661	90460121	80654946	35	23298										
FSCN1	6624	hgsc.bcm.edu	37	chr7	5633032	5633032	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cgtaagcgctacgcgcacctGagcgcgcggccggccgacga	15	16	0	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr7:5633032G>A	ENST00000382361.3	+	1	579	c.465G>A	c.(463-465)ctG>ctA	p.L155L	FSCN1_ENST00000340250.6_Silent_p.L134L	NM_003088.3	NP_003079.1	Q16658	FSCN1_HUMAN	fascin actin-bundling protein 1	155					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|cell motility (GO:0048870)|cell proliferation (GO:0008283)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|invadopodium (GO:0071437)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|drug binding (GO:0008144)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)		ACGCGCACCTGAGCGCGCGGC	0.687																																					p.L155L		Atlas-SNP	.											.	FSCN1	29	.	0			c.G465A						.						31	26	28					7																	5633032		2193	4290	6483	SO:0001819	synonymous_variant	6624	exon1			GCACCTGAGCGCG	U03057	CCDS5342.1	7p22	2014-02-03	2014-02-03	2002-09-20	ENSG00000075618	ENSG00000075618		"Fascins"	11148	protein-coding gene	gene with protein product	"Singed, drosophila, homolog-like", "actin bundling protein"	602689	"singed (Drosophila)-like (sea urchin fascin homolog like)", "fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus)"	SNL		8068206, 10783262	Standard	NM_003088		Approved	p55, FLJ38511	uc003sou.3	Q16658	OTTHUMG00000090599	ENST00000382361.3:c.465G>A	chr7.hg19:g.5633032G>A		200.0	0.0		244.0	74.0	NM_003088	A6NI89|B2RE97|Q96IC5|Q96IH1|Q9BRF1	Silent	SNP	ENST00000382361.3	hg19	CCDS5342.1																																																																																			.	.		0.687	FSCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207153.3	NM_003088		A	5633032	G	A	5633032	2	1	151	1	0	0	0	0	0	0	0	1	6075	1277	45	3		3	FSCN1	7	5633032	Silent	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		5633032	153505631	36	23299										
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80374511	80374511	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	agttgatcttggctatggtcTgcttgaaactattttctgta	9	6	3	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr7:80374511T>C	ENST00000265361.3	-	18	2516	c.1955A>G	c.(1954-1956)cAg>cGg	p.Q652R	SEMA3C_ENST00000419255.2_Missense_Mutation_p.Q652R|SEMA3C_ENST00000544525.1_Missense_Mutation_p.Q670R	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	652	Ig-like C2-type.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GGCTATGGTCTGCTTGAAACT	0.473																																					p.Q652R		Atlas-SNP	.											.	SEMA3C	106	.	0			c.A1955G						.						83	79	80					7																	80374511		2203	4300	6503	SO:0001583	missense	10512	exon18			ATGGTCTGCTTGA	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"Semaphorins", "Immunoglobulin superfamily / I-set domain containing"	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1955A>G	chr7.hg19:g.80374511T>C	ENSP00000265361:p.Gln652Arg	126.0	0.0		116.0	24.0	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	hg19	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.226688	0.39300	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	T;T;T	0.67865	-0.29;-0.29;-0.29	5.56	5.56	0.83823	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.051625	0.85682	D	0.000000	T	0.50086	0.1595	N	0.11870	0.19	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.11329	0.003;0.006	T	0.43442	-0.9391	10	0.30854	T	0.27	.	15.7177	0.77681	0.0:0.0:0.0:1.0	.	670;652	F5H1Z7;Q99985	.;SEM3C_HUMAN	R	652;652;670	ENSP00000265361:Q652R;ENSP00000411193:Q652R;ENSP00000445649:Q670R	ENSP00000265361:Q652R	Q	-	2	0	SEMA3C	80212447	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.628000	0.67791	2.130000	0.65690	0.528000	0.53228	CAG	.	.		0.473	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		C	80374511	T	C	80374511	3	2	151	1	0	0	0	0	1	0	0	0	14041	1580	55	2	304	2	SEMA3C	7	80374511	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	74741479	80374511	78764152	37	23300										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83610774	83610774	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	agctgggcaaccccagccgtTgaaccaatatatagttgttg	10	10	0	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr7:83610774T>A	ENST00000265362.4	-	14	1829	c.1515A>T	c.(1513-1515)tcA>tcT	p.S505S	SEMA3A_ENST00000436949.1_Silent_p.S505S	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	505	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CCCCAGCCGTTGAACCAATAT	0.433																																					p.S505S		Atlas-SNP	.											.	SEMA3A	121	.	0			c.A1515T						.						55	56	55					7																	83610774		2203	4300	6503	SO:0001819	synonymous_variant	10371	exon14			AGCCGTTGAACCA	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1515A>T	chr7.hg19:g.83610774T>A		135.0	0.0		161.0	33.0	NM_006080		Silent	SNP	ENST00000265362.4	hg19	CCDS5599.1																																																																																			.	.		0.433	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		A	83610774	T	A	83610774	2	1	151	1	0	0	0	0	0	0	0	1	14039	1799	63	4		4	SEMA3A	7	83610774	Silent	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	3236263	83610774	75527889	38	23301										
PODXL	5420	hgsc.bcm.edu	37	chr7	131241029	131241029	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ggccactcaccattctgggaGggcgacggcgacggcgacgg	17	13	2	0	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000322985.9_Silent_p.P30P|PODXL_ENST00000541194.1_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		Atlas-SNP	.											.	PODXL	53	.	0			c.C90G						.						5	7	6					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	chr7.hg19:g.131241029G>C		92.0	0.0		127.0	10.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		C	131241029	G	C	131241029	2	2	151	1	0	0	0	0	0	0	0	1	12189	987	35	4		4	PODXL	7	131241029	Silent	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	47630255	131241029	27897634	39	23302			1	25		2	2	27	N	G_A	7.138742e-05
PODXL	5420	hgsc.bcm.edu	37	chr7	131241055	131241055	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cggcgacggcgacggcgacgAcggcagcagcggcggcgttg	20	13	0	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr7:131241055A>G	ENST00000378555.3	-	1	311	c.64T>C	c.(64-66)Tcg>Ccg	p.S22P	PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Missense_Mutation_p.S22P|PODXL_ENST00000322985.9_Missense_Mutation_p.S22P|PODXL_ENST00000541194.1_Missense_Mutation_p.S22P			O00592	PODXL_HUMAN	podocalyxin-like	22					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					gacggcgacgacggcagcagc	0.741																																					p.S22P		Atlas-SNP	.											.	PODXL	53	.	0			c.T64C						.						5	8	7					7																	131241055		1914	3836	5750	SO:0001583	missense	5420	exon1			GCGACGACGGCAG		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.64T>C	chr7.hg19:g.131241055A>G	ENSP00000367817:p.Ser22Pro	101.0	0.0		130.0	9.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	hg19	CCDS34755.1	.	.	.	.	.	.	.	.	.	.	A	10.93	1.488975	0.26686	.	.	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000378555;ENST00000322985	T;T;T;T	0.12774	2.82;2.65;2.82;2.85	.	.	.	.	7739.210000	0.00166	U	0.000000	T	0.08670	0.0215	N	0.14661	0.345	0.09310	N	0.999994	.	.	.	.	.	.	T	0.24728	-1.0152	6	0.29301	T	0.29	.	.	.	.	.	22;22	O00592-2;O00592	.;PODXL_HUMAN	P	22	ENSP00000440518:S22P;ENSP00000442655:S22P;ENSP00000367817:S22P;ENSP00000319782:S22P	ENSP00000319782:S22P	S	-	1	0	PODXL	130891595	0.001000	0.12720	0.027000	0.17364	0.027000	0.11550	0.743000	0.26231	0.056000	0.16144	0.055000	0.15244	TCG	.	.		0.741	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		G	131241055	A	G	131241055	3	3	151	1	0	0	0	0	1	0	0	0	12189	275	10	2	1648	2	PODXL	7	131241055	Missense_Mutation	SNP	A	TCGA-DD-AAC9-01A-11D-A40R-10	26	131241055	27897608	40	23303			1	25		2	2	27	N	G_A	7.138742e-05
BNIP3L	665	hgsc.bcm.edu	37	chr8	26265768	26265768	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tccacttcagacaccctaaaCgttctgtgtctttaagcatg	6	12	3	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr8:26265768C>T	ENST00000380629.2	+	5	720	c.487C>T	c.(487-489)Cgt>Tgt	p.R163C	BNIP3L_ENST00000518611.1_Missense_Mutation_p.R123C|BNIP3L_ENST00000521254.1_3'UTR|BNIP3L_ENST00000520409.1_Missense_Mutation_p.R123C|BNIP3L_ENST00000523515.1_Missense_Mutation_p.R123C	NM_004331.2	NP_004322.1	O60238	BNI3L_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 3-like	163					defense response to virus (GO:0051607)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrial protein catabolic process (GO:0035694)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			large_intestine(3)|lung(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0019)|Epithelial(17;1.59e-12)|all cancers(2;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(2;2.57e-08)|Colorectal(74;0.135)		ACACCCTAAACGTTCTGTGTC	0.448																																					p.R163C		Atlas-SNP	.											.	BNIP3L	7	.	0			c.C487T						.						86	83	84					8																	26265768		2203	4300	6503	SO:0001583	missense	665	exon5			CCTAAACGTTCTG	AB004788	CCDS6050.1	8p21	2014-05-13	2002-08-29		ENSG00000104765	ENSG00000104765			1085	protein-coding gene	gene with protein product		605368	"BCL2/adenovirus E1B 19kD-interacting protein 3-like"			9523198, 9973195	Standard	NM_004331		Approved	Nix, BNIP3a	uc003xex.1	O60238	OTTHUMG00000099433	ENST00000380629.2:c.487C>T	chr8.hg19:g.26265768C>T	ENSP00000370003:p.Arg163Cys	139.0	0.0		127.0	38.0	NM_004331	B0AZS9|Q5JW63|Q8NF87	Missense_Mutation	SNP	ENST00000380629.2	hg19	CCDS6050.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.494572	0.85069	.	.	ENSG00000104765	ENST00000380629;ENST00000221209;ENST00000523949;ENST00000523515;ENST00000520409;ENST00000518611	.	.	.	6.16	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.79015	0.4375	M	0.84326	2.69	0.80722	D	1	D;D	0.76494	0.999;0.999	P;D	0.63597	0.877;0.916	T	0.82752	-0.0302	9	0.87932	D	0	.	14.5092	0.67772	0.2672:0.7328:0.0:0.0	.	123;163	B0AZS9;O60238	.;BNI3L_HUMAN	C	163;163;141;123;123;123	.	ENSP00000221209:R163C	R	+	1	0	BNIP3L	26321685	1.000000	0.71417	0.762000	0.31397	0.986000	0.74619	5.618000	0.67722	1.598000	0.50083	0.650000	0.86243	CGT	.	.		0.448	BNIP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216895.1	NM_004331		T	26265768	C	T	26265768	3	4	151	1	0	0	0	0	1	0	0	0	1479	536	19	1	505	1	BNIP3L	8	26265768	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10		26265768	120098254	41	23304										
RIMS2	9699	hgsc.bcm.edu	37	chr8	104778484	104778484	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gtatgtaatttgtgccgaaaAcaacaagaaatcctcactaa	6	8	1	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr8:104778484A>G	ENST00000406091.3	+	3	417	c.417A>G	c.(415-417)aaA>aaG	p.K139K		NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	170	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TGTGCCGAAAACAACAAGAAA	0.358										HNSCC(12;0.0054)																											p.K139K		Atlas-SNP	.											.	RIMS2	1357	.	0			c.A417G						.						78	73	74					8																	104778484		1860	4096	5956	SO:0001819	synonymous_variant	9699	exon3			CCGAAAACAACAA	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000406091.3:c.417A>G	chr8.hg19:g.104778484A>G		132.0	0.0		199.0	30.0	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000406091.3	hg19	CCDS55269.1																																																																																			.	.		0.358	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001100117		G	104778484	A	G	104778484	2	3	151	1	0	0	0	0	0	0	0	1	13383	40	2	2		2	RIMS2	8	104778484	Silent	SNP	A	TCGA-DD-AAC9-01A-11D-A40R-10	78512716	104778484	41585538	42	23305										
HAUS6	54801	hgsc.bcm.edu	37	chr9	19102558	19102558	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gcgacacgatctttccgcagGcaatggttgccgggcctggc	14	13	1	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr9:19102558G>A	ENST00000380502.3	-	1	559	c.92C>T	c.(91-93)gCc>gTc	p.A31V		NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	31					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTTTCCGCAGGCAATGGTTGC	0.682																																					p.A31V		Atlas-SNP	.											.	HAUS6	66	.	0			c.C92T						.						34	37	36					9																	19102558		2203	4299	6502	SO:0001583	missense	54801	exon1			CCGCAGGCAATGG	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"HAUS augmin-like complex subunits"	25948	protein-coding gene	gene with protein product		613433	"family with sequence similarity 29, member A"	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.92C>T	chr9.hg19:g.19102558G>A	ENSP00000369871:p.Ala31Val	204.0	0.0		218.0	59.0	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	hg19	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	G	9.349	1.064996	0.20067	.	.	ENSG00000147874	ENST00000380502	T	0.22945	1.93	5.52	2.13	0.27403	.	0.626539	0.17585	N	0.168973	T	0.20007	0.0481	L	0.57536	1.79	0.18873	N	0.999984	B	0.25955	0.138	B	0.28465	0.09	T	0.18935	-1.0321	10	0.33141	T	0.24	1.4026	1.1407	0.01765	0.1911:0.151:0.4312:0.2268	.	31	Q7Z4H7	HAUS6_HUMAN	V	31	ENSP00000369871:A31V	ENSP00000369871:A31V	A	-	2	0	HAUS6	19092558	0.140000	0.22579	0.010000	0.14722	0.138000	0.21146	1.141000	0.31528	0.770000	0.33336	-0.175000	0.13238	GCC	.	.		0.682	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645		A	19102558	G	A	19102558	3	1	151	1	0	0	0	0	1	0	0	0	6979	1203	42	3	2843	3	HAUS6	9	19102558	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		19102558	122110873	43	23306										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21971101	21971101	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tgtccaggaagccctcccggGcagcgtcgtgcacgggtcgg	16	14	0	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr9:21971101G>T	ENST00000304494.5	-	2	527	c.257C>A	c.(256-258)gCc>gAc	p.A86D	CDKN2A_ENST00000579755.1_Nonsense_Mutation_p.C100*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000361570.3_Nonsense_Mutation_p.C141*|CDKN2A_ENST00000498124.1_Missense_Mutation_p.A86D|CDKN2A_ENST00000530628.2_Nonsense_Mutation_p.C100*|CDKN2A_ENST00000578845.2_Missense_Mutation_p.A35D|CDKN2A_ENST00000497750.1_Missense_Mutation_p.A35D|CDKN2A_ENST00000479692.2_Missense_Mutation_p.A35D|CDKN2A_ENST00000498628.2_Missense_Mutation_p.A35D|CDKN2A_ENST00000494262.1_Missense_Mutation_p.A35D|CDKN2A_ENST00000579122.1_Missense_Mutation_p.A86D|CDKN2A_ENST00000446177.1_Missense_Mutation_p.A86D	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	86					cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(44)|p.H83fs*2(2)|p.D84_F90del(1)|p.0(1)|p.V82_G89>G(1)|p.E61_L94del(1)|p.R137fs*48(1)|p.A68fs*3(1)|p.A86fs*34(1)|p.V82_E88del(1)|p.A86V(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GCCCTCCCGGGCAGCGTCGTG	0.746		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.C100X		Atlas-SNP	.											CDKN2A,NS,carcinoma,0,1	CDKN2A	4810	.	1370	Whole gene deletion(1316)|Unknown(44)|Deletion - Frameshift(4)|Deletion - In frame(3)|Insertion - Frameshift(1)|Complex - deletion inframe(1)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(283)|skin(175)|central_nervous_system(167)|lung(148)|urinary_tract(91)|bone(74)|soft_tissue(57)|oesophagus(52)|pleura(51)|upper_aerodigestive_tract(50)|ovary(36)|kidney(32)|breast(32)|pancreas(31)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(9)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.C300A						.						12	15	14					9																	21971101		2171	4256	6427	SO:0001583	missense	1029	exon2			TCCCGGGCAGCGT	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.257C>A	chr9.hg19:g.21971101G>T	ENSP00000307101:p.Ala86Asp	139.0	0.0		133.0	43.0	NM_058195	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Nonsense_Mutation	SNP	ENST00000304494.5	hg19	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.491908|8.491908	0.98834|0.98834	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000304494;ENST00000446177|ENST00000361570;ENST00000530628	T;T|.	0.72615|.	-0.67;-0.67|.	5.93|5.93	5.93|5.93	0.95920|0.95920	Ankyrin repeat-containing domain (4);|.	.|1.401910	.|0.04941	.|N	.|0.458690	T|.	0.74824|.	0.3767|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	D|.	0.76494|.	0.999|.	P|.	0.60173|.	0.87|.	T|.	0.68534|.	-0.5383|.	7|.	0.87932|0.72032	D|D	0|0.01	-12.7152|-12.7152	19.1221|19.1221	0.93367|0.93367	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	86|.	P42771|.	CD2A1_HUMAN|.	D|X	86|141;100	ENSP00000307101:A86D;ENSP00000394932:A86D|.	ENSP00000307101:A86D|ENSP00000355153:C141X	A|C	-|-	2|3	0|2	CDKN2A|CDKN2A	21961101|21961101	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.959000|0.959000	0.62525|0.62525	8.665000|8.665000	0.91144|0.91144	2.808000|2.808000	0.96608|0.96608	0.655000|0.655000	0.94253|0.94253	GCC|TGC	.	.		0.746	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		T	21971101	G	T	21971101	3	4	151	1	0	0	0	0	1	0	0	0	3163	1204	42	3	221	3	CDKN2A	9	21971101	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	2868543	21971101	119242330	44	23307										
FGD3	89846	hgsc.bcm.edu	37	chr9	95780428	95780428	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gccccttcaggtgcaggataTcgtcaagccaaacacagcac	9	14	2	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr9:95780428T>A	ENST00000375482.3	+	11	1782	c.1286T>A	c.(1285-1287)aTc>aAc	p.I429N	FGD3_ENST00000538555.1_Missense_Mutation_p.I32N|FGD3_ENST00000337352.6_Missense_Mutation_p.I429N|FGD3_ENST00000416701.2_Missense_Mutation_p.I429N	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	429	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						GTGCAGGATATCGTCAAGCCA	0.463																																					p.I429N		Atlas-SNP	.											.	FGD3	116	.	0			c.T1286A						.						124	124	124					9																	95780428		1966	4166	6132	SO:0001583	missense	89846	exon11			AGGATATCGTCAA	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16027	protein-coding gene	gene with protein product			"FGD1 family, member 3"			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.1286T>A	chr9.hg19:g.95780428T>A	ENSP00000364631:p.Ile429Asn	80.0	0.0		65.0	19.0	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Missense_Mutation	SNP	ENST00000375482.3	hg19	CCDS43849.1	.	.	.	.	.	.	.	.	.	.	T	1.998	-0.430075	0.04701	.	.	ENSG00000127084	ENST00000375482;ENST00000416701;ENST00000337352;ENST00000538555	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	4.7	-2.41	0.06562	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.679389	0.12147	N	0.495305	T	0.72415	0.3457	N	0.17474	0.49	0.18873	N	0.999984	B;B;B	0.11235	0.003;0.004;0.001	B;B;B	0.13407	0.005;0.009;0.009	T	0.58295	-0.7661	10	0.41790	T	0.15	.	5.645	0.17584	0.0:0.3628:0.2595:0.3777	.	429;429;429	Q5JSP0-2;F8W7P2;Q5JSP0	.;.;FGD3_HUMAN	N	429;429;429;32	ENSP00000364631:I429N;ENSP00000413833:I429N;ENSP00000336914:I429N;ENSP00000442560:I32N	ENSP00000336914:I429N	I	+	2	0	FGD3	94820249	0.077000	0.21312	0.006000	0.13384	0.029000	0.11900	-0.428000	0.06991	-0.265000	0.09352	-0.411000	0.06167	ATC	.	.		0.463	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086		A	95780428	T	A	95780428	3	1	151	1	0	0	0	0	1	0	0	0	5842	1435	50	4	1320	4	FGD3	9	95780428	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	73809327	95780428	45433003	45	23308										
FKBP15	23307	hgsc.bcm.edu	37	chr9	115959216	115959216	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	agagagtttcactcacccgcCtaacctccacctcgaacacc	5	18	2	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr9:115959216C>A	ENST00000238256.3	-	9	977	c.860G>T	c.(859-861)aGg>aTg	p.R287M		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	287	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						ACTCACCCGCCTAACCTCCAC	0.463																																					p.R287M		Atlas-SNP	.											.	FKBP15	128	.	0			c.G860T						.						82	82	82					9																	115959216		1967	4137	6104	SO:0001583	missense	23307	exon9			ACCCGCCTAACCT	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23397	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 76", "WASP and FKBP-like protein"		"KIAA0674"	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.860G>T	chr9.hg19:g.115959216C>A	ENSP00000238256:p.Arg287Met	103.0	0.0		120.0	19.0	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	hg19	CCDS48007.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.069615	0.55539	.	.	ENSG00000119321	ENST00000446284;ENST00000238256;ENST00000414250	T;T;T	0.42131	0.98;0.98;0.98	5.33	-0.433	0.12287	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (1);	.	.	.	.	T	0.38799	0.1054	L	0.27053	0.805	0.31269	N	0.692028	P;P;D	0.53462	0.951;0.895;0.96	P;P;P	0.56514	0.698;0.532;0.8	T	0.46205	-0.9208	9	0.72032	D	0.01	-3.7993	5.5401	0.17033	0.0:0.4308:0.1415:0.4278	.	287;287;287	Q5T1M5-2;Q5T1M5-3;Q5T1M5	.;.;FKB15_HUMAN	M	312;287;312	ENSP00000416158:R312M;ENSP00000238256:R287M;ENSP00000415733:R312M	ENSP00000238256:R287M	R	-	2	0	FKBP15	114999037	0.729000	0.28090	0.987000	0.45799	0.563000	0.35712	0.675000	0.25232	0.003000	0.14656	-0.136000	0.14681	AGG	.	.		0.463	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258		A	115959216	C	A	115959216	3	1	151	1	0	0	0	0	1	0	0	0	5913	681	24	3	2879	3	FKBP15	9	115959216	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	20178788	115959216	25254215	46	23309										
CCDC7	79741	hgsc.bcm.edu	37	chr10	32833205	32833205	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ccagaaaaagagtttaaaatAaaagaagatttggatcaagt	8	3	1	4			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr10:32833205A>G	ENST00000362006.5	+	14	1653	c.1110A>G	c.(1108-1110)atA>atG	p.I370M	C10orf68_ENST00000572165.1_3'UTR|CCDC7_ENST00000277657.6_Missense_Mutation_p.I370M	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	370										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				AGTTTAAAATAAAAGAAGATT	0.303																																					p.I370M		Atlas-SNP	.											CCDC7,parotid,carcinoma,0,1	CCDC7	47	.	0			c.A1110G						.						80	83	82					10																	32833205		2203	4286	6489	SO:0001583	missense	221016	exon14			TAAAATAAAAGAA	BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 68"	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.1110A>G	chr10.hg19:g.32833205A>G	ENSP00000355078:p.Ile370Met	396.0	0.0		417.0	127.0	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Missense_Mutation	SNP	ENST00000362006.5	hg19	CCDS7173.1	.	.	.	.	.	.	.	.	.	.	A	9.396	1.076804	0.20227	.	.	ENSG00000216937	ENST00000277657;ENST00000362006;ENST00000435402	T;T;T	0.55930	1.34;1.34;0.49	3.19	-0.791	0.10929	.	.	.	.	.	T	0.29588	0.0738	N	0.19112	0.55	0.09310	N	0.999997	B	0.14012	0.009	B	0.14023	0.01	T	0.20207	-1.0282	9	0.46703	T	0.11	-38.2876	0.5368	0.00638	0.4384:0.2199:0.1286:0.2132	.	370	Q96M83	CCDC7_HUMAN	M	370;370;39	ENSP00000277657:I370M;ENSP00000355078:I370M;ENSP00000401923:I39M	ENSP00000277657:I370M	I	+	3	3	CCDC7	32873211	0.000000	0.05858	0.064000	0.19789	0.308000	0.27856	-0.035000	0.12205	-0.154000	0.11118	0.528000	0.53228	ATA	.	.		0.303	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023		G	32833205	A	G	32833205	3	3	151	1	0	0	0	0	1	0	0	0	2844	352	13	2	1160	2	CCDC7	10	32833205	Missense_Mutation	SNP	A	TCGA-DD-AAC9-01A-11D-A40R-10		32833205	102701542	47	23310										
DENND5A	23258	hgsc.bcm.edu	37	chr11	9225351	9225351	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	acttggtctctggcagattaTtggcccatagaccccagaaa	9	11	1	3			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:9225351T>C	ENST00000328194.3	-	4	1125	c.805A>G	c.(805-807)Ata>Gta	p.I269V	DENND5A_ENST00000530044.1_Missense_Mutation_p.I269V	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	269	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TGGCAGATTATTGGCCCATAG	0.507																																					p.I269V		Atlas-SNP	.											.	DENND5A	84	.	0			c.A805G						.						66	71	69					11																	9225351		2201	4296	6497	SO:0001583	missense	23258	exon4			AGATTATTGGCCC	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"DENN/MADD domain containing"	19344	protein-coding gene	gene with protein product			"RAB6 interacting protein 1"	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.805A>G	chr11.hg19:g.9225351T>C	ENSP00000328524:p.Ile269Val	163.0	0.0		198.0	43.0	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	hg19	CCDS31423.1	.	.	.	.	.	.	.	.	.	.	T	7.933	0.741139	0.15642	.	.	ENSG00000184014	ENST00000328194;ENST00000530044	T;T	0.12039	2.72;2.72	5.31	1.64	0.23874	DENN (3);	0.259259	0.44688	N	0.000440	T	0.10551	0.0258	L	0.41906	1.305	0.80722	D	1	B;B	0.14805	0.011;0.003	B;B	0.22880	0.042;0.024	T	0.20472	-1.0274	10	0.23302	T	0.38	.	8.4273	0.32735	0.0:0.2402:0.0:0.7598	.	269;269	E9PS91;Q6IQ26	.;DEN5A_HUMAN	V	269	ENSP00000328524:I269V;ENSP00000435866:I269V	ENSP00000328524:I269V	I	-	1	0	DENND5A	9181927	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.629000	0.37071	0.027000	0.15297	0.528000	0.53228	ATA	.	.		0.507	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		C	9225351	T	C	9225351	3	2	151	1	0	0	0	0	1	0	0	0	4438	1493	52	2	3138	2	DENND5A	11	9225351	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10		9225351	125781165	48	23311										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17496563	17496563	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gatgtgcaccttggagctctGacttccccatcctgcaggga	11	13	1	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:17496563G>A	ENST00000389817.3	-	2	228	c.160C>T	c.(160-162)Cag>Tag	p.Q54*	ABCC8_ENST00000302539.4_Nonsense_Mutation_p.Q54*			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	54					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	TTGGAGCTCTGACTTCCCCAT	0.582																																					p.Q54X		Atlas-SNP	.											.	ABCC8	170	.	0			c.C160T	GRCh37	CM086731	ABCC8	M		.						176	110	132					11																	17496563		2200	4293	6493	SO:0001587	stop_gained	6833	exon2			AGCTCTGACTTCC	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.160C>T	chr11.hg19:g.17496563G>A	ENSP00000374467:p.Gln54*	92.0	0.0		114.0	22.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Nonsense_Mutation	SNP	ENST00000389817.3	hg19	CCDS31437.1	.	.	.	.	.	.	.	.	.	.	G	38	6.795783	0.97845	.	.	ENSG00000006071	ENST00000389817;ENST00000302539;ENST00000379493	.	.	.	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	18.7138	0.91668	0.0:0.0:1.0:0.0	.	.	.	.	X	54;54;68	.	ENSP00000303960:Q54X	Q	-	1	0	ABCC8	17453139	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.854000	0.99522	2.414000	0.81942	0.585000	0.79938	CAG	.	.		0.582	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		A	17496563	G	A	17496563	4	1	151	1	0	0	0	0	0	1	0	0	58	1299	45	3	4737	3	ABCC8	11	17496563	Nonsense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	8271212	17496563	117509953	49	23312										
CHST1	8534	hgsc.bcm.edu	37	chr11	45672282	45672282	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ctgcgcgtggtggccaggatGaggatgtgggtcttgcggga	20	7	1	1	rs200379237		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:45672282G>A	ENST00000308064.2	-	4	862	c.192C>T	c.(190-192)ctC>ctT	p.L64L	CHST1_ENST00000533673.1_5'Flank|RP11-495O11.1_ENST00000525563.1_RNA	NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	64					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	keratan sulfotransferase activity (GO:0045130)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(10)|lung(17)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)		TGGCCAGGATGAGGATGTGGG	0.647																																					p.L64L		Atlas-SNP	.											.	CHST1	81	.	0			c.C192T						.						83	80	81					11																	45672282		2203	4299	6502	SO:0001819	synonymous_variant	8534	exon4			CAGGATGAGGATG	U65637	CCDS7913.1	11p11.2	2010-04-29			ENSG00000175264	ENSG00000175264		"Sulfotransferases, membrane-bound"	1969	protein-coding gene	gene with protein product		603797				9405439, 9639683	Standard	NM_003654		Approved	C6ST, KSGal6ST	uc001mys.2	O43916		ENST00000308064.2:c.192C>T	chr11.hg19:g.45672282G>A		113.0	0.0		132.0	6.0	NM_003654	D3DQP2	Silent	SNP	ENST00000308064.2	hg19	CCDS7913.1																																																																																			.	G|0.999;A|0.001		0.647	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654		A	45672282	G	A	45672282	2	1	151	1	0	0	0	0	0	0	0	1	3399	1277	45	3		3	CHST1	11	45672282	Silent	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	28175719	45672282	89334234	50	23313										
OR5L2	26338	hgsc.bcm.edu	37	chr11	55594822	55594822	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	agtcacgttgttagccaatcTgggcatgactgcactgattc	10	10	2	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:55594822T>A	ENST00000378397.1	+	1	128	c.128T>A	c.(127-129)cTg>cAg	p.L43Q		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	43						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				TTAGCCAATCTGGGCATGACT	0.493										HNSCC(27;0.073)																											p.L43Q		Atlas-SNP	.											.	OR5L2	135	.	0			c.T128A						.						324	283	297					11																	55594822		2200	4296	6496	SO:0001583	missense	26338	exon1			CCAATCTGGGCAT	AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"GPCR / Class A : Olfactory receptors"	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.128T>A	chr11.hg19:g.55594822T>A	ENSP00000367650:p.Leu43Gln	102.0	0.0		94.0	23.0	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	hg19	CCDS31511.1	.	.	.	.	.	.	.	.	.	.	.	12.63	1.996585	0.35226	.	.	ENSG00000205030	ENST00000378397	T	0.00433	7.43	5.31	5.31	0.75309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38663	N	0.001608	T	0.02156	0.0067	H	0.97186	3.955	0.09310	N	1	D	0.89917	1.0	D	0.70487	0.969	T	0.15752	-1.0426	10	0.87932	D	0	-12.0656	14.5472	0.68041	0.0:0.0:0.0:1.0	.	43	Q8NGL0	OR5L2_HUMAN	Q	43	ENSP00000367650:L43Q	ENSP00000367650:L43Q	L	+	2	0	OR5L2	55351398	0.001000	0.12720	0.965000	0.40720	0.160000	0.22226	1.202000	0.32271	2.173000	0.68751	0.509000	0.49947	CTG	.	.		0.493	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739		A	55594822	T	A	55594822	3	1	151	1	0	0	0	0	1	0	0	0	11180	1580	55	4	130	4	OR5L2	11	55594822	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	9922540	55594822	79411694	51	23314										
DCUN1D5	84259	hgsc.bcm.edu	37	chr11	102935046	102935046	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	actaagatcagcatggactgTtctgctgaattctaatacat	7	8	3	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:102935046T>A	ENST00000260247.5	-	7	958	c.616A>T	c.(616-618)Aca>Tca	p.T206S	DCUN1D5_ENST00000531543.1_Missense_Mutation_p.T121S	NM_032299.3	NP_115675.1	Q9BTE7	DCNL5_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 5	206	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.									NS(1)|central_nervous_system(1)|endometrium(2)	4		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.00032)|Epithelial(105;0.0689)|all cancers(92;0.186)		GCATGGACTGTTCTGCTGAAT	0.269																																					p.T206S		Atlas-SNP	.											.	DCUN1D5	11	.	0			c.A616T						.						135	130	131					11																	102935046		2202	4294	6496	SO:0001583	missense	84259	exon7			GGACTGTTCTGCT		CCDS8325.1	11q22.3	2013-06-10	2013-06-10		ENSG00000137692	ENSG00000137692			28409	protein-coding gene	gene with protein product			"DCN1, defective in cullin neddylation 1, domain containing 5 (S. cerevisiae)"			15988528	Standard	NM_032299		Approved	MGC2714, FLJ32431	uc001phm.3	Q9BTE7	OTTHUMG00000165822	ENST00000260247.5:c.616A>T	chr11.hg19:g.102935046T>A	ENSP00000260247:p.Thr206Ser	55.0	0.0		74.0	20.0	NM_032299	Q3ZTT2	Missense_Mutation	SNP	ENST00000260247.5	hg19	CCDS8325.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846962	0.71603	.	.	ENSG00000137692	ENST00000260247;ENST00000531543	T	0.21734	1.99	5.91	5.91	0.95273	Domain of unknown function DUF298 (2);	0.000000	0.85682	D	0.000000	T	0.21509	0.0518	L	0.38953	1.18	0.80722	D	1	B	0.26672	0.156	B	0.33799	0.17	T	0.05566	-1.0877	10	0.20519	T	0.43	-12.7153	16.35	0.83199	0.0:0.0:0.0:1.0	.	206	Q9BTE7	DCNL5_HUMAN	S	206;121	ENSP00000260247:T206S	ENSP00000260247:T206S	T	-	1	0	DCUN1D5	102440256	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	8.040000	0.89188	2.270000	0.75569	0.528000	0.53228	ACA	.	.		0.269	DCUN1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386382.2	NM_032299		A	102935046	T	A	102935046	3	1	151	1	0	0	0	0	1	0	0	0	4319	1725	60	4	105	4	DCUN1D5	11	102935046	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	47340224	102935046	32071470	52	23315										
OR8D4	338662	hgsc.bcm.edu	37	chr11	123777473	123777473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tgtttgtgttatttctgaatGctacatgctggcagccatgg	11	7	1	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:123777473G>A	ENST00000321355.2	+	1	365	c.335G>A	c.(334-336)tGc>tAc	p.C112Y		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		ATTTCTGAATGCTACATGCTG	0.478																																					p.C112Y		Atlas-SNP	.											.	OR8D4	62	.	0			c.G335A						.						200	195	197					11																	123777473		2202	4299	6501	SO:0001583	missense	338662	exon1			CTGAATGCTACAT	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"GPCR / Class A : Olfactory receptors"	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.335G>A	chr11.hg19:g.123777473G>A	ENSP00000325381:p.Cys112Tyr	86.0	0.0		79.0	19.0	NM_001005197	Q6IFE9	Missense_Mutation	SNP	ENST00000321355.2	hg19	CCDS31698.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.747228	0.49257	.	.	ENSG00000181518	ENST00000321355	T	0.00463	7.25	5.68	4.77	0.60923	GPCR, rhodopsin-like superfamily (1);	0.129861	0.35677	N	0.003052	T	0.00754	0.0025	M	0.80847	2.515	0.32616	N	0.523972	P	0.45986	0.87	P	0.46320	0.512	T	0.41680	-0.9495	10	0.52906	T	0.07	.	9.758	0.40515	0.0774:0.1416:0.781:0.0	.	112	Q8NGM9	OR8D4_HUMAN	Y	112	ENSP00000325381:C112Y	ENSP00000325381:C112Y	C	+	2	0	OR8D4	123282683	0.055000	0.20627	0.989000	0.46669	0.819000	0.46315	0.496000	0.22499	1.405000	0.46838	0.561000	0.74099	TGC	.	.		0.478	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197		A	123777473	G	A	123777473	3	1	151	1	0	0	0	0	1	0	0	0	11242	1319	46	3	337	3	OR8D4	11	123777473	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	20842427	123777473	11229043	53	23316										
AMHR2	269	hgsc.bcm.edu	37	chr12	53825147	53825147	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	aagactgtacttcaattcctGcccctaccatcctcccctgt	4	17	1	1	rs116281343		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr12:53825147G>T	ENST00000257863.4	+	11	1692	c.1612G>T	c.(1612-1614)Gcc>Tcc	p.A538S	AMHR2_ENST00000379791.3_Missense_Mutation_p.A443S|AMHR2_ENST00000550311.1_3'UTR	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	538					Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	TTCAATTCCTGCCCCTACCAT	0.602																																					p.A538S		Atlas-SNP	.											.	AMHR2	61	.	0			c.G1612T						.						122	103	110					12																	53825147		2203	4300	6503	SO:0001583	missense	269	exon11			ATTCCTGCCCCTA	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"Muellerian inhibiting substance type II receptor"	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.1612G>T	chr12.hg19:g.53825147G>T	ENSP00000257863:p.Ala538Ser	86.0	0.0		85.0	22.0	NM_020547	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Missense_Mutation	SNP	ENST00000257863.4	hg19	CCDS8858.1	.	.	.	.	.	.	.	.	.	.	G	9.890	1.203978	0.22205	.	.	ENSG00000135409	ENST00000257863;ENST00000379791	D;D	0.93659	-3.14;-3.26	4.86	1.91	0.25777	.	0.209202	0.24245	N	0.040237	T	0.82079	0.4959	N	0.12182	0.205	0.21020	N	0.99981	B	0.13594	0.008	B	0.06405	0.002	T	0.67389	-0.5683	10	0.22109	T	0.4	.	4.7842	0.13217	0.2333:0.2907:0.4761:0.0	.	538	Q16671	AMHR2_HUMAN	S	538;443	ENSP00000257863:A538S;ENSP00000369117:A443S	ENSP00000257863:A538S	A	+	1	0	AMHR2	52111414	0.003000	0.15002	0.269000	0.24586	0.764000	0.43329	0.244000	0.18124	0.301000	0.22738	0.563000	0.77884	GCC	.	G|0.999;A|0.001		0.602	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547		T	53825147	G	T	53825147	3	4	151	1	0	0	0	0	1	0	0	0	573	1319	46	3	1654	3	AMHR2	12	53825147	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		53825147	80026748	54	23317										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112721009	112721009	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tataccgagaaagtctacttAgaagcatctcattaatgctt	6	8	2	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr12:112721009A>G	ENST00000430131.2	-	8	1396	c.251T>C	c.(250-252)cTa>cCa	p.L84P	HECTD4_ENST00000550722.1_Missense_Mutation_p.L334P|HECTD4_ENST00000377560.5_Missense_Mutation_p.L334P			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	84					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										AAGTCTACTTAGAAGCATCTC	0.458																																					p.L334P		Atlas-SNP	.											.	.	.	.	0			c.T1001C						.						112	102	105					12																	112721009		1906	4133	6039	SO:0001583	missense	283450	exon8			CTACTTAGAAGCA	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.251T>C	chr12.hg19:g.112721009A>G	ENSP00000404379:p.Leu84Pro	154.0	0.0		174.0	43.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	A	31	5.079173	0.94050	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.63913	0.01;-0.07;-0.05	5.62	5.62	0.85841	.	.	.	.	.	T	0.66167	0.2762	N	0.14661	0.345	0.80722	D	1	D	0.65815	0.995	D	0.75484	0.986	T	0.72757	-0.4197	9	0.87932	D	0	.	15.8154	0.78595	1.0:0.0:0.0:0.0	.	84	Q9Y4D8	K0614_HUMAN	P	334;84;334	ENSP00000366783:L334P;ENSP00000404379:L84P;ENSP00000449784:L334P	ENSP00000366783:L334P	L	-	2	0	C12orf51	111205392	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.923000	0.92808	2.152000	0.67230	0.459000	0.35465	CTA	.	.		0.458	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		G	112721009	A	G	112721009	3	3	151	1	0	0	0	0	1	0	0	0	1698	420	15	2	12011	2	C12orf51	12	112721009	Missense_Mutation	SNP	A	TCGA-DD-AAC9-01A-11D-A40R-10	58895862	112721009	21130886	55	23318										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130185090	130185090	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	aaatcagaaatgactccaccCgggactgcaggctggagttc	11	11	1	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr12:130185090C>T	ENST00000422113.2	-	2	559	c.233G>A	c.(232-234)cGg>cAg	p.R78Q	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	78					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGACTCCACCCGGGACTGCAG	0.547																																					p.R78Q		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G233A						.						60	56	58					12																	130185090		2203	4300	6503	SO:0001583	missense	121256	exon2			TCCACCCGGGACT	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.233G>A	chr12.hg19:g.130185090C>T	ENSP00000408581:p.Arg78Gln	156.0	0.0		144.0	36.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.919068	0.92249	.	.	ENSG00000151952	ENST00000422113	T	0.16897	2.31	5.33	5.33	0.75918	.	0.000000	0.56097	D	0.000030	T	0.44498	0.1296	M	0.75884	2.315	0.36095	D	0.84371	D	0.89917	1.0	D	0.77557	0.99	T	0.52026	-0.8630	9	.	.	.	-42.2379	19.0288	0.92946	0.0:1.0:0.0:0.0	.	78	Q14C87	T132D_HUMAN	Q	78	ENSP00000408581:R78Q	.	R	-	2	0	TMEM132D	128751043	0.999000	0.42202	0.931000	0.37212	0.983000	0.72400	5.910000	0.69931	2.472000	0.83506	0.555000	0.69702	CGG	.	.		0.547	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	130185090	C	T	130185090	3	4	151	1	0	0	0	0	1	0	0	0	16062	652	23	1	3098	1	TMEM132D	12	130185090	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	17464081	130185090	3666805	56	23319										
OR4N2	390429	hgsc.bcm.edu	37	chr14	20296452	20296452	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cacagtgatttttcctttgtTgaatcctgtcatttataccc	5	10	1	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr14:20296452T>C	ENST00000315947.1	+	1	845	c.845T>C	c.(844-846)tTg>tCg	p.L282S	OR4N2_ENST00000568211.1_3'UTR	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTCCTTTGTTGAATCCTGTC	0.433																																					p.L282S		Atlas-SNP	.											.	OR4N2	125	.	0			c.T845C						.						66	68	68					14																	20296452		2203	4300	6503	SO:0001583	missense	390429	exon1			CTTTGTTGAATCC		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"GPCR / Class A : Olfactory receptors"	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.845T>C	chr14.hg19:g.20296452T>C	ENSP00000319601:p.Leu282Ser	125.0	0.0		152.0	32.0	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	hg19	CCDS32022.1	.	.	.	.	.	.	.	.	.	.	.	18.00	3.524762	0.64747	.	.	ENSG00000176294	ENST00000315947	T	0.48836	0.8	4.57	4.57	0.56435	GPCR, rhodopsin-like superfamily (1);	0.184888	0.26146	N	0.026063	T	0.66086	0.2754	H	0.96208	3.785	0.31464	N	0.669204	P	0.45428	0.858	P	0.45794	0.493	T	0.79564	-0.1751	10	0.87932	D	0	-4.6361	12.161	0.54103	0.0:0.0:0.0:1.0	.	282	Q8NGD1	OR4N2_HUMAN	S	282	ENSP00000319601:L282S	ENSP00000319601:L282S	L	+	2	0	OR4N2	19366292	0.997000	0.39634	0.991000	0.47740	0.888000	0.51559	7.022000	0.76431	2.037000	0.60232	0.482000	0.46254	TTG	.	.		0.433	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2			C	20296452	T	C	20296452	3	2	151	1	0	0	0	0	1	0	0	0	11086	1821	63	2	847	2	OR4N2	14	20296452	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10		20296452	87053088	57	23320										
ITPK1	3705	hgsc.bcm.edu	37	chr14	93408041	93408041	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tcggcctcagccttccagggCgcgtcctggcccatcatgct	11	17	2	0	rs532039520		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr14:93408041C>T	ENST00000267615.6	-	11	1283	c.1110G>A	c.(1108-1110)gcG>gcA	p.A370A	ITPK1_ENST00000354313.3_Intron|ITPK1_ENST00000555495.1_Silent_p.A251A|ITPK1_ENST00000556603.2_Silent_p.A370A			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	370					blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		CCTTCCAGGGCGCGTCCTGGC	0.731													c|||	1	0.000199681	8e-04	0	5008	,	,		13516	0		0	False		,,,				2504	0				p.A370A		Atlas-SNP	.											.	ITPK1	53	.	0			c.G1110A						.						3	4	4					14																	93408041		1857	3656	5513	SO:0001819	synonymous_variant	3705	exon11			CCAGGGCGCGTCC	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.1110G>A	chr14.hg19:g.93408041C>T		29.0	0.0		45.0	10.0	NM_001142593	Q9BTL6|Q9H2E7	Silent	SNP	ENST00000267615.6	hg19	CCDS9907.1																																																																																			.	.		0.731	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		T	93408041	C	T	93408041	2	4	151	1	0	0	0	0	0	0	0	1	7925	755	27	1		1	ITPK1	14	93408041	Silent	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	73111589	93408041	13941499	58	23321										
NEO1	4756	hgsc.bcm.edu	37	chr15	73552722	73552722	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	acattgtggtcagaggttacGccattggttatggcattggc	13	7	1	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr15:73552722G>A	ENST00000339362.5	+	16	2761	c.2314G>A	c.(2314-2316)Gcc>Acc	p.A772T	NEO1_ENST00000558964.1_Missense_Mutation_p.A772T|NEO1_ENST00000560262.1_Missense_Mutation_p.A772T|NEO1_ENST00000261908.6_Missense_Mutation_p.A772T			Q92859	NEO1_HUMAN	neogenin 1	772	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						CAGAGGTTACGCCATTGGTTA	0.483																																					p.A772T		Atlas-SNP	.											.	NEO1	102	.	0			c.G2314A						.						124	104	111					15																	73552722		2198	4297	6495	SO:0001583	missense	4756	exon15			GGTTACGCCATTG	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.2314G>A	chr15.hg19:g.73552722G>A	ENSP00000341198:p.Ala772Thr	129.0	0.0		150.0	12.0	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	hg19	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	G	9.537	1.112265	0.20795	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.56275	0.47;0.47	5.2	5.2	0.72013	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.192709	0.56097	D	0.000040	T	0.22166	0.0534	N	0.00468	-1.46	0.58432	D	0.99999	B;B;B;B	0.28233	0.204;0.023;0.014;0.099	B;B;B;B	0.29716	0.106;0.024;0.015;0.078	T	0.36601	-0.9741	10	0.09338	T	0.73	-16.963	19.1117	0.93318	0.0:0.0:1.0:0.0	.	772;772;510;772	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	T	772;510;772	ENSP00000341198:A772T;ENSP00000261908:A772T	ENSP00000261908:A772T	A	+	1	0	NEO1	71339775	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	5.003000	0.63959	2.593000	0.87608	0.655000	0.94253	GCC	.	.		0.483	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		A	73552722	G	A	73552722	3	1	151	1	0	0	0	0	1	0	0	0	10345	1087	38	1	2372	1	NEO1	15	73552722	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		73552722	28978670	59	23322										
UNC45A	55898	hgsc.bcm.edu	37	chr15	91493443	91493443	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cagacaaaggcagcccaggcCcttgccaagctcaccatcac	8	17	2	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr15:91493443C>T	ENST00000418476.2	+	16	2173	c.2133C>T	c.(2131-2133)gcC>gcT	p.A711A	UNC45A_ENST00000394275.2_Silent_p.A696A|AC068831.6_ENST00000553321.1_RNA	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	711					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CAGCCCAGGCCCTTGCCAAGC	0.642																																					p.A711A		Atlas-SNP	.											.	UNC45A	57	.	0			c.C2133T						.						88	74	79					15																	91493443		1989	3817	5806	SO:0001819	synonymous_variant	55898	exon16			CCAGGCCCTTGCC		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"smooth muscle cell associated protein-1"	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.2133C>T	chr15.hg19:g.91493443C>T		97.0	0.0		134.0	10.0	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Silent	SNP	ENST00000418476.2	hg19	CCDS10367.1																																																																																			.	.		0.642	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671		T	91493443	C	T	91493443	2	4	151	1	0	0	0	0	0	0	0	1	17003	610	22	3		3	UNC45A	15	91493443	Silent	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	17940721	91493443	11037949	60	23323										
ABCC6	368	hgsc.bcm.edu	37	chr16	16248587	16248587	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ccagggctgcccagatagccTcgtccgagtgctcctgcagc	12	16	0	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr16:16248587T>G	ENST00000205557.7	-	29	4135	c.4106A>C	c.(4105-4107)gAg>gCg	p.E1369A		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1369	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CCAGATAGCCTCGTCCGAGTG	0.677																																					p.E1369A		Atlas-SNP	.											.	ABCC6	110	.	0			c.A4106C						.						33	28	30					16																	16248587		2197	4300	6497	SO:0001583	missense	368	exon29			ATAGCCTCGTCCG	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.4106A>C	chr16.hg19:g.16248587T>G	ENSP00000205557:p.Glu1369Ala	148.0	0.0		137.0	47.0	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	hg19	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	T	8.125	0.781884	0.16189	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.91295	-2.82	4.59	3.5	0.40072	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.697795	0.12253	U	0.485469	T	0.81959	0.4933	N	0.12637	0.245	0.80722	D	1	P;P	0.42827	0.791;0.791	B;B	0.43155	0.41;0.41	T	0.78797	-0.2063	10	0.46703	T	0.11	.	6.3997	0.21632	0.0:0.0874:0.1596:0.753	.	1369;1369	O95255;A8Y988	MRP6_HUMAN;.	A	1369;307	ENSP00000205557:E1369A	ENSP00000205557:E1369A	E	-	2	0	ABCC6	16156088	0.318000	0.24598	0.175000	0.22980	0.104000	0.19210	2.229000	0.42990	1.708000	0.51301	0.381000	0.24937	GAG	.	.		0.677	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			G	16248587	T	G	16248587	3	3	151	1	0	0	0	0	1	0	0	0	57	1551	54	5	417	5	ABCC6	16	16248587	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10		16248587	74106166	61	23324										
FAM57B	83723	hgsc.bcm.edu	37	chr16	30041827	30041827	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tccggggaacaccaccccccCggccaccatcggggtcagca	11	19	1	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr16:30041827C>A	ENST00000380495.4	-	1	753	c.22G>T	c.(22-24)Ggg>Tgg	p.G8W	FAM57B_ENST00000567037.1_5'Flank|FAM57B_ENST00000279389.4_5'Flank|FAM57B_ENST00000564806.1_5'Flank	NM_031478.4	NP_113666.2	Q71RH2	FA57B_HUMAN	family with sequence similarity 57, member B	8					ceramide biosynthetic process (GO:0046513)|negative regulation of fat cell differentiation (GO:0045599)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sphingosine N-acyltransferase activity (GO:0050291)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						ACCACCCCCCCGGCCACCATC	0.677																																					p.G8W		Atlas-SNP	.											.	FAM57B	26	.	0			c.G22T						.						13	16	15					16																	30041827		1866	4081	5947	SO:0001583	missense	83723	exon1			CCCCCCCGGCCAC	AF370365	CCDS10667.2	16p11.2	2013-02-19			ENSG00000149926	ENSG00000149926			25295	protein-coding gene	gene with protein product		615175				11230166, 23275342	Standard	NM_031478		Approved	DKFZP434I2117	uc002dvt.3	Q71RH2	OTTHUMG00000132105	ENST00000380495.4:c.22G>T	chr16.hg19:g.30041827C>A	ENSP00000369863:p.Gly8Trp	143.0	0.0		156.0	41.0	NM_031478	Q9H0J1	Missense_Mutation	SNP	ENST00000380495.4	hg19	CCDS10667.2	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756147	0.89843	.	.	ENSG00000149926	ENST00000380495	.	.	.	4.68	4.68	0.58851	.	0.203505	0.41097	D	0.000943	T	0.77631	0.4159	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80632	-0.1296	9	0.87932	D	0	0.0637	14.8742	0.70483	0.0:1.0:0.0:0.0	.	8	Q71RH2	FA57B_HUMAN	W	8	.	ENSP00000369863:G8W	G	-	1	0	FAM57B	29949328	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.043000	0.71004	2.320000	0.78422	0.561000	0.74099	GGG	.	.		0.677	FAM57B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255142.2	NM_031478		A	30041827	C	A	30041827	3	1	151	1	0	0	0	0	1	0	0	0	5597	652	23	1	822	1	FAM57B	16	30041827	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	13793240	30041827	60312926	62	23325										
NFATC3	4775	hgsc.bcm.edu	37	chr16	68160388	68160388	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cactagactggcctttaccaGctcattttggacaatgtgaa	8	10	1	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr16:68160388G>T	ENST00000346183.3	+	3	1300	c.1276G>T	c.(1276-1278)Gct>Tct	p.A426S	NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Missense_Mutation_p.A426S|NFATC3_ENST00000329524.4_Missense_Mutation_p.A426S|NFATC3_ENST00000349223.5_Missense_Mutation_p.A426S	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	426	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		GCCTTTACCAGCTCATTTTGG	0.408																																					p.A426S		Atlas-SNP	.											.	NFATC3	190	.	0			c.G1276T						.						146	113	124					16																	68160388		2198	4300	6498	SO:0001583	missense	4775	exon3			TTACCAGCTCATT	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"Nuclear factor of activated T-cells"	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.1276G>T	chr16.hg19:g.68160388G>T	ENSP00000300659:p.Ala426Ser	122.0	0.0		143.0	39.0	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	hg19	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	G	5.647	0.303946	0.10678	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524	T;T;T	0.38240	1.15;1.15;1.15	5.48	0.75	0.18387	Rel homology (2);p53-like transcription factor, DNA-binding (1);	0.128661	0.64402	D	0.000001	T	0.04815	0.0130	N	0.00062	-2.325	0.25068	N	0.991016	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.41106	-0.9527	10	0.02654	T	1	-3.0191	4.7376	0.12995	0.6508:0.0:0.22:0.1292	.	426;426;426;426	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	S	426	ENSP00000264008:A426S;ENSP00000300659:A426S;ENSP00000331324:A426S	ENSP00000331324:A426S	A	+	1	0	NFATC3	66717889	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	4.268000	0.58883	0.065000	0.16485	-0.378000	0.06908	GCT	.	.		0.408	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		T	68160388	G	T	68160388	3	4	151	1	0	0	0	0	1	0	0	0	10373	971	34	3	1286	3	NFATC3	16	68160388	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	38118561	68160388	22194365	63	23326										
PELP1	27043	hgsc.bcm.edu	37	chr17	4580066	4580066	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	acctgttggagctgagggctCaaggcatccaccctagacag	12	12	1	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr17:4580066C>A	ENST00000574876.1	-	6	701	c.684G>T	c.(682-684)ttG>ttT	p.L228F	PELP1_ENST00000301396.4_Missense_Mutation_p.L228F|PELP1_ENST00000572293.1_Missense_Mutation_p.L278F|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000436683.2_Missense_Mutation_p.L81F|PELP1_ENST00000269230.7_Missense_Mutation_p.L228F			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	228					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GCTGAGGGCTCAAGGCATCCA	0.557																																					p.L228F		Atlas-SNP	.											.	PELP1	102	.	0			c.G684T						.						45	44	44					17																	4580066		1954	4131	6085	SO:0001583	missense	27043	exon6			AGGGCTCAAGGCA		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"proline, glutamic acid and leucine rich protein 1"			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.684G>T	chr17.hg19:g.4580066C>A	ENSP00000461625:p.Leu228Phe	186.0	0.0		196.0	28.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	hg19	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.934795	0.52866	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.68479	-0.3;-0.18;-0.33	5.31	5.31	0.75309	.	0.626193	0.15140	N	0.278359	T	0.73590	0.3606	L	0.44542	1.39	0.34133	D	0.66551	D;D	0.62365	0.991;0.983	P;P	0.60949	0.881;0.799	T	0.77938	-0.2400	10	0.49607	T	0.09	-1.0784	14.3972	0.67020	0.0:1.0:0.0:0.0	.	81;228	E7EV54;Q8IZL8	.;PELP1_HUMAN	F	228;228;81	ENSP00000301396:L228F;ENSP00000269230:L228F;ENSP00000416231:L81F	ENSP00000269230:L228F	L	-	3	2	AC091153.1	4526815	1.000000	0.71417	0.999000	0.59377	0.776000	0.43924	1.708000	0.37899	2.774000	0.95407	0.650000	0.86243	TTG	.	.		0.557	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		A	4580066	C	A	4580066	3	1	151	1	0	0	0	0	1	0	0	0	11734	825	29	3	2756	3	PELP1	17	4580066	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10		4580066	76615144	64	23327										
SLFN12L	100506736	hgsc.bcm.edu	37	chr17	33806550	33806550	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	taacaacttttcagtcgagaAgttttttatttcaacgtgtg	7	6	2	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr17:33806550A>C	ENST00000260908.7	-	2	796	c.679T>G	c.(679-681)Ttc>Gtc	p.F227V	RP11-686D22.9_ENST00000587076.1_RNA|SLFN12L_ENST00000449046.1_Missense_Mutation_p.F258V|SLFN12L_ENST00000361112.4_Missense_Mutation_p.F256V	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	227						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						TCAGTCGAGAAGTTTTTTATT	0.338																																					p.F227V		Atlas-SNP	.											.	SLFN12L	140	.	0			c.T679G						.						103	83	89					17																	33806550		692	1591	2283	SO:0001583	missense	100506736	exon2			TCGAGAAGTTTTT	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.679T>G	chr17.hg19:g.33806550A>C	ENSP00000437635:p.Phe227Val	93.0	0.0		119.0	19.0	NM_001195790	F5H6G3	Missense_Mutation	SNP	ENST00000260908.7	hg19	CCDS56026.1	.	.	.	.	.	.	.	.	.	.	A	12.43	1.936605	0.34189	.	.	ENSG00000205045	ENST00000260908;ENST00000361112;ENST00000449046	T;T;T	0.28666	1.6;1.6;1.6	2.62	1.46	0.22682	.	.	.	.	.	T	0.39306	0.1073	L	0.45051	1.395	0.09310	N	1	D	0.71674	0.998	D	0.66847	0.947	T	0.13845	-1.0494	9	0.49607	T	0.09	.	4.7657	0.13130	0.7221:0.0:0.0:0.2779	.	256	Q6IEE8-2	.	V	227;256;258	ENSP00000437635:F227V;ENSP00000354412:F256V;ENSP00000389348:F258V	ENSP00000437635:F227V	F	-	1	0	SLFN12L	30830663	0.022000	0.18835	0.000000	0.03702	0.009000	0.06853	2.261000	0.43276	0.209000	0.20645	0.338000	0.21704	TTC	.	.		0.338	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206		C	33806550	A	C	33806550	3	2	151	1	0	0	0	0	1	0	0	0	14750	72	3	5	1099	5	SLFN12L	17	33806550	Missense_Mutation	SNP	A	TCGA-DD-AAC9-01A-11D-A40R-10	29226484	33806550	47388660	65	23328										
HOXB4	3214	hgsc.bcm.edu	37	chr17	46655393	46655393	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gaggagggccccggcgggtgGcggcgcaggagcccgagggg	24	11	0	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr17:46655393G>A	ENST00000332503.5	-	1	2080	c.289C>T	c.(289-291)Cca>Tca	p.P97S	MIR10A_ENST00000385043.1_RNA|HOXB3_ENST00000498678.1_Intron|HOXB3_ENST00000485909.2_5'Flank|HOXB3_ENST00000489475.1_Intron|HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000465120.3_Intron|HOXB3_ENST00000472863.1_Intron|HOXB3_ENST00000552000.2_Intron|HOXB3_ENST00000460160.1_Intron|HOXB3_ENST00000476342.1_Intron	NM_024015.4	NP_076920.1	P17483	HXB4_HUMAN	homeobox B4	97	Pro-rich (part of the transcriptional activation domain).				anterior/posterior pattern specification (GO:0009952)|bone marrow development (GO:0048539)|cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|hematopoietic stem cell differentiation (GO:0060218)|morphogenesis of an epithelial sheet (GO:0002011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell division (GO:0048103)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	9						CCGGCGGGTGGCGGCGCAGGA	0.831																																					p.P97S		Atlas-SNP	.											.	HOXB4	16	.	0			c.C289T						.						3	3	3					17																	46655393		990	2253	3243	SO:0001583	missense	3214	exon1			CGGGTGGCGGCGC		CCDS11529.1	17q21.32	2011-06-20	2005-12-22		ENSG00000182742	ENSG00000182742		"Homeoboxes / ANTP class : HOXL subclass"	5115	protein-coding gene	gene with protein product		142965	"homeo box B4"	HOX2, HOX2F		1973146, 1358459	Standard	NM_024015		Approved		uc002inp.3	P17483	OTTHUMG00000159920	ENST00000332503.5:c.289C>T	chr17.hg19:g.46655393G>A	ENSP00000328928:p.Pro97Ser	17.0	0.0		30.0	7.0	NM_024015	Q9NTA0	Missense_Mutation	SNP	ENST00000332503.5	hg19	CCDS11529.1	.	.	.	.	.	.	.	.	.	.	G	6.741	0.505545	0.12822	.	.	ENSG00000182742	ENST00000332503	T	0.50277	0.75	3.38	1.25	0.21368	.	0.399441	0.24422	N	0.038663	T	0.31327	0.0793	L	0.40543	1.245	0.31863	N	0.620736	B	0.02656	0.0	B	0.01281	0.0	T	0.35126	-0.9801	10	0.10377	T	0.69	.	8.2615	0.31788	0.2141:0.0:0.7859:0.0	.	97	P17483	HXB4_HUMAN	S	97	ENSP00000328928:P97S	ENSP00000328928:P97S	P	-	1	0	HOXB4	44010392	0.821000	0.29204	0.065000	0.19835	0.423000	0.31445	1.967000	0.40491	-0.004000	0.14419	0.313000	0.20887	CCA	.	.		0.831	HOXB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358259.2			A	46655393	G	A	46655393	3	1	151	1	0	0	0	0	1	0	0	0	7312	1203	42	3	474	3	HOXB4	17	46655393	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	12848843	46655393	34539817	66	23329										
DCXR	51181	hgsc.bcm.edu	37	chr17	79995521	79995521	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gcccacctttgcctgccccgGtgaccagcacccggcggccc	11	21	0	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr17:79995521G>A	ENST00000306869.2	-	1	87	c.38C>T	c.(37-39)aCc>aTc	p.T13I	DCXR_ENST00000584318.1_5'Flank|RP13-650J16.1_ENST00000584705.1_RNA|RP13-650J16.1_ENST00000582558.1_RNA	NM_001195218.1|NM_016286.3	NP_001182147.1|NP_057370.1	Q7Z4W1	DCXR_HUMAN	dicarbonyl/L-xylulose reductase	13					D-xylose metabolic process (GO:0042732)|glucose metabolic process (GO:0006006)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|xylulose metabolic process (GO:0005997)	brush border (GO:0005903)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)	L-xylulose reductase (NADP+) activity (GO:0050038)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)			kidney(1)|lung(3)	4	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GCCTGCCCCGGTGACCAGCAC	0.726																																					p.T13I		Atlas-SNP	.											.	DCXR	10	.	0			c.C38T						.						5	6	6					17																	79995521		1987	4035	6022	SO:0001583	missense	51181	exon1			GCCCCGGTGACCA	AB013846	CCDS11799.1	17q25.3	2011-09-14				ENSG00000169738	1.1.1.10	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18985	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 20C, member 1"	608347				11882650, 19027726	Standard	NM_016286		Approved	KIDCR, DCR, SDR20C1	uc002kdg.3	Q7Z4W1		ENST00000306869.2:c.38C>T	chr17.hg19:g.79995521G>A	ENSP00000303356:p.Thr13Ile	78.0	0.0		94.0	18.0	NM_001195218	Q9BTZ3|Q9UHY9	Missense_Mutation	SNP	ENST00000306869.2	hg19	CCDS11799.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.697988	0.48307	.	.	ENSG00000169738	ENST00000306869	T	0.38401	1.14	3.85	3.85	0.44370	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.61751	0.2372	M	0.82056	2.57	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	T	0.67738	-0.5593	9	.	.	.	.	15.9235	0.79592	0.0:0.0:1.0:0.0	.	13	Q7Z4W1	DCXR_HUMAN	I	13	ENSP00000303356:T13I	.	T	-	2	0	DCXR	77588810	1.000000	0.71417	0.994000	0.49952	0.830000	0.47004	5.009000	0.63998	1.969000	0.57287	0.491000	0.48974	ACC	.	.		0.726	DCXR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442153.2			A	79995521	G	A	79995521	3	1	151	1	0	0	0	0	1	0	0	0	4321	1261	44	3	728	3	DCXR	17	79995521	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	33340128	79995521	1199689	67	23330										
FASN	2194	hgsc.bcm.edu	37	chr17	80051184	80051184	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tgttgggcttcagcaggacaTtgatgccccccacgatggcg	13	12	1	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr17:80051184T>G	ENST00000306749.2	-	5	784	c.566A>C	c.(565-567)aAt>aCt	p.N189T		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	189	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CAGCAGGACATTGATGCCCCC	0.657																																					p.N189T	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.A566C						.						43	31	35					17																	80051184		2182	4285	6467	SO:0001583	missense	2194	exon5			AGGACATTGATGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.566A>C	chr17.hg19:g.80051184T>G	ENSP00000304592:p.Asn189Thr	155.0	0.0		191.0	68.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.380592	0.42207	.	.	ENSG00000169710	ENST00000306749	T	0.32988	1.43	4.77	4.77	0.60923	Beta-ketoacyl synthase, N-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	T	0.34600	0.0903	L	0.59436	1.845	0.58432	D	0.999997	P	0.40619	0.724	P	0.45232	0.474	T	0.08827	-1.0703	10	0.37606	T	0.19	-55.651	9.664	0.39972	0.1554:0.0:0.0:0.8446	.	189	P49327	FAS_HUMAN	T	189	ENSP00000304592:N189T	ENSP00000304592:N189T	N	-	2	0	FASN	77644473	1.000000	0.71417	0.849000	0.33467	0.109000	0.19521	4.982000	0.63825	1.783000	0.52377	0.379000	0.24179	AAT	.	.		0.657	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		G	80051184	T	G	80051184	3	3	151	1	0	0	0	0	1	0	0	0	5691	1493	52	5	7125	5	FASN	17	80051184	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	55663	80051184	1144026	68	23331										
CDH7	1005	hgsc.bcm.edu	37	chr18	63481780	63481780	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	atcctacatatggcaacagtGccagagtggtctacagtatt	9	9	1	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr18:63481780G>A	ENST00000397968.2	+	4	991	c.565G>A	c.(565-567)Gcc>Acc	p.A189T	CDH7_ENST00000323011.3_Missense_Mutation_p.A189T|CDH7_ENST00000536984.2_Missense_Mutation_p.A189T	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	189	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				TGGCAACAGTGCCAGAGTGGT	0.433																																					p.A189T		Atlas-SNP	.											.	CDH7	362	.	0			c.G565A						.						179	159	166					18																	63481780		2203	4300	6503	SO:0001583	missense	1005	exon4			AACAGTGCCAGAG	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.565G>A	chr18.hg19:g.63481780G>A	ENSP00000381058:p.Ala189Thr	109.0	0.0		130.0	39.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	hg19	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	G	36	5.652508	0.96724	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.60797	0.16;0.16;0.16	5.75	5.75	0.90469	Cadherin (4);Cadherin-like (1);	0.126750	0.52532	D	0.000066	T	0.77198	0.4095	M	0.72353	2.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.78321	-0.2249	10	0.87932	D	0	.	19.9478	0.97189	0.0:0.0:1.0:0.0	.	189;189	F5H5X9;Q9ULB5	.;CADH7_HUMAN	T	189	ENSP00000319166:A189T;ENSP00000443030:A189T;ENSP00000381058:A189T	ENSP00000319166:A189T	A	+	1	0	CDH7	61632760	1.000000	0.71417	0.965000	0.40720	0.975000	0.68041	9.325000	0.96381	2.712000	0.92718	0.591000	0.81541	GCC	.	.		0.433	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		A	63481780	G	A	63481780	3	1	151	1	0	0	0	0	1	0	0	0	3117	1319	46	3	575	3	CDH7	18	63481780	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		63481780	14595468	69	23332										
C19orf21	126353	hgsc.bcm.edu	37	chr19	758004	758004	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cccgtccctctacgtgcagcGggacatagtacaggagacac	11	14	1	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:758004G>A	ENST00000215582.6	+	2	1161	c.1058G>A	c.(1057-1059)cGg>cAg	p.R353Q		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	353					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											TACGTGCAGCGGGACATAGTA	0.687																																					p.R353Q		Atlas-SNP	.											.	C19orf21	56	.	0			c.G1058A						.						16	19	18					19																	758004		2196	4292	6488	SO:0001583	missense	126353	exon2			TGCAGCGGGACAT	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.1058G>A	chr19.hg19:g.758004G>A	ENSP00000215582:p.Arg353Gln	38.0	0.0		37.0	8.0	NM_173481		Missense_Mutation	SNP	ENST00000215582.6	hg19	CCDS12042.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.847148	0.71603	.	.	ENSG00000099812	ENST00000215582	T	0.46063	0.88	4.13	4.13	0.48395	.	0.376195	0.23760	N	0.044825	T	0.60547	0.2277	M	0.64997	1.995	0.43588	D	0.995935	D	0.89917	1.0	D	0.79784	0.993	T	0.65071	-0.6257	10	0.87932	D	0	-25.5125	13.9053	0.63831	0.0:0.0:1.0:0.0	.	353	Q8IVT2	CS021_HUMAN	Q	353	ENSP00000215582:R353Q	ENSP00000215582:R353Q	R	+	2	0	C19orf21	709004	0.998000	0.40836	0.997000	0.53966	0.153000	0.21895	3.558000	0.53749	2.036000	0.60181	0.491000	0.48974	CGG	.	.		0.687	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		A	758004	G	A	758004	3	1	151	1	0	0	0	0	1	0	0	0	1915	1116	39	1	1060	1	C19orf21	19	758004	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		758004	58370979	70	23333										
NFIC	4782	hgsc.bcm.edu	37	chr19	3452573	3452573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cacctacttcccccacacggCcatccgctacccacctcatc	3	23	1	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:3452573C>T	ENST00000443272.2	+	8	1229	c.1178C>T	c.(1177-1179)gCc>gTc	p.A393V	NFIC_ENST00000589123.1_Missense_Mutation_p.A384V|NFIC_ENST00000395111.3_Missense_Mutation_p.A384V|NFIC_ENST00000346156.5_Missense_Mutation_p.A360V|NFIC_ENST00000341919.3_Missense_Mutation_p.A393V|NFIC_ENST00000590282.1_Missense_Mutation_p.A393V|NFIC_ENST00000586919.1_Missense_Mutation_p.A360V	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	393					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		CCCCACACGGCCATCCGCTAC	0.652																																					p.A393V		Atlas-SNP	.											NFIC,colon,carcinoma,0,1	NFIC	36	.	0			c.C1178T						.						187	159	168					19																	3452573		2203	4300	6503	SO:0001583	missense	4782	exon8			ACACGGCCATCCG	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.1178C>T	chr19.hg19:g.3452573C>T	ENSP00000396843:p.Ala393Val	74.0	0.0		79.0	9.0	NM_001245004	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	hg19	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890863	0.91889	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T	0.53640	0.61;0.61;0.61	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.66117	0.2757	M	0.65498	2.005	0.52501	D	0.999953	D;D;D;D;D	0.76494	0.999;0.999;0.998;0.972;0.998	D;D;D;P;D	0.83275	0.996;0.996;0.994;0.592;0.994	T	0.69614	-0.5098	10	0.54805	T	0.06	.	15.0657	0.71992	0.0:1.0:0.0:0.0	.	393;393;384;393;384	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	V	384;384;360;393;393;393	ENSP00000378543:A384V;ENSP00000301935:A360V;ENSP00000342194:A393V	ENSP00000269778:A393V	A	+	2	0	NFIC	3403573	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.240000	0.78192	1.874000	0.54306	0.555000	0.69702	GCC	.	.		0.652	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597		T	3452573	C	T	3452573	3	4	151	1	0	0	0	0	1	0	0	0	10381	739	26	3	1215	3	NFIC	19	3452573	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	2694569	3452573	55676410	71	23334										
ZNF626	199777	hgsc.bcm.edu	37	chr19	20807134	20807300	+	Frame_Shift_Del	DEL	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	-													0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ggtgtgaggaccgcttgaagGctttgccacattcttcacat					rs200411264|rs4808252|rs4808251|rs190319020|rs4809071|rs4809072|rs547337333|rs76605719|rs10408597|rs71332197|rs549423118|rs78715171|rs4808250|rs376295094|rs78217174|rs375690494|rs35575803|rs71174721	byFrequency	TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:20807134_20807300delGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	ENST00000601440.1	-	4	1529_1695	c.1383_1549delTTTTAAGTGCTCCTCTAACCTTACTACACATAAGAAAATTCATACTGGAGAGAGACCCTACAAATGTGAAGAATGTGGCAAAGCCTTCAACCAGTCCTCAATCCTTACTACACATGAGAGAATCATACTGGAGAGAAATTCTACAAATGTGAAGAATGTGGCAAAGC	c.(1381-1551)gcttttaagtgctcctctaaccttactacacataagaaaattcatactggagagagaccctacaaatgtgaagaatgtggcaaagccttcaaccagtcctcaatccttactacacatgagagaatcatactggagagaaattctacaaatgtgaagaatgtggcaaagcctfs	p.FKCSSNLTTHKKIHTGERPYKCEECGKAFNQSSILTTHERIILERNSTNVKNVAKP462fs	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	462					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K473R(2)|p.E484K(1)|p.I502F(1)		breast(1)|endometrium(1)|lung(3)|skin(1)	6						CCGCTTGAAGGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAAGCTTTGCCAC	0.384																																					p.462_517del		Pindel	.											.	ZNF626	121	.	4	Substitution - Missense(4)	lung(3)|central_nervous_system(1)	c.1384_1550del						.																																			SO:0001589	frameshift_variant	199777	exon4			.	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"Zinc fingers, C2H2-type", "-"	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.1383_1549delTTTTAAGTGCTCCTCTAACCTTACTACACATAAGAAAATTCATACTGGAGAGAGACCCTACAAATGTGAAGAATGTGGCAAAGCCTTCAACCAGTCCTCAATCCTTACTACACATGAGAGAATCATACTGGAGAGAAATTCTACAAATGTGAAGAATGTGGCAAAGC	chr19.hg19:g.20807134_20807300delGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	ENSP00000469958:p.Phe462fs	29.0	0.0		23.0	10.0	NM_001076675	Q8N8T4|Q96QM1	Frame_Shift_Del	DEL	ENST00000601440.1	hg19	CCDS42535.1																																																																																			.	.		0.384	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		-	20807300	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	-	20807134	7	5	151	1	0	1	0	1	0	0	0	0	18065	1203	42	0	41	0	ZNF626	19	20807134	Frame_Shift_Del	DEL	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	TCGA-DD-AAC9-01A-11D-A40R-10	17354561	20807134	38321849	72	23335										
ZNF99	7652	hgsc.bcm.edu	37	chr19	22941303	22941303	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	agtatgaattatctcatgttTtctaagggctgaaaaattgc	8	5	2	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:22941303T>C	ENST00000596209.1	-	4	1498	c.1408A>G	c.(1408-1410)Aaa>Gaa	p.K470E	ZNF99_ENST00000397104.3_Missense_Mutation_p.K379E	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	470					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				ATCTCATGTTTTCTAAGGGCT	0.348																																					p.K470E		Atlas-SNP	.											.	ZNF99	273	.	0			c.A1408G						.						68	70	69					19																	22941303		2005	4209	6214	SO:0001583	missense	7652	exon4			CATGTTTTCTAAG	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1408A>G	chr19.hg19:g.22941303T>C	ENSP00000472969:p.Lys470Glu	67.0	0.0		105.0	29.0	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	N	0.004	-2.247202	0.00271	.	.	ENSG00000213973	ENST00000397104	T	0.06687	3.27	1.28	0.17	0.15021	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04815	0.0130	N	0.20530	0.585	0.09310	N	1	P	0.40534	0.72	P	0.45474	0.482	T	0.18085	-1.0348	9	0.02654	T	1	.	2.2405	0.04018	0.2521:0.1924:0.0:0.5554	.	379	A8MXY4	ZNF99_HUMAN	E	379	ENSP00000380293:K379E	ENSP00000380293:K379E	K	-	1	0	ZNF99	22733143	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-3.434000	0.00472	0.566000	0.29273	0.325000	0.21440	AAA	.	.		0.348	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		C	22941303	T	C	22941303	3	2	151	1	0	0	0	0	1	0	0	0	18219	1850	64	2	1989	2	ZNF99	19	22941303	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10	2134169	22941303	36187680	73	23336										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40434029	40434029	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gactccccgggcctcactgtGaccttctttgaggtgttgtc	11	13	2	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:40434029G>T	ENST00000221347.6	-	2	247	c.240C>A	c.(238-240)gtC>gtA	p.V80V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	80	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCCTCACTGTGACCTTCTTTG	0.567																																					p.V80V		Atlas-SNP	.											.	FCGBP	416	.	0			c.C240A						.						123	106	112					19																	40434029		2203	4300	6503	SO:0001819	synonymous_variant	8857	exon2			CACTGTGACCTTC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.240C>A	chr19.hg19:g.40434029G>T		131.0	0.0		146.0	34.0	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.		0.567	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40434029	G	T	40434029	2	4	151	1	0	0	0	0	0	0	0	1	5786	1277	45	3		3	FCGBP	19	40434029	Silent	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	17492726	40434029	18694954	74	23337										
HAS1	3036	hgsc.bcm.edu	37	chr19	52220241	52220241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ctagaggaccgctgatgcagGatacacagtggaagtagctc	13	9	0	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:52220241G>A	ENST00000222115.1	-	3	942	c.908C>T	c.(907-909)tCc>tTc	p.S303F	HAS1_ENST00000594621.1_Missense_Mutation_p.S157F|HAS1_ENST00000601714.1_Missense_Mutation_p.S310F|HAS1_ENST00000540069.2_Missense_Mutation_p.S302F	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	303					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GCTGATGCAGGATACACAGTG	0.577																																					p.S303F	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.C908T						.						108	103	104					19																	52220241		2203	4300	6503	SO:0001583	missense	3036	exon3			ATGCAGGATACAC	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.908C>T	chr19.hg19:g.52220241G>A	ENSP00000222115:p.Ser303Phe	67.0	0.0		83.0	19.0	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	hg19	CCDS12838.1	.	.	.	.	.	.	.	.	.	.	g	19.12	3.764912	0.69878	.	.	ENSG00000105509	ENST00000540069;ENST00000222115;ENST00000376737;ENST00000376738	T;T	0.43294	0.95;0.95	3.96	3.96	0.45880	.	0.070349	0.64402	U	0.000017	T	0.61160	0.2325	M	0.66506	2.035	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	D;D;D	0.75484	0.964;0.986;0.986	T	0.65882	-0.6060	10	0.66056	D	0.02	-25.9268	13.9492	0.64106	0.0:0.0:1.0:0.0	.	302;303;302	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	F	302;303;160;157	ENSP00000445021:S302F;ENSP00000222115:S303F	ENSP00000222115:S303F	S	-	2	0	HAS1	56912053	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	4.454000	0.60068	1.947000	0.56498	0.489000	0.48404	TCC	.	.		0.577	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		A	52220241	G	A	52220241	3	1	151	1	0	0	0	0	1	0	0	0	6970	1174	41	3	840	3	HAS1	19	52220241	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	11786212	52220241	6908742	75	23338										
LILRB5	10990	hgsc.bcm.edu	37	chr19	54757883	54757883	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tcagagcccctcactcaccaCtctggggatccaaccccgtg	8	18	4	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:54757883C>A	ENST00000316219.5	-	8	1459	c.1352G>T	c.(1351-1353)aGt>aTt	p.S451I	LILRB5_ENST00000345866.6_Missense_Mutation_p.S352I|LILRB5_ENST00000450632.1_Missense_Mutation_p.S443I|LILRB5_ENST00000449561.2_Missense_Mutation_p.S452I	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	451					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TCACTCACCACTCTGGGGATC	0.672																																					p.S452I		Atlas-SNP	.											.	LILRB5	176	.	0			c.G1355T						.						24	24	24					19																	54757883		2194	4295	6489	SO:0001583	missense	10990	exon8			TCACCACTCTGGG	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1352G>T	chr19.hg19:g.54757883C>A	ENSP00000320390:p.Ser451Ile	210.0	0.0		212.0	9.0	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	hg19	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	C	6.471	0.454991	0.12283	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00490	7.05;7.03;7.05;7.05	1.53	-3.05	0.05396	.	7739.210000	0.00166	N	0.000000	T	0.00356	0.0011	L	0.42581	1.335	0.09310	N	1	P;B;B;B	0.41265	0.744;0.022;0.261;0.0	B;B;B;B	0.32864	0.154;0.037;0.076;0.0	T	0.43426	-0.9392	10	0.66056	D	0.02	.	3.7018	0.08386	0.0:0.2555:0.4111:0.3334	.	443;352;452;451	C9JMK7;O75023-2;O75023-3;O75023	.;.;.;LIRB5_HUMAN	I	451;443;452;352	ENSP00000320390:S451I;ENSP00000414225:S443I;ENSP00000406478:S452I;ENSP00000263430:S352I	ENSP00000320390:S451I	S	-	2	0	LILRB5	59449695	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.309000	0.02728	-1.453000	0.01928	0.430000	0.28490	AGT	.	.		0.672	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			A	54757883	C	A	54757883	3	1	151	1	0	0	0	0	1	0	0	0	8803	565	20	3	444	3	LILRB5	19	54757883	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	2537642	54757883	4371100	76	23339										
ZNF787	126208	hgsc.bcm.edu	37	chr19	56600216	56600216	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gatgcgccggtgctgcaccaGgtgcgagctctgcgagaagg	17	11	1	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:56600216G>C	ENST00000270459.3	-	3	443	c.325C>G	c.(325-327)Ctg>Gtg	p.L109V		NM_001002836.2	NP_001002836	Q6DD87	ZN787_HUMAN	zinc finger protein 787	109					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)	5		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0559)		TGCTGCACCAGGTGCGAGCTC	0.682																																					p.L109V		Atlas-SNP	.											.	ZNF787	20	.	0			c.C325G						.						21	23	23					19																	56600216		2203	4299	6502	SO:0001583	missense	126208	exon3			GCACCAGGTGCGA	BC077728, AF000560	CCDS42634.1	19q13.42	2013-01-08				ENSG00000142409		"Zinc fingers, C2H2-type"	26998	protein-coding gene	gene with protein product							Standard	NM_001002836		Approved		uc010eth.1	Q6DD87		ENST00000270459.3:c.325C>G	chr19.hg19:g.56600216G>C	ENSP00000270459:p.Leu109Val	80.0	0.0		90.0	20.0	NM_001002836	O00455	Missense_Mutation	SNP	ENST00000270459.3	hg19	CCDS42634.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.111009	0.56398	.	.	ENSG00000142409	ENST00000270459	T	0.52983	0.64	3.46	2.36	0.29203	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.58991	0.2161	L	0.60845	1.875	0.80722	D	1	D	0.69078	0.997	D	0.67725	0.953	T	0.58747	-0.7582	9	0.62326	D	0.03	-21.1662	9.1854	0.37168	0.1163:0.0:0.8836:0.0	.	109	Q6DD87	ZN787_HUMAN	V	109	ENSP00000270459:L109V	ENSP00000270459:L109V	L	-	1	2	ZNF787	61292028	0.859000	0.29813	1.000000	0.80357	0.914000	0.54420	0.892000	0.28322	0.748000	0.32831	0.462000	0.41574	CTG	.	.		0.682	ZNF787-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457498.1	NM_001002836		C	56600216	G	C	56600216	3	2	151	1	0	0	0	0	1	0	0	0	18174	991	35	4	830	4	ZNF787	19	56600216	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	1842333	56600216	2528767	77	23340										
DDX27	55661	hgsc.bcm.edu	37	chr20	47855523	47855523	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	cgggacaagattgagaaaatGgagaaagatgtgtatgcagt	14	3	0	4			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr20:47855523G>T	ENST00000371764.4	+	15	1827	c.1818G>T	c.(1816-1818)atG>atT	p.M606I	ZNFX1_ENST00000469991.1_5'UTR|ZNFX1_ENST00000371754.4_Silent_p.S1247S|DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	606						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.M606I(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TTGAGAAAATGGAGAAAGATG	0.478																																					p.M606I		Atlas-SNP	.											DDX27,NS,carcinoma,0,1	DDX27	74	.	1	Substitution - Missense(1)	lung(1)	c.G1818T						.						64	59	61					20																	47855523		2203	4300	6503	SO:0001583	missense	55661	exon15			GAAAATGGAGAAA	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"DEAD-boxes"	15837	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.1818G>T	chr20.hg19:g.47855523G>T	ENSP00000360828:p.Met606Ile	64.0	0.0		106.0	5.0	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	hg19	CCDS13416.1	.	.	.	.	.	.	.	.	.	.	G	15.11	2.736757	0.49045	.	.	ENSG00000124228	ENST00000371764	T	0.01430	4.9	5.23	5.23	0.72850	.	0.169570	0.53938	D	0.000045	T	0.02193	0.0068	L	0.43923	1.385	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.56860	-0.7909	10	0.45353	T;T	0.12;0.12	-27.0788	16.3221	0.82954	0.0:0.0:1.0:0.0	.	606	Q96GQ7	DDX27_HUMAN	I	606	ENSP00000360828:M606I	ENSP00000360828:M606I;ENSP00000360828:M606I	M	+	3	0	DDX27	47288930	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.260000	0.65490	2.438000	0.82558	0.655000	0.94253	ATG	.	.		0.478	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1			T	47855523	G	T	47855523	3	4	151	1	0	0	0	0	1	0	0	0	4356	1348	47	3	1876	3	DDX27	20	47855523	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10		47855523	15169997	78	23341										
CTCFL	140690	hgsc.bcm.edu	37	chr20	56090848	56090848	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ctggcaacactgaaaggggcGctccccagtgtgggatcgga	15	11	0	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr20:56090848G>T	ENST00000608263.1	-	5	1763	c.1102C>A	c.(1102-1104)Cgc>Agc	p.R368S	CTCFL_ENST00000422869.2_Missense_Mutation_p.R368S|CTCFL_ENST00000502686.2_Missense_Mutation_p.R106S|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000243914.3_Missense_Mutation_p.R368S|CTCFL_ENST00000423479.3_Missense_Mutation_p.R368S|CTCFL_ENST00000539382.1_Missense_Mutation_p.R163S|CTCFL_ENST00000609232.1_Missense_Mutation_p.R368S|CTCFL_ENST00000608440.1_Missense_Mutation_p.R368S|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000433949.3_Missense_Mutation_p.R163S|CTCFL_ENST00000608425.1_Missense_Mutation_p.R368S|CTCFL_ENST00000371196.2_Missense_Mutation_p.R368S|CTCFL_ENST00000608903.1_Missense_Mutation_p.R106S|CTCFL_ENST00000429804.3_Missense_Mutation_p.R368S	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	368					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			TGAAAGGGGCGCTCCCCAGTG	0.478																																					p.R368S		Atlas-SNP	.											.	CTCFL	97	.	0			c.C1102A						.						163	156	159					20																	56090848		2203	4300	6503	SO:0001583	missense	140690	exon5			AGGGGCGCTCCCC		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1102C>A	chr20.hg19:g.56090848G>T	ENSP00000476783:p.Arg368Ser	65.0	0.0		61.0	14.0	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	hg19	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	G	32	5.108533	0.94292	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000502686;ENST00000422109;ENST00000426658;ENST00000539382;ENST00000422869	T;T;T;T;T;T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16	5.24	5.24	0.73138	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44902	D	0.000406	T	0.49983	0.1589	M	0.78344	2.41	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.999;1.0;1.0;1.0	T	0.53287	-0.8460	10	0.87932	D	0	-44.5807	17.9607	0.89084	0.0:0.0:1.0:0.0	.	368;368;368;368;368	A6XGM9;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;CTCFL_HUMAN	S	368;368;368;368;368;106;368;368;163;368	ENSP00000415579:R368S;ENSP00000243914:R368S;ENSP00000360239:R368S;ENSP00000415329:R368S;ENSP00000392034:R368S;ENSP00000437999:R106S;ENSP00000413713:R368S;ENSP00000403369:R368S;ENSP00000439998:R163S;ENSP00000399061:R368S	ENSP00000243914:R368S	R	-	1	0	CTCFL	55524254	1.000000	0.71417	0.972000	0.41901	0.782000	0.44232	6.387000	0.73191	2.608000	0.88229	0.650000	0.86243	CGC	.	.		0.478	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		T	56090848	G	T	56090848	3	4	151	1	0	0	0	0	1	0	0	0	4003	1087	38	1	913	1	CTCFL	20	56090848	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	8235325	56090848	6934672	79	23342										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885585	29885586	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC													0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	caaagtcccctgagaaggccINSaagtccccagagaaggaaga					rs200984527|rs267607533		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr22:29885585_29885586insAAGTCCCCTGAGAAGGCC	ENST00000310624.6	+	4	1989_1990	c.1956_1957insAAGTCCCCTGAGAAGGCC	c.(1957-1959)aag>AAGTCCCCTGAGAAGGCCaag	p.653_653K>KSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	659	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CTGAGAAGGCCAAGTCCCCAGA	0.564																																					p.A652delinsAKSPEKA		Atlas-INDEL	.											.,1	NEFH	178	.	0			c.1956_1957insAAGTCCCCTGAGAAGGCC						.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1939_1956dupAAGTCCCCTGAGAAGGCC	chr22.hg19:g.29885585_29885586insAAGTCCCCTGAGAAGGCC	ENSP00000311997:p.SerProGluLysAlaLys653dup	247.0	0.0		274.0	136.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.564	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		AAGTCCCCTGAGAAGGCC	29885586	-	AAGTCCCCTGAGAAGGCC	29885585	7	5	151	1	0	1	1	0	0	0	0	0	10323	581	21	0	1970	0	NEFH	22	29885585	In_Frame_Ins	INS	-	TCGA-DD-AAC9-01A-11D-A40R-10		29885585	21418981	80	23343										
KAL1	3730	hgsc.bcm.edu	37	chrX	8503661	8503661	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gatctgggactgtgaaataaTgctgttgggtaggctgttct	14	5	2	1			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chrX:8503661T>A	ENST00000262648.3	-	12	1962	c.1813A>T	c.(1813-1815)Att>Ttt	p.I605F	KAL1_ENST00000481896.1_5'UTR	NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	605	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.I605F(1)		breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						TGTGAAATAATGCTGTTGGGT	0.493																																					p.I605F		Atlas-SNP	.											.	KAL1	78	.	1	Substitution - Missense(1)	lung(1)	c.A1813T						.						171	127	142					X																	8503661		2203	4300	6503	SO:0001583	missense	3730	exon12			AAATAATGCTGTT		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"WAP four-disulfide core domain containing", "Fibronectin type III domain containing"	6211	protein-coding gene	gene with protein product	"anosmin-1", "WAP four-disulfide core domain 19"	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.1813A>T	chrX.hg19:g.8503661T>A	ENSP00000262648:p.Ile605Phe	186.0	0.0		196.0	106.0	NM_000216	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	hg19	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.233337	0.39498	.	.	ENSG00000011201	ENST00000262648	T	0.78707	-1.2	4.43	1.81	0.25067	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.055572	0.64402	D	0.000001	T	0.81088	0.4750	L	0.44542	1.39	0.43841	D	0.996423	D	0.69078	0.997	D	0.74348	0.983	T	0.78585	-0.2147	10	0.72032	D	0.01	-22.6232	9.7523	0.40483	0.0:0.0:0.3297:0.6703	.	605	P23352	KALM_HUMAN	F	605	ENSP00000262648:I605F	ENSP00000262648:I605F	I	-	1	0	KAL1	8463661	1.000000	0.71417	0.966000	0.40874	0.112000	0.19704	3.081000	0.50120	-0.004000	0.14419	0.486000	0.48141	ATT	.	.		0.493	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216		A	8503661	T	A	8503661	3	1	151	1	0	0	0	0	1	0	0	0	7983	1464	51	4	241	4	KAL1	23	8503661	Missense_Mutation	SNP	T	TCGA-DD-AAC9-01A-11D-A40R-10		8503661	146766899	81	23344										
PHEX	5251	hgsc.bcm.edu	37	chrX	22263484	22263484	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ctacagaccagaagctgcccGagaacaagtccaaattggtg	10	11	0	3			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chrX:22263484G>A	ENST00000379374.4	+	21	2670	c.2105G>A	c.(2104-2106)cGa>cAa	p.R702Q	PHEX_ENST00000535894.1_Missense_Mutation_p.R605Q|PHEX_ENST00000537599.1_Intron|PHEX_ENST00000418858.3_Missense_Mutation_p.R405Q	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	702					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						GAAGCTGCCCGAGAACAAGTC	0.458																																					p.R702Q		Atlas-SNP	.											.	PHEX	95	.	0			c.G2105A						.						169	154	159					X																	22263484		2203	4300	6503	SO:0001583	missense	5251	exon21			CTGCCCGAGAACA	U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.2105G>A	chrX.hg19:g.22263484G>A	ENSP00000368682:p.Arg702Gln	106.0	0.0		107.0	11.0	NM_000444	O00678|Q13646|Q2M325|Q93032|Q99827	Missense_Mutation	SNP	ENST00000379374.4	hg19	CCDS14204.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.017292	0.93404	.	.	ENSG00000102174	ENST00000379374;ENST00000535894;ENST00000418858	D;D;D	0.90004	-2.6;-2.6;-2.6	5.82	5.82	0.92795	Peptidase M13, neprilysin, C-terminal (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.83257	0.5215	L	0.35793	1.09	0.47862	D	0.999536	P	0.39903	0.694	B	0.33620	0.167	T	0.82432	-0.0460	10	0.28530	T	0.3	-19.6123	17.2568	0.87059	0.0:0.0:1.0:0.0	.	702	P78562	PHEX_HUMAN	Q	702;605;405	ENSP00000368682:R702Q;ENSP00000439418:R605Q;ENSP00000443531:R405Q	ENSP00000368682:R702Q	R	+	2	0	PHEX	22173405	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.354000	0.79424	2.457000	0.83068	0.544000	0.68410	CGA	.	.		0.458	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		A	22263484	G	A	22263484	3	1	151	1	0	0	0	0	1	0	0	0	11828	1058	37	1	2187	1	PHEX	23	22263484	Missense_Mutation	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	13759823	22263484	133007076	82	23345										
KCND1	3750	hgsc.bcm.edu	37	chrX	48823176	48823176	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	gccccgacccacctcaaggcCcccattctgcttgtactgca	7	19	2	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chrX:48823176C>T	ENST00000218176.3	-	3	2657	c.1360G>A	c.(1360-1362)Ggc>Agc	p.G454S	KCND1_ENST00000376477.1_Missense_Mutation_p.G77S	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	454					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	ACCTCAAGGCCCCCATTCTGC	0.577																																					p.G454S		Atlas-SNP	.											.	KCND1	63	.	0			c.G1360A						.						93	79	84					X																	48823176		2203	4300	6503	SO:0001583	missense	3750	exon3			CAAGGCCCCCATT	AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.1360G>A	chrX.hg19:g.48823176C>T	ENSP00000218176:p.Gly454Ser	26.0	0.0		28.0	10.0	NM_004979	A6NEF1|B2RCG0|O75671	Missense_Mutation	SNP	ENST00000218176.3	hg19	CCDS14314.1	.	.	.	.	.	.	.	.	.	.	C	9.057	0.993445	0.19043	.	.	ENSG00000102057	ENST00000376477;ENST00000218176	D;D	0.81821	-1.54;-1.54	5.7	4.84	0.62591	Potassium channel, voltage dependent, Kv4, C-terminal (1);	0.195954	0.40640	N	0.001050	T	0.68348	0.2991	L	0.31294	0.92	0.45194	D	0.998201	B	0.14012	0.009	B	0.18263	0.021	T	0.60161	-0.7317	10	0.09338	T	0.73	.	12.7154	0.57111	0.0:0.9172:0.0:0.0828	.	454	Q9NSA2	KCND1_HUMAN	S	77;454	ENSP00000365660:G77S;ENSP00000218176:G454S	ENSP00000218176:G454S	G	-	1	0	KCND1	48708120	0.969000	0.33509	0.989000	0.46669	0.762000	0.43233	1.830000	0.39131	1.157000	0.42530	0.594000	0.82650	GGC	.	.		0.577	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979		T	48823176	C	T	48823176	3	4	151	1	0	0	0	0	1	0	0	0	8027	623	22	3	599	3	KCND1	23	48823176	Missense_Mutation	SNP	C	TCGA-DD-AAC9-01A-11D-A40R-10	26559692	48823176	106447384	83	23346										
ATP7A	538	hgsc.bcm.edu	37	chrX	77245380	77245380	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	tagcaatgggactgttgagtAtgatcctctactaacctctc	8	10	2	2			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chrX:77245380A>G	ENST00000341514.6	+	4	1417	c.1262A>G	c.(1261-1263)tAt>tGt	p.Y421C	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Missense_Mutation_p.Y421C	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	421	HMA 4. {ECO:0000255|PROSITE- ProRule:PRU00280}.				blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ACTGTTGAGTATGATCCTCTA	0.398																																					p.Y421C		Atlas-SNP	.											.	ATP7A	248	.	0			c.A1262G						.						91	83	86					X																	77245380		2203	4296	6499	SO:0001583	missense	538	exon4			TTGAGTATGATCC	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.1262A>G	chrX.hg19:g.77245380A>G	ENSP00000345728:p.Tyr421Cys	284.0	0.0		258.0	138.0	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	hg19	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	A	15.32	2.797715	0.50208	.	.	ENSG00000165240	ENST00000343533;ENST00000341514;ENST00000355691	D;D	0.86497	-2.13;-2.13	5.77	3.19	0.36642	Heavy metal-associated domain, HMA (3);Heavy metal-associated domain, copper ion-binding (1);	0.202249	0.44285	D	0.000467	D	0.94248	0.8153	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.97110	0.969;1.0	D	0.93978	0.7255	10	0.87932	D	0	-0.7507	10.2368	0.43288	0.7332:0.0:0.0:0.2668	.	421;431	Q04656;Q59HD1	ATP7A_HUMAN;.	C	421;421;431	ENSP00000343026:Y421C;ENSP00000345728:Y421C	ENSP00000345728:Y421C	Y	+	2	0	ATP7A	77132036	1.000000	0.71417	0.996000	0.52242	0.954000	0.61252	4.210000	0.58500	0.780000	0.33566	0.481000	0.45027	TAT	.	.		0.398	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		G	77245380	A	G	77245380	3	3	151	1	0	0	0	0	1	0	0	0	1190	449	16	2	1272	2	ATP7A	23	77245380	Missense_Mutation	SNP	A	TCGA-DD-AAC9-01A-11D-A40R-10	28422204	77245380	78025180	84	23347										
CXorf57	55086	hgsc.bcm.edu	37	chrX	105879772	105879772	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0352941176470588	3	1	0.812040441176471	0	0.952047413793103	0.192307692307692	0.751940625889747	0	ataagtgtttttgttctctaGtggcatattttgtgtgtaca	9	4	1	0			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chrX:105879772G>T	ENST00000372548.4	+	7	1412		c.e7-1		CXorf57_ENST00000372544.2_Splice_Site	NM_018015.5	NP_060485.4	Q6NSI4	CX057_HUMAN	chromosome X open reading frame 57								poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	31						TTGTTCTCTAGTGGCATATTT	0.343																																					.		Atlas-SNP	.											.	CXorf57	107	.	0			c.1304-1G>T						.						146	131	136					X																	105879772		2203	4299	6502	SO:0001630	splice_region_variant	55086	exon7			TCTCTAGTGGCAT	AK024253	CCDS14519.1, CCDS55470.1	Xq22.3	2008-02-05			ENSG00000147231	ENSG00000147231			25486	protein-coding gene	gene with protein product							Standard	NM_018015		Approved	FLJ14191, FLJ10178	uc004emi.4	Q6NSI4	OTTHUMG00000022150	ENST00000372548.4:c.1304-1G>T	chrX.hg19:g.105879772G>T		64.0	0.0		74.0	39.0	NM_001184782	H7BY89|Q4G0L7|Q5JQS1|Q5JRF9|Q6PHY5|Q6PII9|Q6PJU8|Q9H7W5|Q9NWA6	Splice_Site	SNP	ENST00000372548.4	hg19	CCDS14519.1	.	.	.	.	.	.	.	.	.	.	g	10.31	1.314334	0.23908	.	.	ENSG00000147231	ENST00000372544;ENST00000372548;ENST00000421550	.	.	.	4.33	4.33	0.51752	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3433	0.60557	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CXorf57	105766428	1.000000	0.71417	0.725000	0.30721	0.210000	0.24377	5.358000	0.66064	2.083000	0.62718	0.425000	0.28330	.	.	.		0.343	CXorf57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057800.2	NM_018015	Intron	T	105879772	G	T	105879772	5	4	151	1	0	0	0	0	0	0	1	0	4115	1043	36	3	1329	3	CXorf57	23	105879772	Splice_Site	SNP	G	TCGA-DD-AAC9-01A-11D-A40R-10	28634392	105879772	49390788	85	23348										
C1orf168	199920	hgsc.bcm.edu	37	chr1	57206372	57206372	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tttaaagggactttttacctTaagttttctttcgacttggt	7	6	1	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr1:57206372T>C	ENST00000343433.6	-	13	1781	c.1701A>G	c.(1699-1701)ttA>ttG	p.L567L	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	567										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						CTTTTTACCTTAAGTTTTCTT	0.363																																					p.L567L		Atlas-SNP	.											.	C1orf168	102	.	0			c.A1701G						.						101	92	95					1																	57206372		2201	4297	6498	SO:0001819	synonymous_variant	199920	exon13			TTACCTTAAGTTT	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.1701A>G	1.37:g.57206372T>C		107.0	0.0		56.0	22.0	NM_001004303	Q63HM3|Q6ZUY6	Silent	SNP	ENST00000343433.6	37	CCDS30729.1																																																																																			.	.		0.363	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303		C	57206372	T	C	57206372	2	2	152	1	0	0	0	0	0	0	0	1	2014	1751	61	2		2	C1orf168	1	57206372	Silent	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10		57206372	192044249	1	23349										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103405915	103405915	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ttccccaggggagccggcagGaccagctggccctgggagac	16	14	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr1:103405915G>T	ENST00000370096.3	-	43	3664	c.3352C>A	c.(3352-3354)Cct>Act	p.P1118T	COL11A1_ENST00000512756.1_Missense_Mutation_p.P1002T|COL11A1_ENST00000358392.2_Missense_Mutation_p.P1130T|COL11A1_ENST00000353414.4_Missense_Mutation_p.P1079T	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1118	Triple-helical region.		Missing (in STL2). {ECO:0000269|PubMed:20513134}.		cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GAGCCGGCAGGACCAGCTGGC	0.473																																					p.P1130T		Atlas-SNP	.											COL11A1_ENST00000370096,NS,carcinoma,0,2	COL11A1	972	2	0			c.C3388A						.						56	62	60					1																	103405915		2203	4300	6503	SO:0001583	missense	1301	exon43			CGGCAGGACCAGC	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3352C>A	1.37:g.103405915G>T	ENSP00000359114:p.Pro1118Thr	240.0	1.0		102.0	31.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.272323	0.40194	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.96651	-4.08;-4.08;-4.08;-4.08	5.46	5.46	0.80206	.	0.061344	0.64402	D	0.000002	D	0.97980	0.9335	M	0.79123	2.44	0.58432	D	0.999999	P;D;P;P;P	0.67145	0.734;0.996;0.925;0.877;0.59	B;D;P;B;B	0.75484	0.254;0.986;0.621;0.417;0.346	D	0.98681	1.0692	10	0.87932	D	0	.	19.3174	0.94220	0.0:0.0:1.0:0.0	.	1002;1079;1130;1118;338	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	T	1118;1130;1079;338;1002	ENSP00000359114:P1118T;ENSP00000351163:P1130T;ENSP00000302551:P1079T;ENSP00000426533:P1002T	ENSP00000302551:P1079T	P	-	1	0	COL11A1	103178503	1.000000	0.71417	0.978000	0.43139	0.173000	0.22820	7.922000	0.87538	2.569000	0.86673	0.650000	0.86243	CCT	.	.		0.473	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		T	103405915	G	T	103405915	3	4	152	1	0	0	0	0	1	0	0	0	3669	1174	41	3	2168	3	COL11A1	1	103405915	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	46199543	103405915	145844706	2	23350										
KCNA3	3738	hgsc.bcm.edu	37	chr1	111216298	111216298	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tgcagccccttggagtggcgCgacagcttgaagatgcggaa	15	10	0	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr1:111216298C>T	ENST00000369769.2	-	1	1357	c.1134G>A	c.(1132-1134)tcG>tcA	p.S378S		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	378					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	TGGAGTGGCGCGACAGCTTGA	0.592																																					p.S378S		Atlas-SNP	.											KCNA3,NS,carcinoma,-1,1	KCNA3	91	1	0			c.G1134A						.						105	104	105					1																	111216298		2203	4300	6503	SO:0001819	synonymous_variant	3738	exon1			GTGGCGCGACAGC	L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.1134G>A	1.37:g.111216298C>T		67.0	0.0		79.0	40.0	NM_002232	Q5VWN2	Silent	SNP	ENST00000369769.2	37	CCDS828.2																																																																																			.	.		0.592	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		T	111216298	C	T	111216298	2	4	152	1	0	0	0	0	0	0	0	1	8013	755	27	1		1	KCNA3	1	111216298	Silent	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	7810383	111216298	138034323	3	23351										
KCND3	3752	hgsc.bcm.edu	37	chr1	112525100	112525100	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	acctcggggtcccggtcgaaGaagtactccttggtgtcctc	12	13	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr1:112525100G>T	ENST00000315987.2	-	2	728	c.249C>A	c.(247-249)ttC>ttA	p.F83L	KCND3_ENST00000302127.4_Missense_Mutation_p.F83L|KCND3_ENST00000369697.1_Missense_Mutation_p.F83L	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	83					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	CCCGGTCGAAGAAGTACTCCT	0.622																																					p.F83L		Atlas-SNP	.											KCND3_ENST00000315987,NS,carcinoma,0,2	KCND3	150	2	0			c.C249A						.						126	114	119					1																	112525100		2203	4300	6503	SO:0001583	missense	3752	exon2			GTCGAAGAAGTAC	AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6239	protein-coding gene	gene with protein product		605411	"spinocerebellar ataxia 22", "spinocerebellar ataxia 19"	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.249C>A	1.37:g.112525100G>T	ENSP00000319591:p.Phe83Leu	96.0	0.0		97.0	37.0	NM_004980	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Missense_Mutation	SNP	ENST00000315987.2	37	CCDS843.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.986080	0.74589	.	.	ENSG00000171385	ENST00000369697;ENST00000315987;ENST00000302127	D;D;D	0.83591	-1.74;-1.74;-1.74	5.74	4.83	0.62350	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.88058	0.6335	M	0.84219	2.685	0.80722	D	1	D;D	0.65815	0.995;0.995	D;D	0.65443	0.935;0.935	D	0.89939	0.4071	10	0.87932	D	0	.	11.5885	0.50933	0.1448:0.0:0.8552:0.0	.	83;83	Q14D71;Q9UK17	.;KCND3_HUMAN	L	83	ENSP00000358711:F83L;ENSP00000319591:F83L;ENSP00000306923:F83L	ENSP00000306923:F83L	F	-	3	2	KCND3	112326623	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.523000	0.67099	1.443000	0.47586	0.655000	0.94253	TTC	.	.		0.622	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198		T	112525100	G	T	112525100	3	4	152	1	0	0	0	0	1	0	0	0	8029	933	33	3	1746	3	KCND3	1	112525100	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	1308802	112525100	136725521	4	23352										
PHTF1	10745	hgsc.bcm.edu	37	chr1	114249252	114249253	+	Frame_Shift_Ins	INS	-	-	A													0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cacttatttccaacacagacINSatatccatctttttgcactc							TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr1:114249252_114249253insA	ENST00000369604.1	-	12	1844_1845	c.1361_1362insT	c.(1360-1362)atgfs	p.M454fs	PHTF1_ENST00000357783.2_Frame_Shift_Ins_p.M454fs|PHTF1_ENST00000474926.1_5'UTR|PHTF1_ENST00000393357.2_Frame_Shift_Ins_p.M454fs|PHTF1_ENST00000369596.2_Frame_Shift_Ins_p.M401fs|PHTF1_ENST00000369600.1_Frame_Shift_Ins_p.M401fs|PHTF1_ENST00000369598.1_Frame_Shift_Ins_p.M409fs|PHTF1_ENST00000447664.2_3'UTR			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	454					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCAACACAGACATATCCATCTT	0.366																																					p.M454fs		Atlas-Indel	.											.	PHTF1	69	.	0			c.1362_1363insT						.																																			SO:0001589	frameshift_variant	10745	exon11			.	AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.1362dupT	1.37:g.114249253_114249253dupA	ENSP00000358617:p.Met454fs	349.0	0.0		162.0	57.0	NM_006608	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Frame_Shift_Ins	INS	ENST00000369604.1	37	CCDS861.1																																																																																			.	.		0.366	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608		A	114249253	-	A	114249252	7	5	152	1	0	1	1	0	0	0	0	0	11871	478	17	0	958	0	PHTF1	1	114249252	Frame_Shift_Ins	INS	-	TCGA-DD-AACA-01A-11D-A40R-10	1724152	114249252	135001369	5	23353										
ADAM30	11085	hgsc.bcm.edu	37	chr1	120438632	120438632	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cacggagcccatgtagttgcAgtcctttggtatgtaaggat	12	8	0	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr1:120438632A>C	ENST00000369400.1	-	1	486	c.328T>G	c.(328-330)Tgc>Ggc	p.C110G		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	110					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		ATGTAGTTGCAGTCCTTTGGT	0.488																																					p.C110G		Atlas-SNP	.											.	ADAM30	88	.	0			c.T328G						.						66	65	66					1																	120438632		2203	4300	6503	SO:0001583	missense	11085	exon1			AGTTGCAGTCCTT	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.328T>G	1.37:g.120438632A>C	ENSP00000358407:p.Cys110Gly	128.0	0.0		71.0	42.0	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	.	.	.	.	.	.	.	.	.	.	A	18.93	3.728480	0.69074	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.12361	2.69	4.34	4.34	0.51931	Peptidase M12B, propeptide (1);	0.000000	0.41001	U	0.000963	T	0.41073	0.1143	H	0.97874	4.095	0.32740	N	0.507848	D	0.89917	1.0	D	0.91635	0.999	T	0.61217	-0.7107	10	0.72032	D	0.01	.	9.8364	0.40971	1.0:0.0:0.0:0.0	.	110	Q9UKF2	ADA30_HUMAN	G	110	ENSP00000358407:C110G	ENSP00000358407:C110G	C	-	1	0	ADAM30	120240155	1.000000	0.71417	0.942000	0.38095	0.270000	0.26580	4.900000	0.63252	1.819000	0.53055	0.379000	0.24179	TGC	.	.		0.488	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		C	120438632	A	C	120438632	3	2	152	1	0	0	0	0	1	0	0	0	248	188	7	5	2048	5	ADAM30	1	120438632	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	6189380	120438632	128811989	6	23354										
FLG	2312	hgsc.bcm.edu	37	chr1	152282404	152282404	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tctctgcatgacgagtgcctGattgtctggagctctctgca	11	11	3	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr1:152282404G>A	ENST00000368799.1	-	3	4993	c.4958C>T	c.(4957-4959)tCa>tTa	p.S1653L	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1653	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACGAGTGCCTGATTGTCTGGA	0.567									Ichthyosis																												p.S1653L		Atlas-SNP	.											.	FLG	900	.	0			c.C4958T						.						269	271	270					1																	152282404		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTGCCTGATTGTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4958C>T	1.37:g.152282404G>A	ENSP00000357789:p.Ser1653Leu	137.0	0.0		93.0	33.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	9.866	1.197604	0.22037	.	.	ENSG00000143631	ENST00000368799	T	0.00848	5.62	3.56	3.56	0.40772	.	.	.	.	.	T	0.01627	0.0052	M	0.75447	2.3	0.09310	N	1	D	0.69078	0.997	P	0.58577	0.841	T	0.45279	-0.9272	9	0.56958	D	0.05	.	11.02	0.47711	0.0:0.0:1.0:0.0	.	1653	P20930	FILA_HUMAN	L	1653	ENSP00000357789:S1653L	ENSP00000357789:S1653L	S	-	2	0	FLG	150549028	0.001000	0.12720	0.003000	0.11579	0.007000	0.05969	0.786000	0.26844	1.721000	0.51461	0.306000	0.20318	TCA	.	.		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152282404	G	A	152282404	3	1	152	1	0	0	0	0	1	0	0	0	5930	1294	45	3	7231	3	FLG	1	152282404	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	31843772	152282404	96968217	7	23355										
SLAMF1	6504	hgsc.bcm.edu	37	chr1	160604639	160604639	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gtatcaaggtgcaggtcccgTtctcctgggtcttgtttaaa	11	9	3	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr1:160604639T>G	ENST00000302035.6	-	3	813	c.464A>C	c.(463-465)aAc>aCc	p.N155T	SLAMF1_ENST00000538290.1_Missense_Mutation_p.N155T|SLAMF1_ENST00000355199.3_Missense_Mutation_p.N155T|SLAMF1_ENST00000235739.5_Missense_Mutation_p.N155T	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	155	Ig-like C2-type.				lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GCAGGTCCCGTTCTCCTGGGT	0.552																																					p.N155T		Atlas-SNP	.											SLAMF1,NS,carcinoma,+1,1	SLAMF1	74	1	0			c.A464C						.						91	91	91					1																	160604639		2203	4300	6503	SO:0001583	missense	6504	exon3			GTCCCGTTCTCCT	U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10903	protein-coding gene	gene with protein product		603492	"signaling lymphocytic activation molecule"	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.464A>C	1.37:g.160604639T>G	ENSP00000306190:p.Asn155Thr	119.0	0.0		93.0	37.0	NM_003037	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	37	CCDS1207.1	.	.	.	.	.	.	.	.	.	.	T	7.028	0.560124	0.13498	.	.	ENSG00000117090	ENST00000302035;ENST00000235739;ENST00000538290;ENST00000355199	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	4.09	0.543	0.17179	Immunoglobulin-like (1);	0.753844	0.13658	N	0.371768	T	0.16171	0.0389	M	0.69358	2.11	0.09310	N	1	B	0.16396	0.017	B	0.13407	0.009	T	0.24225	-1.0166	10	0.40728	T	0.16	0.0403	3.2926	0.06954	0.0:0.2211:0.2114:0.5675	.	155	Q13291	SLAF1_HUMAN	T	155	ENSP00000306190:N155T;ENSP00000235739:N155T;ENSP00000438406:N155T;ENSP00000347333:N155T	ENSP00000235739:N155T	N	-	2	0	SLAMF1	158871263	0.002000	0.14202	0.007000	0.13788	0.958000	0.62258	0.299000	0.19138	0.075000	0.16796	0.533000	0.62120	AAC	.	.		0.552	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1			G	160604639	T	G	160604639	3	3	152	1	0	0	0	0	1	0	0	0	14382	1725	60	5	563	5	SLAMF1	1	160604639	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	8322235	160604639	88645982	8	23356										
ZBTB41	360023	hgsc.bcm.edu	37	chr1	197157558	197157558	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tgtggtcttcgagtaaaagaTttcttacaaatctaaattaa	6	5	3	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr1:197157558T>C	ENST00000367405.4	-	4	1478	c.1410A>G	c.(1408-1410)aaA>aaG	p.K470K	ZBTB41_ENST00000467322.1_5'UTR	NM_194314.2	NP_919290.2	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	470					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(11)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	40						GAGTAAAAGATTTCTTACAAA	0.279																																					p.K470K		Atlas-SNP	.											ZBTB41,NS,carcinoma,-2,1	ZBTB41	116	1	0			c.A1410G						.						43	42	43					1																	197157558		2201	4299	6500	SO:0001819	synonymous_variant	360023	exon4			AAAAGATTTCTTA		CCDS30960.1	1q31.3	2013-01-08			ENSG00000177888	ENSG00000177888		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	24819	protein-coding gene	gene with protein product							Standard	NM_194314		Approved	FRBZ1, FLJ36199, DKFZp686C06120, ZNF924	uc001gtx.1	Q5SVQ8	OTTHUMG00000036275	ENST00000367405.4:c.1410A>G	1.37:g.197157558T>C		49.0	0.0		34.0	11.0	NM_194314	A2RUA8|Q6MZT8|Q6ZR25|Q7Z4T1|Q8IZ99	Silent	SNP	ENST00000367405.4	37	CCDS30960.1																																																																																			.	.		0.279	ZBTB41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088249.2	NM_194314		C	197157558	T	C	197157558	2	2	152	1	0	0	0	0	0	0	0	1	17558	1490	52	2		2	ZBTB41	1	197157558	Silent	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	36552919	197157558	52093063	9	23357										
NUP133	55746	hgsc.bcm.edu	37	chr1	229625781	229625781	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cattatcttctattgttatcAgagagtaatagatgagacat	7	5	3	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr1:229625781A>T	ENST00000261396.3	-	9	1206	c.1115T>A	c.(1114-1116)cTg>cAg	p.L372Q	NUP133_ENST00000537506.1_Missense_Mutation_p.L356Q	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	372					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TATTGTTATCAGAGAGTAATA	0.373																																					p.L372Q		Atlas-SNP	.											.	NUP133	111	.	0			c.T1115A						.						62	61	61					1																	229625781		2203	4300	6503	SO:0001583	missense	55746	exon9			GTTATCAGAGAGT		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1115T>A	1.37:g.229625781A>T	ENSP00000261396:p.Leu372Gln	161.0	0.0		84.0	39.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107287	0.77096	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.36520	1.25;1.25;1.25	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.066940	0.64402	D	0.000010	T	0.59528	0.2200	M	0.72118	2.19	0.58432	D	0.999997	D	0.76494	0.999	D	0.70016	0.967	T	0.63010	-0.6732	10	0.66056	D	0.02	-18.8712	15.9649	0.79961	1.0:0.0:0.0:0.0	.	372	Q8WUM0	NU133_HUMAN	Q	372;372;372;356	ENSP00000261396:L372Q;ENSP00000355640:L372Q;ENSP00000443496:L356Q	ENSP00000261396:L372Q	L	-	2	0	NUP133	227692404	1.000000	0.71417	0.535000	0.28026	0.835000	0.47333	7.911000	0.87458	2.232000	0.73038	0.533000	0.62120	CTG	.	.		0.373	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		T	229625781	A	T	229625781	3	4	152	1	0	0	0	0	1	0	0	0	10763	188	7	4	2427	4	NUP133	1	229625781	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	32468223	229625781	19624840	10	23358										
ZNF512	84450	hgsc.bcm.edu	37	chr2	27822456	27822456	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gtatggtacttcagggtcagGtggagtatcagccaagggga	16	6	3	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr2:27822456G>T	ENST00000355467.4	+	4	367	c.284G>T	c.(283-285)gGt>gTt	p.G95V	ZNF512_ENST00000413371.2_Missense_Mutation_p.G18V|ZNF512_ENST00000494548.1_3'UTR|ZNF512_ENST00000379717.1_Missense_Mutation_p.G94V|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000416005.2_Missense_Mutation_p.G94V|ZNF512_ENST00000556601.1_Missense_Mutation_p.V6L	NM_001271287.1|NM_001271288.1|NM_001271289.1|NM_001271318.1|NM_032434.3	NP_001258216.1|NP_001258217.1|NP_001258218.1|NP_001258247.1|NP_115810.2	Q96ME7	ZN512_HUMAN	zinc finger protein 512	95					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)					TCAGGGTCAGGTGGAGTATCA	0.408																																					p.G95V		Atlas-SNP	.											.	ZNF512	54	.	0			c.G284T						.						100	103	102					2																	27822456		2203	4300	6503	SO:0001583	missense	84450	exon4			GGTCAGGTGGAGT	AL833748	CCDS1758.1, CCDS59428.1, CCDS59429.1	2p23	2008-02-05			ENSG00000243943	ENSG00000243943		"Zinc fingers, C2H2-type"	29380	protein-coding gene	gene with protein product						11347906	Standard	NM_032434		Approved	KIAA1805	uc002rla.4	Q96ME7	OTTHUMG00000097786	ENST00000355467.4:c.284G>T	2.37:g.27822456G>T	ENSP00000347648:p.Gly95Val	198.0	0.0		99.0	38.0	NM_032434	B4DSM5|Q53RZ7|Q86XK6|Q96JM0	Missense_Mutation	SNP	ENST00000355467.4	37	CCDS1758.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.28|16.28	3.079673|3.079673	0.55753|0.55753	.|.	.|.	ENSG00000243943|ENSG00000243943	ENST00000379717;ENST00000355467;ENST00000416005;ENST00000413371|ENST00000556601	.|.	.|.	.|.	5.86|5.86	4.97|4.97	0.65823|0.65823	.|.	0.435767|.	0.22087|.	N|.	0.064813|.	T|T	0.29288|0.29288	0.0729|0.0729	N|N	0.12182|0.12182	0.205|0.205	0.20821|0.20821	N|N	0.999844|0.999844	P;P;P|.	0.50443|.	0.931;0.935;0.935|.	B;B;B|.	0.35413|.	0.202;0.202;0.202|.	T|T	0.19712|0.19712	-1.0297|-1.0297	9|5	0.72032|.	D|.	0.01|.	-7.9976|-7.9976	13.2925|13.2925	0.60278|0.60278	0.0:0.3033:0.6967:0.0|0.0:0.3033:0.6967:0.0	.|.	18;94;95|.	B4DES6;B4DSM5;Q96ME7|.	.;.;ZN512_HUMAN|.	V|L	94;95;94;18|6	.|.	ENSP00000347648:G95V|.	G|V	+|+	2|1	0|0	ZNF512|ZNF512	27675960|27675960	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.992000|0.992000	0.81027|0.81027	3.510000|3.510000	0.53393|0.53393	1.464000|1.464000	0.47987|0.47987	0.655000|0.655000	0.94253|0.94253	GGT|GTG	.	.		0.408	ZNF512-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215029.2	NM_032434		T	27822456	G	T	27822456	3	4	152	1	0	0	0	0	1	0	0	0	17971	1261	44	3	298	3	ZNF512	2	27822456	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10		27822456	215376917	11	23359										
HAAO	23498	hgsc.bcm.edu	37	chr2	43015676	43015676	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cagtcaaacctacctcttcaCcctcttcgatgtgatagtcc	5	15	4	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr2:43015676C>T	ENST00000294973.6	-	2	207	c.152G>A	c.(151-153)gGt>gAt	p.G51D		NM_012205.2	NP_036337.2			3-hydroxyanthranilate 3,4-dioxygenase											breast(2)|cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(2)	11						TACCTCTTCACCCTCTTCGAT	0.602																																					p.G51D		Atlas-SNP	.											.	HAAO	26	.	0			c.G152A						.						249	173	199					2																	43015676		2203	4300	6503	SO:0001583	missense	23498	exon2			TCTTCACCCTCTT	Z29481	CCDS33187.1	2p	2008-02-05			ENSG00000162882	ENSG00000162882	1.13.11.6		4796	protein-coding gene	gene with protein product		604521				7514594	Standard	NM_012205		Approved		uc002rst.4	P46952	OTTHUMG00000152348	ENST00000294973.6:c.152G>A	2.37:g.43015676C>T	ENSP00000294973:p.Gly51Asp	49.0	0.0		61.0	30.0	NM_012205		Missense_Mutation	SNP	ENST00000294973.6	37	CCDS33187.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.290516	0.80914	.	.	ENSG00000162882	ENST00000294973;ENST00000431905	T;T	0.37235	1.21;1.21	5.44	4.56	0.56223	Cupin, RmlC-type (1);	0.000000	0.85682	D	0.000000	T	0.64136	0.2571	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70092	-0.4967	10	0.66056	D	0.02	.	12.4725	0.55795	0.0:0.916:0.0:0.084	.	51	P46952	3HAO_HUMAN	D	51;17	ENSP00000294973:G51D;ENSP00000412601:G17D	ENSP00000294973:G51D	G	-	2	0	HAAO	42869180	1.000000	0.71417	0.995000	0.50966	0.964000	0.63967	5.910000	0.69931	2.554000	0.86153	0.655000	0.94253	GGT	.	.		0.602	HAAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325948.2			T	43015676	C	T	43015676	3	4	152	1	0	0	0	0	1	0	0	0	6946	507	18	3	744	3	HAAO	2	43015676	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	15193220	43015676	200183697	12	23360										
ABCG8	64241	hgsc.bcm.edu	37	chr2	44102319	44102319	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tccggagcactgtgcctacaTcatcatctacgggatgccca	9	14	3	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr2:44102319T>G	ENST00000272286.2	+	11	1613	c.1523T>G	c.(1522-1524)aTc>aGc	p.I508S		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	508	ABC transmembrane type-2.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	TGTGCCTACATCATCATCTAC	0.552																																					p.I508S		Atlas-SNP	.											.	ABCG8	98	.	0			c.T1523G						.						85	79	81					2																	44102319		2203	4300	6503	SO:0001583	missense	64241	exon11			CCTACATCATCAT	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"ATP binding cassette transporters / subfamily G"	13887	protein-coding gene	gene with protein product	"gallbladder disease 4", "sterolin 2"	605460	"ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.1523T>G	2.37:g.44102319T>G	ENSP00000272286:p.Ile508Ser	50.0	0.0		42.0	14.0	NM_022437	Q53QN8	Missense_Mutation	SNP	ENST00000272286.2	37	CCDS1815.1	.	.	.	.	.	.	.	.	.	.	T	9.207	1.030060	0.19512	.	.	ENSG00000143921	ENST00000272286	T	0.70749	-0.51	4.62	3.46	0.39613	ABC-2 type transporter (1);	0.516766	0.21777	N	0.069269	T	0.51278	0.1665	N	0.14661	0.345	0.09310	N	0.999997	B;B	0.20459	0.045;0.024	B;B	0.21151	0.031;0.033	T	0.38286	-0.9668	10	0.33141	T	0.24	.	9.8422	0.41006	0.0:0.0815:0.0:0.9185	.	507;508	Q9H221-2;Q9H221	.;ABCG8_HUMAN	S	508	ENSP00000272286:I508S	ENSP00000272286:I508S	I	+	2	0	ABCG8	43955823	0.998000	0.40836	0.009000	0.14445	0.786000	0.44442	3.690000	0.54713	0.642000	0.30620	0.383000	0.25322	ATC	.	.		0.552	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437		G	44102319	T	G	44102319	3	3	152	1	0	0	0	0	1	0	0	0	72	1435	50	5	1565	5	ABCG8	2	44102319	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	1086643	44102319	199097054	13	23361										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131522066	131522066	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gcccggtggagttcccagggCcaccatccagaaagcctggg	14	14	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr2:131522066C>A	ENST00000423981.1	+	2	2531	c.2421C>A	c.(2419-2421)ggC>ggA	p.G807G	AMER3_ENST00000321420.4_Silent_p.G807G	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	807					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										GTTCCCAGGGCCACCATCCAG	0.667																																					p.G807G		Atlas-SNP	.											.	.	.	.	0			c.C2421A						.						11	12	12					2																	131522066		2197	4293	6490	SO:0001819	synonymous_variant	205147	exon2			CCAGGGCCACCAT	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.2421C>A	2.37:g.131522066C>A		66.0	0.0		97.0	33.0	NM_152698	B7ZLH6	Silent	SNP	ENST00000423981.1	37	CCDS2164.1																																																																																			.	.		0.667	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		A	131522066	C	A	131522066	2	1	152	1	0	0	0	0	0	0	0	1	5429	726	26	3		3	FAM123C	2	131522066	Silent	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	87419747	131522066	111677307	14	23362										
MFF	56947	hgsc.bcm.edu	37	chr2	228197291	228197291	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	agaaagacctcctacaacccCtcaaaatgaagaagtaagta	6	10	1	4			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr2:228197291C>T	ENST00000353339.3	+	5	857	c.416C>T	c.(415-417)cCt>cTt	p.P139L	MFF_ENST00000524634.1_5'UTR|MFF_ENST00000337110.7_Missense_Mutation_p.P113L|MFF_ENST00000392059.1_Missense_Mutation_p.P139L|MFF_ENST00000476924.1_3'UTR|MFF_ENST00000349901.7_Missense_Mutation_p.P113L|MFF_ENST00000304593.9_Missense_Mutation_p.P113L|MFF_ENST00000409616.1_Missense_Mutation_p.P113L|MFF_ENST00000409565.1_Missense_Mutation_p.P113L|MFF_ENST00000354503.6_Missense_Mutation_p.P113L	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	139					mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)			breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						CCTACAACCCCTCAAAATGAA	0.388																																					p.P139L		Atlas-SNP	.											.	MFF	48	.	0			c.C416T						.						176	192	187					2																	228197291		2203	4300	6503	SO:0001583	missense	56947	exon5			CAACCCCTCAAAA	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"chromosome 2 open reading frame 33"	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.416C>T	2.37:g.228197291C>T	ENSP00000302037:p.Pro139Leu	256.0	0.0		140.0	57.0	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Missense_Mutation	SNP	ENST00000353339.3	37	CCDS2465.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.269825	0.80469	.	.	ENSG00000168958	ENST00000304593;ENST00000353339;ENST00000354503;ENST00000409565;ENST00000452930;ENST00000409616;ENST00000337110;ENST00000349901;ENST00000392059	T;T	0.34072	1.38;1.38	5.02	5.02	0.67125	.	0.165377	0.53938	D	0.000050	T	0.54319	0.1851	L	0.49350	1.555	0.80722	D	1	D;B;B;P;D;P	0.76494	0.994;0.284;0.004;0.467;0.999;0.815	P;B;B;B;D;P	0.65233	0.9;0.188;0.013;0.103;0.933;0.5	T	0.55598	-0.8116	10	0.59425	D	0.04	-18.5936	18.6891	0.91576	0.0:1.0:0.0:0.0	.	113;113;113;113;113;139	Q9GZY8-4;Q9GZY8-3;Q9GZY8-5;C9JHF5;Q9GZY8-2;Q9GZY8	.;.;.;.;.;MFF_HUMAN	L	113;139;113;113;113;113;113;113;139	ENSP00000302037:P139L;ENSP00000375912:P139L	ENSP00000304898:P113L	P	+	2	0	MFF	227905535	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.123000	0.50453	2.478000	0.83669	0.563000	0.77884	CCT	.	.		0.388	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194		T	228197291	C	T	228197291	3	4	152	1	0	0	0	0	1	0	0	0	9528	681	24	3	426	3	MFF	2	228197291	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	96675225	228197291	15002082	15	23363										
TTLL3	26140	hgsc.bcm.edu	37	chr3	9867563	9867563	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	agcagctgcaggccgtggtaCcccagatagacatggaaggg	15	10	0	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr3:9867563C>T	ENST00000547186.1	+	8	1021	c.805C>T	c.(805-807)Ccc>Tcc	p.P269S	TTLL3_ENST00000397241.1_Missense_Mutation_p.P57S|ARPC4-TTLL3_ENST00000397256.1_Missense_Mutation_p.P330S|TTLL3_ENST00000426895.4_Missense_Mutation_p.P412S|TTLL3_ENST00000455274.1_Missense_Mutation_p.P57S|TTLL3_ENST00000383827.1_Missense_Mutation_p.P57S|TTLL3_ENST00000430793.1_Missense_Mutation_p.P57S|TTLL3_ENST00000427853.3_Missense_Mutation_p.P57S|TTLL3_ENST00000466245.1_3'UTR	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	269	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					GGCCGTGGTACCCCAGATAGA	0.607																																					p.P412S		Atlas-SNP	.											.	TTLL3	51	.	0			c.C1234T						.						80	69	73					3																	9867563		2203	4300	6503	SO:0001583	missense	26140	exon8			GTGGTACCCCAGA		CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"Tubulin tyrosine ligase-like family"	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.805C>T	3.37:g.9867563C>T	ENSP00000446659:p.Pro269Ser	351.0	1.0		318.0	158.0	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Missense_Mutation	SNP	ENST00000547186.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.5|25.5	4.649280|4.649280	0.87958|0.87958	.|.	.|.	ENSG00000250151;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021|ENSG00000214021	ENST00000397256;ENST00000426895;ENST00000547186;ENST00000397241;ENST00000427853;ENST00000443148;ENST00000383827;ENST00000455274;ENST00000430793|ENST00000310252;ENST00000452823	T;T;T;T;T;T;T;T;T|.	0.46451|.	0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87|.	4.86|4.86	3.97|3.97	0.46021|0.46021	.|.	0.075472|.	0.53938|.	U|.	0.000049|.	T|T	0.69124|0.69124	0.3076|0.3076	M|M	0.64676|0.64676	1.99|1.99	0.58432|0.58432	D|D	0.999997|0.999997	D;D;D;D;D;D|.	0.71674|.	0.998;0.969;0.998;0.972;0.975;0.981|.	D;P;D;D;D;P|.	0.70016|.	0.967;0.868;0.936;0.919;0.951;0.871|.	T|T	0.68164|0.68164	-0.5481|-0.5481	10|5	0.87932|.	D|.	0|.	.|.	12.556|12.556	0.56254|0.56254	0.0:0.9182:0.0:0.0818|0.0:0.9182:0.0:0.0818	.|.	208;57;57;57;269;330|.	B4DM47;Q9Y4R7-2;B2RCJ2;Q9Y4R7-5;Q9Y4R7;E7ETI0|.	.;.;.;.;TTLL3_HUMAN;.|.	S|I	330;412;269;57;57;207;57;57;57|224;186	ENSP00000380427:P330S;ENSP00000392549:P412S;ENSP00000446659:P269S;ENSP00000380416:P57S;ENSP00000394462:P57S;ENSP00000398097:P207S;ENSP00000373338:P57S;ENSP00000409632:P57S;ENSP00000403874:P57S|.	ENSP00000380416:P57S|.	P|T	+|+	1|2	0|0	ARPC4-TTLL3;TTLL3|TTLL3	9842563|9842563	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.990000|0.990000	0.78478|0.78478	5.691000|5.691000	0.68249|0.68249	2.420000|2.420000	0.82092|0.82092	0.561000|0.561000	0.74099|0.74099	CCC|ACC	.	.		0.607	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2		T	9867563	C	T	9867563	3	4	152	1	0	0	0	0	1	0	0	0	16743	507	18	3	831	3	TTLL3	3	9867563	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10		9867563	188154867	16	23364										
PLCL2	23228	hgsc.bcm.edu	37	chr3	17053189	17053189	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tgtggtagatccttatgtctAtgttgaaatccatggaatcc	9	7	1	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr3:17053189A>G	ENST00000418129.2	+	2	2438	c.1973A>G	c.(1972-1974)tAt>tGt	p.Y658C	PLCL2_ENST00000432376.1_Missense_Mutation_p.Y658C|PLCL2_ENST00000396755.2_Missense_Mutation_p.Y658C	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	784	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						CCTTATGTCTATGTTGAAATC	0.428																																					p.Y658C		Atlas-SNP	.											.	PLCL2	145	.	0			c.A1973G						.						76	76	76					3																	17053189		2203	4300	6503	SO:0001583	missense	23228	exon2			ATGTCTATGTTGA	AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"phospholipase C, epsilon 2"	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.1973A>G	3.37:g.17053189A>G	ENSP00000409637:p.Tyr658Cys	132.0	0.0		92.0	42.0	NM_015184	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Missense_Mutation	SNP	ENST00000418129.2	37	CCDS33713.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.697|5.697	0.313067|0.313067	0.10789|0.10789	.|.	.|.	ENSG00000154822|ENSG00000154822	ENST00000419842|ENST00000418129;ENST00000285094;ENST00000396755;ENST00000432376	.|T;T;T	.|0.68765	.|-0.35;-0.35;-0.35	4.96|4.96	4.96|4.96	0.65561|0.65561	.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|0.057327	.|0.64402	.|D	.|0.000001	T|T	0.59074|0.59074	0.2167|0.2167	.|.	.|.	.|.	0.58432|0.58432	D|D	0.999999|0.999999	.|B	.|0.11235	.|0.004	.|B	.|0.17979	.|0.02	T|T	0.55872|0.55872	-0.8072|-0.8072	4|9	.|0.38643	.|T	.|0.18	.|.	14.9278|14.9278	0.70893|0.70893	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|784	.|Q9UPR0	.|PLCL2_HUMAN	V|C	402|658;785;658;658	.|ENSP00000409637:Y658C;ENSP00000379979:Y658C;ENSP00000412836:Y658C	.|ENSP00000285094:Y785C	M|Y	+|+	1|2	0|0	PLCL2|PLCL2	17028193|17028193	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.018000|0.018000	0.09664|0.09664	7.386000|7.386000	0.79775|0.79775	1.983000|1.983000	0.57843|0.57843	0.459000|0.459000	0.35465|0.35465	ATG|TAT	.	.		0.428	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3			G	17053189	A	G	17053189	3	3	152	1	0	0	0	0	1	0	0	0	12049	449	16	2	2351	2	PLCL2	3	17053189	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	7185626	17053189	180969241	17	23365										
NGLY1	55768	hgsc.bcm.edu	37	chr3	25777623	25777623	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ctgctgagaaggagaatagaCttctgtccagacatggtcta	11	8	2	4			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr3:25777623C>G	ENST00000280700.5	-	7	1181	c.1021G>C	c.(1021-1023)Gtc>Ctc	p.V341L	NGLY1_ENST00000467224.1_5'Flank|NGLY1_ENST00000422724.2_3'UTR|NGLY1_ENST00000396649.3_Missense_Mutation_p.V341L|NGLY1_ENST00000428257.1_Intron|NGLY1_ENST00000417874.2_Missense_Mutation_p.V299L	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	341					glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						GGAGAATAGACTTCTGTCCAG	0.413																																					p.V341L		Atlas-SNP	.											.	NGLY1	57	.	0			c.G1021C						.						50	47	48					3																	25777623		2203	4300	6503	SO:0001583	missense	55768	exon7			AATAGACTTCTGT	AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.1021G>C	3.37:g.25777623C>G	ENSP00000280700:p.Val341Leu	146.0	0.0		68.0	22.0	NM_018297	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Missense_Mutation	SNP	ENST00000280700.5	37	CCDS33719.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.114416	0.77210	.	.	ENSG00000151092	ENST00000280700;ENST00000396649;ENST00000417874	T;T;T	0.38401	1.14;1.14;1.14	5.66	5.66	0.87406	Transglutaminase-like (2);	0.000000	0.85682	D	0.000000	T	0.56601	0.1996	H	0.94423	3.535	0.80722	D	1	B;B;B	0.34255	0.085;0.445;0.355	B;B;B	0.34779	0.123;0.177;0.189	T	0.66740	-0.5847	10	0.62326	D	0.03	-10.8079	20.1253	0.97977	0.0:1.0:0.0:0.0	.	299;341;341	B4DJE9;Q96IV0-3;Q96IV0	.;.;NGLY1_HUMAN	L	341;341;299	ENSP00000280700:V341L;ENSP00000379886:V341L;ENSP00000389888:V299L	ENSP00000280700:V341L	V	-	1	0	NGLY1	25752627	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.894000	0.63206	2.832000	0.97577	0.655000	0.94253	GTC	.	.		0.413	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2			G	25777623	C	G	25777623	3	3	152	1	0	0	0	0	1	0	0	0	10407	565	20	4	967	4	NGLY1	3	25777623	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	8724434	25777623	172244807	18	23366										
EOMES	8320	hgsc.bcm.edu	37	chr3	27763429	27763429	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gcggcggcggcggcggcggcTgcagcggcggagggcagctc	23	13	0	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr3:27763429T>G	ENST00000295743.4	-	1	560	c.357A>C	c.(355-357)gcA>gcC	p.A119A	EOMES_ENST00000449599.1_Silent_p.A119A|EOMES_ENST00000461503.1_Intron|EOMES_ENST00000537516.1_Intron			O95936	EOMES_HUMAN	eomesodermin	119	Ala-rich.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						cggcggcggctgcagcggcgg	0.766																																					p.A119A		Atlas-SNP	.											.	EOMES	65	.	0			c.A357C						.						1	1	1					3																	27763429		553	1356	1909	SO:0001819	synonymous_variant	8320	exon1			GGCGGCTGCAGCG	BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"T-boxes"	3372	protein-coding gene	gene with protein product	"T-box brain2"	604615	"eomesodermin (Xenopus laevis) homolog"			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.357A>C	3.37:g.27763429T>G		29.0	0.0		65.0	18.0	NM_005442	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Silent	SNP	ENST00000295743.4	37	CCDS2646.1																																																																																			.	.		0.766	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442		G	27763429	T	G	27763429	2	3	152	1	0	0	0	0	0	0	0	1	5149	1567	55	5		5	EOMES	3	27763429	Silent	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	1985806	27763429	170259001	19	23367										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266101	41266101	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gcaacagtcttacctggactCtggaatccattctggtgcca	9	12	3	0	rs121913416|rs121913400		TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr3:41266101C>T	ENST00000349496.5	+	3	378	c.98C>T	c.(97-99)tCt>tTt	p.S33F	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,435	CTNNB1	4904	435	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98T						.						92	77	82					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>T	3.37:g.41266101C>T	ENSP00000344456:p.Ser33Phe	154.0	0.0		70.0	22.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.498846	0.85069	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	F	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26F;ENSP00000385604:S33F;ENSP00000412219:S33F;ENSP00000379486:S33F;ENSP00000344456:S33F;ENSP00000411226:S26F;ENSP00000379488:S33F;ENSP00000409302:S33F;ENSP00000401599:S33F	ENSP00000344456:S33F	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266101	C	T	41266101	3	4	152	1	0	0	0	0	1	0	0	0	4018	913	32	3	104	3	CTNNB1	3	41266101	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	13502672	41266101	156756329	20	23368										
CDCP1	64866	hgsc.bcm.edu	37	chr3	45152154	45152154	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gatgtagtattcaacccgctCctccttcctctcacagttgg	7	14	2	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr3:45152154C>A	ENST00000296129.1	-	4	969	c.835G>T	c.(835-837)Gag>Tag	p.E279*	CDCP1_ENST00000425231.2_Nonsense_Mutation_p.E279*|CDCP1_ENST00000490471.1_5'Flank	NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	279						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		TCAACCCGCTCCTCCTTCCTC	0.577																																					p.E279X		Atlas-SNP	.											.	CDCP1	61	.	0			c.G835T						.						125	118	121					3																	45152154		2203	4300	6503	SO:0001587	stop_gained	64866	exon4			CCCGCTCCTCCTT	AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"CD molecules"	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.835G>T	3.37:g.45152154C>A	ENSP00000296129:p.Glu279*	156.0	0.0		155.0	75.0	NM_178181	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Nonsense_Mutation	SNP	ENST00000296129.1	37	CCDS2727.1	.	.	.	.	.	.	.	.	.	.	C	36	5.802050	0.96960	.	.	ENSG00000163814	ENST00000296129;ENST00000425231	.	.	.	5.87	3.95	0.45737	.	0.459206	0.26650	N	0.023218	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	16.3177	0.82934	0.0:0.7506:0.2494:0.0	.	.	.	.	X	279	.	ENSP00000296129:E279X	E	-	1	0	CDCP1	45127158	0.997000	0.39634	1.000000	0.80357	0.997000	0.91878	2.299000	0.43611	1.593000	0.50029	0.655000	0.94253	GAG	.	.		0.577	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842		A	45152154	C	A	45152154	4	1	152	1	0	0	0	0	0	1	0	0	3095	864	30	3	1707	3	CDCP1	3	45152154	Nonsense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	3886053	45152154	152870276	21	23369										
FEZF2	55079	hgsc.bcm.edu	37	chr3	62356922	62356922	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aaagcctttgccgcaaaattCgcagacgaagggcttgtagc	11	10	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr3:62356922C>A	ENST00000283268.3	-	4	1384	c.1090G>T	c.(1090-1092)Gaa>Taa	p.E364*	FEZF2_ENST00000475839.1_Nonsense_Mutation_p.E364*|PTPRG-AS1_ENST00000495542.1_RNA|PTPRG-AS1_ENST00000490916.1_RNA|FEZF2_ENST00000486811.1_Nonsense_Mutation_p.E364*	NM_018008.3	NP_060478.3	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2	364					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cerebral cortex GABAergic interneuron migration (GO:0021853)|dendrite development (GO:0016358)|dentate gyrus development (GO:0021542)|forebrain anterior/posterior pattern specification (GO:0021797)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|lung(8)|skin(1)	20		Lung SC(41;0.0262)		BRCA - Breast invasive adenocarcinoma(55;0.000221)|KIRC - Kidney renal clear cell carcinoma(15;0.00834)|Kidney(15;0.00957)		CCGCAAAATTCGCAGACGAAG	0.572																																					p.E364X	NSCLC(170;1772 2053 12525 15604 23984)	Atlas-SNP	.											.	FEZF2	46	.	0			c.G1090T						.						110	107	108					3																	62356922		2203	4300	6503	SO:0001587	stop_gained	55079	exon4			AAAATTCGCAGAC	AF064845	CCDS2897.1	3p21.1	2013-01-08	2006-08-15	2006-08-15	ENSG00000153266	ENSG00000153266		"Zinc fingers, C2H2-type"	13506	protein-coding gene	gene with protein product		607414	"zinc finger protein 312"	ZNF312			Standard	NM_018008		Approved	FLJ10142, FKSG36, TOF, FEZL, Zfp312	uc003dli.2	Q8TBJ5	OTTHUMG00000158705	ENST00000283268.3:c.1090G>T	3.37:g.62356922C>A	ENSP00000283268:p.Glu364*	94.0	0.0		79.0	31.0	NM_018008	A8K349|Q9BZ91|Q9NWB9	Nonsense_Mutation	SNP	ENST00000283268.3	37	CCDS2897.1	.	.	.	.	.	.	.	.	.	.	C	37	6.259302	0.97421	.	.	ENSG00000153266	ENST00000486811;ENST00000283268;ENST00000475839	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-18.9899	20.6525	0.99598	0.0:1.0:0.0:0.0	.	.	.	.	X	364	.	ENSP00000283268:E364X	E	-	1	0	FEZF2	62331962	1.000000	0.71417	1.000000	0.80357	0.118000	0.20060	7.818000	0.86416	2.890000	0.99128	0.585000	0.79938	GAA	.	.		0.572	FEZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351813.1	NM_018008		A	62356922	C	A	62356922	4	1	152	1	0	0	0	0	0	1	0	0	5834	893	31	1	297	1	FEZF2	3	62356922	Nonsense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	17204768	62356922	135665508	22	23370										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64582563	64582563	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ccggattcacaggctctttgCtcatcaggttttattctctc	7	12	5	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr3:64582563C>T	ENST00000498707.1	-	27	4464	c.4122G>A	c.(4120-4122)gaG>gaA	p.E1374E	ADAMTS9_ENST00000295903.4_Silent_p.E1346E	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1374	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		AGGCTCTTTGCTCATCAGGTT	0.498																																					p.E1374E		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G4122A						.						112	94	100					3																	64582563		2203	4300	6503	SO:0001819	synonymous_variant	56999	exon27			TCTTTGCTCATCA	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.4122G>A	3.37:g.64582563C>T		74.0	0.0		61.0	21.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Silent	SNP	ENST00000498707.1	37	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	C	9.687	1.150868	0.21371	.	.	ENSG00000163638	ENST00000481060	.	.	.	5.4	3.59	0.41128	.	.	.	.	.	T	0.62768	0.2455	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59963	-0.7355	4	.	.	.	.	12.2158	0.54406	0.0:0.8604:0.0:0.1396	.	.	.	.	N	430	.	.	S	-	2	0	ADAMTS9	64557603	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.177000	0.42509	0.821000	0.34540	0.591000	0.81541	AGC	.	.		0.498	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			T	64582563	C	T	64582563	2	4	152	1	0	0	0	0	0	0	0	1	273	796	28	3		3	ADAMTS9	3	64582563	Silent	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	2225641	64582563	133439867	23	23371										
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69362608	69362608	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gtgggccacacctacctgaaCcagcagctccagtctcctat	8	16	1	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr3:69362608C>A	ENST00000398540.3	-	2	306	c.223G>T	c.(223-225)Gtt>Ttt	p.V75F	FRMD4B_ENST00000542259.1_Missense_Mutation_p.V21F	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	75	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		CCTACCTGAACCAGCAGCTCC	0.577																																					p.V75F		Atlas-SNP	.											.	FRMD4B	90	.	0			c.G223T						.						53	56	55					3																	69362608		2060	4184	6244	SO:0001583	missense	23150	exon2			CCTGAACCAGCAG	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.223G>T	3.37:g.69362608C>A	ENSP00000381549:p.Val75Phe	92.0	0.0		56.0	24.0	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	C	29.4	4.999024	0.93227	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000473029;ENST00000460709;ENST00000459638;ENST00000497880	T;T;T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36;-1.36;-1.36	6.08	6.08	0.98989	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.89451	0.6719	M	0.71206	2.165	0.80722	D	1	D;P	0.67145	0.996;0.938	D;P	0.70487	0.969;0.906	D	0.89263	0.3599	10	0.72032	D	0.01	-15.967	19.4349	0.94788	0.0:1.0:0.0:0.0	.	180;75	Q6PEW6;Q9Y2L6	.;FRM4B_HUMAN	F	75;21;21;21;21;21	ENSP00000381549:V75F;ENSP00000437658:V21F;ENSP00000418373:V21F;ENSP00000418023:V21F;ENSP00000417550:V21F;ENSP00000417765:V21F	ENSP00000381549:V75F	V	-	1	0	FRMD4B	69445298	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.500000	0.73687	2.894000	0.99253	0.655000	0.94253	GTT	.	.		0.577	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			A	69362608	C	A	69362608	3	1	152	1	0	0	0	0	1	0	0	0	6060	507	18	3	2969	3	FRMD4B	3	69362608	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	4780045	69362608	128659822	24	23372										
PDE6B	5158	hgsc.bcm.edu	37	chr4	619713	619713	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gcctcttcatgtaccgccagCgcaacggcgtggccgagctg	13	15	2	0	rs537263212		TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr4:619713C>A	ENST00000496514.1	+	1	319	c.298C>A	c.(298-300)Cgc>Agc	p.R100S	PDE6B_ENST00000255622.6_Missense_Mutation_p.R100S			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	100	GAF 1.		R -> H (in RP40). {ECO:0000269|PubMed:22334370}.		cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	GTACCGCCAGCGCAACGGCGT	0.672																																					p.R100S	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.C298A						.						13	12	12					4																	619713		2193	4289	6482	SO:0001583	missense	5158	exon1			CGCCAGCGCAACG	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"Phosphodiesterases"	8786	protein-coding gene	gene with protein product	"congenital stationary night blindness 3, autosomal dominant"	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.298C>A	4.37:g.619713C>A	ENSP00000420295:p.Arg100Ser	68.0	0.0		87.0	47.0	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	37	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.604494	0.66445	.	.	ENSG00000133256	ENST00000255622;ENST00000496514	T;T	0.68479	-0.33;-0.33	4.98	4.04	0.47022	GAF (2);	0.000000	0.85682	D	0.000000	T	0.76673	0.4020	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.75536	-0.3283	10	0.41790	T	0.15	.	9.3606	0.38192	0.3641:0.6359:0.0:0.0	.	100;100	P35913;P35913-2	PDE6B_HUMAN;.	S	100	ENSP00000255622:R100S;ENSP00000420295:R100S	ENSP00000255622:R100S	R	+	1	0	PDE6B	609713	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	0.754000	0.26390	2.326000	0.78906	0.561000	0.74099	CGC	.	.		0.672	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		A	619713	C	A	619713	3	1	152	1	0	0	0	0	1	0	0	0	11655	768	27	1	300	1	PDE6B	4	619713	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10		619713	190534563	25	23373										
C4orf31	79625	hgsc.bcm.edu	37	chr4	121966814	121966814	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	agggagaatacctcttaggtGtatctctaaagagataactg	10	6	2	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr4:121966814G>C	ENST00000379692.4	-	2	705	c.179C>G	c.(178-180)aCa>aGa	p.T60R		NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	60					cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						CCTCTTAGGTGTATCTCTAAA	0.368																																					p.T60R		Atlas-SNP	.											.	NDNF	72	.	0			c.C179G						.						61	58	58					4																	121966814		1817	4081	5898	SO:0001583	missense	79625	exon2			TTAGGTGTATCTC	BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 31"	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.179C>G	4.37:g.121966814G>C	ENSP00000369014:p.Thr60Arg	158.0	0.0		72.0	34.0	NM_024574	A8K0Q0|Q6UWE5|Q9H5P7	Missense_Mutation	SNP	ENST00000379692.4	37	CCDS3717.2	.	.	.	.	.	.	.	.	.	.	G	15.69	2.908950	0.52439	.	.	ENSG00000173376	ENST00000379692;ENST00000515757;ENST00000511408	.	.	.	5.72	5.72	0.89469	.	0.048637	0.85682	D	0.000000	T	0.54598	0.1868	L	0.51422	1.61	0.58432	D	0.999999	P	0.41313	0.745	B	0.41236	0.351	T	0.53556	-0.8422	9	0.36615	T	0.2	-23.1078	14.7034	0.69171	0.0:0.0:0.8552:0.1448	.	60	Q8TB73	NDNF_HUMAN	R	60	.	ENSP00000369014:T60R	T	-	2	0	NDNF	122186264	1.000000	0.71417	0.996000	0.52242	0.886000	0.51366	7.500000	0.81588	2.717000	0.92951	0.655000	0.94253	ACA	.	.		0.368	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574		C	121966814	G	C	121966814	3	2	152	1	0	0	0	0	1	0	0	0	2263	1377	48	4	1539	4	C4orf31	4	121966814	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	121347101	121966814	69187462	26	23374										
ADCY2	108	hgsc.bcm.edu	37	chr5	7698485	7698485	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ctggacatgtgtgaagccatAaagtaagtggactgcttagt	12	6	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr5:7698485A>G	ENST00000338316.4	+	7	1196	c.1107A>G	c.(1105-1107)atA>atG	p.I369M	ADCY2_ENST00000537121.1_Missense_Mutation_p.I189M	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	369					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						GTGAAGCCATAAAGTAAGTGG	0.418																																					p.I369M		Atlas-SNP	.											.	ADCY2	337	.	0			c.A1107G						.						136	132	133					5																	7698485		2203	4300	6503	SO:0001583	missense	108	exon7			AGCCATAAAGTAA	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1107A>G	5.37:g.7698485A>G	ENSP00000342952:p.Ile369Met	53.0	0.0		28.0	15.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	A	17.72	3.459733	0.63401	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	D;D	0.85088	-1.94;-1.94	5.8	0.245	0.15512	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.88306	0.6401	M	0.63208	1.945	0.38297	D	0.942866	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.999	D	0.85769	0.1354	10	0.87932	D	0	.	6.742	0.23441	0.4119:0.2473:0.0:0.3408	.	189;369	B7Z2C1;Q08462	.;ADCY2_HUMAN	M	369;220;189	ENSP00000342952:I369M;ENSP00000444803:I189M	ENSP00000342952:I369M	I	+	3	3	ADCY2	7751485	1.000000	0.71417	0.997000	0.53966	0.929000	0.56500	1.513000	0.35823	-0.179000	0.10654	-0.313000	0.08912	ATA	.	.		0.418	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		G	7698485	A	G	7698485	3	3	152	1	0	0	0	0	1	0	0	0	294	352	13	2	1133	2	ADCY2	5	7698485	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10		7698485	173216775	27	23375										
C5orf22	55322	hgsc.bcm.edu	37	chr5	31541416	31541416	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ggtagatattgttgatactcGaattcatcaattagaggatt	9	4	2	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr5:31541416G>A	ENST00000325366.9	+	6	1026	c.899G>A	c.(898-900)cGa>cAa	p.R300Q	C5orf22_ENST00000355907.3_5'UTR	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	300										kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						GTTGATACTCGAATTCATCAA	0.348																																					p.R300Q		Atlas-SNP	.											C5orf22,NS,carcinoma,0,1	C5orf22	48	1	0			c.G899A						.						108	109	109					5																	31541416		2203	4300	6503	SO:0001583	missense	55322	exon6			ATACTCGAATTCA	AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.899G>A	5.37:g.31541416G>A	ENSP00000326879:p.Arg300Gln	104.0	0.0		48.0	24.0	NM_018356	Q8ND28|Q8WU61|Q9NUR1	Missense_Mutation	SNP	ENST00000325366.9	37	CCDS3895.1	.	.	.	.	.	.	.	.	.	.	G	35	5.457909	0.96240	.	.	ENSG00000082213	ENST00000325366;ENST00000543911	T	0.46451	0.87	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.69575	0.3126	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74222	-0.3735	10	0.87932	D	0	-11.6748	19.2415	0.93886	0.0:0.0:1.0:0.0	.	300	Q49AR2	CE022_HUMAN	Q	300;35	ENSP00000326879:R300Q	ENSP00000326879:R300Q	R	+	2	0	C5orf22	31577173	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.884000	0.92432	2.538000	0.85594	0.591000	0.81541	CGA	.	.		0.348	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356		A	31541416	G	A	31541416	3	1	152	1	0	0	0	0	1	0	0	0	2287	1058	37	1	921	1	C5orf22	5	31541416	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	23842931	31541416	149373844	28	23376										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33630934	33630934	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tgctgttgccgccttcaaagCaaggggtaccatcaatgaca	10	11	2	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr5:33630934C>A	ENST00000504830.1	-	13	2308	c.1973G>T	c.(1972-1974)tGc>tTc	p.C658F	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Intron	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	658	Cys-rich.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GCCTTCAAAGCAAGGGGTACC	0.408										HNSCC(64;0.19)																											p.C658F		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.G1973T						.						106	106	106					5																	33630934		2203	4300	6503	SO:0001583	missense	81792	exon13			TCAAAGCAAGGGG	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.1973G>T	5.37:g.33630934C>A	ENSP00000422554:p.Cys658Phe	273.0	0.0		142.0	54.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756722	0.89843	.	.	ENSG00000151388	ENST00000504830	T	0.73363	-0.74	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.90865	0.7130	H	0.95114	3.625	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.93118	0.6522	10	0.87932	D	0	.	19.618	0.95643	0.0:1.0:0.0:0.0	.	658	P58397	ATS12_HUMAN	F	658	ENSP00000422554:C658F	ENSP00000422554:C658F	C	-	2	0	ADAMTS12	33666691	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.741000	0.84997	2.635000	0.89317	0.650000	0.86243	TGC	.	.		0.408	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33630934	C	A	33630934	3	1	152	1	0	0	0	0	1	0	0	0	257	710	25	3	2859	3	ADAMTS12	5	33630934	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	2089518	33630934	147284326	29	23377										
TGFBI	7045	hgsc.bcm.edu	37	chr5	135388596	135388596	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tgagtctgtttggaccccagAcctgctgaacaaccacatct	8	13	2	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr5:135388596A>G	ENST00000442011.2	+	8	1075	c.914A>G	c.(913-915)gAc>gGc	p.D305G	TGFBI_ENST00000305126.8_Splice_Site_p.D305G	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	305	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGGACCCCAGACCTGCTGAAC	0.572																																					p.D305G		Atlas-SNP	.											.	TGFBI	76	.	0			c.A914G						.						62	67	65					5																	135388596		2142	4247	6389	SO:0001630	splice_region_variant	7045	exon8			CCCCAGACCTGCT	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"transforming growth factor, beta-induced, 68kD"	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.914-1A>G	5.37:g.135388596A>G		82.0	0.0		49.0	21.0	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Missense_Mutation	SNP	ENST00000442011.2	37	CCDS47266.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.487155	0.44249	.	.	ENSG00000120708	ENST00000442011;ENST00000398813;ENST00000305126	D;D	0.90732	-2.72;-2.72	5.65	5.65	0.86999	FAS1 domain (5);	0.000000	0.85682	D	0.000000	D	0.92024	0.7473	L	0.28504	0.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.99	D	0.91247	0.5026	9	.	.	.	.	16.1566	0.81673	1.0:0.0:0.0:0.0	.	38;305	B9ZVW9;Q15582	.;BGH3_HUMAN	G	305;38;305	ENSP00000416330:D305G;ENSP00000306306:D305G	.	D	+	2	0	TGFBI	135416495	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	4.659000	0.61504	2.268000	0.75426	0.533000	0.62120	GAC	.	.		0.572	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		Missense_Mutation	G	135388596	A	G	135388596	5	3	152	1	0	0	0	0	0	0	1	0	15835	289	10	2	944	2	TGFBI	5	135388596	Splice_Site	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	101757662	135388596	45526664	30	23378										
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140168107	140168107	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	actctggtgtgctccagcgcGttggggagctggtcgaactc	15	11	1	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr5:140168107G>C	ENST00000504120.2	+	1	2232	c.2232G>C	c.(2230-2232)gcG>gcC	p.A744A	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000378133.3_Silent_p.A744A	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	744	5 X 4 AA repeats of P-X-X-P.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTCCAGCGCGTTGGGGAGCT	0.657																																					p.A744A		Atlas-SNP	.											PCDHA1_ENST00000504120,NS,carcinoma,+2,2	PCDHA1	387	2	0			c.G2232C						.						45	41	42					5																	140168107		2203	4300	6503	SO:0001819	synonymous_variant	56147	exon1			CAGCGCGTTGGGG	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"Cadherins / Protocadherins : Clustered"	8663	other	complex locus constituent	"KIAA0345-like 13"	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.2232G>C	5.37:g.140168107G>C		164.0	0.0		152.0	64.0	NM_031410	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	37	CCDS54913.1																																																																																			.	.		0.657	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		C	140168107	G	C	140168107	2	2	152	1	0	0	0	0	0	0	0	1	11528	1132	40	4		4	PCDHA1	5	140168107	Silent	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	4779511	140168107	40747153	31	23379										
CAMK2A	815	hgsc.bcm.edu	37	chr5	149602646	149602646	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	acgggtctcctccgactgggCggtgcgtgggatgccgccag	17	13	1	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr5:149602646C>T	ENST00000348628.6	-	17	2004	c.1339G>A	c.(1339-1341)Gcc>Acc	p.A447T	CAMK2A_ENST00000351010.6_5'UTR|CAMK2A_ENST00000398376.3_Missense_Mutation_p.A458T	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	447					calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCGACTGGGCGGTGCGTGGG	0.642																																					p.A458T		Atlas-SNP	.											CAMK2A,NS,carcinoma,+2,1	CAMK2A	42	1	0			c.G1372A						.						64	74	71					5																	149602646		2201	4298	6499	SO:0001583	missense	815	exon18			ACTGGGCGGTGCG	AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"CaM-kinase II alpha chain", "calcium/calmodulin-dependent protein kinase II alpha-B subunit", "CaM kinase II alpha subunit", "CaMK-II alpha subunit", "calcium/calmodulin-dependent protein kinase type II alpha chain"	114078	"calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.1339G>A	5.37:g.149602646C>T	ENSP00000261793:p.Ala447Thr	59.0	0.0		61.0	24.0	NM_015981	Q9UL21|Q9Y2H4|Q9Y352	Missense_Mutation	SNP	ENST00000348628.6	37	CCDS43386.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.844078	0.32606	.	.	ENSG00000070808	ENST00000348628;ENST00000398376	T;T	0.43294	0.95;0.95	5.15	5.15	0.70609	Protein kinase-like domain (1);Calcium/calmodulin-dependent protein kinase II, association-domain (1);	0.000000	0.64402	U	0.000001	T	0.24392	0.0591	N	0.05230	-0.09	0.45150	D	0.998166	B;B;B	0.12630	0.006;0.002;0.006	B;B;B	0.18263	0.004;0.021;0.004	T	0.10590	-1.0623	10	0.10377	T	0.69	.	18.6945	0.91596	0.0:1.0:0.0:0.0	.	447;458;447	Q9UQM7;A8K161;Q7LDD5	KCC2A_HUMAN;.;.	T	447;458	ENSP00000261793:A447T;ENSP00000381412:A458T	ENSP00000261793:A447T	A	-	1	0	CAMK2A	149582839	0.395000	0.25254	0.992000	0.48379	0.929000	0.56500	1.077000	0.30741	2.419000	0.82065	0.555000	0.69702	GCC	.	.		0.642	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981		T	149602646	C	T	149602646	3	4	152	1	0	0	0	0	1	0	0	0	2601	768	27	1	105	1	CAMK2A	5	149602646	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	9434539	149602646	31312614	32	23380										
RNF145	153830	hgsc.bcm.edu	37	chr5	158586026	158586026	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aaatgactgcaaggcgtgatCacagcagatttcatgtccta	9	9	2	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr5:158586026C>A	ENST00000424310.2	-	11	2003	c.1644G>T	c.(1642-1644)gtG>gtT	p.V548V	RNF145_ENST00000519865.1_Silent_p.V548V|RNF145_ENST00000518284.1_5'UTR|RNF145_ENST00000518802.1_Silent_p.V578V|RNF145_ENST00000520638.1_Silent_p.V562V|RNF145_ENST00000521606.2_Silent_p.V565V|RNF145_ENST00000274542.2_Silent_p.V576V	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	548						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AAGGCGTGATCACAGCAGATT	0.433																																					p.V578V		Atlas-SNP	.											.	RNF145	110	.	0			c.G1734T						.						47	49	48					5																	158586026		2195	4283	6478	SO:0001819	synonymous_variant	153830	exon11			CGTGATCACAGCA	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"RING-type (C3HC4) zinc fingers"	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.1644G>T	5.37:g.158586026C>A		65.0	0.0		32.0	12.0	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Silent	SNP	ENST00000424310.2	37	CCDS56390.1																																																																																			.	.		0.433	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		A	158586026	C	A	158586026	2	1	152	1	0	0	0	0	0	0	0	1	13462	813	29	3		3	RNF145	5	158586026	Silent	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	8983380	158586026	22329234	33	23381										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161115970	161115970	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cttaggagtatacgatggatGtttttttccgccagacctgg	11	8	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr5:161115970G>T	ENST00000274545.5	+	4	674	c.241G>T	c.(241-243)Gtt>Ttt	p.V81F	GABRA6_ENST00000523217.1_Intron|GABRA6_ENST00000522269.1_3'UTR|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	81					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.V81F(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TACGATGGATGTTTTTTTCCG	0.403										TCGA Ovarian(5;0.080)																											p.V81F		Atlas-SNP	.											GABRA6,NS,carcinoma,0,1	GABRA6	139	1	1	Substitution - Missense(1)	endometrium(1)	c.G241T						.						79	80	80					5																	161115970		2203	4299	6502	SO:0001583	missense	2559	exon4			ATGGATGTTTTTT		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.241G>T	5.37:g.161115970G>T	ENSP00000274545:p.Val81Phe	49.0	0.0		39.0	20.0	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	37	CCDS4356.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.0|21.0	4.082017|4.082017	0.76528|0.76528	.|.	.|.	ENSG00000145863|ENSG00000145863	ENST00000520000|ENST00000274545;ENST00000517823	.|T;T	.|0.80994	.|-1.44;-1.44	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Neurotransmitter-gated ion-channel ligand-binding (3);	.|0.054895	.|0.64402	.|D	.|0.000001	T|T	0.75117|0.75117	0.3806|0.3806	L|L	0.28115|0.28115	0.83|0.83	0.80722|0.80722	D|D	1|1	.|B	.|0.27700	.|0.186	.|B	.|0.37387	.|0.248	T|T	0.74659|0.74659	-0.3591|-0.3591	5|10	.|0.87932	.|D	.|0	.|.	13.3239|13.3239	0.60449|0.60449	0.0722:0.0:0.9278:0.0|0.0722:0.0:0.9278:0.0	.|.	.|81	.|Q16445	.|GBRA6_HUMAN	I|F	20|81;28	.|ENSP00000274545:V81F;ENSP00000430212:V28F	.|ENSP00000274545:V81F	M|V	+|+	3|1	0|0	GABRA6|GABRA6	161048548|161048548	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.942000|0.942000	0.58702|0.58702	7.895000|7.895000	0.87343|0.87343	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	ATG|GTT	.	.		0.403	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			T	161115970	G	T	161115970	3	4	152	1	0	0	0	0	1	0	0	0	6173	1377	48	3	255	3	GABRA6	5	161115970	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	2529944	161115970	19799290	34	23382										
FOXC1	2296	hgsc.bcm.edu	37	chr6	1612042	1612042	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ggcggcggcggcggcggcggGggaggccaggaggccggcca	25	12	0	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr6:1612042G>C	ENST00000380874.2	+	1	1362	c.1362G>C	c.(1360-1362)ggG>ggC	p.G454G		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	454	Poly-Gly.				artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		gcggcggcggGGGAGGCCAGG	0.751																																					p.G454G	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.G1362C						.						1	1	1					6																	1612042		591	1329	1920	SO:0001819	synonymous_variant	2296	exon1			CGGCGGGGGAGGC	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"Forkhead boxes"	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.1362G>C	6.37:g.1612042G>C		188.0	0.0		346.0	31.0	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Silent	SNP	ENST00000380874.2	37	CCDS4473.1																																																																																			.	.		0.751	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			C	1612042	G	C	1612042	2	2	152	1	0	0	0	0	0	0	0	1	6002	1219	43	4		4	FOXC1	6	1612042	Silent	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10		1612042	169503025	35	23383										
VPS52	6293	hgsc.bcm.edu	37	chr6	33231576	33231576	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	acacccagcatcatgtcataGttgttgatcagaaacacaag	7	10	3	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr6:33231576G>C	ENST00000445902.2	-	16	1919	c.1701C>G	c.(1699-1701)aaC>aaG	p.N567K	VPS52_ENST00000478934.1_5'UTR|VPS52_ENST00000436044.2_Missense_Mutation_p.N442K|VPS52_ENST00000482399.1_3'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	567					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						TCATGTCATAGTTGTTGATCA	0.502																																					p.N567K		Atlas-SNP	.											.	VPS52	56	.	0			c.C1701G						.						118	101	107					6																	33231576		2203	4300	6503	SO:0001583	missense	6293	exon16			GTCATAGTTGTTG	AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"SAC2 suppressor of actin mutations 2-like (yeast)", "vacuolar protein sorting 52 (yeast)"	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.1701C>G	6.37:g.33231576G>C	ENSP00000409952:p.Asn567Lys	85.0	0.0		72.0	4.0	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Missense_Mutation	SNP	ENST00000445902.2	37	CCDS4770.2	.	.	.	.	.	.	.	.	.	.	G	25.6	4.655637	0.88056	.	.	ENSG00000223501	ENST00000445902;ENST00000418054;ENST00000436044	.	.	.	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.82976	0.5154	M	0.89601	3.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85677	0.1298	9	0.87932	D	0	-19.2835	16.3679	0.83341	0.0:0.0:1.0:0.0	.	378;567	B3KMF7;Q8N1B4	.;VPS52_HUMAN	K	567;545;442	.	ENSP00000414785:N545K	N	-	3	2	VPS52	33339554	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.007000	0.88571	2.819000	0.97034	0.573000	0.79308	AAC	.	.		0.502	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553		C	33231576	G	C	33231576	3	2	152	1	0	0	0	0	1	0	0	0	17229	1020	36	4	490	4	VPS52	6	33231576	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	31619534	33231576	137883491	36	23384										
USP45	85015	hgsc.bcm.edu	37	chr6	99883624	99883624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ttcatagaaaagaaggtaggCttgtgcactaagtgctcttg	11	6	2	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr6:99883624C>T	ENST00000327681.6	-	18	2945	c.2413G>A	c.(2413-2415)Gcc>Acc	p.A805T	USP45_ENST00000369233.2_Missense_Mutation_p.A757T|USP45_ENST00000539675.1_Missense_Mutation_p.A98T|USP45_ENST00000500704.2_Missense_Mutation_p.A805T|USP45_ENST00000392738.2_Missense_Mutation_p.A485T	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	805	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		AGAAGGTAGGCTTGTGCACTA	0.358																																					p.A805T		Atlas-SNP	.											.	USP45	56	.	0			c.G2413A						.						120	123	122					6																	99883624		2203	4300	6503	SO:0001583	missense	85015	exon18			GGTAGGCTTGTGC	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"Ubiquitin-specific peptidases"	20080	protein-coding gene	gene with protein product			"ubiquitin specific protease 45"			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.2413G>A	6.37:g.99883624C>T	ENSP00000333376:p.Ala805Thr	62.0	0.0		22.0	8.0	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	37	CCDS34501.1	.	.	.	.	.	.	.	.	.	.	C	34	5.397139	0.96009	.	.	ENSG00000123552	ENST00000392738;ENST00000500704;ENST00000327681;ENST00000539675;ENST00000369233	T;T;T;T;T	0.55588	0.51;3.21;3.21;0.51;0.51	5.75	5.75	0.90469	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.057388	0.64402	D	0.000002	T	0.79493	0.4455	H	0.94306	3.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84590	0.0666	10	0.87932	D	0	.	19.9376	0.97146	0.0:1.0:0.0:0.0	.	805;485	Q70EL2;Q70EL2-3	UBP45_HUMAN;.	T	485;805;805;98;757	ENSP00000376495:A485T;ENSP00000424372:A805T;ENSP00000333376:A805T;ENSP00000439569:A98T;ENSP00000358236:A757T	ENSP00000333376:A805T	A	-	1	0	USP45	99990345	1.000000	0.71417	1.000000	0.80357	0.720000	0.41350	7.060000	0.76692	2.711000	0.92665	0.655000	0.94253	GCC	.	.		0.358	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929		T	99883624	C	T	99883624	3	4	152	1	0	0	0	0	1	0	0	0	17091	797	28	3	35	3	USP45	6	99883624	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	66652048	99883624	71231443	37	23385										
SEC63	11231	hgsc.bcm.edu	37	chr6	108194082	108194082	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	acacagtatactgataatttCcaggcttgcctggtgcagga	10	9	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr6:108194082C>T	ENST00000369002.4	-	20	2248	c.2069G>A	c.(2068-2070)gGa>gAa	p.G690E		NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	690	SEC63 2.				liver development (GO:0001889)|multicellular organismal aging (GO:0010259)|nitrogen compound metabolic process (GO:0006807)|posttranslational protein targeting to membrane (GO:0006620)|posttranslational protein targeting to membrane, translocation (GO:0031204)|protein targeting to membrane (GO:0006612)|renal system development (GO:0072001)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		ctgataatttccaggcttgcc	0.373																																					p.G690E		Atlas-SNP	.											.	SEC63	79	.	0			c.G2069A						.						37	36	37					6																	108194082		2092	4094	6186	SO:0001583	missense	11231	exon20			TAATTTCCAGGCT	BC048287	CCDS5061.1	6q21	2011-09-05	2006-09-12		ENSG00000025796	ENSG00000025796		"Heat shock proteins / DNAJ (HSP40)"	21082	protein-coding gene	gene with protein product		608648	"SEC63-like (S. cerevisiae)"			10219736, 10543453	Standard	NM_007214		Approved	SEC63L, PRO2507, ERdj2, DNAJC23	uc003psc.4	Q9UGP8	OTTHUMG00000015316	ENST00000369002.4:c.2069G>A	6.37:g.108194082C>T	ENSP00000357998:p.Gly690Glu	203.0	0.0		89.0	39.0	NM_007214	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	Missense_Mutation	SNP	ENST00000369002.4	37	CCDS5061.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.499067	0.85069	.	.	ENSG00000025796	ENST00000369002;ENST00000437345	T	0.60548	0.18	4.93	4.93	0.64822	Sec63 domain (2);	0.000000	0.85682	D	0.000000	T	0.79563	0.4467	M	0.92507	3.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.84115	0.0403	10	0.87932	D	0	-18.4453	17.4262	0.87527	0.0:1.0:0.0:0.0	.	690;690	Q9UGP8;B3KQF0	SEC63_HUMAN;.	E	690;308	ENSP00000357998:G690E	ENSP00000357998:G690E	G	-	2	0	SEC63	108300775	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	3.160000	0.50739	2.725000	0.93324	0.591000	0.81541	GGA	.	.		0.373	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214		T	108194082	C	T	108194082	3	4	152	1	0	0	0	0	1	0	0	0	14020	855	30	3	221	3	SEC63	6	108194082	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	8310458	108194082	62920985	38	23386										
REV3L	5980	hgsc.bcm.edu	37	chr6	111652972	111652972	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ctcagagaggtacagccaaaTttgaactcatcatacctgtt	7	10	3	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr6:111652972T>C	ENST00000358835.3	-	25	8395	c.7941A>G	c.(7939-7941)aaA>aaG	p.K2647K	REV3L_ENST00000435970.1_Silent_p.K2569K|REV3L_ENST00000368802.3_Silent_p.K2647K|REV3L_ENST00000368805.1_Silent_p.K2647K			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2647					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TACAGCCAAATTTGAACTCAT	0.363								DNA polymerases (catalytic subunits)																													p.K2647K		Atlas-SNP	.											.	REV3L	386	.	0			c.A7941G						.						109	106	107					6																	111652972		2203	4300	6503	SO:0001819	synonymous_variant	5980	exon24			GCCAAATTTGAAC	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.7941A>G	6.37:g.111652972T>C		115.0	0.0		42.0	16.0	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																			.	.		0.363	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		C	111652972	T	C	111652972	2	2	152	1	0	0	0	0	0	0	0	1	13255	1490	52	2		2	REV3L	6	111652972	Silent	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	3458890	111652972	59462095	39	23387										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129723605	129723605	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tgagagccacgcagctcagtTgaatgactcatctgctgtcc	10	12	3	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr6:129723605T>C	ENST00000421865.2	+	39	5748	c.5699T>C	c.(5698-5700)tTg>tCg	p.L1900S		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1900	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GCAGCTCAGTTGAATGACTCA	0.413																																					p.L1900S		Atlas-SNP	.											.	LAMA2	481	.	0			c.T5699C						.						123	92	103					6																	129723605		2203	4300	6503	SO:0001583	missense	3908	exon39			CTCAGTTGAATGA	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.5699T>C	6.37:g.129723605T>C	ENSP00000400365:p.Leu1900Ser	68.0	0.0		26.0	16.0	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.133415	0.77662	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.24151	1.87	5.63	5.63	0.86233	.	0.000000	0.64402	D	0.000004	T	0.44456	0.1294	M	0.73598	2.24	0.52099	D	0.999946	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.49542	-0.8929	10	0.87932	D	0	.	15.8438	0.78871	0.0:0.0:0.0:1.0	.	1900;1900	A6NF00;P24043	.;LAMA2_HUMAN	S	1900	ENSP00000400365:L1900S	ENSP00000346769:L1900S	L	+	2	0	LAMA2	129765298	1.000000	0.71417	0.955000	0.39395	0.921000	0.55340	6.862000	0.75484	2.132000	0.65825	0.454000	0.30748	TTG	.	.		0.413	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			C	129723605	T	C	129723605	3	2	152	1	0	0	0	0	1	0	0	0	8615	1821	63	2	5853	2	LAMA2	6	129723605	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	18070633	129723605	41391462	40	23388										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138483281	138483281	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ccgggagcaagtacaaagccAtcaaggagagctgcacctgg	13	11	1	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr6:138483281A>G	ENST00000251691.4	+	1	224	c.58A>G	c.(58-60)Atc>Gtc	p.I20V		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		GTACAAAGCCATCAAGGAGAG	0.697																																					p.I20V		Atlas-SNP	.											.	KIAA1244	236	.	0			c.A58G						.						40	51	47					6																	138483281		1937	4142	6079	SO:0001583	missense	57221	exon1			AAAGCCATCAAGG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.58A>G	6.37:g.138483281A>G	ENSP00000251691:p.Ile20Val	144.0	0.0		220.0	85.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	A	14.33	2.504165	0.44558	.	.	ENSG00000112379	ENST00000251691	T	0.19394	2.15	4.07	4.07	0.47477	.	.	.	.	.	T	0.09291	0.0229	L	0.43152	1.355	0.35530	D	0.802199	B	0.25312	0.123	B	0.18871	0.023	T	0.05632	-1.0873	9	0.62326	D	0.03	-13.3507	12.2239	0.54449	1.0:0.0:0.0:0.0	.	20	Q5TH69	BIG3_HUMAN	V	20	ENSP00000251691:I20V	ENSP00000251691:I20V	I	+	1	0	KIAA1244	138524974	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.935000	0.56560	1.487000	0.48415	0.374000	0.22700	ATC	.	.		0.697	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		G	138483281	A	G	138483281	3	3	152	1	0	0	0	0	1	0	0	0	8226	217	8	2	60	2	KIAA1244	6	138483281	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	8759676	138483281	32631786	41	23389										
REPS1	85021	hgsc.bcm.edu	37	chr6	139234056	139234056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gagttatgaggccatcggcaTccactgggcgatgcacagca	13	11	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr6:139234056T>C	ENST00000450536.2	-	16	2391	c.1817A>G	c.(1816-1818)gAt>gGt	p.D606G	REPS1_ENST00000258062.5_Missense_Mutation_p.D605G|REPS1_ENST00000367663.4_Missense_Mutation_p.D579G|REPS1_ENST00000415951.2_Missense_Mutation_p.D579G|REPS1_ENST00000409812.2_Missense_Mutation_p.D515G			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	606					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		GCCATCGGCATCCACTGGGCG	0.473																																					p.D605G		Atlas-SNP	.											REPS1,NS,carcinoma,0,1	REPS1	58	1	0			c.A1814G						.						92	80	85					6																	139234056		2203	4300	6503	SO:0001583	missense	85021	exon16			TCGGCATCCACTG		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"EF-hand domain containing"	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.1817A>G	6.37:g.139234056T>C	ENSP00000392065:p.Asp606Gly	59.0	1.0		35.0	15.0	NM_031922	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	ENST00000450536.2	37		.	.	.	.	.	.	.	.	.	.	T	17.46	3.394232	0.62066	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668;ENST00000530255	T;T;T;T;T;T	0.31510	1.51;1.49;1.49;1.53;1.51;1.59	6.07	6.07	0.98685	.	0.051097	0.85682	D	0.000000	T	0.28764	0.0713	N	0.22421	0.69	0.44627	D	0.997606	P;P;D;P;B	0.67145	0.873;0.89;0.996;0.799;0.001	P;B;P;B;B	0.61874	0.461;0.272;0.895;0.272;0.001	T	0.05599	-1.0875	10	0.37606	T	0.19	-18.2411	16.6407	0.85098	0.0:0.0:0.0:1.0	.	605;554;515;606;579	Q96D71-3;B2R7D3;Q96D71-2;Q96D71;E9PMG1	.;.;.;REPS1_HUMAN;.	G	606;579;564;515;605;579;554;129	ENSP00000392065:D606G;ENSP00000356635:D579G;ENSP00000434251:D564G;ENSP00000386699:D515G;ENSP00000258062:D605G;ENSP00000397941:D579G	ENSP00000258062:D605G	D	-	2	0	REPS1	139275749	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.421000	0.66447	2.326000	0.78906	0.533000	0.62120	GAT	.	.		0.473	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			C	139234056	T	C	139234056	3	2	152	1	0	0	0	0	1	0	0	0	13243	1435	50	2	593	2	REPS1	6	139234056	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	750775	139234056	31881011	42	23390										
MTRF1L	54516	hgsc.bcm.edu	37	chr6	153316417	153316417	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cttccaggatcaaatcatttTcatctgtttcttctgaggga	7	9	6	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr6:153316417T>C	ENST00000367233.5	-	3	376	c.377A>G	c.(376-378)gAa>gGa	p.E126G	MTRF1L_ENST00000367231.5_Missense_Mutation_p.E126G|MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367230.1_Missense_Mutation_p.E126G	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	126						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		CAAATCATTTTCATCTGTTTC	0.308																																					p.E126G		Atlas-SNP	.											.	MTRF1L	21	.	0			c.A377G						.						25	25	25					6																	153316417		2194	4295	6489	SO:0001583	missense	54516	exon3			TCATTTTCATCTG	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.377A>G	6.37:g.153316417T>C	ENSP00000356202:p.Glu126Gly	165.0	0.0		69.0	31.0	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Missense_Mutation	SNP	ENST00000367233.5	37	CCDS5243.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.022417	0.35701	.	.	ENSG00000112031	ENST00000367233;ENST00000367231;ENST00000367230;ENST00000414771	T;T;T;T	0.45668	0.89;0.89;0.89;2.76	5.43	2.99	0.34606	Peptide chain release factor (2);	0.655706	0.16258	N	0.222370	T	0.15305	0.0369	L	0.49350	1.555	0.21473	N	0.999673	B;B;B;B	0.12630	0.002;0.005;0.001;0.006	B;B;B;B	0.12156	0.003;0.003;0.003;0.007	T	0.24261	-1.0165	10	0.30078	T	0.28	-5.9767	7.4452	0.27207	0.0:0.0758:0.1442:0.7801	.	126;126;126;126	B4DMX1;Q9UGC7-2;Q9UGC7-4;Q9UGC7	.;.;.;RF1ML_HUMAN	G	126;126;126;13	ENSP00000356202:E126G;ENSP00000356200:E126G;ENSP00000356199:E126G;ENSP00000414383:E13G	ENSP00000356199:E126G	E	-	2	0	MTRF1L	153358110	0.984000	0.35163	0.984000	0.44739	0.985000	0.73830	2.576000	0.46033	0.351000	0.24027	0.477000	0.44152	GAA	.	.		0.308	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041		C	153316417	T	C	153316417	3	2	152	1	0	0	0	0	1	0	0	0	9969	1783	62	2	785	2	MTRF1L	6	153316417	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	14082361	153316417	17798650	43	23391										
PLG	5340	hgsc.bcm.edu	37	chr6	161134133	161134133	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	atccagaaaagagatatgacTactgcgacattcttgagtgt	9	7	1	4			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr6:161134133T>A	ENST00000308192.9	+	5	586	c.523T>A	c.(523-525)Tac>Aac	p.Y175N	PLG_ENST00000462918.1_3'UTR	NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	175	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	GAGATATGACTACTGCGACAT	0.468																																					p.Y175N		Atlas-SNP	.											.	PLG	150	.	0			c.T523A						.						147	143	144					6																	161134133		2203	4300	6503	SO:0001583	missense	5340	exon5			TATGACTACTGCG	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.523T>A	6.37:g.161134133T>A	ENSP00000308938:p.Tyr175Asn	53.0	0.0		49.0	15.0	NM_000301	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	ENST00000308192.9	37	CCDS5279.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.322488	0.41096	.	.	ENSG00000122194	ENST00000308192	T	0.66460	-0.21	5.11	5.11	0.69529	Kringle (4);Kringle-like fold (1);	0.000000	0.35903	U	0.002905	T	0.75627	0.3875	M	0.91459	3.21	0.46654	D	0.99914	P	0.50066	0.931	P	0.51615	0.675	T	0.82446	-0.0453	10	0.72032	D	0.01	.	14.1696	0.65500	0.0:0.0:0.0:1.0	.	175	P00747	PLMN_HUMAN	N	175	ENSP00000308938:Y175N	ENSP00000308938:Y175N	Y	+	1	0	PLG	161054123	0.968000	0.33430	0.864000	0.33941	0.330000	0.28571	1.849000	0.39318	2.054000	0.61138	0.528000	0.53228	TAC	.	.		0.468	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		A	161134133	T	A	161134133	3	1	152	1	0	0	0	0	1	0	0	0	12095	1522	53	4	545	4	PLG	6	161134133	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	7817716	161134133	9980934	44	23392										
CHPF2	54480	hgsc.bcm.edu	37	chr7	150935715	150935715	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cctggaggggctagggggccGtgcccagctggctatggctc	18	12	0	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr7:150935715G>C	ENST00000035307.2	+	4	3780	c.2267G>C	c.(2266-2268)cGt>cCt	p.R756P	RP4-548D19.3_ENST00000607902.1_RNA|CHPF2_ENST00000495645.1_Missense_Mutation_p.R748P|MIR671_ENST00000390183.1_RNA	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	756					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						CTAGGGGGCCGTGCCCAGCTG	0.622																																					p.R756P		Atlas-SNP	.											.	CHPF2	52	.	0			c.G2267C						.						17	17	17					7																	150935715		2200	4300	6500	SO:0001583	missense	54480	exon4			GGGGCCGTGCCCA	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.2267G>C	7.37:g.150935715G>C	ENSP00000035307:p.Arg756Pro	69.0	0.0		95.0	23.0	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	37	CCDS34779.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.388043	0.82902	.	.	ENSG00000033100	ENST00000495645;ENST00000035307	T;T	0.16743	2.32;2.32	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.45478	0.1344	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.46442	-0.9191	10	0.54805	T	0.06	-12.2	17.0841	0.86606	0.0:0.0:1.0:0.0	.	756;748	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	P	748;756	ENSP00000418914:R748P;ENSP00000035307:R756P	ENSP00000035307:R756P	R	+	2	0	CHPF2	150566648	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	9.648000	0.98483	2.492000	0.84095	0.655000	0.94253	CGT	.	.		0.622	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015		C	150935715	G	C	150935715	3	2	152	1	0	0	0	0	1	0	0	0	3371	1145	40	4	2281	4	CHPF2	7	150935715	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10		150935715	8202948	45	23393										
XKR6	286046	hgsc.bcm.edu	37	chr8	10782179	10782179	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cgctgttcttctggagcatgAtgtagagctgtagcaccagt	12	9	2	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr8:10782179A>G	ENST00000416569.2	-	2	952	c.926T>C	c.(925-927)aTc>aCc	p.I309T	XKR6_ENST00000304437.2_Missense_Mutation_p.I30T	NM_173683.3	NP_775954.2	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related family, member 6	309						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(8)|ovary(2)|prostate(1)|skin(3)	31				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		CTGGAGCATGATGTAGAGCTG	0.647																																					p.I309T		Atlas-SNP	.											.	XKR6	85	.	0			c.T926C						.						87	84	85					8																	10782179		2203	4300	6503	SO:0001583	missense	286046	exon2			AGCATGATGTAGA	BC024146	CCDS5978.2	8p23.1	2009-05-27	2006-01-12	2005-07-28	ENSG00000171044	ENSG00000171044			27806	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 7", "chromosome 8 open reading frame 21", "X Kell blood group precursor-related family, member 6", "chromosome 8 open reading frame 5"	C8orf7, C8orf21, C8orf5			Standard	NM_173683		Approved		uc003wtk.1	Q5GH73	OTTHUMG00000129351	ENST00000416569.2:c.926T>C	8.37:g.10782179A>G	ENSP00000416707:p.Ile309Thr	64.0	0.0		38.0	17.0	NM_173683	Q8TBA0	Missense_Mutation	SNP	ENST00000416569.2	37	CCDS5978.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	22.8|22.8	4.341404|4.341404	0.81911|0.81911	.|.	.|.	ENSG00000171044|ENSG00000171044	ENST00000304437;ENST00000416569|ENST00000382461	T;T|.	0.74106|.	-0.81;-0.81|.	4.84|4.84	4.84|4.84	0.62591|0.62591	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80380|0.80380	0.4612|0.4612	M|M	0.90705|0.90705	3.14|3.14	0.80722|0.80722	D|D	1|1	D|.	0.69078|.	0.997|.	D|.	0.80764|.	0.994|.	D|D	0.84462|0.84462	0.0594|0.0594	10|5	0.87932|.	D|.	0|.	-0.4384|-0.4384	13.5992|13.5992	0.62010|0.62010	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	309|.	Q5GH73|.	XKR6_HUMAN|.	T|P	30;309|86	ENSP00000307120:I30T;ENSP00000416707:I309T|.	ENSP00000307120:I30T|.	I|S	-|-	2|1	0|0	XKR6|XKR6	10819589|10819589	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.894000|0.894000	0.52154|0.52154	9.095000|9.095000	0.94175|0.94175	1.797000|1.797000	0.52628|0.52628	0.375000|0.375000	0.23000|0.23000	ATC|TCA	.	.		0.647	XKR6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383958.1	NM_173683		G	10782179	A	G	10782179	3	3	152	1	0	0	0	0	1	0	0	0	17450	333	12	2	1007	2	XKR6	8	10782179	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10		10782179	135581843	46	23394										
PSD3	23362	hgsc.bcm.edu	37	chr8	18662113	18662113	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ctagtttgctaaattcgttgCtataagaaaacagaatagac	7	6	0	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr8:18662113C>A	ENST00000327040.8	-	6	1932		c.e6-1		PSD3_ENST00000286485.8_Splice_Site|PSD3_ENST00000440756.2_Splice_Site|PSD3_ENST00000523619.1_Splice_Site	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3						neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		AAATTCGTTGCTATAAGAAAA	0.373																																					.		Atlas-SNP	.											.	PSD3	142	.	0			c.1830-1G>T						.						98	102	100					8																	18662113		2203	4300	6503	SO:0001630	splice_region_variant	23362	exon7			TCGTTGCTATAAG	AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"Pleckstrin homology (PH) domain containing"	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.1830-1G>T	8.37:g.18662113C>A		101.0	0.0		46.0	22.0	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Splice_Site	SNP	ENST00000327040.8	37	CCDS43720.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.589004	0.46110	.	.	ENSG00000156011	ENST00000327040;ENST00000440756;ENST00000286485;ENST00000523619;ENST00000520858;ENST00000519851;ENST00000521027	.	.	.	6.07	6.07	0.98685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1532	0.89682	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PSD3	18706393	1.000000	0.71417	0.998000	0.56505	0.455000	0.32408	6.959000	0.76031	2.885000	0.99019	0.655000	0.94253	.	.	.		0.373	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310	Intron	A	18662113	C	A	18662113	5	1	152	1	0	0	0	0	0	0	1	0	12660	811	28	3	1358	3	PSD3	8	18662113	Splice_Site	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	7879934	18662113	127701909	47	23395										
ADAM28	10863	hgsc.bcm.edu	37	chr8	24199212	24199212	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	atgtaaaacatttgatcctgAagacacaagtcaagaaatag	7	6	1	4			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr8:24199212A>C	ENST00000265769.4	+	16	1882	c.1772A>C	c.(1771-1773)gAa>gCa	p.E591A	ADAM28_ENST00000397649.3_Missense_Mutation_p.E338A|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	591	Cys-rich.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TTTGATCCTGAAGACACAAGT	0.413																																					p.E591A	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.A1772C						.						206	195	199					8																	24199212		2203	4300	6503	SO:0001583	missense	10863	exon16			ATCCTGAAGACAC	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.1772A>C	8.37:g.24199212A>C	ENSP00000265769:p.Glu591Ala	199.0	0.0		106.0	53.0	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.307|6.307	0.424674|0.424674	0.11928|0.11928	.|.	.|.	ENSG00000042980|ENSG00000042980	ENST00000265769;ENST00000397649|ENST00000521629;ENST00000518326	T;T|.	0.01725|.	4.77;4.67|.	5.82|5.82	5.82|5.82	0.92795|0.92795	ADAM, cysteine-rich (1);|.	.|.	.|.	.|.	.|.	T|.	0.66703|.	0.2816|.	M|M	0.68317|0.68317	2.08|2.08	0.33797|0.33797	D|D	0.626131|0.626131	D;D|.	0.56746|.	0.977;0.977|.	P;P|.	0.52424|.	0.698;0.698|.	T|.	0.76152|.	-0.3064|.	9|.	0.07813|.	T|.	0.8|.	.|.	12.574|12.574	0.56354|0.56354	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	591;591|.	B2RMV5;Q9UKQ2|.	.;ADA28_HUMAN|.	A|C	591;338|223;16	ENSP00000265769:E591A;ENSP00000380770:E338A|.	ENSP00000265769:E591A|.	E|X	+|+	2|3	0|0	ADAM28|ADAM28	24255157|24255157	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.126000|0.126000	0.20510|0.20510	2.739000|2.739000	0.47409|0.47409	2.236000|2.236000	0.73375|0.73375	0.523000|0.523000	0.50628|0.50628	GAA|TGA	.	.		0.413	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		C	24199212	A	C	24199212	3	2	152	1	0	0	0	0	1	0	0	0	246	246	9	5	1890	5	ADAM28	8	24199212	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	5537099	24199212	122164810	48	23396										
SLCO5A1	81796	hgsc.bcm.edu	37	chr8	70744717	70744717	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tcctggtggcccgaagaatcCacacagccaaaggccgggtt	12	13	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr8:70744717C>A	ENST00000260126.4	-	2	898	c.192G>T	c.(190-192)gtG>gtT	p.V64V	RP11-159H10.3_ENST00000528800.2_RNA|SLCO5A1_ENST00000530307.1_Silent_p.V64V|SLCO5A1_ENST00000528658.1_5'UTR|RP11-159H10.3_ENST00000533300.1_RNA|RP11-159H10.3_ENST00000501104.2_RNA|SLCO5A1_ENST00000524945.1_Silent_p.V64V	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			CCGAAGAATCCACACAGCCAA	0.642											OREG0018815	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V64V		Atlas-SNP	.											.	SLCO5A1	142	.	0			c.G192T						.						36	40	39					8																	70744717		2203	4300	6503	SO:0001819	synonymous_variant	81796	exon2			AGAATCCACACAG	AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"Solute carriers"	19046	protein-coding gene	gene with protein product		613543	"solute carrier family 21 (organic anion transporter), member 15"	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.192G>T	8.37:g.70744717C>A		78.0	0.0	1124	105.0	68.0	NM_030958	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Silent	SNP	ENST00000260126.4	37	CCDS6205.1																																																																																			.	.		0.642	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958		A	70744717	C	A	70744717	2	1	152	1	0	0	0	0	0	0	0	1	14746	581	21	3		3	SLCO5A1	8	70744717	Silent	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	46545505	70744717	75619305	49	23397										
SPAG1	6674	hgsc.bcm.edu	37	chr8	101206459	101206459	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tccgaagatgaagaaggaaaAagcggaagaaaacatgaaga	12	4	0	6	rs56246127	byFrequency	TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr8:101206459A>C	ENST00000388798.2	+	10	1250	c.1059A>C	c.(1057-1059)aaA>aaC	p.K353N	SPAG1_ENST00000251809.3_Missense_Mutation_p.K353N|SPAG1_ENST00000520508.1_Missense_Mutation_p.K353N|SPAG1_ENST00000520643.1_Missense_Mutation_p.K353N	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	353					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		AAGAAGGAAAAAGCGGAAGAA	0.358																																					p.K353N		Atlas-SNP	.											.	SPAG1	80	.	0			c.A1059C						.						64	64	64					8																	101206459		2203	4300	6503	SO:0001583	missense	6674	exon10			AGGAAAAAGCGGA	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.1059A>C	8.37:g.101206459A>C	ENSP00000373450:p.Lys353Asn	577.0	0.0		370.0	20.0	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	37	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	A	0.762	-0.768896	0.02974	.	.	ENSG00000104450	ENST00000520643;ENST00000251809;ENST00000520508;ENST00000388798	T;T;T;T	0.63417	2.83;-0.04;2.83;-0.04	5.39	0.943	0.19531	.	0.615169	0.15977	N	0.235509	T	0.48370	0.1496	L	0.41824	1.3	0.09310	N	1	P;P	0.44195	0.828;0.804	B;B	0.41764	0.366;0.16	T	0.32188	-0.9916	10	0.32370	T	0.25	-15.8264	6.443	0.21861	0.5813:0.0:0.4187:0.0	.	353;353	Q07617;G3XAM3	SPAG1_HUMAN;.	N	353	ENSP00000427716:K353N;ENSP00000251809:K353N;ENSP00000428070:K353N;ENSP00000373450:K353N	ENSP00000251809:K353N	K	+	3	2	SPAG1	101275635	0.154000	0.22792	0.011000	0.14972	0.025000	0.11179	1.135000	0.31454	0.261000	0.21753	-0.425000	0.05940	AAA	.	.		0.358	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		C	101206459	A	C	101206459	3	2	152	1	0	0	0	0	1	0	0	0	14990	11	1	5	1093	5	SPAG1	8	101206459	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	30461742	101206459	45157563	50	23398										
EFR3A	23167	hgsc.bcm.edu	37	chr8	132966069	132966069	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ttttttttttttataggataCgaattgctggaattagaggt	9	2	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr8:132966069C>T	ENST00000254624.5	+	6	718	c.493C>T	c.(493-495)Cga>Tga	p.R165*	EFR3A_ENST00000519656.1_Nonsense_Mutation_p.R129*|EFR3A_ENST00000334503.4_Nonsense_Mutation_p.R165*	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	165						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			TTATAGGATACGAATTGCTGG	0.348																																					p.R165X		Atlas-SNP	.											.	EFR3A	96	.	0			c.C493T						.						29	26	27					8																	132966069		2200	4282	6482	SO:0001587	stop_gained	23167	exon6			AGGATACGAATTG	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.493C>T	8.37:g.132966069C>T	ENSP00000254624:p.Arg165*	97.0	0.0		48.0	10.0	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Nonsense_Mutation	SNP	ENST00000254624.5	37	CCDS34942.2	.	.	.	.	.	.	.	.	.	.	C	34	5.298382	0.95574	.	.	ENSG00000132294	ENST00000254624;ENST00000522709;ENST00000377917;ENST00000334503;ENST00000519656	.	.	.	5.6	3.77	0.43336	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0935	5.6691	0.17713	0.144:0.6428:0.139:0.0743	.	.	.	.	X	165;129;165;165;129	.	ENSP00000254624:R165X	R	+	1	2	EFR3A	133035251	1.000000	0.71417	0.973000	0.42090	0.716000	0.41182	4.744000	0.62118	0.693000	0.31634	0.484000	0.47621	CGA	.	.		0.348	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		T	132966069	C	T	132966069	4	4	152	1	0	0	0	0	0	1	0	0	4960	528	19	1	515	1	EFR3A	8	132966069	Nonsense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	31759610	132966069	13397953	51	23399										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139856352	139856352	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	atttccttggttcctccattGgtgtgcttaaagcgatctcc	8	11	1	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr8:139856352G>T	ENST00000303045.6	-	4	1154	c.708C>A	c.(706-708)acC>acA	p.T236T	COL22A1_ENST00000435777.1_Silent_p.T236T	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	236					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TTCCTCCATTGGTGTGCTTAA	0.458										HNSCC(7;0.00092)																											p.T236T		Atlas-SNP	.											.	COL22A1	390	.	0			c.C708A						.						374	326	342					8																	139856352		2203	4300	6503	SO:0001819	synonymous_variant	169044	exon4			TCCATTGGTGTGC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.708C>A	8.37:g.139856352G>T		79.0	0.0		64.0	20.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			.	.		0.458	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		T	139856352	G	T	139856352	2	4	152	1	0	0	0	0	0	0	0	1	3683	1335	47	3		3	COL22A1	8	139856352	Silent	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	6890283	139856352	6507670	52	23400										
VCP	7415	hgsc.bcm.edu	37	chr9	35068306	35068306	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cttcatcaacaattaaccgaTtgggacggttcttctgtttg	8	9	4	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr9:35068306T>G	ENST00000358901.6	-	2	966	c.71A>C	c.(70-72)aAt>aCt	p.N24T		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	24					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			AATTAACCGATTGGGACGGTT	0.473																																					p.N24T		Atlas-SNP	.											.	VCP	64	.	0			c.A71C						.						342	308	320					9																	35068306		2203	4300	6503	SO:0001583	missense	7415	exon2			AACCGATTGGGAC	AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"ATPases / AAA-type"	12666	protein-coding gene	gene with protein product		601023	"valosin-containing protein"			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.71A>C	9.37:g.35068306T>G	ENSP00000351777:p.Asn24Thr	73.0	0.0		59.0	25.0	NM_007126	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Missense_Mutation	SNP	ENST00000358901.6	37	CCDS6573.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.902443	0.72754	.	.	ENSG00000165280	ENST00000358901	D	0.83075	-1.68	6.06	6.06	0.98353	Aspartate decarboxylase-like fold (2);	0.000000	0.85682	D	0.000000	D	0.86785	0.6016	M	0.91300	3.195	0.80722	D	1	P	0.46395	0.877	B	0.42214	0.38	D	0.87026	0.2132	10	0.28530	T	0.3	-1.4889	15.1804	0.72952	0.0:0.0:0.0:1.0	.	24	P55072	TERA_HUMAN	T	24	ENSP00000351777:N24T	ENSP00000351777:N24T	N	-	2	0	VCP	35058306	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.922000	0.87538	2.324000	0.78689	0.533000	0.62120	AAT	.	.		0.473	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126		G	35068306	T	G	35068306	3	3	152	1	0	0	0	0	1	0	0	0	17155	1493	52	5	2413	5	VCP	9	35068306	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10		35068306	106145125	53	23401										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137703411	137703411	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aggtgatgaaggtcccagagGctttcctggaccccctgggc	14	12	0	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr9:137703411G>A	ENST00000371817.3	+	46	4070	c.3656G>A	c.(3655-3657)gGc>gAc	p.G1219D		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1219	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GGTCCCAGAGGCTTTCCTGGA	0.652											OREG0019605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G1219D		Atlas-SNP	.											.	COL5A1	323	.	0			c.G3656A						.						21	21	21					9																	137703411		2144	4217	6361	SO:0001583	missense	1289	exon46			CCAGAGGCTTTCC	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.3656G>A	9.37:g.137703411G>A	ENSP00000360882:p.Gly1219Asp	132.0	0.0	1635	117.0	45.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.358006	0.61403	.	.	ENSG00000130635	ENST00000371817	D	0.99619	-6.28	4.0	4.0	0.46444	.	0.000000	0.85682	U	0.000000	D	0.99764	0.9904	H	0.96720	3.87	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.96824	0.9606	10	0.87932	D	0	.	16.112	0.81271	0.0:0.0:1.0:0.0	.	1219	P20908	CO5A1_HUMAN	D	1219	ENSP00000360882:G1219D	ENSP00000360882:G1219D	G	+	2	0	COL5A1	136843232	1.000000	0.71417	0.197000	0.23402	0.601000	0.36947	9.718000	0.98758	1.780000	0.52325	0.544000	0.68410	GGC	.	.		0.652	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137703411	G	A	137703411	3	1	152	1	0	0	0	0	1	0	0	0	3698	1203	42	3	3838	3	COL5A1	9	137703411	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	102635105	137703411	3510020	54	23402										
ANAPC2	29882	hgsc.bcm.edu	37	chr9	140077646	140077646	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aagggtccagcacgcgcagcGccttgatggcagagatatag	14	10	0	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr9:140077646G>A	ENST00000323927.2	-	6	1221	c.1217C>T	c.(1216-1218)gCg>gTg	p.A406V		NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	406					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		CACGCGCAGCGCCTTGATGGC	0.627																																					p.A406V		Atlas-SNP	.											.	ANAPC2	57	.	0			c.C1217T						.						138	137	137					9																	140077646		2203	4300	6503	SO:0001583	missense	29882	exon6			CGCAGCGCCTTGA	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"Anaphase promoting complex subunits"	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.1217C>T	9.37:g.140077646G>A	ENSP00000314004:p.Ala406Val	101.0	0.0		104.0	40.0	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Missense_Mutation	SNP	ENST00000323927.2	37	CCDS7033.1	.	.	.	.	.	.	.	.	.	.	G	31	5.066762	0.93898	.	.	ENSG00000176248	ENST00000323927	T	0.71579	-0.58	4.83	4.83	0.62350	.	0.050390	0.85682	D	0.000000	T	0.80199	0.4579	M	0.62723	1.935	0.80722	D	1	D;D	0.76494	0.999;0.998	D;P	0.63877	0.919;0.868	T	0.79797	-0.1652	10	0.42905	T	0.14	-14.5684	15.4405	0.75178	0.0:0.0:1.0:0.0	.	406;403	Q9UJX6;Q9UJX6-2	ANC2_HUMAN;.	V	406	ENSP00000314004:A406V	ENSP00000314004:A406V	A	-	2	0	ANAPC2	139197467	1.000000	0.71417	0.957000	0.39632	0.817000	0.46193	9.112000	0.94314	2.515000	0.84797	0.561000	0.74099	GCG	.	.		0.627	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366		A	140077646	G	A	140077646	3	1	152	1	0	0	0	0	1	0	0	0	603	1087	38	1	1283	1	ANAPC2	9	140077646	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	2374235	140077646	1135785	55	23403										
CUBN	8029	hgsc.bcm.edu	37	chr10	17113430	17113430	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ttttttccctcttacctcaaCataatctgtttcacagtggg	5	11	4	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr10:17113430C>T	ENST00000377833.4	-	19	2685	c.2620G>A	c.(2620-2622)Gtt>Att	p.V874I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	874	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CTTACCTCAACATAATCTGTT	0.363																																					p.V874I		Atlas-SNP	.											.	CUBN	515	.	0			c.G2620A						.						72	71	71					10																	17113430		2203	4300	6503	SO:0001583	missense	8029	exon19			CCTCAACATAATC	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2620G>A	10.37:g.17113430C>T	ENSP00000367064:p.Val874Ile	116.0	0.0		69.0	6.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	4.433	0.080178	0.08533	.	.	ENSG00000107611	ENST00000377833	T	0.37411	1.2	5.47	-5.88	0.02290	CUB (5);	0.805314	0.10456	N	0.672549	T	0.26231	0.0640	L	0.38175	1.15	0.80722	D	1	B	0.11235	0.004	B	0.19148	0.024	T	0.43393	-0.9394	10	0.09843	T	0.71	.	18.8206	0.92096	0.0:0.7513:0.0:0.2487	.	874	O60494	CUBN_HUMAN	I	874	ENSP00000367064:V874I	ENSP00000367064:V874I	V	-	1	0	CUBN	17153436	0.990000	0.36364	0.888000	0.34837	0.566000	0.35808	0.228000	0.17814	-1.017000	0.03367	-0.540000	0.04249	GTT	.	.		0.363	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	17113430	C	T	17113430	3	4	152	1	0	0	0	0	1	0	0	0	4053	478	17	3	8447	3	CUBN	10	17113430	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10		17113430	118421317	56	23404										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24727389	24727389	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gtttaatcacacaccaaaaaCtatgaatggagacatgaggg	9	7	1	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr10:24727389C>T	ENST00000376454.3	+	5	857	c.827C>T	c.(826-828)aCt>aTt	p.T276I	KIAA1217_ENST00000430453.2_Missense_Mutation_p.T197I|KIAA1217_ENST00000458595.1_Missense_Mutation_p.T276I|KIAA1217_ENST00000376462.1_Missense_Mutation_p.T196I|KIAA1217_ENST00000376452.3_Missense_Mutation_p.T276I	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	276					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						ACACCAAAAACTATGAATGGA	0.398																																					p.T276I		Atlas-SNP	.											.	KIAA1217	235	.	0			c.C827T						.						208	178	188					10																	24727389		2203	4300	6503	SO:0001583	missense	56243	exon5			CAAAAACTATGAA	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.827C>T	10.37:g.24727389C>T	ENSP00000365637:p.Thr276Ile	104.0	0.0		69.0	27.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348988	0.41599	.	.	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000376454;ENST00000376452;ENST00000438429;ENST00000430453	T;T;T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03;0.03;0.03	5.46	5.46	0.80206	.	0.227354	0.45606	D	0.000352	T	0.52565	0.1742	L	0.31664	0.95	0.34613	D	0.717826	P;P;P;P	0.42203	0.554;0.601;0.634;0.773	B;B;B;B	0.40506	0.218;0.331;0.3;0.316	T	0.57562	-0.7790	10	0.14252	T	0.57	.	19.3041	0.94153	0.0:1.0:0.0:0.0	.	276;276;276;276	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	I	196;276;276;276;276;126;197	ENSP00000365645:T196I;ENSP00000365639:T276I;ENSP00000392625:T276I;ENSP00000365637:T276I;ENSP00000365635:T276I;ENSP00000404798:T126I;ENSP00000389680:T197I	ENSP00000365635:T276I	T	+	2	0	KIAA1217	24767395	1.000000	0.71417	0.483000	0.27378	0.669000	0.39330	4.321000	0.59209	2.583000	0.87209	0.573000	0.79308	ACT	.	.		0.398	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		T	24727389	C	T	24727389	3	4	152	1	0	0	0	0	1	0	0	0	8225	565	20	3	845	3	KIAA1217	10	24727389	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	7613959	24727389	110807358	57	23405										
GRID1	2894	hgsc.bcm.edu	37	chr10	87966273	87966273	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ggtggcatgcggtgcgtggcGaccctcccgggttgcgctgg	19	12	0	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr10:87966273G>A	ENST00000327946.7	-	3	453	c.368C>T	c.(367-369)tCg>tTg	p.S123L		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	123					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.S123L(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						GGTGCGTGGCGACCCTCCCGG	0.627										Multiple Myeloma(13;0.14)																											p.S123L		Atlas-SNP	.											GRID1,extremity,malignant_melanoma,0,1	GRID1	204	1	1	Substitution - Missense(1)	skin(1)	c.C368T						.						182	114	137					10																	87966273		2203	4300	6503	SO:0001583	missense	2894	exon3			CGTGGCGACCCTC	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.368C>T	10.37:g.87966273G>A	ENSP00000330148:p.Ser123Leu	88.0	0.0		94.0	36.0	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.315816	0.81469	.	.	ENSG00000182771	ENST00000327946	D	0.87029	-2.2	6.06	6.06	0.98353	Extracellular ligand-binding receptor (1);	0.156570	0.43579	D	0.000554	D	0.84465	0.5478	L	0.44542	1.39	0.80722	D	1	D	0.53462	0.96	B	0.41374	0.355	D	0.84894	0.0838	10	0.46703	T	0.11	.	19.609	0.95594	0.0:0.0:1.0:0.0	.	123	Q9ULK0	GRID1_HUMAN	L	123	ENSP00000330148:S123L	ENSP00000330148:S123L	S	-	2	0	GRID1	87956253	1.000000	0.71417	0.462000	0.27118	0.902000	0.53008	9.863000	0.99569	2.882000	0.98803	0.655000	0.94253	TCG	.	.		0.627	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		A	87966273	G	A	87966273	3	1	152	1	0	0	0	0	1	0	0	0	6780	1059	37	1	2717	1	GRID1	10	87966273	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	63238884	87966273	47568474	58	23406										
MUC2	4583	hgsc.bcm.edu	37	chr11	1093375	1093375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ccaccaccactacggtgaccCcaaccccaacacccaccggc	5	23	0	1	rs552937801	byFrequency	TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr11:1093375C>T	ENST00000441003.2	+	30	5221	c.5194C>T	c.(5194-5196)Cca>Tca	p.P1732S	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Missense_Mutation_p.P20S|MUC2_ENST00000359061.5_Missense_Mutation_p.P1699S	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	tacggtgaccccaaccccaac	0.657																																					p.P1732S		Atlas-SNP	.											.	MUC2	614	.	0			c.C5194T						.																																			SO:0001583	missense	4583	exon30			GTGACCCCAACCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5194C>T	11.37:g.1093375C>T	ENSP00000415183:p.Pro1732Ser	39.0	0.0		39.0	5.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	0.065	-1.214378	0.01555	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.10288	3.1;3.17;2.89	1.49	-1.27	0.09347	.	498.391000	0.02047	N	0.049780	T	0.06050	0.0157	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28902	-1.0029	9	0.20519	T	0.43	.	2.7543	0.05288	0.4674:0.3566:0.0:0.176	.	1732	E7EUV1	.	S	1732;1699;20	ENSP00000415183:P1732S;ENSP00000351956:P1699S;ENSP00000331373:P20S	ENSP00000331373:P20S	P	+	1	0	MUC2	1083375	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-2.627000	0.00874	-0.601000	0.05783	-1.152000	0.01820	CCA	.	.		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093375	C	T	1093375	3	4	152	1	0	0	0	0	1	0	0	0	9984	623	22	3	5312	3	MUC2	11	1093375	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10		1093375	133913141	59	23407										
MYEOV	26579	hgsc.bcm.edu	37	chr11	69063143	69063143	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	agggctccaaagccggcagaTcccggggccgcctctgtctc	13	16	2	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr11:69063143T>C	ENST00000308946.3	+	3	676	c.226T>C	c.(226-228)Tcc>Ccc	p.S76P	MYEOV_ENST00000441339.2_Missense_Mutation_p.S76P|MYEOV_ENST00000535407.1_Missense_Mutation_p.S18P	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	76										endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|urinary_tract(1)	24	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		AGCCGGCAGATCCCGGGGCCG	0.607																																					p.S76P		Atlas-SNP	.											.	MYEOV	42	.	0			c.T226C						.						50	59	56					11																	69063143		2200	4294	6494	SO:0001583	missense	26579	exon3			GGCAGATCCCGGG	AJ223366	CCDS8190.1, CCDS73340.1	11q13.2	2013-03-27	2013-03-27			ENSG00000172927			7563	protein-coding gene	gene with protein product		605625	"myeloma overexpressed (in a subset of t(11;14) positive multiple myelomas)"			10753852	Standard	XM_005273908		Approved	OCIM	uc001oov.3	Q96EZ4		ENST00000308946.3:c.226T>C	11.37:g.69063143T>C	ENSP00000308330:p.Ser76Pro	66.0	0.0		73.0	36.0	NM_138768	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	.	.	.	.	.	.	.	.	.	.	T	8.577	0.881480	0.17467	.	.	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.24350	1.87;1.87;1.86	1.38	-1.15	0.09709	.	.	.	.	.	T	0.11580	0.0282	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25222	-1.0138	9	0.87932	D	0	.	5.4883	0.16761	0.0:0.7029:0.0:0.2971	.	76	Q96EZ4	MYEOV_HUMAN	P	76;76;18	ENSP00000412482:S76P;ENSP00000308330:S76P;ENSP00000438100:S18P	ENSP00000308330:S76P	S	+	1	0	MYEOV	68819719	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.389000	0.07342	-0.347000	0.08299	-0.512000	0.04463	TCC	.	.		0.607	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1			C	69063143	T	C	69063143	3	2	152	1	0	0	0	0	1	0	0	0	10034	1435	50	2	232	2	MYEOV	11	69063143	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	67969768	69063143	65943373	60	23408										
ALG9	91893	hgsc.bcm.edu	37	chr11	111742145	111742145	+	IGR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cagcttgtccgcagccggggCgcgtatccccactgctggcc	13	17	0	0	rs10708475|rs200786242		TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr11:111742145C>G	ENST00000260257.4	-	0	2789				ALG9_ENST00000524880.1_Missense_Mutation_p.R254P|ALG9_ENST00000527377.1_5'UTR|ALG9_ENST00000398006.2_5'Flank|ALG9_ENST00000531154.1_5'Flank|ALG9_ENST00000527228.1_5'UTR	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1						phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						GCAGCCGGGGCGCGTATCCCC	0.711																																					p.A21P		Atlas-SNP	.											.	ALG9	77	.	0			c.G61C						.						1	1	1					11																	111742145		776	1973	2749	SO:0001628	intergenic_variant	79796	exon2			CCGGGGCGCGTAT		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"hypothetical protein BC006136"						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795		11.37:g.111742145C>G		650.0	0.0		759.0	35.0	NM_001077690	A0PJW7|B4DUU2	Missense_Mutation	SNP	ENST00000260257.4	37	CCDS44729.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.83|11.83	1.756102|1.756102	0.31137|0.31137	.|.	.|.	ENSG00000086848|ENSG00000086848	ENST00000428306|ENST00000428306	.|.	.|.	.|.	4.98|4.98	0.976|0.976	0.19727|0.19727	.|.	.|.	.|.	.|.	.|.	.|T	.|0.17831	.|0.0428	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	0.99999|0.99999	.|B;B	.|0.21147	.|0.0;0.052	.|B;B	.|0.16722	.|0.0;0.016	.|T	.|0.23940	.|-1.0174	.|8	.|0.26408	.|T	.|0.33	.|.	4.2702|4.2702	0.10783|0.10783	0.1565:0.5847:0.0:0.2588|0.1565:0.5847:0.0:0.2588	.|.	.|21;21	.|Q9H6U8-3;Q9H6U8	.|.;ALG9_HUMAN	.|P	-1|254	.|.	.|ENSP00000387627:A254P	.|A	-|-	.|1	.|0	ALG9|ALG9	111247355|111247355	0.130000|0.130000	0.22417|0.22417	0.101000|0.101000	0.21167|0.21167	0.687000|0.687000	0.40016|0.40016	0.758000|0.758000	0.26447|0.26447	0.032000|0.032000	0.15435|0.15435	-0.291000|-0.291000	0.09656|0.09656	.|GCC	.	.		0.711	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378		G	111742145	C	G	111742145	1	3	152	0	1	0	0	0	0	0	0	0	524	768	27	4		4	ALG9	11	111742145	IGR	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	42679002	111742145	23264371	61	23409										
APOA1	335	hgsc.bcm.edu	37	chr11	116706843	116706843	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ccagtgggctcagcttctctTgcagctcgtgcagcttctgg	12	13	3	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr11:116706843T>G	ENST00000236850.4	-	4	850	c.485A>C	c.(484-486)cAa>cCa	p.Q162P	AP006216.12_ENST00000444200.1_RNA|APOA1_ENST00000375323.1_Missense_Mutation_p.Q162P|APOA1_ENST00000359492.2_Missense_Mutation_p.Q162P|APOA1_ENST00000375329.2_Missense_Mutation_p.Q140P|APOA1_ENST00000375320.1_Missense_Mutation_p.Q162P	NM_000039.1	NP_000030.1	P02647	APOA1_HUMAN	apolipoprotein A-I	162	10 X approximate tandem repeats.				adrenal gland development (GO:0030325)|blood coagulation (GO:0007596)|blood vessel endothelial cell migration (GO:0043534)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endothelial cell proliferation (GO:0001935)|G-protein coupled receptor signaling pathway (GO:0007186)|glucocorticoid metabolic process (GO:0008211)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|integrin-mediated signaling pathway (GO:0007229)|lipid storage (GO:0019915)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|negative chemotaxis (GO:0050919)|negative regulation of cell adhesion molecule production (GO:0060354)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of lipase activity (GO:0060192)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of very-low-density lipoprotein particle remodeling (GO:0010903)|organ regeneration (GO:0031100)|peptidyl-methionine modification (GO:0018206)|peripheral nervous system axon regeneration (GO:0014012)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of hydrolase activity (GO:0051345)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transferase activity (GO:0051347)|protein oxidation (GO:0018158)|protein stabilization (GO:0050821)|regulation of Cdc42 protein signal transduction (GO:0032489)|regulation of intestinal cholesterol absorption (GO:0030300)|regulation of protein phosphorylation (GO:0001932)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to nutrient (GO:0007584)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule lumen (GO:0034774)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)|vesicle (GO:0031982)	apolipoprotein A-I receptor binding (GO:0034191)|apolipoprotein receptor binding (GO:0034190)|beta-amyloid binding (GO:0001540)|chemorepellent activity (GO:0045499)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|enzyme binding (GO:0019899)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor binding (GO:0070653)|identical protein binding (GO:0042802)|lipase inhibitor activity (GO:0055102)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)			cervix(1)|endometrium(1)|lung(4)|prostate(1)|skin(2)	9	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.59e-05)|all cancers(92;0.000162)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		CAGCTTCTCTTGCAGCTCGTG	0.687																																					p.Q162P		Atlas-SNP	.											.	APOA1	19	.	0			c.A485C						.						24	25	24					11																	116706843		2201	4291	6492	SO:0001583	missense	335	exon4			TTCTCTTGCAGCT	X02162	CCDS8378.1	11q23-q24	2014-09-17			ENSG00000118137	ENSG00000118137		"Apolipoproteins"	600	protein-coding gene	gene with protein product		107680					Standard	NM_000039		Approved		uc001ppv.1	P02647	OTTHUMG00000046112	ENST00000236850.4:c.485A>C	11.37:g.116706843T>G	ENSP00000236850:p.Gln162Pro	51.0	0.0		40.0	18.0	NM_000039	A8K866|Q6LDN9|Q6Q785|Q9UCS8|Q9UCT8	Missense_Mutation	SNP	ENST00000236850.4	37	CCDS8378.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.688098	0.48097	.	.	ENSG00000118137	ENST00000375320;ENST00000359492;ENST00000375329;ENST00000375323;ENST00000236850	T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02	5.17	4.03	0.46877	Apolipoprotein/apolipophorin (1);	0.950518	0.08651	U	0.913947	D	0.87977	0.6314	M	0.83012	2.62	0.38490	D	0.947941	D	0.54964	0.969	D	0.66847	0.947	T	0.81743	-0.0793	10	0.56958	D	0.05	-4.7239	9.7196	0.40295	0.0:0.0834:0.0:0.9166	.	162	P02647	APOA1_HUMAN	P	162;162;140;162;162	ENSP00000364469:Q162P;ENSP00000352471:Q162P;ENSP00000364478:Q140P;ENSP00000364472:Q162P;ENSP00000236850:Q162P	ENSP00000236850:Q162P	Q	-	2	0	APOA1	116212053	0.996000	0.38824	0.714000	0.30535	0.033000	0.12548	2.672000	0.46850	0.799000	0.34018	0.379000	0.24179	CAA	.	.		0.687	APOA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106281.2	NM_000039		G	116706843	T	G	116706843	3	3	152	1	0	0	0	0	1	0	0	0	780	1812	63	5	322	5	APOA1	11	116706843	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	4964698	116706843	18299673	62	23410										
CEP164	22897	hgsc.bcm.edu	37	chr11	117222658	117222658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	taagaagaagaaaaaaaaaaAggaaaagaaagacaagaagg	10	1	0	6			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr11:117222658A>G	ENST00000278935.3	+	5	494	c.347A>G	c.(346-348)aAg>aGg	p.K116R		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	116	Interaction with ATRIP.|Lys-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		aaaaaaaaaaaggaaaagaaa	0.502																																					p.K116R		Atlas-SNP	.											CEP164,caecum,carcinoma,0,1	CEP164	121	1	0			c.A347G						.						33	34	34					11																	117222658		2201	4296	6497	SO:0001583	missense	22897	exon4			AAAAAAAGGAAAA	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.347A>G	11.37:g.117222658A>G	ENSP00000278935:p.Lys116Arg	87.0	0.0		53.0	3.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744661	0.49151	.	.	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000533570;ENST00000529538	T;T;T;T	0.76060	-0.34;-0.03;-0.29;-0.99	5.95	4.82	0.62117	.	0.243999	0.29172	N	0.012934	T	0.80221	0.4583	M	0.62723	1.935	0.34770	D	0.733632	D;P;B;D	0.56521	0.959;0.482;0.023;0.976	P;B;B;P	0.56960	0.65;0.11;0.01;0.81	D	0.85776	0.1358	10	0.62326	D	0.03	-27.2573	11.2799	0.49188	0.9276:0.0:0.0724:0.0	.	116;70;116;116	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	R	70;116;70;70;116;116	ENSP00000436034:K70R;ENSP00000278935:K116R;ENSP00000435759:K70R;ENSP00000431302:K116R	ENSP00000278935:K116R	K	+	2	0	CEP164	116727868	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.713000	0.91408	1.068000	0.40764	0.533000	0.62120	AAG	.	.		0.502	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		G	117222658	A	G	117222658	3	3	152	1	0	0	0	0	1	0	0	0	3251	72	3	2	357	2	CEP164	11	117222658	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	515815	117222658	17783858	63	23411										
PLEKHG6	55200	hgsc.bcm.edu	37	chr12	6424240	6424240	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tgtttgggatgccccggctgCcccctgaggaccggcggcac	15	15	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr12:6424240C>T	ENST00000396988.3	+	4	594	c.364C>T	c.(364-366)Ccc>Tcc	p.P122S	PLEKHG6_ENST00000449001.2_Missense_Mutation_p.P90S|PLEKHG6_ENST00000536531.1_Missense_Mutation_p.P122S|PLEKHG6_ENST00000011684.7_Missense_Mutation_p.P122S	NM_001144856.1	NP_001138328.1	Q3KR16	PKHG6_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	122						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(4)	23						GCCCCGGCTGCCCCCTGAGGA	0.642																																					p.P122S		Atlas-SNP	.											.	PLEKHG6	62	.	0			c.C364T						.						76	70	72					12																	6424240		2203	4300	6503	SO:0001583	missense	55200	exon4			CGGCTGCCCCCTG	AK001527	CCDS8541.1, CCDS44808.1	12p13.31	2013-01-11			ENSG00000008323	ENSG00000008323		"Pleckstrin homology (PH) domain containing"	25562	protein-coding gene	gene with protein product		611743					Standard	NM_018173		Approved	FLJ10665	uc001qnr.3	Q3KR16	OTTHUMG00000168266	ENST00000396988.3:c.364C>T	12.37:g.6424240C>T	ENSP00000380185:p.Pro122Ser	61.0	0.0		47.0	16.0	NM_001144856	Q3SWR1|Q8N1P1|Q8WYY1|Q9H8F4|Q9NVK9	Missense_Mutation	SNP	ENST00000396988.3	37	CCDS8541.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.468019	0.84533	.	.	ENSG00000008323	ENST00000011684;ENST00000536531;ENST00000396988;ENST00000449001	T;T;T;T	0.72051	-0.49;-0.31;-0.49;-0.62	5.0	5.0	0.66597	.	0.000000	0.51477	D	0.000086	D	0.83096	0.5180	M	0.77103	2.36	0.80722	D	1	P;D;D	0.89917	0.953;1.0;0.999	P;D;D	0.76575	0.821;0.988;0.946	D	0.84419	0.0570	10	0.59425	D	0.04	-19.2803	13.6539	0.62327	0.0:1.0:0.0:0.0	.	90;122;122	Q3KR16-2;F5H731;Q3KR16	.;.;PKHG6_HUMAN	S	122;122;122;90	ENSP00000011684:P122S;ENSP00000442836:P122S;ENSP00000380185:P122S;ENSP00000393194:P90S	ENSP00000011684:P122S	P	+	1	0	PLEKHG6	6294501	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.047000	0.64232	2.600000	0.87896	0.591000	0.81541	CCC	.	.		0.642	PLEKHG6-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399031.1	NM_018173		T	6424240	C	T	6424240	3	4	152	1	0	0	0	0	1	0	0	0	12083	739	26	3	420	3	PLEKHG6	12	6424240	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10		6424240	127427655	64	23412										
CLEC2D	29121	hgsc.bcm.edu	37	chr12	9833543	9833543	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tctgcattcaaaagagcattCtattaaagctaccttaattt	4	8	3	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr12:9833543C>G	ENST00000290855.6	+	2	108	c.86C>G	c.(85-87)tCt>tGt	p.S29C	CLEC2D_ENST00000487752.1_3'UTR|CLEC2D_ENST00000261339.6_Intron|CLEC2D_ENST00000543300.1_Missense_Mutation_p.S29C|CLEC2D_ENST00000545918.1_Intron|CLEC2D_ENST00000261340.7_Missense_Mutation_p.S29C	NM_013269.5	NP_037401.1	Q9UHP7	CLC2D_HUMAN	C-type lectin domain family 2, member D	29					cell surface receptor signaling pathway (GO:0007166)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|stomach(1)	9						AAAGAGCATTCTATTAAAGCT	0.313																																					p.S29C		Atlas-SNP	.											.	CLEC2D	54	.	0			c.C86G						.						129	124	126					12																	9833543		2202	4297	6499	SO:0001583	missense	29121	exon2			AGCATTCTATTAA	AF133299	CCDS8602.1, CCDS31741.1, CCDS55800.1, CCDS55801.1, CCDS55802.1	12p13.31	2011-05-24	2005-09-29		ENSG00000069493	ENSG00000069493		"C-type lectin domain containing"	14351	protein-coding gene	gene with protein product	"C-type lectin related f", "lectin-like transcript 1"	605659	"C-type lectin superfamily 2, member D"				Standard	NM_013269		Approved	LLT1, CLAX, OCIL	uc001qwf.3	Q9UHP7	OTTHUMG00000168369	ENST00000290855.6:c.86C>G	12.37:g.9833543C>G	ENSP00000290855:p.Ser29Cys	72.0	0.0		26.0	8.0	NM_001004419	D6CI39|D6CI40|D6CI41|Q6YID5|Q8WUP7|Q9HD37|Q9HD38	Missense_Mutation	SNP	ENST00000290855.6	37	CCDS8602.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.451488	0.26074	.	.	ENSG00000069493	ENST00000261340;ENST00000290855;ENST00000543300;ENST00000430909;ENST00000544322	T;T;T;T;T	0.11277	4.42;4.57;2.83;4.32;2.79	1.31	1.31	0.21738	.	.	.	.	.	T	0.13841	0.0335	N	0.19112	0.55	0.18873	N	0.999989	D;D	0.71674	0.998;0.989	D;D	0.67725	0.953;0.924	T	0.23476	-1.0187	8	.	.	.	-1.3815	6.0258	0.19654	0.0:1.0:0.0:0.0	.	29;29	Q9UHP7;Q9UHP7-3	CLC2D_HUMAN;.	C	29;29;29;8;3	ENSP00000261340:S29C;ENSP00000290855:S29C;ENSP00000443065:S29C;ENSP00000413045:S8C;ENSP00000437861:S3C	.	S	+	2	0	CLEC2D	9724810	0.001000	0.12720	0.026000	0.17262	0.055000	0.15305	0.002000	0.13061	1.051000	0.40369	0.436000	0.28706	TCT	.	.		0.313	CLEC2D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000335424.2	NM_013269		G	9833543	C	G	9833543	3	3	152	1	0	0	0	0	1	0	0	0	3510	913	32	4	92	4	CLEC2D	12	9833543	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	3409303	9833543	124018352	65	23413										
CDKN1B	1027	hgsc.bcm.edu	37	chr12	12871044	12871044	+	Frame_Shift_Del	DEL	C	C	-													0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tgcccgagttctactacagaCccccgcggccccccaaaggt							TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr12:12871044delC	ENST00000228872.4	+	1	987	c.271delC	c.(271-273)cccfs	p.P92fs	CDKN1B_ENST00000396340.1_Frame_Shift_Del_p.P92fs|CDKN1B_ENST00000477087.1_Intron	NM_004064.3	NP_004055.1	P46527	CDN1B_HUMAN	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	92					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|cellular response to antibiotic (GO:0071236)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular component movement (GO:0051271)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of kinase activity (GO:0033673)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|potassium ion transport (GO:0006813)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein phosphatase binding (GO:0019903)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)			breast(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(5)	13		Prostate(47;0.0322)|all_epithelial(100;0.159)		BRCA - Breast invasive adenocarcinoma(232;0.0336)		CTACTACAGACCCCCGCGGCC	0.617																																					p.R90fs		Atlas-Indel	.											.	CDKN1B	48	.	0			c.270delA						.						47	57	54					12																	12871044		2203	4300	6503	SO:0001589	frameshift_variant	1027	exon1			.	AF480891	CCDS8653.1	12p13.1-p12	2008-08-04			ENSG00000111276	ENSG00000111276			1785	protein-coding gene	gene with protein product		600778				8033212	Standard	NM_004064		Approved	KIP1, P27KIP1	uc001rat.2	P46527	OTTHUMG00000149914	ENST00000228872.4:c.271delC	12.37:g.12871044delC	ENSP00000228872:p.Pro92fs	651.0	0.0		519.0	190.0	NM_004064	Q16307|Q5U0H2|Q9BUS6	Frame_Shift_Del	DEL	ENST00000228872.4	37	CCDS8653.1																																																																																			.	.		0.617	CDKN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313878.2	NM_004064		-	12871044	C	-	12871044	7	5	152	1	0	1	0	1	0	0	0	0	3161	507	18	0	273	0	CDKN1B	12	12871044	Frame_Shift_Del	DEL	C	TCGA-DD-AACA-01A-11D-A40R-10	3037501	12871044	120980851	66	23414										
TMBIM6	7009	hgsc.bcm.edu	37	chr12	50153095	50153095	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ggccgaacatggagatcaagAttatatctggtgagtgtggg	15	5	2	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr12:50153095A>G	ENST00000267115.5	+	8	690	c.605A>G	c.(604-606)gAt>gGt	p.D202G	TMBIM6_ENST00000423828.1_Missense_Mutation_p.D260G|TMBIM6_ENST00000395006.4_Missense_Mutation_p.D202G|TMBIM6_ENST00000547798.1_Missense_Mutation_p.D165G|TMBIM6_ENST00000549385.1_Missense_Mutation_p.D202G|TMBIM6_ENST00000552699.1_Missense_Mutation_p.D260G	NM_003217.2	NP_003208.2	P55061	BI1_HUMAN	transmembrane BAX inhibitor motif containing 6	202					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)				lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	6						GGAGATCAAGATTATATCTGG	0.438																																					p.D260G		Atlas-SNP	.											.	TMBIM6	26	.	0			c.A779G						.						166	152	157					12																	50153095		2203	4300	6503	SO:0001583	missense	7009	exon8			ATCAAGATTATAT	X75861	CCDS31797.1, CCDS44875.1	12q13.12	2013-10-08	2008-09-17	2008-09-17	ENSG00000139644	ENSG00000139644			11723	protein-coding gene	gene with protein product	"BAX inhibitor 1"	600748	"testis enhanced gene transcript"	TEGT		8530040, 9660918	Standard	NM_001098576		Approved	BI-1, BAXI1	uc001ruy.2	P55061	OTTHUMG00000169652	ENST00000267115.5:c.605A>G	12.37:g.50153095A>G	ENSP00000267115:p.Asp202Gly	67.0	0.0		36.0	16.0	NM_001098576	B2R5M4|F8W034|O14938|Q643A7|Q96J50	Missense_Mutation	SNP	ENST00000267115.5	37	CCDS31797.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.928452	0.92389	.	.	ENSG00000139644	ENST00000552699;ENST00000267115;ENST00000549385;ENST00000423828;ENST00000542631;ENST00000552370;ENST00000395006;ENST00000547798	T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.71962	0.3402	M	0.92412	3.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79676	-0.1704	10	0.87932	D	0	.	14.3706	0.66836	1.0:0.0:0.0:0.0	.	260;202	F8W034;P55061	.;BI1_HUMAN	G	260;202;202;260;202;202;202;165	ENSP00000446734:D260G;ENSP00000267115:D202G;ENSP00000448036:D202G;ENSP00000389277:D260G;ENSP00000450158:D202G;ENSP00000378454:D202G;ENSP00000447030:D165G	ENSP00000267115:D202G	D	+	2	0	TMBIM6	48439362	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.284000	0.89912	2.240000	0.73641	0.528000	0.53228	GAT	.	.		0.438	TMBIM6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405289.1	NM_003217		G	50153095	A	G	50153095	3	3	152	1	0	0	0	0	1	0	0	0	15998	333	12	2	809	2	TMBIM6	12	50153095	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	37282051	50153095	83698800	67	23415										
INHBE	83729	hgsc.bcm.edu	37	chr12	57850023	57850023	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tcttccgatggggaccaaggAggaggcgccaagggtcccgc	16	12	1	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr12:57850023A>G	ENST00000266646.2	+	2	661	c.445A>G	c.(445-447)Agg>Ggg	p.R149G	INHBE_ENST00000551553.1_3'UTR	NM_031479.3	NP_113667.1	P58166	INHBE_HUMAN	inhibin, beta E	149					growth (GO:0040007)	extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	15						GGGACCAAGGAGGAGGCGCCA	0.617											OREG0021944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R149G	GBM(191;1808 2166 15720 36624 50371)	Atlas-SNP	.											.	INHBE	38	.	0			c.A445G						.						152	147	149					12																	57850023		2203	4300	6503	SO:0001583	missense	83729	exon2			CCAAGGAGGAGGC		CCDS8939.1	12q13.2	2008-02-05				ENSG00000139269			24029	protein-coding gene	gene with protein product		612031				12242034	Standard	NM_031479		Approved	activin, MGC4638	uc001snw.3	P58166		ENST00000266646.2:c.445A>G	12.37:g.57850023A>G	ENSP00000266646:p.Arg149Gly	102.0	0.0	1026	69.0	31.0	NM_031479		Missense_Mutation	SNP	ENST00000266646.2	37	CCDS8939.1	.	.	.	.	.	.	.	.	.	.	A	0.385	-0.926804	0.02377	.	.	ENSG00000139269	ENST00000547970;ENST00000266646	T;T	0.81330	-1.48;-0.17	4.5	2.07	0.26955	Transforming growth factor-beta, N-terminal (1);	0.427931	0.20301	N	0.095035	T	0.67373	0.2886	L	0.39898	1.24	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.50259	-0.8849	10	0.22706	T	0.39	-4.2841	5.9334	0.19152	0.7434:0.1664:0.0902:0.0	.	149	P58166	INHBE_HUMAN	G	94;149	ENSP00000450212:R94G;ENSP00000266646:R149G	ENSP00000266646:R149G	R	+	1	2	INHBE	56136290	0.000000	0.05858	0.012000	0.15200	0.008000	0.06430	0.125000	0.15749	0.323000	0.23307	-0.313000	0.08912	AGG	.	.		0.617	INHBE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406773.1	NM_031479		G	57850023	A	G	57850023	3	3	152	1	0	0	0	0	1	0	0	0	7753	295	11	2	451	2	INHBE	12	57850023	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	7696928	57850023	76001872	68	23416										
EXOC5	10640	hgsc.bcm.edu	37	chr14	57686092	57686092	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tttgtcaaaaagatgaaaaaTagtattggcctgttgcacaa	8	5	1	2	rs370435401		TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr14:57686092T>C	ENST00000413566.2	-	14	1833	c.1474A>G	c.(1474-1476)Att>Gtt	p.I492V	EXOC5_ENST00000340918.7_Missense_Mutation_p.I427V	NM_006544.3	NP_006535.1	O00471	EXOC5_HUMAN	exocyst complex component 5	492					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|vesicle docking (GO:0048278)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(3)|endometrium(1)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	22						AGATGAAAAATAGTATTGGCC	0.313													T|||	1	0.000199681	0	0	5008	,	,		15036	0.001		0	False		,,,				2504	0				p.I492V		Atlas-SNP	.											EXOC5,NS,carcinoma,+2,1	EXOC5	45	1	0			c.A1474G						.						51	46	47					14																	57686092		1828	4058	5886	SO:0001583	missense	10640	exon14			GAAAAATAGTATT	U85946	CCDS45111.1	14q22.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000070367	ENSG00000070367			10696	protein-coding gene	gene with protein product		604469	"SEC10 (S. cerevisiae)-like 1", "SEC10-like 1 (S. cerevisiae)"	SEC10L1		9119050	Standard	XM_005267272		Approved	SEC10, SEC10P	uc001xct.3	O00471	OTTHUMG00000171309	ENST00000413566.2:c.1474A>G	14.37:g.57686092T>C	ENSP00000389934:p.Ile492Val	404.0	1.0		149.0	54.0	NM_006544	B2R6C5	Missense_Mutation	SNP	ENST00000413566.2	37	CCDS45111.1	.	.	.	.	.	.	.	.	.	.	T	16.36	3.100964	0.56183	.	.	ENSG00000070367	ENST00000413566;ENST00000340918	T;T	0.58210	0.41;0.35	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.41834	0.1176	N	0.21194	0.64	0.80722	D	1	P;B	0.36110	0.537;0.361	B;B	0.36666	0.203;0.23	T	0.42932	-0.9422	10	0.49607	T	0.09	-12.5892	15.3357	0.74250	0.0:0.0:0.0:1.0	.	427;492	F8W9B8;O00471	.;EXOC5_HUMAN	V	492;427	ENSP00000389934:I492V;ENSP00000342100:I427V	ENSP00000342100:I427V	I	-	1	0	EXOC5	56755845	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.159000	0.64923	2.087000	0.62958	0.528000	0.53228	ATT	.	.		0.313	EXOC5-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412905.1	NM_006544		C	57686092	T	C	57686092	3	2	152	1	0	0	0	0	1	0	0	0	5309	1406	49	2	672	2	EXOC5	14	57686092	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10		57686092	49663448	69	23417										
C14orf179	112752	hgsc.bcm.edu	37	chr14	76488730	76488730	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gggcaggtgattccgtgaagGcttcgaagtgagtaccagca	15	8	0	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr14:76488730G>T	ENST00000314067.6	+	3	242	c.208G>T	c.(208-210)Gct>Tct	p.A70S	IFT43_ENST00000238628.6_Missense_Mutation_p.A70S|IFT43_ENST00000553338.1_3'UTR|IFT43_ENST00000556742.1_Missense_Mutation_p.A70S	NM_001102564.1	NP_001096034.1	Q96FT9	IFT43_HUMAN	intraflagellar transport 43	70					cilium morphogenesis (GO:0060271)|intraciliary retrograde transport (GO:0035721)	cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)				endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						TTCCGTGAAGGCTTCGAAGTG	0.478																																					p.A70S		Atlas-SNP	.											.	IFT43	63	.	0			c.G208T						.						141	141	141					14																	76488730		2203	4300	6503	SO:0001583	missense	112752	exon3			GTGAAGGCTTCGA	BC010436	CCDS9847.1, CCDS41973.1, CCDS58330.1	14q24.3	2014-07-03	2014-07-03	2011-06-09				"Intraflagellar transport homologs"	29669	protein-coding gene	gene with protein product		614068	"chromosome 14 open reading frame 179", "intraflagellar transport 43 homolog (Chlamydomonas)"	C14orf179		21378380	Standard	NM_052873		Approved	FLJ32173, MGC16028	uc010asm.1	Q96FT9		ENST00000314067.6:c.208G>T	14.37:g.76488730G>T	ENSP00000324177:p.Ala70Ser	192.0	0.0		60.0	43.0	NM_001102564	B3KPT6|B4DZI9|G3V385|O95418|Q9ULA9	Missense_Mutation	SNP	ENST00000314067.6	37	CCDS41973.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.155818	0.00325	.	.	ENSG00000119650	ENST00000314067;ENST00000238628;ENST00000556742	T;T	0.38077	1.16;1.16	4.7	-9.39	0.00619	.	2.866800	0.00848	N	0.001801	T	0.10723	0.0262	N	0.02142	-0.665	0.09310	N	1	B;B;B;B	0.11235	0.004;0.004;0.004;0.0	B;B;B;B	0.08055	0.003;0.003;0.003;0.001	T	0.18209	-1.0344	10	0.16896	T	0.51	-15.0556	3.3446	0.07131	0.5156:0.0979:0.208:0.1786	.	70;70;70;70	Q96FT9;Q96FT9-3;Q96FT9-2;G3V385	IFT43_HUMAN;.;.;.	S	70	ENSP00000324177:A70S;ENSP00000238628:A70S	ENSP00000238628:A70S	A	+	1	0	IFT43	75558483	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.865000	0.01649	-2.611000	0.00445	-1.887000	0.00540	GCT	.	.		0.478	IFT43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052873		T	76488730	G	T	76488730	3	4	152	1	0	0	0	0	1	0	0	0	1764	1203	42	3	218	3	C14orf179	14	76488730	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	18802638	76488730	30860810	70	23418										
RTF1	23168	hgsc.bcm.edu	37	chr15	41771302	41771302	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aacttattttctctctcagtCcagagacccagctgttcaag	6	12	3	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr15:41771302C>T	ENST00000389629.4	+	16	1832	c.1820C>T	c.(1819-1821)tCc>tTc	p.S607F		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	607					DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		CTCTCTCAGTCCAGAGACCCA	0.463																																					p.S607F		Atlas-SNP	.											.	RTF1	76	.	0			c.C1820T						.						86	82	83					15																	41771302		2203	4300	6503	SO:0001630	splice_region_variant	23168	exon16			CTCAGTCCAGAGA	D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"KIAA0252"	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.1819-1C>T	15.37:g.41771302C>T		68.0	0.0		60.0	20.0	NM_015138	Q96BX6	Missense_Mutation	SNP	ENST00000389629.4	37	CCDS32200.2	.	.	.	.	.	.	.	.	.	.	C	19.49	3.838150	0.71373	.	.	ENSG00000137815	ENST00000389629	.	.	.	5.47	5.47	0.80525	.	0.053218	0.85682	D	0.000000	T	0.55369	0.1916	L	0.43923	1.385	0.80722	D	1	P	0.44578	0.838	B	0.41271	0.352	T	0.61451	-0.7060	9	0.72032	D	0.01	-9.0335	19.3293	0.94278	0.0:1.0:0.0:0.0	.	607	Q92541	RTF1_HUMAN	F	607	.	ENSP00000374280:S607F	S	+	2	0	RTF1	39558594	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	6.962000	0.76048	2.574000	0.86865	0.563000	0.77884	TCC	.	.		0.463	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138	Missense_Mutation	T	41771302	C	T	41771302	5	4	152	1	0	0	0	0	0	0	1	0	13736	869	30	3	1882	3	RTF1	15	41771302	Splice_Site	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10		41771302	60760090	71	23419										
TYRO3	7301	hgsc.bcm.edu	37	chr15	41854916	41854916	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	catctgttttaaatgtaacaGgtgagcagcctcagaagggg	12	7	2	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr15:41854916G>A	ENST00000263798.3	+	4	804	c.580G>A	c.(580-582)Ggg>Agg	p.G194R	TYRO3_ENST00000559066.1_Splice_Site_p.G149R	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	194	Ig-like C2-type 2.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		AAATGTAACAGGTGAGCAGCC	0.577																																					p.G194R		Atlas-SNP	.											.	TYRO3	169	.	0			c.G580A						.						22	22	22					15																	41854916		2203	4300	6503	SO:0001630	splice_region_variant	7301	exon4			GTAACAGGTGAGC	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.580+1G>A	15.37:g.41854916G>A		55.0	0.0		45.0	19.0	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	g	23.9	4.471522	0.84533	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	T	0.12039	2.72	4.8	3.89	0.44902	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.40640	N	0.001058	T	0.37320	0.0999	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.29058	-1.0024	10	0.87932	D	0	-18.1417	12.8527	0.57867	0.0787:0.0:0.9213:0.0	.	194	Q06418	TYRO3_HUMAN	R	126;194	ENSP00000263798:G194R	ENSP00000263798:G194R	G	+	1	0	TYRO3	39642208	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.377000	0.79668	1.239000	0.43787	0.472000	0.43445	GGG	.	.		0.577	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Missense_Mutation	A	41854916	G	A	41854916	5	1	152	1	0	0	0	0	0	0	1	0	16829	1014	35	3	594	3	TYRO3	15	41854916	Splice_Site	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	83614	41854916	60676476	72	23420										
TLN2	83660	hgsc.bcm.edu	37	chr15	62999360	62999360	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	taaaggcaaagaatgttgccCaagtggccgaagacactgtc	11	9	0	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr15:62999360C>T	ENST00000561311.1	+	19	2310	c.2080C>T	c.(2080-2082)Caa>Taa	p.Q694*	TLN2_ENST00000306829.6_Nonsense_Mutation_p.Q694*			Q9Y4G6	TLN2_HUMAN	talin 2	694					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						GAATGTTGCCCAAGTGGCCGA	0.493																																					p.Q694X		Atlas-SNP	.											.	TLN2	253	.	0			c.C2080T						.						132	110	117					15																	62999360		2203	4300	6503	SO:0001587	stop_gained	83660	exon17			GTTGCCCAAGTGG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.2080C>T	15.37:g.62999360C>T	ENSP00000453508:p.Gln694*	92.0	0.0		64.0	21.0	NM_015059	A6NLB8	Nonsense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	c	43	10.104317	0.99337	.	.	ENSG00000171914	ENST00000306829	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	-12.4641	19.6558	0.95837	0.0:1.0:0.0:0.0	.	.	.	.	X	694	.	ENSP00000303476:Q694X	Q	+	1	0	TLN2	60786652	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.743000	0.85020	2.719000	0.93026	0.655000	0.94253	CAA	.	.		0.493	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	62999360	C	T	62999360	4	4	152	1	0	0	0	0	0	1	0	0	15963	595	21	3	2146	3	TLN2	15	62999360	Nonsense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	21144444	62999360	39532032	73	23421										
NOX5	79400	hgsc.bcm.edu	37	chr15	69329420	69329432	+	Frame_Shift_Del	DEL	TTCATGGGCCCAA	TTCATGGGCCCAA	-													0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cgtgtggcttctgctcatctTtcatgggcccaacttctgga					rs139472034		TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	TTCATGGGCCCAA	TTCATGGGCCCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr15:69329420_69329432delTTCATGGGCCCAA	ENST00000388866.3	+	8	1282_1294	c.1241_1253delTTCATGGGCCCAA	c.(1240-1254)tttcatgggcccaacfs	p.FHGPN414fs	NOX5_ENST00000448182.3_Frame_Shift_Del_p.FHGPN368fs|NOX5_ENST00000260364.5_Frame_Shift_Del_p.FHGPN396fs|NOX5_ENST00000530406.2_Frame_Shift_Del_p.FHGPN386fs|RP11-809H16.4_ENST00000559495.1_RNA|NOX5_ENST00000455873.3_Frame_Shift_Del_p.FHGPN379fs	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	414	Ferric oxidoreductase.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						CTGCTCATCTTTCATGGGCCCAACTTCTGGAAG	0.573																																					p.414_418del		Atlas-Indel	.											.	NOX5	60	.	0			c.1240_1252del						.																																			SO:0001589	frameshift_variant	79400	exon8			.	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"EF-hand domain containing"	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.1241_1253delTTCATGGGCCCAA	15.37:g.69329420_69329432delTTCATGGGCCCAA	ENSP00000373518:p.Phe414fs	132.0	0.0		76.0	16.0	NM_024505	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Frame_Shift_Del	DEL	ENST00000388866.3	37	CCDS32276.2																																																																																			.	.		0.573	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505		-	69329432	TTCATGGGCCCAA	-	69329420	7	5	152	1	0	1	0	1	0	0	0	0	10568	1841	64	0	1304	0	NOX5	15	69329420	Frame_Shift_Del	DEL	TTCATGGGCCCAA	TCGA-DD-AACA-01A-11D-A40R-10	6330060	69329420	33201972	74	23422										
PDIA2	64714	hgsc.bcm.edu	37	chr16	336642	336642	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gaccacgaggacatcatcatTgctgagctggatgccacggc	12	12	2	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr16:336642T>C	ENST00000219406.6	+	9	1347	c.1329T>C	c.(1327-1329)atT>atC	p.I443I	PDIA2_ENST00000404312.1_Silent_p.I440I	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	443	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				ACATCATCATTGCTGAGCTGG	0.602																																					p.I443I		Atlas-SNP	.											.	PDIA2	51	.	0			c.T1329C						.						48	51	50					16																	336642		2156	4243	6399	SO:0001819	synonymous_variant	64714	exon9			CATCATTGCTGAG	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"Protein disulfide isomerases"	14180	protein-coding gene	gene with protein product		608012	"protein disulfide isomerase, pancreatic", "protein disulfide isomerase-associated 2"	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.1329T>C	16.37:g.336642T>C		90.0	0.0		60.0	20.0	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Silent	SNP	ENST00000219406.6	37	CCDS42089.1																																																																																			.	.		0.602	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849		C	336642	T	C	336642	2	2	152	1	0	0	0	0	0	0	0	1	11677	1800	63	2		2	PDIA2	16	336642	Silent	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10		336642	90018111	75	23423										
SRL	6345	hgsc.bcm.edu	37	chr16	4242284	4242284	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cctgagtgatggcccgctcaAtcttctccagaaagcaacct	8	14	3	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr16:4242284A>G	ENST00000399609.3	-	6	1304	c.1292T>C	c.(1291-1293)aTt>aCt	p.I431T	SRL_ENST00000537996.1_Missense_Mutation_p.I389T	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	890	Acidic domain, probably binds calcium. {ECO:0000250}.					sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						GGCCCGCTCAATCTTCTCCAG	0.552																																					p.I431T		Atlas-SNP	.											.	SRL	56	.	0			c.T1292C						.						74	78	77					16																	4242284		1895	4103	5998	SO:0001583	missense	6345	exon6			CGCTCAATCTTCT	AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739			11295	protein-coding gene	gene with protein product		604992				2762314	Standard	NM_001098814		Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.1292T>C	16.37:g.4242284A>G	ENSP00000382518:p.Ile431Thr	140.0	0.0		111.0	56.0	NM_001098814		Missense_Mutation	SNP	ENST00000399609.3	37	CCDS42113.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.002624	0.74932	.	.	ENSG00000185739	ENST00000399609;ENST00000330063;ENST00000537996	T;T	0.36699	1.24;1.24	5.83	5.83	0.93111	.	0.000000	0.85682	U	0.000000	T	0.44477	0.1295	M	0.68952	2.095	0.80722	D	1	P	0.50272	0.933	P	0.44811	0.461	T	0.50197	-0.8856	10	0.87932	D	0	-11.4226	16.1905	0.81986	1.0:0.0:0.0:0.0	.	431	Q86TD4-2	.	T	431;889;389	ENSP00000382518:I431T;ENSP00000440350:I389T	ENSP00000333285:I889T	I	-	2	0	SRL	4182285	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	9.339000	0.96797	2.212000	0.71576	0.533000	0.62120	ATT	.	.		0.552	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152		G	4242284	A	G	4242284	3	3	152	1	0	0	0	0	1	0	0	0	15165	101	4	2	133	2	SRL	16	4242284	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	3905642	4242284	86112469	76	23424										
USP7	7874	hgsc.bcm.edu	37	chr16	8992449	8992449	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	actgtagaagatctcttaaaGtaccttcataattatgtcta	5	7	3	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr16:8992449G>A	ENST00000344836.4	-	24	2777	c.2579C>T	c.(2578-2580)aCt>aTt	p.T860I	USP7_ENST00000381886.4_Missense_Mutation_p.T844I|USP7_ENST00000535863.1_Missense_Mutation_p.T761I	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	860					maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						ATCTCTTAAAGTACCTTCATA	0.338																																					p.T860I		Atlas-SNP	.											.	USP7	116	.	0			c.C2579T						.						69	72	71					16																	8992449		2197	4300	6497	SO:0001583	missense	7874	exon24			CTTAAAGTACCTT	Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"Ubiquitin-specific peptidases"	12630	protein-coding gene	gene with protein product		602519	"ubiquitin specific protease 7 (herpes virus-associated)"	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.2579C>T	16.37:g.8992449G>A	ENSP00000343535:p.Thr860Ile	62.0	0.0		33.0	14.0	NM_003470	A6NMY8|B7Z815|H0Y3G8	Missense_Mutation	SNP	ENST00000344836.4	37	CCDS32385.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.347182	0.82022	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863;ENST00000544549	T;T	0.08634	3.07;3.09	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.28433	0.0703	M	0.68317	2.08	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.64237	0.923;0.923	T	0.00010	-1.2455	10	0.42905	T	0.14	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	860;844	Q93009;B7Z815	UBP7_HUMAN;.	I	860;868;761;761	ENSP00000343535:T860I;ENSP00000443646:T761I	ENSP00000343535:T860I	T	-	2	0	USP7	8899950	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.491000	0.97954	2.941000	0.99782	0.655000	0.94253	ACT	.	.		0.338	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			A	8992449	G	A	8992449	3	1	152	1	0	0	0	0	1	0	0	0	17103	1029	36	3	761	3	USP7	16	8992449	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	4750165	8992449	81362304	77	23425										
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15069069	15069069	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cctcagccatggacgcgtccCtggagaaggtccgtgccggg	15	14	1	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr16:15069069C>T	ENST00000396410.4	+	1	110	c.13C>T	c.(13-15)Ctg>Ttg	p.L5L	PDXDC1_ENST00000455313.2_Silent_p.L5L|PDXDC1_ENST00000563679.1_Intron|PDXDC1_ENST00000325823.7_Intron|PDXDC1_ENST00000535621.2_Silent_p.L5L|PDXDC1_ENST00000450288.2_Silent_p.L5L|PDXDC1_ENST00000447912.2_Intron|PDXDC1_ENST00000569715.1_Silent_p.L5L	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	5					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GGACGCGTCCCTGGAGAAGGT	0.721																																					p.L5L		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C13T						.						6	10	9					16																	15069069		1769	3522	5291	SO:0001819	synonymous_variant	23042	exon1			GCGTCCCTGGAGA	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.13C>T	16.37:g.15069069C>T		52.0	0.0		105.0	53.0	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	37	CCDS32393.1																																																																																			.	.		0.721	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		T	15069069	C	T	15069069	2	4	152	1	0	0	0	0	0	0	0	1	11705	680	24	3		3	PDXDC1	16	15069069	Silent	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	6076620	15069069	75285684	78	23426										
CDH15	1013	hgsc.bcm.edu	37	chr16	89260253	89260253	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gcagagatgccccgcagggcCgcctgcacccccagccaccc	11	21	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr16:89260253C>T	ENST00000289746.2	+	13	2148	c.2083C>T	c.(2083-2085)Cgc>Tgc	p.R695C		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	695					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		CCCGCAGGGCCGCCTGCACCC	0.677																																					p.R695C		Atlas-SNP	.											.	CDH15	54	.	0			c.C2083T						.						13	17	15					16																	89260253		2141	4243	6384	SO:0001583	missense	1013	exon13			CAGGGCCGCCTGC	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"Cadherins / Major cadherins"	1754	protein-coding gene	gene with protein product		114019	"cadherin 15, M-cadherin (myotubule)"	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.2083C>T	16.37:g.89260253C>T	ENSP00000289746:p.Arg695Cys	100.0	0.0		86.0	42.0	NM_004933		Missense_Mutation	SNP	ENST00000289746.2	37	CCDS10976.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.533399	0.45073	.	.	ENSG00000129910	ENST00000289746	T	0.77620	-1.11	4.52	0.197	0.15164	Cadherin, cytoplasmic domain (1);	1.799820	0.03367	N	0.198394	T	0.79505	0.4457	L	0.37750	1.13	0.09310	N	1	D	0.69078	0.997	D	0.63793	0.918	T	0.62831	-0.6771	10	0.38643	T	0.18	.	4.0149	0.09639	0.1613:0.4729:0.0:0.3658	.	695	P55291	CAD15_HUMAN	C	695	ENSP00000289746:R695C	ENSP00000289746:R695C	R	+	1	0	CDH15	87787754	0.002000	0.14202	0.000000	0.03702	0.020000	0.10135	0.040000	0.13905	0.015000	0.14971	0.557000	0.71058	CGC	.	.		0.677	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		T	89260253	C	T	89260253	3	4	152	1	0	0	0	0	1	0	0	0	3102	652	23	1	2133	1	CDH15	16	89260253	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	74191184	89260253	1094500	79	23427										
MPDU1	9526	hgsc.bcm.edu	37	chr17	7490856	7490856	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aaagcctccccacaagcagaAaaaggcgcagtagagccagc	10	13	0	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr17:7490856A>C	ENST00000250124.6	+	7	947	c.731A>C	c.(730-732)aAa>aCa	p.K244T	MPDU1_ENST00000396501.4_3'UTR|MPDU1_ENST00000423172.2_Intron	NM_004870.3	NP_004861.2	O75352	MPU1_HUMAN	mannose-P-dolichol utilization defect 1	244					dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|oligosaccharide biosynthetic process (GO:0009312)|protein folding (GO:0006457)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)				central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(1)	7						CACAAGCAGAAAAAGGCGCAG	0.572																																					p.K244T		Atlas-SNP	.											.	MPDU1	14	.	0			c.A731C						.						84	83	84					17																	7490856		2203	4300	6503	SO:0001583	missense	9526	exon7			AGCAGAAAAAGGC	AF038961	CCDS11115.1	17p13.1-p12	2008-07-03			ENSG00000129255	ENSG00000129255			7207	protein-coding gene	gene with protein product		604041				8663248, 9653160, 11733564	Standard	NM_004870		Approved	SL15, Lec35, PQLC5, CDGIf	uc002ghw.3	O75352	OTTHUMG00000108147	ENST00000250124.6:c.731A>C	17.37:g.7490856A>C	ENSP00000250124:p.Lys244Thr	65.0	0.0		35.0	28.0	NM_004870	B3KQP1|B4DT74|Q9BUU8	Missense_Mutation	SNP	ENST00000250124.6	37	CCDS11115.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.41|13.41	2.230082|2.230082	0.39399|0.39399	.|.	.|.	ENSG00000129255|ENSG00000129255	ENST00000359822|ENST00000250124	.|T	.|0.76839	.|-1.05	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	0.429988|.	0.22246|.	N|.	0.062618|.	T|T	0.79522|0.79522	0.4460|0.4460	M|M	0.78456|0.78456	2.415|2.415	0.80722|0.80722	D|D	1|1	.|P	.|0.51791	.|0.948	.|P	.|0.45037	.|0.467	T|T	0.82857|0.82857	-0.0250|-0.0250	7|9	0.59425|0.72032	D|D	0.04|0.01	-0.2512|-0.2512	11.7153|11.7153	0.51650|0.51650	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|244	.|O75352	.|MPU1_HUMAN	D|T	243|244	.|ENSP00000250124:K244T	ENSP00000352876:E243D|ENSP00000250124:K244T	E|K	+|+	3|2	2|0	MPDU1|MPDU1	7431580|7431580	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.183000|0.183000	0.23260|0.23260	3.965000|3.965000	0.56788|0.56788	2.254000|2.254000	0.74563|0.74563	0.533000|0.533000	0.62120|0.62120	GAA|AAA	.	.		0.572	MPDU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226950.4			C	7490856	A	C	7490856	3	2	152	1	0	0	0	0	1	0	0	0	9730	14	1	5	757	5	MPDU1	17	7490856	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10		7490856	73704354	80	23428										
PER1	5187	hgsc.bcm.edu	37	chr17	8049752	8049752	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cgtcgtcagaggctgaggagGtggtataggaggaggaggag	21	4	1	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr17:8049752G>A	ENST00000317276.4	-	16	2213	c.1976C>T	c.(1975-1977)aCc>aTc	p.T659I	PER1_ENST00000354903.5_Missense_Mutation_p.T643I|PER1_ENST00000578089.1_5'UTR|PER1_ENST00000581082.1_Missense_Mutation_p.T639I	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	659	Required for phosphorylation by CSNK1E. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GGCTGAGGAGGTGGTATAGGA	0.592			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.T659I		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.C1976T						.						81	86	84					17																	8049752		2203	4300	6503	SO:0001583	missense	5187	exon16			GAGGAGGTGGTAT	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"period (Drosophila) homolog 1", "period homolog 1 (Drosophila)"	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.1976C>T	17.37:g.8049752G>A	ENSP00000314420:p.Thr659Ile	48.0	0.0		26.0	14.0	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	G	11.88	1.769948	0.31320	.	.	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.39787	2.45;1.06	5.28	4.3	0.51218	.	0.397228	0.26349	N	0.024881	T	0.31104	0.0786	L	0.34521	1.04	0.28987	N	0.888274	B;B	0.33583	0.418;0.181	B;B	0.26969	0.075;0.046	T	0.31586	-0.9938	10	0.72032	D	0.01	-1.5602	13.2862	0.60245	0.0:0.0:0.8401:0.1599	.	643;659	B4DI49;O15534	.;PER1_HUMAN	I	659;643	ENSP00000314420:T659I;ENSP00000346979:T643I	ENSP00000314420:T659I	T	-	2	0	PER1	7990477	0.883000	0.30277	0.275000	0.24674	0.334000	0.28698	2.525000	0.45598	1.350000	0.45770	0.563000	0.77884	ACC	.	.		0.592	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			A	8049752	G	A	8049752	3	1	152	1	0	0	0	0	1	0	0	0	11738	1261	44	3	1928	3	PER1	17	8049752	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	558896	8049752	73145458	81	23429										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11797765	11797765	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tctccagtgcagacgggcacCgccagccccgtggagttcct	12	16	1	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr17:11797765C>A	ENST00000262442.4	+	59	11426	c.11358C>A	c.(11356-11358)acC>acA	p.T3786T	DNAH9_ENST00000454412.2_Silent_p.T3786T|DNAH9_ENST00000608377.1_Silent_p.T98T|DNAH9_ENST00000396001.2_3'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3786					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGACGGGCACCGCCAGCCCCG	0.517																																					p.T3786T		Atlas-SNP	.											DNAH9,NS,carcinoma,0,1	DNAH9	695	1	0			c.C11358A						.						87	87	87					17																	11797765		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon59			GGGCACCGCCAGC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.11358C>A	17.37:g.11797765C>A		47.0	0.0		15.0	11.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			.	.		0.517	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11797765	C	A	11797765	2	1	152	1	0	0	0	0	0	0	0	1	4610	639	23	1		1	DNAH9	17	11797765	Silent	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	3748013	11797765	69397445	82	23430										
SARM1	113235	hgsc.bcm.edu	37	chr17	26723213	26723213	+	3'UTR	SNP	A	A	G													0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aggaggccaccattgagaagAtcatccgcttcctgcagggc							TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr17:26723213A>G	ENST00000440501.1	-	0	4934				SARM1_ENST00000457710.3_Missense_Mutation_p.I661V|SLC46A1_ENST00000584729.1_5'UTR|SARM1_ENST00000379061.4_3'UTR|SLC46A1_ENST00000321666.5_3'UTR	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1						cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	CATTGAGAAGATCATCCGCTT	0.602																																					p.I694V		Atlas-SNP	.											SARM1,colon,carcinoma,-1,1	SARM1	40	1	0			c.A2080G						.						85	75	78					17																	26723213		2203	4300	6503	SO:0001624	3_prime_UTR_variant	23098	exon10			GAGAAGATCATCC	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"Solute carriers"	30521	protein-coding gene	gene with protein product	"heme carrier protein 1", "proton-coupled folate transporter"	611672	"solute carrier family 46, member 1"			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.*3459T>C	17.37:g.26723213A>G		48.0	0.0		69.0	35.0	NM_015077	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Missense_Mutation	SNP	ENST00000440501.1	37		.	.	.	.	.	.	.	.	.	.	A	13.60	2.286217	0.40394	.	.	ENSG00000004139	ENST00000457710;ENST00000003834	.	.	.	4.84	4.84	0.62591	Toll/interleukin-1 receptor homology (TIR) domain (1);	0.000000	0.85682	D	0.000000	T	0.43077	0.1231	.	.	.	0.80722	D	1	B	0.28082	0.2	B	0.28385	0.089	T	0.30001	-0.9993	8	0.19590	T	0.45	-20.2746	11.1654	0.48539	0.846:0.154:0.0:0.0	.	695	Q6SZW1	SARM1_HUMAN	V	693;661	.	ENSP00000003834:I661V	I	+	1	0	SARM1	23747340	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.155000	0.71833	1.803000	0.52742	0.459000	0.35465	ATC	.	.		0.602	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		G	26723213	A	G	26723213	1	3	152	0	1	0	0	0	0	0	0	0	13857	333	12	2		2	SARM1	17	26723213	3'UTR	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	14925448	26723213	54471997	83	23431	103	2								
SARM1	113235	hgsc.bcm.edu	37	chr17	26723216	26723216	+	3'UTR	SNP	A	A	G													0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aggccaccattgagaagatcAtccgcttcctgcagggccgc							TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr17:26723216A>G	ENST00000440501.1	-	0	4931				SARM1_ENST00000457710.3_Missense_Mutation_p.I662V|SLC46A1_ENST00000584729.1_5'UTR|SARM1_ENST00000379061.4_3'UTR|SLC46A1_ENST00000321666.5_3'UTR	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1						cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	TGAGAAGATCATCCGCTTCCT	0.607																																					p.I695V		Atlas-SNP	.											.	SARM1	40	.	0			c.A2083G						.						85	76	79					17																	26723216		2203	4300	6503	SO:0001624	3_prime_UTR_variant	23098	exon10			AAGATCATCCGCT	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"Solute carriers"	30521	protein-coding gene	gene with protein product	"heme carrier protein 1", "proton-coupled folate transporter"	611672	"solute carrier family 46, member 1"			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.*3456T>C	17.37:g.26723216A>G		45.0	0.0		63.0	32.0	NM_015077	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Missense_Mutation	SNP	ENST00000440501.1	37		.	.	.	.	.	.	.	.	.	.	A	9.897	1.205791	0.22205	.	.	ENSG00000004139	ENST00000457710;ENST00000003834	.	.	.	4.84	4.84	0.62591	Toll/interleukin-1 receptor homology (TIR) domain (1);	0.068407	0.64402	D	0.000012	T	0.35828	0.0945	.	.	.	0.80722	D	1	B	0.19073	0.033	B	0.19666	0.026	T	0.25187	-1.0139	8	0.05436	T	0.98	-20.6578	14.4401	0.67309	1.0:0.0:0.0:0.0	.	696	Q6SZW1	SARM1_HUMAN	V	694;662	.	ENSP00000003834:I662V	I	+	1	0	SARM1	23747343	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.215000	0.42862	1.803000	0.52742	0.459000	0.35465	ATC	.	.		0.607	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		G	26723216	A	G	26723216	1	3	152	0	1	0	0	0	0	0	0	0	13857	217	8	2		2	SARM1	17	26723216	3'UTR	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	3	26723216	54471994	84	23432	103	2								
KRT20	54474	hgsc.bcm.edu	37	chr17	39036387	39036387	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ttctttggcctcttgaaggtTcttctgggccatgacttcat	9	10	5	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr17:39036387T>A	ENST00000167588.3	-	4	798	c.757A>T	c.(757-759)Aac>Tac	p.N253Y		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	253	Coil 2.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				TCTTGAAGGTTCTTCTGGGCC	0.468																																					p.N253Y		Atlas-SNP	.											.	KRT20	38	.	0			c.A757T						.						218	189	199					17																	39036387		2203	4300	6503	SO:0001583	missense	54474	exon4			GAAGGTTCTTCTG	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"-", "Intermediate filaments type I, keratins (acidic)"	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.757A>T	17.37:g.39036387T>A	ENSP00000167588:p.Asn253Tyr	69.0	0.0		53.0	33.0	NM_019010	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	37	CCDS11379.1	.	.	.	.	.	.	.	.	.	.	T	17.78	3.472801	0.63737	.	.	ENSG00000171431	ENST00000167588	D	0.89681	-2.55	5.29	1.55	0.23275	Filament (1);	0.178499	0.38720	N	0.001582	D	0.91399	0.7286	M	0.89030	3	0.42093	D	0.991303	P	0.51537	0.946	P	0.49528	0.614	D	0.90731	0.4642	10	0.72032	D	0.01	.	10.4525	0.44531	0.3921:0.0:0.0:0.6079	.	253	P35900	K1C20_HUMAN	Y	253	ENSP00000167588:N253Y	ENSP00000167588:N253Y	N	-	1	0	KRT20	36289913	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	2.406000	0.44557	0.286000	0.22352	-0.669000	0.03829	AAC	.	.		0.468	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2			A	39036387	T	A	39036387	3	1	152	1	0	0	0	0	1	0	0	0	8467	1783	62	4	537	4	KRT20	17	39036387	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	12313171	39036387	42158823	85	23433										
CDC27	996	hgsc.bcm.edu	37	chr17	45234727	45234727	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	taaagatgtgaatttaaatgTttggtcaggatctggctttt	10	3	2	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr17:45234727T>A	ENST00000066544.3	-	6	592	c.499A>T	c.(499-501)Aca>Tca	p.T167S	CDC27_ENST00000446365.2_Missense_Mutation_p.T106S|CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000531206.1_Missense_Mutation_p.T167S|CDC27_ENST00000527547.1_Missense_Mutation_p.T167S	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	167					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						AATTTAAATGTTTGGTCAGGA	0.368																																					p.T167S		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,+2,10	CDC27	337	10	0			c.A499T						.						73	73	73					17																	45234727		2203	4300	6503	SO:0001583	missense	996	exon6			TAAATGTTTGGTC	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.499A>T	17.37:g.45234727T>A	ENSP00000066544:p.Thr167Ser	126.0	2.0		95.0	4.0	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.623232	0.46840	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.67171	-0.25;-0.25;0.04;-0.25;0.89	5.39	5.39	0.77823	.	0.119985	0.64402	D	0.000020	T	0.47192	0.1432	N	0.08118	0	0.39122	D	0.961682	P;P;P;B	0.38677	0.475;0.528;0.642;0.211	B;B;B;B	0.36092	0.049;0.217;0.204;0.067	T	0.59762	-0.7393	10	0.72032	D	0.01	-19.1215	13.3763	0.60741	0.0:0.0:0.0:1.0	.	106;167;167;167	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	S	167;167;106;167;167	ENSP00000066544:T167S;ENSP00000434614:T167S;ENSP00000392802:T106S;ENSP00000437339:T167S;ENSP00000432105:T167S	ENSP00000066544:T167S	T	-	1	0	CDC27	42589726	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.374000	0.66167	2.053000	0.61076	0.528000	0.53228	ACA	.	.		0.368	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			A	45234727	T	A	45234727	3	1	152	1	0	0	0	0	1	0	0	0	3068	1725	60	4	2049	4	CDC27	17	45234727	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	6198340	45234727	35960483	86	23434										
NAT9	26151	hgsc.bcm.edu	37	chr17	72767893	72767893	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tctgccgacccatctctgtaAggcttctcttccacgtggct	8	15	3	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr17:72767893A>C	ENST00000357814.3	-	7	667	c.594T>G	c.(592-594)ccT>ccG	p.P198P	NAT9_ENST00000580216.1_5'Flank|NAT9_ENST00000578822.1_Silent_p.P203P|NAT9_ENST00000582870.1_Silent_p.P202P|NAT9_ENST00000580301.1_Silent_p.P197P|NAT9_ENST00000581136.1_Silent_p.P193P|NAT9_ENST00000580632.1_Silent_p.P198P|NAT9_ENST00000583757.1_3'UTR	NM_015654.3	NP_056469.2	Q9BTE0	NAT9_HUMAN	N-acetyltransferase 9 (GCN5-related, putative)	198						protein complex (GO:0043234)	N-acetyltransferase activity (GO:0008080)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)	8						CATCTCTGTAAGGCTTCTCTT	0.577																																					p.P198P		Atlas-SNP	.											.	NAT9	16	.	0			c.T594G						.						55	51	52					17																	72767893		2203	4300	6503	SO:0001819	synonymous_variant	26151	exon7			TCTGTAAGGCTTC	AK123115	CCDS11706.1	17q25.2	2011-11-25	2008-09-24		ENSG00000109065	ENSG00000109065			23133	protein-coding gene	gene with protein product			"N-acetyltransferase 9"			14608357	Standard	NM_015654		Approved	DKFZP564C103	uc002jlq.3	Q9BTE0		ENST00000357814.3:c.594T>G	17.37:g.72767893A>C		58.0	0.0		52.0	16.0	NM_015654	B2R7F0|Q9BTD0|Q9Y3T3	Silent	SNP	ENST00000357814.3	37	CCDS11706.1																																																																																			.	.		0.577	NAT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443700.1	NM_015654		C	72767893	A	C	72767893	2	2	152	1	0	0	0	0	0	0	0	1	10191	59	3	5		5	NAT9	17	72767893	Silent	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	27533166	72767893	8427317	87	23435										
NPLOC4	55666	hgsc.bcm.edu	37	chr17	79536080	79536080	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	atcccggttttcaataggaaAtggattttgcgaaatagaaa	9	5	1	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr17:79536080A>C	ENST00000331134.6	-	14	1626	c.1411T>G	c.(1411-1413)Ttt>Gtt	p.F471V	NPLOC4_ENST00000374747.5_Missense_Mutation_p.F471V|NPLOC4_ENST00000573876.1_5'Flank|NPLOC4_ENST00000539314.1_Missense_Mutation_p.F310V|NPLOC4_ENST00000572760.1_5'Flank	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	471					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			TCAATAGGAAATGGATTTTGC	0.363																																					p.F471V		Atlas-SNP	.											.	NPLOC4	27	.	0			c.T1411G						.						99	98	99					17																	79536080		1863	4106	5969	SO:0001583	missense	55666	exon14			TAGGAAATGGATT	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.1411T>G	17.37:g.79536080A>C	ENSP00000331487:p.Phe471Val	129.0	0.0		121.0	61.0	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Missense_Mutation	SNP	ENST00000331134.6	37	CCDS45812.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.941528	0.73557	.	.	ENSG00000182446	ENST00000331134;ENST00000374747;ENST00000539314	.	.	.	5.63	5.63	0.86233	Nuclear pore localisation protein NPL4 (1);	0.092279	0.85682	D	0.000000	D	0.86830	0.6027	H	0.95328	3.655	0.80722	D	1	D;D;D	0.71674	0.996;0.997;0.998	D;D;D	0.77557	0.99;0.928;0.957	D	0.90682	0.4606	9	0.87932	D	0	-18.1206	14.8257	0.70110	1.0:0.0:0.0:0.0	.	310;471;471	B4DG89;Q8TAT6-2;Q8TAT6	.;.;NPL4_HUMAN	V	471;470;310	.	ENSP00000331487:F471V	F	-	1	0	NPLOC4	77146517	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.744000	0.91596	2.152000	0.67230	0.460000	0.39030	TTT	.	.		0.363	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1			C	79536080	A	C	79536080	3	2	152	1	0	0	0	0	1	0	0	0	10595	101	4	5	431	5	NPLOC4	17	79536080	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	6768187	79536080	1659130	88	23436										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5396258	5396258	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gaactactggcacttccttcGtggaaatttctagctttact	7	10	1	0	rs79592897	byFrequency	TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr18:5396258G>C	ENST00000341928.2	-	19	3255	c.2915C>G	c.(2914-2916)aCg>aGg	p.T972R	EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000542146.1_Missense_Mutation_p.T277R|EPB41L3_ENST00000400111.3_Missense_Mutation_p.T750R|EPB41L3_ENST00000544123.1_Missense_Mutation_p.T803R|EPB41L3_ENST00000342933.3_Missense_Mutation_p.T972R|EPB41L3_ENST00000427684.2_Missense_Mutation_p.T269R|EPB41L3_ENST00000540638.2_Missense_Mutation_p.T750R	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	972	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						CACTTCCTTCGTGGAAATTTC	0.473																																					p.T972R		Atlas-SNP	.											.	EPB41L3	222	.	0			c.C2915G						.						239	219	226					18																	5396258		2203	4300	6503	SO:0001583	missense	23136	exon19			TCCTTCGTGGAAA	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2915C>G	18.37:g.5396258G>C	ENSP00000343158:p.Thr972Arg	104.0	0.0		42.0	16.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.326926	0.81690	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.84	5.84	0.93424	Band 4.1, C-terminal (1);	0.196730	0.53938	D	0.000051	D	0.88496	0.6452	M	0.84219	2.685	0.53005	D	0.999965	D;D;D;P;P;P;D;P	0.89917	1.0;1.0;1.0;0.905;0.81;0.932;0.999;0.618	D;D;D;P;P;P;D;P	0.97110	0.998;1.0;0.994;0.688;0.474;0.821;0.988;0.657	D	0.89500	0.3763	10	0.87932	D	0	.	14.3232	0.66502	0.0705:0.0:0.9295:0.0	.	803;269;277;364;641;750;972;207	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	R	972;641;803;641;269;277;972;750	ENSP00000343158:T972R;ENSP00000441174:T803R;ENSP00000392195:T269R;ENSP00000442233:T277R;ENSP00000341138:T972R;ENSP00000382981:T750R	ENSP00000343158:T972R	T	-	2	0	EPB41L3	5386258	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	6.654000	0.74387	2.764000	0.94973	0.650000	0.86243	ACG	.	G|0.998;A|0.002		0.473	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		C	5396258	G	C	5396258	3	2	152	1	0	0	0	0	1	0	0	0	5156	1145	40	4	364	4	EPB41L3	18	5396258	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10		5396258	72680990	89	23437										
CBLN2	147381	hgsc.bcm.edu	37	chr18	70205486	70205486	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aggttgcctctctcaagtttGagatgcactttgtcttccct	8	11	3	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr18:70205486G>C	ENST00000269503.4	-	5	1373	c.600C>G	c.(598-600)ctC>ctG	p.L200L	CBLN2_ENST00000585159.1_Silent_p.L200L|CBLN2_ENST00000584764.1_Silent_p.L84L|CBLN2_ENST00000581073.1_Silent_p.L86L|CBLN2_ENST00000583651.1_5'UTR	NM_182511.3	NP_872317.1	Q8IUK8	CBLN2_HUMAN	cerebellin 2 precursor	200	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				positive regulation of synapse assembly (GO:0051965)	extracellular space (GO:0005615)				endometrium(2)|lung(15)	17		Esophageal squamous(42;0.131)				TCTCAAGTTTGAGATGCACTT	0.532																																					p.L200L		Atlas-SNP	.											CBLN2,NS,carcinoma,-1,1	CBLN2	41	1	0			c.C600G						.						117	111	113					18																	70205486		2203	4300	6503	SO:0001819	synonymous_variant	147381	exon5			AAGTTTGAGATGC	BC035789	CCDS11999.1	18q22.3	2007-11-19			ENSG00000141668	ENSG00000141668			1544	protein-coding gene	gene with protein product		600433				7877445	Standard	NM_182511		Approved		uc002lkv.2	Q8IUK8	OTTHUMG00000132825	ENST00000269503.4:c.600C>G	18.37:g.70205486G>C		108.0	0.0		77.0	34.0	NM_182511	Q53Z56	Silent	SNP	ENST00000269503.4	37	CCDS11999.1																																																																																			.	.		0.532	CBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256288.1	NM_182511		C	70205486	G	C	70205486	2	2	152	1	0	0	0	0	0	0	0	1	2707	1277	45	4		4	CBLN2	18	70205486	Silent	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	64809228	70205486	7871762	90	23438										
CIRBP	1153	hgsc.bcm.edu	37	chr19	1271585	1271585	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gctatggggggaaccggttcGagtccaggagtgggggctac	19	8	0	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:1271585G>A	ENST00000588030.1	+	5	645	c.385G>A	c.(385-387)Gag>Aag	p.E129K	CIRBP-AS1_ENST00000585832.1_RNA|CIRBP_ENST00000591935.1_Missense_Mutation_p.E129K|CIRBP_ENST00000589686.1_Missense_Mutation_p.E129K|CIRBP_ENST00000589710.1_Missense_Mutation_p.E129K|CIRBP_ENST00000587323.1_Missense_Mutation_p.E129K|CIRBP_ENST00000444172.2_Missense_Mutation_p.E76K|CIRBP_ENST00000588230.1_Missense_Mutation_p.E129K|CIRBP-AS1_ENST00000600215.1_RNA|CIRBP_ENST00000585630.1_Missense_Mutation_p.E129K|CIRBP_ENST00000413636.2_Missense_Mutation_p.E95K|CIRBP_ENST00000586773.1_Missense_Mutation_p.E129K|CIRBP_ENST00000587896.1_Missense_Mutation_p.E129K|CIRBP_ENST00000589235.1_Missense_Mutation_p.E129K|CIRBP_ENST00000588090.1_Missense_Mutation_p.E129K|CIRBP_ENST00000320936.5_Missense_Mutation_p.E129K|CIRBP_ENST00000589660.1_Missense_Mutation_p.E129K|CIRBP_ENST00000586472.1_Missense_Mutation_p.E129K			Q14011	CIRBP_HUMAN	cold inducible RNA binding protein	129	Gly-rich.				mRNA stabilization (GO:0048255)|positive regulation of translation (GO:0045727)|response to cold (GO:0009409)|response to UV (GO:0009411)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|small ribosomal subunit rRNA binding (GO:0070181)|translation repressor activity (GO:0030371)			endometrium(1)|large_intestine(1)|lung(3)	5		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAACCGGTTCGAGTCCAGGAG	0.627																																					p.E129K		Atlas-SNP	.											.	CIRBP	19	.	0			c.G385A						.						22	27	25					19																	1271585		2190	4277	6467	SO:0001583	missense	1153	exon5			CGGTTCGAGTCCA	D78134	CCDS12059.1, CCDS74244.1, CCDS74245.1	19p13.3	2013-02-12	2001-11-28		ENSG00000099622	ENSG00000099622		"RNA binding motif (RRM) containing"	1982	protein-coding gene	gene with protein product	"Cold-inducible RNA-binding protein", "glycine-rich RNA binding protein"	602649	"cold inducible RNA-binding protein"			9434172, 9151692	Standard	NM_001280		Approved	CIRP	uc002lrr.4	Q14011		ENST00000588030.1:c.385G>A	19.37:g.1271585G>A	ENSP00000468788:p.Glu129Lys	61.0	0.0		58.0	23.0	NM_001280	B3KT17|B4E2X2	Missense_Mutation	SNP	ENST00000588030.1	37	CCDS12059.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.525886	0.64860	.	.	ENSG00000099622	ENST00000320936;ENST00000413636;ENST00000444172	T;T	0.73789	0.21;-0.78	4.23	3.18	0.36537	.	0.520575	0.20137	N	0.098463	T	0.51736	0.1692	L	0.29908	0.895	0.37410	D	0.913192	P;B;B;B	0.38504	0.634;0.034;0.377;0.088	B;B;B;B	0.23150	0.044;0.002;0.044;0.006	T	0.51647	-0.8679	10	0.13470	T	0.59	-8.4619	9.2426	0.37506	0.1044:0.0:0.8956:0.0	.	95;129;129;129	B4E2X2;Q53XX5;D6W5Y5;Q14011	.;.;.;CIRBP_HUMAN	K	129;95;76	ENSP00000322887:E129K;ENSP00000412831:E95K	ENSP00000322887:E129K	E	+	1	0	CIRBP	1222585	1.000000	0.71417	0.973000	0.42090	0.936000	0.57629	4.191000	0.58372	0.767000	0.33267	0.462000	0.41574	GAG	.	.		0.627	CIRBP-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449969.1	NM_001280		A	1271585	G	A	1271585	3	1	152	1	0	0	0	0	1	0	0	0	3435	1059	37	1	399	1	CIRBP	19	1271585	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10		1271585	57857398	91	23439										
REEP6	92840	hgsc.bcm.edu	37	chr19	1495318	1495341	+	In_Frame_Del	DEL	TCTGCTGTTCGGCTACGGAGCGTC	TCTGCTGTTCGGCTACGGAGCGTC	-													0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gtcactctgctaagcctgtaTctgctgttcggctacggagc					rs200733401|rs371810396|rs537764971|rs79574672	byFrequency	TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	TCTGCTGTTCGGCTACGGAGCGTC	TCTGCTGTTCGGCTACGGAGCGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:1495318_1495341delTCTGCTGTTCGGCTACGGAGCGTC	ENST00000233596.3	+	2	245_268	c.141_164delTCTGCTGTTCGGCTACGGAGCGTC	c.(139-165)tatctgctgttcggctacggagcgtct>tat	p.LLFGYGAS48del		NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6	48					regulation of intracellular transport (GO:0032386)	apical part of cell (GO:0045177)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.G51V(1)|p.R118R(1)		lung(1)|ovary(1)	2		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TAAGCCTGTATCTGCTGTTCGGCTACGGAGCGTCTCTGCTGTGC	0.665																																					p.47_55del		Atlas-Indel	.											.	REEP6	21	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)	c.140_163del						.																																			SO:0001651	inframe_deletion	92840	exon2			.	BC008201	CCDS12070.1	19p13.3	2012-12-20	2006-02-08	2006-02-07	ENSG00000115255	ENSG00000115255		"Receptor accessory proteins"	30078	protein-coding gene	gene with protein product	"polyposis locus protein 1-like 1", "deleted in polyposis 1-like 1"	609346	"chromosome 19 open reading frame 32"	C19orf32		16271481, 15550249	Standard	NM_138393		Approved	DP1L1, FLJ25383	uc002ltc.3	Q96HR9	OTTHUMG00000180072	ENST00000233596.3:c.141_164delTCTGCTGTTCGGCTACGGAGCGTC	19.37:g.1495318_1495341delTCTGCTGTTCGGCTACGGAGCGTC	ENSP00000233596:p.Leu48_Ser55del	45.0	0.0		28.0	12.0	NM_138393	B2RE01|D6W5Z0|Q96LM0	In_Frame_Del	DEL	ENST00000233596.3	37	CCDS12070.1																																																																																			.	.		0.665	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393		-	1495341	TCTGCTGTTCGGCTACGGAGCGTC	-	1495318	7	5	152	1	0	1	0	1	0	0	0	0	13224	1442	50	0	147	0	REEP6	19	1495318	In_Frame_Del	DEL	TCTGCTGTTCGGCTACGGAGCGTC	TCGA-DD-AACA-01A-11D-A40R-10	223733	1495318	57633665	92	23440										
TMED1	11018	hgsc.bcm.edu	37	chr19	10945612	10945612	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	agcgcagcctggacacacctTgatgtcctccattttaacat	7	13	0	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:10945612T>G	ENST00000214869.2	-	3	561	c.463A>C	c.(463-465)Aag>Cag	p.K155Q	TMED1_ENST00000591695.1_Intron|C19orf38_ENST00000592854.1_5'Flank|TMED1_ENST00000588289.1_Missense_Mutation_p.K10Q	NM_006858.2	NP_006849.1	Q13445	TMED1_HUMAN	transmembrane emp24 protein transport domain containing 1	155					cell-cell signaling (GO:0007267)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|lung(2)|ovary(3)|prostate(1)|skin(1)	10						GGACACACCTTGATGTCCTCC	0.592																																					p.K155Q		Atlas-SNP	.											.	TMED1	22	.	0			c.A463C						.						167	160	162					19																	10945612		2203	4300	6503	SO:0001583	missense	11018	exon3			ACACCTTGATGTC	U41804	CCDS12249.1	19p13.2	2008-02-05	2005-08-26			ENSG00000099203			17291	protein-coding gene	gene with protein product		605395	"transmembrane emp24 domain containing 1"			11466339, 8621446	Standard	NM_006858		Approved	ST2L, MGC1270, IL1RL1LG, Il1rl1l	uc002mpy.3	Q13445		ENST00000214869.2:c.463A>C	19.37:g.10945612T>G	ENSP00000214869:p.Lys155Gln	61.0	0.0		44.0	17.0	NM_006858		Missense_Mutation	SNP	ENST00000214869.2	37	CCDS12249.1	.	.	.	.	.	.	.	.	.	.	T	9.514	1.106519	0.20632	.	.	ENSG00000099203	ENST00000214869	T	0.15834	2.39	5.02	5.02	0.67125	GOLD (1);	0.058548	0.64402	D	0.000003	T	0.15478	0.0373	L	0.36672	1.1	0.36480	D	0.867795	B	0.18013	0.025	B	0.19666	0.026	T	0.08994	-1.0695	10	0.34782	T	0.22	-34.4991	13.7375	0.62827	0.0:0.0:0.0:1.0	.	155	Q13445	TMED1_HUMAN	Q	155	ENSP00000214869:K155Q	ENSP00000214869:K155Q	K	-	1	0	TMED1	10806612	1.000000	0.71417	1.000000	0.80357	0.566000	0.35808	2.541000	0.45735	1.895000	0.54865	0.379000	0.24179	AAG	.	.		0.592	TMED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452614.1	NM_006858		G	10945612	T	G	10945612	3	3	152	1	0	0	0	0	1	0	0	0	16017	1821	63	5	228	5	TMED1	19	10945612	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	9450294	10945612	48183371	93	23441			1	26		2	2	14	T		4.787215e-05
TMED1	11018	hgsc.bcm.edu	37	chr19	10945625	10945625	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cacaccttgatgtcctccatTttaacatccagcatctcctc	3	16	1	1			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:10945625T>G	ENST00000214869.2	-	3	548	c.450A>C	c.(448-450)aaA>aaC	p.K150N	TMED1_ENST00000591695.1_Intron|C19orf38_ENST00000592854.1_5'Flank|TMED1_ENST00000588289.1_Missense_Mutation_p.K5N	NM_006858.2	NP_006849.1	Q13445	TMED1_HUMAN	transmembrane emp24 protein transport domain containing 1	150					cell-cell signaling (GO:0007267)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|lung(2)|ovary(3)|prostate(1)|skin(1)	10						TGTCCTCCATTTTAACATCCA	0.587																																					p.K150N		Atlas-SNP	.											.	TMED1	22	.	0			c.A450C						.						174	164	168					19																	10945625		2203	4300	6503	SO:0001583	missense	11018	exon3			CTCCATTTTAACA	U41804	CCDS12249.1	19p13.2	2008-02-05	2005-08-26			ENSG00000099203			17291	protein-coding gene	gene with protein product		605395	"transmembrane emp24 domain containing 1"			11466339, 8621446	Standard	NM_006858		Approved	ST2L, MGC1270, IL1RL1LG, Il1rl1l	uc002mpy.3	Q13445		ENST00000214869.2:c.450A>C	19.37:g.10945625T>G	ENSP00000214869:p.Lys150Asn	60.0	0.0		43.0	15.0	NM_006858		Missense_Mutation	SNP	ENST00000214869.2	37	CCDS12249.1	.	.	.	.	.	.	.	.	.	.	T	16.43	3.120503	0.56613	.	.	ENSG00000099203	ENST00000214869	T	0.19806	2.12	5.02	-1.68	0.08212	GOLD (1);	0.095235	0.64402	D	0.000001	T	0.38241	0.1033	M	0.84156	2.68	0.49389	D	0.99978	P	0.49447	0.924	P	0.60068	0.868	T	0.23583	-1.0184	10	0.33940	T	0.23	-30.1085	9.8445	0.41019	0.0:0.5911:0.0:0.4089	.	150	Q13445	TMED1_HUMAN	N	150	ENSP00000214869:K150N	ENSP00000214869:K150N	K	-	3	2	TMED1	10806625	0.999000	0.42202	0.952000	0.39060	0.943000	0.58893	0.684000	0.25364	-0.224000	0.09928	0.379000	0.24179	AAA	.	.		0.587	TMED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452614.1	NM_006858		G	10945625	T	G	10945625	3	3	152	1	0	0	0	0	1	0	0	0	16017	1838	64	5	241	5	TMED1	19	10945625	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	13	10945625	48183358	94	23442			1	26		2	2	14	T		4.787215e-05
SLC5A5	6528	hgsc.bcm.edu	37	chr19	18001706	18001706	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gcctctcaggccccaccaagCgcagcaccctggccccggga	11	20	1	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:18001706C>T	ENST00000222248.3	+	14	2010	c.1663C>T	c.(1663-1665)Cgc>Tgc	p.R555C		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	555					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						CCCCACCAAGCGCAGCACCCT	0.602																																					p.R555C	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.C1663T						.						85	92	90					19																	18001706		2203	4300	6503	SO:0001583	missense	6528	exon14			ACCAAGCGCAGCA		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"Solute carriers"	11040	protein-coding gene	gene with protein product		601843	"solute carrier family 5 (sodium iodide symporter), member 5"			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.1663C>T	19.37:g.18001706C>T	ENSP00000222248:p.Arg555Cys	60.0	0.0		53.0	22.0	NM_000453	O43702|Q2M335|Q9NYB6	Missense_Mutation	SNP	ENST00000222248.3	37	CCDS12368.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150244	0.37923	.	.	ENSG00000105641	ENST00000222248	D	0.85861	-2.04	4.71	3.62	0.41486	.	0.166361	0.46758	D	0.000272	D	0.88826	0.6542	M	0.69823	2.125	0.48696	D	0.999698	D	0.89917	1.0	P	0.60286	0.872	D	0.88515	0.3092	10	0.54805	T	0.06	.	10.2325	0.43264	0.3282:0.6718:0.0:0.0	.	555	Q92911	SC5A5_HUMAN	C	555	ENSP00000222248:R555C	ENSP00000222248:R555C	R	+	1	0	SLC5A5	17862706	0.999000	0.42202	0.993000	0.49108	0.037000	0.13140	0.659000	0.24994	2.457000	0.83068	0.491000	0.48974	CGC	.	.		0.602	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			T	18001706	C	T	18001706	3	4	152	1	0	0	0	0	1	0	0	0	14683	768	27	1	1717	1	SLC5A5	19	18001706	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	7056081	18001706	41127277	95	23443										
LSR	51599	hgsc.bcm.edu	37	chr19	35758280	35758280	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cccacgagtaatggtgggagAagccgggcctacatgccccc	13	14	0	1	rs112715995		TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:35758280A>G	ENST00000361790.3	+	9	1716	c.1557A>G	c.(1555-1557)agA>agG	p.R519R	LSR_ENST00000360798.3_Silent_p.R451R|LSR_ENST00000354900.3_Silent_p.R500R|USF2_ENST00000343550.5_5'Flank|USF2_ENST00000379134.3_5'Flank|USF2_ENST00000595068.1_5'Flank|AD000684.2_ENST00000602262.1_RNA|USF2_ENST00000594064.1_5'Flank|USF2_ENST00000222305.3_5'Flank|LSR_ENST00000427250.1_Silent_p.R363R|LSR_ENST00000602122.1_Silent_p.R499R|LSR_ENST00000347609.4_Silent_p.R461R	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	519					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			ATGGTGGGAGAAGCCGGGCCT	0.716																																					p.R519R		Atlas-SNP	.											.	LSR	60	.	0			c.A1557G						.						11	16	15					19																	35758280		2117	4161	6278	SO:0001819	synonymous_variant	51599	exon9			TGGGAGAAGCCGG	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1557A>G	19.37:g.35758280A>G		94.0	0.0		83.0	9.0	NM_205834	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Silent	SNP	ENST00000361790.3	37	CCDS12450.1																																																																																			.	.		0.716	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		G	35758280	A	G	35758280	2	3	152	1	0	0	0	0	0	0	0	1	9073	243	9	2		2	LSR	19	35758280	Silent	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	17756574	35758280	23370703	96	23444										
FFAR2	2867	hgsc.bcm.edu	37	chr19	35940857	35940857	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gctggtacctgcccaaggtcGtctgcgccctcacgagtttt	11	14	2	0	rs539042139		TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:35940857G>T	ENST00000599180.2	+	2	321	c.241G>T	c.(241-243)Gtc>Ttc	p.V81F	FFAR2_ENST00000246549.2_Missense_Mutation_p.V81F|FFAR2_ENST00000601590.1_Intron			O15552	FFAR2_HUMAN	free fatty acid receptor 2	81					cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GCCCAAGGTCGTCTGCGCCCT	0.627																																					p.V81F	GBM(40;139 809 9833 23358 48736)	Atlas-SNP	.											.	FFAR2	39	.	0			c.G241T						.						58	46	50					19																	35940857		2203	4300	6503	SO:0001583	missense	2867	exon1			AAGGTCGTCTGCG	AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"GPCR / Class A : Fatty acid receptors"	4501	protein-coding gene	gene with protein product		603823	"G protein-coupled receptor 43"	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.241G>T	19.37:g.35940857G>T	ENSP00000473159:p.Val81Phe	39.0	0.0		57.0	26.0	NM_005306	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Missense_Mutation	SNP	ENST00000599180.2	37	CCDS12461.1	.	.	.	.	.	.	.	.	.	.	G	6.324	0.427788	0.11987	.	.	ENSG00000126262	ENST00000246549	T	0.36878	1.23	5.48	-5.01	0.02991	GPCR, rhodopsin-like superfamily (1);	0.513281	0.18689	N	0.133935	T	0.16938	0.0407	N	0.12637	0.245	0.09310	N	0.999998	B	0.13145	0.007	B	0.15870	0.014	T	0.19031	-1.0318	10	0.54805	T	0.06	-12.1557	10.6757	0.45785	0.2136:0.5825:0.2039:0.0	.	81	O15552	FFAR2_HUMAN	F	81	ENSP00000246549:V81F	ENSP00000246549:V81F	V	+	1	0	FFAR2	40632697	0.165000	0.22948	0.000000	0.03702	0.002000	0.02628	0.705000	0.25675	-0.427000	0.07350	-0.254000	0.11334	GTC	.	.		0.627	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306		T	35940857	G	T	35940857	3	4	152	1	0	0	0	0	1	0	0	0	5836	1145	40	1	243	1	FFAR2	19	35940857	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	182577	35940857	23188126	97	23445										
NAPA	8775	hgsc.bcm.edu	37	chr19	47995285	47995285	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gtgctaccttggcgttgagcAtgtcgatgcagaagtggcag	15	8	0	2	rs149012477	byFrequency	TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:47995285A>C	ENST00000263354.3	-	8	952	c.653T>G	c.(652-654)aTg>aGg	p.M218R	NAPA-AS1_ENST00000593284.1_RNA|NAPA_ENST00000595227.1_Missense_Mutation_p.M179R|NAPA-AS1_ENST00000594367.1_RNA	NM_003827.3	NP_003818.2	P54920	SNAA_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, alpha	218					apical protein localization (GO:0045176)|brain development (GO:0007420)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron differentiation (GO:0030182)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)	11		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000466)|all cancers(93;0.000739)|Epithelial(262;0.0168)|GBM - Glioblastoma multiforme(486;0.049)		GGCGTTGAGCATGTCGATGCA	0.622																																					p.M218R	Ovarian(185;1135 2042 27703 31345 42493)	Atlas-SNP	.											.	NAPA	34	.	0			c.T653G						.						219	171	187					19																	47995285		2203	4300	6503	SO:0001583	missense	8775	exon8			TTGAGCATGTCGA	U39412	CCDS12702.1	19q13.33	2012-08-16			ENSG00000105402	ENSG00000105402			7641	protein-coding gene	gene with protein product	"alpha SNAP"	603215				9269766	Standard	NM_003827		Approved		uc002pha.2	P54920		ENST00000263354.3:c.653T>G	19.37:g.47995285A>C	ENSP00000263354:p.Met218Arg	51.0	0.0		48.0	18.0	NM_003827	A8K879|Q96IK3|Q9BVJ3	Missense_Mutation	SNP	ENST00000263354.3	37	CCDS12702.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.611197	0.28712	.	.	ENSG00000105402	ENST00000263354	T	0.75589	-0.95	5.24	4.23	0.50019	Tetratricopeptide-like helical (1);	0.117280	0.85682	D	0.000000	T	0.69851	0.3157	M	0.71581	2.175	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.63752	-0.6566	10	0.26408	T	0.33	-12.6147	9.973	0.41765	0.9193:0.0:0.0807:0.0	.	218	P54920	SNAA_HUMAN	R	218	ENSP00000263354:M218R	ENSP00000263354:M218R	M	-	2	0	NAPA	52687097	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	1.806000	0.38892	1.030000	0.39839	0.418000	0.28097	ATG	.	A|1.000;G|0.000		0.622	NAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466048.2	NM_003827		C	47995285	A	C	47995285	3	2	152	1	0	0	0	0	1	0	0	0	10170	217	8	5	250	5	NAPA	19	47995285	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	12054428	47995285	11133698	98	23446										
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305624	48305624	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ggcctgggtttgggcctgagAttgggcctgagattgggcct	18	8	0	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:48305624A>T	ENST00000322175.3	-	2	799	c.644T>A	c.(643-645)aTc>aAc	p.I215N	TPRX1_ENST00000543508.1_Missense_Mutation_p.I205N|TPRX1_ENST00000535759.1_Missense_Mutation_p.I312N	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	215	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		tgggcctgagattgggcctga	0.667																																					p.I215N	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.T644A						.						13	10	11					19																	48305624		1860	3655	5515	SO:0001583	missense	284355	exon2			CCTGAGATTGGGC		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"Homeoboxes / PRD class"	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.644T>A	19.37:g.48305624A>T	ENSP00000323455:p.Ile215Asn	12.0	0.0		71.0	31.0	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	t	0.005	-2.226762	0.00283	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.40225	1.04;1.04;1.04	0.365	-0.73	0.11154	.	.	.	.	.	T	0.18002	0.0432	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21724	-1.0237	8	0.16896	T	0.51	.	.	.	.	.	215	Q8N7U7	TPRX1_HUMAN	N	215;312;205	ENSP00000323455:I215N;ENSP00000438832:I312N;ENSP00000438712:I205N	ENSP00000323455:I215N	I	-	2	0	TPRX1	52997436	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.499000	0.06413	-2.038000	0.00918	-2.153000	0.00332	ATC	.	.		0.667	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		T	48305624	A	T	48305624	3	4	152	1	0	0	0	0	1	0	0	0	16437	333	12	4	595	4	TPRX1	19	48305624	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	310339	48305624	10823359	99	23447			2	27	37359999	2	2	15	N	T_A	5.155453e-05
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305638	48305638	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cctgagattgggcctgagatTgggcctgggatcgggcctgg	18	9	0	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:48305638T>C	ENST00000322175.3	-	2	785	c.630A>G	c.(628-630)ccA>ccG	p.P210P	TPRX1_ENST00000543508.1_Silent_p.P200P|TPRX1_ENST00000535759.1_Silent_p.P307P	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	210	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P210P(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		ggcctgagattgggcctggga	0.672																																					p.P210P	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,NS,carcinoma,0,1	TPRX1	46	1	1	Substitution - coding silent(1)	endometrium(1)	c.A630G						.						13	10	11					19																	48305638		1836	3551	5387	SO:0001819	synonymous_variant	284355	exon2			TGAGATTGGGCCT		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"Homeoboxes / PRD class"	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.630A>G	19.37:g.48305638T>C		61.0	0.0		79.0	23.0	NM_198479	A5D8Y3|B2RPL5	Silent	SNP	ENST00000322175.3	37	CCDS33066.1																																																																																			.	.		0.672	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		C	48305638	T	C	48305638	2	2	152	1	0	0	0	0	0	0	0	1	16437	1799	63	2		2	TPRX1	19	48305638	Silent	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	14	48305638	10823345	100	23448			2	27	37359999	2	2	15	N	T_A	5.155453e-05
IZUMO1	284359	hgsc.bcm.edu	37	chr19	49244664	49244664	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aggctggaggcttatggacgActccgtggtcgcctcccccg	14	14	0	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:49244664A>G	ENST00000332955.2	-	9	1373	c.826T>C	c.(826-828)Tcg>Ccg	p.S276P	RASIP1_ENST00000594232.1_5'Flank|RASIP1_ENST00000222145.4_5'Flank	NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	276					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		CTTATGGACGACTCCGTGGTC	0.552																																					p.S276P		Atlas-SNP	.											.	IZUMO1	30	.	0			c.T826C						.						64	69	67					19																	49244664		2203	4300	6503	SO:0001583	missense	284359	exon9			TGGACGACTCCGT	BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"-"	28539	protein-coding gene	gene with protein product	"oocyte binding/fusion factor"	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.826T>C	19.37:g.49244664A>G	ENSP00000327786:p.Ser276Pro	53.0	0.0		35.0	19.0	NM_182575	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	37	CCDS12732.1	.	.	.	.	.	.	.	.	.	.	A	13.49	2.253735	0.39797	.	.	ENSG00000182264	ENST00000332955	T	0.23754	1.89	4.96	-9.93	0.00452	.	8.737100	0.00166	N	0.000001	T	0.12817	0.0311	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.10660	-1.0620	10	0.30078	T	0.28	0.7108	3.4906	0.07636	0.1483:0.1196:0.4509:0.2813	.	276	Q8IYV9	IZUM1_HUMAN	P	276	ENSP00000327786:S276P	ENSP00000327786:S276P	S	-	1	0	IZUMO1	53936476	0.000000	0.05858	0.000000	0.03702	0.549000	0.35272	-2.457000	0.01001	-2.774000	0.00363	0.482000	0.46254	TCG	.	.		0.552	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575		G	49244664	A	G	49244664	3	3	152	1	0	0	0	0	1	0	0	0	7942	275	10	2	234	2	IZUMO1	19	49244664	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	939026	49244664	9884319	101	23449										
NLRP7	199713	hgsc.bcm.edu	37	chr19	55452329	55452329	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	taactccgagtcttcttctgCatctcccagctcaggattat	6	13	5	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr19:55452329C>T	ENST00000590030.1	-	2	362	c.322G>A	c.(322-324)Gca>Aca	p.A108T	NLRP7_ENST00000446217.1_Missense_Mutation_p.A136T|NLRP7_ENST00000592784.1_Missense_Mutation_p.A108T|NLRP7_ENST00000448121.2_Missense_Mutation_p.A108T|NLRP7_ENST00000588756.1_Missense_Mutation_p.A108T|NLRP7_ENST00000340844.2_Missense_Mutation_p.A108T|NLRP7_ENST00000328092.5_Missense_Mutation_p.A108T			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	108							ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TCTTCTTCTGCATCTCCCAGC	0.443																																					p.A108T		Atlas-SNP	.											.	NLRP7	411	.	0			c.G322A						.						252	201	218					19																	55452329		2203	4300	6503	SO:0001583	missense	199713	exon3			CTTCTGCATCTCC	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.322G>A	19.37:g.55452329C>T	ENSP00000465520:p.Ala108Thr	55.0	0.0		37.0	10.0	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	C	0.075	-1.194146	0.01594	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.73897	-0.73;-0.73;-0.79;-0.76	1.8	-3.6	0.04570	.	.	.	.	.	T	0.40670	0.1126	N	0.08118	0	0.09310	N	1	B;B;B;B	0.33477	0.005;0.013;0.167;0.413	B;B;B;B	0.29077	0.002;0.002;0.028;0.098	T	0.37244	-0.9714	9	0.13853	T	0.58	.	0.2545	0.00210	0.2056:0.289:0.2032:0.3021	.	136;108;108;108	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	T	108;108;108;136	ENSP00000329568:A108T;ENSP00000409137:A108T;ENSP00000339491:A108T;ENSP00000414273:A136T	ENSP00000329568:A108T	A	-	1	0	NLRP7	60144141	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.461000	0.06712	-0.971000	0.03564	-1.401000	0.01141	GCA	.	.		0.443	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		T	55452329	C	T	55452329	3	4	152	1	0	0	0	0	1	0	0	0	10491	710	25	3	2827	3	NLRP7	19	55452329	Missense_Mutation	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	6207665	55452329	3676654	102	23450										
DEFB129	140881	hgsc.bcm.edu	37	chr20	210326	210326	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ccaaagaaagcagagattctGccactgcctcgccaccacca	7	16	1	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr20:210326G>A	ENST00000246105.4	+	2	497	c.466G>A	c.(466-468)Gcc>Acc	p.A156T		NM_080831.3	NP_543021.1	Q9H1M3	DB129_HUMAN	defensin, beta 129	156					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|stomach(1)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			CAGAGATTCTGCCACTGCCTC	0.512																																					p.A156T		Atlas-SNP	.											DEFB129,NS,carcinoma,0,2	DEFB129	24	2	0			c.G466A						.						125	112	116					20																	210326		2203	4300	6503	SO:0001583	missense	140881	exon2			GATTCTGCCACTG	AY358186	CCDS12992.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125903	ENSG00000125903		"Defensins, beta"	16218	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 87"	C20orf87		11854508	Standard	NM_080831		Approved	bA530N10.3, DEFB-29	uc002wda.3	Q9H1M3	OTTHUMG00000031618	ENST00000246105.4:c.466G>A	20.37:g.210326G>A	ENSP00000246105:p.Ala156Thr	62.0	0.0		28.0	11.0	NM_080831	Q8NES7	Missense_Mutation	SNP	ENST00000246105.4	37	CCDS12992.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.666106	0.47677	.	.	ENSG00000125903	ENST00000246105	T	0.46063	0.88	4.26	2.27	0.28462	.	0.891435	0.09560	N	0.785724	T	0.36138	0.0956	L	0.32530	0.975	0.09310	N	1	D	0.58620	0.983	P	0.47864	0.559	T	0.15809	-1.0424	10	0.51188	T	0.08	-1.1742	6.0935	0.20007	0.1032:0.1901:0.7067:0.0	.	156	Q9H1M3	DB129_HUMAN	T	156	ENSP00000246105:A156T	ENSP00000246105:A156T	A	+	1	0	DEFB129	158326	0.002000	0.14202	0.001000	0.08648	0.040000	0.13550	0.768000	0.26590	0.732000	0.32470	0.462000	0.41574	GCC	.	.		0.512	DEFB129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077430.2	NM_080831		A	210326	G	A	210326	3	1	152	1	0	0	0	0	1	0	0	0	4417	1319	46	3	472	3	DEFB129	20	210326	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10		210326	62815194	103	23451										
SLC32A1	140679	hgsc.bcm.edu	37	chr20	37357190	37357190	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	aagtcttcttcgacgtcgccAtcttcgtcatcggcggcatc	9	14	4	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr20:37357190A>G	ENST00000217420.1	+	2	1749	c.1486A>G	c.(1486-1488)Atc>Gtc	p.I496V		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	496					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	CGACGTCGCCATCTTCGTCAT	0.642																																					p.I496V		Atlas-SNP	.											.	SLC32A1	81	.	0			c.A1486G						.						23	23	23					20																	37357190		2202	4300	6502	SO:0001583	missense	140679	exon2			GTCGCCATCTTCG	AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"Solute carriers"	11018	protein-coding gene	gene with protein product			"vesicular inhibitory amino acid transporter"	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.1486A>G	20.37:g.37357190A>G	ENSP00000217420:p.Ile496Val	123.0	0.0		104.0	42.0	NM_080552	Q8N489	Missense_Mutation	SNP	ENST00000217420.1	37	CCDS13307.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.091026	0.55968	.	.	ENSG00000101438	ENST00000217420	T	0.02236	4.38	4.95	4.95	0.65309	.	0.101862	0.64402	D	0.000004	T	0.03136	0.0092	N	0.21508	0.67	0.80722	D	1	P	0.39903	0.694	P	0.45610	0.487	T	0.64601	-0.6369	10	0.37606	T	0.19	-21.4989	12.8433	0.57815	1.0:0.0:0.0:0.0	.	496	Q9H598	VIAAT_HUMAN	V	496	ENSP00000217420:I496V	ENSP00000217420:I496V	I	+	1	0	SLC32A1	36790604	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.218000	0.95166	1.987000	0.57996	0.533000	0.62120	ATC	.	.		0.642	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		G	37357190	A	G	37357190	3	3	152	1	0	0	0	0	1	0	0	0	14580	217	8	2	1492	2	SLC32A1	20	37357190	Missense_Mutation	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	37146864	37357190	25668330	104	23452										
CD40	958	hgsc.bcm.edu	37	chr20	44756975	44756975	+	Frame_Shift_Del	DEL	T	T	-													0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	ttttttttttttagaaaaggTggccaagaagccaaccaata							TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr20:44756975delT	ENST00000372285.3	+	8	725	c.653delT	c.(652-654)gtgfs	p.V218fs	CD40_ENST00000489304.1_3'UTR|CD40_ENST00000372276.3_Frame_Shift_Del_p.G198fs	NM_001250.4	NP_001241.1	P25942	TNR5_HUMAN	CD40 molecule, TNF receptor superfamily member 5	218					B cell proliferation (GO:0042100)|cellular calcium ion homeostasis (GO:0006874)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|protein complex assembly (GO:0006461)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	CD40 receptor complex (GO:0035631)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|enzyme binding (GO:0019899)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		Myeloproliferative disorder(115;0.0122)				ttAGAAAAGGTGGCCAAGAAG	0.498									Immune Deficiency with Hyper-IgM		OREG0025991	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V218fs		Atlas-Indel	.											CD40,NS,carcinoma,0,1	CD40	33	1	0			c.652delG						.																																			SO:0001589	frameshift_variant	958	exon8	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	.	X60592	CCDS13393.1, CCDS13394.1	20q12-q13.2	2014-09-17	2006-03-28	2005-01-14	ENSG00000101017	ENSG00000101017		"Tumor necrosis factor receptor superfamily", "CD molecules"	11919	protein-coding gene	gene with protein product		109535	"tumor necrosis factor receptor superfamily, member 5"	TNFRSF5		7687385, 2998589	Standard	XM_005260617		Approved	p50, Bp50	uc002xrg.1	P25942	OTTHUMG00000033053	ENST00000372285.3:c.653delT	20.37:g.44756975delT	ENSP00000361359:p.Val218fs	95.0	0.0	926	87.0	10.0	NM_001250	E1P5S9|Q53GN5|Q5JY15|Q5U007|Q7M4Q8|Q86YK5|Q9BYU0	Frame_Shift_Del	DEL	ENST00000372285.3	37	CCDS13393.1																																																																																			.	.		0.498	CD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080376.1	NM_001250		-	44756975	T	-	44756975	7	5	152	1	0	1	0	1	0	0	0	0	3017	1696	59	0	683	0	CD40	20	44756975	Frame_Shift_Del	DEL	T	TCGA-DD-AACA-01A-11D-A40R-10	7399785	44756975	18268545	105	23453										
EWSR1	2130	hgsc.bcm.edu	37	chr22	29695754	29695754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tggctttggtggaggaagacGaggtggccctggggggcccc	20	9	0	1	rs201365388		TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr22:29695754G>A	ENST00000397938.2	+	16	2163	c.1844G>A	c.(1843-1845)cGa>cAa	p.R615Q	EWSR1_ENST00000414183.2_Missense_Mutation_p.R620Q|EWSR1_ENST00000332035.6_Missense_Mutation_p.R559Q|EWSR1_ENST00000332050.6_Missense_Mutation_p.R542Q|EWSR1_ENST00000406548.1_Missense_Mutation_p.R614Q|EWSR1_ENST00000331029.7_Missense_Mutation_p.R577Q	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1	615	Arg/Gly/Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GGAGGAAGACGAGGTGGCCCT	0.612			T	"FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"	"Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"																																p.R620Q		Atlas-SNP	.		Dom	yes		22	22q12	2130	Ewing sarcoma breakpoint region 1 (EWS)		"L, M"	EWSR1_ENST00000414183,brain,glioma,0,2	EWSR1	104	2	0			c.G1859A						.																																			SO:0001583	missense	2130	exon17			GAAGACGAGGTGG		CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944		"RNA binding motif (RRM) containing"	3508	protein-coding gene	gene with protein product		133450	"Ewing sarcoma breakpoint region 1"			1522903	Standard	NM_005243		Approved	EWS	uc003aev.3	Q01844	OTTHUMG00000151107	ENST00000397938.2:c.1844G>A	22.37:g.29695754G>A	ENSP00000381031:p.Arg615Gln	84.0	0.0		79.0	5.0	NM_013986	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	Missense_Mutation	SNP	ENST00000397938.2	37	CCDS13851.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.277579	0.59758	.	.	ENSG00000182944	ENST00000332050;ENST00000397938;ENST00000406548;ENST00000331029;ENST00000414183;ENST00000332035	D;D;D;D;D;D	0.96774	-4.05;-3.54;-3.67;-4.12;-3.68;-3.56	4.91	3.89	0.44902	.	0.000000	0.64402	U	0.000002	D	0.91653	0.7362	N	0.19112	0.55	0.38032	D	0.9352	B;B;B;B;B	0.14438	0.003;0.01;0.01;0.01;0.01	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	D	0.88575	0.3132	10	0.52906	T	0.07	.	13.0918	0.59171	0.0784:0.0:0.9216:0.0	.	559;614;559;620;615	Q96MN4;Q96FE8;B0QYK1;Q96MX4;Q01844	.;.;.;.;EWS_HUMAN	Q	542;615;614;577;620;559	ENSP00000330896:R542Q;ENSP00000381031:R615Q;ENSP00000385726:R614Q;ENSP00000330516:R577Q;ENSP00000400142:R620Q;ENSP00000331699:R559Q	ENSP00000330516:R577Q	R	+	2	0	EWSR1	28025754	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.112000	0.89566	1.052000	0.40392	0.305000	0.20034	CGA	.	G|0.994;A|0.006		0.612	EWSR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321345.1	NM_005243		A	29695754	G	A	29695754	3	1	152	1	0	0	0	0	1	0	0	0	5298	1058	37	1	2023	1	EWSR1	22	29695754	Missense_Mutation	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10		29695754	21608812	106	23454										
TST	7263	hgsc.bcm.edu	37	chr22	37407302	37407302	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tctgggcccttctcgaagccAtcctcagtcaggaagtccat	9	14	4	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr22:37407302A>G	ENST00000403892.3	-	2	1394	c.660T>C	c.(658-660)gaT>gaC	p.D220D	TST_ENST00000249042.3_Silent_p.D220D|Y_RNA_ENST00000516603.1_RNA	NM_001270483.1	NP_001257412.1	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase (rhodanese)	220	Rhodanese 2. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cellular nitrogen compound metabolic process (GO:0034641)|cyanate catabolic process (GO:0009440)|epithelial cell differentiation (GO:0030855)|rRNA import into mitochondrion (GO:0035928)|rRNA transport (GO:0051029)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|thiosulfate sulfurtransferase activity (GO:0004792)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	7						TCTCGAAGCCATCCTCAGTCA	0.587																																					p.D220D		Atlas-SNP	.											.	TST	22	.	0			c.T660C						.						55	44	48					22																	37407302		2203	4300	6503	SO:0001819	synonymous_variant	7263	exon3			GAAGCCATCCTCA	Z73420	CCDS13938.1	22q13.1	2002-02-05			ENSG00000128311	ENSG00000128311	2.8.1.1		12388	protein-coding gene	gene with protein product		180370				1953758	Standard	NM_003312		Approved	RDS	uc003aqh.4	Q16762	OTTHUMG00000150533	ENST00000403892.3:c.660T>C	22.37:g.37407302A>G		90.0	0.0		102.0	50.0	NM_003312	B3KRM1|Q6IB06	Silent	SNP	ENST00000403892.3	37	CCDS13938.1																																																																																			.	.		0.587	TST-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318790.1			G	37407302	A	G	37407302	2	3	152	1	0	0	0	0	0	0	0	1	16688	214	8	2		2	TST	22	37407302	Silent	SNP	A	TCGA-DD-AACA-01A-11D-A40R-10	7711548	37407302	13897264	107	23455										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38120691	38120691	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gggacgatcccagagcctccTctcctaacagaaccacccaa	7	17	1	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr22:38120691T>G	ENST00000406386.3	+	7	2383	c.2128T>G	c.(2128-2130)Tct>Gct	p.S710A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	710					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAGAGCCTCCTCTCCTAACAG	0.577																																					p.S710A		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	0			c.T2128G						.						171	186	181					22																	38120691		1944	4150	6094	SO:0001583	missense	11078	exon7			GCCTCCTCTCCTA	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.2128T>G	22.37:g.38120691T>G	ENSP00000384312:p.Ser710Ala	157.0	0.0		149.0	57.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.602126	0.66445	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.21361	2.01	4.35	4.35	0.52113	.	.	.	.	.	T	0.21631	0.0521	M	0.64404	1.975	0.80722	D	1	P	0.45715	0.865	B	0.40602	0.334	T	0.02365	-1.1170	9	0.33141	T	0.24	.	10.1536	0.42809	0.0:0.0:0.0:1.0	.	710	Q9H2D6	TARA_HUMAN	A	710	ENSP00000384312:S710A	ENSP00000384312:S710A	S	+	1	0	TRIOBP	36450637	0.478000	0.25917	0.191000	0.23289	0.010000	0.07245	1.135000	0.31454	1.977000	0.57605	0.456000	0.33151	TCT	.	.		0.577	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			G	38120691	T	G	38120691	3	3	152	1	0	0	0	0	1	0	0	0	16568	1551	54	5	2146	5	TRIOBP	22	38120691	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	713389	38120691	13183875	108	23456										
MICALL1	85377	hgsc.bcm.edu	37	chr22	38302534	38302534	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	agctccttccgggacggcctGgccttctgcgccatcctgca	11	17	1	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chr22:38302534G>T	ENST00000215957.6	+	1	231	c.105G>T	c.(103-105)ctG>ctT	p.L35L		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	35	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					GGGACGGCCTGGCCTTCTGCG	0.801																																					p.L35L		Atlas-SNP	.											.	MICALL1	53	.	0			c.G105T						.						5	5	5					22																	38302534		1818	3519	5337	SO:0001819	synonymous_variant	85377	exon1			CGGCCTGGCCTTC	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"molecule interacting with Rab13"					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.105G>T	22.37:g.38302534G>T		23.0	0.0		37.0	14.0	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Silent	SNP	ENST00000215957.6	37	CCDS13961.1																																																																																			.	.		0.801	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		T	38302534	G	T	38302534	2	4	152	1	0	0	0	0	0	0	0	1	9582	1335	47	3		3	MICALL1	22	38302534	Silent	SNP	G	TCGA-DD-AACA-01A-11D-A40R-10	181843	38302534	13002032	109	23457										
KAL1	3730	hgsc.bcm.edu	37	chrX	8553366	8553366	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cctcgagttccatgcacattCacagcagccactcgaaactg	7	15	1	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chrX:8553366C>T	ENST00000262648.3	-	6	947	c.798G>A	c.(796-798)gtG>gtA	p.V266V		NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	266	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						CATGCACATTCACAGCAGCCA	0.517																																					p.V266V		Atlas-SNP	.											.	KAL1	78	.	0			c.G798A						.						173	120	138					X																	8553366		2203	4300	6503	SO:0001819	synonymous_variant	3730	exon6			CACATTCACAGCA		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"WAP four-disulfide core domain containing", "Fibronectin type III domain containing"	6211	protein-coding gene	gene with protein product	"anosmin-1", "WAP four-disulfide core domain 19"	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.798G>A	X.37:g.8553366C>T		34.0	0.0		31.0	25.0	NM_000216	B2RPF8	Silent	SNP	ENST00000262648.3	37	CCDS14130.1																																																																																			.	.		0.517	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216		T	8553366	C	T	8553366	2	4	152	1	0	0	0	0	0	0	0	1	7983	813	29	3		3	KAL1	23	8553366	Silent	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10		8553366	146717194	110	23458										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382442	24382453	+	IGR	DEL	TAGCTGCTGCTG	TAGCTGCTGCTG	-													0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tgctgctcctgctcctgctcTagctgctgctgctgctcctg					rs112697166		TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	TAGCTGCTGCTG	TAGCTGCTGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chrX:24382442_24382453delTAGCTGCTGCTG								AC004552.1 (15419 upstream) : PDK3 (100884 downstream)																							gctcctgctctagctgctgctgctgctcctgc	0.623																																					p.522_525del		Atlas-Indel	.											.	.	.	.	0			c.1564_1575del						.																																			SO:0001628	intergenic_variant	100130302	exon1			.																													X.37:g.24382442_24382453delTAGCTGCTGCTG		87.0	0.0		78.0	18.0	NM_001136234		In_Frame_Del	DEL		37																																																																																				.	.	0	0.623									-	24382453	TAGCTGCTGCTG	-	24382442	6	5	152	0	1	1	0	1	0	0	0	0	5581	1522	53	0		0	FAM48B1	23	24382442	IGR	DEL	TAGCTGCTGCTG	TCGA-DD-AACA-01A-11D-A40R-10	15829076	24382442	130888118	111	23459										
HEPH	9843	hgsc.bcm.edu	37	chrX	65408259	65408259	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	gtagaccatgatttcttcctCctcttcagtgtggtagatga	9	9	3	4			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chrX:65408259C>T	ENST00000343002.2	+	4	1348	c.684C>T	c.(682-684)ctC>ctT	p.L228L	HEPH_ENST00000519389.1_Silent_p.L282L|HEPH_ENST00000419594.1_Silent_p.L231L|HEPH_ENST00000441993.2_Silent_p.L231L|HEPH_ENST00000374727.3_Silent_p.L231L|HEPH_ENST00000336279.5_5'UTR			Q9BQS7	HEPH_HUMAN	hephaestin	228	Plastocyanin-like 2.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						ATTTCTTCCTCCTCTTCAGTG	0.488																																					p.L282L		Atlas-SNP	.											.	HEPH	224	.	0			c.C846T						.						105	78	87					X																	65408259		2203	4300	6503	SO:0001819	synonymous_variant	9843	exon5			CTTCCTCCTCTTC	AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.684C>T	X.37:g.65408259C>T		138.0	0.0		69.0	64.0	NM_138737	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Silent	SNP	ENST00000343002.2	37																																																																																				.	.		0.488	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737		T	65408259	C	T	65408259	2	4	152	1	0	0	0	0	0	0	0	1	7063	842	30	3		3	HEPH	23	65408259	Silent	SNP	C	TCGA-DD-AACA-01A-11D-A40R-10	41025817	65408259	89862301	112	23460										
MED12	9968	hgsc.bcm.edu	37	chrX	70349274	70349274	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tgttctcaaggctgtgtttgTacttggtacgggggtaggaa	15	5	1	0			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chrX:70349274T>A	ENST00000374080.3	+	26	3718	c.3686T>A	c.(3685-3687)gTa>gAa	p.V1229E	MED12_ENST00000333646.6_Missense_Mutation_p.V1229E|MED12_ENST00000374102.1_Missense_Mutation_p.V1229E			Q93074	MED12_HUMAN	mediator complex subunit 12	1229					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					GCTGTGTTTGTACTTGGTACG	0.562			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome				OREG0019857	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V1229E		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.T3686A						.						41	43	43					X																	70349274		2063	4183	6246	SO:0001583	missense	9968	exon26			TGTTTGTACTTGG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.3686T>A	X.37:g.70349274T>A	ENSP00000363193:p.Val1229Glu	43.0	0.0	1121	44.0	36.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	20.6	4.010611	0.75046	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.37411	1.2;1.2;1.2;1.2	5.09	5.09	0.68999	.	0.053332	0.85682	D	0.000000	T	0.47432	0.1445	L	0.48642	1.525	0.80722	D	1	P;P;P;P	0.52170	0.713;0.944;0.951;0.59	B;P;P;B	0.55871	0.433;0.462;0.786;0.258	T	0.48768	-0.9006	10	0.72032	D	0.01	-10.3987	14.2257	0.65858	0.0:0.0:0.0:1.0	.	1229;1076;1229;1229	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	E	1229;1229;1229;1229;1197	ENSP00000333125:V1229E;ENSP00000363215:V1229E;ENSP00000363193:V1229E;ENSP00000414203:V1197E	ENSP00000333125:V1229E	V	+	2	0	MED12	70265999	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.283000	0.78640	2.003000	0.58678	0.430000	0.28490	GTA	.	.		0.562	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		A	70349274	T	A	70349274	3	1	152	1	0	0	0	0	1	0	0	0	9437	1638	57	4	3788	4	MED12	23	70349274	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	4941015	70349274	84921286	113	23461										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107925029	107925029	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	tccttcaggacagagtatcaTaattaaaggagatgctggtc	10	7	2	2			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chrX:107925029T>C	ENST00000361603.2	+	45	4353	c.4109T>C	c.(4108-4110)aTa>aCa	p.I1370T	COL4A5_ENST00000328300.6_Missense_Mutation_p.I1376T	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1370	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						CAGAGTATCATAATTAAAGGA	0.483									Alport syndrome with Diffuse Leiomyomatosis																												p.I1370T		Atlas-SNP	.											.	COL4A5	262	.	0			c.T4109C						.						113	100	104					X																	107925029		2203	4300	6503	SO:0001583	missense	1287	exon45	Familial Cancer Database		GTATCATAATTAA	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.4109T>C	X.37:g.107925029T>C	ENSP00000354505:p.Ile1370Thr	129.0	0.0		71.0	55.0	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.578862	0.46006	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.94000	-3.33;-2.61	4.86	4.86	0.63082	.	0.664334	0.15080	N	0.281691	D	0.86289	0.5897	N	0.19112	0.55	0.24919	N	0.991991	B;B	0.19583	0.037;0.018	B;B	0.19391	0.025;0.007	T	0.74009	-0.3802	10	0.21540	T	0.41	.	9.3044	0.37865	0.1625:0.0:0.0:0.8375	.	1373;1370	E7EVY4;P29400	.;CO4A5_HUMAN	T	1376;1370;1376	ENSP00000331902:I1376T;ENSP00000354505:I1370T	ENSP00000331902:I1376T	I	+	2	0	COL4A5	107811685	0.993000	0.37304	0.992000	0.48379	0.774000	0.43823	4.044000	0.57361	1.706000	0.51276	0.412000	0.27726	ATA	.	.		0.483	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			C	107925029	T	C	107925029	3	2	152	1	0	0	0	0	1	0	0	0	3696	1406	49	2	4298	2	COL4A5	23	107925029	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	37575755	107925029	47345531	114	23462										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123514834	123514834	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.043859649122807	5	1	0.892760565556672	1.53554817275748	0.697976442162489	1	1	0	cttcctccagagacccaagcTtaatgaagtagtgagtgtcc	9	11	0	3			TCGA-DD-AACA-01A-11D-A40R-10	TCGA-DD-AACA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fee6db1a-5aa7-490d-a841-3b5b430ec874	99678528-a049-4ed5-9eb9-d70563f8d53f	g.chrX:123514834T>A	ENST00000371130.3	-	31	7793	c.7730A>T	c.(7729-7731)aAg>aTg	p.K2577M	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.K2584M	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2577					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AGACCCAAGCTTAATGAAGTA	0.493																																					p.K2584M		Atlas-SNP	.											.	.	.	.	0			c.A7751T						.						98	75	83					X																	123514834		2203	4300	6503	SO:0001583	missense	10178	exon32			CCAAGCTTAATGA	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7730A>T	X.37:g.123514834T>A	ENSP00000360171:p.Lys2577Met	103.0	0.0		67.0	61.0	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	18.06	3.538653	0.65085	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.91180	-2.8;-2.77	5.83	5.83	0.93111	.	0.047957	0.85682	D	0.000000	D	0.94650	0.8275	M	0.72353	2.195	0.80722	D	1	D;D;D	0.89917	0.996;0.999;1.0	P;D;D	0.72075	0.862;0.921;0.976	D	0.95135	0.8258	10	0.87932	D	0	.	15.1686	0.72850	0.0:0.0:0.0:1.0	.	2583;2584;2577	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	M	2577;2584	ENSP00000360171:K2577M;ENSP00000403954:K2584M	ENSP00000360171:K2577M	K	-	2	0	ODZ1	123342515	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.040000	0.89188	1.965000	0.57142	0.486000	0.48141	AAG	.	.		0.493	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123514834	T	A	123514834	3	1	152	1	0	0	0	0	1	0	0	0	10843	1609	56	4	451	4	ODZ1	23	123514834	Missense_Mutation	SNP	T	TCGA-DD-AACA-01A-11D-A40R-10	15589805	123514834	31755726	115	23463										
SSU72	29101	hgsc.bcm.edu	37	chr1	1500211	1500211	+	Frame_Shift_Del	DEL	C	C	-													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gtcatatgtggttttgaaatCataaacattgggcttgtcgg							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr1:1500211delC	ENST00000291386.3	-	2	477	c.166delG	c.(166-168)gatfs	p.D56fs	SSU72_ENST00000359060.4_Frame_Shift_Del_p.D56fs	NM_014188.2	NP_054907.1	Q9NP77	SSU72_HUMAN	SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)	56					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|mRNA polyadenylation (GO:0006378)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)			large_intestine(2)|lung(5)	7	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		GTTTTGAAATCATAAACATTG	0.483																																					p.D56fs		Atlas-INDEL	.											.	SSU72	15	.	0			c.167delA						.						150	150	150					1																	1500211		2203	4300	6503	SO:0001589	frameshift_variant	29101	exon2			.	AJ276409	CCDS32.1	1p36	2010-03-24	2006-04-04		ENSG00000160075	ENSG00000160075			25016	protein-coding gene	gene with protein product			"Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)"			15125841, 15659578	Standard	NM_014188		Approved	HSPC182	uc001agd.3	Q9NP77	OTTHUMG00000000576	ENST00000291386.3:c.166delG	chr1.hg19:g.1500211delC	ENSP00000291386:p.Asp56fs	110.0	0.0		103.0	40.0	NM_014188	Q9BZS6|Q9H933	Frame_Shift_Del	DEL	ENST00000291386.3	hg19	CCDS32.1																																																																																			.	.		0.483	SSU72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001366.1	NM_014188		-	1500211	C	-	1500211	7	5	153	1	0	1	0	1	0	0	0	0	15217	826	29	0	434	0	SSU72	1	1500211	Frame_Shift_Del	DEL	C	TCGA-DD-AACB-01A-11D-A40R-10		1500211	247750410	1	23464										
RPS6KA1	6195	hgsc.bcm.edu	37	chr1	26900660	26900660	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	catccatcctggcccagcggCgagtgaggaagttgccatcc	12	14	0	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr1:26900660C>A	ENST00000374168.2	+	22	2330	c.2176C>A	c.(2176-2178)Cga>Aga	p.R726R	RPS6KA1_ENST00000530003.1_Silent_p.R710R|RPS6KA1_ENST00000374166.4_Silent_p.R715R|RPS6KA1_ENST00000374162.2_Silent_p.R634R|RPS6KA1_ENST00000526792.1_Silent_p.R634R|RPS6KA1_ENST00000531382.1_Silent_p.R735R	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	726					axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		GGCCCAGCGGCGAGTGAGGAA	0.627																																					p.R735R		Atlas-SNP	.											.	RPS6KA1	65	.	0			c.C2203A						.						114	97	103					1																	26900660		2203	4300	6503	SO:0001819	synonymous_variant	6195	exon21			CAGCGGCGAGTGA	BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"ribosomal protein S6 kinase, 90kD, polypeptide 1"			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.2176C>A	chr1.hg19:g.26900660C>A		58.0	0.0		44.0	15.0	NM_001006665	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Silent	SNP	ENST00000374168.2	hg19	CCDS284.1																																																																																			.	.		0.627	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011431.1	NM_002953		A	26900660	C	A	26900660	2	1	153	1	0	0	0	0	0	0	0	1	13665	760	27	1		1	RPS6KA1	1	26900660	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	25400449	26900660	222349961	2	23465										
STIL	6491	hgsc.bcm.edu	37	chr1	47746604	47746604	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggttccctttcttataggcaGgtggctgtcttactttgcag	11	9	2	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr1:47746604G>A	ENST00000360380.3	-	13	1889	c.1526C>T	c.(1525-1527)cCt>cTt	p.P509L	STIL_ENST00000371877.3_Missense_Mutation_p.P509L|STIL_ENST00000396221.2_Missense_Mutation_p.P509L|STIL_ENST00000337817.5_Missense_Mutation_p.P509L|STIL_ENST00000243182.6_Missense_Mutation_p.P509L	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	509					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				CTTATAGGCAGGTGGCTGTCT	0.423																																					p.P509L		Atlas-SNP	.											.	STIL	91	.	0			c.C1526T						.						94	90	91					1																	47746604		2203	4300	6503	SO:0001583	missense	6491	exon12			TAGGCAGGTGGCT	M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"TAL1 (SCL) interrupting locus"	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.1526C>T	chr1.hg19:g.47746604G>A	ENSP00000353544:p.Pro509Leu	123.0	0.0		119.0	50.0	NM_003035	Q5T0C5|Q68CN9	Missense_Mutation	SNP	ENST00000360380.3	hg19	CCDS548.1	.	.	.	.	.	.	.	.	.	.	G	2.344	-0.350347	0.05173	.	.	ENSG00000123473	ENST00000360380;ENST00000337817;ENST00000371877;ENST00000396221;ENST00000243182;ENST00000447475	T;T;T;T;T;T	0.44083	2.27;2.27;2.29;2.27;2.27;0.93	4.96	4.04	0.47022	.	0.896444	0.09985	N	0.730472	T	0.25494	0.0620	N	0.08118	0	0.09310	N	0.999999	B;B;B;B;B	0.10296	0.003;0.003;0.003;0.003;0.003	B;B;B;B;B	0.12156	0.004;0.007;0.004;0.007;0.004	T	0.17137	-1.0379	10	0.40728	T	0.16	-6.1906	10.4565	0.44553	0.1691:0.0:0.8309:0.0	.	509;462;509;509;509	E9PSF2;Q5T0C7;B7ZLW5;Q15468-2;Q15468	.;.;.;.;STIL_HUMAN	L	509;509;509;509;509;462	ENSP00000353544:P509L;ENSP00000337367:P509L;ENSP00000360944:P509L;ENSP00000379523:P509L;ENSP00000243182:P509L;ENSP00000411664:P462L	ENSP00000243182:P509L	P	-	2	0	STIL	47519191	0.937000	0.31787	0.318000	0.25279	0.063000	0.16089	3.395000	0.52558	1.318000	0.45170	-0.150000	0.13652	CCT	.	.		0.423	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035		A	47746604	G	A	47746604	3	1	153	1	0	0	0	0	1	0	0	0	15297	1000	35	3	2364	3	STIL	1	47746604	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	20845944	47746604	201504017	3	23466										
ITLN1	55600	hgsc.bcm.edu	37	chr1	160849202	160849202	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	aacaaatcccgcagtgaattCccctgaaaacaagaggcaga	8	11	0	4			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr1:160849202C>T	ENST00000326245.3	-	7	803	c.688G>A	c.(688-690)Gaa>Aaa	p.E230K	ITLN1_ENST00000487531.1_5'UTR	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	230	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			GCAGTGAATTCCCCTGAAAAC	0.488																																					p.E230K		Atlas-SNP	.											.	ITLN1	45	.	0			c.G688A						.						91	81	84					1																	160849202		2203	4300	6503	SO:0001583	missense	55600	exon7			TGAATTCCCCTGA	AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.688G>A	chr1.hg19:g.160849202C>T	ENSP00000323587:p.Glu230Lys	82.0	0.0		100.0	32.0	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Missense_Mutation	SNP	ENST00000326245.3	hg19	CCDS1211.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.657680	0.47467	.	.	ENSG00000179914	ENST00000326245	T	0.18810	2.19	3.96	3.96	0.45880	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (1);	0.172533	0.37304	N	0.002157	T	0.17789	0.0427	M	0.89214	3.015	0.20764	N	0.999853	B	0.17038	0.02	B	0.23150	0.044	T	0.11155	-1.0599	10	0.40728	T	0.16	-17.238	13.5475	0.61713	0.0:1.0:0.0:0.0	.	230	Q8WWA0	ITLN1_HUMAN	K	230	ENSP00000323587:E230K	ENSP00000323587:E230K	E	-	1	0	ITLN1	159115826	0.034000	0.19679	0.044000	0.18714	0.358000	0.29455	0.894000	0.28350	2.016000	0.59253	0.655000	0.94253	GAA	.	.		0.488	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625		T	160849202	C	T	160849202	3	4	153	1	0	0	0	0	1	0	0	0	7919	864	30	3	261	3	ITLN1	1	160849202	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	113102598	160849202	88401419	4	23467										
RGS5	8490	hgsc.bcm.edu	37	chr1	163117258	163117258	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gaaggttccaccaggttcttCattgtgatgtccttagtgaa	10	8	2	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr1:163117258C>A	ENST00000313961.5	-	5	697	c.420G>T	c.(418-420)atG>atT	p.M140I	RGS5_ENST00000527988.1_Missense_Mutation_p.M32I|RGS5_ENST00000530507.1_Missense_Mutation_p.M144I|RGS5_ENST00000367903.3_Missense_Mutation_p.M160I	NM_001254749.1|NM_003617.3	NP_001241678.1|NP_003608.1	O15539	RGS5_HUMAN	regulator of G-protein signaling 5	140	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(1)|lung(12)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20			LUSC - Lung squamous cell carcinoma(543;0.187)			CCAGGTTCTTCATTGTGATGT	0.478																																					p.M144I		Atlas-SNP	.											.	RGS5	29	.	0			c.G432T						.						149	140	143					1																	163117258		2203	4300	6503	SO:0001583	missense	8490	exon5			GTTCTTCATTGTG	AF030108	CCDS1244.1, CCDS55652.1, CCDS58041.1	1q23.1	2008-02-05	2007-08-14		ENSG00000143248	ENSG00000143248		"Regulators of G-protein signaling"	10001	protein-coding gene	gene with protein product		603276	"regulator of G-protein signalling 5"			9747037	Standard	NM_003617		Approved		uc021pdt.1	O15539	OTTHUMG00000034441	ENST00000313961.5:c.420G>T	chr1.hg19:g.163117258C>A	ENSP00000319308:p.Met140Ile	117.0	0.0		152.0	52.0	NM_001254749	E9PMP5|Q53XA9|Q599J0	Missense_Mutation	SNP	ENST00000313961.5	hg19	CCDS1244.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.039002	0.35989	.	.	ENSG00000143248	ENST00000313961;ENST00000367903;ENST00000530507;ENST00000527988	T;T;T;T	0.01871	4.59;4.59;4.59;4.59	5.76	5.76	0.90799	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.406007	0.31257	N	0.007978	T	0.00906	0.0030	N	0.12569	0.235	0.37266	D	0.907191	B	0.02656	0.0	B	0.01281	0.0	T	0.59118	-0.7514	9	0.40728	T	0.16	.	17.4698	0.87642	0.0:1.0:0.0:0.0	.	140	O15539	RGS5_HUMAN	I	140;160;144;32	ENSP00000319308:M140I;ENSP00000356879:M160I;ENSP00000433001:M144I;ENSP00000432313:M32I	ENSP00000319308:M140I	M	-	3	0	RGS5	161383882	1.000000	0.71417	0.993000	0.49108	0.999000	0.98932	2.516000	0.45520	2.713000	0.92767	0.655000	0.94253	ATG	.	.		0.478	RGS5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083264.1	NM_003617		A	163117258	C	A	163117258	3	1	153	1	0	0	0	0	1	0	0	0	13323	826	29	3	129	3	RGS5	1	163117258	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	2268056	163117258	86133363	5	23468										
PBX1	5087	hgsc.bcm.edu	37	chr1	164769105	164769105	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	cgaggcggtgatgatcctgcGttcccgatttctggatgcgc	14	11	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr1:164769105G>A	ENST00000420696.2	+	4	868	c.680G>A	c.(679-681)cGt>cAt	p.R227H	PBX1_ENST00000560641.1_Missense_Mutation_p.R122H|PBX1_ENST00000540236.1_Missense_Mutation_p.R227H|PBX1_ENST00000559240.1_Missense_Mutation_p.R227H|PBX1_ENST00000401534.1_Missense_Mutation_p.R227H|PBX1_ENST00000367897.1_Missense_Mutation_p.R227H|PBX1_ENST00000540246.1_Missense_Mutation_p.R122H	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	227					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						ATGATCCTGCGTTCCCGATTT	0.612			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.R227H		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1	60	.	0			c.G680A						.						117	94	102					1																	164769105		2203	4300	6503	SO:0001583	missense	5087	exon4			TCCTGCGTTCCCG	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"Homeoboxes / TALE class"	8632	protein-coding gene	gene with protein product		176310	"pre-B-cell leukemia transcription factor 1"				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.680G>A	chr1.hg19:g.164769105G>A	ENSP00000405890:p.Arg227His	106.0	0.0		107.0	32.0	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	hg19	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.849231	0.91277	.	.	ENSG00000185630	ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09	5.64	5.64	0.86602	PBX (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.59445	0.2194	M	0.87758	2.905	.	.	.	B;P;P;P;P	0.52692	0.31;0.726;0.858;0.88;0.955	B;B;B;P;P	0.54706	0.149;0.444;0.316;0.563;0.759	T	0.67245	-0.5719	9	0.87932	D	0	-8.2355	19.3125	0.94195	0.0:0.0:1.0:0.0	.	122;227;227;227;227	B7Z774;A8K5V0;F5H4U9;P40424;Q53YC7	.;.;.;PBX1_HUMAN;.	H	227;227;227;227;122	ENSP00000405890:R227H;ENSP00000356872:R227H;ENSP00000439943:R227H;ENSP00000384856:R227H;ENSP00000440869:R122H	ENSP00000356872:R227H	R	+	2	0	PBX1	163035729	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.338000	0.96553	2.653000	0.90120	0.655000	0.94253	CGT	.	.		0.612	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		A	164769105	G	A	164769105	3	1	153	1	0	0	0	0	1	0	0	0	11501	1145	40	1	694	1	PBX1	1	164769105	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	1651847	164769105	84481516	6	23469										
TPR	7175	hgsc.bcm.edu	37	chr1	186304629	186304629	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tgctgatctaaggctccattCctttgtttaagctcctcatt	6	11	2	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr1:186304629C>T	ENST00000367478.4	-	34	5048	c.4752G>A	c.(4750-4752)agG>agA	p.R1584R		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1584					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		AGGCTCCATTCCTTTGTTTAA	0.353			T	NTRK1	papillary thyroid																																p.R1584R		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.G4752A						.						150	135	140					1																	186304629		1853	4098	5951	SO:0001819	synonymous_variant	7175	exon34			TCCATTCCTTTGT	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.4752G>A	chr1.hg19:g.186304629C>T		94.0	0.0		76.0	9.0	NM_003292	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	hg19	CCDS41446.1																																																																																			.	.		0.353	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		T	186304629	C	T	186304629	2	4	153	1	0	0	0	0	0	0	0	1	16431	854	30	3		3	TPR	1	186304629	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	21535524	186304629	62945992	7	23470										
ASPM	259266	hgsc.bcm.edu	37	chr1	197065148	197065148	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	cgtgttctctctagtttggtAtagaagcaaccttgaataat	8	7	2	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr1:197065148A>G	ENST00000367409.4	-	19	9223	c.8967T>C	c.(8965-8967)taT>taC	p.Y2989Y	ASPM_ENST00000294732.7_Silent_p.Y1404Y|ASPM_ENST00000367408.1_Silent_p.Y654Y	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2989					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						CTAGTTTGGTATAGAAGCAAC	0.348																																					p.Y2989Y		Atlas-SNP	.											.	ASPM	444	.	0			c.T8967C						.						108	117	114					1																	197065148		2203	4299	6502	SO:0001819	synonymous_variant	259266	exon19			TTTGGTATAGAAG	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.8967T>C	chr1.hg19:g.197065148A>G		81.0	0.0		108.0	42.0	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	hg19	CCDS1389.1																																																																																			.	.		0.348	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		G	197065148	A	G	197065148	2	3	153	1	0	0	0	0	0	0	0	1	1056	456	16	2		2	ASPM	1	197065148	Silent	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	10760519	197065148	52185473	8	23471										
NUAK2	81788	hgsc.bcm.edu	37	chr1	205277742	205277742	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tgcacggcagagacgatctgCcggaagaaatgcctagcttc	12	11	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr1:205277742C>A	ENST00000367157.3	-	3	597	c.471G>T	c.(469-471)cgG>cgT	p.R157R		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			AGACGATCTGCCGGAAGAAAT	0.572																																					p.R157R		Atlas-SNP	.											.	NUAK2	107	.	0			c.G471T						.						64	59	61					1																	205277742		2203	4300	6503	SO:0001819	synonymous_variant	81788	exon3			GATCTGCCGGAAG	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"SNF1/AMP activated protein kinase"	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.471G>T	chr1.hg19:g.205277742C>A		92.0	0.0		123.0	53.0	NM_030952		Silent	SNP	ENST00000367157.3	hg19	CCDS1453.1																																																																																			.	.		0.572	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		A	205277742	C	A	205277742	2	1	153	1	0	0	0	0	0	0	0	1	10722	726	26	3		3	NUAK2	1	205277742	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	8212594	205277742	43972879	9	23472										
OR14A16	284532	hgsc.bcm.edu	37	chr1	247978833	247978833	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tgaaataaggcagagatccaAgaaagatagattcttcaaga	9	5	2	6			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr1:247978833A>T	ENST00000357627.1	-	1	198	c.199T>A	c.(199-201)Ttg>Atg	p.L67M		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	67						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(32)|skin(2)|stomach(1)	45						CAGAGATCCAAGAAAGATAGA	0.433																																					p.L67M	Ovarian(112;180 1586 15073 21914 33526)	Atlas-SNP	.											.	OR14A16	90	.	0			c.T199A						.						73	74	74					1																	247978833		2203	4300	6503	SO:0001583	missense	284532	exon1			GATCCAAGAAAGA	BK004366	CCDS31097.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000196772	ENSG00000196772		"GPCR / Class A : Olfactory receptors"	15022	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily AT, member 1"	OR5AT1			Standard	NM_001001966		Approved		uc001idm.1	Q8NHC5	OTTHUMG00000040199	ENST00000357627.1:c.199T>A	chr1.hg19:g.247978833A>T	ENSP00000350248:p.Leu67Met	205.0	0.0		287.0	45.0	NM_001001966	Q6IF96	Missense_Mutation	SNP	ENST00000357627.1	hg19	CCDS31097.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.272788	0.40194	.	.	ENSG00000196772	ENST00000357627	T	0.14391	2.51	3.32	-2.19	0.07015	GPCR, rhodopsin-like superfamily (1);	2.080570	0.02996	U	0.147493	T	0.34424	0.0897	M	0.75777	2.31	0.09310	N	1	D	0.71674	0.998	D	0.68353	0.957	T	0.35699	-0.9778	10	0.87932	D	0	.	6.9312	0.24442	0.4113:0.1391:0.4496:0.0	.	67	Q8NHC5	O14AG_HUMAN	M	67	ENSP00000350248:L67M	ENSP00000350248:L67M	L	-	1	2	OR14A16	246045456	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-2.580000	0.00907	-0.555000	0.06142	0.481000	0.45027	TTG	.	.		0.433	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1	NM_001001966		T	247978833	A	T	247978833	3	4	153	1	0	0	0	0	1	0	0	0	10954	69	3	4	734	4	OR14A16	1	247978833	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	42701091	247978833	1271788	10	23473										
APOB	338	hgsc.bcm.edu	37	chr2	21256268	21256268	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	attgaagagattagctctctGgatattttgctcagagatgg	11	5	2	3			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr2:21256268G>A	ENST00000233242.1	-	9	1154	c.1027C>T	c.(1027-1029)Cag>Tag	p.Q343*	APOB_ENST00000399256.4_Nonsense_Mutation_p.Q343*	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	343	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTAGCTCTCTGGATATTTTGC	0.458																																					p.Q343X		Atlas-SNP	.											.	APOB	761	.	0			c.C1027T						.						150	144	146					2																	21256268		2203	4300	6503	SO:0001587	stop_gained	338	exon9			CTCTCTGGATATT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1027C>T	chr2.hg19:g.21256268G>A	ENSP00000233242:p.Gln343*	76.0	0.0		62.0	28.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Nonsense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990275	0.74589	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	.	.	.	5.53	3.68	0.42216	.	0.111526	0.40222	N	0.001146	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	14.3639	0.66792	0.0:0.0:0.614:0.386	.	.	.	.	X	343	.	ENSP00000233242:Q343X	Q	-	1	0	APOB	21109773	1.000000	0.71417	0.666000	0.29783	0.083000	0.17756	2.443000	0.44881	0.764000	0.33197	0.655000	0.94253	CAG	.	.		0.458	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21256268	G	A	21256268	4	1	153	1	0	0	0	0	0	1	0	0	785	1357	47	3	12748	3	APOB	2	21256268	Nonsense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10		21256268	221943105	11	23474										
IMP4	92856	hgsc.bcm.edu	37	chr2	131103253	131103253	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	accgatctgctggtcgttcaCgagcatcggggcacacctgg	13	13	2	0	rs201275845		TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr2:131103253C>T	ENST00000259239.3	+	5	1128	c.420C>T	c.(418-420)caC>caT	p.H140H	IMP4_ENST00000409935.1_Silent_p.H140H	NM_033416.1	NP_219484.1	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein	140	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				rRNA processing (GO:0006364)	nucleolus (GO:0005730)|ribonucleoprotein complex (GO:0030529)				central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	18	Colorectal(110;0.1)					TGGTCGTTCACGAGCATCGGG	0.662																																					p.H140H		Atlas-SNP	.											.	IMP4	35	.	0			c.C420T						.						54	56	55					2																	131103253		2203	4300	6503	SO:0001819	synonymous_variant	92856	exon5			CGTTCACGAGCAT	BC010042	CCDS2160.1	2q21.1	2014-02-19	2014-02-19		ENSG00000136718	ENSG00000136718			30856	protein-coding gene	gene with protein product		612981	"IMP4, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			8619474, 9110174, 12655004	Standard	NM_033416		Approved	MGC19606, BXDC4	uc002tra.1	Q96G21	OTTHUMG00000131627	ENST00000259239.3:c.420C>T	chr2.hg19:g.131103253C>T		66.0	0.0		59.0	25.0	NM_033416	Q3ZTT3	Silent	SNP	ENST00000259239.3	hg19	CCDS2160.1	.	.	.	.	.	.	.	.	.	.	C	1.148	-0.647416	0.03506	.	.	ENSG00000136718	ENST00000452955	.	.	.	5.06	-10.1	0.00402	.	.	.	.	.	T	0.61825	0.2378	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72899	-0.4152	4	.	.	.	-24.2336	16.8772	0.86055	0.0:0.2819:0.0:0.7181	.	.	.	.	M	129	.	.	T	+	2	0	IMP4	130819723	0.002000	0.14202	0.136000	0.22124	0.233000	0.25261	-1.893000	0.01609	-2.171000	0.00775	-0.436000	0.05848	ACG	.	C|0.999;T|0.001		0.662	IMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254520.2	NM_033416		T	131103253	C	T	131103253	2	4	153	1	0	0	0	0	0	0	0	1	7729	535	19	1		1	IMP4	2	131103253	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	109846985	131103253	112096120	12	23475										
FAM168B	130074	hgsc.bcm.edu	37	chr2	131812878	131812878	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	catggtggtcccagccaccaTgcccatggtgaccccgttgc	11	16	0	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr2:131812878T>A	ENST00000409185.1	-	5	549	c.442A>T	c.(442-444)Atg>Ttg	p.M148L	FAM168B_ENST00000389915.3_Missense_Mutation_p.M148L	NM_001009993.2	NP_001009993.2	A1KXE4	F168B_HUMAN	family with sequence similarity 168, member B	148						cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|lung(2)	5						CCAGCCACCATGCCCATGGTG	0.632																																					p.M148L		Atlas-SNP	.											.	FAM168B	15	.	0			c.A442T						.						92	103	99					2																	131812878		2077	4197	6274	SO:0001583	missense	130074	exon5			CCACCATGCCCAT		CCDS42755.1	2q21.1	2008-08-08			ENSG00000152102	ENSG00000152102			27016	protein-coding gene	gene with protein product							Standard	NM_001009993		Approved	KIAA0280L	uc002tsd.3	A1KXE4	OTTHUMG00000153473	ENST00000409185.1:c.442A>T	chr2.hg19:g.131812878T>A	ENSP00000387051:p.Met148Leu	103.0	0.0		79.0	37.0	NM_001009993	Q2TAZ6|Q6NZ40	Missense_Mutation	SNP	ENST00000409185.1	hg19	CCDS42755.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.791850	0.90453	.	.	ENSG00000152102	ENST00000409185;ENST00000389915	.	.	.	5.54	5.54	0.83059	.	0.071529	0.85682	D	0.000000	T	0.61615	0.2361	L	0.32530	0.975	0.80722	D	1	B	0.24533	0.105	P	0.44623	0.455	T	0.54820	-0.8236	9	0.11485	T	0.65	-12.7669	13.9286	0.63978	0.0:0.0:0.0:1.0	.	148	A1KXE4	F168B_HUMAN	L	148	.	ENSP00000374565:M148L	M	-	1	0	FAM168B	131529348	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.812000	0.69194	2.227000	0.72691	0.533000	0.62120	ATG	.	.		0.632	FAM168B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331299.2	NM_001009993		A	131812878	T	A	131812878	3	1	153	1	0	0	0	0	1	0	0	0	5491	1464	51	4	153	4	FAM168B	2	131812878	Missense_Mutation	SNP	T	TCGA-DD-AACB-01A-11D-A40R-10	709625	131812878	111386495	13	23476										
PKP4	8502	hgsc.bcm.edu	37	chr2	159481723	159481723	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	accaaaccaccgccagagtgGggtccccactgaccctgacg	10	17	0	3			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr2:159481723G>A	ENST00000389759.3	+	7	1049	c.937G>A	c.(937-939)Ggg>Agg	p.G313R	PKP4_ENST00000389757.3_Missense_Mutation_p.G313R	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	313					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						CGCCAGAGTGGGGTCCCCACT	0.632										HNSCC(62;0.18)																											p.G313R		Atlas-SNP	.											.	PKP4	133	.	0			c.G937A						.						47	45	46					2																	159481723		2203	4300	6503	SO:0001583	missense	8502	exon7			AGAGTGGGGTCCC	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.937G>A	chr2.hg19:g.159481723G>A	ENSP00000374409:p.Gly313Arg	122.0	0.0		110.0	39.0	NM_001005476	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.195294	0.78902	.	.	ENSG00000144283	ENST00000428353;ENST00000389757;ENST00000389759	T;T	0.75704	-0.96;-0.95	5.87	5.87	0.94306	.	0.052726	0.85682	D	0.000000	D	0.83797	0.5332	L	0.54323	1.7	0.80722	D	1	D;D;D;D	0.63880	0.989;0.961;0.969;0.993	D;P;P;D	0.66979	0.913;0.886;0.827;0.948	T	0.80730	-0.1252	10	0.39692	T	0.17	-8.2235	20.5827	0.99408	0.0:0.0:1.0:0.0	.	165;313;313;165	Q6LCG8;Q99569-2;Q99569;F8W7E2	.;.;PKP4_HUMAN;.	R	165;313;313	ENSP00000374407:G313R;ENSP00000374409:G313R	ENSP00000374407:G313R	G	+	1	0	PKP4	159189969	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.742000	0.68646	2.941000	0.99782	0.655000	0.94253	GGG	.	.		0.632	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			A	159481723	G	A	159481723	3	1	153	1	0	0	0	0	1	0	0	0	11996	1232	43	3	959	3	PKP4	2	159481723	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	27668845	159481723	83717650	14	23477										
TANC1	85461	hgsc.bcm.edu	37	chr2	160027239	160027239	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tgggaagacggcaatcatttCcaagttggtggccctgagct	13	9	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr2:160027239C>T	ENST00000263635.6	+	10	1511	c.1274C>T	c.(1273-1275)tCc>tTc	p.S425F	TANC1_ENST00000454300.1_Missense_Mutation_p.S319F	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	425					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GCAATCATTTCCAAGTTGGTG	0.498																																					p.S425F		Atlas-SNP	.											.	TANC1	157	.	0			c.C1274T						.						110	123	119					2																	160027239		1936	4132	6068	SO:0001583	missense	85461	exon10			TCATTTCCAAGTT	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.1274C>T	chr2.hg19:g.160027239C>T	ENSP00000263635:p.Ser425Phe	234.0	1.0		256.0	127.0	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	hg19	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.785479	0.90282	.	.	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.22336	1.96;1.96	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.49762	0.1576	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.964	D;D;P	0.87578	0.996;0.998;0.791	T	0.42548	-0.9445	10	0.38643	T	0.18	.	19.2792	0.94046	0.0:1.0:0.0:0.0	.	417;319;425	B9EK39;Q9C0D5-2;Q9C0D5	.;.;TANC1_HUMAN	F	319;425	ENSP00000396339:S319F;ENSP00000263635:S425F	ENSP00000263635:S425F	S	+	2	0	TANC1	159735485	1.000000	0.71417	0.997000	0.53966	0.948000	0.59901	4.858000	0.62947	2.632000	0.89209	0.655000	0.94253	TCC	.	.		0.498	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			T	160027239	C	T	160027239	3	4	153	1	0	0	0	0	1	0	0	0	15559	855	30	3	1304	3	TANC1	2	160027239	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	545516	160027239	83172134	15	23478										
ZAK	51776	hgsc.bcm.edu	37	chr2	174047653	174047653	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	aggagatggatatggatcacAttatgacctgggccactgat	12	7	1	3			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr2:174047653A>G	ENST00000375213.3	+	4	397	c.319A>G	c.(319-321)Att>Gtt	p.I107V	MLK7-AS1_ENST00000419609.1_RNA|MLTK_ENST00000539448.1_Missense_Mutation_p.I107V|MLTK_ENST00000338983.3_Missense_Mutation_p.I107V|MLTK_ENST00000431503.2_Missense_Mutation_p.I6V|MLTK_ENST00000480606.1_3'UTR|MLK7-AS1_ENST00000422703.1_RNA|MLTK_ENST00000409176.2_Missense_Mutation_p.I107V	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		107	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										TATGGATCACATTATGACCTG	0.363																																					p.I107V		Atlas-SNP	.											.	ZAK	62	.	0			c.A319G						.						74	76	75					2																	174047653		2203	4299	6502	SO:0001583	missense	0	exon4			GATCACATTATGA																												ENST00000375213.3:c.319A>G	chr2.hg19:g.174047653A>G	ENSP00000364361:p.Ile107Val	443.0	1.0		439.0	174.0	NM_133646	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	hg19	CCDS42777.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.400021	0.62177	.	.	ENSG00000091436	ENST00000539448;ENST00000409176;ENST00000338983;ENST00000431503;ENST00000375213;ENST00000422149	D;D;D;D;D;D	0.89050	-2.46;-2.46;-2.46;-2.46;-2.46;-2.46	5.74	5.74	0.90152	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.044394	0.85682	D	0.000000	D	0.85570	0.5727	L	0.28344	0.845	0.58432	D	0.999999	B;B;P;B;B	0.44776	0.143;0.118;0.843;0.143;0.004	B;B;P;B;B	0.44860	0.191;0.12;0.462;0.191;0.006	D	0.87237	0.2264	10	0.59425	D	0.04	.	16.0343	0.80612	1.0:0.0:0.0:0.0	.	107;107;107;107;107	A8K710;Q9NYL2-2;Q9NYL2;D4Q8H0;Q9NYL2-3	.;.;MLTK_HUMAN;.;.	V	107;107;107;6;107;107	ENSP00000439414:I107V;ENSP00000387259:I107V;ENSP00000340257:I107V;ENSP00000399787:I6V;ENSP00000364361:I107V;ENSP00000411923:I107V	ENSP00000340257:I107V	I	+	1	0	AC013461.1	173755899	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.113000	0.71553	2.198000	0.70561	0.533000	0.62120	ATT	.	.		0.363	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1			G	174047653	A	G	174047653	3	3	153	1	0	0	0	0	1	0	0	0	17527	217	8	2	329	2	ZAK	2	174047653	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	14020414	174047653	69151720	16	23479										
SCRN3	79634	hgsc.bcm.edu	37	chr2	175292518	175292518	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gagatggaatcaatccttcaAaacaagcatcttgatgtgga	9	7	3	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr2:175292518A>G	ENST00000272732.6	+	8	1252	c.1170A>G	c.(1168-1170)caA>caG	p.Q390Q	SCRN3_ENST00000409673.3_Silent_p.Q383Q|SCRN3_ENST00000548921.1_3'UTR	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	390							dipeptidase activity (GO:0016805)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			CAATCCTTCAAAACAAGCATC	0.299																																					p.Q390Q		Atlas-SNP	.											.	SCRN3	76	.	0			c.A1170G						.						79	78	78					2																	175292518		2202	4295	6497	SO:0001819	synonymous_variant	79634	exon8			CCTTCAAAACAAG	AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.1170A>G	chr2.hg19:g.175292518A>G		410.0	0.0		451.0	126.0	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Silent	SNP	ENST00000272732.6	hg19	CCDS2258.1																																																																																			.	.		0.299	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583		G	175292518	A	G	175292518	2	3	153	1	0	0	0	0	0	0	0	1	13955	11	1	2		2	SCRN3	2	175292518	Silent	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	1244865	175292518	67906855	17	23480										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196619135	196619135	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	caagaagatcaataggaattGtgtatttcctggcgtagttc	10	6	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr2:196619135G>T	ENST00000312428.6	-	63	11790	c.11690C>A	c.(11689-11691)aCa>aAa	p.T3897K	DNAH7_ENST00000409063.1_Missense_Mutation_p.T380K	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3897					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AATAGGAATTGTGTATTTCCT	0.483																																					p.T3897K		Atlas-SNP	.											.	DNAH7	512	.	0			c.C11690A						.						122	120	121					2																	196619135		1915	4123	6038	SO:0001583	missense	56171	exon63			GGAATTGTGTATT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.11690C>A	chr2.hg19:g.196619135G>T	ENSP00000311273:p.Thr3897Lys	153.0	0.0		144.0	43.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	G	1.593	-0.528666	0.04112	.	.	ENSG00000118997	ENST00000312428;ENST00000409063	T;T	0.07114	3.22;3.22	5.55	5.55	0.83447	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.05227	0.0139	N	0.05280	-0.08	0.80722	D	1	B	0.21225	0.053	B	0.28011	0.085	T	0.20306	-1.0279	10	0.02654	T	1	.	19.2868	0.94082	0.0:0.0:1.0:0.0	.	3897	Q8WXX0	DYH7_HUMAN	K	3897;380	ENSP00000311273:T3897K;ENSP00000386912:T380K	ENSP00000311273:T3897K	T	-	2	0	DNAH7	196327380	1.000000	0.71417	0.980000	0.43619	0.279000	0.26890	4.191000	0.58372	2.885000	0.99019	0.655000	0.94253	ACA	.	.		0.483	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196619135	G	T	196619135	3	4	153	1	0	0	0	0	1	0	0	0	4608	1377	48	3	396	3	DNAH7	2	196619135	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	21326617	196619135	46580238	18	23481										
NRP2	8828	hgsc.bcm.edu	37	chr2	206562324	206562324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ctggctatatcacctctcccGgttacccccaggactacccc	6	19	2	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr2:206562324G>A	ENST00000357785.5	+	2	161	c.130G>A	c.(130-132)Ggt>Agt	p.G44S	NRP2_ENST00000357118.4_Missense_Mutation_p.G44S|NRP2_ENST00000540841.1_Missense_Mutation_p.G44S|NRP2_ENST00000412873.2_Missense_Mutation_p.G44S|NRP2_ENST00000355117.4_Missense_Mutation_p.G44S|NRP2_ENST00000540178.1_Missense_Mutation_p.G44S|NRP2_ENST00000417189.1_Missense_Mutation_p.G44S|NRP2_ENST00000272849.3_Missense_Mutation_p.G44S|NRP2_ENST00000360409.3_Missense_Mutation_p.G44S			Q99435	NELL2_HUMAN	neuropilin 2	0						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						CACCTCTCCCGGTTACCCCCA	0.498																																					p.G44S		Atlas-SNP	.											.	NRP2	179	.	0			c.G130A						.						306	293	298					2																	206562324		2203	4300	6503	SO:0001583	missense	8828	exon2			TCTCCCGGTTACC	AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.130G>A	chr2.hg19:g.206562324G>A	ENSP00000350432:p.Gly44Ser	150.0	0.0		115.0	51.0	NM_201279	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000357785.5	hg19	CCDS46496.1	.	.	.	.	.	.	.	.	.	.	G	32	5.128780	0.94473	.	.	ENSG00000118257	ENST00000340626;ENST00000360409;ENST00000540178;ENST00000540841;ENST00000355117;ENST00000450507;ENST00000417189;ENST00000357118;ENST00000357785;ENST00000412873;ENST00000272849	T;T;T;T;T;T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.49;1.23;1.23;1.23;1.23;1.23	5.28	5.28	0.74379	CUB (5);	0.000000	0.85682	D	0.000000	T	0.60077	0.2241	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;1.0;1.0	T	0.63042	-0.6725	10	0.87932	D	0	-17.0866	18.9047	0.92455	0.0:0.0:1.0:0.0	.	44;44;44;44;44;44	O60462-2;O60462-3;O60462;O60462-4;O60462-5;E9PF66	.;.;NRP2_HUMAN;.;.;.	S	44	ENSP00000353582:G44S;ENSP00000439658:G44S;ENSP00000439261:G44S;ENSP00000347238:G44S;ENSP00000404279:G44S;ENSP00000387519:G44S;ENSP00000349632:G44S;ENSP00000350432:G44S;ENSP00000407626:G44S;ENSP00000272849:G44S	ENSP00000272849:G44S	G	+	1	0	NRP2	206270569	1.000000	0.71417	0.450000	0.26969	0.995000	0.86356	9.869000	0.99810	2.450000	0.82876	0.655000	0.94253	GGT	.	.		0.498	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1			A	206562324	G	A	206562324	3	1	153	1	0	0	0	0	1	0	0	0	10670	1116	39	1	136	1	NRP2	2	206562324	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	9943189	206562324	36637049	19	23482										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230656743	230656743	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tctccaatataaaactgcagCctgtgtcttacatttcctga	5	11	2	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr2:230656743C>T	ENST00000283943.5	-	28	4207	c.4029G>A	c.(4027-4029)agG>agA	p.R1343R	TRIP12_ENST00000389044.4_Silent_p.R1391R|TRIP12_ENST00000389045.3_Silent_p.R1073R	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1343					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		AAAACTGCAGCCTGTGTCTTA	0.393																																					p.R1343R		Atlas-SNP	.											.	TRIP12	207	.	0			c.G4029A						.						128	126	127					2																	230656743		2203	4300	6503	SO:0001819	synonymous_variant	9320	exon28			CTGCAGCCTGTGT	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.4029G>A	chr2.hg19:g.230656743C>T		250.0	1.0		300.0	133.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.		0.393	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		T	230656743	C	T	230656743	2	4	153	1	0	0	0	0	0	0	0	1	16571	738	26	3		3	TRIP12	2	230656743	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	24094419	230656743	12542630	20	23483										
PLCL2	23228	hgsc.bcm.edu	37	chr3	17051428	17051429	+	Frame_Shift_Ins	INS	-	-	A													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	atcaaggaagtgagaacaggINSaaaaaacacagacatattcc					rs77416948		TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr3:17051428_17051429insA	ENST00000418129.2	+	2	677_678	c.212_213insA	c.(211-216)ggaaaafs	p.GK71fs	PLCL2_ENST00000432376.1_Frame_Shift_Ins_p.GK71fs|PLCL2_ENST00000396755.2_Frame_Shift_Ins_p.GK71fs|PLCL2_ENST00000460467.1_3'UTR	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	197					B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.G71E(2)		breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						GTGAGAACAGGAAAAAACACAG	0.416																																					p.G71fs		Atlas-INDEL	.											PLCL2,NS,carcinoma,0,2	PLCL2	145	.	2	Substitution - Missense(2)	cervix(1)|skin(1)	c.212_213insA						.																																			SO:0001589	frameshift_variant	23228	exon2			.	AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"phospholipase C, epsilon 2"	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.218dupA	chr3.hg19:g.17051434_17051434dupA	ENSP00000409637:p.Gly71fs	185.0	0.0		172.0	38.0	NM_015184	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Frame_Shift_Ins	INS	ENST00000418129.2	hg19	CCDS33713.1																																																																																			.	.		0.416	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3			A	17051429	-	A	17051428	7	5	153	1	0	1	1	0	0	0	0	0	12049	1174	41	0	590	0	PLCL2	3	17051428	Frame_Shift_Ins	INS	-	TCGA-DD-AACB-01A-11D-A40R-10		17051428	180971002	21	23484										
EPM2AIP1	9852	hgsc.bcm.edu	37	chr3	37034022	37034022	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gttctcataggccacaaaagCctggtcgtccaaggcaagag	11	11	1	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr3:37034022C>T	ENST00000322716.5	-	1	773	c.547G>A	c.(547-549)Gct>Act	p.A183T	MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000539477.1_5'Flank|MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000536378.1_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	183					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						GCCACAAAAGCCTGGTCGTCC	0.498																																					p.A183T		Atlas-SNP	.											.	EPM2AIP1	47	.	0			c.G547A						.						74	74	74					3																	37034022		1935	4130	6065	SO:0001583	missense	9852	exon1			CAAAAGCCTGGTC	AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.547G>A	chr3.hg19:g.37034022C>T	ENSP00000406027:p.Ala183Thr	93.0	0.0		61.0	11.0	NM_014805	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	hg19	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	C	11.28	1.590723	0.28357	.	.	ENSG00000178567	ENST00000322716	T	0.08807	3.05	5.26	4.34	0.51931	.	.	.	.	.	T	0.05547	0.0146	N	0.25647	0.755	0.29997	N	0.816353	B	0.24576	0.106	B	0.20955	0.032	T	0.15896	-1.0421	9	0.02654	T	1	-4.7113	11.8748	0.52541	0.0:0.8252:0.1748:0.0	.	183	Q7L775	EPMIP_HUMAN	T	183	ENSP00000406027:A183T	ENSP00000406027:A183T	A	-	1	0	EPM2AIP1	37009026	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.049000	0.41288	2.731000	0.93534	0.557000	0.71058	GCT	.	.		0.498	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805		T	37034022	C	T	37034022	3	4	153	1	0	0	0	0	1	0	0	0	5186	739	26	3	1280	3	EPM2AIP1	3	37034022	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	19982594	37034022	160988408	22	23485										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr3:41266098A>G	ENST00000349496.5	+	3	375	c.95A>G	c.(94-96)gAc>gGc	p.D32G	CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95G						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>G	chr3.hg19:g.41266098A>G	ENSP00000344456:p.Asp32Gly	165.0	1.0		138.0	35.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308122	0.81247	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69788	0.3150	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.74137	-0.3762	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	G	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25G;ENSP00000385604:D32G;ENSP00000412219:D32G;ENSP00000379486:D32G;ENSP00000344456:D32G;ENSP00000411226:D25G;ENSP00000379488:D32G;ENSP00000409302:D32G;ENSP00000401599:D32G	ENSP00000344456:D32G	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266098	A	G	41266098	3	3	153	1	0	0	0	0	1	0	0	0	4018	275	10	2	101	2	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	4232076	41266098	156756332	23	23486										
TRAK1	22906	hgsc.bcm.edu	37	chr3	42265035	42265035	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	cccttgttcccagaggcctgGtacctgagggcctgcccctc	11	17	0	2	rs546729861		TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr3:42265035G>T	ENST00000327628.5	+	16	3068	c.2668G>T	c.(2668-2670)Gta>Tta	p.V890L	TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000396175.1_Missense_Mutation_p.V832L|RNU4-78P_ENST00000410940.1_RNA	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	890					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						CAGAGGCCTGGTACCTGAGGG	0.662																																					p.V890L	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.G2668T						.						31	34	33					3																	42265035		1967	4137	6104	SO:0001583	missense	22906	exon16			GGCCTGGTACCTG		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.2668G>T	chr3.hg19:g.42265035G>T	ENSP00000328998:p.Val890Leu	87.0	0.0		64.0	34.0	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	hg19	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.651623	0.47362	.	.	ENSG00000182606	ENST00000327628;ENST00000396175	T;T	0.08370	3.11;3.1	4.74	4.74	0.60224	.	0.445672	0.20342	N	0.094201	T	0.06325	0.0163	N	0.14661	0.345	0.80722	D	1	B;B	0.17038	0.02;0.02	B;B	0.17433	0.018;0.011	T	0.42103	-0.9471	10	0.18276	T	0.48	.	16.882	0.86065	0.0:0.0:1.0:0.0	.	832;890	C9JC32;Q9UPV9	.;TRAK1_HUMAN	L	890;832	ENSP00000328998:V890L;ENSP00000379478:V832L	ENSP00000328998:V890L	V	+	1	0	TRAK1	42240039	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	3.904000	0.56325	2.482000	0.83794	0.591000	0.81541	GTA	.	.		0.662	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		T	42265035	G	T	42265035	3	4	153	1	0	0	0	0	1	0	0	0	16464	1261	44	3	3118	3	TRAK1	3	42265035	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	998937	42265035	155757395	24	23487										
FAM19A1	407738	hgsc.bcm.edu	37	chr3	68466449	68466449	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gaaggagggacgtgtgaagtGatagcagcacaccgatgttg	16	6	0	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr3:68466449G>A	ENST00000478136.1	+	3	628	c.138G>A	c.(136-138)gtG>gtA	p.V46V	FAM19A1_ENST00000491017.1_3'UTR|FAM19A1_ENST00000496687.1_Silent_p.V46V	NM_213609.3	NP_998774.2	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A1	46						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	7		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)		CGTGTGAAGTGATAGCAGCAC	0.483																																					p.V46V		Atlas-SNP	.											.	FAM19A1	58	.	0			c.G138A						.						106	103	104					3																	68466449		1965	4145	6110	SO:0001819	synonymous_variant	407738	exon3			TGAAGTGATAGCA	AY325114	CCDS54606.1	3p14.1	2005-01-20			ENSG00000183662	ENSG00000183662			21587	protein-coding gene	gene with protein product						15028294	Standard	NM_213609		Approved	TAFA-1	uc003dnd.3	Q7Z5A9	OTTHUMG00000158745	ENST00000478136.1:c.138G>A	chr3.hg19:g.68466449G>A		126.0	0.0		108.0	13.0	NM_213609	A8K0V3|Q8TCL8	Silent	SNP	ENST00000478136.1	hg19	CCDS54606.1																																																																																			.	.		0.483	FAM19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352004.1	NM_213609		A	68466449	G	A	68466449	2	1	153	1	0	0	0	0	0	0	0	1	5536	1277	45	3		3	FAM19A1	3	68466449	Silent	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	26201414	68466449	129555981	25	23488										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77671422	77671422	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tccacagcctccagttccacCgttaggttatgtgtctggag	10	12	1	0	rs376068100		TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr3:77671422C>A	ENST00000461745.1	+	23	4499	c.3599C>A	c.(3598-3600)cCg>cAg	p.P1200Q	ROBO2_ENST00000332191.8_Missense_Mutation_p.P1200Q|ROBO2_ENST00000487694.3_Missense_Mutation_p.P1216Q	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1200					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CCAGTTCCACCGTTAGGTTAT	0.408																																					p.P1200Q		Atlas-SNP	.											ROBO2_ENST00000487694,colon,carcinoma,0,4	ROBO2	527	.	0			c.C3599A						.						107	107	107					3																	77671422		1893	4118	6011	SO:0001583	missense	6092	exon23			TTCCACCGTTAGG	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3599C>A	chr3.hg19:g.77671422C>A	ENSP00000417164:p.Pro1200Gln	124.0	1.0		149.0	77.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.864022	0.32884	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000461745;ENST00000332191	T;T;T	0.72725	-0.68;-0.63;-0.47	5.56	5.56	0.83823	.	0.000000	0.45606	D	0.000343	T	0.81446	0.4824	L	0.48642	1.525	0.30094	N	0.8080229999999999	P;D;P	0.89917	0.933;1.0;0.933	B;D;B	0.91635	0.397;0.999;0.397	T	0.82554	-0.0399	9	0.87932	D	0	.	19.5083	0.95130	0.0:1.0:0.0:0.0	.	1216;1200;1200	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	Q	1216;1216;1200;1200	ENSP00000417335:P1216Q;ENSP00000417164:P1200Q;ENSP00000327536:P1200Q	ENSP00000327536:P1200Q	P	+	2	0	ROBO2	77754112	1.000000	0.71417	0.999000	0.59377	0.202000	0.24057	7.487000	0.81328	2.611000	0.88343	0.650000	0.86243	CCG	.	.		0.408	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		A	77671422	C	A	77671422	3	1	153	1	0	0	0	0	1	0	0	0	13529	652	23	1	3691	1	ROBO2	3	77671422	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	9204973	77671422	120351008	26	23489										
SLCO2A1	6578	hgsc.bcm.edu	37	chr3	133674014	133674014	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ccaatgcttctggcagagctCggcctgcaagcggctgttgt	13	12	1	1	rs148547180		TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr3:133674014C>T	ENST00000310926.4	-	4	694	c.421G>A	c.(421-423)Gag>Aag	p.E141K	SLCO2A1_ENST00000493729.1_Intron|SLCO2A1_ENST00000478651.1_5'Flank	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	141					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	TGGCAGAGCTCGGCCTGCAAG	0.627																																					p.E141K		Atlas-SNP	.											SLCO2A1,NS,carcinoma,0,1	SLCO2A1	72	.	0			c.G421A						.	C	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	48	48	48		421	4.3	0.6	3	dbSNP_134	48	0,8600		0,0,4300	no	missense	SLCO2A1	NM_005630.2	56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	141/644	133674014	1,13005	2203	4300	6503	SO:0001583	missense	6578	exon4			AGAGCTCGGCCTG		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"Solute carriers"	10955	protein-coding gene	gene with protein product		601460	"solute carrier family 21 (prostaglandin transporter), member 2", "matrin F/G 1"	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.421G>A	chr3.hg19:g.133674014C>T	ENSP00000311291:p.Glu141Lys	76.0	0.0		80.0	25.0	NM_005630	Q86V98|Q8IUN2	Missense_Mutation	SNP	ENST00000310926.4	hg19	CCDS3084.1	.	.	.	.	.	.	.	.	.	.	C	7.457	0.643906	0.14451	2.27E-4	0.0	ENSG00000174640	ENST00000310926	T	0.38240	1.15	5.18	4.31	0.51392	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.941565	0.08803	N	0.891450	T	0.24198	0.0586	N	0.20807	0.61	0.80722	D	1	B	0.18166	0.026	B	0.14578	0.011	T	0.07065	-1.0792	10	0.35671	T	0.21	.	6.9043	0.24301	0.0:0.703:0.1443:0.1527	.	141	Q92959	SO2A1_HUMAN	K	141	ENSP00000311291:E141K	ENSP00000311291:E141K	E	-	1	0	SLCO2A1	135156704	0.062000	0.20869	0.620000	0.29132	0.078000	0.17371	0.942000	0.29017	1.324000	0.45282	0.462000	0.41574	GAG	.	C|1.000;T|0.000		0.627	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630		T	133674014	C	T	133674014	3	4	153	1	0	0	0	0	1	0	0	0	14741	893	31	1	1554	1	SLCO2A1	3	133674014	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	56002592	133674014	64348416	27	23490										
STK32B	55351	hgsc.bcm.edu	37	chr4	5461929	5461929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gggacgcggtgttcaagaagGcactgatgcccggctttgtg	16	9	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr4:5461929G>A	ENST00000282908.5	+	9	1305	c.883G>A	c.(883-885)Gca>Aca	p.A295T	STK32B_ENST00000508728.1_3'UTR|STK32B_ENST00000510398.1_Missense_Mutation_p.A248T|RN7SKP275_ENST00000364626.1_RNA|STK32B_ENST00000512636.1_Missense_Mutation_p.A218T	NM_018401.1	NP_060871.1			serine/threonine kinase 32B									p.A295T(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						GTTCAAGAAGGCACTGATGCC	0.587											OREG0016061	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A295T		Atlas-SNP	.											STK32B,colon,carcinoma,0,1	STK32B	87	.	1	Substitution - Missense(1)	large_intestine(1)	c.G883A						.						157	129	138					4																	5461929		2203	4300	6503	SO:0001583	missense	55351	exon9			AAGAAGGCACTGA	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.883G>A	chr4.hg19:g.5461929G>A	ENSP00000282908:p.Ala295Thr	99.0	0.0	626	67.0	21.0	NM_018401		Missense_Mutation	SNP	ENST00000282908.5	hg19	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	G	7.326	0.618000	0.14129	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.24538	1.85;1.85;1.85	4.51	2.77	0.32553	Protein kinase-like domain (1);	0.161832	0.28354	N	0.015656	T	0.14657	0.0354	L	0.27053	0.805	0.24748	N	0.992998	B	0.18610	0.029	B	0.14023	0.01	T	0.17806	-1.0357	10	0.33141	T	0.24	.	5.1475	0.14993	0.1781:0.0:0.6589:0.163	.	295	Q9NY57	ST32B_HUMAN	T	295;218;248	ENSP00000282908:A295T;ENSP00000423209:A218T;ENSP00000420984:A248T	ENSP00000282908:A295T	A	+	1	0	STK32B	5512830	0.625000	0.27111	0.199000	0.23439	0.088000	0.18126	0.251000	0.18257	0.453000	0.26858	-0.309000	0.09137	GCA	.	.		0.587	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		A	5461929	G	A	5461929	3	1	153	1	0	0	0	0	1	0	0	0	15313	1203	42	3	917	3	STK32B	4	5461929	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10		5461929	185692347	28	23491										
NAP1L5	266812	hgsc.bcm.edu	37	chr4	89618757	89618768	+	In_Frame_Del	DEL	TGACCAGCCGCG	TGACCAGCCGCG	-													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tctggggctcctcagccatcTgaccagccgcgctgtcaggg					rs546469739|rs561100902	byFrequency	TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	TGACCAGCCGCG	TGACCAGCCGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr4:89618757_89618768delTGACCAGCCGCG	ENST00000323061.5	-	1	618_629	c.138_149delCGCGGCTGGTCA	c.(136-150)agcgcggctggtcag>agg	p.46_50SAAGQ>R	HERC3_ENST00000264345.3_Intron|HERC3_ENST00000402738.1_Intron|HERC3_ENST00000543130.1_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	46					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.G49V(1)		endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(123;0.000181)		CTCAGCCATCTGACCAGCCGCGCTGTCAGGGT	0.646																																					p.47_50del		Atlas-INDEL	.											.	NAP1L5	23	.	1	Substitution - Missense(1)	endometrium(1)	c.139_150del						.																																			SO:0001651	inframe_deletion	266812	exon1			.	NM_153757	CCDS3632.1	4q21-q22	2006-04-12			ENSG00000177432	ENSG00000177432			19968	protein-coding gene	gene with protein product		612203				12383514	Standard	NM_153757		Approved	DRLM	uc003hrx.3	Q96NT1	OTTHUMG00000130950	ENST00000323061.5:c.138_149delCGCGGCTGGTCA	chr4.hg19:g.89618757_89618768delTGACCAGCCGCG	ENSP00000320488:p.Ser46_Gln50delinsArg	63.0	0.0		38.0	29.0	NM_153757		In_Frame_Del	DEL	ENST00000323061.5	hg19	CCDS3632.1																																																																																			.	.		0.646	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757		-	89618768	TGACCAGCCGCG	-	89618757	7	5	153	1	0	1	0	1	0	0	0	0	10169	1580	55	0	403	0	NAP1L5	4	89618757	In_Frame_Del	DEL	TGACCAGCCGCG	TCGA-DD-AACB-01A-11D-A40R-10	84156828	89618757	101535519	29	23492										
ANK2	287	hgsc.bcm.edu	37	chr4	114208800	114208800	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	accttgcagcccaggaagatAaagtgaatgttgctgatatt	10	7	0	3			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr4:114208800A>C	ENST00000357077.4	+	19	2172	c.2119A>C	c.(2119-2121)Aaa>Caa	p.K707Q	ANK2_ENST00000264366.6_Missense_Mutation_p.K707Q|ANK2_ENST00000394537.3_Missense_Mutation_p.K707Q|ANK2_ENST00000506722.1_Missense_Mutation_p.K686Q	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	707					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CCAGGAAGATAAAGTGAATGT	0.418																																					p.K707Q		Atlas-SNP	.											.	ANK2	576	.	0			c.A2119C						.						130	112	118					4																	114208800		2203	4300	6503	SO:0001583	missense	287	exon19			GAAGATAAAGTGA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.2119A>C	chr4.hg19:g.114208800A>C	ENSP00000349588:p.Lys707Gln	81.0	0.0		41.0	16.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	A	13.69	2.311235	0.40895	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056	T;T;T;T;T;T;T	0.64438	-0.06;-0.06;-0.06;-0.06;-0.1;-0.06;-0.06	5.49	4.29	0.51040	Ankyrin repeat-containing domain (3);	0.000000	0.56097	D	0.000036	T	0.63224	0.2493	N	0.14661	0.345	0.80722	D	1	D;D;D;D;P	0.76494	0.999;0.998;0.998;0.975;0.734	D;D;D;P;P	0.76575	0.988;0.925;0.969;0.757;0.562	T	0.65026	-0.6268	10	0.46703	T	0.11	.	12.6506	0.56759	0.8617:0.1383:0.0:0.0	.	707;707;707;686;686	Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	ANK2_HUMAN;.;.;.;.	Q	686;653;686;722;707;707;707;686	ENSP00000423799:K686Q;ENSP00000421011:K653Q;ENSP00000421067:K686Q;ENSP00000424722:K722Q;ENSP00000378044:K707Q;ENSP00000349588:K707Q;ENSP00000264366:K707Q	ENSP00000264366:K707Q	K	+	1	0	ANK2	114428249	1.000000	0.71417	1.000000	0.80357	0.010000	0.07245	6.048000	0.71046	0.880000	0.35969	-0.323000	0.08544	AAA	.	.		0.418	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		C	114208800	A	C	114208800	3	2	153	1	0	0	0	0	1	0	0	0	621	363	13	5	2218	5	ANK2	4	114208800	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	24590043	114208800	76945476	30	23493										
FBXL7	23194	hgsc.bcm.edu	37	chr5	15928473	15928473	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tggctgcaggcggctcacagAccgagggctgtacaccatcg	14	13	1	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr5:15928473A>T	ENST00000504595.1	+	3	1083	c.602A>T	c.(601-603)gAc>gTc	p.D201V	FBXL7_ENST00000510662.1_Missense_Mutation_p.D154V|FBXL7_ENST00000329673.7_Missense_Mutation_p.D189V	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	201					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						CGGCTCACAGACCGAGGGCTG	0.602																																					p.D201V		Atlas-SNP	.											.	FBXL7	138	.	0			c.A602T						.						40	45	43					5																	15928473		2084	4208	6292	SO:0001583	missense	23194	exon3			TCACAGACCGAGG	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.602A>T	chr5.hg19:g.15928473A>T	ENSP00000423630:p.Asp201Val	113.0	0.0		144.0	67.0	NM_012304	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	hg19	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935533	0.73442	.	.	ENSG00000183580	ENST00000504595;ENST00000510662;ENST00000329673	T;T;T	0.46819	0.86;0.86;0.86	5.36	4.19	0.49359	.	0.000000	0.85682	D	0.000000	T	0.74504	0.3725	H	0.95004	3.61	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.79403	-0.1818	10	0.72032	D	0.01	.	10.9576	0.47366	0.9261:0.0:0.0739:0.0	.	201	Q9UJT9	FBXL7_HUMAN	V	201;154;189	ENSP00000423630:D201V;ENSP00000425184:D154V;ENSP00000329632:D189V	ENSP00000329632:D189V	D	+	2	0	FBXL7	15981473	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	9.300000	0.96151	0.875000	0.35847	0.459000	0.35465	GAC	.	.		0.602	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		T	15928473	A	T	15928473	3	4	153	1	0	0	0	0	1	0	0	0	5732	275	10	4	612	4	FBXL7	5	15928473	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10		15928473	164986787	31	23494										
RNF180	285671	hgsc.bcm.edu	37	chr5	63510007	63510007	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ttcctttcagaatccatccaGttttgatcctagtatgctgc	6	11	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr5:63510007G>T	ENST00000389100.4	+	4	926	c.854G>T	c.(853-855)aGt>aTt	p.S285I	RNF180_ENST00000296615.6_Missense_Mutation_p.S285I|RNF180_ENST00000381081.2_Intron	NM_001113561.1	NP_001107033.1	Q86T96	RN180_HUMAN	ring finger protein 180	285	Interaction with ZIC2. {ECO:0000250}.				adult behavior (GO:0030534)|norepinephrine metabolic process (GO:0042415)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|regulation of catalytic activity (GO:0050790)|serotonin metabolic process (GO:0042428)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	20		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)		AATCCATCCAGTTTTGATCCT	0.428																																					p.S285I		Atlas-SNP	.											.	RNF180	94	.	0			c.G854T						.						85	92	90					5																	63510007		2203	4300	6503	SO:0001583	missense	285671	exon4			CATCCAGTTTTGA	AK090756	CCDS34169.1, CCDS47219.1	5q12.3	2013-01-09			ENSG00000164197	ENSG00000164197		"RING-type (C3HC4) zinc fingers"	27752	protein-coding gene	gene with protein product							Standard	NM_178532		Approved		uc003jti.3	Q86T96	OTTHUMG00000162278	ENST00000389100.4:c.854G>T	chr5.hg19:g.63510007G>T	ENSP00000373752:p.Ser285Ile	108.0	0.0		102.0	22.0	NM_001113561	Q0JSU3|Q495A8|Q8NBD1	Missense_Mutation	SNP	ENST00000389100.4	hg19	CCDS47219.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.433355	0.43224	.	.	ENSG00000164197	ENST00000296615;ENST00000389100	T	0.54479	0.57	5.98	3.15	0.36227	.	0.547089	0.20944	N	0.082871	T	0.44286	0.1286	L	0.51422	1.61	0.80722	D	1	P;P	0.45474	0.8;0.859	B;B	0.40444	0.293;0.329	T	0.42344	-0.9457	10	0.87932	D	0	-4.8301	7.7947	0.29140	0.1451:0.2482:0.6067:0.0	.	285;285	Q86T96;Q86T96-2	RN180_HUMAN;.	I	285	ENSP00000373752:S285I	ENSP00000296615:S285I	S	+	2	0	RNF180	63545763	0.997000	0.39634	0.995000	0.50966	0.990000	0.78478	0.880000	0.28159	0.802000	0.34089	-0.165000	0.13383	AGT	.	.		0.428	RNF180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368394.1	NM_178532		T	63510007	G	T	63510007	3	4	153	1	0	0	0	0	1	0	0	0	13479	1029	36	3	864	3	RNF180	5	63510007	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	47581534	63510007	117405253	32	23495										
MAST4	375449	hgsc.bcm.edu	37	chr5	66398386	66398386	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ctggacgttctcccgcctgcTgtgaccatgaaataattatg	9	11	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr5:66398386T>A	ENST00000403625.2	+	9	1388	c.1093T>A	c.(1093-1095)Tgt>Agt	p.C365S	MAST4_ENST00000490016.2_Missense_Mutation_p.C176S|MAST4_ENST00000261569.7_Missense_Mutation_p.C171S|MAST4_ENST00000404260.3_Missense_Mutation_p.C368S|MAST4_ENST00000403666.1_Missense_Mutation_p.C176S|MAST4_ENST00000405643.1_Missense_Mutation_p.C186S	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	368						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TCCCGCCTGCTGTGACCATGA	0.393																																					p.C365S		Atlas-SNP	.											.	MAST4	218	.	0			c.T1093A						.						131	126	127					5																	66398386		1874	4112	5986	SO:0001583	missense	375449	exon9			GCCTGCTGTGACC	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.1093T>A	chr5.hg19:g.66398386T>A	ENSP00000385727:p.Cys365Ser	233.0	0.0		186.0	42.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	T	19.11	3.763654	0.69878	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000490016;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399	T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62	5.4	5.4	0.78164	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.172789	0.39083	U	0.001462	T	0.21427	0.0516	N	0.12182	0.205	0.38245	D	0.941436	P;B;B;B;B	0.37688	0.605;0.392;0.34;0.057;0.066	B;B;B;B;B	0.39379	0.298;0.262;0.237;0.113;0.071	T	0.14924	-1.0455	10	0.30854	T	0.27	-8.0332	15.4348	0.75137	0.0:0.0:0.0:1.0	.	186;368;171;176;176	E7EWQ5;O15021;O15021-2;O15021-3;D6RAK1	.;MAST4_HUMAN;.;.;.	S	368;365;176;176;186;186;171;171	ENSP00000385048:C368S;ENSP00000385727:C365S;ENSP00000421739:C176S;ENSP00000384313:C176S;ENSP00000384099:C186S;ENSP00000261569:C171S	ENSP00000261569:C171S	C	+	1	0	MAST4	66434142	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.048000	0.60808	0.533000	0.62120	TGT	.	.		0.393	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66398386	T	A	66398386	3	1	153	1	0	0	0	0	1	0	0	0	9336	1580	55	4	1257	4	MAST4	5	66398386	Missense_Mutation	SNP	T	TCGA-DD-AACB-01A-11D-A40R-10	2888379	66398386	114516874	33	23496										
CD83	9308	hgsc.bcm.edu	37	chr6	14118268	14118268	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	caccgccccctgggatccgcAggttccctacacggtctcct	9	19	1	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr6:14118268A>T	ENST00000379153.3	+	2	296	c.125A>T	c.(124-126)cAg>cTg	p.Q42L		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	42	Ig-like V-type.				defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				TGGGATCCGCAGGTTCCCTAC	0.617																																					p.Q42L		Atlas-SNP	.											.	CD83	23	.	0			c.A125T						.						27	28	28					6																	14118268		2203	4300	6503	SO:0001583	missense	9308	exon2			ATCCGCAGGTTCC	Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1703	protein-coding gene	gene with protein product		604534	"CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)", "CD83 molecule "			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.125A>T	chr6.hg19:g.14118268A>T	ENSP00000368450:p.Gln42Leu	51.0	0.0		68.0	25.0	NM_004233	Q5THX9	Missense_Mutation	SNP	ENST00000379153.3	hg19	CCDS4532.1	.	.	.	.	.	.	.	.	.	.	A	9.875	1.199915	0.22121	.	.	ENSG00000112149	ENST00000379153	T	0.64991	-0.13	4.56	-6.73	0.01749	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.543413	0.18136	N	0.150580	T	0.18467	0.0443	L	0.35854	1.095	0.09310	N	1	B	0.12013	0.005	B	0.17433	0.018	T	0.20207	-1.0282	10	0.22109	T	0.4	-2.8511	5.2775	0.15657	0.2678:0.0:0.4507:0.2815	.	42	Q01151	CD83_HUMAN	L	42	ENSP00000368450:Q42L	ENSP00000368450:Q42L	Q	+	2	0	CD83	14226247	0.000000	0.05858	0.009000	0.14445	0.256000	0.26092	-0.644000	0.05415	-1.439000	0.01962	-0.669000	0.03829	CAG	.	.		0.617	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1			T	14118268	A	T	14118268	3	4	153	1	0	0	0	0	1	0	0	0	3043	188	7	4	131	4	CD83	6	14118268	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10		14118268	156996799	34	23497										
ZBTB12	221527	hgsc.bcm.edu	37	chr6	31868141	31868141	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggcaggggtccccggctgccCcccgcccccaggctgccccc	13	23	0	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr6:31868141C>T	ENST00000375527.2	-	2	1117	c.942G>A	c.(940-942)ggG>ggA	p.G314G	EHMT2_ENST00000375537.4_5'Flank|C2_ENST00000469372.1_Intron|C2_ENST00000452323.2_5'Flank|EHMT2_ENST00000375530.4_5'Flank	NM_181842.2	NP_862825.1	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	314	Gly-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(5)|prostate(1)|skin(1)	10						cccggctgccccccgccccca	0.716																																					p.G314G		Atlas-SNP	.											.	ZBTB12	25	.	0			c.G942A						.						4	5	5					6																	31868141		1919	3769	5688	SO:0001819	synonymous_variant	221527	exon2			GCTGCCCCCCGCC	BC043609	CCDS4727.1	6p21.31	2013-01-08	2004-04-15	2004-04-16	ENSG00000204366	ENSG00000204366		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	19066	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 46"	C6orf46		9545376	Standard	NM_181842		Approved	G10, NG35, D6S59E	uc003nyd.1	Q9Y330	OTTHUMG00000031169	ENST00000375527.2:c.942G>A	chr6.hg19:g.31868141C>T		33.0	0.0		43.0	9.0	NM_181842	B0UY00|Q5JQ98	Silent	SNP	ENST00000375527.2	hg19	CCDS4727.1																																																																																			.	.		0.716	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842		T	31868141	C	T	31868141	2	4	153	1	0	0	0	0	0	0	0	1	17540	610	22	3		3	ZBTB12	6	31868141	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	17749873	31868141	139246926	35	23498										
GRM4	2914	hgsc.bcm.edu	37	chr6	34004308	34004308	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	cactgtcttcttccgctcacCcggttggcagggcaggctgc	12	15	3	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr6:34004308C>G	ENST00000538487.2	-	9	2022	c.1579G>C	c.(1579-1581)Ggt>Cgt	p.G527R	GRM4_ENST00000535756.1_Missense_Mutation_p.G394R|GRM4_ENST00000455714.2_Missense_Mutation_p.G387R|GRM4_ENST00000374181.4_Missense_Mutation_p.G527R|GRM4_ENST00000609222.1_Missense_Mutation_p.G394R|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000374177.3_Missense_Mutation_p.G411R|GRM4_ENST00000544773.2_Missense_Mutation_p.G358R	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	527					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						TTCCGCTCACCCGGTTGGCAG	0.632																																					p.G527R		Atlas-SNP	.											.	GRM4	317	.	0			c.G1579C						.						56	47	50					6																	34004308		2203	4300	6503	SO:0001583	missense	2914	exon9			GCTCACCCGGTTG	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.1579G>C	chr6.hg19:g.34004308C>G	ENSP00000440556:p.Gly527Arg	61.0	0.0		71.0	17.0	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	hg19	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.536246	0.64972	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000545715;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	D;D;D;D;D;D;D	0.95137	-3.62;-3.62;-3.62;-3.62;-3.62;-3.62;-3.62	4.79	4.79	0.61399	GPCR, family 3, nine cysteines domain (1);	0.000000	0.85682	D	0.000000	D	0.98277	0.9429	H	0.96943	3.91	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999	D;D;D;D;D	0.97110	0.996;0.993;1.0;1.0;0.973	D	0.99624	1.0984	10	0.87932	D	0	.	17.6327	0.88113	0.0:1.0:0.0:0.0	.	480;358;387;527;394	B7ZLU9;B7Z1T9;F5GXM5;Q14833;B3KVL9	.;.;.;GRM4_HUMAN;.	R	527;411;219;394;358;527;387	ENSP00000363296:G527R;ENSP00000363292:G411R;ENSP00000445533:G219R;ENSP00000437925:G394R;ENSP00000437730:G358R;ENSP00000440556:G527R;ENSP00000398456:G387R	ENSP00000363292:G411R	G	-	1	0	GRM4	34112286	1.000000	0.71417	0.438000	0.26821	0.473000	0.32948	7.644000	0.83416	2.481000	0.83766	0.551000	0.68910	GGT	.	.		0.632	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			G	34004308	C	G	34004308	3	3	153	1	0	0	0	0	1	0	0	0	6808	623	22	4	1171	4	GRM4	6	34004308	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	2136167	34004308	137110759	36	23499										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42196221	42196221	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	aggatgtccacatccttgatGggtttgatcagactcagctg	11	9	2	3			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr6:42196221G>A	ENST00000372922.4	-	18	4027	c.3465C>T	c.(3463-3465)ccC>ccT	p.P1155P	TRERF1_ENST00000541110.1_Silent_p.P1175P|TRERF1_ENST00000340840.2_Silent_p.P1084P|TRERF1_ENST00000372917.4_Silent_p.P1084P|TRERF1_ENST00000354325.2_Silent_p.P1072P	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1155	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CATCCTTGATGGGTTTGATCA	0.597																																					p.P1155P		Atlas-SNP	.											.	TRERF1	124	.	0			c.C3465T						.						150	154	152					6																	42196221		2203	4300	6503	SO:0001819	synonymous_variant	55809	exon18			CTTGATGGGTTTG	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.3465C>T	chr6.hg19:g.42196221G>A		65.0	0.0		100.0	30.0	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	hg19	CCDS4867.1																																																																																			.	.		0.597	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		A	42196221	G	A	42196221	2	1	153	1	0	0	0	0	0	0	0	1	16490	1335	47	3		3	TRERF1	6	42196221	Silent	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	8191913	42196221	128918846	37	23500										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5427597	5427597	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggtgggcgcaggctcgggttTcatggtgcccaaacctccaa	14	12	1	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr7:5427597T>C	ENST00000430969.1	-	5	2206	c.1858A>G	c.(1858-1860)Aaa>Gaa	p.K620E	TNRC18_ENST00000399537.4_Missense_Mutation_p.K620E	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	620							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GGCTCGGGTTTCATGGTGCCC	0.692																																					p.K620E		Atlas-SNP	.											.	TNRC18	311	.	0			c.A1858G						.						6	10	9					7																	5427597		1980	4099	6079	SO:0001583	missense	84629	exon5			CGGGTTTCATGGT	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.1858A>G	chr7.hg19:g.5427597T>C	ENSP00000395538:p.Lys620Glu	140.0	0.0		105.0	28.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	t	13.04	2.118578	0.37436	.	.	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000413081	T;T	0.22945	1.94;1.93	4.83	4.83	0.62350	.	.	.	.	.	T	0.46541	0.1398	M	0.73962	2.25	0.31015	N	0.71881	D	0.67145	0.996	P	0.57620	0.824	T	0.56842	-0.7912	9	0.87932	D	0	.	14.419	0.67171	0.0:0.0:0.0:1.0	.	620	O15417	TNC18_HUMAN	E	620;620;22	ENSP00000382452:K620E;ENSP00000395538:K620E	ENSP00000382452:K620E	K	-	1	0	TNRC18	5394123	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	4.058000	0.57463	1.804000	0.52760	0.454000	0.30748	AAA	.	.		0.692	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	5427597	T	C	5427597	3	2	153	1	0	0	0	0	1	0	0	0	16354	1792	62	2	7152	2	TNRC18	7	5427597	Missense_Mutation	SNP	T	TCGA-DD-AACB-01A-11D-A40R-10		5427597	153711066	38	23501										
ANK1	286	hgsc.bcm.edu	37	chr8	41542087	41542087	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	atctgggagggtgacagcgaGtagtcgcggtcggtgtgccg	19	8	1	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr8:41542087G>A	ENST00000347528.4	-	37	4595	c.4512C>T	c.(4510-4512)taC>taT	p.Y1504Y	ANK1_ENST00000352337.4_Silent_p.Y1504Y|ANK1_ENST00000265709.8_Silent_p.Y1545Y|ANK1_ENST00000289734.7_Silent_p.Y1504Y|ANK1_ENST00000379758.2_Silent_p.Y1504Y|ANK1_ENST00000396942.1_Silent_p.Y1504Y|ANK1_ENST00000396945.1_Silent_p.Y1504Y	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1504	55 kDa regulatory domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GTGACAGCGAGTAGTCGCGGT	0.612																																					p.Y1545Y		Atlas-SNP	.											.	ANK1	497	.	0			c.C4635T						.						84	64	71					8																	41542087		2203	4300	6503	SO:0001819	synonymous_variant	286	exon38			CAGCGAGTAGTCG	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.4512C>T	chr8.hg19:g.41542087G>A		46.0	0.0		73.0	48.0	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	hg19	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	G	3.508	-0.100308	0.06967	.	.	ENSG00000029534	ENST00000520299	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	T	0.59932	0.2230	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58457	-0.7633	4	.	.	.	.	8.7271	0.34476	0.0782:0.0:0.7711:0.1507	.	.	.	.	F	826	.	.	L	-	1	0	ANK1	41661244	0.995000	0.38212	1.000000	0.80357	0.315000	0.28087	0.523000	0.22925	2.572000	0.86782	0.655000	0.94253	CTC	.	.		0.612	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		A	41542087	G	A	41542087	2	1	153	1	0	0	0	0	0	0	0	1	620	1024	36	3		3	ANK1	8	41542087	Silent	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10		41542087	104821935	39	23502										
XKR9	389668	hgsc.bcm.edu	37	chr8	71646299	71646299	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	aaaaacaacacccagttttgTacttgtataagtatggaatt	6	6	0	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr8:71646299T>A	ENST00000408926.3	+	5	1296	c.762T>A	c.(760-762)tgT>tgA	p.C254*	XKR9_ENST00000520030.1_Nonsense_Mutation_p.C254*|XKR9_ENST00000520273.1_Intron	NM_001011720.1	NP_001011720.1	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related family, member 9	254						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)			CCCAGTTTTGTACTTGTATAA	0.279																																					p.C254X		Atlas-SNP	.											.	XKR9	43	.	0			c.T762A						.						121	120	120					8																	71646299		2201	4297	6498	SO:0001587	stop_gained	389668	exon5			GTTTTGTACTTGT	AY534247	CCDS34905.1	8q13.3	2006-01-12	2006-01-12			ENSG00000221947			20937	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 9"				Standard	NM_001287258		Approved		uc003xyq.3	Q5GH70		ENST00000408926.3:c.762T>A	chr8.hg19:g.71646299T>A	ENSP00000386141:p.Cys254*	107.0	0.0		228.0	20.0	NM_001011720	B2RNS9|B9EH74	Nonsense_Mutation	SNP	ENST00000408926.3	hg19	CCDS34905.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.938285	0.92526	.	.	ENSG00000221947	ENST00000408926;ENST00000520030	.	.	.	4.89	2.45	0.29901	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	-19.1733	7.8315	0.29344	0.0:0.3387:0.0:0.6613	.	.	.	.	X	254	.	ENSP00000386141:C254X	C	+	3	2	XKR9	71808853	1.000000	0.71417	0.978000	0.43139	0.107000	0.19398	1.193000	0.32162	0.340000	0.23745	0.460000	0.39030	TGT	.	.		0.279	XKR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378752.1	NM_001011720		A	71646299	T	A	71646299	4	1	153	1	0	0	0	0	0	1	0	0	17453	1644	57	4	772	4	XKR9	8	71646299	Nonsense_Mutation	SNP	T	TCGA-DD-AACB-01A-11D-A40R-10	30104212	71646299	74717723	40	23503										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113317133	113317133	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gataaaggaattgatgcttgGacatgtaacaactatacaaa	8	5	0	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr8:113317133G>T	ENST00000297405.5	-	52	8327	c.8083C>A	c.(8083-8085)Cca>Aca	p.P2695T	CSMD3_ENST00000352409.3_Missense_Mutation_p.P2625T|CSMD3_ENST00000455883.2_Intron|CSMD3_ENST00000343508.3_Missense_Mutation_p.P2655T	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2695	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTGATGCTTGGACATGTAACA	0.378										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.P2695T		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C8083A						.						64	54	58					8																	113317133		2203	4300	6503	SO:0001583	missense	114788	exon52			TGCTTGGACATGT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8083C>A	chr8.hg19:g.113317133G>T	ENSP00000297405:p.Pro2695Thr	124.0	0.0		188.0	25.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111483	0.77210	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000352409	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.18	5.18	0.71444	Complement control module (3);Sushi/SCR/CCP (3);	0.083622	0.48286	D	0.000195	D	0.83972	0.5370	M	0.87900	2.915	0.54753	D	0.999984	P;D	0.76494	0.923;0.999	P;D	0.74023	0.811;0.982	D	0.83958	0.0320	10	0.36615	T	0.2	.	19.0673	0.93116	0.0:0.0:1.0:0.0	.	2695;2655	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	T	2655;2695;1965;2625	ENSP00000345799:P2655T;ENSP00000297405:P2695T;ENSP00000341558:P1965T;ENSP00000343124:P2625T	ENSP00000297405:P2695T	P	-	1	0	CSMD3	113386309	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.923000	0.87546	2.547000	0.85894	0.655000	0.94253	CCA	.	.		0.378	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113317133	G	T	113317133	3	4	153	1	0	0	0	0	1	0	0	0	3948	1174	41	3	3120	3	CSMD3	8	113317133	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	41670834	113317133	33046889	41	23504										
DMRT1	1761	hgsc.bcm.edu	37	chr9	842074	842074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gctgcccaagtgcgcacgctGcaggaaccacggctacgcct	12	16	0	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr9:842074G>A	ENST00000382276.3	+	1	385	c.236G>A	c.(235-237)tGc>tAc	p.C79Y	DMRT1_ENST00000569227.1_5'Flank	NM_021951.2	NP_068770.2	Q9Y5R6	DMRT1_HUMAN	doublesex and mab-3 related transcription factor 1	79					cell morphogenesis (GO:0000902)|germ cell migration (GO:0008354)|intracellular signal transduction (GO:0035556)|male germ cell proliferation (GO:0002176)|male sex determination (GO:0030238)|male sex differentiation (GO:0046661)|negative regulation of meiosis (GO:0045835)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oocyte development (GO:0048599)|positive regulation of male gonad development (GO:2000020)|positive regulation of meiosis I (GO:0060903)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of nodal signaling pathway (GO:1900107)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(2)|lung(10)|ovary(1)	13		all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232)		Lung(218;0.037)		TGCGCACGCTGCAGGAACCAC	0.701																																					p.C79Y		Atlas-SNP	.											.	DMRT1	38	.	0			c.G236A						.						5	5	5					9																	842074		2065	4086	6151	SO:0001583	missense	1761	exon1			CACGCTGCAGGAA	AF130728	CCDS6442.1	9p24.3	2014-01-21			ENSG00000137090	ENSG00000137090			2934	protein-coding gene	gene with protein product	"DM domain expressed in testis 1"	602424				9490411, 10332030	Standard	XM_006716732		Approved	DMT1, CT154	uc003zgv.3	Q9Y5R6	OTTHUMG00000019435	ENST00000382276.3:c.236G>A	chr9.hg19:g.842074G>A	ENSP00000371711:p.Cys79Tyr	69.0	0.0		83.0	42.0	NM_021951	B2R913|Q6T1H8|Q6T1H9|Q8IW77	Missense_Mutation	SNP	ENST00000382276.3	hg19	CCDS6442.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.631948	0.87660	.	.	ENSG00000137090	ENST00000451501;ENST00000382276	D	0.82984	-1.67	4.05	4.05	0.47172	DM DNA-binding (6);	0.000000	0.85682	D	0.000000	D	0.94699	0.8290	H	0.98370	4.215	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.998;1.0	D	0.97211	0.9871	10	0.87932	D	0	.	16.5834	0.84720	0.0:0.0:1.0:0.0	.	79;79	Q9Y5R6;Q6T1H9	DMRT1_HUMAN;.	Y	79	ENSP00000371711:C79Y	ENSP00000371711:C79Y	C	+	2	0	DMRT1	832074	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.911000	0.92721	1.960000	0.56953	0.561000	0.74099	TGC	.	.		0.701	DMRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051489.2	NM_021951		A	842074	G	A	842074	3	1	153	1	0	0	0	0	1	0	0	0	4587	1319	46	3	238	3	DMRT1	9	842074	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10		842074	140371357	42	23505										
ELAVL2	1993	hgsc.bcm.edu	37	chr9	23762193	23762193	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggtggttggaccattggctgTgttattgcaagttggcccat	14	7	0	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr9:23762193T>C	ENST00000397312.2	-	2	314	c.40A>G	c.(40-42)Aca>Gca	p.T14A	ELAVL2_ENST00000544538.1_Missense_Mutation_p.T14A|ELAVL2_ENST00000462649.1_5'Flank|ELAVL2_ENST00000380110.4_Missense_Mutation_p.T43A|ELAVL2_ENST00000223951.6_Missense_Mutation_p.T14A|ELAVL2_ENST00000380117.1_Missense_Mutation_p.T14A	NM_004432.3	NP_004423.2	Q12926	ELAV2_HUMAN	ELAV like neuron-specific RNA binding protein 2	14					regulation of transcription, DNA-templated (GO:0006355)		mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		CCATTGGCTGTGTTATTGCAA	0.413																																					p.T14A		Atlas-SNP	.											.	ELAVL2	80	.	0			c.A40G						.						309	284	292					9																	23762193		2203	4299	6502	SO:0001583	missense	1993	exon2			TGGCTGTGTTATT	BC030692	CCDS6515.1, CCDS55298.1	9p21	2013-10-03	2013-10-03		ENSG00000107105	ENSG00000107105		"RNA binding motif (RRM) containing"	3313	protein-coding gene	gene with protein product	"Hu antigen B"	601673	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2", "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"			8812435	Standard	NM_004432		Approved	HuB, HEL-N1	uc003zpu.3	Q12926	OTTHUMG00000019700	ENST00000397312.2:c.40A>G	chr9.hg19:g.23762193T>C	ENSP00000380479:p.Thr14Ala	143.0	0.0		137.0	45.0	NM_001171195	D3DRK3|Q13235|Q59G15|Q8NEM4|Q9H1Q8	Missense_Mutation	SNP	ENST00000397312.2	hg19	CCDS6515.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.326561	0.24080	.	.	ENSG00000107105	ENST00000223951;ENST00000397312;ENST00000544538;ENST00000380110;ENST00000380117;ENST00000359598;ENST00000440102	T;T;T;T;T	0.13657	2.57;2.97;2.97;2.97;2.91	5.92	5.92	0.95590	.	0.053959	0.64402	D	0.000001	T	0.09069	0.0224	N	0.12182	0.205	0.47994	D	0.999562	B;B	0.09022	0.0;0.002	B;B	0.09377	0.001;0.004	T	0.30297	-0.9983	10	0.17832	T	0.49	.	16.371	0.83361	0.0:0.0:0.0:1.0	.	14;14	Q12926;Q12926-2	ELAV2_HUMAN;.	A	14;14;14;14;14;42;14	ENSP00000223951:T14A;ENSP00000380479:T14A;ENSP00000440998:T14A;ENSP00000369460:T14A;ENSP00000412602:T14A	ENSP00000223951:T14A	T	-	1	0	ELAVL2	23752193	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.704000	0.61831	2.267000	0.75376	0.477000	0.44152	ACA	.	.		0.413	ELAVL2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051943.2	NM_004432		C	23762193	T	C	23762193	3	2	153	1	0	0	0	0	1	0	0	0	5052	1696	59	2	1063	2	ELAVL2	9	23762193	Missense_Mutation	SNP	T	TCGA-DD-AACB-01A-11D-A40R-10	22920119	23762193	117451238	43	23506										
HINT2	84681	hgsc.bcm.edu	37	chr9	35813496	35813496	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggaatgggcttcttaggaatGaccaggaagtgcacaggagc	15	7	1	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr9:35813496G>T	ENST00000259667.5	-	3	314	c.273C>A	c.(271-273)gtC>gtA	p.V91V	HINT2_ENST00000474908.1_5'UTR|SPAG8_ENST00000484764.1_5'Flank|SPAG8_ENST00000340291.2_5'Flank|SPAG8_ENST00000396638.2_5'Flank|AL133410.1_ENST00000582432.1_RNA|SPAG8_ENST00000479751.1_5'Flank|TMEM8B_ENST00000377996.1_5'Flank	NM_032593.2	NP_115982.1	Q9BX68	HINT2_HUMAN	histidine triad nucleotide binding protein 2	91	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.				apoptotic process (GO:0006915)|steroid biosynthetic process (GO:0006694)	mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)			NS(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	7	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)			TCTTAGGAATGACCAGGAAGT	0.582											OREG0019179	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V91V	GBM(185;1694 2122 5473 25431 37228)	Atlas-SNP	.											.	HINT2	15	.	0			c.C273A						.						57	55	56					9																	35813496		2203	4300	6503	SO:0001819	synonymous_variant	84681	exon3			AGGAATGACCAGG	AY033094	CCDS6594.1	9p11.2	2005-12-20			ENSG00000137133	ENSG00000137133			18344	protein-coding gene	gene with protein product		609997					Standard	NM_032593		Approved		uc003zyh.3	Q9BX68	OTTHUMG00000019886	ENST00000259667.5:c.273C>A	chr9.hg19:g.35813496G>T		104.0	0.0	858	83.0	24.0	NM_032593	Q5TCW3	Silent	SNP	ENST00000259667.5	hg19	CCDS6594.1																																																																																			.	.		0.582	HINT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052390.1	NM_032593		T	35813496	G	T	35813496	2	4	153	1	0	0	0	0	0	0	0	1	7121	1277	45	3		3	HINT2	9	35813496	Silent	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	12051303	35813496	105399935	44	23507										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73151320	73151320	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tgtccgcaattgcttgagggGcattgacacaccttgtgtca	11	10	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr9:73151320G>A	ENST00000377110.3	-	25	4916	c.4673C>T	c.(4672-4674)gCc>gTc	p.A1558V	TRPM3_ENST00000396285.1_Missense_Mutation_p.A1417V|TRPM3_ENST00000423814.3_Missense_Mutation_p.A1585V|TRPM3_ENST00000360823.2_Missense_Mutation_p.A1420V|TRPM3_ENST00000396292.4_Missense_Mutation_p.A1430V|TRPM3_ENST00000377105.1_Missense_Mutation_p.A1417V|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396280.5_Missense_Mutation_p.A1407V|TRPM3_ENST00000408909.2_Missense_Mutation_p.A1417V|TRPM3_ENST00000358082.3_Missense_Mutation_p.A1420V|TRPM3_ENST00000377106.1_Missense_Mutation_p.A1430V|TRPM3_ENST00000357533.2_Missense_Mutation_p.A1562V			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1583					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TGCTTGAGGGGCATTGACACA	0.483																																					p.A1558V		Atlas-SNP	.											.	TRPM3	700	.	0			c.C4673T						.						97	90	93					9																	73151320		2203	4300	6503	SO:0001583	missense	80036	exon25			TGAGGGGCATTGA	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.4673C>T	chr9.hg19:g.73151320G>A	ENSP00000366314:p.Ala1558Val	113.0	0.0		88.0	56.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377110.3	hg19	CCDS43835.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.069013	0.55539	.	.	ENSG00000083067	ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	T;T;T;T;T;T;T;T;T;T	0.56776	0.53;0.47;0.47;0.44;0.53;0.44;0.45;0.47;0.47;0.53	5.87	5.87	0.94306	.	0.057558	0.64402	D	0.000001	T	0.48447	0.1500	L	0.27053	0.805	0.48571	D	0.999677	B;B;B;B;B;B;B	0.33612	0.419;0.026;0.19;0.295;0.288;0.253;0.19	B;B;B;B;B;B;B	0.38500	0.275;0.014;0.068;0.068;0.143;0.059;0.068	T	0.39231	-0.9624	10	0.38643	T	0.18	-20.6562	20.2181	0.98305	0.0:0.0:1.0:0.0	.	1558;1548;1562;1420;1417;1530;1417	Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.;.;.;.;.;.;.	V	1558;1430;1420;1417;1562;1417;1417;1430;1420;1585	ENSP00000366314:A1558V;ENSP00000366310:A1430V;ENSP00000354066:A1420V;ENSP00000366309:A1417V;ENSP00000350140:A1562V;ENSP00000386127:A1417V;ENSP00000379581:A1417V;ENSP00000379587:A1430V;ENSP00000350791:A1420V;ENSP00000389542:A1585V	ENSP00000350140:A1562V	A	-	2	0	TRPM3	72341140	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.230000	0.95299	2.785000	0.95823	0.655000	0.94253	GCC	.	.		0.483	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945		A	73151320	G	A	73151320	3	1	153	1	0	0	0	0	1	0	0	0	16602	1203	42	3	454	3	TRPM3	9	73151320	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	37337824	73151320	68062111	45	23508										
AGPAT2	10555	hgsc.bcm.edu	37	chr9	139568320	139568320	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggtgtccacgagcgcagggaCgtccgccgcagtgaggccgc	17	14	0	1	rs11545228		TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr9:139568320C>A	ENST00000371696.2	-	6	786	c.721G>T	c.(721-723)Gtc>Ttc	p.V241F	AGPAT2_ENST00000538402.1_Missense_Mutation_p.V241F|AGPAT2_ENST00000371694.3_Missense_Mutation_p.V209F	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	241					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|epidermis development (GO:0008544)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)	6	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		AGCGCAGGGACGTCCGCCGCA	0.667																																					p.V241F		Atlas-SNP	.											.	AGPAT2	17	.	0			c.G721T						.						40	40	40					9																	139568320		2192	4295	6487	SO:0001583	missense	10555	exon6			CAGGGACGTCCGC	AF000237	CCDS7003.1, CCDS35181.1	9q34.3	2013-02-05	2013-02-05		ENSG00000169692	ENSG00000169692	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	325	protein-coding gene	gene with protein product	"LPAAT-beta", "lysophosphatidic acid acyltransferase, beta"	603100	"Berardinelli-Seip congenital lipodystrophy", "1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)"	BSCL		9242711, 9212163	Standard	NM_006412		Approved		uc004cii.1	O15120	OTTHUMG00000020936	ENST00000371696.2:c.721G>T	chr9.hg19:g.139568320C>A	ENSP00000360761:p.Val241Phe	127.0	0.0		83.0	54.0	NM_006412	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Missense_Mutation	SNP	ENST00000371696.2	hg19	CCDS7003.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.242802	0.39598	.	.	ENSG00000169692	ENST00000371694;ENST00000371696;ENST00000538402	D;D;D	0.93953	-3.32;-3.32;-3.32	5.23	0.704	0.18121	.	0.395578	0.24033	N	0.042179	D	0.96116	0.8734	M	0.87328	2.875	0.41433	D	0.987874	D;D	0.89917	1.0;0.999	D;D	0.78314	0.991;0.965	D	0.94909	0.8063	10	0.72032	D	0.01	-40.9283	9.6943	0.40147	0.0:0.5952:0.0:0.4048	rs11545228;rs17845113;rs17857906	209;241	O15120-2;O15120	.;PLCB_HUMAN	F	209;241;241	ENSP00000360759:V209F;ENSP00000360761:V241F;ENSP00000438919:V241F	ENSP00000360759:V209F	V	-	1	0	AGPAT2	138688141	0.988000	0.35896	0.011000	0.14972	0.003000	0.03518	0.820000	0.27323	0.220000	0.20860	-0.150000	0.13652	GTC	.	C|1.000		0.667	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412		A	139568320	C	A	139568320	3	1	153	1	0	0	0	0	1	0	0	0	387	536	19	1	119	1	AGPAT2	9	139568320	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	66417000	139568320	1645111	46	23509										
ADARB2	105	hgsc.bcm.edu	37	chr10	1405325	1405325	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gcggcctgaccccgggccagCttcttgctgcgccccgagcc	13	19	1	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr10:1405325C>A	ENST00000381312.1	-	3	1300	c.975G>T	c.(973-975)aaG>aaT	p.K325N	RP11-398B16.2_ENST00000432987.1_RNA	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	325	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CCCGGGCCAGCTTCTTGCTGC	0.726																																					p.K325N		Atlas-SNP	.											.	ADARB2	95	.	0			c.G975T						.						6	7	7					10																	1405325		2072	4107	6179	SO:0001583	missense	105	exon3			GGCCAGCTTCTTG	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.975G>T	chr10.hg19:g.1405325C>A	ENSP00000370713:p.Lys325Asn	25.0	0.0		29.0	11.0	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	hg19	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.662592	0.88251	.	.	ENSG00000185736	ENST00000381312	D	0.86230	-2.09	5.24	5.24	0.73138	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.096500	0.64402	D	0.000001	D	0.96074	0.8721	H	0.97103	3.94	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97510	1.0066	10	0.87932	D	0	-43.8987	18.8514	0.92232	0.0:1.0:0.0:0.0	.	325	Q9NS39	RED2_HUMAN	N	325	ENSP00000370713:K325N	ENSP00000370713:K325N	K	-	3	2	ADARB2	1395325	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	3.891000	0.56227	2.445000	0.82738	0.561000	0.74099	AAG	.	.		0.726	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		A	1405325	C	A	1405325	3	1	153	1	0	0	0	0	1	0	0	0	283	796	28	3	1276	3	ADARB2	10	1405325	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10		1405325	134129422	47	23510										
PFKFB3	5209	hgsc.bcm.edu	37	chr10	6262815	6262815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gggcgactcaggcctgtccaGccggggcaagaaggtgcggg	19	11	1	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr10:6262815G>A	ENST00000379775.4	+	8	1148	c.818G>A	c.(817-819)aGc>aAc	p.S273N	PFKFB3_ENST00000317350.4_Missense_Mutation_p.S273N|PFKFB3_ENST00000379789.4_Missense_Mutation_p.S253N|PFKFB3_ENST00000379785.1_Missense_Mutation_p.S273N|PFKFB3_ENST00000536985.1_3'UTR|PFKFB3_ENST00000540253.1_Missense_Mutation_p.S287N|PFKFB3_ENST00000360521.2_Missense_Mutation_p.S273N|PFKFB3_ENST00000379782.3_Missense_Mutation_p.S273N	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	273	Fructose-2,6-bisphosphatase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						GGCCTGTCCAGCCGGGGCAAG	0.662																																					p.S273N		Atlas-SNP	.											.	PFKFB3	82	.	0			c.G818A						.						38	42	41					10																	6262815		2203	4299	6502	SO:0001583	missense	5209	exon8			TGTCCAGCCGGGG		CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.818G>A	chr10.hg19:g.6262815G>A	ENSP00000369100:p.Ser273Asn	44.0	0.0		50.0	8.0	NM_004566	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Missense_Mutation	SNP	ENST00000379775.4	hg19	CCDS7078.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.254403	0.39896	.	.	ENSG00000170525	ENST00000379789;ENST00000379784;ENST00000540253;ENST00000317350;ENST00000379785;ENST00000379782;ENST00000360521;ENST00000379775;ENST00000358499	T;T;T;T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59;-0.59;-0.59;-0.59	5.93	-3.76	0.04359	Histidine phosphatase superfamily, clade-1 (2);	1.102000	0.06548	N	0.744417	T	0.59142	0.2172	L	0.56280	1.765	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.0	T	0.44802	-0.9304	10	0.35671	T	0.21	0.0404	4.3813	0.11295	0.0924:0.1686:0.1984:0.5407	.	287;273;273;253	B7Z955;Q16875-2;Q16875;Q5VX15	.;.;F263_HUMAN;.	N	253;34;287;273;273;273;273;273;273	ENSP00000369115:S253N;ENSP00000446384:S287N;ENSP00000369105:S273N;ENSP00000369111:S273N;ENSP00000369108:S273N;ENSP00000353712:S273N;ENSP00000369100:S273N	ENSP00000369105:S273N	S	+	2	0	PFKFB3	6302821	0.000000	0.05858	0.709000	0.30452	0.979000	0.70002	-0.070000	0.11523	-0.429000	0.07329	0.561000	0.74099	AGC	.	.		0.662	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1			A	6262815	G	A	6262815	3	1	153	1	0	0	0	0	1	0	0	0	11771	971	34	3	868	3	PFKFB3	10	6262815	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	4857490	6262815	129271932	48	23511										
PSAP	5660	hgsc.bcm.edu	37	chr10	73594188	73594188	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	cactgccccgcagtcggacgCcgtcttcacattctggcacc	9	18	3	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr10:73594188C>T	ENST00000394936.3	-	2	262	c.115G>A	c.(115-117)Gcg>Acg	p.A39T	PSAP_ENST00000394934.1_Missense_Mutation_p.A39T			P07602	SAP_HUMAN	prosaposin	39	Saposin A-type 1. {ECO:0000255|PROSITE- ProRule:PRU00414}.				blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						CAGTCGGACGCCGTCTTCACA	0.607																																					p.A39T		Atlas-SNP	.											.	PSAP	43	.	0			c.G115A						.						50	41	44					10																	73594188		2203	4300	6503	SO:0001583	missense	5660	exon2			CGGACGCCGTCTT	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"Endogenous ligands"	9498	protein-coding gene	gene with protein product	"variant Gaucher disease and variant metachromatic leukodystrophy"	176801	"sphingolipid activator protein-1"	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.115G>A	chr10.hg19:g.73594188C>T	ENSP00000378394:p.Ala39Thr	65.0	0.0		89.0	36.0	NM_001042466	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Missense_Mutation	SNP	ENST00000394936.3	hg19	CCDS7311.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.306115	0.81247	.	.	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000394929;ENST00000404083	T;T	0.80033	-1.33;-1.33	5.67	5.67	0.87782	Saposin type A (3);	0.047988	0.85682	D	0.000000	D	0.91327	0.7265	M	0.86805	2.84	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.92312	0.5858	10	0.87932	D	0	3.834	18.5336	0.91001	0.0:1.0:0.0:0.0	.	39	P07602	SAP_HUMAN	T	39;39;39;39;39;42	ENSP00000378394:A39T;ENSP00000378392:A39T	ENSP00000350063:A39T	A	-	1	0	PSAP	73264194	1.000000	0.71417	0.873000	0.34254	0.253000	0.25986	6.364000	0.73086	2.680000	0.91292	0.563000	0.77884	GCG	.	.		0.607	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778		T	73594188	C	T	73594188	3	4	153	1	0	0	0	0	1	0	0	0	12655	739	26	3	1527	3	PSAP	10	73594188	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	67331373	73594188	61940559	49	23512										
USP54	159195	hgsc.bcm.edu	37	chr10	75296083	75296083	+	Frame_Shift_Del	DEL	G	G	-													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	actggaactcagcttggggaGgcaggtcctgggtggaaact							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr10:75296083delG	ENST00000339859.4	-	10	1188	c.1088delC	c.(1087-1089)cctfs	p.P364fs	USP54_ENST00000408019.1_Frame_Shift_Del_p.P364fs|USP54_ENST00000428547.1_Frame_Shift_Del_p.P214fs|USP54_ENST00000497106.1_5'UTR|USP54_ENST00000394811.2_5'UTR|USP54_ENST00000319786.7_Frame_Shift_Del_p.P364fs			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	364					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					AGCTTGGGGAGGCAGGTCCTG	0.552																																					p.P363fs	Colon(195;880 2046 8854 25025 38456)	Atlas-INDEL	.											.	USP54	178	.	0			c.1089delT						.						88	94	92					10																	75296083		1990	4164	6154	SO:0001589	frameshift_variant	159195	exon9			.	AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"Ubiquitin-specific peptidases"	23513	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 29", "ubiquitin specific protease 54"	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.1088delC	chr10.hg19:g.75296083delG	ENSP00000345216:p.Pro364fs	113.0	0.0		107.0	19.0	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Frame_Shift_Del	DEL	ENST00000339859.4	hg19	CCDS7329.2																																																																																			.	.		0.552	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		-	75296083	G	-	75296083	7	5	153	1	0	1	0	1	0	0	0	0	17100	1000	35	0	4022	0	USP54	10	75296083	Frame_Shift_Del	DEL	G	TCGA-DD-AACB-01A-11D-A40R-10	1701895	75296083	60238664	50	23513										
RPLP2	6181	hgsc.bcm.edu	37	chr11	812569	812569	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gccagtgtacctgctggtggGgctgtagccgtctctgctgc	15	12	1	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr11:812569G>T	ENST00000321153.4	+	4	601	c.207G>T	c.(205-207)ggG>ggT	p.G69G	RPLP2_ENST00000530797.1_Silent_p.G69G|RPLP2_ENST00000532004.1_3'UTR|SNORA52_ENST00000362915.1_RNA	NM_001004.3	NP_000995.1	P05387	RLA2_HUMAN	ribosomal protein, large, P2	69					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			lung(1)	1		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGCTGGTGGGGCTGTAGCCG	0.632																																					p.G69G		Atlas-SNP	.											.	RPLP2	2	.	0			c.G207T						.						59	48	52					11																	812569		2203	4299	6502	SO:0001819	synonymous_variant	6181	exon4			TGGTGGGGCTGTA	M17887	CCDS7717.1	11p15.5	2011-07-29			ENSG00000177600	ENSG00000177600		"L ribosomal proteins"	10377	protein-coding gene	gene with protein product	"60S acidic ribosomal protein P2", "acidic ribosomal phosphoprotein P2"	180530		D11S2243E		3323886	Standard	NM_001004		Approved	P2, RPP2, MGC71408, LP2	uc001lrq.1	P05387	OTTHUMG00000133317	ENST00000321153.4:c.207G>T	chr11.hg19:g.812569G>T		43.0	0.0		32.0	10.0	NM_001004	Q6FG96	Silent	SNP	ENST00000321153.4	hg19	CCDS7717.1	.	.	.	.	.	.	.	.	.	.	G	7.661	0.684927	0.14973	.	.	ENSG00000177600	ENST00000530398	.	.	.	4.82	-0.824	0.10812	.	0.000000	0.85682	D	0.000000	T	0.54447	0.1859	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51411	-0.8709	6	0.59425	D	0.04	-12.9596	3.7639	0.08615	0.3469:0.0:0.1896:0.4635	.	.	.	.	V	46	.	ENSP00000433443:G46V	G	+	2	0	RPLP2	802569	0.772000	0.28567	0.994000	0.49952	0.704000	0.40688	-0.188000	0.09642	0.163000	0.19507	0.561000	0.74099	GGG	.	.		0.632	RPLP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257115.2	NM_001004		T	812569	G	T	812569	2	4	153	1	0	0	0	0	0	0	0	1	13621	1219	43	3		3	RPLP2	11	812569	Silent	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10		812569	134193947	51	23514										
FOLH1	2346	hgsc.bcm.edu	37	chr11	49214430	49214430	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ctggaggaggtggttcaaatAatgatgtgttgaaaatctag	13	3	2	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr11:49214430A>G	ENST00000256999.2	-	4	688	c.428T>C	c.(427-429)tTa>tCa	p.L143S	FOLH1_ENST00000343844.4_5'UTR|FOLH1_ENST00000356696.3_Missense_Mutation_p.L143S|FOLH1_ENST00000340334.7_Missense_Mutation_p.L128S|FOLH1_ENST00000533034.1_Missense_Mutation_p.L128S	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	143					folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TGGTTCAAATAATGATGTGTT	0.313																																					p.L143S		Atlas-SNP	.											.	FOLH1	141	.	0			c.T428C						.						62	69	67					11																	49214430		2201	4295	6496	SO:0001583	missense	2346	exon4			TCAAATAATGATG	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"glutamate carboxylase II", "glutamate carboxypeptidase II"	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.428T>C	chr11.hg19:g.49214430A>G	ENSP00000256999:p.Leu143Ser	191.0	0.0		143.0	24.0	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	hg19	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	A	10.49	1.364573	0.24684	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	3.45	3.45	0.39498	.	0.000000	0.38720	N	0.001599	T	0.47040	0.1424	M	0.64404	1.975	0.80722	D	1	B;B;B;B;B	0.23128	0.065;0.056;0.004;0.03;0.08	B;B;B;B;B	0.26770	0.073;0.029;0.005;0.059;0.03	T	0.38585	-0.9654	10	0.22706	T	0.39	.	9.9921	0.41877	1.0:0.0:0.0:0.0	.	128;128;128;143;143	Q04609-9;Q04609-7;A4UU13;Q04609-8;Q04609	.;.;.;.;FOLH1_HUMAN	S	143;143;128;128;143	ENSP00000256999:L143S;ENSP00000349129:L143S;ENSP00000344131:L128S;ENSP00000431463:L128S	ENSP00000256999:L143S	L	-	2	0	FOLH1	49171006	0.997000	0.39634	0.983000	0.44433	0.980000	0.70556	6.246000	0.72405	1.454000	0.47793	0.329000	0.21502	TTA	.	.		0.313	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476		G	49214430	A	G	49214430	3	3	153	1	0	0	0	0	1	0	0	0	5987	372	13	2	1888	2	FOLH1	11	49214430	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	48401861	49214430	85792086	52	23515										
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57080662	57080662	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gcggcctcactggcttcagtGatgggggagggaggcgggga	21	8	2	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr11:57080662G>A	ENST00000532437.1	-	4	1811	c.1500C>T	c.(1498-1500)atC>atT	p.I500I	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Silent_p.I500I			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	500	Acidic.|Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TGGCTTCAGTGATGGGGGAGG	0.647																																					p.I500I		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.C1500T						.						17	20	19					11																	57080662		1993	4010	6003	SO:0001819	synonymous_variant	85456	exon5			TTCAGTGATGGGG	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.1500C>T	chr11.hg19:g.57080662G>A		73.0	0.0		52.0	10.0	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	hg19	CCDS7951.1																																																																																			.	.		0.647	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		A	57080662	G	A	57080662	2	1	153	1	0	0	0	0	0	0	0	1	16335	1280	45	3		3	TNKS1BP1	11	57080662	Silent	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	7866232	57080662	77925854	53	23516										
MS4A6E	245802	hgsc.bcm.edu	37	chr11	60107405	60107405	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tagctgtgctcactgctgtgCtgcagtggaaacagactgtc	12	10	1	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr11:60107405C>T	ENST00000300182.4	+	3	486	c.421C>T	c.(421-423)Ctg>Ttg	p.L141L		NM_139249.2	NP_640342.1	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member 6E	141						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(9)|stomach(1)	13						CACTGCTGTGCTGCAGTGGAA	0.473																																					p.L141L		Atlas-SNP	.											.	MS4A6E	22	.	0			c.C421T						.						231	211	218					11																	60107405		2203	4300	6503	SO:0001819	synonymous_variant	245802	exon3			GCTGTGCTGCAGT	AF354931	CCDS7984.1	11q12	2008-03-25				ENSG00000166926			14285	protein-coding gene	gene with protein product		608402				11486273	Standard	NM_139249		Approved		uc001npd.3	Q96DS6		ENST00000300182.4:c.421C>T	chr11.hg19:g.60107405C>T		63.0	0.0		35.0	17.0	NM_139249	Q3MIL2|Q8NE56|Q96PG4|Q96PG5	Silent	SNP	ENST00000300182.4	hg19	CCDS7984.1																																																																																			.	.		0.473	MS4A6E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394296.1			T	60107405	C	T	60107405	2	4	153	1	0	0	0	0	0	0	0	1	9874	796	28	3		3	MS4A6E	11	60107405	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	3026743	60107405	74899111	54	23517										
C11orf20	25858	hgsc.bcm.edu	37	chr11	64070996	64070996	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	actcaatattgcgaagcacaTgccccatcgagcctactggg	9	13	1	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr11:64070996T>A	ENST00000328404.6	+	3	415	c.395T>A	c.(394-396)aTg>aAg	p.M132K	TEX40_ENST00000539943.1_Missense_Mutation_p.M90K|ESRRA_ENST00000405666.1_5'Flank|ESRRA_ENST00000406310.1_5'Flank|RP11-783K16.10_ENST00000539086.1_RNA|ESRRA_ENST00000000442.6_5'Flank	NM_001039496.1	NP_001034585.1	Q9NTU4	TEX40_HUMAN	testis expressed 40	132					cell differentiation (GO:0030154)|male meiosis (GO:0007140)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)											GCGAAGCACATGCCCCATCGA	0.557																																					p.M132K		Atlas-SNP	.											.	.	.	.	0			c.T395A						.						57	60	59					11																	64070996		2015	4175	6190	SO:0001583	missense	25858	exon3			AGCACATGCCCCA			11q13.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000219435	ENSG00000219435			19231	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 20"	C11orf20			Standard	NM_001039496		Approved	DKFZP566E164	uc009ypm.3	Q9NTU4	OTTHUMG00000167820	ENST00000328404.6:c.395T>A	chr11.hg19:g.64070996T>A	ENSP00000330877:p.Met132Lys	68.0	0.0		56.0	20.0	NM_001039496		Missense_Mutation	SNP	ENST00000328404.6	hg19		.	.	.	.	.	.	.	.	.	.	T	2.914	-0.224602	0.06061	.	.	ENSG00000219435	ENST00000328404;ENST00000539943	T;T	0.39997	1.06;1.05	3.39	-1.87	0.07737	.	.	.	.	.	T	0.14743	0.0356	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.31392	-0.9945	9	0.14252	T	0.57	1.6415	7.4432	0.27196	0.0:0.4305:0.0:0.5695	.	132	Q9NTU4	CK020_HUMAN	K	132;90	ENSP00000330877:M132K;ENSP00000443917:M90K	ENSP00000330877:M132K	M	+	2	0	C11orf20	63827572	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.330000	0.07925	-0.391000	0.07763	-1.044000	0.02363	ATG	.	.		0.557	TEX40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039496		A	64070996	T	A	64070996	3	1	153	1	0	0	0	0	1	0	0	0	1636	1464	51	4	405	4	C11orf20	11	64070996	Missense_Mutation	SNP	T	TCGA-DD-AACB-01A-11D-A40R-10	3963591	64070996	70935520	55	23518										
CNTN5	53942	hgsc.bcm.edu	37	chr11	100211261	100211261	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tcaaaactagagggaatgagTctttcgtcatcctaacagga	9	8	3	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr11:100211261T>C	ENST00000524871.1	+	22	3087	c.2797T>C	c.(2797-2799)Tct>Cct	p.S933P	CNTN5_ENST00000524560.1_3'UTR|CNTN5_ENST00000528682.1_Missense_Mutation_p.S933P|CNTN5_ENST00000418526.2_Missense_Mutation_p.S859P|CNTN5_ENST00000279463.3_Missense_Mutation_p.S933P	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	933	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		AGGGAATGAGTCTTTCGTCAT	0.413																																					p.S933P		Atlas-SNP	.											.	CNTN5	324	.	0			c.T2797C						.						94	94	94					11																	100211261		1926	4150	6076	SO:0001583	missense	53942	exon21			AATGAGTCTTTCG	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.2797T>C	chr11.hg19:g.100211261T>C	ENSP00000435637:p.Ser933Pro	171.0	0.0		141.0	43.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.906925	0.33628	.	.	ENSG00000149972	ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	5.18	5.18	0.71444	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.196018	0.46145	D	0.000317	T	0.36744	0.0978	N	0.17248	0.465	0.47009	D	0.999286	P;P	0.47191	0.664;0.891	B;P	0.45377	0.346;0.478	T	0.13764	-1.0497	9	.	.	.	.	14.1943	0.65659	0.0:0.0:0.0:1.0	.	859;933	O94779-2;O94779	.;CNTN5_HUMAN	P	933;933;859;933	ENSP00000436185:S933P;ENSP00000435637:S933P;ENSP00000393229:S859P;ENSP00000279463:S933P	.	S	+	1	0	CNTN5	99716471	1.000000	0.71417	0.965000	0.40720	0.006000	0.05464	4.146000	0.58072	1.952000	0.56665	0.482000	0.46254	TCT	.	.		0.413	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		C	100211261	T	C	100211261	3	2	153	1	0	0	0	0	1	0	0	0	3646	1667	58	2	2875	2	CNTN5	11	100211261	Missense_Mutation	SNP	T	TCGA-DD-AACB-01A-11D-A40R-10	36140265	100211261	34795255	56	23519										
KBTBD3	143879	hgsc.bcm.edu	37	chr11	105923599	105923600	+	Missense_Mutation	DNP	CA	CA	AT													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	aagcacatagattagaaaacCatgggtctctgtatttatta							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr11:105923599_105923600CA>AT	ENST00000526793.1	-	3	1975_1976	c.1816_1817TG>AT	c.(1816-1818)TGg>ATg	p.W606M	KBTBD3_ENST00000534815.1_Missense_Mutation_p.W527M|KBTBD3_ENST00000531837.1_Missense_Mutation_p.W606M	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	602										NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		ATTAGAAAACCATGGGTCTCTG	0.356																																					p.W606L|p.W606R		Atlas-SNP	.											.	KBTBD3	59	.	0			c.G1817T|c.T1816A						.																																			SO:0001583	missense	143879	exon3			GAAAACCATGGGT|AAAACCATGGGTC	AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"BTB/POZ domain containing"	22934	protein-coding gene	gene with protein product			"BTB and kelch domain containing 3"	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.1816_1817delinsAT	chr11.hg19:g.105923599_105923600delinsAT	ENSP00000436262:p.Trp606Met	134.0	0.0		122.0|123.0	31.0	NM_152433	Q6N066|Q86X38|Q96NK5	Missense_Mutation	SNP	ENST00000526793.1	hg19	CCDS8334.1																																																																																			.	.		0.356	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433		AT	105923600	CA	AT	105923599	3	1	153	1	0	0	0	0	1	0	0	0	8003	595	21	3	25	3	KBTBD3	11	105923599	Missense_Mutation	DNP	CA	TCGA-DD-AACB-01A-11D-A40R-10	5712338	105923599	29082917	57	23520										
MLL	4297	hgsc.bcm.edu	37	chr11	118374231	118374231	+	Missense_Mutation	SNP	C	C	A													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	agagtcaatccaaaaatgccCtgaaagaaagtagtcctgct							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr11:118374231C>A	ENST00000389506.5	+	27	7615	c.7615C>A	c.(7615-7617)Ctg>Atg	p.L2539M	KMT2A_ENST00000534358.1_Missense_Mutation_p.L2542M|KMT2A_ENST00000354520.4_Missense_Mutation_p.L2501M			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2539					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CAAAAATGCCCTGAAAGAAAG	0.458																																					p.L2542M		Atlas-SNP	.											.	MLL	548	.	0			c.C7624A						.						62	59	60					11																	118374231		2200	4296	6496	SO:0001583	missense	4297	exon27			AATGCCCTGAAAG	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.7615C>A	chr11.hg19:g.118374231C>A	ENSP00000374157:p.Leu2539Met	111.0	0.0		73.0	24.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	7.111	0.575989	0.13623	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.81739	-1.53;-1.53;-1.5	5.95	2.47	0.30058	.	0.369458	0.27019	N	0.021325	T	0.62588	0.2440	N	0.19112	0.55	0.09310	N	1	P;P	0.37955	0.612;0.612	B;B	0.33890	0.172;0.172	T	0.57207	-0.7851	10	0.59425	D	0.04	.	6.7541	0.23503	0.1272:0.6366:0.0:0.2363	.	2542;2539	E9PQG7;Q03164	.;MLL1_HUMAN	M	2542;2539;2501;1449	ENSP00000436786:L2542M;ENSP00000374157:L2539M;ENSP00000346516:L2501M	ENSP00000346516:L2501M	L	+	1	2	MLL	117879441	0.212000	0.23540	0.903000	0.35520	0.905000	0.53344	1.695000	0.37763	0.765000	0.33221	0.655000	0.94253	CTG	.	.		0.458	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118374231	C	A	118374231	3	1	153	1	0	0	0	0	1	0	0	0	9629	680	24	3	7721	3	MLL	11	118374231	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	12450632	118374231	16632285	58	23521	104	2								
MLL	4297	hgsc.bcm.edu	37	chr11	118374237	118374238	+	Frame_Shift_Ins	INS	-	-	TC													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	atccaaaaatgccctgaaagINSaaagtagtcctgcttcccct							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr11:118374237_118374238insTC	ENST00000389506.5	+	27	7621_7622	c.7621_7622insTC	c.(7621-7623)gaafs	p.E2541fs	KMT2A_ENST00000534358.1_Frame_Shift_Ins_p.E2544fs|KMT2A_ENST00000354520.4_Frame_Shift_Ins_p.E2503fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2541					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TGCCCTGAAAGAAAGTAGTCCT	0.46																																					p.E2544fs		Atlas-INDEL	.											.	MLL	548	.	0			c.7630_7631insTC						.																																			SO:0001589	frameshift_variant	4297	exon27			.	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	Exception_encountered	chr11.hg19:g.118374237_118374238insTC	ENSP00000374157:p.Glu2541fs	105.0	0.0		73.0	24.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Ins	INS	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.46	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		TC	118374238	-	TC	118374237	7	5	153	1	0	1	1	0	0	0	0	0	9629	943	33	0	7727	0	MLL	11	118374237	Frame_Shift_Ins	INS	-	TCGA-DD-AACB-01A-11D-A40R-10	6	118374237	16632279	59	23522	104	2								
TAS2R42	353164	hgsc.bcm.edu	37	chr12	11339508	11339508	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	atgatgaattctgctattgcCagaatcagaaagattttgtc	8	6	2	5			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr12:11339508C>T	ENST00000334266.1	-	1	35	c.36G>A	c.(34-36)ctG>ctA	p.L12L		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	12					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			CTGCTATTGCCAGAATCAGAA	0.378																																					p.L12L	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.G36A						.						79	83	82					12																	11339508		2203	4300	6503	SO:0001819	synonymous_variant	353164	exon1			TATTGCCAGAATC	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.36G>A	chr12.hg19:g.11339508C>T		62.0	0.0		76.0	20.0	NM_181429	A2RRP4|Q645X0	Silent	SNP	ENST00000334266.1	hg19	CCDS31747.1																																																																																			.	.		0.378	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429		T	11339508	C	T	11339508	2	4	153	1	0	0	0	0	0	0	0	1	15595	581	21	3		3	TAS2R42	12	11339508	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10		11339508	122512387	60	23523										
SP1	6667	hgsc.bcm.edu	37	chr12	53775951	53775951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	cttgcagcagaattgagtcaCccaatgagaacagcaacaac	8	11	1	3			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr12:53775951C>T	ENST00000327443.4	+	3	318	c.220C>T	c.(220-222)Ccc>Tcc	p.P74S	SP1_ENST00000426431.2_Missense_Mutation_p.P67S	NM_001251825.1|NM_138473.2	NP_001238754.1|NP_612482.2	P08047	SP1_HUMAN	Sp1 transcription factor	74	Repressor domain.|Ser/Thr-rich.				cellular lipid metabolic process (GO:0044255)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|gene expression (GO:0010467)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|ossification (GO:0001503)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	bHLH transcription factor binding (GO:0043425)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|histone deacetylase binding (GO:0042826)|HMG box domain binding (GO:0071837)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.00527)		AATTGAGTCACCCAATGAGAA	0.557											OREG0021870	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P74S		Atlas-SNP	.											.	SP1	57	.	0			c.C220T						.						61	60	60					12																	53775951		2203	4300	6503	SO:0001583	missense	6667	exon3			GAGTCACCCAATG	J03133	CCDS8857.1, CCDS44898.1	12q13.1	2013-01-08						"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11205	protein-coding gene	gene with protein product	"specificity protein 1"	189906				1662663	Standard	NM_003109		Approved		uc001scw.3	P08047	OTTHUMG00000170047	ENST00000327443.4:c.220C>T	chr12.hg19:g.53775951C>T	ENSP00000329357:p.Pro74Ser	57.0	0.0	995	54.0	10.0	NM_138473	E4Z9M7|G5E9M8|Q86TN8|Q9H3Q5|Q9NR51|Q9NY21|Q9NYE7	Missense_Mutation	SNP	ENST00000327443.4	hg19	CCDS8857.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.065361	0.55432	.	.	ENSG00000185591	ENST00000327443;ENST00000426431	T;T	0.11821	2.76;2.74	4.13	4.13	0.48395	.	0.000000	0.53938	D	0.000046	T	0.27278	0.0669	L	0.60455	1.87	0.53005	D	0.999967	D	0.64830	0.994	P	0.55345	0.774	T	0.03278	-1.1053	10	0.72032	D	0.01	.	15.6957	0.77494	0.0:1.0:0.0:0.0	.	74	P08047	SP1_HUMAN	S	74;67	ENSP00000329357:P74S;ENSP00000404263:P67S	ENSP00000329357:P74S	P	+	1	0	SP1	52062218	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.129000	0.77225	2.306000	0.77630	0.467000	0.42956	CCC	.	.		0.557	SP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407044.1			T	53775951	C	T	53775951	3	4	153	1	0	0	0	0	1	0	0	0	14974	507	18	3	230	3	SP1	12	53775951	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	42436443	53775951	80075944	61	23524										
HSP90B1	7184	hgsc.bcm.edu	37	chr12	104327962	104327962	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ataaggttattgtcacttcaAaacacaacaacgatacccag	5	10	2	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr12:104327962A>G	ENST00000299767.5	+	5	822	c.640A>G	c.(640-642)Aaa>Gaa	p.K214E		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	214					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	TGTCACTTCAAAACACAACAA	0.453																																					p.K214E		Atlas-SNP	.											.	HSP90B1	72	.	0			c.A640G						.						103	97	99					12																	104327962		2203	4300	6503	SO:0001583	missense	7184	exon5			ACTTCAAAACACA	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.640A>G	chr12.hg19:g.104327962A>G	ENSP00000299767:p.Lys214Glu	238.0	0.0		229.0	21.0	NM_003299	Q96A97	Missense_Mutation	SNP	ENST00000299767.5	hg19	CCDS9094.1	.	.	.	.	.	.	.	.	.	.	A	32	5.152833	0.94645	.	.	ENSG00000166598	ENST00000299767;ENST00000537375	D	0.89746	-2.56	5.93	5.93	0.95920	Heat shock protein Hsp90, N-terminal (1);ATPase-like, ATP-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.97266	0.9106	H	0.99600	4.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99143	1.0856	10	0.87932	D	0	.	16.3943	0.83563	1.0:0.0:0.0:0.0	.	240;214	Q59FC6;P14625	.;ENPL_HUMAN	E	214	ENSP00000299767:K214E	ENSP00000299767:K214E	K	+	1	0	HSP90B1	102852092	1.000000	0.71417	0.944000	0.38274	0.994000	0.84299	9.336000	0.96533	2.281000	0.76405	0.533000	0.62120	AAA	.	.		0.453	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		G	104327962	A	G	104327962	3	3	153	1	0	0	0	0	1	0	0	0	7412	15	1	2	658	2	HSP90B1	12	104327962	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	50552011	104327962	29523933	62	23525										
ATP12A	479	hgsc.bcm.edu	37	chr13	25283923	25283923	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	cctgcgggtagaatgggagaAggactacgtgaatgacttga	15	6	0	5			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr13:25283923A>T	ENST00000381946.3	+	19	2887	c.2720A>T	c.(2719-2721)aAg>aTg	p.K907M	ATP12A_ENST00000218548.6_Missense_Mutation_p.K913M			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	907					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		GAATGGGAGAAGGACTACGTG	0.542																																					p.K913M	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.A2738T						.						127	123	124					13																	25283923		2203	4300	6503	SO:0001583	missense	479	exon19			GGGAGAAGGACTA	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2720A>T	chr13.hg19:g.25283923A>T	ENSP00000371372:p.Lys907Met	84.0	0.0		94.0	20.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	A	9.707	1.155956	0.21454	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.88586	-2.4;-2.4	5.79	-1.37	0.09056	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	1.083730	0.06933	N	0.811393	D	0.83422	0.5251	L	0.28192	0.835	0.09310	N	1	P;P	0.35982	0.531;0.53	P;B	0.45474	0.482;0.44	T	0.73078	-0.4096	10	0.87932	D	0	.	1.6346	0.02740	0.3959:0.2735:0.0804:0.2502	.	913;907	P54707-2;P54707	.;AT12A_HUMAN	M	913;907	ENSP00000218548:K913M;ENSP00000371372:K907M	ENSP00000218548:K913M	K	+	2	0	ATP12A	24181923	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	1.520000	0.35899	-0.448000	0.07128	-0.313000	0.08912	AAG	.	.		0.542	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25283923	A	T	25283923	3	4	153	1	0	0	0	0	1	0	0	0	1122	72	3	4	2812	4	ATP12A	13	25283923	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10		25283923	89885955	63	23526										
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42385467	42385467	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggtagaaagtgatgccgctaAtgattgtgcctatcaaaaga	11	6	1	4			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr13:42385467A>G	ENST00000379310.3	-	17	2025	c.1957T>C	c.(1957-1959)Tta>Cta	p.L653L	VWA8_ENST00000281496.6_Silent_p.L653L	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	653						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										GATGCCGCTAATGATTGTGCC	0.388																																					p.L653L		Atlas-SNP	.											.	.	.	.	0			c.T1957C						.						112	113	113					13																	42385467		2203	4300	6503	SO:0001819	synonymous_variant	23078	exon17			CCGCTAATGATTG	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.1957T>C	chr13.hg19:g.42385467A>G		116.0	0.0		94.0	11.0	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Silent	SNP	ENST00000379310.3	hg19	CCDS41881.1																																																																																			.	.		0.388	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		G	42385467	A	G	42385467	2	3	153	1	0	0	0	0	0	0	0	1	8194	98	4	2		2	KIAA0564	13	42385467	Silent	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	17101544	42385467	72784411	64	23527										
ING1	3621	hgsc.bcm.edu	37	chr13	111371917	111371917	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	agcgcaacaacgagaaccgtGagaacgcgtccagcaaccac	10	14	0	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr13:111371917G>A	ENST00000375774.3	+	2	1369	c.907G>A	c.(907-909)Gag>Aag	p.E303K	ING1_ENST00000338450.7_Missense_Mutation_p.E116K|ING1_ENST00000333219.7_Missense_Mutation_p.E160K|ING1_ENST00000375775.3_Missense_Mutation_p.E91K	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	303					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CGAGAACCGTGAGAACGCGTC	0.652																																					p.E303K		Atlas-SNP	.											.	ING1	106	.	0			c.G907A						.						51	42	45					13																	111371917		2200	4299	6499	SO:0001583	missense	3621	exon2			AACCGTGAGAACG		CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"Zinc fingers, PHD-type"	6062	protein-coding gene	gene with protein product	"inhibitor of growth 1", "tumor suppressor ING1", "growth inhibitor ING1", "growth inhibitory protein ING1"	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.907G>A	chr13.hg19:g.111371917G>A	ENSP00000364929:p.Glu303Lys	239.0	0.0		289.0	69.0	NM_005537	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Missense_Mutation	SNP	ENST00000375774.3	hg19	CCDS9517.1	.	.	.	.	.	.	.	.	.	.	G	13.92	2.381824	0.42207	.	.	ENSG00000153487	ENST00000338450;ENST00000333219;ENST00000375775;ENST00000375774	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.36	5.36	0.76844	.	0.049125	0.85682	D	0.000000	T	0.59376	0.2189	L	0.60455	1.87	0.58432	D	0.999998	D;P;D	0.69078	0.997;0.877;0.99	P;B;D	0.72982	0.815;0.411;0.979	T	0.51332	-0.8719	10	0.12430	T	0.62	-37.3868	19.0766	0.93165	0.0:0.0:1.0:0.0	.	303;160;116	Q9UK53;Q5T9H0;Q9UK53-4	ING1_HUMAN;.;.	K	116;160;91;303	ENSP00000345202:E116K;ENSP00000328436:E160K;ENSP00000364930:E91K;ENSP00000364929:E303K	ENSP00000328436:E160K	E	+	1	0	ING1	110169918	1.000000	0.71417	0.945000	0.38365	0.133000	0.20885	7.219000	0.78000	2.506000	0.84524	0.491000	0.48974	GAG	.	.		0.652	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537		A	111371917	G	A	111371917	3	1	153	1	0	0	0	0	1	0	0	0	7744	1291	45	3	1061	3	ING1	13	111371917	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	68986450	111371917	3797961	65	23528										
CUL4A	8451	hgsc.bcm.edu	37	chr13	113882334	113882334	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tttaaagaagattaacacgtGctggcaggaccactgcagac	10	9	0	3			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr13:113882334G>T	ENST00000375440.4	+	4	497	c.413G>T	c.(412-414)tGc>tTc	p.C138F	CUL4A_ENST00000326335.4_Missense_Mutation_p.C38F|CUL4A_ENST00000463426.1_3'UTR|CUL4A_ENST00000451881.1_Missense_Mutation_p.C38F|CUL4A_ENST00000375441.3_Missense_Mutation_p.C38F	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	138					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			ATTAACACGTGCTGGCAGGAC	0.383																																					p.C138F		Atlas-SNP	.											.	CUL4A	50	.	0			c.G413T						.						85	82	83					13																	113882334		2203	4300	6503	SO:0001583	missense	8451	exon4			ACACGTGCTGGCA	U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.413G>T	chr13.hg19:g.113882334G>T	ENSP00000364589:p.Cys138Phe	116.0	0.0		110.0	40.0	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	hg19	CCDS41908.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.620332	0.46736	.	.	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78	5.51	5.51	0.81932	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.047489	0.85682	D	0.000000	T	0.71298	0.3323	L	0.59436	1.845	0.80722	D	1	B	0.14438	0.01	B	0.20384	0.029	T	0.66980	-0.5786	10	0.09843	T	0.71	-28.2997	19.4545	0.94882	0.0:0.0:1.0:0.0	.	138	Q13619	CUL4A_HUMAN	F	38;38;38;138	ENSP00000364590:C38F;ENSP00000389118:C38F;ENSP00000322132:C38F;ENSP00000364589:C138F	ENSP00000322132:C38F	C	+	2	0	CUL4A	112930335	1.000000	0.71417	0.998000	0.56505	0.363000	0.29612	9.553000	0.98118	2.590000	0.87494	0.650000	0.86243	TGC	.	.		0.383	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589		T	113882334	G	T	113882334	3	4	153	1	0	0	0	0	1	0	0	0	4059	1319	46	3	427	3	CUL4A	13	113882334	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	2510417	113882334	1287544	66	23529										
JKAMP	112849	hgsc.bcm.edu	37	chr14	59953512	59953512	+	5'Flank	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tggctcaactgaaatatatgGagaatgtggggtaagtctta	12	4	2	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr14:59953512G>A	ENST00000247194.4	-	0	0				JKAMP_ENST00000356057.5_Missense_Mutation_p.G37E|JKAMP_ENST00000425728.2_Missense_Mutation_p.G23E|JKAMP_ENST00000554271.1_Missense_Mutation_p.G43E|JKAMP_ENST00000557560.1_3'UTR|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000261247.9_Missense_Mutation_p.G29E|JKAMP_ENST00000556985.1_Missense_Mutation_p.G29E	NM_144581.1	NP_653182.1	Q96EM0	T3HPD_HUMAN	L-3-hydroxyproline dehydratase (trans-)						metabolic process (GO:0008152)		hydro-lyase activity (GO:0016836)|trans-L-3-hydroxyproline dehydratase activity (GO:0050346)									L-Proline(DB00172)	GAAATATATGGAGAATGTGGG	0.299																																					p.G29E		Atlas-SNP	.											JKAMP_ENST00000356057,NS,carcinoma,0,2	JKAMP	49	.	0			c.G86A						.						82	80	81					14																	59953512		1791	4067	5858	SO:0001631	upstream_gene_variant	51528	exon2			TATATGGAGAATG	AI762327	CCDS9739.1	14q23.1	2012-08-15	2012-08-15	2012-08-15	ENSG00000126790	ENSG00000126790	4.2.1.77		20488	protein-coding gene	gene with protein product	"trans-L-3-hydroxyproline dehydratase"	614811	"chromosome 14 open reading frame 149"	C14orf149		22528483	Standard	NM_144581		Approved	FLJ25436	uc001xee.1	Q96EM0	OTTHUMG00000028941		chr14.hg19:g.59953512G>A	Exception_encountered	85.0	0.0		96.0	17.0	NM_016475	Q96LJ5	Missense_Mutation	SNP	ENST00000247194.4	hg19	CCDS9739.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.942180	0.73672	.	.	ENSG00000050130	ENST00000261247;ENST00000425728;ENST00000556985;ENST00000554271;ENST00000554795;ENST00000356057	.	.	.	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.77405	0.4125	M	0.66939	2.045	0.58432	D	0.999999	D;D;D;D	0.71674	0.998;0.998;0.998;0.998	D;D;D;D	0.66847	0.947;0.947;0.947;0.947	T	0.78780	-0.2070	9	0.56958	D	0.05	-14.4716	18.4684	0.90763	0.0:0.0:1.0:0.0	.	43;23;37;29	G3V2M4;Q9P055-3;Q9P055-5;Q9P055-4	.;.;.;.	E	29;23;29;43;37;37	.	ENSP00000261247:G29E	G	+	2	0	JKAMP	59023265	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.802000	0.62539	2.541000	0.85698	0.655000	0.94253	GGA	.	.		0.299	L3HYPDH-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072254.5	NM_144581		A	59953512	G	A	59953512	1	1	153	0	1	0	0	0	0	0	0	0	7958	1174	41	3		3	JKAMP	14	59953512	5'Flank	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10		59953512	47396028	67	23530										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089391	86089391	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gaagacaccatttgttcagaGgccaccacccatgcctccta	7	15	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr14:86089391G>A	ENST00000330753.4	+	2	2300	c.1533G>A	c.(1531-1533)gaG>gaA	p.E511E	FLRT2_ENST00000554746.1_Silent_p.E511E	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	511	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TTTGTTCAGAGGCCACCACCC	0.557																																					p.E511E		Atlas-SNP	.											.	FLRT2	168	.	0			c.G1533A						.						122	114	117					14																	86089391		2203	4300	6503	SO:0001819	synonymous_variant	23768	exon2			TTCAGAGGCCACC	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1533G>A	chr14.hg19:g.86089391G>A		150.0	0.0		153.0	40.0	NM_013231	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	hg19	CCDS9877.1																																																																																			.	.		0.557	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			A	86089391	G	A	86089391	2	1	153	1	0	0	0	0	0	0	0	1	5947	991	35	3		3	FLRT2	14	86089391	Silent	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	26135879	86089391	21260149	68	23531										
TMC3	342125	hgsc.bcm.edu	37	chr15	81625501	81625501	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tgaaagtcttttcggaaaagAggttctgagtgtacatcttc	10	6	3	3			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr15:81625501A>T	ENST00000359440.5	-	22	2697	c.2562T>A	c.(2560-2562)ccT>ccA	p.P854P	RP11-761I4.3_ENST00000559781.1_RNA|RP11-761I4.3_ENST00000560851.1_RNA|RP11-761I4.3_ENST00000560973.1_RNA|TMC3_ENST00000558726.1_Silent_p.P855P	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						TTCGGAAAAGAGGTTCTGAGT	0.537																																					p.P854P		Atlas-SNP	.											.	TMC3	112	.	0			c.T2562A						.						146	143	144					15																	81625501		1987	4184	6171	SO:0001819	synonymous_variant	342125	exon22			GAAAAGAGGTTCT	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.2562T>A	chr15.hg19:g.81625501A>T		135.0	0.0		115.0	14.0	NM_001080532		Silent	SNP	ENST00000359440.5	hg19	CCDS45324.1																																																																																			.	.		0.537	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		T	81625501	A	T	81625501	2	4	153	1	0	0	0	0	0	0	0	1	16001	291	11	4		4	TMC3	15	81625501	Silent	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10		81625501	20905891	69	23532										
ZSCAN2	54993	hgsc.bcm.edu	37	chr15	85164886	85164886	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggagagcttcagctggagctCcaacctcctcaagcaccaga	10	14	2	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr15:85164886C>A	ENST00000448803.2	+	3	1752	c.1460C>A	c.(1459-1461)tCc>tAc	p.S487Y	ZSCAN2_ENST00000485222.2_Intron|ZSCAN2_ENST00000541040.1_Intron|ZSCAN2_ENST00000327179.6_Missense_Mutation_p.S486Y|ZSCAN2_ENST00000538076.1_Intron|ZSCAN2_ENST00000546148.1_Missense_Mutation_p.S487Y|ZSCAN2_ENST00000358472.3_Missense_Mutation_p.S337Y	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2	487					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|liver(2)|lung(4)|ovary(1)|pancreas(1)	19				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		AGCTGGAGCTCCAACCTCCTC	0.577																																					p.S487Y		Atlas-SNP	.											.	ZSCAN2	43	.	0			c.C1460A						.						87	78	81					15																	85164886		2203	4299	6502	SO:0001583	missense	54993	exon3			GGAGCTCCAACCT	BC041620	CCDS10329.2, CCDS32315.1, CCDS32316.1	15q25.2	2013-01-08	2004-11-01	2004-11-02	ENSG00000176371	ENSG00000176371		"-", "Zinc fingers, C2H2-type"	20994	protein-coding gene	gene with protein product			"zinc finger protein 29"	ZFP29		1937051	Standard	NM_017894		Approved	FLJ20595, ZNF854	uc002bkr.3	Q7Z7L9	OTTHUMG00000074027	ENST00000448803.2:c.1460C>A	chr15.hg19:g.85164886C>A	ENSP00000410198:p.Ser487Tyr	65.0	0.0		78.0	10.0	NM_181877	A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Missense_Mutation	SNP	ENST00000448803.2	hg19	CCDS10329.2	.	.	.	.	.	.	.	.	.	.	C	15.75	2.926048	0.52759	.	.	ENSG00000176371	ENST00000448803;ENST00000546148;ENST00000358472;ENST00000327179;ENST00000379353	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	4.87	4.87	0.63330	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000040	T	0.30947	0.0781	L	0.38649	1.16	0.80722	D	1	D;P	0.89917	1.0;0.649	D;B	0.74674	0.984;0.092	T	0.01561	-1.1324	9	.	.	.	-34.5536	15.4721	0.75446	0.0:1.0:0.0:0.0	.	487;487	A8K5A9;Q7Z7L9	.;ZSCA2_HUMAN	Y	487;487;337;486;468	ENSP00000410198:S487Y;ENSP00000445451:S487Y;ENSP00000351257:S337Y;ENSP00000325123:S486Y	.	S	+	2	0	ZSCAN2	82965890	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	0.269000	0.18589	2.237000	0.73441	0.655000	0.94253	TCC	.	.		0.577	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894		A	85164886	C	A	85164886	3	1	153	1	0	0	0	0	1	0	0	0	18246	855	30	3	1556	3	ZSCAN2	15	85164886	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	3539385	85164886	17366506	70	23533										
CENPT	80152	hgsc.bcm.edu	37	chr16	67862725	67862725	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggatgcctgaccaacagaggCtctgcaggctctgaagataa	12	10	2	4			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr16:67862725C>T	ENST00000562787.1	-	14	1850	c.1302G>A	c.(1300-1302)gaG>gaA	p.E434E	CENPT_ENST00000564817.1_Silent_p.E379E|CENPT_ENST00000440851.2_Silent_p.E434E|CENPT_ENST00000562947.1_5'Flank|CENPT_ENST00000219172.3_Silent_p.E434E	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T	434					chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		CCAACAGAGGCTCTGCAGGCT	0.582																																					p.E434E		Atlas-SNP	.											.	CENPT	26	.	0			c.G1302A						.						56	62	60					16																	67862725		1915	4125	6040	SO:0001819	synonymous_variant	80152	exon14			CAGAGGCTCTGCA	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3		ENST00000562787.1:c.1302G>A	chr16.hg19:g.67862725C>T		62.0	0.0		69.0	17.0	NM_025082	Q96I29|Q96IC6|Q96NK9|Q9H901	Silent	SNP	ENST00000562787.1	hg19	CCDS42182.1																																																																																			.	.		0.582	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		T	67862725	C	T	67862725	2	4	153	1	0	0	0	0	0	0	0	1	3244	796	28	3		3	CENPT	16	67862725	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10		67862725	22492028	71	23534										
ST3GAL2	6483	hgsc.bcm.edu	37	chr16	70432255	70432255	+	Frame_Shift_Del	DEL	A	A	-													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ccgagagcctctccttgctgAggcgctgcaggccggcatag							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr16:70432255delA	ENST00000393640.4	-	1	2286	c.179delT	c.(178-180)ctcfs	p.L60fs	ST3GAL2_ENST00000342907.2_Frame_Shift_Del_p.L60fs|RP11-529K1.4_ENST00000566960.1_RNA|ST3GAL2_ENST00000566097.1_5'Flank			Q16842	SIA4B_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	60					amino sugar metabolic process (GO:0006040)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)	11		Ovarian(137;0.0694)				CTCCTTGCTGAGGCGCTGCAG	0.657																																					p.L60fs		Atlas-INDEL	.											.	ST3GAL2	23	.	0			c.180delC						.						48	51	50					16																	70432255		2198	4300	6498	SO:0001589	frameshift_variant	6483	exon2			.	U63090	CCDS10890.1	16q22.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000157350	ENSG00000157350	2.4.99.4	"Sialyltransferases"	10863	protein-coding gene	gene with protein product		607188	"sialyltransferase 4B (beta-galactosidase alpha-2,3-sialytransferase)"	SIAT4B		9266697, 8920913	Standard	NM_006927		Approved	ST3GALII, ST3GalA.2	uc002eyx.2	Q16842	OTTHUMG00000137580	ENST00000393640.4:c.179delT	chr16.hg19:g.70432255delA	ENSP00000377257:p.Leu60fs	79.0	0.0		80.0	19.0	NM_006927	O00654	Frame_Shift_Del	DEL	ENST00000393640.4	hg19	CCDS10890.1																																																																																			.	.		0.657	ST3GAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268968.1	NM_006927		-	70432255	A	-	70432255	7	5	153	1	0	1	0	1	0	0	0	0	15230	304	11	0	897	0	ST3GAL2	16	70432255	Frame_Shift_Del	DEL	A	TCGA-DD-AACB-01A-11D-A40R-10	2569530	70432255	19922498	72	23535										
TP53	7157	hgsc.bcm.edu	37	chr17	7577095	7577095	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ttctcttcctctgtgcgccgGtctctcccaggacaggcaca	9	16	3	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr17:7577095G>C	ENST00000269305.4	-	8	1032	c.843C>G	c.(841-843)gaC>gaG	p.D281E	TP53_ENST00000420246.2_Missense_Mutation_p.D281E|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.D281E|TP53_ENST00000455263.2_Missense_Mutation_p.D281E|TP53_ENST00000445888.2_Missense_Mutation_p.D281E	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	281	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		D -> A (in sporadic cancers; somatic mutation).|D -> E (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1459726}.|D -> G (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).|D -> H (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|D -> N (in LFS; germline mutation and in sporadic cancers; somatic mutation).|D -> R (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|D -> V (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|D -> Y (in sporadic cancers; somatic mutation).|DR -> EW (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.D281E(28)|p.R282W(10)|p.0?(8)|p.D281D(5)|p.?(2)|p.D281fs*63(2)|p.R280_D281delRD(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282fs*24(1)|p.D281R(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.F270_D281del12(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGTGCGCCGGTCTCTCCCAG	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.D281E	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,adenocarcinoma,-1,1	TP53	33396	.	72	Substitution - Missense(39)|Deletion - In frame(8)|Whole gene deletion(8)|Substitution - coding silent(5)|Deletion - Frameshift(4)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - Frameshift(1)|Insertion - In frame(1)	skin(12)|upper_aerodigestive_tract(8)|ovary(8)|haematopoietic_and_lymphoid_tissue(7)|breast(6)|lung(5)|central_nervous_system(4)|bone(4)|urinary_tract(3)|oesophagus(3)|liver(3)|stomach(2)|endometrium(2)|large_intestine(1)|vulva(1)|genital_tract(1)|pancreas(1)|prostate(1)	c.C843G						.						82	70	74					17																	7577095		2203	4300	6503	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GCGCCGGTCTCTC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.843C>G	chr17.hg19:g.7577095G>C	ENSP00000269305:p.Asp281Glu	89.0	0.0		64.0	40.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.105939	0.77096	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99861	-7.26;-7.26;-7.26;-7.26;-7.26;-7.26	4.99	0.696	0.18075	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99832	0.9924	M	0.92649	3.33	0.53005	D	0.999961	D;D;D;P	0.71674	0.993;0.998;0.995;0.916	D;D;D;D	0.91635	0.965;0.999;0.951;0.943	D	0.98567	1.0644	10	0.87932	D	0	-25.6697	7.6418	0.28298	0.4422:0.0:0.5578:0.0	.	281;281;281;281	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	E	281;281;281;281;281;270;149	ENSP00000352610:D281E;ENSP00000269305:D281E;ENSP00000398846:D281E;ENSP00000391127:D281E;ENSP00000391478:D281E;ENSP00000425104:D149E	ENSP00000269305:D281E	D	-	3	2	TP53	7517820	1.000000	0.71417	0.915000	0.36163	0.964000	0.63967	1.949000	0.40313	0.286000	0.22352	0.462000	0.41574	GAC	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577095	G	C	7577095	3	2	153	1	0	0	0	0	1	0	0	0	16396	1252	44	4	443	4	TP53	17	7577095	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10		7577095	73618115	73	23536										
ACACA	31	hgsc.bcm.edu	37	chr17	35486338	35486338	+	Frame_Shift_Del	DEL	T	T	-													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	atcgaggatcgtatggggtcTttgtgggaacaaactcgatg							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr17:35486338delT	ENST00000394406.2	-	47	5976	c.5786delA	c.(5785-5787)aagfs	p.K1929fs	ACACA_ENST00000335166.5_Frame_Shift_Del_p.K1851fs|ACACA_ENST00000360679.3_Frame_Shift_Del_p.K1871fs|ACACA_ENST00000361253.5_Frame_Shift_Del_p.K55fs|ACACA_ENST00000353139.5_Frame_Shift_Del_p.K1966fs	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1929	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	GTATGGGGTCTTTGTGGGAAC	0.473																																					p.K1966fs	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-INDEL	.											.	ACACA	395	.	0			c.5898delG						.						155	129	138					17																	35486338		2203	4300	6503	SO:0001589	frameshift_variant	31	exon47			.	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.5786delA	chr17.hg19:g.35486338delT	ENSP00000377928:p.Lys1929fs	143.0	0.0		128.0	46.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Frame_Shift_Del	DEL	ENST00000394406.2	hg19	CCDS11317.1																																																																																			.	.		0.473	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		-	35486338	T	-	35486338	7	5	153	1	0	1	0	1	0	0	0	0	106	1609	56	0	1294	0	ACACA	17	35486338	Frame_Shift_Del	DEL	T	TCGA-DD-AACB-01A-11D-A40R-10	27909243	35486338	45708872	74	23537										
RPL19	6143	hgsc.bcm.edu	37	chr17	37357506	37357506	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggctcgcctctagtgtcctcCgctgtggcaagaagaaggtc	13	12	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr17:37357506C>T	ENST00000225430.4	+	2	108	c.46C>T	c.(46-48)Cgc>Tgc	p.R16C	RPL19_ENST00000582193.1_Missense_Mutation_p.R14C|RPL19_ENST00000579260.1_Missense_Mutation_p.R14C|RPL19_ENST00000579374.1_Missense_Mutation_p.R13C	NM_000981.3	NP_000972.1	P84098	RL19_HUMAN	ribosomal protein L19	16					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7						TAGTGTCCTCCGCTGTGGCAA	0.498																																					p.R16C		Atlas-SNP	.											.	RPL19	18	.	0			c.C46T						.						90	87	88					17																	37357506		1894	4120	6014	SO:0001583	missense	6143	exon2			GTCCTCCGCTGTG		CCDS42312.1	17q12	2012-09-20			ENSG00000108298	ENSG00000108298		"L ribosomal proteins"	10312	protein-coding gene	gene with protein product	"60S ribosomal protein L19", "ribosomal protein L19, cytosolic, N-terminus truncated"	180466				1577483	Standard	XM_005257564		Approved	FLJ27452, MGC71997, DKFZp779D216, L19	uc002hrq.1	P84098	OTTHUMG00000178979	ENST00000225430.4:c.46C>T	chr17.hg19:g.37357506C>T	ENSP00000225430:p.Arg16Cys	50.0	0.0		66.0	11.0	NM_000981	B2R4K2|P14118|P22908|Q502Y6|Q7Z6E4	Missense_Mutation	SNP	ENST00000225430.4	hg19	CCDS42312.1	.	.	.	.	.	.	.	.	.	.	c	15.76	2.927553	0.52759	.	.	ENSG00000108298	ENST00000225430	.	.	.	4.7	3.68	0.42216	Ribosomal protein L19/L19e conserved site (1);Ribosomal protein L19/L19e (2);Ribosomal protein L19/L19e, domain 1 (1);	0.068449	0.64402	D	0.000018	T	0.45657	0.1353	L	0.40543	1.245	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.45527	-0.9255	9	0.46703	T	0.11	.	9.5757	0.39457	0.1407:0.7818:0.0:0.0775	.	16	P84098	RL19_HUMAN	C	16	.	ENSP00000225430:R16C	R	+	1	0	RPL19	34611032	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	4.680000	0.61656	2.169000	0.68431	0.313000	0.20887	CGC	.	.		0.498	RPL19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444190.1	NM_000981		T	37357506	C	T	37357506	3	4	153	1	0	0	0	0	1	0	0	0	13581	652	23	1	52	1	RPL19	17	37357506	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	1871168	37357506	43837704	75	23538										
ABCC3	8714	hgsc.bcm.edu	37	chr17	48746279	48746279	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	acctgccccccactctgcacAggtaccagcttctcccactc	5	21	2	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr17:48746279A>C	ENST00000285238.8	+	15	2016	c.1936A>C	c.(1936-1938)Agc>Cgc	p.S646R		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	646	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	CACTCTGCACAGGTACCAGCT	0.597																																					p.S646R		Atlas-SNP	.											.	ABCC3	138	.	0			c.A1936C						.						102	74	83					17																	48746279		2203	4300	6503	SO:0001630	splice_region_variant	8714	exon15			CTGCACAGGTACC	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"ATP binding cassette transporters / subfamily C"	54	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter 2"	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.1937+1A>C	chr17.hg19:g.48746279A>C		76.0	0.0		86.0	37.0	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	hg19	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	A	6.733	0.503938	0.12822	.	.	ENSG00000108846	ENST00000285238	D	0.90620	-2.7	4.8	3.71	0.42584	ABC transporter-like (1);	0.237616	0.40222	N	0.001157	T	0.81702	0.4878	N	0.21508	0.67	0.45541	D	0.998491	P	0.48503	0.911	P	0.45037	0.467	T	0.77965	-0.2389	10	0.32370	T	0.25	-31.5622	2.6457	0.04983	0.6218:0.0:0.1667:0.2115	.	646	O15438	MRP3_HUMAN	R	646	ENSP00000285238:S646R	ENSP00000285238:S646R	S	+	1	0	ABCC3	46101278	1.000000	0.71417	1.000000	0.80357	0.320000	0.28249	1.475000	0.35409	1.935000	0.56089	0.397000	0.26171	AGC	.	.		0.597	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	Missense_Mutation	C	48746279	A	C	48746279	5	2	153	1	0	0	0	0	0	0	1	0	54	202	7	5	2078	5	ABCC3	17	48746279	Splice_Site	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	11388773	48746279	32448931	76	23539										
EXOC7	23265	hgsc.bcm.edu	37	chr17	74093950	74093950	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	agcacgctctcgggcaggtgCtccagggtcacgtcctcctg	13	15	2	0	rs117225564		TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr17:74093950C>A	ENST00000335146.7	-	5	620	c.567G>T	c.(565-567)gaG>gaT	p.E189D	EXOC7_ENST00000467929.2_Missense_Mutation_p.E148D|EXOC7_ENST00000405575.4_Missense_Mutation_p.E189D|EXOC7_ENST00000589210.1_Missense_Mutation_p.E189D|EXOC7_ENST00000332065.5_Missense_Mutation_p.E189D|EXOC7_ENST00000607838.1_Missense_Mutation_p.E189D|EXOC7_ENST00000411744.2_Missense_Mutation_p.E189D			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	189					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CGGGCAGGTGCTCCAGGGTCA	0.597																																					p.E189D		Atlas-SNP	.											.	EXOC7	47	.	0			c.G567T						.						104	86	92					17																	74093950		2203	4300	6503	SO:0001583	missense	23265	exon5			CAGGTGCTCCAGG	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.567G>T	chr17.hg19:g.74093950C>A	ENSP00000334100:p.Glu189Asp	124.0	0.0		144.0	63.0	NM_001145298	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.697089	0.68386	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744;ENST00000405068;ENST00000420116	.	.	.	4.99	4.99	0.66335	Cullin repeat-like-containing domain (1);	0.111990	0.64402	D	0.000013	T	0.63686	0.2532	L	0.55481	1.735	0.80722	D	1	P;B;P;B;P;B;D;B	0.71674	0.707;0.114;0.509;0.294;0.819;0.131;0.998;0.043	P;B;B;B;B;B;D;B	0.65987	0.518;0.038;0.034;0.199;0.337;0.044;0.94;0.025	T	0.59096	-0.7518	9	0.07030	T	0.85	-36.6713	11.1089	0.48221	0.0:0.9157:0.0:0.0843	.	189;189;148;148;189;189;189;189	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5-4;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;.;EXOC7_HUMAN;.;.	D	189;109;189;189;189;148;189;189;74	.	ENSP00000333806:E189D	E	-	3	2	EXOC7	71605545	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	0.757000	0.26433	2.598000	0.87819	0.563000	0.77884	GAG	.	C|0.999;T|0.001		0.597	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		A	74093950	C	A	74093950	3	1	153	1	0	0	0	0	1	0	0	0	5312	796	28	3	1704	3	EXOC7	17	74093950	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	25347671	74093950	7101260	77	23540										
FASN	2194	hgsc.bcm.edu	37	chr17	80050789	80050793	+	Frame_Shift_Del	DEL	ATCTG	ATCTG	-													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ccaccttgctccttgaagccAtctgtattggtgccggcgtt							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	ATCTG	ATCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr17:80050789_80050793delATCTG	ENST00000306749.2	-	6	976_980	c.758_762delCAGAT	c.(757-762)acagatfs	p.TD253fs		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	253	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CCTTGAAGCCATCTGTATTGGTGCC	0.688																																					p.253_255del	Colon(59;314 1043 11189 28578 32273)	Atlas-INDEL	.											.	FASN	154	.	0			c.759_763del						.																																			SO:0001589	frameshift_variant	2194	exon6			.	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.758_762delCAGAT	chr17.hg19:g.80050789_80050793delATCTG	ENSP00000304592:p.Thr253fs	91.0	0.0		93.0	37.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Frame_Shift_Del	DEL	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.688	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		-	80050793	ATCTG	-	80050789	7	5	153	1	0	1	0	1	0	0	0	0	5691	214	8	0	6925	0	FASN	17	80050789	Frame_Shift_Del	DEL	ATCTG	TCGA-DD-AACB-01A-11D-A40R-10	5956839	80050789	1144421	78	23541										
RALBP1	10928	hgsc.bcm.edu	37	chr18	9535711	9535711	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	aagcaattcatgaggagcgcGaggccatcatcgagctgcgc	13	11	2	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr18:9535711G>A	ENST00000019317.4	+	10	1967	c.1744G>A	c.(1744-1746)Gag>Aag	p.E582K	RALBP1_ENST00000383432.3_Missense_Mutation_p.E582K			Q15311	RBP1_HUMAN	ralA binding protein 1	582					ATP catabolic process (GO:0006200)|chemotaxis (GO:0006935)|positive regulation of Cdc42 GTPase activity (GO:0043089)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|transport (GO:0006810)	cytosol (GO:0005829)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ATPase activity, coupled to movement of substances (GO:0043492)|GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	14					Carbamazepine(DB00564)|Doxorubicin(DB00997)|Sorafenib(DB00398)|Vincristine(DB00541)	TGAGGAGCGCGAGGCCATCAT	0.557																																					p.E582K		Atlas-SNP	.											.	RALBP1	48	.	0			c.G1744A						.						21	19	20					18																	9535711		2203	4299	6502	SO:0001583	missense	10928	exon10			GAGCGCGAGGCCA	L42542	CCDS11845.1	18p11.22	2006-04-22			ENSG00000017797	ENSG00000017797			9841	protein-coding gene	gene with protein product		605801				7673236	Standard	NM_006788		Approved	RLIP76, RIP1, RIP	uc002koc.3	Q15311	OTTHUMG00000131596	ENST00000019317.4:c.1744G>A	chr18.hg19:g.9535711G>A	ENSP00000019317:p.Glu582Lys	103.0	0.0		87.0	22.0	NM_006788	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	hg19	CCDS11845.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.081002	0.76528	.	.	ENSG00000017797	ENST00000019317;ENST00000383432	T;T	0.11277	2.79;2.79	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.11793	0.0287	M	0.63843	1.955	0.80722	D	1	P	0.47302	0.893	B	0.30105	0.111	T	0.15350	-1.0440	10	0.36615	T	0.2	-13.122	18.7058	0.91637	0.0:0.0:1.0:0.0	.	582	Q15311	RBP1_HUMAN	K	582	ENSP00000019317:E582K;ENSP00000372924:E582K	ENSP00000019317:E582K	E	+	1	0	RALBP1	9525711	1.000000	0.71417	0.961000	0.40146	0.870000	0.49936	9.144000	0.94629	2.478000	0.83669	0.655000	0.94253	GAG	.	.		0.557	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788		A	9535711	G	A	9535711	3	1	153	1	0	0	0	0	1	0	0	0	13027	1059	37	1	1778	1	RALBP1	18	9535711	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10		9535711	68541537	79	23542										
SPIRE1	56907	hgsc.bcm.edu	37	chr18	12464951	12464951	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gctggtcgacttgtgcagcgTttcttcctgagcaaagtaca	11	10	1	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr18:12464951T>C	ENST00000409402.4	-	11	1678	c.1411A>G	c.(1411-1413)Acg>Gcg	p.T471A	SPIRE1_ENST00000464481.1_5'UTR|SPIRE1_ENST00000453447.2_Missense_Mutation_p.T337A|SPIRE1_ENST00000410092.3_Missense_Mutation_p.T457A|SPIRE1_ENST00000383356.2_Missense_Mutation_p.T298A|SPIRE1_ENST00000309836.5_Missense_Mutation_p.T260A	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1											breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						TTGTGCAGCGTTTCTTCCTGA	0.453																																					p.T471A		Atlas-SNP	.											.	SPIRE1	120	.	0			c.A1411G						.						75	62	66					18																	12464951		2203	4300	6503	SO:0001583	missense	56907	exon11			GCAGCGTTTCTTC	AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"spire homolog 1 (Drosophila)", "spire family actin nucleation factor 1"			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.1411A>G	chr18.hg19:g.12464951T>C	ENSP00000387266:p.Thr471Ala	38.0	0.0		43.0	20.0	NM_001128626		Missense_Mutation	SNP	ENST00000409402.4	hg19	CCDS45829.1	.	.	.	.	.	.	.	.	.	.	T	0.968	-0.700975	0.03255	.	.	ENSG00000134278	ENST00000453447;ENST00000409402;ENST00000410092;ENST00000309836;ENST00000383356	T;T;T;T;T	0.42513	0.98;1.59;1.56;0.98;0.97	5.49	-3.27	0.05048	.	0.787769	0.12303	N	0.480905	T	0.25975	0.0633	L	0.46157	1.445	0.09310	N	1	B;B;B	0.12013	0.005;0.001;0.004	B;B;B	0.10450	0.005;0.002;0.004	T	0.36744	-0.9735	10	0.08179	T	0.78	-3.1922	6.2809	0.21007	0.1592:0.3839:0.0:0.4569	.	457;260;471	Q08AE8-2;B4DWX0;Q08AE8	.;.;SPIR1_HUMAN	A	337;471;457;260;298	ENSP00000407050:T337A;ENSP00000387266:T471A;ENSP00000387226:T457A;ENSP00000309661:T260A;ENSP00000372847:T298A	ENSP00000309661:T260A	T	-	1	0	SPIRE1	12454951	0.046000	0.20272	0.023000	0.16930	0.461000	0.32589	-0.096000	0.11059	-0.334000	0.08463	0.460000	0.39030	ACG	.	.		0.453	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818		C	12464951	T	C	12464951	3	2	153	1	0	0	0	0	1	0	0	0	15086	1725	60	2	887	2	SPIRE1	18	12464951	Missense_Mutation	SNP	T	TCGA-DD-AACB-01A-11D-A40R-10	2929240	12464951	65612297	80	23543										
C18orf19	125228	hgsc.bcm.edu	37	chr18	13681644	13681644	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tgttccaaaccaaacaccagAagttattagatgcactggaa	7	9	0	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr18:13681644A>T	ENST00000322247.3	-	3	820	c.433T>A	c.(433-435)Tct>Act	p.S145T	FAM210A_ENST00000588475.1_5'UTR|FAM210A_ENST00000402563.1_Missense_Mutation_p.S145T	NM_001098801.1	NP_001092271.1	Q96ND0	F210A_HUMAN	family with sequence similarity 210, member A	145	DUF1279.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)											CAAACACCAGAAGTTATTAGA	0.333																																					p.S145T		Atlas-SNP	.											.	.	.	.	0			c.T433A						.						81	79	80					18																	13681644		2203	4300	6503	SO:0001583	missense	125228	exon3			CACCAGAAGTTAT	AK055618	CCDS11866.1	18p11.21	2011-11-24	2011-11-24	2011-11-24	ENSG00000177150	ENSG00000177150			28346	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 19"	C18orf19		14702039	Standard	NM_152352		Approved	MGC24180, HsT2329	uc010dli.3	Q96ND0	OTTHUMG00000131719	ENST00000322247.3:c.433T>A	chr18.hg19:g.13681644A>T	ENSP00000323635:p.Ser145Thr	189.0	0.0		162.0	48.0	NM_001098801	D3DUJ4	Missense_Mutation	SNP	ENST00000322247.3	hg19	CCDS11866.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.824976	0.90955	.	.	ENSG00000177150	ENST00000322247;ENST00000402563	T;T	0.40476	1.03;1.03	5.51	5.51	0.81932	Domain of unknown function DUF1279 (1);	0.000000	0.85682	D	0.000000	T	0.71126	0.3303	M	0.90542	3.125	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78191	-0.2300	10	0.72032	D	0.01	-21.9681	15.6324	0.76920	1.0:0.0:0.0:0.0	.	145	Q96ND0	CR019_HUMAN	T	145	ENSP00000323635:S145T;ENSP00000386115:S145T	ENSP00000323635:S145T	S	-	1	0	C18orf19	13671644	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.198000	0.94994	2.080000	0.62538	0.533000	0.62120	TCT	.	.		0.333	FAM210A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254637.1	NM_152352		T	13681644	A	T	13681644	3	4	153	1	0	0	0	0	1	0	0	0	1898	246	9	4	397	4	C18orf19	18	13681644	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	1216693	13681644	64395604	81	23544										
C19orf20	91978	hgsc.bcm.edu	37	chr19	519039	519039	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	cccgaggaggtggtggcgccGctgctgcgcaaggtgcagtg	19	11	0	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr19:519039G>A	ENST00000359315.5	+	2	697	c.489G>A	c.(487-489)ccG>ccA	p.P163P		NM_033513.2	NP_277048.2	Q6ZTW0	TPGS1_HUMAN	tubulin polyglutamylase complex subunit 1	163					adult behavior (GO:0030534)|multicellular organismal development (GO:0007275)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|synaptic transmission (GO:0007268)|vesicle localization (GO:0051648)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)	tubulin-glutamic acid ligase activity (GO:0070740)										TGGTGGCGCCGCTGCTGCGCA	0.726																																					p.P163P		Atlas-SNP	.											.	.	.	.	0			c.G489A						.						5	8	7					19																	519039		1999	4033	6032	SO:0001819	synonymous_variant	91978	exon2			GGCGCCGCTGCTG	BC009520	CCDS42454.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000141933	ENSG00000141933			25058	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 20"	C19orf20		11441184, 12972506	Standard	NM_033513		Approved	GTRGEO22, PGs1	uc002lou.3	Q6ZTW0		ENST00000359315.5:c.489G>A	chr19.hg19:g.519039G>A		62.0	0.0		49.0	21.0	NM_033513	Q96GE2	Silent	SNP	ENST00000359315.5	hg19	CCDS42454.1																																																																																			.	.		0.726	TPGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451887.2	NM_033513		A	519039	G	A	519039	2	1	153	1	0	0	0	0	0	0	0	1	1914	1074	38	1		1	C19orf20	19	519039	Silent	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10		519039	58609944	82	23545										
LPPR3	79948	hgsc.bcm.edu	37	chr19	815228	815228	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	caggaaggagttgaagttgcAgccgccggcgttgatgctgc	16	9	0	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr19:815228A>G	ENST00000520876.3	-	4	439	c.361T>C	c.(361-363)Tgc>Cgc	p.C121R	MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Missense_Mutation_p.C121R	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		121						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										TTGAAGTTGCAGCCGCCGGCG	0.697																																					p.C121R		Atlas-SNP	.											.	.	.	.	0			c.T361C						.						18	23	21					19																	815228		2170	4274	6444	SO:0001583	missense	0	exon4			AGTTGCAGCCGCC																												ENST00000520876.3:c.361T>C	chr19.hg19:g.815228A>G	ENSP00000430297:p.Cys121Arg	57.0	0.0		56.0	39.0	NM_001270366	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	hg19	CCDS58636.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.515767	0.85495	.	.	ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876;ENST00000521445	T;T	0.50813	0.73;0.73	4.32	4.32	0.51571	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	U	0.000000	T	0.68851	0.3046	M	0.82517	2.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.73757	-0.3882	10	0.87932	D	0	-30.2469	11.4343	0.50060	1.0:0.0:0.0:0.0	.	121;121;121	Q6T4P5-2;Q6T4P5;Q6T4P5-3	.;LPPR3_HUMAN;.	R	121	ENSP00000352962:C121R;ENSP00000430297:C121R	ENSP00000300947:C121R	C	-	1	0	AC006273.1	766228	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	7.024000	0.76443	1.585000	0.49928	0.374000	0.22700	TGC	.	.		0.697	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3			G	815228	A	G	815228	3	3	153	1	0	0	0	0	1	0	0	0	8935	188	7	2	1895	2	LPPR3	19	815228	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	296189	815228	58313755	83	23546										
GTF2F1	2962	hgsc.bcm.edu	37	chr19	6387475	6387475	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gtgtgaaattgtaccagttgTgcacggggaaggcctcgaag	15	7	0	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr19:6387475T>C	ENST00000394456.5	-	5	886	c.422A>G	c.(421-423)cAc>cGc	p.H141R	GTF2F1_ENST00000429701.2_Intron|CTB-180A7.6_ENST00000599584.1_RNA	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	141					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						GTACCAGTTGTGCACGGGGAA	0.627																																					p.H141R		Atlas-SNP	.											.	GTF2F1	39	.	0			c.A422G						.						160	141	147					19																	6387475		2203	4300	6503	SO:0001583	missense	2962	exon5			CAGTTGTGCACGG		CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"General transcription factors"	4652	protein-coding gene	gene with protein product		189968	"general transcription factor IIF, polypeptide 1 (74kD subunit)"			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.422A>G	chr19.hg19:g.6387475T>C	ENSP00000377969:p.His141Arg	95.0	0.0		91.0	62.0	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	hg19	CCDS12165.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.976948	0.53720	.	.	ENSG00000125651	ENST00000394456;ENST00000542045	T	0.41400	1.0	5.39	5.39	0.77823	Transcription Factor IIF, Rap30/Rap74, interaction (1);	0.281476	0.39083	N	0.001462	T	0.38612	0.1047	L	0.55990	1.75	0.80722	D	1	B	0.19583	0.037	B	0.21360	0.034	T	0.25916	-1.0118	10	0.48119	T	0.1	-44.3265	10.5418	0.45037	0.0:0.0:0.1621:0.8379	.	141	P35269	T2FA_HUMAN	R	141;201	ENSP00000377969:H141R	ENSP00000377969:H141R	H	-	2	0	GTF2F1	6338475	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	2.502000	0.45398	2.024000	0.59613	0.533000	0.62120	CAC	.	.		0.627	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096		C	6387475	T	C	6387475	3	2	153	1	0	0	0	0	1	0	0	0	6867	1696	59	2	1167	2	GTF2F1	19	6387475	Missense_Mutation	SNP	T	TCGA-DD-AACB-01A-11D-A40R-10	5572247	6387475	52741508	84	23547										
MUC16	94025	hgsc.bcm.edu	37	chr19	9089258	9089258	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tagatgagtggaaggagtagAtgaagaaaatgtggttttga	15	0	0	6			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr19:9089258A>T	ENST00000397910.4	-	1	2760	c.2557T>A	c.(2557-2559)Tct>Act	p.S853T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	853	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAAGGAGTAGATGAAGAAAAT	0.453																																					p.S853T		Atlas-SNP	.											.	MUC16	4315	.	0			c.T2557A						.						107	103	105					19																	9089258		1939	4137	6076	SO:0001583	missense	94025	exon1			GAGTAGATGAAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.2557T>A	chr19.hg19:g.9089258A>T	ENSP00000381008:p.Ser853Thr	100.0	0.0		95.0	66.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	3.896	-0.022967	0.07634	.	.	ENSG00000181143	ENST00000397910	T	0.02552	4.25	1.45	1.45	0.22620	.	.	.	.	.	T	0.01661	0.0053	N	0.14661	0.345	.	.	.	D	0.55172	0.97	B	0.37387	0.248	T	0.46555	-0.9183	8	0.87932	D	0	.	5.0127	0.14321	1.0:0.0:0.0:0.0	.	853	B5ME49	.	T	853	ENSP00000381008:S853T	ENSP00000381008:S853T	S	-	1	0	MUC16	8950258	0.000000	0.05858	0.003000	0.11579	0.015000	0.08874	-0.029000	0.12329	0.918000	0.36919	0.172000	0.16884	TCT	.	.		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9089258	A	T	9089258	3	4	153	1	0	0	0	0	1	0	0	0	9982	333	12	4	41302	4	MUC16	19	9089258	Missense_Mutation	SNP	A	TCGA-DD-AACB-01A-11D-A40R-10	2701783	9089258	50039725	85	23548										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610330	10610330	+	Frame_Shift_Del	DEL	C	C	-													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ccatgaccttggggtggataCcctcaatggacaccacctcc							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr19:10610330delC	ENST00000171111.5	-	2	927	c.380delG	c.(379-381)ggtfs	p.G127fs	KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Frame_Shift_Del_p.G127fs	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	127	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GGGGTGGATACCCTCAATGGA	0.597																																					p.G127fs		Atlas-INDEL	.											.	KEAP1	182	.	0			c.381delT						.						127	102	110					19																	10610330		2203	4300	6503	SO:0001589	frameshift_variant	9817	exon2			.	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.380delG	chr19.hg19:g.10610330delC	ENSP00000171111:p.Gly127fs	76.0	0.0		69.0	50.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Frame_Shift_Del	DEL	ENST00000171111.5	hg19	CCDS12239.1																																																																																			.	.		0.597	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		-	10610330	C	-	10610330	7	5	153	1	0	1	0	1	0	0	0	0	8150	507	18	0	1514	0	KEAP1	19	10610330	Frame_Shift_Del	DEL	C	TCGA-DD-AACB-01A-11D-A40R-10	1521072	10610330	48518653	86	23549										
PGLYRP2	114770	hgsc.bcm.edu	37	chr19	15586526	15586526	+	Frame_Shift_Del	DEL	G	G	-													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	agcagcaccgttctgccgtcGgaagttgctgcggaaccctg							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr19:15586526delG	ENST00000340880.4	-	2	1435	c.955delC	c.(955-957)cgafs	p.R320fs	PGLYRP2_ENST00000292609.4_Frame_Shift_Del_p.R320fs	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	320					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						TTCTGCCGTCGGAAGTTGCTG	0.637																																					p.R319fs		Atlas-INDEL	.											.	PGLYRP2	116	.	0			c.956delG						.						45	44	44					19																	15586526		2203	4300	6503	SO:0001589	frameshift_variant	114770	exon2			.	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"peptidoglycan recognition protein L precursor", "peptidoglycan recognition protein-like", "N-acetylmuramoyl-L-alanine amidase"	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.955delC	chr19.hg19:g.15586526delG	ENSP00000345968:p.Arg320fs	78.0	0.0		64.0	17.0	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Frame_Shift_Del	DEL	ENST00000340880.4	hg19	CCDS12330.2																																																																																			.	.		0.637	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		-	15586526	G	-	15586526	7	5	153	1	0	1	0	1	0	0	0	0	11803	1124	39	0	791	0	PGLYRP2	19	15586526	Frame_Shift_Del	DEL	G	TCGA-DD-AACB-01A-11D-A40R-10	4976196	15586526	43542457	87	23550										
LILRA2	11027	hgsc.bcm.edu	37	chr19	55086934	55086934	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggccctgtgagcccctcccaCgggggccagtacagatgcta	13	15	0	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr19:55086934C>T	ENST00000251377.3	+	6	1000	c.867C>T	c.(865-867)caC>caT	p.H289H	LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000391737.1_Silent_p.H277H|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000418536.2_Intron|LILRA2_ENST00000391738.3_Silent_p.H289H|LILRA2_ENST00000251376.3_Silent_p.H289H			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	289	Ig-like C2-type 3.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		GCCCCTCCCACGGGGGCCAGT	0.652																																					p.H289H		Atlas-SNP	.											.	LILRA2	99	.	0			c.C867T						.						49	51	50					19																	55086934		2203	4299	6502	SO:0001819	synonymous_variant	11027	exon5			CTCCCACGGGGGC	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.867C>T	chr19.hg19:g.55086934C>T		160.0	0.0		141.0	42.0	NM_001130917	O75020	Silent	SNP	ENST00000251377.3	hg19	CCDS46179.1																																																																																			.	.		0.652	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			T	55086934	C	T	55086934	2	4	153	1	0	0	0	0	0	0	0	1	8794	535	19	1		1	LILRA2	19	55086934	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	39500408	55086934	4042049	88	23551										
CHGB	1114	hgsc.bcm.edu	37	chr20	5903753	5903754	+	Frame_Shift_Ins	INS	-	-	G													0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	acgtcagcatggccagtttaINSggggaaaagagggaccacca							TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr20:5903753_5903754insG	ENST00000378961.4	+	4	1167_1168	c.963_964insG	c.(964-966)gggfs	p.G322fs		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	322						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						TGGCCAGTTTAGGGGAAAAGAG	0.545																																					p.L321fs		Atlas-INDEL	.											.	CHGB	112	.	0			c.963_964insG						.																																			SO:0001589	frameshift_variant	1114	exon4			.		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.967dupG	chr20.hg19:g.5903757_5903757dupG	ENSP00000368244:p.Gly322fs	145.0	0.0		186.0	33.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Frame_Shift_Ins	INS	ENST00000378961.4	hg19	CCDS13092.1																																																																																			.	.		0.545	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		G	5903754	-	G	5903753	7	5	153	1	0	1	1	0	0	0	0	0	3341	417	15	0	977	0	CHGB	20	5903753	Frame_Shift_Ins	INS	-	TCGA-DD-AACB-01A-11D-A40R-10		5903753	57121767	89	23552										
RPN2	6185	hgsc.bcm.edu	37	chr20	35812641	35812641	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gccagcacctgggctctgacGcccactcactacctcaccaa	7	19	3	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr20:35812641G>T	ENST00000237530.6	+	2	383	c.72G>T	c.(70-72)acG>acT	p.T24T	RPN2_ENST00000373622.5_Silent_p.T24T	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II	24					aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				GGGCTCTGACGCCCACTCACT	0.522																																					p.T24T		Atlas-SNP	.											.	RPN2	45	.	0			c.G72T						.						134	106	116					20																	35812641		2203	4300	6503	SO:0001819	synonymous_variant	6185	exon2			TCTGACGCCCACT	Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"oligosaccharyltransferase complex subunit (non-catalytic)"	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.72G>T	chr20.hg19:g.35812641G>T		137.0	0.0		145.0	25.0	NM_002951	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Silent	SNP	ENST00000237530.6	hg19	CCDS13291.1																																																																																			.	.		0.522	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079076.2	NM_002951		T	35812641	G	T	35812641	2	4	153	1	0	0	0	0	0	0	0	1	13623	1074	38	1		1	RPN2	20	35812641	Silent	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	29908888	35812641	27212879	90	23553										
EMILIN3	90187	hgsc.bcm.edu	37	chr20	39992390	39992390	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggtgaggcagccccatggtcCgtgaggtgctcagggcagcg	18	11	1	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr20:39992390C>A	ENST00000332312.3	-	3	594	c.402G>T	c.(400-402)acG>acT	p.T134T		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	134						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)		p.T134T(1)		biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				CCCCATGGTCCGTGAGGTGCT	0.627																																					p.T134T		Atlas-SNP	.											EMILIN3,caecum,carcinoma,0,1	EMILIN3	63	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G402T						.						97	82	87					20																	39992390		2203	4300	6503	SO:0001819	synonymous_variant	90187	exon3			ATGGTCCGTGAGG	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"EMI domain containing"	16123	protein-coding gene	gene with protein product	"chromosome 20 open reading frame 130"	608929	"elastin microfibril interfacer 5"	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.402G>T	chr20.hg19:g.39992390C>A		121.0	0.0		125.0	22.0	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	hg19	CCDS13316.1																																																																																			.	.		0.627	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741		A	39992390	C	A	39992390	2	1	153	1	0	0	0	0	0	0	0	1	5097	639	23	1		1	EMILIN3	20	39992390	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	4179749	39992390	23033130	91	23554										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40827954	40827954	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	cgctgagcttggtggtgggtTtgtcggcagaggccacaggc	18	9	0	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr20:40827954T>A	ENST00000373187.1	-	16	2416	c.2417A>T	c.(2416-2418)aAa>aTa	p.K806I	PTPRT_ENST00000373201.1_Missense_Mutation_p.K796I|PTPRT_ENST00000373184.1_Missense_Mutation_p.K796I|PTPRT_ENST00000373190.1_Missense_Mutation_p.K806I|PTPRT_ENST00000373198.4_Missense_Mutation_p.K825I|PTPRT_ENST00000373193.3_Missense_Mutation_p.K809I|PTPRT_ENST00000356100.2_Missense_Mutation_p.K815I			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	806					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				GGTGGTGGGTTTGTCGGCAGA	0.557																																					p.K825I		Atlas-SNP	.											.	PTPRT	372	.	0			c.A2474T						.						184	195	191					20																	40827954		2046	4199	6245	SO:0001583	missense	11122	exon17			GTGGGTTTGTCGG	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.2417A>T	chr20.hg19:g.40827954T>A	ENSP00000362283:p.Lys806Ile	136.0	0.0		128.0	16.0	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.176104	0.78564	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.37752	1.18;1.19;1.2;1.2;1.19;1.2;1.2	6.03	6.03	0.97812	.	0.046442	0.85682	D	0.000000	T	0.44746	0.1308	L	0.52573	1.65	0.53688	D	0.999972	P;P	0.47034	0.889;0.823	P;B	0.48454	0.578;0.374	T	0.38222	-0.9671	10	0.62326	D	0.03	.	16.5582	0.84512	0.0:0.0:0.0:1.0	.	828;806	O14522-1;O14522	.;PTPRT_HUMAN	I	806;806;809;815;828;796;796	ENSP00000362286:K806I;ENSP00000362283:K806I;ENSP00000362289:K809I;ENSP00000348408:K815I;ENSP00000362294:K828I;ENSP00000362280:K796I;ENSP00000362297:K796I	ENSP00000348408:K815I	K	-	2	0	PTPRT	40261368	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.632000	0.67819	2.308000	0.77769	0.533000	0.62120	AAA	.	.		0.557	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	40827954	T	A	40827954	3	1	153	1	0	0	0	0	1	0	0	0	12827	1841	64	4	1972	4	PTPRT	20	40827954	Missense_Mutation	SNP	T	TCGA-DD-AACB-01A-11D-A40R-10	835564	40827954	22197566	92	23555										
NCOA5	57727	hgsc.bcm.edu	37	chr20	44692024	44692024	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	agagagtcggtgctgctcctCatcagccgctccttccgctc	10	16	2	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr20:44692024C>T	ENST00000290231.6	-	7	1289	c.1125G>A	c.(1123-1125)atG>atA	p.M375I		NM_020967.2	NP_066018.1	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	375					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				TGCTGCTCCTCATCAGCCGCT	0.567																																					p.M375I		Atlas-SNP	.											.	NCOA5	58	.	0			c.G1125A						.						60	54	56					20																	44692024		2203	4300	6503	SO:0001583	missense	57727	exon7			GCTCCTCATCAGC		CCDS13392.1	20q12-q13.12	2008-07-02			ENSG00000124160	ENSG00000124160			15909	protein-coding gene	gene with protein product	"coactivator independent of AF-2"					11780052, 11113208	Standard	XM_005260474		Approved	bA465L10.6, CIA	uc002xre.3	Q9HCD5	OTTHUMG00000032639	ENST00000290231.6:c.1125G>A	chr20.hg19:g.44692024C>T	ENSP00000290231:p.Met375Ile	35.0	0.0		43.0	26.0	NM_020967	B2RTV9|E1P5R0|Q6HA99|Q9H1F2|Q9H2T2|Q9H4Y9	Missense_Mutation	SNP	ENST00000290231.6	hg19	CCDS13392.1	.	.	.	.	.	.	.	.	.	.	C	8.872	0.949552	0.18356	.	.	ENSG00000124160	ENST00000290231	T	0.39787	1.06	5.41	3.31	0.37934	.	0.437392	0.28796	N	0.014106	T	0.17662	0.0424	N	0.03608	-0.345	0.22171	N	0.999313	B	0.02656	0.0	B	0.04013	0.001	T	0.08827	-1.0703	10	0.49607	T	0.09	-12.6995	5.3686	0.16127	0.1485:0.6233:0.1442:0.084	.	375	Q9HCD5	NCOA5_HUMAN	I	375	ENSP00000290231:M375I	ENSP00000290231:M375I	M	-	3	0	NCOA5	44125431	0.991000	0.36638	0.970000	0.41538	0.759000	0.43091	0.366000	0.20365	1.478000	0.48253	0.561000	0.74099	ATG	.	.		0.567	NCOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079559.1	NM_020967		T	44692024	C	T	44692024	3	4	153	1	0	0	0	0	1	0	0	0	10241	826	29	3	622	3	NCOA5	20	44692024	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10	3864070	44692024	18333496	93	23556										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58489238	58489238	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	tgaaaaccactgatgtgccaGttcttgtctttgtttttctg	8	8	3	2			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr20:58489238G>A	ENST00000357552.3	-	11	928	c.703C>T	c.(703-705)Ctg>Ttg	p.L235L	SYCP2_ENST00000371001.2_Silent_p.L235L			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	235					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			TGATGTGCCAGTTCTTGTCTT	0.299																																					p.L235L		Atlas-SNP	.											.	SYCP2	204	.	0			c.C703T						.						91	87	88					20																	58489238		2202	4295	6497	SO:0001819	synonymous_variant	10388	exon10			GTGCCAGTTCTTG	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.703C>T	chr20.hg19:g.58489238G>A		133.0	0.0		160.0	11.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Silent	SNP	ENST00000357552.3	hg19	CCDS13482.1																																																																																			.	.		0.299	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		A	58489238	G	A	58489238	2	1	153	1	0	0	0	0	0	0	0	1	15447	1020	36	3		3	SYCP2	20	58489238	Silent	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	13797214	58489238	4536282	94	23557										
SRMS	6725	hgsc.bcm.edu	37	chr20	62172284	62172284	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gagcacgtagacctccgccgGgcaggcagccgggcgcggca	17	15	0	1			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr20:62172284G>A	ENST00000217188.1	-	8	1394	c.1354C>T	c.(1354-1356)Ccg>Tcg	p.P452S		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	452	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> L (in dbSNP:rs8120713). {ECO:0000269|PubMed:17344846}.		peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			ACCTCCGCCGGGCAGGCAGCC	0.687																																					p.P452S		Atlas-SNP	.											.	SRMS	48	.	0			c.C1354T						.						61	65	63					20																	62172284		2202	4297	6499	SO:0001583	missense	6725	exon8			CCGCCGGGCAGGC		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"SH2 domain containing"	11298	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 148"	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.1354C>T	chr20.hg19:g.62172284G>A	ENSP00000217188:p.Pro452Ser	45.0	0.0		47.0	7.0	NM_080823		Missense_Mutation	SNP	ENST00000217188.1	hg19	CCDS13525.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.362583	0.41902	.	.	ENSG00000125508	ENST00000217188	T	0.10763	2.84	5.17	2.92	0.33932	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.226361	0.31370	N	0.007769	T	0.12220	0.0297	L	0.47016	1.485	0.44388	D	0.997299	P	0.35944	0.529	B	0.41917	0.37	T	0.04178	-1.0971	10	0.66056	D	0.02	.	7.1483	0.25595	0.1577:0.1748:0.6675:0.0	.	452	Q9H3Y6	SRMS_HUMAN	S	452	ENSP00000217188:P452S	ENSP00000217188:P452S	P	-	1	0	SRMS	61642728	1.000000	0.71417	0.988000	0.46212	0.054000	0.15201	4.452000	0.60054	1.150000	0.42419	0.655000	0.94253	CCG	.	.		0.687	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823		A	62172284	G	A	62172284	3	1	153	1	0	0	0	0	1	0	0	0	15167	1232	43	3	116	3	SRMS	20	62172284	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10	3683046	62172284	853236	95	23558										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41416170	41416170	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	atagcggtttctcgctgtggGcccagccttggcattcctcc	11	14	1	0	rs36025081		TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr21:41416170G>A	ENST00000400454.1	-	31	5695	c.5218C>T	c.(5218-5220)Ccc>Tcc	p.P1740S		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1740					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CTCGCTGTGGGCCCAGCCTTG	0.592																																					p.P1740S	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C5218T						.						77	86	83					21																	41416170		2131	4240	6371	SO:0001583	missense	1826	exon31			CTGTGGGCCCAGC	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.5218C>T	chr21.hg19:g.41416170G>A	ENSP00000383303:p.Pro1740Ser	53.0	0.0		68.0	5.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	g	19.59	3.856661	0.71834	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.58060	0.36;0.46	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.60586	0.2280	L	0.27053	0.805	0.52501	D	0.999954	D	0.89917	1.0	D	0.83275	0.996	T	0.52660	-0.8546	10	0.14656	T	0.56	.	19.4936	0.95062	0.0:0.0:1.0:0.0	.	1740	O60469	DSCAM_HUMAN	S	1740;1492	ENSP00000383303:P1740S;ENSP00000385342:P1492S	ENSP00000383303:P1740S	P	-	1	0	DSCAM	40338040	1.000000	0.71417	0.993000	0.49108	0.536000	0.34869	9.751000	0.98889	2.605000	0.88082	0.655000	0.94253	CCC	.	.		0.592	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41416170	G	A	41416170	3	1	153	1	0	0	0	0	1	0	0	0	4770	1203	42	3	832	3	DSCAM	21	41416170	Missense_Mutation	SNP	G	TCGA-DD-AACB-01A-11D-A40R-10		41416170	6713725	96	23559										
LIF	3976	hgsc.bcm.edu	37	chr22	30640879	30640879	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	gtgatggggagggggctcccCgccccatgtttccagtgcag	16	12	0	1	rs368278663		TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chr22:30640879C>T	ENST00000249075.3	-	2	218	c.63G>A	c.(61-63)gcG>gcA	p.A21A	RP1-102K2.8_ENST00000608354.1_RNA|LIF_ENST00000403987.3_Intron|RP1-102K2.8_ENST00000593843.1_RNA	NM_002309.4	NP_002300.1	P15018	LIF_HUMAN	leukemia inhibitory factor	21					blood vessel remodeling (GO:0001974)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|immune response (GO:0006955)|leukemia inhibitory factor signaling pathway (GO:0048861)|lung alveolus development (GO:0048286)|lung lobe morphogenesis (GO:0060463)|lung vasculature development (GO:0060426)|multicellular organismal development (GO:0007275)|muscle organ morphogenesis (GO:0048644)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of hormone secretion (GO:0046888)|negative regulation of meiosis (GO:0045835)|neuron development (GO:0048666)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cell proliferation (GO:0008284)|positive regulation of histone H3-K27 acetylation (GO:1901676)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|spongiotrophoblast differentiation (GO:0060708)|stem cell maintenance (GO:0019827)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|leukemia inhibitory factor receptor binding (GO:0005146)|receptor binding (GO:0005102)|RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001135)			breast(1)|lung(3)|skin(3)	7			Epithelial(10;0.171)			GGGGGCTCCCCGCCCCATGTT	0.597																																					p.A21A		Atlas-SNP	.											.	LIF	18	.	0			c.G63A						.	C		0,4406		0,0,2203	131	116	121		63	-8.8	0	22		121	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	LIF	NM_002309.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		21/203	30640879	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3976	exon2			GCTCCCCGCCCCA		CCDS13872.1, CCDS58799.1	22q12.2	2012-02-09	2012-02-09		ENSG00000128342	ENSG00000128342			6596	protein-coding gene	gene with protein product	"differentiation inhibitory activity", "differentiation-inducing factor", "hepatocyte-stimulating factor III", "cholinergic differentiation factor", "human interleukin in DA cells"	159540				1714745, 8058719	Standard	NM_002309		Approved	CDF, DIA, HILDA	uc003agz.3	P15018	OTTHUMG00000150910	ENST00000249075.3:c.63G>A	chr22.hg19:g.30640879C>T		125.0	0.0		127.0	6.0	NM_002309	B2RCW7|B5MC23|Q52LZ2	Silent	SNP	ENST00000249075.3	hg19	CCDS13872.1																																																																																			.	.		0.597	LIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320508.1	NM_002309		T	30640879	C	T	30640879	2	4	153	1	0	0	0	0	0	0	0	1	8788	639	23	1		1	LIF	22	30640879	Silent	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10		30640879	20663687	97	23560										
NAP1L3	4675	hgsc.bcm.edu	37	chrX	92927344	92927344	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0412371134020619	4	1	0.818454935622318	0	0.861531511181387	0.06993006993007	0.521678321678322	0	ggcccgagcttgtcaacattCtttaaaacaatcagccaata	6	11	3	0			TCGA-DD-AACB-01A-11D-A40R-10	TCGA-DD-AACB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c89647e-854d-47b7-bf48-df5f8112ba84	035d1a22-9937-469e-a65c-1e9eb89fc338	g.chrX:92927344C>A	ENST00000373079.3	-	1	1223	c.960G>T	c.(958-960)aaG>aaT	p.K320N	FAM133A_ENST00000332647.4_5'Flank|NAP1L3_ENST00000475430.2_Missense_Mutation_p.K313N|FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000322139.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	320					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						TGTCAACATTCTTTAAAACAA	0.438																																					p.K320N		Atlas-SNP	.											.	NAP1L3	81	.	0			c.G960T						.						60	55	57					X																	92927344		2203	4298	6501	SO:0001583	missense	4675	exon1			AACATTCTTTAAA		CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.960G>T	chrX.hg19:g.92927344C>A	ENSP00000362171:p.Lys320Asn	212.0	0.0		117.0	37.0	NM_004538	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	hg19	CCDS14465.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.752359	0.49362	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.28255	1.62	3.68	2.81	0.32909	.	0.048073	0.85682	D	0.000000	T	0.49218	0.1544	M	0.76002	2.32	0.32679	N	0.515783	D	0.89917	1.0	D	0.91635	0.999	T	0.59300	-0.7480	10	0.72032	D	0.01	.	6.0749	0.19909	0.0:0.8573:0.0:0.1427	.	320	Q99457	NP1L3_HUMAN	N	320;313	ENSP00000362171:K320N	ENSP00000362171:K320N	K	-	3	2	NAP1L3	92814000	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	1.818000	0.39012	0.923000	0.37045	0.529000	0.55759	AAG	.	.		0.438	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538		A	92927344	C	A	92927344	3	1	153	1	0	0	0	0	1	0	0	0	10167	912	32	3	564	3	NAP1L3	23	92927344	Missense_Mutation	SNP	C	TCGA-DD-AACB-01A-11D-A40R-10		92927344	62343216	98	23561										
C1orf173	127254	hgsc.bcm.edu	37	chr1	75072555	75072556	+	Frame_Shift_Ins	INS	-	-	T													0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ctagatttcggcaaagacggINSttttttgtcaaggcccattg							TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr1:75072555_75072556insT	ENST00000326665.5	-	10	1436_1437	c.1218_1219insA	c.(1216-1221)aaaccgfs	p.P407fs	C1orf173_ENST00000420661.2_Frame_Shift_Ins_p.P210fs|RP4-612J11.1_ENST00000416017.1_RNA	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		407										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						GGCAAAGACGGTTTTTTGTCAA	0.421																																					p.P407fs		Atlas-INDEL	.											C1orf173,NS,carcinoma,+2,1	C1orf173	380	.	0			c.1219_1220insA						.																																			SO:0001589	frameshift_variant	127254	exon10			.																												ENST00000326665.5:c.1219dupA	chr1.hg19:g.75072561_75072561dupT	ENSP00000322609:p.Pro407fs	78.0	0.0		79.0	12.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Frame_Shift_Ins	INS	ENST00000326665.5	hg19	CCDS30755.1																																																																																			.	.		0.421	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			T	75072556	-	T	75072555	7	5	154	1	0	1	1	0	0	0	0	0	2016	1261	44	0	3393	0	C1orf173	1	75072555	Frame_Shift_Ins	INS	-	TCGA-DD-AACC-01A-11D-A40R-10		75072555	174178066	1	23562										
AGL	178	hgsc.bcm.edu	37	chr1	100366399	100366399	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	cctacagatgattctgctccTttgcctgctggcacactggt	9	13	1	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr1:100366399T>G	ENST00000294724.4	+	26	4048	c.3570T>G	c.(3568-3570)ccT>ccG	p.P1190P	AGL_ENST00000361522.4_Silent_p.P1173P|AGL_ENST00000361302.3_Silent_p.P1174P|AGL_ENST00000370163.3_Silent_p.P1190P|AGL_ENST00000370165.3_Silent_p.P1190P|AGL_ENST00000370161.2_Silent_p.P1174P|AGL_ENST00000361915.3_Silent_p.P1190P	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	1190					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		ATTCTGCTCCTTTGCCTGCTG	0.343																																					p.P1190P		Atlas-SNP	.											.	AGL	137	.	0			c.T3570G						.						149	142	144					1																	100366399		2203	4300	6503	SO:0001819	synonymous_variant	178	exon26			TGCTCCTTTGCCT	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.3570T>G	chr1.hg19:g.100366399T>G		125.0	0.0		120.0	19.0	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	hg19	CCDS759.1																																																																																			.	.		0.343	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		G	100366399	T	G	100366399	2	3	154	1	0	0	0	0	0	0	0	1	384	1596	56	5		5	AGL	1	100366399	Silent	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	25293844	100366399	148884222	2	23563										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118574431	118574431	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggtcactataacaggaaccaCtgttggagtgagtgctgaag	13	7	1	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr1:118574431C>A	ENST00000336338.5	-	25	3558	c.3493G>T	c.(3493-3495)Gtg>Ttg	p.V1165L		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1165						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ACAGGAACCACTGTTGGAGTG	0.353																																					p.V1165L		Atlas-SNP	.											.	SPAG17	263	.	0			c.G3493T						.						137	129	132					1																	118574431		2203	4300	6503	SO:0001583	missense	200162	exon25			GAACCACTGTTGG		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.3493G>T	chr1.hg19:g.118574431C>A	ENSP00000337804:p.Val1165Leu	159.0	0.0		152.0	30.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	4.535	0.099225	0.08681	.	.	ENSG00000155761	ENST00000336338	T	0.29397	1.57	5.52	3.66	0.41972	.	0.824566	0.10906	N	0.621108	T	0.05547	0.0146	N	0.22421	0.69	0.09310	N	1	B	0.28350	0.208	B	0.29598	0.104	T	0.41502	-0.9505	10	0.13853	T	0.58	.	3.0627	0.06204	0.1411:0.5653:0.1368:0.1568	.	1165	Q6Q759	SPG17_HUMAN	L	1165	ENSP00000337804:V1165L	ENSP00000337804:V1165L	V	-	1	0	SPAG17	118375954	0.041000	0.20044	0.688000	0.30117	0.254000	0.26022	0.643000	0.24750	0.701000	0.31803	0.655000	0.94253	GTG	.	.		0.353	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118574431	C	A	118574431	3	1	154	1	0	0	0	0	1	0	0	0	14994	565	20	3	3274	3	SPAG17	1	118574431	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	18208032	118574431	130676190	3	23564										
ANP32E	81611	hgsc.bcm.edu	37	chr1	150204152	150204152	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	agctgggaagccgggccagcGaacttagttccacattagcc	12	12	0	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr1:150204152G>A	ENST00000314136.8	-	2	536	c.167C>T	c.(166-168)tCg>tTg	p.S56L	ANP32E_ENST00000369119.3_Missense_Mutation_p.S8L|ANP32E_ENST00000369116.4_Intron|ANP32E_ENST00000533654.1_Missense_Mutation_p.S56L|ANP32E_ENST00000369115.2_Intron|ANP32E_ENST00000369114.5_Missense_Mutation_p.S56L|ANP32E_ENST00000436748.2_Missense_Mutation_p.S56L	NM_001136478.2|NM_001280559.1|NM_030920.3	NP_001129950.1|NP_001267488.1|NP_112182.1	Q9BTT0	AN32E_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	56					histone exchange (GO:0043486)|negative regulation of catalytic activity (GO:0043086)	cytoplasmic membrane-bounded vesicle (GO:0016023)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	histone binding (GO:0042393)|phosphatase inhibitor activity (GO:0019212)			breast(3)|endometrium(3)|lung(7)|skin(1)|urinary_tract(1)	15	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCGGGCCAGCGAACTTAGTTC	0.413																																					p.S56L		Atlas-SNP	.											.	ANP32E	28	.	0			c.C167T						.						106	104	105					1																	150204152		2203	4300	6503	SO:0001583	missense	81611	exon2			GCCAGCGAACTTA	AK092672	CCDS946.1, CCDS44214.1, CCDS44215.1, CCDS60245.1	1q22	2008-02-05			ENSG00000143401	ENSG00000143401		"ANP32 acidic nuclear phosphoproteins"	16673	protein-coding gene	gene with protein product		609611				12438741	Standard	NM_030920		Approved	LANPL, MGC5350, LANP-L	uc001etw.3	Q9BTT0	OTTHUMG00000012547	ENST00000314136.8:c.167C>T	chr1.hg19:g.150204152G>A	ENSP00000324074:p.Ser56Leu	64.0	0.0		101.0	9.0	NM_030920	B4E0I6|E9PEA6|Q5TB18|Q5TB20|Q8N1S4|Q8WWW9	Missense_Mutation	SNP	ENST00000314136.8	hg19	CCDS946.1	.	.	.	.	.	.	.	.	.	.	G	35	5.563696	0.96527	.	.	ENSG00000143401	ENST00000314136;ENST00000369119;ENST00000436748;ENST00000369114;ENST00000533654	T;T;T;T;T	0.00408	7.54;7.54;7.54;7.54;7.54	6.06	6.06	0.98353	.	0.059521	0.64402	D	0.000001	T	0.01189	0.0039	M	0.91663	3.23	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;0.988;0.997	T	0.57877	-0.7735	10	0.87932	D	0	.	19.609	0.95594	0.0:0.0:1.0:0.0	.	56;56;56;8	E9PLC4;E9PEA6;Q9BTT0;Q5TB20	.;.;AN32E_HUMAN;.	L	56;8;56;56;56	ENSP00000324074:S56L;ENSP00000358115:S8L;ENSP00000393718:S56L;ENSP00000358110:S56L;ENSP00000435215:S56L	ENSP00000324074:S56L	S	-	2	0	ANP32E	148470776	1.000000	0.71417	0.993000	0.49108	0.987000	0.75469	9.202000	0.95026	2.882000	0.98803	0.655000	0.94253	TCG	.	.		0.413	ANP32E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035056.1	NM_030920		A	150204152	G	A	150204152	3	1	154	1	0	0	0	0	1	0	0	0	709	1059	37	1	663	1	ANP32E	1	150204152	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	31629721	150204152	99046469	4	23565										
TROVE2	6738	hgsc.bcm.edu	37	chr1	193045776	193045776	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	taatgaaaaactattaaaaaAggtaagcattatcattgttc	5	4	1	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr1:193045776A>G	ENST00000367446.3	+	4	1157	c.947A>G	c.(946-948)aAg>aGg	p.K316R	TROVE2_ENST00000400968.2_Splice_Site_p.K316R|TROVE2_ENST00000432079.1_Splice_Site_p.K41R|TROVE2_ENST00000416058.2_Splice_Site_p.K41R|TROVE2_ENST00000460715.2_3'UTR|TROVE2_ENST00000367441.1_Splice_Site_p.K316R|TROVE2_ENST00000367445.3_Splice_Site_p.K316R|TROVE2_ENST00000367443.1_Splice_Site_p.K316R|TROVE2_ENST00000367444.3_Splice_Site_p.K316R	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2	316	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)			biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						CTATTAAAAAAGGTAAGCATT	0.318																																					p.K316R		Atlas-SNP	.											.	TROVE2	50	.	0			c.A947G						.						71	70	70					1																	193045776		1804	4066	5870	SO:0001630	splice_region_variant	6738	exon4			TAAAAAAGGTAAG	BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.948+1A>G	chr1.hg19:g.193045776A>G		219.0	0.0		298.0	44.0	NM_004600	B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Missense_Mutation	SNP	ENST00000367446.3	hg19	CCDS1379.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.830097	0.71258	.	.	ENSG00000116747	ENST00000400968;ENST00000416058;ENST00000367446;ENST00000367443;ENST00000367445;ENST00000367444;ENST00000367441	T;T;T;T;T;T;T	0.12569	2.67;2.67;2.67;2.67;2.67;2.67;2.67	5.38	4.25	0.50352	TROVE (2);	0.044639	0.85682	N	0.000000	T	0.20007	0.0481	L	0.39514	1.22	0.53005	D	0.999965	B;B;B;D	0.63880	0.04;0.04;0.127;0.993	B;B;B;P	0.59761	0.075;0.075;0.092;0.863	T	0.04565	-1.0942	10	0.11794	T	0.64	-19.8266	11.1853	0.48653	0.9278:0.0:0.0722:0.0	.	316;316;316;316	Q5LJ99;Q5LJ98;Q5LJA0;P10155	.;.;.;RO60_HUMAN	R	316;41;316;316;316;316;316	ENSP00000383752:K316R;ENSP00000411421:K41R;ENSP00000356416:K316R;ENSP00000356413:K316R;ENSP00000356415:K316R;ENSP00000356414:K316R;ENSP00000356411:K316R	ENSP00000356411:K316R	K	+	2	0	TROVE2	191312399	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.691000	0.74573	1.003000	0.39130	0.456000	0.33151	AAG	.	.		0.318	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	NM_004600	Missense_Mutation	G	193045776	A	G	193045776	5	3	154	1	0	0	0	0	0	0	1	0	16591	86	3	2	957	2	TROVE2	1	193045776	Splice_Site	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	42841624	193045776	56204845	5	23566										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232649711	232649711	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ctggttttctctgggcacttCcaagacggagacacctgcat	10	12	1	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr1:232649711C>T	ENST00000366630.1	-	2	1733	c.1375G>A	c.(1375-1377)Gaa>Aaa	p.E459K	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.E459K			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	459					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CTGGGCACTTCCAAGACGGAG	0.483																																					p.E459K		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G1375A						.						153	149	150					1																	232649711		1965	4160	6125	SO:0001583	missense	57568	exon1			GCACTTCCAAGAC	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.1375G>A	chr1.hg19:g.232649711C>T	ENSP00000355589:p.Glu459Lys	99.0	0.0		119.0	39.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.981252	0.93044	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	D;D	0.86030	-2.06;-2.06	5.39	5.39	0.77823	.	0.055252	0.64402	D	0.000001	D	0.93779	0.8011	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.94331	0.7562	10	0.87932	D	0	-36.6723	19.3561	0.94414	0.0:1.0:0.0:0.0	.	459	Q9P2F8	SI1L2_HUMAN	K	459	ENSP00000355589:E459K;ENSP00000262861:E459K	ENSP00000262861:E459K	E	-	1	0	SIPA1L2	230716334	1.000000	0.71417	0.997000	0.53966	0.981000	0.71138	7.651000	0.83577	2.810000	0.96702	0.650000	0.86243	GAA	.	.		0.483	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		T	232649711	C	T	232649711	3	4	154	1	0	0	0	0	1	0	0	0	14345	864	30	3	3877	3	SIPA1L2	1	232649711	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	39603935	232649711	16600910	6	23567										
MSH6	2956	hgsc.bcm.edu	37	chr2	48010529	48010544	+	Frame_Shift_Del	DEL	GCTGGGCCTGGGCCCA	GCTGGGCCTGGGCCCA	-													0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gggatgcggcctggagcgagGctgggcctgggcccaggccc					rs63751098		TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	GCTGGGCCTGGGCCCA	GCTGGGCCTGGGCCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr2:48010529_48010544delGCTGGGCCTGGGCCCA	ENST00000234420.5	+	1	309_324	c.157_172delGCTGGGCCTGGGCCCA	c.(157-174)gctgggcctgggcccaggfs	p.AGPGPR53fs	MSH6_ENST00000538136.1_5'Flank|MSH6_ENST00000540021.1_Frame_Shift_Del_p.AGPGPR53fs|RNU6-688P_ENST00000516063.1_RNA	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	53				AAPGASPSPGGDAAWSEAGPGP -> GCPRGLSFPRRGCGL ERGWAWA (in Ref. 2; BAA23674/BAA23675). {ECO:0000305}.	ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTGGAGCGAGGCTGGGCCTGGGCCCAGGCCCTTGGC	0.75			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.52_57del		Atlas-INDEL	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.156_171del	GRCh37	CM034828	MSH6	M	rs63751098	.																																			SO:0001589	frameshift_variant	2956	exon1	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	.	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.157_172delGCTGGGCCTGGGCCCA	chr2.hg19:g.48010529_48010544delGCTGGGCCTGGGCCCA	ENSP00000234420:p.Ala53fs	74.0	0.0		86.0	14.0	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Frame_Shift_Del	DEL	ENST00000234420.5	hg19	CCDS1836.1																																																																																			.	.		0.75	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		-	48010544	GCTGGGCCTGGGCCCA	-	48010529	7	5	154	1	0	1	0	1	0	0	0	0	9883	1203	42	0	159	0	MSH6	2	48010529	Frame_Shift_Del	DEL	GCTGGGCCTGGGCCCA	TCGA-DD-AACC-01A-11D-A40R-10		48010529	195188844	7	23568										
PCBP1	5093	hgsc.bcm.edu	37	chr2	70315623	70315623	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gacaacagtctcactttgccAtgatgcacggcgggaccgga	12	12	1	1	rs548418658		TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr2:70315623A>G	ENST00000303577.5	+	1	1039	c.748A>G	c.(748-750)Atg>Gtg	p.M250V	PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000439670.2_RNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000458698.2_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	250					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						TCACTTTGCCATGATGCACGG	0.527																																					p.M250V	Colon(85;1146 1307 3484 18706 25380)	Atlas-SNP	.											.	PCBP1	28	.	0			c.A748G						.						77	72	73					2																	70315623		2203	4300	6503	SO:0001583	missense	5093	exon1			TTTGCCATGATGC		CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.748A>G	chr2.hg19:g.70315623A>G	ENSP00000305556:p.Met250Val	139.0	0.0		140.0	23.0	NM_006196	Q13157|Q14975	Missense_Mutation	SNP	ENST00000303577.5	hg19	CCDS1898.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.192143	0.38707	.	.	ENSG00000169564	ENST00000303577	T	0.29397	1.57	4.32	4.32	0.51571	.	0.420286	0.18063	N	0.152899	T	0.33030	0.0849	M	0.69823	2.125	0.42082	D	0.991251	B	0.25563	0.129	B	0.29942	0.109	T	0.09058	-1.0692	10	0.15499	T	0.54	.	12.0954	0.53752	1.0:0.0:0.0:0.0	.	250	Q15365	PCBP1_HUMAN	V	250	ENSP00000305556:M250V	ENSP00000305556:M250V	M	+	1	0	PCBP1	70169127	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.928000	0.48908	2.181000	0.69327	0.533000	0.62120	ATG	.	.		0.527	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		G	70315623	A	G	70315623	3	3	154	1	0	0	0	0	1	0	0	0	11509	217	8	2	750	2	PCBP1	2	70315623	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	22305094	70315623	172883750	8	23569										
SLC39A10	57181	hgsc.bcm.edu	37	chr2	196593046	196593046	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tttgcagtcactgcaggcatGttcctctatgtagccttggt	10	10	2	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr2:196593046G>A	ENST00000409086.3	+	9	2585	c.2310G>A	c.(2308-2310)atG>atA	p.M770I	SLC39A10_ENST00000359634.5_Missense_Mutation_p.M770I|SLC39A10_ENST00000541054.1_Missense_Mutation_p.M320I	NM_001127257.1	NP_001120729.1	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter), member 10	770					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(16)|pancreas(1)|prostate(1)|skin(2)	34			OV - Ovarian serous cystadenocarcinoma(117;0.221)			CTGCAGGCATGTTCCTCTATG	0.413																																					p.M770I		Atlas-SNP	.											.	SLC39A10	89	.	0			c.G2310A						.						224	190	202					2																	196593046		2203	4300	6503	SO:0001583	missense	57181	exon9			AGGCATGTTCCTC		CCDS33353.1	2q33.1	2013-05-22			ENSG00000196950	ENSG00000196950		"Solute carriers"	20861	protein-coding gene	gene with protein product		608733	"solute carrier family 39 (metal ion transporter), member 10"			12659941	Standard	NM_020342		Approved	KIAA1265, FLJ90515, DKFZp564L2123	uc002utg.4	Q9ULF5	OTTHUMG00000154380	ENST00000409086.3:c.2310G>A	chr2.hg19:g.196593046G>A	ENSP00000386766:p.Met770Ile	131.0	0.0		149.0	27.0	NM_020342	A8K5C6|B4DGU0|Q3MJA4|Q68CR5|Q6DKH6|Q9Y3Z1	Missense_Mutation	SNP	ENST00000409086.3	hg19	CCDS33353.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.690335	0.68271	.	.	ENSG00000196950	ENST00000409086;ENST00000359634;ENST00000541054	T;T;T	0.46063	0.88;0.88;0.88	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.50205	0.1602	L	0.50919	1.6	0.80722	D	1	B	0.32968	0.392	B	0.44224	0.444	T	0.40175	-0.9577	10	0.34782	T	0.22	.	19.0594	0.93081	0.0:0.0:1.0:0.0	.	770	Q9ULF5	S39AA_HUMAN	I	770;770;320	ENSP00000386766:M770I;ENSP00000352655:M770I;ENSP00000437787:M320I	ENSP00000352655:M770I	M	+	3	0	SLC39A10	196301291	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.614000	0.82996	2.750000	0.94351	0.561000	0.74099	ATG	.	.		0.413	SLC39A10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335186.1	XM_047707		A	196593046	G	A	196593046	3	1	154	1	0	0	0	0	1	0	0	0	14628	1377	48	3	2340	3	SLC39A10	2	196593046	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	126277423	196593046	46606327	9	23570										
PTH2R	5746	hgsc.bcm.edu	37	chr2	209345847	209345847	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	agttctagctaccaaaatctGggagaccaatgcagttgggc	11	9	2	1	rs151296979		TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr2:209345847G>T	ENST00000272847.2	+	10	1247	c.1034G>T	c.(1033-1035)tGg>tTg	p.W345L	PTH2R_ENST00000413482.1_3'UTR|AC019185.4_ENST00000424628.1_RNA	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	345					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)	p.W345L(2)		breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	ACCAAAATCTGGGAGACCAAT	0.358													G|||	1	0.000199681	0	0	5008	,	,		17253	0		0.001	False		,,,				2504	0				p.W345L		Atlas-SNP	.											PTH2R,NS,carcinoma,0,2	PTH2R	92	.	2	Substitution - Missense(2)	lung(2)	c.G1034T						.	G	LEU/TRP	0,4406		0,0,2203	101	99	99		1034	4.7	1	2	dbSNP_134	99	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PTH2R	NM_005048.2	61	0,2,6501	TT,TG,GG		0.0233,0.0,0.0154	probably-damaging	345/551	209345847	2,13004	2203	4300	6503	SO:0001583	missense	5746	exon10			AAATCTGGGAGAC	BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"GPCR / Class B : Parathyroid hormone receptors"	9609	protein-coding gene	gene with protein product		601469	"parathyroid hormone receptor 2"	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1034G>T	chr2.hg19:g.209345847G>T	ENSP00000272847:p.Trp345Leu	218.0	0.0		259.0	21.0	NM_005048	Q8N429	Missense_Mutation	SNP	ENST00000272847.2	hg19	CCDS2383.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.987720	0.74589	0.0	2.33E-4	ENSG00000144407	ENST00000272847	T	0.31769	1.48	5.54	4.66	0.58398	GPCR, family 2-like (1);	0.000000	0.47093	D	0.000255	T	0.43942	0.1270	L	0.45228	1.405	0.40834	D	0.983611	D;D	0.63880	0.993;0.993	D;D	0.66497	0.944;0.944	T	0.30504	-0.9976	9	.	.	.	.	12.6927	0.56985	0.081:0.0:0.919:0.0	.	234;345	B4DFN8;P49190	.;PTH2R_HUMAN	L	345	ENSP00000272847:W345L	.	W	+	2	0	PTH2R	209054092	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.302000	0.96175	1.477000	0.48234	0.650000	0.86243	TGG	.	G|1.000;T|0.000		0.358	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048		T	209345847	G	T	209345847	3	4	154	1	0	0	0	0	1	0	0	0	12773	1357	47	3	1072	3	PTH2R	2	209345847	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	12752801	209345847	33853526	10	23571										
GRM7	2917	hgsc.bcm.edu	37	chr3	7620315	7620315	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	aggcccaatgaaaatcgaacCggatgccaggatattcccat	9	11	0	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:7620315C>T	ENST00000357716.4	+	8	1996	c.1722C>T	c.(1720-1722)acC>acT	p.T574T	GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000402647.2_Silent_p.T574T|GRM7_ENST00000486284.1_Silent_p.T574T|GRM7_ENST00000389336.4_Silent_p.T574T|GRM7_ENST00000403881.1_Silent_p.T574T	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	574					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						AAAATCGAACCGGATGCCAGG	0.522																																					p.T574T		Atlas-SNP	.											.	GRM7	223	.	0			c.C1722T						.						137	135	136					3																	7620315		2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			TCGAACCGGATGC	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1722C>T	chr3.hg19:g.7620315C>T		110.0	0.0		109.0	12.0	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	hg19	CCDS43042.1																																																																																			.	.		0.522	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		T	7620315	C	T	7620315	2	4	154	1	0	0	0	0	0	0	0	1	6811	639	23	1		1	GRM7	3	7620315	Silent	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10		7620315	190402115	11	23572										
SH3BP5	9467	hgsc.bcm.edu	37	chr3	15300545	15300545	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggcctgcaggtcatccacagTctttttcagttgctgatcaa	9	11	4	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:15300545T>C	ENST00000383791.3	-	7	902	c.682A>G	c.(682-684)Act>Gct	p.T228A	SH3BP5-AS1_ENST00000420195.1_RNA|SH3BP5-AS1_ENST00000436602.1_RNA|SH3BP5_ENST00000253688.5_Missense_Mutation_p.T71A|SH3BP5_ENST00000426925.1_Missense_Mutation_p.T71A|SH3BP5_ENST00000408919.3_Missense_Mutation_p.T71A|SH3BP5-AS1_ENST00000413977.1_RNA	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	228					intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	protein kinase inhibitor activity (GO:0004860)			NS(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	12						TCATCCACAGTCTTTTTCAGT	0.488																																					p.T228A		Atlas-SNP	.											.	SH3BP5	32	.	0			c.A682G						.						77	65	69					3																	15300545		2203	4300	6503	SO:0001583	missense	9467	exon7			CCACAGTCTTTTT	AB005047	CCDS2625.2, CCDS43055.1	3p24.3	2008-07-10			ENSG00000131370	ENSG00000131370			10827	protein-coding gene	gene with protein product	"SH3 binding protein"	605612				9571151, 10339589	Standard	NM_004844		Approved	Sab	uc003bzp.2	O60239	OTTHUMG00000129859	ENST00000383791.3:c.682A>G	chr3.hg19:g.15300545T>C	ENSP00000373301:p.Thr228Ala	85.0	0.0		89.0	7.0	NM_004844	B3KQW6|Q5JWV9	Missense_Mutation	SNP	ENST00000383791.3	hg19	CCDS2625.2	.	.	.	.	.	.	.	.	.	.	T	8.882	0.951889	0.18431	.	.	ENSG00000131370	ENST00000383791;ENST00000426925;ENST00000253688;ENST00000408919;ENST00000366391	T;T	0.78246	-1.16;2.35	5.36	2.88	0.33553	.	0.254800	0.44097	D	0.000487	T	0.59115	0.2170	N	0.19112	0.55	0.41422	D	0.987801	B	0.02656	0.0	B	0.08055	0.003	T	0.48340	-0.9044	10	0.13853	T	0.58	-4.9378	9.8627	0.41125	0.0:0.1458:0.0:0.8542	.	228	O60239	3BP5_HUMAN	A	228;71;71;71;71	ENSP00000373301:T228A;ENSP00000394115:T71A	ENSP00000253688:T71A	T	-	1	0	SH3BP5	15275549	1.000000	0.71417	0.952000	0.39060	0.258000	0.26162	3.313000	0.51935	0.852000	0.35287	0.414000	0.27820	ACT	.	.		0.488	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844		C	15300545	T	C	15300545	3	2	154	1	0	0	0	0	1	0	0	0	14262	1667	58	2	697	2	SH3BP5	3	15300545	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	7680230	15300545	182721885	12	23573										
NR1D2	9975	hgsc.bcm.edu	37	chr3	24009404	24009404	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggatgatttacactcaatggGagcaggggatctgctaaact	12	7	2	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:24009404G>T	ENST00000312521.4	+	7	1752	c.1433G>T	c.(1432-1434)gGa>gTa	p.G478V	NR1D2_ENST00000492552.1_3'UTR	NM_001145425.1|NM_005126.4	NP_001138897.1|NP_005117	Q14995	NR1D2_HUMAN	nuclear receptor subfamily 1, group D, member 2	478	Interaction with ZNHIT1.|Ligand-binding.				gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lipid homeostasis (GO:0055088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of inflammatory response (GO:0050727)|regulation of lipid metabolic process (GO:0019216)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.G478fs*6(1)		NS(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	22						CACTCAATGGGAGCAGGGGAT	0.388																																					p.G478V		Atlas-SNP	.											.,2	NR1D2	52	.	1	Deletion - Frameshift(1)	prostate(1)	c.G1433T						.						143	138	140					3																	24009404		2203	4300	6503	SO:0001583	missense	9975	exon7			CAATGGGAGCAGG	BC045613	CCDS33718.1	3p24.1	2013-01-16			ENSG00000174738	ENSG00000174738		"Nuclear hormone receptors"	7963	protein-coding gene	gene with protein product		602304				7997240, 10198169	Standard	NM_005126		Approved	BD73, RVR, EAR-1r, HZF2, Hs.37288	uc003ccs.2	Q14995	OTTHUMG00000155659	ENST00000312521.4:c.1433G>T	chr3.hg19:g.24009404G>T	ENSP00000310006:p.Gly478Val	105.0	0.0		108.0	23.0	NM_005126	B2R8Q3|O00402|Q86XD4	Missense_Mutation	SNP	ENST00000312521.4	hg19	CCDS33718.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.873683	0.72180	.	.	ENSG00000174738	ENST00000312521;ENST00000396676	D	0.96619	-4.07	5.94	5.07	0.68467	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.98492	0.9497	M	0.92317	3.295	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99482	1.0948	10	0.87932	D	0	.	15.1079	0.72334	0.0677:0.0:0.9322:0.0	.	478	Q14995	NR1D2_HUMAN	V	478	ENSP00000310006:G478V	ENSP00000310006:G478V	G	+	2	0	NR1D2	23984408	1.000000	0.71417	1.000000	0.80357	0.647000	0.38526	9.789000	0.99068	1.516000	0.48900	-0.136000	0.14681	GGA	.	.		0.388	NR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341017.3			T	24009404	G	T	24009404	3	4	154	1	0	0	0	0	1	0	0	0	10625	1174	41	3	1459	3	NR1D2	3	24009404	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	8708859	24009404	174013026	13	23574										
SLC4A7	9497	hgsc.bcm.edu	37	chr3	27490188	27490188	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tctttatctgattctttatcTtttcttctccggtggtgatg	7	8	6	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:27490188T>G	ENST00000295736.5	-	3	286	c.216A>C	c.(214-216)aaA>aaC	p.K72N	SLC4A7_ENST00000437179.1_Missense_Mutation_p.K77N|SLC4A7_ENST00000425128.2_Missense_Mutation_p.K77N|SLC4A7_ENST00000428386.1_Missense_Mutation_p.K72N|SLC4A7_ENST00000455077.1_Missense_Mutation_p.K77N|SLC4A7_ENST00000446700.1_Missense_Mutation_p.K77N|SLC4A7_ENST00000454389.1_Missense_Mutation_p.K81N|SLC4A7_ENST00000440156.1_Missense_Mutation_p.K81N|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000445684.1_Missense_Mutation_p.K81N|SLC4A7_ENST00000435667.2_Missense_Mutation_p.K81N	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	72					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	ATTCTTTATCTTTTCTTCTCC	0.413																																					p.K77N		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A231C						.						241	217	225					3																	27490188		2203	4300	6503	SO:0001583	missense	9497	exon3			TTTATCTTTTCTT	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"Solute carriers"	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.216A>C	chr3.hg19:g.27490188T>G	ENSP00000295736:p.Lys72Asn	133.0	0.0		98.0	12.0	NM_001258379	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	hg19	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.627193	0.46944	.	.	ENSG00000033867	ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000425128;ENST00000428179	T;T;T;T;T;T;T;T;T;T;T	0.79247	-1.16;-1.18;-1.17;-1.25;-1.18;-1.24;-1.18;-1.24;-1.18;0.26;-1.18	5.56	5.56	0.83823	.	0.060857	0.64402	D	0.000003	T	0.74772	0.3760	L	0.42245	1.32	0.58432	D	0.999999	P;B;P;P;P;B;B;P;B	0.38992	0.653;0.178;0.653;0.647;0.546;0.435;0.249;0.546;0.178	B;B;B;B;B;B;B;B;B	0.43809	0.357;0.15;0.357;0.432;0.156;0.347;0.274;0.156;0.15	T	0.71248	-0.4649	10	0.20046	T	0.44	.	15.3698	0.74554	0.0:0.0:0.0:1.0	.	81;77;77;81;81;77;72;72;77	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;B6DY53;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	N	72;72;81;81;77;77;77;81;81;77;72	ENSP00000295736:K72N;ENSP00000416368:K72N;ENSP00000390394:K81N;ENSP00000414797:K81N;ENSP00000394252:K77N;ENSP00000406605:K77N;ENSP00000407382:K77N;ENSP00000406804:K81N;ENSP00000395336:K81N;ENSP00000401949:K77N;ENSP00000388703:K72N	ENSP00000295736:K72N	K	-	3	2	SLC4A7	27465192	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.488000	0.35551	2.106000	0.64143	0.528000	0.53228	AAA	.	.		0.413	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		G	27490188	T	G	27490188	3	3	154	1	0	0	0	0	1	0	0	0	14673	1606	56	5	3520	5	SLC4A7	3	27490188	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	3480784	27490188	170532242	14	23575										
CADPS	8618	hgsc.bcm.edu	37	chr3	62860303	62860303	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	atgtcggtgggctgcttggcAttaaaggggtaggcgatgca	17	6	0	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:62860303A>C	ENST00000383710.4	-	1	751	c.402T>G	c.(400-402)aaT>aaG	p.N134K	CADPS_ENST00000490353.2_Missense_Mutation_p.N134K|CADPS_ENST00000357948.3_Missense_Mutation_p.N134K|CADPS_ENST00000283269.9_Missense_Mutation_p.N134K	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	134					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		GCTGCTTGGCATTAAAGGGGT	0.632																																					p.N134K		Atlas-SNP	.											.	CADPS	387	.	0			c.T402G						.						41	35	37					3																	62860303		2193	4274	6467	SO:0001583	missense	8618	exon1			CTTGGCATTAAAG	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.402T>G	chr3.hg19:g.62860303A>C	ENSP00000373215:p.Asn134Lys	92.0	0.0		92.0	13.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	A	16.74	3.206270	0.58343	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000490353	D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76	4.73	0.664	0.17890	.	0.260090	0.37761	N	0.001960	D	0.88720	0.6513	M	0.81112	2.525	0.47308	D	0.999381	D;D;D	0.69078	0.997;0.989;0.997	D;D;D	0.75484	0.959;0.969;0.986	D	0.86393	0.1737	10	0.87932	D	0	.	7.8723	0.29573	0.4265:0.0:0.5735:0.0	.	134;134;134	Q9ULU8-2;Q9ULU8-3;Q9ULU8	.;.;CAPS1_HUMAN	K	134	ENSP00000373215:N134K;ENSP00000350632:N134K;ENSP00000283269:N134K;ENSP00000418736:N134K	ENSP00000283269:N134K	N	-	3	2	CADPS	62835343	0.997000	0.39634	1.000000	0.80357	0.957000	0.61999	0.337000	0.19841	0.083000	0.17047	-1.145000	0.01858	AAT	.	.		0.632	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		C	62860303	A	C	62860303	3	2	154	1	0	0	0	0	1	0	0	0	2572	214	8	5	3852	5	CADPS	3	62860303	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	35370115	62860303	135162127	15	23576										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108373111	108373111	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggattctgcaatggaagacaAgttctatagcctggatgaat	11	6	2	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:108373111A>G	ENST00000361582.3	+	19	2383	c.2153A>G	c.(2152-2154)aAg>aGg	p.K718R	DZIP3_ENST00000463306.1_Missense_Mutation_p.K718R	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	718					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						ATGGAAGACAAGTTCTATAGC	0.408																																					p.K718R		Atlas-SNP	.											.	DZIP3	111	.	0			c.A2153G						.						192	173	179					3																	108373111		2203	4300	6503	SO:0001583	missense	9666	exon19			AAGACAAGTTCTA	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2153A>G	chr3.hg19:g.108373111A>G	ENSP00000355028:p.Lys718Arg	148.0	0.0		120.0	21.0	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	hg19	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.284897	0.59867	.	.	ENSG00000198919	ENST00000361582;ENST00000463306	T;T	0.32023	1.47;1.47	4.81	3.66	0.41972	.	0.123171	0.36932	N	0.002337	T	0.32763	0.0840	L	0.44542	1.39	0.28799	N	0.898899	P;D	0.55172	0.948;0.97	B;P	0.51833	0.428;0.681	T	0.14952	-1.0454	10	0.56958	D	0.05	-9.4436	7.0365	0.24996	0.8978:0.0:0.1022:0.0	.	336;718	D3DN61;Q86Y13	.;DZIP3_HUMAN	R	718	ENSP00000355028:K718R;ENSP00000419981:K718R	ENSP00000355028:K718R	K	+	2	0	DZIP3	109855801	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	3.944000	0.56629	0.869000	0.35703	-0.361000	0.07541	AAG	.	.		0.408	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		G	108373111	A	G	108373111	3	3	154	1	0	0	0	0	1	0	0	0	4867	72	3	2	2223	2	DZIP3	3	108373111	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	45512808	108373111	89649319	16	23577										
POLQ	10721	hgsc.bcm.edu	37	chr3	121209009	121209009	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gaactcttagtttgggatatAaatgtgtgttcctttacttc	8	6	1	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:121209009A>T	ENST00000264233.5	-	16	2897	c.2769T>A	c.(2767-2769)ttT>ttA	p.F923L		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	923					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TTTGGGATATAAATGTGTGTT	0.328								DNA polymerases (catalytic subunits)																													p.F923L	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.T2769A						.						71	65	67					3																	121209009		2203	4300	6503	SO:0001583	missense	10721	exon16			GGATATAAATGTG	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.2769T>A	chr3.hg19:g.121209009A>T	ENSP00000264233:p.Phe923Leu	138.0	0.0		116.0	21.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.662092	0.29515	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.45276	0.9	5.62	1.7	0.24286	.	1.019970	0.07777	N	0.952772	T	0.27629	0.0679	L	0.32530	0.975	0.09310	N	1	B;B	0.11235	0.0;0.004	B;B	0.15484	0.002;0.013	T	0.29274	-1.0017	10	0.15066	T	0.55	.	3.9949	0.09553	0.406:0.3698:0.2242:0.0	.	923;95	O75417;O75417-2	DPOLQ_HUMAN;.	L	546;923;1059	ENSP00000264233:F923L	ENSP00000264233:F923L	F	-	3	2	POLQ	122691699	0.000000	0.05858	0.003000	0.11579	0.926000	0.56050	0.047000	0.14056	0.407000	0.25591	0.455000	0.32223	TTT	.	.		0.328	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121209009	A	T	121209009	3	4	154	1	0	0	0	0	1	0	0	0	12217	359	13	4	5063	4	POLQ	3	121209009	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	12835898	121209009	76813421	17	23578										
ITGB5	3693	hgsc.bcm.edu	37	chr3	124592378	124592378	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	cactagtgcatatgttgagaCctttaaagcaagataaagat	8	6	0	3			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:124592378C>G	ENST00000296181.4	-	2	367	c.71G>C	c.(70-72)gGt>gCt	p.G24A		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	24					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		TATGTTGAGACCTTTAAAGCA	0.438																																					p.G24A		Atlas-SNP	.											.	ITGB5	66	.	0			c.G71C						.						282	270	274					3																	124592378		2203	4300	6503	SO:0001630	splice_region_variant	3693	exon2			TTGAGACCTTTAA	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.71-1G>C	chr3.hg19:g.124592378C>G		109.0	0.0		102.0	18.0	NM_002213	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	hg19	CCDS3030.1	.	.	.	.	.	.	.	.	.	.	C	16.68	3.191633	0.58017	.	.	ENSG00000082781	ENST00000296181	D	0.90732	-2.72	5.04	5.04	0.67666	.	0.000000	0.85682	U	0.000000	T	0.78553	0.4301	N	0.08118	0	0.53688	D	0.999975	P	0.37122	0.583	B	0.20767	0.031	T	0.82456	-0.0448	10	0.62326	D	0.03	.	15.402	0.74849	0.0:1.0:0.0:0.0	.	24	P18084	ITB5_HUMAN	A	24	ENSP00000296181:G24A	ENSP00000296181:G24A	G	-	2	0	ITGB5	126075068	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	5.400000	0.66320	2.613000	0.88420	0.462000	0.41574	GGT	.	.		0.438	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213	Missense_Mutation	G	124592378	C	G	124592378	5	3	154	1	0	0	0	0	0	0	1	0	7907	521	18	4	2384	4	ITGB5	3	124592378	Splice_Site	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	3383369	124592378	73430052	18	23579										
KLF15	28999	hgsc.bcm.edu	37	chr3	126071187	126071235	+	Frame_Shift_Del	DEL	GGAACAGCGCTCTCTCCCGCTGGACCCAGGATGGAGGTGGCTCTTGTGT	GGAACAGCGCTCTCTCCCGCTGGACCCAGGATGGAGGTGGCTCTTGTGT	-													0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ctggcaccacctggtggaggGgaacagcgctctctcccgct					rs374592098|rs538422160|rs201547298		TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	GGAACAGCGCTCTCTCCCGCTGGACCCAGGATGGAGGTGGCTCTTGTGT	GGAACAGCGCTCTCTCCCGCTGGACCCAGGATGGAGGTGGCTCTTGTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:126071187_126071235delGGAACAGCGCTCTCTCCCGCTGGACCCAGGATGGAGGTGGCTCTTGTGT	ENST00000296233.3	-	2	761_809	c.531_579delACACAAGAGCCACCTCCATCCTGGGTCCAGCGGGAGAGAGCGCTGTTCC	c.(529-579)ccacacaagagccacctccatcctgggtccagcgggagagagcgctgttccfs	p.PHKSHLHPGSSGRERCS177fs	KLF15_ENST00000509675.1_5'Flank	NM_014079.3	NP_054798.1	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	177					cardiac muscle hypertrophy in response to stress (GO:0014898)|cellular response to peptide (GO:1901653)|glial cell differentiation (GO:0010001)|glomerular visceral epithelial cell differentiation (GO:0072112)|glucose transport (GO:0015758)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(7)|ovary(2)|skin(2)	12				GBM - Glioblastoma multiforme(114;0.147)		CTGGTGGAGGGGAACAGCGCTCTCTCCCGCTGGACCCAGGATGGAGGTGGCTCTTGTGTGGCCCAGCTG	0.643																																					p.178_194del		Atlas-INDEL	.											.	KLF15	40	.	0			c.532_580del						.																																			SO:0001589	frameshift_variant	28999	exon2			.	AB029254	CCDS3036.1	3q21.3	2013-01-08			ENSG00000163884	ENSG00000163884		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	14536	protein-coding gene	gene with protein product	"kidney-enriched Kruppel-like factor"	606465				10982849	Standard	NM_014079		Approved	KKLF	uc011bkk.1	Q9UIH9	OTTHUMG00000162689	ENST00000296233.3:c.531_579delACACAAGAGCCACCTCCATCCTGGGTCCAGCGGGAGAGAGCGCTGTTCC	chr3.hg19:g.126071187_126071235delGGAACAGCGCTCTCTCCCGCTGGACCCAGGATGGAGGTGGCTCTTGTGT	ENSP00000296233:p.Pro177fs	125.0	0.0		120.0	11.0	NM_014079		Frame_Shift_Del	DEL	ENST00000296233.3	hg19	CCDS3036.1																																																																																			.	.		0.643	KLF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370096.1	NM_014079		-	126071235	GGAACAGCGCTCTCTCCCGCTGGACCCAGGATGGAGGTGGCTCTTGTGT	-	126071187	7	5	154	1	0	1	0	1	0	0	0	0	8352	1219	43	0	679	0	KLF15	3	126071187	Frame_Shift_Del	DEL	GGAACAGCGCTCTCTCCCGCTGGACCCAGGATGGAGGTGGCTCTTGTGT	TCGA-DD-AACC-01A-11D-A40R-10	1478809	126071187	71951243	19	23580										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130346161	130346161	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	taatcaattgctctgtttacAgggcaatgatggcagtccag	10	8	2	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:130346161A>C	ENST00000358511.6	+	25	4972		c.e25-1		COL6A6_ENST00000453409.2_Splice_Site	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6						cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CTCTGTTTACAGGGCAATGAT	0.428																																					.		Atlas-SNP	.											.	COL6A6	497	.	0			c.4942-2A>C						.						177	176	176					3																	130346161		1903	4125	6028	SO:0001630	splice_region_variant	131873	exon25			GTTTACAGGGCAA	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.4942-1A>C	chr3.hg19:g.130346161A>C		160.0	0.0		182.0	32.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Splice_Site	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.586269	0.28268	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9756	0.53089	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL6A6	131828851	0.997000	0.39634	0.962000	0.40283	0.130000	0.20726	4.593000	0.61034	2.143000	0.66587	0.528000	0.53228	.	.	.		0.428	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	Intron	C	130346161	A	C	130346161	5	2	154	1	0	0	0	0	0	0	1	0	3705	202	7	5	5038	5	COL6A6	3	130346161	Splice_Site	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	4274974	130346161	67676269	20	23581										
ACTL6A	86	hgsc.bcm.edu	37	chr3	179304415	179304415	+	Missense_Mutation	SNP	T	T	C													0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ttggcggctccattctagccTctttggttagtagatgagct							TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:179304415T>C	ENST00000429709.2	+	13	1417	c.1204T>C	c.(1204-1206)Tct>Cct	p.S402P	ACTL6A_ENST00000392662.1_Missense_Mutation_p.S360P|RP11-15L13.4_ENST00000608818.1_RNA|ACTL6A_ENST00000450518.2_Missense_Mutation_p.S360P|RP11-145M9.6_ENST00000610007.1_RNA	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A	402					ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			CATTCTAGCCTCTTTGGTTAG	0.338																																					p.S402P		Atlas-SNP	.											.	ACTL6A	43	.	0			c.T1204C						.						84	84	84					3																	179304415		2203	4300	6503	SO:0001583	missense	86	exon13			CTAGCCTCTTTGG	AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"INO80 complex subunits"	24124	protein-coding gene	gene with protein product	"BAF complex 53 kDa subunit", "BRG1-associated factor", "actin-related protein 4", "INO80 complex subunit K"	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.1204T>C	chr3.hg19:g.179304415T>C	ENSP00000397552:p.Ser402Pro	44.0	0.0		51.0	10.0	NM_004301	B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Missense_Mutation	SNP	ENST00000429709.2	hg19	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.496203	0.85069	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	D;D;D	0.95518	-3.73;-3.73;-3.73	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.98469	0.9490	H	0.95470	3.675	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99671	1.0996	10	0.87932	D	0	.	16.3483	0.83171	0.0:0.0:0.0:1.0	.	402	O96019	ACL6A_HUMAN	P	402;360;360	ENSP00000397552:S402P;ENSP00000394014:S360P;ENSP00000376430:S360P	ENSP00000376430:S360P	S	+	1	0	ACTL6A	180787109	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	7.616000	0.83018	2.254000	0.74563	0.533000	0.62120	TCT	.	.		0.338	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	NM_004301		C	179304415	T	C	179304415	3	2	154	1	0	0	0	0	1	0	0	0	198	1551	54	2	1254	2	ACTL6A	3	179304415	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	48958254	179304415	18718015	21	23582	105	2								
ACTL6A	86	hgsc.bcm.edu	37	chr3	179304422	179304422	+	Splice_Site	SNP	T	T	G													0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ctccattctagcctctttggTtagtagatgagctactttgc							TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:179304422T>G	ENST00000429709.2	+	13	1422		c.e13+2		ACTL6A_ENST00000392662.1_Splice_Site|RP11-15L13.4_ENST00000608818.1_RNA|ACTL6A_ENST00000450518.2_Splice_Site|RP11-145M9.6_ENST00000610007.1_RNA	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A						ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			GCCTCTTTGGTTAGTAGATGA	0.338																																					.		Atlas-SNP	.											.	ACTL6A	43	.	0			c.1083+2T>G						.						83	82	82					3																	179304422		2203	4300	6503	SO:0001630	splice_region_variant	86	exon13			CTTTGGTTAGTAG	AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"INO80 complex subunits"	24124	protein-coding gene	gene with protein product	"BAF complex 53 kDa subunit", "BRG1-associated factor", "actin-related protein 4", "INO80 complex subunit K"	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.1209+2T>G	chr3.hg19:g.179304422T>G		41.0	0.0		50.0	11.0	NM_178042	B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Splice_Site	SNP	ENST00000429709.2	hg19	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.586884	0.46110	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	.	.	.	5.76	4.59	0.56863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1116	0.59277	0.0:0.0:0.1338:0.8662	.	.	.	.	.	-1	.	.	.	+	.	.	ACTL6A	180787116	1.000000	0.71417	0.998000	0.56505	0.556000	0.35491	7.616000	0.83018	0.981000	0.38548	0.533000	0.62120	.	.	.		0.338	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	NM_004301	Intron	G	179304422	T	G	179304422	5	3	154	1	0	0	0	0	0	0	1	0	198	1739	60	5	1261	5	ACTL6A	3	179304422	Splice_Site	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	7	179304422	18718008	22	23583	105	2								
MAP3K13	9175	hgsc.bcm.edu	37	chr3	185146704	185146704	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggacggagagagcacaagcgGaactgaagacataaagattc	13	7	0	4			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:185146704G>T	ENST00000265026.3	+	2	669	c.335G>T	c.(334-336)gGa>gTa	p.G112V	MAP3K13_ENST00000446828.1_Intron|MAP3K13_ENST00000424227.1_Missense_Mutation_p.G112V|MAP3K13_ENST00000535426.1_Intron|MAP3K13_ENST00000443863.1_Intron	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			AGCACAAGCGGAACTGAAGAC	0.493																																					p.G112V		Atlas-SNP	.											.	MAP3K13	209	.	0			c.G335T						.						107	99	102					3																	185146704		2203	4300	6503	SO:0001583	missense	9175	exon2			CAAGCGGAACTGA	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.335G>T	chr3.hg19:g.185146704G>T	ENSP00000265026:p.Gly112Val	153.0	0.0		186.0	24.0	NM_004721		Missense_Mutation	SNP	ENST00000265026.3	hg19	CCDS3270.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.934304	0.34096	.	.	ENSG00000073803	ENST00000447637;ENST00000424227;ENST00000428617;ENST00000265026	T;T;T;T	0.76448	0.31;-1.02;0.78;-1.02	5.61	4.73	0.59995	.	0.484890	0.21493	N	0.073653	T	0.62356	0.2421	N	0.08118	0	0.27651	N	0.9474	B	0.31054	0.306	B	0.33042	0.157	T	0.54774	-0.8243	10	0.28530	T	0.3	.	16.1836	0.81929	0.0:0.2507:0.7493:0.0	.	112	O43283	M3K13_HUMAN	V	112	ENSP00000389495:G112V;ENSP00000399910:G112V;ENSP00000405163:G112V;ENSP00000265026:G112V	ENSP00000265026:G112V	G	+	2	0	MAP3K13	186629398	1.000000	0.71417	0.015000	0.15790	0.772000	0.43724	4.100000	0.57762	1.346000	0.45694	0.655000	0.94253	GGA	.	.		0.493	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		T	185146704	G	T	185146704	3	4	154	1	0	0	0	0	1	0	0	0	9256	1174	41	3	337	3	MAP3K13	3	185146704	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	5842282	185146704	12875726	23	23584										
BCL6	604	hgsc.bcm.edu	37	chr3	187446200	187446200	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tctcccatctcctcagggaaCgtggggccagcggtgtggag	15	12	3	0	rs370060611		TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr3:187446200C>T	ENST00000406870.2	-	6	1854	c.1488G>A	c.(1486-1488)acG>acA	p.T496T	RP11-211G3.3_ENST00000437407.1_Intron|BCL6_ENST00000232014.4_Silent_p.T496T|BCL6_ENST00000450123.2_Silent_p.T496T|RP11-211G3.3_ENST00000449623.1_Intron	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	496					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		CCTCAGGGAACGTGGGGCCAG	0.597			"T, Mis"	"IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"	"NHL, CLL"								C|||	1	0.000199681	0	0.0014	5008	,	,		19897	0		0	False		,,,				2504	0				p.T496T		Atlas-SNP	.		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	.	BCL6	107	.	0			c.G1488A						.	C	,,	0,4406		0,0,2203	60	52	55		1488,1488,1488	-4.4	1	3		55	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	BCL6	NM_001130845.1,NM_001134738.1,NM_001706.4	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	496/707,496/651,496/707	187446200	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	604	exon5			AGGGAACGTGGGG		CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1001	protein-coding gene	gene with protein product		109565	"zinc finger protein 51"	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.1488G>A	chr3.hg19:g.187446200C>T		98.0	0.0		101.0	19.0	NM_001134738	A7E241|B8PSA7|D3DNV5	Silent	SNP	ENST00000406870.2	hg19	CCDS3289.1																																																																																			.	.		0.597	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931		T	187446200	C	T	187446200	2	4	154	1	0	0	0	0	0	0	0	1	1376	523	19	1		1	BCL6	3	187446200	Silent	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	2299496	187446200	10576230	24	23585										
C1QTNF7	114905	hgsc.bcm.edu	37	chr4	15443998	15443998	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gaagcatcgtgctcaaatccGccttttctgttggcatcaca	8	12	3	0	rs372857232		TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr4:15443998G>A	ENST00000444304.2	+	3	771	c.445G>A	c.(445-447)Gcc>Acc	p.A149T	C1QTNF7_ENST00000429690.1_Missense_Mutation_p.A149T|C1QTNF7_ENST00000295297.4_Missense_Mutation_p.A156T			Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7	149	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	16						GCTCAAATCCGCCTTTTCTGT	0.517																																					p.A156T		Atlas-SNP	.											.	C1QTNF7	36	.	0			c.G466A						.	G	THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	221	231	228		466,445,445	5.8	1	4		228	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	C1QTNF7	NM_001135170.1,NM_001135171.1,NM_031911.4	58,58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	156/297,149/290,149/290	15443998	1,13005	2203	4300	6503	SO:0001583	missense	114905	exon3			AAATCCGCCTTTT	AF329839	CCDS3414.1, CCDS47025.1	4p15.3	2008-08-29			ENSG00000163145	ENSG00000163145			14342	protein-coding gene	gene with protein product							Standard	NM_001135170		Approved	CTRP7	uc003gnp.3	Q9BXJ2	OTTHUMG00000097095	ENST00000444304.2:c.445G>A	chr4.hg19:g.15443998G>A	ENSP00000388914:p.Ala149Thr	210.0	0.0		240.0	46.0	NM_001135170	B2RBT3|J3KPW3	Missense_Mutation	SNP	ENST00000444304.2	hg19	CCDS3414.1	.	.	.	.	.	.	.	.	.	.	G	34	5.367332	0.95900	0.0	1.16E-4	ENSG00000163145	ENST00000295297;ENST00000429690;ENST00000444304	D;D;D	0.84873	-1.91;-1.91;-1.91	5.8	5.8	0.92144	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.000000	0.85682	D	0.000000	D	0.95376	0.8499	H	0.95982	3.75	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96191	0.9138	9	.	.	.	.	20.0545	0.97645	0.0:0.0:1.0:0.0	.	149	Q9BXJ2	C1QT7_HUMAN	T	156;149;149	ENSP00000295297:A156T;ENSP00000410722:A149T;ENSP00000388914:A149T	.	A	+	1	0	C1QTNF7	15053096	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	9.830000	0.99415	2.748000	0.94277	0.655000	0.94253	GCC	.	.		0.517	C1QTNF7-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250891.2			A	15443998	G	A	15443998	3	1	154	1	0	0	0	0	1	0	0	0	1970	1087	38	1	476	1	C1QTNF7	4	15443998	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10		15443998	175710278	25	23586										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46060363	46060363	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tcttctgctcaggtcaaaaaAaattgtcatgataacataat	5	7	5	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr4:46060363A>G	ENST00000295452.4	-	7	954	c.787T>C	c.(787-789)Ttt>Ctt	p.F263L		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	263					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AGGTCAAAAAAAATTGTCATG	0.284																																					p.F263L		Atlas-SNP	.											.	GABRG1	172	.	0			c.T787C						.						93	97	95					4																	46060363		2203	4300	6503	SO:0001583	missense	2565	exon7			CAAAAAAAATTGT	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.787T>C	chr4.hg19:g.46060363A>G	ENSP00000295452:p.Phe263Leu	383.0	0.0		352.0	55.0	NM_173536	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	A	19.46	3.832567	0.71258	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	T	0.78924	-1.22	5.82	5.82	0.92795	Neurotransmitter-gated ion-channel ligand-binding (3);	0.050552	0.85682	D	0.000000	T	0.70351	0.3214	N	0.20766	0.605	0.45806	D	0.998682	B	0.33549	0.417	B	0.39935	0.314	T	0.71886	-0.4457	10	0.49607	T	0.09	.	15.4084	0.74900	1.0:0.0:0.0:0.0	.	263	Q8N1C3	GBRG1_HUMAN	L	263	ENSP00000295452:F263L	ENSP00000295452:F263L	F	-	1	0	GABRG1	45755120	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.201000	0.95017	2.236000	0.73375	0.524000	0.50904	TTT	.	.		0.284	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		G	46060363	A	G	46060363	3	3	154	1	0	0	0	0	1	0	0	0	6179	14	1	2	622	2	GABRG1	4	46060363	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	30616365	46060363	145093913	26	23587										
DSPP	1834	hgsc.bcm.edu	37	chr4	88535860	88535861	+	In_Frame_Ins	INS	-	-	AGCAGCAGTAGCAGTGAC													0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	acagcagcagtagcagtgacINSagcagcaacagcagtgatag							TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr4:88535860_88535861insAGCAGCAGTAGCAGTGAC	ENST00000282478.7	+	4	2079_2080	c.2046_2047insAGCAGCAGTAGCAGTGAC	c.(2047-2049)agc>AGCAGCAGTAGCAGTGACagc	p.683_683S>SSSSSDS	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_In_Frame_Ins_p.683_683S>SSSSSDS			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	683	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtagcagtgacagcagcaacag	0.475																																					p.D682delinsDSSSSSD		Atlas-INDEL	.											.	DSPP	174	.	0			c.2046_2047insAGCAGCAGTAGCAGTGAC						.																																			SO:0001652	inframe_insertion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2029_2046dupAGCAGCAGTAGCAGTGAC	chr4.hg19:g.88535860_88535861insAGCAGCAGTAGCAGTGAC	ENSP00000282478:p.SerSerSerSerAspSer683dup	218.0	0.0		202.0	27.0	NM_014208	A8MUI0|O95815	In_Frame_Ins	INS	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.475	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		AGCAGCAGTAGCAGTGAC	88535861	-	AGCAGCAGTAGCAGTGAC	88535860	7	5	154	1	0	1	1	0	0	0	0	0	4784	477	17	0	2060	0	DSPP	4	88535860	In_Frame_Ins	INS	-	TCGA-DD-AACC-01A-11D-A40R-10	42475497	88535860	102618416	27	23588										
FGA	2243	hgsc.bcm.edu	37	chr4	155507643	155507643	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ttgcagtccctccagtcccaGagctcccagggtttcggttt	10	14	0	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr4:155507643G>A	ENST00000302053.3	-	5	1016	c.938C>T	c.(937-939)tCt>tTt	p.S313F	FGA_ENST00000403106.3_Missense_Mutation_p.S313F	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	313					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	TCCAGTCCCAGAGCTCCCAGG	0.572																																					p.S313F	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.C938T						.						101	110	107					4																	155507643		2203	4300	6503	SO:0001583	missense	2243	exon5			GTCCCAGAGCTCC		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.938C>T	chr4.hg19:g.155507643G>A	ENSP00000306361:p.Ser313Phe	168.0	0.0		103.0	11.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.685721	0.47991	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.80480	-1.38;-1.38	4.85	4.0	0.46444	.	.	.	.	.	T	0.79305	0.4423	M	0.62723	1.935	0.09310	N	1	P;P	0.43094	0.799;0.531	P;B	0.45610	0.487;0.154	T	0.72004	-0.4421	9	0.62326	D	0.03	.	6.0833	0.19952	0.1018:0.1936:0.7046:0.0	.	313;313	P02671-2;P02671	.;FIBA_HUMAN	F	313	ENSP00000306361:S313F;ENSP00000385981:S313F	ENSP00000306361:S313F	S	-	2	0	FGA	155727093	0.174000	0.23070	0.003000	0.11579	0.032000	0.12392	3.489000	0.53237	2.212000	0.71576	0.563000	0.77884	TCT	.	.		0.572	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		A	155507643	G	A	155507643	3	1	154	1	0	0	0	0	1	0	0	0	5838	942	33	3	1714	3	FGA	4	155507643	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	66971783	155507643	35646633	28	23589										
IRX1	79192	hgsc.bcm.edu	37	chr5	3599554	3599556	+	In_Frame_Del	DEL	CAT	CAT	-													0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggcgagaagatcatgctggcCatcatcaccaagatgaccct							TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr5:3599554_3599556delCAT	ENST00000302006.3	+	2	544_546	c.492_494delCAT	c.(490-495)gccatc>gcc	p.I166del	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	166					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TCATGCTGGCCATCATCACCAAG	0.626																																					p.164_165del		Atlas-INDEL	.											IRX1,NS,carcinoma,0,1	IRX1	106	.	0			c.491_493del						.																																			SO:0001651	inframe_deletion	79192	exon2			.	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.492_494delCAT	chr5.hg19:g.3599557_3599559delCAT	ENSP00000305244:p.Ile166del	131.0	0.0		139.0	12.0	NM_024337	Q7Z2F8|Q8N312	In_Frame_Del	DEL	ENST00000302006.3	hg19	CCDS34132.1																																																																																			.	.		0.626	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		-	3599556	CAT	-	3599554	7	5	154	1	0	1	0	1	0	0	0	0	7852	581	21	0	498	0	IRX1	5	3599554	In_Frame_Del	DEL	CAT	TCGA-DD-AACC-01A-11D-A40R-10		3599554	177315706	29	23590										
TARS	6897	hgsc.bcm.edu	37	chr5	33455170	33455170	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	atgacatgtacctcgaagaaGggtaagccatcaactagata	9	8	1	3			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr5:33455170G>T	ENST00000265112.3	+	5	885	c.574G>T	c.(574-576)Ggg>Tgg	p.G192W	TARS_ENST00000455217.2_Splice_Site_p.G225W|TARS_ENST00000414361.2_Splice_Site_p.G71W|TARS_ENST00000541634.1_Splice_Site_p.G88W|TARS_ENST00000502553.1_Splice_Site_p.G192W	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	192					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)			NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	CCTCGAAGAAGGGTAAGCCAT	0.383																																					p.G225W		Atlas-SNP	.											.	TARS	66	.	0			c.G673T						.						80	75	77					5																	33455170		2203	4300	6503	SO:0001630	splice_region_variant	6897	exon6			GAAGAAGGGTAAG	AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	11572	protein-coding gene	gene with protein product	"threonine tRNA ligase 1, cytoplasmic"	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.575+1G>T	chr5.hg19:g.33455170G>T		82.0	0.0		68.0	9.0	NM_001258438	A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Missense_Mutation	SNP	ENST00000265112.3	hg19	CCDS3899.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.907597	0.72868	.	.	ENSG00000113407	ENST00000502553;ENST00000265112;ENST00000541634;ENST00000455217;ENST00000414361	T;T;T;T;T	0.06933	3.24;3.24;3.24;3.24;3.24	5.86	5.86	0.93980	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.046695	0.85682	D	0.000000	T	0.18215	0.0437	L	0.41492	1.28	0.54753	D	0.999983	P;D;D;D	0.59357	0.94;0.985;0.957;0.972	P;P;P;P	0.54210	0.571;0.745;0.649;0.571	T	0.00036	-1.2257	10	0.87932	D	0	-24.8767	20.2429	0.98386	0.0:0.0:1.0:0.0	.	71;225;88;192	E7ERI3;B4DEG8;G3XAN9;P26639	.;.;.;SYTC_HUMAN	W	192;192;88;225;71	ENSP00000424387:G192W;ENSP00000265112:G192W;ENSP00000438469:G88W;ENSP00000387710:G225W;ENSP00000394291:G71W	ENSP00000265112:G192W	G	+	1	0	TARS	33490927	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	4.327000	0.59247	2.797000	0.96272	0.644000	0.83932	GGG	.	.		0.383	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295	Missense_Mutation	T	33455170	G	T	33455170	5	4	154	1	0	0	0	0	0	0	1	0	15574	1014	35	3	592	3	TARS	5	33455170	Splice_Site	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	29855616	33455170	147460090	30	23591										
FYB	2533	hgsc.bcm.edu	37	chr5	39135012	39135012	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tctgggttgtctgtgatgcgGatgatttcaatttgctctcc	11	8	4	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr5:39135012G>T	ENST00000351578.6	-	8	1810	c.1620C>A	c.(1618-1620)atC>atA	p.I540I	FYB_ENST00000512982.1_Silent_p.I540I|FYB_ENST00000515010.1_Silent_p.I540I|FYB_ENST00000505428.1_Silent_p.I540I|FYB_ENST00000540520.1_Silent_p.I550I	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	540	SH3.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			CTGTGATGCGGATGATTTCAA	0.438																																					p.I550I		Atlas-SNP	.											.	FYB	354	.	0			c.C1650A						.						202	186	191					5																	39135012		1890	4140	6030	SO:0001819	synonymous_variant	2533	exon8			GATGCGGATGATT	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1620C>A	chr5.hg19:g.39135012G>T		129.0	0.0		138.0	18.0	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	hg19	CCDS47200.1																																																																																			.	.		0.438	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		T	39135012	G	T	39135012	2	4	154	1	0	0	0	0	0	0	0	1	6132	1164	41	3		3	FYB	5	39135012	Silent	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	5679842	39135012	141780248	31	23592										
MEGF10	84466	hgsc.bcm.edu	37	chr5	126758426	126758426	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ccacgcagatggctgccaccCtaccacgggccattgccgct	10	18	0	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr5:126758426C>T	ENST00000274473.6	+	14	1922	c.1655C>T	c.(1654-1656)cCt>cTt	p.P552L	MEGF10_ENST00000418761.2_Missense_Mutation_p.P552L|MEGF10_ENST00000503335.2_Missense_Mutation_p.P552L|MEGF10_ENST00000508365.1_Missense_Mutation_p.P552L	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	552	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		GGCTGCCACCCTACCACGGGC	0.582																																					p.P552L		Atlas-SNP	.											.	MEGF10	152	.	0			c.C1655T						.						35	34	34					5																	126758426		2203	4300	6503	SO:0001583	missense	84466	exon14			GCCACCCTACCAC	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.1655C>T	chr5.hg19:g.126758426C>T	ENSP00000274473:p.Pro552Leu	181.0	0.0		223.0	47.0	NM_032446	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	hg19	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.108842	0.77096	.	.	ENSG00000145794	ENST00000503335;ENST00000508365;ENST00000418761;ENST00000274473	T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58	5.28	5.28	0.74379	EGF-like, laminin (1);Epidermal growth factor-like, type 3 (1);	0.326765	0.28161	N	0.016371	D	0.87317	0.6147	M	0.91196	3.185	0.80722	D	1	P;D	0.57899	0.912;0.981	P;D	0.65773	0.662;0.938	D	0.89000	0.3421	10	0.54805	T	0.06	-2.0654	19.2744	0.94026	0.0:1.0:0.0:0.0	.	552;552	Q96KG7-2;Q96KG7	.;MEG10_HUMAN	L	552	ENSP00000423354:P552L;ENSP00000423195:P552L;ENSP00000416284:P552L;ENSP00000274473:P552L	ENSP00000274473:P552L	P	+	2	0	MEGF10	126786325	0.934000	0.31675	0.998000	0.56505	0.985000	0.73830	3.183000	0.50918	2.636000	0.89361	0.650000	0.86243	CCT	.	.		0.582	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		T	126758426	C	T	126758426	3	4	154	1	0	0	0	0	1	0	0	0	9469	681	24	3	1701	3	MEGF10	5	126758426	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	87623414	126758426	54156834	32	23593										
SLC12A2	6558	hgsc.bcm.edu	37	chr5	127483379	127483379	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	atattttcagccactctttcTtcagcattagcatccctagt	4	12	4	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr5:127483379T>G	ENST00000262461.2	+	11	2028	c.1839T>G	c.(1837-1839)tcT>tcG	p.S613S	SLC12A2_ENST00000343225.4_Silent_p.S613S	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	613					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	CCACTCTTTCTTCAGCATTAG	0.328																																					p.S613S		Atlas-SNP	.											.	SLC12A2	119	.	0			c.T1839G						.						122	121	121					5																	127483379		2203	4296	6499	SO:0001819	synonymous_variant	6558	exon11			TCTTTCTTCAGCA		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.1839T>G	chr5.hg19:g.127483379T>G		111.0	0.0		156.0	47.0	NM_001046	Q8N713|Q8WWH7	Silent	SNP	ENST00000262461.2	hg19	CCDS4144.1																																																																																			.	.		0.328	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		G	127483379	T	G	127483379	2	3	154	1	0	0	0	0	0	0	0	1	14398	1596	56	5		5	SLC12A2	5	127483379	Silent	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	724953	127483379	53431881	33	23594										
HSPA9	3313	hgsc.bcm.edu	37	chr5	137897301	137897301	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	agtcatgccacccacaagaaTcacttctcctatgtcactct	4	15	5	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr5:137897301T>G	ENST00000297185.3	-	10	1275	c.1150A>C	c.(1150-1152)Att>Ctt	p.I384L	HSPA9_ENST00000501917.2_Intron|SNORD63_ENST00000384262.1_RNA|SNORD63_ENST00000411005.1_RNA	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	384					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CCCACAAGAATCACTTCTCCT	0.483																																					p.I384L		Atlas-SNP	.											.	HSPA9	49	.	0			c.A1150C						.						127	104	112					5																	137897301		2203	4300	6503	SO:0001583	missense	3313	exon10			CAAGAATCACTTC	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"Heat shock proteins / HSP70"	5244	protein-coding gene	gene with protein product		600548	"heat shock 70kDa protein 9B (mortalin-2)"	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.1150A>C	chr5.hg19:g.137897301T>G	ENSP00000297185:p.Ile384Leu	104.0	0.0		125.0	32.0	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	hg19	CCDS4208.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.284501	0.23392	.	.	ENSG00000113013	ENST00000297185;ENST00000541333;ENST00000540484	T	0.01025	5.43	5.37	4.2	0.49525	Heat shock protein 70, conserved site (1);	0.112190	0.64402	D	0.000009	T	0.00724	0.0024	N	0.16833	0.445	0.41132	D	0.98589	B;B	0.02656	0.0;0.0	B;B	0.11329	0.003;0.006	T	0.58674	-0.7595	10	0.13853	T	0.58	-13.3409	8.4308	0.32757	0.0:0.1523:0.0:0.8477	.	315;384	B7Z1V7;P38646	.;GRP75_HUMAN	L	384;337;370	ENSP00000297185:I384L	ENSP00000297185:I384L	I	-	1	0	HSPA9	137925200	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.105000	0.41825	0.985000	0.38656	0.533000	0.62120	ATT	.	.		0.483	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134		G	137897301	T	G	137897301	3	3	154	1	0	0	0	0	1	0	0	0	7426	1435	50	5	921	5	HSPA9	5	137897301	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	10413922	137897301	43017959	34	23595										
CPEB4	80315	hgsc.bcm.edu	37	chr5	173382953	173382953	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	cttggatgatcagctgtgtgAtgaatgtcagggggcccgtt	15	7	2	3			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr5:173382953A>T	ENST00000265085.5	+	10	3457	c.2003A>T	c.(2002-2004)gAt>gTt	p.D668V	CPEB4_ENST00000517880.1_Missense_Mutation_p.D261V|CPEB4_ENST00000334035.5_Missense_Mutation_p.D651V|CPEB4_ENST00000519467.1_3'UTR|CPEB4_ENST00000520867.1_Missense_Mutation_p.D643V|CPEB4_ENST00000522336.1_Missense_Mutation_p.D278V	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	668					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CAGCTGTGTGATGAATGTCAG	0.433																																					p.D668V		Atlas-SNP	.											.	CPEB4	54	.	0			c.A2003T						.						107	107	107					5																	173382953		2203	4300	6503	SO:0001583	missense	80315	exon10			TGTGTGATGAATG	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.2003A>T	chr5.hg19:g.173382953A>T	ENSP00000265085:p.Asp668Val	90.0	0.0		93.0	24.0	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Missense_Mutation	SNP	ENST00000265085.5	hg19	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.584464	0.65992	.	.	ENSG00000113742	ENST00000265085;ENST00000520867;ENST00000334035;ENST00000522336;ENST00000517880	T;T;T;T;T	0.20200	2.09;2.09;2.09;2.09;2.09	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.51686	0.1689	M	0.83774	2.66	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	1.0;0.998;0.999;0.998	T	0.57412	-0.7816	10	0.87932	D	0	-23.7175	16.4288	0.83833	1.0:0.0:0.0:0.0	.	643;651;278;668	B7ZLQ8;Q17RY0-2;E5RFP2;Q17RY0	.;.;.;CPEB4_HUMAN	V	668;643;651;278;261	ENSP00000265085:D668V;ENSP00000429092:D643V;ENSP00000334533:D651V;ENSP00000430345:D278V;ENSP00000427990:D261V	ENSP00000265085:D668V	D	+	2	0	CPEB4	173315559	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.284000	0.95882	2.282000	0.76494	0.533000	0.62120	GAT	.	.		0.433	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		T	173382953	A	T	173382953	3	4	154	1	0	0	0	0	1	0	0	0	3805	333	12	4	2041	4	CPEB4	5	173382953	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	35485652	173382953	7532307	35	23596										
HIST1H1T	3010	hgsc.bcm.edu	37	chr6	26108149	26108149	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	caaccaaagacatacctactCgttcctgtgacactgaaagg	7	12	0	3			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr6:26108149C>T	ENST00000338379.4	-	1	215	c.173G>A	c.(172-174)cGa>cAa	p.R58Q		NM_005323.3	NP_005314.2	P22492	H1T_HUMAN	histone cluster 1, H1t	58	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|nucleosome assembly (GO:0006334)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(1)|lung(3)|ovary(2)|prostate(1)	9						CATACCTACTCGTTCCTGTGA	0.532																																					p.R58Q		Atlas-SNP	.											.	HIST1H1T	40	.	0			c.G173A						.						128	109	116					6																	26108149		2203	4300	6503	SO:0001583	missense	3010	exon1			CCTACTCGTTCCT	M60094	CCDS34349.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000187475	ENSG00000187475		"Histones / Replication-dependent"	4720	protein-coding gene	gene with protein product		142712	"H1 histone family, member T (testis-specific)", "histone 1, H1t"	H1FT		8175896, 12408966	Standard	NM_005323		Approved	H1t	uc003ngj.3	P22492	OTTHUMG00000014430	ENST00000338379.4:c.173G>A	chr6.hg19:g.26108149C>T	ENSP00000341214:p.Arg58Gln	105.0	0.0		114.0	7.0	NM_005323	Q6ISI1|Q8IUE8	Missense_Mutation	SNP	ENST00000338379.4	hg19	CCDS34349.1	.	.	.	.	.	.	.	.	.	.	.	34	5.378140	0.95945	.	.	ENSG00000187475	ENST00000338379	T	0.33654	1.4	5.35	5.35	0.76521	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.130748	0.52532	D	0.000067	T	0.73233	0.3561	H	0.98646	4.29	0.51767	D	0.999934	D	0.89917	1.0	D	0.85130	0.997	D	0.83868	0.0272	10	0.87932	D	0	-9.4827	18.2308	0.89934	0.0:1.0:0.0:0.0	.	58	P22492	H1T_HUMAN	Q	58	ENSP00000341214:R58Q	ENSP00000341214:R58Q	R	-	2	0	HIST1H1T	26216128	0.997000	0.39634	0.012000	0.15200	0.008000	0.06430	5.917000	0.69989	2.780000	0.95670	0.655000	0.94253	CGA	.	.		0.532	HIST1H1T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040093.2	NM_005323		T	26108149	C	T	26108149	3	4	154	1	0	0	0	0	1	0	0	0	7136	884	31	1	454	1	HIST1H1T	6	26108149	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10		26108149	145006918	36	23597										
VPS52	6293	hgsc.bcm.edu	37	chr6	33231842	33231842	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggaattgtctggttgatactGacaagagcggaggagaactc	14	6	1	4			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr6:33231842G>A	ENST00000445902.2	-	15	1781	c.1563C>T	c.(1561-1563)gtC>gtT	p.V521V	VPS52_ENST00000436044.2_Silent_p.V396V|VPS52_ENST00000482399.1_3'UTR|VPS52_ENST00000478934.1_5'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	521					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						GGTTGATACTGACAAGAGCGG	0.547																																					p.V521V		Atlas-SNP	.											.	VPS52	56	.	0			c.C1563T						.						158	149	152					6																	33231842		2203	4300	6503	SO:0001819	synonymous_variant	6293	exon15			GATACTGACAAGA	AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"SAC2 suppressor of actin mutations 2-like (yeast)", "vacuolar protein sorting 52 (yeast)"	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.1563C>T	chr6.hg19:g.33231842G>A		72.0	0.0		97.0	12.0	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	hg19	CCDS4770.2																																																																																			.	.		0.547	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553		A	33231842	G	A	33231842	2	1	154	1	0	0	0	0	0	0	0	1	17229	1277	45	3		3	VPS52	6	33231842	Silent	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	7123693	33231842	137883225	37	23598										
ZNF318	24149	hgsc.bcm.edu	37	chr6	43309850	43309850	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gtggcaaaaaggaaacatacCttttgcaggaacagttatct	9	7	1	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr6:43309850C>G	ENST00000361428.2	-	8	3453	c.3376G>C	c.(3376-3378)Ggc>Cgc	p.G1126R	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1126					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			GGAAACATACCTTTTGCAGGA	0.468																																					p.G1126R		Atlas-SNP	.											.	ZNF318	175	.	0			c.G3376C						.						211	159	177					6																	43309850		2203	4300	6503	SO:0001630	splice_region_variant	24149	exon8			ACATACCTTTTGC	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.3376+1G>C	chr6.hg19:g.43309850C>G		70.0	0.0		77.0	17.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	C	17.74	3.463657	0.63513	.	.	ENSG00000171467	ENST00000361428	T	0.72505	-0.66	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.80813	0.4695	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80721	-0.1256	9	.	.	.	-12.1032	16.6605	0.85239	0.0:1.0:0.0:0.0	.	1126	Q5VUA4	ZN318_HUMAN	R	1126	ENSP00000354964:G1126R	.	G	-	1	0	ZNF318	43417828	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.019000	0.70818	2.596000	0.87737	0.563000	0.77884	GGC	.	.		0.468	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	Missense_Mutation	G	43309850	C	G	43309850	5	3	154	1	0	0	0	0	0	0	1	0	17851	695	24	4	3475	4	ZNF318	6	43309850	Splice_Site	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	10078008	43309850	127805217	38	23599										
MAP3K7	6885	hgsc.bcm.edu	37	chr6	91281491	91281491	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tcttttgctctccacttagcTttgcaaacaactccaaaggc	5	13	2	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr6:91281491T>A	ENST00000369329.3	-	2	317	c.156A>T	c.(154-156)aaA>aaT	p.K52N	MAP3K7_ENST00000369327.3_Missense_Mutation_p.K52N|MAP3K7_ENST00000369332.3_Missense_Mutation_p.K52N|MAP3K7_ENST00000369325.3_Missense_Mutation_p.K52N	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	52	Interaction with MAPK8IP1. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		TCCACTTAGCTTTGCAAACAA	0.343																																					p.K52N		Atlas-SNP	.											.	MAP3K7	100	.	0			c.A156T						.						128	120	123					6																	91281491		2203	4299	6502	SO:0001583	missense	6885	exon2			CTTAGCTTTGCAA	AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.156A>T	chr6.hg19:g.91281491T>A	ENSP00000358335:p.Lys52Asn	81.0	0.0		95.0	17.0	NM_145333	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Missense_Mutation	SNP	ENST00000369329.3	hg19	CCDS5028.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.928857	0.73327	.	.	ENSG00000135341	ENST00000369332;ENST00000369329;ENST00000369325;ENST00000369327;ENST00000450832	T;T;T;T	0.38560	1.13;1.13;1.13;1.13	5.57	4.21	0.49690	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.080378	0.85682	D	0.000000	T	0.59756	0.2217	M	0.89287	3.02	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.80764	0.989;0.983;0.993;0.994	T	0.67401	-0.5680	10	0.87932	D	0	.	10.1804	0.42963	0.0:0.1225:0.0:0.8775	.	52;52;52;52	O43318-4;O43318-2;O43318-3;O43318	.;.;.;M3K7_HUMAN	N	52	ENSP00000358338:K52N;ENSP00000358335:K52N;ENSP00000358331:K52N;ENSP00000358333:K52N	ENSP00000358331:K52N	K	-	3	2	MAP3K7	91338212	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.318000	0.33643	2.122000	0.65172	0.455000	0.32223	AAA	.	.		0.343	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331		A	91281491	T	A	91281491	3	1	154	1	0	0	0	0	1	0	0	0	9264	1606	56	4	1728	4	MAP3K7	6	91281491	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	47971641	91281491	79833576	39	23600										
UST	10090	hgsc.bcm.edu	37	chr6	149340294	149340294	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggatatcaatgagtgtattcTtgaaaactatcccgagtgct	9	7	2	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr6:149340294T>A	ENST00000367463.4	+	6	804	c.701T>A	c.(700-702)cTt>cAt	p.L234H		NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	234					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		GAGTGTATTCTTGAAAACTAT	0.418																																					p.L234H		Atlas-SNP	.											.	UST	42	.	0			c.T701A						.						176	165	169					6																	149340294		2203	4300	6503	SO:0001583	missense	10090	exon6			GTATTCTTGAAAA	AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"Sulfotransferases, membrane-bound"	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.701T>A	chr6.hg19:g.149340294T>A	ENSP00000356433:p.Leu234His	70.0	0.0		58.0	13.0	NM_005715	B2RCX6	Missense_Mutation	SNP	ENST00000367463.4	hg19	CCDS5213.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450040	0.84101	.	.	ENSG00000111962	ENST00000367463	T	0.51325	0.71	5.95	5.95	0.96441	.	0.063973	0.64402	D	0.000005	T	0.59622	0.2207	M	0.72479	2.2	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	T	0.58853	-0.7563	10	0.36615	T	0.2	-20.3248	16.4237	0.83790	0.0:0.0:0.0:1.0	.	234	Q9Y2C2	UST_HUMAN	H	234	ENSP00000356433:L234H	ENSP00000356433:L234H	L	+	2	0	UST	149381987	1.000000	0.71417	0.988000	0.46212	0.958000	0.62258	8.015000	0.88690	2.279000	0.76181	0.533000	0.62120	CTT	.	.		0.418	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715		A	149340294	T	A	149340294	3	1	154	1	0	0	0	0	1	0	0	0	17108	1609	56	4	723	4	UST	6	149340294	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	58058803	149340294	21774773	40	23601										
AKAP12	9590	hgsc.bcm.edu	37	chr6	151673861	151673861	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gaaacaggtgaaacgttggaGcctgcaggtgcacatttagt	13	7	0	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr6:151673861G>T	ENST00000253332.1	+	3	4524	c.4335G>T	c.(4333-4335)gaG>gaT	p.E1445D	AKAP12_ENST00000354675.6_Missense_Mutation_p.E1347D|AKAP12_ENST00000402676.2_Missense_Mutation_p.E1445D|AKAP12_ENST00000359755.5_Missense_Mutation_p.E1340D			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1445					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		AAACGTTGGAGCCTGCAGGTG	0.488																																					p.E1445D	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.G4335T						.						85	89	88					6																	151673861		2203	4300	6503	SO:0001583	missense	9590	exon4			GTTGGAGCCTGCA	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.4335G>T	chr6.hg19:g.151673861G>T	ENSP00000253332:p.Glu1445Asp	113.0	0.0		106.0	5.0	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	hg19	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	G	11.69	1.714171	0.30413	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.15139	2.45;2.45;2.48;2.48	4.86	0.261	0.15592	.	0.503502	0.14876	N	0.293280	T	0.03220	0.0094	L	0.34521	1.04	0.09310	N	1	B;B;B	0.19706	0.013;0.037;0.038	B;B;B	0.18561	0.022;0.022;0.01	T	0.41680	-0.9495	10	0.33940	T	0.23	.	3.6095	0.08055	0.1507:0.0992:0.5608:0.1894	.	1340;1347;1445	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	D	1445;1445;1347;1340	ENSP00000384537:E1445D;ENSP00000253332:E1445D;ENSP00000346702:E1347D;ENSP00000352794:E1340D	ENSP00000253332:E1445D	E	+	3	2	AKAP12	151715554	0.000000	0.05858	0.016000	0.15963	0.116000	0.19942	0.310000	0.19356	0.102000	0.17638	0.650000	0.86243	GAG	.	.		0.488	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			T	151673861	G	T	151673861	3	4	154	1	0	0	0	0	1	0	0	0	448	962	34	3	4374	3	AKAP12	6	151673861	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	2333567	151673861	19441206	41	23602										
DAGLB	221955	hgsc.bcm.edu	37	chr7	6476018	6476018	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	cacgacggttgcgatgatgcCgtttacaactgtcctgtcgc	11	12	0	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr7:6476018C>T	ENST00000297056.6	-	3	563	c.394G>A	c.(394-396)Ggc>Agc	p.G132S	DAGLB_ENST00000421761.2_Intron|DAGLB_ENST00000428902.2_Intron|DAGLB_ENST00000479922.2_5'UTR|DAGLB_ENST00000425398.2_Missense_Mutation_p.G132S|DAGLB_ENST00000436575.1_Missense_Mutation_p.G91S	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	132					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		GCGATGATGCCGTTTACAACT	0.522																																					p.G132S		Atlas-SNP	.											.	DAGLB	74	.	0			c.G394A						.						159	142	148					7																	6476018		2203	4300	6503	SO:0001583	missense	221955	exon3			TGATGCCGTTTAC	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.394G>A	chr7.hg19:g.6476018C>T	ENSP00000297056:p.Gly132Ser	158.0	0.0		180.0	25.0	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Missense_Mutation	SNP	ENST00000297056.6	hg19	CCDS5350.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.662530	0.47572	.	.	ENSG00000164535	ENST00000297056;ENST00000425398;ENST00000436575;ENST00000471132;ENST00000432248	T;T;T	0.40756	1.04;1.02;1.03	5.87	5.87	0.94306	.	0.180091	0.47852	D	0.000220	T	0.39708	0.1088	L	0.54323	1.7	0.80722	D	1	P;P	0.52316	0.952;0.87	B;B	0.38655	0.278;0.084	T	0.20907	-1.0261	10	0.17832	T	0.49	-4.2775	20.5827	0.99408	0.0:1.0:0.0:0.0	.	132;132	B4DQU0;Q8NCG7	.;DGLB_HUMAN	S	132;132;91;132;132	ENSP00000297056:G132S;ENSP00000391171:G132S;ENSP00000404785:G91S	ENSP00000297056:G132S	G	-	1	0	DAGLB	6442543	1.000000	0.71417	0.962000	0.40283	0.051000	0.14879	6.986000	0.76200	2.941000	0.99782	0.655000	0.94253	GGC	.	.		0.522	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179		T	6476018	C	T	6476018	3	4	154	1	0	0	0	0	1	0	0	0	4229	652	23	1	1676	1	DAGLB	7	6476018	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10		6476018	152662645	42	23603										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48626793	48626793	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	cttacacctcgaagcccacgCggacaaacctgtggccacct	8	17	0	0	rs563692415		TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr7:48626793C>T	ENST00000435803.1	+	57	14573	c.14549C>T	c.(14548-14550)gCg>gTg	p.A4850V	ABCA13_ENST00000544596.1_Missense_Mutation_p.A580V	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4850	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GAAGCCCACGCGGACAAACCT	0.557																																					p.A4850V		Atlas-SNP	.											ABCA13_ENST00000435803,rectum,carcinoma,+1,2	ABCA13	1192	.	0			c.C14549T						.						43	48	46					7																	48626793		2024	4188	6212	SO:0001583	missense	154664	exon57			CCCACGCGGACAA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.14549C>T	chr7.hg19:g.48626793C>T	ENSP00000411096:p.Ala4850Val	65.0	0.0		64.0	6.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	1.942	-0.443420	0.04604	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.94184	-3.37;-3.37;-3.37	5.71	-0.712	0.11226	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.760684	0.11485	N	0.559299	D	0.89174	0.6640	L	0.58428	1.81	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.002	T	0.76105	-0.3081	10	0.30854	T	0.27	.	7.0876	0.25266	0.1224:0.1475:0.0:0.7301	.	580;2552;4850	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	V	4850;623;580	ENSP00000411096:A4850V;ENSP00000391042:A623V;ENSP00000442634:A580V	ENSP00000391042:A623V	A	+	2	0	ABCA13	48597339	0.097000	0.21791	0.017000	0.16124	0.151000	0.21798	0.423000	0.21313	-0.283000	0.09115	-0.143000	0.13931	GCG	.	.		0.557	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48626793	C	T	48626793	3	4	154	1	0	0	0	0	1	0	0	0	31	768	27	1	14604	1	ABCA13	7	48626793	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	42150775	48626793	110511870	43	23604										
TAC1	6863	hgsc.bcm.edu	37	chr7	97363076	97363076	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gagcatcttctgcagagaatCgcccggagacccaagcctca	10	14	3	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr7:97363076C>A	ENST00000319273.5	+	3	462	c.165C>A	c.(163-165)atC>atA	p.I55I	TAC1_ENST00000350485.4_Silent_p.I55I|TAC1_ENST00000346867.4_Silent_p.I55I	NM_003182.2	NP_003173.1	P20366	TKN1_HUMAN	tachykinin, precursor 1	55					associative learning (GO:0008306)|cell-cell signaling (GO:0007267)|detection of abiotic stimulus (GO:0009582)|inflammatory response (GO:0006954)|insemination (GO:0007320)|long-term memory (GO:0007616)|negative regulation of heart rate (GO:0010459)|neuropeptide signaling pathway (GO:0007218)|positive regulation of action potential (GO:0045760)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of corticosterone secretion (GO:2000854)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of ossification (GO:0045778)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of saliva secretion (GO:0046878)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of blood pressure (GO:0008217)|response to hormone (GO:0009725)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)|tachykinin receptor signaling pathway (GO:0007217)	axon (GO:0030424)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				large_intestine(4)|lung(6)|urinary_tract(1)	11	all_cancers(62;3.95e-09)|all_epithelial(64;1.1e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0358)|all_lung(186;0.0384)					TGCAGAGAATCGCCCGGAGAC	0.592																																					p.I55I		Atlas-SNP	.											.	TAC1	21	.	0			c.C165A						.						97	88	91					7																	97363076		2203	4300	6503	SO:0001819	synonymous_variant	6863	exon3			GAGAATCGCCCGG	M68907	CCDS5649.1, CCDS5650.1, CCDS5651.1	7q21-q22	2013-02-26	2008-01-17		ENSG00000006128	ENSG00000006128		"Endogenous ligands"	11517	protein-coding gene	gene with protein product	"substance K", "substance P", "neurokinin 1", "neurokinin 2", "neuromedin L", "neurokinin alpha", "neuropeptide K", "neuropeptide gamma", "preprotachykinin"	162320	"tachykinin, precursor 1 (substance K, substance P, neurokinin 1, neurokinin 2, neuromedin L, neurokinin alpha, neuropeptide K, neuropeptide gamma)"	TAC2, NKNA		1708336	Standard	NM_003182		Approved	NPK	uc003uop.4	P20366	OTTHUMG00000154069	ENST00000319273.5:c.165C>A	chr7.hg19:g.97363076C>A		121.0	0.0		142.0	25.0	NM_003182	O60600|O60601|Q00072|Q53GH4|Q549V0|Q549V1|Q549V2|Q6FHM1	Silent	SNP	ENST00000319273.5	hg19	CCDS5649.1																																																																																			.	.		0.592	TAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333696.1	NM_003182		A	97363076	C	A	97363076	2	1	154	1	0	0	0	0	0	0	0	1	15513	874	31	1		1	TAC1	7	97363076	Silent	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	48736283	97363076	61775587	44	23605										
ASNS	440	hgsc.bcm.edu	37	chr7	97482512	97482512	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	aaacgtctctctcaggagatGtttttctatcccattctgac	6	11	4	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr7:97482512G>A	ENST00000394309.3	-	12	1807	c.1336C>T	c.(1336-1338)Cat>Tat	p.H446Y	ASNS_ENST00000394308.3_Missense_Mutation_p.H446Y|ASNS_ENST00000444334.1_Missense_Mutation_p.H425Y|ASNS_ENST00000437628.1_Missense_Mutation_p.H363Y|ASNS_ENST00000455086.1_Missense_Mutation_p.H363Y|ASNS_ENST00000422745.1_Missense_Mutation_p.H425Y|ASNS_ENST00000175506.4_Missense_Mutation_p.H446Y	NM_133436.3	NP_597680.2	P08243	ASNS_HUMAN	asparagine synthetase (glutamine-hydrolyzing)	446	Asparagine synthetase.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|asparagine biosynthetic process (GO:0006529)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular protein metabolic process (GO:0044267)|cellular response to glucose starvation (GO:0042149)|cellular response to hormone stimulus (GO:0032870)|endoplasmic reticulum unfolded protein response (GO:0030968)|glutamine metabolic process (GO:0006541)|L-asparagine biosynthetic process (GO:0070981)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|positive regulation of mitotic cell cycle (GO:0045931)|response to amino acid (GO:0043200)|response to follicle-stimulating hormone (GO:0032354)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)|ATP binding (GO:0005524)|cofactor binding (GO:0048037)			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	CTCAGGAGATGTTTTTCTATC	0.378																																					p.H446Y	Melanoma(70;6 1280 3108 3799 51123)|GBM(6;275 291 425 9929 27738)	Atlas-SNP	.											.	ASNS	97	.	0			c.C1336T						.						53	51	52					7																	97482512		2199	4298	6497	SO:0001583	missense	440	exon12			GGAGATGTTTTTC	M27396	CCDS5652.1, CCDS55131.1, CCDS55132.1	7q21.3	2012-10-02	2010-05-07		ENSG00000070669	ENSG00000070669	6.3.5.4		753	protein-coding gene	gene with protein product		108370	"asparagine synthetase"				Standard	NM_001673		Approved		uc003uov.4	P08243	OTTHUMG00000022892	ENST00000394309.3:c.1336C>T	chr7.hg19:g.97482512G>A	ENSP00000377846:p.His446Tyr	91.0	0.0		74.0	14.0	NM_133436	A4D1I8|B4DXZ1|B7ZAA9|D6W5R3|E9PCI3|E9PCX6|P08184|Q15666|Q549T9|Q96HD0	Missense_Mutation	SNP	ENST00000394309.3	hg19	CCDS5652.1	.	.	.	.	.	.	.	.	.	.	G	0.524	-0.860980	0.02610	.	.	ENSG00000070669	ENST00000175506;ENST00000394309;ENST00000437628;ENST00000394308;ENST00000422745;ENST00000455086;ENST00000444334	T;T;T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08;1.08;1.08	3.63	2.74	0.32292	Rossmann-like alpha/beta/alpha sandwich fold (1);Asparagine synthase (1);	0.273854	0.41823	D	0.000804	T	0.14743	0.0356	N	0.03016	-0.435	0.40279	D	0.978379	B	0.06786	0.001	B	0.12156	0.007	T	0.07888	-1.0749	10	0.09590	T	0.72	-24.2124	6.02	0.19625	0.2296:0.0:0.7704:0.0	.	446	P08243	ASNS_HUMAN	Y	446;446;363;446;425;363;425	ENSP00000175506:H446Y;ENSP00000377846:H446Y;ENSP00000414379:H363Y;ENSP00000377845:H446Y;ENSP00000414901:H425Y;ENSP00000408472:H363Y;ENSP00000406994:H425Y	ENSP00000175506:H446Y	H	-	1	0	ASNS	97320448	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	3.381000	0.52455	1.100000	0.41517	0.561000	0.74099	CAT	.	.		0.378	ASNS-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333645.1	NM_001673, NM_183356		A	97482512	G	A	97482512	3	1	154	1	0	0	0	0	1	0	0	0	1048	1377	48	3	357	3	ASNS	7	97482512	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	119436	97482512	61656151	45	23606										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98529221	98529221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tgtgaggaagcaggccatgcAttcgctgcaggtgttggccc	15	10	0	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr7:98529221A>G	ENST00000359863.4	+	26	3994	c.3785A>G	c.(3784-3786)cAt>cGt	p.H1262R	TRRAP_ENST00000355540.3_Missense_Mutation_p.H1262R|TRRAP_ENST00000446306.3_Missense_Mutation_p.H1261R	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1262					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			CAGGCCATGCATTCGCTGCAG	0.527																																					p.H1262R		Atlas-SNP	.											.	TRRAP	863	.	0			c.A3785G						.						91	79	83					7																	98529221		2203	4300	6503	SO:0001583	missense	8295	exon26			CCATGCATTCGCT	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.3785A>G	chr7.hg19:g.98529221A>G	ENSP00000352925:p.His1262Arg	150.0	0.0		160.0	22.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.16|13.16	2.155382|2.155382	0.38021|0.38021	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306|ENST00000456197	T;T|.	0.63744|.	3.64;-0.06|.	6.06|6.06	6.06|6.06	0.98353|0.98353	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.56775|0.56775	0.2008|0.2008	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	P;B;P|.	0.39311|.	0.667;0.055;0.596|.	B;B;B|.	0.37989|.	0.262;0.022;0.177|.	T|T	0.52555|0.52555	-0.8560|-0.8560	10|5	0.15499|.	T|.	0.54|.	.|.	16.6127|16.6127	0.84892|0.84892	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1262;976;1262|.	Q9Y4A5-2;Q59FH1;Q9Y4A5|.	.;.;TRRAP_HUMAN|.	R|V	1262;1262;1260|977	ENSP00000352925:H1262R;ENSP00000347733:H1262R|.	ENSP00000347733:H1262R|.	H|I	+|+	2|1	0|0	TRRAP|TRRAP	98367157|98367157	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.992000|0.992000	0.81027|0.81027	8.958000|8.958000	0.93099|0.93099	2.322000|2.322000	0.78497|0.78497	0.528000|0.528000	0.53228|0.53228	CAT|ATT	.	.		0.527	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		G	98529221	A	G	98529221	3	3	154	1	0	0	0	0	1	0	0	0	16616	217	8	2	3883	2	TRRAP	7	98529221	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	1046709	98529221	60609442	46	23607										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131895838	131895838	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggaggttcttggccttcagcGtgataggcttgatcacctcc	12	11	3	2	rs377154325		TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr7:131895838G>A	ENST00000359827.3	-	10	3124	c.2162C>T	c.(2161-2163)aCg>aTg	p.T721M	PLXNA4_ENST00000321063.4_Missense_Mutation_p.T721M			Q9HCM2	PLXA4_HUMAN	plexin A4	721					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						GGCCTTCAGCGTGATAGGCTT	0.652																																					p.T721M		Atlas-SNP	.											PLXNA4_ENST00000359827,right_upper_lobe,carcinoma,0,2	PLXNA4	873	.	0			c.C2162T						.						31	35	34					7																	131895838		2147	4271	6418	SO:0001583	missense	91584	exon10			TTCAGCGTGATAG	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2162C>T	chr7.hg19:g.131895838G>A	ENSP00000352882:p.Thr721Met	60.0	0.0		61.0	6.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.005611	0.93287	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.01059	5.39;5.39	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.10981	0.0268	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.00603	-1.1649	10	0.59425	D	0.04	.	19.7362	0.96205	0.0:0.0:1.0:0.0	.	721	Q9HCM2	PLXA4_HUMAN	M	721	ENSP00000323194:T721M;ENSP00000352882:T721M	ENSP00000323194:T721M	T	-	2	0	PLXNA4	131546378	1.000000	0.71417	0.974000	0.42286	0.986000	0.74619	9.796000	0.99103	2.661000	0.90470	0.655000	0.94253	ACG	.	.		0.652	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	131895838	G	A	131895838	3	1	154	1	0	0	0	0	1	0	0	0	12131	1145	40	1	3614	1	PLXNA4	7	131895838	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	33366617	131895838	27242825	47	23608										
GPR124	25960	hgsc.bcm.edu	37	chr8	37697733	37697733	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggagctcacctggagggcacCccctccgcaagaaggggacc	14	15	1	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr8:37697733C>A	ENST00000412232.2	+	17	2619	c.2606C>A	c.(2605-2607)cCc>cAc	p.P869H	GPR124_ENST00000315215.7_Missense_Mutation_p.P652H	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	869					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			TGGAGGGCACCCCCTCCGCAA	0.607																																					p.P869H		Atlas-SNP	.											.	GPR124	85	.	0			c.C2606A						.						71	61	64					8																	37697733		2203	4300	6503	SO:0001583	missense	25960	exon17			GGGCACCCCCTCC	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.2606C>A	chr8.hg19:g.37697733C>A	ENSP00000406367:p.Pro869His	35.0	0.0		39.0	6.0	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	C	16.06	3.015195	0.54468	.	.	ENSG00000020181	ENST00000416514;ENST00000315215;ENST00000412232	T;T	0.60299	0.2;0.41	3.91	3.91	0.45181	GPCR, family 2-like (1);	0.128231	0.53938	D	0.000054	T	0.69387	0.3105	L	0.58810	1.83	0.48135	D	0.999591	D;D	0.89917	0.999;1.0	D;D	0.77004	0.948;0.989	T	0.69921	-0.5014	10	0.48119	T	0.1	-32.445	11.7443	0.51811	0.1762:0.8238:0.0:0.0	.	652;869	Q96PE1-2;Q96PE1	.;GP124_HUMAN	H	862;652;869	ENSP00000323508:P652H;ENSP00000406367:P869H	ENSP00000323508:P652H	P	+	2	0	GPR124	37816891	0.997000	0.39634	0.932000	0.37286	0.311000	0.27955	3.688000	0.54699	2.188000	0.69820	0.650000	0.86243	CCC	.	.		0.607	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			A	37697733	C	A	37697733	3	1	154	1	0	0	0	0	1	0	0	0	6646	623	22	3	2651	3	GPR124	8	37697733	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10		37697733	108666289	48	23609										
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48647955	48647955	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	accgcccacccgaccagctgCattggattggaggaaatcga	11	13	0	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr8:48647955C>T	ENST00000297423.4	+	20	3075	c.2691C>T	c.(2689-2691)tgC>tgT	p.C897C	SPIDR_ENST00000518060.1_3'UTR|SPIDR_ENST00000518074.1_Missense_Mutation_p.H838Y|SPIDR_ENST00000517693.1_Silent_p.C372C|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Silent_p.C827C	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	897					cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											CGACCAGCTGCATTGGATTGG	0.522																																					p.C897C		Atlas-SNP	.											.	KIAA0146	64	.	0			c.C2691T						.						114	123	120					8																	48647955		1974	4150	6124	SO:0001819	synonymous_variant	23514	exon20			CAGCTGCATTGGA	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"KIAA0146"	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.2691C>T	chr8.hg19:g.48647955C>T		158.0	0.0		172.0	26.0	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Silent	SNP	ENST00000297423.4	hg19	CCDS43737.1	.	.	.	.	.	.	.	.	.	.	C	4.216	0.038919	0.08148	.	.	ENSG00000164808	ENST00000518074	.	.	.	5.73	3.91	0.45181	.	.	.	.	.	T	0.53642	0.1809	.	.	.	0.80722	D	1	D	0.54964	0.969	P	0.51016	0.656	T	0.54234	-0.8324	7	0.56958	D	0.05	.	4.0397	0.09745	0.1658:0.5675:0.0:0.2667	.	838	B4E0Y6	.	Y	838	.	ENSP00000429487:H838Y	H	+	1	0	KIAA0146	48810508	0.002000	0.14202	0.220000	0.23810	0.103000	0.19146	-0.027000	0.12371	0.744000	0.32741	0.511000	0.50034	CAT	.	.		0.522	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		T	48647955	C	T	48647955	2	4	154	1	0	0	0	0	0	0	0	1	8166	718	25	3		3	KIAA0146	8	48647955	Silent	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	10950222	48647955	97716067	49	23610										
GDAP1	54332	hgsc.bcm.edu	37	chr8	75274140	75274140	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ccaaattggaaacacagagtCtgagctgaagaaacttgctg	10	8	1	4			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr8:75274140C>T	ENST00000220822.7	+	4	586	c.506C>T	c.(505-507)tCt>tTt	p.S169F	GDAP1_ENST00000434412.2_Missense_Mutation_p.S101F|GDAP1_ENST00000521096.1_3'UTR	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	169	GST C-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			AACACAGAGTCTGAGCTGAAG	0.373																																					p.S169F		Atlas-SNP	.											.	GDAP1	36	.	0			c.C506T						.						108	102	104					8																	75274140		2203	4300	6503	SO:0001583	missense	54332	exon4			CAGAGTCTGAGCT		CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"Charcot-Marie-Tooth neuropathy 4A"	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.506C>T	chr8.hg19:g.75274140C>T	ENSP00000220822:p.Ser169Phe	93.0	0.0		101.0	10.0	NM_018972	A8K957|E7FJF3|E7FJF4	Missense_Mutation	SNP	ENST00000220822.7	hg19	CCDS34911.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.705255	0.89018	.	.	ENSG00000104381	ENST00000220822;ENST00000434412	D;D	0.99113	-5.44;-5.44	5.27	5.27	0.74061	Glutathione S-transferase/chloride channel, C-terminal (1);	0.126959	0.53938	D	0.000042	D	0.97920	0.9316	L	0.29908	0.895	0.58432	D	0.999995	P	0.50819	0.939	P	0.49421	0.61	D	0.98956	1.0796	10	0.72032	D	0.01	-20.1664	19.0885	0.93215	0.0:1.0:0.0:0.0	.	169	Q8TB36	GDAP1_HUMAN	F	169;101	ENSP00000220822:S169F;ENSP00000417006:S101F	ENSP00000220822:S169F	S	+	2	0	GDAP1	75436695	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.958000	0.76025	2.758000	0.94735	0.561000	0.74099	TCT	.	.		0.373	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379061.1	NM_018972		T	75274140	C	T	75274140	3	4	154	1	0	0	0	0	1	0	0	0	6315	913	32	3	520	3	GDAP1	8	75274140	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	26626185	75274140	71089882	50	23611										
MATN2	4147	hgsc.bcm.edu	37	chr8	98900398	98900398	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tcctcctccctgccgaggccAgggagcggtcacgtgggagg	16	14	1	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr8:98900398A>G	ENST00000520016.1	+	1	194	c.70A>G	c.(70-72)Agg>Ggg	p.R24G	MATN2_ENST00000521689.1_Missense_Mutation_p.R24G|MATN2_ENST00000254898.5_Missense_Mutation_p.R24G|MATN2_ENST00000522025.2_Intron|MATN2_ENST00000524308.1_Missense_Mutation_p.R24G			O00339	MATN2_HUMAN	matrilin 2	24						proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TGCCGAGGCCAGGGAGCGGTC	0.622																																					p.R24G		Atlas-SNP	.											.	MATN2	165	.	0			c.A70G						.						33	34	34					8																	98900398		1969	4169	6138	SO:0001583	missense	4147	exon2			GAGGCCAGGGAGC	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.70A>G	chr8.hg19:g.98900398A>G	ENSP00000430487:p.Arg24Gly	45.0	0.0		37.0	8.0	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	hg19	CCDS55264.1	.	.	.	.	.	.	.	.	.	.	A	8.106	0.777825	0.16120	.	.	ENSG00000132561	ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000520016	D;T;D;T	0.83250	-1.68;-0.83;-1.7;-0.8	5.02	1.07	0.20283	.	0.000000	0.47093	D	0.000260	T	0.66761	0.2822	N	0.24115	0.695	0.23215	N	0.998105	B;B;B	0.27498	0.003;0.001;0.18	B;B;B	0.21917	0.002;0.001;0.037	T	0.57963	-0.7720	10	0.72032	D	0.01	-9.9689	4.9832	0.14176	0.503:0.1701:0.0:0.3269	.	24;24;24	O00339-2;O00339;Q8N2G3	.;MATN2_HUMAN;.	G	24	ENSP00000429977:R24G;ENSP00000254898:R24G;ENSP00000430221:R24G;ENSP00000430487:R24G	ENSP00000254898:R24G	R	+	1	2	MATN2	98969574	1.000000	0.71417	0.113000	0.21522	0.012000	0.07955	0.985000	0.29578	0.027000	0.15297	-0.333000	0.08304	AGG	.	.		0.622	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			G	98900398	A	G	98900398	3	3	154	1	0	0	0	0	1	0	0	0	9343	179	7	2	72	2	MATN2	8	98900398	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	23626258	98900398	47463624	51	23612										
C9orf96	169436	hgsc.bcm.edu	37	chr9	136245946	136245946	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ctggggccttgggggtgaacCtggtggtggaggaaatggaa	20	5	0	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr9:136245946C>T	ENST00000371957.3	+	2	234	c.127C>T	c.(127-129)Ctg>Ttg	p.L43L	SURF4_ENST00000485435.2_5'Flank|C9orf96_ENST00000468046.1_3'UTR|C9orf96_ENST00000426926.2_Silent_p.L43L|SURF4_ENST00000371989.3_5'Flank|C9orf96_ENST00000371955.1_5'UTR	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		43	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GGGGGTGAACCTGGTGGTGGA	0.493																																					p.L43L		Atlas-SNP	.											.	C9orf96	77	.	0			c.C127T						.						114	98	103					9																	136245946		2203	4300	6503	SO:0001819	synonymous_variant	169436	exon2			GTGAACCTGGTGG																												ENST00000371957.3:c.127C>T	chr9.hg19:g.136245946C>T		113.0	0.0		124.0	26.0	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Silent	SNP	ENST00000371957.3	hg19	CCDS35169.1																																																																																			.	.		0.493	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1			T	136245946	C	T	136245946	2	4	154	1	0	0	0	0	0	0	0	1	2510	680	24	3		3	C9orf96	9	136245946	Silent	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10		136245946	4967485	52	23613										
CDK1	983	hgsc.bcm.edu	37	chr10	62551796	62551796	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggattcagaaattgatcaacTcttcaggattttcaggtagc	9	7	5	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr10:62551796T>C	ENST00000395284.3	+	6	780	c.638T>C	c.(637-639)cTc>cCc	p.L213P	CDK1_ENST00000448257.2_Missense_Mutation_p.L213P|CDK1_ENST00000316629.4_Missense_Mutation_p.L156P|CDK1_ENST00000373809.2_Missense_Mutation_p.L156P	NM_001786.4	NP_001777.1	P06493	CDK1_HUMAN	cyclin-dependent kinase 1	213	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell aging (GO:0007569)|cell migration (GO:0016477)|cellular response to hydrogen peroxide (GO:0070301)|centrosome cycle (GO:0007098)|chromosome condensation (GO:0030261)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|pronuclear fusion (GO:0007344)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|Ras protein signal transduction (GO:0007265)|regulation of embryonic development (GO:0045995)|regulation of Schwann cell differentiation (GO:0014038)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to activity (GO:0014823)|response to amine (GO:0014075)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organic cyclic compound (GO:0014070)|response to toxic substance (GO:0009636)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac muscle cell development (GO:0055015)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|histone kinase activity (GO:0035173)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			ovary(1)	1						ATTGATCAACTCTTCAGGATT	0.323																																					p.L213P		Atlas-SNP	.											.	CDK1	24	.	0			c.T638C						.						72	73	73					10																	62551796		2203	4299	6502	SO:0001583	missense	983	exon6			ATCAACTCTTCAG	BC014563	CCDS7260.1, CCDS44408.1	10q21.2	2011-11-08	2009-12-16	2009-12-16	ENSG00000170312	ENSG00000170312		"Cyclin-dependent kinases"	1722	protein-coding gene	gene with protein product		116940	"cell division cycle 2, G1 to S and G2 to M"	CDC2		3553962, 19884882	Standard	NM_001786		Approved	CDC28A	uc001jld.3	P06493	OTTHUMG00000018290	ENST00000395284.3:c.638T>C	chr10.hg19:g.62551796T>C	ENSP00000378699:p.Leu213Pro	156.0	0.0		176.0	14.0	NM_001786	A8K7C4|C9J497|O60764	Missense_Mutation	SNP	ENST00000395284.3	hg19	CCDS44408.1	.	.	.	.	.	.	.	.	.	.	T	19.69	3.874754	0.72180	.	.	ENSG00000170312	ENST00000395284;ENST00000316629;ENST00000448257;ENST00000373809	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	5.81	5.81	0.92471	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.80048	0.4552	M	0.94063	3.49	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.985;1.0;0.995	D	0.85517	0.1201	10	0.87932	D	0	-17.9858	16.1708	0.81812	0.0:0.0:0.0:1.0	.	156;219;213	P06493-2;Q5H9N4;P06493	.;.;CDK1_HUMAN	P	213;156;213;156	ENSP00000378699:L213P;ENSP00000325970:L156P;ENSP00000397973:L213P;ENSP00000362915:L156P	ENSP00000325970:L156P	L	+	2	0	CDK1	62221802	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.953000	0.87836	2.225000	0.72522	0.533000	0.62120	CTC	.	.		0.323	CDK1-007	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048211.2	NM_001786		C	62551796	T	C	62551796	3	2	154	1	0	0	0	0	1	0	0	0	3126	1551	54	2	668	2	CDK1	10	62551796	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10		62551796	72982951	53	23614										
HERC4	26091	hgsc.bcm.edu	37	chr10	69748547	69748547	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	caacttccttaaaaagttctActatcttgaggaatagtgga	7	7	2	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr10:69748547A>G	ENST00000395198.3	-	15	1926	c.1679T>C	c.(1678-1680)gTa>gCa	p.V560A	HERC4_ENST00000277817.6_Missense_Mutation_p.V450A|HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000373700.4_Missense_Mutation_p.V560A|HERC4_ENST00000412272.2_Missense_Mutation_p.V560A	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	560					cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						AAAAAGTTCTACTATCTTGAG	0.318																																					p.V560A		Atlas-SNP	.											.	HERC4	78	.	0			c.T1679C						.						109	119	116					10																	69748547		2202	4294	6496	SO:0001583	missense	26091	exon15			AGTTCTACTATCT	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"hect domain and RLD 4"			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.1679T>C	chr10.hg19:g.69748547A>G	ENSP00000378624:p.Val560Ala	332.0	0.0		363.0	52.0	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	hg19	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.857521	0.51376	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.56444	0.69;0.47;0.46;0.46	5.49	5.49	0.81192	.	0.053101	0.85682	D	0.000000	T	0.54127	0.1839	L	0.56199	1.76	0.80722	D	1	B;B;B;B;B;B	0.30563	0.285;0.245;0.002;0.159;0.245;0.159	B;B;B;B;B;B	0.36335	0.122;0.222;0.008;0.111;0.222;0.111	T	0.56986	-0.7888	10	0.62326	D	0.03	.	15.5826	0.76455	1.0:0.0:0.0:0.0	.	560;450;560;410;560;560	Q5GLZ8-3;Q5GLZ8-6;A8K9U4;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;.;HERC4_HUMAN	A	450;560;560;560	ENSP00000277817:V450A;ENSP00000416504:V560A;ENSP00000378624:V560A;ENSP00000362804:V560A	ENSP00000277817:V450A	V	-	2	0	HERC4	69418553	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.619000	0.74219	2.073000	0.62155	0.533000	0.62120	GTA	.	.		0.318	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601		G	69748547	A	G	69748547	3	3	154	1	0	0	0	0	1	0	0	0	7069	391	14	2	1542	2	HERC4	10	69748547	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	7196751	69748547	65786200	54	23615										
CDH23	64072	hgsc.bcm.edu	37	chr10	73563052	73563052	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	agttcagtctgaccgtggtgGccacagatggtggagagccc	15	10	2	3			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr10:73563052G>T	ENST00000224721.6	+	54	7767	c.7762G>T	c.(7762-7764)Gcc>Tcc	p.A2588S	CDH23_ENST00000475158.1_3'UTR|CDH23_ENST00000398788.3_Missense_Mutation_p.A343S	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2583	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> Q (in dbSNP:rs41281338). {ECO:0000269|PubMed:11138009, ECO:0000269|PubMed:12075507, ECO:0000269|PubMed:18429043}.		calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GACCGTGGTGGCCACAGATGG	0.617																																					p.A2583S		Atlas-SNP	.											.	CDH23	365	.	0			c.G7747T						.						26	31	29					10																	73563052		2048	4180	6228	SO:0001583	missense	64072	exon53			GTGGTGGCCACAG	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.7762G>T	chr10.hg19:g.73563052G>T	ENSP00000224721:p.Ala2588Ser	82.0	0.0		83.0	9.0	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	G	17.80	3.479062	0.63849	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.75477	-0.94	5.02	3.16	0.36331	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.89143	0.6631	H	0.96142	3.775	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.79108	0.983;0.992	D	0.89925	0.4062	10	0.62326	D	0.03	.	11.2263	0.48886	0.1498:0.0:0.8502:0.0	.	2583;2583	E9PEX1;Q9H251	.;CAD23_HUMAN	S	2588;2583;2586;343	ENSP00000381768:A343S	ENSP00000224721:A2588S	A	+	1	0	CDH23	73233058	1.000000	0.71417	1.000000	0.80357	0.330000	0.28571	9.739000	0.98837	0.632000	0.30432	-0.269000	0.10298	GCC	.	.		0.617	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73563052	G	T	73563052	3	4	154	1	0	0	0	0	1	0	0	0	3110	1203	42	3	8306	3	CDH23	10	73563052	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	3814505	73563052	61971695	55	23616										
CCDC147	159686	hgsc.bcm.edu	37	chr10	106128252	106128252	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gctaaacttcagcaagagaaTgaacagcacagtttggtctg	10	8	2	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr10:106128252T>G	ENST00000369704.3	+	6	998	c.864T>G	c.(862-864)aaT>aaG	p.N288K	CCDC147_ENST00000312902.5_De_novo_Start_OutOfFrame	NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		288						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		AGCAAGAGAATGAACAGCACA	0.438																																					p.N288K		Atlas-SNP	.											.	CCDC147	137	.	0			c.T864G						.						118	106	110					10																	106128252		2203	4300	6503	SO:0001583	missense	159686	exon6			AGAGAATGAACAG																												ENST00000369704.3:c.864T>G	chr10.hg19:g.106128252T>G	ENSP00000358718:p.Asn288Lys	99.0	0.0		141.0	18.0	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	hg19	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	T	9.881	1.201489	0.22121	.	.	ENSG00000120051	ENST00000369704	T	0.33654	1.4	6.17	-6.95	0.01628	.	0.284681	0.44285	D	0.000468	T	0.30262	0.0759	L	0.51422	1.61	0.80722	D	1	B	0.33583	0.418	B	0.35655	0.207	T	0.05550	-1.0878	10	0.34782	T	0.22	-28.6057	18.5683	0.91124	0.0:0.1865:0.0:0.8135	.	288	Q5T655	CC147_HUMAN	K	288	ENSP00000358718:N288K	ENSP00000358718:N288K	N	+	3	2	CCDC147	106118242	0.010000	0.17322	0.734000	0.30879	0.341000	0.28922	-1.361000	0.02597	-1.265000	0.02449	-0.912000	0.02778	AAT	.	.		0.438	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			G	106128252	T	G	106128252	3	3	154	1	0	0	0	0	1	0	0	0	2783	1461	51	5	886	5	CCDC147	10	106128252	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	32565200	106128252	29406495	56	23617										
TACC2	10579	hgsc.bcm.edu	37	chr10	123970808	123970808	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	cccctcctaccaaaaagataGgcaaaaagccagttgccaaa	6	13	0	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr10:123970808G>T	ENST00000369005.1	+	9	7208	c.6868G>T	c.(6868-6870)Ggc>Tgc	p.G2290C	TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000334433.3_Missense_Mutation_p.G2290C|TACC2_ENST00000360561.3_Missense_Mutation_p.G368C|TACC2_ENST00000368999.1_Missense_Mutation_p.G368C|TACC2_ENST00000513429.1_Missense_Mutation_p.G436C|TACC2_ENST00000260733.3_Missense_Mutation_p.G368C|TACC2_ENST00000515273.1_Missense_Mutation_p.G2294C|TACC2_ENST00000453444.2_Missense_Mutation_p.G2294C|TACC2_ENST00000369004.3_Missense_Mutation_p.G368C|TACC2_ENST00000515603.1_Missense_Mutation_p.G2245C|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000358010.1_Missense_Mutation_p.G436C	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2290					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CAAAAAGATAGGCAAAAAGCC	0.517																																					p.G2290C		Atlas-SNP	.											.	TACC2	271	.	0			c.G6868T						.						53	61	58					10																	123970808		2203	4300	6503	SO:0001583	missense	10579	exon9			AAGATAGGCAAAA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.6868G>T	chr10.hg19:g.123970808G>T	ENSP00000358001:p.Gly2290Cys	199.0	0.0		222.0	32.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	hg19	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.132741	0.77662	.	.	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000514539;ENST00000496913	T;T;T;T;T;T;T;T;T;T;T;T;T	0.39056	2.45;2.05;2.59;2.52;2.45;2.05;2.59;1.89;1.9;1.87;1.9;1.73;1.1	5.12	5.12	0.69794	.	0.000000	0.37623	N	0.002017	T	0.68311	0.2987	M	0.82056	2.57	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	T	0.72437	-0.4294	10	0.66056	D	0.02	-13.2516	18.9406	0.92604	0.0:0.0:1.0:0.0	.	385;2294;368;2245;2294;368;368;436;2290	E9PGB3;E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	C	2290;436;2294;2245;2290;436;2294;2280;368;368;368;368;385;29	ENSP00000358001:G2290C;ENSP00000425062:G436C;ENSP00000424467:G2294C;ENSP00000427618:G2245C;ENSP00000334280:G2290C;ENSP00000350701:G436C;ENSP00000395048:G2294C;ENSP00000353763:G368C;ENSP00000357995:G368C;ENSP00000422815:G368C;ENSP00000260733:G368C;ENSP00000420967:G385C;ENSP00000422725:G29C	ENSP00000260733:G368C	G	+	1	0	TACC2	123960798	1.000000	0.71417	0.986000	0.45419	0.896000	0.52359	9.632000	0.98428	2.557000	0.86248	0.555000	0.69702	GGC	.	.		0.517	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123970808	G	T	123970808	3	4	154	1	0	0	0	0	1	0	0	0	15517	1000	35	3	6970	3	TACC2	10	123970808	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	17842556	123970808	11563939	57	23618										
CDHR5	53841	hgsc.bcm.edu	37	chr11	618860	618860	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ggtctgtgctgtgcccccacTgggtgtggctggttggtggg	19	9	1	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr11:618860T>C	ENST00000358353.3	-	14	2021	c.1699A>G	c.(1699-1701)Agt>Ggt	p.S567G	CDHR5_ENST00000349570.7_Intron|IRF7_ENST00000397562.3_5'Flank|CDHR5_ENST00000397542.2_Missense_Mutation_p.S567G|IRF7_ENST00000397570.1_5'Flank|IRF7_ENST00000330243.5_5'Flank|IRF7_ENST00000397574.2_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	567	4 X 31 AA approximate tandem repeats.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						GTGCCCCCACTGGGTGTGGCT	0.672																																					p.S567G		Atlas-SNP	.											.	CDHR5	77	.	0			c.A1699G						.																																			SO:0001583	missense	53841	exon13			CCCCACTGGGTGT	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.1699A>G	chr11.hg19:g.618860T>C	ENSP00000351118:p.Ser567Gly	116.0	0.0		166.0	8.0	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Missense_Mutation	SNP	ENST00000358353.3	hg19	CCDS7707.1	.	.	.	.	.	.	.	.	.	.	C	3.103	-0.184385	0.06340	.	.	ENSG00000099834	ENST00000397542;ENST00000358353	T;T	0.50277	0.75;0.75	2.59	-2.0	0.07433	.	.	.	.	.	T	0.18383	0.0441	N	0.02916	-0.46	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30327	-0.9982	9	0.07990	T	0.79	.	9.3241	0.37982	0.0:0.2294:0.0:0.7706	.	561;567	Q9HBB8-4;Q9HBB8	.;CDHR5_HUMAN	G	567	ENSP00000380676:S567G;ENSP00000351118:S567G	ENSP00000351118:S567G	S	-	1	0	CDHR5	608860	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.029000	0.03585	-0.744000	0.04778	-0.222000	0.12452	AGT	.	.		0.672	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		C	618860	T	C	618860	3	2	154	1	0	0	0	0	1	0	0	0	3124	1580	55	2	850	2	CDHR5	11	618860	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10		618860	134387656	58	23619										
RSF1	51773	hgsc.bcm.edu	37	chr11	77409660	77409660	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tttttcactgccagacccttCactttcatcattgctggaat	5	12	4	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr11:77409660C>T	ENST00000308488.6	-	7	2889	c.2587G>A	c.(2587-2589)Gaa>Aaa	p.E863K	RSF1_ENST00000480887.1_Missense_Mutation_p.E611K|RSF1_ENST00000360355.2_Missense_Mutation_p.E832K			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	863					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.E863*(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			CCAGACCCTTCACTTTCATCA	0.403																																					p.E863K		Atlas-SNP	.											RSF1,NS,carcinoma,0,1	RSF1	105	.	1	Substitution - Nonsense(1)	lung(1)	c.G2587A						.						162	153	156					11																	77409660		2200	4292	6492	SO:0001583	missense	51773	exon7			ACCCTTCACTTTC	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"Zinc fingers, PHD-type"	18118	protein-coding gene	gene with protein product		608522	"hepatitis B virus x associated protein"	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.2587G>A	chr11.hg19:g.77409660C>T	ENSP00000311513:p.Glu863Lys	127.0	0.0		127.0	22.0	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	hg19	CCDS8253.1	.	.	.	.	.	.	.	.	.	.	C	32	5.135599	0.94517	.	.	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000526324	D;D;D;D	0.86497	-2.12;-2.13;-2.13;-2.07	4.68	4.68	0.58851	Zinc finger, FYVE/PHD-type (1);	0.000000	0.52532	D	0.000077	T	0.82111	0.4966	L	0.29908	0.895	0.51482	D	0.999926	P	0.43094	0.799	B	0.40066	0.318	D	0.84601	0.0672	10	0.54805	T	0.06	-12.7817	17.7579	0.88455	0.0:1.0:0.0:0.0	.	863	Q96T23	RSF1_HUMAN	K	863;611;832;664	ENSP00000311513:E863K;ENSP00000434509:E611K;ENSP00000353511:E832K;ENSP00000432022:E664K	ENSP00000311513:E863K	E	-	1	0	RSF1	77087308	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.929000	0.63455	2.580000	0.87095	0.591000	0.81541	GAA	.	.		0.403	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		T	77409660	C	T	77409660	3	4	154	1	0	0	0	0	1	0	0	0	13714	835	29	3	1778	3	RSF1	11	77409660	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	76790800	77409660	57596856	59	23620										
BCL9L	283149	hgsc.bcm.edu	37	chr11	118771950	118771950	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	aactgtgaaggcatcagcatCttctgcgggccgcccatcac	10	14	4	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr11:118771950C>T	ENST00000334801.3	-	6	3466	c.2502G>A	c.(2500-2502)aaG>aaA	p.K834K	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	834	Met-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GCATCAGCATCTTCTGCGGGC	0.647																																					p.K834K		Atlas-SNP	.											.	BCL9L	254	.	0			c.G2502A						.						72	70	70					11																	118771950		2200	4295	6495	SO:0001819	synonymous_variant	283149	exon6			CAGCATCTTCTGC	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.2502G>A	chr11.hg19:g.118771950C>T		47.0	0.0		55.0	14.0	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	hg19	CCDS8403.1																																																																																			.	.		0.647	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		T	118771950	C	T	118771950	2	4	154	1	0	0	0	0	0	0	0	1	1382	912	32	3		3	BCL9L	11	118771950	Silent	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	41362290	118771950	16234566	60	23621										
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120318992	120318992	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	atatgaagcatttgggagtaAaagtgaaagagcctcgaaat	11	4	0	3			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr11:120318992A>C	ENST00000397843.2	+	20	1838	c.1672A>C	c.(1672-1674)Aaa>Caa	p.K558Q	ARHGEF12_ENST00000356641.3_Missense_Mutation_p.K539Q|ARHGEF12_ENST00000532993.1_Missense_Mutation_p.K455Q	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	558	RGSL.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		TTTGGGAGTAAAAGTGAAAGA	0.418			T	MLL	AML																																p.K558Q		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.A1672C						.						93	91	92					11																	120318992		1860	4087	5947	SO:0001583	missense	23365	exon20			GGAGTAAAAGTGA	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.1672A>C	chr11.hg19:g.120318992A>C	ENSP00000380942:p.Lys558Gln	91.0	0.0		108.0	19.0	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	hg19	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.486866	0.84854	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	D;D;D	0.83673	-1.75;-1.75;-1.75	5.28	5.28	0.74379	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.123853	0.36134	N	0.002761	D	0.88040	0.6330	M	0.71581	2.175	0.33793	D	0.625737	P;P;D	0.53885	0.909;0.954;0.963	P;P;P	0.55260	0.745;0.662;0.772	D	0.92849	0.6295	10	0.72032	D	0.01	-19.2225	15.213	0.73241	1.0:0.0:0.0:0.0	.	455;539;558	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	Q	558;539;455	ENSP00000380942:K558Q;ENSP00000349056:K539Q;ENSP00000432984:K455Q	ENSP00000349056:K539Q	K	+	1	0	ARHGEF12	119824202	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.940000	0.75917	1.995000	0.58328	0.477000	0.44152	AAA	.	.		0.418	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		C	120318992	A	C	120318992	3	2	154	1	0	0	0	0	1	0	0	0	897	15	1	5	1750	5	ARHGEF12	11	120318992	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	1547042	120318992	14687524	61	23622										
SNX19	399979	hgsc.bcm.edu	37	chr11	130785826	130785826	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tggaacggtggcactgtttcTgtcttcatggctgaacggac	13	9	3	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr11:130785826T>C	ENST00000265909.4	-	1	578	c.9A>G	c.(7-9)acA>acG	p.T3T	SNX19_ENST00000539184.1_Intron|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000530356.1_Intron|SNX19_ENST00000533214.1_Silent_p.T3T|SNX19_ENST00000533318.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	3					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GCACTGTTTCTGTCTTCATGG	0.522																																					p.T3T		Atlas-SNP	.											.	SNX19	84	.	0			c.A9G						.						47	42	44					11																	130785826		2201	4297	6498	SO:0001819	synonymous_variant	399979	exon1			TGTTTCTGTCTTC	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.9A>G	chr11.hg19:g.130785826T>C		65.0	0.0		56.0	12.0	NM_014758	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	hg19	CCDS31721.1																																																																																			.	.		0.522	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		C	130785826	T	C	130785826	2	2	154	1	0	0	0	0	0	0	0	1	14905	1567	55	2		2	SNX19	11	130785826	Silent	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	10466834	130785826	4220690	62	23623										
NOP2	4839	hgsc.bcm.edu	37	chr12	6669440	6669440	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ctaggcccgtgggcaccagtCgcacattcctctttttcaga	9	14	2	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr12:6669440C>A	ENST00000322166.5	-	15	1734	c.1613G>T	c.(1612-1614)cGa>cTa	p.R538L	NOP2_ENST00000399466.2_Missense_Mutation_p.R534L|NOP2_ENST00000537442.1_Missense_Mutation_p.R538L|NOP2_ENST00000382421.3_Missense_Mutation_p.R571L|NOP2_ENST00000545200.1_Missense_Mutation_p.R534L|NOP2_ENST00000542015.1_5'UTR|NOP2_ENST00000541778.1_Missense_Mutation_p.R534L	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	538					positive regulation of cell proliferation (GO:0008284)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	19						GGGCACCAGTCGCACATTCCT	0.542																																					p.R571L		Atlas-SNP	.											.	NOP2	44	.	0			c.G1712T						.						69	71	70					12																	6669440		1931	4140	6071	SO:0001583	missense	4839	exon16			ACCAGTCGCACAT		CCDS44811.1, CCDS58202.1, CCDS58203.1, CCDS58204.1	12p13	2012-12-10	2012-12-10	2008-10-13	ENSG00000111641	ENSG00000111641		"NOP2/Sun domain containing"	7867	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 1"	164031	"nucleolar protein 1 (120kD)", "nucleolar protein 1, 120kDa", "nucleolar protein 2 homolog (yeast)", "NOP2 nucleolar protein homolog (yeast)"	NOL1		8088812	Standard	NM_006170		Approved	NOP120, NSUN1, p120	uc021qtz.2	P46087	OTTHUMG00000169163	ENST00000322166.5:c.1613G>T	chr12.hg19:g.6669440C>A	ENSP00000313272:p.Arg538Leu	83.0	0.0		83.0	14.0	NM_001258309	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Missense_Mutation	SNP	ENST00000322166.5	hg19	CCDS58203.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.510252	0.85282	.	.	ENSG00000111641	ENST00000537442;ENST00000382421;ENST00000545200;ENST00000399466;ENST00000322166;ENST00000541778	T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88	4.95	4.95	0.65309	.	0.122440	0.56097	D	0.000027	T	0.39784	0.1091	L	0.41961	1.31	0.80722	D	1	D;P	0.65815	0.995;0.943	D;P	0.66497	0.944;0.493	T	0.14727	-1.0462	10	0.87932	D	0	-23.2785	11.8077	0.52165	0.0:0.9199:0.0:0.0801	.	534;534	Q05BA7;P46087-2	.;.	L	538;571;534;534;538;534	ENSP00000444437:R538L;ENSP00000371858:R571L;ENSP00000439422:R534L;ENSP00000382392:R534L;ENSP00000313272:R538L;ENSP00000443150:R534L	ENSP00000313272:R538L	R	-	2	0	NOP2	6539701	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.767000	0.68850	2.569000	0.86673	0.655000	0.94253	CGA	.	.		0.542	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170		A	6669440	C	A	6669440	3	1	154	1	0	0	0	0	1	0	0	0	10547	884	31	1	833	1	NOP2	12	6669440	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10		6669440	127182455	63	23624										
GRIN2B	2904	hgsc.bcm.edu	37	chr12	13906726	13906726	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	cttgtttacaaagtcctggtAgccagggaaataggtggtga	13	6	0	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr12:13906726A>T	ENST00000609686.1	-	3	744	c.535T>A	c.(535-537)Tac>Aac	p.Y179N		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	179					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AAGTCCTGGTAGCCAGGGAAA	0.483																																					p.Y179N		Atlas-SNP	.											.	GRIN2B	303	.	0			c.T535A						.						128	122	124					12																	13906726		2203	4300	6503	SO:0001583	missense	2904	exon3			CCTGGTAGCCAGG		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.535T>A	chr12.hg19:g.13906726A>T	ENSP00000477455:p.Tyr179Asn	183.0	0.0		166.0	10.0	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	hg19	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.259110	0.80246	.	.	ENSG00000150086	ENST00000279593	D	0.86097	-2.07	5.13	5.13	0.70059	Extracellular ligand-binding receptor (1);	0.061515	0.64402	D	0.000002	D	0.92743	0.7693	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93686	0.7003	10	0.62326	D	0.03	.	14.9427	0.71006	1.0:0.0:0.0:0.0	.	179	Q13224	NMDE2_HUMAN	N	179	ENSP00000279593:Y179N	ENSP00000279593:Y179N	Y	-	1	0	GRIN2B	13797993	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.259000	0.95561	1.923000	0.55706	0.459000	0.35465	TAC	.	.		0.483	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			T	13906726	A	T	13906726	3	4	154	1	0	0	0	0	1	0	0	0	6789	420	15	4	3963	4	GRIN2B	12	13906726	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	7237286	13906726	119945169	64	23625										
KRT71	112802	hgsc.bcm.edu	37	chr12	52940080	52940080	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ccccgcccacctgcactcctCgctctccagtagcttgcgat	7	20	1	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr12:52940080C>T	ENST00000267119.5	-	7	1384	c.1315G>A	c.(1315-1317)Gag>Aag	p.E439K		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	439	Coil 2.|Rod.				hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		CTGCACTCCTCGCTCTCCAGT	0.612																																					p.E439K		Atlas-SNP	.											.	KRT71	70	.	0			c.G1315A						.						56	50	52					12																	52940080		2203	4300	6503	SO:0001583	missense	112802	exon7			ACTCCTCGCTCTC	AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"-", "Intermediate filaments type II, keratins (basic)"	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.1315G>A	chr12.hg19:g.52940080C>T	ENSP00000267119:p.Glu439Lys	90.0	0.0		86.0	4.0	NM_033448	B3KVC1|Q3SY85|Q96DU2	Missense_Mutation	SNP	ENST00000267119.5	hg19	CCDS8831.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.719502	0.89205	.	.	ENSG00000139648	ENST00000267119	D	0.93366	-3.21	4.34	3.44	0.39384	Filament (1);	0.000000	0.40640	N	0.001047	D	0.96682	0.8917	M	0.86420	2.815	0.48040	D	0.99957	D	0.89917	1.0	D	0.91635	0.999	D	0.97060	0.9770	10	0.87932	D	0	.	13.2682	0.60146	0.0:0.92:0.0:0.08	.	439	Q3SY84	K2C71_HUMAN	K	439	ENSP00000267119:E439K	ENSP00000267119:E439K	E	-	1	0	KRT71	51226347	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	6.048000	0.71046	1.136000	0.42199	0.561000	0.74099	GAG	.	.		0.612	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448		T	52940080	C	T	52940080	3	4	154	1	0	0	0	0	1	0	0	0	8493	893	31	1	268	1	KRT71	12	52940080	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	39033354	52940080	80911815	65	23626										
CAND1	55832	hgsc.bcm.edu	37	chr12	67691629	67691629	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	aagcctttgaatcatttgtaAgaaggtaagtttttaagatc	8	4	1	3			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr12:67691629A>G	ENST00000545606.1	+	6	1287	c.850A>G	c.(850-852)Aga>Gga	p.R284G		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	284					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		ATCATTTGTAAGAAGGTAAGT	0.323																																					p.R284G		Atlas-SNP	.											.	CAND1	100	.	0			c.A850G						.						68	73	72					12																	67691629		2201	4296	6497	SO:0001583	missense	55832	exon6			TTTGTAAGAAGGT		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.850A>G	chr12.hg19:g.67691629A>G	ENSP00000442318:p.Arg284Gly	64.0	0.0		65.0	10.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	A	12.23	1.876108	0.33162	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047	T	0.32515	1.45	5.81	4.64	0.57946	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.31231	0.0790	L	0.49699	1.58	0.80722	D	1	P	0.41624	0.757	B	0.41813	0.367	T	0.02533	-1.1145	9	.	.	.	-15.6081	12.9803	0.58559	0.8649:0.1351:0.0:0.0	.	284	Q86VP6	CAND1_HUMAN	G	284;284;126	ENSP00000442318:R284G	.	R	+	1	2	CAND1	65977896	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.195000	0.58400	1.004000	0.39156	0.528000	0.53228	AGA	.	.		0.323	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		G	67691629	A	G	67691629	3	3	154	1	0	0	0	0	1	0	0	0	2617	64	3	2	872	2	CAND1	12	67691629	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	14751549	67691629	66160266	66	23627										
ACACB	32	hgsc.bcm.edu	37	chr12	109692117	109692117	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ccctacgacccccggtggatGcttgcaggaaggcctcaccc	11	17	1	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr12:109692117G>T	ENST00000338432.7	+	44	6263	c.6144G>T	c.(6142-6144)atG>atT	p.M2048I	ACACB_ENST00000543201.1_Missense_Mutation_p.M714I|ACACB_ENST00000377854.5_Missense_Mutation_p.M1978I|ACACB_ENST00000377848.3_Missense_Mutation_p.M2048I			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2048	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	CCCGGTGGATGCTTGCAGGAA	0.507																																					p.M2048I		Atlas-SNP	.											.	ACACB	330	.	0			c.G6144T						.						139	142	141					12																	109692117		2203	4300	6503	SO:0001583	missense	32	exon43			GTGGATGCTTGCA	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.6144G>T	chr12.hg19:g.109692117G>T	ENSP00000341044:p.Met2048Ile	105.0	0.0		137.0	31.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.000214	0.74818	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027;ENST00000543201	D;D;D;D	0.97232	-4.3;-4.3;-4.3;-4.3	5.27	5.27	0.74061	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.113610	0.85682	D	0.000000	D	0.96728	0.8932	M	0.64567	1.98	0.80722	D	1	B	0.28082	0.2	B	0.37451	0.25	D	0.95614	0.8675	10	0.56958	D	0.05	.	18.8734	0.92325	0.0:0.0:1.0:0.0	.	2048	O00763	ACACB_HUMAN	I	2048;2048;1978;1279;714	ENSP00000341044:M2048I;ENSP00000367079:M2048I;ENSP00000367085:M1978I;ENSP00000444075:M714I	ENSP00000341044:M2048I	M	+	3	0	ACACB	108176500	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.605000	0.74155	2.648000	0.89879	0.655000	0.94253	ATG	.	.		0.507	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109692117	G	T	109692117	3	4	154	1	0	0	0	0	1	0	0	0	107	1319	46	3	6314	3	ACACB	12	109692117	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	42000488	109692117	24159778	67	23628										
B3GNT4	79369	hgsc.bcm.edu	37	chr12	122691390	122691390	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tcaacctgacgctcaaggagCtgcacctgcagcgctgggtg	13	13	2	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr12:122691390C>A	ENST00000324189.4	+	3	948	c.592C>A	c.(592-594)Ctg>Atg	p.L198M	B3GNT4_ENST00000545141.1_Intron|B3GNT4_ENST00000535274.1_Missense_Mutation_p.L173M|B3GNT4_ENST00000546192.1_Missense_Mutation_p.L173M	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	198					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		GCTCAAGGAGCTGCACCTGCA	0.577																																					p.L198M		Atlas-SNP	.											.	B3GNT4	35	.	0			c.C592A						.						44	47	46					12																	122691390		2203	4300	6503	SO:0001583	missense	79369	exon3			AAGGAGCTGCACC	AB049586	CCDS9227.1	12q24	2013-02-19						"Beta 3-glycosyltransferases"	15683	protein-coding gene	gene with protein product		605864				11042166	Standard	NM_030765		Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000324189.4:c.592C>A	chr12.hg19:g.122691390C>A	ENSP00000319636:p.Leu198Met	55.0	0.0		52.0	7.0	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Missense_Mutation	SNP	ENST00000324189.4	hg19	CCDS9227.1	.	.	.	.	.	.	.	.	.	.	C	17.69	3.450887	0.63290	.	.	ENSG00000176383	ENST00000324189;ENST00000546192;ENST00000535274	T;T;T	0.57273	0.41;0.41;0.41	5.2	4.29	0.51040	.	0.158628	0.29293	N	0.012575	T	0.57725	0.2073	L	0.35542	1.07	0.34620	D	0.718496	D	0.71674	0.998	D	0.74348	0.983	T	0.64188	-0.6466	10	0.29301	T	0.29	.	10.6445	0.45613	0.149:0.7073:0.1437:0.0	.	198	Q9C0J1	B3GN4_HUMAN	M	198;173;173	ENSP00000319636:L198M;ENSP00000438840:L173M;ENSP00000444534:L173M	ENSP00000319636:L198M	L	+	1	2	B3GNT4	121257343	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.003000	0.29809	1.275000	0.44379	0.655000	0.94253	CTG	.	.		0.577	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765		A	122691390	C	A	122691390	3	1	154	1	0	0	0	0	1	0	0	0	1259	796	28	3	598	3	B3GNT4	12	122691390	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	12999273	122691390	11160505	68	23629										
MGAT2	4247	hgsc.bcm.edu	37	chr14	50089289	50089289	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	atggagggtggggagatattAgggaccatgaactctgtaaa	15	4	1	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr14:50089289A>G	ENST00000305386.2	+	1	1801	c.1303A>G	c.(1303-1305)Agg>Ggg	p.R435G	RPL36AL_ENST00000298289.6_5'Flank|RP11-649E7.5_ENST00000555043.1_RNA	NM_002408.3	NP_002399.1	Q10469	MGAT2_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	435					cellular protein metabolic process (GO:0044267)|oligosaccharide biosynthetic process (GO:0009312)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0008455)|carbohydrate binding (GO:0030246)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)	11	all_epithelial(31;0.0021)|Breast(41;0.0124)					GGGAGATATTAGGGACCATGA	0.368																																					p.R435G		Atlas-SNP	.											.	MGAT2	26	.	0			c.A1303G						.						40	44	43					14																	50089289		2191	4289	6480	SO:0001583	missense	4247	exon1			GATATTAGGGACC	U15128	CCDS9690.1	14q21	2013-02-25			ENSG00000168282	ENSG00000168282	2.4.1.143	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7045	protein-coding gene	gene with protein product		602616				7635144	Standard	NM_002408		Approved	GNT-II	uc001wwr.3	Q10469	OTTHUMG00000140271	ENST00000305386.2:c.1303A>G	chr14.hg19:g.50089289A>G	ENSP00000307423:p.Arg435Gly	82.0	0.0		70.0	7.0	NM_002408	B3KPC5|B3KQM0	Missense_Mutation	SNP	ENST00000305386.2	hg19	CCDS9690.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.801054	0.50315	.	.	ENSG00000168282	ENST00000305386;ENST00000504161	D	0.94280	-3.39	6.14	4.95	0.65309	.	0.000000	0.85682	D	0.000000	D	0.96830	0.8965	M	0.87547	2.89	0.48901	D	0.999727	D	0.89917	1.0	D	0.97110	1.0	D	0.97385	0.9985	10	0.87932	D	0	-14.2725	14.0596	0.64790	0.7236:0.2764:0.0:0.0	.	435	Q10469	MGAT2_HUMAN	G	435;441	ENSP00000307423:R435G	ENSP00000307423:R435G	R	+	1	2	MGAT2	49159039	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.215000	0.42862	2.367000	0.80283	0.529000	0.55759	AGG	.	.		0.368	MGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276807.1	NM_002408		G	50089289	A	G	50089289	3	3	154	1	0	0	0	0	1	0	0	0	9552	411	15	2	1305	2	MGAT2	14	50089289	Missense_Mutation	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10		50089289	57260251	69	23630										
DDHD1	80821	hgsc.bcm.edu	37	chr14	53540535	53540535	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gcatggttggaaaaatgcctTtcttctatttttcttgcagc	8	8	3	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr14:53540535T>C	ENST00000323669.5	-	5	1319	c.1320A>G	c.(1318-1320)gaA>gaG	p.E440E	DDHD1_ENST00000395606.1_Silent_p.E447E|DDHD1_ENST00000357758.3_Silent_p.E440E	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	440					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					AAAAATGCCTTTCTTCTATTT	0.308																																					p.E447E		Atlas-SNP	.											.	DDHD1	202	.	0			c.A1341G						.						87	88	87					14																	53540535		2203	4300	6503	SO:0001819	synonymous_variant	80821	exon6			ATGCCTTTCTTCT	AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"phosphatidic acid-preferring phospholipase A1"	614603	"spastic paraplegia 28 (autosomal recessive)"	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.1320A>G	chr14.hg19:g.53540535T>C		163.0	0.0		175.0	22.0	NM_001160147	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Silent	SNP	ENST00000323669.5	hg19	CCDS53895.1																																																																																			.	.		0.308	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1			C	53540535	T	C	53540535	2	2	154	1	0	0	0	0	0	0	0	1	4328	1838	64	2		2	DDHD1	14	53540535	Silent	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	3451246	53540535	53809005	70	23631										
VSX2	338917	hgsc.bcm.edu	37	chr14	74726418	74726418	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	atggtgcggcactccatcccCctgcccgagtccatcctcaa	8	18	1	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr14:74726418C>A	ENST00000261980.2	+	4	783	c.693C>A	c.(691-693)ccC>ccA	p.P231P		NM_182894.2	NP_878314.1	P58304	VSX2_HUMAN	visual system homeobox 2	231	CVC. {ECO:0000255|PROSITE- ProRule:PRU00829}.				cell fate commitment (GO:0045165)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7				BRCA - Breast invasive adenocarcinoma(234;0.00154)		ACTCCATCCCCCTGCCCGAGT	0.652																																					p.P231P		Atlas-SNP	.											.	VSX2	32	.	0			c.C693A						.						111	90	97					14																	74726418		2203	4300	6503	SO:0001819	synonymous_variant	338917	exon4			CATCCCCCTGCCC	AC005519	CCDS9827.1	14q24.3	2011-06-20	2007-08-21	2007-08-21		ENSG00000119614		"Homeoboxes / PRD class"	1975	protein-coding gene	gene with protein product		142993	"C elegans ceh-10 homeo domain-containing homolog", "ceh-10 homeo domain containing homolog (C. elegans)", "ceh-10 homeodomain containing homolog (C. elegans)"	HOX10, CHX10		1973146	Standard	NM_182894		Approved	RET1	uc001xpq.3	P58304		ENST00000261980.2:c.693C>A	chr14.hg19:g.74726418C>A		93.0	0.0		132.0	25.0	NM_182894	A1A4X6	Silent	SNP	ENST00000261980.2	hg19	CCDS9827.1																																																																																			.	.		0.652	VSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412323.1	NM_182894		A	74726418	C	A	74726418	2	1	154	1	0	0	0	0	0	0	0	1	17247	610	22	3		3	VSX2	14	74726418	Silent	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	21185883	74726418	32623122	71	23632										
TJP1	7082	hgsc.bcm.edu	37	chr15	29997825	29997825	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ttcgggaatggctccttgagGgataattatactaacaccag	10	8	0	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr15:29997825G>A	ENST00000346128.6	-	26	5449	c.4975C>T	c.(4975-4977)Cct>Tct	p.P1659S	TJP1_ENST00000356107.6_Missense_Mutation_p.P1659S|TJP1_ENST00000545208.2_Missense_Mutation_p.P1579S|TJP1_ENST00000400011.2_Missense_Mutation_p.P1583S	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1659	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		GCTCCTTGAGGGATAATTATA	0.463																																					p.P1659S	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.C4975T						.						90	88	89					15																	29997825		1910	4134	6044	SO:0001583	missense	7082	exon26			CTTGAGGGATAAT		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.4975C>T	chr15.hg19:g.29997825G>A	ENSP00000281537:p.Pro1659Ser	140.0	0.0		141.0	23.0	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	hg19	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	G	33	5.195963	0.94960	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	D;D	0.82167	-1.58;-1.58	4.96	4.96	0.65561	ZU5 (3);	0.111165	0.64402	D	0.000007	D	0.92110	0.7499	M	0.84948	2.725	0.80722	D	1	D;D;D;D	0.89917	0.991;0.97;0.972;1.0	P;P;D;D	0.85130	0.857;0.696;0.918;0.997	D	0.93222	0.6609	10	0.87932	D	0	.	18.4059	0.90536	0.0:0.0:1.0:0.0	.	1652;1579;1659;1583	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	S	1659;1583;1659;1579;1579	ENSP00000281537:P1659S;ENSP00000382890:P1583S	ENSP00000281537:P1659S	P	-	1	0	TJP1	27785117	1.000000	0.71417	0.996000	0.52242	0.965000	0.64279	9.657000	0.98554	2.585000	0.87301	0.655000	0.94253	CCT	.	.		0.463	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		A	29997825	G	A	29997825	3	1	154	1	0	0	0	0	1	0	0	0	15944	1232	43	3	283	3	TJP1	15	29997825	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10		29997825	72533567	72	23633										
JMJD7	100137047	hgsc.bcm.edu	37	chr15	42127787	42127787	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tctgccttctgccctgcaggAaagatgcccgatgctgtgaa	11	12	2	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr15:42127787A>G	ENST00000397299.4	+	4	514	c.474A>G	c.(472-474)ggA>ggG	p.G158G	PLA2G4B_ENST00000542534.2_Splice_Site_p.G158G|JMJD7_ENST00000408047.1_Splice_Site_p.G59G|PLA2G4B_ENST00000452633.1_5'Flank|JMJD7-PLA2G4B_ENST00000342159.4_Splice_Site_p.G158G|JMJD7-PLA2G4B_ENST00000476036.1_3'UTR|JMJD7-PLA2G4B_ENST00000382448.4_Splice_Site_p.G158G	NM_001114632.1	NP_001108104.1	P0C870	JMJD7_HUMAN	jumonji domain containing 7	158	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.									NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)	8						GCCCTGCAGGAAAGATGCCCG	0.567																																					p.G158G		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.A474G						.						87	83	84					15																	42127787		2203	4300	6503	SO:0001630	splice_region_variant	8681	exon4			TGCAGGAAAGATG		CCDS45240.1	15q15.1	2011-02-10			ENSG00000243789	ENSG00000243789			34397	protein-coding gene	gene with protein product							Standard	NM_001114632		Approved			P0C870	OTTHUMG00000156810	ENST00000397299.4:c.473-1A>G	chr15.hg19:g.42127787A>G		99.0	0.0		120.0	8.0	NM_005090	A5D6V5|O95712|Q59GF9|Q8TB10|Q9UKV7	Silent	SNP	ENST00000397299.4	hg19	CCDS45240.1																																																																																			.	.		0.567	JMJD7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326082.1	NM_001114632	Silent	G	42127787	A	G	42127787	5	3	154	1	0	0	0	0	0	0	1	0	7963	260	9	2	488	2	JMJD7	15	42127787	Splice_Site	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	12129962	42127787	60403605	73	23634										
LCTL	197021	hgsc.bcm.edu	37	chr15	66857654	66857654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tccgggcggcccccagcctgGgcaccagcagtagcatccac	12	18	0	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr15:66857654G>A	ENST00000341509.5	-	1	181	c.50C>T	c.(49-51)cCc>cTc	p.P17L	LCTL_ENST00000537670.1_Intron|LCTL_ENST00000563438.1_Intron	NM_207338.2	NP_997221.2	Q6UWM7	LCTL_HUMAN	lactase-like	17					carbohydrate metabolic process (GO:0005975)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CCCCAGCCTGGGCACCAGCAG	0.632																																					p.P17L		Atlas-SNP	.											.	LCTL	73	.	0			c.C50T						.						35	36	36					15																	66857654		2200	4299	6499	SO:0001583	missense	197021	exon1			AGCCTGGGCACCA	AY358729	CCDS10220.1, CCDS61678.1	15q21.3	2008-02-05			ENSG00000188501	ENSG00000188501			15583	protein-coding gene	gene with protein product	"klotho gamma", "KL lactase phlorizin hydrolase"					12084582	Standard	NM_207338		Approved	KLPH, FLJ33279, KLG	uc002aqc.3	Q6UWM7	OTTHUMG00000133207	ENST00000341509.5:c.50C>T	chr15.hg19:g.66857654G>A	ENSP00000343490:p.Pro17Leu	242.0	0.0		242.0	45.0	NM_207338	B3KQY0	Missense_Mutation	SNP	ENST00000341509.5	hg19	CCDS10220.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.710072	0.00094	.	.	ENSG00000188501	ENST00000341509	T	0.30981	1.51	4.18	-0.0437	0.13858	.	0.981786	0.08343	N	0.960539	T	0.12732	0.0309	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34800	-0.9814	10	0.09843	T	0.71	-1.7633	5.6031	0.17365	0.2793:0.1482:0.5725:0.0	.	17	Q6UWM7	LCTL_HUMAN	L	17	ENSP00000343490:P17L	ENSP00000343490:P17L	P	-	2	0	LCTL	64644708	0.000000	0.05858	0.015000	0.15790	0.002000	0.02628	0.291000	0.18994	-0.173000	0.10761	-1.728000	0.00702	CCC	.	.		0.632	LCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256921.2	NM_207338		A	66857654	G	A	66857654	3	1	154	1	0	0	0	0	1	0	0	0	8703	1232	43	3	1705	3	LCTL	15	66857654	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	24729867	66857654	35673738	74	23635										
IREB2	3658	hgsc.bcm.edu	37	chr15	78758781	78758781	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tcaggaacattttcttcgcaGattgagaatacacccatcct	6	11	2	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr15:78758781G>A	ENST00000258886.8	+	5	728	c.579G>A	c.(577-579)caG>caA	p.Q193Q	IREB2_ENST00000560440.1_Silent_p.Q193Q|IREB2_ENST00000559427.1_3'UTR	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	193					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		TTTCTTCGCAGATTGAGAATA	0.433																																					p.Q193Q	NSCLC(200;764 2208 35157 49871 50830)	Atlas-SNP	.											.	IREB2	106	.	0			c.G579A						.						128	125	126					15																	78758781		2196	4293	6489	SO:0001819	synonymous_variant	3658	exon5			TTCGCAGATTGAG	M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.579G>A	chr15.hg19:g.78758781G>A		140.0	0.0		150.0	15.0	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Silent	SNP	ENST00000258886.8	hg19	CCDS10302.1																																																																																			.	.		0.433	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		A	78758781	G	A	78758781	2	1	154	1	0	0	0	0	0	0	0	1	7835	933	33	3		3	IREB2	15	78758781	Silent	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	11901127	78758781	23772611	75	23636										
MESP1	55897	hgsc.bcm.edu	37	chr15	90294296	90294296	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	cccggagggtgcctggccgcGcggggctcgccacggggctg	20	15	0	0	rs3841586|rs71934166		TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr15:90294296G>A	ENST00000300057.4	-	1	245	c.167C>T	c.(166-168)gCg>gTg	p.A56V	MESP1_ENST00000559894.1_5'UTR	NM_018670.3	NP_061140.1	Q9BRJ9	MESP1_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 1	56					cardiac atrium formation (GO:0003210)|cardiac cell fate determination (GO:0060913)|cardiac muscle cell differentiation (GO:0055007)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cardiac ventricle formation (GO:0003211)|cardioblast anterior-lateral migration (GO:0003259)|cardioblast migration to the midline involved in heart field formation (GO:0060975)|embryonic heart tube morphogenesis (GO:0003143)|endothelial cell differentiation (GO:0045446)|gastrulation (GO:0007369)|growth involved in heart morphogenesis (GO:0003241)|heart looping (GO:0001947)|lateral mesoderm development (GO:0048368)|mesodermal cell migration (GO:0008078)|negative regulation of endodermal cell fate specification (GO:0042664)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of transcription, DNA-templated (GO:0045892)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway (GO:0090082)|positive regulation of hepatocyte differentiation (GO:0070368)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of Notch signaling pathway involved in heart induction (GO:0035481)|positive regulation of striated muscle cell differentiation (GO:0051155)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|secondary heart field specification (GO:0003139)|signal transduction involved in regulation of gene expression (GO:0023019)|sinoatrial node cell differentiation (GO:0060921)|sinus venosus morphogenesis (GO:0003236)	nucleus (GO:0005634)	enhancer binding (GO:0035326)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|kidney(1)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			GCCTGGCCGCGCGGGGCTCGC	0.786																																					p.A56V		Atlas-SNP	.											.	MESP1	7	.	0			c.C167T						.						2	3	2					15																	90294296		862	2258	3120	SO:0001583	missense	55897	exon1			GGCCGCGCGGGGC		CCDS10355.1	15q26.1	2014-06-30	2014-06-30		ENSG00000166823	ENSG00000166823		"Basic helix-loop-helix proteins"	29658	protein-coding gene	gene with protein product		608689	"mesoderm posterior 1 homolog (mouse)"			8787751, 11578861	Standard	NM_018670		Approved	MGC10676, bHLHc5	uc002bol.3	Q9BRJ9	OTTHUMG00000149810	ENST00000300057.4:c.167C>T	chr15.hg19:g.90294296G>A	ENSP00000300057:p.Ala56Val	5.0	0.0		13.0	5.0	NM_018670	Q9NSF1|Q9NSF2	Missense_Mutation	SNP	ENST00000300057.4	hg19	CCDS10355.1	.	.	.	.	.	.	.	.	.	.	G	11.97	1.797307	0.31777	.	.	ENSG00000166823	ENST00000300057	T	0.79940	-1.32	3.11	-3.69	0.04450	.	.	.	.	.	T	0.55146	0.1902	N	0.19112	0.55	0.09310	N	1	P	0.42692	0.787	B	0.27262	0.078	T	0.50118	-0.8865	9	0.25106	T	0.35	.	7.6367	0.28270	0.0:0.4869:0.2532:0.2599	.	56	Q9BRJ9	MESP1_HUMAN	V	56	ENSP00000300057:A56V	ENSP00000300057:A56V	A	-	2	0	MESP1	88095300	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.025000	0.12413	-0.477000	0.06832	0.448000	0.29417	GCG	.	.		0.786	MESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313421.1	NM_018670		A	90294296	G	A	90294296	3	1	154	1	0	0	0	0	1	0	0	0	9491	1087	38	1	647	1	MESP1	15	90294296	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	11535515	90294296	12237096	76	23637										
MVP	9961	hgsc.bcm.edu	37	chr16	29848234	29848234	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tgcgtgattctcgaccctgtCggaccggatggcaagaatca	12	11	2	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr16:29848234C>T	ENST00000357402.5	+	7	1002	c.864C>T	c.(862-864)gtC>gtT	p.V288V	MVP_ENST00000452209.2_Missense_Mutation_p.R103W|MVP_ENST00000395353.1_Silent_p.V288V	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	288					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						TCGACCCTGTCGGACCGGATG	0.617																																					p.V288V		Atlas-SNP	.											.	MVP	80	.	0			c.C864T						.						68	53	58					16																	29848234		2197	4300	6497	SO:0001819	synonymous_variant	9961	exon7			CCCTGTCGGACCG	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"lung resistance-related protein"	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.864C>T	chr16.hg19:g.29848234C>T		102.0	0.0		112.0	23.0	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Silent	SNP	ENST00000357402.5	hg19	CCDS10656.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.242225	0.39598	.	.	ENSG00000013364	ENST00000452209	T	0.64991	-0.13	5.47	-10.9	0.00192	.	.	.	.	.	T	0.53769	0.1817	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.63857	-0.6542	6	0.87932	D	0	-16.0431	8.2486	0.31704	0.0646:0.3999:0.4325:0.103	.	.	.	.	W	103	ENSP00000387916:R103W	ENSP00000387916:R103W	R	+	1	2	MVP	29755735	0.001000	0.12720	0.000000	0.03702	0.843000	0.47879	-2.758000	0.00787	-3.446000	0.00162	0.462000	0.41574	CGG	.	.		0.617	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115		T	29848234	C	T	29848234	2	4	154	1	0	0	0	0	0	0	0	1	10005	871	31	1		1	MVP	16	29848234	Silent	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10		29848234	60506519	77	23638										
KIFC3	3801	hgsc.bcm.edu	37	chr16	57796115	57796115	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tgtactcccagtcagacgccTtctcctgcacctcggagaag	9	15	2	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr16:57796115T>G	ENST00000379655.4	-	13	1942	c.1685A>C	c.(1684-1686)aAg>aCg	p.K562T	KIFC3_ENST00000541240.1_Missense_Mutation_p.K584T|KIFC3_ENST00000543930.1_Missense_Mutation_p.K420T|KIFC3_ENST00000445690.2_Missense_Mutation_p.K562T|KIFC3_ENST00000562903.1_Missense_Mutation_p.K423T|KIFC3_ENST00000465878.2_Missense_Mutation_p.K423T|KIFC3_ENST00000540079.2_Missense_Mutation_p.K460T|KIFC3_ENST00000539578.1_Missense_Mutation_p.K504T|KIFC3_ENST00000421376.2_Missense_Mutation_p.K423T	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	562	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				GTCAGACGCCTTCTCCTGCAC	0.637																																					p.K562T		Atlas-SNP	.											.	KIFC3	55	.	0			c.A1685C						.						48	45	46					16																	57796115		2198	4300	6498	SO:0001583	missense	3801	exon13			GACGCCTTCTCCT	BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"Kinesins"	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.1685A>C	chr16.hg19:g.57796115T>G	ENSP00000368976:p.Lys562Thr	33.0	0.0		32.0	8.0	NM_001130100	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Missense_Mutation	SNP	ENST00000379655.4	hg19	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	T	19.41	3.822928	0.71028	.	.	ENSG00000140859	ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578	T;T;T;T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9;-0.9;-0.9;-0.9	4.42	4.42	0.53409	Kinesin, motor domain (4);	0.049261	0.85682	D	0.000000	T	0.65575	0.2704	L	0.27944	0.81	0.53688	D	0.999971	P;P;P;B;B;P;P	0.44816	0.641;0.844;0.641;0.01;0.077;0.792;0.756	B;B;P;B;B;P;B	0.47102	0.337;0.402;0.456;0.021;0.082;0.537;0.429	T	0.67393	-0.5682	10	0.59425	D	0.04	.	7.48	0.27400	0.0:0.0993:0.0:0.9007	.	584;504;420;460;267;562;423	B7Z484;F5H4I9;B7Z896;F5H3M2;B7Z3I6;Q9BVG8;A8K6S2	.;.;.;.;.;KIFC3_HUMAN;.	T	562;562;423;584;460;420;504	ENSP00000368976:K562T;ENSP00000401696:K562T;ENSP00000396399:K423T;ENSP00000442008:K584T;ENSP00000438805:K460T;ENSP00000444012:K420T;ENSP00000444884:K504T	ENSP00000368976:K562T	K	-	2	0	KIFC3	56353616	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	3.081000	0.50120	1.636000	0.50526	0.482000	0.46254	AAG	.	.		0.637	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550		G	57796115	T	G	57796115	3	3	154	1	0	0	0	0	1	0	0	0	8323	1609	56	5	853	5	KIFC3	16	57796115	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	27947881	57796115	32558638	78	23639										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58572172	58572172	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tcgacattcaattaggcaccTagaaaaagttcaatatcttt	5	8	3	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr16:58572172T>C	ENST00000317147.5	-	37	5468		c.e37-2		CNOT1_ENST00000245138.4_Splice_Site|CNOT1_ENST00000569240.1_Splice_Site	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1						gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		ATTAGGCACCTAGAAAAAGTT	0.358																																					.		Atlas-SNP	.											.	CNOT1	359	.	0			c.5136-2A>G						.						59	57	58					16																	58572172		2198	4300	6498	SO:0001630	splice_region_variant	23019	exon38			GGCACCTAGAAAA	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.5136-2A>G	chr16.hg19:g.58572172T>C		86.0	0.0		97.0	10.0	NM_016284	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Splice_Site	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.132861	0.77662	.	.	ENSG00000125107	ENST00000317147;ENST00000245138;ENST00000394200	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0121	0.80409	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CNOT1	57129673	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	8.040000	0.89188	2.180000	0.69256	0.482000	0.46254	.	.	.		0.358	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	Intron	C	58572172	T	C	58572172	5	2	154	1	0	0	0	0	0	0	1	0	3619	1536	53	2	2048	2	CNOT1	16	58572172	Splice_Site	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	776057	58572172	31782581	79	23640										
CDH8	1006	hgsc.bcm.edu	37	chr16	61687819	61687819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gcaaatctggtttaatatccTtacggggtaaaaatccatta	7	7	1	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr16:61687819T>C	ENST00000577390.1	-	12	3047	c.2093A>G	c.(2092-2094)aAg>aGg	p.K698R	CDH8_ENST00000577730.1_Intron|CDH8_ENST00000299345.6_Missense_Mutation_p.K698R	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	698					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		TTTAATATCCTTACGGGGTAA	0.418																																					p.K698R		Atlas-SNP	.											.	CDH8	273	.	0			c.A2093G						.						105	105	105					16																	61687819		2203	4300	6503	SO:0001583	missense	1006	exon12			ATATCCTTACGGG	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.2093A>G	chr16.hg19:g.61687819T>C	ENSP00000462701:p.Lys698Arg	127.0	0.0		150.0	22.0	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	hg19	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	T	0.539	-0.854473	0.02630	.	.	ENSG00000150394	ENST00000299345	T	0.75821	-0.97	5.7	4.61	0.57282	Cadherin, cytoplasmic domain (1);	0.048168	0.85682	N	0.000000	T	0.49029	0.1533	N	0.10629	0.01	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44406	-0.9330	10	0.02654	T	1	.	10.8247	0.46625	0.0:0.0736:0.0:0.9264	.	698	P55286	CADH8_HUMAN	R	698	ENSP00000299345:K698R	ENSP00000299345:K698R	K	-	2	0	CDH8	60245320	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.937000	0.70162	0.993000	0.38866	0.533000	0.62120	AAG	.	.		0.418	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		C	61687819	T	C	61687819	3	2	154	1	0	0	0	0	1	0	0	0	3118	1609	56	2	310	2	CDH8	16	61687819	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	3115647	61687819	28666934	80	23641										
OVCA2	124641	hgsc.bcm.edu	37	chr17	1945365	1945365	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gccgcgcagcgacccctgcgGgtcctgtgcctggcgggctt	16	16	0	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr17:1945365G>T	ENST00000572195.1	+	1	39	c.24G>T	c.(22-24)cgG>cgT	p.R8R	DPH1_ENST00000570477.1_Intron|DPH1_ENST00000263083.6_Intron|RP11-667K14.3_ENST00000572790.1_lincRNA|RP11-667K14.4_ENST00000572404.1_RNA	NM_080822.2	NP_543012.1	Q8WZ82	OVCA2_HUMAN	ovarian tumor suppressor candidate 2	8					metabolic process (GO:0008152)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)										GACCCCTGCGGGTCCTGTGCC	0.716											OREG0024078	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R8R		Atlas-SNP	.											.	.	.	.	0			c.G24T						.						4	5	5					17																	1945365		1952	3954	5906	SO:0001819	synonymous_variant	124641	exon1			CCTGCGGGTCCTG	AF321875	CCDS11015.1	17p13.3	2012-10-08			ENSG00000262664	ENSG00000262664			24203	protein-coding gene	gene with protein product	"candidate tumor suppressor in ovarian cancer 2"	607896				11979432, 8616839, 16368187	Standard	NM_080822		Approved		uc002ftx.3	Q8WZ82	OTTHUMG00000132471	ENST00000572195.1:c.24G>T	chr17.hg19:g.1945365G>T		44.0	0.0	599	38.0	8.0	NM_080822	Q86XN3|Q8IW87|Q9UCX9	Silent	SNP	ENST00000572195.1	hg19	CCDS11015.1																																																																																			.	.		0.716	OVCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255636.5	NM_080822		T	1945365	G	T	1945365	2	4	154	1	0	0	0	0	0	0	0	1	11331	1219	43	3		3	OVCA2	17	1945365	Silent	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10		1945365	79249845	81	23642										
TXNDC17	84817	hgsc.bcm.edu	37	chr17	6545140	6545140	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gtgttcatctactgccaagtAggagaaaagccttagtaagt	10	7	2	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr17:6545140A>G	ENST00000250101.5	+	2	538	c.213A>G	c.(211-213)gtA>gtG	p.V71V	KIAA0753_ENST00000361413.3_5'Flank|TXNDC17_ENST00000577146.1_3'UTR|TXNDC17_ENST00000570330.1_Silent_p.V46V|TXNDC17_ENST00000574838.1_Silent_p.V71V|KIAA0753_ENST00000572370.1_5'Flank	NM_032731.3	NP_116120.1	Q9BRA2	TXD17_HUMAN	thioredoxin domain containing 17	71	Thioredoxin.				oxidation-reduction process (GO:0055114)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|peroxidase activity (GO:0004601)|protein-disulfide reductase activity (GO:0047134)			endometrium(1)|kidney(1)|ovary(1)	3						ACTGCCAAGTAGGAGAAAAGC	0.448																																					p.V71V		Atlas-SNP	.											.	TXNDC17	10	.	0			c.A213G						.						98	98	98					17																	6545140		2203	4300	6503	SO:0001819	synonymous_variant	84817	exon2			CCAAGTAGGAGAA	BC006405	CCDS11077.1	17p13.2	2007-08-16	2007-08-16	2007-08-16	ENSG00000129235	ENSG00000129235			28218	protein-coding gene	gene with protein product	"thioredoxin (Trx)-related protein, 14 kDa"		"thioredoxin-like 5"	TXNL5		14607844, 14607843	Standard	NM_032731		Approved	MGC14353, TRP14	uc002gdf.4	Q9BRA2	OTTHUMG00000102053	ENST00000250101.5:c.213A>G	chr17.hg19:g.6545140A>G		102.0	0.0		90.0	4.0	NM_032731	A8K7E8	Silent	SNP	ENST00000250101.5	hg19	CCDS11077.1																																																																																			.	.		0.448	TXNDC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219854.2	NM_032731		G	6545140	A	G	6545140	2	3	154	1	0	0	0	0	0	0	0	1	16811	407	15	2		2	TXNDC17	17	6545140	Silent	SNP	A	TCGA-DD-AACC-01A-11D-A40R-10	4599775	6545140	74650070	82	23643										
TTC19	54902	hgsc.bcm.edu	37	chr17	15903433	15903433	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tcagagccccttcccgcagcGctcgcctggttctcgaggcc	11	18	2	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr17:15903433G>T	ENST00000261647.5	+	2	655	c.186G>T	c.(184-186)gcG>gcT	p.A62A	ZSWIM7_ENST00000472495.1_5'Flank|ZSWIM7_ENST00000486655.1_5'Flank|ZSWIM7_ENST00000399277.1_5'Flank|TTC19_ENST00000486880.2_Splice_Site_p.A183A|TTC19_ENST00000497842.2_3'UTR|ZSWIM7_ENST00000399280.2_5'Flank	NM_001271420.1|NM_017775.3	NP_001258349.1|NP_060245.3	Q6DKK2	TTC19_HUMAN	tetratricopeptide repeat domain 19	62					cytokinesis (GO:0000910)|mitochondrial respiratory chain complex III assembly (GO:0034551)	centrosome (GO:0005813)|midbody (GO:0030496)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				central_nervous_system(1)|lung(2)|skin(1)|stomach(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TTCCCGCAGCGCTCGCCTGGT	0.796																																					p.A62A		Atlas-SNP	.											.	TTC19	10	.	0			c.G186T						.						4	7	6					17																	15903433		1860	3797	5657	SO:0001630	splice_region_variant	54902	exon2			CGCAGCGCTCGCC	AK094819	CCDS11174.1, CCDS11174.2	17p11.2	2013-01-11			ENSG00000011295	ENSG00000011295		"Tetratricopeptide (TTC) repeat domain containing"	26006	protein-coding gene	gene with protein product		613814					Standard	NM_017775		Approved	FLJ20343, MGC19520	uc002gph.3	Q6DKK2	OTTHUMG00000059306	ENST00000261647.5:c.185-1G>T	chr17.hg19:g.15903433G>T		614.0	1.0		532.0	93.0	NM_017775	A8MZ52|B3KP62|B4DN65|Q2M248|Q7L3U8|Q9H6G3|Q9NXB2	Silent	SNP	ENST00000261647.5	hg19	CCDS11174.2																																																																																			.	.		0.796	TTC19-001	NOVEL	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000131725.6	NM_017775	Silent	T	15903433	G	T	15903433	5	4	154	1	0	0	0	0	0	0	1	0	16701	1101	38	1	555	1	TTC19	17	15903433	Splice_Site	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	9358293	15903433	65291777	83	23644										
MEOX1	4222	hgsc.bcm.edu	37	chr17	41738603	41738603	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gagttgggcctgcgccgggcGtctgagacagggaagtgcca	18	10	1	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr17:41738603G>T	ENST00000318579.4	-	1	719	c.300C>A	c.(298-300)gaC>gaA	p.D100E	MEOX1_ENST00000393661.2_5'UTR|MEOX1_ENST00000329168.3_Missense_Mutation_p.D100E|MEOX1_ENST00000549132.1_Missense_Mutation_p.T71K	NM_001040002.1|NM_004527.3	NP_001035091.1|NP_004518.1	P50221	MEOX1_HUMAN	mesenchyme homeobox 1	100					multicellular organismal development (GO:0007275)|somite specification (GO:0001757)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)		TGCGCCGGGCGTCTGAGACAG	0.667																																					p.D100E		Atlas-SNP	.											.	MEOX1	29	.	0			c.C300A						.						49	56	54					17																	41738603		2203	4300	6503	SO:0001583	missense	4222	exon1			CCGGGCGTCTGAG		CCDS11466.1, CCDS11467.1, CCDS42343.1	17q21.31	2014-07-15	2005-12-22					"Homeoboxes / ANTP class : HOXL subclass"	7013	protein-coding gene	gene with protein product		600147	"mesenchyme homeo box 1"			7987315	Standard	NM_013999		Approved	MOX1	uc002idz.3	P50221	OTTHUMG00000170513	ENST00000318579.4:c.300C>A	chr17.hg19:g.41738603G>T	ENSP00000321684:p.Asp100Glu	101.0	0.0		103.0	14.0	NM_004527	A8K524|A8MWF9|Q15069	Missense_Mutation	SNP	ENST00000318579.4	hg19	CCDS11466.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.092|0.092	-1.165880|-1.165880	0.01673|0.01673	.|.	.|.	ENSG00000005102|ENSG00000005102	ENST00000318579;ENST00000329168|ENST00000549132	D;T|.	0.89681|.	-2.55;1.48|.	4.63|4.63	0.13|0.13	0.14746|0.14746	.|.	0.105878|.	0.64402|.	N|.	0.000005|.	T|T	0.06645|0.06645	0.0170|0.0170	N|N	0.00210|0.00210	-1.845|-1.845	0.19775|0.19775	N|N	0.99995|0.99995	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.28364|0.28364	-1.0046|-1.0046	10|6	0.02654|0.87932	T|D	1|0	-20.2265|-20.2265	6.095|6.095	0.20015|0.20015	0.0:0.5446:0.2891:0.1663|0.0:0.5446:0.2891:0.1663	.|.	100;100|.	Q15069;P50221|.	.;MEOX1_HUMAN|.	E|K	100|71	ENSP00000321684:D100E;ENSP00000328678:D100E|.	ENSP00000321684:D100E|ENSP00000449049:T71K	D|T	-|-	3|2	2|0	MEOX1|MEOX1	39094129|39094129	0.962000|0.962000	0.33011|0.33011	0.978000|0.978000	0.43139|0.43139	0.417000|0.417000	0.31264|0.31264	0.141000|0.141000	0.16076|0.16076	0.152000|0.152000	0.19188|0.19188	-0.128000|-0.128000	0.14901|0.14901	GAC|ACG	.	.		0.667	MEOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409452.1			T	41738603	G	T	41738603	3	4	154	1	0	0	0	0	1	0	0	0	9482	1136	40	1	476	1	MEOX1	17	41738603	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	25835170	41738603	39456607	84	23645										
KCNH6	81033	hgsc.bcm.edu	37	chr17	61623214	61623214	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	tgttcccaagcagctggactTccagagacatggctcagatc	10	12	1	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr17:61623214T>C	ENST00000583023.1	+	14	2947	c.2936T>C	c.(2935-2937)tTc>tCc	p.F979S	KCNH6_ENST00000581784.1_Missense_Mutation_p.F890S|KCNH6_ENST00000314672.5_Missense_Mutation_p.F943S|KCNH6_ENST00000456941.2_Missense_Mutation_p.F890S	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	979					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	CAGCTGGACTTCCAGAGACAT	0.552																																					p.F979S		Atlas-SNP	.											.	KCNH6	122	.	0			c.T2936C						.						90	86	88					17																	61623214		2203	4300	6503	SO:0001583	missense	81033	exon14			TGGACTTCCAGAG	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2936T>C	chr17.hg19:g.61623214T>C	ENSP00000463533:p.Phe979Ser	60.0	0.0		50.0	4.0	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	hg19	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	T	16.16	3.044176	0.55110	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D	0.99270	-5.66	4.57	3.48	0.39840	.	0.570419	0.15330	U	0.268084	D	0.97461	0.9169	L	0.44542	1.39	0.32052	N	0.596766	B;B;B;B	0.27559	0.004;0.181;0.066;0.112	B;B;B;B	0.26310	0.004;0.042;0.068;0.063	D	0.99975	1.2161	10	0.87932	D	0	.	9.708	0.40227	0.0:0.0826:0.0:0.9174	.	820;943;890;979	B4DPJ3;B4DKC0;Q9H252-2;Q9H252	.;.;.;KCNH6_HUMAN	S	979;890	ENSP00000396900:F890S	ENSP00000318212:F979S	F	+	2	0	KCNH6	58976946	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.531000	0.45650	1.810000	0.52873	0.460000	0.39030	TTC	.	.		0.552	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		C	61623214	T	C	61623214	3	2	154	1	0	0	0	0	1	0	0	0	8045	1783	62	2	2990	2	KCNH6	17	61623214	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	19884611	61623214	19571996	85	23646										
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72998511	72998511	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	agtgagtcagccaaggatcaGaaagcagcgaacccgtacgt	12	10	2	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr18:72998511G>T	ENST00000580243.1	+	2	1497	c.1149G>T	c.(1147-1149)caG>caT	p.Q383H	TSHZ1_ENST00000322038.5_Missense_Mutation_p.Q338H			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	383					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		CCAAGGATCAGAAAGCAGCGA	0.627																																					p.Q338H		Atlas-SNP	.											.	TSHZ1	104	.	0			c.G1014T						.						103	108	106					18																	72998511		2203	4300	6503	SO:0001583	missense	10194	exon2			GGATCAGAAAGCA	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	10669	protein-coding gene	gene with protein product		614427	"serologically defined colon cancer antigen 33", "teashirt zinc finger 1", "teashirt family zinc finger 1"	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1149G>T	chr18.hg19:g.72998511G>T	ENSP00000464391:p.Gln383His	107.0	0.0		126.0	7.0	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	hg19		.	.	.	.	.	.	.	.	.	.	G	2.165	-0.391360	0.04932	.	.	ENSG00000179981	ENST00000322038	T	0.13901	2.55	5.27	3.37	0.38596	.	0.299193	0.32952	N	0.005442	T	0.14743	0.0356	L	0.41824	1.3	0.36632	D	0.876367	D	0.56521	0.976	P	0.49999	0.628	T	0.05146	-1.0903	10	0.48119	T	0.1	-32.1355	6.7208	0.23328	0.1539:0.1471:0.699:0.0	.	383	Q6ZSZ6	TSH1_HUMAN	H	338	ENSP00000323584:Q338H	ENSP00000323584:Q338H	Q	+	3	2	TSHZ1	71127499	1.000000	0.71417	0.990000	0.47175	0.273000	0.26683	1.583000	0.36579	1.986000	0.57962	0.459000	0.35465	CAG	.	.		0.627	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		T	72998511	G	T	72998511	3	4	154	1	0	0	0	0	1	0	0	0	16638	933	33	3	1016	3	TSHZ1	18	72998511	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10		72998511	5078737	86	23647										
C19orf29	58509	hgsc.bcm.edu	37	chr19	3623843	3623843	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gtgcgcgcttctcctcgggcGtctcgaaggccttcatcagc	12	15	4	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr19:3623843G>A	ENST00000429344.2	-	2	537	c.485C>T	c.(484-486)aCg>aTg	p.T162M	CACTIN_ENST00000221899.3_Missense_Mutation_p.T94M|CACTIN_ENST00000248420.5_Missense_Mutation_p.T162M	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	162					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CTCCTCGGGCGTCTCGAAGGC	0.687																																					p.T162M		Atlas-SNP	.											.	.	.	.	0			c.C485T						.						30	37	34					19																	3623843		2095	4196	6291	SO:0001583	missense	58509	exon2			TCGGGCGTCTCGA	BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"NY REN 24 antigen", "functional spliceosome-associated protein c", "cactin homolog (Drosophila)"		"chromosome 19 open reading frame 29"	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.485C>T	chr19.hg19:g.3623843G>A	ENSP00000415078:p.Thr162Met	42.0	0.0		40.0	7.0	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Missense_Mutation	SNP	ENST00000429344.2	hg19	CCDS45920.1	.	.	.	.	.	.	.	.	.	.	G	18.10	3.548248	0.65311	.	.	ENSG00000105298	ENST00000429344;ENST00000248420;ENST00000221899	.	.	.	5.09	5.09	0.68999	.	0.054374	0.64402	D	0.000002	D	0.82917	0.5141	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85628	0.1268	9	0.87932	D	0	.	17.4868	0.87691	0.0:0.0:1.0:0.0	.	162	Q8WUQ7	CS029_HUMAN	M	162;162;94	.	ENSP00000221899:T94M	T	-	2	0	C19orf29	3574843	1.000000	0.71417	0.938000	0.37757	0.087000	0.18053	9.695000	0.98691	2.379000	0.81126	0.561000	0.74099	ACG	.	.		0.687	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2			A	3623843	G	A	3623843	3	1	154	1	0	0	0	0	1	0	0	0	1920	1145	40	1	1827	1	C19orf29	19	3623843	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10		3623843	55505140	87	23648										
FSD1	79187	hgsc.bcm.edu	37	chr19	4310529	4310529	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gcgaaggtcagtgacaacatGagtcacctcatggtggactt	12	9	3	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr19:4310529G>A	ENST00000221856.6	+	6	573	c.426G>A	c.(424-426)atG>atA	p.M142I	FSD1_ENST00000598010.1_3'UTR|FSD1_ENST00000597590.1_Missense_Mutation_p.M142I	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	142	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.				mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGACAACATGAGTCACCTCA	0.607																																					p.M142I		Atlas-SNP	.											.	FSD1	51	.	0			c.G426A						.						84	73	76					19																	4310529		2203	4300	6503	SO:0001583	missense	79187	exon6			CAACATGAGTCAC	AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"Fibronectin type III domain containing"	13745	protein-coding gene	gene with protein product		609828	"fibronectin type 3 and SPRY domain containing 1"			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.426G>A	chr19.hg19:g.4310529G>A	ENSP00000221856:p.Met142Ile	85.0	0.0		98.0	7.0	NM_024333	B2RDT0|Q9BXN0|Q9HAG4	Missense_Mutation	SNP	ENST00000221856.6	hg19	CCDS12127.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.074849	0.76415	.	.	ENSG00000105255	ENST00000221856	T	0.46063	0.88	5.23	5.23	0.72850	COS domain (1);	0.000000	0.85682	D	0.000000	T	0.60353	0.2262	M	0.66939	2.045	0.80722	D	1	D;P	0.63046	0.992;0.462	P;B	0.61722	0.893;0.258	T	0.62590	-0.6822	10	0.56958	D	0.05	.	16.2944	0.82763	0.0:0.0:1.0:0.0	.	129;142	B4DIC5;Q9BTV5	.;FSD1_HUMAN	I	142	ENSP00000221856:M142I	ENSP00000221856:M142I	M	+	3	0	FSD1	4261529	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.254000	0.95512	2.453000	0.82957	0.511000	0.50034	ATG	.	.		0.607	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333		A	4310529	G	A	4310529	3	1	154	1	0	0	0	0	1	0	0	0	6078	1290	45	3	448	3	FSD1	19	4310529	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10	686686	4310529	54818454	88	23649										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22155400	22155400	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	gttgagaccttactaaaggtTttgccacattcttcacattt	6	9	2	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr19:22155400T>G	ENST00000397126.4	-	4	2584	c.2436A>C	c.(2434-2436)aaA>aaC	p.K812N	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	812					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TACTAAAGGTTTTGCCACATT	0.373																																					p.K812N		Atlas-SNP	.											.	ZNF208	817	.	0			c.A2436C						.						57	66	63					19																	22155400		2087	4239	6326	SO:0001583	missense	7757	exon4			AAAGGTTTTGCCA	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2436A>C	chr19.hg19:g.22155400T>G	ENSP00000380315:p.Lys812Asn	77.0	0.0		76.0	9.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	12.80	2.047636	0.36085	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.27890	1.64	2.57	0.183	0.15082	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.48409	0.1498	.	.	.	0.22562	N	0.998987	D	0.89917	1.0	D	0.81914	0.995	T	0.29518	-1.0009	8	0.87932	D	0	.	6.4872	0.22095	0.0:0.2483:0.0:0.7517	.	712	O43345	ZN208_HUMAN	N	812;712	ENSP00000380315:K812N	ENSP00000380315:K812N	K	-	3	2	ZNF208	21947240	0.002000	0.14202	0.079000	0.20413	0.169000	0.22640	-0.456000	0.06754	0.005000	0.14708	0.232000	0.17820	AAA	.	.		0.373	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		G	22155400	T	G	22155400	3	3	154	1	0	0	0	0	1	0	0	0	17781	1838	64	5	1410	5	ZNF208	19	22155400	Missense_Mutation	SNP	T	TCGA-DD-AACC-01A-11D-A40R-10	17844871	22155400	36973583	89	23650										
FFAR1	2864	hgsc.bcm.edu	37	chr19	35842806	35842806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	ccttgggctaccaagccttcCggaggccgtgctattcctgg	12	14	0	0			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr19:35842806C>T	ENST00000246553.2	+	1	362	c.352C>T	c.(352-354)Cgg>Tgg	p.R118W		NM_005303.2	NP_005294.1	O14842	FFAR1_HUMAN	free fatty acid receptor 1	118					energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|positive regulation of GTPase activity (GO:0043547)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)	p.R118W(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;4.58e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.67e-19)|all cancers(14;2.01e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)		Icosapent(DB00159)	CCAAGCCTTCCGGAGGCCGTG	0.677																																					p.R118W		Atlas-SNP	.											FFAR1,caecum,carcinoma,-2,1	FFAR1	33	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.C352T						.						50	51	51					19																	35842806		2203	4300	6503	SO:0001583	missense	2864	exon1			GCCTTCCGGAGGC	AF024687	CCDS12458.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000126266	ENSG00000126266		"GPCR / Class A : Fatty acid receptors"	4498	protein-coding gene	gene with protein product		603820	"G protein-coupled receptor 40"	GPR40		15684720	Standard	NM_005303		Approved	FFA1R	uc002nzc.2	O14842		ENST00000246553.2:c.352C>T	chr19.hg19:g.35842806C>T	ENSP00000246553:p.Arg118Trp	76.0	0.0		77.0	18.0	NM_005303	Q0VAS2|Q4VBL4	Missense_Mutation	SNP	ENST00000246553.2	hg19	CCDS12458.1	.	.	.	.	.	.	.	.	.	.	C	15.19	2.760021	0.49468	.	.	ENSG00000126266	ENST00000246553	T	0.39787	1.06	4.23	4.23	0.50019	GPCR, rhodopsin-like superfamily (1);	0.083641	0.45867	D	0.000323	T	0.60818	0.2298	M	0.74467	2.265	0.39849	D	0.973219	D	0.89917	1.0	D	0.87578	0.998	T	0.65796	-0.6081	10	0.72032	D	0.01	-23.9206	9.3832	0.38327	0.2129:0.7871:0.0:0.0	.	118	O14842	FFAR1_HUMAN	W	118	ENSP00000246553:R118W	ENSP00000246553:R118W	R	+	1	2	FFAR1	40534646	0.798000	0.28890	0.744000	0.31058	0.028000	0.11728	1.397000	0.34543	2.171000	0.68590	0.561000	0.74099	CGG	.	.		0.677	FFAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466112.2	NM_005303		T	35842806	C	T	35842806	3	4	154	1	0	0	0	0	1	0	0	0	5835	643	23	1	354	1	FFAR1	19	35842806	Missense_Mutation	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	13687406	35842806	23286177	90	23651										
ZNF350	59348	hgsc.bcm.edu	37	chr19	52472325	52472325	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	aggtccttctgagcagcgccCaggagttgccactcctccca	10	16	1	1			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chr19:52472325C>A	ENST00000243644.4	-	3	302	c.75G>T	c.(73-75)ctG>ctT	p.L25L	HCCAT3_ENST00000595010.1_RNA|HCCAT3_ENST00000600253.1_RNA|ZNF350_ENST00000600703.1_5'UTR	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	25	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		GAGCAGCGCCCAGGAGTTGCC	0.512																																					p.L25L		Atlas-SNP	.											.	ZNF350	48	.	0			c.G75T						.						171	151	158					19																	52472325		2203	4300	6503	SO:0001819	synonymous_variant	59348	exon3			AGCGCCCAGGAGT	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"Zinc fingers, C2H2-type", "-"	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.75G>T	chr19.hg19:g.52472325C>A		124.0	0.0		147.0	27.0	NM_021632	Q96G73|Q9HAQ4	Silent	SNP	ENST00000243644.4	hg19	CCDS12845.1																																																																																			.	.		0.512	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632		A	52472325	C	A	52472325	2	1	154	1	0	0	0	0	0	0	0	1	17878	581	21	3		3	ZNF350	19	52472325	Silent	SNP	C	TCGA-DD-AACC-01A-11D-A40R-10	16629519	52472325	6656658	91	23652										
ZNF185	7739	hgsc.bcm.edu	37	chrX	152128322	152128322	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.72839506172839	0	1.85185185185185	0.0013986013986014	0.0474253019707566	0	acaggcctggagccccaagaGgtggccaaggagacccagct	14	13	0	2			TCGA-DD-AACC-01A-11D-A40R-10	TCGA-DD-AACC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2bc7ba7-16b9-4c71-9492-c0e1b05f9fec	145154db-d25e-4815-923c-613aace5297a	g.chrX:152128322G>T	ENST00000370268.4	+	17	1523	c.1486G>T	c.(1486-1488)Ggt>Tgt	p.G496C	ZNF185_ENST00000535861.1_Missense_Mutation_p.G528C|ZNF185_ENST00000539731.1_Missense_Mutation_p.G499C|ZNF185_ENST00000318529.8_Missense_Mutation_p.G275C|ZNF185_ENST00000318504.7_Missense_Mutation_p.G437C|ZNF185_ENST00000454925.1_Missense_Mutation_p.G134C|ZNF185_ENST00000449285.2_Missense_Mutation_p.G497C|ZNF185_ENST00000370270.2_Missense_Mutation_p.G528C|ZNF185_ENST00000324823.6_Missense_Mutation_p.G264C			O15231	ZN185_HUMAN	zinc finger protein 185 (LIM domain)	496						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(3)	12	Acute lymphoblastic leukemia(192;6.56e-05)					AGCCCCAAGAGGTGGCCAAGG	0.582																																					p.G528C		Atlas-SNP	.											.	ZNF185	92	.	0			c.G1582T						.						46	51	49					X																	152128322		1983	4131	6114	SO:0001583	missense	7739	exon18			CCAAGAGGTGGCC	AK056517	CCDS48184.1, CCDS55528.1, CCDS55529.1, CCDS55530.1, CCDS55531.1, CCDS55532.1, CCDS69832.1	Xq28	2012-08-08			ENSG00000147394	ENSG00000147394		"Zinc fingers, C2H2-type"	12976	protein-coding gene	gene with protein product		300381				9268636	Standard	NM_001178106		Approved		uc011myg.2	O15231	OTTHUMG00000024187	ENST00000370268.4:c.1486G>T	chrX.hg19:g.152128322G>T	ENSP00000359291:p.Gly496Cys	131.0	0.0		142.0	42.0	NM_001178106	A4FTV3|A6NME5|B4DLE9|B7Z771|B8K2L9|B8K2M0|B8K2M1|B8K2M2|E9PFR6|F5GXF7|F5GZL4|F8W8V7|H0Y4M8|O00345|Q8N1R8|Q9NSD2	Missense_Mutation	SNP	ENST00000370268.4	hg19	CCDS48184.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	9.541|9.541|9.541	1.113407|1.113407|1.113407	0.20795|0.20795|0.20795	.|.|.	.|.|.	ENSG00000147394|ENSG00000147394|ENSG00000147394	ENST00000454925|ENST00000535861;ENST00000539731;ENST00000449285;ENST00000318504;ENST00000535156;ENST00000324823;ENST00000370268;ENST00000318529;ENST00000370270;ENST00000436731|ENST00000426821	.|T;T;T;T;T|.	.|0.47869|.	.|0.83;0.83;0.83;0.83;0.83|.	3.99|3.99|3.99	-0.954|-0.954|-0.954	0.10359|0.10359|0.10359	.|.|.	.|1.172330|.	.|0.06385|.	.|N|.	.|0.715848|.	T|T|T	0.26919|0.26919|0.26919	0.0659|0.0659|0.0659	L|L|L	0.34521|0.34521|0.34521	1.04|1.04|1.04	0.09310|0.09310|0.09310	N|N|N	1|1|1	.|P;B;B;P;P;P;B;D;P|.	.|0.76494|.	.|0.649;0.4;0.009;0.587;0.644;0.649;0.338;0.999;0.506|.	.|B;B;B;B;B;B;B;D;B|.	.|0.65874|.	.|0.149;0.11;0.017;0.146;0.207;0.21;0.168;0.939;0.126|.	T|T|T	0.31503|0.31503|0.31503	-0.9941|-0.9941|-0.9941	5|10|6	.|0.66056|0.72032	.|D|D	.|0.02|0.01	0.1733|0.1733|0.1733	3.3893|3.3893|3.3893	0.07283|0.07283|0.07283	0.4573:0.0:0.3543:0.1884|0.4573:0.0:0.3543:0.1884|0.4573:0.0:0.3543:0.1884	.|.|.	.|497;437;467;499;528;496;134;275;259|.	.|O15231-3;B8K2L9;B8K2M0;F5GZL4;F5GXF7;O15231;Q8N1R8;F8W8V7;O15231-2|.	.|.;.;.;.;.;ZN185_HUMAN;.;.;.|.	D|C|M	136|528;499;497;437;331;264;496;275;259;201|281	.|ENSP00000440847:G528C;ENSP00000444367:G499C;ENSP00000395228:G497C;ENSP00000312782:G437C;ENSP00000359291:G496C|.	.|ENSP00000312782:G437C|ENSP00000409121:R281M	E|G|R	+|+|+	3|1|2	2|0|0	ZNF185|ZNF185|ZNF185	151878978|151878978|151878978	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.062000|0.062000|0.062000	0.15995|0.15995|0.15995	0.009000|0.009000|0.009000	0.13219|0.13219|0.13219	-0.361000|-0.361000|-0.361000	0.08125|0.08125|0.08125	-0.297000|-0.297000|-0.297000	0.09499|0.09499|0.09499	GAG|GGT|AGG	.	.		0.582	ZNF185-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377480.1	NM_007150		T	152128322	G	T	152128322	3	4	154	1	0	0	0	0	1	0	0	0	17767	1000	35	3	1796	3	ZNF185	23	152128322	Missense_Mutation	SNP	G	TCGA-DD-AACC-01A-11D-A40R-10		152128322	3142238	92	23653										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7798171	7798171	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	cactgagtctggaagagccaAatatcaggaagcaaagccct	10	10	2	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:7798171A>C	ENST00000303635.7	+	16	4018	c.3811A>C	c.(3811-3813)Aat>Cat	p.N1271H	CAMTA1_ENST00000439411.2_Missense_Mutation_p.N1271H	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		GGAAGAGCCAAATATCAGGAA	0.527			T	WWTR1	epitheliod hemangioendothelioma																																p.N1271H		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.A3811C						.						67	64	65					1																	7798171		2203	4300	6503	SO:0001583	missense	23261	exon16			GAGCCAAATATCA	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3811A>C	chr1.hg19:g.7798171A>C	ENSP00000306522:p.Asn1271His	65.0	0.0		84.0	30.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	hg19	CCDS30576.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.00|12.00	1.806086|1.806086	0.31961|0.31961	.|.	.|.	ENSG00000171735|ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646|ENST00000495233	T;T|.	0.20463|.	2.07;2.08|.	4.87|4.87	4.87|4.87	0.63330|0.63330	.|.	0.531870|.	0.22050|.	N|.	0.065339|.	T|T	0.20088|0.20088	0.0483|0.0483	N|N	0.08118|0.08118	0|0	0.24320|0.24320	N|N	0.995041|0.995041	P;B;B;P|.	0.43352|.	0.804;0.291;0.412;0.511|.	B;B;B;B|.	0.40534|.	0.332;0.087;0.125;0.135|.	T|T	0.16958|0.16958	-1.0385|-1.0385	10|5	0.30078|.	T|.	0.28|.	-4.1565|-4.1565	9.028|9.028	0.36241|0.36241	0.7155:0.0:0.0:0.2845|0.7155:0.0:0.0:0.2845	.|.	1271;358;227;1271|.	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1|.	.;.;.;CMTA1_HUMAN|.	H|H	1271;1271;358;227|227	ENSP00000306522:N1271H;ENSP00000402561:N1271H|.	ENSP00000306522:N1271H|.	N|Q	+|+	1|3	0|2	CAMTA1|CAMTA1	7720758|7720758	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.365000|2.365000	0.44196|0.44196	1.943000|1.943000	0.56356|0.56356	0.533000|0.533000	0.62120|0.62120	AAT|CAA	.	.		0.527	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		C	7798171	A	C	7798171	3	2	155	1	0	0	0	0	1	0	0	0	2615	14	1	5	3873	5	CAMTA1	1	7798171	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10		7798171	241452450	1	23654										
SRRM1	10250	hgsc.bcm.edu	37	chr1	24998064	24998064	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	attagcacaggaagagccagTggcagcgccagagccgaaga	14	10	0	3			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:24998064T>C	ENST00000323848.9	+	16	2903	c.2588T>C	c.(2587-2589)gTg>gCg	p.V863A	SRRM1_ENST00000447431.2_Missense_Mutation_p.V875A|SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Missense_Mutation_p.V872A	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	863	Ala-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		GAAGAGCCAGTGGCAGCGCCA	0.488																																					p.V863A	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.T2588C						.						50	51	51					1																	24998064		2203	4300	6503	SO:0001583	missense	10250	exon16			AGCCAGTGGCAGC	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.2588T>C	chr1.hg19:g.24998064T>C	ENSP00000326261:p.Val863Ala	203.0	0.0		218.0	67.0	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	hg19	CCDS255.1	.	.	.	.	.	.	.	.	.	.	T	8.417	0.845535	0.16963	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.41065	1.01;1.01;1.01	5.95	3.6	0.41247	.	0.320352	0.26804	N	0.022414	T	0.18341	0.0440	N	0.03608	-0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.03969	-1.0988	10	0.32370	T	0.25	-0.0034	7.2221	0.25994	0.7034:0.1507:0.0:0.1459	.	875;863	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	A	863;875;872	ENSP00000326261:V863A;ENSP00000391430:V875A;ENSP00000363510:V872A	ENSP00000326261:V863A	V	+	2	0	SRRM1	24870651	0.999000	0.42202	0.233000	0.24025	0.015000	0.08874	1.311000	0.33562	0.479000	0.27511	-0.347000	0.07816	GTG	.	.		0.488	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		C	24998064	T	C	24998064	3	2	155	1	0	0	0	0	1	0	0	0	15183	1696	59	2	2650	2	SRRM1	1	24998064	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	17199893	24998064	224252557	2	23655										
CTPS	1503	hgsc.bcm.edu	37	chr1	41449049	41449049	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gtgggcacaatactcaagtcAtgtggtttacatgtaacttc	9	8	2	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:41449049A>G	ENST00000372621.4	+	2	595	c.87A>G	c.(85-87)tcA>tcG	p.S29S	CTPS1_ENST00000475060.1_3'UTR|CTPS1_ENST00000543104.1_Silent_p.S36S|CTPS1_ENST00000372616.1_Silent_p.S29S|CTPS1_ENST00000541520.1_Intron	NM_001905.2	NP_001896.2			CTP synthase 1											endometrium(3)|lung(10)	13						TACTCAAGTCATGTGGTTTAC	0.393																																					p.S29S		Atlas-SNP	.											.	CTPS1	34	.	0			c.A87G						.						192	165	174					1																	41449049		2203	4300	6503	SO:0001819	synonymous_variant	1503	exon2			CAAGTCATGTGGT	BC009408	CCDS459.1	1p34.1	2012-05-02	2012-05-02	2012-05-02	ENSG00000171793	ENSG00000171793	6.3.4.2		2519	protein-coding gene	gene with protein product		123860	"CTP synthase"	CTPS		1783378	Standard	XM_005270536		Approved		uc001cgk.4	P17812	OTTHUMG00000005712	ENST00000372621.4:c.87A>G	chr1.hg19:g.41449049A>G		231.0	0.0		257.0	84.0	NM_001905		Silent	SNP	ENST00000372621.4	hg19	CCDS459.1																																																																																			.	.		0.393	CTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015629.1	NM_001905		G	41449049	A	G	41449049	2	3	155	1	0	0	0	0	0	0	0	1	4024	204	8	2		2	CTPS	1	41449049	Silent	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	16450985	41449049	207801572	3	23656										
CCDC17	149483	hgsc.bcm.edu	37	chr1	46087108	46087108	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	cttagttgcacccaaatccaGgaagcctcaaggccccgcag	9	15	1	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:46087108G>A	ENST00000528266.1	-	10	1380	c.1233C>T	c.(1231-1233)tcC>tcT	p.S411S	CCDC17_ENST00000343901.2_Silent_p.S379S|CCDC17_ENST00000464739.1_Intron|CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000421127.2_Silent_p.S402S			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	411										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					CCCAAATCCAGGAAGCCTCAA	0.572																																					p.S411S		Atlas-SNP	.											.	CCDC17	54	.	0			c.C1233T						.						41	39	40					1																	46087108		2203	4298	6501	SO:0001819	synonymous_variant	149483	exon10			AATCCAGGAAGCC		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.1233C>T	chr1.hg19:g.46087108G>A		250.0	0.0		234.0	84.0	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Silent	SNP	ENST00000528266.1	hg19	CCDS44131.2																																																																																			.	.		0.572	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500		A	46087108	G	A	46087108	2	1	155	1	0	0	0	0	0	0	0	1	2795	987	35	3		3	CCDC17	1	46087108	Silent	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	4638059	46087108	203163513	4	23657										
JAK1	3716	hgsc.bcm.edu	37	chr1	65305399	65305399	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tacctccactctcaggcttcAgagatttaacagccacctgc	6	15	2	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:65305399A>G	ENST00000342505.4	-	20	2977	c.2729T>C	c.(2728-2730)cTg>cCg	p.L910P	JAK1_ENST00000465376.1_5'Flank	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	910	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CTCAGGCTTCAGAGATTTAAC	0.478			Mis		ALL																																p.L910P		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	JAK1,NS,carcinoma,0,2	JAK1	209	.	0			c.T2729C						.						150	138	142					1																	65305399		1917	4139	6056	SO:0001583	missense	3716	exon20			GGCTTCAGAGATT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2729T>C	chr1.hg19:g.65305399A>G	ENSP00000343204:p.Leu910Pro	99.0	0.0		78.0	24.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.517041	0.85495	.	.	ENSG00000162434	ENST00000342505	D	0.91351	-2.83	5.13	5.13	0.70059	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.94525	0.8237	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95349	0.8445	9	0.87932	D	0	-3.8222	15.1086	0.72338	1.0:0.0:0.0:0.0	.	910	P23458	JAK1_HUMAN	P	910	ENSP00000343204:L910P	ENSP00000343204:L910P	L	-	2	0	JAK1	65077987	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.703000	0.91344	2.146000	0.66826	0.533000	0.62120	CTG	.	.		0.478	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		G	65305399	A	G	65305399	3	3	155	1	0	0	0	0	1	0	0	0	7946	188	7	2	759	2	JAK1	1	65305399	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	19218291	65305399	183945222	5	23658										
TMEM56	148534	hgsc.bcm.edu	37	chr1	95609466	95609466	+	Frame_Shift_Del	DEL	C	C	-													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ggttgaagaaatatggagatCaacacaaaactgctcatcag							TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:95609466delC	ENST00000370203.4	+	2	300	c.9delC	c.(7-9)atcfs	p.I3fs	TMEM56_ENST00000463375.1_3'UTR|RP11-57H12.6_ENST00000604534.1_Frame_Shift_Del_p.I3fs	NM_001199679.1|NM_152487.2	NP_001186608.1|NP_689700.1	Q96MV1	TMM56_HUMAN	transmembrane protein 56	3						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(2)|skin(1)|urinary_tract(1)	12		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.133)		ATATGGAGATCAACACAAAAC	0.313																																					p.I3fs		Atlas-INDEL	.											.	TMEM56	24	.	0			c.8delT						.						113	114	113					1																	95609466		2203	4300	6503	SO:0001589	frameshift_variant	148534	exon2			.		CCDS753.1	1p21.3	2008-02-05			ENSG00000152078	ENSG00000152078			26477	protein-coding gene	gene with protein product							Standard	NM_152487		Approved	FLJ31842	uc001drb.3	Q96MV1	OTTHUMG00000010847	ENST00000370203.4:c.9delC	chr1.hg19:g.95609466delC	ENSP00000359222:p.Ile3fs	111.0	0.0		117.0	25.0	NM_001199679	B2RPI2|D3DT48	Frame_Shift_Del	DEL	ENST00000370203.4	hg19	CCDS753.1																																																																																			.	.		0.313	TMEM56-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029935.1	NM_152487		-	95609466	C	-	95609466	7	5	155	1	0	1	0	1	0	0	0	0	16198	816	29	0	11	0	TMEM56	1	95609466	Frame_Shift_Del	DEL	C	TCGA-DD-AACD-01A-11D-A40R-10	30304067	95609466	153641155	6	23659										
MAN1A2	10905	hgsc.bcm.edu	37	chr1	117948198	117948198	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aacatgcttgggataactatAggacatatgggtggggacat	13	5	0	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:117948198A>T	ENST00000356554.3	+	3	1321	c.586A>T	c.(586-588)Agg>Tgg	p.R196W	MAN1A2_ENST00000482811.1_Intron	NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	196					cellular protein metabolic process (GO:0044267)|lung alveolus development (GO:0048286)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	27	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		GGATAACTATAGGACATATGG	0.308																																					p.R196W	Ovarian(33;199 881 8228 13687 31538)	Atlas-SNP	.											.	MAN1A2	50	.	0			c.A586T						.						109	116	113					1																	117948198		2203	4299	6502	SO:0001583	missense	10905	exon3			AACTATAGGACAT	AF027156	CCDS895.1	1p13	2008-02-05			ENSG00000198162	ENSG00000198162			6822	protein-coding gene	gene with protein product		604345				9592125	Standard	NM_006699		Approved	MAN1B	uc001ehd.1	O60476	OTTHUMG00000012149	ENST00000356554.3:c.586A>T	chr1.hg19:g.117948198A>T	ENSP00000348959:p.Arg196Trp	586.0	1.0		628.0	216.0	NM_006699	Q9H510	Missense_Mutation	SNP	ENST00000356554.3	hg19	CCDS895.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.177175	0.78564	.	.	ENSG00000198162	ENST00000356554	T	0.72835	-0.69	5.84	5.84	0.93424	.	0.089867	0.85682	D	0.000000	D	0.82595	0.5071	M	0.89214	3.015	0.50632	D	0.999883	P	0.52316	0.952	D	0.63957	0.92	D	0.86287	0.1671	10	0.87932	D	0	-15.6024	14.1576	0.65428	1.0:0.0:0.0:0.0	.	196	O60476	MA1A2_HUMAN	W	196	ENSP00000348959:R196W	ENSP00000348959:R196W	R	+	1	2	MAN1A2	117749721	0.999000	0.42202	0.954000	0.39281	0.979000	0.70002	4.038000	0.57318	2.220000	0.72140	0.533000	0.62120	AGG	.	.		0.308	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033593.1	NM_006699		T	117948198	A	T	117948198	3	4	155	1	0	0	0	0	1	0	0	0	9220	411	15	4	596	4	MAN1A2	1	117948198	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	22338732	117948198	131302423	7	23660										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144916634	144916634	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gaatgatactctcttgttccTtctgccaacggctaaatttg	7	10	2	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:144916634T>C	ENST00000369354.3	-	13	1910	c.1721A>G	c.(1720-1722)aAg>aGg	p.K574R	PDE4DIP_ENST00000313431.9_Missense_Mutation_p.K737R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.K640R|PDE4DIP_ENST00000479408.2_Missense_Mutation_p.K361R|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.K737R|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.K711R|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.K711R|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.K574R|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.K574R|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.K574R			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	574					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTCTTGTTCCTTCTGCCAACG	0.443			T	PDGFRB	MPD																																p.K737R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A2210G						.						613	641	631					1																	144916634		2203	4296	6499	SO:0001583	missense	9659	exon9			TGTTCCTTCTGCC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.1721A>G	chr1.hg19:g.144916634T>C	ENSP00000358360:p.Lys574Arg	125.0	0.0		133.0	19.0	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.620675	0.46736	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	T;T;T;T;T;T;T;T;T;T	0.64618	4.76;4.88;4.88;4.87;4.87;3.89;3.9;2.85;2.84;-0.11	5.83	5.83	0.93111	.	.	.	.	.	T	0.56277	0.1974	L	0.32530	0.975	0.80722	D	1	P;D;P;P;D;D	0.69078	0.921;0.968;0.865;0.935;0.993;0.997	P;P;B;P;P;D	0.63703	0.601;0.818;0.421;0.7;0.903;0.917	T	0.53933	-0.8368	9	0.18710	T	0.47	.	14.4902	0.67645	0.0:0.0:0.0:1.0	.	737;361;574;737;640;574	E9PL24;E9PQG4;Q5VU43-7;Q5VU43-2;Q5VU43-3;Q5VU43	.;.;.;.;.;MYOME_HUMAN	R	640;574;574;737;711;711;574;574;737;737;361	ENSP00000327209:K640R;ENSP00000358360:K574R;ENSP00000358363:K574R;ENSP00000435654:K711R;ENSP00000358366:K711R;ENSP00000358357:K574R;ENSP00000358355:K574R;ENSP00000316434:K737R;ENSP00000433392:K737R;ENSP00000436791:K361R	ENSP00000327209:K640R	K	-	2	0	PDE4DIP	143627991	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.192000	0.50989	2.364000	0.80123	0.524000	0.50904	AAG	.	.		0.443	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144916634	T	C	144916634	3	2	155	1	0	0	0	0	1	0	0	0	11652	1609	56	2	5457	2	PDE4DIP	1	144916634	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	26968436	144916634	104333987	8	23661										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157509048	157509048	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tcatgatgaaactggtacagGatggggagtgaacctctctg	13	7	2	3			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:157509048G>C	ENST00000361835.3	-	7	1387	c.1230C>G	c.(1228-1230)atC>atG	p.I410M	FCRL5_ENST00000368190.3_Missense_Mutation_p.I410M|FCRL5_ENST00000368191.3_Missense_Mutation_p.I325M|FCRL5_ENST00000356953.4_Missense_Mutation_p.I410M|FCRL5_ENST00000368189.3_Missense_Mutation_p.I410M	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	410	Ig-like C2-type 4.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				ACTGGTACAGGATGGGGAGTG	0.552																																					p.I410M		Atlas-SNP	.											.	FCRL5	177	.	0			c.C1230G						.						85	77	80					1																	157509048		2203	4300	6503	SO:0001583	missense	83416	exon7			GTACAGGATGGGG	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.1230C>G	chr1.hg19:g.157509048G>C	ENSP00000354691:p.Ile410Met	75.0	0.0		82.0	22.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	hg19	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.287377	0.40494	.	.	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191;ENST00000368189	T;T;T;T;T	0.12774	2.65;2.65;2.65;2.65;2.65	3.04	2.09	0.27110	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.159289	0.28933	N	0.013667	T	0.30947	0.0781	H	0.96269	3.795	0.18873	N	0.999989	D;D;D;D;D;D	0.89917	1.0;1.0;0.989;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.996;0.919;0.998;1.0;0.997	T	0.12760	-1.0535	10	0.72032	D	0.01	.	6.4583	0.21942	0.146:0.0:0.854:0.0	.	441;325;410;410;410;410	B4DW39;F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9-4;Q96RD9	.;.;.;.;.;FCRL5_HUMAN	M	410;410;410;325;410	ENSP00000354691:I410M;ENSP00000349434:I410M;ENSP00000357173:I410M;ENSP00000357174:I325M;ENSP00000357172:I410M	ENSP00000349434:I410M	I	-	3	3	FCRL5	155775672	0.825000	0.29262	0.004000	0.12327	0.274000	0.26718	1.368000	0.34216	0.583000	0.29574	0.313000	0.20887	ATC	.	.		0.552	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		C	157509048	G	C	157509048	3	2	155	1	0	0	0	0	1	0	0	0	5806	1164	41	4	1747	4	FCRL5	1	157509048	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	12592414	157509048	91741573	9	23662										
C1orf156	92342	hgsc.bcm.edu	37	chr1	169761806	169761807	+	Frame_Shift_Ins	INS	-	-	T													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tctggtcttaaaaacatctcINStttcttctacaaacttctga							TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:169761806_169761807insT	ENST00000310392.4	-	2	1383_1384	c.1030_1031insA	c.(1030-1032)agafs	p.R344fs	METTL18_ENST00000303469.2_Frame_Shift_Ins_p.R344fs|C1orf112_ENST00000413811.2_5'Flank|C1orf112_ENST00000359326.4_5'Flank|C1orf112_ENST00000456684.1_5'Flank|C1orf112_ENST00000498289.1_Intron|C1orf112_ENST00000286031.6_5'Flank	NM_033418.2	NP_219486.1	O95568	MET18_HUMAN	methyltransferase like 18	344						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			kidney(1)|large_intestine(3)|lung(4)	8						AAAAACATCTCTTTCTTCTACA	0.327																																					p.R344fs		Atlas-INDEL	.											.	METTL18	23	.	0			c.1031_1032insA						.																																			SO:0001589	frameshift_variant	92342	exon2			.	AL035369	CCDS1284.1	1q24.2	2013-10-11	2011-03-02	2011-03-02	ENSG00000171806	ENSG00000171806			28793	protein-coding gene	gene with protein product	"histidine protein methyltransferase 1"	615255	"chromosome 1 open reading frame 156"	C1orf156		20864530	Standard	NM_033418		Approved	MGC9084, AsTP2, HPM1	uc001ggn.4	O95568	OTTHUMG00000035813	ENST00000310392.4:c.1031dupA	chr1.hg19:g.169761809_169761809dupT	ENSP00000307975:p.Arg344fs	298.0	0.0		339.0	107.0	NM_033418	B2R9T5	Frame_Shift_Ins	INS	ENST00000310392.4	hg19	CCDS1284.1																																																																																			.	.		0.327	METTL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087109.1	NM_033418		T	169761807	-	T	169761806	7	5	155	1	0	1	1	0	0	0	0	0	2008	913	32	0	91	0	C1orf156	1	169761806	Frame_Shift_Ins	INS	-	TCGA-DD-AACD-01A-11D-A40R-10	12252758	169761806	79488815	10	23663										
SDCCAG8	10806	hgsc.bcm.edu	37	chr1	243434288	243434288	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tttgctctatagttaatcagCtcaaagatttgttgcgccaa	7	8	3	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:243434288C>G	ENST00000366541.3	+	3	347	c.229C>G	c.(229-231)Ctc>Gtc	p.L77V	SDCCAG8_ENST00000391846.1_Missense_Mutation_p.L77V|SDCCAG8_ENST00000343783.6_Intron|SDCCAG8_ENST00000355875.4_Missense_Mutation_p.L77V	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	77					establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		AGTTAATCAGCTCAAAGATTT	0.378																																					p.L77V		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.C229G						.						114	106	109					1																	243434288		2203	4300	6503	SO:0001583	missense	10806	exon3			AATCAGCTCAAAG	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.229C>G	chr1.hg19:g.243434288C>G	ENSP00000355499:p.Leu77Val	225.0	0.0		226.0	75.0	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	hg19	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.074740	0.76415	.	.	ENSG00000054282	ENST00000355875;ENST00000391846;ENST00000366541	T;T	0.75477	-0.94;-0.55	5.52	4.59	0.56863	.	0.000000	0.85682	D	0.000000	D	0.83834	0.5340	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.84012	0.0349	10	0.54805	T	0.06	-3.856	12.4439	0.55639	0.0:0.916:0.0:0.084	.	77	Q86SQ7	SDCG8_HUMAN	V	77	ENSP00000348137:L77V;ENSP00000355499:L77V	ENSP00000348137:L77V	L	+	1	0	SDCCAG8	241500911	0.991000	0.36638	0.988000	0.46212	0.948000	0.59901	2.963000	0.49184	2.752000	0.94435	0.655000	0.94253	CTC	.	.		0.378	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		G	243434288	C	G	243434288	3	3	155	1	0	0	0	0	1	0	0	0	13974	797	28	4	239	4	SDCCAG8	1	243434288	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	73672482	243434288	5816333	11	23664										
OR2T6	254879	hgsc.bcm.edu	37	chr1	248551453	248551453	+	Frame_Shift_Del	DEL	C	C	-													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	atcactttttctgtgaggcaCccaccatgctgaggctggcc					rs548026945		TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr1:248551453delC	ENST00000355728.2	+	1	544	c.544delC	c.(544-546)cccfs	p.P182fs		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTGTGAGGCACCCACCATGCT	0.527																																					p.A181fs		Atlas-INDEL	.											.	OR2T6	101	.	0			c.543delA						.						138	115	123					1																	248551453		2203	4300	6503	SO:0001589	frameshift_variant	254879	exon1			.	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"GPCR / Class A : Olfactory receptors"	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.544delC	chr1.hg19:g.248551453delC	ENSP00000347965:p.Pro182fs	121.0	0.0		138.0	30.0	NM_001005471	A6NE36	Frame_Shift_Del	DEL	ENST00000355728.2	hg19	CCDS31114.1																																																																																			.	.		0.527	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471		-	248551453	C	-	248551453	7	5	155	1	0	1	0	1	0	0	0	0	11038	507	18	0	546	0	OR2T6	1	248551453	Frame_Shift_Del	DEL	C	TCGA-DD-AACD-01A-11D-A40R-10	5117165	248551453	699168	12	23665										
TMEM214	54867	hgsc.bcm.edu	37	chr2	27260542	27260542	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tttcctgtccagagccacccCtagctgtccccctgagatga	8	16	0	3			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr2:27260542C>A	ENST00000238788.9	+	9	1186	c.1124C>A	c.(1123-1125)cCt>cAt	p.P375H	TMEM214_ENST00000404032.3_Missense_Mutation_p.P330H	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	375					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						AGAGCCACCCCTAGCTGTCCC	0.552																																					p.P375H		Atlas-SNP	.											.	TMEM214	41	.	0			c.C1124A						.						99	100	100					2																	27260542		1907	4121	6028	SO:0001583	missense	54867	exon9			CCACCCCTAGCTG		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.1124C>A	chr2.hg19:g.27260542C>A	ENSP00000238788:p.Pro375His	98.0	0.0		122.0	41.0	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	hg19	CCDS42664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.980336|3.980336	0.74474|0.74474	.|.	.|.	ENSG00000119777|ENSG00000119777	ENST00000425720|ENST00000238788;ENST00000404032;ENST00000537397	.|T;T	.|0.51574	.|0.7;0.7	5.69|5.69	4.81|4.81	0.61882|0.61882	.|.	.|0.049473	.|0.85682	.|N	.|0.000000	T|T	0.66896|0.66896	0.2836|0.2836	M|M	0.72894|0.72894	2.215|2.215	0.54753|0.54753	D|D	0.999981|0.999981	.|D;D	.|0.89917	.|1.0;0.998	.|D;D	.|0.80764	.|0.994;0.986	T|T	0.70335|0.70335	-0.4900|-0.4900	5|10	.|0.62326	.|D	.|0.03	-8.2946|-8.2946	14.0468|14.0468	0.64710|0.64710	0.1512:0.8488:0.0:0.0|0.1512:0.8488:0.0:0.0	.|.	.|330;375	.|Q6NUQ4-2;Q6NUQ4	.|.;TM214_HUMAN	I|H	134|375;330;115	.|ENSP00000238788:P375H;ENSP00000384417:P330H	.|ENSP00000238788:P375H	L|P	+|+	1|2	2|0	TMEM214|TMEM214	27114046|27114046	1.000000|1.000000	0.71417|0.71417	0.892000|0.892000	0.35008|0.35008	0.962000|0.962000	0.63368|0.63368	4.496000|4.496000	0.60360|0.60360	1.400000|1.400000	0.46741|0.46741	-0.314000|-0.314000	0.08810|0.08810	CTA|CCT	.	.		0.552	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727		A	27260542	C	A	27260542	3	1	155	1	0	0	0	0	1	0	0	0	16152	681	24	3	1158	3	TMEM214	2	27260542	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10		27260542	215938831	13	23666										
XDH	7498	hgsc.bcm.edu	37	chr2	31625953	31625953	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gatcatacttggagagcatcActgtgcaagccccgcagccc	10	14	2	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr2:31625953A>G	ENST00000379416.3	-	3	206	c.158T>C	c.(157-159)gTg>gCg	p.V53A		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	53	2Fe-2S ferredoxin-type. {ECO:0000255|PROSITE-ProRule:PRU00465}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GGAGAGCATCACTGTGCAAGC	0.577																																					p.V53A	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.T158C						.						108	101	103					2																	31625953		2203	4300	6503	SO:0001583	missense	7498	exon3			AGCATCACTGTGC	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.158T>C	chr2.hg19:g.31625953A>G	ENSP00000368727:p.Val53Ala	59.0	0.0		66.0	20.0	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	hg19	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.561967	0.86335	.	.	ENSG00000158125	ENST00000379416	T	0.58506	0.33	6.04	6.04	0.98038	Xanthine dehydrogenase, small subunit (1);Beta-grasp fold, ferredoxin-type (1);Ferredoxin (3);	0.000000	0.85682	D	0.000000	D	0.83087	0.5178	H	0.96333	3.805	0.80722	D	1	D	0.69078	0.997	D	0.68483	0.958	D	0.88314	0.2958	10	0.72032	D	0.01	.	15.5589	0.76223	1.0:0.0:0.0:0.0	.	53	P47989	XDH_HUMAN	A	53	ENSP00000368727:V53A	ENSP00000368727:V53A	V	-	2	0	XDH	31479457	1.000000	0.71417	0.997000	0.53966	0.906000	0.53458	6.761000	0.74945	2.317000	0.78254	0.459000	0.35465	GTG	.	.		0.577	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		G	31625953	A	G	31625953	3	3	155	1	0	0	0	0	1	0	0	0	17441	159	6	2	3979	2	XDH	2	31625953	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	4365411	31625953	211573420	14	23667										
SIX2	10736	hgsc.bcm.edu	37	chr2	45233483	45233483	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ggcagcccagggggcggcggGctgaggagcagtgcggggct	23	10	0	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr2:45233483G>A	ENST00000303077.6	-	2	1021	c.702C>T	c.(700-702)agC>agT	p.S234S		NM_016932.4	NP_058628.3	Q9NPC8	SIX2_HUMAN	SIX homeobox 2	234					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|kidney development (GO:0001822)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesenchymal stem cell proliferation (GO:0097168)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|middle ear morphogenesis (GO:0042474)|nephron development (GO:0072006)|nephron morphogenesis (GO:0072028)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus (GO:0006606)|regulation of branching involved in ureteric bud morphogenesis (GO:0090189)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|large_intestine(3)|lung(8)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	22		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GGGGCGGCGGGCTGAGGAGCA	0.701																																					p.S234S		Atlas-SNP	.											.	SIX2	39	.	0			c.C702T						.						63	68	66					2																	45233483		2203	4300	6503	SO:0001819	synonymous_variant	10736	exon2			CGGCGGGCTGAGG	AF136939	CCDS1822.1	2p21	2011-06-20	2007-07-13		ENSG00000170577	ENSG00000170577		"Homeoboxes / SINE class"	10888	protein-coding gene	gene with protein product		604994	"sine oculis homeobox (Drosophila) homolog 2", "sine oculis homeobox homolog 2 (Drosophila)"				Standard	NM_016932		Approved		uc002ruo.3	Q9NPC8	OTTHUMG00000152421	ENST00000303077.6:c.702C>T	chr2.hg19:g.45233483G>A		54.0	0.0		75.0	22.0	NM_016932	Q9BXH7	Silent	SNP	ENST00000303077.6	hg19	CCDS1822.1																																																																																			.	.		0.701	SIX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326188.2			A	45233483	G	A	45233483	2	1	155	1	0	0	0	0	0	0	0	1	14362	1194	42	3		3	SIX2	2	45233483	Silent	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	13607530	45233483	197965890	15	23668										
MPHOSPH10	10199	hgsc.bcm.edu	37	chr2	71361819	71361824	+	In_Frame_Del	DEL	AGTGAC	AGTGAC	-													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	cataaagaaagcttgaaaagAgtgacctttgctttaccaga					rs147873518		TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	AGTGAC	AGTGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr2:71361819_71361824delAGTGAC	ENST00000244230.2	+	4	1342_1347	c.990_995delAGTGAC	c.(988-996)agagtgacc>agc	p.330_332RVT>S	MPHOSPH10_ENST00000498451.2_In_Frame_Del_p.330_332RVT>S	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	330					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						GCTTGAAAAGAGTGACCTTTGCTTTA	0.311																																					p.330_332del		Atlas-INDEL	.											.	MPHOSPH10	81	.	0			c.989_994del						.																																			SO:0001651	inframe_deletion	10199	exon4			.	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 106"	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.990_995delAGTGAC	chr2.hg19:g.71361819_71361824delAGTGAC	ENSP00000244230:p.Arg330_Thr332delinsSer	301.0	0.0		273.0	60.0	NM_005791	A0AVJ8	In_Frame_Del	DEL	ENST00000244230.2	hg19	CCDS1916.1																																																																																			.	.		0.311	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791		-	71361824	AGTGAC	-	71361819	7	5	155	1	0	1	0	1	0	0	0	0	9734	301	11	0	1004	0	MPHOSPH10	2	71361819	In_Frame_Del	DEL	AGTGAC	TCGA-DD-AACD-01A-11D-A40R-10	26128336	71361819	171837554	16	23669										
WDR33	55339	hgsc.bcm.edu	37	chr2	128466455	128466455	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gggagtatcacgaaaatgttCatgacctggccctgaaacaa	10	9	2	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr2:128466455C>A	ENST00000322313.4	-	21	3735	c.3577G>T	c.(3577-3579)Gaa>Taa	p.E1193*		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	1193					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CGAAAATGTTCATGACCTGGC	0.517																																					p.E1193X		Atlas-SNP	.											.	WDR33	136	.	0			c.G3577T						.						49	47	48					2																	128466455		2203	4300	6503	SO:0001587	stop_gained	55339	exon21			AATGTTCATGACC		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.3577G>T	chr2.hg19:g.128466455C>A	ENSP00000325377:p.Glu1193*	50.0	0.0		64.0	27.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Nonsense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	C	43	10.241364	0.99367	.	.	ENSG00000136709	ENST00000322313	.	.	.	5.56	5.56	0.83823	.	0.063932	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-15.8068	16.2544	0.82505	0.0:1.0:0.0:0.0	.	.	.	.	X	1193	.	ENSP00000325377:E1193X	E	-	1	0	WDR33	128182925	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.298000	0.51818	2.640000	0.89533	0.655000	0.94253	GAA	.	.		0.517	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		A	128466455	C	A	128466455	4	1	155	1	0	0	0	0	0	1	0	0	17302	835	29	3	441	3	WDR33	2	128466455	Nonsense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	57104636	128466455	114732918	17	23670										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227924168	227924168	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ctctgggtccttttatccctGgcactcctgaaagacccctc	7	16	1	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr2:227924168G>T	ENST00000396625.3	-	28	2543	c.2336C>A	c.(2335-2337)cCa>cAa	p.P779Q	COL4A4_ENST00000329662.7_Missense_Mutation_p.P779Q	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	779	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TTTTATCCCTGGCACTCCTGA	0.572																																					p.P779Q		Atlas-SNP	.											.	COL4A4	215	.	0			c.C2336A						.						135	142	139					2																	227924168		1863	4085	5948	SO:0001583	missense	1286	exon28			ATCCCTGGCACTC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.2336C>A	chr2.hg19:g.227924168G>T	ENSP00000379866:p.Pro779Gln	190.0	0.0		179.0	61.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	hg19	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.994827	0.54041	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.93712	-3.27;-3.27	5.99	4.18	0.49190	.	.	.	.	.	D	0.89753	0.6806	L	0.49571	1.57	0.19945	N	0.999941	P	0.37330	0.59	B	0.35182	0.197	T	0.80634	-0.1295	9	0.39692	T	0.17	.	9.3804	0.38311	0.0724:0.0:0.7839:0.1437	.	779	P53420	CO4A4_HUMAN	Q	779	ENSP00000379866:P779Q;ENSP00000328553:P779Q	ENSP00000328553:P779Q	P	-	2	0	COL4A4	227632412	1.000000	0.71417	0.054000	0.19295	0.828000	0.46876	5.485000	0.66850	0.852000	0.35287	0.655000	0.94253	CCA	.	.		0.572	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		T	227924168	G	T	227924168	3	4	155	1	0	0	0	0	1	0	0	0	3695	1348	47	3	2820	3	COL4A4	2	227924168	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	99457713	227924168	15275205	18	23671										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1367631	1367631	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aaatggtgaacgactcaaccCagaggtaagcaactatgttg	10	8	1	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr3:1367631C>A	ENST00000446702.2	+	9	1706	c.1079C>A	c.(1078-1080)cCa>cAa	p.P360Q	CNTN6_ENST00000539053.1_Missense_Mutation_p.P288Q|CNTN6_ENST00000350110.2_Missense_Mutation_p.P360Q			Q9UQ52	CNTN6_HUMAN	contactin 6	360	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		CGACTCAACCCAGAGGTAAGC	0.358																																					p.P360Q		Atlas-SNP	.											CNTN6,NS,carcinoma,0,1	CNTN6	245	.	0			c.C1079A						.						95	92	93					3																	1367631		2203	4300	6503	SO:0001583	missense	27255	exon9			TCAACCCAGAGGT	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1079C>A	chr3.hg19:g.1367631C>A	ENSP00000407822:p.Pro360Gln	117.0	0.0		104.0	26.0	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	hg19	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.201901	0.38905	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.66460	-0.21;-0.21;-0.21	5.26	4.39	0.52855	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.507528	0.18288	N	0.145790	T	0.63200	0.2491	L	0.45051	1.395	0.21878	N	0.999491	B	0.32467	0.372	B	0.39258	0.295	T	0.59241	-0.7491	10	0.56958	D	0.05	.	12.1998	0.54319	0.0:0.9213:0.0:0.0787	.	360	Q9UQ52	CNTN6_HUMAN	Q	360;288;360	ENSP00000407822:P360Q;ENSP00000442791:P288Q;ENSP00000341882:P360Q	ENSP00000341882:P360Q	P	+	2	0	CNTN6	1342631	0.188000	0.23250	0.779000	0.31741	0.854000	0.48673	1.590000	0.36654	1.227000	0.43598	0.650000	0.86243	CCA	.	.		0.358	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		A	1367631	C	A	1367631	3	1	155	1	0	0	0	0	1	0	0	0	3647	594	21	3	1109	3	CNTN6	3	1367631	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10		1367631	196654799	19	23672										
IQSEC1	9922	hgsc.bcm.edu	37	chr3	12963694	12963694	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tgcgcctggaatttcctgagGgcctcatccagctccatggt	11	13	1	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr3:12963694G>T	ENST00000273221.4	-	5	2037	c.1821C>A	c.(1819-1821)gcC>gcA	p.A607A		NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1	607	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ATTTCCTGAGGGCCTCATCCA	0.622																																					p.A607A		Atlas-SNP	.											.	IQSEC1	88	.	0			c.C1821A						.						74	68	70					3																	12963694		2202	4300	6502	SO:0001819	synonymous_variant	9922	exon5			CCTGAGGGCCTCA	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"brefeldin A-resistant ARF-GEF2"	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.1821C>A	chr3.hg19:g.12963694G>T		80.0	0.0		77.0	16.0	NM_014869	O94863|Q96D85	Silent	SNP	ENST00000273221.4	hg19	CCDS33703.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.625736	0.28889	.	.	ENSG00000144711	ENST00000450726	.	.	.	4.84	0.263	0.15602	.	.	.	.	.	T	0.50990	0.1648	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40905	-0.9538	4	.	.	.	.	5.1968	0.15243	0.293:0.0:0.5109:0.1961	.	.	.	.	T	608	.	.	P	-	1	0	IQSEC1	12938694	0.684000	0.27642	0.998000	0.56505	0.999000	0.98932	-0.141000	0.10327	0.402000	0.25451	0.655000	0.94253	CCT	.	.		0.622	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869		T	12963694	G	T	12963694	2	4	155	1	0	0	0	0	0	0	0	1	7826	1219	43	3		3	IQSEC1	3	12963694	Silent	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	11596063	12963694	185058736	20	23673										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37402755	37402755	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ttacttcacctcgcagtggtAtcttctgagtaaaccatcag	7	11	4	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr3:37402755A>G	ENST00000361924.2	+	23	7059	c.6685A>G	c.(6685-6687)Atc>Gtc	p.I2229V	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	2229					Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TCGCAGTGGTATCTTCTGAGT	0.353																																					p.I2229V		Atlas-SNP	.											.	GOLGA4	173	.	0			c.A6685G						.						185	160	168					3																	37402755		2203	4300	6503	SO:0001583	missense	2803	exon23			AGTGGTATCTTCT	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.6685A>G	chr3.hg19:g.37402755A>G	ENSP00000354486:p.Ile2229Val	107.0	0.0		119.0	37.0	NM_002078	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	hg19	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.673577	0.47781	.	.	ENSG00000144674	ENST00000361924	T	0.24908	1.83	5.7	4.52	0.55395	.	.	.	.	.	T	0.16514	0.0397	N	0.08118	0	0.80722	D	1	D	0.53312	0.959	B	0.43950	0.437	T	0.05971	-1.0853	9	0.87932	D	0	.	12.939	0.58331	0.8646:0.1354:0.0:0.0	.	2229	Q13439	GOGA4_HUMAN	V	2229	ENSP00000354486:I2229V	ENSP00000354486:I2229V	I	+	1	0	GOLGA4	37377759	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.894000	0.56250	0.971000	0.38288	0.460000	0.39030	ATC	.	.		0.353	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		G	37402755	A	G	37402755	3	3	155	1	0	0	0	0	1	0	0	0	6563	449	16	2	6845	2	GOLGA4	3	37402755	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	24439061	37402755	160619675	21	23674										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38159099	38159099	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	attcccgagcagccctgctcTggggtgagtgtgctgccacc	13	14	1	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr3:38159099T>C	ENST00000308059.6	+	32	4503	c.4482T>C	c.(4480-4482)tcT>tcC	p.S1494S	DLEC1_ENST00000346219.3_Silent_p.S1494S|DLEC1_ENST00000452631.2_Silent_p.S1497S					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		AGCCCTGCTCTGGGGTGAGTG	0.592											OREG0015476	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1494S		Atlas-SNP	.											.	DLEC1	278	.	0			c.T4482C						.						50	57	55					3																	38159099		2055	4212	6267	SO:0001819	synonymous_variant	9940	exon32			CTGCTCTGGGGTG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.4482T>C	chr3.hg19:g.38159099T>C		120.0	0.0	876	126.0	27.0	NM_007337		Silent	SNP	ENST00000308059.6	hg19	CCDS2672.2																																																																																			.	.		0.592	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		C	38159099	T	C	38159099	2	2	155	1	0	0	0	0	0	0	0	1	4554	1567	55	2		2	DLEC1	3	38159099	Silent	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	756344	38159099	159863331	22	23675										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266110	41266110	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ttacctggactctggaatccAttctggtgccactaccacag	8	13	2	0	rs121913416		TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr3:41266110A>C	ENST00000349496.5	+	3	387	c.107A>C	c.(106-108)cAt>cCt	p.H36P	CTNNB1_ENST00000396185.3_Missense_Mutation_p.H36P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.H36P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.H29P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.H36P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	36					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.H36P(24)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.H36R(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.I35_S37>T(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.S29_H36del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTGGAATCCATTCTGGTGCC	0.498		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.H36P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	159	Deletion - In frame(104)|Substitution - Missense(27)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(119)|large_intestine(20)|stomach(7)|kidney(6)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.A107C						.						95	80	85					3																	41266110		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GAATCCATTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.107A>C	chr3.hg19:g.41266110A>C	ENSP00000344456:p.His36Pro	158.0	0.0		175.0	52.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824526	0.50739	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88	5.76	5.76	0.90799	.	0.093481	0.85682	D	0.000000	T	0.51210	0.1661	M	0.64170	1.965	0.80722	D	1	P	0.40398	0.716	P	0.45946	0.498	T	0.54807	-0.8238	10	0.72032	D	0.01	-2.3155	16.0676	0.80897	1.0:0.0:0.0:0.0	.	36	P35222	CTNB1_HUMAN	P	29;36;36;36;36;29;36;36;36	ENSP00000400508:H29P;ENSP00000385604:H36P;ENSP00000412219:H36P;ENSP00000379486:H36P;ENSP00000344456:H36P;ENSP00000411226:H29P;ENSP00000379488:H36P;ENSP00000409302:H36P;ENSP00000401599:H36P	ENSP00000344456:H36P	H	+	2	0	CTNNB1	41241114	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	CAT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266110	A	C	41266110	3	2	155	1	0	0	0	0	1	0	0	0	4018	217	8	5	113	5	CTNNB1	3	41266110	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	3107011	41266110	156756320	23	23676										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140401928	140401928	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tctttccacaatggccacgaCaccattagcctcatcgacgc	6	16	2	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr3:140401928C>A	ENST00000286349.3	+	2	1157	c.966C>A	c.(964-966)gaC>gaA	p.D322E		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	322						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ATGGCCACGACACCATTAGCC	0.562																																					p.D322E		Atlas-SNP	.											.	TRIM42	143	.	0			c.C966A						.						215	188	197					3																	140401928		2203	4300	6503	SO:0001583	missense	287015	exon2			CCACGACACCATT	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.966C>A	chr3.hg19:g.140401928C>A	ENSP00000286349:p.Asp322Glu	140.0	0.0		130.0	42.0	NM_152616	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	hg19	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.904855	0.52333	.	.	ENSG00000155890	ENST00000286349	T	0.39997	1.05	5.46	4.58	0.56647	Zinc finger, B-box (2);	0.089094	0.48767	D	0.000163	T	0.19287	0.0463	N	0.12182	0.205	0.29538	N	0.852261	P	0.39535	0.677	B	0.36378	0.223	T	0.11421	-1.0588	10	0.07030	T	0.85	-28.4889	9.1765	0.37116	0.0:0.9033:0.0:0.0967	.	322	Q8IWZ5	TRI42_HUMAN	E	322	ENSP00000286349:D322E	ENSP00000286349:D322E	D	+	3	2	TRIM42	141884618	0.625000	0.27111	1.000000	0.80357	0.925000	0.55904	0.551000	0.23361	2.567000	0.86603	0.561000	0.74099	GAC	.	.		0.562	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		A	140401928	C	A	140401928	3	1	155	1	0	0	0	0	1	0	0	0	16532	477	17	3	972	3	TRIM42	3	140401928	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	99135818	140401928	57620502	24	23677										
EVC2	132884	hgsc.bcm.edu	37	chr4	5664973	5664973	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	cttgctctcatactgccaaaCcttcaggagaattgcggaaa	8	11	2	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr4:5664973C>T	ENST00000344408.5	-	9	1059	c.1006G>A	c.(1006-1008)Gtt>Att	p.V336I	EVC2_ENST00000310917.2_Splice_Site_p.V256I|EVC2_ENST00000344938.1_Splice_Site_p.V336I	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	336					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TACTGCCAAACCTTCAGGAGA	0.498																																					p.V336I		Atlas-SNP	.											.	EVC2	202	.	0			c.G1006A						.						114	115	115					4																	5664973		2203	4300	6503	SO:0001630	splice_region_variant	132884	exon9			GCCAAACCTTCAG	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1006-1G>A	chr4.hg19:g.5664973C>T		87.0	0.0		78.0	19.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	12.32	1.903520	0.33628	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.76448	-1.02;-1.02;-1.02	5.27	4.42	0.53409	.	0.729745	0.13477	N	0.385008	T	0.72236	0.3435	L	0.57536	1.79	0.24000	N	0.996212	B	0.17667	0.023	B	0.15052	0.012	T	0.58340	-0.7653	10	0.22706	T	0.39	-2.3607	10.6002	0.45362	0.0:0.9082:0.0:0.0918	.	336	Q86UK5	LBN_HUMAN	I	336;256;336	ENSP00000339954:V336I;ENSP00000311683:V256I;ENSP00000342144:V336I	ENSP00000311683:V256I	V	-	1	0	EVC2	5715874	0.219000	0.23619	0.294000	0.24946	0.112000	0.19704	0.538000	0.23160	1.306000	0.44926	0.655000	0.94253	GTT	.	.		0.498	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	Missense_Mutation	T	5664973	C	T	5664973	5	4	155	1	0	0	0	0	0	0	1	0	5288	521	18	3	2976	3	EVC2	4	5664973	Splice_Site	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10		5664973	185489303	25	23678										
REST	5978	hgsc.bcm.edu	37	chr4	57797002	57797002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	agatggaggtggttcaggagGggcctgctcagaaggagctg	19	6	2	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr4:57797002G>A	ENST00000309042.7	+	4	2292	c.1978G>A	c.(1978-1980)Ggg>Agg	p.G660R		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	660	Pro-rich.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					GGTTCAGGAGGGGCCTGCTCA	0.617																																					p.G660R		Atlas-SNP	.											.	REST	104	.	0			c.G1978A						.						42	46	45					4																	57797002		2203	4300	6503	SO:0001583	missense	5978	exon4			CAGGAGGGGCCTG	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.1978G>A	chr4.hg19:g.57797002G>A	ENSP00000311816:p.Gly660Arg	105.0	0.0		113.0	36.0	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	hg19	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	G	17.24	3.338866	0.60963	.	.	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.08193	3.12	3.24	3.24	0.37175	.	.	.	.	.	T	0.10337	0.0253	L	0.60455	1.87	0.09310	N	1	B;B	0.21520	0.047;0.057	B;B	0.21917	0.037;0.014	T	0.24297	-1.0164	9	0.17369	T	0.5	0.0593	12.7223	0.57149	0.0:0.0:1.0:0.0	.	637;660	F8WAN5;Q13127	.;REST_HUMAN	R	660;637	ENSP00000311816:G660R	ENSP00000311816:G660R	G	+	1	0	REST	57491759	0.009000	0.17119	0.024000	0.17045	0.416000	0.31233	1.730000	0.38125	1.771000	0.52183	0.462000	0.41574	GGG	.	.		0.617	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		A	57797002	G	A	57797002	3	1	155	1	0	0	0	0	1	0	0	0	13249	1232	43	3	1988	3	REST	4	57797002	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	52132029	57797002	133357274	26	23679										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537513	88537513	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gacagcagtgacagcaatgaAagcagcgacagcagtgacag	13	9	0	3	rs112275895		TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr4:88537513A>C	ENST00000282478.7	+	4	3732	c.3699A>C	c.(3697-3699)gaA>gaC	p.E1233D	DSPP_ENST00000399271.1_Missense_Mutation_p.E1233D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1233	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcaatgaaagcagcgaca	0.547																																					p.E1233D		Atlas-SNP	.											.	DSPP	174	.	0			c.A3699C						.																																			SO:0001583	missense	1834	exon5			CAATGAAAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3699A>C	chr4.hg19:g.88537513A>C	ENSP00000282478:p.Glu1233Asp	298.0	0.0		362.0	48.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.785366	0.00628	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	2.61	-5.21	0.02815	.	.	.	.	.	T	0.57213	0.2038	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.57347	-0.7827	9	0.02654	T	1	.	0.7125	0.00926	0.2623:0.1881:0.1298:0.4197	.	1233	Q9NZW4	DSPP_HUMAN	D	1233	ENSP00000382213:E1233D;ENSP00000282478:E1233D	ENSP00000282478:E1233D	E	+	3	2	DSPP	88756537	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-2.769000	0.00780	-2.252000	0.00699	-3.496000	0.00033	GAA	.	A|0.500;C|0.500		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537513	A	C	88537513	3	2	155	1	0	0	0	0	1	0	0	0	4784	11	1	5	3713	5	DSPP	4	88537513	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	30740511	88537513	102616763	27	23680										
PCDH18	54510	hgsc.bcm.edu	37	chr4	138452132	138452132	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tgtatcaataggatccccttCaaaaatataagatatttctt	4	7	3	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr4:138452132C>T	ENST00000344876.4	-	1	1497	c.1111G>A	c.(1111-1113)Gaa>Aaa	p.E371K	PCDH18_ENST00000507846.1_Missense_Mutation_p.E151K|PCDH18_ENST00000412923.2_Missense_Mutation_p.E371K|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000510305.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	371	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					GGATCCCCTTCAAAAATATAA	0.353																																					p.E371K		Atlas-SNP	.											.	PCDH18	229	.	0			c.G1111A						.						47	50	49					4																	138452132		2203	4299	6502	SO:0001583	missense	54510	exon1			CCCCTTCAAAAAT	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.1111G>A	chr4.hg19:g.138452132C>T	ENSP00000355082:p.Glu371Lys	207.0	0.0		238.0	77.0	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	hg19	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.706878	0.89018	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846	T;T;T	0.76316	-1.01;-1.01;-1.01	5.92	5.92	0.95590	Cadherin (3);Cadherin-like (1);	0.000000	0.44097	D	0.000483	D	0.93979	0.8072	H	0.99197	4.465	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.95872	0.8892	10	0.87932	D	0	.	20.3167	0.98654	0.0:1.0:0.0:0.0	.	151;371;371	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	K	371;371;151	ENSP00000355082:E371K;ENSP00000390688:E371K;ENSP00000425903:E151K	ENSP00000355082:E371K	E	-	1	0	PCDH18	138671582	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.770000	0.85390	2.809000	0.96659	0.557000	0.71058	GAA	.	.		0.353	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		T	138452132	C	T	138452132	3	4	155	1	0	0	0	0	1	0	0	0	11522	835	29	3	2312	3	PCDH18	4	138452132	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	49914619	138452132	52702144	28	23681										
ALDH7A1	501	hgsc.bcm.edu	37	chr5	125918580	125918580	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ggtcctccaatcatccttgaTaaaccaacagcatagtcaca	5	13	2	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr5:125918580T>C	ENST00000409134.3	-	5	699	c.480A>G	c.(478-480)ttA>ttG	p.L160L	ALDH7A1_ENST00000413020.1_5'UTR|ALDH7A1_ENST00000553117.1_Silent_p.L160L|ALDH7A1_ENST00000447989.2_Silent_p.L187L	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	160					cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|glycine betaine biosynthetic process from choline (GO:0019285)|lysine catabolic process (GO:0006554)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|betaine-aldehyde dehydrogenase activity (GO:0008802)|L-aminoadipate-semialdehyde dehydrogenase activity (GO:0004043)			endometrium(1)|kidney(4)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)		TCATCCTTGATAAACCAACAG	0.373																																					p.L187L		Atlas-SNP	.											.	ALDH7A1	57	.	0			c.A561G						.						115	104	108					5																	125918580		2203	4300	6503	SO:0001819	synonymous_variant	501	exon5			CCTTGATAAACCA	S74728	CCDS4137.2, CCDS56380.1	5q31	2013-06-03			ENSG00000164904	ENSG00000164904	1.2.1.31	"Aldehyde dehydrogenases"	877	protein-coding gene	gene with protein product	"antiquitin 1", "26g turgor protein homolog", "alpha-aminoadipic semialdehyde dehydrogenase", "alpha-AASA dehydrogenase", "delta1-piperideine-6-carboxylate dehydrogenease", "P6c dehydrogenase"	107323		ATQ1		9417906	Standard	NM_001182		Approved	EPD, PDE	uc003ktx.3	P49419	OTTHUMG00000128942	ENST00000409134.3:c.480A>G	chr5.hg19:g.125918580T>C		267.0	0.0		325.0	172.0	NM_001202404	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Silent	SNP	ENST00000409134.3	hg19	CCDS4137.2																																																																																			.	.		0.373	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182		C	125918580	T	C	125918580	2	2	155	1	0	0	0	0	0	0	0	1	504	1403	49	2		2	ALDH7A1	5	125918580	Silent	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10		125918580	54996680	29	23682										
RGL2	5863	hgsc.bcm.edu	37	chr6	33259901	33259901	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	agaacagtgcccgtgcaatcTtcctccctgtggccttgatc	9	14	1	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr6:33259901T>G	ENST00000497454.1	-	18	2807	c.2312A>C	c.(2311-2313)aAg>aCg	p.K771T	WDR46_ENST00000477718.1_5'Flank|RGL2_ENST00000437840.2_5'UTR|WDR46_ENST00000374617.4_5'Flank|PFDN6_ENST00000463584.1_Intron	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2	771					positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						CCGTGCAATCTTCCTCCCTGT	0.572																																					p.K771T		Atlas-SNP	.											.	RGL2	58	.	0			c.A2312C						.						62	54	57					6																	33259901		2203	4300	6503	SO:0001583	missense	5863	exon18			GCAATCTTCCTCC		CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"RAB2, member RAS oncogene family-like"	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.2312A>C	chr6.hg19:g.33259901T>G	ENSP00000420211:p.Lys771Thr	82.0	0.0		107.0	22.0	NM_004761	B4DG72|Q5STK0|Q9Y3F3	Missense_Mutation	SNP	ENST00000497454.1	hg19	CCDS4774.1	.	.	.	.	.	.	.	.	.	.	T	15.44	2.833583	0.50951	.	.	ENSG00000237441	ENST00000497454	T	0.13778	2.56	5.5	5.5	0.81552	.	0.060904	0.64402	D	0.000004	T	0.08980	0.0222	N	0.19112	0.55	0.80722	D	1	D	0.53885	0.963	P	0.52554	0.702	T	0.06643	-1.0815	10	0.87932	D	0	.	12.0031	0.53243	0.0:0.0:0.0:1.0	.	771	O15211	RGL2_HUMAN	T	771	ENSP00000420211:K771T	ENSP00000420211:K771T	K	-	2	0	RGL2	33367879	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.553000	0.53713	2.084000	0.62774	0.448000	0.29417	AAG	.	.		0.572	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2			G	33259901	T	G	33259901	3	3	155	1	0	0	0	0	1	0	0	0	13292	1609	56	5	25	5	RGL2	6	33259901	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10		33259901	137855166	30	23683										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72806711	72806711	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gagaaaaataggggaagaagCgcggcgttaccagggcgagc	17	7	0	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr6:72806711C>A	ENST00000521978.1	+	3	305	c.305C>A	c.(304-306)gCg>gAg	p.A102E	RIMS1_ENST00000348717.5_Missense_Mutation_p.A102E|RIMS1_ENST00000520567.1_Missense_Mutation_p.A102E|RIMS1_ENST00000518273.1_Missense_Mutation_p.A102E|RIMS1_ENST00000522291.1_Missense_Mutation_p.A102E|RIMS1_ENST00000517960.1_Missense_Mutation_p.A102E|RIMS1_ENST00000491071.2_Missense_Mutation_p.A102E|RIMS1_ENST00000264839.7_Missense_Mutation_p.A102E	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	102	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GGGGAAGAAGCGCGGCGTTAC	0.438																																					p.A102E		Atlas-SNP	.											RIMS1,NS,carcinoma,0,1	RIMS1	278	.	0			c.C305A						.						82	77	79					6																	72806711		1931	4135	6066	SO:0001583	missense	22999	exon3			AAGAAGCGCGGCG	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.305C>A	chr6.hg19:g.72806711C>A	ENSP00000428417:p.Ala102Glu	204.0	0.0		119.0	63.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.787299	0.90367	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29	5.81	5.81	0.92471	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE/PHD-type (1);	0.093571	0.45361	D	0.000364	T	0.32285	0.0824	L	0.55481	1.735	0.80722	D	1	P	0.46784	0.884	B	0.43575	0.424	T	0.13282	-1.0515	10	0.59425	D	0.04	-17.8794	20.0804	0.97772	0.0:1.0:0.0:0.0	.	102	Q86UR5	RIMS1_HUMAN	E	102	ENSP00000430101:A102E;ENSP00000275037:A102E;ENSP00000264839:A102E;ENSP00000429959:A102E;ENSP00000430408:A102E;ENSP00000430502:A102E;ENSP00000430932:A102E;ENSP00000428417:A102E	ENSP00000264839:A102E	A	+	2	0	RIMS1	72863432	1.000000	0.71417	0.964000	0.40570	0.745000	0.42441	7.798000	0.85924	2.738000	0.93877	0.655000	0.94253	GCG	.	.		0.438	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			A	72806711	C	A	72806711	3	1	155	1	0	0	0	0	1	0	0	0	13382	768	27	1	315	1	RIMS1	6	72806711	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	39546810	72806711	98308356	31	23684										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75904605	75904605	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ggatcaactggttttgcccaTgacatatgaacagtattttc	8	8	1	2	rs201454637		TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr6:75904605T>C	ENST00000322507.8	-	3	441	c.132A>G	c.(130-132)tcA>tcG	p.S44S	COL12A1_ENST00000483888.2_Silent_p.S44S|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Silent_p.S44S	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	44	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						GTTTTGCCCATGACATATGAA	0.363																																					p.S44S		Atlas-SNP	.											.	COL12A1	385	.	0			c.A132G						.	T	,	0,3650		0,0,1825	112	106	108		132,	3.3	1	6		108	7,8155		0,7,4074	no	coding-synonymous,intron	COL12A1	NM_004370.5,NM_080645.2	,	0,7,5899	CC,CT,TT		0.0858,0.0,0.0593	,	44/3064,	75904605	7,11805	1825	4081	5906	SO:0001819	synonymous_variant	1303	exon3			TGCCCATGACATA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.132A>G	chr6.hg19:g.75904605T>C		72.0	0.0		61.0	33.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	T|0.999;C|0.001		0.363	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75904605	T	C	75904605	2	2	155	1	0	0	0	0	0	0	0	1	3671	1451	51	2		2	COL12A1	6	75904605	Silent	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	3097894	75904605	95210462	32	23685										
SENP6	26054	hgsc.bcm.edu	37	chr6	76386824	76386861	+	Frame_Shift_Del	DEL	TTAATGAAATTGGTATAAAGAATAACATCTCCAATTTT	TTAATGAAATTGGTATAAAGAATAACATCTCCAATTTT	-													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tatggtatttgaaagtatcaTtaatgaaattggtataaaga					rs561416792|rs202019332|rs373276113	byFrequency	TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	TTAATGAAATTGGTATAAAGAATAACATCTCCAATTTT	TTAATGAAATTGGTATAAAGAATAACATCTCCAATTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr6:76386824_76386861delTTAATGAAATTGGTATAAAGAATAACATCTCCAATTTT	ENST00000447266.2	+	14	2178_2215	c.1700_1737delTTAATGAAATTGGTATAAAGAATAACATCTCCAATTTT	c.(1699-1737)attaatgaaattggtataaagaataacatctccaattttfs	p.INEIGIKNNISNF567fs	SENP6_ENST00000327284.8_Frame_Shift_Del_p.INEIGIKNNISNF560fs|SENP6_ENST00000370014.3_Frame_Shift_Del_p.INEIGIKNNISNF567fs|SENP6_ENST00000541192.1_Frame_Shift_Del_p.INEIGIKNNISNF163fs|SENP6_ENST00000370010.2_Frame_Shift_Del_p.INEIGIKNNISNF560fs	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	567					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				GAAAGTATCATTAATGAAATTGGTATAAAGAATAACATCTCCAATTTTTTTGCGAAAA	0.311																																					p.567_579del		Atlas-INDEL	.											.	SENP6	189	.	0			c.1699_1736del						.																																			SO:0001589	frameshift_variant	26054	exon14			.		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.1700_1737delTTAATGAAATTGGTATAAAGAATAACATCTCCAATTTT	chr6.hg19:g.76386824_76386861delTTAATGAAATTGGTATAAAGAATAACATCTCCAATTTT	ENSP00000402527:p.Ile567fs	436.0	0.0		218.0	25.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Frame_Shift_Del	DEL	ENST00000447266.2	hg19	CCDS47454.1																																																																																			.	.		0.311	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		-	76386861	TTAATGAAATTGGTATAAAGAATAACATCTCCAATTTT	-	76386824	7	5	155	1	0	1	0	1	0	0	0	0	14065	1493	52	0	1754	0	SENP6	6	76386824	Frame_Shift_Del	DEL	TTAATGAAATTGGTATAAAGAATAACATCTCCAATTTT	TCGA-DD-AACD-01A-11D-A40R-10	482219	76386824	94728243	33	23686										
SENP6	26054	hgsc.bcm.edu	37	chr6	76386867	76386867	+	Frame_Shift_Del	DEL	G	G	-													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aacatctccaatttttttgcGaaaattccctttgaagaagc							TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr6:76386867delG	ENST00000447266.2	+	14	2221	c.1743delG	c.(1741-1743)gcgfs	p.A581fs	SENP6_ENST00000327284.8_Frame_Shift_Del_p.A574fs|SENP6_ENST00000370014.3_Frame_Shift_Del_p.A581fs|SENP6_ENST00000541192.1_Frame_Shift_Del_p.A177fs|SENP6_ENST00000370010.2_Frame_Shift_Del_p.A574fs	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	581					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				ATTTTTTTGCGAAAATTCCCT	0.333																																					p.A581fs		Atlas-INDEL	.											.	SENP6	189	.	0			c.1742delC						.						35	34	34					6																	76386867		1807	4066	5873	SO:0001589	frameshift_variant	26054	exon14			.		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.1743delG	chr6.hg19:g.76386867delG	ENSP00000402527:p.Ala581fs	605.0	0.0		282.0	72.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Frame_Shift_Del	DEL	ENST00000447266.2	hg19	CCDS47454.1																																																																																			.	.		0.333	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		-	76386867	G	-	76386867	7	5	155	1	0	1	0	1	0	0	0	0	14065	1045	37	0	1797	0	SENP6	6	76386867	Frame_Shift_Del	DEL	G	TCGA-DD-AACD-01A-11D-A40R-10	43	76386867	94728200	34	23687										
NOD1	10392	hgsc.bcm.edu	37	chr7	30492539	30492539	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	cattgctgaagccaaccagcTccatgatggtgtccatgtag	10	11	0	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr7:30492539T>C	ENST00000222823.4	-	6	1019	c.494A>G	c.(493-495)gAg>gGg	p.E165G	NOD1_ENST00000423334.2_Missense_Mutation_p.E165G	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	165					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						GCCAACCAGCTCCATGATGGT	0.597																																					p.E165G		Atlas-SNP	.											.	NOD1	79	.	0			c.A494G						.						124	103	110					7																	30492539		2203	4300	6503	SO:0001583	missense	10392	exon6			ACCAGCTCCATGA	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"Nucleotide-binding domain and leucine rich repeat containing"	16390	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1", "NLR family, CARD domain containing 1"	605980	"caspase recruitment domain family, member 4"	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.494A>G	chr7.hg19:g.30492539T>C	ENSP00000222823:p.Glu165Gly	65.0	0.0		67.0	32.0	NM_006092	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	hg19	CCDS5427.1	.	.	.	.	.	.	.	.	.	.	T	15.91	2.971382	0.53614	.	.	ENSG00000106100	ENST00000222823;ENST00000423334	T	0.73789	-0.78	5.56	5.56	0.83823	.	0.094006	0.64402	D	0.000001	D	0.83133	0.5188	M	0.68952	2.095	0.58432	D	0.999999	D;D	0.71674	0.995;0.998	P;P	0.61722	0.541;0.893	D	0.85292	0.1068	10	0.87932	D	0	.	14.9019	0.70687	0.0:0.0:0.0:1.0	.	165;165	B4DTU3;Q9Y239	.;NOD1_HUMAN	G	165	ENSP00000222823:E165G	ENSP00000222823:E165G	E	-	2	0	NOD1	30459064	1.000000	0.71417	1.000000	0.80357	0.451000	0.32288	6.259000	0.72494	2.110000	0.64415	0.533000	0.62120	GAG	.	.		0.597	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2			C	30492539	T	C	30492539	3	2	155	1	0	0	0	0	1	0	0	0	10525	1551	54	2	2403	2	NOD1	7	30492539	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10		30492539	128646124	35	23688										
ACHE	43	hgsc.bcm.edu	37	chr7	100491063	100491063	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ccaccgtggcccagggtccaTtgggggcaccgctctgcagc	14	16	1	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr7:100491063T>A	ENST00000412389.1	-	1	946	c.791A>T	c.(790-792)aAt>aTt	p.N264I	ACHE_ENST00000302913.4_Missense_Mutation_p.N264I|ACHE_ENST00000497647.1_5'Flank|ACHE_ENST00000411582.1_Missense_Mutation_p.N264I|ACHE_ENST00000428317.1_Missense_Mutation_p.N264I|ACHE_ENST00000419336.2_Missense_Mutation_p.N264I|ACHE_ENST00000241069.5_Missense_Mutation_p.N264I			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	264					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	CCAGGGTCCATTGGGGGCACC	0.721																																					p.N264I		Atlas-SNP	.											.	ACHE	80	.	0			c.A791T						.						22	25	24					7																	100491063		2201	4297	6498	SO:0001583	missense	43	exon2			GGTCCATTGGGGG		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"Blood group antigens"	108	protein-coding gene	gene with protein product	"Yt blood group"	100740	"acetylcholinesterase (YT blood group)", "acetylcholinesterase (Yt blood group)", "acetylcholinesterase"	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.791A>T	chr7.hg19:g.100491063T>A	ENSP00000394976:p.Asn264Ile	34.0	0.0		55.0	23.0	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	hg19	CCDS5709.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.872199	0.51695	.	.	ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000302913;ENST00000412389;ENST00000426415;ENST00000430554;ENST00000411582;ENST00000422451	T;T;T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96	4.95	3.78	0.43462	Carboxylesterase, type B (1);	0.099065	0.64402	D	0.000002	T	0.30262	0.0759	L	0.33668	1.02	0.53688	D	0.999975	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.998;0.999	T	0.01899	-1.1251	10	0.31617	T	0.26	.	8.6379	0.33959	0.0:0.0937:0.0:0.9063	.	264;264;264;264	B7WPI6;P22303-3;P22303-2;P22303	.;.;.;ACES_HUMAN	I	264	ENSP00000403474:N264I;ENSP00000241069:N264I;ENSP00000414858:N264I;ENSP00000303211:N264I;ENSP00000394976:N264I;ENSP00000397143:N264I;ENSP00000399725:N264I;ENSP00000404865:N264I	ENSP00000241069:N264I	N	-	2	0	ACHE	100328999	1.000000	0.71417	0.992000	0.48379	0.775000	0.43874	3.644000	0.54381	0.721000	0.32231	0.397000	0.26171	AAT	.	.		0.721	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831		A	100491063	T	A	100491063	3	1	155	1	0	0	0	0	1	0	0	0	141	1493	52	4	1204	4	ACHE	7	100491063	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	69998524	100491063	58647600	36	23689										
SLC13A4	26266	hgsc.bcm.edu	37	chr7	135370360	135370360	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	acgaggatgcatgccagcagGgtgacagcccacggtgggag	17	10	0	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr7:135370360G>C	ENST00000354042.4	-	14	2204	c.1515C>G	c.(1513-1515)acC>acG	p.T505T	C7orf73_ENST00000422968.1_Intron|SLC13A4_ENST00000491630.1_5'UTR	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	505					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						ATGCCAGCAGGGTGACAGCCC	0.542																																					p.T505T		Atlas-SNP	.											.	SLC13A4	56	.	0			c.C1515G						.						201	175	184					7																	135370360		2203	4300	6503	SO:0001819	synonymous_variant	26266	exon14			CAGCAGGGTGACA	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1515C>G	chr7.hg19:g.135370360G>C		104.0	0.0		138.0	33.0	NM_012450	A4D1Q4|Q8N631	Silent	SNP	ENST00000354042.4	hg19	CCDS5840.1																																																																																			.	.		0.542	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		C	135370360	G	C	135370360	2	2	155	1	0	0	0	0	0	0	0	1	14409	1219	43	4		4	SLC13A4	7	135370360	Silent	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	34879297	135370360	23768303	37	23690										
ZNF282	8427	hgsc.bcm.edu	37	chr7	148892729	148892729	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	cctcagcagctgggcatccaGggcctggggctggacagcgg	17	13	1	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr7:148892729G>A	ENST00000262085.3	+	1	153	c.48G>A	c.(46-48)caG>caA	p.Q16Q	ZNF282_ENST00000479907.1_Silent_p.Q16Q	NM_003575.2	NP_003566.1	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	16					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	17	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)		TGGGCATCCAGGGCCTGGGGC	0.687																																					p.Q16Q		Atlas-SNP	.											.	ZNF282	42	.	0			c.G48A						.						13	15	14					7																	148892729		2198	4288	6486	SO:0001819	synonymous_variant	8427	exon1			CATCCAGGGCCTG	D30612	CCDS5895.1	7q36.1	2013-01-08			ENSG00000170265	ENSG00000170265		"Zinc fingers, C2H2-type", "-"	13076	protein-coding gene	gene with protein product		603397				9396811	Standard	NM_003575		Approved	HUB1	uc003wfm.3	Q9UDV7	OTTHUMG00000158974	ENST00000262085.3:c.48G>A	chr7.hg19:g.148892729G>A		118.0	0.0		150.0	73.0	NM_003575	B4DRI5|O43691|Q6DKK0	Silent	SNP	ENST00000262085.3	hg19	CCDS5895.1																																																																																			.	.		0.687	ZNF282-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352746.1	NM_003575		A	148892729	G	A	148892729	2	1	155	1	0	0	0	0	0	0	0	1	17834	991	35	3		3	ZNF282	7	148892729	Silent	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	13522369	148892729	10245934	38	23691										
WDR60	55112	hgsc.bcm.edu	37	chr7	158705686	158705686	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tgtttttaaggcatatgttcAgtgtaacgaagataatgttg	10	3	1	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr7:158705686A>T	ENST00000407559.3	+	13	1759	c.1601A>T	c.(1600-1602)cAg>cTg	p.Q534L		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	534					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		GCATATGTTCAGTGTAACGAA	0.383																																					p.Q534L		Atlas-SNP	.											.	WDR60	94	.	0			c.A1601T						.						100	98	99					7																	158705686		1865	4097	5962	SO:0001583	missense	55112	exon13			ATGTTCAGTGTAA		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"WD repeat domain containing"	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.1601A>T	chr7.hg19:g.158705686A>T	ENSP00000384290:p.Gln534Leu	134.0	0.0		189.0	81.0	NM_018051	Q9NW58	Missense_Mutation	SNP	ENST00000407559.3	hg19	CCDS47757.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.411950	0.83340	.	.	ENSG00000126870	ENST00000407559	T	0.80994	-1.44	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.81133	0.4759	M	0.85777	2.775	0.80722	D	1	P;P	0.40431	0.717;0.476	B;B	0.35039	0.194;0.172	D	0.84599	0.0671	10	0.87932	D	0	-22.407	13.4283	0.61039	1.0:0.0:0.0:0.0	.	17;534	A4D230;Q8WVS4	.;WDR60_HUMAN	L	534	ENSP00000384290:Q534L	ENSP00000384290:Q534L	Q	+	2	0	WDR60	158398447	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	7.671000	0.83941	2.050000	0.60909	0.460000	0.39030	CAG	.	.		0.383	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051		T	158705686	A	T	158705686	3	4	155	1	0	0	0	0	1	0	0	0	17326	188	7	4	1651	4	WDR60	7	158705686	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	9812957	158705686	432977	39	23692										
FAM92A1	137392	hgsc.bcm.edu	37	chr8	94730901	94730901	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tcaattctttggttttttttAgactatattttctgaattta	4	4	3	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr8:94730901A>G	ENST00000518322.1	+	7	684		c.e7-1		FAM92A1_ENST00000423990.2_Intron|FAM92A1_ENST00000517718.1_Splice_Site|CTD-2006H14.2_ENST00000607706.1_RNA|FAM92A1_ENST00000519679.1_Splice_Site|RP11-10N23.2_ENST00000520562.1_RNA	NM_145269.3	NP_660312.2	A1XBS5	F92A1_HUMAN	family with sequence similarity 92, member A1											NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)	7	Breast(36;2.4e-06)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			GGTTTTTTTTAGACTATATTT	0.269																																					.		Atlas-SNP	.											.	FAM92A1	22	.	0			c.544-2A>G						.						22	18	19					8																	94730901		1770	4036	5806	SO:0001630	splice_region_variant	137392	exon6			TTTTTTAGACTAT		CCDS47892.1, CCDS64933.1	8q22.1	2005-09-22			ENSG00000188343	ENSG00000188343			30452	protein-coding gene	gene with protein product						12477932	Standard	XM_005250783		Approved	FLJ38979	uc022ayd.1	A1XBS5	OTTHUMG00000164238	ENST00000518322.1:c.544-1A>G	chr8.hg19:g.94730901A>G		97.0	0.0		249.0	81.0	NM_145269	A1XBS4|Q32ND3|Q6AHW7|Q8N8R1|Q96L09	Splice_Site	SNP	ENST00000518322.1	hg19	CCDS47892.1	.	.	.	.	.	.	.	.	.	.	A	16.99	3.274104	0.59649	.	.	ENSG00000188343	ENST00000518322;ENST00000341186;ENST00000540007;ENST00000517718;ENST00000521641;ENST00000519679	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5602	0.84551	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAM92A1	94800077	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	8.339000	0.90041	2.367000	0.80283	0.528000	0.53228	.	.	.		0.269	FAM92A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377890.4	NM_145269	Intron	G	94730901	A	G	94730901	5	3	155	1	0	0	0	0	0	0	1	0	5660	434	15	2	564	2	FAM92A1	8	94730901	Splice_Site	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10		94730901	51633121	40	23693										
SNX31	169166	hgsc.bcm.edu	37	chr8	101612592	101612592	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ttcacctttgtttgactgtcTtctttctggaaagcttctaa	6	9	5	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr8:101612592T>C	ENST00000311812.2	-	9	909	c.759A>G	c.(757-759)gaA>gaG	p.E253E	SNX31_ENST00000428383.2_Silent_p.E154E	NM_152628.3	NP_689841.3	Q8N9S9	SNX31_HUMAN	sorting nexin 31	253					protein transport (GO:0015031)	protein complex (GO:0043234)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|skin(3)|urinary_tract(1)	26	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)			TTTGACTGTCTTCTTTCTGGA	0.358																																					p.E253E		Atlas-SNP	.											.	SNX31	66	.	0			c.A759G						.						217	200	206					8																	101612592		2202	4300	6502	SO:0001819	synonymous_variant	169166	exon9			ACTGTCTTCTTTC		CCDS6288.1	8q22.3	2011-05-03			ENSG00000174226	ENSG00000174226		"Sorting nexins"	28605	protein-coding gene	gene with protein product						16782399	Standard	NM_152628		Approved	MGC39715	uc003yjr.3	Q8N9S9	OTTHUMG00000164725	ENST00000311812.2:c.759A>G	chr8.hg19:g.101612592T>C		103.0	0.0		215.0	55.0	NM_152628	C9J6L9|Q8N0U9	Silent	SNP	ENST00000311812.2	hg19	CCDS6288.1																																																																																			.	.		0.358	SNX31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379910.1	NM_152628		C	101612592	T	C	101612592	2	2	155	1	0	0	0	0	0	0	0	1	14916	1606	56	2		2	SNX31	8	101612592	Silent	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	6881691	101612592	44751430	41	23694										
DOCK8	81704	hgsc.bcm.edu	37	chr9	434955	434955	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aggaccacagctacctgcccGtgggcagtgtcagcttccag	12	14	1	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr9:434955G>A	ENST00000453981.1	+	39	5171	c.5059G>A	c.(5059-5061)Gtg>Atg	p.V1687M	DOCK8_ENST00000382329.1_Missense_Mutation_p.V1154M|DOCK8_ENST00000469391.1_Missense_Mutation_p.V1587M|DOCK8_ENST00000432829.2_Missense_Mutation_p.V1619M			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1687	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CTACCTGCCCGTGGGCAGTGT	0.587																																					p.V1687M		Atlas-SNP	.											.	DOCK8	401	.	0			c.G5059A						.						85	82	83					9																	434955		2203	4300	6503	SO:0001583	missense	81704	exon39			CTGCCCGTGGGCA	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.5059G>A	chr9.hg19:g.434955G>A	ENSP00000408464:p.Val1687Met	49.0	0.0		43.0	15.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	21.0	4.081486	0.76528	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.68624	2.51;-0.34;-0.34;-0.34	5.04	5.04	0.67666	.	0.059925	0.64402	D	0.000003	T	0.77698	0.4169	M	0.64567	1.98	0.80722	D	1	D;P;D	0.69078	0.997;0.948;0.964	P;P;P	0.62435	0.902;0.528;0.528	T	0.74272	-0.3719	10	0.28530	T	0.3	.	18.5837	0.91181	0.0:0.0:1.0:0.0	.	1587;1154;1687	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	M	1687;1655;1619;1587;1154	ENSP00000408464:V1687M;ENSP00000394888:V1619M;ENSP00000419438:V1587M;ENSP00000371766:V1154M	ENSP00000287364:V1655M	V	+	1	0	DOCK8	424955	1.000000	0.71417	0.959000	0.39883	0.989000	0.77384	4.654000	0.61469	2.615000	0.88500	0.609000	0.83330	GTG	.	.		0.587	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		A	434955	G	A	434955	3	1	155	1	0	0	0	0	1	0	0	0	4695	1145	40	1	5213	1	DOCK8	9	434955	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10		434955	140778476	42	23695										
ANUBL1	93550	hgsc.bcm.edu	37	chr10	46121665	46121665	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ggaaataacatcagatctttTcccaagtgaatcaactttaa	5	8	3	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr10:46121665T>C	ENST00000344646.5	-	7	1821	c.1606A>G	c.(1606-1608)Aaa>Gaa	p.K536E	ZFAND4_ENST00000374370.1_5'UTR|ZFAND4_ENST00000374371.2_Intron|ZFAND4_ENST00000374366.3_Missense_Mutation_p.K462E	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	536							zinc ion binding (GO:0008270)										TCAGATCTTTTCCCAAGTGAA	0.378																																					p.K536E		Atlas-SNP	.											.	.	.	.	0			c.A1606G						.						82	85	84					10																	46121665		2203	4300	6503	SO:0001583	missense	93550	exon7			ATCTTTTCCCAAG	AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"Zinc fingers, AN1-type domain containing"	23504	protein-coding gene	gene with protein product			"AN1, ubiquitin-like, homolog (Xenopus laevis)"	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.1606A>G	chr10.hg19:g.46121665T>C	ENSP00000339484:p.Lys536Glu	151.0	0.0		132.0	43.0	NM_001128324	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	hg19	CCDS7214.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.644900	0.87859	.	.	ENSG00000172671	ENST00000344646;ENST00000374366;ENST00000374370	T;T	0.32515	1.45;1.47	5.73	5.73	0.89815	.	5.101160	0.00496	N	0.000146	T	0.61837	0.2379	M	0.75264	2.295	0.58432	D	0.999996	D	0.67145	0.996	D	0.66351	0.943	T	0.14755	-1.0461	10	0.87932	D	0	-13.0771	13.973	0.64252	0.0:0.0:0.0:1.0	.	536	Q86XD8	ANUB1_HUMAN	E	536;462;418	ENSP00000339484:K536E;ENSP00000363486:K462E	ENSP00000339484:K536E	K	-	1	0	ANUBL1	45441671	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.371000	0.79600	2.186000	0.69663	0.459000	0.35465	AAA	.	.		0.378	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890		C	46121665	T	C	46121665	3	2	155	1	0	0	0	0	1	0	0	0	713	1792	62	2	593	2	ANUBL1	10	46121665	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10		46121665	89413082	43	23696										
MYPN	84665	hgsc.bcm.edu	37	chr10	69926386	69926386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ccccagagccttcttcccccGtgaaagagccccctccagtt	7	19	1	3			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr10:69926386G>A	ENST00000358913.5	+	10	2424	c.1936G>A	c.(1936-1938)Gtg>Atg	p.V646M	MYPN_ENST00000354393.2_Missense_Mutation_p.V371M|MYPN_ENST00000540630.1_Missense_Mutation_p.V646M	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	646					sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						TTCTTCCCCCGTGAAAGAGCC	0.512																																					p.V646M		Atlas-SNP	.											.	MYPN	189	.	0			c.G1936A						.						40	40	40					10																	69926386		2203	4300	6503	SO:0001583	missense	84665	exon10			TCCCCCGTGAAAG	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1936G>A	chr10.hg19:g.69926386G>A	ENSP00000351790:p.Val646Met	163.0	0.0		151.0	19.0	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	hg19	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.560993	0.27827	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.58797	0.31;0.41;0.38	5.43	-2.38	0.06622	.	1.051730	0.07396	N	0.889937	T	0.36276	0.0961	N	0.24115	0.695	0.09310	N	1	P;P;P	0.46706	0.883;0.771;0.661	B;B;B	0.36666	0.212;0.23;0.105	T	0.25813	-1.0121	9	.	.	.	.	8.2643	0.31804	0.6831:0.0:0.137:0.1799	.	646;371;646	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	M	371;371;646;646	ENSP00000346369:V371M;ENSP00000351790:V646M;ENSP00000441668:V646M	.	V	+	1	0	MYPN	69596392	0.001000	0.12720	0.104000	0.21259	0.807000	0.45602	-0.123000	0.10611	-0.695000	0.05105	-0.140000	0.14226	GTG	.	.		0.512	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		A	69926386	G	A	69926386	3	1	155	1	0	0	0	0	1	0	0	0	10107	1145	40	1	1970	1	MYPN	10	69926386	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	23804721	69926386	65608361	44	23697										
CRTAC1	55118	hgsc.bcm.edu	37	chr10	99696049	99696049	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gcgcgtagtagggtgagctgCgctcatcgaccgcgatgttc	15	11	1	1	rs375692428	byFrequency	TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr10:99696049C>T	ENST00000370597.3	-	3	654	c.299G>A	c.(298-300)cGc>cAc	p.R100H	CRTAC1_ENST00000298819.4_Missense_Mutation_p.R100H|CRTAC1_ENST00000370591.2_Missense_Mutation_p.R100H	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	100						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		GGGTGAGCTGCGCTCATCGAC	0.642													C|||	2	0.000399361	0	0	5008	,	,		18224	0		0	False		,,,				2504	0.002				p.R100H		Atlas-SNP	.											.	CRTAC1	86	.	0			c.G299A						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	64	53	57		299,299	4.8	1	10		57	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CRTAC1	NM_001206528.2,NM_018058.6	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	100/646,100/662	99696049	1,13005	2203	4300	6503	SO:0001583	missense	55118	exon3			GAGCTGCGCTCAT	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.299G>A	chr10.hg19:g.99696049C>T	ENSP00000359629:p.Arg100His	81.0	0.0		75.0	25.0	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	ENST00000370597.3	hg19	CCDS31266.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.409456	0.42715	0.0	1.16E-4	ENSG00000095713	ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591	T;T;T;T	0.75938	-0.98;1.31;-0.13;-0.13	4.76	4.76	0.60689	.	0.058751	0.64402	D	0.000002	T	0.64271	0.2583	L	0.33485	1.01	0.49213	D	0.99976	B;B	0.19583	0.011;0.037	B;B	0.12156	0.004;0.007	T	0.59825	-0.7381	10	0.15066	T	0.55	-18.3388	17.7666	0.88480	0.0:1.0:0.0:0.0	.	100;100	Q9NQ79-2;Q9NQ79	.;CRAC1_HUMAN	H	100;100;92;100	ENSP00000359629:R100H;ENSP00000298819:R100H;ENSP00000310810:R92H;ENSP00000359623:R100H	ENSP00000298819:R100H	R	-	2	0	CRTAC1	99686039	0.998000	0.40836	1.000000	0.80357	0.665000	0.39181	1.563000	0.36364	2.204000	0.70986	0.313000	0.20887	CGC	.	.		0.642	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058		T	99696049	C	T	99696049	3	4	155	1	0	0	0	0	1	0	0	0	3898	768	27	1	1738	1	CRTAC1	10	99696049	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	29769663	99696049	35838698	45	23698										
CALHM2	51063	hgsc.bcm.edu	37	chr10	105207130	105207130	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gttgagcgccacaaagccaaAgaagcggcgcacattgttgg	13	10	0	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr10:105207130A>G	ENST00000260743.5	-	4	1274	c.751T>C	c.(751-753)Ttt>Ctt	p.F251L	RP11-225H22.7_ENST00000608063.1_RNA|CALHM2_ENST00000369788.3_Missense_Mutation_p.F251L|CALHM2_ENST00000494180.1_5'Flank	NM_015916.4	NP_057000.2	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	251					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|skin(1)	11						ACAAAGCCAAAGAAGCGGCGC	0.617																																					p.F251L		Atlas-SNP	.											.	CALHM2	30	.	0			c.T751C						.						86	77	80					10																	105207130		2203	4300	6503	SO:0001583	missense	51063	exon4			AGCCAAAGAAGCG	BC000039	CCDS7549.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000138172	ENSG00000138172			23493	protein-coding gene	gene with protein product		612235	"family with sequence similarity 26, member B"	FAM26B		18585350	Standard	NM_015916		Approved		uc001kxa.3	Q9HA72	OTTHUMG00000018990	ENST00000260743.5:c.751T>C	chr10.hg19:g.105207130A>G	ENSP00000260743:p.Phe251Leu	106.0	0.0		107.0	8.0	NM_015916	D3DR94|O95893|Q6ZUV9	Missense_Mutation	SNP	ENST00000260743.5	hg19	CCDS7549.1	.	.	.	.	.	.	.	.	.	.	A	34	5.341577	0.95783	.	.	ENSG00000138172	ENST00000369788;ENST00000260743	T;T	0.56444	0.46;0.46	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.73385	0.3580	M	0.84326	2.69	0.80722	D	1	D	0.69078	0.997	D	0.66497	0.944	T	0.78575	-0.2151	10	0.87932	D	0	-18.8865	15.3625	0.74492	1.0:0.0:0.0:0.0	.	251	Q9HA72	CAHM2_HUMAN	L	251	ENSP00000358803:F251L;ENSP00000260743:F251L	ENSP00000260743:F251L	F	-	1	0	CALHM2	105197120	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.296000	0.89940	2.045000	0.60652	0.459000	0.35465	TTT	.	.		0.617	CALHM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050159.1	NM_015916		G	105207130	A	G	105207130	3	3	155	1	0	0	0	0	1	0	0	0	2585	72	3	2	224	2	CALHM2	10	105207130	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	5511081	105207130	30327617	46	23699										
COL17A1	1308	hgsc.bcm.edu	37	chr10	105803274	105803274	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ctgacctggggcacctggagGtcctgggggtcccatggctc	16	13	0	1	rs543835020	byFrequency	TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr10:105803274G>C	ENST00000353479.5	-	35	2790	c.2500C>G	c.(2500-2502)Cct>Gct	p.P834A	COL17A1_ENST00000369733.3_Missense_Mutation_p.P834A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	834	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GCACCTGGAGGTCCTGGGGGT	0.542																																					p.P834A		Atlas-SNP	.											.	COL17A1	149	.	0			c.C2500G						.						25	27	26					10																	105803274		2203	4300	6503	SO:0001583	missense	1308	exon35			CTGGAGGTCCTGG	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.2500C>G	chr10.hg19:g.105803274G>C	ENSP00000340937:p.Pro834Ala	227.0	0.0		188.0	14.0	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	hg19	CCDS7554.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.879548	0.51801	.	.	ENSG00000065618	ENST00000353479;ENST00000369733	D;D	0.96554	-4.05;-4.05	5.77	5.77	0.91146	.	0.000000	0.46442	D	0.000286	D	0.94608	0.8262	L	0.31476	0.935	0.80722	D	1	D	0.62365	0.991	P	0.58820	0.846	D	0.91037	0.4868	10	0.08179	T	0.78	-9.8049	10.8478	0.46753	0.0848:0.0:0.9152:0.0	.	834	Q9UMD9	COHA1_HUMAN	A	834	ENSP00000340937:P834A;ENSP00000358748:P834A	ENSP00000340937:P834A	P	-	1	0	COL17A1	105793264	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.524000	0.60552	2.724000	0.93272	0.561000	0.74099	CCT	.	.		0.542	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		C	105803274	G	C	105803274	3	2	155	1	0	0	0	0	1	0	0	0	3676	1261	44	4	2081	4	COL17A1	10	105803274	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	596144	105803274	29731473	47	23700										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62290619	62290619	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ccacatcgcccttgactttgGggcccttcaggtttaaatca	8	13	2	1	rs551324364		TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr11:62290619G>A	ENST00000378024.4	-	5	11544	c.11270C>T	c.(11269-11271)cCc>cTc	p.P3757L	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3757					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CTTGACTTTGGGGCCCTTCAG	0.468																																					p.P3757L		Atlas-SNP	.											.	AHNAK	532	.	0			c.C11270T						.						126	129	128					11																	62290619		2202	4299	6501	SO:0001583	missense	79026	exon5			ACTTTGGGGCCCT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11270C>T	chr11.hg19:g.62290619G>A	ENSP00000367263:p.Pro3757Leu	85.0	0.0		89.0	29.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	17.97	3.517346	0.64634	.	.	ENSG00000124942	ENST00000378024	T	0.25912	1.77	5.33	5.33	0.75918	.	0.181406	0.26820	N	0.022337	T	0.67277	0.2876	H	0.96943	3.91	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.79586	-0.1742	10	0.72032	D	0.01	-6.8964	18.6223	0.91326	0.0:0.0:1.0:0.0	.	3757	Q09666	AHNK_HUMAN	L	3757	ENSP00000367263:P3757L	ENSP00000367263:P3757L	P	-	2	0	AHNAK	62047195	1.000000	0.71417	0.331000	0.25455	0.010000	0.07245	5.658000	0.68003	2.493000	0.84123	0.579000	0.79373	CCC	.	.		0.468	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62290619	G	A	62290619	3	1	155	1	0	0	0	0	1	0	0	0	414	1232	43	3	6522	3	AHNAK	11	62290619	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10		62290619	72715897	48	23701										
STIP1	10963	hgsc.bcm.edu	37	chr11	63965043	63965043	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tgaagtggggagagaaaaccGagaagactatcgacagattg	14	5	0	5			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr11:63965043G>A	ENST00000305218.4	+	7	1025	c.878G>A	c.(877-879)cGa>cAa	p.R293Q	STIP1_ENST00000358794.5_Missense_Mutation_p.R340Q|STIP1_ENST00000538945.1_Missense_Mutation_p.R269Q	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	293					response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						AGAGAAAACCGAGAAGACTAT	0.498																																					p.R293Q		Atlas-SNP	.											.	STIP1	63	.	0			c.G878A						.						64	67	66					11																	63965043		2201	4297	6498	SO:0001583	missense	10963	exon7			AAAACCGAGAAGA	BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"Tetratricopeptide (TTC) repeat domain containing"	11387	protein-coding gene	gene with protein product	"Hsp70/Hsp90-organizing protein"	605063	"stress-induced-phosphoprotein 1"			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.878G>A	chr11.hg19:g.63965043G>A	ENSP00000305958:p.Arg293Gln	81.0	0.0		111.0	14.0	NM_006819	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Missense_Mutation	SNP	ENST00000305218.4	hg19	CCDS8058.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.049361	0.93740	.	.	ENSG00000168439	ENST00000358794;ENST00000305218;ENST00000538945	T;T;T	0.16073	2.38;2.62;2.37	5.73	5.73	0.89815	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.19087	0.0458	M	0.67517	2.055	0.80722	D	1	P;P	0.46784	0.884;0.815	B;B	0.30646	0.118;0.072	T	0.05903	-1.0857	10	0.45353	T	0.12	-8.0877	19.059	0.93080	0.0:0.0:1.0:0.0	.	269;293	F5H0T1;P31948	.;STIP1_HUMAN	Q	340;293;269	ENSP00000351646:R340Q;ENSP00000305958:R293Q;ENSP00000445957:R269Q	ENSP00000305958:R293Q	R	+	2	0	STIP1	63721619	1.000000	0.71417	0.993000	0.49108	0.991000	0.79684	7.320000	0.79064	2.882000	0.98803	0.655000	0.94253	CGA	.	.		0.498	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819		A	63965043	G	A	63965043	3	1	155	1	0	0	0	0	1	0	0	0	15300	1058	37	1	904	1	STIP1	11	63965043	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	1674424	63965043	71041473	49	23702										
SYVN1	84447	hgsc.bcm.edu	37	chr11	64898776	64898776	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gtacatgggccggatggcaaAgagtgggaaggtgtgcacct	17	7	0	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr11:64898776A>G	ENST00000377190.3	-	8	821	c.727T>C	c.(727-729)Ttt>Ctt	p.F243L	SYVN1_ENST00000294256.8_Missense_Mutation_p.F243L|SYVN1_ENST00000307289.6_Missense_Mutation_p.F192L|SYVN1_ENST00000526121.1_5'UTR|SYVN1_ENST00000526060.1_Missense_Mutation_p.F243L	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	243	Interaction with p53/TP53.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						CGGATGGCAAAGAGTGGGAAG	0.582																																					p.F243L		Atlas-SNP	.											.	SYVN1	55	.	0			c.T727C						.						124	110	115					11																	64898776		2201	4297	6498	SO:0001583	missense	84447	exon8			TGGCAAAGAGTGG	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"RING-type (C3HC4) zinc fingers"	20738	protein-coding gene	gene with protein product	"HMG-coA reductase degradation 1 homolog (S. cerevisiae)"	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.727T>C	chr11.hg19:g.64898776A>G	ENSP00000366395:p.Phe243Leu	120.0	0.0		127.0	41.0	NM_172230	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Missense_Mutation	SNP	ENST00000377190.3	hg19	CCDS31605.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.852810	0.91355	.	.	ENSG00000162298	ENST00000377190;ENST00000294256;ENST00000434219;ENST00000307289;ENST00000526060;ENST00000531018;ENST00000528487	T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.63827	0.2544	M	0.84948	2.725	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.998	D;D;D	0.76071	0.978;0.987;0.979	T	0.64901	-0.6298	10	0.14656	T	0.56	-10.7716	12.7103	0.57086	1.0:0.0:0.0:0.0	.	192;243;243	Q86TM6-2;Q86TM6-3;Q86TM6	.;.;SYVN1_HUMAN	L	243;243;243;192;243;183;228	ENSP00000366395:F243L;ENSP00000294256:F243L;ENSP00000302035:F192L;ENSP00000436984:F243L;ENSP00000431215:F183L;ENSP00000431720:F228L	ENSP00000294256:F243L	F	-	1	0	SYVN1	64655352	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	8.973000	0.93428	1.883000	0.54544	0.460000	0.39030	TTT	.	.		0.582	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431		G	64898776	A	G	64898776	3	3	155	1	0	0	0	0	1	0	0	0	15502	72	3	2	1162	2	SYVN1	11	64898776	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	933733	64898776	70107740	50	23703										
PRCP	5547	hgsc.bcm.edu	37	chr11	82536165	82536165	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aggggtctagttcaccattgCtgcaagtgaaaaaaagaaga	11	6	2	3			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr11:82536165C>T	ENST00000313010.3	-	9	1469		c.e9-1		PRCP_ENST00000535099.1_Splice_Site|PRCP_ENST00000525772.1_Splice_Site|PRCP_ENST00000393399.2_Splice_Site	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)						angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						TTCACCATTGCTGCAAGTGAA	0.393																																					.		Atlas-SNP	.											.	PRCP	69	.	0			c.1275-1G>A						.						52	48	49					11																	82536165		2203	4300	6503	SO:0001630	splice_region_variant	5547	exon10			CCATTGCTGCAAG	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.1275-1G>A	chr11.hg19:g.82536165C>T		71.0	0.0		58.0	15.0	NM_005040	A8MU24|B2R7B7|B3KRK5|B5BU34	Splice_Site	SNP	ENST00000313010.3	hg19	CCDS8262.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.008138	0.75046	.	.	ENSG00000137509	ENST00000313010;ENST00000393399;ENST00000535099	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2129	0.93765	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRCP	82213813	1.000000	0.71417	0.998000	0.56505	0.881000	0.50899	6.484000	0.73621	2.629000	0.89072	0.467000	0.42956	.	.	.		0.393	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040	Intron	T	82536165	C	T	82536165	5	4	155	1	0	0	0	0	0	0	1	0	12461	811	28	3	220	3	PRCP	11	82536165	Splice_Site	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	17637389	82536165	52470351	51	23704										
C11orf73	51501	hgsc.bcm.edu	37	chr11	86017465	86017465	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aatgccagtatggcaactccTaggatttgtcacgaatggga	11	8	1	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr11:86017465T>G	ENST00000278483.3	+	2	435	c.209T>G	c.(208-210)cTa>cGa	p.L70R	C11orf73_ENST00000533986.1_Missense_Mutation_p.L70R|C11orf73_ENST00000530208.1_3'UTR	NM_016401.3	NP_057485.2	Q53FT3	HIKES_HUMAN	chromosome 11 open reading frame 73	70					cellular response to heat (GO:0034605)|Golgi organization (GO:0007030)|lung development (GO:0030324)|protein import into nucleus (GO:0006606)|protein transport (GO:0015031)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	Hsp70 protein binding (GO:0030544)|protein transporter activity (GO:0008565)			kidney(1)|large_intestine(1)|urinary_tract(1)	3		Acute lymphoblastic leukemia(157;1.17e-07)|all_hematologic(158;0.000556)				TGGCAACTCCTAGGATTTGTC	0.368																																					p.L70R		Atlas-SNP	.											.	C11orf73	9	.	0			c.T209G						.						64	65	65					11																	86017465		2202	4299	6501	SO:0001583	missense	51501	exon2			AACTCCTAGGATT	BC015991	CCDS8275.1	11q14.2	2013-03-12			ENSG00000149196	ENSG00000149196			26938	protein-coding gene	gene with protein product		614908				11042152, 22541429	Standard	NM_016401		Approved	HSPC138, HSPC179, Hikeshi, OPI10	uc001pbu.3	Q53FT3	OTTHUMG00000167212	ENST00000278483.3:c.209T>G	chr11.hg19:g.86017465T>G	ENSP00000278483:p.Leu70Arg	70.0	0.0		72.0	29.0	NM_016401	Q8WVE8|Q9NVQ2|Q9NZZ1|Q9P022|Q9P0N1	Missense_Mutation	SNP	ENST00000278483.3	hg19	CCDS8275.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185282	0.78677	.	.	ENSG00000149196	ENST00000533986;ENST00000278483	T;T	0.58210	0.35;0.35	5.07	5.07	0.68467	.	0.000000	0.64402	D	0.000001	T	0.79358	0.4432	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.85384	0.1121	9	.	.	.	-18.5147	15.1285	0.72500	0.0:0.0:0.0:1.0	.	70;70	Q53FT3;E9PPG8	CK073_HUMAN;.	R	70	ENSP00000432699:L70R;ENSP00000278483:L70R	.	L	+	2	0	C11orf73	85695113	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.521000	0.81832	2.042000	0.60477	0.533000	0.62120	CTA	.	.		0.368	C11orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393747.1	NM_016401		G	86017465	T	G	86017465	3	3	155	1	0	0	0	0	1	0	0	0	1663	1522	53	5	215	5	C11orf73	11	86017465	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	3481300	86017465	48989051	52	23705										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26731667	26731667	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	cacttcagccaaagttctgaTacaggattccactgaggctt	8	11	2	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr12:26731667T>C	ENST00000381340.3	-	34	5025	c.4609A>G	c.(4609-4611)Atc>Gtc	p.I1537V		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1537					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	AAAGTTCTGATACAGGATTCC	0.408																																					p.I1537V		Atlas-SNP	.											.	ITPR2	270	.	0			c.A4609G						.						135	131	132					12																	26731667		1844	4091	5935	SO:0001583	missense	3709	exon34			TTCTGATACAGGA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4609A>G	chr12.hg19:g.26731667T>C	ENSP00000370744:p.Ile1537Val	113.0	0.0		115.0	38.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	T	13.21	2.167694	0.38315	.	.	ENSG00000123104	ENST00000381340	T	0.68903	-0.36	5.12	3.98	0.46160	.	0.099123	0.64402	D	0.000002	T	0.62368	0.2422	M	0.64404	1.975	0.80722	D	1	B	0.14438	0.01	B	0.18263	0.021	T	0.60177	-0.7314	10	0.51188	T	0.08	.	10.6123	0.45429	0.0:0.0752:0.0:0.9248	.	1537	Q14571	ITPR2_HUMAN	V	1537	ENSP00000370744:I1537V	ENSP00000370744:I1537V	I	-	1	0	ITPR2	26622934	1.000000	0.71417	0.926000	0.36857	0.793000	0.44817	5.800000	0.69108	0.979000	0.38497	0.477000	0.44152	ATC	.	.		0.408	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		C	26731667	T	C	26731667	3	2	155	1	0	0	0	0	1	0	0	0	7930	1406	49	2	3592	2	ITPR2	12	26731667	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10		26731667	107120228	53	23706										
ARID2	196528	hgsc.bcm.edu	37	chr12	46246408	46246408	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ccattctcctgccctatcatCtgacgttcggtctacaaatg	6	14	4	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr12:46246408C>T	ENST00000334344.6	+	15	4674	c.4502C>T	c.(4501-4503)tCt>tTt	p.S1501F	ARID2_ENST00000457135.1_Missense_Mutation_p.S109F|ARID2_ENST00000444670.1_Missense_Mutation_p.S1111F|ARID2_ENST00000422737.1_Missense_Mutation_p.S1352F|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1501					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GCCCTATCATCTGACGTTCGG	0.443			"N, S, F"		hepatocellular carcinoma																																p.S1501F		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.C4502T						.						106	100	102					12																	46246408		2203	4300	6503	SO:0001583	missense	196528	exon15			TATCATCTGACGT		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4502C>T	chr12.hg19:g.46246408C>T	ENSP00000335044:p.Ser1501Phe	161.0	0.0		189.0	62.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.773481	0.49786	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670;ENST00000457135	T	0.35973	1.28	6.02	6.02	0.97574	.	0.234273	0.45126	D	0.000388	T	0.35566	0.0936	N	0.24115	0.695	0.50313	D	0.999861	B;B;B	0.33857	0.25;0.429;0.412	B;B;B	0.40228	0.323;0.323;0.172	T	0.07654	-1.0761	10	0.44086	T	0.13	-7.333	20.5407	0.99260	0.0:1.0:0.0:0.0	.	1501;1111;1501	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	F	1501;618;618;1352;1111;109	ENSP00000335044:S1501F	ENSP00000335044:S1501F	S	+	2	0	ARID2	44532675	1.000000	0.71417	0.990000	0.47175	0.968000	0.65278	7.043000	0.76572	2.865000	0.98341	0.655000	0.94253	TCT	.	.		0.443	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46246408	C	T	46246408	3	4	155	1	0	0	0	0	1	0	0	0	915	913	32	3	4560	3	ARID2	12	46246408	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	19514741	46246408	87605487	54	23707										
WNT10B	7480	hgsc.bcm.edu	37	chr12	49364298	49364298	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gagggcggaggccgcggccgGggctcctccagcatgtcgaa	18	13	0	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr12:49364298G>A	ENST00000301061.4	-	2	363	c.15C>T	c.(13-15)ccC>ccT	p.P5P	WNT10B_ENST00000407467.1_Silent_p.P5P|WNT10B_ENST00000403957.1_Silent_p.P5P	NM_003394.3	NP_003385.2	O00744	WN10B_HUMAN	wingless-type MMTV integration site family, member 10B	5					bone trabecula formation (GO:0060346)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to cAMP (GO:0071320)|cellular response to hydrostatic pressure (GO:0071464)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fungiform papilla development (GO:0061196)|G2/M transition of mitotic cell cycle (GO:0000086)|hematopoietic stem cell proliferation (GO:0071425)|lipid metabolic process (GO:0006629)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of anagen (GO:0051885)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of skeletal muscle tissue development (GO:0048641)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			central_nervous_system(1)|large_intestine(5)|lung(12)|prostate(1)|skin(4)	23						GCCGCGGCCGGGGCTCCTCCA	0.672																																					p.P5P		Atlas-SNP	.											.	WNT10B	41	.	0			c.C15T						.						8	13	12					12																	49364298		2173	4264	6437	SO:0001819	synonymous_variant	7480	exon2			CGGCCGGGGCTCC	X97057	CCDS8775.1	12q13	2009-01-02			ENSG00000169884	ENSG00000169884		"Wingless-type MMTV integration sites"	12775	protein-coding gene	gene with protein product		601906				9121776, 9284937, 18515319	Standard	NM_003394		Approved	WNT-12, SHFM6	uc001rss.3	O00744	OTTHUMG00000150734	ENST00000301061.4:c.15C>T	chr12.hg19:g.49364298G>A		388.0	0.0		398.0	128.0	NM_003394	B2R7A5|O00747|Q4VAJ4|Q4VAJ5|Q8WZ97	Silent	SNP	ENST00000301061.4	hg19	CCDS8775.1																																																																																			.	.		0.672	WNT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319864.1	NM_003394		A	49364298	G	A	49364298	2	1	155	1	0	0	0	0	0	0	0	1	17398	1219	43	3		3	WNT10B	12	49364298	Silent	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	3117890	49364298	84487597	55	23708										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56488188	56488188	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	cttctctcttccactcagggCtctgatacttgtgctcaatg	7	13	5	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr12:56488188C>A	ENST00000267101.3	+	15	2147	c.1707C>A	c.(1705-1707)ggC>ggA	p.G569G	ERBB3_ENST00000553131.1_5'Flank|ERBB3_ENST00000415288.2_Silent_p.G510G|ERBB3_ENST00000450146.2_Intron	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	569					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CCACTCAGGGCTCTGATACTT	0.522																																					p.G569G		Atlas-SNP	.											.	ERBB3	350	.	0			c.C1707A						.						115	120	118					12																	56488188		2203	4300	6503	SO:0001819	synonymous_variant	2065	exon15			TCAGGGCTCTGAT	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.1707C>A	chr12.hg19:g.56488188C>A		37.0	0.0		24.0	7.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Silent	SNP	ENST00000267101.3	hg19	CCDS31833.1																																																																																			.	.		0.522	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			A	56488188	C	A	56488188	2	1	155	1	0	0	0	0	0	0	0	1	5210	784	28	3		3	ERBB3	12	56488188	Silent	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	7123890	56488188	77363707	56	23709										
PIP4K2C	79837	hgsc.bcm.edu	37	chr12	57995105	57995105	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	atgctaagaagaaagcagctCatgcagccaaaactgtcaag	9	9	2	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr12:57995105C>A	ENST00000354947.5	+	9	1175	c.1159C>A	c.(1159-1161)Cat>Aat	p.H387N	PIP4K2C_ENST00000550465.1_Missense_Mutation_p.H369N|PIP4K2C_ENST00000540759.2_Missense_Mutation_p.H387N|PIP4K2C_ENST00000422156.3_Missense_Mutation_p.H339N			Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, gamma	387	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(13)|pancreas(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Melanoma(17;0.122)					GAAAGCAGCTCATGCAGCCAA	0.473																																					p.H387N		Atlas-SNP	.											.	PIP4K2C	50	.	0			c.C1159A						.						76	79	78					12																	57995105		2203	4300	6503	SO:0001583	missense	79837	exon9			GCAGCTCATGCAG	AK125526	CCDS8946.1, CCDS53808.1, CCDS55839.1	12q13.3	2014-09-04	2007-08-14	2007-08-14	ENSG00000166908	ENSG00000166908			23786	protein-coding gene	gene with protein product			"phosphatidylinositol-4-phosphate 5-kinase, type II, gamma"	PIP5K2C		9367159	Standard	NM_024779		Approved	FLJ22055	uc001sot.3	Q8TBX8	OTTHUMG00000170144	ENST00000354947.5:c.1159C>A	chr12.hg19:g.57995105C>A	ENSP00000347032:p.His387Asn	129.0	0.0		119.0	31.0	NM_001146258	B2RDL3|B4DM11|B4DY44|Q9H6N2	Missense_Mutation	SNP	ENST00000354947.5	hg19	CCDS8946.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.588983	0.66105	.	.	ENSG00000166908	ENST00000422156;ENST00000540759;ENST00000550465;ENST00000354947	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	4.56	4.56	0.56223	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.55386	0.1917	M	0.75264	2.295	0.58432	D	0.999998	P;B;D	0.67145	0.877;0.41;0.996	P;B;D	0.70487	0.781;0.349;0.969	T	0.59048	-0.7527	10	0.56958	D	0.05	-14.9835	16.6342	0.85042	0.0:1.0:0.0:0.0	.	339;369;387	B4DM11;B4DY44;Q8TBX8	.;.;PI42C_HUMAN	N	339;387;369;387	ENSP00000412035:H339N;ENSP00000439878:H387N;ENSP00000447390:H369N;ENSP00000347032:H387N	ENSP00000347032:H387N	H	+	1	0	PIP4K2C	56281372	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.188000	0.77739	2.534000	0.85438	0.655000	0.94253	CAT	.	.		0.473	PIP4K2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407644.1	NM_024779		A	57995105	C	A	57995105	3	1	155	1	0	0	0	0	1	0	0	0	11947	826	29	3	1193	3	PIP4K2C	12	57995105	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	1506917	57995105	75856790	57	23710										
IFNG	3458	hgsc.bcm.edu	37	chr12	68551852	68551852	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	taaaaggagacaatttggctCtgcattatttttctgtcact	7	7	3	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr12:68551852C>T	ENST00000229135.3	-	3	338	c.207G>A	c.(205-207)caG>caA	p.Q69Q	IFNG-AS1_ENST00000536914.1_RNA	NM_000619.2	NP_000610.2	P01579	IFNG_HUMAN	interferon, gamma	69					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell cycle arrest (GO:0007050)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to interleukin-18 (GO:0071351)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|extrinsic apoptotic signaling pathway (GO:0097191)|humoral immune response (GO:0006959)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of myelination (GO:0031642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil apoptotic process (GO:0001781)|neutrophil chemotaxis (GO:0030593)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity (GO:0060550)|positive regulation of fructose 1,6-bisphosphate metabolic process (GO:0060552)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|regulation of insulin secretion (GO:0050796)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of the force of heart contraction (GO:0002026)|response to drug (GO:0042493)|response to virus (GO:0009615)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|interferon-gamma receptor binding (GO:0005133)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Glucosamine(DB01296)|Olsalazine(DB01250)	CAATTTGGCTCTGCATTATTT	0.373																																					p.Q69Q		Atlas-SNP	.											.	IFNG	38	.	0			c.G207A						.						85	86	85					12																	68551852		2202	4300	6502	SO:0001819	synonymous_variant	3458	exon3			TTGGCTCTGCATT		CCDS8980.1	12q14	2007-10-17			ENSG00000111537	ENSG00000111537		"Interferons"	5438	protein-coding gene	gene with protein product		147570					Standard	NM_000619		Approved		uc001stw.1	P01579	OTTHUMG00000169113	ENST00000229135.3:c.207G>A	chr12.hg19:g.68551852C>T		78.0	0.0		79.0	20.0	NM_000619	B5BU88|Q53ZV4	Silent	SNP	ENST00000229135.3	hg19	CCDS8980.1																																																																																			.	.		0.373	IFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402301.1			T	68551852	C	T	68551852	2	4	155	1	0	0	0	0	0	0	0	1	7557	912	32	3		3	IFNG	12	68551852	Silent	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	10556747	68551852	65300043	58	23711										
ACAD10	80724	hgsc.bcm.edu	37	chr12	112147442	112147443	+	Frame_Shift_Ins	INS	-	-	AACAAATCTAA													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	atctttcttgatgaccttggINSaacaaatctaaaagaagctg					rs375834504		TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr12:112147442_112147443insAACAAATCTAA	ENST00000313698.4	+	5	799_800	c.644_645insAACAAATCTAA	c.(643-648)ggaacafs	p.-219fs	ACAD10_ENST00000413681.3_3'UTR|ACAD10_ENST00000392636.2_5'UTR|ACAD10_ENST00000549590.1_Frame_Shift_Ins_p.-219fs|ACAD10_ENST00000455480.2_Frame_Shift_Ins_p.-219fs	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10							mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						GATGACCTTGGAACAAATCTAA	0.47																																					p.G215fs		Atlas-INDEL	.											.	ACAD10	93	.	0			c.644_645insAACAAATCTAA						.																																			SO:0001589	frameshift_variant	80724	exon5			.	AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"acyl-Coenzyme A dehydrogenase family, member 10"			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.645_655dupAACAAATCTAA	chr12.hg19:g.112147443_112147453dupAACAAATCTAA	ENSP00000325137:p.Lys219fs	88.0	0.0		118.0	13.0	NM_001136538	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Frame_Shift_Ins	INS	ENST00000313698.4	hg19	CCDS31903.1																																																																																			.	.		0.47	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		AACAAATCTAA	112147443	-	AACAAATCTAA	112147442	7	5	155	1	0	1	1	0	0	0	0	0	108	1174	41	0	658	0	ACAD10	12	112147442	Frame_Shift_Ins	INS	-	TCGA-DD-AACD-01A-11D-A40R-10	43595590	112147442	21704453	59	23712										
NOS1	4842	hgsc.bcm.edu	37	chr12	117723914	117723914	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gacttcaccacctacctgcaGcttggaccactggatcctgc	8	16	1	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr12:117723914G>C	ENST00000338101.4	-	5	1289	c.1285C>G	c.(1285-1287)Ctg>Gtg	p.L429V	NOS1_ENST00000317775.6_Missense_Mutation_p.L429V|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CCTACCTGCAGCTTGGACCAC	0.537																																					p.L429V	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C1285G						.						118	118	118					12																	117723914		2168	4293	6461	SO:0001583	missense	4842	exon6			CCTGCAGCTTGGA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1285C>G	chr12.hg19:g.117723914G>C	ENSP00000337459:p.Leu429Val	77.0	0.0		79.0	32.0	NM_000620		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.998288	0.74818	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.59364	0.27;0.27	4.93	4.93	0.64822	Nitric oxide synthase, oxygenase domain (3);	0.000000	0.64402	D	0.000001	T	0.80363	0.4609	H	0.96142	3.775	0.80722	D	1	P	0.48230	0.907	P	0.53313	0.723	D	0.87174	0.2223	10	0.87932	D	0	-11.4483	18.3299	0.90264	0.0:0.0:1.0:0.0	.	429	P29475	NOS1_HUMAN	V	429	ENSP00000320758:L429V;ENSP00000337459:L429V	ENSP00000320758:L429V	L	-	1	2	NOS1	116208297	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.427000	0.66483	2.559000	0.86315	0.591000	0.81541	CTG	.	.		0.537	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			C	117723914	G	C	117723914	3	2	155	1	0	0	0	0	1	0	0	0	10550	962	34	4	3115	4	NOS1	12	117723914	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	5576472	117723914	16127981	60	23713										
GPR183	1880	hgsc.bcm.edu	37	chr13	99947896	99947896	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tcctgctttgacatagggttGatgaggagtgggagtgtctg	16	5	1	3			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr13:99947896G>A	ENST00000376414.4	-	2	587	c.504C>T	c.(502-504)atC>atT	p.I168I	UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	168					G-protein coupled receptor signaling pathway (GO:0007186)|humoral immune response (GO:0006959)|immune response (GO:0006955)|mature B cell differentiation involved in immune response (GO:0002313)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|oxysterol binding (GO:0008142)			cervix(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	23						ACATAGGGTTGATGAGGAGTG	0.428																																					p.I168I		Atlas-SNP	.											.	GPR183	38	.	0			c.C504T						.						125	105	112					13																	99947896		2203	4300	6503	SO:0001819	synonymous_variant	1880	exon2			AGGGTTGATGAGG	L08177	CCDS9492.1	13q32.3	2012-08-21	2008-07-21	2008-07-21	ENSG00000169508	ENSG00000169508		"GPCR / Class A : Orphans"	3128	protein-coding gene	gene with protein product	"EBV-induced G-protein coupled receptor 2"	605741	"Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor)"	EBI2		8383238	Standard	NM_004951		Approved		uc001vog.3	P32249	OTTHUMG00000017263	ENST00000376414.4:c.504C>T	chr13.hg19:g.99947896G>A		95.0	0.0		119.0	25.0	NM_004951	B2R8N5|Q53F99|Q5JUH7	Silent	SNP	ENST00000376414.4	hg19	CCDS9492.1																																																																																			.	.		0.428	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045582.2	NM_004951		A	99947896	G	A	99947896	2	1	155	1	0	0	0	0	0	0	0	1	6686	1280	45	3		3	GPR183	13	99947896	Silent	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10		99947896	15221982	61	23714										
OR10G2	26534	hgsc.bcm.edu	37	chr14	22102622	22102622	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gacatattgctaggtacctgTcataggccatcaaggtgtag	11	8	2	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr14:22102622T>G	ENST00000542433.1	-	1	474	c.377A>C	c.(376-378)gAc>gCc	p.D126A		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		TAGGTACCTGTCATAGGCCAT	0.542																																					p.D126A		Atlas-SNP	.											.	OR10G2	35	.	0			c.A377C						.						38	43	41					14																	22102622		2203	4294	6497	SO:0001583	missense	26534	exon1			TACCTGTCATAGG		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"GPCR / Class A : Olfactory receptors"	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.377A>C	chr14.hg19:g.22102622T>G	ENSP00000445383:p.Asp126Ala	302.0	0.0		259.0	76.0	NM_001005466	B2RPD0	Missense_Mutation	SNP	ENST00000542433.1	hg19	CCDS32047.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.445246	0.63178	.	.	ENSG00000255582	ENST00000542433	T	0.55413	0.52	3.78	3.78	0.43462	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45867	D	0.000323	T	0.81221	0.4777	H	0.98487	4.245	0.40470	D	0.980331	D	0.89917	1.0	D	0.87578	0.998	D	0.86602	0.1867	10	0.87932	D	0	-12.9343	10.4989	0.44794	0.0:0.0:0.0:1.0	.	126	Q8NGC3	O10G2_HUMAN	A	126	ENSP00000445383:D126A	ENSP00000445383:D126A	D	-	2	0	OR10G2	21172462	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.606000	0.82863	1.582000	0.49881	0.455000	0.32223	GAC	.	.		0.542	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1			G	22102622	T	G	22102622	3	3	155	1	0	0	0	0	1	0	0	0	10908	1667	58	5	558	5	OR10G2	14	22102622	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10		22102622	85246918	62	23715										
SPATA7	55812	hgsc.bcm.edu	37	chr14	88892812	88892812	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gccctgtatggcagaaggccCagaagcacattcccaaattc	9	13	0	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr14:88892812C>G	ENST00000393545.4	+	6	898	c.609C>G	c.(607-609)ccC>ccG	p.P203P	SPATA7_ENST00000045347.7_Silent_p.P203P|SPATA7_ENST00000556553.1_Silent_p.P171P|SPATA7_ENST00000356583.5_Silent_p.P171P	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	203					response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						GCAGAAGGCCCAGAAGCACAT	0.507																																					p.P203P		Atlas-SNP	.											.	SPATA7	58	.	0			c.C609G						.						62	60	61					14																	88892812		2203	4300	6503	SO:0001819	synonymous_variant	55812	exon6			AAGGCCCAGAAGC	AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"Leber congenital amaurosis 3"	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.609C>G	chr14.hg19:g.88892812C>G		144.0	0.0		134.0	35.0	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Silent	SNP	ENST00000393545.4	hg19	CCDS9883.1																																																																																			.	.		0.507	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1			G	88892812	C	G	88892812	2	3	155	1	0	0	0	0	0	0	0	1	15029	581	21	4		4	SPATA7	14	88892812	Silent	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	66790190	88892812	18456728	63	23716										
BLM	641	hgsc.bcm.edu	37	chr15	91358483	91358483	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	agcctataaatagaccgtttCttaagccttcatatgcattc	5	10	2	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr15:91358483C>A	ENST00000355112.3	+	22	4346	c.4228C>A	c.(4228-4230)Ctt>Att	p.L1410I	BLM_ENST00000560509.1_Missense_Mutation_p.L1279I	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1410					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TAGACCGTTTCTTAAGCCTTC	0.423			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.L1410I		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	.	BLM	122	.	0			c.C4228A						.						141	133	135					15																	91358483		2198	4298	6496	SO:0001583	missense	641	exon22	Familial Cancer Database		CCGTTTCTTAAGC	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"Bloom syndrome"			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.4228C>A	chr15.hg19:g.91358483C>A	ENSP00000347232:p.Leu1410Ile	89.0	0.0		89.0	10.0	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	hg19	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.443626	0.43429	.	.	ENSG00000197299	ENST00000355112;ENST00000536925	T	0.61627	0.09	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.77798	0.4184	M	0.77103	2.36	0.28434	N	0.91713	D;D	0.69078	0.997;0.997	D;D	0.78314	0.991;0.991	T	0.73408	-0.3992	10	0.87932	D	0	-6.0224	18.3732	0.90420	0.0:1.0:0.0:0.0	.	1410;1410	B2RAN0;P54132	.;BLM_HUMAN	I	1410;1040	ENSP00000347232:L1410I	ENSP00000347232:L1410I	L	+	1	0	BLM	89159487	1.000000	0.71417	0.593000	0.28771	0.132000	0.20833	4.695000	0.61767	2.941000	0.99782	0.655000	0.94253	CTT	.	.		0.423	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			A	91358483	C	A	91358483	3	1	155	1	0	0	0	0	1	0	0	0	1445	913	32	3	4310	3	BLM	15	91358483	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10		91358483	11172909	64	23717										
ADAMTS17	170691	hgsc.bcm.edu	37	chr15	100514721	100514721	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ttcttttctcggatgacccgGcaatataccgtccactggtc	8	13	2	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr15:100514721G>A	ENST00000268070.4	-	22	3279	c.3174C>T	c.(3172-3174)tgC>tgT	p.C1058C	CTD-3076O17.1_ENST00000528696.3_RNA|CTD-3076O17.2_ENST00000559400.1_RNA	NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	1058	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		GGATGACCCGGCAATATACCG	0.562																																					p.C1058C		Atlas-SNP	.											.	ADAMTS17	127	.	0			c.C3174T						.						117	94	102					15																	100514721		2203	4300	6503	SO:0001819	synonymous_variant	170691	exon22			GACCCGGCAATAT	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.3174C>T	chr15.hg19:g.100514721G>A		95.0	0.0		84.0	26.0	NM_139057	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	hg19	CCDS10383.1																																																																																			.	.		0.562	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		A	100514721	G	A	100514721	2	1	155	1	0	0	0	0	0	0	0	1	262	1195	42	3		3	ADAMTS17	15	100514721	Silent	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	9156238	100514721	2016671	65	23718										
TPSD1	23430	hgsc.bcm.edu	37	chr16	1306936	1306936	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	accggggcggacatcgccctGctggagctggaggagcccgt	17	13	0	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr16:1306936G>T	ENST00000211076.3	+	3	541	c.393G>T	c.(391-393)ctG>ctT	p.L131L	TPSD1_ENST00000397534.2_Silent_p.L124L|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	131	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				ACATCGCCCTGCTGGAGCTGG	0.652																																					p.L131L		Atlas-SNP	.											.	TPSD1	47	.	0			c.G393T						.						65	65	65					16																	1306936		2199	4300	6499	SO:0001819	synonymous_variant	23430	exon3			CGCCCTGCTGGAG	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"mMCP-7-like II", "mMCP-7-like I", "MMCP-7-LIKE-2"	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.393G>T	chr16.hg19:g.1306936G>T		266.0	0.0		293.0	47.0	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	hg19	CCDS10432.1																																																																																			.	.		0.652	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2			T	1306936	G	T	1306936	2	4	155	1	0	0	0	0	0	0	0	1	16440	1306	46	3		3	TPSD1	16	1306936	Silent	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10		1306936	89047817	66	23719										
PRKCB	5579	hgsc.bcm.edu	37	chr16	24202547	24202547	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ccagcccccttataagccaaAagctgtaagtagcccattct	6	14	1	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr16:24202547A>T	ENST00000321728.7	+	16	2034	c.1859A>T	c.(1858-1860)aAa>aTa	p.K620I	PRKCB_ENST00000303531.7_Missense_Mutation_p.K620I	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	620	AGC-kinase C-terminal.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	TATAAGCCAAAAGCTGTAAGT	0.473																																					p.K620I		Atlas-SNP	.											.	PRKCB	383	.	0			c.A1859T						.						106	111	109					16																	24202547		2197	4300	6497	SO:0001583	missense	5579	exon16			AGCCAAAAGCTGT	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"protein kinase C, beta 1"	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.1859A>T	chr16.hg19:g.24202547A>T	ENSP00000318315:p.Lys620Ile	112.0	0.0		101.0	37.0	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	hg19	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.687970	0.88639	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	T;T	0.55234	0.53;0.53	5.73	5.73	0.89815	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.107337	0.64402	D	0.000010	T	0.63896	0.2550	M	0.89095	3.005	0.58432	D	0.999999	B;B	0.09022	0.002;0.001	B;B	0.28849	0.058;0.095	T	0.66148	-0.5996	10	0.87932	D	0	.	13.9858	0.64334	1.0:0.0:0.0:0.0	.	620;620	P05771-2;P05771	.;KPCB_HUMAN	I	620	ENSP00000318315:K620I;ENSP00000305355:K620I	ENSP00000305355:K620I	K	+	2	0	PRKCB	24110048	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.497000	0.53295	2.189000	0.69895	0.528000	0.53228	AAA	.	.		0.473	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		T	24202547	A	T	24202547	3	4	155	1	0	0	0	0	1	0	0	0	12520	14	1	4	1921	4	PRKCB	16	24202547	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	22895611	24202547	66152206	67	23720										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31409166	31409166	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ggggagaactcatactcaaaGggttcctgcctcctgctggg	13	11	2	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr16:31409166G>C	ENST00000389202.2	+	5	412	c.363G>C	c.(361-363)aaG>aaC	p.K121N		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	121					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CATACTCAAAGGGTTCCTGCC	0.642																																					p.K121N		Atlas-SNP	.											.	ITGAD	154	.	0			c.G363C						.						42	38	39					16																	31409166		2197	4300	6497	SO:0001583	missense	3681	exon5			CTCAAAGGGTTCC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.363G>C	chr16.hg19:g.31409166G>C	ENSP00000373854:p.Lys121Asn	41.0	0.0		36.0	13.0	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.143|1.143	-0.649007|-0.649007	0.03506|0.03506	.|.	.|.	ENSG00000156886|ENSG00000156886	ENST00000444228;ENST00000389202|ENST00000316569	T|.	0.70516|.	-0.49|.	4.19|4.19	-0.674|-0.674	0.11369|0.11369	.|.	.|.	.|.	.|.	.|.	T|T	0.10551|0.10551	0.0258|0.0258	N|N	0.02412|0.02412	-0.56|-0.56	0.09310|0.09310	N|N	1|1	B;B;B|.	0.17268|.	0.021;0.007;0.004|.	B;B;B|.	0.18871|.	0.023;0.004;0.004|.	T|T	0.22452|0.22452	-1.0216|-1.0216	9|6	0.08599|0.46703	T|T	0.76|0.11	.|.	3.8259|3.8259	0.08853|0.08853	0.3627:0.0:0.4411:0.1962|0.3627:0.0:0.4411:0.1962	.|.	121;137;121|.	B7Z6V7;Q59H14;Q13349|.	.;.;ITAD_HUMAN|.	N|T	137;121|29	ENSP00000373854:K121N|.	ENSP00000373854:K121N|ENSP00000323325:R29T	K|R	+|+	3|2	2|0	ITGAD|ITGAD	31316667|31316667	0.001000|0.001000	0.12720|0.12720	0.128000|0.128000	0.21923|0.21923	0.213000|0.213000	0.24496|0.24496	-1.093000|-1.093000	0.03362|0.03362	-0.037000|-0.037000	0.13646|0.13646	-0.302000|-0.302000	0.09304|0.09304	AAG|AGG	.	.		0.642	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		C	31409166	G	C	31409166	3	2	155	1	0	0	0	0	1	0	0	0	7893	991	35	4	381	4	ITGAD	16	31409166	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	7206619	31409166	58945587	68	23721										
HSF4	3299	hgsc.bcm.edu	37	chr16	67201742	67201742	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gacagcccccccgccactgcCtgtggctgtggtgcaggcca	13	17	0	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr16:67201742C>A	ENST00000521374.1	+	9	974	c.974C>A	c.(973-975)cCt>cAt	p.P325H	HSF4_ENST00000421453.1_Missense_Mutation_p.P295H|HSF4_ENST00000264009.8_Missense_Mutation_p.P325H|NOL3_ENST00000564053.1_5'Flank|HSF4_ENST00000584272.1_Missense_Mutation_p.P295H|NOL3_ENST00000432069.2_5'Flank			Q9ULV5	HSF4_HUMAN	heat shock transcription factor 4	325					camera-type eye development (GO:0043010)|cell development (GO:0048468)|histone H3-K9 demethylation (GO:0033169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotrimerization (GO:0070207)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		CCGCCACTGCCTGTGGCTGTG	0.667																																					p.P325H		Atlas-SNP	.											.	HSF4	33	.	0			c.C974A						.						11	18	16					16																	67201742		1892	4092	5984	SO:0001583	missense	3299	exon11			CACTGCCTGTGGC	D87673	CCDS42175.1, CCDS45510.1	16q21	2013-01-22			ENSG00000102878	ENSG00000102878			5227	protein-coding gene	gene with protein product		602438	"cataract, Marner"	CTM		8972228, 10488131, 12089525	Standard	NM_001538		Approved		uc002erl.2	Q9ULV5	OTTHUMG00000178325	ENST00000521374.1:c.974C>A	chr16.hg19:g.67201742C>A	ENSP00000430947:p.Pro325His	106.0	0.0		95.0	4.0	NM_001040667	Q99472|Q9ULV6	Missense_Mutation	SNP	ENST00000521374.1	hg19	CCDS42175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.2|27.2	4.805303|4.805303	0.90623|0.90623	.|.	.|.	ENSG00000102878|ENSG00000102878	ENST00000520304|ENST00000421453;ENST00000264009;ENST00000521374	.|.	.|.	.|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.060140	.|0.64402	.|D	.|0.000002	T|T	0.64757|0.64757	0.2627|0.2627	L|L	0.32530|0.32530	0.975|0.975	0.58432|0.58432	D|D	0.999999|0.999999	.|D;P	.|0.61697	.|0.99;0.898	.|P;B	.|0.60473	.|0.875;0.428	T|T	0.66484|0.66484	-0.5912|-0.5912	5|9	.|0.59425	.|D	.|0.04	-2.5728|-2.5728	16.8974|16.8974	0.86104|0.86104	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|295;325	.|Q9ULV5-2;Q9ULV5	.|.;HSF4_HUMAN	M|H	1|295;325;325	.|.	.|ENSP00000264009:P325H	L|P	+|+	1|2	2|0	HSF4|HSF4	65759243|65759243	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	6.375000|6.375000	0.73137|0.73137	2.586000|2.586000	0.87340|0.87340	0.561000|0.561000	0.74099|0.74099	CTG|CCT	.	.		0.667	HSF4-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375080.1	NM_001538		A	67201742	C	A	67201742	3	1	155	1	0	0	0	0	1	0	0	0	7407	681	24	3	1022	3	HSF4	16	67201742	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	35792576	67201742	23153011	69	23722										
CTRL	1506	hgsc.bcm.edu	37	chr16	67963973	67963973	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	cccatgtgtttcccttctggCagacaagagggcctccggag	12	13	1	2	rs142873279	byFrequency	TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr16:67963973C>T	ENST00000574481.1	-	7	1220	c.659G>A	c.(658-660)tGc>tAc	p.C220Y	CTRL_ENST00000576408.1_5'Flank	NM_001907.2	NP_001898.1	P40313	CTRL_HUMAN	chymotrypsin-like	220	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|urinary_tract(1)	4		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		TCCCTTCTGGCAGACAAGAGG	0.562																																					p.C220Y		Atlas-SNP	.											.	CTRL	11	.	0			c.G659A						.						100	107	105					16																	67963973		2198	4300	6498	SO:0001583	missense	1506	exon7			TTCTGGCAGACAA		CCDS10852.1	16q22.1	2008-02-05			ENSG00000141086	ENSG00000141086			2524	protein-coding gene	gene with protein product		118888				8268911	Standard	NM_001907		Approved		uc002euw.3	P40313	OTTHUMG00000137552	ENST00000574481.1:c.659G>A	chr16.hg19:g.67963973C>T	ENSP00000458537:p.Cys220Tyr	107.0	0.0		112.0	37.0	NM_001907		Missense_Mutation	SNP	ENST00000574481.1	hg19	CCDS10852.1	.	.	.	.	.	.	.	.	.	.	C	18.72	3.684589	0.68157	.	.	ENSG00000141086	ENST00000319955	.	.	.	5.74	3.79	0.43588	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.523574	0.22012	N	0.065847	T	0.62672	0.2447	M	0.74647	2.275	0.80722	D	1	P	0.42620	0.785	P	0.46237	0.508	T	0.66590	-0.5885	9	0.56958	D	0.05	-18.0625	11.0735	0.48016	0.0:0.7968:0.0:0.2032	.	220	P40313	CTRL_HUMAN	Y	220	.	ENSP00000322629:C220Y	C	-	2	0	CTRL	66521474	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.912000	0.28597	1.432000	0.47375	0.491000	0.48974	TGC	.	C|0.999;A|0.001		0.562	CTRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268886.3			T	67963973	C	T	67963973	3	4	155	1	0	0	0	0	1	0	0	0	4030	710	25	3	139	3	CTRL	16	67963973	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	762231	67963973	22390780	70	23723										
SENP3	26168	hgsc.bcm.edu	37	chr17	7466636	7466636	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	agtgaagaggaggaagaagaGgaggaggaggaggatgaaga	21	0	0	6			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr17:7466636G>A	ENST00000429205.2	+	2	292	c.243G>A	c.(241-243)gaG>gaA	p.E81E	SENP3_ENST00000578868.1_3'UTR|SENP3_ENST00000321337.7_Silent_p.E81E|SENP3-EIF4A1_ENST00000579777.1_RNA			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	81	Glu-rich.					cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				aggaagaagaggaggaggagg	0.622																																					p.E81E		Atlas-SNP	.											.	SENP3	18	.	0			c.G243A						.																																			SO:0001819	synonymous_variant	26168	exon2			AGAAGAGGAGGAG	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"SUMO1/sentrin/SMT3 specific protease 3"			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.243G>A	chr17.hg19:g.7466636G>A		98.0	0.0		117.0	6.0	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	hg19																																																																																				.	.		0.622	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670		A	7466636	G	A	7466636	2	1	155	1	0	0	0	0	0	0	0	1	14063	991	35	3		3	SENP3	17	7466636	Silent	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10		7466636	73728574	71	23724										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27442455	27442455	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	cactccagtgcactcagtttCgggcctgtggggcaggggga	16	11	1	0	rs368144764		TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr17:27442455C>T	ENST00000527372.1	-	13	2412	c.2232G>A	c.(2230-2232)ccG>ccA	p.P744P	MYO18A_ENST00000354329.4_Silent_p.P744P|MYO18A_ENST00000533112.1_Silent_p.P744P|MYO18A_ENST00000531253.1_Silent_p.P744P	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	744	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CACTCAGTTTCGGGCCTGTGG	0.657																																					p.P744P	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.G2232A						.	C	,	0,3932		0,0,1966	31	40	37		2232,2232	1.1	1	17		37	1,8279		0,1,4139	no	coding-synonymous,coding-synonymous	MYO18A	NM_078471.3,NM_203318.1	,	0,1,6105	TT,TC,CC		0.0121,0.0,0.0082	,	744/2055,744/2040	27442455	1,12211	1966	4140	6106	SO:0001819	synonymous_variant	399687	exon13			CAGTTTCGGGCCT	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.2232G>A	chr17.hg19:g.27442455C>T		67.0	0.0		66.0	23.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	hg19	CCDS45642.1																																																																																			.	.		0.657	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		T	27442455	C	T	27442455	2	4	155	1	0	0	0	0	0	0	0	1	10074	871	31	1		1	MYO18A	17	27442455	Silent	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	19975819	27442455	53752755	72	23725										
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274487	39274488	+	Missense_Mutation	DNP	GG	GG	TT													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	caggtggtctcacagcagctGgggcggcagcaggtctcctg							TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr17:39274487_39274488GG>TT	ENST00000391413.2	-	1	118_119	c.80_81CC>AA	c.(79-81)cCC>cAA	p.P27Q		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	27	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CACAGCAGCTGGGGCGGCAGCA	0.634																																					p.P27P|p.P27H		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.C81A|c.C80A						.																																			SO:0001583	missense	653240	exon1			GCAGCTGGGGCGG|CAGCTGGGGCGGC	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"Keratin associated proteins"	18911	protein-coding gene	gene with protein product			"keratin associated protein 4-14"	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.80_81delinsTT	chr17.hg19:g.39274487_39274488delinsTT	ENSP00000375232:p.Pro27Gln	72.0|71.0	0.0		66.0|67.0	27.0	NM_033059	A0AUY2	Silent|Missense_Mutation	SNP	ENST00000391413.2	hg19	CCDS45675.1																																																																																			.	.		0.634	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			TT	39274488	GG	TT	39274487	3	4	155	1	0	0	0	0	1	0	0	0	8558	1335	47	3	510	3	KRTAP4-11	17	39274487	Missense_Mutation	DNP	GG	TCGA-DD-AACD-01A-11D-A40R-10	11832032	39274487	41920723	73	23726										
RUNDC3A	10900	hgsc.bcm.edu	37	chr17	42389993	42389993	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aagtacacagcggagcccatCgatgactcatcggaggagtt	12	10	1	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr17:42389993C>T	ENST00000426726.3	+	2	427	c.153C>T	c.(151-153)atC>atT	p.I51I	AC003102.3_ENST00000588097.1_RNA|RUNDC3A_ENST00000590941.1_Silent_p.I51I|RUNDC3A_ENST00000225441.7_Silent_p.I51I	NM_001144825.1	NP_001138297.1	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A	51	Interaction with RAP2A. {ECO:0000250}.				positive regulation of cGMP biosynthetic process (GO:0030828)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanylate cyclase activator activity (GO:0030250)|small GTPase regulator activity (GO:0005083)			large_intestine(1)|lung(1)|ovary(2)	4		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CGGAGCCCATCGATGACTCAT	0.597																																					p.I51I	Pancreas(82;1061 1416 11136 20771 23901)	Atlas-SNP	.											RUNDC3A_ENST00000225441,colon,carcinoma,0,2	RUNDC3A	30	.	0			c.C153T						.						46	51	49					17																	42389993		2001	4174	6175	SO:0001819	synonymous_variant	10900	exon2			GCCCATCGATGAC	AF055026	CCDS45698.1, CCDS45699.1, CCDS59294.1	17q21.31	2008-02-05			ENSG00000108309	ENSG00000108309			16984	protein-coding gene	gene with protein product		605448				9523700	Standard	NM_006695		Approved	RPIP8, RAP2IP	uc002igl.4	Q59EK9	OTTHUMG00000169259	ENST00000426726.3:c.153C>T	chr17.hg19:g.42389993C>T		49.0	0.0		38.0	14.0	NM_001144825	B2R974|O15483|O60651|Q7Z3S2|Q9UF50	Silent	SNP	ENST00000426726.3	hg19	CCDS45698.1																																																																																			.	.		0.597	RUNDC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403173.2	NM_006695		T	42389993	C	T	42389993	2	4	155	1	0	0	0	0	0	0	0	1	13759	874	31	1		1	RUNDC3A	17	42389993	Silent	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	3115506	42389993	38805217	74	23727										
SPATA20	64847	hgsc.bcm.edu	37	chr17	48626198	48626198	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ctccacctgccactggtgccAcatgatggaagaggagtcct	11	13	0	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr17:48626198A>G	ENST00000356488.4	+	4	424	c.341A>G	c.(340-342)cAc>cGc	p.H114R	SPATA20_ENST00000393244.3_Missense_Mutation_p.H70R|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000006658.6_Missense_Mutation_p.H130R	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	114					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CACTGGTGCCACATGATGGAA	0.617																																					p.H130R		Atlas-SNP	.											.	SPATA20	59	.	0			c.A389G						.						124	92	103					17																	48626198		2203	4300	6503	SO:0001583	missense	64847	exon5			GGTGCCACATGAT		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.341A>G	chr17.hg19:g.48626198A>G	ENSP00000348878:p.His114Arg	72.0	0.0		71.0	30.0	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	hg19	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.519018	0.85495	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.51071	0.72;0.72;0.72	4.78	4.78	0.61160	Thioredoxin-like fold (2);Domain of unknown function DUF255 (1);	0.000000	0.85682	D	0.000000	T	0.73644	0.3613	M	0.89785	3.06	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.80473	-0.1367	10	0.87932	D	0	-18.7784	14.3103	0.66413	1.0:0.0:0.0:0.0	.	114;114;130	B4DZC5;Q8TB22;Q8TB22-2	.;SPT20_HUMAN;.	R	130;114;70	ENSP00000006658:H130R;ENSP00000348878:H114R;ENSP00000376935:H70R	ENSP00000006658:H130R	H	+	2	0	SPATA20	45981197	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.962000	0.93254	1.788000	0.52465	0.402000	0.26972	CAC	.	.		0.617	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		G	48626198	A	G	48626198	3	3	155	1	0	0	0	0	1	0	0	0	15021	159	6	2	407	2	SPATA20	17	48626198	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	6236205	48626198	32569012	75	23728										
POLG2	11232	hgsc.bcm.edu	37	chr17	62488797	62488797	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	gcagtacctttctccaccacTggagtcgatgacgtaaccag	9	13	1	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr17:62488797T>C	ENST00000539111.2	-	3	849	c.782A>G	c.(781-783)cAg>cGg	p.Q261R		NM_007215.3	NP_009146.2	Q9UHN1	DPOG2_HUMAN	polymerase (DNA directed), gamma 2, accessory subunit	261					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)	extracellular vesicular exosome (GO:0070062)|mitochondrial chromosome (GO:0000262)|mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(4)|skin(2)|stomach(1)|urinary_tract(1)	15	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			TCTCCACCACTGGAGTCGATG	0.358																																					p.Q261R	Colon(3;18 21 435 17652 48887)	Atlas-SNP	.											.	POLG2	29	.	0			c.A782G						.						47	43	44					17																	62488797		2203	4300	6503	SO:0001583	missense	11232	exon3			CACCACTGGAGTC	U94703	CCDS32706.1	17q23.3	2012-05-18			ENSG00000256525	ENSG00000256525		"DNA polymerases"	9180	protein-coding gene	gene with protein product		604983				9153213	Standard	NM_007215		Approved	MTPOLB, HP55	uc002jei.3	Q9UHN1		ENST00000539111.2:c.782A>G	chr17.hg19:g.62488797T>C	ENSP00000442563:p.Gln261Arg	1769.0	0.0		1900.0	604.0	NM_007215	O00419|Q0IJ81|Q96GW2|Q9UK35|Q9UK94	Missense_Mutation	SNP	ENST00000539111.2	hg19	CCDS32706.1	.	.	.	.	.	.	.	.	.	.	T	5.366	0.252741	0.10185	.	.	ENSG00000256525	ENST00000539111	T	0.77098	-1.07	5.44	3.15	0.36227	.	0.281419	0.32802	N	0.005638	T	0.69169	0.3081	L	0.50333	1.59	0.30041	N	0.812619	B;B	0.24823	0.112;0.112	B;B	0.19148	0.024;0.024	T	0.61850	-0.6978	10	0.33940	T	0.23	-4.096	10.6405	0.45590	0.418:0.0:0.0:0.582	.	261;261	E5KS15;Q9UHN1	.;DPOG2_HUMAN	R	261	ENSP00000442563:Q261R	ENSP00000442563:Q261R	Q	-	2	0	POLG2	59919259	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	2.313000	0.43735	0.408000	0.25621	-0.339000	0.08088	CAG	.	.		0.358	POLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443820.1	NM_007215		C	62488797	T	C	62488797	3	2	155	1	0	0	0	0	1	0	0	0	12210	1580	55	2	699	2	POLG2	17	62488797	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	13862599	62488797	18706413	76	23729										
ATP5A1	498	hgsc.bcm.edu	37	chr18	43667308	43667308	+	Splice_Site	SNP	T	T	C													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aaaatttatttcctttgaccTgtttggataagtcgtcatag							TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr18:43667308T>C	ENST00000398752.6	-	7	1071	c.950A>G	c.(949-951)cAg>cGg	p.Q317R	ATP5A1_ENST00000593152.2_Splice_Site_p.Q267R|ATP5A1_ENST00000282050.2_Splice_Site_p.Q317R|ATP5A1_ENST00000590665.1_Splice_Site_p.Q295R	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	317					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						TCCTTTGACCTGTTTGGATAA	0.353																																					p.Q317R		Atlas-SNP	.											.	ATP5A1	52	.	0			c.A950G						.						65	67	66					18																	43667308		2203	4299	6502	SO:0001630	splice_region_variant	498	exon7			TTGACCTGTTTGG	D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.951+1A>G	chr18.hg19:g.43667308T>C		160.0	0.0		222.0	97.0	NM_004046	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	hg19	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.178808	0.78564	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	T;T	0.79454	-1.27;-1.27	4.53	4.53	0.55603	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.92031	0.7475	H	0.98980	4.39	0.80722	D	1	D	0.54047	0.964	P	0.62184	0.899	D	0.94810	0.7978	10	0.87932	D	0	-18.2648	13.8784	0.63667	0.0:0.0:0.0:1.0	.	317	P25705	ATPA_HUMAN	R	317;317;267	ENSP00000282050:Q317R;ENSP00000381736:Q317R	ENSP00000282050:Q317R	Q	-	2	0	ATP5A1	41921306	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.953000	0.87836	1.686000	0.51046	0.460000	0.39030	CAG	.	.		0.353	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046	Missense_Mutation	C	43667308	T	C	43667308	5	2	155	1	0	0	0	0	0	0	1	0	1147	1594	55	2	735	2	ATP5A1	18	43667308	Splice_Site	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10		43667308	34409940	77	23730	106	2								
ATP5A1	498	hgsc.bcm.edu	37	chr18	43667311	43667311	+	Missense_Mutation	SNP	T	T	C													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	atttatttcctttgacctgtTtggataagtcgtcatagatg							TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr18:43667311T>C	ENST00000398752.6	-	7	1068	c.947A>G	c.(946-948)aAa>aGa	p.K316R	ATP5A1_ENST00000593152.2_Missense_Mutation_p.K266R|ATP5A1_ENST00000282050.2_Missense_Mutation_p.K316R|ATP5A1_ENST00000590665.1_Missense_Mutation_p.K294R	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	316					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						TTTGACCTGTTTGGATAAGTC	0.363																																					p.K316R		Atlas-SNP	.											.	ATP5A1	52	.	0			c.A947G						.						67	69	68					18																	43667311		2203	4300	6503	SO:0001583	missense	498	exon7			ACCTGTTTGGATA	D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.947A>G	chr18.hg19:g.43667311T>C	ENSP00000381736:p.Lys316Arg	159.0	0.0		219.0	93.0	NM_004046	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	hg19	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.446750	0.84101	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	T;T	0.77750	-1.12;-1.12	4.53	4.53	0.55603	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.045477	0.85682	D	0.000000	D	0.87410	0.6170	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89157	0.3527	10	0.87932	D	0	-16.2311	13.8784	0.63667	0.0:0.0:0.0:1.0	.	316	P25705	ATPA_HUMAN	R	316;316;266	ENSP00000282050:K316R;ENSP00000381736:K316R	ENSP00000282050:K316R	K	-	2	0	ATP5A1	41921309	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.953000	0.87836	1.686000	0.51046	0.460000	0.39030	AAA	.	.		0.363	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046		C	43667311	T	C	43667311	3	2	155	1	0	0	0	0	1	0	0	0	1147	1841	64	2	738	2	ATP5A1	18	43667311	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	3	43667311	34409937	78	23731	106	2								
SMAD4	4089	hgsc.bcm.edu	37	chr18	48593405	48593405	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	taaggttgcacataggcaaaGgtgtgcagttggaatgtaaa	13	4	0	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr18:48593405G>A	ENST00000342988.3	+	10	1694	c.1156G>A	c.(1156-1158)Ggt>Agt	p.G386S	SMAD4_ENST00000588745.1_Missense_Mutation_p.G290S|SMAD4_ENST00000398417.2_Missense_Mutation_p.G386S	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	386	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		G -> D (in JP/HHT; dbSNP:rs28936393). {ECO:0000269|PubMed:15031030}.		atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.G386R(5)|p.?(2)|p.G386C(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		CATAGGCAAAGGTGTGCAGTT	0.363																																					p.G386S		Atlas-SNP	.											SMAD4,colon,carcinoma,0,7	SMAD4	822	.	44	Whole gene deletion(36)|Substitution - Missense(6)|Unknown(2)	pancreas(26)|large_intestine(8)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|ovary(1)	c.G1156A						.						200	165	177					18																	48593405		2203	4300	6503	SO:0001583	missense	4089	exon10			GGCAAAGGTGTGC	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1156G>A	chr18.hg19:g.48593405G>A	ENSP00000341551:p.Gly386Ser	134.0	0.0		142.0	42.0	NM_005359	A8K405	Missense_Mutation	SNP	ENST00000342988.3	hg19	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.957718	0.92726	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.99872	-7.37;-7.37	5.65	4.78	0.61160	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.046058	0.85682	N	0.000000	D	0.99898	0.9951	H	0.96080	3.765	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96254	0.9185	10	0.87932	D	0	.	13.5117	0.61517	0.0761:0.0:0.9239:0.0	.	386	Q13485	SMAD4_HUMAN	S	386	ENSP00000341551:G386S;ENSP00000381452:G386S	ENSP00000341551:G386S	G	+	1	0	SMAD4	46847403	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.759000	0.98931	1.395000	0.46643	0.563000	0.77884	GGT	.	.		0.363	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48593405	G	A	48593405	3	1	155	1	0	0	0	0	1	0	0	0	14775	1000	35	3	1190	3	SMAD4	18	48593405	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	4926094	48593405	29483843	79	23732										
TXNL1	9352	hgsc.bcm.edu	37	chr18	54291666	54291666	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aacaaaaatgtaggtgttgcTgatatattgttggtggcagc	12	4	0	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr18:54291666T>A	ENST00000217515.6	-	3	426	c.222A>T	c.(220-222)tcA>tcT	p.S74S	TXNL1_ENST00000590954.1_Silent_p.S74S|TXNL1_ENST00000540155.1_5'UTR	NM_004786.2	NP_004777.1	O43396	TXNL1_HUMAN	thioredoxin-like 1	74	Thioredoxin.				cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	disulfide oxidoreductase activity (GO:0015036)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)		TAGGTGTTGCTGATATATTGT	0.353																																					p.S74S		Atlas-SNP	.											.	TXNL1	30	.	0			c.A222T						.						177	175	175					18																	54291666		2203	4300	6503	SO:0001819	synonymous_variant	9352	exon3			TGTTGCTGATATA	AF003938	CCDS11961.1	18q21.31	2011-01-17	2004-05-06	2004-05-07	ENSG00000091164	ENSG00000091164			12436	protein-coding gene	gene with protein product	"thioredoxin-like, 32kD"	603049	"thioredoxin-like, 32kDa"	TXNL		9473519, 9668102	Standard	NM_004786		Approved	Txl, TRP32	uc002lgg.3	O43396	OTTHUMG00000132722	ENST00000217515.6:c.222A>T	chr18.hg19:g.54291666T>A		81.0	0.0		91.0	20.0	NM_004786		Silent	SNP	ENST00000217515.6	hg19	CCDS11961.1																																																																																			.	.		0.353	TXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256064.2			A	54291666	T	A	54291666	2	1	155	1	0	0	0	0	0	0	0	1	16819	1567	55	4		4	TXNL1	18	54291666	Silent	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	5698261	54291666	23785582	80	23733										
SERPINB7	8710	hgsc.bcm.edu	37	chr18	61449699	61449699	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aatggaaatgtgttcttttcCtctctgagcctcttcgctgc	8	11	3	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr18:61449699C>G	ENST00000398019.2	+	2	418	c.93C>G	c.(91-93)tcC>tcG	p.S31S	SERPINB7_ENST00000546027.1_Silent_p.S31S|SERPINB7_ENST00000540675.1_Silent_p.S31S|SERPINB7_ENST00000336429.2_Silent_p.S31S	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	31					negative regulation of endopeptidase activity (GO:0010951)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of transforming growth factor beta1 production (GO:0032914)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	27		Esophageal squamous(42;0.129)				TGTTCTTTTCCTCTCTGAGCC	0.483																																					p.S31S		Atlas-SNP	.											.	SERPINB7	66	.	0			c.C93G						.						127	101	110					18																	61449699		2203	4300	6503	SO:0001819	synonymous_variant	8710	exon2			CTTTTCCTCTCTG	AF027866	CCDS11988.1, CCDS58633.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166396	ENSG00000166396		"Serine (or cysteine) peptidase inhibitors"	13902	protein-coding gene	gene with protein product		603357	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 7"			24172014	Standard	NM_003784		Approved	MEGSIN	uc002ljl.4	O75635	OTTHUMG00000060591	ENST00000398019.2:c.93C>G	chr18.hg19:g.61449699C>G		73.0	0.0		108.0	27.0	NM_001261830	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Silent	SNP	ENST00000398019.2	hg19	CCDS11988.1																																																																																			.	.		0.483	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134007.1	NM_003784		G	61449699	C	G	61449699	2	3	155	1	0	0	0	0	0	0	0	1	14121	668	24	4		4	SERPINB7	18	61449699	Silent	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	7158033	61449699	16627549	81	23734										
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4171378	4171378	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	actctgccgctgtctccaccAggtcctgttgctgtcctttg	9	15	2	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr19:4171378A>G	ENST00000078445.2	+	9	1122		c.e9-1		CREB3L3_ENST00000595923.1_Splice_Site|CREB3L3_ENST00000602147.1_Splice_Site|CREB3L3_ENST00000602257.1_Splice_Site|CREB3L3_ENST00000252587.3_Splice_Site	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		TGTCTCCACCAGGTCCTGTTG	0.607																																					.		Atlas-SNP	.											.	CREB3L3	53	.	0			c.973-2A>G						.						91	79	83					19																	4171378		2203	4300	6503	SO:0001630	splice_region_variant	84699	exon9			TCCACCAGGTCCT		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.976-1A>G	chr19.hg19:g.4171378A>G		66.0	0.0		78.0	21.0	NM_001271995	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Splice_Site	SNP	ENST00000078445.2	hg19	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	A	13.39	2.221787	0.39300	.	.	ENSG00000060566	ENST00000078445;ENST00000381943;ENST00000252587	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8958	0.52656	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CREB3L3	4122378	1.000000	0.71417	0.988000	0.46212	0.273000	0.26683	6.155000	0.71833	1.700000	0.51204	0.459000	0.35465	.	.	.		0.607	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	Intron	G	4171378	A	G	4171378	5	3	155	1	0	0	0	0	0	0	1	0	3860	202	7	2	1008	2	CREB3L3	19	4171378	Splice_Site	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10		4171378	54957605	82	23735										
KDM4B	23030	hgsc.bcm.edu	37	chr19	5131976	5131976	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tgggccggccgcccacccggTccccactgtcggtggtgaag	15	16	0	1			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr19:5131976T>C	ENST00000159111.4	+	13	2082	c.1864T>C	c.(1864-1866)Tcc>Ccc	p.S622P	KDM4B_ENST00000536461.1_Missense_Mutation_p.S656P	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	622					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						GCCCACCCGGTCCCCACTGTC	0.637																																					p.S622P		Atlas-SNP	.											.	KDM4B	120	.	0			c.T1864C						.						21	26	25					19																	5131976		2194	4294	6488	SO:0001583	missense	23030	exon13			ACCCGGTCCCCAC	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1864T>C	chr19.hg19:g.5131976T>C	ENSP00000159111:p.Ser622Pro	241.0	0.0		259.0	80.0	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	hg19	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.153137	0.78001	.	.	ENSG00000127663	ENST00000159111;ENST00000536461	T;T	0.53423	0.62;0.62	4.12	4.12	0.48240	.	0.126301	0.56097	D	0.000033	T	0.65144	0.2663	M	0.77103	2.36	0.43448	D	0.995637	D;D	0.71674	0.994;0.998	P;D	0.63381	0.865;0.914	T	0.68265	-0.5454	10	0.46703	T	0.11	-39.7167	13.1392	0.59426	0.0:0.0:0.0:1.0	.	656;622	F5GX28;O94953	.;KDM4B_HUMAN	P	622;656	ENSP00000159111:S622P;ENSP00000440495:S656P	ENSP00000159111:S622P	S	+	1	0	KDM4B	5082976	1.000000	0.71417	0.891000	0.34965	0.774000	0.43823	3.688000	0.54699	1.512000	0.48834	0.459000	0.35465	TCC	.	.		0.637	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		C	5131976	T	C	5131976	3	2	155	1	0	0	0	0	1	0	0	0	8138	1667	58	2	1906	2	KDM4B	19	5131976	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	960598	5131976	53997007	83	23736										
SLC35E1	79939	hgsc.bcm.edu	37	chr19	16678874	16678874	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	aaatgttctgaagcgagaagCacagcgtggcggcgagggcg	17	8	1	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr19:16678874C>A	ENST00000595753.1	-	3	616	c.599G>T	c.(598-600)tGc>tTc	p.C200F	CTD-3222D19.10_ENST00000597851.1_RNA|CTD-3222D19.2_ENST00000409035.1_Intron|SLC35E1_ENST00000431408.1_Missense_Mutation_p.C44F	NM_024881.4	NP_079157.3	Q96K37	S35E1_HUMAN	solute carrier family 35, member E1	200					transport (GO:0006810)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(2)|ovary(1)	15						AAGCGAGAAGCACAGCGTGGC	0.562																																					p.C200F		Atlas-SNP	.											.	SLC35E1	48	.	0			c.G599T						.						93	86	89					19																	16678874		2203	4300	6503	SO:0001583	missense	79939	exon3			GAGAAGCACAGCG	AK024313	CCDS12346.2	19p13.11	2013-05-22			ENSG00000127526	ENSG00000127526		"Solute carriers"	20803	protein-coding gene	gene with protein product							Standard	NM_024881		Approved	FLJ14251	uc010xph.2	Q96K37	OTTHUMG00000152575	ENST00000595753.1:c.599G>T	chr19.hg19:g.16678874C>A	ENSP00000470652:p.Cys200Phe	58.0	0.0		55.0	14.0	NM_024881	Q8NBQ2|Q96JV7	Missense_Mutation	SNP	ENST00000595753.1	hg19	CCDS12346.2	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364801	0.82463	.	.	ENSG00000127526	ENST00000409648;ENST00000431408	T	0.62105	0.05	5.13	5.13	0.70059	Domain of unknown function DUF250 (1);	0.000000	0.85682	D	0.000000	T	0.71013	0.3290	L	0.44542	1.39	0.80722	D	1	D;P	0.71674	0.998;0.9	D;P	0.68943	0.961;0.668	T	0.65635	-0.6120	10	0.20046	T	0.44	-40.764	17.5838	0.87976	0.0:1.0:0.0:0.0	.	200;56	Q96K37;Q9H7U6	S35E1_HUMAN;.	F	200;44	ENSP00000397670:C44F	ENSP00000387152:C200F	C	-	2	0	SLC35E1	16539874	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.201000	0.77847	2.387000	0.81309	0.555000	0.69702	TGC	.	.		0.562	SLC35E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326809.2	NM_024881		A	16678874	C	A	16678874	3	1	155	1	0	0	0	0	1	0	0	0	14599	710	25	3	649	3	SLC35E1	19	16678874	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	11546898	16678874	42450109	84	23737										
ZNF527	84503	hgsc.bcm.edu	37	chr19	37880628	37880629	+	Missense_Mutation	DNP	TG	TG	GT													0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ccctatgaatgtagtgaatgTgggaaggcttttcatcagat							TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr19:37880628_37880629TG>GT	ENST00000436120.2	+	5	1784_1785	c.1677_1678TG>GT	c.(1675-1680)tgTGgg>tgGTgg	p.559_560CG>WW	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	559					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTAGTGAATGTGGGAAGGCTTT	0.376																																					p.C559W|p.G560W		Atlas-SNP	.											.	ZNF527	78	.	0			c.T1677G|c.G1678T						.																																			SO:0001583	missense	84503	exon5			TGAATGTGGGAAG|GAATGTGGGAAGG	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"Zinc fingers, C2H2-type", "-"	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	Exception_encountered	chr19.hg19:g.37880628_37880629delinsGT	ENSP00000390179:p.C559_G560delinsWW	61.0	0.0		48.0|47.0	20.0|19.0	NM_032453	B4DVL5	Missense_Mutation	SNP	ENST00000436120.2	hg19	CCDS42559.1																																																																																			.	.		0.376	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453		GT	37880629	TG	GT	37880628	3	3	155	1	0	0	0	0	1	0	0	0	17983	1702	59	5	1691	5	ZNF527	19	37880628	Missense_Mutation	DNP	TG	TCGA-DD-AACD-01A-11D-A40R-10	21201754	37880628	21248355	85	23738										
CKM	1158	hgsc.bcm.edu	37	chr19	45821217	45821217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	atcaccagccacgcagcccaCggtcatgatgaaggggtgac	12	13	2	3	rs1803285		TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr19:45821217C>T	ENST00000221476.3	-	3	388	c.214G>A	c.(214-216)Gtg>Atg	p.V72M		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	72	Phosphagen kinase N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00842}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.V72M(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	ACGCAGCCCACGGTCATGATG	0.592																																					p.V72M		Atlas-SNP	.											CKM,colon,carcinoma,0,1	CKM	40	.	1	Substitution - Missense(1)	large_intestine(1)	c.G214A						.						64	54	57					19																	45821217		2203	4300	6503	SO:0001583	missense	1158	exon3			AGCCCACGGTCAT	M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.214G>A	chr19.hg19:g.45821217C>T	ENSP00000221476:p.Val72Met	83.0	0.0		94.0	36.0	NM_001824	Q96QL9	Missense_Mutation	SNP	ENST00000221476.3	hg19	CCDS12659.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.649634	0.87958	.	.	ENSG00000104879	ENST00000221476	T	0.70399	-0.48	4.62	4.62	0.57501	ATP:guanido phosphotransferase, N-terminal (4);	0.070689	0.56097	D	0.000026	T	0.78078	0.4227	M	0.86097	2.795	0.58432	D	0.999999	D	0.54772	0.968	P	0.47626	0.552	D	0.83635	0.0147	10	0.87932	D	0	-32.9684	15.0581	0.71930	0.0:1.0:0.0:0.0	rs1803285	72	P06732	KCRM_HUMAN	M	72	ENSP00000221476:V72M	ENSP00000221476:V72M	V	-	1	0	CKM	50513057	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	7.283000	0.78640	2.418000	0.82041	0.650000	0.86243	GTG	.	.		0.592	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1			T	45821217	C	T	45821217	3	4	155	1	0	0	0	0	1	0	0	0	3450	536	19	1	955	1	CKM	19	45821217	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	7940589	45821217	13307766	86	23739										
ZNF761	388561	hgsc.bcm.edu	37	chr19	53959745	53959745	+	RNA	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ttcatactggagagaaacctTacaagtgtaatgagtgtggc	11	6	1	2	rs146356671	byFrequency	TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr19:53959745T>G	ENST00000454407.1	+	0	2437							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		AGAGAAACCTTACAAGTGTAA	0.383																																					p.Y662D		Atlas-SNP	.											.	ZNF761	104	.	0			c.T1984G						.						81	87	85					19																	53959745		2203	4300	6503			388561	exon7			AAACCTTACAAGT	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		chr19.hg19:g.53959745T>G		77.0	0.0		87.0	33.0	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	hg19																																																																																				.	T|0.999;C|0.001		0.383	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		G	53959745	T	G	53959745	1	3	155	0	1	0	0	0	0	0	0	0	18151	1754	61	5		5	ZNF761	19	53959745	RNA	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10	8138528	53959745	5169238	87	23740										
SLC4A11	83959	hgsc.bcm.edu	37	chr20	3214949	3214949	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	atctcttccttgaagttcttTaacttcaggtactgagggga	9	8	3	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr20:3214949T>G	ENST00000380056.3	-	4	398	c.351A>C	c.(349-351)ttA>ttC	p.L117F	SLC4A11_ENST00000380059.3_Missense_Mutation_p.L144F|SLC4A11_ENST00000539553.2_Missense_Mutation_p.L101F	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	117					bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						TGAAGTTCTTTAACTTCAGGT	0.607																																					p.L144F	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.A432C						.						57	55	56					20																	3214949		2203	4300	6503	SO:0001583	missense	83959	exon5			GTTCTTTAACTTC	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"Solute carriers"	16438	protein-coding gene	gene with protein product		610206	"corneal endothelial dystrophy 2 (autosomal recessive)", "solute carrier family 4, sodium bicarbonate transporter-like, member 11", "corneal dystrophy and perceptive deafness 1"	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.351A>C	chr20.hg19:g.3214949T>G	ENSP00000369396:p.Leu117Phe	87.0	0.0		92.0	24.0	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	hg19	CCDS13052.1	.	.	.	.	.	.	.	.	.	.	T	13.70	2.316836	0.40996	.	.	ENSG00000088836	ENST00000380059;ENST00000380056;ENST00000539553;ENST00000437836	D;D;D;D	0.83250	-1.66;-1.64;-1.63;-1.7	5.2	1.66	0.24008	Phosphotransferase/anion transporter (1);	0.387849	0.21342	N	0.076118	T	0.76097	0.3940	L	0.52364	1.645	0.58432	D	0.99999	B;B;B	0.30104	0.268;0.175;0.175	B;B;B	0.31442	0.13;0.101;0.101	T	0.69165	-0.5217	10	0.48119	T	0.1	.	8.2353	0.31622	0.0:0.2364:0.0:0.7636	.	101;144;117	G3V1M3;B4DKC8;Q8NBS3	.;.;S4A11_HUMAN	F	144;117;101;101	ENSP00000369399:L144F;ENSP00000369396:L117F;ENSP00000441370:L101F;ENSP00000404271:L101F	ENSP00000369396:L117F	L	-	3	2	SLC4A11	3162949	0.904000	0.30761	1.000000	0.80357	0.990000	0.78478	-0.036000	0.12185	0.290000	0.22444	0.533000	0.62120	TTA	.	.		0.607	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1			G	3214949	T	G	3214949	3	3	155	1	0	0	0	0	1	0	0	0	14667	1751	61	5	2388	5	SLC4A11	20	3214949	Missense_Mutation	SNP	T	TCGA-DD-AACD-01A-11D-A40R-10		3214949	59810571	88	23741										
ADIG	57148	hgsc.bcm.edu	37	chr20	37209925	37209925	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tttgatgccgctggtgaacgAcctcacattttctttcctgg	9	11	2	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr20:37209925A>G	ENST00000262879.6	+	0	8661				ADIG_ENST00000373348.3_Missense_Mutation_p.D11G|ADIG_ENST00000537425.1_Missense_Mutation_p.D6G			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)						activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						CTGGTGAACGACCTCACATTT	0.557																																					p.D11G		Atlas-SNP	.											.	ADIG	16	.	0			c.A32G						.						182	188	186					20																	37209925		1980	4158	6138	SO:0001628	intergenic_variant	149685	exon1			TGAACGACCTCAC	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"KIAA1219"	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270		chr20.hg19:g.37209925A>G		118.0	0.0		108.0	27.0	NM_001018082	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	hg19	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.453783	0.63290	.	.	ENSG00000182035	ENST00000537425;ENST00000373348	.	.	.	5.15	5.15	0.70609	.	0.667620	0.12253	N	0.485482	T	0.39989	0.1099	.	.	.	0.19775	N	0.999951	P	0.36633	0.562	B	0.38500	0.275	T	0.36553	-0.9743	8	0.62326	D	0.03	.	11.6597	0.51339	1.0:0.0:0.0:0.0	.	11	Q0VDE8	ADIG_HUMAN	G	6;11	.	ENSP00000362445:D11G	D	+	2	0	ADIG	36643339	0.701000	0.27806	0.187000	0.23214	0.945000	0.59286	4.660000	0.61511	2.053000	0.61076	0.533000	0.62120	GAC	.	.		0.557	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		G	37209925	A	G	37209925	1	3	155	0	1	0	0	0	0	0	0	0	316	275	10	2		2	ADIG	20	37209925	IGR	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	33994976	37209925	25815595	89	23742										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61528235	61528235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	agcaaaagaagacttctttgGcacgaggtttctaggtgcag	12	7	2	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr20:61528235G>A	ENST00000266070.4	-	7	2027	c.1702C>T	c.(1702-1704)Cca>Tca	p.P568S	DIDO1_ENST00000395343.1_Missense_Mutation_p.P568S|DIDO1_ENST00000395340.1_Missense_Mutation_p.P568S|DIDO1_ENST00000395335.2_Missense_Mutation_p.P568S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	568					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GACTTCTTTGGCACGAGGTTT	0.577																																					p.P568S	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1,NS,malignant_melanoma,0,1	DIDO1	321	.	0			c.C1702T						.						45	46	46					20																	61528235		2203	4300	6503	SO:0001583	missense	11083	exon7			TCTTTGGCACGAG	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.1702C>T	chr20.hg19:g.61528235G>A	ENSP00000266070:p.Pro568Ser	135.0	0.0		156.0	47.0	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	G	10.34	1.324076	0.24080	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.12879	2.98;2.98;2.64;2.64	5.71	4.75	0.60458	.	0.175580	0.27130	N	0.020795	T	0.14570	0.0352	L	0.58669	1.825	0.80722	D	1	B;B	0.30281	0.275;0.18	B;B	0.26202	0.067;0.03	T	0.01874	-1.1256	10	0.42905	T	0.14	-12.1361	11.5841	0.50908	0.1401:0.0:0.8599:0.0	.	568;568	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	S	568	ENSP00000266070:P568S;ENSP00000378752:P568S;ENSP00000378749:P568S;ENSP00000378744:P568S	ENSP00000266070:P568S	P	-	1	0	DIDO1	60998680	0.988000	0.35896	0.913000	0.36048	0.076000	0.17211	1.575000	0.36493	2.685000	0.91497	0.563000	0.77884	CCA	.	.		0.577	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		A	61528235	G	A	61528235	3	1	155	1	0	0	0	0	1	0	0	0	4524	1203	42	3	5089	3	DIDO1	20	61528235	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10	24318310	61528235	1497285	90	23743										
APP	351	hgsc.bcm.edu	37	chr21	27372473	27372473	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	tcattgctcggcacggccccGtctcggcttgttcagagcac	11	15	3	1	rs557227002		TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr21:27372473G>T	ENST00000346798.3	-	7	923	c.890C>A	c.(889-891)aCg>aAg	p.T297K	APP_ENST00000440126.3_Missense_Mutation_p.T292K|APP_ENST00000448388.2_Intron|APP_ENST00000354192.3_Intron|APP_ENST00000348990.5_Intron|APP_ENST00000439274.2_Missense_Mutation_p.T241K|APP_ENST00000359726.3_Intron|APP_ENST00000358918.3_Missense_Mutation_p.T297K|APP_ENST00000357903.3_Missense_Mutation_p.T297K	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	297	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.				adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				GCACGGCCCCGTCTCGGCTTG	0.517																																					p.T297K		Atlas-SNP	.											.	APP	90	.	0			c.C890A						.						79	66	70					21																	27372473		2203	4300	6503	SO:0001583	missense	351	exon7			GGCCCCGTCTCGG	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.890C>A	chr21.hg19:g.27372473G>T	ENSP00000284981:p.Thr297Lys	94.0	0.0		73.0	18.0	NM_001204302	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	hg19	CCDS13576.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.5|29.5	5.015149|5.015149	0.93404|0.93404	.|.	.|.	ENSG00000142192|ENSG00000142192	ENST00000448850|ENST00000346798;ENST00000357903;ENST00000358918;ENST00000440126;ENST00000439274	.|T;T;T;T;T	.|0.57752	.|0.38;0.38;0.38;0.38;0.38	5.08|5.08	5.08|5.08	0.68730|0.68730	.|Proteinase inhibitor I2, Kunitz metazoa (6);	.|0.105878	.|0.64402	.|D	.|0.000005	T|T	0.65344|0.65344	0.2682|0.2682	L|L	0.42487|0.42487	1.325|1.325	0.80722|0.80722	D|D	1|1	.|D;P;P;D	.|0.69078	.|0.997;0.919;0.901;0.997	.|P;P;P;D	.|0.64595	.|0.902;0.705;0.58;0.927	T|T	0.67929|0.67929	-0.5543|-0.5543	5|10	.|0.87932	.|D	.|0	-17.4333|-17.4333	18.2555|18.2555	0.90019|0.90019	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|241;292;297;297	.|E9PG40;B4DII8;P05067-8;P05067	.|.;.;.;A4_HUMAN	E|K	218|297;297;297;292;241	.|ENSP00000284981:T297K;ENSP00000350578:T297K;ENSP00000351796:T297K;ENSP00000387483:T292K;ENSP00000398879:T241K	.|ENSP00000284981:T297K	D|T	-|-	3|2	2|0	APP|APP	26294344|26294344	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.307000|7.307000	0.78920|0.78920	2.648000|2.648000	0.89879|0.89879	0.650000|0.650000	0.86243|0.86243	GAC|ACG	.	.		0.517	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		T	27372473	G	T	27372473	3	4	155	1	0	0	0	0	1	0	0	0	815	1145	40	1	1470	1	APP	21	27372473	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10		27372473	20757422	91	23744										
SUSD2	56241	hgsc.bcm.edu	37	chr22	24581750	24581750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	actggggcgcacccccgttcCgcacgccaccccgagtgccc	11	21	0	0			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr22:24581750C>T	ENST00000358321.3	+	8	1453	c.1192C>T	c.(1192-1194)Cgc>Tgc	p.R398C		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	398	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						ACCCCCGTTCCGCACGCCACC	0.672																																					p.R398C		Atlas-SNP	.											.	SUSD2	68	.	0			c.C1192T						.						29	27	28					22																	24581750		2201	4296	6497	SO:0001583	missense	56241	exon8			CCGTTCCGCACGC	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.1192C>T	chr22.hg19:g.24581750C>T	ENSP00000351075:p.Arg398Cys	61.0	0.0		47.0	11.0	NM_019601	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	hg19	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.154112	0.57259	.	.	ENSG00000099994	ENST00000358321	T	0.21361	2.01	4.77	3.69	0.42338	AMOP (3);	0.755868	0.12111	N	0.498488	T	0.42449	0.1203	M	0.72118	2.19	0.09310	N	0.999998	D	0.89917	1.0	D	0.65773	0.938	T	0.11470	-1.0586	10	0.59425	D	0.04	-20.2557	11.0138	0.47677	0.2816:0.7184:0.0:0.0	.	398	Q9UGT4	SUSD2_HUMAN	C	398	ENSP00000351075:R398C	ENSP00000351075:R398C	R	+	1	0	SUSD2	22911750	0.002000	0.14202	0.362000	0.25862	0.926000	0.56050	0.092000	0.15066	2.396000	0.81511	0.456000	0.33151	CGC	.	.		0.672	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		T	24581750	C	T	24581750	3	4	155	1	0	0	0	0	1	0	0	0	15423	652	23	1	1222	1	SUSD2	22	24581750	Missense_Mutation	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10		24581750	26722816	92	23745										
ZBED4	9889	hgsc.bcm.edu	37	chr22	50279247	50279247	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ctcttttgatgacaccaatgAgaagttttacgattctcacc	6	10	2	3			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chr22:50279247A>T	ENST00000216268.5	+	2	2414	c.1937A>T	c.(1936-1938)gAg>gTg	p.E646V		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	646						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GACACCAATGAGAAGTTTTAC	0.493																																					p.E646V		Atlas-SNP	.											.	ZBED4	102	.	0			c.A1937T						.						52	57	56					22																	50279247		2203	4300	6503	SO:0001583	missense	9889	exon2			CCAATGAGAAGTT	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"Zinc fingers, BED-type"	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.1937A>T	chr22.hg19:g.50279247A>T	ENSP00000216268:p.Glu646Val	74.0	0.0		86.0	24.0	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	hg19	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.134213	0.77662	.	.	ENSG00000100426	ENST00000216268	T	0.48836	0.8	5.36	5.36	0.76844	.	0.120058	0.56097	D	0.000039	T	0.52224	0.1721	M	0.72118	2.19	0.58432	D	0.999997	D	0.54397	0.966	B	0.44315	0.446	T	0.59327	-0.7475	10	0.52906	T	0.07	-13.1138	15.3501	0.74376	1.0:0.0:0.0:0.0	.	646	O75132	ZBED4_HUMAN	V	646	ENSP00000216268:E646V	ENSP00000216268:E646V	E	+	2	0	ZBED4	48665251	1.000000	0.71417	0.992000	0.48379	0.963000	0.63663	8.723000	0.91458	2.017000	0.59298	0.533000	0.62120	GAG	.	.		0.493	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		T	50279247	A	T	50279247	3	4	155	1	0	0	0	0	1	0	0	0	17535	304	11	4	1939	4	ZBED4	22	50279247	Missense_Mutation	SNP	A	TCGA-DD-AACD-01A-11D-A40R-10	25697497	50279247	1025319	93	23746										
USP9X	8239	hgsc.bcm.edu	37	chrX	41048571	41048571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	taattttacagaccaatgcaGgcaatgagccagacttggaa	9	8	0	3			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chrX:41048571G>A	ENST00000324545.8	+	26	4453	c.3820G>A	c.(3820-3822)Ggc>Agc	p.G1274S	USP9X_ENST00000378308.2_Missense_Mutation_p.G1274S	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1274					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						GACCAATGCAGGCAATGAGCC	0.383																																					p.G1274S	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.G3820A						.						147	133	138					X																	41048571		2199	4300	6499	SO:0001583	missense	8239	exon26			AATGCAGGCAATG	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.3820G>A	chrX.hg19:g.41048571G>A	ENSP00000316357:p.Gly1274Ser	116.0	0.0		227.0	11.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	hg19	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	G	9.927	1.213781	0.22289	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.02709	4.2;4.19	5.78	5.78	0.91487	.	0.046433	0.85682	D	0.000000	T	0.02083	0.0065	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.46527	-0.9185	10	0.06099	T	0.92	.	18.9742	0.92728	0.0:0.0:1.0:0.0	.	1274;1274	Q93008-1;Q93008	.;USP9X_HUMAN	S	1274	ENSP00000367558:G1274S;ENSP00000316357:G1274S	ENSP00000316357:G1274S	G	+	1	0	USP9X	40933515	1.000000	0.71417	1.000000	0.80357	0.698000	0.40448	9.444000	0.97578	2.429000	0.82318	0.513000	0.50165	GGC	.	.		0.383	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		A	41048571	G	A	41048571	3	1	155	1	0	0	0	0	1	0	0	0	17105	1000	35	3	3918	3	USP9X	23	41048571	Missense_Mutation	SNP	G	TCGA-DD-AACD-01A-11D-A40R-10		41048571	114221989	94	23747										
DRP2	1821	hgsc.bcm.edu	37	chrX	100507604	100507604	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0531914893617021	5	1	1.1025641025641	0	1.4292497625831	0.0256410256410257	0.304738562091504	0	ctcccccaaggtaccggagtCtgaagcaattcaacgttgac	9	13	2	2			TCGA-DD-AACD-01A-11D-A40R-10	TCGA-DD-AACD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c59fe787-da95-4adc-aac0-30431d975acb	9f8086f5-832e-4885-8836-e959e0921ea7	g.chrX:100507604C>T	ENST00000395209.3	+	17	2403	c.1876C>T	c.(1876-1878)Ctg>Ttg	p.L626L	DRP2_ENST00000541709.1_Silent_p.L548L|DRP2_ENST00000402866.1_Silent_p.L626L|DRP2_ENST00000538510.1_Silent_p.L626L	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	626					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						GTACCGGAGTCTGAAGCAATT	0.507																																					p.L626L		Atlas-SNP	.											.	DRP2	98	.	0			c.C1876T						.						123	91	102					X																	100507604		2203	4300	6503	SO:0001819	synonymous_variant	1821	exon17			CGGAGTCTGAAGC	U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.1876C>T	chrX.hg19:g.100507604C>T		171.0	1.0		229.0	162.0	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Silent	SNP	ENST00000395209.3	hg19	CCDS14480.2																																																																																			.	.		0.507	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		T	100507604	C	T	100507604	2	4	155	1	0	0	0	0	0	0	0	1	4766	912	32	3		3	DRP2	23	100507604	Silent	SNP	C	TCGA-DD-AACD-01A-11D-A40R-10	59459033	100507604	54762956	95	23748										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32131184	32131184	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tttgtgtcttcttcactcacCggtgggcccggaaagcctgg	12	12	4	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr1:32131184C>T	ENST00000373672.3	-	55	4008	c.3492G>A	c.(3490-3492)ccG>ccA	p.P1164P	COL16A1_ENST00000271069.6_Splice_Site_p.P1164P	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1164	Triple-helical region 2 (COL2) with 2 imperfections.			P -> T (in Ref. 1; AAA58427). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CTTCACTCACCGGTGGGCCCG	0.632																																					p.P1164P	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.G3492A						.						82	86	85					1																	32131184		1975	4142	6117	SO:0001630	splice_region_variant	1307	exon55			ACTCACCGGTGGG	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.3492+1G>A	chr1.hg19:g.32131184C>T		66.0	0.0		65.0	21.0	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.		0.632	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	Silent	T	32131184	C	T	32131184	5	4	156	1	0	0	0	0	0	0	1	0	3675	666	23	1	1390	1	COL16A1	1	32131184	Splice_Site	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10		32131184	217119437	1	23749										
ERMAP	114625	hgsc.bcm.edu	37	chr1	43296622	43296622	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gaaggaccaggatgaagatcTgatgccggaatataagggga	15	5	1	3			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr1:43296622T>A	ENST00000372517.2	+	4	513	c.269T>A	c.(268-270)cTg>cAg	p.L90Q	ERMAP_ENST00000328249.3_5'UTR|ERMAP_ENST00000372514.3_Missense_Mutation_p.L90Q|ERMAP_ENST00000487556.1_Intron	NM_001017922.1	NP_001017922.1	Q96PL5	ERMAP_HUMAN	erythroblast membrane-associated protein (Scianna blood group)	90	Ig-like V-type.					cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GATGAAGATCTGATGCCGGAA	0.587																																					p.L90Q		Atlas-SNP	.											.	ERMAP	30	.	0			c.T269A						.						113	98	103					1																	43296622		2203	4300	6503	SO:0001583	missense	114625	exon4			AAGATCTGATGCC	AF311284	CCDS475.1	1p34	2014-07-19	2006-02-23		ENSG00000164010	ENSG00000164010		"Blood group antigens", "Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	15743	protein-coding gene	gene with protein product		609017	"Radin blood group", "Scianna blood group", "erythroblast membrane-associated protein", "erythroblast membrane-associated protein (RD and SC blood groups)"	RD, SC		11549310	Standard	XM_005270415		Approved	BTN5	uc001cie.1	Q96PL5	OTTHUMG00000007619	ENST00000372517.2:c.269T>A	chr1.hg19:g.43296622T>A	ENSP00000361595:p.Leu90Gln	166.0	0.0		137.0	74.0	NM_001017922	D3DPW8|Q5VV53|Q6DUE0|Q7Z3X0|Q8NCV8|Q8NCW2|Q8NCW3|Q96PL6	Missense_Mutation	SNP	ENST00000372517.2	hg19	CCDS475.1	.	.	.	.	.	.	.	.	.	.	T	10.38	1.335536	0.24253	.	.	ENSG00000164010	ENST00000372517;ENST00000372514	T;T	0.64803	-0.12;-0.12	4.83	-1.73	0.08081	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.598870	0.04053	N	0.305068	T	0.24236	0.0587	N	0.00405	-1.535	0.09310	N	0.999991	B;B	0.23249	0.082;0.003	B;B	0.23275	0.045;0.008	T	0.18147	-1.0346	10	0.13108	T	0.6	.	5.0935	0.14721	0.604:0.0974:0.0:0.2986	.	151;90	B7Z3C6;Q96PL5	.;ERMAP_HUMAN	Q	90	ENSP00000361595:L90Q;ENSP00000361592:L90Q	ENSP00000361592:L90Q	L	+	2	0	ERMAP	43069209	0.207000	0.23482	0.000000	0.03702	0.581000	0.36288	0.265000	0.18515	-0.072000	0.12864	0.377000	0.23210	CTG	.	.		0.587	ERMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020180.1	NM_018538		A	43296622	T	A	43296622	3	1	156	1	0	0	0	0	1	0	0	0	5236	1580	55	4	275	4	ERMAP	1	43296622	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10	11165438	43296622	205953999	2	23750										
NRAS	4893	hgsc.bcm.edu	37	chr1	115256600	115256600	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	acttgttttctgtaagaatcCtgggggtgtggagggtaagg	16	4	1	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr1:115256600C>T	ENST00000369535.4	-	3	365		c.e3-1			NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog						actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)			NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGTAAGAATCCTGGGGGTGTG	0.438		50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																											.		Atlas-SNP	.		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	.	NRAS	3766	.	0			c.112-1G>A						.						93	95	95					1																	115256600		2203	4300	6503	SO:0001630	splice_region_variant	4893	exon4	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	AGAATCCTGGGGG	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.112-1G>A	chr1.hg19:g.115256600C>T		63.0	0.0		60.0	38.0	NM_002524	Q14971|Q15104|Q15282	Splice_Site	SNP	ENST00000369535.4	hg19	CCDS877.1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.507519	0.64410	.	.	ENSG00000213281	ENST00000369535	.	.	.	3.72	3.72	0.42706	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7925	0.85593	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NRAS	115058123	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	7.547000	0.82146	2.378000	0.81104	0.655000	0.94253	.	.	.		0.438	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524	Intron	T	115256600	C	T	115256600	5	4	156	1	0	0	0	0	0	0	1	0	10649	695	24	3	470	3	NRAS	1	115256600	Splice_Site	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	71959978	115256600	133994021	3	23751										
TCHHL1	126637	hgsc.bcm.edu	37	chr1	152057498	152057498	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ccagcctctctctctgagggTgaccttgcttatcttccaag	8	14	3	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr1:152057498T>C	ENST00000368806.1	-	3	2724	c.2660A>G	c.(2659-2661)cAc>cGc	p.H887R		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	887							calcium ion binding (GO:0005509)			breast(4)|endometrium(1)|kidney(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(1)|skin(7)|stomach(1)	60	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			TCTCTGAGGGTGACCTTGCTT	0.507																																					p.H887R		Atlas-SNP	.											.	TCHHL1	132	.	0			c.A2660G						.						161	156	157					1																	152057498		2203	4300	6503	SO:0001583	missense	126637	exon3			TGAGGGTGACCTT		CCDS30857.1	1q21.3	2011-10-11	2004-10-05	2006-01-27	ENSG00000182898	ENSG00000182898		"S100 calcium binding proteins"	31796	protein-coding gene	gene with protein product			"S100 calcium binding protein A17"	S100A17, THHL1			Standard	NM_001008536		Approved		uc001ezo.1	Q5QJ38	OTTHUMG00000013058	ENST00000368806.1:c.2660A>G	chr1.hg19:g.152057498T>C	ENSP00000357796:p.His887Arg	104.0	0.0		209.0	71.0	NM_001008536	B2RPK8|Q5VTJ9	Missense_Mutation	SNP	ENST00000368806.1	hg19	CCDS30857.1	.	.	.	.	.	.	.	.	.	.	.	0.012	-1.676200	0.00751	.	.	ENSG00000182898	ENST00000368806	T	0.23552	1.9	3.7	-3.25	0.05079	.	0.711616	0.11587	N	0.549165	T	0.02649	0.0080	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45454	-0.9260	10	0.02654	T	1	1.678	9.2382	0.37479	0.0:0.5568:0.0:0.4432	.	887	Q5QJ38	TCHL1_HUMAN	R	887	ENSP00000357796:H887R	ENSP00000357796:H887R	H	-	2	0	TCHHL1	150324122	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.679000	0.05203	-0.836000	0.04229	0.482000	0.46254	CAC	.	.		0.507	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104		C	152057498	T	C	152057498	3	2	156	1	0	0	0	0	1	0	0	0	15716	1696	59	2	58	2	TCHHL1	1	152057498	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10	36800898	152057498	97193123	4	23752										
INTS3	11000	hgsc.bcm.edu	37	chr1	153745721	153745721	+	5'Flank	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gcggaaacgaaaagggtcctCtgcagtgggctctgacagtg	15	9	2	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr1:153745721C>T	ENST00000368661.3	+	0	0				INTS3_ENST00000512605.1_Missense_Mutation_p.S895F|INTS3_ENST00000318967.2_Missense_Mutation_p.S1035F|INTS3_ENST00000456435.1_Missense_Mutation_p.S895F|INTS3_ENST00000476843.1_3'UTR|SLC27A3_ENST00000271857.2_5'Flank|INTS3_ENST00000435409.2_Missense_Mutation_p.S1035F	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3						fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AAAGGGTCCTCTGCAGTGGGC	0.562																																					p.S1035F		Atlas-SNP	.											.	INTS3	83	.	0			c.C3104T						.						175	177	177					1																	153745721		2203	4300	6503	SO:0001631	upstream_gene_variant	65123	exon30			GGTCCTCTGCAGT	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"Acyl-CoA synthetase family", "Solute carriers"	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155		chr1.hg19:g.153745721C>T	Exception_encountered	93.0	0.0		189.0	146.0	NM_023015	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	hg19	CCDS1053.1	.	.	.	.	.	.	.	.	.	.	C	18.43	3.623310	0.66901	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.44159	0.1280	L	0.34521	1.04	0.29630	N	0.845506	D;D;D	0.64830	0.994;0.99;0.994	D;D;D	0.74348	0.983;0.962;0.983	T	0.28522	-1.0041	9	0.36615	T	0.2	.	13.5491	0.61721	0.0:1.0:0.0:0.0	.	895;1036;1035	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	F	1035;895;1035;895	.	ENSP00000318641:S1035F	S	+	2	0	INTS3	152012345	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.020000	0.70826	2.569000	0.86673	0.485000	0.47835	TCT	.	.		0.562	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330		T	153745721	C	T	153745721	1	4	156	0	1	0	0	0	0	0	0	0	7788	913	32	3		3	INTS3	1	153745721	5'Flank	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	1688223	153745721	95504900	5	23753										
F5	2153	hgsc.bcm.edu	37	chr1	169555596	169555596	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tggtgcccaagaccaccaggAcccagaggcgtgggcagcct	14	14	0	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr1:169555596A>C	ENST00000367797.3	-	1	230	c.29T>G	c.(28-30)gTc>gGc	p.V10G	F5_ENST00000546081.1_5'UTR|F5_ENST00000367796.3_Missense_Mutation_p.V10G	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	10					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GACCACCAGGACCCAGAGGCG	0.647																																					p.V10G		Atlas-SNP	.											.	F5	301	.	0			c.T29G						.						54	43	47					1																	169555596		2203	4300	6503	SO:0001583	missense	2153	exon1			ACCAGGACCCAGA	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.29T>G	chr1.hg19:g.169555596A>C	ENSP00000356771:p.Val10Gly	50.0	0.0		86.0	57.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	hg19	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.130688	0.56828	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.98567	-5.0;-5.0	5.41	3.08	0.35506	.	1.061280	0.07373	N	0.886136	D	0.93789	0.8014	L	0.29908	0.895	0.80722	D	1	P	0.49635	0.926	P	0.44597	0.454	D	0.88066	0.2797	10	0.87932	D	0	-4.3159	7.0736	0.25191	0.8193:0.0:0.1807:0.0	.	10	P12259	FA5_HUMAN	G	10	ENSP00000356771:V10G;ENSP00000356770:V10G	ENSP00000356770:V10G	V	-	2	0	F5	167822220	1.000000	0.71417	0.999000	0.59377	0.600000	0.36913	2.849000	0.48286	0.352000	0.24053	-0.290000	0.09829	GTC	.	.		0.647	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		C	169555596	A	C	169555596	3	2	156	1	0	0	0	0	1	0	0	0	5350	275	10	5	6745	5	F5	1	169555596	Missense_Mutation	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	15809875	169555596	79695025	6	23754										
SMG7	9887	hgsc.bcm.edu	37	chr1	183510238	183510238	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gattgctgataatcagccaaGgtaagtctggaacttctggt	11	7	3	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr1:183510238G>A	ENST00000347615.2	+	13	1534	c.1415G>A	c.(1414-1416)aGg>aAg	p.R472K	SMG7_ENST00000456731.2_Splice_Site_p.R430K|SMG7_ENST00000508461.1_Splice_Site_p.R430K|SMG7_ENST00000367537.3_Splice_Site_p.R501K|SMG7_ENST00000507469.1_Splice_Site_p.R472K|SMG7_ENST00000515829.2_Splice_Site_p.R472K	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	472					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						AATCAGCCAAGGTAAGTCTGG	0.478																																					p.R472K		Atlas-SNP	.											.	SMG7	165	.	0			c.G1415A						.						182	173	176					1																	183510238		2203	4300	6503	SO:0001630	splice_region_variant	9887	exon13			AGCCAAGGTAAGT	D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.1415+1G>A	chr1.hg19:g.183510238G>A		343.0	0.0		518.0	75.0	NM_201569	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	hg19	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.505476	0.44558	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000419169;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T;T	0.18657	2.2;2.2;2.2;2.2;2.2;2.2;2.2	5.57	5.57	0.84162	.	0.050293	0.85682	D	0.000000	T	0.10252	0.0251	N	0.14661	0.345	0.53688	D	0.999979	B;B;B;B;B;B	0.28801	0.091;0.042;0.042;0.07;0.146;0.223	B;B;B;B;B;B	0.21151	0.015;0.015;0.015;0.033;0.024;0.026	T	0.07501	-1.0769	10	0.05351	T	0.99	-8.9689	12.8444	0.57821	0.0743:0.0:0.9257:0.0	.	430;501;430;472;472;472	E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;.;SMG7_HUMAN;.	K	430;501;430;430;472;472;472	ENSP00000407629:R430K;ENSP00000356507:R501K;ENSP00000426915:R430K;ENSP00000388390:R430K;ENSP00000340766:R472K;ENSP00000425133:R472K;ENSP00000421358:R472K	ENSP00000340766:R472K	R	+	2	0	SMG7	181776861	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	6.978000	0.76147	2.619000	0.88677	0.650000	0.86243	AGG	.	.		0.478	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837	Missense_Mutation	A	183510238	G	A	183510238	5	1	156	1	0	0	0	0	0	0	1	0	14813	1014	35	3	1465	3	SMG7	1	183510238	Splice_Site	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	13954642	183510238	65740383	7	23755										
INTS7	25896	hgsc.bcm.edu	37	chr1	212118308	212118308	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ccggggcgatggtgacagagCaagctggaatgccaacactc	14	11	0	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr1:212118308C>G	ENST00000366994.3	-	19	2523	c.2419G>C	c.(2419-2421)Gct>Cct	p.A807P	INTS7_ENST00000366992.3_Missense_Mutation_p.A787P|INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000366993.3_Missense_Mutation_p.A793P|INTS7_ENST00000440600.2_Missense_Mutation_p.A758P	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	807					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		GGTGACAGAGCAAGCTGGAAT	0.488																																					p.A807P		Atlas-SNP	.											.	INTS7	68	.	0			c.G2419C						.						60	58	58					1																	212118308		2203	4300	6503	SO:0001583	missense	25896	exon19			ACAGAGCAAGCTG	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.2419G>C	chr1.hg19:g.212118308C>G	ENSP00000355961:p.Ala807Pro	69.0	0.0		123.0	5.0	NM_015434	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	hg19	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.024062	0.93462	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992;ENST00000440600	T;T;T;T	0.53640	0.7;0.68;0.61;0.69	5.64	5.64	0.86602	.	0.096924	0.64402	D	0.000001	T	0.69124	0.3076	M	0.65498	2.005	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.996;0.991;0.996;0.997	T	0.68633	-0.5357	10	0.52906	T	0.07	-18.8202	19.7094	0.96085	0.0:1.0:0.0:0.0	.	758;787;793;807	B4DLZ6;Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;.;INT7_HUMAN	P	807;793;787;758	ENSP00000355961:A807P;ENSP00000355960:A793P;ENSP00000355959:A787P;ENSP00000388908:A758P	ENSP00000355959:A787P	A	-	1	0	INTS7	210184931	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.591000	0.67536	2.662000	0.90505	0.655000	0.94253	GCT	.	.		0.488	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434		G	212118308	C	G	212118308	3	3	156	1	0	0	0	0	1	0	0	0	7792	710	25	4	477	4	INTS7	1	212118308	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	28608070	212118308	37132313	8	23756										
AGT	183	hgsc.bcm.edu	37	chr1	230838957	230838957	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tggcgctttgatcatacacaGcaaacaggaatgggcggttc	12	9	1	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr1:230838957G>A	ENST00000366667.4	-	5	1602	c.1388C>T	c.(1387-1389)gCt>gTt	p.A463V		NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	463					activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ATCATACACAGCAAACAGGAA	0.587																																					p.A463V		Atlas-SNP	.											.	AGT	62	.	0			c.C1388T						.						149	133	138					1																	230838957		2203	4300	6503	SO:0001583	missense	183	exon5			TACACAGCAAACA	K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"Serine (or cysteine) peptidase inhibitors", "Endogenous ligands"	333	protein-coding gene	gene with protein product	"alpha-1 antiproteinase, antitrypsin"	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.1388C>T	chr1.hg19:g.230838957G>A	ENSP00000355627:p.Ala463Val	153.0	0.0		264.0	105.0	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	hg19	CCDS1585.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.367362	0.41902	.	.	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.83419	-1.72	5.45	2.36	0.29203	Serpin domain (3);Protease inhibitor I4, serpin, conserved site (1);	0.353208	0.31636	N	0.007313	T	0.69851	0.3157	L	0.52011	1.625	0.09310	N	0.999998	P;P	0.49635	0.926;0.926	B;B	0.37833	0.259;0.259	T	0.62835	-0.6770	10	0.07325	T	0.83	.	8.0777	0.30726	0.2826:0.0:0.7174:0.0	.	463;463	B0ZBE2;P01019	.;ANGT_HUMAN	V	463;381	ENSP00000355627:A463V	ENSP00000355627:A463V	A	-	2	0	AGT	228905580	0.324000	0.24652	0.057000	0.19452	0.283000	0.27025	2.899000	0.48679	0.615000	0.30124	0.655000	0.94253	GCT	.	.		0.587	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		A	230838957	G	A	230838957	3	1	156	1	0	0	0	0	1	0	0	0	399	971	34	3	73	3	AGT	1	230838957	Missense_Mutation	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	18720649	230838957	18411664	9	23757										
EDARADD	128178	hgsc.bcm.edu	37	chr1	236590697	236590697	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ttttttttttcctagctgaaGaatgtgatacaattactttg	6	5	0	3			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr1:236590697G>C	ENST00000334232.4	+	4	333	c.166G>C	c.(166-168)Gaa>Caa	p.E56Q	EDARADD_ENST00000359362.5_Missense_Mutation_p.E46Q	NM_145861.2	NP_665860.2	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain	56					cell differentiation (GO:0030154)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|stomach(1)	12	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			cCTAGCTGAAGAATGTGATAC	0.318																																					p.E56Q		Atlas-SNP	.											.	EDARADD	31	.	0			c.G166C						.						30	32	31					1																	236590697		2199	4294	6493	SO:0001583	missense	128178	exon4			GCTGAAGAATGTG	AY028914	CCDS1610.1, CCDS31065.1	1q42.3	2013-05-22			ENSG00000186197	ENSG00000186197			14341	protein-coding gene	gene with protein product		606603				11780064	Standard	NM_145861		Approved		uc001hxu.1	Q8WWZ3	OTTHUMG00000039954	ENST00000334232.4:c.166G>C	chr1.hg19:g.236590697G>C	ENSP00000335076:p.Glu56Gln	263.0	0.0		417.0	65.0	NM_145861	A2VCK5|A8K7B5|B1AL54|B9ZVW5|Q5VYJ7	Missense_Mutation	SNP	ENST00000334232.4	hg19	CCDS1610.1	.	.	.	.	.	.	.	.	.	.	G	11.23	1.577957	0.28180	.	.	ENSG00000186197	ENST00000439430;ENST00000334232;ENST00000359362	T;T;D	0.81821	0.63;-0.98;-1.54	4.08	4.08	0.47627	.	0.239067	0.25391	U	0.031005	T	0.75810	0.3900	L	0.45228	1.405	0.28815	N	0.898019	P;B	0.34522	0.455;0.247	B;B	0.39771	0.309;0.214	T	0.71659	-0.4526	10	0.40728	T	0.16	.	12.0785	0.53657	0.0:0.0:1.0:0.0	.	46;56	A8K7B5;Q8WWZ3	.;EDAD_HUMAN	Q	34;56;46	ENSP00000405815:E34Q;ENSP00000335076:E56Q;ENSP00000352320:E46Q	ENSP00000335076:E56Q	E	+	1	0	EDARADD	234657320	0.814000	0.29104	0.515000	0.27774	0.073000	0.16967	3.731000	0.55013	2.542000	0.85734	0.655000	0.94253	GAA	.	.		0.318	EDARADD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096368.1	NM_145861		C	236590697	G	C	236590697	3	2	156	1	0	0	0	0	1	0	0	0	4908	943	33	4	215	4	EDARADD	1	236590697	Missense_Mutation	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	5751740	236590697	12659924	10	23758										
ODC1	4953	hgsc.bcm.edu	37	chr2	10580969	10580969	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tacttcgggtgggaagtcggGgttctggaattgctgcatga	16	6	1	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr2:10580969G>A	ENST00000234111.4	-	12	1777	c.1267C>T	c.(1267-1269)Ccc>Tcc	p.P423S	ODC1_ENST00000405333.1_Missense_Mutation_p.P423S	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	423					cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)			NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	GGGAAGTCGGGGTTCTGGAAT	0.512																																					p.P423S		Atlas-SNP	.											.	ODC1	40	.	0			c.C1267T						.						93	92	92					2																	10580969		2203	4300	6503	SO:0001583	missense	4953	exon12			AGTCGGGGTTCTG		CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4.1.1.17		8109	protein-coding gene	gene with protein product		165640					Standard	NM_002539		Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.1267C>T	chr2.hg19:g.10580969G>A	ENSP00000234111:p.Pro423Ser	129.0	0.0		82.0	39.0	NM_002539	Q53TU3|Q6LDS9	Missense_Mutation	SNP	ENST00000234111.4	hg19	CCDS1672.1	.	.	.	.	.	.	.	.	.	.	G	10.76	1.441013	0.25900	.	.	ENSG00000115758	ENST00000234111;ENST00000405333;ENST00000537630	T;T	0.39787	1.06;1.06	5.82	4.92	0.64577	.	0.542887	0.22838	N	0.055011	T	0.28797	0.0714	N	0.22421	0.69	0.23855	N	0.996658	B	0.02656	0.0	B	0.01281	0.0	T	0.11717	-1.0576	10	0.08599	T	0.76	.	16.085	0.81038	0.0:0.0:0.8649:0.1351	.	423	P11926	DCOR_HUMAN	S	423;423;294	ENSP00000234111:P423S;ENSP00000385333:P423S	ENSP00000234111:P423S	P	-	1	0	ODC1	10498420	0.967000	0.33354	0.078000	0.20375	0.711000	0.40976	4.756000	0.62205	1.423000	0.47198	0.591000	0.81541	CCC	.	.		0.512	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206896.2			A	10580969	G	A	10580969	3	1	156	1	0	0	0	0	1	0	0	0	10834	1232	43	3	122	3	ODC1	2	10580969	Missense_Mutation	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10		10580969	232618404	11	23759										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32774378	32774378	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	aattaatttcaacaatttttAggttcttgccagttacataa	4	6	2	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr2:32774378A>G	ENST00000421745.2	+	65	13109		c.e65-1			NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6						apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AACAATTTTTAGGTTCTTGCC	0.348																																					.	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.12976-2A>G						.						95	92	93					2																	32774378		2203	4300	6503	SO:0001630	splice_region_variant	57448	exon65			ATTTTTAGGTTCT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.12976-1A>G	chr2.hg19:g.32774378A>G		413.0	0.0		269.0	105.0	NM_016252	Q9ULD1	Splice_Site	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	19.69	3.874485	0.72180	.	.	ENSG00000115760	ENST00000421745	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9227	0.79589	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BIRC6	32627882	1.000000	0.71417	0.922000	0.36590	0.689000	0.40095	9.264000	0.95635	2.157000	0.67596	0.528000	0.53228	.	.	.		0.348	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	Intron	G	32774378	A	G	32774378	5	3	156	1	0	0	0	0	0	0	1	0	1438	434	15	2	13232	2	BIRC6	2	32774378	Splice_Site	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	22193409	32774378	210424995	12	23760										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613065	73613065	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gaggaggaggaggaggaggaGgaggaagaggaggaggctgc	25	2	0	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr2:73613065G>A	ENST00000264448.6	+	1	180	c.69G>A	c.(67-69)gaG>gaA	p.E23E	ALMS1_ENST00000409009.1_Silent_p.E23E|ALMS1_ENST00000377715.1_Silent_p.E23E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	23	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						aggaggaggaggaggaagagg	0.687																																					p.E23E		Atlas-SNP	.											.	ALMS1	384	.	0			c.G69A						.						6	9	8					2																	73613065		1849	3831	5680	SO:0001819	synonymous_variant	7840	exon1			GGAGGAGGAGGAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.69G>A	chr2.hg19:g.73613065G>A		551.0	0.0		444.0	30.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.687	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73613065	G	A	73613065	2	1	156	1	0	0	0	0	0	0	0	1	535	991	35	3		3	ALMS1	2	73613065	Silent	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	40838687	73613065	169586308	13	23761										
HK2	3099	hgsc.bcm.edu	37	chr2	75113492	75113492	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	atgacctgtggctttgaagaCcctcactgtgaagttggcct	11	10	1	4			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr2:75113492C>T	ENST00000290573.2	+	14	2607	c.2007C>T	c.(2005-2007)gaC>gaT	p.D669D	HK2_ENST00000409174.1_Silent_p.D641D	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	669	Catalytic.|Hexokinase type-1 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						GCTTTGAAGACCCTCACTGTG	0.537																																					p.D669D		Atlas-SNP	.											.	HK2	85	.	0			c.C2007T						.						229	186	201					2																	75113492		2203	4300	6503	SO:0001819	synonymous_variant	3099	exon14			TGAAGACCCTCAC		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.2007C>T	chr2.hg19:g.75113492C>T		102.0	0.0		71.0	25.0	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	hg19	CCDS1956.1																																																																																			.	.		0.537	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189		T	75113492	C	T	75113492	2	4	156	1	0	0	0	0	0	0	0	1	7200	506	18	3		3	HK2	2	75113492	Silent	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	1500427	75113492	168085881	14	23762										
KIF5C	3800	hgsc.bcm.edu	37	chr2	149803415	149803415	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	aactattttccttttcagacAtgaatgaacacagctctaga	5	9	2	4			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr2:149803415A>G	ENST00000435030.1	+	8	960	c.592A>G	c.(592-594)Atg>Gtg	p.M198V	KIF5C_ENST00000397413.1_5'Flank|KIF5C_ENST00000414838.2_Missense_Mutation_p.M103V			O60282	KIF5C_HUMAN	kinesin family member 5C	198	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		CTTTTCAGACATGAATGAACA	0.338																																					p.M198V		Atlas-SNP	.											.	KIF5C	166	.	0			c.A592G						.						90	82	85					2																	149803415		1841	4106	5947	SO:0001583	missense	3800	exon8			TCAGACATGAATG	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.592A>G	chr2.hg19:g.149803415A>G	ENSP00000393379:p.Met198Val	202.0	0.0		152.0	64.0	NM_004522	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	hg19		.	.	.	.	.	.	.	.	.	.	A	24.1	4.491804	0.84962	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436	T;T	0.74947	-0.89;-0.89	5.64	5.64	0.86602	Kinesin, motor domain (5);	0.000000	0.85682	D	0.000000	T	0.81583	0.4853	.	.	.	0.80722	D	1	P	0.49185	0.92	P	0.52343	0.696	D	0.84016	0.0351	9	0.87932	D	0	.	16.0238	0.80522	1.0:0.0:0.0:0.0	.	198	O60282	KIF5C_HUMAN	V	198;103;101	ENSP00000393379:M198V;ENSP00000410115:M103V	ENSP00000334176:M101V	M	+	1	0	KIF5C	149511661	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.139000	0.94554	2.367000	0.80283	0.528000	0.53228	ATG	.	.		0.338	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		G	149803415	A	G	149803415	3	3	156	1	0	0	0	0	1	0	0	0	8316	217	8	2	544	2	KIF5C	2	149803415	Missense_Mutation	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	74689923	149803415	93395958	15	23763										
TTN	7273	hgsc.bcm.edu	37	chr2	179500897	179500897	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ctctttgtttaactcgcagcTcaagtacaatggctgtcctt	7	11	2	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr2:179500897T>A	ENST00000591111.1	-	176	36702	c.36478A>T	c.(36478-36480)Agc>Tgc	p.S12160C	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S4861C|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S4736C|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S4928C|TTN-AS1_ENST00000418062.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S11233C|TTN_ENST00000589042.1_Missense_Mutation_p.S13801C|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12160	Ig-like 81.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AACTCGCAGCTCAAGTACAAT	0.453																																					p.S13801C		Atlas-SNP	.											.	TTN	18412	.	0			c.A41401T						.						61	58	59					2																	179500897		2008	4172	6180	SO:0001583	missense	7273	exon226			CGCAGCTCAAGTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.36478A>T	chr2.hg19:g.179500897T>A	ENSP00000465570:p.Ser12160Cys	108.0	0.0		73.0	29.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.69	2.909197	0.52439	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.05199	3.48;3.48;3.48;3.48	5.8	5.8	0.92144	Immunoglobulin subtype (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.13415	0.0325	L	0.41492	1.28	0.41298	D	0.987024	D;D;D;D	0.61697	0.99;0.99;0.99;0.978	P;P;P;P	0.53722	0.733;0.733;0.733;0.733	T	0.00485	-1.1711	9	0.87932	D	0	.	16.1445	0.81555	0.0:0.0:0.0:1.0	.	4736;4861;4928;12160	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	11233;4736;4928;4861;4736	ENSP00000343764:S11233C;ENSP00000434586:S4736C;ENSP00000340554:S4928C;ENSP00000352154:S4861C	ENSP00000340554:S4928C	S	-	1	0	TTN	179209142	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.175000	0.71949	2.223000	0.72356	0.477000	0.44152	AGC	.	.		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179500897	T	A	179500897	3	1	156	1	0	0	0	0	1	0	0	0	16750	1551	54	4	66840	4	TTN	2	179500897	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10	29697482	179500897	63698476	16	23764										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207174808	207174808	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ctggtgaaggagtttagggaAggtcgtttccactgttactt	13	6	0	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr2:207174808A>G	ENST00000374423.3	+	5	5942	c.5556A>G	c.(5554-5556)gaA>gaG	p.E1852E		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1852							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGTTTAGGGAAGGTCGTTTCC	0.423																																					p.E1852E		Atlas-SNP	.											.	ZDBF2	531	.	0			c.A5556G						.						79	75	76					2																	207174808		1874	4109	5983	SO:0001819	synonymous_variant	57683	exon5			TAGGGAAGGTCGT	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5556A>G	chr2.hg19:g.207174808A>G		164.0	0.0		107.0	43.0	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	hg19	CCDS46501.1																																																																																			.	.		0.423	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		G	207174808	A	G	207174808	2	3	156	1	0	0	0	0	0	0	0	1	17614	69	3	2		2	ZDBF2	2	207174808	Silent	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	27673911	207174808	36024565	17	23765										
COL4A3	1285	hgsc.bcm.edu	37	chr2	228141109	228141109	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	aatttccttaaggccctaggGgagagctcagtgtttcaaca	10	9	2	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr2:228141109G>T	ENST00000396578.3	+	27	2098	c.1936G>T	c.(1936-1938)Gga>Tga	p.G646*	AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000433324.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	646	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		AGGCCCTAGGGGAGAGCTCAG	0.498																																					p.G646X		Atlas-SNP	.											.	COL4A3	293	.	0			c.G1936T						.						68	70	69					2																	228141109		1889	4105	5994	SO:0001587	stop_gained	1285	exon27			CCTAGGGGAGAGC		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.1936G>T	chr2.hg19:g.228141109G>T	ENSP00000379823:p.Gly646*	105.0	0.0		81.0	28.0	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Nonsense_Mutation	SNP	ENST00000396578.3	hg19	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	G	40	7.940454	0.98571	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	.	.	.	5.33	5.33	0.75918	.	0.000000	0.56097	D	0.000025	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	14.8911	0.70609	0.0:0.0:1.0:0.0	.	.	.	.	X	646	.	ENSP00000323334:G646X	G	+	1	0	COL4A3	227849353	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	5.456000	0.66665	2.650000	0.89964	0.655000	0.94253	GGA	.	.		0.498	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		T	228141109	G	T	228141109	4	4	156	1	0	0	0	0	0	1	0	0	3693	1233	43	3	2042	3	COL4A3	2	228141109	Nonsense_Mutation	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	20966301	228141109	15058264	18	23766										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48698559	48698559	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tcatagctttccatgtgctcGcggtccactcggccgctggt	11	14	1	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr3:48698559G>A	ENST00000164024.4	-	1	1789	c.1509C>T	c.(1507-1509)cgC>cgT	p.R503R	CELSR3_ENST00000544264.1_Silent_p.R503R|RP11-148G20.1_ENST00000421275.1_RNA	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	503	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CCATGTGCTCGCGGTCCACTC	0.677																																					p.R503R		Atlas-SNP	.											.	CELSR3	237	.	0			c.C1509T						.						24	21	22					3																	48698559		2201	4298	6499	SO:0001819	synonymous_variant	1951	exon1			GTGCTCGCGGTCC	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.1509C>T	chr3.hg19:g.48698559G>A		129.0	0.0		131.0	33.0	NM_001407	O75092	Silent	SNP	ENST00000164024.4	hg19	CCDS2775.1																																																																																			.	.		0.677	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48698559	G	A	48698559	2	1	156	1	0	0	0	0	0	0	0	1	3225	1074	38	1		1	CELSR3	3	48698559	Silent	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10		48698559	149323871	19	23767										
ITIH3	3699	hgsc.bcm.edu	37	chr3	52834993	52834993	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tccaacaggtgagagcagacCcgaaaaaatccaagagaatg	10	9	0	3			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr3:52834993C>A	ENST00000449956.2	+	11	1220	c.1214C>A	c.(1213-1215)cCc>cAc	p.P405H	ITIH3_ENST00000416872.2_Missense_Mutation_p.P405H|ITIH3_ENST00000465243.2_3'UTR	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	405	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GAGAGCAGACCCGAAAAAATC	0.542																																					p.P405H		Atlas-SNP	.											.	ITIH3	132	.	0			c.C1214A						.						127	129	128					3																	52834993		1952	4147	6099	SO:0001583	missense	3699	exon11			GCAGACCCGAAAA		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.1214C>A	chr3.hg19:g.52834993C>A	ENSP00000415769:p.Pro405His	158.0	0.0		162.0	30.0	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	hg19	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	C	8.172	0.791978	0.16258	.	.	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	D;D	0.84223	-1.82;-1.82	4.82	3.86	0.44501	von Willebrand factor, type A (3);	0.419833	0.26082	N	0.026459	D	0.83413	0.5249	L	0.56280	1.765	0.09310	N	1	P;P	0.51933	0.949;0.923	P;P	0.56343	0.753;0.796	T	0.72184	-0.4367	10	0.14252	T	0.57	-8.4461	3.3063	0.07001	0.2292:0.5825:0.0:0.1884	.	405;405	E7ET33;Q06033	.;ITIH3_HUMAN	H	405;393;400;405;405	ENSP00000413922:P405H;ENSP00000415769:P405H	ENSP00000273291:P400H	P	+	2	0	ITIH3	52810033	0.012000	0.17670	0.742000	0.31022	0.032000	0.12392	1.830000	0.39131	2.502000	0.84385	0.655000	0.94253	CCC	.	.		0.542	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		A	52834993	C	A	52834993	3	1	156	1	0	0	0	0	1	0	0	0	7914	623	22	3	1256	3	ITIH3	3	52834993	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	4136434	52834993	145187437	20	23768										
CNTN3	5067	hgsc.bcm.edu	37	chr3	74334612	74334612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tttcatcttactggatgattCctcctttccacccccattcc	3	16	2	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr3:74334612C>T	ENST00000263665.6	-	19	2575	c.2548G>A	c.(2548-2550)Gaa>Aaa	p.E850K		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	850	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CTGGATGATTCCTCCTTTCCA	0.493																																					p.E850K		Atlas-SNP	.											.	CNTN3	174	.	0			c.G2548A						.						170	150	157					3																	74334612		2203	4300	6503	SO:0001583	missense	5067	exon19			ATGATTCCTCCTT	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.2548G>A	chr3.hg19:g.74334612C>T	ENSP00000263665:p.Glu850Lys	149.0	0.0		130.0	72.0	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	hg19	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.668143	0.29604	.	.	ENSG00000113805	ENST00000263665	T	0.54675	0.56	4.68	4.68	0.58851	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.451038	0.25578	N	0.029702	T	0.45478	0.1344	L	0.48935	1.535	0.41524	D	0.988417	B	0.14012	0.009	B	0.29176	0.099	T	0.31503	-0.9941	10	0.09338	T	0.73	.	13.2524	0.60060	0.0:0.7064:0.2936:0.0	.	850	Q9P232	CNTN3_HUMAN	K	850	ENSP00000263665:E850K	ENSP00000263665:E850K	E	-	1	0	CNTN3	74417302	0.994000	0.37717	0.015000	0.15790	0.232000	0.25224	2.340000	0.43974	2.269000	0.75478	0.655000	0.94253	GAA	.	.		0.493	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		T	74334612	C	T	74334612	3	4	156	1	0	0	0	0	1	0	0	0	3644	864	30	3	554	3	CNTN3	3	74334612	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	21499619	74334612	123687818	21	23769										
OR5H14	403273	hgsc.bcm.edu	37	chr3	97868504	97868504	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	cttagctaagagtaagatgaTatctctctctgaatgcaaga	8	7	2	5			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr3:97868504T>A	ENST00000437310.1	+	1	335	c.275T>A	c.(274-276)aTa>aAa	p.I92K	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	92						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						AGTAAGATGATATCTCTCTCT	0.393																																					p.I92K		Atlas-SNP	.											.	OR5H14	56	.	0			c.T275A						.						226	229	228					3																	97868504		2203	4299	6502	SO:0001583	missense	403273	exon1			AGATGATATCTCT		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"GPCR / Class A : Olfactory receptors"	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.275T>A	chr3.hg19:g.97868504T>A	ENSP00000401706:p.Ile92Lys	188.0	0.0		199.0	53.0	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	hg19	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.549848	0.45383	.	.	ENSG00000236032	ENST00000437310	T	0.00484	7.08	2.49	1.27	0.21489	GPCR, rhodopsin-like superfamily (1);	0.396031	0.21269	N	0.077344	T	0.01695	0.0054	H	0.98849	4.35	0.22446	N	0.99909	P	0.49358	0.923	P	0.55345	0.774	T	0.33343	-0.9872	10	0.87932	D	0	.	4.4478	0.11606	0.0:0.3322:0.0:0.6678	.	92	A6NHG9	O5H14_HUMAN	K	92	ENSP00000401706:I92K	ENSP00000401706:I92K	I	+	2	0	OR5H14	99351194	1.000000	0.71417	0.024000	0.17045	0.071000	0.16799	5.078000	0.64425	0.198000	0.20407	0.164000	0.16699	ATA	.	.		0.393	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			A	97868504	T	A	97868504	3	1	156	1	0	0	0	0	1	0	0	0	11169	1406	49	4	277	4	OR5H14	3	97868504	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10	23533892	97868504	100153926	22	23770										
A4GNT	51146	hgsc.bcm.edu	37	chr3	137849889	137849889	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	atcttggcagcagactctacGgaacaggagaccaaatgggg	13	9	2	2	rs374392631		TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr3:137849889G>A	ENST00000236709.3	-	2	411	c.210C>T	c.(208-210)tcC>tcT	p.S70S		NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	70					carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						CAGACTCTACGGAACAGGAGA	0.532																																					p.S70S		Atlas-SNP	.											.	A4GNT	42	.	0			c.C210T						.						102	102	102					3																	137849889		2203	4300	6503	SO:0001819	synonymous_variant	51146	exon2			CTCTACGGAACAG	AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.210C>T	chr3.hg19:g.137849889G>A		247.0	0.0		227.0	112.0	NM_016161	Q0VDK1|Q0VDK2	Silent	SNP	ENST00000236709.3	hg19	CCDS3097.1																																																																																			.	.		0.532	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	NM_016161		A	137849889	G	A	137849889	2	1	156	1	0	0	0	0	0	0	0	1	7	1103	39	1		1	A4GNT	3	137849889	Silent	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	39981385	137849889	60172541	23	23771										
FAM53A	152877	hgsc.bcm.edu	37	chr4	1657010	1657010	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ctcgctgctgtccacgaagcCgccgctggcggaggacggcc	15	16	0	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr4:1657010C>A	ENST00000308132.6	-	4	769	c.577G>T	c.(577-579)Ggc>Tgc	p.G193C	FAM53A_ENST00000472884.2_Missense_Mutation_p.G193C|FAM53A_ENST00000461064.1_Missense_Mutation_p.G193C|FAM53A_ENST00000489363.1_Missense_Mutation_p.G193C	NM_001174070.1	NP_001167541.1	Q6NSI3	FA53A_HUMAN	family with sequence similarity 53, member A	193						nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		all_epithelial(65;0.206)|Breast(71;0.212)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)			TCCACGAAGCCGCCGCTGGCG	0.751																																					p.G193C		Atlas-SNP	.											.	FAM53A	25	.	0			c.G577T						.						3	4	4					4																	1657010		1546	3374	4920	SO:0001583	missense	152877	exon4			CGAAGCCGCCGCT	BC070112	CCDS33939.1, CCDS75091.1	4p16.3	2005-08-09			ENSG00000174137	ENSG00000174137			31860	protein-coding gene	gene with protein product							Standard	NM_001013622		Approved	DNTNP	uc021xkl.1	Q6NSI3	OTTHUMG00000159855	ENST00000308132.6:c.577G>T	chr4.hg19:g.1657010C>A	ENSP00000310057:p.Gly193Cys	73.0	0.0		41.0	15.0	NM_001013622	Q6ZUL5	Missense_Mutation	SNP	ENST00000308132.6	hg19	CCDS33939.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530876	0.27387	.	.	ENSG00000174137	ENST00000308132;ENST00000489363;ENST00000461064;ENST00000472884	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	4.21	3.35	0.38373	.	0.110085	0.39407	U	0.001372	T	0.63248	0.2495	M	0.68593	2.085	0.44201	D	0.997027	D;D	0.89917	1.0;1.0	D;D	0.81914	0.991;0.995	T	0.60786	-0.7194	10	0.35671	T	0.21	-0.3812	12.1503	0.54046	0.0:0.9142:0.0:0.0858	.	193;193	Q6NSI3;C9JYQ7	FA53A_HUMAN;.	C	193	ENSP00000310057:G193C;ENSP00000419044:G193C;ENSP00000418243:G193C;ENSP00000426260:G193C	ENSP00000310057:G193C	G	-	1	0	FAM53A	1626807	0.973000	0.33851	0.018000	0.16275	0.065000	0.16274	0.653000	0.24902	0.752000	0.32923	0.467000	0.42956	GGC	.	.		0.751	FAM53A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359224.1	NM_001013622		A	1657010	C	A	1657010	3	1	156	1	0	0	0	0	1	0	0	0	5587	652	23	1	627	1	FAM53A	4	1657010	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10		1657010	189497266	24	23772										
CLNK	116449	hgsc.bcm.edu	37	chr4	10567642	10567642	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ccaaacgttacctgcatattCagattcctttataggccggg	8	11	1	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr4:10567642C>G	ENST00000226951.6	-	6	522	c.283G>C	c.(283-285)Gaa>Caa	p.E95Q	CLNK_ENST00000507719.1_Missense_Mutation_p.E53Q|CLNK_ENST00000442825.2_Missense_Mutation_p.E53Q	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	95					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						CCTGCATATTCAGATTCCTTT	0.428																																					p.E95Q	GBM(87;402 1286 6949 13902 35851)	Atlas-SNP	.											.	CLNK	85	.	0			c.G283C						.						55	54	54					4																	10567642		1860	4103	5963	SO:0001583	missense	116449	exon6			CATATTCAGATTC	AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"SH2 domain containing"	17438	protein-coding gene	gene with protein product	"mast cell immunoreceptor signal transducer"	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.283G>C	chr4.hg19:g.10567642C>G	ENSP00000226951:p.Glu95Gln	78.0	0.0		51.0	22.0	NM_052964	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	hg19	CCDS47024.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.543609	0.45280	.	.	ENSG00000109684	ENST00000226951;ENST00000429087;ENST00000442825;ENST00000507719	T;T;T	0.52754	1.74;0.65;0.65	5.55	4.66	0.58398	.	0.089086	0.41605	D	0.000842	T	0.45776	0.1359	N	0.24115	0.695	0.30591	N	0.761542	D;P	0.60160	0.987;0.911	P;B	0.53518	0.728;0.382	T	0.50816	-0.8783	10	0.66056	D	0.02	-24.9468	13.2003	0.59763	0.0:0.8256:0.1743:0.0	.	53;95	Q7Z7G1-2;Q7Z7G1	.;CLNK_HUMAN	Q	95;95;53;53	ENSP00000226951:E95Q;ENSP00000390744:E53Q;ENSP00000427208:E53Q	ENSP00000226951:E95Q	E	-	1	0	CLNK	10176740	0.967000	0.33354	0.987000	0.45799	0.469000	0.32828	2.195000	0.42677	2.616000	0.88540	0.585000	0.79938	GAA	.	.		0.428	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964		G	10567642	C	G	10567642	3	3	156	1	0	0	0	0	1	0	0	0	3549	835	29	4	1059	4	CLNK	4	10567642	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	8910632	10567642	180586634	25	23773										
TMEM165	55858	hgsc.bcm.edu	37	chr4	56284075	56284077	+	In_Frame_Del	DEL	CAA	CAA	-													0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ttatttcacccatttttgttCaagctcttacattaacattc							TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr4:56284075_56284077delCAA	ENST00000381334.5	+	4	948_950	c.715_717delCAA	c.(715-717)caadel	p.Q239del	TMEM165_ENST00000514904.1_3'UTR|TMEM165_ENST00000506198.1_Intron|TMEM165_ENST00000542052.1_In_Frame_Del_p.Q176del	NM_018475.4	NP_060945.2	Q9HC07	TM165_HUMAN	transmembrane protein 165	239					cellular calcium ion homeostasis (GO:0006874)|Golgi calcium ion transport (GO:0032472)|protein N-linked glycosylation (GO:0006487)|regulation of lysosomal lumen pH (GO:0035751)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				endometrium(1)|kidney(1)|large_intestine(2)	4	Lung NSC(11;0.00545)|Glioma(25;0.08)|all_neural(26;0.101)|all_epithelial(27;0.135)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0103)			CATTTTTGTTCAAGCTCTTACAT	0.399																																					p.238_239del		Atlas-INDEL	.											.	TMEM165	12	.	0			c.714_716del						.																																			SO:0001651	inframe_deletion	55858	exon4			.	AF183409	CCDS3499.1	4q12	2014-03-13			ENSG00000134851	ENSG00000134851			30760	protein-coding gene	gene with protein product	"TPA regulated locus"	614726				3202867, 22683087, 23575229	Standard	NM_018475		Approved	TMPT27, TPARL, GDT1	uc003hax.3	Q9HC07	OTTHUMG00000128735	ENST00000381334.5:c.715_717delCAA	chr4.hg19:g.56284075_56284077delCAA	ENSP00000370736:p.Gln239del	255.0	0.0		159.0	60.0	NM_018475	A8K3P8|B4DHW1|Q9BTN9|Q9NZ34	In_Frame_Del	DEL	ENST00000381334.5	hg19	CCDS3499.1																																																																																			.	.		0.399	TMEM165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250646.4	NM_018475		-	56284077	CAA	-	56284075	7	5	156	1	0	1	0	1	0	0	0	0	16095	827	29	0	729	0	TMEM165	4	56284075	In_Frame_Del	DEL	CAA	TCGA-DD-AACE-01A-11D-A40R-10	45716433	56284075	134870201	26	23774										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62897286	62897286	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	accattttcaattctctacaGggaatgtttatatttatttt	4	6	2	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr4:62897286G>T	ENST00000514591.1	+	22	3674	c.3345G>T	c.(3343-3345)caG>caT	p.Q1115H	LPHN3_ENST00000508946.1_Missense_Mutation_p.Q1115H|LPHN3_ENST00000507625.1_Missense_Mutation_p.Q1174H|LPHN3_ENST00000512091.2_Missense_Mutation_p.Q1115H|LPHN3_ENST00000508693.1_Missense_Mutation_p.Q1183H|LPHN3_ENST00000509896.1_Missense_Mutation_p.Q1183H|LPHN3_ENST00000514157.1_Missense_Mutation_p.Q1106H|LPHN3_ENST00000514996.1_Missense_Mutation_p.Q1106H|LPHN3_ENST00000506700.1_Missense_Mutation_p.Q1106H|LPHN3_ENST00000506746.1_Missense_Mutation_p.Q1174H|LPHN3_ENST00000504896.1_Missense_Mutation_p.Q1115H|LPHN3_ENST00000506720.1_Missense_Mutation_p.Q1183H|LPHN3_ENST00000507164.1_Missense_Mutation_p.Q1174H|LPHN3_ENST00000545650.1_Missense_Mutation_p.Q1115H|LPHN3_ENST00000511324.1_Missense_Mutation_p.Q1174H			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1093					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						ATTCTCTACAGGGAATGTTTA	0.343																																					p.Q1115H		Atlas-SNP	.											.	LPHN3	800	.	0			c.G3345T						.						94	89	91					4																	62897286		1823	4083	5906	SO:0001583	missense	23284	exon20			TCTACAGGGAATG	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.3345G>T	chr4.hg19:g.62897286G>T	ENSP00000422533:p.Gln1115His	128.0	0.0		83.0	28.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.63|18.63	3.664606|3.664606	0.67700|0.67700	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000502815|ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.60424	.|0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19	5.49|5.49	4.65|4.65	0.58169|0.58169	.|GPCR, family 2-like (1);GPCR, family 2, secretin-like, conserved site (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.80470|0.80470	0.4629|0.4629	M|M	0.90977|0.90977	3.165|3.165	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.71674	.|0.998;0.998;0.998	.|D;D;D	.|0.83275	.|0.996;0.996;0.994	D|D	0.85130|0.85130	0.0974|0.0974	5|10	.|0.87932	.|D	.|0	.|.	14.2726|14.2726	0.66159|0.66159	0.0716:0.0:0.9284:0.0|0.0716:0.0:0.9284:0.0	.|.	.|1115;1093;1115	.|E9PE04;Q9HAR2;Q9HAR2-2	.|.;LPHN3_HUMAN;.	W|H	564|1115;1115;1183;1174;1106;1115;1093;1115;1174;1183;1174;1106;1115;1115;1183;1174;1106	.|ENSP00000423388:Q1115H;ENSP00000422533:Q1115H;ENSP00000423787:Q1183H;ENSP00000425033:Q1174H;ENSP00000424120:Q1106H;ENSP00000439831:Q1115H;ENSP00000421476:Q1174H;ENSP00000424030:Q1183H;ENSP00000421372:Q1174H;ENSP00000425201:Q1106H;ENSP00000423434:Q1115H;ENSP00000421627:Q1115H;ENSP00000420931:Q1183H;ENSP00000425884:Q1174H;ENSP00000424258:Q1106H	.|ENSP00000280009:Q1115H	G|Q	+|+	1|3	0|2	LPHN3|LPHN3	62579881|62579881	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.422000|3.422000	0.52749|0.52749	1.322000|1.322000	0.45245|0.45245	0.655000|0.655000	0.94253|0.94253	GGG|CAG	.	.		0.343	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			T	62897286	G	T	62897286	3	4	156	1	0	0	0	0	1	0	0	0	8926	991	35	3	3423	3	LPHN3	4	62897286	Missense_Mutation	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	6613211	62897286	128256990	27	23775										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79360143	79360143	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	atggaccacaaccatctggaTaatcagatatttaccatcat	5	10	3	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr4:79360143T>C	ENST00000325942.6	+	40	5894	c.5454T>C	c.(5452-5454)gaT>gaC	p.D1818D	FRAS1_ENST00000264895.6_Silent_p.D1818D	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1818					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ACCATCTGGATAATCAGATAT	0.383																																					p.D1818D		Atlas-SNP	.											.	FRAS1	779	.	0			c.T5454C						.						211	212	211					4																	79360143		1898	4106	6004	SO:0001819	synonymous_variant	80144	exon40			TCTGGATAATCAG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.5454T>C	chr4.hg19:g.79360143T>C		72.0	0.0		52.0	24.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	T	9.385	1.074084	0.20227	.	.	ENSG00000138759	ENST00000510944;ENST00000512123	.	.	.	5.92	2.1	0.27182	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3334	0.26596	0.2425:0.6293:0.0:0.1282	.	.	.	.	Q	268;47	.	.	X	+	1	0	FRAS1	79579167	0.958000	0.32768	0.998000	0.56505	0.972000	0.66771	0.042000	0.13949	0.094000	0.17404	-0.292000	0.09595	TAA	.	.		0.383	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			C	79360143	T	C	79360143	2	2	156	1	0	0	0	0	0	0	0	1	6050	1403	49	2		2	FRAS1	4	79360143	Silent	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10	16462857	79360143	111794133	28	23776										
LRIT3	345193	hgsc.bcm.edu	37	chr4	110772751	110772751	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gcatagagaagactgtcatcCgcagaatctctgcggaggcc	12	11	2	3	rs544073628	byFrequency	TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr4:110772751C>T	ENST00000594814.1	+	2	208	c.208C>T	c.(208-210)Cgc>Tgc	p.R70C	LRIT3_ENST00000327908.3_5'UTR|LRIT3_ENST00000379920.3_Missense_Mutation_p.R25C	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	70					regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		GACTGTCATCCGCAGAATCTC	0.507													C|||	3	0.000599042	0	0	5008	,	,		18474	0		0	False		,,,				2504	0.0031				p.R70C		Atlas-SNP	.											.	LRIT3	107	.	0			c.C208T						.						84	78	80					4																	110772751		692	1591	2283	SO:0001583	missense	345193	exon2			GTCATCCGCAGAA	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"Immunoglobulin superfamily / I-set domain containing"	24783	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 4"	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.208C>T	chr4.hg19:g.110772751C>T	ENSP00000469759:p.Arg70Cys	104.0	0.0		89.0	36.0	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	hg19	CCDS3688.3	.	.	.	.	.	.	.	.	.	.	C	17.33	3.362117	0.61403	.	.	ENSG00000183423	ENST00000379920	T	0.59638	0.25	6.02	5.17	0.71159	.	.	.	.	.	T	0.71500	0.3347	L	0.49455	1.56	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.74349	-0.3694	9	0.66056	D	0.02	.	16.4149	0.83730	0.1392:0.8608:0.0:0.0	.	25	Q3SXY7	LRIT3_HUMAN	C	25	ENSP00000369252:R25C	ENSP00000369252:R25C	R	+	1	0	LRIT3	110992200	1.000000	0.71417	0.200000	0.23457	0.415000	0.31203	3.638000	0.54332	1.521000	0.48983	0.655000	0.94253	CGC	.	.		0.507	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506		T	110772751	C	T	110772751	3	4	156	1	0	0	0	0	1	0	0	0	8958	652	23	1	75	1	LRIT3	4	110772751	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	31412608	110772751	80381525	29	23777										
LARP1B	55132	hgsc.bcm.edu	37	chr4	129028555	129028555	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ttatttattttcagtttattTagatttgataggaaaattaa	5	1	1	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr4:129028555T>G	ENST00000326639.6	+	9	1199				LARP1B_ENST00000264584.5_Intron|LARP1B_ENST00000512292.1_Intron|LARP1B_ENST00000394288.3_Intron|LARP1B_ENST00000354456.3_Intron|LARP1B_ENST00000432347.2_Nonstop_Mutation_p.*359E|LARP1B_ENST00000441387.1_Intron|LARP1B_ENST00000427266.1_Intron	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B							nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						tcagtttatttaGATTTGATA	0.294																																					p.X359E		Atlas-SNP	.											.	LARP1B	120	.	0			c.T1075G						.						16	18	17					4																	129028555		1281	2299	3580	SO:0001627	intron_variant	55132	exon9			TTTATTTAGATTT		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.988+87T>G	chr4.hg19:g.129028555T>G		107.0	0.0		67.0	25.0	NM_032239	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Missense_Mutation	SNP	ENST00000326639.6	hg19	CCDS3738.1	.	.	.	.	.	.	.	.	.	.	T	0.013	-1.620350	0.00828	.	.	ENSG00000138709	ENST00000432347	.	.	.	4.97	1.13	0.20643	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.285	0.10850	0.0:0.2814:0.2432:0.4754	.	.	.	.	E	359	.	.	X	+	1	0	LARP1B	129248005	0.076000	0.21285	0.000000	0.03702	0.015000	0.08874	0.400000	0.20932	0.037000	0.15575	0.460000	0.39030	TAG	.	.		0.294	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		G	129028555	T	G	129028555	1	3	156	0	1	0	0	0	0	0	0	0	8638	1767	61	5		5	LARP1B	4	129028555	Intron	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10	18255804	129028555	62125721	30	23778										
TMEM144	55314	hgsc.bcm.edu	37	chr4	159162713	159162713	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	acctgctgttggttcatagcAaatcactctctgagtgctgt	9	10	3	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr4:159162713A>C	ENST00000296529.6	+	11	1375	c.855A>C	c.(853-855)gcA>gcC	p.A285A	TMEM144_ENST00000503404.1_3'UTR	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	285						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		GGTTCATAGCAAATCACTCTC	0.398																																					p.A285A		Atlas-SNP	.											.	TMEM144	34	.	0			c.A855C						.						288	260	270					4																	159162713		2203	4300	6503	SO:0001819	synonymous_variant	55314	exon11			CATAGCAAATCAC	AK002017	CCDS3799.1	4q32.1	2008-02-05			ENSG00000164124	ENSG00000164124			25633	protein-coding gene	gene with protein product						12477932	Standard	NM_018342		Approved	FLJ11155	uc003ipx.3	Q7Z5S9	OTTHUMG00000162013	ENST00000296529.6:c.855A>C	chr4.hg19:g.159162713A>C		57.0	0.0		43.0	10.0	NM_018342	D3DP24|Q49A05|Q9NUT3	Silent	SNP	ENST00000296529.6	hg19	CCDS3799.1																																																																																			.	.		0.398	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342		C	159162713	A	C	159162713	2	2	156	1	0	0	0	0	0	0	0	1	16073	117	5	5		5	TMEM144	4	159162713	Silent	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	30134158	159162713	31991563	31	23779										
HCN1	348980	hgsc.bcm.edu	37	chr5	45267245	45267245	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	aaaggctctcctcatcattgGatattcctccaggacctcgt	7	13	3	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr5:45267245G>T	ENST00000303230.4	-	7	1786	c.1729C>A	c.(1729-1731)Cca>Aca	p.P577T		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	577					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						CTCATCATTGGATATTCCTCC	0.433																																					p.P577T		Atlas-SNP	.											.	HCN1	298	.	0			c.C1729A						.						165	151	156					5																	45267245		2203	4300	6503	SO:0001583	missense	348980	exon7			TCATTGGATATTC	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1729C>A	chr5.hg19:g.45267245G>T	ENSP00000307342:p.Pro577Thr	127.0	0.0		149.0	44.0	NM_021072		Missense_Mutation	SNP	ENST00000303230.4	hg19	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	G	33	5.224588	0.95139	.	.	ENSG00000164588	ENST00000303230	D	0.98012	-4.66	5.91	5.91	0.95273	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.64402	D	0.000002	D	0.99155	0.9708	H	0.94423	3.535	0.80722	D	1	D	0.71674	0.998	D	0.71414	0.973	D	0.99143	1.0856	10	0.87932	D	0	.	20.2963	0.98556	0.0:0.0:1.0:0.0	.	577	O60741	HCN1_HUMAN	T	577	ENSP00000307342:P577T	ENSP00000307342:P577T	P	-	1	0	HCN1	45303002	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.813000	0.96785	0.655000	0.94253	CCA	.	.		0.433	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		T	45267245	G	T	45267245	3	4	156	1	0	0	0	0	1	0	0	0	7005	1174	41	3	951	3	HCN1	5	45267245	Missense_Mutation	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10		45267245	135648015	32	23780										
HCN1	348980	hgsc.bcm.edu	37	chr5	45645564	45645564	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tcccagtcctaaaattcatgAtcaggtccaataggaaaact	6	10	2	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr5:45645564A>G	ENST00000303230.4	-	2	629	c.572T>C	c.(571-573)aTc>aCc	p.I191T		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	191					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						AAAATTCATGATCAGGTCCAA	0.378																																					p.I191T		Atlas-SNP	.											.	HCN1	298	.	0			c.T572C						.						96	93	94					5																	45645564		2203	4300	6503	SO:0001583	missense	348980	exon2			TTCATGATCAGGT	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.572T>C	chr5.hg19:g.45645564A>G	ENSP00000307342:p.Ile191Thr	98.0	0.0		110.0	34.0	NM_021072		Missense_Mutation	SNP	ENST00000303230.4	hg19	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	A	15.72	2.917585	0.52546	.	.	ENSG00000164588	ENST00000303230	D	0.98732	-5.1	5.37	5.37	0.77165	Ion transport (1);	0.101606	0.41097	D	0.000944	D	0.97145	0.9067	L	0.39020	1.185	0.45528	D	0.998486	B	0.17268	0.021	B	0.32393	0.145	D	0.95460	0.8542	10	0.87932	D	0	.	15.3658	0.74519	1.0:0.0:0.0:0.0	.	191	O60741	HCN1_HUMAN	T	191	ENSP00000307342:I191T	ENSP00000307342:I191T	I	-	2	0	HCN1	45681321	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.038000	0.60285	0.454000	0.30748	ATC	.	.		0.378	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		G	45645564	A	G	45645564	3	3	156	1	0	0	0	0	1	0	0	0	7005	333	12	2	2128	2	HCN1	5	45645564	Missense_Mutation	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	378319	45645564	135269696	33	23781										
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67576424	67576424	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ggtcgcctagcatacctcatCagtattggcttacgcttcag	9	12	3	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr5:67576424C>T	ENST00000521381.1	+	6	1319	c.703C>T	c.(703-705)Cag>Tag	p.Q235*	PIK3R1_ENST00000274335.5_Nonsense_Mutation_p.Q235*|PIK3R1_ENST00000396611.1_Nonsense_Mutation_p.Q235*|PIK3R1_ENST00000521657.1_Nonsense_Mutation_p.Q235*	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	235	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CATACCTCATCAGTATTGGCT	0.333			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.Q235X		Atlas-SNP	.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1	869	.	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	c.C703T						.						127	141	136					5																	67576424		2203	4300	6503	SO:0001587	stop_gained	5295	exon6			CCTCATCAGTATT	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.703C>T	chr5.hg19:g.67576424C>T	ENSP00000428056:p.Gln235*	175.0	0.0		162.0	90.0	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Nonsense_Mutation	SNP	ENST00000521381.1	hg19	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	C	36	5.844556	0.97016	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-15.2429	20.0361	0.97558	0.0:1.0:0.0:0.0	.	.	.	.	X	235	.	ENSP00000274335:Q235X	Q	+	1	0	PIK3R1	67612180	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.294000	0.78760	2.745000	0.94114	0.462000	0.41574	CAG	.	.		0.333	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		T	67576424	C	T	67576424	4	4	156	1	0	0	0	0	0	1	0	0	11927	827	29	3	721	3	PIK3R1	5	67576424	Nonsense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	21930860	67576424	113338836	34	23782										
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140857013	140857013	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tctcagcccttacaatagtgCgtgttcaagtgtccgacatc	8	12	2	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr5:140857013C>T	ENST00000308177.3	+	1	1434	c.1330C>T	c.(1330-1332)Cgt>Tgt	p.R444C	PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB2_ENST00000522605.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	444	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R444C(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACAATAGTGCGTGTTCAAGT	0.522																																					p.R444C		Atlas-SNP	.											PCDHGC3_ENST00000308177,colon,NS,0,2	PCDHGC3	173	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1330T						.						124	124	124					5																	140857013		2203	4300	6503	SO:0001583	missense	5098	exon1			ATAGTGCGTGTTC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.1330C>T	chr5.hg19:g.140857013C>T	ENSP00000312070:p.Arg444Cys	150.0	0.0		128.0	77.0	NM_032402	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	hg19	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	C	9.017	0.984037	0.18889	.	.	ENSG00000240184	ENST00000308177	T	0.54279	0.58	5.19	0.914	0.19360	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.48095	0.1481	M	0.62209	1.925	0.09310	N	1	P;D	0.57257	0.941;0.979	B;B	0.43360	0.417;0.409	T	0.37384	-0.9708	9	0.38643	T	0.18	.	8.9568	0.35823	0.4851:0.4446:0.0:0.0703	.	444;444	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	C	444	ENSP00000312070:R444C	ENSP00000312070:R444C	R	+	1	0	PCDHGC3	140837197	0.000000	0.05858	0.134000	0.22075	0.431000	0.31685	0.205000	0.17356	0.362000	0.24319	0.655000	0.94253	CGT	.	.		0.522	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		T	140857013	C	T	140857013	3	4	156	1	0	0	0	0	1	0	0	0	11578	768	27	1	1332	1	PCDHGC3	5	140857013	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	73280589	140857013	40058247	35	23783										
TCOF1	6949	hgsc.bcm.edu	37	chr5	149758589	149758589	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tgcagctgctcaagccaagcAgaggtctccatccaaggcaa	10	13	2	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr5:149758589A>G	ENST00000504761.2	+	15	2462	c.2462A>G	c.(2461-2463)cAg>cGg	p.Q821R	TCOF1_ENST00000506063.1_3'UTR|TCOF1_ENST00000445265.2_Missense_Mutation_p.Q744R|TCOF1_ENST00000377797.3_Missense_Mutation_p.Q821R|TCOF1_ENST00000513346.1_Missense_Mutation_p.Q821R|TCOF1_ENST00000323668.7_Missense_Mutation_p.Q744R|TCOF1_ENST00000451292.1_Missense_Mutation_p.Q821R|TCOF1_ENST00000439160.2_Missense_Mutation_p.Q821R|TCOF1_ENST00000394269.3_Missense_Mutation_p.Q821R			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	821					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAAGCCAAGCAGAGGTCTCCA	0.592																																					p.Q821R		Atlas-SNP	.											.	TCOF1	154	.	0			c.A2462G						.						66	68	67					5																	149758589		2203	4300	6503	SO:0001583	missense	6949	exon15			CCAAGCAGAGGTC		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.2462A>G	chr5.hg19:g.149758589A>G	ENSP00000421655:p.Gln821Arg	197.0	0.0		147.0	84.0	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	hg19	CCDS54936.1	.	.	.	.	.	.	.	.	.	.	A	0.334	-0.954543	0.02285	.	.	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000394269;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14	4.84	-2.63	0.06133	Treacher Collins syndrome, treacle (1);	0.827549	0.10185	N	0.705343	T	0.48040	0.1478	L	0.59436	1.845	0.09310	N	1	B;B;B;B;B;B;B	0.25850	0.005;0.004;0.004;0.004;0.136;0.004;0.004	B;B;B;B;B;B;B	0.26517	0.007;0.004;0.004;0.004;0.07;0.004;0.004	T	0.44360	-0.9333	10	0.39692	T	0.17	-0.3141	0.2487	0.00202	0.3007:0.1411:0.1949:0.3632	.	330;821;744;821;821;744;821	B4DRA2;Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8;Q13428-5	.;.;.;.;TCOF_HUMAN;.;.	R	821;821;744;744;821;821;821;821;821	ENSP00000400939:Q821R;ENSP00000367028:Q821R;ENSP00000409944:Q744R;ENSP00000325223:Q744R;ENSP00000406888:Q821R;ENSP00000377811:Q821R;ENSP00000390717:Q821R;ENSP00000421655:Q821R;ENSP00000427484:Q821R	ENSP00000325223:Q744R	Q	+	2	0	TCOF1	149738782	0.000000	0.05858	0.270000	0.24601	0.046000	0.14306	-0.501000	0.06398	-0.172000	0.10779	0.459000	0.35465	CAG	.	.		0.592	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656		G	149758589	A	G	149758589	3	3	156	1	0	0	0	0	1	0	0	0	15723	188	7	2	2520	2	TCOF1	5	149758589	Missense_Mutation	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	8901576	149758589	31156671	36	23784										
FOXC1	2296	hgsc.bcm.edu	37	chr6	1612042	1612042	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ggcggcggcggcggcggcggGggaggccaggaggccggcca	25	12	0	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr6:1612042G>C	ENST00000380874.2	+	1	1362	c.1362G>C	c.(1360-1362)ggG>ggC	p.G454G		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	454	Poly-Gly.				artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		gcggcggcggGGGAGGCCAGG	0.751																																					p.G454G	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.G1362C						.						1	1	1					6																	1612042		591	1329	1920	SO:0001819	synonymous_variant	2296	exon1			CGGCGGGGGAGGC	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"Forkhead boxes"	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.1362G>C	chr6.hg19:g.1612042G>C		269.0	0.0		483.0	31.0	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Silent	SNP	ENST00000380874.2	hg19	CCDS4473.1																																																																																			.	.		0.751	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			C	1612042	G	C	1612042	2	2	156	1	0	0	0	0	0	0	0	1	6002	1219	43	4		4	FOXC1	6	1612042	Silent	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10		1612042	169503025	37	23785										
TREM1	54210	hgsc.bcm.edu	37	chr6	41250225	41250225	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gatacagtccagaatcttccActtgaaggttgaccattcgg	9	10	1	3			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr6:41250225A>G	ENST00000244709.4	-	2	377	c.314T>C	c.(313-315)gTg>gCg	p.V105A	TREM1_ENST00000589614.1_Missense_Mutation_p.V105A|TREM1_ENST00000334475.6_Missense_Mutation_p.V105A|TREM1_ENST00000591620.1_Missense_Mutation_p.V105A	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	105	Ig-like V-type.				blood coagulation (GO:0007596)|chemokine metabolic process (GO:0050755)|cytokine secretion involved in immune response (GO:0002374)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|neutrophil mediated killing of gram-negative bacterium (GO:0070945)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			NS(1)|breast(2)|endometrium(2)|large_intestine(5)|lung(5)|skin(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					AGAATCTTCCACTTGAAGGTT	0.512																																					p.V105A		Atlas-SNP	.											.	TREM1	38	.	0			c.T314C						.						102	75	84					6																	41250225		2203	4300	6503	SO:0001583	missense	54210	exon2			TCTTCCACTTGAA	AF196329	CCDS4854.1, CCDS56427.1, CCDS59499.1	6p21.1	2013-01-11			ENSG00000124731	ENSG00000124731		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	17760	protein-coding gene	gene with protein product		605085				11922939, 10799849	Standard	NM_018643		Approved	TREM-1, CD354	uc003oqf.2	Q9NP99	OTTHUMG00000014674	ENST00000244709.4:c.314T>C	chr6.hg19:g.41250225A>G	ENSP00000244709:p.Val105Ala	82.0	0.0		171.0	17.0	NM_001242590	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Missense_Mutation	SNP	ENST00000244709.4	hg19	CCDS4854.1	.	.	.	.	.	.	.	.	.	.	A	9.321	1.058110	0.19987	.	.	ENSG00000124731	ENST00000244709;ENST00000334475	T;T	0.64438	-0.1;-0.1	4.37	0.231	0.15377	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.188597	0.26159	N	0.025996	T	0.16727	0.0402	L	0.27053	0.805	0.09310	N	1	P;B	0.41910	0.764;0.376	B;B	0.41946	0.338;0.371	T	0.32295	-0.9912	10	0.06891	T	0.86	-5.9515	1.1955	0.01874	0.5214:0.1906:0.1042:0.1839	.	105;105	Q9NP99-2;Q9NP99	.;TREM1_HUMAN	A	105	ENSP00000244709:V105A;ENSP00000334284:V105A	ENSP00000244709:V105A	V	-	2	0	TREM1	41358203	0.000000	0.05858	0.056000	0.19401	0.242000	0.25591	-0.389000	0.07342	0.292000	0.22492	0.482000	0.46254	GTG	.	.		0.512	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040505.2	NM_018643		G	41250225	A	G	41250225	3	3	156	1	0	0	0	0	1	0	0	0	16485	159	6	2	402	2	TREM1	6	41250225	Missense_Mutation	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	39638183	41250225	129864842	38	23786										
RUNX2	860	hgsc.bcm.edu	37	chr6	45390469	45390469	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	cagcagcagcagcagcaacaGcagcagcagcagcaggaggc	14	13	0	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr6:45390469G>A	ENST00000371438.1	+	2	556	c.198G>A	c.(196-198)caG>caA	p.Q66Q	RUNX2_ENST00000352853.5_Silent_p.Q134Q|RUNX2_ENST00000576263.1_Silent_p.Q66Q|RUNX2_ENST00000371432.3_Silent_p.Q52Q|RUNX2_ENST00000371436.6_Silent_p.Q66Q|RUNX2_ENST00000359524.5_Silent_p.Q52Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000541979.1_Silent_p.Q134Q|RUNX2_ENST00000465038.2_Silent_p.Q66Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	66	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcaacagcagcagcagc	0.731																																					p.Q66Q		Atlas-SNP	.											.	RUNX2	128	.	0			c.G198A						.						9	14	13					6																	45390469		1431	3046	4477	SO:0001819	synonymous_variant	860	exon3			GCAACAGCAGCAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.198G>A	chr6.hg19:g.45390469G>A		66.0	0.0		149.0	7.0	NM_001024630	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	hg19	CCDS43467.2																																																																																			.	.		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		A	45390469	G	A	45390469	2	1	156	1	0	0	0	0	0	0	0	1	13763	962	34	3		3	RUNX2	6	45390469	Silent	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	4140244	45390469	125724598	39	23787										
SLC22A2	6582	hgsc.bcm.edu	37	chr6	160677694	160677694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	agccaataaagaatcctacaTtcactgatgactggaatagg	8	8	1	3			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr6:160677694T>C	ENST00000366953.3	-	2	728	c.470A>G	c.(469-471)aAt>aGt	p.N157S	SLC22A2_ENST00000491092.1_Intron|SLC22A2_ENST00000366952.1_Missense_Mutation_p.N136S	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	157					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	GAATCCTACATTCACTGATGA	0.443																																					p.N157S		Atlas-SNP	.											.	SLC22A2	78	.	0			c.A470G						.						129	121	124					6																	160677694		2203	4300	6503	SO:0001583	missense	6582	exon2			CCTACATTCACTG	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"Solute carriers"	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.470A>G	chr6.hg19:g.160677694T>C	ENSP00000355920:p.Asn157Ser	134.0	0.0		129.0	38.0	NM_003058	Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Missense_Mutation	SNP	ENST00000366953.3	hg19	CCDS5276.1	.	.	.	.	.	.	.	.	.	.	T	12.58	1.979359	0.34942	.	.	ENSG00000112499	ENST00000366953;ENST00000366952	T;T	0.73152	-0.72;-0.72	5.8	5.8	0.92144	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.050014	0.85682	D	0.000000	T	0.67050	0.2852	M	0.83312	2.635	0.40267	D	0.978246	B;B;P	0.36378	0.343;0.186;0.55	B;B;B	0.40901	0.343;0.302;0.259	T	0.68667	-0.5348	10	0.22706	T	0.39	.	16.1508	0.81622	0.0:0.0:0.0:1.0	.	157;157;157	O15244-3;O15244;O15244-2	.;S22A2_HUMAN;.	S	157;136	ENSP00000355920:N157S;ENSP00000355919:N136S	ENSP00000355919:N136S	N	-	2	0	SLC22A2	160597684	1.000000	0.71417	0.986000	0.45419	0.081000	0.17604	5.594000	0.67557	2.207000	0.71202	0.528000	0.53228	AAT	.	.		0.443	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058		C	160677694	T	C	160677694	3	2	156	1	0	0	0	0	1	0	0	0	14465	1493	52	2	1237	2	SLC22A2	6	160677694	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10	115287225	160677694	10437373	40	23788										
MYO1G	64005	hgsc.bcm.edu	37	chr7	45005789	45005789	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ccaaaggccacgtccccctgCagcccgtgctgctccaggag	11	18	0	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr7:45005789C>A	ENST00000258787.7	-	16	2176	c.2040G>T	c.(2038-2040)ctG>ctT	p.L680L		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	680	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						CGTCCCCCTGCAGCCCGTGCT	0.627																																					p.L680L		Atlas-SNP	.											.	MYO1G	86	.	0			c.G2040T						.						56	51	53					7																	45005789		2202	4300	6502	SO:0001819	synonymous_variant	64005	exon16			CCCCTGCAGCCCG	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"Myosins / Myosin superfamily : Class I"	13880	protein-coding gene	gene with protein product	"minor histocompatibility antigen HA-2"	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.2040G>T	chr7.hg19:g.45005789C>A		31.0	0.0		56.0	19.0	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Silent	SNP	ENST00000258787.7	hg19	CCDS34629.1																																																																																			.	.		0.627	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2			A	45005789	C	A	45005789	2	1	156	1	0	0	0	0	0	0	0	1	10083	697	25	3		3	MYO1G	7	45005789	Silent	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10		45005789	114132874	41	23789										
PON3	5446	hgsc.bcm.edu	37	chr7	94996796	94996796	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	acaacataaagatacacagtAttgtctacatggaaaaaagg	7	6	1	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr7:94996796A>T	ENST00000265627.5	-	5	382	c.372T>A	c.(370-372)aaT>aaA	p.N124K	PON3_ENST00000427422.1_Missense_Mutation_p.N124K|PON3_ENST00000451904.1_Missense_Mutation_p.N124K|PON1_ENST00000542556.1_Intron	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	124					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	GATACACAGTATTGTCTACAT	0.338																																					p.N124K		Atlas-SNP	.											.	PON3	59	.	0			c.T372A						.						106	112	110					7																	94996796		2203	4300	6503	SO:0001583	missense	5446	exon5			CACAGTATTGTCT	L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"Paraoxonases"	9206	protein-coding gene	gene with protein product	"arylesterase 3"	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.372T>A	chr7.hg19:g.94996796A>T	ENSP00000265627:p.Asn124Lys	82.0	0.0		140.0	55.0	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Missense_Mutation	SNP	ENST00000265627.5	hg19	CCDS5639.1	.	.	.	.	.	.	.	.	.	.	A	3.988	-0.004988	0.07773	.	.	ENSG00000105852	ENST00000265627;ENST00000427422	T;T	0.16743	2.32;2.32	4.78	-4.22	0.03800	Six-bladed beta-propeller, TolB-like (1);	0.383815	0.30235	N	0.010081	T	0.10380	0.0254	L	0.49778	1.585	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.001	T	0.16867	-1.0388	10	0.49607	T	0.09	-0.2762	1.0575	0.01593	0.401:0.1062:0.2663:0.2265	.	172;124	B4E2I0;Q15166	.;PON3_HUMAN	K	124	ENSP00000265627:N124K;ENSP00000413276:N124K	ENSP00000265627:N124K	N	-	3	2	PON3	94834732	0.005000	0.15991	0.015000	0.15790	0.018000	0.09664	-0.349000	0.07731	-0.849000	0.04158	-0.449000	0.05564	AAT	.	.		0.338	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940		T	94996796	A	T	94996796	3	4	156	1	0	0	0	0	1	0	0	0	12259	446	16	4	712	4	PON3	7	94996796	Missense_Mutation	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	49991007	94996796	64141867	42	23790										
FBXO24	26261	hgsc.bcm.edu	37	chr7	100187289	100187289	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gtgggaaagccagcaggaacGggggggccaagggcctagga	20	8	0	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr7:100187289G>A	ENST00000241071.6	+	2	361				PCOLCE-AS1_ENST00000442166.2_RNA|FBXO24_ENST00000465843.1_Intron|FBXO24_ENST00000498195.1_Intron|FBXO24_ENST00000468962.1_Intron|FBXO24_ENST00000427939.2_Missense_Mutation_p.R9Q|FBXO24_ENST00000360609.2_Intron	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24						protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CAGCAGGAACGGGGGGGCCAA	0.647																																					p.R9Q		Atlas-SNP	.											FBXO24_ENST00000427939,NS,carcinoma,0,3	FBXO24	125	.	0			c.G26A						.						31	35	34					7																	100187289		692	1591	2283	SO:0001627	intron_variant	26261	exon1			AGGAACGGGGGGG	AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"F-boxes /  "other""	13595	protein-coding gene	gene with protein product		609097	"F-box only protein 24"			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.40-311G>A	chr7.hg19:g.100187289G>A		199.0	0.0		217.0	20.0	NM_012172	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	hg19	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	g	4.423	0.078205	0.08485	.	.	ENSG00000106336	ENST00000427939	T	0.14022	2.54	2.59	0.365	0.16131	.	.	.	.	.	T	0.09555	0.0235	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31916	-0.9926	8	0.87932	D	0	.	4.4001	0.11383	0.2602:0.4827:0.2571:0.0	.	9	B4DX91	.	Q	9	ENSP00000416558:R9Q	ENSP00000416558:R9Q	R	+	2	0	FBXO24	100025225	0.719000	0.27986	0.002000	0.10522	0.217000	0.24651	0.736000	0.26130	0.416000	0.25844	-0.993000	0.02533	CGG	.	.		0.647	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1			A	100187289	G	A	100187289	1	1	156	0	1	0	0	0	0	0	0	0	5743	1116	39	1		1	FBXO24	7	100187289	Intron	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	5190493	100187289	58951374	43	23791										
EPHB4	2050	hgsc.bcm.edu	37	chr7	100420008	100420008	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tagaggctggggctggggccAggggcggggacggcatccac	21	10	0	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr7:100420008A>T	ENST00000358173.3	-	4	1161	c.693T>A	c.(691-693)ccT>ccA	p.P231P	RN7SL750P_ENST00000582814.1_RNA|EPHB4_ENST00000477446.1_5'UTR|EPHB4_ENST00000360620.3_Silent_p.P231P	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	231	Cys-rich.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					GGCTGGGGCCAGGGGCGGGGA	0.692																																					p.P231P	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.T693A						.						11	13	12					7																	100420008		2181	4257	6438	SO:0001819	synonymous_variant	2050	exon4			GGGGCCAGGGGCG	AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3395	protein-coding gene	gene with protein product		600011	"EphB4"	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.693T>A	chr7.hg19:g.100420008A>T		108.0	0.0		149.0	61.0	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Silent	SNP	ENST00000358173.3	hg19	CCDS5706.1																																																																																			.	.		0.692	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		T	100420008	A	T	100420008	2	4	156	1	0	0	0	0	0	0	0	1	5179	175	7	4		4	EPHB4	7	100420008	Silent	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	232719	100420008	58718655	44	23792										
LHFPL3	375612	hgsc.bcm.edu	37	chr7	103969251	103969251	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	cccggagccgccgccgctgcCgccgccgccgccgccgcgat	14	23	0	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr7:103969251C>T	ENST00000535008.1	+	1	148	c.24C>T	c.(22-24)gcC>gcT	p.A8A	LHFPL3_ENST00000401970.2_5'UTR|LHFPL3_ENST00000543266.1_Silent_p.A8A|LHFPL3_ENST00000424859.1_5'UTR			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	8						integral component of membrane (GO:0016021)		p.A8A(1)		kidney(1)|large_intestine(2)|lung(6)	9						ccgccgctgccgccgccgccg	0.721																																					p.A8A		Atlas-SNP	.											LHFPL3,NS,carcinoma,0,1	LHFPL3	24	.	1	Substitution - coding silent(1)	kidney(1)	c.C24T						.						11	14	13					7																	103969251		1949	4092	6041	SO:0001819	synonymous_variant	375612	exon1			CGCTGCCGCCGCC	AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416			6589	protein-coding gene	gene with protein product		609719	"lipoma HMGIC fusion partner-like 4"	LHFPL4		10329012	Standard	NM_199000		Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000535008.1:c.24C>T	chr7.hg19:g.103969251C>T		38.0	0.0		50.0	2.0	NM_199000	A1L383|A4D0Q5	Silent	SNP	ENST00000535008.1	hg19																																																																																				.	.		0.721	LHFPL3-201	KNOWN	basic	protein_coding	protein_coding		NM_199000		T	103969251	C	T	103969251	2	4	156	1	0	0	0	0	0	0	0	1	8775	639	23	1		1	LHFPL3	7	103969251	Silent	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	3549243	103969251	55169412	45	23793										
GCC1	79571	hgsc.bcm.edu	37	chr7	127225186	127225186	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tgggtctctatagtctccagCaagtccttcttgctcgggcc	10	13	3	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr7:127225186C>T	ENST00000321407.2	-	1	475	c.51G>A	c.(49-51)ttG>ttA	p.L17L	GCC1_ENST00000497650.1_Intron	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	17					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TAGTCTCCAGCAAGTCCTTCT	0.552											OREG0003808	type=REGULATORY REGION|Gene=GCC1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.L17L		Atlas-SNP	.											.	GCC1	83	.	0			c.G51A						.						81	87	85					7																	127225186		2203	4300	6503	SO:0001819	synonymous_variant	79571	exon1			CTCCAGCAAGTCC	AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"golgi coiled-coil 1"			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.51G>A	chr7.hg19:g.127225186C>T		64.0	0.0	1555	101.0	50.0	NM_024523	Q9H6N7	Silent	SNP	ENST00000321407.2	hg19	CCDS5796.1																																																																																			.	.		0.552	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523		T	127225186	C	T	127225186	2	4	156	1	0	0	0	0	0	0	0	1	6293	709	25	3		3	GCC1	7	127225186	Silent	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	23255935	127225186	31913477	46	23794										
ZNF282	8427	hgsc.bcm.edu	37	chr7	148895528	148895528	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ccgcatgatgcgagagccccAgttgcccacagcagagatct	11	14	1	3			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr7:148895528A>T	ENST00000262085.3	+	2	374	c.269A>T	c.(268-270)cAg>cTg	p.Q90L	ZNF282_ENST00000479907.1_Missense_Mutation_p.Q90L	NM_003575.2	NP_003566.1	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	90					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	17	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)		CGAGAGCCCCAGTTGCCCACA	0.607																																					p.Q90L		Atlas-SNP	.											.	ZNF282	42	.	0			c.A269T						.						49	47	48					7																	148895528		2203	4300	6503	SO:0001583	missense	8427	exon2			AGCCCCAGTTGCC	D30612	CCDS5895.1	7q36.1	2013-01-08			ENSG00000170265	ENSG00000170265		"Zinc fingers, C2H2-type", "-"	13076	protein-coding gene	gene with protein product		603397				9396811	Standard	NM_003575		Approved	HUB1	uc003wfm.3	Q9UDV7	OTTHUMG00000158974	ENST00000262085.3:c.269A>T	chr7.hg19:g.148895528A>T	ENSP00000262085:p.Gln90Leu	91.0	0.0		134.0	69.0	NM_003575	B4DRI5|O43691|Q6DKK0	Missense_Mutation	SNP	ENST00000262085.3	hg19	CCDS5895.1	.	.	.	.	.	.	.	.	.	.	A	13.34	2.207887	0.39003	.	.	ENSG00000170265	ENST00000430197;ENST00000262085;ENST00000479907	T;T	0.07021	3.23;5.05	4.26	4.26	0.50523	.	0.000000	0.40554	N	0.001072	T	0.07324	0.0185	N	0.24115	0.695	0.36109	D	0.844665	P;B;B;B	0.41313	0.745;0.18;0.18;0.281	B;B;B;B	0.41813	0.367;0.052;0.11;0.11	T	0.30822	-0.9965	10	0.56958	D	0.05	-31.88	10.0483	0.42199	1.0:0.0:0.0:0.0	.	90;41;62;90	B4DRI5;Q86YG2;Q7Z2V4;Q9UDV7	.;.;.;ZN282_HUMAN	L	5;90;90	ENSP00000262085:Q90L;ENSP00000418840:Q90L	ENSP00000262085:Q90L	Q	+	2	0	ZNF282	148526461	0.988000	0.35896	0.998000	0.56505	0.797000	0.45037	2.740000	0.47418	1.704000	0.51252	0.260000	0.18958	CAG	.	.		0.607	ZNF282-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352746.1	NM_003575		T	148895528	A	T	148895528	3	4	156	1	0	0	0	0	1	0	0	0	17834	188	7	4	275	4	ZNF282	7	148895528	Missense_Mutation	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	21670342	148895528	10243135	47	23795										
EXTL3	2137	hgsc.bcm.edu	37	chr8	28573960	28573960	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gagaacgccaagcaggacctGctccagctcaagaatgtcat	10	12	2	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr8:28573960G>T	ENST00000220562.4	+	3	1286	c.384G>T	c.(382-384)ctG>ctT	p.L128L	EXTL3_ENST00000523149.1_Intron|EXTL3_ENST00000519886.1_Intron	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	128					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)			biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		AGCAGGACCTGCTCCAGCTCA	0.567																																					p.L128L		Atlas-SNP	.											.	EXTL3	83	.	0			c.G384T						.						47	41	43					8																	28573960		2203	4300	6503	SO:0001819	synonymous_variant	2137	exon3			GGACCTGCTCCAG	U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"Exostosin glycosyltransferase family"	3518	protein-coding gene	gene with protein product	"REG receptor", "glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"	605744	"exostoses (multiple)-like 3"			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.384G>T	chr8.hg19:g.28573960G>T		66.0	0.0		60.0	15.0	NM_001440	D3DST8|O00225|Q53XT3	Silent	SNP	ENST00000220562.4	hg19	CCDS6070.1																																																																																			.	.		0.567	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440		T	28573960	G	T	28573960	2	4	156	1	0	0	0	0	0	0	0	1	5329	1306	46	3		3	EXTL3	8	28573960	Silent	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10		28573960	117790062	48	23796										
PREX2	80243	hgsc.bcm.edu	37	chr8	69046429	69046429	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ggaaaatgagatggaaacttGggaagccagcaggaggtggc	17	5	0	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr8:69046429G>C	ENST00000288368.4	+	32	4179	c.3902G>C	c.(3901-3903)tGg>tCg	p.W1301S		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1301					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						ATGGAAACTTGGGAAGCCAGC	0.493																																					p.W1301S		Atlas-SNP	.											.	PREX2	614	.	0			c.G3902C						.						113	104	107					8																	69046429		2203	4300	6503	SO:0001583	missense	80243	exon32			AAACTTGGGAAGC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3902G>C	chr8.hg19:g.69046429G>C	ENSP00000288368:p.Trp1301Ser	108.0	0.0		108.0	38.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	10.01	1.233571	0.22626	.	.	ENSG00000046889	ENST00000288368	T	0.39229	1.09	5.42	4.53	0.55603	.	0.662276	0.15201	N	0.275005	T	0.21801	0.0525	N	0.08118	0	0.36684	D	0.879239	B	0.02656	0.0	B	0.01281	0.0	T	0.11203	-1.0597	10	0.45353	T	0.12	.	5.9928	0.19476	0.0748:0.1288:0.6457:0.1506	.	1301	Q70Z35	PREX2_HUMAN	S	1301	ENSP00000288368:W1301S	ENSP00000288368:W1301S	W	+	2	0	PREX2	69208983	0.950000	0.32346	0.984000	0.44739	0.991000	0.79684	1.693000	0.37742	1.282000	0.44496	-0.176000	0.13171	TGG	.	.		0.493	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		C	69046429	G	C	69046429	3	2	156	1	0	0	0	0	1	0	0	0	12489	1357	47	4	4257	4	PREX2	8	69046429	Missense_Mutation	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	40472469	69046429	77317593	49	23797										
ZNF696	79943	hgsc.bcm.edu	37	chr8	144375190	144375190	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	agatggagccaggaggagagCccacaggtgctaaagagagc	16	8	0	3			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr8:144375190C>G	ENST00000330143.3	+	2	428	c.19C>G	c.(19-21)Ccc>Gcc	p.P7A	ZNF696_ENST00000520333.1_Missense_Mutation_p.P7A|RP13-582O9.7_ENST00000607376.1_RNA|ZNF696_ENST00000521537.1_Missense_Mutation_p.P7A	NM_030895.2	NP_112157.2	Q9H7X3	ZN696_HUMAN	zinc finger protein 696	7					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			AGGAGGAGAGCCCACAGGTGC	0.522																																					p.P7A		Atlas-SNP	.											.	ZNF696	18	.	0			c.C19G						.						87	76	80					8																	144375190		2203	4300	6503	SO:0001583	missense	79943	exon2			GGAGAGCCCACAG	AK024191	CCDS6399.1	8q24.3	2013-01-08				ENSG00000185730		"Zinc fingers, C2H2-type"	25872	protein-coding gene	gene with protein product							Standard	NM_030895		Approved	FLJ14129	uc003yxy.4	Q9H7X3		ENST00000330143.3:c.19C>G	chr8.hg19:g.144375190C>G	ENSP00000328515:p.Pro7Ala	118.0	0.0		127.0	46.0	NM_030895	A0AVE2	Missense_Mutation	SNP	ENST00000330143.3	hg19	CCDS6399.1	.	.	.	.	.	.	.	.	.	.	C	0.599	-0.829883	0.02734	.	.	ENSG00000185730	ENST00000523891;ENST00000518575;ENST00000330143;ENST00000521537;ENST00000518432	T;T	0.06687	3.27;3.36	1.09	-2.13	0.07144	.	.	.	.	.	T	0.03220	0.0094	N	0.08118	0	0.09310	N	1	B	0.24132	0.098	B	0.14578	0.011	T	0.45220	-0.9276	9	0.21540	T	0.41	.	5.0439	0.14473	0.0:0.5056:0.0:0.4944	.	7	Q9H7X3	ZN696_HUMAN	A	23;7;7;7;7	ENSP00000427857:P7A;ENSP00000328515:P7A	ENSP00000328515:P7A	P	+	1	0	ZNF696	144446565	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.069000	0.11542	-0.873000	0.04032	-0.253000	0.11424	CCC	.	.		0.522	ZNF696-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381164.2	NM_030895		G	144375190	C	G	144375190	3	3	156	1	0	0	0	0	1	0	0	0	18114	739	26	4	21	4	ZNF696	8	144375190	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	75328761	144375190	1988832	50	23798										
MAMDC2	256691	hgsc.bcm.edu	37	chr9	72723289	72723289	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	cagccagctgaacctctacaTgagatttgaagatgaaagct	9	9	1	5			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr9:72723289T>A	ENST00000377182.4	+	3	928	c.311T>A	c.(310-312)aTg>aAg	p.M104K	MAMDC2-AS1_ENST00000591368.1_RNA|MAMDC2-AS1_ENST00000414515.3_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	104	MAM 1. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						AACCTCTACATGAGATTTGAA	0.488																																					p.M104K		Atlas-SNP	.											.	MAMDC2	55	.	0			c.T311A						.						75	74	75					9																	72723289		2203	4300	6503	SO:0001583	missense	256691	exon3			TCTACATGAGATT	BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.311T>A	chr9.hg19:g.72723289T>A	ENSP00000366387:p.Met104Lys	113.0	0.0		89.0	34.0	NM_153267	Q5VW47|Q8WX43|Q96BM4	Missense_Mutation	SNP	ENST00000377182.4	hg19	CCDS6631.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.056845	0.55325	.	.	ENSG00000165072	ENST00000377182	T	0.02158	4.42	5.93	5.93	0.95920	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.648767	0.16015	N	0.233581	T	0.03390	0.0098	L	0.32530	0.975	0.35152	D	0.76989	B	0.15719	0.014	B	0.24006	0.05	T	0.47736	-0.9094	10	0.40728	T	0.16	-6.8559	16.3701	0.83353	0.0:0.0:0.0:1.0	.	104	Q7Z304	MAMC2_HUMAN	K	104	ENSP00000366387:M104K	ENSP00000366387:M104K	M	+	2	0	MAMDC2	71913109	0.884000	0.30299	0.987000	0.45799	0.990000	0.78478	2.667000	0.46808	2.257000	0.74773	0.528000	0.53228	ATG	.	.		0.488	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267		A	72723289	T	A	72723289	3	1	156	1	0	0	0	0	1	0	0	0	9212	1464	51	4	321	4	MAMDC2	9	72723289	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10		72723289	68490142	51	23799										
C10orf47	254427	hgsc.bcm.edu	37	chr10	11912120	11912120	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gctccgcggggcccggcgctGgccaacggcttcccaagtgc	15	17	0	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr10:11912120G>A	ENST00000277570.5	+	4	1177	c.1023G>A	c.(1021-1023)ctG>ctA	p.L341L	PROSER2_ENST00000379200.1_Silent_p.L145L|PROSER2-AS1_ENST00000453242.1_RNA|PROSER2-AS1_ENST00000445498.1_RNA	NM_153256.3	NP_694988.3	Q86WR7	PRSR2_HUMAN	proline and serine rich 2	341																	GCCCGGCGCTGGCCAACGGCT	0.781																																					p.L341L		Atlas-SNP	.											.	.	.	.	0			c.G1023A						.						2	2	2					10																	11912120		1194	2378	3572	SO:0001819	synonymous_variant	254427	exon4			GGCGCTGGCCAAC	BC017269	CCDS7085.1	10p14	2014-02-19	2014-02-19	2012-12-05	ENSG00000148426	ENSG00000148426			23728	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 47", "proline and serine-rich protein 2"	C10orf47		12477932	Standard	NM_153256		Approved	MGC35403	uc001ikx.3	Q86WR7	OTTHUMG00000017673	ENST00000277570.5:c.1023G>A	chr10.hg19:g.11912120G>A		10.0	0.0		26.0	7.0	NM_153256	D3DRR8|Q5W0J9|Q5W0K0|Q5W0K1|Q5W0K2|Q6PJC8|Q8N317	Silent	SNP	ENST00000277570.5	hg19	CCDS7085.1																																																																																			.	.		0.781	PROSER2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090189.2	NM_153256		A	11912120	G	A	11912120	2	1	156	1	0	0	0	0	0	0	0	1	1607	1335	47	3		3	C10orf47	10	11912120	Silent	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10		11912120	123622627	52	23800										
CUBN	8029	hgsc.bcm.edu	37	chr10	17169878	17169878	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tatattttgaggcagaccaaTtgcactcccttttaactcta	5	10	1	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr10:17169878T>C	ENST00000377833.4	-	3	363	c.298A>G	c.(298-300)Att>Gtt	p.I100V	CUBN_ENST00000377823.1_Missense_Mutation_p.I100V	NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	100					cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GGCAGACCAATTGCACTCCCT	0.323																																					p.I100V		Atlas-SNP	.											.	CUBN	515	.	0			c.A298G						.						210	206	208					10																	17169878		2202	4300	6502	SO:0001583	missense	8029	exon3			GACCAATTGCACT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.298A>G	chr10.hg19:g.17169878T>C	ENSP00000367064:p.Ile100Val	83.0	0.0		82.0	47.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	1.333	-0.596367	0.03771	.	.	ENSG00000107611	ENST00000377833;ENST00000377823	T;D	0.88741	-0.91;-2.42	5.39	-1.93	0.07594	.	2.469160	0.01861	N	0.036620	T	0.74831	0.3768	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.63910	-0.6530	10	0.28530	T	0.3	.	11.7449	0.51815	0.0:0.6798:0.0:0.3202	.	100	O60494	CUBN_HUMAN	V	100	ENSP00000367064:I100V;ENSP00000367054:I100V	ENSP00000367054:I100V	I	-	1	0	CUBN	17209884	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-0.986000	0.03747	-0.593000	0.05844	-0.297000	0.09499	ATT	.	.		0.323	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	17169878	T	C	17169878	3	2	156	1	0	0	0	0	1	0	0	0	4053	1493	52	2	10833	2	CUBN	10	17169878	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10	5257758	17169878	118364869	53	23801										
HK1	3098	hgsc.bcm.edu	37	chr10	71158366	71158366	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	cacagtgaccgattagcactGctccaggtccgggctatcct	10	14	0	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr10:71158366G>A	ENST00000359426.6	+	17	2495	c.2391G>A	c.(2389-2391)ctG>ctA	p.L797L	HK1_ENST00000298649.3_Silent_p.L796L|HK1_ENST00000360289.2_Silent_p.L785L|HK1_ENST00000448642.2_Silent_p.L832L|HK1_ENST00000404387.2_Silent_p.L801L	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	797	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GATTAGCACTGCTCCAGGTCC	0.622																																					p.L801L		Atlas-SNP	.											.	HK1	170	.	0			c.G2403A						.						43	37	39					10																	71158366		2203	4300	6503	SO:0001819	synonymous_variant	3098	exon20			AGCACTGCTCCAG	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.2391G>A	chr10.hg19:g.71158366G>A		48.0	0.0		54.0	16.0	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	hg19	CCDS7292.1																																																																																			.	.		0.622	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		A	71158366	G	A	71158366	2	1	156	1	0	0	0	0	0	0	0	1	7199	1306	46	3		3	HK1	10	71158366	Silent	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	53988488	71158366	64376381	54	23802										
ECHS1	1892	hgsc.bcm.edu	37	chr10	135180466	135180466	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	atcgccagcgacttcccaacAgcacgggtgagtctctgggt	12	13	1	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr10:135180466A>T	ENST00000368547.3	-	5	901	c.546T>A	c.(544-546)gcT>gcA	p.A182A		NM_004092.3	NP_004083.3	P30084	ECHM_HUMAN	enoyl CoA hydratase, short chain, 1, mitochondrial	182					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	10		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;1.62e-06)|OV - Ovarian serous cystadenocarcinoma(35;5.75e-06)|Epithelial(32;7.58e-06)		ACTTCCCAACAGCACGGGTGA	0.627																																					p.A182A	GBM(132;1720 1771 5373 10277 21402)	Atlas-SNP	.											.	ECHS1	31	.	0			c.T546A						.						67	52	57					10																	135180466		2202	4300	6502	SO:0001819	synonymous_variant	1892	exon5			CCCAACAGCACGG		CCDS7681.1	10q26.2-q26.3	2010-05-04	2010-04-30		ENSG00000127884	ENSG00000127884	4.2.1.17		3151	protein-coding gene	gene with protein product		602292	"enoyl Coenzyme A hydratase, short chain, 1, mitochondrial"			8012501	Standard	NM_004092		Approved	SCEH	uc001lmu.3	P30084	OTTHUMG00000019320	ENST00000368547.3:c.546T>A	chr10.hg19:g.135180466A>T		58.0	0.0		44.0	15.0	NM_004092	O00739|Q5VWY1|Q96H54	Silent	SNP	ENST00000368547.3	hg19	CCDS7681.1																																																																																			.	.		0.627	ECHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051156.1			T	135180466	A	T	135180466	2	4	156	1	0	0	0	0	0	0	0	1	4898	175	7	4		4	ECHS1	10	135180466	Silent	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	64022100	135180466	354281	55	23803										
DRD2	1813	hgsc.bcm.edu	37	chr11	113281524	113281524	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tagatgatggggttcacggcGctgttgacatagcccagcca	13	10	1	3	rs79932566		TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr11:113281524G>T	ENST00000362072.3	-	8	1601	c.1257C>A	c.(1255-1257)agC>agA	p.S419R	RP11-159N11.3_ENST00000546284.1_RNA|DRD2_ENST00000346454.3_Missense_Mutation_p.S390R|DRD2_ENST00000542968.1_Missense_Mutation_p.S419R|DRD2_ENST00000355319.2_Missense_Mutation_p.S421R|DRD2_ENST00000538967.1_Missense_Mutation_p.S421R|DRD2_ENST00000544518.1_Missense_Mutation_p.S418R	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	419					activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GGTTCACGGCGCTGTTGACAT	0.567																																					p.S419R		Atlas-SNP	.											.	DRD2	98	.	0			c.C1257A						.						266	195	219					11																	113281524		2201	4296	6497	SO:0001583	missense	1813	exon8			CACGGCGCTGTTG	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.1257C>A	chr11.hg19:g.113281524G>T	ENSP00000354859:p.Ser419Arg	104.0	0.0		129.0	47.0	NM_000795	Q9NZR3|Q9UPA9	Missense_Mutation	SNP	ENST00000362072.3	hg19	CCDS8361.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.556537	0.65425	.	.	ENSG00000149295	ENST00000355319;ENST00000346454;ENST00000362072;ENST00000544518;ENST00000542968;ENST00000538967	T;T;T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29;-1.29;-1.29	5.62	0.915	0.19366	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.93635	0.7967	H	0.99794	4.785	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.92482	0.5993	10	0.87932	D	0	.	10.3645	0.44015	0.4574:0.0:0.5426:0.0	.	418;390;419	F8VUV1;P14416-2;P14416	.;.;DRD2_HUMAN	R	421;390;419;418;419;421	ENSP00000347474:S421R;ENSP00000278597:S390R;ENSP00000354859:S419R;ENSP00000441068:S418R;ENSP00000442172:S419R;ENSP00000438215:S421R	ENSP00000278597:S390R	S	-	3	2	DRD2	112786734	0.839000	0.29477	1.000000	0.80357	0.862000	0.49288	0.011000	0.13264	0.143000	0.18926	0.655000	0.94253	AGC	.	G|1.000;A|0.000		0.567	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		T	113281524	G	T	113281524	3	4	156	1	0	0	0	0	1	0	0	0	4759	1078	38	1	78	1	DRD2	11	113281524	Missense_Mutation	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10		113281524	21724992	56	23804										
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51857460	51857460	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	cacatagaacaggaaccacaTgggggtcacagtgggccaga	13	10	1	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr12:51857460T>A	ENST00000453097.2	+	11	1528	c.1311T>A	c.(1309-1311)caT>caA	p.H437Q	SLC4A8_ENST00000358657.3_Missense_Mutation_p.H464Q|SLC4A8_ENST00000394856.1_Missense_Mutation_p.H384Q|SLC4A8_ENST00000535225.2_Missense_Mutation_p.H384Q|SLC4A8_ENST00000514353.3_Missense_Mutation_p.H384Q	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		AGGAACCACATGGGGGTCACA	0.453																																					p.H437Q		Atlas-SNP	.											.	SLC4A8	292	.	0			c.T1311A						.						106	108	107					12																	51857460		2203	4300	6503	SO:0001583	missense	9498	exon11			ACCACATGGGGGT	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"Solute carriers"	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1311T>A	chr12.hg19:g.51857460T>A	ENSP00000405812:p.His437Gln	148.0	0.0		85.0	37.0	NM_001039960		Missense_Mutation	SNP	ENST00000453097.2	hg19	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	T	13.20	2.165626	0.38217	.	.	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000551071	T;T;T;T;T	0.76060	-0.36;-0.99;-0.98;-0.36;-0.36	5.42	0.377	0.16198	.	0.100410	0.64402	D	0.000002	T	0.64649	0.2617	L	0.50333	1.59	0.50467	D	0.999876	P;B;B;B;B;B	0.35077	0.483;0.013;0.382;0.053;0.029;0.029	B;B;B;B;B;B	0.41571	0.212;0.026;0.36;0.067;0.142;0.142	T	0.50833	-0.8781	10	0.21540	T	0.41	.	4.2938	0.10892	0.1482:0.332:0.0:0.5198	.	384;464;384;437;437;437	E7EML0;Q2Y0W8-2;F5GZ31;Q2Y0W8;Q2Y0W8-3;Q2Y0W8-6	.;.;.;S4A8_HUMAN;.;.	Q	384;464;437;384;437;384;384	ENSP00000441520:H384Q;ENSP00000351483:H464Q;ENSP00000405812:H437Q;ENSP00000378325:H384Q;ENSP00000442561:H384Q	ENSP00000315789:H437Q	H	+	3	2	SLC4A8	50143727	0.381000	0.25140	1.000000	0.80357	0.986000	0.74619	-0.397000	0.07269	0.108000	0.17862	0.533000	0.62120	CAT	.	.		0.453	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		A	51857460	T	A	51857460	3	1	156	1	0	0	0	0	1	0	0	0	14674	1461	51	4	1353	4	SLC4A8	12	51857460	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10		51857460	81994435	57	23805										
SLC26A10	65012	hgsc.bcm.edu	37	chr12	58019464	58019464	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tgcagctgcttatgccctggGgagcctgttaaggggcagta	15	9	0	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr12:58019464G>T	ENST00000320442.4	+	14	1939	c.1628G>T	c.(1627-1629)gGg>gTg	p.G543V	SLC26A10_ENST00000379218.2_3'UTR|SLC26A10_ENST00000490243.1_3'UTR	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	543						integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					TATGCCCTGGGGAGCCTGTTA	0.637																																					p.G543V		Atlas-SNP	.											.	SLC26A10	89	.	0			c.G1628T						.						52	54	53					12																	58019464		2203	4300	6503	SO:0001583	missense	65012	exon14			CCCTGGGGAGCCT		CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"Solute carriers"	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.1628G>T	chr12.hg19:g.58019464G>T	ENSP00000320217:p.Gly543Val	37.0	0.0		40.0	16.0	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Missense_Mutation	SNP	ENST00000320442.4	hg19	CCDS8949.2	.	.	.	.	.	.	.	.	.	.	.	10.63	1.403390	0.25291	.	.	ENSG00000135502	ENST00000320442	D	0.92965	-3.14	4.62	2.2	0.27929	.	.	.	.	.	T	0.79452	0.4448	N	0.08118	0	0.80722	D	1	B	0.20671	0.047	B	0.17433	0.018	T	0.66748	-0.5845	9	0.31617	T	0.26	.	4.2778	0.10818	0.6862:0.2046:0.1092:0.0	.	543	Q8NG04	S2610_HUMAN	V	543	ENSP00000320217:G543V	ENSP00000320217:G543V	G	+	2	0	SLC26A10	56305731	1.000000	0.71417	0.996000	0.52242	0.761000	0.43186	1.226000	0.32563	0.364000	0.24374	-0.484000	0.04775	GGG	.	.		0.637	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2			T	58019464	G	T	58019464	3	4	156	1	0	0	0	0	1	0	0	0	14530	1232	43	3	1682	3	SLC26A10	12	58019464	Missense_Mutation	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	6162004	58019464	75832431	58	23806										
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123475098	123475098	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	cctggtatactcactctgggCgatgctggatgccgtgtagc	13	11	2	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr12:123475098C>T	ENST00000542749.1	-	15	2626	c.2563G>A	c.(2563-2565)Gcc>Acc	p.A855T	PITPNM2_ENST00000280562.5_Missense_Mutation_p.A903T|PITPNM2_ENST00000392428.1_Missense_Mutation_p.A576T|PITPNM2_ENST00000320201.4_Missense_Mutation_p.A855T			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	855	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		TCACTCTGGGCGATGCTGGAT	0.627																																					p.A855T		Atlas-SNP	.											.	PITPNM2	105	.	0			c.G2563A						.						64	51	56					12																	123475098		2202	4300	6502	SO:0001583	missense	57605	exon16			TCTGGGCGATGCT	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.2563G>A	chr12.hg19:g.123475098C>T	ENSP00000437611:p.Ala855Thr	42.0	0.0		25.0	9.0	NM_020845	Q9P271	Missense_Mutation	SNP	ENST00000542749.1	hg19	CCDS9242.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.975435	0.92919	.	.	ENSG00000090975	ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749	T;T;T;T	0.50813	1.24;1.07;0.73;1.07	5.35	5.35	0.76521	DDHD (2);	0.063724	0.64402	D	0.000008	T	0.59169	0.2174	L	0.37800	1.135	0.58432	D	0.999993	P;D	0.89917	0.723;1.0	B;D	0.91635	0.131;0.999	T	0.50566	-0.8813	10	0.17369	T	0.5	-36.4578	19.0766	0.93165	0.0:1.0:0.0:0.0	.	903;855	Q9BZ72-2;Q9BZ72	.;PITM2_HUMAN	T	903;855;576;855	ENSP00000280562:A903T;ENSP00000322218:A855T;ENSP00000376223:A576T;ENSP00000437611:A855T	ENSP00000280562:A903T	A	-	1	0	PITPNM2	122041051	1.000000	0.71417	0.997000	0.53966	0.910000	0.53928	6.055000	0.71103	2.495000	0.84180	0.462000	0.41574	GCC	.	.		0.627	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		T	123475098	C	T	123475098	3	4	156	1	0	0	0	0	1	0	0	0	11960	768	27	1	1526	1	PITPNM2	12	123475098	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	65455634	123475098	10376797	59	23807										
COL4A1	1282	hgsc.bcm.edu	37	chr13	110822980	110822980	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	atcccggtaaccccggctgtCcctggggccccggaggaccc	13	18	0	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr13:110822980C>A	ENST00000375820.4	-	42	3777	c.3656G>T	c.(3655-3657)gGa>gTa	p.G1219V		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1219	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CCCCGGCTGTCCCTGGGGCCC	0.652																																					p.G1219V		Atlas-SNP	.											.	COL4A1	372	.	0			c.G3656T						.						23	28	26					13																	110822980		2203	4300	6503	SO:0001583	missense	1282	exon42			GGCTGTCCCTGGG	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.3656G>T	chr13.hg19:g.110822980C>A	ENSP00000364979:p.Gly1219Val	85.0	0.0		187.0	47.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.299205	0.60195	.	.	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198	D	0.99488	-6.0	5.07	4.2	0.49525	.	0.115129	0.64402	D	0.000017	D	0.99677	0.9879	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97501	1.0060	10	0.87932	D	0	.	15.2375	0.73441	0.0:0.8586:0.1413:0.0	.	1219	P02462	CO4A1_HUMAN	V	862;1219;868	ENSP00000364979:G1219V	ENSP00000364973:G862V	G	-	2	0	COL4A1	109620981	1.000000	0.71417	1.000000	0.80357	0.389000	0.30415	7.171000	0.77595	1.067000	0.40740	0.650000	0.86243	GGA	.	.		0.652	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			A	110822980	C	A	110822980	3	1	156	1	0	0	0	0	1	0	0	0	3691	855	30	3	1397	3	COL4A1	13	110822980	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10		110822980	4346898	60	23808										
FOXG1	2290	hgsc.bcm.edu	37	chr14	29237416	29237416	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gctccctctactggcccatgTcgcccttcctgtccctgcac	7	20	1	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr14:29237416T>A	ENST00000313071.4	+	1	1130	c.931T>A	c.(931-933)Tcg>Acg	p.S311T	RP11-966I7.1_ENST00000546560.1_RNA|RP11-966I7.1_ENST00000551395.1_RNA|FOXG1_ENST00000382535.3_Missense_Mutation_p.S311T|RP11-966I7.1_ENST00000549487.1_RNA	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	311				RAGSLYWPMSPFLSLHHPR -> APAPSTGPCRPSCPCTTP (in Ref. 1; CAA52240 and 2; CAA55038). {ECO:0000305}.	aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		CTGGCCCATGTCGCCCTTCCT	0.687																																					p.S311T		Atlas-SNP	.											.	FOXG1	92	.	0			c.T931A						.						59	70	66					14																	29237416		2203	4300	6503	SO:0001583	missense	2290	exon1			CCCATGTCGCCCT		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.931T>A	chr14.hg19:g.29237416T>A	ENSP00000339004:p.Ser311Thr	89.0	0.0		50.0	10.0	NM_005249	A6NFY2|P55315|Q14488|Q86XT7	Missense_Mutation	SNP	ENST00000313071.4	hg19	CCDS9636.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.552654	0.65425	.	.	ENSG00000176165	ENST00000382535;ENST00000313071	D;D	0.94232	-3.38;-3.38	4.19	4.19	0.49359	.	0.144430	0.47852	U	0.000215	D	0.88599	0.6480	L	0.29908	0.895	0.58432	D	0.999992	B	0.22683	0.073	B	0.26094	0.066	D	0.84979	0.0887	10	0.35671	T	0.21	.	12.8951	0.58095	0.0:0.0:0.0:1.0	.	311	P55316	FOXG1_HUMAN	T	311	ENSP00000371975:S311T;ENSP00000339004:S311T	ENSP00000339004:S311T	S	+	1	0	FOXG1	28307167	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.066000	0.64351	1.522000	0.49001	0.260000	0.18958	TCG	.	.		0.687	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			A	29237416	T	A	29237416	3	1	156	1	0	0	0	0	1	0	0	0	6015	1667	58	4	933	4	FOXG1	14	29237416	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10		29237416	78112124	61	23809										
NID2	22795	hgsc.bcm.edu	37	chr14	52520493	52520493	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ccgttttcggggtacggtggTggggtttcccaggaaggagc	18	8	0	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr14:52520493T>C	ENST00000216286.5	-	5	1232	c.1233A>G	c.(1231-1233)ccA>ccG	p.P411P	NID2_ENST00000541773.1_Silent_p.P358P	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	411					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GGTACGGTGGTGGGGTTTCCC	0.547																																					p.P411P		Atlas-SNP	.											.	NID2	201	.	0			c.A1233G						.						103	92	95					14																	52520493		2203	4300	6503	SO:0001819	synonymous_variant	22795	exon5			CGGTGGTGGGGTT	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1233A>G	chr14.hg19:g.52520493T>C		152.0	0.0		104.0	35.0	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	hg19	CCDS9706.1																																																																																			.	.		0.547	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			C	52520493	T	C	52520493	2	2	156	1	0	0	0	0	0	0	0	1	10424	1683	59	2		2	NID2	14	52520493	Silent	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10	23283077	52520493	54829047	62	23810										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94173074	94173074	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tatctgcgggactccagcttCgcctccaggctattcagaac	9	14	2	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr14:94173074C>T	ENST00000393151.2	+	50	7732	c.7732C>T	c.(7732-7734)Cgc>Tgc	p.R2578C	UNC79_ENST00000555664.1_Missense_Mutation_p.R2539C|UNC79_ENST00000553484.1_Missense_Mutation_p.R2600C|UNC79_ENST00000256339.4_Missense_Mutation_p.R2401C			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2578					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						ACTCCAGCTTCGCCTCCAGGC	0.587																																					p.R2401C		Atlas-SNP	.											.	UNC79	366	.	0			c.C7201T						.						71	77	75					14																	94173074		2203	4300	6503	SO:0001583	missense	57578	exon50			CAGCTTCGCCTCC	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7732C>T	chr14.hg19:g.94173074C>T	ENSP00000376858:p.Arg2578Cys	124.0	0.0		93.0	35.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	C	20.9	4.068233	0.76301	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.33438	1.41;1.46;1.41;1.41	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.58623	0.2135	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.59300	-0.7480	10	0.87932	D	0	-19.5361	20.0407	0.97588	0.0:1.0:0.0:0.0	.	2600	C9JQL1	.	C	2401;2539;2600;2578;2600	ENSP00000256339:R2401C;ENSP00000450868:R2539C;ENSP00000451360:R2600C;ENSP00000376858:R2578C	ENSP00000256339:R2401C	R	+	1	0	KIAA1409	93242827	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.920000	0.70017	2.746000	0.94184	0.561000	0.74099	CGC	.	.		0.587	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94173074	C	T	94173074	3	4	156	1	0	0	0	0	1	0	0	0	8239	884	31	1	7387	1	KIAA1409	14	94173074	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	41652581	94173074	13176466	63	23811										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105415678	105415678	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	cggcagaagggggctgaatgCtgaggtcagtggtcttcagg	18	7	3	3			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr14:105415678C>T	ENST00000333244.5	-	7	6229	c.6110G>A	c.(6109-6111)aGc>aAc	p.S2037N	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2037						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGGCTGAATGCTGAGGTCAGT	0.657																																					p.S2037N		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G6110A						.						105	71	82					14																	105415678		1923	4055	5978	SO:0001583	missense	113146	exon7			TGAATGCTGAGGT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.6110G>A	chr14.hg19:g.105415678C>T	ENSP00000353114:p.Ser2037Asn	135.0	0.0		128.0	37.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	9.084	0.999954	0.19121	.	.	ENSG00000185567	ENST00000333244	T	0.00873	5.59	3.87	1.93	0.25924	.	.	.	.	.	T	0.02047	0.0064	L	0.45470	1.425	0.09310	N	1	D	0.63046	0.992	P	0.59012	0.85	T	0.51036	-0.8756	9	0.20046	T	0.44	-24.5028	6.8111	0.23805	0.0:0.5564:0.3481:0.0955	.	2037	Q8IVF2	AHNK2_HUMAN	N	2037	ENSP00000353114:S2037N	ENSP00000353114:S2037N	S	-	2	0	AHNAK2	104486723	.	.	0.001000	0.08648	0.034000	0.12701	.	.	0.119000	0.18210	-0.494000	0.04653	AGC	.	.		0.657	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105415678	C	T	105415678	3	4	156	1	0	0	0	0	1	0	0	0	415	797	28	3	11281	3	AHNAK2	14	105415678	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	11242604	105415678	1933862	64	23812										
CHRNA7	1139	hgsc.bcm.edu	37	chr15	32323130	32323130	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	aaggcgagttccagaggaagCtttacaaggagctggtcaag	14	7	1	1	rs199819119		TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr15:32323130C>A	ENST00000306901.3	+	2	182	c.85C>A	c.(85-87)Ctt>Att	p.L29I	CHRNA7_ENST00000454250.3_Missense_Mutation_p.L58I|CHRNA7_ENST00000455693.2_5'UTR	NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)	29					activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)			endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	CCAGAGGAAGCTTTACAAGGA	0.617																																					p.L58I	Esophageal Squamous(193;529 2900 40232 43193)	Atlas-SNP	.											.	CHRNA7	57	.	0			c.C172A						.						60	57	58					15																	32323130		2201	4300	6501	SO:0001583	missense	1139	exon2			AGGAAGCTTTACA	Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1960	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 7 (neuronal)"	118511	"cholinergic receptor, nicotinic, alpha polypeptide 7"			8188270	Standard	NM_001190455		Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.85C>A	chr15.hg19:g.32323130C>A	ENSP00000303727:p.Leu29Ile	76.0	0.0		83.0	53.0	NM_001190455	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	Missense_Mutation	SNP	ENST00000306901.3	hg19	CCDS10027.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888069	0.91814	.	.	ENSG00000175344	ENST00000454250;ENST00000306901;ENST00000449991	D;D	0.83506	-1.73;-1.73	4.41	4.41	0.53225	Neurotransmitter-gated ion-channel ligand-binding (3);	0.076629	0.53938	N	0.000046	D	0.92984	0.7767	M	0.94063	3.49	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.998	D;D;D	0.97110	0.994;0.999;1.0	D	0.94747	0.7924	10	0.87932	D	0	.	14.8598	0.70372	0.0:1.0:0.0:0.0	.	29;45;29	F5H8K5;B1N7F6;P36544	.;.;ACHA7_HUMAN	I	58;29;29	ENSP00000407546:L58I;ENSP00000303727:L29I	ENSP00000303727:L29I	L	+	1	0	CHRNA7	30110422	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	6.789000	0.75110	2.190000	0.69967	0.491000	0.48974	CTT	.	.		0.617	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251410.2			A	32323130	C	A	32323130	3	1	156	1	0	0	0	0	1	0	0	0	3390	797	28	3	91	3	CHRNA7	15	32323130	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10		32323130	70208262	65	23813										
C15orf42	90381	hgsc.bcm.edu	37	chr15	90145127	90145127	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ctttctgtgccttttttgtcAagtgctcgtagatcagtgtc	9	9	3	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr15:90145127A>G	ENST00000268138.7	+	12	2592	c.2487A>G	c.(2485-2487)tcA>tcG	p.S829S	TICRR_ENST00000560985.1_Silent_p.S828S			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	829					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										CTTTTTTGTCAAGTGCTCGTA	0.448																																					p.S829S		Atlas-SNP	.											.	.	.	.	0			c.A2487G						.						126	116	119					15																	90145127		1922	4136	6058	SO:0001819	synonymous_variant	90381	exon12			TTTGTCAAGTGCT	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.2487A>G	chr15.hg19:g.90145127A>G		102.0	0.0		100.0	32.0	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	hg19	CCDS10352.2																																																																																			.	.		0.448	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		G	90145127	A	G	90145127	2	3	156	1	0	0	0	0	0	0	0	1	1798	117	5	2		2	C15orf42	15	90145127	Silent	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	57821997	90145127	12386265	66	23814										
ABCC12	94160	hgsc.bcm.edu	37	chr16	48173219	48173219	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	aggcagcttcaaacaaagaaTagctatcacttgacagtata	7	8	2	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr16:48173219T>C	ENST00000311303.3	-	5	1031	c.686A>G	c.(685-687)tAt>tGt	p.Y229C	ABCC12_ENST00000416054.1_Missense_Mutation_p.Y229C|ABCC12_ENST00000448542.1_Missense_Mutation_p.Y229C	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	229	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				AAACAAAGAATAGCTATCACT	0.453																																					p.Y229C		Atlas-SNP	.											.	ABCC12	190	.	0			c.A686G						.						107	97	101					16																	48173219		2201	4300	6501	SO:0001583	missense	94160	exon5			AAAGAATAGCTAT	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.686A>G	chr16.hg19:g.48173219T>C	ENSP00000311030:p.Tyr229Cys	165.0	0.0		172.0	46.0	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	hg19	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	T	16.97	3.268187	0.59540	.	.	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000416054	D;D;D	0.89810	-2.57;-2.57;-2.57	5.88	5.88	0.94601	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.265286	0.38778	N	0.001580	D	0.91209	0.7230	L	0.44542	1.39	0.51233	D	0.999919	D;P	0.61697	0.99;0.89	P;P	0.61275	0.879;0.886	D	0.91565	0.5267	10	0.54805	T	0.06	.	15.284	0.73814	0.0:0.0:0.0:1.0	.	229;229	Q96J65-2;Q96J65	.;MRP9_HUMAN	C	229	ENSP00000311030:Y229C;ENSP00000401855:Y229C;ENSP00000413046:Y229C	ENSP00000311030:Y229C	Y	-	2	0	ABCC12	46730720	1.000000	0.71417	0.994000	0.49952	0.485000	0.33311	4.703000	0.61824	2.239000	0.73571	0.533000	0.62120	TAT	.	.		0.453	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		C	48173219	T	C	48173219	3	2	156	1	0	0	0	0	1	0	0	0	52	1406	49	2	3493	2	ABCC12	16	48173219	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10		48173219	42181534	67	23815										
PHF23	79142	hgsc.bcm.edu	37	chr17	7139048	7139048	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	cggggacgttggtcttcttaAtcttagcacaggagaggtgg	15	7	3	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr17:7139048A>C	ENST00000320316.3	-	5	1335	c.1109T>G	c.(1108-1110)aTt>aGt	p.I370S	PHF23_ENST00000571362.1_Missense_Mutation_p.I303S|PHF23_ENST00000454255.2_Missense_Mutation_p.I366S|DVL2_ENST00000005340.5_5'Flank|PHF23_ENST00000576955.1_Missense_Mutation_p.I240S|DVL2_ENST00000575458.1_5'Flank|PHF23_ENST00000570753.1_5'Flank	NM_001284518.1|NM_024297.2	NP_001271447.1|NP_077273.2	Q9BUL5	PHF23_HUMAN	PHD finger protein 23	370							zinc ion binding (GO:0008270)			breast(4)|kidney(2)|large_intestine(6)|lung(3)	15						GGTCTTCTTAATCTTAGCACA	0.557																																					p.I370S		Atlas-SNP	.											.	PHF23	38	.	0			c.T1109G						.						149	150	150					17																	7139048		1924	4133	6057	SO:0001583	missense	79142	exon5			TTCTTAATCTTAG	AK122791	CCDS42250.1, CCDS67143.1, CCDS67144.1	17p13.1	2014-08-13			ENSG00000040633	ENSG00000040633		"Zinc fingers, PHD-type"	28428	protein-coding gene	gene with protein product		612910					Standard	NM_024297		Approved	MGC2941, FLJ16355	uc002gfa.3	Q9BUL5	OTTHUMG00000177972	ENST00000320316.3:c.1109T>G	chr17.hg19:g.7139048A>C	ENSP00000322579:p.Ile370Ser	57.0	0.0		30.0	17.0	NM_024297	A1DZ74|B3KVH8|B4DLK6|D3DTN4|Q8IZK0|Q96HG7|Q9H5X0	Missense_Mutation	SNP	ENST00000320316.3	hg19	CCDS42250.1	.	.	.	.	.	.	.	.	.	.	A	18.67	3.673403	0.67928	.	.	ENSG00000040633	ENST00000320316;ENST00000454255	D;D	0.85556	-2.0;-2.0	5.19	5.19	0.71726	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.94522	0.8236	H	0.96365	3.81	0.58432	D	0.999993	D;D	0.89917	1.0;0.992	D;D	0.91635	0.999;0.989	D	0.95806	0.8837	10	0.87932	D	0	-6.5648	12.9762	0.58538	1.0:0.0:0.0:0.0	.	303;370	B4DLK6;Q9BUL5	.;PHF23_HUMAN	S	370;366	ENSP00000322579:I370S;ENSP00000414607:I366S	ENSP00000322579:I370S	I	-	2	0	PHF23	7079772	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.561000	0.90715	1.947000	0.56498	0.260000	0.18958	ATT	.	.		0.557	PHF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440047.1	NM_024297		C	7139048	A	C	7139048	3	2	156	1	0	0	0	0	1	0	0	0	11844	101	4	5	106	5	PHF23	17	7139048	Missense_Mutation	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10		7139048	74056162	68	23816										
TP53	7157	hgsc.bcm.edu	37	chr17	7576863	7576863	+	Frame_Shift_Del	DEL	A	A	-													0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gacttagtacctgaagggtgAaatattctccatccagtggt							TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr17:7576863delA	ENST00000269305.4	-	9	1172	c.983delT	c.(982-984)ttcfs	p.F328fs	TP53_ENST00000420246.2_Frame_Shift_Del_p.F328fs|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Frame_Shift_Del_p.F328fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.F328fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.F328fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	328	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		F -> L (in a sporadic cancer; somatic mutation).|F -> S (in sporadic cancers; somatic mutation).|F -> V (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.T329fs*8(3)|p.F328S(1)|p.?(1)|p.F328fs*9(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGAAGGGTGAAATATTCTCC	0.438		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.F328fs	Pancreas(47;798 1329 9957 10801)	Atlas-INDEL	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53,sinonasal_and_nasal_cavity,lymphoid_neoplasm,0,3	TP53	33396	.	14	Whole gene deletion(8)|Insertion - Frameshift(4)|Substitution - Missense(1)|Unknown(1)	bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|stomach(1)|pancreas(1)	c.984delC						.						122	114	117					17																	7576863		2203	4300	6503	SO:0001589	frameshift_variant	7157	exon9	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.983delT	chr17.hg19:g.7576863delA	ENSP00000269305:p.Phe328fs	186.0	0.0		68.0	41.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.438	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7576863	A	-	7576863	7	5	156	1	0	1	0	1	0	0	0	0	16396	246	9	0	299	0	TP53	17	7576863	Frame_Shift_Del	DEL	A	TCGA-DD-AACE-01A-11D-A40R-10	437815	7576863	73618347	69	23817										
KLHL10	317719	hgsc.bcm.edu	37	chr17	39998197	39998197	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ccggaccgtgcctatcacacCggacaatgtggagaaactgc	11	13	1	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr17:39998197C>T	ENST00000293303.4	+	2	470	c.317C>T	c.(316-318)cCg>cTg	p.P106L	KLHL10_ENST00000485613.1_3'UTR	NM_152467.3	NP_689680.2	Q6JEL2	KLH10_HUMAN	kelch-like family member 10	106	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia morphogenesis (GO:0048808)|male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26		Breast(137;0.000162)				CCTATCACACCGGACAATGTG	0.483																																					p.P106L		Atlas-SNP	.											.	KLHL10	67	.	0			c.C317T						.						125	117	119					17																	39998197		1990	4166	6156	SO:0001583	missense	317719	exon2			TCACACCGGACAA	AK057224	CCDS42340.1	17q21.2	2013-01-30	2013-01-30		ENSG00000161594	ENSG00000161594		"Kelch-like", "BTB/POZ domain containing"	18829	protein-coding gene	gene with protein product		608778	"kelch-like 10 (Drosophila)"				Standard	NM_152467		Approved	FLJ32662	uc010cxr.3	Q6JEL2	OTTHUMG00000152510	ENST00000293303.4:c.317C>T	chr17.hg19:g.39998197C>T	ENSP00000293303:p.Pro106Leu	187.0	0.0		235.0	52.0	NM_152467	Q6NW28|Q96MC0	Missense_Mutation	SNP	ENST00000293303.4	hg19	CCDS42340.1	.	.	.	.	.	.	.	.	.	.	C	14.81	2.647934	0.47258	.	.	ENSG00000161594	ENST00000293303;ENST00000438813	T;T	0.66280	-0.2;-0.2	5.58	5.58	0.84498	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.284900	0.38548	N	0.001643	T	0.42471	0.1204	N	0.14661	0.345	0.44261	D	0.997118	P;P	0.36378	0.529;0.55	B;B	0.25140	0.04;0.058	T	0.38542	-0.9656	9	.	.	.	.	18.1317	0.89604	0.0:1.0:0.0:0.0	.	100;106	B4DXV2;Q6JEL2	.;KLH10_HUMAN	L	106;100	ENSP00000293303:P106L;ENSP00000416221:P100L	.	P	+	2	0	KLHL10	37251723	0.000000	0.05858	0.984000	0.44739	0.934000	0.57294	0.559000	0.23485	2.620000	0.88729	0.655000	0.94253	CCG	.	.		0.483	KLHL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326535.1	NM_152467		T	39998197	C	T	39998197	3	4	156	1	0	0	0	0	1	0	0	0	8375	652	23	1	323	1	KLHL10	17	39998197	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	32421334	39998197	41197013	70	23818										
DHX8	1659	hgsc.bcm.edu	37	chr17	41585264	41585264	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ctcaatacttctatgaagctCccattttcaccatcccaggt	4	14	3	1			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr17:41585264C>A	ENST00000262415.3	+	15	2269	c.2197C>A	c.(2197-2199)Ccc>Acc	p.P733T	DHX8_ENST00000540306.1_Missense_Mutation_p.P733T	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	733	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		CTATGAAGCTCCCATTTTCAC	0.438																																					p.P733T	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.C2197A						.						119	114	116					17																	41585264		2203	4300	6503	SO:0001583	missense	1659	exon15			GAAGCTCCCATTT	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"DEAH-boxes"	2749	protein-coding gene	gene with protein product		600396	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.2197C>A	chr17.hg19:g.41585264C>A	ENSP00000262415:p.Pro733Thr	108.0	0.0		171.0	107.0	NM_004941		Missense_Mutation	SNP	ENST00000262415.3	hg19	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.620732	0.87460	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.03242	4.0;4.0	6.08	6.08	0.98989	DEAD-like helicase (2);	0.049309	0.85682	D	0.000000	T	0.29817	0.0745	H	0.94222	3.51	0.80722	D	1	D;D	0.89917	1.0;0.991	D;D	0.74023	0.982;0.916	T	0.23868	-1.0176	10	0.87932	D	0	.	19.6603	0.95864	0.0:1.0:0.0:0.0	.	733;733	F5H658;Q14562	.;DHX8_HUMAN	T	733	ENSP00000437886:P733T;ENSP00000262415:P733T	ENSP00000262415:P733T	P	+	1	0	DHX8	38940790	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.734000	0.84928	2.894000	0.99253	0.591000	0.81541	CCC	.	.		0.438	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			A	41585264	C	A	41585264	3	1	156	1	0	0	0	0	1	0	0	0	4517	855	30	3	2255	3	DHX8	17	41585264	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	1587067	41585264	39609946	71	23819										
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42956967	42956967	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ggaccactccatctgagatgCgcaagccagctgtgacctca	10	14	2	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr17:42956967C>T	ENST00000426333.2	-	9	956	c.659G>A	c.(658-660)cGc>cAc	p.R220H	EFTUD2_ENST00000591382.1_Missense_Mutation_p.R220H|EFTUD2_ENST00000592576.1_Missense_Mutation_p.R210H|EFTUD2_ENST00000402521.3_Missense_Mutation_p.R185H	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	220	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				ATCTGAGATGCGCAAGCCAGC	0.478																																					p.R220H	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.G659A						.						110	95	100					17																	42956967		2203	4300	6503	SO:0001583	missense	9343	exon9			GAGATGCGCAAGC	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.659G>A	chr17.hg19:g.42956967C>T	ENSP00000392094:p.Arg220His	116.0	0.0		110.0	70.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Missense_Mutation	SNP	ENST00000426333.2	hg19	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	C	36	5.655679	0.96724	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	T;T	0.80214	-1.35;-1.35	6.02	6.02	0.97574	Small GTP-binding protein domain (1);Protein synthesis factor, GTP-binding (2);	0.000000	0.85682	D	0.000000	D	0.92925	0.7749	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.99	D	0.93671	0.6990	10	0.87932	D	0	-6.9932	20.5373	0.99239	0.0:1.0:0.0:0.0	.	210;220	B4DMC0;Q15029	.;U5S1_HUMAN	H	220;210;185	ENSP00000392094:R220H;ENSP00000385873:R185H	ENSP00000262414:R210H	R	-	2	0	EFTUD2	40312493	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.818000	0.86416	2.857000	0.98124	0.650000	0.86243	CGC	.	.		0.478	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		T	42956967	C	T	42956967	3	4	156	1	0	0	0	0	1	0	0	0	4963	768	27	1	2339	1	EFTUD2	17	42956967	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	1371703	42956967	38238243	72	23820										
OSBPL7	114881	hgsc.bcm.edu	37	chr17	45886525	45886525	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	caaagagtcggtggaggacaCggccactccgactgagcaca	13	12	0	2	rs376859496		TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr17:45886525C>A	ENST00000007414.3	-	20	2278	c.2087G>T	c.(2086-2088)cGt>cTt	p.R696L	OSBPL7_ENST00000392507.3_Missense_Mutation_p.R696L	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	696					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)	p.R696H(1)		autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						GTGGAGGACACGGCCACTCCG	0.637																																					p.R696L		Atlas-SNP	.											OSBPL7,NS,carcinoma,0,1	OSBPL7	65	.	1	Substitution - Missense(1)	endometrium(1)	c.G2087T						.						51	55	54					17																	45886525		2203	4300	6503	SO:0001583	missense	114881	exon20			AGGACACGGCCAC	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.2087G>T	chr17.hg19:g.45886525C>A	ENSP00000007414:p.Arg696Leu	74.0	0.0		88.0	54.0	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	hg19	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.705442	0.68615	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.30448	1.53;1.53	5.0	5.0	0.66597	.	0.217614	0.43747	D	0.000529	T	0.34774	0.0909	L	0.48935	1.535	0.31875	N	0.619213	D	0.54601	0.967	P	0.52309	0.695	T	0.46105	-0.9215	10	0.51188	T	0.08	-15.9196	7.7644	0.28972	0.0:0.8204:0.0:0.1796	.	696	Q9BZF2	OSBL7_HUMAN	L	696	ENSP00000007414:R696L;ENSP00000376295:R696L	ENSP00000007414:R696L	R	-	2	0	OSBPL7	43241524	0.321000	0.24625	0.994000	0.49952	0.966000	0.64601	0.793000	0.26944	2.333000	0.79357	0.561000	0.74099	CGT	.	.		0.637	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		A	45886525	C	A	45886525	3	1	156	1	0	0	0	0	1	0	0	0	11291	536	19	1	457	1	OSBPL7	17	45886525	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	2929558	45886525	35308685	73	23821										
RSAD1	55316	hgsc.bcm.edu	37	chr17	48559662	48559662	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	acctctccctctaccagctgTccctggagcggggcaccgca	10	18	2	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr17:48559662T>G	ENST00000258955.2	+	4	770	c.685T>G	c.(685-687)Tcc>Gcc	p.S229A		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	229					porphyrin-containing compound biosynthetic process (GO:0006779)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|coproporphyrinogen oxidase activity (GO:0004109)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CTACCAGCTGTCCCTGGAGCG	0.687											OREG0024567	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S229A		Atlas-SNP	.											.	RSAD1	36	.	0			c.T685G						.						64	64	64					17																	48559662		2203	4299	6502	SO:0001583	missense	55316	exon4			CAGCTGTCCCTGG	AK002026	CCDS11569.1	17q21.33	2004-11-08			ENSG00000136444	ENSG00000136444			25634	protein-coding gene	gene with protein product						12477932	Standard	NM_018346		Approved	FLJ11164	uc002iqw.1	Q9HA92	OTTHUMG00000162126	ENST00000258955.2:c.685T>G	chr17.hg19:g.48559662T>G	ENSP00000258955:p.Ser229Ala	119.0	0.0	955	140.0	81.0	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Missense_Mutation	SNP	ENST00000258955.2	hg19	CCDS11569.1	.	.	.	.	.	.	.	.	.	.	T	17.06	3.293146	0.60086	.	.	ENSG00000136444	ENST00000258955	T	0.23147	1.92	5.37	-0.612	0.11597	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);	0.255459	0.36482	N	0.002576	T	0.19685	0.0473	L	0.41710	1.295	0.24466	N	0.99441	B	0.18461	0.028	B	0.13407	0.009	T	0.28586	-1.0039	10	0.87932	D	0	-9.6367	11.9622	0.53015	0.6486:0.0:0.0:0.3514	.	229	Q9HA92	RSAD1_HUMAN	A	229	ENSP00000258955:S229A	ENSP00000258955:S229A	S	+	1	0	RSAD1	45914661	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	1.533000	0.36040	-0.021000	0.14009	0.533000	0.62120	TCC	.	.		0.687	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346		G	48559662	T	G	48559662	3	3	156	1	0	0	0	0	1	0	0	0	13709	1667	58	5	699	5	RSAD1	17	48559662	Missense_Mutation	SNP	T	TCGA-DD-AACE-01A-11D-A40R-10	2673137	48559662	32635548	74	23822										
ABCA9	10350	hgsc.bcm.edu	37	chr17	66978770	66978770	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	acaggcaacttatagaccatCagggaggagaacctgcgaag	12	9	1	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr17:66978770C>T	ENST00000340001.4	-	37	4864	c.4653G>A	c.(4651-4653)ctG>ctA	p.L1551L	ABCA9_ENST00000453985.2_Silent_p.L1513L|ABCA9_ENST00000370732.2_3'UTR	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1551					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					TATAGACCATCAGGGAGGAGA	0.463																																					p.L1551L		Atlas-SNP	.											.	ABCA9	192	.	0			c.G4653A						.						111	104	106					17																	66978770		2203	4300	6503	SO:0001819	synonymous_variant	10350	exon37			GACCATCAGGGAG	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.4653G>A	chr17.hg19:g.66978770C>T		109.0	0.0		119.0	30.0	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Silent	SNP	ENST00000340001.4	hg19	CCDS11681.1																																																																																			.	.		0.463	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		T	66978770	C	T	66978770	2	4	156	1	0	0	0	0	0	0	0	1	39	813	29	3		3	ABCA9	17	66978770	Silent	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	18419108	66978770	14216440	75	23823										
EVPL	2125	hgsc.bcm.edu	37	chr17	74015086	74015086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gaggggccacatcccggcttCgccgctgcaggtccccagtg	14	16	0	0	rs201678162		TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr17:74015086C>T	ENST00000301607.3	-	11	1446	c.1193G>A	c.(1192-1194)cGa>cAa	p.R398Q	EVPL_ENST00000586740.1_Missense_Mutation_p.R398Q	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	398	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						ATCCCGGCTTCGCCGCTGCAG	0.672																																					p.R398Q		Atlas-SNP	.											.	EVPL	155	.	0			c.G1193A						.	C	GLN/ARG	0,4402		0,0,2201	17	19	18		1193	-4.5	0	17		18	1,8597		0,1,4298	yes	missense	EVPL	NM_001988.2	43	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	benign	398/2034	74015086	1,12999	2201	4299	6500	SO:0001583	missense	2125	exon11			CGGCTTCGCCGCT	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.1193G>A	chr17.hg19:g.74015086C>T	ENSP00000301607:p.Arg398Gln	108.0	0.0		121.0	45.0	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	hg19	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.461988	0.26248	0.0	1.16E-4	ENSG00000167880	ENST00000301607	T	0.69685	-0.42	5.03	-4.47	0.03525	.	0.601694	0.16236	N	0.223365	T	0.49098	0.1537	L	0.47016	1.485	0.09310	N	1	B;B	0.27286	0.051;0.174	B;B	0.16289	0.013;0.015	T	0.29971	-0.9994	10	0.59425	D	0.04	-8.2166	6.6081	0.22735	0.1207:0.3504:0.0:0.5289	.	398;398	B7ZLH8;Q92817	.;EVPL_HUMAN	Q	398	ENSP00000301607:R398Q	ENSP00000301607:R398Q	R	-	2	0	EVPL	71526681	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-1.096000	0.03353	-1.051000	0.03226	-0.500000	0.04577	CGA	.	.		0.672	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		T	74015086	C	T	74015086	3	4	156	1	0	0	0	0	1	0	0	0	5294	884	31	1	4956	1	EVPL	17	74015086	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10	7036316	74015086	7180124	76	23824										
FZR1	51343	hgsc.bcm.edu	37	chr19	3531769	3531769	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	tgcagatctgggacgcagccGcagggaagaagctgtccatg	15	10	1	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr19:3531769G>A	ENST00000395095.3	+	8	778	c.778G>A	c.(778-780)Gca>Aca	p.A260T	FZR1_ENST00000313639.8_Missense_Mutation_p.A171T|FZR1_ENST00000441788.2_Missense_Mutation_p.A260T	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	260					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		GGACGCAGCCGCAGGGAAGAA	0.672																																					p.A260T		Atlas-SNP	.											.	FZR1	42	.	0			c.G778A						.						61	60	60					19																	3531769		1907	3737	5644	SO:0001583	missense	51343	exon8			GCAGCCGCAGGGA	AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"WD repeat domain containing"	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.778G>A	chr19.hg19:g.3531769G>A	ENSP00000378529:p.Ala260Thr	152.0	0.0		126.0	8.0	NM_001136198	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Missense_Mutation	SNP	ENST00000395095.3	hg19	CCDS45916.1	.	.	.	.	.	.	.	.	.	.	G	16.07	3.019289	0.54576	.	.	ENSG00000105325	ENST00000441788;ENST00000395095;ENST00000313639	T;T;T	0.24151	1.87;1.87;5.27	5.18	5.18	0.71444	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.13543	0.0328	N	0.00595	-1.35	0.80722	D	1	B;P;D	0.71674	0.05;0.633;0.998	B;B;P	0.56865	0.006;0.074;0.808	T	0.33266	-0.9875	10	0.02654	T	1	-25.2369	17.2375	0.87004	0.0:0.0:1.0:0.0	.	260;171;260	Q9UM11;Q9UM11-3;Q9UM11-2	FZR_HUMAN;.;.	T	260;260;171	ENSP00000410369:A260T;ENSP00000378529:A260T;ENSP00000321800:A171T	ENSP00000321800:A171T	A	+	1	0	FZR1	3482769	1.000000	0.71417	0.280000	0.24747	0.717000	0.41224	7.687000	0.84139	2.426000	0.82243	0.561000	0.74099	GCA	.	.		0.672	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		A	3531769	G	A	3531769	3	1	156	1	0	0	0	0	1	0	0	0	6146	1087	38	1	808	1	FZR1	19	3531769	Missense_Mutation	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10		3531769	55597214	77	23825										
CHAF1A	10036	hgsc.bcm.edu	37	chr19	4422571	4422571	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	actgtcttgtaggatcaggaGcgtctgggcaagcagctcaa	13	9	4	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr19:4422571G>A	ENST00000301280.5	+	5	1127	c.1026G>A	c.(1024-1026)gaG>gaA	p.E342E		NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	342	Arg/Glu/Lys-rich.				cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGATCAGGAGCGTCTGGGCA	0.577								Chromatin Structure																													p.E342E		Atlas-SNP	.											.	CHAF1A	69	.	0			c.G1026A						.						34	31	32					19																	4422571		2197	4287	6484	SO:0001819	synonymous_variant	10036	exon5			TCAGGAGCGTCTG	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"chromatin assembly factor I (150 kDa)"	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.1026G>A	chr19.hg19:g.4422571G>A		137.0	0.0		79.0	23.0	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Silent	SNP	ENST00000301280.5	hg19	CCDS32875.1																																																																																			.	.		0.577	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483		A	4422571	G	A	4422571	2	1	156	1	0	0	0	0	0	0	0	1	3313	962	34	3		3	CHAF1A	19	4422571	Silent	SNP	G	TCGA-DD-AACE-01A-11D-A40R-10	890802	4422571	54706412	78	23826										
ZNF627	199692	hgsc.bcm.edu	37	chr19	11727702	11727702	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	gatcacactggacgtgaaccAaatgaatatcaggaatatgg	10	7	2	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr19:11727702A>G	ENST00000361113.5	+	4	592	c.384A>G	c.(382-384)ccA>ccG	p.P128P	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	128					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						GACGTGAACCAAATGAATATC	0.448																																					p.P128P	Melanoma(112;173 1614 10731 17751 23322)	Atlas-SNP	.											.	ZNF627	43	.	0			c.A384G						.						122	124	124					19																	11727702		2157	4274	6431	SO:0001819	synonymous_variant	199692	exon4			TGAACCAAATGAA	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"Zinc fingers, C2H2-type", "-"	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.384A>G	chr19.hg19:g.11727702A>G		167.0	0.0		173.0	70.0	NM_145295	O14846|Q4KMP9|Q6NT81|Q9BRG4	Silent	SNP	ENST00000361113.5	hg19	CCDS42502.1																																																																																			.	.		0.448	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295		G	11727702	A	G	11727702	2	3	156	1	0	0	0	0	0	0	0	1	18066	117	5	2		2	ZNF627	19	11727702	Silent	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	7305131	11727702	47401281	79	23827										
PGLS	25796	hgsc.bcm.edu	37	chr19	17626986	17626986	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	cctctgttggctgcagacgcAtcttctctccagactgccga	9	15	3	2			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr19:17626986A>G	ENST00000252603.2	+	2	337	c.293A>G	c.(292-294)cAt>cGt	p.H98R	CTD-3131K8.3_ENST00000596192.1_RNA	NM_012088.2	NP_036220.1	O95336	6PGL_HUMAN	6-phosphogluconolactonase	98					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	6-phosphogluconolactonase activity (GO:0017057)|monosaccharide binding (GO:0048029)			endometrium(1)|lung(1)	2						CTGCAGACGCATCTTCTCTCC	0.537																																					p.H98R		Atlas-SNP	.											.	PGLS	12	.	0			c.A293G						.						111	79	90					19																	17626986		2203	4300	6503	SO:0001583	missense	25796	exon2			AGACGCATCTTCT	AJ243972	CCDS12361.1	19p13.2	2008-02-05				ENSG00000130313	3.1.1.31		8903	protein-coding gene	gene with protein product		604951				10518023	Standard	NM_012088		Approved	6PGL	uc002ngw.3	O95336		ENST00000252603.2:c.293A>G	chr19.hg19:g.17626986A>G	ENSP00000252603:p.His98Arg	115.0	0.0		81.0	26.0	NM_012088		Missense_Mutation	SNP	ENST00000252603.2	hg19	CCDS12361.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.296777	0.23650	.	.	ENSG00000130313	ENST00000252603	T	0.41400	1.0	5.08	5.08	0.68730	Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1);	0.241291	0.42821	D	0.000643	T	0.45558	0.1348	L	0.60012	1.86	0.38377	D	0.945033	P	0.35411	0.5	P	0.45232	0.474	T	0.41574	-0.9501	10	0.16896	T	0.51	-29.1705	11.2135	0.48813	1.0:0.0:0.0:0.0	.	98	O95336	6PGL_HUMAN	R	98	ENSP00000252603:H98R	ENSP00000252603:H98R	H	+	2	0	PGLS	17487986	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	5.441000	0.66569	1.889000	0.54706	0.459000	0.35465	CAT	.	.		0.537	PGLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464154.1			G	17626986	A	G	17626986	3	3	156	1	0	0	0	0	1	0	0	0	11801	217	8	2	299	2	PGLS	19	17626986	Missense_Mutation	SNP	A	TCGA-DD-AACE-01A-11D-A40R-10	5899284	17626986	41501997	80	23828										
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3679945	3679945	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	ggcgtcagtgctggaggccgCggggagcaggaggctgctgc	21	10	1	0			TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chr20:3679945C>A	ENST00000344754.4	-	7	1689	c.1690G>T	c.(1690-1692)Gcg>Tcg	p.A564S	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.A564S	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	564	Ig-like C2-type 5.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CTGGAGGCCGCGGGGAGCAGG	0.672																																					p.A564S		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.G1690T						.						24	21	22					20																	3679945		2203	4297	6500	SO:0001583	missense	6614	exon7			AGGCCGCGGGGAG	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.1690G>T	chr20.hg19:g.3679945C>A	ENSP00000341141:p.Ala564Ser	155.0	0.0		157.0	86.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	hg19	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	C	9.316	1.056711	0.19907	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.10960	2.82;2.82	5.46	0.803	0.18691	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.546274	0.15423	N	0.263131	T	0.04861	0.0131	N	0.05306	-0.075	0.09310	N	1	B;B	0.24882	0.113;0.092	B;B	0.38954	0.286;0.15	T	0.48410	-0.9038	10	0.06494	T	0.89	.	3.2682	0.06873	0.1841:0.5118:0.0:0.3041	.	564;564	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	S	564	ENSP00000341141:A564S;ENSP00000202578:A564S	ENSP00000202578:A564S	A	-	1	0	SIGLEC1	3627945	0.000000	0.05858	0.004000	0.12327	0.739000	0.42172	-0.435000	0.06931	0.669000	0.31146	0.655000	0.94253	GCG	.	.		0.672	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		A	3679945	C	A	3679945	3	1	156	1	0	0	0	0	1	0	0	0	14320	768	27	1	3499	1	SIGLEC1	20	3679945	Missense_Mutation	SNP	C	TCGA-DD-AACE-01A-11D-A40R-10		3679945	59345575	81	23829										
WNK3	65267	hgsc.bcm.edu	37	chrX	54264775	54264776	+	Splice_Site	DEL	CT	CT	-													0.0609756097560976	5	1	1.18639455782313	2.76825396825397	0.859113300492611	1	1	0	attcaatcaaagacacaaacCtggaaccgaccccgctgaaa							TCGA-DD-AACE-01A-11D-A40R-10	TCGA-DD-AACE-10A-01D-A40U-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b4d8378-ded6-4a8c-9839-6e437ce1d88a	ba4f8145-e3ba-4242-a382-1c87a35ed636	g.chrX:54264775_54264776delCT	ENST00000375159.2	-	18	4012_4013	c.4013_4014delAG	c.(4012-4014)cag>c	p.Q1338fs	WNK3_ENST00000354646.2_Splice_Site_p.Q1338fs|WNK3_ENST00000375169.3_Splice_Site_p.Q1291fs			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1338					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AGACACAAACCTGGAACCGACC	0.426																																					p.1338_1338del		Atlas-INDEL	.											.	WNK3	218	.	0			c.4014_4014del						.																																			SO:0001630	splice_region_variant	65267	exon19			.	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.4014+1AG>-	chrX.hg19:g.54264775_54264776delCT		67.0	0.0		65.0	49.0	NM_020922	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Frame_Shift_Del	DEL	ENST00000375159.2	hg19	CCDS14357.1																																																																																			.	.		0.426	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922	Frame_Shift_Del	-	54264776	CT	-	54264775	8	5	156	1	0	1	0	1	0	0	1	0	17394	695	24	0	1412	0	WNK3	23	54264775	Splice_Site	DEL	CT	TCGA-DD-AACE-01A-11D-A40R-10		54264775	101005785	82	23830										
ECE1	1889	hgsc.bcm.edu	37	chr1	21599275	21599275	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	agtggccatcagggactgggTtggccttgatccagccccca	13	13	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:21599275T>C	ENST00000374893.6	-	4	484	c.410A>G	c.(409-411)aAc>aGc	p.N137S	ECE1_ENST00000436918.2_Missense_Mutation_p.N137S|ECE1_ENST00000357071.4_Missense_Mutation_p.N125S|ECE1_ENST00000264205.6_Missense_Mutation_p.N134S|ECE1_ENST00000415912.2_Missense_Mutation_p.N121S	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	137					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)			endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		AGGGACTGGGTTGGCCTTGAT	0.582																																					p.N137S		Atlas-SNP	.											.	ECE1	76	.	0			c.A410G						.						152	134	140					1																	21599275		2203	4300	6503	SO:0001583	missense	1889	exon4			ACTGGGTTGGCCT	D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.410A>G	chr1.hg19:g.21599275T>C	ENSP00000364028:p.Asn137Ser	139.0	0.0		151.0	53.0	NM_001397	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Missense_Mutation	SNP	ENST00000374893.6	hg19	CCDS215.1	.	.	.	.	.	.	.	.	.	.	T	32	5.145815	0.94603	.	.	ENSG00000117298	ENST00000415912;ENST00000357071;ENST00000374893;ENST00000436918;ENST00000264205;ENST00000473505;ENST00000481130	T;T;T;T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87	5.75	5.75	0.90469	Peptidase M13 (1);	0.093907	0.64402	D	0.000001	D	0.84584	0.5504	M	0.80508	2.5	0.80722	D	1	D;D;P;D;D	0.60575	0.975;0.988;0.458;0.986;0.986	P;P;B;P;P	0.59221	0.854;0.75;0.233;0.634;0.768	D	0.86941	0.2079	10	0.87932	D	0	-43.2995	14.8963	0.70646	0.0:0.0:0.0:1.0	.	137;121;137;125;134	B4DKB2;Q2Z2K8;P42892;P42892-2;P42892-4	.;.;ECE1_HUMAN;.;.	S	121;125;137;137;134;23;123	ENSP00000405088:N121S;ENSP00000349581:N125S;ENSP00000364028:N137S;ENSP00000388439:N137S;ENSP00000264205:N134S;ENSP00000431856:N23S;ENSP00000436633:N123S	ENSP00000264205:N134S	N	-	2	0	ECE1	21471862	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.008000	0.88588	2.206000	0.71126	0.533000	0.62120	AAC	.	.		0.582	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397		C	21599275	T	C	21599275	3	2	157	1	0	0	0	0	1	0	0	0	4891	1725	60	2	1966	2	ECE1	1	21599275	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10		21599275	227651346	1	23831										
FAM151A	338094	hgsc.bcm.edu	37	chr1	55085632	55085636	+	Frame_Shift_Del	DEL	AGGTA	AGGTA	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tgatctggcccaggctcagcAggtagtccagcatgtcggca							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	AGGTA	AGGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:55085632_55085636delAGGTA	ENST00000302250.2	-	2	323_327	c.163_167delTACCT	c.(163-168)tacctgfs	p.YL55fs	FAM151A_ENST00000371304.2_Frame_Shift_Del_p.YL55fs|ACOT11_ENST00000371316.3_Intron|RP11-240D10.4_ENST00000416119.1_RNA	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	55						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						CAGGCTCAGCAGGTAGTCCAGCATG	0.61																																					p.55_56del		Atlas-INDEL	.											.	FAM151A	58	.	0			c.164_168del						.																																			SO:0001589	frameshift_variant	338094	exon2			.	AK091901	CCDS594.1	1p32.3	2008-02-05	2007-12-18	2007-12-18	ENSG00000162391	ENSG00000162391			25032	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 179"	C1orf179		17273976	Standard	NM_176782		Approved	MGC27169	uc001cxn.3	Q8WW52	OTTHUMG00000009888	ENST00000302250.2:c.163_167delTACCT	chr1.hg19:g.55085632_55085636delAGGTA	ENSP00000306888:p.Tyr55fs	29.0	0.0		51.0	16.0	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Frame_Shift_Del	DEL	ENST00000302250.2	hg19	CCDS594.1																																																																																			.	.		0.61	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782		-	55085636	AGGTA	-	55085632	7	5	157	1	0	1	0	1	0	0	0	0	5463	188	7	0	1618	0	FAM151A	1	55085632	Frame_Shift_Del	DEL	AGGTA	TCGA-DD-AACF-01A-11D-A40R-10	33486357	55085632	194164989	2	23832										
CLCA1	1179	hgsc.bcm.edu	37	chr1	86960069	86960069	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aattctcagggccagtgtcaCagccctgattgaatcagtga	10	10	3	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:86960069C>A	ENST00000234701.3	+	12	2231	c.1880C>A	c.(1879-1881)aCa>aAa	p.T627K	CLCA1_ENST00000394711.1_Missense_Mutation_p.T627K			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	627					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		GCCAGTGTCACAGCCCTGATT	0.433																																					p.T627K		Atlas-SNP	.											.	CLCA1	109	.	0			c.C1880A						.						69	64	66					1																	86960069		2203	4300	6503	SO:0001583	missense	1179	exon11			GTGTCACAGCCCT		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.1880C>A	chr1.hg19:g.86960069C>A	ENSP00000234701:p.Thr627Lys	138.0	0.0		226.0	106.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	hg19	CCDS709.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.6|21.6	4.171406|4.171406	0.78452|0.78452	.|.	.|.	ENSG00000016490|ENSG00000016490	ENST00000539889|ENST00000234701;ENST00000394711	.|T;T	.|0.32272	.|1.46;1.46	5.93|5.93	5.01|5.01	0.66863|0.66863	.|Domain of unknown function DUF1973 (1);	.|0.305888	.|0.32134	.|N	.|0.006538	T|T	0.45637|0.45637	0.1352|0.1352	M|M	0.73598|0.73598	2.24|2.24	0.37961|0.37961	D|D	0.932973|0.932973	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.79784	.|0.993;0.993	T|T	0.46233|0.46233	-0.9206|-0.9206	6|10	0.87932|0.72032	D|D	0|0.01	-21.8109|-21.8109	11.5342|11.5342	0.50628|0.50628	0.0:0.8637:0.0:0.1363|0.0:0.8637:0.0:0.1363	.|.	.|627;390	.|A8K7I4;B4DUZ6	.|CLCA1_HUMAN;.	Q|K	325|627	.|ENSP00000234701:T627K;ENSP00000378200:T627K	ENSP00000443173:H325Q|ENSP00000234701:T627K	H|T	+|+	3|2	2|0	CLCA1|CLCA1	86732657|86732657	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	0.704000|0.704000	0.25661|0.25661	2.805000|2.805000	0.96524|0.96524	0.655000|0.655000	0.94253|0.94253	CAC|ACA	.	.		0.433	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		A	86960069	C	A	86960069	3	1	157	1	0	0	0	0	1	0	0	0	3459	478	17	3	1922	3	CLCA1	1	86960069	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	31874437	86960069	162290552	3	23833										
GSTM3	2947	hgsc.bcm.edu	37	chr1	110280775	110280775	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	atccattacttggttctctaTgatgtccactcgaatctttt	5	10	2	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:110280775T>C	ENST00000540225.1	-	6	620	c.310A>G	c.(310-312)Ata>Gta	p.I104V	RP4-735C1.4_ENST00000431955.1_RNA|GSTM3_ENST00000488824.1_5'UTR|GSTM3_ENST00000361066.2_Missense_Mutation_p.I104V|GSTM3_ENST00000256594.3_Missense_Mutation_p.I104V			P21266	GSTM3_HUMAN	glutathione S-transferase mu 3 (brain)	104	GST C-terminal.				cellular detoxification of nitrogen compound (GO:0070458)|establishment of blood-nerve barrier (GO:0008065)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|skin(1)	9		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)|Vitamin E(DB00163)	TGGTTCTCTATGATGTCCACT	0.458																																					p.I104V		Atlas-SNP	.											.	GSTM3	21	.	0			c.A310G						.						228	213	218					1																	110280775		2203	4300	6503	SO:0001583	missense	2947	exon6			TCTCTATGATGTC	BC000088	CCDS812.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134202	ENSG00000134202	2.5.1.18	"Glutathione S-transferases / Soluble"	4635	protein-coding gene	gene with protein product		138390	"glutathione S-transferase M3 (brain)"			2345169	Standard	NM_000849		Approved	GST5	uc001dyo.2	P21266	OTTHUMG00000011640	ENST00000540225.1:c.310A>G	chr1.hg19:g.110280775T>C	ENSP00000444978:p.Ile104Val	99.0	0.0		159.0	58.0	NM_000849	O60550|Q96HA3	Missense_Mutation	SNP	ENST00000540225.1	hg19	CCDS812.1	.	.	.	.	.	.	.	.	.	.	T	9.089	1.001164	0.19121	.	.	ENSG00000134202	ENST00000540225;ENST00000256594;ENST00000361066	T;T;T	0.03745	3.82;3.82;3.82	5.41	1.73	0.24493	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.423243	0.31709	N	0.007190	T	0.00580	0.0019	N	0.04132	-0.27	0.23661	N	0.997173	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.48410	-0.9038	10	0.37606	T	0.19	-14.2532	6.33	0.21264	0.0:0.1622:0.1748:0.663	.	104;110;104	Q6FGJ9;Q59EJ5;P21266	.;.;GSTM3_HUMAN	V	104	ENSP00000444978:I104V;ENSP00000256594:I104V;ENSP00000354357:I104V	ENSP00000256594:I104V	I	-	1	0	GSTM3	110082298	0.231000	0.23751	0.995000	0.50966	0.611000	0.37282	-0.095000	0.11077	0.483000	0.27608	-0.400000	0.06385	ATA	.	.		0.458	GSTM3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032182.1	NM_000849		C	110280775	T	C	110280775	3	2	157	1	0	0	0	0	1	0	0	0	6848	1464	51	2	383	2	GSTM3	1	110280775	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	23320706	110280775	138969846	4	23834										
TCHH	7062	hgsc.bcm.edu	37	chr1	152086518	152086518	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gagacatactgattgaaaatTtcagtgatgtcacagatgct	9	6	2	5			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:152086518T>C	ENST00000368804.1	-	1	38	c.39A>G	c.(37-39)gaA>gaG	p.E13E		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	13	S-100-like.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GATTGAAAATTTCAGTGATGT	0.373																																					p.E13E		Atlas-SNP	.											.	TCHH	275	.	0			c.A39G						.						121	109	113					1																	152086518		1864	4099	5963	SO:0001819	synonymous_variant	7062	exon2			GAAAATTTCAGTG	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.39A>G	chr1.hg19:g.152086518T>C		72.0	0.0		145.0	58.0	NM_007113	Q5VUI3	Silent	SNP	ENST00000368804.1	hg19	CCDS41396.1																																																																																			.	.		0.373	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152086518	T	C	152086518	2	2	157	1	0	0	0	0	0	0	0	1	15715	1838	64	2		2	TCHH	1	152086518	Silent	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	41805743	152086518	97164103	5	23835										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153907287	153907287	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tgacacctgctcctgctgctGctgctgctgctgctgctgtt	11	14	0	1	rs3835302|rs199597671		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:153907287G>C	ENST00000361217.4	-	18	3140	c.2722C>G	c.(2722-2724)Cag>Gag	p.Q908E	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	908	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tcctgctgctgctgctgctgc	0.632																																					p.Q908E		Atlas-SNP	.											.	DENND4B	210	.	0			c.C2722G						.						23	27	26					1																	153907287		2184	4281	6465	SO:0001583	missense	9909	exon18			GCTGCTGCTGCTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2722C>G	chr1.hg19:g.153907287G>C	ENSP00000354597:p.Gln908Glu	21.0	0.0		120.0	8.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	1.785	-0.481073	0.04383	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06294	3.33;3.32	2.67	0.673	0.17941	.	5.053470	0.00166	N	0.000001	T	0.00815	0.0027	N	0.14661	0.345	0.19300	N	0.999977	B	0.02656	0.0	B	0.04013	0.001	T	0.26573	-1.0099	10	0.02654	T	1	-2.4288	3.3651	0.07201	0.1454:0.0:0.5849:0.2697	.	908	O75064	DEN4B_HUMAN	E	908;919	ENSP00000354597:Q908E;ENSP00000357635:Q919E	ENSP00000354597:Q908E	Q	-	1	0	DENND4B	152173911	0.943000	0.32029	0.986000	0.45419	0.760000	0.43138	0.537000	0.23144	0.194000	0.20326	0.271000	0.19318	CAG	.	.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153907287	G	C	153907287	3	2	157	1	0	0	0	0	1	0	0	0	4436	1328	46	4	1812	4	DENND4B	1	153907287	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	1820769	153907287	95343334	6	23836										
RPS27	6232	hgsc.bcm.edu	37	chr1	153963600	153963600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gtccctcttagctcgcaaagGatctccttcatccctctcca	5	17	4	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:153963600G>A	ENST00000368567.4	+	2	54	c.16G>A	c.(16-18)Gat>Aat	p.D6N	RPS27_ENST00000493224.1_3'UTR|RPS27_ENST00000392558.4_Missense_Mutation_p.D6N	NM_001030.4	NP_001021.1	P42677	RS27_HUMAN	ribosomal protein S27	6					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|nucleus (GO:0005634)|ribosome (GO:0005840)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|zinc ion binding (GO:0008270)			kidney(1)	1	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GCTCGCAAAGGATCTCCTTCA	0.502																																					p.D6N		Atlas-SNP	.											.	RPS27	6	.	0			c.G16A						.						95	82	87					1																	153963600		2203	4298	6501	SO:0001583	missense	6232	exon2			GCAAAGGATCTCC	U57847	CCDS1059.1	1q21	2011-04-06	2008-08-29		ENSG00000177954	ENSG00000177954		"S ribosomal proteins"	10416	protein-coding gene	gene with protein product	"metallopanstimulin 1"	603702	"ribosomal protein S27 (metallopanstimulin 1)"			8908372, 8407955	Standard	NM_001030		Approved	MPS-1, MPS1, S27	uc001fdv.3	P42677	OTTHUMG00000036591	ENST00000368567.4:c.16G>A	chr1.hg19:g.153963600G>A	ENSP00000357555:p.Asp6Asn	41.0	0.0		119.0	17.0	NM_001030	Q5T4L6	Missense_Mutation	SNP	ENST00000368567.4	hg19	CCDS1059.1	.	.	.	.	.	.	.	.	.	.	G	36	5.779576	0.96929	.	.	ENSG00000177954	ENST00000368567;ENST00000392558	.	.	.	5.06	5.06	0.68205	.	0.000000	0.49916	D	0.000123	T	0.46014	0.1371	.	.	.	0.58432	D	0.999994	B	0.13594	0.008	B	0.16722	0.016	T	0.49523	-0.8931	8	0.72032	D	0.01	-22.5869	17.4153	0.87498	0.0:0.0:1.0:0.0	.	6	P42677	RS27_HUMAN	N	6	.	ENSP00000357555:D6N	D	+	1	0	RPS27	152230224	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.776000	0.91776	2.647000	0.89833	0.555000	0.69702	GAT	.	.		0.502	RPS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088997.1	NM_001030		A	153963600	G	A	153963600	3	1	157	1	0	0	0	0	1	0	0	0	13653	1174	41	3	22	3	RPS27	1	153963600	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	56313	153963600	95287021	7	23837										
SCAMP3	10067	hgsc.bcm.edu	37	chr1	155230399	155230399	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cgagggctgcaaggagggagCtgagggtggaggcaatgggg	23	5	0	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:155230399C>A	ENST00000302631.3	-	3	303	c.196G>T	c.(196-198)Gct>Tct	p.A66S	SCAMP3_ENST00000472397.1_5'Flank|CLK2_ENST00000497188.1_5'Flank|SCAMP3_ENST00000355379.3_Missense_Mutation_p.A40S	NM_005698.3	NP_005689.2	O14828	SCAM3_HUMAN	secretory carrier membrane protein 3	66					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|response to retinoic acid (GO:0032526)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|large_intestine(3)|lung(7)|ovary(4)|urinary_tract(1)	19	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			AAGGAGGGAGCTGAGGGTGGA	0.567																																					p.A66S		Atlas-SNP	.											.	SCAMP3	33	.	0			c.G196T						.						127	131	130					1																	155230399		2203	4300	6503	SO:0001583	missense	10067	exon3			AGGGAGCTGAGGG	AF005039	CCDS1105.1, CCDS1106.1	1q21	2013-02-21			ENSG00000116521	ENSG00000116521		"Secretory carrier membrane proteins"	10565	protein-coding gene	gene with protein product	"Propin 1"	606913		C1orf3		9331372, 9658162	Standard	NM_005698		Approved		uc001fjs.3	O14828	OTTHUMG00000035874	ENST00000302631.3:c.196G>T	chr1.hg19:g.155230399C>A	ENSP00000307275:p.Ala66Ser	45.0	0.0		147.0	76.0	NM_005698	A9Z1W6|B1AVS6|O15128|Q96FR8|Q9BPY0	Missense_Mutation	SNP	ENST00000302631.3	hg19	CCDS1105.1	.	.	.	.	.	.	.	.	.	.	.	13.27	2.188080	0.38609	.	.	ENSG00000116521	ENST00000302631;ENST00000355379	T;T	0.19250	2.45;2.16	4.81	3.88	0.44766	.	0.536026	0.14838	N	0.295477	T	0.05090	0.0136	L	0.32530	0.975	0.40148	D	0.976917	B;B;P	0.35433	0.061;0.065;0.501	B;B;B	0.25140	0.045;0.017;0.058	T	0.20042	-1.0287	10	0.14252	T	0.57	-9.5133	9.2225	0.37386	0.0:0.8993:0.0:0.1007	.	66;40;66	Q6FHJ5;O14828-2;O14828	.;.;SCAM3_HUMAN	S	66;40	ENSP00000307275:A66S;ENSP00000347540:A40S	ENSP00000307275:A66S	A	-	1	0	SCAMP3	153497023	0.986000	0.35501	0.994000	0.49952	0.988000	0.76386	1.391000	0.34475	2.498000	0.84270	0.650000	0.86243	GCT	.	.		0.567	SCAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087399.1	NM_005698		A	155230399	C	A	155230399	3	1	157	1	0	0	0	0	1	0	0	0	13887	797	28	3	875	3	SCAMP3	1	155230399	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	1266799	155230399	94020222	8	23838										
CEP350	9857	hgsc.bcm.edu	37	chr1	180013265	180013265	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	agaagtattctgcttcatatGatagttattctgagtcttca	7	6	5	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:180013265G>T	ENST00000367607.3	+	21	4997	c.4579G>T	c.(4579-4581)Gat>Tat	p.D1527Y		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1527	Ser-rich.				microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TGCTTCATATGATAGTTATTC	0.343																																					p.D1527Y		Atlas-SNP	.											.	CEP350	418	.	0			c.G4579T						.						52	48	49					1																	180013265		2200	4294	6494	SO:0001583	missense	9857	exon21			TCATATGATAGTT	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.4579G>T	chr1.hg19:g.180013265G>T	ENSP00000356579:p.Asp1527Tyr	60.0	0.0		150.0	63.0	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.97|17.97	3.518966|3.518966	0.64634|0.64634	.|.	.|.	ENSG00000135837|ENSG00000135837	ENST00000367607|ENST00000418229	T|.	0.58940|.	0.3|.	5.69|5.69	4.78|4.78	0.61160|0.61160	.|.	0.150636|.	0.30193|.	N|.	0.010181|.	T|.	0.53867|.	0.1823|.	L|L	0.34521|0.34521	1.04|1.04	0.46849|0.46849	D|D	0.999224|0.999224	P;P|.	0.48503|.	0.911;0.911|.	P;P|.	0.48901|.	0.594;0.594|.	T|.	0.50074|.	-0.8870|.	9|.	.|.	.|.	.|.	.|.	12.4244|12.4244	0.55538|0.55538	0.0781:0.0:0.9219:0.0|0.0781:0.0:0.9219:0.0	.|.	1527;1527|.	E7EU22;Q5VT06|.	.;CE350_HUMAN|.	Y|L	1527|135	ENSP00000356579:D1527Y|.	.|.	D|X	+|+	1|2	0|2	CEP350|CEP350	178279888|178279888	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.597000|0.597000	0.36814|0.36814	4.612000|4.612000	0.61169|0.61169	1.418000|1.418000	0.47098|0.47098	0.555000|0.555000	0.69702|0.69702	GAT|TGA	.	.		0.343	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	180013265	G	T	180013265	3	4	157	1	0	0	0	0	1	0	0	0	3256	1290	45	3	4657	3	CEP350	1	180013265	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	24782866	180013265	69237356	9	23839										
PRELP	5549	hgsc.bcm.edu	37	chr1	203452997	203452997	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	acctcatgcagctcaacctgGcccacaacatcctgagaaag	7	15	2	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:203452997G>A	ENST00000343110.2	+	2	812	c.685G>A	c.(685-687)Gcc>Acc	p.A229T		NM_002725.3|NM_201348.1	NP_002716.1|NP_958505.1	P51888	PRELP_HUMAN	proline/arginine-rich end leucine-rich repeat protein	229					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			BRCA - Breast invasive adenocarcinoma(75;0.109)			GCTCAACCTGGCCCACAACAT	0.567																																					p.A229T		Atlas-SNP	.											.	PRELP	63	.	0			c.G685A						.						167	162	164					1																	203452997		2203	4300	6503	SO:0001583	missense	5549	exon2			AACCTGGCCCACA	BC032498	CCDS1438.1	1q32	2008-02-05	2005-07-24		ENSG00000188783	ENSG00000188783		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	9357	protein-coding gene	gene with protein product	"prolargin proteoglycan"	601914	"proline arginine-rich end leucine-rich repeat protein"				Standard	NM_002725		Approved	SLRR2A, prolargin	uc001gzt.3	P51888	OTTHUMG00000035911	ENST00000343110.2:c.685G>A	chr1.hg19:g.203452997G>A	ENSP00000343924:p.Ala229Thr	115.0	0.0		305.0	77.0	NM_201348	Q6FG38	Missense_Mutation	SNP	ENST00000343110.2	hg19	CCDS1438.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200694	0.79015	.	.	ENSG00000188783	ENST00000343110	T	0.57595	0.39	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.59376	0.2189	N	0.20574	0.59	0.52501	D	0.999959	D	0.89917	1.0	D	0.97110	1.0	T	0.65001	-0.6274	10	0.59425	D	0.04	-18.1347	16.3701	0.83353	0.0:0.0:1.0:0.0	.	229	P51888	PRELP_HUMAN	T	229	ENSP00000343924:A229T	ENSP00000343924:A229T	A	+	1	0	PRELP	201719620	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	8.030000	0.88816	2.214000	0.71695	0.462000	0.41574	GCC	.	.		0.567	PRELP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087474.1	NM_002725		A	203452997	G	A	203452997	3	1	157	1	0	0	0	0	1	0	0	0	12485	1203	42	3	687	3	PRELP	1	203452997	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	23439732	203452997	45797624	10	23840										
CR2	1380	hgsc.bcm.edu	37	chr1	207644091	207644091	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gtcctttcatttagaatgccAggcccctcctaacatcctca	5	15	2	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:207644091A>G	ENST00000367058.3	+	7	1421	c.1232A>G	c.(1231-1233)cAg>cGg	p.Q411R	CR2_ENST00000458541.2_Missense_Mutation_p.Q411R|CR2_ENST00000367059.3_Missense_Mutation_p.Q411R|CR2_ENST00000367057.3_Missense_Mutation_p.Q411R	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	411	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						TTAGAATGCCAGGCCCCTCCT	0.393																																					p.Q411R		Atlas-SNP	.											.	CR2	164	.	0			c.A1232G						.						84	81	82					1																	207644091		2203	4300	6503	SO:0001583	missense	1380	exon7			AATGCCAGGCCCC	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1232A>G	chr1.hg19:g.207644091A>G	ENSP00000356025:p.Gln411Arg	61.0	0.0		194.0	42.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.944534	0.53079	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	4.57	2.1	0.27182	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.67776	0.2929	L	0.39514	1.22	0.26031	N	0.981749	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.80764	0.985;0.994;0.953	T	0.56171	-0.8023	9	0.38643	T	0.18	.	9.0435	0.36331	0.6389:0.3611:0.0:0.0	.	411;411;411	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	R	411	ENSP00000356025:Q411R;ENSP00000356024:Q411R;ENSP00000356026:Q411R;ENSP00000404222:Q411R	ENSP00000356024:Q411R	Q	+	2	0	CR2	205710714	0.001000	0.12720	0.233000	0.24025	0.943000	0.58893	0.053000	0.14184	0.293000	0.22520	0.533000	0.62120	CAG	.	.		0.393	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		G	207644091	A	G	207644091	3	3	157	1	0	0	0	0	1	0	0	0	3844	188	7	2	1258	2	CR2	1	207644091	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	4191094	207644091	41606530	11	23841										
GPATCH2	55105	hgsc.bcm.edu	37	chr1	217688227	217688227	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tacccactgggccaggaatgGgtacctacagggagatttaa	12	9	0	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr1:217688227G>A	ENST00000366935.3	-	6	1213	c.1103C>T	c.(1102-1104)cCc>cTc	p.P368L		NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	368					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		GCCAGGAATGGGTACCTACAG	0.353																																					p.P368L		Atlas-SNP	.											.	GPATCH2	53	.	0			c.C1103T						.						40	40	40					1																	217688227		2203	4300	6503	SO:0001583	missense	55105	exon6			GGAATGGGTACCT	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "G patch domain containing"	25499	protein-coding gene	gene with protein product	"cancer/testis antigen 110", "protein phosphatase 1, regulatory subunit 30"			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.1103C>T	chr1.hg19:g.217688227G>A	ENSP00000355902:p.Pro368Leu	271.0	0.0		776.0	194.0	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Missense_Mutation	SNP	ENST00000366935.3	hg19	CCDS1518.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872396	0.51695	.	.	ENSG00000092978	ENST00000366935	T	0.29397	1.57	5.86	4.93	0.64822	.	0.490245	0.24954	N	0.034270	T	0.18759	0.0450	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.02877	-1.1099	10	0.28530	T	0.3	.	16.9629	0.86277	0.0:0.1278:0.8722:0.0	.	368	Q9NW75	GPTC2_HUMAN	L	368	ENSP00000355902:P368L	ENSP00000355902:P368L	P	-	2	0	GPATCH2	215754850	0.998000	0.40836	0.378000	0.26068	0.611000	0.37282	1.160000	0.31761	1.455000	0.47813	0.650000	0.86243	CCC	.	.		0.353	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040		A	217688227	G	A	217688227	3	1	157	1	0	0	0	0	1	0	0	0	6599	1232	43	3	503	3	GPATCH2	1	217688227	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	10044136	217688227	31562394	12	23842										
DNAJC27	51277	hgsc.bcm.edu	37	chr2	25190147	25190147	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gaatcttttctcacagtatcGctttataatacagctctaaa	4	9	3	0	rs147784881		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:25190147G>A	ENST00000264711.2	-	2	292	c.103C>T	c.(103-105)Cga>Tga	p.R35*	DNAJC27_ENST00000468467.1_5'UTR|SNORD14_ENST00000365609.1_RNA|DNAJC27_ENST00000534855.1_5'UTR	NM_001198559.1|NM_016544.2	NP_001185488.1|NP_057628.1	Q9NZQ0	DJC27_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 27	35					small GTPase mediated signal transduction (GO:0007264)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)	p.R35*(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						TCACAGTATCGCTTTATAATA	0.323																																					p.R35X		Atlas-SNP	.											DNAJC27,colon,carcinoma,0,1	DNAJC27	37	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C103T						.	G	stop/ARG,stop/ARG	1,4401	2.1+/-5.4	0,1,2200	72	77	75		103,103	5.8	1	2	dbSNP_134	75	0,8600		0,0,4300	no	stop-gained,stop-gained	DNAJC27	NM_001198559.1,NM_016544.2	,	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	,	35/178,35/274	25190147	1,13001	2201	4300	6501	SO:0001587	stop_gained	51277	exon2			AGTATCGCTTTAT		CCDS1716.1, CCDS74493.1	2p23.3	2011-09-02	2008-08-20	2008-08-20	ENSG00000115137	ENSG00000115137		"Heat shock proteins / DNAJ (HSP40)"	30290	protein-coding gene	gene with protein product		613527	"rab and DnaJ domain containing"	RBJ		14980719	Standard	NM_016544		Approved	RabJS	uc002rft.2	Q9NZQ0	OTTHUMG00000125524	ENST00000264711.2:c.103C>T	chr2.hg19:g.25190147G>A	ENSP00000264711:p.Arg35*	211.0	0.0		297.0	128.0	NM_016544	Q5JV88|Q86Y24	Nonsense_Mutation	SNP	ENST00000264711.2	hg19	CCDS1716.1	.	.	.	.	.	.	.	.	.	.	G	38	6.709763	0.97780	2.27E-4	0.0	ENSG00000115137	ENST00000264711	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.8466	17.0799	0.86596	0.0:0.0:1.0:0.0	.	.	.	.	X	35	.	ENSP00000264711:R35X	R	-	1	2	DNAJC27	25043651	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.022000	0.64078	2.885000	0.99019	0.655000	0.94253	CGA	.	G|1.000;A|0.000		0.323	DNAJC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246855.3	NM_016544		A	25190147	G	A	25190147	4	1	157	1	0	0	0	0	0	1	0	0	4647	1095	38	1	742	1	DNAJC27	2	25190147	Nonsense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10		25190147	218009226	13	23843										
C2orf53	339779	hgsc.bcm.edu	37	chr2	27360538	27360538	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tcgtgtgcgatgcggcggtgCcccagctggaccaccagggc	16	14	0	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:27360538C>A	ENST00000335524.3	-	3	1185	c.660G>T	c.(658-660)ggG>ggT	p.G220G	PREB_ENST00000260643.2_5'Flank	NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		220										cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCGGCGGTGCCCCAGCTGGA	0.657																																					p.G220G		Atlas-SNP	.											.	C2orf53	45	.	0			c.G660T						.						22	26	25					2																	27360538		2195	4290	6485	SO:0001819	synonymous_variant	339779	exon3			GCGGTGCCCCAGC																												ENST00000335524.3:c.660G>T	chr2.hg19:g.27360538C>A		76.0	0.0		126.0	57.0	NM_178553	Q86UE2	Silent	SNP	ENST00000335524.3	hg19	CCDS1739.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.459492	0.26248	.	.	ENSG00000186143	ENST00000432962	.	.	.	4.67	1.43	0.22495	.	.	.	.	.	T	0.61009	0.2313	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61008	-0.7149	5	0.87932	D	0	-12.3653	6.9023	0.24288	0.2034:0.4511:0.3455:0.0	.	.	.	.	S	56	.	ENSP00000393468:A56S	A	-	1	0	C2orf53	27214042	0.997000	0.39634	0.993000	0.49108	0.746000	0.42486	0.391000	0.20784	0.520000	0.28426	0.561000	0.74099	GCA	.	.		0.657	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1			A	27360538	C	A	27360538	2	1	157	1	0	0	0	0	0	0	0	1	2176	726	26	3		3	C2orf53	2	27360538	Silent	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	2170391	27360538	215838835	14	23844										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32695253	32695253	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tagggtcttcatgttactttCctgcattggtcaaagatcac	8	9	4	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:32695253C>G	ENST00000421745.2	+	31	6499	c.6365C>G	c.(6364-6366)tCc>tGc	p.S2122C		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2122					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					ATGTTACTTTCCTGCATTGGT	0.289																																					p.S2122C	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C6365G						.						56	55	56					2																	32695253		2201	4295	6496	SO:0001583	missense	57448	exon31			TACTTTCCTGCAT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.6365C>G	chr2.hg19:g.32695253C>G	ENSP00000393596:p.Ser2122Cys	60.0	0.0		99.0	44.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487440	0.84854	.	.	ENSG00000115760	ENST00000421745	T	0.75367	-0.93	5.14	5.14	0.70334	.	0.139878	0.48286	D	0.000182	D	0.84070	0.5391	L	0.53249	1.67	0.58432	D	0.999999	D	0.76494	0.999	D	0.77557	0.99	D	0.85716	0.1322	10	0.87932	D	0	.	18.6592	0.91467	0.0:1.0:0.0:0.0	.	2122	Q9NR09	BIRC6_HUMAN	C	2122	ENSP00000393596:S2122C	ENSP00000393596:S2122C	S	+	2	0	BIRC6	32548757	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.798000	0.85924	2.411000	0.81874	0.585000	0.79938	TCC	.	.		0.289	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		G	32695253	C	G	32695253	3	3	157	1	0	0	0	0	1	0	0	0	1438	855	30	4	6487	4	BIRC6	2	32695253	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	5334715	32695253	210504120	15	23845										
RTN4	57142	hgsc.bcm.edu	37	chr2	55201875	55201875	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	taaacaaggcaccaacatagGtaaatacccacatcaacact	4	12	1	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:55201875G>A	ENST00000337526.6	-	6	3629	c.3386C>T	c.(3385-3387)aCc>aTc	p.T1129I	RTN4_ENST00000486085.1_Intron|RTN4_ENST00000357732.4_Missense_Mutation_p.T329I|RTN4_ENST00000394609.2_Missense_Mutation_p.T136I|RTN4_ENST00000394611.2_Missense_Mutation_p.T923I|RTN4_ENST00000405240.1_Missense_Mutation_p.T923I|RTN4_ENST00000404909.1_Missense_Mutation_p.T923I|RTN4_ENST00000354474.6_Missense_Mutation_p.T897I|RTN4_ENST00000317610.7_Missense_Mutation_p.T310I|RTN4_ENST00000402434.2_Missense_Mutation_p.T282I|RTN4_ENST00000357376.3_Missense_Mutation_p.T923I	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	1129	Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						ACCAACATAGGTAAATACCCA	0.353																																					p.T1129I		Atlas-SNP	.											.	RTN4	189	.	0			c.C3386T						.						125	110	115					2																	55201875		2203	4300	6503	SO:0001583	missense	57142	exon6			ACATAGGTAAATA	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.3386C>T	chr2.hg19:g.55201875G>A	ENSP00000337838:p.Thr1129Ile	226.0	0.0		359.0	154.0	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	hg19	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	G	31	5.068487	0.93950	.	.	ENSG00000115310	ENST00000394609;ENST00000405240;ENST00000357376;ENST00000337526;ENST00000317610;ENST00000357732;ENST00000394611;ENST00000404909;ENST00000402434;ENST00000354474	T;T;T;T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.78477	0.4289	M	0.92412	3.305	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;1.0	T	0.81797	-0.0768	10	0.87932	D	0	-11.1752	20.8794	0.99867	0.0:0.0:1.0:0.0	.	310;329;1129;136	Q7L7Q6;Q9NQC3-5;Q9NQC3;Q7L7Q5	.;.;RTN4_HUMAN;.	I	136;923;923;1129;310;329;923;923;282;897	ENSP00000378107:T136I;ENSP00000384471:T923I;ENSP00000349944:T923I;ENSP00000337838:T1129I;ENSP00000322147:T310I;ENSP00000350365:T329I;ENSP00000378109:T923I;ENSP00000385650:T923I;ENSP00000384825:T282I;ENSP00000346465:T897I	ENSP00000322147:T310I	T	-	2	0	RTN4	55055379	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.706000	0.91362	2.941000	0.99782	0.655000	0.94253	ACC	.	.		0.353	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			A	55201875	G	A	55201875	3	1	157	1	0	0	0	0	1	0	0	0	13743	1261	44	3	208	3	RTN4	2	55201875	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	22506622	55201875	187997498	16	23846										
CD207	50489	hgsc.bcm.edu	37	chr2	71060902	71060902	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tttgggcatttaaggtactgActtcttcccaacttcttgtt	7	9	2	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:71060902A>G	ENST00000410009.3	-	3	485	c.440T>C	c.(439-441)gTc>gCc	p.V147A		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	147					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						TAAGGTACTGACTTCTTCCCA	0.453																																					p.V147A		Atlas-SNP	.											.	CD207	47	.	0			c.T440C						.						138	125	129					2																	71060902		1897	4129	6026	SO:0001583	missense	50489	exon3			GTACTGACTTCTT	AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"C-type lectin domain containing", "CD molecules"	17935	protein-coding gene	gene with protein product		604862	"CD207 antigen, langerin"			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.440T>C	chr2.hg19:g.71060902A>G	ENSP00000386378:p.Val147Ala	99.0	0.0		144.0	55.0	NM_015717		Missense_Mutation	SNP	ENST00000410009.3	hg19		.	.	.	.	.	.	.	.	.	.	A	7.221	0.597370	0.13875	.	.	ENSG00000116031	ENST00000410009	T	0.27256	1.68	4.23	0.553	0.17235	.	0.728978	0.12311	N	0.480149	T	0.16981	0.0408	L	0.36672	1.1	0.09310	N	1	B	0.14012	0.009	B	0.12156	0.007	T	0.28138	-1.0053	10	0.25751	T	0.34	.	6.2193	0.20673	0.6873:0.0:0.3127:0.0	.	147	Q9UJ71	CLC4K_HUMAN	A	147	ENSP00000386378:V147A	ENSP00000386378:V147A	V	-	2	0	CD207	70914410	0.008000	0.16893	0.001000	0.08648	0.005000	0.04900	1.769000	0.38522	0.087000	0.17167	0.533000	0.62120	GTC	.	.		0.453	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717		G	71060902	A	G	71060902	3	3	157	1	0	0	0	0	1	0	0	0	2985	275	10	2	562	2	CD207	2	71060902	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	15859027	71060902	172138471	17	23847										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84832694	84832694	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ctccaaagatgtgtttatacTgggcggcacagatgacatac	10	9	0	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:84832694T>G	ENST00000237449.6	+	19	3160	c.3152T>G	c.(3151-3153)cTg>cGg	p.L1051R	DNAH6_ENST00000389394.3_Missense_Mutation_p.L1051R|DNAH6_ENST00000398278.2_Missense_Mutation_p.L1051R			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1051	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GTGTTTATACTGGGCGGCACA	0.413																																					p.L1051R		Atlas-SNP	.											.	DNAH6	194	.	0			c.T3152G						.						166	141	148					2																	84832694		692	1591	2283	SO:0001583	missense	1768	exon20			TTATACTGGGCGG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.3152T>G	chr2.hg19:g.84832694T>G	ENSP00000237449:p.Leu1051Arg	79.0	0.0		152.0	63.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.645437	0.87859	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.69685	-0.42;-0.42;-0.42	5.78	5.78	0.91487	Dynein heavy chain, domain-2 (1);	.	.	.	.	D	0.87857	0.6283	H	0.96805	3.885	0.42457	D	0.992775	D	0.89917	1.0	D	0.91635	0.999	D	0.91955	0.5574	9	0.87932	D	0	.	15.103	0.72296	0.0:0.0:0.0:1.0	.	1051	Q9C0G6	DYH6_HUMAN	R	1051	ENSP00000374045:L1051R;ENSP00000381326:L1051R;ENSP00000237449:L1051R	ENSP00000237449:L1051R	L	+	2	0	DNAH6	84686205	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	6.562000	0.73960	2.205000	0.71048	0.533000	0.62120	CTG	.	.		0.413	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84832694	T	G	84832694	3	3	157	1	0	0	0	0	1	0	0	0	4607	1580	55	5	3226	5	DNAH6	2	84832694	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	13771792	84832694	158366679	18	23848										
TMEM150A	129303	hgsc.bcm.edu	37	chr2	85828182	85828182	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tccagggtgcagcaggtcttGggacccccttgctcagcagg	14	13	2	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:85828182G>C	ENST00000409668.1	-	3	629	c.162C>G	c.(160-162)ccC>ccG	p.P54P	TMEM150A_ENST00000334462.5_Silent_p.P54P|TMEM150A_ENST00000306353.3_Missense_Mutation_p.P24R			Q86TG1	T150A_HUMAN	transmembrane protein 150A	54					catabolic process (GO:0009056)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|lung(1)|skin(1)	7						AGCAGGTCTTGGGACCCCCTT	0.647																																					p.P54P		Atlas-SNP	.											.	TMEM150A	15	.	0			c.C162G						.						58	51	53					2																	85828182		2203	4300	6503	SO:0001819	synonymous_variant	129303	exon4			GGTCTTGGGACCC	AK098152	CCDS33233.1	2p11.2	2009-06-12	2009-06-12	2009-06-12	ENSG00000168890	ENSG00000168890			24677	protein-coding gene	gene with protein product			"transmembrane protein 150"	TMEM150		10858565	Standard	NM_001031738		Approved	TM6P1, FLJ90024	uc002spy.2	Q86TG1	OTTHUMG00000130168	ENST00000409668.1:c.162C>G	chr2.hg19:g.85828182G>C		80.0	0.0		118.0	45.0	NM_001031738	A8K764|B7WPQ9|D6W5L2|Q8N2R6	Silent	SNP	ENST00000409668.1	hg19	CCDS33233.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774939	0.49786	.	.	ENSG00000168890	ENST00000306353;ENST00000425160	T	0.50001	0.76	5.06	2.06	0.26882	.	0.000000	0.85682	D	0.000000	T	0.33147	0.0853	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.18023	-1.0350	9	0.87932	D	0	-13.3705	4.0961	0.09991	0.2165:0.1958:0.5877:0.0	.	24	Q86TG1-2	.	R	24	ENSP00000302715:P24R	ENSP00000302715:P24R	P	-	2	0	TMEM150A	85681693	0.989000	0.36119	1.000000	0.80357	0.996000	0.88848	0.072000	0.14617	0.508000	0.28173	0.655000	0.94253	CCA	.	.		0.647	TMEM150A-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329474.1	NM_153342		C	85828182	G	C	85828182	2	2	157	1	0	0	0	0	0	0	0	1	16082	1335	47	4		4	TMEM150A	2	85828182	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	995488	85828182	157371191	19	23849										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141819790	141819790	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tgttcggttcatcccatccaTgtcacatctctccactttgg	6	14	3	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:141819790T>A	ENST00000389484.3	-	8	2037	c.1066A>T	c.(1066-1068)Atg>Ttg	p.M356L		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	356					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATCCCATCCATGTCACATCTC	0.443										TSP Lung(27;0.18)																											p.M356L	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A1066T						.						142	124	130					2																	141819790		2203	4300	6503	SO:0001583	missense	53353	exon8			CATCCATGTCACA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1066A>T	chr2.hg19:g.141819790T>A	ENSP00000374135:p.Met356Leu	58.0	0.0		88.0	33.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.003795	0.35320	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.95690	-3.78	5.63	3.16	0.36331	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.048873	0.85682	N	0.000000	D	0.89649	0.6776	L	0.31371	0.925	0.31964	N	0.608031	B	0.02656	0.0	B	0.01281	0.0	T	0.83339	-0.0009	10	0.27082	T	0.32	.	7.4863	0.27435	0.2476:0.0:0.1294:0.623	.	356	Q9NZR2	LRP1B_HUMAN	L	356;294	ENSP00000374135:M356L	ENSP00000374135:M356L	M	-	1	0	LRP1B	141536260	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.313000	0.51935	0.450000	0.26774	0.533000	0.62120	ATG	.	.		0.443	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141819790	T	A	141819790	3	1	157	1	0	0	0	0	1	0	0	0	8964	1464	51	4	13069	4	LRP1B	2	141819790	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	55991608	141819790	101379583	20	23850										
TTN	7273	hgsc.bcm.edu	37	chr2	179477198	179477198	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ctctcttttccacaatgtagTtggtgatgggggaccctcca	10	11	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:179477198T>C	ENST00000591111.1	-	216	45355	c.45131A>G	c.(45130-45132)aAc>aGc	p.N15044S	TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.N7745S|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.N16685S|TTN_ENST00000342992.6_Missense_Mutation_p.N14117S|TTN_ENST00000460472.2_Missense_Mutation_p.N7620S|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.N7812S|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15044	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACAATGTAGTTGGTGATGGG	0.488																																					p.N16685S		Atlas-SNP	.											.	TTN	18412	.	0			c.A50054G						.						114	100	104					2																	179477198		1922	4138	6060	SO:0001583	missense	7273	exon266			ATGTAGTTGGTGA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.45131A>G	chr2.hg19:g.179477198T>C	ENSP00000465570:p.Asn15044Ser	54.0	0.0		73.0	31.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.21	1.572968	0.28092	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	5.71	4.56	0.56223	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50531	0.1621	L	0.41236	1.265	0.47698	D	0.999495	P;P;P;D	0.53151	0.928;0.928;0.928;0.958	P;P;P;P	0.48488	0.579;0.579;0.579;0.579	T	0.53265	-0.8463	9	0.87932	D	0	.	11.4716	0.50272	0.0:0.0701:0.0:0.9299	.	7620;7745;7812;15044	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	14117;7620;7812;7745;7620	ENSP00000343764:N14117S;ENSP00000434586:N7620S;ENSP00000340554:N7812S;ENSP00000352154:N7745S	ENSP00000340554:N7812S	N	-	2	0	TTN	179185443	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.991000	0.88244	1.006000	0.39211	0.460000	0.39030	AAC	.	.		0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179477198	T	C	179477198	3	2	157	1	0	0	0	0	1	0	0	0	16750	1725	60	2	58027	2	TTN	2	179477198	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	37657408	179477198	63722175	21	23851										
SLC40A1	30061	hgsc.bcm.edu	37	chr2	190428726	190428726	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cctgagtgtaggcgtaccctGtggtgatgcagtcaaagccc	13	11	1	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:190428726G>T	ENST00000261024.2	-	7	1412	c.986C>A	c.(985-987)aCa>aAa	p.T329K		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	329					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			GGCGTACCCTGTGGTGATGCA	0.488																																					p.T329K		Atlas-SNP	.											.	SLC40A1	51	.	0			c.C986A						.						102	82	89					2																	190428726		2203	4300	6503	SO:0001583	missense	30061	exon7			TACCCTGTGGTGA	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"Solute carriers"	10909	protein-coding gene	gene with protein product	"ferroportin 1"	604653	"solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.986C>A	chr2.hg19:g.190428726G>T	ENSP00000261024:p.Thr329Lys	150.0	0.0		219.0	94.0	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	hg19	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	G	34	5.397711	0.96009	.	.	ENSG00000138449	ENST00000261024;ENST00000544056	D	0.94966	-3.57	6.16	6.16	0.99307	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.97654	0.9231	M	0.84511	2.7	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.97415	1.0005	10	0.72032	D	0.01	-25.8042	20.8598	0.99761	0.0:0.0:1.0:0.0	.	329	Q9NP59	S40A1_HUMAN	K	329;64	ENSP00000261024:T329K	ENSP00000261024:T329K	T	-	2	0	SLC40A1	190136971	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.850000	0.99511	2.937000	0.99478	0.650000	0.86243	ACA	.	.		0.488	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			T	190428726	G	T	190428726	3	4	157	1	0	0	0	0	1	0	0	0	14643	1377	48	3	737	3	SLC40A1	2	190428726	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	10951528	190428726	52770647	22	23852										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204078361	204078361	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aaattgattgtagtgggtgtTggcaagcctgctgaggtaaa	14	4	0	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:204078361T>C	ENST00000449802.1	+	54	8301	c.7968T>C	c.(7966-7968)gtT>gtC	p.V2656V		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2656										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TAGTGGGTGTTGGCAAGCCTG	0.418																																					p.V2656V		Atlas-SNP	.											.	NBEAL1	266	.	0			c.T7968C						.						145	132	136					2																	204078361		1894	4120	6014	SO:0001819	synonymous_variant	65065	exon54			GGGTGTTGGCAAG	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.7968T>C	chr2.hg19:g.204078361T>C		97.0	0.0		136.0	65.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Silent	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	T	9.355	1.066636	0.20067	.	.	ENSG00000144426	ENST00000434469	.	.	.	5.61	0.251	0.15540	.	.	.	.	.	T	0.51584	0.1683	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36114	-0.9761	4	.	.	.	.	6.2477	0.20827	0.0:0.1992:0.1234:0.6774	.	.	.	.	S	184	.	.	L	+	2	0	NBEAL1	203786606	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	1.447000	0.35101	-0.180000	0.10637	0.528000	0.53228	TTG	.	.		0.418	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			C	204078361	T	C	204078361	2	2	157	1	0	0	0	0	0	0	0	1	10197	1799	63	2		2	NBEAL1	2	204078361	Silent	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	13649635	204078361	39121012	23	23853										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215854156	215854156	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gaggtggtgtcatcctgaacCggggaggtgtacatattttc	14	7	1	1	rs71428357	byFrequency	TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:215854156C>G	ENST00000272895.7	-	26	3945	c.3726G>C	c.(3724-3726)ccG>ccC	p.P1242P	ABCA12_ENST00000389661.4_Silent_p.P924P	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1242					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CATCCTGAACCGGGGAGGTGT	0.418																																					p.P1242P	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.G3726C						.						111	111	111					2																	215854156		2203	4300	6503	SO:0001819	synonymous_variant	26154	exon26			CTGAACCGGGGAG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.3726G>C	chr2.hg19:g.215854156C>G		224.0	0.0		301.0	129.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	hg19	CCDS33372.1																																																																																			.	C|0.925;T|0.075		0.418	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215854156	C	G	215854156	2	3	157	1	0	0	0	0	0	0	0	1	30	639	23	4		4	ABCA12	2	215854156	Silent	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	11775795	215854156	27345217	24	23854										
CTDSP1	58190	hgsc.bcm.edu	37	chr2	219268052	219268052	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ccaccgggggaactacgtgaAggacctgagccggttgggtc	16	11	0	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr2:219268052A>T	ENST00000273062.2	+	6	905	c.569A>T	c.(568-570)aAg>aTg	p.K190M	CTDSP1_ENST00000443891.1_Missense_Mutation_p.K189M|CTDSP1_ENST00000488627.1_3'UTR|MIR26B_ENST00000362251.2_RNA	NM_021198.2|NM_182642.2	NP_067021.1|NP_872580.1	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	190	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.	Transition state stabilizer.			negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|protein dephosphorylation (GO:0006470)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			NS(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	8		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AACTACGTGAAGGACCTGAGC	0.617																																					p.K190M		Atlas-SNP	.											.	CTDSP1	19	.	0			c.A569T						.						66	74	71					2																	219268052		2203	4300	6503	SO:0001583	missense	58190	exon6			ACGTGAAGGACCT	AF229162	CCDS2416.1, CCDS56166.1	2q35	2010-06-21			ENSG00000144579	ENSG00000144579		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	21614	protein-coding gene	gene with protein product	"nuclear LIM interactor-interacting factor", "small CTD phosphatase 1"	605323				11950066, 12721286	Standard	NM_021198		Approved	NLIIF, SCP1	uc021vwv.1	Q9GZU7	OTTHUMG00000133109	ENST00000273062.2:c.569A>T	chr2.hg19:g.219268052A>T	ENSP00000273062:p.Lys190Met	69.0	0.0		96.0	43.0	NM_021198	C9IYG0|Q7Z5Q3|Q7Z5Q4	Missense_Mutation	SNP	ENST00000273062.2	hg19	CCDS2416.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.4|20.4	3.986744|3.986744	0.74589|0.74589	.|.	.|.	ENSG00000144579|ENSG00000144579	ENST00000443891;ENST00000273062|ENST00000452977;ENST00000428361	T;T|.	0.51574|.	0.7;0.7|.	4.64|4.64	4.64|4.64	0.57946|0.57946	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.91818|0.91818	0.7411|0.7411	H|H	0.99961|0.99961	5.07|5.07	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.94799|0.94799	0.7969|0.7969	10|5	0.87932|.	D|.	0|.	-27.7969|-27.7969	13.051|13.051	0.58954|0.58954	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	190;189|.	Q9GZU7;C9IYG0|.	CTDS1_HUMAN;.|.	M|W	189;190|183;191	ENSP00000392248:K189M;ENSP00000273062:K190M|.	ENSP00000273062:K190M|.	K|R	+|+	2|1	0|2	CTDSP1|CTDSP1	218976296|218976296	1.000000|1.000000	0.71417|0.71417	0.866000|0.866000	0.34008|0.34008	0.725000|0.725000	0.41563|0.41563	9.273000|9.273000	0.95719|0.95719	1.724000|1.724000	0.51502|0.51502	0.402000|0.402000	0.26972|0.26972	AAG|AGG	.	.		0.617	CTDSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256774.1	NM_182642, NM_021198		T	219268052	A	T	219268052	3	4	157	1	0	0	0	0	1	0	0	0	4005	72	3	4	591	4	CTDSP1	2	219268052	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	3413896	219268052	23931321	25	23855										
KIF15	56992	hgsc.bcm.edu	37	chr3	44869717	44869717	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tcaccatagatggcaaaagtAcagaaactagaagagagctt	9	7	1	4			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr3:44869717A>G	ENST00000326047.4	+	24	3017	c.2868A>G	c.(2866-2868)gtA>gtG	p.V956V	KIF15_ENST00000425755.1_Silent_p.V591V	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	956					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		TGGCAAAAGTACAGAAACTAG	0.343																																					p.V956V		Atlas-SNP	.											.	KIF15	103	.	0			c.A2868G						.						68	68	68					3																	44869717		2203	4300	6503	SO:0001819	synonymous_variant	56992	exon24			AAAAGTACAGAAA	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.2868A>G	chr3.hg19:g.44869717A>G		85.0	0.0		95.0	49.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Silent	SNP	ENST00000326047.4	hg19	CCDS33744.1																																																																																			.	.		0.343	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			G	44869717	A	G	44869717	2	3	157	1	0	0	0	0	0	0	0	1	8286	378	14	2		2	KIF15	3	44869717	Silent	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10		44869717	153152713	26	23856										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48614152	48614152	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ctgggaggcctggaggccccTggggtccaaggataccagga	17	11	0	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr3:48614152T>A	ENST00000328333.8	-	67	5764	c.5657A>T	c.(5656-5658)cAg>cTg	p.Q1886L	COL7A1_ENST00000454817.1_Intron|MIR711_ENST00000390201.1_RNA	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1886	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGGAGGCCCCTGGGGTCCAAG	0.597																																					p.Q1886L		Atlas-SNP	.											.	COL7A1	320	.	0			c.A5657T	GRCh37	CD993040	COL7A1	D		.						17	19	19					3																	48614152		2203	4299	6502	SO:0001583	missense	1294	exon67			GGCCCCTGGGGTC	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.5657A>T	chr3.hg19:g.48614152T>A	ENSP00000332371:p.Gln1886Leu	73.0	0.0		101.0	41.0	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	hg19	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	T	10.54	1.377792	0.24944	.	.	ENSG00000114270	ENST00000328333	D	0.95788	-3.81	5.93	4.77	0.60923	.	0.157646	0.29609	N	0.011680	D	0.96433	0.8836	M	0.64567	1.98	0.80722	D	1	D	0.53151	0.958	D	0.66602	0.945	D	0.94720	0.7900	10	0.28530	T	0.3	.	11.9081	0.52723	0.0:0.0:0.4426:0.5574	.	1886	Q02388	CO7A1_HUMAN	L	1886	ENSP00000332371:Q1886L	ENSP00000332371:Q1886L	Q	-	2	0	COL7A1	48589156	1.000000	0.71417	0.995000	0.50966	0.516000	0.34256	1.093000	0.30939	1.053000	0.40415	0.533000	0.62120	CAG	.	.		0.597	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48614152	T	A	48614152	3	1	157	1	0	0	0	0	1	0	0	0	3706	1580	55	4	3385	4	COL7A1	3	48614152	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	3744435	48614152	149408278	27	23857										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48683636	48683636	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ccccttaggaagttgcgtccGtggaacacagccacgctgac	11	14	0	1	rs375748006		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr3:48683636G>A	ENST00000164024.4	-	22	7630	c.7350C>T	c.(7348-7350)caC>caT	p.H2450H	MIR4793_ENST00000577502.1_RNA|CELSR3_ENST00000544264.1_Silent_p.H2455H	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	2450					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AGTTGCGTCCGTGGAACACAG	0.602																																					p.H2450H		Atlas-SNP	.											.	CELSR3	237	.	0			c.C7350T						.			2,4400	4.2+/-10.8	0,2,2199	49	48	49		7350	-4.5	1	3		49	0,8598		0,0,4299	no	coding-synonymous	CELSR3	NM_001407.2		0,2,6498	AA,AG,GG		0.0,0.0454,0.0154		2450/3313	48683636	2,12998	2201	4299	6500	SO:0001819	synonymous_variant	1951	exon22			GCGTCCGTGGAAC	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.7350C>T	chr3.hg19:g.48683636G>A		109.0	0.0		133.0	59.0	NM_001407	O75092	Silent	SNP	ENST00000164024.4	hg19	CCDS2775.1																																																																																			.	.		0.602	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48683636	G	A	48683636	2	1	157	1	0	0	0	0	0	0	0	1	3225	1136	40	1		1	CELSR3	3	48683636	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	69484	48683636	149338794	28	23858										
LRIG1	26018	hgsc.bcm.edu	37	chr3	66434613	66434613	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ggcaatctgagggtttgggtGacctgtggcagcacattcga	15	8	1	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr3:66434613G>A	ENST00000273261.3	-	14	2397	c.1873C>T	c.(1873-1875)Cac>Tac	p.H625Y	LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.H649Y|SLC25A26_ENST00000536651.1_Intron	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	625	Ig-like C2-type 2.				innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		GGGTTTGGGTGACCTGTGGCA	0.562																																					p.H625Y		Atlas-SNP	.											.	LRIG1	138	.	0			c.C1873T						.						166	159	161					3																	66434613		2203	4300	6503	SO:0001583	missense	26018	exon14			TTGGGTGACCTGT	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1873C>T	chr3.hg19:g.66434613G>A	ENSP00000273261:p.His625Tyr	156.0	0.0		210.0	99.0	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	hg19	CCDS33783.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.443981	0.83993	.	.	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.66815	-0.23;-0.23	6.17	6.17	0.99709	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.65831	0.2729	N	0.05199	-0.095	0.80722	D	1	P;P;P	0.46952	0.863;0.786;0.887	P;P;P	0.57548	0.729;0.771;0.823	T	0.72161	-0.4374	10	0.66056	D	0.02	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	649;625;625	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	Y	625;649;528	ENSP00000273261:H625Y;ENSP00000373208:H649Y	ENSP00000273261:H625Y	H	-	1	0	LRIG1	66517303	1.000000	0.71417	1.000000	0.80357	0.207000	0.24258	5.744000	0.68664	2.941000	0.99782	0.655000	0.94253	CAC	.	.		0.562	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		A	66434613	G	A	66434613	3	1	157	1	0	0	0	0	1	0	0	0	8953	1290	45	3	1432	3	LRIG1	3	66434613	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	17750977	66434613	131587817	29	23859										
GPR128	84873	hgsc.bcm.edu	37	chr3	100387946	100387946	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ttctgccttttcaacactacAcaggtatggtgcggattagt	9	9	2	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr3:100387946A>G	ENST00000273352.3	+	15	2401	c.2133A>G	c.(2131-2133)acA>acG	p.T711T	GPR128_ENST00000475887.1_Silent_p.T416T|GPR128_ENST00000481506.1_3'UTR	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	711					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						TCAACACTACACAGGTATGGT	0.373																																					p.T711T	Pancreas(87;185 1975 7223 18722)	Atlas-SNP	.											.	GPR128	126	.	0			c.A2133G						.						101	88	93					3																	100387946		2203	4300	6503	SO:0001819	synonymous_variant	84873	exon15			CACTACACAGGTA	AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"-", "GPCR / Class B : Orphans"	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.2133A>G	chr3.hg19:g.100387946A>G		120.0	0.0		192.0	68.0	NM_032787	Q14D94|Q86SQ2	Silent	SNP	ENST00000273352.3	hg19	CCDS2938.1																																																																																			.	.		0.373	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1			G	100387946	A	G	100387946	2	3	157	1	0	0	0	0	0	0	0	1	6649	146	6	2		2	GPR128	3	100387946	Silent	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	33953333	100387946	97634484	30	23860										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129288753	129288753	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	atgatggccgtctcgctgccCcccagctgcagtgtggcgat	13	14	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr3:129288753C>T	ENST00000324093.4	-	20	3976	c.3798G>A	c.(3796-3798)ggG>ggA	p.G1266G	PLXND1_ENST00000393239.1_Silent_p.G1266G	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1266					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						TCTCGCTGCCCCCCAGCTGCA	0.592																																					p.G1266G	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.G3798A						.						91	77	82					3																	129288753		2203	4300	6503	SO:0001819	synonymous_variant	23129	exon20			GCTGCCCCCCAGC	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.3798G>A	chr3.hg19:g.129288753C>T		47.0	0.0		38.0	7.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	hg19	CCDS33854.1																																																																																			.	.		0.592	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		T	129288753	C	T	129288753	2	4	157	1	0	0	0	0	0	0	0	1	12136	610	22	3		3	PLXND1	3	129288753	Silent	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	28900807	129288753	68733677	31	23861										
ATR	545	hgsc.bcm.edu	37	chr3	142188365	142188365	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tgctctgtgataaccttgttTattttacccaaatcattcct	4	10	2	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr3:142188365T>C	ENST00000350721.4	-	38	6487	c.6366A>G	c.(6364-6366)atA>atG	p.I2122M	RP11-383G6.3_ENST00000460977.1_RNA|ATR_ENST00000383101.3_Missense_Mutation_p.I2058M	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2122	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TAACCTTGTTTATTTTACCCA	0.348								Other conserved DNA damage response genes																													p.I2122M		Atlas-SNP	.											.	ATR	285	.	0			c.A6366G						.						143	152	149					3																	142188365		2202	4300	6502	SO:0001583	missense	545	exon38			CTTGTTTATTTTA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.6366A>G	chr3.hg19:g.142188365T>C	ENSP00000343741:p.Ile2122Met	137.0	0.0		243.0	109.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.694359	0.30052	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.05199	3.48;3.93	5.15	3.98	0.46160	PIK-related kinase (1);	0.094484	0.64402	D	0.000001	T	0.04952	0.0133	L	0.28694	0.88	0.58432	D	0.999998	P	0.39665	0.682	B	0.38562	0.276	T	0.52997	-0.8500	10	0.22706	T	0.39	-13.4247	7.3538	0.26706	0.0:0.0762:0.1444:0.7794	.	2122	Q13535	ATR_HUMAN	M	2122;2058	ENSP00000343741:I2122M;ENSP00000372581:I2058M	ENSP00000343741:I2122M	I	-	3	3	ATR	143671055	1.000000	0.71417	0.997000	0.53966	0.960000	0.62799	3.192000	0.50989	0.791000	0.33826	0.482000	0.46254	ATA	.	.		0.348	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		C	142188365	T	C	142188365	3	2	157	1	0	0	0	0	1	0	0	0	1204	1744	61	2	1608	2	ATR	3	142188365	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	12899612	142188365	55834065	32	23862										
P2RY14	9934	hgsc.bcm.edu	37	chr3	150932059	150932059	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ctgagtgatcaggaggttctGagagcaggattcatctggag	15	6	4	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr3:150932059G>T	ENST00000309170.3	-	3	358	c.46C>A	c.(46-48)Cag>Aag	p.Q16K	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|P2RY14_ENST00000424796.2_Missense_Mutation_p.Q16K	NM_001081455.1|NM_014879.3	NP_001074924.1|NP_055694.3	Q15391	P2Y14_HUMAN	purinergic receptor P2Y, G-protein coupled, 14	16					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|UDP-activated nucleotide receptor activity (GO:0045029)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)	20			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGGAGGTTCTGAGAGCAGGAT	0.453																																					p.Q16K		Atlas-SNP	.											.	P2RY14	50	.	0			c.C46A						.						167	162	164					3																	150932059		2203	4300	6503	SO:0001583	missense	9934	exon3			GGTTCTGAGAGCA	D13626	CCDS3156.1	3q21-q25	2012-08-08	2004-07-12	2004-07-14	ENSG00000174944	ENSG00000174944		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	16442	protein-coding gene	gene with protein product		610116	"G protein-coupled receptor 105"	GPR105			Standard	NM_014879		Approved	KIAA0001	uc003eys.1	Q15391	OTTHUMG00000159859	ENST00000309170.3:c.46C>A	chr3.hg19:g.150932059G>T	ENSP00000308361:p.Gln16Lys	52.0	0.0		69.0	21.0	NM_014879	Q8IYT7	Missense_Mutation	SNP	ENST00000309170.3	hg19	CCDS3156.1	.	.	.	.	.	.	.	.	.	.	G	9.943	1.218083	0.22373	.	.	ENSG00000174944	ENST00000309170;ENST00000424796;ENST00000494668	T;T;T	0.19938	2.11;2.11;2.11	5.71	-11.4	0.00090	.	3.857980	0.00508	N	0.000163	T	0.06142	0.0159	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25502	-1.0130	10	0.05959	T	0.93	1.5069	2.2686	0.04085	0.2461:0.1072:0.1839:0.4628	.	16	Q15391	P2Y14_HUMAN	K	16	ENSP00000308361:Q16K;ENSP00000408733:Q16K;ENSP00000418065:Q16K	ENSP00000308361:Q16K	Q	-	1	0	P2RY14	152414749	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.876000	0.01633	-2.623000	0.00438	-1.491000	0.00971	CAG	.	.		0.453	P2RY14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357789.1	NM_014879		T	150932059	G	T	150932059	3	4	157	1	0	0	0	0	1	0	0	0	11360	1299	45	3	974	3	P2RY14	3	150932059	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	8743694	150932059	47090371	33	23863										
ECT2	1894	hgsc.bcm.edu	37	chr3	172499968	172499968	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ttcaggatgatcttgaagacCttatagttaattgggatgag	11	4	2	4			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr3:172499968C>G	ENST00000392692.3	+	15	1740	c.1564C>G	c.(1564-1566)Ctt>Gtt	p.L522V	ECT2_ENST00000427830.1_Missense_Mutation_p.L491V|ECT2_ENST00000441497.2_Missense_Mutation_p.L491V|ECT2_ENST00000540509.1_Missense_Mutation_p.L522V|ECT2_ENST00000232458.5_Missense_Mutation_p.L491V|ECT2_ENST00000417960.1_Missense_Mutation_p.L490V	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2	522	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				activation of protein kinase activity (GO:0032147)|activation of Rac GTPase activity (GO:0032863)|activation of Rho GTPase activity (GO:0032862)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular response to calcium ion (GO:0071277)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of Rho GTPase activity (GO:0032321)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|centralspindlin complex (GO:0097149)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			TCTTGAAGACCTTATAGTTAA	0.279																																					p.L522V		Atlas-SNP	.											.	ECT2	79	.	0			c.C1564G						.						100	100	100					3																	172499968		2203	4299	6502	SO:0001583	missense	1894	exon15			GAAGACCTTATAG	AA206473	CCDS3220.1, CCDS58860.1	3q26.1-q26.2	2014-03-11	2014-03-11		ENSG00000114346	ENSG00000114346		"Rho guanine nucleotide exchange factors"	3155	protein-coding gene	gene with protein product		600586	"epithelial cell transforming sequence 2 oncogene"			8464478, 10579713	Standard	NM_018098		Approved	ARHGEF31	uc003fil.2	Q9H8V3	OTTHUMG00000156762	ENST00000392692.3:c.1564C>G	chr3.hg19:g.172499968C>G	ENSP00000376457:p.Leu522Val	65.0	0.0		113.0	5.0	NM_001258315	Q0MT80|Q2M269|Q6U836|Q9NSV8|Q9NVW9	Missense_Mutation	SNP	ENST00000392692.3	hg19	CCDS58860.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.338418	0.81911	.	.	ENSG00000114346	ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000441497;ENST00000540509	T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54	5.86	5.86	0.93980	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.40909	0.1136	L	0.35723	1.085	0.80722	D	1	P;D;P;B	0.58970	0.872;0.984;0.508;0.34	P;P;B;B	0.53549	0.593;0.729;0.343;0.343	T	0.02352	-1.1172	10	0.41790	T	0.15	-23.066	20.1581	0.98126	0.0:1.0:0.0:0.0	.	522;522;491;490	Q9H8V3;Q9H8V3-3;G5E9L8;Q9H8V3-2	ECT2_HUMAN;.;.;.	V	491;522;491;490;491;522	ENSP00000232458:L491V;ENSP00000376457:L522V;ENSP00000401910:L491V;ENSP00000415876:L490V;ENSP00000412259:L491V;ENSP00000443160:L522V	ENSP00000232458:L491V	L	+	1	0	ECT2	173982662	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.736000	0.62059	2.937000	0.99478	0.650000	0.86243	CTT	.	.		0.279	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	NM_018098		G	172499968	C	G	172499968	3	3	157	1	0	0	0	0	1	0	0	0	4903	681	24	4	1521	4	ECT2	3	172499968	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	21567909	172499968	25522462	34	23864										
CCDC39	339829	hgsc.bcm.edu	37	chr3	180379687	180379687	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ttccagtattgaagccatctCattttccagccgttgaattt	6	10	1	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr3:180379687C>T	ENST00000442201.2	-	3	438	c.319G>A	c.(319-321)Gag>Aag	p.E107K	CCDC39_ENST00000273654.4_Missense_Mutation_p.E191K	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	107					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			GAAGCCATCTCATTTTCCAGC	0.373																																					p.E107K		Atlas-SNP	.											.	CCDC39	242	.	0			c.G319A						.						83	75	77					3																	180379687		1829	4083	5912	SO:0001583	missense	339829	exon3			CCATCTCATTTTC	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.319G>A	chr3.hg19:g.180379687C>T	ENSP00000405708:p.Glu107Lys	179.0	0.0		259.0	100.0	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	hg19	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.272905	0.59649	.	.	ENSG00000145075	ENST00000273654;ENST00000442201;ENST00000471307	T	0.81163	-1.46	5.38	5.38	0.77491	.	0.093711	0.64402	D	0.000001	D	0.84556	0.5498	M	0.81802	2.56	0.45676	D	0.998597	P	0.43024	0.798	B	0.43123	0.409	D	0.87157	0.2212	10	0.72032	D	0.01	-22.3511	19.1199	0.93358	0.0:1.0:0.0:0.0	.	107	Q9UFE4	CCD39_HUMAN	K	191;107;89	ENSP00000418702:E89K	ENSP00000273654:E191K	E	-	1	0	CCDC39	181862381	1.000000	0.71417	1.000000	0.80357	0.155000	0.21991	3.002000	0.49496	2.502000	0.84385	0.655000	0.94253	GAG	.	.		0.373	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		T	180379687	C	T	180379687	3	4	157	1	0	0	0	0	1	0	0	0	2813	835	29	3	2578	3	CCDC39	3	180379687	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	7879719	180379687	17642743	35	23865										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55156601	55156602	+	Missense_Mutation	DNP	AG	AG	TT													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aaacgaggaagacaagctgaAggactgggagggtggtctgg					rs373642812		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr4:55156601_55156602AG>TT	ENST00000257290.5	+	22	3333_3334	c.3002_3003AG>TT	c.(3001-3003)aAG>aTT	p.K1001I	FIP1L1_ENST00000507166.1_Missense_Mutation_p.K761I	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	1001					adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	GACAAGCTGAAGGACTGGGAGG	0.545			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.K1001M|p.K1001N	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	.	PDGFRA	1583	.	0			c.A3002T|c.G3003T						.																																			SO:0001583	missense	5156	exon22	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	AGCTGAAGGACTG|GCTGAAGGACTGG	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	Exception_encountered	chr4.hg19:g.55156601_55156602delinsTT	ENSP00000257290:p.Lys1001Ile	154.0	0.0		93.0|95.0	60.0|62.0	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	hg19	CCDS3495.1																																																																																			.	.		0.545	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		TT	55156602	AG	TT	55156601	3	4	157	1	0	0	0	0	1	0	0	0	11670	72	3	4	3084	4	PDGFRA	4	55156601	Missense_Mutation	DNP	AG	TCGA-DD-AACF-01A-11D-A40R-10		55156601	135997675	36	23866										
INPP4B	8821	hgsc.bcm.edu	37	chr4	143067061	143067061	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	catcattgttgccgccactgCcttcactgccaccatctctt	5	17	3	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr4:143067061C>G	ENST00000513000.1	-	19	2085	c.1652G>C	c.(1651-1653)gGc>gCc	p.G551A	INPP4B_ENST00000262992.4_Missense_Mutation_p.G551A|INPP4B_ENST00000308502.4_Missense_Mutation_p.G551A|INPP4B_ENST00000509777.1_Missense_Mutation_p.G551A|INPP4B_ENST00000508116.1_Missense_Mutation_p.G551A	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	551					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					GCCGCCACTGCCTTCACTGCC	0.443																																					p.G551A		Atlas-SNP	.											.	INPP4B	132	.	0			c.G1652C						.						201	167	179					4																	143067061		2203	4300	6503	SO:0001583	missense	8821	exon19			CCACTGCCTTCAC	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.1652G>C	chr4.hg19:g.143067061C>G	ENSP00000425487:p.Gly551Ala	123.0	0.0		110.0	83.0	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	hg19	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	C	0.024	-1.390171	0.01185	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55	5.48	1.77	0.24775	.	0.330559	0.21414	N	0.074933	T	0.16514	0.0397	L	0.38175	1.15	0.09310	N	1	B;B	0.33940	0.001;0.433	B;B	0.35182	0.003;0.197	T	0.12967	-1.0527	10	0.08837	T	0.75	.	1.568	0.02608	0.1189:0.3909:0.1777:0.3126	.	422;551	B7Z6T2;O15327	.;INP4B_HUMAN	A	551;551;551;422;551;551;366;366;551;422	ENSP00000425487:G551A;ENSP00000262992:G551A;ENSP00000308441:G551A;ENSP00000423954:G551A;ENSP00000422793:G551A;ENSP00000426207:G366A;ENSP00000427250:G551A;ENSP00000421065:G422A	ENSP00000262992:G551A	G	-	2	0	INPP4B	143286511	0.000000	0.05858	0.002000	0.10522	0.247000	0.25773	0.119000	0.15626	0.287000	0.22375	0.650000	0.86243	GGC	.	.		0.443	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		G	143067061	C	G	143067061	3	3	157	1	0	0	0	0	1	0	0	0	7762	739	26	4	1158	4	INPP4B	4	143067061	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	87910460	143067061	48087215	37	23867										
FAM105A	54491	hgsc.bcm.edu	37	chr5	14582020	14582020	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cggcatggcggcgacaaggaGccccacgcgggcaagggagc	18	13	0	0	rs375610503	byFrequency	TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr5:14582020G>A	ENST00000274217.3	+	1	137	c.17G>A	c.(16-18)aGc>aAc	p.S6N		NM_019018.2	NP_061891.1	Q9NUU6	F105A_HUMAN	family with sequence similarity 105, member A	6										large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Lung NSC(4;0.00592)					GCGACAAGGAGCCCCACGCGG	0.806													G|||	32	0.00638978	0	0	5008	,	,		5116	0.0308		0	False		,,,				2504	0.001				p.S6N		Atlas-SNP	.											.	FAM105A	32	.	0			c.G17A						.						1	1	1					5																	14582020		417	1078	1495	SO:0001583	missense	54491	exon1			CAAGGAGCCCCAC		CCDS3884.1	5p15.2	2014-02-24			ENSG00000145569	ENSG00000145569		"OTU domain containing"	25629	protein-coding gene	gene with protein product						12477932	Standard	NM_019018		Approved	FLJ11127, NET20	uc003jfj.3	Q9NUU6	OTTHUMG00000131056	ENST00000274217.3:c.17G>A	chr5.hg19:g.14582020G>A	ENSP00000274217:p.Ser6Asn	0.0	0.0		6.0	6.0	NM_019018	Q53H50|Q9H037	Missense_Mutation	SNP	ENST00000274217.3	hg19	CCDS3884.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.412692	0.25465	.	.	ENSG00000145569	ENST00000274217	T	0.18502	2.21	2.78	2.78	0.32641	.	2.107840	0.02975	U	0.144806	T	0.16300	0.0392	N	0.24115	0.695	0.24488	N	0.994317	B	0.24092	0.097	B	0.29598	0.104	T	0.24728	-1.0152	10	0.87932	D	0	-2.561	9.22	0.37370	0.0:0.0:1.0:0.0	.	6	Q9NUU6	F105A_HUMAN	N	6	ENSP00000274217:S6N	ENSP00000274217:S6N	S	+	2	0	FAM105A	14635020	0.377000	0.25106	0.613000	0.29037	0.044000	0.14063	2.711000	0.47177	1.867000	0.54127	0.491000	0.48974	AGC	.	.		0.806	FAM105A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253710.1	NM_019018		A	14582020	G	A	14582020	3	1	157	1	0	0	0	0	1	0	0	0	5392	971	34	3	19	3	FAM105A	5	14582020	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10		14582020	166333240	38	23868										
MYO10	4651	hgsc.bcm.edu	37	chr5	16766245	16766246	+	Missense_Mutation	DNP	GG	GG	TT													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cctgaggaacattgatctctGggtcaaagcatctgtgagct							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr5:16766245_16766246GG>TT	ENST00000513610.1	-	11	1576_1577	c.1122_1123CC>AA	c.(1120-1125)acCCag>acAAag	p.Q375K		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	375	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						ATTGATCTCTGGGTCAAAGCAT	0.51																																					p.Q375K|p.T374T		Atlas-SNP	.											.	MYO10	198	.	0			c.C1123A|c.C1122A						.																																			SO:0001583	missense	4651	exon11			ATCTCTGGGTCAA|TCTCTGGGTCAAA	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.1122_1123delinsTT	chr5.hg19:g.16766245_16766246delinsTT	ENSP00000421280:p.Gln375Lys	120.0	0.0		203.0	58.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation|Silent	SNP	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.51	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		TT	16766246	GG	TT	16766245	3	4	157	1	0	0	0	0	1	0	0	0	10071	1357	47	3	5177	3	MYO10	5	16766245	Missense_Mutation	DNP	GG	TCGA-DD-AACF-01A-11D-A40R-10	2184225	16766245	164149015	39	23869										
PRKAA1	5562	hgsc.bcm.edu	37	chr5	40764913	40764913	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ttctgccataatatcatttgGtcgactttgacttctaattc	5	9	3	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr5:40764913G>C	ENST00000397128.2	-	7	1257	c.1249C>G	c.(1249-1251)Cca>Gca	p.P417A	PRKAA1_ENST00000354209.3_Missense_Mutation_p.P432A	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	417					activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)			breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	ATATCATTTGGTCGACTTTGA	0.348																																					p.P432A		Atlas-SNP	.											.	PRKAA1	27	.	0			c.C1294G						.						119	105	109					5																	40764913		1857	4114	5971	SO:0001583	missense	5562	exon8			CATTTGGTCGACT		CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"AMPK, alpha, 1"	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.1249C>G	chr5.hg19:g.40764913G>C	ENSP00000380317:p.Pro417Ala	104.0	0.0		208.0	125.0	NM_206907	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Missense_Mutation	SNP	ENST00000397128.2	hg19	CCDS3932.2	.	.	.	.	.	.	.	.	.	.	G	16.12	3.033899	0.54896	.	.	ENSG00000132356	ENST00000397128;ENST00000354209	D;D	0.86497	-1.99;-2.13	6.01	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.90126	0.6915	M	0.91717	3.235	0.80722	D	1	B;B	0.21520	0.034;0.057	B;B	0.24006	0.022;0.05	D	0.88618	0.3161	10	0.62326	D	0.03	-13.6234	15.6824	0.77381	0.0664:0.0:0.9336:0.0	.	417;432	Q13131;Q13131-2	AAPK1_HUMAN;.	A	417;432	ENSP00000380317:P417A;ENSP00000346148:P432A	ENSP00000346148:P432A	P	-	1	0	AC008810.1	40800670	1.000000	0.71417	0.955000	0.39395	0.989000	0.77384	7.642000	0.83385	2.861000	0.98227	0.650000	0.86243	CCA	.	.		0.348	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251		C	40764913	G	C	40764913	3	2	157	1	0	0	0	0	1	0	0	0	12505	1261	44	4	442	4	PRKAA1	5	40764913	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	23998668	40764913	140150347	40	23870										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139828827	139828827	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	atggttcgctttctacttgaAgctggtgcagatcaagagca	11	8	2	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr5:139828827A>T	ENST00000360839.2	+	7	1333	c.1179A>T	c.(1177-1179)gaA>gaT	p.E393D	ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.E393D|ANKHD1_ENST00000394723.3_Missense_Mutation_p.E393D|ANKHD1_ENST00000394722.3_Missense_Mutation_p.E382D|ANKHD1_ENST00000297183.6_Missense_Mutation_p.E393D	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	393						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCTACTTGAAGCTGGTGCAG	0.348																																					p.E393D		Atlas-SNP	.											.	ANKHD1	233	.	0			c.A1179T						.						78	67	71					5																	139828827		2203	4300	6503	SO:0001583	missense	54882	exon7			ACTTGAAGCTGGT	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1179A>T	chr5.hg19:g.139828827A>T	ENSP00000354085:p.Glu393Asp	311.0	0.0		692.0	198.0	NM_024668	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	A	17.01	3.278596	0.59758	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000421134;ENST00000394723;ENST00000394722;ENST00000532219	T;T;T;T;T;T	0.15372	2.44;2.44;2.43;2.43;2.43;2.44	5.97	0.575	0.17374	Ankyrin repeat-containing domain (3);	0.118251	0.56097	N	0.000029	T	0.13457	0.0326	L	0.47716	1.5	0.54753	D	0.999982	B;B;B;B;B	0.16166	0.003;0.001;0.003;0.013;0.016	B;B;B;B;B	0.23852	0.02;0.005;0.009;0.03;0.049	T	0.08743	-1.0707	10	0.33940	T	0.23	.	6.9475	0.24526	0.5081:0.0:0.0714:0.4205	.	393;393;393;382;393	Q8IWZ3-5;Q8IWZ2;Q8IWZ3;Q8IWZ3-3;Q8IWZ3-2	.;.;ANKH1_HUMAN;.;.	D	393;407;393;393;393;393;382;393	ENSP00000354085:E393D;ENSP00000297183:E393D;ENSP00000394489:E393D;ENSP00000378212:E393D;ENSP00000378211:E382D;ENSP00000432016:E393D	ENSP00000432016:E393D	E	+	3	2	ANKHD1-EIF4EBP3;ANKHD1	139809011	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.895000	0.28363	0.125000	0.18397	-0.480000	0.04831	GAA	.	.		0.348	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		T	139828827	A	T	139828827	3	4	157	1	0	0	0	0	1	0	0	0	628	69	3	4	1205	4	ANKHD1	5	139828827	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	99063914	139828827	41086433	41	23871										
PCDHAC1	56135	hgsc.bcm.edu	37	chr5	140308283	140308283	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ctttcctaccacatctcccgGgcgtctgactctagtctctt	6	16	4	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr5:140308283G>A	ENST00000253807.2	+	1	1806	c.1806G>A	c.(1804-1806)cgG>cgA	p.R602R	PCDHA13_ENST00000289272.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHAC1_ENST00000409700.3_Silent_p.R602R|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	602	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACATCTCCCGGGCGTCTGACT	0.522																																					p.R602R		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.G1806A						.						81	84	83					5																	140308283		2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			CTCCCGGGCGTCT	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"Cadherins / Protocadherins : Clustered"	8676	other	complex locus constituent	"PCDH-ALPHA-C1"	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1806G>A	chr5.hg19:g.140308283G>A		61.0	0.0		151.0	44.0	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	hg19	CCDS4241.1																																																																																			.	.		0.522	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		A	140308283	G	A	140308283	2	1	157	1	0	0	0	0	0	0	0	1	11541	1219	43	3		3	PCDHAC1	5	140308283	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	479456	140308283	40606977	42	23872										
NMUR2	56923	hgsc.bcm.edu	37	chr5	151784217	151784217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gggtgctctgcagtttggcgCggaacgggtgtaggatggcc	19	8	1	0	rs370782921		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr5:151784217C>T	ENST00000255262.3	-	1	623	c.458G>A	c.(457-459)cGc>cAc	p.R153H	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	153					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			CAGTTTGGCGCGGAACGGGTG	0.637																																					p.R153H		Atlas-SNP	.											NMUR2,NS,carcinoma,0,1	NMUR2	111	.	0			c.G458A						.						47	53	51					5																	151784217		2203	4300	6503	SO:0001583	missense	56923	exon1			TTGGCGCGGAACG	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.458G>A	chr5.hg19:g.151784217C>T	ENSP00000255262:p.Arg153His	78.0	0.0		159.0	37.0	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	hg19	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.072172	0.55646	.	.	ENSG00000132911	ENST00000255262	T	0.39406	1.08	5.35	5.35	0.76521	GPCR, rhodopsin-like superfamily (1);	0.170414	0.42548	D	0.000689	T	0.58192	0.2105	M	0.62723	1.935	0.44330	D	0.997219	D	0.89917	1.0	D	0.68353	0.957	T	0.57883	-0.7734	10	0.48119	T	0.1	-15.3605	11.5244	0.50571	0.0:0.9184:0.0:0.0816	.	153	Q9GZQ4	NMUR2_HUMAN	H	153	ENSP00000255262:R153H	ENSP00000255262:R153H	R	-	2	0	NMUR2	151764410	0.070000	0.21116	0.918000	0.36340	0.403000	0.30841	0.584000	0.23864	2.502000	0.84385	0.591000	0.81541	CGC	.	.		0.637	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		T	151784217	C	T	151784217	3	4	157	1	0	0	0	0	1	0	0	0	10516	768	27	1	805	1	NMUR2	5	151784217	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	11475934	151784217	29131043	43	23873										
GRM4	2914	hgsc.bcm.edu	37	chr6	34003690	34003690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gaagcgggggtcgagtgtccGctggtcctggaagtccacca	16	11	0	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr6:34003690G>A	ENST00000538487.2	-	9	2640	c.2197C>T	c.(2197-2199)Cgg>Tgg	p.R733W	GRM4_ENST00000544773.2_Missense_Mutation_p.R564W|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000535756.1_Missense_Mutation_p.R600W|GRM4_ENST00000609222.1_Missense_Mutation_p.R600W|GRM4_ENST00000374177.3_Missense_Mutation_p.R617W|GRM4_ENST00000374181.4_Missense_Mutation_p.R733W|GRM4_ENST00000455714.2_Missense_Mutation_p.R593W	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	733					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						TCGAGTGTCCGCTGGTCCTGG	0.622																																					p.R733W		Atlas-SNP	.											GRM4_ENST00000374181,NS,carcinoma,0,6	GRM4	317	.	0			c.C2197T						.						87	84	85					6																	34003690		2203	4300	6503	SO:0001583	missense	2914	exon9			GTGTCCGCTGGTC	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.2197C>T	chr6.hg19:g.34003690G>A	ENSP00000440556:p.Arg733Trp	72.0	0.0		127.0	43.0	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	hg19	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	G	18.87	3.714681	0.68730	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000545715;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	D;D;D;D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44	4.47	4.47	0.54385	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.93864	0.8037	M	0.80183	2.485	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.999;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.967;0.967;0.997;0.983;0.978	D	0.94717	0.7897	10	0.87932	D	0	.	17.3286	0.87257	0.0:0.0:1.0:0.0	.	686;564;593;733;600	B7ZLU9;B7Z1T9;F5GXM5;Q14833;B3KVL9	.;.;.;GRM4_HUMAN;.	W	733;617;425;600;564;733;593	ENSP00000363296:R733W;ENSP00000363292:R617W;ENSP00000445533:R425W;ENSP00000437925:R600W;ENSP00000437730:R564W;ENSP00000440556:R733W;ENSP00000398456:R593W	ENSP00000363292:R617W	R	-	1	2	GRM4	34111668	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.166000	0.64965	2.303000	0.77524	0.455000	0.32223	CGG	.	.		0.622	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			A	34003690	G	A	34003690	3	1	157	1	0	0	0	0	1	0	0	0	6808	1086	38	1	553	1	GRM4	6	34003690	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10		34003690	137111377	44	23874										
C6orf167	253714	hgsc.bcm.edu	37	chr6	97613250	97613250	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gaagctggaagaaatcgcccAatatactgctcaataacatt	7	9	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr6:97613250A>C	ENST00000275053.4	-	21	3358	c.3093T>G	c.(3091-3093)atT>atG	p.I1031M	MMS22L_ENST00000369251.2_Missense_Mutation_p.I991M	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1031					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						GAAATCGCCCAATATACTGCT	0.398																																					p.I1031M		Atlas-SNP	.											.	MMS22L	102	.	0			c.T3093G						.						117	108	111					6																	97613250		2203	4300	6503	SO:0001583	missense	253714	exon21			TCGCCCAATATAC		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"chromosome 6 open reading frame 167"	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3093T>G	chr6.hg19:g.97613250A>C	ENSP00000275053:p.Ile1031Met	90.0	0.0		124.0	66.0	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	hg19	CCDS5039.1	.	.	.	.	.	.	.	.	.	.	A	18.19	3.569039	0.65765	.	.	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.35789	3.48;1.29	5.79	-1.21	0.09524	.	0.166971	0.52532	D	0.000065	T	0.22044	0.0531	L	0.60455	1.87	0.25142	N	0.990492	D;D	0.55172	0.97;0.97	P;P	0.56042	0.79;0.711	T	0.11470	-1.0586	10	0.51188	T	0.08	-5.0302	2.1972	0.03914	0.4931:0.1144:0.2763:0.1162	.	991;1031	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	M	1031;991	ENSP00000275053:I1031M;ENSP00000358254:I991M	ENSP00000275053:I1031M	I	-	3	3	MMS22L	97719971	1.000000	0.71417	0.983000	0.44433	0.992000	0.81027	0.729000	0.26028	-0.435000	0.07264	-0.250000	0.11733	ATT	.	.		0.398	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		C	97613250	A	C	97613250	3	2	157	1	0	0	0	0	1	0	0	0	2344	126	5	5	658	5	C6orf167	6	97613250	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	63609560	97613250	73501817	45	23875										
AIM1	202	hgsc.bcm.edu	37	chr6	106992501	106992501	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	atcagtatttgctagaagaaGgagaatacagggactggaaa	12	4	1	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr6:106992501G>A	ENST00000369066.3	+	10	4358	c.3871G>A	c.(3871-3873)Gga>Aga	p.G1291R	AIM1_ENST00000535438.1_Missense_Mutation_p.G110R|AIM1_ENST00000487681.1_3'UTR	NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GCTAGAAGAAGGAGAATACAG	0.418																																					p.G1291R		Atlas-SNP	.											.	AIM1	161	.	0			c.G3871A						.						93	95	94					6																	106992501		2203	4300	6503	SO:0001583	missense	202	exon10			GAAGAAGGAGAAT	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.3871G>A	chr6.hg19:g.106992501G>A	ENSP00000358062:p.Gly1291Arg	99.0	0.0		147.0	61.0	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.414455	0.83449	.	.	ENSG00000112297	ENST00000369066;ENST00000457437;ENST00000535438	D;D;D	0.94000	-3.33;-3.33;-3.33	5.85	4.99	0.66335	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.97396	0.9148	H	0.95328	3.655	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98614	1.0664	10	0.87932	D	0	.	14.935	0.70948	0.0685:0.0:0.9315:0.0	.	110;1291	B4DU04;Q9Y4K1	.;AIM1_HUMAN	R	1291;110;110	ENSP00000358062:G1291R;ENSP00000391419:G110R;ENSP00000439183:G110R	ENSP00000358062:G1291R	G	+	1	0	AIM1	107099194	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.891000	0.92485	1.490000	0.48466	-0.136000	0.14681	GGA	.	.		0.418	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			A	106992501	G	A	106992501	3	1	157	1	0	0	0	0	1	0	0	0	430	1001	35	3	3909	3	AIM1	6	106992501	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	9379251	106992501	64122566	46	23876										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136599264	136599264	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aaggagtattttttgcagagTgaactgtactgagcatggga	13	4	0	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr6:136599264T>G	ENST00000531224.1	-	4	1007	c.755A>C	c.(754-756)cAc>cCc	p.H252P	BCLAF1_ENST00000527536.1_Missense_Mutation_p.H252P|BCLAF1_ENST00000527759.1_Missense_Mutation_p.H250P|BCLAF1_ENST00000353331.4_Missense_Mutation_p.H250P|BCLAF1_ENST00000392348.2_Missense_Mutation_p.H250P|BCLAF1_ENST00000530767.1_Missense_Mutation_p.H252P	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	252					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		TTTTGCAGAGTGAACTGTACT	0.438																																					p.H252P	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.A755C						.						147	140	142					6																	136599264		2203	4300	6503	SO:0001583	missense	9774	exon4			GCAGAGTGAACTG	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.755A>C	chr6.hg19:g.136599264T>G	ENSP00000435210:p.His252Pro	143.0	0.0		221.0	38.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	T	13.90	2.376065	0.42105	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T;T	0.13778	2.56;2.56;2.56;2.56;2.56;2.56;2.56	5.82	5.82	0.92795	.	0.000000	0.64402	D	0.000001	T	0.06735	0.0172	N	0.08118	0	0.44110	D	0.996885	D;D;D;D	0.64830	0.987;0.994;0.987;0.987	P;P;P;P	0.53912	0.6;0.737;0.6;0.6	T	0.28235	-1.0050	10	0.52906	T	0.07	-3.6276	10.5159	0.44889	0.0:0.0721:0.0:0.9279	.	250;250;252;252	Q9NYF8-2;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;BCLF1_HUMAN;.	P	252;250;252;252;250;250;252	ENSP00000435210:H252P;ENSP00000229446:H250P;ENSP00000435441:H252P;ENSP00000436501:H252P;ENSP00000434826:H250P;ENSP00000376159:H250P;ENSP00000431734:H252P	ENSP00000229446:H250P	H	-	2	0	BCLAF1	136640957	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.854000	0.55949	2.222000	0.72286	0.528000	0.53228	CAC	.	.		0.438	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		G	136599264	T	G	136599264	3	3	157	1	0	0	0	0	1	0	0	0	1383	1696	59	5	2047	5	BCLAF1	6	136599264	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	29606763	136599264	34515803	47	23877										
RADIL	55698	hgsc.bcm.edu	37	chr7	4839835	4839835	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aggcccatccccagcccggaGgggcctcgttccagctccac	11	19	0	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr7:4839835G>T	ENST00000399583.3	-	13	3136	c.2949C>A	c.(2947-2949)ccC>ccA	p.P983P	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Silent_p.P743P	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	983	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CCAGCCCGGAGGGGCCTCGTT	0.692																																					p.P983P		Atlas-SNP	.											.	RADIL	110	.	0			c.C2949A						.						18	22	21					7																	4839835		2006	4164	6170	SO:0001819	synonymous_variant	55698	exon13			CCCGGAGGGGCCT	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2949C>A	chr7.hg19:g.4839835G>T		42.0	0.0		107.0	31.0	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	hg19	CCDS43544.1																																																																																			.	.		0.692	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		T	4839835	G	T	4839835	2	4	157	1	0	0	0	0	0	0	0	1	13012	987	35	3		3	RADIL	7	4839835	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10		4839835	154298828	48	23878										
KRIT1	889	hgsc.bcm.edu	37	chr7	91865731	91865731	+	Frame_Shift_Del	DEL	C	C	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	taacggcatttcttacttatCcaaggctattaacatccttg							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr7:91865731delC	ENST00000340022.2	-	7	1499	c.481delG	c.(481-483)gatfs	p.D161fs	KRIT1_ENST00000394507.1_Frame_Shift_Del_p.D161fs|KRIT1_ENST00000394505.2_Frame_Shift_Del_p.D161fs|KRIT1_ENST00000394503.2_Frame_Shift_Del_p.D161fs|KRIT1_ENST00000412043.2_Frame_Shift_Del_p.D161fs	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	161	N-terminal domain similar to Nudix hydrolase domain.				angiogenesis (GO:0001525)|cell redox homeostasis (GO:0045454)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|positive regulation of protein binding (GO:0032092)|regulation of catalytic activity (GO:0050790)|regulation of establishment of cell polarity (GO:2000114)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(2)|stomach(1)	22	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TCTTACTTATCCAAGGCTATT	0.318																																					p.D161fs		Atlas-INDEL	.											.	KRIT1	66	.	0			c.482delA						.						74	75	74					7																	91865731		2202	4300	6502	SO:0001589	frameshift_variant	889	exon8			.	AJ294850	CCDS5624.1, CCDS34679.1	7q21.2	2014-09-17	2005-03-15	2005-03-17	ENSG00000001631	ENSG00000001631		"Ankyrin repeat domain containing"	1573	protein-coding gene	gene with protein product		604214	"cerebral cavernous malformations 1"	CCM1		7604043, 11342228	Standard	NM_194455		Approved	CAM	uc003ulu.1	O00522	OTTHUMG00000131187	ENST00000340022.2:c.481delG	chr7.hg19:g.91865731delC	ENSP00000344668:p.Asp161fs	39.0	0.0		136.0	54.0	NM_194456	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Frame_Shift_Del	DEL	ENST00000340022.2	hg19	CCDS5624.1																																																																																			.	.		0.318	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1			-	91865731	C	-	91865731	7	5	157	1	0	1	0	1	0	0	0	0	8454	855	30	0	1781	0	KRIT1	7	91865731	Frame_Shift_Del	DEL	C	TCGA-DD-AACF-01A-11D-A40R-10	87025896	91865731	67272932	49	23879										
MUC17	140453	hgsc.bcm.edu	37	chr7	100681743	100681743	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tatgcctgtcagcaccacaaTggtggccagttttgaaacaa	9	10	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr7:100681743T>C	ENST00000306151.4	+	3	7110	c.7046T>C	c.(7045-7047)aTg>aCg	p.M2349T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2349	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AGCACCACAATGGTGGCCAGT	0.493																																					p.M2349T		Atlas-SNP	.											.	MUC17	804	.	0			c.T7046C						.						244	239	241					7																	100681743		2203	4300	6503	SO:0001583	missense	140453	exon3			CCACAATGGTGGC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.7046T>C	chr7.hg19:g.100681743T>C	ENSP00000302716:p.Met2349Thr	68.0	0.0		123.0	74.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.864169	0.00552	.	.	ENSG00000169876	ENST00000306151	T	0.02197	4.4	0.679	-1.36	0.09085	.	.	.	.	.	T	0.00998	0.0033	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48031	-0.9070	9	0.12766	T	0.61	.	5.5977	0.17337	0.0:0.5543:0.0:0.4457	.	2349	Q685J3	MUC17_HUMAN	T	2349	ENSP00000302716:M2349T	ENSP00000302716:M2349T	M	+	2	0	MUC17	100468463	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.837000	0.04377	-1.283000	0.02393	-1.568000	0.00874	ATG	.	.		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100681743	T	C	100681743	3	2	157	1	0	0	0	0	1	0	0	0	9983	1464	51	2	7056	2	MUC17	7	100681743	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	8816012	100681743	58456920	50	23880										
LAMB1	3912	hgsc.bcm.edu	37	chr7	107577640	107577684	+	In_Frame_Del	DEL	CTGTGCTGTTGCTTTGGGAAGTTGTGTCAGATAATTTCACTTCTA	CTGTGCTGTTGCTTTGGGAAGTTGTGTCAGATAATTTCACTTCTA	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tagagaatccagttctttggCtgtgctgttgctttgggaag					rs377388989	byFrequency	TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	CTGTGCTGTTGCTTTGGGAAGTTGTGTCAGATAATTTCACTTCTA	CTGTGCTGTTGCTTTGGGAAGTTGTGTCAGATAATTTCACTTCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr7:107577640_107577684delCTGTGCTGTTGCTTTGGGAAGTTGTGTCAGATAATTTCACTTCTA	ENST00000222399.6	-	26	4030_4074	c.3800_3844delTAGAAGTGAAATTATCTGACACAACTTCCCAAAGCAACAGCACAG	c.(3799-3846)gtagaagtgaaattatctgacacaacttcccaaagcaacagcacagcc>gcc	p.VEVKLSDTTSQSNST1267del	LAMB1_ENST00000393561.1_In_Frame_Del_p.VEVKLSDTTSQSNST1291del|LAMB1_ENST00000474380.1_5'Flank	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1267	Domain II.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						AGTTCTTTGGCTGTGCTGTTGCTTTGGGAAGTTGTGTCAGATAATTTCACTTCTACTTGAGCCAT	0.376																																					p.1267_1282del		Atlas-INDEL	.											.	LAMB1	185	.	0			c.3801_3845del						.																																			SO:0001651	inframe_deletion	3912	exon26			.	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.3800_3844delTAGAAGTGAAATTATCTGACACAACTTCCCAAAGCAACAGCACAG	chr7.hg19:g.107577640_107577684delCTGTGCTGTTGCTTTGGGAAGTTGTGTCAGATAATTTCACTTCTA	ENSP00000222399:p.Val1267_Thr1281del	82.0	0.0		139.0	10.0	NM_002291	Q14D91	In_Frame_Del	DEL	ENST00000222399.6	hg19	CCDS5750.1																																																																																			.	.		0.376	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		-	107577684	CTGTGCTGTTGCTTTGGGAAGTTGTGTCAGATAATTTCACTTCTA	-	107577640	7	5	157	1	0	1	0	1	0	0	0	0	8619	797	28	0	1552	0	LAMB1	7	107577640	In_Frame_Del	DEL	CTGTGCTGTTGCTTTGGGAAGTTGTGTCAGATAATTTCACTTCTA	TCGA-DD-AACF-01A-11D-A40R-10	6895897	107577640	51561023	51	23881										
CADPS2	93664	hgsc.bcm.edu	37	chr7	122056186	122056186	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cagatgaagaatctcttccaGctttctagcaggagatgcct	9	10	2	4			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr7:122056186G>T	ENST00000449022.2	-	18	2528	c.2509C>A	c.(2509-2511)Ctg>Atg	p.L837M	CADPS2_ENST00000334010.7_Missense_Mutation_p.L838M|CADPS2_ENST00000412584.2_Missense_Mutation_p.L834M|RP5-1101C3.1_ENST00000593910.1_RNA|CADPS2_ENST00000313070.7_Missense_Mutation_p.L834M|RP5-1101C3.1_ENST00000591140.1_RNA	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	837	Interaction with DRD2.				cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						ATCTCTTCCAGCTTTCTAGCA	0.373																																					p.L844M		Atlas-SNP	.											.	CADPS2	116	.	0			c.C2530A						.						63	60	61					7																	122056186		1836	4085	5921	SO:0001583	missense	93664	exon19			CTTCCAGCTTTCT		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.2509C>A	chr7.hg19:g.122056186G>T	ENSP00000398481:p.Leu837Met	35.0	0.0		86.0	19.0	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	hg19	CCDS55158.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	22.6|22.6|22.6	4.306552|4.306552|4.306552	0.81247|0.81247|0.81247	.|.|.	.|.|.	ENSG00000081803|ENSG00000081803|ENSG00000081803	ENST00000397721|ENST00000360097;ENST00000313070;ENST00000334010;ENST00000420900;ENST00000545465;ENST00000412584;ENST00000449022|ENST00000462699	.|T;T;T;T|.	.|0.59502|.	.|0.26;0.28;0.26;0.29|.	5.86|5.86|5.86	5.86|5.86|5.86	0.93980|0.93980|0.93980	.|Calcium-dependent secretion activator (1);|.	.|0.000000|.	.|0.64402|.	.|D|.	.|0.000003|.	T|T|T	0.76955|0.76955|0.76955	0.4060|0.4060|0.4060	M|M|M	0.71206|0.71206|0.71206	2.165|2.165|2.165	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;D;D;D|.	.|0.89917|.	.|1.0;1.0;1.0;0.999|.	.|D;D;D;D|.	.|0.91635|.	.|0.999;0.991;0.999;0.997|.	T|T|T	0.74293|0.74293|0.74293	-0.3712|-0.3712|-0.3712	5|10|5	.|0.87932|.	.|D|.	.|0|.	-11.9917|-11.9917|-11.9917	20.1813|20.1813|20.1813	0.98205|0.98205|0.98205	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|844;834;837;834|.	.|B7ZM57;Q86UW7-2;Q86UW7;Q86UW7-3|.	.|.;.;CAPS2_HUMAN;.|.	D|M|R	482|10;834;838;845;801;834;837|30	.|ENSP00000325581:L834M;ENSP00000333940:L838M;ENSP00000400401:L834M;ENSP00000398481:L837M|.	.|ENSP00000325581:L834M|.	A|L|S	-|-|-	2|1|3	0|2|2	CADPS2|CADPS2|CADPS2	121843422|121843422|121843422	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.995000|0.995000|0.995000	0.86356|0.86356|0.86356	5.895000|5.895000|5.895000	0.69814|0.69814|0.69814	2.763000|2.763000|2.763000	0.94921|0.94921|0.94921	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	GCT|CTG|AGC	.	.		0.373	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		T	122056186	G	T	122056186	3	4	157	1	0	0	0	0	1	0	0	0	2573	962	34	3	1452	3	CADPS2	7	122056186	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	14478546	122056186	37082477	52	23882										
ZNF746	155061	hgsc.bcm.edu	37	chr7	149171588	149171588	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ggggctcttgaagggatcagGaggtgcgggcggcgtcggga	22	7	2	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr7:149171588G>A	ENST00000340622.3	-	7	2102	c.1822C>T	c.(1822-1824)Cct>Tct	p.P608S	ZNF746_ENST00000458143.2_Missense_Mutation_p.P609S			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	608					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			AAGGGATCAGGAGGTGCGGGC	0.672																																					p.P609S		Atlas-SNP	.											.	ZNF746	68	.	0			c.C1825T						.						32	32	32					7																	149171588		2201	4297	6498	SO:0001583	missense	155061	exon7			GATCAGGAGGTGC	AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"Zinc fingers, C2H2-type", "-"	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.1822C>T	chr7.hg19:g.149171588G>A	ENSP00000345140:p.Pro608Ser	58.0	0.0		74.0	31.0	NM_001163474	A8K6Z9|Q6ZRF9	Missense_Mutation	SNP	ENST00000340622.3	hg19	CCDS5897.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.662254	0.29515	.	.	ENSG00000181220	ENST00000340622;ENST00000458143	T;T	0.09538	3.01;2.97	5.47	5.47	0.80525	.	0.140546	0.32901	N	0.005502	T	0.18509	0.0444	N	0.24115	0.695	0.09310	N	1	D;D	0.67145	0.996;0.993	D;P	0.64144	0.922;0.838	T	0.15378	-1.0439	10	0.27785	T	0.31	-15.9004	16.8082	0.85711	0.0:0.0:1.0:0.0	.	609;608	Q6NUN9-2;Q6NUN9	.;ZN746_HUMAN	S	608;609	ENSP00000345140:P608S;ENSP00000395007:P609S	ENSP00000345140:P608S	P	-	1	0	ZNF746	148802521	0.997000	0.39634	0.220000	0.23810	0.002000	0.02628	3.735000	0.55044	2.570000	0.86706	0.462000	0.41574	CCT	.	.		0.672	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557		A	149171588	G	A	149171588	3	1	157	1	0	0	0	0	1	0	0	0	18144	1174	41	3	116	3	ZNF746	7	149171588	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	27115402	149171588	9967075	53	23883										
ATP6V1H	51606	hgsc.bcm.edu	37	chr8	54669202	54669202	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gatcatctgacacttccaaaAgttttgtcaagattctgaaa	6	8	4	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr8:54669202A>C	ENST00000359530.2	-	12	1453	c.1190T>G	c.(1189-1191)cTt>cGt	p.L397R	ATP6V1H_ENST00000355221.3_Missense_Mutation_p.L379R|ATP6V1H_ENST00000520188.1_Missense_Mutation_p.L357R|ATP6V1H_ENST00000396774.2_Missense_Mutation_p.L397R|ATP6V1H_ENST00000523899.1_Intron	NM_015941.3	NP_057025.2	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H	397					ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|endocytosis (GO:0006897)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|regulation of catalytic activity (GO:0050790)|regulation of defense response to virus by virus (GO:0050690)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V1 domain (GO:0000221)	enzyme regulator activity (GO:0030234)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	18		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)			CACTTCCAAAAGTTTTGTCAA	0.388																																					p.L397R		Atlas-SNP	.											.	ATP6V1H	66	.	0			c.T1190G						.						80	74	76					8																	54669202		2203	4300	6503	SO:0001583	missense	51606	exon12			TCCAAAAGTTTTG	AF132945	CCDS6153.1, CCDS6154.1	8q11.2	2011-05-24	2002-08-29		ENSG00000047249	ENSG00000047249		"ATPases / V-type"	18303	protein-coding gene	gene with protein product	"vacuolar ATP synthase subunit H"	608861	"ATPase, H+ transporting, lysosomal 50/57kD, V1 subunit H"			9620685, 10810093	Standard	NM_015941		Approved	CGI-11, SFD, VMA13, SFDalpha, SFDbeta	uc003xrm.4	Q9UI12	OTTHUMG00000164231	ENST00000359530.2:c.1190T>G	chr8.hg19:g.54669202A>C	ENSP00000352522:p.Leu397Arg	78.0	0.0		91.0	44.0	NM_015941	B3KMR0|Q6PK44|Q9H3E3|Q9Y300	Missense_Mutation	SNP	ENST00000359530.2	hg19	CCDS6153.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.398468	0.83120	.	.	ENSG00000047249	ENST00000355221;ENST00000520188;ENST00000359530;ENST00000396774	.	.	.	5.63	5.63	0.86233	ATPase, V1 complex, subunit H, C-terminal (2);Armadillo-type fold (1);	0.054698	0.85682	D	0.000000	D	0.84534	0.5493	M	0.90082	3.085	0.80722	D	1	D;D	0.60160	0.957;0.987	D;D	0.74023	0.952;0.982	D	0.87847	0.2655	9	0.87932	D	0	-19.0047	14.8248	0.70104	1.0:0.0:0.0:0.0	.	379;397	Q9UI12-2;Q9UI12	.;VATH_HUMAN	R	379;357;397;397	.	ENSP00000347359:L379R	L	-	2	0	ATP6V1H	54831755	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.526000	0.90588	2.142000	0.66516	0.528000	0.53228	CTT	.	.		0.388	ATP6V1H-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377865.1	NM_015941		C	54669202	A	C	54669202	3	2	157	1	0	0	0	0	1	0	0	0	1189	72	3	5	273	5	ATP6V1H	8	54669202	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10		54669202	91694820	54	23884										
NKAIN3	286183	hgsc.bcm.edu	37	chr8	63161677	63161677	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tcgctcatctgcctctgcgcGctgcagttggtgagtgcccc	12	15	3	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr8:63161677G>T	ENST00000523211.1	+	1	177	c.45G>T	c.(43-45)gcG>gcT	p.A15A	NKAIN3_ENST00000328472.5_Silent_p.A15A|NKAIN3_ENST00000519049.1_3'UTR	NM_173688.2	NP_775959.1	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3	15						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(3)|large_intestine(2)|lung(8)	13	Breast(64;0.127)	Lung NSC(129;0.187)				GCCTCTGCGCGCTGCAGTTGG	0.716																																					p.A15A		Atlas-SNP	.											.	NKAIN3	32	.	0			c.G45T						.						5	8	7					8																	63161677		1822	3534	5356	SO:0001819	synonymous_variant	286183	exon1			CTGCGCGCTGCAG	AK096949	CCDS55239.1	8q12.3	2014-08-12	2007-10-04	2007-10-04	ENSG00000185942	ENSG00000185942		"Na+/K+ transporting ATPase interacting"	26829	protein-coding gene	gene with protein product		612872	"family with sequence similarity 77, member D"	FAM77D		17606467	Standard	NM_173688		Approved	FLJ39630	uc010lyq.1	Q8N8D7	OTTHUMG00000164361	ENST00000523211.1:c.45G>T	chr8.hg19:g.63161677G>T		81.0	0.0		81.0	35.0	NM_173688		Silent	SNP	ENST00000523211.1	hg19	CCDS55239.1																																																																																			.	.		0.716	NKAIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378447.2	NM_173688		T	63161677	G	T	63161677	2	4	157	1	0	0	0	0	0	0	0	1	10446	1074	38	1		1	NKAIN3	8	63161677	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	8492475	63161677	83202345	55	23885										
INTS8	55656	hgsc.bcm.edu	37	chr8	95879510	95879510	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ttttctttttaaaggaggacAttgtgaatgatattacagct	8	4	1	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr8:95879510A>G	ENST00000523731.1	+	20	2492	c.2359A>G	c.(2359-2361)Att>Gtt	p.I787V	INTS8_ENST00000447247.1_Missense_Mutation_p.I787V|INTS8_ENST00000520845.1_3'UTR	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	787					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					AAAGGAGGACATTGTGAATGA	0.274																																					p.I787V		Atlas-SNP	.											.	INTS8	92	.	0			c.A2359G						.						110	112	111					8																	95879510		2203	4291	6494	SO:0001583	missense	55656	exon20			GAGGACATTGTGA	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2359A>G	chr8.hg19:g.95879510A>G	ENSP00000430338:p.Ile787Val	283.0	0.0		624.0	401.0	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Missense_Mutation	SNP	ENST00000523731.1	hg19	CCDS34925.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.167676	0.38315	.	.	ENSG00000164941	ENST00000523731;ENST00000447247	T;T	0.32272	1.46;1.46	5.28	3.99	0.46301	.	0.046974	0.85682	D	0.000000	T	0.27798	0.0684	L	0.60455	1.87	0.52501	D	0.999952	B	0.11235	0.004	B	0.15870	0.014	T	0.07233	-1.0783	10	0.12430	T	0.62	-17.3747	12.4795	0.55833	0.8663:0.0:0.0:0.1337	.	787	Q75QN2	INT8_HUMAN	V	787	ENSP00000430338:I787V;ENSP00000398203:I787V	ENSP00000398203:I787V	I	+	1	0	INTS8	95948686	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.819000	0.75262	1.983000	0.57843	0.455000	0.32223	ATT	.	.		0.274	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		G	95879510	A	G	95879510	3	3	157	1	0	0	0	0	1	0	0	0	7793	217	8	2	2437	2	INTS8	8	95879510	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	32717833	95879510	50484512	56	23886										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100128060	100128060	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ttaaagaaggcgaaatagagGaccttacttgtcataataaa	8	5	1	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr8:100128060G>T	ENST00000358544.2	+	7	1006	c.895G>T	c.(895-897)Gac>Tac	p.D299Y	VPS13B_ENST00000355155.1_Missense_Mutation_p.D299Y|VPS13B_ENST00000357162.2_Missense_Mutation_p.D299Y|VPS13B_ENST00000395996.1_Missense_Mutation_p.D299Y|VPS13B_ENST00000441350.2_Missense_Mutation_p.D299Y	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	299					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CGAAATAGAGGACCTTACTTG	0.299																																					p.D299Y	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.G895T						.						76	78	77					8																	100128060		2203	4296	6499	SO:0001583	missense	157680	exon7			ATAGAGGACCTTA	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.895G>T	chr8.hg19:g.100128060G>T	ENSP00000351346:p.Asp299Tyr	242.0	0.0		570.0	170.0	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.840611	0.51057	.	.	ENSG00000132549	ENST00000355155;ENST00000357162;ENST00000358544;ENST00000395996;ENST00000441350	T;T;T;T;D	0.83673	-1.16;-0.45;-0.45;-0.16;-1.75	5.65	4.78	0.61160	.	0.279655	0.33477	N	0.004876	D	0.83839	0.5341	L	0.46157	1.445	0.52501	D	0.999956	P;P;P;P;P	0.51537	0.946;0.828;0.892;0.786;0.739	P;B;P;P;P	0.55161	0.77;0.44;0.542;0.542;0.501	T	0.82847	-0.0255	10	0.41790	T	0.15	.	10.6553	0.45671	0.1457:0.0:0.8543:0.0	.	299;299;299;299;299	Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3;Q7Z7G8-4;Q7Z7G8-5	.;VP13B_HUMAN;.;.;.	Y	299	ENSP00000347281:D299Y;ENSP00000349685:D299Y;ENSP00000351346:D299Y;ENSP00000379318:D299Y;ENSP00000398472:D299Y	ENSP00000347281:D299Y	D	+	1	0	VPS13B	100197236	1.000000	0.71417	0.320000	0.25306	0.568000	0.35870	5.881000	0.69706	1.396000	0.46663	0.655000	0.94253	GAC	.	.		0.299	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100128060	G	T	100128060	3	4	157	1	0	0	0	0	1	0	0	0	17205	1174	41	3	917	3	VPS13B	8	100128060	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	4248550	100128060	46235962	57	23887										
C8orf33	65265	hgsc.bcm.edu	37	chr8	146278796	146278796	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	atagggctcagatggaagccGaatggcgtgaggccctgcgg	17	9	1	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr8:146278796G>A	ENST00000331434.6	+	4	631	c.517G>A	c.(517-519)Gaa>Aaa	p.E173K		NM_023080.2	NP_075568.1	Q9H7E9	CH033_HUMAN	chromosome 8 open reading frame 33	173										endometrium(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;9.1e-38)|all cancers(56;7.37e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.243)		GATGGAAGCCGAATGGCGTGA	0.567																																					p.E173K		Atlas-SNP	.											.	C8orf33	25	.	0			c.G517A						.						50	56	54					8																	146278796		2203	4300	6503	SO:0001583	missense	65265	exon4			GAAGCCGAATGGC		CCDS34974.1	8q24.3	2012-04-11			ENSG00000182307	ENSG00000182307			26104	protein-coding gene	gene with protein product							Standard	NM_023080		Approved	FLJ20989	uc003zfc.4	Q9H7E9	OTTHUMG00000165256	ENST00000331434.6:c.517G>A	chr8.hg19:g.146278796G>A	ENSP00000330361:p.Glu173Lys	63.0	0.0		107.0	15.0	NM_023080	A6NGC0|Q96BT8	Missense_Mutation	SNP	ENST00000331434.6	hg19	CCDS34974.1	.	.	.	.	.	.	.	.	.	.	.	18.13	3.555884	0.65425	.	.	ENSG00000182307	ENST00000331434	.	.	.	3.75	2.83	0.33086	.	0.126216	0.50627	D	0.000104	T	0.63498	0.2516	M	0.78456	2.415	0.22171	N	0.999316	D	0.89917	1.0	D	0.67103	0.949	T	0.54125	-0.8340	8	.	.	.	-16.0644	9.0264	0.36232	0.0:0.227:0.773:0.0	.	173	Q9H7E9	CH033_HUMAN	K	173	.	.	E	+	1	0	C8orf33	146249600	0.001000	0.12720	0.007000	0.13788	0.036000	0.12997	0.222000	0.17699	0.852000	0.35287	0.460000	0.39030	GAA	.	.		0.567	C8orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382995.1	NM_023080		A	146278796	G	A	146278796	3	1	157	1	0	0	0	0	1	0	0	0	2423	1059	37	1	531	1	C8orf33	8	146278796	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	46150736	146278796	85226	58	23888										
IFNA14	3448	hgsc.bcm.edu	37	chr9	21239511	21239512	+	Missense_Mutation	DNP	CC	CC	AG													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ttggaagtatttcttcacagCcaggatggagtcctcattca							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr9:21239511_21239512CC>AG	ENST00000380222.2	-	1	466_467	c.423_424GG>CT	c.(421-426)ctGGct>ctCTct	p.A142S		NM_002172.2	NP_002163.2	P01570	IFN14_HUMAN	interferon, alpha 14	142					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)	11				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		TTCTTCACAGCCAGGATGGAGT	0.46																																					p.A142S|p.L141L		Atlas-SNP	.											.	IFNA14	29	.	0			c.G424T|c.G423C						.																																			SO:0001583	missense	3448	exon1			TCACAGCCAGGAT|CACAGCCAGGATG		CCDS6501.1	9p22	2010-08-24			ENSG00000228083	ENSG00000228083		"Interferons"	5420	protein-coding gene	gene with protein product		147579				1385305	Standard	NM_002172		Approved	LEIF2H, IFN-alphaH	uc010mis.3	P01570	OTTHUMG00000019665	ENST00000380222.2:c.423_424delinsAG	chr9.hg19:g.21239511_21239512delinsAG	ENSP00000369571:p.Ala142Ser	129.0|130.0	0.0		162.0	19.0|18.0	NM_002172	Q5VZ56|Q7M4S1	Missense_Mutation|Silent	SNP	ENST00000380222.2	hg19	CCDS6501.1																																																																																			.	.		0.46	IFNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051894.1	NM_002172		AG	21239512	CC	AG	21239511	3	1	157	1	0	0	0	0	1	0	0	0	7543	739	26	3	149	3	IFNA14	9	21239511	Missense_Mutation	DNP	CC	TCGA-DD-AACF-01A-11D-A40R-10		21239511	119973920	59	23889										
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84606650	84606650	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ggagagacaagtcaaaaaaaGgggtgatttcctgatgtgga	14	4	1	3	rs368407426		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr9:84606650G>T	ENST00000344803.2	+	4	1312	c.1265G>T	c.(1264-1266)aGg>aTg	p.R422M		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	422					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GTCAAAAAAAGGGGTGATTTC	0.428																																					p.R422M		Atlas-SNP	.											.	.	.	.	0			c.G1265T						.	G	MET/ARG	1,3679		0,1,1839	79	69	72		1265	-0.9	0	9		72	0,8186		0,0,4093	no	missense	FAM75D1	NM_001001670.2	91	0,1,5932	TT,TG,GG		0.0,0.0272,0.0084	probably-damaging	422/1577	84606650	1,11865	1840	4093	5933	SO:0001583	missense	389763	exon4			AAAAAAGGGGTGA		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.1265G>T	chr9.hg19:g.84606650G>T	ENSP00000341988:p.Arg422Met	155.0	0.0		262.0	110.0	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	hg19	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.031487	0.35797	2.72E-4	0.0	ENSG00000214929	ENST00000344803	T	0.06528	3.29	3.41	-0.908	0.10517	.	1.226850	0.05724	N	0.598296	T	0.22399	0.0540	M	0.78637	2.42	0.09310	N	1	D	0.89917	1.0	D	0.78314	0.991	T	0.16748	-1.0392	10	0.72032	D	0.01	-4.4445	6.2473	0.20825	0.571:0.0:0.429:0.0	.	422	Q6ZQQ2	F75D1_HUMAN	M	422	ENSP00000341988:R422M	ENSP00000341988:R422M	R	+	2	0	FAM75D1	83796470	0.005000	0.15991	0.002000	0.10522	0.029000	0.11900	-0.121000	0.10643	-0.046000	0.13446	0.650000	0.86243	AGG	.	.		0.428	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84606650	G	T	84606650	3	4	157	1	0	0	0	0	1	0	0	0	5940	1000	35	3	1279	3	FLJ46321	9	84606650	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	63367139	84606650	56606781	60	23890										
OR1N1	138883	hgsc.bcm.edu	37	chr9	125288746	125288746	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	acatgggagtcactatggtgTacattgcagctgctgcaatg	12	8	1	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr9:125288746T>G	ENST00000304880.2	-	1	826	c.827A>C	c.(826-828)tAc>tCc	p.Y276S		NM_012363.1	NP_036495.1	Q8NGS0	OR1N1_HUMAN	olfactory receptor, family 1, subfamily N, member 1	276						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|large_intestine(2)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						CACTATGGTGTACATTGCAGC	0.493																																					p.Y276S		Atlas-SNP	.											.	OR1N1	38	.	0			c.A827C						.						107	99	102					9																	125288746		2203	4300	6503	SO:0001583	missense	138883	exon1			ATGGTGTACATTG	U86216	CCDS6844.1	9q34.11	2012-08-09			ENSG00000171505	ENSG00000171505		"GPCR / Class A : Olfactory receptors"	8221	protein-coding gene	gene with protein product				OR1N3		9500546	Standard	NM_012363		Approved	OR1-26	uc004bmn.1	Q8NGS0	OTTHUMG00000020608	ENST00000304880.2:c.827A>C	chr9.hg19:g.125288746T>G	ENSP00000306974:p.Tyr276Ser	73.0	0.0		108.0	47.0	NM_012363	A3KFM1|O43870|Q6IF16|Q96R93	Missense_Mutation	SNP	ENST00000304880.2	hg19	CCDS6844.1	.	.	.	.	.	.	.	.	.	.	T	18.63	3.666235	0.67814	.	.	ENSG00000171505	ENST00000304880	T	0.00311	8.15	3.62	2.43	0.29744	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31566	U	0.007432	T	0.00666	0.0022	M	0.89353	3.025	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.27297	-1.0078	10	0.87932	D	0	.	8.2457	0.31686	0.0:0.103:0.0:0.897	.	276	Q8NGS0	OR1N1_HUMAN	S	276	ENSP00000306974:Y276S	ENSP00000306974:Y276S	Y	-	2	0	OR1N1	124328567	0.997000	0.39634	0.016000	0.15963	0.914000	0.54420	3.376000	0.52417	1.559000	0.49555	0.367000	0.22151	TAC	.	.		0.493	OR1N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053938.1			G	125288746	T	G	125288746	3	3	157	1	0	0	0	0	1	0	0	0	10978	1638	57	5	112	5	OR1N1	9	125288746	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	40682096	125288746	15924685	61	23891										
AK1	203	hgsc.bcm.edu	37	chr9	130630625	130630625	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gcacaatgccacgtttctcaTagaaggcgatgacaggttct	10	10	2	2	rs137853203		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr9:130630625T>C	ENST00000373176.1	-	6	643	c.491A>G	c.(490-492)tAt>tGt	p.Y164C	AK1_ENST00000373156.1_Missense_Mutation_p.Y164C|RP11-203J24.9_ENST00000476274.2_RNA|MIR4672_ENST00000583126.1_RNA|AK1_ENST00000223836.10_Missense_Mutation_p.Y180C	NM_000476.2	NP_000467.1			adenylate kinase 1											endometrium(1)|prostate(1)	2						ACGTTTCTCATAGAAGGCGAT	0.597																																					p.Y164C		Atlas-SNP	.											.	AK1	13	.	0			c.A491G	GRCh37	CM970075	AK1	M	rs137853203	.						77	57	64					9																	130630625		2203	4299	6502	SO:0001583	missense	203	exon6			TTCTCATAGAAGG	J04809	CCDS6881.1	9q34.1	2008-02-05			ENSG00000106992	ENSG00000106992	2.7.4.3	"Adenylate kinases"	361	protein-coding gene	gene with protein product		103000					Standard	NM_000476		Approved		uc004bsm.4	P00568	OTTHUMG00000020722	ENST00000373176.1:c.491A>G	chr9.hg19:g.130630625T>C	ENSP00000362271:p.Tyr164Cys	31.0	0.0		41.0	24.0	NM_000476		Missense_Mutation	SNP	ENST00000373176.1	hg19	CCDS6881.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.6|20.6	4.011936|4.011936	0.75046|0.75046	.|.	.|.	ENSG00000106992|ENSG00000106992	ENST00000413016|ENST00000373176;ENST00000373156;ENST00000223836	.|D;D;D	.|0.85171	.|-1.95;-1.95;-1.95	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.95589|0.95589	0.8566|0.8566	H|H	0.98980|0.98980	4.39|4.39	0.80722|0.80722	A|A	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.97247|0.97247	0.9895|0.9895	4|9	.|0.87932	.|D	.|0	-34.4225|-34.4225	14.1613|14.1613	0.65448|0.65448	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|164	.|P00568	.|KAD1_HUMAN	V|C	105|164;164;180	.|ENSP00000362271:Y164C;ENSP00000362249:Y164C;ENSP00000223836:Y180C	.|ENSP00000223836:Y180C	M|Y	-|-	1|2	0|0	AK1|AK1	129670446|129670446	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.722000|0.722000	0.41435|0.41435	7.622000|7.622000	0.83099|0.83099	2.029000|2.029000	0.59856|0.59856	0.459000|0.459000	0.35465|0.35465	ATG|TAT	.	.		0.597	AK1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054307.1			C	130630625	T	C	130630625	3	2	157	1	0	0	0	0	1	0	0	0	439	1406	49	2	101	2	AK1	9	130630625	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	5341879	130630625	10582806	62	23892										
AIF1L	83543	hgsc.bcm.edu	37	chr9	133993147	133993147	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gcttttcccccggcagacctGatgtctttaaagaggatgat	10	10	1	4			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr9:133993147G>T	ENST00000247291.3	+	5	295	c.207G>T	c.(205-207)ctG>ctT	p.L69L	AIF1L_ENST00000372301.2_Silent_p.L13L|AIF1L_ENST00000372297.2_Silent_p.L13L|AIF1L_ENST00000372309.3_Silent_p.L95L|AIF1L_ENST00000372300.1_Silent_p.L69L|AIF1L_ENST00000372312.3_Silent_p.L74L|AIF1L_ENST00000372302.1_Silent_p.L61L|AIF1L_ENST00000372298.1_Silent_p.L69L	NM_031426.3	NP_113614.1	Q9BQI0	AIF1L_HUMAN	allograft inflammatory factor 1-like	69	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			lung(2)	2						CGGCAGACCTGATGTCTTTAA	0.542																																					p.L95L	Esophageal Squamous(95;611 1423 5044 34794 42333)	Atlas-SNP	.											.	AIF1L	15	.	0			c.G285T						.						75	72	73					9																	133993147		2203	4300	6503	SO:0001819	synonymous_variant	83543	exon6			AGACCTGATGTCT	AL136566	CCDS6939.1, CCDS55348.1, CCDS55349.1	9q34.13-q34.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000126878	ENSG00000126878		"EF-hand domain containing"	28904	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 58"	C9orf58		11230166	Standard	NM_001185095		Approved	IBA2, FLJ12783	uc004cad.2	Q9BQI0	OTTHUMG00000020817	ENST00000247291.3:c.207G>T	chr9.hg19:g.133993147G>T		86.0	0.0		81.0	36.0	NM_001185095	B2RBC4|Q6ZR40|Q8NAX7|Q8WU47|Q9H9G0	Silent	SNP	ENST00000247291.3	hg19	CCDS6939.1																																																																																			.	.		0.542	AIF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054703.2	NM_031426		T	133993147	G	T	133993147	2	4	157	1	0	0	0	0	0	0	0	1	425	1277	45	3		3	AIF1L	9	133993147	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	3362522	133993147	7220284	63	23893										
NUP214	8021	hgsc.bcm.edu	37	chr9	134073951	134073951	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	agtctgtttgggcagcagacTggtagcacagccagcacagc	13	11	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr9:134073951T>G	ENST00000359428.5	+	29	5214	c.5070T>G	c.(5068-5070)acT>acG	p.T1690T	NUP214_ENST00000451030.1_Silent_p.T1691T|NUP214_ENST00000483497.2_Silent_p.T516T|NUP214_ENST00000411637.2_Silent_p.T1680T			P35658	NU214_HUMAN	nucleoporin 214kDa	1690	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		GGCAGCAGACTGGTAGCACAG	0.607			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.T1690T	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.T5070G						.						48	50	49					9																	134073951		2203	4300	6503	SO:0001819	synonymous_variant	8021	exon29			GCAGACTGGTAGC	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.5070T>G	chr9.hg19:g.134073951T>G		162.0	0.0		236.0	120.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	ENST00000359428.5	hg19	CCDS6940.1																																																																																			.	.		0.607	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		G	134073951	T	G	134073951	2	3	157	1	0	0	0	0	0	0	0	1	10771	1567	55	5		5	NUP214	9	134073951	Silent	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	80804	134073951	7139480	64	23894										
UBAC1	10422	hgsc.bcm.edu	37	chr9	138825357	138825357	+	Frame_Shift_Del	DEL	A	A	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gggttctccagcatgtcttcAaatgctgcagggaaaacaga							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr9:138825357delA	ENST00000371756.3	-	10	1324	c.1107delT	c.(1105-1107)tttfs	p.F369fs		NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	369	STI1.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		GCATGTCTTCAAATGCTGCAG	0.542																																					p.E370fs	NSCLC(78;973 1398 27381 29552 42415)	Atlas-INDEL	.											.	UBAC1	40	.	0			c.1108delG						.						98	90	93					9																	138825357		2203	4300	6503	SO:0001589	frameshift_variant	10422	exon10			.	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"ubiquitin associated domain containing 1"	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.1107delT	chr9.hg19:g.138825357delA	ENSP00000360821:p.Phe369fs	54.0	0.0		97.0	45.0	NM_016172	O75500|Q9UMW7	Frame_Shift_Del	DEL	ENST00000371756.3	hg19	CCDS35177.1																																																																																			.	.		0.542	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172		-	138825357	A	-	138825357	7	5	157	1	0	1	0	1	0	0	0	0	16849	127	5	0	114	0	UBAC1	9	138825357	Frame_Shift_Del	DEL	A	TCGA-DD-AACF-01A-11D-A40R-10	4751406	138825357	2388074	65	23895										
KIAA0913	23053	hgsc.bcm.edu	37	chr10	75548868	75548868	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ccccaggctgtattcgtgccTggccaatggcagtgcggatg	14	12	0	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr10:75548868T>C	ENST00000605216.1	+	3	594	c.377T>C	c.(376-378)cTg>cCg	p.L126P	ZSWIM8_ENST00000603114.1_Missense_Mutation_p.L126P|ZSWIM8_ENST00000604729.1_Missense_Mutation_p.L126P|ZSWIM8_ENST00000604524.1_Missense_Mutation_p.L126P|ZSWIM8_ENST00000398706.2_Missense_Mutation_p.L126P	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	126							zinc ion binding (GO:0008270)										TATTCGTGCCTGGCCAATGGC	0.562																																					p.L126P		Atlas-SNP	.											.	.	.	.	0			c.T377C						.						99	100	100					10																	75548868		2090	4208	6298	SO:0001583	missense	23053	exon3			CGTGCCTGGCCAA	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"Zinc fingers, SWIM-type"	23528	protein-coding gene	gene with protein product			"KIAA0913"	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.377T>C	chr10.hg19:g.75548868T>C	ENSP00000474748:p.Leu126Pro	63.0	0.0		105.0	42.0	NM_001242488	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Missense_Mutation	SNP	ENST00000605216.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.99|19.99	3.928246|3.928246	0.73327|0.73327	.|.	.|.	ENSG00000214655|ENSG00000214655	ENST00000398706|ENST00000446546	T|.	0.60797|.	0.16|.	5.76|5.76	4.64|4.64	0.57946|0.57946	.|.	.|.	.|.	.|.	.|.	T|T	0.73961|0.73961	0.3654|0.3654	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	D;D;D|.	0.71674|.	0.998;0.998;0.998|.	D;D;D|.	0.69142|.	0.943;0.962;0.943|.	T|T	0.75852|0.75852	-0.3171|-0.3171	9|5	0.87932|.	D|.	0|.	.|.	11.2073|11.2073	0.48778|0.48778	0.0:0.0712:0.0:0.9287|0.0:0.0712:0.0:0.9287	.|.	126;126;126|.	A7E2V4;A7E2V4-5;A7E2V4-4|.	K0913_HUMAN;.;.|.	P|R	126|211	ENSP00000381693:L126P|.	ENSP00000381693:L126P|.	L|W	+|+	2|1	0|0	KIAA0913|KIAA0913	75218874|75218874	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.972000|7.972000	0.88022|0.88022	2.202000|2.202000	0.70862|0.70862	0.533000|0.533000	0.62120|0.62120	CTG|TGG	.	.		0.562	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		C	75548868	T	C	75548868	3	2	157	1	0	0	0	0	1	0	0	0	8209	1580	55	2	387	2	KIAA0913	10	75548868	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10		75548868	59985879	66	23896										
IFIT3	3437	hgsc.bcm.edu	37	chr10	91098522	91098542	+	In_Frame_Del	DEL	GAGTGTGTAACCAGATTGAAT	GAGTGTGTAACCAGATTGAAT	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ctcaagggatctagaagataGagtgtgtaaccagattgaat							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	GAGTGTGTAACCAGATTGAAT	GAGTGTGTAACCAGATTGAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr10:91098522_91098542delGAGTGTGTAACCAGATTGAAT	ENST00000371818.4	+	2	290_310	c.110_130delGAGTGTGTAACCAGATTGAAT	c.(109-132)agagtgtgtaaccagattgaattt>att	p.37_44RVCNQIEF>I	IFIT3_ENST00000371811.4_In_Frame_Del_p.37_44RVCNQIEF>I|LIPA_ENST00000371837.1_Intron|LIPA_ENST00000487618.1_Intron	NM_001549.4	NP_001540.2	O14879	IFIT3_HUMAN	interferon-induced protein with tetratricopeptide repeats 3	37				F -> S (in Ref. 5; AAH04977). {ECO:0000305}.	cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)|urinary_tract(1)	15						CTAGAAGATAGAGTGTGTAACCAGATTGAATTTTTAAACAC	0.425																																					p.37_43del		Atlas-INDEL	.											.	IFIT3	36	.	0			c.109_129del						.																																			SO:0001651	inframe_deletion	3437	exon2			.	U52513	CCDS7402.1, CCDS31241.1	10q23.31	2014-05-22	2004-07-16	2004-07-16	ENSG00000119917	ENSG00000119917		"Tetratricopeptide (TTC) repeat domain containing"	5411	protein-coding gene	gene with protein product		604650	"interferon-induced protein with tetratricopeptide repeats 4"	IFIT4		9828129, 9391139	Standard	NM_001031683		Approved	ISG60, RIG-G, CIG-49, IFI60, GARG-49, IRG2	uc001kgg.3	O14879	OTTHUMG00000018708	ENST00000371818.4:c.110_130delGAGTGTGTAACCAGATTGAAT	chr10.hg19:g.91098522_91098542delGAGTGTGTAACCAGATTGAAT	ENSP00000360883:p.Arg37_Phe44delinsIle	140.0	0.0		176.0	29.0	NM_001549	Q99634|Q9BSK7	In_Frame_Del	DEL	ENST00000371818.4	hg19	CCDS7402.1																																																																																			.	.		0.425	IFIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049294.1	NM_001549		-	91098542	GAGTGTGTAACCAGATTGAAT	-	91098522	7	5	157	1	0	1	0	1	0	0	0	0	7533	942	33	0	125	0	IFIT3	10	91098522	In_Frame_Del	DEL	GAGTGTGTAACCAGATTGAAT	TCGA-DD-AACF-01A-11D-A40R-10	15549654	91098522	44436225	67	23897										
RRM1	6240	hgsc.bcm.edu	37	chr11	4148360	4148360	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	agatacccttttgagagtgcAgaagcccagttactgaataa	9	8	0	4			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr11:4148360A>G	ENST00000300738.5	+	14	1770	c.1566A>G	c.(1564-1566)gcA>gcG	p.A522A	RRM1_ENST00000423050.2_Silent_p.A425A|RRM1_ENST00000537197.1_Silent_p.A184A|RRM1_ENST00000534285.1_Silent_p.A300A	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	522					cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	TTGAGAGTGCAGAAGCCCAGT	0.468																																					p.A522A	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.A1566G						.						117	120	119					11																	4148360		2201	4298	6499	SO:0001819	synonymous_variant	6240	exon14			GAGTGCAGAAGCC	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"ribonucleotide reductase M1 polypeptide"			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.1566A>G	chr11.hg19:g.4148360A>G		103.0	0.0		124.0	56.0	NM_001033	Q9UNN2	Silent	SNP	ENST00000300738.5	hg19	CCDS7750.1																																																																																			.	.		0.468	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		G	4148360	A	G	4148360	2	3	157	1	0	0	0	0	0	0	0	1	13696	175	7	2		2	RRM1	11	4148360	Silent	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10		4148360	130858156	68	23898										
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579631	55579631	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	caccatcctgaagatgggctCtgcagagggcaggcacaaag	13	11	1	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr11:55579631C>T	ENST00000333973.2	+	1	778	c.689C>T	c.(688-690)tCt>tTt	p.S230F		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S230F(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				AAGATGGGCTCTGCAGAGGGC	0.512																																					p.S230F		Atlas-SNP	.											OR5L1,trunk,malignant_melanoma,0,1	OR5L1	145	.	1	Substitution - Missense(1)	skin(1)	c.C689T						.						188	154	166					11																	55579631		2200	4296	6496	SO:0001583	missense	219437	exon1			TGGGCTCTGCAGA	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.689C>T	chr11.hg19:g.55579631C>T	ENSP00000335529:p.Ser230Phe	74.0	0.0		70.0	29.0	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	hg19	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	c	22.6	4.310525	0.81358	.	.	ENSG00000186117	ENST00000333973	T	0.00340	8.04	4.12	4.12	0.48240	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000080	T	0.01254	0.0041	H	0.95004	3.61	0.28435	N	0.91709	D	0.89917	1.0	D	0.97110	1.0	T	0.04178	-1.0971	10	0.87932	D	0	-34.6134	15.121	0.72443	0.0:1.0:0.0:0.0	.	230	Q8NGL2	OR5L1_HUMAN	F	230	ENSP00000335529:S230F	ENSP00000335529:S230F	S	+	2	0	OR5L1	55336207	0.514000	0.26202	0.028000	0.17463	0.902000	0.53008	3.162000	0.50755	1.875000	0.54330	0.428000	0.28381	TCT	.	.		0.512	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		T	55579631	C	T	55579631	3	4	157	1	0	0	0	0	1	0	0	0	11179	913	32	3	691	3	OR5L1	11	55579631	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	51431271	55579631	79426885	69	23899										
DAK	26007	hgsc.bcm.edu	37	chr11	61111672	61111672	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	agcactctcctgggcctggaGgaacacctgaatgccctgga	12	13	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr11:61111672G>T	ENST00000394900.3	+	13	1396	c.1167G>T	c.(1165-1167)gaG>gaT	p.E389D		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	389	DhaL. {ECO:0000255|PROSITE- ProRule:PRU00813}.				carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)			NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						TGGGCCTGGAGGAACACCTGA	0.642																																					p.E389D		Atlas-SNP	.											.	DAK	52	.	0			c.G1167T						.						67	63	64					11																	61111672		2203	4299	6502	SO:0001583	missense	26007	exon13			CCTGGAGGAACAC		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"dihydroxyacetone kinase 2 homolog (yeast)"				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.1167G>T	chr11.hg19:g.61111672G>T	ENSP00000378360:p.Glu389Asp	103.0	0.0		152.0	72.0	NM_015533	Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Missense_Mutation	SNP	ENST00000394900.3	hg19	CCDS8003.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.776826	0.70107	.	.	ENSG00000149476	ENST00000394900;ENST00000529479	T;T	0.37915	1.17;1.18	6.08	4.2	0.49525	Dak phosphatase (2);	0.270973	0.41938	D	0.000786	T	0.56499	0.1989	M	0.87269	2.87	0.41751	D	0.989667	P;P	0.52061	0.9;0.95	P;P	0.55161	0.521;0.77	T	0.65726	-0.6098	10	0.87932	D	0	-37.4166	11.3685	0.49686	0.144:0.0:0.856:0.0	.	389;389	Q2L9C1;Q3LXA3	.;DHAK_HUMAN	D	389;388	ENSP00000378360:E389D;ENSP00000432539:E388D	ENSP00000378360:E389D	E	+	3	2	DAK	60868248	1.000000	0.71417	0.998000	0.56505	0.369000	0.29798	4.793000	0.62474	1.586000	0.49944	0.655000	0.94253	GAG	.	.		0.642	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533		T	61111672	G	T	61111672	3	4	157	1	0	0	0	0	1	0	0	0	4230	991	35	3	1213	3	DAK	11	61111672	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	5532041	61111672	73894844	70	23900										
HNRNPUL2	221092	hgsc.bcm.edu	37	chr11	62484565	62484581	+	Frame_Shift_Del	DEL	TTGTACTTAGTGACAAT	TTGTACTTAGTGACAAT	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gaagcttccttgcctcctccTtgtacttagtgacaatgggc					rs199647392		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	TTGTACTTAGTGACAAT	TTGTACTTAGTGACAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr11:62484565_62484581delTTGTACTTAGTGACAAT	ENST00000301785.5	-	11	2053_2069	c.1861_1877delATTGTCACTAAGTACAA	c.(1861-1878)attgtcactaagtacaagfs	p.IVTKYK621fs	HNRNPUL2-BSCL2_ENST00000403734.2_Frame_Shift_Del_p.IVTKYK621fs	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	621						membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						TGCCTCCTCCTTGTACTTAGTGACAATGGGCTGAGCT	0.525																																					p.621_626del		Atlas-INDEL	.											.	HNRNPUL2	41	.	0			c.1862_1878del						.																																			SO:0001589	frameshift_variant	221092	exon11			.		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.1861_1877delATTGTCACTAAGTACAA	chr11.hg19:g.62484565_62484581delTTGTACTTAGTGACAAT	ENSP00000301785:p.Ile621fs	98.0	0.0		110.0	27.0	NM_001079559	Q8N3B3	Frame_Shift_Del	DEL	ENST00000301785.5	hg19	CCDS41659.1																																																																																			.	.		0.525	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		-	62484581	TTGTACTTAGTGACAAT	-	62484565	7	5	157	1	0	1	0	1	0	0	0	0	7284	1609	56	0	382	0	HNRNPUL2	11	62484565	Frame_Shift_Del	DEL	TTGTACTTAGTGACAAT	TCGA-DD-AACF-01A-11D-A40R-10	1372893	62484565	72521951	71	23901										
CHRM1	1128	hgsc.bcm.edu	37	chr11	62677945	62677945	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ctctgtctcccggtagatgcGccagtagagcgtgcacatga	12	12	2	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr11:62677945G>A	ENST00000306960.3	-	2	1169	c.628C>T	c.(628-630)Cgc>Tgc	p.R210C	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	210					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	CGGTAGATGCGCCAGTAGAGC	0.617																																					p.R210C		Atlas-SNP	.											.	CHRM1	29	.	0			c.C628T						.						74	59	64					11																	62677945		2201	4298	6499	SO:0001583	missense	1128	exon2			AGATGCGCCAGTA	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1950	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 1"	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.628C>T	chr11.hg19:g.62677945G>A	ENSP00000306490:p.Arg210Cys	52.0	0.0		62.0	23.0	NM_000738	Q96RH1	Missense_Mutation	SNP	ENST00000306960.3	hg19	CCDS8040.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.429867	0.62844	.	.	ENSG00000168539	ENST00000306960;ENST00000543973	T;T	0.39592	1.07;1.07	4.48	4.48	0.54585	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000031	T	0.63546	0.2520	M	0.82716	2.605	0.58432	D	0.999997	D	0.89917	1.0	D	0.72625	0.978	T	0.68116	-0.5494	10	0.87932	D	0	-16.9303	9.8437	0.41015	0.0:0.0:0.7955:0.2045	.	210	P11229	ACM1_HUMAN	C	210	ENSP00000306490:R210C;ENSP00000441188:R210C	ENSP00000306490:R210C	R	-	1	0	CHRM1	62434521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.534000	0.36051	2.329000	0.79093	0.563000	0.77884	CGC	.	.		0.617	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738		A	62677945	G	A	62677945	3	1	157	1	0	0	0	0	1	0	0	0	3378	1087	38	1	758	1	CHRM1	11	62677945	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	193380	62677945	72328571	72	23902										
RSF1	51773	hgsc.bcm.edu	37	chr11	77409582	77409582	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tttgcatggttcatcatcatCtgctaggatggcttcttcac	8	10	6	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr11:77409582C>A	ENST00000308488.6	-	7	2967	c.2665G>T	c.(2665-2667)Gat>Tat	p.D889Y	RSF1_ENST00000360355.2_Missense_Mutation_p.D858Y|RSF1_ENST00000480887.1_Missense_Mutation_p.D637Y			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	889					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			TCATCATCATCTGCTAGGATG	0.413																																					p.D889Y		Atlas-SNP	.											.	RSF1	105	.	0			c.G2665T						.						226	206	213					11																	77409582		2200	4292	6492	SO:0001583	missense	51773	exon7			CATCATCTGCTAG	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"Zinc fingers, PHD-type"	18118	protein-coding gene	gene with protein product		608522	"hepatitis B virus x associated protein"	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.2665G>T	chr11.hg19:g.77409582C>A	ENSP00000311513:p.Asp889Tyr	86.0	0.0		147.0	58.0	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	hg19	CCDS8253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.80|17.80	3.477684|3.477684	0.63849|0.63849	.|.	.|.	ENSG00000048649|ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000526324|ENST00000532556	D;D;D;D|.	0.88046|.	-2.33;-2.33;-2.33;-2.33|.	4.68|4.68	4.68|4.68	0.58851|0.58851	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE/PHD-type (1);|.	0.000000|.	0.52532|.	D|.	0.000073|.	T|T	0.55369|0.55369	0.1916|0.1916	N|N	0.25957|0.25957	0.775|0.775	0.53005|0.53005	D|D	0.999964|0.999964	B|.	0.32302|.	0.363|.	B|.	0.35073|.	0.195|.	T|T	0.50575|0.50575	-0.8812|-0.8812	10|5	0.72032|.	D|.	0.01|.	-17.8695|-17.8695	17.7579|17.7579	0.88455|0.88455	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	889|.	Q96T23|.	RSF1_HUMAN|.	Y|H	889;637;858;690|142	ENSP00000311513:D889Y;ENSP00000434509:D637Y;ENSP00000353511:D858Y;ENSP00000432022:D690Y|.	ENSP00000311513:D889Y|.	D|Q	-|-	1|3	0|2	RSF1|RSF1	77087230|77087230	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.955000|0.955000	0.61496|0.61496	4.116000|4.116000	0.57871|0.57871	2.580000|2.580000	0.87095|0.87095	0.591000|0.591000	0.81541|0.81541	GAT|CAG	.	.		0.413	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		A	77409582	C	A	77409582	3	1	157	1	0	0	0	0	1	0	0	0	13714	913	32	3	1700	3	RSF1	11	77409582	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	14731637	77409582	57596934	73	23903										
NFRKB	4798	hgsc.bcm.edu	37	chr11	129754016	129754016	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tttaacattatcttcaggtcActgtcccccagttctacttt	4	12	4	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr11:129754016A>G	ENST00000446488.3	-	7	868	c.765T>C	c.(763-765)agT>agC	p.S255S	NFRKB_ENST00000304521.5_Silent_p.S255S|NFRKB_ENST00000524794.1_Silent_p.S280S|NFRKB_ENST00000524746.1_Silent_p.S255S	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	255					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		TCTTCAGGTCACTGTCCCCCA	0.428																																					p.S280S		Atlas-SNP	.											.	NFRKB	101	.	0			c.T840C						.						287	245	259					11																	129754016		2201	4297	6498	SO:0001819	synonymous_variant	4798	exon6			CAGGTCACTGTCC		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"INO80 complex subunits"	7802	protein-coding gene	gene with protein product	"nuclear factor related to kappa B binding protein", "DNA-binding protein R kappa B", "INO80 complex subunit G"	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.765T>C	chr11.hg19:g.129754016A>G		59.0	0.0		92.0	35.0	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	hg19	CCDS44770.1																																																																																			.	.		0.428	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		G	129754016	A	G	129754016	2	3	157	1	0	0	0	0	0	0	0	1	10393	156	6	2		2	NFRKB	11	129754016	Silent	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	52344434	129754016	5252500	74	23904										
LTBR	4055	hgsc.bcm.edu	37	chr12	6493827	6493827	+	Frame_Shift_Del	DEL	T	T	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ctatgagccccagcaccgcaTctgctgctcccgctgcccgc							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr12:6493827delT	ENST00000228918.4	+	2	496	c.170delT	c.(169-171)atcfs	p.I57fs	LTBR_ENST00000546296.1_3'UTR|LTBR_ENST00000541102.1_5'Flank|LTBR_ENST00000539925.1_Frame_Shift_Del_p.I38fs|LTBR_ENST00000543190.1_5'UTR	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)	57					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						CAGCACCGCATCTGCTGCTCC	0.632																																					p.I57fs		Atlas-INDEL	.											.	LTBR	30	.	0			c.169delA						.						54	58	57					12																	6493827		2203	4300	6503	SO:0001589	frameshift_variant	4055	exon2			.	L04270	CCDS8544.1, CCDS59233.1	12p13	2013-05-22				ENSG00000111321		"Tumor necrosis factor receptor superfamily"	6718	protein-coding gene	gene with protein product		600979		D12S370		8171323, 8486360	Standard	NM_002342		Approved	TNFCR, TNFR-RP, TNFR2-RP, TNF-R-III, TNFRSF3	uc001qny.2	P36941		ENST00000228918.4:c.170delT	chr12.hg19:g.6493827delT	ENSP00000228918:p.Ile57fs	62.0	0.0		97.0	41.0	NM_002342	B7Z1D2|D3DUR2|F5GXE7	Frame_Shift_Del	DEL	ENST00000228918.4	hg19	CCDS8544.1																																																																																			.	.		0.632	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1			-	6493827	T	-	6493827	7	5	157	1	0	1	0	1	0	0	0	0	9086	1435	50	0	176	0	LTBR	12	6493827	Frame_Shift_Del	DEL	T	TCGA-DD-AACF-01A-11D-A40R-10		6493827	127358068	75	23905										
ZNF384	171017	hgsc.bcm.edu	37	chr12	6777070	6777070	+	Missense_Mutation	SNP	T	T	G													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ggaagtgtggtggtggctgtTgctgctgctgctgctgctgc					rs72393318|rs544124628|rs3835029	byFrequency	TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr12:6777070T>G	ENST00000396801.3	-	11	1751	c.1544A>C	c.(1543-1545)cAa>cCa	p.Q515P	ZNF384_ENST00000396795.1_Missense_Mutation_p.Q454P|ZNF384_ENST00000319770.3_Missense_Mutation_p.Q438P|ZNF384_ENST00000361959.3_Missense_Mutation_p.Q515P|RP4-761J14.8_ENST00000586338.1_RNA|ZNF384_ENST00000355772.4_Missense_Mutation_p.Q399P|RP4-761J14.8_ENST00000589924.1_RNA|ZNF384_ENST00000396799.2_Missense_Mutation_p.Q454P	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	515	Gln-rich.				nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.L139delL(6)|p.Q455delQ(3)|p.Q516delQ(3)	EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						TGGTGgctgttgctgctgctg	0.672			T	"EWSR1, TAF15 "	ALL																																p.Q515P		Atlas-SNP	.		Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	ZNF384_ENST00000361959,caecum,carcinoma,+1,4	ZNF384	102	.	12	Deletion - In frame(12)	breast(12)	c.A1544C						.						19	22	21					12																	6777070		2201	4296	6497	SO:0001583	missense	171017	exon11			GGCTGTTGCTGCT	U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"Zinc fingers, C2H2-type"	11955	protein-coding gene	gene with protein product		609951	"trinucleotide repeat containing 1"	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.1544A>C	chr12.hg19:g.6777070T>G	ENSP00000380019:p.Gln515Pro	48.0	0.0		66.0	6.0	NM_001135734	O15407|Q7Z722|Q8N938	Missense_Mutation	SNP	ENST00000396801.3	hg19	CCDS44817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0|0	-2.663886|-2.663886	0.00107|0.00107	.|.	.|.	ENSG00000219410|ENSG00000126746	ENST00000407384|ENST00000319770;ENST00000396795;ENST00000396801;ENST00000361959;ENST00000355772;ENST00000396799	.|T;T;T;T;T;T	.|0.55588	.|0.51;0.51;0.51;0.51;0.51;0.51	0.853|0.853	-0.852|-0.852	0.10713|0.10713	.|.	.|0.088353	.|0.44483	.|N	.|0.000451	T|T	0.22589|0.22589	0.0545|0.0545	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.04013	.|0.0;0.001;0.001;0.001	T|T	0.08764|0.08764	-1.0706|-1.0706	6|10	0.87932|0.21014	D|T	0|0.42	-0.8311|-0.8311	3.6518|3.6518	0.08206|0.08206	0.0:0.0:0.4097:0.5903|0.0:0.0:0.4097:0.5903	.|.	.|515;399;438;454	.|Q8TF68;Q8TF68-3;F8W6Q3;Q8TF68-2	.|ZN384_HUMAN;.;.;.	W|P	125|438;454;515;515;399;454	.|ENSP00000321650:Q438P;ENSP00000380013:Q454P;ENSP00000380019:Q515P;ENSP00000354592:Q515P;ENSP00000348018:Q399P;ENSP00000380017:Q454P	ENSP00000384049:L125W|ENSP00000321650:Q438P	L|Q	+|-	2|2	0|0	AC125494.1|ZNF384	6647331|6647331	0.892000|0.892000	0.30473|0.30473	0.100000|0.100000	0.21137|0.21137	0.041000|0.041000	0.13682|0.13682	0.394000|0.394000	0.20834|0.20834	-0.197000|-0.197000	0.10350|0.10350	-0.815000|-0.815000	0.03128|0.03128	TTG|CAA	.	.		0.672	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400712.1			G	6777070	T	G	6777070	3	3	157	1	0	0	0	0	1	0	0	0	17890	1812	63	5	193	5	ZNF384	12	6777070	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	283243	6777070	127074825	76	23906	107	2								
ZNF384	171017	hgsc.bcm.edu	37	chr12	6777075	6777075	+	Silent	SNP	C	C	T													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tgtggtggtggctgttgctgCtgctgctgctgctgctgctg					rs1052680		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr12:6777075C>T	ENST00000396801.3	-	11	1746	c.1539G>A	c.(1537-1539)caG>caA	p.Q513Q	ZNF384_ENST00000396795.1_Silent_p.Q452Q|ZNF384_ENST00000319770.3_Silent_p.Q436Q|ZNF384_ENST00000361959.3_Silent_p.Q513Q|RP4-761J14.8_ENST00000586338.1_RNA|ZNF384_ENST00000355772.4_Silent_p.Q397Q|RP4-761J14.8_ENST00000589924.1_RNA|ZNF384_ENST00000396799.2_Silent_p.Q452Q	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	513	Gln-rich.				nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)		EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						gctgttgctgctgctgctgct	0.667			T	"EWSR1, TAF15 "	ALL																																p.Q513Q		Atlas-SNP	.		Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	.	ZNF384	102	.	0			c.G1539A						.						18	22	21					12																	6777075		2203	4296	6499	SO:0001819	synonymous_variant	171017	exon11			TTGCTGCTGCTGC	U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"Zinc fingers, C2H2-type"	11955	protein-coding gene	gene with protein product		609951	"trinucleotide repeat containing 1"	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.1539G>A	chr12.hg19:g.6777075C>T		47.0	0.0		62.0	5.0	NM_001135734	O15407|Q7Z722|Q8N938	Silent	SNP	ENST00000396801.3	hg19	CCDS44817.1																																																																																			.	C|1.000;|0.000		0.667	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400712.1			T	6777075	C	T	6777075	2	4	157	1	0	0	0	0	0	0	0	1	17890	796	28	3		3	ZNF384	12	6777075	Silent	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	5	6777075	127074820	77	23907	107	2								
MLL2	8085	hgsc.bcm.edu	37	chr12	49426793	49426793	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ctgctgctgctgctgaagctGctgtaaagagcccatgggct	13	11	0	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr12:49426793G>A	ENST00000301067.7	-	39	11694	c.11695C>T	c.(11695-11697)Cag>Tag	p.Q3899*	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3899	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										tgctgAAGCTGCTGTAAAGAG	0.562																																					p.Q3899X		Atlas-SNP	.											.	MLL2	1173	.	0			c.C11695T						.						15	19	18					12																	49426793		1788	3311	5099	SO:0001587	stop_gained	8085	exon39			GAAGCTGCTGTAA	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.11695C>T	chr12.hg19:g.49426793G>A	ENSP00000301067:p.Gln3899*	29.0	0.0		48.0	21.0	NM_003482	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	51	18.122273	0.99899	.	.	ENSG00000167548	ENST00000301067	.	.	.	4.45	4.45	0.53987	.	0.238912	0.21796	N	0.068994	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.0607	0.86547	0.0:0.0:1.0:0.0	.	.	.	.	X	3899	.	ENSP00000301067:Q3899X	Q	-	1	0	MLL2	47713060	0.008000	0.16893	1.000000	0.80357	0.669000	0.39330	1.691000	0.37721	2.755000	0.94549	0.563000	0.77884	CAG	.	.		0.562	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49426793	G	A	49426793	4	1	157	1	0	0	0	0	0	1	0	0	9630	1328	46	3	4982	3	MLL2	12	49426793	Nonsense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	42649718	49426793	84425102	78	23908										
DGKA	1606	hgsc.bcm.edu	37	chr12	56346653	56346653	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gggatatctatgggatcaacCaggccttaggtgctacagct	12	9	2	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr12:56346653C>G	ENST00000331886.5	+	21	2333	c.1879C>G	c.(1879-1881)Cag>Gag	p.Q627E	DGKA_ENST00000394147.1_Missense_Mutation_p.Q627E|DGKA_ENST00000551156.1_Missense_Mutation_p.Q627E|DGKA_ENST00000549079.2_3'UTR	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	627					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	TGGGATCAACCAGGCCTTAGG	0.547																																					p.Q627E		Atlas-SNP	.											.	DGKA	70	.	0			c.C1879G						.						147	134	139					12																	56346653		2203	4300	6503	SO:0001583	missense	1606	exon21			ATCAACCAGGCCT	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"EF-hand domain containing"	2849	protein-coding gene	gene with protein product		125855	"diacylglycerol kinase, alpha (80kD)"	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.1879C>G	chr12.hg19:g.56346653C>G	ENSP00000328405:p.Gln627Glu	83.0	0.0		128.0	55.0	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Missense_Mutation	SNP	ENST00000331886.5	hg19	CCDS8896.1	.	.	.	.	.	.	.	.	.	.	C	1.665	-0.510526	0.04231	.	.	ENSG00000065357	ENST00000331886;ENST00000394147;ENST00000551156	D;D;D	0.84589	-1.87;-1.87;-1.87	4.91	3.99	0.46301	Diacylglycerol kinase, accessory domain (2);	1.926710	0.02344	N	0.075249	T	0.78291	0.4260	N	0.12569	0.235	0.35026	D	0.758322	B	0.15719	0.014	B	0.29440	0.102	T	0.53968	-0.8363	10	0.15952	T	0.53	.	13.2183	0.59873	0.0:0.9148:0.0:0.0852	.	627	P23743	DGKA_HUMAN	E	627	ENSP00000328405:Q627E;ENSP00000377703:Q627E;ENSP00000450359:Q627E	ENSP00000328405:Q627E	Q	+	1	0	DGKA	54632920	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	1.226000	0.32563	2.432000	0.82394	0.313000	0.20887	CAG	.	.		0.547	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1			G	56346653	C	G	56346653	3	3	157	1	0	0	0	0	1	0	0	0	4467	595	21	4	1957	4	DGKA	12	56346653	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	6919860	56346653	77505242	79	23909										
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72017292	72017293	+	Missense_Mutation	DNP	TG	TG	CA													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gaatgttgaattcaataagaTgtatgtaggccaaccatgcc							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr12:72017292_72017293TG>CA	ENST00000378743.3	-	24	4949_4950	c.4591_4592CA>TG	c.(4591-4593)CAt>TGt	p.H1531C		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1531					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TTCAATAAGATGTATGTAGGCC	0.332																																					p.H1531R|p.H1531Y		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.A4592G|c.C4591T						.																																			SO:0001583	missense	196441	exon24			ATAAGATGTATGT|TAAGATGTATGTA	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.4591_4592delinsCA	chr12.hg19:g.72017292_72017293delinsCA	ENSP00000368017:p.His1531Cys	111.0	0.0		175.0	65.0|64.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	hg19	CCDS41813.1																																																																																			.	.		0.332	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		CA	72017293	TG	CA	72017292	3	2	157	1	0	0	0	0	1	0	0	0	17648	1464	51	2	1425	2	ZFC3H1	12	72017292	Missense_Mutation	DNP	TG	TCGA-DD-AACF-01A-11D-A40R-10	15670639	72017292	61834603	80	23910										
TMTC2	160335	hgsc.bcm.edu	37	chr12	83289601	83289601	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tctcttttggtttcagaggaAgaacttgtcgcttttcctaa	8	8	2	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr12:83289601A>C	ENST00000321196.3	+	3	1366	c.659A>C	c.(658-660)aAg>aCg	p.K220T	TMTC2_ENST00000548305.1_Missense_Mutation_p.K220T|TMTC2_ENST00000549919.1_Missense_Mutation_p.K214T	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	220					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						TTTCAGAGGAAGAACTTGTCG	0.378																																					p.K220T		Atlas-SNP	.											.	TMTC2	100	.	0			c.A659C						.						95	94	94					12																	83289601		2203	4300	6503	SO:0001583	missense	160335	exon3			AGAGGAAGAACTT	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.659A>C	chr12.hg19:g.83289601A>C	ENSP00000322300:p.Lys220Thr	70.0	0.0		96.0	34.0	NM_152588	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	hg19	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	A	17.36	3.369573	0.61624	.	.	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919	T;T;T	0.62639	0.67;0.01;0.56	5.84	5.84	0.93424	.	0.041493	0.85682	D	0.000000	T	0.63462	0.2513	L	0.47190	1.495	0.80722	D	1	P;B	0.47841	0.901;0.397	P;B	0.49999	0.628;0.133	T	0.58457	-0.7633	10	0.13470	T	0.59	-20.9681	16.2167	0.82231	1.0:0.0:0.0:0.0	.	220;220	Q8N394;F8VSH2	TMTC2_HUMAN;.	T	220;220;214	ENSP00000322300:K220T;ENSP00000448292:K220T;ENSP00000447609:K214T	ENSP00000322300:K220T	K	+	2	0	TMTC2	81813732	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.003000	0.63959	2.231000	0.72958	0.533000	0.62120	AAG	.	.		0.378	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		C	83289601	A	C	83289601	3	2	157	1	0	0	0	0	1	0	0	0	16276	72	3	5	669	5	TMTC2	12	83289601	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	11272309	83289601	50562294	81	23911										
ANKRD13A	88455	hgsc.bcm.edu	37	chr12	110465512	110465512	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ctccctacccctctgtagcaGacaggaacccgctggaatct	8	16	2	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr12:110465512G>T	ENST00000261739.4	+	9	1052	c.886G>T	c.(886-888)Gac>Tac	p.D296Y		NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	296				D -> G (in Ref. 1; AAH32833). {ECO:0000305}.		endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						CTCTGTAGCAGACAGGAACCC	0.408																																					p.D296Y		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.G886T						.						114	116	115					12																	110465512		2203	4300	6503	SO:0001583	missense	88455	exon9			GTAGCAGACAGGA	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"Ankyrin repeat domain containing"	21268	protein-coding gene	gene with protein product		615123	"ankyrin repeat domain 13"	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.886G>T	chr12.hg19:g.110465512G>T	ENSP00000261739:p.Asp296Tyr	83.0	0.0		130.0	62.0	NM_033121	O60736	Missense_Mutation	SNP	ENST00000261739.4	hg19	CCDS9140.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.93|18.93	3.728674|3.728674	0.69074|0.69074	.|.	.|.	ENSG00000076513|ENSG00000076513	ENST00000261738;ENST00000547639|ENST00000261739;ENST00000546476	.|T	.|0.44083	.|0.93	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	.|0.042063	.|0.85682	.|D	.|0.000000	.|T	.|0.60431	.|0.2268	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.72982	.|0.979	.|T	.|0.58364	.|-0.7649	.|10	.|0.62326	.|D	.|0.03	.|-21.5399	19.3837|19.3837	0.94548|0.94548	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|296	.|Q8IZ07	.|AN13A_HUMAN	.|Y	-1|296;67	.|ENSP00000261739:D296Y	.|ENSP00000261739:D296Y	.|D	+|+	.|1	.|0	ANKRD13A|ANKRD13A	108949895|108949895	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.728000|0.728000	0.41692|0.41692	7.029000|7.029000	0.76477|0.76477	2.830000|2.830000	0.97506|0.97506	0.655000|0.655000	0.94253|0.94253	.|GAC	.	.		0.408	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		T	110465512	G	T	110465512	3	4	157	1	0	0	0	0	1	0	0	0	641	942	33	3	920	3	ANKRD13A	12	110465512	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	27175911	110465512	23386383	82	23912										
ANAPC7	51434	hgsc.bcm.edu	37	chr12	110812008	110812008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ggccgcctcactgtcgctgcCctccaggtccccttcttccc	8	21	2	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr12:110812008C>T	ENST00000455511.3	-	11	1741	c.1741G>A	c.(1741-1743)Ggc>Agc	p.G581S	ANAPC7_ENST00000481473.1_5'UTR	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	581					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						CTGTCGCTGCCCTCCAGGTCC	0.652																																					p.G581S		Atlas-SNP	.											.	ANAPC7	68	.	0			c.G1741A						.						130	94	106					12																	110812008		2203	4300	6503	SO:0001583	missense	51434	exon11			CGCTGCCCTCCAG	AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	17380	protein-coding gene	gene with protein product		606949					Standard	NM_016238		Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.1741G>A	chr12.hg19:g.110812008C>T	ENSP00000394394:p.Gly581Ser	47.0	0.0		59.0	30.0	NM_016238	Q96AC4|Q96GF4|Q9BU24|Q9NT16	Missense_Mutation	SNP	ENST00000455511.3	hg19	CCDS9145.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.3|28.3	4.905619|4.905619	0.92107|0.92107	.|.	.|.	ENSG00000196510|ENSG00000196510	ENST00000552087|ENST00000455511;ENST00000481473	.|T	.|0.63744	.|-0.06	5.88|5.88	5.0|5.0	0.66597|0.66597	.|.	0.095466|0.095466	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.46619|0.46619	0.1402|0.1402	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|B	.|0.23891	.|0.093	.|B	.|0.21151	.|0.033	T|T	0.35025|0.35025	-0.9805|-0.9805	6|10	.|0.18710	.|T	.|0.47	-30.2176|-30.2176	15.2303|15.2303	0.73383|0.73383	0.0:0.9326:0.0:0.0674|0.0:0.9326:0.0:0.0674	.|.	.|581	.|Q9UJX3	.|APC7_HUMAN	E|S	130|581;155	.|ENSP00000394394:G581S	.|ENSP00000394394:G581S	G|G	-|-	2|1	0|0	ANAPC7|ANAPC7	109296391|109296391	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.487000|7.487000	0.81328|0.81328	1.502000|1.502000	0.48669|0.48669	0.561000|0.561000	0.74099|0.74099	GGG|GGC	.	.		0.652	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347075.3	NM_016238		T	110812008	C	T	110812008	3	4	157	1	0	0	0	0	1	0	0	0	606	623	22	3	62	3	ANAPC7	12	110812008	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	346496	110812008	23039887	83	23913										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124839467	124839467	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	atgctctgagtacgggacgtGgagctggaccgacattccct	13	11	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr12:124839467G>A	ENST00000405201.1	-	25	3400	c.3400C>T	c.(3400-3402)Cac>Tac	p.H1134Y	NCOR2_ENST00000356219.3_Missense_Mutation_p.H1141Y|NCOR2_ENST00000404121.2_Missense_Mutation_p.H695Y|NCOR2_ENST00000429285.2_Missense_Mutation_p.H1124Y|NCOR2_ENST00000397355.1_Missense_Mutation_p.H1125Y|NCOR2_ENST00000404621.1_Missense_Mutation_p.H1124Y			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1142					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TACGGGACGTGGAGCTGGACC	0.652																																					p.H1134Y		Atlas-SNP	.											.	NCOR2	475	.	0			c.C3400T						.						51	58	56					12																	124839467		2009	4152	6161	SO:0001583	missense	9612	exon27			GGACGTGGAGCTG	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.3400C>T	chr12.hg19:g.124839467G>A	ENSP00000384018:p.His1134Tyr	48.0	0.0		77.0	25.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	G	15.74	2.923570	0.52653	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.38887	1.92;2.18;1.91;2.18;1.94;2.18;1.11	4.46	4.46	0.54185	.	0.054285	0.64402	D	0.000001	T	0.50086	0.1595	L	0.50333	1.59	0.41253	D	0.986721	D;B;D	0.58620	0.977;0.039;0.983	P;B;P	0.51453	0.551;0.021;0.67	T	0.57780	-0.7752	10	0.72032	D	0.01	-20.9257	17.0978	0.86641	0.0:0.0:1.0:0.0	.	1124;1125;1134	C9J0Q5;C9J239;C9JFD3	.;.;.	Y	1134;1124;1141;1125;1133;695;1124;1142	ENSP00000384018:H1134Y;ENSP00000384202:H1124Y;ENSP00000348551:H1141Y;ENSP00000380513:H1125Y;ENSP00000385618:H695Y;ENSP00000400281:H1124Y;ENSP00000402808:H1142Y	ENSP00000348551:H1141Y	H	-	1	0	NCOR2	123405420	1.000000	0.71417	0.752000	0.31206	0.848000	0.48234	6.703000	0.74633	2.018000	0.59344	0.407000	0.27541	CAC	.	.		0.652	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124839467	G	A	124839467	3	1	157	1	0	0	0	0	1	0	0	0	10245	1348	47	3	4236	3	NCOR2	12	124839467	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	14027459	124839467	9012428	84	23914										
NUPL1	9818	hgsc.bcm.edu	37	chr13	25895210	25895210	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aacactctcaacattgacaaAttgaaaatagaaactgctca	4	9	2	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr13:25895210A>T	ENST00000381736.3	+	9	1180	c.930A>T	c.(928-930)aaA>aaT	p.K310N	NUPL1_ENST00000381718.3_Missense_Mutation_p.K298N|NUPL1_ENST00000466694.1_3'UTR|NUPL1_ENST00000463407.1_Missense_Mutation_p.K310N	NM_001008564.1|NM_014089.3	NP_001008564.1|NP_054808.1	Q9BVL2	NUPL1_HUMAN	nucleoporin like 1	310	14 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	nucleocytoplasmic transporter activity (GO:0005487)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|stomach(1)|urinary_tract(1)	16		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.0092)|Epithelial(112;0.0477)|OV - Ovarian serous cystadenocarcinoma(117;0.165)|GBM - Glioblastoma multiforme(144;0.244)		ACATTGACAAATTGAAAATAG	0.358																																					p.K310N	Pancreas(166;1040 2004 4560 4728 37041)|GBM(109;1045 1520 7614 9308 19618)	Atlas-SNP	.											.	NUPL1	37	.	0			c.A930T						.						106	109	108					13																	25895210		2203	4300	6503	SO:0001583	missense	9818	exon9			TGACAAATTGAAA	AB007870	CCDS9314.1, CCDS31949.1	13q12.12	2011-04-12			ENSG00000139496	ENSG00000139496			20261	protein-coding gene	gene with protein product		607615				9455477	Standard	NM_014089		Approved	KIAA0410	uc001uqi.3	Q9BVL2	OTTHUMG00000016608	ENST00000381736.3:c.930A>T	chr13.hg19:g.25895210A>T	ENSP00000371155:p.Lys310Asn	194.0	0.0		278.0	115.0	NM_014089	A6NI12|B4DZJ1|O43160|Q5JRG2|Q5JRG5	Missense_Mutation	SNP	ENST00000381736.3	hg19	CCDS9314.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.870922	0.51695	.	.	ENSG00000139496	ENST00000381736;ENST00000381745;ENST00000313619;ENST00000463407;ENST00000381718;ENST00000381747;ENST00000394327	T;T;T;T;T	0.52057	1.27;1.26;1.27;1.23;0.68	5.94	-1.2	0.09554	.	0.041188	0.85682	D	0.000000	T	0.39064	0.1064	M	0.65498	2.005	0.50813	D	0.99989	P;B;B	0.40578	0.722;0.333;0.291	B;B;B	0.34093	0.175;0.175;0.157	T	0.41215	-0.9521	10	0.46703	T	0.11	-3.1368	11.9891	0.53166	0.4874:0.0:0.5126:0.0	.	298;310;310	A6NI12;Q9BVL2;Q9BVL2-2	.;NUPL1_HUMAN;.	N	310;298;287;310;298;310;257	ENSP00000371155:K310N;ENSP00000418555:K310N;ENSP00000371137:K298N;ENSP00000371166:K310N;ENSP00000408147:K257N	ENSP00000318459:K287N	K	+	3	2	NUPL1	24793210	0.592000	0.26832	0.790000	0.31976	0.953000	0.61014	1.000000	0.29770	-0.066000	0.12998	-0.924000	0.02725	AAA	.	.		0.358	NUPL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044228.2			T	25895210	A	T	25895210	3	4	157	1	0	0	0	0	1	0	0	0	10783	98	4	4	964	4	NUPL1	13	25895210	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10		25895210	89274668	85	23915										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58207758	58207758	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tcgtctccgtgcgccaggggGcgctgagcgaggccgcccct	16	16	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr13:58207758G>A	ENST00000377918.3	+	1	1104	c.1078G>A	c.(1078-1080)Gcg>Acg	p.A360T		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	360	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		GCGCCAGGGGGCGCTGAGCGA	0.667																																					p.A360T	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.G1078A						.						42	44	43					13																	58207758		2203	4300	6503	SO:0001583	missense	27253	exon1			CAGGGGGCGCTGA	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1078G>A	chr13.hg19:g.58207758G>A	ENSP00000367151:p.Ala360Thr	32.0	0.0		34.0	24.0	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	hg19	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.057386	0.55325	.	.	ENSG00000118946	ENST00000377918	T	0.50001	0.76	5.46	5.46	0.80206	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.40815	0.1132	N	0.02876	-0.465	0.58432	D	0.999991	D;P	0.52996	0.957;0.932	P;P	0.56865	0.709;0.808	T	0.48670	-0.9015	9	.	.	.	.	19.3194	0.94231	0.0:0.0:1.0:0.0	.	360;360	O14917-2;O14917	.;PCD17_HUMAN	T	360	ENSP00000367151:A360T	.	A	+	1	0	PCDH17	57105759	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.831000	0.75324	2.588000	0.87417	0.650000	0.86243	GCG	.	.		0.667	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		A	58207758	G	A	58207758	3	1	157	1	0	0	0	0	1	0	0	0	11521	1203	42	3	1080	3	PCDH17	13	58207758	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	32312548	58207758	56962120	86	23916										
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60616914	60616914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ccattttcagctcatgaatgAattcctgaggtgagatctgt	9	8	3	4			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr13:60616914A>G	ENST00000400324.4	-	5	756	c.536T>C	c.(535-537)tTc>tCc	p.F179S	DIAPH3_ENST00000400319.1_Missense_Mutation_p.F109S|DIAPH3_ENST00000400330.1_Missense_Mutation_p.F179S|DIAPH3-AS1_ENST00000435636.1_RNA|DIAPH3-AS1_ENST00000432995.1_RNA|DIAPH3_ENST00000377908.2_Missense_Mutation_p.F168S|DIAPH3_ENST00000267215.4_Missense_Mutation_p.F179S|DIAPH3_ENST00000400320.1_Missense_Mutation_p.F133S|DIAPH3-AS1_ENST00000422052.1_RNA	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	179	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		CTCATGAATGAATTCCTGAGG	0.403																																					p.F179S		Atlas-SNP	.											.	DIAPH3	139	.	0			c.T536C						.						92	88	89					13																	60616914		1838	4088	5926	SO:0001583	missense	81624	exon5			TGAATGAATTCCT	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.536T>C	chr13.hg19:g.60616914A>G	ENSP00000383178:p.Phe179Ser	55.0	0.0		84.0	34.0	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	hg19	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.312323	0.81358	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000453990	D;D;D;D;D;D	0.90324	-2.65;-2.65;-2.65;-2.65;-2.65;-2.65	5.65	5.65	0.86999	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.000000	0.85682	D	0.000000	D	0.94886	0.8347	M	0.73598	2.24	0.45979	D	0.998797	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.91635	0.997;0.999;0.999;0.977	D	0.95374	0.8467	10	0.87932	D	0	.	14.8661	0.70416	1.0:0.0:0.0:0.0	.	109;133;168;179	A8MYX0;C9JL55;C9JDG1;Q9NSV4	.;.;.;DIAP3_HUMAN	S	179;179;168;133;109;168;109;133;179;179	ENSP00000383178:F179S;ENSP00000383184:F179S;ENSP00000367141:F168S;ENSP00000383173:F109S;ENSP00000383174:F133S;ENSP00000267215:F179S	ENSP00000267215:F179S	F	-	2	0	DIAPH3	59514915	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.354000	0.73036	2.153000	0.67306	0.477000	0.44152	TTC	.	.		0.403	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		G	60616914	A	G	60616914	3	3	157	1	0	0	0	0	1	0	0	0	4522	246	9	2	3161	2	DIAPH3	13	60616914	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	2409156	60616914	54552964	87	23917										
OR4N2	390429	hgsc.bcm.edu	37	chr14	20296045	20296045	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	acctgctatgcaatgatgttGgctctgtggcttgggggttt	14	7	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr14:20296045G>A	ENST00000315947.1	+	1	438	c.438G>A	c.(436-438)ttG>ttA	p.L146L	OR4N2_ENST00000568211.1_Silent_p.L146L	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CAATGATGTTGGCTCTGTGGC	0.522																																					p.L146L		Atlas-SNP	.											.	OR4N2	125	.	0			c.G438A						.						179	192	188					14																	20296045		2203	4300	6503	SO:0001819	synonymous_variant	390429	exon1			GATGTTGGCTCTG		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"GPCR / Class A : Olfactory receptors"	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.438G>A	chr14.hg19:g.20296045G>A		95.0	0.0		237.0	111.0	NM_001004723	Q6IEY9|Q6IFA2	Silent	SNP	ENST00000315947.1	hg19	CCDS32022.1																																																																																			.	.		0.522	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2			A	20296045	G	A	20296045	2	1	157	1	0	0	0	0	0	0	0	1	11086	1339	47	3		3	OR4N2	14	20296045	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10		20296045	87053495	88	23918										
REM2	161253	hgsc.bcm.edu	37	chr14	23355418	23355418	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aacaagagcgacttggcccgCtcccgggaggtatcactgga	13	12	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr14:23355418C>T	ENST00000267396.4	+	4	828	c.705C>T	c.(703-705)cgC>cgT	p.R235R	REM2_ENST00000536884.1_Missense_Mutation_p.L211F	NM_173527.2	NP_775798.2	Q8IYK8	REM2_HUMAN	RAS (RAD and GEM)-like GTP binding 2	235					small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|large_intestine(2)|ovary(1)	5	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.012)		ACTTGGCCCGCTCCCGGGAGG	0.567																																					p.R235R		Atlas-SNP	.											.	REM2	21	.	0			c.C705T						.						23	27	26					14																	23355418		1917	4121	6038	SO:0001819	synonymous_variant	161253	exon4			GGCCCGCTCCCGG		CCDS45082.1	14q11.2	2014-05-09	2006-12-14		ENSG00000139890	ENSG00000139890			20248	protein-coding gene	gene with protein product			"RAS (RAD and GEM) like GTP binding 2"			10727423	Standard	NM_173527		Approved	FLJ38964	uc001whf.1	Q8IYK8	OTTHUMG00000170277	ENST00000267396.4:c.705C>T	chr14.hg19:g.23355418C>T		86.0	0.0		268.0	15.0	NM_173527	B7Z5P1|Q8N8R8	Silent	SNP	ENST00000267396.4	hg19	CCDS45082.1	.	.	.	.	.	.	.	.	.	.	C	8.252	0.809124	0.16537	.	.	ENSG00000139890	ENST00000536884	T	0.39056	1.1	5.34	1.39	0.22231	.	.	.	.	.	T	0.31482	0.0798	.	.	.	0.26574	N	0.973501	B	0.14805	0.011	B	0.16722	0.016	T	0.30909	-0.9962	8	0.87932	D	0	.	6.954	0.24560	0.0:0.5882:0.1211:0.2907	.	211	B7Z5P1	.	F	211	ENSP00000442774:L211F	ENSP00000442774:L211F	L	+	1	0	REM2	22425258	0.664000	0.27457	1.000000	0.80357	0.387000	0.30353	-0.153000	0.10144	0.321000	0.23259	-0.253000	0.11424	CTC	.	.		0.567	REM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408290.1	NM_173527		T	23355418	C	T	23355418	2	4	157	1	0	0	0	0	0	0	0	1	13238	784	28	3		3	REM2	14	23355418	Silent	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	3059373	23355418	83994122	89	23919										
C14orf93	60686	hgsc.bcm.edu	37	chr14	23459032	23459032	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cagaagaaacttcactactgAaatattccaagaggacttga	7	8	1	5			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr14:23459032A>C	ENST00000299088.6	-	5	1432	c.1003T>G	c.(1003-1005)Tca>Gca	p.S335A	RP11-298I3.4_ENST00000556503.1_RNA|RP11-298I3.4_ENST00000555294.1_RNA|C14orf93_ENST00000397377.1_Missense_Mutation_p.S155A|C14orf93_ENST00000341470.4_Missense_Mutation_p.S335A|C14orf93_ENST00000397382.4_Missense_Mutation_p.S335A|RP11-298I3.4_ENST00000557615.1_RNA|C14orf93_ENST00000406429.2_Missense_Mutation_p.S335A|C14orf93_ENST00000397379.3_Missense_Mutation_p.S335A	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93	335						extracellular region (GO:0005576)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	17	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		TTCACTACTGAAATATTCCAA	0.413																																					p.S335A		Atlas-SNP	.											.	C14orf93	33	.	0			c.T1003G						.						89	86	87					14																	23459032		2203	4300	6503	SO:0001583	missense	60686	exon5			CTACTGAAATATT	AK023026	CCDS9583.1, CCDS61399.1, CCDS61400.1	14q11.1	2012-09-25			ENSG00000100802	ENSG00000100802			20162	protein-coding gene	gene with protein product							Standard	XM_005267971		Approved	FLJ12154	uc001wih.3	Q9H972	OTTHUMG00000028712	ENST00000299088.6:c.1003T>G	chr14.hg19:g.23459032A>C	ENSP00000299088:p.Ser335Ala	80.0	0.0		249.0	116.0	NM_021944	B7WP03|D3DS38|D3DS39|Q86SE6|Q96CF7|Q9HA68	Missense_Mutation	SNP	ENST00000299088.6	hg19	CCDS9583.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.153965	0.78114	.	.	ENSG00000100802	ENST00000299088;ENST00000341470;ENST00000397379;ENST00000397382;ENST00000397377;ENST00000406429	T;T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41;0.41	5.85	4.69	0.59074	.	0.097947	0.44902	N	0.000406	T	0.43233	0.1238	L	0.29908	0.895	0.34975	D	0.753575	B;B	0.30146	0.202;0.27	B;B	0.32533	0.104;0.147	T	0.56147	-0.8027	10	0.87932	D	0	-27.5673	12.3485	0.55134	0.8587:0.1413:0.0:0.0	.	335;335	Q9H972;Q9H972-2	CN093_HUMAN;.	A	335;335;335;335;155;335	ENSP00000299088:S335A;ENSP00000341353:S335A;ENSP00000380535:S335A;ENSP00000380538:S335A;ENSP00000380533:S155A;ENSP00000384768:S335A	ENSP00000299088:S335A	S	-	1	0	C14orf93	22528872	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.499000	0.35671	1.020000	0.39573	0.533000	0.62120	TCA	.	.		0.413	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	NM_021944		C	23459032	A	C	23459032	3	2	157	1	0	0	0	0	1	0	0	0	1784	246	9	5	625	5	C14orf93	14	23459032	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	103614	23459032	83890508	90	23920										
RABGGTA	5875	hgsc.bcm.edu	37	chr14	24737796	24737796	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gtatgttggggcaactggtcGttgagggaggcagcaggcag	19	6	0	1	rs370715682		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr14:24737796G>A	ENST00000399409.3	-	9	1413	c.930C>T	c.(928-930)aaC>aaT	p.N310N	RABGGTA_ENST00000559586.1_5'Flank|RABGGTA_ENST00000216840.6_Silent_p.N310N|RABGGTA_ENST00000560777.1_Intron	NM_004581.5	NP_004572.3	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase, alpha subunit	310					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)	12				GBM - Glioblastoma multiforme(265;0.0184)		GCAACTGGTCGTTGAGGGAGG	0.552																																					p.N310N		Atlas-SNP	.											.	RABGGTA	43	.	0			c.C930T						.	G	,	0,4152		0,0,2076	89	94	93		930,930	-0.2	1	14		93	1,8411		0,1,4205	no	coding-synonymous,coding-synonymous	RABGGTA	NM_004581.3,NM_182836.1	,	0,1,6281	AA,AG,GG		0.0119,0.0,0.0080	,	310/568,310/568	24737796	1,12563	2076	4206	6282	SO:0001819	synonymous_variant	5875	exon9			CTGGTCGTTGAGG		CCDS45088.1	14q11.2	2011-06-27				ENSG00000100949		"Prenyltransferase alpha subunit repeat containing"	9795	protein-coding gene	gene with protein product	"protein prenyltransferase alpha subunit repeat containing 3"	601905				8954794	Standard	NM_182836		Approved	PTAR3	uc001wog.4	Q92696		ENST00000399409.3:c.930C>T	chr14.hg19:g.24737796G>A		41.0	0.0		105.0	50.0	NM_004581	A8K5N2|D3DS69	Silent	SNP	ENST00000399409.3	hg19	CCDS45088.1																																																																																			.	.		0.552	RABGGTA-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415308.5	NM_182836		A	24737796	G	A	24737796	2	1	157	1	0	0	0	0	0	0	0	1	12982	1136	40	1		1	RABGGTA	14	24737796	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	1278764	24737796	82611744	91	23921										
NIPA2	81614	hgsc.bcm.edu	37	chr15	23006742	23006743	+	Frame_Shift_Del	DEL	TT	TT	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ggagactgaaaacgcgccgaTtacagagcagattgttatgt							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr15:23006742_23006743delTT	ENST00000337451.3	-	8	1173_1174	c.561_562delAA	c.(559-564)gtaatcfs	p.I188fs	NIPA2_ENST00000398013.3_Frame_Shift_Del_p.I188fs|NIPA2_ENST00000398014.2_Frame_Shift_Del_p.I188fs|NIPA2_ENST00000359727.4_Frame_Shift_Del_p.I169fs|NIPA2_ENST00000539711.2_Frame_Shift_Del_p.I169fs	NM_030922.6	NP_112184.4	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 2	188						early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(4)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		AACGCGCCGATTACAGAGCAGA	0.51																																					p.188_188del		Atlas-INDEL	.											.	NIPA2	49	.	0			c.562_563del						.																																			SO:0001589	frameshift_variant	81614	exon10			.	AY732242	CCDS73693.1, CCDS73694.1	15q11.2	2008-02-05			ENSG00000140157	ENSG00000140157			17044	protein-coding gene	gene with protein product		608146				14508708	Standard	NM_001008860		Approved		uc001yuz.3	Q8N8Q9	OTTHUMG00000129101	ENST00000337451.3:c.561_562delAA	chr15.hg19:g.23006742_23006743delTT	ENSP00000337618:p.Ile188fs	123.0	0.0		105.0	82.0	NM_001184889	F8W7Y8|Q96F03|Q9BVS2	Frame_Shift_Del	DEL	ENST00000337451.3	hg19	CCDS10010.1																																																																																			.	.		0.51	NIPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251137.1	NM_030922		-	23006743	TT	-	23006742	7	5	157	1	0	1	0	1	0	0	0	0	10432	1493	52	0	524	0	NIPA2	15	23006742	Frame_Shift_Del	DEL	TT	TCGA-DD-AACF-01A-11D-A40R-10		23006742	79524650	92	23922										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51768790	51768790	+	Frame_Shift_Del	DEL	C	C	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tcatttaaattctcaccaggCcattgagcaggagatgaatt							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr15:51768790delC	ENST00000251076.5	-	27	7244	c.6957delG	c.(6955-6957)tggfs	p.W2319fs	DMXL2_ENST00000449909.3_Frame_Shift_Del_p.W1683fs|DMXL2_ENST00000543779.2_Frame_Shift_Del_p.W2320fs|RP11-707P17.1_ENST00000561007.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2319						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TCTCACCAGGCCATTGAGCAG	0.378																																					p.P2321fs		Atlas-INDEL	.											.	DMXL2	262	.	0			c.6961delC						.						143	136	138					15																	51768790		2196	4293	6489	SO:0001589	frameshift_variant	23312	exon27			.	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.6957delG	chr15.hg19:g.51768790delC	ENSP00000251076:p.Trp2319fs	35.0	0.0		75.0	29.0	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Frame_Shift_Del	DEL	ENST00000251076.5	hg19	CCDS10141.1																																																																																			.	.		0.378	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		-	51768790	C	-	51768790	7	5	157	1	0	1	0	1	0	0	0	0	4597	740	26	0	2221	0	DMXL2	15	51768790	Frame_Shift_Del	DEL	C	TCGA-DD-AACF-01A-11D-A40R-10	28762048	51768790	50762602	93	23923										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54306076	54306076	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	caagcctgagatttttaaatGtgactgaagaaagatttgaa	9	4	0	6			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr15:54306076G>A	ENST00000260323.11	+	1	976	c.976G>A	c.(976-978)Gtg>Atg	p.V326M	UNC13C_ENST00000545554.1_Missense_Mutation_p.V326M|UNC13C_ENST00000537900.1_Missense_Mutation_p.V326M	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	326					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ATTTTTAAATGTGACTGAAGA	0.363																																					p.V326M		Atlas-SNP	.											.	UNC13C	674	.	0			c.G976A						.						96	94	95					15																	54306076		1843	4088	5931	SO:0001583	missense	440279	exon1			TTAAATGTGACTG	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.976G>A	chr15.hg19:g.54306076G>A	ENSP00000260323:p.Val326Met	103.0	0.0		157.0	80.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.074718	0.76415	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.86230	-2.09;-2.09;-2.09	5.08	5.08	0.68730	.	.	.	.	.	D	0.89622	0.6768	L	0.27053	0.805	0.54753	D	0.999987	D	0.76494	0.999	D	0.85130	0.997	D	0.91242	0.5022	9	0.72032	D	0.01	.	17.4827	0.87677	0.0:0.0:1.0:0.0	.	326	Q8NB66	UN13C_HUMAN	M	326	ENSP00000260323:V326M;ENSP00000438156:V326M;ENSP00000442569:V326M	ENSP00000260323:V326M	V	+	1	0	UNC13C	52093368	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.785000	0.99042	2.343000	0.79666	0.655000	0.94253	GTG	.	.		0.363	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54306076	G	A	54306076	3	1	157	1	0	0	0	0	1	0	0	0	17001	1377	48	3	978	3	UNC13C	15	54306076	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	2537286	54306076	48225316	94	23924										
PARP16	54956	hgsc.bcm.edu	37	chr15	65559101	65559101	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ccagtcagcttttggatcttTtcaaacttgaaaacatgaag	7	8	3	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr15:65559101T>A	ENST00000261888.6	-	3	763	c.318A>T	c.(316-318)gaA>gaT	p.E106D	PARP16_ENST00000444347.2_Intron|PARP16_ENST00000558873.1_5'UTR	NM_017851.4	NP_060321.3	Q8N5Y8	PAR16_HUMAN	poly (ADP-ribose) polymerase family, member 16	106	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell death (GO:0060548)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum tubular network (GO:0071782)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	kinase binding (GO:0019900)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|protein serine/threonine kinase activator activity (GO:0043539)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						TTTGGATCTTTTCAAACTTGA	0.443																																					p.E106D	NSCLC(50;885 1163 13509 21242 41978)	Atlas-SNP	.											.	PARP16	23	.	0			c.A318T						.						44	45	44					15																	65559101		2201	4299	6500	SO:0001583	missense	54956	exon3			GATCTTTTCAAAC	AK000516	CCDS10204.1	15q22.2	2010-02-16	2004-08-25	2004-08-25	ENSG00000138617	ENSG00000138617		"Poly (ADP-ribose) polymerases"	26040	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 30"	C15orf30		15273990	Standard	NM_017851		Approved	FLJ20509, FLJ25281, pART15	uc002aoq.3	Q8N5Y8	OTTHUMG00000133138	ENST00000261888.6:c.318A>T	chr15.hg19:g.65559101T>A	ENSP00000261888:p.Glu106Asp	96.0	0.0		147.0	58.0	NM_017851	Q6PK64|Q9NX03	Missense_Mutation	SNP	ENST00000261888.6	hg19	CCDS10204.1	.	.	.	.	.	.	.	.	.	.	T	10.65	1.409134	0.25378	.	.	ENSG00000138617	ENST00000261888	T	0.14893	2.47	5.58	1.81	0.25067	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.295240	0.37348	N	0.002132	T	0.06826	0.0174	N	0.11313	0.125	0.80722	D	1	B;B	0.16166	0.012;0.016	B;B	0.20955	0.019;0.032	T	0.25847	-1.0120	10	0.23891	T	0.37	-19.2437	3.0532	0.06175	0.0:0.337:0.2388:0.4242	.	106;106	Q8N5Y8-3;Q8N5Y8	.;PAR16_HUMAN	D	106	ENSP00000261888:E106D	ENSP00000261888:E106D	E	-	3	2	PARP16	63346154	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.805000	0.27112	0.972000	0.38314	0.379000	0.24179	GAA	.	.		0.443	PARP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256827.2	NM_017851		A	65559101	T	A	65559101	3	1	157	1	0	0	0	0	1	0	0	0	11469	1838	64	4	669	4	PARP16	15	65559101	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	11253025	65559101	36972291	95	23925										
DENND4A	10260	hgsc.bcm.edu	37	chr15	66015255	66015255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	acatggcttctttggaagtaTcttccaggctacatttttct	7	9	3	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr15:66015255T>C	ENST00000431932.2	-	12	1727	c.1519A>G	c.(1519-1521)Ata>Gta	p.I507V	DENND4A_ENST00000443035.3_Missense_Mutation_p.I507V	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	507					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						TTTGGAAGTATCTTCCAGGCT	0.323																																					p.I507V		Atlas-SNP	.											.	DENND4A	217	.	0			c.A1519G						.						107	91	96					15																	66015255		1803	4064	5867	SO:0001583	missense	10260	exon12			GAAGTATCTTCCA	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.1519A>G	chr15.hg19:g.66015255T>C	ENSP00000396830:p.Ile507Val	55.0	0.0		92.0	30.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	hg19	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336467	0.60963	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.04970	3.52;3.53	5.12	3.99	0.46301	.	0.198286	0.52532	D	0.000078	T	0.17450	0.0419	L	0.53249	1.67	0.58432	D	0.999995	B;D;D	0.67145	0.006;0.996;0.988	B;D;D	0.77557	0.008;0.99;0.968	T	0.00998	-1.1486	10	0.31617	T	0.26	.	11.1857	0.48655	0.0:0.0733:0.0:0.9267	.	507;507;507	B7Z5Y3;E7EPL3;Q7Z401	.;.;MYCPP_HUMAN	V	507	ENSP00000391167:I507V;ENSP00000396830:I507V	ENSP00000396830:I507V	I	-	1	0	DENND4A	63802309	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.767000	0.47637	0.881000	0.35993	0.533000	0.62120	ATA	.	.		0.323	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		C	66015255	T	C	66015255	3	2	157	1	0	0	0	0	1	0	0	0	4435	1435	50	2	4289	2	DENND4A	15	66015255	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	456154	66015255	36516137	96	23926										
MAN2C1	4123	hgsc.bcm.edu	37	chr15	75660501	75660501	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gtctctccggcgtcaggaagCtggagagcacagccacaggg	15	12	2	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr15:75660501C>A	ENST00000267978.5	-	2	186	c.140G>T	c.(139-141)aGc>aTc	p.S47I	MAN2C1_ENST00000565683.1_Missense_Mutation_p.S47I|MAN2C1_ENST00000563622.1_Missense_Mutation_p.S47I|MAN2C1_ENST00000569482.1_Missense_Mutation_p.S47I|MAN2C1_ENST00000563539.1_5'UTR|RP11-817O13.8_ENST00000563278.1_lincRNA	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	47					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						CGTCAGGAAGCTGGAGAGCAC	0.701																																					p.S47I		Atlas-SNP	.											.	MAN2C1	76	.	0			c.G140T						.						8	11	10					15																	75660501		2147	4226	6373	SO:0001583	missense	4123	exon2			AGGAAGCTGGAGA	AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.140G>T	chr15.hg19:g.75660501C>A	ENSP00000267978:p.Ser47Ile	93.0	0.0		141.0	69.0	NM_001256494	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Missense_Mutation	SNP	ENST00000267978.5	hg19	CCDS32298.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.474139	0.26423	.	.	ENSG00000140400	ENST00000267978;ENST00000421803	T	0.16743	2.32	5.11	4.19	0.49359	.	0.331114	0.32868	N	0.005545	T	0.08447	0.0210	N	0.14661	0.345	0.33651	D	0.608456	B;B;B	0.28470	0.213;0.212;0.136	B;B;B	0.26202	0.067;0.03;0.03	T	0.17471	-1.0368	10	0.22706	T	0.39	-14.3641	6.8949	0.24251	0.0:0.8067:0.0:0.1933	.	47;47;47	B4DH23;Q68EM8;Q9NTJ4	.;.;MA2C1_HUMAN	I	47	ENSP00000267978:S47I	ENSP00000267978:S47I	S	-	2	0	MAN2C1	73447554	1.000000	0.71417	0.995000	0.50966	0.221000	0.24807	1.150000	0.31639	2.366000	0.80165	0.491000	0.48974	AGC	.	.		0.701	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1			A	75660501	C	A	75660501	3	1	157	1	0	0	0	0	1	0	0	0	9227	797	28	3	3082	3	MAN2C1	15	75660501	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	9645246	75660501	26870891	97	23927										
CHSY1	22856	hgsc.bcm.edu	37	chr15	101718463	101718463	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gggagctgaaaggggacgagCttcttcagggagtttgagag	18	5	2	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr15:101718463C>G	ENST00000254190.3	-	3	2014	c.1539G>C	c.(1537-1539)aaG>aaC	p.K513N	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	513					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AGGGGACGAGCTTCTTCAGGG	0.468																																					p.K513N		Atlas-SNP	.											.	CHSY1	60	.	0			c.G1539C						.						92	98	96					15																	101718463		2203	4300	6503	SO:0001583	missense	22856	exon3			GACGAGCTTCTTC	AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	17198	protein-coding gene	gene with protein product		608183	"carbohydrate (chondroitin) synthase 1"			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.1539G>C	chr15.hg19:g.101718463C>G	ENSP00000254190:p.Lys513Asn	42.0	0.0		76.0	44.0	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Missense_Mutation	SNP	ENST00000254190.3	hg19	CCDS10390.1	.	.	.	.	.	.	.	.	.	.	C	2.634	-0.285615	0.05605	.	.	ENSG00000131873	ENST00000254190;ENST00000543813	T	0.35236	1.32	5.8	3.93	0.45458	.	0.196582	0.49916	N	0.000131	T	0.18551	0.0445	N	0.02916	-0.46	0.38310	D	0.943234	B	0.28470	0.213	B	0.35770	0.21	T	0.12116	-1.0560	10	0.17369	T	0.5	-44.7939	12.4709	0.55785	0.0:0.865:0.0:0.135	.	513	Q86X52	CHSS1_HUMAN	N	513;241	ENSP00000254190:K513N	ENSP00000254190:K513N	K	-	3	2	CHSY1	99535986	1.000000	0.71417	0.995000	0.50966	0.344000	0.29017	3.871000	0.56077	0.798000	0.33994	0.655000	0.94253	AAG	.	.		0.468	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918		G	101718463	C	G	101718463	3	3	157	1	0	0	0	0	1	0	0	0	3414	796	28	4	873	4	CHSY1	15	101718463	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	26057962	101718463	812929	98	23928										
MVP	9961	hgsc.bcm.edu	37	chr16	29859235	29859235	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gccagtgggcccagccctggGgaggggatatccccccagtc	15	15	0	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr16:29859235G>T	ENST00000357402.5	+	15	2745	c.2607G>T	c.(2605-2607)ggG>ggT	p.G869G	MVP_ENST00000395353.1_Silent_p.G869G	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	869					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						CCAGCCCTGGGGAGGGGATAT	0.612																																					p.G869G		Atlas-SNP	.											.	MVP	80	.	0			c.G2607T						.						50	53	52					16																	29859235		2197	4300	6497	SO:0001819	synonymous_variant	9961	exon15			CCCTGGGGAGGGG	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"lung resistance-related protein"	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.2607G>T	chr16.hg19:g.29859235G>T		62.0	0.0		100.0	40.0	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Silent	SNP	ENST00000357402.5	hg19	CCDS10656.1																																																																																			.	.		0.612	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115		T	29859235	G	T	29859235	2	4	157	1	0	0	0	0	0	0	0	1	10005	1219	43	3		3	MVP	16	29859235	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10		29859235	60495518	99	23929										
CYBA	1535	hgsc.bcm.edu	37	chr16	88713512	88713512	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	agcaggaggagactcaccagCgctccatggtggagcccttc	13	13	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr16:88713512C>T	ENST00000261623.3	-	3	338	c.200G>A	c.(199-201)cGc>cAc	p.R67H	CYBA_ENST00000567174.1_Missense_Mutation_p.R67H|CYBA_ENST00000561972.1_5'Flank|CYBA_ENST00000569359.1_Missense_Mutation_p.R67H	NM_000101.3	NP_000092.2	P13498	CY24A_HUMAN	cytochrome b-245, alpha polypeptide	67					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to amino acid stimulus (GO:0071230)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|cytochrome complex assembly (GO:0017004)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|negative regulation of glomerular filtration by angiotensin (GO:0003106)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of cell growth (GO:0030307)|positive regulation of endothelial cell proliferation (GO:0001938)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|response to nutrient levels (GO:0031667)|smooth muscle hypertrophy (GO:0014895)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|secretory granule (GO:0030141)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)			endometrium(1)|liver(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0478)	Dextromethorphan(DB00514)	GACTCACCAGCGCTCCATGGT	0.642																																					p.R67H		Atlas-SNP	.											.	CYBA	12	.	0			c.G200A						.						34	30	32					16																	88713512		2198	4300	6498	SO:0001583	missense	1535	exon3			CACCAGCGCTCCA		CCDS32504.1	16q24	2014-09-17				ENSG00000051523		"Cytochrome b genes"	2577	protein-coding gene	gene with protein product	"flavocytochrome b-558 alpha polypeptide"	608508				2243141	Standard	NM_000101		Approved	p22-PHOX	uc002flb.4	P13498		ENST00000261623.3:c.200G>A	chr16.hg19:g.88713512C>T	ENSP00000261623:p.Arg67His	27.0	0.0		18.0	12.0	NM_000101	Q14090|Q9BR72	Missense_Mutation	SNP	ENST00000261623.3	hg19	CCDS32504.1	.	.	.	.	.	.	.	.	.	.	C	32	5.135334	0.94517	.	.	ENSG00000051523	ENST00000261623	D	0.90324	-2.65	4.61	4.61	0.57282	.	0.107163	0.64402	D	0.000018	D	0.95494	0.8536	M	0.84433	2.695	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.96249	0.9182	10	0.87932	D	0	.	15.1962	0.73092	0.0:1.0:0.0:0.0	.	3;67	B4DT46;P13498	.;CY24A_HUMAN	H	67	ENSP00000261623:R67H	ENSP00000261623:R67H	R	-	2	0	CYBA	87241013	1.000000	0.71417	0.993000	0.49108	0.960000	0.62799	5.657000	0.67996	2.107000	0.64212	0.549000	0.68633	CGC	.	.		0.642	CYBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422765.1	NM_000101		T	88713512	C	T	88713512	3	4	157	1	0	0	0	0	1	0	0	0	4133	768	27	1	403	1	CYBA	16	88713512	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	58854277	88713512	1641241	100	23930										
TRPV3	162514	hgsc.bcm.edu	37	chr17	3417211	3417211	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	accagctctgggttccgcttCtacaccgaggtttccgggaa	11	13	2	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr17:3417211C>T	ENST00000576742.1	-	18	2694	c.2373G>A	c.(2371-2373)taG>taA	p.*791*	TRPV3_ENST00000301365.4_Silent_p.*792*|SPATA22_ENST00000541913.1_5'Flank	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	0					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	GGTTCCGCTTCTACACCGAGG	0.537																																					p.X792X		Atlas-SNP	.											.	TRPV3	85	.	0			c.G2376A						.						113	102	106					17																	3417211		2203	4300	6503	SO:0001819	synonymous_variant	162514	exon18			CCGCTTCTACACC	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.2373G>A	chr17.hg19:g.3417211C>T		51.0	0.0		50.0	41.0	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Silent	SNP	ENST00000576742.1	hg19	CCDS11029.1																																																																																			.	.		0.537	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		T	3417211	C	T	3417211	2	4	157	1	0	0	0	0	0	0	0	1	16612	924	32	3		3	TRPV3	17	3417211	Silent	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10		3417211	77777999	101	23931										
ANKFY1	51479	hgsc.bcm.edu	37	chr17	4111281	4111281	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cacgtcttctctctccacttTgatggctttatgtagcgggt	9	11	3	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr17:4111281T>C	ENST00000341657.4	-	6	714	c.679A>G	c.(679-681)Aaa>Gaa	p.K227E	ANKFY1_ENST00000433651.1_Missense_Mutation_p.K227E|ANKFY1_ENST00000570535.1_Missense_Mutation_p.K269E|ANKFY1_ENST00000574367.1_Missense_Mutation_p.K227E	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	227					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CTCTCCACTTTGATGGCTTTA	0.448																																					p.K269E		Atlas-SNP	.											.	ANKFY1	81	.	0			c.A805G						.						196	186	189					17																	4111281		1918	4132	6050	SO:0001583	missense	51479	exon6			CCACTTTGATGGC	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"Zinc fingers, FYVE domain containing", "BTB/POZ domain containing", "Ankyrin repeat domain containing"	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.679A>G	chr17.hg19:g.4111281T>C	ENSP00000343362:p.Lys227Glu	67.0	0.0		65.0	44.0	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	hg19		.	.	.	.	.	.	.	.	.	.	T	16.95	3.264619	0.59431	.	.	ENSG00000185722	ENST00000341657;ENST00000535427;ENST00000433651	T;T	0.53423	0.62;0.66	5.58	4.43	0.53597	Ankyrin repeat-containing domain (3);	0.116434	0.64402	D	0.000020	T	0.28896	0.0717	N	0.12502	0.225	0.54753	D	0.999987	P;P;B;B;B	0.39480	0.675;0.622;0.01;0.185;0.288	B;B;B;B;B	0.36666	0.23;0.164;0.006;0.05;0.079	T	0.11591	-1.0581	10	0.32370	T	0.25	-20.6206	13.2594	0.60097	0.0:0.0:0.1409:0.8591	.	168;227;227;227;269	F5H754;Q9P2R3-3;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;.;ANFY1_HUMAN;.;.	E	227;168;227	ENSP00000343362:K227E;ENSP00000416005:K227E	ENSP00000343362:K227E	K	-	1	0	ANKFY1	4058030	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.151000	0.71806	2.131000	0.65755	0.533000	0.62120	AAA	.	.		0.448	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		C	4111281	T	C	4111281	3	2	157	1	0	0	0	0	1	0	0	0	626	1821	63	2	3005	2	ANKFY1	17	4111281	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	694070	4111281	77083929	102	23932										
TP53	7157	hgsc.bcm.edu	37	chr17	7578477	7578504	+	Frame_Shift_Del	DEL	GGGTGTGGAATCAACCCACAGCTGCACA	GGGTGTGGAATCAACCCACAGCTGCACA	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cggacgcgggtgccgggcggGggtgtggaatcaacccacag					rs587782197|rs28934874|rs137852790|rs137852791|rs587782620		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	GGGTGTGGAATCAACCCACAGCTGCACA	GGGTGTGGAATCAACCCACAGCTGCACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr17:7578477_7578504delGGGTGTGGAATCAACCCACAGCTGCACA	ENST00000269305.4	-	5	615_642	c.426_453delTGTGCAGCTGTGGGTTGATTCCACACCC	c.(424-453)cctgtgcagctgtgggttgattccacacccfs	p.PVQLWVDSTP142fs	TP53_ENST00000359597.4_Frame_Shift_Del_p.PVQLWVDSTP142fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.PVQLWVDSTP142fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.PVQLWVDSTP142fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Del_p.PVQLWVDSTP142fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.PVQLWVDSTP142fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	142	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> R (in a sporadic cancer; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.W146*(72)|p.P151S(68)|p.Q144*(36)|p.P151H(31)|p.V143M(19)|p.V143A(18)|p.L145Q(17)|p.L145P(17)|p.P151T(16)|p.P151A(13)|p.P151P(12)|p.P152fs*18(11)|p.P151R(9)|p.L145L(8)|p.Q144L(8)|p.0?(8)|p.L145R(7)|p.P151fs*30(7)|p.P151L(7)|p.T150fs*16(6)|p.S149F(6)|p.S149S(6)|p.V147G(6)|p.V147I(6)|p.P152fs*29(5)|p.V143E(5)|p.V147fs*23(5)|p.?(5)|p.W146R(5)|p.S149fs*32(5)|p.V147D(5)|p.V143L(4)|p.T150I(4)|p.Q144H(4)|p.D148E(4)|p.D148N(4)|p.Q144R(4)|p.Q144P(4)|p.S149P(4)|p.W146S(4)|p.W14*(3)|p.W53*(3)|p.Q144fs*25(3)|p.Q144fs*26(3)|p.S149fs*21(3)|p.P142P(3)|p.V147V(3)|p.Q12*(2)|p.V143fs*27(2)|p.D148fs*33(2)|p.P152fs*28(2)|p.P58H(2)|p.P58S(2)|p.V143V(2)|p.Q51*(2)|p.Q144del(2)|p.V11A(2)|p.Q144K(2)|p.V50A(2)|p.L145V(2)|p.D148V(2)|p.Q144Q(2)|p.S149T(2)|p.P58A(2)|p.D148fs*23(2)|p.D148fs*22(2)|p.W146C(2)|p.V147A(2)|p.P19S(2)|p.P19H(2)|p.P19A(2)|p.L137_W146del10(1)|p.V143fs*29(1)|p.D148fs*34(1)|p.D148fs*32(1)|p.L145del(1)|p.W146fs*25(1)|p.W146fs*22(1)|p.W146fs*23(1)|p.W146fs*1(1)|p.W14S(1)|p.P58T(1)|p.P58R(1)|p.Q144_G154del11(1)|p.W146_V147insXXXXXXX(1)|p.Q144fs*32(1)|p.T150fs*31(1)|p.T150fs*23(1)|p.W53S(1)|p.T57fs*16(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.Q51fs*25(1)|p.P152del(1)|p.V143G(1)|p.S149fs*72(1)|p.Q144fs*16(1)|p.L145M(1)|p.V11M(1)|p.K139fs*4(1)|p.C141fs*5(1)|p.P152_P153del(1)|p.T150R(1)|p.V50M(1)|p.T150K(1)|p.P151del(1)|p.W146_S149>C(1)|p.D148del(1)|p.S149fs*17(1)|p.V143_S149del(1)|p.P152fs*14(1)|p.T150_P151delTP(1)|p.Q144fs*4(1)|p.P142_Q144delPVQ(1)|p.P153fs*16(1)|p.D148Y(1)|p.P151_V173del23(1)|p.D148D(1)|p.D148H(1)|p.A138_V143delAKTCPV(1)|p.P153fs*28(1)|p.S149fs*31(1)|p.W146G(1)|p.V147E(1)|p.V147F(1)|p.P19R(1)|p.P19T(1)|p.T18fs*16(1)|p.D148*(1)|p.Q12fs*25(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCT	0.588		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.143_152del	Pancreas(47;798 1329 9957 10801)	Atlas-INDEL	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,+1,1	TP53	33396	.	613	Substitution - Missense(344)|Substitution - Nonsense(119)|Deletion - Frameshift(55)|Substitution - coding silent(37)|Insertion - Frameshift(26)|Deletion - In frame(16)|Whole gene deletion(8)|Unknown(5)|Complex - frameshift(1)|Complex - deletion inframe(1)|Insertion - In frame(1)	large_intestine(84)|lung(72)|upper_aerodigestive_tract(69)|breast(57)|oesophagus(48)|haematopoietic_and_lymphoid_tissue(45)|ovary(41)|stomach(31)|urinary_tract(28)|endometrium(22)|central_nervous_system(20)|liver(19)|skin(16)|prostate(16)|soft_tissue(11)|pancreas(10)|biliary_tract(8)|bone(5)|vulva(4)|thyroid(2)|salivary_gland(2)|pleura(1)|peritoneum(1)|cervix(1)	c.427_454del	GRCh37	CD044990|CM012662|CM023462|CM941326	TP53	D|M	rs28934874	.																																			SO:0001589	frameshift_variant	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.426_453delTGTGCAGCTGTGGGTTGATTCCACACCC	chr17.hg19:g.7578477_7578504delGGGTGTGGAATCAACCCACAGCTGCACA	ENSP00000269305:p.Pro142fs	105.0	0.0		50.0	17.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.588	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7578504	GGGTGTGGAATCAACCCACAGCTGCACA	-	7578477	7	5	157	1	0	1	0	1	0	0	0	0	16396	1219	43	0	845	0	TP53	17	7578477	Frame_Shift_Del	DEL	GGGTGTGGAATCAACCCACAGCTGCACA	TCGA-DD-AACF-01A-11D-A40R-10	3467196	7578477	73616733	103	23933										
MYH4	4622	hgsc.bcm.edu	37	chr17	10350423	10350423	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gtccgttccagggatgccctGagctcttcaacttcagcctg	10	14	3	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr17:10350423G>T	ENST00000255381.2	-	35	5186	c.5076C>A	c.(5074-5076)ctC>ctA	p.L1692L	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1692					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						GGGATGCCCTGAGCTCTTCAA	0.517																																					p.L1692L		Atlas-SNP	.											.	MYH4	349	.	0			c.C5076A						.						174	138	150					17																	10350423		2203	4300	6503	SO:0001819	synonymous_variant	4622	exon35			TGCCCTGAGCTCT		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.5076C>A	chr17.hg19:g.10350423G>T		55.0	0.0		81.0	35.0	NM_017533		Silent	SNP	ENST00000255381.2	hg19	CCDS11154.1																																																																																			.	.		0.517	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10350423	G	T	10350423	2	4	157	1	0	0	0	0	0	0	0	1	10046	1277	45	3		3	MYH4	17	10350423	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	2771946	10350423	70844787	104	23934										
MYH4	4622	hgsc.bcm.edu	37	chr17	10363541	10363541	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tgctgcacagtctggcctttGgttacgaactcattgccgac	10	12	2	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr17:10363541G>T	ENST00000255381.2	-	13	1355	c.1245C>A	c.(1243-1245)acC>acA	p.T415T	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	415	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						TCTGGCCTTTGGTTACGAACT	0.428																																					p.T415T		Atlas-SNP	.											.	MYH4	349	.	0			c.C1245A						.						122	111	115					17																	10363541		2203	4300	6503	SO:0001819	synonymous_variant	4622	exon13			GCCTTTGGTTACG		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.1245C>A	chr17.hg19:g.10363541G>T		104.0	0.0		169.0	69.0	NM_017533		Silent	SNP	ENST00000255381.2	hg19	CCDS11154.1																																																																																			.	.		0.428	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10363541	G	T	10363541	2	4	157	1	0	0	0	0	0	0	0	1	10046	1335	47	3		3	MYH4	17	10363541	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	13118	10363541	70831669	105	23935										
SAMD14	201191	hgsc.bcm.edu	37	chr17	48194991	48194991	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aggcagaaagagcccccggcCggggaccccgggcctgagtg	17	14	0	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr17:48194991C>A	ENST00000330175.4	-	4	596	c.279G>T	c.(277-279)ccG>ccT	p.P93P	SAMD14_ENST00000503131.1_Silent_p.P93P|SAMD14_ENST00000503734.1_5'UTR	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	93										breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						AGCCCCCGGCCGGGGACCCCG	0.741																																					p.P93P		Atlas-SNP	.											.	SAMD14	36	.	0			c.G279T						.						4	5	5					17																	48194991		1561	3449	5010	SO:0001819	synonymous_variant	201191	exon4			CCCGGCCGGGGAC		CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"Sterile alpha motif (SAM) domain containing"	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.279G>T	chr17.hg19:g.48194991C>A		51.0	0.0		80.0	31.0	NM_001257359	A5D8V1|Q8N2X0	Silent	SNP	ENST00000330175.4	hg19	CCDS58562.1																																																																																			.	.		0.741	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920		A	48194991	C	A	48194991	2	1	157	1	0	0	0	0	0	0	0	1	13834	639	23	1		1	SAMD14	17	48194991	Silent	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	37831450	48194991	33000219	106	23936										
YES1	7525	hgsc.bcm.edu	37	chr18	743374	743375	+	Frame_Shift_Del	DEL	GA	GA	-													0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	agtctgaggtttcacagttgGacacacagttgtcaacttgt							TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr18:743374_743375delGA	ENST00000584307.1	-	7	935_936	c.765_766delTC	c.(763-768)tgtccafs	p.P256fs	YES1_ENST00000314574.4_Frame_Shift_Del_p.P256fs|YES1_ENST00000577961.1_Frame_Shift_Del_p.P261fs			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	256					blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glucose transport (GO:0015758)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|regulation of vascular permeability (GO:0043114)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)	17					Dasatinib(DB01254)	TTCACAGTTGGACACACAGTTG	0.386																																					p.256_256del		Atlas-INDEL	.											.	YES1	50	.	0			c.766_767del						.																																			SO:0001589	frameshift_variant	7525	exon7			.	M15990	CCDS11824.1	18p11.31-p11.21	2014-06-26	2014-06-26		ENSG00000176105	ENSG00000176105		"SH2 domain containing"	12841	protein-coding gene	gene with protein product		164880	"v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1"			2983418	Standard	NM_005433		Approved	Yes, c-yes, HsT441	uc002kky.3	P07947	OTTHUMG00000131472	ENST00000584307.1:c.765_766delTC	chr18.hg19:g.743374_743375delGA	ENSP00000462468:p.Pro256fs	53.0	0.0		121.0	72.0	NM_005433	A6NLB3|D3DUH1	Frame_Shift_Del	DEL	ENST00000584307.1	hg19	CCDS11824.1																																																																																			.	.		0.386	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440827.2	NM_005433		-	743375	GA	-	743374	7	5	157	1	0	1	0	1	0	0	0	0	17489	1174	41	0	889	0	YES1	18	743374	Frame_Shift_Del	DEL	GA	TCGA-DD-AACF-01A-11D-A40R-10		743374	77333874	107	23937										
FBN3	84467	hgsc.bcm.edu	37	chr19	8196466	8196466	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ttggcaggacaaagctggcaGggctccccaaaaccgtggtc	13	12	0	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr19:8196466G>A	ENST00000600128.1	-	15	2376	c.1962C>T	c.(1960-1962)ccC>ccT	p.P654P	FBN3_ENST00000270509.2_Silent_p.P654P|FBN3_ENST00000601739.1_Silent_p.P654P			Q75N90	FBN3_HUMAN	fibrillin 3	654	TB 3.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						AAAGCTGGCAGGGCTCCCCAA	0.637																																					p.P654P		Atlas-SNP	.											.	FBN3	300	.	0			c.C1962T						.						58	63	61					19																	8196466		2203	4300	6503	SO:0001819	synonymous_variant	84467	exon14			CTGGCAGGGCTCC		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.1962C>T	chr19.hg19:g.8196466G>A		99.0	0.0		128.0	44.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	hg19	CCDS12196.1																																																																																			.	.		0.637	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8196466	G	A	8196466	2	1	157	1	0	0	0	0	0	0	0	1	5712	987	35	3		3	FBN3	19	8196466	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10		8196466	50932517	108	23938										
MUC16	94025	hgsc.bcm.edu	37	chr19	9083169	9083169	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gtagactgtgggatcccccaAgttgggggagctgtagtcag	16	8	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr19:9083169A>T	ENST00000397910.4	-	1	8849	c.8646T>A	c.(8644-8646)acT>acA	p.T2882T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2883	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGATCCCCCAAGTTGGGGGAG	0.527																																					p.T2882T		Atlas-SNP	.											.	MUC16	4315	.	0			c.T8646A						.						63	59	60					19																	9083169		1918	4137	6055	SO:0001819	synonymous_variant	94025	exon1			CCCCCAAGTTGGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8646T>A	chr19.hg19:g.9083169A>T		147.0	0.0		212.0	97.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9083169	A	T	9083169	2	4	157	1	0	0	0	0	0	0	0	1	9982	59	3	4		4	MUC16	19	9083169	Silent	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	886703	9083169	50045814	109	23939										
BEST2	54831	hgsc.bcm.edu	37	chr19	12865364	12865364	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cccattccccgctcccctgcAggcttttatgtgacgctggt	9	16	0	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr19:12865364A>G	ENST00000549706.1	+	4	571		c.e4-1		BEST2_ENST00000042931.1_Splice_Site|BEST2_ENST00000553030.1_Splice_Site			Q8NFU1	BEST2_HUMAN	bestrophin 2						chloride transmembrane transport (GO:1902476)|membrane depolarization (GO:0051899)|sensory perception of smell (GO:0007608)	chloride channel complex (GO:0034707)|cilium (GO:0005929)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	12						GCTCCCCTGCAGGCTTTTATG	0.662																																					.		Atlas-SNP	.											.	BEST2	35	.	0			c.248-2A>G						.						13	13	13					19																	12865364		1979	4160	6139	SO:0001630	splice_region_variant	54831	exon3			CCCTGCAGGCTTT	AF440756	CCDS42506.1	19p13.13	2014-08-12	2006-10-18	2006-10-18	ENSG00000039987	ENSG00000039987		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17107	protein-coding gene	gene with protein product		607335	"vitelliform macular dystrophy 2-like 1"	VMD2L1		12032738, 16912113	Standard	NM_017682		Approved	FLJ20132	uc002mux.3	Q8NFU1	OTTHUMG00000169293	ENST00000549706.1:c.248-1A>G	chr19.hg19:g.12865364A>G		40.0	0.0		65.0	29.0	NM_017682	Q53YQ8|Q9NXP0	Splice_Site	SNP	ENST00000549706.1	hg19	CCDS42506.1	.	.	.	.	.	.	.	.	.	.	A	10.77	1.445309	0.25987	.	.	ENSG00000039987	ENST00000549706;ENST00000553030;ENST00000042931	.	.	.	4.41	4.41	0.53225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9116	0.58182	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BEST2	12726364	1.000000	0.71417	0.998000	0.56505	0.061000	0.15899	9.143000	0.94623	1.763000	0.52060	0.379000	0.24179	.	.	.		0.662	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682	Intron	G	12865364	A	G	12865364	5	3	157	1	0	0	0	0	0	0	1	0	1405	202	7	2	256	2	BEST2	19	12865364	Splice_Site	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	3782195	12865364	46263619	110	23940										
UNC13A	23025	hgsc.bcm.edu	37	chr19	17738725	17738725	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cagctgaactcgtagctgttGagtgttattcatgagaatgc	11	7	1	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr19:17738725G>T	ENST00000519716.2	-	32	3777	c.3778C>A	c.(3778-3780)Caa>Aaa	p.Q1260K	UNC13A_ENST00000428389.2_Missense_Mutation_p.Q1348K|UNC13A_ENST00000252773.7_Missense_Mutation_p.Q1260K|UNC13A_ENST00000550896.1_Missense_Mutation_p.Q1258K|UNC13A_ENST00000552293.1_Missense_Mutation_p.Q1260K|UNC13A_ENST00000551649.1_Missense_Mutation_p.Q1260K	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1260					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CGTAGCTGTTGAGTGTTATTC	0.612																																					p.Q1260K		Atlas-SNP	.											UNC13A_ENST00000519716,NS,carcinoma,0,2	UNC13A	299	.	0			c.C3778A						.						647	577	600					19																	17738725		2012	4180	6192	SO:0001583	missense	23025	exon31			GCTGTTGAGTGTT	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.3778C>A	chr19.hg19:g.17738725G>T	ENSP00000429562:p.Gln1260Lys	19.0	0.0		29.0	11.0	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	18.03	3.533519	0.64972	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91;-0.91;-0.91	3.68	3.68	0.42216	.	0.140928	0.48767	U	0.000165	T	0.79724	0.4495	M	0.82630	2.6	0.53005	D	0.999965	P	0.51653	0.947	P	0.48089	0.566	D	0.84046	0.0367	10	0.87932	D	0	.	12.9701	0.58508	0.0:0.0:1.0:0.0	.	1260	Q9UPW8	UN13A_HUMAN	K	1260;1348;1260;1260;1260;1258	ENSP00000429562:Q1260K;ENSP00000400409:Q1348K;ENSP00000252773:Q1260K;ENSP00000447236:Q1260K;ENSP00000447572:Q1260K;ENSP00000446831:Q1258K	ENSP00000252773:Q1260K	Q	-	1	0	UNC13A	17599725	1.000000	0.71417	1.000000	0.80357	0.536000	0.34869	9.633000	0.98432	1.616000	0.50265	0.306000	0.20318	CAA	.	.		0.612	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17738725	G	T	17738725	3	4	157	1	0	0	0	0	1	0	0	0	16999	1299	45	3	1381	3	UNC13A	19	17738725	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	4873361	17738725	41390258	111	23941										
FCHO1	23149	hgsc.bcm.edu	37	chr19	17883504	17883504	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aacgtcagcgtggagatgctActcaggaagtttgcagagag	14	7	2	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr19:17883504A>G	ENST00000596536.1	+	11	1027	c.744A>G	c.(742-744)ctA>ctG	p.L248L	FCHO1_ENST00000600676.1_Silent_p.L248L|FCHO1_ENST00000595033.1_Silent_p.L198L|FCHO1_ENST00000594202.1_Silent_p.L248L|FCHO1_ENST00000389133.4_Silent_p.L248L|FCHO1_ENST00000596951.1_Silent_p.L248L|FCHO1_ENST00000252771.7_Silent_p.L248L|FCHO1_ENST00000597512.1_Silent_p.L255L|FCHO1_ENST00000539407.1_Silent_p.L248L	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	248	Mediates membrane-binding.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						TGGAGATGCTACTCAGGAAGT	0.607																																					p.L248L		Atlas-SNP	.											.	FCHO1	69	.	0			c.A744G						.						103	91	95					19																	17883504		2203	4300	6503	SO:0001819	synonymous_variant	23149	exon10			GATGCTACTCAGG	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.744A>G	chr19.hg19:g.17883504A>G		93.0	0.0		128.0	47.0	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Silent	SNP	ENST00000596536.1	hg19	CCDS32955.1																																																																																			.	.		0.607	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122		G	17883504	A	G	17883504	2	3	157	1	0	0	0	0	0	0	0	1	5795	378	14	2		2	FCHO1	19	17883504	Silent	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	144779	17883504	41245479	112	23942										
HKR1	284459	hgsc.bcm.edu	37	chr19	37853629	37853629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ggaatgtgggcgaggctttaCgtggaagtcaaacctgatca	14	7	2	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr19:37853629C>T	ENST00000324411.4	+	6	1201	c.932C>T	c.(931-933)aCg>aTg	p.T311M	HKR1_ENST00000591134.1_Intron|HKR1_ENST00000392153.3_Missense_Mutation_p.T292M|HKR1_ENST00000541583.2_Missense_Mutation_p.T250M|HKR1_ENST00000544914.1_Missense_Mutation_p.T38M|HKR1_ENST00000591471.1_Missense_Mutation_p.T38M|HKR1_ENST00000589392.1_Missense_Mutation_p.T293M	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	311					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CGAGGCTTTACGTGGAAGTCA	0.507																																					p.T311M		Atlas-SNP	.											.	HKR1	74	.	0			c.C932T						.						99	92	94					19																	37853629		2203	4300	6503	SO:0001583	missense	284459	exon6			GCTTTACGTGGAA	M20675	CCDS12502.1	19q13.13	2013-01-08	2010-05-04			ENSG00000181666		"Zinc fingers, C2H2-type", "-"	4928	protein-coding gene	gene with protein product	"oncogene HKR1"	165250	"GLI-Kruppel family member HKR1"			2850480, 9813242	Standard	NM_181786		Approved	ZNF875	uc002ogb.3	P10072		ENST00000324411.4:c.932C>T	chr19.hg19:g.37853629C>T	ENSP00000315505:p.Thr311Met	98.0	0.0		114.0	48.0	NM_181786	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Missense_Mutation	SNP	ENST00000324411.4	hg19	CCDS12502.1	.	.	.	.	.	.	.	.	.	.	C	13.53	2.263720	0.39995	.	.	ENSG00000181666	ENST00000544914;ENST00000392153;ENST00000542144;ENST00000324411;ENST00000541583	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	3.37	0.927	0.19437	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46268	0.1384	L	0.52759	1.655	0.42482	D	0.992865	D;P;D;D	0.76494	0.999;0.625;0.997;0.997	D;B;D;P	0.67725	0.953;0.119;0.931;0.765	T	0.45160	-0.9280	9	0.72032	D	0.01	-3.7279	7.0879	0.25267	0.3273:0.5229:0.1498:0.0	.	250;292;311;293	Q7Z6E1;P10072-2;P10072;B4DSY3	.;.;HKR1_HUMAN;.	M	38;292;347;311;250	ENSP00000437774:T38M;ENSP00000375994:T292M;ENSP00000315505:T311M;ENSP00000438261:T250M	ENSP00000315505:T311M	T	+	2	0	HKR1	42545469	0.000000	0.05858	0.998000	0.56505	0.995000	0.86356	-3.352000	0.00501	0.710000	0.31997	0.650000	0.86243	ACG	.	.		0.507	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786		T	37853629	C	T	37853629	3	4	157	1	0	0	0	0	1	0	0	0	7203	536	19	1	946	1	HKR1	19	37853629	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	19970125	37853629	21275354	113	23943										
SIRT2	22933	hgsc.bcm.edu	37	chr19	39371780	39371780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aacgcgctgggaggctctcaCcaaaaaagacgatatctgag	11	10	2	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr19:39371780C>T	ENST00000249396.7	-	11	1008	c.707G>A	c.(706-708)gGt>gAt	p.G236D	RINL_ENST00000340740.3_5'Flank|RINL_ENST00000591812.1_5'Flank|SIRT2_ENST00000358931.5_Missense_Mutation_p.G236D|SIRT2_ENST00000392081.2_Missense_Mutation_p.G199D	NM_012237.3	NP_036369.2	Q8IXJ6	SIR2_HUMAN	sirtuin 2	236	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.|Peptide inhibitor binding.				autophagy (GO:0006914)|cellular lipid catabolic process (GO:0044242)|cellular response to caloric restriction (GO:0061433)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to hypoxia (GO:0071456)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to oxidative stress (GO:0034599)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|chromatin silencing at telomere (GO:0006348)|gene silencing (GO:0016458)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|innate immune response (GO:0045087)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|myelination in peripheral nervous system (GO:0022011)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)|negative regulation of defense response to bacterium (GO:1900425)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of oligodendrocyte progenitor proliferation (GO:0070446)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cell division (GO:0051781)|positive regulation of DNA binding (GO:0043388)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of meiosis (GO:0045836)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)|protein kinase B signaling (GO:0043491)|regulation of cell cycle (GO:0051726)|regulation of exit from mitosis (GO:0007096)|regulation of myelination (GO:0031641)|regulation of phosphorylation (GO:0042325)|response to redox state (GO:0051775)|ripoptosome assembly involved in necroptotic process (GO:1901026)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)	centriole (GO:0005814)|centrosome (GO:0005813)|chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|glial cell projection (GO:0097386)|juxtaparanode region of axon (GO:0044224)|lateral loop (GO:0043219)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|myelin sheath (GO:0043209)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|spindle (GO:0005819)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|NAD-dependent protein deacetylase activity (GO:0034979)|protein deacetylase activity (GO:0033558)|transcription factor binding (GO:0008134)|tubulin deacetylase activity (GO:0042903)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(5)|skin(1)	9	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00125)|LUSC - Lung squamous cell carcinoma(53;0.00191)			GAGGCTCTCACCAAAAAAGAC	0.622																																					p.G236D		Atlas-SNP	.											.	SIRT2	29	.	0			c.G707A						.						79	72	74					19																	39371780		2203	4300	6503	SO:0001583	missense	22933	exon11			CTCTCACCAAAAA	AF083107	CCDS12523.1, CCDS46069.1, CCDS74361.1	19q13	2010-06-25	2010-06-25		ENSG00000068903	ENSG00000068903			10886	protein-coding gene	gene with protein product		604480	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 2", "sirtuin (silent mating type information regulation 2 homolog) 2 (S. cerevisiae)"	SIR2L		10393250, 10381378	Standard	NM_012237		Approved		uc002ojt.2	Q8IXJ6	OTTHUMG00000150480	ENST00000249396.7:c.707G>A	chr19.hg19:g.39371780C>T	ENSP00000249396:p.Gly236Asp	115.0	0.0		136.0	18.0	NM_012237	A8K3V1|B2RB45|O95889|Q924Y7|Q9P0G8|Q9UNT0|Q9Y6E9|U5TP13	Missense_Mutation	SNP	ENST00000249396.7	hg19	CCDS12523.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.205605	0.79127	.	.	ENSG00000068903	ENST00000249396;ENST00000392081;ENST00000358931;ENST00000456703;ENST00000414941	T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99	4.96	4.96	0.65561	.	0.126864	0.52532	D	0.000076	D	0.89729	0.6799	M	0.94021	3.485	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.92577	0.6071	10	0.87932	D	0	-11.8713	16.9718	0.86302	0.0:1.0:0.0:0.0	.	236;199;236;216	Q8IXJ6-4;Q8IXJ6-2;Q8IXJ6;Q8IXJ6-3	.;.;SIRT2_HUMAN;.	D	236;199;236;221;199	ENSP00000249396:G236D;ENSP00000375931:G199D;ENSP00000351809:G236D;ENSP00000404309:G199D	ENSP00000249396:G236D	G	-	2	0	SIRT2	44063620	1.000000	0.71417	0.608000	0.28969	0.515000	0.34225	6.598000	0.74122	2.304000	0.77564	0.511000	0.50034	GGT	.	.		0.622	SIRT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318278.1			T	39371780	C	T	39371780	3	4	157	1	0	0	0	0	1	0	0	0	14353	507	18	3	486	3	SIRT2	19	39371780	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	1518151	39371780	19757203	114	23944										
LIPE	3991	hgsc.bcm.edu	37	chr19	42910418	42910418	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	aggctgcagcattgtggccgGgtaggctgccatgatgccat	15	10	0	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr19:42910418G>C	ENST00000244289.4	-	7	2536	c.2260C>G	c.(2260-2262)Ccg>Gcg	p.P754A	LIPE-AS1_ENST00000594624.2_RNA|LIPE_ENST00000602000.1_5'Flank|LIPE-AS1_ENST00000593491.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000599276.1_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	754					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				ATTGTGGCCGGGTAGGCTGCC	0.667																																					p.P754A		Atlas-SNP	.											.	LIPE	83	.	0			c.C2260G						.						49	46	47					19																	42910418		2203	4300	6503	SO:0001583	missense	3991	exon7			TGGCCGGGTAGGC	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2260C>G	chr19.hg19:g.42910418G>C	ENSP00000244289:p.Pro754Ala	63.0	0.0		105.0	42.0	NM_005357	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	hg19	CCDS12607.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.066104	0.76187	.	.	ENSG00000079435	ENST00000244289	T	0.41065	1.01	5.09	5.09	0.68999	Alpha/beta hydrolase fold-3 (1);	0.000000	0.85682	D	0.000000	T	0.65954	0.2741	M	0.81239	2.535	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	T	0.63377	-0.6651	10	0.24483	T	0.36	-33.719	17.6625	0.88196	0.0:0.0:1.0:0.0	.	754	Q05469	LIPS_HUMAN	A	754	ENSP00000244289:P754A	ENSP00000244289:P754A	P	-	1	0	LIPE	47602258	1.000000	0.71417	0.998000	0.56505	0.897000	0.52465	8.497000	0.90488	2.531000	0.85337	0.645000	0.84053	CCG	.	.		0.667	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		C	42910418	G	C	42910418	3	2	157	1	0	0	0	0	1	0	0	0	8830	1232	43	4	986	4	LIPE	19	42910418	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	3538638	42910418	16218565	115	23945										
BAX	581	hgsc.bcm.edu	37	chr19	49464086	49464086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ggccctgtgcaccaaggtgcCggaactgatcagaaccatca	11	13	2	2	rs369660551		TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr19:49464086C>T	ENST00000345358.7	+	5	441	c.389C>T	c.(388-390)cCg>cTg	p.P130L	BAX_ENST00000415969.2_Missense_Mutation_p.P130L|BAX_ENST00000539787.1_Missense_Mutation_p.R163W|BAX_ENST00000391871.3_3'UTR|BAX_ENST00000293288.8_Missense_Mutation_p.P130L|BAX_ENST00000354470.3_Missense_Mutation_p.P81L	NM_138761.3|NM_138764.4	NP_620116.1|NP_620119.2	Q07812	BAX_HUMAN	BCL2-associated X protein	130					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell homeostatic proliferation (GO:0002358)|B cell negative selection (GO:0002352)|B cell receptor apoptotic signaling pathway (GO:1990117)|blood vessel remodeling (GO:0001974)|cellular response to organic substance (GO:0071310)|cellular response to UV (GO:0034644)|cerebral cortex development (GO:0021987)|development of secondary sexual characteristics (GO:0045136)|ectopic germ cell programmed cell death (GO:0035234)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells within a tissue (GO:0048873)|hypothalamus development (GO:0021854)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein binding (GO:0032091)|neuron apoptotic process (GO:0051402)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic DNA fragmentation (GO:1902512)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of developmental pigmentation (GO:0048087)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-embryonic camera-type eye morphogenesis (GO:0048597)|protein homooligomerization (GO:0051260)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)|protein oligomerization (GO:0051259)|regulation of cell cycle (GO:0051726)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|release of matrix enzymes from mitochondria (GO:0032976)|response to axon injury (GO:0048678)|response to gamma radiation (GO:0010332)|response to salt stress (GO:0009651)|response to toxic substance (GO:0009636)|retina development in camera-type eye (GO:0060041)|retinal cell apoptotic process (GO:1990009)|retinal cell programmed cell death (GO:0046666)|Sertoli cell proliferation (GO:0060011)|spermatid differentiation (GO:0048515)|T cell homeostatic proliferation (GO:0001777)|thymocyte apoptotic process (GO:0070242)|transformed cell apoptotic process (GO:0006927)|vagina development (GO:0060068)|viral process (GO:0016032)	BAX complex (GO:0097144)|Bcl-2 family protein complex (GO:0097136)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrial permeability transition pore complex (GO:0005757)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(4)	17		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)		ACCAAGGTGCCGGAACTGATC	0.592																																					p.P130L		Atlas-SNP	.											.	BAX	69	.	0			c.C389T						.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	110	95	100		389,389,242,389	2	0.9	19		100	0,8600		0,0,4300	no	missense,missense,missense,missense	BAX	NM_004324.3,NM_138761.3,NM_138763.3,NM_138764.4	98,98,98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	130/219,130/193,81/144,130/180	49464086	1,13005	2203	4300	6503	SO:0001583	missense	581	exon5			AGGTGCCGGAACT		CCDS12742.1, CCDS12743.1, CCDS12744.1, CCDS12745.1, CCDS12745.2	19q13.3-q13.4	2014-03-07			ENSG00000087088	ENSG00000087088			959	protein-coding gene	gene with protein product		600040				8358790	Standard	NM_138761		Approved	BCL2L4	uc002plf.1	Q07812	OTTHUMG00000160476	ENST00000345358.7:c.389C>T	chr19.hg19:g.49464086C>T	ENSP00000263262:p.Pro130Leu	53.0	0.0		86.0	32.0	NM_004324	A8K4W1|P55269|Q07814|Q07815|Q8WZ49|Q9NR76|Q9NYG7|Q9UCZ6|Q9UCZ7|Q9UQD6	Missense_Mutation	SNP	ENST00000345358.7	hg19	CCDS12742.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.362|9.362	1.068359|1.068359	0.20067|0.20067	2.27E-4|2.27E-4	0.0|0.0	ENSG00000087088|ENSG00000087088	ENST00000345358;ENST00000415969;ENST00000354470;ENST00000293288|ENST00000539787;ENST00000506183	T;T;T;T|T	0.34667|0.12039	1.35;2.73;1.35;2.73|2.72	3.1|3.1	2.03|2.03	0.26663|0.26663	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.20700|0.20700	0.0498|0.0498	L|L	0.56340|0.56340	1.77|1.77	0.80722|0.80722	D|D	1|1	P;D;D;D|.	0.71674|.	0.912;0.996;0.986;0.998|.	B;P;B;P|.	0.55577|.	0.158;0.707;0.394;0.779|.	T|T	0.01909|0.01909	-1.1249|-1.1249	10|7	0.19147|0.87932	T|D	0.46|0	-8.9341|-8.9341	8.1459|8.1459	0.31110|0.31110	0.0:0.751:0.249:0.0|0.0:0.751:0.249:0.0	.|.	81;130;130;130|.	Q07812-4;Q07812;Q07812-8;Q07812-2|.	.;BAX_HUMAN;.;.|.	L|W	130;130;81;130|163;64	ENSP00000263262:P130L;ENSP00000389971:P130L;ENSP00000346461:P81L;ENSP00000293288:P130L|ENSP00000441413:R163W	ENSP00000293288:P130L|ENSP00000348871:R163W	P|R	+|+	2|1	0|2	BAX|BAX	54155898|54155898	0.999000|0.999000	0.42202|0.42202	0.929000|0.929000	0.37066|0.37066	0.161000|0.161000	0.22273|0.22273	5.205000|5.205000	0.65186|0.65186	0.835000|0.835000	0.34877|0.34877	-0.333000|-0.333000	0.08304|0.08304	CCG|CGG	.	.		0.592	BAX-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360767.1	NM_138763		T	49464086	C	T	49464086	3	4	157	1	0	0	0	0	1	0	0	0	1328	652	23	1	407	1	BAX	19	49464086	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	6553668	49464086	9664897	116	23946										
KLK4	9622	hgsc.bcm.edu	37	chr19	51412004	51412004	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ttgtactctgggtgccgtacGgagaggctggcctccaccat	13	12	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr19:51412004G>T	ENST00000324041.1	-	3	305	c.306C>A	c.(304-306)tcC>tcA	p.S102S	KLK4_ENST00000597441.1_5'Flank|KLK4_ENST00000431178.2_Silent_p.S53S	NM_004917.3	NP_004908.3	Q9Y5K2	KLK4_HUMAN	kallikrein-related peptidase 4	102	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amelogenesis (GO:0097186)|extracellular matrix disassembly (GO:0022617)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(8)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00624)|GBM - Glioblastoma multiforme(134;0.00878)		GGTGCCGTACGGAGAGGCTGG	0.612																																					p.S102S		Atlas-SNP	.											.	KLK4	46	.	0			c.C306A						.						110	85	93					19																	51412004		2203	4300	6503	SO:0001819	synonymous_variant	9622	exon3			CCGTACGGAGAGG	AF113141	CCDS12809.1	19q13.41	2014-09-04	2006-10-27		ENSG00000167749	ENSG00000167749		"Kallikreins", "Serine peptidases / Serine peptidases"	6365	protein-coding gene	gene with protein product		603767	"kallikrein 4 (prostase, enamel matrix, prostate)"	PRSS17		10077646, 10438493, 16800724, 10863090, 9465170	Standard	XM_005259441		Approved	EMSP, EMSP1, PSTS, KLK-L1	uc002pua.1	Q9Y5K2	OTTHUMG00000182964	ENST00000324041.1:c.306C>A	chr19.hg19:g.51412004G>T		45.0	0.0		77.0	28.0	NM_004917	Q4VB16|Q96RU5|Q9GZL6|Q9UBJ6	Silent	SNP	ENST00000324041.1	hg19	CCDS12809.1																																																																																			.	.		0.612	KLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464449.1	NM_004917		T	51412004	G	T	51412004	2	4	157	1	0	0	0	0	0	0	0	1	8415	1103	39	1		1	KLK4	19	51412004	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	1947918	51412004	7716979	117	23947										
CPXM1	56265	hgsc.bcm.edu	37	chr20	2775922	2775922	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gggccgggacgcagatccgaCctgctccaggtaggtgagga	17	11	0	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr20:2775922C>T	ENST00000380605.2	-	12	1925		c.e12+1			NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						GCAGATCCGACCTGCTCCAGG	0.572																																					.		Atlas-SNP	.											.	CPXM1	107	.	0			c.1860+1G>A						.						95	86	89					20																	2775922		2203	4300	6503	SO:0001630	splice_region_variant	56265	exon13			ATCCGACCTGCTC	AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"carboxypeptidase-like protein X1"	609555	"carboxypeptidase X (M14 family)"	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.1860+1G>A	chr20.hg19:g.2775922C>T		62.0	0.0		98.0	45.0	NM_019609	Q6P4G8|Q6UW65|Q9NUB5	Splice_Site	SNP	ENST00000380605.2	hg19	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.422347	0.62622	.	.	ENSG00000088882	ENST00000380605;ENST00000421947	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7195	0.85406	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CPXM1	2723922	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	7.651000	0.83577	2.814000	0.96858	0.563000	0.77884	.	.	.		0.572	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609	Intron	T	2775922	C	T	2775922	5	4	157	1	0	0	0	0	0	0	1	0	3839	521	18	3	355	3	CPXM1	20	2775922	Splice_Site	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10		2775922	60249598	118	23948										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46264396	46264396	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ccaaaccagcagaatatcatGatttctcctcgtaatcgtgg	7	11	2	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr20:46264396G>T	ENST00000371998.3	+	11	1634	c.1443G>T	c.(1441-1443)atG>atT	p.M481I	NCOA3_ENST00000372004.3_Missense_Mutation_p.M481I|NCOA3_ENST00000371997.3_Missense_Mutation_p.M491I|NCOA3_ENST00000341724.6_Missense_Mutation_p.M491I			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	481					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						AGAATATCATGATTTCTCCTC	0.433																																					p.M491I		Atlas-SNP	.											.	NCOA3	156	.	0			c.G1473T						.						80	75	76					20																	46264396		2203	4300	6503	SO:0001583	missense	8202	exon11			TATCATGATTTCT	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.1443G>T	chr20.hg19:g.46264396G>T	ENSP00000361066:p.Met481Ile	103.0	0.0		133.0	55.0	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	hg19	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643271	0.67244	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997;ENST00000542882	T;T;T;T	0.16324	2.35;2.35;2.35;2.35	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.38585	0.1046	M	0.78637	2.42	0.52501	D	0.999955	P;P;P;P;P;P	0.50710	0.898;0.928;0.898;0.805;0.938;0.898	P;P;P;P;P;P	0.53549	0.642;0.671;0.54;0.459;0.729;0.54	T	0.29792	-1.0000	10	0.66056	D	0.02	-4.7133	18.9045	0.92455	0.0:0.0:1.0:0.0	.	481;491;485;481;481;481	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	I	481;491;481;481;491;247	ENSP00000342123:M491I;ENSP00000361073:M481I;ENSP00000361066:M481I;ENSP00000361065:M491I	ENSP00000345671:M481I	M	+	3	0	NCOA3	45697803	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.108000	0.64609	2.459000	0.83118	0.563000	0.77884	ATG	.	.		0.433	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		T	46264396	G	T	46264396	3	4	157	1	0	0	0	0	1	0	0	0	10239	1290	45	3	1507	3	NCOA3	20	46264396	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	43488474	46264396	16761124	119	23949										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60898879	60898879	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	ggtttgcagaggcactgggtGcggccgcctcgcaggacaca	16	12	0	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr20:60898879G>A	ENST00000252999.3	-	44	5868	c.5802C>T	c.(5800-5802)cgC>cgT	p.R1934R		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1934	Laminin EGF-like 18. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGCACTGGGTGCGGCCGCCTC	0.677																																					p.R1934R		Atlas-SNP	.											.	LAMA5	268	.	0			c.C5802T						.						24	26	25					20																	60898879		2183	4287	6470	SO:0001819	synonymous_variant	3911	exon44			CTGGGTGCGGCCG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.5802C>T	chr20.hg19:g.60898879G>A		94.0	0.0		137.0	56.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	hg19	CCDS33502.1																																																																																			.	.		0.677	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60898879	G	A	60898879	2	1	157	1	0	0	0	0	0	0	0	1	8618	1306	46	3		3	LAMA5	20	60898879	Silent	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	14634483	60898879	2126641	120	23950										
ZGPAT	84619	hgsc.bcm.edu	37	chr20	62366733	62366733	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	caatgaaaagctgcaaggtcAggctcctggggccctagaag	13	10	1	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr20:62366733A>C	ENST00000328969.5	+	6	1401	c.1274A>C	c.(1273-1275)cAg>cCg	p.Q425P	LIME1_ENST00000309546.3_5'Flank|ZGPAT_ENST00000369967.3_Missense_Mutation_p.Q405P|ZGPAT_ENST00000448100.2_Missense_Mutation_p.Q405P|ZGPAT_ENST00000357119.4_Missense_Mutation_p.Q396P|RP4-583P15.14_ENST00000467211.1_5'Flank|RP4-583P15.15_ENST00000490623.2_Silent_p.R311R|ZGPAT_ENST00000355969.6_Missense_Mutation_p.Q405P	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	425					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					CTGCAAGGTCAGGCTCCTGGG	0.667																																					p.Q425P		Atlas-SNP	.											.	ZGPAT	57	.	0			c.A1274C						.						22	25	24					20																	62366733		2184	4294	6478	SO:0001583	missense	84619	exon6			AAGGTCAGGCTCC	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"Zinc fingers, CCCH-type domain containing", "G patch domain containing"	15948	protein-coding gene	gene with protein product			"KIAA1847"	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.1274A>C	chr20.hg19:g.62366733A>C	ENSP00000332013:p.Gln425Pro	96.0	0.0		135.0	53.0	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Missense_Mutation	SNP	ENST00000328969.5	hg19	CCDS13534.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.670044	0.29693	.	.	ENSG00000197114	ENST00000448100;ENST00000355969;ENST00000357119;ENST00000369967;ENST00000328969	T;T;T;T;T	0.24538	1.85;1.85;1.87;1.85;1.87	5.47	0.61	0.17580	.	0.673691	0.14239	N	0.332201	T	0.26412	0.0645	L	0.47716	1.5	0.21675	N	0.999591	P;P;P	0.51240	0.666;0.943;0.938	B;B;P	0.46975	0.277;0.424;0.533	T	0.12041	-1.0563	10	0.66056	D	0.02	-1.0295	9.2376	0.37475	0.6128:0.0:0.3872:0.0	.	396;425;405	Q8N5A5-3;Q8N5A5;Q8N5A5-2	.;ZGPAT_HUMAN;.	P	405;405;396;405;425	ENSP00000391176:Q405P;ENSP00000348242:Q405P;ENSP00000349634:Q396P;ENSP00000358984:Q405P;ENSP00000332013:Q425P	ENSP00000332013:Q425P	Q	+	2	0	ZGPAT	61837177	0.449000	0.25689	0.004000	0.12327	0.121000	0.20230	0.873000	0.28052	-0.166000	0.10890	0.460000	0.39030	CAG	.	.		0.667	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		C	62366733	A	C	62366733	3	2	157	1	0	0	0	0	1	0	0	0	17689	188	7	5	1292	5	ZGPAT	20	62366733	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	1467854	62366733	658787	121	23951			1	28		2	2	19	A		7.442374e-05
ZGPAT	84619	hgsc.bcm.edu	37	chr20	62366751	62366751	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	tcaggctcctggggccctagAagccggggcggccccagcgg	17	15	1	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr20:62366751A>G	ENST00000328969.5	+	6	1419	c.1292A>G	c.(1291-1293)gAa>gGa	p.E431G	LIME1_ENST00000309546.3_5'Flank|ZGPAT_ENST00000369967.3_Missense_Mutation_p.E411G|ZGPAT_ENST00000448100.2_Missense_Mutation_p.E411G|ZGPAT_ENST00000357119.4_Missense_Mutation_p.E402G|RP4-583P15.14_ENST00000467211.1_5'Flank|RP4-583P15.15_ENST00000490623.2_Missense_Mutation_p.K317E|ZGPAT_ENST00000355969.6_Missense_Mutation_p.E411G	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	431					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					GGGGCCCTAGAAGCCGGGGCG	0.657																																					p.E431G		Atlas-SNP	.											.	ZGPAT	57	.	0			c.A1292G						.						18	22	21					20																	62366751		2186	4290	6476	SO:0001583	missense	84619	exon6			CCCTAGAAGCCGG	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"Zinc fingers, CCCH-type domain containing", "G patch domain containing"	15948	protein-coding gene	gene with protein product			"KIAA1847"	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.1292A>G	chr20.hg19:g.62366751A>G	ENSP00000332013:p.Glu431Gly	102.0	0.0		152.0	61.0	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Missense_Mutation	SNP	ENST00000328969.5	hg19	CCDS13534.1	.	.	.	.	.	.	.	.	.	.	A	10.37	1.331475	0.24167	.	.	ENSG00000197114	ENST00000448100;ENST00000355969;ENST00000357119;ENST00000369967;ENST00000328969	T;T;T;T;T	0.25912	1.77;1.77;1.8;1.77;1.78	5.47	5.47	0.80525	.	0.810459	0.11647	N	0.543122	T	0.25531	0.0621	L	0.56769	1.78	0.23473	N	0.997603	B;P;B	0.35745	0.313;0.518;0.313	B;B;B	0.31101	0.124;0.114;0.124	T	0.16129	-1.0413	10	0.38643	T	0.18	-31.0128	10.7781	0.46361	0.8416:0.1584:0.0:0.0	.	402;431;411	Q8N5A5-3;Q8N5A5;Q8N5A5-2	.;ZGPAT_HUMAN;.	G	411;411;402;411;431	ENSP00000391176:E411G;ENSP00000348242:E411G;ENSP00000349634:E402G;ENSP00000358984:E411G;ENSP00000332013:E431G	ENSP00000332013:E431G	E	+	2	0	ZGPAT	61837195	1.000000	0.71417	0.036000	0.18154	0.016000	0.09150	3.568000	0.53820	2.070000	0.61991	0.460000	0.39030	GAA	.	.		0.657	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		G	62366751	A	G	62366751	3	3	157	1	0	0	0	0	1	0	0	0	17689	246	9	2	1310	2	ZGPAT	20	62366751	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10	18	62366751	658769	122	23952			1	28		2	2	19	A		7.442374e-05
PCNT	5116	hgsc.bcm.edu	37	chr21	47783767	47783767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gcagccagtgtgggcgggagCcgcccacagcccaggacggg	18	14	0	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr21:47783767C>T	ENST00000359568.5	+	14	2634	c.2527C>T	c.(2527-2529)Ccg>Tcg	p.P843S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	843					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TGGGCGGGAGCCGCCCACAGC	0.667																																					p.P843S		Atlas-SNP	.											.	PCNT	283	.	0			c.C2527T						.						69	81	77					21																	47783767		2193	4280	6473	SO:0001583	missense	5116	exon14			CGGGAGCCGCCCA	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.2527C>T	chr21.hg19:g.47783767C>T	ENSP00000352572:p.Pro843Ser	82.0	0.0		80.0	34.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	C	7.170	0.587374	0.13812	.	.	ENSG00000160299	ENST00000359568	T	0.23147	1.92	4.43	0.104	0.14531	.	.	.	.	.	T	0.16811	0.0404	M	0.62723	1.935	0.19775	N	0.999956	B;P	0.39809	0.015;0.689	B;B	0.34590	0.005;0.186	T	0.19582	-1.0301	9	0.07813	T	0.8	.	2.9953	0.05996	0.262:0.3765:0.2735:0.088	.	725;843	O95613-2;O95613	.;PCNT_HUMAN	S	843	ENSP00000352572:P843S	ENSP00000352572:P843S	P	+	1	0	PCNT	46608195	0.406000	0.25344	0.196000	0.23383	0.216000	0.24613	0.632000	0.24583	0.006000	0.14734	-0.325000	0.08501	CCG	.	.		0.667	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47783767	C	T	47783767	3	4	157	1	0	0	0	0	1	0	0	0	11599	739	26	3	2581	3	PCNT	21	47783767	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10		47783767	346128	123	23953										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18371957	18371957	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	atgtcaaaggccagttggttAttcttctccacattttgctc	7	10	3	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr22:18371957A>T	ENST00000441493.2	-	13	2086	c.1734T>A	c.(1732-1734)aaT>aaA	p.N578K	MICAL3_ENST00000383094.3_Missense_Mutation_p.N578K|MICAL3_ENST00000414725.2_Missense_Mutation_p.N578K|MICAL3_ENST00000400561.2_Missense_Mutation_p.N578K|MICAL3_ENST00000444520.1_Missense_Mutation_p.N578K|MICAL3_ENST00000207726.7_Missense_Mutation_p.N578K|MICAL3_ENST00000585038.1_Missense_Mutation_p.N578K|MICAL3_ENST00000429452.1_Missense_Mutation_p.N578K	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	578	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		CCAGTTGGTTATTCTTCTCCA	0.438																																					p.N578K		Atlas-SNP	.											.	MICAL3	53	.	0			c.T1734A						.						126	113	117					22																	18371957		1568	3582	5150	SO:0001583	missense	57553	exon13			TTGGTTATTCTTC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.1734T>A	chr22.hg19:g.18371957A>T	ENSP00000416015:p.Asn578Lys	75.0	0.0		146.0	63.0	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.195705	0.78902	.	.	ENSG00000093100;ENSG00000093100;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156	ENST00000441493;ENST00000429452;ENST00000400561;ENST00000444520;ENST00000414725;ENST00000383094;ENST00000207726	D;D;D;D;D;D;D	0.97575	-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44	5.55	2.31	0.28768	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.98648	0.9547	H	0.96080	3.765	0.50039	D	0.99984	D;D;P;D;D	0.89917	0.999;1.0;0.907;1.0;0.999	D;D;P;D;D	0.91635	0.999;0.994;0.878;0.995;0.999	D	0.98068	1.0397	10	0.51188	T	0.08	.	9.5881	0.39528	0.8071:0.0:0.1929:0.0	.	578;578;578;578;578	B2RXJ5;Q7RTP6-3;Q7RTP6-2;Q7RTP6-4;Q7RTP6	.;.;.;.;MICA3_HUMAN	K	578	ENSP00000416015:N578K;ENSP00000414846:N578K;ENSP00000383406:N578K;ENSP00000410315:N578K;ENSP00000391827:N578K;ENSP00000372574:N578K;ENSP00000207726:N578K	ENSP00000207726:N578K	N	-	3	2	XXbac-B461K10.4;MICAL3	16751957	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.567000	0.36407	0.952000	0.37798	0.533000	0.62120	AAT	.	.		0.438	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18371957	A	T	18371957	3	4	157	1	0	0	0	0	1	0	0	0	9580	446	16	4	5091	4	MICAL3	22	18371957	Missense_Mutation	SNP	A	TCGA-DD-AACF-01A-11D-A40R-10		18371957	32932609	124	23954										
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29439309	29439309	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gaaccagggctctgaagaccCgctcaagaggccggtggtgt	15	11	2	3			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chr22:29439309C>A	ENST00000544604.2	+	4	699	c.524C>A	c.(523-525)cCg>cAg	p.P175Q	ZNRF3_ENST00000406323.3_Missense_Mutation_p.P75Q|ZNRF3_ENST00000402174.1_Missense_Mutation_p.P75Q|ZNRF3_ENST00000332811.4_Missense_Mutation_p.P75Q	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	175					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						TCTGAAGACCCGCTCAAGAGG	0.517																																					p.P175Q		Atlas-SNP	.											.	ZNRF3	75	.	0			c.C524A						.						59	62	61					22																	29439309		1921	4124	6045	SO:0001583	missense	84133	exon4			AAGACCCGCTCAA	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"RING-type (C3HC4) zinc fingers"	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.524C>A	chr22.hg19:g.29439309C>A	ENSP00000443824:p.Pro175Gln	61.0	0.0		63.0	23.0	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	hg19	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.510296	0.85282	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000402174;ENST00000406323	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.51109	0.1655	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.71870	0.975	T	0.42982	-0.9419	10	0.33940	T	0.23	-0.5131	19.6321	0.95713	0.0:1.0:0.0:0.0	.	175	Q9ULT6	ZNRF3_HUMAN	Q	175;75;75;75	ENSP00000443824:P175Q;ENSP00000328614:P75Q;ENSP00000384456:P75Q;ENSP00000384553:P75Q	ENSP00000328614:P75Q	P	+	2	0	ZNRF3	27769309	1.000000	0.71417	0.971000	0.41717	0.653000	0.38743	7.272000	0.78516	2.884000	0.98904	0.655000	0.94253	CCG	.	.		0.517	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		A	29439309	C	A	29439309	3	1	157	1	0	0	0	0	1	0	0	0	18228	652	23	1	234	1	ZNRF3	22	29439309	Missense_Mutation	SNP	C	TCGA-DD-AACF-01A-11D-A40R-10	11067352	29439309	21865257	125	23955										
NHS	4810	hgsc.bcm.edu	37	chrX	17746244	17746244	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	caacagatgtaagcaatcaaTttaagcatcaatttgttatg	6	6	2	1	rs3747295	byFrequency	TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chrX:17746244T>G	ENST00000380060.3	+	6	4293	c.3955T>G	c.(3955-3957)Ttt>Gtt	p.F1319V	NHS_ENST00000398097.3_Missense_Mutation_p.F1163V	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1340					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					AAGCAATCAATTTAAGCATCA	0.423																																					p.F1319V		Atlas-SNP	.											.	NHS	302	.	0			c.T3955G						.						110	95	100					X																	17746244		2203	4300	6503	SO:0001583	missense	4810	exon6			AATCAATTTAAGC		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.3955T>G	chrX.hg19:g.17746244T>G	ENSP00000369400:p.Phe1319Val	81.0	0.0		246.0	235.0	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	hg19	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	C	2.021	-0.424761	0.04734	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.39787	1.06;1.06	5.74	0.689	0.18033	.	1.134220	0.06265	N	0.694590	T	0.17280	0.0415	N	0.02539	-0.55	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.28681	-1.0036	9	0.14656	T	0.56	0.9957	6.2175	0.20663	0.0:0.464:0.2082:0.3278	.	1340;1161;1163;1319	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	V	1319;1163;1161	ENSP00000369400:F1319V;ENSP00000381170:F1163V	ENSP00000369397:F1161V	F	+	1	0	NHS	17656165	0.103000	0.21917	0.090000	0.20809	0.257000	0.26127	0.002000	0.13061	-0.603000	0.05767	-0.992000	0.02543	TTT	.	0|0.003;C|0.382		0.423	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		G	17746244	T	G	17746244	3	3	157	1	0	0	0	0	1	0	0	0	10420	1493	52	5	4082	5	NHS	23	17746244	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10		17746244	137524316	126	23956										
CHST7	56548	hgsc.bcm.edu	37	chrX	46433907	46433907	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	cgggggaccccgctgcgcgcGccccggacacggccaatctt	14	18	1	0			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chrX:46433907G>A	ENST00000276055.3	+	1	689	c.541G>A	c.(541-543)Gcc>Acc	p.A181T		NM_019886.2	NP_063939.2	Q9NS84	CHST7_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 7	181					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|N-acetylglucosamine metabolic process (GO:0006044)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)			breast(3)|endometrium(2)|kidney(1)|lung(2)	8						cgctgcgcgcgccccggACAC	0.716																																					p.A181T		Atlas-SNP	.											.	CHST7	23	.	0			c.G541A						.						8	10	9					X																	46433907		2045	4032	6077	SO:0001583	missense	56548	exon1			GCGCGCGCCCCGG	AB040711	CCDS14268.1	Xp11.3	2008-02-05			ENSG00000147119	ENSG00000147119		"Sulfotransferases, membrane-bound"	13817	protein-coding gene	gene with protein product		300375				10781596	Standard	NM_019886		Approved	C6ST-2, C6ST2	uc004dgt.3	Q9NS84	OTTHUMG00000021423	ENST00000276055.3:c.541G>A	chrX.hg19:g.46433907G>A	ENSP00000276055:p.Ala181Thr	35.0	0.0		101.0	50.0	NM_019886	O75667	Missense_Mutation	SNP	ENST00000276055.3	hg19	CCDS14268.1	.	.	.	.	.	.	.	.	.	.	g	8.588	0.883919	0.17467	.	.	ENSG00000147119	ENST00000276055	D	0.97378	-4.36	3.5	1.64	0.23874	Sulfotransferase domain (1);	0.471116	0.15575	U	0.255203	D	0.90707	0.7084	N	0.19112	0.55	0.20074	N	0.999939	B	0.27416	0.178	B	0.19946	0.027	T	0.81422	-0.0940	10	0.22109	T	0.4	.	6.2169	0.20659	0.0:0.3873:0.412:0.2007	.	181	Q9NS84	CHST7_HUMAN	T	181	ENSP00000276055:A181T	ENSP00000276055:A181T	A	+	1	0	CHST7	46318851	0.988000	0.35896	0.161000	0.22692	0.498000	0.33706	-0.276000	0.08514	0.072000	0.16694	0.431000	0.28591	GCC	.	.		0.716	CHST7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056362.1	NM_019886		A	46433907	G	A	46433907	3	1	157	1	0	0	0	0	1	0	0	0	3411	1087	38	1	543	1	CHST7	23	46433907	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	28687663	46433907	108836653	127	23957										
ZMYM3	9203	hgsc.bcm.edu	37	chrX	70468643	70468643	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	gcggcagaagctgcagggtcGgggagggcctggggcataga	21	8	0	2			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chrX:70468643G>C	ENST00000353904.2	-	9	1817	c.1630C>G	c.(1630-1632)Cga>Gga	p.R544G	ZMYM3_ENST00000489332.1_5'UTR|ZMYM3_ENST00000373988.1_Missense_Mutation_p.R546G|ZMYM3_ENST00000373984.3_Missense_Mutation_p.R546G|ZMYM3_ENST00000314425.5_Missense_Mutation_p.R544G|ZMYM3_ENST00000373998.1_Missense_Mutation_p.R544G	NM_005096.3	NP_005087.1	Q14202	ZMYM3_HUMAN	zinc finger, MYM-type 3	544					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(7)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(17)|ovary(1)|prostate(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(35;0.156)					CTGCAGGGTCGGGGAGGGCCT	0.562																																					p.R544G		Atlas-SNP	.											.	ZMYM3	137	.	0			c.C1630G						.						23	24	24					X																	70468643		2199	4293	6492	SO:0001583	missense	9203	exon9			AGGGTCGGGGAGG	AB002383	CCDS14409.1, CCDS55443.1, CCDS55444.1	Xq13.1	2013-01-08	2005-12-19	2005-12-19	ENSG00000147130	ENSG00000147130		"Zinc fingers, MYM type"	13054	protein-coding gene	gene with protein product		300061	"zinc finger protein 261"	ZNF261		10486218	Standard	NM_201599		Approved	ZNF198L2, DXS6673E, KIAA0385, MYM	uc004dzh.2	Q14202	OTTHUMG00000021799	ENST00000353904.2:c.1630C>G	chrX.hg19:g.70468643G>C	ENSP00000343909:p.Arg544Gly	53.0	0.0		162.0	29.0	NM_005096	D3DVV3|O15089|Q96E26	Missense_Mutation	SNP	ENST00000353904.2	hg19	CCDS14409.1	.	.	.	.	.	.	.	.	.	.	g	10.91	1.483624	0.26598	.	.	ENSG00000147130	ENST00000314425;ENST00000373998;ENST00000353904;ENST00000373984;ENST00000373988	T;T;T;T;T	0.44482	1.51;0.92;1.51;1.5;1.51	5.51	5.51	0.81932	Zinc finger, MYM-type (1);	0.000000	0.53938	D	0.000058	T	0.43055	0.1230	L	0.54323	1.7	0.80722	D	1	P;P	0.41345	0.702;0.746	B;B	0.43754	0.304;0.43	T	0.21280	-1.0250	10	0.22109	T	0.4	-4.9165	14.0345	0.64636	0.0:0.0:0.8485:0.1515	.	544;544	Q14202-2;Q14202	.;ZMYM3_HUMAN	G	544;544;544;546;546	ENSP00000322845:R544G;ENSP00000363110:R544G;ENSP00000343909:R544G;ENSP00000363096:R546G;ENSP00000363100:R546G	ENSP00000322845:R544G	R	-	1	2	ZMYM3	70385368	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	3.511000	0.53400	2.313000	0.78055	0.365000	0.22127	CGA	.	.		0.562	ZMYM3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057154.1	NM_201599		C	70468643	G	C	70468643	3	2	157	1	0	0	0	0	1	0	0	0	17716	1124	39	4	2550	4	ZMYM3	23	70468643	Missense_Mutation	SNP	G	TCGA-DD-AACF-01A-11D-A40R-10	24034736	70468643	84801917	128	23958										
AIFM1	9131	hgsc.bcm.edu	37	chrX	129270145	129270145	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.03125	4	1	0.622835601559006	0	0.813146479813146	0.093167701863354	0.617038875103394	0	caggcccacagctgccactaTgtggtcagtttctacctgag	10	13	2	1			TCGA-DD-AACF-01A-11D-A40R-10	TCGA-DD-AACF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10de1a6c-59f9-4819-ae33-a37b0f025bd2	a93a98e3-6c06-4078-bdc4-f6d5306dd50c	g.chrX:129270145T>C	ENST00000287295.3	-	12	1410	c.1180A>G	c.(1180-1182)Ata>Gta	p.I394V	AIFM1_ENST00000319908.3_Missense_Mutation_p.I390V|AIFM1_ENST00000535724.1_3'UTR|AIFM1_ENST00000346424.2_Missense_Mutation_p.I107V|AIFM1_ENST00000460436.2_Missense_Mutation_p.I55V|AIFM1_ENST00000440263.1_Missense_Mutation_p.I42V	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	394	FAD-dependent oxidoreductase. {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	GCTGCCACTATGTGGTCAGTT	0.468																																					p.I394V		Atlas-SNP	.											.	AIFM1	75	.	0			c.A1180G						.						45	42	43					X																	129270145		2202	4300	6502	SO:0001583	missense	9131	exon12			CCACTATGTGGTC	AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"programmed cell death 8 (apoptosis-inducing factor)", "neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.1180A>G	chrX.hg19:g.129270145T>C	ENSP00000287295:p.Ile394Val	88.0	0.0		205.0	186.0	NM_004208	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Missense_Mutation	SNP	ENST00000287295.3	hg19	CCDS14618.1	.	.	.	.	.	.	.	.	.	.	T	5.931	0.355743	0.11239	.	.	ENSG00000156709	ENST00000460436;ENST00000346424;ENST00000319908;ENST00000440263;ENST00000287295	T;T;T;T;T	0.71698	2.09;2.11;-0.59;2.06;-0.59	6.01	6.01	0.97437	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.40670	0.1126	N	0.01152	-0.98	0.80722	D	1	B;B;B	0.15473	0.002;0.01;0.013	B;B;B	0.18263	0.002;0.012;0.021	T	0.50701	-0.8797	10	0.02654	T	1	-17.2902	15.3956	0.74790	0.0:0.0:0.0:1.0	.	107;390;394	O95831-2;O95831-3;O95831	.;.;AIFM1_HUMAN	V	55;107;390;42;394	ENSP00000431222:I55V;ENSP00000316320:I107V;ENSP00000315122:I390V;ENSP00000405879:I42V;ENSP00000287295:I394V	ENSP00000287295:I394V	I	-	1	0	AIFM1	129097826	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.773000	0.55333	2.020000	0.59435	0.486000	0.48141	ATA	.	.		0.468	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2			C	129270145	T	C	129270145	3	2	157	1	0	0	0	0	1	0	0	0	426	1464	51	2	681	2	AIFM1	23	129270145	Missense_Mutation	SNP	T	TCGA-DD-AACF-01A-11D-A40R-10	58801502	129270145	26000415	129	23959										
ACTRT2	140625	hgsc.bcm.edu	37	chr1	2938945	2938945	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ggagcccgagaaggagctttCccggaggccggaggaggtcc	18	11	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:2938945C>T	ENST00000378404.2	+	1	900	c.695C>T	c.(694-696)tCc>tTc	p.S232F		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	232						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		AAGGAGCTTTCCCGGAGGCCG	0.652																																					p.S232F		Atlas-SNP	.											.	ACTRT2	69	.	0			c.C695T						.						36	41	39					1																	2938945		2203	4300	6503	SO:0001583	missense	140625	exon1			AGCTTTCCCGGAG	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.695C>T	chr1.hg19:g.2938945C>T	ENSP00000367658:p.Ser232Phe	171.0	0.0		152.0	25.0	NM_080431	B1AN52|Q8NHS6|Q8TDG1	Missense_Mutation	SNP	ENST00000378404.2	hg19	CCDS45.1	.	.	.	.	.	.	.	.	.	.	C	8.373	0.835796	0.16820	.	.	ENSG00000169717	ENST00000378404;ENST00000543312	D	0.94723	-3.5	4.85	-0.658	0.11428	.	1.896970	0.02817	N	0.125078	D	0.95004	0.8383	M	0.62723	1.935	0.09310	N	1	P	0.37573	0.6	P	0.46110	0.504	D	0.85943	0.1459	10	0.87932	D	0	.	10.8114	0.46549	0.196:0.1629:0.6411:0.0	.	232	Q8TDY3	ACTT2_HUMAN	F	232	ENSP00000367658:S232F	ENSP00000367658:S232F	S	+	2	0	ACTRT2	2928805	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.662000	0.05305	-0.468000	0.06922	-1.083000	0.02208	TCC	.	.		0.652	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431		T	2938945	C	T	2938945	3	4	158	1	0	0	0	0	1	0	0	0	219	855	30	3	697	3	ACTRT2	1	2938945	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10		2938945	246311676	1	23960										
UBXN10	127733	hgsc.bcm.edu	37	chr1	20517360	20517360	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	atccctgagctgcagcagcaAgtacccactggggcttcctc	10	15	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:20517360A>G	ENST00000375099.3	+	2	390	c.306A>G	c.(304-306)caA>caG	p.Q102Q		NM_152376.3	NP_689589.1	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	102										endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|skin(2)	14						TGCAGCAGCAAGTACCCACTG	0.517																																					p.Q102Q		Atlas-SNP	.											.	UBXN10	29	.	0			c.A306G						.						54	59	57					1																	20517360		2203	4300	6503	SO:0001819	synonymous_variant	127733	exon2			GCAGCAAGTACCC	AK058158	CCDS205.1	1p36.13	2008-07-25	2008-07-25	2008-07-25	ENSG00000162543	ENSG00000162543		"UBX domain containing"	26354	protein-coding gene	gene with protein product			"UBX domain containing 3"	UBXD3		12477932	Standard	NM_152376		Approved	FLJ25429	uc001bdb.3	Q96LJ8	OTTHUMG00000002708	ENST00000375099.3:c.306A>G	chr1.hg19:g.20517360A>G		137.0	0.0		151.0	27.0	NM_152376	Q5R386	Silent	SNP	ENST00000375099.3	hg19	CCDS205.1																																																																																			.	.		0.517	UBXN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007693.1	NM_152376		G	20517360	A	G	20517360	2	3	158	1	0	0	0	0	0	0	0	1	16927	69	3	2		2	UBXN10	1	20517360	Silent	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	17578415	20517360	228733261	2	23961										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27023218	27023222	+	Frame_Shift_Del	DEL	CCCTA	CCCTA	-													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	aactcgaacgggaacgcgggCcctaggcccgccctgaacaa							TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	CCCTA	CCCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:27023218_27023222delCCCTA	ENST00000324856.7	+	1	695_699	c.324_328delCCCTA	c.(322-330)ggccctaggfs	p.PR109fs	RP5-968P14.2_ENST00000569378.1_RNA|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.PR109fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	109					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.A107fs*4(1)|p.N106fs*4(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GGAACGCGGGCCCTAGGCCCGCCCT	0.771			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.108_109del		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	2	Deletion - Frameshift(2)	liver(2)	c.323_327del						.																																			SO:0001589	frameshift_variant	8289	exon1			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.324_328delCCCTA	chr1.hg19:g.27023218_27023222delCCCTA	ENSP00000320485:p.Pro109fs	29.0	0.0		18.0	11.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.771	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27023222	CCCTA	-	27023218	7	5	158	1	0	1	0	1	0	0	0	0	913	726	26	0	326	0	ARID1A	1	27023218	Frame_Shift_Del	DEL	CCCTA	TCGA-DD-AACG-01A-11D-A40R-10	6505858	27023218	222227403	3	23962										
SCP2	6342	hgsc.bcm.edu	37	chr1	53504627	53504637	+	Frame_Shift_Del	DEL	TGCCTTCAAGG	TGCCTTCAAGG	-													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	aagaaaatcggtggtattttTgccttcaaggtgaaagatgg							TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	TGCCTTCAAGG	TGCCTTCAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:53504627_53504637delTGCCTTCAAGG	ENST00000528311.1	+	13	1430_1440	c.1134_1144delTGCCTTCAAGG	c.(1132-1146)tttgccttcaaggtgfs	p.AFKV379fs	SCP2_ENST00000488965.1_Intron|SCP2_ENST00000435345.2_Frame_Shift_Del_p.AFKV56fs|SCP2_ENST00000408941.3_Intron|SCP2_ENST00000371509.4_Frame_Shift_Del_p.AFKV416fs|SCP2_ENST00000430330.2_Frame_Shift_Del_p.AFKV53fs|SCP2_ENST00000371514.3_Frame_Shift_Del_p.AFKV460fs|SCP2_ENST00000407246.2_Frame_Shift_Del_p.AFKV436fs	NM_001193617.1	NP_001180546.1	Q9BX26	SYCP2_HUMAN	sterol carrier protein 2	1252					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	15						GTGGTATTTTTGCCTTCAAGGTGAAAGATGG	0.455																																					p.459_462del		Atlas-INDEL	.											.	SCP2	44	.	0			c.1376_1386del						.																																			SO:0001589	frameshift_variant	6342	exon14			.	M75884	CCDS572.1, CCDS30719.1, CCDS41338.1, CCDS44149.1, CCDS44150.1, CCDS53317.1, CCDS53318.1, CCDS53319.1	1p32	2010-08-20			ENSG00000116171	ENSG00000116171			10606	protein-coding gene	gene with protein product		184755				1703300, 1718316	Standard	NM_001007098		Approved		uc001cur.2	P22307	OTTHUMG00000008936	ENST00000528311.1:c.1134_1144delTGCCTTCAAGG	chr1.hg19:g.53504627_53504637delTGCCTTCAAGG	ENSP00000434132:p.Ala379fs	141.0	0.0		128.0	14.0	NM_002979	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Frame_Shift_Del	DEL	ENST00000528311.1	hg19	CCDS53319.1																																																																																			.	.		0.455	SCP2-010	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387558.1	NM_002979		-	53504637	TGCCTTCAAGG	-	53504627	7	5	158	1	0	1	0	1	0	0	0	0	13949	1809	63	0	1455	0	SCP2	1	53504627	Frame_Shift_Del	DEL	TGCCTTCAAGG	TCGA-DD-AACG-01A-11D-A40R-10	26481409	53504627	195745994	4	23963										
FAM69A	388650	hgsc.bcm.edu	37	chr1	93309540	93309540	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agagaggtatattcaacactTtccatcacatagaggtcacc	7	10	3	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:93309540T>A	ENST00000370310.4	-	5	757	c.687A>T	c.(685-687)gaA>gaT	p.E229D	SNORA51_ENST00000384295.1_RNA	NM_001006605.4|NM_001252269.1|NM_001252271.1	NP_001006606.2|NP_001239198.1|NP_001239200.1	Q5T7M9	FA69A_HUMAN	family with sequence similarity 69, member A	229						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)		ATTCAACACTTTCCATCACAT	0.388																																					p.E229D		Atlas-SNP	.											.	FAM69A	30	.	0			c.A687T						.						137	112	120					1																	93309540		692	1591	2283	SO:0001583	missense	388650	exon5			AACACTTTCCATC	AK027146	CCDS44173.1, CCDS72822.1, CCDS72823.1, CCDS72824.1, CCDS72825.1	1p22	2014-06-25			ENSG00000154511	ENSG00000154511			32213	protein-coding gene	gene with protein product		614542				21334309	Standard	NM_001006605		Approved	FLJ23493	uc001dpg.3	Q5T7M9	OTTHUMG00000010894	ENST00000370310.4:c.687A>T	chr1.hg19:g.93309540T>A	ENSP00000359333:p.Glu229Asp	127.0	0.0		125.0	27.0	NM_001006605	Q6IRV2	Missense_Mutation	SNP	ENST00000370310.4	hg19	CCDS44173.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.911830	0.72983	.	.	ENSG00000154511	ENST00000370310	T	0.63913	-0.07	5.82	4.69	0.59074	.	0.044304	0.85682	D	0.000000	T	0.73337	0.3574	M	0.81942	2.565	0.58432	D	0.999997	D;D	0.76494	0.997;0.999	D;D	0.80764	0.992;0.994	T	0.77656	-0.2506	10	0.72032	D	0.01	-15.1303	11.7636	0.51918	0.0:0.0705:0.0:0.9295	.	222;229	B4E174;Q5T7M9	.;FA69A_HUMAN	D	229	ENSP00000359333:E229D	ENSP00000359333:E229D	E	-	3	2	FAM69A	93082128	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.864000	0.56024	2.218000	0.71995	0.533000	0.62120	GAA	.	.		0.388	FAM69A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030046.2	NM_001006605		A	93309540	T	A	93309540	3	1	158	1	0	0	0	0	1	0	0	0	5610	1838	64	4	603	4	FAM69A	1	93309540	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	39804913	93309540	155941081	5	23964										
CLK2	1196	hgsc.bcm.edu	37	chr1	155238148	155238148	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	tcctaaggtgctaacgatttCatctgaaatgaaagagagca	9	7	2	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:155238148C>A	ENST00000368361.4	-	5	805	c.490G>T	c.(490-492)Gaa>Taa	p.E164*	CLK2_ENST00000536801.1_Nonsense_Mutation_p.E164*|CLK2_ENST00000355560.4_Nonsense_Mutation_p.E162*|CLK2_ENST00000361168.5_Nonsense_Mutation_p.E163*|CLK2_ENST00000497188.1_5'UTR			P49760	CLK2_HUMAN	CDC-like kinase 2	164	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CTAACGATTTCATCTGAAATG	0.527								Other conserved DNA damage response genes																													p.E163X		Atlas-SNP	.											.	CLK2	55	.	0			c.G487T						.						51	51	51					1																	155238148		2203	4300	6503	SO:0001587	stop_gained	1196	exon5			CGATTTCATCTGA	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"CDC-like kinases"	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.490G>T	chr1.hg19:g.155238148C>A	ENSP00000357345:p.Glu164*	122.0	0.0		109.0	17.0	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Nonsense_Mutation	SNP	ENST00000368361.4	hg19		.	.	.	.	.	.	.	.	.	.	.	26.1	4.703077	0.88924	.	.	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000536801	.	.	.	5.41	5.41	0.78517	.	0.046935	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	17.9201	0.88963	0.0:1.0:0.0:0.0	.	.	.	.	X	163;164;162;164	.	ENSP00000347759:E162X	E	-	1	0	CLK2	153504772	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.651000	0.83577	2.815000	0.96918	0.561000	0.74099	GAA	.	.		0.527	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993		A	155238148	C	A	155238148	4	1	158	1	0	0	0	0	0	1	0	0	3539	835	29	3	1045	3	CLK2	1	155238148	Nonsense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	61928608	155238148	94012473	6	23965										
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156498714	156498714	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	aaagcagcacctacttggagTcgggggccaggtggtccagg	16	10	0	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:156498714T>C	ENST00000361170.2	-	35	4575	c.4565A>G	c.(4564-4566)gAc>gGc	p.D1522G	snoU13_ENST00000458777.1_RNA	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1522					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTACTTGGAGTCGGGGGCCAG	0.572																																					p.D1522G		Atlas-SNP	.											.	IQGAP3	146	.	0			c.A4565G						.						87	87	87					1																	156498714		2203	4300	6503	SO:0001583	missense	128239	exon35			TTGGAGTCGGGGG	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.4565A>G	chr1.hg19:g.156498714T>C	ENSP00000354451:p.Asp1522Gly	69.0	0.0		73.0	45.0	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	hg19	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	T	9.060	0.994334	0.19043	.	.	ENSG00000183856	ENST00000361170	T	0.42131	0.98	4.41	2.47	0.30058	RasGAP protein, C-terminal (1);	0.761500	0.12908	N	0.429198	T	0.07908	0.0198	N	0.08118	0	0.25885	N	0.983547	B	0.02656	0.0	B	0.01281	0.0	T	0.32079	-0.9920	10	0.37606	T	0.19	-0.256	6.6198	0.22796	0.0:0.6774:0.0:0.3226	.	1522	Q86VI3	IQGA3_HUMAN	G	1522	ENSP00000354451:D1522G	ENSP00000354451:D1522G	D	-	2	0	IQGAP3	154765338	0.230000	0.23740	0.961000	0.40146	0.320000	0.28249	0.568000	0.23623	0.564000	0.29238	-0.415000	0.06103	GAC	.	.		0.572	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		C	156498714	T	C	156498714	3	2	158	1	0	0	0	0	1	0	0	0	7825	1667	58	2	346	2	IQGAP3	1	156498714	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	1260566	156498714	92751907	7	23966										
DARS2	55157	hgsc.bcm.edu	37	chr1	173806173	173806173	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	aagcaacttctgatggttggCggtttagacaggtgagcttt	13	6	1	3	rs149916824		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:173806173C>T	ENST00000361951.4	+	8	1486	c.759C>T	c.(757-759)ggC>ggT	p.G253G	DARS2_ENST00000239457.5_5'UTR	NM_018122.4	NP_060592.2	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial	253					gene expression (GO:0010467)|mitochondrial asparaginyl-tRNA aminoacylation (GO:0070145)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aspartate-tRNA ligase activity (GO:0004815)|aspartate-tRNA(Asn) ligase activity (GO:0050560)|ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)			breast(4)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	30					L-Aspartic Acid(DB00128)	TGATGGTTGGCGGTTTAGACA	0.403																																					p.G253G		Atlas-SNP	.											.	DARS2	61	.	0			c.C759T						.						133	149	143					1																	173806173		2203	4300	6503	SO:0001819	synonymous_variant	55157	exon8			GGTTGGCGGTTTA	AK022754	CCDS1311.1	1q25.1	2011-07-01	2007-02-23		ENSG00000117593	ENSG00000117593	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	25538	protein-coding gene	gene with protein product	"aspartate tRNA ligase 2, mitochondrial"	610956				15779907	Standard	NM_018122		Approved	FLJ10514	uc001gjh.2	Q6PI48	OTTHUMG00000034803	ENST00000361951.4:c.759C>T	chr1.hg19:g.173806173C>T		111.0	0.0		105.0	22.0	NM_018122		Silent	SNP	ENST00000361951.4	hg19	CCDS1311.1																																																																																			.	C|1.000;A|0.000		0.403	DARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084220.1	NM_018122		T	173806173	C	T	173806173	2	4	158	1	0	0	0	0	0	0	0	1	4244	755	27	1		1	DARS2	1	173806173	Silent	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	17307459	173806173	75444448	8	23967										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190250737	190250737	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gtgtcccatatttcttgataAggttttctgtgatttgctga	9	6	2	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:190250737A>T	ENST00000367462.3	-	3	611	c.380T>A	c.(379-381)cTt>cAt	p.L127H	RP11-547I7.1_ENST00000452178.1_RNA|BRINP3_ENST00000534846.1_Intron	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	127	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											TTTCTTGATAAGGTTTTCTGT	0.458																																					p.L127H		Atlas-SNP	.											.	FAM5C	343	.	0			c.T380A						.						91	89	90					1																	190250737		2203	4300	6503	SO:0001583	missense	339479	exon3			TTGATAAGGTTTT	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.380T>A	chr1.hg19:g.190250737A>T	ENSP00000356432:p.Leu127His	293.0	0.0		270.0	173.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.690914	0.88735	.	.	ENSG00000162670	ENST00000367462	D	0.87256	-2.23	5.67	5.67	0.87782	Membrane attack complex component/perforin (MACPF) domain (2);	0.000000	0.64402	D	0.000001	D	0.89357	0.6692	L	0.59436	1.845	0.80722	D	1	D	0.55172	0.97	P	0.53266	0.722	D	0.90431	0.4424	10	0.87932	D	0	.	13.8533	0.63510	1.0:0.0:0.0:0.0	.	127	Q76B58	FAM5C_HUMAN	H	127	ENSP00000356432:L127H	ENSP00000356432:L127H	L	-	2	0	FAM5C	188517360	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.309000	0.96252	2.162000	0.67917	0.477000	0.44152	CTT	.	.		0.458	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190250737	A	T	190250737	3	4	158	1	0	0	0	0	1	0	0	0	5602	72	3	4	1944	4	FAM5C	1	190250737	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	16444564	190250737	58999884	9	23968										
CHRM3	1131	hgsc.bcm.edu	37	chr1	240071289	240071289	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cgctcacgtaccgagccaaaCgaacaacaaagagagccggt	10	13	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:240071289C>G	ENST00000255380.4	+	5	1317	c.538C>G	c.(538-540)Cga>Gga	p.R180G		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	180					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CCGAGCCAAACGAACAACAAA	0.488																																					p.R180G		Atlas-SNP	.											.	CHRM3	118	.	0			c.C538G						.						162	165	164					1																	240071289		2203	4300	6503	SO:0001583	missense	1131	exon5			GCCAAACGAACAA	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.538C>G	chr1.hg19:g.240071289C>G	ENSP00000255380:p.Arg180Gly	79.0	0.0		94.0	18.0	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	hg19	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.328672	0.60743	.	.	ENSG00000133019	ENST00000255380	T	0.39406	1.08	5.9	0.454	0.16644	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.65893	0.2735	M	0.83012	2.62	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.72207	-0.4360	10	0.87932	D	0	-7.6239	16.5734	0.84631	0.5576:0.4424:0.0:0.0	.	180	P20309	ACM3_HUMAN	G	180	ENSP00000255380:R180G	ENSP00000255380:R180G	R	+	1	2	CHRM3	238137912	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	0.835000	0.27531	-0.161000	0.10983	0.650000	0.86243	CGA	.	.		0.488	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		G	240071289	C	G	240071289	3	3	158	1	0	0	0	0	1	0	0	0	3380	528	19	4	540	4	CHRM3	1	240071289	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	49820552	240071289	9179332	10	23969										
APOB	338	hgsc.bcm.edu	37	chr2	21229519	21229519	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	acagtactgttatgactaccCtccacaaatttgttgctcag	6	11	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:21229519C>A	ENST00000233242.1	-	26	10348	c.10221G>T	c.(10219-10221)gaG>gaT	p.E3407D		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3407	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATGACTACCCTCCACAAATT	0.408																																					p.E3407D		Atlas-SNP	.											.	APOB	761	.	0			c.G10221T						.						164	163	163					2																	21229519		2203	4300	6503	SO:0001583	missense	338	exon26			ACTACCCTCCACA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10221G>T	chr2.hg19:g.21229519C>A	ENSP00000233242:p.Glu3407Asp	95.0	0.0		86.0	53.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.469527	0.26423	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.39787	1.06	5.74	-2.06	0.07298	.	0.307999	0.27811	N	0.017751	T	0.42268	0.1195	M	0.84585	2.705	0.80722	D	1	P	0.34780	0.468	B	0.36464	0.225	T	0.35871	-0.9771	10	0.42905	T	0.14	.	8.1747	0.31275	0.0:0.446:0.1206:0.4334	.	3407	P04114	APOB_HUMAN	D	3407	ENSP00000233242:E3407D	ENSP00000233242:E3407D	E	-	3	2	APOB	21083024	0.772000	0.28567	0.772000	0.31596	0.117000	0.20001	-0.005000	0.12855	-0.127000	0.11661	-0.302000	0.09304	GAG	.	.		0.408	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21229519	C	A	21229519	3	1	158	1	0	0	0	0	1	0	0	0	785	680	24	3	3486	3	APOB	2	21229519	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10		21229519	221969854	11	23970										
CLIP4	79745	hgsc.bcm.edu	37	chr2	29366802	29366802	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ggggatcgtgttgttattgcAggacagaaggtacagtaagt	15	4	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:29366802A>T	ENST00000320081.5	+	7	1131	c.876A>T	c.(874-876)gcA>gcT	p.A292A	CLIP4_ENST00000404424.1_Silent_p.A292A|CLIP4_ENST00000401605.1_Silent_p.A292A|CLIP4_ENST00000401617.2_Silent_p.A185A	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	292										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					TTGTTATTGCAGGACAGAAGG	0.443																																					p.A292A		Atlas-SNP	.											.	CLIP4	69	.	0			c.A876T						.						236	212	220					2																	29366802		2203	4300	6503	SO:0001819	synonymous_variant	79745	exon7			TATTGCAGGACAG	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"Ankyrin repeat domain containing"	26108	protein-coding gene	gene with protein product			"restin-like 2"	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.876A>T	chr2.hg19:g.29366802A>T		144.0	0.0		144.0	86.0	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Silent	SNP	ENST00000320081.5	hg19	CCDS1770.1																																																																																			.	.		0.443	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		T	29366802	A	T	29366802	2	4	158	1	0	0	0	0	0	0	0	1	3537	175	7	4		4	CLIP4	2	29366802	Silent	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	8137283	29366802	213832571	12	23971										
DHX57	90957	hgsc.bcm.edu	37	chr2	39053721	39053721	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	catcgatggttatggatgtcTcagcaatgttggtggaaatt	12	5	1	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:39053721T>A	ENST00000295373.6	-	15	2876	c.2750A>T	c.(2749-2751)gAg>gTg	p.E917V		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	917	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TATGGATGTCTCAGCAATGTT	0.408																																					p.E917V	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.A2750T						.						161	145	150					2																	39053721		2203	4300	6503	SO:0001583	missense	90957	exon15			GATGTCTCAGCAA	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.2750A>T	chr2.hg19:g.39053721T>A	ENSP00000295373:p.Glu917Val	116.0	0.0		99.0	53.0	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	hg19	CCDS1800.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.2|27.2	4.810992|4.810992	0.90707|0.90707	.|.	.|.	ENSG00000163214|ENSG00000163214	ENST00000295373|ENST00000452978	T|.	0.77877|.	-1.13|.	5.38|5.38	5.38|5.38	0.77491|0.77491	Helicase, C-terminal (3);|.	0.000000|.	0.52532|.	D|.	0.000062|.	D|.	0.90943|.	0.7153|.	H|H	0.99286|0.99286	4.5|4.5	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	D|.	0.94682|.	0.7866|.	10|.	0.87932|.	D|.	0|.	.|.	15.3782|15.3782	0.74630|0.74630	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	917;917;309|.	Q6P158;B4DKW2;Q59G60|.	DHX57_HUMAN;.;.|.	V|C	917|240	ENSP00000295373:E917V|.	ENSP00000295373:E917V|.	E|X	-|-	2|3	0|0	DHX57|DHX57	38907225|38907225	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	7.930000|7.930000	0.87610|0.87610	2.026000|2.026000	0.59711|0.59711	0.460000|0.460000	0.39030|0.39030	GAG|TGA	.	.		0.408	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		A	39053721	T	A	39053721	3	1	158	1	0	0	0	0	1	0	0	0	4515	1551	54	4	1450	4	DHX57	2	39053721	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	9686919	39053721	204145652	13	23972										
R3HDM1	23518	hgsc.bcm.edu	37	chr2	136481727	136481727	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ttggcctccacctacaccgtCttagccacattcccctccat	4	19	1	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:136481727C>G	ENST00000264160.4	+	26	3535	c.3165C>G	c.(3163-3165)gtC>gtG	p.V1055V	R3HDM1_ENST00000409606.1_Silent_p.V1056V|R3HDM1_ENST00000409478.1_Silent_p.V927V|R3HDM1_ENST00000410054.1_Silent_p.V1000V|R3HDM1_ENST00000329971.3_Silent_p.V926V	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	1055							poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		CCTACACCGTCTTAGCCACAT	0.502																																					p.V1055V		Atlas-SNP	.											.	R3HDM1	84	.	0			c.C3165G						.						91	87	88					2																	136481727		2203	4300	6503	SO:0001819	synonymous_variant	23518	exon26			CACCGTCTTAGCC	D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing"	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.3165C>G	chr2.hg19:g.136481727C>G		170.0	0.0		206.0	48.0	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Silent	SNP	ENST00000264160.4	hg19	CCDS2177.1	.	.	.	.	.	.	.	.	.	.	C	3.741	-0.053617	0.07362	.	.	ENSG00000048991	ENST00000429703	.	.	.	5.74	3.92	0.45320	.	.	.	.	.	T	0.56031	0.1958	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53436	-0.8439	4	.	.	.	-7.4794	6.8462	0.23990	0.0:0.6622:0.0:0.3378	.	.	.	.	V	779	.	.	L	+	1	0	R3HDM1	136198197	0.987000	0.35691	1.000000	0.80357	0.981000	0.71138	1.067000	0.30616	1.574000	0.49760	0.561000	0.74099	CTT	.	.		0.502	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		G	136481727	C	G	136481727	2	3	158	1	0	0	0	0	0	0	0	1	12902	900	32	4		4	R3HDM1	2	136481727	Silent	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	97428006	136481727	106717646	14	23973										
DARS	1615	hgsc.bcm.edu	37	chr2	136691481	136691481	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	tcataagtataatttttaccTcttctccttctgcctcaggc	4	12	5	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:136691481T>A	ENST00000264161.4	-	6	718	c.503A>T	c.(502-504)gAg>gTg	p.E168V	DARS_ENST00000537273.1_Splice_Site_p.E68V	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	168					aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	AATTTTTACCTCTTCTCCTTC	0.403																																					p.E168V		Atlas-SNP	.											.	DARS	44	.	0			c.A503T						.						48	48	48					2																	136691481		2203	4300	6503	SO:0001630	splice_region_variant	1615	exon6			TTTACCTCTTCTC	J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	2678	protein-coding gene	gene with protein product	"aspartate tRNA ligase 1, cytoplasmic"	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.504+1A>T	chr2.hg19:g.136691481T>A		331.0	0.0		347.0	212.0	NM_001349	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Missense_Mutation	SNP	ENST00000264161.4	hg19	CCDS2180.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901975	0.72754	.	.	ENSG00000115866	ENST00000264161;ENST00000537273;ENST00000441323;ENST00000456565;ENST00000449218	D;T	0.83755	-1.76;-1.37	4.94	4.94	0.65067	.	0.139089	0.64402	D	0.000004	D	0.83940	0.5363	M	0.72576	2.205	0.80722	D	1	B	0.26845	0.161	B	0.35182	0.197	T	0.82782	-0.0287	10	0.45353	T	0.12	-12.7829	14.4276	0.67227	0.0:0.0:0.0:1.0	.	168	P14868	SYDC_HUMAN	V	168;68;135;135;135	ENSP00000264161:E168V;ENSP00000444192:E68V	ENSP00000264161:E168V	E	-	2	0	DARS	136407951	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.572000	0.82409	2.086000	0.62901	0.472000	0.43445	GAG	.	.		0.403	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254660.5	NM_001349	Missense_Mutation	A	136691481	T	A	136691481	5	1	158	1	0	0	0	0	0	0	1	0	4243	1565	54	4	1046	4	DARS	2	136691481	Splice_Site	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	209754	136691481	106507892	15	23974										
COBLL1	22837	hgsc.bcm.edu	37	chr2	165559721	165559721	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cctgactggaaagcccagggTgaaaggtttctgccaaagaa	12	9	1	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:165559721T>C	ENST00000392717.2	-	10	1353	c.1349A>G	c.(1348-1350)cAc>cGc	p.H450R	COBLL1_ENST00000194871.6_Missense_Mutation_p.H478R|COBLL1_ENST00000342193.4_Missense_Mutation_p.H412R|COBLL1_ENST00000491126.2_Intron|COBLL1_ENST00000409184.3_Intron|COBLL1_ENST00000375458.2_Intron			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	450						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						AAGCCCAGGGTGAAAGGTTTC	0.478																																					p.H412R		Atlas-SNP	.											.	COBLL1	122	.	0			c.A1235G						.						92	88	89					2																	165559721		2203	4300	6503	SO:0001583	missense	22837	exon9			CCAGGGTGAAAGG	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1349A>G	chr2.hg19:g.165559721T>C	ENSP00000376478:p.His450Arg	85.0	0.0		51.0	11.0	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	hg19		.	.	.	.	.	.	.	.	.	.	T	0.457	-0.891058	0.02491	.	.	ENSG00000082438	ENST00000342193;ENST00000392717;ENST00000194871	.	.	.	4.68	2.88	0.33553	.	0.299368	0.28996	N	0.013465	T	0.16085	0.0387	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.19976	-1.0289	9	0.21014	T	0.42	-0.8433	7.2693	0.26248	0.0:0.7987:0.0:0.2013	.	478	B7Z2P5	.	R	412;450;478	.	ENSP00000194871:H478R	H	-	2	0	COBLL1	165267967	0.438000	0.25602	0.271000	0.24616	0.009000	0.06853	0.164000	0.16542	0.706000	0.31912	-0.766000	0.03442	CAC	.	.		0.478	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		C	165559721	T	C	165559721	3	2	158	1	0	0	0	0	1	0	0	0	3656	1696	59	2	2289	2	COBLL1	2	165559721	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	28868240	165559721	77639652	16	23975										
ARMC9	80210	hgsc.bcm.edu	37	chr2	232123721	232123721	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	taggaaattgaaggatgtccCattactgccctccttggatt	9	9	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:232123721C>T	ENST00000349938.4	+	11	1126	c.932C>T	c.(931-933)cCa>cTa	p.P311L	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	311						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		AAGGATGTCCCATTACTGCCC	0.453																																					p.P311L		Atlas-SNP	.											ARMC9_ENST00000359743,NS,neuroblastoma,0,2	ARMC9	129	.	0			c.C932T						.						157	143	148					2																	232123721		2203	4300	6503	SO:0001583	missense	80210	exon11			ATGTCCCATTACT	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"Armadillo repeat containing"	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.932C>T	chr2.hg19:g.232123721C>T	ENSP00000258417:p.Pro311Leu	76.0	0.0		91.0	59.0	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	hg19	CCDS2484.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.3|22.3	4.273584|4.273584	0.80580|0.80580	.|.	.|.	ENSG00000135931|ENSG00000135931	ENST00000424740|ENST00000349938;ENST00000359743;ENST00000436339	.|T	.|0.19669	.|2.13	4.7|4.7	4.7|4.7	0.59300|0.59300	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.40619|0.40619	0.1124|0.1124	L|L	0.52573|0.52573	1.65|1.65	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.69307	.|0.963	T|T	0.22417|0.22417	-1.0217|-1.0217	5|10	.|0.59425	.|D	.|0.04	-13.3684|-13.3684	16.7969|16.7969	0.85604|0.85604	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|311	.|Q7Z3E5	.|ARMC9_HUMAN	Y|L	14|311;311;28	.|ENSP00000258417:P311L	.|ENSP00000258417:P311L	H|P	+|+	1|2	0|0	ARMC9|ARMC9	231831965|231831965	1.000000|1.000000	0.71417|0.71417	0.936000|0.936000	0.37596|0.37596	0.989000|0.989000	0.77384|0.77384	6.553000|6.553000	0.73918|0.73918	2.344000|2.344000	0.79699|0.79699	0.561000|0.561000	0.74099|0.74099	CAT|CCA	.	.		0.453	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139		T	232123721	C	T	232123721	3	4	158	1	0	0	0	0	1	0	0	0	958	594	21	3	970	3	ARMC9	2	232123721	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	66564000	232123721	11075652	17	23976										
SLC6A11	6538	hgsc.bcm.edu	37	chr3	10970945	10970945	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	acatgtaccccaaggttttcCggaggggttaccggcgggag	15	10	0	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:10970945C>T	ENST00000254488.2	+	10	1357	c.1291C>T	c.(1291-1293)Cgg>Tgg	p.R431W		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	431					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	CAAGGTTTTCCGGAGGGGTTA	0.542																																					p.R431W		Atlas-SNP	.											SLC6A11,NS,adenocarcinoma,-1,1	SLC6A11	87	.	0			c.C1291T						.						212	206	208					3																	10970945		2203	4300	6503	SO:0001583	missense	6538	exon10			GTTTTCCGGAGGG	S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"Solute carriers"	11044	protein-coding gene	gene with protein product	"GABA transporter 3"	607952	"solute carrier family 6 (neurotransmitter transporter, GABA), member 11"			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.1291C>T	chr3.hg19:g.10970945C>T	ENSP00000254488:p.Arg431Trp	148.0	0.0		173.0	58.0	NM_014229	B2R6U6|Q8IYC9	Missense_Mutation	SNP	ENST00000254488.2	hg19	CCDS2602.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201112	0.79015	.	.	ENSG00000132164	ENST00000254488	T	0.76316	-1.01	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.89863	0.6838	M	0.91090	3.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91822	0.5468	10	0.87932	D	0	.	13.5363	0.61648	0.1558:0.8442:0.0:0.0	.	431	P48066	S6A11_HUMAN	W	431	ENSP00000254488:R431W	ENSP00000254488:R431W	R	+	1	2	SLC6A11	10945945	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.379000	0.34340	2.376000	0.81061	0.462000	0.41574	CGG	.	.		0.542	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229		T	10970945	C	T	10970945	3	4	158	1	0	0	0	0	1	0	0	0	14689	643	23	1	1329	1	SLC6A11	3	10970945	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10		10970945	187051485	18	23977										
COLQ	8292	hgsc.bcm.edu	37	chr3	15507879	15507879	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gggcctgggggccccggacgGccaggttgaccagaaggccc	18	14	0	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:15507879G>T	ENST00000383788.5	-	12	908	c.783C>A	c.(781-783)ggC>ggA	p.G261G	COLQ_ENST00000383785.2_3'UTR|COLQ_ENST00000435459.2_Silent_p.G251G|COLQ_ENST00000603808.1_Silent_p.G261G|COLQ_ENST00000383781.4_Silent_p.G251G|COLQ_ENST00000383786.5_Silent_p.G227G|COLQ_ENST00000383787.2_Silent_p.G252G	NM_005677.3	NP_005668.2	Q9Y215	COLQ_HUMAN	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	261	Collagen-like 1.				acetylcholine catabolic process in synaptic cleft (GO:0001507)|asymmetric protein localization (GO:0008105)	basal lamina (GO:0005605)|cell junction (GO:0030054)|collagen trimer (GO:0005581)|extracellular space (GO:0005615)|synapse (GO:0045202)				endometrium(2)|large_intestine(4)|lung(10)|skin(3)	19						GCCCCGGACGGCCAGGTTGAC	0.602																																					p.G261G		Atlas-SNP	.											.	COLQ	82	.	0			c.C783A						.						50	54	53					3																	15507879		2203	4300	6503	SO:0001819	synonymous_variant	8292	exon12			CGGACGGCCAGGT	AF057036	CCDS33709.1, CCDS43057.1, CCDS46768.1	3p	2008-07-18			ENSG00000206561	ENSG00000206561			2226	protein-coding gene	gene with protein product	"single strand of homotrimeric collagen-like tail subunit of asymmetric acetylcholinesterase", "collagenic tail of endplate acetylcholinesterase", "AChE Q subunit", "acetylcholinesterase-associated collagen"	603033				9689136	Standard	NM_005677		Approved	EAD	uc003bzx.3	Q9Y215	OTTHUMG00000156233	ENST00000383788.5:c.783C>A	chr3.hg19:g.15507879G>T		298.0	0.0		376.0	62.0	NM_005677	B3KY09|Q6DK18|Q6YH18|Q6YH19|Q6YH20|Q6YH21|Q9NP18|Q9NP19|Q9NP20|Q9NP21|Q9NP22|Q9NP23|Q9NP24|Q9UP88	Silent	SNP	ENST00000383788.5	hg19	CCDS33709.1																																																																																			.	.		0.602	COLQ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343575.1	NM_005677		T	15507879	G	T	15507879	2	4	158	1	0	0	0	0	0	0	0	1	3715	1190	42	3		3	COLQ	3	15507879	Silent	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	4536934	15507879	182514551	19	23978										
TOP2B	7155	hgsc.bcm.edu	37	chr3	25686805	25686805	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	aattacctgcgtcaatggctCcactgacccaatatatgtat	6	11	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:25686805C>G	ENST00000264331.4	-	2	225	c.226G>C	c.(226-228)Gag>Cag	p.E76Q	TOP2B_ENST00000435706.2_Missense_Mutation_p.E71Q	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	76					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	GTCAATGGCTCCACTGACCCA	0.313																																					p.E71Q		Atlas-SNP	.											.	TOP2B	98	.	0			c.G211C						.						179	166	170					3																	25686805		1859	4099	5958	SO:0001583	missense	7155	exon2			ATGGCTCCACTGA	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.226G>C	chr3.hg19:g.25686805C>G	ENSP00000264331:p.Glu76Gln	188.0	0.0		934.0	334.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	hg19		.	.	.	.	.	.	.	.	.	.	C	21.8	4.208803	0.79240	.	.	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225;ENST00000535930	T;T	0.53423	0.62;0.62	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.64034	0.2562	M	0.73372	2.23	0.80722	D	1	D	0.53151	0.958	P	0.54060	0.741	T	0.67047	-0.5769	10	0.87932	D	0	-0.4432	19.8426	0.96695	0.0:1.0:0.0:0.0	.	71	Q02880-2	.	Q	71;76;71;53	ENSP00000396704:E71Q;ENSP00000264331:E76Q	ENSP00000264331:E76Q	E	-	1	0	TOP2B	25661809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.775000	0.95449	0.655000	0.94253	GAG	.	.		0.313	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				G	25686805	C	G	25686805	3	3	158	1	0	0	0	0	1	0	0	0	16381	864	30	4	4794	4	TOP2B	3	25686805	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	10178926	25686805	172335625	20	23979										
SCN11A	11280	hgsc.bcm.edu	37	chr3	38904741	38904741	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	atcctaattttttcattgcaTtatagtatttcttctgttct	3	7	4	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:38904741T>A	ENST00000302328.3	-	24	4199	c.4001A>T	c.(4000-4002)aAt>aTt	p.N1334I	SCN11A_ENST00000444237.2_Missense_Mutation_p.N1334I|SCN11A_ENST00000450244.1_Missense_Mutation_p.N1334I|SCN11A_ENST00000456224.3_Missense_Mutation_p.N1296I	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1334					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTTCATTGCATTATAGTATTT	0.328																																					p.N1334I		Atlas-SNP	.											.	SCN11A	296	.	0			c.A4001T						.						143	130	134					3																	38904741		2203	4300	6503	SO:0001583	missense	11280	exon24			ATTGCATTATAGT	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.4001A>T	chr3.hg19:g.38904741T>A	ENSP00000307599:p.Asn1334Ile	54.0	0.0		82.0	36.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	hg19	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.351754	0.82132	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.96554	-4.05;-4.05;-4.02;-3.93	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.98529	0.9509	M	0.93150	3.385	0.52099	D	0.999946	D	0.89917	1.0	D	0.71184	0.972	D	0.99671	1.0996	10	0.87932	D	0	.	15.6082	0.76692	0.0:0.0:0.0:1.0	.	1334	Q9UI33	SCNBA_HUMAN	I	1334;1334;1296;1334	ENSP00000307599:N1334I;ENSP00000400945:N1334I;ENSP00000416757:N1296I;ENSP00000408028:N1334I	ENSP00000307599:N1334I	N	-	2	0	SCN11A	38879745	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.217000	0.72218	2.169000	0.68431	0.533000	0.62120	AAT	.	.		0.328	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		A	38904741	T	A	38904741	3	1	158	1	0	0	0	0	1	0	0	0	13928	1493	52	4	1386	4	SCN11A	3	38904741	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	13217936	38904741	159117689	21	23980										
ZNF502	91392	hgsc.bcm.edu	37	chr3	44763599	44763599	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cggcaccagagaagtcacacTggagaaaaaccctataaatg	9	10	1	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:44763599T>A	ENST00000296091.4	+	4	1546	c.1290T>A	c.(1288-1290)acT>acA	p.T430T	ZNF502_ENST00000436624.2_Silent_p.T430T|ZNF502_ENST00000449836.1_Silent_p.T430T	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		GAAGTCACACTGGAGAAAAAC	0.428																																					p.T430T		Atlas-SNP	.											.	ZNF502	58	.	0			c.T1290A						.						73	78	76					3																	44763599		2203	4300	6503	SO:0001819	synonymous_variant	91392	exon4			TCACACTGGAGAA	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"Zinc fingers, C2H2-type"	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.1290T>A	chr3.hg19:g.44763599T>A		122.0	0.0		146.0	58.0	NM_001134440		Silent	SNP	ENST00000296091.4	hg19	CCDS2719.1	.	.	.	.	.	.	.	.	.	.	T	8.715	0.912974	0.17907	.	.	ENSG00000196653	ENST00000427783	.	.	.	4.42	-1.48	0.08745	.	.	.	.	.	T	0.53514	0.1801	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54768	-0.8244	5	0.87932	D	0	-10.8818	1.4648	0.02403	0.3845:0.082:0.2621:0.2714	.	.	.	.	Q	430	.	ENSP00000397812:L430Q	L	+	2	0	ZNF502	44738603	0.001000	0.12720	0.996000	0.52242	0.998000	0.95712	-2.759000	0.00787	-0.305000	0.08831	0.533000	0.62120	CTG	.	.		0.428	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		A	44763599	T	A	44763599	2	1	158	1	0	0	0	0	0	0	0	1	17965	1567	55	4		4	ZNF502	3	44763599	Silent	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	5858858	44763599	153258831	22	23981										
SETD2	29072	hgsc.bcm.edu	37	chr3	47165225	47165225	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agaacctgtttttttacagcTcagactaatcttagaactat	5	8	2	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:47165225T>A	ENST00000409792.3	-	3	943	c.901A>T	c.(901-903)Agc>Tgc	p.S301C		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	301					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTTTTACAGCTCAGACTAATC	0.353			"N, F, S, Mis"		clear cell renal carcinoma																																p.S301C		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.A901T						.						136	107	116					3																	47165225		692	1591	2283	SO:0001583	missense	29072	exon3			TACAGCTCAGACT	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.901A>T	chr3.hg19:g.47165225T>A	ENSP00000386759:p.Ser301Cys	102.0	0.0		87.0	34.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	4.103	0.017112	0.07959	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792;ENST00000412450	T;T	0.16073	2.37;2.37	4.88	-0.167	0.13347	.	.	.	.	.	T	0.08714	0.0216	N	0.19112	0.55	0.28774	N	0.900188	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37526	-0.9702	8	.	.	.	.	4.9808	0.14164	0.3411:0.1273:0.0:0.5316	.	301;301	F2Z317;Q9BYW2	.;SETD2_HUMAN	C	301;301;301;257	ENSP00000386759:S301C;ENSP00000416401:S257C	.	S	-	1	0	SETD2	47140229	0.002000	0.14202	0.998000	0.56505	0.975000	0.68041	0.257000	0.18369	0.150000	0.19136	-0.433000	0.05886	AGC	.	.		0.353	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47165225	T	A	47165225	3	1	158	1	0	0	0	0	1	0	0	0	14146	1551	54	4	6869	4	SETD2	3	47165225	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	2401626	47165225	150857205	23	23982										
CCDC52	152185	hgsc.bcm.edu	37	chr3	113212129	113212129	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ccacaatgggaccctgagagGaatcaggagccactgttaca	11	11	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:113212129G>T	ENST00000295872.4	-	6	675	c.416C>A	c.(415-417)tCc>tAc	p.S139Y		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	139					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						ACCCTGAGAGGAATCAGGAGC	0.398																																					p.S139Y		Atlas-SNP	.											.	SPICE1	130	.	0			c.C416A						.						98	93	95					3																	113212129		2203	4300	6503	SO:0001583	missense	152185	exon6			TGAGAGGAATCAG	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.416C>A	chr3.hg19:g.113212129G>T	ENSP00000295872:p.Ser139Tyr	82.0	0.0		104.0	43.0	NM_144718	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	hg19	CCDS2973.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645383	0.67358	.	.	ENSG00000163611	ENST00000295872;ENST00000495812;ENST00000480527	T	0.37058	1.22	5.22	4.28	0.50868	.	0.161352	0.56097	D	0.000028	T	0.53738	0.1815	L	0.60455	1.87	0.43907	D	0.996544	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.982	T	0.55560	-0.8122	10	0.72032	D	0.01	-6.5994	12.8312	0.57746	0.0:0.1645:0.8355:0.0	.	35;139	B3KX77;Q8N0Z3	.;SPICE_HUMAN	Y	139	ENSP00000295872:S139Y	ENSP00000295872:S139Y	S	-	2	0	SPICE1	114694819	1.000000	0.71417	0.995000	0.50966	0.931000	0.56810	2.960000	0.49161	2.577000	0.86979	0.563000	0.77884	TCC	.	.		0.398	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		T	113212129	G	T	113212129	3	4	158	1	0	0	0	0	1	0	0	0	2824	1174	41	3	2203	3	CCDC52	3	113212129	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	66046904	113212129	84810301	24	23983										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129282004	129282004	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gtgtgtagcgggccttgcctGtgatggcgtcgatggagccc	17	10	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:129282004G>C	ENST00000324093.4	-	26	4779	c.4601C>G	c.(4600-4602)aCa>aGa	p.T1534R	PLXND1_ENST00000393239.1_Missense_Mutation_p.T1534R	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1534					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GGCCTTGCCTGTGATGGCGTC	0.637																																					p.T1534R	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C4601G						.						72	64	67					3																	129282004		2203	4300	6503	SO:0001583	missense	23129	exon26			TTGCCTGTGATGG	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.4601C>G	chr3.hg19:g.129282004G>C	ENSP00000317128:p.Thr1534Arg	66.0	0.0		51.0	22.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.449403	0.84101	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.16324	2.35;2.35	5.25	5.25	0.73442	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.182670	0.47852	D	0.000219	T	0.50154	0.1599	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.997;0.999	T	0.58934	-0.7548	10	0.87932	D	0	.	18.8662	0.92293	0.0:0.0:1.0:0.0	.	129;1534	B4DRU3;Q9Y4D7	.;PLXD1_HUMAN	R	1534	ENSP00000317128:T1534R;ENSP00000376931:T1534R	ENSP00000317128:T1534R	T	-	2	0	PLXND1	130764694	1.000000	0.71417	0.944000	0.38274	0.539000	0.34962	6.813000	0.75231	2.454000	0.82982	0.462000	0.41574	ACA	.	.		0.637	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		C	129282004	G	C	129282004	3	2	158	1	0	0	0	0	1	0	0	0	12136	1377	48	4	1220	4	PLXND1	3	129282004	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	16069875	129282004	68740426	25	23984										
ACPP	55	hgsc.bcm.edu	37	chr3	132086623	132086623	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	actactgtttatccacattcGccgtggactctgctggcaga	9	12	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:132086623G>C	ENST00000351273.7	+	11	1264	c.1214G>C	c.(1213-1215)cGc>cCc	p.R405P		NM_001134194.1	NP_001127666.1	P15309	PPAP_HUMAN	acid phosphatase, prostate	0					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						ATCCACATTCGCCGTGGACTC	0.468																																					p.R405P		Atlas-SNP	.											ACPP_ENST00000351273,NS,carcinoma,0,1	ACPP	118	.	0			c.G1214C						.						394	334	352					3																	132086623		1568	3582	5150	SO:0001583	missense	55	exon11			ACATTCGCCGTGG		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000351273.7:c.1214G>C	chr3.hg19:g.132086623G>C	ENSP00000323036:p.Arg405Pro	53.0	0.0		73.0	8.0	NM_001134194	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Missense_Mutation	SNP	ENST00000351273.7	hg19	CCDS46916.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.067088	0.36470	.	.	ENSG00000014257	ENST00000351273	T	0.07444	3.19	4.96	3.13	0.36017	.	0.424638	0.22602	N	0.057947	T	0.18341	0.0440	.	.	.	0.19300	N	0.999974	D	0.67145	0.996	D	0.65443	0.935	T	0.04811	-1.0925	9	0.30078	T	0.28	.	9.3876	0.38352	0.1456:0.0:0.8544:0.0	.	405	P15309-2	.	P	405	ENSP00000323036:R405P	ENSP00000323036:R405P	R	+	2	0	ACPP	133569313	0.891000	0.30450	0.498000	0.27564	0.192000	0.23643	1.862000	0.39448	0.765000	0.33221	0.655000	0.94253	CGC	.	.		0.468	ACPP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356701.1	NM_001099		C	132086623	G	C	132086623	3	2	158	1	0	0	0	0	1	0	0	0	167	1087	38	4	1279	4	ACPP	3	132086623	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	2804619	132086623	65935807	26	23985										
ZNF518B	85460	hgsc.bcm.edu	37	chr4	10446373	10446373	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gtgatgcagcaaatgggagtAactgctgtgagctactgtgt	14	6	0	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr4:10446373A>T	ENST00000326756.3	-	3	2018	c.1580T>A	c.(1579-1581)tTa>tAa	p.L527*		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	527					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						AAATGGGAGTAACTGCTGTGA	0.408																																					p.L527X		Atlas-SNP	.											ZNF518B,colon,carcinoma,0,1	ZNF518B	116	.	0			c.T1580A						.						93	93	93					4																	10446373		2203	4300	6503	SO:0001587	stop_gained	85460	exon3			GGGAGTAACTGCT	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.1580T>A	chr4.hg19:g.10446373A>T	ENSP00000317614:p.Leu527*	247.0	0.0		164.0	58.0	NM_053042	Q96LN8	Nonsense_Mutation	SNP	ENST00000326756.3	hg19	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	A	38	7.267662	0.98175	.	.	ENSG00000178163	ENST00000326756	.	.	.	5.36	1.72	0.24424	.	1.629630	0.04159	N	0.322733	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-0.0026	0.8378	0.01143	0.4076:0.164:0.2709:0.1574	.	.	.	.	X	527	.	ENSP00000317614:L527X	L	-	2	0	ZNF518B	10055471	0.003000	0.15002	0.000000	0.03702	0.032000	0.12392	1.112000	0.31172	0.503000	0.28060	0.496000	0.49642	TTA	.	.		0.408	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		T	10446373	A	T	10446373	4	4	158	1	0	0	0	0	0	1	0	0	17978	372	13	4	1648	4	ZNF518B	4	10446373	Nonsense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10		10446373	180707903	27	23986										
N4BP2	55728	hgsc.bcm.edu	37	chr4	40154482	40154482	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cagggaggagttgctcgcatCaaaccagctgtcattaagta	11	9	2	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr4:40154482C>G	ENST00000261435.6	+	17	5642	c.5226C>G	c.(5224-5226)atC>atG	p.I1742M		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1742	Smr. {ECO:0000255|PROSITE- ProRule:PRU00321}.				nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TTGCTCGCATCAAACCAGCTG	0.423																																					p.I1742M		Atlas-SNP	.											.	N4BP2	166	.	0			c.C5226G						.						161	143	149					4																	40154482		2203	4300	6503	SO:0001583	missense	55728	exon17			TCGCATCAAACCA	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.5226C>G	chr4.hg19:g.40154482C>G	ENSP00000261435:p.Ile1742Met	121.0	0.0		172.0	42.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.77|15.77	2.931636|2.931636	0.52866|0.52866	.|.	.|.	ENSG00000078177|ENSG00000078177	ENST00000261435;ENST00000381804|ENST00000513269	T|.	0.28454|.	1.61|.	5.83|5.83	5.0|5.0	0.66597|0.66597	Smr protein/MutS2 C-terminal (2);|.	0.079922|.	0.64402|.	D|.	0.000019|.	T|T	0.75882|0.75882	0.3910|0.3910	M|M	0.84683|0.84683	2.71|2.71	0.52501|0.52501	D|D	0.999959|0.999959	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.999;1.0|.	T|T	0.78048|0.78048	-0.2356|-0.2356	10|5	0.87932|.	D|.	0|.	-9.2451|-9.2451	11.0507|11.0507	0.47884|0.47884	0.0:0.8589:0.0:0.1411|0.0:0.8589:0.0:0.1411	.|.	1725;1742|.	Q86UW6-2;Q86UW6|.	.;N4BP2_HUMAN|.	M|E	1742;1662|1372	ENSP00000261435:I1742M|.	ENSP00000261435:I1742M|.	I|Q	+|+	3|1	3|0	N4BP2|N4BP2	39830877|39830877	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.435000|0.435000	0.31806|0.31806	2.834000|2.834000	0.48167|0.48167	1.485000|1.485000	0.48380|0.48380	-0.140000|-0.140000	0.14226|0.14226	ATC|CAA	.	.		0.423	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		G	40154482	C	G	40154482	3	3	158	1	0	0	0	0	1	0	0	0	10119	816	29	4	5284	4	N4BP2	4	40154482	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	29708109	40154482	150999794	28	23987										
PRDM9	56979	hgsc.bcm.edu	37	chr5	23526821	23526821	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ttaaatcagatgttattacaCaccaaaggacacatacaggg	7	8	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr5:23526821C>A	ENST00000296682.3	+	11	1806	c.1624C>A	c.(1624-1626)Cac>Aac	p.H542N		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	542					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						TGTTATTACACACCAAAGGAC	0.468										HNSCC(3;0.000094)																											p.H542N		Atlas-SNP	.											.	PRDM9	344	.	0			c.C1624A						.						93	99	97					5																	23526821		2160	4288	6448	SO:0001583	missense	56979	exon11			ATTACACACCAAA	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1624C>A	chr5.hg19:g.23526821C>A	ENSP00000296682:p.His542Asn	174.0	0.0		304.0	79.0	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	hg19	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	5.291	0.239000	0.10023	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	D	0.86865	-2.18	2.39	1.48	0.22813	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.89518	0.6738	H	0.94264	3.515	0.40517	D	0.980796	B	0.18863	0.031	B	0.26517	0.07	D	0.86779	0.1978	9	0.62326	D	0.03	-9.746	8.3235	0.32142	0.2374:0.7626:0.0:0.0	.	542	Q9NQV7	PRDM9_HUMAN	N	542;336	ENSP00000296682:H542N	ENSP00000253473:H336N	H	+	1	0	PRDM9	23562578	0.396000	0.25262	0.522000	0.27862	0.066000	0.16364	1.723000	0.38053	0.521000	0.28445	0.400000	0.26472	CAC	.	.		0.468	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		A	23526821	C	A	23526821	3	1	158	1	0	0	0	0	1	0	0	0	12475	478	17	3	1662	3	PRDM9	5	23526821	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10		23526821	157388439	29	23988										
PLCXD3	345557	hgsc.bcm.edu	37	chr5	41382470	41382470	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agatcaaaataacgaattccAgctcctagctggccagtaaa	7	10	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr5:41382470A>T	ENST00000377801.3	-	2	344	c.270T>A	c.(268-270)gcT>gcA	p.A90A	PLCXD3_ENST00000328457.3_Silent_p.A90A			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	90	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						AACGAATTCCAGCTCCTAGCT	0.438																																					p.A90A		Atlas-SNP	.											.	PLCXD3	86	.	0			c.T270A						.						65	70	68					5																	41382470		2203	4300	6503	SO:0001819	synonymous_variant	345557	exon2			AATTCCAGCTCCT		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.270T>A	chr5.hg19:g.41382470A>T		134.0	0.0		220.0	129.0	NM_001005473	A6NL04	Silent	SNP	ENST00000377801.3	hg19	CCDS34150.1																																																																																			.	.		0.438	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875		T	41382470	A	T	41382470	2	4	158	1	0	0	0	0	0	0	0	1	12052	175	7	4		4	PLCXD3	5	41382470	Silent	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	17855649	41382470	139532790	30	23989										
C5orf28	64417	hgsc.bcm.edu	37	chr5	43446574	43446574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agtctttgagcttgaaaaggTgcatagtaaatttcagggtc	11	5	2	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr5:43446574T>C	ENST00000500337.2	-	5	729	c.398A>G	c.(397-399)cAc>cGc	p.H133R	C5orf28_ENST00000397080.3_Missense_Mutation_p.H133R|C5orf28_ENST00000512085.1_Missense_Mutation_p.H133R|C5orf28_ENST00000510130.1_Missense_Mutation_p.H31R|C5orf28_ENST00000511525.1_5'UTR|C5orf28_ENST00000537319.1_Missense_Mutation_p.H2R			Q0VDI3	CE028_HUMAN	chromosome 5 open reading frame 28	133						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(5)	9	Lung NSC(6;2.07e-05)					CTTGAAAAGGTGCATAGTAAA	0.458																																					p.H133R		Atlas-SNP	.											.	C5orf28	25	.	0			c.A398G						.						97	89	92					5																	43446574		2203	4300	6503	SO:0001583	missense	64417	exon3			AAAAGGTGCATAG	AK025310	CCDS3945.1	5p12	2011-01-25			ENSG00000151881	ENSG00000151881			26139	protein-coding gene	gene with protein product						12477932	Standard	NM_022483		Approved	FLJ21657	uc003jny.3	Q0VDI3	OTTHUMG00000131150	ENST00000500337.2:c.398A>G	chr5.hg19:g.43446574T>C	ENSP00000426067:p.His133Arg	104.0	0.0		174.0	108.0	NM_022483	B2RDA6|Q9H6Z2	Missense_Mutation	SNP	ENST00000500337.2	hg19	CCDS3945.1	.	.	.	.	.	.	.	.	.	.	T	13.46	2.242650	0.39598	.	.	ENSG00000151881	ENST00000500337;ENST00000537319;ENST00000397080;ENST00000512085;ENST00000510130;ENST00000506860	.	.	.	5.95	5.95	0.96441	.	0.316960	0.42420	D	0.000707	T	0.59321	0.2185	L	0.56396	1.775	0.37729	D	0.925205	B	0.17667	0.023	B	0.23852	0.049	T	0.58657	-0.7598	9	0.13108	T	0.6	-23.8459	16.4025	0.83647	0.0:0.0:0.0:1.0	.	133	Q0VDI3	CE028_HUMAN	R	133;2;133;133;31;133	.	ENSP00000380270:H133R	H	-	2	0	C5orf28	43482331	1.000000	0.71417	0.916000	0.36221	0.970000	0.65996	4.658000	0.61497	2.268000	0.75426	0.533000	0.62120	CAC	.	.		0.458	C5orf28-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368003.1	NM_022483		C	43446574	T	C	43446574	3	2	158	1	0	0	0	0	1	0	0	0	2291	1696	59	2	253	2	C5orf28	5	43446574	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	2064104	43446574	137468686	31	23990										
CEP120	153241	hgsc.bcm.edu	37	chr5	122754208	122754208	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ggacgtttggggaaatgccgAcctggagaaacagaatatat	13	6	0	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr5:122754208A>C	ENST00000306467.5	-	2	355	c.51T>G	c.(49-51)ggT>ggG	p.G17G	CEP120_ENST00000306481.6_5'UTR|CEP120_ENST00000328236.5_Splice_Site_p.G17G|CEP120_ENST00000395431.2_Splice_Site_p.G17G|CEP120_ENST00000515110.1_Splice_Site_p.S54A			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	17					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						GGAAATGCCGACCTGGAGAAA	0.383																																					p.G17G		Atlas-SNP	.											.	CEP120	72	.	0			c.T51G						.						85	76	79					5																	122754208		1848	4085	5933	SO:0001630	splice_region_variant	153241	exon3			ATGCCGACCTGGA	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"coiled-coil domain containing 100"	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.50-1T>G	chr5.hg19:g.122754208A>C		85.0	0.0		79.0	16.0	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Silent	SNP	ENST00000306467.5	hg19	CCDS4134.2	.	.	.	.	.	.	.	.	.	.	A	9.890	1.203870	0.22121	.	.	ENSG00000168944	ENST00000515110	.	.	.	5.18	2.51	0.30379	.	.	.	.	.	T	0.50871	0.1641	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54529	-0.8280	5	0.87932	D	0	.	1.1814	0.01846	0.3153:0.2666:0.0854:0.3327	.	.	.	.	A	54	.	ENSP00000428303:S54A	S	-	1	0	CEP120	122782107	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	0.881000	0.28173	0.859000	0.35456	0.533000	0.62120	TCG	.	.		0.383	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	Silent	C	122754208	A	C	122754208	5	2	158	1	0	0	0	0	0	0	1	0	3248	289	10	5	2985	5	CEP120	5	122754208	Splice_Site	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	79307634	122754208	58161052	32	23991										
PDE6A	5145	hgsc.bcm.edu	37	chr5	149247346	149247346	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cttgttcccagaattcagcaGccaccagcagagctacctgc	8	15	1	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr5:149247346G>T	ENST00000255266.5	-	19	2335	c.2216C>A	c.(2215-2217)gCt>gAt	p.A739D		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	739					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	GAATTCAGCAGCCACCAGCAG	0.572																																					p.A739D		Atlas-SNP	.											.	PDE6A	98	.	0			c.C2216A						.						96	69	78					5																	149247346		2203	4300	6503	SO:0001583	missense	5145	exon19			TCAGCAGCCACCA		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.2216C>A	chr5.hg19:g.149247346G>T	ENSP00000255266:p.Ala739Asp	53.0	0.0		60.0	14.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.884058	0.91814	.	.	ENSG00000132915	ENST00000255266	D	0.82081	-1.57	5.42	5.42	0.78866	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.178771	0.47852	D	0.000220	D	0.91546	0.7330	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91889	0.5522	10	0.52906	T	0.07	.	16.72	0.85408	0.0:0.0:1.0:0.0	.	739	P16499	PDE6A_HUMAN	D	739	ENSP00000255266:A739D	ENSP00000255266:A739D	A	-	2	0	PDE6A	149227539	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.994000	0.93529	2.544000	0.85801	0.407000	0.27541	GCT	.	.		0.572	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			T	149247346	G	T	149247346	3	4	158	1	0	0	0	0	1	0	0	0	11654	971	34	3	382	3	PDE6A	5	149247346	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	26493138	149247346	31667914	33	23992										
BAT1	7919	hgsc.bcm.edu	37	chr6	31507007	31507007	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gcccgacttggcctggcacaGgacatccattcccagaatgg	11	14	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:31507007G>C	ENST00000396172.1	-	3	886	c.256C>G	c.(256-258)Ctg>Gtg	p.L86V	SNORD117_ENST00000364915.1_RNA|ATP6V1G2-DDX39B_ENST00000475917.1_5'Flank|DDX39B_ENST00000449074.2_Missense_Mutation_p.L86V|SNORD84_ENST00000584275.1_RNA|DDX39B_ENST00000417556.2_Missense_Mutation_p.L86V|DDX39B_ENST00000376177.2_Missense_Mutation_p.L86V|DDX39B_ENST00000458640.1_Missense_Mutation_p.L86V|DDX39B_ENST00000453105.2_Intron|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR|DDX39B_ENST00000415382.2_Intron	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	86	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						GCCTGGCACAGGACATCCATT	0.517																																					p.L86V		Atlas-SNP	.											.	DDX39B	38	.	0			c.C256G						.						137	138	138					6																	31507007		1511	2709	4220	SO:0001583	missense	7919	exon3			GGCACAGGACATC	Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"DEAD-boxes"	13917	protein-coding gene	gene with protein product	"U2AF65-associated protein 56"	142560	"HLA-B associated transcript 1"	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.256C>G	chr6.hg19:g.31507007G>C	ENSP00000379475:p.Leu86Val	102.0	0.0		81.0	40.0	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Missense_Mutation	SNP	ENST00000396172.1	hg19	CCDS4697.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.699928	0.48307	.	.	ENSG00000198563	ENST00000376177;ENST00000458640;ENST00000396172;ENST00000417556;ENST00000427214;ENST00000428098;ENST00000419338;ENST00000456662;ENST00000449074;ENST00000428450;ENST00000449757;ENST00000456976;ENST00000418897;ENST00000419020;ENST00000458215	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.49720	0.77;2.23;2.23;2.23;0.77;0.77;0.77;2.23;0.77;0.77;0.77;2.23;2.23;0.77	5.53	4.47	0.54385	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.64402	D	0.000016	T	0.26955	0.0660	L	0.31664	0.95	0.58432	D	0.999998	B;B;B	0.26363	0.147;0.012;0.087	B;B;B	0.35607	0.206;0.092;0.13	T	0.12863	-1.0531	10	0.41790	T	0.15	-10.6604	12.514	0.56021	0.0953:0.0:0.9047:0.0	.	106;86;86	Q59G92;Q13838;Q5STU3	.;DX39B_HUMAN;.	V	86;86;86;86;86;86;86;86;86;86;109;86;101;86;86	ENSP00000365347:L86V;ENSP00000416269:L86V;ENSP00000379475:L86V;ENSP00000412582:L86V;ENSP00000399371:L86V;ENSP00000392672:L86V;ENSP00000410313:L86V;ENSP00000416350:L86V;ENSP00000391946:L86V;ENSP00000405707:L86V;ENSP00000409426:L109V;ENSP00000393984:L86V;ENSP00000399841:L101V;ENSP00000405245:L86V	ENSP00000365347:L86V	L	-	1	2	DDX39B	31614986	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.430000	0.52807	2.592000	0.87571	0.563000	0.77884	CTG	.	.		0.517	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640		C	31507007	G	C	31507007	3	2	158	1	0	0	0	0	1	0	0	0	1318	991	35	4	1066	4	BAT1	6	31507007	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10		31507007	139608060	34	23993										
LST1	259197	hgsc.bcm.edu	37	chr6	31555456	31555456	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gcctggggctgggcgggctcCtgcttctggcagtggtcctt	17	12	1	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:31555456C>T	ENST00000340027.5	-	0	1042				LST1_ENST00000303757.8_Silent_p.L20L|LST1_ENST00000376086.3_Intron|LST1_ENST00000339530.4_Silent_p.L20L|NCR3_ENST00000491161.1_5'Flank|LST1_ENST00000396101.3_Silent_p.L20L|LST1_ENST00000376111.4_5'UTR|LST1_ENST00000376092.3_Intron|LST1_ENST00000376099.1_Intron|LST1_ENST00000376096.1_Intron|LST1_ENST00000418507.2_Intron|LST1_ENST00000438075.2_Silent_p.L20L|LST1_ENST00000376090.2_Intron|LST1_ENST00000376089.2_Intron|LST1_ENST00000376093.2_Silent_p.L20L|LST1_ENST00000376110.3_Intron|LST1_ENST00000211921.7_Intron|LST1_ENST00000376102.3_Silent_p.S14S|LST1_ENST00000419073.1_3'UTR|LST1_ENST00000376100.3_Intron	NM_147130.2	NP_667341.1	O14931	NCTR3_HUMAN	natural cytotoxicity triggering receptor 3						cell recognition (GO:0008037)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	integral component of plasma membrane (GO:0005887)				cervix(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)	9						GGGCGGGCTCCTGCTTCTGGC	0.627																																					p.L20L		Atlas-SNP	.											.	LST1	6	.	0			c.C58T						.						12	14	13					6																	31555456		1980	4138	6118	SO:0001628	intergenic_variant	7940	exon2			GGGCTCCTGCTTC	AB055881	CCDS34397.1, CCDS47401.1, CCDS47402.1	6p21.3	2013-01-11	2002-11-13	2002-11-15	ENSG00000204475	ENSG00000204475		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	19077	protein-coding gene	gene with protein product		611550	"lymphocyte antigen 117"	LY117		8824804, 11782277	Standard	NM_001145466		Approved	1C7, NKp30, CD337	uc003nuv.2	O14931	OTTHUMG00000031123		chr6.hg19:g.31555456C>T		46.0	0.0		42.0	12.0	NM_205840	B0S8F2|B0S8F4|B0S8F5|O14930|O14932|O95667|O95668|O95669|Q5ST89|Q5ST90|Q5ST91|Q5ST92|Q5STA3	Silent	SNP	ENST00000340027.5	hg19	CCDS34397.1	.	.	.	.	.	.	.	.	.	.	C	7.548	0.662115	0.14645	.	.	ENSG00000204482	ENST00000464044	.	.	.	4.47	4.47	0.54385	.	.	.	.	.	T	0.53965	0.1829	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53995	-0.8359	4	.	.	.	-5.8203	12.5067	0.55986	0.0:1.0:0.0:0.0	.	.	.	.	L	4	.	.	P	+	2	0	LST1	31663435	0.975000	0.34042	0.326000	0.25389	0.069000	0.16628	1.878000	0.39608	2.310000	0.77875	0.561000	0.74099	CCT	.	.		0.627	NCR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076210.2			T	31555456	C	T	31555456	1	4	158	0	1	0	0	0	0	0	0	0	9076	680	24	3		3	LST1	6	31555456	IGR	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	48449	31555456	139559611	35	23994										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33135050	33135051	+	Frame_Shift_Ins	INS	-	-	G													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agtcactcaccacaggacctINSgggggcccagcctggcctgt							TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:33135050_33135051insG	ENST00000374708.4	-	55	4166_4167	c.3908_3909insC	c.(3907-3909)ccafs	p.P1303fs	COL11A2_ENST00000357486.1_Frame_Shift_Ins_p.P1368fs|COL11A2_ENST00000374714.1_Frame_Shift_Ins_p.P1363fs|COL11A2_ENST00000395197.1_Frame_Shift_Ins_p.P1329fs|COL11A2_ENST00000341947.2_Frame_Shift_Ins_p.P1389fs|COL11A2_ENST00000374712.1_Frame_Shift_Ins_p.P1308fs|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374713.1_Frame_Shift_Ins_p.P1342fs|COL11A2_ENST00000361917.1_Frame_Shift_Ins_p.P1282fs	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1389	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CCACAGGACCTGGGGGCCCAGC	0.649																																					p.P1389fs	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.4167_4168insC						.																																			SO:0001589	frameshift_variant	1302	exon57			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.3909dupC	chr6.hg19:g.33135055_33135055dupG	ENSP00000363840:p.Pro1303fs	119.0	0.0		122.0	50.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Ins	INS	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.649	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			G	33135051	-	G	33135050	7	5	158	1	0	1	1	0	0	0	0	0	3670	1567	55	0	1083	0	COL11A2	6	33135050	Frame_Shift_Ins	INS	-	TCGA-DD-AACG-01A-11D-A40R-10	1579594	33135050	137980017	36	23995										
PIM1	5292	hgsc.bcm.edu	37	chr6	37139141	37139141	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ccgtgcggcactgccacaacTgcggggtgctccaccgcgac	13	17	0	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:37139141T>A	ENST00000373509.5	+	4	854	c.481T>A	c.(481-483)Tgc>Agc	p.C161S		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	252	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	CTGCCACAACTGCGGGGTGCT	0.612			T	BCL6	NHL																																p.C252S		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.T754A						.						46	51	49					6																	37139141		2203	4300	6503	SO:0001583	missense	5292	exon4			CACAACTGCGGGG		CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"pim-1 oncogene"	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.481T>A	chr6.hg19:g.37139141T>A	ENSP00000362608:p.Cys161Ser	165.0	0.0		174.0	69.0	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	hg19	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	T	10.47	1.360168	0.24598	.	.	ENSG00000137193	ENST00000373509	T	0.63744	-0.06	4.36	4.36	0.52297	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.126933	0.56097	D	0.000040	T	0.22126	0.0533	N	0.11106	0.095	0.47065	D	0.999301	B	0.21753	0.06	B	0.20384	0.029	T	0.12192	-1.0557	10	0.11794	T	0.64	.	12.658	0.56797	0.0:0.0:0.0:1.0	.	252	P11309	PIM1_HUMAN	S	161	ENSP00000362608:C161S	ENSP00000362608:C161S	C	+	1	0	PIM1	37247119	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	3.844000	0.55873	1.827000	0.53221	0.368000	0.22195	TGC	.	.		0.612	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37139141	T	A	37139141	3	1	158	1	0	0	0	0	1	0	0	0	11936	1580	55	4	495	4	PIM1	6	37139141	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	4004091	37139141	133975926	37	23996										
XPO5	57510	hgsc.bcm.edu	37	chr6	43492327	43492327	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ccagtgagtccttctgtattTcagggatttgctccattaca	8	10	2	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:43492327T>A	ENST00000265351.7	-	31	3569	c.3359A>T	c.(3358-3360)gAa>gTa	p.E1120V	POLR1C_ENST00000304004.3_Intron	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	1120					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			CTTCTGTATTTCAGGGATTTG	0.493																																					p.E1120V		Atlas-SNP	.											.	XPO5	79	.	0			c.A3359T						.						149	151	150					6																	43492327		1919	4124	6043	SO:0001583	missense	57510	exon31			TGTATTTCAGGGA	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.3359A>T	chr6.hg19:g.43492327T>A	ENSP00000265351:p.Glu1120Val	112.0	0.0		120.0	48.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Missense_Mutation	SNP	ENST00000265351.7	hg19	CCDS47430.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.7|20.7	4.026845|4.026845	0.75390|0.75390	.|.	.|.	ENSG00000124571|ENSG00000124571	ENST00000265351;ENST00000372258;ENST00000439465|ENST00000455285	T|.	0.68903|.	-0.36|.	6.06|6.06	6.06|6.06	0.98353|0.98353	Armadillo-type fold (1);|.	0.160919|.	0.56097|.	D|.	0.000028|.	T|.	0.52273|.	0.1724|.	L|L	0.44542|0.44542	1.39|1.39	0.47476|0.47476	D|D	0.999434|0.999434	B|.	0.27068|.	0.167|.	B|.	0.25614|.	0.062|.	T|.	0.50294|.	-0.8845|.	10|.	0.54805|.	T|.	0.06|.	-9.1451|-9.1451	16.6093|16.6093	0.84858|0.84858	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1120|.	Q9HAV4|.	XPO5_HUMAN|.	V|X	1120;660;748|235	ENSP00000265351:E1120V|.	ENSP00000265351:E1120V|.	E|K	-|-	2|1	0|0	XPO5|XPO5	43600305|43600305	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.499000|7.499000	0.81566|0.81566	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	GAA|AAA	.	.		0.493	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		A	43492327	T	A	43492327	3	1	158	1	0	0	0	0	1	0	0	0	17462	1783	62	4	263	4	XPO5	6	43492327	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	6353186	43492327	127622740	38	23997										
TFAP2B	7021	hgsc.bcm.edu	37	chr6	50803905	50803905	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ctctgctcagttcaacttcgAagtacaaagtaactgtggga	9	9	3	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:50803905A>G	ENST00000393655.3	+	4	902	c.733A>G	c.(733-735)Aag>Gag	p.K245E	TFAP2B_ENST00000263046.4_Missense_Mutation_p.K254E	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	245					aorta morphogenesis (GO:0035909)|calcium ion homeostasis (GO:0055074)|cellular ammonia homeostasis (GO:0097275)|cellular creatinine homeostasis (GO:0097276)|cellular urea homeostasis (GO:0097277)|collecting duct development (GO:0072044)|distal tubule development (GO:0072017)|ductus arteriosus closure (GO:0097070)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hindlimb morphogenesis (GO:0035137)|kidney development (GO:0001822)|magnesium ion homeostasis (GO:0010960)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphate ion homeostasis (GO:0055062)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|potassium ion homeostasis (GO:0055075)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell differentiation (GO:0045595)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|renal water homeostasis (GO:0003091)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|retina layer formation (GO:0010842)|skin development (GO:0043588)|sodium ion homeostasis (GO:0055078)|sympathetic nervous system development (GO:0048485)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)	40	Lung NSC(77;0.156)					TTCAACTTCGAAGTACAAAGT	0.537																																					p.K245E	Pancreas(116;1373 2332 5475 10752)	Atlas-SNP	.											.	TFAP2B	91	.	0			c.A733G						.						67	65	66					6																	50803905		2203	4300	6503	SO:0001583	missense	7021	exon4			ACTTCGAAGTACA	X95694	CCDS4934.2	6p12	2008-02-05	2001-11-28		ENSG00000008196	ENSG00000008196			11743	protein-coding gene	gene with protein product		601601	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)"			7555706, 8661133	Standard	NM_003221		Approved	AP2-B	uc003pag.3	Q92481	OTTHUMG00000014836	ENST00000393655.3:c.733A>G	chr6.hg19:g.50803905A>G	ENSP00000377265:p.Lys245Glu	74.0	0.0		83.0	36.0	NM_003221	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	hg19	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	A	18.85	3.711761	0.68730	.	.	ENSG00000008196	ENST00000393655;ENST00000263046	D;D	0.97831	-4.56;-4.56	5.44	5.44	0.79542	Transcription factor AP-2, C-terminal (1);	0.098510	0.64402	D	0.000002	D	0.98324	0.9444	M	0.91561	3.22	0.80722	D	1	D	0.59767	0.986	P	0.53490	0.727	D	0.98968	1.0800	10	0.87932	D	0	-15.3874	15.5056	0.75739	1.0:0.0:0.0:0.0	.	245	Q92481	AP2B_HUMAN	E	245;254	ENSP00000377265:K245E;ENSP00000263046:K254E	ENSP00000263046:K254E	K	+	1	0	TFAP2B	50911864	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	9.339000	0.96797	2.071000	0.62044	0.528000	0.53228	AAG	.	.		0.537	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221		G	50803905	A	G	50803905	3	3	158	1	0	0	0	0	1	0	0	0	15803	247	9	2	747	2	TFAP2B	6	50803905	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	7311578	50803905	120311162	39	23998										
SIM1	6492	hgsc.bcm.edu	37	chr6	100896528	100896528	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	tccaggctgtactggcggatCttcaagtagccgctgcagtg	13	11	2	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:100896528C>A	ENST00000369208.3	-	7	1352	c.570G>T	c.(568-570)aaG>aaT	p.K190N	SIM1_ENST00000262901.4_Missense_Mutation_p.K190N			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	190					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		ACTGGCGGATCTTCAAGTAGC	0.627																																					p.K190N		Atlas-SNP	.											.	SIM1	173	.	0			c.G570T						.						35	37	37					6																	100896528		2203	4300	6503	SO:0001583	missense	6492	exon6			GCGGATCTTCAAG	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"Basic helix-loop-helix proteins"	10882	protein-coding gene	gene with protein product		603128	"single-minded (Drosophila) homolog 1", "single-minded homolog 1 (Drosophila)"			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.570G>T	chr6.hg19:g.100896528C>A	ENSP00000358210:p.Lys190Asn	21.0	0.0		24.0	7.0	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	hg19	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	C	33	5.288765	0.95517	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.70749	-0.51;-0.51	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.86493	0.5946	M	0.91872	3.25	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	D	0.88940	0.3379	10	0.87932	D	0	.	19.5581	0.95361	0.0:1.0:0.0:0.0	.	190	P81133	SIM1_HUMAN	N	190	ENSP00000358210:K190N;ENSP00000262901:K190N	ENSP00000262901:K190N	K	-	3	2	SIM1	101003249	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.328000	0.52052	2.614000	0.88457	0.655000	0.94253	AAG	.	.		0.627	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		A	100896528	C	A	100896528	3	1	158	1	0	0	0	0	1	0	0	0	14338	912	32	3	1754	3	SIM1	6	100896528	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	50092623	100896528	70218539	40	23999										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128403764	128403764	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gaactgcaggatcaaatgatCttatactgctatagctgatc	8	8	2	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:128403764C>A	ENST00000368215.3	-	10	1594	c.1595G>T	c.(1594-1596)aGa>aTa	p.R532I	RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000368207.3_Missense_Mutation_p.R532I|PTPRK_ENST00000532331.1_Missense_Mutation_p.R532I|PTPRK_ENST00000368210.3_Missense_Mutation_p.R532I|PTPRK_ENST00000368226.4_Missense_Mutation_p.R532I|PTPRK_ENST00000368213.5_Missense_Mutation_p.R532I|PTPRK_ENST00000368227.3_Missense_Mutation_p.R532I|PTPRK_ENST00000524481.1_5'UTR			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	532	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		ATCAAATGATCTTATACTGCT	0.363																																					p.R532I		Atlas-SNP	.											.	PTPRK	330	.	0			c.G1595T						.						81	72	75					6																	128403764		2203	4300	6503	SO:0001583	missense	5796	exon10			AATGATCTTATAC	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.1595G>T	chr6.hg19:g.128403764C>A	ENSP00000357198:p.Arg532Ile	97.0	0.0		118.0	26.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	hg19		.	.	.	.	.	.	.	.	.	.	C	19.77	3.888976	0.72524	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000427676	T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36	5.46	5.46	0.80206	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.097739	0.64402	D	0.000002	T	0.41650	0.1168	N	0.19112	0.55	0.53688	D	0.999977	B;P;P;B;P;P	0.48834	0.371;0.916;0.898;0.451;0.857;0.828	B;P;P;B;P;B	0.54026	0.31;0.74;0.622;0.306;0.508;0.374	T	0.40739	-0.9547	10	0.51188	T	0.08	.	14.8552	0.70332	0.0:0.9288:0.0:0.0712	.	532;532;532;389;532;532	B4DHC3;B7ZMG0;Q15262-3;F5GWP2;Q15262;Q15262-2	.;.;.;.;PTPRK_HUMAN;.	I	532;532;532;532;532;532;532;389	ENSP00000357209:R532I;ENSP00000357210:R532I;ENSP00000432973:R532I;ENSP00000357196:R532I;ENSP00000357193:R532I;ENSP00000357198:R532I;ENSP00000357190:R532I	ENSP00000357190:R532I	R	-	2	0	PTPRK	128445457	0.972000	0.33761	0.989000	0.46669	0.966000	0.64601	2.407000	0.44565	2.718000	0.92993	0.650000	0.86243	AGA	.	.		0.363	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			A	128403764	C	A	128403764	3	1	158	1	0	0	0	0	1	0	0	0	12820	913	32	3	2833	3	PTPRK	6	128403764	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	27507236	128403764	42711303	41	24000										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151161379	151161380	+	Frame_Shift_Del	DEL	AA	AA	-													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	tttacaactccttgggtcggAaagggatcagcgctaaatct							TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:151161379_151161380delAA	ENST00000358517.2	+	16	3716_3717	c.3505_3506delAA	c.(3505-3507)aaafs	p.K1169fs	PLEKHG1_ENST00000367328.1_Frame_Shift_Del_p.K1169fs			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	1169							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		CTTGGGTCGGAAAGGGATCAGC	0.495																																					p.1168_1169del		Atlas-INDEL	.											.	PLEKHG1	97	.	0			c.3504_3505del						.																																			SO:0001589	frameshift_variant	57480	exon17			.	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.3505_3506delAA	chr6.hg19:g.151161379_151161380delAA	ENSP00000351318:p.Lys1169fs	83.0	0.0		77.0	28.0	NM_001029884	Q5T1F2	Frame_Shift_Del	DEL	ENST00000358517.2	hg19	CCDS34552.1																																																																																			.	.		0.495	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			-	151161380	AA	-	151161379	7	5	158	1	0	1	0	1	0	0	0	0	12077	247	9	0	3563	0	PLEKHG1	6	151161379	Frame_Shift_Del	DEL	AA	TCGA-DD-AACG-01A-11D-A40R-10	22757615	151161379	19953688	42	24001										
WIPF3	644150	hgsc.bcm.edu	37	chr7	29874406	29874406	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ccgcctctgggggctcctccCcctcccccaccatcagcacc	7	24	2	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:29874406C>G	ENST00000409290.1	+	1	66	c.66C>G	c.(64-66)ccC>ccG	p.P22P	WIPF3_ENST00000242140.5_Silent_p.P22P|WIPF3_ENST00000409123.1_Silent_p.P22P	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	22					cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						gggctcctccccctcccccac	0.552																																					p.P22P		Atlas-SNP	.											.	WIPF3	46	.	0			c.C66G						.						13	14	13					7																	29874406		931	2074	3005	SO:0001819	synonymous_variant	644150	exon2			TCCTCCCCCTCCC	AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.66C>G	chr7.hg19:g.29874406C>G		288.0	0.0		332.0	81.0	NM_001080529	B8ZZV2	Silent	SNP	ENST00000409290.1	hg19	CCDS56472.1																																																																																			.	.		0.552	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1			G	29874406	C	G	29874406	2	3	158	1	0	0	0	0	0	0	0	1	17384	610	22	4		4	WIPF3	7	29874406	Silent	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10		29874406	129264257	43	24002										
MYO1G	64005	hgsc.bcm.edu	37	chr7	45016656	45016656	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	caccgatgtaggtgtagatgCggcccttctcgaacctggac	12	12	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:45016656C>T	ENST00000258787.7	-	2	246	c.110G>A	c.(109-111)cGc>cAc	p.R37H		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	37	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						GGTGTAGATGCGGCCCTTCTC	0.637																																					p.R37H		Atlas-SNP	.											.	MYO1G	86	.	0			c.G110A						.						58	54	56					7																	45016656		2203	4300	6503	SO:0001583	missense	64005	exon2			TAGATGCGGCCCT	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"Myosins / Myosin superfamily : Class I"	13880	protein-coding gene	gene with protein product	"minor histocompatibility antigen HA-2"	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.110G>A	chr7.hg19:g.45016656C>T	ENSP00000258787:p.Arg37His	68.0	0.0		82.0	5.0	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	hg19	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518945	0.44866	.	.	ENSG00000136286	ENST00000258787	T	0.71698	-0.59	3.93	2.02	0.26589	Myosin head, motor domain (2);	0.000000	0.37437	N	0.002082	T	0.68485	0.3006	N	0.25789	0.76	0.49389	D	0.999789	D	0.69078	0.997	D	0.63283	0.913	T	0.66614	-0.5879	10	0.59425	D	0.04	.	7.4484	0.27223	0.1644:0.744:0.0:0.0915	.	37	B0I1T2	MYO1G_HUMAN	H	37	ENSP00000258787:R37H	ENSP00000258787:R37H	R	-	2	0	MYO1G	44983181	0.978000	0.34361	0.998000	0.56505	0.791000	0.44710	2.517000	0.45529	0.402000	0.25451	0.655000	0.94253	CGC	.	.		0.637	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2			T	45016656	C	T	45016656	3	4	158	1	0	0	0	0	1	0	0	0	10083	768	27	1	3030	1	MYO1G	7	45016656	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	15142250	45016656	114122007	44	24003										
POM121L12	285877	hgsc.bcm.edu	37	chr7	53104142	53104142	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cttccgtgctggtccagcccGccccatccgccatctgggac	10	19	1	0	rs202031574	byFrequency	TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:53104142G>A	ENST00000408890.4	+	1	794	c.778G>A	c.(778-780)Gcc>Acc	p.A260T		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	260										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GGTCCAGCCCGCCCCATCCGC	0.657																																					p.A260T		Atlas-SNP	.											POM121L12,NS,carcinoma,0,1	POM121L12	146	.	0			c.G778A						.						50	57	54					7																	53104142		2017	4174	6191	SO:0001583	missense	285877	exon1			CAGCCCGCCCCAT		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.778G>A	chr7.hg19:g.53104142G>A	ENSP00000386133:p.Ala260Thr	26.0	0.0		37.0	15.0	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	hg19	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	G	7.673	0.687324	0.14973	.	.	ENSG00000221900	ENST00000408890	T	0.25912	1.77	2.16	-4.31	0.03698	.	.	.	.	.	T	0.09335	0.0230	N	0.08118	0	0.09310	N	1	B	0.28419	0.211	B	0.19391	0.025	T	0.12889	-1.0530	9	0.56958	D	0.05	.	2.3928	0.04382	0.1725:0.1362:0.5107:0.1807	.	260	Q8N7R1	P1L12_HUMAN	T	260	ENSP00000386133:A260T	ENSP00000386133:A260T	A	+	1	0	POM121L12	53071636	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.248000	0.00541	-2.674000	0.00412	-0.410000	0.06199	GCC	.	.		0.657	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		A	53104142	G	A	53104142	3	1	158	1	0	0	0	0	1	0	0	0	12250	1087	38	1	780	1	POM121L12	7	53104142	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	8087486	53104142	106034521	45	24004										
CPA4	51200	hgsc.bcm.edu	37	chr7	129962512	129962512	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gcatgtgcgggacaacctctActaggcgatggctctgctct	12	12	3	0	rs376985428		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:129962512A>T	ENST00000222482.4	+	11	1290	c.1262A>T	c.(1261-1263)tAc>tTc	p.Y421F	CPA4_ENST00000493259.1_Missense_Mutation_p.Y317F|CPA4_ENST00000445470.2_Missense_Mutation_p.Y388F	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	421					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					GACAACCTCTACTAGGCGATG	0.537																																					p.Y421F		Atlas-SNP	.											.	CPA4	47	.	0			c.A1262T						.						181	147	159					7																	129962512		2203	4300	6503	SO:0001583	missense	51200	exon11			ACCTCTACTAGGC	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"carboxypeptidase A3"	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1262A>T	chr7.hg19:g.129962512A>T	ENSP00000222482:p.Tyr421Phe	70.0	0.0		61.0	24.0	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	hg19	CCDS5818.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.089189	0.55968	.	.	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.14144	2.74;2.8;2.53	5.63	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.37320	0.0999	M	0.79258	2.445	0.47511	D	0.999444	D;D	0.71674	0.998;0.994	D;D	0.87578	0.998;0.989	T	0.15435	-1.0437	10	0.66056	D	0.02	.	12.1272	0.53922	0.8563:0.1437:0.0:0.0	.	388;421	B7Z576;Q9UI42	.;CBPA4_HUMAN	F	388;421;226;317	ENSP00000412947:Y388F;ENSP00000222482:Y421F;ENSP00000419660:Y317F	ENSP00000222482:Y421F	Y	+	2	0	CPA4	129749748	1.000000	0.71417	1.000000	0.80357	0.094000	0.18550	3.959000	0.56744	0.947000	0.37659	0.460000	0.39030	TAC	.	.		0.537	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352		T	129962512	A	T	129962512	3	4	158	1	0	0	0	0	1	0	0	0	3794	391	14	4	1304	4	CPA4	7	129962512	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	76858370	129962512	29176151	46	24005										
CREB3L2	64764	hgsc.bcm.edu	37	chr7	137567230	137567230	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agataatgaaatggggaagaTccacatccggcctggactcc	11	10	0	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:137567230T>A	ENST00000330387.6	-	11	1766	c.1415A>T	c.(1414-1416)gAt>gTt	p.D472V		NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	472					cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)		FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						ATGGGGAAGATCCACATCCGG	0.592			T	FUS	fibromyxoid sarcoma																																p.D472V		Atlas-SNP	.		Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	.	CREB3L2	62	.	0			c.A1415T						.						78	73	74					7																	137567230		2203	4300	6503	SO:0001583	missense	64764	exon11			GGAAGATCCACAT	AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158		"basic leucine zipper proteins"	23720	protein-coding gene	gene with protein product		608834					Standard	NM_194071		Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.1415A>T	chr7.hg19:g.137567230T>A	ENSP00000329140:p.Asp472Val	129.0	0.0		180.0	74.0	NM_194071	Q6P454|Q6ZMR6	Missense_Mutation	SNP	ENST00000330387.6	hg19	CCDS34760.1	.	.	.	.	.	.	.	.	.	.	T	15.73	2.920532	0.52653	.	.	ENSG00000182158	ENST00000330387	T	0.59638	0.25	5.59	3.15	0.36227	.	0.519429	0.21454	N	0.074281	T	0.38268	0.1034	N	0.22421	0.69	0.80722	D	1	B	0.23735	0.09	B	0.18263	0.021	T	0.13926	-1.0491	10	0.31617	T	0.26	-0.3458	7.5117	0.27577	0.0:0.0728:0.1409:0.7863	.	472	Q70SY1	CR3L2_HUMAN	V	472	ENSP00000329140:D472V	ENSP00000329140:D472V	D	-	2	0	CREB3L2	137217770	0.932000	0.31603	0.997000	0.53966	0.989000	0.77384	2.435000	0.44811	0.935000	0.37341	0.454000	0.30748	GAT	.	.		0.592	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341462.1	NM_194071		A	137567230	T	A	137567230	3	1	158	1	0	0	0	0	1	0	0	0	3859	1435	50	4	155	4	CREB3L2	7	137567230	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	7604718	137567230	21571433	47	24006										
KLRG2	346689	hgsc.bcm.edu	37	chr7	139168233	139168233	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cccgccgccttctccacggcCccggccggacttgggctgct	12	20	1	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:139168233C>G	ENST00000340940.4	-	1	225	c.156G>C	c.(154-156)ggG>ggC	p.G52G	KLRG2_ENST00000393039.2_Silent_p.G52G	NM_198508.2	NP_940910.1	A4D1S0	KLRG2_HUMAN	killer cell lectin-like receptor subfamily G, member 2	52	Pro-rich.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|large_intestine(2)|lung(3)	6	Melanoma(164;0.233)					TCTCCACGGCCCCGGCCGGAC	0.731																																					p.G52G		Atlas-SNP	.											.	KLRG2	22	.	0			c.G156C						.						12	14	14					7																	139168233		1932	4005	5937	SO:0001819	synonymous_variant	346689	exon1			CACGGCCCCGGCC	AK126174	CCDS5854.1	7q34	2011-08-30			ENSG00000188883	ENSG00000188883		"Killer cell lectin-like receptors", "C-type lectin domain containing"	24778	protein-coding gene	gene with protein product	"C-type lectin domain family 15, member B"						Standard	XM_005250311		Approved	FLJ44186, CLEC15B	uc003vvb.3	A4D1S0	OTTHUMG00000157705	ENST00000340940.4:c.156G>C	chr7.hg19:g.139168233C>G		47.0	0.0		63.0	10.0	NM_198508	Q2NL79|Q6ZTV6	Silent	SNP	ENST00000340940.4	hg19	CCDS5854.1																																																																																			.	.		0.731	KLRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349433.1	NM_198508		G	139168233	C	G	139168233	2	3	158	1	0	0	0	0	0	0	0	1	8431	610	22	4		4	KLRG2	7	139168233	Silent	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	1601003	139168233	19970430	48	24007										
ZNF282	8427	hgsc.bcm.edu	37	chr7	148907790	148907790	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gagccatccctacggaatccAttaccggtgagtgagccaag	11	12	0	2	rs141109561		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:148907790A>G	ENST00000262085.3	+	5	1051	c.946A>G	c.(946-948)Att>Gtt	p.I316V	ZNF282_ENST00000479907.1_Missense_Mutation_p.I316V	NM_003575.2	NP_003566.1	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	316					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	17	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)		TACGGAATCCATTACCGGTGA	0.637																																					p.I316V		Atlas-SNP	.											.	ZNF282	42	.	0			c.A946G						.	A	VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	54	47	49		946	3	0.1	7	dbSNP_134	49	0,8598		0,0,4299	no	missense	ZNF282	NM_003575.2	29	0,1,6501	GG,GA,AA		0.0,0.0227,0.0077	benign	316/672	148907790	1,13003	2203	4299	6502	SO:0001583	missense	8427	exon5			GAATCCATTACCG	D30612	CCDS5895.1	7q36.1	2013-01-08			ENSG00000170265	ENSG00000170265		"Zinc fingers, C2H2-type", "-"	13076	protein-coding gene	gene with protein product		603397				9396811	Standard	NM_003575		Approved	HUB1	uc003wfm.3	Q9UDV7	OTTHUMG00000158974	ENST00000262085.3:c.946A>G	chr7.hg19:g.148907790A>G	ENSP00000262085:p.Ile316Val	260.0	0.0		275.0	127.0	NM_003575	B4DRI5|O43691|Q6DKK0	Missense_Mutation	SNP	ENST00000262085.3	hg19	CCDS5895.1	.	.	.	.	.	.	.	.	.	.	A	3.715	-0.058831	0.07317	2.27E-4	0.0	ENSG00000170265	ENST00000262085;ENST00000479907	T;T	0.05580	3.42;5.25	5.29	2.95	0.34219	.	0.335009	0.21348	N	0.076011	T	0.03739	0.0106	N	0.21448	0.665	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.43734	-0.9373	10	0.18710	T	0.47	-7.401	4.7612	0.13110	0.7082:0.0:0.2918:0.0	.	316;288;316	B4DRI5;Q7Z2V4;Q9UDV7	.;.;ZN282_HUMAN	V	316	ENSP00000262085:I316V;ENSP00000418840:I316V	ENSP00000262085:I316V	I	+	1	0	ZNF282	148538723	0.020000	0.18652	0.126000	0.21872	0.471000	0.32888	0.601000	0.24119	0.857000	0.35407	0.460000	0.39030	ATT	.	A|1.000;G|0.000		0.637	ZNF282-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352746.1	NM_003575		G	148907790	A	G	148907790	3	3	158	1	0	0	0	0	1	0	0	0	17834	217	8	2	964	2	ZNF282	7	148907790	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	9739557	148907790	10230873	49	24008										
NUDT18	79873	hgsc.bcm.edu	37	chr8	21965221	21965221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agccacgagccgctggcagaCcagatcacagggtagctctt	12	13	2	2	rs554932005		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr8:21965221C>T	ENST00000309188.6	-	5	680	c.562G>A	c.(562-564)Gtc>Atc	p.V188I	NUDT18_ENST00000521807.2_3'UTR|NUDT18_ENST00000522405.1_Missense_Mutation_p.V111I	NM_024815.3	NP_079091.3	Q6ZVK8	NUD18_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 18	188					dADP catabolic process (GO:0046057)|dGDP catabolic process (GO:0046067)|GDP catabolic process (GO:0046712)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	8-hydroxy-dADP phosphatase activity (GO:0044717)|8-oxo-dGDP phosphatase activity (GO:0044715)|8-oxo-GDP phosphatase activity (GO:0044716)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|lung(2)	4				Colorectal(74;0.00185)|COAD - Colon adenocarcinoma(73;0.0608)|READ - Rectum adenocarcinoma(5;0.0986)		CGCTGGCAGACCAGATCACAG	0.612																																					p.V188I		Atlas-SNP	.											.	NUDT18	13	.	0			c.G562A						.						64	76	72					8																	21965221		2141	4232	6373	SO:0001583	missense	79873	exon5			GGCAGACCAGATC		CCDS75706.1	8p21.3	2012-07-31				ENSG00000275074		"Nudix motif containing"	26194	protein-coding gene	gene with protein product	"mutT human homolog 3"	615791				22556419	Standard	NM_024815		Approved	FLJ22494, MTH3	uc003xaq.1	Q6ZVK8		ENST00000309188.6:c.562G>A	chr8.hg19:g.21965221C>T	ENSP00000307852:p.Val188Ile	94.0	0.0		28.0	15.0	NM_024815	Q8IZ75|Q9H687	Missense_Mutation	SNP	ENST00000309188.6	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.600|9.600	1.128556|1.128556	0.21041|0.21041	.|.	.|.	ENSG00000173566|ENSG00000173566	ENST00000522379|ENST00000522405;ENST00000309188	.|.	.|.	.|.	5.37|5.37	3.32|3.32	0.38043|0.38043	.|.	.|0.312145	.|0.30320	.|N	.|0.009883	T|T	0.34395|0.34395	0.0896|0.0896	L|L	0.39633|0.39633	1.23|1.23	0.32039|0.32039	N|N	0.598503|0.598503	.|B	.|0.10296	.|0.003	.|B	.|0.08055	.|0.003	T|T	0.33650|0.33650	-0.9860|-0.9860	5|9	.|0.33141	.|T	.|0.24	-18.3948|-18.3948	7.4638|7.4638	0.27310|0.27310	0.0:0.7468:0.0:0.2532|0.0:0.7468:0.0:0.2532	.|.	.|188	.|Q6ZVK8	.|NUD18_HUMAN	D|I	223|111;188	.|.	.|ENSP00000307852:V188I	G|V	-|-	2|1	0|0	NUDT18|NUDT18	22021166|22021166	0.003000|0.003000	0.15002|0.15002	1.000000|1.000000	0.80357|0.80357	0.806000|0.806000	0.45545|0.45545	-0.111000|-0.111000	0.10807|0.10807	1.260000|1.260000	0.44134|0.44134	0.655000|0.655000	0.94253|0.94253	GGT|GTC	.	.		0.612	NUDT18-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_024815		T	21965221	C	T	21965221	3	4	158	1	0	0	0	0	1	0	0	0	10744	507	18	3	413	3	NUDT18	8	21965221	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10		21965221	124398801	50	24009										
EYA1	2138	hgsc.bcm.edu	37	chr8	72182014	72182014	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	taggacccagtaagcaaggaGtggaaaacaatgattgtctc	11	7	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr8:72182014G>A	ENST00000340726.3	-	11	1650	c.1011C>T	c.(1009-1011)caC>caT	p.H337H	EYA1_ENST00000388742.4_Silent_p.H337H|EYA1_ENST00000303824.7_Silent_p.H331H|EYA1_ENST00000388740.3_Silent_p.H304H|EYA1_ENST00000388741.2_Silent_p.H303H|EYA1_ENST00000388743.2_Silent_p.H336H|EYA1_ENST00000419131.1_Silent_p.H332H	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	337					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			TAAGCAAGGAGTGGAAAACAA	0.403																																					p.H337H		Atlas-SNP	.											.	EYA1	108	.	0			c.C1011T						.						172	156	161					8																	72182014		2203	4300	6503	SO:0001819	synonymous_variant	2138	exon11			CAAGGAGTGGAAA	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"Protein tyrosine phosphatases / Asp-based PTPs"	3519	protein-coding gene	gene with protein product		601653	"eyes absent (Drosophila) homolog 1", "eyes absent homolog 1 (Drosophila)"	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.1011C>T	chr8.hg19:g.72182014G>A		94.0	0.0		130.0	31.0	NM_000503	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Silent	SNP	ENST00000340726.3	hg19	CCDS34906.1																																																																																			.	.		0.403	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		A	72182014	G	A	72182014	2	1	158	1	0	0	0	0	0	0	0	1	5330	1020	36	3		3	EYA1	8	72182014	Silent	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	50216793	72182014	74182008	51	24010										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5921873	5921873	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	atcaccactgccagtggtgtGgcctaatgtaagtttgagat	11	8	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:5921873G>A	ENST00000399933.3	-	8	4122	c.4123C>T	c.(4123-4125)Cac>Tac	p.H1375Y	KIAA2026_ENST00000381461.2_Missense_Mutation_p.H1345Y	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1375	Ser-rich.									breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		CCAGTGGTGTGGCCTAATGTA	0.443																																					p.H1375Y		Atlas-SNP	.											.	KIAA2026	231	.	0			c.C4123T						.						155	150	151					9																	5921873		1883	4120	6003	SO:0001583	missense	158358	exon8			TGGTGTGGCCTAA	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.4123C>T	chr9.hg19:g.5921873G>A	ENSP00000382815:p.His1375Tyr	79.0	0.0		54.0	45.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	hg19		.	.	.	.	.	.	.	.	.	.	G	0.013	-1.630739	0.00813	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	3.9	2.98	0.34508	.	0.273622	0.24568	N	0.037402	T	0.20170	0.0485	N	0.08118	0	0.18873	N	0.999989	B	0.22851	0.076	B	0.19946	0.027	T	0.23762	-1.0179	9	0.02654	T	1	0.4025	14.2375	0.65937	0.0827:0.0:0.9173:0.0	.	1375	Q5HYC2	K2026_HUMAN	Y	1375;1345	.	ENSP00000370870:H1345Y	H	-	1	0	KIAA2026	5911873	1.000000	0.71417	0.235000	0.24058	0.073000	0.16967	4.572000	0.60886	0.342000	0.23796	-1.233000	0.01565	CAC	.	.		0.443	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		A	5921873	G	A	5921873	3	1	158	1	0	0	0	0	1	0	0	0	8279	1348	47	3	2192	3	KIAA2026	9	5921873	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10		5921873	135291558	52	24011										
SHB	6461	hgsc.bcm.edu	37	chr9	38068423	38068428	+	In_Frame_Del	DEL	TGTCGT	TGTCGT	-													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gaggtcgctggtgctgccgcTgtcgtcgggcagcgagcccg							TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	TGTCGT	TGTCGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:38068423_38068428delTGTCGT	ENST00000377707.3	-	1	780_785	c.215_220delACGACA	c.(214-222)gacgacagc>ggc	p.72_74DDS>G	RP11-613M10.9_ENST00000540557.1_In_Frame_Del_p.72_74DDS>G|SHB_ENST00000377700.4_In_Frame_Del_p.72_74DDS>G	NM_003028.2	NP_003019.2	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein B	72	Mediates interaction with LAT, PTK2/FAK1, JAK1 and JAK3.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(4)|lung(1)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)	11		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)		GTGCTGCCGCTGTCGTCGGGCAGCGA	0.728																																					p.72_74del		Atlas-INDEL	.											.	SHB	31	.	0			c.216_221del						.																																			SO:0001651	inframe_deletion	6461	exon1			.		CCDS43806.1	9p13.2	2013-09-23	2005-05-24		ENSG00000107338	ENSG00000107338		"SH2 domain containing"	10838	protein-coding gene	gene with protein product		600314	"SHB adaptor protein (a Src homology 2 protein)", "SHB (Src homology 2 domain containing) adaptor protein B"			7713524	Standard	NM_003028		Approved		uc004aax.3	Q15464	OTTHUMG00000019936	ENST00000377707.3:c.215_220delACGACA	chr9.hg19:g.38068423_38068428delTGTCGT	ENSP00000366936:p.Asp72_Ser74delinsGly	81.0	0.0		72.0	26.0	NM_003028	B9EGM0|D3DRQ5|Q504U5|Q5VUM8	In_Frame_Del	DEL	ENST00000377707.3	hg19	CCDS43806.1																																																																																			.	.		0.728	SHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052490.1			-	38068428	TGTCGT	-	38068423	7	5	158	1	0	1	0	1	0	0	0	0	14283	1580	55	0	1333	0	SHB	9	38068423	In_Frame_Del	DEL	TGTCGT	TCGA-DD-AACG-01A-11D-A40R-10	32146550	38068423	103145008	53	24012										
NCBP1	4686	hgsc.bcm.edu	37	chr9	100423350	100423375	+	Splice_Site	DEL	GGTAAGTGGAATTCAGTATTTCTTAA	GGTAAGTGGAATTCAGTATTTCTTAA	-													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ctaaccaggatgatgacgacGgtaagtggaattcagtattt							TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	GGTAAGTGGAATTCAGTATTTCTTAA	GGTAAGTGGAATTCAGTATTTCTTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:100423350_100423375delGGTAAGTGGAATTCAGTATTTCTTAA	ENST00000375147.3	+	16	1856	c.1600delGGTAAGTGGAATTCAGTATTTCTTAA	c.(1600-1602)ggt>gt	p.G534fs		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	534					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				TGATGACGACGGTAAGTGGAATTCAGTATTTCTTAAGTGGAACTAT	0.376																																					p.533_534del	Ovarian(36;879 898 2893 44212 50307)	Atlas-INDEL	.											.	NCBP1	64	.	0			c.1599_1600del						.																																			SO:0001630	splice_region_variant	4686	exon16			.	BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.1600+1GGTAAGTGGAATTCAGTATTTCTTAA>-	chr9.hg19:g.100423350_100423375delGGTAAGTGGAATTCAGTATTTCTTAA		40.0	0.0		41.0	11.0	NM_002486	B2R718|Q59G76|Q5T1V0|Q5T7X2	Frame_Shift_Del	DEL	ENST00000375147.3	hg19	CCDS6728.1																																																																																			.	.		0.376	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486	Frame_Shift_Del	-	100423375	GGTAAGTGGAATTCAGTATTTCTTAA	-	100423350	8	5	158	1	0	1	0	1	0	0	1	0	10220	1130	39	0	1662	0	NCBP1	9	100423350	Splice_Site	DEL	GGTAAGTGGAATTCAGTATTTCTTAA	TCGA-DD-AACG-01A-11D-A40R-10	62354927	100423350	40790081	54	24013										
FAM125B	89853	hgsc.bcm.edu	37	chr9	129148868	129148868	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	tggggaacgtgttagtagatAtgaagctcattgacatcaag	12	5	2	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:129148868A>G	ENST00000361171.3	+	4	421	c.340A>G	c.(340-342)Atg>Gtg	p.M114V	MVB12B_ENST00000545391.1_Missense_Mutation_p.M114V|MVB12B_ENST00000535766.1_Missense_Mutation_p.M107V|MVB12B_ENST00000436593.3_Missense_Mutation_p.M99V	NM_033446.2	NP_258257.1	Q9H7P6	MB12B_HUMAN	multivesicular body subunit 12B	114	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	lipid binding (GO:0008289)										GTTAGTAGATATGAAGCTCAT	0.453																																					p.M114V		Atlas-SNP	.											.	.	.	.	0			c.A340G						.						121	95	104					9																	129148868		2203	4300	6503	SO:0001583	missense	89853	exon4			GTAGATATGAAGC	AK000001	CCDS35142.1	9q34.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000196814	ENSG00000196814			23368	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 28", "family with sequence similarity 125, member B"	C9orf28, FAM125B		18005716, 20654576, 22232651	Standard	NM_033446		Approved	FLJ00001	uc004bqh.2	Q9H7P6	OTTHUMG00000020687	ENST00000361171.3:c.340A>G	chr9.hg19:g.129148868A>G	ENSP00000354772:p.Met114Val	51.0	0.0		58.0	18.0	NM_001011703	Q8N6S7	Missense_Mutation	SNP	ENST00000361171.3	hg19	CCDS35142.1	.	.	.	.	.	.	.	.	.	.	A	14.17	2.456758	0.43634	.	.	ENSG00000196814	ENST00000361171;ENST00000545391;ENST00000402437;ENST00000436593;ENST00000535766	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06	5.29	5.29	0.74685	MABP domain (1);	0.000000	0.85682	D	0.000000	T	0.41073	0.1143	L	0.58101	1.795	0.58432	D	0.999996	P;P;P	0.39535	0.677;0.476;0.476	B;B;B	0.40199	0.322;0.223;0.223	T	0.23691	-1.0181	10	0.13470	T	0.59	-1.0168	15.2378	0.73443	1.0:0.0:0.0:0.0	.	107;99;114	B7Z4X0;B7Z1P9;Q9H7P6	.;.;F125B_HUMAN	V	114;114;99;99;107	ENSP00000354772:M114V;ENSP00000441988:M114V;ENSP00000384751:M99V;ENSP00000401379:M99V;ENSP00000442846:M107V	ENSP00000354772:M114V	M	+	1	0	FAM125B	128188689	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.088000	0.76901	2.003000	0.58678	0.528000	0.53228	ATG	.	.		0.453	MVB12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054110.1	XM_088525		G	129148868	A	G	129148868	3	3	158	1	0	0	0	0	1	0	0	0	5433	449	16	2	354	2	FAM125B	9	129148868	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	28725518	129148868	12064563	55	24014										
RALGDS	5900	hgsc.bcm.edu	37	chr9	135985072	135985072	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	taggggaggatgcagccgtaTctagaggaggccgtgagggc	19	7	1	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:135985072T>C	ENST00000372050.3	-	4	546	c.525A>G	c.(523-525)agA>agG	p.R175R	RALGDS_ENST00000393157.3_Silent_p.R174R|RALGDS_ENST00000372047.3_Splice_Site_p.R163R|RALGDS_ENST00000393160.3_Silent_p.R120R|RALGDS_ENST00000542690.1_Silent_p.R246R|RALGDS_ENST00000469972.1_5'Flank|RALGDS_ENST00000372062.3_Splice_Site_p.R146R	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	175	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		TGCAGCCGTATCTAGAGGAGG	0.567			T	CIITA	"PMBL, Hodgkin Lymphona, "																																p.R175R	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.A525G						.						178	138	152					9																	135985072		2202	4300	6502	SO:0001819	synonymous_variant	5900	exon4			GCCGTATCTAGAG	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.525A>G	chr9.hg19:g.135985072T>C		88.0	0.0		90.0	34.0	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	hg19	CCDS6959.1																																																																																			.	.		0.567	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266		C	135985072	T	C	135985072	2	2	158	1	0	0	0	0	0	0	0	1	13031	1432	50	2		2	RALGDS	9	135985072	Silent	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	6836204	135985072	5228359	56	24015										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138660742	138660742	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	caactgccccctctacgtccAgatcctcaaacctgaaaaca	4	17	2	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:138660742A>G	ENST00000263604.3	+	15	1412	c.1412A>G	c.(1411-1413)cAg>cGg	p.Q471R	KCNT1_ENST00000487664.1_Missense_Mutation_p.Q445R|KCNT1_ENST00000488444.2_Missense_Mutation_p.Q471R|KCNT1_ENST00000371757.2_Missense_Mutation_p.Q490R|KCNT1_ENST00000486577.2_Missense_Mutation_p.Q451R|KCNT1_ENST00000491806.2_Missense_Mutation_p.Q457R|KCNT1_ENST00000490355.2_Missense_Mutation_p.Q471R|KCNT1_ENST00000298480.5_Missense_Mutation_p.Q490R			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	471					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		CTCTACGTCCAGATCCTCAAA	0.617																																					p.Q490R		Atlas-SNP	.											.	KCNT1	139	.	0			c.A1469G						.						122	105	111					9																	138660742		2201	4300	6501	SO:0001583	missense	57582	exon15			ACGTCCAGATCCT	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.1412A>G	chr9.hg19:g.138660742A>G	ENSP00000263604:p.Gln471Arg	39.0	0.0		33.0	13.0	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	A	21.0	4.083107	0.76642	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	3.75	3.75	0.43078	NAD(P)-binding domain (1);	0.000000	0.64402	D	0.000001	T	0.78799	0.4340	M	0.85542	2.76	0.80722	D	1	D;D;D;D	0.67145	0.983;0.996;0.99;0.983	D;D;D;P	0.70487	0.917;0.969;0.948;0.889	T	0.82325	-0.0513	10	0.87932	D	0	-10.1884	11.7981	0.52112	1.0:0.0:0.0:0.0	.	457;490;445;471	C9JYL2;B9EGP2;G5E9V0;Q5JUK3	.;.;.;KCNT1_HUMAN	R	445;490;490;451;457;471;471;471	ENSP00000417851:Q445R;ENSP00000298480:Q490R;ENSP00000360822:Q490R;ENSP00000263604:Q471R	ENSP00000263604:Q471R	Q	+	2	0	KCNT1	137800563	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	8.919000	0.92770	1.550000	0.49438	0.402000	0.26972	CAG	.	.		0.617	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		G	138660742	A	G	138660742	3	3	158	1	0	0	0	0	1	0	0	0	8100	188	7	2	1527	2	KCNT1	9	138660742	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	2675670	138660742	2552689	57	24016										
GBF1	8729	hgsc.bcm.edu	37	chr10	104140434	104140434	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	atgaactcttcaagcagaccGtcatccagggtagggggctc	12	11	3	2	rs142268101		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr10:104140434G>C	ENST00000369983.3	+	38	5421	c.5161G>C	c.(5161-5163)Gtc>Ctc	p.V1721L		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1721					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CAAGCAGACCGTCATCCAGGG	0.577																																					p.V1721L		Atlas-SNP	.											.	GBF1	142	.	0			c.G5161C						.						165	183	177					10																	104140434		2203	4300	6503	SO:0001583	missense	8729	exon38			CAGACCGTCATCC	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.5161G>C	chr10.hg19:g.104140434G>C	ENSP00000359000:p.Val1721Leu	69.0	0.0		53.0	34.0	NM_004193	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.979964	0.53827	.	.	ENSG00000107862	ENST00000369983	T	0.09911	2.93	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.31167	0.0788	L	0.57536	1.79	0.80722	D	1	P;D;D	0.63880	0.495;0.993;0.993	B;D;D	0.72075	0.062;0.976;0.976	T	0.00141	-1.1999	10	0.28530	T	0.3	-22.5885	20.2985	0.98592	0.0:0.0:1.0:0.0	.	1717;1717;1721	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	L	1721	ENSP00000359000:V1721L	ENSP00000359000:V1721L	V	+	1	0	GBF1	104130424	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.836000	0.86788	2.793000	0.96121	0.655000	0.94253	GTC	.	G|1.000;A|0.000		0.577	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			C	104140434	G	C	104140434	3	2	158	1	0	0	0	0	1	0	0	0	6279	1145	40	4	5307	4	GBF1	10	104140434	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10		104140434	31394313	58	24017										
ARL3	403	hgsc.bcm.edu	37	chr10	104465227	104465227	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ctggtgcacttttcaacttgCgcaaaattgagagcaagccc	9	11	1	1	rs368901451		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr10:104465227C>T	ENST00000260746.5	-	2	154	c.23G>A	c.(22-24)cGc>cAc	p.R8H		NM_004311.3	NP_004302.1	P36405	ARL3_HUMAN	ADP-ribosylation factor-like 3	8					cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|intraciliary transport (GO:0042073)|kidney development (GO:0001822)|photoreceptor cell development (GO:0042461)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|spindle microtubule (GO:0005876)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			large_intestine(2)	2		Colorectal(252;0.122)		Epithelial(162;4.88e-09)|all cancers(201;1.29e-07)|BRCA - Breast invasive adenocarcinoma(275;0.22)		TTTCAACTTGCGCAAAATTGA	0.463																																					p.R8H		Atlas-SNP	.											.	ARL3	13	.	0			c.G23A						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	107	90	96		23	4.2	1	10		96	0,8600		0,0,4300	no	missense	ARL3	NM_004311.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	8/183	104465227	1,13005	2203	4300	6503	SO:0001583	missense	403	exon2			AACTTGCGCAAAA	U07151	CCDS7538.1	10q23.3	2014-05-09			ENSG00000138175	ENSG00000138175		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	694	protein-coding gene	gene with protein product		604695				8034651, 10072593	Standard	NM_004311		Approved	ARFL3	uc001kwa.3	P36405	OTTHUMG00000018965	ENST00000260746.5:c.23G>A	chr10.hg19:g.104465227C>T	ENSP00000260746:p.Arg8His	84.0	0.0		61.0	31.0	NM_004311	B2R6C7|Q53X83|Q5JSM2	Missense_Mutation	SNP	ENST00000260746.5	hg19	CCDS7538.1	.	.	.	.	.	.	.	.	.	.	C	31	5.066753	0.93898	2.27E-4	0.0	ENSG00000138175	ENST00000260746	T	0.64618	-0.11	6.03	4.17	0.49024	.	0.882556	0.09697	N	0.767547	T	0.79240	0.4412	M	0.86502	2.82	0.80722	D	1	D	0.76494	0.999	P	0.58210	0.835	T	0.78250	-0.2277	10	0.62326	D	0.03	-22.8469	13.1907	0.59709	0.0:0.8695:0.0:0.1305	.	8	P36405	ARL3_HUMAN	H	8	ENSP00000260746:R8H	ENSP00000260746:R8H	R	-	2	0	ARL3	104455217	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.060000	0.71141	1.572000	0.49736	0.555000	0.69702	CGC	.	.		0.463	ARL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050088.2	NM_004311		T	104465227	C	T	104465227	3	4	158	1	0	0	0	0	1	0	0	0	935	768	27	1	545	1	ARL3	10	104465227	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	324793	104465227	31069520	59	24018										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124336218	124336218	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	taactgtggccatggtgaagAtgctggtgttatctgctcag	13	7	2	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr10:124336218A>G	ENST00000338354.3	+	7	693	c.587A>G	c.(586-588)gAt>gGt	p.D196G	DMBT1_ENST00000368956.2_Missense_Mutation_p.D196G|DMBT1_ENST00000344338.3_Missense_Mutation_p.D196G|DMBT1_ENST00000359586.6_Missense_Mutation_p.D196G|DMBT1_ENST00000330163.4_Missense_Mutation_p.D196G|DMBT1_ENST00000368955.3_Missense_Mutation_p.D196G|DMBT1_ENST00000368909.3_Missense_Mutation_p.D196G			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	196	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CATGGTGAAGATGCTGGTGTT	0.562																																					p.D196G	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.A587G						.						113	111	112					10																	124336218		2056	4193	6249	SO:0001583	missense	1755	exon7			GTGAAGATGCTGG		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.587A>G	chr10.hg19:g.124336218A>G	ENSP00000342210:p.Asp196Gly	95.0	0.0		84.0	20.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	a	33	5.207083	0.95033	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58	4.63	4.63	0.57726	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	D	0.83069	0.5174	H	0.98701	4.305	0.44175	D	0.996983	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.997;1.0;1.0;0.994;0.999;1.0	D	0.89635	0.3858	9	0.62326	D	0.03	.	14.3417	0.66630	1.0:0.0:0.0:0.0	.	196;196;196;196;196;196	F8WEF7;Q9UGM3-4;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;DMBT1_HUMAN	G	196	ENSP00000342210:D196G;ENSP00000343175:D196G;ENSP00000327747:D196G;ENSP00000357905:D196G;ENSP00000357951:D196G;ENSP00000357952:D196G;ENSP00000352593:D196G	ENSP00000331522:D196G	D	+	2	0	DMBT1	124326208	1.000000	0.71417	0.034000	0.17996	0.728000	0.41692	7.112000	0.77086	1.853000	0.53794	0.533000	0.62120	GAT	.	.		0.562	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		G	124336218	A	G	124336218	3	3	158	1	0	0	0	0	1	0	0	0	4579	333	12	2	613	2	DMBT1	10	124336218	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	19870991	124336218	11198529	60	24019										
MKI67	4288	hgsc.bcm.edu	37	chr10	129913465	129913465	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agctgcatcttcaactttagCtggtgttcgatttctagttg	9	8	3	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr10:129913465C>G	ENST00000368654.3	-	7	1582	c.1207G>C	c.(1207-1209)Gct>Cct	p.A403P	MKI67_ENST00000484853.1_5'Flank|MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	403					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TCAACTTTAGCTGGTGTTCGA	0.438																																					p.A403P		Atlas-SNP	.											.	MKI67	363	.	0			c.G1207C						.						91	93	92					10																	129913465		2203	4300	6503	SO:0001583	missense	4288	exon7			CTTTAGCTGGTGT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.1207G>C	chr10.hg19:g.129913465C>G	ENSP00000357643:p.Ala403Pro	118.0	0.0		110.0	31.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.436079	0.43224	.	.	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.01516	4.81	4.0	-5.46	0.02608	.	3.288320	0.00866	N	0.001962	T	0.02807	0.0084	N	0.19112	0.55	0.09310	N	1	D	0.61080	0.989	P	0.50708	0.648	T	0.40213	-0.9575	10	0.87932	D	0	.	12.4406	0.55623	0.0:0.2242:0.0:0.7758	.	403	P46013	KI67_HUMAN	P	403	ENSP00000357643:A403P	ENSP00000357643:A403P	A	-	1	0	MKI67	129803455	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	-2.827000	0.00746	-1.180000	0.02734	-0.302000	0.09304	GCT	.	.		0.438	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		G	129913465	C	G	129913465	3	3	158	1	0	0	0	0	1	0	0	0	9607	797	28	4	8599	4	MKI67	10	129913465	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	5577247	129913465	5621282	61	24020										
CYP2E1	1571	hgsc.bcm.edu	37	chr10	135352460	135352460	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	acaaactctgtgtcattcccCgctcatgagtgtgtggagga	11	10	3	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr10:135352460C>T	ENST00000463117.2	+	11	1746	c.1474C>T	c.(1474-1476)Cgc>Tgc	p.R492C	SPRN_ENST00000541506.1_Intron|CYP2E1_ENST00000252945.3_Missense_Mutation_p.R492C			P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E, polypeptide 1	492					drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organonitrogen compound (GO:0010243)|response to ozone (GO:0010193)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|triglyceride metabolic process (GO:0006641)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(7)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Aldesleukin(DB00041)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminophylline(DB01223)|Amitriptyline(DB00321)|Antipyrine(DB01435)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupropion(DB01156)|Caffeine(DB00201)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Citalopram(DB00215)|Clevidipine(DB04920)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonazepam(DB01068)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Dacarbazine(DB00851)|Dalfampridine(DB06637)|Dapsone(DB00250)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Disulfiram(DB00822)|Econazole(DB01127)|Enflurane(DB00228)|Enfuvirtide(DB00109)|Estrone(DB00655)|Ethanol(DB00898)|Ethanolamine Oleate(DB06689)|Ethosuximide(DB00593)|Etoposide(DB00773)|Etoricoxib(DB01628)|Felbamate(DB00949)|Fingolimod(DB08868)|Flunitrazepam(DB01544)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluvoxamine(DB00176)|Folic Acid(DB00158)|Fomepizole(DB01213)|Glucosamine(DB01296)|Halothane(DB01159)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imipramine(DB00458)|Isoflurane(DB00753)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Itraconazole(DB01167)|Menadione(DB00170)|Meprobamate(DB00371)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Mexiletine(DB00379)|Miconazole(DB01110)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nitrazepam(DB01595)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Orphenadrine(DB01173)|Oxaliplatin(DB00526)|Paramethadione(DB00617)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Pimozide(DB01100)|Proguanil(DB01131)|Propofol(DB00818)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rufinamide(DB06201)|S-Adenosylmethionine(DB00118)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulfadiazine(DB00359)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiopental(DB00599)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Ursodeoxycholic acid(DB01586)|Zafirlukast(DB00549)|Zopiclone(DB01198)	TGTCATTCCCCGCTCATGAGT	0.453									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.R492C		Atlas-SNP	.											.	CYP2E1	69	.	0			c.C1474T						.						103	84	90					10																	135352460		2203	4300	6503	SO:0001583	missense	1571	exon9	Familial Cancer Database	incl.: Familial Head and Neck Cancer	ATTCCCCGCTCAT	J02843	CCDS7686.1	10q26.3	2013-05-03	2003-01-14	2002-09-13	ENSG00000130649	ENSG00000130649		"Cytochrome P450s"	2631	protein-coding gene	gene with protein product		124040	"cytochrome P450, subfamily IIE (ethanol-inducible), polypeptide 1"	CYP2E			Standard	NM_000773		Approved		uc001lnj.1	P05181	OTTHUMG00000019322	ENST00000463117.2:c.1474C>T	chr10.hg19:g.135352460C>T	ENSP00000440689:p.Arg492Cys	77.0	0.0		53.0	23.0	NM_000773	Q5VZD5|Q6NWT9|Q9UK47	Missense_Mutation	SNP	ENST00000463117.2	hg19	CCDS7686.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.372590	0.42003	.	.	ENSG00000130649	ENST00000463117;ENST00000252945	T;T	0.66638	-0.22;-0.22	4.64	3.73	0.42828	.	0.000000	0.85682	D	0.000000	T	0.77903	0.4200	M	0.64170	1.965	0.41488	D	0.988206	D	0.89917	1.0	D	0.85130	0.997	T	0.80132	-0.1510	10	0.72032	D	0.01	.	12.1856	0.54236	0.1721:0.8279:0.0:0.0	.	492	P05181	CP2E1_HUMAN	C	492	ENSP00000440689:R492C;ENSP00000252945:R492C	ENSP00000252945:R492C	R	+	1	0	CYP2E1	135202450	0.064000	0.20934	0.549000	0.28204	0.064000	0.16182	1.363000	0.34159	1.299000	0.44798	0.491000	0.48974	CGC	.	.		0.453	CYP2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051161.2	NM_000773		T	135352460	C	T	135352460	3	4	158	1	0	0	0	0	1	0	0	0	4172	652	23	1	1508	1	CYP2E1	10	135352460	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	5438995	135352460	182287	62	24021										
HBD	3045	hgsc.bcm.edu	37	chr11	5254217	5254217	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	atggtacttgtgagccagggCattagccacaccagccacca	10	13	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:5254217C>A	ENST00000380299.3	-	3	635	c.421G>T	c.(421-423)Gcc>Tcc	p.A141S	HBD_ENST00000292901.3_Intron	NM_000519.3	NP_000510.1	P02042	HBD_HUMAN	hemoglobin, delta	141			A -> V (in Bagheria). {ECO:0000269|PubMed:17145605}.		blood coagulation (GO:0007596)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			endometrium(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	16		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;5.69e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGAGCCAGGGCATTAGCCACA	0.493																																					p.A141S		Atlas-SNP	.											.	HBD	35	.	0			c.G421T						.						158	138	145					11																	5254217		2201	4298	6499	SO:0001583	missense	3045	exon3			CCAGGGCATTAGC	AY034468	CCDS31376.1	11p15.5	2012-10-02			ENSG00000223609	ENSG00000223609			4829	protein-coding gene	gene with protein product		142000				2649166	Standard	NM_000519		Approved		uc001maf.1	P02042	OTTHUMG00000066674	ENST00000380299.3:c.421G>T	chr11.hg19:g.5254217C>A	ENSP00000369654:p.Ala141Ser	91.0	0.0		87.0	18.0	NM_000519	Q3Y5H3|Q8WXT7	Missense_Mutation	SNP	ENST00000380299.3	hg19	CCDS31376.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	14.13|14.13	2.442754|2.442754	0.43326|0.43326	.|.	.|.	ENSG00000223609|ENSG00000223609	ENST00000380299|ENST00000417377	D|D	0.94537|0.86432	-3.45|-2.12	4.8|4.8	2.92|2.92	0.33932|0.33932	Globin-like (1);Globin, structural domain (1);|.	.|.	.|.	.|.	.|.	D|D	0.91229|0.91229	0.7236|0.7236	M|M	0.88310|0.88310	2.945|2.945	0.22001|0.22001	N|N	0.999425|0.999425	D|.	0.61697|.	0.99|.	D|.	0.75484|.	0.986|.	D|D	0.83916|0.83916	0.0298|0.0298	9|7	0.87932|0.87932	D|D	0|0	.|.	7.8913|7.8913	0.29680|0.29680	0.0:0.8148:0.0:0.1852|0.0:0.8148:0.0:0.1852	.|.	141|.	P02042|.	HBD_HUMAN|.	S|I	141|66	ENSP00000369654:A141S|ENSP00000414741:M66I	ENSP00000369654:A141S|ENSP00000414741:M66I	A|M	-|-	1|3	0|0	HBD|HBD	5210793|5210793	0.236000|0.236000	0.23804|0.23804	0.017000|0.017000	0.16124|0.16124	0.491000|0.491000	0.33493|0.33493	1.473000|1.473000	0.35387|0.35387	0.737000|0.737000	0.32582|0.32582	0.650000|0.650000	0.86243|0.86243	GCC|ATG	.	.		0.493	HBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142970.1	NM_000519		A	5254217	C	A	5254217	3	1	158	1	0	0	0	0	1	0	0	0	6988	710	25	3	26	3	HBD	11	5254217	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10		5254217	129752299	63	24022										
CD44	960	hgsc.bcm.edu	37	chr11	35208383	35208383	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ttttcctacctcatagctccAcctgaagaagattgtacatc	5	12	1	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:35208383A>T	ENST00000428726.2	+	4	495	c.372A>T	c.(370-372)ccA>ccT	p.P124P	CD44_ENST00000526669.2_Intron|CD44_ENST00000434472.2_Silent_p.P124P|CD44_ENST00000263398.6_Silent_p.P124P|CD44_ENST00000433354.2_Silent_p.P124P|CD44_ENST00000278386.6_Intron|CD44_ENST00000437706.2_Silent_p.P124P|CD44_ENST00000352818.4_Silent_p.P124P|CD44_ENST00000360158.4_Silent_p.P124P|CD44_ENST00000433892.2_Silent_p.P124P|CD44_ENST00000449691.2_Silent_p.P124P|CD44_ENST00000415148.2_Silent_p.P124P	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	124					blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	TCATAGCTCCACCTGAAGAAG	0.348																																					p.P124P		Atlas-SNP	.											.	CD44	48	.	0			c.A372T						.						147	140	143					11																	35208383		2202	4298	6500	SO:0001819	synonymous_variant	960	exon4			AGCTCCACCTGAA	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"CD molecules", "Blood group antigens", "Proteoglycans / Cell surface : Other"	1681	protein-coding gene	gene with protein product	"hematopoietic cell E- and L-selectin ligand", "chondroitin sulfate proteoglycan 8"	107269	"CD44 antigen (homing function and Indian blood group system)"	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.372A>T	chr11.hg19:g.35208383A>T		79.0	0.0		78.0	29.0	NM_001001391	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	hg19	CCDS7897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.12|13.12	2.142421|2.142421	0.37825|0.37825	.|.	.|.	ENSG00000026508|ENSG00000026508	ENST00000527889;ENST00000531873|ENST00000442151;ENST00000528455	.|.	.|.	.|.	4.76|4.76	-6.03|-6.03	0.02185|0.02185	.|.	.|.	.|.	.|.	.|.	T|T	0.47284|0.47284	0.1437|0.1437	.|.	.|.	.|.	0.33917|0.33917	D|D	0.64039|0.64039	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.58880|0.58880	-0.7558|-0.7558	4|5	.|0.87932	.|D	.|0	-1.0333|-1.0333	4.403|4.403	0.11395|0.11395	0.3457:0.0:0.3983:0.256|0.3457:0.0:0.3983:0.256	.|.	.|.	.|.	.|.	L|S	80;45|124;61	.|.	.|ENSP00000395953:T80S	H|T	+|+	2|1	0|0	CD44|CD44	35164959|35164959	0.000000|0.000000	0.05858|0.05858	0.005000|0.005000	0.12908|0.12908	0.007000|0.007000	0.05969|0.05969	-0.790000|-0.790000	0.04604|0.04604	-1.146000|-1.146000	0.02854|0.02854	-0.366000|-0.366000	0.07423|0.07423	CAC|ACC	.	.		0.348	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610		T	35208383	A	T	35208383	2	4	158	1	0	0	0	0	0	0	0	1	3019	146	6	4		4	CD44	11	35208383	Silent	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	29954166	35208383	99798133	64	24023										
PTPMT1	114971	hgsc.bcm.edu	37	chr11	47591365	47591365	+	Frame_Shift_Del	DEL	G	G	-													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	tttgctctcaagtaccagtcGctgggccagtgtgtttacgt							TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:47591365delG	ENST00000326674.9	+	3	391	c.369delG	c.(367-369)tcgfs	p.S123fs	PTPMT1_ENST00000426530.2_Intron|PTPMT1_ENST00000527079.2_3'UTR|PTPMT1_ENST00000534775.1_Frame_Shift_Del_p.A160fs|PTPMT1_ENST00000326656.8_Intron|NDUFS3_ENST00000533507.1_Intron	NM_175732.2	NP_783859.1	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	123	Tyrosine-protein phosphatase.				cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|inositol phosphate dephosphorylation (GO:0046855)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylglycerophosphatase activity (GO:0008962)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	6						AGTACCAGTCGCTGGGCCAGT	0.547																																					p.S123fs		Atlas-INDEL	.											.	PTPMT1	17	.	0			c.368delC						.						110	112	112					11																	47591365		2013	4163	6176	SO:0001589	frameshift_variant	114971	exon3			.	BC014048	CCDS41643.1, CCDS44593.1	11p11.2	2011-06-09			ENSG00000110536	ENSG00000110536	3.1.3.36	"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	26965	protein-coding gene	gene with protein product		609538				12477932	Standard	NM_175732		Approved	PLIP, DUSP23, MOSP	uc001nfs.4	Q8WUK0	OTTHUMG00000166892	ENST00000326674.9:c.369delG	chr11.hg19:g.47591365delG	ENSP00000325958:p.Ser123fs	86.0	0.0		89.0	33.0	NM_175732	E9PAT8|Q7Z557|Q96CR2|Q9BXV8	Frame_Shift_Del	DEL	ENST00000326674.9	hg19	CCDS41643.1																																																																																			.	.		0.547	PTPMT1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391746.1	XM_374879		-	47591365	G	-	47591365	7	5	158	1	0	1	0	1	0	0	0	0	12791	1074	38	0	484	0	PTPMT1	11	47591365	Frame_Shift_Del	DEL	G	TCGA-DD-AACG-01A-11D-A40R-10	12382982	47591365	87415151	65	24024										
GLYATL1	92292	hgsc.bcm.edu	37	chr11	58723497	58723497	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ccacagaatctagttccattTtagacaatgaagctgcttag	7	9	1	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:58723497T>G	ENST00000317391.4	+	8	1246	c.906T>G	c.(904-906)ttT>ttG	p.F302L	GLYATL1_ENST00000300079.5_Missense_Mutation_p.F333L|RP11-142C4.6_ENST00000533954.1_RNA|RP11-142C4.6_ENST00000525714.1_RNA	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	302						mitochondrion (GO:0005739)	glutamine N-acyltransferase activity (GO:0047946)|glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|skin(4)|urinary_tract(1)	34					Glycine(DB00145)	TAGTTCCATTTTAGACAATGA	0.423																																					p.F333L		Atlas-SNP	.											.	GLYATL1	89	.	0			c.T999G						.						46	47	47					11																	58723497		2201	4292	6493	SO:0001583	missense	92292	exon7			TCCATTTTAGACA	AK091965	CCDS31556.1, CCDS55768.1	11q12.1	2014-08-12			ENSG00000166840	ENSG00000166840			30519	protein-coding gene	gene with protein product		614761				12477932	Standard	NM_080661		Approved	MGC15397, FLJ34646	uc001nnh.2	Q969I3	OTTHUMG00000167221	ENST00000317391.4:c.906T>G	chr11.hg19:g.58723497T>G	ENSP00000322223:p.Phe302Leu	75.0	0.0		80.0	36.0	NM_080661	A6NDT0|Q7Z510|Q8NAW8	Missense_Mutation	SNP	ENST00000317391.4	hg19	CCDS55768.1	.	.	.	.	.	.	.	.	.	.	.	3.217	-0.160382	0.06502	.	.	ENSG00000166840	ENST00000444580;ENST00000317391;ENST00000300079	T;T	0.20598	2.55;2.06	1.67	-0.859	0.10685	.	1.074110	0.07478	N	0.903386	T	0.10508	0.0257	N	0.16478	0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38090	-0.9677	10	0.19147	T	0.46	.	4.1596	0.10277	0.0:0.4767:0.0:0.5233	.	333;302	Q969I3-2;Q969I3	.;GLYL1_HUMAN	L	279;302;333	ENSP00000322223:F302L;ENSP00000300079:F333L	ENSP00000300079:F333L	F	+	3	2	GLYATL1	58480073	0.021000	0.18746	0.004000	0.12327	0.116000	0.19942	1.550000	0.36223	-0.063000	0.13065	0.338000	0.21704	TTT	.	.		0.423	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	NM_080661		G	58723497	T	G	58723497	3	3	158	1	0	0	0	0	1	0	0	0	6488	1838	64	5	1025	5	GLYATL1	11	58723497	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	11132132	58723497	76283019	66	24025										
MS4A7	58475	hgsc.bcm.edu	37	chr11	60157018	60157018	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ttgccttattcggagtactaTtatccaatatatgaaatcaa	5	7	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:60157018T>C	ENST00000300184.3	+	5	691	c.495T>C	c.(493-495)taT>taC	p.Y165Y	MS4A7_ENST00000534016.1_Silent_p.Y120Y|MS4A7_ENST00000530234.2_Intron|MS4A7_ENST00000358246.1_Silent_p.Y120Y|MS4A14_ENST00000531787.1_Intron	NM_021201.4|NM_206939.1	NP_067024.1|NP_996822.1	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member 7	165						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(8)|ovary(1)|skin(1)	20						CGGAGTACTATTATCCAATAT	0.418																																					p.Y165Y		Atlas-SNP	.											.	MS4A7	38	.	0			c.T495C						.						124	115	118					11																	60157018		2203	4300	6503	SO:0001819	synonymous_variant	58475	exon5			GTACTATTATCCA	AB026043	CCDS7985.1, CCDS7986.1	11q12	2008-03-25				ENSG00000166927			13378	protein-coding gene	gene with protein product		606502				11245982, 11401424	Standard	NM_021201		Approved	CD20L4, CFFM4, MS4A8	uc001npf.3	Q9GZW8		ENST00000300184.3:c.495T>C	chr11.hg19:g.60157018T>C		60.0	0.0		58.0	18.0	NM_021201	A6NP53|Q6IAG8	Silent	SNP	ENST00000300184.3	hg19	CCDS7985.1																																																																																			.	.		0.418	MS4A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394299.1			C	60157018	T	C	60157018	2	2	158	1	0	0	0	0	0	0	0	1	9875	1500	52	2		2	MS4A7	11	60157018	Silent	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	1433521	60157018	74849498	67	24026										
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94603926	94603926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cttgctgcacaagcccgagtTccctgatggagagatgatgg	13	10	0	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:94603926T>C	ENST00000433060.2	+	13	2978	c.2837T>C	c.(2836-2838)tTc>tCc	p.F946S	AMOTL1_ENST00000317829.8_Missense_Mutation_p.F896S|AMOTL1_ENST00000317837.9_Missense_Mutation_p.F533S	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	946					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				AAGCCCGAGTTCCCTGATGGA	0.522																																					p.F946S		Atlas-SNP	.											.	AMOTL1	95	.	0			c.T2837C						.						34	36	35					11																	94603926		1954	4145	6099	SO:0001583	missense	154810	exon13			CCGAGTTCCCTGA	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"junction-enriched and associated protein"	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2837T>C	chr11.hg19:g.94603926T>C	ENSP00000387739:p.Phe946Ser	47.0	0.0		45.0	17.0	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	hg19	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	T	19.35	3.811101	0.70797	.	.	ENSG00000166025	ENST00000317829;ENST00000317837;ENST00000433060	T;T;T	0.61392	1.75;0.11;1.7	5.56	5.56	0.83823	.	0.152891	0.45867	D	0.000329	T	0.70404	0.3220	L	0.57536	1.79	0.24328	N	0.995018	D;P	0.69078	0.997;0.771	P;B	0.62184	0.899;0.226	T	0.65606	-0.6127	10	0.56958	D	0.05	-10.5661	15.7213	0.77713	0.0:0.0:0.0:1.0	.	896;946	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	S	896;533;946	ENSP00000320968:F896S;ENSP00000323474:F533S;ENSP00000387739:F946S	ENSP00000320968:F896S	F	+	2	0	AMOTL1	94243574	1.000000	0.71417	0.989000	0.46669	0.413000	0.31143	5.322000	0.65852	2.127000	0.65507	0.379000	0.24179	TTC	.	.		0.522	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		C	94603926	T	C	94603926	3	2	158	1	0	0	0	0	1	0	0	0	583	1783	62	2	2887	2	AMOTL1	11	94603926	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	34446908	94603926	40402590	68	24027										
CEP164	22897	hgsc.bcm.edu	37	chr11	117251354	117251359	+	In_Frame_Del	DEL	GACAAG	GACAAG	-													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agcaaccactgggaatagaaGacaaggatgacagccagtcc					rs144135343		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	GACAAG	GACAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:117251354_117251359delGACAAG	ENST00000278935.3	+	12	1489_1494	c.1342_1347delGACAAG	c.(1342-1347)gacaagdel	p.DK448del	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	448					cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		GGGAATAGAAGACAAGGATGACAGCC	0.549																																					p.447_449del		Atlas-INDEL	.											.	CEP164	121	.	0			c.1341_1346del						.																																			SO:0001651	inframe_deletion	22897	exon11			.	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.1342_1347delGACAAG	chr11.hg19:g.117251354_117251359delGACAAG	ENSP00000278935:p.Asp448_Lys449del	68.0	0.0		54.0	19.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	In_Frame_Del	DEL	ENST00000278935.3	hg19	CCDS31683.1																																																																																			.	.		0.549	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		-	117251359	GACAAG	-	117251354	7	5	158	1	0	1	0	1	0	0	0	0	3251	942	33	0	1380	0	CEP164	11	117251354	In_Frame_Del	DEL	GACAAG	TCGA-DD-AACG-01A-11D-A40R-10	22647428	117251354	17755162	69	24028										
USP2	9099	hgsc.bcm.edu	37	chr11	119243744	119243744	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gaggtccggaggctggagaaAtcccgggccaggtctgattg	17	9	1	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:119243744A>G	ENST00000260187.2	-	2	741	c.447T>C	c.(445-447)gaT>gaC	p.D149D	RP11-334E6.3_ENST00000530918.2_RNA|USP2_ENST00000455332.2_Intron	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	149	Necessary for interaction with MDM4.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		GGCTGGAGAAATCCCGGGCCA	0.627																																					p.D149D		Atlas-SNP	.											.	USP2	71	.	0			c.T447C						.						55	63	61					11																	119243744		2199	4295	6494	SO:0001819	synonymous_variant	9099	exon2			GGAGAAATCCCGG	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"Ubiquitin-specific peptidases"	12618	protein-coding gene	gene with protein product		604725	"ubiquitin specific protease 2"			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.447T>C	chr11.hg19:g.119243744A>G		84.0	0.0		70.0	26.0	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	hg19	CCDS8422.1																																																																																			.	.		0.627	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997		G	119243744	A	G	119243744	2	3	158	1	0	0	0	0	0	0	0	1	17066	98	4	2		2	USP2	11	119243744	Silent	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	1992390	119243744	15762772	70	24029										
VWF	7450	hgsc.bcm.edu	37	chr12	6182863	6182863	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ctggcaggtcctggcgcaagGggacacacactgcctatact	12	13	0	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:6182863G>A	ENST00000261405.5	-	8	1173	c.919C>T	c.(919-921)Cct>Tct	p.P307S		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	307	TIL 1.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.P307S(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CTGGCGCAAGGGGACACACAC	0.557																																					p.P307S		Atlas-SNP	.											VWF,NS,carcinoma,0,1	VWF	338	.	1	Substitution - Missense(1)	lung(1)	c.C919T						.						124	101	109					12																	6182863		2203	4300	6503	SO:0001583	missense	7450	exon8			CGCAAGGGGACAC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.919C>T	chr12.hg19:g.6182863G>A	ENSP00000261405:p.Pro307Ser	28.0	0.0		39.0	18.0	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	hg19	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.304563	0.60305	.	.	ENSG00000110799	ENST00000261405	D	0.90133	-2.62	5.07	5.07	0.68467	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	0.000000	0.41097	D	0.000949	D	0.90762	0.7100	N	0.17082	0.46	0.80722	D	1	P;D	0.89917	0.623;1.0	B;D	0.87578	0.401;0.998	D	0.89663	0.3878	10	0.26408	T	0.33	.	17.0171	0.86422	0.0:0.0:1.0:0.0	.	307;307	B4DNX0;P04275	.;VWF_HUMAN	S	307	ENSP00000261405:P307S	ENSP00000261405:P307S	P	-	1	0	VWF	6053124	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	4.058000	0.57463	2.352000	0.79861	0.491000	0.48974	CCT	.	.		0.557	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6182863	G	A	6182863	3	1	158	1	0	0	0	0	1	0	0	0	17261	1232	43	3	7702	3	VWF	12	6182863	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10		6182863	127669032	71	24030										
CLEC9A	283420	hgsc.bcm.edu	37	chr12	10205329	10205329	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cctctcttcagtgggatagcCcagcaccagacacttaccag	8	15	2	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:10205329C>G	ENST00000355819.1	+	4	656	c.43C>G	c.(43-45)Cca>Gca	p.P15A	CLEC9A_ENST00000544751.1_3'UTR	NM_207345.2	NP_997228.1	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A	15					positive regulation of cytokine secretion (GO:0050715)|receptor-mediated endocytosis (GO:0006898)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	22						GTGGGATAGCCCAGCACCAGA	0.418																																					p.P15A		Atlas-SNP	.											.	CLEC9A	41	.	0			c.C43G						.						118	109	112					12																	10205329		2203	4300	6503	SO:0001583	missense	283420	exon4			GATAGCCCAGCAC		CCDS8611.1	12p13.31	2010-04-27				ENSG00000197992		"C-type lectin domain containing"	26705	protein-coding gene	gene with protein product		612252					Standard	NM_207345		Approved	UNQ9341, HEEE9341	uc001qxa.3	Q6UXN8		ENST00000355819.1:c.43C>G	chr12.hg19:g.10205329C>G	ENSP00000348074:p.Pro15Ala	103.0	0.0		54.0	26.0	NM_207345	B0ZBM2	Missense_Mutation	SNP	ENST00000355819.1	hg19	CCDS8611.1	.	.	.	.	.	.	.	.	.	.	C	8.653	0.898740	0.17686	.	.	ENSG00000197992	ENST00000355819	T	0.01438	4.89	4.2	3.31	0.37934	.	0.380726	0.19384	N	0.115570	T	0.02230	0.0069	L	0.50333	1.59	0.09310	N	1	P	0.48834	0.916	P	0.45712	0.491	T	0.47433	-0.9118	10	0.45353	T	0.12	.	7.8528	0.29464	0.0:0.8894:0.0:0.1106	.	15	Q6UXN8	CLC9A_HUMAN	A	15	ENSP00000348074:P15A	ENSP00000348074:P15A	P	+	1	0	CLEC9A	10096596	0.001000	0.12720	0.005000	0.12908	0.056000	0.15407	0.454000	0.21827	1.361000	0.45981	0.655000	0.94253	CCA	.	.		0.418	CLEC9A-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000399564.1	NM_207345		G	10205329	C	G	10205329	3	3	158	1	0	0	0	0	1	0	0	0	3524	623	22	4	45	4	CLEC9A	12	10205329	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	4022466	10205329	123646566	72	24031										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32136720	32136720	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agaaccagaaaaacaattagAtaataccactgaaaataaag	5	6	0	4			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:32136720A>G	ENST00000312561.4	+	4	3245	c.2831A>G	c.(2830-2832)gAt>gGt	p.D944G	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	944																	AAACAATTAGATAATACCACT	0.378																																					p.D944G		Atlas-SNP	.											.	.	.	.	0			c.A2831G						.						38	37	38					12																	32136720		2203	4300	6503	SO:0001583	missense	55196	exon4			AATTAGATAATAC	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.2831A>G	chr12.hg19:g.32136720A>G	ENSP00000310338:p.Asp944Gly	79.0	0.0		42.0	19.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	A	16.28	3.079373	0.55753	.	.	ENSG00000174718	ENST00000312561	T	0.12879	2.64	5.67	4.54	0.55810	.	1.377390	0.04380	N	0.360631	T	0.25975	0.0633	L	0.54323	1.7	0.09310	N	1	D	0.56746	0.977	P	0.51016	0.656	T	0.12863	-1.0531	9	.	.	.	.	9.7098	0.40238	0.9214:0.0:0.0786:0.0	.	944	Q9HCM1	CL035_HUMAN	G	944	ENSP00000310338:D944G	.	D	+	2	0	C12orf35	32027987	0.025000	0.19082	0.001000	0.08648	0.011000	0.07611	1.719000	0.38011	0.993000	0.38866	0.459000	0.35465	GAT	.	.		0.378	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		G	32136720	A	G	32136720	3	3	158	1	0	0	0	0	1	0	0	0	1684	333	12	2	2833	2	C12orf35	12	32136720	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	21931391	32136720	101715175	73	24032										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41900359	41900359	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	caggtgttaaggcgaacaccTcttagtagaccagcctatgg	11	10	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:41900359T>C	ENST00000402685.2	+	4	953	c.945T>C	c.(943-945)ccT>ccC	p.P315P	PDZRN4_ENST00000298919.7_Silent_p.P55P|PDZRN4_ENST00000539469.2_Silent_p.P57P	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	315							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				GGCGAACACCTCTTAGTAGAC	0.512																																					p.P315P		Atlas-SNP	.											.	PDZRN4	346	.	0			c.T945C						.						140	118	126					12																	41900359		2203	4300	6503	SO:0001819	synonymous_variant	29951	exon4			AACACCTCTTAGT	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.945T>C	chr12.hg19:g.41900359T>C		87.0	0.0		59.0	39.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	hg19	CCDS53777.1																																																																																			.	.		0.512	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		C	41900359	T	C	41900359	2	2	158	1	0	0	0	0	0	0	0	1	11719	1538	54	2		2	PDZRN4	12	41900359	Silent	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	9763639	41900359	91951536	74	24033										
LRP1	4035	hgsc.bcm.edu	37	chr12	57594875	57594875	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	aacaccaaccgctgtattccCggcatcttccgctgcaatgg	8	15	1	0	rs551393670		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:57594875C>T	ENST00000243077.3	+	65	10750	c.10284C>T	c.(10282-10284)ccC>ccT	p.P3428P		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3428	LDL-receptor class A 23. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GCTGTATTCCCGGCATCTTCC	0.597																																					p.P3428P		Atlas-SNP	.											.	LRP1	428	.	0			c.C10284T						.						241	200	214					12																	57594875		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon65			TATTCCCGGCATC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.10284C>T	chr12.hg19:g.57594875C>T		55.0	0.0		60.0	15.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.597	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57594875	C	T	57594875	2	4	158	1	0	0	0	0	0	0	0	1	8960	639	23	1		1	LRP1	12	57594875	Silent	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	15694516	57594875	76257020	75	24034										
CIT	11113	hgsc.bcm.edu	37	chr12	120220408	120220408	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gtcatcctcctgggacacctCcatccgtgcttgctccaaac	7	17	1	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:120220408C>T	ENST00000261833.7	-	13	1631	c.1579G>A	c.(1579-1581)Gag>Aag	p.E527K	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Missense_Mutation_p.E527K	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	527					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		TGGGACACCTCCATCCGTGCT	0.473																																					p.E527K		Atlas-SNP	.											.	CIT	535	.	0			c.G1579A						.						106	96	99					12																	120220408		2203	4300	6503	SO:0001583	missense	11113	exon13			ACACCTCCATCCG	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.1579G>A	chr12.hg19:g.120220408C>T	ENSP00000261833:p.Glu527Lys	65.0	0.0		49.0	27.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.380699|5.380699	0.95945|0.95945	.|.	.|.	ENSG00000122966|ENSG00000122966	ENST00000392521;ENST00000261833|ENST00000392520	T;T|.	0.64438|.	-0.1;-0.1|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.59280|.	0.2182|.	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D;P;P|.	0.60575|.	0.988;0.851;0.908|.	P;B;B|.	0.55508|.	0.777;0.253;0.436|.	T|.	0.49173|.	-0.8967|.	10|.	0.33940|.	T|.	0.23|.	.|.	20.8794|20.8794	0.99867|0.99867	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	527;527;60|.	Q2M5E1;O14578;O14578-3|.	.;CTRO_HUMAN;.|.	K|X	527|154	ENSP00000376306:E527K;ENSP00000261833:E527K|.	ENSP00000261833:E527K|.	E|W	-|-	1|3	0|0	CIT|CIT	118704791|118704791	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.999000|5.999000	0.70665|0.70665	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GAG|TGG	.	.		0.473	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120220408	C	T	120220408	3	4	158	1	0	0	0	0	1	0	0	0	3440	864	30	3	4644	3	CIT	12	120220408	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	62625533	120220408	13631487	76	24035										
TMTC4	84899	hgsc.bcm.edu	37	chr13	101289831	101289831	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gcaaaggaggccgggttgtcCacctcggtgaaggccggcgg	18	11	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr13:101289831C>A	ENST00000376234.3	-	8	1092	c.903G>T	c.(901-903)gtG>gtT	p.V301V	TMTC4_ENST00000342624.5_Silent_p.V320V|TMTC4_ENST00000328767.5_Silent_p.V190V|TMTC4_ENST00000462211.1_5'UTR	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	301						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CCGGGTTGTCCACCTCGGTGA	0.637																																					p.V320V		Atlas-SNP	.											.	TMTC4	103	.	0			c.G960T						.						61	67	65					13																	101289831		2203	4300	6503	SO:0001819	synonymous_variant	84899	exon9			GTTGTCCACCTCG		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"Tetratricopeptide (TTC) repeat domain containing"	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.903G>T	chr13.hg19:g.101289831C>A		88.0	0.0		65.0	24.0	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	hg19	CCDS41904.1																																																																																			.	.		0.637	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		A	101289831	C	A	101289831	2	1	158	1	0	0	0	0	0	0	0	1	16278	581	21	3		3	TMTC4	13	101289831	Silent	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10		101289831	13880047	77	24036										
PRPF39	55015	hgsc.bcm.edu	37	chr14	45571737	45571737	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	aatttaatttttcagaacttTtgagcatgctgttctagctg	7	6	2	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr14:45571737T>G	ENST00000355765.6	+	5	745	c.575T>G	c.(574-576)tTt>tGt	p.F192C		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	192					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						TTCAGAACTTTTGAGCATGCT	0.313																																					p.F192C		Atlas-SNP	.											.	PRPF39	46	.	0			c.T575G						.						52	55	54					14																	45571737		2202	4300	6502	SO:0001583	missense	55015	exon5			GAACTTTTGAGCA	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"PRP39 pre-mRNA processing factor 39 homolog (yeast)", "PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.575T>G	chr14.hg19:g.45571737T>G	ENSP00000348010:p.Phe192Cys	74.0	0.0		43.0	23.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	T	18.15	3.560757	0.65538	.	.	ENSG00000185246	ENST00000355765;ENST00000355846	T	0.36878	1.23	5.62	5.62	0.85841	.	0.157792	0.64402	D	0.000018	T	0.55337	0.1914	M	0.68317	2.08	0.41612	D	0.988919	D;D	0.76494	0.999;0.998	D;P	0.70016	0.967;0.891	T	0.60000	-0.7348	10	0.87932	D	0	-24.4203	10.5592	0.45135	0.1806:0.0:0.0:0.8193	.	192;71	Q86UA1;F5H1P0	PRP39_HUMAN;.	C	192;71	ENSP00000348010:F192C	ENSP00000348010:F192C	F	+	2	0	PRPF39	44641487	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.403000	0.59729	2.137000	0.66172	0.533000	0.62120	TTT	.	.		0.313	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			G	45571737	T	G	45571737	3	3	158	1	0	0	0	0	1	0	0	0	12581	1841	64	5	589	5	PRPF39	14	45571737	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10		45571737	61777803	78	24037										
PRPF39	55015	hgsc.bcm.edu	37	chr14	45571769	45571769	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ttctagctgcaggaacagatTtccgttctgacagactgtgg	11	9	2	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr14:45571769T>G	ENST00000355765.6	+	5	777	c.607T>G	c.(607-609)Ttc>Gtc	p.F203V		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	203					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						AGGAACAGATTTCCGTTCTGA	0.333																																					p.F203V		Atlas-SNP	.											.	PRPF39	46	.	0			c.T607G						.						89	92	91					14																	45571769		2203	4300	6503	SO:0001583	missense	55015	exon5			ACAGATTTCCGTT	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"PRP39 pre-mRNA processing factor 39 homolog (yeast)", "PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.607T>G	chr14.hg19:g.45571769T>G	ENSP00000348010:p.Phe203Val	106.0	0.0		58.0	23.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	T	25.9	4.681776	0.88542	.	.	ENSG00000185246	ENST00000355765;ENST00000355846	T	0.34275	1.37	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.63307	0.2500	M	0.84948	2.725	0.80722	D	1	D;P	0.71674	0.998;0.638	D;B	0.77004	0.989;0.225	T	0.64719	-0.6341	10	0.31617	T	0.26	-7.2579	15.4843	0.75551	0.0:0.0:0.0:1.0	.	203;82	Q86UA1;F5H1P0	PRP39_HUMAN;.	V	203;82	ENSP00000348010:F203V	ENSP00000348010:F203V	F	+	1	0	PRPF39	44641519	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.137000	0.66172	0.533000	0.62120	TTC	.	.		0.333	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			G	45571769	T	G	45571769	3	3	158	1	0	0	0	0	1	0	0	0	12581	1841	64	5	621	5	PRPF39	14	45571769	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	32	45571769	61777771	79	24038										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24922750	24922750	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ccctgaagtagttaatatggAtactactgccccatctcagg	8	11	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:24922750A>T	ENST00000329468.2	+	1	2210	c.1736A>T	c.(1735-1737)gAt>gTt	p.D579V		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	579					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											GTTAATATGGATACTACTGCC	0.468																																					p.D579V		Atlas-SNP	.											.	.	.	.	0			c.A1736T						.						114	107	109					15																	24922750		2203	4300	6503	SO:0001583	missense	23742	exon1			ATATGGATACTAC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.1736A>T	chr15.hg19:g.24922750A>T	ENSP00000333735:p.Asp579Val	98.0	0.0		84.0	20.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	13.67	2.306848	0.40795	.	.	ENSG00000185823	ENST00000329468	T	0.18502	2.21	2.12	2.12	0.27331	.	0.333628	0.21904	N	0.067419	T	0.20129	0.0484	L	0.34521	1.04	0.18873	N	0.999988	D	0.89917	1.0	D	0.66351	0.943	T	0.11324	-1.0592	10	0.12103	T	0.63	.	6.205	0.20598	1.0:0.0:0.0:0.0	.	579	Q9NZP6	CO002_HUMAN	V	579	ENSP00000333735:D579V	ENSP00000333735:D579V	D	+	2	0	C15orf2	22473843	0.036000	0.19791	0.089000	0.20774	0.196000	0.23810	0.076000	0.14712	1.223000	0.43536	0.172000	0.16884	GAT	.	.		0.468	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24922750	A	T	24922750	3	4	158	1	0	0	0	0	1	0	0	0	1786	333	12	4	1738	4	C15orf2	15	24922750	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10		24922750	77608642	80	24039										
DUOX2	50506	hgsc.bcm.edu	37	chr15	45388244	45388244	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gccttggggcctctggaattGcaggtaggtcactcctggag	15	10	2	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:45388244G>T	ENST00000603300.1	-	30	4064	c.3862C>A	c.(3862-3864)Caa>Aaa	p.Q1288K	DUOX2_ENST00000389039.6_Missense_Mutation_p.Q1288K	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1288	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CTCTGGAATTGCAGGTAGGTC	0.577																																					p.Q1288K		Atlas-SNP	.											.	DUOX2	137	.	0			c.C3862A						.						67	57	60					15																	45388244		2198	4298	6496	SO:0001583	missense	50506	exon30			GGAATTGCAGGTA	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"EF-hand domain containing"	13273	protein-coding gene	gene with protein product	"dual oxidase-like domains 2", "nicotinamide adenine dinucleotide phosphate oxidase", "flavoprotein NADPH oxidase", "NADPH thyroid oxidase 2", "NADH/NADPH thyroid oxidase p138-tox", "NADPH oxidase/peroxidase DUOX2"	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.3862C>A	chr15.hg19:g.45388244G>T	ENSP00000475084:p.Gln1288Lys	89.0	0.0		71.0	17.0	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	hg19	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	G	0.674	-0.800649	0.02841	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.69	2.61	0.31194	Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.426166	0.27618	N	0.018571	T	0.28532	0.0706	N	0.16862	0.45	0.29131	N	0.879665	B	0.02656	0.0	B	0.06405	0.002	T	0.19484	-1.0304	9	0.02654	T	1	-5.0647	16.6592	0.85237	0.0:0.5324:0.4676:0.0	.	1288	Q9NRD8	DUOX2_HUMAN	K	1288	.	ENSP00000373691:Q1288K	Q	-	1	0	DUOX2	43175536	0.999000	0.42202	0.972000	0.41901	0.436000	0.31835	1.551000	0.36233	0.723000	0.32274	0.561000	0.74099	CAA	.	.		0.577	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		T	45388244	G	T	45388244	3	4	158	1	0	0	0	0	1	0	0	0	4803	1328	46	3	804	3	DUOX2	15	45388244	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	20465494	45388244	57143148	81	24040										
DIS3L	115752	hgsc.bcm.edu	37	chr15	66599227	66599227	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ttgcattctctttgctaatgAattccagcaatgctgctatc	6	10	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:66599227A>G	ENST00000319212.4	+	3	409	c.359A>G	c.(358-360)gAa>gGa	p.E120G	DIS3L_ENST00000319194.5_Missense_Mutation_p.E37G|DIS3L_ENST00000441424.2_Intron	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	120					RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TTTGCTAATGAATTCCAGCAA	0.473																																					p.E120G		Atlas-SNP	.											.	DIS3L	175	.	0			c.A359G						.						135	108	117					15																	66599227		2201	4299	6500	SO:0001583	missense	115752	exon3			CTAATGAATTCCA		CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938			28698	protein-coding gene	gene with protein product		614183	"DIS3 mitotic control homolog (S. cerevisiae)-like"			20531386	Standard	NM_001143688		Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.359A>G	chr15.hg19:g.66599227A>G	ENSP00000321711:p.Glu120Gly	48.0	0.0		61.0	21.0	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Missense_Mutation	SNP	ENST00000319212.4	hg19	CCDS45286.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.937762	0.92458	.	.	ENSG00000166938	ENST00000319194;ENST00000525134;ENST00000319212;ENST00000532580;ENST00000530615	T;T	0.39997	1.05;1.14	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.69540	0.3122	M	0.87269	2.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.972;0.994	T	0.75479	-0.3303	10	0.87932	D	0	-8.2493	15.6296	0.76893	1.0:0.0:0.0:0.0	.	120;120	Q8TF46;Q8TF46-3	DI3L1_HUMAN;.	G	37;37;120;37;37	ENSP00000321583:E37G;ENSP00000321711:E120G	ENSP00000321583:E37G	E	+	2	0	DIS3L	64386281	1.000000	0.71417	0.890000	0.34922	0.780000	0.44128	8.494000	0.90477	2.285000	0.76669	0.533000	0.62120	GAA	.	.		0.473	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375		G	66599227	A	G	66599227	3	3	158	1	0	0	0	0	1	0	0	0	4538	246	9	2	369	2	DIS3L	15	66599227	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	21210983	66599227	35932165	82	24041										
ISLR2	57611	hgsc.bcm.edu	37	chr15	74426696	74426696	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gcgcctactctatctgtgtcCagcggggggcggcgcggcag	17	13	2	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:74426696C>T	ENST00000361742.3	+	4	2370	c.1601C>T	c.(1600-1602)cCa>cTa	p.P534L	ISLR2_ENST00000453268.2_Missense_Mutation_p.P534L|ISLR2_ENST00000435464.1_Missense_Mutation_p.P534L|ISLR2_ENST00000445793.1_Missense_Mutation_p.P534L|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000565159.1_Missense_Mutation_p.P534L|ISLR2_ENST00000419208.1_Missense_Mutation_p.P534L|ISLR2_ENST00000565540.1_Missense_Mutation_p.P534L	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	534					positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						TATCTGTGTCCAGCGGGGGGC	0.746																																					p.P534L		Atlas-SNP	.											.	ISLR2	78	.	0			c.C1601T						.						5	7	6					15																	74426696		2034	4098	6132	SO:0001583	missense	57611	exon4			TGTGTCCAGCGGG		CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.1601C>T	chr15.hg19:g.74426696C>T	ENSP00000355402:p.Pro534Leu	35.0	0.0		44.0	30.0	NM_001130138	A8K352|Q9P263	Missense_Mutation	SNP	ENST00000361742.3	hg19	CCDS10259.1	.	.	.	.	.	.	.	.	.	.	C	10.92	1.487186	0.26686	.	.	ENSG00000167178	ENST00000445793;ENST00000361742;ENST00000435464;ENST00000453268;ENST00000419208	T;T;T;T;T	0.05081	3.5;3.5;3.5;3.5;3.5	4.83	3.91	0.45181	.	0.371892	0.27549	N	0.018869	T	0.03827	0.0108	N	0.14661	0.345	0.31337	N	0.684065	B	0.27351	0.176	B	0.20184	0.028	T	0.11372	-1.0590	10	0.59425	D	0.04	.	7.3605	0.26744	0.1658:0.7452:0.0:0.089	.	534	Q6UXK2	ISLR2_HUMAN	L	534	ENSP00000403244:P534L;ENSP00000355402:P534L;ENSP00000411443:P534L;ENSP00000411834:P534L;ENSP00000408872:P534L	ENSP00000355402:P534L	P	+	2	0	ISLR2	72213749	0.669000	0.27502	0.954000	0.39281	0.874000	0.50279	1.709000	0.37909	1.017000	0.39495	0.313000	0.20887	CCA	.	.		0.746	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851		T	74426696	C	T	74426696	3	4	158	1	0	0	0	0	1	0	0	0	7868	594	21	3	1603	3	ISLR2	15	74426696	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	7827469	74426696	28104696	83	24042										
ZNF592	9640	hgsc.bcm.edu	37	chr15	85327987	85327987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gggcagtgccagtccccctcCtccagccttgccactctacc	8	20	1	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:85327987C>T	ENST00000560079.2	+	4	2369	c.2081C>T	c.(2080-2082)cCt>cTt	p.P694L	ZNF592_ENST00000299927.3_Missense_Mutation_p.P694L	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	694					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGTCCCCCTCCTCCAGCCTTG	0.592																																					p.P694L		Atlas-SNP	.											.	ZNF592	95	.	0			c.C2081T						.						85	78	80					15																	85327987		2203	4299	6502	SO:0001583	missense	9640	exon4			CCCCTCCTCCAGC	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"Zinc fingers, C2H2-type"	28986	protein-coding gene	gene with protein product		613624	"spinocerebellar ataxia, autosomal recessive 5"	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.2081C>T	chr15.hg19:g.85327987C>T	ENSP00000452877:p.Pro694Leu	71.0	0.0		59.0	26.0	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	hg19	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	14.12	2.439993	0.43326	.	.	ENSG00000166716	ENST00000299927	T	0.30981	1.51	5.93	1.11	0.20524	.	0.594857	0.18557	N	0.137746	T	0.13798	0.0334	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24693	-1.0153	10	0.26408	T	0.33	0.3876	8.7519	0.34620	0.0:0.597:0.0:0.403	.	694	Q92610	ZN592_HUMAN	L	694	ENSP00000299927:P694L	ENSP00000299927:P694L	P	+	2	0	ZNF592	83128991	0.011000	0.17503	0.000000	0.03702	0.881000	0.50899	1.032000	0.30178	-0.080000	0.12685	-0.136000	0.14681	CCT	.	.		0.592	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		T	85327987	C	T	85327987	3	4	158	1	0	0	0	0	1	0	0	0	18037	681	24	3	2083	3	ZNF592	15	85327987	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	10901291	85327987	17203405	84	24043										
ARRDC4	91947	hgsc.bcm.edu	37	chr15	98512602	98512602	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cattatcagagtggactattCcttagctgtaagcaaagctc	8	9	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:98512602C>A	ENST00000268042.6	+	5	1039	c.875C>A	c.(874-876)tCc>tAc	p.S292Y	ARRDC4_ENST00000538249.1_Missense_Mutation_p.S205Y	NM_183376.2	NP_899232.2	Q8NCT1	ARRD4_HUMAN	arrestin domain containing 4	292					positive regulation of ubiquitin-protein transferase activity (GO:0051443)	endosome (GO:0005768)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|skin(3)	16	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)			GTGGACTATTCCTTAGCTGTA	0.393																																					p.S292Y		Atlas-SNP	.											.	ARRDC4	30	.	0			c.C875A						.						88	80	83					15																	98512602		2197	4298	6495	SO:0001583	missense	91947	exon5			ACTATTCCTTAGC	BC028704	CCDS10377.1	15q26.2	2005-08-16			ENSG00000140450	ENSG00000140450			28087	protein-coding gene	gene with protein product						12477932	Standard	NM_183376		Approved	FLJ36045	uc010bom.3	Q8NCT1	OTTHUMG00000149849	ENST00000268042.6:c.875C>A	chr15.hg19:g.98512602C>A	ENSP00000268042:p.Ser292Tyr	99.0	0.0		85.0	44.0	NM_183376	Q6NSI9	Missense_Mutation	SNP	ENST00000268042.6	hg19	CCDS10377.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.263852	0.80358	.	.	ENSG00000140450	ENST00000538249;ENST00000268042	T;T	0.15718	2.4;2.4	5.22	4.29	0.51040	Immunoglobulin E-set (1);Arrestin-like, C-terminal (1);	0.078649	0.53938	D	0.000041	T	0.28699	0.0711	L	0.43152	1.355	0.58432	D	0.999998	D;D	0.60160	0.987;0.984	P;P	0.59115	0.852;0.656	T	0.01074	-1.1460	10	0.72032	D	0.01	-25.6166	13.5324	0.61629	0.0:0.9242:0.0:0.0758	.	292;205	Q8NCT1;F5H824	ARRD4_HUMAN;.	Y	205;292	ENSP00000443774:S205Y;ENSP00000268042:S292Y	ENSP00000268042:S292Y	S	+	2	0	ARRDC4	96313606	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	5.666000	0.68059	2.597000	0.87782	0.591000	0.81541	TCC	.	.		0.393	ARRDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313535.1	NM_183376		A	98512602	C	A	98512602	3	1	158	1	0	0	0	0	1	0	0	0	985	855	30	3	893	3	ARRDC4	15	98512602	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	13184615	98512602	4018790	85	24044										
TP53	7157	hgsc.bcm.edu	37	chr17	7578275	7578275	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ttccactcggataagatgctGaggaggggccagacctaaga	13	9	0	4			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:7578275G>A	ENST00000269305.4	-	6	763	c.574C>T	c.(574-576)Cag>Tag	p.Q192*	TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q192*|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q192*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	192	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Q -> H (in sporadic cancers; somatic mutation).|Q -> K (in a sporadic cancer; somatic mutation).|Q -> L (in sporadic cancers; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q192*(83)|p.0?(8)|p.Q99*(6)|p.?(6)|p.Q60*(6)|p.P191del(4)|p.P191delP(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.G187fs*16(2)|p.P59delP(2)|p.P98delP(2)|p.P191fs*6(1)|p.A189_Q192>E(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P191_Q192delPQ(1)|p.Q192K(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.Q192del(1)|p.Q192fs*16(1)|p.L188_P191del(1)|p.Q192fs*30(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATAAGATGCTGAGGAGGGGCC	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Q192X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	144	Substitution - Nonsense(95)|Deletion - In frame(19)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - deletion inframe(6)|Unknown(6)|Insertion - Frameshift(1)|Complex - frameshift(1)|Substitution - Missense(1)	breast(26)|ovary(20)|urinary_tract(15)|lung(12)|upper_aerodigestive_tract(10)|skin(8)|biliary_tract(7)|oesophagus(7)|large_intestine(6)|kidney(6)|stomach(5)|haematopoietic_and_lymphoid_tissue(5)|liver(5)|bone(4)|central_nervous_system(3)|pancreas(2)|cervix(1)|endometrium(1)|eye(1)	c.C574T						.						89	80	83					17																	7578275		2203	4300	6503	SO:0001587	stop_gained	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGCTGAGGAGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.574C>T	chr17.hg19:g.7578275G>A	ENSP00000269305:p.Gln192*	153.0	0.0		87.0	64.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.269040	0.40095	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.41	3.36	0.38483	.	0.242461	0.43260	D	0.000594	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-22.6404	8.6971	0.34303	0.0:0.1484:0.545:0.3066	.	.	.	.	X	192;192;192;192;192;192;181;99;60;99;60	.	ENSP00000269305:Q192X	Q	-	1	0	TP53	7519000	1.000000	0.71417	0.987000	0.45799	0.035000	0.12851	2.163000	0.42377	0.732000	0.32470	0.655000	0.94253	CAG	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578275	G	A	7578275	4	1	158	1	0	0	0	0	0	1	0	0	16396	1299	45	3	720	3	TP53	17	7578275	Nonsense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10		7578275	73616935	86	24045										
RARA	5914	hgsc.bcm.edu	37	chr17	38508601	38508601	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agaacaacagctcagaacaaCgtgtctctctggacattgac	8	11	3	3			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:38508601C>A	ENST00000254066.5	+	6	1104	c.649C>A	c.(649-651)Cgt>Agt	p.R217S	RARA_ENST00000394089.2_Missense_Mutation_p.R217S|RARA_ENST00000394086.3_Missense_Mutation_p.R233S|RARA_ENST00000394081.3_Missense_Mutation_p.R212S|RARA_ENST00000425707.3_Missense_Mutation_p.R120S|RARA_ENST00000420042.1_3'UTR	NM_000964.3	NP_000955.1	P10276	RARA_HUMAN	retinoic acid receptor, alpha	217	Ligand-binding.				apoptotic cell clearance (GO:0043277)|cellular response to estrogen stimulus (GO:0071391)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|chondroblast differentiation (GO:0060591)|embryonic camera-type eye development (GO:0031076)|face development (GO:0060324)|female pregnancy (GO:0007565)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|intracellular estrogen receptor signaling pathway (GO:0030520)|limb development (GO:0060173)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translational initiation (GO:0045947)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of binding (GO:0051099)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein phosphorylation (GO:0006468)|regulation of myelination (GO:0031641)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|retinoic acid receptor signaling pathway (GO:0048384)|Sertoli cell fate commitment (GO:0060010)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chromatin DNA binding (GO:0031490)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|mRNA 5'-UTR binding (GO:0048027)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein kinase A binding (GO:0051018)|protein kinase B binding (GO:0043422)|receptor binding (GO:0005102)|retinoic acid binding (GO:0001972)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|translation repressor activity, nucleic acid binding (GO:0000900)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|urinary_tract(2)	16		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)	CTCAGAACAACGTGTCTCTCT	0.582			T	"PML, ZNF145, TIF1, NUMA1, NPM1"	APL																																p.R217S		Atlas-SNP	.		Dom	yes		17	17q12	5914	"retinoic acid receptor, alpha"		L	.	RARA	52	.	0			c.C649A						.						171	147	155					17																	38508601		2203	4300	6503	SO:0001583	missense	5914	exon6			GAACAACGTGTCT	X06538	CCDS11366.1, CCDS42317.1, CCDS45671.1	17q21.1	2014-01-20			ENSG00000131759	ENSG00000131759		"Nuclear hormone receptors"	9864	protein-coding gene	gene with protein product		180240				2825036, 8244378	Standard	NM_001145301		Approved	RAR, NR1B1	uc002huk.2	P10276	OTTHUMG00000133328	ENST00000254066.5:c.649C>A	chr17.hg19:g.38508601C>A	ENSP00000254066:p.Arg217Ser	59.0	0.0		50.0	12.0	NM_000964	B8Y636|P78456|Q13440|Q13441|Q96S41|Q9NQS0	Missense_Mutation	SNP	ENST00000254066.5	hg19	CCDS11366.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.396|8.396	0.840786|0.840786	0.16891|0.16891	.|.	.|.	ENSG00000131759|ENSG00000131759	ENST00000319149|ENST00000254066;ENST00000425707;ENST00000394089;ENST00000394086;ENST00000394081;ENST00000420042	.|T;D;T;T;T	.|0.92699	.|1.48;-3.09;1.48;1.48;1.48	4.34|4.34	4.34|4.34	0.51931|0.51931	.|Nuclear hormone receptor, ligand-binding (2);	0.378221|.	0.27595|.	N|.	0.018673|.	D|D	0.93416|0.93416	0.7900|0.7900	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|D;P;D	.|0.89917	.|1.0;0.513;1.0	.|D;B;D	.|0.91635	.|0.997;0.284;0.999	D|D	0.93060|0.93060	0.6473|0.6473	7|9	0.22109|0.40728	T|T	0.4|0.16	.|.	15.7766|15.7766	0.78224|0.78224	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|120;212;217	.|B8Y636;F1D8N9;P10276	.|.;.;RARA_HUMAN	K|S	210|217;120;217;233;212;104	.|ENSP00000254066:R217S;ENSP00000389993:R120S;ENSP00000377649:R217S;ENSP00000377648:R233S;ENSP00000377643:R212S	ENSP00000316769:N210K|ENSP00000254066:R217S	N|R	+|+	3|1	2|0	RARA|RARA	35762127|35762127	1.000000|1.000000	0.71417|0.71417	0.260000|0.260000	0.24451|0.24451	0.018000|0.018000	0.09664|0.09664	5.906000|5.906000	0.69900|0.69900	2.219000|2.219000	0.72066|0.72066	0.460000|0.460000	0.39030|0.39030	AAC|CGT	.	.		0.582	RARA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257136.2			A	38508601	C	A	38508601	3	1	158	1	0	0	0	0	1	0	0	0	13067	536	19	1	834	1	RARA	17	38508601	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	30930326	38508601	42686609	87	24046										
KRT13	3860	hgsc.bcm.edu	37	chr17	39659035	39659036	+	Missense_Mutation	DNP	GG	GG	TT													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gtctgaatcatggcagtgttGgtagacacctccttgttcag							TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:39659035_39659036GG>TT	ENST00000246635.3	-	5	972_973	c.926_927CC>AA	c.(925-927)aCC>aAA	p.T309K	KRT13_ENST00000587118.1_5'Flank|AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000336861.3_Missense_Mutation_p.T309K|KRT13_ENST00000587544.1_Missense_Mutation_p.T309K	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	309	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.T309T(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				TGGCAGTGTTGGTAGACACCTC	0.569																																					p.T309T|p.T309N		Atlas-SNP	.											KRT13,bladder,carcinoma,0,1|.	KRT13	72	.	1	Substitution - coding silent(1)	urinary_tract(1)	c.C927A|c.C926A						.																																			SO:0001583	missense	3860	exon5			AGTGTTGGTAGAC|GTGTTGGTAGACA		CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"-", "Intermediate filaments type I, keratins (acidic)"	6415	protein-coding gene	gene with protein product	"keratin, type I cytoskeletal 13", "cytokeratin 13"	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.926_927delinsTT	chr17.hg19:g.39659035_39659036delinsTT	ENSP00000246635:p.Thr309Lys	52.0	0.0		68.0	26.0|27.0	NM_002274	Q53G54|Q6AZK5|Q8N240	Silent|Missense_Mutation	SNP	ENST00000246635.3	hg19	CCDS11396.1																																																																																			.	.		0.569	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		TT	39659036	GG	TT	39659035	3	4	158	1	0	0	0	0	1	0	0	0	8459	1335	47	3	465	3	KRT13	17	39659035	Missense_Mutation	DNP	GG	TCGA-DD-AACG-01A-11D-A40R-10	1150434	39659035	41536175	88	24047										
SOX9	6662	hgsc.bcm.edu	37	chr17	70117638	70117638	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	actccgcgggctcgccctgcCcgtcgggctccggctcggac	14	19	0	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:70117638C>T	ENST00000245479.2	+	1	478	c.106C>T	c.(106-108)Ccg>Tcg	p.P36S		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	36					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			CTCGCCCTGCCCGTCGGGCTC	0.672																																					p.P36S	Pancreas(42;83 1041 2320 35205 39456)	Atlas-SNP	.											.	SOX9	91	.	0			c.C106T						.						13	14	14					17																	70117638		2196	4288	6484	SO:0001583	missense	6662	exon1			CCCTGCCCGTCGG	S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.106C>T	chr17.hg19:g.70117638C>T	ENSP00000245479:p.Pro36Ser	244.0	0.0		272.0	111.0	NM_000346	Q53Y80	Missense_Mutation	SNP	ENST00000245479.2	hg19	CCDS11689.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026531	0.75390	.	.	ENSG00000125398	ENST00000245479;ENST00000455872	T	0.75050	-0.9	4.39	4.39	0.52855	.	0.120496	0.56097	U	0.000025	D	0.85504	0.5712	M	0.77406	2.37	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84697	0.0726	10	0.29301	T	0.29	.	16.9671	0.86288	0.0:1.0:0.0:0.0	.	36	P48436	SOX9_HUMAN	S	36	ENSP00000245479:P36S	ENSP00000245479:P36S	P	+	1	0	SOX9	67629233	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	4.489000	0.60309	1.997000	0.58415	0.491000	0.48974	CCG	.	.		0.672	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		T	70117638	C	T	70117638	3	4	158	1	0	0	0	0	1	0	0	0	14973	623	22	3	108	3	SOX9	17	70117638	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	30458603	70117638	11077572	89	24048										
CBX4	8535	hgsc.bcm.edu	37	chr17	77808306	77808306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gtgcgggtggtgtgagggcgGgtgcgtgttccgggccgggt	24	7	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:77808306G>A	ENST00000269397.4	-	5	1312	c.1135C>T	c.(1135-1137)Ccg>Tcg	p.P379S		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	379	His-rich.|Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			tgTGAGGGCGGGTGCGTGTTC	0.697																																					p.P379S		Atlas-SNP	.											.	CBX4	40	.	0			c.C1135T						.						11	13	12					17																	77808306		2190	4282	6472	SO:0001583	missense	8535	exon5			AGGGCGGGTGCGT	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"NS5ATP1-binding protein 16", "Pc class 2 homolog (Drosophila)"	603079	"chromobox homolog 4 (Drosophila Pc class)"			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.1135C>T	chr17.hg19:g.77808306G>A	ENSP00000269397:p.Pro379Ser	44.0	0.0		51.0	17.0	NM_003655	B1PJR7|Q6TPI8|Q96C04	Missense_Mutation	SNP	ENST00000269397.4	hg19	CCDS32758.1	.	.	.	.	.	.	.	.	.	.	g	1.031	-0.681816	0.03353	.	.	ENSG00000141582	ENST00000269397	.	.	.	3.67	2.66	0.31614	.	555.879000	0.00166	N	0.000003	T	0.50017	0.1591	L	0.48642	1.525	0.80722	D	1	B	0.26935	0.164	B	0.19946	0.027	T	0.28933	-1.0028	9	0.09338	T	0.73	.	8.8709	0.35316	0.0:0.2315:0.7685:0.0	.	379	O00257	CBX4_HUMAN	S	379	.	ENSP00000269397:P379S	P	-	1	0	CBX4	75422901	0.902000	0.30710	0.020000	0.16555	0.022000	0.10575	1.431000	0.34925	0.487000	0.27698	0.306000	0.20318	CCG	.	.		0.697	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655		A	77808306	G	A	77808306	3	1	158	1	0	0	0	0	1	0	0	0	2722	1232	43	3	551	3	CBX4	17	77808306	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	7690668	77808306	3386904	90	24049										
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29488760	29488760	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ttttctctatatgtggcaaaAggccccgaaatgtgaactct	8	9	2	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr18:29488760A>G	ENST00000283351.4	-	7	1414	c.1079T>C	c.(1078-1080)cTt>cCt	p.L360P	TRAPPC8_ENST00000582513.1_Missense_Mutation_p.L360P|TRAPPC8_ENST00000582539.1_Missense_Mutation_p.L306P	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	360					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						ATGTGGCAAAAGGCCCCGAAA	0.294																																					p.L360P		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.T1079C						.						57	53	54					18																	29488760		2203	4300	6503	SO:0001583	missense	22878	exon7			GGCAAAAGGCCCC	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.1079T>C	chr18.hg19:g.29488760A>G	ENSP00000283351:p.Leu360Pro	82.0	0.0		86.0	4.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	hg19	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.317904	0.40996	.	.	ENSG00000153339	ENST00000283351	T	0.26810	1.71	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000001	T	0.56761	0.2007	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.64063	-0.6495	10	0.87932	D	0	.	15.97	0.80008	1.0:0.0:0.0:0.0	.	360;360	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	P	360	ENSP00000283351:L360P	ENSP00000283351:L360P	L	-	2	0	TRAPPC8	27742758	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.615000	0.90920	2.181000	0.69327	0.459000	0.35465	CTT	.	.		0.294	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		G	29488760	A	G	29488760	3	3	158	1	0	0	0	0	1	0	0	0	8213	72	3	2	3320	2	KIAA1012	18	29488760	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10		29488760	48588488	91	24050										
SALL3	27164	hgsc.bcm.edu	37	chr18	76755362	76755362	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gtgcgggaagaccttctcctCggccagcgccctgcagatcc	12	16	1	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr18:76755362C>A	ENST00000537592.2	+	2	3371	c.3371C>A	c.(3370-3372)tCg>tAg	p.S1124*	SALL3_ENST00000536229.3_Nonsense_Mutation_p.S919*|SALL3_ENST00000575389.2_Nonsense_Mutation_p.S1052*	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1124					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		ACCTTCTCCTCGGCCAGCGCC	0.692																																					p.S1124X		Atlas-SNP	.											SALL3,colon,carcinoma,0,1	SALL3	162	.	0			c.C3371A						.						10	10	10					18																	76755362		2159	4238	6397	SO:0001587	stop_gained	27164	exon2			TCTCCTCGGCCAG	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.3371C>A	chr18.hg19:g.76755362C>A	ENSP00000441823:p.Ser1124*	23.0	0.0		28.0	10.0	NM_171999	Q9UGH1	Nonsense_Mutation	SNP	ENST00000537592.2	hg19	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	C	36	5.679248	0.96774	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	.	.	.	5.35	3.56	0.40772	.	0.137147	0.33057	N	0.005322	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.8292	10.9437	0.47289	0.0:0.7997:0.1301:0.0701	.	.	.	.	X	1124;1052;784	.	ENSP00000299466:S1124X	S	+	2	0	SALL3	74856350	1.000000	0.71417	0.811000	0.32455	0.912000	0.54170	5.990000	0.70595	0.628000	0.30357	0.655000	0.94253	TCG	.	.		0.692	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		A	76755362	C	A	76755362	4	1	158	1	0	0	0	0	0	1	0	0	13827	893	31	1	3377	1	SALL3	18	76755362	Nonsense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	47266602	76755362	1321886	92	24051										
ZNF317	57693	hgsc.bcm.edu	37	chr19	9271261	9271281	+	In_Frame_Del	DEL	GCTTACGGCCGGAGCTGCCAC	GCTTACGGCCGGAGCTGCCAC	-													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agtgtgatcagtgcgggaagGcttacggccggagctgccac							TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	GCTTACGGCCGGAGCTGCCAC	GCTTACGGCCGGAGCTGCCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr19:9271261_9271281delGCTTACGGCCGGAGCTGCCAC	ENST00000247956.6	+	7	1245_1265	c.940_960delGCTTACGGCCGGAGCTGCCAC	c.(940-960)gcttacggccggagctgccacdel	p.AYGRSCH314del	ZNF317_ENST00000360385.3_In_Frame_Del_p.AYGRSCH282del	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	314					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R317Q(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						GTGCGGGAAGGCTTACGGCCGGAGCTGCCACCTCATCGCAC	0.579																																					p.313_320del		Atlas-INDEL	.											.	ZNF317	61	.	1	Substitution - Missense(1)	endometrium(1)	c.939_959del						.																																			SO:0001651	inframe_deletion	57693	exon7			.	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"Zinc fingers, C2H2-type", "-"	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.940_960delGCTTACGGCCGGAGCTGCCAC	chr19.hg19:g.9271261_9271281delGCTTACGGCCGGAGCTGCCAC	ENSP00000247956:p.Ala314_His320del	64.0	0.0		26.0	18.0	NM_020933	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	In_Frame_Del	DEL	ENST00000247956.6	hg19	CCDS12210.1																																																																																			.	.		0.579	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933		-	9271281	GCTTACGGCCGGAGCTGCCAC	-	9271261	7	5	158	1	0	1	0	1	0	0	0	0	17850	1203	42	0	962	0	ZNF317	19	9271261	In_Frame_Del	DEL	GCTTACGGCCGGAGCTGCCAC	TCGA-DD-AACG-01A-11D-A40R-10		9271261	49857722	93	24052										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22154761	22154761	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	tcacatttgtagggtgtctcTccagtgtgaattttcttatg	9	7	3	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr19:22154761T>C	ENST00000397126.4	-	4	3223	c.3075A>G	c.(3073-3075)ggA>ggG	p.G1025G	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	1025					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGGGTGTCTCTCCAGTGTGAA	0.413																																					p.G1025G		Atlas-SNP	.											.	ZNF208	817	.	0			c.A3075G						.						98	106	103					19																	22154761		2135	4254	6389	SO:0001819	synonymous_variant	7757	exon4			TGTCTCTCCAGTG	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.3075A>G	chr19.hg19:g.22154761T>C		138.0	0.0		292.0	46.0	NM_007153		Silent	SNP	ENST00000397126.4	hg19	CCDS54240.1																																																																																			.	.		0.413	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		C	22154761	T	C	22154761	2	2	158	1	0	0	0	0	0	0	0	1	17781	1538	54	2		2	ZNF208	19	22154761	Silent	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10	12883500	22154761	36974222	94	24053										
SIX5	147912	hgsc.bcm.edu	37	chr19	46268971	46268972	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ctctgttcctgcgcttagttCcagccctgctgaccagacag							TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr19:46268971_46268972CC>AA	ENST00000317578.6	-	3	2388_2389	c.2007_2008GG>TT	c.(2005-2010)ctGGaa>ctTTaa	p.E670*	AC074212.5_ENST00000559756.1_RNA|SIX5_ENST00000560168.1_3'UTR|AC074212.6_ENST00000590076.1_RNA|AC074212.5_ENST00000592217.2_RNA	NM_175875.4	NP_787071	Q8N196	SIX5_HUMAN	SIX homeobox 5	670					lens development in camera-type eye (GO:0002088)|negative regulation of cell proliferation (GO:0008285)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)		GCGCTTAGTTCCAGCCCTGCTG	0.688																																					p.E670X|p.L669L		Atlas-SNP	.											.	SIX5	35	.	0			c.G2008T|c.G2007T						.																																			SO:0001587	stop_gained	147912	exon3			TTAGTTCCAGCCC|TAGTTCCAGCCCT	L08835	CCDS12673.1	19q13.32	2011-06-20	2007-07-13			ENSG00000177045		"Homeoboxes / SINE class"	10891	protein-coding gene	gene with protein product		600963	"sine oculis homeobox (Drosophila) homolog 5", "sine oculis homeobox homolog 5 (Drosophila)"	DMAHP		8595416	Standard	NM_175875		Approved		uc002pdb.3	Q8N196		ENST00000317578.6:c.2007_2008delinsAA	chr19.hg19:g.46268971_46268972delinsAA	ENSP00000316842:p.Glu670*	56.0	0.0		112.0|111.0	79.0|78.0	NM_175875		Nonsense_Mutation|Silent	SNP	ENST00000317578.6	hg19	CCDS12673.1																																																																																			.	.		0.688	SIX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417341.3	NM_175875		AA	46268972	CC	AA	46268971	4	1	158	1	0	0	0	0	0	1	0	0	14365	864	30	3	215	3	SIX5	19	46268971	Nonsense_Mutation	DNP	CC	TCGA-DD-AACG-01A-11D-A40R-10	24114210	46268971	12860012	95	24054										
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13912332	13912332	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	gattcttctttttctccaggAgattttctcttttattgatt	5	7	4	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr20:13912332A>G	ENST00000284951.5	-	3	274	c.200T>C	c.(199-201)cTc>cCc	p.L67P	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Missense_Mutation_p.L67P			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	67						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						TTTCTCCAGGAGATTTTCTCT	0.259																																					p.L67P		Atlas-SNP	.											.	SEL1L2	103	.	0			c.T200C						.						69	61	64					20																	13912332		1779	4041	5820	SO:0001583	missense	80343	exon3			TCCAGGAGATTTT	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.200T>C	chr20.hg19:g.13912332A>G	ENSP00000284951:p.Leu67Pro	84.0	0.0		99.0	48.0	NM_001271539	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	hg19		.	.	.	.	.	.	.	.	.	.	A	6.378	0.437767	0.12104	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.23348	1.91;2.23	5.34	1.35	0.21983	.	1.324090	0.05221	N	0.508542	T	0.12774	0.0310	N	0.08118	0	0.25756	N	0.985008	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.26677	-1.0096	10	0.31617	T	0.26	2.4044	3.8076	0.08783	0.513:0.2536:0.2334:0.0	.	67;67	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	P	67	ENSP00000367312:L67P;ENSP00000284951:L67P	ENSP00000284951:L67P	L	-	2	0	SEL1L2	13860332	0.981000	0.34729	0.403000	0.26384	0.602000	0.36980	0.953000	0.29162	0.420000	0.25954	0.533000	0.62120	CTC	.	.		0.259	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		G	13912332	A	G	13912332	3	3	158	1	0	0	0	0	1	0	0	0	14026	304	11	2	1938	2	SEL1L2	20	13912332	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10		13912332	49113188	96	24055										
ZFP64	55734	hgsc.bcm.edu	37	chr20	50781292	50781292	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ccataagcagtcttgaattgGcaacctaaaaaaaaaaagga	7	7	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr20:50781292G>A	ENST00000216923.4	-	4	802	c.453C>T	c.(451-453)tgC>tgT	p.C151C	ZFP64_ENST00000346617.4_Silent_p.C97C|ZFP64_ENST00000477786.1_5'UTR|ZFP64_ENST00000361387.2_Silent_p.C151C|ZFP64_ENST00000371518.2_Silent_p.C151C|ZFP64_ENST00000371515.4_Silent_p.C149C	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						TCTTGAATTGGCAACCTAAAA	0.378																																					p.C151C		Atlas-SNP	.											.	ZFP64	240	.	0			c.C453T						.						87	81	83					20																	50781292		2203	4300	6503	SO:0001819	synonymous_variant	55734	exon4			GAATTGGCAACCT	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.453C>T	chr20.hg19:g.50781292G>A		39.0	0.0		43.0	15.0	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	hg19	CCDS13440.1																																																																																			.	.		0.378	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197		A	50781292	G	A	50781292	2	1	158	1	0	0	0	0	0	0	0	1	17667	1195	42	3		3	ZFP64	20	50781292	Silent	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	36868960	50781292	12244228	97	24056										
OGFR	11054	hgsc.bcm.edu	37	chr20	61443981	61443981	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ccagagcatagcaagggtggGggcagggtggacgaggggcc	21	8	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr20:61443981G>T	ENST00000290291.6	+	7	1039	c.1014G>T	c.(1012-1014)ggG>ggT	p.G338G	OGFR_ENST00000370461.1_Silent_p.G286G	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	338					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					GCAAGGGTGGGGGCAGGGTGG	0.721																																					p.G338G		Atlas-SNP	.											.	OGFR	63	.	0			c.G1014T						.						3	4	4					20																	61443981		1956	3966	5922	SO:0001819	synonymous_variant	11054	exon7			GGGTGGGGGCAGG	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1014G>T	chr20.hg19:g.61443981G>T		142.0	0.0		110.0	41.0	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Silent	SNP	ENST00000290291.6	hg19	CCDS13504.1																																																																																			.	.		0.721	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			T	61443981	G	T	61443981	2	4	158	1	0	0	0	0	0	0	0	1	10852	1219	43	3		3	OGFR	20	61443981	Silent	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	10662689	61443981	1581539	98	24057										
BRWD1	54014	hgsc.bcm.edu	37	chr21	40568678	40568678	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ttgtcttactaaaaggagccTttccataggtcctgagtctt	8	9	2	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr21:40568678T>C	ENST00000333229.2	-	41	6644	c.6317A>G	c.(6316-6318)aAg>aGg	p.K2106R	BRWD1_ENST00000380800.3_Missense_Mutation_p.K2106R|BRWD1_ENST00000342449.3_Missense_Mutation_p.K2106R	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2106					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				AAAAGGAGCCTTTCCATAGGT	0.413																																					p.K2106R	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A6317G						.						174	166	169					21																	40568678		2203	4299	6502	SO:0001583	missense	54014	exon41			GGAGCCTTTCCAT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.6317A>G	chr21.hg19:g.40568678T>C	ENSP00000330753:p.Lys2106Arg	58.0	0.0		42.0	11.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	hg19	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.194740	0.58017	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.58797	0.31;0.49;0.43	5.53	4.39	0.52855	.	0.256906	0.34178	N	0.004189	T	0.47911	0.1471	L	0.46885	1.475	0.80722	D	1	B;B	0.19583	0.037;0.022	B;B	0.19148	0.024;0.011	T	0.47686	-0.9098	10	0.44086	T	0.13	-14.0862	9.1127	0.36737	0.0:0.141:0.0:0.859	.	2106;2106	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	R	2106	ENSP00000330753:K2106R;ENSP00000344333:K2106R;ENSP00000370178:K2106R	ENSP00000330753:K2106R	K	-	2	0	BRWD1	39490548	0.471000	0.25862	1.000000	0.80357	0.995000	0.86356	1.058000	0.30504	2.100000	0.63781	0.533000	0.62120	AAG	.	.		0.413	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		C	40568678	T	C	40568678	3	2	158	1	0	0	0	0	1	0	0	0	1527	1609	56	2	892	2	BRWD1	21	40568678	Missense_Mutation	SNP	T	TCGA-DD-AACG-01A-11D-A40R-10		40568678	7561217	99	24058										
SLC37A1	54020	hgsc.bcm.edu	37	chr21	43955639	43955639	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ctactccttcctgtgcgcctAtgccgtggggatgtacctca	10	14	1	0	rs564499706		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr21:43955639A>G	ENST00000352133.2	+	5	1311	c.329A>G	c.(328-330)tAt>tGt	p.Y110C	SLC37A1_ENST00000398341.3_Missense_Mutation_p.Y110C			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	110					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						CTGTGCGCCTATGCCGTGGGG	0.507													A|||	1	0.000199681	0	0	5008	,	,		20100	0		0.001	False		,,,				2504	0				p.Y110C		Atlas-SNP	.											.	SLC37A1	48	.	0			c.A329G						.						174	167	169					21																	43955639		2203	4300	6503	SO:0001583	missense	54020	exon6			GCGCCTATGCCGT	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"Solute carriers"	11024	protein-coding gene	gene with protein product		608094	"solute carrier family 37 (glycerol-3-phosphate transporter), member 1"			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.329A>G	chr21.hg19:g.43955639A>G	ENSP00000344648:p.Tyr110Cys	93.0	0.0		69.0	29.0	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	hg19	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.087246	0.55968	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.61742	0.08;0.08	4.65	4.65	0.58169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.81945	0.4930	H	0.94698	3.57	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87380	0.2356	10	0.87932	D	0	-15.6574	14.3838	0.66929	1.0:0.0:0.0:0.0	.	110	P57057	GLPT_HUMAN	C	110	ENSP00000381383:Y110C;ENSP00000344648:Y110C	ENSP00000344648:Y110C	Y	+	2	0	SLC37A1	42828708	1.000000	0.71417	0.034000	0.17996	0.341000	0.28922	8.763000	0.91715	1.858000	0.53909	0.460000	0.39030	TAT	.	.		0.507	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1			G	43955639	A	G	43955639	3	3	158	1	0	0	0	0	1	0	0	0	14612	449	16	2	343	2	SLC37A1	21	43955639	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10	3386961	43955639	4174256	100	24059										
CCDC116	164592	hgsc.bcm.edu	37	chr22	21989329	21989329	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ggctgtggataagctccgtgGcgcccactgccgcgacggcc	15	15	0	0			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr22:21989329G>C	ENST00000292779.3	+	4	1138	c.977G>C	c.(976-978)gGc>gCc	p.G326A	CCDC116_ENST00000607942.1_Missense_Mutation_p.G326A	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	326										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					AAGCTCCGTGGCGCCCACTGC	0.662																																					p.G326A		Atlas-SNP	.											.	CCDC116	56	.	0			c.G977C						.						36	38	37					22																	21989329		2203	4300	6503	SO:0001583	missense	164592	exon4			TCCGTGGCGCCCA	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.977G>C	chr22.hg19:g.21989329G>C	ENSP00000292779:p.Gly326Ala	72.0	0.0		70.0	38.0	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	hg19	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	G	9.629	1.135800	0.21123	.	.	ENSG00000161180	ENST00000292779	T	0.11712	2.75	3.83	-0.833	0.10782	.	1.489690	0.03821	N	0.267551	T	0.09862	0.0242	L	0.39898	1.24	0.09310	N	1	B;B	0.27882	0.093;0.192	B;B	0.27170	0.077;0.029	T	0.37126	-0.9719	10	0.62326	D	0.03	-22.3123	3.5073	0.07695	0.3558:0.197:0.4472:0.0	.	326;326	B7Z7H5;Q8IYX3-2	.;.	A	326	ENSP00000292779:G326A	ENSP00000292779:G326A	G	+	2	0	CCDC116	20319329	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.113000	0.10774	-0.046000	0.13446	0.561000	0.74099	GGC	.	.		0.662	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612		C	21989329	G	C	21989329	3	2	158	1	0	0	0	0	1	0	0	0	2755	1203	42	4	987	4	CCDC116	22	21989329	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10		21989329	29315237	101	24060										
LARGE	9215	hgsc.bcm.edu	37	chr22	33733771	33733771	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	tcacccggagcttcttggggGagttccagtgaatgacctgg	14	10	2	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr22:33733771G>C	ENST00000354992.2	-	11	1719	c.1148C>G	c.(1147-1149)tCc>tGc	p.S383C	LARGE_ENST00000402320.1_Intron|LARGE_ENST00000437602.2_Missense_Mutation_p.S383C|LARGE_ENST00000452586.2_Missense_Mutation_p.S182C|LARGE_ENST00000397394.2_Missense_Mutation_p.S383C|LARGE_ENST00000337431.2_Intron	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	383					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				CTTCTTGGGGGAGTTCCAGTG	0.557																																					p.S383C	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											.	LARGE	98	.	0			c.C1148G						.						62	58	59					22																	33733771		2203	4300	6503	SO:0001583	missense	9215	exon11			TTGGGGGAGTTCC	AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"Glycosyltransferase family 8 domain containing"	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1148C>G	chr22.hg19:g.33733771G>C	ENSP00000347088:p.Ser383Cys	155.0	0.0		118.0	50.0	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	ENST00000354992.2	hg19	CCDS13912.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.660247	0.88154	.	.	ENSG00000133424	ENST00000443693;ENST00000429788;ENST00000445431;ENST00000354992;ENST00000397394;ENST00000452586;ENST00000437602;ENST00000421768	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.66557	0.2801	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.80764	0.994;0.985;0.992	T	0.70669	-0.4808	10	0.87932	D	0	-5.7369	18.8007	0.92015	0.0:0.0:1.0:0.0	.	383;182;383	B7Z2I9;E9PH73;O95461	.;.;LARGE_HUMAN	C	60;60;60;383;383;182;383;182	ENSP00000347088:S383C;ENSP00000380549:S383C;ENSP00000407917:S182C;ENSP00000388544:S383C;ENSP00000403841:S182C	ENSP00000347088:S383C	S	-	2	0	LARGE	32063771	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.171000	0.94802	2.437000	0.82529	0.655000	0.94253	TCC	.	.		0.557	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		C	33733771	G	C	33733771	3	2	158	1	0	0	0	0	1	0	0	0	8636	1174	41	4	1146	4	LARGE	22	33733771	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	11744442	33733771	17570795	102	24061										
PRR5	55615	hgsc.bcm.edu	37	chr22	45132994	45132994	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	ctccctgccccgctccagccCggagaacctggtggaccaga	11	18	0	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr22:45132994C>T	ENST00000336985.6	+	8	1311	c.1034C>T	c.(1033-1035)cCg>cTg	p.P345L	ARHGAP8_ENST00000517296.3_Intron|PRR5-ARHGAP8_ENST00000361473.5_Intron|ARHGAP8_ENST00000389773.5_Intron|PRR5_ENST00000006251.7_Missense_Mutation_p.P336L|PRR5_ENST00000477331.1_3'UTR|PRR5-ARHGAP8_ENST00000352766.7_Intron|PRR5_ENST00000403581.1_Missense_Mutation_p.P368L	NM_181333.3	NP_851850.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	345					cell cycle (GO:0007049)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)	TORC2 complex (GO:0031932)				central_nervous_system(1)|endometrium(2)|lung(6)|prostate(1)|skin(1)	11		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		CGCTCCAGCCCGGAGAACCTG	0.667																																					p.P368L		Atlas-SNP	.											.	PRR5	75	.	0			c.C1103T						.						25	29	28					22																	45132994		2203	4296	6499	SO:0001583	missense	55615	exon10			CCAGCCCGGAGAA	AF177331	CCDS14058.1, CCDS14059.1, CCDS56232.1, CCDS74875.1	22q13.3	2011-02-10			ENSG00000186654	ENSG00000186654			31682	protein-coding gene	gene with protein product	"protein observed with Rictor-1"	609406				15718101, 17599906	Standard	NM_001017528		Approved	PP610, FLJ20185k, Protor-1		P85299	OTTHUMG00000150460	ENST00000336985.6:c.1034C>T	chr22.hg19:g.45132994C>T	ENSP00000337464:p.Pro345Leu	93.0	0.0		85.0	40.0	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000336985.6	hg19	CCDS14058.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.1|20.1	3.932598|3.932598	0.73442|0.73442	.|.	.|.	ENSG00000186654|ENSG00000186654	ENST00000006251;ENST00000404016;ENST00000403581;ENST00000336985|ENST00000455389	T;T;T|.	0.38560|.	1.18;1.13;1.18|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	.|.	.|.	.|.	.|.	T|T	0.74741|0.74741	0.3756|0.3756	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D;P;D;P;P|.	0.89917|.	1.0;0.822;1.0;0.696;0.696|.	D;B;D;B;B|.	0.83275|.	0.991;0.171;0.996;0.099;0.099|.	T|T	0.71303|0.71303	-0.4633|-0.4633	8|5	.|.	.|.	.|.	.|.	19.6803|19.6803	0.95960|0.95960	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	309;368;244;345;345|.	B1AHF5;B1AHF6;P85299-2;P85299;A8K699|.	.;.;.;PRR5_HUMAN;.|.	L|W	336;309;368;345|305	ENSP00000006251:P336L;ENSP00000384848:P368L;ENSP00000337464:P345L|.	.|.	P|R	+|+	2|1	0|2	PRR5|PRR5	43511658|43511658	1.000000|1.000000	0.71417|0.71417	0.969000|0.969000	0.41365|0.41365	0.491000|0.491000	0.33493|0.33493	5.369000|5.369000	0.66138|0.66138	2.756000|2.756000	0.94617|0.94617	0.561000|0.561000	0.74099|0.74099	CCG|CGG	.	.		0.667	PRR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318200.2	NM_001017528		T	45132994	C	T	45132994	3	4	158	1	0	0	0	0	1	0	0	0	12612	652	23	1	1064	1	PRR5	22	45132994	Missense_Mutation	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	11399223	45132994	6171572	103	24062										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51113605	51113605	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cgccctcccggggccgcgccGgcaagttcctggatgaggag	16	15	0	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr22:51113605G>T	ENST00000414786.2	+	2	420	c.193G>T	c.(193-195)Ggc>Tgc	p.G65C	SHANK3_ENST00000262795.3_Missense_Mutation_p.G65C|SHANK3_ENST00000445220.2_Missense_Mutation_p.G65C			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	65	Intramolecular interaction with the ANK repeats. {ECO:0000250}.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		GGGCCGCGCCGGCAAGTTCCT	0.701																																					p.G65C		Atlas-SNP	.											.	SHANK3	96	.	0			c.G193T						.						5	6	6					22																	51113605		1713	3725	5438	SO:0001583	missense	85358	exon2			CGCGCCGGCAAGT	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.193G>T	chr22.hg19:g.51113605G>T	ENSP00000464552:p.Gly65Cys	105.0	0.0		87.0	5.0	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	G	20.2	3.944295	0.73672	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.17213	2.29;2.29	3.91	1.58	0.23477	.	.	.	.	.	T	0.37999	0.1024	M	0.79123	2.44	0.30951	N	0.72475	D	0.89917	1.0	D	0.85130	0.997	T	0.34750	-0.9816	9	0.87932	D	0	.	7.2035	0.25895	0.1041:0.1703:0.7256:0.0	.	65	F2Z3L0	.	C	65	ENSP00000442518:G65C;ENSP00000446078:G65C	ENSP00000442518:G65C	G	+	1	0	SHANK3	49460471	1.000000	0.71417	0.994000	0.49952	0.905000	0.53344	5.229000	0.65316	0.620000	0.30215	0.185000	0.17295	GGC	.	.		0.701	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		T	51113605	G	T	51113605	3	4	158	1	0	0	0	0	1	0	0	0	14281	1116	39	1	199	1	SHANK3	22	51113605	Missense_Mutation	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	5980611	51113605	190961	104	24063										
UBA1	7317	hgsc.bcm.edu	37	chrX	47065414	47065414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	acatatccgggtgacaagccAccagaaccgtgtgggtcctg	12	12	0	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chrX:47065414A>G	ENST00000335972.6	+	15	1826	c.1643A>G	c.(1642-1644)cAc>cGc	p.H548R	UBA1_ENST00000377269.3_5'Flank|UBA1_ENST00000377351.4_Missense_Mutation_p.H548R|INE1_ENST00000456273.1_RNA|UBA1_ENST00000490869.1_Intron	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	548	2 approximate repeats.				cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GTGACAAGCCACCAGAACCGT	0.527																																					p.H548R		Atlas-SNP	.											.	UBA1	89	.	0			c.A1643G						.						54	39	44					X																	47065414		2202	4300	6502	SO:0001583	missense	7317	exon15			CAAGCCACCAGAA	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"Ubiquitin-like modifier activating enzymes"	12469	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog (yeast)", "POC20 centriolar protein homolog (Chlamydomonas)"	314370	"ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)", "ubiquitin-activating enzyme E1"	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.1643A>G	chrX.hg19:g.47065414A>G	ENSP00000338413:p.His548Arg	120.0	0.0		113.0	52.0	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	hg19	CCDS14275.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.170785	0.38315	.	.	ENSG00000130985	ENST00000377351;ENST00000335972	T;T	0.44881	0.91;0.91	4.63	4.63	0.57726	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.50701	0.1631	M	0.68728	2.09	0.80722	D	1	P	0.38767	0.646	P	0.49012	0.598	T	0.44498	-0.9324	10	0.21540	T	0.41	-22.4795	12.3933	0.55370	1.0:0.0:0.0:0.0	.	548	P22314	UBA1_HUMAN	R	548	ENSP00000366568:H548R;ENSP00000338413:H548R	ENSP00000338413:H548R	H	+	2	0	UBA1	46950358	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.443000	0.59994	1.630000	0.50440	0.483000	0.47432	CAC	.	.		0.527	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334		G	47065414	A	G	47065414	3	3	158	1	0	0	0	0	1	0	0	0	16842	159	6	2	1697	2	UBA1	23	47065414	Missense_Mutation	SNP	A	TCGA-DD-AACG-01A-11D-A40R-10		47065414	108205146	105	24064										
RBMX2	51634	hgsc.bcm.edu	37	chrX	129546795	129546795	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	tcccgggagcgggagtcttcGaatcccagtgaccgttggcg	15	12	1	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chrX:129546795G>T	ENST00000305536.6	+	6	1006	c.942G>T	c.(940-942)tcG>tcT	p.S314S		NM_016024.2	NP_057108.2	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2	314	Arg-rich.			SSDAHSSWYNGRSEGRSYRSRSRSRDKSHRHKRARRSRERE SSNPSDRWRH -> LQMHILAGIMGVLKGVVIEVEVGAEIN PIGIKGPDAPGRGVLRIPVTVGVTEDFSCTVDLEIIMFFKC SQIQLGGYYFCI (in Ref. 1; AAD34074). {ECO:0000305}.			nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(2)|large_intestine(1)|liver(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	19						GGGAGTCTTCGAATCCCAGTG	0.473																																					p.S314S		Atlas-SNP	.											.	RBMX2	46	.	0			c.G942T						.						29	30	29					X																	129546795		1815	4061	5876	SO:0001819	synonymous_variant	51634	exon6			GTCTTCGAATCCC	AF078865	CCDS43993.1	Xq26.1	2013-02-12			ENSG00000134597	ENSG00000134597		"RNA binding motif (RRM) containing"	24282	protein-coding gene	gene with protein product						10810093	Standard	NM_016024		Approved	CGI-79	uc004evt.3	Q9Y388	OTTHUMG00000022395	ENST00000305536.6:c.942G>T	chrX.hg19:g.129546795G>T		124.0	0.0		121.0	5.0	NM_016024	A8K9Z0|Q5JY82|Q9Y3I8	Silent	SNP	ENST00000305536.6	hg19	CCDS43993.1																																																																																			.	.		0.473	RBMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058265.1	NM_016024		T	129546795	G	T	129546795	2	4	158	1	0	0	0	0	0	0	0	1	13167	1045	37	1		1	RBMX2	23	129546795	Silent	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	82481381	129546795	25723765	106	24065										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140984732	140984732	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	agtcctcctgagattcctccCcagggtcctcccaagatctc	7	17	1	2			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chrX:140984732C>A	ENST00000298296.1	+	7	1188	c.1188C>A	c.(1186-1188)ccC>ccA	p.P396P	MAGEC3_ENST00000443323.2_Silent_p.P18P|MAGEC3_ENST00000544766.1_Silent_p.P98P|MAGEC3_ENST00000483584.1_3'UTR|MAGEC3_ENST00000409007.1_Silent_p.P98P|MAGEC3_ENST00000536088.1_Silent_p.P98P	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	396	Pro-rich.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					AGATtcctccccagggtcctc	0.577																																					p.P396P		Atlas-SNP	.											.	MAGEC3	228	.	0			c.C1188A						.						34	31	32					X																	140984732		2189	4271	6460	SO:0001819	synonymous_variant	139081	exon7			TCCTCCCCAGGGT	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1188C>A	chrX.hg19:g.140984732C>A		48.0	0.0		44.0	39.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Silent	SNP	ENST00000298296.1	hg19	CCDS14676.1																																																																																			.	.		0.577	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		A	140984732	C	A	140984732	2	1	158	1	0	0	0	0	0	0	0	1	9191	610	22	3		3	MAGEC3	23	140984732	Silent	SNP	C	TCGA-DD-AACG-01A-11D-A40R-10	11437937	140984732	14285828	107	24066										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140994996	140994996	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0277777777777778	3	1	0.719262295081967	1.23302107728337	0.392324888226528	1	1	0	cctcagagccctcctcagggGgaggactccatgtctcctct	10	16	4	1			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chrX:140994996G>T	ENST00000285879.4	+	4	2092	c.1806G>T	c.(1804-1806)ggG>ggT	p.G602G	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	602										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CTCCTCAGGGGGAGGACTCCA	0.582										HNSCC(15;0.026)																											p.G602G		Atlas-SNP	.											.	MAGEC1	317	.	0			c.G1806T						.						205	219	214					X																	140994996		2203	4300	6503	SO:0001819	synonymous_variant	9947	exon4			TCAGGGGGAGGAC	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.1806G>T	chrX.hg19:g.140994996G>T		100.0	0.0		102.0	39.0	NM_005462	A0PK03|O75451|Q8TCV4	Silent	SNP	ENST00000285879.4	hg19	CCDS35417.1																																																																																			.	.		0.582	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		T	140994996	G	T	140994996	2	4	158	1	0	0	0	0	0	0	0	1	9189	1219	43	3		3	MAGEC1	23	140994996	Silent	SNP	G	TCGA-DD-AACG-01A-11D-A40R-10	10264	140994996	14275564	108	24067										
RPL11	6135	hgsc.bcm.edu	37	chr1	24020395	24020395	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cagaagaaatcttggagaagGgtctaaaggtgagcctaatc	12	6	2	4			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr1:24020395G>T	ENST00000374550.3	+	3	301	c.256G>T	c.(256-258)Ggt>Tgt	p.G86C	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	86					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		CTTGGAGAAGGGTCTAAAGGT	0.428																																					p.G86C		Atlas-SNP	.											.	RPL11	21	.	0			c.G256T						.						107	90	96					1																	24020395		2203	4300	6503	SO:0001583	missense	6135	exon3			GAGAAGGGTCTAA	L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"L ribosomal proteins"	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.256G>T	chr1.hg19:g.24020395G>T	ENSP00000363676:p.Gly86Cys	68.0	0.0		96.0	43.0	NM_000975	P25121|P39026|Q8TDH2|Q9Y674	Missense_Mutation	SNP	ENST00000374550.3	hg19	CCDS238.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.561797	0.86335	.	.	ENSG00000142676	ENST00000374550;ENST00000443624;ENST00000458455	T;T;T	0.77098	-1.07;-1.07;-1.07	5.47	5.47	0.80525	Ribosomal protein L5 domain (2);	0.000000	0.85682	D	0.000000	D	0.91858	0.7423	H	0.94620	3.56	0.80722	D	1	D;D	0.76494	0.992;0.999	D;D	0.83275	0.99;0.996	D	0.93767	0.7071	10	0.87932	D	0	-0.2468	19.3166	0.94216	0.0:0.0:1.0:0.0	.	85;86	P62913-2;P62913	.;RL11_HUMAN	C	86;84;84	ENSP00000363676:G86C;ENSP00000390839:G84C;ENSP00000398888:G84C	ENSP00000363676:G86C	G	+	1	0	RPL11	23892982	1.000000	0.71417	0.998000	0.56505	0.593000	0.36681	9.654000	0.98509	2.572000	0.86782	0.655000	0.94253	GGT	.	.		0.428	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975		T	24020395	G	T	24020395	3	4	159	1	0	0	0	0	1	0	0	0	13572	1232	43	3	266	3	RPL11	1	24020395	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10		24020395	225230226	1	24068										
IL22RA1	58985	hgsc.bcm.edu	37	chr1	24448089	24448089	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ctgtggagctcctgcgggctCcctgggtccagacaccctga	13	15	0	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr1:24448089C>G	ENST00000270800.1	-	7	969	c.931G>C	c.(931-933)Gag>Cag	p.E311Q		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	311					cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		CCTGCGGGCTCCCTGGGTCCA	0.632																																					p.E311Q		Atlas-SNP	.											.	IL22RA1	62	.	0			c.G931C						.						57	59	58					1																	24448089		2203	4300	6503	SO:0001583	missense	58985	exon7			CGGGCTCCCTGGG	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"Interleukins and interleukin receptors"	13700	protein-coding gene	gene with protein product		605457	"interleukin 22 receptor"	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.931G>C	chr1.hg19:g.24448089C>G	ENSP00000270800:p.Glu311Gln	77.0	0.0		82.0	24.0	NM_021258	A8K839|B2R9Y9|Q9HB22	Missense_Mutation	SNP	ENST00000270800.1	hg19	CCDS247.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.711474	0.48517	.	.	ENSG00000142677	ENST00000270800	T	0.12672	2.66	4.89	4.89	0.63831	.	1.053850	0.07523	N	0.910839	T	0.25344	0.0616	L	0.32530	0.975	0.29920	N	0.822852	D;D	0.71674	0.998;0.994	P;P	0.59761	0.863;0.796	T	0.11036	-1.0604	10	0.37606	T	0.19	-7.6637	13.5568	0.61763	0.0:1.0:0.0:0.0	.	243;311	B4E2V9;Q8N6P7	.;I22R1_HUMAN	Q	311	ENSP00000270800:E311Q	ENSP00000270800:E311Q	E	-	1	0	IL22RA1	24320676	0.916000	0.31088	0.945000	0.38365	0.064000	0.16182	3.549000	0.53681	2.263000	0.75096	0.462000	0.41574	GAG	.	.		0.632	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1			G	24448089	C	G	24448089	3	3	159	1	0	0	0	0	1	0	0	0	7682	864	30	4	797	4	IL22RA1	1	24448089	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	427694	24448089	224802532	2	24069										
EPHA10	284656	hgsc.bcm.edu	37	chr1	38187384	38187384	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tggctatggtcaaactggccCagcgtgagggcctcggccag	15	12	1	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr1:38187384C>T	ENST00000373048.4	-	11	2093	c.2094G>A	c.(2092-2094)ctG>ctA	p.L698L	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000427468.2_Silent_p.L698L|EPHA10_ENST00000330210.7_Silent_p.L193L|EPHA10_ENST00000540011.1_3'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	698	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CAAACTGGCCCAGCGTGAGGG	0.677																																					p.L698L		Atlas-SNP	.											.	EPHA10	120	.	0			c.G2094A						.						17	21	20					1																	38187384		2037	4177	6214	SO:0001819	synonymous_variant	284656	exon11			CTGGCCCAGCGTG	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2094G>A	chr1.hg19:g.38187384C>T		190.0	0.0		214.0	85.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	hg19	CCDS41305.1																																																																																			.	.		0.677	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		T	38187384	C	T	38187384	2	4	159	1	0	0	0	0	0	0	0	1	5168	581	21	3		3	EPHA10	1	38187384	Silent	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	13739295	38187384	211063237	3	24070										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79392770	79392770	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	aatatacaaatgcaactgcaAcattgcctatcaatcaaata	3	9	2	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr1:79392770A>G	ENST00000370742.3	-	8	947	c.884T>C	c.(883-885)gTt>gCt	p.V295A		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	295					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		TGCAACTGCAACATTGCCTAT	0.269																																					p.V295A		Atlas-SNP	.											.	ELTD1	143	.	0			c.T884C						.						48	45	46					1																	79392770		1793	4068	5861	SO:0001583	missense	64123	exon8			ACTGCAACATTGC	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.884T>C	chr1.hg19:g.79392770A>G	ENSP00000359778:p.Val295Ala	122.0	0.0		128.0	49.0	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	a	12.24	1.877362	0.33162	.	.	ENSG00000162618	ENST00000370742	T	0.09911	2.93	6.02	2.44	0.29823	Domain of unknown function DUF3497 (1);	0.439444	0.26255	N	0.025421	T	0.04272	0.0118	L	0.58101	1.795	0.36834	D	0.887066	B	0.10296	0.003	B	0.20577	0.03	T	0.22208	-1.0223	9	.	.	.	.	9.4887	0.38946	0.8013:0.0:0.1987:0.0	.	295	Q9HBW9	ELTD1_HUMAN	A	295	ENSP00000359778:V295A	.	V	-	2	0	ELTD1	79165358	0.924000	0.31332	0.993000	0.49108	0.984000	0.73092	1.698000	0.37794	0.169000	0.19679	0.445000	0.29226	GTT	.	.		0.269	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		G	79392770	A	G	79392770	3	3	159	1	0	0	0	0	1	0	0	0	5086	43	2	2	1220	2	ELTD1	1	79392770	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	41205386	79392770	169857851	4	24071										
FLG	2312	hgsc.bcm.edu	37	chr1	152277071	152277071	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gtgtccacgaatggtgtcctGaccctcttgggacgctgagt	13	11	1	2	rs545185518		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr1:152277071G>T	ENST00000368799.1	-	3	10326	c.10291C>A	c.(10291-10293)Cag>Aag	p.Q3431K	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3431	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGGTGTCCTGACCCTCTTGG	0.607									Ichthyosis				G|||	1	0.000199681	0	0	5008	,	,		19214	0		0	False		,,,				2504	0.001				p.Q3431K		Atlas-SNP	.											.	FLG	900	.	0			c.C10291A						.						252	259	257					1																	152277071		2203	4299	6502	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGTCCTGACCCTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10291C>A	chr1.hg19:g.152277071G>T	ENSP00000357789:p.Gln3431Lys	65.0	0.0		171.0	14.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.828712	0.32329	.	.	ENSG00000143631	ENST00000368799	T	0.01629	4.72	4.06	1.94	0.25998	.	.	.	.	.	T	0.02494	0.0076	M	0.79805	2.47	0.09310	N	1	D	0.57571	0.98	D	0.71656	0.974	T	0.22138	-1.0225	9	0.06365	T	0.9	.	9.9333	0.41537	0.0:0.4413:0.5587:0.0	.	3431	P20930	FILA_HUMAN	K	3431	ENSP00000357789:Q3431K	ENSP00000357789:Q3431K	Q	-	1	0	FLG	150543695	0.000000	0.05858	0.009000	0.14445	0.031000	0.12232	-0.088000	0.11198	0.818000	0.34468	0.454000	0.30748	CAG	.	.		0.607	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152277071	G	T	152277071	3	4	159	1	0	0	0	0	1	0	0	0	5930	1299	45	3	1898	3	FLG	1	152277071	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	72884301	152277071	96973550	5	24072										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156908219	156908219	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	aaagttattacccgtagcctTtgttccgccttccacttcag	6	13	1	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr1:156908219T>A	ENST00000361409.2	-	37	4805	c.4063A>T	c.(4063-4065)Aag>Tag	p.K1355*	ARHGEF11_ENST00000315174.8_Nonsense_Mutation_p.K771*|MIR765_ENST00000390226.1_RNA|ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000368194.3_Nonsense_Mutation_p.K1395*	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1355					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCCGTAGCCTTTGTTCCGCCT	0.582																																					p.K1395X		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.A4183T						.						112	97	102					1																	156908219		2203	4300	6503	SO:0001587	stop_gained	9826	exon38			TAGCCTTTGTTCC	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.4063A>T	chr1.hg19:g.156908219T>A	ENSP00000354644:p.Lys1355*	40.0	0.0		133.0	98.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Nonsense_Mutation	SNP	ENST00000361409.2	hg19	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	T	48	14.397898	0.99793	.	.	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	.	.	.	5.35	-3.43	0.04810	.	0.579300	0.15749	N	0.246528	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-6.9366	6.3238	0.21232	0.0:0.2319:0.325:0.443	.	.	.	.	X	1395;1355;771	.	ENSP00000313470:K771X	K	-	1	0	ARHGEF11	155174843	0.620000	0.27068	0.954000	0.39281	0.988000	0.76386	-0.524000	0.06222	-0.517000	0.06461	0.533000	0.62120	AAG	.	.		0.582	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		A	156908219	T	A	156908219	4	1	159	1	0	0	0	0	0	1	0	0	896	1850	64	4	521	4	ARHGEF11	1	156908219	Nonsense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	4631148	156908219	92342402	6	24073										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167097070	167097070	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gagcttccgatattcttcccGcagtaattcccagaaacctg	7	13	1	1	rs61748781	byFrequency	TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr1:167097070G>T	ENST00000361200.2	+	6	2868	c.2702G>T	c.(2701-2703)cGc>cTc	p.R901L	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.R901L|DUSP27_ENST00000443333.1_Missense_Mutation_p.R901L			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	901	Ser-rich.				protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						TATTCTTCCCGCAGTAATTCC	0.498																																					p.R901L		Atlas-SNP	.											.	DUSP27	235	.	0			c.G2702T						.						93	82	86					1																	167097070		2203	4300	6503	SO:0001583	missense	92235	exon5			CTTCCCGCAGTAA	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2702G>T	chr1.hg19:g.167097070G>T	ENSP00000354483:p.Arg901Leu	42.0	0.0		111.0	78.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.639224	0.29157	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03607	3.87;3.87;3.87	5.25	2.11	0.27256	.	2.098730	0.01678	N	0.025950	T	0.02047	0.0064	L	0.51422	1.61	0.34339	D	0.68856	B	0.32893	0.389	B	0.32090	0.14	T	0.20273	-1.0280	10	0.87932	D	0	-7.7281	7.5309	0.27683	0.4518:0.0:0.5482:0.0	.	901	Q5VZP5	DUS27_HUMAN	L	901	ENSP00000354483:R901L;ENSP00000271385:R901L;ENSP00000404874:R901L	ENSP00000271385:R901L	R	+	2	0	DUSP27	165363694	0.989000	0.36119	0.998000	0.56505	0.817000	0.46193	0.818000	0.27295	0.482000	0.27582	-0.148000	0.13756	CGC	.	G|0.987;A|0.013		0.498	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		T	167097070	G	T	167097070	3	4	159	1	0	0	0	0	1	0	0	0	4826	1087	38	1	2720	1	DUSP27	1	167097070	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	10188851	167097070	82153551	7	24074										
DHX9	1660	hgsc.bcm.edu	37	chr1	182856333	182856333	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gcggtggctatagcagtggaGgctatggtagcggaggctat	18	6	0	0	rs533935555		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr1:182856333G>T	ENST00000367549.3	+	28	3687	c.3577G>T	c.(3577-3579)Ggc>Tgc	p.G1193C	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	1193	NTD.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						TAGCAGTGGAGGCTATGGTAG	0.562																																					p.G1193C	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G3577T						.						107	119	115					1																	182856333		1991	4170	6161	SO:0001583	missense	1660	exon28			AGTGGAGGCTATG	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.3577G>T	chr1.hg19:g.182856333G>T	ENSP00000356520:p.Gly1193Cys	126.0	0.0		109.0	5.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.024993	0.35701	.	.	ENSG00000135829	ENST00000367549	D	0.84873	-1.91	4.18	4.18	0.49190	.	0.000000	0.56097	U	0.000029	D	0.83764	0.5325	N	0.08118	0	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.86659	0.1903	10	0.54805	T	0.06	.	14.0001	0.64429	0.0:0.0:1.0:0.0	.	472;1193	B3KU66;Q08211	.;DHX9_HUMAN	C	1193	ENSP00000356520:G1193C	ENSP00000356520:G1193C	G	+	1	0	DHX9	181122956	1.000000	0.71417	0.864000	0.33941	0.659000	0.38960	8.554000	0.90689	1.862000	0.54008	0.561000	0.74099	GGC	.	.		0.562	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		T	182856333	G	T	182856333	3	4	159	1	0	0	0	0	1	0	0	0	4518	1000	35	3	3683	3	DHX9	1	182856333	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	15759263	182856333	66394288	8	24075										
KIF14	9928	hgsc.bcm.edu	37	chr1	200522691	200522691	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tataagtttcccagggtttcAacaaatcagggctttcttca	7	9	4	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr1:200522691A>G	ENST00000367350.4	-	30	5210	c.4772T>C	c.(4771-4773)tTg>tCg	p.L1591S		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1591	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						CCAGGGTTTCAACAAATCAGG	0.393																																					p.L1591S		Atlas-SNP	.											.	KIF14	156	.	0			c.T4772C						.						127	115	119					1																	200522691		2203	4300	6503	SO:0001583	missense	9928	exon30			GGTTTCAACAAAT	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.4772T>C	chr1.hg19:g.200522691A>G	ENSP00000356319:p.Leu1591Ser	173.0	0.0		428.0	291.0	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	hg19	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	A	9.432	1.085785	0.20390	.	.	ENSG00000118193	ENST00000367350	T	0.74106	-0.81	5.59	-5.22	0.02806	.	0.830394	0.10390	N	0.680579	T	0.53514	0.1801	L	0.31294	0.92	0.09310	N	1	B	0.18461	0.028	B	0.14578	0.011	T	0.35699	-0.9778	10	0.18276	T	0.48	.	7.0655	0.25149	0.2982:0.3512:0.3506:0.0	.	1591	Q15058	KIF14_HUMAN	S	1591	ENSP00000356319:L1591S	ENSP00000356319:L1591S	L	-	2	0	KIF14	198789314	0.001000	0.12720	0.000000	0.03702	0.492000	0.33523	0.739000	0.26173	-1.346000	0.02211	0.533000	0.62120	TTG	.	.		0.393	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		G	200522691	A	G	200522691	3	3	159	1	0	0	0	0	1	0	0	0	8285	131	5	2	178	2	KIF14	1	200522691	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	17666358	200522691	48727930	9	24076										
RYR2	6262	hgsc.bcm.edu	37	chr1	237961396	237961396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	atcagtgaattacttggcatGgacaaggcagctctggactt	11	8	2	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr1:237961396G>A	ENST00000366574.2	+	97	14333	c.14016G>A	c.(14014-14016)atG>atA	p.M4672I	RYR2_ENST00000360064.6_Missense_Mutation_p.M4678I|RYR2_ENST00000542537.1_Missense_Mutation_p.M4656I	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4672					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TACTTGGCATGGACAAGGCAG	0.433																																					p.M4672I		Atlas-SNP	.											.	RYR2	1273	.	0			c.G14016A						.						97	100	99					1																	237961396		1914	4127	6041	SO:0001583	missense	6262	exon97			TGGCATGGACAAG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.14016G>A	chr1.hg19:g.237961396G>A	ENSP00000355533:p.Met4672Ile	117.0	0.0		246.0	189.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.280352	0.59758	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000536033	D;D;D	0.91631	-2.88;-2.88;-2.88	5.72	5.72	0.89469	.	0.000000	0.85682	U	0.000000	D	0.90466	0.7014	L	0.49126	1.545	0.58432	D	0.999998	B;B	0.25667	0.002;0.131	B;B	0.19946	0.011;0.027	D	0.87163	0.2216	10	0.62326	D	0.03	.	19.8806	0.96895	0.0:0.0:1.0:0.0	.	105;4672	F5H3C7;Q92736	.;RYR2_HUMAN	I	4672;4678;4656;105	ENSP00000355533:M4672I;ENSP00000353174:M4678I;ENSP00000443798:M4656I	ENSP00000353174:M4678I	M	+	3	0	RYR2	236028019	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.809000	0.86057	2.704000	0.92352	0.650000	0.86243	ATG	.	.		0.433	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237961396	G	A	237961396	3	1	159	1	0	0	0	0	1	0	0	0	13784	1348	47	3	14402	3	RYR2	1	237961396	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	37438705	237961396	11289225	10	24077										
CENPA	1058	hgsc.bcm.edu	37	chr2	27015082	27015082	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	agaagagcacacacctcttgAtaaggaagctgcccttcagc	9	12	2	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr2:27015082A>G	ENST00000335756.4	+	2	384	c.184A>G	c.(184-186)Ata>Gta	p.I62V	CENPA_ENST00000233505.8_Missense_Mutation_p.I62V|CENPA_ENST00000475662.1_3'UTR	NM_001809.3	NP_001800.1	P49450	CENPA_HUMAN	centromere protein A	62	H3-like.				CENP-A containing nucleosome assembly (GO:0034080)|establishment of mitotic spindle orientation (GO:0000132)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|protein localization to chromosome, centromeric region (GO:0071459)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|condensed chromosome inner kinetochore (GO:0000939)|condensed nuclear chromosome kinetochore (GO:0000778)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(3)|lung(3)|urinary_tract(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACACCTCTTGATAAGGAAGCT	0.527																																					p.I62V	Pancreas(28;769 878 30250 30578 41330)	Atlas-SNP	.											.	CENPA	13	.	0			c.A184G						.						64	60	61					2																	27015082		2203	4300	6503	SO:0001583	missense	1058	exon2			CTCTTGATAAGGA	U14518	CCDS1729.1, CCDS42662.1	2p23.3	2013-11-05	2006-06-16		ENSG00000115163	ENSG00000115163			1851	protein-coding gene	gene with protein product	"centromere-specific histone", "histone H3-like centromeric protein A"	117139	"centromere protein A (17kD)", "centromere protein A, 17kDa"				Standard	NM_001042426		Approved	CENP-A, CenH3	uc002rhr.3	P49450	OTTHUMG00000097073	ENST00000335756.4:c.184A>G	chr2.hg19:g.27015082A>G	ENSP00000336868:p.Ile62Val	89.0	0.0		90.0	32.0	NM_001042426	D6W544|Q53T74|Q9BVW2	Missense_Mutation	SNP	ENST00000335756.4	hg19	CCDS1729.1	.	.	.	.	.	.	.	.	.	.	A	16.69	3.193222	0.58017	.	.	ENSG00000115163	ENST00000335756;ENST00000233505	T;T	0.50548	0.74;0.74	5.7	-11.4	0.00090	Histone-fold (2);Histone core (1);	0.534882	0.18069	N	0.152694	T	0.45034	0.1322	M	0.85859	2.78	0.09310	N	1	B;B	0.31351	0.32;0.279	B;B	0.39068	0.091;0.289	T	0.46693	-0.9173	10	0.72032	D	0.01	-17.6173	8.2788	0.31887	0.3967:0.4436:0.0:0.1597	.	62;62	P49450-2;P49450	.;CENPA_HUMAN	V	62	ENSP00000336868:I62V;ENSP00000233505:I62V	ENSP00000233505:I62V	I	+	1	0	CENPA	26868586	0.000000	0.05858	0.000000	0.03702	0.411000	0.31082	-4.525000	0.00221	-1.847000	0.01173	-0.309000	0.09137	ATA	.	.		0.527	CENPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214190.2	NM_001809		G	27015082	A	G	27015082	3	3	159	1	0	0	0	0	1	0	0	0	3228	333	12	2	190	2	CENPA	2	27015082	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10		27015082	216184291	11	24078										
R3HDM1	23518	hgsc.bcm.edu	37	chr2	136437817	136437817	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gttatgttccctaatcagtcTaatcaaggatctatgcccac	6	11	4	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr2:136437817T>A	ENST00000264160.4	+	20	2647	c.2277T>A	c.(2275-2277)tcT>tcA	p.S759S	R3HDM1_ENST00000410054.1_Silent_p.S704S|R3HDM1_ENST00000409606.1_Silent_p.S760S|R3HDM1_ENST00000409478.1_Silent_p.S631S|R3HDM1_ENST00000329971.3_Silent_p.S630S	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	759							poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		CTAATCAGTCTAATCAAGGAT	0.388																																					p.S759S		Atlas-SNP	.											.	R3HDM1	84	.	0			c.T2277A						.						135	131	133					2																	136437817		2203	4300	6503	SO:0001819	synonymous_variant	23518	exon20			TCAGTCTAATCAA	D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing"	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.2277T>A	chr2.hg19:g.136437817T>A		114.0	0.0		133.0	56.0	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Silent	SNP	ENST00000264160.4	hg19	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.41|10.41	1.341281|1.341281	0.24339|0.24339	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000445855|ENST00000429703	.|.	.|.	.|.	5.99|5.99	3.64|3.64	0.41730|0.41730	.|.	.|.	.|.	.|.	.|.	T|.	0.47655|.	0.1457|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.40308|.	-0.9570|.	4|.	.|.	.|.	.|.	-1.9477|-1.9477	4.0916|4.0916	0.09972|0.09972	0.1457:0.2934:0.0:0.561|0.1457:0.2934:0.0:0.561	.|.	.|.	.|.	.|.	Q|K	55|483	.|.	.|.	L|X	+|+	2|1	0|0	R3HDM1|R3HDM1	136154287|136154287	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	0.704000|0.704000	0.25661|0.25661	1.077000|1.077000	0.40990|0.40990	0.533000|0.533000	0.62120|0.62120	CTA|TAA	.	.		0.388	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		A	136437817	T	A	136437817	2	1	159	1	0	0	0	0	0	0	0	1	12902	1509	53	4		4	R3HDM1	2	136437817	Silent	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	109422735	136437817	106761556	12	24079										
ITGB6	3694	hgsc.bcm.edu	37	chr2	161052096	161052096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ccgggtagtcctcagtctggCggacatgcacctgcagagtc	13	13	2	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr2:161052096C>T	ENST00000283249.2	-	4	614	c.377G>A	c.(376-378)cGc>cAc	p.R126H	ITGB6_ENST00000409872.1_Missense_Mutation_p.R126H|ITGB6_ENST00000409967.2_Missense_Mutation_p.R126H|ITGB6_ENST00000485635.1_5'UTR|ITGB6_ENST00000428609.2_Missense_Mutation_p.R84H	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	126					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						CTCAGTCTGGCGGACATGCAC	0.537																																					p.R126H		Atlas-SNP	.											.	ITGB6	68	.	0			c.G377A						.						79	72	74					2																	161052096		2203	4300	6503	SO:0001583	missense	3694	exon4			GTCTGGCGGACAT		CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"Integrins"	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.377G>A	chr2.hg19:g.161052096C>T	ENSP00000283249:p.Arg126His	58.0	0.0		58.0	16.0	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Missense_Mutation	SNP	ENST00000283249.2	hg19	CCDS2212.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.781161	0.90282	.	.	ENSG00000115221	ENST00000283249;ENST00000428609;ENST00000409967;ENST00000409872	D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22	6.05	6.05	0.98169	Integrin beta subunit, N-terminal (2);	0.110420	0.64402	D	0.000004	D	0.96087	0.8725	M	0.63428	1.95	0.54753	D	0.99998	D;D	0.71674	0.998;0.998	D;D	0.65773	0.938;0.938	D	0.95193	0.8310	10	0.51188	T	0.08	.	20.6013	0.99457	0.0:1.0:0.0:0.0	.	84;126	E9PEE8;P18564	.;ITB6_HUMAN	H	126;84;126;126	ENSP00000283249:R126H;ENSP00000408024:R84H;ENSP00000386828:R126H;ENSP00000386367:R126H	ENSP00000283249:R126H	R	-	2	0	ITGB6	160760342	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.991000	0.56973	2.878000	0.98634	0.650000	0.86243	CGC	.	.		0.537	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888		T	161052096	C	T	161052096	3	4	159	1	0	0	0	0	1	0	0	0	7908	768	27	1	2037	1	ITGB6	2	161052096	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	24614279	161052096	82147277	13	24080										
STK39	27347	hgsc.bcm.edu	37	chr2	168986092	168986092	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gtctggtgttcttgtaagcaGcttctcaatcaggtactctc	9	10	5	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr2:168986092G>A	ENST00000355999.4	-	10	1753	c.1048C>T	c.(1048-1050)Ctg>Ttg	p.L350L		NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	350					cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						CTTGTAAGCAGCTTCTCAATC	0.398																																					p.L350L		Atlas-SNP	.											.	STK39	95	.	0			c.C1048T						.						311	284	292					2																	168986092		1898	4112	6010	SO:0001819	synonymous_variant	27347	exon10			TAAGCAGCTTCTC	AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648			17717	protein-coding gene	gene with protein product	"STE20/SPS1 homolog (yeast)"	607648				10980603	Standard	NM_013233		Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.1048C>T	chr2.hg19:g.168986092G>A		128.0	0.0		169.0	59.0	NM_013233	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	Silent	SNP	ENST00000355999.4	hg19	CCDS42770.1																																																																																			.	.		0.398	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258112.2	NM_013233		A	168986092	G	A	168986092	2	1	159	1	0	0	0	0	0	0	0	1	15320	962	34	3		3	STK39	2	168986092	Silent	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	7933996	168986092	74213281	14	24081										
TTN	7273	hgsc.bcm.edu	37	chr2	179455790	179455790	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tactgcttccggaagagacaAcaccccacgtgtctttcctt	7	14	1	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr2:179455790A>C	ENST00000591111.1	-	254	55963	c.55739T>G	c.(55738-55740)gTt>gGt	p.V18580G	TTN_ENST00000589042.1_Missense_Mutation_p.V20221G|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V17653G|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V11348G|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V11281G|TTN_ENST00000460472.2_Missense_Mutation_p.V11156G|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18580	Fibronectin type-III 34. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGAAGAGACAACACCCCACGT	0.433																																					p.V20221G		Atlas-SNP	.											.	TTN	18412	.	0			c.T60662G						.						151	146	148					2																	179455790		1893	4116	6009	SO:0001583	missense	7273	exon304			GAGACAACACCCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.55739T>G	chr2.hg19:g.179455790A>C	ENSP00000465570:p.Val18580Gly	109.0	0.0		150.0	28.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.761	1.170205	0.21621	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	6.11	6.11	0.99139	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46092	0.1375	L	0.33710	1.025	0.80722	D	1	B;B;B;B	0.09022	0.002;0.002;0.002;0.002	B;B;B;B	0.08055	0.003;0.003;0.003;0.003	T	0.35574	-0.9783	9	0.87932	D	0	.	16.7021	0.85357	1.0:0.0:0.0:0.0	.	11156;11281;11348;18580	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	17653;11156;11348;11281;11154	ENSP00000343764:V17653G;ENSP00000434586:V11156G;ENSP00000340554:V11348G;ENSP00000352154:V11281G	ENSP00000340554:V11348G	V	-	2	0	TTN	179164036	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.756000	0.68757	2.343000	0.79666	0.533000	0.62120	GTT	.	.		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179455790	A	C	179455790	3	2	159	1	0	0	0	0	1	0	0	0	16750	43	2	5	47553	5	TTN	2	179455790	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	10469698	179455790	63743583	15	24082										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187559065	187559065	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cagcaacaacaacaacaacaGcaaaagcagctggaggaggc	10	11	0	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr2:187559065G>A	ENST00000304698.5	+	1	368	c.165G>A	c.(163-165)caG>caA	p.Q55Q	AC017101.10_ENST00000453665.1_RNA	NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	55	Gln-rich.					integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						aacaacaacagcaaaagcagc	0.642																																					p.Q55Q		Atlas-SNP	.											.	FAM171B	146	.	0			c.G165A						.						28	31	30					2																	187559065		2202	4300	6502	SO:0001819	synonymous_variant	165215	exon1			ACAACAGCAAAAG	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.165G>A	chr2.hg19:g.187559065G>A		109.0	0.0		116.0	8.0	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Silent	SNP	ENST00000304698.5	hg19	CCDS33347.1																																																																																			.	.		0.642	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		A	187559065	G	A	187559065	2	1	159	1	0	0	0	0	0	0	0	1	5496	962	34	3		3	FAM171B	2	187559065	Silent	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	8103275	187559065	55640308	16	24083										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189873710	189873710	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ctcctggtgcccctggtcctTgctgtggtggtgttggagcc	15	12	0	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr2:189873710T>C	ENST00000304636.3	+	48	3756	c.3586T>C	c.(3586-3588)Tgc>Cgc	p.C1196R	COL3A1_ENST00000317840.5_Missense_Mutation_p.C893R	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	1196	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	CCCTGGTCCTTGCTGTGGTGG	0.537																																					p.C1196R		Atlas-SNP	.											.	COL3A1	292	.	0			c.T3586C						.						67	75	72					2																	189873710		2203	4300	6503	SO:0001583	missense	1281	exon48			GGTCCTTGCTGTG	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.3586T>C	chr2.hg19:g.189873710T>C	ENSP00000304408:p.Cys1196Arg	128.0	0.0		173.0	70.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	hg19	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	T	14.67	2.604879	0.46423	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.96522	-4.04;-4.04	5.54	5.54	0.83059	.	0.000000	0.56097	D	0.000026	D	0.96959	0.9007	M	0.80508	2.5	0.38538	D	0.949147	D	0.55800	0.973	P	0.53224	0.721	D	0.96981	0.9715	10	0.19590	T	0.45	.	15.6737	0.77297	0.0:0.0:0.0:1.0	.	1196	P02461	CO3A1_HUMAN	R	1196;893	ENSP00000304408:C1196R;ENSP00000315243:C893R	ENSP00000304408:C1196R	C	+	1	0	COL3A1	189581955	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	5.919000	0.70005	2.103000	0.63969	0.533000	0.62120	TGC	.	.		0.537	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		C	189873710	T	C	189873710	3	2	159	1	0	0	0	0	1	0	0	0	3690	1812	63	2	3776	2	COL3A1	2	189873710	Missense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	2314645	189873710	53325663	17	24084										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209195391	209195391	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tatcagcatacaattcttacAtattcctggtgtagaatctg	6	8	3	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr2:209195391A>G	ENST00000264380.4	+	23	4094	c.3936A>G	c.(3934-3936)acA>acG	p.T1312T		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1312					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						CAATTCTTACATATTCCTGGT	0.363																																					p.T1312T		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.A3936G						.						161	162	162					2																	209195391		2203	4300	6503	SO:0001819	synonymous_variant	200576	exon23			TCTTACATATTCC	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.3936A>G	chr2.hg19:g.209195391A>G		88.0	0.0		75.0	34.0	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	hg19	CCDS2382.1																																																																																			.	.		0.363	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		G	209195391	A	G	209195391	2	3	159	1	0	0	0	0	0	0	0	1	11933	204	8	2		2	PIKFYVE	2	209195391	Silent	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	19321681	209195391	34003982	18	24085										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64132537	64132537	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gacagggccagggattccatGgagccccgaggggtctgctc	16	12	1	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr3:64132537G>T	ENST00000295902.6	-	7	2214	c.1629C>A	c.(1627-1629)tcC>tcA	p.S543S	PRICKLE2_ENST00000564377.1_Silent_p.S599S	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	543					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		GGGATTCCATGGAGCCCCGAG	0.557																																					p.S543S		Atlas-SNP	.											.	PRICKLE2	88	.	0			c.C1629A						.						69	71	70					3																	64132537		2203	4300	6503	SO:0001819	synonymous_variant	166336	exon7			TTCCATGGAGCCC	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.1629C>A	chr3.hg19:g.64132537G>T		60.0	0.0		63.0	25.0	NM_198859	Q0VF44	Silent	SNP	ENST00000295902.6	hg19	CCDS2902.1																																																																																			.	.		0.557	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		T	64132537	G	T	64132537	2	4	159	1	0	0	0	0	0	0	0	1	12499	1335	47	3		3	PRICKLE2	3	64132537	Silent	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10		64132537	133889893	19	24086										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376412	113376412	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	agggatctgactgaccatcaTttgagtttggtcagaaatgg	12	6	3	4			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr3:113376412T>C	ENST00000478658.1	-	5	4134	c.4117A>G	c.(4117-4119)Atg>Gtg	p.M1373V	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.M1373V			Q68DE3	K2018_HUMAN	KIAA2018	1373						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						CTGACCATCATTTGAGTTTGG	0.468																																					p.M1373V		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A4117G						.						104	102	103					3																	113376412		1989	4160	6149	SO:0001583	missense	205717	exon7			CCATCATTTGAGT	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4117A>G	chr3.hg19:g.113376412T>C	ENSP00000420721:p.Met1373Val	76.0	0.0		82.0	37.0	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	hg19	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	T	11.86	1.766023	0.31228	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.19105	2.17;2.17	5.68	4.54	0.55810	.	0.182532	0.64402	D	0.000018	T	0.13841	0.0335	L	0.34521	1.04	0.53005	D	0.999969	B	0.16396	0.017	B	0.12837	0.008	T	0.05053	-1.0909	10	0.07644	T	0.81	-5.2402	11.0849	0.48080	0.0:0.0721:0.0:0.9278	.	1373	Q68DE3	K2018_HUMAN	V	1373	ENSP00000320794:M1373V;ENSP00000420721:M1373V	ENSP00000320794:M1373V	M	-	1	0	KIAA2018	114859102	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	3.851000	0.55926	2.169000	0.68431	0.402000	0.26972	ATG	.	.		0.468	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		C	113376412	T	C	113376412	3	2	159	1	0	0	0	0	1	0	0	0	8277	1493	52	2	2624	2	KIAA2018	3	113376412	Missense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	49243875	113376412	84646018	20	24087										
GFM1	85476	hgsc.bcm.edu	37	chr3	158363556	158363556	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tttactacactggcagaattGcaaagatgcatgaggtatat	9	6	0	3	rs140377587	byFrequency	TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr3:158363556G>C	ENST00000486715.1	+	2	577	c.220G>C	c.(220-222)Gca>Cca	p.A74P	GFM1_ENST00000264263.5_Missense_Mutation_p.A74P|GFM1_ENST00000478576.1_Missense_Mutation_p.A74P	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			TGGCAGAATTGCAAAGATGCA	0.323																																					p.A74P		Atlas-SNP	.											.	GFM1	83	.	0			c.G220C						.						120	122	121					3																	158363556		2203	4300	6503	SO:0001583	missense	85476	exon2			AGAATTGCAAAGA	AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"G translation elongation factor, mitochondrial"			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.220G>C	chr3.hg19:g.158363556G>C	ENSP00000419038:p.Ala74Pro	115.0	0.0		108.0	43.0	NM_024996		Missense_Mutation	SNP	ENST00000486715.1	hg19	CCDS33885.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.483722	0.84854	.	.	ENSG00000168827	ENST00000486715;ENST00000478576;ENST00000264263	T;T;T	0.74002	-0.8;-0.8;-0.8	5.68	5.68	0.88126	Small GTP-binding protein domain (1);Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	T	0.78136	0.4236	L	0.37507	1.11	0.80722	D	1	P;P	0.47677	0.757;0.899	P;P	0.53102	0.718;0.718	T	0.79507	-0.1775	10	0.72032	D	0.01	-4.6008	19.8773	0.96884	0.0:0.0:1.0:0.0	.	74;74	Q96RP9;C9IZ01	EFGM_HUMAN;.	P	74	ENSP00000419038:A74P;ENSP00000418755:A74P;ENSP00000264263:A74P	ENSP00000264263:A74P	A	+	1	0	GFM1	159846250	1.000000	0.71417	0.691000	0.30163	0.968000	0.65278	6.049000	0.71053	2.687000	0.91594	0.650000	0.86243	GCA	.	G|0.998;T|0.002		0.323	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996		C	158363556	G	C	158363556	3	2	159	1	0	0	0	0	1	0	0	0	6349	1319	46	4	226	4	GFM1	3	158363556	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	44987144	158363556	39658874	21	24088										
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57173769	57173769	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	attcccatgaataaggcaaaCagtggagaggctagcttaga	11	7	0	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr4:57173769C>T	ENST00000504228.1	+	3	294	c.189C>T	c.(187-189)aaC>aaT	p.N63N	KIAA1211_ENST00000264229.6_Silent_p.N63N|KIAA1211_ENST00000541073.1_Silent_p.N56N			Q6ZU35	K1211_HUMAN	KIAA1211	63										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					ATAAGGCAAACAGTGGAGAGG	0.478																																					p.N63N		Atlas-SNP	.											.	KIAA1211	178	.	0			c.C189T						.						89	90	90					4																	57173769		2001	4167	6168	SO:0001819	synonymous_variant	57482	exon5			GGCAAACAGTGGA	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.189C>T	chr4.hg19:g.57173769C>T		86.0	0.0		107.0	35.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	hg19	CCDS43230.1																																																																																			.	.		0.478	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		T	57173769	C	T	57173769	2	4	159	1	0	0	0	0	0	0	0	1	8224	477	17	3		3	KIAA1211	4	57173769	Silent	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10		57173769	133980507	22	24089										
TMPRSS11D	9407	hgsc.bcm.edu	37	chr4	68703989	68703989	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tttcattgatgctccattgtTatttctagtgaattgaaatt	6	5	2	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr4:68703989T>C	ENST00000283916.6	-	5	474	c.376A>G	c.(376-378)Aac>Gac	p.N126D	TMPRSS11D_ENST00000509584.1_5'UTR|TMPRSS11D_ENST00000545541.1_Missense_Mutation_p.N9D|UBA6-AS1_ENST00000500538.2_RNA	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	126	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				proteolysis (GO:0006508)|respiratory gaseous exchange (GO:0007585)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GCTCCATTGTTATTTCTAGTG	0.333																																					p.N126D		Atlas-SNP	.											.	TMPRSS11D	68	.	0			c.A376G						.						97	91	93					4																	68703989		2202	4300	6502	SO:0001583	missense	9407	exon5			CATTGTTATTTCT	AB002134	CCDS3518.1	4q13.2	2010-04-13			ENSG00000153802	ENSG00000153802		"Serine peptidases / Transmembrane"	24059	protein-coding gene	gene with protein product	"airway trypsin like protease"	605369				9565616, 9070615	Standard	XM_005265710		Approved		uc003hdq.3	O60235	OTTHUMG00000129300	ENST00000283916.6:c.376A>G	chr4.hg19:g.68703989T>C	ENSP00000283916:p.Asn126Asp	91.0	0.0		114.0	43.0	NM_004262	Q08AF6	Missense_Mutation	SNP	ENST00000283916.6	hg19	CCDS3518.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.507216	0.27036	.	.	ENSG00000153802	ENST00000283916;ENST00000545541	T;D	0.87571	1.61;-2.27	5.16	3.94	0.45596	SEA (3);	0.457587	0.20162	N	0.097923	D	0.85159	0.5633	L	0.52206	1.635	0.09310	N	1	P	0.51537	0.946	P	0.51487	0.671	T	0.73547	-0.3948	10	0.14252	T	0.57	.	8.3659	0.32387	0.1752:0.0:0.0:0.8248	.	126	O60235	TM11D_HUMAN	D	126;9	ENSP00000283916:N126D;ENSP00000442045:N9D	ENSP00000283916:N126D	N	-	1	0	TMPRSS11D	68386584	0.000000	0.05858	0.008000	0.14137	0.974000	0.67602	0.472000	0.22116	0.869000	0.35703	0.533000	0.62120	AAC	.	.		0.333	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3	NM_004262		C	68703989	T	C	68703989	3	2	159	1	0	0	0	0	1	0	0	0	16256	1754	61	2	904	2	TMPRSS11D	4	68703989	Missense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	11530220	68703989	122450287	23	24090										
ALB	213	hgsc.bcm.edu	37	chr4	74286009	74286012	+	Frame_Shift_Del	DEL	CTTA	CTTA	-													0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gcaagtcaagctgccttaggCttataacatcacatttaaaa							TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	CTTA	CTTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr4:74286009_74286012delCTTA	ENST00000503124.1	+	12	1581_1584	c.1374_1377delCTTA	c.(1372-1377)ggcttafs	p.GL458fs	ALB_ENST00000509063.1_Intron|ALB_ENST00000295897.4_Frame_Shift_Del_p.GL608fs|ALB_ENST00000415165.2_Frame_Shift_Del_p.GL416fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Frame_Shift_Del_p.GL493fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTGCCTTAGGCTTATAACATCACA	0.284																																					p.608_609del		Atlas-INDEL	.											.	ALB	132	.	0			c.1823_1826del						.																																			SO:0001589	frameshift_variant	213	exon14			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1374_1377delCTTA	chr4.hg19:g.74286009_74286012delCTTA	ENSP00000421027:p.Gly458fs	166.0	0.0		168.0	67.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.284	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74286012	CTTA	-	74286009	7	5	159	1	0	1	0	1	0	0	0	0	486	784	28	0	1878	0	ALB	4	74286009	Frame_Shift_Del	DEL	CTTA	TCGA-DD-AACH-01A-11D-A40R-10	5582020	74286009	116868267	24	24091										
ADH4	127	hgsc.bcm.edu	37	chr4	100057655	100057655	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	agccccatagccagttgaaaAcccacatccaagcagacaaa	6	14	0	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr4:100057655A>C	ENST00000265512.7	-	5	618	c.544T>G	c.(544-546)Ttt>Gtt	p.F182V	ADH4_ENST00000423445.1_Missense_Mutation_p.F201V|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000508393.1_Missense_Mutation_p.F201V|ADH4_ENST00000505590.1_Missense_Mutation_p.F201V	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	182					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		CCAGTTGAAAACCCACATCCA	0.403																																					p.F182V		Atlas-SNP	.											.	ADH4	35	.	0			c.T544G						.						190	169	176					4																	100057655		2203	4300	6503	SO:0001583	missense	127	exon5			TTGAAAACCCACA	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"Alcohol dehydrogenases"	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.544T>G	chr4.hg19:g.100057655A>C	ENSP00000265512:p.Phe182Val	70.0	0.0		80.0	31.0	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Missense_Mutation	SNP	ENST00000265512.7	hg19	CCDS34032.1	.	.	.	.	.	.	.	.	.	.	A	8.932	0.963597	0.18583	.	.	ENSG00000198099	ENST00000508393;ENST00000265512;ENST00000423445;ENST00000505590;ENST00000512499;ENST00000504125	T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;4.06;4.06	4.55	4.55	0.56014	GroES-like (1);	0.238899	0.35179	N	0.003399	T	0.16769	0.0403	N	0.16656	0.425	0.41841	D	0.99012	B;B	0.30727	0.185;0.292	B;B	0.42995	0.362;0.404	T	0.02676	-1.1125	10	0.02654	T	1	-12.4301	14.0991	0.65042	1.0:0.0:0.0:0.0	.	201;182	P08319-2;P08319	.;ADH4_HUMAN	V	201;182;201;201;201;164	ENSP00000424630:F201V;ENSP00000265512:F182V;ENSP00000397939:F201V;ENSP00000425416:F201V;ENSP00000423571:F201V;ENSP00000427525:F164V	ENSP00000265512:F182V	F	-	1	0	ADH4	100276678	0.846000	0.29590	0.880000	0.34516	0.713000	0.41058	1.683000	0.37638	1.925000	0.55765	0.528000	0.53228	TTT	.	.		0.403	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670		C	100057655	A	C	100057655	3	2	159	1	0	0	0	0	1	0	0	0	310	43	2	5	618	5	ADH4	4	100057655	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	25771646	100057655	91096621	25	24092										
NUDT6	11162	hgsc.bcm.edu	37	chr4	123814266	123814266	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ttaggcggcagatgatatacAtatctgacttcccaaaagct	8	9	1	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr4:123814266A>G	ENST00000304430.5	-	5	701	c.668T>C	c.(667-669)aTg>aCg	p.M223T	FGF2_ENST00000608478.1_3'UTR|NUDT6_ENST00000502270.1_Missense_Mutation_p.M54T|NUDT6_ENST00000339154.2_Missense_Mutation_p.M54T|NUDT6_ENST00000608639.1_5'Flank|FGF2_ENST00000264498.3_3'UTR	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	223	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)			endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						GATGATATACATATCTGACTT	0.423																																					p.M223T		Atlas-SNP	.											.	NUDT6	50	.	0			c.T668C						.						107	108	108					4																	123814266		2203	4300	6503	SO:0001583	missense	11162	exon5			ATATACATATCTG	AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"Nudix motif containing"	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.668T>C	chr4.hg19:g.123814266A>G	ENSP00000306070:p.Met223Thr	52.0	0.0		63.0	26.0	NM_007083	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	hg19	CCDS43268.1	.	.	.	.	.	.	.	.	.	.	A	17.94	3.511451	0.64522	.	.	ENSG00000170917	ENST00000304430;ENST00000339154;ENST00000502270	T;T;T	0.27104	1.69;1.69;1.69	5.41	4.16	0.48862	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.129061	0.64402	D	0.000002	T	0.34019	0.0883	L	0.56769	1.78	0.58432	D	0.999999	P	0.43633	0.813	P	0.48552	0.581	T	0.15578	-1.0432	10	0.87932	D	0	-9.9271	11.2964	0.49280	0.8637:0.0:0.0:0.1363	.	223	P53370	NUDT6_HUMAN	T	223;54;54	ENSP00000306070:M223T;ENSP00000344011:M54T;ENSP00000424117:M54T	ENSP00000306070:M223T	M	-	2	0	NUDT6	124033716	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.508000	0.73721	2.054000	0.61138	0.528000	0.53228	ATG	.	.		0.423	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083		G	123814266	A	G	123814266	3	3	159	1	0	0	0	0	1	0	0	0	10752	217	8	2	286	2	NUDT6	4	123814266	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	23756611	123814266	67340010	26	24093										
FGA	2243	hgsc.bcm.edu	37	chr4	155507834	155507834	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tgcggcatgtctgttaatgcCttccactctgggggtacctt	11	11	2	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr4:155507834C>G	ENST00000302053.3	-	5	825	c.747G>C	c.(745-747)aaG>aaC	p.K249N	FGA_ENST00000403106.3_Missense_Mutation_p.K249N	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	249					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	CTGTTAATGCCTTCCACTCTG	0.473																																					p.K249N	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.G747C						.						132	138	136					4																	155507834		2203	4300	6503	SO:0001583	missense	2243	exon5			TAATGCCTTCCAC		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.747G>C	chr4.hg19:g.155507834C>G	ENSP00000306361:p.Lys249Asn	101.0	0.0		104.0	37.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	C	11.29	1.594928	0.28445	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.61980	0.06;0.06	5.43	-2.1	0.07210	.	3.162610	0.00424	N	0.000078	T	0.50069	0.1594	L	0.45698	1.435	0.09310	N	1	B;B	0.15473	0.003;0.013	B;B	0.12156	0.007;0.003	T	0.15665	-1.0429	10	0.38643	T	0.18	.	0.3637	0.00368	0.2467:0.2719:0.2277:0.2537	.	249;249	P02671-2;P02671	.;FIBA_HUMAN	N	249	ENSP00000306361:K249N;ENSP00000385981:K249N	ENSP00000306361:K249N	K	-	3	2	FGA	155727284	0.000000	0.05858	0.010000	0.14722	0.024000	0.10985	-0.849000	0.04322	-0.131000	0.11578	0.655000	0.94253	AAG	.	.		0.473	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		G	155507834	C	G	155507834	3	3	159	1	0	0	0	0	1	0	0	0	5838	680	24	4	1905	4	FGA	4	155507834	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	31693568	155507834	35646442	27	24094										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13876819	13876819	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ggtggagttgataattgtgcTaagcacagaaactaatttta	10	4	0	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr5:13876819T>A	ENST00000265104.4	-	22	3474	c.3370A>T	c.(3370-3372)Agc>Tgc	p.S1124C	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1124	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					ATAATTGTGCTAAGCACAGAA	0.388									Kartagener syndrome																												p.S1124C		Atlas-SNP	.											.	DNAH5	868	.	0			c.A3370T						.						127	129	128					5																	13876819		2203	4300	6503	SO:0001583	missense	1767	exon22	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TTGTGCTAAGCAC	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3370A>T	chr5.hg19:g.13876819T>A	ENSP00000265104:p.Ser1124Cys	163.0	0.0		145.0	69.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.016737	0.54468	.	.	ENSG00000039139	ENST00000265104	T	0.25749	1.78	5.6	4.44	0.53790	.	0.079143	0.85682	D	0.000000	T	0.30039	0.0752	M	0.71036	2.16	0.51233	D	0.999918	B	0.13145	0.007	B	0.16722	0.016	T	0.08207	-1.0733	10	0.59425	D	0.04	.	11.699	0.51560	0.0:0.0694:0.0:0.9306	.	1124	Q8TE73	DYH5_HUMAN	C	1124	ENSP00000265104:S1124C	ENSP00000265104:S1124C	S	-	1	0	DNAH5	13929819	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	5.670000	0.68088	1.066000	0.40716	0.533000	0.62120	AGC	.	.		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13876819	T	A	13876819	3	1	159	1	0	0	0	0	1	0	0	0	4606	1522	53	4	10736	4	DNAH5	5	13876819	Missense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10		13876819	167038441	28	24095										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37213755	37213755	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	taggcagccatgaaacgagcCatggactggacgactctcac	11	12	1	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr5:37213755C>A	ENST00000508244.1	-	15	2919	c.2826G>T	c.(2824-2826)atG>atT	p.M942I	C5orf42_ENST00000425232.2_Missense_Mutation_p.M942I|C5orf42_ENST00000274258.7_5'UTR			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	942						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TGAAACGAGCCATGGACTGGA	0.478																																					p.M942I		Atlas-SNP	.											.	C5orf42	422	.	0			c.G2826T						.						104	86	91					5																	37213755		692	1591	2283	SO:0001583	missense	65250	exon16			ACGAGCCATGGAC		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.2826G>T	chr5.hg19:g.37213755C>A	ENSP00000421690:p.Met942Ile	390.0	1.0		417.0	164.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	19.10	3.762870	0.69763	.	.	ENSG00000197603	ENST00000508244;ENST00000425232	T;T	0.27557	1.66;1.66	5.44	5.44	0.79542	.	0.079006	0.52532	U	0.000067	T	0.47154	0.1430	M	0.73598	2.24	0.80722	D	1	D	0.59767	0.986	P	0.53593	0.73	T	0.49370	-0.8947	10	0.59425	D	0.04	-13.5991	13.5522	0.61738	0.0:0.9251:0.0:0.0749	.	942	E9PH94	.	I	942	ENSP00000421690:M942I;ENSP00000389014:M942I	ENSP00000389014:M942I	M	-	3	0	C5orf42	37249512	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	2.652000	0.46682	2.542000	0.85734	0.491000	0.48974	ATG	.	.		0.478	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37213755	C	A	37213755	3	1	159	1	0	0	0	0	1	0	0	0	2303	594	21	3	6915	3	C5orf42	5	37213755	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	23336936	37213755	143701505	29	24096										
MAST4	375449	hgsc.bcm.edu	37	chr5	66430370	66430370	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ggtctgtggcacacctgaatAcattgcaccagaagtgattc	10	10	1	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr5:66430370A>G	ENST00000403625.2	+	18	2541	c.2246A>G	c.(2245-2247)tAc>tGc	p.Y749C	MAST4_ENST00000404260.3_Missense_Mutation_p.Y752C|MAST4_ENST00000405643.1_Missense_Mutation_p.Y570C|MAST4_ENST00000261569.7_Missense_Mutation_p.Y555C|MAST4_ENST00000403666.1_Missense_Mutation_p.Y560C	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	752	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		ACACCTGAATACATTGCACCA	0.413																																					p.Y749C		Atlas-SNP	.											.	MAST4	218	.	0			c.A2246G						.						109	117	114					5																	66430370		1858	4103	5961	SO:0001583	missense	375449	exon18			CTGAATACATTGC	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.2246A>G	chr5.hg19:g.66430370A>G	ENSP00000385727:p.Tyr749Cys	103.0	0.0		100.0	38.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	A	17.02	3.281120	0.59758	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399	T;T;T;T;T	0.59638	0.25;0.25;0.25;0.25;0.25	5.56	5.56	0.83823	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84088	0.5395	H	0.97051	3.93	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.997;0.998	D	0.89641	0.3862	10	0.87932	D	0	-19.1959	15.7031	0.77558	1.0:0.0:0.0:0.0	.	570;752;555;560	E7EWQ5;O15021;O15021-2;O15021-3	.;MAST4_HUMAN;.;.	C	752;749;560;570;570;555;555	ENSP00000385048:Y752C;ENSP00000385727:Y749C;ENSP00000384313:Y560C;ENSP00000384099:Y570C;ENSP00000261569:Y555C	ENSP00000261569:Y555C	Y	+	2	0	MAST4	66466126	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.124000	0.65301	0.528000	0.53228	TAC	.	.		0.413	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			G	66430370	A	G	66430370	3	3	159	1	0	0	0	0	1	0	0	0	9336	391	14	2	2446	2	MAST4	5	66430370	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	29216615	66430370	114484890	30	24097										
CRHBP	1393	hgsc.bcm.edu	37	chr5	76254694	76254694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ctgatcttaccctgggacacGtaaatggtcttcagttaaag	9	9	3	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr5:76254694G>A	ENST00000274368.4	+	5	1095	c.673G>A	c.(673-675)Gta>Ata	p.V225I	CRHBP_ENST00000506501.1_Missense_Mutation_p.V225I|CRHBP_ENST00000514258.1_3'UTR	NM_001882.3	NP_001873.2	P24387	CRHBP_HUMAN	corticotropin releasing hormone binding protein	225					behavioral response to ethanol (GO:0048149)|cellular response to calcium ion (GO:0071277)|cellular response to cAMP (GO:0071320)|cellular response to cocaine (GO:0071314)|cellular response to drug (GO:0035690)|cellular response to estradiol stimulus (GO:0071392)|cellular response to estrogen stimulus (GO:0071391)|cellular response to gonadotropin-releasing hormone (GO:0097211)|cellular response to potassium ion (GO:0035865)|cellular response to stress (GO:0033554)|cellular response to tumor necrosis factor (GO:0071356)|female pregnancy (GO:0007565)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|inflammatory response (GO:0006954)|learning or memory (GO:0007611)|maternal aggressive behavior (GO:0002125)|negative regulation of corticotropin secretion (GO:0051460)|negative regulation of corticotropin-releasing hormone receptor activity (GO:1900011)|regulated secretory pathway (GO:0045055)|regulation of corticotropin secretion (GO:0051459)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|synaptic transmission, dopaminergic (GO:0001963)	axon terminus (GO:0043679)|dendrite (GO:0030425)|dense core granule (GO:0031045)|extracellular space (GO:0005615)|intracellular (GO:0005622)|microtubule (GO:0005874)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|perikaryon (GO:0043204)|secondary lysosome (GO:0005767)|secretory granule (GO:0030141)|varicosity (GO:0043196)	corticotropin-releasing hormone binding (GO:0051424)|peptide binding (GO:0042277)			kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	16		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)		CCTGGGACACGTAAATGGTCT	0.413																																					p.V225I		Atlas-SNP	.											.	CRHBP	46	.	0			c.G673A						.						100	81	87					5																	76254694		2203	4300	6503	SO:0001583	missense	1393	exon5			GGACACGTAAATG	X58022	CCDS4034.1	5q	2008-07-18	2001-11-28		ENSG00000145708	ENSG00000145708			2356	protein-coding gene	gene with protein product		122559	"corticotropin releasing hormone-binding protein"			8198617	Standard	NM_001882		Approved	CRF-BP, CRFBP	uc003ker.3	P24387	OTTHUMG00000102133	ENST00000274368.4:c.673G>A	chr5.hg19:g.76254694G>A	ENSP00000274368:p.Val225Ile	51.0	0.0		103.0	9.0	NM_001882	Q53F32|Q6FHT5	Missense_Mutation	SNP	ENST00000274368.4	hg19	CCDS4034.1	.	.	.	.	.	.	.	.	.	.	G	9.252	1.041074	0.19669	.	.	ENSG00000145708	ENST00000274368;ENST00000506501	.	.	.	5.22	-1.6	0.08426	.	1.143080	0.06278	N	0.696820	T	0.14614	0.0353	N	0.03608	-0.345	0.09310	N	1	B;B	0.11235	0.004;0.001	B;B	0.06405	0.002;0.002	T	0.24368	-1.0162	9	0.17832	T	0.49	2.4636	5.9571	0.19279	0.0:0.171:0.2459:0.5831	.	225;225	D6RHH7;P24387	.;CRHBP_HUMAN	I	225	.	ENSP00000274368:V225I	V	+	1	0	CRHBP	76290450	0.055000	0.20627	0.024000	0.17045	0.811000	0.45836	0.271000	0.18626	-0.531000	0.06340	-0.738000	0.03535	GTA	.	.		0.413	CRHBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219972.2	NM_001882		A	76254694	G	A	76254694	3	1	159	1	0	0	0	0	1	0	0	0	3872	1145	40	1	691	1	CRHBP	5	76254694	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	9824324	76254694	104660566	31	24098										
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138269736	138269736	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cagaagaagcacgtgaacccGgtgcaggccctcagcgagtt	13	12	1	3	rs1059181		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr5:138269736G>A	ENST00000302763.7	+	18	2769	c.2679G>A	c.(2677-2679)ccG>ccA	p.P893P	CTNNA1_ENST00000355078.5_Silent_p.P790P|CTNNA1_ENST00000518825.1_3'UTR|CTNNA1_ENST00000540387.1_Silent_p.P523P	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	893					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACGTGAACCCGGTGCAGGCCC	0.547																																					p.P893P		Atlas-SNP	.											.	CTNNA1	114	.	0			c.G2679A						.						52	51	51					5																	138269736		2203	4300	6503	SO:0001819	synonymous_variant	1495	exon18			GAACCCGGTGCAG	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2679G>A	chr5.hg19:g.138269736G>A		33.0	0.0		74.0	46.0	NM_001903	Q12795|Q8N1C0	Silent	SNP	ENST00000302763.7	hg19	CCDS34243.1																																																																																			.	.		0.547	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		A	138269736	G	A	138269736	2	1	159	1	0	0	0	0	0	0	0	1	4014	1103	39	1		1	CTNNA1	5	138269736	Silent	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	62015042	138269736	42645524	32	24099										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140262783	140262783	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	acaaaaggcaaactagatttCgaagaaaagaaattatatga	7	4	0	4	rs145698462		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr5:140262783C>T	ENST00000289272.2	+	1	930	c.930C>T	c.(928-930)ttC>ttT	p.F310F	PCDHA12_ENST00000398631.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA13_ENST00000409494.1_Silent_p.F310F|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	310	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACTAGATTTCGAAGAAAAGA	0.378																																					p.F310F	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.C930T						.						56	64	61					5																	140262783		2203	4300	6503	SO:0001819	synonymous_variant	56136	exon1			AGATTTCGAAGAA	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.930C>T	chr5.hg19:g.140262783C>T		137.0	0.0		180.0	110.0	NM_031865	O75277	Silent	SNP	ENST00000289272.2	hg19	CCDS4240.1																																																																																			.	C|1.000;A|0.000		0.378	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		T	140262783	C	T	140262783	2	4	159	1	0	0	0	0	0	0	0	1	11532	883	31	1		1	PCDHA13	5	140262783	Silent	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	1993047	140262783	40652477	33	24100										
PCDHGB5	56102	hgsc.bcm.edu	37	chr5	140779699	140779699	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	acagcttgcaggaggtgctgCcggatatcactgaccgccct	12	13	1	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr5:140779699C>T	ENST00000576222.1	+	1	2546				PCDHGA2_ENST00000394576.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_5'Flank|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGGTGCTGCCGGATATCAC	0.622																																					p.P669S		Atlas-SNP	.											.	.	.	.	0			c.C2005T						.						144	155	152					5																	140779699		2181	4265	6446	SO:0001627	intron_variant	56101	exon1			GTGCTGCCGGATA	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+27323C>T	chr5.hg19:g.140779699C>T		55.0	0.0		91.0	61.0	NM_018925	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.		0.622	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		T	140779699	C	T	140779699	1	4	159	0	1	0	0	0	0	0	0	0	11575	739	26	3		3	PCDHGB5	5	140779699	Intron	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	516916	140779699	40135561	34	24101										
NMUR2	56923	hgsc.bcm.edu	37	chr5	151784456	151784456	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gtgggcgtcttcatagcctgGtgctgcagaatcaccaggca	13	11	3	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr5:151784456G>A	ENST00000255262.3	-	1	384	c.219C>T	c.(217-219)caC>caT	p.H73H	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	73					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			TCATAGCCTGGTGCTGCAGAA	0.567																																					p.H73H		Atlas-SNP	.											.	NMUR2	111	.	0			c.C219T						.						106	100	102					5																	151784456		2203	4300	6503	SO:0001819	synonymous_variant	56923	exon1			AGCCTGGTGCTGC	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.219C>T	chr5.hg19:g.151784456G>A		118.0	0.0		185.0	60.0	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Silent	SNP	ENST00000255262.3	hg19	CCDS4321.1																																																																																			.	.		0.567	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		A	151784456	G	A	151784456	2	1	159	1	0	0	0	0	0	0	0	1	10516	1252	44	3		3	NMUR2	5	151784456	Silent	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	11004757	151784456	29130804	35	24102										
HLA-DPB1	3115	hgsc.bcm.edu	37	chr6	33053995	33053995	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	acctttcgtctttcatttcaGttcaacgaggatctgcataa	6	10	5	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr6:33053995G>T	ENST00000418931.2	+	5	873		c.e5-1			NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						TTTCATTTCAGTTCAACGAGG	0.408																																					.		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.758-1G>T						.						183	197	192					6																	33053995		2203	4300	6503	SO:0001630	splice_region_variant	3115	exon5			ATTTCAGTTCAAC		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.758-1G>T	chr6.hg19:g.33053995G>T		93.0	0.0		79.0	18.0	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Splice_Site	SNP	ENST00000418931.2	hg19	CCDS4765.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.356465	0.41700	.	.	ENSG00000223865	ENST00000418931;ENST00000411942;ENST00000422592;ENST00000416804	.	.	.	2.95	2.05	0.26809	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.867	0.29543	0.0:0.2569:0.7431:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HLA-DPB1	33161973	0.001000	0.12720	0.004000	0.12327	0.773000	0.43773	0.479000	0.22228	0.780000	0.33566	0.643000	0.83706	.	.	.		0.408	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	Intron	T	33053995	G	T	33053995	5	4	159	1	0	0	0	0	0	0	1	0	7212	1043	36	3	775	3	HLA-DPB1	6	33053995	Splice_Site	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10		33053995	138061072	36	24103										
C7orf16	10842	hgsc.bcm.edu	37	chr7	31735231	31735231	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ctgcacatcccacctttcatAccaggtaatggacaaagtca	6	13	2	0	rs367575540		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr7:31735231A>T	ENST00000342032.3	+	3	859	c.231A>T	c.(229-231)atA>atT	p.I77I	PPP1R17_ENST00000409146.3_Intron	NM_006658.4	NP_006649.2	O96001	PPR17_HUMAN	protein phosphatase 1, regulatory subunit 17	77					central nervous system development (GO:0007417)|intracellular signal transduction (GO:0035556)|regulation of phosphatase activity (GO:0010921)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)										CACCTTTCATACCAGGTAATG	0.433																																					p.I77I		Atlas-SNP	.											.	.	.	.	0			c.A231T						.						116	113	114					7																	31735231		2203	4300	6503	SO:0001819	synonymous_variant	10842	exon3			TTTCATACCAGGT	AF071789	CCDS5436.1, CCDS47570.1	7p15	2012-04-17	2011-10-11	2011-10-11	ENSG00000106341	ENSG00000106341		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16973	protein-coding gene	gene with protein product	"G-substrate"	604088	"chromosome 7 open reading frame 16"	C7orf16		10051666, 9920894	Standard	NM_006658		Approved	GSBS	uc003tcl.3	O96001	OTTHUMG00000128629	ENST00000342032.3:c.231A>T	chr7.hg19:g.31735231A>T		106.0	0.0		228.0	130.0	NM_006658	B4DE58|Q9UDQ0	Silent	SNP	ENST00000342032.3	hg19	CCDS5436.1																																																																																			.	.		0.433	PPP1R17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250498.1	NM_006658		T	31735231	A	T	31735231	2	4	159	1	0	0	0	0	0	0	0	1	2380	381	14	4		4	C7orf16	7	31735231	Silent	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10		31735231	127403432	37	24104										
TBX20	57057	hgsc.bcm.edu	37	chr7	35288373	35288373	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ggtacctcttgttgtccacaGggacgatgtccatcaggact	11	11	2	0	rs112862467		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr7:35288373G>A	ENST00000408931.3	-	3	987	c.461C>T	c.(460-462)cCt>cTt	p.P154L		NM_001077653.2|NM_001166220.1	NP_001071121.1|NP_001159692.1	Q9UMR3	TBX20_HUMAN	T-box 20	154					aortic valve morphogenesis (GO:0003180)|atrial septum morphogenesis (GO:0060413)|blood circulation (GO:0008015)|cardiac chamber formation (GO:0003207)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|dorsal/ventral pattern formation (GO:0009953)|embryonic heart tube elongation (GO:0036306)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion formation (GO:0003272)|endocardial cushion morphogenesis (GO:0003203)|endoderm formation (GO:0001706)|foramen ovale closure (GO:0035922)|heart looping (GO:0001947)|lateral mesoderm formation (GO:0048370)|muscle contraction (GO:0006936)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|outflow tract septum morphogenesis (GO:0003148)|patterning of blood vessels (GO:0001569)|pericardium morphogenesis (GO:0003344)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve formation (GO:0003193)|pulmonary vein morphogenesis (GO:0060577)|tricuspid valve development (GO:0003175)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(9)|prostate(1)|skin(1)|stomach(1)	18						GTTGTCCACAGGGACGATGTC	0.597																																					p.P154L		Atlas-SNP	.											.	TBX20	96	.	0			c.C461T						.						105	95	98					7																	35288373		2203	4300	6503	SO:0001583	missense	57057	exon3			TCCACAGGGACGA	AJ237589	CCDS43568.1	7p14.3	2014-09-17			ENSG00000164532	ENSG00000164532		"T-boxes"	11598	protein-coding gene	gene with protein product		606061				10936053	Standard	NM_001077653		Approved		uc011kas.2	Q9UMR3	OTTHUMG00000099411	ENST00000408931.3:c.461C>T	chr7.hg19:g.35288373G>A	ENSP00000386170:p.Pro154Leu	111.0	0.0		187.0	102.0	NM_001077653	A4D1Y6|Q000T4|Q0IJ70|Q0VAS1|Q9Y2N5	Missense_Mutation	SNP	ENST00000408931.3	hg19	CCDS43568.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.033544	0.93575	.	.	ENSG00000164532	ENST00000408931	D	0.89415	-2.51	5.87	4.98	0.66077	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.94361	0.8187	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95097	0.8227	10	0.87932	D	0	.	16.6795	0.85288	0.0:0.0:0.8692:0.1308	.	154	Q9UMR3	TBX20_HUMAN	L	154	ENSP00000386170:P154L	ENSP00000386170:P154L	P	-	2	0	TBX20	35254898	1.000000	0.71417	0.900000	0.35374	0.997000	0.91878	9.813000	0.99286	1.602000	0.50124	0.655000	0.94253	CCT	.	G|0.998;C|0.002		0.597	TBX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216870.2	NM_020417		A	35288373	G	A	35288373	3	1	159	1	0	0	0	0	1	0	0	0	15671	1000	35	3	907	3	TBX20	7	35288373	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	3553142	35288373	123850290	38	24105										
ZNF713	349075	hgsc.bcm.edu	37	chr7	55990926	55990926	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gaccagctgtaccctgcccaAaagaacctctatcgagacgt	8	14	1	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr7:55990926A>T	ENST00000429591.2	+	2	158	c.120A>T	c.(118-120)caA>caT	p.Q40H	ZNF713_ENST00000482436.1_3'UTR|MRPS17_ENST00000426595.1_Missense_Mutation_p.Q40H	NM_182633.1	NP_872439.1	Q8N859	ZN713_HUMAN	zinc finger protein 713	40	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			ACCCTGCCCAAAAGAACCTCT	0.537																																					p.Q40H		Atlas-SNP	.											.	ZNF713	47	.	0			c.A120T						.						154	128	137					7																	55990926		2203	4300	6503	SO:0001583	missense	349075	exon2			TGCCCAAAAGAAC	AK097282	CCDS34639.1	7p11.2	2013-01-08			ENSG00000178665	ENSG00000178665		"Zinc fingers, C2H2-type", "-"	22043	protein-coding gene	gene with protein product							Standard	NM_182633		Approved	FLJ39963	uc003trc.1	Q8N859	OTTHUMG00000156175	ENST00000429591.2:c.120A>T	chr7.hg19:g.55990926A>T	ENSP00000416662:p.Gln40His	79.0	0.0		98.0	16.0	NM_182633		Missense_Mutation	SNP	ENST00000429591.2	hg19	CCDS34639.1	.	.	.	.	.	.	.	.	.	.	A	13.82	2.351738	0.41700	.	.	ENSG00000249773;ENSG00000178665	ENST00000426595;ENST00000429591	T;T	0.09445	2.98;2.98	2.93	0.0208	0.14126	Krueppel-associated box (4);	.	.	.	.	T	0.44371	0.1290	H	0.97874	4.095	0.24003	N	0.996205	D	0.69078	0.997	D	0.83275	0.996	T	0.28138	-1.0053	9	0.46703	T	0.11	.	9.5826	0.39497	0.2193:0.0:0.7807:0.0	.	40	Q8N859	ZN713_HUMAN	H	40	ENSP00000390331:Q40H;ENSP00000416662:Q40H	ENSP00000390331:Q40H	Q	+	3	2	RP11-15K19.2;ZNF713	55958420	0.998000	0.40836	0.998000	0.56505	0.506000	0.33950	0.463000	0.21972	-0.006000	0.14370	-1.241000	0.01538	CAA	.	.		0.537	ZNF713-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343297.1	NM_182633		T	55990926	A	T	55990926	3	4	159	1	0	0	0	0	1	0	0	0	18132	11	1	4	126	4	ZNF713	7	55990926	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	20702553	55990926	103147737	39	24106										
SLC25A13	10165	hgsc.bcm.edu	37	chr7	95820436	95820436	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ctcacccttagtcacttcaaCatctttcctggtgccagcca	5	16	4	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr7:95820436C>A	ENST00000265631.5	-	7	875	c.739G>T	c.(739-741)Gtt>Ttt	p.V247F	SLC25A13_ENST00000542654.1_Missense_Mutation_p.V139F|SLC25A13_ENST00000416240.2_Missense_Mutation_p.V247F			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	247					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	GTCACTTCAACATCTTTCCTG	0.363																																					p.V247F		Atlas-SNP	.											.	SLC25A13	131	.	0			c.G739T						.						207	207	207					7																	95820436		2203	4300	6503	SO:0001583	missense	10165	exon7			CTTCAACATCTTT	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"Solute carriers", "EF-hand domain containing"	10983	protein-coding gene	gene with protein product	"mitochondrial aspartate glutamate carrier 2"	603859	"solute carrier family 25, member 13 (citrin)"	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.739G>T	chr7.hg19:g.95820436C>A	ENSP00000265631:p.Val247Phe	47.0	0.0		48.0	42.0	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Missense_Mutation	SNP	ENST00000265631.5	hg19	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	C	2.079	-0.411131	0.04799	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	T;T;T	0.79454	-1.27;-1.27;-1.27	5.18	4.3	0.51218	EF-hand-like domain (1);	0.071501	0.53938	D	0.000042	T	0.69958	0.3169	L	0.47716	1.5	0.45733	D	0.998639	B;B;B	0.33528	0.416;0.413;0.413	B;B;B	0.34722	0.188;0.092;0.092	T	0.70923	-0.4740	10	0.54805	T	0.06	-17.6928	9.6195	0.39712	0.1435:0.7819:0.0:0.0745	.	139;247;247	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	F	247;247;139	ENSP00000265631:V247F;ENSP00000400101:V247F;ENSP00000440484:V139F	ENSP00000265631:V247F	V	-	1	0	SLC25A13	95658372	0.976000	0.34144	0.994000	0.49952	0.524000	0.34500	0.794000	0.26958	2.868000	0.98415	0.557000	0.71058	GTT	.	.		0.363	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		A	95820436	C	A	95820436	3	1	159	1	0	0	0	0	1	0	0	0	14490	478	17	3	1339	3	SLC25A13	7	95820436	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	39829510	95820436	63318227	40	24107										
LMBR1	64327	hgsc.bcm.edu	37	chr7	156555801	156555801	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tcaagtctgaaaaatacttaCagagaagtaacaaacatccc	5	9	2	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr7:156555801C>A	ENST00000353442.5	-	7	856		c.e7+1		LMBR1_ENST00000354505.4_Splice_Site|LMBR1_ENST00000359422.4_Splice_Site|LMBR1_ENST00000540390.1_Splice_Site	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1						embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		AAAATACTTACAGAGAAGTAA	0.279																																					.		Atlas-SNP	.											.	LMBR1	35	.	0			c.619+1G>T						.						29	32	31					7																	156555801		2193	4273	6466	SO:0001630	splice_region_variant	64327	exon8			TACTTACAGAGAA	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"chromosome 7 open reading frame 2", "limb region 1 homolog (mouse)"	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.619+1G>T	chr7.hg19:g.156555801C>A		278.0	1.0		445.0	225.0	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Splice_Site	SNP	ENST00000353442.5	hg19	CCDS5945.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070462	0.76301	.	.	ENSG00000105983	ENST00000353442;ENST00000359422;ENST00000415428;ENST00000354505;ENST00000540390	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8532	0.92241	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LMBR1	156248562	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.989000	0.76219	2.547000	0.85894	0.655000	0.94253	.	.	.		0.279	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	Intron	A	156555801	C	A	156555801	5	1	159	1	0	0	0	0	0	0	1	0	8849	492	17	3	896	3	LMBR1	7	156555801	Splice_Site	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	60735365	156555801	2582862	41	24108										
C8orf40	114926	hgsc.bcm.edu	37	chr8	42401693	42401693	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gaagcctggaatgaagccacCaatgtttacttgatagttat	9	7	0	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr8:42401693C>G	ENST00000438528.3	+	2	127	c.78C>G	c.(76-78)acC>acG	p.T26T	SMIM19_ENST00000414154.2_Silent_p.T26T|SMIM19_ENST00000416469.2_Silent_p.T26T|SMIM19_ENST00000529505.1_3'UTR|SMIM19_ENST00000417410.2_Silent_p.T26T|SMIM19_ENST00000490331.2_Silent_p.T26T	NM_001135676.1	NP_001129148.1	Q96E16	SMI19_HUMAN	small integral membrane protein 19	26						integral component of membrane (GO:0016021)											ATGAAGCCACCAATGTTTACT	0.403																																					p.T26T		Atlas-SNP	.											.	.	.	.	0			c.C78G						.						240	208	219					8																	42401693		2203	4300	6503	SO:0001819	synonymous_variant	0	exon2			AGCCACCAATGTT	BC013035	CCDS6133.2	8p11.21	2013-03-08	2013-03-08	2013-03-08	ENSG00000176209	ENSG00000176209			25166	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 40"	C8orf40		12477932	Standard	NM_001135674		Approved		uc011lcv.2	Q96E16	OTTHUMG00000157060	ENST00000438528.3:c.78C>G	chr8.hg19:g.42401693C>G		121.0	0.0		107.0	36.0	NM_001135675	B2R4S6|D3DSY4	Silent	SNP	ENST00000438528.3	hg19	CCDS6133.2																																																																																			.	.		0.403	SMIM19-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347309.2	NM_138436		G	42401693	C	G	42401693	2	3	159	1	0	0	0	0	0	0	0	1	2428	581	21	4		4	C8orf40	8	42401693	Silent	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10		42401693	103962329	42	24109										
SLCO5A1	81796	hgsc.bcm.edu	37	chr8	70591797	70591797	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ctgacttcgctgtcccacggTgggtggagtgatcacttggc	14	11	1	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr8:70591797T>A	ENST00000260126.4	-	8	2546	c.1840A>T	c.(1840-1842)Acc>Tcc	p.T614S	SLCO5A1_ENST00000530307.1_Missense_Mutation_p.T559S|SLCO5A1_ENST00000524945.1_Missense_Mutation_p.T614S	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	614						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			TGTCCCACGGTGGGTGGAGTG	0.468																																					p.T614S		Atlas-SNP	.											.	SLCO5A1	142	.	0			c.A1840T						.						150	143	145					8																	70591797		2203	4300	6503	SO:0001583	missense	81796	exon8			CCACGGTGGGTGG	AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"Solute carriers"	19046	protein-coding gene	gene with protein product		613543	"solute carrier family 21 (organic anion transporter), member 15"	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.1840A>T	chr8.hg19:g.70591797T>A	ENSP00000260126:p.Thr614Ser	86.0	0.0		152.0	36.0	NM_030958	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Missense_Mutation	SNP	ENST00000260126.4	hg19	CCDS6205.1	.	.	.	.	.	.	.	.	.	.	T	9.842	1.191410	0.21954	.	.	ENSG00000137571	ENST00000260126;ENST00000524945;ENST00000530307	T;T;T	0.41065	1.15;1.55;1.01	5.8	5.8	0.92144	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.32704	0.0838	N	0.16903	0.455	0.49582	D	0.999806	B;B;B	0.27166	0.17;0.028;0.037	B;B;B	0.34536	0.185;0.025;0.028	T	0.12967	-1.0527	10	0.23891	T	0.37	.	16.1549	0.81657	0.0:0.0:0.0:1.0	.	559;614;614	E9PKK5;Q9H2Y9;G3V1C0	.;SO5A1_HUMAN;.	S	614;614;559	ENSP00000260126:T614S;ENSP00000434422:T614S;ENSP00000431611:T559S	ENSP00000260126:T614S	T	-	1	0	SLCO5A1	70754351	1.000000	0.71417	0.995000	0.50966	0.050000	0.14768	4.103000	0.57783	2.209000	0.71365	0.533000	0.62120	ACC	.	.		0.468	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958		A	70591797	T	A	70591797	3	1	159	1	0	0	0	0	1	0	0	0	14746	1696	59	4	718	4	SLCO5A1	8	70591797	Missense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	28190104	70591797	75772225	43	24110										
CRISPLD1	83690	hgsc.bcm.edu	37	chr8	75932274	75932274	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cttgtgaaacaactgtggaaCagctctgtccatttcataag	8	9	2	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr8:75932274C>T	ENST00000262207.4	+	12	1672	c.1204C>T	c.(1204-1206)Cag>Tag	p.Q402*	CRISPLD1_ENST00000523524.1_Nonsense_Mutation_p.Q214*|CRISPLD1_ENST00000517786.1_Nonsense_Mutation_p.Q216*	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	402	LCCL 2. {ECO:0000255|PROSITE- ProRule:PRU00123}.				face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			AACTGTGGAACAGCTCTGTCC	0.413																																					p.Q402X		Atlas-SNP	.											.	CRISPLD1	94	.	0			c.C1204T						.						137	125	129					8																	75932274		2203	4300	6503	SO:0001587	stop_gained	83690	exon12			GTGGAACAGCTCT	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.1204C>T	chr8.hg19:g.75932274C>T	ENSP00000262207:p.Gln402*	120.0	0.0		155.0	47.0	NM_031461	B2RA60|B7Z929	Nonsense_Mutation	SNP	ENST00000262207.4	hg19	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	C	42	9.172352	0.99089	.	.	ENSG00000121005	ENST00000262207;ENST00000523524;ENST00000517786	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	14.9966	0.71436	0.0:0.8581:0.1419:0.0	.	.	.	.	X	402;214;216	.	ENSP00000262207:Q402X	Q	+	1	0	CRISPLD1	76094829	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.504000	0.53347	2.834000	0.97654	0.650000	0.86243	CAG	.	.		0.413	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		T	75932274	C	T	75932274	4	4	159	1	0	0	0	0	0	1	0	0	3884	479	17	3	1246	3	CRISPLD1	8	75932274	Nonsense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	5340477	75932274	70431748	44	24111										
SLC25A32	81034	hgsc.bcm.edu	37	chr8	104415462	104415462	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	caaacattcctttatattgtCggtgtggggagttaacaaca	9	7	0	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr8:104415462C>A	ENST00000297578.4	-	4	648	c.482G>T	c.(481-483)cGa>cTa	p.R161L	SLC25A32_ENST00000523701.1_5'Flank|SLC25A32_ENST00000543107.1_Missense_Mutation_p.R29L	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32	161					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	TTTATATTGTCGGTGTGGGGA	0.338																																					p.R161L		Atlas-SNP	.											.	SLC25A32	36	.	0			c.G482T						.						104	103	104					8																	104415462		2203	4300	6503	SO:0001583	missense	81034	exon4			TATTGTCGGTGTG	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"Solute carriers"	29683	protein-coding gene	gene with protein product		610815	"solute carrier family 25, member 32"			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790	ENST00000297578.4:c.482G>T	chr8.hg19:g.104415462C>A	ENSP00000297578:p.Arg161Leu	106.0	0.0		138.0	32.0	NM_030780	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	hg19	CCDS6300.1	.	.	.	.	.	.	.	.	.	.	C	9.837	1.190108	0.21954	.	.	ENSG00000164933	ENST00000297578;ENST00000424899;ENST00000543107	T;T	0.79247	-1.25;-1.25	6.06	3.02	0.34903	Mitochondrial carrier domain (2);	0.105224	0.64402	D	0.000009	T	0.61627	0.2362	N	0.20304	0.555	0.48452	D	0.999658	B	0.10296	0.003	B	0.16289	0.015	T	0.49532	-0.8930	10	0.29301	T	0.29	-15.9841	10.2325	0.43264	0.0:0.764:0.0:0.236	.	161	Q9H2D1	MFTC_HUMAN	L	161;145;29	ENSP00000297578:R161L;ENSP00000443497:R29L	ENSP00000297578:R161L	R	-	2	0	SLC25A32	104484638	0.361000	0.24972	0.353000	0.25747	0.475000	0.33008	1.010000	0.29898	0.317000	0.23160	-0.234000	0.12200	CGA	.	.		0.338	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780		A	104415462	C	A	104415462	3	1	159	1	0	0	0	0	1	0	0	0	14511	884	31	1	481	1	SLC25A32	8	104415462	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	28483188	104415462	41948560	45	24112										
DDX58	23586	hgsc.bcm.edu	37	chr9	32457126	32457126	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ttgaggacctgatatcatttGgacatttctgctggatcaaa	9	7	3	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr9:32457126G>T	ENST00000379883.2	-	18	2929	c.2772C>A	c.(2770-2772)tcC>tcA	p.S924S	DDX58_ENST00000379868.1_Silent_p.S721S|DDX58_ENST00000542096.1_Silent_p.S853S|DDX58_ENST00000379882.1_Silent_p.S879S	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	924	Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		GATATCATTTGGACATTTCTG	0.418																																					p.S924S		Atlas-SNP	.											.	DDX58	82	.	0			c.C2772A						.						61	58	59					9																	32457126		2203	4300	6503	SO:0001819	synonymous_variant	23586	exon18			TCATTTGGACATT	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2772C>A	chr9.hg19:g.32457126G>T		69.0	0.0		83.0	18.0	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Silent	SNP	ENST00000379883.2	hg19	CCDS6526.1																																																																																			.	.		0.418	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		T	32457126	G	T	32457126	2	4	159	1	0	0	0	0	0	0	0	1	4377	1335	47	3		3	DDX58	9	32457126	Silent	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10		32457126	108756305	46	24113										
SLC2A6	11182	hgsc.bcm.edu	37	chr9	136338644	136338644	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	actcgctttccaggcccgcaGtgctgttggggctcagaggc	14	13	1	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr9:136338644G>C	ENST00000371899.4	-	8	1192	c.1115C>G	c.(1114-1116)aCt>aGt	p.T372S	SLC2A6_ENST00000371897.4_Intron|SLC2A6_ENST00000485978.1_5'UTR	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	372					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		CAGGCCCGCAGTGCTGTTGGG	0.657																																					p.T372S		Atlas-SNP	.											.	SLC2A6	31	.	0			c.C1115G						.						34	35	34					9																	136338644		2198	4298	6496	SO:0001583	missense	11182	exon8			CCCGCAGTGCTGT	AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"Solute carriers"	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.1115C>G	chr9.hg19:g.136338644G>C	ENSP00000360966:p.Thr372Ser	129.0	0.0		107.0	22.0	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	hg19	CCDS6975.1	.	.	.	.	.	.	.	.	.	.	G	1.463	-0.562006	0.03939	.	.	ENSG00000160326	ENST00000371899	D	0.82433	-1.61	4.94	4.03	0.46877	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.139140	0.06579	N	0.749930	T	0.72906	0.3519	N	0.17082	0.46	0.31736	N	0.636381	B	0.18968	0.032	B	0.23716	0.048	T	0.54735	-0.8249	10	0.07175	T	0.84	.	14.337	0.66598	0.0:0.1494:0.8506:0.0	.	372	Q9UGQ3	GTR6_HUMAN	S	372	ENSP00000360966:T372S	ENSP00000360966:T372S	T	-	2	0	SLC2A6	135328465	0.996000	0.38824	0.461000	0.27105	0.050000	0.14768	3.128000	0.50492	1.066000	0.40716	0.561000	0.74099	ACT	.	.		0.657	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585		C	136338644	G	C	136338644	3	2	159	1	0	0	0	0	1	0	0	0	14564	1029	36	4	420	4	SLC2A6	9	136338644	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	103881518	136338644	4874787	47	24114										
DDX50	79009	hgsc.bcm.edu	37	chr10	70673827	70673827	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tatttaagattctgaagacaAtcctcagactttactttttt	4	7	2	4	rs202146235		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr10:70673827A>G	ENST00000373585.3	+	7	1063	c.956A>G	c.(955-957)aAt>aGt	p.N319S	RNU6-571P_ENST00000384128.1_RNA	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	319	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						TCTGAAGACAATCCTCAGACT	0.343																																					p.N319S		Atlas-SNP	.											.	DDX50	65	.	0			c.A956G						.						45	45	45					10																	70673827		2203	4300	6503	SO:0001583	missense	79009	exon7			AAGACAATCCTCA	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.956A>G	chr10.hg19:g.70673827A>G	ENSP00000362687:p.Asn319Ser	150.0	0.0		97.0	68.0	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	hg19	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.199549	0.58126	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.04809	3.55	5.49	5.49	0.81192	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.039376	0.85682	D	0.000000	T	0.06050	0.0157	N	0.25647	0.755	0.52099	D	0.999945	B;B	0.24258	0.1;0.086	B;B	0.33121	0.098;0.158	T	0.48927	-0.8991	10	0.27785	T	0.31	-17.6164	15.8838	0.79226	1.0:0.0:0.0:0.0	.	319;319	Q9BQ39;B4DED6	DDX50_HUMAN;.	S	319	ENSP00000362687:N319S	ENSP00000362687:N319S	N	+	2	0	DDX50	70343833	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.216000	0.71823	0.379000	0.24179	AAT	.	A|0.999;G|0.001		0.343	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		G	70673827	A	G	70673827	3	3	159	1	0	0	0	0	1	0	0	0	4370	101	4	2	982	2	DDX50	10	70673827	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10		70673827	64860920	48	24115										
TLX1	3195	hgsc.bcm.edu	37	chr10	102891823	102891823	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ctcactggcctcaccttcccCtggatggagagtaaccgcag	10	15	2	1	rs2742016		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr10:102891823C>G	ENST00000370196.6	+	1	2567	c.525C>G	c.(523-525)ccC>ccG	p.P175P	TLX1NB_ENST00000445873.1_5'Flank|TLX1NB_ENST00000425505.1_5'Flank|TLX1_ENST00000467928.2_Silent_p.P175P			P31314	TLX1_HUMAN	T-cell leukemia homeobox 1	175					cell fate commitment (GO:0045165)|central nervous system development (GO:0007417)|neuron differentiation (GO:0030182)|organ formation (GO:0048645)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spleen development (GO:0048536)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|upper_aerodigestive_tract(1)	2				Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		TCACCTTCCCCTGGATGGAGA	0.701			T	"TRB@, TRD@"	T-ALL																																p.P175P		Atlas-SNP	.		Dom	yes		10	10q24	3195	" T-cell leukemia, homeobox 1 (HOX11)"		L	.	TLX1	20	.	0			c.C525G						.						27	30	29					10																	102891823		2169	4231	6400	SO:0001819	synonymous_variant	3195	exon1			CTTCCCCTGGATG	M62626	CCDS7510.1, CCDS55725.1	10q24.32	2011-06-20	2005-12-22	2002-05-31	ENSG00000107807	ENSG00000107807		"Homeoboxes / ANTP class : NKL subclass"	5056	protein-coding gene	gene with protein product	"Homeo box-11 (T-cell leukemia-3 associated breakpoint, homologous to Drosophila Notch)", "homeo box 11 (T-cell lymphoma 3-associated breakpoint)"	186770	"homeo box 11 (T-cell lymphoma 3-associated breakpoint)", "T-cell leukemia, homeobox 1"	TCL3, HOX11		1676542, 1973146	Standard	NM_005521		Approved		uc001ksw.3	P31314	OTTHUMG00000019341	ENST00000370196.6:c.525C>G	chr10.hg19:g.102891823C>G		3.0	0.0		7.0	7.0	NM_005521	A1L4G3|O75699|Q5VXP2|Q9HCA0|Q9UD59	Silent	SNP	ENST00000370196.6	hg19	CCDS7510.1																																																																																			.	.		0.701	TLX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051193.3	NM_005521		G	102891823	C	G	102891823	2	3	159	1	0	0	0	0	0	0	0	1	15974	668	24	4		4	TLX1	10	102891823	Silent	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	32217996	102891823	32642924	49	24116										
DUSP5	1847	hgsc.bcm.edu	37	chr10	112258097	112258097	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gcccgacgaggcggcgcgcgCgcggctcctgcaggagggcg	20	15	0	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr10:112258097C>A	ENST00000369583.3	+	1	502	c.218C>A	c.(217-219)gCg>gAg	p.A73E	RP11-525A16.4_ENST00000609514.1_lincRNA	NM_004419.3	NP_004410.3	Q16690	DUS5_HUMAN	dual specificity phosphatase 5	73	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				endoderm formation (GO:0001706)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			kidney(2)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	13		Breast(234;0.0848)		Epithelial(162;0.000276)|all cancers(201;0.00465)|BRCA - Breast invasive adenocarcinoma(275;0.12)		GCGGCGCGCGCGCGGCTCCTG	0.776																																					p.A73E		Atlas-SNP	.											.	DUSP5	62	.	0			c.C218A						.						2	2	2					10																	112258097		930	2016	2946	SO:0001583	missense	1847	exon1			CGCGCGCGCGGCT	U16996	CCDS7566.1	10q25	2011-06-09			ENSG00000138166	ENSG00000138166		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3071	protein-coding gene	gene with protein product		603069				7806236	Standard	NM_004419		Approved	HVH3	uc001kzd.3	Q16690	OTTHUMG00000019040	ENST00000369583.3:c.218C>A	chr10.hg19:g.112258097C>A	ENSP00000358596:p.Ala73Glu	21.0	0.0		28.0	23.0	NM_004419	Q12997|Q5T603	Missense_Mutation	SNP	ENST00000369583.3	hg19	CCDS7566.1	.	.	.	.	.	.	.	.	.	.	c	21.9	4.222657	0.79464	.	.	ENSG00000138166	ENST00000369583	T	0.38887	1.11	4.98	4.98	0.66077	Rhodanese-like (5);	0.190857	0.47852	D	0.000208	T	0.38957	0.1060	L	0.51422	1.61	0.36547	D	0.871621	P	0.43169	0.8	B	0.42593	0.392	T	0.38802	-0.9644	10	0.06891	T	0.86	.	17.248	0.87033	0.0:1.0:0.0:0.0	.	73	Q16690	DUS5_HUMAN	E	73	ENSP00000358596:A73E	ENSP00000358596:A73E	A	+	2	0	DUSP5	112248087	0.998000	0.40836	0.999000	0.59377	0.989000	0.77384	1.815000	0.38981	2.309000	0.77851	0.461000	0.40582	GCG	.	.		0.776	DUSP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050333.1	NM_004419		A	112258097	C	A	112258097	3	1	159	1	0	0	0	0	1	0	0	0	4830	768	27	1	220	1	DUSP5	10	112258097	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	9366274	112258097	23276650	50	24117										
MUC6	4588	hgsc.bcm.edu	37	chr11	1028253	1028253	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ctggctcatggagcaggggtCagtctcacgctccagagcgg	15	12	3	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr11:1028253C>A	ENST00000421673.2	-	14	1776	c.1726G>T	c.(1726-1728)Gac>Tac	p.D576Y		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	576	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAGCAGGGGTCAGTCTCACGC	0.667																																					p.D576Y		Atlas-SNP	.											.	MUC6	408	.	0			c.G1726T						.						21	26	24					11																	1028253		1938	4118	6056	SO:0001583	missense	4588	exon14			AGGGGTCAGTCTC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.1726G>T	chr11.hg19:g.1028253C>A	ENSP00000406861:p.Asp576Tyr	143.0	0.0		256.0	32.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	15.77	2.930742	0.52866	.	.	ENSG00000184956	ENST00000421673	T	0.22336	1.96	4.52	4.52	0.55395	von Willebrand factor, type D domain (1);	0.000000	0.32190	U	0.006450	T	0.50973	0.1647	M	0.90814	3.15	0.32187	N	0.579598	D	0.89917	1.0	D	0.75484	0.986	T	0.66893	-0.5808	10	0.87932	D	0	.	11.1958	0.48711	0.0:0.9142:0.0:0.0858	.	576	Q6W4X9	MUC6_HUMAN	Y	576	ENSP00000406861:D576Y	ENSP00000406861:D576Y	D	-	1	0	MUC6	1018253	0.957000	0.32711	0.985000	0.45067	0.981000	0.71138	2.182000	0.42556	2.261000	0.74972	0.491000	0.48974	GAC	.	.		0.667	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1028253	C	A	1028253	3	1	159	1	0	0	0	0	1	0	0	0	9989	826	29	3	5673	3	MUC6	11	1028253	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10		1028253	133978263	51	24118										
MUC6	4588	hgsc.bcm.edu	37	chr11	1028287	1028287	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	agagcggccggacagttcccCgcccgccaggagtccacaaa	12	16	0	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr11:1028287C>G	ENST00000421673.2	-	14	1742	c.1692G>C	c.(1690-1692)gcG>gcC	p.A564A		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	564	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GACAGTTCCCCGCCCGCCAGG	0.662																																					p.A564A		Atlas-SNP	.											.	MUC6	408	.	0			c.G1692C						.						25	32	30					11																	1028287		2025	4143	6168	SO:0001819	synonymous_variant	4588	exon14			GTTCCCCGCCCGC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.1692G>C	chr11.hg19:g.1028287C>G		171.0	0.0		281.0	45.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	hg19	CCDS44513.1																																																																																			.	.		0.662	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		G	1028287	C	G	1028287	2	3	159	1	0	0	0	0	0	0	0	1	9989	639	23	4		4	MUC6	11	1028287	Silent	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	34	1028287	133978229	52	24119										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1247915	1247915	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cactacaagaccttcgacggCgacgtcttccgcttccctgg	9	16	1	1	rs377569377		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr11:1247915C>T	ENST00000529681.1	+	4	328	c.270C>T	c.(268-270)ggC>ggT	p.G90G	MUC5B_ENST00000447027.1_Silent_p.G90G	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	90	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCTTCGACGGCGACGTCTTCC	0.647																																					p.G90G		Atlas-SNP	.											.	MUC5B	473	.	0			c.C270T						.	C		1,4281		0,1,2140	37	39	39		270	-7.2	0	11		39	0,8524		0,0,4262	no	coding-synonymous	MUC5B	NM_002458.2		0,1,6402	TT,TC,CC		0.0,0.0234,0.0078		90/5763	1247915	1,12805	2141	4262	6403	SO:0001819	synonymous_variant	727897	exon4			CGACGGCGACGTC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.270C>T	chr11.hg19:g.1247915C>T		80.0	0.0		109.0	44.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1247915	C	T	1247915	2	4	159	1	0	0	0	0	0	0	0	1	9988	755	27	1		1	MUC5B	11	1247915	Silent	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	219628	1247915	133758601	53	24120										
OR2AG1	144125	hgsc.bcm.edu	37	chr11	6806660	6806660	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ggccatttgtcatcctctgaCatacatgaccctcatgagct	7	13	3	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr11:6806660C>A	ENST00000307401.4	+	1	413	c.392C>A	c.(391-393)aCa>aAa	p.T131K		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	131						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATCCTCTGACATACATGACC	0.532																																					p.T131K		Atlas-SNP	.											OR2AG1,NS,carcinoma,0,2	OR2AG1	57	.	0			c.C392A						.						108	97	101					11																	6806660		2201	4296	6497	SO:0001583	missense	144125	exon1			CTCTGACATACAT	AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"GPCR / Class A : Olfactory receptors"	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.392C>A	chr11.hg19:g.6806660C>A	ENSP00000307447:p.Thr131Lys	87.0	0.0		164.0	8.0	NM_001004489	B9EKV7|Q6IFG7|Q96R26	Missense_Mutation	SNP	ENST00000307401.4	hg19	CCDS31414.1	.	.	.	.	.	.	.	.	.	.	c	5.147	0.212688	0.09757	.	.	ENSG00000170803	ENST00000307401	T	0.01388	4.95	3.89	1.47	0.22746	GPCR, rhodopsin-like superfamily (1);	0.367913	0.23209	N	0.050698	T	0.00998	0.0033	N	0.14661	0.345	0.21445	N	0.999683	B	0.02656	0.0	B	0.04013	0.001	T	0.48043	-0.9069	10	0.56958	D	0.05	.	4.8236	0.13405	0.5093:0.3885:0.1023:0.0	.	131	Q9H205	O2AG1_HUMAN	K	131	ENSP00000307447:T131K	ENSP00000307447:T131K	T	+	2	0	OR2AG1	6763236	0.000000	0.05858	0.999000	0.59377	0.157000	0.22087	-0.317000	0.08060	0.174000	0.19809	-0.339000	0.08088	ACA	.	.		0.532	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385980.1	NM_001004489		A	6806660	C	A	6806660	3	1	159	1	0	0	0	0	1	0	0	0	10993	478	17	3	394	3	OR2AG1	11	6806660	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	5558745	6806660	128199856	54	24121										
OR5T2	219464	hgsc.bcm.edu	37	chr11	55999712	55999712	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gcaagggaatcacaatggtgTaaaatattgacactatcatg	9	6	2	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr11:55999712T>C	ENST00000313264.4	-	1	1025	c.950A>G	c.(949-951)tAc>tGc	p.Y317C		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	317						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					CACAATGGTGTAAAATATTGA	0.378																																					p.Y317C		Atlas-SNP	.											.	OR5T2	107	.	0			c.A950G						.						168	149	155					11																	55999712		2201	4296	6497	SO:0001583	missense	219464	exon1			ATGGTGTAAAATA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.950A>G	chr11.hg19:g.55999712T>C	ENSP00000323688:p.Tyr317Cys	88.0	0.0		94.0	37.0	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	hg19	CCDS31523.1	.	.	.	.	.	.	.	.	.	.	T	12.65	2.002287	0.35320	.	.	ENSG00000181718	ENST00000313264	T	0.00318	8.12	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38217	U	0.001771	T	0.00875	0.0029	M	0.92268	3.29	0.09310	N	1	D	0.59357	0.985	D	0.63957	0.92	T	0.18681	-1.0329	10	0.87932	D	0	.	13.9683	0.64223	0.0:0.0:0.0:1.0	.	317	Q8NGG2	OR5T2_HUMAN	C	317	ENSP00000323688:Y317C	ENSP00000323688:Y317C	Y	-	2	0	OR5T2	55756288	0.916000	0.31088	0.940000	0.37924	0.618000	0.37518	2.371000	0.44248	2.041000	0.60428	0.391000	0.25812	TAC	.	.		0.378	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		C	55999712	T	C	55999712	3	2	159	1	0	0	0	0	1	0	0	0	11191	1638	57	2	128	2	OR5T2	11	55999712	Missense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	49193052	55999712	79006804	55	24122										
CLCF1	23529	hgsc.bcm.edu	37	chr11	67135046	67135046	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gattgagagctggcactgcaGggaggtgccagagcaccgtg	17	9	0	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr11:67135046G>A	ENST00000312438.7	-	2	265	c.68C>T	c.(67-69)cCt>cTt	p.P23L	AP003419.11_ENST00000543494.1_RNA|CLCF1_ENST00000533438.1_Missense_Mutation_p.P13L|CLCF1_ENST00000528474.1_Missense_Mutation_p.P13L	NM_013246.2	NP_037378.1	Q9UBD9	CLCF1_HUMAN	cardiotrophin-like cytokine factor 1	23				P -> L (in Ref. 7; AAH66231). {ECO:0000305}.	B cell differentiation (GO:0030183)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)	CNTFR-CLCF1 complex (GO:0097059)|CRLF-CLCF1 complex (GO:0097058)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	ciliary neurotrophic factor receptor binding (GO:0005127)|cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			endometrium(1)|urinary_tract(1)	2			BRCA - Breast invasive adenocarcinoma(15;2.39e-06)			TGGCACTGCAGGGAGGTGCCA	0.662																																					p.P23L		Atlas-SNP	.											.	CLCF1	15	.	0			c.C68T						.						101	81	88					11																	67135046		2200	4295	6495	SO:0001583	missense	23529	exon2			ACTGCAGGGAGGT	BC012939	CCDS31617.1, CCDS53666.1	11q13.3	2014-01-28	2006-07-03		ENSG00000175505	ENSG00000175505			17412	protein-coding gene	gene with protein product	"B-cell stimulating factor 3", "cold-induced sweating syndrome 2", "novel neurotrophin-1"	607672	"CRLF1 associated cytokine-like factor 1"			10500198, 10448081, 16782820	Standard	NM_001166212		Approved	NNT1, BSF3, CLC, NR6, CISS2, BSF-3, NNT-1	uc010rpp.2	Q9UBD9	OTTHUMG00000167669	ENST00000312438.7:c.68C>T	chr11.hg19:g.67135046G>A	ENSP00000309338:p.Pro23Leu	43.0	0.0		57.0	8.0	NM_013246	B4DNT4|Q6NZA4	Missense_Mutation	SNP	ENST00000312438.7	hg19	CCDS31617.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.640479	0.67244	.	.	ENSG00000175505	ENST00000312438;ENST00000533438;ENST00000528474	T;T;T	0.76060	-0.99;-0.98;-0.98	5.26	5.26	0.73747	.	0.372941	0.23962	N	0.042858	T	0.65637	0.2710	N	0.08118	0	0.46203	D	0.998928	P	0.52061	0.95	P	0.47864	0.559	T	0.74188	-0.3746	10	0.87932	D	0	-10.2951	18.8589	0.92265	0.0:0.0:1.0:0.0	.	23	Q9UBD9	CLCF1_HUMAN	L	23;13;13	ENSP00000309338:P23L;ENSP00000434122:P13L;ENSP00000432553:P13L	ENSP00000309338:P23L	P	-	2	0	CLCF1	66891622	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.796000	0.69080	2.646000	0.89796	0.591000	0.81541	CCT	.	.		0.662	CLCF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395478.1	NM_013246		A	67135046	G	A	67135046	3	1	159	1	0	0	0	0	1	0	0	0	3463	1000	35	3	617	3	CLCF1	11	67135046	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	11135334	67135046	67871470	56	24123										
RPUSD4	84881	hgsc.bcm.edu	37	chr11	126075666	126075666	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tgagggcatggggacatgcaCagtgatggccctgggggtga	19	7	0	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr11:126075666C>A	ENST00000298317.4	-	4	621	c.568G>T	c.(568-570)Gtg>Ttg	p.V190L	RP11-50B3.4_ENST00000532866.1_RNA|RPUSD4_ENST00000534393.1_5'UTR|RPUSD4_ENST00000533628.1_Missense_Mutation_p.V190L	NM_032795.2	NP_116184.2	Q96CM3	RUSD4_HUMAN	RNA pseudouridylate synthase domain containing 4	190					pseudouridine synthesis (GO:0001522)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0761)		GGGACATGCACAGTGATGGCC	0.572																																					p.V190L		Atlas-SNP	.											.	RPUSD4	36	.	0			c.G568T						.						51	43	46					11																	126075666		2201	4299	6500	SO:0001583	missense	84881	exon4			CATGCACAGTGAT	BC014131	CCDS8469.1, CCDS53721.1	11q24.2	2013-02-11			ENSG00000165526	ENSG00000165526		"RNA pseudouridylate synthase domain containing"	25898	protein-coding gene	gene with protein product							Standard	NM_032795		Approved	FLJ14494	uc001qde.3	Q96CM3	OTTHUMG00000165815	ENST00000298317.4:c.568G>T	chr11.hg19:g.126075666C>A	ENSP00000298317:p.Val190Leu	35.0	0.0		59.0	18.0	NM_001144827	E9PML2|Q96K56	Missense_Mutation	SNP	ENST00000298317.4	hg19	CCDS8469.1	.	.	.	.	.	.	.	.	.	.	C	13.58	2.280807	0.40294	.	.	ENSG00000165526	ENST00000298317;ENST00000533628	T;T	0.14144	2.53;2.53	5.89	3.03	0.35002	Pseudouridine synthase, RsuA and RluB/C/D/E/F (1);Pseudouridine synthase, catalytic domain (1);	0.121669	0.56097	D	0.000034	T	0.09024	0.0223	N	0.26130	0.795	0.22330	N	0.99919	B;B	0.17852	0.02;0.024	B;B	0.24269	0.038;0.052	T	0.32903	-0.9889	10	0.28530	T	0.3	-35.9459	6.7022	0.23230	0.0:0.6595:0.1267:0.2138	.	190;190	E9PML2;Q96CM3	.;RUSD4_HUMAN	L	190	ENSP00000298317:V190L;ENSP00000433065:V190L	ENSP00000298317:V190L	V	-	1	0	RPUSD4	125580876	0.925000	0.31364	0.021000	0.16686	0.923000	0.55619	2.035000	0.41155	0.400000	0.25396	0.655000	0.94253	GTG	.	.		0.572	RPUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386336.1	NM_032795		A	126075666	C	A	126075666	3	1	159	1	0	0	0	0	1	0	0	0	13684	478	17	3	581	3	RPUSD4	11	126075666	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	58940620	126075666	8930850	57	24124										
TIRAP	114609	hgsc.bcm.edu	37	chr11	126162928	126162930	+	In_Frame_Del	DEL	AGT	AGT	-													0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cctgatggtggctttcgtcaAgtcaaagaagctgtcatgcg							TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	AGT	AGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr11:126162928_126162930delAGT	ENST00000392680.2	+	5	1029_1031	c.624_626delAGT	c.(622-627)caagtc>cac	p.208_209QV>H	TIRAP_ENST00000392678.3_In_Frame_Del_p.208_209QV>H|TIRAP_ENST00000392679.1_In_Frame_Del_p.208_209QV>H|RP11-712L6.7_ENST00000533378.1_RNA|RP11-712L6.5_ENST00000528876.1_5'Flank	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	208	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)			breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		GCTTTCGTCAAGTCAAAGAAGCT	0.542																																					p.208_209del		Atlas-INDEL	.											.	TIRAP	37	.	0			c.623_625del						.																																			SO:0001651	inframe_deletion	114609	exon5			.	AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"MyD88 adapter-like"	606252	"Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.624_626delAGT	chr11.hg19:g.126162928_126162930delAGT	ENSP00000376447:p.Gln208_Val209delinsHis	58.0	0.0		59.0	14.0	NM_148910	B3KW65|Q56UH9|Q56UI0|Q8N5E5	In_Frame_Del	DEL	ENST00000392680.2	hg19	CCDS8472.1																																																																																			.	.		0.542	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910		-	126162930	AGT	-	126162928	7	5	159	1	0	1	0	1	0	0	0	0	15942	69	3	0	630	0	TIRAP	11	126162928	In_Frame_Del	DEL	AGT	TCGA-DD-AACH-01A-11D-A40R-10	87262	126162928	8843588	58	24125	108	2								
TIRAP	114609	hgsc.bcm.edu	37	chr11	126162932	126162935	+	Frame_Shift_Del	DEL	AAAG	AAAG	-													0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	atggtggctttcgtcaagtcAaagaagctgtcatgcgttgt							TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr11:126162932_126162935delAAAG	ENST00000392680.2	+	5	1033_1036	c.628_631delAAAG	c.(628-633)aaagaafs	p.KE210fs	TIRAP_ENST00000392678.3_Frame_Shift_Del_p.KE210fs|TIRAP_ENST00000392679.1_Frame_Shift_Del_p.KE210fs|RP11-712L6.7_ENST00000533378.1_RNA|RP11-712L6.5_ENST00000528876.1_5'Flank	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	210	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)			breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		TCGTCAAGTCAAAGAAGCTGTCAT	0.544																																					p.209_210del		Atlas-INDEL	.											.	TIRAP	37	.	0			c.627_630del						.																																			SO:0001589	frameshift_variant	114609	exon5			.	AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"MyD88 adapter-like"	606252	"Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.628_631delAAAG	chr11.hg19:g.126162932_126162935delAAAG	ENSP00000376447:p.Lys210fs	58.0	0.0		61.0	12.0	NM_148910	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Frame_Shift_Del	DEL	ENST00000392680.2	hg19	CCDS8472.1																																																																																			.	.		0.544	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910		-	126162935	AAAG	-	126162932	7	5	159	1	0	1	0	1	0	0	0	0	15942	131	5	0	634	0	TIRAP	11	126162932	Frame_Shift_Del	DEL	AAAG	TCGA-DD-AACH-01A-11D-A40R-10	4	126162932	8843584	59	24126	108	2								
CELA1	1990	hgsc.bcm.edu	37	chr12	51723540	51723540	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ctggagacattacagccccgGctggacacaaagctggtcac	11	13	1	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr12:51723540G>T	ENST00000293636.1	-	7	727	c.687C>A	c.(685-687)agC>agA	p.S229R		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	229	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						TACAGCCCCGGCTGGACACAA	0.512																																					p.S229R		Atlas-SNP	.											.	CELA1	39	.	0			c.C687A						.						79	79	79					12																	51723540		2203	4300	6503	SO:0001583	missense	1990	exon7			GCCCCGGCTGGAC		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"elastase 1, pancreatic"	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.687C>A	chr12.hg19:g.51723540G>T	ENSP00000293636:p.Ser229Arg	53.0	0.0		58.0	18.0	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Missense_Mutation	SNP	ENST00000293636.1	hg19	CCDS8812.1	.	.	.	.	.	.	.	.	.	.	G	2.454	-0.325591	0.05350	.	.	ENSG00000139610	ENST00000293636	D	0.89050	-2.46	5.51	-1.26	0.09376	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.478838	0.24618	N	0.036995	T	0.76593	0.4009	N	0.21324	0.655	0.09310	N	1	B	0.13145	0.007	B	0.26693	0.072	T	0.63355	-0.6656	10	0.51188	T	0.08	-8.7379	2.2082	0.03941	0.3175:0.2067:0.3722:0.1036	.	229	Q9UNI1	CELA1_HUMAN	R	229	ENSP00000293636:S229R	ENSP00000293636:S229R	S	-	3	2	CELA1	50009807	0.000000	0.05858	0.333000	0.25482	0.011000	0.07611	-1.255000	0.02872	-0.358000	0.08162	-2.056000	0.00403	AGC	.	.		0.512	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971		T	51723540	G	T	51723540	3	4	159	1	0	0	0	0	1	0	0	0	3212	1194	42	3	97	3	CELA1	12	51723540	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10		51723540	82128355	60	24127										
MFSD5	84975	hgsc.bcm.edu	37	chr12	53647163	53647163	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ccttctggaaccatgtgctgGctgtagtggcaggtgtggca	15	9	1	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr12:53647163G>T	ENST00000329548.4	+	2	735	c.544G>T	c.(544-546)Gct>Tct	p.A182S	MFSD5_ENST00000534842.1_Missense_Mutation_p.A289S	NM_032889.4	NP_116278.3	Q6N075	MFSD5_HUMAN	major facilitator superfamily domain containing 5	182					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(3)|urinary_tract(1)	16						CCATGTGCTGGCTGTAGTGGC	0.612																																					p.A289S		Atlas-SNP	.											.	MFSD5	40	.	0			c.G865T						.						129	131	130					12																	53647163		2203	4300	6503	SO:0001583	missense	84975	exon2			GTGCTGGCTGTAG	AK097576	CCDS8851.1, CCDS53796.1	12q13.13	2012-03-09			ENSG00000182544	ENSG00000182544			28156	protein-coding gene	gene with protein product							Standard	NM_032889		Approved	MGC11308	uc001sch.2	Q6N075	OTTHUMG00000170028	ENST00000329548.4:c.544G>T	chr12.hg19:g.53647163G>T	ENSP00000332624:p.Ala182Ser	39.0	0.0		45.0	19.0	NM_001170790	G3V1N7|Q6NW04|Q8N7W8|Q8NCK0|Q96IA5	Missense_Mutation	SNP	ENST00000329548.4	hg19	CCDS8851.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.492264	0.64074	.	.	ENSG00000182544	ENST00000551660;ENST00000534842;ENST00000328704;ENST00000329548	T;T	0.80824	-1.42;-1.42	4.36	4.36	0.52297	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.81098	0.4752	L	0.48260	1.515	0.80722	D	1	P;P	0.46784	0.825;0.884	P;P	0.49597	0.468;0.616	T	0.81611	-0.0854	10	0.42905	T	0.14	-0.8003	15.8223	0.78667	0.0:0.0:1.0:0.0	.	182;289	Q6N075;G3V1N7	MFSD5_HUMAN;.	S	289;289;289;182	ENSP00000442688:A289S;ENSP00000332624:A182S	ENSP00000331231:A289S	A	+	1	0	MFSD5	51933430	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.305000	0.96197	2.268000	0.75426	0.561000	0.74099	GCT	.	.		0.612	MFSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406896.1	NM_032889		T	53647163	G	T	53647163	3	4	159	1	0	0	0	0	1	0	0	0	9543	1203	42	3	871	3	MFSD5	12	53647163	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	1923623	53647163	80204732	61	24128										
MUCL1	118430	hgsc.bcm.edu	37	chr12	55248916	55248916	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tcagagaatccgacaacagcTgctccagctgacacgtatcc	8	14	1	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr12:55248916T>A	ENST00000308796.6	+	2	121	c.75T>A	c.(73-75)gcT>gcA	p.A25A	MUCL1_ENST00000547990.1_3'UTR|MUCL1_ENST00000546809.1_Silent_p.A20A	NM_058173.2	NP_477521.1	Q96DR8	MUCL1_HUMAN	mucin-like 1	25	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|membrane (GO:0016020)				breast(1)|kidney(1)|lung(1)	3						CGACAACAGCTGCTCCAGCTG	0.428																																					p.A25A		Atlas-SNP	.											.	MUCL1	11	.	0			c.T75A						.						87	79	82					12																	55248916		2203	4300	6503	SO:0001819	synonymous_variant	118430	exon2			AACAGCTGCTCCA	AF414087	CCDS8885.1	12q13.2	2007-07-02							30588	protein-coding gene	gene with protein product	"small breast epithelial mucin"	610857				12019145	Standard	NM_058173		Approved	SBEM	uc001sgk.3	Q96DR8		ENST00000308796.6:c.75T>A	chr12.hg19:g.55248916T>A		86.0	0.0		89.0	34.0	NM_058173	Q0VG95|Q32ZB5	Silent	SNP	ENST00000308796.6	hg19	CCDS8885.1																																																																																			.	.		0.428	MUCL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406062.1	NM_058173		A	55248916	T	A	55248916	2	1	159	1	0	0	0	0	0	0	0	1	9991	1567	55	4		4	MUCL1	12	55248916	Silent	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	1601753	55248916	78602979	62	24129										
LEMD3	23592	hgsc.bcm.edu	37	chr12	65563653	65563653	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ccgcggggatgggggtccggCcggtctcgggcgacctctcc	18	15	2	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr12:65563653C>T	ENST00000308330.2	+	1	303	c.277C>T	c.(277-279)Ccg>Tcg	p.P93S	LEMD3_ENST00000541171.1_3'UTR	NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	93					negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of cell cycle (GO:0051726)|skeletal muscle cell differentiation (GO:0035914)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	36			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		gggggTCCGGCCGGTCTCGGG	0.716																																					p.P93S		Atlas-SNP	.											.	LEMD3	68	.	0			c.C277T						.						1	1	1					12																	65563653		891	2014	2905	SO:0001583	missense	23592	exon1			GTCCGGCCGGTCT	AF263918	CCDS8972.1	12q14	2008-02-05			ENSG00000174106	ENSG00000174106			28887	protein-coding gene	gene with protein product		607844				10671519, 15489854	Standard	NM_014319		Approved	MAN1	uc001ssl.2	Q9Y2U8	OTTHUMG00000168840	ENST00000308330.2:c.277C>T	chr12.hg19:g.65563653C>T	ENSP00000308369:p.Pro93Ser	737.0	1.0		779.0	304.0	NM_001167614	Q9NT47|Q9NYA5	Missense_Mutation	SNP	ENST00000308330.2	hg19	CCDS8972.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.526354	0.44969	.	.	ENSG00000174106	ENST00000308330	T	0.51325	0.71	3.49	2.56	0.30785	.	0.082180	0.48286	D	0.000194	T	0.28863	0.0716	N	0.24115	0.695	0.35061	D	0.76156	B;B	0.16603	0.018;0.018	B;B	0.15870	0.014;0.014	T	0.24333	-1.0163	9	.	.	.	-3.2809	8.6594	0.34084	0.0:0.7651:0.2349:0.0	.	93;93	B4E2K7;Q9Y2U8	.;MAN1_HUMAN	S	93	ENSP00000308369:P93S	.	P	+	1	0	LEMD3	63849920	1.000000	0.71417	0.997000	0.53966	0.372000	0.29890	1.553000	0.36255	0.992000	0.38840	0.462000	0.41574	CCG	.	.		0.716	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401312.2			T	65563653	C	T	65563653	3	4	159	1	0	0	0	0	1	0	0	0	8730	739	26	3	279	3	LEMD3	12	65563653	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	10314737	65563653	68288242	63	24130										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70953387	70953387	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	aatgtcagcaaatgacataaGactgggaggacttggagctg	13	6	1	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr12:70953387G>C	ENST00000261266.5	-	16	3825	c.3796C>G	c.(3796-3798)Ctt>Gtt	p.L1266V	PTPRB_ENST00000551525.1_Missense_Mutation_p.L1483V|PTPRB_ENST00000538708.1_Missense_Mutation_p.L1176V|PTPRB_ENST00000451516.2_Missense_Mutation_p.L1176V|PTPRB_ENST00000334414.6_Missense_Mutation_p.L1484V|PTPRB_ENST00000550358.1_Missense_Mutation_p.L1396V|PTPRB_ENST00000550857.1_Missense_Mutation_p.L1176V	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1266	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			AATGACATAAGACTGGGAGGA	0.453																																					p.L1484V		Atlas-SNP	.											.	PTPRB	676	.	0			c.C4450G						.						101	98	99					12																	70953387		1915	4143	6058	SO:0001583	missense	5787	exon18			ACATAAGACTGGG	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.3796C>G	chr12.hg19:g.70953387G>C	ENSP00000261266:p.Leu1266Val	115.0	0.0		111.0	52.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	G	10.43	1.346808	0.24426	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41;0.41;0.41;3.7	6.11	2.48	0.30137	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.458009	0.24836	N	0.035204	T	0.36193	0.0958	N	0.25647	0.755	0.25703	N	0.985567	B;B;B;B;B;B;B	0.30281	0.022;0.01;0.212;0.275;0.217;0.156;0.217	B;B;B;B;B;B;B	0.36186	0.037;0.037;0.065;0.219;0.138;0.158;0.138	T	0.15037	-1.0451	10	0.38643	T	0.18	.	4.4825	0.11774	0.2447:0.0:0.5022:0.2531	.	1176;1176;1363;1483;1484;1266;1396	P23467-2;F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;PTPRB_HUMAN;.	V	1484;1176;1396;1176;1176;1266;1483;1363	ENSP00000334928:L1484V;ENSP00000393028:L1176V;ENSP00000448058:L1396V;ENSP00000438927:L1176V;ENSP00000447302:L1176V;ENSP00000261266:L1266V;ENSP00000448349:L1483V;ENSP00000446982:L1363V	ENSP00000261266:L1266V	L	-	1	0	PTPRB	69239654	0.866000	0.29940	0.998000	0.56505	0.966000	0.64601	0.755000	0.26405	1.596000	0.50062	0.655000	0.94253	CTT	.	.		0.453	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			C	70953387	G	C	70953387	3	2	159	1	0	0	0	0	1	0	0	0	12811	942	33	4	2265	4	PTPRB	12	70953387	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	5389734	70953387	62898508	64	24131										
FBXW8	26259	hgsc.bcm.edu	37	chr12	117383227	117383227	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gctgtggtacaggctgtgccAgcaggaagggcaccttccgg	16	11	0	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr12:117383227A>T	ENST00000309909.5	+	3	564	c.482A>T	c.(481-483)cAg>cTg	p.Q161L	FBXW8_ENST00000455858.2_Missense_Mutation_p.Q95L			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	161					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|labyrinthine layer blood vessel development (GO:0060716)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|spongiotrophoblast layer development (GO:0060712)	Cul7-RING ubiquitin ligase complex (GO:0031467)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)				endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		AGGCTGTGCCAGCAGGAAGGG	0.493																																					p.Q161L		Atlas-SNP	.											.	FBXW8	53	.	0			c.A482T						.						134	111	118					12																	117383227		2203	4300	6503	SO:0001583	missense	26259	exon3			TGTGCCAGCAGGA	AF176707	CCDS9182.1, CCDS44988.1	12q24.23	2013-01-09	2007-02-08	2003-06-13				"F-boxes / WD-40 domains", "WD repeat domain containing"	13597	protein-coding gene	gene with protein product		609073	"F-box only protein 29", "F-box and WD-40 domain protein 8"	FBXO29		10531035, 10531037	Standard	NM_012174		Approved	FBX29, FBW6, FBW8	uc001twg.1	Q8N3Y1	OTTHUMG00000169329	ENST00000309909.5:c.482A>T	chr12.hg19:g.117383227A>T	ENSP00000310686:p.Gln161Leu	76.0	0.0		82.0	24.0	NM_153348	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	hg19	CCDS9182.1	.	.	.	.	.	.	.	.	.	.	A	8.270	0.813058	0.16537	.	.	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.33865	1.39;1.39	6.17	2.59	0.31030	F-box domain, Skp2-like (1);	0.454593	0.23989	N	0.042582	T	0.19327	0.0464	N	0.11724	0.165	0.28627	N	0.907861	B;B	0.18741	0.03;0.024	B;B	0.23275	0.045;0.015	T	0.16217	-1.0410	10	0.29301	T	0.29	-11.6751	8.5595	0.33503	0.7197:0.0:0.2803:0.0	.	161;95	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	L	161;95;95	ENSP00000310686:Q161L;ENSP00000389144:Q95L	ENSP00000310686:Q161L	Q	+	2	0	FBXW8	115867610	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	1.063000	0.30567	0.215000	0.20761	0.533000	0.62120	CAG	.	.		0.493	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174		T	117383227	A	T	117383227	3	4	159	1	0	0	0	0	1	0	0	0	5778	188	7	4	492	4	FBXW8	12	117383227	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	46429840	117383227	16468668	65	24132										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	129566302	129566302	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ggatttttttttttttttttAcctgaatggtggtcatccca	7	6	1	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr12:129566302A>G	ENST00000422113.2	-	7	2250		c.e7+1		TMEM132D_ENST00000389441.4_Splice_Site	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D						negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TTTTTTTTTTACCTGAATGGT	0.483																																					.		Atlas-SNP	.											.	TMEM132D	299	.	0			c.1923+2T>C						.						27	29	28					12																	129566302		2201	4294	6495	SO:0001630	splice_region_variant	121256	exon8			TTTTTTACCTGAA	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1923+1T>C	chr12.hg19:g.129566302A>G		69.0	0.0		104.0	41.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Splice_Site	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	A	16.10	3.027425	0.54683	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.837	0.63415	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM132D	128132255	1.000000	0.71417	0.984000	0.44739	0.620000	0.37586	9.104000	0.94239	1.660000	0.50760	0.459000	0.35465	.	.	.		0.483	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	Intron	G	129566302	A	G	129566302	5	3	159	1	0	0	0	0	0	0	1	0	16062	405	14	2	1386	2	TMEM132D	12	129566302	Splice_Site	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	12183075	129566302	4285593	66	24133										
POSTN	10631	hgsc.bcm.edu	37	chr13	38154710	38154710	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	aggcttacctaaagcgcttaTcttgttttaacttttcatgg	7	8	2	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr13:38154710T>C	ENST00000379747.4	-	11	1634	c.1517A>G	c.(1516-1518)gAt>gGt	p.D506G	POSTN_ENST00000541179.1_Missense_Mutation_p.D506G|POSTN_ENST00000379749.4_Missense_Mutation_p.D506G|POSTN_ENST00000541481.1_Missense_Mutation_p.D506G|POSTN_ENST00000379743.4_Missense_Mutation_p.D506G|POSTN_ENST00000379742.4_Missense_Mutation_p.D506G	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	506	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		AAAGCGCTTATCTTGTTTTAA	0.438																																					p.D506G		Atlas-SNP	.											.	POSTN	161	.	0			c.A1517G						.						287	274	278					13																	38154710		2203	4300	6503	SO:0001583	missense	10631	exon11			CGCTTATCTTGTT	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1517A>G	chr13.hg19:g.38154710T>C	ENSP00000369071:p.Asp506Gly	70.0	0.0		78.0	40.0	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	hg19	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.458623	0.84317	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.91843	-2.92;-2.92;-2.92;-2.92;-2.92;-2.92	5.02	5.02	0.67125	FAS1 domain (3);	0.094148	0.64402	D	0.000001	D	0.96334	0.8804	M	0.86573	2.825	0.51233	D	0.999914	D;D;D;D;D;D;D	0.76494	0.998;0.998;0.985;0.999;0.999;0.984;0.985	D;D;P;D;D;P;P	0.87578	0.995;0.998;0.826;0.998;0.994;0.853;0.826	D	0.96873	0.9641	10	0.62326	D	0.03	-25.7735	15.0317	0.71713	0.0:0.0:0.0:1.0	.	506;506;506;506;506;506;506	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	G	506	ENSP00000437959:D506G;ENSP00000369073:D506G;ENSP00000369071:D506G;ENSP00000369067:D506G;ENSP00000369066:D506G;ENSP00000437953:D506G	ENSP00000369066:D506G	D	-	2	0	POSTN	37052710	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	7.408000	0.80041	2.000000	0.58554	0.455000	0.32223	GAT	.	.		0.438	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		C	38154710	T	C	38154710	3	2	159	1	0	0	0	0	1	0	0	0	12268	1435	50	2	1045	2	POSTN	13	38154710	Missense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10		38154710	77015168	67	24134										
IPO4	79711	hgsc.bcm.edu	37	chr14	24653203	24653203	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gcccacccaccctttgctcaCcacaatgccctcggtggaac	7	19	1	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr14:24653203C>G	ENST00000354464.6	-	18	2046		c.e18+1		RP11-468E2.2_ENST00000561419.1_Splice_Site	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4						DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CCTTTGCTCACCACAATGCCC	0.632																																					.		Atlas-SNP	.											.	IPO4	74	.	0			c.1869+1G>C						.						28	27	27					14																	24653203		1893	4088	5981	SO:0001630	splice_region_variant	79711	exon19			TGCTCACCACAAT	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"Importins"	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1869+1G>C	chr14.hg19:g.24653203C>G		44.0	0.0		45.0	18.0	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Splice_Site	SNP	ENST00000354464.6	hg19	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.202111	0.79127	.	.	ENSG00000196497	ENST00000354464;ENST00000399536	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1124	0.93321	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IPO4	23723043	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.575000	0.74018	2.814000	0.96858	0.655000	0.94253	.	.	.		0.632	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	Intron	G	24653203	C	G	24653203	5	3	159	1	0	0	0	0	0	0	1	0	7804	521	18	4	1427	4	IPO4	14	24653203	Splice_Site	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10		24653203	82696337	68	24135										
TRAPPC6B	122553	hgsc.bcm.edu	37	chr14	39623438	39623438	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	agatgcatgttctaaatactGttttcctgcagacatctgag	8	8	2	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr14:39623438G>A	ENST00000330149.5	-	4	554	c.328C>T	c.(328-330)Cag>Tag	p.Q110*	TRAPPC6B_ENST00000347691.5_Intron|TRAPPC6B_ENST00000557764.1_5'UTR	NM_001079537.1	NP_001073005.1	Q86SZ2	TPC6B_HUMAN	trafficking protein particle complex 6B	110					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0128)		TCTAAATACTGTTTTCCTGCA	0.353																																					p.Q110X		Atlas-SNP	.											.	TRAPPC6B	13	.	0			c.C328T						.						109	101	103					14																	39623438		1835	4079	5914	SO:0001587	stop_gained	122553	exon4			AATACTGTTTTCC	AK025437	CCDS9670.1, CCDS41947.1	14q13.3	2011-10-10			ENSG00000182400	ENSG00000182400		"Trafficking protein particle complex"	23066	protein-coding gene	gene with protein product		610397					Standard	NM_177452		Approved		uc001wut.1	Q86SZ2	OTTHUMG00000140259	ENST00000330149.5:c.328C>T	chr14.hg19:g.39623438G>A	ENSP00000330289:p.Gln110*	54.0	0.0		89.0	21.0	NM_001079537	B3KPS2|Q5JPD6|Q86U35|Q86X35	Nonsense_Mutation	SNP	ENST00000330149.5	hg19	CCDS41947.1	.	.	.	.	.	.	.	.	.	.	G	37	6.260483	0.97421	.	.	ENSG00000182400	ENST00000330149	.	.	.	6.08	5.2	0.72013	.	0.178535	0.53938	D	0.000053	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-1.8261	15.3715	0.74568	0.0664:0.0:0.9336:0.0	.	.	.	.	X	110	.	ENSP00000330289:Q110X	Q	-	1	0	TRAPPC6B	38693189	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.007000	0.93597	1.594000	0.50039	0.591000	0.81541	CAG	.	.		0.353	TRAPPC6B-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276775.1	NM_177452		A	39623438	G	A	39623438	4	1	159	1	0	0	0	0	0	1	0	0	16479	1386	48	3	160	3	TRAPPC6B	14	39623438	Nonsense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	14970235	39623438	67726102	69	24136										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96809568	96809568	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gagcaaaagcagtgggttgaTgcacattaattcctgaggat	12	6	0	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr14:96809568T>C	ENST00000359933.4	-	5	1525	c.632A>G	c.(631-633)cAt>cGt	p.H211R		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	211					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AGTGGGTTGATGCACATTAAT	0.433																																					p.H211R		Atlas-SNP	.											.	ATG2B	169	.	0			c.A632G						.						118	114	115					14																	96809568		1925	4125	6050	SO:0001583	missense	55102	exon5			GGTTGATGCACAT	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.632A>G	chr14.hg19:g.96809568T>C	ENSP00000353010:p.His211Arg	99.0	0.0		51.0	33.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	T	22.2	4.261047	0.80246	.	.	ENSG00000066739	ENST00000359933	T	0.10099	2.91	5.27	5.27	0.74061	.	0.000000	0.64402	U	0.000001	T	0.12347	0.0300	L	0.42245	1.32	0.58432	D	0.999991	B	0.24258	0.1	B	0.26864	0.074	T	0.05386	-1.0888	10	0.36615	T	0.2	.	15.1796	0.72945	0.0:0.0:0.0:1.0	.	211	Q96BY7	ATG2B_HUMAN	R	211	ENSP00000353010:H211R	ENSP00000353010:H211R	H	-	2	0	ATG2B	95879321	1.000000	0.71417	0.921000	0.36526	0.979000	0.70002	7.499000	0.81566	1.995000	0.58328	0.482000	0.46254	CAT	.	.		0.433	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		C	96809568	T	C	96809568	3	2	159	1	0	0	0	0	1	0	0	0	1094	1464	51	2	5756	2	ATG2B	14	96809568	Missense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	57186130	96809568	10539972	70	24137										
LPCAT4	254531	hgsc.bcm.edu	37	chr15	34659273	34659274	+	Frame_Shift_Ins	INS	-	-	C													0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gggggtgggatctaggggggINScccagtcccccggacttccc							TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr15:34659273_34659274insC	ENST00000314891.6	-	1	205_206	c.28_29insG	c.(28-30)gccfs	p.A10fs	LPCAT4_ENST00000562431.1_5'Flank	NM_153613.2	NP_705841.2	Q643R3	LPCT4_HUMAN	lysophosphatidylcholine acyltransferase 4	10					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphoethanolamine O-acyltransferase activity (GO:0047166)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|calcium ion binding (GO:0005509)|lysophospholipid acyltransferase activity (GO:0071617)			NS(1)|breast(1)|large_intestine(2)|lung(5)|prostate(1)	10						ATCTAGGGGGGCCCAGTCCCCC	0.673																																					p.A10fs		Atlas-INDEL	.											.	LPCAT4	36	.	0			c.29_30insG						.																																			SO:0001589	frameshift_variant	254531	exon1			.	AF542964	CCDS32191.1	15q14	2008-07-02	2008-06-24	2008-06-24		ENSG00000176454			30059	protein-coding gene	gene with protein product	"lysophosphatidylethanolamine acyltransferase 2"	612039	"acyltransferase like 3", "1-acylglycerol-3-phosphate O-acyltransferase 7 (lysophosphatidic acid acyltransferase, eta)"	AYTL3, AGPAT7		8619474, 9110174, 16243729, 18458083	Standard	XR_243087		Approved	FLJ10257, LPAAT-eta, LPEAT2	uc001zig.3	Q643R3		ENST00000314891.6:c.29dupG	chr15.hg19:g.34659276_34659276dupC	ENSP00000317300:p.Ala10fs	149.0	0.0		178.0	18.0	NM_153613	A8K2K8|O43412|Q7Z4P4|Q8IUL7|Q8TB38	Frame_Shift_Ins	INS	ENST00000314891.6	hg19	CCDS32191.1																																																																																			.	.		0.673	LPCAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418028.2	NM_153613		C	34659274	-	C	34659273	7	5	159	1	0	1	1	0	0	0	0	0	8922	1203	42	0	1601	0	LPCAT4	15	34659273	Frame_Shift_Ins	INS	-	TCGA-DD-AACH-01A-11D-A40R-10		34659273	67872119	71	24138										
PLA2G4E	123745	hgsc.bcm.edu	37	chr15	42287601	42287601	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gatgtagctggcacagtccaGgaggttcagcttctgcagcc	13	11	2	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr15:42287601G>A	ENST00000399518.3	-	12	1690	c.1204C>T	c.(1204-1206)Ctg>Ttg	p.L402L	PLA2G4E_ENST00000413860.2_Silent_p.L373L|CTD-2382E5.1_ENST00000499478.2_RNA	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	390	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		GCACAGTCCAGGAGGTTCAGC	0.607																																					p.L402L		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.C1204T						.						60	64	63					15																	42287601		2040	4199	6239	SO:0001819	synonymous_variant	123745	exon12			AGTCCAGGAGGTT		CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.1204C>T	chr15.hg19:g.42287601G>A		65.0	0.0		84.0	30.0	NM_001206670	Q6ZSC0	Silent	SNP	ENST00000399518.3	hg19	CCDS55962.1																																																																																			.	.		0.607	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442		A	42287601	G	A	42287601	2	1	159	1	0	0	0	0	0	0	0	1	12014	991	35	3		3	PLA2G4E	15	42287601	Silent	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	7628328	42287601	60243791	72	24139										
CD19	930	hgsc.bcm.edu	37	chr16	28947906	28947906	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	acgtgctgtctctccccacaCccacctcaggcctcggtaag	8	18	2	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr16:28947906C>T	ENST00000324662.3	+	7	1113	c.1069C>T	c.(1069-1071)Ccc>Tcc	p.P357S	CD19_ENST00000567541.1_Missense_Mutation_p.P357S|CD19_ENST00000538922.1_Missense_Mutation_p.P357S			P15391	CD19_HUMAN	CD19 molecule	357					B cell receptor signaling pathway (GO:0050853)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor signaling protein activity (GO:0005057)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(4)|urinary_tract(1)	29						TCTCCCCACACCCACCTCAGG	0.642																																					p.P357S		Atlas-SNP	.											CD19,NS,neuroblastoma,0,1	CD19	65	.	0			c.C1069T						.						48	45	46					16																	28947906		2197	4300	6497	SO:0001583	missense	930	exon7			CCCACACCCACCT		CCDS10644.1, CCDS53998.1	16p11.2	2014-09-17	2006-03-28		ENSG00000177455	ENSG00000177455		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1633	protein-coding gene	gene with protein product		107265	"CD19 antigen"				Standard	NM_001770		Approved		uc010byo.2	P15391	OTTHUMG00000097049	ENST00000324662.3:c.1069C>T	chr16.hg19:g.28947906C>T	ENSP00000313419:p.Pro357Ser	33.0	0.0		37.0	18.0	NM_001178098	A0N0P9|F5H635|Q96S68|Q9BRD6	Missense_Mutation	SNP	ENST00000324662.3	hg19	CCDS10644.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.474141	0.63737	.	.	ENSG00000177455	ENST00000538922;ENST00000380673;ENST00000324662;ENST00000537306	T;T	0.39997	1.05;1.05	4.14	0.677	0.17964	.	1.085380	0.07160	N	0.850521	T	0.22322	0.0538	N	0.14661	0.345	0.09310	N	1	B;B	0.21753	0.06;0.036	B;B	0.20767	0.031;0.014	T	0.24977	-1.0145	10	0.21014	T	0.42	-3.9298	3.5093	0.07703	0.2334:0.53:0.0:0.2366	.	357;357	F5H635;P15391	.;CD19_HUMAN	S	357;164;357;206	ENSP00000437940:P357S;ENSP00000313419:P357S	ENSP00000313419:P357S	P	+	1	0	CD19	28855407	0.035000	0.19736	0.046000	0.18839	0.851000	0.48451	-0.299000	0.08254	0.050000	0.15949	0.305000	0.20034	CCC	.	.		0.642	CD19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214152.2			T	28947906	C	T	28947906	3	4	159	1	0	0	0	0	1	0	0	0	2975	507	18	3	1095	3	CD19	16	28947906	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10		28947906	61406847	73	24140										
FAM65A	79567	hgsc.bcm.edu	37	chr16	67575468	67575468	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gtaccatcaagctcagcctgGaagtcacatggaggttggtg	13	9	3	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr16:67575468G>A	ENST00000379312.3	+	11	1070	c.949G>A	c.(949-951)Gaa>Aaa	p.E317K	CTD-2012K14.2_ENST00000567122.1_RNA|CTD-2012K14.3_ENST00000563083.1_RNA|FAM65A_ENST00000540839.3_Missense_Mutation_p.E333K|CTD-2012K14.4_ENST00000564717.1_RNA|FAM65A_ENST00000042381.4_Missense_Mutation_p.E313K|FAM65A_ENST00000428437.2_Missense_Mutation_p.E327K|FAM65A_ENST00000422602.2_Missense_Mutation_p.E333K	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	317						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		GCTCAGCCTGGAAGTCACATG	0.602																																					p.E333K		Atlas-SNP	.											.	FAM65A	104	.	0			c.G997A						.						110	100	104					16																	67575468		2198	4300	6498	SO:0001583	missense	79567	exon11			AGCCTGGAAGTCA	AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.949G>A	chr16.hg19:g.67575468G>A	ENSP00000368614:p.Glu317Lys	94.0	0.0		57.0	41.0	NM_001193523	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	hg19	CCDS54028.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.267522|5.267522	0.95399|0.95399	.|.	.|.	ENSG00000039523|ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839|ENST00000428437	T;T;T|.	0.03441|.	3.93;3.93;3.93|.	4.9|4.9	4.9|4.9	0.64082|0.64082	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78155|0.78155	0.4239|0.4239	M|M	0.80616|0.80616	2.505|2.505	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.83275|.	0.996;0.996;0.996;0.996|.	T|T	0.79952|0.79952	-0.1586|-0.1586	10|5	0.54805|.	T|.	0.06|.	-7.3884|-7.3884	18.0724|18.0724	0.89413|0.89413	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	327;333;317;333|.	B4DIM2;E9PBS3;Q6ZS17;B4DEQ9|.	.;.;FA65A_HUMAN;.|.	K|E	317;313;333;327|307	ENSP00000368614:E317K;ENSP00000042381:E313K;ENSP00000400099:E333K|.	ENSP00000042381:E313K|.	E|G	+|+	1|2	0|0	FAM65A|FAM65A	66132969|66132969	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	9.458000|9.458000	0.97634|0.97634	2.266000|2.266000	0.75297|0.75297	0.555000|0.555000	0.69702|0.69702	GAA|GGA	.	.		0.602	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		A	67575468	G	A	67575468	3	1	159	1	0	0	0	0	1	0	0	0	5607	1175	41	3	975	3	FAM65A	16	67575468	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	38627562	67575468	22779285	74	24141										
AKAP10	11216	hgsc.bcm.edu	37	chr17	19827755	19827755	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ttgatataaagattctggatCcagacttgccgcatccacaa	7	10	1	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr17:19827755C>A	ENST00000225737.6	-	11	1874	c.1717G>T	c.(1717-1719)Gat>Tat	p.D573Y	AKAP10_ENST00000395536.3_Missense_Mutation_p.D515Y	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	573					blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					GATTCTGGATCCAGACTTGCC	0.318																																					p.D573Y		Atlas-SNP	.											.	AKAP10	47	.	0			c.G1717T						.						68	69	68					17																	19827755		2203	4300	6503	SO:0001583	missense	11216	exon11			CTGGATCCAGACT	AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"A-kinase anchor proteins"	368	protein-coding gene	gene with protein product	"dual-specificity A-kinase anchoring protein 2", "protein kinase A anchoring protein 10", "mitochondrial A kinase PPKA anchor protein 10"	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.1717G>T	chr17.hg19:g.19827755C>A	ENSP00000225737:p.Asp573Tyr	328.0	0.0		294.0	67.0	NM_007202	B2R650|Q96AJ7	Missense_Mutation	SNP	ENST00000225737.6	hg19	CCDS11214.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.435059	0.83885	.	.	ENSG00000108599	ENST00000225737;ENST00000395536	T	0.38401	1.14	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.62344	0.2420	M	0.74881	2.28	0.58432	D	0.999998	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.98	T	0.66384	-0.5937	10	0.87932	D	0	-11.6057	17.8951	0.88885	0.0:1.0:0.0:0.0	.	515;515;573	E7EMD6;Q2XPN4;O43572	.;.;AKA10_HUMAN	Y	573;515	ENSP00000225737:D573Y	ENSP00000225737:D573Y	D	-	1	0	AKAP10	19768347	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.882000	0.75589	2.468000	0.83385	0.591000	0.81541	GAT	.	.		0.318	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202		A	19827755	C	A	19827755	3	1	159	1	0	0	0	0	1	0	0	0	446	855	30	3	291	3	AKAP10	17	19827755	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10		19827755	61367455	75	24142										
TAOK1	57551	hgsc.bcm.edu	37	chr17	27869796	27869796	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tactgggggtccaggacctcActggggtcatcccatgggtg	15	11	2	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr17:27869796A>G	ENST00000261716.3	+	20	3281	c.2762A>G	c.(2761-2763)cAc>cGc	p.H921R	TAOK1_ENST00000536202.1_Missense_Mutation_p.H773R	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	921					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|execution phase of apoptosis (GO:0097194)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of cytoskeleton organization (GO:0051493)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28			Colorectal(6;0.198)			CCAGGACCTCACTGGGGTCAT	0.587																																					p.H921R		Atlas-SNP	.											.	TAOK1	151	.	0			c.A2762G						.						59	64	62					17																	27869796		2203	4300	6503	SO:0001583	missense	57551	exon20			GACCTCACTGGGG	AB037782	CCDS32601.1, CCDS56024.1	17q11.2	2014-01-28				ENSG00000160551			29259	protein-coding gene	gene with protein product		610266				10718198, 14517247	Standard	NM_020791		Approved	KIAA1361, MARKK, PSK2, MAP3K16, FLJ14314, TAO1	uc002hdz.2	Q7L7X3		ENST00000261716.3:c.2762A>G	chr17.hg19:g.27869796A>G	ENSP00000261716:p.His921Arg	143.0	0.0		173.0	75.0	NM_020791	A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Missense_Mutation	SNP	ENST00000261716.3	hg19	CCDS32601.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.634436	0.47049	.	.	ENSG00000160551	ENST00000261716;ENST00000536202	T;T	0.73363	-0.67;-0.74	5.79	5.79	0.91817	Protein kinase-like domain (1);	0.048258	0.85682	D	0.000000	T	0.72078	0.3416	L	0.57536	1.79	0.25172	N	0.990277	B;B	0.19331	0.035;0.02	B;B	0.15052	0.012;0.012	T	0.64356	-0.6427	10	0.49607	T	0.09	.	16.1307	0.81436	1.0:0.0:0.0:0.0	.	773;921	B7ZLV6;Q7L7X3	.;TAOK1_HUMAN	R	921;773	ENSP00000261716:H921R;ENSP00000438819:H773R	ENSP00000261716:H921R	H	+	2	0	TAOK1	24893922	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.256000	0.78350	2.209000	0.71365	0.459000	0.35465	CAC	.	.		0.587	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791		G	27869796	A	G	27869796	3	3	159	1	0	0	0	0	1	0	0	0	15562	159	6	2	2836	2	TAOK1	17	27869796	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	8042041	27869796	53325414	76	24143										
KRTAP1-3	81850	hgsc.bcm.edu	37	chr17	39190968	39190968	+	Frame_Shift_Del	DEL	G	G	-													0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ggtctggcagcagcttggctGgcagcagctggtctcacagc							TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr17:39190968delG	ENST00000344363.5	-	1	139	c.106delC	c.(106-108)cagfs	p.Q36fs		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	36						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCTTGGCTGGCAGCAGCTG	0.607																																					p.Q36fs		Atlas-INDEL	.											.	KRTAP1-3	18	.	0			c.107delA						.						35	44	41					17																	39190968		1964	4161	6125	SO:0001589	frameshift_variant	81850	exon1			.	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"Keratin associated proteins"	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.106delC	chr17.hg19:g.39190968delG	ENSP00000344420:p.Gln36fs	69.0	0.0		83.0	14.0	NM_030966	Q07628|Q8IUG0|Q9BYS2	Frame_Shift_Del	DEL	ENST00000344363.5	hg19	CCDS42323.1																																																																																			.	.		0.607	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			-	39190968	G	-	39190968	7	5	159	1	0	1	0	1	0	0	0	0	8512	1357	47	0	401	0	KRTAP1-3	17	39190968	Frame_Shift_Del	DEL	G	TCGA-DD-AACH-01A-11D-A40R-10	11321172	39190968	42004242	77	24144										
KRTAP1-1	81851	hgsc.bcm.edu	37	chr17	39197544	39197544	+	Frame_Shift_Del	DEL	G	G	-													0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ggtctcacagcagcgtggctGgcaggagctggtctcacagc							TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr17:39197544delG	ENST00000306271.4	-	1	169	c.106delC	c.(106-108)cagfs	p.Q36fs		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	36			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)				NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCGTGGCTGGCAGGAGCTG	0.607																																					p.Q36fs		Atlas-INDEL	.											.	KRTAP1-1	23	.	0			c.107delA						.						50	64	60					17																	39197544		2017	4199	6216	SO:0001589	frameshift_variant	81851	exon1			.	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"Keratin associated proteins"	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.106delC	chr17.hg19:g.39197544delG	ENSP00000305975:p.Gln36fs	82.0	0.0		83.0	21.0	NM_030967	A6NC32|Q96S60|Q96S67	Frame_Shift_Del	DEL	ENST00000306271.4	hg19	CCDS42324.1																																																																																			.	.		0.607	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967		-	39197544	G	-	39197544	7	5	159	1	0	1	0	1	0	0	0	0	8511	1357	47	0	431	0	KRTAP1-1	17	39197544	Frame_Shift_Del	DEL	G	TCGA-DD-AACH-01A-11D-A40R-10	6576	39197544	41997666	78	24145										
HCRT	3060	hgsc.bcm.edu	37	chr17	40336391	40336391	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	agcgtgaggatgccggccgcGtgattgcccgcgccgtgcag	17	13	0	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr17:40336391G>A	ENST00000293330.1	-	2	263	c.177C>T	c.(175-177)caC>caT	p.H59H		NM_001524.1	NP_001515.1	O43612	OREX_HUMAN	hypocretin (orexin) neuropeptide precursor	59					eating behavior (GO:0042755)|negative regulation of DNA replication (GO:0008156)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of transmission of nerve impulse (GO:0051970)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of transmission of nerve impulse (GO:0051971)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)				breast(1)|central_nervous_system(1)	2		all_cancers(22;1.39e-06)|all_epithelial(22;9.98e-06)|Breast(137;0.000143)|Ovarian(249;0.0221)|Myeloproliferative disorder(1115;0.0255)|Colorectal(1115;0.069)		BRCA - Breast invasive adenocarcinoma(366;0.124)		TGCCGGCCGCGTGATTGCCCG	0.721																																					p.H59H		Atlas-SNP	.											.	HCRT	3	.	0			c.C177T						.						6	7	7					17																	40336391		2005	3992	5997	SO:0001819	synonymous_variant	3060	exon2			GGCCGCGTGATTG	AF041240	CCDS11421.1	17q21	2013-02-28				ENSG00000161610		"Endogenous ligands"	4847	protein-coding gene	gene with protein product	"prepro-orexin"	602358				9419374, 9491897	Standard	NM_001524		Approved	PPOX, OX	uc002hzc.1	O43612		ENST00000293330.1:c.177C>T	chr17.hg19:g.40336391G>A		44.0	0.0		49.0	8.0	NM_001524		Silent	SNP	ENST00000293330.1	hg19	CCDS11421.1																																																																																			.	.		0.721	HCRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449792.1	NM_001524		A	40336391	G	A	40336391	2	1	159	1	0	0	0	0	0	0	0	1	7009	1136	40	1		1	HCRT	17	40336391	Silent	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	1138847	40336391	40858819	79	24146										
TMC6	11322	hgsc.bcm.edu	37	chr17	76121927	76121927	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gcaccgaagctgcaccgtgcGgttgtagtactgggagatga	15	9	0	2	rs117065924	byFrequency	TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr17:76121927G>T	ENST00000590602.1	-	5	469	c.310C>A	c.(310-312)Cgc>Agc	p.R104S	TMC6_ENST00000392467.3_Missense_Mutation_p.R104S|TMC6_ENST00000306591.7_Missense_Mutation_p.R104S|TMC6_ENST00000592076.1_5'Flank|TMC6_ENST00000322933.4_5'UTR|TMC6_ENST00000589553.1_5'UTR|TMC6_ENST00000322914.3_Missense_Mutation_p.R104S			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	104					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			TGCACCGTGCGGTTGTAGTAC	0.706																																					p.R104S		Atlas-SNP	.											.	TMC6	42	.	0			c.C310A						.						24	24	24					17																	76121927		2097	4143	6240	SO:0001583	missense	11322	exon5			CCGTGCGGTTGTA	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"epidermodysplasia verruciformis 1"	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.310C>A	chr17.hg19:g.76121927G>T	ENSP00000465261:p.Arg104Ser	135.0	0.0		111.0	22.0	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	hg19	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	g	16.81	3.225403	0.58668	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000306591	T;T;T	0.53423	0.62;0.62;0.62	4.02	4.02	0.46733	.	1.723940	0.03486	U	0.215803	T	0.69214	0.3086	M	0.66939	2.045	0.80722	D	1	D;P	0.62365	0.991;0.928	P;P	0.61592	0.891;0.496	T	0.54629	-0.8265	10	0.48119	T	0.1	-22.0581	15.7704	0.78164	0.0:0.0:1.0:0.0	.	104;104	Q7Z403-2;Q7Z403	.;TMC6_HUMAN	S	104	ENSP00000313408:R104S;ENSP00000376260:R104S;ENSP00000306405:R104S	ENSP00000306405:R104S	R	-	1	0	TMC6	73633522	1.000000	0.71417	0.916000	0.36221	0.227000	0.25037	5.112000	0.64634	1.797000	0.52628	0.556000	0.70494	CGC	.	G|0.996;A|0.004		0.706	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			T	76121927	G	T	76121927	3	4	159	1	0	0	0	0	1	0	0	0	16004	1116	39	1	2171	1	TMC6	17	76121927	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	35785536	76121927	5073283	80	24147										
MC2R	4158	hgsc.bcm.edu	37	chr18	13884907	13884907	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ggagggtggagatcttcctgGtgtgggatcgagccagcagg	19	7	1	1	rs202040791		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr18:13884907G>T	ENST00000327606.3	-	2	791	c.611C>A	c.(610-612)aCc>aAc	p.T204N		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	204					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)			breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	GATCTTCCTGGTGTGGGATCG	0.572																																					p.T204N	Colon(141;1584 1782 35999 48227 48692)	Atlas-SNP	.											.	MC2R	78	.	0			c.C611A						.						107	89	95					18																	13884907		2203	4300	6503	SO:0001583	missense	4158	exon2			TTCCTGGTGTGGG		CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"GPCR / Class A : Melanocortin receptors"	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.611C>A	chr18.hg19:g.13884907G>T	ENSP00000333821:p.Thr204Asn	136.0	0.0		158.0	74.0	NM_000529	A8K016|Q3MI45|Q504X6	Missense_Mutation	SNP	ENST00000327606.3	hg19	CCDS11869.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.072766	0.55646	.	.	ENSG00000185231	ENST00000327606;ENST00000399821	T	0.37584	1.19	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.170809	0.51477	D	0.000086	T	0.33904	0.0879	L	0.29908	0.895	0.28875	N	0.894714	B	0.26876	0.162	B	0.31495	0.131	T	0.37888	-0.9686	10	0.72032	D	0.01	.	18.6835	0.91556	0.0:0.0:1.0:0.0	.	204	Q01718	ACTHR_HUMAN	N	204	ENSP00000333821:T204N	ENSP00000333821:T204N	T	-	2	0	MC2R	13874907	1.000000	0.71417	0.971000	0.41717	0.870000	0.49936	3.462000	0.53042	2.411000	0.81874	0.655000	0.94253	ACC	.	.		0.572	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2			T	13884907	G	T	13884907	3	4	159	1	0	0	0	0	1	0	0	0	9373	1261	44	3	286	3	MC2R	18	13884907	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10		13884907	64192341	81	24148										
ATP8B1	5205	hgsc.bcm.edu	37	chr18	55373803	55373803	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tacttgcgatcgtttgctttGacttgccatgtacattcttt	7	9	1	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr18:55373803G>C	ENST00000283684.4	-	2	197	c.198C>G	c.(196-198)gtC>gtG	p.V66V	RP11-35G9.3_ENST00000599199.1_RNA|ATP8B1_ENST00000589147.1_5'UTR|ATP8B1_ENST00000536015.1_Silent_p.V66V|RP11-35G9.5_ENST00000588925.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	66					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				CGTTTGCTTTGACTTGCCATG	0.353																																					p.V66V		Atlas-SNP	.											.	ATP8B1	126	.	0			c.C198G						.						130	110	116					18																	55373803		2203	4300	6503	SO:0001819	synonymous_variant	5205	exon3			TGCTTTGACTTGC	AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"ATPases / P-type"	3706	protein-coding gene	gene with protein product		602397	"ATPase, Class I, type 8B, member 1", "ATPase, class I, type 8B, member 1"	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.198C>G	chr18.hg19:g.55373803G>C		93.0	0.0		74.0	6.0	NM_005603	Q9BTP8	Silent	SNP	ENST00000283684.4	hg19	CCDS11965.1																																																																																			.	.		0.353	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603		C	55373803	G	C	55373803	2	2	159	1	0	0	0	0	0	0	0	1	1194	1277	45	4		4	ATP8B1	18	55373803	Silent	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	41488896	55373803	22703445	82	24149										
SEC11C	90701	hgsc.bcm.edu	37	chr18	56819870	56819870	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	atagttgtttttaaagttgaAggacgagacattccaatagt	9	4	0	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr18:56819870A>T	ENST00000587834.1	+	3	772	c.300A>T	c.(298-300)gaA>gaT	p.E100D	SEC11C_ENST00000588875.1_Missense_Mutation_p.E100D	NM_033280.2	NP_150596.1	Q9BY50	SC11C_HUMAN	SEC11 homolog C (S. cerevisiae)	100					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	serine-type peptidase activity (GO:0008236)			endometrium(1)|large_intestine(4)|liver(2)|lung(2)	9		Colorectal(73;0.175)				TTAAAGTTGAAGGACGAGACA	0.393																																					p.E100D		Atlas-SNP	.											.	SEC11C	17	.	0			c.A300T						.						99	103	102					18																	56819870		2203	4300	6503	SO:0001583	missense	90701	exon3			AGTTGAAGGACGA	AF212233	CCDS11970.1	18q21.32	2006-11-07	2006-11-07	2006-11-07	ENSG00000166562	ENSG00000166562			23400	protein-coding gene	gene with protein product			"SEC11-like 3 (S. cerevisiae)"	SEC11L3			Standard	NM_033280		Approved	SPC21, SPCS4C	uc002lht.3	Q9BY50	OTTHUMG00000132762	ENST00000587834.1:c.300A>T	chr18.hg19:g.56819870A>T	ENSP00000468633:p.Glu100Asp	122.0	0.0		107.0	45.0	NM_033280	B2RAA3	Missense_Mutation	SNP	ENST00000587834.1	hg19	CCDS11970.1	.	.	.	.	.	.	.	.	.	.	A	13.36	2.213675	0.39102	.	.	ENSG00000166562	ENST00000299714;ENST00000509791	.	.	.	5.48	4.28	0.50868	Peptidase S24/S26A/S26B/S26C (1);Peptidase S24/S26A/S26B/S26C, beta-ribbon domain (1);Peptidase S24/S26A/S26B (1);	0.000000	0.64402	D	0.000001	T	0.38241	0.1033	N	0.21240	0.645	0.58432	D	0.999996	B	0.17038	0.02	B	0.20384	0.029	T	0.22591	-1.0212	9	0.25751	T	0.34	-31.0153	6.2582	0.20885	0.7834:0.0:0.075:0.1416	.	100	Q9BY50	SC11C_HUMAN	D	100	.	ENSP00000299714:E100D	E	+	3	2	SEC11C	54970850	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.231000	0.51294	2.081000	0.62600	0.533000	0.62120	GAA	.	.		0.393	SEC11C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256134.2	NM_033280		T	56819870	A	T	56819870	3	4	159	1	0	0	0	0	1	0	0	0	13994	69	3	4	310	4	SEC11C	18	56819870	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	1446067	56819870	21257378	83	24150										
EMR1	2015	hgsc.bcm.edu	37	chr19	6928158	6928158	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tcctatttctctccacagctGctggctgaatacagagacag	8	12	1	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr19:6928158G>A	ENST00000312053.4	+	17	2262	c.2225G>A	c.(2224-2226)tGc>tAc	p.C742Y	EMR1_ENST00000250572.8_Missense_Mutation_p.C677Y|EMR1_ENST00000381404.4_Missense_Mutation_p.C690Y|EMR1_ENST00000381407.5_Missense_Mutation_p.C601Y|EMR1_ENST00000450315.3_Missense_Mutation_p.C565Y	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	742					cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					CTCCACAGCTGCTGGCTGAAT	0.498																																					p.C742Y		Atlas-SNP	.											.	EMR1	153	.	0			c.G2225A						.						178	166	170					19																	6928158		2203	4300	6503	SO:0001583	missense	2015	exon17			ACAGCTGCTGGCT	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.2225G>A	chr19.hg19:g.6928158G>A	ENSP00000311545:p.Cys742Tyr	42.0	0.0		30.0	20.0	NM_001974	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	hg19	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	g	16.41	3.114514	0.56505	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.61980	0.06;0.06;0.06;0.06;0.06	3.78	3.78	0.43462	GPCR, family 2-like (1);	.	.	.	.	D	0.85375	0.5682	H	0.98111	4.15	0.40877	D	0.983962	D;D;D;D;D	0.76494	0.986;0.995;0.999;0.995;0.982	P;D;D;D;P	0.71656	0.873;0.917;0.974;0.917;0.832	D	0.90761	0.4665	9	0.87932	D	0	.	13.1242	0.59344	0.0:0.0:1.0:0.0	.	565;601;677;690;742	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	Y	677;742;690;677;601;565	ENSP00000311545:C742Y;ENSP00000370811:C690Y;ENSP00000250572:C677Y;ENSP00000370814:C601Y;ENSP00000405974:C565Y	ENSP00000250572:C677Y	C	+	2	0	EMR1	6879158	1.000000	0.71417	0.989000	0.46669	0.709000	0.40893	7.847000	0.86896	1.642000	0.50584	0.609000	0.83330	TGC	.	.		0.498	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			A	6928158	G	A	6928158	3	1	159	1	0	0	0	0	1	0	0	0	5106	1319	46	3	2291	3	EMR1	19	6928158	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10		6928158	52200825	84	24151										
MUC16	94025	hgsc.bcm.edu	37	chr19	8994527	8994527	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gagggtgaatagtatcaggaGatggctggcagctgtagtgg	18	4	1	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr19:8994527G>C	ENST00000397910.4	-	64	41568	c.41365C>G	c.(41365-41367)Ctc>Gtc	p.L13789V	MUC16_ENST00000380951.5_Missense_Mutation_p.L430V	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13791	SEA 12. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGTATCAGGAGATGGCTGGCA	0.428																																					p.L13789V		Atlas-SNP	.											.	MUC16	4315	.	0			c.C41365G						.						176	157	163					19																	8994527		1963	4160	6123	SO:0001583	missense	94025	exon64			TCAGGAGATGGCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.41365C>G	chr19.hg19:g.8994527G>C	ENSP00000381008:p.Leu13789Val	134.0	0.0		82.0	54.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	2.230|2.230	-0.376399|-0.376399	0.05000|0.05000	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.32515	.|1.45;1.45	2.69|2.69	-5.39|-5.39	0.02664|0.02664	.|.	.|.	.|.	.|.	.|.	T|T	0.32041|0.32041	0.0816|0.0816	L|L	0.45581|0.45581	1.43|1.43	.|.	.|.	.|.	.|B;P	.|0.48911	.|0.002;0.917	.|B;D	.|0.65684	.|0.001;0.937	T|T	0.16453|0.16453	-1.0402|-1.0402	4|8	.|0.16420	.|T	.|0.52	.|.	0.2962|0.2962	0.00266|0.00266	0.2416:0.1729:0.2809:0.3046|0.2416:0.1729:0.2809:0.3046	.|.	.|21434;13789	.|Q8WXI7;B5ME49	.|MUC16_HUMAN;.	M|V	628|13789;430	.|ENSP00000381008:L13789V;ENSP00000370338:L430V	.|ENSP00000370338:L430V	I|L	-|-	3|1	3|0	MUC16|MUC16	8855527|8855527	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-6.734000|-6.734000	0.00055|0.00055	-2.040000|-2.040000	0.00916|0.00916	-0.259000|-0.259000	0.10710|0.10710	ATC|CTC	.	.		0.428	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	8994527	G	C	8994527	3	2	159	1	0	0	0	0	1	0	0	0	9982	942	33	4	2242	4	MUC16	19	8994527	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	2066369	8994527	50134456	85	24152										
GGN	199720	hgsc.bcm.edu	37	chr19	38876196	38876196	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tagctgccccagtctgagagGccccgctgccaccaccccct	9	20	1	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr19:38876196G>T	ENST00000334928.6	-	3	1838	c.1706C>A	c.(1705-1707)gCc>gAc	p.A569D	AC005789.9_ENST00000585411.1_RNA|GGN_ENST00000591809.1_Intron|SPRED3_ENST00000587013.1_5'Flank	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	569	Interactions with ZNF403/GGNBP2 and OAZ3. {ECO:0000250}.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGTCTGAGAGGCCCCGCTGCC	0.647																																					p.A569D		Atlas-SNP	.											.	GGN	50	.	0			c.C1706A						.						41	33	36					19																	38876196		2203	4300	6503	SO:0001583	missense	199720	exon3			TGAGAGGCCCCGC	AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.1706C>A	chr19.hg19:g.38876196G>T	ENSP00000334940:p.Ala569Asp	134.0	0.0		153.0	44.0	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Missense_Mutation	SNP	ENST00000334928.6	hg19	CCDS12516.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.254092	0.59212	.	.	ENSG00000179168	ENST00000334928	.	.	.	2.71	1.65	0.23941	.	0.393637	0.18577	N	0.137170	T	0.19644	0.0472	N	0.24115	0.695	0.09310	N	1	P	0.48016	0.904	B	0.43728	0.429	T	0.07404	-1.0774	9	0.54805	T	0.06	1.0967	5.733	0.18051	0.1549:0.0:0.8451:0.0	.	569	Q86UU5	GGN_HUMAN	D	569	.	ENSP00000334940:A569D	A	-	2	0	GGN	43568036	0.113000	0.22115	0.059000	0.19551	0.438000	0.31896	3.002000	0.49496	0.690000	0.31570	0.455000	0.32223	GCC	.	.		0.647	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		T	38876196	G	T	38876196	3	4	159	1	0	0	0	0	1	0	0	0	6366	1203	42	3	260	3	GGN	19	38876196	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	29881669	38876196	20252787	86	24153										
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39329533	39329533	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ctcccgagcctgagcacctaCcagacattcagcttctgccc	7	18	2	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr19:39329533C>T	ENST00000221419.5	-	9	1722		c.e9+1		AC104534.3_ENST00000594769.1_Splice_Site|HNRNPL_ENST00000600873.1_Splice_Site	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L						gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			TGAGCACCTACCAGACATTCA	0.597																																					.		Atlas-SNP	.											.	HNRNPL	67	.	0			c.1355+1G>A						.						117	95	102					19																	39329533		2203	4300	6503	SO:0001630	splice_region_variant	3191	exon10			CACCTACCAGACA	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1355+1G>A	chr19.hg19:g.39329533C>T		62.0	0.0		47.0	21.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Splice_Site	SNP	ENST00000221419.5	hg19	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	C	32	5.161363	0.94727	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750	.	.	.	6.09	6.09	0.99107	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4664	0.94945	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HNRNPL	44021373	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.512000	0.81728	2.899000	0.99337	0.655000	0.94253	.	.	.		0.597	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1		Intron	T	39329533	C	T	39329533	5	4	159	1	0	0	0	0	0	0	1	0	7279	521	18	3	433	3	HNRNPL	19	39329533	Splice_Site	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	453337	39329533	19799450	87	24154										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40408687	40408687	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ccacacaggccacacatctgCtggtagtagtttccggggac	11	13	1	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr19:40408687C>A	ENST00000221347.6	-	8	4159	c.4152G>T	c.(4150-4152)caG>caT	p.Q1384H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1384	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CACACATCTGCTGGTAGTAGT	0.562																																					p.Q1384H		Atlas-SNP	.											.	FCGBP	416	.	0			c.G4152T						.						143	123	130					19																	40408687		2203	4300	6503	SO:0001583	missense	8857	exon8			CATCTGCTGGTAG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4152G>T	chr19.hg19:g.40408687C>A	ENSP00000221347:p.Gln1384His	328.0	0.0		298.0	106.0	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	5.981	0.364972	0.11296	.	.	ENSG00000090920	ENST00000221347	T	0.59364	0.27	4.71	-0.825	0.10809	von Willebrand factor, type D domain (3);	1.244280	0.05942	N	0.637270	T	0.40862	0.1134	N	0.11201	0.11	0.09310	N	1	P	0.46656	0.882	P	0.48488	0.579	T	0.30387	-0.9980	10	0.52906	T	0.07	.	1.6164	0.02705	0.2218:0.4029:0.1997:0.1757	.	1384	Q9Y6R7	FCGBP_HUMAN	H	1384	ENSP00000221347:Q1384H	ENSP00000221347:Q1384H	Q	-	3	2	FCGBP	45100527	0.000000	0.05858	0.935000	0.37517	0.109000	0.19521	-0.211000	0.09332	0.093000	0.17368	-0.194000	0.12790	CAG	.	.		0.562	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40408687	C	A	40408687	3	1	159	1	0	0	0	0	1	0	0	0	5786	796	28	3	12181	3	FCGBP	19	40408687	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	1079154	40408687	18720296	88	24155										
KCNC3	3748	hgsc.bcm.edu	37	chr19	50826433	50826433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gggtggcggcgggctgatgcCcccgctgccgtggtgcgggt	21	12	0	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr19:50826433C>T	ENST00000477616.1	-	2	2071	c.1777G>A	c.(1777-1779)Ggc>Agc	p.G593S	KCNC3_ENST00000391818.2_Intron|KCNC3_ENST00000474951.1_Intron|KCNC3_ENST00000376959.2_Missense_Mutation_p.G593S	NM_004977.2	NP_004968.2	Q14003	KCNC3_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 3	593					cell death (GO:0008219)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axolemma (GO:0030673)|axon terminus (GO:0043679)|dendrite membrane (GO:0032590)|neuromuscular junction (GO:0031594)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)	13		all_neural(266;0.057)|Ovarian(192;0.208)		OV - Ovarian serous cystadenocarcinoma(262;0.00283)|GBM - Glioblastoma multiforme(134;0.0181)	Dalfampridine(DB06637)	GGGCTGATGCCCCCGCTGCCG	0.751																																					p.G593S	Melanoma(91;1496 2324 50908)	Atlas-SNP	.											.	KCNC3	41	.	0			c.G1777A						.						1	1	1					19																	50826433		928	2154	3082	SO:0001583	missense	3748	exon2			TGATGCCCCCGCT	AB208930	CCDS12793.1	19q13.33	2014-09-17			ENSG00000131398	ENSG00000131398		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6235	protein-coding gene	gene with protein product		176264	"spinocerebellar ataxia 13"	SCA13		1740329, 8111118, 16382104	Standard	NM_004977		Approved	Kv3.3	uc002pru.1	Q14003	OTTHUMG00000044580	ENST00000477616.1:c.1777G>A	chr19.hg19:g.50826433C>T	ENSP00000434241:p.Gly593Ser	45.0	0.0		29.0	8.0	NM_004977		Missense_Mutation	SNP	ENST00000477616.1	hg19	CCDS12793.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.091035	0.36855	.	.	ENSG00000131398	ENST00000376959;ENST00000477616;ENST00000443843	D;D	0.97976	-4.63;-4.64	2.83	0.593	0.17478	.	.	.	.	.	D	0.89815	0.6824	N	0.08118	0	0.80722	D	1	B;B	0.23854	0.0;0.092	B;B	0.14578	0.001;0.011	T	0.81590	-0.0863	9	0.07175	T	0.84	.	7.3735	0.26815	0.0:0.7669:0.0:0.2331	.	593;593	Q14003;E7ETH1	KCNC3_HUMAN;.	S	593;593;407	ENSP00000366158:G593S;ENSP00000434241:G593S	ENSP00000366158:G593S	G	-	1	0	KCNC3	55518245	0.453000	0.25721	0.559000	0.28332	0.146000	0.21551	1.259000	0.32956	0.253000	0.21552	0.462000	0.41574	GGC	.	.		0.751	KCNC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314288.2	NM_004977		T	50826433	C	T	50826433	3	4	159	1	0	0	0	0	1	0	0	0	8025	623	22	3	508	3	KCNC3	19	50826433	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	10417746	50826433	8302550	89	24156										
POLD1	5424	hgsc.bcm.edu	37	chr19	50921101	50921101	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ccctgcccccacccgcagccGggactgccccatcttctaca	7	22	2	0	rs541931950		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr19:50921101G>A	ENST00000440232.2	+	27	3274	c.3221G>A	c.(3220-3222)cGg>cAg	p.R1074Q	CTD-2545M3.6_ENST00000599632.1_Intron|SPIB_ENST00000596074.1_5'Flank|SPIB_ENST00000270632.7_5'Flank|POLD1_ENST00000595904.1_Missense_Mutation_p.R1100Q|SPIB_ENST00000595883.1_5'Flank|SPIB_ENST00000439922.2_5'Flank|SPIB_ENST00000597855.1_5'Flank|POLD1_ENST00000599857.1_Missense_Mutation_p.R1074Q	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	1074					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		ACCCGCAGCCGGGACTGCCCC	0.692								DNA polymerases (catalytic subunits)					-|||	1	0.000199681	0	0	5008	,	,		9593	0		0	False		,,,				2504	0.001				p.R1074Q		Atlas-SNP	.											.	POLD1	174	.	0			c.G3221A						.						18	19	19					19																	50921101		2197	4296	6493	SO:0001583	missense	5424	exon27			GCAGCCGGGACTG		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.3221G>A	chr19.hg19:g.50921101G>A	ENSP00000406046:p.Arg1074Gln	129.0	0.0		148.0	68.0	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	hg19	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	g	31	5.092539	0.94149	.	.	ENSG00000062822	ENST00000440232	T	0.45668	0.89	3.87	3.87	0.44632	.	0.000000	0.64402	U	0.000002	T	0.68705	0.3030	M	0.88241	2.94	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.99;0.994	T	0.76702	-0.2862	10	0.62326	D	0.03	-27.1432	15.0385	0.71767	0.0:0.0:1.0:0.0	.	1100;1074	E7EVW0;P28340	.;DPOD1_HUMAN	Q	1074	ENSP00000406046:R1074Q	ENSP00000406046:R1074Q	R	+	2	0	POLD1	55612913	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	5.331000	0.65905	1.913000	0.55393	0.444000	0.29173	CGG	.	.		0.692	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			A	50921101	G	A	50921101	3	1	159	1	0	0	0	0	1	0	0	0	12199	1116	39	1	3323	1	POLD1	19	50921101	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	94668	50921101	8207882	90	24157										
LAIR1	3903	hgsc.bcm.edu	37	chr19	54868132	54868132	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gattctggcgatggaggcagAagaggaccaggaggaggaga	19	5	1	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr19:54868132A>C	ENST00000391742.2	-	6	703	c.551T>G	c.(550-552)tTc>tGc	p.F184C	LAIR1_ENST00000434277.2_Missense_Mutation_p.F183C|LAIR1_ENST00000463489.1_5'UTR|LAIR1_ENST00000474878.1_Missense_Mutation_p.F166C|LAIR1_ENST00000391743.3_Missense_Mutation_p.F166C|LAIR1_ENST00000313038.6_Missense_Mutation_p.F177C|LAIR1_ENST00000348231.4_Missense_Mutation_p.F167C			Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like receptor 1	184					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(4)|prostate(1)|stomach(3)	26	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)		ATGGAGGCAGAAGAGGACCAG	0.547																																					p.F184C		Atlas-SNP	.											.	LAIR1	44	.	0			c.T551G						.						101	106	104					19																	54868132		2203	4300	6503	SO:0001583	missense	3903	exon6			AGGCAGAAGAGGA	AF013249	CCDS12891.1, CCDS12892.1, CCDS74448.1, CCDS74449.1, CCDS74450.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167613	ENSG00000167613		"Leukocyte-associated Ig like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6477	protein-coding gene	gene with protein product		602992	"leukocyte-associated Ig-like receptor 1"			9285412	Standard	XM_005258924		Approved	CD305	uc002qfk.1	Q6GTX8	OTTHUMG00000065545	ENST00000391742.2:c.551T>G	chr19.hg19:g.54868132A>C	ENSP00000375622:p.Phe184Cys	74.0	0.0		96.0	41.0	NM_002287		Missense_Mutation	SNP	ENST00000391742.2	hg19	CCDS12891.1	.	.	.	.	.	.	.	.	.	.	.	11.85	1.760802	0.31137	.	.	ENSG00000167613	ENST00000391743;ENST00000391742;ENST00000434277;ENST00000348231;ENST00000313038;ENST00000474878	T;T;T;T;T;T	0.00524	6.82;6.89;6.93;6.82;6.88;6.83	4.39	2.24	0.28232	.	1.069840	0.07396	N	0.889958	T	0.01489	0.0048	M	0.79123	2.44	0.09310	N	1	D;D;D;D;B;D	0.89917	1.0;0.999;0.999;0.976;0.107;0.999	D;P;D;P;B;P	0.69479	0.964;0.894;0.951;0.711;0.079;0.894	T	0.49925	-0.8887	10	0.87932	D	0	.	4.5526	0.12120	0.7019:0.1964:0.1017:0.0	.	184;166;166;183;167;184	Q6GTX8-4;A8MZ84;Q6GTX8-3;D3YTC8;Q6GTX8-2;Q6GTX8	.;.;.;.;.;LAIR1_HUMAN	C	166;184;183;167;177;166	ENSP00000375623:F166C;ENSP00000375622:F184C;ENSP00000391003:F183C;ENSP00000301193:F167C;ENSP00000319204:F177C;ENSP00000418998:F166C	ENSP00000319204:F177C	F	-	2	0	LAIR1	59559944	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.386000	0.20702	0.422000	0.26005	0.528000	0.53228	TTC	.	.		0.547	LAIR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140506.1			C	54868132	A	C	54868132	3	2	159	1	0	0	0	0	1	0	0	0	8611	246	9	5	332	5	LAIR1	19	54868132	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	3947031	54868132	4260851	91	24158										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55494016	55494016	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	gaagaagccggtgcccgtccTcctggggagtttgctgaaca	14	11	0	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr19:55494016T>A	ENST00000543010.1	+	6	1093	c.950T>A	c.(949-951)cTc>cAc	p.L317H	NLRP2_ENST00000538819.1_Missense_Mutation_p.L293H|NLRP2_ENST00000427260.2_Missense_Mutation_p.L294H|NLRP2_ENST00000537859.1_Missense_Mutation_p.L295H|NLRP2_ENST00000448584.2_Missense_Mutation_p.L317H|NLRP2_ENST00000391721.4_Missense_Mutation_p.L293H|NLRP2_ENST00000339757.7_Missense_Mutation_p.L295H|NLRP2_ENST00000263437.6_Missense_Mutation_p.L314H	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	317	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GTGCCCGTCCTCCTGGGGAGT	0.647																																					p.L317H		Atlas-SNP	.											.	NLRP2	161	.	0			c.T950A						.						45	42	43					19																	55494016		2203	4300	6503	SO:0001583	missense	55655	exon6			CCGTCCTCCTGGG	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.950T>A	chr19.hg19:g.55494016T>A	ENSP00000445135:p.Leu317His	71.0	0.0		74.0	26.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.138920	0.56936	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	D;D;D;D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	1.55	1.55	0.23275	NACHT nucleoside triphosphatase (1);	.	.	.	.	D	0.91717	0.7381	M	0.93197	3.39	0.24777	N	0.992834	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.80752	-0.1242	9	0.87932	D	0	.	7.1971	0.25860	0.0:0.0:0.0:1.0	.	294;295;314;293;317	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	H	317;293;295;317;295;294;293;314	ENSP00000445135:L317H;ENSP00000375601:L293H;ENSP00000344074:L295H;ENSP00000409370:L317H;ENSP00000440601:L295H;ENSP00000402474:L294H;ENSP00000441133:L293H;ENSP00000263437:L314H	ENSP00000263437:L314H	L	+	2	0	NLRP2	60185828	0.002000	0.14202	0.062000	0.19696	0.292000	0.27327	1.259000	0.32956	0.998000	0.38996	0.397000	0.26171	CTC	.	.		0.647	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		A	55494016	T	A	55494016	3	1	159	1	0	0	0	0	1	0	0	0	10486	1551	54	4	968	4	NLRP2	19	55494016	Missense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	625884	55494016	3634967	92	24159										
KRTAP22-1	337979	hgsc.bcm.edu	37	chr21	31973566	31973577	+	In_Frame_Del	DEL	TGGTTTTCTGGC	TGGTTTTCTGGC	-													0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	catggtgttatgaaagatctTggttttctggctgcttctga							TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	TGGTTTTCTGGC	TGGTTTTCTGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr21:31973566_31973577delTGGTTTTCTGGC	ENST00000334680.2	+	1	153_164	c.127_138delTGGTTTTCTGGC	c.(127-138)tggttttctggcdel	p.WFSG43del	KRTAP6-2_ENST00000334897.3_5'Flank	NM_181620.1	NP_853651.1	Q3MIV0	KR221_HUMAN	keratin associated protein 22-1	43						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	8						TGAAAGATCTTGGTTTTCTGGCTGCTTCTGAG	0.462																																					p.42_46del		Atlas-INDEL	.											.	KRTAP22-1	16	.	0			c.126_137del						.																																			SO:0001651	inframe_deletion	337979	exon1			.	AP001708	CCDS13601.1	21q22.1	2011-02-10			ENSG00000186924	ENSG00000186924		"Keratin associated proteins"	18947	protein-coding gene	gene with protein product						12359730	Standard	NM_181620		Approved	KAP22.1	uc011add.2	Q3MIV0	OTTHUMG00000057778	ENST00000334680.2:c.127_138delTGGTTTTCTGGC	chr21.hg19:g.31973566_31973577delTGGTTTTCTGGC	ENSP00000333887:p.Trp43_Gly46del	84.0	0.0		75.0	20.0	NM_181620		In_Frame_Del	DEL	ENST00000334680.2	hg19	CCDS13601.1																																																																																			.	.		0.462	KRTAP22-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128230.2			-	31973577	TGGTTTTCTGGC	-	31973566	7	5	159	1	0	1	0	1	0	0	0	0	8549	1812	63	0	129	0	KRTAP22-1	21	31973566	In_Frame_Del	DEL	TGGTTTTCTGGC	TCGA-DD-AACH-01A-11D-A40R-10		31973566	16156329	93	24160										
BRWD1	54014	hgsc.bcm.edu	37	chr21	40608663	40608663	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ttcttaaaggaggctgcaaaTtgatgcccgcatcagctgtc	10	10	2	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr21:40608663T>C	ENST00000333229.2	-	23	2951	c.2624A>G	c.(2623-2625)aAt>aGt	p.N875S	BRWD1_ENST00000342449.3_Missense_Mutation_p.N875S|BRWD1_ENST00000380800.3_Missense_Mutation_p.N875S	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	875					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				AGGCTGCAAATTGATGCCCGC	0.398																																					p.N875S	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											BRWD1_ENST00000333229,caecum,carcinoma,0,2	BRWD1	325	.	0			c.A2624G						.						114	108	110					21																	40608663		2203	4300	6503	SO:0001583	missense	54014	exon23			TGCAAATTGATGC	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.2624A>G	chr21.hg19:g.40608663T>C	ENSP00000330753:p.Asn875Ser	89.0	0.0		95.0	33.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	hg19	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.517254	0.64634	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.53857	0.6;0.6;0.6	5.32	4.16	0.48862	.	0.134195	0.50627	D	0.000114	T	0.67126	0.2860	M	0.77486	2.375	0.80722	D	1	B;P;B	0.51147	0.013;0.942;0.071	B;P;B	0.58266	0.011;0.836;0.038	T	0.68808	-0.5311	10	0.59425	D	0.04	-6.0218	10.8914	0.46998	0.0:0.0741:0.0:0.9259	.	542;875;875	Q5R2U6;Q9NSI6-2;Q9NSI6	.;.;BRWD1_HUMAN	S	875	ENSP00000330753:N875S;ENSP00000344333:N875S;ENSP00000370178:N875S	ENSP00000330753:N875S	N	-	2	0	BRWD1	39530533	1.000000	0.71417	0.835000	0.33067	0.782000	0.44232	7.527000	0.81931	0.862000	0.35528	0.528000	0.53228	AAT	.	.		0.398	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		C	40608663	T	C	40608663	3	2	159	1	0	0	0	0	1	0	0	0	1527	1493	52	2	4657	2	BRWD1	21	40608663	Missense_Mutation	SNP	T	TCGA-DD-AACH-01A-11D-A40R-10	8635097	40608663	7521232	94	24161										
PES1	23481	hgsc.bcm.edu	37	chr22	30985180	30985180	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cggtccctctatattcacctAaagtcagccaagctcagctg	7	14	4	0			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr22:30985180A>T	ENST00000354694.7	-	2	208	c.102T>A	c.(100-102)ttT>ttA	p.F34L	PES1_ENST00000402284.3_Missense_Mutation_p.F34L|PES1_ENST00000335214.6_Missense_Mutation_p.F34L|PES1_ENST00000405677.1_5'UTR|PES1_ENST00000402281.1_5'UTR	NM_001243225.1|NM_014303.3	NP_001230154.1|NP_055118.1			pescadillo ribosomal biogenesis factor 1											breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	29						ATATTCACCTAAAGTCAGCCA	0.517																																					p.F34L		Atlas-SNP	.											.	PES1	55	.	0			c.T102A						.						61	52	55					22																	30985180		2203	4300	6503	SO:0001583	missense	23481	exon2			TCACCTAAAGTCA	U78310	CCDS13880.1, CCDS58802.1, CCDS74842.1	22q12.1	2012-02-23	2012-02-23		ENSG00000100029	ENSG00000100029			8848	protein-coding gene	gene with protein product		605819	"pescadillo (zebrafish) homolog 1, containing BRCT domain", "pescadillo homolog 1, containing BRCT domain (zebrafish)"			8985183, 10591208, 17353269	Standard	NM_014303		Approved	PES	uc003aij.2	O00541	OTTHUMG00000151077	ENST00000354694.7:c.102T>A	chr22.hg19:g.30985180A>T	ENSP00000346725:p.Phe34Leu	28.0	0.0		62.0	31.0	NM_014303		Missense_Mutation	SNP	ENST00000354694.7	hg19	CCDS13880.1	.	.	.	.	.	.	.	.	.	.	A	32	5.112796	0.94339	.	.	ENSG00000100029	ENST00000354694;ENST00000402284;ENST00000335214;ENST00000433575	T;T;T;T	0.61980	0.06;0.06;0.06;0.06	5.42	4.31	0.51392	.	0.049658	0.85682	D	0.000000	T	0.82208	0.4987	M	0.93062	3.375	0.80722	D	1	D;D;D;D	0.89917	1.0;0.994;0.995;1.0	D;D;P;D	0.91635	0.999;0.972;0.862;0.999	D	0.85171	0.0998	10	0.87932	D	0	-32.7	11.2474	0.49004	0.1004:0.0:0.8996:0.0	.	34;34;34;34	B2RDF2;B5MCF9;O00541-2;O00541	.;.;.;PESC_HUMAN	L	34	ENSP00000346725:F34L;ENSP00000384252:F34L;ENSP00000334612:F34L;ENSP00000388071:F34L	ENSP00000334612:F34L	F	-	3	2	PES1	29315180	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	4.849000	0.62882	1.107000	0.41642	-0.417000	0.06048	TTT	.	.		0.517	PES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321188.3	NM_014303		T	30985180	A	T	30985180	3	4	159	1	0	0	0	0	1	0	0	0	11742	359	13	4	1720	4	PES1	22	30985180	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10		30985180	20319386	95	24162										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40058779	40058779	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cgctccgtcctcctcttgctAgaccctgtgcttccgcgtcc	8	19	1	1			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr22:40058779A>T	ENST00000402142.3	+	18	3372		c.e18-1		CACNA1I_ENST00000407673.1_Splice_Site|CACNA1I_ENST00000404898.1_Splice_Site|CACNA1I_ENST00000336649.4_Splice_Site|CACNA1I_ENST00000401624.1_Splice_Site|CACNA1I_ENST00000400164.3_Splice_Site	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit						axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	TCCTCTTGCTAGACCCTGTGC	0.652																																					.		Atlas-SNP	.											.	CACNA1I	264	.	0			c.3373-2A>T						.						31	34	33					22																	40058779		2174	4262	6436	SO:0001630	splice_region_variant	8911	exon18			CTTGCTAGACCCT	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.3373-1A>T	chr22.hg19:g.40058779A>T		56.0	0.0		42.0	25.0	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Splice_Site	SNP	ENST00000402142.3	hg19	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.101898	0.76983	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3929	0.74760	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1I	38388725	1.000000	0.71417	0.997000	0.53966	0.465000	0.32709	8.925000	0.92832	2.031000	0.59945	0.523000	0.50628	.	.	.		0.652	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	Intron	T	40058779	A	T	40058779	5	4	159	1	0	0	0	0	0	0	1	0	2548	434	15	4	3441	4	CACNA1I	22	40058779	Splice_Site	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	9073599	40058779	11245787	96	24163										
SGSM3	57591	hgsc.bcm.edu	37	chr22	40804805	40804805	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ggtgtcccctcaggttggatGaagatggcaaagtcctgacc	13	10	1	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr22:40804805G>T	ENST00000355630.3	-	0	4496				SGSM3_ENST00000248929.9_Nonsense_Mutation_p.E621*|SGSM3_ENST00000454798.2_Nonsense_Mutation_p.E554*	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1						negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						CAGGTTGGATGAAGATGGCAA	0.662			T	RBM15	acute megakaryocytic leukemia																																p.E621X		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	SGSM3	48	.	0			c.G1861T						.						43	50	47					22																	40804805		2203	4300	6503	SO:0001628	intergenic_variant	27352	exon18			TTGGATGAAGATG	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146		chr22.hg19:g.40804805G>T		72.0	0.0		71.0	29.0	NM_015705	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Nonsense_Mutation	SNP	ENST00000355630.3	hg19	CCDS14003.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.497789|7.497789	0.98322|0.98322	.|.	.|.	ENSG00000100359|ENSG00000100359	ENST00000248929;ENST00000454798;ENST00000427834|ENST00000417424	.|.	.|.	.|.	3.92|3.92	3.92|3.92	0.45320|0.45320	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.87932|.	D|.	0|.	.|.	16.7997|16.7997	0.85611|0.85611	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	621;554;66|3	.|.	ENSP00000248929:E621X|.	E|X	+|+	1|2	0|2	SGSM3|SGSM3	39134751|39134751	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.552000|0.552000	0.35366|0.35366	6.554000|6.554000	0.73923|0.73923	2.145000|2.145000	0.66743|0.66743	0.313000|0.313000	0.20887|0.20887	GAA|TGA	.	.		0.662	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		T	40804805	G	T	40804805	1	4	159	0	1	0	0	0	0	0	0	0	14239	1291	45	3		3	SGSM3	22	40804805	IGR	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	746026	40804805	10499761	97	24164										
EP300	2033	hgsc.bcm.edu	37	chr22	41569712	41569712	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cagcctgagtaggggcaacaAgaagaaacccgggatgccca	13	11	0	3			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr22:41569712A>G	ENST00000263253.7	+	29	5922	c.4703A>G	c.(4702-4704)aAg>aGg	p.K1568R	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1568	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AGGGGCAACAAGAAGAAACCC	0.448			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.K1568R		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.A4703G						.						148	157	154					22																	41569712		2203	4300	6503	SO:0001583	missense	2033	exon29	Familial Cancer Database	Broad Thumb-Hallux syndrome	GCAACAAGAAGAA	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.4703A>G	chr22.hg19:g.41569712A>G	ENSP00000263253:p.Lys1568Arg	259.0	0.0		301.0	115.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.024448	0.93518	.	.	ENSG00000100393	ENST00000263253	D	0.93712	-3.27	5.52	5.52	0.82312	.	0.000000	0.48767	D	0.000170	D	0.96463	0.8846	M	0.78285	2.405	0.46078	D	0.99885	D	0.76494	0.999	D	0.83275	0.996	D	0.96561	0.9415	10	0.52906	T	0.07	-14.6587	15.643	0.77020	1.0:0.0:0.0:0.0	.	1568	Q09472	EP300_HUMAN	R	1568	ENSP00000263253:K1568R	ENSP00000263253:K1568R	K	+	2	0	EP300	39899658	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.237000	0.95368	2.094000	0.63399	0.533000	0.62120	AAG	.	.		0.448	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41569712	A	G	41569712	3	3	159	1	0	0	0	0	1	0	0	0	5150	72	3	2	4817	2	EP300	22	41569712	Missense_Mutation	SNP	A	TCGA-DD-AACH-01A-11D-A40R-10	764907	41569712	9734854	98	24165										
PNPLA5	150379	hgsc.bcm.edu	37	chr22	44285214	44285214	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cagggccagacctacctcgaGgctggggggtatgagacata	15	10	0	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chr22:44285214G>C	ENST00000597664.1	-	4	826	c.697C>G	c.(697-699)Ctc>Gtc	p.L233V	PNPLA5_ENST00000593866.1_Missense_Mutation_p.L119V|PNPLA5_ENST00000216177.4_Missense_Mutation_p.L233V|PNPLA5_ENST00000381198.2_Missense_Mutation_p.L119V			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	233					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)	p.L233I(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				CCTACCTCGAGGCTGGGGGGT	0.577																																					p.L233V		Atlas-SNP	.											PNPLA5,NS,carcinoma,0,1	PNPLA5	46	.	1	Substitution - Missense(1)	lung(1)	c.C697G						.						53	57	56					22																	44285214		2203	4300	6503	SO:0001583	missense	150379	exon4			CCTCGAGGCTGGG	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"Patatin-like phospholipase domain containing"	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.697C>G	chr22.hg19:g.44285214G>C	ENSP00000471069:p.Leu233Val	38.0	0.0		40.0	14.0	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	hg19		.	.	.	.	.	.	.	.	.	.	G	1.095	-0.662893	0.03454	.	.	ENSG00000100341	ENST00000216177;ENST00000381198	T;T	0.79454	-1.27;0.91	4.87	0.232	0.15381	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.693493	0.12851	N	0.433906	T	0.58906	0.2155	N	0.21373	0.66	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39057	-0.9632	10	0.22706	T	0.39	-0.8965	6.233	0.20747	0.2337:0.1337:0.6326:0.0	.	119;233	Q7Z6Z6-2;Q7Z6Z6	.;PLPL5_HUMAN	V	233;119	ENSP00000216177:L233V;ENSP00000370595:L119V	ENSP00000216177:L233V	L	-	1	0	PNPLA5	42616547	0.047000	0.20315	0.000000	0.03702	0.007000	0.05969	1.114000	0.31196	-0.040000	0.13580	0.491000	0.48974	CTC	.	.		0.577	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814		C	44285214	G	C	44285214	3	2	159	1	0	0	0	0	1	0	0	0	12177	1000	35	4	616	4	PNPLA5	22	44285214	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	2715502	44285214	7019352	99	24166										
TCEANC	170082	hgsc.bcm.edu	37	chrX	13680785	13680786	+	Frame_Shift_Del	DEL	AC	AC	-													0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	agatgtggtcagagctgtgtAcagagtcctcaaaaactgcc							TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chrX:13680785_13680786delAC	ENST00000380600.1	+	2	245_246	c.158_159delAC	c.(157-159)tacfs	p.Y53fs	TCEANC_ENST00000545566.1_Frame_Shift_Del_p.Y53fs|TCEANC_ENST00000544987.1_Frame_Shift_Del_p.Y53fs|TCEANC_ENST00000314720.4_Frame_Shift_Del_p.Y83fs|TCEANC_ENST00000490617.1_3'UTR			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	53	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						AGAGCTGTGTACAGAGTCCTCA	0.431																																					p.83_83del		Atlas-INDEL	.											.	TCEANC	29	.	0			c.247_248del						.																																			SO:0001589	frameshift_variant	170082	exon4			.		CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.158_159delAC	chrX.hg19:g.13680785_13680786delAC	ENSP00000369974:p.Tyr53fs	92.0	0.0		113.0	87.0	NM_152634	A6NI06|B2RDM3	Frame_Shift_Del	DEL	ENST00000380600.1	hg19																																																																																				.	.		0.431	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055796.1	NM_152634		-	13680786	AC	-	13680785	7	5	159	1	0	1	0	1	0	0	0	0	15693	391	14	0	254	0	TCEANC	23	13680785	Frame_Shift_Del	DEL	AC	TCGA-DD-AACH-01A-11D-A40R-10		13680785	141589775	100	24167										
FANCB	2187	hgsc.bcm.edu	37	chrX	14863073	14863078	+	In_Frame_Del	DEL	TTAGGA	TTAGGA	-													0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	cacacacaacataacgatctTtaggacagttaccactttct							TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	TTAGGA	TTAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chrX:14863073_14863078delTTAGGA	ENST00000324138.3	-	7	1980_1985	c.1827_1832delTCCTAA	c.(1825-1833)tgtcctaaa>tga	p.609_611CPK>*	FANCB_ENST00000398334.1_In_Frame_Del_p.609_611CPK>*	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	609					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					ATAACGATCTTTAGGACAGTTACCAC	0.35								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.610_611del		Atlas-INDEL	.											.	FANCB	78	.	0			c.1828_1833del						.																																			SO:0001651	inframe_deletion	2187	exon7	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"Fanconi anemia, complementation groups"	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.1827_1832delTCCTAA	chrX.hg19:g.14863073_14863078delTTAGGA	ENSP00000326819:p.Cys609_Lys611delins*	178.0	0.0		98.0	54.0	NM_152633	B2RMZ4|Q7Z2U2|Q86XG1	In_Frame_Del	DEL	ENST00000324138.3	hg19	CCDS14161.1																																																																																			.	.		0.35	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633		-	14863078	TTAGGA	-	14863073	7	5	159	1	0	1	0	1	0	0	0	0	5671	1841	64	0	759	0	FANCB	23	14863073	In_Frame_Del	DEL	TTAGGA	TCGA-DD-AACH-01A-11D-A40R-10	1182288	14863073	140407487	101	24168	109	2								
FANCB	2187	hgsc.bcm.edu	37	chrX	14863080	14863093	+	Frame_Shift_Del	DEL	AGTTACCACTTTCT	AGTTACCACTTTCT	-													0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	aacataacgatctttaggacAgttaccactttctctctcca					rs148560784		TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	AGTTACCACTTTCT	AGTTACCACTTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chrX:14863080_14863093delAGTTACCACTTTCT	ENST00000324138.3	-	7	1965_1978	c.1812_1825delAGAAAGTGGTAACT	c.(1810-1827)agagaaagtggtaactgtfs	p.ESGNC605fs	FANCB_ENST00000398334.1_Frame_Shift_Del_p.ESGNC605fs	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	605					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					TCTTTAGGACAGTTACCACTTTCTCTCTCCATAA	0.355								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.605_609del		Atlas-INDEL	.											.	FANCB	78	.	0			c.1813_1826del						.																																			SO:0001589	frameshift_variant	2187	exon7	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"Fanconi anemia, complementation groups"	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.1812_1825delAGAAAGTGGTAACT	chrX.hg19:g.14863080_14863093delAGTTACCACTTTCT	ENSP00000326819:p.Glu605fs	183.0	0.0		92.0	54.0	NM_152633	B2RMZ4|Q7Z2U2|Q86XG1	Frame_Shift_Del	DEL	ENST00000324138.3	hg19	CCDS14161.1																																																																																			.	.		0.355	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633		-	14863093	AGTTACCACTTTCT	-	14863080	7	5	159	1	0	1	0	1	0	0	0	0	5671	188	7	0	766	0	FANCB	23	14863080	Frame_Shift_Del	DEL	AGTTACCACTTTCT	TCGA-DD-AACH-01A-11D-A40R-10	7	14863080	140407480	102	24169	109	2								
HUWE1	10075	hgsc.bcm.edu	37	chrX	53617377	53617377	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	tagttacctcaggtgactctGccctttgatccattggaata	8	10	2	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chrX:53617377G>A	ENST00000342160.3	-	34	4635	c.4178C>T	c.(4177-4179)gCa>gTa	p.A1393V	HUWE1_ENST00000262854.6_Missense_Mutation_p.A1393V|HUWE1_ENST00000218328.8_Missense_Mutation_p.A1393V			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	1393					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						AGGTGACTCTGCCCTTTGATC	0.423																																					p.A1393V		Atlas-SNP	.											.	HUWE1	724	.	0			c.C4178T						.						185	153	164					X																	53617377		2203	4300	6503	SO:0001583	missense	10075	exon35			GACTCTGCCCTTT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.4178C>T	chrX.hg19:g.53617377G>A	ENSP00000340648:p.Ala1393Val	50.0	0.0		43.0	37.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.518964	0.64634	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328	T;T;T	0.48522	1.13;1.13;0.81	5.93	5.06	0.68205	Armadillo-like helical (1);	0.135447	0.51477	D	0.000087	T	0.40145	0.1105	N	0.14661	0.345	0.41691	D	0.989343	D;P	0.57257	0.979;0.874	P;B	0.49999	0.628;0.443	T	0.24190	-1.0167	10	0.28530	T	0.3	.	14.984	0.71332	0.0:0.1398:0.8602:0.0	.	1393;1393	Q7Z6Z7;Q7Z6Z7-2	HUWE1_HUMAN;.	V	1393	ENSP00000340648:A1393V;ENSP00000262854:A1393V;ENSP00000218328:A1393V	ENSP00000218328:A1393V	A	-	2	0	HUWE1	53634102	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.307000	0.96226	1.247000	0.43917	0.600000	0.82982	GCA	.	.		0.423	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		A	53617377	G	A	53617377	3	1	159	1	0	0	0	0	1	0	0	0	7470	1319	46	3	9146	3	HUWE1	23	53617377	Missense_Mutation	SNP	G	TCGA-DD-AACH-01A-11D-A40R-10	38754297	53617377	101653183	103	24170										
MAGEH1	28986	hgsc.bcm.edu	37	chrX	55478905	55478905	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	3	1	0.616396761133603	1.95192307692308	0	0.181818181818182	0.751940625889747	0	ggcctcagaggcctccgagaCccctatggccgcctctgtgg	13	16	2	2			TCGA-DD-AACH-01A-11D-A40R-10	TCGA-DD-AACH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb4838f-fd57-4ed4-8bc8-5d42e7fb0fac	62e49f6d-fde8-4259-a620-199fc7b700e0	g.chrX:55478905C>A	ENST00000342972.1	+	1	368	c.98C>A	c.(97-99)aCc>aAc	p.T33N	hsa-mir-4536-2_ENST00000583537.1_RNA	NM_014061.3	NP_054780.2	Q9H213	MAGH1_HUMAN	melanoma antigen family H, 1	33	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|skin(2)	15						GCCTCCGAGACCCCTATGGCC	0.642																																					p.T33N		Atlas-SNP	.											.	MAGEH1	37	.	0			c.C98A						.						21	24	23					X																	55478905		2200	4299	6499	SO:0001583	missense	28986	exon1			CCGAGACCCCTAT	AF320912	CCDS14369.1	Xp11.22	2008-02-05			ENSG00000187601	ENSG00000187601			24092	protein-coding gene	gene with protein product		300548				12414813, 9485030	Standard	NM_014061		Approved	APR1	uc004dum.3	Q9H213	OTTHUMG00000021655	ENST00000342972.1:c.98C>A	chrX.hg19:g.55478905C>A	ENSP00000343706:p.Thr33Asn	46.0	0.0		58.0	44.0	NM_014061	B2R8V9|Q5JRJ3|Q9Y5M2	Missense_Mutation	SNP	ENST00000342972.1	hg19	CCDS14369.1	.	.	.	.	.	.	.	.	.	.	.	4.917	0.170395	0.09391	.	.	ENSG00000187601	ENST00000342972	T	0.15256	2.44	3.03	1.25	0.21368	.	0.229983	0.22467	N	0.059668	T	0.07007	0.0178	N	0.08118	0	0.09310	N	1	B	0.24721	0.11	B	0.21360	0.034	T	0.26503	-1.0101	10	0.45353	T	0.12	.	4.7194	0.12912	0.0:0.6853:0.0:0.3147	.	33	Q9H213	MAGH1_HUMAN	N	33	ENSP00000343706:T33N	ENSP00000343706:T33N	T	+	2	0	MAGEH1	55495630	0.007000	0.16637	0.006000	0.13384	0.015000	0.08874	0.171000	0.16685	0.210000	0.20664	0.529000	0.55759	ACC	.	.		0.642	MAGEH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056868.1	NM_014061		A	55478905	C	A	55478905	3	1	159	1	0	0	0	0	1	0	0	0	9197	507	18	3	100	3	MAGEH1	23	55478905	Missense_Mutation	SNP	C	TCGA-DD-AACH-01A-11D-A40R-10	1861528	55478905	99791655	104	24171										
CDK11B	8510	hgsc.bcm.edu	37	chr1	1571767	1571767	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggaggttgttgtaggggtgcTcgctgaaggtcatcttcttg	16	6	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:1571767T>A	ENST00000356026.5	+	0	1326				CDK11B_ENST00000407249.3_Missense_Mutation_p.E668V|CDK11B_ENST00000341832.6_Missense_Mutation_p.E621V|CDK11B_ENST00000317673.7_Missense_Mutation_p.E666V|CDK11B_ENST00000340677.5_Missense_Mutation_p.E655V			O75900	MMP23_HUMAN	matrix metallopeptidase 23B						proteolysis (GO:0006508)|reproduction (GO:0000003)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			large_intestine(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)	Marimastat(DB00786)	GTAGGGGTGCTCGCTGAAGGT	0.592																																					p.E663V		Atlas-SNP	.											.	CDK11B	37	.	0			c.A1988T						.						88	69	75					1																	1571767		1973	4134	6107	SO:0001628	intergenic_variant	984	exon18			GGGTGCTCGCTGA		CCDS30559.1	1p36.3	2013-01-11	2005-08-08		ENSG00000189409	ENSG00000189409		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7171	protein-coding gene	gene with protein product	"matrix metalloproteinase 22", "femalysin", "matrix metalloproteinase in the female reproductive tract"	603321	"matrix metalloproteinase 23B"	MMP22		9740677, 9750192	Standard	XM_005244810		Approved	MIFR, MIFR-1	uc001agp.3	O75900	OTTHUMG00000074713		chr1.hg19:g.1571767T>A		96.0	0.0		91.0	38.0	NM_033486	A2AGN0|A2AGN1|O75894|O75895|Q5QPQ8|Q76P96|Q7LDM6|Q7LDM7|Q9UBR9|Q9UJK8	Missense_Mutation	SNP	ENST00000356026.5	hg19	CCDS30559.1																																																																																			.	.		0.592	MMP23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158492.2	NM_006983		A	1571767	T	A	1571767	1	1	160	0	1	0	0	0	0	0	0	0	3129	1551	54	4		4	CDK11B	1	1571767	IGR	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10		1571767	247678854	1	24172										
ESPN	83715	hgsc.bcm.edu	37	chr1	6500800	6500800	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gctggctgctgctgcacggcGgggagatctcggctgacctg	17	12	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:6500800G>T	ENST00000377828.1	+	4	958	c.790G>T	c.(790-792)Ggg>Tgg	p.G264W	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	264					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GCTGCACGGCGGGGAGATCTC	0.741																																					p.G264W		Atlas-SNP	.											.	ESPN	32	.	0			c.G790T						.						5	5	5					1																	6500800		2003	4015	6018	SO:0001583	missense	83715	exon4			CACGGCGGGGAGA	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"Ankyrin repeat domain containing"	13281	protein-coding gene	gene with protein product		606351	"deafness, autosomal recessive 36"	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.790G>T	chr1.hg19:g.6500800G>T	ENSP00000367059:p.Gly264Trp	759.0	1.0		732.0	277.0	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	hg19	CCDS70.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.585132	0.86748	.	.	ENSG00000187017	ENST00000377828;ENST00000418286	T;T	0.34072	2.36;1.38	3.84	3.84	0.44239	Ankyrin repeat-containing domain (5);	0.237219	0.35466	N	0.003191	T	0.45458	0.1343	L	0.31157	0.91	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	T	0.48293	-0.9048	10	0.87932	D	0	-10.8417	12.6418	0.56714	0.0:0.0:1.0:0.0	.	264	B1AK53	ESPN_HUMAN	W	264;49	ENSP00000367059:G264W;ENSP00000401793:G49W	ENSP00000367059:G264W	G	+	1	0	ESPN	6423387	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.052000	0.76634	1.989000	0.58080	0.430000	0.28490	GGG	.	.		0.741	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		T	6500800	G	T	6500800	3	4	160	1	0	0	0	0	1	0	0	0	5256	1116	39	1	804	1	ESPN	1	6500800	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	4929033	6500800	242749821	2	24173										
H6PD	9563	hgsc.bcm.edu	37	chr1	9324489	9324489	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cctgctgcagcacgtccggaTcccctactacaacatccacc	6	19	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:9324489T>A	ENST00000377403.2	+	5	2239	c.1937T>A	c.(1936-1938)aTc>aAc	p.I646N	H6PD_ENST00000602477.1_Missense_Mutation_p.I657N	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	646	6-phosphogluconolactonase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		CACGTCCGGATCCCCTACTAC	0.657																																					p.I646N		Atlas-SNP	.											.	H6PD	71	.	0			c.T1937A						.						40	43	42					1																	9324489		2203	4295	6498	SO:0001583	missense	9563	exon5			TCCGGATCCCCTA	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"glucose dehyrogenase"	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.1937T>A	chr1.hg19:g.9324489T>A	ENSP00000366620:p.Ile646Asn	155.0	0.0		119.0	12.0	NM_004285	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	hg19	CCDS101.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250853	0.80135	.	.	ENSG00000049239	ENST00000377403	T	0.50813	0.73	5.72	5.72	0.89469	Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1);	0.167672	0.52532	D	0.000080	T	0.68311	0.2987	M	0.88842	2.985	0.34413	D	0.696598	D	0.53885	0.963	P	0.54629	0.757	T	0.82663	-0.0346	10	0.87932	D	0	-33.1888	15.1805	0.72952	0.0:0.0:0.0:1.0	.	646	O95479	G6PE_HUMAN	N	646	ENSP00000366620:I646N	ENSP00000366620:I646N	I	+	2	0	H6PD	9247076	1.000000	0.71417	0.829000	0.32907	0.900000	0.52787	7.592000	0.82676	2.187000	0.69744	0.459000	0.35465	ATC	.	.		0.657	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		A	9324489	T	A	9324489	3	1	160	1	0	0	0	0	1	0	0	0	6945	1435	50	4	1951	4	H6PD	1	9324489	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2823689	9324489	239926132	3	24174										
SPSB1	80176	hgsc.bcm.edu	37	chr1	9416188	9416188	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcatctttcaccggcatccgGtggcccagagcacggacgct	11	15	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:9416188G>A	ENST00000328089.6	+	2	579	c.238G>A	c.(238-240)Gtg>Atg	p.V80M	SPSB1_ENST00000377399.2_Missense_Mutation_p.V80M|SPSB1_ENST00000357898.3_Missense_Mutation_p.V80M	NM_025106.3	NP_079382.2	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box containing 1	80	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(2)|lung(5)|prostate(2)	13	all_lung(157;0.194)	all_epithelial(116;4.38e-15)|all_lung(118;0.000156)|Lung NSC(185;0.000446)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.72e-07)|COAD - Colon adenocarcinoma(227;9.12e-05)|Kidney(185;0.000296)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00193)|BRCA - Breast invasive adenocarcinoma(304;0.00202)|READ - Rectum adenocarcinoma(331;0.0419)		CCGGCATCCGGTGGCCCAGAG	0.582																																					p.V80M		Atlas-SNP	.											SPSB1,right_lower_lobe,carcinoma,0,1	SPSB1	22	.	0			c.G238A						.						153	154	154					1																	9416188		2203	4300	6503	SO:0001583	missense	80176	exon2			CATCCGGTGGCCC		CCDS102.1	1p36.22	2008-02-05			ENSG00000171621	ENSG00000171621			30628	protein-coding gene	gene with protein product		611657				15713673, 12076535	Standard	NM_025106		Approved	SSB-1	uc010oae.2	Q96BD6	OTTHUMG00000001279	ENST00000328089.6:c.238G>A	chr1.hg19:g.9416188G>A	ENSP00000330221:p.Val80Met	129.0	0.0		134.0	13.0	NM_025106	A2A275|Q59FA1|Q5TIH9|Q9BRY9|Q9H6C5	Missense_Mutation	SNP	ENST00000328089.6	hg19	CCDS102.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.665618	0.88251	.	.	ENSG00000171621	ENST00000328089;ENST00000450402;ENST00000357898;ENST00000377399	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.32	5.32	0.75619	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.000000	0.85682	D	0.000000	T	0.80649	0.4663	H	0.94734	3.575	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.85590	0.1245	10	0.56958	D	0.05	-10.2896	17.997	0.89187	0.0:0.0:1.0:0.0	.	80	Q96BD6	SPSB1_HUMAN	M	80	ENSP00000330221:V80M;ENSP00000409235:V80M;ENSP00000350573:V80M;ENSP00000366616:V80M	ENSP00000330221:V80M	V	+	1	0	SPSB1	9338775	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.995000	0.88328	2.485000	0.83878	0.655000	0.94253	GTG	.	.		0.582	SPSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003727.2	NM_025106		A	9416188	G	A	9416188	3	1	160	1	0	0	0	0	1	0	0	0	15127	1261	44	3	240	3	SPSB1	1	9416188	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	91699	9416188	239834433	4	24175										
CLCN6	1185	hgsc.bcm.edu	37	chr1	11897423	11897423	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cactccctaccccaacctatAccctgaccagtccccaagtg	4	20	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:11897423A>G	ENST00000346436.6	+	20	2214	c.2162A>G	c.(2161-2163)tAc>tGc	p.Y721C	CLCN6_ENST00000376496.3_Missense_Mutation_p.Y721C|CLCN6_ENST00000376487.3_Missense_Mutation_p.Y699C|CLCN6_ENST00000312413.6_3'UTR	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	721					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CCCAACCTATACCCTGACCAG	0.587																																					p.Y721C		Atlas-SNP	.											.	CLCN6	77	.	0			c.A2162G						.						132	124	127					1																	11897423		2203	4300	6503	SO:0001583	missense	1185	exon20			ACCTATACCCTGA	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"Ion channels / Chloride channels : Voltage-sensitive"	2024	protein-coding gene	gene with protein product		602726	"chloride channel 6"			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.2162A>G	chr1.hg19:g.11897423A>G	ENSP00000234488:p.Tyr721Cys	83.0	0.0		90.0	9.0	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	hg19	CCDS138.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.147386	0.77888	.	.	ENSG00000011021	ENST00000346436;ENST00000376487;ENST00000376496	D;D;D	0.91843	-2.88;-2.87;-2.92	5.67	5.67	0.87782	.	0.055154	0.85682	D	0.000000	D	0.91452	0.7302	L	0.44542	1.39	0.80722	D	1	D;P	0.53619	0.961;0.934	P;B	0.50378	0.639;0.338	D	0.91017	0.4854	10	0.40728	T	0.16	-28.6138	15.1051	0.72315	1.0:0.0:0.0:0.0	.	699;721	F8W9R3;P51797	.;CLCN6_HUMAN	C	721;699;721	ENSP00000234488:Y721C;ENSP00000365670:Y699C;ENSP00000365679:Y721C	ENSP00000234488:Y721C	Y	+	2	0	CLCN6	11820010	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.962000	0.93254	2.163000	0.67991	0.459000	0.35465	TAC	.	.		0.587	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		G	11897423	A	G	11897423	3	3	160	1	0	0	0	0	1	0	0	0	3469	391	14	2	2250	2	CLCN6	1	11897423	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2481235	11897423	237353198	5	24176										
TNFRSF1B	7133	hgsc.bcm.edu	37	chr1	12251908	12251908	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccggctggtactgcgcgctgAgcaagcaggaggggtgccgg	19	11	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:12251908A>G	ENST00000376259.3	+	4	474	c.385A>G	c.(385-387)Agc>Ggc	p.S129G	TNFRSF1B_ENST00000536782.1_Missense_Mutation_p.S129G|MIR4632_ENST00000584158.1_RNA|TNFRSF1B_ENST00000492361.1_3'UTR	NM_001066.2	NP_001057.1	P20333	TNR1B_HUMAN	tumor necrosis factor receptor superfamily, member 1B	129					aging (GO:0007568)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lipopolysaccharide (GO:0071222)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of inflammatory response (GO:0050728)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|RNA destabilization (GO:0050779)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|varicosity (GO:0043196)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|liver(1)|lung(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)	CTGCGCGCTGAGCAAGCAGGA	0.692																																					p.S129G		Atlas-SNP	.											.	TNFRSF1B	28	.	0			c.A385G						.						25	26	26					1																	12251908		2203	4300	6503	SO:0001583	missense	7133	exon4			GCGCTGAGCAAGC	M32315	CCDS145.1	1p36.22	2008-02-05			ENSG00000028137	ENSG00000028137		"Tumor necrosis factor receptor superfamily", "CD molecules"	11917	protein-coding gene	gene with protein product		191191		TNFR2		2158863, 8702885	Standard	NM_001066		Approved	TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b	uc001att.3	P20333	OTTHUMG00000001829	ENST00000376259.3:c.385A>G	chr1.hg19:g.12251908A>G	ENSP00000365435:p.Ser129Gly	218.0	0.0		174.0	32.0	NM_001066	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Missense_Mutation	SNP	ENST00000376259.3	hg19	CCDS145.1	.	.	.	.	.	.	.	.	.	.	A	10.14	1.267486	0.23136	.	.	ENSG00000028137	ENST00000376259;ENST00000400863;ENST00000536782	T;T	0.73152	0.65;-0.72	4.12	-6.95	0.01628	TNFR/CD27/30/40/95 cysteine-rich region (2);	.	.	.	.	T	0.26122	0.0637	N	0.00142	-2.005	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43637	-0.9379	9	0.25751	T	0.34	0.3146	8.5316	0.33337	0.317:0.1378:0.5452:0.0	.	129	P20333	TNR1B_HUMAN	G	129	ENSP00000365435:S129G;ENSP00000440425:S129G	ENSP00000365435:S129G	S	+	1	0	TNFRSF1B	12174495	0.000000	0.05858	0.000000	0.03702	0.246000	0.25737	-2.446000	0.01010	-1.660000	0.01486	-0.421000	0.06004	AGC	.	.		0.692	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066		G	12251908	A	G	12251908	3	3	160	1	0	0	0	0	1	0	0	0	16309	304	11	2	399	2	TNFRSF1B	1	12251908	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	354485	12251908	236998713	6	24177										
EPHB2	2048	hgsc.bcm.edu	37	chr1	23235588	23235588	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gttcacctcggccagtgatgTgtggagctacggcattgtca	13	10	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:23235588T>C	ENST00000400191.3	+	13	2444	c.2426T>C	c.(2425-2427)gTg>gCg	p.V809A	EPHB2_ENST00000374632.3_Missense_Mutation_p.V810A|EPHB2_ENST00000374630.3_Missense_Mutation_p.V809A|EPHB2_ENST00000374627.1_Missense_Mutation_p.V804A	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	809	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		GCCAGTGATGTGTGGAGCTAC	0.577																																					p.V810A		Atlas-SNP	.											.	EPHB2	257	.	0			c.T2429C						.						133	119	124					1																	23235588		2203	4300	6503	SO:0001583	missense	2048	exon13			GTGATGTGTGGAG	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3393	protein-coding gene	gene with protein product		600997	"EphB2"	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.2426T>C	chr1.hg19:g.23235588T>C	ENSP00000383053:p.Val809Ala	137.0	0.0		112.0	41.0	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	hg19		.	.	.	.	.	.	.	.	.	.	T	17.94	3.511541	0.64522	.	.	ENSG00000133216	ENST00000374625;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	D;D;D;D	0.88124	-2.34;-2.34;-2.34;-2.34	4.96	4.96	0.65561	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.160375	0.40818	N	0.001019	D	0.94817	0.8326	H	0.94385	3.53	0.80722	D	1	D;D;D;B	0.59357	0.983;0.985;0.973;0.415	P;D;D;P	0.75484	0.866;0.986;0.979;0.771	D	0.94918	0.8071	10	0.38643	T	0.18	.	13.64	0.62243	0.0:0.0:0.0:1.0	.	751;809;827;810	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	A	751;809;809;810;804	ENSP00000363761:V809A;ENSP00000383053:V809A;ENSP00000363763:V810A;ENSP00000363758:V804A	ENSP00000363755:V751A	V	+	2	0	EPHB2	23108175	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	3.211000	0.51137	2.088000	0.63022	0.524000	0.50904	GTG	.	.		0.577	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		C	23235588	T	C	23235588	3	2	160	1	0	0	0	0	1	0	0	0	5177	1696	59	2	2479	2	EPHB2	1	23235588	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	10983680	23235588	226015033	7	24178										
PHC2	1912	hgsc.bcm.edu	37	chr1	33794569	33794569	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgcccaccaggtcccgcataTgcatgtcggggagctccagg	13	14	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:33794569T>C	ENST00000257118.5	-	13	2377	c.2324A>G	c.(2323-2325)cAt>cGt	p.H775R	PHC2_ENST00000373418.3_Missense_Mutation_p.H240R|PHC2_ENST00000485928.1_5'UTR|PHC2_ENST00000419414.2_Missense_Mutation_p.H776R|PHC2_ENST00000373422.3_Missense_Mutation_p.H381R|PHC2_ENST00000373416.1_Missense_Mutation_p.H240R|PHC2_ENST00000431992.1_Missense_Mutation_p.H746R|RP11-415J8.3_ENST00000457957.2_RNA	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	775					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GTCCCGCATATGCATGTCGGG	0.577																																					p.H775R		Atlas-SNP	.											.	PHC2	78	.	0			c.A2324G						.						90	87	88					1																	33794569		2203	4300	6503	SO:0001583	missense	1912	exon13			CGCATATGCATGT	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"Sterile alpha motif (SAM) domain containing"	3183	protein-coding gene	gene with protein product		602979	"early development regulator 2 (homolog of polyhomeotic 2)", "polyhomeotic-like 2 (Drosophila)"	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.2324A>G	chr1.hg19:g.33794569T>C	ENSP00000257118:p.His775Arg	58.0	0.0		47.0	11.0	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	hg19	CCDS378.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.43|19.43	3.826442|3.826442	0.71143|0.71143	.|.	.|.	ENSG00000134686|ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000373422;ENST00000373418;ENST00000419414;ENST00000373416|ENST00000307890	T;T;T;T|.	0.40225|.	2.05;1.64;1.04;2.05|.	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	0.255382|.	0.45126|.	D|.	0.000383|.	T|T	0.56775|0.56775	0.2008|0.2008	L|L	0.50333|0.50333	1.59|1.59	0.51012|0.51012	D|D	0.999906|0.999906	D;D;D;D|.	0.76494|.	0.993;0.993;0.993;0.999|.	D;D;D;D|.	0.80764|.	0.977;0.977;0.977;0.994|.	T|T	0.51647|0.51647	-0.8679|-0.8679	10|6	0.16896|0.07325	T|T	0.51|0.83	-23.9181|-23.9181	14.2004|14.2004	0.65699|0.65699	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	776;747;775;190|.	A8KA40;B7ZLY0;Q8IXK0;Q8IXK0-3|.	.;.;PHC2_HUMAN;.|.	R|V	746;775;381;240;776;240|352	ENSP00000389436:H746R;ENSP00000257118:H775R;ENSP00000362521:H381R;ENSP00000391440:H776R|.	ENSP00000257118:H775R|ENSP00000310685:I352V	H|I	-|-	2|1	0|0	PHC2|PHC2	33567156|33567156	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	1.129000|1.129000	0.31381|0.31381	2.237000|2.237000	0.73441|0.73441	0.459000|0.459000	0.35465|0.35465	CAT|ATA	.	.		0.577	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		C	33794569	T	C	33794569	3	2	160	1	0	0	0	0	1	0	0	0	11826	1464	51	2	260	2	PHC2	1	33794569	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	10558981	33794569	215456052	8	24179										
RLF	6018	hgsc.bcm.edu	37	chr1	40701476	40701476	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acttacaggcacaagatgctGgtcttggggtgtcaatttta	11	7	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:40701476G>T	ENST00000372771.4	+	8	1129	c.1102G>T	c.(1102-1104)Ggt>Tgt	p.G368C		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	368					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			ACAAGATGCTGGTCTTGGGGT	0.338																																					p.G368C		Atlas-SNP	.											.	RLF	152	.	0			c.G1102T						.						73	75	74					1																	40701476		2203	4300	6503	SO:0001583	missense	6018	exon8			GATGCTGGTCTTG		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.1102G>T	chr1.hg19:g.40701476G>T	ENSP00000361857:p.Gly368Cys	279.0	0.0		262.0	42.0	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	hg19	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.236631	0.58886	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.46451	0.87	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.68961	0.3058	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.69727	-0.5067	10	0.87932	D	0	-16.009	20.6593	0.99626	0.0:0.0:1.0:0.0	.	61;368	F5H2M5;Q13129	.;RLF_HUMAN	C	368;61	ENSP00000361857:G368C	ENSP00000361857:G368C	G	+	1	0	RLF	40474063	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.827000	0.99397	2.885000	0.99019	0.655000	0.94253	GGT	.	.		0.338	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		T	40701476	G	T	40701476	3	4	160	1	0	0	0	0	1	0	0	0	13404	1348	47	3	1132	3	RLF	1	40701476	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	6906907	40701476	208549145	9	24180										
INADL	10207	hgsc.bcm.edu	37	chr1	62263013	62263013	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atgatgttgttgaagtattaCgaaatgcagggcaggtggta	14	3	0	2	rs200079447		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:62263013C>T	ENST00000371158.2	+	11	1429	c.1315C>T	c.(1315-1317)Cga>Tga	p.R439*	INADL_ENST00000316485.6_Nonsense_Mutation_p.R439*	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	439	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.R439*(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TGAAGTATTACGAAATGCAGG	0.423																																					p.R439X		Atlas-SNP	.											INADL,NS,carcinoma,0,2	INADL	179	.	1	Substitution - Nonsense(1)	pancreas(1)	c.C1315T						.						216	194	201					1																	62263013		2203	4300	6503	SO:0001587	stop_gained	10207	exon11			GTATTACGAAATG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.1315C>T	chr1.hg19:g.62263013C>T	ENSP00000360200:p.Arg439*	107.0	0.0		126.0	46.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Nonsense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	C	35	5.582251	0.96578	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	.	.	.	4.96	3.05	0.35203	.	0.104080	0.38720	N	0.001582	.	.	.	.	.	.	0.42996	D	0.994504	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.0196	0.58779	0.3098:0.6902:0.0:0.0	.	.	.	.	X	439	.	ENSP00000255202:R439X	R	+	1	2	INADL	62035601	0.998000	0.40836	0.014000	0.15608	0.304000	0.27724	1.755000	0.38379	0.652000	0.30806	0.591000	0.81541	CGA	.	C|0.999;T|0.001		0.423	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		T	62263013	C	T	62263013	4	4	160	1	0	0	0	0	0	1	0	0	7740	528	19	1	1353	1	INADL	1	62263013	Nonsense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	21561537	62263013	186987608	10	24181										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67855778	67855778	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gaaattccagatccagcaaaTagcacttgcgctaagaaata	7	9	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:67855778T>C	ENST00000262345.1	+	15	2653	c.2013T>C	c.(2011-2013)aaT>aaC	p.N671N	IL12RB2_ENST00000544434.1_Silent_p.N585N|IL12RB2_ENST00000371000.1_Intron|IL12RB2_ENST00000465396.1_3'UTR|IL12RB2_ENST00000541374.1_Intron	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	671					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						ATCCAGCAAATAGCACTTGCG	0.433																																					p.N671N		Atlas-SNP	.											.	IL12RB2	94	.	0			c.T2013C						.						125	114	117					1																	67855778		2203	4300	6503	SO:0001819	synonymous_variant	3595	exon15			AGCAAATAGCACT	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.2013T>C	chr1.hg19:g.67855778T>C		94.0	0.0		66.0	8.0	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Silent	SNP	ENST00000262345.1	hg19	CCDS638.1																																																																																			.	.		0.433	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		C	67855778	T	C	67855778	2	2	160	1	0	0	0	0	0	0	0	1	7636	1403	49	2		2	IL12RB2	1	67855778	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	5592765	67855778	181394843	11	24182										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79383362	79383362	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctataaaactccaaataaagTtgttttcggtgctaagccaa	6	8	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:79383362T>A	ENST00000370742.3	-	12	1769	c.1706A>T	c.(1705-1707)aAc>aTc	p.N569I		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	569					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		CCAAATAAAGTTGTTTTCGGT	0.284																																					p.N569I		Atlas-SNP	.											.	ELTD1	143	.	0			c.A1706T						.						60	57	58					1																	79383362		1805	4065	5870	SO:0001583	missense	64123	exon12			ATAAAGTTGTTTT	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1706A>T	chr1.hg19:g.79383362T>A	ENSP00000359778:p.Asn569Ile	371.0	0.0		359.0	51.0	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.357362	0.82243	.	.	ENSG00000162618	ENST00000370742;ENST00000401034	T;T	0.45276	0.9;0.9	5.89	5.89	0.94794	GPCR, family 2-like (1);	0.044830	0.85682	D	0.000000	T	0.42607	0.1210	L	0.31845	0.965	0.58432	D	0.999997	D	0.65815	0.995	D	0.67725	0.953	T	0.27157	-1.0082	9	.	.	.	.	16.3123	0.82883	0.0:0.0:0.0:1.0	.	569	Q9HBW9	ELTD1_HUMAN	I	569;27	ENSP00000359778:N569I;ENSP00000383813:N27I	.	N	-	2	0	ELTD1	79155950	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.719000	0.61937	2.254000	0.74563	0.459000	0.35465	AAC	.	.		0.284	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		A	79383362	T	A	79383362	3	1	160	1	0	0	0	0	1	0	0	0	5086	1725	60	4	382	4	ELTD1	1	79383362	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	11527584	79383362	169867259	12	24183										
MCOLN3	55283	hgsc.bcm.edu	37	chr1	85487861	85487861	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttgggcagcgctgcctgaagGgtcaaaatgaggagctggga	17	7	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:85487861G>A	ENST00000370589.2	-	11	1264	c.1212C>T	c.(1210-1212)acC>acT	p.T404T	MCOLN3_ENST00000341115.4_Silent_p.T348T|MCOLN3_ENST00000474447.1_5'UTR|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	404					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		CTGCCTGAAGGGTCAAAATGA	0.478																																					p.T404T		Atlas-SNP	.											.	MCOLN3	74	.	0			c.C1212T						.						82	80	81					1																	85487861		2203	4300	6503	SO:0001819	synonymous_variant	55283	exon11			CTGAAGGGTCAAA	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.1212C>T	chr1.hg19:g.85487861G>A		208.0	0.0		212.0	82.0	NM_018298	Q5T4H5|Q5T4H6|Q9NV09	Silent	SNP	ENST00000370589.2	hg19	CCDS701.1																																																																																			.	.		0.478	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		A	85487861	G	A	85487861	2	1	160	1	0	0	0	0	0	0	0	1	9406	1219	43	3		3	MCOLN3	1	85487861	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	6104499	85487861	163762760	13	24184										
PKN2	5586	hgsc.bcm.edu	37	chr1	89226006	89226006	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aattggatatagaacttaaaGtaaaacaaggtgcagagaat	9	3	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:89226006G>A	ENST00000370521.3	+	3	810	c.451G>A	c.(451-453)Gta>Ata	p.V151I	PKN2_ENST00000370505.3_5'UTR|PKN2_ENST00000370513.5_Missense_Mutation_p.V151I|PKN2_ENST00000316005.7_Missense_Mutation_p.V151I	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	151					apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		AGAACTTAAAGTAAAACAAGG	0.333																																					p.V151I		Atlas-SNP	.											.	PKN2	109	.	0			c.G451A						.						91	95	94					1																	89226006		1817	4068	5885	SO:0001583	missense	5586	exon3			CTTAAAGTAAAAC	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"cardiolipin-activated protein kinase Pak2"	602549	"protein kinase C-like 2"	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.451G>A	chr1.hg19:g.89226006G>A	ENSP00000359552:p.Val151Ile	345.0	0.0		325.0	129.0	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	hg19	CCDS714.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.895418	0.91962	.	.	ENSG00000065243	ENST00000370521;ENST00000316005;ENST00000370513	T;T;T	0.16196	2.36;2.36;2.36	4.5	4.5	0.54988	.	0.000000	0.40469	U	0.001090	T	0.39708	0.1088	M	0.91406	3.205	0.80722	D	1	P;P;P;P	0.51147	0.933;0.776;0.942;0.638	P;P;P;B	0.59288	0.855;0.598;0.778;0.348	T	0.53556	-0.8422	10	0.59425	D	0.04	.	17.5792	0.87960	0.0:0.0:1.0:0.0	.	151;151;151;151	B4DTP5;E7ESL7;Q16513;B1AL79	.;.;PKN2_HUMAN;.	I	151	ENSP00000359552:V151I;ENSP00000317851:V151I;ENSP00000359544:V151I	ENSP00000317851:V151I	V	+	1	0	PKN2	88998594	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.586000	0.82596	2.218000	0.71995	0.591000	0.81541	GTA	.	.		0.333	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		A	89226006	G	A	89226006	3	1	160	1	0	0	0	0	1	0	0	0	11989	1029	36	3	461	3	PKN2	1	89226006	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	3738145	89226006	160024615	14	24185										
EVI5	7813	hgsc.bcm.edu	37	chr1	93131551	93131551	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tattttctgtgcgtaacctcTgccaagaaaaaaaaagtttt	6	7	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:93131551T>G	ENST00000370331.1	-	11	1300		c.e11-2		EVI5_ENST00000543509.1_Splice_Site|EVI5_ENST00000540033.1_Splice_Site|EVI5_ENST00000491940.1_5'Flank	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5						cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		GCGTAACCTCTGCCAAGAAAA	0.323																																					.		Atlas-SNP	.											.	EVI5	94	.	0			c.1291-2A>C						.						101	100	100					1																	93131551		2202	4298	6500	SO:0001630	splice_region_variant	7813	exon12			AACCTCTGCCAAG	AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1291-2A>C	chr1.hg19:g.93131551T>G		46.0	0.0		58.0	12.0	NM_005665	A6NKX8|B9A6J0|Q9H1Y9	Splice_Site	SNP	ENST00000370331.1	hg19	CCDS30774.1	.	.	.	.	.	.	.	.	.	.	T	18.40	3.616173	0.66672	.	.	ENSG00000067208	ENST00000370331;ENST00000540033;ENST00000543509;ENST00000338689	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8205	0.70068	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EVI5	92904139	1.000000	0.71417	0.983000	0.44433	0.924000	0.55760	7.405000	0.80007	1.887000	0.54652	0.477000	0.44152	.	.	.		0.323	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665	Intron	G	93131551	T	G	93131551	5	3	160	1	0	0	0	0	0	0	1	0	5291	1594	55	5	1175	5	EVI5	1	93131551	Splice_Site	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	3905545	93131551	156119070	15	24186										
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95330430	95330430	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tccgagaatcattgtcatgtAcatgcaaaacgcactgaaag	8	9	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:95330430A>T	ENST00000271227.6	+	11	1472	c.1370A>T	c.(1369-1371)tAc>tTc	p.Y457F	SLC44A3_ENST00000532427.1_Missense_Mutation_p.Y377F|SLC44A3_ENST00000446120.2_Missense_Mutation_p.Y421F|SLC44A3_ENST00000529450.1_Missense_Mutation_p.Y425F|SLC44A3_ENST00000467909.1_Missense_Mutation_p.Y409F|SLC44A3_ENST00000527077.1_Missense_Mutation_p.Y389F|SLC44A3_ENST00000530397.1_3'UTR	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	457					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	ATTGTCATGTACATGCAAAAC	0.428																																					p.Y457F		Atlas-SNP	.											.	SLC44A3	109	.	0			c.A1370T						.						205	191	196					1																	95330430		2203	4300	6503	SO:0001583	missense	126969	exon11			TCATGTACATGCA	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"Solute carriers"	28689	protein-coding gene	gene with protein product			"solute carrier family, member 3"			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.1370A>T	chr1.hg19:g.95330430A>T	ENSP00000271227:p.Tyr457Phe	46.0	0.0		48.0	5.0	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	hg19	CCDS44176.1	.	.	.	.	.	.	.	.	.	.	A	12.55	1.971662	0.34754	.	.	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427	T;T;T;T;T;T	0.26067	1.76;1.76;1.76;1.76;1.76;1.76	5.84	-2.67	0.06059	.	0.974275	0.08449	N	0.944221	T	0.10723	0.0262	M	0.67625	2.065	0.19775	N	0.999955	B;B;B;B;B	0.22080	0.015;0.064;0.015;0.015;0.003	B;B;B;B;B	0.29716	0.018;0.106;0.018;0.018;0.012	T	0.47971	-0.9075	10	0.72032	D	0.01	0.2618	4.3337	0.11076	0.4195:0.1013:0.3807:0.0984	.	377;421;389;425;457	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	F	421;457;389;425;409;377	ENSP00000389143:Y421F;ENSP00000271227:Y457F;ENSP00000433641:Y389F;ENSP00000431836:Y425F;ENSP00000432789:Y409F;ENSP00000436661:Y377F	ENSP00000271227:Y457F	Y	+	2	0	SLC44A3	95103018	0.077000	0.21312	0.000000	0.03702	0.001000	0.01503	0.621000	0.24418	-0.785000	0.04522	-0.408000	0.06270	TAC	.	.		0.428	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		T	95330430	A	T	95330430	3	4	160	1	0	0	0	0	1	0	0	0	14652	391	14	4	1412	4	SLC44A3	1	95330430	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2198879	95330430	153920191	16	24187										
RSBN1	54665	hgsc.bcm.edu	37	chr1	114354782	114354782	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agatcggcgctgccgtttaaCtccccgcggggagaccccag	13	15	0	2	rs372385428		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:114354782C>G	ENST00000261441.5	-	1	316	c.253G>C	c.(253-255)Gtt>Ctt	p.V85L	RP5-1073O3.2_ENST00000418238.1_RNA|RP5-1073O3.2_ENST00000429398.1_RNA	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	85						nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGCCGTTTAACTCCCCGCGGG	0.711																																					p.V85L		Atlas-SNP	.											.	RSBN1	71	.	0			c.G253C						.						23	33	29					1																	114354782		2170	4286	6456	SO:0001583	missense	54665	exon1			GTTTAACTCCCCG	AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.253G>C	chr1.hg19:g.114354782C>G	ENSP00000261441:p.Val85Leu	70.0	0.0		61.0	11.0	NM_018364	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Missense_Mutation	SNP	ENST00000261441.5	hg19	CCDS862.1	.	.	.	.	.	.	.	.	.	.	C	18.26	3.583608	0.65992	.	.	ENSG00000081019	ENST00000261441	.	.	.	5.11	4.12	0.48240	.	0.365028	0.20479	N	0.091528	T	0.08358	0.0208	N	0.08118	0	0.25877	N	0.983638	B	0.26147	0.143	B	0.27608	0.081	T	0.08911	-1.0699	9	0.52906	T	0.07	-6.5303	7.6603	0.28400	0.0:0.8848:0.0:0.1152	.	85	Q5VWQ0	RSBN1_HUMAN	L	85	.	ENSP00000261441:V85L	V	-	1	0	RSBN1	114156305	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	1.356000	0.34079	2.659000	0.90383	0.561000	0.74099	GTT	.	.		0.711	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364		G	114354782	C	G	114354782	3	3	160	1	0	0	0	0	1	0	0	0	13711	565	20	4	2183	4	RSBN1	1	114354782	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	19024352	114354782	134895839	17	24188										
CRNN	49860	hgsc.bcm.edu	37	chr1	152382558	152382558	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctggctggtctggctcctgcCttgaccgtggatctcagtcc	12	14	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:152382558C>A	ENST00000271835.3	-	3	1062	c.1000G>T	c.(1000-1002)Ggc>Tgc	p.G334C	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	334	Gln-rich.				response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGCTCCTGCCTTGACCGTGG	0.592																																					p.G334C		Atlas-SNP	.											.	CRNN	78	.	0			c.G1000T						.						235	207	216					1																	152382558		2203	4300	6503	SO:0001583	missense	49860	exon3			TCCTGCCTTGACC	AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"EF-hand domain containing"	1230	protein-coding gene	gene with protein product		611312	"chromosome 1 open reading frame 10"	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.1000G>T	chr1.hg19:g.152382558C>A	ENSP00000271835:p.Gly334Cys	147.0	0.0		308.0	56.0	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	hg19	CCDS1010.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.457724	0.43634	.	.	ENSG00000143536	ENST00000271835	T	0.05139	3.49	4.61	2.66	0.31614	.	0.860398	0.10200	N	0.703486	T	0.02571	0.0078	L	0.29908	0.895	0.09310	N	1	D	0.59357	0.985	P	0.46796	0.527	T	0.45190	-0.9278	10	0.59425	D	0.04	.	6.5679	0.22523	0.0:0.716:0.1827:0.1013	.	334	Q9UBG3	CRNN_HUMAN	C	334	ENSP00000271835:G334C	ENSP00000271835:G334C	G	-	1	0	CRNN	150649182	0.001000	0.12720	0.022000	0.16811	0.017000	0.09413	-0.201000	0.09464	1.122000	0.41944	0.536000	0.68110	GGC	.	.		0.592	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190		A	152382558	C	A	152382558	3	1	160	1	0	0	0	0	1	0	0	0	3894	681	24	3	491	3	CRNN	1	152382558	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	38027776	152382558	96868063	18	24189										
SPRR2A	6700	hgsc.bcm.edu	37	chr1	153029021	153029021	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcttcggtggatactttgacTggcagggtggggaaggtgtc	17	6	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:153029021T>A	ENST00000392653.2	-	2	276	c.191A>T	c.(190-192)cAg>cTg	p.Q64L		NM_005988.2	NP_005979.1	P35326	SPR2A_HUMAN	small proline-rich protein 2A	64					epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				large_intestine(2)|ovary(1)	3	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ATACTTTGACTGGCAGGGTGG	0.537																																					p.Q64L		Atlas-SNP	.											.	SPRR2A	9	.	0			c.A191T						.						227	209	216					1																	153029021		2203	4300	6503	SO:0001583	missense	6700	exon2			TTTGACTGGCAGG	X53064	CCDS1034.1	1q21-q22	2008-02-05			ENSG00000241794	ENSG00000241794			11261	protein-coding gene	gene with protein product		182267				8325635	Standard	NM_005988		Approved		uc001fbd.3	P35326	OTTHUMG00000014395	ENST00000392653.2:c.191A>T	chr1.hg19:g.153029021T>A	ENSP00000376423:p.Gln64Leu	85.0	0.0		170.0	11.0	NM_005988	B2R4T3|D3DV35|Q5T529	Missense_Mutation	SNP	ENST00000392653.2	hg19	CCDS1034.1	.	.	.	.	.	.	.	.	.	.	T	9.305	1.054054	0.19907	.	.	ENSG00000241794	ENST00000392653	T	0.33865	1.39	2.83	2.83	0.33086	.	0.000000	0.33670	N	0.004669	T	0.31949	0.0813	.	.	.	0.23739	N	0.996973	P	0.51449	0.945	P	0.56648	0.803	T	0.05289	-1.0894	9	0.87932	D	0	.	7.3682	0.26785	0.0:0.0:0.0:1.0	.	64	P35326	SPR2A_HUMAN	L	64	ENSP00000376423:Q64L	ENSP00000376423:Q64L	Q	-	2	0	SPRR2A	151295645	0.991000	0.36638	0.969000	0.41365	0.053000	0.15095	3.196000	0.51020	1.274000	0.44362	0.334000	0.21626	CAG	.	.		0.537	SPRR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040049.1	NM_005988		A	153029021	T	A	153029021	3	1	160	1	0	0	0	0	1	0	0	0	15112	1580	55	4	31	4	SPRR2A	1	153029021	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	646463	153029021	96221600	19	24190										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154744565	154744565	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcatgacaaagcgggtgttgAagttgatcttgttgagggcc	14	6	2	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:154744565A>G	ENST00000271915.4	-	3	1649	c.1334T>C	c.(1333-1335)tTc>tCc	p.F445S	KCNN3_ENST00000358505.2_Missense_Mutation_p.F132S|KCNN3_ENST00000361147.4_Missense_Mutation_p.F140S	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	450					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	GCGGGTGTTGAAGTTGATCTT	0.577																																					p.F445S		Atlas-SNP	.											.	KCNN3	141	.	0			c.T1334C						.						142	106	118					1																	154744565		2203	4300	6503	SO:0001583	missense	3782	exon3			GTGTTGAAGTTGA	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.1334T>C	chr1.hg19:g.154744565A>G	ENSP00000271915:p.Phe445Ser	105.0	0.0		226.0	10.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	A	17.04	3.288440	0.59976	.	.	ENSG00000143603	ENST00000361147;ENST00000271915;ENST00000358505	D;D;D	0.98901	-5.22;-4.06;-5.22	4.66	4.66	0.58398	.	0.000000	0.56097	D	0.000021	D	0.99013	0.9663	M	0.84511	2.7	0.80722	D	1	D;D;D	0.76494	0.999;0.995;0.995	D;D;D	0.80764	0.994;0.979;0.962	D	0.99793	1.1032	10	0.87932	D	0	-16.2721	13.9313	0.63998	1.0:0.0:0.0:0.0	.	451;450;140	Q6JXY2;Q9UGI6;Q9UGI6-2	.;KCNN3_HUMAN;.	S	140;445;132	ENSP00000354764:F140S;ENSP00000271915:F445S;ENSP00000351295:F132S	ENSP00000271915:F445S	F	-	2	0	KCNN3	153011189	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.135000	0.94478	1.954000	0.56735	0.459000	0.35465	TTC	.	.		0.577	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		G	154744565	A	G	154744565	3	3	160	1	0	0	0	0	1	0	0	0	8089	246	9	2	885	2	KCNN3	1	154744565	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1715544	154744565	94506056	20	24191										
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156496381	156496381	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccacaccctcatactggagcTgcaggagatcctaggaggga	12	12	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:156496381T>A	ENST00000361170.2	-	38	4803	c.4793A>T	c.(4792-4794)cAg>cTg	p.Q1598L	snoU13_ENST00000458777.1_RNA	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1598					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ATACTGGAGCTGCAGGAGATC	0.493																																					p.Q1598L		Atlas-SNP	.											.	IQGAP3	146	.	0			c.A4793T						.						77	69	72					1																	156496381		2203	4300	6503	SO:0001583	missense	128239	exon38			TGGAGCTGCAGGA	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.4793A>T	chr1.hg19:g.156496381T>A	ENSP00000354451:p.Gln1598Leu	66.0	0.0		116.0	10.0	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	hg19	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.650199	0.87958	.	.	ENSG00000183856	ENST00000361170	T	0.03580	3.88	4.76	4.76	0.60689	.	0.066807	0.64402	D	0.000007	T	0.13200	0.0320	M	0.89715	3.055	0.58432	D	0.999998	D	0.63046	0.992	D	0.63381	0.914	T	0.00907	-1.1519	10	0.87932	D	0	-21.9106	13.2453	0.60020	0.0:0.0:0.0:1.0	.	1598	Q86VI3	IQGA3_HUMAN	L	1598	ENSP00000354451:Q1598L	ENSP00000354451:Q1598L	Q	-	2	0	IQGAP3	154763005	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.799000	0.85936	2.003000	0.58678	0.459000	0.35465	CAG	.	.		0.493	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		A	156496381	T	A	156496381	3	1	160	1	0	0	0	0	1	0	0	0	7825	1580	55	4	106	4	IQGAP3	1	156496381	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1751816	156496381	92754240	21	24192										
GPATCH4	54865	hgsc.bcm.edu	37	chr1	156565217	156565217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctccaagacccccatcttctCctcttcatggtgccacctct	4	19	5	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:156565217C>T	ENST00000438976.2	-	8	946	c.916G>A	c.(916-918)Gag>Aag	p.E306K	GPATCH4_ENST00000368232.4_Missense_Mutation_p.E301K|GPATCH4_ENST00000497287.1_5'Flank			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	301							poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(3)|stomach(1)	17	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCCATCTTCTCCTCTTCATGG	0.537																																					p.E306K		Atlas-SNP	.											.	GPATCH4	34	.	0			c.G916A						.						243	235	238					1																	156565217		2203	4300	6503	SO:0001583	missense	54865	exon8			TCTTCTCCTCTTC	BC056904	CCDS1146.1, CCDS44245.1	1q22	2013-01-28		2006-12-13	ENSG00000160818	ENSG00000160818		"G patch domain containing"	25982	protein-coding gene	gene with protein product				GPATC4		12477932	Standard	NM_015590		Approved	FLJ20249, DKFZP434F1735	uc001fpl.3	Q5T3I0	OTTHUMG00000033203	ENST00000438976.2:c.916G>A	chr1.hg19:g.156565217C>T	ENSP00000396441:p.Glu306Lys	110.0	0.0		236.0	12.0	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Missense_Mutation	SNP	ENST00000438976.2	hg19	CCDS44245.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.032211	0.54790	.	.	ENSG00000160818	ENST00000368232;ENST00000368229;ENST00000438976	T;T	0.43294	0.95;0.95	4.84	3.89	0.44902	.	3.316370	0.00695	N	0.000747	T	0.19805	0.0476	L	0.42245	1.32	0.53005	D	0.999969	B;B	0.17465	0.022;0.022	B;B	0.10450	0.005;0.005	T	0.16689	-1.0394	10	0.14656	T	0.56	-19.8176	10.8507	0.46769	0.0:0.8993:0.0:0.1007	.	306;301	E9PAV9;Q5T3I0	.;GPTC4_HUMAN	K	301;301;306	ENSP00000357215:E301K;ENSP00000396441:E306K	ENSP00000357212:E301K	E	-	1	0	GPATCH4	154831841	0.000000	0.05858	0.046000	0.18839	0.763000	0.43281	-0.805000	0.04530	1.284000	0.44531	0.557000	0.71058	GAG	.	.		0.537	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725		T	156565217	C	T	156565217	3	4	160	1	0	0	0	0	1	0	0	0	6601	864	30	3	215	3	GPATCH4	1	156565217	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	68836	156565217	92685404	22	24193										
NES	10763	hgsc.bcm.edu	37	chr1	156640722	156640722	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gactcacccatggcaggctcTgaccccaacatgacctctgg	9	16	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:156640722T>A	ENST00000368223.3	-	4	3390	c.3258A>T	c.(3256-3258)tcA>tcT	p.S1086S		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1086	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGGCAGGCTCTGACCCCAACA	0.682																																					p.S1086S		Atlas-SNP	.											.	NES	196	.	0			c.A3258T						.						23	26	25					1																	156640722		2202	4289	6491	SO:0001819	synonymous_variant	10763	exon4			AGGCTCTGACCCC	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3258A>T	chr1.hg19:g.156640722T>A		152.0	0.0		318.0	22.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	hg19	CCDS1151.1																																																																																			.	.		0.682	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		A	156640722	T	A	156640722	2	1	160	1	0	0	0	0	0	0	0	1	10346	1567	55	4		4	NES	1	156640722	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	75505	156640722	92609899	23	24194										
ISG20L2	81875	hgsc.bcm.edu	37	chr1	156697395	156697395	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tggcatttccttctaatgccTttttgggaggaggttcccca	10	10	1	0	rs35218759		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:156697395T>A	ENST00000313146.6	-	1	832	c.50A>T	c.(49-51)aAg>aTg	p.K17M	RRNAD1_ENST00000368216.4_5'Flank|ISG20L2_ENST00000368219.1_Missense_Mutation_p.K17M|RRNAD1_ENST00000368218.4_5'Flank|ISG20L2_ENST00000472824.2_5'Flank|RRNAD1_ENST00000524343.1_5'Flank	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene 20kDa-like 2	17					ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTCTAATGCCTTTTTGGGAGG	0.463																																					p.K17M		Atlas-SNP	.											.	ISG20L2	43	.	0			c.A50T						.						70	78	75					1																	156697395		2203	4300	6503	SO:0001583	missense	81875	exon1			AATGCCTTTTTGG	AK095697	CCDS1153.1	1q23.1	2013-10-11			ENSG00000143319	ENSG00000143319			25745	protein-coding gene	gene with protein product		611930				18065403	Standard	NM_030980		Approved	FLJ12671	uc001fps.1	Q9H9L3	OTTHUMG00000041301	ENST00000313146.6:c.50A>T	chr1.hg19:g.156697395T>A	ENSP00000323424:p.Lys17Met	38.0	0.0		112.0	13.0	NM_030980	D3DVC6|Q64KA2	Missense_Mutation	SNP	ENST00000313146.6	hg19	CCDS1153.1	.	.	.	.	.	.	.	.	.	.	T	19.90	3.913471	0.72983	.	.	ENSG00000143319	ENST00000313146;ENST00000368219	T;T	0.33654	1.4;1.4	5.41	4.28	0.50868	.	.	.	.	.	T	0.23965	0.0580	L	0.34521	1.04	0.33313	D	0.566358	D	0.67145	0.996	P	0.54499	0.754	T	0.13575	-1.0504	9	0.72032	D	0.01	-13.1106	8.1337	0.31041	0.0:0.0895:0.0:0.9105	.	17	Q9H9L3	I20L2_HUMAN	M	17	ENSP00000323424:K17M;ENSP00000357202:K17M	ENSP00000323424:K17M	K	-	2	0	ISG20L2	154964019	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	2.179000	0.42528	1.058000	0.40530	0.533000	0.62120	AAG	.	.		0.463	ISG20L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098969.1	NM_030980		A	156697395	T	A	156697395	3	1	160	1	0	0	0	0	1	0	0	0	7864	1609	56	4	1023	4	ISG20L2	1	156697395	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	56673	156697395	92553226	24	24195										
KIRREL	55243	hgsc.bcm.edu	37	chr1	158064686	158064686	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acacaaccagccagctgtccTacgagaactatgagaagttc	8	12	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:158064686T>A	ENST00000359209.6	+	15	2117	c.2050T>A	c.(2050-2052)Tac>Aac	p.Y684N	KIRREL_ENST00000368172.1_Missense_Mutation_p.Y498N|KIRREL_ENST00000360089.4_Missense_Mutation_p.Y520N|KIRREL_ENST00000392272.2_Missense_Mutation_p.Y581N|KIRREL_ENST00000368173.3_Missense_Mutation_p.Y700N|KIRREL_ENST00000416935.2_Missense_Mutation_p.Y584N			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	684					excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					CCAGCTGTCCTACGAGAACTA	0.647																																					p.Y684N		Atlas-SNP	.											.	KIRREL	346	.	0			c.T2050A						.						51	53	52					1																	158064686		2203	4300	6503	SO:0001583	missense	55243	exon15			CTGTCCTACGAGA	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15734	protein-coding gene	gene with protein product	"nephrin-like protein 1"	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.2050T>A	chr1.hg19:g.158064686T>A	ENSP00000352138:p.Tyr684Asn	242.0	0.0		429.0	35.0	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Missense_Mutation	SNP	ENST00000359209.6	hg19	CCDS1172.2	.	.	.	.	.	.	.	.	.	.	T	17.45	3.391766	0.62066	.	.	ENSG00000183853	ENST00000360089;ENST00000368173;ENST00000392272;ENST00000359209;ENST00000416935;ENST00000368172	T;T;T;T;T;T	0.73469	0.23;-0.75;-0.13;-0.38;-0.29;0.07	4.76	4.76	0.60689	.	0.000000	0.39274	N	0.001420	T	0.65481	0.2695	N	0.24115	0.695	0.53005	D	0.99996	D;D;D;D	0.71674	0.998;0.996;0.978;0.996	D;P;P;P	0.63488	0.915;0.853;0.758;0.853	T	0.66528	-0.5901	10	0.28530	T	0.3	-13.5334	12.2244	0.54451	0.0:0.0:0.0:1.0	.	584;520;498;684	B4DN67;Q5W0F9;Q5W0G0;Q96J84	.;.;.;KIRR1_HUMAN	N	520;700;581;684;584;498	ENSP00000353202:Y520N;ENSP00000357155:Y700N;ENSP00000376098:Y581N;ENSP00000352138:Y684N;ENSP00000389674:Y584N;ENSP00000357154:Y498N	ENSP00000352138:Y684N	Y	+	1	0	KIRREL	156331310	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.577000	0.67444	1.765000	0.52091	0.459000	0.35465	TAC	.	.		0.647	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240		A	158064686	T	A	158064686	3	1	160	1	0	0	0	0	1	0	0	0	8333	1522	53	4	2108	4	KIRREL	1	158064686	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1367291	158064686	91185935	25	24196										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158592934	158592934	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtccttcaggtcagtgatctCgggaagtctctcttgctgga	12	10	5	1	rs533909383		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:158592934C>A	ENST00000368147.4	-	43	6139	c.5959G>T	c.(5959-5961)Gag>Tag	p.E1987*		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1987					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TCAGTGATCTCGGGAAGTCTC	0.498																																					p.E1987X		Atlas-SNP	.											.	SPTA1	720	.	0			c.G5959T						.						292	295	294					1																	158592934		1927	4133	6060	SO:0001587	stop_gained	6708	exon43			TGATCTCGGGAAG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5959G>T	chr1.hg19:g.158592934C>A	ENSP00000357129:p.Glu1987*	182.0	0.0		391.0	39.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Nonsense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	44	10.671078	0.99447	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	.	.	.	4.78	2.7	0.31948	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	6.4875	0.22097	0.0:0.5424:0.0:0.4576	.	.	.	.	X	1987;1984	.	ENSP00000357129:E1984X	E	-	1	0	SPTA1	156859558	0.977000	0.34250	0.436000	0.26797	0.304000	0.27724	1.767000	0.38501	0.422000	0.26005	0.655000	0.94253	GAG	.	.		0.498	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158592934	C	A	158592934	4	1	160	1	0	0	0	0	0	1	0	0	15131	893	31	1	1340	1	SPTA1	1	158592934	Nonsense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	528248	158592934	90657687	26	24197										
VSIG8	391123	hgsc.bcm.edu	37	chr1	159825697	159825698	+	Missense_Mutation	DNP	CA	CA	GT													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctcactagccaagtcgccgCaggcccctccgccgaccccg							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:159825697_159825698CA>GT	ENST00000368100.1	-	6	1081_1082	c.946_947TG>AC	c.(946-948)TGc>ACc	p.C316T	C1orf204_ENST00000491974.1_5'Flank|C1orf204_ENST00000368102.1_5'Flank	NM_001013661.1	NP_001013683.1	Q5VU13	VSIG8_HUMAN	V-set and immunoglobulin domain containing 8	316						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	8	all_hematologic(112;0.0597)					CAAgtcgccgcaggcccctccg	0.713																																					p.C316S		Atlas-SNP	.											.	VSIG8	24	.	0			c.G947C|c.T946A						.																																			SO:0001583	missense	391123	exon6			TCGCCGCAGGCCC|CGCCGCAGGCCCC		CCDS30913.1	1q23.2	2013-01-11			ENSG00000243284	ENSG00000243284		"Immunoglobulin superfamily / V-set domain containing"	32063	protein-coding gene	gene with protein product							Standard	NM_001013661		Approved		uc001fuh.3	Q5VU13	OTTHUMG00000168834	ENST00000368100.1:c.946_947delinsGT	chr1.hg19:g.159825697_159825698delinsGT	ENSP00000357080:p.Cys316Thr	52.0|55.0	0.0		157.0	27.0|28.0	NM_001013661	Q5VU14	Missense_Mutation	SNP	ENST00000368100.1	hg19	CCDS30913.1																																																																																			.	.		0.713	VSIG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085978.8	NM_001013661		GT	159825698	CA	GT	159825697	3	3	160	1	0	0	0	0	1	0	0	0	17241	710	25	4	305	4	VSIG8	1	159825697	Missense_Mutation	DNP	CA	TCGA-DD-AACI-01A-11D-A40R-10	1232763	159825697	89424924	27	24198										
NDUFS2	4720	hgsc.bcm.edu	37	chr1	161180452	161180452	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gccctatgatgtttacgaccAggttgagtttgatgttcctg	11	8	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:161180452A>T	ENST00000367993.3	+	10	1386	c.938A>T	c.(937-939)cAg>cTg	p.Q313L	NDUFS2_ENST00000476409.2_Missense_Mutation_p.Q215L|NDUFS2_ENST00000392179.4_Missense_Mutation_p.Q313L|NDUFS2_ENST00000465923.1_3'UTR	NM_004550.4	NP_004541.1	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)	313					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|quinone binding (GO:0048038)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	18	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Doxorubicin(DB00997)	GTTTACGACCAGGTTGAGTTT	0.532																																					p.Q313L		Atlas-SNP	.											.	NDUFS2	33	.	0			c.A938T						.						152	119	130					1																	161180452		2203	4300	6503	SO:0001583	missense	4720	exon9			ACGACCAGGTTGA	BC008868	CCDS1224.1, CCDS53404.1	1q23.3	2011-07-04	2002-08-29		ENSG00000158864	ENSG00000158864	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7708	protein-coding gene	gene with protein product	"complex I 49kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial"	602985	"NADH dehydrogenase (ubiquinone) Fe-S protein 2 (49kD) (NADH-coenzyme Q reductase)"			1832859, 9585441	Standard	NM_004550		Approved	CI-49	uc001fyw.3	O75306	OTTHUMG00000034344	ENST00000367993.3:c.938A>T	chr1.hg19:g.161180452A>T	ENSP00000356972:p.Gln313Leu	145.0	0.0		321.0	22.0	NM_001166159	D3DVG7|J3KPM7|Q5VTW0|Q969P3|Q9UEV3	Missense_Mutation	SNP	ENST00000367993.3	hg19	CCDS1224.1	.	.	.	.	.	.	.	.	.	.	A	15.58	2.874660	0.51695	.	.	ENSG00000158864	ENST00000367993;ENST00000392179;ENST00000476409	D;D;D	0.87809	-2.3;-2.3;-2.3	5.14	5.14	0.70334	NADH-quinone oxidoreductase, subunit D (1);	0.184651	0.47455	D	0.000231	T	0.69378	0.3104	L	0.31065	0.9	0.39344	D	0.965631	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.09377	0.002;0.002;0.004;0.004	T	0.64875	-0.6304	9	0.22109	T	0.4	.	14.0779	0.64903	1.0:0.0:0.0:0.0	.	262;215;313;313	B7Z792;B7Z9L2;Q53HG2;O75306	.;.;.;NDUS2_HUMAN	L	313;313;215	ENSP00000356972:Q313L;ENSP00000376018:Q313L;ENSP00000446447:Q215L	ENSP00000356972:Q313L	Q	+	2	0	NDUFS2	159447076	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.347000	0.90062	2.155000	0.67459	0.454000	0.30748	CAG	.	.		0.532	NDUFS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083015.1	NM_004550		T	161180452	A	T	161180452	3	4	160	1	0	0	0	0	1	0	0	0	10301	188	7	4	972	4	NDUFS2	1	161180452	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1354755	161180452	88070169	28	24199										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096866	167096866	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctttgctgacaatgtggaccTaaaggaacttggccggaagg	13	8	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:167096866T>A	ENST00000361200.2	+	6	2664	c.2498T>A	c.(2497-2499)cTa>cAa	p.L833Q	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.L833Q|DUSP27_ENST00000443333.1_Missense_Mutation_p.L833Q			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	833					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						AATGTGGACCTAAAGGAACTT	0.522																																					p.L833Q		Atlas-SNP	.											.	DUSP27	235	.	0			c.T2498A						.						76	73	74					1																	167096866		2203	4300	6503	SO:0001583	missense	92235	exon5			TGGACCTAAAGGA	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2498T>A	chr1.hg19:g.167096866T>A	ENSP00000354483:p.Leu833Gln	164.0	0.0		343.0	30.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	T	11.03	1.519566	0.27211	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.08282	3.11;3.11;3.11	5.36	4.23	0.50019	.	0.118708	0.35708	N	0.003037	T	0.16214	0.0390	M	0.69823	2.125	0.44477	D	0.997416	D	0.89917	1.0	D	0.87578	0.998	T	0.00684	-1.1611	10	0.87932	D	0	-9.3483	11.0427	0.47840	0.0:0.073:0.0:0.927	.	833	Q5VZP5	DUS27_HUMAN	Q	833	ENSP00000354483:L833Q;ENSP00000271385:L833Q;ENSP00000404874:L833Q	ENSP00000271385:L833Q	L	+	2	0	DUSP27	165363490	1.000000	0.71417	0.116000	0.21606	0.002000	0.02628	7.687000	0.84139	0.861000	0.35504	-0.389000	0.06534	CTA	.	.		0.522	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		A	167096866	T	A	167096866	3	1	160	1	0	0	0	0	1	0	0	0	4826	1522	53	4	2516	4	DUSP27	1	167096866	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	5916414	167096866	82153755	29	24200										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172577940	172577940	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcaagttttctccagaaaagAaggtaattgtttatttcttt	6	5	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:172577940A>T	ENST00000263688.3	+	23	3538	c.3319A>T	c.(3319-3321)Aag>Tag	p.K1107*	SUCO_ENST00000608151.1_Nonsense_Mutation_p.K1259*|SUCO_ENST00000610051.1_Nonsense_Mutation_p.K736*|SUCO_ENST00000367723.4_Nonsense_Mutation_p.K1258*	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	1107					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											TCCAGAAAAGAAGGTAATTGT	0.284																																					p.K1107X		Atlas-SNP	.											.	.	.	.	0			c.A3319T						.						66	78	74					1																	172577940		2200	4289	6489	SO:0001587	stop_gained	51430	exon23			GAAAAGAAGGTAA	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.3319A>T	chr1.hg19:g.172577940A>T	ENSP00000263688:p.Lys1107*	312.0	0.0		669.0	61.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Nonsense_Mutation	SNP	ENST00000263688.3	hg19	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	A	42	9.549242	0.99202	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.116	13.4922	0.61402	1.0:0.0:0.0:0.0	.	.	.	.	X	1259;1107	.	ENSP00000263688:K1107X	K	+	1	0	C1orf9	170844563	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.986000	0.88173	2.082000	0.62665	0.459000	0.35465	AAG	.	.		0.284	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		T	172577940	A	T	172577940	4	4	160	1	0	0	0	0	0	1	0	0	2069	247	9	4	3409	4	C1orf9	1	172577940	Nonsense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	5481074	172577940	76672681	30	24201										
TNR	7143	hgsc.bcm.edu	37	chr1	175293604	175293604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tagtcactgcaacatcattgTctctatcctctgtggagaaa	7	10	4	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:175293604T>C	ENST00000367674.2	-	22	4553	c.3845A>G	c.(3844-3846)gAc>gGc	p.D1282G	RP3-518E13.2_ENST00000569593.1_RNA|TNR_ENST00000263525.2_Missense_Mutation_p.D1282G			Q92752	TENR_HUMAN	tenascin R	1282	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					AACATCATTGTCTCTATCCTC	0.488																																					p.D1282G		Atlas-SNP	.											.	TNR	399	.	0			c.A3845G						.						257	205	222					1																	175293604		2203	4300	6503	SO:0001583	missense	7143	exon22			TCATTGTCTCTAT	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.3845A>G	chr1.hg19:g.175293604T>C	ENSP00000356646:p.Asp1282Gly	125.0	0.0		298.0	70.0	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.931683	0.92389	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	D;D	0.86297	-2.1;-2.1	5.66	5.66	0.87406	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.95510	0.8541	H	0.95043	3.615	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96791	0.9582	10	0.87932	D	0	.	15.5673	0.76303	0.0:0.0:0.0:1.0	.	1282	Q92752	TENR_HUMAN	G	1282;1282;1192	ENSP00000356646:D1282G;ENSP00000263525:D1282G	ENSP00000263525:D1282G	D	-	2	0	TNR	173560227	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.930000	0.87610	2.154000	0.67381	0.533000	0.62120	GAC	.	.		0.488	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		C	175293604	T	C	175293604	3	2	160	1	0	0	0	0	1	0	0	0	16353	1667	58	2	239	2	TNR	1	175293604	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2715664	175293604	73957017	31	24202										
TNR	7143	hgsc.bcm.edu	37	chr1	175334337	175334337	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gaatgagtctgtctgctgggGgagatggatcactccaagtg	15	7	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:175334337G>C	ENST00000367674.2	-	12	3104	c.2396C>G	c.(2395-2397)cCc>cGc	p.P799R	TNR_ENST00000263525.2_Missense_Mutation_p.P799R			Q92752	TENR_HUMAN	tenascin R	799	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					GTCTGCTGGGGGAGATGGATC	0.522																																					p.P799R		Atlas-SNP	.											.	TNR	399	.	0			c.C2396G						.						103	97	99					1																	175334337		2203	4300	6503	SO:0001583	missense	7143	exon12			GCTGGGGGAGATG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.2396C>G	chr1.hg19:g.175334337G>C	ENSP00000356646:p.Pro799Arg	116.0	0.0		266.0	144.0	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.635445	0.87760	.	.	ENSG00000116147	ENST00000367674;ENST00000263525	T;T	0.54866	0.55;0.55	5.91	5.91	0.95273	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.68339	0.2990	L	0.45228	1.405	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68051	-0.5511	10	0.66056	D	0.02	.	19.8936	0.96942	0.0:0.0:1.0:0.0	.	799	Q92752	TENR_HUMAN	R	799	ENSP00000356646:P799R;ENSP00000263525:P799R	ENSP00000263525:P799R	P	-	2	0	TNR	173600960	1.000000	0.71417	0.996000	0.52242	0.959000	0.62525	9.296000	0.96104	2.793000	0.96121	0.655000	0.94253	CCC	.	.		0.522	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		C	175334337	G	C	175334337	3	2	160	1	0	0	0	0	1	0	0	0	16353	1232	43	4	1728	4	TNR	1	175334337	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	40733	175334337	73916284	32	24203										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179497527	179497527	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggagaagatgaaaatgttcaTtccaaacctctatttgaaac	7	7	2	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:179497527T>C	ENST00000367618.3	+	23	3063	c.2676T>C	c.(2674-2676)caT>caC	p.H892H		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	892	Glu-rich.									NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						AAAATGTTCATTCCAAACCTC	0.373																																					p.H892H		Atlas-SNP	.											.	AXDND1	142	.	0			c.T2676C						.						127	112	117					1																	179497527		2203	4300	6503	SO:0001819	synonymous_variant	126859	exon23			TGTTCATTCCAAA	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2676T>C	chr1.hg19:g.179497527T>C		64.0	0.0		153.0	24.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Silent	SNP	ENST00000367618.3	hg19	CCDS30948.1																																																																																			.	.		0.373	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179497527	T	C	179497527	2	2	160	1	0	0	0	0	0	0	0	1	1995	1490	52	2		2	C1orf125	1	179497527	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4163190	179497527	69753094	33	24204										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181685267	181685267	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gttgatatctcctctgtgggTgagtggatccagttagatct	12	7	3	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:181685267T>A	ENST00000367573.2	+	10	1315		c.e10+2		CACNA1E_ENST00000357570.5_Splice_Site|CACNA1E_ENST00000367567.4_Splice_Site|CACNA1E_ENST00000367570.1_Splice_Site|CACNA1E_ENST00000360108.3_Splice_Site|CACNA1E_ENST00000526775.1_Splice_Site|CACNA1E_ENST00000358338.5_Splice_Site	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit						calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CCTCTGTGGGTGAGTGGATCC	0.498																																					.		Atlas-SNP	.											.	CACNA1E	778	.	0			c.1315+2T>A						.						67	75	73					1																	181685267		1946	4142	6088	SO:0001630	splice_region_variant	777	exon10			TGTGGGTGAGTGG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1315+2T>A	chr1.hg19:g.181685267T>A		67.0	0.0		126.0	10.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Splice_Site	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	T	10.55	1.380247	0.24944	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	.	.	.	5.51	4.37	0.52481	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.1938	0.31385	0.0:0.0714:0.1361:0.7926	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1E	179951890	1.000000	0.71417	1.000000	0.80357	0.015000	0.08874	3.774000	0.55341	1.003000	0.39130	-0.313000	0.08912	.	.	.		0.498	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	Intron	A	181685267	T	A	181685267	5	1	160	1	0	0	0	0	0	0	1	0	2544	1710	59	4	1355	4	CACNA1E	1	181685267	Splice_Site	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2187740	181685267	67565354	34	24205										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181767735	181767735	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cgagccctacttggccctgcAcgaagactcccacgcctcag	9	18	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:181767735A>G	ENST00000367573.2	+	48	6707	c.6707A>G	c.(6706-6708)cAc>cGc	p.H2236R	CACNA1E_ENST00000357570.5_Missense_Mutation_p.H2187R|CACNA1E_ENST00000367567.4_Missense_Mutation_p.H1800R|CACNA1E_ENST00000367570.1_Missense_Mutation_p.H2193R|CACNA1E_ENST00000360108.3_Missense_Mutation_p.H2217R|CACNA1E_ENST00000526775.1_Missense_Mutation_p.H2174R|CACNA1E_ENST00000358338.5_Missense_Mutation_p.H2125R	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2236					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TTGGCCCTGCACGAAGACTCC	0.612																																					p.H2236R		Atlas-SNP	.											.	CACNA1E	778	.	0			c.A6707G						.						41	46	44					1																	181767735		2141	4256	6397	SO:0001583	missense	777	exon48			CCCTGCACGAAGA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6707A>G	chr1.hg19:g.181767735A>G	ENSP00000356545:p.His2236Arg	72.0	0.0		126.0	14.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	7.992	0.753440	0.15778	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.95756	-3.73;-3.73;-3.73;-3.73;-3.8;-3.74;-3.73	5.55	5.55	0.83447	.	0.344130	0.31507	N	0.007539	D	0.87708	0.6245	N	0.10916	0.065	0.53688	D	0.999976	B;B	0.24823	0.112;0.001	B;B	0.17722	0.019;0.003	D	0.84359	0.0537	10	0.02654	T	1	.	15.432	0.75108	1.0:0.0:0.0:0.0	.	2174;2193	Q15878-2;Q15878-3	.;.	R	2193;2174;2187;2125;1800;2217;2236	ENSP00000356542:H2193R;ENSP00000434814:H2174R;ENSP00000350183:H2187R;ENSP00000351101:H2125R;ENSP00000356539:H1800R;ENSP00000353222:H2217R;ENSP00000356545:H2236R	ENSP00000350183:H2187R	H	+	2	0	CACNA1E	180034358	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.669000	0.74462	2.117000	0.64856	0.456000	0.33151	CAC	.	.		0.612	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		G	181767735	A	G	181767735	3	3	160	1	0	0	0	0	1	0	0	0	2544	159	6	2	6764	2	CACNA1E	1	181767735	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	82468	181767735	67482886	35	24206										
DHX9	1660	hgsc.bcm.edu	37	chr1	182811771	182811771	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgaccccatcctatgaaattAgagcagtggggaacaaaaac	9	9	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:182811771A>G	ENST00000367549.3	+	2	180	c.70A>G	c.(70-72)Aga>Gga	p.R24G		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	24	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.|Interaction with CREBBP.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						CTATGAAATTAGAGCAGTGGG	0.378																																					p.R24G	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.A70G						.						109	101	104					1																	182811771		1856	4091	5947	SO:0001583	missense	1660	exon2			GAAATTAGAGCAG	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.70A>G	chr1.hg19:g.182811771A>G	ENSP00000356520:p.Arg24Gly	123.0	0.0		270.0	26.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.299585	0.81136	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	T	0.77098	-1.07	5.46	5.46	0.80206	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.86764	0.6011	M	0.81179	2.53	0.58432	D	0.999999	D	0.71674	0.998	D	0.70487	0.969	D	0.88041	0.2781	10	0.72032	D	0.01	.	10.4261	0.44378	0.7254:0.2746:0.0:0.0	.	24	Q08211	DHX9_HUMAN	G	24	ENSP00000356520:R24G	ENSP00000356520:R24G	R	+	1	2	DHX9	181078394	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.753000	0.68736	2.195000	0.70347	0.528000	0.53228	AGA	.	.		0.378	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		G	182811771	A	G	182811771	3	3	160	1	0	0	0	0	1	0	0	0	4518	412	15	2	72	2	DHX9	1	182811771	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1044036	182811771	66438850	36	24207										
DHX9	1660	hgsc.bcm.edu	37	chr1	182827944	182827944	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	accatctcagcgacaaaaccAagtgggtgtggttccttggt	11	10	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:182827944A>G	ENST00000367549.3	+	10	1087	c.977A>G	c.(976-978)cAa>cGa	p.Q326R		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	326					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						CGACAAAACCAAGTGGGTGTG	0.443																																					p.Q326R	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.A977G						.						111	100	104					1																	182827944		1898	4132	6030	SO:0001583	missense	1660	exon10			AAAACCAAGTGGG	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.977A>G	chr1.hg19:g.182827944A>G	ENSP00000356520:p.Gln326Arg	131.0	0.0		309.0	25.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.574025	0.28092	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	T	0.08720	3.06	5.73	3.35	0.38373	.	0.609442	0.18284	N	0.145934	T	0.06188	0.0160	N	0.22421	0.69	0.21719	N	0.999575	B	0.06786	0.001	B	0.06405	0.002	T	0.38802	-0.9644	10	0.18276	T	0.48	.	12.5524	0.56233	0.7276:0.2724:0.0:0.0	.	326	Q08211	DHX9_HUMAN	R	326	ENSP00000356520:Q326R	ENSP00000356520:Q326R	Q	+	2	0	DHX9	181094567	0.973000	0.33851	0.957000	0.39632	0.998000	0.95712	3.001000	0.49488	0.491000	0.27793	0.533000	0.62120	CAA	.	.		0.443	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		G	182827944	A	G	182827944	3	3	160	1	0	0	0	0	1	0	0	0	4518	130	5	2	1011	2	DHX9	1	182827944	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	16173	182827944	66422677	37	24208										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185987388	185987388	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	taaatggacgcaaactggttAttgctcaggctcaagtgtca	10	8	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:185987388A>G	ENST00000271588.4	+	34	5603	c.5374A>G	c.(5374-5376)Att>Gtt	p.I1792V	HMCN1_ENST00000367492.2_Missense_Mutation_p.I1792V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1792	Ig-like C2-type 15.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CAAACTGGTTATTGCTCAGGC	0.423																																					p.I1792V		Atlas-SNP	.											.	HMCN1	797	.	0			c.A5374G						.						157	154	155					1																	185987388		2203	4300	6503	SO:0001583	missense	83872	exon34			CTGGTTATTGCTC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.5374A>G	chr1.hg19:g.185987388A>G	ENSP00000271588:p.Ile1792Val	123.0	0.0		240.0	26.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	14.48	2.549278	0.45383	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.77750	-1.12;-1.12	5.89	3.58	0.41010	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.103566	0.64402	N	0.000004	T	0.68174	0.2972	L	0.41079	1.255	0.43103	D	0.994796	B	0.30068	0.267	B	0.32090	0.14	T	0.60601	-0.7231	10	0.31617	T	0.26	.	10.3095	0.43699	0.8672:0.0:0.1328:0.0	.	1792	Q96RW7	HMCN1_HUMAN	V	1792	ENSP00000271588:I1792V;ENSP00000356462:I1792V	ENSP00000271588:I1792V	I	+	1	0	HMCN1	184254011	0.976000	0.34144	0.986000	0.45419	0.795000	0.44927	1.704000	0.37857	0.491000	0.27793	-0.360000	0.07572	ATT	.	.		0.423	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	185987388	A	G	185987388	3	3	160	1	0	0	0	0	1	0	0	0	7229	449	16	2	5508	2	HMCN1	1	185987388	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	3159444	185987388	63263233	38	24209										
LMOD1	25802	hgsc.bcm.edu	37	chr1	201915422	201915422	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctccagcaggctgtcgatgTcggggtcttcactcacctgc	11	14	4	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:201915422T>A	ENST00000367288.4	-	1	293	c.47A>T	c.(46-48)gAc>gTc	p.D16V		NM_012134.2	NP_036266.2	P29536	LMOD1_HUMAN	leiomodin 1 (smooth muscle)	16					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GCTGTCGATGTCGGGGTCTTC	0.617																																					p.D16V		Atlas-SNP	.											.	LMOD1	59	.	0			c.A47T						.						36	39	38					1																	201915422		1997	4165	6162	SO:0001583	missense	25802	exon1			TCGATGTCGGGGT	X54162	CCDS53457.1	1q32.1	2008-05-22			ENSG00000163431	ENSG00000163431			6647	protein-coding gene	gene with protein product		602715					Standard	NM_012134		Approved	64kD, D1, 1D	uc021phl.1	P29536	OTTHUMG00000035802	ENST00000367288.4:c.47A>T	chr1.hg19:g.201915422T>A	ENSP00000356257:p.Asp16Val	112.0	0.0		252.0	25.0	NM_012134	B1APV6|C4AMB1|Q68EN2	Missense_Mutation	SNP	ENST00000367288.4	hg19	CCDS53457.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.903171	0.92035	.	.	ENSG00000163431	ENST00000367288;ENST00000400965;ENST00000412469	T	0.41758	0.99	5.93	5.93	0.95920	.	0.000000	0.41712	D	0.000828	T	0.69931	0.3166	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.76263	-0.3023	10	0.87932	D	0	-50.1905	14.335	0.66584	0.0:0.0:0.0:1.0	.	16;16	B4E3S9;P29536	.;LMOD1_HUMAN	V	16	ENSP00000356257:D16V	ENSP00000356257:D16V	D	-	2	0	LMOD1	200182045	1.000000	0.71417	0.990000	0.47175	0.959000	0.62525	7.985000	0.88162	2.271000	0.75665	0.459000	0.35465	GAC	.	.		0.617	LMOD1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087085.2			A	201915422	T	A	201915422	3	1	160	1	0	0	0	0	1	0	0	0	8865	1667	58	4	1767	4	LMOD1	1	201915422	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	15928034	201915422	47335199	39	24210										
LAX1	54900	hgsc.bcm.edu	37	chr1	203734781	203734781	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgactccccgcagcctggacAggtgagtgactcagggtggt	15	11	1	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:203734781A>T	ENST00000442561.2	+	1	478	c.88A>T	c.(88-90)Aga>Tga	p.R30*	LAX1_ENST00000367217.5_Intron	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	30					antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)			central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CAGCCTGGACAGGTGAGTGAC	0.562																																					p.R30X		Atlas-SNP	.											.	LAX1	48	.	0			c.A88T						.						74	58	63					1																	203734781		2203	4300	6503	SO:0001630	splice_region_variant	54900	exon1			CTGGACAGGTGAG	AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188			26005	protein-coding gene	gene with protein product	"LAT-like membrane associated protein", "linker for activation of x cells"					12359715	Standard	NM_017773		Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.89+1A>T	chr1.hg19:g.203734781A>T		104.0	0.0		210.0	20.0	NM_017773	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	Nonsense_Mutation	SNP	ENST00000442561.2	hg19	CCDS1441.2	.	.	.	.	.	.	.	.	.	.	A	40	8.172012	0.98688	.	.	ENSG00000122188	ENST00000442561	.	.	.	4.17	-1.85	0.07784	.	0.741182	0.11919	N	0.516927	.	.	.	.	.	.	0.21020	N	0.999801	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-0.5129	9.6788	0.40056	0.2674:0.0:0.7326:0.0	.	.	.	.	X	30	.	ENSP00000406970:R30X	R	+	1	2	LAX1	202001404	0.107000	0.21998	0.100000	0.21137	0.730000	0.41778	0.141000	0.16076	-0.304000	0.08843	0.460000	0.39030	AGA	.	.		0.562	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087468.3	NM_017773	Nonsense_Mutation	T	203734781	A	T	203734781	5	4	160	1	0	0	0	0	0	0	1	0	8657	202	7	4	135	4	LAX1	1	203734781	Splice_Site	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1819359	203734781	45515840	40	24211										
ACBD3	64746	hgsc.bcm.edu	37	chr1	226340311	226340311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tggatggagctgctattactGgaagagattctaaaggcaat	12	5	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:226340311G>A	ENST00000366812.5	-	7	1154	c.1100C>T	c.(1099-1101)cCa>cTa	p.P367L	RP11-275I14.4_ENST00000440540.1_RNA|ACBD3_ENST00000464927.1_5'Flank	NM_022735.3	NP_073572.2	Q9H3P7	GCP60_HUMAN	acyl-CoA binding domain containing 3	367					steroid biosynthetic process (GO:0006694)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)			breast(2)|endometrium(3)|large_intestine(5)|lung(7)|skin(1)|urinary_tract(2)	20	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.121)		TGCTATTACTGGAAGAGATTC	0.438																																					p.P367L		Atlas-SNP	.											.	ACBD3	38	.	0			c.C1100T						.						116	122	120					1																	226340311		2203	4300	6503	SO:0001583	missense	64746	exon7			ATTACTGGAAGAG	AB043587	CCDS1551.1	1q41	2013-10-16	2010-04-30	2003-11-12	ENSG00000182827	ENSG00000182827		"A-kinase anchor proteins"	15453	protein-coding gene	gene with protein product	"PBR- and PKA-associated protein 7"	606809	"golgi complex associated protein 1, 60kDa", "acyl-Coenzyme A binding domain containing 3"	GOLPH1, GOCAP1		12692076, 20150326	Standard	NM_022735		Approved	GCP60, PAP7	uc001hpy.3	Q9H3P7	OTTHUMG00000037560	ENST00000366812.5:c.1100C>T	chr1.hg19:g.226340311G>A	ENSP00000355777:p.Pro367Leu	77.0	0.0		175.0	106.0	NM_022735	B2RB29|Q5VTJ0|Q6P9F1|Q8IZC5|Q8N4D6|Q9H6U3	Missense_Mutation	SNP	ENST00000366812.5	hg19	CCDS1551.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.164340	0.38217	.	.	ENSG00000182827	ENST00000366812	T	0.52057	0.68	5.29	5.29	0.74685	.	0.097704	0.64402	D	0.000001	T	0.56630	0.1998	M	0.80028	2.48	0.80722	D	1	B	0.24721	0.11	B	0.28638	0.092	T	0.60234	-0.7303	10	0.72032	D	0.01	-10.2805	18.9418	0.92608	0.0:0.0:1.0:0.0	.	367	Q9H3P7	GCP60_HUMAN	L	367	ENSP00000355777:P367L	ENSP00000355777:P367L	P	-	2	0	ACBD3	224406934	1.000000	0.71417	1.000000	0.80357	0.028000	0.11728	9.397000	0.97276	2.488000	0.83962	0.655000	0.94253	CCA	.	.		0.438	ACBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091528.1	NM_022735		A	226340311	G	A	226340311	3	1	160	1	0	0	0	0	1	0	0	0	123	1348	47	3	494	3	ACBD3	1	226340311	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	22605530	226340311	22910310	41	24212										
NID1	4811	hgsc.bcm.edu	37	chr1	236205357	236205357	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccggcgcggggagaggacgcTgggcacactgtatgtgtcag	18	10	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:236205357T>A	ENST00000264187.6	-	4	1070	c.988A>T	c.(988-990)Agc>Tgc	p.S330C	NID1_ENST00000366595.3_Missense_Mutation_p.S330C	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	330					basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	GAGAGGACGCTGGGCACACTG	0.617																																					p.S330C		Atlas-SNP	.											.	NID1	196	.	0			c.A988T						.						88	83	85					1																	236205357		2203	4300	6503	SO:0001583	missense	4811	exon4			GGACGCTGGGCAC	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.988A>T	chr1.hg19:g.236205357T>A	ENSP00000264187:p.Ser330Cys	137.0	0.0		212.0	27.0	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	hg19	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	T	12.76	2.034920	0.35893	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	D;D	0.88664	-1.76;-2.41	5.57	-1.18	0.09617	.	1.392310	0.03689	N	0.246823	D	0.82674	0.5088	L	0.40543	1.245	0.09310	N	1	D;P	0.55800	0.973;0.556	B;B	0.42653	0.394;0.221	T	0.71715	-0.4509	10	0.52906	T	0.07	.	2.0473	0.03563	0.1302:0.1756:0.4018:0.2924	.	330;330	P14543-2;P14543	.;NID1_HUMAN	C	330	ENSP00000264187:S330C;ENSP00000355554:S330C	ENSP00000264187:S330C	S	-	1	0	NID1	234271980	0.011000	0.17503	0.002000	0.10522	0.008000	0.06430	0.847000	0.27696	-0.477000	0.06832	-0.376000	0.06991	AGC	.	.		0.617	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		A	236205357	T	A	236205357	3	1	160	1	0	0	0	0	1	0	0	0	10423	1580	55	4	2823	4	NID1	1	236205357	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	9865046	236205357	13045264	42	24213										
RYR2	6262	hgsc.bcm.edu	37	chr1	237729922	237729922	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aggttccgaatcttccgtgcCgagaagacctatgcagtgaa	11	10	1	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:237729922C>T	ENST00000366574.2	+	28	3587	c.3270C>T	c.(3268-3270)gcC>gcT	p.A1090A	RYR2_ENST00000542537.1_Silent_p.A1074A|RYR2_ENST00000360064.6_Silent_p.A1088A	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1090	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TCTTCCGTGCCGAGAAGACCT	0.552																																					p.A1090A		Atlas-SNP	.											.	RYR2	1273	.	0			c.C3270T						.						98	98	98					1																	237729922		1926	4131	6057	SO:0001819	synonymous_variant	6262	exon28			CCGTGCCGAGAAG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.3270C>T	chr1.hg19:g.237729922C>T		122.0	0.0		284.0	54.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.552	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237729922	C	T	237729922	2	4	160	1	0	0	0	0	0	0	0	1	13784	639	23	1		1	RYR2	1	237729922	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	1524565	237729922	11520699	43	24214										
RYR2	6262	hgsc.bcm.edu	37	chr1	237972236	237972236	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggcttattagctgttgttgtAtacctatacactgtggtggc	11	7	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:237972236A>T	ENST00000366574.2	+	100	14651	c.14334A>T	c.(14332-14334)gtA>gtT	p.V4778V	RYR2_ENST00000542537.1_Silent_p.V4762V|RYR2_ENST00000360064.6_Silent_p.V4784V	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4778					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CTGTTGTTGTATACCTATACA	0.373																																					p.V4778V		Atlas-SNP	.											.	RYR2	1273	.	0			c.A14334T						.						335	325	328					1																	237972236		1898	4114	6012	SO:0001819	synonymous_variant	6262	exon100			TGTTGTATACCTA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.14334A>T	chr1.hg19:g.237972236A>T		133.0	0.0		281.0	24.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.373	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237972236	A	T	237972236	2	4	160	1	0	0	0	0	0	0	0	1	13784	436	16	4		4	RYR2	1	237972236	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	242314	237972236	11278385	44	24215										
CHRM3	1131	hgsc.bcm.edu	37	chr1	240072372	240072372	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acatcaacagcaccgtgaacCccgtgtgctatgctctgtgc	9	14	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:240072372C>G	ENST00000255380.4	+	5	2400	c.1621C>G	c.(1621-1623)Ccc>Gcc	p.P541A		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	541					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CACCGTGAACCCCGTGTGCTA	0.483																																					p.P541A		Atlas-SNP	.											.	CHRM3	118	.	0			c.C1621G						.						96	83	87					1																	240072372		2203	4300	6503	SO:0001583	missense	1131	exon5			GTGAACCCCGTGT	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.1621C>G	chr1.hg19:g.240072372C>G	ENSP00000255380:p.Pro541Ala	183.0	0.0		346.0	28.0	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	hg19	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.962856	0.74016	.	.	ENSG00000133019	ENST00000255380	D	0.98807	-5.15	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.99233	0.9733	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99616	1.0982	10	0.87932	D	0	-22.4672	19.5758	0.95444	0.0:1.0:0.0:0.0	.	541	P20309	ACM3_HUMAN	A	541	ENSP00000255380:P541A	ENSP00000255380:P541A	P	+	1	0	CHRM3	238138995	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.818000	0.86416	2.632000	0.89209	0.655000	0.94253	CCC	.	.		0.483	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		G	240072372	C	G	240072372	3	3	160	1	0	0	0	0	1	0	0	0	3380	623	22	4	1623	4	CHRM3	1	240072372	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	2100136	240072372	9178249	45	24216										
ZNF124	7678	hgsc.bcm.edu	37	chr1	247320351	247320351	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctttcatggtcacgaaggtgActggaacgactgaaggcttt	12	8	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:247320351A>G	ENST00000543802.2	-	4	662	c.573T>C	c.(571-573)agT>agC	p.S191S	ZNF124_ENST00000491356.1_Intron|ZNF124_ENST00000472531.1_Intron|ZNF124_ENST00000491848.1_5'UTR|ZNF124_ENST00000340684.6_Silent_p.S129S			Q15973	ZN124_HUMAN	zinc finger protein 124	191					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(3)|urinary_tract(2)	14	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)			CACGAAGGTGACTGGAACGAC	0.428																																					p.S129S		Atlas-SNP	.											.	ZNF124	39	.	0			c.T387C						.						87	81	83					1																	247320351		2203	4300	6503	SO:0001819	synonymous_variant	7678	exon4			AAGGTGACTGGAA	S54641	CCDS31089.1, CCDS58067.1, CCDS73057.1	1q44	2013-01-08	2006-06-13		ENSG00000196418	ENSG00000196418		"Zinc fingers, C2H2-type", "-"	12907	protein-coding gene	gene with protein product		194631	"zinc finger protein 124 (HZF-16)"			7916577	Standard	XM_005273256		Approved	HZF16, HZF-16	uc001icj.1	Q15973	OTTHUMG00000041112	ENST00000543802.2:c.573T>C	chr1.hg19:g.247320351A>G		100.0	0.0		213.0	15.0	NM_003431	B3KNP3|J3KSE1|Q15974|Q4VAJ7|Q5T2V4	Silent	SNP	ENST00000543802.2	hg19																																																																																				.	.		0.428	ZNF124-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000447393.1	NM_003431		G	247320351	A	G	247320351	2	3	160	1	0	0	0	0	0	0	0	1	17735	272	10	2		2	ZNF124	1	247320351	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	7247979	247320351	1930270	46	24217										
OR2AK2	391191	hgsc.bcm.edu	37	chr1	248128887	248128887	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cagtcagctctccatcgttgAcctcatgtacatctccacca	5	16	4	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:248128887A>C	ENST00000366480.3	+	1	353	c.254A>C	c.(253-255)gAc>gCc	p.D85A	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, member 2	85						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TCCATCGTTGACCTCATGTAC	0.473																																					p.D85A	Melanoma(45;390 1181 23848 28461 41504)	Atlas-SNP	.											.	OR2AK2	90	.	0			c.A254C						.						201	177	185					1																	248128887		2203	4300	6503	SO:0001583	missense	391191	exon1			TCGTTGACCTCAT	BK004457	CCDS31102.1	1q44	2012-08-09			ENSG00000187080	ENSG00000187080		"GPCR / Class A : Olfactory receptors"	19569	protein-coding gene	gene with protein product				OR2AK1P			Standard	NM_001004491		Approved		uc010pzd.2	Q8NG84	OTTHUMG00000040201	ENST00000366480.3:c.254A>C	chr1.hg19:g.248128887A>C	ENSP00000355436:p.Asp85Ala	65.0	0.0		108.0	14.0	NM_001004491	B2RND1|Q6IF05	Missense_Mutation	SNP	ENST00000366480.3	hg19	CCDS31102.1	.	.	.	.	.	.	.	.	.	.	.	13.82	2.349908	0.41599	.	.	ENSG00000187080	ENST00000366480	T	0.01172	5.23	3.15	3.15	0.36227	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.10895	0.0266	H	0.98388	4.22	0.09310	N	1	D	0.64830	0.994	P	0.60415	0.874	T	0.13045	-1.0524	9	0.87932	D	0	.	10.7706	0.46321	1.0:0.0:0.0:0.0	.	85	Q8NG84	O2AK2_HUMAN	A	85	ENSP00000355436:D85A	ENSP00000355436:D85A	D	+	2	0	OR2AK2	246195510	0.996000	0.38824	0.002000	0.10522	0.001000	0.01503	4.198000	0.58419	1.421000	0.47157	0.374000	0.22700	GAC	.	.		0.473	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	NM_001004491		C	248128887	A	C	248128887	3	2	160	1	0	0	0	0	1	0	0	0	10995	275	10	5	256	5	OR2AK2	1	248128887	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	808536	248128887	1121734	47	24218										
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458294	248458294	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acacacagcagatgtacatgGcgttttcgaagactgaagtg	11	8	0	3	rs536165632		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr1:248458294G>T	ENST00000317996.1	-	1	586	c.587C>A	c.(586-588)gCc>gAc	p.A196D		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	196						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			GATGTACATGGCGTTTTCGAA	0.532																																					p.A196D		Atlas-SNP	.											.	OR2T12	113	.	0			c.C587A						.						74	58	63					1																	248458294		2201	4295	6496	SO:0001583	missense	127064	exon1			TACATGGCGTTTT	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.587C>A	chr1.hg19:g.248458294G>T	ENSP00000324583:p.Ala196Asp	527.0	0.0		952.0	81.0	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	hg19	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	g	13.21	2.169254	0.38315	.	.	ENSG00000177201	ENST00000317996	T	0.37752	1.18	1.55	-1.11	0.09840	GPCR, rhodopsin-like superfamily (1);	0.548063	0.13454	U	0.386692	T	0.47322	0.1439	M	0.71871	2.18	0.09310	N	1	D	0.58970	0.984	P	0.59643	0.861	T	0.36040	-0.9764	10	0.87932	D	0	.	5.5786	0.17236	0.6177:0.0:0.3823:0.0	.	196	Q8NG77	O2T12_HUMAN	D	196	ENSP00000324583:A196D	ENSP00000324583:A196D	A	-	2	0	OR2T12	246524917	0.000000	0.05858	0.002000	0.10522	0.213000	0.24496	-0.381000	0.07417	-0.207000	0.10187	0.175000	0.17021	GCC	.	.		0.532	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		T	248458294	G	T	248458294	3	4	160	1	0	0	0	0	1	0	0	0	11028	1203	42	3	378	3	OR2T12	1	248458294	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	329407	248458294	792327	48	24219										
SOX11	6664	hgsc.bcm.edu	37	chr2	5833868	5833868	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cgcccgcgtcctcgcgctcgGtgtccacctcctcgtccagc	10	21	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:5833868G>A	ENST00000322002.3	+	1	1070	c.1015G>A	c.(1015-1017)Gtg>Atg	p.V339M	AC010729.1_ENST00000455579.2_RNA|AC108025.2_ENST00000420221.1_RNA|AC108025.2_ENST00000453678.1_RNA|AC107057.2_ENST00000458264.1_RNA	NM_003108.3	NP_003099.1	P35716	SOX11_HUMAN	SRY (sex determining region Y)-box 11	339	Poly-Ser.				cardiac ventricle formation (GO:0003211)|closure of optic fissure (GO:0061386)|cornea development in camera-type eye (GO:0061303)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|eyelid development in camera-type eye (GO:0061029)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|hard palate development (GO:0060022)|kidney development (GO:0001822)|lens morphogenesis in camera-type eye (GO:0002089)|limb bud formation (GO:0060174)|lung morphogenesis (GO:0060425)|negative regulation of cell death (GO:0060548)|negative regulation of gene expression (GO:0010629)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural crest cell development (GO:0014032)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|neuron differentiation (GO:0030182)|noradrenergic neuron differentiation (GO:0003357)|oligodendrocyte development (GO:0014003)|outflow tract morphogenesis (GO:0003151)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of hippo signaling (GO:0035332)|positive regulation of hormone secretion (GO:0046887)|positive regulation of lens epithelial cell proliferation (GO:2001111)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|signal transduction involved in cell cycle checkpoint (GO:0072395)|skeletal muscle cell differentiation (GO:0035914)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)|somite development (GO:0061053)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|translation (GO:0006412)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|translation factor activity, nucleic acid binding (GO:0008135)			central_nervous_system(5)|cervix(1)|endometrium(1)|liver(1)|lung(4)|stomach(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)		CTCGCGCTCGGTGTCCACCTC	0.677																																					p.V339M		Atlas-SNP	.											.	SOX11	69	.	0			c.G1015A						.						5	6	6					2																	5833868		2050	4019	6069	SO:0001583	missense	6664	exon1			CGCTCGGTGTCCA		CCDS1654.1	2p25	2008-05-21			ENSG00000176887	ENSG00000176887		"SRY (sex determining region Y)-boxes"	11191	protein-coding gene	gene with protein product	"SRY-related HMG-box gene 11"	600898				8666406, 12637543	Standard	NM_003108		Approved		uc002qyj.3	P35716	OTTHUMG00000090333	ENST00000322002.3:c.1015G>A	chr2.hg19:g.5833868G>A	ENSP00000322568:p.Val339Met	53.0	0.0		64.0	7.0	NM_003108	Q4ZFV8	Missense_Mutation	SNP	ENST00000322002.3	hg19	CCDS1654.1	.	.	.	.	.	.	.	.	.	.	G	7.791	0.711507	0.15306	.	.	ENSG00000176887	ENST00000322002	D	0.97906	-4.6	4.6	4.6	0.57074	.	12.374300	0.01040	U	0.004299	D	0.97451	0.9166	M	0.65975	2.015	0.33597	D	0.601824	P	0.45902	0.868	P	0.45506	0.483	D	0.91581	0.5279	10	0.34782	T	0.22	.	11.47	0.50264	0.0966:0.0:0.9034:0.0	.	339	P35716	SOX11_HUMAN	M	339	ENSP00000322568:V339M	ENSP00000322568:V339M	V	+	1	0	SOX11	5751319	1.000000	0.71417	1.000000	0.80357	0.304000	0.27724	3.308000	0.51896	2.110000	0.64415	0.561000	0.74099	GTG	.	.		0.677	SOX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206698.1	NM_003108		A	5833868	G	A	5833868	3	1	160	1	0	0	0	0	1	0	0	0	14957	1261	44	3	1017	3	SOX11	2	5833868	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10		5833868	237365505	49	24220										
FAM179A	165186	hgsc.bcm.edu	37	chr2	29226472	29226472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cggttgcagcgaccccctccCgtgtgcctggctcccttccc	10	20	0	0	rs559495685		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:29226472C>T	ENST00000379558.4	+	6	1105	c.754C>T	c.(754-756)Cgt>Tgt	p.R252C	FAM179A_ENST00000403861.2_Missense_Mutation_p.R252C	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	252										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GACCCCCTCCCGTGTGCCTGG	0.627													C|||	1	0.000199681	8e-04	0	5008	,	,		18665	0		0	False		,,,				2504	0				p.R252C		Atlas-SNP	.											.	FAM179A	106	.	0			c.C754T						.						31	36	35					2																	29226472		2025	4143	6168	SO:0001583	missense	165186	exon6			CCCTCCCGTGTGC	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.754C>T	chr2.hg19:g.29226472C>T	ENSP00000368876:p.Arg252Cys	251.0	0.0		279.0	38.0	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	hg19	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	C	5.783	0.328894	0.10956	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.09817	3.1;2.94	4.95	-9.91	0.00458	.	.	.	.	.	T	0.02970	0.0088	N	0.03608	-0.345	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.04013	0.001;0.001	T	0.41378	-0.9512	9	0.46703	T	0.11	.	1.432	0.02336	0.2177:0.2439:0.3354:0.2029	.	252;252	F8W8E4;Q6ZUX3	.;F179A_HUMAN	C	252	ENSP00000368876:R252C;ENSP00000384699:R252C	ENSP00000368876:R252C	R	+	1	0	FAM179A	29079976	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.734000	0.00192	-4.333000	0.00056	-1.579000	0.00862	CGT	.	.		0.627	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		T	29226472	C	T	29226472	3	4	160	1	0	0	0	0	1	0	0	0	5510	652	23	1	772	1	FAM179A	2	29226472	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	23392604	29226472	213972901	50	24221										
XPO1	7514	hgsc.bcm.edu	37	chr2	61711207	61711207	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agcctgaagtagtaagaaaaAgttcgttctatgttcaggat	10	5	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:61711207A>C	ENST00000401558.2	-	21	3269	c.2542T>G	c.(2542-2544)Ttt>Gtt	p.F848V	XPO1_ENST00000404992.2_Missense_Mutation_p.F848V|RP11-355B11.2_ENST00000605437.1_RNA|RP11-355B11.2_ENST00000603652.1_RNA|RP11-355B11.2_ENST00000603028.1_RNA|XPO1_ENST00000406957.1_Missense_Mutation_p.F848V|RP11-355B11.2_ENST00000578974.2_RNA	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	848					gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			AGTAAGAAAAAGTTCGTTCTA	0.373			Mis		CLL																																p.F848V		Atlas-SNP	.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1	108	.	0			c.T2542G						.						99	103	102					2																	61711207		2203	4300	6503	SO:0001583	missense	7514	exon21			AGAAAAAGTTCGT	Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.2542T>G	chr2.hg19:g.61711207A>C	ENSP00000384863:p.Phe848Val	127.0	0.0		174.0	41.0	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	hg19	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.993189	0.93167	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	T;T;T	0.66638	-0.22;-0.22;-0.22	5.62	5.62	0.85841	Armadillo-like helical (1);Armadillo-type fold (2);Exportin 1, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.86855	0.6033	H	0.94925	3.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90550	0.4508	10	0.87932	D	0	-19.9212	16.1283	0.81408	1.0:0.0:0.0:0.0	.	495;848	B3KWD0;O14980	.;XPO1_HUMAN	V	848	ENSP00000384863:F848V;ENSP00000385942:F848V;ENSP00000385559:F848V	ENSP00000384863:F848V	F	-	1	0	XPO1	61564711	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.287000	0.95975	2.263000	0.75096	0.533000	0.62120	TTT	.	.		0.373	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		C	61711207	A	C	61711207	3	2	160	1	0	0	0	0	1	0	0	0	17460	72	3	5	693	5	XPO1	2	61711207	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	32484735	61711207	181488166	51	24222										
CCT7	10574	hgsc.bcm.edu	37	chr2	73477551	73477551	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	catgatgccatcatgatcgtCaggagggccatcaaggtact	11	10	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:73477551C>A	ENST00000258091.5	+	10	1329	c.1188C>A	c.(1186-1188)gtC>gtA	p.V396V	CCT7_ENST00000538797.1_Silent_p.V268V|CCT7_ENST00000398422.2_Silent_p.V192V|CCT7_ENST00000539919.1_Silent_p.V352V|CCT7_ENST00000540468.1_Silent_p.V309V|CCT7_ENST00000537131.1_Silent_p.V296V	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	396					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						TCATGATCGTCAGGAGGGCCA	0.557																																					p.V396V		Atlas-SNP	.											.	CCT7	60	.	0			c.C1188A						.						95	105	102					2																	73477551		2084	4220	6304	SO:0001819	synonymous_variant	10574	exon10			GATCGTCAGGAGG	AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"Heat Shock Proteins / Chaperonins"	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	ENST00000258091.5:c.1188C>A	chr2.hg19:g.73477551C>A		108.0	0.0		98.0	5.0	NM_006429	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Silent	SNP	ENST00000258091.5	hg19	CCDS46336.1																																																																																			.	.		0.557	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2			A	73477551	C	A	73477551	2	1	160	1	0	0	0	0	0	0	0	1	2961	813	29	3		3	CCT7	2	73477551	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	11766344	73477551	169721822	52	24223										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613037	+	Missense_Mutation	DNP	GA	GA	CT													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	catggccgggcgagctggagGaggaggaggaggaggaggag					rs61156725|rs72319667|rs3074417	byFrequency	TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:73613036_73613037GA>CT	ENST00000264448.6	+	1	151_152	c.40_41GA>CT	c.(40-42)GAg>CTg	p.E14L	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14L|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggaggag	0.693																																					p.E14Q|p.E14V		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C|c.A41T						.																																			SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG|TGGAGGAGGAGGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	Exception_encountered	chr2.hg19:g.73613036_73613037delinsCT	ENSP00000264448:p.Glu14Leu	195.0	0.0		317.0|321.0	17.0|23.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.693	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		CT	73613037	GA	CT	73613036	3	2	160	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	DNP	GA	TCGA-DD-AACI-01A-11D-A40R-10	135485	73613036	169586337	53	24224										
SLC4A5	57835	hgsc.bcm.edu	37	chr2	74475529	74475529	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gatgaggatgggccccgtgcTgctgagaatgatgagaggct	17	7	0	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:74475529T>G	ENST00000377634.4	-	18	2137	c.1738A>C	c.(1738-1740)Agc>Cgc	p.S580R	SLC4A5_ENST00000423644.1_Missense_Mutation_p.S580R|SLC4A5_ENST00000346834.4_Missense_Mutation_p.S580R|SLC4A5_ENST00000358683.4_Missense_Mutation_p.S516R|SLC4A5_ENST00000357822.5_Missense_Mutation_p.S580R|SLC4A5_ENST00000359484.4_Missense_Mutation_p.S516R|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000394019.2_Missense_Mutation_p.S580R|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Missense_Mutation_p.S580R					solute carrier family 4 (sodium bicarbonate cotransporter), member 5											breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						GGCCCCGTGCTGCTGAGAATG	0.587																																					p.S580R		Atlas-SNP	.											.	SLC4A5	215	.	0			c.A1738C						.						93	90	91					2																	74475529		2203	4300	6503	SO:0001583	missense	57835	exon13			CCGTGCTGCTGAG	AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"Solute carriers"	18168	protein-coding gene	gene with protein product		606757	"solute carrier family 4, sodium bicarbonate cotransporter, member 5"			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.1738A>C	chr2.hg19:g.74475529T>G	ENSP00000366861:p.Ser580Arg	93.0	0.0		125.0	39.0	NM_021196		Missense_Mutation	SNP	ENST00000377634.4	hg19	CCDS1936.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145117	0.77888	.	.	ENSG00000188687	ENST00000394019;ENST00000451608;ENST00000346834;ENST00000359484;ENST00000423644;ENST00000358683;ENST00000357822;ENST00000377632;ENST00000377634;ENST00000425249	T;T;T;T;T;T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38	4.85	4.85	0.62838	Bicarbonate transporter, C-terminal (1);	0.192108	0.56097	D	0.000035	D	0.91865	0.7425	H	0.94385	3.53	0.54753	D	0.999987	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.999;1.0;1.0;0.998	D	0.93646	0.6969	10	0.87932	D	0	.	12.7399	0.57246	0.0:0.0:0.0:1.0	.	580;580;516;580;580	Q9BY07-4;E7EQT3;Q9BY07-7;Q9BY07;Q9BY07-3	.;.;.;S4A5_HUMAN;.	R	580;580;580;516;580;516;580;580;580;580	ENSP00000377587:S580R;ENSP00000251768:S580R;ENSP00000352461:S516R;ENSP00000395804:S580R;ENSP00000351513:S516R;ENSP00000350475:S580R;ENSP00000366859:S580R;ENSP00000366861:S580R;ENSP00000405678:S580R	ENSP00000251768:S580R	S	-	1	0	SLC4A5	74329037	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.901000	0.63259	2.187000	0.69744	0.523000	0.50628	AGC	.	.		0.587	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3			G	74475529	T	G	74475529	3	3	160	1	0	0	0	0	1	0	0	0	14672	1580	55	5	1731	5	SLC4A5	2	74475529	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	862493	74475529	168723844	54	24225										
PROM2	150696	hgsc.bcm.edu	37	chr2	95943753	95943753	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctccagcatggtccaggagGtgagagccacctggtctgcc	13	13	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:95943753G>T	ENST00000317620.9	+	8	1183		c.e8+1		PROM2_ENST00000317668.4_Splice_Site|PROM2_ENST00000403131.2_Splice_Site|PROM2_ENST00000542147.1_Splice_Site	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2						negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						GGTCCAGGAGGTGAGAGCCAC	0.567																																					.		Atlas-SNP	.											.	PROM2	78	.	0			c.1050+1G>T						.						71	54	60					2																	95943753		2203	4300	6503	SO:0001630	splice_region_variant	150696	exon8			CAGGAGGTGAGAG	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.1050+1G>T	chr2.hg19:g.95943753G>T		53.0	0.0		59.0	25.0	NM_144707	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Splice_Site	SNP	ENST00000317620.9	hg19	CCDS2012.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.710877	0.68730	.	.	ENSG00000155066	ENST00000403131;ENST00000317668;ENST00000317620;ENST00000542147	.	.	.	5.17	5.17	0.71159	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0525	0.64747	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PROM2	95307480	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.605000	0.61119	2.703000	0.92315	0.655000	0.94253	.	.	.		0.567	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707	Intron	T	95943753	G	T	95943753	5	4	160	1	0	0	0	0	0	0	1	0	12568	1275	44	3	1081	3	PROM2	2	95943753	Splice_Site	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	21468224	95943753	147255620	55	24226										
TBC1D8	11138	hgsc.bcm.edu	37	chr2	101666875	101666875	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	actttcacctcttggtgatcTggctcggctcctgcagatcg	10	13	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:101666875T>G	ENST00000376840.4	-	5	814	c.815A>C	c.(814-816)cAg>cCg	p.Q272P	TBC1D8_ENST00000409318.1_Missense_Mutation_p.Q287P			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	272					blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						CTTGGTGATCTGGCTCGGCTC	0.557																																					p.Q272P		Atlas-SNP	.											.	TBC1D8	169	.	0			c.A815C						.						46	48	47					2																	101666875		1992	4165	6157	SO:0001583	missense	11138	exon5			GTGATCTGGCTCG	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"BUB2-like protein 1", "vascular Rab-GAP/TBC-containing protein"					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.815A>C	chr2.hg19:g.101666875T>G	ENSP00000366036:p.Gln272Pro	60.0	0.0		66.0	14.0	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Missense_Mutation	SNP	ENST00000376840.4	hg19	CCDS46375.1	.	.	.	.	.	.	.	.	.	.	T	16.82	3.227399	0.58668	.	.	ENSG00000204634	ENST00000376840;ENST00000409318	T;T	0.03386	3.95;3.95	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000004	T	0.11281	0.0275	L	0.48642	1.525	0.41935	D	0.990581	B;D	0.65815	0.013;0.995	B;P	0.62649	0.017;0.905	T	0.22906	-1.0203	10	0.27785	T	0.31	-36.4977	15.3821	0.74664	0.0:0.0:0.0:1.0	.	287;272	B7Z6L4;O95759	.;TBCD8_HUMAN	P	272;287	ENSP00000366036:Q272P;ENSP00000386856:Q287P	ENSP00000366036:Q272P	Q	-	2	0	TBC1D8	101033307	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	3.892000	0.56235	2.032000	0.59987	0.459000	0.35465	CAG	.	.		0.557	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063		G	101666875	T	G	101666875	3	3	160	1	0	0	0	0	1	0	0	0	15640	1580	55	5	2671	5	TBC1D8	2	101666875	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	5723122	101666875	141532498	56	24227										
IL1R1	3554	hgsc.bcm.edu	37	chr2	102789169	102789169	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tggaaaatcctgcaaacaaaAgaaggagtaccctcatcaca	7	10	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:102789169A>G	ENST00000410023.1	+	9	1180	c.862A>G	c.(862-864)Aga>Gga	p.R288G	IL1R1_ENST00000424272.1_Missense_Mutation_p.R288G|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000409929.1_Missense_Mutation_p.R288G|IL1R1_ENST00000409329.1_Missense_Mutation_p.R288G|IL1R1_ENST00000409288.1_Missense_Mutation_p.R288G|IL1R1_ENST00000409589.1_Intron|IL1R1_ENST00000233946.3_Missense_Mutation_p.R288G			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	288	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	TGCAAACAAAAGAAGGAGTAC	0.338																																					p.R288G		Atlas-SNP	.											.	IL1R1	52	.	0			c.A862G						.						109	100	103					2																	102789169		2203	4300	6503	SO:0001583	missense	3554	exon8			AACAAAAGAAGGA	M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.862A>G	chr2.hg19:g.102789169A>G	ENSP00000386380:p.Arg288Gly	170.0	0.0		208.0	35.0	NM_000877	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	hg19	CCDS2055.1	.	.	.	.	.	.	.	.	.	.	A	9.381	1.072896	0.20147	.	.	ENSG00000115594	ENST00000409929;ENST00000424272;ENST00000409329;ENST00000428279;ENST00000409288;ENST00000410023;ENST00000233946	T;T;T;T;T;T;T	0.02709	4.19;4.19;4.19;4.19;4.19;4.19;4.19	4.87	3.72	0.42706	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.640031	0.17631	N	0.167371	T	0.03564	0.0102	L	0.59436	1.845	0.09310	N	1	B;B;B	0.13145	0.0;0.0;0.007	B;B;B	0.14023	0.003;0.003;0.01	T	0.42310	-0.9459	10	0.18710	T	0.47	.	7.1863	0.25801	0.9004:0.0:0.0996:0.0	.	288;288;288	B8ZZW4;P14778;B8ZZ73	.;IL1R1_HUMAN;.	G	288;288;288;144;288;288;288	ENSP00000386776:R288G;ENSP00000415366:R288G;ENSP00000387131:R288G;ENSP00000410461:R144G;ENSP00000386478:R288G;ENSP00000386380:R288G;ENSP00000233946:R288G	ENSP00000233946:R288G	R	+	1	2	IL1R1	102155601	0.000000	0.05858	0.003000	0.11579	0.099000	0.18886	0.688000	0.25422	1.000000	0.39049	0.482000	0.46254	AGA	.	.		0.338	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1			G	102789169	A	G	102789169	3	3	160	1	0	0	0	0	1	0	0	0	7667	64	3	2	888	2	IL1R1	2	102789169	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1122294	102789169	140410204	57	24228										
CCDC138	165055	hgsc.bcm.edu	37	chr2	109408129	109408129	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgatacaattatttttttaaAgcctagatgatgaactggat	7	4	0	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:109408129A>T	ENST00000295124.4	+	4	326		c.e4-1		CCDC138_ENST00000412964.2_Splice_Site|CCDC138_ENST00000470608.1_Intron	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138											endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						ATTTTTTTAAAGCCTAGATGA	0.279																																					.		Atlas-SNP	.											.	CCDC138	49	.	0			c.267-2A>T						.						82	98	93					2																	109408129		2197	4282	6479	SO:0001630	splice_region_variant	165055	exon4			TTTTAAAGCCTAG	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.267-1A>T	chr2.hg19:g.109408129A>T		92.0	0.0		85.0	15.0	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Splice_Site	SNP	ENST00000295124.4	hg19	CCDS2080.1	.	.	.	.	.	.	.	.	.	.	A	14.14	2.445713	0.43429	.	.	ENSG00000163006	ENST00000412964;ENST00000295124	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6091	0.62065	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCDC138	108774561	1.000000	0.71417	1.000000	0.80357	0.543000	0.35085	5.587000	0.67510	2.198000	0.70561	0.533000	0.62120	.	.	.		0.279	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	Intron	T	109408129	A	T	109408129	5	4	160	1	0	0	0	0	0	0	1	0	2774	86	3	4	279	4	CCDC138	2	109408129	Splice_Site	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	6618960	109408129	133791244	58	24229										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125204373	125204373	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agcagcttgccctctgccacCctgggcagcctcctggatga	11	16	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:125204373C>G	ENST00000431078.1	+	6	1141	c.777C>G	c.(775-777)acC>acG	p.T259T		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	259	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CCTCTGCCACCCTGGGCAGCC	0.602																																					p.T259T		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.C777G						.						54	58	57					2																	125204373		2152	4271	6423	SO:0001819	synonymous_variant	129684	exon6			TGCCACCCTGGGC	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.777C>G	chr2.hg19:g.125204373C>G		165.0	0.0		152.0	53.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	hg19	CCDS46401.1																																																																																			.	.		0.602	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			G	125204373	C	G	125204373	2	3	160	1	0	0	0	0	0	0	0	1	3652	610	22	4		4	CNTNAP5	2	125204373	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	15796244	125204373	117995000	59	24230										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125504881	125504881	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gggaggttcccctcctggggTccagcagtgtgagtgtggcc	17	11	0	1	rs35085748	byFrequency	TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:125504881T>G	ENST00000431078.1	+	14	2514	c.2150T>G	c.(2149-2151)gTc>gGc	p.V717G		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	717	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CCTCCTGGGGTCCAGCAGTGT	0.517																																					p.V717G		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.T2150G						.						121	120	120					2																	125504881		2056	4213	6269	SO:0001583	missense	129684	exon14			CTGGGGTCCAGCA	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2150T>G	chr2.hg19:g.125504881T>G	ENSP00000399013:p.Val717Gly	158.0	0.0		167.0	20.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	T	8.458	0.854649	0.17106	.	.	ENSG00000155052	ENST00000431078	T	0.18810	2.19	6.04	2.41	0.29592	.	0.465395	0.17848	N	0.159955	T	0.26304	0.0642	M	0.84846	2.72	0.80722	D	1	B	0.24258	0.1	B	0.21708	0.036	T	0.03060	-1.1077	10	0.23302	T	0.38	.	9.3168	0.37939	0.0:0.202:0.0:0.798	.	717	Q8WYK1	CNTP5_HUMAN	G	717	ENSP00000399013:V717G	ENSP00000399013:V717G	V	+	2	0	CNTNAP5	125221351	1.000000	0.71417	0.061000	0.19648	0.004000	0.04260	5.193000	0.65120	0.184000	0.20083	-0.256000	0.11100	GTC	.	T|0.993;C|0.007		0.517	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			G	125504881	T	G	125504881	3	3	160	1	0	0	0	0	1	0	0	0	3652	1667	58	5	2204	5	CNTNAP5	2	125504881	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	300508	125504881	117694492	60	24231										
CYP27C1	339761	hgsc.bcm.edu	37	chr2	127960995	127960995	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cattgacattggtcacggttTctccatcttctgcctggctc	8	13	4	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:127960995T>C	ENST00000335247.7	-	2	261	c.131A>G	c.(130-132)gAa>gGa	p.E44G	CYP27C1_ENST00000409327.1_Missense_Mutation_p.E44G	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	44						membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		GGTCACGGTTTCTCCATCTTC	0.428																																					p.E44G		Atlas-SNP	.											.	CYP27C1	52	.	0			c.A131G						.						181	171	175					2																	127960995		2203	4300	6503	SO:0001583	missense	339761	exon2			ACGGTTTCTCCAT	AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684		"Cytochrome P450s"	33480	protein-coding gene	gene with protein product							Standard	NM_001001665		Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.131A>G	chr2.hg19:g.127960995T>C	ENSP00000334128:p.Glu44Gly	94.0	0.0		95.0	14.0	NM_001001665	Q6ZNI7	Missense_Mutation	SNP	ENST00000335247.7	hg19	CCDS33285.1	.	.	.	.	.	.	.	.	.	.	T	7.457	0.643869	0.14451	.	.	ENSG00000186684	ENST00000335247;ENST00000409327	T;T	0.35421	1.31;1.31	4.23	4.23	0.50019	.	0.371485	0.27349	N	0.019767	T	0.22360	0.0539	N	0.24115	0.695	0.30804	N	0.739587	B	0.02656	0.0	B	0.06405	0.002	T	0.12167	-1.0558	10	0.26408	T	0.33	-1.0388	8.862	0.35263	0.1672:0.0:0.0:0.8328	.	44	Q4G0S4	C27C1_HUMAN	G	44	ENSP00000334128:E44G;ENSP00000387198:E44G	ENSP00000334128:E44G	E	-	2	0	CYP27C1	127677465	0.987000	0.35691	0.982000	0.44146	0.422000	0.31414	2.106000	0.41835	1.564000	0.49628	0.402000	0.26972	GAA	.	.		0.428	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665		C	127960995	T	C	127960995	3	2	160	1	0	0	0	0	1	0	0	0	4162	1783	62	2	1015	2	CYP27C1	2	127960995	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2456114	127960995	115238378	61	24232										
LIMS2	55679	hgsc.bcm.edu	37	chr2	128412026	128412026	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	attcttcacaaagcccaggtCagccagctccacatcacaca	5	16	4	0	rs371008915		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:128412026C>A	ENST00000355119.4	-	4	496	c.331G>T	c.(331-333)Gac>Tac	p.D111Y	LIMS2_ENST00000324938.5_Missense_Mutation_p.D135Y|LIMS2_ENST00000410011.1_Missense_Mutation_p.D106Y|LIMS2_ENST00000409455.1_Missense_Mutation_p.D106Y|LIMS2_ENST00000409808.2_Missense_Mutation_p.D106Y|LIMS2_ENST00000545738.2_Missense_Mutation_p.D133Y	NM_001161403.1	NP_001154875.1	Q7Z4I7	LIMS2_HUMAN	LIM and senescent cell antigen-like domains 2	111	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.			D -> G (in Ref. 5; BAG60013). {ECO:0000305}.	cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0681)		AAGCCCAGGTCAGCCAGCTCC	0.612																																					p.D135Y		Atlas-SNP	.											.	LIMS2	33	.	0			c.G403T						.						120	115	117					2																	128412026		2203	4300	6503	SO:0001583	missense	55679	exon4			CCAGGTCAGCCAG	AF520987	CCDS2147.1, CCDS54394.1, CCDS54395.1, CCDS54396.1, CCDS58725.1	2q21.1	2008-02-05			ENSG00000072163	ENSG00000072163			16084	protein-coding gene	gene with protein product		607908					Standard	NM_017980		Approved		uc002tox.3	Q7Z4I7	OTTHUMG00000131529	ENST00000355119.4:c.331G>T	chr2.hg19:g.128412026C>A	ENSP00000347240:p.Asp111Tyr	207.0	0.0		193.0	76.0	NM_017980	A6NLH0|B4DMV1|F5H6E6|Q7Z4I2|Q7Z4I6|Q7Z4I8|Q8NFE7|Q9HA13	Missense_Mutation	SNP	ENST00000355119.4	hg19	CCDS54395.1	.	.	.	.	.	.	.	.	.	.	.	31	5.091942	0.94149	.	.	ENSG00000072163	ENST00000545738;ENST00000355119;ENST00000324938;ENST00000409455;ENST00000410109;ENST00000409808;ENST00000410011;ENST00000544917;ENST00000422034	D;D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32;-2.32	5.37	5.37	0.77165	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.95959	0.8684	H	0.95917	3.74	0.80722	D	1	D;D;D	0.89917	0.998;0.998;1.0	D;D;D	0.85130	0.967;0.996;0.997	D	0.97165	0.9840	10	0.87932	D	0	.	19.0997	0.93269	0.0:1.0:0.0:0.0	.	133;111;135	F5H6E6;Q7Z4I7;Q7Z4I7-2	.;LIMS2_HUMAN;.	Y	133;111;135;106;106;106;106;133;106	ENSP00000443794:D133Y;ENSP00000347240:D111Y;ENSP00000326888:D135Y;ENSP00000386383:D106Y;ENSP00000386637:D106Y;ENSP00000387002:D106Y	ENSP00000326888:D135Y	D	-	1	0	LIMS2	128128496	1.000000	0.71417	0.993000	0.49108	0.954000	0.61252	7.707000	0.84623	2.523000	0.85059	0.609000	0.83330	GAC	.	.		0.612	LIMS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331133.2	NM_017980		A	128412026	C	A	128412026	3	1	160	1	0	0	0	0	1	0	0	0	8813	826	29	3	722	3	LIMS2	2	128412026	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	451031	128412026	114787347	62	24233										
TMEM163	81615	hgsc.bcm.edu	37	chr2	135308172	135308172	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atgggcagagtgcacagcggCcgcgttgctgtaacgccaca	14	12	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:135308172C>A	ENST00000281924.6	-	4	491	c.427G>T	c.(427-429)Gcc>Tcc	p.A143S		NM_030923.4	NP_112185.1	Q8TC26	TM163_HUMAN	transmembrane protein 163	143						cell junction (GO:0030054)|early endosome membrane (GO:0031901)|integral component of synaptic vesicle membrane (GO:0030285)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.154)		TGCACAGCGGCCGCGTTGCTG	0.537																																					p.A143S		Atlas-SNP	.											.	TMEM163	34	.	0			c.G427T						.						115	110	112					2																	135308172		2203	4300	6503	SO:0001583	missense	81615	exon4			CAGCGGCCGCGTT		CCDS2172.1	2q21.3	2008-02-05			ENSG00000152128	ENSG00000152128			25380	protein-coding gene	gene with protein product						17623043	Standard	NM_030923		Approved	DKFZP566N034, SV31	uc002ttx.3	Q8TC26	OTTHUMG00000131713	ENST00000281924.6:c.427G>T	chr2.hg19:g.135308172C>A	ENSP00000281924:p.Ala143Ser	80.0	0.0		98.0	18.0	NM_030923	Q53QM3|Q53SV7|Q69YH3|Q9UFG3	Missense_Mutation	SNP	ENST00000281924.6	hg19	CCDS2172.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098331	0.56183	.	.	ENSG00000152128	ENST00000281924;ENST00000537539	T	0.62941	-0.01	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.73102	0.3544	L	0.51422	1.61	0.54753	D	0.999988	D	0.71674	0.998	D	0.80764	0.994	T	0.65598	-0.6129	10	0.13108	T	0.6	.	18.3542	0.90351	0.0:1.0:0.0:0.0	.	143	Q8TC26	TM163_HUMAN	S	143;82	ENSP00000281924:A143S	ENSP00000281924:A143S	A	-	1	0	TMEM163	135024642	1.000000	0.71417	0.138000	0.22173	0.168000	0.22595	7.115000	0.77110	2.640000	0.89533	0.563000	0.77884	GCC	.	.		0.537	TMEM163-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254631.2	NM_030923		A	135308172	C	A	135308172	3	1	160	1	0	0	0	0	1	0	0	0	16093	739	26	3	462	3	TMEM163	2	135308172	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	6896146	135308172	107891201	63	24234										
ZEB2	9839	hgsc.bcm.edu	37	chr2	145156008	145156008	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tggtcgtagcccaggaatacTggtctggactggtggcatga	15	8	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:145156008T>A	ENST00000558170.2	-	8	3930	c.2746A>T	c.(2746-2748)Agt>Tgt	p.S916C	ZEB2_ENST00000303660.4_Missense_Mutation_p.S916C|ZEB2_ENST00000539609.3_Missense_Mutation_p.S892C|ZEB2_ENST00000409487.3_Missense_Mutation_p.S916C	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	916					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		CCAGGAATACTGGTCTGGACT	0.493																																					p.S916C	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											.	ZEB2	218	.	0			c.A2746T						.						171	167	168					2																	145156008		2203	4300	6503	SO:0001583	missense	9839	exon8			GAATACTGGTCTG	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.2746A>T	chr2.hg19:g.145156008T>A	ENSP00000454157:p.Ser916Cys	152.0	0.0		180.0	42.0	NM_014795	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	hg19	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	T	14.86	2.662434	0.47572	.	.	ENSG00000169554	ENST00000539609;ENST00000303660;ENST00000409487	T;T;T	0.15603	2.42;2.41;2.41	5.83	4.69	0.59074	.	0.075006	0.85682	D	0.000000	T	0.31327	0.0793	L	0.54323	1.7	0.58432	D	0.999998	D;D;P;P	0.76494	0.999;0.975;0.876;0.876	D;P;B;B	0.65987	0.94;0.671;0.417;0.417	T	0.02087	-1.1216	10	0.59425	D	0.04	-9.8811	8.5945	0.33707	0.0:0.1429:0.0:0.8571	.	892;781;915;916	F5H814;Q53TD9;A0JP08;O60315	.;.;.;ZEB2_HUMAN	C	892;916;916	ENSP00000443792:S892C;ENSP00000302501:S916C;ENSP00000386854:S916C	ENSP00000302501:S916C	S	-	1	0	ZEB2	144872478	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.615000	0.46368	2.231000	0.72958	0.460000	0.39030	AGT	.	.		0.493	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		A	145156008	T	A	145156008	3	1	160	1	0	0	0	0	1	0	0	0	17639	1580	55	4	910	4	ZEB2	2	145156008	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	9847836	145156008	98043365	64	24235										
KIF5C	3800	hgsc.bcm.edu	37	chr2	149633278	149633279	+	Missense_Mutation	DNP	CC	CC	AG													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccgcggggacaaattcatccCcaaatttaaaggcgatgaga							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:149633278_149633279CC>AG	ENST00000435030.1	+	1	460_461	c.92_93CC>AG	c.(91-93)cCC>cAG	p.P31Q	AC105402.4_ENST00000601658.1_RNA|AC105402.4_ENST00000446781.2_RNA			O60282	KIF5C_HUMAN	kinesin family member 5C	31	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		AAATTCATCCCCAAATTTAAAG	0.644																																					p.P31H|p.P31P		Atlas-SNP	.											.	KIF5C	166	.	0			c.C92A|c.C93G						.																																			SO:0001583	missense	3800	exon1			TCATCCCCAAATT|CATCCCCAAATTT	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	Exception_encountered	chr2.hg19:g.149633278_149633279delinsAG	ENSP00000393379:p.Pro31Gln	277.0|275.0	0.0		282.0	84.0|85.0	NM_004522	O95079|Q2YDC5	Missense_Mutation|Silent	SNP	ENST00000435030.1	hg19																																																																																				.	.		0.644	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		AG	149633279	CC	AG	149633278	3	1	160	1	0	0	0	0	1	0	0	0	8316	623	22	3	94	3	KIF5C	2	149633278	Missense_Mutation	DNP	CC	TCGA-DD-AACI-01A-11D-A40R-10	4477270	149633278	93566095	65	24236										
XIRP2	129446	hgsc.bcm.edu	37	chr2	167992512	167992512	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgaaagattcagacaagaaaGgcaaggaaacatcttttgac	9	6	2	5			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:167992512G>T	ENST00000409728.1	+	3	591	c.502G>T	c.(502-504)Ggc>Tgc	p.G168C	XIRP2_ENST00000295237.9_Missense_Mutation_p.G168C|XIRP2_ENST00000409195.1_Missense_Mutation_p.G168C|XIRP2_ENST00000420519.1_Missense_Mutation_p.G168C|XIRP2-AS1_ENST00000525330.1_RNA|XIRP2_ENST00000409043.1_Missense_Mutation_p.G168C|XIRP2_ENST00000409756.2_Missense_Mutation_p.G168C	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGACAAGAAAGGCAAGGAAAC	0.438																																					p.G168C		Atlas-SNP	.											.	XIRP2	914	.	0			c.G502T						.						98	97	98					2																	167992512		1904	4129	6033	SO:0001583	missense	129446	exon3			AAGAAAGGCAAGG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.502G>T	chr2.hg19:g.167992512G>T	ENSP00000386619:p.Gly168Cys	61.0	0.0		75.0	5.0	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	hg19	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.076034	0.36662	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409195;ENST00000409756;ENST00000420519;ENST00000295237	T;T;T;T;T;T	0.78924	-1.13;-1.22;4.21;-1.13;-1.22;4.21	5.51	-0.0527	0.13821	.	.	.	.	.	T	0.79776	0.4504	.	.	.	0.09310	N	0.999998	D;D	0.60575	0.988;0.988	P;P	0.56514	0.8;0.8	T	0.67669	-0.5611	8	0.56958	D	0.05	-0.563	6.0957	0.20019	0.4423:0.1261:0.4316:0.0	.	168;168	A4UGR9-4;A4UGR9-6	.;.	C	168	ENSP00000386454:G168C;ENSP00000386619:G168C;ENSP00000386840:G168C;ENSP00000386724:G168C;ENSP00000415541:G168C;ENSP00000295237:G168C	ENSP00000295237:G168C	G	+	1	0	XIRP2	167700758	0.042000	0.20092	0.067000	0.19924	0.664000	0.39144	0.103000	0.15292	-0.066000	0.12998	-0.226000	0.12346	GGC	.	.		0.438	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		T	167992512	G	T	167992512	3	4	160	1	0	0	0	0	1	0	0	0	17445	1000	35	3	508	3	XIRP2	2	167992512	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	18359234	167992512	75206861	66	24237										
LRP2	4036	hgsc.bcm.edu	37	chr2	170136923	170136923	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tagtggaaagccacacccacGgccactccacgattctgaga	9	14	1	1	rs373521676		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:170136923G>T	ENST00000263816.3	-	11	1563	c.1278C>A	c.(1276-1278)gcC>gcA	p.A426A	LRP2_ENST00000443831.1_Silent_p.A426A	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	426					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CCACACCCACGGCCACTCCAC	0.458																																					p.A426A		Atlas-SNP	.											.	LRP2	751	.	0			c.C1278A						.						75	77	76					2																	170136923		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon11			ACCCACGGCCACT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.1278C>A	chr2.hg19:g.170136923G>T		118.0	0.0		115.0	5.0	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.		0.458	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170136923	G	T	170136923	2	4	160	1	0	0	0	0	0	0	0	1	8965	1103	39	1		1	LRP2	2	170136923	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	2144411	170136923	73062450	67	24238										
PPIG	9360	hgsc.bcm.edu	37	chr2	170488352	170488352	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtccagaagagatccctcctAtacctgaaaatagattccta	6	11	0	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:170488352A>G	ENST00000260970.3	+	11	1058	c.838A>G	c.(838-840)Ata>Gta	p.I280V	PPIG_ENST00000462903.1_Missense_Mutation_p.I280V|PPIG_ENST00000409714.3_Missense_Mutation_p.I265V|PPIG_ENST00000482772.1_3'UTR|PPIG_ENST00000448752.2_Missense_Mutation_p.I280V	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	280					protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	GATCCCTCCTATACCTGAAAA	0.413																																					p.I280V		Atlas-SNP	.											.	PPIG	100	.	0			c.A838G						.						120	108	112					2																	170488352		2203	4300	6503	SO:0001583	missense	9360	exon11			CCTCCTATACCTG	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"SR-related CTD-associated factor 10"	606093	"peptidyl-prolyl isomerase G (cyclophilin G)"			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.838A>G	chr2.hg19:g.170488352A>G	ENSP00000260970:p.Ile280Val	78.0	0.0		80.0	4.0	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	hg19	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	A	14.30	2.493290	0.44352	.	.	ENSG00000138398	ENST00000260970;ENST00000530133;ENST00000433207;ENST00000409714;ENST00000462903;ENST00000448752	T;T;T;T;T	0.21361	2.72;2.26;2.76;2.01;2.72	5.3	4.11	0.48088	.	0.051438	0.85682	D	0.000000	T	0.08802	0.0218	N	0.12569	0.235	0.45554	D	0.998509	B;B;B;B;B	0.26483	0.011;0.001;0.15;0.001;0.001	B;B;B;B;B	0.23419	0.008;0.002;0.046;0.005;0.002	T	0.15292	-1.0442	10	0.02654	T	1	-18.2541	7.4588	0.27283	0.781:0.1445:0.0745:0.0	.	273;265;265;280;280	C9JM79;E9PG73;Q2NKQ6;Q13427-2;Q13427	.;.;.;.;PPIG_HUMAN	V	280;280;273;265;280;280	ENSP00000260970:I280V;ENSP00000408683:I273V;ENSP00000386245:I265V;ENSP00000435987:I280V;ENSP00000407083:I280V	ENSP00000260970:I280V	I	+	1	0	PPIG	170196598	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.327000	0.52045	0.806000	0.34183	0.383000	0.25322	ATA	.	.		0.413	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			G	170488352	A	G	170488352	3	3	160	1	0	0	0	0	1	0	0	0	12336	449	16	2	872	2	PPIG	2	170488352	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	351429	170488352	72711021	68	24239										
CIR1	9541	hgsc.bcm.edu	37	chr2	175213317	175213317	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtctgtgccatggcttctgcTgtcatttcttctgctttgct	9	11	5	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:175213317T>A	ENST00000342016.3	-	10	1353	c.1261A>T	c.(1261-1263)Agc>Tgc	p.S421C	CIR1_ENST00000362053.5_3'UTR	NM_004882.3	NP_004873.3	Q86X95	CIR1_HUMAN	corepressor interacting with RBPJ, 1	421	Arg/Ser-rich (RS domain).				mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(5)|skin(1)	15						TGGCTTCTGCTGTCATTTCTT	0.478																																					p.S421C		Atlas-SNP	.											.	CIR1	38	.	0			c.A1261T						.						221	213	216					2																	175213317		2203	4300	6503	SO:0001583	missense	9541	exon10			TTCTGCTGTCATT	AF098297	CCDS2256.1	2q31.1	2009-07-14			ENSG00000138433	ENSG00000138433			24217	protein-coding gene	gene with protein product	"recepin", "CBF1 interacting corepressor"	605228				15652350, 11222720, 9874765	Standard	NM_004882		Approved	CIR	uc002uim.3	Q86X95	OTTHUMG00000132338	ENST00000342016.3:c.1261A>T	chr2.hg19:g.175213317T>A	ENSP00000339723:p.Ser421Cys	78.0	0.0		95.0	14.0	NM_004882	A6NFI6|A8K8M4|O95367|Q12804|Q4G1B9|Q6PJI4|Q8IWI2	Missense_Mutation	SNP	ENST00000342016.3	hg19	CCDS2256.1	.	.	.	.	.	.	.	.	.	.	T	8.179	0.793354	0.16327	.	.	ENSG00000138433	ENST00000342016	.	.	.	5.82	-3.21	0.05140	.	0.997396	0.08125	N	0.994164	T	0.15522	0.0374	N	0.14661	0.345	0.09310	N	1	B	0.30709	0.291	B	0.27262	0.078	T	0.21655	-1.0239	9	0.44086	T	0.13	.	0.8178	0.01105	0.2397:0.2274:0.1109:0.422	.	421	Q86X95	CIR1_HUMAN	C	421	.	ENSP00000339723:S421C	S	-	1	0	CIR1	174921563	0.000000	0.05858	0.000000	0.03702	0.105000	0.19272	-0.692000	0.05127	-0.123000	0.11745	0.455000	0.32223	AGC	.	.		0.478	CIR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255460.1	NM_004882		A	175213317	T	A	175213317	3	1	160	1	0	0	0	0	1	0	0	0	3434	1580	55	4	95	4	CIR1	2	175213317	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4724965	175213317	67986056	69	24240										
HOXD12	3238	hgsc.bcm.edu	37	chr2	176965409	176965409	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gctgaacctcagcgaccagcAagtcaaaatctggttccaga	9	12	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:176965409A>T	ENST00000406506.2	+	2	806	c.734A>T	c.(733-735)cAa>cTa	p.Q245L	HOXD12_ENST00000404162.2_3'UTR			P35452	HXD12_HUMAN	homeobox D12	245					embryonic digit morphogenesis (GO:0042733)|pattern specification process (GO:0007389)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		AGCGACCAGCAAGTCAAAATC	0.562																																					p.Q245L		Atlas-SNP	.											.	HOXD12	25	.	0			c.A734T						.						41	43	43					2																	176965409		1992	4201	6193	SO:0001583	missense	3238	exon2			ACCAGCAAGTCAA		CCDS46456.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170178	ENSG00000170178		"Homeoboxes / ANTP class : HOXL subclass"	5135	protein-coding gene	gene with protein product		142988	"homeo box D12"	HOX4H		1675198, 1973146	Standard	NM_021193		Approved		uc010zev.1	P35452	OTTHUMG00000150358	ENST00000406506.2:c.734A>T	chr2.hg19:g.176965409A>T	ENSP00000385586:p.Gln245Leu	320.0	0.0		345.0	53.0	NM_021193	B5MCP0|Q0VAD7|Q0VAD8|Q9NS03	Missense_Mutation	SNP	ENST00000406506.2	hg19	CCDS46456.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.848979	0.91277	.	.	ENSG00000170178	ENST00000406506	D	0.97114	-4.25	5.81	5.81	0.92471	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99193	0.9720	H	0.98901	4.365	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98816	1.0745	10	0.87932	D	0	.	16.1699	0.81801	1.0:0.0:0.0:0.0	.	245	P35452	HXD12_HUMAN	L	245	ENSP00000385586:Q245L	ENSP00000385586:Q245L	Q	+	2	0	HOXD12	176673655	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.339000	0.96797	2.217000	0.71921	0.533000	0.62120	CAA	.	.		0.562	HOXD12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359253.2	NM_021193		T	176965409	A	T	176965409	3	4	160	1	0	0	0	0	1	0	0	0	7330	130	5	4	740	4	HOXD12	2	176965409	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1752092	176965409	66233964	70	24241										
TTN	7273	hgsc.bcm.edu	37	chr2	179424917	179424917	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aggagatggtaggaacactgGatcttctgccctaattaagg	12	7	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:179424917G>T	ENST00000591111.1	-	276	81243	c.81019C>A	c.(81019-81021)Cca>Aca	p.P27007T	TTN_ENST00000342992.6_Missense_Mutation_p.P26080T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P19775T|TTN_ENST00000460472.2_Missense_Mutation_p.P19583T|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P19708T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P28648T			Q8WZ42	TITIN_HUMAN	titin	27007	Fibronectin type-III 96. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGGAACACTGGATCTTCTGCC	0.458																																					p.P28648T		Atlas-SNP	.											.	TTN	18412	.	0			c.C85942A						.						111	109	110					2																	179424917		1917	4118	6035	SO:0001583	missense	7273	exon326			ACACTGGATCTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.81019C>A	chr2.hg19:g.179424917G>T	ENSP00000465570:p.Pro27007Thr	147.0	0.0		161.0	46.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.38	2.815275	0.50527	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	6.08	6.08	0.98989	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.71324	0.3326	L	0.55834	1.745	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.997;0.997;0.997	T	0.70710	-0.4797	9	0.87932	D	0	.	20.6647	0.99678	0.0:0.0:1.0:0.0	.	19583;19708;19775;27007	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	26080;19583;19775;19708;19580	ENSP00000343764:P26080T;ENSP00000434586:P19583T;ENSP00000340554:P19775T;ENSP00000352154:P19708T	ENSP00000340554:P19775T	P	-	1	0	TTN	179133163	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.903000	0.87398	2.890000	0.99128	0.655000	0.94253	CCA	.	.		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179424917	G	T	179424917	3	4	160	1	0	0	0	0	1	0	0	0	16750	1174	41	3	22185	3	TTN	2	179424917	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	2459508	179424917	63774456	71	24242										
ZSWIM2	151112	hgsc.bcm.edu	37	chr2	187713768	187713768	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atctctcgtaggaggtagatGctgctactcagcgcctggtc	12	11	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:187713768G>C	ENST00000295131.2	-	1	129	c.90C>G	c.(88-90)agC>agG	p.S30R		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	30					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			GGAGGTAGATGCTGCTACTCA	0.607																																					p.S30R		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.C90G						.						58	53	55					2																	187713768		2203	4300	6503	SO:0001583	missense	151112	exon1			GTAGATGCTGCTA	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.90C>G	chr2.hg19:g.187713768G>C	ENSP00000295131:p.Ser30Arg	136.0	0.0		168.0	48.0	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	hg19	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	G	7.128	0.579348	0.13686	.	.	ENSG00000163012	ENST00000295131	T	0.19532	2.14	4.91	3.12	0.35913	.	0.341983	0.25820	N	0.028086	T	0.12475	0.0303	L	0.27053	0.805	0.34231	D	0.676501	B	0.26400	0.148	B	0.29440	0.102	T	0.21793	-1.0235	10	0.11794	T	0.64	-7.0701	7.5742	0.27926	0.1933:0.0:0.8067:0.0	.	30	Q8NEG5	ZSWM2_HUMAN	R	30	ENSP00000295131:S30R	ENSP00000295131:S30R	S	-	3	2	ZSWIM2	187422013	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	1.126000	0.31344	0.786000	0.33708	-0.142000	0.14014	AGC	.	.		0.607	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		C	187713768	G	C	187713768	3	2	160	1	0	0	0	0	1	0	0	0	18256	1310	46	4	1847	4	ZSWIM2	2	187713768	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	8288851	187713768	55485605	72	24243										
TMEFF2	23671	hgsc.bcm.edu	37	chr2	192862989	192862989	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agaagaaaatattatgtaccTgcataatctgttcttgcata	6	6	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:192862989T>A	ENST00000272771.5	-	7	1928	c.744A>T	c.(742-744)gcA>gcT	p.A248A	TMEFF2_ENST00000392314.1_Splice_Site_p.A248A|TMEFF2_ENST00000487771.1_5'UTR|AC098617.1_ENST00000424116.2_RNA|AC098617.1_ENST00000428980.2_RNA	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2	248						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(12)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			ATTATGTACCTGCATAATCTG	0.323																																					p.A248A	Pancreas(50;1277 1381 28487 47072)	Atlas-SNP	.											.	TMEFF2	54	.	0			c.A744T						.						92	96	95					2																	192862989		2203	4298	6501	SO:0001630	splice_region_variant	23671	exon7			TGTACCTGCATAA	AB017269	CCDS2314.1	2q32.3	2010-05-04			ENSG00000144339	ENSG00000144339			11867	protein-coding gene	gene with protein product	"transmembrane protein TENB2", "tomoregulin", "cancer/testis antigen family 120, member 2"	605734				10903839	Standard	NM_016192		Approved	TENB2, HPP1, TR, TPEF, CT120.2	uc002utc.3	Q9UIK5	OTTHUMG00000132723	ENST00000272771.5:c.745+1A>T	chr2.hg19:g.192862989T>A		47.0	0.0		52.0	9.0	NM_016192	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Silent	SNP	ENST00000272771.5	hg19	CCDS2314.1																																																																																			.	.		0.323	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192	Silent	A	192862989	T	A	192862989	5	1	160	1	0	0	0	0	0	0	1	0	16029	1594	55	4	396	4	TMEFF2	2	192862989	Splice_Site	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	5149221	192862989	50336384	73	24244										
NRP2	8828	hgsc.bcm.edu	37	chr2	206641001	206641001	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctgccagggaccgagcccacAgtggacacggtgcccatgca	13	15	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:206641001A>T	ENST00000357118.4	+	16	2488	c.2457A>T	c.(2455-2457)acA>acT	p.T819T	NRP2_ENST00000540841.1_Intron|NRP2_ENST00000540178.1_Intron|NRP2_ENST00000357785.5_Intron|NRP2_ENST00000360409.3_Intron|NRP2_ENST00000272849.3_Silent_p.T824T|NRP2_ENST00000412873.2_Intron	NM_201267.1	NP_957719	Q99435	NELL2_HUMAN	neuropilin 2	0						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						CCGAGCCCACAGTGGACACGG	0.607											OREG0015157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T824T		Atlas-SNP	.											.	NRP2	179	.	0			c.A2472T						.						81	85	84					2																	206641001		2203	4300	6503	SO:0001819	synonymous_variant	8828	exon16			GCCCACAGTGGAC	AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357118.4:c.2457A>T	chr2.hg19:g.206641001A>T		54.0	0.0	2161	53.0	9.0	NM_018534	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000357118.4	hg19	CCDS46498.1																																																																																			.	.		0.607	NRP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336465.1			T	206641001	A	T	206641001	2	4	160	1	0	0	0	0	0	0	0	1	10670	175	7	4		4	NRP2	2	206641001	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	13778012	206641001	36558372	74	24245										
PTPRN	5798	hgsc.bcm.edu	37	chr2	220156208	220156208	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccacctgcagtgcacgatgaTggggcaggagcggccccggt	16	13	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:220156208T>A	ENST00000295718.2	-	20	2953	c.2713A>T	c.(2713-2715)Atc>Ttc	p.I905F	PTPRN_ENST00000423636.2_Missense_Mutation_p.I815F|PTPRN_ENST00000409251.3_Missense_Mutation_p.I876F|PTPRN_ENST00000497977.1_5'UTR|MIR153-1_ENST00000384914.1_RNA	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	905	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		TGCACGATGATGGGGCAGGAG	0.592																																					p.I905F		Atlas-SNP	.											.	PTPRN	138	.	0			c.A2713T						.						87	70	76					2																	220156208		2203	4300	6503	SO:0001583	missense	5798	exon20			CGATGATGGGGCA		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.2713A>T	chr2.hg19:g.220156208T>A	ENSP00000295718:p.Ile905Phe	240.0	0.0		246.0	40.0	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	hg19	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.197849	0.79015	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.18960	2.18;2.18;2.18	4.86	3.7	0.42460	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.057258	0.64402	D	0.000002	T	0.51176	0.1659	M	0.91818	3.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.57248	-0.7844	10	0.87932	D	0	.	9.5145	0.39098	0.0:0.085:0.0:0.915	.	876;905	Q6NSL1;Q16849	.;PTPRN_HUMAN	F	876;905;876;815	ENSP00000386638:I876F;ENSP00000295718:I905F;ENSP00000444244:I815F	ENSP00000295718:I905F	I	-	1	0	PTPRN	219864452	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.650000	0.54424	0.878000	0.35920	0.459000	0.35465	ATC	.	.		0.592	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			A	220156208	T	A	220156208	3	1	160	1	0	0	0	0	1	0	0	0	12822	1464	51	4	242	4	PTPRN	2	220156208	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	13515207	220156208	23043165	75	24246										
ACSL3	2181	hgsc.bcm.edu	37	chr2	223795465	223795465	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tttctttgaagatgaaaatgGacaaaggtggctctgtactg	11	5	2	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:223795465G>T	ENST00000357430.3	+	14	2198	c.1667G>T	c.(1666-1668)gGa>gTa	p.G556V	AC013476.1_ENST00000582868.1_RNA|ACSL3_ENST00000392066.3_Missense_Mutation_p.G556V	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	556					brain development (GO:0007420)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty acid import (GO:0044539)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)|positive regulation of phosphatidylcholine biosynthetic process (GO:2001247)|positive regulation of secretion (GO:0051047)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)|skin(2)	22		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	GATGAAAATGGACAAAGGTGG	0.378			T	ETV1	prostate																																p.G556V		Atlas-SNP	.		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	.	ACSL3	107	.	0			c.G1667T						.						102	106	104					2																	223795465		2203	4300	6503	SO:0001583	missense	2181	exon13			AAAATGGACAAAG	D89053	CCDS2455.1	2q34-q35	2008-02-05	2004-02-19	2004-02-20	ENSG00000123983	ENSG00000123983		"Acyl-CoA synthetase family"	3570	protein-coding gene	gene with protein product		602371	"fatty-acid-Coenzyme A ligase, long-chain 3"	FACL3			Standard	NM_004457		Approved	ACS3, PRO2194	uc002vnj.3	O95573	OTTHUMG00000133160	ENST00000357430.3:c.1667G>T	chr2.hg19:g.223795465G>T	ENSP00000350012:p.Gly556Val	149.0	0.0		152.0	50.0	NM_203372	Q60I92|Q8IUM9	Missense_Mutation	SNP	ENST00000357430.3	hg19	CCDS2455.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.9|26.9	4.778557|4.778557	0.90195|0.90195	.|.	.|.	ENSG00000123983|ENSG00000123983	ENST00000407441|ENST00000357430;ENST00000392066	.|T;T	.|0.21361	.|2.01;2.01	5.74|5.74	5.74|5.74	0.90152|0.90152	.|AMP-dependent synthetase/ligase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.68550|0.68550	0.3013|0.3013	H|H	0.99238|0.99238	4.48|4.48	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	T|T	0.82774|0.82774	-0.0291|-0.0291	5|10	.|0.87932	.|D	.|0	-19.7837|-19.7837	19.9187|19.9187	0.97077|0.97077	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|556	.|O95573	.|ACSL3_HUMAN	Y|V	57|556	.|ENSP00000350012:G556V;ENSP00000375918:G556V	.|ENSP00000350012:G556V	D|G	+|+	1|2	0|0	ACSL3|ACSL3	223503709|223503709	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.876000|7.876000	0.87215|0.87215	2.702000|2.702000	0.92279|0.92279	0.591000|0.591000	0.81541|0.81541	GAC|GGA	.	.		0.378	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457		T	223795465	G	T	223795465	3	4	160	1	0	0	0	0	1	0	0	0	178	1174	41	3	1709	3	ACSL3	2	223795465	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	3639257	223795465	19403908	76	24247										
SP140	11262	hgsc.bcm.edu	37	chr2	231109739	231109739	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttgtgagcagttagctctccCaaaggctggtggaggagatg	15	7	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:231109739C>T	ENST00000392045.3	+	6	722	c.608C>T	c.(607-609)cCa>cTa	p.P203L	SP140_ENST00000420434.3_Missense_Mutation_p.P203L|SP140_ENST00000486687.2_Missense_Mutation_p.P203L|SP140_ENST00000343805.6_Missense_Mutation_p.P203L|SP140_ENST00000417495.3_Missense_Mutation_p.P203L|SP140_ENST00000350136.5_Missense_Mutation_p.P183L	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	203					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		TTAGCTCTCCCAAAGGCTGGT	0.463																																					p.P203L		Atlas-SNP	.											.	SP140	121	.	0			c.C608T						.						137	127	130					2																	231109739		1927	4149	6076	SO:0001583	missense	11262	exon6			CTCTCCCAAAGGC	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.608C>T	chr2.hg19:g.231109739C>T	ENSP00000375899:p.Pro203Leu	64.0	0.0		70.0	25.0	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	hg19	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	C	9.108	1.005734	0.19199	.	.	ENSG00000079263	ENST00000486687;ENST00000392044;ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434	T;T;T;T;T	0.58940	0.66;0.94;0.66;0.3;0.69	2.46	0.00307	0.14053	.	.	.	.	.	T	0.47893	0.1470	N	0.24115	0.695	0.09310	N	1	D;B;B;B;B	0.65815	0.995;0.183;0.278;0.242;0.183	P;B;B;B;B	0.54889	0.763;0.021;0.079;0.075;0.036	T	0.32745	-0.9895	9	0.41790	T	0.15	-0.4126	2.9781	0.05945	0.5557:0.284:0.1603:0.0	.	203;203;203;203;203	E7EUR5;E7ESH9;E9PFJ6;Q13342;E7EX75	.;.;.;LY10_HUMAN;.	L	203;203;183;203;203;203;203	ENSP00000440107:P203L;ENSP00000345846:P183L;ENSP00000375899:P203L;ENSP00000342096:P203L;ENSP00000398210:P203L	ENSP00000342096:P203L	P	+	2	0	SP140	230817983	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.048000	0.14078	-0.004000	0.14419	-0.493000	0.04662	CCA	.	.		0.463	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		T	231109739	C	T	231109739	3	4	160	1	0	0	0	0	1	0	0	0	14977	594	21	3	747	3	SP140	2	231109739	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	7314274	231109739	12089634	77	24248										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234854632	234854632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccactgtcgaagcaaagctcCggaatcagctagagaagtat	10	10	1	1	rs200066478		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr2:234854632C>T	ENST00000324695.4	+	7	872	c.832C>T	c.(832-834)Cgg>Tgg	p.R278W	AC005538.5_ENST00000455991.1_RNA|TRPM8_ENST00000433712.2_5'UTR	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	278					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	AGCAAAGCTCCGGAATCAGCT	0.478																																					p.R278W		Atlas-SNP	.											.	TRPM8	146	.	0			c.C832T						.						104	90	95					2																	234854632		2203	4300	6503	SO:0001583	missense	79054	exon7			AAGCTCCGGAATC	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.832C>T	chr2.hg19:g.234854632C>T	ENSP00000323926:p.Arg278Trp	120.0	0.0		119.0	13.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	hg19	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.663770	0.67700	.	.	ENSG00000144481	ENST00000324695	T	0.68903	-0.36	5.75	5.75	0.90469	.	0.000000	0.64402	D	0.000007	D	0.84929	0.5581	M	0.89968	3.075	0.80722	D	1	D	0.89917	1.0	D	0.65987	0.94	D	0.87538	0.2457	10	0.87932	D	0	-22.1091	18.5163	0.90936	0.0:1.0:0.0:0.0	.	278	Q7Z2W7	TRPM8_HUMAN	W	278	ENSP00000323926:R278W	ENSP00000323926:R278W	R	+	1	2	TRPM8	234519371	0.993000	0.37304	0.823000	0.32752	0.020000	0.10135	3.009000	0.49552	2.719000	0.93026	0.655000	0.94253	CGG	.	.		0.478	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		T	234854632	C	T	234854632	3	4	160	1	0	0	0	0	1	0	0	0	16607	643	23	1	854	1	TRPM8	2	234854632	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	3744893	234854632	8344741	78	24249										
FBLN2	2199	hgsc.bcm.edu	37	chr3	13659731	13659731	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atactgtgggttcttaccacTgtgcctgctttcctggcttc	9	12	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:13659731T>A	ENST00000295760.7	+	6	1954	c.1885T>A	c.(1885-1887)Tgt>Agt	p.C629S	FBLN2_ENST00000492059.1_Missense_Mutation_p.C629S|FBLN2_ENST00000535798.1_Missense_Mutation_p.C655S|FBLN2_ENST00000404922.3_Missense_Mutation_p.C629S	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	629	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			TTCTTACCACTGTGCCTGCTT	0.622																																					p.C629S		Atlas-SNP	.											.	FBLN2	137	.	0			c.T1885A						.						95	100	98					3																	13659731		2083	4208	6291	SO:0001583	missense	2199	exon6			TACCACTGTGCCT	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"Fibulins"	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.1885T>A	chr3.hg19:g.13659731T>A	ENSP00000295760:p.Cys629Ser	97.0	0.0		79.0	17.0	NM_001998	B7Z9C5|Q8IUI0|Q8IUI1	Missense_Mutation	SNP	ENST00000295760.7	hg19	CCDS46762.1	.	.	.	.	.	.	.	.	.	.	t	18.21	3.574379	0.65878	.	.	ENSG00000163520	ENST00000535798;ENST00000404922;ENST00000295760;ENST00000492059	D;D;D;D	0.99966	-10.09;-10.09;-10.09;-10.09	5.2	5.2	0.72013	EGF-like calcium-binding, conserved site (1);EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99984	0.9995	H	0.99777	4.77	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.98948	1.0793	10	0.87932	D	0	.	13.3197	0.60426	0.0:0.0:0.0:1.0	.	629;629;655	P98095;P98095-2;F5H1F3	FBLN2_HUMAN;.;.	S	655;629;629;629	ENSP00000445705:C655S;ENSP00000384169:C629S;ENSP00000295760:C629S;ENSP00000420042:C629S	ENSP00000295760:C629S	C	+	1	0	FBLN2	13634732	1.000000	0.71417	0.748000	0.31131	0.346000	0.29079	6.174000	0.71943	1.976000	0.57569	0.520000	0.50463	TGT	.	.		0.622	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019		A	13659731	T	A	13659731	3	1	160	1	0	0	0	0	1	0	0	0	5707	1580	55	4	593	4	FBLN2	3	13659731	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10		13659731	184362699	79	24250										
BTD	686	hgsc.bcm.edu	37	chr3	15686472	15686472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aattttgtcaggcgatccgtActgtgagaaggatgctcagg	13	7	2	1	rs148193489		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:15686472A>G	ENST00000303498.5	+	4	1218	c.1109A>G	c.(1108-1110)tAc>tGc	p.Y370C	BTD_ENST00000449107.1_Missense_Mutation_p.Y372C|BTD_ENST00000383778.4_Missense_Mutation_p.Y350C|BTD_ENST00000437172.1_Missense_Mutation_p.Y372C	NM_000060.2|NM_001281723.1	NP_000051.1|NP_001268652.1	P43251	BTD_HUMAN	biotinidase	370					biotin metabolic process (GO:0006768)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	biotin carboxylase activity (GO:0004075)|biotinidase activity (GO:0047708)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	18						GGCGATCCGTACTGTGAGAAG	0.463																																					p.Y370C		Atlas-SNP	.											.	BTD	49	.	0			c.A1109G						.	A	CYS/TYR	0,4406		0,0,2203	115	113	114		1109	-3.2	0	3	dbSNP_134	114	1,8599	1.2+/-3.3	0,1,4299	no	missense	BTD	NM_000060.2	194	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	370/544	15686472	1,13005	2203	4300	6503	SO:0001583	missense	686	exon4			ATCCGTACTGTGA	AF018631	CCDS2628.1, CCDS63563.1, CCDS63564.1, CCDS63565.1	3p25	2007-03-26			ENSG00000169814	ENSG00000169814	3.5.1.12		1122	protein-coding gene	gene with protein product		609019				8001986	Standard	NM_001281723		Approved		uc003cah.3	P43251	OTTHUMG00000129861	ENST00000303498.5:c.1109A>G	chr3.hg19:g.15686472A>G	ENSP00000306477:p.Tyr370Cys	124.0	0.0		132.0	24.0	NM_000060	A6NHF2|B2R865|B4DFX1|B4DLJ9|B7Z7C9|F8W1Q3|Q96EM9	Missense_Mutation	SNP	ENST00000303498.5	hg19	CCDS2628.1	.	.	.	.	.	.	.	.	.	.	A	9.875	1.200039	0.22121	0.0	1.16E-4	ENSG00000169814	ENST00000449107;ENST00000303498;ENST00000437172;ENST00000383778	D;D;D;D	0.89617	-2.54;-2.54;-2.54;-2.54	5.58	-3.24	0.05094	.	1.897250	0.01784	N	0.031925	D	0.86830	0.6027	M	0.77103	2.36	0.18873	N	0.999989	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.10450	0.005;0.005;0.005	T	0.65627	-0.6122	10	0.44086	T	0.13	-44.1713	3.1763	0.06570	0.1927:0.4041:0.0731:0.33	.	372;372;370	A6NHF2;B4DLJ9;P43251	.;.;BTD_HUMAN	C	372;370;372;350	ENSP00000388212:Y372C;ENSP00000306477:Y370C;ENSP00000400995:Y372C;ENSP00000373288:Y350C	ENSP00000306477:Y370C	Y	+	2	0	BTD	15661476	0.000000	0.05858	0.045000	0.18777	0.720000	0.41350	-0.692000	0.05127	-0.176000	0.10707	0.459000	0.35465	TAC	.	A|1.000;G|0.000		0.463	BTD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252103.2	NM_000060		G	15686472	A	G	15686472	3	3	160	1	0	0	0	0	1	0	0	0	1552	391	14	2	1123	2	BTD	3	15686472	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2026741	15686472	182335958	80	24251										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19575195	19575195	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccccaacgaactggagctcaTgagcaaaatcctgcagacag	9	13	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:19575195T>C	ENST00000328405.2	+	16	3194	c.2928T>C	c.(2926-2928)caT>caC	p.H976H		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	976	Ser-rich.				potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						CTGGAGCTCATGAGCAAAATC	0.453																																					p.H976H	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.T2928C						.						119	119	119					3																	19575195		2203	4300	6503	SO:0001819	synonymous_variant	131096	exon16			AGCTCATGAGCAA	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2928T>C	chr3.hg19:g.19575195T>C		94.0	0.0		90.0	15.0	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	hg19	CCDS2632.1																																																																																			.	.		0.453	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		C	19575195	T	C	19575195	2	2	160	1	0	0	0	0	0	0	0	1	8047	1461	51	2		2	KCNH8	3	19575195	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	3888723	19575195	178447235	81	24252										
DCLK3	85443	hgsc.bcm.edu	37	chr3	36778744	36778744	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cggtggacaatgctcttgtcGtgcatgtggacgagggcttt	15	8	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:36778744G>A	ENST00000416516.2	-	2	1897	c.1407C>T	c.(1405-1407)caC>caT	p.H469H		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	469	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						TGCTCTTGTCGTGCATGTGGA	0.483																																					p.H469H		Atlas-SNP	.											.	DCLK3	95	.	0			c.C1407T						.						80	77	78					3																	36778744		1983	4168	6151	SO:0001819	synonymous_variant	85443	exon2			CTTGTCGTGCATG	AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"doublecortin and CaM kinase-like 3"	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.1407C>T	chr3.hg19:g.36778744G>A		152.0	0.0		155.0	32.0	NM_033403		Silent	SNP	ENST00000416516.2	hg19	CCDS43064.1																																																																																			.	.		0.483	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355		A	36778744	G	A	36778744	2	1	160	1	0	0	0	0	0	0	0	1	4295	1136	40	1		1	DCLK3	3	36778744	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	17203549	36778744	161243686	82	24253										
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37133031	37133031	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccttaaggtcatagatatccTgcaggacataggaatgaacc	9	9	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:37133031T>C	ENST00000336686.4	-	18	1116		c.e18-2		LRRFIP2_ENST00000396428.2_Intron|LRRFIP2_ENST00000440230.1_Splice_Site|LRRFIP2_ENST00000354379.4_Intron|Y_RNA_ENST00000383918.1_RNA|LRRFIP2_ENST00000421307.1_Splice_Site|LRRFIP2_ENST00000421276.2_Splice_Site			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2						Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						ATAGATATCCTGCAGGACATA	0.418																																					.		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.1036-2A>G						.						151	131	138					3																	37133031		2203	4300	6503	SO:0001630	splice_region_variant	9209	exon20			ATATCCTGCAGGA	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.1036-2A>G	chr3.hg19:g.37133031T>C		98.0	0.0		92.0	8.0	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Splice_Site	SNP	ENST00000336686.4	hg19	CCDS2664.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.584811	0.86748	.	.	ENSG00000093167	ENST00000421307;ENST00000336686;ENST00000421276;ENST00000440230;ENST00000416425	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9672	0.79984	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRRFIP2	37108035	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.674000	0.83992	2.181000	0.69327	0.460000	0.39030	.	.	.		0.418	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	Intron	C	37133031	T	C	37133031	5	2	160	1	0	0	0	0	0	0	1	0	9037	1594	55	2	1175	2	LRRFIP2	3	37133031	Splice_Site	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	354287	37133031	160889399	83	24254										
CXCR6	10663	hgsc.bcm.edu	37	chr3	45988540	45988540	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	catgacgaggcaatttccacTgtggttcttgccacccagat	9	12	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:45988540T>A	ENST00000458629.1	+	1	2030	c.567T>A	c.(565-567)acT>acA	p.T189T	CXCR6_ENST00000438735.1_Silent_p.T189T|CXCR6_ENST00000304552.4_Silent_p.T189T|FYCO1_ENST00000535325.1_Intron|CXCR6_ENST00000457814.1_Silent_p.T189T|FYCO1_ENST00000438446.1_Intron|FYCO1_ENST00000296137.2_Intron			O00574	CXCR6_HUMAN	chemokine (C-X-C motif) receptor 6	189					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|viral genome replication (GO:0019079)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(3)|lung(1)|prostate(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CAATTTCCACTGTGGTTCTTG	0.463																																					p.T189T	Esophageal Squamous(63;1005 1117 15521 45762 47089)	Atlas-SNP	.											.	CXCR6	17	.	0			c.T567A						.						127	127	127					3																	45988540		2203	4300	6503	SO:0001819	synonymous_variant	10663	exon2			TTCCACTGTGGTT	AF007545	CCDS2735.1	3p21	2012-08-08			ENSG00000172215	ENSG00000172215		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	16647	protein-coding gene	gene with protein product		605163				9166430, 9230441	Standard	XM_005264809		Approved	TYMSTR, STRL33, BONZO, CD186	uc003cpc.1	O00574	OTTHUMG00000133448	ENST00000458629.1:c.567T>A	chr3.hg19:g.45988540T>A		79.0	0.0		86.0	16.0	NM_006564	O00575|Q9HCA5	Silent	SNP	ENST00000458629.1	hg19	CCDS2735.1																																																																																			.	.		0.463	CXCR6-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344395.1			A	45988540	T	A	45988540	2	1	160	1	0	0	0	0	0	0	0	1	4097	1567	55	4		4	CXCR6	3	45988540	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	8855509	45988540	152033890	84	24255										
MST1R	4486	hgsc.bcm.edu	37	chr3	49928638	49928638	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctggactctcacatgcagttCcgcgcagccaggtccctgtg	11	15	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:49928638C>A	ENST00000296474.3	-	17	3663	c.3636G>T	c.(3634-3636)cgG>cgT	p.R1212R	MST1R_ENST00000344206.4_Silent_p.R1163R	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	1212	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		ACATGCAGTTCCGCGCAGCCA	0.617																																					p.R1212R		Atlas-SNP	.											.	MST1R	205	.	0			c.G3636T						.						66	58	61					3																	49928638		2203	4300	6503	SO:0001819	synonymous_variant	4486	exon17			GCAGTTCCGCGCA	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.3636G>T	chr3.hg19:g.49928638C>A		58.0	0.0		51.0	9.0	NM_002447	B5A944|B5A945|B5A946|B5A947	Silent	SNP	ENST00000296474.3	hg19	CCDS2807.1	.	.	.	.	.	.	.	.	.	.	.	7.962	0.747232	0.15710	.	.	ENSG00000164078	ENST00000434765;ENST00000440292	.	.	.	5.37	3.56	0.40772	.	.	.	.	.	T	0.57961	0.2089	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50110	-0.8866	4	.	.	.	-25.672	8.172	0.31260	0.0:0.6754:0.1175:0.207	.	.	.	.	V	190;233	.	.	G	-	2	0	MST1R	49903642	0.997000	0.39634	1.000000	0.80357	0.901000	0.52897	0.467000	0.22035	0.258000	0.21686	-0.829000	0.03081	GGA	.	.		0.617	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			A	49928638	C	A	49928638	2	1	160	1	0	0	0	0	0	0	0	1	9900	842	30	3		3	MST1R	3	49928638	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	3940098	49928638	148093792	85	24256										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51266174	51266174	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggactacaatggctgccctaAtattccttctagcctcatct	6	13	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:51266174A>G	ENST00000266037.9	+	18	1753	c.1730A>G	c.(1729-1731)aAt>aGt	p.N577S		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	577	DHR-1.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		GGCTGCCCTAATATTCCTTCT	0.478																																					p.N577S		Atlas-SNP	.											.	DOCK3	397	.	0			c.A1730G						.						114	114	114					3																	51266174		1965	4158	6123	SO:0001583	missense	1795	exon18			GCCCTAATATTCC	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.1730A>G	chr3.hg19:g.51266174A>G	ENSP00000266037:p.Asn577Ser	133.0	0.0		134.0	29.0	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	A	9.742	1.165175	0.21538	.	.	ENSG00000088538	ENST00000266037	T	0.04758	3.56	5.45	5.45	0.79879	.	0.134765	0.64402	D	0.000003	T	0.05502	0.0145	L	0.41824	1.3	0.45427	D	0.998405	B	0.29552	0.248	B	0.30179	0.112	T	0.38001	-0.9681	10	0.10111	T	0.7	.	15.5099	0.75772	1.0:0.0:0.0:0.0	.	577	Q8IZD9	DOCK3_HUMAN	S	577	ENSP00000266037:N577S	ENSP00000266037:N577S	N	+	2	0	DOCK3	51241214	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	4.103000	0.57783	2.060000	0.61445	0.533000	0.62120	AAT	.	.		0.478	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		G	51266174	A	G	51266174	3	3	160	1	0	0	0	0	1	0	0	0	4690	101	4	2	1800	2	DOCK3	3	51266174	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1337536	51266174	146756256	86	24257										
GRM2	2912	hgsc.bcm.edu	37	chr3	51746843	51746843	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtgcccgcgtggctgtcctgTtcacccgttctgaggatgcc	13	14	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:51746843T>A	ENST00000395052.3	+	3	1039	c.805T>A	c.(805-807)Ttc>Atc	p.F269I	GRM2_ENST00000442933.2_Missense_Mutation_p.F269I|GRM2_ENST00000475478.1_Intron	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	269					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGCTGTCCTGTTCACCCGTTC	0.677																																					p.F269I		Atlas-SNP	.											.	GRM2	91	.	0			c.T805A						.						28	29	28					3																	51746843		2202	4298	6500	SO:0001583	missense	2912	exon3			GTCCTGTTCACCC	L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.805T>A	chr3.hg19:g.51746843T>A	ENSP00000378492:p.Phe269Ile	75.0	0.0		75.0	20.0	NM_000839	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Missense_Mutation	SNP	ENST00000395052.3	hg19	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	t	27.3	4.821056	0.90873	.	.	ENSG00000164082	ENST00000395052;ENST00000442933	D;D	0.84370	-1.84;-1.84	5.23	5.23	0.72850	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.93331	0.7874	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94572	0.7772	10	0.87932	D	0	.	15.4555	0.75311	0.0:0.0:0.0:1.0	.	269	Q14416	GRM2_HUMAN	I	269	ENSP00000378492:F269I;ENSP00000408906:F269I	ENSP00000296479:F269I	F	+	1	0	GRM2	51721883	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	8.026000	0.88783	2.128000	0.65567	0.524000	0.50904	TTC	.	.		0.677	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			A	51746843	T	A	51746843	3	1	160	1	0	0	0	0	1	0	0	0	6806	1725	60	4	811	4	GRM2	3	51746843	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	480669	51746843	146275587	87	24258										
OR5H1	26341	hgsc.bcm.edu	37	chr3	97852435	97852435	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctgagaaataagcaagtcacAgtttcattcacaaaaatgtt	6	7	3	1	rs376802329		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:97852435A>T	ENST00000354565.2	+	1	894	c.894A>T	c.(892-894)acA>acT	p.T298T	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						AGCAAGTCACAGTTTCATTCA	0.323																																					p.T298T		Atlas-SNP	.											.	OR5H1	71	.	0			c.A894T						.	A		0,4404		0,0,2202	73	78	77		894	2.1	0	3		77	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	OR5H1	NM_001005338.1		0,1,6498	TT,TA,AA		0.0116,0.0,0.0077		298/314	97852435	1,12997	2202	4297	6499	SO:0001819	synonymous_variant	26341	exon1			AGTCACAGTTTCA	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"GPCR / Class A : Olfactory receptors"	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.894A>T	chr3.hg19:g.97852435A>T		66.0	0.0		68.0	10.0	NM_001005338		Silent	SNP	ENST00000354565.2	hg19	CCDS33797.1																																																																																			.	.		0.323	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338		T	97852435	A	T	97852435	2	4	160	1	0	0	0	0	0	0	0	1	11168	175	7	4		4	OR5H1	3	97852435	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	46105592	97852435	100169995	88	24259										
KCNAB1	7881	hgsc.bcm.edu	37	chr3	156009781	156009781	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgagcaagcagagctccaccGcccccaatgtggtgaacgca	11	14	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr3:156009781G>A	ENST00000490337.1	+	2	339				KCNAB1_ENST00000389634.5_Missense_Mutation_p.A29T|KCNAB1_ENST00000389636.5_Intron|KCNAB1_ENST00000302490.8_Missense_Mutation_p.A29T|KCNAB1_ENST00000471742.1_Intron	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1						learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GAGCTCCACCGCCCCCAATGT	0.582																																					p.A29T		Atlas-SNP	.											.	KCNAB1	176	.	0			c.G85A						.						68	64	65					3																	156009781		2203	4300	6503	SO:0001627	intron_variant	7881	exon1			TCCACCGCCCCCA	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.276-129624G>A	chr3.hg19:g.156009781G>A		253.0	0.0		226.0	25.0	NM_172159	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	hg19	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.824992	0.50739	.	.	ENSG00000169282	ENST00000302490;ENST00000389634	T;T	0.10288	3.23;2.89	5.04	4.15	0.48705	.	0.172150	0.40385	N	0.001116	T	0.04861	0.0131	N	0.03608	-0.345	0.37360	D	0.911163	B;B	0.14012	0.009;0.006	B;B	0.06405	0.002;0.002	T	0.33369	-0.9871	10	0.38643	T	0.18	.	10.0896	0.42439	0.1573:0.0:0.8427:0.0	.	29;29	F8W6W4;B3KPZ4	.;.	T	29	ENSP00000305858:A29T;ENSP00000374285:A29T	ENSP00000305858:A29T	A	+	1	0	KCNAB1	157492475	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.339000	0.59322	2.349000	0.79799	0.460000	0.39030	GCC	.	.		0.582	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		A	156009781	G	A	156009781	1	1	160	0	1	0	0	0	0	0	0	0	8018	1087	38	1		1	KCNAB1	3	156009781	Intron	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	58157346	156009781	42012649	89	24260										
PDE6B	5158	hgsc.bcm.edu	37	chr4	656887	656887	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acctccaccacctgtgtaacAggtcccagaaccccttggct	7	17	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:656887A>T	ENST00000496514.1	+	15	1853		c.e15-1		RP11-1191J2.5_ENST00000609172.1_RNA|PDE6B_ENST00000255622.6_Splice_Site|PDE6B_ENST00000429163.2_Splice_Site			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta						cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	CCTGTGTAACAGGTCCCAGAA	0.602																																					.	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.1833-2A>T						.						97	91	93					4																	656887		2203	4300	6503	SO:0001630	splice_region_variant	5158	exon15			TGTAACAGGTCCC	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"Phosphodiesterases"	8786	protein-coding gene	gene with protein product	"congenital stationary night blindness 3, autosomal dominant"	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.1833-1A>T	chr4.hg19:g.656887A>T		101.0	0.0		114.0	11.0	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Splice_Site	SNP	ENST00000496514.1	hg19	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.610525	0.28712	.	.	ENSG00000133256	ENST00000255622;ENST00000496514;ENST00000429163	.	.	.	4.01	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8803	0.46935	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PDE6B	646887	1.000000	0.71417	0.493000	0.27502	0.098000	0.18820	8.533000	0.90617	1.453000	0.47775	0.449000	0.29647	.	.	.		0.602	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283	Intron	T	656887	A	T	656887	5	4	160	1	0	0	0	0	0	0	1	0	11655	202	7	4	1889	4	PDE6B	4	656887	Splice_Site	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10		656887	190497389	90	24261										
SLC2A9	56606	hgsc.bcm.edu	37	chr4	9828041	9828041	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttaaggccttccatttatctTaccatcagtgacagctgagt	7	10	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:9828041T>C	ENST00000264784.3	-	12	1656	c.1603A>G	c.(1603-1605)Aag>Gag	p.K535E	SLC2A9_ENST00000506583.1_Missense_Mutation_p.K506E|SLC2A9_ENST00000309065.3_Missense_Mutation_p.K506E	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	535					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	CCATTTATCTTACCATCAGTG	0.408																																					p.K535E		Atlas-SNP	.											.	SLC2A9	158	.	0			c.A1603G						.						179	156	164					4																	9828041		2203	4300	6503	SO:0001583	missense	56606	exon12			TTATCTTACCATC	AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"Solute carriers"	13446	protein-coding gene	gene with protein product	"urate voltage-driven efflux transporter 1"	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.1603A>G	chr4.hg19:g.9828041T>C	ENSP00000264784:p.Lys535Glu	117.0	0.0		146.0	23.0	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	hg19	CCDS3407.1	.	.	.	.	.	.	.	.	.	.	T	13.65	2.299674	0.40694	.	.	ENSG00000109667	ENST00000506583;ENST00000264784;ENST00000309065	D;D;D	0.82255	-1.59;-1.52;-1.59	5.96	4.74	0.60224	.	2.528880	0.01133	N	0.006032	T	0.78000	0.4215	L	0.27053	0.805	0.09310	N	1	B;B	0.29862	0.216;0.259	B;B	0.34242	0.178;0.118	T	0.64740	-0.6336	10	0.46703	T	0.11	.	6.9308	0.24439	0.0:0.0836:0.163:0.7534	.	506;535	Q9NRM0-2;Q9NRM0	.;GTR9_HUMAN	E	506;535;506	ENSP00000422209:K506E;ENSP00000264784:K535E;ENSP00000311383:K506E	ENSP00000264784:K535E	K	-	1	0	SLC2A9	9437139	0.115000	0.22152	0.008000	0.14137	0.013000	0.08279	1.969000	0.40510	2.284000	0.76573	0.528000	0.53228	AAG	.	.		0.408	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1			C	9828041	T	C	9828041	3	2	160	1	0	0	0	0	1	0	0	0	14567	1763	61	2	23	2	SLC2A9	4	9828041	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	9171154	9828041	181326235	91	24262										
PPARGC1A	10891	hgsc.bcm.edu	37	chr4	23826123	23826123	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cagaggaagagataaagttgTtggtttggctaaagaaaaaa	12	2	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:23826123T>C	ENST00000264867.2	-	6	885	c.766A>G	c.(766-768)Aca>Gca	p.T256A	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	256					androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				GATAAAGTTGTTGGTTTGGCT	0.343																																					p.T256A	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.A766G						.						154	167	163					4																	23826123		2203	4300	6503	SO:0001583	missense	10891	exon6			AAGTTGTTGGTTT	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"RNA binding motif (RRM) containing"	9237	protein-coding gene	gene with protein product		604517	"peroxisome proliferative activated receptor, gamma, coactivator 1", "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.766A>G	chr4.hg19:g.23826123T>C	ENSP00000264867:p.Thr256Ala	47.0	0.0		44.0	7.0	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	hg19	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	T	11.09	1.536981	0.27475	.	.	ENSG00000109819	ENST00000264867	T	0.24538	1.85	5.71	4.53	0.55603	.	0.048621	0.85682	D	0.000000	T	0.30759	0.0775	M	0.77820	2.39	0.80722	D	1	B	0.26483	0.15	B	0.26310	0.068	T	0.05225	-1.0898	10	0.32370	T	0.25	-6.752	11.7914	0.52072	0.0:0.0687:0.0:0.9313	.	256	Q9UBK2	PRGC1_HUMAN	A	256	ENSP00000264867:T256A	ENSP00000264867:T256A	T	-	1	0	PPARGC1A	23435221	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	5.981000	0.70524	0.998000	0.38996	-0.589000	0.04120	ACA	.	.		0.343	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261		C	23826123	T	C	23826123	3	2	160	1	0	0	0	0	1	0	0	0	12309	1725	60	2	1662	2	PPARGC1A	4	23826123	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	13998082	23826123	167328153	92	24263										
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25836852	25836852	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcctctggcgtcgagtggccTccagctctcggttccgaaac	11	15	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:25836852T>A	ENST00000399878.3	-	3	949	c.827A>T	c.(826-828)gAg>gTg	p.E276V	SEL1L3_ENST00000264868.5_Missense_Mutation_p.E241V|SEL1L3_ENST00000502949.1_Missense_Mutation_p.E123V|SEL1L3_ENST00000513364.1_5'UTR	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	276						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						TCGAGTGGCCTCCAGCTCTCG	0.537																																					p.E276V		Atlas-SNP	.											.	SEL1L3	62	.	0			c.A827T						.						123	126	125					4																	25836852		1979	4144	6123	SO:0001583	missense	23231	exon3			GTGGCCTCCAGCT	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.827A>T	chr4.hg19:g.25836852T>A	ENSP00000382767:p.Glu276Val	87.0	0.0		99.0	21.0	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.329476	0.81690	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.14766	2.48;2.48;2.48	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.35970	0.0950	M	0.68952	2.095	0.43073	D	0.99471	D	0.89917	1.0	D	0.81914	0.995	T	0.08638	-1.0712	10	0.87932	D	0	-27.0413	14.0679	0.64841	0.0:0.0:0.0:1.0	.	276	Q68CR1	SE1L3_HUMAN	V	276;241;123	ENSP00000382767:E276V;ENSP00000264868:E241V;ENSP00000425438:E123V	ENSP00000264868:E241V	E	-	2	0	SEL1L3	25445950	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	4.438000	0.59961	2.311000	0.77944	0.533000	0.62120	GAG	.	.		0.537	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		A	25836852	T	A	25836852	3	1	160	1	0	0	0	0	1	0	0	0	14027	1551	54	4	2659	4	SEL1L3	4	25836852	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2010729	25836852	165317424	93	24264										
RFC1	5981	hgsc.bcm.edu	37	chr4	39304373	39304373	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ataccttaatctgttcaaccCgaggtctttgaaaacgaaga	7	9	3	2	rs199688793		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:39304373C>T	ENST00000381897.1	-	17	2460	c.2327G>A	c.(2326-2328)cGg>cAg	p.R776Q	RFC1_ENST00000349703.2_Missense_Mutation_p.R775Q	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	776					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						CTGTTCAACCCGAGGTCTTTG	0.303																																					p.R776Q	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.G2327A						.						44	45	45					4																	39304373		2203	4299	6502	SO:0001583	missense	5981	exon17			TCAACCCGAGGTC	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.2327G>A	chr4.hg19:g.39304373C>T	ENSP00000371321:p.Arg776Gln	256.0	0.0		281.0	60.0	NM_001204747	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	hg19	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.033828	0.93575	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.16597	2.33;2.33	6.02	5.18	0.71444	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.30885	0.0779	L	0.31526	0.94	0.80722	D	1	D;D	0.89917	0.994;1.0	D;D	0.97110	0.932;1.0	T	0.05225	-1.0898	10	0.59425	D	0.04	-9.9506	15.146	0.72653	0.0:0.9328:0.0:0.0672	.	776;775	P35251;P35251-2	RFC1_HUMAN;.	Q	776;775	ENSP00000371321:R776Q;ENSP00000261424:R775Q	ENSP00000261424:R775Q	R	-	2	0	RFC1	38980768	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	7.786000	0.85741	1.567000	0.49668	0.655000	0.94253	CGG	.	.		0.303	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		T	39304373	C	T	39304373	3	4	160	1	0	0	0	0	1	0	0	0	13259	652	23	1	1155	1	RFC1	4	39304373	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	13467521	39304373	151849903	94	24265										
NFXL1	152518	hgsc.bcm.edu	37	chr4	47900865	47900865	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tactaactcttggacaaggcTgacagcttcctaaaaccaga	7	11	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:47900865T>A	ENST00000507489.1	-	8	1174	c.998A>T	c.(997-999)cAg>cTg	p.Q333L	NFXL1_ENST00000329043.3_Missense_Mutation_p.Q333L|NFXL1_ENST00000381538.3_Missense_Mutation_p.Q333L	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	333						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						TGGACAAGGCTGACAGCTTCC	0.358																																					p.Q333L		Atlas-SNP	.											.	NFXL1	79	.	0			c.A998T						.						142	138	139					4																	47900865		2203	4300	6503	SO:0001583	missense	152518	exon8			CAAGGCTGACAGC	AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"ovarian zinc finger protein"						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.998A>T	chr4.hg19:g.47900865T>A	ENSP00000422037:p.Gln333Leu	175.0	0.0		221.0	51.0	NM_152995	B1Q2K1|Q86VG1|Q8WVH1	Missense_Mutation	SNP	ENST00000507489.1	hg19	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	T	6.309	0.425150	0.11987	.	.	ENSG00000170448	ENST00000381538;ENST00000507489;ENST00000329043	T;T;T	0.60040	0.22;0.22;0.22	5.15	-0.334	0.12666	Zinc finger, NF-X1-type (2);	0.836379	0.10770	N	0.636150	T	0.41351	0.1155	N	0.25144	0.715	0.19775	N	0.999959	B	0.02656	0.0	B	0.04013	0.001	T	0.21827	-1.0234	10	0.29301	T	0.29	0.0826	12.0732	0.53628	0.1023:0.0:0.628:0.2697	.	333	Q6ZNB6	NFXL1_HUMAN	L	333	ENSP00000370949:Q333L;ENSP00000422037:Q333L;ENSP00000333113:Q333L	ENSP00000333113:Q333L	Q	-	2	0	NFXL1	47595622	0.002000	0.14202	0.400000	0.26346	0.828000	0.46876	-0.149000	0.10204	-0.276000	0.09206	-0.320000	0.08662	CAG	.	.		0.358	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995		A	47900865	T	A	47900865	3	1	160	1	0	0	0	0	1	0	0	0	10397	1580	55	4	1801	4	NFXL1	4	47900865	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	8596492	47900865	143253411	95	24266										
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69198561	69198561	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aatttctcatgcttcttttcTgaacctgtatttagccaaag	5	9	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:69198561T>C	ENST00000344157.4	-	6	1313	c.978A>G	c.(976-978)tcA>tcG	p.S326S	YTHDC1_ENST00000355665.3_Intron|YTHDC1_ENST00000579690.1_Silent_p.S326S	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	326					mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						GCTTCTTTTCTGAACCTGTAT	0.318																																					p.S326S		Atlas-SNP	.											.	YTHDC1	81	.	0			c.A978G						.						88	79	82					4																	69198561		2202	4299	6501	SO:0001819	synonymous_variant	91746	exon6			CTTTTCTGAACCT	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.978A>G	chr4.hg19:g.69198561T>C		62.0	0.0		59.0	15.0	NM_001031732	Q4W5Q3|Q7Z622|Q8TF35	Silent	SNP	ENST00000344157.4	hg19	CCDS33992.1																																																																																			.	.		0.318	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		C	69198561	T	C	69198561	2	2	160	1	0	0	0	0	0	0	0	1	17511	1567	55	2		2	YTHDC1	4	69198561	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	21297696	69198561	121955715	96	24267										
DSPP	1834	hgsc.bcm.edu	37	chr4	88534079	88534079	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aattccgatgggagtcctagTgggaatggagcagatgagga	16	5	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:88534079T>G	ENST00000282478.7	+	3	774	c.741T>G	c.(739-741)agT>agG	p.S247R	DSPP_ENST00000399271.1_Missense_Mutation_p.S247R|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	247					biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		GGAGTCCTAGTGGGAATGGAG	0.493																																					p.S247R		Atlas-SNP	.											.	DSPP	174	.	0			c.T741G						.						109	121	117					4																	88534079		2057	4195	6252	SO:0001583	missense	1834	exon4			TCCTAGTGGGAAT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.741T>G	chr4.hg19:g.88534079T>G	ENSP00000282478:p.Ser247Arg	242.0	0.0		287.0	130.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.287097	0.40494	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.96745	-4.11;-4.11	4.59	-0.459	0.12179	.	.	.	.	.	D	0.96355	0.8811	L	0.59436	1.845	0.28904	N	0.893098	D	0.76494	0.999	D	0.74674	0.984	D	0.90345	0.4362	9	0.62326	D	0.03	-7.9015	4.4745	0.11729	0.1524:0.3763:0.0:0.4713	.	247	Q9NZW4	DSPP_HUMAN	R	247	ENSP00000382213:S247R;ENSP00000282478:S247R	ENSP00000282478:S247R	S	+	3	2	DSPP	88753103	0.998000	0.40836	0.996000	0.52242	0.936000	0.57629	0.114000	0.15520	-0.214000	0.10078	-0.385000	0.06624	AGT	.	.		0.493	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		G	88534079	T	G	88534079	3	3	160	1	0	0	0	0	1	0	0	0	4784	1693	59	5	751	5	DSPP	4	88534079	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	19335518	88534079	102620197	97	24268										
DSPP	1834	hgsc.bcm.edu	37	chr4	88534092	88534092	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtcctagtgggaatggagcaGatgaggatgaagacgagggt	18	4	0	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:88534092G>C	ENST00000282478.7	+	3	787	c.754G>C	c.(754-756)Gat>Cat	p.D252H	DSPP_ENST00000399271.1_Missense_Mutation_p.D252H|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	252					biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		GAATGGAGCAGATGAGGATGA	0.507																																					p.D252H		Atlas-SNP	.											.	DSPP	174	.	0			c.G754C						.						117	129	125					4																	88534092		2061	4194	6255	SO:0001583	missense	1834	exon4			GGAGCAGATGAGG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.754G>C	chr4.hg19:g.88534092G>C	ENSP00000282478:p.Asp252His	243.0	0.0		272.0	119.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318612	0.40996	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.92595	-3.07;-3.07	4.4	4.4	0.53042	.	.	.	.	.	D	0.94085	0.8104	L	0.55481	1.735	0.25521	N	0.987364	D	0.89917	1.0	D	0.74023	0.982	D	0.86844	0.2019	9	0.66056	D	0.02	-3.0903	10.2175	0.43177	0.0966:0.0:0.9034:0.0	.	252	Q9NZW4	DSPP_HUMAN	H	252	ENSP00000382213:D252H;ENSP00000282478:D252H	ENSP00000282478:D252H	D	+	1	0	DSPP	88753116	0.995000	0.38212	0.897000	0.35233	0.933000	0.57130	2.576000	0.46033	2.284000	0.76573	0.557000	0.71058	GAT	.	.		0.507	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88534092	G	C	88534092	3	2	160	1	0	0	0	0	1	0	0	0	4784	942	33	4	764	4	DSPP	4	88534092	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	13	88534092	102620184	98	24269										
CENPE	1062	hgsc.bcm.edu	37	chr4	104066278	104066278	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aagggcctcctgtactctttTcatttcctctttttccttaa	4	12	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:104066278T>A	ENST00000265148.3	-	32	4875	c.4786A>T	c.(4786-4788)Aaa>Taa	p.K1596*	CENPE_ENST00000380026.3_Nonsense_Mutation_p.K1571*	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1596					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TGTACTCTTTTCATTTCCTCT	0.328																																					p.K1596X		Atlas-SNP	.											.	CENPE	253	.	0			c.A4786T						.						139	131	134					4																	104066278		2203	4298	6501	SO:0001587	stop_gained	1062	exon32			CTCTTTTCATTTC	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.4786A>T	chr4.hg19:g.104066278T>A	ENSP00000265148:p.Lys1596*	55.0	0.0		56.0	9.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Nonsense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	T	41	8.815695	0.98964	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	.	.	.	4.06	2.79	0.32731	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.9088	0.24323	0.0:0.1189:0.0:0.8811	.	.	.	.	X	1596;1596;1571	.	ENSP00000265148:K1596X	K	-	1	0	CENPE	104285727	0.039000	0.19947	0.805000	0.32314	0.317000	0.28152	0.227000	0.17795	0.538000	0.28769	0.368000	0.22195	AAA	.	.		0.328	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104066278	T	A	104066278	4	1	160	1	0	0	0	0	0	1	0	0	3232	1792	62	4	3391	4	CENPE	4	104066278	Nonsense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	15532186	104066278	87087998	99	24270										
TET2	54790	hgsc.bcm.edu	37	chr4	106157691	106157691	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aagacccaaaacttgcatcaCatgcaatattttccaaataa	3	10	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:106157691C>T	ENST00000540549.1	+	3	3452	c.2592C>T	c.(2590-2592)caC>caT	p.H864H	TET2_ENST00000513237.1_Silent_p.H885H|TET2_ENST00000545826.1_Silent_p.H864H|TET2_ENST00000380013.4_Silent_p.H864H|TET2_ENST00000394764.1_Silent_p.H864H|TET2_ENST00000305737.2_Silent_p.H864H|TET2_ENST00000413648.2_Silent_p.H864H			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	864	Gln-rich.				5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ACTTGCATCACATGCAATATT	0.388			"Mis N, F"		MDS																																p.H864H		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.C2592T						.						71	68	69					4																	106157691		2203	4300	6503	SO:0001819	synonymous_variant	54790	exon3			GCATCACATGCAA	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.2592C>T	chr4.hg19:g.106157691C>T		259.0	0.0		252.0	62.0	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	hg19	CCDS47120.1																																																																																			.	.		0.388	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106157691	C	T	106157691	2	4	160	1	0	0	0	0	0	0	0	1	15785	477	17	3		3	TET2	4	106157691	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	2091413	106157691	84996585	100	24271										
BBS12	166379	hgsc.bcm.edu	37	chr4	123663523	123663523	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atttagtgtaagtttgtgtcCttttctacaggtcccttcag	8	8	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:123663523C>T	ENST00000314218.3	+	2	669	c.476C>T	c.(475-477)cCt>cTt	p.P159L	BBS12_ENST00000542236.1_Missense_Mutation_p.P159L	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	159			P -> L (in BBS12; pathogenicity uncertain; significantly reduces the interaction with MKKS; the interaction with BBS10 is not affected by this mutation). {ECO:0000269|PubMed:17160889}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						AGTTTGTGTCCTTTTCTACAG	0.383									Bardet-Biedl syndrome																												p.P159L		Atlas-SNP	.											.	BBS12	63	.	0			c.C476T	GRCh37	CM070034	BBS12	M		.						110	98	102					4																	123663523		2203	4300	6503	SO:0001583	missense	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TGTGTCCTTTTCT	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"Heat Shock Proteins / Chaperonins"	26648	protein-coding gene	gene with protein product		610683	"chromosome 4 open reading frame 24"	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.476C>T	chr4.hg19:g.123663523C>T	ENSP00000319062:p.Pro159Leu	157.0	0.0		160.0	37.0	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	hg19	CCDS3728.1	.	.	.	.	.	.	.	.	.	.	C	10.90	1.480328	0.26598	.	.	ENSG00000181004	ENST00000314218;ENST00000542236;ENST00000433287	T;T;T	0.72835	-0.69;-0.69;-0.66	5.2	3.41	0.39046	.	0.268407	0.29466	N	0.012067	T	0.52533	0.1740	L	0.34521	1.04	0.09310	N	0.999999	B	0.15473	0.013	B	0.15052	0.012	T	0.43245	-0.9403	10	0.51188	T	0.08	-23.6558	1.8051	0.03079	0.3112:0.3989:0.1539:0.136	.	159	Q6ZW61	BBS12_HUMAN	L	159	ENSP00000319062:P159L;ENSP00000438273:P159L;ENSP00000398912:P159L	ENSP00000319062:P159L	P	+	2	0	BBS12	123882973	0.493000	0.26035	0.015000	0.15790	0.290000	0.27261	0.846000	0.27682	1.287000	0.44583	0.650000	0.86243	CCT	.	.		0.383	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618		T	123663523	C	T	123663523	3	4	160	1	0	0	0	0	1	0	0	0	1337	681	24	3	478	3	BBS12	4	123663523	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	17505832	123663523	67490753	101	24272										
ZNF827	152485	hgsc.bcm.edu	37	chr4	146770559	146770559	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctgggggtactctgccctcTggcatcttctgtaagggttc	12	11	5	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:146770559T>C	ENST00000508784.1	-	6	2363	c.2136A>G	c.(2134-2136)ccA>ccG	p.P712P	ZNF827_ENST00000379448.4_Silent_p.P712P|ZNF827_ENST00000511534.1_5'UTR|ZNF827_ENST00000513320.1_Silent_p.P362P			Q17R98	ZN827_HUMAN	zinc finger protein 827	712					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					CTCTGCCCTCTGGCATCTTCT	0.493																																					p.P712P		Atlas-SNP	.											.	ZNF827	102	.	0			c.A2136G						.						108	117	114					4																	146770559		2203	4300	6503	SO:0001819	synonymous_variant	152485	exon6			GCCCTCTGGCATC	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.2136A>G	chr4.hg19:g.146770559T>C		121.0	0.0		144.0	40.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Silent	SNP	ENST00000508784.1	hg19																																																																																				.	.		0.493	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		C	146770559	T	C	146770559	2	2	160	1	0	0	0	0	0	0	0	1	18195	1567	55	2		2	ZNF827	4	146770559	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	23107036	146770559	44383717	102	24273										
ZNF827	152485	hgsc.bcm.edu	37	chr4	146770637	146770637	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttccggctgggtgatatcgaGacatgggagtcctggatgtc	15	8	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:146770637G>C	ENST00000508784.1	-	6	2285	c.2058C>G	c.(2056-2058)gtC>gtG	p.V686V	ZNF827_ENST00000379448.4_Silent_p.V686V|ZNF827_ENST00000511534.1_5'UTR|ZNF827_ENST00000513320.1_Silent_p.V336V			Q17R98	ZN827_HUMAN	zinc finger protein 827	686					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					GTGATATCGAGACATGGGAGT	0.498																																					p.V686V		Atlas-SNP	.											.	ZNF827	102	.	0			c.C2058G						.						147	142	144					4																	146770637		2203	4300	6503	SO:0001819	synonymous_variant	152485	exon6			TATCGAGACATGG	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.2058C>G	chr4.hg19:g.146770637G>C		83.0	0.0		122.0	47.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Silent	SNP	ENST00000508784.1	hg19																																																																																				.	.		0.498	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		C	146770637	G	C	146770637	2	2	160	1	0	0	0	0	0	0	0	1	18195	929	33	4		4	ZNF827	4	146770637	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	78	146770637	44383639	103	24274										
PRSS48	345062	hgsc.bcm.edu	37	chr4	152203321	152203321	+	Frame_Shift_Del	DEL	T	T	-													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acctggactactttttcataTactgtgtggctaggatcgat							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:152203321delT	ENST00000455694.2	+	3	239	c.237delT	c.(235-237)tatfs	p.Y79fs	PRSS48_ENST00000441586.2_Intron|SH3D19_ENST00000604030.1_Intron	NM_183375.2	NP_899231.2	Q7RTY5	PRS48_HUMAN	protease, serine, 48	79	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8						CTTTTTCATATACTGTGTGGC	0.473																																					p.Y79fs		Atlas-INDEL	.											.	PRSS48	91	.	0			c.236delA						.						257	237	244					4																	152203321		1942	4144	6086	SO:0001589	frameshift_variant	345062	exon3			.	BN000134	CCDS47145.1	4q31.3	2010-05-07			ENSG00000189099	ENSG00000189099		"Serine peptidases / Serine peptidases"	24635	protein-coding gene	gene with protein product						12838346	Standard	NM_183375		Approved	ESSPL	uc011cif.2	Q7RTY5	OTTHUMG00000161673	ENST00000455694.2:c.237delT	chr4.hg19:g.152203321delT	ENSP00000401328:p.Tyr79fs	94.0	0.0		135.0	21.0	NM_183375	Q08E82|Q0VAD4	Frame_Shift_Del	DEL	ENST00000455694.2	hg19	CCDS47145.1																																																																																			.	.		0.473	PRSS48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365685.3	NM_183375		-	152203321	T	-	152203321	7	5	160	1	0	1	0	1	0	0	0	0	12642	1413	49	0	247	0	PRSS48	4	152203321	Frame_Shift_Del	DEL	T	TCGA-DD-AACI-01A-11D-A40R-10	5432684	152203321	38950955	104	24275										
MAP9	79884	hgsc.bcm.edu	37	chr4	156289851	156289851	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	caattcttcactgagggcagTttctttatcttctagtccat	6	10	5	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr4:156289851T>A	ENST00000311277.4	-	5	858	c.595A>T	c.(595-597)Act>Tct	p.T199S	MAP9_ENST00000379248.2_Missense_Mutation_p.T126S|AC097467.2_ENST00000598890.1_RNA|AC097467.2_ENST00000596165.1_RNA|AC097467.2_ENST00000600928.1_RNA|MAP9_ENST00000515654.1_Missense_Mutation_p.T199S|AC097467.2_ENST00000597831.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	199					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		CTGAGGGCAGTTTCTTTATCT	0.418																																					p.T199S		Atlas-SNP	.											.	MAP9	79	.	0			c.A595T						.						204	190	195					4																	156289851		2203	4300	6503	SO:0001583	missense	79884	exon5			GGGCAGTTTCTTT	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"aster-associated protein"	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.595A>T	chr4.hg19:g.156289851T>A	ENSP00000310593:p.Thr199Ser	118.0	0.0		141.0	34.0	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	hg19	CCDS35493.1	.	.	.	.	.	.	.	.	.	.	T	9.785	1.176486	0.21704	.	.	ENSG00000164114	ENST00000311277;ENST00000515654;ENST00000433024;ENST00000393836;ENST00000379248	T;T;T;T	0.30981	2.27;2.29;1.51;3.24	4.8	-9.6	0.00553	.	1.302380	0.05401	N	0.540762	T	0.12561	0.0305	L	0.28274	0.84	0.09310	N	1	B;P;B;B	0.43938	0.058;0.822;0.137;0.137	B;B;B;B	0.41510	0.059;0.359;0.037;0.037	T	0.32824	-0.9892	10	0.06891	T	0.86	1.6013	0.5456	0.00653	0.2886:0.2134:0.2926:0.2054	.	198;126;199;199	B4DVG9;A8MSM7;B9EJB6;Q49MG5	.;.;.;MAP9_HUMAN	S	199;199;198;199;126	ENSP00000310593:T199S;ENSP00000427402:T199S;ENSP00000394048:T198S;ENSP00000368550:T126S	ENSP00000310593:T199S	T	-	1	0	MAP9	156509301	0.000000	0.05858	0.000000	0.03702	0.785000	0.44390	-0.871000	0.04223	-2.213000	0.00735	-0.456000	0.05471	ACT	.	.		0.418	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580		A	156289851	T	A	156289851	3	1	160	1	0	0	0	0	1	0	0	0	9279	1725	60	4	1388	4	MAP9	4	156289851	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4086530	156289851	34864425	105	24276										
CDH18	1016	hgsc.bcm.edu	37	chr5	19591188	19591188	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctttaaagaaaggattcctTctctggtctctttgtcagtg	8	8	4	1	rs528650652		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:19591188T>C	ENST00000507958.1	-	9	1967	c.977A>G	c.(976-978)gAa>gGa	p.E326G	CDH18_ENST00000511273.1_Missense_Mutation_p.E326G|CDH18_ENST00000274170.4_Missense_Mutation_p.E326G|CDH18_ENST00000502796.1_Missense_Mutation_p.E326G|CDH18_ENST00000506372.1_Missense_Mutation_p.E326G|CDH18_ENST00000382275.1_Missense_Mutation_p.E326G			Q13634	CAD18_HUMAN	cadherin 18, type 2	326	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					AAGGATTCCTTCTCTGGTCTC	0.393																																					p.E326G		Atlas-SNP	.											.	CDH18	561	.	0			c.A977G						.						110	96	100					5																	19591188		2203	4300	6503	SO:0001583	missense	1016	exon7			ATTCCTTCTCTGG	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.977A>G	chr5.hg19:g.19591188T>C	ENSP00000425093:p.Glu326Gly	63.0	0.0		78.0	10.0	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411282	0.83340	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17;1.17;1.17	5.24	5.24	0.73138	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.69584	0.3127	H	0.94734	3.575	0.54753	D	0.999989	D;D	0.76494	0.999;0.996	D;D	0.80764	0.994;0.955	T	0.79235	-0.1887	9	.	.	.	.	13.9607	0.64177	0.0:0.0:0.0:1.0	.	326;326	B4DHG6;Q13634	.;CAD18_HUMAN	G	326;326;326;326;326;326;272;326	ENSP00000371710:E326G;ENSP00000425093:E326G;ENSP00000274170:E326G;ENSP00000424931:E326G;ENSP00000422138:E326G;ENSP00000427383:E272G;ENSP00000425854:E326G	.	E	-	2	0	CDH18	19626945	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.556000	0.82233	1.966000	0.57179	0.528000	0.53228	GAA	.	.		0.393	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		C	19591188	T	C	19591188	3	2	160	1	0	0	0	0	1	0	0	0	3105	1783	62	2	1423	2	CDH18	5	19591188	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10		19591188	161324072	106	24277										
NPR3	4883	hgsc.bcm.edu	37	chr5	32712409	32712409	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgagtactcgcacctcacgcGcgtggcgcccgcctacgcca	11	18	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:32712409G>A	ENST00000265074.8	+	1	870	c.527G>A	c.(526-528)cGc>cAc	p.R176H	NPR3_ENST00000415685.2_Intron|NPR3_ENST00000434067.2_Intron|NPR3_ENST00000415167.2_Missense_Mutation_p.R176H	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3	176					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	CACCTCACGCGCGTGGCGCCC	0.677																																					p.R176H		Atlas-SNP	.											.	NPR3	65	.	0			c.G527A						.						37	44	42					5																	32712409		2068	4192	6260	SO:0001583	missense	4883	exon1			TCACGCGCGTGGC		CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"guanylate cyclase C"	108962	"chromosome 5 open reading frame 23", "atrionatriuretic peptide receptor C", "natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)", "natriuretic peptide receptor C"	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.527G>A	chr5.hg19:g.32712409G>A	ENSP00000265074:p.Arg176His	106.0	0.0		141.0	25.0	NM_000908	A2RRD1|B4DT84|E7EPG9	Missense_Mutation	SNP	ENST00000265074.8	hg19	CCDS56357.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.931256	0.92389	.	.	ENSG00000113389	ENST00000265074;ENST00000415167	D;D	0.91295	-2.82;-2.82	4.89	4.89	0.63831	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.96253	0.8778	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96990	0.9721	10	0.87932	D	0	-26.0128	18.2354	0.89948	0.0:0.0:1.0:0.0	.	176;176	P17342;Q60I31	ANPRC_HUMAN;.	H	176	ENSP00000265074:R176H;ENSP00000398028:R176H	ENSP00000265074:R176H	R	+	2	0	NPR3	32748166	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	9.429000	0.97481	2.551000	0.86045	0.561000	0.74099	CGC	.	.		0.677	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908		A	32712409	G	A	32712409	3	1	160	1	0	0	0	0	1	0	0	0	10605	1087	38	1	529	1	NPR3	5	32712409	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	13121221	32712409	148202851	107	24278										
NUP155	9631	hgsc.bcm.edu	37	chr5	37370982	37370982	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acatgcggtcctcttgcaacTgacggtcgatgagccgtcca	11	13	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:37370982T>C	ENST00000231498.3	-	1	301	c.98A>G	c.(97-99)cAg>cGg	p.Q33R	NUP155_ENST00000513532.1_Missense_Mutation_p.Q33R|NUP155_ENST00000381843.2_5'Flank	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	33					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTCTTGCAACTGACGGTCGAT	0.572																																					p.Q33R		Atlas-SNP	.											.	NUP155	116	.	0			c.A98G						.						104	100	102					5																	37370982		2203	4300	6503	SO:0001583	missense	9631	exon1			TGCAACTGACGGT	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.98A>G	chr5.hg19:g.37370982T>C	ENSP00000231498:p.Gln33Arg	70.0	0.0		97.0	12.0	NM_153485	Q9UBE9|Q9UFL5	Missense_Mutation	SNP	ENST00000231498.3	hg19	CCDS3921.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.302556	0.60195	.	.	ENSG00000113569	ENST00000231498;ENST00000513532	T;T	0.77489	-1.09;-1.1	4.28	4.28	0.50868	.	0.116985	0.64402	D	0.000014	T	0.62636	0.2444	L	0.43152	1.355	0.31353	N	0.682312	P;B	0.34562	0.457;0.432	B;B	0.27887	0.084;0.048	T	0.61038	-0.7143	10	0.10377	T	0.69	.	9.1292	0.36835	0.1627:0.0:0.0:0.8373	.	33;33	E9PF10;O75694	.;NU155_HUMAN	R	33	ENSP00000231498:Q33R;ENSP00000422019:Q33R	ENSP00000231498:Q33R	Q	-	2	0	NUP155	37406739	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	4.254000	0.58798	1.810000	0.52873	0.529000	0.55759	CAG	.	.		0.572	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		C	37370982	T	C	37370982	3	2	160	1	0	0	0	0	1	0	0	0	10765	1580	55	2	4217	2	NUP155	5	37370982	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4658573	37370982	143544278	108	24279										
C9	735	hgsc.bcm.edu	37	chr5	39341729	39341729	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gctctgtgggcacacactgtCgtctgtctcccacagcgtcg	11	15	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:39341729C>T	ENST00000263408.4	-	3	352	c.257G>A	c.(256-258)cGa>cAa	p.R86Q	C9_ENST00000509186.1_5'UTR	NM_001737.3	NP_001728.1	P02748	CO9_HUMAN	complement component 9	86	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|hemolysis by symbiont of host erythrocytes (GO:0019836)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane attack complex (GO:0005579)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)			CACACACTGTCGTCTGTCTCC	0.453																																					p.R86Q		Atlas-SNP	.											C9,right_upper_lobe,carcinoma,0,1	C9	116	.	0			c.G257A						.						118	109	112					5																	39341729		2203	4300	6503	SO:0001583	missense	735	exon3			CACTGTCGTCTGT		CCDS3929.1	5p14-p12	2014-09-17			ENSG00000113600	ENSG00000113600		"Complement system"	1358	protein-coding gene	gene with protein product		120940					Standard	NM_001737		Approved		uc003jlv.4	P02748	OTTHUMG00000094767	ENST00000263408.4:c.257G>A	chr5.hg19:g.39341729C>T	ENSP00000263408:p.Arg86Gln	146.0	0.0		173.0	26.0	NM_001737		Missense_Mutation	SNP	ENST00000263408.4	hg19	CCDS3929.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.313980	0.23908	.	.	ENSG00000113600	ENST00000263408	T	0.49720	0.77	5.51	-1.46	0.08800	.	1.143940	0.06279	N	0.697008	T	0.25680	0.0625	N	0.11106	0.095	0.09310	N	1	B	0.16802	0.019	B	0.11329	0.006	T	0.29305	-1.0016	10	0.02654	T	1	-0.6749	12.6649	0.56835	0.0:0.2587:0.0:0.7413	.	86	P02748	CO9_HUMAN	Q	86	ENSP00000263408:R86Q	ENSP00000263408:R86Q	R	-	2	0	C9	39377486	0.000000	0.05858	0.000000	0.03702	0.372000	0.29890	-0.171000	0.09883	-0.692000	0.05128	-0.291000	0.09656	CGA	.	.		0.453	C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211576.3			T	39341729	C	T	39341729	3	4	160	1	0	0	0	0	1	0	0	0	2445	884	31	1	1458	1	C9	5	39341729	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	1970747	39341729	141573531	109	24280										
C5orf28	64417	hgsc.bcm.edu	37	chr5	43446346	43446346	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agacatcaatacgaactccaTgttttgaagacatcatttgt	6	8	2	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:43446346T>A	ENST00000500337.2	-	5	957	c.626A>T	c.(625-627)cAt>cTt	p.H209L	C5orf28_ENST00000537319.1_Missense_Mutation_p.H78L|C5orf28_ENST00000397080.3_Missense_Mutation_p.H209L|C5orf28_ENST00000510130.1_Missense_Mutation_p.H107L|C5orf28_ENST00000511525.1_5'UTR|C5orf28_ENST00000512085.1_Missense_Mutation_p.H209L			Q0VDI3	CE028_HUMAN	chromosome 5 open reading frame 28	209						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(5)	9	Lung NSC(6;2.07e-05)					ACGAACTCCATGTTTTGAAGA	0.348																																					p.H209L		Atlas-SNP	.											.	C5orf28	25	.	0			c.A626T						.						102	100	100					5																	43446346		2203	4300	6503	SO:0001583	missense	64417	exon3			ACTCCATGTTTTG	AK025310	CCDS3945.1	5p12	2011-01-25			ENSG00000151881	ENSG00000151881			26139	protein-coding gene	gene with protein product						12477932	Standard	NM_022483		Approved	FLJ21657	uc003jny.3	Q0VDI3	OTTHUMG00000131150	ENST00000500337.2:c.626A>T	chr5.hg19:g.43446346T>A	ENSP00000426067:p.His209Leu	87.0	0.0		100.0	13.0	NM_022483	B2RDA6|Q9H6Z2	Missense_Mutation	SNP	ENST00000500337.2	hg19	CCDS3945.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.463696	0.84425	.	.	ENSG00000151881	ENST00000500337;ENST00000537319;ENST00000397080;ENST00000512085;ENST00000510130	.	.	.	6.06	6.06	0.98353	.	0.174023	0.64402	D	0.000007	T	0.65238	0.2672	M	0.73962	2.25	0.58432	D	0.999998	B	0.31548	0.328	B	0.31101	0.124	T	0.67389	-0.5683	9	0.72032	D	0.01	-13.3332	16.6093	0.84858	0.0:0.0:0.0:1.0	.	209	Q0VDI3	CE028_HUMAN	L	209;78;209;209;107	.	ENSP00000380270:H209L	H	-	2	0	C5orf28	43482103	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.985000	0.70556	2.324000	0.78689	0.533000	0.62120	CAT	.	.		0.348	C5orf28-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368003.1	NM_022483		A	43446346	T	A	43446346	3	1	160	1	0	0	0	0	1	0	0	0	2291	1464	51	4	25	4	C5orf28	5	43446346	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4104617	43446346	137468914	110	24281										
PTCD2	79810	hgsc.bcm.edu	37	chr5	71618053	71618053	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	attaaaagaatttcaacaaaAgaaagtggctgttgcatgta	8	4	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:71618053A>G	ENST00000380639.5	+	2	198	c.182A>G	c.(181-183)aAg>aGg	p.K61R	MRPS27_ENST00000513900.1_5'Flank|PTCD2_ENST00000536805.1_5'UTR|PTCD2_ENST00000503868.1_Missense_Mutation_p.K61R|MRPS27_ENST00000261413.5_5'Flank|MRPS27_ENST00000515404.1_5'Flank|PTCD2_ENST00000543322.1_Missense_Mutation_p.K61R|MRPS27_ENST00000457646.4_5'Flank|MRPS27_ENST00000522095.1_5'Flank	NM_024754.3	NP_079030.3	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	61					kidney development (GO:0001822)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|muscle fiber development (GO:0048747)|regulation of mRNA processing (GO:0050684)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(1)|skin(1)	11		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)		TTTCAACAAAAGAAAGTGGCT	0.279																																					p.K61R		Atlas-SNP	.											.	PTCD2	31	.	0			c.A182G						.						119	129	126					5																	71618053		1808	4070	5878	SO:0001583	missense	79810	exon2			AACAAAAGAAAGT	BC018720	CCDS4014.2, CCDS68891.1, CCDS68892.1, CCDS75258.1	5q13.2	2008-02-05			ENSG00000049883	ENSG00000049883			25734	protein-coding gene	gene with protein product		615484				12477932	Standard	XM_005248601		Approved	FLJ12598	uc003kcb.3	Q8WV60	OTTHUMG00000100953	ENST00000380639.5:c.182A>G	chr5.hg19:g.71618053A>G	ENSP00000370013:p.Lys61Arg	99.0	0.0		107.0	11.0	NM_024754	B7Z5D0|B7Z8L7|E9PFV7|Q6IA65|Q9H9R0	Missense_Mutation	SNP	ENST00000380639.5	hg19	CCDS4014.2	.	.	.	.	.	.	.	.	.	.	A	13.20	2.165411	0.38217	.	.	ENSG00000049883	ENST00000380639;ENST00000543322;ENST00000503868	T;T	0.48522	0.81;0.81	5.85	3.36	0.38483	.	0.413624	0.29028	N	0.013377	T	0.42810	0.1219	M	0.73598	2.24	0.80722	D	1	P;P	0.43231	0.763;0.801	B;B	0.41374	0.311;0.355	T	0.36601	-0.9741	10	0.08599	T	0.76	.	9.2507	0.37554	0.756:0.1241:0.0:0.1199	.	61;61	E9PFV7;Q8WV60	.;PTCD2_HUMAN	R	61	ENSP00000370013:K61R;ENSP00000438810:K61R	ENSP00000308948:K61R	K	+	2	0	PTCD2	71653809	0.982000	0.34865	0.999000	0.59377	0.283000	0.27025	0.839000	0.27586	2.238000	0.73509	0.533000	0.62120	AAG	.	.		0.279	PTCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218562.6	NM_024754		G	71618053	A	G	71618053	3	3	160	1	0	0	0	0	1	0	0	0	12740	72	3	2	188	2	PTCD2	5	71618053	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	28171707	71618053	109297207	111	24282										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79025753	79025753	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cacccgacacacctgcaactAtgttcctgagaacaacaaag	6	14	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:79025753A>G	ENST00000446378.2	+	2	1196	c.1165A>G	c.(1165-1167)Atg>Gtg	p.M389V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	389					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		ACCTGCAACTATGTTCCTGAG	0.473																																					p.M389V		Atlas-SNP	.											.	CMYA5	643	.	0			c.A1165G						.						79	80	79					5																	79025753		2165	4279	6444	SO:0001583	missense	202333	exon2			GCAACTATGTTCC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.1165A>G	chr5.hg19:g.79025753A>G	ENSP00000394770:p.Met389Val	192.0	0.0		187.0	25.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	A	7.494	0.651254	0.14516	.	.	ENSG00000164309	ENST00000446378	T	0.35605	1.3	5.93	0.0595	0.14332	.	2.769760	0.01243	N	0.008670	T	0.21186	0.0510	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11767	-1.0574	10	0.15066	T	0.55	.	5.6339	0.17526	0.4814:0.0:0.3873:0.1313	.	389	Q8N3K9	CMYA5_HUMAN	V	389	ENSP00000394770:M389V	ENSP00000394770:M389V	M	+	1	0	CMYA5	79061509	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.537000	0.23144	0.138000	0.18790	-0.230000	0.12252	ATG	.	.		0.473	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		G	79025753	A	G	79025753	3	3	160	1	0	0	0	0	1	0	0	0	3592	449	16	2	1171	2	CMYA5	5	79025753	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	7407700	79025753	101889507	112	24283										
LIX1	167410	hgsc.bcm.edu	37	chr5	96478229	96478229	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gactagagccggatctctgtGaggcaagacttgggcaatga	14	8	1	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:96478229G>A	ENST00000274382.4	-	1	347	c.52C>T	c.(52-54)Cac>Tac	p.H18Y	CTD-2215E18.1_ENST00000509481.1_Intron	NM_153234.4	NP_694966.3	Q8N485	LIX1_HUMAN	Lix1 homolog (chicken)	18										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)	10		all_cancers(142;4.28e-07)|all_epithelial(76;1.06e-09)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0318)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.0733)		GGATCTCTGTGAGGCAAGACT	0.453																																					p.H18Y		Atlas-SNP	.											.	LIX1	41	.	0			c.C52T						.						178	150	159					5																	96478229		2203	4300	6503	SO:0001583	missense	167410	exon1			CTCTGTGAGGCAA		CCDS4088.1	5q15	2008-03-06	2008-03-06	2005-02-07	ENSG00000145721	ENSG00000145721			18581	protein-coding gene	gene with protein product		610466	"chromosome 5 open reading frame 11", "Lix1 homolog (mouse)"	C5orf11		11731258	Standard	NM_153234		Approved		uc003kmy.4	Q8N485	OTTHUMG00000128720	ENST00000274382.4:c.52C>T	chr5.hg19:g.96478229G>A	ENSP00000274382:p.His18Tyr	109.0	0.0		114.0	19.0	NM_153234	A8K4R9|Q8N7I2	Missense_Mutation	SNP	ENST00000274382.4	hg19	CCDS4088.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.823534	0.32237	.	.	ENSG00000145721	ENST00000274382	T	0.43294	0.95	5.86	4.99	0.66335	.	0.521381	0.24136	N	0.041209	T	0.33760	0.0874	N	0.22421	0.69	0.38721	D	0.953451	B	0.25105	0.118	B	0.25140	0.058	T	0.27773	-1.0064	10	0.87932	D	0	-12.7766	16.4499	0.83976	0.0:0.0:0.8675:0.1325	.	18	Q8N485	LIX1_HUMAN	Y	18	ENSP00000274382:H18Y	ENSP00000274382:H18Y	H	-	1	0	LIX1	96503985	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	6.283000	0.72646	1.611000	0.50210	-0.175000	0.13238	CAC	.	.		0.453	LIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250625.1	NM_153234		A	96478229	G	A	96478229	3	1	160	1	0	0	0	0	1	0	0	0	8840	1290	45	3	820	3	LIX1	5	96478229	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	17452476	96478229	84437031	113	24284										
PAM	5066	hgsc.bcm.edu	37	chr5	102326046	102326046	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggccaggtttctggggtggcTctagaccctaagaataacct	12	10	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:102326046T>C	ENST00000438793.3	+	15	2024	c.1554T>C	c.(1552-1554)gcT>gcC	p.A518A	PAM_ENST00000348126.2_Silent_p.A411A|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000304400.7_Silent_p.A518A|PAM_ENST00000455264.2_Silent_p.A518A|PAM_ENST00000274392.9_Silent_p.A421A|PAM_ENST00000346918.2_Silent_p.A518A	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	518	Peptidyl-alpha-hydroxyglycine alpha- amidating lyase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	CTGGGGTGGCTCTAGACCCTA	0.393																																					p.A518A		Atlas-SNP	.											.	PAM	180	.	0			c.T1554C						.						64	62	63					5																	102326046		2203	4300	6503	SO:0001819	synonymous_variant	5066	exon15			GGTGGCTCTAGAC	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.1554T>C	chr5.hg19:g.102326046T>C		131.0	0.0		152.0	17.0	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Silent	SNP	ENST00000438793.3	hg19	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.336513	0.24253	.	.	ENSG00000145730	ENST00000379799	.	.	.	5.45	0.274	0.15654	.	.	.	.	.	T	0.50171	0.1600	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35176	-0.9799	4	.	.	.	-20.6332	4.6454	0.12570	0.1581:0.4453:0.0:0.3966	.	.	.	.	P	291	.	.	S	+	1	0	PAM	102353945	0.132000	0.22450	0.998000	0.56505	0.917000	0.54804	-0.534000	0.06150	0.059000	0.16252	0.454000	0.30748	TCT	.	.		0.393	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		C	102326046	T	C	102326046	2	2	160	1	0	0	0	0	0	0	0	1	11421	1538	54	2		2	PAM	5	102326046	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	5847817	102326046	78589214	114	24285										
GIN1	54826	hgsc.bcm.edu	37	chr5	102432263	102432263	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	accttgttcactggattctcTtatgtagggcttaaggtggg	12	7	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:102432263T>A	ENST00000399004.2	-	7	1370	c.1276A>T	c.(1276-1278)Aga>Tga	p.R426*	GIN1_ENST00000508629.1_Intron	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	426					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		CTGGATTCTCTTATGTAGGGC	0.378																																					p.R426X		Atlas-SNP	.											.	GIN1	53	.	0			c.A1276T						.						175	164	168					5																	102432263		1862	4095	5957	SO:0001587	stop_gained	54826	exon7			ATTCTCTTATGTA	BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"gypsy integrase 1", "Ty3/Gypsy integrase 1"		"zinc finger, H2C2 domain containing"	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.1276A>T	chr5.hg19:g.102432263T>A	ENSP00000381970:p.Arg426*	97.0	0.0		123.0	20.0	NM_017676	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Nonsense_Mutation	SNP	ENST00000399004.2	hg19	CCDS43349.1	.	.	.	.	.	.	.	.	.	.	T	35	5.592189	0.96590	.	.	ENSG00000145723	ENST00000399004	.	.	.	5.77	4.6	0.57074	.	0.000000	0.46758	U	0.000265	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	7.6812	11.9118	0.52743	0.0:0.0:0.1453:0.8547	.	.	.	.	X	426	.	ENSP00000381970:R426X	R	-	1	2	GIN1	102460162	1.000000	0.71417	0.777000	0.31699	0.434000	0.31775	4.896000	0.63222	0.996000	0.38943	0.533000	0.62120	AGA	.	.		0.378	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		A	102432263	T	A	102432263	4	1	160	1	0	0	0	0	0	1	0	0	6394	1617	56	4	300	4	GIN1	5	102432263	Nonsense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	106217	102432263	78482997	115	24286										
APC	324	hgsc.bcm.edu	37	chr5	112179022	112179022	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcttcaattctttctgcttcAtcagaatccagtgaaaaagc	5	10	6	2	rs537187449		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:112179022A>T	ENST00000457016.1	+	16	8111	c.7731A>T	c.(7729-7731)tcA>tcT	p.S2577S	APC_ENST00000257430.4_Silent_p.S2577S|APC_ENST00000508376.2_Silent_p.S2577S|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	2577	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTTCTGCTTCATCAGAATCCA	0.398		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.S2577S	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	1	Unknown(1)	skin(1)	c.A7731T						.						69	72	71					5																	112179022		2202	4300	6502	SO:0001819	synonymous_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TGCTTCATCAGAA	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.7731A>T	chr5.hg19:g.112179022A>T		111.0	0.0		122.0	14.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112179022	A	T	112179022	2	4	160	1	0	0	0	0	0	0	0	1	763	204	8	4		4	APC	5	112179022	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	9746759	112179022	68736238	116	24287										
MCC	4163	hgsc.bcm.edu	37	chr5	112363149	112363149	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agtttgttttgatgctttttCtttgctttctcataggcagc	8	7	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:112363149C>G	ENST00000302475.4	-	17	2903	c.2340G>C	c.(2338-2340)aaG>aaC	p.K780N	MCC_ENST00000514701.3_5'UTR|MCC_ENST00000515367.2_Missense_Mutation_p.K717N|MCC_ENST00000408903.3_Missense_Mutation_p.K970N	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	780					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		GATGCTTTTTCTTTGCTTTCT	0.453																																					p.K970N		Atlas-SNP	.											.	MCC	234	.	0			c.G2910C						.						206	177	187					5																	112363149		2202	4300	6502	SO:0001583	missense	4163	exon19			CTTTTTCTTTGCT		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"EF-hand domain containing"	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.2340G>C	chr5.hg19:g.112363149C>G	ENSP00000305617:p.Lys780Asn	60.0	0.0		75.0	31.0	NM_001085377	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	hg19	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.782453	0.90282	.	.	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.51071	0.72;0.72;0.72	5.83	5.83	0.93111	Usher syndrome type-1C protein-binding protein 1, PDZ domain (1);	0.000000	0.56097	U	0.000032	T	0.66208	0.2766	L	0.52759	1.655	0.80722	D	1	D;D	0.67145	0.996;0.991	D;D	0.77557	0.99;0.987	T	0.65977	-0.6037	10	0.72032	D	0.01	-33.4093	20.1374	0.98035	0.0:1.0:0.0:0.0	.	970;780	P23508-2;P23508	.;CRCM_HUMAN	N	780;717;970	ENSP00000305617:K780N;ENSP00000421615:K717N;ENSP00000386227:K970N	ENSP00000305617:K780N	K	-	3	2	MCC	112391048	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.206000	0.58473	2.763000	0.94921	0.563000	0.77884	AAG	.	.		0.453	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377		G	112363149	C	G	112363149	3	3	160	1	0	0	0	0	1	0	0	0	9382	912	32	4	153	4	MCC	5	112363149	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	184127	112363149	68552111	117	24288										
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121786551	121786551	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gttagccaggctgagacagcTgatgcagaggtcactgagtg	15	8	1	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:121786551T>G	ENST00000261368.8	+	10	2271	c.2009T>G	c.(2008-2010)cTg>cGg	p.L670R	SNCAIP_ENST00000379536.2_Missense_Mutation_p.L610R|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000261367.7_Missense_Mutation_p.L717R|SNCAIP_ENST00000379538.3_Missense_Mutation_p.L304R|SNCAIP_ENST00000504884.2_3'UTR|CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000503116.2_3'UTR|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000414317.2_Missense_Mutation_p.L272R|SNCAIP_ENST00000379533.2_Missense_Mutation_p.L717R|SNCAIP_ENST00000542191.1_Missense_Mutation_p.L228R|CTC-210G5.1_ENST00000509993.1_RNA|CTC-210G5.1_ENST00000505546.1_RNA	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	670					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		CTGAGACAGCTGATGCAGAGG	0.527																																					p.L670R		Atlas-SNP	.											.	SNCAIP	308	.	0			c.T2009G						.						44	46	45					5																	121786551		2203	4300	6503	SO:0001583	missense	9627	exon10			GACAGCTGATGCA	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.2009T>G	chr5.hg19:g.121786551T>G	ENSP00000261368:p.Leu670Arg	88.0	0.0		121.0	10.0	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	hg19	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	T	19.19	3.780473	0.70222	.	.	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317;ENST00000447854	T;T;T;T;T;T;T;T	0.20598	3.9;4.45;2.14;2.06;4.45;4.35;2.06;4.11	6.06	6.06	0.98353	.	0.067299	0.64402	D	0.000012	T	0.48960	0.1529	M	0.76574	2.34	0.48288	D	0.99962	D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;1.0;0.999;0.999;0.999	D;D;D;D;D;D;D;D	0.91635	0.998;0.996;0.993;0.974;0.999;0.974;0.996;0.942	T	0.50381	-0.8835	10	0.87932	D	0	-12.8429	16.6093	0.84858	0.0:0.0:0.0:1.0	.	610;298;272;610;304;304;717;670	D6R9G8;Q9NVG1;B7Z995;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;SNCAP_HUMAN	R	228;610;670;717;610;304;717;272;310	ENSP00000441681:L228R;ENSP00000422106:L610R;ENSP00000261368:L670R;ENSP00000368848:L717R;ENSP00000368851:L610R;ENSP00000368854:L304R;ENSP00000261367:L717R;ENSP00000394392:L272R	ENSP00000261367:L717R	L	+	2	0	SNCAIP	121814450	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.812000	0.69194	2.324000	0.78689	0.533000	0.62120	CTG	.	.		0.527	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			G	121786551	T	G	121786551	3	3	160	1	0	0	0	0	1	0	0	0	14856	1580	55	5	2043	5	SNCAIP	5	121786551	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	9423402	121786551	59128709	118	24289										
ALDH7A1	501	hgsc.bcm.edu	37	chr5	125903957	125903957	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aagccaacacttaccaaaccTctcctgcaccatcaggccca	4	18	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:125903957T>A	ENST00000409134.3	-	9	1084	c.865A>T	c.(865-867)Agg>Tgg	p.R289W	ALDH7A1_ENST00000447989.2_Missense_Mutation_p.R316W|ALDH7A1_ENST00000413020.1_5'UTR|ALDH7A1_ENST00000553117.1_Missense_Mutation_p.R289W	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	289					cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|glycine betaine biosynthetic process from choline (GO:0019285)|lysine catabolic process (GO:0006554)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|betaine-aldehyde dehydrogenase activity (GO:0008802)|L-aminoadipate-semialdehyde dehydrogenase activity (GO:0004043)			endometrium(1)|kidney(4)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)		TTACCAAACCTCTCCTGCACC	0.458																																					p.R316W		Atlas-SNP	.											.	ALDH7A1	57	.	0			c.A946T						.						161	146	151					5																	125903957		2203	4300	6503	SO:0001583	missense	501	exon9			CAAACCTCTCCTG	S74728	CCDS4137.2, CCDS56380.1	5q31	2013-06-03			ENSG00000164904	ENSG00000164904	1.2.1.31	"Aldehyde dehydrogenases"	877	protein-coding gene	gene with protein product	"antiquitin 1", "26g turgor protein homolog", "alpha-aminoadipic semialdehyde dehydrogenase", "alpha-AASA dehydrogenase", "delta1-piperideine-6-carboxylate dehydrogenease", "P6c dehydrogenase"	107323		ATQ1		9417906	Standard	NM_001182		Approved	EPD, PDE	uc003ktx.3	P49419	OTTHUMG00000128942	ENST00000409134.3:c.865A>T	chr5.hg19:g.125903957T>A	ENSP00000387123:p.Arg289Trp	63.0	0.0		83.0	10.0	NM_001202404	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Missense_Mutation	SNP	ENST00000409134.3	hg19	CCDS4137.2	.	.	.	.	.	.	.	.	.	.	T	20.4	3.977848	0.74360	.	.	ENSG00000164904	ENST00000409134;ENST00000553117;ENST00000447989;ENST00000437170	D;D;D	0.91521	-2.86;-2.86;-2.86	5.16	3.97	0.46021	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	D	0.96688	0.8919	H	0.97214	3.96	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96625	0.9462	10	0.87932	D	0	.	10.886	0.46968	0.0:0.0:0.1576:0.8424	.	316;316;289	E7EPT3;B4DMA0;P49419	.;.;AL7A1_HUMAN	W	289;289;316;97	ENSP00000387123:R289W;ENSP00000448593:R289W;ENSP00000414132:R316W	ENSP00000387123:R289W	R	-	1	2	ALDH7A1	125931856	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.815000	0.38981	1.050000	0.40346	0.533000	0.62120	AGG	.	.		0.458	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182		A	125903957	T	A	125903957	3	1	160	1	0	0	0	0	1	0	0	0	504	1550	54	4	794	4	ALDH7A1	5	125903957	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4117406	125903957	55011303	119	24290										
LMNB1	4001	hgsc.bcm.edu	37	chr5	126141268	126141268	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttttccttgtaatagttggaAgcctccttagctgcagccaa	8	10	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:126141268A>G	ENST00000261366.5	+	3	883	c.522A>G	c.(520-522)gaA>gaG	p.E174E	LMNB1_ENST00000460265.1_3'UTR|LMNB1_ENST00000395354.1_Silent_p.E174E	NM_001198557.1|NM_005573.3	NP_001185486.1|NP_005564.1	P20700	LMNB1_HUMAN	lamin B1	174	Coil 1B.|Rod.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	lamin filament (GO:0005638)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		AATAGTTGGAAGCCTCCTTAG	0.328																																					p.E174E		Atlas-SNP	.											.	LMNB1	49	.	0			c.A522G						.						73	75	74					5																	126141268		2203	4300	6503	SO:0001819	synonymous_variant	4001	exon3			GTTGGAAGCCTCC	L37737	CCDS4140.1	5q23.2	2013-01-16			ENSG00000113368	ENSG00000113368		"Intermediate filaments type V, lamins"	6637	protein-coding gene	gene with protein product		150340				7557986, 8838815	Standard	NM_005573		Approved		uc003kud.2	P20700	OTTHUMG00000128969	ENST00000261366.5:c.522A>G	chr5.hg19:g.126141268A>G		58.0	0.0		75.0	5.0	NM_005573	B2R6J6|Q3SYN7|Q96EI6	Silent	SNP	ENST00000261366.5	hg19	CCDS4140.1																																																																																			.	.		0.328	LMNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250956.2	NM_005573		G	126141268	A	G	126141268	2	3	160	1	0	0	0	0	0	0	0	1	8858	69	3	2		2	LMNB1	5	126141268	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	237311	126141268	54773992	120	24291										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	129019947	129019947	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cacacaagctgggaagattgCgatgccacttgtggaggagg	15	8	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:129019947C>T	ENST00000274487.4	+	18	2926	c.2781C>T	c.(2779-2781)tgC>tgT	p.C927C	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	927	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GGGAAGATTGCGATGCCACTT	0.403																																					p.C927C		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.C2781T						.						80	77	78					5																	129019947		2203	4300	6503	SO:0001819	synonymous_variant	171019	exon18			AGATTGCGATGCC	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.2781C>T	chr5.hg19:g.129019947C>T		123.0	0.0		120.0	12.0	NM_133638		Silent	SNP	ENST00000274487.4	hg19	CCDS4146.1																																																																																			.	.		0.403	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		T	129019947	C	T	129019947	2	4	160	1	0	0	0	0	0	0	0	1	264	776	27	1		1	ADAMTS19	5	129019947	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	2878679	129019947	51895313	121	24292										
IL5	3567	hgsc.bcm.edu	37	chr5	131879078	131879078	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gaaagcagtgccaaggtctcTttcaccaatgcacttgtggg	11	10	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:131879078T>A	ENST00000231454.1	-	1	136	c.93A>T	c.(91-93)aaA>aaT	p.K31N		NM_000879.2	NP_000870.1	P05113	IL5_HUMAN	interleukin 5	31					cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of eosinophil differentiation (GO:0045645)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of podosome assembly (GO:0071803)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-5 receptor binding (GO:0005137)			endometrium(1)|large_intestine(1)|stomach(1)|upper_aerodigestive_tract(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Pranlukast(DB01411)	CCAAGGTCTCTTTCACCAATG	0.443																																					p.K31N		Atlas-SNP	.											.	IL5	7	.	0			c.A93T						.						183	163	170					5																	131879078		2203	4300	6503	SO:0001583	missense	3567	exon1			GGTCTCTTTCACC	X04688	CCDS4156.1	5q23-q31	2014-04-04	2014-04-04		ENSG00000113525	ENSG00000113525		"Interleukins and interleukin receptors"	6016	protein-coding gene	gene with protein product	"interleukin-5", "T-cell replacing factor", "B cell differentiation factor I", "eosinophil differentiation factor", "colony-stimulating factor, eosinophil"	147850	"interleukin 5 (colony-stimulating factor, eosinophil)"			3498940	Standard	NM_000879		Approved	IL-5, EDF, TRF	uc003kxe.1	P05113	OTTHUMG00000059496	ENST00000231454.1:c.93A>T	chr5.hg19:g.131879078T>A	ENSP00000231454:p.Lys31Asn	116.0	0.0		142.0	20.0	NM_000879	Q13840	Missense_Mutation	SNP	ENST00000231454.1	hg19	CCDS4156.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.560203	0.45590	.	.	ENSG00000113525	ENST00000231454	.	.	.	5.8	4.62	0.57501	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.773340	0.11636	N	0.544332	T	0.50820	0.1638	L	0.44542	1.39	0.36384	D	0.862085	B	0.29936	0.262	B	0.32762	0.152	T	0.50600	-0.8809	9	0.34782	T	0.22	-1.5035	9.8389	0.40987	0.0:0.0:0.1726:0.8274	.	31	P05113	IL5_HUMAN	N	31	.	ENSP00000231454:K31N	K	-	3	2	IL5	131906977	0.940000	0.31905	0.986000	0.45419	0.457000	0.32468	0.936000	0.28938	0.990000	0.38787	0.533000	0.62120	AAA	.	.		0.443	IL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132339.1	NM_000879		A	131879078	T	A	131879078	3	1	160	1	0	0	0	0	1	0	0	0	7708	1606	56	4	327	4	IL5	5	131879078	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2859131	131879078	49036182	122	24293										
C5orf15	56951	hgsc.bcm.edu	37	chr5	133292672	133292672	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccatttcctgctttgaaccaGaagaaaaatctggaaaacag	7	9	1	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:133292672G>C	ENST00000231512.3	-	3	878	c.676C>G	c.(676-678)Ctg>Gtg	p.L226V	C5orf15_ENST00000507191.1_5'Flank	NM_020199.2	NP_064584.1	Q8NC54	KCT2_HUMAN	chromosome 5 open reading frame 15	226						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)			CTTTGAACCAGAAGAAAAATC	0.353																																					p.L226V		Atlas-SNP	.											.	C5orf15	20	.	0			c.C676G						.						84	83	83					5																	133292672		2203	4300	6503	SO:0001583	missense	56951	exon3			GAACCAGAAGAAA	AF226055	CCDS4167.1	5q31.1	2012-02-22			ENSG00000113583	ENSG00000113583			20656	protein-coding gene	gene with protein product	"keratinocytes associated transmembrane protein 2"						Standard	NM_020199		Approved	KCT2, HTGN29	uc003kyo.3	Q8NC54	OTTHUMG00000129125	ENST00000231512.3:c.676C>G	chr5.hg19:g.133292672G>C	ENSP00000231512:p.Leu226Val	188.0	0.0		230.0	36.0	NM_020199	B2RD10|D3DQ92|Q9NRG2	Missense_Mutation	SNP	ENST00000231512.3	hg19	CCDS4167.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.026892	0.35797	.	.	ENSG00000113583	ENST00000231512;ENST00000451255	.	.	.	5.34	1.05	0.20165	.	0.131815	0.33572	N	0.004780	T	0.43478	0.1249	L	0.59436	1.845	0.42936	D	0.994339	P	0.44946	0.846	B	0.39531	0.302	T	0.39292	-0.9621	9	0.72032	D	0.01	-9.0093	7.4695	0.27340	0.2859:0.0:0.5965:0.1175	.	226	Q8NC54	KCT2_HUMAN	V	226;126	.	ENSP00000231512:L226V	L	-	1	2	C5orf15	133320571	0.960000	0.32886	0.997000	0.53966	0.986000	0.74619	0.923000	0.28757	0.265000	0.21872	-0.145000	0.13849	CTG	.	.		0.353	C5orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251175.1	NM_020199		C	133292672	G	C	133292672	3	2	160	1	0	0	0	0	1	0	0	0	2285	933	33	4	125	4	C5orf15	5	133292672	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	1413594	133292672	47622588	123	24294										
TXNDC15	79770	hgsc.bcm.edu	37	chr5	134210212	134210212	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gctgggacttcccgtccgcgGcgtggagggtgagtgtgggc	20	10	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:134210212G>T	ENST00000358387.4	+	1	720	c.95G>T	c.(94-96)gGc>gTc	p.G32V	TXNDC15_ENST00000546290.1_5'Flank	NM_024715.3	NP_078991.3	Q96J42	TXD15_HUMAN	thioredoxin domain containing 15	32					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCCGTCCGCGGCGTGGAGGGT	0.716																																					p.G32V		Atlas-SNP	.											.	TXNDC15	37	.	0			c.G95T						.						51	57	55					5																	134210212		2201	4298	6499	SO:0001583	missense	79770	exon1			TCCGCGGCGTGGA	AK026278	CCDS4180.1	5q31.1	2008-02-05	2007-08-16	2007-08-16	ENSG00000113621	ENSG00000113621			20652	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 14"	C5orf14			Standard	NM_024715		Approved	2310047H23Rik, FLJ22625	uc003lac.1	Q96J42	OTTHUMG00000129115	ENST00000358387.4:c.95G>T	chr5.hg19:g.134210212G>T	ENSP00000351157:p.Gly32Val	86.0	0.0		80.0	24.0	NM_024715	D3DQA9|Q96MT2|Q9H639	Missense_Mutation	SNP	ENST00000358387.4	hg19	CCDS4180.1	.	.	.	.	.	.	.	.	.	.	G	8.738	0.918243	0.17982	.	.	ENSG00000113621	ENST00000441965;ENST00000358387;ENST00000506916	T	0.59083	0.29	4.7	3.82	0.43975	.	0.477014	0.19837	N	0.104956	T	0.50086	0.1595	N	0.24115	0.695	0.80722	D	1	P	0.52463	0.953	P	0.48795	0.59	T	0.54423	-0.8296	10	0.72032	D	0.01	0.2974	11.4885	0.50367	0.0:0.1824:0.8175:0.0	.	32	Q96J42	TXD15_HUMAN	V	32	ENSP00000351157:G32V	ENSP00000351157:G32V	G	+	2	0	TXNDC15	134238111	1.000000	0.71417	1.000000	0.80357	0.088000	0.18126	1.772000	0.38552	1.276000	0.44395	0.563000	0.77884	GGC	.	.		0.716	TXNDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251160.1	NM_024715		T	134210212	G	T	134210212	3	4	160	1	0	0	0	0	1	0	0	0	16809	1203	42	3	97	3	TXNDC15	5	134210212	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	917540	134210212	46705048	124	24295										
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140257026	140257026	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tggtgaaggaccacggtgagCccgcgctgacgtccacggcc	15	14	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:140257026C>T	ENST00000398631.2	+	1	1969	c.1969C>T	c.(1969-1971)Ccc>Tcc	p.P657S	PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	657	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACGGTGAGCCCGCGCTGAC	0.692																																					p.P657S	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.C1969T						.						83	84	84					5																	140257026		2203	4299	6502	SO:0001583	missense	56137	exon1			GGTGAGCCCGCGC	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1969C>T	chr5.hg19:g.140257026C>T	ENSP00000381628:p.Pro657Ser	158.0	0.0		194.0	14.0	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	hg19	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.352664	0.41700	.	.	ENSG00000251664	ENST00000398631	T	0.56776	0.44	4.81	3.94	0.45596	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.79879	0.4522	H	0.95470	3.675	0.37860	D	0.929683	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.87319	0.2317	9	0.72032	D	0.01	.	14.1944	0.65659	0.1509:0.8491:0.0:0.0	.	657;657	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	S	657	ENSP00000381628:P657S	ENSP00000381628:P657S	P	+	1	0	PCDHA12	140237210	0.001000	0.12720	0.949000	0.38748	0.013000	0.08279	1.250000	0.32850	1.027000	0.39758	-0.226000	0.12346	CCC	.	.		0.692	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		T	140257026	C	T	140257026	3	4	160	1	0	0	0	0	1	0	0	0	11531	739	26	3	1971	3	PCDHA12	5	140257026	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	6046814	140257026	40658234	125	24296										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140562781	140562781	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	attaaccctgacagcgctggAtggtggctctccaccgcgat	11	13	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:140562781A>T	ENST00000361016.2	+	1	1802	c.647A>T	c.(646-648)gAt>gTt	p.D216V		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	216	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACAGCGCTGGATGGTGGCTCT	0.507																																					p.D216V		Atlas-SNP	.											.	PCDHB16	159	.	0			c.A647T						.						65	65	65					5																	140562781		2203	4300	6503	SO:0001583	missense	57717	exon1			CGCTGGATGGTGG	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.647A>T	chr5.hg19:g.140562781A>T	ENSP00000354293:p.Asp216Val	68.0	0.0		68.0	9.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	A	16.76	3.211812	0.58452	.	.	ENSG00000196963	ENST00000361016	T	0.68624	-0.34	4.69	4.69	0.59074	Cadherin (4);Cadherin-like (1);	0.000000	0.35555	N	0.003123	D	0.89829	0.6828	H	0.99764	4.76	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94000	0.7274	10	0.87932	D	0	.	14.1404	0.65316	1.0:0.0:0.0:0.0	.	216	Q9NRJ7	PCDBG_HUMAN	V	216	ENSP00000354293:D216V	ENSP00000354293:D216V	D	+	2	0	PCDHB16	140542965	1.000000	0.71417	1.000000	0.80357	0.101000	0.19017	7.433000	0.80362	1.737000	0.51674	0.533000	0.62120	GAT	.	.		0.507	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		T	140562781	A	T	140562781	3	4	160	1	0	0	0	0	1	0	0	0	11550	333	12	4	649	4	PCDHB16	5	140562781	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	305755	140562781	40352479	126	24297										
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140589743	140589743	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccgagtacaacatcaccatcAccgtcaccgacttggggacc	8	16	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:140589743A>G	ENST00000239450.2	+	1	1453	c.1264A>G	c.(1264-1266)Acc>Gcc	p.T422A	PCDHB12_ENST00000541609.1_Missense_Mutation_p.T85A	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	422	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CATCACCATCACCGTCACCGA	0.517																																					p.T422A		Atlas-SNP	.											.	PCDHB12	179	.	0			c.A1264G						.						98	95	96					5																	140589743		2203	4300	6503	SO:0001583	missense	56124	exon1			ACCATCACCGTCA	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1264A>G	chr5.hg19:g.140589743A>G	ENSP00000239450:p.Thr422Ala	131.0	0.0		144.0	28.0	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	hg19	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.507041	0.27036	.	.	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.03181	4.02;4.02	3.83	2.6	0.31112	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.16981	0.0408	M	0.94101	3.495	0.09310	N	1	P	0.49559	0.925	P	0.56648	0.803	T	0.08106	-1.0738	9	0.66056	D	0.02	.	5.5298	0.16978	0.5311:0.3052:0.0:0.1637	.	422	Q9Y5F1	PCDBC_HUMAN	A	85;422;42	ENSP00000440199:T85A;ENSP00000239450:T422A	ENSP00000239450:T422A	T	+	1	0	PCDHB12	140569927	0.000000	0.05858	0.846000	0.33378	0.369000	0.29798	0.660000	0.25009	0.427000	0.26145	0.397000	0.26171	ACC	.	.		0.517	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		G	140589743	A	G	140589743	3	3	160	1	0	0	0	0	1	0	0	0	11546	159	6	2	1266	2	PCDHB12	5	140589743	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	26962	140589743	40325517	127	24298										
SYNPO	11346	hgsc.bcm.edu	37	chr5	149997966	149997966	+	Missense_Mutation	SNP	C	C	G													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcccacctccgccccttgcaCccagcgaagggaggcctacc							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:149997966C>G	ENST00000394243.1	+	2	411	c.37C>G	c.(37-39)Ccc>Gcc	p.P13A	SYNPO_ENST00000522122.1_Missense_Mutation_p.P13A	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	13					positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)			NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCCCCTTGCACCCAGCGAAGG	0.667																																					p.P13A		Atlas-SNP	.											.	SYNPO	147	.	0			c.C37G						.						21	27	25					5																	149997966		692	1591	2283	SO:0001583	missense	11346	exon2			CTTGCACCCAGCG	AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.37C>G	chr5.hg19:g.149997966C>G	ENSP00000377789:p.Pro13Ala	189.0	0.0		178.0	30.0	NM_001166209	A5PKZ8|D3DQG8|O15271|Q9UPX1	Missense_Mutation	SNP	ENST00000394243.1	hg19	CCDS54937.1	.	.	.	.	.	.	.	.	.	.	C	2.838	-0.241060	0.05906	.	.	ENSG00000171992	ENST00000394243;ENST00000522122	T;T	0.25250	1.81;1.81	4.91	1.95	0.26073	.	0.666403	0.12477	N	0.465511	T	0.11580	0.0282	N	0.08118	0	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.25117	-1.0141	10	0.02654	T	1	-2.8157	13.0666	0.59036	0.0:0.5346:0.4654:0.0	.	13	Q8N3V7	SYNPO_HUMAN	A	13	ENSP00000377789:P13A;ENSP00000428378:P13A	ENSP00000377789:P13A	P	+	1	0	SYNPO	149978159	0.064000	0.20934	0.007000	0.13788	0.497000	0.33675	0.034000	0.13776	0.439000	0.26476	-0.304000	0.09214	CCC	.	.		0.667	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286		G	149997966	C	G	149997966	3	3	160	1	0	0	0	0	1	0	0	0	15471	507	18	4	39	4	SYNPO	5	149997966	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	9408223	149997966	30917294	128	24299	110	2								
SYNPO	11346	hgsc.bcm.edu	37	chr5	149997969	149997969	+	Missense_Mutation	SNP	A	A	T													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cacctccgccccttgcacccAgcgaagggaggcctaccccc							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:149997969A>T	ENST00000394243.1	+	2	414	c.40A>T	c.(40-42)Agc>Tgc	p.S14C	SYNPO_ENST00000522122.1_Missense_Mutation_p.S14C	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	14					positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)			NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTTGCACCCAGCGAAGGGAG	0.667																																					p.S14C		Atlas-SNP	.											.	SYNPO	147	.	0			c.A40T						.						21	26	24					5																	149997969		692	1591	2283	SO:0001583	missense	11346	exon2			GCACCCAGCGAAG	AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.40A>T	chr5.hg19:g.149997969A>T	ENSP00000377789:p.Ser14Cys	193.0	0.0		183.0	30.0	NM_001166209	A5PKZ8|D3DQG8|O15271|Q9UPX1	Missense_Mutation	SNP	ENST00000394243.1	hg19	CCDS54937.1	.	.	.	.	.	.	.	.	.	.	A	12.87	2.067358	0.36470	.	.	ENSG00000171992	ENST00000394243;ENST00000522122	T;T	0.33216	1.42;1.42	5.12	1.38	0.22167	.	0.912783	0.09141	N	0.842883	T	0.23572	0.0570	L	0.44542	1.39	0.09310	N	0.999999	B	0.22683	0.073	B	0.19148	0.024	T	0.33214	-0.9877	10	0.87932	D	0	-0.134	3.2873	0.06936	0.6409:0.0:0.1883:0.1708	.	14	Q8N3V7	SYNPO_HUMAN	C	14	ENSP00000377789:S14C;ENSP00000428378:S14C	ENSP00000377789:S14C	S	+	1	0	SYNPO	149978162	0.057000	0.20700	0.001000	0.08648	0.659000	0.38960	0.957000	0.29215	-0.001000	0.14495	0.459000	0.35465	AGC	.	.		0.667	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286		T	149997969	A	T	149997969	3	4	160	1	0	0	0	0	1	0	0	0	15471	188	7	4	42	4	SYNPO	5	149997969	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	3	149997969	30917291	129	24300	110	2								
FAT2	2196	hgsc.bcm.edu	37	chr5	150925156	150925156	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aataatacagggcttccttgGtcatggacatagacacagaa	9	8	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:150925156G>T	ENST00000261800.5	-	9	5544	c.5532C>A	c.(5530-5532)gaC>gaA	p.D1844E		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1844	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGCTTCCTTGGTCATGGACAT	0.433																																					p.D1844E		Atlas-SNP	.											.	FAT2	465	.	0			c.C5532A						.						73	79	77					5																	150925156		2203	4300	6503	SO:0001583	missense	2196	exon9			TCCTTGGTCATGG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.5532C>A	chr5.hg19:g.150925156G>T	ENSP00000261800:p.Asp1844Glu	189.0	0.0		173.0	53.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.901133	0.52227	.	.	ENSG00000086570	ENST00000261800	T	0.67865	-0.29	5.25	2.5	0.30297	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000010	D	0.85261	0.5656	H	0.97131	3.945	0.48341	D	0.999632	D	0.89917	1.0	D	0.87578	0.998	D	0.85276	0.1059	10	0.87932	D	0	.	8.2442	0.31677	0.3022:0.0:0.6978:0.0	.	1844	Q9NYQ8	FAT2_HUMAN	E	1844	ENSP00000261800:D1844E	ENSP00000261800:D1844E	D	-	3	2	FAT2	150905349	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	2.390000	0.44416	0.607000	0.29982	0.467000	0.42956	GAC	.	.		0.433	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150925156	G	T	150925156	3	4	160	1	0	0	0	0	1	0	0	0	5698	1252	44	3	7577	3	FAT2	5	150925156	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	927187	150925156	29990104	130	24301										
CPEB4	80315	hgsc.bcm.edu	37	chr5	173372134	173372134	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	taggcggattgcctccagacAttgatgaaggtatgtttaga	12	6	0	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:173372134A>G	ENST00000265085.5	+	5	2901	c.1447A>G	c.(1447-1449)Att>Gtt	p.I483V	CPEB4_ENST00000517880.1_Missense_Mutation_p.I76V|CPEB4_ENST00000334035.5_Missense_Mutation_p.I466V|CPEB4_ENST00000519467.1_3'UTR|CPEB4_ENST00000522336.1_Missense_Mutation_p.I93V|CPEB4_ENST00000520867.1_Missense_Mutation_p.I458V|CPEB4_ENST00000519835.1_Missense_Mutation_p.I458V	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	483	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GCCTCCAGACATTGATGAAGG	0.458																																					p.I483V		Atlas-SNP	.											.	CPEB4	54	.	0			c.A1447G						.						124	114	117					5																	173372134		2203	4300	6503	SO:0001583	missense	80315	exon5			CCAGACATTGATG	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.1447A>G	chr5.hg19:g.173372134A>G	ENSP00000265085:p.Ile483Val	140.0	0.0		136.0	22.0	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Missense_Mutation	SNP	ENST00000265085.5	hg19	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.076398	0.76415	.	.	ENSG00000113742	ENST00000265085;ENST00000520867;ENST00000334035;ENST00000519835;ENST00000522336;ENST00000517880	T;T;T;T;T;T	0.14893	2.47;2.47;2.47;2.47;2.47;2.47	5.37	5.37	0.77165	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.30230	0.0758	N	0.20401	0.57	0.58432	D	0.999995	B;B;B;B;B	0.30851	0.297;0.159;0.048;0.082;0.297	P;P;P;P;P	0.57548	0.7;0.475;0.61;0.482;0.823	T	0.35599	-0.9782	10	0.44086	T	0.13	-11.2425	15.6695	0.77262	1.0:0.0:0.0:0.0	.	458;466;458;93;483	B7ZLQ8;Q17RY0-2;E5RJM0;E5RFP2;Q17RY0	.;.;.;.;CPEB4_HUMAN	V	483;458;466;458;93;76	ENSP00000265085:I483V;ENSP00000429092:I458V;ENSP00000334533:I466V;ENSP00000429048:I458V;ENSP00000430345:I93V;ENSP00000427990:I76V	ENSP00000265085:I483V	I	+	1	0	CPEB4	173304740	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.213000	0.95133	2.178000	0.69098	0.533000	0.62120	ATT	.	.		0.458	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		G	173372134	A	G	173372134	3	3	160	1	0	0	0	0	1	0	0	0	3805	217	8	2	1465	2	CPEB4	5	173372134	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	22446978	173372134	7543126	131	24302										
TRIM7	81786	hgsc.bcm.edu	37	chr5	180626894	180626894	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tttgagctgtctcctggatcTggctgctgagcttggacagc	13	10	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr5:180626894T>A	ENST00000274773.7	-	3	867	c.806A>T	c.(805-807)cAg>cTg	p.Q269L	CTC-338M12.6_ENST00000502812.2_RNA|CTC-338M12.6_ENST00000509080.1_RNA|TRIM7_ENST00000422067.2_Missense_Mutation_p.Q61L|TRIM7_ENST00000393319.3_Missense_Mutation_p.Q87L|CTC-338M12.6_ENST00000419707.2_RNA|TRIM7_ENST00000393315.1_Missense_Mutation_p.Q61L|CTC-338M12.6_ENST00000514784.1_RNA|CTC-338M12.6_ENST00000512508.1_RNA|TRIM7_ENST00000504241.1_5'Flank|TRIM7_ENST00000361809.3_Missense_Mutation_p.Q61L|CTC-338M12.6_ENST00000511517.1_RNA	NM_203293.1	NP_976038.1	Q9C029	TRIM7_HUMAN	tripartite motif containing 7	269						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|stomach(1)	17	all_cancers(89;6.03e-06)|all_epithelial(37;7.1e-07)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000172)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;2e-06)|Epithelial(171;1.35e-05)|OV - Ovarian serous cystadenocarcinoma(192;0.000128)|Kidney(146;0.0674)|GBM - Glioblastoma multiforme(465;0.0802)		CTCCTGGATCTGGCTGCTGAG	0.582																																					p.Q269L	Esophageal Squamous(128;2258 2308 35507 48647)	Atlas-SNP	.											.	TRIM7	56	.	0			c.A806T						.						63	54	57					5																	180626894		2203	4300	6503	SO:0001583	missense	81786	exon3			TGGATCTGGCTGC	AF220032	CCDS4462.1, CCDS4463.1, CCDS4464.1, CCDS43414.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146054	ENSG00000146054		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16278	protein-coding gene	gene with protein product	"glycogenin-interacting protein", "tripartite motif protein TRIM7"	609315	"tripartite motif-containing 7"			11331580	Standard	NM_203294		Approved	RNF90, GNIP	uc003mmz.1	Q9C029	OTTHUMG00000130963	ENST00000274773.7:c.806A>T	chr5.hg19:g.180626894T>A	ENSP00000274773:p.Gln269Leu	73.0	0.0		80.0	8.0	NM_203293	A2RUE4|D3DWR7|Q969F5|Q96F67|Q96J89|Q96J90	Missense_Mutation	SNP	ENST00000274773.7	hg19	CCDS4462.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.064513	0.55432	.	.	ENSG00000146054	ENST00000274773;ENST00000393315;ENST00000361809;ENST00000393319;ENST00000422067	T;T;T;T;T	0.04758	3.56;3.56;3.56;3.56;3.56	5.34	5.34	0.76211	.	0.108661	0.40064	N	0.001193	T	0.05960	0.0155	L	0.50333	1.59	0.31710	N	0.639627	B;P	0.37276	0.003;0.589	B;B	0.32677	0.002;0.15	T	0.05649	-1.0872	10	0.52906	T	0.07	.	11.7196	0.51675	0.0:0.0:0.0:1.0	.	269;87	Q9C029;Q9C029-4	TRIM7_HUMAN;.	L	269;61;61;87;61	ENSP00000274773:Q269L;ENSP00000376991:Q61L;ENSP00000355059:Q61L;ENSP00000376994:Q87L;ENSP00000391458:Q61L	ENSP00000274773:Q269L	Q	-	2	0	TRIM7	180559500	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	3.317000	0.51968	2.018000	0.59344	0.379000	0.24179	CAG	.	.		0.582	TRIM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253569.3	NM_203296		A	180626894	T	A	180626894	3	1	160	1	0	0	0	0	1	0	0	0	16558	1580	55	4	749	4	TRIM7	5	180626894	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	7254760	180626894	288366	132	24303										
SSR1	6745	hgsc.bcm.edu	37	chr6	7301679	7301679	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcagaggaagagctgtgaaaTtctggatataaaactggtag	12	4	2	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:7301679T>G	ENST00000244763.4	-	4	493	c.407A>C	c.(406-408)aAt>aCt	p.N136T	SSR1_ENST00000479365.1_Missense_Mutation_p.N136T|SSR1_ENST00000488834.1_5'UTR|SSR1_ENST00000534851.1_Missense_Mutation_p.N109T|SSR1_ENST00000474597.1_Missense_Mutation_p.N136T|RP11-69L16.4_ENST00000379928.4_RNA|SSR1_ENST00000397511.2_Missense_Mutation_p.N136T|SSR1_ENST00000489567.1_Intron|SSR1_ENST00000462112.1_Missense_Mutation_p.N136T	NM_003144.3	NP_003135.2	P43307	SSRA_HUMAN	signal sequence receptor, alpha	136					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|positive regulation of cell proliferation (GO:0008284)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(1)	9	Ovarian(93;0.0398)					AGCTGTGAAATTCTGGATATA	0.453																																					p.N136T		Atlas-SNP	.											.	SSR1	21	.	0			c.A407C						.						95	101	99					6																	7301679		2203	4300	6503	SO:0001583	missense	6745	exon4			GTGAAATTCTGGA		CCDS4499.1	6p24.3	2010-11-24	2008-08-26		ENSG00000124783	ENSG00000124783			11323	protein-coding gene	gene with protein product	"translocon-associated protein alpha"	600868					Standard	NM_001292008		Approved	TRAPA	uc003mxf.4	P43307	OTTHUMG00000014202	ENST00000244763.4:c.407A>C	chr6.hg19:g.7301679T>G	ENSP00000244763:p.Asn136Thr	130.0	0.0		177.0	23.0	NM_003144	A8K685|Q53GX2|Q53H19|Q5TAM3|Q6IB43|Q8NBH9|Q96IA2|Q9TNQ8|Q9UN49	Missense_Mutation	SNP	ENST00000244763.4	hg19	CCDS4499.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.939404	0.92526	.	.	ENSG00000124783	ENST00000474597;ENST00000244763;ENST00000397511;ENST00000534851;ENST00000479365;ENST00000462112	T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.73575	0.3604	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	T	0.80313	-0.1435	10	0.87932	D	0	.	15.5577	0.76213	0.0:0.0:0.0:1.0	.	136;136	C9J5W0;P43307	.;SSRA_HUMAN	T	136;136;136;109;136;136	ENSP00000418617:N136T;ENSP00000244763:N136T;ENSP00000380647:N136T;ENSP00000443020:N109T;ENSP00000417911:N136T;ENSP00000417290:N136T	ENSP00000244763:N136T	N	-	2	0	SSR1	7246678	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.859000	0.86982	2.263000	0.75096	0.533000	0.62120	AAT	.	.		0.453	SSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039775.2			G	7301679	T	G	7301679	3	3	160	1	0	0	0	0	1	0	0	0	15205	1493	52	5	473	5	SSR1	6	7301679	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10		7301679	163813388	133	24304										
NKAPL	222698	hgsc.bcm.edu	37	chr6	28227649	28227649	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aacgcatcagaaaagcagcaGttcagattccaactcggaag	9	10	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:28227649G>T	ENST00000343684.3	+	1	552	c.500G>T	c.(499-501)aGt>aTt	p.S167I	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	167										breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						AAAAGCAGCAGTTCAGATTCC	0.428																																					p.S167I		Atlas-SNP	.											.	NKAPL	72	.	0			c.G500T						.						57	65	62					6																	28227649		2203	4300	6503	SO:0001583	missense	222698	exon1			GCAGCAGTTCAGA	BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 194"	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.500G>T	chr6.hg19:g.28227649G>T	ENSP00000345716:p.Ser167Ile	129.0	0.0		142.0	18.0	NM_001007531	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	hg19	CCDS34353.1	.	.	.	.	.	.	.	.	.	.	G	4.091	0.014799	0.07959	.	.	ENSG00000189134	ENST00000343684	T	0.14391	2.51	4.5	0.348	0.16026	.	0.423784	0.30277	N	0.009997	T	0.02610	0.0079	L	0.34521	1.04	0.19300	N	0.999972	B	0.06786	0.001	B	0.11329	0.006	T	0.38824	-0.9643	10	0.49607	T	0.09	-0.1449	3.076	0.06247	0.0968:0.3346:0.3966:0.1719	.	167	Q5M9Q1	NKAPL_HUMAN	I	167	ENSP00000345716:S167I	ENSP00000345716:S167I	S	+	2	0	NKAPL	28335628	0.905000	0.30787	0.001000	0.08648	0.003000	0.03518	0.921000	0.28718	0.242000	0.21303	0.655000	0.94253	AGT	.	.		0.428	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1			T	28227649	G	T	28227649	3	4	160	1	0	0	0	0	1	0	0	0	10449	1029	36	3	502	3	NKAPL	6	28227649	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	20925970	28227649	142887418	134	24305										
OR2J2	26707	hgsc.bcm.edu	37	chr6	29141609	29141609	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aatgtacttcttcctttcaaAcctctcatttctggatctct	3	12	5	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:29141609A>C	ENST00000377167.2	+	1	299	c.197A>C	c.(196-198)aAc>aCc	p.N66T		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						TTCCTTTCAAACCTCTCATTT	0.488																																					p.N66T		Atlas-SNP	.											.	OR2J2	51	.	0			c.A197C						.						155	146	149					6																	29141609		2026	4226	6252	SO:0001583	missense	26707	exon1			TTTCAAACCTCTC		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"GPCR / Class A : Olfactory receptors"	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.197A>C	chr6.hg19:g.29141609A>C	ENSP00000366372:p.Asn66Thr	101.0	0.0		144.0	22.0	NM_030905	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Missense_Mutation	SNP	ENST00000377167.2	hg19	CCDS43434.1	.	.	.	.	.	.	.	.	.	.	A	13.54	2.266755	0.40095	.	.	ENSG00000204700	ENST00000377167	T	0.12984	2.63	2.3	2.3	0.28687	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.17408	0.0418	M	0.88775	2.98	0.39205	D	0.963211	P	0.46142	0.873	P	0.48627	0.584	T	0.03829	-1.1000	9	0.87932	D	0	.	9.0762	0.36522	1.0:0.0:0.0:0.0	.	66	O76002	OR2J2_HUMAN	T	66	ENSP00000366372:N66T	ENSP00000366372:N66T	N	+	2	0	OR2J2	29249588	0.009000	0.17119	1.000000	0.80357	0.383000	0.30230	2.263000	0.43293	1.039000	0.40074	0.172000	0.16884	AAC	.	.		0.488	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2			C	29141609	A	C	29141609	3	2	160	1	0	0	0	0	1	0	0	0	11012	43	2	5	199	5	OR2J2	6	29141609	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	913960	29141609	141973458	135	24306										
PPP1R10	5514	hgsc.bcm.edu	37	chr6	30570416	30570416	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcacctccccggggagggggTggaggacccagaagacgtgg	18	11	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:30570416T>A	ENST00000376511.2	-	19	2562	c.2010A>T	c.(2008-2010)ccA>ccT	p.P670P		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	670	Gly-rich.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						GGGGAGGGGGTGGAGGACCCA	0.652																																					p.P670P		Atlas-SNP	.											.	PPP1R10	60	.	0			c.A2010T						.						10	14	13					6																	30570416		1455	2617	4072	SO:0001819	synonymous_variant	5514	exon19			AGGGGGTGGAGGA	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9284	protein-coding gene	gene with protein product	"phosphatase 1 nuclear targeting subunit", "HLA-C associated transcript 53"	603771	"protein phosphatase 1, regulatory (inhibitor) subunit 10"			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.2010A>T	chr6.hg19:g.30570416T>A		35.0	0.0		46.0	8.0	NM_002714	O00405	Silent	SNP	ENST00000376511.2	hg19	CCDS4681.1																																																																																			.	.		0.652	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		A	30570416	T	A	30570416	2	1	160	1	0	0	0	0	0	0	0	1	12364	1683	59	4		4	PPP1R10	6	30570416	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1428807	30570416	140544651	136	24307										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33144072	33144072	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cccttcagaccccgaattccGtccacaccctagaattagag	6	16	1	3	rs138650682		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:33144072G>A	ENST00000374708.4	-	26	2178	c.1920C>T	c.(1918-1920)gaC>gaT	p.D640D	COL11A2_ENST00000361917.1_Silent_p.D619D|COL11A2_ENST00000357486.1_Silent_p.D705D|COL11A2_ENST00000374714.1_Silent_p.D700D|COL11A2_ENST00000341947.2_Silent_p.D726D|COL11A2_ENST00000374712.1_Silent_p.D645D|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374713.1_Silent_p.D679D|COL11A2_ENST00000395197.1_Silent_p.D666D	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	726	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.D726D(1)		biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CCCGAATTCCGTCCACACCCT	0.552																																					p.D726D	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											COL11A2,NS,carcinoma,0,1	COL11A2	124	.	1	Substitution - coding silent(1)	prostate(1)	c.C2178T						.	G	,,	0,3022		0,0,1511	63	39	47		1857,2178,1920	-0.1	1	6	dbSNP_134	47	1,5417		0,1,2708	no	coding-synonymous,coding-synonymous,coding-synonymous	COL11A2	NM_080679.2,NM_080680.2,NM_080681.2	,,	0,1,4219	AA,AG,GG		0.0185,0.0,0.0118	,,	619/1630,726/1737,640/1651	33144072	1,8439	1511	2709	4220	SO:0001819	synonymous_variant	1302	exon28			AATTCCGTCCACA	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.1920C>T	chr6.hg19:g.33144072G>A		112.0	0.0		153.0	17.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	G|1.000;A|0.000		0.552	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			A	33144072	G	A	33144072	2	1	160	1	0	0	0	0	0	0	0	1	3670	1136	40	1		1	COL11A2	6	33144072	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	2573656	33144072	137970995	137	24308										
ANKS1A	23294	hgsc.bcm.edu	37	chr6	35051203	35051203	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtttcctgtagaaatctacgGagcacatgaagaagatcccc	9	10	1	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:35051203G>C	ENST00000360359.3	+	20	3055	c.2917G>C	c.(2917-2919)Gag>Cag	p.E973Q	ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	973	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						GAAATCTACGGAGCACATGAA	0.527																																					p.E973Q		Atlas-SNP	.											.	ANKS1A	123	.	0			c.G2917C						.						195	162	173					6																	35051203		2203	4300	6503	SO:0001583	missense	23294	exon20			TCTACGGAGCACA	D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20961	protein-coding gene	gene with protein product		608994	"ankyrin repeat and SAM domain containing 1", "ankyrin repeat and sterile alpha motif domain containing 1"	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.2917G>C	chr6.hg19:g.35051203G>C	ENSP00000353518:p.Glu973Gln	96.0	0.0		128.0	15.0	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	hg19	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.599708	0.87055	.	.	ENSG00000064999	ENST00000360359;ENST00000373990	T	0.13778	2.56	4.76	4.76	0.60689	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.46758	D	0.000277	T	0.24851	0.0603	L	0.51914	1.62	0.80722	D	1	D;P;D	0.89917	0.996;0.87;1.0	D;P;D	0.87578	0.983;0.81;0.998	T	0.02683	-1.1124	10	0.72032	D	0.01	-22.0481	17.7722	0.88496	0.0:0.0:1.0:0.0	.	299;299;973	Q49AR9;E7EM84;Q92625	.;.;ANS1A_HUMAN	Q	973;299	ENSP00000353518:E973Q	ENSP00000353518:E973Q	E	+	1	0	ANKS1A	35159181	1.000000	0.71417	0.981000	0.43875	0.799000	0.45148	9.842000	0.99487	2.194000	0.70268	0.655000	0.94253	GAG	.	.		0.527	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		C	35051203	G	C	35051203	3	2	160	1	0	0	0	0	1	0	0	0	688	1175	41	4	2995	4	ANKS1A	6	35051203	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	1907131	35051203	136063864	138	24309										
CUL9	23113	hgsc.bcm.edu	37	chr6	43160940	43160940	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtcttggtgcagcaggctggGctggcggtgagtacattggg	19	7	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:43160940G>A	ENST00000252050.4	+	9	2466	c.2382G>A	c.(2380-2382)ggG>ggA	p.G794G	CUL9_ENST00000372647.2_Silent_p.G794G|CUL9_ENST00000354495.3_Silent_p.G684G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	794					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						AGCAGGCTGGGCTGGCGGTGA	0.567																																					p.G794G		Atlas-SNP	.											.	CUL9	248	.	0			c.G2382A						.						89	89	89					6																	43160940		2202	4299	6501	SO:0001819	synonymous_variant	23113	exon9			GGCTGGGCTGGCG	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.2382G>A	chr6.hg19:g.43160940G>A		67.0	0.0		85.0	33.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	hg19	CCDS4890.1																																																																																			.	.		0.567	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43160940	G	A	43160940	2	1	160	1	0	0	0	0	0	0	0	1	4063	1190	42	3		3	CUL9	6	43160940	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	8109737	43160940	127954127	139	24310										
CUL9	23113	hgsc.bcm.edu	37	chr6	43182826	43182827	+	Missense_Mutation	DNP	GC	GC	TT													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctcctatccaggtgctggagGcctggcagaagggtccaaat					rs146106470		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:43182826_43182827GC>TT	ENST00000252050.4	+	30	5782_5783	c.5698_5699GC>TT	c.(5698-5700)GCc>TTc	p.A1900F	CUL9_ENST00000372647.2_Missense_Mutation_p.A1872F|CUL9_ENST00000354495.3_Missense_Mutation_p.A1790F|RP3-330M21.5_ENST00000500590.1_RNA	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1900					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GGTGCTGGAGGCCTGGCAGAAG	0.559																																					p.A1900S|p.A1900V		Atlas-SNP	.											.	CUL9	248	.	0			c.G5698T|c.C5699T						.																																			SO:0001583	missense	23113	exon30			CTGGAGGCCTGGC|TGGAGGCCTGGCA	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	Exception_encountered	chr6.hg19:g.43182826_43182827delinsTT	ENSP00000252050:p.Ala1900Phe	76.0|78.0	0.0		84.0|83.0	4.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1																																																																																			.	.|C|1.000;T|0.000		0.559	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		TT	43182827	GC	TT	43182826	3	4	160	1	0	0	0	0	1	0	0	0	4063	1203	42	3	5812	3	CUL9	6	43182826	Missense_Mutation	DNP	GC	TCGA-DD-AACI-01A-11D-A40R-10	21886	43182826	127932241	140	24311										
SLC22A7	10864	hgsc.bcm.edu	37	chr6	43269998	43269998	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtgtcggggctggggctgaaCgtgtaccagacacagctgtt	16	9	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:43269998C>T	ENST00000372585.5	+	8	1217	c.1122C>T	c.(1120-1122)aaC>aaT	p.N374N	SLC22A7_ENST00000372589.3_Silent_p.N372N|SLC22A7_ENST00000372574.3_Silent_p.N372N	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	374					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	TGGGGCTGAACGTGTACCAGA	0.602																																					p.N374N		Atlas-SNP	.											.	SLC22A7	69	.	0			c.C1122T						.						121	105	110					6																	43269998		2203	4300	6503	SO:0001819	synonymous_variant	10864	exon7			GCTGAACGTGTAC	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.1122C>T	chr6.hg19:g.43269998C>T		106.0	0.0		149.0	19.0	NM_153320	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Silent	SNP	ENST00000372585.5	hg19	CCDS4893.2																																																																																			.	.		0.602	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			T	43269998	C	T	43269998	2	4	160	1	0	0	0	0	0	0	0	1	14474	535	19	1		1	SLC22A7	6	43269998	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	87172	43269998	127845069	141	24312										
DST	667	hgsc.bcm.edu	37	chr6	56380255	56380255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acaccaggcttacccgatgtTcttcctgctgctgccttaga	8	14	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:56380255T>C	ENST00000361203.3	-	67	17616	c.17609A>G	c.(17608-17610)gAa>gGa	p.E5870G	DST_ENST00000370769.4_Missense_Mutation_p.E5981G|DST_ENST00000421834.2_Missense_Mutation_p.E3893G|DST_ENST00000370754.5_Missense_Mutation_p.E6159G|DST_ENST00000370788.2_Missense_Mutation_p.E3784G|DST_ENST00000244364.6_Missense_Mutation_p.E3567G|DST_ENST00000340834.4_5'UTR|DST_ENST00000446842.2_Missense_Mutation_p.E5655G|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	5870					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TACCCGATGTTCTTCCTGCTG	0.408																																					p.E3567G		Atlas-SNP	.											.	DST	1427	.	0			c.A10700G						.						99	95	97					6																	56380255		1885	4133	6018	SO:0001583	missense	667	exon53			CGATGTTCTTCCT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.17609A>G	chr6.hg19:g.56380255T>C	ENSP00000354508:p.Glu5870Gly	57.0	0.0		69.0	9.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	T	19.89	3.910763	0.72983	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7;0.7;0.7	5.8	5.8	0.92144	.	0.000000	0.52532	D	0.000065	T	0.54983	0.1892	L	0.50333	1.59	0.33373	D	0.573864	P;D;D;P;P	0.76494	0.931;0.999;0.998;0.939;0.935	P;D;D;P;P	0.73380	0.761;0.98;0.949;0.739;0.811	T	0.57659	-0.7773	9	0.49607	T	0.09	.	16.1508	0.81622	0.0:0.0:0.0:1.0	.	3893;5981;6159;5979;3567	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	G	3567;6159;5981;3893;5655;3784;5870	ENSP00000244364:E3567G;ENSP00000359790:E6159G;ENSP00000359805:E5981G;ENSP00000400883:E3893G;ENSP00000393645:E5655G;ENSP00000359824:E3784G;ENSP00000354508:E5870G	ENSP00000244364:E3567G	E	-	2	0	DST	56488214	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	8.040000	0.89188	2.207000	0.71202	0.528000	0.53228	GAA	.	.		0.408	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56380255	T	C	56380255	3	2	160	1	0	0	0	0	1	0	0	0	4785	1783	62	2	4943	2	DST	6	56380255	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	13110257	56380255	114734812	142	24313										
DST	667	hgsc.bcm.edu	37	chr6	56380272	56380272	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgttcttcctgctgctgcctTagagtttcatattcaagggc	9	10	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:56380272T>G	ENST00000361203.3	-	67	17599	c.17592A>C	c.(17590-17592)ctA>ctC	p.L5864L	DST_ENST00000370769.4_Silent_p.L5975L|DST_ENST00000421834.2_Silent_p.L3887L|DST_ENST00000370754.5_Silent_p.L6153L|DST_ENST00000370788.2_Silent_p.L3778L|DST_ENST00000244364.6_Silent_p.L3561L|DST_ENST00000340834.4_5'UTR|DST_ENST00000446842.2_Silent_p.L5649L|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	5864					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GCTGCTGCCTTAGAGTTTCAT	0.418																																					p.L3561L		Atlas-SNP	.											.	DST	1427	.	0			c.A10683C						.						109	105	107					6																	56380272		1883	4139	6022	SO:0001819	synonymous_variant	667	exon53			CTGCCTTAGAGTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.17592A>C	chr6.hg19:g.56380272T>G		72.0	0.0		83.0	9.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.418	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56380272	T	G	56380272	2	3	160	1	0	0	0	0	0	0	0	1	4785	1741	61	5		5	DST	6	56380272	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	17	56380272	114734795	143	24314										
EYS	346007	hgsc.bcm.edu	37	chr6	65300985	65300985	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtgcataccagctggctaatAtcgctgagttcatccagaat	9	10	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:65300985A>T	ENST00000370621.3	-	26	5301	c.4775T>A	c.(4774-4776)aTa>aAa	p.I1592K	EYS_ENST00000370616.2_Missense_Mutation_p.I1592K|EYS_ENST00000503581.1_Missense_Mutation_p.I1592K			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1592					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GCTGGCTAATATCGCTGAGTT	0.398																																					p.I1592K		Atlas-SNP	.											.	EYS	527	.	0			c.T4775A						.						25	22	23					6																	65300985		692	1590	2282	SO:0001583	missense	346007	exon26			GCTAATATCGCTG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4775T>A	chr6.hg19:g.65300985A>T	ENSP00000359655:p.Ile1592Lys	75.0	0.0		66.0	14.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	A	14.18	2.458146	0.43634	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84589	-1.87;-1.85;-1.85	5.84	3.41	0.39046	.	.	.	.	.	T	0.61060	0.2317	N	0.08118	0	0.80722	D	1	P;P	0.49358	0.923;0.875	P;B	0.46110	0.504;0.307	T	0.66767	-0.5840	9	0.87932	D	0	.	7.18	0.25768	0.7787:0.1469:0.0744:0.0	.	1592;1592	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	K	1592	ENSP00000424243:I1592K;ENSP00000359655:I1592K;ENSP00000359650:I1592K	ENSP00000359650:I1592K	I	-	2	0	EYS	65357706	1.000000	0.71417	0.945000	0.38365	0.998000	0.95712	4.186000	0.58337	0.460000	0.27045	0.482000	0.46254	ATA	.	.		0.398	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		T	65300985	A	T	65300985	3	4	160	1	0	0	0	0	1	0	0	0	5334	449	16	4	4576	4	EYS	6	65300985	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	8920713	65300985	105814082	144	24315										
OOEP	441161	hgsc.bcm.edu	37	chr6	74079023	74079023	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cgcccgaaaacggtgatttcGactaggttccctgagtcaac	10	12	1	2	rs372105159	byFrequency	TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:74079023G>A	ENST00000370359.5	-	2	275	c.276C>T	c.(274-276)gtC>gtT	p.V92V	OOEP_ENST00000370363.1_Silent_p.V37V|OOEP-AS1_ENST00000445350.2_RNA	NM_001080507.2	NP_001073976.1	A6NGQ2	OOEP_HUMAN	oocyte expressed protein	92	KH; atypical.		V -> A (in dbSNP:rs496530). {ECO:0000269|Ref.1}.		cellular protein complex assembly (GO:0043623)|embryo implantation (GO:0007566)|embryonic pattern specification (GO:0009880)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|protein phosphorylation (GO:0006468)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|protein complex (GO:0043234)	RNA binding (GO:0003723)			large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	8						CGGTGATTTCGACTAGGTTCC	0.557													G|||	2	0.000399361	0.0015	0	5008	,	,		19368	0		0	False		,,,				2504	0				p.V92V		Atlas-SNP	.											.	OOEP	18	.	0			c.C276T						.	G		2,3928		0,2,1963	50	49	49		276	-7.4	0	6		49	0,8278		0,0,4139	no	coding-synonymous	OOEP	NM_001080507.2		0,2,6102	AA,AG,GG		0.0,0.0509,0.0164		92/150	74079023	2,12206	1965	4139	6104	SO:0001819	synonymous_variant	441161	exon2			GATTTCGACTAGG	BC024931	CCDS47451.1	6q13	2012-02-22	2012-02-22	2007-11-13	ENSG00000203907	ENSG00000203907			21382	protein-coding gene	gene with protein product	"KH homology domain containing 2"	611689	"chromosome 6 open reading frame 156", "oocyte expressed protein homolog (dog)"	C6orf156		17913455	Standard	NM_001080507		Approved	Em:AC019205.2, KHDC2	uc003pgu.4	A6NGQ2	OTTHUMG00000150057	ENST00000370359.5:c.276C>T	chr6.hg19:g.74079023G>A		130.0	0.0		133.0	65.0	NM_001080507	A6NIN5|A9UIB7	Silent	SNP	ENST00000370359.5	hg19	CCDS47451.1																																																																																			.	.		0.557	OOEP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108414.2	NM_001080507		A	74079023	G	A	74079023	2	1	160	1	0	0	0	0	0	0	0	1	10879	1045	37	1		1	OOEP	6	74079023	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	8778038	74079023	97036044	145	24316										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75875410	75875410	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	catgagaccctgtaaccgcgAaccattcctggagcagatgt	10	12	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:75875410A>G	ENST00000322507.8	-	14	3105	c.2796T>C	c.(2794-2796)gtT>gtC	p.V932V	COL12A1_ENST00000483888.2_Silent_p.V932V|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Silent_p.V932V	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	932	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TGTAACCGCGAACCATTCCTG	0.403																																					p.V932V		Atlas-SNP	.											.	COL12A1	385	.	0			c.T2796C						.						121	113	115					6																	75875410		1878	4108	5986	SO:0001819	synonymous_variant	1303	exon14			ACCGCGAACCATT	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2796T>C	chr6.hg19:g.75875410A>G		145.0	0.0		103.0	18.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.403	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		G	75875410	A	G	75875410	2	3	160	1	0	0	0	0	0	0	0	1	3671	233	9	2		2	COL12A1	6	75875410	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1796387	75875410	95239657	146	24317										
SFRS18	25957	hgsc.bcm.edu	37	chr6	99851737	99851737	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gggaagccagtgcactggacTgtgccagctgttttgcagga	15	9	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:99851737T>A	ENST00000369239.5	-	10	1328	c.1124A>T	c.(1123-1125)cAg>cTg	p.Q375L	PNISR_ENST00000438806.1_Missense_Mutation_p.Q375L	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	375						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						TGCACTGGACTGTGCCAGCTG	0.438																																					p.Q375L		Atlas-SNP	.											.	PNISR	74	.	0			c.A1124T						.						82	70	74					6																	99851737		2203	4300	6503	SO:0001583	missense	25957	exon9			CTGGACTGTGCCA	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 111", "splicing factor, arginine/serine-rich 18"	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.1124A>T	chr6.hg19:g.99851737T>A	ENSP00000358242:p.Gln375Leu	210.0	0.0		178.0	46.0	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Missense_Mutation	SNP	ENST00000369239.5	hg19	CCDS5043.1	.	.	.	.	.	.	.	.	.	.	T	17.25	3.342148	0.61073	.	.	ENSG00000132424	ENST00000369239;ENST00000438806	.	.	.	5.7	5.7	0.88788	.	0.104260	0.64402	D	0.000002	T	0.67998	0.2953	L	0.59436	1.845	0.80722	D	1	D	0.61080	0.989	D	0.72625	0.978	T	0.64537	-0.6384	9	0.24483	T	0.36	.	16.2651	0.82574	0.0:0.0:0.0:1.0	.	375	Q8TF01	PNISR_HUMAN	L	375	.	ENSP00000358242:Q375L	Q	-	2	0	PNISR	99958458	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.556000	0.82233	2.304000	0.77564	0.523000	0.50628	CAG	.	.		0.438	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870		A	99851737	T	A	99851737	3	1	160	1	0	0	0	0	1	0	0	0	14189	1580	55	4	1305	4	SFRS18	6	99851737	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	23976327	99851737	71263330	147	24318										
SFRS18	25957	hgsc.bcm.edu	37	chr6	99854007	99854007	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctttcccactacttgcagccTcaacattttcagtgtcttct	4	14	4	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:99854007T>C	ENST00000369239.5	-	8	1106	c.902A>G	c.(901-903)gAg>gGg	p.E301G	PNISR_ENST00000438806.1_Missense_Mutation_p.E301G	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	301						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						ACTTGCAGCCTCAACATTTTC	0.393																																					p.E301G		Atlas-SNP	.											.	PNISR	74	.	0			c.A902G						.						207	185	193					6																	99854007		2203	4300	6503	SO:0001583	missense	25957	exon7			GCAGCCTCAACAT	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 111", "splicing factor, arginine/serine-rich 18"	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.902A>G	chr6.hg19:g.99854007T>C	ENSP00000358242:p.Glu301Gly	104.0	0.0		79.0	22.0	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Missense_Mutation	SNP	ENST00000369239.5	hg19	CCDS5043.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.849913	0.91277	.	.	ENSG00000132424	ENST00000369239;ENST00000438806	T;T	0.54071	0.59;0.59	5.57	5.57	0.84162	.	0.046027	0.85682	D	0.000000	T	0.53658	0.1810	L	0.51422	1.61	0.80722	D	1	D	0.63046	0.992	P	0.57620	0.824	T	0.54655	-0.8261	10	0.45353	T	0.12	.	16.0108	0.80402	0.0:0.0:0.0:1.0	.	301	Q8TF01	PNISR_HUMAN	G	301	ENSP00000358242:E301G;ENSP00000387997:E301G	ENSP00000358242:E301G	E	-	2	0	PNISR	99960728	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.302000	0.72788	2.242000	0.73789	0.482000	0.46254	GAG	.	.		0.393	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870		C	99854007	T	C	99854007	3	2	160	1	0	0	0	0	1	0	0	0	14189	1551	54	2	1535	2	SFRS18	6	99854007	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2270	99854007	71261060	148	24319										
MAN1A1	4121	hgsc.bcm.edu	37	chr6	119669665	119669665	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttttctcgcggatggcggcgTcggcgggctcccggctctcc	15	15	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:119669665T>A	ENST00000368468.3	-	2	1007	c.566A>T	c.(565-567)gAc>gTc	p.D189V	MAN1A1_ENST00000368466.2_Missense_Mutation_p.D189V	NM_005907.3	NP_005898.2	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	189					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|mannosidase activity (GO:0015923)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|skin(3)	24		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		GATGGCGGCGTCGGCGGGCTC	0.662																																					p.D189V	Ovarian(136;8 1825 12608 33541 47587)	Atlas-SNP	.											.	MAN1A1	77	.	0			c.A566T						.						22	29	26					6																	119669665		2194	4289	6483	SO:0001583	missense	4121	exon2			GCGGCGTCGGCGG	AK025599	CCDS5122.1	6q22	2008-08-29			ENSG00000111885	ENSG00000111885	3.2.1.113		6821	protein-coding gene	gene with protein product		604344				8223597	Standard	NM_005907		Approved		uc003pym.2	P33908	OTTHUMG00000015472	ENST00000368468.3:c.566A>T	chr6.hg19:g.119669665T>A	ENSP00000357453:p.Asp189Val	111.0	0.0		89.0	21.0	NM_005907	E7EU32|Q6P052|Q9NU44|Q9UJI3	Missense_Mutation	SNP	ENST00000368468.3	hg19	CCDS5122.1	.	.	.	.	.	.	.	.	.	.	T	15.47	2.843243	0.51057	.	.	ENSG00000111885	ENST00000368468;ENST00000368466	T;D	0.81996	-0.84;-1.56	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.83922	0.5359	M	0.65975	2.015	0.80722	D	1	D;B	0.61080	0.989;0.222	P;B	0.55615	0.78;0.13	D	0.84467	0.0597	9	.	.	.	-10.026	14.7849	0.69796	0.0:0.0:0.0:1.0	.	189;189	Q6P052;P33908	.;MA1A1_HUMAN	V	189	ENSP00000357453:D189V;ENSP00000357451:D189V	.	D	-	2	0	MAN1A1	119711364	1.000000	0.71417	0.170000	0.22879	0.232000	0.25224	7.131000	0.77243	1.985000	0.57927	0.374000	0.22700	GAC	.	.		0.662	MAN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042015.1	NM_005907		A	119669665	T	A	119669665	3	1	160	1	0	0	0	0	1	0	0	0	9219	1667	58	4	1443	4	MAN1A1	6	119669665	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	19815658	119669665	51445402	149	24320										
ENPP1	5167	hgsc.bcm.edu	37	chr6	132189188	132189188	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccttgcagagggttgatggtAtggttggtatgctgatggat	16	4	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:132189188A>T	ENST00000360971.2	+	12	1215	c.1195A>T	c.(1195-1197)Atg>Ttg	p.M399L		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	399	Phosphodiesterase.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	GGTTGATGGTATGGTTGGTAT	0.403																																					p.M399L	Colon(104;336 1535 5856 11019 33782)	Atlas-SNP	.											.	ENPP1	108	.	0			c.A1195T						.						243	217	226					6																	132189188		2203	4300	6503	SO:0001583	missense	5167	exon12			GATGGTATGGTTG	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.1195A>T	chr6.hg19:g.132189188A>T	ENSP00000354238:p.Met399Leu	93.0	0.0		80.0	19.0	NM_006208	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Missense_Mutation	SNP	ENST00000360971.2	hg19	CCDS5150.2	.	.	.	.	.	.	.	.	.	.	A	10.55	1.380504	0.24944	.	.	ENSG00000197594	ENST00000360971	T	0.73469	-0.75	5.76	3.33	0.38152	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.280341	0.43579	N	0.000552	T	0.31040	0.0784	N	0.16307	0.4	0.30384	N	0.781628	B;B	0.06786	0.001;0.001	B;B	0.11329	0.006;0.004	T	0.10941	-1.0608	10	0.15066	T	0.55	-7.5435	6.9604	0.24593	0.7411:0.1264:0.1325:0.0	.	399;29	P22413;Q7Z3P5	ENPP1_HUMAN;.	L	399	ENSP00000354238:M399L	ENSP00000354238:M399L	M	+	1	0	ENPP1	132230881	0.998000	0.40836	0.709000	0.30452	0.416000	0.31233	3.853000	0.55941	0.509000	0.28195	0.533000	0.62120	ATG	.	.		0.403	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2			T	132189188	A	T	132189188	3	4	160	1	0	0	0	0	1	0	0	0	5131	449	16	4	1241	4	ENPP1	6	132189188	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	12519523	132189188	38925879	150	24321										
EYA4	2070	hgsc.bcm.edu	37	chr6	133767789	133767789	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctatggaaatgcaggacctAgcaagtcctcatactcttgt	8	10	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:133767789A>T	ENST00000367895.5	+	4	569	c.105A>T	c.(103-105)ctA>ctT	p.L35L	EYA4_ENST00000355167.3_Silent_p.L35L|EYA4_ENST00000531901.1_Silent_p.L35L|EYA4_ENST00000430974.2_Silent_p.L35L|EYA4_ENST00000525849.1_Silent_p.L35L|EYA4_ENST00000355286.6_Silent_p.L35L|EYA4_ENST00000431403.2_Silent_p.L35L|EYA4_ENST00000452339.2_Silent_p.L35L	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	35					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		TGCAGGACCTAGCAAGTCCTC	0.393																																					p.L35L	Melanoma(57;398 1237 3528 4702 7415)	Atlas-SNP	.											.	EYA4	196	.	0			c.A105T						.						116	110	112					6																	133767789		2203	4300	6503	SO:0001819	synonymous_variant	2070	exon4			GGACCTAGCAAGT	Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"Protein tyrosine phosphatases / Asp-based PTPs"	3522	protein-coding gene	gene with protein product		603550	"eyes absent (Drosophila) homolog 4", "eyes absent homolog 4 (Drosophila)"	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.105A>T	chr6.hg19:g.133767789A>T		137.0	0.0		93.0	18.0	NM_172105	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Silent	SNP	ENST00000367895.5	hg19	CCDS5165.1																																																																																			.	.		0.393	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100		T	133767789	A	T	133767789	2	4	160	1	0	0	0	0	0	0	0	1	5333	407	15	4		4	EYA4	6	133767789	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1578601	133767789	37347278	151	24322										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136597258	136597258	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttttgtagtgctaggcctttCcactacatatccagtctctt	6	11	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:136597258C>A	ENST00000531224.1	-	5	1657	c.1405G>T	c.(1405-1407)Gaa>Taa	p.E469*	BCLAF1_ENST00000530767.1_Intron|BCLAF1_ENST00000353331.4_Nonsense_Mutation_p.E467*|BCLAF1_ENST00000527536.1_Nonsense_Mutation_p.E469*|BCLAF1_ENST00000527759.1_Nonsense_Mutation_p.E467*|BCLAF1_ENST00000392348.2_Nonsense_Mutation_p.E467*	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	469					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.E469fs*20(1)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		CTAGGCCTTTCCACTACATAT	0.343																																					p.E469X	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.,1	BCLAF1	203	.	1	Deletion - Frameshift(1)	lung(1)	c.G1405T						.						133	138	136					6																	136597258		2203	4300	6503	SO:0001587	stop_gained	9774	exon5			GCCTTTCCACTAC	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.1405G>T	chr6.hg19:g.136597258C>A	ENSP00000435210:p.Glu469*	102.0	0.0		107.0	17.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Nonsense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	37	6.531036	0.97641	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000527759;ENST00000392348;ENST00000529826	.	.	.	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	-11.3047	12.5417	0.56174	0.0:0.9237:0.0:0.0763	.	.	.	.	X	469;467;469;467;467;469	.	ENSP00000229446:E467X	E	-	1	0	BCLAF1	136638951	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.938000	0.70170	2.611000	0.88343	0.644000	0.83932	GAA	.	.		0.343	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		A	136597258	C	A	136597258	4	1	160	1	0	0	0	0	0	1	0	0	1383	864	30	3	1393	3	BCLAF1	6	136597258	Nonsense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	2829469	136597258	34517809	152	24323										
MAP7	9053	hgsc.bcm.edu	37	chr6	136693743	136693743	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtgtgcagctttgtagggcaTgatgatggggctgcaagatg	17	5	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:136693743T>C	ENST00000354570.3	-	8	1182	c.772A>G	c.(772-774)Atg>Gtg	p.M258V	MAP7_ENST00000544465.1_Missense_Mutation_p.M243V|MAP7_ENST00000454590.1_Missense_Mutation_p.M280V|MAP7_ENST00000438100.2_Missense_Mutation_p.M243V|MAP7_ENST00000432797.2_Missense_Mutation_p.M112V	NM_001198616.1|NM_001198617.1|NM_001198619.1|NM_003980.4	NP_001185545.1|NP_001185546.1|NP_001185548.1|NP_003971.1	Q14244	MAP7_HUMAN	microtubule-associated protein 7	258					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|establishment or maintenance of cell polarity (GO:0007163)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells (GO:0048872)|Leydig cell differentiation (GO:0033327)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nucleus organization (GO:0006997)|organ growth (GO:0035265)|protein localization to plasma membrane (GO:0072659)|response to osmotic stress (GO:0006970)|response to retinoic acid (GO:0032526)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(11)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		TTGTAGGGCATGATGATGGGG	0.488																																					p.M288V		Atlas-SNP	.											.	MAP7	63	.	0			c.A862G						.						193	168	177					6																	136693743		2203	4300	6503	SO:0001583	missense	9053	exon8			AGGGCATGATGAT	X73882	CCDS5178.1, CCDS56452.1, CCDS56453.1, CCDS56454.1, CCDS56455.1, CCDS75527.1, CCDS75528.1, CCDS75529.1	6q23.2	2008-07-28			ENSG00000135525	ENSG00000135525			6869	protein-coding gene	gene with protein product		604108				8408219	Standard	NM_003980		Approved	E-MAP-115	uc011edg.2	Q14244	OTTHUMG00000015646	ENST00000354570.3:c.772A>G	chr6.hg19:g.136693743T>C	ENSP00000346581:p.Met258Val	138.0	0.0		102.0	56.0	NM_001198609	B7Z290|B7Z400|B7Z5S7|B7Z9U7|C9JPS0|E9PCP3|F5H1E2|Q7Z6S0|Q8TAU5|Q9NY82|Q9NY83	Missense_Mutation	SNP	ENST00000354570.3	hg19	CCDS5178.1	.	.	.	.	.	.	.	.	.	.	T	9.679	1.148811	0.21288	.	.	ENSG00000135525	ENST00000354570;ENST00000454590;ENST00000544465;ENST00000438100;ENST00000432797;ENST00000345567	T;T;T;T;T	0.11063	2.81;2.81;2.81;2.81;2.81	5.67	5.67	0.87782	.	0.193905	0.35970	N	0.002870	T	0.04770	0.0129	L	0.53249	1.67	0.29112	N	0.880792	B;B;B;B;B;B;B;B	0.17667	0.013;0.013;0.023;0.013;0.002;0.023;0.023;0.013	B;B;B;B;B;B;B;B	0.18561	0.01;0.01;0.022;0.01;0.001;0.022;0.022;0.01	T	0.21245	-1.0251	10	0.28530	T	0.3	-11.9308	11.4179	0.49962	0.0:0.0:0.2728:0.7272	.	243;280;243;280;280;164;221;258	B7Z290;B7ZB64;F5H1E2;E9PCP3;B7Z400;F8W783;Q14244-2;Q14244	.;.;.;.;.;.;.;MAP7_HUMAN	V	258;280;243;243;112;164	ENSP00000346581:M258V;ENSP00000414712:M280V;ENSP00000445737:M243V;ENSP00000400790:M243V;ENSP00000414879:M112V	ENSP00000344217:M164V	M	-	1	0	MAP7	136735436	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.153000	0.42282	2.163000	0.67991	0.482000	0.46254	ATG	.	.		0.488	MAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042382.2	NM_003980		C	136693743	T	C	136693743	3	2	160	1	0	0	0	0	1	0	0	0	9275	1464	51	2	1521	2	MAP7	6	136693743	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	96485	136693743	34421324	153	24324										
EPM2A	7957	hgsc.bcm.edu	37	chr6	146056478	146056478	+	Frame_Shift_Del	DEL	C	C	-													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	caggcccggctcctgcagggCcagggccccgtcgcccgccg							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:146056478delC	ENST00000367519.3	-	1	682	c.157delG	c.(157-159)gccfs	p.A53fs	RP3-466P17.2_ENST00000603042.1_lincRNA|RP3-466P17.1_ENST00000603994.1_lincRNA	NM_005670.3	NP_005661.1	O95278	EPM2A_HUMAN	epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)	53	CBM20. {ECO:0000255|PROSITE- ProRule:PRU00594}.				autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|habituation (GO:0046959)|inositol phosphate dephosphorylation (GO:0046855)|nervous system development (GO:0007399)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polysome (GO:0005844)	carbohydrate phosphatase activity (GO:0019203)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|starch binding (GO:2001070)			kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	7		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)		TCCTGCAGGGCCAGGGCCCCG	0.801																																					p.A53fs		Atlas-INDEL	.											.	EPM2A	21	.	0			c.158delC						.						1	1	1					6																	146056478		904	2006	2910	SO:0001589	frameshift_variant	7957	exon1			.	AF284580	CCDS5206.1	6q24	2011-06-09			ENSG00000112425	ENSG00000112425		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3413	protein-coding gene	gene with protein product		607566	"epilepsy, progressive myoclonus type 2, Lafora disease (laforin)"			9222970, 7485240	Standard	XM_006715564		Approved	LDE, LD	uc003qkw.3	B3EWF7	OTTHUMG00000015747	ENST00000367519.3:c.157delG	chr6.hg19:g.146056478delC	ENSP00000356489:p.Ala53fs	150.0	0.0		164.0	36.0	NM_001018041	B3KMU5|B4DRZ2|O95483|Q5T3F5|Q6IS15|Q8IU96|Q8IX24|Q8IX25|Q9BS66|Q9UEN2	Frame_Shift_Del	DEL	ENST00000367519.3	hg19	CCDS5206.1																																																																																			.	.		0.801	EPM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042564.1			-	146056478	C	-	146056478	7	5	160	1	0	1	0	1	0	0	0	0	5185	739	26	0	888	0	EPM2A	6	146056478	Frame_Shift_Del	DEL	C	TCGA-DD-AACI-01A-11D-A40R-10	9362735	146056478	25058589	154	24325										
ESR1	2099	hgsc.bcm.edu	37	chr6	152415601	152415601	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agtcctggacaagatcacagAcactttgatccacctgatgg	9	11	1	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr6:152415601A>G	ENST00000206249.3	+	7	1813	c.1451A>G	c.(1450-1452)gAc>gGc	p.D484G	ESR1_ENST00000406599.1_Missense_Mutation_p.D223G|ESR1_ENST00000440973.1_Missense_Mutation_p.D484G|ESR1_ENST00000427531.2_Intron|ESR1_ENST00000338799.5_Missense_Mutation_p.D484G|ESR1_ENST00000456483.2_Missense_Mutation_p.D372G|ESR1_ENST00000443427.1_Missense_Mutation_p.D484G	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	484	Interaction with AKAP13.|Self-association.|Steroid-binding.|Transactivation AF-2.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	AAGATCACAGACACTTTGATC	0.567																																					p.D484G		Atlas-SNP	.											.	ESR1	94	.	0			c.A1451G						.						101	90	94					6																	152415601		2203	4300	6503	SO:0001583	missense	2099	exon7			TCACAGACACTTT	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"Nuclear hormone receptors"	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.1451A>G	chr6.hg19:g.152415601A>G	ENSP00000206249:p.Asp484Gly	101.0	0.0		65.0	16.0	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Missense_Mutation	SNP	ENST00000206249.3	hg19	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.840954	0.91197	.	.	ENSG00000091831	ENST00000440973;ENST00000338799;ENST00000456483;ENST00000443427;ENST00000206249;ENST00000406599;ENST00000431590	D;D;D;D;D;D	0.96913	-4.17;-4.17;-4.17;-4.17;-4.17;-4.17	5.43	5.43	0.79202	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.97993	0.9339	M	0.85197	2.74	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.998;1.0;0.986;0.997;0.997;0.997	D;D;D;P;D;D;D	0.91635	0.999;0.998;0.999;0.861;0.99;0.976;0.986	D	0.99232	1.0882	10	0.87932	D	0	.	15.4875	0.75578	1.0:0.0:0.0:0.0	.	49;179;223;411;483;484;484	B5LY05;C8CJL6;Q9H2M1;B4E3R5;A8KAF4;G4XH65;P03372	.;.;.;.;.;.;ESR1_HUMAN	G	484;484;372;484;484;223;412	ENSP00000405330:D484G;ENSP00000342630:D484G;ENSP00000415934:D372G;ENSP00000387500:D484G;ENSP00000206249:D484G;ENSP00000384064:D223G	ENSP00000206249:D484G	D	+	2	0	ESR1	152457294	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.962000	0.93254	2.066000	0.61787	0.454000	0.30748	GAC	.	.		0.567	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1			G	152415601	A	G	152415601	3	3	160	1	0	0	0	0	1	0	0	0	5258	275	10	2	1477	2	ESR1	6	152415601	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	6359123	152415601	18699466	155	24326										
EIF2AK1	27102	hgsc.bcm.edu	37	chr7	6080784	6080784	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccaaagcgtttttctttttcTggggtgggctcagcaaagat	11	8	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:6080784T>A	ENST00000199389.6	-	9	1004	c.858A>T	c.(856-858)ccA>ccT	p.P286P	EIF2AK1_ENST00000495565.1_5'UTR|EIF2AK1_ENST00000536084.1_Silent_p.P162P	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	286	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		TTTCTTTTTCTGGGGTGGGCT	0.358																																					p.P286P		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.A858T						.						97	103	101					7																	6080784		2203	4300	6503	SO:0001819	synonymous_variant	27102	exon9			TTTTTCTGGGGTG	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"heme regulated initiation factor 2 alpha kinase"	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.858A>T	chr7.hg19:g.6080784T>A		108.0	0.0		144.0	19.0	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Silent	SNP	ENST00000199389.6	hg19	CCDS5345.1																																																																																			.	.		0.358	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		A	6080784	T	A	6080784	2	1	160	1	0	0	0	0	0	0	0	1	4998	1567	55	4		4	EIF2AK1	7	6080784	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10		6080784	153057879	156	24327										
INHBA	3624	hgsc.bcm.edu	37	chr7	41729994	41729994	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gctgccctgcgggtgcttctGctgctggaagaggcggatgg	18	10	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:41729994G>C	ENST00000242208.4	-	3	781	c.535C>G	c.(535-537)Cag>Gag	p.Q179E	INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Missense_Mutation_p.Q179E|AC005027.3_ENST00000416150.1_RNA	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	179					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GGGTGCTTCTGCTGCTGGAAG	0.562										TSP Lung(11;0.080)																											p.Q179E		Atlas-SNP	.											.	INHBA	118	.	0			c.C535G						.						101	94	97					7																	41729994		2203	4300	6503	SO:0001583	missense	3624	exon3			GCTTCTGCTGCTG		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.535C>G	chr7.hg19:g.41729994G>C	ENSP00000242208:p.Gln179Glu	67.0	0.0		93.0	11.0	NM_002192	Q14599	Missense_Mutation	SNP	ENST00000242208.4	hg19	CCDS5464.1	.	.	.	.	.	.	.	.	.	.	.	15.04	2.714918	0.48622	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.63580	-0.05;-0.05	5.81	5.81	0.92471	Transforming growth factor-beta, N-terminal (1);	0.554170	0.20607	N	0.089047	T	0.54159	0.1841	L	0.42245	1.32	0.46521	D	0.999082	B	0.02656	0.0	B	0.14023	0.01	T	0.53872	-0.8377	10	0.02654	T	1	-18.9698	20.0699	0.97718	0.0:0.0:1.0:0.0	.	179	P08476	INHBA_HUMAN	E	179	ENSP00000242208:Q179E;ENSP00000397197:Q179E	ENSP00000242208:Q179E	Q	-	1	0	INHBA	41696519	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.018000	0.70811	2.741000	0.93983	0.655000	0.94253	CAG	.	.		0.562	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			C	41729994	G	C	41729994	3	2	160	1	0	0	0	0	1	0	0	0	7750	1328	46	4	749	4	INHBA	7	41729994	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	35649210	41729994	117408669	157	24328										
INHBA	3624	hgsc.bcm.edu	37	chr7	41730010	41730010	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttctgctgctggaagaggcgGatggtgactttggtcctggt	16	7	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:41730010G>A	ENST00000242208.4	-	3	765	c.519C>T	c.(517-519)atC>atT	p.I173I	INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Silent_p.I173I|AC005027.3_ENST00000416150.1_RNA	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	173					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)	p.I173I(1)		biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GGAAGAGGCGGATGGTGACTT	0.577										TSP Lung(11;0.080)																											p.I173I		Atlas-SNP	.											INHBA,NS,carcinoma,0,1	INHBA	118	.	1	Substitution - coding silent(1)	lung(1)	c.C519T						.						107	99	102					7																	41730010		2203	4300	6503	SO:0001819	synonymous_variant	3624	exon3			GAGGCGGATGGTG		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.519C>T	chr7.hg19:g.41730010G>A		56.0	0.0		79.0	9.0	NM_002192	Q14599	Silent	SNP	ENST00000242208.4	hg19	CCDS5464.1																																																																																			.	.		0.577	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			A	41730010	G	A	41730010	2	1	160	1	0	0	0	0	0	0	0	1	7750	1164	41	3		3	INHBA	7	41730010	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	16	41730010	117408653	158	24329										
DDC	1644	hgsc.bcm.edu	37	chr7	50563117	50563117	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agttgaatgaatctgcaaacTgccaaagaacaagagtaaga	9	6	1	5			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:50563117T>A	ENST00000444124.2	-	9	1077		c.e9-2		DDC_ENST00000426377.1_Splice_Site|DDC_ENST00000380984.4_Splice_Site|DDC_ENST00000431062.1_Splice_Site|DDC_ENST00000357936.5_Splice_Site	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)						catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021)	amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170)	p.?(2)		breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1)	40	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968)	ATCTGCAAACTGCCAAAGAAC	0.338																																					.		Atlas-SNP	.											DDC_ENST00000380984,NS,carcinoma,0,2	DDC	100	.	2	Unknown(2)	lung(2)	c.598-2A>T						.						64	61	62					7																	50563117		2203	4300	6503	SO:0001630	splice_region_variant	1644	exon8			GCAAACTGCCAAA		CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1	7p12.1	2012-08-30			ENSG00000132437	ENSG00000132437	4.1.1.28		2719	protein-coding gene	gene with protein product		107930				1612608	Standard	NM_001082971		Approved	AADC	uc003tpf.4	P20711	OTTHUMG00000023353	ENST00000444124.2:c.877-2A>T	chr7.hg19:g.50563117T>A		59.0	0.0		111.0	17.0	NM_001242889	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Splice_Site	SNP	ENST00000444124.2	hg19	CCDS5511.1	.	.	.	.	.	.	.	.	.	.	T	17.68	3.449805	0.63290	.	.	ENSG00000132437	ENST00000357936;ENST00000431062;ENST00000426377;ENST00000444124;ENST00000430300;ENST00000380984	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3483	0.66682	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DDC	50530611	1.000000	0.71417	0.996000	0.52242	0.697000	0.40408	7.001000	0.76297	2.085000	0.62840	0.533000	0.62120	.	.	.		0.338	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1		Intron	A	50563117	T	A	50563117	5	1	160	1	0	0	0	0	0	0	1	0	4327	1594	55	4	591	4	DDC	7	50563117	Splice_Site	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	8833107	50563117	108575546	159	24330										
EGFR	1956	hgsc.bcm.edu	37	chr7	55248998	55248999	+	In_Frame_Ins	INS	-	-	TGGCCAGCG													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cctccaggaagcctacgtgaINStggccagcgtggacaacccc							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:55248998_55248999insTGGCCAGCG	ENST00000275493.2	+	20	2473_2474	c.2296_2297insTGGCCAGCG	c.(2296-2298)atg>aTGGCCAGCGtg	p.769_770insASV	EGFR_ENST00000442591.1_Intron|EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000455089.1_In_Frame_Ins_p.724_725insASV|EGFR_ENST00000454757.2_In_Frame_Ins_p.716_717insASV	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	769	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> M (found in a lung cancer sample; dbSNP:rs147149347). {ECO:0000269|PubMed:15623594}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.M766T(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	AGCCTACGTGATGGCCAGCGTG	0.644		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.M766delinsMASV		Atlas-INDEL	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	EGFR,caecum,carcinoma,0,1	EGFR	20426	.	1	Substitution - Missense(1)	lung(1)	c.2296_2297insTGGCCAGCG						.																																			SO:0001652	inframe_insertion	1956	exon20	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	.		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2297_2305dupTGGCCAGCG	chr7.hg19:g.55248999_55249007dupTGGCCAGCG	ENSP00000275493:p.Ala767_Val769dup	110.0	0.0		145.0	19.0	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	In_Frame_Ins	INS	ENST00000275493.2	hg19	CCDS5514.1																																																																																			.	.		0.644	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		TGGCCAGCG	55248999	-	TGGCCAGCG	55248998	7	5	160	1	0	1	1	0	0	0	0	0	4969	333	12	0	2638	0	EGFR	7	55248998	In_Frame_Ins	INS	-	TCGA-DD-AACI-01A-11D-A40R-10	4685881	55248998	103889665	160	24331										
ZNF679	168417	hgsc.bcm.edu	37	chr7	63726363	63726363	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	taccaagaagatatggaaaaAgtggacatgacaatttacaa	8	5	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:63726363A>T	ENST00000421025.1	+	5	621	c.352A>T	c.(352-354)Agt>Tgt	p.S118C	ZNF679_ENST00000255746.4_Missense_Mutation_p.S118C	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	118					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						ATATGGAAAAAGTGGACATGA	0.373																																					p.S118C		Atlas-SNP	.											.	ZNF679	80	.	0			c.A352T						.						162	138	145					7																	63726363		692	1591	2283	SO:0001583	missense	168417	exon5			GGAAAAAGTGGAC	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"Zinc fingers, C2H2-type", "-"	28650	protein-coding gene	gene with protein product	"hypothetical protein MGC42415"					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.352A>T	chr7.hg19:g.63726363A>T	ENSP00000416809:p.Ser118Cys	142.0	0.0		227.0	31.0	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	hg19	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.423716	0.00186	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.06608	3.28;3.28	0.819	-1.64	0.08318	.	.	.	.	.	T	0.01320	0.0043	N	0.00855	-1.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38265	-0.9669	9	0.02654	T	1	.	1.5151	0.02504	0.3311:0.0:0.3295:0.3394	.	118	Q8IYX0	ZN679_HUMAN	C	118	ENSP00000416809:S118C;ENSP00000255746:S118C	ENSP00000255746:S118C	S	+	1	0	ZNF679	63363798	0.000000	0.05858	0.019000	0.16419	0.019000	0.09904	-1.587000	0.02108	-1.207000	0.02637	-1.236000	0.01555	AGT	.	.		0.373	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		T	63726363	A	T	63726363	3	4	160	1	0	0	0	0	1	0	0	0	18101	72	3	4	366	4	ZNF679	7	63726363	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	8477365	63726363	95412300	161	24332										
PCLO	27445	hgsc.bcm.edu	37	chr7	82582621	82582621	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggaaggcaatttataatctgCtgaagtcactaaatttaagg	9	5	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:82582621C>A	ENST00000333891.9	-	5	7985	c.7648G>T	c.(7648-7650)Gca>Tca	p.A2550S	PCLO_ENST00000423517.2_Missense_Mutation_p.A2550S|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTATAATCTGCTGAAGTCACT	0.403																																					p.A2550S		Atlas-SNP	.											.	PCLO	1506	.	0			c.G7648T						.						92	90	91					7																	82582621		1878	4108	5986	SO:0001583	missense	27445	exon5			AATCTGCTGAAGT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.7648G>T	chr7.hg19:g.82582621C>A	ENSP00000334319:p.Ala2550Ser	132.0	0.0		139.0	16.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	7.338	0.620407	0.14193	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17528	2.28;2.27	4.66	2.81	0.32909	.	.	.	.	.	T	0.14700	0.0355	L	0.43152	1.355	0.28256	N	0.92507	B;B	0.32829	0.103;0.386	B;B	0.31101	0.085;0.124	T	0.13282	-1.0515	9	0.87932	D	0	.	8.4034	0.32601	0.0:0.7532:0.0:0.2468	.	2550;2550	Q9Y6V0-5;Q9Y6V0-6	.;.	S	2481;2550;2550	ENSP00000334319:A2550S;ENSP00000388393:A2550S	ENSP00000334319:A2550S	A	-	1	0	PCLO	82420557	0.801000	0.28930	0.988000	0.46212	0.908000	0.53690	0.019000	0.13444	0.961000	0.38030	0.484000	0.47621	GCA	.	.		0.403	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82582621	C	A	82582621	3	1	160	1	0	0	0	0	1	0	0	0	11592	797	28	3	7881	3	PCLO	7	82582621	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	18856258	82582621	76556042	162	24333										
PCLO	27445	hgsc.bcm.edu	37	chr7	82595525	82595525	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agtttactctcttcttgtttTtgatctgtggttaccatagg	8	7	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:82595525T>A	ENST00000333891.9	-	4	3916	c.3579A>T	c.(3577-3579)caA>caT	p.Q1193H	PCLO_ENST00000423517.2_Missense_Mutation_p.Q1193H	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTTCTTGTTTTTGATCTGTGG	0.343																																					p.Q1193H		Atlas-SNP	.											.	PCLO	1506	.	0			c.A3579T						.						135	126	129					7																	82595525		1801	4082	5883	SO:0001583	missense	27445	exon4			TTGTTTTTGATCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.3579A>T	chr7.hg19:g.82595525T>A	ENSP00000334319:p.Gln1193His	89.0	0.0		121.0	35.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	10.80	1.451591	0.26074	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16897	2.31;2.31	5.89	-1.98	0.07480	.	.	.	.	.	T	0.12433	0.0302	L	0.32530	0.975	0.24335	N	0.994987	B;B	0.14438	0.01;0.01	B;B	0.17433	0.018;0.01	T	0.32666	-0.9898	9	0.87932	D	0	.	8.1693	0.31245	0.0:0.396:0.1112:0.4928	.	1193;1193	Q9Y6V0-5;Q9Y6V0-6	.;.	H	1132;1193;1193	ENSP00000334319:Q1193H;ENSP00000388393:Q1193H	ENSP00000334319:Q1193H	Q	-	3	2	PCLO	82433461	0.016000	0.18221	0.413000	0.26509	0.802000	0.45316	0.085000	0.14912	-0.341000	0.08376	-0.256000	0.11100	CAA	.	.		0.343	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82595525	T	A	82595525	3	1	160	1	0	0	0	0	1	0	0	0	11592	1838	64	4	11954	4	PCLO	7	82595525	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	12904	82595525	76543138	163	24334										
PCLO	27445	hgsc.bcm.edu	37	chr7	82764329	82764329	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccttcttttgtacggggtcaActtgtttttgacctttgctc	8	10	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:82764329A>T	ENST00000333891.9	-	3	2874	c.2537T>A	c.(2536-2538)gTt>gAt	p.V846D	PCLO_ENST00000423517.2_Missense_Mutation_p.V846D	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TACGGGGTCAACTTGTTTTTG	0.448																																					p.V846D		Atlas-SNP	.											.	PCLO	1506	.	0			c.T2537A						.						153	155	154					7																	82764329		1913	4129	6042	SO:0001583	missense	27445	exon3			GGGTCAACTTGTT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.2537T>A	chr7.hg19:g.82764329A>T	ENSP00000334319:p.Val846Asp	161.0	0.0		191.0	17.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	5.689	0.311765	0.10789	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.15952	2.39;2.38	5.98	0.758	0.18432	.	.	.	.	.	T	0.07369	0.0186	N	0.08118	0	0.09310	N	0.999995	B;B	0.13145	0.007;0.007	B;B	0.09377	0.004;0.004	T	0.33523	-0.9865	9	0.87932	D	0	.	2.0716	0.03614	0.5152:0.121:0.2471:0.1167	.	846;846	Q9Y6V0-5;Q9Y6V0-6	.;.	D	792;846;846	ENSP00000334319:V846D;ENSP00000388393:V846D	ENSP00000334319:V846D	V	-	2	0	PCLO	82602265	0.000000	0.05858	0.041000	0.18516	0.860000	0.49131	-0.197000	0.09518	-0.091000	0.12440	-0.313000	0.08912	GTT	.	.		0.448	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82764329	A	T	82764329	3	4	160	1	0	0	0	0	1	0	0	0	11592	43	2	4	13000	4	PCLO	7	82764329	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	168804	82764329	76374334	164	24335										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83610729	83610729	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cactcagcacacgctttcccGtaaatatcacaccggtgtaa	6	14	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:83610729G>A	ENST00000265362.4	-	14	1874	c.1560C>T	c.(1558-1560)taC>taT	p.Y520Y	SEMA3A_ENST00000436949.1_Silent_p.Y520Y	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	520					apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						ACGCTTTCCCGTAAATATCAC	0.483																																					p.Y520Y		Atlas-SNP	.											.	SEMA3A	121	.	0			c.C1560T						.						76	70	72					7																	83610729		2203	4300	6503	SO:0001819	synonymous_variant	10371	exon14			TTTCCCGTAAATA	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1560C>T	chr7.hg19:g.83610729G>A		172.0	0.0		213.0	10.0	NM_006080		Silent	SNP	ENST00000265362.4	hg19	CCDS5599.1																																																																																			.	.		0.483	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		A	83610729	G	A	83610729	2	1	160	1	0	0	0	0	0	0	0	1	14039	1140	40	1		1	SEMA3A	7	83610729	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	846400	83610729	75527934	165	24336										
SAMD9	54809	hgsc.bcm.edu	37	chr7	92731091	92731091	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctagttgttgattttctggCcagaataagagggaagctag	12	5	2	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:92731091C>G	ENST00000379958.2	-	3	4589	c.4320G>C	c.(4318-4320)tgG>tgC	p.W1440C		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1440						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			GATTTTCTGGCCAGAATAAGA	0.358																																					p.W1440C		Atlas-SNP	.											.	SAMD9	239	.	0			c.G4320C						.						108	108	108					7																	92731091		2203	4300	6503	SO:0001583	missense	54809	exon2			TTCTGGCCAGAAT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.4320G>C	chr7.hg19:g.92731091C>G	ENSP00000369292:p.Trp1440Cys	142.0	0.0		171.0	33.0	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	hg19	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.062126	0.55432	.	.	ENSG00000205413	ENST00000379958	T	0.53640	0.61	4.35	4.35	0.52113	.	0.000000	0.64402	U	0.000003	T	0.63663	0.2530	L	0.55990	1.75	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.67620	-0.5624	10	0.87932	D	0	.	15.9323	0.79672	0.0:1.0:0.0:0.0	.	1440	Q5K651	SAMD9_HUMAN	C	1440	ENSP00000369292:W1440C	ENSP00000369292:W1440C	W	-	3	0	SAMD9	92569027	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.220000	0.78008	2.411000	0.81874	0.603000	0.83216	TGG	.	.		0.358	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		G	92731091	C	G	92731091	3	3	160	1	0	0	0	0	1	0	0	0	13841	740	26	4	453	4	SAMD9	7	92731091	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	9120362	92731091	66407572	166	24337										
DLX5	1749	hgsc.bcm.edu	37	chr7	96650106	96650106	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtaaggagcccggcggcggcAggtgggaattgattgagctg	19	7	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:96650106A>T	ENST00000222598.4	-	3	1285	c.812T>A	c.(811-813)cTg>cAg	p.L271Q	DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	271					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					CGGCGGCGGCAGGTGGGAATT	0.592																																					p.L271Q		Atlas-SNP	.											.	DLX5	52	.	0			c.T812A						.						50	55	54					7																	96650106		2203	4300	6503	SO:0001583	missense	1749	exon3			GGCGGCAGGTGGG		CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"Homeoboxes / ANTP class : NKL subclass"	2918	protein-coding gene	gene with protein product		600028	"distal-less homeo box 5"			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.812T>A	chr7.hg19:g.96650106A>T	ENSP00000222598:p.Leu271Gln	115.0	0.0		117.0	12.0	NM_005221	B7Z4P3|Q9UPL1	Missense_Mutation	SNP	ENST00000222598.4	hg19	CCDS5647.1	.	.	.	.	.	.	.	.	.	.	A	16.58	3.163084	0.57476	.	.	ENSG00000105880	ENST00000222598	D	0.91011	-2.77	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.93164	0.7823	M	0.70275	2.135	0.58432	D	0.999995	D	0.67145	0.996	P	0.59703	0.862	D	0.91501	0.5219	10	0.22109	T	0.4	-11.4203	15.1094	0.72343	1.0:0.0:0.0:0.0	.	271	P56178	DLX5_HUMAN	Q	271	ENSP00000222598:L271Q	ENSP00000222598:L271Q	L	-	2	0	DLX5	96488042	1.000000	0.71417	1.000000	0.80357	0.642000	0.38348	6.270000	0.72563	2.217000	0.71921	0.533000	0.62120	CTG	.	.		0.592	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			T	96650106	A	T	96650106	3	4	160	1	0	0	0	0	1	0	0	0	4576	188	7	4	61	4	DLX5	7	96650106	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	3919015	96650106	62488557	167	24338										
MUC17	140453	hgsc.bcm.edu	37	chr7	100680019	100680019	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	accctttcagcaactcctatTgacaccagcacccctgtgac	5	17	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:100680019T>C	ENST00000306151.4	+	3	5386	c.5322T>C	c.(5320-5322)atT>atC	p.I1774I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1774	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CAACTCCTATTGACACCAGCA	0.498																																					p.I1774I		Atlas-SNP	.											.	MUC17	804	.	0			c.T5322C						.						275	288	283					7																	100680019		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TCCTATTGACACC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5322T>C	chr7.hg19:g.100680019T>C		86.0	0.0		103.0	23.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100680019	T	C	100680019	2	2	160	1	0	0	0	0	0	0	0	1	9983	1800	63	2		2	MUC17	7	100680019	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4029913	100680019	58458644	168	24339										
MUC17	140453	hgsc.bcm.edu	37	chr7	100680551	100680551	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccctttcaacaactcttgctGacaccaggacacctgtgacc	6	16	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:100680551G>A	ENST00000306151.4	+	3	5918	c.5854G>A	c.(5854-5856)Gac>Aac	p.D1952N		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1952	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AACTCTTGCTGACACCAGGAC	0.488																																					p.D1952N		Atlas-SNP	.											.	MUC17	804	.	0			c.G5854A						.						249	245	246					7																	100680551		2203	4300	6503	SO:0001583	missense	140453	exon3			CTTGCTGACACCA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5854G>A	chr7.hg19:g.100680551G>A	ENSP00000302716:p.Asp1952Asn	81.0	0.0		94.0	24.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	6.997	0.554014	0.13374	.	.	ENSG00000169876	ENST00000306151	T	0.02890	4.12	0.932	0.932	0.19466	.	.	.	.	.	T	0.03220	0.0094	N	0.24115	0.695	0.09310	N	1	P	0.51933	0.949	P	0.51297	0.665	T	0.45425	-0.9262	9	0.12103	T	0.63	.	7.8581	0.29493	0.0:0.0:1.0:0.0	.	1952	Q685J3	MUC17_HUMAN	N	1952	ENSP00000302716:D1952N	ENSP00000302716:D1952N	D	+	1	0	MUC17	100467271	0.000000	0.05858	0.004000	0.12327	0.018000	0.09664	-0.182000	0.09726	0.857000	0.35407	0.134000	0.15878	GAC	.	.		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100680551	G	A	100680551	3	1	160	1	0	0	0	0	1	0	0	0	9983	1290	45	3	5864	3	MUC17	7	100680551	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	532	100680551	58458112	169	24340										
PMPCB	9512	hgsc.bcm.edu	37	chr7	102944347	102944347	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttgggagaagcagagattgaAcgtgagcgtggagtaatcct	15	5	0	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:102944347A>T	ENST00000249269.4	+	5	554	c.516A>T	c.(514-516)gaA>gaT	p.E172D	PMPCB_ENST00000428154.1_Missense_Mutation_p.E172D|PMPCB_ENST00000420236.2_Missense_Mutation_p.E67D	NM_004279.2	NP_004270.2	O75439	MPPB_HUMAN	peptidase (mitochondrial processing) beta	172					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(9)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CAGAGATTGAACGTGAGCGTG	0.348																																					p.E172D		Atlas-SNP	.											.	PMPCB	35	.	0			c.A516T						.						101	97	98					7																	102944347		2203	4300	6503	SO:0001583	missense	9512	exon5			GATTGAACGTGAG	AF054182	CCDS5730.1	7q22.1	2007-07-30			ENSG00000105819	ENSG00000105819			9119	protein-coding gene	gene with protein product		603131				9653160	Standard	XM_005250717		Approved	MPPB, MPPP52	uc003vbl.3	O75439	OTTHUMG00000157205	ENST00000249269.4:c.516A>T	chr7.hg19:g.102944347A>T	ENSP00000249269:p.Glu172Asp	127.0	0.0		165.0	17.0	NM_004279	O60416|Q96FV4	Missense_Mutation	SNP	ENST00000249269.4	hg19	CCDS5730.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.051710	0.55218	.	.	ENSG00000105819	ENST00000249269;ENST00000428154;ENST00000420236	T;T;T	0.18810	2.19;2.19;2.19	5.2	1.43	0.22495	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.17492	0.0420	L	0.48218	1.51	0.47621	D	0.999476	B;B;B;B;B;B;B	0.21821	0.002;0.028;0.037;0.037;0.061;0.061;0.007	B;B;B;B;B;B;B	0.23018	0.037;0.027;0.025;0.043;0.043;0.043;0.028	T	0.05402	-1.0887	10	0.46703	T	0.11	.	8.8961	0.35465	0.6893:0.0:0.3107:0.0	.	67;67;172;172;163;172;172	E7ERZ4;B4DM90;A8K1E9;B3KM34;Q96CP5;O75439;G3V0E4	.;.;.;.;.;MPPB_HUMAN;.	D	172;172;67	ENSP00000249269:E172D;ENSP00000390035:E172D;ENSP00000410393:E67D	ENSP00000249269:E172D	E	+	3	2	PMPCB	102731583	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.778000	0.26732	0.269000	0.21961	0.528000	0.53228	GAA	.	.		0.348	PMPCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347913.1	NM_004279		T	102944347	A	T	102944347	3	4	160	1	0	0	0	0	1	0	0	0	12150	40	2	4	534	4	PMPCB	7	102944347	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2263796	102944347	56194316	170	24341										
SYPL1	6856	hgsc.bcm.edu	37	chr7	105752947	105752947	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggccgagtcgactgatccgcTggcgaaccaagtagatgttg	14	10	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:105752947T>A	ENST00000011473.2	-	1	75	c.29A>T	c.(28-30)cAg>cTg	p.Q10L	SYPL1_ENST00000455385.2_5'Flank|SYPL1_ENST00000470347.1_5'Flank	NM_006754.3	NP_006745.1	Q16563	SYPL1_HUMAN	synaptophysin-like 1	10					synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|integral component of synaptic vesicle membrane (GO:0030285)|secretory granule (GO:0030141)	transporter activity (GO:0005215)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	7						actgatccgctGGCGAACCAA	0.716																																					p.Q10L		Atlas-SNP	.											.	SYPL1	20	.	0			c.A29T						.						17	14	15					7																	105752947		2184	4268	6452	SO:0001583	missense	6856	exon1			ATCCGCTGGCGAA		CCDS5736.1, CCDS47685.1	7q22.2	2005-05-24	2005-05-24	2005-05-24	ENSG00000008282	ENSG00000008282			11507	protein-coding gene	gene with protein product			"synaptophysin-like protein"	SYPL			Standard	NM_006754		Approved		uc003vdp.4	Q16563	OTTHUMG00000157587	ENST00000011473.2:c.29A>T	chr7.hg19:g.105752947T>A	ENSP00000011473:p.Gln10Leu	65.0	0.0		94.0	21.0	NM_006754	A4D0R2|Q96AR8	Missense_Mutation	SNP	ENST00000011473.2	hg19	CCDS5736.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.286968	0.40494	.	.	ENSG00000008282	ENST00000011473	T	0.30182	1.54	3.26	3.26	0.37387	.	0.277566	0.29730	N	0.011348	T	0.38852	0.1056	L	0.40543	1.245	0.80722	D	1	D	0.54601	0.967	P	0.62382	0.901	T	0.16988	-1.0384	10	0.59425	D	0.04	.	8.2466	0.31693	0.0:0.0:0.0:1.0	.	10	Q16563	SYPL1_HUMAN	L	10	ENSP00000011473:Q10L	ENSP00000011473:Q10L	Q	-	2	0	SYPL1	105540183	1.000000	0.71417	1.000000	0.80357	0.373000	0.29922	2.836000	0.48183	1.702000	0.51228	0.402000	0.26972	CAG	.	.		0.716	SYPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349221.1			A	105752947	T	A	105752947	3	1	160	1	0	0	0	0	1	0	0	0	15477	1580	55	4	774	4	SYPL1	7	105752947	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2808600	105752947	53385716	171	24342										
ST7	7982	hgsc.bcm.edu	37	chr7	116862960	116862960	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agttcagggactggaattgcAagagtattttcatgcgtgtt	12	5	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:116862960A>T	ENST00000265437.5	+	16	1898	c.1684A>T	c.(1684-1686)Aag>Tag	p.K562*	ST7_ENST00000393444.3_Intron|ST7_ENST00000422922.1_Intron|ST7_ENST00000393446.2_Intron|ST7_ENST00000323984.3_Intron|ST7_ENST00000393449.1_Intron|ST7_ENST00000393443.1_Intron|ST7_ENST00000393451.3_Intron|ST7_ENST00000393447.4_Intron|ST7_ENST00000432298.1_Intron	NM_021908.2	NP_068708.1	Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		CTGGAATTGCAAGAGTATTTT	0.448																																					p.K562X		Atlas-SNP	.											.	ST7	64	.	0			c.A1684T						.						146	141	143					7																	116862960		2203	4300	6503	SO:0001587	stop_gained	7982	exon16			AATTGCAAGAGTA	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000265437.5:c.1684A>T	chr7.hg19:g.116862960A>T	ENSP00000265437:p.Lys562*	92.0	0.0		91.0	11.0	NM_021908	A8K137|B4DRQ2	Nonsense_Mutation	SNP	ENST00000265437.5	hg19	CCDS5770.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.460773	0.84317	.	.	ENSG00000004866	ENST00000265437	.	.	.	4.5	-8.99	0.00751	.	1.592400	0.03719	N	0.251483	.	.	.	.	.	.	0.31265	N	0.692463	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	0.5236	2.8234	0.05478	0.2072:0.3556:0.3208:0.1165	.	.	.	.	X	562	.	ENSP00000265437:K562X	K	+	1	0	ST7	116650196	0.977000	0.34250	0.724000	0.30704	0.469000	0.32828	-0.107000	0.10873	-1.562000	0.01682	-0.250000	0.11733	AAG	.	.		0.448	ST7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141622.1	NM_021908		T	116862960	A	T	116862960	4	4	160	1	0	0	0	0	0	1	0	0	15244	131	5	4	1746	4	ST7	7	116862960	Nonsense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	11110013	116862960	42275703	172	24343										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117361141	117361141	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttttgttttgacagagaagcAttcctgttacaattcagctg	8	7	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:117361141A>G	ENST00000160373.3	-	20	4582	c.4491T>C	c.(4489-4491)aaT>aaC	p.N1497N		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1497					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		ACAGAGAAGCATTCCTGTTAC	0.308																																					p.N1497N		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.T4491C						.						165	163	164					7																	117361141		2202	4299	6501	SO:0001819	synonymous_variant	83992	exon20			AGAAGCATTCCTG		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.4491T>C	chr7.hg19:g.117361141A>G		78.0	0.0		91.0	30.0	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	A	1.185	-0.637094	0.03557	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.39	0.707	0.18139	.	.	.	.	.	T	0.21227	0.0511	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.22034	-1.0228	4	.	.	.	-9.3533	1.8968	0.03259	0.2797:0.139:0.427:0.1544	.	.	.	.	R	985	.	.	C	-	1	0	CTTNBP2	117148377	0.000000	0.05858	0.079000	0.20413	0.498000	0.33706	0.109000	0.15417	0.155000	0.19261	-0.911000	0.02809	TGC	.	.		0.308	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		G	117361141	A	G	117361141	2	3	160	1	0	0	0	0	0	0	0	1	4047	214	8	2		2	CTTNBP2	7	117361141	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	498181	117361141	41777522	173	24344										
FLNC	2318	hgsc.bcm.edu	37	chr7	128486380	128486380	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	catctggtggaggtcctgtaTgatgaggtcgctgtgcccaa	14	9	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:128486380T>A	ENST00000325888.8	+	23	4251	c.3990T>A	c.(3988-3990)taT>taA	p.Y1330*	FLNC_ENST00000346177.6_Nonsense_Mutation_p.Y1330*	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1330					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						AGGTCCTGTATGATGAGGTCG	0.667																																					p.Y1330X		Atlas-SNP	.											.	FLNC	339	.	0			c.T3990A						.						45	57	53					7																	128486380		2131	4219	6350	SO:0001587	stop_gained	2318	exon23			CCTGTATGATGAG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.3990T>A	chr7.hg19:g.128486380T>A	ENSP00000327145:p.Tyr1330*	78.0	0.0		82.0	12.0	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Nonsense_Mutation	SNP	ENST00000325888.8	hg19	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	T	44	10.785616	0.99467	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	.	.	.	5.07	-4.36	0.03645	.	0.133902	0.51477	D	0.000086	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.461	0.67450	0.0:0.5351:0.0:0.4649	.	.	.	.	X	1330	.	ENSP00000327145:Y1330X	Y	+	3	2	FLNC	128273616	0.000000	0.05858	0.948000	0.38648	0.868000	0.49771	-1.914000	0.01579	-0.905000	0.03871	0.454000	0.30748	TAT	.	.		0.667	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128486380	T	A	128486380	4	1	160	1	0	0	0	0	0	1	0	0	5943	1471	51	4	4080	4	FLNC	7	128486380	Nonsense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	11125239	128486380	30652283	174	24345										
FLNC	2318	hgsc.bcm.edu	37	chr7	128497184	128497184	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gcccccaggtgtgtcatcagAgttcatcgtgaacaccctga	10	13	3	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:128497184A>T	ENST00000325888.8	+	46	7835	c.7574A>T	c.(7573-7575)gAg>gTg	p.E2525V	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Missense_Mutation_p.E2492V	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2525	Interaction with INPPL1.				cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GTGTCATCAGAGTTCATCGTG	0.637																																					p.E2525V		Atlas-SNP	.											.	FLNC	339	.	0			c.A7574T						.						125	130	128					7																	128497184		1961	4135	6096	SO:0001583	missense	2318	exon46			CATCAGAGTTCAT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.7574A>T	chr7.hg19:g.128497184A>T	ENSP00000327145:p.Glu2525Val	57.0	0.0		72.0	9.0	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	hg19	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	a	15.91	2.973378	0.53614	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.84944	-1.92;-1.92	5.41	5.41	0.78517	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.113585	0.64402	D	0.000018	D	0.90300	0.6966	M	0.69823	2.125	0.58432	D	0.999997	D;P	0.53312	0.959;0.784	P;P	0.58520	0.84;0.603	D	0.91301	0.5067	10	0.66056	D	0.02	.	15.4618	0.75363	1.0:0.0:0.0:0.0	.	2492;2525	Q14315-2;Q14315	.;FLNC_HUMAN	V	2525;2492	ENSP00000327145:E2525V;ENSP00000344002:E2492V	ENSP00000327145:E2525V	E	+	2	0	FLNC	128284420	1.000000	0.71417	1.000000	0.80357	0.164000	0.22412	9.307000	0.96226	2.059000	0.61396	0.528000	0.53228	GAG	.	.		0.637	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128497184	A	T	128497184	3	4	160	1	0	0	0	0	1	0	0	0	5943	304	11	4	7756	4	FLNC	7	128497184	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	10804	128497184	30641479	175	24346										
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138566238	138566238	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttcagaggtcctggcagtggCgctggctcatgaataatcaa	12	9	3	2	rs377023001		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:138566238C>T	ENST00000422774.1	-	11	4173	c.4125G>A	c.(4123-4125)gcG>gcA	p.A1375A	KIAA1549_ENST00000440172.1_Silent_p.A1375A|KIAA1549_ENST00000242365.4_Silent_p.A1325A			Q9HCM3	K1549_HUMAN	KIAA1549	1375						integral component of membrane (GO:0016021)		p.A1375A(1)|p.A1325A(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CTGGCAGTGGCGCTGGCTCAT	0.507			O	BRAF	pilocytic astrocytoma																																p.A1375A	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	KIAA1549_ENST00000422774,rectum,carcinoma,0,2	KIAA1549	314	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G4125A						.	C	,	1,4167		0,1,2083	116	121	119		4125,4125	-11.5	0	7		119	0,8434		0,0,4217	no	coding-synonymous,coding-synonymous	KIAA1549	NM_001164665.1,NM_020910.2	,	0,1,6300	TT,TC,CC		0.0,0.024,0.0079	,	1375/1951,1375/1935	138566238	1,12601	2084	4217	6301	SO:0001819	synonymous_variant	57670	exon11			CAGTGGCGCTGGC		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4125G>A	chr7.hg19:g.138566238C>T		135.0	0.0		143.0	35.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	hg19	CCDS56513.1																																																																																			.	.		0.507	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			T	138566238	C	T	138566238	2	4	160	1	0	0	0	0	0	0	0	1	8253	755	27	1		1	KIAA1549	7	138566238	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	10069054	138566238	20572425	176	24347										
WEE2	494551	hgsc.bcm.edu	37	chr7	141424074	141424074	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggctaatgagattttgcaagAggtatagattagggaaatgg	14	2	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:141424074A>T	ENST00000397541.2	+	8	1626	c.1220A>T	c.(1219-1221)gAg>gTg	p.E407V	WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000486906.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000484172.1_RNA|WEE2-AS1_ENST00000471512.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	407	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					ATTTTGCAAGAGGTATAGATT	0.363																																					p.E407V		Atlas-SNP	.											.	WEE2	59	.	0			c.A1220T						.						109	108	108					7																	141424074		1833	4079	5912	SO:0001630	splice_region_variant	494551	exon8			TGCAAGAGGTATA	AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.1221+1A>T	chr7.hg19:g.141424074A>T		194.0	0.0		248.0	49.0	NM_001105558		Missense_Mutation	SNP	ENST00000397541.2	hg19	CCDS43660.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.995772	0.93167	.	.	ENSG00000214102	ENST00000397541;ENST00000493845	T;T	0.66099	1.01;-0.19	5.93	5.93	0.95920	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	U	0.000000	D	0.85405	0.5689	H	0.95816	3.725	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.89753	0.3941	10	0.87932	D	0	.	16.3871	0.83514	1.0:0.0:0.0:0.0	.	407	P0C1S8	WEE2_HUMAN	V	407;182	ENSP00000380675:E407V;ENSP00000420388:E182V	ENSP00000380675:E407V	E	+	2	0	WEE2	141070543	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.433000	0.90291	2.270000	0.75569	0.482000	0.46254	GAG	.	.		0.363	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558	Missense_Mutation	T	141424074	A	T	141424074	5	4	160	1	0	0	0	0	0	0	1	0	17360	318	11	4	1250	4	WEE2	7	141424074	Splice_Site	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2857836	141424074	17714589	177	24348										
MGAM	8972	hgsc.bcm.edu	37	chr7	141736006	141736006	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tggctttgctttggacacccCtgaggagctctgtaggcggt	14	10	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:141736006C>A	ENST00000549489.2	+	17	2092	c.1997C>A	c.(1996-1998)cCt>cAt	p.P666H	MGAM_ENST00000475668.2_Missense_Mutation_p.P666H	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	666	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTGGACACCCCTGAGGAGCTC	0.498																																					p.P666H		Atlas-SNP	.											.	MGAM	767	.	0			c.C1997A						.						127	124	125					7																	141736006		1966	4160	6126	SO:0001583	missense	8972	exon17			ACACCCCTGAGGA	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.1997C>A	chr7.hg19:g.141736006C>A	ENSP00000447378:p.Pro666His	133.0	0.0		187.0	56.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.239019	0.79800	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.92911	-3.13	5.34	4.43	0.53597	Glycoside hydrolase, superfamily (1);	1.387040	0.04708	N	0.417019	D	0.89287	0.6672	N	0.14661	0.345	0.09310	N	1	P	0.40731	0.728	B	0.43754	0.43	T	0.81084	-0.1093	10	0.87932	D	0	.	13.9752	0.64268	0.1578:0.8422:0.0:0.0	.	666	O43451	MGA_HUMAN	H	666;666;543	ENSP00000447378:P666H	ENSP00000316431:P543H	P	+	2	0	MGAM	141382475	0.027000	0.19231	0.168000	0.22838	0.804000	0.45430	2.414000	0.44627	1.422000	0.47177	0.650000	0.86243	CCT	.	.		0.498	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			A	141736006	C	A	141736006	3	1	160	1	0	0	0	0	1	0	0	0	9550	681	24	3	2059	3	MGAM	7	141736006	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	311932	141736006	17402657	178	24349										
GIMAP6	474344	hgsc.bcm.edu	37	chr7	150325135	150325135	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcacatccagccaggcaaggGcctggttgttggtctctcgc	12	13	2	0	rs368001704		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:150325135G>T	ENST00000328902.5	-	3	767	c.551C>A	c.(550-552)gCc>gAc	p.A184D	GIMAP6_ENST00000493969.1_3'UTR	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	184	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)			endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCAGGCAAGGGCCTGGTTGTT	0.627																																					p.A254D		Atlas-SNP	.											.	GIMAP6	60	.	0			c.C761A						.						119	123	121					7																	150325135		2203	4300	6503	SO:0001583	missense	474344	exon3			GCAAGGGCCTGGT	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"GTPases, IMAP"	21918	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 6"					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.551C>A	chr7.hg19:g.150325135G>T	ENSP00000330374:p.Ala184Asp	72.0	0.0		95.0	14.0	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	hg19	CCDS34778.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.732380	0.30684	.	.	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.33654	1.4	4.29	-8.58	0.00897	AIG1 (1);	2.089860	0.02501	N	0.090478	T	0.17066	0.0410	N	0.16602	0.42	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.17722	0.019;0.0	T	0.16808	-1.0390	10	0.10902	T	0.67	.	5.075	0.14626	0.1002:0.2639:0.4873:0.1486	.	184;104	Q6P9H5;Q6P9H5-2	GIMA6_HUMAN;.	D	184;245	ENSP00000330374:A184D	ENSP00000330374:A184D	A	-	2	0	GIMAP6	149956068	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.672000	0.01952	-2.714000	0.00392	-0.305000	0.09177	GCC	.	.		0.627	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711		T	150325135	G	T	150325135	3	4	160	1	0	0	0	0	1	0	0	0	6391	1203	42	3	331	3	GIMAP6	7	150325135	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	8589129	150325135	8813528	179	24350										
GIMAP2	26157	hgsc.bcm.edu	37	chr7	150389814	150389814	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cacaattgtcctctttacccAcaaggaagacctcaatggtg	7	12	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:150389814A>T	ENST00000223293.5	+	3	534	c.440A>T	c.(439-441)cAc>cTc	p.H147L		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	147	AIG1-type G.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(8)|skin(2)|urinary_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTCTTTACCCACAAGGAAGAC	0.537																																					p.H147L		Atlas-SNP	.											.	GIMAP2	39	.	0			c.A440T						.						75	53	60					7																	150389814		2203	4300	6503	SO:0001583	missense	26157	exon3			TTACCCACAAGGA	AL110151	CCDS5905.1	7q36.1	2014-04-04			ENSG00000106560	ENSG00000106560		"GTPases, IMAP"	21789	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 12"	608085				15474311	Standard	NM_015660		Approved	DKFZp586D0824, HIMAP2, IMAP2, IAN12	uc003who.3	Q9UG22	OTTHUMG00000157488	ENST00000223293.5:c.440A>T	chr7.hg19:g.150389814A>T	ENSP00000223293:p.His147Leu	120.0	0.0		163.0	42.0	NM_015660	Q96L25	Missense_Mutation	SNP	ENST00000223293.5	hg19	CCDS5905.1	.	.	.	.	.	.	.	.	.	.	A	13.10	2.135994	0.37728	.	.	ENSG00000106560	ENST00000223293	T	0.61040	0.14	3.9	-3.16	0.05217	AIG1 (1);	0.269330	0.28098	N	0.016602	T	0.52256	0.1723	M	0.78456	2.415	0.09310	N	0.999999	P	0.37781	0.608	B	0.36534	0.227	T	0.54768	-0.8244	10	0.66056	D	0.02	.	10.511	0.44862	0.3262:0.0:0.6737:0.0	.	147	Q9UG22	GIMA2_HUMAN	L	147	ENSP00000223293:H147L	ENSP00000223293:H147L	H	+	2	0	GIMAP2	150020747	0.000000	0.05858	0.975000	0.42487	0.880000	0.50808	-0.059000	0.11731	-0.451000	0.07097	-0.314000	0.08810	CAC	.	.		0.537	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660		T	150389814	A	T	150389814	3	4	160	1	0	0	0	0	1	0	0	0	6388	159	6	4	446	4	GIMAP2	7	150389814	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	64679	150389814	8748849	180	24351										
GBX1	2636	hgsc.bcm.edu	37	chr7	150864157	150864157	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gaggtggtgggggctctgccActttctcccgggccggcagc	17	13	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:150864157A>G	ENST00000297537.4	-	1	478	c.479T>C	c.(478-480)gTg>gCg	p.V160A	GBX1_ENST00000475831.1_5'UTR	NM_001098834.1	NP_001092304.1	Q14549	GBX1_HUMAN	gastrulation brain homeobox 1	160	Pro-rich.				adult walking behavior (GO:0007628)|neuron fate commitment (GO:0048663)|proprioception (GO:0019230)|regulation of transcription, DNA-templated (GO:0006355)|sensory neuron axon guidance (GO:0097374)|spinal cord motor neuron differentiation (GO:0021522)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(5)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GGGCTCTGCCACTTTCTCCCG	0.701																																					p.V160A		Atlas-SNP	.											.	GBX1	21	.	0			c.T479C						.						24	31	29					7																	150864157		1874	4103	5977	SO:0001583	missense	2636	exon1			TCTGCCACTTTCT	L11239	CCDS43682.1	7q36.1	2012-03-09	2005-12-22		ENSG00000164900	ENSG00000164900		"Homeoboxes / ANTP class : HOXL subclass"	4185	protein-coding gene	gene with protein product		603354	"gastrulation brain homeo box 1"			7903253	Standard	NM_001098834		Approved		uc011kvg.2	Q14549	OTTHUMG00000158751	ENST00000297537.4:c.479T>C	chr7.hg19:g.150864157A>G	ENSP00000297537:p.Val160Ala	156.0	0.0		183.0	22.0	NM_001098834		Missense_Mutation	SNP	ENST00000297537.4	hg19	CCDS43682.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.488|8.488	0.861437|0.861437	0.17178|0.17178	.|.	.|.	ENSG00000164900|ENSG00000164900	ENST00000297537|ENST00000475831	D|.	0.91631|.	-2.88|.	4.15|4.15	1.81|1.81	0.25067|0.25067	.|.	0.233514|.	0.27912|.	U|.	0.017349|.	T|T	0.18635|0.18635	0.0447|0.0447	N|N	0.14661|0.14661	0.345|0.345	0.19945|0.19945	N|N	0.999945|0.999945	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.24404|0.24404	-1.0161|-1.0161	10|5	0.19147|.	T|.	0.46|.	-4.4166|-4.4166	4.1043|4.1043	0.10030|0.10030	0.6243:0.2548:0.1209:0.0|0.6243:0.2548:0.1209:0.0	.|.	160|.	Q14549|.	GBX1_HUMAN|.	A|R	160|10	ENSP00000297537:V160A|.	ENSP00000297537:V160A|.	V|W	-|-	2|1	0|0	GBX1|GBX1	150495090|150495090	0.049000|0.049000	0.20398|0.20398	0.881000|0.881000	0.34555|0.34555	0.962000|0.962000	0.63368|0.63368	-0.335000|-0.335000	0.07873|0.07873	0.194000|0.194000	0.20326|0.20326	0.391000|0.391000	0.25812|0.25812	GTG|TGG	.	.		0.701	GBX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352029.1			G	150864157	A	G	150864157	3	3	160	1	0	0	0	0	1	0	0	0	6288	159	6	2	619	2	GBX1	7	150864157	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	474343	150864157	8274506	181	24352										
DNAJB6	10049	hgsc.bcm.edu	37	chr7	157160104	157160104	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agtccatttgaatttggcttCacattccgtaacccagatga	7	10	1	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr7:157160104C>T	ENST00000262177.4	+	5	478	c.273C>T	c.(271-273)ttC>ttT	p.F91F	DNAJB6_ENST00000452797.2_Silent_p.F42F|DNAJB6_ENST00000429029.2_Silent_p.F91F|DNAJB6_ENST00000443280.1_Silent_p.F91F	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	91	Gly/Phe-rich.|Interaction with HSP70.				intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		AATTTGGCTTCACATTCCGTA	0.388																																					p.F91F	Esophageal Squamous(46;195 967 1350 20350 43814)	Atlas-SNP	.											.	DNAJB6	39	.	0			c.C273T						.						160	149	153					7																	157160104		2203	4299	6502	SO:0001819	synonymous_variant	10049	exon5			TGGCTTCACATTC	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"Heat shock proteins / DNAJ (HSP40)"	14888	protein-coding gene	gene with protein product		611332	"limb girdle muscular dystrophy 1D (autosomal dominant)"	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.273C>T	chr7.hg19:g.157160104C>T		86.0	0.0		139.0	30.0	NM_058246	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Silent	SNP	ENST00000262177.4	hg19	CCDS5946.1																																																																																			.	.		0.388	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2			T	157160104	C	T	157160104	2	4	160	1	0	0	0	0	0	0	0	1	4626	825	29	3		3	DNAJB6	7	157160104	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	6295947	157160104	1978559	182	24353										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3087715	3087715	+	Frame_Shift_Del	DEL	G	G	-													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tccatagcgggtgccattttGgggcatacctggatcgttac							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:3087715delG	ENST00000520002.1	-	28	4750	c.4195delC	c.(4195-4197)caafs	p.Q1399fs	CSMD1_ENST00000542608.1_Frame_Shift_Del_p.Q1398fs|CSMD1_ENST00000602557.1_Frame_Shift_Del_p.Q1399fs|CSMD1_ENST00000539096.1_Frame_Shift_Del_p.Q1398fs|CSMD1_ENST00000537824.1_Frame_Shift_Del_p.Q1398fs|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602723.1_Frame_Shift_Del_p.Q1399fs|CSMD1_ENST00000400186.3_Frame_Shift_Del_p.Q1399fs			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1399	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GTGCCATTTTGGGGCATACCT	0.522																																					p.Q1398fs		Atlas-INDEL	.											.	CSMD1	1469	.	0			c.4193delA						.						62	62	62					8																	3087715		2004	4189	6193	SO:0001589	frameshift_variant	64478	exon27			.			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4195delC	chr8.hg19:g.3087715delG	ENSP00000430733:p.Gln1399fs	109.0	0.0		155.0	13.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Frame_Shift_Del	DEL	ENST00000520002.1	hg19																																																																																				.	.		0.522	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		-	3087715	G	-	3087715	7	5	160	1	0	1	0	1	0	0	0	0	3946	1357	47	0	6678	0	CSMD1	8	3087715	Frame_Shift_Del	DEL	G	TCGA-DD-AACI-01A-11D-A40R-10		3087715	143276307	183	24354										
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24259501	24259501	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	accttttatctcagaaaccaAagtgcctgctgcaagcacct	6	13	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:24259501A>G	ENST00000256412.4	+	12	1436	c.1216A>G	c.(1216-1218)Aag>Gag	p.K406E	ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.K327E|RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.K327E|RP11-624C23.1_ENST00000523578.1_RNA	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	406	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TCAGAAACCAAAGTGCCTGCT	0.403																																					p.K406E	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.A1216G						.						107	106	107					8																	24259501		2203	4300	6503	SO:0001583	missense	27299	exon12			AAACCAAAGTGCC	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.1216A>G	chr8.hg19:g.24259501A>G	ENSP00000256412:p.Lys406Glu	78.0	0.0		79.0	10.0	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	hg19	CCDS6044.1	.	.	.	.	.	.	.	.	.	.	A	10.33	1.321703	0.23994	.	.	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.63417	-0.04;-0.04;-0.04	6.16	6.16	0.99307	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.610934	0.17160	N	0.184723	T	0.55049	0.1896	L	0.31294	0.92	0.25588	N	0.986727	B	0.26512	0.151	B	0.34038	0.174	T	0.53315	-0.8456	10	0.45353	T	0.12	-6.6935	13.1979	0.59749	1.0:0.0:0.0:0.0	.	406	O15204	ADEC1_HUMAN	E	406;327;327	ENSP00000256412:K406E;ENSP00000442592:K327E;ENSP00000428993:K327E	ENSP00000256412:K406E	K	+	1	0	ADAMDEC1	24315446	0.024000	0.19004	0.974000	0.42286	0.209000	0.24338	1.300000	0.33436	2.367000	0.80283	0.528000	0.53228	AAG	.	.		0.403	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		G	24259501	A	G	24259501	3	3	160	1	0	0	0	0	1	0	0	0	254	15	1	2	1262	2	ADAMDEC1	8	24259501	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	21171786	24259501	122104521	184	24355										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36642022	36642022	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cagcattcattctctcttccTttgtgaccttcttcagtgga	6	12	5	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:36642022T>C	ENST00000399881.3	+	1	131	c.94T>C	c.(94-96)Ttt>Ctt	p.F32L		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	32					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TCTCTCTTCCTTTGTGACCTT	0.413																																					p.F32L		Atlas-SNP	.											.	KCNU1	359	.	0			c.T94C						.						168	155	159					8																	36642022		1954	4147	6101	SO:0001583	missense	157855	exon1			TCTTCCTTTGTGA	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.94T>C	chr8.hg19:g.36642022T>C	ENSP00000382770:p.Phe32Leu	92.0	0.0		145.0	28.0	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	hg19	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	T	1.844	-0.466694	0.04476	.	.	ENSG00000215262	ENST00000523973;ENST00000399881	T;T	0.24350	1.86;1.9	5.49	-0.268	0.12934	.	.	.	.	.	T	0.08802	0.0218	N	0.11427	0.14	0.46564	D	0.9991	B	0.12013	0.005	B	0.09377	0.004	T	0.29058	-1.0024	9	0.10111	T	0.7	.	1.8418	0.03151	0.273:0.0814:0.1408:0.5048	.	32	A8MYU2	KCNU1_HUMAN	L	32	ENSP00000429951:F32L;ENSP00000382770:F32L	ENSP00000382770:F32L	F	+	1	0	KCNU1	36761180	0.069000	0.21087	0.836000	0.33094	0.081000	0.17604	-0.280000	0.08468	0.088000	0.17205	0.528000	0.53228	TTT	.	.		0.413	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		C	36642022	T	C	36642022	3	2	160	1	0	0	0	0	1	0	0	0	8102	1609	56	2	96	2	KCNU1	8	36642022	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	12382521	36642022	109722000	185	24356										
LSM1	27257	hgsc.bcm.edu	37	chr8	38029501	38029501	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	accaaattgatcaatgcttcTtaaaaagcctataagtgtcc	5	9	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:38029501T>C	ENST00000311351.4	-	2	492	c.97A>G	c.(97-99)Aga>Gga	p.R33G	LSM1_ENST00000520755.1_Missense_Mutation_p.R33G|LSM1_ENST00000522515.1_5'UTR	NM_014462.2	NP_055277.1	O15116	LSM1_HUMAN	LSM1, U6 small nuclear RNA associated	33					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(3)|lung(2)	7	Colorectal(12;0.000442)					TCAATGCTTCTTAAAAAGCCT	0.333											OREG0018720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R33G		Atlas-SNP	.											.	LSM1	14	.	0			c.A97G						.						96	100	99					8																	38029501		2203	4300	6503	SO:0001583	missense	27257	exon2			TGCTTCTTAAAAA	AF000177	CCDS6103.1	8p11.2	2014-02-14	2014-02-14		ENSG00000175324	ENSG00000175324			20472	protein-coding gene	gene with protein product		607281	"LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)"			12515382, 11953827	Standard	NM_014462		Approved	CASM, YJL124C	uc003xkw.3	O15116	OTTHUMG00000164051	ENST00000311351.4:c.97A>G	chr8.hg19:g.38029501T>C	ENSP00000310596:p.Arg33Gly	89.0	0.0	875	141.0	17.0	NM_014462	B2R5E6	Missense_Mutation	SNP	ENST00000311351.4	hg19	CCDS6103.1	.	.	.	.	.	.	.	.	.	.	T	18.37	3.608888	0.66558	.	.	ENSG00000175324	ENST00000311351;ENST00000520755	T;T	0.46063	0.88;0.88	5.93	4.73	0.59995	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.088985	0.85682	D	0.000000	T	0.77343	0.4116	H	0.99026	4.405	0.80722	D	1	D	0.62365	0.991	D	0.72075	0.976	D	0.85921	0.1446	10	0.87932	D	0	-29.3368	13.0482	0.58939	0.0:0.0:0.1762:0.8238	.	33	O15116	LSM1_HUMAN	G	33	ENSP00000310596:R33G;ENSP00000430021:R33G	ENSP00000310596:R33G	R	-	1	2	LSM1	38148658	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	1.752000	0.38349	2.273000	0.75805	0.482000	0.46254	AGA	.	.		0.333	LSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376965.1	NM_014462		C	38029501	T	C	38029501	3	2	160	1	0	0	0	0	1	0	0	0	9059	1617	56	2	316	2	LSM1	8	38029501	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1387479	38029501	108334521	186	24357										
CNBD1	168975	hgsc.bcm.edu	37	chr8	88365869	88365869	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atatttttttaacagaaaagAtctcaaaaacttgtttatat	3	4	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:88365869A>G	ENST00000518476.1	+	10	1209	c.1158A>G	c.(1156-1158)agA>agG	p.R386R		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	386										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						AACAGAAAAGATCTCAAAAAC	0.318																																					p.R386R		Atlas-SNP	.											.	CNBD1	206	.	0			c.A1158G						.						56	56	56					8																	88365869		1798	4061	5859	SO:0001819	synonymous_variant	168975	exon10			GAAAAGATCTCAA	AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.1158A>G	chr8.hg19:g.88365869A>G		352.0	0.0		552.0	31.0	NM_173538		Silent	SNP	ENST00000518476.1	hg19	CCDS55259.1	.	.	.	.	.	.	.	.	.	.	A	0.218	-1.031014	0.02029	.	.	ENSG00000176571	ENST00000523299;ENST00000521593	.	.	.	4.98	2.61	0.31194	.	.	.	.	.	T	0.54029	0.1833	.	.	.	0.44275	D	0.997137	.	.	.	.	.	.	T	0.46386	-0.9195	4	.	.	.	-21.8253	5.8986	0.18953	0.7926:0.0:0.2074:0.0	.	.	.	.	G	78;23	.	.	D	+	2	0	CNBD1	88434985	0.833000	0.29383	0.584000	0.28653	0.023000	0.10783	1.390000	0.34464	0.755000	0.32990	0.454000	0.30748	GAT	.	.		0.318	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		G	88365869	A	G	88365869	2	3	160	1	0	0	0	0	0	0	0	1	3593	330	12	2		2	CNBD1	8	88365869	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	50336368	88365869	57998153	187	24358										
MATN2	4147	hgsc.bcm.edu	37	chr8	99033508	99033508	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgggaattcctacatctgcaAatgctcagagggatttgttc	10	8	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:99033508A>C	ENST00000520016.1	+	12	2019	c.1895A>C	c.(1894-1896)aAa>aCa	p.K632T	MATN2_ENST00000521689.1_Missense_Mutation_p.K632T|MATN2_ENST00000524308.1_Missense_Mutation_p.K591T|MATN2_ENST00000254898.5_Missense_Mutation_p.K632T|MATN2_ENST00000522025.2_Missense_Mutation_p.K348T			O00339	MATN2_HUMAN	matrilin 2	632	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TACATCTGCAAATGCTCAGAG	0.443																																					p.K632T		Atlas-SNP	.											.	MATN2	165	.	0			c.A1895C						.						134	130	131					8																	99033508		1890	4121	6011	SO:0001583	missense	4147	exon13			TCTGCAAATGCTC	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1895A>C	chr8.hg19:g.99033508A>C	ENSP00000430487:p.Lys632Thr	116.0	0.0		184.0	21.0	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	hg19	CCDS55264.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.844|8.844	0.942875|0.942875	0.18281|0.18281	.|.	.|.	ENSG00000132561|ENSG00000132561	ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016|ENST00000518154	D;D;D;D;D|.	0.96232|.	-3.95;-3.95;-3.95;-3.95;-3.95|.	5.58|5.58	2.48|2.48	0.30137|0.30137	Epidermal growth factor-like (1);EGF-like region, conserved site (1);|.	0.181219|.	0.38720|.	N|.	0.001582|.	T|T	0.13243|0.13243	0.0321|0.0321	N|N	0.02412|0.02412	-0.56|-0.56	0.28643|0.28643	N|N	0.907045|0.907045	B;P;P;P|.	0.42078|.	0.418;0.77;0.726;0.77|.	B;B;B;B|.	0.43052|.	0.145;0.316;0.406;0.316|.	T|T	0.28586|0.28586	-1.0039|-1.0039	10|5	0.13853|.	T|.	0.58|.	-14.3116|-14.3116	7.643|7.643	0.28305|0.28305	0.782:0.0:0.218:0.0|0.782:0.0:0.218:0.0	.|.	591;632;632;632|.	C9JH87;E9PF03;O00339-2;O00339|.	.;.;.;MATN2_HUMAN|.	T|H	632;632;591;591;348;632|414	ENSP00000429977:K632T;ENSP00000254898:K632T;ENSP00000430221:K591T;ENSP00000429010:K348T;ENSP00000430487:K632T|.	ENSP00000254898:K632T|.	K|Q	+|+	2|3	0|2	MATN2|MATN2	99102684|99102684	0.036000|0.036000	0.19791|0.19791	0.998000|0.998000	0.56505|0.56505	0.598000|0.598000	0.36846|0.36846	0.892000|0.892000	0.28322|0.28322	0.191000|0.191000	0.20236|0.20236	0.533000|0.533000	0.62120|0.62120	AAA|CAA	.	.		0.443	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			C	99033508	A	C	99033508	3	2	160	1	0	0	0	0	1	0	0	0	9343	14	1	5	1941	5	MATN2	8	99033508	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	10667639	99033508	47330514	188	24359										
SPAG1	6674	hgsc.bcm.edu	37	chr8	101178179	101178179	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttttacagctgaagaatgggAaaaaattgatggtgatataa	10	2	0	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:101178179A>G	ENST00000388798.2	+	3	469	c.278A>G	c.(277-279)gAa>gGa	p.E93G	SPAG1_ENST00000251809.3_Missense_Mutation_p.E93G|SPAG1_ENST00000520643.1_Missense_Mutation_p.E93G|SPAG1_ENST00000520508.1_Missense_Mutation_p.E93G	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	93					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GAAGAATGGGAAAAAATTGAT	0.363																																					p.E93G		Atlas-SNP	.											.	SPAG1	80	.	0			c.A278G						.						62	63	63					8																	101178179		2203	4300	6503	SO:0001583	missense	6674	exon3			AATGGGAAAAAAT	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.278A>G	chr8.hg19:g.101178179A>G	ENSP00000373450:p.Glu93Gly	164.0	0.0		261.0	33.0	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	hg19	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	A	18.58	3.654484	0.67472	.	.	ENSG00000104450	ENST00000520643;ENST00000251809;ENST00000520508;ENST00000388798	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	5.81	4.66	0.58398	.	0.585351	0.19443	N	0.114132	T	0.20251	0.0487	M	0.72894	2.215	0.33026	D	0.529559	P;P	0.50272	0.933;0.804	P;P	0.46479	0.518;0.462	T	0.36089	-0.9762	10	0.72032	D	0.01	-15.938	6.9829	0.24713	0.7739:0.1495:0.0766:0.0	.	93;93	Q07617;G3XAM3	SPAG1_HUMAN;.	G	93	ENSP00000427716:E93G;ENSP00000251809:E93G;ENSP00000428070:E93G;ENSP00000373450:E93G	ENSP00000251809:E93G	E	+	2	0	SPAG1	101247355	0.976000	0.34144	0.911000	0.35937	0.995000	0.86356	2.111000	0.41883	1.037000	0.40024	0.533000	0.62120	GAA	.	.		0.363	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		G	101178179	A	G	101178179	3	3	160	1	0	0	0	0	1	0	0	0	14990	246	9	2	284	2	SPAG1	8	101178179	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2144671	101178179	45185843	189	24360										
PABPC1	26986	hgsc.bcm.edu	37	chr8	101733713	101733713	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atggagaggatgggcccggcCgggctgaacttctcgtagag	17	9	1	3	rs148248545		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:101733713C>G	ENST00000318607.5	-	1	1227	c.99G>C	c.(97-99)ccG>ccC	p.P33P	PABPC1_ENST00000519004.1_Intron|PABPC1_ENST00000522387.1_Silent_p.P33P	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	33	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TGGGCCCGGCCGGGCTGAACT	0.662																																					p.P33P		Atlas-SNP	.											.	PABPC1	76	.	0			c.G99C						.						26	30	29					8																	101733713		2203	4299	6502	SO:0001819	synonymous_variant	26986	exon1			CCCGGCCGGGCTG	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"RNA binding motif (RRM) containing"	8554	protein-coding gene	gene with protein product		604679	"poly(A)-binding protein, cytoplasmic 2"	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.99G>C	chr8.hg19:g.101733713C>G		233.0	0.0		387.0	162.0	NM_002568	Q15097|Q93004	Silent	SNP	ENST00000318607.5	hg19	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	C	8.417	0.845519	0.16963	.	.	ENSG00000070756	ENST00000523555	.	.	.	3.45	1.55	0.23275	.	.	.	.	.	T	0.44095	0.1277	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21143	-1.0254	4	.	.	.	.	2.8039	0.05422	0.3151:0.4362:0.1542:0.0945	.	.	.	.	R	28	.	.	G	-	1	0	PABPC1	101802889	0.934000	0.31675	0.999000	0.59377	0.914000	0.54420	-0.032000	0.12266	0.099000	0.17552	-0.321000	0.08615	GGC	.	C|1.000;T|0.000		0.662	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568		G	101733713	C	G	101733713	2	3	160	1	0	0	0	0	0	0	0	1	11372	639	23	4		4	PABPC1	8	101733713	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	555534	101733713	44630309	190	24361										
EXT1	2131	hgsc.bcm.edu	37	chr8	118834756	118834756	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agataagatgaatactgtggTagtacgaacaatcctccagg	10	7	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:118834756T>A	ENST00000378204.2	-	5	2171	c.1365A>T	c.(1363-1365)ctA>ctT	p.L455L		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	455					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			AATACTGTGGTAGTACGAACA	0.363			"Mis, N, F, S"			"exostoses, osteosarcoma"			Langer-Giedion syndrome;Hereditary Multiple Exostoses																												p.L455L		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	EXT1	98	.	0			c.A1365T						.						133	129	130					8																	118834756		2203	4300	6503	SO:0001819	synonymous_variant	2131	exon5	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	CTGTGGTAGTACG	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3512	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608177	"Langer-Giedion syndrome chromosome region", "exostoses (multiple) 1", "exostosin 1"	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.1365A>T	chr8.hg19:g.118834756T>A		85.0	0.0		116.0	9.0	NM_000127	B2R7V2|Q9BVI9	Silent	SNP	ENST00000378204.2	hg19	CCDS6324.1																																																																																			.	.		0.363	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127		A	118834756	T	A	118834756	2	1	160	1	0	0	0	0	0	0	0	1	5325	1625	57	4		4	EXT1	8	118834756	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	17101043	118834756	27529266	191	24362										
ADCY8	114	hgsc.bcm.edu	37	chr8	131916177	131916177	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcaggctgcttaattaagtaAgtttcgatattatgcttcct	7	7	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:131916177A>G	ENST00000286355.5	-	7	3844	c.1752T>C	c.(1750-1752)acT>acC	p.T584T	ADCY8_ENST00000377928.3_Silent_p.T584T	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	584					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.T584T(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TAATTAAGTAAGTTTCGATAT	0.483										HNSCC(32;0.087)																											p.T584T		Atlas-SNP	.											ADCY8,colon,carcinoma,0,2	ADCY8	291	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1752C						.						151	138	142					8																	131916177		2203	4300	6503	SO:0001819	synonymous_variant	114	exon7			TAAGTAAGTTTCG	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1752T>C	chr8.hg19:g.131916177A>G		103.0	0.0		184.0	39.0	NM_001115		Silent	SNP	ENST00000286355.5	hg19	CCDS6363.1																																																																																			.	.		0.483	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			G	131916177	A	G	131916177	2	3	160	1	0	0	0	0	0	0	0	1	300	59	3	2		2	ADCY8	8	131916177	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	13081421	131916177	14447845	192	24363										
TG	7038	hgsc.bcm.edu	37	chr8	133894143	133894143	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgtgaccttcagttccttccAgaggaggttccctgaggtat	11	10	1	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:133894143A>C	ENST00000220616.4	+	6	714	c.674A>C	c.(673-675)cAg>cCg	p.Q225P	TG_ENST00000377869.1_Missense_Mutation_p.Q225P	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	225	Thyroglobulin type-1 3. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AGTTCCTTCCAGAGGAGGTTC	0.498																																					p.Q225P		Atlas-SNP	.											.	TG	416	.	0			c.A674C						.						126	109	115					8																	133894143		2203	4300	6503	SO:0001583	missense	7038	exon6			CCTTCCAGAGGAG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.674A>C	chr8.hg19:g.133894143A>C	ENSP00000220616:p.Gln225Pro	87.0	0.0		128.0	14.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	A	12.84	2.057174	0.36277	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.63913	-0.07;-0.07	5.36	1.52	0.23074	Thyroglobulin type-1 (2);	0.466052	0.19105	N	0.122600	T	0.33411	0.0862	N	0.08118	0	0.23464	N	0.997621	P	0.38335	0.627	B	0.25759	0.063	T	0.17379	-1.0371	10	0.87932	D	0	.	9.204	0.37278	0.3058:0.0:0.6942:0.0	.	225	P01266	THYG_HUMAN	P	225	ENSP00000367100:Q225P;ENSP00000220616:Q225P	ENSP00000220616:Q225P	Q	+	2	0	TG	133963325	1.000000	0.71417	0.979000	0.43373	0.423000	0.31445	2.780000	0.47742	-0.001000	0.14495	-0.468000	0.05107	CAG	.	.		0.498	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	133894143	A	C	133894143	3	2	160	1	0	0	0	0	1	0	0	0	15828	188	7	5	696	5	TG	8	133894143	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1977966	133894143	12469879	193	24364										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139727943	139727943	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	accttttcacctcggtcaccTttcagtcctggaagtcccag	7	15	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:139727943T>C	ENST00000303045.6	-	30	2945	c.2499A>G	c.(2497-2499)aaA>aaG	p.K833K	COL22A1_ENST00000435777.1_Silent_p.K833K|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	833	Collagen-like 6.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CTCGGTCACCTTTCAGTCCTG	0.373										HNSCC(7;0.00092)																											p.K833K		Atlas-SNP	.											.	COL22A1	390	.	0			c.A2499G						.						92	99	96					8																	139727943		2203	4300	6503	SO:0001819	synonymous_variant	169044	exon30			GTCACCTTTCAGT	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2499A>G	chr8.hg19:g.139727943T>C		64.0	0.0		126.0	8.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.373	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		C	139727943	T	C	139727943	2	2	160	1	0	0	0	0	0	0	0	1	3683	1606	56	2		2	COL22A1	8	139727943	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	5833800	139727943	6636079	194	24365										
DENND3	22898	hgsc.bcm.edu	37	chr8	142160957	142160957	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttaacatgaagtcgctccagAttgtgttacctgcccgagca	9	11	0	2	rs531863353		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:142160957A>G	ENST00000262585.2	+	6	798	c.520A>G	c.(520-522)Att>Gtt	p.I174V	DENND3_ENST00000519811.1_Missense_Mutation_p.I254V|DENND3_ENST00000424248.1_Missense_Mutation_p.I174V	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	174	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			GTCGCTCCAGATTGTGTTACC	0.547													A|||	1	0.000199681	0	0	5008	,	,		16755	0		0	False		,,,				2504	0.001				p.I174V		Atlas-SNP	.											.	DENND3	127	.	0			c.A520G						.						150	143	145					8																	142160957		2203	4300	6503	SO:0001583	missense	22898	exon6			CTCCAGATTGTGT	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.520A>G	chr8.hg19:g.142160957A>G	ENSP00000262585:p.Ile174Val	74.0	0.0		130.0	53.0	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	hg19	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.593|2.593	-0.294721|-0.294721	0.05568|0.05568	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000518668|ENST00000262585;ENST00000424248;ENST00000519811;ENST00000520986;ENST00000523058	.|T;T;T;T;T	.|0.46819	.|2.72;2.72;2.72;2.72;0.86	5.4|5.4	-1.02|-1.02	0.10135|0.10135	.|DENN (3);	.|0.270871	.|0.40144	.|N	.|0.001163	T|T	0.31358|0.31358	0.0794|0.0794	L|L	0.29908|0.29908	0.895|0.895	0.35351|0.35351	D|D	0.78735|0.78735	.|B;B	.|0.25772	.|0.134;0.031	.|B;B	.|0.28465	.|0.09;0.058	T|T	0.25433|0.25433	-1.0132|-1.0132	5|10	.|0.22706	.|T	.|0.39	-4.0707|-4.0707	11.2567|11.2567	0.49058|0.49058	0.7414:0.0:0.2586:0.0|0.7414:0.0:0.2586:0.0	.|.	.|254;174	.|E9PF32;A2RUS2	.|.;DEND3_HUMAN	G|V	230|174;174;254;176;275	.|ENSP00000262585:I174V;ENSP00000410594:I174V;ENSP00000428714:I254V;ENSP00000429780:I176V;ENSP00000430786:I275V	.|ENSP00000262585:I174V	D|I	+|+	2|1	0|0	DENND3|DENND3	142230139|142230139	0.954000|0.954000	0.32549|0.32549	0.691000|0.691000	0.30163|0.30163	0.006000|0.006000	0.05464|0.05464	0.419000|0.419000	0.21247|0.21247	-0.018000|-0.018000	0.14079|0.14079	-0.441000|-0.441000	0.05720|0.05720	GAT|ATT	.	.		0.547	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		G	142160957	A	G	142160957	3	3	160	1	0	0	0	0	1	0	0	0	4434	333	12	2	538	2	DENND3	8	142160957	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2433014	142160957	4203065	195	24366										
COMMD5	28991	hgsc.bcm.edu	37	chr8	146076399	146076399	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctcctggagctggtccctgaAggtgtcaggcttcaggctgg	15	11	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr8:146076399A>C	ENST00000305103.3	-	2	577	c.325T>G	c.(325-327)Ttc>Gtc	p.F109V	COMMD5_ENST00000450361.2_Missense_Mutation_p.F109V|COMMD5_ENST00000402718.3_Missense_Mutation_p.F109V|AF235103.1_ENST00000578937.1_RNA	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	109						nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			TGGTCCCTGAAGGTGTCAGGC	0.662																																					p.F109V		Atlas-SNP	.											.	COMMD5	18	.	0			c.T325G						.						13	15	14					8																	146076399		2188	4275	6463	SO:0001583	missense	28991	exon2			CCCTGAAGGTGTC	AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.325T>G	chr8.hg19:g.146076399A>C	ENSP00000304544:p.Phe109Val	76.0	0.0		166.0	34.0	NM_001081004	D3DWN7|Q9NVN6|Q9UHX5	Missense_Mutation	SNP	ENST00000305103.3	hg19	CCDS6436.1	.	.	.	.	.	.	.	.	.	.	A	11.56	1.673715	0.29693	.	.	ENSG00000170619	ENST00000402718;ENST00000450361;ENST00000305103;ENST00000529143;ENST00000533270	T;T;T;T;T	0.10005	2.92;2.92;2.92;2.92;2.92	4.32	3.14	0.36123	.	0.000000	0.85682	D	0.000000	T	0.21307	0.0513	M	0.76838	2.35	0.22185	N	0.999304	D	0.56746	0.977	P	0.52672	0.706	T	0.05419	-1.0886	10	0.51188	T	0.08	-0.7699	7.9679	0.30111	0.7914:0.2086:0.0:0.0	.	109	Q9GZQ3	COMD5_HUMAN	V	109	ENSP00000385793:F109V;ENSP00000394331:F109V;ENSP00000304544:F109V;ENSP00000435552:F109V;ENSP00000433758:F109V	ENSP00000304544:F109V	F	-	1	0	COMMD5	146047203	0.009000	0.17119	0.517000	0.27799	0.009000	0.06853	1.236000	0.32683	0.794000	0.33899	-0.472000	0.04984	TTC	.	.		0.662	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382962.1	NM_014066		C	146076399	A	C	146076399	3	2	160	1	0	0	0	0	1	0	0	0	3721	72	3	5	353	5	COMMD5	8	146076399	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	3915442	146076399	287623	196	24367										
JAK2	3717	hgsc.bcm.edu	37	chr9	5069060	5069060	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tataaacactgtttgattacAaaaaatgagaatgaagagta	7	3	0	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:5069060A>G	ENST00000381652.3	+	11	1859	c.1365A>G	c.(1363-1365)acA>acG	p.T455T	JAK2_ENST00000544510.1_Silent_p.T306T|JAK2_ENST00000539801.1_Silent_p.T455T	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	455	SH2; atypical. {ECO:0000255|PROSITE- ProRule:PRU00191}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GTTTGATTACAAAAAATGAGA	0.343		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.T455T		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.A1365G						.						71	73	72					9																	5069060		2203	4299	6502	SO:0001819	synonymous_variant	3717	exon11	Familial Cancer Database		GATTACAAAAAAT		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1365A>G	chr9.hg19:g.5069060A>G		169.0	0.0		169.0	30.0	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	hg19	CCDS6457.1																																																																																			.	.		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			G	5069060	A	G	5069060	2	3	160	1	0	0	0	0	0	0	0	1	7947	117	5	2		2	JAK2	9	5069060	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10		5069060	136144371	197	24368										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8404601	8404601	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acattcgcgtatctattcttTggtttgtttacttccaagtt	6	8	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:8404601T>A	ENST00000381196.4	-	33	4689	c.4146A>T	c.(4144-4146)ccA>ccT	p.P1382P	PTPRD_ENST00000397611.3_Silent_p.P972P|PTPRD_ENST00000397606.3_Silent_p.P975P|PTPRD_ENST00000360074.4_Silent_p.P1369P|PTPRD_ENST00000486161.1_Silent_p.P975P|PTPRD_ENST00000540109.1_Silent_p.P1382P|PTPRD_ENST00000356435.5_Silent_p.P1382P|PTPRD_ENST00000537002.1_Silent_p.P972P|PTPRD_ENST00000355233.5_Silent_p.P976P|PTPRD_ENST00000397617.3_Silent_p.P975P|PTPRD_ENST00000358503.5_Silent_p.P1360P	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1382	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		ATCTATTCTTTGGTTTGTTTA	0.373										TSP Lung(15;0.13)																											p.P1382P		Atlas-SNP	.											.	PTPRD	1348	.	0			c.A4146T						.						186	159	168					9																	8404601		2203	4300	6503	SO:0001819	synonymous_variant	5789	exon36			ATTCTTTGGTTTG	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.4146A>T	chr9.hg19:g.8404601T>A		114.0	0.0		81.0	18.0	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	hg19	CCDS43786.1																																																																																			.	.		0.373	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			A	8404601	T	A	8404601	2	1	160	1	0	0	0	0	0	0	0	1	12814	1799	63	4		4	PTPRD	9	8404601	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	3335541	8404601	132808830	198	24369										
IFNA16	3449	hgsc.bcm.edu	37	chr9	21217203	21217203	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aggagtatcaaggccctcctAttacccaggctgtgagtctg	11	11	2	1	rs372911133		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:21217203A>G	ENST00000380216.1	-	1	107	c.102T>C	c.(100-102)aaT>aaC	p.N34N		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	34					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		AGGCCCTCCTATTACCCAGGC	0.507																																					p.N34N		Atlas-SNP	.											.	IFNA16	27	.	0			c.T102C						.						92	93	93					9																	21217203		2203	4298	6501	SO:0001819	synonymous_variant	3449	exon1			CCTCCTATTACCC		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"Interferons"	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.102T>C	chr9.hg19:g.21217203A>G		209.0	0.0		195.0	40.0	NM_002173	Q5VV12	Silent	SNP	ENST00000380216.1	hg19	CCDS34996.1																																																																																			.	.		0.507	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173		G	21217203	A	G	21217203	2	3	160	1	0	0	0	0	0	0	0	1	7544	446	16	2		2	IFNA16	9	21217203	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	12812602	21217203	119996228	199	24370										
KIF24	347240	hgsc.bcm.edu	37	chr9	34311028	34311028	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgctggcatttctgtctttaTtgtcagcaggagaatcaaaa	9	7	4	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:34311028T>A	ENST00000402558.2	-	1	341	c.317A>T	c.(316-318)aAt>aTt	p.N106I	KIF24_ENST00000379166.2_Missense_Mutation_p.N106I|KIF24_ENST00000379174.3_Missense_Mutation_p.N106I|KIF24_ENST00000345050.2_Missense_Mutation_p.N106I			Q5T7B8	KIF24_HUMAN	kinesin family member 24	106					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			TCTGTCTTTATTGTCAGCAGG	0.433																																					p.N106I		Atlas-SNP	.											.	KIF24	64	.	0			c.A317T						.						93	85	87					9																	34311028		1893	4127	6020	SO:0001583	missense	347240	exon2			TCTTTATTGTCAG	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"Kinesins", "Sterile alpha motif (SAM) domain containing"	19916	protein-coding gene	gene with protein product		613747	"chromosome 9 open reading frame 48"	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.317A>T	chr9.hg19:g.34311028T>A	ENSP00000384433:p.Asn106Ile	123.0	0.0		121.0	23.0	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Missense_Mutation	SNP	ENST00000402558.2	hg19	CCDS6551.2	.	.	.	.	.	.	.	.	.	.	T	8.982	0.975524	0.18736	.	.	ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188	T;T;T;T	0.71698	-0.4;-0.59;-0.4;-0.59	5.33	-4.14	0.03892	.	0.754197	0.11456	N	0.562281	T	0.55689	0.1936	L	0.44542	1.39	0.09310	N	1	B;B	0.20671	0.047;0.028	B;B	0.21360	0.034;0.015	T	0.41858	-0.9485	10	0.36615	T	0.2	.	7.6252	0.28208	0.0:0.4459:0.1312:0.4229	.	106;106	Q5T7B8-4;Q5T7B8	.;KIF24_HUMAN	I	106	ENSP00000384433:N106I;ENSP00000368472:N106I;ENSP00000368464:N106I;ENSP00000340179:N106I	ENSP00000340179:N106I	N	-	2	0	KIF24	34301028	0.006000	0.16342	0.068000	0.19968	0.266000	0.26442	0.032000	0.13732	-0.841000	0.04200	-0.280000	0.10049	AAT	.	.		0.433	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5			A	34311028	T	A	34311028	3	1	160	1	0	0	0	0	1	0	0	0	8301	1493	52	4	3837	4	KIF24	9	34311028	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	13093825	34311028	106902403	200	24371										
KIAA1045	23349	hgsc.bcm.edu	37	chr9	34977626	34977626	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	caagaccctgctgcccacagAgcaggagtccaggtgagtag	13	12	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:34977626A>T	ENST00000242315.3	+	7	1176	c.1094A>T	c.(1093-1095)gAg>gTg	p.E365V	KIAA1045_ENST00000544237.1_Missense_Mutation_p.E365V|KIAA1045_ENST00000476115.2_3'UTR	NM_015297.1	NP_056112.1	Q9UPV7	K1045_HUMAN	KIAA1045	365							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			LUSC - Lung squamous cell carcinoma(32;0.00575)			CTGCCCACAGAGCAGGAGTCC	0.582																																					p.E365V		Atlas-SNP	.											.	KIAA1045	60	.	0			c.A1094T						.						28	33	31					9																	34977626		2145	4245	6390	SO:0001583	missense	23349	exon7			CCACAGAGCAGGA	AB028968	CCDS43796.1	9p13.2	2008-02-05			ENSG00000122733	ENSG00000122733			29180	protein-coding gene	gene with protein product						10470851	Standard	NM_015297		Approved		uc003zvr.3	Q9UPV7	OTTHUMG00000019844	ENST00000242315.3:c.1094A>T	chr9.hg19:g.34977626A>T	ENSP00000242315:p.Glu365Val	166.0	0.0		177.0	33.0	NM_015297	B7Z253|Q58FE9|Q5T662	Missense_Mutation	SNP	ENST00000242315.3	hg19	CCDS43796.1	.	.	.	.	.	.	.	.	.	.	A	18.00	3.526022	0.64860	.	.	ENSG00000122733	ENST00000544237;ENST00000242315	.	.	.	5.43	5.43	0.79202	.	0.798454	0.11351	N	0.572965	T	0.48978	0.1530	N	0.24115	0.695	0.47621	D	0.999472	B	0.24043	0.096	B	0.30943	0.122	T	0.41963	-0.9479	9	0.52906	T	0.07	0.353	12.8631	0.57924	1.0:0.0:0.0:0.0	.	365	Q9UPV7	K1045_HUMAN	V	365	.	ENSP00000242315:E365V	E	+	2	0	KIAA1045	34967626	1.000000	0.71417	0.994000	0.49952	0.992000	0.81027	4.767000	0.62286	2.069000	0.61940	0.533000	0.62120	GAG	.	.		0.582	KIAA1045-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052256.2	XM_048592		T	34977626	A	T	34977626	3	4	160	1	0	0	0	0	1	0	0	0	8216	304	11	4	1116	4	KIAA1045	9	34977626	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	666598	34977626	106235805	201	24372										
C9orf131	138724	hgsc.bcm.edu	37	chr9	35043491	35043491	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	catcactactcctccatctgAggcccttccctgtggaccac	6	18	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:35043491A>T	ENST00000312292.5	+	2	912	c.865A>T	c.(865-867)Agg>Tgg	p.R289W	FLJ00273_ENST00000595331.1_5'Flank|C9orf131_ENST00000421362.2_Missense_Mutation_p.R241W|C9orf131_ENST00000354479.5_Missense_Mutation_p.R216W	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	289										cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			CCTCCATCTGAGGCCCTTCCC	0.562																																					p.R289W		Atlas-SNP	.											.	C9orf131	71	.	0			c.A865T						.						124	116	119					9																	35043491		2203	4300	6503	SO:0001583	missense	138724	exon2			CATCTGAGGCCCT	BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.865A>T	chr9.hg19:g.35043491A>T	ENSP00000308279:p.Arg289Trp	91.0	0.0		98.0	22.0	NM_203299	A6NLE6|E9PB26|Q86XC6|Q9UF74	Missense_Mutation	SNP	ENST00000312292.5	hg19	CCDS6572.2	.	.	.	.	.	.	.	.	.	.	A	17.01	3.278764	0.59758	.	.	ENSG00000174038	ENST00000421362;ENST00000354479;ENST00000312292;ENST00000378745	T;T;T;T	0.33865	2.38;2.38;2.38;1.39	4.84	2.33	0.28932	.	0.903341	0.09370	N	0.811445	T	0.39279	0.1072	L	0.44542	1.39	0.09310	N	1	P;P;P	0.50443	0.935;0.935;0.935	P;P;P	0.49528	0.614;0.614;0.614	T	0.22800	-1.0206	10	0.87932	D	0	-0.6903	8.7327	0.34510	0.6228:0.3772:0.0:0.0	.	289;216;241	Q5VYM1;A6NLE6;E9PB26	CI131_HUMAN;.;.	W	241;216;289;254	ENSP00000393683:R241W;ENSP00000346472:R216W;ENSP00000308279:R289W;ENSP00000368019:R254W	ENSP00000308279:R289W	R	+	1	2	C9orf131	35033491	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	0.554000	0.23407	0.287000	0.22375	0.533000	0.62120	AGG	.	.		0.562	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299		T	35043491	A	T	35043491	3	4	160	1	0	0	0	0	1	0	0	0	2459	295	11	4	887	4	C9orf131	9	35043491	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	65865	35043491	106169940	202	24373										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79320733	79320733	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttctgcattggatgggacaaActcccgtccaggctcataaa	9	11	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:79320733A>G	ENST00000376718.3	-	8	6580	c.6457T>C	c.(6457-6459)Ttt>Ctt	p.F2153L	PRUNE2_ENST00000428286.1_Missense_Mutation_p.F1794L	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2153					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GATGGGACAAACTCCCGTCCA	0.512																																					p.F2153L		Atlas-SNP	.											.	PRUNE2	331	.	0			c.T6457C						.						124	114	117					9																	79320733		1568	3582	5150	SO:0001583	missense	158471	exon8			GGACAAACTCCCG	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.6457T>C	chr9.hg19:g.79320733A>G	ENSP00000365908:p.Phe2153Leu	67.0	0.0		42.0	11.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.125|2.125	-0.400496|-0.400496	0.04865|0.04865	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.39787|.	1.06;1.06|.	5.25|5.25	2.81|2.81	0.32909|0.32909	.|.	1.041720|.	0.07533|.	N|.	0.912570|.	T|T	0.37404|0.37404	0.1002|0.1002	L|L	0.47716|0.47716	1.5|1.5	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.24693|0.24693	-1.0153|-1.0153	10|5	0.02654|.	T|.	1|.	0.136|0.136	4.9378|4.9378	0.13950|0.13950	0.7173:0.0:0.1426:0.1401|0.7173:0.0:0.1426:0.1401	.|.	2153|.	Q8WUY3|.	PRUN2_HUMAN|.	L|A	2153;1794;2152|1474	ENSP00000365908:F2153L;ENSP00000397425:F1794L|.	ENSP00000365908:F2153L|.	F|V	-|-	1|2	0|0	PRUNE2|PRUNE2	78510553|78510553	0.000000|0.000000	0.05858|0.05858	0.017000|0.017000	0.16124|0.16124	0.011000|0.011000	0.07611|0.07611	0.839000|0.839000	0.27586|0.27586	0.972000|0.972000	0.38314|0.38314	0.533000|0.533000	0.62120|0.62120	TTT|GTT	.	.		0.512	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		G	79320733	A	G	79320733	3	3	160	1	0	0	0	0	1	0	0	0	12653	43	2	2	2857	2	PRUNE2	9	79320733	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	44277242	79320733	61892698	203	24374										
WNK2	65268	hgsc.bcm.edu	37	chr9	95992093	95992093	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cttctgggagtccagcgccaAgggcaagcggtgcattgtgc	15	11	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:95992093A>T	ENST00000297954.4	+	2	797	c.797A>T	c.(796-798)aAg>aTg	p.K266M	WNK2_ENST00000349097.3_De_novo_Start_OutOfFrame|WNK2_ENST00000427277.2_De_novo_Start_OutOfFrame|WNK2_ENST00000395475.2_Missense_Mutation_p.K252M|WNK2_ENST00000356055.3_De_novo_Start_OutOfFrame|WNK2_ENST00000395477.2_Missense_Mutation_p.K266M	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	266	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TCCAGCGCCAAGGGCAAGCGG	0.622																																					p.K266M		Atlas-SNP	.											.	WNK2	277	.	0			c.A797T						.						70	55	60					9																	95992093		2203	4300	6503	SO:0001583	missense	65268	exon2			GCGCCAAGGGCAA	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.797A>T	chr9.hg19:g.95992093A>T	ENSP00000297954:p.Lys266Met	64.0	0.0		64.0	11.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.55|17.55	3.418189|3.418189	0.62622|0.62622	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000448039;ENST00000297954;ENST00000395477;ENST00000395475|ENST00000432730	T;T;T;T|.	0.73363|.	-0.74;-0.66;-0.65;-0.74|.	5.43|5.43	2.97|2.97	0.34412|0.34412	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.109140|.	0.64402|.	D|.	0.000010|.	T|T	0.56077|0.56077	0.1961|0.1961	L|L	0.43757|0.43757	1.38|1.38	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.71674|.	0.998;0.996;0.998;0.998|.	P;P;P;D|.	0.65684|.	0.854;0.854;0.854;0.937|.	T|T	0.46582|0.46582	-0.9181|-0.9181	10|5	0.87932|.	D|.	0|.	.|.	11.5841|11.5841	0.50908|0.50908	0.9182:0.0:0.0818:0.0|0.9182:0.0:0.0818:0.0	.|.	266;266;266;266|.	Q9Y3S1-2;Q9Y3S1-4;F8W9F9;Q9Y3S1|.	.;.;.;WNK2_HUMAN|.	M|W	266;266;266;252|262	ENSP00000412465:K266M;ENSP00000297954:K266M;ENSP00000378860:K266M;ENSP00000378858:K252M|.	ENSP00000297954:K266M|.	K|R	+|+	2|1	0|2	WNK2|WNK2	95031914|95031914	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.995000|0.995000	0.86356|0.86356	3.918000|3.918000	0.56432|0.56432	0.325000|0.325000	0.23359|0.23359	0.533000|0.533000	0.62120|0.62120	AAG|AGG	.	.		0.622	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		T	95992093	A	T	95992093	3	4	160	1	0	0	0	0	1	0	0	0	17393	72	3	4	803	4	WNK2	9	95992093	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	16671360	95992093	45221338	204	24375										
OR13C5	138799	hgsc.bcm.edu	37	chr9	107360745	107360745	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcacctttctcatttacttgTtaaaattttttcttctcagt	2	9	4	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:107360745T>A	ENST00000374779.2	-	1	1043	c.950A>T	c.(949-951)aAc>aTc	p.N317I		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	317						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CATTTACTTGTTAAAATTTTT	0.343																																					p.N317I		Atlas-SNP	.											.	OR13C5	60	.	0			c.A950T						.						75	84	81					9																	107360745		2203	4300	6503	SO:0001583	missense	138799	exon1			TACTTGTTAAAAT		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"GPCR / Class A : Olfactory receptors"	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.950A>T	chr9.hg19:g.107360745T>A	ENSP00000363911:p.Asn317Ile	58.0	0.0		61.0	12.0	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	hg19	CCDS35091.1	.	.	.	.	.	.	.	.	.	.	T	6.960	0.547096	0.13312	.	.	ENSG00000255800	ENST00000374779	T	0.09163	3.01	2.83	-1.12	0.09808	.	1.248280	0.06317	U	0.703833	T	0.04770	0.0129	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.42548	-0.9445	10	0.27082	T	0.32	.	2.8935	0.05684	0.1955:0.2601:0.0:0.5444	.	317	Q8NGS8	O13C5_HUMAN	I	317	ENSP00000363911:N317I	ENSP00000363911:N317I	N	-	2	0	OR13C5	106400566	0.000000	0.05858	0.002000	0.10522	0.026000	0.11368	-1.732000	0.01851	-0.083000	0.12618	0.528000	0.53228	AAC	.	.		0.343	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482		A	107360745	T	A	107360745	3	1	160	1	0	0	0	0	1	0	0	0	10946	1725	60	4	8	4	OR13C5	9	107360745	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	11368652	107360745	33852686	205	24376										
C5	727	hgsc.bcm.edu	37	chr9	123789473	123789473	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgctgtttgcatcatttcttTttgatcatcttttaagtctt	5	7	5	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:123789473T>A	ENST00000223642.1	-	8	867	c.838A>T	c.(838-840)Aaa>Taa	p.K280*		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	280					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	ATCATTTCTTTTTGATCATCT	0.343																																					p.K280X		Atlas-SNP	.											.	C5	124	.	0			c.A838T						.						283	207	233					9																	123789473		2202	4299	6501	SO:0001587	stop_gained	727	exon8			TTTCTTTTTGATC	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.838A>T	chr9.hg19:g.123789473T>A	ENSP00000223642:p.Lys280*	42.0	0.0		39.0	6.0	NM_001735	Q14CJ0|Q27I61	Nonsense_Mutation	SNP	ENST00000223642.1	hg19	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	T	35	5.548472	0.96488	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	.	.	.	5.75	4.62	0.57501	.	0.000000	0.52532	D	0.000062	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.4505	0.38723	0.0:0.0794:0.0:0.9206	.	.	.	.	X	280;351	.	ENSP00000223642:K280X	K	-	1	0	C5	122829294	0.997000	0.39634	0.795000	0.32087	0.984000	0.73092	3.255000	0.51484	1.020000	0.39573	0.533000	0.62120	AAA	.	.		0.343	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		A	123789473	T	A	123789473	4	1	160	1	0	0	0	0	0	1	0	0	2282	1850	64	4	4328	4	C5	9	123789473	Nonsense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	16428728	123789473	17423958	206	24377										
OR1N2	138882	hgsc.bcm.edu	37	chr9	125316382	125316382	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcatttatagcttgaggaacAgagacatgaaggaggctttg	12	5	1	3	rs369499080		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:125316382A>C	ENST00000373688.2	+	1	992	c.934A>C	c.(934-936)Aga>Cga	p.R312R		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						CTTGAGGAACAGAGACATGAA	0.403																																					p.R312R		Atlas-SNP	.											.	OR1N2	51	.	0			c.A934C						.						109	109	109					9																	125316382		2203	4300	6503	SO:0001819	synonymous_variant	138882	exon1			AGGAACAGAGACA		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"GPCR / Class A : Olfactory receptors"	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.934A>C	chr9.hg19:g.125316382A>C		61.0	0.0		59.0	5.0	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Silent	SNP	ENST00000373688.2	hg19	CCDS35123.1																																																																																			.	.		0.403	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2			C	125316382	A	C	125316382	2	2	160	1	0	0	0	0	0	0	0	1	10979	180	7	5		5	OR1N2	9	125316382	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1526909	125316382	15897049	207	24378										
NR5A1	2516	hgsc.bcm.edu	37	chr9	127262932	127262932	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cttctgctgtttcagggcccGgtcccgcttgtacatcggcc	11	15	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:127262932G>A	ENST00000373588.4	-	4	503	c.307C>T	c.(307-309)Cgg>Tgg	p.R103W		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	103					adrenal gland development (GO:0030325)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|hormone metabolic process (GO:0042445)|intracellular receptor signaling pathway (GO:0030522)|luteinization (GO:0001553)|maintenance of protein location in nucleus (GO:0051457)|male gonad development (GO:0008584)|multicellular organismal aging (GO:0010259)|negative regulation of female gonad development (GO:2000195)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|primary sex determination (GO:0007538)|regulation of steroid biosynthetic process (GO:0050810)|tissue development (GO:0009888)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)	2						TTCAGGGCCCGGTCCCGCTTG	0.667																																					p.R103W		Atlas-SNP	.											.	NR5A1	32	.	0			c.C307T						.						40	45	43					9																	127262932		2137	4088	6225	SO:0001583	missense	2516	exon4			GGGCCCGGTCCCG	D88155	CCDS6856.1	9q33	2013-01-16			ENSG00000136931	ENSG00000136931		"Nuclear hormone receptors"	7983	protein-coding gene	gene with protein product		184757		FTZF1		7789992	Standard	NM_004959		Approved	FTZ1, SF-1, ELP, AD4BP	uc004boo.1	Q13285	OTTHUMG00000020655	ENST00000373588.4:c.307C>T	chr9.hg19:g.127262932G>A	ENSP00000362690:p.Arg103Trp	70.0	0.0		74.0	14.0	NM_004959	O15196|Q5T6F5	Missense_Mutation	SNP	ENST00000373588.4	hg19	CCDS6856.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.709003	0.68615	.	.	ENSG00000136931	ENST00000373588;ENST00000455734	D;D	0.94862	-3.54;-3.47	4.54	2.64	0.31445	Zinc finger, NHR/GATA-type (1);Nuclear hormone receptor, ligand-binding (1);	0.056932	0.64402	D	0.000001	D	0.96673	0.8914	M	0.80982	2.52	0.50632	D	0.999885	D	0.76494	0.999	D	0.70716	0.97	D	0.96120	0.9084	10	0.87932	D	0	.	12.7537	0.57321	0.0:0.0:0.7408:0.2592	.	103	Q13285	STF1_HUMAN	W	103	ENSP00000362690:R103W;ENSP00000393245:R103W	ENSP00000362690:R103W	R	-	1	2	NR5A1	126302753	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	2.600000	0.46240	0.335000	0.23614	0.561000	0.74099	CGG	.	.		0.667	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959		A	127262932	G	A	127262932	3	1	160	1	0	0	0	0	1	0	0	0	10644	1115	39	1	1094	1	NR5A1	9	127262932	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	1946550	127262932	13950499	208	24379										
NUP214	8021	hgsc.bcm.edu	37	chr9	134026017	134026017	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctacagattgcacactttcaGaaggagttggaagagttaaa	10	6	1	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:134026017G>T	ENST00000359428.5	+	16	2286	c.2142G>T	c.(2140-2142)caG>caT	p.Q714H	NUP214_ENST00000451030.1_Missense_Mutation_p.Q715H|RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.Q704H|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	714	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)	p.Q714H(1)		NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		CACACTTTCAGAAGGAGTTGG	0.458			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.Q714H	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	NUP214,bladder,carcinoma,0,1	NUP214	166	.	1	Substitution - Missense(1)	urinary_tract(1)	c.G2142T						.						95	99	98					9																	134026017		2203	4300	6503	SO:0001583	missense	8021	exon16			CTTTCAGAAGGAG	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.2142G>T	chr9.hg19:g.134026017G>T	ENSP00000352400:p.Gln714His	126.0	0.0		137.0	18.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.904419	0.72868	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605	T;T;T	0.36878	1.25;1.23;1.23	5.84	2.44	0.29823	.	0.000000	0.41712	D	0.000825	T	0.33673	0.0871	N	0.08118	0	0.54753	D	0.999988	D;D;D;D	0.89917	0.996;1.0;0.994;1.0	D;D;D;D	0.91635	0.989;0.999;0.943;0.999	T	0.25187	-1.0139	10	0.87932	D	0	-13.6507	6.2748	0.20975	0.5255:0.0:0.4745:0.0	.	703;308;704;714	P35658-2;Q5JUP9;P35658-4;P35658	.;.;.;NU214_HUMAN	H	714;704;715;703;308;143	ENSP00000352400:Q714H;ENSP00000396576:Q704H;ENSP00000405014:Q715H	ENSP00000352400:Q714H	Q	+	3	2	NUP214	133015838	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.883000	0.39658	0.400000	0.25396	0.655000	0.94253	CAG	.	.		0.458	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		T	134026017	G	T	134026017	3	4	160	1	0	0	0	0	1	0	0	0	10771	933	33	3	2204	3	NUP214	9	134026017	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	6763085	134026017	7187414	209	24380										
WDR5	11091	hgsc.bcm.edu	37	chr9	137023062	137023062	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	caacagaaaacatcatcgccTctgctgcgctagaaaatgac	7	12	2	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:137023062T>C	ENST00000358625.3	+	14	1123	c.952T>C	c.(952-954)Tct>Cct	p.S318P	WDR5_ENST00000425041.1_Missense_Mutation_p.S318P	NM_017588.2	NP_060058.1	P61964	WDR5_HUMAN	WD repeat domain 5	318					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|histone H3-K4 methylation (GO:0051568)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|positive regulation of gluconeogenesis (GO:0045722)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|histone acetyltransferase complex (GO:0000123)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)				endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123)		Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154)		CATCATCGCCTCTGCTGCGCT	0.517																																					p.S318P		Atlas-SNP	.											.	WDR5	29	.	0			c.T952C						.						155	129	138					9																	137023062		2203	4300	6503	SO:0001583	missense	11091	exon13			ATCGCCTCTGCTG	AJ011376	CCDS6981.1	9q34	2014-09-03			ENSG00000196363	ENSG00000196363		"WD repeat domain containing"	12757	protein-coding gene	gene with protein product	"SWD3, Set1c WD40 repeat protein, homolog (S. cerevisiae)", "cilia and flagella associated protein 89"	609012				11551928	Standard	XM_005272163		Approved	SWD3, CFAP89	uc004cey.3	P61964	OTTHUMG00000131707	ENST00000358625.3:c.952T>C	chr9.hg19:g.137023062T>C	ENSP00000351446:p.Ser318Pro	101.0	0.0		89.0	18.0	NM_052821	Q91VA5|Q9NWX7|Q9UGP9	Missense_Mutation	SNP	ENST00000358625.3	hg19	CCDS6981.1	.	.	.	.	.	.	.	.	.	.	T	19.65	3.866752	0.72065	.	.	ENSG00000196363	ENST00000358625;ENST00000425041	T;T	0.72725	-0.68;-0.68	4.19	4.19	0.49359	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.245923	0.35040	N	0.003496	D	0.84705	0.5531	H	0.95402	3.665	0.80722	D	1	D	0.56746	0.977	P	0.54372	0.75	D	0.89180	0.3543	10	0.87932	D	0	.	12.7294	0.57189	0.0:0.0:0.0:1.0	.	318	P61964	WDR5_HUMAN	P	318	ENSP00000351446:S318P;ENSP00000401889:S318P	ENSP00000351446:S318P	S	+	1	0	WDR5	136012883	1.000000	0.71417	0.987000	0.45799	0.600000	0.36913	7.202000	0.77856	1.677000	0.50941	0.459000	0.35465	TCT	.	.		0.517	WDR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254621.1	NM_052821		C	137023062	T	C	137023062	3	2	160	1	0	0	0	0	1	0	0	0	17318	1551	54	2	1002	2	WDR5	9	137023062	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2997045	137023062	4190369	210	24381										
INPP5E	56623	hgsc.bcm.edu	37	chr9	139324161	139324161	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agatggtgctggagttctgaCtctgtagtgcttgctgcctc	13	9	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr9:139324161C>G	ENST00000371712.3	-	10	2303	c.1901G>C	c.(1900-1902)aGt>aCt	p.S634T		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		GGAGTTCTGACTCTGTAGTGC	0.463																																					p.S634T		Atlas-SNP	.											.	INPP5E	18	.	0			c.G1901C						.						249	232	238					9																	139324161		2203	4300	6503	SO:0001583	missense	56623	exon10			TTCTGACTCTGTA	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"Joubert syndrome 1"	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1901G>C	chr9.hg19:g.139324161C>G	ENSP00000360777:p.Ser634Thr	76.0	0.0		69.0	7.0	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371712.3	hg19	CCDS7000.1	.	.	.	.	.	.	.	.	.	.	C	5.899	0.350029	0.11182	.	.	ENSG00000148384	ENST00000371712	D	0.97505	-4.41	5.27	-6.52	0.01872	.	0.692933	0.14651	N	0.306610	D	0.89908	0.6851	N	0.22421	0.69	0.09310	N	1	B;B	0.18166	0.007;0.026	B;B	0.11329	0.006;0.005	T	0.79624	-0.1726	10	0.30078	T	0.28	-7.7169	6.3837	0.21550	0.0:0.3211:0.3875:0.2914	.	600;634	Q9NRR6-2;Q9NRR6	.;INP5E_HUMAN	T	634	ENSP00000360777:S634T	ENSP00000360777:S634T	S	-	2	0	INPP5E	138443982	0.260000	0.24053	0.000000	0.03702	0.002000	0.02628	-0.214000	0.09292	-1.509000	0.01798	-1.290000	0.01357	AGT	.	.		0.463	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892		G	139324161	C	G	139324161	3	3	160	1	0	0	0	0	1	0	0	0	7766	565	20	4	37	4	INPP5E	9	139324161	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	2301099	139324161	1889270	211	24382										
NEBL	10529	hgsc.bcm.edu	37	chr10	21169807	21169807	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	taatctgagaatcctttggcAgcatcatgtttctgcttgta	8	8	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr10:21169807A>T	ENST00000377122.4	-	5	792	c.396T>A	c.(394-396)gcT>gcA	p.A132A	NEBL_ENST00000377159.4_Intron|NEBL_ENST00000377119.1_Silent_p.A132A|NEBL_ENST00000417816.2_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	132				KHDAAKGFSD -> NMMLPRILS (in Ref. 2; AAF24858). {ECO:0000305}.	cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						ATCCTTTGGCAGCATCATGTT	0.413																																					p.A132A		Atlas-SNP	.											.	NEBL	199	.	0			c.T396A						.						131	132	132					10																	21169807		2203	4300	6503	SO:0001819	synonymous_variant	10529	exon5			TTTGGCAGCATCA	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.396T>A	chr10.hg19:g.21169807A>T		78.0	0.0		70.0	11.0	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Silent	SNP	ENST00000377122.4	hg19	CCDS7134.1																																																																																			.	.		0.413	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		T	21169807	A	T	21169807	2	4	160	1	0	0	0	0	0	0	0	1	10312	175	7	4		4	NEBL	10	21169807	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10		21169807	114364940	212	24383										
FAM13C	220965	hgsc.bcm.edu	37	chr10	61043201	61043201	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gactccatgcacctgagcagCttcttcctggtttgttaaaa	8	11	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr10:61043201C>T	ENST00000373868.2	-	6	601	c.514G>A	c.(514-516)Gct>Act	p.A172T	FAM13C_ENST00000442566.3_Missense_Mutation_p.A193T|FAM13C_ENST00000277705.6_Missense_Mutation_p.A193T|RP11-443O13.3_ENST00000433249.1_RNA|FAM13C_ENST00000422313.2_Missense_Mutation_p.A172T|FAM13C_ENST00000373867.3_Missense_Mutation_p.A89T|FAM13C_ENST00000419214.2_Missense_Mutation_p.A172T|FAM13C_ENST00000435852.2_Missense_Mutation_p.A172T|FAM13C_ENST00000468840.2_Missense_Mutation_p.A89T	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	172										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACCTGAGCAGCTTCTTCCTGG	0.537																																					p.A172T		Atlas-SNP	.											.	FAM13C	124	.	0			c.G514A						.						132	130	131					10																	61043201		2203	4300	6503	SO:0001583	missense	220965	exon6			GAGCAGCTTCTTC	U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"family with sequence similarity 13, member C1"	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.514G>A	chr10.hg19:g.61043201C>T	ENSP00000362975:p.Ala172Thr	50.0	0.0		65.0	9.0	NM_198215	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	hg19	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.737195	0.30774	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000419214;ENST00000468840;ENST00000435852;ENST00000422313	T;T;T;T;T;T;T;T	0.77358	-1.08;0.97;-1.09;-1.09;0.95;-1.08;0.97;0.97	4.85	3.93	0.45458	.	0.365106	0.26227	N	0.025594	T	0.62060	0.2397	L	0.35414	1.06	0.26536	N	0.974178	B;B;B;B;B	0.21147	0.023;0.007;0.052;0.005;0.007	B;B;B;B;B	0.17433	0.018;0.006;0.018;0.007;0.01	T	0.42310	-0.9459	10	0.14252	T	0.57	-4.4575	7.8516	0.29457	0.0:0.8044:0.0:0.1956	.	172;89;172;172;172	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31-3;Q8NE31	.;.;.;.;FA13C_HUMAN	T	89;172;193;193;172;89;172;172	ENSP00000362974:A89T;ENSP00000362975:A172T;ENSP00000395661:A193T;ENSP00000277705:A193T;ENSP00000391993:A172T;ENSP00000423896:A89T;ENSP00000392302:A172T;ENSP00000400241:A172T	ENSP00000277705:A193T	A	-	1	0	FAM13C	60713207	0.990000	0.36364	0.998000	0.56505	0.963000	0.63663	1.946000	0.40283	2.388000	0.81334	0.563000	0.77884	GCT	.	.		0.537	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			T	61043201	C	T	61043201	3	4	160	1	0	0	0	0	1	0	0	0	5459	797	28	3	1279	3	FAM13C	10	61043201	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	39873394	61043201	74491546	213	24384										
FAM13C	220965	hgsc.bcm.edu	37	chr10	61112104	61112104	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cctggacttgaagttgcccaTgctgggtcgcaatacgctgt	12	11	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr10:61112104T>C	ENST00000373868.2	-	3	337	c.250A>G	c.(250-252)Atg>Gtg	p.M84V	FAM13C_ENST00000442566.3_Missense_Mutation_p.M84V|FAM13C_ENST00000277705.6_Missense_Mutation_p.M84V|FAM13C_ENST00000422313.2_Missense_Mutation_p.M84V|FAM13C_ENST00000373867.3_Start_Codon_SNP_p.M1V|FAM13C_ENST00000419214.2_Missense_Mutation_p.M84V|FAM13C_ENST00000435852.2_Missense_Mutation_p.M84V|FAM13C_ENST00000468840.2_Start_Codon_SNP_p.M1V	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	84										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						AAGTTGCCCATGCTGGGTCGC	0.602																																					p.M84V		Atlas-SNP	.											.	FAM13C	124	.	0			c.A250G						.						79	78	78					10																	61112104		2203	4300	6503	SO:0001583	missense	220965	exon3			TGCCCATGCTGGG	U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"family with sequence similarity 13, member C1"	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.250A>G	chr10.hg19:g.61112104T>C	ENSP00000362975:p.Met84Val	57.0	0.0		69.0	20.0	NM_198215	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	hg19	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.357715	0.61403	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000419214;ENST00000468840;ENST00000435852;ENST00000422313;ENST00000512919;ENST00000503444	T;T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03;-0.03	5.93	5.93	0.95920	.	0.142968	0.50627	D	0.000108	T	0.74951	0.3784	L	0.56769	1.78	0.80722	D	1	B;D;B;D;B	0.58268	0.264;0.982;0.264;0.982;0.167	B;D;B;D;B	0.68943	0.085;0.961;0.085;0.961;0.053	T	0.77067	-0.2725	10	0.72032	D	0.01	.	13.8054	0.63227	0.0:0.0:0.0:1.0	.	84;1;84;84;84	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31-3;Q8NE31	.;.;.;.;FA13C_HUMAN	V	1;84;84;84;84;1;84;84;1;1	ENSP00000362975:M84V;ENSP00000395661:M84V;ENSP00000277705:M84V;ENSP00000391993:M84V;ENSP00000392302:M84V;ENSP00000400241:M84V	ENSP00000277705:M84V	M	-	1	0	FAM13C	60782110	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.258000	0.58822	2.281000	0.76405	0.529000	0.55759	ATG	.	.		0.602	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			C	61112104	T	C	61112104	3	2	160	1	0	0	0	0	1	0	0	0	5459	1464	51	2	1555	2	FAM13C	10	61112104	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	68903	61112104	74422643	214	24385										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720791	89720791	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cgtgcagataatgacaaggaAtatctagtacttactttaac	7	7	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr10:89720791A>G	ENST00000371953.3	+	8	2299	c.942A>G	c.(940-942)gaA>gaG	p.E314E	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	314	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.E314fs*3(2)|p.G165_*404del(1)|p.W274_F341del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		ATGACAAGGAATATCTAGTAC	0.338		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.E314E		Atlas-SNP	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,NS,other,+2,2	PTEN	3652	.	52	Whole gene deletion(37)|Deletion - Frameshift(11)|Deletion - In frame(2)|Unknown(2)	prostate(16)|central_nervous_system(13)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)|endometrium(1)	c.A942G						.						103	101	101					10																	89720791		2203	4299	6502	SO:0001819	synonymous_variant	5728	exon8	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	CAAGGAATATCTA	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.942A>G	chr10.hg19:g.89720791A>G		389.0	0.0		313.0	50.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	hg19	CCDS31238.1																																																																																			.	.		0.338	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89720791	A	G	89720791	2	3	160	1	0	0	0	0	0	0	0	1	12750	98	4	2		2	PTEN	10	89720791	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	28608687	89720791	45813956	215	24386										
IFIT2	3433	hgsc.bcm.edu	37	chr10	91066479	91066479	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttcttcgcagtgcagccaagTtttatcgaagaaaagatgag	10	7	1	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr10:91066479T>A	ENST00000371826.3	+	2	935	c.766T>A	c.(766-768)Ttt>Att	p.F256I	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	256					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				TGCAGCCAAGTTTTATCGAAG	0.443																																					p.F256I		Atlas-SNP	.											.	IFIT2	39	.	0			c.T766A						.						91	90	91					10																	91066479		1972	4182	6154	SO:0001583	missense	3433	exon2			GCCAAGTTTTATC	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"Tetratricopeptide (TTC) repeat domain containing"	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.766T>A	chr10.hg19:g.91066479T>A	ENSP00000360891:p.Phe256Ile	118.0	0.0		187.0	20.0	NM_001547	Q5T767	Missense_Mutation	SNP	ENST00000371826.3	hg19	CCDS41548.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.740146	0.49045	.	.	ENSG00000119922	ENST00000371826	T	0.35048	1.33	4.58	-0.607	0.11615	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.230914	0.35646	U	0.003076	T	0.43634	0.1256	M	0.86651	2.83	0.31969	N	0.607455	P	0.43392	0.805	B	0.44224	0.444	T	0.57596	-0.7784	10	0.87932	D	0	-0.9185	9.019	0.36188	0.0:0.262:0.0:0.738	.	256	P09913	IFIT2_HUMAN	I	256	ENSP00000360891:F256I	ENSP00000360891:F256I	F	+	1	0	IFIT2	91056459	0.980000	0.34600	0.013000	0.15412	0.208000	0.24298	1.896000	0.39789	-0.085000	0.12573	-0.242000	0.12053	TTT	.	.		0.443	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547		A	91066479	T	A	91066479	3	1	160	1	0	0	0	0	1	0	0	0	7532	1725	60	4	772	4	IFIT2	10	91066479	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1345688	91066479	44468268	216	24387										
SFRP5	6425	hgsc.bcm.edu	37	chr10	99527306	99527306	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cgccccgtagaagaaagggtAgtagagggagcaggggtagg	19	6	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr10:99527306A>T	ENST00000266066.3	-	3	1037	c.919T>A	c.(919-921)Tac>Aac	p.Y307N		NM_003015.3	NP_003006.2	Q5T4F7	SFRP5_HUMAN	secreted frizzled-related protein 5	307					anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cell differentiation (GO:0030154)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|establishment or maintenance of cell polarity (GO:0007163)|gonad development (GO:0008406)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of Wnt signaling pathway involved in digestive tract morphogenesis (GO:2000057)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|post-anal tail morphogenesis (GO:0036342)|signal transduction (GO:0007165)|vasculature development (GO:0001944)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			large_intestine(1)|lung(4)	5		Colorectal(252;0.234)		Epithelial(162;4.98e-10)|all cancers(201;3.58e-08)		AAGAAAGGGTAGTAGAGGGAG	0.582																																					p.Y307N		Atlas-SNP	.											.	SFRP5	32	.	0			c.T919A						.						56	44	48					10																	99527306		2200	4299	6499	SO:0001583	missense	6425	exon3			AAGGGTAGTAGAG	AF017988	CCDS7472.1	10q24	2008-07-10			ENSG00000120057	ENSG00000120057		"Secreted frizzled-related proteins"	10779	protein-coding gene	gene with protein product	"secreted apoptosis related protein 3"	604158				9391078	Standard	NM_003015		Approved	SARP3	uc001kor.4	Q5T4F7	OTTHUMG00000018866	ENST00000266066.3:c.919T>A	chr10.hg19:g.99527306A>T	ENSP00000266066:p.Tyr307Asn	104.0	0.0		99.0	27.0	NM_003015	O14780|Q86TH7	Missense_Mutation	SNP	ENST00000266066.3	hg19	CCDS7472.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.159064	0.38119	.	.	ENSG00000120057	ENST00000266066	T	0.29142	1.58	5.74	5.74	0.90152	Tissue inhibitor of metalloproteinases-like, OB-fold (1);	0.194860	0.44483	D	0.000451	T	0.19005	0.0456	N	0.22421	0.69	0.34179	D	0.670694	B	0.29253	0.239	B	0.26517	0.07	T	0.25363	-1.0134	10	0.46703	T	0.11	.	6.8138	0.23819	0.7651:0.1534:0.0815:0.0	.	307	Q5T4F7	SFRP5_HUMAN	N	307	ENSP00000266066:Y307N	ENSP00000266066:Y307N	Y	-	1	0	SFRP5	99517296	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.258000	0.58822	2.189000	0.69895	0.459000	0.35465	TAC	.	.		0.582	SFRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049742.1	NM_003015		T	99527306	A	T	99527306	3	4	160	1	0	0	0	0	1	0	0	0	14179	420	15	4	38	4	SFRP5	10	99527306	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	8460827	99527306	36007441	217	24388										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106865232	106865232	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cttttgcccgctccattgacAtcagttccctggttgtccag	8	14	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr10:106865232A>C	ENST00000369701.3	+	7	1398	c.1171A>C	c.(1171-1173)Atc>Ctc	p.I391L		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	391					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CTCCATTGACATCAGTTCCCT	0.502																																					p.I391L	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.A1171C						.						182	153	163					10																	106865232		2203	4300	6503	SO:0001583	missense	22986	exon7			ATTGACATCAGTT	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1171A>C	chr10.hg19:g.106865232A>C	ENSP00000358715:p.Ile391Leu	94.0	0.0		75.0	16.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	A	9.222	1.033532	0.19590	.	.	ENSG00000156395	ENST00000369701	T	0.29655	1.56	5.43	1.85	0.25348	VPS10 (1);	0.294151	0.37715	N	0.001979	T	0.15739	0.0379	L	0.34521	1.04	0.34961	D	0.752204	B	0.24618	0.107	B	0.19391	0.025	T	0.15636	-1.0430	10	0.11182	T	0.66	.	3.1378	0.06444	0.638:0.0:0.1865:0.1754	.	391	Q9UPU3	SORC3_HUMAN	L	391	ENSP00000358715:I391L	ENSP00000358715:I391L	I	+	1	0	SORCS3	106855222	0.989000	0.36119	1.000000	0.80357	0.994000	0.84299	0.273000	0.18662	0.354000	0.24105	0.379000	0.24179	ATC	.	.		0.502	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		C	106865232	A	C	106865232	3	2	160	1	0	0	0	0	1	0	0	0	14947	217	8	5	1197	5	SORCS3	10	106865232	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	7337926	106865232	28669515	218	24389										
FAM160B1	57700	hgsc.bcm.edu	37	chr10	116608453	116608453	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aaaatcctcctaccatgttgAgggcacaggatatgacactt	8	10	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr10:116608453A>G	ENST00000369248.4	+	13	2095	c.1760A>G	c.(1759-1761)gAg>gGg	p.E587G	FAM160B1_ENST00000369250.3_Missense_Mutation_p.E587G	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	587										NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						TACCATGTTGAGGGCACAGGA	0.423																																					p.E587G		Atlas-SNP	.											.	FAM160B1	107	.	0			c.A1760G						.						127	98	108					10																	116608453		2203	4300	6503	SO:0001583	missense	57700	exon13			ATGTTGAGGGCAC	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"KIAA1600"	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.1760A>G	chr10.hg19:g.116608453A>G	ENSP00000358251:p.Glu587Gly	64.0	0.0		92.0	15.0	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Missense_Mutation	SNP	ENST00000369248.4	hg19	CCDS31290.1	.	.	.	.	.	.	.	.	.	.	A	17.35	3.368553	0.61624	.	.	ENSG00000151553	ENST00000369248;ENST00000369250	T;T	0.16897	2.33;2.31	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.18299	0.0439	L	0.40543	1.245	0.80722	D	1	B;B	0.24043	0.096;0.018	B;B	0.29862	0.108;0.018	T	0.03641	-1.1017	10	0.30078	T	0.28	-23.6696	16.0529	0.80775	1.0:0.0:0.0:0.0	.	587;587	Q5W0V3-2;Q5W0V3	.;F16B1_HUMAN	G	587	ENSP00000358251:E587G;ENSP00000358253:E587G	ENSP00000358251:E587G	E	+	2	0	FAM160B1	116598443	1.000000	0.71417	0.998000	0.56505	0.670000	0.39368	8.971000	0.93419	2.257000	0.74773	0.459000	0.35465	GAG	.	.		0.423	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351		G	116608453	A	G	116608453	3	3	160	1	0	0	0	0	1	0	0	0	5475	304	11	2	1810	2	FAM160B1	10	116608453	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	9743221	116608453	18926294	219	24390										
C10orf90	118611	hgsc.bcm.edu	37	chr10	128150126	128150126	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttcttacattcctttattttTacaaccaagtcacagcatgt	3	10	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr10:128150126T>A	ENST00000284694.7	-	5	1683	c.1563A>T	c.(1561-1563)gtA>gtT	p.V521V	C10orf90_ENST00000544758.1_Silent_p.V618V|C10orf90_ENST00000454341.1_Silent_p.V424V|C10orf90_ENST00000480379.1_5'UTR|C10orf90_ENST00000356858.3_Silent_p.V474V	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	521					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		CCTTTATTTTTACAACCAAGT	0.522																																					p.V521V		Atlas-SNP	.											.	C10orf90	121	.	0			c.A1563T						.						70	69	69					10																	128150126		2203	4300	6503	SO:0001819	synonymous_variant	118611	exon5			TATTTTTACAACC	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.1563A>T	chr10.hg19:g.128150126T>A		103.0	0.0		80.0	7.0	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Silent	SNP	ENST00000284694.7	hg19	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	T	1.076	-0.668350	0.03428	.	.	ENSG00000154493	ENST00000424927	.	.	.	4.81	-9.63	0.00544	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.982	4.56	0.12156	0.1801:0.3712:0.344:0.1046	.	.	.	.	L	64	.	.	X	-	2	2	C10orf90	128140116	0.010000	0.17322	0.002000	0.10522	0.268000	0.26511	-0.977000	0.03782	-2.852000	0.00330	-1.288000	0.01363	TAA	.	.		0.522	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		A	128150126	T	A	128150126	2	1	160	1	0	0	0	0	0	0	0	1	1625	1741	61	4		4	C10orf90	10	128150126	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	11541673	128150126	7384621	220	24391										
C10orf90	118611	hgsc.bcm.edu	37	chr10	128193605	128193605	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tattctcatcaatcatctggGagatgactatggatgaaatc	8	7	4	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr10:128193605G>A	ENST00000284694.7	-	3	284	c.164C>T	c.(163-165)tCc>tTc	p.S55F	C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000544758.1_Missense_Mutation_p.S152F|C10orf90_ENST00000454341.1_Missense_Mutation_p.S55F|C10orf90_ENST00000392694.1_Missense_Mutation_p.S8F|C10orf90_ENST00000356858.3_Missense_Mutation_p.S8F	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	55					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		AATCATCTGGGAGATGACTAT	0.433																																					p.S55F		Atlas-SNP	.											.	C10orf90	121	.	0			c.C164T						.						117	110	112					10																	128193605		2203	4300	6503	SO:0001583	missense	118611	exon3			ATCTGGGAGATGA	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.164C>T	chr10.hg19:g.128193605G>A	ENSP00000284694:p.Ser55Phe	59.0	0.0		71.0	17.0	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	hg19	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.489742	0.44249	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.51325	0.99;0.94;1.12;1.01;0.71	4.76	4.76	0.60689	.	0.137327	0.34088	N	0.004277	T	0.67316	0.2880	M	0.65498	2.005	0.35554	D	0.804104	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.76575	0.988;0.988;0.983;0.977;0.961	T	0.77032	-0.2738	10	0.87932	D	0	-11.8858	16.9636	0.86279	0.0:0.0:1.0:0.0	.	152;152;8;55;55	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	F	8;55;55;152;55;8;8	ENSP00000284694:S55F;ENSP00000398786:S55F;ENSP00000444369:S152F;ENSP00000405995:S55F;ENSP00000376459:S8F	ENSP00000284694:S55F	S	-	2	0	C10orf90	128183595	1.000000	0.71417	0.150000	0.22450	0.043000	0.13939	6.002000	0.70693	2.473000	0.83533	0.561000	0.74099	TCC	.	.		0.433	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		A	128193605	G	A	128193605	3	1	160	1	0	0	0	0	1	0	0	0	1625	1174	41	3	1963	3	C10orf90	10	128193605	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	43479	128193605	7341142	221	24392										
CD151	977	hgsc.bcm.edu	37	chr11	836089	836089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gatgggtgagttcaacgagaAgaagacaacatgtggcaccg	14	7	1	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:836089A>G	ENST00000397420.3	+	3	269	c.20A>G	c.(19-21)aAg>aGg	p.K7R	CD151_ENST00000397421.1_Missense_Mutation_p.K7R|CD151_ENST00000322008.4_Missense_Mutation_p.K7R|CD151_ENST00000528011.1_Missense_Mutation_p.K7R			P48509	CD151_HUMAN	CD151 molecule (Raph blood group)	7					cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|T cell proliferation (GO:0042098)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	3		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;1.54e-25)|Epithelial(43;1.22e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.91e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TTCAACGAGAAGAAGACAACA	0.632																																					p.K7R	Esophageal Squamous(14;501 559 15826 37823 38305)	Atlas-SNP	.											.	CD151	7	.	0			c.A20G						.						100	80	87					11																	836089		2198	4295	6493	SO:0001583	missense	977	exon2			ACGAGAAGAAGAC	AL161965, BC013302, D29963	CCDS7719.1	11p15.5	2014-07-18	2006-03-28		ENSG00000177697	ENSG00000177697		"CD molecules", "Blood group antigens", "Tetraspanins"	1630	protein-coding gene	gene with protein product		602243	"CD151 antigen", "CD151 antigen (Raph blood group)"			9070943	Standard	NM_004357		Approved	SFA-1, PETA-3, TSPAN24, RAPH	uc001lsb.3	P48509	OTTHUMG00000133311	ENST00000397420.3:c.20A>G	chr11.hg19:g.836089A>G	ENSP00000380565:p.Lys7Arg	97.0	0.0		99.0	16.0	NM_139030	A8KAK8|E9PI15|Q14826|Q86U54|Q96TE3	Missense_Mutation	SNP	ENST00000397420.3	hg19	CCDS7719.1	.	.	.	.	.	.	.	.	.	.	A	11.48	1.650800	0.29336	.	.	ENSG00000177697	ENST00000397420;ENST00000525718;ENST00000322008;ENST00000397421;ENST00000529810;ENST00000528143;ENST00000526693;ENST00000525333;ENST00000524748;ENST00000527341;ENST00000528867;ENST00000530320;ENST00000526439;ENST00000528011	T;T;T;T;T;T;T;T;T;T;T;T;T	0.37411	1.2;1.92;1.2;1.2;1.44;2.01;1.9;2.07;2.07;1.92;2.01;1.44;1.2	4.72	4.72	0.59763	.	0.484709	0.24267	N	0.040030	T	0.30572	0.0769	L	0.36672	1.1	0.43947	D	0.996618	B	0.25772	0.134	B	0.23419	0.046	T	0.08848	-1.0702	10	0.44086	T	0.13	.	14.343	0.66641	1.0:0.0:0.0:0.0	.	7	P48509	CD151_HUMAN	R	7	ENSP00000380565:K7R;ENSP00000435854:K7R;ENSP00000324101:K7R;ENSP00000380566:K7R;ENSP00000432258:K7R;ENSP00000435054:K7R;ENSP00000431671:K7R;ENSP00000431403:K7R;ENSP00000436591:K7R;ENSP00000433752:K7R;ENSP00000433787:K7R;ENSP00000434663:K7R;ENSP00000432990:K7R	ENSP00000324101:K7R	K	+	2	0	CD151	826089	1.000000	0.71417	0.944000	0.38274	0.081000	0.17604	6.344000	0.72991	1.989000	0.58080	0.459000	0.35465	AAG	.	.		0.632	CD151-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257108.1	NM_004357		G	836089	A	G	836089	3	3	160	1	0	0	0	0	1	0	0	0	2967	72	3	2	22	2	CD151	11	836089	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10		836089	134170427	222	24393										
MUC6	4588	hgsc.bcm.edu	37	chr11	1030299	1030299	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcacgcaggccgagccgcacTcctggtacacctggttggcc	12	16	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:1030299T>A	ENST00000421673.2	-	8	979	c.929A>T	c.(928-930)gAg>gTg	p.E310V		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	310	TIL.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGAGCCGCACTCCTGGTACAC	0.706																																					p.E310V		Atlas-SNP	.											.	MUC6	408	.	0			c.A929T						.						10	14	13					11																	1030299		1953	3805	5758	SO:0001583	missense	4588	exon8			CCGCACTCCTGGT	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.929A>T	chr11.hg19:g.1030299T>A	ENSP00000406861:p.Glu310Val	136.0	0.0		121.0	20.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	t	13.85	2.361108	0.41801	.	.	ENSG00000184956	ENST00000421673	D	0.91521	-2.86	4.33	3.16	0.36331	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	.	.	.	.	D	0.94032	0.8088	M	0.75150	2.29	0.37776	D	0.926849	D	0.89917	1.0	D	0.83275	0.996	D	0.94082	0.7345	9	0.87932	D	0	.	10.1612	0.42853	0.0:0.0819:0.0:0.9181	.	310	Q6W4X9	MUC6_HUMAN	V	310	ENSP00000406861:E310V	ENSP00000406861:E310V	E	-	2	0	MUC6	1020299	1.000000	0.71417	0.416000	0.26546	0.500000	0.33767	4.308000	0.59129	0.606000	0.29965	0.409000	0.27619	GAG	.	.		0.706	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1030299	T	A	1030299	3	1	160	1	0	0	0	0	1	0	0	0	9989	1551	54	4	6494	4	MUC6	11	1030299	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	194210	1030299	133976217	223	24394										
TSSC4	10078	hgsc.bcm.edu	37	chr11	2424234	2424234	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgacaacggaggcttcaagcGgcccctagcgccctcaggcc	12	16	2	1	rs1008265	byFrequency	TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:2424234G>T	ENST00000333256.6	+	3	814	c.371G>T	c.(370-372)cGg>cTg	p.R124L	TSSC4_ENST00000451491.2_Missense_Mutation_p.R124L|AC124057.5_ENST00000433035.1_RNA|TSSC4_ENST00000380992.1_Missense_Mutation_p.R60L|TSSC4_ENST00000380996.5_Missense_Mutation_p.R60L			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	124			R -> Q (in dbSNP:rs1008265).							endometrium(3)|large_intestine(1)|lung(4)	8		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGCTTCAAGCGGCCCCTAGCG	0.682																																					p.R124L		Atlas-SNP	.											.	TSSC4	19	.	0			c.G371T						.						16	18	17					11																	2424234		2196	4292	6488	SO:0001583	missense	10078	exon2			TCAAGCGGCCCCT	AF125568	CCDS7735.1, CCDS73241.1	11p15.5	2008-02-05			ENSG00000184281	ENSG00000184281			12386	protein-coding gene	gene with protein product		603852				10072438	Standard	XM_005252722		Approved		uc001lwl.3	Q9Y5U2	OTTHUMG00000009895	ENST00000333256.6:c.371G>T	chr11.hg19:g.2424234G>T	ENSP00000331087:p.Arg124Leu	156.0	0.0		135.0	22.0	NM_005706	C9JS66|Q86VL2|Q9BRS6	Missense_Mutation	SNP	ENST00000333256.6	hg19	CCDS7735.1	.	.	.	.	.	.	.	.	.	.	G	4.270	0.049272	0.08243	.	.	ENSG00000184281	ENST00000380996;ENST00000333256;ENST00000380992;ENST00000437110;ENST00000440813;ENST00000496468;ENST00000451491	T;T;T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66;0.66;0.66	3.52	-3.56	0.04626	.	0.407543	0.21227	U	0.078048	T	0.32615	0.0835	L	0.52266	1.64	0.20196	N	0.999926	B;B	0.24768	0.111;0.111	B;B	0.23275	0.045;0.045	T	0.14783	-1.0460	10	0.26408	T	0.33	-0.1386	7.1129	0.25401	0.4049:0.0:0.4887:0.1064	.	124;60	Q9Y5U2;Q9Y5U2-2	TSSC4_HUMAN;.	L	60;124;60;124;60;124;124	ENSP00000370384:R60L;ENSP00000331087:R124L;ENSP00000370380:R60L;ENSP00000396925:R124L;ENSP00000416937:R60L;ENSP00000435013:R124L;ENSP00000411224:R124L	ENSP00000331087:R124L	R	+	2	0	TSSC4	2380810	0.017000	0.18338	0.000000	0.03702	0.005000	0.04900	0.245000	0.18142	-1.474000	0.01879	-1.587000	0.00848	CGG	.	G|0.988;A|0.012		0.682	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706		T	2424234	G	T	2424234	3	4	160	1	0	0	0	0	1	0	0	0	16682	1116	39	1	373	1	TSSC4	11	2424234	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	1393935	2424234	132582282	224	24395										
OR56B1	387748	hgsc.bcm.edu	37	chr11	5757966	5757966	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccatgtatattttccttggcAtcctctgtatggtagacatg	8	9	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:5757966A>T	ENST00000317121.3	+	1	286	c.220A>T	c.(220-222)Atc>Ttc	p.I74F	TRIM5_ENST00000380027.1_Intron	NM_001005180.2	NP_001005180.1	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B, member 1	74						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.086)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.184)		TTTCCTTGGCATCCTCTGTAT	0.483																																					p.I74F		Atlas-SNP	.											.	OR56B1	38	.	0			c.A220T						.						197	174	181					11																	5757966		2201	4297	6498	SO:0001583	missense	387748	exon1			CTTGGCATCCTCT	BK004386	CCDS31395.1	11p15.4	2012-08-09		2004-03-10	ENSG00000181023	ENSG00000181023		"GPCR / Class A : Olfactory receptors"	15245	protein-coding gene	gene with protein product				OR56B1P			Standard	NM_001005180		Approved		uc001mbt.2	Q8NGI3	OTTHUMG00000066891	ENST00000317121.3:c.220A>T	chr11.hg19:g.5757966A>T	ENSP00000322939:p.Ile74Phe	117.0	0.0		98.0	19.0	NM_001005180	B2RNY6|B3KV42|Q6IF76	Missense_Mutation	SNP	ENST00000317121.3	hg19	CCDS31395.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.049610	0.36181	.	.	ENSG00000181023	ENST00000317121	T	0.02974	4.09	5.91	3.64	0.41730	GPCR, rhodopsin-like superfamily (1);	0.366108	0.19923	U	0.103057	T	0.02970	0.0088	L	0.35249	1.045	0.32892	D	0.512035	B	0.26775	0.159	B	0.30105	0.111	T	0.12116	-1.0560	10	0.72032	D	0.01	-3.4468	6.3772	0.21513	0.7459:0.0:0.2541:0.0	.	74	Q8NGI3	O56B1_HUMAN	F	74	ENSP00000322939:I74F	ENSP00000322939:I74F	I	+	1	0	OR56B1	5714542	0.017000	0.18338	0.976000	0.42696	0.736000	0.42039	2.819000	0.48049	1.074000	0.40909	0.533000	0.62120	ATC	.	.		0.483	OR56B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143354.1	NM_001005180		T	5757966	A	T	5757966	3	4	160	1	0	0	0	0	1	0	0	0	11146	217	8	4	222	4	OR56B1	11	5757966	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	3333732	5757966	129248550	225	24396										
USP47	55031	hgsc.bcm.edu	37	chr11	11944273	11944273	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	taattatgtcttattaagaaAtctcctcagactgaaagttg	6	6	3	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:11944273A>G	ENST00000399455.2	+	12	1401	c.1281A>G	c.(1279-1281)aaA>aaG	p.K427K	USP47_ENST00000539466.1_5'UTR|USP47_ENST00000527733.1_Silent_p.K407K|USP47_ENST00000339865.5_Silent_p.K339K	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	427	USP.				base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		TTATTAAGAAATCTCCTCAGA	0.333																																					p.K339K		Atlas-SNP	.											.	USP47	91	.	0			c.A1017G						.						64	59	61					11																	11944273		1837	4094	5931	SO:0001819	synonymous_variant	55031	exon10			TAAGAAATCTCCT	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.1281A>G	chr11.hg19:g.11944273A>G		126.0	0.0		109.0	18.0	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Silent	SNP	ENST00000399455.2	hg19																																																																																				.	.		0.333	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		G	11944273	A	G	11944273	2	3	160	1	0	0	0	0	0	0	0	1	17093	98	4	2		2	USP47	11	11944273	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	6186307	11944273	123062243	226	24397										
LUZP2	338645	hgsc.bcm.edu	37	chr11	24936037	24936037	+	Missense_Mutation	SNP	G	G	T													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tacagtcaaaaaaaatccaaGcccagctgaaggagcttcgt							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:24936037G>T	ENST00000336930.6	+	7	541	c.475G>T	c.(475-477)Gcc>Tcc	p.A159S	LUZP2_ENST00000533227.1_Missense_Mutation_p.A73S			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	159						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						AAAAATCCAAGCCCAGCTGAA	0.338																																					p.A159S		Atlas-SNP	.											.	LUZP2	90	.	0			c.G475T						.						89	90	89					11																	24936037		2203	4300	6503	SO:0001583	missense	338645	exon7			ATCCAAGCCCAGC	AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.475G>T	chr11.hg19:g.24936037G>T	ENSP00000336817:p.Ala159Ser	286.0	0.0		322.0	39.0	NM_001009909	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Missense_Mutation	SNP	ENST00000336930.6	hg19	CCDS31446.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.436867	0.43224	.	.	ENSG00000187398	ENST00000336930;ENST00000533227	T;T	0.24151	1.87;1.87	5.54	2.61	0.31194	.	0.226555	0.37577	N	0.002031	T	0.13798	0.0334	N	0.20986	0.625	0.34678	D	0.724451	B	0.30709	0.291	B	0.29598	0.104	T	0.27365	-1.0076	10	0.15066	T	0.55	-5.5054	7.9728	0.30138	0.0763:0.0:0.6397:0.284	.	159	Q86TE4	LUZP2_HUMAN	S	159;73	ENSP00000336817:A159S;ENSP00000432952:A73S	ENSP00000336817:A159S	A	+	1	0	LUZP2	24892613	1.000000	0.71417	0.999000	0.59377	0.920000	0.55202	4.184000	0.58323	0.280000	0.22209	0.467000	0.42956	GCC	.	.		0.338	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909		T	24936037	G	T	24936037	3	4	160	1	0	0	0	0	1	0	0	0	9096	971	34	3	501	3	LUZP2	11	24936037	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	12991764	24936037	110070479	227	24398	111	2								
LUZP2	338645	hgsc.bcm.edu	37	chr11	24936045	24936045	+	Silent	SNP	G	G	A													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aaaaaaatccaagcccagctGaaggagcttcgttatgggaa							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:24936045G>A	ENST00000336930.6	+	7	549	c.483G>A	c.(481-483)ctG>ctA	p.L161L	LUZP2_ENST00000533227.1_Silent_p.L75L			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	161						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						AAGCCCAGCTGAAGGAGCTTC	0.323																																					p.L161L		Atlas-SNP	.											.	LUZP2	90	.	0			c.G483A						.						90	92	91					11																	24936045		2203	4300	6503	SO:0001819	synonymous_variant	338645	exon7			CCAGCTGAAGGAG	AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.483G>A	chr11.hg19:g.24936045G>A		280.0	0.0		325.0	41.0	NM_001009909	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Silent	SNP	ENST00000336930.6	hg19	CCDS31446.1																																																																																			.	.		0.323	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909		A	24936045	G	A	24936045	2	1	160	1	0	0	0	0	0	0	0	1	9096	1277	45	3		3	LUZP2	11	24936045	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	8	24936045	110070471	228	24399	111	2								
WT1	7490	hgsc.bcm.edu	37	chr11	32413561	32413561	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtgtgggtcttcaggtggtcGgaccgggagaactttcgctg	17	8	2	1	rs374799820		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:32413561G>T	ENST00000379079.2	-	9	1026	c.753C>A	c.(751-753)tcC>tcA	p.S251S	WT1_ENST00000530998.1_Silent_p.S234S|WT1_ENST00000332351.3_Silent_p.S463S|WT1_ENST00000448076.3_Silent_p.S463S	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	395					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.V380_S410del(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			TCAGGTGGTCGGACCGGGAGA	0.423			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																												p.S463S		Atlas-SNP	.	yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	.	WT1	744	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1389A						.						194	190	191					11																	32413561		2202	4299	6501	SO:0001819	synonymous_variant	7490	exon9	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	GTGGTCGGACCGG		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.753C>A	chr11.hg19:g.32413561G>T		109.0	0.0		129.0	24.0	NM_024424	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Silent	SNP	ENST00000379079.2	hg19	CCDS55751.1																																																																																			.	.		0.423	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378		T	32413561	G	T	32413561	2	4	160	1	0	0	0	0	0	0	0	1	17423	1103	39	1		1	WT1	11	32413561	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	7477516	32413561	102592955	229	24400										
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48188835	48188835	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aaaagtagatcttatctaccAgaacacaactgcaatgacaa	5	9	2	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:48188835A>G	ENST00000418331.2	+	25	4287	c.3935A>G	c.(3934-3936)cAg>cGg	p.Q1312R		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	1312					contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CTTATCTACCAGAACACAACT	0.393																																					p.Q1312R		Atlas-SNP	.											.	PTPRJ	225	.	0			c.A3935G						.						174	159	164					11																	48188835		2201	4298	6499	SO:0001583	missense	5795	exon25			TCTACCAGAACAC	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.3935A>G	chr11.hg19:g.48188835A>G	ENSP00000400010:p.Gln1312Arg	116.0	0.0		96.0	19.0	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	hg19	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	A	19.10	3.761987	0.69763	.	.	ENSG00000149177	ENST00000418331	T	0.15834	2.39	5.19	5.19	0.71726	.	.	.	.	.	T	0.29914	0.0748	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.02208	-1.1195	9	0.51188	T	0.08	.	12.9886	0.58606	1.0:0.0:0.0:0.0	.	1312	Q12913	PTPRJ_HUMAN	R	1312	ENSP00000400010:Q1312R	ENSP00000400010:Q1312R	Q	+	2	0	PTPRJ	48145411	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	8.561000	0.90715	1.968000	0.57251	0.377000	0.23210	CAG	.	.		0.393	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			G	48188835	A	G	48188835	3	3	160	1	0	0	0	0	1	0	0	0	12819	188	7	2	4042	2	PTPRJ	11	48188835	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	15775274	48188835	86817681	230	24401										
OR5B21	219968	hgsc.bcm.edu	37	chr11	58275100	58275100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agaaggagagtctgaaggtgCctgctgcatggatagaggca	16	6	1	4	rs376076638		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:58275100C>T	ENST00000360374.2	-	1	478	c.479G>A	c.(478-480)gGc>gAc	p.G160D		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	160						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TCTGAAGGTGCCTGCTGCATG	0.507																																					p.G160D		Atlas-SNP	.											.	OR5B21	59	.	0			c.G479A						.	C	ASP/GLY	1,4401	2.1+/-5.4	0,1,2200	86	73	77		479	2.7	0.4	11		77	0,8590		0,0,4295	no	missense	OR5B21	NM_001005218.1	94	0,1,6495	TT,TC,CC		0.0,0.0227,0.0077	benign	160/310	58275100	1,12991	2201	4295	6496	SO:0001583	missense	219968	exon1			AAGGTGCCTGCTG		CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"GPCR / Class A : Olfactory receptors"	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.479G>A	chr11.hg19:g.58275100C>T	ENSP00000353537:p.Gly160Asp	88.0	0.0		102.0	6.0	NM_001005218		Missense_Mutation	SNP	ENST00000360374.2	hg19	CCDS31552.1	.	.	.	.	.	.	.	.	.	.	C	3.171	-0.169907	0.06461	2.27E-4	0.0	ENSG00000198283	ENST00000360374	T	0.00091	8.74	5.04	2.74	0.32292	GPCR, rhodopsin-like superfamily (1);	0.425169	0.16326	N	0.219324	T	0.00073	0.0002	N	0.12422	0.21	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.05989	-1.0852	10	0.33940	T	0.23	-2.1452	6.9943	0.24774	0.0:0.2707:0.0:0.7293	.	160	A6NL26	OR5BL_HUMAN	D	160	ENSP00000353537:G160D	ENSP00000353537:G160D	G	-	2	0	OR5B21	58031676	0.000000	0.05858	0.376000	0.26042	0.474000	0.32979	-0.971000	0.03806	0.410000	0.25675	-0.302000	0.09304	GGC	.	.		0.507	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218		T	58275100	C	T	58275100	3	4	160	1	0	0	0	0	1	0	0	0	11160	739	26	3	452	3	OR5B21	11	58275100	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	10086265	58275100	76731416	231	24402										
PLAC1L	219990	hgsc.bcm.edu	37	chr11	59814496	59814496	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cttttattgctgactttcagAcaacagcagaagagttagga	9	7	1	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:59814496A>G	ENST00000278855.2	+	4	612	c.427A>G	c.(427-429)Aca>Gca	p.T143A		NM_173801.3	NP_776162.2	Q86WS3	OOSP2_HUMAN		143						extracellular region (GO:0005576)				breast(1)|lung(9)|ovary(2)|prostate(2)|skin(1)	15						TGACTTTCAGACAACAGCAGA	0.368																																					p.T143A		Atlas-SNP	.											.	PLAC1L	36	.	0			c.A427G						.						123	122	122					11																	59814496		2201	4295	6496	SO:0001583	missense	219990	exon4			TTTCAGACAACAG																												ENST00000278855.2:c.427A>G	chr11.hg19:g.59814496A>G	ENSP00000278855:p.Thr143Ala	113.0	0.0		123.0	47.0	NM_173801	E9PJA4|Q8N9U6	Missense_Mutation	SNP	ENST00000278855.2	hg19	CCDS7979.1	.	.	.	.	.	.	.	.	.	.	A	0.119	-1.127778	0.01770	.	.	ENSG00000149507	ENST00000278855	.	.	.	3.28	-2.03	0.07365	.	0.524017	0.14407	N	0.321537	T	0.19846	0.0477	N	0.10874	0.06	0.35961	D	0.834628	B	0.11235	0.004	B	0.09377	0.004	T	0.16512	-1.0400	9	0.15952	T	0.53	-2.1544	4.1675	0.10313	0.3359:0.4144:0.2497:0.0	.	143	Q86WS3	PLACL_HUMAN	A	143	.	ENSP00000278855:T143A	T	+	1	0	PLAC1L	59571072	0.000000	0.05858	0.240000	0.24138	0.885000	0.51271	-0.214000	0.09292	-0.433000	0.07286	-0.410000	0.06199	ACA	.	.		0.368	PLAC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394411.1			G	59814496	A	G	59814496	3	3	160	1	0	0	0	0	1	0	0	0	12022	275	10	2	441	2	PLAC1L	11	59814496	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1539396	59814496	75192020	232	24403										
MS4A12	54860	hgsc.bcm.edu	37	chr11	60264908	60264908	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cctctgggttcaatcaacttAgaaaaccaagctcagggtgc	9	11	4	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:60264908A>T	ENST00000016913.4	+	2	174	c.117A>T	c.(115-117)ttA>ttT	p.L39F	MS4A12_ENST00000537076.1_Missense_Mutation_p.L39F|MS4A12_ENST00000525951.1_3'UTR	NM_017716.2	NP_060186.2	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member 12	39						integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)	17						CAATCAACTTAGAAAACCAAG	0.483																																					p.L39F		Atlas-SNP	.											.	MS4A12	44	.	0			c.A117T						.						91	88	89					11																	60264908		2203	4300	6503	SO:0001583	missense	54860	exon2			CAACTTAGAAAAC	AK000224	CCDS7988.1, CCDS53638.1	11q12	2008-03-25				ENSG00000071203			13370	protein-coding gene	gene with protein product		606550				11401424, 11486273	Standard	NM_017716		Approved	Ms4a10, FLJ20217	uc001npr.3	Q9NXJ0		ENST00000016913.4:c.117A>T	chr11.hg19:g.60264908A>T	ENSP00000016913:p.Leu39Phe	188.0	0.0		166.0	12.0	NM_017716	F5GX98|Q8N6L4	Missense_Mutation	SNP	ENST00000016913.4	hg19	CCDS7988.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.362249	0.24684	.	.	ENSG00000071203	ENST00000537076;ENST00000526784;ENST00000016913;ENST00000530007	T;T;T;T	0.48836	1.87;0.87;3.36;0.8	4.22	-3.93	0.04143	.	7739.210000	0.00166	N	0.000000	T	0.29190	0.0726	N	0.19112	0.55	0.09310	N	1	P;P	0.43094	0.799;0.697	B;B	0.41764	0.366;0.154	T	0.18241	-1.0343	10	0.09084	T	0.74	.	5.4813	0.16725	0.2853:0.3225:0.3922:0.0	.	39;39	E9PNI3;Q9NXJ0	.;M4A12_HUMAN	F	39	ENSP00000440424:L39F;ENSP00000431959:L39F;ENSP00000016913:L39F;ENSP00000434783:L39F	ENSP00000016913:L39F	L	+	3	2	MS4A12	60021484	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.492000	0.06467	-0.660000	0.05352	0.460000	0.39030	TTA	.	.		0.483	MS4A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383627.1			T	60264908	A	T	60264908	3	4	160	1	0	0	0	0	1	0	0	0	9865	417	15	4	119	4	MS4A12	11	60264908	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	450412	60264908	74741608	233	24404										
STX5	6811	hgsc.bcm.edu	37	chr11	62594819	62594819	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccccaagaacactcacagatTgtcagcttctccagcttggc	7	15	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:62594819T>C	ENST00000294179.3	-	4	501	c.348A>G	c.(346-348)acA>acG	p.T116T	STX5_ENST00000541317.1_Silent_p.T20T|STX5_ENST00000394690.1_Silent_p.T62T|STX5_ENST00000377897.4_Silent_p.T116T	NM_001244666.1|NM_003164.4	NP_001231595.1|NP_003155.2	Q13190	STX5_HUMAN	syntaxin 5	116					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion with Golgi apparatus (GO:0048280)|vesicle targeting (GO:0006903)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|SNARE complex (GO:0031201)	protein N-terminus binding (GO:0047485)|SNAP receptor activity (GO:0005484)			breast(2)|endometrium(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	18						ACTCACAGATTGTCAGCTTCT	0.493																																					p.T116T		Atlas-SNP	.											.	STX5	42	.	0			c.A348G						.						179	161	167					11																	62594819		2201	4299	6500	SO:0001819	synonymous_variant	6811	exon4			ACAGATTGTCAGC	U26648	CCDS8038.2, CCDS58140.1	11q12.3	2008-02-05	2006-04-25	2006-04-25	ENSG00000162236	ENSG00000162236			11440	protein-coding gene	gene with protein product		603189	"syntaxin 5A"	STX5A		9188044, 11959998	Standard	NM_003164		Approved	SED5	uc001nvh.3	Q13190	OTTHUMG00000143864	ENST00000294179.3:c.348A>G	chr11.hg19:g.62594819T>C		102.0	0.0		111.0	12.0	NM_003164	B2R8T2|F8W8Q9|Q5U0D4|Q7Z3T6|Q9BUG1	Silent	SNP	ENST00000294179.3	hg19	CCDS8038.2																																																																																			.	.		0.493	STX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290113.1	NM_003164		C	62594819	T	C	62594819	2	2	160	1	0	0	0	0	0	0	0	1	15363	1799	63	2		2	STX5	11	62594819	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2329911	62594819	72411697	234	24405										
SLC3A2	6520	hgsc.bcm.edu	37	chr11	62648792	62648792	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctcggcatgcttgctggtgcCgtggtcataatcgtgcgagc	14	11	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:62648792C>A	ENST00000377890.2	+	4	768	c.600C>A	c.(598-600)gcC>gcA	p.A200A	SLC3A2_ENST00000377889.2_Silent_p.A138A|SLC3A2_ENST00000536981.1_5'Flank|SLC3A2_ENST00000338663.7_Silent_p.A99A|SLC3A2_ENST00000535296.1_Silent_p.A169A|SLC3A2_ENST00000377891.2_Silent_p.A201A|SLC3A2_ENST00000377892.1_Silent_p.A231A	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	200					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						TTGCTGGTGCCGTGGTCATAA	0.682											OREG0021031	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A201A		Atlas-SNP	.											.	SLC3A2	55	.	0			c.C603A						.						12	12	12					11																	62648792		2188	4283	6471	SO:0001819	synonymous_variant	6520	exon4			TGGTGCCGTGGTC		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"Solute carriers"	11026	protein-coding gene	gene with protein product	"antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43", "antigen defined by monoclonal antibody 4F2", "heavy chain", "4F2 heavy chain", "CD98 heavy chain", "monoclonal antibody 44D7", "4F2 cell-surface antigen heavy chain", "lymphocyte activation antigen 4F2 large subunit"	158070	"solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.600C>A	chr11.hg19:g.62648792C>A		79.0	0.0	1062	71.0	17.0	NM_001012662	Q13543	Silent	SNP	ENST00000377890.2	hg19	CCDS8039.2	.	.	.	.	.	.	.	.	.	.	C	13.06	2.123616	0.37436	.	.	ENSG00000168003	ENST00000538084	.	.	.	5.04	-0.591	0.11675	.	.	.	.	.	T	0.54822	0.1882	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48714	-0.9011	4	.	.	.	-22.1282	8.835	0.35107	0.0:0.2947:0.5591:0.1462	.	.	.	.	Q	171	.	.	P	+	2	0	SLC3A2	62405368	0.985000	0.35326	0.998000	0.56505	0.941000	0.58515	0.137000	0.15995	-0.004000	0.14419	0.561000	0.74099	CCG	.	.		0.682	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661		A	62648792	C	A	62648792	2	1	160	1	0	0	0	0	0	0	0	1	14642	639	23	1		1	SLC3A2	11	62648792	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	53973	62648792	72357724	235	24406										
NPAS4	266743	hgsc.bcm.edu	37	chr11	66189687	66189687	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctgcttgtgttcacagccgAggggaaattgctctacctgt	11	10	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:66189687A>G	ENST00000311034.2	+	2	448	c.272A>G	c.(271-273)gAg>gGg	p.E91G		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	91	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						TTCACAGCCGAGGGGAAATTG	0.597																																					p.E91G		Atlas-SNP	.											.	NPAS4	133	.	0			c.A272G						.						89	81	84					11																	66189687		2200	4295	6495	SO:0001583	missense	266743	exon2			CAGCCGAGGGGAA	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"Basic helix-loop-helix proteins"	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.272A>G	chr11.hg19:g.66189687A>G	ENSP00000311196:p.Glu91Gly	72.0	0.0		60.0	10.0	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	hg19	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	A	18.97	3.735815	0.69189	.	.	ENSG00000174576	ENST00000311034	T	0.19105	2.17	4.8	4.8	0.61643	PAS (2);	0.000000	0.56097	D	0.000026	T	0.25195	0.0612	M	0.63169	1.94	0.80722	D	1	B	0.25955	0.138	B	0.28638	0.092	T	0.06770	-1.0808	10	0.72032	D	0.01	-12.1785	12.6089	0.56540	1.0:0.0:0.0:0.0	.	91	Q8IUM7	NPAS4_HUMAN	G	91	ENSP00000311196:E91G	ENSP00000311196:E91G	E	+	2	0	NPAS4	65946263	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	5.525000	0.67110	2.142000	0.66516	0.460000	0.39030	GAG	.	.		0.597	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		G	66189687	A	G	66189687	3	3	160	1	0	0	0	0	1	0	0	0	10574	304	11	2	278	2	NPAS4	11	66189687	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	3540895	66189687	68816829	236	24407										
B3GNT6	192134	hgsc.bcm.edu	37	chr11	76751320	76751320	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cctgcaggcgcagccacccgGccgccacctgttctccggcc	11	21	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:76751320G>A	ENST00000533140.1	+	2	863	c.725G>A	c.(724-726)gGc>gAc	p.G242D	B3GNT6_ENST00000354301.5_Missense_Mutation_p.G242D|B3GNT6_ENST00000421061.1_Missense_Mutation_p.G153D			O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						CAGCCACCCGGCCGCCACCTG	0.697																																					p.G242D		Atlas-SNP	.											.	B3GNT6	27	.	0			c.G725A						.						12	16	15					11																	76751320		2165	4256	6421	SO:0001583	missense	192134	exon2			CACCCGGCCGCCA	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"Beta 3-glycosyltransferases"	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000533140.1:c.725G>A	chr11.hg19:g.76751320G>A	ENSP00000435352:p.Gly242Asp	33.0	0.0		29.0	10.0	NM_138706	Q4TTN0	Missense_Mutation	SNP	ENST00000533140.1	hg19	CCDS53681.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.124239	0.00342	.	.	ENSG00000198488	ENST00000533140;ENST00000354301;ENST00000421061	T;T;T	0.39997	1.05;1.05;1.05	2.71	-1.1	0.09872	.	0.533626	0.20401	N	0.093046	T	0.08537	0.0212	N	0.00317	-1.655	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.38672	-0.9650	10	0.06757	T	0.87	.	6.7572	0.23520	0.5492:0.0:0.4508:0.0	.	242	Q6ZMB0	B3GN6_HUMAN	D	242;242;153	ENSP00000435352:G242D;ENSP00000346256:G242D;ENSP00000403463:G153D	ENSP00000346256:G242D	G	+	2	0	B3GNT6	76428968	0.001000	0.12720	0.012000	0.15200	0.014000	0.08584	0.286000	0.18902	-0.257000	0.09459	-0.379000	0.06801	GGC	.	.		0.697	B3GNT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382740.2	NM_138706		A	76751320	G	A	76751320	3	1	160	1	0	0	0	0	1	0	0	0	1261	1203	42	3	727	3	B3GNT6	11	76751320	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	10561633	76751320	58255196	237	24408										
GRM5	2915	hgsc.bcm.edu	37	chr11	88780420	88780420	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acataggtccagttgtacctCttcactatgtccaccatggc	7	13	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:88780420C>A	ENST00000305447.4	-	1	770	c.621G>T	c.(619-621)aaG>aaT	p.K207N	GRM5_ENST00000418177.2_Missense_Mutation_p.K207N|GRM5_ENST00000305432.5_Missense_Mutation_p.K207N|GRM5_ENST00000393294.3_Missense_Mutation_p.K207N|GRM5_ENST00000393297.1_Missense_Mutation_p.K207N|GRM5_ENST00000455756.2_Missense_Mutation_p.K207N	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	207					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	AGTTGTACCTCTTCACTATGT	0.433																																					p.K207N		Atlas-SNP	.											.	GRM5	414	.	0			c.G621T						.						105	96	99					11																	88780420		2201	4299	6500	SO:0001583	missense	2915	exon2			GTACCTCTTCACT	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.621G>T	chr11.hg19:g.88780420C>A	ENSP00000306138:p.Lys207Asn	120.0	0.0		113.0	15.0	NM_000842	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	hg19	CCDS44694.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.92|16.92	3.255355|3.255355	0.59321|0.59321	.|.	.|.	ENSG00000168959|ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297;ENST00000393294|ENST00000449371	D;D;D;D;D;D|.	0.84370|.	-1.84;-1.84;-1.84;-1.84;-1.84;-1.84|.	5.41|5.41	0.874|0.874	0.19124|0.19124	Extracellular ligand-binding receptor (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73536|0.73536	0.3599|0.3599	M|M	0.84082|0.84082	2.675|2.675	0.49130|0.49130	D|D	0.999754|0.999754	D;D;D|.	0.89917|.	0.968;1.0;1.0|.	P;D;D|.	0.83275|.	0.773;0.995;0.996|.	T|T	0.74206|0.74206	-0.3740|-0.3740	9|5	.|.	.|.	.|.	.|.	12.0599|12.0599	0.53557|0.53557	0.0:0.6557:0.0:0.3443|0.0:0.6557:0.0:0.3443	.|.	207;207;207|.	A8MT20;P41594-2;P41594|.	.;.;GRM5_HUMAN|.	N|I	207|40	ENSP00000402912:K207N;ENSP00000405690:K207N;ENSP00000305905:K207N;ENSP00000306138:K207N;ENSP00000376975:K207N;ENSP00000376972:K207N|.	.|.	K|R	-|-	3|2	2|0	GRM5|GRM5	88420068|88420068	0.999000|0.999000	0.42202|0.42202	0.998000|0.998000	0.56505|0.56505	0.985000|0.985000	0.73830|0.73830	0.782000|0.782000	0.26788|0.26788	0.254000|0.254000	0.21573|0.21573	-0.251000|-0.251000	0.11542|0.11542	AAG|AGA	.	.		0.433	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		A	88780420	C	A	88780420	3	1	160	1	0	0	0	0	1	0	0	0	6809	912	32	3	3053	3	GRM5	11	88780420	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	12029100	88780420	46226096	238	24409										
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110451149	110451149	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctctgagcagcgccgatgtgTccttggacccttgagggcat	13	12	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:110451149T>C	ENST00000260283.4	-	16	2805	c.2521A>G	c.(2521-2523)Aca>Gca	p.T841A	ARHGAP20_ENST00000529591.1_Missense_Mutation_p.T384A|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.T815A|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.T805A|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.T815A|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.T805A|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.T818A	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	841					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		CGCCGATGTGTCCTTGGACCC	0.488																																					p.T841A		Atlas-SNP	.											.	ARHGAP20	150	.	0			c.A2521G						.						118	112	114					11																	110451149		2201	4298	6499	SO:0001583	missense	57569	exon16			GATGTGTCCTTGG	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.2521A>G	chr11.hg19:g.110451149T>C	ENSP00000260283:p.Thr841Ala	126.0	0.0		102.0	26.0	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	hg19	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	T	9.603	1.129115	0.21041	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.08282	3.11;3.11;3.16;3.11;3.11;3.11;3.11	4.65	2.31	0.28768	.	0.616334	0.15563	N	0.255846	T	0.02970	0.0088	N	0.02011	-0.69	0.20703	N	0.999869	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.41998	-0.9477	10	0.40728	T	0.16	.	5.8693	0.18795	0.1476:0.0816:0.0:0.7709	.	815;841;818	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	A	841;815;384;818;805;815;805	ENSP00000260283:T841A;ENSP00000349660:T815A;ENSP00000437905:T384A;ENSP00000432076:T818A;ENSP00000436319:T805A;ENSP00000436522:T815A;ENSP00000431399:T805A	ENSP00000260283:T841A	T	-	1	0	ARHGAP20	109956359	0.336000	0.24757	0.030000	0.17652	0.618000	0.37518	2.000000	0.40816	0.308000	0.22923	0.533000	0.62120	ACA	.	.		0.488	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		C	110451149	T	C	110451149	3	2	160	1	0	0	0	0	1	0	0	0	870	1667	58	2	1058	2	ARHGAP20	11	110451149	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	21670729	110451149	24555367	239	24410										
MLL	4297	hgsc.bcm.edu	37	chr11	118359362	118359362	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aagtctgttgtgagcccttcCacaagttttgtttagaggag	11	7	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:118359362C>T	ENST00000389506.5	+	11	4366	c.4366C>T	c.(4366-4368)Cac>Tac	p.H1456Y	KMT2A_ENST00000534358.1_Missense_Mutation_p.H1456Y|KMT2A_ENST00000354520.4_Missense_Mutation_p.H1418Y			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1456					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TGAGCCCTTCCACAAGTTTTG	0.413																																					p.H1456Y		Atlas-SNP	.											.	MLL	548	.	0			c.C4366T						.						141	130	134					11																	118359362		2200	4296	6496	SO:0001583	missense	4297	exon11			CCCTTCCACAAGT	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.4366C>T	chr11.hg19:g.118359362C>T	ENSP00000374157:p.His1456Tyr	124.0	0.0		83.0	18.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.132936	0.77662	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313;ENST00000392873	D;D;D;D	0.99329	-5.01;-4.95;-4.81;-5.75	5.52	5.52	0.82312	Zinc finger, PHD-finger (1);Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.99450	0.9805	M	0.83012	2.62	0.80722	D	1	D;D	0.69078	0.978;0.997	D;D	0.75484	0.969;0.986	D	0.99047	1.0826	10	0.87932	D	0	.	19.8024	0.96513	0.0:1.0:0.0:0.0	.	1456;1456	E9PQG7;Q03164	.;MLL1_HUMAN	Y	1456;1456;1418;366;168	ENSP00000436786:H1456Y;ENSP00000374157:H1456Y;ENSP00000346516:H1418Y;ENSP00000376612:H168Y	ENSP00000346516:H1418Y	H	+	1	0	MLL	117864572	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.442000	0.80503	2.752000	0.94435	0.655000	0.94253	CAC	.	.		0.413	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118359362	C	T	118359362	3	4	160	1	0	0	0	0	1	0	0	0	9629	594	21	3	4408	3	MLL	11	118359362	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	7908213	118359362	16647154	240	24411										
NTM	50863	hgsc.bcm.edu	37	chr11	132081914	132081914	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcattctgtcttgtttccacAgtatctcccaaaattgtaga	5	10	4	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr11:132081914A>T	ENST00000374786.1	+	3	879		c.e3-1		NTM_ENST00000427481.2_Splice_Site|NTM_ENST00000374791.3_Splice_Site|NTM_ENST00000539799.1_Splice_Site|NTM_ENST00000374784.1_Splice_Site|NTM_ENST00000474900.1_Splice_Site|NTM_ENST00000425719.2_Splice_Site	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin						cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.?(2)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						TTGTTTCCACAGTATCTCCCA	0.383																																					.		Atlas-SNP	.											NTM_ENST00000374791,NS,carcinoma,0,2	NTM	253	.	2	Unknown(2)	prostate(2)	c.401-2A>T						.						59	60	60					11																	132081914		2201	4297	6498	SO:0001630	splice_region_variant	50863	exon4			TTCCACAGTATCT	AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"Immunoglobulin superfamily / I-set domain containing"	17941	protein-coding gene	gene with protein product	"neurotrimin", "IgLON family member 2"	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.401-1A>T	chr11.hg19:g.132081914A>T		82.0	0.0		70.0	22.0	NM_001048209	A0MTT2|Q6UXJ3|Q86VJ9	Splice_Site	SNP	ENST00000374786.1	hg19	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.062881	0.76187	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000550167;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5764	0.84681	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NTM	131587124	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.420000	0.90256	2.371000	0.80710	0.533000	0.62120	.	.	.		0.383	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522	Intron	T	132081914	A	T	132081914	5	4	160	1	0	0	0	0	0	0	1	0	10708	202	7	4	495	4	NTM	11	132081914	Splice_Site	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	13722552	132081914	2924602	241	24412										
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	667798	667798	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccccatggtgatgaggctgcAttgtggggccaccccccagt	13	14	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:667798A>T	ENST00000266383.5	+	18	2745	c.2732A>T	c.(2731-2733)cAt>cTt	p.H911L		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	911					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			ATGAGGCTGCATTGTGGGGCC	0.582																																					p.H911L		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.A2732T						.						106	87	93					12																	667798		2203	4300	6503	SO:0001583	missense	283358	exon18			GGCTGCATTGTGG	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.2732A>T	chr12.hg19:g.667798A>T	ENSP00000266383:p.His911Leu	87.0	0.0		132.0	31.0	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	A	15.66	2.898015	0.52227	.	.	ENSG00000139044	ENST00000266383	T	0.33865	1.39	4.84	4.84	0.62591	.	0.309743	0.34067	N	0.004298	T	0.39937	0.1097	L	0.53249	1.67	0.36045	D	0.840368	B	0.33345	0.409	B	0.38755	0.281	T	0.53865	-0.8378	10	0.52906	T	0.07	-26.7237	14.7232	0.69323	1.0:0.0:0.0:0.0	.	911	Q6L9W6	B4GN3_HUMAN	L	911	ENSP00000266383:H911L	ENSP00000266383:H911L	H	+	2	0	B4GALNT3	538059	1.000000	0.71417	0.972000	0.41901	0.993000	0.82548	5.271000	0.65553	1.929000	0.55896	0.374000	0.22700	CAT	.	.		0.582	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		T	667798	A	T	667798	3	4	160	1	0	0	0	0	1	0	0	0	1268	217	8	4	2802	4	B4GALNT3	12	667798	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10		667798	133184097	242	24413										
EPS8	2059	hgsc.bcm.edu	37	chr12	15777209	15777209	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acgtcttcacatcctctggtGtggagtcgtaagtgatattg	11	8	3	1	rs150904526	byFrequency	TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:15777209G>T	ENST00000281172.5	-	19	2613	c.2177C>A	c.(2176-2178)aCa>aAa	p.T726K	EPS8_ENST00000540613.1_Missense_Mutation_p.T466K|EPS8_ENST00000543523.1_Missense_Mutation_p.T726K|EPS8_ENST00000543612.1_Missense_Mutation_p.T726K|EPS8_ENST00000542903.1_Missense_Mutation_p.T466K	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	726	Effector region. {ECO:0000250}.|Helix bundle 1. {ECO:0000250}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		ATCCTCTGGTGTGGAGTCGTA	0.468																																					p.T726K		Atlas-SNP	.											.	EPS8	70	.	0			c.C2177A						.						185	148	161					12																	15777209		2203	4300	6503	SO:0001583	missense	2059	exon19			TCTGGTGTGGAGT	U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.2177C>A	chr12.hg19:g.15777209G>T	ENSP00000281172:p.Thr726Lys	147.0	0.0		210.0	66.0	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Missense_Mutation	SNP	ENST00000281172.5	hg19	CCDS31753.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.093235	0.36952	.	.	ENSG00000151491	ENST00000543523;ENST00000281172;ENST00000543612;ENST00000540613;ENST00000542903	T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02	5.43	5.43	0.79202	.	0.405817	0.26700	N	0.022952	T	0.19248	0.0462	L	0.32530	0.975	0.41863	D	0.990237	B	0.12013	0.005	B	0.10450	0.005	T	0.05886	-1.0858	10	0.19590	T	0.45	-11.2335	19.4372	0.94801	0.0:0.0:1.0:0.0	.	726	Q12929	EPS8_HUMAN	K	726;726;726;466;466	ENSP00000441867:T726K;ENSP00000281172:T726K;ENSP00000442388:T726K;ENSP00000441888:T466K;ENSP00000437806:T466K	ENSP00000281172:T726K	T	-	2	0	EPS8	15668476	0.997000	0.39634	0.733000	0.30861	0.007000	0.05969	5.815000	0.69215	2.827000	0.97445	0.650000	0.86243	ACA	.	G|0.999;A|0.001		0.468	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			T	15777209	G	T	15777209	3	4	160	1	0	0	0	0	1	0	0	0	5196	1377	48	3	303	3	EPS8	12	15777209	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	15109411	15777209	118074686	243	24414										
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18435472	18435472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	catcattcacaagtttggatAaaattaatctagagaaagaa	6	5	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:18435472A>G	ENST00000266497.5	+	1	495	c.457A>G	c.(457-459)Aaa>Gaa	p.K153E	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.K153E|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.K153E|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.K153E|RERGL_ENST00000541632.1_Intron			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	153					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				AAGTTTGGATAAAATTAATCT	0.348																																					p.K153E		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A457G						.						53	54	54					12																	18435472		1809	4063	5872	SO:0001583	missense	5288	exon2			TTGGATAAAATTA	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.457A>G	chr12.hg19:g.18435472A>G	ENSP00000266497:p.Lys153Glu	69.0	0.0		101.0	15.0	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.818037	0.32145	.	.	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.62105	1.36;0.06;0.06;0.05	4.68	-6.98	0.01611	.	10.947600	0.00166	N	0.000000	T	0.41073	0.1143	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.002	T	0.23940	-1.0174	10	0.22109	T	0.4	-0.7851	9.4284	0.38595	0.345:0.1253:0.5298:0.0	.	153;153	F5H369;O75747	.;P3C2G_HUMAN	E	153	ENSP00000443850:K153E;ENSP00000404845:K153E;ENSP00000266497:K153E;ENSP00000445381:K153E	ENSP00000266497:K153E	K	+	1	0	PIK3C2G	18326739	0.001000	0.12720	0.000000	0.03702	0.412000	0.31113	-0.346000	0.07760	-1.465000	0.01899	0.533000	0.62120	AAA	.	.		0.348	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		G	18435472	A	G	18435472	3	3	160	1	0	0	0	0	1	0	0	0	11920	363	13	2	459	2	PIK3C2G	12	18435472	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2658263	18435472	115416423	244	24415										
GYS2	2998	hgsc.bcm.edu	37	chr12	21695505	21695505	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	attcgtggtcacactggggaTacccatcacagtgcattcag	10	11	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:21695505T>C	ENST00000261195.2	-	13	1824	c.1570A>G	c.(1570-1572)Atc>Gtc	p.I524V		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	524					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						ACACTGGGGATACCCATCACA	0.517																																					p.I524V	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											.	GYS2	110	.	0			c.A1570G						.						92	74	80					12																	21695505		2203	4300	6503	SO:0001583	missense	2998	exon13			TGGGGATACCCAT		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1570A>G	chr12.hg19:g.21695505T>C	ENSP00000261195:p.Ile524Val	282.0	0.0		313.0	58.0	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	hg19	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	T	16.32	3.089348	0.55968	.	.	ENSG00000111713	ENST00000261195	T	0.62498	0.02	5.34	5.34	0.76211	.	0.055179	0.64402	N	0.000001	T	0.63827	0.2544	N	0.20304	0.555	0.80722	D	1	P	0.50819	0.939	D	0.68943	0.961	T	0.58014	-0.7711	10	0.11794	T	0.64	-15.5221	15.4691	0.75426	0.0:0.0:0.0:1.0	.	524	P54840	GYS2_HUMAN	V	524	ENSP00000261195:I524V	ENSP00000261195:I524V	I	-	1	0	GYS2	21586772	1.000000	0.71417	0.929000	0.37066	0.981000	0.71138	7.854000	0.86942	2.240000	0.73641	0.528000	0.53228	ATC	.	.		0.517	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		C	21695505	T	C	21695505	3	2	160	1	0	0	0	0	1	0	0	0	6922	1406	49	2	557	2	GYS2	12	21695505	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	3260033	21695505	112156390	245	24416										
PPHLN1	51535	hgsc.bcm.edu	37	chr12	42835193	42835193	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agatccttcattagaaaagtCtatacagtttgcattgaggc	8	7	2	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:42835193C>G	ENST00000395568.2	+	10	1070	c.986C>G	c.(985-987)tCt>tGt	p.S329C	PPHLN1_ENST00000256678.8_Missense_Mutation_p.S209C|PPHLN1_ENST00000337898.6_Missense_Mutation_p.S274C|PPHLN1_ENST00000395580.3_Missense_Mutation_p.S336C|PPHLN1_ENST00000317560.9_Missense_Mutation_p.S262C|PPHLN1_ENST00000432191.2_Missense_Mutation_p.S274C|PPHLN1_ENST00000358314.7_Missense_Mutation_p.S329C|PPHLN1_ENST00000552761.1_Missense_Mutation_p.S281C|PPHLN1_ENST00000549190.1_Missense_Mutation_p.S347C|PPHLN1_ENST00000449194.2_Missense_Mutation_p.S310C	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	329					keratinization (GO:0031424)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	16	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		TTAGAAAAGTCTATACAGTTT	0.378																																					p.S336C		Atlas-SNP	.											.	PPHLN1	101	.	0			c.C1007G						.						157	154	155					12																	42835193		2203	4300	6503	SO:0001583	missense	51535	exon11			AAAAGTCTATACA	AY157850	CCDS8741.1, CCDS31777.1, CCDS41773.1, CCDS44860.1, CCDS44861.1, CCDS55817.1	12q12	2006-10-24				ENSG00000134283			19369	protein-coding gene	gene with protein product		608150					Standard	NM_016488		Approved		uc001rng.1	Q8NEY8		ENST00000395568.2:c.986C>G	chr12.hg19:g.42835193C>G	ENSP00000378935:p.Ser329Cys	76.0	0.0		110.0	11.0	NM_201515	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Missense_Mutation	SNP	ENST00000395568.2	hg19	CCDS31777.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612481	0.46631	.	.	ENSG00000134283	ENST00000549190;ENST00000395580;ENST00000337898;ENST00000358314;ENST00000395568;ENST00000256678;ENST00000449194;ENST00000552761;ENST00000317560;ENST00000432191	.	.	.	5.72	4.77	0.60923	.	0.488214	0.25148	N	0.032767	T	0.55401	0.1918	M	0.65975	2.015	0.32020	N	0.600909	B;B;B;B;B;B;B;B;B;B;B;B	0.31625	0.072;0.311;0.209;0.332;0.089;0.311;0.209;0.044;0.089;0.148;0.148;0.044	B;B;B;B;B;B;B;B;B;B;B;B	0.38954	0.066;0.187;0.161;0.286;0.109;0.134;0.161;0.081;0.103;0.222;0.178;0.099	T	0.65861	-0.6065	9	0.59425	D	0.04	-4.7703	11.5942	0.50964	0.1385:0.7278:0.1336:0.0	.	262;209;255;274;262;274;329;310;329;281;336;347	F8WF16;F8W6A0;B7Z695;B7Z8L1;B7Z615;Q8NEY8-3;Q8NEY8;E9PAX8;Q8NEY8-8;Q8NEY8-6;Q8NEY8-2;F8W0Q9	.;.;.;.;.;.;PPHLN_HUMAN;.;.;.;.;.	C	347;336;274;329;329;209;310;281;262;274	.	ENSP00000256678:S209C	S	+	2	0	PPHLN1	41121460	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.085000	0.50151	2.878000	0.98634	0.650000	0.86243	TCT	.	.		0.378	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515		G	42835193	C	G	42835193	3	3	160	1	0	0	0	0	1	0	0	0	12324	913	32	4	1057	4	PPHLN1	12	42835193	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	21139688	42835193	91016702	246	24417										
KRT76	51350	hgsc.bcm.edu	37	chr12	53163335	53163335	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tttgaatgggctacttacaaAtgcacacggcactctgacat	8	10	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:53163335A>G	ENST00000332411.2	-	8	1570	c.1517T>C	c.(1516-1518)aTt>aCt	p.I506T		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	506	Tail.				cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTACTTACAAATGCACACGGC	0.453																																					p.I506T		Atlas-SNP	.											.	KRT76	72	.	0			c.T1517C						.						126	118	121					12																	53163335		2203	4300	6503	SO:0001583	missense	51350	exon8			TTACAAATGCACA	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"-", "Intermediate filaments type II, keratins (basic)"	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.1517T>C	chr12.hg19:g.53163335A>G	ENSP00000330101:p.Ile506Thr	66.0	0.0		95.0	13.0	NM_015848	B4DRR3|Q7Z795	Missense_Mutation	SNP	ENST00000332411.2	hg19	CCDS8838.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.948659	0.73787	.	.	ENSG00000185069	ENST00000332411	D	0.83075	-1.68	4.83	4.83	0.62350	.	0.000000	0.46758	D	0.000262	T	0.82061	0.4955	N	0.08118	0	0.49213	D	0.999763	D	0.76494	0.999	D	0.79108	0.992	D	0.86398	0.1740	10	0.87932	D	0	.	14.7779	0.69743	1.0:0.0:0.0:0.0	.	506	Q01546	K22O_HUMAN	T	506	ENSP00000330101:I506T	ENSP00000330101:I506T	I	-	2	0	KRT76	51449602	0.993000	0.37304	0.997000	0.53966	0.942000	0.58702	3.091000	0.50199	2.100000	0.63781	0.533000	0.62120	ATT	.	.		0.453	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848		G	53163335	A	G	53163335	3	3	160	1	0	0	0	0	1	0	0	0	8498	101	4	2	407	2	KRT76	12	53163335	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	10328142	53163335	80688560	247	24418										
KRT18	3875	hgsc.bcm.edu	37	chr12	53343284	53343284	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	accgagaaccggaggctggaGagcaaaatccgggagcactt	14	10	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:53343284G>A	ENST00000388835.3	+	1	537	c.327G>A	c.(325-327)gaG>gaA	p.E109E	AC107016.2_ENST00000581256.1_RNA|KRT8_ENST00000552551.1_5'UTR|KRT8_ENST00000546897.1_Intron|KRT18_ENST00000388837.2_Silent_p.E109E|KRT18_ENST00000550600.1_Silent_p.E109E|KRT8_ENST00000549198.1_5'UTR	NM_000224.2	NP_000215.1	P05783	K1C18_HUMAN	keratin 18	109	Coil 1A.|Interaction with TRADD.|Necessary for interaction with PNN.|Rod.				anatomical structure morphogenesis (GO:0009653)|cell cycle (GO:0007049)|extrinsic apoptotic signaling pathway (GO:0097191)|Golgi to plasma membrane CFTR protein transport (GO:0043000)|hepatocyte apoptotic process (GO:0097284)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of apoptotic process (GO:0043066)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell periphery (GO:0071944)|centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)			central_nervous_system(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	11						GGAGGCTGGAGAGCAAAATCC	0.572																																					p.E109E		Atlas-SNP	.											.	KRT18	31	.	0			c.G327A						.						29	35	33					12																	53343284		2203	4294	6497	SO:0001819	synonymous_variant	3875	exon1			GCTGGAGAGCAAA		CCDS31809.1	12q13	2013-01-16			ENSG00000111057	ENSG00000111057		"-", "Intermediate filaments type I, keratins (acidic)"	6430	protein-coding gene	gene with protein product		148070				1705144, 16831889	Standard	NM_000224		Approved		uc001sbg.3	P05783	OTTHUMG00000169882	ENST00000388835.3:c.327G>A	chr12.hg19:g.53343284G>A		81.0	0.0		106.0	14.0	NM_000224	Q53G38|Q5U0N8|Q9BW26	Silent	SNP	ENST00000388835.3	hg19	CCDS31809.1																																																																																			.	.		0.572	KRT18-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406405.1	NM_199187		A	53343284	G	A	53343284	2	1	160	1	0	0	0	0	0	0	0	1	8464	933	33	3		3	KRT18	12	53343284	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	179949	53343284	80508611	248	24419										
CAND1	55832	hgsc.bcm.edu	37	chr12	67692842	67692842	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aagatgaagatgaaaatgcaAtggatgctgatggtggtgat	14	2	0	6			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:67692842A>G	ENST00000545606.1	+	7	1404	c.967A>G	c.(967-969)Atg>Gtg	p.M323V		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	323	Asp-rich.				cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		tgaaaatgcaatggatgctga	0.294																																					p.M323V		Atlas-SNP	.											.	CAND1	100	.	0			c.A967G						.						48	45	46					12																	67692842		2199	4297	6496	SO:0001583	missense	55832	exon7			AATGCAATGGATG		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.967A>G	chr12.hg19:g.67692842A>G	ENSP00000442318:p.Met323Val	36.0	0.0		50.0	11.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	A	12.69	2.012736	0.35511	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047;ENST00000544619	T;T	0.30448	1.53;1.53	5.57	5.57	0.84162	Armadillo-type fold (1);	0.078727	0.85682	N	0.000000	T	0.43787	0.1263	L	0.58969	1.84	0.80722	D	1	B;B	0.28667	0.219;0.005	P;B	0.44623	0.455;0.006	T	0.31138	-0.9954	9	.	.	.	-4.4344	15.3948	0.74784	1.0:0.0:0.0:0.0	.	323;323	Q86VP6-2;Q86VP6	.;CAND1_HUMAN	V	323;323;165;31	ENSP00000442318:M323V;ENSP00000444089:M31V	.	M	+	1	0	CAND1	65979109	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.951000	0.93025	2.102000	0.63906	0.533000	0.62120	ATG	.	.		0.294	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		G	67692842	A	G	67692842	3	3	160	1	0	0	0	0	1	0	0	0	2617	101	4	2	993	2	CAND1	12	67692842	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	14349558	67692842	66159053	249	24420										
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72037930	72037930	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcatgaatcgattgtactgtTcttcctgatttgagagatct	8	7	3	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:72037930T>C	ENST00000378743.3	-	5	1806	c.1448A>G	c.(1447-1449)gAa>gGa	p.E483G		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	483					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ATTGTACTGTTCTTCCTGATT	0.358																																					p.E483G		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.A1448G						.						176	160	165					12																	72037930		1854	4103	5957	SO:0001583	missense	196441	exon5			TACTGTTCTTCCT	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.1448A>G	chr12.hg19:g.72037930T>C	ENSP00000368017:p.Glu483Gly	122.0	0.0		121.0	15.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	hg19	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.663776	0.88251	.	.	ENSG00000133858	ENST00000378743	T	0.58652	0.32	5.0	5.0	0.66597	.	0.000000	0.64402	D	0.000001	T	0.63721	0.2535	N	0.24115	0.695	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.68522	-0.5386	10	0.66056	D	0.02	.	14.7156	0.69265	0.0:0.0:0.0:1.0	.	483	O60293	ZC3H1_HUMAN	G	483	ENSP00000368017:E483G	ENSP00000368017:E483G	E	-	2	0	ZFC3H1	70324197	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.134000	0.77268	1.876000	0.54355	0.533000	0.62120	GAA	.	.		0.358	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		C	72037930	T	C	72037930	3	2	160	1	0	0	0	0	1	0	0	0	17648	1783	62	2	4645	2	ZFC3H1	12	72037930	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4345088	72037930	61813965	250	24421										
E2F7	144455	hgsc.bcm.edu	37	chr12	77426865	77426865	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	attttctgtctatagacagcTgccaggcttccaatttctaa	6	10	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:77426865T>A	ENST00000322886.7	-	9	1582	c.1347A>T	c.(1345-1347)gcA>gcT	p.A449A	E2F7_ENST00000416496.2_Silent_p.A449A	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	449					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						TATAGACAGCTGCCAGGCTTC	0.348																																					p.A449A		Atlas-SNP	.											.	E2F7	201	.	0			c.A1347T						.						80	85	83					12																	77426865		2203	4300	6503	SO:0001819	synonymous_variant	144455	exon9			GACAGCTGCCAGG	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.1347A>T	chr12.hg19:g.77426865T>A		73.0	0.0		77.0	14.0	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	hg19	CCDS9016.1																																																																																			.	.		0.348	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		A	77426865	T	A	77426865	2	1	160	1	0	0	0	0	0	0	0	1	4874	1567	55	4		4	E2F7	12	77426865	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	5388935	77426865	56425030	251	24422										
ACSS3	79611	hgsc.bcm.edu	37	chr12	81647343	81647343	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tagacagaacattggccctgTggctgcttttcgaaatgcag	11	9	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:81647343T>A	ENST00000548058.1	+	15	2799	c.1889T>A	c.(1888-1890)gTg>gAg	p.V630E	ACSS3_ENST00000261206.3_Missense_Mutation_p.V629E|ACSS3_ENST00000548324.1_Missense_Mutation_p.V312E			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	630						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						ATTGGCCCTGTGGCTGCTTTT	0.438																																					p.V630E		Atlas-SNP	.											.	ACSS3	118	.	0			c.T1889A						.						101	103	102					12																	81647343		2203	4300	6503	SO:0001583	missense	79611	exon15			GCCCTGTGGCTGC		CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"Acyl-CoA synthetase family"	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.1889T>A	chr12.hg19:g.81647343T>A	ENSP00000449535:p.Val630Glu	188.0	0.0		191.0	33.0	NM_024560	Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	hg19	CCDS9022.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.890877	0.91889	.	.	ENSG00000111058	ENST00000548058;ENST00000261206;ENST00000548324	T;T;T	0.59083	0.29;0.29;0.29	6.03	6.03	0.97812	.	0.117511	0.56097	D	0.000023	T	0.77864	0.4194	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.76575	0.988;0.977	T	0.80852	-0.1197	10	0.87932	D	0	-12.8112	16.5724	0.84622	0.0:0.0:0.0:1.0	.	312;630	Q9H6R3-2;Q9H6R3	.;ACSS3_HUMAN	E	630;629;312	ENSP00000449535:V630E;ENSP00000261206:V629E;ENSP00000448965:V312E	ENSP00000261206:V629E	V	+	2	0	ACSS3	80171474	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	7.665000	0.83852	2.313000	0.78055	0.455000	0.32223	GTG	.	.		0.438	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560		A	81647343	T	A	81647343	3	1	160	1	0	0	0	0	1	0	0	0	190	1696	59	4	1947	4	ACSS3	12	81647343	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4220478	81647343	52204552	252	24423										
TMTC2	160335	hgsc.bcm.edu	37	chr12	83251361	83251361	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	attacctaccatttacaaagTaagtgattgttggctcttga	7	7	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:83251361T>A	ENST00000321196.3	+	2	1361		c.e2+2		TMTC2_ENST00000548305.1_Splice_Site|TMTC2_ENST00000549919.1_Splice_Site	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2						calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						ATTTACAAAGTAAGTGATTGT	0.373																																					.		Atlas-SNP	.											.	TMTC2	100	.	0			c.654+2T>A						.						58	53	55					12																	83251361		2203	4300	6503	SO:0001630	splice_region_variant	160335	exon2			ACAAAGTAAGTGA	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.654+2T>A	chr12.hg19:g.83251361T>A		82.0	0.0		94.0	14.0	NM_152588	B2RCU7|Q8N2K8	Splice_Site	SNP	ENST00000321196.3	hg19	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.032002	0.75504	.	.	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6569	0.68838	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMTC2	81775492	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.377000	0.79668	2.251000	0.74343	0.528000	0.53228	.	.	.		0.373	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588	Intron	A	83251361	T	A	83251361	5	1	160	1	0	0	0	0	0	0	1	0	16276	1652	57	4	662	4	TMTC2	12	83251361	Splice_Site	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1604018	83251361	50600534	253	24424										
TMTC3	160418	hgsc.bcm.edu	37	chr12	88542128	88542128	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctaaaagaaataaccttaatAgtaggtgtggttactgcctg	9	6	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:88542128A>T	ENST00000266712.6	+	2	256	c.36A>T	c.(34-36)atA>atT	p.I12I		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	12					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						TAACCTTAATAGTAGGTGTGG	0.328																																					p.I12I		Atlas-SNP	.											.	TMTC3	75	.	0			c.A36T						.						131	124	126					12																	88542128		2203	4300	6503	SO:0001819	synonymous_variant	160418	exon2			CTTAATAGTAGGT		CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"Tetratricopeptide (TTC) repeat domain containing"	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.36A>T	chr12.hg19:g.88542128A>T		145.0	0.0		212.0	41.0	NM_181783	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Silent	SNP	ENST00000266712.6	hg19	CCDS9032.1																																																																																			.	.		0.328	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783		T	88542128	A	T	88542128	2	4	160	1	0	0	0	0	0	0	0	1	16277	410	15	4		4	TMTC3	12	88542128	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	5290767	88542128	45309767	254	24425										
ATP2B1	490	hgsc.bcm.edu	37	chr12	90020267	90020267	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aacagccagttttgtaagttTcccttgtaaaacagattttt	6	7	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:90020267T>A	ENST00000428670.3	-	8	1549	c.1093A>T	c.(1093-1095)Aaa>Taa	p.K365*	ATP2B1_ENST00000393164.2_Nonsense_Mutation_p.K108*|ATP2B1_ENST00000348959.3_Nonsense_Mutation_p.K365*|ATP2B1_ENST00000359142.3_Nonsense_Mutation_p.K365*|ATP2B1_ENST00000261173.2_Nonsense_Mutation_p.K365*			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	365					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						TTTGTAAGTTTCCCTTGTAAA	0.328																																					p.K365X		Atlas-SNP	.											.	ATP2B1	191	.	0			c.A1093T						.						94	92	93					12																	90020267		2203	4300	6503	SO:0001587	stop_gained	490	exon7			TAAGTTTCCCTTG	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.1093A>T	chr12.hg19:g.90020267T>A	ENSP00000392043:p.Lys365*	64.0	0.0		65.0	9.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Nonsense_Mutation	SNP	ENST00000428670.3	hg19	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	T	43	10.122574	0.99342	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-27.4303	15.9838	0.80133	0.0:0.0:0.0:1.0	.	.	.	.	X	365;365;365;365;108	.	.	K	-	1	0	ATP2B1	88544398	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.040000	0.89188	2.178000	0.69098	0.533000	0.62120	AAA	.	.		0.328	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		A	90020267	T	A	90020267	4	1	160	1	0	0	0	0	0	1	0	0	1139	1792	62	4	2783	4	ATP2B1	12	90020267	Nonsense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1478139	90020267	43831628	255	24426										
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99898358	99898358	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctcattttctgaaggaaatGtatccagagaagcagatggt	10	6	2	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:99898358G>T	ENST00000547776.2	-	10	1333	c.1334C>A	c.(1333-1335)aCa>aAa	p.T445K	ANKS1B_ENST00000547010.1_Missense_Mutation_p.T25K|ANKS1B_ENST00000329257.7_Missense_Mutation_p.T445K	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	445						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TGAAGGAAATGTATCCAGAGA	0.383																																					p.T445K		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1334A						.						61	60	60					12																	99898358		1826	4080	5906	SO:0001583	missense	56899	exon10			GGAAATGTATCCA	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1334C>A	chr12.hg19:g.99898358G>T	ENSP00000449629:p.Thr445Lys	64.0	0.0		118.0	16.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.842736	0.51057	.	.	ENSG00000185046	ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000549866	T;T;T;T	0.59906	1.01;0.23;1.01;0.93	5.68	4.78	0.61160	.	0.404248	0.24499	N	0.037995	T	0.35219	0.0924	N	0.08118	0	0.80722	D	1	B;B;B	0.16603	0.018;0.018;0.005	B;B;B	0.21360	0.034;0.034;0.007	T	0.17319	-1.0373	9	.	.	.	-0.3752	12.3544	0.55167	0.0775:0.0:0.9225:0.0	.	411;25;445	F8VVQ4;Q7Z6G8-6;Q7Z6G8	.;.;ANS1B_HUMAN	K	445;25;445;24;411	ENSP00000449629:T445K;ENSP00000448512:T25K;ENSP00000331381:T445K;ENSP00000449894:T411K	.	T	-	2	0	ANKS1B	98422489	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.201000	0.42734	2.694000	0.91930	0.650000	0.86243	ACA	.	.		0.383	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		T	99898358	G	T	99898358	3	4	160	1	0	0	0	0	1	0	0	0	689	1377	48	3	2768	3	ANKS1B	12	99898358	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	9878091	99898358	33953537	256	24427										
RFX4	5992	hgsc.bcm.edu	37	chr12	107075779	107075779	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gttgacttacagatcataagGcagcagtttcctcagttaac	8	9	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:107075779G>T	ENST00000392842.1	+	5	738	c.324G>T	c.(322-324)agG>agT	p.R108S	RP11-482D24.2_ENST00000547531.1_RNA|RFX4_ENST00000229387.5_5'Flank|RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000357881.4_Missense_Mutation_p.R117S	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	108					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						AGATCATAAGGCAGCAGTTTC	0.493																																					p.R117S		Atlas-SNP	.											.	RFX4	218	.	0			c.G351T						.						149	134	139					12																	107075779		2203	4300	6503	SO:0001583	missense	5992	exon5			CATAAGGCAGCAG	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.324G>T	chr12.hg19:g.107075779G>T	ENSP00000376585:p.Arg108Ser	89.0	0.0		99.0	15.0	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Missense_Mutation	SNP	ENST00000392842.1	hg19	CCDS9106.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.351733	0.82132	.	.	ENSG00000111783	ENST00000392842;ENST00000549040;ENST00000357881;ENST00000266774;ENST00000551640	D;D;D;D	0.86432	-2.12;-2.12;-2.12;-2.12	5.29	1.91	0.25777	Winged helix-turn-helix transcription repressor DNA-binding (1);DNA-binding RFX (1);	0.000000	0.85682	D	0.000000	D	0.91469	0.7307	M	0.81179	2.53	0.80722	D	1	D;P;P	0.57899	0.981;0.873;0.684	D;B;B	0.69142	0.962;0.385;0.258	D	0.90154	0.4223	10	0.87932	D	0	-23.1125	7.6718	0.28463	0.4644:0.0:0.5356:0.0	.	117;117;108	Q33E94-2;Q33E94-4;Q33E94	.;.;RFX4_HUMAN	S	108;25;117;117;53	ENSP00000376585:R108S;ENSP00000447735:R25S;ENSP00000350552:R117S;ENSP00000448694:R53S	ENSP00000266774:R117S	R	+	3	2	RFX4	105599909	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.120000	0.41968	0.691000	0.31592	0.609000	0.83330	AGG	.	.		0.493	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491		T	107075779	G	T	107075779	3	4	160	1	0	0	0	0	1	0	0	0	13280	1194	42	3	416	3	RFX4	12	107075779	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	7177421	107075779	26776116	257	24428										
TBX5	6910	hgsc.bcm.edu	37	chr12	114793650	114793650	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtagcctgtccatgggctgcAcggtggtgacggtgcagctg	17	10	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:114793650A>G	ENST00000310346.4	-	9	1910	c.1244T>C	c.(1243-1245)gTg>gCg	p.V415A	TBX5_ENST00000405440.2_Missense_Mutation_p.V415A|TBX5_ENST00000349716.5_Missense_Mutation_p.V365A	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	415					apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		CATGGGCTGCACGGTGGTGAC	0.657																																					p.V415A	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											.	TBX5	188	.	0			c.T1244C						.						45	40	42					12																	114793650		2202	4300	6502	SO:0001583	missense	6910	exon9			GGCTGCACGGTGG	U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"T-boxes"	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.1244T>C	chr12.hg19:g.114793650A>G	ENSP00000309913:p.Val415Ala	60.0	0.0		73.0	15.0	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	hg19	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	A	17.46	3.395396	0.62066	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000448888;ENST00000405440	T;T;T	0.46451	0.87;0.87;0.87	4.99	4.99	0.66335	.	0.050104	0.85682	D	0.000000	T	0.32285	0.0824	L	0.36672	1.1	0.80722	D	1	B	0.20368	0.044	B	0.19148	0.024	T	0.10683	-1.0619	10	0.11485	T	0.65	.	14.7159	0.69269	1.0:0.0:0.0:0.0	.	415	Q99593	TBX5_HUMAN	A	365;415;312;415	ENSP00000337723:V365A;ENSP00000309913:V415A;ENSP00000384152:V415A	ENSP00000309913:V415A	V	-	2	0	TBX5	113278033	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	8.701000	0.91331	1.883000	0.54544	0.533000	0.62120	GTG	.	.		0.657	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		G	114793650	A	G	114793650	3	3	160	1	0	0	0	0	1	0	0	0	15676	159	6	2	316	2	TBX5	12	114793650	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	7717871	114793650	19058245	258	24429										
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123472882	123472882	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cagctccaagatgctggagtTgtcatgcctcatgacctggg	12	11	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:123472882T>A	ENST00000542749.1	-	18	2959	c.2896A>T	c.(2896-2898)Aac>Tac	p.N966Y	PITPNM2_ENST00000320201.4_Missense_Mutation_p.N966Y|PITPNM2_ENST00000280562.5_Missense_Mutation_p.N960Y|PITPNM2_ENST00000392428.1_Missense_Mutation_p.N687Y			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	966					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		ATGCTGGAGTTGTCATGCCTC	0.637																																					p.N966Y		Atlas-SNP	.											.	PITPNM2	105	.	0			c.A2896T						.						131	128	129					12																	123472882		2203	4300	6503	SO:0001583	missense	57605	exon19			TGGAGTTGTCATG	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.2896A>T	chr12.hg19:g.123472882T>A	ENSP00000437611:p.Asn966Tyr	42.0	0.0		55.0	13.0	NM_020845	Q9P271	Missense_Mutation	SNP	ENST00000542749.1	hg19	CCDS9242.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.466733	0.84425	.	.	ENSG00000090975	ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749	T;T;T;T	0.45668	1.22;1.21;0.89;1.21	5.21	5.21	0.72293	.	0.105878	0.64402	D	0.000007	T	0.44953	0.1318	L	0.44542	1.39	0.58432	D	0.999992	B;P	0.47962	0.014;0.903	B;P	0.49502	0.026;0.613	T	0.23547	-1.0185	10	0.28530	T	0.3	-12.6398	15.2349	0.73422	0.0:0.0:0.0:1.0	.	960;966	Q9BZ72-2;Q9BZ72	.;PITM2_HUMAN	Y	960;966;687;966	ENSP00000280562:N960Y;ENSP00000322218:N966Y;ENSP00000376223:N687Y;ENSP00000437611:N966Y	ENSP00000280562:N960Y	N	-	1	0	PITPNM2	122038835	1.000000	0.71417	0.903000	0.35520	0.954000	0.61252	7.799000	0.85936	2.193000	0.70182	0.397000	0.26171	AAC	.	.		0.637	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		A	123472882	T	A	123472882	3	1	160	1	0	0	0	0	1	0	0	0	11960	1812	63	4	1181	4	PITPNM2	12	123472882	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	8679232	123472882	10379013	259	24430										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124335527	124335527	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cgcacggagctgcccgagtcGgtgaaggcgctgttcaggcc	16	13	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:124335527G>A	ENST00000409039.3	+	34	5866	c.5841G>A	c.(5839-5841)tcG>tcA	p.S1947S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1947	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TGCCCGAGTCGGTGAAGGCGC	0.617																																					p.S1947S		Atlas-SNP	.											.	DNAH10	888	.	0			c.G5841A						.						41	45	44					12																	124335527		2146	4283	6429	SO:0001819	synonymous_variant	196385	exon34			CGAGTCGGTGAAG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.5841G>A	chr12.hg19:g.124335527G>A		101.0	0.0		108.0	19.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.617	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124335527	G	A	124335527	2	1	160	1	0	0	0	0	0	0	0	1	4600	1103	39	1		1	DNAH10	12	124335527	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	862645	124335527	9516368	260	24431										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126139052	126139052	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tatgagaaagaaattaaaaaTgaacctatgaattcttcggg	8	4	1	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:126139052T>C	ENST00000299308.3	+	9	3041	c.3033T>C	c.(3031-3033)aaT>aaC	p.N1011N	TMEM132B_ENST00000535886.1_Silent_p.N523N	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	1011						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		AAATTAAAAATGAACCTATGA	0.468																																					p.N1011N		Atlas-SNP	.											.	TMEM132B	207	.	0			c.T3033C						.						48	48	48					12																	126139052		1856	4092	5948	SO:0001819	synonymous_variant	114795	exon9			TAAAAATGAACCT	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.3033T>C	chr12.hg19:g.126139052T>C		88.0	0.0		90.0	13.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	hg19	CCDS41859.1																																																																																			.	.		0.468	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		C	126139052	T	C	126139052	2	2	160	1	0	0	0	0	0	0	0	1	16061	1461	51	2		2	TMEM132B	12	126139052	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1803525	126139052	7712843	261	24432										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	129558522	129558522	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atgtcatcctcgctactcatCacgatggagttcctggtggg	11	11	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr12:129558522C>G	ENST00000422113.2	-	9	3524	c.3198G>C	c.(3196-3198)gtG>gtC	p.V1066V	TMEM132D_ENST00000389441.4_Silent_p.V604V	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	1066					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CGCTACTCATCACGATGGAGT	0.512																																					p.V1066V		Atlas-SNP	.											TMEM132D,colon,carcinoma,0,1	TMEM132D	299	.	0			c.G3198C						.						174	165	168					12																	129558522		2203	4300	6503	SO:0001819	synonymous_variant	121256	exon9			ACTCATCACGATG	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.3198G>C	chr12.hg19:g.129558522C>G		128.0	1.0		159.0	51.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	hg19	CCDS9266.1																																																																																			.	.		0.512	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		G	129558522	C	G	129558522	2	3	160	1	0	0	0	0	0	0	0	1	16062	813	29	4		4	TMEM132D	12	129558522	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	3419470	129558522	4293373	262	24433										
FAM123A	219287	hgsc.bcm.edu	37	chr13	25745258	25745258	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccgagcgcccgttcttcttcAgcagcgagaagaagctgtgc	12	13	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr13:25745258A>G	ENST00000515384.1	-	1	1167	c.500T>C	c.(499-501)cTg>cCg	p.L167P	AMER2-AS1_ENST00000413501.1_lincRNA|AMER2_ENST00000357816.2_Missense_Mutation_p.L167P|AMER2_ENST00000381853.3_Missense_Mutation_p.L167P			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	167					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)										GTTCTTCTTCAGCAGCGAGAA	0.721																																					p.L167P		Atlas-SNP	.											.	.	.	.	0			c.T500C						.						11	14	13					13																	25745258		2139	4227	6366	SO:0001583	missense	219287	exon1			TTCTTCAGCAGCG	AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"-"	26360	protein-coding gene	gene with protein product		614659	"family with sequence similarity 123A"	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.500T>C	chr13.hg19:g.25745258A>G	ENSP00000426528:p.Leu167Pro	83.0	0.0		73.0	9.0	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	hg19	CCDS53859.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.590154	0.46214	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.22945	1.93;1.93;1.93	3.53	3.53	0.40419	.	0.338611	0.24198	U	0.040647	T	0.44414	0.1292	M	0.69358	2.11	0.21527	N	0.999652	D;D	0.63046	0.992;0.99	D;D	0.66847	0.947;0.912	T	0.18587	-1.0332	10	0.41790	T	0.15	-27.2837	11.4076	0.49906	1.0:0.0:0.0:0.0	.	167;167	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	P	167	ENSP00000350469:L167P;ENSP00000371277:L167P;ENSP00000426528:L167P	ENSP00000350469:L167P	L	-	2	0	FAM123A	24643258	0.997000	0.39634	0.003000	0.11579	0.956000	0.61745	5.084000	0.64462	1.471000	0.48121	0.254000	0.18369	CTG	.	.		0.721	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704		G	25745258	A	G	25745258	3	3	160	1	0	0	0	0	1	0	0	0	5427	188	7	2	1519	2	FAM123A	13	25745258	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10		25745258	89424620	263	24434										
ALG5	29880	hgsc.bcm.edu	37	chr13	37563694	37563694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctttgtcacttccatatttcTggcaatatttaaaagctacc	4	10	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr13:37563694T>C	ENST00000239891.3	-	5	440	c.374A>G	c.(373-375)cAg>cGg	p.Q125R	ALG5_ENST00000496689.1_5'UTR|ALG5_ENST00000413537.2_Missense_Mutation_p.Q125R|ALG5_ENST00000443765.1_Splice_Site	NM_013338.4	NP_037470.1	Q9Y673	ALG5_HUMAN	ALG5, dolichyl-phosphate beta-glucosyltransferase	125					cellular protein metabolic process (GO:0044267)|determination of left/right symmetry (GO:0007368)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dolichyl-phosphate beta-glucosyltransferase activity (GO:0004581)|oligosaccharyl transferase activity (GO:0004576)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;5.79e-07)|Epithelial(112;1.81e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00785)|BRCA - Breast invasive adenocarcinoma(63;0.0127)|GBM - Glioblastoma multiforme(144;0.0472)		TCCATATTTCTGGCAATATTT	0.303																																					p.Q125R		Atlas-SNP	.											.	ALG5	28	.	0			c.A374G						.						82	79	80					13																	37563694		2202	4299	6501	SO:0001583	missense	29880	exon5			TATTTCTGGCAAT	AF088028	CCDS9361.1, CCDS45033.1	13q13.1	2013-02-22	2013-02-21		ENSG00000120697	ENSG00000120697	2.4.1.117	"Glycosyltransferase family 2 domain containing"	20266	protein-coding gene	gene with protein product		604565	"asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate beta-glucosyltransferase)", "asparagine-linked glycosylation 5, dolichyl-phosphate beta-glucosyltransferase homolog (S. cerevisiae)"			10359825	Standard	NM_013338		Approved	bA421P11.2	uc001uvy.3	Q9Y673	OTTHUMG00000016741	ENST00000239891.3:c.374A>G	chr13.hg19:g.37563694T>C	ENSP00000239891:p.Gln125Arg	89.0	0.0		79.0	15.0	NM_013338	B4DR37|Q5TBA6	Missense_Mutation	SNP	ENST00000239891.3	hg19	CCDS9361.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.1|21.1	4.103337|4.103337	0.76983|0.76983	.|.	.|.	ENSG00000120697|ENSG00000120697	ENST00000443765|ENST00000239891;ENST00000413537	.|T;T	.|0.61627	.|0.09;0.09	5.91|5.91	5.91|5.91	0.95273|0.95273	.|Glycosyl transferase, family 2 (1);	.|0.263259	.|0.43416	.|D	.|0.000573	.|T	.|0.37046	.|0.0989	N|N	0.05050|0.05050	-0.12|-0.12	0.36269|0.36269	D|D	0.855048|0.855048	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	.|T	.|0.39165	.|-0.9627	.|10	.|0.19147	.|T	.|0.46	.|-20.6184	16.0084|16.0084	0.80380|0.80380	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|125	.|Q9Y673	.|ALG5_HUMAN	.|R	-1|125	.|ENSP00000239891:Q125R;ENSP00000389647:Q125R	.|ENSP00000239891:Q125R	.|Q	-|-	.|2	.|0	ALG5|ALG5	36461694|36461694	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.914000|0.914000	0.54420|0.54420	2.284000|2.284000	0.43478|0.43478	2.263000|2.263000	0.75096|0.75096	0.528000|0.528000	0.53228|0.53228	.|CAG	.	.		0.303	ALG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044528.2	NM_013338		C	37563694	T	C	37563694	3	2	160	1	0	0	0	0	1	0	0	0	521	1594	55	2	624	2	ALG5	13	37563694	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	11818436	37563694	77606184	264	24435										
OR4K15	81127	hgsc.bcm.edu	37	chr14	20443792	20443792	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gggtgacagaatttgtgttgCtgggactgtctagttcaagg	15	5	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:20443792C>A	ENST00000305051.5	+	1	190	c.115C>A	c.(115-117)Ctg>Atg	p.L39M		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATTTGTGTTGCTGGGACTGTC	0.403																																					p.L39M		Atlas-SNP	.											.	OR4K15	82	.	0			c.C115A						.						122	130	127					14																	20443792		2203	4299	6502	SO:0001583	missense	81127	exon1			GTGTTGCTGGGAC		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"GPCR / Class A : Olfactory receptors"	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.115C>A	chr14.hg19:g.20443792C>A	ENSP00000304077:p.Leu39Met	49.0	0.0		52.0	9.0	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	hg19	CCDS32026.1	.	.	.	.	.	.	.	.	.	.	.	12.47	1.948700	0.34377	.	.	ENSG00000169488	ENST00000305051	T	0.00637	6.05	3.41	0.211	0.15236	.	0.000000	0.34025	N	0.004321	T	0.01695	0.0054	M	0.76170	2.325	0.09310	N	1	D	0.71674	0.998	D	0.64237	0.923	T	0.48246	-0.9052	10	0.72032	D	0.01	.	0.7415	0.00974	0.1891:0.3871:0.1856:0.2381	.	39	Q8NH41	OR4KF_HUMAN	M	39	ENSP00000304077:L39M	ENSP00000304077:L39M	L	+	1	2	OR4K15	19513632	0.000000	0.05858	0.726000	0.30738	0.954000	0.61252	-1.281000	0.02802	0.104000	0.17725	0.467000	0.42956	CTG	.	.		0.403	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1			A	20443792	C	A	20443792	3	1	160	1	0	0	0	0	1	0	0	0	11079	796	28	3	117	3	OR4K15	14	20443792	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10		20443792	86905748	265	24436										
MYH7	4625	hgsc.bcm.edu	37	chr14	23885305	23885305	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gatctccatctcattgaggtCtccttccatcttcttcttca	4	14	7	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:23885305C>A	ENST00000355349.3	-	34	5023	c.4861G>T	c.(4861-4863)Gac>Tac	p.D1621Y	MIR208B_ENST00000401172.1_RNA|CTD-2201G16.1_ENST00000557368.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1621					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCATTGAGGTCTCCTTCCATC	0.612																																					p.D1621Y		Atlas-SNP	.											.	MYH7	349	.	0			c.G4861T						.						197	146	164					14																	23885305		2203	4300	6503	SO:0001583	missense	4625	exon34			TGAGGTCTCCTTC	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.4861G>T	chr14.hg19:g.23885305C>A	ENSP00000347507:p.Asp1621Tyr	85.0	0.0		76.0	10.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.135468	0.77662	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	T	0.81415	-1.49	4.55	4.55	0.56014	Myosin tail (1);	.	.	.	.	D	0.93236	0.7845	H	0.97131	3.945	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.95480	0.8559	9	0.87932	D	0	.	17.8682	0.88803	0.0:1.0:0.0:0.0	.	1621	P12883	MYH7_HUMAN	Y	1621;1626	ENSP00000347507:D1621Y	ENSP00000347507:D1621Y	D	-	1	0	MYH7	22955145	1.000000	0.71417	0.988000	0.46212	0.980000	0.70556	7.170000	0.77587	2.537000	0.85549	0.655000	0.94253	GAC	.	.		0.612	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23885305	C	A	23885305	3	1	160	1	0	0	0	0	1	0	0	0	10048	913	32	3	974	3	MYH7	14	23885305	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	3441513	23885305	83464235	266	24437										
FAM179B	23116	hgsc.bcm.edu	37	chr14	45473485	45473485	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctcaaattcctggcctcttAaaagcttcgaaggactatca	6	11	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:45473485A>T	ENST00000361577.3	+	4	2774	c.2560A>T	c.(2560-2562)Aaa>Taa	p.K854*	FAM179B_ENST00000382233.2_Nonsense_Mutation_p.K854*|FAM179B_ENST00000361462.2_Nonsense_Mutation_p.K854*|KLHL28_ENST00000553817.1_Intron	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	854										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						CTGGCCTCTTAAAAGCTTCGA	0.388																																					p.K854X		Atlas-SNP	.											.	FAM179B	115	.	0			c.A2560T						.						67	71	69					14																	45473485		2203	4300	6503	SO:0001587	stop_gained	23116	exon4			CCTCTTAAAAGCT	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.2560A>T	chr14.hg19:g.45473485A>T	ENSP00000355045:p.Lys854*	132.0	0.0		134.0	24.0	NM_015091	Q68D66|Q6PG27	Nonsense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	A	38	7.167669	0.98111	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233;ENST00000555874	.	.	.	5.24	5.24	0.73138	.	0.162866	0.41823	D	0.000814	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.7371	13.3595	0.60648	1.0:0.0:0.0:0.0	.	.	.	.	X	854;854;854;854;173	.	ENSP00000354917:K854X	K	+	1	0	FAM179B	44543235	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	5.925000	0.70062	1.980000	0.57719	0.383000	0.25322	AAA	.	.		0.388	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		T	45473485	A	T	45473485	4	4	160	1	0	0	0	0	0	1	0	0	5511	363	13	4	2574	4	FAM179B	14	45473485	Nonsense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	21588180	45473485	61876055	267	24438										
NID2	22795	hgsc.bcm.edu	37	chr14	52486849	52486849	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gaaggaaccaggagtattgtAgcaggtagctgcagggtgac	16	6	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:52486849A>T	ENST00000216286.5	-	13	2721	c.2722T>A	c.(2722-2724)Tac>Aac	p.Y908N	NID2_ENST00000541773.1_Missense_Mutation_p.Y807N	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	908	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GGAGTATTGTAGCAGGTAGCT	0.463																																					p.Y908N		Atlas-SNP	.											.	NID2	201	.	0			c.T2722A						.						127	110	116					14																	52486849		2203	4300	6503	SO:0001583	missense	22795	exon13			TATTGTAGCAGGT	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.2722T>A	chr14.hg19:g.52486849A>T	ENSP00000216286:p.Tyr908Asn	106.0	0.0		123.0	23.0	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.08|14.08	2.428638|2.428638	0.43122|0.43122	.|.	.|.	ENSG00000087303|ENSG00000087303	ENST00000556572|ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	.|D;D	.|0.89485	.|-2.52;-2.52	5.46|5.46	1.8|1.8	0.24995|0.24995	.|Thyroglobulin type-1 (1);EGF domain, merozoite surface protein 1-like (1);EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.|0.868339	.|0.10587	.|N	.|0.657154	D|D	0.84683|0.84683	0.5526|0.5526	N|N	0.14661|0.14661	0.345|0.345	0.33452|0.33452	D|D	0.583855|0.583855	.|B;P;P;P	.|0.48764	.|0.096;0.7;0.605;0.915	.|B;B;B;P	.|0.58780	.|0.102;0.111;0.34;0.845	T|T	0.80125|0.80125	-0.1513|-0.1513	5|10	.|0.30078	.|T	.|0.28	.|.	4.372|4.372	0.11253|0.11253	0.5085:0.0:0.3431:0.1484|0.5085:0.0:0.3431:0.1484	.|.	.|502;807;910;908	.|E7EPP3;Q14112-2;Q5CZI2;Q14112	.|.;.;.;NID2_HUMAN	Q|N	176|908;502;807;910	.|ENSP00000216286:Y908N;ENSP00000443730:Y807N	.|ENSP00000216286:Y908N	L|Y	-|-	2|1	0|0	NID2|NID2	51556599|51556599	0.811000|0.811000	0.29063|0.29063	0.997000|0.997000	0.53966|0.53966	0.990000|0.990000	0.78478|0.78478	0.469000|0.469000	0.22067|0.22067	0.383000|0.383000	0.24910|0.24910	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.		0.463	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			T	52486849	A	T	52486849	3	4	160	1	0	0	0	0	1	0	0	0	10424	420	15	4	1445	4	NID2	14	52486849	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	7013364	52486849	54862691	268	24439										
C14orf39	317761	hgsc.bcm.edu	37	chr14	60923752	60923752	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttcgtggaaaattctcagctCtctcttctacttcatcacta	4	12	6	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:60923752C>G	ENST00000321731.3	-	15	1400	c.1241G>C	c.(1240-1242)aGa>aCa	p.R414T		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	414					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		ATTCTCAGCTCTCTCTTCTAC	0.343																																					p.R414T		Atlas-SNP	.											.	C14orf39	79	.	0			c.G1241C						.						86	99	94					14																	60923752		2203	4299	6502	SO:0001583	missense	317761	exon15			TCAGCTCTCTCTT	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1241G>C	chr14.hg19:g.60923752C>G	ENSP00000324920:p.Arg414Thr	192.0	0.0		182.0	30.0	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	hg19	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	C	1.243	-0.620798	0.03636	.	.	ENSG00000179008	ENST00000321731	T	0.23552	1.9	5.32	-1.26	0.09376	.	0.885729	0.10032	N	0.724558	T	0.17704	0.0425	L	0.51422	1.61	0.09310	N	1	B	0.32160	0.358	B	0.25140	0.058	T	0.20371	-1.0277	10	0.52906	T	0.07	1.5903	3.5547	0.07860	0.2745:0.401:0.0:0.3245	.	414	Q8N1H7	S6OS1_HUMAN	T	414	ENSP00000324920:R414T	ENSP00000324920:R414T	R	-	2	0	C14orf39	59993505	0.003000	0.15002	0.012000	0.15200	0.006000	0.05464	-0.335000	0.07873	-0.140000	0.11394	-0.253000	0.11424	AGA	.	.		0.343	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		G	60923752	C	G	60923752	3	3	160	1	0	0	0	0	1	0	0	0	1774	913	32	4	538	4	C14orf39	14	60923752	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	8436903	60923752	46425788	269	24440										
RHOJ	57381	hgsc.bcm.edu	37	chr14	63757723	63757723	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acgctgttctgagggtcacaGctgctgttcaattatctgag	11	9	4	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:63757723G>A	ENST00000316754.3	+	5	1088	c.626G>A	c.(625-627)aGc>aAc	p.S209N		NM_020663.4	NP_065714.1	Q9H4E5	RHOJ_HUMAN	ras homolog family member J	209					actin cytoskeleton organization (GO:0030036)|GTP catabolic process (GO:0006184)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.00326)|all cancers(60;0.031)|BRCA - Breast invasive adenocarcinoma(234;0.119)		GAGGGTCACAGCTGCTGTTCA	0.498																																					p.S209N		Atlas-SNP	.											.	RHOJ	45	.	0			c.G626A						.						102	94	96					14																	63757723		2203	4300	6503	SO:0001583	missense	57381	exon5			GTCACAGCTGCTG	AK027351	CCDS9757.1	14q23.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000126785	ENSG00000126785			688	protein-coding gene	gene with protein product		607653	"RAS-like, family 7, member B", "ras homolog gene family, member J"	RASL7B, ARHJ		10967094	Standard	NM_020663		Approved	FLJ14445, TCL	uc001xgb.2	Q9H4E5	OTTHUMG00000140342	ENST00000316754.3:c.626G>A	chr14.hg19:g.63757723G>A	ENSP00000316729:p.Ser209Asn	70.0	0.0		84.0	19.0	NM_020663	Q96KC1	Missense_Mutation	SNP	ENST00000316754.3	hg19	CCDS9757.1	.	.	.	.	.	.	.	.	.	.	G	8.763	0.923982	0.18056	.	.	ENSG00000126785	ENST00000316754	T	0.67698	-0.28	5.86	2.09	0.27110	.	3.757210	0.00659	N	0.000582	T	0.45216	0.1331	N	0.03154	-0.405	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18618	-1.0331	10	0.16896	T	0.51	.	9.1268	0.36821	0.3347:0.0:0.6653:0.0	.	209	Q9H4E5	RHOJ_HUMAN	N	209	ENSP00000316729:S209N	ENSP00000316729:S209N	S	+	2	0	RHOJ	62827476	1.000000	0.71417	0.465000	0.27155	0.952000	0.60782	3.740000	0.55082	0.127000	0.18452	0.655000	0.94253	AGC	.	.		0.498	RHOJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276975.3			A	63757723	G	A	63757723	3	1	160	1	0	0	0	0	1	0	0	0	13356	971	34	3	644	3	RHOJ	14	63757723	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	2833971	63757723	43591817	270	24441										
GPHN	10243	hgsc.bcm.edu	37	chr14	67589018	67589018	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	taccagggaagattcgagacAgcaatcgttcaactcttcta	8	10	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:67589018A>T	ENST00000315266.5	+	16	2694	c.1573A>T	c.(1573-1575)Agc>Tgc	p.S525C	GPHN_ENST00000543237.1_Missense_Mutation_p.S571C|GPHN_ENST00000478722.1_Missense_Mutation_p.S558C|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000305960.9_Missense_Mutation_p.S494C	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	525	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		GATTCGAGACAGCAATCGTTC	0.383			T	MLL	AL																																p.S558C		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.A1672T						.						129	115	120					14																	67589018		2203	4300	6503	SO:0001583	missense	10243	exon17			CGAGACAGCAATC	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.1573A>T	chr14.hg19:g.67589018A>T	ENSP00000312771:p.Ser525Cys	142.0	0.0		170.0	33.0	NM_020806	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	hg19	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.957333	0.92726	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000305960;ENST00000555503	T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22	6.17	6.17	0.99709	Molybdenum cofactor synthesis (1);Molybdopterin binding (4);	0.037143	0.85682	D	0.000000	D	0.88969	0.6582	M	0.84156	2.68	0.80722	D	1	P;D;P;D	0.76494	0.722;0.999;0.859;0.999	P;D;P;D	0.72338	0.474;0.966;0.609;0.977	D	0.90249	0.4292	10	0.87932	D	0	-7.7264	16.8222	0.85835	1.0:0.0:0.0:0.0	.	494;571;525;558	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2	.;.;GEPH_HUMAN;.	C	525;558;571;494;50	ENSP00000312771:S525C;ENSP00000417901:S558C;ENSP00000438404:S571C;ENSP00000303019:S494C;ENSP00000452009:S50C	ENSP00000303019:S494C	S	+	1	0	GPHN	66658771	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.911000	0.69939	2.371000	0.80710	0.533000	0.62120	AGC	.	.		0.383	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		T	67589018	A	T	67589018	3	4	160	1	0	0	0	0	1	0	0	0	6618	188	7	4	1738	4	GPHN	14	67589018	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	3831295	67589018	39760522	271	24442										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68264872	68264872	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctttggcttctcaggagggcTgcggctactgatctcatcca	11	12	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:68264872T>A	ENST00000347230.4	-	11	2245	c.2107A>T	c.(2107-2109)Agc>Tgc	p.S703C	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.S703C	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	703					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		TCAGGAGGGCTGCGGCTACTG	0.517																																					p.S703C		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A2107T						.						52	55	54					14																	68264872		2203	4300	6503	SO:0001583	missense	23503	exon11			GAGGGCTGCGGCT	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.2107A>T	chr14.hg19:g.68264872T>A	ENSP00000251119:p.Ser703Cys	65.0	0.0		68.0	9.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.056486	0.36277	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.28666	1.74;1.6	5.95	-11.1	0.00147	.	3.301100	0.00397	N	0.000052	T	0.19765	0.0475	L	0.29908	0.895	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.001;0.001	T	0.17961	-1.0352	10	0.56958	D	0.05	19.721	9.5985	0.39589	0.0817:0.5657:0.1651:0.1874	.	703;703;703	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	C	703;682;703	ENSP00000251119:S703C;ENSP00000450603:S703C	ENSP00000251119:S703C	S	-	1	0	ZFYVE26	67334625	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.022000	0.12480	-2.065000	0.00887	-0.899000	0.02877	AGC	.	.		0.517	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68264872	T	A	68264872	3	1	160	1	0	0	0	0	1	0	0	0	17683	1580	55	4	5640	4	ZFYVE26	14	68264872	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	675854	68264872	39084668	272	24443										
COQ6	51004	hgsc.bcm.edu	37	chr14	74428174	74428177	+	Frame_Shift_Del	DEL	GTCC	GTCC	-													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttagggatgcagcccacagaGtccatccgcttgcaggacag					rs528712914		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	GTCC	GTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:74428174_74428177delGTCC	ENST00000334571.2	+	10	1151_1154	c.1111_1114delGTCC	c.(1111-1116)gtccatfs	p.VH371fs	COQ6_ENST00000238709.4_Frame_Shift_Del_p.VH296fs|COQ6_ENST00000554920.1_Intron|ENTPD5_ENST00000557325.1_Intron|COQ6_ENST00000394026.4_Frame_Shift_Del_p.VH346fs	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	371					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		AGCCCACAGAGTCCATCCGCTTGC	0.529																																					p.370_371del		Atlas-INDEL	.											.	COQ6	27	.	0			c.1110_1113del						.																																			SO:0001589	frameshift_variant	51004	exon10			.	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"coenzyme Q6 homolog (yeast)", "coenzyme Q6 homolog, monooxygenase (yeast)", "coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.1111_1114delGTCC	chr14.hg19:g.74428174_74428177delGTCC	ENSP00000333946:p.Val371fs	79.0	0.0		63.0	13.0	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Frame_Shift_Del	DEL	ENST00000334571.2	hg19	CCDS9823.1																																																																																			.	.		0.529	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1			-	74428177	GTCC	-	74428174	7	5	160	1	0	1	0	1	0	0	0	0	3751	1029	36	0	1149	0	COQ6	14	74428174	Frame_Shift_Del	DEL	GTCC	TCGA-DD-AACI-01A-11D-A40R-10	6163302	74428174	32921366	273	24444										
LTBP2	4053	hgsc.bcm.edu	37	chr14	75018988	75018988	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tccctggaggctccctgtccGgctgcgggataggcaggtgg	17	12	0	0	rs371940681		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:75018988G>A	ENST00000261978.4	-	6	1687	c.1301C>T	c.(1300-1302)cCg>cTg	p.P434L	CTD-2207P18.1_ENST00000554552.1_lincRNA|LTBP2_ENST00000556690.1_Missense_Mutation_p.P434L|LTBP2_ENST00000557425.1_Intron	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	434					protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CTCCCTGTCCGGCTGCGGGAT	0.672																																					p.P434L		Atlas-SNP	.											.	LTBP2	158	.	0			c.C1301T						.		LEU/PRO	0,4404		0,0,2202	33	36	35		1301	-5.3	0	14		35	1,8581		0,1,4290	no	missense	LTBP2	NM_000428.2	98	0,1,6492	AA,AG,GG		0.0117,0.0,0.0077	benign	434/1822	75018988	1,12985	2202	4291	6493	SO:0001583	missense	4053	exon6			CTGTCCGGCTGCG		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.1301C>T	chr14.hg19:g.75018988G>A	ENSP00000261978:p.Pro434Leu	146.0	0.0		102.0	25.0	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	hg19	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	g	11.35	1.614217	0.28712	0.0	1.17E-4	ENSG00000119681	ENST00000261978;ENST00000556690	T;T	0.16897	2.31;2.31	4.63	-5.33	0.02713	.	0.544954	0.13688	N	0.369745	T	0.05686	0.0149	N	0.05510	-0.035	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.41088	-0.9528	10	0.07813	T	0.8	.	9.3654	0.38221	0.2885:0.0:0.5874:0.1241	.	434	Q14767	LTBP2_HUMAN	L	434	ENSP00000261978:P434L;ENSP00000451477:P434L	ENSP00000261978:P434L	P	-	2	0	LTBP2	74088741	0.127000	0.22367	0.001000	0.08648	0.916000	0.54674	0.758000	0.26447	-1.187000	0.02709	-0.387000	0.06579	CCG	.	.		0.672	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		A	75018988	G	A	75018988	3	1	160	1	0	0	0	0	1	0	0	0	9083	1116	39	1	4288	1	LTBP2	14	75018988	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	590814	75018988	32330552	274	24445										
KCNK13	56659	hgsc.bcm.edu	37	chr14	90650745	90650745	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gcacagcctccatcctcatcTcttgctgcgcctcagccatg	7	18	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:90650745T>C	ENST00000282146.4	+	2	1066	c.625T>C	c.(625-627)Tct>Cct	p.S209P		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	209					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				CATCCTCATCTCTTGCTGCGC	0.562																																					p.S209P		Atlas-SNP	.											.	KCNK13	76	.	0			c.T625C						.						168	141	150					14																	90650745		2203	4300	6503	SO:0001583	missense	56659	exon2			CTCATCTCTTGCT	AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.625T>C	chr14.hg19:g.90650745T>C	ENSP00000282146:p.Ser209Pro	109.0	0.0		78.0	22.0	NM_022054	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	hg19	CCDS9889.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.687762	0.48097	.	.	ENSG00000152315	ENST00000282146	T	0.45668	0.89	5.31	5.31	0.75309	Ion transport 2 (1);	0.295030	0.21561	N	0.072576	T	0.62612	0.2442	M	0.73598	2.24	0.80722	D	1	D	0.58620	0.983	D	0.63703	0.917	T	0.63368	-0.6653	10	0.42905	T	0.14	.	15.2351	0.73422	0.0:0.0:0.0:1.0	.	209	Q9HB14	KCNKD_HUMAN	P	209	ENSP00000282146:S209P	ENSP00000282146:S209P	S	+	1	0	KCNK13	89720498	1.000000	0.71417	0.981000	0.43875	0.312000	0.27988	6.166000	0.71896	2.003000	0.58678	0.533000	0.62120	TCT	.	.		0.562	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		C	90650745	T	C	90650745	3	2	160	1	0	0	0	0	1	0	0	0	8070	1551	54	2	631	2	KCNK13	14	90650745	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	15631757	90650745	16698795	275	24446										
DICER1	23405	hgsc.bcm.edu	37	chr14	95577654	95577654	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctgttctaaccaatactaacTgcttttgggtagcactgcct	7	11	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:95577654T>A	ENST00000526495.1	-	16	2547	c.2256A>T	c.(2254-2256)gcA>gcT	p.A752A	DICER1_ENST00000527414.1_Splice_Site_p.A752A|DICER1_ENST00000393063.1_Splice_Site_p.A752A|DICER1_ENST00000343455.3_Splice_Site_p.A752A|DICER1_ENST00000541352.1_Splice_Site_p.A752A			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	752					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		CAATACTAACTGCTTTTGGGT	0.443			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.A752A		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.A2256T						.						271	252	259					14																	95577654		2203	4300	6503	SO:0001630	splice_region_variant	23405	exon15	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	ACTAACTGCTTTT	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.2256+1A>T	chr14.hg19:g.95577654T>A		103.0	0.0		72.0	9.0	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Silent	SNP	ENST00000526495.1	hg19	CCDS9931.1																																																																																			.	.		0.443	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1		Silent	A	95577654	T	A	95577654	5	1	160	1	0	0	0	0	0	0	1	0	4523	1594	55	4	3568	4	DICER1	14	95577654	Splice_Site	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4926909	95577654	11771886	276	24447										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414392	105414392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cgccacagacaggtccccctCcagccacgcaccatccagct	7	21	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr14:105414392C>T	ENST00000333244.5	-	7	7515	c.7396G>A	c.(7396-7398)Gag>Aag	p.E2466K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2466						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			AGGTCCCCCTCCAGCCACGCA	0.622																																					p.E2466K		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G7396A						.						124	147	139					14																	105414392		2061	4199	6260	SO:0001583	missense	113146	exon7			CCCCCTCCAGCCA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7396G>A	chr14.hg19:g.105414392C>T	ENSP00000353114:p.Glu2466Lys	137.0	0.0		98.0	21.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	9.667	1.145750	0.21288	.	.	ENSG00000185567	ENST00000333244	T	0.00776	5.71	3.74	2.82	0.32997	.	.	.	.	.	T	0.00724	0.0024	L	0.37750	1.13	0.09310	N	1	B	0.32467	0.372	B	0.29077	0.098	T	0.36648	-0.9739	9	0.05959	T	0.93	.	10.3572	0.43972	0.1969:0.8031:0.0:0.0	.	2466	Q8IVF2	AHNK2_HUMAN	K	2466	ENSP00000353114:E2466K	ENSP00000353114:E2466K	E	-	1	0	AHNAK2	104485437	0.233000	0.23772	0.028000	0.17463	0.038000	0.13279	1.257000	0.32932	0.532000	0.28657	0.485000	0.47835	GAG	.	.		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105414392	C	T	105414392	3	4	160	1	0	0	0	0	1	0	0	0	415	864	30	3	9995	3	AHNAK2	14	105414392	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	9836738	105414392	1935148	277	24448										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25971123	25971123	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gctgaaaacagagacatgcaAacaaggagcaggacacacca	10	10	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:25971123A>G	ENST00000356865.6	-	5	1065	c.954T>C	c.(952-954)gtT>gtC	p.V318V		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	318					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GAGACATGCAAACAAGGAGCA	0.562																																					p.V318V		Atlas-SNP	.											.	ATP10A	270	.	0			c.T954C						.						134	108	117					15																	25971123		2203	4300	6503	SO:0001819	synonymous_variant	57194	exon5			CATGCAAACAAGG	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.954T>C	chr15.hg19:g.25971123A>G		55.0	0.0		44.0	13.0	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	hg19	CCDS32178.1																																																																																			.	.		0.562	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		G	25971123	A	G	25971123	2	3	160	1	0	0	0	0	0	0	0	1	1116	1	1	2		2	ATP10A	15	25971123	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10		25971123	76560269	278	24449										
RYR3	6263	hgsc.bcm.edu	37	chr15	34072456	34072456	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctggcctcgctggcagctgCcataccagtggcattcctgg	12	14	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:34072456C>T	ENST00000389232.4	+	65	9252	c.9182C>T	c.(9181-9183)gCc>gTc	p.A3061V	RYR3_ENST00000415757.3_Missense_Mutation_p.A3061V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3061					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CTGGCAGCTGCCATACCAGTG	0.567																																					p.A3061V		Atlas-SNP	.											.	RYR3	760	.	0			c.C9182T						.						52	55	54					15																	34072456		1946	4155	6101	SO:0001583	missense	6263	exon65			CAGCTGCCATACC		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.9182C>T	chr15.hg19:g.34072456C>T	ENSP00000373884:p.Ala3061Val	129.0	0.0		99.0	14.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	35	5.522190	0.96416	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.62788	-0.0;-0.0	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.81312	0.4796	M	0.84433	2.695	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.66084	0.941;0.913	D	0.83775	0.0222	10	0.72032	D	0.01	.	19.1786	0.93614	0.0:1.0:0.0:0.0	.	3061;3061	Q15413-2;Q15413	.;RYR3_HUMAN	V	3061	ENSP00000373884:A3061V;ENSP00000399610:A3061V	ENSP00000354735:A3061V	A	+	2	0	RYR3	31859748	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.492000	0.81482	2.768000	0.95171	0.650000	0.86243	GCC	.	.		0.567	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34072456	C	T	34072456	3	4	160	1	0	0	0	0	1	0	0	0	13785	739	26	3	9440	3	RYR3	15	34072456	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	8101333	34072456	68458936	279	24450										
AQR	9716	hgsc.bcm.edu	37	chr15	35253000	35253000	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tttgacaatctctttttcatAtatatcttcaataacctgtt	2	8	4	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:35253000A>G	ENST00000156471.5	-	3	373	c.148T>C	c.(148-150)Tat>Cat	p.Y50H		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	50					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TCTTTTTCATATATATCTTCA	0.274																																					p.Y50H		Atlas-SNP	.											.	AQR	139	.	0			c.T148C						.						49	45	46					15																	35253000		1752	4024	5776	SO:0001583	missense	9716	exon3			TTTCATATATATC	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.148T>C	chr15.hg19:g.35253000A>G	ENSP00000156471:p.Tyr50His	164.0	0.0		195.0	39.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	hg19	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	A	19.50	3.839892	0.71488	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.96396	-4.0	5.26	5.26	0.73747	.	0.244719	0.42964	D	0.000632	D	0.98394	0.9466	M	0.93375	3.41	0.58432	D	0.999994	D	0.89917	1.0	D	0.80764	0.994	D	0.98850	1.0758	10	0.49607	T	0.09	-16.7426	12.6656	0.56840	1.0:0.0:0.0:0.0	.	50	O60306	AQR_HUMAN	H	50	ENSP00000156471:Y50H	ENSP00000156471:Y50H	Y	-	1	0	AQR	33040292	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.367000	0.52350	2.205000	0.71048	0.455000	0.32223	TAT	.	.		0.274	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		G	35253000	A	G	35253000	3	3	160	1	0	0	0	0	1	0	0	0	835	449	16	2	4441	2	AQR	15	35253000	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1180544	35253000	67278392	280	24451										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48062884	48062884	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gagtccgcccagtcatgcacAgactccagtggaagttttgc	11	12	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:48062884A>G	ENST00000316364.5	+	19	2563	c.2124A>G	c.(2122-2124)acA>acG	p.T708T	SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000537942.1_Silent_p.T646T|SEMA6D_ENST00000389432.2_Silent_p.T665T|SEMA6D_ENST00000536845.2_Silent_p.T708T|SEMA6D_ENST00000389433.2_Silent_p.T689T|SEMA6D_ENST00000354744.4_Silent_p.T652T|SEMA6D_ENST00000389428.3_Silent_p.T633T|SEMA6D_ENST00000358066.4_Silent_p.T646T|SEMA6D_ENST00000558014.1_Silent_p.T646T|SEMA6D_ENST00000355997.3_3'UTR	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	708					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AGTCATGCACAGACTCCAGTG	0.443																																					p.T708T		Atlas-SNP	.											.	SEMA6D	322	.	0			c.A2124G						.						96	90	92					15																	48062884		2198	4297	6495	SO:0001819	synonymous_variant	80031	exon19			ATGCACAGACTCC	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.2124A>G	chr15.hg19:g.48062884A>G		114.0	0.0		95.0	30.0	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	hg19	CCDS32225.1																																																																																			.	.		0.443	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		G	48062884	A	G	48062884	2	3	160	1	0	0	0	0	0	0	0	1	14057	175	7	2		2	SEMA6D	15	48062884	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	12809884	48062884	54468508	281	24452										
LEO1	123169	hgsc.bcm.edu	37	chr15	52244087	52244087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	caggatcacgaccagccattGgcaagattctaatcttctgt	8	11	4	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:52244087G>A	ENST00000299601.5	-	9	1625	c.1565C>T	c.(1564-1566)cCa>cTa	p.P522L	LEO1_ENST00000315141.5_Missense_Mutation_p.P462L	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	522					endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		ACCAGCCATTGGCAAGATTCT	0.443																																					p.P522L	Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)	Atlas-SNP	.											.	LEO1	46	.	0			c.C1565T						.						195	161	172					15																	52244087		2195	4293	6488	SO:0001583	missense	123169	exon9			GCCATTGGCAAGA	AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.1565C>T	chr15.hg19:g.52244087G>A	ENSP00000299601:p.Pro522Leu	62.0	0.0		62.0	10.0	NM_138792	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	hg19	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	.	33	5.287477	0.95517	.	.	ENSG00000166477	ENST00000299601;ENST00000538386;ENST00000315141	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.75606	0.3872	M	0.62723	1.935	0.80722	D	1	D;D	0.76494	0.978;0.999	P;D	0.72338	0.883;0.977	T	0.68352	-0.5431	9	0.11794	T	0.64	.	19.6961	0.96026	0.0:0.0:1.0:0.0	.	462;522	Q8WVC0-2;Q8WVC0	.;LEO1_HUMAN	L	522;500;462	.	ENSP00000299601:P522L	P	-	2	0	LEO1	50031379	1.000000	0.71417	0.984000	0.44739	0.993000	0.82548	9.623000	0.98386	2.654000	0.90174	0.650000	0.86243	CCA	.	.		0.443	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792		A	52244087	G	A	52244087	3	1	160	1	0	0	0	0	1	0	0	0	8735	1348	47	3	451	3	LEO1	15	52244087	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	4181203	52244087	50287305	282	24453										
RNF111	54778	hgsc.bcm.edu	37	chr15	59350608	59350608	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tggaatcacaagctactagcGcttccattaacaattcaaat	5	10	2	0	rs201513331	byFrequency	TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:59350608G>C	ENST00000557998.1	+	5	1512	c.1225G>C	c.(1225-1227)Gct>Cct	p.A409P	RNF111_ENST00000348370.4_Missense_Mutation_p.A409P|RNF111_ENST00000561186.1_Missense_Mutation_p.A409P|RNF111_ENST00000434298.1_Missense_Mutation_p.A409P|RNF111_ENST00000559209.1_Missense_Mutation_p.A409P	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	409	Ser-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		AGCTACTAGCGCTTCCATTAA	0.413																																					p.A409P	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.G1225C						.						214	214	214					15																	59350608		2192	4291	6483	SO:0001583	missense	54778	exon5			ACTAGCGCTTCCA	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1225G>C	chr15.hg19:g.59350608G>C	ENSP00000452732:p.Ala409Pro	80.0	0.0		78.0	8.0	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Missense_Mutation	SNP	ENST00000557998.1	hg19	CCDS58366.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.952249	0.73787	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	T;T	0.16597	2.33;2.33	5.98	2.79	0.32731	.	0.354886	0.33272	N	0.005082	T	0.12689	0.0308	N	0.14661	0.345	0.34297	D	0.683947	P;P;P	0.47604	0.898;0.895;0.874	P;B;P	0.49192	0.602;0.397;0.521	T	0.18903	-1.0322	10	0.87932	D	0	-8.5652	5.7735	0.18267	0.2461:0.0:0.5898:0.1641	.	409;409;409	Q6ZNA4-3;Q6ZNA4;Q6ZNA4-2	.;RN111_HUMAN;.	P	409	ENSP00000288199:A409P;ENSP00000393641:A409P	ENSP00000288199:A409P	A	+	1	0	RNF111	57137900	0.993000	0.37304	0.992000	0.48379	0.964000	0.63967	0.329000	0.19698	0.824000	0.34613	0.585000	0.79938	GCT	.	G|1.000;A|0.000		0.413	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		C	59350608	G	C	59350608	3	2	160	1	0	0	0	0	1	0	0	0	13440	1087	38	4	1239	4	RNF111	15	59350608	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	7106521	59350608	43180784	283	24454										
HCN4	10021	hgsc.bcm.edu	37	chr15	73636059	73636059	+	Frame_Shift_Del	DEL	G	G	-													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttgaagacaatccagggtgtGgtgttctcatccttgaagaa							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:73636059delG	ENST00000261917.3	-	2	1869	c.876delC	c.(874-876)accfs	p.T293fs	RP11-272D12.1_ENST00000558742.1_RNA|RP11-272D12.1_ENST00000557981.1_RNA	NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	293					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		TCCAGGGTGTGGTGTTCTCAT	0.507																																					p.T293fs		Atlas-INDEL	.											.	HCN4	150	.	0			c.877delA						.						99	88	92					15																	73636059		2198	4297	6495	SO:0001589	frameshift_variant	10021	exon2			.	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.876delC	chr15.hg19:g.73636059delG	ENSP00000261917:p.Thr293fs	125.0	0.0		159.0	37.0	NM_005477	Q9UMQ7	Frame_Shift_Del	DEL	ENST00000261917.3	hg19	CCDS10248.1																																																																																			.	.		0.507	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		-	73636059	G	-	73636059	7	5	160	1	0	1	0	1	0	0	0	0	7008	1335	47	0	2763	0	HCN4	15	73636059	Frame_Shift_Del	DEL	G	TCGA-DD-AACI-01A-11D-A40R-10	14285451	73636059	28895333	284	24455										
C15orf60	283677	hgsc.bcm.edu	37	chr15	73843382	73843382	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gctggcacaatacataaccgTgcaggtgcctgatggaaaca	11	10	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:73843382T>C	ENST00000331090.6	+	4	465	c.437T>C	c.(436-438)gTg>gCg	p.V146A	C15orf60_ENST00000560581.1_Missense_Mutation_p.V118A	NM_001042367.1	NP_001035826.1	Q7Z4M0	RE114_HUMAN		146					DNA recombination (GO:0006310)|meiotic nuclear division (GO:0007126)					endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|pancreas(1)|prostate(2)	17						TACATAACCGTGCAGGTGCCT	0.532																																					p.V146A		Atlas-SNP	.											.	C15orf60	26	.	0			c.T437C						.						65	67	66					15																	73843382		1979	4149	6128	SO:0001583	missense	283677	exon4			TAACCGTGCAGGT																												ENST00000331090.6:c.437T>C	chr15.hg19:g.73843382T>C	ENSP00000328423:p.Val146Ala	193.0	0.0		180.0	42.0	NM_001042367		Missense_Mutation	SNP	ENST00000331090.6	hg19	CCDS45296.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.689407	0.68271	.	.	ENSG00000183324	ENST00000331090	T	0.58940	0.3	5.52	5.52	0.82312	.	0.067578	0.64402	D	0.000018	T	0.73666	0.3616	M	0.68952	2.095	0.18873	N	0.999988	D	0.71674	0.998	D	0.77557	0.99	T	0.68288	-0.5448	10	0.72032	D	0.01	-22.7799	14.4641	0.67472	0.0:0.0:0.0:1.0	.	146	Q7Z4M0	CO060_HUMAN	A	146	ENSP00000328423:V146A	ENSP00000328423:V146A	V	+	2	0	C15orf60	71630435	0.986000	0.35501	0.020000	0.16555	0.076000	0.17211	3.731000	0.55013	2.079000	0.62486	0.496000	0.49642	GTG	.	.		0.532	C15orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419069.1			C	73843382	T	C	73843382	3	2	160	1	0	0	0	0	1	0	0	0	1810	1696	59	2	451	2	C15orf60	15	73843382	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	207323	73843382	28688010	285	24456										
CLK3	1198	hgsc.bcm.edu	37	chr15	74914530	74914530	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aggagggtcacctggtgtgcCggatcggcgattggctccaa	16	10	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:74914530C>A	ENST00000395066.3	+	4	1344	c.883C>A	c.(883-885)Cgg>Agg	p.R295R	CLK3_ENST00000352989.5_Silent_p.R147R|CLK3_ENST00000345005.4_Silent_p.R147R|CLK3_ENST00000348245.3_Intron	NM_001130028.1	NP_001123500.1	P49761	CLK3_HUMAN	CDC-like kinase 3	295					protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	cytoplasmic vesicle (GO:0031410)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)|stomach(2)|urinary_tract(1)	15						CCTGGTGTGCCGGATCGGCGA	0.572																																					p.R295R	Ovarian(133;694 1754 28950 29027 31859)	Atlas-SNP	.											CLK3_ENST00000454830,colon,carcinoma,0,2	CLK3	78	.	0			c.C883A						.						144	117	126					15																	74914530		2197	4296	6493	SO:0001819	synonymous_variant	1198	exon4			GTGTGCCGGATCG	L29220	CCDS10265.1, CCDS45304.1	15q24	2008-05-02			ENSG00000179335	ENSG00000179335		"CDC-like kinases"	2071	protein-coding gene	gene with protein product		602990				7990150, 9856501	Standard	NM_003992		Approved	clk3	uc010uln.2	P49761	OTTHUMG00000141320	ENST00000395066.3:c.883C>A	chr15.hg19:g.74914530C>A		108.0	0.0		113.0	39.0	NM_001130028	D3DW59|Q53Y48|Q9BRS3|Q9BUJ7	Silent	SNP	ENST00000395066.3	hg19	CCDS45304.1																																																																																			.	.		0.572	CLK3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390442.3			A	74914530	C	A	74914530	2	1	160	1	0	0	0	0	0	0	0	1	3540	643	23	1		1	CLK3	15	74914530	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	1071148	74914530	27616862	286	24457										
IREB2	3658	hgsc.bcm.edu	37	chr15	78765662	78765662	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	accagaggtggttggatgtgAgttaactgggtcatcaaacc	13	7	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:78765662A>T	ENST00000258886.8	+	8	1111	c.962A>T	c.(961-963)gAg>gTg	p.E321V	IREB2_ENST00000560440.1_Missense_Mutation_p.E321V	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	321					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		GTTGGATGTGAGTTAACTGGG	0.398																																					p.E321V	NSCLC(200;764 2208 35157 49871 50830)	Atlas-SNP	.											.	IREB2	106	.	0			c.A962T						.						262	234	244					15																	78765662		2196	4293	6489	SO:0001583	missense	3658	exon8			GATGTGAGTTAAC	M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.962A>T	chr15.hg19:g.78765662A>T	ENSP00000258886:p.Glu321Val	141.0	0.0		138.0	24.0	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	hg19	CCDS10302.1	.	.	.	.	.	.	.	.	.	.	A	34	5.316948	0.95682	.	.	ENSG00000136381	ENST00000258886	T	0.47177	0.85	6.08	6.08	0.98989	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 2 (1);	0.042164	0.85682	D	0.000000	T	0.64316	0.2587	M	0.63208	1.945	0.58432	D	0.999999	D;D	0.58970	0.984;0.983	P;P	0.60236	0.855;0.871	T	0.66870	-0.5814	10	0.87932	D	0	.	16.6512	0.85203	1.0:0.0:0.0:0.0	.	321;321	P48200;Q8WVK6	IREB2_HUMAN;.	V	321	ENSP00000258886:E321V	ENSP00000258886:E321V	E	+	2	0	IREB2	76552717	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.261000	0.78400	2.333000	0.79357	0.482000	0.46254	GAG	.	.		0.398	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		T	78765662	A	T	78765662	3	4	160	1	0	0	0	0	1	0	0	0	7835	304	11	4	992	4	IREB2	15	78765662	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	3851132	78765662	23765730	287	24458										
UNC45A	55898	hgsc.bcm.edu	37	chr15	91483701	91483701	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tttgctctgagcatcagtcaCgggtaggtggagtggagagg	17	6	3	2	rs144625807		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr15:91483701C>T	ENST00000418476.2	+	6	725	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	UNC45A_ENST00000394275.2_Missense_Mutation_p.R214W|UNC45A_ENST00000553671.2_3'UTR	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	229					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GCATCAGTCACGGGTAGGTGG	0.567																																					p.R229W		Atlas-SNP	.											.	UNC45A	57	.	0			c.C685T						.	C	TRP/ARG,TRP/ARG	1,4395	2.1+/-5.4	0,1,2197	158	118	131		640,685	5.5	1	15	dbSNP_134	131	0,8596		0,0,4298	no	missense,missense	UNC45A	NM_001039675.1,NM_018671.3	101,101	0,1,6495	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	214/930,229/945	91483701	1,12991	2198	4298	6496	SO:0001583	missense	55898	exon6			CAGTCACGGGTAG		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"smooth muscle cell associated protein-1"	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.685C>T	chr15.hg19:g.91483701C>T	ENSP00000407487:p.Arg229Trp	71.0	0.0		84.0	4.0	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	hg19	CCDS10367.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.177737	0.78564	2.27E-4	0.0	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.48836	0.8;0.8	5.52	5.52	0.82312	Armadillo-like helical (1);Armadillo-type fold (1);	0.220197	0.37530	N	0.002057	T	0.70561	0.3238	M	0.74881	2.28	0.58432	D	0.999996	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;P	0.91635	0.998;0.999;0.998;0.893	T	0.69752	-0.5060	10	0.48119	T	0.1	-26.9622	19.8567	0.96761	0.0:1.0:0.0:0.0	.	229;221;229;214	B4DZL0;B4DLE6;Q9H3U1;A8K6F7	.;.;UN45A_HUMAN;.	W	214;229	ENSP00000377816:R214W;ENSP00000407487:R229W	ENSP00000377816:R214W	R	+	1	2	UNC45A	89284705	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	4.938000	0.63519	2.764000	0.94973	0.650000	0.86243	CGG	.	C|1.000;T|0.000		0.567	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671		T	91483701	C	T	91483701	3	4	160	1	0	0	0	0	1	0	0	0	17003	527	19	1	707	1	UNC45A	15	91483701	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	12718039	91483701	11047691	288	24459										
RHBDF1	64285	hgsc.bcm.edu	37	chr16	111826	111826	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccatgtcctcgatctggcgcTtgacgaagctgtcgatgcgc	12	13	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:111826T>A	ENST00000262316.6	-	8	1320	c.1178A>T	c.(1177-1179)aAg>aTg	p.K393M	RHBDF1_ENST00000454039.2_Missense_Mutation_p.K393M	NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	393					cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				GATCTGGCGCTTGACGAAGCT	0.687																																					p.K393M		Atlas-SNP	.											.	RHBDF1	54	.	0			c.A1178T						.						33	36	35					16																	111826		2199	4293	6492	SO:0001583	missense	64285	exon8			TGGCGCTTGACGA	BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"chromosome 16 open reading frame 8", "rhomboid family 1 (Drosophila)"	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.1178A>T	chr16.hg19:g.111826T>A	ENSP00000262316:p.Lys393Met	48.0	0.0		68.0	7.0	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Missense_Mutation	SNP	ENST00000262316.6	hg19	CCDS32344.1	.	.	.	.	.	.	.	.	.	.	.	22.5	4.295451	0.81025	.	.	ENSG00000007384	ENST00000262316;ENST00000454039	T;T	0.69306	0.54;-0.39	4.43	3.3	0.37823	.	0.094770	0.64402	D	0.000001	T	0.71005	0.3289	L	0.52011	1.625	0.80722	D	1	D;D;P	0.62365	0.986;0.991;0.939	P;P;P	0.59288	0.855;0.847;0.615	T	0.71354	-0.4618	10	0.66056	D	0.02	-25.3162	9.5759	0.39457	0.0:0.085:0.0:0.915	.	393;416;393	F5GWL4;B4E3Q0;Q96CC6	.;.;RHDF1_HUMAN	M	393	ENSP00000262316:K393M;ENSP00000392133:K393M	ENSP00000262316:K393M	K	-	2	0	RHBDF1	51826	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	3.291000	0.51764	0.802000	0.34089	0.379000	0.24179	AAG	.	.		0.687	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450		A	111826	T	A	111826	3	1	160	1	0	0	0	0	1	0	0	0	13334	1609	56	4	1433	4	RHBDF1	16	111826	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10		111826	90242927	289	24460										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1261288	1261288	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atcatttttggcattttgggTgtgcaggtgtgtggccccca	13	8	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:1261288T>A	ENST00000348261.5	+	22	4592	c.4344T>A	c.(4342-4344)ggT>ggA	p.G1448G	CACNA1H_ENST00000358590.4_Silent_p.G1448G|CACNA1H_ENST00000565831.1_Silent_p.G1448G	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1448					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GCATTTTGGGTGTGCAGGTGT	0.632																																					p.G1448G		Atlas-SNP	.											.	CACNA1H	317	.	0			c.T4344A						.						111	125	120					16																	1261288		2158	4243	6401	SO:0001819	synonymous_variant	8912	exon22			TTTGGGTGTGCAG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.4344T>A	chr16.hg19:g.1261288T>A		83.0	0.0		92.0	12.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	hg19	CCDS45375.1																																																																																			.	.		0.632	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		A	1261288	T	A	1261288	2	1	160	1	0	0	0	0	0	0	0	1	2547	1683	59	4		4	CACNA1H	16	1261288	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1149462	1261288	89093465	290	24461										
CLCN7	1186	hgsc.bcm.edu	37	chr16	1496643	1496643	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggctgggcctcacgtctgggCcagcgagagctcctccaagc	14	15	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:1496643C>T	ENST00000382745.4	-	25	3012	c.2407G>A	c.(2407-2409)Gcc>Acc	p.A803T	LA16c-390E6.5_ENST00000566287.1_RNA|CLCN7_ENST00000262318.8_Missense_Mutation_p.G779D|CCDC154_ENST00000409671.1_5'Flank|CLCN7_ENST00000448525.1_Missense_Mutation_p.A779T|CCDC154_ENST00000389176.3_5'Flank	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	803					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				CACGTCTGGGCCAGCGAGAGC	0.642																																					p.A803T		Atlas-SNP	.											.	CLCN7	53	.	0			c.G2407A						.						37	25	29					16																	1496643		2172	4268	6440	SO:0001583	missense	1186	exon25			TCTGGGCCAGCGA	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ion channels / Chloride channels : Voltage-sensitive"	2025	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 63"	602727	"chloride channel 7"			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.2407G>A	chr16.hg19:g.1496643C>T	ENSP00000372193:p.Ala803Thr	167.0	0.0		156.0	23.0	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Missense_Mutation	SNP	ENST00000382745.4	hg19	CCDS32361.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.167382	0.78339	.	.	ENSG00000103249	ENST00000448525;ENST00000262318;ENST00000382745;ENST00000428756	D;D	0.89939	-2.54;-2.59	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.88562	0.6470	L	0.29908	0.895	0.80722	D	1	B;D;B	0.58620	0.172;0.983;0.307	B;P;B	0.53490	0.023;0.727;0.031	D	0.89400	0.3695	10	0.54805	T	0.06	-39.1491	16.6309	0.85032	0.0:1.0:0.0:0.0	.	779;803;252	E9PDB9;P51798;B3KUD9	.;CLCN7_HUMAN;.	T	779;756;803;745	ENSP00000410907:A779T;ENSP00000372193:A803T	ENSP00000262318:A756T	A	-	1	0	CLCN7	1436644	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	3.005000	0.49521	2.521000	0.84997	0.561000	0.74099	GCC	.	.		0.642	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		T	1496643	C	T	1496643	3	4	160	1	0	0	0	0	1	0	0	0	3470	739	26	3	14	3	CLCN7	16	1496643	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	235355	1496643	88858110	291	24462										
ABCA3	21	hgsc.bcm.edu	37	chr16	2348419	2348419	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ataaaggtgctctgcgactgTcaagttgtcaaacaggatgt	11	7	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:2348419T>C	ENST00000301732.5	-	15	2564	c.1864A>G	c.(1864-1866)Aca>Gca	p.T622A	ABCA3_ENST00000382381.3_Missense_Mutation_p.T564A	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	622	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	TCTGCGACTGTCAAGTTGTCA	0.562																																					p.T622A		Atlas-SNP	.											.	ABCA3	176	.	0			c.A1864G						.						156	150	152					16																	2348419		2198	4300	6498	SO:0001583	missense	21	exon15			CGACTGTCAAGTT	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.1864A>G	chr16.hg19:g.2348419T>C	ENSP00000301732:p.Thr622Ala	146.0	0.0		185.0	25.0	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	hg19	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	T	19.28	3.797639	0.70567	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.94966	-3.57	6.08	6.08	0.98989	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.047260	0.85682	D	0.000000	D	0.98197	0.9404	H	0.96333	3.805	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.91635	0.993;0.999;0.984	D	0.99402	1.0928	10	0.87932	D	0	.	15.4788	0.75508	0.0:0.0:0.0:1.0	.	622;626;622	A7MBM9;Q4LE27;Q99758	.;.;ABCA3_HUMAN	A	622;626	ENSP00000301732:T622A	ENSP00000301732:T622A	T	-	1	0	ABCA3	2288420	1.000000	0.71417	0.998000	0.56505	0.019000	0.09904	6.078000	0.71282	2.333000	0.79357	0.533000	0.62120	ACA	.	.		0.562	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		C	2348419	T	C	2348419	3	2	160	1	0	0	0	0	1	0	0	0	33	1667	58	2	3326	2	ABCA3	16	2348419	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	851776	2348419	88006334	292	24463										
ADCY9	115	hgsc.bcm.edu	37	chr16	4015970	4015970	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtcagaacccagagatgtctTgtccacatactggacagaag	10	10	2	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:4015970T>C	ENST00000294016.3	-	11	4406	c.3868A>G	c.(3868-3870)Aag>Gag	p.K1290E		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	1290					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AGAGATGTCTTGTCCACATAC	0.602																																					p.K1290E		Atlas-SNP	.											.	ADCY9	151	.	0			c.A3868G						.						97	87	90					16																	4015970		2197	4300	6497	SO:0001583	missense	115	exon11			ATGTCTTGTCCAC	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.3868A>G	chr16.hg19:g.4015970T>C	ENSP00000294016:p.Lys1290Glu	86.0	0.0		121.0	21.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	hg19	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.673805	0.29693	.	.	ENSG00000162104	ENST00000294016	D	0.83163	-1.69	5.45	3.13	0.36017	.	0.593517	0.18649	N	0.135072	T	0.68979	0.3060	N	0.17082	0.46	0.35247	D	0.778372	B	0.10296	0.003	B	0.04013	0.001	T	0.62487	-0.6844	10	0.18276	T	0.48	.	12.4153	0.55490	0.0:0.0:0.2789:0.7211	.	1290	O60503	ADCY9_HUMAN	E	1290	ENSP00000294016:K1290E	ENSP00000294016:K1290E	K	-	1	0	ADCY9	3955971	1.000000	0.71417	0.978000	0.43139	0.697000	0.40408	2.531000	0.45650	0.425000	0.26087	0.533000	0.62120	AAG	.	.		0.602	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			C	4015970	T	C	4015970	3	2	160	1	0	0	0	0	1	0	0	0	301	1821	63	2	197	2	ADCY9	16	4015970	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1667551	4015970	86338783	293	24464										
CORO7	79585	hgsc.bcm.edu	37	chr16	4405166	4405166	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acgggggcgcaggctagtccTggggcgaaacaccaagaggt	17	10	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:4405166T>A	ENST00000251166.4	-	28	2918		c.e28-2		CORO7_ENST00000539968.1_Splice_Site|PAM16_ENST00000576217.1_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000574025.1_Splice_Site|CORO7-PAM16_ENST00000572274.1_Intron|CORO7_ENST00000537233.2_Splice_Site	NM_024535.4	NP_078811.3	P57737	CORO7_HUMAN	coronin 7						actin filament polymerization (GO:0030041)|Golgi to endosome transport (GO:0006895)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)			breast(3)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|prostate(2)|skin(2)|urinary_tract(2)	23						AGGCTAGTCCTGGGGCGAAAC	0.652																																					.		Atlas-SNP	.											.	CORO7	73	.	0			c.2518-2A>T						.						98	72	81					16																	4405166		2193	4292	6485	SO:0001630	splice_region_variant	79585	exon27			TAGTCCTGGGGCG	AK097238	CCDS10513.1, CCDS55982.1, CCDS58417.1	16p13.3	2013-01-10			ENSG00000262246	ENSG00000262246		"Coronins", "WD repeat domain containing"	26161	protein-coding gene	gene with protein product		611668				15327992	Standard	NM_024535		Approved	FLJ22021		P57737	OTTHUMG00000129465	ENST00000251166.4:c.2773-2A>T	chr16.hg19:g.4405166T>A		152.0	0.0		159.0	23.0	NM_001201473	B4DFD6|B4DL18|I3L416|Q17RK4	Splice_Site	SNP	ENST00000251166.4	hg19	CCDS10513.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.020451	0.54576	.	.	ENSG00000103426	ENST00000251166;ENST00000537233;ENST00000539968	.	.	.	4.63	4.63	0.57726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.714	0.51641	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CORO7	4345167	0.998000	0.40836	1.000000	0.80357	0.743000	0.42351	1.794000	0.38774	1.853000	0.53794	0.482000	0.46254	.	.	.		0.652	CORO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251628.2	NM_024535	Intron	A	4405166	T	A	4405166	5	1	160	1	0	0	0	0	0	0	1	0	3761	1594	55	4	10	4	CORO7	16	4405166	Splice_Site	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	389196	4405166	85949587	294	24465										
CIITA	4261	hgsc.bcm.edu	37	chr16	11001808	11001808	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccacgaggccgaggaggctgGaatttggcagcacgtggtac	16	10	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:11001808G>T	ENST00000324288.8	+	11	2592	c.2459G>T	c.(2458-2460)gGa>gTa	p.G820V	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	820					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						GAGGAGGCTGGAATTTGGCAG	0.667			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.G820V		Atlas-SNP	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.G2459T						.						29	35	33					16																	11001808		2196	4297	6493	SO:0001583	missense	4261	exon11			AGGCTGGAATTTG	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2459G>T	chr16.hg19:g.11001808G>T	ENSP00000316328:p.Gly820Val	85.0	0.0		86.0	12.0	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	hg19	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	G	2.105	-0.405138	0.04832	.	.	ENSG00000179583	ENST00000324288;ENST00000388910	T	0.72835	-0.69	5.0	-1.51	0.08664	.	1.197730	0.05977	N	0.643481	T	0.72407	0.3456	L	0.53249	1.67	0.09310	N	1	P;B;P;D	0.65815	0.594;0.399;0.716;0.995	B;B;B;P	0.60068	0.215;0.147;0.386;0.868	T	0.58956	-0.7544	10	0.37606	T	0.19	.	1.4533	0.02380	0.2263:0.2919:0.3349:0.147	.	820;820;772;820	A0N0N9;P33076;F2Z2G8;Q96KL4	.;C2TA_HUMAN;.;.	V	820;772	ENSP00000316328:G820V	ENSP00000316328:G820V	G	+	2	0	CIITA	10909309	0.001000	0.12720	0.002000	0.10522	0.004000	0.04260	0.569000	0.23638	-0.104000	0.12154	-0.181000	0.13052	GGA	.	.		0.667	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		T	11001808	G	T	11001808	3	4	160	1	0	0	0	0	1	0	0	0	3430	1174	41	3	2501	3	CIITA	16	11001808	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	6596642	11001808	79352945	295	24466										
RSL1D1	26156	hgsc.bcm.edu	37	chr16	11933580	11933580	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tttcattagctggagtcttcTttcctattggtaccagctgt	8	9	3	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:11933580T>C	ENST00000571133.1	-	8	1190	c.1118A>G	c.(1117-1119)aAg>aGg	p.K373R	RSL1D1_ENST00000542106.1_Missense_Mutation_p.K153R	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	373					osteoblast differentiation (GO:0001649)|regulation of apoptotic process (GO:0042981)|regulation of cellular senescence (GO:2000772)|regulation of protein localization (GO:0032880)	membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						TGGAGTCTTCTTTCCTATTGG	0.423																																					p.K373R		Atlas-SNP	.											.	RSL1D1	40	.	0			c.A1118G						.						241	214	223					16																	11933580		2197	4300	6497	SO:0001583	missense	26156	exon8			GTCTTCTTTCCTA	AY154473	CCDS10551.1	16p13.13	2011-08-12			ENSG00000171490	ENSG00000171490			24534	protein-coding gene	gene with protein product		615874				15334068, 9859858	Standard	NM_015659		Approved	PBK1, L12, DKFZP564M182, CSIG, UTP30	uc002dbp.1	O76021	OTTHUMG00000129824	ENST00000571133.1:c.1118A>G	chr16.hg19:g.11933580T>C	ENSP00000460871:p.Lys373Arg	79.0	0.0		85.0	10.0	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Missense_Mutation	SNP	ENST00000571133.1	hg19	CCDS10551.1	.	.	.	.	.	.	.	.	.	.	T	9.758	1.169380	0.21621	.	.	ENSG00000171490	ENST00000355674;ENST00000396503;ENST00000542106	T;T	0.47869	1.0;0.83	4.05	-1.67	0.08238	.	1.286670	0.05069	N	0.481365	T	0.32496	0.0831	L	0.34521	1.04	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.16158	-1.0412	10	0.15952	T	0.53	-3.0125	6.3403	0.21319	0.0:0.1187:0.5773:0.304	.	373;373	Q32Q62;O76021	.;RL1D1_HUMAN	R	372;373;153	ENSP00000347897:K372R;ENSP00000442089:K153R	ENSP00000347897:K372R	K	-	2	0	RSL1D1	11841081	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-0.799000	0.04560	-0.067000	0.12976	-0.648000	0.03929	AAG	.	.		0.423	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659		C	11933580	T	C	11933580	3	2	160	1	0	0	0	0	1	0	0	0	13715	1609	56	2	362	2	RSL1D1	16	11933580	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	931772	11933580	78421173	296	24467										
USP31	57478	hgsc.bcm.edu	37	chr16	23083412	23083412	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atctccacggactcagagagCgacgccagggaggtgcgtct	14	12	3	1	rs546697725	byFrequency	TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:23083412C>A	ENST00000219689.7	-	15	2441	c.2442G>T	c.(2440-2442)tcG>tcT	p.S814S	USP31_ENST00000567975.1_Silent_p.S107S	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	DUSP 3. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		ACTCAGAGAGCGACGCCAGGG	0.567																																					p.S814S		Atlas-SNP	.											.	USP31	122	.	0			c.G2442T						.						142	139	140					16																	23083412		2197	4300	6497	SO:0001819	synonymous_variant	57478	exon15			AGAGAGCGACGCC	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2442G>T	chr16.hg19:g.23083412C>A		56.0	0.0		64.0	21.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000219689.7	hg19	CCDS10607.1																																																																																			.	.		0.567	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		A	23083412	C	A	23083412	2	1	160	1	0	0	0	0	0	0	0	1	17077	755	27	1		1	USP31	16	23083412	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	11149832	23083412	67271341	297	24468										
LAT	27040	hgsc.bcm.edu	37	chr16	28996206	28996206	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gaggccacggctgccagctgGcaggtggctgtccccgtctt	15	14	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:28996206G>T	ENST00000360872.5	+	0	0				LAT_ENST00000395456.2_5'Flank|LAT_ENST00000454369.2_5'Flank|LAT_ENST00000354453.4_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000566177.1_5'Flank|LAT_ENST00000395461.3_Missense_Mutation_p.W8C|LAT_ENST00000564277.1_5'Flank			O43561	LAT_HUMAN	linker for activation of T cells						blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|gene expression (GO:0010467)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lymphocyte homeostasis (GO:0002260)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|regulation of T cell activation (GO:0050863)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(2)|lung(3)|urinary_tract(1)	6		Hepatocellular(780;0.244)				CTGCCAGCTGGCAGGTGGCTG	0.711																																					p.W8C		Atlas-SNP	.											.	LAT	22	.	0			c.G24T						.						9	10	10					16																	28996206		691	1588	2279	SO:0001631	upstream_gene_variant	27040	exon1			CAGCTGGCAGGTG	AF036905	CCDS10647.1, CCDS32425.1, CCDS45455.1, CCDS53999.1	16q13	2011-11-01			ENSG00000213658	ENSG00000213658			18874	protein-coding gene	gene with protein product	"linker for activation of T cells, transmembrane adaptor"	602354				9489702	Standard	NM_014387		Approved	LAT1	uc010vdj.2	O43561	OTTHUMG00000131761		chr16.hg19:g.28996206G>T	Exception_encountered	124.0	0.0		138.0	19.0	NM_001014989	B7WPI0|C7C5T6|G5E9K3|O43919	Missense_Mutation	SNP	ENST00000360872.5	hg19	CCDS10647.1	.	.	.	.	.	.	.	.	.	.	G	6.988	0.552434	0.13374	.	.	ENSG00000213658	ENST00000395461	.	.	.	3.5	0.0307	0.14168	.	.	.	.	.	T	0.15998	0.0385	N	0.08118	0	0.09310	N	0.999999	P	0.38788	0.647	B	0.40165	0.321	T	0.16958	-1.0385	8	0.87932	D	0	.	6.2162	0.20656	0.1209:0.4336:0.4455:0.0	.	8	B7WPI0	.	C	8	.	ENSP00000378845:W8C	W	+	3	0	LAT	28903707	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	-0.385000	0.07379	-0.048000	0.13401	0.561000	0.74099	TGG	.	.		0.711	LAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254688.2			T	28996206	G	T	28996206	1	4	160	0	1	0	0	0	0	0	0	0	8653	1212	42	3		3	LAT	16	28996206	5'Flank	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	5912794	28996206	61358547	298	24469										
ITGAX	3687	hgsc.bcm.edu	37	chr16	31374277	31374277	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcggctcctacttcggggccTccctctgctccgtggacgta	11	16	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:31374277T>A	ENST00000268296.4	+	13	1502	c.1381T>A	c.(1381-1383)Tcc>Acc	p.S461T	ITGAX_ENST00000562522.1_Missense_Mutation_p.S461T	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	461					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CTTCGGGGCCTCCCTCTGCTC	0.672																																					p.S461T		Atlas-SNP	.											.	ITGAX	198	.	0			c.T1381A						.						67	70	69					16																	31374277		2197	4300	6497	SO:0001583	missense	3687	exon13			GGGGCCTCCCTCT	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1381T>A	chr16.hg19:g.31374277T>A	ENSP00000268296:p.Ser461Thr	174.0	0.0		184.0	38.0	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	hg19	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	T	4.756	0.140591	0.09083	.	.	ENSG00000140678	ENST00000268296	T	0.09163	3.01	3.58	2.24	0.28232	.	.	.	.	.	T	0.18173	0.0436	L	0.48986	1.54	0.21290	N	0.999731	D	0.71674	0.998	D	0.65443	0.935	T	0.18241	-1.0343	9	0.24483	T	0.36	.	3.3128	0.07022	0.2998:0.0:0.1979:0.5023	.	461	P20702	ITAX_HUMAN	T	461	ENSP00000268296:S461T	ENSP00000268296:S461T	S	+	1	0	ITGAX	31281778	0.056000	0.20664	1.000000	0.80357	0.141000	0.21300	1.047000	0.30367	1.413000	0.46997	0.248000	0.18094	TCC	.	.		0.672	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		A	31374277	T	A	31374277	3	1	160	1	0	0	0	0	1	0	0	0	7898	1551	54	4	1431	4	ITGAX	16	31374277	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2378071	31374277	58980476	299	24470										
CES2	51647	hgsc.bcm.edu	37	chr16	66969499	66969499	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cagcctctgggtgaacagcaGcgtgtccgccggcagcgaac	14	14	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:66969499G>T	ENST00000422424.2	-	0	0				CES2_ENST00000317091.4_Missense_Mutation_p.Q51H|CES2_ENST00000417689.1_Missense_Mutation_p.Q51H	NM_016062.3	NP_057146.1	Q9Y3D0	MIP18_HUMAN	family with sequence similarity 96, member B						chromosome segregation (GO:0007059)|small molecule metabolic process (GO:0044281)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)				kidney(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)		GTGAACAGCAGCGTGTCCGCC	0.677																																					p.Q51H		Atlas-SNP	.											.	CES2	43	.	0			c.G153T						.						47	54	52					16																	66969499		2200	4299	6499	SO:0001631	upstream_gene_variant	8824	exon1			ACAGCAGCGTGTC		CCDS45506.1	16q22.1	2014-01-16			ENSG00000166595	ENSG00000166595			24261	protein-coding gene	gene with protein product		614778				11042152, 10810093, 23891004	Standard	NM_016062		Approved	CGI-128	uc021tjy.2	Q9Y3D0	OTTHUMG00000175408		chr16.hg19:g.66969499G>T	Exception_encountered	95.0	0.0		55.0	15.0	NM_003869		Missense_Mutation	SNP	ENST00000422424.2	hg19	CCDS45506.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.844987	0.51164	.	.	ENSG00000172831	ENST00000417689;ENST00000317091	T;T	0.68331	-0.31;-0.32	3.39	1.26	0.21427	.	17.756700	0.00397	U	0.000048	T	0.47948	0.1473	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42275	-0.9461	10	0.56958	D	0.05	.	5.691	0.17829	0.0:0.2488:0.5371:0.2141	.	51	A8K367	.	H	51	ENSP00000394452:Q51H;ENSP00000317842:Q51H	ENSP00000317842:Q51H	Q	+	3	2	CES2	65527000	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.582000	0.05814	0.350000	0.24002	-0.211000	0.12701	CAG	.	.		0.677	FAM96B-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429890.1	NM_016062		T	66969499	G	T	66969499	1	4	160	0	1	0	0	0	0	0	0	0	3272	962	34	3		3	CES2	16	66969499	5'Flank	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	35595222	66969499	23385254	300	24471										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72830306	72830306	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gcgagaagatgggcagctccAtcggcatggagagctgggtg	18	8	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr16:72830306A>G	ENST00000268489.5	-	9	6947	c.6275T>C	c.(6274-6276)aTg>aCg	p.M2092T	ZFHX3_ENST00000397992.5_Missense_Mutation_p.M1178T	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2092					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				GGGCAGCTCCATCGGCATGGA	0.652																																					p.M2092T		Atlas-SNP	.											.	ZFHX3	404	.	0			c.T6275C						.						72	61	65					16																	72830306		2198	4300	6498	SO:0001583	missense	463	exon9			AGCTCCATCGGCA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.6275T>C	chr16.hg19:g.72830306A>G	ENSP00000268489:p.Met2092Thr	48.0	0.0		36.0	11.0	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	hg19	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	A	15.90	2.970550	0.53614	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.73258	-0.73;-0.71	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000009	T	0.65101	0.2659	L	0.46157	1.445	0.80722	D	1	D	0.53885	0.963	B	0.40940	0.344	T	0.69731	-0.5066	10	0.52906	T	0.07	.	15.4346	0.75137	1.0:0.0:0.0:0.0	.	2092	Q15911	ZFHX3_HUMAN	T	2092;1178	ENSP00000268489:M2092T;ENSP00000438926:M1178T	ENSP00000268489:M2092T	M	-	2	0	ZFHX3	71387807	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	9.331000	0.96430	2.041000	0.60428	0.533000	0.62120	ATG	.	.		0.652	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		G	72830306	A	G	72830306	3	3	160	1	0	0	0	0	1	0	0	0	17649	217	8	2	4844	2	ZFHX3	16	72830306	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	5860807	72830306	17524447	301	24472										
FAM57A	79850	hgsc.bcm.edu	37	chr17	644672	644672	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cagcagggactaagcctgctCcaagtacccttcagcatccc	8	16	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:644672C>G	ENST00000308278.8	+	5	872	c.636C>G	c.(634-636)ctC>ctG	p.L212L	FAM57A_ENST00000301324.8_Silent_p.L180L	NM_024792.1	NP_079068.1	Q8TBR7	FA57A_HUMAN	family with sequence similarity 57, member A	212	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(2)|urinary_tract(2)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0217)		TAAGCCTGCTCCAAGTACCCT	0.557																																					p.L212L		Atlas-SNP	.											.	FAM57A	17	.	0			c.C636G						.						160	124	136					17																	644672		2203	4300	6503	SO:0001819	synonymous_variant	79850	exon5			CCTGCTCCAAGTA	AK025935	CCDS10996.1	17p13.3	2014-08-14				ENSG00000167695			29646	protein-coding gene	gene with protein product		611627				12270127	Standard	NM_024792		Approved	FLJ22282, CT120	uc002frp.3	Q8TBR7		ENST00000308278.8:c.636C>G	chr17.hg19:g.644672C>G		76.0	0.0		79.0	8.0	NM_024792	A8K7Q0|Q7Z464|Q96D97|Q9H6H3	Silent	SNP	ENST00000308278.8	hg19	CCDS10996.1																																																																																			.	.		0.557	FAM57A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437155.2	NM_024792		G	644672	C	G	644672	2	3	160	1	0	0	0	0	0	0	0	1	5596	842	30	4		4	FAM57A	17	644672	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10		644672	80550538	302	24473										
ALOX15B	247	hgsc.bcm.edu	37	chr17	7946179	7946179	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgagatgaaaaggatcttcaActtccggaggaccccagcag	11	10	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:7946179A>T	ENST00000380183.4	+	5	792	c.653A>T	c.(652-654)aAc>aTc	p.N218I	ALOX15B_ENST00000572022.1_Missense_Mutation_p.N218I|ALOX15B_ENST00000573359.1_Missense_Mutation_p.N218I|ALOX15B_ENST00000380173.2_Missense_Mutation_p.N218I	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	218	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						AGGATCTTCAACTTCCGGAGG	0.567																																					p.N218I		Atlas-SNP	.											.	ALOX15B	66	.	0			c.A653T						.						34	31	32					17																	7946179		2176	4250	6426	SO:0001583	missense	247	exon5			TCTTCAACTTCCG	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"Arachidonate lipoxygenases"	434	protein-coding gene	gene with protein product		603697	"arachidonate 15-lipoxygenase, second type"			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.653A>T	chr17.hg19:g.7946179A>T	ENSP00000369530:p.Asn218Ile	102.0	0.0		108.0	21.0	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	hg19	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	A	10.64	1.406422	0.25378	.	.	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	T;T	0.76709	-1.04;-1.04	4.42	0.477	0.16784	Lipoxygenase, C-terminal (3);	0.727387	0.14403	N	0.321775	T	0.53722	0.1814	N	0.16201	0.385	0.29488	N	0.855847	B;B;B;B	0.19200	0.034;0.027;0.01;0.012	B;B;B;B	0.23018	0.043;0.026;0.015;0.026	T	0.38265	-0.9669	10	0.17832	T	0.49	-19.3584	3.0325	0.06111	0.5119:0.0:0.1082:0.3799	.	218;218;218;218	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	I	218	ENSP00000369520:N218I;ENSP00000369530:N218I	ENSP00000344337:N218I	N	+	2	0	ALOX15B	7886904	0.000000	0.05858	0.830000	0.32933	0.043000	0.13939	-1.136000	0.03222	0.254000	0.21573	-0.379000	0.06801	AAC	.	.		0.567	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2			T	7946179	A	T	7946179	3	4	160	1	0	0	0	0	1	0	0	0	539	43	2	4	671	4	ALOX15B	17	7946179	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	7301507	7946179	73249031	303	24474										
NTN1	9423	hgsc.bcm.edu	37	chr17	8926031	8926031	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cctcaccgacctcaacaaccCgcacaacctgacgtgctggc	7	19	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:8926031C>T	ENST00000173229.2	+	2	448	c.341C>T	c.(340-342)cCg>cTg	p.P114L	NTN1_ENST00000546090.1_Missense_Mutation_p.P114L|NTN1_ENST00000538852.1_Missense_Mutation_p.P114L	NM_004822.2	NP_004813.2	O95631	NET1_HUMAN	netrin 1	114	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|establishment of nucleus localization (GO:0040023)|inner ear morphogenesis (GO:0042472)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of axon extension (GO:0030517)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of cell proliferation (GO:0008284)|regulation of cell migration (GO:0030334)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)			NTN1/ACLY(2)	central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(5)	13						CTCAACAACCCGCACAACCTG	0.647																																					p.P114L		Atlas-SNP	.											.	NTN1	31	.	0			c.C341T						.						21	14	16					17																	8926031		2110	4164	6274	SO:0001583	missense	9423	exon2			ACAACCCGCACAA	U75586	CCDS11148.1	17p13-p12	2013-03-01			ENSG00000065320	ENSG00000065320		"Netrins"	8029	protein-coding gene	gene with protein product	"Netrin-1"	601614				9950216	Standard	NM_004822		Approved	NTN1L	uc002glw.4	O95631	OTTHUMG00000130257	ENST00000173229.2:c.341C>T	chr17.hg19:g.8926031C>T	ENSP00000173229:p.Pro114Leu	104.0	0.0		117.0	15.0	NM_004822	E9KL51	Missense_Mutation	SNP	ENST00000173229.2	hg19	CCDS11148.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.062819	0.76187	.	.	ENSG00000065320	ENST00000173229;ENST00000538852;ENST00000546090	T;T;T	0.76448	-1.02;-1.02;-1.02	4.71	4.71	0.59529	Laminin, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.81375	0.4809	M	0.87971	2.92	0.80722	D	1	P	0.36633	0.562	B	0.36608	0.229	D	0.83480	0.0064	10	0.41790	T	0.15	.	17.262	0.87072	0.0:1.0:0.0:0.0	.	114	O95631	NET1_HUMAN	L	114	ENSP00000173229:P114L;ENSP00000443259:P114L;ENSP00000441611:P114L	ENSP00000173229:P114L	P	+	2	0	NTN1	8866756	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.967000	0.70403	2.170000	0.68504	0.536000	0.68110	CCG	.	.		0.647	NTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252583.1			T	8926031	C	T	8926031	3	4	160	1	0	0	0	0	1	0	0	0	10709	652	23	1	343	1	NTN1	17	8926031	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	979852	8926031	72269179	304	24475										
MYH4	4622	hgsc.bcm.edu	37	chr17	10350413	10350413	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gcctctctcagtccgttccaGggatgccctgagctcttcaa	9	15	4	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:10350413G>C	ENST00000255381.2	-	35	5196	c.5086C>G	c.(5086-5088)Ctg>Gtg	p.L1696V	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1696					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						GTCCGTTCCAGGGATGCCCTG	0.517																																					p.L1696V		Atlas-SNP	.											.	MYH4	349	.	0			c.C5086G						.						170	135	147					17																	10350413		2203	4300	6503	SO:0001583	missense	4622	exon35			GTTCCAGGGATGC		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.5086C>G	chr17.hg19:g.10350413G>C	ENSP00000255381:p.Leu1696Val	70.0	0.0		90.0	4.0	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.821619	0.50633	.	.	ENSG00000141048	ENST00000255381	D	0.81579	-1.51	5.29	3.18	0.36537	Myosin tail (1);	0.000000	0.30011	U	0.010639	D	0.82393	0.5027	M	0.76328	2.33	0.42162	D	0.991604	P	0.41345	0.746	P	0.47827	0.558	T	0.80139	-0.1507	10	0.44086	T	0.13	.	9.5163	0.39106	0.2429:0.0:0.7571:0.0	.	1696	Q9Y623	MYH4_HUMAN	V	1696	ENSP00000255381:L1696V	ENSP00000255381:L1696V	L	-	1	2	MYH4	10291138	0.980000	0.34600	0.987000	0.45799	0.959000	0.62525	1.775000	0.38584	0.637000	0.30526	-0.251000	0.11542	CTG	.	.		0.517	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		C	10350413	G	C	10350413	3	2	160	1	0	0	0	0	1	0	0	0	10046	991	35	4	757	4	MYH4	17	10350413	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	1424382	10350413	70844797	305	24476										
MPRIP	23164	hgsc.bcm.edu	37	chr17	17075128	17075128	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agcgggagctagagaaacttCgagaagagaaagaccgcctc	13	9	0	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:17075128C>T	ENST00000341712.4	+	16	2260	c.2260C>T	c.(2260-2262)Cga>Tga	p.R754*	MPRIP_ENST00000395804.3_Nonsense_Mutation_p.R754*|MPRIP_ENST00000395811.5_Nonsense_Mutation_p.R754*|RNU6-767P_ENST00000384132.1_RNA|RP11-45M22.3_ENST00000584203.1_RNA|MPRIP_ENST00000444976.1_Nonsense_Mutation_p.R716*			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	754	Interaction with RHOA.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						AGAGAAACTTCGAGAAGAGAA	0.587																																					p.R754X		Atlas-SNP	.											.	MPRIP	87	.	0			c.C2260T						.						61	71	68					17																	17075128		2203	4300	6503	SO:0001587	stop_gained	23164	exon16			AAACTTCGAGAAG	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"Pleckstrin homology (PH) domain containing"	30321	protein-coding gene	gene with protein product	"Rho interacting protein 3"	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.2260C>T	chr17.hg19:g.17075128C>T	ENSP00000342379:p.Arg754*	266.0	0.0		286.0	54.0	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Nonsense_Mutation	SNP	ENST00000341712.4	hg19	CCDS32578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	7.086633|7.086633	0.98055|0.98055	.|.	.|.	ENSG00000133030|ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712|ENST00000313485	.|.	.|.	.|.	5.79|5.79	-1.8|-1.8	0.07907|0.07907	.|.	0.156344|.	0.39210|.	N|.	0.001430|.	.|T	.|0.62636	.|0.2444	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69731	.|-0.5066	.|3	0.05351|.	T|.	0.99|.	-7.8984|-7.8984	17.4731|17.4731	0.87652|0.87652	0.645:0.355:0.0:0.0|0.645:0.355:0.0:0.0	.|.	.|.	.|.	.|.	X|L	716;754;754;754|1118	.|.	ENSP00000342379:R754X|.	R|S	+|+	1|2	2|0	MPRIP|MPRIP	17015853|17015853	1.000000|1.000000	0.71417|0.71417	0.556000|0.556000	0.28293|0.28293	0.896000|0.896000	0.52359|0.52359	1.456000|1.456000	0.35201|0.35201	-0.165000|-0.165000	0.10908|0.10908	0.655000|0.655000	0.94253|0.94253	CGA|TCG	.	.		0.587	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		T	17075128	C	T	17075128	4	4	160	1	0	0	0	0	0	1	0	0	9752	876	31	1	2322	1	MPRIP	17	17075128	Nonsense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	6724715	17075128	64120082	306	24477										
AKAP10	11216	hgsc.bcm.edu	37	chr17	19844215	19844215	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tttacctcagagaaataaaaGagggctgactcacagaagag	10	7	2	5			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:19844215G>A	ENST00000225737.6	-	7	1327	c.1170C>T	c.(1168-1170)ctC>ctT	p.L390L	AKAP10_ENST00000395536.3_Silent_p.L390L	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	390	RGS 2. {ECO:0000255|PROSITE- ProRule:PRU00171}.				blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					AGAAATAAAAGAGGGCTGACT	0.433																																					p.L390L		Atlas-SNP	.											.	AKAP10	47	.	0			c.C1170T						.						58	56	57					17																	19844215		2203	4299	6502	SO:0001819	synonymous_variant	11216	exon7			ATAAAAGAGGGCT	AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"A-kinase anchor proteins"	368	protein-coding gene	gene with protein product	"dual-specificity A-kinase anchoring protein 2", "protein kinase A anchoring protein 10", "mitochondrial A kinase PPKA anchor protein 10"	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.1170C>T	chr17.hg19:g.19844215G>A		298.0	0.0		370.0	33.0	NM_007202	B2R650|Q96AJ7	Silent	SNP	ENST00000225737.6	hg19	CCDS11214.1																																																																																			.	.		0.433	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202		A	19844215	G	A	19844215	2	1	160	1	0	0	0	0	0	0	0	1	446	929	33	3		3	AKAP10	17	19844215	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	2769087	19844215	61350995	307	24478										
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28296107	28296107	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gccaaagagtggtttaatacTgacagcatgacactgaataa	9	7	0	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:28296107T>A	ENST00000394835.3	+	4	681	c.489T>A	c.(487-489)acT>acA	p.T163T	EFCAB5_ENST00000378738.3_Silent_p.T163T|EFCAB5_ENST00000394832.2_Silent_p.T163T|EFCAB5_ENST00000541045.1_Intron|EFCAB5_ENST00000320856.5_Silent_p.T163T|EFCAB5_ENST00000534836.2_Intron|EFCAB5_ENST00000536908.2_Silent_p.T107T	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	163							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						GGTTTAATACTGACAGCATGA	0.348																																					p.T163T		Atlas-SNP	.											.	EFCAB5	122	.	0			c.T489A						.						40	39	39					17																	28296107		1841	4086	5927	SO:0001819	synonymous_variant	374786	exon4			TAATACTGACAGC	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.489T>A	chr17.hg19:g.28296107T>A		221.0	0.0		253.0	32.0	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	hg19	CCDS11254.2																																																																																			.	.		0.348	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		A	28296107	T	A	28296107	2	1	160	1	0	0	0	0	0	0	0	1	4940	1567	55	4		4	EFCAB5	17	28296107	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	8451892	28296107	52899103	308	24479										
LHX1	3975	hgsc.bcm.edu	37	chr17	35297689	35297689	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cacctgaactgcttcacctgCatgatgtgtaacaagcagct	8	12	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:35297689C>T	ENST00000254457.5	+	2	1684	c.273C>T	c.(271-273)tgC>tgT	p.C91C	RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	91	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				GCTTCACCTGCATGATGTGTA	0.527																																					p.C91C		Atlas-SNP	.											.	LHX1	48	.	0			c.C273T						.						88	72	77					17																	35297689		2203	4300	6503	SO:0001819	synonymous_variant	3975	exon2			CACCTGCATGATG	U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"Homeoboxes / LIM class"	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.273C>T	chr17.hg19:g.35297689C>T		89.0	0.0		113.0	17.0	NM_005568	Q3MIW0	Silent	SNP	ENST00000254457.5	hg19	CCDS11316.1																																																																																			.	.		0.527	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3	NM_005568		T	35297689	C	T	35297689	2	4	160	1	0	0	0	0	0	0	0	1	8779	718	25	3		3	LHX1	17	35297689	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	7001582	35297689	45897521	309	24480										
ACACA	31	hgsc.bcm.edu	37	chr17	35614734	35614734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	actgaaatatccccaaacatTcttattgctgcggaaattta	5	9	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:35614734T>C	ENST00000394406.2	-	14	1796	c.1606A>G	c.(1606-1608)Aat>Gat	p.N536D	ACACA_ENST00000360679.3_Missense_Mutation_p.N478D|ACACA_ENST00000353139.5_Missense_Mutation_p.N573D|ACACA_ENST00000335166.5_Missense_Mutation_p.N458D	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	536	Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	CCCCAAACATTCTTATTGCTG	0.418																																					p.N573D	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.A1717G						.						93	90	91					17																	35614734		2203	4300	6503	SO:0001583	missense	31	exon14			AAACATTCTTATT	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.1606A>G	chr17.hg19:g.35614734T>C	ENSP00000377928:p.Asn536Asp	90.0	0.0		80.0	9.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	hg19	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.047507	0.75846	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44	5.93	5.93	0.95920	Rudiment single hybrid motif (1);ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);Biotin carboxylase, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.77512	0.4141	N	0.25380	0.74	0.80722	D	1	B;B;B	0.31503	0.041;0.326;0.279	B;B;B	0.42087	0.059;0.375;0.258	T	0.76326	-0.3000	10	0.42905	T	0.14	-19.7328	15.5755	0.76380	0.0:0.0:0.0:1.0	.	573;536;478	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	D	573;478;536;560;458	ENSP00000344789:N573D;ENSP00000353898:N478D;ENSP00000377928:N536D;ENSP00000335323:N458D	ENSP00000335323:N458D	N	-	1	0	ACACA	32688847	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.040000	0.89188	2.281000	0.76405	0.533000	0.62120	AAT	.	.		0.418	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		C	35614734	T	C	35614734	3	2	160	1	0	0	0	0	1	0	0	0	106	1783	62	2	5606	2	ACACA	17	35614734	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	317045	35614734	45580476	310	24481										
KRTAP17-1	83902	hgsc.bcm.edu	37	chr17	39471826	39471826	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cgcagcagccacagcagcccGgctgacagcagcactcttca	10	17	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:39471826G>A	ENST00000334202.3	-	1	121	c.77C>T	c.(76-78)cCg>cTg	p.P26L		NM_031964.1	NP_114170.1	Q9BYP8	KR171_HUMAN	keratin associated protein 17-1	26						intermediate filament (GO:0005882)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			acagcagCCCGGCTGACAGCA	0.692																																					p.P26L		Atlas-SNP	.											.	KRTAP17-1	14	.	0			c.C77T						.						15	18	17					17																	39471826		2196	4282	6478	SO:0001583	missense	83902	exon1			CAGCCCGGCTGAC	AJ406952	CCDS11387.1	17q21.2	2013-06-20			ENSG00000186860	ENSG00000186860		"Keratin associated proteins"	18917	protein-coding gene	gene with protein product							Standard	NM_031964		Approved	KAP17.1	uc002hwj.3	Q9BYP8	OTTHUMG00000133433	ENST00000334202.3:c.77C>T	chr17.hg19:g.39471826G>A	ENSP00000333993:p.Pro26Leu	80.0	0.0		86.0	10.0	NM_031964		Missense_Mutation	SNP	ENST00000334202.3	hg19	CCDS11387.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.358358	0.24598	.	.	ENSG00000186860	ENST00000334202	.	.	.	4.26	3.25	0.37280	.	.	.	.	.	T	0.25082	0.0609	N	0.14661	0.345	0.40845	D	0.983709	P	0.39022	0.655	B	0.28784	0.094	T	0.12656	-1.0539	8	0.87932	D	0	-13.7877	8.864	0.35276	0.0:0.0:0.766:0.234	.	26	Q9BYP8	KR171_HUMAN	L	26	.	ENSP00000333993:P26L	P	-	2	0	KRTAP17-1	36725352	0.878000	0.30173	0.991000	0.47740	0.852000	0.48524	1.075000	0.30716	0.937000	0.37394	0.462000	0.41574	CCG	.	.		0.692	KRTAP17-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257296.1			A	39471826	G	A	39471826	3	1	160	1	0	0	0	0	1	0	0	0	8536	1116	39	1	244	1	KRTAP17-1	17	39471826	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	3857092	39471826	41723384	311	24482										
ACLY	47	hgsc.bcm.edu	37	chr17	40063809	40063810	+	Frame_Shift_Ins	INS	-	-	C													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccaagtcaaggacatagactINSccatctttggtcactacttc							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:40063809_40063810insC	ENST00000352035.2	-	7	762_763	c.632_633insG	c.(631-633)ggafs	p.G211fs	ACLY_ENST00000353196.1_Frame_Shift_Ins_p.G211fs|ACLY_ENST00000537919.1_Intron|ACLY_ENST00000590151.1_Frame_Shift_Ins_p.G211fs|ACLY_ENST00000393896.2_Frame_Shift_Ins_p.G211fs	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	211	ATP-grasp.				ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				GGACATAGACTCCATCTTTGGT	0.574																																					p.G211fs	Colon(64;807 1396 15971 30971)	Atlas-INDEL	.											.	ACLY	85	.	0			c.633_634insG						.																																			SO:0001589	frameshift_variant	47	exon7			.	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.633dupG	chr17.hg19:g.40063811_40063811dupC	ENSP00000253792:p.Gly211fs	77.0	0.0		92.0	39.0	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Frame_Shift_Ins	INS	ENST00000352035.2	hg19	CCDS11412.1																																																																																			.	.		0.574	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		C	40063810	-	C	40063809	7	5	160	1	0	1	1	0	0	0	0	0	143	1538	54	0	2764	0	ACLY	17	40063809	Frame_Shift_Ins	INS	-	TCGA-DD-AACI-01A-11D-A40R-10	591983	40063809	41131401	312	24483										
SGCA	6442	hgsc.bcm.edu	37	chr17	48245087	48245087	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cccagaagatcgtgggctccAggtcattgaggtgccgtcag	14	11	2	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:48245087A>T	ENST00000262018.3	+	3	338	c.302A>T	c.(301-303)cAg>cTg	p.Q101L	SGCA_ENST00000543315.1_Missense_Mutation_p.Q101L|SGCA_ENST00000513942.1_Intron|RP11-893F2.14_ENST00000572855.1_RNA|SGCA_ENST00000451235.2_Intron|SGCA_ENST00000344627.6_Missense_Mutation_p.Q101L	NM_000023.2	NP_000014.1	Q16586	SGCA_HUMAN	sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein)	101					muscle contraction (GO:0006936)|muscle organ development (GO:0007517)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						CGTGGGCTCCAGGTCATTGAG	0.632																																					p.Q101L		Atlas-SNP	.											.	SGCA	35	.	0			c.A302T						.						20	21	21					17																	48245087		2203	4300	6503	SO:0001583	missense	6442	exon3			GGCTCCAGGTCAT	L34355	CCDS32679.1, CCDS45729.1	17q21	2014-09-17	2002-08-29		ENSG00000108823	ENSG00000108823			10805	protein-coding gene	gene with protein product	"50kD DAG", "Sarcoglycan, alpha (50kD dystrophin-associated glycoprotein; adhalin)", "adhalin (limb girdle muscular dystrophy 2D)"	600119	"sarcoglycan, alpha (50kD dystrophin-associated glycoprotein)"	ADL		7937874	Standard	NM_000023		Approved	SCARMD1, LGMD2D, adhalin, DMDA2, A2	uc002iqi.3	Q16586	OTTHUMG00000162024	ENST00000262018.3:c.302A>T	chr17.hg19:g.48245087A>T	ENSP00000262018:p.Gln101Leu	94.0	0.0		90.0	18.0	NM_001135697	A6NEB8|A8K3K7|Q13710|Q13712	Missense_Mutation	SNP	ENST00000262018.3	hg19	CCDS32679.1	.	.	.	.	.	.	.	.	.	.	A	11.53	1.665845	0.29604	.	.	ENSG00000108823	ENST00000344627;ENST00000262018;ENST00000543315	D;D;D	0.98178	-4.77;-4.77;-4.77	4.53	3.36	0.38483	Dystroglycan-type cadherin-like (1);Cadherin-like (1);	0.322034	0.29431	N	0.012178	D	0.97031	0.9030	L	0.27053	0.805	0.80722	D	1	D;B	0.67145	0.996;0.046	D;B	0.77557	0.99;0.066	D	0.94612	0.7805	10	0.25106	T	0.35	-21.717	8.0867	0.30775	0.8198:0.0:0.0:0.1802	.	101;101	Q16586-2;Q16586	.;SGCA_HUMAN	L	101	ENSP00000345522:Q101L;ENSP00000262018:Q101L;ENSP00000444539:Q101L	ENSP00000262018:Q101L	Q	+	2	0	SGCA	45600086	0.971000	0.33674	0.984000	0.44739	0.628000	0.37860	1.019000	0.30014	1.802000	0.52723	0.379000	0.24179	CAG	.	.		0.632	SGCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366841.1	NM_000023		T	48245087	A	T	48245087	3	4	160	1	0	0	0	0	1	0	0	0	14214	188	7	4	312	4	SGCA	17	48245087	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	8181278	48245087	32950123	313	24484										
MBTD1	54799	hgsc.bcm.edu	37	chr17	49302381	49302381	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atactcacccatgccagattTaccatctgggtatgtgtaga	8	10	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:49302381T>C	ENST00000586178.1	-	3	485	c.142A>G	c.(142-144)Aaa>Gaa	p.K48E	MBTD1_ENST00000593259.1_5'Flank|MBTD1_ENST00000415868.1_Missense_Mutation_p.K48E|MBTD1_ENST00000376381.2_Missense_Mutation_p.K48E	NM_017643.2	NP_060113.2	Q05BQ5	MBTD1_HUMAN	mbt domain containing 1	48					chromatin modification (GO:0016568)|embryonic skeletal system development (GO:0048706)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)			ATGCCAGATTTACCATCTGGG	0.423																																					p.K48E		Atlas-SNP	.											.	MBTD1	44	.	0			c.A142G						.						150	139	142					17																	49302381		692	1591	2283	SO:0001583	missense	54799	exon3			CAGATTTACCATC	AK000062	CCDS11581.2	17q24.1	2003-01-15			ENSG00000011258	ENSG00000011258			19866	protein-coding gene	gene with protein product							Standard	NM_017643		Approved	SA49P01, FLJ20055	uc002itr.4	Q05BQ5	OTTHUMG00000150442	ENST00000586178.1:c.142A>G	chr17.hg19:g.49302381T>C	ENSP00000468304:p.Lys48Glu	72.0	0.0		91.0	15.0	NM_017643	Q6ZVU7|Q9NXU1	Missense_Mutation	SNP	ENST00000586178.1	hg19	CCDS11581.2	.	.	.	.	.	.	.	.	.	.	T	27.6	4.843128	0.91197	.	.	ENSG00000011258	ENST00000405860;ENST00000415868;ENST00000376381	T;T	0.24908	1.83;1.84	5.21	5.21	0.72293	Zinc finger, FCS-type (1);	0.044023	0.85682	D	0.000000	T	0.42359	0.1199	L	0.48642	1.525	0.80722	D	1	D;D	0.67145	0.985;0.996	P;D	0.76071	0.576;0.987	T	0.11421	-1.0588	10	0.21540	T	0.41	.	15.3505	0.74380	0.0:0.0:0.0:1.0	.	48;48	Q05BQ5;Q05BQ5-2	MBTD1_HUMAN;.	E	48	ENSP00000403946:K48E;ENSP00000365561:K48E	ENSP00000365561:K48E	K	-	1	0	MBTD1	46657380	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.965000	0.87945	2.089000	0.63090	0.482000	0.46254	AAA	.	.		0.423	MBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318124.1			C	49302381	T	C	49302381	3	2	160	1	0	0	0	0	1	0	0	0	9369	1763	61	2	1804	2	MBTD1	17	49302381	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1057294	49302381	31892829	314	24485										
DGKE	8526	hgsc.bcm.edu	37	chr17	54939189	54939189	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gcgagtagcactgcccagctTggaaggtattatagttctga	12	8	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:54939189T>A	ENST00000284061.3	+	10	1502	c.1322T>A	c.(1321-1323)tTg>tAg	p.L441*		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	441					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					CTGCCCAGCTTGGAAGGTATT	0.463																																					p.L441X		Atlas-SNP	.											.	DGKE	47	.	0			c.T1322A						.						181	179	180					17																	54939189		2203	4300	6503	SO:0001587	stop_gained	8526	exon10			CCAGCTTGGAAGG	U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"diacylglycerol kinase, epsilon (64kD)"			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.1322T>A	chr17.hg19:g.54939189T>A	ENSP00000284061:p.Leu441*	91.0	0.0		77.0	7.0	NM_003647	Q8TBM4|Q9UKQ3	Nonsense_Mutation	SNP	ENST00000284061.3	hg19	CCDS11590.1	.	.	.	.	.	.	.	.	.	.	T	38	6.840181	0.97877	.	.	ENSG00000153933	ENST00000284061	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.9436	0.79776	0.0:0.0:0.0:1.0	.	.	.	.	X	441	.	ENSP00000284061:L441X	L	+	2	0	DGKE	52294188	1.000000	0.71417	0.984000	0.44739	0.962000	0.63368	7.580000	0.82523	2.150000	0.67090	0.529000	0.55759	TTG	.	.		0.463	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647		A	54939189	T	A	54939189	4	1	160	1	0	0	0	0	0	1	0	0	4470	1821	63	4	1356	4	DGKE	17	54939189	Nonsense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	5636808	54939189	26256021	315	24486										
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56382773	56382773	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agaaaccgtcatcgtccatgCccccaaacacagtaatgaca	6	14	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:56382773C>A	ENST00000343736.4	-	29	5571	c.5408G>T	c.(5407-5409)gGc>gTc	p.G1803V	BZRAP1_ENST00000355701.3_Missense_Mutation_p.G1803V|BZRAP1_ENST00000268893.6_Missense_Mutation_p.G1743V			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1803	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ATCGTCCATGCCCCCAAACAC	0.582																																					p.G1803V		Atlas-SNP	.											.	BZRAP1	287	.	0			c.G5408T						.						127	115	119					17																	56382773		2203	4300	6503	SO:0001583	missense	9256	exon29			TCCATGCCCCCAA	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.5408G>T	chr17.hg19:g.56382773C>A	ENSP00000345824:p.Gly1803Val	162.0	0.0		147.0	16.0	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	hg19	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.035305	0.35893	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.08896	3.04;3.04;3.04	5.39	-6.81	0.01704	Src homology-3 domain (3);Variant SH3 (1);	0.958653	0.08680	N	0.909552	T	0.06781	0.0173	N	0.08118	0	0.32326	N	0.56176	B;P;P	0.49307	0.213;0.454;0.922	B;B;P	0.53360	0.139;0.363;0.724	T	0.38564	-0.9655	10	0.48119	T	0.1	.	10.3478	0.43916	0.0:0.1372:0.5599:0.303	.	1794;1743;1803	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	V	1803;1803;1743	ENSP00000347929:G1803V;ENSP00000345824:G1803V;ENSP00000268893:G1743V	ENSP00000268893:G1743V	G	-	2	0	BZRAP1	53737772	0.110000	0.22057	0.210000	0.23637	0.958000	0.62258	0.774000	0.26675	-0.896000	0.03915	-0.502000	0.04539	GGC	.	.		0.582	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		A	56382773	C	A	56382773	3	1	160	1	0	0	0	0	1	0	0	0	1579	739	26	3	177	3	BZRAP1	17	56382773	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	1443584	56382773	24812437	316	24487										
TANC2	26115	hgsc.bcm.edu	37	chr17	61278235	61278235	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tacactcccacccatcagtaCaaatgcaactgccaaggact	5	15	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:61278235C>A	ENST00000424789.2	+	5	468	c.464C>A	c.(463-465)aCa>aAa	p.T155K	TANC2_ENST00000389520.4_Missense_Mutation_p.T155K|AC037445.1_ENST00000581421.1_RNA	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	155					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						CCCATCAGTACAAATGCAACT	0.507																																					p.T155K		Atlas-SNP	.											.	TANC2	266	.	0			c.C464A						.						149	145	146					17																	61278235		1980	4152	6132	SO:0001583	missense	26115	exon5			TCAGTACAAATGC	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.464C>A	chr17.hg19:g.61278235C>A	ENSP00000387593:p.Thr155Lys	218.0	0.0		236.0	40.0	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Missense_Mutation	SNP	ENST00000424789.2	hg19	CCDS45754.1	.	.	.	.	.	.	.	.	.	.	C	14.57	2.574538	0.45902	.	.	ENSG00000170921	ENST00000389520;ENST00000424789	T;T	0.38077	1.16;1.16	5.76	5.76	0.90799	.	.	.	.	.	T	0.35335	0.0928	L	0.29908	0.895	0.41456	D	0.988016	P;B	0.35033	0.481;0.349	B;B	0.38500	0.275;0.142	T	0.09618	-1.0666	9	0.45353	T	0.12	.	19.9658	0.97266	0.0:1.0:0.0:0.0	.	155;155	Q9HCD6-2;Q9HCD6	.;TANC2_HUMAN	K	155	ENSP00000374171:T155K;ENSP00000387593:T155K	ENSP00000374171:T155K	T	+	2	0	TANC2	58631967	0.999000	0.42202	1.000000	0.80357	0.168000	0.22595	5.898000	0.69838	2.721000	0.93114	0.591000	0.81541	ACA	.	.		0.507	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			A	61278235	C	A	61278235	3	1	160	1	0	0	0	0	1	0	0	0	15560	478	17	3	482	3	TANC2	17	61278235	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	4895462	61278235	19916975	317	24488										
CYB561	1534	hgsc.bcm.edu	37	chr17	61513081	61513081	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	caggacaaagacaaggatccCgcaccagctgtgtaggctgt	12	11	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:61513081C>T	ENST00000392976.1	-	4	672	c.373G>A	c.(373-375)Ggg>Agg	p.G125R	CYB561_ENST00000582997.1_Missense_Mutation_p.G132R|CYB561_ENST00000392975.2_Missense_Mutation_p.G125R|CYB561_ENST00000582297.1_Missense_Mutation_p.G125R|CYB561_ENST00000581163.1_5'UTR|CYB561_ENST00000542042.1_Missense_Mutation_p.G192R|CYB561_ENST00000582034.1_Missense_Mutation_p.G96R|CYB561_ENST00000360793.3_Missense_Mutation_p.G125R|CYB561_ENST00000581573.1_Missense_Mutation_p.G125R|CYB561_ENST00000584031.1_Silent_p.A140A|CYB561_ENST00000448884.2_Missense_Mutation_p.G125R	NM_001017916.1	NP_001017916.1	P49447	CY561_HUMAN	cytochrome b561	125	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				electron transport chain (GO:0022900)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|transmembrane electron transfer carrier (GO:0022865)			lung(2)|ovary(1)|prostate(1)	4				READ - Rectum adenocarcinoma(1115;0.0689)		ACAAGGATCCCGCACCAGCTG	0.607																																					p.G125R		Atlas-SNP	.											.	CYB561	15	.	0			c.G373A						.						130	123	125					17																	61513081		2203	4300	6503	SO:0001583	missense	1534	exon4			GGATCCCGCACCA		CCDS11636.1	17q23.3	2013-03-14	2013-03-14		ENSG00000008283	ENSG00000008283		"Cytochrome b genes"	2571	protein-coding gene	gene with protein product	"ferric-chelate reductase 2", "cytochrome b561 family, member A1"	600019				7959749, 23249217	Standard	XM_005257091		Approved	FRRS2, CYB561A1	uc002jas.3	P49447		ENST00000392976.1:c.373G>A	chr17.hg19:g.61513081C>T	ENSP00000376702:p.Gly125Arg	135.0	0.0		137.0	16.0	NM_001915	B2RE96|B7Z775|D3DU11|Q5BJG9|Q9BU05|Q9BWR9	Missense_Mutation	SNP	ENST00000392976.1	hg19	CCDS11636.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.074125	0.55646	.	.	ENSG00000008283	ENST00000360793;ENST00000392976;ENST00000392975;ENST00000448884;ENST00000542042	D;D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35;-2.35	4.43	4.43	0.53597	Cytochrome b561, eukaryote (1);Cytochrome b561/ferric reductase transmembrane (2);	0.000000	0.85682	D	0.000000	D	0.95771	0.8624	M	0.94101	3.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96930	0.9680	10	0.87932	D	0	-23.8694	15.8184	0.78621	0.0:1.0:0.0:0.0	.	125;192;125	B7Z775;F5H757;P49447	.;.;CY561_HUMAN	R	125;125;125;125;192	ENSP00000354028:G125R;ENSP00000376702:G125R;ENSP00000376701:G125R;ENSP00000400350:G125R;ENSP00000442773:G192R	ENSP00000354028:G125R	G	-	1	0	CYB561	58866813	1.000000	0.71417	0.866000	0.34008	0.994000	0.84299	5.516000	0.67055	2.297000	0.77311	0.561000	0.74099	GGG	.	.		0.607	CYB561-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444843.1	NM_001915		T	61513081	C	T	61513081	3	4	160	1	0	0	0	0	1	0	0	0	4121	652	23	1	394	1	CYB561	17	61513081	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	234846	61513081	19682129	318	24489										
CCDC45	90799	hgsc.bcm.edu	37	chr17	62533182	62533182	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcattgctggcagaagccatAtcacaggaacatcaagaact	8	10	3	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:62533182A>G	ENST00000556440.2	+	19	2751	c.2241A>G	c.(2239-2241)atA>atG	p.I747M	CEP95_ENST00000553412.1_Missense_Mutation_p.I583M	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	747						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						CAGAAGCCATATCACAGGAAC	0.343																																					p.I747M		Atlas-SNP	.											.	CEP95	103	.	0			c.A2241G						.						42	39	40					17																	62533182		1817	4078	5895	SO:0001583	missense	90799	exon19			AGCCATATCACAG	AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.2241A>G	chr17.hg19:g.62533182A>G	ENSP00000450461:p.Ile747Met	386.0	0.0		425.0	109.0	NM_138363	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	hg19	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.886267	0.51908	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	T;T	0.34072	1.4;1.38	5.34	1.5	0.22942	.	0.170777	0.51477	D	0.000087	T	0.29524	0.0736	N	0.19112	0.55	0.33229	D	0.555721	P	0.42203	0.773	P	0.48840	0.592	T	0.42258	-0.9462	10	0.72032	D	0.01	-12.7041	8.2556	0.31754	0.4833:0.3954:0.0:0.1214	.	747	Q96GE4	CEP95_HUMAN	M	682;747;583	ENSP00000450461:I747M;ENSP00000450906:I583M	ENSP00000438458:I682M	I	+	3	3	CEP95	59963644	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.997000	0.29731	0.377000	0.24735	0.379000	0.24179	ATA	.	.		0.343	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		G	62533182	A	G	62533182	3	3	160	1	0	0	0	0	1	0	0	0	2818	439	16	2	2315	2	CCDC45	17	62533182	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1020101	62533182	18662028	319	24490										
PRKAR1A	5573	hgsc.bcm.edu	37	chr17	66521090	66521090	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttctatgtgattgatcaaggAgagacggatgtaagatttac	11	4	2	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:66521090A>C	ENST00000589228.1	+	6	668	c.540A>C	c.(538-540)ggA>ggC	p.G180G	PRKAR1A_ENST00000588188.2_Silent_p.G180G|PRKAR1A_ENST00000586397.1_Silent_p.G180G|PRKAR1A_ENST00000536854.2_Silent_p.G180G|PRKAR1A_ENST00000358598.2_Silent_p.G180G|PRKAR1A_ENST00000392711.1_Silent_p.G180G	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	180					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					TTGATCAAGGAGAGACGGATG	0.313			"T, Mis, N, F, S"	RET	papillary thyroid	"myxoma, endocrine, papillary thyroid"			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of																												p.G180G	Ovarian(167;637 1670 33025 39608 46699 51856)	Atlas-SNP	.	yes	"Dom, Rec"	yes	Carney complex	17	17q23-q24	5573	"protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"		"E, M"	.	PRKAR1A	48	.	0			c.A540C						.						123	132	129					17																	66521090		2203	4300	6503	SO:0001819	synonymous_variant	5573	exon5	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;	TCAAGGAGAGACG		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"Carney complex type 1"	188830	"tissue specific extinguisher 1"	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.540A>C	chr17.hg19:g.66521090A>C		64.0	0.0		96.0	22.0	NM_001276290	K7ER48|Q567S7	Silent	SNP	ENST00000589228.1	hg19	CCDS11678.1																																																																																			.	.		0.313	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449884.1			C	66521090	A	C	66521090	2	2	160	1	0	0	0	0	0	0	0	1	12515	291	11	5		5	PRKAR1A	17	66521090	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	3987908	66521090	14674120	320	24491										
CD300LF	146722	hgsc.bcm.edu	37	chr17	72694567	72694567	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aggcggccaccaaaagcagcAgcaatatggtgaagatgagg	14	8	0	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:72694567A>T	ENST00000326165.6	-	4	611	c.500T>A	c.(499-501)cTg>cAg	p.L167Q	RAB37_ENST00000340415.3_Intron|CD300LF_ENST00000343125.4_Intron|CD300LF_ENST00000464910.1_Missense_Mutation_p.L170Q|CD300LF_ENST00000361254.4_Missense_Mutation_p.L185Q|CD300LF_ENST00000581500.1_Missense_Mutation_p.L185Q|RAB37_ENST00000402449.4_Intron|CD300LF_ENST00000469092.1_Intron|CD300LF_ENST00000301573.9_Silent_p.A182A|CD300LF_ENST00000583937.1_Missense_Mutation_p.L182Q	NM_139018.3	NP_620587.2	Q8TDQ1	CLM1_HUMAN	CD300 molecule-like family member f	167					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						CAAAAGCAGCAGCAATATGGT	0.587																																					p.L167Q		Atlas-SNP	.											.	CD300LF	55	.	0			c.T500A						.						107	76	87					17																	72694567		2203	4300	6503	SO:0001583	missense	146722	exon4			AGCAGCAGCAATA	BC028199	CCDS11704.1, CCDS74148.1, CCDS74149.1, CCDS74150.1, CCDS74151.1, CCDS74152.1	17q25.2	2013-01-11	2006-03-29		ENSG00000186074	ENSG00000186074		"Immunoglobulin superfamily / V-set domain containing"	29883	protein-coding gene	gene with protein product		609807	"CD300 antigen like family member F"			12975309	Standard	NM_139018		Approved	IREM1, NKIR, IGSF13, CD300f, CLM1	uc002jlg.3	Q8TDQ1	OTTHUMG00000067609	ENST00000326165.6:c.500T>A	chr17.hg19:g.72694567A>T	ENSP00000327075:p.Leu167Gln	87.0	0.0		92.0	14.0	NM_139018	B2RCL2|C9JDN3|Q3Y6P0|Q6UX24|Q7Z6A6|Q7Z7I4|Q7Z7I5|Q8N6D0|Q8NAF5	Missense_Mutation	SNP	ENST00000326165.6	hg19	CCDS11704.1	.	.	.	.	.	.	.	.	.	.	A	5.751	0.323065	0.10900	.	.	ENSG00000186074	ENST00000361254;ENST00000326165	T;T	0.70631	-0.5;-0.5	5.66	4.59	0.56863	.	0.428603	0.17017	N	0.190251	T	0.82185	0.4982	M	0.80422	2.495	0.20703	N	0.999864	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.982;0.999;1.0	T	0.72513	-0.4270	10	0.62326	D	0.03	.	7.5656	0.27876	0.9066:0.0:0.0934:0.0	.	182;185;167;170	E7EME0;Q8TDQ1-2;Q8TDQ1;Q8TDQ1-6	.;.;CLM1_HUMAN;.	Q	185;167	ENSP00000355294:L185Q;ENSP00000327075:L167Q	ENSP00000327075:L167Q	L	-	2	0	CD300LF	70206162	0.948000	0.32251	0.836000	0.33094	0.041000	0.13682	2.772000	0.47678	2.154000	0.67381	0.460000	0.39030	CTG	.	.		0.587	CD300LF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000145085.1	NM_139018		T	72694567	A	T	72694567	3	4	160	1	0	0	0	0	1	0	0	0	3003	188	7	4	388	4	CD300LF	17	72694567	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	6173477	72694567	8500643	321	24492										
FAM100B	283991	hgsc.bcm.edu	37	chr17	74266433	74266433	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aacttcagccccttctgggcCtcgtccccgcccagccacca	7	21	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:74266433C>T	ENST00000327490.6	+	3	646	c.342C>T	c.(340-342)gcC>gcT	p.A114A	UBALD2_ENST00000589240.1_Silent_p.A54A	NM_182565.3	NP_872371.1	Q8IYN6	UBAD2_HUMAN	UBA-like domain containing 2	114																	CCTTCTGGGCCTCGTCCCCGC	0.706																																					p.A114A		Atlas-SNP	.											.	.	.	.	0			c.C342T						.						16	13	14					17																	74266433		2171	4281	6452	SO:0001819	synonymous_variant	283991	exon3			CTGGGCCTCGTCC		CCDS11742.1	17q25.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000185262	ENSG00000185262			28438	protein-coding gene	gene with protein product			"family with sequence similarity 100, member B"	FAM100B			Standard	NM_182565		Approved	MGC29814	uc010wsy.1	Q8IYN6	OTTHUMG00000132666	ENST00000327490.6:c.342C>T	chr17.hg19:g.74266433C>T		56.0	0.0		88.0	16.0	NM_182565		Silent	SNP	ENST00000327490.6	hg19	CCDS11742.1																																																																																			.	.		0.706	UBALD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255920.1	NM_182565		T	74266433	C	T	74266433	2	4	160	1	0	0	0	0	0	0	0	1	5384	668	24	3		3	FAM100B	17	74266433	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	1571866	74266433	6928777	322	24493										
TMC6	11322	hgsc.bcm.edu	37	chr17	76121042	76121042	+	Frame_Shift_Del	DEL	C	C	-													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cccggctggcccctccacttCcccctcggggtcctgctctt							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:76121042delC	ENST00000590602.1	-	7	720	c.561delG	c.(559-561)gggfs	p.G187fs	TMC6_ENST00000392467.3_Frame_Shift_Del_p.G187fs|TMC6_ENST00000592076.1_5'Flank|TMC6_ENST00000306591.7_Frame_Shift_Del_p.G187fs|TMC6_ENST00000322914.3_Frame_Shift_Del_p.G187fs|TMC6_ENST00000591436.1_5'Flank|TMC6_ENST00000322933.4_5'UTR|TMC6_ENST00000589553.1_Intron			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	187					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CCCTCCACTTCCCCCTCGGGG	0.682																																					p.K188fs		Atlas-INDEL	.											.	TMC6	42	.	0			c.562delA						.						8	10	9					17																	76121042		2174	4271	6445	SO:0001589	frameshift_variant	11322	exon7			.	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"epidermodysplasia verruciformis 1"	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.561delG	chr17.hg19:g.76121042delC	ENSP00000465261:p.Gly187fs	100.0	0.0		95.0	10.0	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Frame_Shift_Del	DEL	ENST00000590602.1	hg19	CCDS32748.1																																																																																			.	.		0.682	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			-	76121042	C	-	76121042	7	5	160	1	0	1	0	1	0	0	0	0	16004	842	30	0	1912	0	TMC6	17	76121042	Frame_Shift_Del	DEL	C	TCGA-DD-AACI-01A-11D-A40R-10	1854609	76121042	5074168	323	24494										
CYTH1	9267	hgsc.bcm.edu	37	chr17	76778291	76778291	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggggcgcactgaccgtagctGtcgtcctcctccatggtgcg	14	14	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:76778291G>C	ENST00000446868.3	-	1	85	c.15C>G	c.(13-15)gaC>gaG	p.D5E	CYTH1_ENST00000591455.1_Missense_Mutation_p.D5E|CYTH1_ENST00000589296.1_Missense_Mutation_p.D5E|CYTH1_ENST00000361101.4_Missense_Mutation_p.D5E			Q15438	CYH1_HUMAN	cytohesin 1	5					establishment of epithelial cell polarity (GO:0090162)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	19						GACCGTAGCTGTCGTCCTCCT	0.801																																					p.D5E		Atlas-SNP	.											.	CYTH1	36	.	0			c.C15G						.						3	3	3					17																	76778291		1374	2726	4100	SO:0001583	missense	9267	exon1			GTAGCTGTCGTCC	M85169	CCDS32754.1, CCDS42392.2	17q25	2014-05-02	2008-08-14	2008-08-14	ENSG00000108669	ENSG00000108669		"Pleckstrin homology (PH) domain containing"	9501	protein-coding gene	gene with protein product		182115	"pleckstrin homology, Sec7 and coiled-coil domains 1"	PSCD1		1511013, 8449036, 21628335, 20018626	Standard	XM_006722180		Approved	B2-1, D17S811E, cytohesin-1	uc002jvw.3	Q15438	OTTHUMG00000150253	ENST00000446868.3:c.15C>G	chr17.hg19:g.76778291G>C	ENSP00000389095:p.Asp5Glu	50.0	0.0		67.0	6.0	NM_017456	A6NFW7|B7Z1T4|Q9P123|Q9P124	Missense_Mutation	SNP	ENST00000446868.3	hg19		.	.	.	.	.	.	.	.	.	.	g	11.20	1.569107	0.28003	.	.	ENSG00000108669	ENST00000446868;ENST00000361101;ENST00000392457;ENST00000262763	T;T	0.12255	2.7;2.7	2.44	2.44	0.29823	.	1.450410	0.04036	N	0.302257	T	0.10766	0.0263	L	0.27053	0.805	0.25886	N	0.983538	B	0.09022	0.002	B	0.09377	0.004	T	0.24584	-1.0156	10	0.15499	T	0.54	.	8.5166	0.33250	0.0:0.0:1.0:0.0	.	5	Q15438-2	.	E	5	ENSP00000389095:D5E;ENSP00000354398:D5E	ENSP00000262763:D5E	D	-	3	2	CYTH1	74289886	0.998000	0.40836	1.000000	0.80357	0.828000	0.46876	0.498000	0.22530	1.672000	0.50884	0.282000	0.19409	GAC	.	.		0.801	CYTH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317099.1	NM_004762		C	76778291	G	C	76778291	3	2	160	1	0	0	0	0	1	0	0	0	4205	1368	48	4	1233	4	CYTH1	17	76778291	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	657249	76778291	4416919	324	24495										
AATK	9625	hgsc.bcm.edu	37	chr17	79095855	79095855	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aaggcggccacgccccagtcTgcatcctccgctcctccctc	8	21	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr17:79095855T>A	ENST00000326724.4	-	11	1905	c.1881A>T	c.(1879-1881)gcA>gcT	p.A627A	AATK_ENST00000572339.1_5'Flank|AATK_ENST00000417379.1_Silent_p.A524A	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	627					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CGCCCCAGTCTGCATCCTCCG	0.726																																					p.A627A		Atlas-SNP	.											.	AATK	102	.	0			c.A1881T						.						10	13	12					17																	79095855		1882	4021	5903	SO:0001819	synonymous_variant	9625	exon11			CCAGTCTGCATCC	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.1881A>T	chr17.hg19:g.79095855T>A		64.0	0.0		75.0	9.0	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	hg19	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	T	10.14	1.269169	0.23221	.	.	ENSG00000181409	ENST00000417379	.	.	.	4.19	-7.01	0.01594	.	.	.	.	.	T	0.15046	0.0363	.	.	.	0.19575	N	0.999969	.	.	.	.	.	.	T	0.23940	-1.0174	4	.	.	.	.	0.4576	0.00511	0.3097:0.2576:0.2528:0.1799	.	.	.	.	L	580	.	.	Q	-	2	0	AATK	76710450	0.000000	0.05858	0.020000	0.16555	0.173000	0.22820	-1.287000	0.02785	-1.514000	0.01786	0.402000	0.26972	CAG	.	.		0.726	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		A	79095855	T	A	79095855	2	1	160	1	0	0	0	0	0	0	0	1	26	1567	55	4		4	AATK	17	79095855	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2317564	79095855	2099355	325	24496										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7013922	7013922	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cagtcacagggaacacagtcGggaaagtctctgtaacccaa	10	11	2	0	rs375804587		TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr18:7013922G>A	ENST00000389658.3	-	23	3348	c.3255C>T	c.(3253-3255)ccC>ccT	p.P1085P		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1085	Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.P1085P(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GAACACAGTCGGGAAAGTCTC	0.612																																					p.P1085P		Atlas-SNP	.											LAMA1,NS,carcinoma,0,1	LAMA1	458	.	1	Substitution - coding silent(1)	ovary(1)	c.C3255T						.	G		0,4406		0,0,2203	58	49	52		3255	-3.2	1	18		52	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LAMA1	NM_005559.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		1085/3076	7013922	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon23			ACAGTCGGGAAAG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.3255C>T	chr18.hg19:g.7013922G>A		156.0	0.0		103.0	20.0	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.612	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		A	7013922	G	A	7013922	2	1	160	1	0	0	0	0	0	0	0	1	8614	1103	39	1		1	LAMA1	18	7013922	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10		7013922	71063326	326	24497										
DSG4	147409	hgsc.bcm.edu	37	chr18	28979346	28979346	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aaatgcacccaacccctgtgAgaattcaagttgttgatgtg	9	9	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr18:28979346A>T	ENST00000308128.4	+	9	1252	c.1117A>T	c.(1117-1119)Aga>Tga	p.R373*	RP11-534N16.1_ENST00000581856.1_RNA|DSG4_ENST00000359747.4_Nonsense_Mutation_p.R373*|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	373	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			AACCCCTGTGAGAATTCAAGT	0.403																																					p.R373X		Atlas-SNP	.											.	DSG4	343	.	0			c.A1117T						.						128	123	125					18																	28979346		2203	4300	6503	SO:0001587	stop_gained	147409	exon9			CCTGTGAGAATTC	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.1117A>T	chr18.hg19:g.28979346A>T	ENSP00000311859:p.Arg373*	152.0	0.0		110.0	23.0	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Nonsense_Mutation	SNP	ENST00000308128.4	hg19	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	A	38	6.660009	0.97743	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	.	.	.	5.33	4.14	0.48551	.	0.000000	0.36665	N	0.002468	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	7.0959	0.25309	0.7763:0.1494:0.0742:0.0	.	.	.	.	X	373	.	ENSP00000311859:R373X	R	+	1	2	DSG4	27233344	0.998000	0.40836	1.000000	0.80357	0.637000	0.38172	3.888000	0.56204	0.927000	0.37143	0.528000	0.53228	AGA	.	.		0.403	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		T	28979346	A	T	28979346	4	4	160	1	0	0	0	0	0	1	0	0	4781	296	11	4	1151	4	DSG4	18	28979346	Nonsense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	21965424	28979346	49097902	327	24498										
CDC34	997	hgsc.bcm.edu	37	chr19	541500	541500	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cggcgaggtggaggaggaggCcgacagctgcttcggggacg	21	9	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:541500C>T	ENST00000215574.4	+	5	877	c.659C>T	c.(658-660)gCc>gTc	p.A220V	GZMM_ENST00000264553.3_5'Flank	NM_004359.1	NP_004350.1	P49427	UB2R1_HUMAN	cell division cycle 34	220	Asp/Glu-rich (acidic).|SCF-binding.				cellular protein modification process (GO:0006464)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of neuron apoptotic process (GO:0043525)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|response to growth factor (GO:0070848)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(1)	2		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGAGGAGGCCGACAGCTGC	0.627																																					p.A220V		Atlas-SNP	.											.	CDC34	5	.	0			c.C659T						.						58	51	53					19																	541500		2203	4300	6503	SO:0001583	missense	997	exon5			AGGAGGCCGACAG	L22005	CCDS12030.1	19p13.3	2013-01-17	2013-01-17					"Ubiquitin-conjugating enzymes E2"	1734	protein-coding gene	gene with protein product		116948	"cell division cycle 34", "cell division cycle 34 homolog (S. cerevisiae)"			8248134, 16210246	Standard	NM_004359		Approved	E2-CDC34, UBE2R1, UBC3	uc002lov.3	P49427		ENST00000215574.4:c.659C>T	chr19.hg19:g.541500C>T	ENSP00000215574:p.Ala220Val	101.0	0.0		115.0	12.0	NM_004359	A8K689	Missense_Mutation	SNP	ENST00000215574.4	hg19	CCDS12030.1	.	.	.	.	.	.	.	.	.	.	C	9.249	1.040337	0.19669	.	.	ENSG00000099804	ENST00000215574	T	0.44482	0.92	5.45	4.4	0.53042	.	1.436810	0.04575	N	0.393903	T	0.39009	0.1062	L	0.34521	1.04	0.37336	D	0.910168	B	0.26635	0.155	B	0.32864	0.154	T	0.05435	-1.0885	10	0.13470	T	0.59	-33.7016	12.5535	0.56240	0.3028:0.6972:0.0:0.0	.	220	P49427	UB2R1_HUMAN	V	220	ENSP00000215574:A220V	ENSP00000215574:A220V	A	+	2	0	CDC34	492500	0.977000	0.34250	0.464000	0.27143	0.002000	0.02628	2.459000	0.45023	1.306000	0.44926	-0.187000	0.12897	GCC	.	.		0.627	CDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451889.2	NM_004359		T	541500	C	T	541500	3	4	160	1	0	0	0	0	1	0	0	0	3069	739	26	3	677	3	CDC34	19	541500	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10		541500	58587483	328	24499										
GRIN3B	116444	hgsc.bcm.edu	37	chr19	1003596	1003596	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gccatccatgacattgtgcaActggtggcccgggcgctggg	15	12	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:1003596A>T	ENST00000234389.3	+	2	913	c.894A>T	c.(892-894)caA>caT	p.Q298H	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	298					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ACATTGTGCAACTGGTGGCCC	0.766																																					p.Q298H		Atlas-SNP	.											.	GRIN3B	46	.	0			c.A894T						.						2	3	3					19																	1003596		1638	3485	5123	SO:0001583	missense	116444	exon2			TGTGCAACTGGTG		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.894A>T	chr19.hg19:g.1003596A>T	ENSP00000234389:p.Gln298His	100.0	0.0		112.0	9.0	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	hg19	CCDS32861.1	.	.	.	.	.	.	.	.	.	.	a	8.581	0.882389	0.17467	.	.	ENSG00000116032	ENST00000234389	D	0.86164	-2.08	3.94	-1.25	0.09405	.	0.191195	0.33401	U	0.004946	T	0.72700	0.3493	N	0.24115	0.695	0.09310	N	0.99999	P	0.41748	0.761	B	0.38500	0.275	T	0.66834	-0.5823	10	0.66056	D	0.02	.	4.2075	0.10495	0.3239:0.3248:0.3512:0.0	.	298	O60391	NMD3B_HUMAN	H	298	ENSP00000234389:Q298H	ENSP00000234389:Q298H	Q	+	3	2	GRIN3B	954596	1.000000	0.71417	0.009000	0.14445	0.003000	0.03518	1.997000	0.40786	-0.500000	0.06614	-1.685000	0.00733	CAA	.	.		0.766	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2			T	1003596	A	T	1003596	3	4	160	1	0	0	0	0	1	0	0	0	6793	40	2	4	900	4	GRIN3B	19	1003596	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	462096	1003596	58125387	329	24500										
KLF16	83855	hgsc.bcm.edu	37	chr19	1854493	1854493	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ggctgggctgggcgcggggcTgggcgcagggctcccggcca	22	13	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:1854493T>A	ENST00000250916.4	-	2	794	c.724A>T	c.(724-726)Agc>Tgc	p.S242C	KLF16_ENST00000592313.1_5'UTR|CTB-31O20.6_ENST00000592884.1_RNA	NM_031918.3	NP_114124.1	Q9BXK1	KLF16_HUMAN	Kruppel-like factor 16	242	Pro/Ser-rich.				dopamine receptor signaling pathway (GO:0007212)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)	1		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCGCGGGGCTGGGCGCAGGG	0.751																																					p.S242C		Atlas-SNP	.											.	KLF16	9	.	0			c.A724T						.						3	5	4					19																	1854493		1468	3274	4742	SO:0001583	missense	83855	exon2			CGGGGCTGGGCGC	AF327440	CCDS12075.1	19p13.3	2013-10-15			ENSG00000129911	ENSG00000129911		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	16857	protein-coding gene	gene with protein product		606139				11438660	Standard	NM_031918		Approved	NSLP2, BTEB4, DRRF	uc002luc.3	Q9BXK1	OTTHUMG00000179994	ENST00000250916.4:c.724A>T	chr19.hg19:g.1854493T>A	ENSP00000250916:p.Ser242Cys	52.0	0.0		67.0	24.0	NM_031918		Missense_Mutation	SNP	ENST00000250916.4	hg19	CCDS12075.1	.	.	.	.	.	.	.	.	.	.	T	15.67	2.901152	0.52227	.	.	ENSG00000129911	ENST00000250916;ENST00000541015	T;T	0.13901	2.55;2.55	3.34	3.34	0.38264	.	.	.	.	.	T	0.28599	0.0708	L	0.50333	1.59	0.29023	N	0.886157	D	0.76494	0.999	D	0.74674	0.984	T	0.03354	-1.1045	9	0.72032	D	0.01	.	9.7369	0.40392	0.0:0.0:0.0:1.0	.	242	Q9BXK1	KLF16_HUMAN	C	242	ENSP00000250916:S242C;ENSP00000439973:S242C	ENSP00000250916:S242C	S	-	1	0	KLF16	1805493	1.000000	0.71417	0.995000	0.50966	0.611000	0.37282	1.022000	0.30052	1.392000	0.46585	0.391000	0.25812	AGC	.	.		0.751	KLF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449214.1			A	1854493	T	A	1854493	3	1	160	1	0	0	0	0	1	0	0	0	8353	1580	55	4	38	4	KLF16	19	1854493	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	850897	1854493	57274490	330	24501										
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4171378	4171378	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	actctgccgctgtctccaccAggtcctgttgctgtcctttg	9	15	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:4171378A>G	ENST00000078445.2	+	9	1122		c.e9-1		CREB3L3_ENST00000602147.1_Splice_Site|CREB3L3_ENST00000602257.1_Splice_Site|CREB3L3_ENST00000595923.1_Splice_Site|CREB3L3_ENST00000252587.3_Splice_Site	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		TGTCTCCACCAGGTCCTGTTG	0.607																																					.		Atlas-SNP	.											.	CREB3L3	53	.	0			c.973-2A>G						.						91	79	83					19																	4171378		2203	4300	6503	SO:0001630	splice_region_variant	84699	exon9			TCCACCAGGTCCT		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.976-1A>G	chr19.hg19:g.4171378A>G		73.0	0.0		70.0	29.0	NM_001271995	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Splice_Site	SNP	ENST00000078445.2	hg19	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	A	13.39	2.221787	0.39300	.	.	ENSG00000060566	ENST00000078445;ENST00000381943;ENST00000252587	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8958	0.52656	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CREB3L3	4122378	1.000000	0.71417	0.988000	0.46212	0.273000	0.26683	6.155000	0.71833	1.700000	0.51204	0.459000	0.35465	.	.	.		0.607	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	Intron	G	4171378	A	G	4171378	5	3	160	1	0	0	0	0	0	0	1	0	3860	202	7	2	1008	2	CREB3L3	19	4171378	Splice_Site	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2316885	4171378	54957605	331	24502										
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4171711	4171711	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtggctgctgatgctgtgccAggctccgaggccccaggacc	15	14	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:4171711A>T	ENST00000078445.2	+	10	1278	c.1131A>T	c.(1129-1131)ccA>ccT	p.P377P	CREB3L3_ENST00000602147.1_3'UTR|CREB3L3_ENST00000602257.1_Silent_p.P375P|CREB3L3_ENST00000595923.1_Silent_p.P376P|CREB3L3_ENST00000252587.3_Missense_Mutation_p.Q266L	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	377					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGCTGTGCCAGGCTCCGAGG	0.647																																					p.P377P		Atlas-SNP	.											.	CREB3L3	53	.	0			c.A1131T						.						60	72	67					19																	4171711		2201	4294	6495	SO:0001819	synonymous_variant	84699	exon10			TGTGCCAGGCTCC		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.1131A>T	chr19.hg19:g.4171711A>T		184.0	0.0		171.0	11.0	NM_032607	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	hg19	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	A	9.219	1.032845	0.19590	.	.	ENSG00000060566	ENST00000252587	T	0.78707	-1.2	3.53	-1.35	0.09114	.	.	.	.	.	T	0.67664	0.2917	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.57659	-0.7773	6	0.41790	T	0.15	-31.4195	4.5208	0.11958	0.6057:0.1686:0.2258:0.0	.	.	.	.	L	266	ENSP00000252587:Q266L	ENSP00000252587:Q266L	Q	+	2	0	CREB3L3	4122711	0.000000	0.05858	0.006000	0.13384	0.002000	0.02628	-1.567000	0.02146	-0.523000	0.06409	-1.277000	0.01392	CAG	.	.		0.647	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607		T	4171711	A	T	4171711	2	4	160	1	0	0	0	0	0	0	0	1	3860	175	7	4		4	CREB3L3	19	4171711	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	333	4171711	54957272	332	24503										
TNFSF14	8740	hgsc.bcm.edu	37	chr19	6670072	6670072	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	actgagggccgtacgacactCtcctccatgcccaaggtgtc	10	15	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:6670072C>G	ENST00000599359.1	-	2	390	c.9G>C	c.(7-9)gaG>gaC	p.E3D	TNFSF14_ENST00000326176.9_Missense_Mutation_p.E3D|TNFSF14_ENST00000245912.3_Missense_Mutation_p.E3D			O43557	TNF14_HUMAN	tumor necrosis factor (ligand) superfamily, member 14	3					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of T cell chemotaxis (GO:0010820)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|receptor binding (GO:0005102)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18						GTACGACACTCTCCTCCATGC	0.602																																					p.E3D		Atlas-SNP	.											.	TNFSF14	40	.	0			c.G9C						.						95	72	80					19																	6670072		2203	4300	6503	SO:0001583	missense	8740	exon2			GACACTCTCCTCC	AF036581	CCDS12171.1, CCDS45939.1	19p13.3	2008-02-05				ENSG00000125735		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11930	protein-coding gene	gene with protein product		604520				9462508	Standard	NM_172014		Approved	LIGHT, LTg, HVEM-L, CD258	uc002mfk.2	O43557		ENST00000599359.1:c.9G>C	chr19.hg19:g.6670072C>G	ENSP00000469049:p.Glu3Asp	48.0	0.0		58.0	4.0	NM_003807	A8K7M2|C9J5H4|O75476|Q6FHA1|Q8WVF8|Q96LD2	Missense_Mutation	SNP	ENST00000599359.1	hg19	CCDS12171.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.688277	0.29962	.	.	ENSG00000125735	ENST00000245912;ENST00000326176	T;T	0.37752	1.18;1.18	5.04	-4.44	0.03557	.	0.712502	0.12707	N	0.445841	T	0.21590	0.0520	L	0.28740	0.885	0.09310	N	1	B;B	0.12013	0.003;0.005	B;B	0.16722	0.007;0.016	T	0.23940	-1.0174	10	0.33141	T	0.24	-1.6926	9.5391	0.39240	0.2534:0.2734:0.4732:0.0	.	3;3	O43557;O43557-2	TNF14_HUMAN;.	D	3	ENSP00000245912:E3D;ENSP00000326940:E3D	ENSP00000245912:E3D	E	-	3	2	TNFSF14	6621072	0.000000	0.05858	0.009000	0.14445	0.028000	0.11728	-3.607000	0.00416	-0.382000	0.07870	0.563000	0.77884	GAG	.	.		0.602	TNFSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457863.1			G	6670072	C	G	6670072	3	3	160	1	0	0	0	0	1	0	0	0	16322	912	32	4	729	4	TNFSF14	19	6670072	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	2498361	6670072	52458911	333	24504										
KANK3	6234	hgsc.bcm.edu	37	chr19	8387768	8387768	+	3'UTR	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ttgtcaccgcattctccttcAccaggtgtggctgtctggga	11	12	4	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:8387768A>C	ENST00000600659.2	+	0	870				KANK3_ENST00000330915.3_Silent_p.G807G|NDUFA7_ENST00000598884.1_5'Flank|NDUFA7_ENST00000301457.2_5'Flank	NM_001031.4	NP_001022.1	P62857	RS28_HUMAN	ribosomal protein S28						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)										ATTCTCCTTCACCAGGTGTGG	0.587																																					p.G807G		Atlas-SNP	.											.	KANK3	35	.	0			c.T2421G						.						84	67	73					19																	8387768		2203	4300	6503	SO:0001624	3_prime_UTR_variant	256949	exon11			TCCTTCACCAGGT	D14530	CCDS45953.1	19p13.2	2011-04-06				ENSG00000233927		"S ribosomal proteins"	10418	protein-coding gene	gene with protein product	"40S ribosomal protein S28"	603685				8415000, 9582194	Standard	NM_001031		Approved	S28	uc002mjn.3	P62857		ENST00000600659.2:c.*629A>C	chr19.hg19:g.8387768A>C		41.0	0.0		58.0	8.0	NM_198471	P25112	Silent	SNP	ENST00000600659.2	hg19	CCDS45953.1																																																																																			.	.		0.587	RPS28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461377.3	NM_001031		C	8387768	A	C	8387768	1	2	160	0	1	0	0	0	0	0	0	0	7987	146	6	5		5	KANK3	19	8387768	3'UTR	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1717696	8387768	50741215	334	24505										
MUC16	94025	hgsc.bcm.edu	37	chr19	8966763	8966763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgtctactctccgagccagtGgcgagaagttacacagggag	13	10	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:8966763G>A	ENST00000397910.4	-	81	43393	c.43190C>T	c.(43189-43191)cCa>cTa	p.P14397L	MUC16_ENST00000380951.5_Missense_Mutation_p.P1038L	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	14495				Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCGAGCCAGTGGCGAGAAGTT	0.532																																					p.P14397L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C43190T						.						27	30	29					19																	8966763		1954	4136	6090	SO:0001583	missense	94025	exon81			GCCAGTGGCGAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.43190C>T	chr19.hg19:g.8966763G>A	ENSP00000381008:p.Pro14397Leu	97.0	0.0		102.0	15.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	9.742|9.742	1.165075|1.165075	0.21538|0.21538	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.34072	.|1.38;1.38	4.22|4.22	2.07|2.07	0.26955|0.26955	.|SEA (2);	0.466719|.	0.18197|.	N|.	0.148652|.	T|T	0.54303|0.54303	0.1850|0.1850	M|M	0.88570|0.88570	2.965|2.965	.|.	.|.	.|.	.|P;D	.|0.57257	.|0.823;0.979	.|B;P	.|0.55923	.|0.405;0.787	T|T	0.64947|0.64947	-0.6287|-0.6287	5|8	.|0.66056	.|D	.|0.02	.|.	6.6835|6.6835	0.23132|0.23132	0.2181:0.0:0.7819:0.0|0.2181:0.0:0.7819:0.0	.|.	.|22042;14397	.|Q8WXI7;B5ME49	.|MUC16_HUMAN;.	Y|L	1220|14397;1038	.|ENSP00000381008:P14397L;ENSP00000370338:P1038L	.|ENSP00000370338:P1038L	H|P	-|-	1|2	0|0	MUC16|MUC16	8827763|8827763	0.001000|0.001000	0.12720|0.12720	0.007000|0.007000	0.13788|0.13788	0.029000|0.029000	0.11900|0.11900	0.849000|0.849000	0.27723|0.27723	0.541000|0.541000	0.28827|0.28827	0.651000|0.651000	0.88453|0.88453	CAC|CCA	.	.		0.532	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	8966763	G	A	8966763	3	1	160	1	0	0	0	0	1	0	0	0	9982	1348	47	3	349	3	MUC16	19	8966763	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	578995	8966763	50162220	335	24506										
ZNF491	126069	hgsc.bcm.edu	37	chr19	11917800	11917800	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctgccaagtacattcgaatAcatggaaggactcacactgg	9	10	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:11917800A>T	ENST00000323169.5	+	3	1363	c.1032A>T	c.(1030-1032)atA>atT	p.I344I	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	344					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						ACATTCGAATACATGGAAGGA	0.443																																					p.I344I		Atlas-SNP	.											.	ZNF491	61	.	0			c.A1032T						.						63	64	63					19																	11917800		2203	4300	6503	SO:0001819	synonymous_variant	126069	exon3			TCGAATACATGGA	AK092110	CCDS12267.1	19p13.2	2013-01-08			ENSG00000177599	ENSG00000177599		"Zinc fingers, C2H2-type"	23706	protein-coding gene	gene with protein product							Standard	XM_005259730		Approved	FLJ34791	uc002mso.1	Q8N8L2	OTTHUMG00000156529	ENST00000323169.5:c.1032A>T	chr19.hg19:g.11917800A>T		91.0	0.0		89.0	28.0	NM_152356	Q3MJ35|Q8NAT8	Silent	SNP	ENST00000323169.5	hg19	CCDS12267.1																																																																																			.	.		0.443	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356		T	11917800	A	T	11917800	2	4	160	1	0	0	0	0	0	0	0	1	17957	381	14	4		4	ZNF491	19	11917800	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2951037	11917800	47211183	336	24507										
ZNF709	163051	hgsc.bcm.edu	37	chr19	12575440	12575440	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcatgtattcgaacagaactGgaacaactgaaggctttacc	8	9	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:12575440G>T	ENST00000397732.3	-	4	1467	c.1296C>A	c.(1294-1296)tcC>tcA	p.S432S	CTD-3105H18.18_ENST00000598753.1_Intron|ZNF709_ENST00000428311.1_Silent_p.S432S	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	432					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|upper_aerodigestive_tract(3)	6						GAACAGAACTGGAACAACTGA	0.423																																					p.S432S	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											.	ZNF709	80	.	0			c.C1296A						.						112	117	116					19																	12575440		2203	4299	6502	SO:0001819	synonymous_variant	163051	exon4			AGAACTGGAACAA	AK095600	CCDS42504.1	19p13.2	2013-01-08			ENSG00000242852	ENSG00000242852		"Zinc fingers, C2H2-type", "-"	20629	protein-coding gene	gene with protein product							Standard	NM_152601		Approved	FLJ38281	uc002mtv.4	Q8N972	OTTHUMG00000156406	ENST00000397732.3:c.1296C>A	chr19.hg19:g.12575440G>T		96.0	0.0		101.0	16.0	NM_152601	A8K4E6	Silent	SNP	ENST00000397732.3	hg19	CCDS42504.1																																																																																			.	.		0.423	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		T	12575440	G	T	12575440	2	4	160	1	0	0	0	0	0	0	0	1	18128	1335	47	3		3	ZNF709	19	12575440	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	657640	12575440	46553543	337	24508										
CCDC130	81576	hgsc.bcm.edu	37	chr19	13873731	13873731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aactgagacccccaagtgcaGcagcccgagggggcaggaag	15	12	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:13873731G>A	ENST00000586600.1	+	11	1543	c.1040G>A	c.(1039-1041)aGc>aAc	p.S347N	MRI1_ENST00000319545.8_5'Flank|MRI1_ENST00000040663.6_5'Flank|CCDC130_ENST00000587019.1_3'UTR|CCDC130_ENST00000221554.8_Missense_Mutation_p.S347N			P13994	CC130_HUMAN	coiled-coil domain containing 130	347					response to virus (GO:0009615)					endometrium(2)|kidney(1)|large_intestine(3)|ovary(1)|skin(2)|urinary_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)			CCCAAGTGCAGCAGCCCGAGG	0.697																																					p.S347N		Atlas-SNP	.											.	CCDC130	25	.	0			c.G1040A						.						12	16	15					19																	13873731		2189	4277	6466	SO:0001583	missense	81576	exon10			AGTGCAGCAGCCC	AF250306	CCDS12296.1	19p13.13	2008-02-05				ENSG00000104957			28118	protein-coding gene	gene with protein product						3203696	Standard	NM_030818		Approved	MGC10471	uc002mxc.1	P13994		ENST00000586600.1:c.1040G>A	chr19.hg19:g.13873731G>A	ENSP00000465776:p.Ser347Asn	161.0	0.0		155.0	58.0	NM_030818	Q9BQ72	Missense_Mutation	SNP	ENST00000586600.1	hg19	CCDS12296.1	.	.	.	.	.	.	.	.	.	.	G	9.245	1.039253	0.19669	.	.	ENSG00000104957	ENST00000221554	T	0.32753	1.44	3.14	2.07	0.26955	.	1.923890	0.01721	N	0.028272	T	0.30293	0.0760	L	0.57536	1.79	0.09310	N	0.999999	P;B	0.36354	0.549;0.324	B;B	0.34536	0.185;0.129	T	0.19031	-1.0318	10	0.18276	T	0.48	.	6.7732	0.23604	0.1457:0.0:0.8543:0.0	.	347;347	B3KUZ1;P13994	.;CC130_HUMAN	N	347	ENSP00000221554:S347N	ENSP00000221554:S347N	S	+	2	0	CCDC130	13734731	0.001000	0.12720	0.001000	0.08648	0.012000	0.07955	0.882000	0.28186	0.626000	0.30322	0.313000	0.20887	AGC	.	.		0.697	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818		A	13873731	G	A	13873731	3	1	160	1	0	0	0	0	1	0	0	0	2768	971	34	3	1074	3	CCDC130	19	13873731	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	1298291	13873731	45255252	338	24509										
UPF1	5976	hgsc.bcm.edu	37	chr19	18961531	18961531	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gccagagcagcctcaaggacAtcaactgggacagctcgcag	12	13	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:18961531A>T	ENST00000599848.1	+	5	873	c.664A>T	c.(664-666)Atc>Ttc	p.I222F	UPF1_ENST00000600310.1_3'UTR|UPF1_ENST00000262803.5_Missense_Mutation_p.I222F			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	222	Sufficient for interaction with RENT2.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						CCTCAAGGACATCAACTGGGA	0.692																																					p.I222F		Atlas-SNP	.											.	UPF1	88	.	0			c.A664T						.						24	22	23					19																	18961531		2199	4296	6495	SO:0001583	missense	5976	exon5			AAGGACATCAACT	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"UP Frameshift 1", "smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"	601430	"regulator of nonsense transcripts 1"	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.664A>T	chr19.hg19:g.18961531A>T	ENSP00000470142:p.Ile222Phe	105.0	0.0		105.0	7.0	NM_002911	O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	ENST00000599848.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.96	3.516612	0.64634	.	.	ENSG00000005007	ENST00000262803	D	0.89617	-2.54	4.63	4.63	0.57726	RNA helicase UPF1, UPF2-interacting domain (1);	0.054008	0.64402	D	0.000001	D	0.88529	0.6461	M	0.62723	1.935	0.80722	D	1	B;B	0.26041	0.14;0.012	B;B	0.34138	0.176;0.024	D	0.87636	0.2519	10	0.62326	D	0.03	-26.121	13.4865	0.61369	1.0:0.0:0.0:0.0	.	222;222	Q92900;Q92900-2	RENT1_HUMAN;.	F	222	ENSP00000262803:I222F	ENSP00000262803:I222F	I	+	1	0	UPF1	18822531	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.618000	0.90932	1.843000	0.53566	0.482000	0.46254	ATC	.	.		0.692	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		T	18961531	A	T	18961531	3	4	160	1	0	0	0	0	1	0	0	0	17018	217	8	4	682	4	UPF1	19	18961531	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	5087800	18961531	40167452	339	24510										
ETHE1	23474	hgsc.bcm.edu	37	chr19	44012166	44012166	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tcctcacagctgagggtgagCcgagggttcagagtcctctc	13	12	3	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:44012166C>T	ENST00000292147.2	-	6	708	c.642G>A	c.(640-642)cgG>cgA	p.R214R	ETHE1_ENST00000600651.1_Silent_p.R214R	NM_014297.3	NP_055112.2	O95571	ETHE1_HUMAN	ethylmalonic encephalopathy 1	214					cellular nitrogen compound metabolic process (GO:0034641)|glutathione metabolic process (GO:0006749)|hydrogen sulfide metabolic process (GO:0070813)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|sulfur dioxygenase activity (GO:0050313)			central_nervous_system(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	5		Prostate(69;0.0153)				TGAGGGTGAGCCGAGGGTTCA	0.567																																					p.R214R		Atlas-SNP	.											.	ETHE1	7	.	0			c.G642A						.						82	65	71					19																	44012166		2203	4300	6503	SO:0001819	synonymous_variant	23474	exon6			GGTGAGCCGAGGG		CCDS12622.1	19q13.32	2014-06-20				ENSG00000105755	1.13.11.18		23287	protein-coding gene	gene with protein product		608451				19136963	Standard	NM_014297		Approved	YF13H12, HSCO	uc002owp.3	O95571		ENST00000292147.2:c.642G>A	chr19.hg19:g.44012166C>T		62.0	0.0		75.0	8.0	NM_014297	Q96HR0|Q9H001	Silent	SNP	ENST00000292147.2	hg19	CCDS12622.1																																																																																			.	.		0.567	ETHE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463184.1	NM_014297		T	44012166	C	T	44012166	2	4	160	1	0	0	0	0	0	0	0	1	5274	726	26	3		3	ETHE1	19	44012166	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	25050635	44012166	15116817	340	24511										
ZNF221	7638	hgsc.bcm.edu	37	chr19	44469460	44469460	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gaagatgaagacaacaagccAaagagaagggaattcaggta	12	5	1	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:44469460A>T	ENST00000251269.5	+	5	612	c.284A>T	c.(283-285)cAa>cTa	p.Q95L	ZNF221_ENST00000587682.1_Missense_Mutation_p.Q95L|ZNF221_ENST00000592350.1_Missense_Mutation_p.Q95L	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	95	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				ACAACAAGCCAAAGAGAAGGG	0.423																																					p.Q95L		Atlas-SNP	.											.	ZNF221	59	.	0			c.A284T						.						92	85	87					19																	44469460		2203	4300	6503	SO:0001583	missense	7638	exon5			CAAGCCAAAGAGA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.284A>T	chr19.hg19:g.44469460A>T	ENSP00000251269:p.Gln95Leu	198.0	0.0		183.0	19.0	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	hg19	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	A	2.119	-0.401963	0.04865	.	.	ENSG00000159905	ENST00000251269	T	0.05580	3.42	2.02	0.904	0.19302	Krueppel-associated box (1);	.	.	.	.	T	0.06142	0.0159	N	0.17278	0.47	0.09310	N	1	D	0.60160	0.987	P	0.55455	0.776	T	0.31081	-0.9956	9	0.11182	T	0.66	.	5.4263	0.16427	0.75:0.0:0.0:0.25	.	95	Q9UK13	ZN221_HUMAN	L	95	ENSP00000251269:Q95L	ENSP00000251269:Q95L	Q	+	2	0	ZNF221	49161300	0.002000	0.14202	0.001000	0.08648	0.008000	0.06430	1.569000	0.36428	0.176000	0.19873	0.379000	0.24179	CAA	.	.		0.423	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			T	44469460	A	T	44469460	3	4	160	1	0	0	0	0	1	0	0	0	17790	130	5	4	294	4	ZNF221	19	44469460	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	457294	44469460	14659523	341	24512										
CCDC114	93233	hgsc.bcm.edu	37	chr19	48806026	48806026	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctcagcctccgagtgcacctTgtccatgcgctgctgcaaca	9	16	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:48806026T>A	ENST00000315396.7	-	10	1736	c.1054A>T	c.(1054-1056)Aag>Tag	p.K352*		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	352					outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		GAGTGCACCTTGTCCATGCGC	0.637																																					p.K352X		Atlas-SNP	.											.	CCDC114	100	.	0			c.A1054T						.						93	86	88					19																	48806026		2203	4300	6503	SO:0001587	stop_gained	93233	exon10			GCACCTTGTCCAT	BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.1054A>T	chr19.hg19:g.48806026T>A	ENSP00000318429:p.Lys352*	61.0	0.0		62.0	9.0	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Nonsense_Mutation	SNP	ENST00000315396.7	hg19	CCDS12714.2	.	.	.	.	.	.	.	.	.	.	t	41	8.817285	0.98964	.	.	ENSG00000105479	ENST00000315396	.	.	.	3.88	0.208	0.15221	.	0.718496	0.11355	N	0.572600	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.5373	2.8307	0.05499	0.0:0.3042:0.2487:0.4471	.	.	.	.	X	352	.	ENSP00000318429:K352X	K	-	1	0	CCDC114	53497838	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.353000	0.07691	-0.016000	0.14127	0.440000	0.28878	AAG	.	.		0.637	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577		A	48806026	T	A	48806026	4	1	160	1	0	0	0	0	0	1	0	0	2753	1821	63	4	978	4	CCDC114	19	48806026	Nonsense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4336566	48806026	10322957	342	24513										
PIH1D1	55011	hgsc.bcm.edu	37	chr19	49954058	49954058	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccaggctgaggctggatttgTgtcgattctggtctggttgt	15	7	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:49954058T>A	ENST00000262265.5	-	2	373	c.138A>T	c.(136-138)acA>acT	p.T46T	ALDH16A1_ENST00000293350.4_5'Flank|PIH1D1_ENST00000596049.1_Silent_p.T46T|ALDH16A1_ENST00000455361.2_5'Flank|ALDH16A1_ENST00000540132.1_5'Flank|ALDH16A1_ENST00000433981.2_5'Flank	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	46					box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		GCTGGATTTGTGTCGATTCTG	0.552																																					p.T46T		Atlas-SNP	.											.	PIH1D1	23	.	0			c.A138T						.						196	171	180					19																	49954058		2203	4300	6503	SO:0001819	synonymous_variant	55011	exon2			GATTTGTGTCGAT	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.138A>T	chr19.hg19:g.49954058T>A		67.0	0.0		77.0	29.0	NM_017916	B4DGN7|B4E2X7|Q9BVL0	Silent	SNP	ENST00000262265.5	hg19	CCDS12765.1																																																																																			.	.		0.552	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916		A	49954058	T	A	49954058	2	1	160	1	0	0	0	0	0	0	0	1	11915	1683	59	4		4	PIH1D1	19	49954058	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1148032	49954058	9174925	343	24514										
MYH14	79784	hgsc.bcm.edu	37	chr19	50752386	50752386	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cctggacatcgcgggctttgAgatcttccaggtccaccctt	10	14	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:50752386A>T	ENST00000596571.1	+	11	1448	c.1448A>T	c.(1447-1449)gAg>gTg	p.E483V	MYH14_ENST00000440075.2_Missense_Mutation_p.E491V|MYH14_ENST00000262269.8_Missense_Mutation_p.E491V|MYH14_ENST00000425460.1_Missense_Mutation_p.E491V|MYH14_ENST00000376970.2_Missense_Mutation_p.E483V|MYH14_ENST00000601313.1_Missense_Mutation_p.E491V|MYH14_ENST00000598205.1_Missense_Mutation_p.E491V			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	483	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GCGGGCTTTGAGATCTTCCAG	0.652																																					p.E491V		Atlas-SNP	.											.	MYH14	261	.	0			c.A1472T						.						16	19	18					19																	50752386		2025	4189	6214	SO:0001583	missense	79784	exon13			GCTTTGAGATCTT	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.1448A>T	chr19.hg19:g.50752386A>T	ENSP00000472819:p.Glu483Val	135.0	0.0		153.0	14.0	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.324635	0.81580	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45	4.4	4.4	0.53042	Myosin head, motor domain (3);	.	.	.	.	D	0.94059	0.8096	H	0.99619	4.66	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.994;0.999;0.999	D	0.95515	0.8589	9	0.87932	D	0	.	11.888	0.52613	1.0:0.0:0.0:0.0	.	491;483;491	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	V	483;491;483;491;483;491	ENSP00000406273:E491V;ENSP00000366169:E483V;ENSP00000407879:E491V;ENSP00000262269:E491V	ENSP00000262269:E491V	E	+	2	0	MYH14	55444198	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	8.956000	0.93066	1.981000	0.57761	0.459000	0.35465	GAG	.	.		0.652	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50752386	A	T	50752386	3	4	160	1	0	0	0	0	1	0	0	0	10042	304	11	4	1518	4	MYH14	19	50752386	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	798328	50752386	8376597	344	24515										
C19orf63	284361	hgsc.bcm.edu	37	chr19	50984225	50984225	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	caggagcagaagtccttcttCgccaaatacgtgagtggggc	13	10	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:50984225C>T	ENST00000334976.6	+	6	715	c.669C>T	c.(667-669)ttC>ttT	p.F223F	EMC10_ENST00000598585.1_Silent_p.F223F|CTD-2545M3.2_ENST00000598194.1_RNA|EMC10_ENST00000376918.3_Silent_p.F223F	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	223						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											AGTCCTTCTTCGCCAAATACG	0.642																																					p.F223F		Atlas-SNP	.											.	.	.	.	0			c.C669T						.						61	79	73					19																	50984225		2203	4300	6503	SO:0001819	synonymous_variant	284361	exon6			CTTCTTCGCCAAA	BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"hematopoietic signal peptide-containing secreted 1", "hematopoietic signal peptide-containing membrane domain-containing 1"	614545	"chromosome 19 open reading frame 63"	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.669C>T	chr19.hg19:g.50984225C>T		144.0	0.0		149.0	27.0	NM_175063	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Silent	SNP	ENST00000334976.6	hg19	CCDS12796.1																																																																																			.	.		0.642	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063		T	50984225	C	T	50984225	2	4	160	1	0	0	0	0	0	0	0	1	1947	883	31	1		1	C19orf63	19	50984225	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	231839	50984225	8144758	345	24516										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51201148	51201148	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cacttcttccaggcagtcagAggggaaccagccaacacgac	10	14	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:51201148A>T	ENST00000293441.1	-	12	1831	c.1813T>A	c.(1813-1815)Tct>Act	p.S605T	SHANK1_ENST00000359082.3_Missense_Mutation_p.S605T|SHANK1_ENST00000391814.1_Missense_Mutation_p.S605T	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	605	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		AGGCAGTCAGAGGGGAACCAG	0.557																																					p.S605T		Atlas-SNP	.											.	SHANK1	210	.	0			c.T1813A						.						95	82	86					19																	51201148		2203	4299	6502	SO:0001583	missense	50944	exon12			AGTCAGAGGGGAA	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.1813T>A	chr19.hg19:g.51201148A>T	ENSP00000293441:p.Ser605Thr	57.0	0.0		41.0	12.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	hg19	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	A	15.60	2.882279	0.51908	.	.	ENSG00000161681	ENST00000293441;ENST00000359082;ENST00000391814	T;T;T	0.09163	3.01;3.01;3.01	3.27	3.27	0.37495	Src homology-3 domain (3);Variant SH3 (1);	0.181082	0.35235	U	0.003343	T	0.27697	0.0681	M	0.65975	2.015	0.47621	D	0.999476	D	0.58620	0.983	D	0.70227	0.968	T	0.01982	-1.1235	10	0.72032	D	0.01	-15.0275	11.0375	0.47811	1.0:0.0:0.0:0.0	.	605	Q9Y566	SHAN1_HUMAN	T	605	ENSP00000293441:S605T;ENSP00000351984:S605T;ENSP00000375690:S605T	ENSP00000293441:S605T	S	-	1	0	SHANK1	55892960	0.992000	0.36948	0.999000	0.59377	0.917000	0.54804	3.067000	0.50010	1.498000	0.48600	0.375000	0.23000	TCT	.	.		0.557	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		T	51201148	A	T	51201148	3	4	160	1	0	0	0	0	1	0	0	0	14279	304	11	4	4720	4	SHANK1	19	51201148	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	216923	51201148	7927835	346	24517										
ZNF320	162967	hgsc.bcm.edu	37	chr19	53384338	53384338	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctccagtatgaatcctcctAtgtctttcaagatgtgattt	6	9	3	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:53384338A>T	ENST00000595635.1	-	8	1542	c.1041T>A	c.(1039-1041)caT>caA	p.H347Q	ZNF320_ENST00000600930.1_Intron|ZNF320_ENST00000391781.2_Missense_Mutation_p.H347Q|ZNF320_ENST00000597909.1_Intron	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	347					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		GAATCCTCCTATGTCTTTCAA	0.423																																					p.H347Q		Atlas-SNP	.											.	ZNF320	67	.	0			c.T1041A						.						105	101	103					19																	53384338		2203	4300	6503	SO:0001583	missense	162967	exon4			CCTCCTATGTCTT	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"Zinc fingers, C2H2-type", "-"	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.1041T>A	chr19.hg19:g.53384338A>T	ENSP00000473091:p.His347Gln	77.0	0.0		81.0	23.0	NM_207333	Q8NDR6	Missense_Mutation	SNP	ENST00000595635.1	hg19	CCDS33095.1	.	.	.	.	.	.	.	.	.	.	-	12.75	2.032273	0.35893	.	.	ENSG00000182986	ENST00000391781	D	0.86865	-2.18	1.8	0.716	0.18191	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94298	0.8168	H	0.96333	3.805	0.23501	N	0.997543	D	0.89917	1.0	D	0.97110	1.0	D	0.84949	0.0870	9	0.87932	D	0	.	5.9339	0.19154	0.8496:0.0:0.1504:0.0	.	347	A2RRD8	ZN320_HUMAN	Q	347	ENSP00000375660:H347Q	ENSP00000375660:H347Q	H	-	3	2	ZNF320	58076150	0.005000	0.15991	0.004000	0.12327	0.012000	0.07955	-0.259000	0.08721	-0.005000	0.14395	-0.925000	0.02716	CAT	.	.		0.423	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333		T	53384338	A	T	53384338	3	4	160	1	0	0	0	0	1	0	0	0	17854	446	16	4	492	4	ZNF320	19	53384338	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	2183190	53384338	5744645	347	24518										
VSTM1	284415	hgsc.bcm.edu	37	chr19	54545063	54545063	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	accctttccatattggataaAtctgcctctgagtgagaaag	8	9	2	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:54545063A>G	ENST00000338372.2	-	8	736	c.561T>C	c.(559-561)gaT>gaC	p.D187D	VSTM1_ENST00000376626.1_Silent_p.D156D|VSTM1_ENST00000366170.2_Silent_p.D99D|VSTM1_ENST00000425006.2_3'UTR	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	187					immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		TATTGGATAAATCTGCCTCTG	0.483																																					p.D187D		Atlas-SNP	.											.	VSTM1	30	.	0			c.T561C						.						56	52	53					19																	54545063		2203	4300	6503	SO:0001819	synonymous_variant	284415	exon8			GGATAAATCTGCC	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.561T>C	chr19.hg19:g.54545063A>G		84.0	0.0		58.0	11.0	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Silent	SNP	ENST00000338372.2	hg19	CCDS12872.1																																																																																			.	.		0.483	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481		G	54545063	A	G	54545063	2	3	160	1	0	0	0	0	0	0	0	1	17243	98	4	2		2	VSTM1	19	54545063	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	1160725	54545063	4583920	348	24519										
FIZ1	84922	hgsc.bcm.edu	37	chr19	56109118	56109118	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgccgggcaaagtggcgccgCaggtctgagcggtagcggaa	18	10	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:56109118C>G	ENST00000221665.3	-	2	203	c.114G>C	c.(112-114)ctG>ctC	p.L38L	ZNF524_ENST00000301073.3_5'Flank|FIZ1_ENST00000592585.1_Silent_p.L38L	NM_032836.2	NP_116225.2	Q96SL8	FIZ1_HUMAN	FLT3-interacting zinc finger 1	38					positive regulation of protein phosphorylation (GO:0001934)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)	11			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		AGTGGCGCCGCAGGTCTGAGC	0.672																																					p.L38L		Atlas-SNP	.											.	FIZ1	29	.	0			c.G114C						.						45	42	43					19																	56109118		2202	4299	6501	SO:0001819	synonymous_variant	84922	exon2			GCGCCGCAGGTCT	AK027674	CCDS12928.1	19q13.42	2013-01-08				ENSG00000179943		"Zinc fingers, C2H2-type"	25917	protein-coding gene	gene with protein product		609133				12566383	Standard	NM_032836		Approved	FLJ14768, ZNF798	uc002qli.4	Q96SL8		ENST00000221665.3:c.114G>C	chr19.hg19:g.56109118C>G		193.0	0.0		202.0	18.0	NM_032836	A2RU72|Q6ZMJ7	Silent	SNP	ENST00000221665.3	hg19	CCDS12928.1																																																																																			.	.		0.672	FIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453350.1	NM_032836		G	56109118	C	G	56109118	2	3	160	1	0	0	0	0	0	0	0	1	5908	697	25	4		4	FIZ1	19	56109118	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	1564055	56109118	3019865	349	24520										
ZNF582	147948	hgsc.bcm.edu	37	chr19	56896349	56896349	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	caaaagtgggcatttcttcaTgtctgatgatcatctgatgg	10	7	5	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr19:56896349T>A	ENST00000301310.4	-	5	595	c.437A>T	c.(436-438)cAt>cTt	p.H146L	AC006116.12_ENST00000589671.1_RNA|ZNF582_ENST00000586929.1_Missense_Mutation_p.H146L	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		CATTTCTTCATGTCTGATGAT	0.373																																					p.H146L	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.A437T						.						155	153	154					19																	56896349		2203	4300	6503	SO:0001583	missense	147948	exon5			TCTTCATGTCTGA	AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"Zinc fingers, C2H2-type", "-"	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.437A>T	chr19.hg19:g.56896349T>A	ENSP00000301310:p.His146Leu	73.0	0.0		70.0	28.0	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Missense_Mutation	SNP	ENST00000301310.4	hg19	CCDS33121.1	.	.	.	.	.	.	.	.	.	.	T	10.19	1.282265	0.23392	.	.	ENSG00000018869	ENST00000301310	T	0.06142	3.34	4.23	-0.207	0.13189	.	0.560961	0.13669	N	0.371007	T	0.03263	0.0095	N	0.12182	0.205	0.09310	N	1	B;B	0.23058	0.079;0.079	B;B	0.20955	0.032;0.032	T	0.41875	-0.9484	10	0.40728	T	0.16	.	5.3398	0.15976	0.0:0.3487:0.1523:0.4991	.	146;177	Q96NG8;B4DQZ9	ZN582_HUMAN;.	L	146	ENSP00000301310:H146L	ENSP00000301310:H146L	H	-	2	0	ZNF582	61588161	0.925000	0.31364	0.000000	0.03702	0.159000	0.22180	0.208000	0.17415	-0.131000	0.11578	0.482000	0.46254	CAT	.	.		0.373	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		A	56896349	T	A	56896349	3	1	160	1	0	0	0	0	1	0	0	0	18029	1464	51	4	1120	4	ZNF582	19	56896349	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	787231	56896349	2232634	350	24521										
CDC25B	994	hgsc.bcm.edu	37	chr20	3781408	3781408	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	aggtgaggctgctgggccacAgccccgtgcttcggaacatc	14	13	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:3781408A>T	ENST00000245960.5	+	6	1175	c.478A>T	c.(478-480)Agc>Tgc	p.S160C	CDC25B_ENST00000467519.1_3'UTR|CDC25B_ENST00000379598.5_Missense_Mutation_p.S96C|CDC25B_ENST00000439880.2_Missense_Mutation_p.S146C|CDC25B_ENST00000344256.6_Missense_Mutation_p.S96C|CDC25B_ENST00000340833.4_Intron	NM_004358.3|NM_021872.2|NM_021873.2	NP_004349.1|NP_068658.1|NP_068659.1	P30305	MPIP2_HUMAN	cell division cycle 25B	160					female meiosis I (GO:0007144)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|oocyte maturation (GO:0001556)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein kinase activity (GO:0045860)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(1)	18						GCTGGGCCACAGCCCCGTGCT	0.667																																					p.S160C		Atlas-SNP	.											.	CDC25B	76	.	0			c.A478T						.						35	40	39					20																	3781408		2196	4294	6490	SO:0001583	missense	994	exon6			GGCCACAGCCCCG		CCDS13065.1, CCDS13066.1, CCDS13067.1, CCDS74700.1, CCDS74701.1	20p13	2013-01-17	2013-01-17		ENSG00000101224	ENSG00000101224		"Protein tyrosine phosphatases / Class III Cys-based PTPs"	1726	protein-coding gene	gene with protein product		116949	"cell division cycle 25B", "cell division cycle 25 homolog B (S. cerevisiae)", "cell division cycle 25 homolog B (S. pombe)"			1836978	Standard	NM_021873		Approved		uc002wjn.3	P30305	OTTHUMG00000031764	ENST00000245960.5:c.478A>T	chr20.hg19:g.3781408A>T	ENSP00000245960:p.Ser160Cys	106.0	0.0		97.0	14.0	NM_021873	D3DVY1|D3DVY2|D3DVY3|D3DVY4|O43551|Q13971|Q5JX77|Q6RSS1|Q9BRA6	Missense_Mutation	SNP	ENST00000245960.5	hg19	CCDS13067.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.390118	0.61956	.	.	ENSG00000101224	ENST00000344256;ENST00000379598;ENST00000245960;ENST00000439880	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.59088	0.2168	M	0.79123	2.44	0.47341	D	0.999398	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999	T	0.63611	-0.6598	10	0.72032	D	0.01	-5.6901	11.3224	0.49430	1.0:0.0:0.0:0.0	.	96;82;96;146;160	B4DQZ3;B4DRC3;B4DIG0;P30305-2;P30305	.;.;.;.;MPIP2_HUMAN	C	96;96;160;146	ENSP00000339125:S96C;ENSP00000368918:S96C;ENSP00000245960:S160C;ENSP00000405972:S146C	ENSP00000245960:S160C	S	+	1	0	CDC25B	3729408	0.988000	0.35896	1.000000	0.80357	0.652000	0.38707	1.057000	0.30492	2.124000	0.65301	0.459000	0.35465	AGC	.	.		0.667	CDC25B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077779.2	NM_021874		T	3781408	A	T	3781408	3	4	160	1	0	0	0	0	1	0	0	0	3065	188	7	4	500	4	CDC25B	20	3781408	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10		3781408	59244112	351	24522										
SMOX	54498	hgsc.bcm.edu	37	chr20	4163397	4163397	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgagcgctacggccatgtgcTgagcggctggatctgcgggg	18	10	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:4163397T>A	ENST00000305958.4	+	5	1496	c.1271T>A	c.(1270-1272)cTg>cAg	p.L424Q	SMOX_ENST00000379460.2_Missense_Mutation_p.L424Q|SMOX_ENST00000339123.6_Missense_Mutation_p.L371Q|SMOX_ENST00000346595.2_Intron|SMOX_ENST00000278795.3_Missense_Mutation_p.L371Q	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	424					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	GGCCATGTGCTGAGCGGCTGG	0.612																																					p.L424Q		Atlas-SNP	.											.	SMOX	119	.	0			c.T1271A						.						84	77	79					20																	4163397		2203	4300	6503	SO:0001583	missense	54498	exon5			ATGTGCTGAGCGG	AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"chromosome 20 open reading frame 16"	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.1271T>A	chr20.hg19:g.4163397T>A	ENSP00000307252:p.Leu424Gln	57.0	0.0		85.0	31.0	NM_175839	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Missense_Mutation	SNP	ENST00000305958.4	hg19	CCDS13075.1	.	.	.	.	.	.	.	.	.	.	T	18.77	3.694385	0.68386	.	.	ENSG00000088826	ENST00000339123;ENST00000305958;ENST00000278795;ENST00000379460;ENST00000457205	D;D;D;D;D	0.95918	-3.85;-3.85;-3.85;-3.85;-3.85	5.5	5.5	0.81552	Amine oxidase (1);	0.067148	0.64402	D	0.000009	D	0.98595	0.9530	H	0.98133	4.155	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.996;1.0;0.994;0.996	D	0.99521	1.0958	10	0.87932	D	0	-11.7321	13.6121	0.62086	0.0:0.0:0.0:1.0	.	348;424;424;371;371	B4DE63;Q9NWM0-6;Q9NWM0;Q9NWM0-2;Q9NWM0-4	.;.;SMOX_HUMAN;.;.	Q	371;424;371;424;281	ENSP00000344595:L371Q;ENSP00000307252:L424Q;ENSP00000278795:L371Q;ENSP00000368773:L424Q;ENSP00000407269:L281Q	ENSP00000278795:L371Q	L	+	2	0	SMOX	4111397	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	8.035000	0.88872	2.103000	0.63969	0.529000	0.55759	CTG	.	.		0.612	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842		A	4163397	T	A	4163397	3	1	160	1	0	0	0	0	1	0	0	0	14818	1580	55	4	1285	4	SMOX	20	4163397	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	381989	4163397	58862123	352	24523										
XRN2	22803	hgsc.bcm.edu	37	chr20	21362681	21362681	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cctcctccccttttccagcaGcaaaggtttgacaggtaata	7	13	0	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:21362681G>A	ENST00000377191.3	+	28	2729	c.2634G>A	c.(2632-2634)caG>caA	p.Q878Q	XRN2_ENST00000430571.2_Silent_p.Q802Q|XRN2_ENST00000539513.1_Silent_p.Q824Q	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	878					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						TTTTCCAGCAGCAAAGGTTTG	0.383																																					p.Q878Q		Atlas-SNP	.											.	XRN2	90	.	0			c.G2634A						.						52	56	54					20																	21362681		2203	4300	6503	SO:0001819	synonymous_variant	22803	exon28			CCAGCAGCAAAGG	AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.2634G>A	chr20.hg19:g.21362681G>A		54.0	0.0		84.0	13.0	NM_012255	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Silent	SNP	ENST00000377191.3	hg19	CCDS13144.1																																																																																			.	.		0.383	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255		A	21362681	G	A	21362681	2	1	160	1	0	0	0	0	0	0	0	1	17475	962	34	3		3	XRN2	20	21362681	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	17199284	21362681	41662839	353	24524										
THBD	7056	hgsc.bcm.edu	37	chr20	23028430	23028430	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccgctcagagtctctgcggcGtccgctcggtccgcacgtgc	13	17	2	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:23028430G>A	ENST00000377103.2	-	1	1948	c.1712C>T	c.(1711-1713)aCg>aTg	p.T571M		NM_000361.2	NP_000352.1	P07204	TRBM_HUMAN	thrombomodulin	571					blood coagulation (GO:0007596)|female pregnancy (GO:0007565)|leukocyte migration (GO:0050900)|negative regulation of blood coagulation (GO:0030195)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|response to cAMP (GO:0051591)|response to lipopolysaccharide (GO:0032496)|response to X-ray (GO:0010165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|large_intestine(3)|ovary(1)|skin(1)	7	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)				Drotrecogin alfa(DB00055)|Ibuprofen(DB01050)	TCTCTGCGGCGTCCGCTCGGT	0.667																																					p.T571M		Atlas-SNP	.											.	THBD	26	.	0			c.C1712T						.						17	16	16					20																	23028430		2194	4291	6485	SO:0001583	missense	7056	exon1			TGCGGCGTCCGCT		CCDS13148.1	20p11.21	2014-09-17			ENSG00000178726	ENSG00000178726		"CD molecules"	11784	protein-coding gene	gene with protein product		188040					Standard	NM_000361		Approved	CD141	uc002wss.3	P07204	OTTHUMG00000032053	ENST00000377103.2:c.1712C>T	chr20.hg19:g.23028430G>A	ENSP00000366307:p.Thr571Met	104.0	0.0		144.0	8.0	NM_000361	Q8IV29|Q9UC32	Missense_Mutation	SNP	ENST00000377103.2	hg19	CCDS13148.1	.	.	.	.	.	.	.	.	.	.	G	5.169	0.216766	0.09810	.	.	ENSG00000178726	ENST00000377103;ENST00000503590	T	0.79749	-1.3	5.29	-0.487	0.12060	.	1.479610	0.04348	N	0.355171	T	0.65863	0.2732	N	0.17674	0.51	0.09310	N	1	B	0.24317	0.101	B	0.13407	0.009	T	0.49021	-0.8982	10	0.29301	T	0.29	-5.7256	6.3627	0.21437	0.2248:0.0:0.5543:0.2209	.	571	P07204	TRBM_HUMAN	M	571;553	ENSP00000366307:T571M	ENSP00000366307:T571M	T	-	2	0	THBD	22976430	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.408000	0.07169	-0.188000	0.10499	-1.367000	0.01198	ACG	.	.		0.667	THBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078307.2			A	23028430	G	A	23028430	3	1	160	1	0	0	0	0	1	0	0	0	15867	1145	40	1	19	1	THBD	20	23028430	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	1665749	23028430	39997090	354	24525										
REM1	28954	hgsc.bcm.edu	37	chr20	30070206	30070206	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gagctccgcatccagctgcgGcgcacacatcaggcagacca	11	16	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:30070206G>T	ENST00000201979.2	+	4	833	c.540G>T	c.(538-540)cgG>cgT	p.R180R		NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	180					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			TCCAGCTGCGGCGCACACATC	0.607																																					p.R180R		Atlas-SNP	.											.	REM1	54	.	0			c.G540T						.						93	82	85					20																	30070206		2203	4300	6503	SO:0001819	synonymous_variant	28954	exon4			GCTGCGGCGCACA	AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"GTPase GES"	610388	"RAS (RAD and GEM)-like GTP-binding"	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.540G>T	chr20.hg19:g.30070206G>T		79.0	0.0		71.0	9.0	NM_014012	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Silent	SNP	ENST00000201979.2	hg19	CCDS13181.1																																																																																			.	.		0.607	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012		T	30070206	G	T	30070206	2	4	160	1	0	0	0	0	0	0	0	1	13237	1190	42	3		3	REM1	20	30070206	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	7041776	30070206	32955314	355	24526										
MYLK2	85366	hgsc.bcm.edu	37	chr20	30408220	30408220	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	caagaagcccaaggctgagcAgggagcctcaggcagccagg	15	12	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:30408220A>T	ENST00000375994.2	+	2	617	c.344A>T	c.(343-345)cAg>cTg	p.Q115L	MYLK2_ENST00000375985.4_Missense_Mutation_p.Q115L			Q9H1R3	MYLK2_HUMAN	myosin light chain kinase 2	115					cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|neuromuscular synaptic transmission (GO:0007274)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of gene expression (GO:0010628)|protein autophosphorylation (GO:0046777)|regulation of muscle filament sliding (GO:0032971)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle satellite cell differentiation (GO:0014816)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			AAGGCTGAGCAGGGAGCCTCA	0.692																																					p.Q115L		Atlas-SNP	.											.	MYLK2	76	.	0			c.A344T						.						27	31	30					20																	30408220		2202	4297	6499	SO:0001583	missense	85366	exon3			CTGAGCAGGGAGC	AF325549	CCDS13191.1	20q13.31	2014-09-17	2008-01-23		ENSG00000101306	ENSG00000101306	2.7.11.18		16243	protein-coding gene	gene with protein product	"skeletal muscle myosin light chain kinase"	606566	"myosin light chain kinase 2, skeletal muscle"				Standard	NM_033118		Approved	skMLCK, KMLC, MLCK2	uc002wwq.2	Q9H1R3	OTTHUMG00000032194	ENST00000375994.2:c.344A>T	chr20.hg19:g.30408220A>T	ENSP00000365162:p.Gln115Leu	1187.0	0.0		1612.0	314.0	NM_033118	Q569L1|Q96I84	Missense_Mutation	SNP	ENST00000375994.2	hg19	CCDS13191.1	.	.	.	.	.	.	.	.	.	.	A	12.66	2.005545	0.35415	.	.	ENSG00000101306	ENST00000375994;ENST00000375985	T;T	0.67523	-0.27;-0.27	4.7	4.7	0.59300	.	.	.	.	.	T	0.51753	0.1693	L	0.32530	0.975	0.09310	N	1	B	0.32245	0.361	B	0.24155	0.051	T	0.40459	-0.9562	9	0.32370	T	0.25	.	10.49	0.44746	1.0:0.0:0.0:0.0	.	115	Q9H1R3	MYLK2_HUMAN	L	115	ENSP00000365162:Q115L;ENSP00000365152:Q115L	ENSP00000365152:Q115L	Q	+	2	0	MYLK2	29871881	0.000000	0.05858	0.053000	0.19242	0.056000	0.15407	0.385000	0.20685	1.972000	0.57404	0.459000	0.35465	CAG	.	.		0.692	MYLK2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078583.2	NM_033118		T	30408220	A	T	30408220	3	4	160	1	0	0	0	0	1	0	0	0	10066	188	7	4	350	4	MYLK2	20	30408220	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	338014	30408220	32617300	356	24527										
E2F1	1869	hgsc.bcm.edu	37	chr20	32266109	32266109	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cctgcagctgtcggaggtccTgggtcaacccctcaagccgt	12	15	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:32266109T>A	ENST00000343380.5	-	4	762	c.623A>T	c.(622-624)cAg>cTg	p.Q208L	RP1-63M2.5_ENST00000606866.1_RNA	NM_005225.2	NP_005216.1	Q01094	E2F1_HUMAN	E2F transcription factor 1	208	Dimerization. {ECO:0000255}.|Required for interaction with TRIM28.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|DNA damage checkpoint (GO:0000077)|forebrain development (GO:0030900)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|mRNA stabilization (GO:0048255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(2)|breast(1)|endometrium(3)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	16						TCGGAGGTCCTGGGTCAACCC	0.642																																					p.Q208L		Atlas-SNP	.											.	E2F1	41	.	0			c.A623T						.						43	39	40					20																	32266109		2203	4300	6503	SO:0001583	missense	1869	exon4			AGGTCCTGGGTCA		CCDS13224.1	20q11	2008-05-14			ENSG00000101412	ENSG00000101412			3113	protein-coding gene	gene with protein product		189971		RBBP3		8964493	Standard	NM_005225		Approved	RBP3	uc002wzu.4	Q01094	OTTHUMG00000032265	ENST00000343380.5:c.623A>T	chr20.hg19:g.32266109T>A	ENSP00000345571:p.Gln208Leu	132.0	0.0		175.0	38.0	NM_005225	Q13143|Q92768	Missense_Mutation	SNP	ENST00000343380.5	hg19	CCDS13224.1	.	.	.	.	.	.	.	.	.	.	T	13.65	2.301664	0.40694	.	.	ENSG00000101412	ENST00000343380	D	0.84223	-1.82	5.34	4.25	0.50352	.	0.861550	0.10388	N	0.680701	T	0.80623	0.4658	L	0.41573	1.285	0.33273	D	0.561248	B	0.21381	0.055	B	0.23852	0.049	T	0.78894	-0.2024	10	0.59425	D	0.04	-11.5257	10.0921	0.42453	0.0:0.0793:0.0:0.9207	.	208	Q01094	E2F1_HUMAN	L	208	ENSP00000345571:Q208L	ENSP00000345571:Q208L	Q	-	2	0	E2F1	31729770	1.000000	0.71417	0.998000	0.56505	0.449000	0.32228	3.120000	0.50430	1.063000	0.40649	0.533000	0.62120	CAG	.	.		0.642	E2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078731.2			A	32266109	T	A	32266109	3	1	160	1	0	0	0	0	1	0	0	0	4868	1580	55	4	706	4	E2F1	20	32266109	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1857889	32266109	30759411	357	24528										
MAP1LC3A	84557	hgsc.bcm.edu	37	chr20	33147194	33147194	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgagaagcagctgcccgtccTggacaagaccaagtttttgg	12	10	0	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:33147194T>A	ENST00000360668.3	+	3	901	c.140T>A	c.(139-141)cTg>cAg	p.L47Q	MAP1LC3A_ENST00000476428.1_3'UTR|MAP1LC3A_ENST00000397709.1_Missense_Mutation_p.L47Q|MAP1LC3A_ENST00000374837.3_Missense_Mutation_p.L51Q			Q9H492	MLP3A_HUMAN	microtubule-associated protein 1 light chain 3 alpha	47					autophagic vacuole assembly (GO:0000045)|mitochondrion degradation (GO:0000422)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|late endosome (GO:0005770)|microtubule (GO:0005874)|organelle membrane (GO:0031090)	phosphatidylethanolamine binding (GO:0008429)|phospholipid binding (GO:0005543)			cervix(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(2)	5						CTGCCCGTCCTGGACAAGACC	0.662																																					p.L51Q		Atlas-SNP	.											.	MAP1LC3A	10	.	0			c.T152A						.						44	44	44					20																	33147194		2199	4296	6495	SO:0001583	missense	84557	exon4			CCGTCCTGGACAA		CCDS13237.1, CCDS13238.1	20q11.22	2014-02-12			ENSG00000101460	ENSG00000101460			6838	protein-coding gene	gene with protein product		601242				8833088, 17580304	Standard	NM_032514		Approved	MAP1BLC3, MAP1ALC3, LC3, LC3A, ATG8E	uc002xaq.2	Q9H492	OTTHUMG00000032306	ENST00000360668.3:c.140T>A	chr20.hg19:g.33147194T>A	ENSP00000353886:p.Leu47Gln	103.0	0.0		131.0	17.0	NM_181509	E1P5P4|E1P5P5|Q9BXW5	Missense_Mutation	SNP	ENST00000360668.3	hg19	CCDS13238.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.838694	0.91117	.	.	ENSG00000101460	ENST00000374837;ENST00000360668;ENST00000397709	T;T;T	0.55234	0.53;0.53;0.53	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.77638	0.4160	M	0.91249	3.19	0.80722	D	1	P;D	0.89917	0.766;1.0	P;D	0.79108	0.901;0.992	D	0.83482	0.0065	10	0.87932	D	0	-7.232	14.499	0.67709	0.0:0.0:0.0:1.0	.	47;51	Q9H492;Q9H492-2	MLP3A_HUMAN;.	Q	51;47;47	ENSP00000363970:L51Q;ENSP00000353886:L47Q;ENSP00000380821:L47Q	ENSP00000353886:L47Q	L	+	2	0	MAP1LC3A	32610855	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.940000	0.87693	1.908000	0.55244	0.260000	0.18958	CTG	.	.		0.662	MAP1LC3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078801.2	NM_181509		A	33147194	T	A	33147194	3	1	160	1	0	0	0	0	1	0	0	0	9239	1580	55	4	206	4	MAP1LC3A	20	33147194	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	881085	33147194	29878326	358	24529										
DHX35	60625	hgsc.bcm.edu	37	chr20	37662954	37662954	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gctccacacttttatcaacaAggaacggtaggaatgaactg	9	9	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:37662954A>G	ENST00000252011.3	+	21	2094	c.2061A>G	c.(2059-2061)caA>caG	p.Q687Q	DHX35_ENST00000373323.4_Silent_p.Q656Q|DHX35_ENST00000373325.2_Silent_p.Q663Q	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	687					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				TTTATCAACAAGGAACGGTAG	0.443																																					p.Q687Q		Atlas-SNP	.											.	DHX35	82	.	0			c.A2061G						.						86	80	82					20																	37662954		2203	4300	6503	SO:0001819	synonymous_variant	60625	exon21			TCAACAAGGAACG	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.2061A>G	chr20.hg19:g.37662954A>G		45.0	0.0		73.0	19.0	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Silent	SNP	ENST00000252011.3	hg19	CCDS13310.1																																																																																			.	.		0.443	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		G	37662954	A	G	37662954	2	3	160	1	0	0	0	0	0	0	0	1	4510	69	3	2		2	DHX35	20	37662954	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	4515760	37662954	25362566	359	24530										
HNF4A	3172	hgsc.bcm.edu	37	chr20	43058295	43058295	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gccgaccatcaccaagcaggAagttatctagcaagccgctg	10	13	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:43058295A>T	ENST00000316099.4	+	10	1504	c.1415A>T	c.(1414-1416)gAa>gTa	p.E472V	HNF4A_ENST00000457232.1_Missense_Mutation_p.E440V|HNF4A_ENST00000415691.2_Missense_Mutation_p.E462V|HNF4A_ENST00000316673.4_Missense_Mutation_p.E450V	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	472					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			ACCAAGCAGGAAGTTATCTAG	0.632																																					p.E472V	Colon(79;2 1269 8820 14841 52347)	Atlas-SNP	.											.	HNF4A	150	.	0			c.A1415T						.						61	64	63					20																	43058295		2203	4300	6503	SO:0001583	missense	3172	exon10			AGCAGGAAGTTAT	X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"Nuclear hormone receptors"	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.1415A>T	chr20.hg19:g.43058295A>T	ENSP00000312987:p.Glu472Val	121.0	0.0		132.0	15.0	NM_000457	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316099.4	hg19	CCDS13330.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.953070	0.92660	.	.	ENSG00000101076	ENST00000316673;ENST00000457232;ENST00000316099;ENST00000338692;ENST00000415691	T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72	5.36	5.36	0.76844	.	1.610870	0.04225	N	0.334197	D	0.84844	0.5562	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D	0.89917	0.993;0.993;0.999;0.993;1.0	P;P;D;P;D	0.87578	0.782;0.843;0.996;0.722;0.998	T	0.70550	-0.4841	10	0.87932	D	0	.	14.0703	0.64856	1.0:0.0:0.0:0.0	.	465;472;462;450;440	Q5QPB7;P41235;F1D8S2;F1D8T0;P41235-6	.;HNF4A_HUMAN;.;.;.	V	450;440;472;502;462	ENSP00000315180:E450V;ENSP00000396216:E440V;ENSP00000312987:E472V;ENSP00000412111:E462V	ENSP00000312987:E472V	E	+	2	0	HNF4A	42491709	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.707000	0.91367	2.250000	0.74265	0.533000	0.62120	GAA	.	.		0.632	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			T	43058295	A	T	43058295	3	4	160	1	0	0	0	0	1	0	0	0	7262	246	9	4	1631	4	HNF4A	20	43058295	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	5395341	43058295	19967225	360	24531										
PABPC1L	80336	hgsc.bcm.edu	37	chr20	43566766	43566766	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gctggcaagatcacgggcatGctgctggagattgacaactc	13	10	1	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:43566766G>C	ENST00000217073.2	+	13	1710	c.1710G>C	c.(1708-1710)atG>atC	p.M570I	PABPC1L_ENST00000537323.1_3'UTR|PABPC1L_ENST00000217075.2_Missense_Mutation_p.M124I|PABPC1L_ENST00000490798.1_Intron|PABPC1L_ENST00000372819.1_Missense_Mutation_p.M124I|PABPC1L_ENST00000255136.3_Missense_Mutation_p.M570I|PABPC1L_ENST00000372824.1_Missense_Mutation_p.M124I			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	570	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.				mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						TCACGGGCATGCTGCTGGAGA	0.587																																					p.M570I		Atlas-SNP	.											.	PABPC1L	59	.	0			c.G1710C						.						71	63	65					20																	43566766		1568	3582	5150	SO:0001583	missense	80336	exon13			GGGCATGCTGCTG	AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"RNA binding motif (RRM) containing"	15797	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 119"	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.1710G>C	chr20.hg19:g.43566766G>C	ENSP00000217073:p.Met570Ile	117.0	0.0		126.0	10.0	NM_001124756	Q4VY17	Missense_Mutation	SNP	ENST00000217073.2	hg19	CCDS42878.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.1|27.1	4.800764|4.800764	0.90538|0.90538	.|.	.|.	ENSG00000101104|ENSG00000101104	ENST00000372821;ENST00000372826;ENST00000372822|ENST00000255136;ENST00000421240;ENST00000217073;ENST00000372824;ENST00000372819;ENST00000217075	.|T;T;T;T;T	.|0.58506	.|0.33;0.33;0.33;0.33;0.33	4.72|4.72	4.72|4.72	0.59763|0.59763	.|Polyadenylate-binding protein/Hyperplastic disc protein (5);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.77691|0.77691	0.4168|0.4168	M|M	0.80616|0.80616	2.505|2.505	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.997;0.998	.|D;D	.|0.78314	.|0.951;0.991	T|T	0.81581|0.81581	-0.0867|-0.0867	6|10	0.56958|0.87932	D|D	0.05|0	.|.	17.8816|17.8816	0.88842|0.88842	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|570;124	.|Q4VXU2;G5E9L3	.|PAP1L_HUMAN;.	S|I	152;106;93|570;124;570;124;124;124	.|ENSP00000255136:M570I;ENSP00000217073:M570I;ENSP00000361911:M124I;ENSP00000361906:M124I;ENSP00000217075:M124I	ENSP00000361908:C152S|ENSP00000217073:M570I	C|M	+|+	2|3	0|0	PABPC1L|PABPC1L	43000180|43000180	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.657000|9.657000	0.98554|0.98554	2.459000|2.459000	0.83118|0.83118	0.591000|0.591000	0.81541|0.81541	TGC|ATG	.	.		0.587	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2			C	43566766	G	C	43566766	3	2	160	1	0	0	0	0	1	0	0	0	11373	1319	46	4	1760	4	PABPC1L	20	43566766	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	508471	43566766	19458754	361	24532										
ZNF335	63925	hgsc.bcm.edu	37	chr20	44596976	44596976	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gtggtctcggccccgccatcCtcagcactggtcacagtgat	11	15	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:44596976C>T	ENST00000322927.2	-	4	568	c.468G>A	c.(466-468)gaG>gaA	p.E156E	ZNF335_ENST00000494955.1_5'UTR|ZNF335_ENST00000426788.1_Intron	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	156					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				CCCCGCCATCCTCAGCACTGG	0.662																																					p.E156E		Atlas-SNP	.											.	ZNF335	115	.	0			c.G468A						.						132	116	122					20																	44596976		2203	4300	6503	SO:0001819	synonymous_variant	63925	exon4			GCCATCCTCAGCA	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.468G>A	chr20.hg19:g.44596976C>T		59.0	0.0		79.0	7.0	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	hg19	CCDS13389.1																																																																																			.	.		0.662	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		T	44596976	C	T	44596976	2	4	160	1	0	0	0	0	0	0	0	1	17867	680	24	3		3	ZNF335	20	44596976	Silent	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	1030210	44596976	18428544	362	24533										
PREX1	57580	hgsc.bcm.edu	37	chr20	47361579	47361579	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cacgaattttaagaaaacatTcccaagttcatgctgagact	6	9	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:47361579T>A	ENST00000371941.3	-	3	419	c.397A>T	c.(397-399)Aat>Tat	p.N133Y	PREX1_ENST00000396220.1_Missense_Mutation_p.N133Y	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	133	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			AAGAAAACATTCCCAAGTTCA	0.502																																					p.N133Y		Atlas-SNP	.											.	PREX1	441	.	0			c.A397T						.						111	114	113					20																	47361579		2203	4300	6503	SO:0001583	missense	57580	exon3			AAACATTCCCAAG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.397A>T	chr20.hg19:g.47361579T>A	ENSP00000361009:p.Asn133Tyr	109.0	0.0		164.0	18.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	T	12.39	1.924235	0.34002	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.69040	-0.37;-0.37	4.85	4.85	0.62838	Dbl homology (DH) domain (5);	0.118844	0.35555	U	0.003128	T	0.53674	0.1811	L	0.39326	1.205	0.42336	D	0.992312	P	0.41188	0.741	B	0.38921	0.285	T	0.59825	-0.7381	10	0.72032	D	0.01	.	5.9556	0.19271	0.0:0.085:0.168:0.747	.	133	Q8TCU6	PREX1_HUMAN	Y	133	ENSP00000361009:N133Y;ENSP00000379522:N133Y	ENSP00000361009:N133Y	N	-	1	0	PREX1	46794986	1.000000	0.71417	0.993000	0.49108	0.559000	0.35586	3.641000	0.54360	2.039000	0.60335	0.459000	0.35465	AAT	.	.		0.502	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47361579	T	A	47361579	3	1	160	1	0	0	0	0	1	0	0	0	12488	1783	62	4	4734	4	PREX1	20	47361579	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2764603	47361579	15663941	363	24534										
STX16	8675	hgsc.bcm.edu	37	chr20	57246334	57246334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgaaatattcagggacttagGggcgatgattgtagaacagg	14	4	1	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:57246334G>A	ENST00000371141.4	+	7	1497	c.773G>A	c.(772-774)gGg>gAg	p.G258E	STX16-NPEPL1_ENST00000530122.1_Missense_Mutation_p.G258E|STX16_ENST00000371132.4_Missense_Mutation_p.G237E|STX16_ENST00000496003.1_Intron|STX16_ENST00000355957.5_Missense_Mutation_p.G241E|STX16_ENST00000361770.5_Missense_Mutation_p.G241E|STX16_ENST00000361830.3_Missense_Mutation_p.G258E|STX16_ENST00000358029.4_Missense_Mutation_p.G254E|STX16_ENST00000359617.4_Missense_Mutation_p.G205E	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	258	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			AGGGACTTAGGGGCGATGATT	0.478																																					p.G258E		Atlas-SNP	.											.	STX16	36	.	0			c.G773A						.						154	142	146					20																	57246334		2203	4300	6503	SO:0001583	missense	8675	exon7			ACTTAGGGGCGAT	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.773G>A	chr20.hg19:g.57246334G>A	ENSP00000360183:p.Gly258Glu	98.0	0.0		125.0	15.0	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Missense_Mutation	SNP	ENST00000371141.4	hg19	CCDS13468.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.808187	0.90707	.	.	ENSG00000124222	ENST00000355957;ENST00000361770;ENST00000359617;ENST00000371141;ENST00000371138;ENST00000371132;ENST00000358029;ENST00000361830;ENST00000435446	T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92	5.75	5.75	0.90469	t-SNARE (1);Syntaxin/epimorphin, conserved site (1);Target SNARE coiled-coil domain (3);	0.064326	0.64402	U	0.000014	T	0.35098	0.0920	L	0.31752	0.955	0.53005	D	0.999969	B;P;P;D	0.53885	0.389;0.837;0.696;0.963	B;B;B;P	0.59221	0.403;0.444;0.274;0.854	T	0.02437	-1.1159	10	0.52906	T	0.07	.	14.5995	0.68429	0.0:0.1454:0.8546:0.0	.	254;241;237;258	Q6GMS8;O14662-4;O14662-2;O14662	.;.;.;STX16_HUMAN	E	241;241;205;258;205;237;254;258;72	ENSP00000348229:G241E;ENSP00000355408:G241E;ENSP00000352634:G205E;ENSP00000360183:G258E;ENSP00000360173:G237E;ENSP00000350723:G254E;ENSP00000354445:G258E	ENSP00000360180:G205E	G	+	2	0	STX16	56679740	1.000000	0.71417	0.770000	0.31555	0.950000	0.60333	6.788000	0.75105	2.727000	0.93392	0.644000	0.83932	GGG	.	.		0.478	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433		A	57246334	G	A	57246334	3	1	160	1	0	0	0	0	1	0	0	0	15354	1232	43	3	799	3	STX16	20	57246334	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	9884755	57246334	5779186	364	24535										
BIRC7	79444	hgsc.bcm.edu	37	chr20	61869278	61869278	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	atcaggacaaggtgaggtgcTtcttctgctatgggggcctg	15	8	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr20:61869278T>A	ENST00000217169.3	+	2	587	c.373T>A	c.(373-375)Ttc>Atc	p.F125I	BIRC7_ENST00000395306.1_5'Flank|MIR3196_ENST00000579556.1_RNA|BIRC7_ENST00000342412.6_Missense_Mutation_p.F125I	NM_139317.1	NP_647478.1	Q96CA5	BIRC7_HUMAN	baculoviral IAP repeat containing 7	125					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of natural killer cell apoptotic process (GO:0070247)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(9)|ovary(1)	12	all_cancers(38;2.72e-09)					GGTGAGGTGCTTCTTCTGCTA	0.682																																					p.F125I		Atlas-SNP	.											.	BIRC7	25	.	0			c.T373A						.						39	40	39					20																	61869278		2203	4298	6501	SO:0001583	missense	79444	exon2			AGGTGCTTCTTCT	AF301009	CCDS13512.1, CCDS13513.1	20q13.3	2011-01-25	2011-01-25		ENSG00000101197	ENSG00000101197		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	13702	protein-coding gene	gene with protein product	"melanoma inhibitor of apoptosis protein", "kidney inhibitor of apoptosis protein", "livin inhibitor-of-apoptosis", "livin"	605737	"baculoviral IAP repeat-containing 7"			11024045, 11162435	Standard	NM_139317		Approved	mliap, ML-IAP, KIAP, RNF50	uc002yej.3	Q96CA5	OTTHUMG00000032957	ENST00000217169.3:c.373T>A	chr20.hg19:g.61869278T>A	ENSP00000217169:p.Phe125Ile	140.0	0.0		180.0	26.0	NM_139317	Q9BQV0|Q9H2A8|Q9HAP7	Missense_Mutation	SNP	ENST00000217169.3	hg19	CCDS13513.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.578791	0.86645	.	.	ENSG00000101197	ENST00000342412;ENST00000217169	T;T	0.05081	3.5;3.5	5.16	5.16	0.70880	Baculoviral inhibition of apoptosis protein repeat (5);	0.142736	0.32836	N	0.005593	T	0.37785	0.1016	H	0.95917	3.74	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.998	T	0.56902	-0.7902	10	0.87932	D	0	.	14.6667	0.68913	0.0:0.0:0.0:1.0	.	125;125;125	Q6R308;Q96CA5;Q96CA5-2	.;BIRC7_HUMAN;.	I	125	ENSP00000345213:F125I;ENSP00000217169:F125I	ENSP00000217169:F125I	F	+	1	0	BIRC7	61339723	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	4.296000	0.59055	1.941000	0.56285	0.459000	0.35465	TTC	.	.		0.682	BIRC7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080114.2	NM_139317		A	61869278	T	A	61869278	3	1	160	1	0	0	0	0	1	0	0	0	1439	1609	56	4	379	4	BIRC7	20	61869278	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	4622944	61869278	1156242	365	24536										
APP	351	hgsc.bcm.edu	37	chr21	27328044	27328044	+	Frame_Shift_Del	DEL	T	T	-													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gttctgcgcggacatacttcTttagcatattgaacacgtga							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr21:27328044delT	ENST00000346798.3	-	12	1517	c.1484delA	c.(1483-1485)aagfs	p.K496fs	APP_ENST00000440126.3_Frame_Shift_Del_p.K472fs|APP_ENST00000439274.2_Frame_Shift_Del_p.K440fs|APP_ENST00000348990.5_Frame_Shift_Del_p.K421fs|APP_ENST00000358918.3_Frame_Shift_Del_p.K496fs|APP_ENST00000448388.2_Frame_Shift_Del_p.K386fs|APP_ENST00000354192.3_Frame_Shift_Del_p.K365fs|APP_ENST00000359726.3_Frame_Shift_Del_p.K440fs|APP_ENST00000357903.3_Frame_Shift_Del_p.K477fs	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	496	Heparin-binding.				adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				GACATACTTCTTTAGCATATT	0.483																																					p.K495fs		Atlas-INDEL	.											.	APP	90	.	0			c.1485delG						.						218	175	190					21																	27328044		2203	4300	6503	SO:0001589	frameshift_variant	351	exon12			.	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1484delA	chr21.hg19:g.27328044delT	ENSP00000284981:p.Lys496fs	149.0	0.0		98.0	19.0	NM_001204301	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Frame_Shift_Del	DEL	ENST00000346798.3	hg19	CCDS13576.1																																																																																			.	.		0.483	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		-	27328044	T	-	27328044	7	5	160	1	0	1	0	1	0	0	0	0	815	1609	56	0	856	0	APP	21	27328044	Frame_Shift_Del	DEL	T	TCGA-DD-AACI-01A-11D-A40R-10		27328044	20801851	366	24537										
IFNAR2	3455	hgsc.bcm.edu	37	chr21	34625087	34625087	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acagtgatgagcaagcagtaAtaaagtctcccttaaaatgc	8	8	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr21:34625087A>G	ENST00000342136.4	+	7	987	c.661A>G	c.(661-663)Ata>Gta	p.I221V	IFNAR2_ENST00000382264.3_Missense_Mutation_p.I221V|IFNAR2_ENST00000404220.3_Missense_Mutation_p.I221V|IFNAR2_ENST00000342101.3_Missense_Mutation_p.I221V|IFNAR2_ENST00000382241.3_Missense_Mutation_p.I221V|AP000295.9_ENST00000433395.2_Silent_p.*128*|IFNAR2_ENST00000413881.1_Missense_Mutation_p.I149V			P48551	INAR2_HUMAN	interferon (alpha, beta and omega) receptor 2	221					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|type I interferon binding (GO:0019962)|type I interferon receptor activity (GO:0004905)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	11					"""Interferon Alfa-2a(DB00034)|""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"	GCAAGCAGTAATAAAGTCTCC	0.358																																					p.I221V		Atlas-SNP	.											.	IFNAR2	44	.	0			c.A661G						.						117	104	108					21																	34625087		2203	4300	6503	SO:0001583	missense	3455	exon7			GCAGTAATAAAGT		CCDS13621.1, CCDS13622.1, CCDS74782.1	21q22.1	2010-08-17			ENSG00000159110	ENSG00000159110		"Interferons"	5433	protein-coding gene	gene with protein product		602376		IFNABR		8181059	Standard	NM_207585		Approved		uc002yrd.3	P48551	OTTHUMG00000065127	ENST00000342136.4:c.661A>G	chr21.hg19:g.34625087A>G	ENSP00000343957:p.Ile221Val	181.0	0.0		169.0	34.0	NM_207585	A8KAJ4|D3DSE8|D3DSE9|Q15467|Q6FHD7	Missense_Mutation	SNP	ENST00000342136.4	hg19	CCDS13621.1	.	.	.	.	.	.	.	.	.	.	A	0.029	-1.349584	0.01266	.	.	ENSG00000159110	ENST00000382264;ENST00000404220;ENST00000382241;ENST00000342136;ENST00000342101;ENST00000413881;ENST00000443073	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	3.44	-5.84	0.02318	Fibronectin, type III (1);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	5.089080	0.00531	N	0.000209	T	0.30070	0.0753	L	0.29908	0.895	0.09310	N	1	B;B;B	0.22683	0.03;0.037;0.073	B;B;B	0.25884	0.038;0.064;0.063	T	0.32824	-0.9892	10	0.87932	D	0	.	5.7758	0.18279	0.2622:0.4437:0.294:0.0	.	221;221;221	P48551-3;P48551;P48551-2	.;INAR2_HUMAN;.	V	221;221;221;221;221;149;149	ENSP00000371699:I221V;ENSP00000384309:I221V;ENSP00000371676:I221V;ENSP00000343957:I221V;ENSP00000343289:I221V;ENSP00000413160:I149V;ENSP00000403569:I149V	ENSP00000447913:I11V	I	+	1	0	IFNAR2	33546957	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.380000	0.07427	-1.280000	0.02402	-0.441000	0.05720	ATA	.	.		0.358	IFNAR2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139825.1			G	34625087	A	G	34625087	3	3	160	1	0	0	0	0	1	0	0	0	7554	101	4	2	683	2	IFNAR2	21	34625087	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	7297043	34625087	13504808	367	24538										
HLCS	3141	hgsc.bcm.edu	37	chr21	38308987	38308987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tgcttgtcacctgaaagccaCcaaaggtgaaggatgaagac	11	9	1	4			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr21:38308987C>T	ENST00000399120.1	-	5	1988	c.758G>A	c.(757-759)gGt>gAt	p.G253D	HLCS_ENST00000336648.4_Missense_Mutation_p.G253D	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	253					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	CTGAAAGCCACCAAAGGTGAA	0.537																																					p.G253D		Atlas-SNP	.											.	HLCS	64	.	0			c.G758A						.						74	72	73					21																	38308987		2203	4300	6503	SO:0001583	missense	3141	exon5			AAGCCACCAAAGG		CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)", "holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.758G>A	chr21.hg19:g.38308987C>T	ENSP00000382071:p.Gly253Asp	166.0	0.0		116.0	23.0	NM_000411	B2RAH1|D3DSG6|Q99451	Missense_Mutation	SNP	ENST00000399120.1	hg19	CCDS13647.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.726766	0.30593	.	.	ENSG00000159267	ENST00000399120;ENST00000336648	D;D	0.98437	-4.93;-4.93	5.91	3.13	0.36017	.	0.301675	0.40908	N	0.000982	D	0.94169	0.8129	N	0.21448	0.665	0.42614	D	0.993329	B;B	0.23735	0.09;0.043	B;B	0.21151	0.033;0.027	D	0.89163	0.3531	10	0.49607	T	0.09	.	7.5862	0.27993	0.0:0.6352:0.1429:0.2219	.	253;253	B2RAH1;P50747	.;BPL1_HUMAN	D	253	ENSP00000382071:G253D;ENSP00000338387:G253D	ENSP00000338387:G253D	G	-	2	0	HLCS	37230857	0.729000	0.28090	0.307000	0.25127	0.921000	0.55340	1.170000	0.31883	0.388000	0.25054	0.655000	0.94253	GGT	.	.		0.537	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2			T	38308987	C	T	38308987	3	4	160	1	0	0	0	0	1	0	0	0	7222	507	18	3	1454	3	HLCS	21	38308987	Missense_Mutation	SNP	C	TCGA-DD-AACI-01A-11D-A40R-10	3683900	38308987	9820908	368	24539										
SLC5A1	6523	hgsc.bcm.edu	37	chr22	32462982	32462982	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	actttgtggggctggccgggActggggcagcttcaggcatc	17	10	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr22:32462982A>C	ENST00000266088.4	+	3	518	c.268A>C	c.(268-270)Act>Cct	p.T90P	SLC5A1_ENST00000543737.1_5'UTR	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	90					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	GCTGGCCGGGACTGGGGCAGC	0.552																																					p.T90P		Atlas-SNP	.											.	SLC5A1	80	.	0			c.A268C						.						79	78	78					22																	32462982		2203	4300	6503	SO:0001583	missense	6523	exon3			GCCGGGACTGGGG		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"Solute carriers"	11036	protein-coding gene	gene with protein product	"sodium/glucose cotransporter 1"	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.268A>C	chr22.hg19:g.32462982A>C	ENSP00000266088:p.Thr90Pro	105.0	0.0		88.0	7.0	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Missense_Mutation	SNP	ENST00000266088.4	hg19	CCDS13902.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.596112	0.46318	.	.	ENSG00000100170	ENST00000266088	D	0.88896	-2.44	5.1	4.05	0.47172	.	0.044280	0.85682	D	0.000000	D	0.93877	0.8041	M	0.90977	3.165	0.80722	D	1	P	0.50272	0.933	P	0.57057	0.812	D	0.93764	0.7069	10	0.87932	D	0	.	10.459	0.44567	0.8539:0.0:0.0:0.1461	.	90	P13866	SC5A1_HUMAN	P	90	ENSP00000266088:T90P	ENSP00000266088:T90P	T	+	1	0	SLC5A1	30792982	1.000000	0.71417	0.486000	0.27416	0.061000	0.15899	5.684000	0.68197	0.871000	0.35750	0.533000	0.62120	ACT	.	.		0.552	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343		C	32462982	A	C	32462982	3	2	160	1	0	0	0	0	1	0	0	0	14676	275	10	5	278	5	SLC5A1	22	32462982	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10		32462982	18841584	369	24540										
TXN2	25828	hgsc.bcm.edu	37	chr22	36876815	36876815	+	Frame_Shift_Del	DEL	A	A	-													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tctggaagtgaggggtggccActgaccctgagagggcttcc							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr22:36876815delA	ENST00000216185.2	-	2	536	c.70delT	c.(70-72)tggfs	p.W24fs	TXN2_ENST00000403313.1_Frame_Shift_Del_p.W24fs|TXN2_ENST00000487725.1_Intron|TXN2_ENST00000416967.1_5'UTR			Q99757	THIOM_HUMAN	thioredoxin 2	24					cell redox homeostasis (GO:0045454)|cellular response to nutrient levels (GO:0031669)|glycerol ether metabolic process (GO:0006662)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)	dendrite (GO:0030425)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)	protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|lung(1)|prostate(1)	3						AGGGGTGGCCACTGACCCTGA	0.587																																					p.W24fs		Atlas-INDEL	.											.	TXN2	15	.	0			c.71delG						.						91	86	88					22																	36876815		2203	4300	6503	SO:0001589	frameshift_variant	25828	exon2			.	U78678	CCDS13928.1	22q13.1	2008-06-11			ENSG00000100348	ENSG00000100348			17772	protein-coding gene	gene with protein product		609063				9006939, 17220299	Standard	NM_012473		Approved	MT-TRX	uc003apk.1	Q99757	OTTHUMG00000150596	ENST00000216185.2:c.70delT	chr22.hg19:g.36876815delA	ENSP00000216185:p.Trp24fs	101.0	0.0		82.0	15.0	NM_012473	Q5JZA0|Q6FH60|Q9UH29	Frame_Shift_Del	DEL	ENST00000216185.2	hg19	CCDS13928.1																																																																																			.	.		0.587	TXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319016.1	NM_012473		-	36876815	A	-	36876815	7	5	160	1	0	1	0	1	0	0	0	0	16806	159	6	0	442	0	TXN2	22	36876815	Frame_Shift_Del	DEL	A	TCGA-DD-AACI-01A-11D-A40R-10	4413833	36876815	14427751	370	24541										
TOMM22	56993	hgsc.bcm.edu	37	chr22	39078014	39078014	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ccgtcgctgctgccggtgcaGgggaaccccagtccccggac	14	17	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chr22:39078014G>A	ENST00000216034.4	+	1	62	c.31G>A	c.(31-33)Ggg>Agg	p.G11R	RP3-508I15.9_ENST00000431924.2_RNA|RP3-508I15.9_ENST00000444381.1_RNA|RP3-508I15.9_ENST00000412067.1_RNA	NM_020243.4	NP_064628.1	Q9NS69	TOM22_HUMAN	translocase of outer mitochondrial membrane 22 homolog (yeast)	11					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			large_intestine(1)|lung(2)	3	Melanoma(58;0.04)					TGCCGGTGCAGGGGAACCCCA	0.662																																					p.G11R		Atlas-SNP	.											.	TOMM22	10	.	0			c.G31A						.						13	14	14					22																	39078014		2199	4293	6492	SO:0001583	missense	56993	exon1			GGTGCAGGGGAAC	AB040119	CCDS13975.1	22q12-q13	2010-07-29			ENSG00000100216	ENSG00000100216			18002	protein-coding gene	gene with protein product		607046				10982837, 10900208	Standard	NM_020243		Approved	TOM22	uc003awe.3	Q9NS69	OTTHUMG00000150991	ENST00000216034.4:c.31G>A	chr22.hg19:g.39078014G>A	ENSP00000216034:p.Gly11Arg	161.0	0.0		129.0	25.0	NM_020243		Missense_Mutation	SNP	ENST00000216034.4	hg19	CCDS13975.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981173	0.34942	.	.	ENSG00000100216	ENST00000216034	.	.	.	4.92	3.85	0.44370	.	0.147639	0.42821	D	0.000650	T	0.45216	0.1331	M	0.65975	2.015	0.18873	N	0.999982	B	0.06786	0.001	B	0.14578	0.011	T	0.42241	-0.9463	9	0.52906	T	0.07	-11.1439	11.2416	0.48972	0.0:0.1839:0.8161:0.0	.	11	Q9NS69	TOM22_HUMAN	R	11	.	ENSP00000216034:G11R	G	+	1	0	TOMM22	37407960	0.998000	0.40836	0.372000	0.25991	0.028000	0.11728	4.271000	0.58902	2.547000	0.85894	0.655000	0.94253	GGG	.	.		0.662	TOMM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320842.1			A	39078014	G	A	39078014	3	1	160	1	0	0	0	0	1	0	0	0	16371	1000	35	3	33	3	TOMM22	22	39078014	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	2201199	39078014	12226552	371	24542										
PHEX	5251	hgsc.bcm.edu	37	chrX	22231054	22231054	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agagctccagaagcctttctTttggggaacagaatatcctc	9	10	1	3			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:22231054T>C	ENST00000379374.4	+	16	2244	c.1679T>C	c.(1678-1680)tTt>tCt	p.F560S	PHEX_ENST00000535894.1_Missense_Mutation_p.F463S|PHEX_ENST00000537599.1_Missense_Mutation_p.F560S|PHEX_ENST00000418858.3_Missense_Mutation_p.F263S	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	560					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						AAGCCTTTCTTTTGGGGAACA	0.398																																					p.F560S		Atlas-SNP	.											.	PHEX	95	.	0			c.T1679C						.						106	103	104					X																	22231054		2203	4300	6503	SO:0001583	missense	5251	exon16			CTTTCTTTTGGGG	U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.1679T>C	chrX.hg19:g.22231054T>C	ENSP00000368682:p.Phe560Ser	178.0	0.0		206.0	65.0	NM_000444	O00678|Q13646|Q2M325|Q93032|Q99827	Missense_Mutation	SNP	ENST00000379374.4	hg19	CCDS14204.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.527753	0.85706	.	.	ENSG00000102174	ENST00000379374;ENST00000537599;ENST00000535894;ENST00000418858	D;D;D;D	0.94687	-3.49;-3.49;-3.49;-3.49	5.69	5.69	0.88448	Peptidase M13, neprilysin, C-terminal (2);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97539	0.9194	M	0.90759	3.145	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.68483	0.929;0.958	D	0.98333	1.0534	10	0.87932	D	0	.	14.916	0.70798	0.0:0.0:0.0:1.0	.	560;560	F5GXU4;P78562	.;PHEX_HUMAN	S	560;560;463;263	ENSP00000368682:F560S;ENSP00000440362:F560S;ENSP00000439418:F463S;ENSP00000443531:F263S	ENSP00000368682:F560S	F	+	2	0	PHEX	22140975	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.941000	0.75922	1.904000	0.55121	0.486000	0.48141	TTT	.	.		0.398	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		C	22231054	T	C	22231054	3	2	160	1	0	0	0	0	1	0	0	0	11828	1841	64	2	1741	2	PHEX	23	22231054	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10		22231054	133039506	372	24543										
WDR45	11152	hgsc.bcm.edu	37	chrX	48935320	48935320	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	acctgagatctctgagaactTgggactactaccaccgccca	8	14	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:48935320T>A	ENST00000376372.3	-	4	398	c.217A>T	c.(217-219)Aag>Tag	p.K73*	WDR45_ENST00000376368.2_Nonsense_Mutation_p.K73*|WDR45_ENST00000356463.3_Nonsense_Mutation_p.K73*|AF196779.12_ENST00000376358.3_Intron|WDR45_ENST00000473974.1_Nonsense_Mutation_p.K73*|WDR45_ENST00000465431.1_Intron|WDR45_ENST00000485908.1_Intron|WDR45_ENST00000553851.1_Intron|WDR45_ENST00000322995.8_Nonsense_Mutation_p.K73*|WDR45_ENST00000396681.4_Nonsense_Mutation_p.K73*	NM_001029896.1	NP_001025067.1	Q9Y484	WIPI4_HUMAN	WD repeat domain 45	73					autophagy (GO:0006914)|cell death (GO:0008219)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	19						TCTGAGAACTTGGGACTACTA	0.597																																					p.K73X		Atlas-SNP	.											.	WDR45	40	.	0			c.A217T						.						49	30	37					X																	48935320		2200	4298	6498	SO:0001587	stop_gained	11152	exon5			AGAACTTGGGACT	BC003037	CCDS14318.1, CCDS35250.1	Xp11.23	2013-06-06	2004-09-02	2004-09-03	ENSG00000196998	ENSG00000196998		"WD repeat domain containing"	28912	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 5"	300526	"WD repeat domain, X-linked 1"	WDRX1		12477932	Standard	NM_007075		Approved	JM5, WIPI4, NBIA5	uc004dmk.1	Q9Y484	OTTHUMG00000034500	ENST00000376372.3:c.217A>T	chrX.hg19:g.48935320T>A	ENSP00000365551:p.Lys73*	66.0	0.0		75.0	23.0	NM_007075	A6NGH5|B7WPI2|Q5MNZ5|Q6IBS7|Q6NT94|Q96H03	Nonsense_Mutation	SNP	ENST00000376372.3	hg19	CCDS35250.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.5|24.5	4.533205|4.533205	0.85812|0.85812	.|.	.|.	ENSG00000196998|ENSG00000196998	ENST00000376372;ENST00000322995;ENST00000356463;ENST00000473974;ENST00000376368;ENST00000396681;ENST00000471338;ENST00000474053;ENST00000419567;ENST00000465382|ENST00000367375	.|.	.|.	.|.	3.81|3.81	3.81|3.81	0.43845|0.43845	.|.	0.058895|.	0.64402|.	D|.	0.000005|.	.|T	.|0.61515	.|0.2353	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.60177	.|-0.7314	.|4	0.02654|.	T|.	1|.	-11.4686|-11.4686	11.4195|11.4195	0.49974|0.49974	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	X|L	73|29	.|.	ENSP00000365543:K73X|.	K|Q	-|-	1|2	0|0	WDR45|WDR45	48822264|48822264	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.939000|0.939000	0.58152|0.58152	7.259000|7.259000	0.78381|0.78381	1.723000|1.723000	0.51488|0.51488	0.430000|0.430000	0.28490|0.28490	AAG|CAA	.	.		0.597	WDR45-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083418.2	NM_007075		A	48935320	T	A	48935320	4	1	160	1	0	0	0	0	0	1	0	0	17312	1821	63	4	900	4	WDR45	23	48935320	Nonsense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	26704266	48935320	106335240	373	24544										
ALAS2	212	hgsc.bcm.edu	37	chrX	55052401	55052401	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gggccccgggcaagcactggGcagcactgtagcagcatggc	16	13	0	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:55052401G>A	ENST00000330807.5	-	2	170	c.33C>T	c.(31-33)tgC>tgT	p.C11C	ALAS2_ENST00000335854.4_Silent_p.C11C|ALAS2_ENST00000396198.3_Silent_p.C35C	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	11					cellular iron ion homeostasis (GO:0006879)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|hemoglobin biosynthetic process (GO:0042541)|oxygen homeostasis (GO:0032364)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5-aminolevulinate synthase activity (GO:0003870)|coenzyme binding (GO:0050662)|glycine binding (GO:0016594)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)	17					Glycine(DB00145)	CAAGCACTGGGCAGCACTGTA	0.552																																					p.C35C		Atlas-SNP	.											.	ALAS2	163	.	0			c.C105T						.						78	59	66					X																	55052401		2203	4300	6503	SO:0001819	synonymous_variant	212	exon3			CACTGGGCAGCAC		CCDS14366.1, CCDS35303.1, CCDS43960.1	Xp11.21	2008-02-05	2008-02-04		ENSG00000158578	ENSG00000158578	2.3.1.37		397	protein-coding gene	gene with protein product	"sideroblastic/hypochromic anemia"	301300	"aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)"	ASB		1577484	Standard	NM_000032		Approved		uc004dua.4	P22557	OTTHUMG00000021641	ENST00000330807.5:c.33C>T	chrX.hg19:g.55052401G>A		66.0	0.0		54.0	24.0	NM_001037968	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Silent	SNP	ENST00000330807.5	hg19	CCDS14366.1																																																																																			.	.		0.552	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032		A	55052401	G	A	55052401	2	1	160	1	0	0	0	0	0	0	0	1	485	1195	42	3		3	ALAS2	23	55052401	Silent	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	6117081	55052401	100218159	374	24545										
KLF8	11279	hgsc.bcm.edu	37	chrX	56295811	56295811	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	ctccctttctttgcttttagTgaaagttgaccccacctcca	5	14	1	2			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:56295811T>A	ENST00000468660.1	+	4	935	c.647T>A	c.(646-648)gTg>gAg	p.V216E	KLF8_ENST00000374928.3_Splice_Site_p.V216E	NM_007250.4	NP_009181.2	O95600	KLF8_HUMAN	Kruppel-like factor 8	216					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(4)|large_intestine(6)|lung(5)|ovary(1)	16						TTGCTTTTAGTGAAAGTTGAC	0.468																																					p.V216E		Atlas-SNP	.											.	KLF8	38	.	0			c.T647A						.						104	79	88					X																	56295811		2203	4299	6502	SO:0001630	splice_region_variant	11279	exon5			TTTTAGTGAAAGT	U28282	CCDS14373.1, CCDS55428.1	Xp11.21	2013-01-08			ENSG00000102349	ENSG00000102349		"Zinc fingers, C2H2-type", "Kruppel-like transcription factors"	6351	protein-coding gene	gene with protein product		300286					Standard	NM_007250		Approved	BKLF3, ZNF741, DXS741	uc004dur.3	O95600	OTTHUMG00000021666	ENST00000468660.1:c.647-1T>A	chrX.hg19:g.56295811T>A		26.0	0.0		36.0	11.0	NM_001159296	B4DJN3|E7EQQ8|L0R3U8|L0R4U2|Q2M246|Q59GV5|Q5HYQ5|Q5JXP7|Q6MZJ7|Q9UGC4	Missense_Mutation	SNP	ENST00000468660.1	hg19	CCDS14373.1	.	.	.	.	.	.	.	.	.	.	T	19.85	3.903155	0.72754	.	.	ENSG00000102349	ENST00000374928;ENST00000468660	T	0.07567	3.18	4.65	4.65	0.58169	.	0.310345	0.27371	N	0.019673	T	0.19886	0.0478	M	0.65975	2.015	0.48830	D	0.999712	D;D	0.62365	0.989;0.991	P;P	0.58454	0.839;0.766	T	0.00605	-1.1648	9	.	.	.	.	9.7981	0.40748	0.0:0.0:0.0:1.0	.	216;216	E7EQQ8;O95600	.;KLF8_HUMAN	E	216	ENSP00000417303:V216E	.	V	+	2	0	KLF8	56312536	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.319000	0.43788	1.647000	0.50633	0.486000	0.48141	GTG	.	.		0.468	KLF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056887.2	NM_007250	Missense_Mutation	A	56295811	T	A	56295811	5	1	160	1	0	0	0	0	0	0	1	0	8361	1710	59	4	661	4	KLF8	23	56295811	Splice_Site	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	1243410	56295811	98974749	375	24546										
RBM41	55285	hgsc.bcm.edu	37	chrX	106312542	106312542	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	agtcatcattcggaattgaaTtggaggtccttttttctcct	8	8	3	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:106312542T>A	ENST00000372479.3	-	6	1048	c.1018A>T	c.(1018-1020)Att>Ttt	p.I340F	RBM41_ENST00000372487.1_Missense_Mutation_p.I340F	NM_018301.3	NP_060771.3	Q96IZ5	RBM41_HUMAN	RNA binding motif protein 41	340	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	13						CGGAATTGAATTGGAGGTCCT	0.443																																					p.I340F		Atlas-SNP	.											.	RBM41	34	.	0			c.A1018T						.						152	142	145					X																	106312542		2203	4300	6503	SO:0001583	missense	55285	exon6			ATTGAATTGGAGG	BC006986	CCDS14526.1, CCDS55472.1	Xq22.3	2013-02-12			ENSG00000089682	ENSG00000089682		"RNA binding motif (RRM) containing"	25617	protein-coding gene	gene with protein product						12477932	Standard	NM_001171080		Approved	FLJ11016	uc004emz.3	Q96IZ5	OTTHUMG00000022156	ENST00000372479.3:c.1018A>T	chrX.hg19:g.106312542T>A	ENSP00000361557:p.Ile340Phe	92.0	0.0		110.0	34.0	NM_001171080	Q5JSN7|Q5JSN8|Q9H8F7|Q9NV04	Missense_Mutation	SNP	ENST00000372479.3	hg19	CCDS14526.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.002109	0.74932	.	.	ENSG00000089682	ENST00000372487;ENST00000372479	T;T	0.49432	0.78;0.78	5.83	4.66	0.58398	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.192266	0.45361	D	0.000379	T	0.47691	0.1459	N	0.16368	0.405	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.42413	-0.9453	10	0.34782	T	0.22	.	7.7853	0.29089	0.0:0.0953:0.0:0.9047	.	340	Q96IZ5	RBM41_HUMAN	F	340	ENSP00000361565:I340F;ENSP00000361557:I340F	ENSP00000361557:I340F	I	-	1	0	RBM41	106199198	0.991000	0.36638	0.955000	0.39395	0.874000	0.50279	2.323000	0.43823	0.805000	0.34159	-0.360000	0.07572	ATT	.	.		0.443	RBM41-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057819.1	NM_018301		A	106312542	T	A	106312542	3	1	160	1	0	0	0	0	1	0	0	0	13150	1493	52	4	240	4	RBM41	23	106312542	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	50016731	106312542	48958018	376	24547										
IRS4	8471	hgsc.bcm.edu	37	chrX	107975901	107975901	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cagaatcttctctctccgggGgtcttggcacccggcgactg	12	14	4	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:107975901G>T	ENST00000372129.2	-	1	3750	c.3674C>A	c.(3673-3675)cCc>cAc	p.P1225H	RP6-24A23.6_ENST00000563887.1_Missense_Mutation_p.P6H	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	1225					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						TCTCTCCGGGGGTCTTGGCAC	0.582																																					p.P1225H		Atlas-SNP	.											.	IRS4	253	.	0			c.C3674A						.						104	105	105					X																	107975901		2203	4300	6503	SO:0001583	missense	8471	exon1			TCCGGGGGTCTTG	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.3674C>A	chrX.hg19:g.107975901G>T	ENSP00000361202:p.Pro1225His	150.0	0.0		150.0	79.0	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	hg19	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.518846	0.44763	.	.	ENSG00000133124	ENST00000372129	T	0.38401	1.14	4.39	3.45	0.39498	.	0.432236	0.20549	N	0.090145	T	0.36413	0.0966	L	0.27053	0.805	0.30234	N	0.795633	D	0.71674	0.998	P	0.58013	0.831	T	0.26710	-1.0095	10	0.72032	D	0.01	-5.8904	6.3692	0.21471	0.1501:0.0:0.8499:0.0	.	1225	O14654	IRS4_HUMAN	H	1225	ENSP00000361202:P1225H	ENSP00000361202:P1225H	P	-	2	0	IRS4	107862557	0.912000	0.30974	0.902000	0.35471	0.527000	0.34593	1.493000	0.35605	1.074000	0.40909	0.600000	0.82982	CCC	.	.		0.582	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		T	107975901	G	T	107975901	3	4	160	1	0	0	0	0	1	0	0	0	7851	1232	43	3	103	3	IRS4	23	107975901	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	1663359	107975901	47294659	377	24548										
THOC2	57187	hgsc.bcm.edu	37	chrX	122755374	122755374	+	Nonsense_Mutation	SNP	T	T	A													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	tggagtagtagctggagtctTttcttttttctctttttctt							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:122755374T>A	ENST00000245838.8	-	31	3881	c.3850A>T	c.(3850-3852)Aag>Tag	p.K1284*	THOC2_ENST00000355725.4_Nonsense_Mutation_p.K1284*|THOC2_ENST00000497887.1_5'Flank|THOC2_ENST00000491737.1_Nonsense_Mutation_p.K1169*	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1284	Lys-rich.				mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						GCTGGAGtcttttcttttttc	0.348																																					p.K1284X		Atlas-SNP	.											.	THOC2	310	.	0			c.A3850T						.						94	80	84					X																	122755374		1796	4063	5859	SO:0001587	stop_gained	57187	exon31			GAGTCTTTTCTTT	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.3850A>T	chrX.hg19:g.122755374T>A	ENSP00000245838:p.Lys1284*	38.0	0.0		73.0	11.0	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Nonsense_Mutation	SNP	ENST00000245838.8	hg19	CCDS43988.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	42|42|42	9.595869|9.595869|9.595869	0.99214|0.99214|0.99214	.|.|.	.|.|.	ENSG00000125676|ENSG00000125676|ENSG00000125676	ENST00000438358|ENST00000441692|ENST00000245838;ENST00000355725;ENST00000491737	.|.|.	.|.|.	.|.|.	5.05|5.05|5.05	5.05|5.05|5.05	0.67936|0.67936|0.67936	.|.|.	0.180201|0.180201|0.180201	0.37483|0.37483|0.37483	N|N|N	0.002065|0.002065|0.002065	T|T|.	0.34513|0.34513|.	0.0900|0.0900|.	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|.	0.35425|0.35425|.	-0.9789|-0.9789|.	4|4|.	.|.|0.02654	.|.|T	.|.|1	-9.9393|-9.9393|-9.9393	13.8245|13.8245|13.8245	0.63342|0.63342|0.63342	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|.|.	.|.|.	.|.|.	I|N|X	378|51|1284;1284;1169	.|.|.	.|.|ENSP00000245838:K1284X	K|K|K	-|-|-	2|3|1	0|2|0	THOC2|THOC2|THOC2	122583055|122583055|122583055	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	7.603000|7.603000|7.603000	0.82811|0.82811|0.82811	1.793000|1.793000|1.793000	0.52555|0.52555|0.52555	0.486000|0.486000|0.486000	0.48141|0.48141|0.48141	AAA|AAA|AAG	.	.		0.348	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			A	122755374	T	A	122755374	4	1	160	1	0	0	0	0	0	1	0	0	15880	1850	64	4	963	4	THOC2	23	122755374	Nonsense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	14779473	122755374	32515186	378	24549	112	2								
THOC2	57187	hgsc.bcm.edu	37	chrX	122755376	122755376	+	Missense_Mutation	SNP	T	T	G													0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gagtagtagctggagtctttTcttttttctctttttctttc							TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:122755376T>G	ENST00000245838.8	-	31	3879	c.3848A>C	c.(3847-3849)gAa>gCa	p.E1283A	THOC2_ENST00000355725.4_Missense_Mutation_p.E1283A|THOC2_ENST00000497887.1_5'Flank|THOC2_ENST00000491737.1_Missense_Mutation_p.E1168A	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1283	Lys-rich.				mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						TGGAGtcttttcttttttctc	0.348																																					p.E1283A		Atlas-SNP	.											.	THOC2	310	.	0			c.A3848C						.						90	76	81					X																	122755376		1796	4062	5858	SO:0001583	missense	57187	exon31			GTCTTTTCTTTTT	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.3848A>C	chrX.hg19:g.122755376T>G	ENSP00000245838:p.Glu1283Ala	38.0	0.0		71.0	11.0	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	hg19	CCDS43988.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	15.90|15.90|15.90	2.969961|2.969961|2.969961	0.53614|0.53614|0.53614	.|.|.	.|.|.	ENSG00000125676|ENSG00000125676|ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737|ENST00000441692|ENST00000438358	T;T;T|.|.	0.41065|.|.	1.01;1.01;1.01|.|.	4.81|4.81|4.81	4.81|4.81|4.81	0.61882|0.61882|0.61882	.|.|.	0.359735|.|.	0.23832|.|.	N|.|.	0.044134|.|.	T|T|T	0.54431|0.54431|0.54431	0.1858|0.1858|0.1858	L|L|L	0.32530|0.32530|0.32530	0.975|0.975|0.975	0.80722|0.80722|0.80722	D|D|D	1|1|1	P|.|.	0.39060|.|.	0.657|.|.	B|.|.	0.35182|.|.	0.197|.|.	T|T|T	0.51505|0.51505|0.51505	-0.8697|-0.8697|-0.8697	10|5|5	0.12766|.|.	T|.|.	0.61|.|.	-14.4696|-14.4696|-14.4696	13.4607|13.4607|13.4607	0.61225|0.61225|0.61225	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	1283|.|.	Q8NI27|.|.	THOC2_HUMAN|.|.	A|Q|S	1283;1283;1168|51|377	ENSP00000245838:E1283A;ENSP00000347959:E1283A;ENSP00000419795:E1168A|.|.	ENSP00000245838:E1283A|.|.	E|K|R	-|-|-	2|1|3	0|0|2	THOC2|THOC2|THOC2	122583057|122583057|122583057	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	7.603000|7.603000|7.603000	0.82811|0.82811|0.82811	1.705000|1.705000|1.705000	0.51264|0.51264|0.51264	0.486000|0.486000|0.486000	0.48141|0.48141|0.48141	GAA|AAA|AGA	.	.		0.348	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			G	122755376	T	G	122755376	3	3	160	1	0	0	0	0	1	0	0	0	15880	1783	62	5	965	5	THOC2	23	122755376	Missense_Mutation	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	2	122755376	32515184	379	24550	112	2								
DCAF12L2	340578	hgsc.bcm.edu	37	chrX	125299819	125299819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	gaggcccctctccgtccgccGccgctaaaccctgcgacgac	10	20	1	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:125299819G>A	ENST00000360028.2	-	1	115	c.89C>T	c.(88-90)gCg>gTg	p.A30V	DCAF12L2_ENST00000538699.1_Missense_Mutation_p.A30V			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	30										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						TCCGTCCGCCGCCGCTAAACC	0.701																																					p.A30V		Atlas-SNP	.											.	DCAF12L2	157	.	0			c.C89T						.						9	12	11					X																	125299819		1890	3817	5707	SO:0001583	missense	340578	exon1			TCCGCCGCCGCTA	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"WD repeat domain containing"	32950	protein-coding gene	gene with protein product			"WD repeat domain 40C"	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.89C>T	chrX.hg19:g.125299819G>A	ENSP00000353128:p.Ala30Val	65.0	0.0		152.0	23.0	NM_001013628	B2RN42	Missense_Mutation	SNP	ENST00000360028.2	hg19	CCDS43991.1	.	.	.	.	.	.	.	.	.	.	g	13.17	2.158466	0.38119	.	.	ENSG00000198354	ENST00000538699;ENST00000360028	T;T	0.20738	2.05;2.05	3.0	1.08	0.20341	.	.	.	.	.	T	0.18882	0.0453	L	0.57536	1.79	0.09310	N	1	B	0.24368	0.102	B	0.15484	0.013	T	0.19386	-1.0307	9	0.46703	T	0.11	.	6.5328	0.22336	0.0:0.1937:0.6044:0.2019	.	30	Q5VW00	DC122_HUMAN	V	30	ENSP00000441489:A30V;ENSP00000353128:A30V	ENSP00000353128:A30V	A	-	2	0	DCAF12L2	125127500	0.006000	0.16342	0.000000	0.03702	0.173000	0.22820	1.506000	0.35747	0.150000	0.19136	0.287000	0.19450	GCG	.	.		0.701	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		A	125299819	G	A	125299819	3	1	160	1	0	0	0	0	1	0	0	0	4267	1087	38	1	1306	1	DCAF12L2	23	125299819	Missense_Mutation	SNP	G	TCGA-DD-AACI-01A-11D-A40R-10	2544443	125299819	29970741	380	24551										
USP26	83844	hgsc.bcm.edu	37	chrX	132161579	132161579	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	attctcttctaactcttttaActtcaattgtttctctcgat	2	10	5	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:132161579A>G	ENST00000511190.1	-	6	1139	c.670T>C	c.(670-672)Tta>Cta	p.L224L	USP26_ENST00000370832.1_Silent_p.L224L|USP26_ENST00000406273.1_Silent_p.L224L	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	224					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					AACTCTTTTAACTTCAATTGT	0.358																																					p.L224L	NSCLC(104;342 1621 36940 47097 52632)	Atlas-SNP	.											.	USP26	135	.	0			c.T670C						.						80	66	70					X																	132161579		2203	4300	6503	SO:0001819	synonymous_variant	83844	exon1			CTTTTAACTTCAA	AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"Ubiquitin-specific peptidases"	13485	protein-coding gene	gene with protein product		300309	"ubiquitin specific protease 26"			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.670T>C	chrX.hg19:g.132161579A>G		54.0	0.0		108.0	27.0	NM_031907	B9WRT6|Q5H9H4	Silent	SNP	ENST00000511190.1	hg19	CCDS14635.1																																																																																			.	.		0.358	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907		G	132161579	A	G	132161579	2	3	160	1	0	0	0	0	0	0	0	1	17072	40	2	2		2	USP26	23	132161579	Silent	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	6861760	132161579	23108981	381	24552										
FHL1	2273	hgsc.bcm.edu	37	chrX	135291566	135291566	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	cgtgggtggtggttctttatAgaaaaaatcgaagcttagca	12	5	1	1			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:135291566A>G	ENST00000345434.3	+	6	934	c.853A>G	c.(853-855)Aga>Gga	p.R285G	FHL1_ENST00000543669.1_Intron|FHL1_ENST00000370690.3_Intron|FHL1_ENST00000370683.1_Intron|FHL1_ENST00000370676.3_Intron|FHL1_ENST00000394153.2_Intron|FHL1_ENST00000539015.1_Intron|FHL1_ENST00000394155.2_Missense_Mutation_p.R285G|FHL1_ENST00000535737.1_Intron			Q13642	FHL1_HUMAN	four and a half LIM domains 1	285					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|organ morphogenesis (GO:0009887)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane depolarization (GO:0003254)|regulation of potassium ion transmembrane transporter activity (GO:1901016)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel binding (GO:0044325)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(192;0.000127)					GGTTCTTTATAGAAAAAATCG	0.587											OREG0019943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R285G		Atlas-SNP	.											.	FHL1	114	.	0			c.A853G						.						61	54	56					X																	135291566		1568	3582	5150	SO:0001583	missense	2273	exon7			CTTTATAGAAAAA	U60115	CCDS14655.1, CCDS55505.1, CCDS55506.1, CCDS55507.1, CCDS76036.1	Xq26.3	2014-09-17			ENSG00000022267	ENSG00000022267			3702	protein-coding gene	gene with protein product	"Four-and-a-half LIM domains 1", "LIM protein SLIMMER"	300163				8753811, 9714789	Standard	NM_001449		Approved	SLIM1, KYO-T, bA535K18.1, FHL1B, XMPMA, FLH1A, MGC111107	uc004ezo.3	Q13642	OTTHUMG00000022504	ENST00000345434.3:c.853A>G	chrX.hg19:g.135291566A>G	ENSP00000071281:p.Arg285Gly	50.0	0.0	1617	96.0	23.0	NM_001159702	B7Z5T4|B7Z793|O95212|Q13230|Q13645|Q5JXI7|Q5M7Y6|Q6IB30|Q9NZ40|Q9UKZ8|Q9Y630	Missense_Mutation	SNP	ENST00000345434.3	hg19	CCDS55507.1	.	.	.	.	.	.	.	.	.	.	a	12.79	2.042172	0.35989	.	.	ENSG00000022267	ENST00000394155;ENST00000345434	T;T	0.65916	-0.18;-0.18	4.47	4.47	0.54385	.	0.092585	0.44483	D	0.000449	T	0.46151	0.1378	N	0.08118	0	0.28244	N	0.925542	P	0.48350	0.909	P	0.48704	0.587	T	0.37056	-0.9722	10	0.33141	T	0.24	.	9.1475	0.36942	1.0:0.0:0.0:0.0	.	285	Q13642	FHL1_HUMAN	G	285	ENSP00000377710:R285G;ENSP00000071281:R285G	ENSP00000071281:R285G	R	+	1	2	FHL1	135119232	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.861000	0.56002	1.758000	0.51981	0.352000	0.21897	AGA	.	.		0.587	FHL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058461.1	NM_001449		G	135291566	A	G	135291566	3	3	160	1	0	0	0	0	1	0	0	0	5886	412	15	2	988	2	FHL1	23	135291566	Missense_Mutation	SNP	A	TCGA-DD-AACI-01A-11D-A40R-10	3129987	135291566	19978994	382	24553										
BRS3	680	hgsc.bcm.edu	37	chrX	135570516	135570516	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0342105263157895	13	1	0.985437861559944	2.27408737283064	0.516838039279691	0.488676307007786	1	0	accaaatccatgcaaacagtTccaaatattttcatcaccag	3	12	2	0			TCGA-DD-AACI-01A-11D-A40R-10	TCGA-DD-AACI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	247f1556-4111-4fee-ab12-312a9cd3b2ce	145d1bb3-e78f-4ac7-9b82-12983f7080e4	g.chrX:135570516T>A	ENST00000370648.3	+	1	471	c.243T>A	c.(241-243)gtT>gtA	p.V81V	Z97632.1_ENST00000580943.1_RNA	NM_001727.1	NP_001718.1	P32247	BRS3_HUMAN	bombesin-like receptor 3	81					adult feeding behavior (GO:0008343)|glucose metabolic process (GO:0006006)|regulation of blood pressure (GO:0008217)	integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)			endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|pancreas(1)|prostate(1)	23	Acute lymphoblastic leukemia(192;0.000127)					TGCAAACAGTTCCAAATATTT	0.413																																					p.V81V		Atlas-SNP	.											.	BRS3	62	.	0			c.T243A						.						153	135	141					X																	135570516		2203	4300	6503	SO:0001819	synonymous_variant	680	exon1			AACAGTTCCAAAT		CCDS14656.1	Xq26.3	2014-02-21			ENSG00000102239	ENSG00000102239		"GPCR / Class A : Bombesin receptors"	1113	protein-coding gene	gene with protein product		300107				8383682	Standard	NM_001727		Approved	BB3	uc004ezv.1	P32247	OTTHUMG00000022726	ENST00000370648.3:c.243T>A	chrX.hg19:g.135570516T>A		89.0	0.0		187.0	41.0	NM_001727		Silent	SNP	ENST00000370648.3	hg19	CCDS14656.1																																																																																			.	.		0.413	BRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059005.1	NM_001727		A	135570516	T	A	135570516	2	1	160	1	0	0	0	0	0	0	0	1	1524	1770	62	4		4	BRS3	23	135570516	Silent	SNP	T	TCGA-DD-AACI-01A-11D-A40R-10	278950	135570516	19700044	383	24554										
OR6K2	81448	hgsc.bcm.edu	37	chr1	158669714	158669714	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gaaaagacaatgaagtgagaGacacacgtggaaaatgctgt	12	5	0	4			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr1:158669714G>A	ENST00000359610.2	-	1	772	c.729C>T	c.(727-729)gtC>gtT	p.V243V		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					TGAAGTGAGAGACACACGTGG	0.478																																					p.V243V		Atlas-SNP	.											.	OR6K2	104	.	0			c.C729T						.						120	109	113					1																	158669714		2203	4300	6503	SO:0001819	synonymous_variant	81448	exon1			GTGAGAGACACAC	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.729C>T	chr1.hg19:g.158669714G>A		223.0	0.0		330.0	42.0	NM_001005279	B9EH33|Q6IFR6	Silent	SNP	ENST00000359610.2	hg19	CCDS30902.1																																																																																			.	.		0.478	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		A	158669714	G	A	158669714	2	1	161	1	0	0	0	0	0	0	0	1	11211	929	33	3		3	OR6K2	1	158669714	Silent	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10		158669714	90580907	1	24555										
OR6N1	128372	hgsc.bcm.edu	37	chr1	158735540	158735540	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ctctcagccccaactcatgcCaatatcccaattctctttag	3	16	3	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr1:158735540C>T	ENST00000335094.2	-	1	952	c.933G>A	c.(931-933)ttG>ttA	p.L311L		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					CAACTCATGCCAATATCCCAA	0.532																																					p.L311L		Atlas-SNP	.											OR6N1,NS,carcinoma,0,1	OR6N1	96	.	0			c.G933A						.						136	133	134					1																	158735540		2203	4300	6503	SO:0001819	synonymous_variant	128372	exon1			TCATGCCAATATC	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"GPCR / Class A : Olfactory receptors"	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.933G>A	chr1.hg19:g.158735540C>T		61.0	0.0		96.0	15.0	NM_001005185	Q5VUU8|Q96R35	Silent	SNP	ENST00000335094.2	hg19	CCDS30905.1																																																																																			.	.		0.532	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185		T	158735540	C	T	158735540	2	4	161	1	0	0	0	0	0	0	0	1	11215	593	21	3		3	OR6N1	1	158735540	Silent	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	65826	158735540	90515081	2	24556										
GPR161	23432	hgsc.bcm.edu	37	chr1	168066166	168066166	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	atcctcctccacgatgacgaCtgtgccacagtgcaccttgc	8	16	0	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr1:168066166C>T	ENST00000367838.1	-	5	992	c.679G>A	c.(679-681)Gtc>Atc	p.V227I	GPR161_ENST00000537209.1_Missense_Mutation_p.V247I|GPR161_ENST00000539777.1_Missense_Mutation_p.V149I|GPR161_ENST00000361697.2_Missense_Mutation_p.V227I|GPR161_ENST00000367836.1_Missense_Mutation_p.V95I|GPR161_ENST00000367835.1_Missense_Mutation_p.V227I|GPR161_ENST00000271357.5_Missense_Mutation_p.V227I|GPR161_ENST00000546300.1_Missense_Mutation_p.V113I	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	227					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					ACGATGACGACTGTGCCACAG	0.592																																					p.V247I		Atlas-SNP	.											.	GPR161	56	.	0			c.G739A						.						88	87	87					1																	168066166		2203	4300	6503	SO:0001583	missense	23432	exon4			TGACGACTGTGCC	AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"GPCR / Class A : Orphans"	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.679G>A	chr1.hg19:g.168066166C>T	ENSP00000356812:p.Val227Ile	154.0	0.0		171.0	17.0	NM_001267609	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Missense_Mutation	SNP	ENST00000367838.1	hg19	CCDS1268.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.292717	0.59976	.	.	ENSG00000143147	ENST00000367838;ENST00000271357;ENST00000367836;ENST00000367835;ENST00000546300;ENST00000539777;ENST00000537209;ENST00000361697	T;T;D;T;T;T;T;T	0.81739	-0.04;-0.04;-1.53;-0.04;-1.07;-1.03;0.05;-0.04	5.48	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.78941	0.4363	L	0.41415	1.275	0.38105	D	0.937396	P;D;D;P;B;P	0.67145	0.48;0.992;0.996;0.529;0.244;0.659	B;D;D;B;B;P	0.77557	0.198;0.923;0.99;0.376;0.099;0.499	T	0.77552	-0.2545	9	0.24483	T	0.36	-28.9782	13.9679	0.64221	0.0:0.9261:0.0:0.0739	.	247;113;149;247;227;227	F5GXD6;B7Z5E8;F5H6J7;B7Z5Z6;Q8N6U8-2;Q8N6U8	.;.;.;.;.;GP161_HUMAN	I	227;227;95;227;113;149;247;227	ENSP00000356812:V227I;ENSP00000271357:V227I;ENSP00000356810:V95I;ENSP00000356809:V227I;ENSP00000444348:V113I;ENSP00000437576:V149I;ENSP00000441039:V247I;ENSP00000355194:V227I	ENSP00000271357:V227I	V	-	1	0	GPR161	166332790	1.000000	0.71417	0.941000	0.38009	0.727000	0.41649	4.824000	0.62701	1.442000	0.47568	0.561000	0.74099	GTC	.	.		0.592	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369		T	168066166	C	T	168066166	3	4	161	1	0	0	0	0	1	0	0	0	6673	565	20	3	926	3	GPR161	1	168066166	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	9330626	168066166	81184455	3	24557										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176762739	176762739	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gtaatcccccccagtgacccCgtgatgctacctgagaatat	8	14	0	3			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr1:176762739C>T	ENST00000367662.3	+	20	6228	c.5064C>T	c.(5062-5064)ccC>ccT	p.P1688P		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1688	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CCAGTGACCCCGTGATGCTAC	0.478																																					p.P1688P		Atlas-SNP	.											.	PAPPA2	665	.	0			c.C5064T						.						187	185	186					1																	176762739		1980	4158	6138	SO:0001819	synonymous_variant	60676	exon20			TGACCCCGTGATG	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.5064C>T	chr1.hg19:g.176762739C>T		127.0	0.0		162.0	108.0	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.		0.478	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176762739	C	T	176762739	2	4	161	1	0	0	0	0	0	0	0	1	11442	639	23	1		1	PAPPA2	1	176762739	Silent	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	8696573	176762739	72487882	4	24558										
KDM5B	10765	hgsc.bcm.edu	37	chr1	202702884	202702884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	attgaatcataggggcagctGgggccttctgacataggcag	14	8	2	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr1:202702884G>A	ENST00000367265.3	-	23	4718	c.3554C>T	c.(3553-3555)cCa>cTa	p.P1185L	KDM5B_ENST00000367264.2_Missense_Mutation_p.P1221L	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1185					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						AGGGGCAGCTGGGGCCTTCTG	0.502																																					p.P1185L		Atlas-SNP	.											.	KDM5B	166	.	0			c.C3554T						.						74	79	77					1																	202702884		2203	4300	6503	SO:0001583	missense	10765	exon23			GCAGCTGGGGCCT	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	18039	protein-coding gene	gene with protein product	"cancer/testis antigen 31", "protein phosphatase 1, regulatory subunit 98"	605393	"Jumonji, AT rich interactive domain 1B (RBP2-like)", "jumonji, AT rich interactive domain 1B"	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3554C>T	chr1.hg19:g.202702884G>A	ENSP00000356234:p.Pro1185Leu	146.0	0.0		195.0	44.0	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	hg19	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.974774	0.92919	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	D;D;D	0.84873	-1.91;-1.91;-1.91	6.09	6.09	0.99107	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.91788	0.7402	M	0.75615	2.305	0.80722	D	1	D;B	0.76494	0.999;0.05	D;B	0.70935	0.971;0.135	D	0.87505	0.2436	10	0.17832	T	0.49	-16.8674	20.6935	0.99705	0.0:0.0:1.0:0.0	.	1221;1185	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	L	1185;1027;1221;1027	ENSP00000356234:P1185L;ENSP00000356233:P1221L;ENSP00000235790:P1027L	ENSP00000235790:P1027L	P	-	2	0	KDM5B	200969507	1.000000	0.71417	0.994000	0.49952	0.996000	0.88848	9.473000	0.97714	2.897000	0.99335	0.643000	0.83706	CCA	.	.		0.502	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		A	202702884	G	A	202702884	3	1	161	1	0	0	0	0	1	0	0	0	8143	1348	47	3	1100	3	KDM5B	1	202702884	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	25940145	202702884	46547737	5	24559										
LYST	1130	hgsc.bcm.edu	37	chr1	235955183	235955183	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	aacggcaggtggactggggcTatgtgccaagatgaaagcag	16	7	0	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr1:235955183T>C	ENST00000389794.3	-	12	4533	c.4359A>G	c.(4357-4359)atA>atG	p.I1453M	LYST_ENST00000536965.1_Intron|LYST_ENST00000389793.2_Missense_Mutation_p.I1453M			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1453					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GGACTGGGGCTATGTGCCAAG	0.502																																					p.I1453M		Atlas-SNP	.											.	LYST	370	.	0			c.A4359G						.						99	98	98					1																	235955183		2203	4300	6503	SO:0001583	missense	1130	exon12			TGGGGCTATGTGC	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.4359A>G	chr1.hg19:g.235955183T>C	ENSP00000374444:p.Ile1453Met	134.0	0.0		166.0	77.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.209811	0.58343	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.63417	-0.04;-0.04	5.76	0.669	0.17918	.	0.618960	0.18131	N	0.150736	T	0.53530	0.1802	L	0.44542	1.39	0.80722	D	1	P;P	0.46512	0.879;0.684	P;P	0.47528	0.549;0.453	T	0.50668	-0.8801	10	0.62326	D	0.03	.	3.9591	0.09403	0.3351:0.2793:0.0:0.3856	.	1453;1453	Q99698-3;Q99698	.;LYST_HUMAN	M	1453	ENSP00000374444:I1453M;ENSP00000374443:I1453M	ENSP00000374443:I1453M	I	-	3	3	LYST	234021806	0.009000	0.17119	0.823000	0.32752	0.885000	0.51271	-0.782000	0.04643	0.139000	0.18822	0.528000	0.53228	ATA	.	.		0.502	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			C	235955183	T	C	235955183	3	2	161	1	0	0	0	0	1	0	0	0	9137	1512	53	2	7214	2	LYST	1	235955183	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	33252299	235955183	13295438	6	24560										
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112256	248112256	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tcttcattctcattgttttcAttttcctgatggctctaatt	4	9	5	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr1:248112256A>G	ENST00000357191.3	+	1	97	c.97A>G	c.(97-99)Att>Gtt	p.I33V	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			CATTGTTTTCATTTTCCTGAT	0.398																																					p.I33V		Atlas-SNP	.											.	OR2L8	92	.	0			c.A97G						.						240	223	229					1																	248112256		2203	4300	6503	SO:0001583	missense	391190	exon1			GTTTTCATTTTCC	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.97A>G	chr1.hg19:g.248112256A>G	ENSP00000349719:p.Ile33Val	131.0	0.0		208.0	95.0	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	hg19	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	A	0.738	-0.777436	0.02929	.	.	ENSG00000196936	ENST00000357191	T	0.04970	3.52	1.48	0.19	0.15125	.	.	.	.	.	T	0.03520	0.0101	N	0.20483	0.58	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.48581	-0.9023	9	0.15066	T	0.55	.	4.4784	0.11755	0.7911:0.0:0.2089:0.0	.	33	Q8NGY9	OR2L8_HUMAN	V	33	ENSP00000349719:I33V	ENSP00000349719:I33V	I	+	1	0	OR2L8	246178879	0.000000	0.05858	0.002000	0.10522	0.123000	0.20343	-2.291000	0.01147	-0.115000	0.11915	0.248000	0.18094	ATT	.	.		0.398	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			G	248112256	A	G	248112256	3	3	161	1	0	0	0	0	1	0	0	0	11018	217	8	2	99	2	OR2L8	1	248112256	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	12157073	248112256	1138365	7	24561										
NLRC4	58484	hgsc.bcm.edu	37	chr2	32476106	32476106	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	actcagtggtagtggtgacgAtgaccatgttcttgaagcgg	14	7	2	3			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr2:32476106A>T	ENST00000404025.2	-	5	1315	c.827T>A	c.(826-828)aTc>aAc	p.I276N	NLRC4_ENST00000342905.6_Intron|NLRC4_ENST00000360906.5_Missense_Mutation_p.I276N|NLRC4_ENST00000402280.1_Missense_Mutation_p.I276N			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	276	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.|Nucleotide-binding domain (NBD). {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					AGTGGTGACGATGACCATGTT	0.517																																					p.I276N		Atlas-SNP	.											.	NLRC4	165	.	0			c.T827A						.						135	111	119					2																	32476106		2203	4300	6503	SO:0001583	missense	58484	exon4			GTGACGATGACCA	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.827T>A	chr2.hg19:g.32476106A>T	ENSP00000385090:p.Ile276Asn	65.0	0.0		56.0	23.0	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	hg19	CCDS33174.1	.	.	.	.	.	.	.	.	.	.	A	16.63	3.176411	0.57692	.	.	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000404025	T;T;T	0.26810	1.71;1.71;1.71	3.27	3.27	0.37495	.	0.252759	0.25030	N	0.033689	T	0.34716	0.0907	L	0.55481	1.735	0.36283	D	0.855908	P	0.46457	0.878	P	0.51895	0.683	T	0.53781	-0.8390	9	0.87932	D	0	-1.9877	11.0079	0.47646	1.0:0.0:0.0:0.0	.	276	Q9NPP4	NLRC4_HUMAN	N	276	ENSP00000354159:I276N;ENSP00000385428:I276N;ENSP00000385090:I276N	ENSP00000354159:I276N	I	-	2	0	NLRC4	32329610	0.794000	0.28838	0.944000	0.38274	0.897000	0.52465	2.480000	0.45206	1.497000	0.48584	0.443000	0.29094	ATC	.	.		0.517	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		T	32476106	A	T	32476106	3	4	161	1	0	0	0	0	1	0	0	0	10478	333	12	4	2271	4	NLRC4	2	32476106	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10		32476106	210723267	8	24562										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32724675	32724675	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tgaagctcttagaattcactCtggagcagaattttgaagtc	9	7	3	4			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr2:32724675C>T	ENST00000421745.2	+	46	8664	c.8530C>T	c.(8530-8532)Ctg>Ttg	p.L2844L		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2844					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AGAATTCACTCTGGAGCAGAA	0.443																																					p.L2844L	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,NS,carcinoma,0,2	BIRC6	838	.	0			c.C8530T						.						92	87	89					2																	32724675		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon46			TTCACTCTGGAGC	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.8530C>T	chr2.hg19:g.32724675C>T		75.0	0.0		66.0	23.0	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.		0.443	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32724675	C	T	32724675	2	4	161	1	0	0	0	0	0	0	0	1	1438	912	32	3		3	BIRC6	2	32724675	Silent	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	248569	32724675	210474698	9	24563										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99012481	99012481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ccgcctactgaagttttcccGgctctttgaattctttgacc	7	13	2	3	rs104893614		TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr2:99012481G>A	ENST00000272602.2	+	7	887	c.848G>A	c.(847-849)cGg>cAg	p.R283Q	CNGA3_ENST00000436404.2_Missense_Mutation_p.R265Q|CNGA3_ENST00000409937.1_Missense_Mutation_p.R287Q|CNGA3_ENST00000393504.1_Missense_Mutation_p.R283Q			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	283			R -> Q (in ACHM2; does not reveal any detectable calcium influx upon agonist application at 37 degrees Celsius; the channel function could be restored by incubating the transfected cells at 27 degrees Celsius; the dose-response relationship for cGMP-activation is not significantly different from that of wild-type CNGA3; the dose-response relationship of the mutant CNGA3 + CNGB3 is similar to that of the wild-type protein; a substantial reduction of macroscopic cGMP maximum current to only one-third of the mean value for wild-type CNGA3 + CNGB3 is observed for the mutant CNGA3 + CNGB3; the channel density into the cell membrane is considerably improved by decreasing the cultivation temparature). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:18521937, ECO:0000269|PubMed:9662398}.|R -> W (in ACHM2; also found in patients with cone-rod dystrophy). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:24903488, ECO:0000269|PubMed:9662398}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AAGTTTTCCCGGCTCTTTGAA	0.493													G|||	1	0.000199681	8e-04	0	5008	,	,		19479	0		0	False		,,,				2504	0				p.R283Q		Atlas-SNP	.											CNGA3,colon,carcinoma,+1,1	CNGA3	118	.	0			c.G848A	GRCh37	CM980375	CNGA3	M	rs104893614	.	G	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	84	79	81	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	794,848	5.2	1	2	dbSNP_132	81	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CNGA3	NM_001079878.1,NM_001298.2	43,43	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	265/677,283/695	99012481	2,13004	2203	4300	6503	SO:0001583	missense	1261	exon8			TTTCCCGGCTCTT	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.848G>A	chr2.hg19:g.99012481G>A	ENSP00000272602:p.Arg283Gln	179.0	0.0		165.0	61.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.790138	0.90367	2.27E-4	1.16E-4	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.99511	-6.05;-6.05;-6.05;-6.05	5.15	5.15	0.70609	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99600	0.9855	M	0.90369	3.11	0.80722	A	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	0.998;1.0;0.965	D	0.98050	1.0387	9	0.87932	D	0	.	17.5731	0.87940	0.0:0.0:1.0:0.0	.	287;265;283	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	Q	283;265;283;287	ENSP00000377140:R283Q;ENSP00000410070:R265Q;ENSP00000272602:R283Q;ENSP00000386761:R287Q	ENSP00000272602:R283Q	R	+	2	0	CNGA3	98378913	0.999000	0.42202	1.000000	0.80357	0.972000	0.66771	9.263000	0.95617	2.677000	0.91161	0.563000	0.77884	CGG	.	G|1.000;A|0.000		0.493	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		A	99012481	G	A	99012481	3	1	161	1	0	0	0	0	1	0	0	0	3600	1116	39	1	874	1	CNGA3	2	99012481	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	66287806	99012481	144186892	10	24564										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109381547	109381547	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ctgctacttctattccaacaCctgcctcttttaagtttggt	5	12	2	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr2:109381547C>T	ENST00000283195.6	+	20	4678	c.4552C>T	c.(4552-4554)Cct>Tct	p.P1518S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1518					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TATTCCAACACCTGCCTCTTT	0.413																																					p.P1518S		Atlas-SNP	.											.	RANBP2	488	.	0			c.C4552T						.						95	96	96					2																	109381547		2203	4300	6503	SO:0001583	missense	5903	exon20			CCAACACCTGCCT	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.4552C>T	chr2.hg19:g.109381547C>T	ENSP00000283195:p.Pro1518Ser	109.0	0.0		86.0	31.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	2.833	-0.242171	0.05906	.	.	ENSG00000153201	ENST00000283195	T	0.28255	1.62	4.93	1.12	0.20585	.	.	.	.	.	T	0.18299	0.0439	N	0.19112	0.55	0.23287	N	0.997978	B	0.02656	0.0	B	0.04013	0.001	T	0.22626	-1.0211	9	0.34782	T	0.22	-2.4032	8.2095	0.31476	0.0:0.6032:0.0:0.3967	.	1518	P49792	RBP2_HUMAN	S	1518	ENSP00000283195:P1518S	ENSP00000283195:P1518S	P	+	1	0	RANBP2	108747979	0.000000	0.05858	0.125000	0.21846	0.532000	0.34746	-0.480000	0.06559	-0.081000	0.12662	-0.137000	0.14449	CCT	.	.		0.413	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		T	109381547	C	T	109381547	3	4	161	1	0	0	0	0	1	0	0	0	13043	507	18	3	4630	3	RANBP2	2	109381547	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	10369066	109381547	133817826	11	24565										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167288893	167288893	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	atccagattttctatatcagAttctcctgaagcaattggta	6	8	3	3			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr2:167288893A>T	ENST00000409855.1	-	15	2653	c.2527T>A	c.(2527-2529)Tct>Act	p.S843T		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	843					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TCTATATCAGATTCTCCTGAA	0.403																																					p.S843T		Atlas-SNP	.											.	SCN7A	410	.	0			c.T2527A						.						112	111	111					2																	167288893		1904	4105	6009	SO:0001583	missense	6332	exon15			TATCAGATTCTCC	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.2527T>A	chr2.hg19:g.167288893A>T	ENSP00000386796:p.Ser843Thr	99.0	0.0		51.0	22.0	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	hg19	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716541	0.89205	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992	D;D	0.86627	-2.15;-2.15	5.05	5.05	0.67936	Sodium ion transport-associated (1);	0.000000	0.56097	D	0.000040	D	0.93736	0.7998	M	0.90542	3.125	0.38146	D	0.938582	D	0.71674	0.998	D	0.67103	0.949	D	0.95231	0.8342	10	0.54805	T	0.06	.	12.8014	0.57588	1.0:0.0:0.0:0.0	.	843	Q01118	SCN7A_HUMAN	T	843	ENSP00000386796:S843T;ENSP00000413699:S843T	ENSP00000259060:S843T	S	-	1	0	SCN7A	166997139	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	6.046000	0.71029	2.134000	0.65973	0.459000	0.35465	TCT	.	.		0.403	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			T	167288893	A	T	167288893	3	4	161	1	0	0	0	0	1	0	0	0	13938	333	12	4	2565	4	SCN7A	2	167288893	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	57907346	167288893	75910480	12	24566										
NUP35	129401	hgsc.bcm.edu	37	chr2	184022187	184022187	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ttcaggtttcctcaagcatcTgcttcctacatattactaca	4	12	3	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr2:184022187T>A	ENST00000295119.4	+	6	658	c.555T>A	c.(553-555)tcT>tcA	p.S185S	NUP35_ENST00000409798.1_Silent_p.S168S|NUP35_ENST00000541912.1_Silent_p.S50S	NM_138285.3	NP_612142.2	Q8NFH5	NUP53_HUMAN	nucleoporin 35kDa	185	RRM Nup35-type. {ECO:0000255|PROSITE- ProRule:PRU00804}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	8						CTCAAGCATCTGCTTCCTACA	0.328																																					p.S185S		Atlas-SNP	.											.	NUP35	28	.	0			c.T555A						.						145	143	144					2																	184022187		2202	4300	6502	SO:0001819	synonymous_variant	129401	exon6			AGCATCTGCTTCC	AF514993	CCDS2290.1, CCDS74614.1	2q32	2008-02-05			ENSG00000163002	ENSG00000163002			29797	protein-coding gene	gene with protein product		608140					Standard	XM_005246284		Approved	MP44	uc002upf.3	Q8NFH5	OTTHUMG00000132621	ENST00000295119.4:c.555T>A	chr2.hg19:g.184022187T>A		42.0	0.0		47.0	17.0	NM_138285	B4DP57|B4DYB4|Q4ZFZ9|Q53S95|Q8TDJ1	Silent	SNP	ENST00000295119.4	hg19	CCDS2290.1																																																																																			.	.		0.328	NUP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255865.1	NM_138285		A	184022187	T	A	184022187	2	1	161	1	0	0	0	0	0	0	0	1	10772	1567	55	4		4	NUP35	2	184022187	Silent	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	16733294	184022187	59177186	13	24567										
MFSD6	54842	hgsc.bcm.edu	37	chr2	191334570	191334570	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ctggactgttctccccatggAagttcttcaaggtaagttaa	9	9	3	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr2:191334570A>C	ENST00000392328.1	+	4	1943	c.1619A>C	c.(1618-1620)gAa>gCa	p.E540A	MFSD6_ENST00000535751.1_Missense_Mutation_p.E2A|MFSD6_ENST00000281416.7_Missense_Mutation_p.E540A|MFSD6_ENST00000489793.1_3'UTR	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	540					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						CTCCCCATGGAAGTTCTTCAA	0.433																																					p.E540A		Atlas-SNP	.											.	MFSD6	58	.	0			c.A1619C						.						68	67	68					2																	191334570		2203	4300	6503	SO:0001583	missense	54842	exon4			CCATGGAAGTTCT		CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.1619A>C	chr2.hg19:g.191334570A>C	ENSP00000376141:p.Glu540Ala	76.0	0.0		64.0	29.0	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Missense_Mutation	SNP	ENST00000392328.1	hg19	CCDS2306.1	.	.	.	.	.	.	.	.	.	.	A	15.67	2.900893	0.52227	.	.	ENSG00000151690	ENST00000392328;ENST00000281416;ENST00000444317;ENST00000542423;ENST00000535751	T;T	0.56103	0.48;0.48	6.16	5.0	0.66597	Major facilitator superfamily domain, general substrate transporter (1);	0.091877	0.85682	D	0.000000	T	0.75781	0.3896	M	0.88842	2.985	0.54753	D	0.999987	D	0.89917	1.0	D	0.85130	0.997	T	0.79926	-0.1597	10	0.72032	D	0.01	-13.493	12.7598	0.57356	0.8629:0.1371:0.0:0.0	.	540	Q6ZSS7	MFSD6_HUMAN	A	540;540;2;2;2	ENSP00000376141:E540A;ENSP00000281416:E540A	ENSP00000281416:E540A	E	+	2	0	MFSD6	191042815	1.000000	0.71417	1.000000	0.80357	0.019000	0.09904	8.729000	0.91490	1.133000	0.42147	-0.321000	0.08615	GAA	.	.		0.433	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1			C	191334570	A	C	191334570	3	2	161	1	0	0	0	0	1	0	0	0	9544	246	9	5	1625	5	MFSD6	2	191334570	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	7312383	191334570	51864803	14	24568										
NIF3L1	60491	hgsc.bcm.edu	37	chr2	201761868	201761868	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ctgtctccctggcaaccatgAttgatcgaataaaaagacac	7	11	1	3			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr2:201761868A>C	ENST00000409020.1	+	5	1090	c.796A>C	c.(796-798)Att>Ctt	p.I266L	NIF3L1_ENST00000359683.4_Missense_Mutation_p.I239L|NIF3L1_ENST00000416651.1_Missense_Mutation_p.I266L|NIF3L1_ENST00000409588.1_Intron|NIF3L1_ENST00000409357.1_Missense_Mutation_p.I266L|RNU6-762P_ENST00000517107.1_RNA			Q9GZT8	GTPC1_HUMAN	NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae)	266					7,8-dihydroneopterin 3'-triphosphate biosynthetic process (GO:0035998)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTP cyclohydrolase I activity (GO:0003934)|metal ion binding (GO:0046872)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(2)	13						GGCAACCATGATTGATCGAAT	0.438																																					p.I266L		Atlas-SNP	.											.	NIF3L1	51	.	0			c.A796C						.						132	122	125					2																	201761868		1931	4127	6058	SO:0001583	missense	60491	exon5			ACCATGATTGATC	AB038949	CCDS42797.1, CCDS46485.1, CCDS46486.1	2q33	2011-11-10	2011-11-10		ENSG00000196290	ENSG00000196290			13390	protein-coding gene	gene with protein product		605778	"NIF3 (Ngg1 interacting factor 3, S.pombe homolog)-like 1", "NIF3 NGG1 interacting factor 3-like 1 (S. pombe)"	ALS2CR1		11124544, 11161814, 12522100	Standard	NM_001136039		Approved	CALS-7, MDS015	uc002uwm.2	Q9GZT8	OTTHUMG00000154588	ENST00000409020.1:c.796A>C	chr2.hg19:g.201761868A>C	ENSP00000386394:p.Ile266Leu	151.0	0.0		80.0	34.0	NM_001136039	Q53TX4|Q6X735|Q9H2D2|Q9HC18	Missense_Mutation	SNP	ENST00000409020.1	hg19	CCDS46485.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.82|13.82	2.351135|2.351135	0.41599|0.41599	.|.	.|.	ENSG00000196290|ENSG00000196290	ENST00000416651;ENST00000409020;ENST00000359683;ENST00000409357|ENST00000436412	T;T;T;T|.	0.44083|.	0.93;0.93;0.93;0.93|.	6.01|6.01	2.44|2.44	0.29823|0.29823	.|.	0.368655|.	0.31438|.	N|.	0.007653|.	T|.	0.33089|.	0.0851|.	L|L	0.38953|0.38953	1.18|1.18	0.30342|0.30342	N|N	0.785597|0.785597	B|.	0.20164|.	0.042|.	B|.	0.19148|.	0.024|.	T|.	0.30297|.	-0.9983|.	10|.	0.25106|.	T|.	0.35|.	-11.4911|-11.4911	5.3599|5.3599	0.16081|0.16081	0.5456:0.1417:0.3127:0.0|0.5456:0.1417:0.3127:0.0	.|.	266|.	Q9GZT8|.	NIF3L_HUMAN|.	L|C	266;266;239;266|24	ENSP00000400787:I266L;ENSP00000386394:I266L;ENSP00000352711:I239L;ENSP00000387315:I266L|.	ENSP00000352711:I239L|.	I|X	+|+	1|3	0|0	NIF3L1|NIF3L1	201470113|201470113	0.005000|0.005000	0.15991|0.15991	0.998000|0.998000	0.56505|0.56505	0.839000|0.839000	0.47603|0.47603	0.223000|0.223000	0.17719|0.17719	0.182000|0.182000	0.20032|0.20032	0.533000|0.533000	0.62120|0.62120	ATT|TGA	.	.		0.438	NIF3L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336201.1	NM_021824		C	201761868	A	C	201761868	3	2	161	1	0	0	0	0	1	0	0	0	10425	333	12	5	810	5	NIF3L1	2	201761868	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	10427298	201761868	41437505	15	24569										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215852376	215852376	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	accgacttgtcttactggcaGatgggttggtgttctgcatc	12	9	2	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr2:215852376G>T	ENST00000272895.7	-	27	4190	c.3971C>A	c.(3970-3972)tCt>tAt	p.S1324Y	ABCA12_ENST00000389661.4_Missense_Mutation_p.S1006Y	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1324					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CTTACTGGCAGATGGGTTGGT	0.408																																					p.S1324Y	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											ABCA12,bladder,carcinoma,0,1	ABCA12	368	.	0			c.C3971A						.						116	98	104					2																	215852376		2203	4300	6503	SO:0001583	missense	26154	exon27			CTGGCAGATGGGT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.3971C>A	chr2.hg19:g.215852376G>T	ENSP00000272895:p.Ser1324Tyr	255.0	0.0		222.0	11.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.614320	0.46631	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.89415	-2.51;-2.51	5.26	5.26	0.73747	.	0.000000	0.53938	D	0.000047	D	0.86789	0.6017	M	0.77616	2.38	0.80722	D	1	P;P	0.37612	0.602;0.506	B;B	0.39419	0.237;0.299	T	0.83035	-0.0160	10	0.02654	T	1	.	11.4959	0.50408	0.086:0.0:0.914:0.0	.	1324;1006	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	Y	1324;1006	ENSP00000272895:S1324Y;ENSP00000374312:S1006Y	ENSP00000272895:S1324Y	S	-	2	0	ABCA12	215560621	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	2.958000	0.49145	2.464000	0.83262	0.561000	0.74099	TCT	.	.		0.408	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215852376	G	T	215852376	3	4	161	1	0	0	0	0	1	0	0	0	30	942	33	3	3924	3	ABCA12	2	215852376	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	14090508	215852376	27346997	16	24570										
PRKAG3	53632	hgsc.bcm.edu	37	chr2	219692330	219692330	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gagatggagaccagaggcttGaagcagccttgcaggtagat	15	7	0	5			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr2:219692330G>C	ENST00000529249.1	-	8	1158	c.843C>G	c.(841-843)ttC>ttG	p.F281L	PRKAG3_ENST00000439262.2_Missense_Mutation_p.F256L|PRKAG3_ENST00000545803.1_Missense_Mutation_p.F97L|PRKAG3_ENST00000392098.3_Nonsense_Mutation_p.S266*			Q9UGI9	AAKG3_HUMAN	protein kinase, AMP-activated, gamma 3 non-catalytic subunit	281	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)	AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|protein kinase binding (GO:0019901)			large_intestine(7)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Acetylsalicylic acid(DB00945)	CCAGAGGCTTGAAGCAGCCTT	0.592																																					p.F281L		Atlas-SNP	.											.	PRKAG3	47	.	0			c.C843G						.						117	118	118					2																	219692330		2203	4300	6503	SO:0001583	missense	53632	exon8			AGGCTTGAAGCAG	AF214519	CCDS2424.1	2q35	2012-09-20			ENSG00000115592	ENSG00000115592			9387	protein-coding gene	gene with protein product		604976				10818001	Standard	NM_017431		Approved		uc002vjb.1	Q9UGI9	OTTHUMG00000133078	ENST00000529249.1:c.843C>G	chr2.hg19:g.219692330G>C	ENSP00000436068:p.Phe281Leu	92.0	0.0		90.0	32.0	NM_017431	Q4QQG8|Q4V779|Q9NRL1	Missense_Mutation	SNP	ENST00000529249.1	hg19	CCDS2424.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.6|28.6	4.931104|4.931104	0.92389|0.92389	.|.	.|.	ENSG00000115592|ENSG00000115592	ENST00000439262;ENST00000545803;ENST00000529249|ENST00000392098	D;D;D|.	0.91011|.	-2.77;-2.77;-2.77|.	4.54|4.54	2.75|2.75	0.32379|0.32379	Cystathionine beta-synthase, core (1);|.	0.293673|.	0.38436|.	N|.	0.001690|.	T|.	0.40448|.	0.1117|.	L|L	0.28400|0.28400	0.85|0.85	0.80722|0.80722	A|A	1|1	B|.	0.09022|.	0.002|.	B|.	0.08055|.	0.003|.	T|.	0.51092|.	-0.8749|.	9|.	0.16420|0.38643	T|T	0.52|0.18	-15.4959|-15.4959	9.7489|9.7489	0.40464|0.40464	0.1674:0.0:0.8326:0.0|0.1674:0.0:0.8326:0.0	.|.	281|.	Q9UGI9|.	AAKG3_HUMAN|.	L|X	256;97;281|266	ENSP00000397133:F256L;ENSP00000444536:F97L;ENSP00000436068:F281L|.	ENSP00000233944:F281L|ENSP00000375947:S266X	F|S	-|-	3|2	2|0	PRKAG3|PRKAG3	219400574|219400574	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	3.891000|3.891000	0.56227|0.56227	0.554000|0.554000	0.29061|0.29061	-0.136000|-0.136000	0.14681|0.14681	TTC|TCA	.	.		0.592	PRKAG3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385992.1			C	219692330	G	C	219692330	3	2	161	1	0	0	0	0	1	0	0	0	12514	1281	45	4	650	4	PRKAG3	2	219692330	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	3839954	219692330	23507043	17	24571										
ACVR2B	93	hgsc.bcm.edu	37	chr3	38520626	38520626	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	cccccggcctcaggacaagcAgtcgtggcagagtgaacggg	15	13	1	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr3:38520626A>G	ENST00000352511.4	+	6	1146	c.674A>G	c.(673-675)cAg>cGg	p.Q225R		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		CAGGACAAGCAGTCGTGGCAG	0.587																																					p.Q225R		Atlas-SNP	.											.	ACVR2B	88	.	0			c.A674G						.						139	138	138					3																	38520626		2203	4300	6503	SO:0001583	missense	93	exon6			ACAAGCAGTCGTG	X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	ENST00000352511.4:c.674A>G	chr3.hg19:g.38520626A>G	ENSP00000340361:p.Gln225Arg	254.0	0.0		191.0	76.0	NM_001106	Q4VAV0	Missense_Mutation	SNP	ENST00000352511.4	hg19	CCDS2679.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.944240	0.53079	.	.	ENSG00000114739	ENST00000352511	D	0.93076	-3.16	4.75	4.75	0.60458	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.117840	0.64402	D	0.000015	D	0.87904	0.6295	N	0.20445	0.575	0.54753	D	0.999981	B	0.14438	0.01	B	0.16289	0.015	D	0.84871	0.0825	10	0.59425	D	0.04	.	14.4386	0.67301	1.0:0.0:0.0:0.0	.	225	Q13705	AVR2B_HUMAN	R	225	ENSP00000340361:Q225R	ENSP00000340361:Q225R	Q	+	2	0	ACVR2B	38495630	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	5.025000	0.64097	1.992000	0.58205	0.460000	0.39030	CAG	.	.		0.587	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106		G	38520626	A	G	38520626	3	3	161	1	0	0	0	0	1	0	0	0	224	188	7	2	696	2	ACVR2B	3	38520626	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10		38520626	159501804	18	24572										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266124	41266124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gaatccattctggtgccactAccacagctccttctctgagt	7	14	2	1	rs121913412		TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr3:41266124A>G	ENST00000349496.5	+	3	401	c.121A>G	c.(121-123)Acc>Gcc	p.T41A	CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41A|CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34A|CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	41			T -> A (in hepatoblastoma and hepatocellular carcinoma; also in a desmoid tumor; strongly reduces phosphorylation and degradation; abolishes phosphorylation on Ser-33 and Ser-37 and enhances transactivation of target genes). {ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10398436, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10655994, ECO:0000269|PubMed:9927029}.|T -> I (in PTR, hepatocellular carcinoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T41A(550)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41P(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.A39_T42del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGTGCCACTACCACAGCTCC	0.507	T41A(CCK81_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.T41A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	681	Substitution - Missense(559)|Deletion - In frame(96)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)	soft_tissue(387)|liver(158)|large_intestine(61)|endometrium(17)|kidney(11)|stomach(8)|biliary_tract(7)|ovary(6)|small_intestine(4)|lung(4)|prostate(4)|adrenal_gland(3)|haematopoietic_and_lymphoid_tissue(3)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|salivary_gland(1)|pituitary(1)|pancreas(1)	c.A121G						.						89	77	81					3																	41266124		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCCACTACCACAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.121A>G	chr3.hg19:g.41266124A>G	ENSP00000344456:p.Thr41Ala	190.0	1.0		134.0	53.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449381	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.63117	0.2484	M	0.79258	2.445	0.80722	D	1	P	0.50943	0.94	P	0.52267	0.694	T	0.68561	-0.5376	10	0.87932	D	0	-8.9189	16.3453	0.83126	1.0:0.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	A	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34A;ENSP00000385604:T41A;ENSP00000412219:T41A;ENSP00000379486:T41A;ENSP00000344456:T41A;ENSP00000411226:T34A;ENSP00000379488:T41A;ENSP00000409302:T41A;ENSP00000401599:T41A	ENSP00000344456:T41A	T	+	1	0	CTNNB1	41241128	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	ACC	.	.		0.507	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266124	A	G	41266124	3	3	161	1	0	0	0	0	1	0	0	0	4018	391	14	2	127	2	CTNNB1	3	41266124	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	2745498	41266124	156756306	19	24573										
RAD54L2	23132	hgsc.bcm.edu	37	chr3	51664804	51664804	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tcagtgaagatgatgaggaaGaagagaagggtggcacccat	15	5	1	6			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr3:51664804G>T	ENST00000409535.2	+	6	807	c.682G>T	c.(682-684)Gaa>Taa	p.E228*	RAD54L2_ENST00000296477.3_5'UTR	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	228						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		TGATGAGGAAGAAGAGAAGGG	0.498																																					p.E228X		Atlas-SNP	.											.	RAD54L2	94	.	0			c.G682T						.						109	93	98					3																	51664804		2203	4300	6503	SO:0001587	stop_gained	23132	exon6			GAGGAAGAAGAGA	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.682G>T	chr3.hg19:g.51664804G>T	ENSP00000386520:p.Glu228*	61.0	0.0		55.0	27.0	NM_015106	Q8TB57|Q9BV54	Nonsense_Mutation	SNP	ENST00000409535.2	hg19	CCDS33765.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.2|22.2	4.264694|4.264694	0.80358|0.80358	.|.	.|.	ENSG00000164080|ENSG00000164080	ENST00000409535|ENST00000432863	.|.	.|.	.|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.408168|.	0.30742|.	N|.	0.008973|.	.|T	.|0.64907	.|0.2641	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.62282	.|-0.6887	.|4	0.15499|.	T|.	0.54|.	-18.7537|-18.7537	12.3782|12.3782	0.55291|0.55291	0.0762:0.0:0.9238:0.0|0.0762:0.0:0.9238:0.0	.|.	.|.	.|.	.|.	X|I	228|56	.|.	ENSP00000386520:E228X|.	E|R	+|+	1|2	0|0	RAD54L2|RAD54L2	51639844|51639844	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	6.377000|6.377000	0.73145|0.73145	2.744000|2.744000	0.94065|0.94065	0.655000|0.655000	0.94253|0.94253	GAA|AGA	.	.		0.498	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		T	51664804	G	T	51664804	4	4	161	1	0	0	0	0	0	1	0	0	13009	943	33	3	700	3	RAD54L2	3	51664804	Nonsense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	10398680	51664804	146357626	20	24574										
PSMD6	9861	hgsc.bcm.edu	37	chr3	64004653	64004653	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tcacgaatagccacacaataAagaccctgatacacttttag	5	11	1	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr3:64004653A>C	ENST00000295901.4	-	4	698	c.558T>G	c.(556-558)ctT>ctG	p.L186L	PSMD6_ENST00000394431.2_Silent_p.L148L|PSMD6_ENST00000482510.1_Silent_p.L147L|RP11-245J9.4_ENST00000462717.1_RNA|RP11-245J9.6_ENST00000605919.1_RNA|PSMD6_ENST00000492933.1_Silent_p.L239L	NM_014814.1	NP_055629.1	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	186					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATPase activity (GO:0016887)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(1)	13		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)		CCACACAATAAAGACCCTGAT	0.378																																					p.L239L		Atlas-SNP	.											.	PSMD6	30	.	0			c.T717G						.						163	167	166					3																	64004653		2203	4300	6503	SO:0001819	synonymous_variant	9861	exon5			ACAATAAAGACCC	AF215935	CCDS2901.1, CCDS63677.1, CCDS63678.1, CCDS63679.1	3p14.1	2008-05-22			ENSG00000163636	ENSG00000163636		"Proteasome (prosome, macropain) subunits"	9564	protein-coding gene	gene with protein product						10723133	Standard	NM_001271779		Approved	S10, p44S10, KIAA0107, Rpn7	uc003dmb.2	Q15008	OTTHUMG00000158765	ENST00000295901.4:c.558T>G	chr3.hg19:g.64004653A>C		257.0	0.0		184.0	62.0	NM_001271779	A8K2E0|E9PHI9|Q6UV22	Silent	SNP	ENST00000295901.4	hg19	CCDS2901.1	.	.	.	.	.	.	.	.	.	.	A	9.613	1.131798	0.21041	.	.	ENSG00000163636	ENST00000480205	.	.	.	5.84	-0.758	0.11049	.	0.000000	0.85682	D	0.000000	T	0.38983	0.1061	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.08889	-1.0700	6	0.26408	T	0.33	-1.0257	2.1961	0.03911	0.3797:0.3295:0.1843:0.1066	.	.	.	.	V	34	.	ENSP00000418843:L34V	L	-	1	2	PSMD6	63979693	0.607000	0.26958	0.938000	0.37757	0.986000	0.74619	-0.032000	0.12266	-0.341000	0.08376	0.459000	0.35465	TTA	.	.		0.378	PSMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352082.1	NM_014814		C	64004653	A	C	64004653	2	2	161	1	0	0	0	0	0	0	0	1	12714	1	1	5		5	PSMD6	3	64004653	Silent	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	12339849	64004653	134017777	21	24575										
SHQ1	55164	hgsc.bcm.edu	37	chr3	72873605	72873605	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	atgattttcttgttcctgacTcttttccaaaaaggccatca	5	10	3	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr3:72873605T>C	ENST00000325599.8	-	6	836	c.697A>G	c.(697-699)Agt>Ggt	p.S233G	SHQ1_ENST00000463369.1_Missense_Mutation_p.S205G	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	233					negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		TGTTCCTGACTCTTTTCCAAA	0.353																																					p.S233G		Atlas-SNP	.											.	SHQ1	60	.	0			c.A697G						.						95	92	93					3																	72873605		2201	4298	6499	SO:0001583	missense	55164	exon6			CCTGACTCTTTTC	BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"SHQ1 homolog (S. cerevisiae)"			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.697A>G	chr3.hg19:g.72873605T>C	ENSP00000315182:p.Ser233Gly	106.0	0.0		70.0	25.0	NM_018130	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Missense_Mutation	SNP	ENST00000325599.8	hg19	CCDS33788.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.209440	0.39003	.	.	ENSG00000144736	ENST00000325599;ENST00000463369	T;T	0.33865	1.4;1.39	5.61	4.45	0.53987	SHQ1 protein (1);	0.759174	0.13015	N	0.420586	T	0.33818	0.0876	L	0.47716	1.5	0.43803	D	0.996355	B	0.14012	0.009	B	0.19391	0.025	T	0.06110	-1.0845	10	0.48119	T	0.1	-8.289	10.7416	0.46156	0.0:0.0759:0.0:0.9241	.	233	Q6PI26	SHQ1_HUMAN	G	233;205	ENSP00000315182:S233G;ENSP00000417452:S205G	ENSP00000315182:S233G	S	-	1	0	SHQ1	72956295	0.000000	0.05858	0.934000	0.37439	0.077000	0.17291	0.732000	0.26072	0.964000	0.38108	-0.290000	0.09829	AGT	.	.		0.353	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130		C	72873605	T	C	72873605	3	2	161	1	0	0	0	0	1	0	0	0	14307	1551	54	2	1060	2	SHQ1	3	72873605	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	8868952	72873605	125148825	22	24576										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121410757	121410757	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gtcgctcttccagctgttgaTagtcacccactatgcggtct	9	13	3	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr3:121410757T>C	ENST00000340645.5	-	14	7564	c.7439A>G	c.(7438-7440)tAt>tGt	p.Y2480C	GOLGB1_ENST00000393667.3_Missense_Mutation_p.Y2485C	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2480					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CAGCTGTTGATAGTCACCCAC	0.403																																					p.Y2485C		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A7454G						.						164	163	163					3																	121410757		2203	4300	6503	SO:0001583	missense	2804	exon14			TGTTGATAGTCAC	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.7439A>G	chr3.hg19:g.121410757T>C	ENSP00000341848:p.Tyr2480Cys	144.0	0.0		90.0	39.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	12.77	2.038514	0.35989	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.27402	1.67;1.67	5.55	5.55	0.83447	.	0.000000	0.56097	D	0.000030	T	0.55673	0.1935	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.986	T	0.56426	-0.7981	10	0.39692	T	0.17	.	13.648	0.62292	0.0:0.0:0.0:1.0	.	2485;2485;2480	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	C	2480;2485	ENSP00000341848:Y2480C;ENSP00000377275:Y2485C	ENSP00000341848:Y2480C	Y	-	2	0	GOLGB1	122893447	1.000000	0.71417	0.987000	0.45799	0.878000	0.50629	7.634000	0.83273	2.102000	0.63906	0.460000	0.39030	TAT	.	.		0.403	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121410757	T	C	121410757	3	2	161	1	0	0	0	0	1	0	0	0	6573	1406	49	2	2376	2	GOLGB1	3	121410757	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	48537152	121410757	76611673	23	24577										
DTX3L	151636	hgsc.bcm.edu	37	chr3	122284854	122284854	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	caatcacaagcagaaacaccGtctggtgatatgcatcaaca	7	11	3	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr3:122284854G>A	ENST00000296161.4	+	2	525	c.336G>A	c.(334-336)ccG>ccA	p.P112P	PARP9_ENST00000360356.2_5'Flank|PARP9_ENST00000477522.2_5'Flank|PARP9_ENST00000462315.1_5'Flank|PARP9_ENST00000492382.1_5'Flank|PARP9_ENST00000471785.1_5'Flank|DTX3L_ENST00000383661.3_Silent_p.P112P	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	112					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		CAGAAACACCGTCTGGTGATA	0.438																																					p.P112P		Atlas-SNP	.											.	DTX3L	59	.	0			c.G336A						.						105	93	97					3																	122284854		2203	4300	6503	SO:0001819	synonymous_variant	151636	exon2			AACACCGTCTGGT		CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"RING-type (C3HC4) zinc fingers"	30323	protein-coding gene	gene with protein product	"rhysin 2"	613143	"deltex 3-like (Drosophila)"			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.336G>A	chr3.hg19:g.122284854G>A		166.0	0.0		109.0	40.0	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Silent	SNP	ENST00000296161.4	hg19	CCDS3015.1																																																																																			.	.		0.438	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287		A	122284854	G	A	122284854	2	1	161	1	0	0	0	0	0	0	0	1	4798	1132	40	1		1	DTX3L	3	122284854	Silent	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	874097	122284854	75737576	24	24578										
P2RY1	5028	hgsc.bcm.edu	37	chr3	152554320	152554320	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tttgatttacaaagatctggAcaactctcctctgaggagaa	8	8	3	4			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr3:152554320A>T	ENST00000305097.3	+	1	1585	c.749A>T	c.(748-750)gAc>gTc	p.D250V	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	250					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			AAAGATCTGGACAACTCTCCT	0.438																																					p.D250V		Atlas-SNP	.											.	P2RY1	49	.	0			c.A749T						.						105	100	102					3																	152554320		2203	4300	6503	SO:0001583	missense	5028	exon1			ATCTGGACAACTC	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.749A>T	chr3.hg19:g.152554320A>T	ENSP00000304767:p.Asp250Val	109.0	0.0		83.0	38.0	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	hg19	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.260760	0.39995	.	.	ENSG00000169860	ENST00000305097	T	0.20463	2.07	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.062065	0.64402	D	0.000002	T	0.17662	0.0424	N	0.05554	-0.025	0.80722	D	1	P	0.45396	0.857	P	0.49387	0.609	T	0.13845	-1.0494	10	0.29301	T	0.29	.	14.9343	0.70941	1.0:0.0:0.0:0.0	.	250	P47900	P2RY1_HUMAN	V	250	ENSP00000304767:D250V	ENSP00000304767:D250V	D	+	2	0	P2RY1	154037010	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.098000	0.71458	2.117000	0.64856	0.460000	0.39030	GAC	.	.		0.438	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		T	152554320	A	T	152554320	3	4	161	1	0	0	0	0	1	0	0	0	11355	275	10	4	751	4	P2RY1	3	152554320	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	30269466	152554320	45468110	25	24579										
REST	5978	hgsc.bcm.edu	37	chr4	57796354	57796355	+	Frame_Shift_Ins	INS	-	-	A													0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gcctgataatattaccaatgINSaaaaaacagaaatagaacaa							TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr4:57796354_57796355insA	ENST00000309042.7	+	4	1644_1645	c.1330_1331insA	c.(1330-1332)gaafs	p.E444fs		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	444	Lys-rich.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					TATTACCAATGAAAAAACAGAA	0.337																																					p.E444fs		Atlas-INDEL	.											.	REST	104	.	0			c.1330_1331insA						.																																			SO:0001589	frameshift_variant	5978	exon4			.	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.1336dupA	chr4.hg19:g.57796360_57796360dupA	ENSP00000311816:p.Glu444fs	236.0	0.0		185.0	84.0	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Frame_Shift_Ins	INS	ENST00000309042.7	hg19	CCDS3509.1																																																																																			.	.		0.337	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		A	57796355	-	A	57796354	7	5	161	1	0	1	1	0	0	0	0	0	13249	1291	45	0	1340	0	REST	4	57796354	Frame_Shift_Ins	INS	-	TCGA-DD-AACJ-01A-11D-A40R-10		57796354	133357922	26	24580										
WWC2	80014	hgsc.bcm.edu	37	chr4	184180883	184180883	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tgcattcacaacttaaaaggTgagcttatcagatttttgag	8	6	2	3			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr4:184180883T>G	ENST00000403733.3	+	10	1485		c.e10+2		WWC2_ENST00000378925.3_Splice_Site|WWC2_ENST00000513834.1_Splice_Site|WWC2_ENST00000448232.2_Splice_Site|WWC2_ENST00000504005.1_Splice_Site	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2						negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		ACTTAAAAGGTGAGCTTATCA	0.318																																					.		Atlas-SNP	.											.	WWC2	78	.	0			c.1286+2T>G						.						39	42	41					4																	184180883		2085	4052	6137	SO:0001630	splice_region_variant	80014	exon10			AAAAGGTGAGCTT	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.1286+2T>G	chr4.hg19:g.184180883T>G		285.0	1.0		208.0	93.0	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Splice_Site	SNP	ENST00000403733.3	hg19	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812925	0.50527	.	.	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232;ENST00000504005	.	.	.	4.99	2.54	0.30619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.4802	0.38895	0.0:0.1446:0.0:0.8554	.	.	.	.	.	-1	.	.	.	+	.	.	WWC2	184417877	1.000000	0.71417	0.732000	0.30844	0.796000	0.44982	3.729000	0.54999	0.471000	0.27319	0.459000	0.35465	.	.	.		0.318	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	Intron	G	184180883	T	G	184180883	5	3	161	1	0	0	0	0	0	0	1	0	17427	1710	59	5	1326	5	WWC2	4	184180883	Splice_Site	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	126384529	184180883	6973393	27	24581										
FAT1	2195	hgsc.bcm.edu	37	chr4	187510117	187510117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	acccgcggcaggcatgtctcTaggagggtggatggattcaa	15	9	2	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr4:187510117T>C	ENST00000441802.2	-	27	13605	c.13396A>G	c.(13396-13398)Aga>Gga	p.R4466G		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4466					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GGCATGTCTCTAGGAGGGTGG	0.502										HNSCC(5;0.00058)																											p.R4466G	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A13396G						.						210	212	212					4																	187510117		1909	4110	6019	SO:0001583	missense	2195	exon27			TGTCTCTAGGAGG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.13396A>G	chr4.hg19:g.187510117T>C	ENSP00000406229:p.Arg4466Gly	217.0	0.0		194.0	63.0	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.14|11.14	1.549765|1.549765	0.27652|0.27652	.|.	.|.	ENSG00000083857|ENSG00000083857	ENST00000441802;ENST00000260147|ENST00000512772;ENST00000507105	T|.	0.23754|.	1.89|.	5.37|5.37	2.9|2.9	0.33743|0.33743	.|.	0.094242|.	0.64402|.	N|.	0.000002|.	T|.	0.57666|.	0.2069|.	L|L	0.54323|0.54323	1.7|1.7	0.47949|0.47949	D|D	0.999556|0.999556	B|.	0.25441|.	0.126|.	B|.	0.27500|.	0.08|.	T|.	0.50693|.	-0.8798|.	10|.	0.34782|.	T|.	0.22|.	.|.	8.2943|8.2943	0.31976|0.31976	0.0:0.0689:0.1335:0.7976|0.0:0.0689:0.1335:0.7976	.|.	4466|.	Q14517|.	FAT1_HUMAN|.	G|W	4466;4468|245;233	ENSP00000406229:R4466G|.	ENSP00000260147:R4468G|.	R|X	-|-	1|2	2|0	FAT1|FAT1	187747111|187747111	0.949000|0.949000	0.32298|0.32298	0.524000|0.524000	0.27887|0.27887	0.618000|0.618000	0.37518|0.37518	1.621000|1.621000	0.36986|0.36986	0.468000|0.468000	0.27243|0.27243	0.374000|0.374000	0.22700|0.22700	AGA|TAG	.	.		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		C	187510117	T	C	187510117	3	2	161	1	0	0	0	0	1	0	0	0	5697	1530	53	2	374	2	FAT1	4	187510117	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	3329234	187510117	3644159	28	24582										
ST8SIA4	7903	hgsc.bcm.edu	37	chr5	100231434	100231434	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gattgaagagccagcctttcGaatgattttatcagagctat	9	7	1	4			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr5:100231434G>A	ENST00000231461.5	-	2	479	c.169C>T	c.(169-171)Cga>Tga	p.R57*	ST8SIA4_ENST00000451528.2_Nonsense_Mutation_p.R57*	NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	57					axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)	p.R57*(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		CCAGCCTTTCGAATGATTTTA	0.373																																					p.R57X		Atlas-SNP	.											ST8SIA4,NS,carcinoma,+1,1	ST8SIA4	77	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C169T						.						112	109	110					5																	100231434		2203	4299	6502	SO:0001587	stop_gained	7903	exon2			CCTTTCGAATGAT	L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532		"Sialyltransferases"	10871	protein-coding gene	gene with protein product	"ST8Sia IV"	602547	"sialyltransferase 8 (alpha-2, 8-polysialytransferase) D"	SIAT8D		7624364	Standard	NM_005668		Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.169C>T	chr5.hg19:g.100231434G>A	ENSP00000231461:p.Arg57*	119.0	0.0		137.0	39.0	NM_175052	A8KA07|G3V104|Q8N1F4|Q92693	Nonsense_Mutation	SNP	ENST00000231461.5	hg19	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	G	37	6.260157	0.97421	.	.	ENSG00000113532	ENST00000231461;ENST00000451528	.	.	.	5.96	5.96	0.96718	.	0.083749	0.50627	D	0.000120	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	19.3963	0.94608	0.0:0.0:1.0:0.0	.	.	.	.	X	57	.	ENSP00000231461:R57X	R	-	1	2	ST8SIA4	100259333	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	3.235000	0.51328	2.814000	0.96858	0.655000	0.94253	CGA	.	.		0.373	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668		A	100231434	G	A	100231434	4	1	161	1	0	0	0	0	0	1	0	0	15249	1066	37	1	930	1	ST8SIA4	5	100231434	Nonsense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10		100231434	80683826	29	24583										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128861992	128861992	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tgcagataaaggaagacctaGgtctagaaaaatagcagaaa	10	5	1	4			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr5:128861992G>C	ENST00000274487.4	+	4	1056	c.911G>C	c.(910-912)aGg>aCg	p.R304T	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	304						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GGAAGACCTAGGTCTAGAAAA	0.348																																					p.R304T		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.G911C						.						63	60	61					5																	128861992		2203	4300	6503	SO:0001583	missense	171019	exon4			GACCTAGGTCTAG	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.911G>C	chr5.hg19:g.128861992G>C	ENSP00000274487:p.Arg304Thr	315.0	0.0		345.0	210.0	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	G	12.68	2.011789	0.35511	.	.	ENSG00000145808	ENST00000274487	T	0.66280	-0.2	4.45	2.68	0.31781	.	0.139461	0.46758	D	0.000274	T	0.33498	0.0865	N	0.08118	0	0.33325	D	0.567825	B	0.27117	0.168	B	0.15052	0.012	T	0.34403	-0.9830	9	.	.	.	.	7.4419	0.27187	0.3295:0.0:0.6705:0.0	.	304	Q8TE59	ATS19_HUMAN	T	304	ENSP00000274487:R304T	.	R	+	2	0	ADAMTS19	128889891	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.858000	0.27845	0.825000	0.34637	0.557000	0.71058	AGG	.	.		0.348	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		C	128861992	G	C	128861992	3	2	161	1	0	0	0	0	1	0	0	0	264	1000	35	4	925	4	ADAMTS19	5	128861992	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	28630558	128861992	52053268	30	24584										
UBR2	23304	hgsc.bcm.edu	37	chr6	42629942	42629942	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	aaaaatatgatccattattcAtgcaccctgatctgtcttgt	5	9	3	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr6:42629942A>G	ENST00000372899.1	+	31	3721	c.3463A>G	c.(3463-3465)Atg>Gtg	p.M1155V	UBR2_ENST00000372901.1_Missense_Mutation_p.M1155V|UBR2_ENST00000372883.3_3'UTR|RNU6-890P_ENST00000384121.1_RNA	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1155					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TCCATTATTCATGCACCCTGA	0.318																																					p.M1155V		Atlas-SNP	.											.	UBR2	134	.	0			c.A3463G						.						178	167	170					6																	42629942		2203	4300	6503	SO:0001583	missense	23304	exon31			TTATTCATGCACC	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.3463A>G	chr6.hg19:g.42629942A>G	ENSP00000361990:p.Met1155Val	60.0	0.0		66.0	14.0	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	hg19	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154915	0.38021	.	.	ENSG00000024048	ENST00000372899;ENST00000372901	T;T	0.45668	0.89;0.89	5.16	5.16	0.70880	Zinc finger, RING-type (1);	0.036871	0.85682	D	0.000000	T	0.19525	0.0469	L	0.43757	1.38	0.80722	D	1	B;B	0.12013	0.005;0.002	B;B	0.14023	0.01;0.006	T	0.07790	-1.0754	10	0.13853	T	0.58	-10.1973	15.295	0.73898	1.0:0.0:0.0:0.0	.	1155;1155	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	V	1155	ENSP00000361990:M1155V;ENSP00000361992:M1155V	ENSP00000361990:M1155V	M	+	1	0	UBR2	42737920	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	6.014000	0.70784	2.086000	0.62901	0.379000	0.24179	ATG	.	.		0.318	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		G	42629942	A	G	42629942	3	3	161	1	0	0	0	0	1	0	0	0	16917	217	8	2	3731	2	UBR2	6	42629942	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10		42629942	128485125	31	24585										
C6orf142	90523	hgsc.bcm.edu	37	chr6	54095631	54095631	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	catgctgactgtcttgccccAggacccttcagtcatctgtc	8	15	4	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr6:54095631A>G	ENST00000274897.5	+	11	1346	c.1233A>G	c.(1231-1233)ccA>ccG	p.P411P	MLIP_ENST00000509997.1_Intron|MLIP_ENST00000502396.1_Silent_p.P946P|MLIP_ENST00000370877.2_Intron|MLIP_ENST00000370876.2_Intron|MLIP_ENST00000358276.5_Intron	NM_138569.2	NP_612636.2	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein	411						nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						GTCTTGCCCCAGGACCCTTCA	0.512																																					p.P411P		Atlas-SNP	.											.	MLIP	84	.	0			c.A1233G						.						262	231	241					6																	54095631		2203	4300	6503	SO:0001819	synonymous_variant	90523	exon11			TGCCCCAGGACCC	AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147			21355	protein-coding gene	gene with protein product	"muscle-enriched A-type lamin interacting protein"	614106	"chromosome 6 open reading frame 142"	C6orf142		21498514	Standard	NM_138569		Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000274897.5:c.1233A>G	chr6.hg19:g.54095631A>G		66.0	0.0		73.0	40.0	NM_138569	B7Z2N0|D6RE05|Q96H08|Q96NF7	Silent	SNP	ENST00000274897.5	hg19	CCDS4954.1																																																																																			.	.		0.512	MLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040979.3	NM_138569		G	54095631	A	G	54095631	2	3	161	1	0	0	0	0	0	0	0	1	2335	175	7	2		2	C6orf142	6	54095631	Silent	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	11465689	54095631	117019436	32	24586										
GPR63	81491	hgsc.bcm.edu	37	chr6	97246634	97246634	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tggtgaatggggcccagcagAcaatgaagacagcaaagaga	14	7	0	5			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr6:97246634A>G	ENST00000229955.3	-	2	1319	c.974T>C	c.(973-975)gTc>gCc	p.V325A	RP3-417O22.3_ENST00000442184.1_RNA|GPR63_ENST00000417980.1_Missense_Mutation_p.V325A	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	325						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		GGCCCAGCAGACAATGAAGAC	0.453																																					p.V325A		Atlas-SNP	.											.	GPR63	60	.	0			c.T974C						.						107	90	96					6																	97246634		2203	4300	6503	SO:0001583	missense	81491	exon2			CAGCAGACAATGA	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.974T>C	chr6.hg19:g.97246634A>G	ENSP00000229955:p.Val325Ala	166.0	0.0		169.0	53.0	NM_030784	Q9UJH3	Missense_Mutation	SNP	ENST00000229955.3	hg19	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.042816	0.36085	.	.	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	T;T;T	0.41758	0.99;0.99;0.99	5.2	5.2	0.72013	GPCR, rhodopsin-like superfamily (1);	0.160895	0.41194	D	0.000926	T	0.21468	0.0517	L	0.31294	0.92	0.43647	D	0.996056	B	0.06786	0.001	B	0.19391	0.025	T	0.08207	-1.0733	10	0.62326	D	0.03	-0.2317	15.3582	0.74443	1.0:0.0:0.0:0.0	.	325	Q9BZJ6	GPR63_HUMAN	A	349;325;325;325	ENSP00000393170:V325A;ENSP00000229955:V325A;ENSP00000358273:V325A	ENSP00000229955:V325A	V	-	2	0	GPR63	97353355	1.000000	0.71417	0.978000	0.43139	0.998000	0.95712	5.927000	0.70080	2.097000	0.63578	0.528000	0.53228	GTC	.	.		0.453	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			G	97246634	A	G	97246634	3	3	161	1	0	0	0	0	1	0	0	0	6712	275	10	2	289	2	GPR63	6	97246634	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	43151003	97246634	73868433	33	24587										
TFB1M	51106	hgsc.bcm.edu	37	chr6	155632360	155632360	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tcgagtgtccttttcaaccaCcagaagttcagcgacgtcgg	10	12	2	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr6:155632360C>A	ENST00000367166.4	-	2	302	c.247G>T	c.(247-249)Gtg>Ttg	p.V83L	TFB1M_ENST00000480390.1_5'UTR	NM_016020.3	NP_057104.2	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	83					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)		TTTTCAACCACCAGAAGTTCA	0.438																																					p.V83L		Atlas-SNP	.											.	TFB1M	30	.	0			c.G247T						.						128	116	120					6																	155632360		2203	4300	6503	SO:0001583	missense	51106	exon2			CAACCACCAGAAG	AF151833	CCDS5248.1	6q25.1-q25.3	2011-01-28			ENSG00000029639	ENSG00000029639			17037	protein-coding gene	gene with protein product	"dimethyladenosine transferase 1, mitochondrial"	607033				10810093, 11809803	Standard	NM_016020		Approved	mtTFB, CGI-75	uc003qqj.4	Q8WVM0	OTTHUMG00000015881	ENST00000367166.4:c.247G>T	chr6.hg19:g.155632360C>A	ENSP00000356134:p.Val83Leu	106.0	0.0		130.0	46.0	NM_016020	Q05DR0|Q9Y384	Missense_Mutation	SNP	ENST00000367166.4	hg19	CCDS5248.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.553728	0.65425	.	.	ENSG00000029639	ENST00000367166	T	0.27720	1.65	5.96	5.96	0.96718	Ribosomal RNA adenine methylase transferase, conserved site (1);Ribosomal RNA adenine methylase transferase, N-terminal (1);	0.057121	0.64402	D	0.000001	T	0.21921	0.0528	L	0.49455	1.56	0.58432	D	0.999994	B	0.22541	0.071	B	0.33690	0.168	T	0.02683	-1.1124	10	0.36615	T	0.2	-27.1362	14.7978	0.69891	0.1794:0.8206:0.0:0.0	.	83	Q8WVM0	TFB1M_HUMAN	L	83	ENSP00000356134:V83L	ENSP00000356134:V83L	V	-	1	0	TFB1M	155674052	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.452000	0.60054	2.832000	0.97577	0.655000	0.94253	GTG	.	.		0.438	TFB1M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042809.1			A	155632360	C	A	155632360	3	1	161	1	0	0	0	0	1	0	0	0	15808	507	18	3	817	3	TFB1M	6	155632360	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	58385726	155632360	15482707	34	24588										
RADIL	55698	hgsc.bcm.edu	37	chr7	4917682	4917682	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ggtacttgtagctcagcgtcCgggacagcatgctggacaac	13	11	1	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr7:4917682C>T	ENST00000399583.3	-	2	276	c.89G>A	c.(88-90)cGg>cAg	p.R30Q	RADIL_ENST00000536091.1_Missense_Mutation_p.R30Q	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	30					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		GCTCAGCGTCCGGGACAGCAT	0.632																																					p.R30Q		Atlas-SNP	.											.	RADIL	110	.	0			c.G89A						.						22	26	25					7																	4917682		2070	4203	6273	SO:0001583	missense	55698	exon2			AGCGTCCGGGACA	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.89G>A	chr7.hg19:g.4917682C>T	ENSP00000382492:p.Arg30Gln	71.0	0.0		58.0	26.0	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	hg19	CCDS43544.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227487	0.79576	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000536091;ENST00000457174	T;T	0.28255	3.0;1.62	5.84	5.84	0.93424	.	0.068935	0.64402	D	0.000016	T	0.41627	0.1167	M	0.63843	1.955	0.41280	D	0.986906	D	0.58620	0.983	P	0.47470	0.548	T	0.38156	-0.9674	10	0.87932	D	0	-54.2171	17.2991	0.87177	0.0:1.0:0.0:0.0	.	30	Q96JH8	RADIL_HUMAN	Q	30;4;30;30	ENSP00000382492:R30Q;ENSP00000442533:R30Q	ENSP00000320946:R4Q	R	-	2	0	RADIL	4884208	1.000000	0.71417	0.999000	0.59377	0.368000	0.29767	5.450000	0.66626	2.769000	0.95229	0.561000	0.74099	CGG	.	.		0.632	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		T	4917682	C	T	4917682	3	4	161	1	0	0	0	0	1	0	0	0	13012	652	23	1	3194	1	RADIL	7	4917682	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10		4917682	154220981	35	24589										
ANKMY2	57037	hgsc.bcm.edu	37	chr7	16666729	16666729	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tgatgacaatttacatcggcTccatgtcgcagtagtaattt	8	8	0	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr7:16666729T>A	ENST00000306999.2	-	3	450	c.207A>T	c.(205-207)ggA>ggT	p.G69G	ANKMY2_ENST00000421746.1_5'UTR	NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	69						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TTACATCGGCTCCATGTCGCA	0.353																																					p.G69G		Atlas-SNP	.											.	ANKMY2	46	.	0			c.A207T						.						97	84	89					7																	16666729		2203	4300	6503	SO:0001819	synonymous_variant	57037	exon3			ATCGGCTCCATGT	AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.207A>T	chr7.hg19:g.16666729T>A		77.0	0.0		61.0	17.0	NM_020319	A4D124|Q659G1|Q96BL3	Silent	SNP	ENST00000306999.2	hg19	CCDS5361.1																																																																																			.	.		0.353	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319		A	16666729	T	A	16666729	2	1	161	1	0	0	0	0	0	0	0	1	635	1538	54	4		4	ANKMY2	7	16666729	Silent	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	11749047	16666729	142471934	36	24590										
PLEKHA8	84725	hgsc.bcm.edu	37	chr7	30102308	30102308	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	aggtctcaaatttttgaaggGatttttgacagaagtgaaaa	10	3	1	4			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr7:30102308G>T	ENST00000449726.1	+	12	1600	c.1250G>T	c.(1249-1251)gGa>gTa	p.G417V	PLEKHA8_ENST00000396259.1_Missense_Mutation_p.G417V|PLEKHA8_ENST00000396257.2_Missense_Mutation_p.G417V|PLEKHA8_ENST00000258679.7_Missense_Mutation_p.G417V	NM_001197027.1	NP_001183956.1	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	417	Glycolipid transfer protein homology domain.				ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						TTTTTGAAGGGATTTTTGACA	0.343																																					p.G417V		Atlas-SNP	.											.	PLEKHA8	68	.	0			c.G1250T						.						74	77	76					7																	30102308		2203	4300	6503	SO:0001583	missense	84725	exon12			TGAAGGGATTTTT	BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086		"Pleckstrin homology (PH) domain containing"	30037	protein-coding gene	gene with protein product		608639				11001876	Standard	NM_001197027		Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000449726.1:c.1250G>T	chr7.hg19:g.30102308G>T	ENSP00000397947:p.Gly417Val	58.0	0.0		54.0	18.0	NM_001197027	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	Missense_Mutation	SNP	ENST00000449726.1	hg19	CCDS56473.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.383723	0.61845	.	.	ENSG00000106086	ENST00000258679;ENST00000449726;ENST00000396257;ENST00000396259;ENST00000440706	.	.	.	5.15	4.26	0.50523	Glycolipid transfer protein domain (3);	0.189745	0.46145	D	0.000312	T	0.40067	0.1102	N	0.02751	-0.505	0.58432	D	0.999999	P;P;D;P	0.89917	0.617;0.811;1.0;0.72	B;P;D;P	0.91635	0.242;0.516;0.999;0.517	T	0.40308	-0.9570	9	0.34782	T	0.22	-16.2627	9.4036	0.38449	0.1673:0.0:0.8327:0.0	.	417;417;417;417	Q96JA3-2;Q96JA3;Q96JA3-3;B4DH00	.;PKHA8_HUMAN;.;.	V	417;417;417;417;443	.	ENSP00000258679:G417V	G	+	2	0	PLEKHA8	30068833	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.507000	0.45442	2.398000	0.81561	0.655000	0.94253	GGA	.	.		0.343	PLEKHA8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032639		T	30102308	G	T	30102308	3	4	161	1	0	0	0	0	1	0	0	0	12071	1174	41	3	1296	3	PLEKHA8	7	30102308	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	13435579	30102308	129036355	37	24591										
CFTR	1080	hgsc.bcm.edu	37	chr7	117243681	117243681	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ttcgtattatgtgttttacaTttacgtgggagtagccgaca	10	6	0	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr7:117243681T>A	ENST00000003084.6	+	17	2885	c.2753T>A	c.(2752-2754)aTt>aAt	p.I918N	CFTR_ENST00000454343.1_Missense_Mutation_p.I857N|AC000111.6_ENST00000456270.1_RNA	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	918	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	GTGTTTTACATTTACGTGGGA	0.408									Cystic Fibrosis																												p.I918N		Atlas-SNP	.											.	CFTR	171	.	0			c.T2753A						.						217	185	196					7																	117243681		2203	4300	6503	SO:0001583	missense	1080	exon17	Familial Cancer Database	CF	TTTACATTTACGT	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.2753T>A	chr7.hg19:g.117243681T>A	ENSP00000003084:p.Ile918Asn	125.0	0.0		112.0	21.0	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	hg19	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.419619	0.83559	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.91521	-2.86;-2.86;-2.86	5.82	5.82	0.92795	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.96043	0.8711	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96715	0.9528	10	0.87932	D	0	-18.3837	16.179	0.81887	0.0:0.0:0.0:1.0	.	918	P13569	CFTR_HUMAN	N	918;857;888	ENSP00000003084:I918N;ENSP00000403677:I857N;ENSP00000389119:I888N	ENSP00000003084:I918N	I	+	2	0	CFTR	117030917	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	7.990000	0.88215	2.232000	0.73038	0.477000	0.44152	ATT	.	.		0.408	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		A	117243681	T	A	117243681	3	1	161	1	0	0	0	0	1	0	0	0	3296	1493	52	4	2819	4	CFTR	7	117243681	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	87141373	117243681	41894982	38	24592										
LONRF1	91694	hgsc.bcm.edu	37	chr8	12589255	12589255	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	agaaacttactgtgagagttCagcagtttcttcatcatata	7	7	4	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr8:12589255C>A	ENST00000398246.3	-	8	1747	c.1678G>T	c.(1678-1680)Gaa>Taa	p.E560*	LONRF1_ENST00000525024.1_5'Flank|LONRF1_ENST00000533751.1_Nonsense_Mutation_p.E203*	NM_152271.3	NP_689484.3	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger 1	560							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19				READ - Rectum adenocarcinoma(644;0.236)		TGTGAGAGTTCAGCAGTTTCT	0.363																																					p.E560X		Atlas-SNP	.											.	LONRF1	45	.	0			c.G1678T						.						80	74	76					8																	12589255		1811	4070	5881	SO:0001587	stop_gained	91694	exon8			AGAGTTCAGCAGT	AK074329	CCDS5987.2	8p23.1	2013-01-09			ENSG00000154359	ENSG00000154359		"RING-type (C3HC4) zinc fingers"	26302	protein-coding gene	gene with protein product						18253036	Standard	XM_005273685		Approved	FLJ23749, RNF191	uc003wwd.1	Q17RB8	OTTHUMG00000165475	ENST00000398246.3:c.1678G>T	chr8.hg19:g.12589255C>A	ENSP00000381298:p.Glu560*	234.0	1.0		99.0	69.0	NM_152271	B4DM29|B4DU84|Q8TEA0|Q9BSV1	Nonsense_Mutation	SNP	ENST00000398246.3	hg19	CCDS5987.2	.	.	.	.	.	.	.	.	.	.	C	35	5.483070	0.96307	.	.	ENSG00000154359	ENST00000398246;ENST00000533751;ENST00000524526	.	.	.	4.98	4.98	0.66077	.	0.048296	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-18.7649	19.1544	0.93504	0.0:1.0:0.0:0.0	.	.	.	.	X	560;203;163	.	ENSP00000381298:E560X	E	-	1	0	LONRF1	12633626	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.401000	0.79962	2.700000	0.92200	0.557000	0.71058	GAA	.	.		0.363	LONRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251693.2	NM_152271		A	12589255	C	A	12589255	4	1	161	1	0	0	0	0	0	1	0	0	8903	835	29	3	663	3	LONRF1	8	12589255	Nonsense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10		12589255	133774767	39	24593										
TRIB1	10221	hgsc.bcm.edu	37	chr8	126445629	126445629	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gccatcgcacagcaacattaCtggcattgtggaagtgatcc	10	11	0	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr8:126445629C>G	ENST00000311922.3	+	2	1013	c.431C>G	c.(430-432)aCt>aGt	p.T144S	TRIB1_ENST00000520847.1_5'UTR|TRIB1_ENST00000521778.1_3'UTR|TRIB1_ENST00000519576.1_5'Flank	NM_001282985.1|NM_025195.2	NP_001269914.1|NP_079471.1			tribbles pseudokinase 1											NS(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8	all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			AGCAACATTACTGGCATTGTG	0.517																																					p.T144S		Atlas-SNP	.											.	TRIB1	73	.	0			c.C431G						.						188	188	188					8																	126445629		2203	4300	6503	SO:0001583	missense	10221	exon2			ACATTACTGGCAT	AF205437	CCDS6357.1, CCDS64971.1	8q24.13	2013-10-03	2013-10-03			ENSG00000173334			16891	protein-coding gene	gene with protein product		609461	"tribbles homolog 1 (Drosophila)"			9342215, 16715410	Standard	NM_001282985		Approved	C8FW, GIG2, TRB1	uc003yrx.3	Q96RU8		ENST00000311922.3:c.431C>G	chr8.hg19:g.126445629C>G	ENSP00000312150:p.Thr144Ser	138.0	0.0		273.0	53.0	NM_025195		Missense_Mutation	SNP	ENST00000311922.3	hg19	CCDS6357.1	.	.	.	.	.	.	.	.	.	.	C	9.235	1.036721	0.19669	.	.	ENSG00000173334	ENST00000311922	T	0.65549	-0.16	4.91	4.02	0.46733	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.34223	U	0.004152	T	0.49490	0.1560	N	0.24115	0.695	0.80722	D	1	P	0.37352	0.591	B	0.38156	0.266	T	0.54748	-0.8247	10	0.66056	D	0.02	-18.8068	12.6457	0.56733	0.3011:0.6989:0.0:0.0	.	144	Q96RU8	TRIB1_HUMAN	S	144	ENSP00000312150:T144S	ENSP00000312150:T144S	T	+	2	0	TRIB1	126514811	0.991000	0.36638	0.693000	0.30195	0.919000	0.55068	3.068000	0.50018	1.184000	0.42957	0.511000	0.50034	ACT	.	.		0.517	TRIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381430.1	NM_025195		G	126445629	C	G	126445629	3	3	161	1	0	0	0	0	1	0	0	0	16497	565	20	4	437	4	TRIB1	8	126445629	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	113856374	126445629	19918393	40	24594										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139895407	139895407	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gccacagcgttccctcggagGccggccatggctctcctgtt	12	16	1	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr8:139895407G>T	ENST00000303045.6	-	2	455	c.9C>A	c.(7-9)ggC>ggA	p.G3G	COL22A1_ENST00000435777.1_Silent_p.G3G	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	3					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TCCCTCGGAGGCCGGCCATGG	0.662										HNSCC(7;0.00092)																											p.G3G		Atlas-SNP	.											.	COL22A1	390	.	0			c.C9A						.						18	23	21					8																	139895407		2189	4289	6478	SO:0001819	synonymous_variant	169044	exon2			TCGGAGGCCGGCC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.9C>A	chr8.hg19:g.139895407G>T		74.0	0.0		154.0	82.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.662	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		T	139895407	G	T	139895407	2	4	161	1	0	0	0	0	0	0	0	1	3683	1190	42	3		3	COL22A1	8	139895407	Silent	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	13449778	139895407	6468615	41	24595										
IGFBPL1	347252	hgsc.bcm.edu	37	chr9	38411534	38411534	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	cacaccctcatcctcctttcGcagggggttgatctagaaat	8	13	2	2	rs375493692		TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr9:38411534G>T	ENST00000377694.1	-	4	722	c.700C>A	c.(700-702)Cga>Aga	p.R234R		NM_001007563.1	NP_001007564.1	Q8WX77	IBPL1_HUMAN	insulin-like growth factor binding protein-like 1	234	Ig-like C2-type.				regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)				endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	4				GBM - Glioblastoma multiforme(29;0.0437)|Lung(182;0.116)		TCCTCCTTTCGCAGGGGGTTG	0.448																																					p.R234R		Atlas-SNP	.											.	IGFBPL1	8	.	0			c.C700A						.						97	81	86					9																	38411534		2203	4300	6503	SO:0001819	synonymous_variant	347252	exon4			CCTTTCGCAGGGG		CCDS35017.1	9p12	2013-01-11			ENSG00000137142	ENSG00000137142		"Immunoglobulin superfamily / I-set domain containing"	20081	protein-coding gene	gene with protein product		610413					Standard	NM_001007563		Approved	bA113O24.1	uc004aaz.3	Q8WX77	OTTHUMG00000019937	ENST00000377694.1:c.700C>A	chr9.hg19:g.38411534G>T		76.0	0.0		70.0	20.0	NM_001007563		Silent	SNP	ENST00000377694.1	hg19	CCDS35017.1																																																																																			.	.		0.448	IGFBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052491.1	XM_294567		T	38411534	G	T	38411534	2	4	161	1	0	0	0	0	0	0	0	1	7594	1095	38	1		1	IGFBPL1	9	38411534	Silent	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10		38411534	102801897	42	24596										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87635234	87635234	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ggggtcgtgttgtgggagatTttcacctatggcaaacagcc	14	8	1	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr9:87635234T>A	ENST00000323115.4	+	16	2591	c.2238T>A	c.(2236-2238)atT>atA	p.I746I	NTRK2_ENST00000376213.1_Silent_p.I746I|NTRK2_ENST00000277120.3_Silent_p.I762I|NTRK2_ENST00000376214.1_Silent_p.I762I			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	746	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	TGTGGGAGATTTTCACCTATG	0.557										TSP Lung(25;0.17)																											p.I762I		Atlas-SNP	.											.	NTRK2	331	.	0			c.T2286A						.						132	121	125					9																	87635234		2203	4300	6503	SO:0001819	synonymous_variant	4915	exon20			GGAGATTTTCACC	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.2238T>A	chr9.hg19:g.87635234T>A		153.0	0.0		114.0	37.0	NM_006180	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Silent	SNP	ENST00000323115.4	hg19	CCDS35050.1																																																																																			.	.		0.557	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			A	87635234	T	A	87635234	2	1	161	1	0	0	0	0	0	0	0	1	10716	1829	64	4		4	NTRK2	9	87635234	Silent	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	49223700	87635234	53578197	43	24597										
PTCHD3	374308	hgsc.bcm.edu	37	chr10	27702854	27702854	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tgtgacagcggtgccggtgcCtgcagatggccgtgggttcg	18	10	0	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr10:27702854C>T	ENST00000438700.3	-	1	443	c.326G>A	c.(325-327)aGg>aAg	p.R109K		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	109					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						GTGCCGGTGCCTGCAGATGGC	0.706																																					p.R109K		Atlas-SNP	.											.	PTCHD3	140	.	0			c.G326A						.						32	34	33					10																	27702854		2203	4299	6502	SO:0001583	missense	374308	exon1			CGGTGCCTGCAGA	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.326G>A	chr10.hg19:g.27702854C>T	ENSP00000417658:p.Arg109Lys	67.0	0.0		38.0	13.0	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	hg19	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	C	0.016	-1.539085	0.00942	.	.	ENSG00000182077	ENST00000438700	D	0.87571	-2.27	1.66	1.66	0.24008	.	.	.	.	.	T	0.73458	0.3589	L	0.29908	0.895	0.09310	N	1	B	0.14805	0.011	B	0.11329	0.006	T	0.55598	-0.8116	9	0.07482	T	0.82	.	3.4831	0.07610	0.0:0.7102:0.0:0.2898	.	109	Q3KNS1	PTHD3_HUMAN	K	109	ENSP00000417658:R109K	ENSP00000417658:R109K	R	-	2	0	PTCHD3	27742860	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.963000	0.03837	0.681000	0.31386	0.313000	0.20887	AGG	.	.		0.706	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		T	27702854	C	T	27702854	3	4	161	1	0	0	0	0	1	0	0	0	12746	681	24	3	1993	3	PTCHD3	10	27702854	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10		27702854	107831893	44	24598										
UNC5B	219699	hgsc.bcm.edu	37	chr10	73050696	73050696	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ggaggcctcaggggatgcggCgctgtatgcggggctcgtgg	21	9	1	0	rs533838225		TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr10:73050696C>T	ENST00000335350.6	+	9	1540	c.1124C>T	c.(1123-1125)gCg>gTg	p.A375V	UNC5B_ENST00000373192.4_Missense_Mutation_p.A364V	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	375					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						GGGGATGCGGCGCTGTATGCG	0.667													C|||	1	0.000199681	0	0	5008	,	,		17337	0		0	False		,,,				2504	0.001				p.A375V		Atlas-SNP	.											.	UNC5B	123	.	0			c.C1124T						.						133	137	136					10																	73050696		2203	4300	6503	SO:0001583	missense	219699	exon9			ATGCGGCGCTGTA	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"Immunoglobulin superfamily / I-set domain containing"	12568	protein-coding gene	gene with protein product		607870	"unc5 (C.elegans homolog) b"				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.1124C>T	chr10.hg19:g.73050696C>T	ENSP00000334329:p.Ala375Val	69.0	0.0		47.0	22.0	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	hg19	CCDS7309.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.411414	0.83340	.	.	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.56275	0.58;0.47	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.75824	0.3902	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.78033	-0.2362	10	0.51188	T	0.08	-28.5221	18.8547	0.92247	0.0:1.0:0.0:0.0	.	364;375	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	V	375;364	ENSP00000334329:A375V;ENSP00000362288:A364V	ENSP00000334329:A375V	A	+	2	0	UNC5B	72720702	1.000000	0.71417	0.998000	0.56505	0.221000	0.24807	7.786000	0.85741	2.466000	0.83321	0.563000	0.77884	GCG	.	.		0.667	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		T	73050696	C	T	73050696	3	4	161	1	0	0	0	0	1	0	0	0	17007	768	27	1	1158	1	UNC5B	10	73050696	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	45347842	73050696	62484051	45	24599										
ABCC2	1244	hgsc.bcm.edu	37	chr10	101590535	101590535	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	cttgaaaactcggaatgtgaAtagcctgaaggaagacgaag	12	6	0	4			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr10:101590535A>G	ENST00000370449.4	+	21	2923	c.2810A>G	c.(2809-2811)aAt>aGt	p.N937S		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	937					cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CGGAATGTGAATAGCCTGAAG	0.433																																					p.N937S		Atlas-SNP	.											.	ABCC2	160	.	0			c.A2810G						.						92	90	91					10																	101590535		2203	4300	6503	SO:0001583	missense	1244	exon21			ATGTGAATAGCCT	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.2810A>G	chr10.hg19:g.101590535A>G	ENSP00000359478:p.Asn937Ser	170.0	0.0		96.0	49.0	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	hg19	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	A	2.914	-0.224710	0.06022	.	.	ENSG00000023839	ENST00000370449	D	0.88586	-2.4	5.67	-0.967	0.10316	.	1.212080	0.05452	N	0.549609	T	0.77438	0.4130	L	0.29908	0.895	0.09310	N	1	B	0.17038	0.02	B	0.11329	0.006	T	0.59721	-0.7401	10	0.08837	T	0.75	0.3298	1.4555	0.02384	0.4352:0.1398:0.2883:0.1367	.	937	Q92887	MRP2_HUMAN	S	937	ENSP00000359478:N937S	ENSP00000359478:N937S	N	+	2	0	ABCC2	101580525	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	0.419000	0.21247	-0.106000	0.12110	0.459000	0.35465	AAT	.	.		0.433	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		G	101590535	A	G	101590535	3	3	161	1	0	0	0	0	1	0	0	0	53	101	4	2	2892	2	ABCC2	10	101590535	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	28539839	101590535	33944212	46	24600										
PKD2L1	9033	hgsc.bcm.edu	37	chr10	102054310	102054310	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	accaggagcacgaagaagacGaagaagacataggtgacaaa	12	7	0	5	rs148570260		TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr10:102054310G>A	ENST00000318222.3	-	9	2023	c.1641C>T	c.(1639-1641)ttC>ttT	p.F547F	PKD2L1_ENST00000338519.3_Silent_p.F472F|PKD2L1_ENST00000353274.3_Silent_p.F547F	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	547					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)			NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		CGAAGAAGACGAAGAAGACAT	0.532																																					p.F547F		Atlas-SNP	.											.	PKD2L1	103	.	0			c.C1641T						.	G		1,4405	2.1+/-5.4	0,1,2202	138	121	127		1641	-1.1	1	10	dbSNP_134	127	0,8600		0,0,4300	no	coding-synonymous	PKD2L1	NM_016112.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		547/806	102054310	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9033	exon9			GAAGACGAAGAAG	AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"Voltage-gated ion channels / Transient receptor potential cation channels"	9011	protein-coding gene	gene with protein product	"transient receptor potential cation channel, subfamily P, member 3"	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.1641C>T	chr10.hg19:g.102054310G>A		151.0	0.0		132.0	50.0	NM_016112	O75972|Q5W039|Q9UP35|Q9UPA2	Silent	SNP	ENST00000318222.3	hg19	CCDS7492.1																																																																																			.	G|1.000;A|0.000		0.532	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112		A	102054310	G	A	102054310	2	1	161	1	0	0	0	0	0	0	0	1	11976	1049	37	1		1	PKD2L1	10	102054310	Silent	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	463775	102054310	33480437	47	24601										
DEAF1	10522	hgsc.bcm.edu	37	chr11	694962	694988	+	In_Frame_Del	DEL	GCCGCCGCCGCCACAGCGGCCGCGGCC	GCCGCCGCCGCCACAGCGGCCGCGGCC	-													0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	cgcctcctgccgcggccgcgGccgccgccgccacagcggcc							TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	GCCGCCGCCGCCACAGCGGCCGCGGCC	GCCGCCGCCGCCACAGCGGCCGCGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:694962_694988delGCCGCCGCCGCCACAGCGGCCGCGGCC	ENST00000382409.3	-	1	544_570	c.60_86delGGCCGCGGCCGCTGTGGCGGCGGCGGC	c.(58-87)gcggccgcggccgctgtggcggcggcggcc>gcc	p.20_29AAAAAVAAAA>A	TMEM80_ENST00000397512.3_5'Flank|TMEM80_ENST00000608174.1_5'Flank|DEAF1_ENST00000338675.6_In_Frame_Del_p.20_29AAAAAVAAAA>A|TMEM80_ENST00000397510.3_5'Flank	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	20	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		cgcggccgcggccgccgccgccacagcggccgcggccgccaccgccg	0.78																																					p.21_29del		Atlas-INDEL	.											DEAF1,NS,carcinoma,0,1	DEAF1	47	.	0			c.61_87del						.																																			SO:0001651	inframe_deletion	10522	exon1			.	AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030		"Zinc fingers, MYND-type"	14677	protein-coding gene	gene with protein product		602635	"deformed epidermal autoregulatory factor 1 (Drosophila)"			9773984	Standard	XR_428838		Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.60_86delGGCCGCGGCCGCTGTGGCGGCGGCGGC	chr11.hg19:g.694962_694988delGCCGCCGCCGCCACAGCGGCCGCGGCC	ENSP00000371846:p.Ala20_Ala28del	18.0	0.0		14.0	13.0	NM_021008	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	In_Frame_Del	DEL	ENST00000382409.3	hg19	CCDS31327.1																																																																																			.	.		0.78	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383614.3	NM_021008		-	694988	GCCGCCGCCGCCACAGCGGCCGCGGCC	-	694962	7	5	161	1	0	1	0	1	0	0	0	0	4382	1203	42	0	1659	0	DEAF1	11	694962	In_Frame_Del	DEL	GCCGCCGCCGCCACAGCGGCCGCGGCC	TCGA-DD-AACJ-01A-11D-A40R-10		694962	134311554	48	24602										
C11orf16	56673	hgsc.bcm.edu	37	chr11	8950997	8950997	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ttgctaggacccatgtgttgGcagcatctccagctcttccc	9	14	2	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:8950997G>A	ENST00000326053.5	-	3	357	c.251C>T	c.(250-252)gCc>gTc	p.A84V	C11orf16_ENST00000528998.1_Intron|C11orf16_ENST00000525780.1_Missense_Mutation_p.A84V	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	84										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	22				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		CCATGTGTTGGCAGCATCTCC	0.567																																					p.A84V		Atlas-SNP	.											.	C11orf16	43	.	0			c.C251T						.						103	100	101					11																	8950997		2201	4296	6497	SO:0001583	missense	56673	exon3			GTGTTGGCAGCAT	AJ400877	CCDS7794.1	11p15.3	2008-06-25			ENSG00000176029	ENSG00000176029			1169	protein-coding gene	gene with protein product						11528127	Standard	NM_020643		Approved		uc001mhb.4	Q9NQ32	OTTHUMG00000165654	ENST00000326053.5:c.251C>T	chr11.hg19:g.8950997G>A	ENSP00000318999:p.Ala84Val	104.0	0.0		73.0	29.0	NM_020643	Q53FB2|Q8N6Y9	Missense_Mutation	SNP	ENST00000326053.5	hg19	CCDS7794.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.366614	0.61513	.	.	ENSG00000176029	ENST00000525780;ENST00000326053;ENST00000526227	T;T	0.31510	1.5;1.49	4.57	2.52	0.30459	.	0.702222	0.13381	N	0.392178	T	0.35364	0.0929	L	0.57536	1.79	0.09310	N	1	P;P	0.47302	0.893;0.893	P;P	0.47981	0.563;0.563	T	0.10291	-1.0636	10	0.39692	T	0.17	-19.5754	9.5443	0.39271	0.0:0.2784:0.5793:0.1423	.	84;84	Q9NQ32-2;Q9NQ32	.;CK016_HUMAN	V	84	ENSP00000436818:A84V;ENSP00000318999:A84V	ENSP00000318999:A84V	A	-	2	0	C11orf16	8907573	0.002000	0.14202	0.326000	0.25389	0.884000	0.51177	0.620000	0.24403	1.241000	0.43820	0.591000	0.81541	GCC	.	.		0.567	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643		A	8950997	G	A	8950997	3	1	161	1	0	0	0	0	1	0	0	0	1633	1203	42	3	1168	3	C11orf16	11	8950997	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	8256035	8950997	126055519	49	24603										
PLEKHA7	144100	hgsc.bcm.edu	37	chr11	16863238	16863238	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	agcccgctgtggagctgttaTagatgagcgctcgcatcccc	12	13	0	2	rs200394760		TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:16863238T>C	ENST00000355661.3	-	9	738	c.728A>G	c.(727-729)tAt>tGt	p.Y243C	PLEKHA7_ENST00000531066.1_Missense_Mutation_p.Y243C|PLEKHA7_ENST00000448080.2_Missense_Mutation_p.Y243C|PLEKHA7_ENST00000532079.1_Intron|RN7SKP90_ENST00000363013.1_RNA			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	243	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						GGAGCTGTTATAGATGAGCGC	0.557																																					p.Y243C		Atlas-SNP	.											.	PLEKHA7	120	.	0			c.A728G						.	T	CYS/TYR	0,4400		0,0,2200	69	59	63		728	1.4	0.9	11		63	4,8584	3.7+/-12.6	0,4,4290	yes	missense	PLEKHA7	NM_175058.4	194	0,4,6490	CC,CT,TT		0.0466,0.0,0.0308	possibly-damaging	243/1122	16863238	4,12984	2200	4294	6494	SO:0001583	missense	144100	exon9			CTGTTATAGATGA	BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"Pleckstrin homology (PH) domain containing"	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.728A>G	chr11.hg19:g.16863238T>C	ENSP00000347883:p.Tyr243Cys	49.0	0.0		37.0	16.0	NM_175058	B4DK33|B4DWC3|Q86VZ7	Missense_Mutation	SNP	ENST00000355661.3	hg19	CCDS31434.1	.	.	.	.	.	.	.	.	.	.	T	10.40	1.340829	0.24339	0.0	4.66E-4	ENSG00000166689	ENST00000531066;ENST00000355661;ENST00000448080	T;T;T	0.06687	3.27;3.27;3.27	5.16	1.41	0.22369	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.441389	0.26820	N	0.022332	T	0.10165	0.0249	M	0.65975	2.015	0.42515	D	0.992983	B;B	0.14438	0.01;0.003	B;B	0.24701	0.055;0.017	T	0.07309	-1.0779	10	0.45353	T	0.12	-1.1366	6.856	0.24040	0.0:0.1435:0.4574:0.3992	.	243;243	E9PKC0;Q6IQ23	.;PKHA7_HUMAN	C	243	ENSP00000435389:Y243C;ENSP00000347883:Y243C;ENSP00000416895:Y243C	ENSP00000347883:Y243C	Y	-	2	0	PLEKHA7	16819814	1.000000	0.71417	0.856000	0.33681	0.496000	0.33645	1.744000	0.38268	0.120000	0.18254	0.528000	0.53228	TAT	.	T|0.999;C|0.001		0.557	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058		C	16863238	T	C	16863238	3	2	161	1	0	0	0	0	1	0	0	0	12070	1406	49	2	2697	2	PLEKHA7	11	16863238	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	7912241	16863238	118143278	50	24604										
API5	8539	hgsc.bcm.edu	37	chr11	43340327	43340327	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gctatcaatgcacagttagaCctctgtgaggatgaagatgt	11	7	2	4			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:43340327C>T	ENST00000531273.1	+	2	346	c.207C>T	c.(205-207)gaC>gaT	p.D69D	API5_ENST00000378852.3_Silent_p.D69D|API5_ENST00000420461.2_Intron|API5_ENST00000455725.2_Silent_p.D58D|API5_ENST00000534600.1_Silent_p.D69D|API5_ENST00000534695.1_Silent_p.D69D			Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5	69	ARM-like and Heat-like helical repeats.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fibroblast apoptotic process (GO:2000270)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	fibroblast growth factor binding (GO:0017134)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20						CACAGTTAGACCTCTGTGAGG	0.373																																					p.D69D	Pancreas(1;98 122 5625 20895 49453)	Atlas-SNP	.											.	API5	91	.	0			c.C207T						.						115	109	111					11																	43340327		2203	4300	6503	SO:0001819	synonymous_variant	8539	exon2			GTTAGACCTCTGT	U83857	CCDS31465.1, CCDS44572.1, CCDS44573.1	11p12	2010-09-30			ENSG00000166181	ENSG00000166181			594	protein-coding gene	gene with protein product	"API5-like 1", "fibroblast growth factor 2-interacting factor 2", "migration-inducing protein MIG8"	609774				9307294	Standard	NR_024625		Approved	AAC-11, API5L1, AAC11	uc010rfh.1	Q9BZZ5	OTTHUMG00000166395	ENST00000531273.1:c.207C>T	chr11.hg19:g.43340327C>T		27.0	0.0		37.0	19.0	NM_006595	B4DGR0|B4DRJ2|D3DR21|O15441|Q9Y4J7	Silent	SNP	ENST00000531273.1	hg19	CCDS44572.1																																																																																			.	.		0.373	API5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389545.1	NM_006595		T	43340327	C	T	43340327	2	4	161	1	0	0	0	0	0	0	0	1	773	506	18	3		3	API5	11	43340327	Silent	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	26477089	43340327	91666189	51	24605										
SPCS2	9789	hgsc.bcm.edu	37	chr11	74687909	74687909	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	cccccatgcttaggtttgatGacaaatacaccttgaagctg	8	11	0	3			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:74687909G>A	ENST00000263672.6	+	5	541	c.502G>A	c.(502-504)Gac>Aac	p.D168N	SPCS2_ENST00000530257.1_Missense_Mutation_p.D99N|SPCS2_ENST00000528265.1_Intron|SPCS2_ENST00000526361.1_Missense_Mutation_p.D29N	NM_014752.2	NP_055567.2	Q15005	SPCS2_HUMAN	signal peptidase complex subunit 2 homolog (S. cerevisiae)	168					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)			breast(1)	1						TAGGTTTGATGACAAATACAC	0.433																																					p.D168N		Atlas-SNP	.											.	SPCS2	17	.	0			c.G502A						.						73	72	72					11																	74687909		1896	4101	5997	SO:0001583	missense	9789	exon5			TTTGATGACAAAT	D14658	CCDS44681.1	11q13.4	2008-02-05			ENSG00000118363	ENSG00000118363			28962	protein-coding gene	gene with protein product						7788527	Standard	NM_014752		Approved	KIAA0102	uc001ovu.2	Q15005	OTTHUMG00000165517	ENST00000263672.6:c.502G>A	chr11.hg19:g.74687909G>A	ENSP00000263672:p.Asp168Asn	367.0	0.0		316.0	110.0	NM_014752	Q15507|Q3KQT0|Q641R4|Q6FG65|Q6IRX0|Q6P1P4|Q96HU9	Missense_Mutation	SNP	ENST00000263672.6	hg19	CCDS44681.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.850321	0.91277	.	.	ENSG00000118363	ENST00000263672;ENST00000530257;ENST00000526361;ENST00000532972	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.71459	0.3342	M	0.81942	2.565	0.80722	D	1	B	0.31256	0.316	B	0.37508	0.252	T	0.68142	-0.5487	9	0.21014	T	0.42	-6.1455	16.9363	0.86203	0.0:0.0:1.0:0.0	.	168	Q15005	SPCS2_HUMAN	N	168;99;29;199	.	ENSP00000263672:D168N	D	+	1	0	SPCS2	74365557	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.795000	0.91872	2.669000	0.90835	0.655000	0.94253	GAC	.	.		0.433	SPCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384587.1	NM_014752		A	74687909	G	A	74687909	3	1	161	1	0	0	0	0	1	0	0	0	15039	1290	45	3	520	3	SPCS2	11	74687909	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	31347582	74687909	60318607	52	24606										
ATM	472	hgsc.bcm.edu	37	chr11	108124684	108124684	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ccagtccagtattggcttctCtgtccaccagaatctcaagg	8	13	2	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:108124684C>G	ENST00000452508.2	+	14	2231	c.2042C>G	c.(2041-2043)tCt>tGt	p.S681C	ATM_ENST00000278616.4_Missense_Mutation_p.S681C			Q13315	ATM_HUMAN	ATM serine/threonine kinase	681					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	ATTGGCTTCTCTGTCCACCAG	0.378			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.S681C		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.C2042G						.						108	103	104					11																	108124684		2201	4298	6499	SO:0001583	missense	472	exon13	Familial Cancer Database	AT, Louis-Bar syndrome	GCTTCTCTGTCCA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2042C>G	chr11.hg19:g.108124684C>G	ENSP00000388058:p.Ser681Cys	64.0	0.0		43.0	16.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	14.84	2.655540	0.47467	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.74842	-0.88;-0.88;-0.88	6.11	4.26	0.50523	Armadillo-type fold (1);	0.409334	0.27080	N	0.021030	T	0.69169	0.3081	L	0.60455	1.87	0.25419	N	0.988287	P	0.47106	0.89	B	0.43155	0.41	T	0.61153	-0.7120	10	0.36615	T	0.2	.	8.5886	0.33672	0.0:0.7667:0.0:0.2333	.	681	Q13315	ATM_HUMAN	C	681	ENSP00000435747:S681C;ENSP00000278616:S681C;ENSP00000388058:S681C	ENSP00000278616:S681C	S	+	2	0	ATM	107629894	1.000000	0.71417	0.996000	0.52242	0.780000	0.44128	1.270000	0.33086	0.922000	0.37019	0.655000	0.94253	TCT	.	.		0.378	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108124684	C	G	108124684	3	3	161	1	0	0	0	0	1	0	0	0	1109	913	32	4	2088	4	ATM	11	108124684	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	33436775	108124684	26881832	53	24607										
C2CD2L	9854	hgsc.bcm.edu	37	chr11	118984970	118984970	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	caagtgtccaggaagcagacGagacaacccgttcggatatt	11	10	0	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:118984970G>A	ENST00000528586.1	+	9	1118	c.1048G>A	c.(1048-1050)Gag>Aag	p.E350K	C2CD2L_ENST00000336702.3_Missense_Mutation_p.E603K			O14523	C2C2L_HUMAN	C2CD2-like	602						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)	13						GGAAGCAGACGAGACAACCCG	0.587																																					p.E603K		Atlas-SNP	.											.	C2CD2L	39	.	0			c.G1807A						.						142	141	141					11																	118984970		2200	4295	6495	SO:0001583	missense	9854	exon13			GCAGACGAGACAA	AK025223	CCDS8413.1	11q23.3	2008-04-22	2008-04-22	2008-04-22		ENSG00000172375			29000	protein-coding gene	gene with protein product			"transmembrane protein 24"	TMEM24		15289880	Standard	XM_005271738		Approved	KIAA0285	uc001pvn.3	O14523		ENST00000528586.1:c.1048G>A	chr11.hg19:g.118984970G>A	ENSP00000433600:p.Glu350Lys	89.0	0.0		60.0	28.0	NM_014807	Q86UT7|Q86V04|Q8N522|Q8TBN4|Q96G10	Missense_Mutation	SNP	ENST00000528586.1	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.340950	0.95783	.	.	ENSG00000172375	ENST00000336702;ENST00000528586	T;T	0.54279	0.58;0.58	5.41	5.41	0.78517	.	0.101724	0.64402	D	0.000003	T	0.62490	0.2432	L	0.44542	1.39	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	P;P	0.61201	0.885;0.885	T	0.54159	-0.8335	10	0.24483	T	0.36	.	18.3582	0.90365	0.0:0.0:1.0:0.0	.	602;603	O14523;O14523-2	C2C2L_HUMAN;.	K	603;350	ENSP00000338885:E603K;ENSP00000433600:E350K	ENSP00000338885:E603K	E	+	1	0	C2CD2L	118490180	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.025000	0.93694	2.798000	0.96311	0.655000	0.94253	GAG	.	.		0.587	C2CD2L-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000388199.2	NM_014807		A	118984970	G	A	118984970	3	1	161	1	0	0	0	0	1	0	0	0	2155	1059	37	1	1857	1	C2CD2L	11	118984970	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	10860286	118984970	16021546	54	24608										
USP2	9099	hgsc.bcm.edu	37	chr11	119243702	119243707	+	In_Frame_Del	DEL	GGGGTC	GGGGTC	-													0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gggctgcggcccaggttcctGgggtctatccggtagctatc							TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	GGGGTC	GGGGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:119243702_119243707delGGGGTC	ENST00000260187.2	-	2	778_783	c.484_489delGACCCC	c.(484-489)gaccccdel	p.DP162del	RP11-334E6.3_ENST00000530918.2_RNA|USP2_ENST00000455332.2_Intron	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	162	Necessary for interaction with MDM4.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		CCAGGTTCCTGGGGTCTATCCGGTAG	0.641																																					p.162_164del		Atlas-INDEL	.											.	USP2	71	.	0			c.485_490del						.																																			SO:0001651	inframe_deletion	9099	exon2			.	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"Ubiquitin-specific peptidases"	12618	protein-coding gene	gene with protein product		604725	"ubiquitin specific protease 2"			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.484_489delGACCCC	chr11.hg19:g.119243702_119243707delGGGGTC	ENSP00000260187:p.Asp162_Pro163del	71.0	0.0		56.0	20.0	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	In_Frame_Del	DEL	ENST00000260187.2	hg19	CCDS8422.1																																																																																			.	.		0.641	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997		-	119243707	GGGGTC	-	119243702	7	5	161	1	0	1	0	1	0	0	0	0	17066	1335	47	0	1527	0	USP2	11	119243702	In_Frame_Del	DEL	GGGGTC	TCGA-DD-AACJ-01A-11D-A40R-10	258732	119243702	15762814	55	24609										
GRAMD1B	57476	hgsc.bcm.edu	37	chr11	123477353	123477353	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tggaggaagaggcgctggagGgagacgggtccctggaaaag	20	6	0	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:123477353G>C	ENST00000529750.1	+	10	1258	c.931G>C	c.(931-933)Gga>Cga	p.G311R	GRAMD1B_ENST00000450171.2_5'Flank|GRAMD1B_ENST00000322282.7_Missense_Mutation_p.G311R|GRAMD1B_ENST00000456860.2_Missense_Mutation_p.G318R	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	311						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		GGCGCTGGAGGGAGACGGGTC	0.552																																					p.G311R		Atlas-SNP	.											.	GRAMD1B	122	.	0			c.G931C						.						39	43	42					11																	123477353		1966	4140	6106	SO:0001583	missense	57476	exon10			CTGGAGGGAGACG	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.931G>C	chr11.hg19:g.123477353G>C	ENSP00000436500:p.Gly311Arg	81.0	0.0		63.0	22.0	NM_020716	Q6UW85|Q9ULL9	Missense_Mutation	SNP	ENST00000529750.1	hg19	CCDS53720.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.215516	0.39102	.	.	ENSG00000023171	ENST00000539133;ENST00000456860;ENST00000322282;ENST00000529750;ENST00000529432;ENST00000534764	T;T;T;T;T	0.28895	2.0;2.0;2.0;2.0;1.59	5.25	5.25	0.73442	.	0.374956	0.28011	N	0.016958	T	0.20210	0.0486	N	0.08118	0	0.38800	D	0.95518	B;P;B;B	0.36683	0.201;0.565;0.09;0.019	B;B;B;B	0.39419	0.054;0.299;0.024;0.011	T	0.12837	-1.0532	10	0.18276	T	0.48	.	17.8325	0.88687	0.0:0.0:1.0:0.0	.	271;318;311;318	B7Z4N9;F5H572;Q3KR37;E7EPH8	.;.;GRM1B_HUMAN;.	R	318;318;311;311;271;307	ENSP00000402457:G318R;ENSP00000325628:G311R;ENSP00000436500:G311R;ENSP00000432987:G271R;ENSP00000434214:G307R	ENSP00000325628:G311R	G	+	1	0	GRAMD1B	122982563	1.000000	0.71417	0.941000	0.38009	0.938000	0.57974	2.353000	0.44089	2.437000	0.82529	0.462000	0.41574	GGA	.	.		0.552	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		C	123477353	G	C	123477353	3	2	161	1	0	0	0	0	1	0	0	0	6757	1233	43	4	969	4	GRAMD1B	11	123477353	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	4233651	123477353	11529163	56	24610										
ACRV1	56	hgsc.bcm.edu	37	chr11	125546342	125546342	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	cattttccttgatcattcatAtaagcacatgtgtagcaatt	5	8	2	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:125546342A>G	ENST00000533904.1	-	3	927	c.585T>C	c.(583-585)taT>taC	p.Y195Y	ACRV1_ENST00000345274.1_Intron|ACRV1_ENST00000348856.3_Silent_p.Y95Y|ACRV1_ENST00000530048.1_Silent_p.Y140Y|ACRV1_ENST00000425431.1_Silent_p.Y51Y|ACRV1_ENST00000353070.1_Intron|ACRV1_ENST00000453509.1_Silent_p.Y106Y|ACRV1_ENST00000527795.1_Silent_p.Y125Y|ACRV1_ENST00000445562.1_Silent_p.Y100Y|ACRV1_ENST00000315608.3_Silent_p.Y176Y			P26436	ASPX_HUMAN	acrosomal vesicle protein 1	195					multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				kidney(1)|large_intestine(3)|lung(2)	6	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0179)|Lung NSC(97;0.0185)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0713)		GATCATTCATATAAGCACATG	0.403																																					p.Y195Y		Atlas-SNP	.											.	ACRV1	21	.	0			c.T585C						.						142	137	139					11																	125546342		2201	4299	6500	SO:0001819	synonymous_variant	56	exon3			ATTCATATAAGCA	AK223335	CCDS8460.1, CCDS8461.1, CCDS44759.1, CCDS44761.1	11q24.2	2012-05-16			ENSG00000134940	ENSG00000134940			127	protein-coding gene	gene with protein product	"sperm protein 10"	102525				1693291, 8288254	Standard	NM_001612		Approved	SPACA2, SP-10, D11S4365	uc001qcs.3	P26436	OTTHUMG00000165854	ENST00000533904.1:c.585T>C	chr11.hg19:g.125546342A>G		69.0	0.0		64.0	30.0	NM_001612	Q53FF4	Silent	SNP	ENST00000533904.1	hg19	CCDS8460.1																																																																																			.	.		0.403	ACRV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386722.1	NM_001612		G	125546342	A	G	125546342	2	3	161	1	0	0	0	0	0	0	0	1	172	456	16	2		2	ACRV1	11	125546342	Silent	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	2068989	125546342	9460174	57	24611										
JAM3	83700	hgsc.bcm.edu	37	chr11	134018452	134018452	+	Frame_Shift_Del	DEL	C	C	-													0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ttttcttcagatgacctgaaCattggcggaattattggggg							TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr11:134018452delC	ENST00000299106.4	+	7	882	c.723delC	c.(721-723)aacfs	p.N241fs	JAM3_ENST00000529443.2_Frame_Shift_Del_p.N286fs|JAM3_ENST00000441717.3_Frame_Shift_Del_p.N190fs|NCAPD3_ENST00000526787.2_5'Flank			Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	241					adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|establishment of cell polarity (GO:0030010)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|myelination (GO:0042552)|myeloid progenitor cell differentiation (GO:0002318)|neutrophil homeostasis (GO:0001780)|regulation of actin cytoskeleton organization by cell-cell adhesion (GO:0090138)|regulation of neutrophil chemotaxis (GO:0090022)|spermatid development (GO:0007286)|transmission of nerve impulse (GO:0019226)	cell-cell contact zone (GO:0044291)|desmosome (GO:0030057)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	integrin binding (GO:0005178)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)	10	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		ATGACCTGAACATTGGCGGAA	0.502																																					p.N241fs		Atlas-INDEL	.											.	JAM3	41	.	0			c.722delA						.						75	71	73					11																	134018452		2201	4297	6498	SO:0001589	frameshift_variant	83700	exon7			.	AF356518	CCDS8494.1, CCDS55799.1, CCDS8494.2	11q25	2013-01-29			ENSG00000166086	ENSG00000166086		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15532	protein-coding gene	gene with protein product		606871					Standard	NM_032801		Approved	JAM-C, JAMC	uc001qhb.3	Q9BX67	OTTHUMG00000167130	ENST00000299106.4:c.723delC	chr11.hg19:g.134018452delC	ENSP00000299106:p.Asn241fs	128.0	0.0		103.0	48.0	NM_032801	B3KWG9|Q8WWL8|Q96FL1	Frame_Shift_Del	DEL	ENST00000299106.4	hg19	CCDS8494.2																																																																																			.	.		0.502	JAM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393303.4	NM_032801		-	134018452	C	-	134018452	7	5	161	1	0	1	0	1	0	0	0	0	7953	477	17	0	884	0	JAM3	11	134018452	Frame_Shift_Del	DEL	C	TCGA-DD-AACJ-01A-11D-A40R-10	8472110	134018452	988064	58	24612										
FAR2	55711	hgsc.bcm.edu	37	chr12	29460716	29460716	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	agagagcaggaacctgaacaTtgccatcataaggccctcca	9	12	1	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr12:29460716T>C	ENST00000536681.3	+	5	917	c.671T>C	c.(670-672)aTt>aCt	p.I224T	FAR2_ENST00000547116.1_Missense_Mutation_p.I127T|FAR2_ENST00000182377.4_Missense_Mutation_p.I224T|RP11-996F15.2_ENST00000553105.1_RNA	NM_001271783.1|NM_001271784.1	NP_001258712.1|NP_001258713.1	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	224					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|prostate(1)|stomach(1)	29						AACCTGAACATTGCCATCATA	0.488																																					p.I224T		Atlas-SNP	.											.	FAR2	60	.	0			c.T671C						.						101	95	97					12																	29460716		2203	4300	6503	SO:0001583	missense	55711	exon5			TGAACATTGCCAT	AL136843	CCDS8717.1, CCDS61084.1	12p11.23	2013-07-30	2008-06-06	2008-06-06	ENSG00000064763	ENSG00000064763	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	25531	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 2"		"male sterility domain containing 1"	MLSTD1		15220348, 15220349, 19027726	Standard	NM_001271783		Approved	FLJ10462, SDR10E2	uc001ris.5	Q96K12	OTTHUMG00000169320	ENST00000536681.3:c.671T>C	chr12.hg19:g.29460716T>C	ENSP00000443291:p.Ile224Thr	65.0	0.0		56.0	25.0	NM_018099	F8VV73|Q9H0D5|Q9NVW8	Missense_Mutation	SNP	ENST00000536681.3	hg19	CCDS8717.1	.	.	.	.	.	.	.	.	.	.	T	13.78	2.338309	0.41398	.	.	ENSG00000064763	ENST00000536681;ENST00000182377;ENST00000547116	T;T;T	0.21543	2.0;2.0;2.0	5.34	2.91	0.33838	NAD(P)-binding domain (1);Male sterility, NAD-binding (1);	0.332943	0.32231	N	0.006384	T	0.18593	0.0446	L	0.52759	1.655	0.32691	N	0.514192	B	0.18013	0.025	B	0.25759	0.063	T	0.10776	-1.0615	10	0.46703	T	0.11	-9.0932	6.4098	0.21684	0.0:0.0842:0.1586:0.7572	.	224	Q96K12	FACR2_HUMAN	T	224;224;127	ENSP00000443291:I224T;ENSP00000182377:I224T;ENSP00000449349:I127T	ENSP00000182377:I224T	I	+	2	0	FAR2	29351983	0.995000	0.38212	0.002000	0.10522	0.908000	0.53690	5.044000	0.64214	0.308000	0.22923	0.533000	0.62120	ATT	.	.		0.488	FAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403479.2	NM_018099		C	29460716	T	C	29460716	3	2	161	1	0	0	0	0	1	0	0	0	5683	1493	52	2	685	2	FAR2	12	29460716	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10		29460716	104391179	59	24613										
STAC3	246329	hgsc.bcm.edu	37	chr12	57642930	57642930	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ttaggaggttctgggggtggCtcctcctcctcctcttcttc	11	13	3	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr12:57642930C>T	ENST00000332782.2	-	3	429	c.228G>A	c.(226-228)gaG>gaA	p.E76E	STAC3_ENST00000554578.1_Silent_p.E37E|STAC3_ENST00000546246.2_Intron	NM_145064.1	NP_659501.1	Q96MF2	STAC3_HUMAN	SH3 and cysteine rich domain 3	76	Poly-Glu.				intracellular signal transduction (GO:0035556)|neuromuscular synaptic transmission (GO:0007274)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)		identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(2)|skin(1)	18						CTGGGGGTGGctcctcctcct	0.552																																					p.E76E		Atlas-SNP	.											.	STAC3	32	.	0			c.G228A						.						74	75	75					12																	57642930		2203	4300	6503	SO:0001819	synonymous_variant	246329	exon3			GGGTGGCTCCTCC	AK057013	CCDS8936.1, CCDS66405.1, CCDS66406.1	12q13.3	2014-08-12			ENSG00000185482	ENSG00000185482			28423	protein-coding gene	gene with protein product		615521				12477932	Standard	NM_001286257		Approved	MGC2793	uc009zpl.2	Q96MF2	OTTHUMG00000171271	ENST00000332782.2:c.228G>A	chr12.hg19:g.57642930C>T		55.0	0.0		42.0	19.0	NM_145064	B4DUK9|Q96HU5	Silent	SNP	ENST00000332782.2	hg19	CCDS8936.1																																																																																			.	.		0.552	STAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412724.2	NM_145064		T	57642930	C	T	57642930	2	4	161	1	0	0	0	0	0	0	0	1	15256	796	28	3		3	STAC3	12	57642930	Silent	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	28182214	57642930	76208965	60	24614										
XPOT	11260	hgsc.bcm.edu	37	chr12	64813856	64813856	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gttttgtattttaggaggctCgtaggaatactctcataaaa	9	5	1	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr12:64813856C>T	ENST00000332707.5	+	7	1025	c.496C>T	c.(496-498)Cgt>Tgt	p.R166C		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	166	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		TTAGGAGGCTCGTAGGAATAC	0.338																																					p.R166C		Atlas-SNP	.											.	XPOT	105	.	0			c.C496T						.						63	62	62					12																	64813856		2203	4300	6503	SO:0001583	missense	11260	exon7			GAGGCTCGTAGGA	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.496C>T	chr12.hg19:g.64813856C>T	ENSP00000327821:p.Arg166Cys	52.0	0.0		40.0	17.0	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Missense_Mutation	SNP	ENST00000332707.5	hg19	CCDS31852.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.570359	0.86542	.	.	ENSG00000184575	ENST00000332707;ENST00000400935	T;T	0.44083	0.93;0.93	4.79	4.79	0.61399	Exportin-1/Importin-beta-like (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.050506	0.85682	D	0.000000	T	0.54029	0.1833	L	0.43152	1.355	0.80722	D	1	D	0.69078	0.997	P	0.60541	0.876	T	0.48948	-0.8989	9	.	.	.	.	18.7197	0.91688	0.0:1.0:0.0:0.0	.	166	O43592	XPOT_HUMAN	C	166	ENSP00000327821:R166C;ENSP00000383722:R166C	.	R	+	1	0	XPOT	63100123	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.657000	0.83745	2.593000	0.87608	0.655000	0.94253	CGT	.	.		0.338	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		T	64813856	C	T	64813856	3	4	161	1	0	0	0	0	1	0	0	0	17465	884	31	1	518	1	XPOT	12	64813856	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	7170926	64813856	69038039	61	24615										
KBTBD6	89890	hgsc.bcm.edu	37	chr13	41705671	41705671	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tttctgctgcagatacaagaGagttgctgctgctactgctg	11	9	1	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr13:41705671G>C	ENST00000379485.1	-	1	1211	c.977C>G	c.(976-978)tCt>tGt	p.S326C	KBTBD6_ENST00000499385.2_Missense_Mutation_p.S260C	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	326										NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		AGATACAAGAGAGTtgctgct	0.527																																					p.S326C		Atlas-SNP	.											.	KBTBD6	83	.	0			c.C977G						.						30	37	35					13																	41705671		2202	4280	6482	SO:0001583	missense	89890	exon1			ACAAGAGAGTTGC	AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"BTB/POZ domain containing"	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.977C>G	chr13.hg19:g.41705671G>C	ENSP00000368799:p.Ser326Cys	294.0	0.0		243.0	76.0	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	hg19	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	g	5.478	0.273208	0.10403	.	.	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.77877	-1.05;-1.13	3.73	1.85	0.25348	.	0.261034	0.25065	N	0.033407	T	0.64000	0.2559	L	0.36672	1.1	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.55373	-0.8151	10	0.56958	D	0.05	.	5.7702	0.18249	0.111:0.393:0.496:0.0	.	260;326	F5GZN7;Q86V97	.;KBTB6_HUMAN	C	326;260	ENSP00000368799:S326C;ENSP00000444326:S260C	ENSP00000368799:S326C	S	-	2	0	KBTBD6	40603671	0.448000	0.25681	0.186000	0.23195	0.905000	0.53344	1.070000	0.30653	0.323000	0.23307	0.462000	0.41574	TCT	.	.		0.527	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		C	41705671	G	C	41705671	3	2	161	1	0	0	0	0	1	0	0	0	8006	942	33	4	1051	4	KBTBD6	13	41705671	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10		41705671	73464207	62	24616										
TEP1	7011	hgsc.bcm.edu	37	chr14	20851711	20851711	+	Frame_Shift_Del	DEL	G	G	-													0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tctggtccactaacctatcaGccccatcgatgatcaggacc							TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr14:20851711delG	ENST00000262715.5	-	26	3843	c.3803delC	c.(3802-3804)gctfs	p.A1268fs	TEP1_ENST00000556935.1_Frame_Shift_Del_p.A1160fs|TEP1_ENST00000545983.1_5'Flank	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1268	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TAACCTATCAGCCCCATCGAT	0.587																																					p.A1268fs		Atlas-INDEL	.											.	TEP1	224	.	0			c.3804delT						.						68	65	66					14																	20851711		2203	4300	6503	SO:0001589	frameshift_variant	7011	exon26			.		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.3803delC	chr14.hg19:g.20851711delG	ENSP00000262715:p.Ala1268fs	100.0	0.0		94.0	43.0	NM_007110	A0AUV9	Frame_Shift_Del	DEL	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	.		0.587	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		-	20851711	G	-	20851711	7	5	161	1	0	1	0	1	0	0	0	0	15774	971	34	0	4200	0	TEP1	14	20851711	Frame_Shift_Del	DEL	G	TCGA-DD-AACJ-01A-11D-A40R-10		20851711	86497829	63	24617										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31576900	31576900	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	agccagttccttcttctcctAaaaattcaacctaaaatatg	3	11	3	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr14:31576900A>G	ENST00000399332.1	-	37	6979	c.6491T>C	c.(6490-6492)tTa>tCa	p.L2164S	HECTD1_ENST00000553700.1_Missense_Mutation_p.L2164S	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2164	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTCTTCTCCTAAAAATTCAAC	0.353																																					p.L2164S		Atlas-SNP	.											.	HECTD1	159	.	0			c.T6491C						.						54	51	52					14																	31576900		1794	4068	5862	SO:0001583	missense	25831	exon37			TCTCCTAAAAATT	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.6491T>C	chr14.hg19:g.31576900A>G	ENSP00000382269:p.Leu2164Ser	71.0	0.0		66.0	28.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.854|4.854	0.158828|0.158828	0.09236|0.09236	.|.	.|.	ENSG00000092148|ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332|ENST00000554882	T;T|.	0.43294|.	0.95;0.95|.	5.28|5.28	5.28|5.28	0.74379|0.74379	HECT (3);|.	0.317042|.	0.23389|.	U|.	0.048708|.	T|.	0.51092|.	0.1654|.	N|N	0.22421|0.22421	0.69|0.69	0.44587|0.44587	D|D	0.99755|0.99755	B|.	0.24186|.	0.099|.	B|.	0.14578|.	0.011|.	T|.	0.48175|.	-0.9058|.	10|.	0.32370|.	T|.	0.25|.	-7.9822|-7.9822	13.7825|13.7825	0.63091|0.63091	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	2164|.	Q9ULT8|.	HECD1_HUMAN|.	S|Q	2164;2166;2164|530	ENSP00000450697:L2164S;ENSP00000382269:L2164S|.	ENSP00000261312:L2166S|.	L|X	-|-	2|1	0|0	HECTD1|HECTD1	30646651|30646651	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	4.375000|4.375000	0.59549|0.59549	1.996000|1.996000	0.58369|0.58369	0.482000|0.482000	0.46254|0.46254	TTA|TAG	.	.		0.353	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			G	31576900	A	G	31576900	3	3	161	1	0	0	0	0	1	0	0	0	7048	372	13	2	1369	2	HECTD1	14	31576900	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	10725189	31576900	75772640	64	24618										
PSEN1	5663	hgsc.bcm.edu	37	chr14	73678608	73678608	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	agtcacgagctgctgtccagGaactttccagcagtatcctc	9	13	1	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr14:73678608G>C	ENST00000324501.5	+	10	1359	c.1087G>C	c.(1087-1089)Gaa>Caa	p.E363Q	PSEN1_ENST00000394164.1_Missense_Mutation_p.E359Q|PSEN1_ENST00000261970.3_Intron|PSEN1_ENST00000344094.3_3'UTR|PSEN1_ENST00000557511.1_Intron|PSEN1_ENST00000357710.4_Missense_Mutation_p.E359Q|PSEN1_ENST00000406768.1_Missense_Mutation_p.E271Q	NM_000021.3|NM_007318.2	NP_000012.1|NP_015557.2	P49768	PSN1_HUMAN	presenilin 1	363	Required for interaction with CTNNB1.				activation of MAPKK activity (GO:0000186)|amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|autophagic vacuole assembly (GO:0000045)|beta-amyloid formation (GO:0034205)|beta-amyloid metabolic process (GO:0050435)|blood vessel development (GO:0001568)|brain morphogenesis (GO:0048854)|Cajal-Retzius cell differentiation (GO:0021870)|calcium ion transmembrane transport (GO:0070588)|canonical Wnt signaling pathway (GO:0060070)|cell fate specification (GO:0001708)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex cell migration (GO:0021795)|choline transport (GO:0015871)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|L-glutamate transport (GO:0015813)|membrane protein ectodomain proteolysis (GO:0006509)|memory (GO:0007613)|mitochondrial transport (GO:0006839)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of axonogenesis (GO:0050771)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of receptor recycling (GO:0001921)|post-embryonic development (GO:0009791)|protein glycosylation (GO:0006486)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of phosphorylation (GO:0042325)|regulation of protein binding (GO:0043393)|regulation of resting membrane potential (GO:0060075)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)|skeletal system morphogenesis (GO:0048705)|skin morphogenesis (GO:0043589)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|somitogenesis (GO:0001756)|synaptic vesicle targeting (GO:0016080)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary rootlet (GO:0035253)|cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)|perinuclear region of cytoplasm (GO:0048471)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|calcium channel activity (GO:0005262)|endopeptidase activity (GO:0004175)|PDZ domain binding (GO:0030165)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075)		TGCTGTCCAGGAACTTTCCAG	0.493																																					p.E363Q		Atlas-SNP	.											.	PSEN1	38	.	0			c.G1087C						.						103	89	94					14																	73678608		2203	4300	6503	SO:0001583	missense	5663	exon10			GTCCAGGAACTTT	AJ008005	CCDS9812.1, CCDS9813.1	14q24.3	2014-09-17	2008-07-28		ENSG00000080815	ENSG00000080815			9508	protein-coding gene	gene with protein product		104311	"Alzheimer disease 3"	AD3		1411576	Standard	NM_007318		Approved	FAD, S182, PS1	uc001xnr.3	P49768	OTTHUMG00000141279	ENST00000324501.5:c.1087G>C	chr14.hg19:g.73678608G>C	ENSP00000326366:p.Glu363Gln	109.0	0.0		106.0	39.0	NM_000021	B2R6D3|O95465|Q14762|Q15719|Q15720|Q96P33|Q9UIF0	Missense_Mutation	SNP	ENST00000324501.5	hg19	CCDS9812.1	.	.	.	.	.	.	.	.	.	.	G	9.613	1.131676	0.21041	.	.	ENSG00000080815	ENST00000324501;ENST00000357710;ENST00000394164;ENST00000406768	D;D;D;D	0.99619	-6.28;-6.28;-6.28;-6.28	6.07	5.18	0.71444	.	0.209202	0.50627	D	0.000120	D	0.97390	0.9146	N	0.04994	-0.135	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.14578	0.003;0.011	D	0.95918	0.8928	10	0.23891	T	0.37	-5.9736	17.5556	0.87888	0.0:0.1235:0.8764:0.0	.	359;363	P49768-2;P49768	.;PSN1_HUMAN	Q	363;359;359;271	ENSP00000326366:E363Q;ENSP00000350342:E359Q;ENSP00000377719:E359Q;ENSP00000385948:E271Q	ENSP00000326366:E363Q	E	+	1	0	PSEN1	72748361	1.000000	0.71417	0.864000	0.33941	0.129000	0.20672	7.429000	0.80309	1.567000	0.49668	0.655000	0.94253	GAA	.	.		0.493	PSEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280500.2			C	73678608	G	C	73678608	3	2	161	1	0	0	0	0	1	0	0	0	12662	1175	41	4	1117	4	PSEN1	14	73678608	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	42101708	73678608	33670932	65	24619										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92488109	92488109	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tgaaggtactgactgagcagCtgactgcagtttcagcaact	11	9	1	4			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr14:92488109C>T	ENST00000267622.4	-	4	752	c.379G>A	c.(379-381)Gct>Act	p.A127T		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	127					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		GACTGAGCAGCTGACTGCAGT	0.433			T	PDGFRB	AML																																p.A127T	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.G379A						.						84	83	83					14																	92488109		2203	4300	6503	SO:0001583	missense	9321	exon4			GAGCAGCTGACTG	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.379G>A	chr14.hg19:g.92488109C>T	ENSP00000267622:p.Ala127Thr	70.0	0.0		43.0	11.0	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	hg19	CCDS9899.1	.	.	.	.	.	.	.	.	.	.	c	9.210	1.030589	0.19512	.	.	ENSG00000100815	ENST00000267622	T	0.66280	-0.2	5.2	4.31	0.51392	.	0.360535	0.28983	N	0.013510	T	0.55289	0.1911	M	0.61703	1.905	0.25971	N	0.982505	B	0.19935	0.04	B	0.24848	0.056	T	0.44205	-0.9343	10	0.18710	T	0.47	.	8.3773	0.32451	0.1543:0.7681:0.0:0.0776	.	127	Q15643	TRIPB_HUMAN	T	127	ENSP00000267622:A127T	ENSP00000267622:A127T	A	-	1	0	TRIP11	91557862	0.943000	0.32029	0.013000	0.15412	0.007000	0.05969	2.060000	0.41394	1.194000	0.43101	0.655000	0.94253	GCT	.	.		0.433	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			T	92488109	C	T	92488109	3	4	161	1	0	0	0	0	1	0	0	0	16570	797	28	3	5632	3	TRIP11	14	92488109	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	18809501	92488109	14861431	66	24620										
GABRB3	2562	hgsc.bcm.edu	37	chr15	26866602	26866602	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	cagccactcgattgtcaagcGtgaggttgagagggatccca	13	10	1	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr15:26866602G>A	ENST00000311550.5	-	4	431	c.320C>T	c.(319-321)aCg>aTg	p.T107M	GABRB3_ENST00000299267.4_Missense_Mutation_p.T107M|GABRB3_ENST00000545868.1_Missense_Mutation_p.T22M|GABRB3_ENST00000400188.3_Missense_Mutation_p.T36M|GABRB3_ENST00000541819.2_Missense_Mutation_p.T163M	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	107					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ATTGTCAAGCGTGAGGTTGAG	0.428																																					p.T107M		Atlas-SNP	.											.	GABRB3	338	.	0			c.C320T						.						105	102	103					15																	26866602		2203	4300	6503	SO:0001583	missense	2562	exon4			TCAAGCGTGAGGT		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.320C>T	chr15.hg19:g.26866602G>A	ENSP00000308725:p.Thr107Met	123.0	0.0		94.0	34.0	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	hg19	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898193	0.91962	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868;ENST00000555094	T;T;T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36;-1.36;-1.36	5.81	5.81	0.92471	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.90848	0.7125	M	0.84156	2.68	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.996;0.998	D	0.91331	0.5090	10	0.72032	D	0.01	.	19.0679	0.93119	0.0:0.0:1.0:0.0	.	163;107;107	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	M	107;163;107;36;22;22	ENSP00000308725:T107M;ENSP00000442408:T163M;ENSP00000299267:T107M;ENSP00000383049:T36M;ENSP00000439169:T22M;ENSP00000452272:T22M	ENSP00000299267:T107M	T	-	2	0	GABRB3	24417695	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.669000	0.98622	2.752000	0.94435	0.467000	0.42956	ACG	.	.		0.428	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			A	26866602	G	A	26866602	3	1	161	1	0	0	0	0	1	0	0	0	6176	1145	40	1	1125	1	GABRB3	15	26866602	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10		26866602	75664790	67	24621										
KIF7	374654	hgsc.bcm.edu	37	chr15	90171679	90171679	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gtttttccggacatcaatcaTccccgggctggctcgtcgca	10	14	2	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr15:90171679T>A	ENST00000394412.3	-	19	4079	c.4003A>T	c.(4003-4005)Atg>Ttg	p.M1335L	KIF7_ENST00000558928.1_Intron	NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	1335					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			ACATCAATCATCCCCGGGCTG	0.647																																					p.M1335L		Atlas-SNP	.											.	KIF7	130	.	0			c.A4003T						.						46	56	53					15																	90171679		2180	4250	6430	SO:0001583	missense	374654	exon19			CAATCATCCCCGG	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"Kinesins"	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.4003A>T	chr15.hg19:g.90171679T>A	ENSP00000377934:p.Met1335Leu	110.0	0.0		94.0	37.0	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	hg19	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	T	5.027	0.190690	0.09547	.	.	ENSG00000166813	ENST00000394412	T	0.66460	-0.21	5.59	5.59	0.84812	.	0.210318	0.49916	D	0.000133	T	0.52885	0.1762	L	0.27053	0.805	0.33303	D	0.565138	B;B	0.11235	0.004;0.0	B;B	0.10450	0.005;0.0	T	0.56360	-0.7992	10	0.12103	T	0.63	.	15.7488	0.77967	0.0:0.0:0.0:1.0	.	821;1335	B7ZKY4;Q2M1P5	.;KIF7_HUMAN	L	1335	ENSP00000377934:M1335L	ENSP00000377934:M1335L	M	-	1	0	KIF7	87972683	0.974000	0.33945	0.939000	0.37840	0.219000	0.24729	3.512000	0.53407	2.128000	0.65567	0.379000	0.24179	ATG	.	.		0.647	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		A	90171679	T	A	90171679	3	1	161	1	0	0	0	0	1	0	0	0	8318	1435	50	4	32	4	KIF7	15	90171679	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	63305077	90171679	12359713	68	24622										
DNAH3	55567	hgsc.bcm.edu	37	chr16	20966168	20966168	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gtttcttctctcttgaacaaCggcgtggaagaaacaaaggc	10	9	3	2	rs142557616	byFrequency	TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr16:20966168C>T	ENST00000261383.3	-	55	11037	c.11038G>A	c.(11038-11040)Gtt>Att	p.V3680I	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3680	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TCTTGAACAACGGCGTGGAAG	0.488																																					p.V3680I		Atlas-SNP	.											.	DNAH3	1142	.	0			c.G11038A						.						117	114	115					16																	20966168		2201	4300	6501	SO:0001583	missense	55567	exon55			GAACAACGGCGTG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.11038G>A	chr16.hg19:g.20966168C>T	ENSP00000261383:p.Val3680Ile	95.0	0.0		75.0	32.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	8.672	0.903178	0.17760	.	.	ENSG00000158486	ENST00000261383	T	0.12147	2.71	5.43	0.641	0.17759	Dynein heavy chain (1);	0.227292	0.38837	N	0.001555	T	0.05593	0.0147	N	0.12182	0.205	0.38697	D	0.952906	B	0.06786	0.001	B	0.04013	0.001	T	0.42068	-0.9473	10	0.13108	T	0.6	.	6.1732	0.20429	0.0:0.3409:0.2323:0.4268	.	3680	Q8TD57	DYH3_HUMAN	I	3680	ENSP00000261383:V3680I	ENSP00000261383:V3680I	V	-	1	0	DNAH3	20873669	0.953000	0.32496	0.566000	0.28421	0.977000	0.68977	0.459000	0.21908	-0.158000	0.11040	-0.238000	0.12139	GTT	.	C|0.996;A|0.004		0.488	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	20966168	C	T	20966168	3	4	161	1	0	0	0	0	1	0	0	0	4605	536	19	1	1343	1	DNAH3	16	20966168	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10		20966168	69388585	69	24623										
RBBP6	5930	hgsc.bcm.edu	37	chr16	24583618	24583618	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	acacaagaaacataaaaagcAtaagaagcataagaaacatg	6	6	0	3			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr16:24583618A>G	ENST00000319715.4	+	18	5663	c.5231A>G	c.(5230-5232)cAt>cGt	p.H1744R	RBBP6_ENST00000381039.3_Missense_Mutation_p.H904R|RBBP6_ENST00000348022.2_Missense_Mutation_p.H1710R	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1744					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		cataaaaagcataagaagcat	0.378																																					p.H1744R		Atlas-SNP	.											.	RBBP6	158	.	0			c.A5231G						.						35	32	33					16																	24583618		2193	4299	6492	SO:0001583	missense	5930	exon18			AAAAGCATAAGAA		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.5231A>G	chr16.hg19:g.24583618A>G	ENSP00000317872:p.His1744Arg	204.0	0.0		212.0	99.0	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	hg19	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	13.42	2.230965	0.39399	.	.	ENSG00000122257	ENST00000381039;ENST00000319715;ENST00000348022	T;T;T	0.36340	1.26;1.68;1.61	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000002	T	0.42810	0.1219	N	0.14661	0.345	0.51012	D	0.9999	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.997;0.997;0.994	T	0.34650	-0.9820	10	0.22706	T	0.39	-16.3606	16.3436	0.83110	1.0:0.0:0.0:0.0	.	904;1710;1744	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9	.;.;RBBP6_HUMAN	R	904;1744;1710	ENSP00000370427:H904R;ENSP00000317872:H1744R;ENSP00000316291:H1710R	ENSP00000317872:H1744R	H	+	2	0	RBBP6	24491119	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.928000	0.87587	2.269000	0.75478	0.533000	0.62120	CAT	.	.		0.378	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		G	24583618	A	G	24583618	3	3	161	1	0	0	0	0	1	0	0	0	13118	217	8	2	5355	2	RBBP6	16	24583618	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	3617450	24583618	65771135	70	24624										
SNX20	124460	hgsc.bcm.edu	37	chr16	50707378	50707378	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tgcctcggggcgtgggcctcCggagctggctctcctccagc	15	16	1	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr16:50707378C>T	ENST00000330943.4	-	4	1061	c.890G>A	c.(889-891)cGg>cAg	p.R297Q	RP11-401P9.5_ENST00000570167.1_RNA|SNX20_ENST00000300590.3_Intron|SNX20_ENST00000423026.2_Intron|RP11-401P9.5_ENST00000570241.2_RNA	NM_182854.2	NP_878274.1	Q7Z614	SNX20_HUMAN	sorting nexin 20	297					protein transport (GO:0015031)	endosome (GO:0005768)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)			kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(2)|stomach(1)	15						CGTGGGCCTCCGGAGCTGGCT	0.667																																					p.R297Q		Atlas-SNP	.											.	SNX20	50	.	0			c.G890A						.						39	43	42					16																	50707378		2193	4297	6490	SO:0001583	missense	124460	exon4			GGCCTCCGGAGCT	AK055837	CCDS10745.1, CCDS10744.1, CCDS45481.1	16q12.1	2008-03-25	2008-03-25		ENSG00000167208	ENSG00000167208		"Sorting nexins"	30390	protein-coding gene	gene with protein product	"selectin ligand interactor cytoplasmic 1"	613281				18196517, 16782399	Standard	NM_182854		Approved	SLIC-1, SLIC1	uc002egk.2	Q7Z614	OTTHUMG00000133173	ENST00000330943.4:c.890G>A	chr16.hg19:g.50707378C>T	ENSP00000332062:p.Arg297Gln	72.0	0.0		58.0	25.0	NM_182854	A8K9D5|Q08E98|Q6P4H2|Q8IV59	Missense_Mutation	SNP	ENST00000330943.4	hg19	CCDS10745.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.378979	0.24944	.	.	ENSG00000167208	ENST00000330943;ENST00000413750	T	0.29655	1.56	5.67	2.22	0.28083	.	0.593626	0.16759	N	0.200718	T	0.20129	0.0484	L	0.38838	1.175	0.25478	N	0.987768	B	0.29037	0.231	B	0.18561	0.022	T	0.12656	-1.0539	10	0.26408	T	0.33	-34.8905	9.464	0.38802	0.0:0.683:0.0:0.317	.	297	Q7Z614	SNX20_HUMAN	Q	297;133	ENSP00000332062:R297Q	ENSP00000332062:R297Q	R	-	2	0	SNX20	49264879	0.017000	0.18338	0.728000	0.30774	0.891000	0.51852	0.564000	0.23563	0.761000	0.33130	0.561000	0.74099	CGG	.	.		0.667	SNX20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256879.2	NM_153337		T	50707378	C	T	50707378	3	4	161	1	0	0	0	0	1	0	0	0	14907	652	23	1	207	1	SNX20	16	50707378	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	26123760	50707378	39647375	71	24625										
KIAA0174	9798	hgsc.bcm.edu	37	chr16	71961659	71961659	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gccagcacctcagcatctgaAgacattgactttgatgatct	8	11	3	5			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr16:71961659A>C	ENST00000378799.6	+	10	1400	c.1044A>C	c.(1042-1044)gaA>gaC	p.E348D	IST1_ENST00000535424.1_Missense_Mutation_p.E361D|RP11-498D10.6_ENST00000573861.1_RNA|IST1_ENST00000538850.1_Missense_Mutation_p.E200D|IST1_ENST00000544564.1_Missense_Mutation_p.E348D|IST1_ENST00000329908.8_Missense_Mutation_p.K347T|IST1_ENST00000541571.2_Missense_Mutation_p.E348D|IST1_ENST00000538565.1_3'UTR|IST1_ENST00000378798.5_Missense_Mutation_p.E317D|RP11-498D10.5_ENST00000567146.1_RNA|PKD1L3_ENST00000534738.1_RNA|IST1_ENST00000606369.1_Missense_Mutation_p.E200D			P53990	IST1_HUMAN	increased sodium tolerance 1 homolog (yeast)	346	Interaction with VPS4A, VTA1, MITD1 STAMBP and USP8.|Interaction with VTA1.				abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of proteolysis (GO:0045862)|protein localization (GO:0008104)|viral capsid secondary envelopment (GO:0046745)|viral release from host cell (GO:0019076)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|midbody (GO:0030496)	MIT domain binding (GO:0090541)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)										CAGCATCTGAAGACATTGACT	0.458																																					p.E361D		Atlas-SNP	.											.	.	.	.	0			c.A1083C						.						191	196	195					16																	71961659		2198	4300	6498	SO:0001583	missense	9798	exon11			ATCTGAAGACATT	BC004359	CCDS10905.1, CCDS59271.1, CCDS59272.1, CCDS59273.1, CCDS59274.1	16q22.2	2011-08-18	2011-08-18	2011-08-18	ENSG00000182149	ENSG00000182149			28977	protein-coding gene	gene with protein product			"KIAA0174"	KIAA0174		8724849, 19129480	Standard	NM_001270975		Approved		uc002fbm.2	P53990	OTTHUMG00000137597	ENST00000378799.6:c.1044A>C	chr16.hg19:g.71961659A>C	ENSP00000368076:p.Glu348Asp	61.0	0.0		53.0	28.0	NM_001270976	A8KAH5|J3QLU7|Q3SYM4|Q9BQ81|Q9BWN2	Missense_Mutation	SNP	ENST00000378799.6	hg19	CCDS59272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.69|12.69	2.012321|2.012321	0.35511|0.35511	.|.	.|.	ENSG00000182149|ENSG00000182149	ENST00000535424;ENST00000378799;ENST00000538963;ENST00000538850;ENST00000378798;ENST00000456820|ENST00000329908	.|.	.|.	.|.	5.44|5.44	-0.794|-0.794	0.10918|0.10918	.|.	0.044330|.	0.85682|.	D|.	0.000000|.	T|T	0.50701|0.50701	0.1631|0.1631	.|.	.|.	.|.	0.53688|0.53688	D|D	0.999972|0.999972	B;B;B|B	0.16166|0.06786	0.009;0.016;0.012|0.001	B;B;B|B	0.14578|0.08055	0.005;0.011;0.007|0.003	T|T	0.46857|0.46857	-0.9161|-0.9161	8|7	0.02654|0.87932	T|D	1|0	-30.4029|-30.4029	10.4073|10.4073	0.44272|0.44272	0.6556:0.0:0.3444:0.0|0.6556:0.0:0.3444:0.0	.|.	346;317;361|347	P53990;P53990-2;A8KAH5|P53990-3	IST1_HUMAN;.;.|.	D|T	361;348;337;200;317;271|347	.|.	ENSP00000368075:E317D|ENSP00000330408:K347T	E|K	+|+	3|2	2|0	KIAA0174|KIAA0174	70519160|70519160	0.985000|0.985000	0.35326|0.35326	0.997000|0.997000	0.53966|0.53966	0.998000|0.998000	0.95712|0.95712	0.308000|0.308000	0.19314|0.19314	-0.057000|-0.057000	0.13199|0.13199	0.528000|0.528000	0.53228|0.53228	GAA|AAG	.	.		0.458	IST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269005.2	NM_014761		C	71961659	A	C	71961659	3	2	161	1	0	0	0	0	1	0	0	0	8167	72	3	5	1074	5	KIAA0174	16	71961659	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	21254281	71961659	18393094	72	24626										
C17orf74	201243	hgsc.bcm.edu	37	chr17	7329876	7329876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ttcctacctggaggaggaggAcaacctgcccttcccgtatc	10	14	0	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr17:7329876A>G	ENST00000333870.3	+	3	640	c.566A>G	c.(565-567)gAc>gGc	p.D189G	C17orf74_ENST00000574034.1_Silent_p.G76G|RP11-104H15.7_ENST00000575310.1_RNA	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	189						integral component of membrane (GO:0016021)				cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	22		Prostate(122;0.157)				GAGGAGGAGGACAACCTGCCC	0.592																																					p.D189G		Atlas-SNP	.											.	C17orf74	56	.	0			c.A566G						.						135	141	139					17																	7329876		2006	4156	6162	SO:0001583	missense	201243	exon3			AGGAGGACAACCT	BC044816	CCDS42255.1	17p13.1	2012-05-30			ENSG00000184560	ENSG00000184560			27315	protein-coding gene	gene with protein product						12477932	Standard	NM_175734		Approved		uc002ggw.3	Q0P670	OTTHUMG00000178190	ENST00000333870.3:c.566A>G	chr17.hg19:g.7329876A>G	ENSP00000328061:p.Asp189Gly	70.0	0.0		30.0	20.0	NM_175734		Missense_Mutation	SNP	ENST00000333870.3	hg19	CCDS42255.1	.	.	.	.	.	.	.	.	.	.	A	11.44	1.638689	0.29157	.	.	ENSG00000184560	ENST00000333870	T	0.42900	0.96	4.1	3.0	0.34707	.	1.675350	0.04018	N	0.299310	T	0.33381	0.0861	L	0.27053	0.805	0.09310	N	0.999999	B	0.11235	0.004	B	0.11329	0.006	T	0.27739	-1.0065	10	0.62326	D	0.03	-13.998	6.4414	0.21851	0.8863:0.0:0.1137:0.0	.	189	Q0P670	CQ074_HUMAN	G	189	ENSP00000328061:D189G	ENSP00000328061:D189G	D	+	2	0	C17orf74	7270600	0.053000	0.20554	0.003000	0.11579	0.006000	0.05464	2.006000	0.40874	0.707000	0.31934	0.402000	0.26972	GAC	.	.		0.592	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734		G	7329876	A	G	7329876	3	3	161	1	0	0	0	0	1	0	0	0	1881	275	10	2	576	2	C17orf74	17	7329876	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10		7329876	73865334	73	24627										
KRBA2	124751	hgsc.bcm.edu	37	chr17	8272535	8272535	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	atccatgtcatcgtccatatCagatctgtctgctccaatct	5	13	5	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr17:8272535C>A	ENST00000331336.2	-	2	1401	c.1396G>T	c.(1396-1398)Gat>Tat	p.D466Y	RP11-849F2.7_ENST00000582471.1_3'UTR|KRBA2_ENST00000396267.1_Missense_Mutation_p.D384Y|RP11-849F2.5_ENST00000580537.1_RNA|RP11-849F2.5_ENST00000583963.1_RNA	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	466					DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)			endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						TCGTCCATATCAGATCTGTCT	0.493																																					p.D466Y		Atlas-SNP	.											.	KRBA2	34	.	0			c.G1396T						.						157	141	146					17																	8272535		2203	4300	6503	SO:0001583	missense	124751	exon2			CCATATCAGATCT	BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"-"	26989	protein-coding gene	gene with protein product			"KRAB A domain containing 2"			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.1396G>T	chr17.hg19:g.8272535C>A	ENSP00000328017:p.Asp466Tyr	101.0	0.0		36.0	25.0	NM_213597	Q8IYY0	Missense_Mutation	SNP	ENST00000331336.2	hg19	CCDS11141.1	.	.	.	.	.	.	.	.	.	.	c	8.382	0.837844	0.16891	.	.	ENSG00000184619	ENST00000396267;ENST00000331336	T;T	0.27256	1.75;1.68	2.78	2.78	0.32641	.	.	.	.	.	T	0.42810	0.1219	L	0.57536	1.79	0.09310	N	1	D	0.89917	1.0	D	0.68621	0.959	T	0.09185	-1.0686	9	0.72032	D	0.01	.	9.2674	0.37650	0.0:1.0:0.0:0.0	.	466	Q6ZNG9	KRBA2_HUMAN	Y	384;466	ENSP00000379565:D384Y;ENSP00000328017:D466Y	ENSP00000328017:D466Y	D	-	1	0	KRBA2	8213260	0.043000	0.20138	0.008000	0.14137	0.121000	0.20230	1.093000	0.30939	1.875000	0.54330	0.650000	0.86243	GAT	.	.		0.493	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597		A	8272535	C	A	8272535	3	1	161	1	0	0	0	0	1	0	0	0	8449	826	29	3	86	3	KRBA2	17	8272535	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	942659	8272535	72922675	74	24628										
ZNF286B	729288	hgsc.bcm.edu	37	chr17	18566384	18566384	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ttagagtcatagacactattCcgtgtcagtctgtctattat	7	8	4	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr17:18566384C>A	ENST00000545289.1	-	5	685	c.435G>T	c.(433-435)cgG>cgT	p.R145R	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	145					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						AGACACTATTCCGTGTCAGTC	0.413																																					p.R145R		Atlas-SNP	.											.	ZNF286B	75	.	0			c.G435T						.						114	101	105					17																	18566384		692	1590	2282	SO:0001819	synonymous_variant	729288	exon5			ACTATTCCGTGTC		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"Zinc fingers, C2H2-type"	33241	protein-coding gene	gene with protein product	"zinc finger protein 590"		"zinc finger protein 286-like", "zinc finger 286C pseudogene"	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.435G>T	chr17.hg19:g.18566384C>A		253.0	1.0		111.0	78.0	NM_001145045		Silent	SNP	ENST00000545289.1	hg19	CCDS58523.1																																																																																			.	.		0.413	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047		A	18566384	C	A	18566384	2	1	161	1	0	0	0	0	0	0	0	1	17839	842	30	3		3	ZNF286B	17	18566384	Silent	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10	10293849	18566384	62628826	75	24629										
SLC13A2	9058	hgsc.bcm.edu	37	chr17	26817351	26817351	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	cagagaccatttccatccagTttcgagagcccaggggaatg	11	11	0	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr17:26817351T>A	ENST00000314669.5	+	3	651				SLC13A2_ENST00000537681.1_5'UTR|SLC13A2_ENST00000444914.3_Missense_Mutation_p.S86R|SLC13A2_ENST00000545060.1_Intron	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2						dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	TTCCATCCAGTTTCGAGAGCC	0.517																																					p.S86R		Atlas-SNP	.											.	SLC13A2	125	.	0			c.T258A						.						17	19	18					17																	26817351		692	1591	2283	SO:0001627	intron_variant	9058	exon3			ATCCAGTTTCGAG	U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"Solute carriers"	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.232-121T>A	chr17.hg19:g.26817351T>A		81.0	0.0		157.0	29.0	NM_001145975	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	hg19	CCDS11231.1	.	.	.	.	.	.	.	.	.	.	T	6.504	0.461280	0.12342	.	.	ENSG00000007216	ENST00000444914	T	0.67345	-0.26	3.83	-1.71	0.08133	.	.	.	.	.	T	0.34890	0.0913	N	0.08118	0	0.09310	N	0.999998	B	0.33413	0.411	B	0.33454	0.164	T	0.21484	-1.0244	9	0.16896	T	0.51	.	0.6745	0.00864	0.3255:0.106:0.1844:0.3841	.	86	E7ETH5	.	R	86	ENSP00000392411:S86R	ENSP00000392411:S86R	S	+	3	2	SLC13A2	23841478	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.177000	0.16801	-0.472000	0.06881	0.528000	0.53228	AGT	.	.		0.517	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984		A	26817351	T	A	26817351	1	1	161	0	1	0	0	0	0	0	0	0	14407	1722	60	4		4	SLC13A2	17	26817351	Intron	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	8250967	26817351	54377859	76	24630										
KRT20	54474	hgsc.bcm.edu	37	chr17	39034466	39034466	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	caagtcgagtctttatgtcaAgaaggatatggtattcgttg	11	5	2	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr17:39034466A>G	ENST00000167588.3	-	6	1111	c.1070T>C	c.(1069-1071)cTt>cCt	p.L357P		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	357	Coil 2.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				CTTTATGTCAAGAAGGATATG	0.473																																					p.L357P		Atlas-SNP	.											.	KRT20	38	.	0			c.T1070C						.						290	243	259					17																	39034466		2203	4300	6503	SO:0001583	missense	54474	exon6			ATGTCAAGAAGGA	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"-", "Intermediate filaments type I, keratins (acidic)"	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.1070T>C	chr17.hg19:g.39034466A>G	ENSP00000167588:p.Leu357Pro	102.0	0.0		136.0	21.0	NM_019010	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	hg19	CCDS11379.1	.	.	.	.	.	.	.	.	.	.	A	18.70	3.679389	0.68042	.	.	ENSG00000171431	ENST00000167588	D	0.93488	-3.23	5.0	5.0	0.66597	Filament (1);	0.243433	0.28996	N	0.013462	D	0.97892	0.9307	H	0.97340	3.985	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.99312	1.0904	10	0.87932	D	0	.	14.6964	0.69124	1.0:0.0:0.0:0.0	.	357	P35900	K1C20_HUMAN	P	357	ENSP00000167588:L357P	ENSP00000167588:L357P	L	-	2	0	KRT20	36287992	1.000000	0.71417	0.982000	0.44146	0.467000	0.32768	5.988000	0.70579	1.873000	0.54277	0.482000	0.46254	CTT	.	.		0.473	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2			G	39034466	A	G	39034466	3	3	161	1	0	0	0	0	1	0	0	0	8467	72	3	2	216	2	KRT20	17	39034466	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	12217115	39034466	42160744	77	24631										
NME1-NME2	4831	hgsc.bcm.edu	37	chr17	49247317	49247317	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ggtctgggaggggctgaacgTggtgaagacaggccgagtga	20	6	1	4			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr17:49247317T>C	ENST00000393193.2	+	7	670	c.593T>C	c.(592-594)gTg>gCg	p.V198A	NME1-NME2_ENST00000514264.2_Missense_Mutation_p.V83A|NME1-NME2_ENST00000393183.3_Missense_Mutation_p.V8A|NME1-NME2_ENST00000393198.3_Missense_Mutation_p.V198A|NME1-NME2_ENST00000503064.1_Missense_Mutation_p.V83A|NME1-NME2_ENST00000608447.1_Missense_Mutation_p.V223A|NME1-NME2_ENST00000513177.1_Missense_Mutation_p.V83A|NME1-NME2_ENST00000512737.1_Missense_Mutation_p.V83A|NME1-NME2_ENST00000393190.1_Missense_Mutation_p.V83A|NME2_ENST00000376392.6_Intron|NME1-NME2_ENST00000393185.1_Missense_Mutation_p.V8A|NME2_ENST00000555572.1_Missense_Mutation_p.V223A			P22392	NDKB_HUMAN	NME/NM23 nucleoside diphosphate kinase 2	83					cell adhesion (GO:0007155)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of apoptotic process (GO:0043066)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside triphosphate biosynthetic process (GO:0009142)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermis development (GO:0045682)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|UTP biosynthetic process (GO:0006228)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)|protein histidine kinase activity (GO:0004673)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	6			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)		Adefovir Dipivoxil(DB00718)|Lamivudine(DB00709)|Tenofovir(DB00300)	GGGCTGAACGTGGTGAAGACA	0.517																																					p.V198A	Esophageal Squamous(49;809 1203 4404 15246)	Atlas-SNP	.											.	NME1-NME2	17	.	0			c.T593C						.						111	102	105					17																	49247317		2203	4300	6503	SO:0001583	missense	654364	exon7			TGAACGTGGTGAA	X58965	CCDS11580.1, CCDS74107.1	17q21.33	2013-04-29	2012-05-18		ENSG00000011052	ENSG00000011052			7850	protein-coding gene	gene with protein product		156491	"non-metastatic cells 2, protein (NM23B) expressed in"			1988104, 19852809	Standard	NM_001018137		Approved	NM23-H2, NDPKB		P22392	OTTHUMG00000154062	ENST00000393193.2:c.593T>C	chr17.hg19:g.49247317T>C	ENSP00000376889:p.Val198Ala	79.0	0.0		188.0	32.0	NM_001018136	A8MWA3|Q1WM23|Q6LCT6	Missense_Mutation	SNP	ENST00000393193.2	hg19	CCDS32682.1	.	.	.	.	.	.	.	.	.	.	T	14.50	2.555218	0.45487	.	.	ENSG00000011052;ENSG00000011052;ENSG00000011052;ENSG00000011052;ENSG00000011052;ENSG00000011052;ENSG00000011052;ENSG00000011052;ENSG00000011052;ENSG00000243678;ENSG00000243678	ENST00000376392;ENST00000555572;ENST00000514264;ENST00000393185;ENST00000513177;ENST00000512737;ENST00000503064;ENST00000393183;ENST00000393190;ENST00000393193;ENST00000393198	T;T;T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78	4.92	4.92	0.64577	.	0.096714	0.40554	U	0.001068	T	0.38719	0.1051	N	0.11560	0.145	0.58432	D	0.999992	B;P	0.36733	0.026;0.567	B;P	0.46110	0.161;0.504	T	0.37430	-0.9706	10	0.35671	T	0.21	-13.2897	14.552	0.68073	0.0:0.0:0.0:1.0	.	83;223	P22392;Q32Q12	NDKB_HUMAN;.	A	198;223;83;8;83;83;83;8;83;198;223	ENSP00000451932:V223A;ENSP00000426976:V83A;ENSP00000376882:V8A;ENSP00000425581:V83A;ENSP00000421064:V83A;ENSP00000426901:V83A;ENSP00000376880:V8A;ENSP00000376886:V83A;ENSP00000376889:V198A	ENSP00000365572:V83A	V	+	2	0	NME2;NME1-NME2	46602316	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	3.921000	0.56454	1.975000	0.57531	0.482000	0.46254	GTG	.	.		0.517	NME2-001	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000268664.2	NM_002512		C	49247317	T	C	49247317	3	2	161	1	0	0	0	0	1	0	0	0	10499	1696	59	2	615	2	NME1-NME2	17	49247317	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	10212851	49247317	31947893	78	24632										
USH1G	124590	hgsc.bcm.edu	37	chr17	72916457	72916457	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	tatcgccgctccatgcgttcGtggtgcctccgctgcagctt	11	15	0	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr17:72916457G>A	ENST00000319642.1	-	2	656	c.474C>T	c.(472-474)caC>caT	p.H158H		NM_001282489.1|NM_173477.2	NP_001269418.1|NP_775748.2	Q495M9	USH1G_HUMAN	Usher syndrome 1G (autosomal recessive)	158					equilibrioception (GO:0050957)|inner ear morphogenesis (GO:0042472)|inner ear receptor cell differentiation (GO:0060113)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	spectrin binding (GO:0030507)		HN1/USH1G(2)	endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14	all_lung(278;0.172)|Lung NSC(278;0.207)					CCATGCGTTCGTGGTGCCTCC	0.692																																					p.H158H		Atlas-SNP	.											.	USH1G	40	.	0			c.C474T						.						63	45	51					17																	72916457		2203	4299	6502	SO:0001819	synonymous_variant	124590	exon2			GCGTTCGTGGTGC	AK091243	CCDS32725.1	17q25.1	2013-01-10			ENSG00000182040	ENSG00000182040		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	16356	protein-coding gene	gene with protein product		607696				12588794	Standard	NM_001282489		Approved	Sans, FLJ33924, ANKS4A	uc002jme.1	Q495M9	OTTHUMG00000178864	ENST00000319642.1:c.474C>T	chr17.hg19:g.72916457G>A		55.0	0.0		90.0	14.0	NM_173477	Q8N251	Silent	SNP	ENST00000319642.1	hg19	CCDS32725.1																																																																																			.	.		0.692	USH1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443676.1	NM_173477		A	72916457	G	A	72916457	2	1	161	1	0	0	0	0	0	0	0	1	17050	1136	40	1		1	USH1G	17	72916457	Silent	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	23669140	72916457	8278753	79	24633										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7008502	7008502	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	cgtacctgacatgagaatccCacagtgccaggaggacagac	11	12	0	3	rs374423781		TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr18:7008502C>A	ENST00000389658.3	-	28	4200	c.4107G>T	c.(4105-4107)gtG>gtT	p.V1369V		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1369	Laminin EGF-like 14; second part. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				ATGAGAATCCCACAGTGCCAG	0.453																																					p.V1369V		Atlas-SNP	.											.	LAMA1	458	.	0			c.G4107T						.	C		1,4405	2.1+/-5.4	0,1,2202	103	91	95		4107	-5	0	18		95	0,8600		0,0,4300	no	coding-synonymous	LAMA1	NM_005559.3		0,1,6502	AA,AC,CC		0.0,0.0227,0.0077		1369/3076	7008502	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon28			GAATCCCACAGTG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.4107G>T	chr18.hg19:g.7008502C>A		67.0	0.0		69.0	31.0	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.453	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		A	7008502	C	A	7008502	2	1	161	1	0	0	0	0	0	0	0	1	8614	581	21	3		3	LAMA1	18	7008502	Silent	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10		7008502	71068746	80	24634										
ZNF397	84307	hgsc.bcm.edu	37	chr18	32825455	32825455	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	agagacctttatgatgaggcTgaaagatgcttgattctaac	10	6	1	6			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr18:32825455T>A	ENST00000330501.7	+	4	939	c.786T>A	c.(784-786)gcT>gcA	p.A262A	ZNF397_ENST00000589420.1_Intron|ZNF397_ENST00000261333.6_Intron|ZNF397_ENST00000355632.4_Intron|ZNF397_ENST00000592264.1_Intron	NM_001135178.2	NP_001128650.1	Q8NF99	ZN397_HUMAN	zinc finger protein 397	262					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)	12						ATGATGAGGCTGAAAGATGCT	0.423																																					p.A262A		Atlas-SNP	.											.	ZNF397	51	.	0			c.T786A						.						80	73	75					18																	32825455		692	1591	2283	SO:0001819	synonymous_variant	84307	exon4			TGAGGCTGAAAGA	BC006172	CCDS32814.1, CCDS45852.1	18p12	2013-01-09	2003-07-22			ENSG00000186812		"-", "Zinc fingers, C2H2-type"	18818	protein-coding gene	gene with protein product		609601	"zinc finger protein 47"	ZNF47			Standard	NM_032347		Approved	ZSCAN15, MGC13250	uc010dmp.3	Q8NF99		ENST00000330501.7:c.786T>A	chr18.hg19:g.32825455T>A		94.0	0.0		105.0	24.0	NM_001135178	Q9BRM2	Silent	SNP	ENST00000330501.7	hg19	CCDS45852.1																																																																																			.	.		0.423	ZNF397-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442398.1	NM_032347		A	32825455	T	A	32825455	2	1	161	1	0	0	0	0	0	0	0	1	17898	1567	55	4		4	ZNF397	18	32825455	Silent	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	25816953	32825455	45251793	81	24635										
LPPR3	79948	hgsc.bcm.edu	37	chr19	813158	813158	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	actgccgccccgctcttctcGgccatcatgagccacttggc	9	18	3	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr19:813158G>A	ENST00000520876.3	-	8	1647	c.1569C>T	c.(1567-1569)gcC>gcT	p.A523A	LPPR3_ENST00000359894.2_Silent_p.A551A|MIR3187_ENST00000583431.1_RNA	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		523						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										CGCTCTTCTCGGCCATCATGA	0.756																																					p.A551A		Atlas-SNP	.											.	.	.	.	0			c.C1653T						.																																			SO:0001819	synonymous_variant	0	exon7			CTTCTCGGCCATC																												ENST00000520876.3:c.1569C>T	chr19.hg19:g.813158G>A		30.0	0.0		28.0	6.0	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Silent	SNP	ENST00000520876.3	hg19	CCDS58636.1																																																																																			.	.		0.756	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3			A	813158	G	A	813158	2	1	161	1	0	0	0	0	0	0	0	1	8935	1103	39	1		1	LPPR3	19	813158	Silent	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10		813158	58315825	82	24636										
MBD3L1	85509	hgsc.bcm.edu	37	chr19	8953470	8953470	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ttacacattcaagaggccagTaacgagaattacaccccatc	6	12	1	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr19:8953470T>C	ENST00000595891.1	+	3	347	c.116T>C	c.(115-117)gTa>gCa	p.V39A	MBD3L1_ENST00000305625.2_Missense_Mutation_p.V39A			Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like 1	39	Transcription repressor.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|large_intestine(5)|liver(1)|lung(2)|skin(2)	12						AAGAGGCCAGTAACGAGAATT	0.502																																					p.V39A		Atlas-SNP	.											.	MBD3L1	24	.	0			c.T116C						.						127	113	118					19																	8953470		2203	4300	6503	SO:0001583	missense	85509	exon1			GGCCAGTAACGAG	AY038022	CCDS12209.1	19p13.2	2011-01-31	2003-03-19	2003-03-21	ENSG00000170948	ENSG00000170948			15774	protein-coding gene	gene with protein product		607963	"methyl-CpG binding domain protein 3-like"	MBD3L		12504854	Standard	NM_145208		Approved		uc002mko.2	Q8WWY6		ENST00000595891.1:c.116T>C	chr19.hg19:g.8953470T>C	ENSP00000471575:p.Val39Ala	157.0	0.0		116.0	53.0	NM_145208	B5BUM6|Q2M291	Missense_Mutation	SNP	ENST00000595891.1	hg19	CCDS12209.1	.	.	.	.	.	.	.	.	.	.	T	12.96	2.093751	0.36952	.	.	ENSG00000170948	ENST00000305625	T	0.68331	-0.32	3.92	3.92	0.45320	.	0.160194	0.25065	N	0.033405	T	0.76219	0.3957	M	0.86097	2.795	0.48040	D	0.999572	D	0.62365	0.991	P	0.54174	0.744	T	0.80120	-0.1515	10	0.87932	D	0	-16.7206	9.4528	0.38736	0.0:0.0:0.0:1.0	.	39	Q8WWY6	MB3L1_HUMAN	A	39	ENSP00000304198:V39A	ENSP00000304198:V39A	V	+	2	0	MBD3L1	8814470	0.982000	0.34865	0.445000	0.26908	0.100000	0.18952	2.980000	0.49321	1.990000	0.58119	0.533000	0.62120	GTA	.	.		0.502	MBD3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459973.1	NM_145208		C	8953470	T	C	8953470	3	2	161	1	0	0	0	0	1	0	0	0	9354	1638	57	2	118	2	MBD3L1	19	8953470	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	8140312	8953470	50175513	83	24637										
FARSA	2193	hgsc.bcm.edu	37	chr19	13035721	13035740	+	Frame_Shift_Del	DEL	CTGGGCAAGGCGGTAGAGCG	CTGGGCAAGGCGGTAGAGCG	-													0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gcctgggccaaccgcaccttCtgggcaaggcggtagagcgc					rs35087277|rs201276620	byFrequency	TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	CTGGGCAAGGCGGTAGAGCG	CTGGGCAAGGCGGTAGAGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr19:13035721_13035740delCTGGGCAAGGCGGTAGAGCG	ENST00000314606.4	-	9	1022_1041	c.1004_1023delCGCTCTACCGCCTTGCCCAG	c.(1003-1023)gcgctctaccgccttgcccagfs	p.ALYRLAQ335fs	FARSA_ENST00000588025.1_Frame_Shift_Del_p.ALYRLAQ375fs|FARSA_ENST00000423140.2_Frame_Shift_Del_p.ALYRLAQ304fs	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	335					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	ACCGCACCTTCTGGGCAAGGCGGTAGAGCGCACGGGCGCT	0.623																																					p.335_342del		Atlas-INDEL	.											.	FARSA	46	.	0			c.1005_1024del						.																																			SO:0001589	frameshift_variant	2193	exon9			.	U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	3592	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 1, alpha, cytoplasmic"	602918	"phenylalanine-tRNA synthetase-like", "phenylalanyl-tRNA synthetase-like, alpha subunit"	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.1004_1023delCGCTCTACCGCCTTGCCCAG	chr19.hg19:g.13035721_13035740delCTGGGCAAGGCGGTAGAGCG	ENSP00000320309:p.Ala335fs	103.0	0.0		89.0	31.0	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Frame_Shift_Del	DEL	ENST00000314606.4	hg19	CCDS12287.1																																																																																			.	.		0.623	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461		-	13035740	CTGGGCAAGGCGGTAGAGCG	-	13035721	7	5	161	1	0	1	0	1	0	0	0	0	5687	912	32	0	523	0	FARSA	19	13035721	Frame_Shift_Del	DEL	CTGGGCAAGGCGGTAGAGCG	TCGA-DD-AACJ-01A-11D-A40R-10	4082251	13035721	46093262	84	24638										
STX10	8677	hgsc.bcm.edu	37	chr19	13260405	13260405	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gcctgggttggcttccactaTacgtgggctgagagtcaagg	15	9	1	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr19:13260405T>C	ENST00000587230.1	-	3	272	c.208A>G	c.(208-210)Ata>Gta	p.I70V	IER2_ENST00000587885.1_5'Flank|STX10_ENST00000589083.1_Missense_Mutation_p.I70V|STX10_ENST00000242770.5_Missense_Mutation_p.I70V|IER2_ENST00000588173.1_5'Flank|IER2_ENST00000292433.3_5'Flank|STX10_ENST00000343587.5_Missense_Mutation_p.I70V	NM_001271609.1	NP_001258538.1	O60499	STX10_HUMAN	syntaxin 10	70					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion (GO:0006906)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|kidney(1)|lung(2)|prostate(1)	6			OV - Ovarian serous cystadenocarcinoma(19;3.41e-21)			GCTTCCACTATACGTGGGCTG	0.622																																					p.I70V		Atlas-SNP	.											.	STX10	12	.	0			c.A208G						.						69	72	71					19																	13260405		2203	4300	6503	SO:0001583	missense	8677	exon3			CCACTATACGTGG	AF035531	CCDS32922.1, CCDS62569.1, CCDS62570.1, CCDS62571.1	19p13.13	2008-07-22				ENSG00000104915			11428	protein-coding gene	gene with protein product		603765				9446797	Standard	NM_003765		Approved	hsyn10, SYN10	uc021upq.2	O60499		ENST00000587230.1:c.208A>G	chr19.hg19:g.13260405T>C	ENSP00000466298:p.Ile70Val	86.0	0.0		72.0	26.0	NM_003765	A6NC41|Q6IAP4|Q96AE8	Missense_Mutation	SNP	ENST00000587230.1	hg19	CCDS32922.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.295183	0.60086	.	.	ENSG00000104915	ENST00000343587;ENST00000242770;ENST00000440593	.	.	.	3.35	3.35	0.38373	t-SNARE (1);Syntaxin 6, N-terminal (1);	0.000000	0.64402	U	0.000004	T	0.71341	0.3328	M	0.74258	2.255	0.50313	D	0.999867	P	0.44139	0.827	P	0.60789	0.879	T	0.68172	-0.5479	9	0.10377	T	0.69	.	10.3814	0.44115	0.0:0.0:0.0:1.0	.	70	O60499	STX10_HUMAN	V	70	.	ENSP00000242770:I70V	I	-	1	0	STX10	13121405	1.000000	0.71417	0.207000	0.23584	0.911000	0.54048	5.059000	0.64306	1.773000	0.52216	0.460000	0.39030	ATA	.	.		0.622	STX10-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452918.1	NM_003765		C	13260405	T	C	13260405	3	2	161	1	0	0	0	0	1	0	0	0	15351	1406	49	2	564	2	STX10	19	13260405	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	224684	13260405	45868578	85	24639										
IFI30	10437	hgsc.bcm.edu	37	chr19	18284678	18284678	+	Frame_Shift_Del	DEL	C	C	-													0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ctgtcgccacttctgctgttCctgccaccgctgctgctgct							TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr19:18284678delC	ENST00000407280.3	+	1	202	c.27delC	c.(25-27)ttcfs	p.F9fs	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	9					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)			endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						TTctgctgttcctgccaccgc	0.637																																					p.F9fs		Atlas-INDEL	.											.	IFI30	12	.	0			c.26delT						.						15	18	17					19																	18284678		2041	3945	5986	SO:0001589	frameshift_variant	10437	exon1			.	J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"gamma-interferon-inducible lysosomal thiol reductase", "interferon gamma-inducible protein 30 preproprotein"	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.27delC	chr19.hg19:g.18284678delC	ENSP00000384886:p.Phe9fs	42.0	0.0		35.0	20.0	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Frame_Shift_Del	DEL	ENST00000407280.3	hg19	CCDS46015.1																																																																																			.	.		0.637	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332		-	18284678	C	-	18284678	7	5	161	1	0	1	0	1	0	0	0	0	7524	854	30	0	29	0	IFI30	19	18284678	Frame_Shift_Del	DEL	C	TCGA-DD-AACJ-01A-11D-A40R-10	5024273	18284678	40844305	86	24640										
ZNF100	163227	hgsc.bcm.edu	37	chr19	21909720	21909720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gttgtgaggaccggttaaagGctttgccacattcgtcacat	11	9	1	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr19:21909720G>A	ENST00000358296.6	-	5	1592	c.1394C>T	c.(1393-1395)gCc>gTc	p.A465V	ZNF100_ENST00000305570.6_Missense_Mutation_p.A401V	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	465					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						CCGGTTAAAGGCTTTGCCACA	0.413																																					p.A465V		Atlas-SNP	.											.	ZNF100	62	.	0			c.C1394T						.																																			SO:0001583	missense	163227	exon5			TTAAAGGCTTTGC	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"Zinc fingers, C2H2-type", "-"	12880	protein-coding gene	gene with protein product		603982	"zinc finger protein 100 (Y1)"			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.1394C>T	chr19.hg19:g.21909720G>A	ENSP00000351042:p.Ala465Val	62.0	0.0		33.0	15.0	NM_173531	Q7M4M0	Missense_Mutation	SNP	ENST00000358296.6	hg19	CCDS42538.1	.	.	.	.	.	.	.	.	.	.	.	13.08	2.130618	0.37630	.	.	ENSG00000197020	ENST00000358296	T	0.19105	2.17	0.867	0.867	0.19085	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16085	0.0387	N	0.04508	-0.205	0.20638	N	0.999872	P;P	0.45902	0.825;0.868	P;P	0.55087	0.58;0.768	T	0.16305	-1.0407	9	0.54805	T	0.06	.	6.2611	0.20901	0.0:0.5619:0.4381:0.0	.	465;519	Q8IYN0;Q4G131	ZN100_HUMAN;.	V	465	ENSP00000351042:A465V	ENSP00000351042:A465V	A	-	2	0	ZNF100	21701560	0.000000	0.05858	0.882000	0.34594	0.881000	0.50899	-1.282000	0.02799	0.284000	0.22305	0.289000	0.19496	GCC	.	.		0.413	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531		A	21909720	G	A	21909720	3	1	161	1	0	0	0	0	1	0	0	0	17728	1203	42	3	238	3	ZNF100	19	21909720	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	3625042	21909720	37219263	87	24641										
ZNF284	342909	hgsc.bcm.edu	37	chr19	44590539	44590539	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ccatagtagatcaaatcttaAtaggcattccatggtccaca	6	10	2	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr19:44590539A>G	ENST00000421176.3	+	5	1124	c.908A>G	c.(907-909)aAt>aGt	p.N303S	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				TCAAATCTTAATAGGCATTCC	0.393																																					p.N303S		Atlas-SNP	.											.	ZNF284	38	.	0			c.A908G						.						85	88	87					19																	44590539		2144	4279	6423	SO:0001583	missense	342909	exon5			ATCTTAATAGGCA	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"Zinc fingers, C2H2-type", "-"	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.908A>G	chr19.hg19:g.44590539A>G	ENSP00000411032:p.Asn303Ser	64.0	0.0		53.0	21.0	NM_001037813	Q86WM1	Missense_Mutation	SNP	ENST00000421176.3	hg19	CCDS46099.1	.	.	.	.	.	.	.	.	.	.	A	9.259	1.042708	0.19748	.	.	ENSG00000186026	ENST00000421176	T	0.17054	2.3	2.59	-0.103	0.13609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12774	0.0310	N	0.11892	0.195	0.09310	N	1	D	0.55605	0.972	P	0.54629	0.757	T	0.21143	-1.0254	9	0.25751	T	0.34	.	4.2442	0.10663	0.5439:0.286:0.0:0.1701	.	303	Q2VY69	ZN284_HUMAN	S	303	ENSP00000411032:N303S	ENSP00000411032:N303S	N	+	2	0	ZNF284	49282379	0.000000	0.05858	0.001000	0.08648	0.601000	0.36947	-5.001000	0.00161	0.183000	0.20059	0.379000	0.24179	AAT	.	.		0.393	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813		G	44590539	A	G	44590539	3	3	161	1	0	0	0	0	1	0	0	0	17836	101	4	2	922	2	ZNF284	19	44590539	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	22680819	44590539	14538444	88	24642										
SIX5	147912	hgsc.bcm.edu	37	chr19	46271365	46271366	+	Missense_Mutation	DNP	GC	GC	AA													0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	cgccggttcttgaaccagttGctgacctgcgtgagcgacag							TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr19:46271365_46271366GC>AA	ENST00000317578.6	-	1	1118_1119	c.737_738GC>TT	c.(736-738)aGC>aTT	p.S246I	SIX5_ENST00000560168.1_Nonsense_Mutation_p.45_46QQ>H*|AC074212.6_ENST00000590076.1_RNA|AC074212.6_ENST00000591530.1_RNA|AC074212.5_ENST00000592217.2_RNA|AC074212.6_ENST00000586251.1_RNA|AC074212.6_ENST00000586498.1_RNA|AC074212.5_ENST00000559756.1_RNA	NM_175875.4	NP_787071	Q8N196	SIX5_HUMAN	SIX homeobox 5	246					lens development in camera-type eye (GO:0002088)|negative regulation of cell proliferation (GO:0008285)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)		TGAACCAGTTGCTGACCTGCGT	0.728																																					p.S246S|p.S246I		Atlas-SNP	.											.	SIX5	35	.	0			c.C738T|c.G737T						.																																			SO:0001583	missense	147912	exon1			CCAGTTGCTGACC|CAGTTGCTGACCT	L08835	CCDS12673.1	19q13.32	2011-06-20	2007-07-13			ENSG00000177045		"Homeoboxes / SINE class"	10891	protein-coding gene	gene with protein product		600963	"sine oculis homeobox (Drosophila) homolog 5", "sine oculis homeobox homolog 5 (Drosophila)"	DMAHP		8595416	Standard	NM_175875		Approved		uc002pdb.3	Q8N196		ENST00000317578.6:c.737_738delinsAA	chr19.hg19:g.46271365_46271366delinsAA	ENSP00000316842:p.Ser246Ile	53.0|55.0	0.0		35.0	13.0	NM_175875		Silent|Missense_Mutation	SNP	ENST00000317578.6	hg19	CCDS12673.1																																																																																			.	.		0.728	SIX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417341.3	NM_175875		AA	46271366	GC	AA	46271365	3	1	161	1	0	0	0	0	1	0	0	0	14365	1310	46	3	1493	3	SIX5	19	46271365	Missense_Mutation	DNP	GC	TCGA-DD-AACJ-01A-11D-A40R-10	1680826	46271365	12857618	89	24643										
ADRA1D	146	hgsc.bcm.edu	37	chr20	4202607	4202607	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gtagacacgccagagagggcGgcggcgccggcgacgacggc	19	13	0	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr20:4202607G>A	ENST00000379453.4	-	2	1398	c.1282C>T	c.(1282-1284)Cgc>Tgc	p.R428C		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	428	Poly-Arg.				adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			endometrium(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	14					Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	CAGAGAGGGCGGCGGCGCCGG	0.741																																					p.R428C		Atlas-SNP	.											.	ADRA1D	36	.	0			c.C1282T						.						3	4	3					20																	4202607		1757	3584	5341	SO:0001583	missense	146	exon2			GAGGGCGGCGGCG	U03864	CCDS13079.1	20p13	2012-08-08	2012-05-09		ENSG00000171873	ENSG00000171873		"GPCR / Class A : Adrenoceptors : alpha"	280	protein-coding gene	gene with protein product		104219	"adrenergic, alpha-1D-, receptor"			8039425	Standard	NM_000678		Approved	ADRA1R, ADRA1A, ADRA1	uc002wkr.2	P25100	OTTHUMG00000031779	ENST00000379453.4:c.1282C>T	chr20.hg19:g.4202607G>A	ENSP00000368766:p.Arg428Cys	62.0	0.0		45.0	19.0	NM_000678	Q9NPY0	Missense_Mutation	SNP	ENST00000379453.4	hg19	CCDS13079.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.882873	0.72410	.	.	ENSG00000171873	ENST00000379453	T	0.38560	1.13	4.1	4.1	0.47936	.	1.869330	0.03293	U	0.187910	T	0.63908	0.2551	M	0.68593	2.085	0.39665	D	0.970662	D	0.89917	1.0	P	0.58928	0.848	T	0.50285	-0.8846	10	0.59425	D	0.04	.	14.1472	0.65357	0.0:0.0:1.0:0.0	.	428	P25100	ADA1D_HUMAN	C	428	ENSP00000368766:R428C	ENSP00000368766:R428C	R	-	1	0	ADRA1D	4150607	0.996000	0.38824	0.967000	0.41034	0.975000	0.68041	3.156000	0.50708	1.953000	0.56701	0.585000	0.79938	CGC	.	.		0.741	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678		A	4202607	G	A	4202607	3	1	161	1	0	0	0	0	1	0	0	0	336	1116	39	1	440	1	ADRA1D	20	4202607	Missense_Mutation	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10		4202607	58822913	90	24644										
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47605200	47605200	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	aaccaaatctactaagcagaGtaaggtctaatggcaaatta	7	7	2	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr20:47605200G>A	ENST00000371917.4	+	18	2533		c.e18+1			NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)						endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			ACTAAGCAGAGTAAGGTCTAA	0.323																																					.	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.2533+1G>A						.						59	57	58					20																	47605200		2203	4298	6501	SO:0001630	splice_region_variant	10564	exon18			AGCAGAGTAAGGT	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.2533+1G>A	chr20.hg19:g.47605200G>A		211.0	0.0		178.0	62.0	NM_006420	Q5TFT9|Q9NTS1	Splice_Site	SNP	ENST00000371917.4	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.915324	0.92178	.	.	ENSG00000124198	ENST00000371917	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2982	0.98569	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARFGEF2	47038607	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.568000	0.98166	2.873000	0.98535	0.563000	0.77884	.	.	.		0.323	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420	Intron	A	47605200	G	A	47605200	5	1	161	1	0	0	0	0	0	0	1	0	853	1043	36	3	2604	3	ARFGEF2	20	47605200	Splice_Site	SNP	G	TCGA-DD-AACJ-01A-11D-A40R-10	43402593	47605200	15420320	91	24645										
KRTAP10-7	386675	hgsc.bcm.edu	37	chr21	46020913	46020913	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	ctgcaagcctgtgtactgtgTgcctgtctgcagtggggatt	14	9	1	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr21:46020913T>C	ENST00000380102.2	+	1	417	c.392T>C	c.(391-393)gTg>gCg	p.V131A	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	131	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GTGTACTGTGTGCCTGTCTGC	0.627																																					p.V126A		Atlas-SNP	.											.	KRTAP10-7	41	.	0			c.T377C						.						179	173	175					21																	46020913		2188	4300	6488	SO:0001583	missense	386675	exon2			ACTGTGTGCCTGT	AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"Keratin associated proteins"	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.392T>C	chr21.hg19:g.46020913T>C	ENSP00000369445:p.Val131Ala	96.0	0.0		70.0	27.0	NM_198689	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	hg19		.	.	.	.	.	.	.	.	.	.	N	0.006	-2.046656	0.00398	.	.	ENSG00000205441	ENST00000380102	T	0.01335	5.0	3.96	-7.91	0.01165	.	.	.	.	.	T	0.01222	0.0040	L	0.58810	1.83	0.09310	N	1	B	0.25441	0.126	B	0.19666	0.026	T	0.50642	-0.8804	9	0.09338	T	0.73	.	3.2367	0.06767	0.099:0.3258:0.3261:0.2491	.	126	P60409-2	.	A	131	ENSP00000369445:V131A	ENSP00000369445:V131A	V	+	2	0	KRTAP10-7	44845341	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-6.391000	0.00004	-1.621000	0.00791	GTG	.	.		0.627	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689		C	46020913	T	C	46020913	3	2	161	1	0	0	0	0	1	0	0	0	8523	1696	59	2	383	2	KRTAP10-7	21	46020913	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10		46020913	2108982	92	24646										
HIRA	7290	hgsc.bcm.edu	37	chr22	19373215	19373215	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gtggagagctgggcctcggtCatgatggctaggctcttgcc	16	10	2	2			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr22:19373215C>T	ENST00000263208.5	-	12	1414	c.1158G>A	c.(1156-1158)atG>atA	p.M386I	HIRA_ENST00000340170.4_Missense_Mutation_p.M386I|HIRA_ENST00000541063.1_Missense_Mutation_p.M342I|HIRA_ENST00000546308.1_Missense_Mutation_p.M342I	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	386					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					GGGCCTCGGTCATGATGGCTA	0.592																																					p.M386I		Atlas-SNP	.											.	HIRA	100	.	0			c.G1158A						.						100	80	86					22																	19373215		2203	4300	6503	SO:0001583	missense	7290	exon12			CTCGGTCATGATG	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"WD repeat domain containing"	4916	protein-coding gene	gene with protein product	"DiGeorge critical region gene 1"	600237	"HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)", "HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.1158G>A	chr22.hg19:g.19373215C>T	ENSP00000263208:p.Met386Ile	68.0	0.0		80.0	26.0	NM_003325	Q05BU9|Q8IXN2	Missense_Mutation	SNP	ENST00000263208.5	hg19	CCDS13759.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687048	0.29962	.	.	ENSG00000100084	ENST00000340170;ENST00000263208;ENST00000541063;ENST00000546308	T;T;T;T	0.70749	-0.28;-0.51;-0.35;-0.3	5.65	5.65	0.86999	.	0.095099	0.64402	D	0.000002	T	0.54532	0.1864	L	0.29908	0.895	0.80722	D	1	B;B;B	0.32467	0.052;0.372;0.031	B;B;B	0.25140	0.008;0.058;0.003	T	0.51260	-0.8728	10	0.17369	T	0.5	-32.0471	13.1248	0.59349	0.0:0.9278:0.0:0.0721	.	342;386;386	F5H4M2;P54198-2;P54198	.;.;HIRA_HUMAN	I	386;386;342;342	ENSP00000345350:M386I;ENSP00000263208:M386I;ENSP00000446073:M342I;ENSP00000441870:M342I	ENSP00000263208:M386I	M	-	3	0	HIRA	17753215	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.740000	0.47418	2.941000	0.99782	0.655000	0.94253	ATG	.	.		0.592	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		T	19373215	C	T	19373215	3	4	161	1	0	0	0	0	1	0	0	0	7129	826	29	3	1951	3	HIRA	22	19373215	Missense_Mutation	SNP	C	TCGA-DD-AACJ-01A-11D-A40R-10		19373215	31931351	93	24647										
BCR	613	hgsc.bcm.edu	37	chr22	23632562	23632562	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	gctctatgggtttctgaatgTcatcgtccactcagccactg	9	12	4	1			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr22:23632562T>C	ENST00000305877.8	+	14	3495	c.2744T>C	c.(2743-2745)gTc>gCc	p.V915A	BCR_ENST00000359540.3_Missense_Mutation_p.V915A	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	915	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)		BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	TTTCTGAATGTCATCGTCCAC	0.547			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"						OREG0026390	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V915A		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.T2744C						.						230	221	224					22																	23632562		2203	4300	6503	SO:0001583	missense	613	exon14			TGAATGTCATCGT		CCDS13806.1, CCDS13807.1	22q11	2013-01-10			ENSG00000186716	ENSG00000186716		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	1014	protein-coding gene	gene with protein product		151410		D22S11, BCR1		1657398, 18070886	Standard	NM_004327		Approved	D22S662, CML, PHL, ALL	uc002zww.3	P11274	OTTHUMG00000150655	ENST00000305877.8:c.2744T>C	chr22.hg19:g.23632562T>C	ENSP00000303507:p.Val915Ala	71.0	0.0	765	73.0	27.0	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Missense_Mutation	SNP	ENST00000305877.8	hg19	CCDS13806.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.489246	0.84962	.	.	ENSG00000186716	ENST00000305877;ENST00000359540;ENST00000334149	T;D	0.86627	0.32;-2.15	4.47	3.41	0.39046	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.063066	0.64402	N	0.000007	D	0.90631	0.7062	M	0.67953	2.075	0.80722	D	1	D;D;D	0.60575	0.976;0.966;0.988	D;P;D	0.67382	0.913;0.872;0.951	D	0.88532	0.3103	10	0.39692	T	0.17	.	9.9686	0.41741	0.0:0.0838:0.0:0.9162	.	504;915;915	B4E065;P11274-2;P11274	.;.;BCR_HUMAN	A	915;915;580	ENSP00000303507:V915A;ENSP00000352535:V915A	ENSP00000303507:V915A	V	+	2	0	BCR	21962562	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.057000	0.71119	0.777000	0.33496	0.529000	0.55759	GTC	.	.		0.547	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		C	23632562	T	C	23632562	3	2	161	1	0	0	0	0	1	0	0	0	1388	1667	58	2	2798	2	BCR	22	23632562	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10	4259347	23632562	27672004	94	24648										
SREBF2	6721	hgsc.bcm.edu	37	chr22	42269979	42269979	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	atcgctcctccatcaatgacAaaatcatcgaattgaaagac	5	11	2	3			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chr22:42269979A>G	ENST00000361204.4	+	5	1211	c.1045A>G	c.(1045-1047)Aaa>Gaa	p.K349E		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	349	Interaction with LMNA. {ECO:0000250}.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						CATCAATGACAAAATCATCGA	0.483																																					p.K349E		Atlas-SNP	.											.	SREBF2	99	.	0			c.A1045G						.						89	76	80					22																	42269979		2203	4300	6503	SO:0001583	missense	6721	exon5			AATGACAAAATCA	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"Basic helix-loop-helix proteins"	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.1045A>G	chr22.hg19:g.42269979A>G	ENSP00000354476:p.Lys349Glu	196.0	0.0		220.0	52.0	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	hg19	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	A	35	5.449729	0.96205	.	.	ENSG00000198911	ENST00000361204;ENST00000444813;ENST00000457567	D	0.98075	-4.7	6.17	6.17	0.99709	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.98520	0.9506	M	0.72576	2.205	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.99744	1.1016	10	0.72032	D	0.01	-13.3427	16.8222	0.85835	1.0:0.0:0.0:0.0	.	349	Q12772	SRBP2_HUMAN	E	349	ENSP00000354476:K349E	ENSP00000354476:K349E	K	+	1	0	SREBF2	40599925	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.329000	0.96413	2.371000	0.80710	0.533000	0.62120	AAA	.	.		0.483	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		G	42269979	A	G	42269979	3	3	161	1	0	0	0	0	1	0	0	0	15157	131	5	2	1063	2	SREBF2	22	42269979	Missense_Mutation	SNP	A	TCGA-DD-AACJ-01A-11D-A40R-10	18637417	42269979	9034587	95	24649										
CHIC1	53344	hgsc.bcm.edu	37	chrX	72783217	72783217	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0729166666666667	7	1	1.10891089108911	2.51202263083451	0.781518151815181	1	1	0	caacgtcgtcgtcgtcgccgTcgtcgtcgtcgtcggtatct	12	14	1	0			TCGA-DD-AACJ-01A-11D-A40R-10	TCGA-DD-AACJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23475083-0f7f-4acb-a446-f65a896c9c60	a29286c8-285a-4358-9bcc-357f531707af	g.chrX:72783217T>C	ENST00000373502.5	+	1	174	c.97T>C	c.(97-99)Tcg>Ccg	p.S33P	MAP2K4P1_ENST00000602584.1_RNA|CHIC1_ENST00000373504.6_Missense_Mutation_p.S33P	NM_001039840.2	NP_001034929.2	Q5VXU3	CHIC1_HUMAN	cysteine-rich hydrophobic domain 1	33	Ser-rich.					cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(2)	4	Renal(35;0.156)					gtcgtcgccgtcgtcgtcgtc	0.602																																					p.S33P		Atlas-SNP	.											.	CHIC1	13	.	0			c.T97C						.						25	13	17					X																	72783217		2126	4135	6261	SO:0001583	missense	53344	exon1			TCGCCGTCGTCGT	Y11897	CCDS35335.2, CCDS75993.1	Xq13.2	2008-05-14			ENSG00000204116	ENSG00000204116			1934	protein-coding gene	gene with protein product		300922				9321471, 11257495	Standard	NM_001039840		Approved	BRX	uc004ebk.4	Q5VXU3	OTTHUMG00000021835	ENST00000373502.5:c.97T>C	chrX.hg19:g.72783217T>C	ENSP00000362601:p.Ser33Pro	104.0	0.0		98.0	4.0	NM_001039840	A0PJZ2|B0QZ87|B9EGS5|Q5CZ84	Missense_Mutation	SNP	ENST00000373502.5	hg19	CCDS35335.2	.	.	.	.	.	.	.	.	.	.	T	15.34	2.804045	0.50315	.	.	ENSG00000204116	ENST00000373502;ENST00000373504	.	.	.	4.12	-3.13	0.05266	.	0.853808	0.09342	N	0.815269	T	0.15435	0.0372	N	0.08118	0	0.23314	N	0.997926	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.20940	-1.0260	9	0.40728	T	0.16	-5.6818	5.0909	0.14708	0.1852:0.5222:0.0:0.2927	.	33;33;33	B7Z3I1;Q5VXU3-2;Q5VXU3	.;.;CHIC1_HUMAN	P	33	.	ENSP00000362601:S33P	S	+	1	0	CHIC1	72699942	1.000000	0.71417	0.954000	0.39281	0.919000	0.55068	0.811000	0.27198	-0.283000	0.09115	0.345000	0.21793	TCG	.	.		0.602	CHIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057233.3			C	72783217	T	C	72783217	3	2	161	1	0	0	0	0	1	0	0	0	3345	1667	58	2	99	2	CHIC1	23	72783217	Missense_Mutation	SNP	T	TCGA-DD-AACJ-01A-11D-A40R-10		72783217	82487343	96	24650										
CCNL2	81669	hgsc.bcm.edu	37	chr1	1334013	1334013	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	acgaaggacttggtataaaaGaaccgctggaacaacacctg	10	9	0	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:1334013G>A	ENST00000400809.3	-	2	332	c.327C>T	c.(325-327)ttC>ttT	p.F109F	CCNL2_ENST00000408918.4_Silent_p.F109F|RP4-758J18.2_ENST00000448629.2_5'Flank|RP4-758J18.2_ENST00000576232.1_5'Flank|RP4-758J18.2_ENST00000444362.1_5'Flank|CCNL2_ENST00000408952.5_5'Flank	NM_030937.4	NP_112199.2	Q96S94	CCNL2_HUMAN	cyclin L2	109	Cyclin-like 1.				regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		TGGTATAAAAGAACCGCTGGA	0.488																																					p.F109F		Atlas-SNP	.											CCNL2_ENST00000408918,NS,carcinoma,0,2	CCNL2	54	.	0			c.C327T						.						107	112	111					1																	1334013		2203	4297	6500	SO:0001819	synonymous_variant	81669	exon2			ATAAAAGAACCGC	AF251294	CCDS30557.1, CCDS30558.1	1p36.33	2014-07-03			ENSG00000221978	ENSG00000221978			20570	protein-coding gene	gene with protein product	"cyclin S"	613482	"cyclin M"	CCNM		14725631	Standard	NM_030937		Approved	ania-6b, PCEE, SB138, HLA-ISO, CCNS	uc001afi.2	Q96S94	OTTHUMG00000002917	ENST00000400809.3:c.327C>T	chr1.hg19:g.1334013G>A		214.0	2.0		146.0	83.0	NM_030937	A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00	Silent	SNP	ENST00000400809.3	hg19	CCDS30557.1																																																																																			.	.		0.488	CCNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008146.2	NM_030937		A	1334013	G	A	1334013	2	1	162	1	0	0	0	0	0	0	0	1	2934	933	33	3		3	CCNL2	1	1334013	Silent	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10		1334013	247916608	1	24651										
SPEN	23013	hgsc.bcm.edu	37	chr1	16255901	16255901	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ctaaaaaaatcaaactggacAgacttaatactgttgccagc	6	9	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:16255901A>T	ENST00000375759.3	+	11	3370	c.3166A>T	c.(3166-3168)Aga>Tga	p.R1056*		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1056					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CAAACTGGACAGACTTAATAC	0.468																																					p.R1056X		Atlas-SNP	.											.	SPEN	374	.	0			c.A3166T						.						53	58	56					1																	16255901		2203	4300	6503	SO:0001587	stop_gained	23013	exon11			CTGGACAGACTTA		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.3166A>T	chr1.hg19:g.16255901A>T	ENSP00000364912:p.Arg1056*	190.0	0.0		182.0	69.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Nonsense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	41	8.983736	0.99025	.	.	ENSG00000065526	ENST00000375759	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.4715	15.7759	0.78214	1.0:0.0:0.0:0.0	.	.	.	.	X	1056	.	ENSP00000364912:R1056X	R	+	1	2	SPEN	16128488	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.977000	0.56874	2.308000	0.77769	0.533000	0.62120	AGA	.	.		0.468	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16255901	A	T	16255901	4	4	162	1	0	0	0	0	0	1	0	0	15053	180	7	4	3208	4	SPEN	1	16255901	Nonsense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	14921888	16255901	232994720	2	24652										
UBR4	23352	hgsc.bcm.edu	37	chr1	19464665	19464665	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gcatcgccataagcactgctCcggccagatactagagggaa	11	12	0	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:19464665C>A	ENST00000375254.3	-	60	8769	c.8742G>T	c.(8740-8742)cgG>cgT	p.R2914R	UBR4_ENST00000375226.2_Silent_p.R2890R|UBR4_ENST00000375267.2_Silent_p.R2914R|UBR4_ENST00000375217.2_Silent_p.R2907R	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2914					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AAGCACTGCTCCGGCCAGATA	0.522																																					p.R2914R		Atlas-SNP	.											.	UBR4	415	.	0			c.G8742T						.						58	56	57					1																	19464665		2203	4300	6503	SO:0001819	synonymous_variant	23352	exon60			ACTGCTCCGGCCA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.8742G>T	chr1.hg19:g.19464665C>A		33.0	0.0		49.0	23.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.		0.522	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19464665	C	A	19464665	2	1	162	1	0	0	0	0	0	0	0	1	16919	842	30	3		3	UBR4	1	19464665	Silent	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	3208764	19464665	229785956	3	24653										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22201403	22201403	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cctggcaggacggcccacggTacccgggtgggcaggagcac	17	14	0	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:22201403T>A	ENST00000374695.3	-	26	3474	c.3395A>T	c.(3394-3396)tAc>tTc	p.Y1132F		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1132	Laminin EGF-like 5; second part. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CGGCCCACGGTACCCGGGTGG	0.692																																					p.Y1132F		Atlas-SNP	.											.	HSPG2	311	.	0			c.A3395T						.						34	32	33					1																	22201403		2200	4299	6499	SO:0001583	missense	3339	exon26			CCACGGTACCCGG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.3395A>T	chr1.hg19:g.22201403T>A	ENSP00000363827:p.Tyr1132Phe	164.0	0.0		153.0	60.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	T	19.34	3.808435	0.70797	.	.	ENSG00000142798	ENST00000374695	T	0.61510	0.1	5.27	4.12	0.48240	EGF-like, laminin (2);EGF-like region, conserved site (2);	0.218239	0.23282	N	0.049895	T	0.76849	0.4045	M	0.86864	2.845	0.49915	D	0.999833	D	0.63046	0.992	D	0.76071	0.987	T	0.78473	-0.2190	10	0.72032	D	0.01	.	10.5147	0.44883	0.0:0.0:0.1631:0.8369	.	1132	P98160	PGBM_HUMAN	F	1132	ENSP00000363827:Y1132F	ENSP00000363827:Y1132F	Y	-	2	0	HSPG2	22073990	1.000000	0.71417	1.000000	0.80357	0.532000	0.34746	4.939000	0.63526	0.818000	0.34468	0.418000	0.28097	TAC	.	.		0.692	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22201403	T	A	22201403	3	1	162	1	0	0	0	0	1	0	0	0	7439	1638	57	4	10068	4	HSPG2	1	22201403	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	2736738	22201403	227049218	4	24654										
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35452801	35452801	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cccaacagatttttttgtttTgactcagtcaaagctgaaaa	6	8	2	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:35452801T>A	ENST00000357182.4	-	16	4109	c.3882A>T	c.(3880-3882)tcA>tcT	p.S1294S	ZMYM6_ENST00000373340.2_Intron|ZMYM6_ENST00000493328.1_5'UTR|ZMYM6_ENST00000487874.1_Intron|ZMYM6NB_ENST00000373337.3_5'Flank|RP11-244H3.1_ENST00000417456.1_RNA	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	1294					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				TTTTTTGTTTTGACTCAGTCA	0.373																																					p.S1294S		Atlas-SNP	.											.	ZMYM6	110	.	0			c.A3882T						.						70	66	67					1																	35452801		1822	4077	5899	SO:0001819	synonymous_variant	9204	exon16			TTGTTTTGACTCA	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"Zinc fingers, MYM type", "Zinc fingers, BED-type"	13050	protein-coding gene	gene with protein product	"zinc finger, BED-type containing 7"	613567	"zinc finger protein 258", "zinc finger, MYM-type containing 6"	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.3882A>T	chr1.hg19:g.35452801T>A		50.0	0.0		50.0	11.0	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Silent	SNP	ENST00000357182.4	hg19	CCDS387.2																																																																																			.	.		0.373	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		A	35452801	T	A	35452801	2	1	162	1	0	0	0	0	0	0	0	1	17719	1799	63	4		4	ZMYM6	1	35452801	Silent	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	13251398	35452801	213797820	5	24655										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35851192	35851192	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gttaaaatggttacttctgcAggtaatattggtttcacaaa	8	5	2	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:35851192A>T	ENST00000314607.6	+	10	1799	c.1719A>T	c.(1717-1719)gcA>gcT	p.A573A	ZMYM4_ENST00000373297.2_Intron	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	573					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTACTTCTGCAGGTAATATTG	0.323																																					p.A573A		Atlas-SNP	.											.	ZMYM4	143	.	0			c.A1719T						.						54	54	54					1																	35851192		2202	4300	6502	SO:0001630	splice_region_variant	9202	exon10			TTCTGCAGGTAAT	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.1720+1A>T	chr1.hg19:g.35851192A>T		67.0	0.0		73.0	29.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Silent	SNP	ENST00000314607.6	hg19	CCDS389.1																																																																																			.	.		0.323	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095	Silent	T	35851192	A	T	35851192	5	4	162	1	0	0	0	0	0	0	1	0	17717	202	7	4	1757	4	ZMYM4	1	35851192	Splice_Site	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	398391	35851192	213399429	6	24656										
CYP4B1	1580	hgsc.bcm.edu	37	chr1	47278193	47278193	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ggcctgctggttcttgagggGcccaagtggttgcagcaccg	16	11	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:47278193G>T	ENST00000271153.4	+	4	429	c.393G>T	c.(391-393)ggG>ggT	p.G131G	CYP4B1_ENST00000371919.4_Silent_p.G116G|CYP4B1_ENST00000452782.2_5'UTR|CYP4B1_ENST00000371923.4_Silent_p.G131G			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	131					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	TTCTTGAGGGGCCCAAGTGGT	0.587																																					p.G131G		Atlas-SNP	.											.	CYP4B1	81	.	0			c.G393T						.						106	83	91					1																	47278193		2203	4300	6503	SO:0001819	synonymous_variant	1580	exon4			TGAGGGGCCCAAG	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"Cytochrome P450s"	2644	protein-coding gene	gene with protein product		124075	"cytochrome P450, subfamily IVB, polypeptide 1"				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.393G>T	chr1.hg19:g.47278193G>T		94.0	0.0		80.0	30.0	NM_000779	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Silent	SNP	ENST00000271153.4	hg19	CCDS542.1																																																																																			.	.		0.587	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779		T	47278193	G	T	47278193	2	4	162	1	0	0	0	0	0	0	0	1	4187	1190	42	3		3	CYP4B1	1	47278193	Silent	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	11427001	47278193	201972428	7	24657										
AGBL4	84871	hgsc.bcm.edu	37	chr1	50317108	50317108	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	aagataagatgtcctttcttGggctgtccacaatagccagt	9	9	1	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:50317108G>C	ENST00000371839.1	-	2	233	c.117C>G	c.(115-117)ccC>ccG	p.P39P	AGBL4_ENST00000497451.1_5'UTR|AGBL4_ENST00000371836.1_Silent_p.P39P|AGBL4_ENST00000371838.1_Silent_p.P39P	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	39					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		GTCCTTTCTTGGGCTGTCCAC	0.353																																					p.P39P		Atlas-SNP	.											.	AGBL4	54	.	0			c.C117G						.						151	130	136					1																	50317108		692	1591	2283	SO:0001819	synonymous_variant	84871	exon2			TTTCTTGGGCTGT	AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 6"					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.117C>G	chr1.hg19:g.50317108G>C		215.0	0.0		212.0	74.0	NM_032785	B3KT26|B4DG37	Silent	SNP	ENST00000371839.1	hg19	CCDS44137.1																																																																																			.	.		0.353	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785		C	50317108	G	C	50317108	2	2	162	1	0	0	0	0	0	0	0	1	377	1335	47	4		4	AGBL4	1	50317108	Silent	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	3038915	50317108	198933513	8	24658										
FOXD3	27022	hgsc.bcm.edu	37	chr1	63789824	63789824	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ggcgccgcgggcaccaccgcGtcgctcatcaagtccgagcc	13	18	2	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:63789824G>A	ENST00000371116.2	+	1	1095	c.1095G>A	c.(1093-1095)gcG>gcA	p.A365A	RP4-792G4.2_ENST00000431294.1_RNA|RP4-792G4.2_ENST00000449386.1_RNA|RP4-792G4.2_ENST00000426393.1_RNA|RP4-792G4.2_ENST00000427268.1_RNA|RP4-792G4.2_ENST00000418244.1_RNA	NM_012183.2	NP_036315.1	Q9UJU5	FOXD3_HUMAN	forkhead box D3	365					embryonic placenta development (GO:0001892)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|trophectodermal cell differentiation (GO:0001829)	nuclear chromatin (GO:0000790)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|lung(2)|upper_aerodigestive_tract(1)	5						gcACCACCGCGTCGCTCATCA	0.746																																					p.A365A	Pancreas(68;276 1750 11966 31252)	Atlas-SNP	.											.	FOXD3	15	.	0			c.G1095A						.						1	1	1					1																	63789824		858	1831	2689	SO:0001819	synonymous_variant	27022	exon1			CACCGCGTCGCTC	AF197560	CCDS624.1	1p31.3	2008-04-10			ENSG00000187140	ENSG00000187140		"Forkhead boxes"	3804	protein-coding gene	gene with protein product		611539				8499623	Standard	NM_012183		Approved	Genesis, HFH2	uc001dax.2	Q9UJU5	OTTHUMG00000009141	ENST00000371116.2:c.1095G>A	chr1.hg19:g.63789824G>A		19.0	0.0		12.0	6.0	NM_012183	Q9BYM2|Q9UDD1	Silent	SNP	ENST00000371116.2	hg19	CCDS624.1																																																																																			.	.		0.746	FOXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025331.1			A	63789824	G	A	63789824	2	1	162	1	0	0	0	0	0	0	0	1	6006	1132	40	1		1	FOXD3	1	63789824	Silent	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	13472716	63789824	185460797	9	24659										
SLC44A5	204962	hgsc.bcm.edu	37	chr1	75672389	75672389	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tttctgtagatccatcatttCtttccagatcttcacctgta	4	11	5	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:75672389C>G	ENST00000370855.5	-	24	2176	c.2063G>C	c.(2062-2064)aGa>aCa	p.R688T	SLC44A5_ENST00000370859.3_Intron|SLC44A5_ENST00000535611.1_Missense_Mutation_p.R558T	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	688				R -> I (in Ref. 1; BAC03655). {ECO:0000305}.	glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						TCCATCATTTCTTTCCAGATC	0.418																																					p.R688T		Atlas-SNP	.											SLC44A5,NS,carcinoma,0,1	SLC44A5	231	.	0			c.G2063C						.						148	142	144					1																	75672389		2203	4300	6503	SO:0001583	missense	204962	exon24			TCATTTCTTTCCA	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.2063G>C	chr1.hg19:g.75672389C>G	ENSP00000359892:p.Arg688Thr	57.0	0.0		39.0	18.0	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Missense_Mutation	SNP	ENST00000370855.5	hg19	CCDS667.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.261379	0.80246	.	.	ENSG00000137968	ENST00000370855;ENST00000535611;ENST00000535790	T;T	0.24908	1.83;1.83	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.38026	0.1025	M	0.63208	1.945	0.80722	D	1	D;D	0.62365	0.991;0.991	D;D	0.74674	0.984;0.978	T	0.03945	-1.0990	10	0.19147	T	0.46	-10.5251	19.0095	0.92867	0.0:1.0:0.0:0.0	.	682;688	B7Z5Y4;Q8NCS7	.;CTL5_HUMAN	T	688;558;681	ENSP00000359892:R688T;ENSP00000443090:R558T	ENSP00000359892:R688T	R	-	2	0	SLC44A5	75444977	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	5.778000	0.68940	2.501000	0.84356	0.591000	0.81541	AGA	.	.		0.418	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		G	75672389	C	G	75672389	3	3	162	1	0	0	0	0	1	0	0	0	14654	913	32	4	211	4	SLC44A5	1	75672389	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	11882565	75672389	173578232	10	24660										
ODF2L	57489	hgsc.bcm.edu	37	chr1	86822189	86822189	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cttccccttgcagcactgcaGactctcctgacactcgtgaa	7	16	1	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:86822189G>T	ENST00000359242.3	-	14	1737	c.1456C>A	c.(1456-1458)Ctg>Atg	p.L486M	ODF2L_ENST00000394731.1_Missense_Mutation_p.L326M|ODF2L_ENST00000370566.3_Intron|ODF2L_ENST00000524695.1_5'UTR|ODF2L_ENST00000317336.7_Missense_Mutation_p.L486M|ODF2L_ENST00000370567.1_Missense_Mutation_p.L457M|ODF2L_ENST00000294678.2_Missense_Mutation_p.L457M	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	486						centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		CAGCACTGCAGACTCTCCTGA	0.557																																					p.L486M		Atlas-SNP	.											.	ODF2L	53	.	0			c.C1456A						.						91	84	87					1																	86822189		2203	4300	6503	SO:0001583	missense	57489	exon14			ACTGCAGACTCTC		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.1456C>A	chr1.hg19:g.86822189G>T	ENSP00000359600:p.Leu486Met	41.0	0.0		70.0	25.0	NM_001007022	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Missense_Mutation	SNP	ENST00000359242.3	hg19	CCDS41354.2	.	.	.	.	.	.	.	.	.	.	G	16.40	3.112763	0.56398	.	.	ENSG00000122417	ENST00000359242;ENST00000460698;ENST00000317336;ENST00000370567;ENST00000394731;ENST00000294678	T;D;T;T;T;T	0.83673	1.37;-1.75;1.4;1.45;1.47;-1.37	6.16	3.19	0.36642	.	0.145714	0.46758	D	0.000271	T	0.79411	0.4441	L	0.53249	1.67	0.21105	N	0.99978	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.992;0.992;0.995	T	0.69997	-0.4993	10	0.33940	T	0.23	0.114	6.9813	0.24704	0.1572:0.1394:0.7034:0.0	.	457;457;486	Q9ULJ1-4;Q9ULJ1-3;Q9ULJ1	.;.;ODF2L_HUMAN	M	486;333;486;457;326;457	ENSP00000359600:L486M;ENSP00000433092:L333M;ENSP00000320165:L486M;ENSP00000359598:L457M;ENSP00000378219:L326M;ENSP00000294678:L457M	ENSP00000294678:L457M	L	-	1	2	ODF2L	86594777	0.939000	0.31865	0.552000	0.28243	0.716000	0.41182	1.412000	0.34714	0.423000	0.26033	-0.355000	0.07637	CTG	.	.		0.557	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			T	86822189	G	T	86822189	3	4	162	1	0	0	0	0	1	0	0	0	10837	933	33	3	650	3	ODF2L	1	86822189	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	11149800	86822189	162428432	11	24661										
GBP2	2634	hgsc.bcm.edu	37	chr1	89587483	89587483	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ttttcttcccagccagcttgTtcatcaggtaggatttgcct	8	11	3	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:89587483T>C	ENST00000370466.3	-	2	435	c.167A>G	c.(166-168)aAc>aGc	p.N56S	GBP2_ENST00000463660.1_5'Flank	NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN	guanylate binding protein 2, interferon-inducible	56	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		AGCCAGCTTGTTCATCAGGTA	0.522																																					p.N56S		Atlas-SNP	.											.	GBP2	58	.	0			c.A167G						.						192	155	167					1																	89587483		2203	4300	6503	SO:0001583	missense	2634	exon2			AGCTTGTTCATCA	BC073163	CCDS719.1	1p22.2	2008-02-05			ENSG00000162645	ENSG00000162645			4183	protein-coding gene	gene with protein product		600412				1715024	Standard	NM_004120		Approved		uc001dmz.1	P32456	OTTHUMG00000010662	ENST00000370466.3:c.167A>G	chr1.hg19:g.89587483T>C	ENSP00000359497:p.Asn56Ser	118.0	0.0		93.0	32.0	NM_004120	Q6GPH0|Q6IAU2|Q86TB0	Missense_Mutation	SNP	ENST00000370466.3	hg19	CCDS719.1	.	.	.	.	.	.	.	.	.	.	T	18.93	3.726831	0.69074	.	.	ENSG00000162645	ENST00000370466	T	0.79141	-1.24	3.43	3.43	0.39272	Guanylate-binding protein, N-terminal (1);	0.000000	0.64402	U	0.000003	T	0.80352	0.4607	M	0.85462	2.755	0.30948	N	0.725035	D	0.62365	0.991	P	0.57204	0.815	T	0.78046	-0.2357	10	0.87932	D	0	-20.762	10.1493	0.42782	0.0:0.0:0.0:1.0	.	56	P32456	GBP2_HUMAN	S	56	ENSP00000359497:N56S	ENSP00000359497:N56S	N	-	2	0	GBP2	89360071	1.000000	0.71417	0.818000	0.32626	0.871000	0.50021	5.343000	0.65976	1.542000	0.49330	0.402000	0.26972	AAC	.	.		0.522	GBP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029406.2	NM_004120		C	89587483	T	C	89587483	3	2	162	1	0	0	0	0	1	0	0	0	6282	1725	60	2	1648	2	GBP2	1	89587483	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	2765294	89587483	159663138	12	24662										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117120047	117120047	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	caccccattcttcccatcagAgttcttgctggagttccggc	8	15	3	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:117120047A>T	ENST00000369486.3	-	11	4237	c.3472T>A	c.(3472-3474)Tct>Act	p.S1158T	IGSF3_ENST00000369483.1_Missense_Mutation_p.S1178T|IGSF3_ENST00000318837.6_Missense_Mutation_p.S1178T	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1158					lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		TTCCCATCAGAGTTCTTGCTG	0.512																																					p.S1178T		Atlas-SNP	.											.	IGSF3	294	.	0			c.T3532A						.						122	120	121					1																	117120047		2203	4300	6503	SO:0001583	missense	3321	exon12			CATCAGAGTTCTT	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3472T>A	chr1.hg19:g.117120047A>T	ENSP00000358498:p.Ser1158Thr	172.0	0.0		160.0	67.0	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	A	17.13	3.310239	0.60414	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.03242	4.0;4.0;4.0	4.89	3.74	0.42951	.	0.157530	0.45606	D	0.000357	T	0.01695	0.0054	N	0.14661	0.345	0.30459	N	0.774477	D;D	0.57257	0.979;0.979	P;P	0.51777	0.679;0.679	T	0.46693	-0.9173	10	0.62326	D	0.03	-15.2187	9.0676	0.36473	0.6359:0.3641:0.0:0.0	.	1158;1178	O75054;A6NJZ6	IGSF3_HUMAN;.	T	1158;1178;1178	ENSP00000358498:S1158T;ENSP00000358495:S1178T;ENSP00000321184:S1178T	ENSP00000321184:S1178T	S	-	1	0	IGSF3	116921570	1.000000	0.71417	0.979000	0.43373	0.854000	0.48673	6.432000	0.73400	0.861000	0.35504	0.533000	0.62120	TCT	.	.		0.512	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		T	117120047	A	T	117120047	3	4	162	1	0	0	0	0	1	0	0	0	7610	304	11	4	116	4	IGSF3	1	117120047	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	27532564	117120047	132130574	13	24663										
ISG20L2	81875	hgsc.bcm.edu	37	chr1	156696883	156696883	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	atgcccctttggtcctgtgcCcaccatctcacagtcaattg	7	15	2	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:156696883C>T	ENST00000313146.6	-	1	1344	c.562G>A	c.(562-564)Ggc>Agc	p.G188S	RRNAD1_ENST00000368218.4_5'Flank|RRNAD1_ENST00000368216.4_5'Flank|RRNAD1_ENST00000524343.1_5'Flank|ISG20L2_ENST00000368219.1_Missense_Mutation_p.G188S|ISG20L2_ENST00000472824.2_5'Flank	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene 20kDa-like 2	188	Exonuclease.				ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGTCCTGTGCCCACCATCTCA	0.512											OREG0013885	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G188S		Atlas-SNP	.											.	ISG20L2	43	.	0			c.G562A						.						184	146	159					1																	156696883		2203	4300	6503	SO:0001583	missense	81875	exon1			CTGTGCCCACCAT	AK095697	CCDS1153.1	1q23.1	2013-10-11			ENSG00000143319	ENSG00000143319			25745	protein-coding gene	gene with protein product		611930				18065403	Standard	NM_030980		Approved	FLJ12671	uc001fps.1	Q9H9L3	OTTHUMG00000041301	ENST00000313146.6:c.562G>A	chr1.hg19:g.156696883C>T	ENSP00000323424:p.Gly188Ser	151.0	0.0	1780	154.0	61.0	NM_030980	D3DVC6|Q64KA2	Missense_Mutation	SNP	ENST00000313146.6	hg19	CCDS1153.1	.	.	.	.	.	.	.	.	.	.	C	36	5.756261	0.96898	.	.	ENSG00000143319	ENST00000313146;ENST00000368219	T;T	0.48836	0.8;0.8	5.17	5.17	0.71159	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.65407	0.2688	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68337	-0.5435	10	0.66056	D	0.02	.	17.4015	0.87461	0.0:1.0:0.0:0.0	.	188	Q9H9L3	I20L2_HUMAN	S	188	ENSP00000323424:G188S;ENSP00000357202:G188S	ENSP00000323424:G188S	G	-	1	0	ISG20L2	154963507	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.431000	0.80335	2.692000	0.91855	0.655000	0.94253	GGC	.	.		0.512	ISG20L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098969.1	NM_030980		T	156696883	C	T	156696883	3	4	162	1	0	0	0	0	1	0	0	0	7864	623	22	3	511	3	ISG20L2	1	156696883	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	39576836	156696883	92553738	14	24664										
F11R	50848	hgsc.bcm.edu	37	chr1	160970507	160970507	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgtatgtcccagtgtcttccCgtgtcacggacttgaaggtg	12	10	2	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:160970507C>G	ENST00000368026.6	-	4	576	c.302G>C	c.(301-303)cGg>cCg	p.R101P	F11R_ENST00000537746.1_Intron|F11R_ENST00000289779.3_3'UTR|F11R_ENST00000472573.1_5'UTR	NM_016946.4	NP_058642.1	Q9Y624	JAM1_HUMAN	F11 receptor	101	Ig-like V-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)	12	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)			AGTGTCTTCCCGTGTCACGGA	0.542																																					p.R101P		Atlas-SNP	.											.	F11R	29	.	0			c.G302C						.						181	126	144					1																	160970507		2203	4300	6503	SO:0001583	missense	50848	exon4			TCTTCCCGTGTCA	AF111713	CCDS1213.1	1q21.2-q21.3	2013-01-29	2003-02-07	2003-02-14	ENSG00000158769	ENSG00000158769		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14685	protein-coding gene	gene with protein product		605721	"junctional adhesion molecule 1"	JAM1		10395639, 7646439	Standard	NM_016946		Approved	PAM-1, JCAM, JAM-1, JAM-A, JAMA, CD321	uc009wtt.3	Q9Y624	OTTHUMG00000028602	ENST00000368026.6:c.302G>C	chr1.hg19:g.160970507C>G	ENSP00000357005:p.Arg101Pro	82.0	0.0		107.0	35.0	NM_016946	B7Z941	Missense_Mutation	SNP	ENST00000368026.6	hg19	CCDS1213.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156836	0.57259	.	.	ENSG00000158769	ENST00000368026;ENST00000335772;ENST00000289779;ENST00000436182	T;T	0.64260	-0.09;-0.09	5.36	5.36	0.76844	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.133822	0.51477	N	0.000096	T	0.70988	0.3287	M	0.62154	1.92	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.993;0.998;0.998;0.997	T	0.68610	-0.5363	10	0.35671	T	0.21	.	16.5755	0.84635	0.0:1.0:0.0:0.0	.	105;101;101;101	B7Z5W1;Q6FIB4;Q9Y624;D3DVF0	.;.;JAM1_HUMAN;.	P	101;101;101;105	ENSP00000357005:R101P;ENSP00000394809:R105P	ENSP00000289779:R101P	R	-	2	0	F11R	159237131	1.000000	0.71417	0.992000	0.48379	0.016000	0.09150	2.701000	0.47094	2.495000	0.84180	0.563000	0.77884	CGG	.	.		0.542	F11R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071458.3	NM_016946		G	160970507	C	G	160970507	3	3	162	1	0	0	0	0	1	0	0	0	5340	652	23	4	625	4	F11R	1	160970507	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	4273624	160970507	88280114	15	24665										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181725136	181725136	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	aaacaagatggaggtgaaggGccgggaatggaagcgccatg	17	6	0	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:181725136G>T	ENST00000367573.2	+	29	4034	c.4034G>T	c.(4033-4035)gGc>gTc	p.G1345V	CACNA1E_ENST00000357570.5_Missense_Mutation_p.G1296V|CACNA1E_ENST00000526775.1_Missense_Mutation_p.G1326V|CACNA1E_ENST00000358338.5_Missense_Mutation_p.G1277V|CACNA1E_ENST00000360108.3_Missense_Mutation_p.G1326V|CACNA1E_ENST00000367570.1_Missense_Mutation_p.G1345V|CACNA1E_ENST00000367567.4_Missense_Mutation_p.G952V	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1345					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.G1345V(2)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GAGGTGAAGGGCCGGGAATGG	0.493																																					p.G1345V		Atlas-SNP	.											CACNA1E_ENST00000367573,NS,carcinoma,0,2	CACNA1E	778	.	2	Substitution - Missense(2)	lung(2)	c.G4034T						.						88	89	89					1																	181725136		1960	4154	6114	SO:0001583	missense	777	exon29			TGAAGGGCCGGGA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.4034G>T	chr1.hg19:g.181725136G>T	ENSP00000356545:p.Gly1345Val	155.0	0.0		137.0	46.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	16.29	3.082052	0.55861	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98649	-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05	5.6	5.6	0.85130	Ion transport (1);	0.212776	0.51477	D	0.000090	D	0.97201	0.9085	L	0.42245	1.32	0.58432	D	0.999994	B;B;B	0.31548	0.008;0.155;0.328	B;B;B	0.33521	0.059;0.158;0.165	D	0.96001	0.8993	10	0.34782	T	0.22	.	19.5773	0.95450	0.0:0.0:1.0:0.0	.	1326;1345;1345	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	V	1345;1326;1296;1277;952;1326;1345	ENSP00000356542:G1345V;ENSP00000434814:G1326V;ENSP00000350183:G1296V;ENSP00000351101:G1277V;ENSP00000356539:G952V;ENSP00000353222:G1326V;ENSP00000356545:G1345V	ENSP00000350183:G1296V	G	+	2	0	CACNA1E	179991759	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.835000	0.48175	2.788000	0.95919	0.650000	0.86243	GGC	.	.		0.493	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181725136	G	T	181725136	3	4	162	1	0	0	0	0	1	0	0	0	2544	1203	42	3	4148	3	CACNA1E	1	181725136	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	20754629	181725136	67525485	16	24666										
CDK18	5129	hgsc.bcm.edu	37	chr1	205497176	205497219	+	Splice_Site	DEL	GACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAAT	GACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAAT	-													0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	agtgacatgtctgcccccagGactggccagggccaagtcag					rs201373119|rs150420895	byFrequency	TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	GACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAAT	GACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr1:205497176_205497219delGACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAAT	ENST00000360066.2	+	10	1155_1198	c.854_897delGACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAAT	c.(853-897)ggactggccagggccaagtcagtgcccacaaagacttactccaat>g	p.GLARAKSVPTKTYSN285fs	CDK18_ENST00000509056.1_3'UTR|CDK18_ENST00000506784.1_Splice_Site_p.GLARAKSVPTKTYSN315fs|CDK18_ENST00000429964.2_Splice_Site_p.GLARAKSVPTKTYSN285fs	NM_002596.3|NM_212502.2|NM_212503.2	NP_002587.2|NP_997667.1|NP_997668.1	Q07002	CDK18_HUMAN	cyclin-dependent kinase 18	283	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|endometrium(2)|large_intestine(2)|lung(10)|stomach(2)|urinary_tract(1)	19						CTGCCCCCAGGACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAATGAGGTGGTGA	0.611																																					p.315_329del	Pancreas(180;489 2072 28461 40831 44265)	Atlas-INDEL	.											.	CDK18	75	.	0			c.944_986del						.																																			SO:0001630	splice_region_variant	5129	exon10			.	X66362	CCDS1454.1, CCDS44300.1	1q31-q32	2011-11-08	2009-12-16	2009-12-16	ENSG00000117266	ENSG00000117266		"Cyclin-dependent kinases"	8751	protein-coding gene	gene with protein product		169190	"PCTAIRE protein kinase 3"	PCTK3		1437147, 19884882	Standard	NM_002596		Approved	PCTAIRE3	uc010pri.2	Q07002	OTTHUMG00000037203	ENST00000360066.2:c.854-1GACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAAT>-	chr1.hg19:g.205497176_205497219delGACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAAT		160.0	0.0		137.0	12.0	NM_212503	Q5VXQ2|Q6V3A2|Q6V3A3|Q96F90	Frame_Shift_Del	DEL	ENST00000360066.2	hg19	CCDS44300.1																																																																																			.	.		0.611	CDK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090407.2	NM_002596	Frame_Shift_Del	-	205497219	GACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAAT	-	205497176	8	5	162	1	0	1	0	1	0	0	1	0	3136	1188	41	0	978	0	CDK18	1	205497176	Splice_Site	DEL	GACTGGCCAGGGCCAAGTCAGTGCCCACAAAGACTTACTCCAAT	TCGA-DD-AACK-01A-11D-A40R-10	23772040	205497176	43753445	17	24667										
AFTPH	54812	hgsc.bcm.edu	37	chr2	64796244	64796244	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	agggaattgctagatgtgtgGactgagctacaggatatcca	13	6	0	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:64796244G>T	ENST00000422803.1	+	4	2420	c.2106G>T	c.(2104-2106)tgG>tgT	p.W702C	AFTPH_ENST00000409933.1_Missense_Mutation_p.W702C|AFTPH_ENST00000487769.1_Intron|AFTPH_ENST00000238856.4_Missense_Mutation_p.W702C|AFTPH_ENST00000238855.7_Missense_Mutation_p.W702C|AFTPH_ENST00000409183.1_Missense_Mutation_p.W333C			Q6ULP2	AFTIN_HUMAN	aftiphilin	702					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						TAGATGTGTGGACTGAGCTAC	0.463																																					p.W702C		Atlas-SNP	.											.	AFTPH	117	.	0			c.G2106T						.						165	153	157					2																	64796244		2203	4300	6503	SO:0001583	missense	54812	exon4			TGTGTGGACTGAG	AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.2106G>T	chr2.hg19:g.64796244G>T	ENSP00000397726:p.Trp702Cys	85.0	0.0		100.0	39.0	NM_017657	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Missense_Mutation	SNP	ENST00000422803.1	hg19		.	.	.	.	.	.	.	.	.	.	G	20.4	3.979530	0.74360	.	.	ENSG00000119844	ENST00000238856;ENST00000422803;ENST00000238855;ENST00000409933;ENST00000409183	T;T;T;T;T	0.65916	0.82;0.91;0.92;0.92;-0.18	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.79058	0.4382	M	0.72118	2.19	0.80722	D	1	D;D;P;D	0.89917	1.0;1.0;0.923;1.0	D;D;P;D	0.91635	0.998;0.999;0.894;0.998	T	0.82000	-0.0674	10	0.87932	D	0	-0.4091	18.2232	0.89907	0.0:0.0:1.0:0.0	.	702;702;702;702	Q6ULP2;Q6ULP2-2;Q6ULP2-5;Q6ULP2-4	AFTIN_HUMAN;.;.;.	C	702;702;702;702;333	ENSP00000238856:W702C;ENSP00000397726:W702C;ENSP00000238855:W702C;ENSP00000387071:W702C;ENSP00000386913:W333C	ENSP00000238855:W702C	W	+	3	0	AFTPH	64649748	1.000000	0.71417	0.979000	0.43373	0.980000	0.70556	9.693000	0.98684	2.362000	0.80069	0.650000	0.86243	TGG	.	.		0.463	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657		T	64796244	G	T	64796244	3	4	162	1	0	0	0	0	1	0	0	0	364	1183	41	3	2116	3	AFTPH	2	64796244	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10		64796244	178403129	18	24668										
CCDC93	54520	hgsc.bcm.edu	37	chr2	118735578	118735578	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgtttttcttaccttctccaTtttgctctggcggctaaatc	6	11	3	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:118735578T>A	ENST00000376300.2	-	8	786	c.649A>T	c.(649-651)Atg>Ttg	p.M217L	CCDC93_ENST00000460781.1_5'UTR|CCDC93_ENST00000319432.5_Missense_Mutation_p.M216L	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	217										breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						ACCTTCTCCATTTTGCTCTGG	0.398																																					p.M217L		Atlas-SNP	.											.	CCDC93	70	.	0			c.A649T						.						166	139	148					2																	118735578		2203	4300	6503	SO:0001583	missense	54520	exon8			TCTCCATTTTGCT	BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.649A>T	chr2.hg19:g.118735578T>A	ENSP00000365477:p.Met217Leu	52.0	0.0		64.0	28.0	NM_019044	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Missense_Mutation	SNP	ENST00000376300.2	hg19	CCDS2121.2	.	.	.	.	.	.	.	.	.	.	T	3.712	-0.059415	0.07317	.	.	ENSG00000125633	ENST00000376300;ENST00000319432	T;T	0.16457	2.34;2.35	4.28	1.83	0.25207	.	0.744408	0.12434	N	0.469254	T	0.04815	0.0130	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43130	-0.9410	10	0.10377	T	0.69	-3.665	3.8996	0.09155	0.0:0.1998:0.1832:0.6171	.	217	Q567U6	CCD93_HUMAN	L	217;216	ENSP00000365477:M217L;ENSP00000324135:M216L	ENSP00000324135:M216L	M	-	1	0	CCDC93	118452048	0.918000	0.31147	1.000000	0.80357	0.771000	0.43674	0.111000	0.15458	0.280000	0.22209	0.459000	0.35465	ATG	.	.		0.398	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044		A	118735578	T	A	118735578	3	1	162	1	0	0	0	0	1	0	0	0	2874	1493	52	4	1314	4	CCDC93	2	118735578	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	53939334	118735578	124463795	19	24669										
MARCO	8685	hgsc.bcm.edu	37	chr2	119752067	119752067	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	atcatgactgcagccacgagGaggacgcaggcgtggagtgc	16	10	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:119752067G>T	ENST00000327097.4	+	17	1669	c.1534G>T	c.(1534-1536)Gag>Tag	p.E512*	MARCO_ENST00000541757.1_Nonsense_Mutation_p.E434*	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	512	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						CAGCCACGAGGAGGACGCAGG	0.592																																					p.E512X	GBM(8;18 374 7467 11269 32796)	Atlas-SNP	.											.	MARCO	120	.	0			c.G1534T						.						119	97	104					2																	119752067		2203	4300	6503	SO:0001587	stop_gained	8685	exon17			CACGAGGAGGACG	AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"scavenger receptor class A, member 2"	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.1534G>T	chr2.hg19:g.119752067G>T	ENSP00000318916:p.Glu512*	65.0	0.0		56.0	16.0	NM_006770	B4DW79|Q9Y5S3	Nonsense_Mutation	SNP	ENST00000327097.4	hg19	CCDS2124.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.480332	0.84747	.	.	ENSG00000019169	ENST00000327097;ENST00000410021;ENST00000541757	.	.	.	5.25	4.38	0.52667	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.869	0.41162	0.0921:0.0:0.9079:0.0	.	.	.	.	X	512;458;434	.	.	E	+	1	0	MARCO	119468537	1.000000	0.71417	0.854000	0.33618	0.004000	0.04260	4.127000	0.57944	1.441000	0.47550	-0.137000	0.14449	GAG	.	.		0.592	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770		T	119752067	G	T	119752067	4	4	162	1	0	0	0	0	0	1	0	0	9320	1175	41	3	1600	3	MARCO	2	119752067	Nonsense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	1016489	119752067	123447306	20	24670										
MCM6	4175	hgsc.bcm.edu	37	chr2	136622693	136622693	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tcatttggttcttaatgctcTcagctgtctgttcctcatct	6	11	6	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:136622693T>A	ENST00000264156.2	-	7	1028	c.968A>T	c.(967-969)gAg>gTg	p.E323V	MCM6_ENST00000492091.1_5'Flank	NM_005915.5	NP_005906.2	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	323					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(15)|prostate(2)|skin(1)	29				BRCA - Breast invasive adenocarcinoma(221;0.166)		CTTAATGCTCTCAGCTGTCTG	0.398																																					p.E323V	Ovarian(196;141 2104 8848 24991 25939)	Atlas-SNP	.											.	MCM6	64	.	0			c.A968T						.						191	175	180					2																	136622693		2203	4300	6503	SO:0001583	missense	4175	exon7			ATGCTCTCAGCTG		CCDS2179.1	2q14-q21	2008-02-05	2007-04-04		ENSG00000076003	ENSG00000076003			6949	protein-coding gene	gene with protein product	"MIS5 homolog (S.pombe)"	601806	"minichromosome maintenance deficient (mis5, S. pombe) 6", "MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, S. pombe) (S. cerevisiae)", "minichromosome maintenance deficient 6 homolog (S. cerevisiae)"				Standard	NM_005915		Approved	Mis5	uc002tuw.4	Q14566	OTTHUMG00000131739	ENST00000264156.2:c.968A>T	chr2.hg19:g.136622693T>A	ENSP00000264156:p.Glu323Val	54.0	0.0		55.0	19.0	NM_005915	B2R6H2|Q13504|Q99859	Missense_Mutation	SNP	ENST00000264156.2	hg19	CCDS2179.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.932652	0.73442	.	.	ENSG00000076003	ENST00000264156	T	0.03801	3.8	5.59	5.59	0.84812	.	0.045250	0.85682	D	0.000000	T	0.10981	0.0268	M	0.75264	2.295	0.80722	D	1	P	0.36412	0.552	B	0.38500	0.275	T	0.01045	-1.1470	10	0.56958	D	0.05	-17.4913	15.7653	0.78120	0.0:0.0:0.0:1.0	.	323	Q14566	MCM6_HUMAN	V	323	ENSP00000264156:E323V	ENSP00000264156:E323V	E	-	2	0	MCM6	136339163	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.644000	0.83416	2.122000	0.65172	0.455000	0.32223	GAG	.	.		0.398	MCM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254658.1	NM_005915		A	136622693	T	A	136622693	3	1	162	1	0	0	0	0	1	0	0	0	9400	1551	54	4	1541	4	MCM6	2	136622693	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	16870626	136622693	106576680	21	24671										
NEB	4703	hgsc.bcm.edu	37	chr2	152529088	152529088	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tcttgtattcacgatcagacTgcagctttgccacattcata	6	11	4	1	rs375155384		TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:152529088T>A	ENST00000172853.10	-	37	4241	c.4094A>T	c.(4093-4095)cAg>cTg	p.Q1365L	NEB_ENST00000603639.1_Missense_Mutation_p.Q1365L|NEB_ENST00000397345.3_Missense_Mutation_p.Q1365L|NEB_ENST00000427231.2_Missense_Mutation_p.Q1365L|NEB_ENST00000604864.1_Missense_Mutation_p.Q1365L|NEB_ENST00000409198.1_Missense_Mutation_p.Q1365L			P20929	NEBU_HUMAN	nebulin	1365					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		ACGATCAGACTGCAGCTTTGC	0.473																																					p.Q1365L		Atlas-SNP	.											.	NEB	1697	.	0			c.A4094T						.	T	LEU/GLN,LEU/GLN,LEU/GLN	0,3920		0,0,1960	137	133	134		4094,4094,4094	5.9	1	2		134	1,8277		0,1,4138	no	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	113,113,113	0,1,6098	AA,AT,TT		0.0121,0.0,0.0082	probably-damaging,probably-damaging,probably-damaging	1365/8526,1365/8526,1365/6670	152529088	1,12197	1960	4139	6099	SO:0001583	missense	4703	exon37			TCAGACTGCAGCT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.4094A>T	chr2.hg19:g.152529088T>A	ENSP00000172853:p.Gln1365Leu	98.0	0.0		91.0	45.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	T	22.4	4.287784	0.80803	0.0	1.21E-4	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.48836	0.8;0.8;0.8;0.8	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.73497	0.3594	M	0.86740	2.835	0.80722	D	1	D	0.71674	0.998	D	0.87578	0.998	T	0.78046	-0.2357	10	0.62326	D	0.03	.	16.3782	0.83418	0.0:0.0:0.0:1.0	.	1365	P20929	NEBU_HUMAN	L	1365	ENSP00000386259:Q1365L;ENSP00000380505:Q1365L;ENSP00000416578:Q1365L;ENSP00000172853:Q1365L	ENSP00000172853:Q1365L	Q	-	2	0	NEB	152237334	1.000000	0.71417	1.000000	0.80357	0.450000	0.32258	8.018000	0.88722	2.277000	0.76020	0.528000	0.53228	CAG	.	.		0.473	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152529088	T	A	152529088	3	1	162	1	0	0	0	0	1	0	0	0	10311	1580	55	4	22176	4	NEB	2	152529088	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	15906395	152529088	90670285	22	24672										
DHRS9	10170	hgsc.bcm.edu	37	chr2	169940058	169940058	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cgttggagggggctatactcCatccaaatatgcagtggaag	13	8	0	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:169940058C>T	ENST00000327239.4	+	6	2037	c.533C>T	c.(532-534)cCa>cTa	p.P178L	DHRS9_ENST00000412271.1_Missense_Mutation_p.P178L|DHRS9_ENST00000436483.2_Missense_Mutation_p.P178L|DHRS9_ENST00000602501.1_Missense_Mutation_p.P178L|DHRS9_ENST00000357546.2_Missense_Mutation_p.P178L|DHRS9_ENST00000428522.1_Missense_Mutation_p.P178L|DHRS9_ENST00000421653.1_Missense_Mutation_p.P31L|DHRS9_ENST00000432060.2_Missense_Mutation_p.P238L	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	178					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						GGCTATACTCCATCCAAATAT	0.393																																					p.P178L		Atlas-SNP	.											.	DHRS9	29	.	0			c.C533T						.						71	67	68					2																	169940058		2203	4300	6503	SO:0001583	missense	10170	exon6			ATACTCCATCCAA	AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	16888	protein-coding gene	gene with protein product	"NADP-dependent retinol dehydrogenase/reductase", "3-alpha hydroxysteroid dehydrogenase", "retinol dehydrogenase homolog", "short chain dehydrogenase/reductase family 9C, member 4"	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.533C>T	chr2.hg19:g.169940058C>T	ENSP00000316670:p.Pro178Leu	52.0	0.0		95.0	34.0	NM_005771	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Missense_Mutation	SNP	ENST00000327239.4	hg19	CCDS2231.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.287639	0.23478	.	.	ENSG00000073737	ENST00000327239;ENST00000357546;ENST00000432060;ENST00000428522;ENST00000421653;ENST00000436483;ENST00000412271	D;D;D;D;D;D;D	0.92545	-2.15;-2.15;-2.15;-2.15;-3.06;-2.15;-2.15	5.93	2.24	0.28232	NAD(P)-binding domain (1);	0.395216	0.31648	N	0.007281	T	0.79185	0.4403	N	0.02697	-0.525	0.28071	N	0.932595	B;B	0.02656	0.0;0.0	B;B	0.11329	0.006;0.002	T	0.67280	-0.5710	10	0.31617	T	0.26	.	10.7832	0.46390	0.0:0.7492:0.0:0.2508	.	238;178	B7Z416;Q9BPW9	.;DHRS9_HUMAN	L	178;178;238;178;31;178;178	ENSP00000316670:P178L;ENSP00000350154:P178L;ENSP00000389241:P238L;ENSP00000388564:P178L;ENSP00000388066:P31L;ENSP00000407167:P178L;ENSP00000407747:P178L	ENSP00000316670:P178L	P	+	2	0	DHRS9	169648304	0.001000	0.12720	0.584000	0.28653	0.848000	0.48234	1.407000	0.34657	0.150000	0.19136	-0.123000	0.14984	CCA	.	.		0.393	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771		T	169940058	C	T	169940058	3	4	162	1	0	0	0	0	1	0	0	0	4500	594	21	3	539	3	DHRS9	2	169940058	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	17410970	169940058	73259315	23	24673										
TTN	7273	hgsc.bcm.edu	37	chr2	179472543	179472543	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gccacagtaacaggttgtgtTtctccaggcggtccttcccc	10	14	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:179472543T>A	ENST00000591111.1	-	226	48272	c.48048A>T	c.(48046-48048)gaA>gaT	p.E16016D	TTN_ENST00000460472.2_Missense_Mutation_p.E8592D|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E8784D|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E17657D|TTN_ENST00000342992.6_Missense_Mutation_p.E15089D|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E8717D|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16016	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGGTTGTGTTTCTCCAGGCG	0.433																																					p.E17657D		Atlas-SNP	.											.	TTN	18412	.	0			c.A52971T						.						95	90	91					2																	179472543		1901	4124	6025	SO:0001583	missense	7273	exon276			TTGTGTTTCTCCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48048A>T	chr2.hg19:g.179472543T>A	ENSP00000465570:p.Glu16016Asp	51.0	0.0		55.0	19.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.74	1.727389	0.30593	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	6.06	2.43	0.29744	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.24928	0.0605	N	0.16708	0.43	0.34907	D	0.747117	P;P;P;P	0.34462	0.454;0.454;0.454;0.454	B;B;B;B	0.29598	0.104;0.104;0.104;0.104	T	0.26292	-1.0107	9	0.87932	D	0	.	10.0208	0.42041	0.0:0.1818:0.0:0.8182	.	8592;8717;8784;16016	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	15089;8592;8784;8717;8592	ENSP00000343764:E15089D;ENSP00000434586:E8592D;ENSP00000340554:E8784D;ENSP00000352154:E8717D	ENSP00000340554:E8784D	E	-	3	2	TTN	179180788	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	0.985000	0.29578	0.181000	0.19994	0.533000	0.62120	GAA	.	.		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179472543	T	A	179472543	3	1	162	1	0	0	0	0	1	0	0	0	16750	1838	64	4	55070	4	TTN	2	179472543	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	9532485	179472543	63726830	24	24674										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196749353	196749353	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	aattgttcctttttcaggaaAtgggacagttagtgcctttg	10	6	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:196749353A>T	ENST00000312428.6	-	35	5819	c.5719T>A	c.(5719-5721)Ttt>Att	p.F1907I		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1907					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TTTTCAGGAAATGGGACAGTT	0.413																																					p.F1907I		Atlas-SNP	.											.	DNAH7	512	.	0			c.T5719A						.						109	105	106					2																	196749353		1911	4117	6028	SO:0001583	missense	56171	exon35			CAGGAAATGGGAC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.5719T>A	chr2.hg19:g.196749353A>T	ENSP00000311273:p.Phe1907Ile	99.0	0.0		114.0	42.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	A	11.50	1.658059	0.29425	.	.	ENSG00000118997	ENST00000312428	T	0.24723	1.84	5.67	4.51	0.55191	.	0.608298	0.16579	N	0.208291	T	0.18299	0.0439	L	0.39397	1.21	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.07966	-1.0745	10	0.22706	T	0.39	.	6.386	0.21561	0.7843:0.0:0.0747:0.141	.	1907	Q8WXX0	DYH7_HUMAN	I	1907	ENSP00000311273:F1907I	ENSP00000311273:F1907I	F	-	1	0	DNAH7	196457598	1.000000	0.71417	0.998000	0.56505	0.700000	0.40528	3.256000	0.51492	2.275000	0.75901	0.533000	0.62120	TTT	.	.		0.413	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196749353	A	T	196749353	3	4	162	1	0	0	0	0	1	0	0	0	4608	101	4	4	6479	4	DNAH7	2	196749353	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	17276810	196749353	46450020	25	24675										
ORC2L	4999	hgsc.bcm.edu	37	chr2	201791508	201791508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tactgatttcacactgattcCaggaaagaagccattgatga	8	8	1	5			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:201791508C>T	ENST00000234296.2	-	12	1282	c.1033G>A	c.(1033-1035)Gga>Aga	p.G345R	RN7SL694P_ENST00000584245.1_RNA	NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	345					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						ACACTGATTCCAGGAAAGAAG	0.373																																					p.G345R		Atlas-SNP	.											.	ORC2	48	.	0			c.G1033A						.						110	107	108					2																	201791508		2203	4300	6503	SO:0001583	missense	4999	exon12			TGATTCCAGGAAA		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"origin recognition complex, subunit 2 (yeast homolog)-like", "origin recognition complex, subunit 2-like (yeast)", "origin recognition complex, subunit 2 homolog (yeast)"	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1033G>A	chr2.hg19:g.201791508C>T	ENSP00000234296:p.Gly345Arg	71.0	0.0		87.0	42.0	NM_006190	Q13204|Q53TX5	Missense_Mutation	SNP	ENST00000234296.2	hg19	CCDS2334.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.766852	0.69878	.	.	ENSG00000115942	ENST00000234296	T	0.44881	0.91	5.77	5.77	0.91146	.	0.236827	0.45126	D	0.000392	T	0.52224	0.1721	L	0.52126	1.63	0.35438	D	0.794656	P;D	0.56968	0.93;0.978	P;D	0.65233	0.756;0.933	T	0.61033	-0.7144	10	0.45353	T	0.12	-10.6798	7.8916	0.29682	0.0:0.8113:0.0:0.1887	.	345;345	B4DYU9;Q13416	.;ORC2_HUMAN	R	345	ENSP00000234296:G345R	ENSP00000234296:G345R	G	-	1	0	ORC2	201499753	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.684000	0.54671	2.890000	0.99128	0.585000	0.79938	GGA	.	.		0.373	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190		T	201791508	C	T	201791508	3	4	162	1	0	0	0	0	1	0	0	0	11271	603	21	3	728	3	ORC2L	2	201791508	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	5042155	201791508	41407865	26	24676										
STK36	27148	hgsc.bcm.edu	37	chr2	219564008	219564008	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gcatgtggagacccccagccAaatgtgaaggaggctgccct	13	12	0	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:219564008A>T	ENST00000295709.3	+	26	4020	c.3741A>T	c.(3739-3741)ccA>ccT	p.P1247P	STK36_ENST00000392106.2_Silent_p.P1226P|STK36_ENST00000392105.3_Silent_p.P1226P|STK36_ENST00000440309.1_Silent_p.P1247P	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		ACCCCCAGCCAAATGTGAAGG	0.562																																					p.P1247P		Atlas-SNP	.											.	STK36	111	.	0			c.A3741T						.						52	56	55					2																	219564008		2203	4300	6503	SO:0001819	synonymous_variant	27148	exon26			CCAGCCAAATGTG	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"fused homolog (Drosophila)"	607652	"serine/threonine kinase 36 (fused homolog, Drosophila)"			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.3741A>T	chr2.hg19:g.219564008A>T		114.0	0.0		118.0	48.0	NM_015690		Silent	SNP	ENST00000295709.3	hg19	CCDS2421.1	.	.	.	.	.	.	.	.	.	.	A	8.424	0.847156	0.17034	.	.	ENSG00000163482	ENST00000431040	.	.	.	5.47	-3.42	0.04825	.	.	.	.	.	T	0.16769	0.0403	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.27640	-1.0068	4	.	.	.	0.3	0.6469	0.00819	0.3172:0.2815:0.2061:0.1953	.	.	.	.	L	440	.	.	Q	+	2	0	STK36	219272252	0.000000	0.05858	0.967000	0.41034	0.985000	0.73830	-1.313000	0.02718	-0.143000	0.11334	0.459000	0.35465	CAA	.	.		0.562	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			T	219564008	A	T	219564008	2	4	162	1	0	0	0	0	0	0	0	1	15317	117	5	4		4	STK36	2	219564008	Silent	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	17772500	219564008	23635365	27	24677										
DNER	92737	hgsc.bcm.edu	37	chr2	230312104	230312104	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	agcacaggggctgagggcacAgaagtcaataagctgggcac	15	9	1	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:230312104A>T	ENST00000341772.4	-	8	1548	c.1414T>A	c.(1414-1416)Tgt>Agt	p.C472S		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	472	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		CTGAGGGCACAGAAGTCAATA	0.602																																					p.C472S		Atlas-SNP	.											.	DNER	129	.	0			c.T1414A						.						51	46	48					2																	230312104		2203	4300	6503	SO:0001583	missense	92737	exon8			GGGCACAGAAGTC	AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.1414T>A	chr2.hg19:g.230312104A>T	ENSP00000345229:p.Cys472Ser	314.0	0.0		326.0	113.0	NM_139072	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Missense_Mutation	SNP	ENST00000341772.4	hg19	CCDS33390.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.403641	0.83230	.	.	ENSG00000187957	ENST00000341772;ENST00000543700	D	0.99992	-12.4	4.94	4.94	0.65067	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99988	0.9998	M	0.93507	3.425	0.80722	D	1	D	0.69078	0.997	P	0.62885	0.908	D	0.99943	1.1432	10	0.87932	D	0	.	14.8962	0.70646	1.0:0.0:0.0:0.0	.	472	Q8NFT8	DNER_HUMAN	S	472;190	ENSP00000345229:C472S	ENSP00000345229:C472S	C	-	1	0	DNER	230020348	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	8.776000	0.91776	1.978000	0.57642	0.533000	0.62120	TGT	.	.		0.602	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072		T	230312104	A	T	230312104	3	4	162	1	0	0	0	0	1	0	0	0	4669	188	7	4	823	4	DNER	2	230312104	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	10748096	230312104	12887269	28	24678										
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233708845	233708845	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tcaggttgggggaatgtcagCaaaccttcaggtaccacgaa	12	9	3	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:233708845C>G	ENST00000409547.1	+	26	3290	c.2979C>G	c.(2977-2979)agC>agG	p.S993R	GIGYF2_ENST00000373566.3_Missense_Mutation_p.S1015R|GIGYF2_ENST00000409451.3_Missense_Mutation_p.S1014R|GIGYF2_ENST00000409480.1_Missense_Mutation_p.S1015R|GIGYF2_ENST00000409196.3_Missense_Mutation_p.S987R|GIGYF2_ENST00000452341.2_Missense_Mutation_p.Q836E|GIGYF2_ENST00000373563.4_Missense_Mutation_p.S993R	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	993	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		GGAATGTCAGCAAACCTTCAG	0.522																																					p.S1014R		Atlas-SNP	.											.	GIGYF2	288	.	0			c.C3042G						.						51	49	50					2																	233708845		2202	4298	6500	SO:0001583	missense	26058	exon26			TGTCAGCAAACCT	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2979C>G	chr2.hg19:g.233708845C>G	ENSP00000386537:p.Ser993Arg	260.0	0.0		274.0	86.0	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.55|14.55	2.567778|2.567778	0.45798|0.45798	.|.	.|.	ENSG00000204120|ENSG00000204120	ENST00000452341|ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000426102	T|T;T;T;T;T;T;T	0.70045|0.73469	-0.45|-0.75;-0.75;-0.75;-0.75;-0.75;-0.74;-0.06	5.31|5.31	3.17|3.17	0.36434|0.36434	.|.	.|0.179769	.|0.64402	.|D	.|0.000011	T|T	0.63710|0.63710	0.2534|0.2534	L|L	0.47716|0.47716	1.5|1.5	0.22728|0.22728	N|N	0.998802|0.998802	P|P;B;B	0.51147|0.42409	0.942|0.779;0.201;0.201	P|B;B;B	0.52386|0.36030	0.697|0.216;0.143;0.143	T|T	0.56135|0.56135	-0.8029|-0.8029	9|10	0.87932|0.30854	D|T	0|0.27	-10.5152|-10.5152	12.6497|12.6497	0.56753|0.56753	0.0:0.791:0.0:0.209|0.0:0.791:0.0:0.209	.|.	836|1014;993;987	E9PC50|A6H8W4;Q6Y7W6;E9PBB0	.|.;PERQ2_HUMAN;.	E|R	836|1015;993;1015;993;987;1014;22	ENSP00000411505:Q836E|ENSP00000362667:S1015R;ENSP00000362664:S993R;ENSP00000386765:S1015R;ENSP00000386537:S993R;ENSP00000387070:S987R;ENSP00000387170:S1014R;ENSP00000415037:S22R	ENSP00000411505:Q836E|ENSP00000362664:S993R	Q|S	+|+	1|3	0|2	GIGYF2|GIGYF2	233417089|233417089	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.553000|0.553000	0.35397|0.35397	1.229000|1.229000	0.32600|0.32600	1.237000|1.237000	0.43756|0.43756	0.561000|0.561000	0.74099|0.74099	CAA|AGC	.	.		0.522	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		G	233708845	C	G	233708845	3	3	162	1	0	0	0	0	1	0	0	0	6386	709	25	4	3135	4	GIGYF2	2	233708845	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	3396741	233708845	9490528	29	24679										
RBM44	375316	hgsc.bcm.edu	37	chr2	238727032	238727032	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	acaagtgcaagaccttctgtAgtatctacatcaagcaacac	6	11	3	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:238727032A>G	ENST00000409864.1	+	3	1727	c.1473A>G	c.(1471-1473)gtA>gtG	p.V491V	RBM44_ENST00000316997.4_Silent_p.V491V|RBM44_ENST00000444524.2_Intron			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	490						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		GACCTTCTGTAGTATCTACAT	0.393																																					p.V491V		Atlas-SNP	.											.	RBM44	167	.	0			c.A1473G						.						87	81	83					2																	238727032		1919	4133	6052	SO:0001819	synonymous_variant	375316	exon3			TTCTGTAGTATCT	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"RNA binding motif (RRM) containing"	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.1473A>G	chr2.hg19:g.238727032A>G		246.0	0.0		211.0	91.0	NM_001080504	A0AUW3	Silent	SNP	ENST00000409864.1	hg19	CCDS46554.1																																																																																			.	.		0.393	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		G	238727032	A	G	238727032	2	3	162	1	0	0	0	0	0	0	0	1	13153	407	15	2		2	RBM44	2	238727032	Silent	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	5018187	238727032	4472341	30	24680										
HDAC4	9759	hgsc.bcm.edu	37	chr2	239975278	239975278	+	Frame_Shift_Del	DEL	C	C	-													0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gctgtggaggttgtgcgctgCaggcagcgccagtacttgcc							TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:239975278delC	ENST00000345617.3	-	26	3884	c.3093delG	c.(3091-3093)ctgfs	p.L1031fs	HDAC4_ENST00000543185.1_Frame_Shift_Del_p.L615fs	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	1031	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		TTGTGCGCTGCAGGCAGCGCC	0.632																																					p.Q1032fs		Atlas-INDEL	.											.	HDAC4	127	.	0			c.3094delC						.						30	35	33					2																	239975278		2203	4299	6502	SO:0001589	frameshift_variant	9759	exon26			.	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.3093delG	chr2.hg19:g.239975278delC	ENSP00000264606:p.Leu1031fs	80.0	0.0		84.0	21.0	NM_006037	Q9UND6	Frame_Shift_Del	DEL	ENST00000345617.3	hg19	CCDS2529.1																																																																																			.	.		0.632	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		-	239975278	C	-	239975278	7	5	162	1	0	1	0	1	0	0	0	0	7018	697	25	0	169	0	HDAC4	2	239975278	Frame_Shift_Del	DEL	C	TCGA-DD-AACK-01A-11D-A40R-10	1248246	239975278	3224095	31	24681	113	2								
HDAC4	9759	hgsc.bcm.edu	37	chr2	239975280	239975281	+	Frame_Shift_Del	DEL	GG	GG	-													0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgtggaggttgtgcgctgcaGgcagcgccagtacttgcctg							TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr2:239975280_239975281delGG	ENST00000345617.3	-	26	3881_3882	c.3090_3091delCC	c.(3088-3093)tgcctgfs	p.L1031fs	HDAC4_ENST00000543185.1_Frame_Shift_Del_p.L615fs	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	1031	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GTGCGCTGCAGGCAGCGCCAGT	0.629																																					p.1031_1031del		Atlas-INDEL	.											.	HDAC4	127	.	0			c.3091_3092del						.																																			SO:0001589	frameshift_variant	9759	exon26			.	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.3090_3091delCC	chr2.hg19:g.239975280_239975281delGG	ENSP00000264606:p.Leu1031fs	79.0	0.0		84.0	21.0	NM_006037	Q9UND6	Frame_Shift_Del	DEL	ENST00000345617.3	hg19	CCDS2529.1																																																																																			.	.		0.629	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		-	239975281	GG	-	239975280	7	5	162	1	0	1	0	1	0	0	0	0	7018	991	35	0	171	0	HDAC4	2	239975280	Frame_Shift_Del	DEL	GG	TCGA-DD-AACK-01A-11D-A40R-10	2	239975280	3224093	32	24682	113	2								
DYNC1LI1	51143	hgsc.bcm.edu	37	chr3	32568308	32568308	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tcttcaagaagcttctccttCcgtaggagatgtaggtgttg	11	8	3	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr3:32568308C>T	ENST00000273130.4	-	13	1658	c.1555G>A	c.(1555-1557)Gaa>Aaa	p.E519K	DYNC1LI1_ENST00000432458.2_Missense_Mutation_p.E403K	NM_016141.3	NP_057225.2	Q9Y6G9	DC1L1_HUMAN	dynein, cytoplasmic 1, light intermediate chain 1	519					microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(1)|lung(3)|ovary(1)	7						GCTTCTCCTTCCGTAGGAGAT	0.398																																					p.E519K		Atlas-SNP	.											DYNC1LI1,NS,carcinoma,0,1	DYNC1LI1	23	.	0			c.G1555A						.						147	141	143					3																	32568308		2203	4300	6503	SO:0001583	missense	51143	exon13			CTCCTTCCGTAGG	AF078849	CCDS2654.1	3p23	2013-01-18	2005-11-25	2005-11-25	ENSG00000144635	ENSG00000144635		"Cytoplasmic dyneins"	18745	protein-coding gene	gene with protein product		615890	"dynein, cytoplasmic, light intermediate polypeptide 1"	DNCLI1		16260502	Standard	NM_016141		Approved		uc003cfb.4	Q9Y6G9	OTTHUMG00000130750	ENST00000273130.4:c.1555G>A	chr3.hg19:g.32568308C>T	ENSP00000273130:p.Glu519Lys	135.0	0.0		130.0	10.0	NM_016141	A2RRG7|Q53HC8|Q53HK7	Missense_Mutation	SNP	ENST00000273130.4	hg19	CCDS2654.1	.	.	.	.	.	.	.	.	.	.	C	31	5.069408	0.93950	.	.	ENSG00000144635	ENST00000273130;ENST00000432458	T;T	0.51574	1.98;0.7	5.53	5.53	0.82687	.	0.358552	0.32301	N	0.006288	T	0.58250	0.2109	N	0.22421	0.69	0.58432	D	0.999999	D;D	0.69078	0.997;0.997	D;D	0.79108	0.992;0.992	T	0.61671	-0.7015	10	0.66056	D	0.02	-31.1411	19.8132	0.96556	0.0:1.0:0.0:0.0	.	403;519	E9PHI6;Q9Y6G9	.;DC1L1_HUMAN	K	519;403	ENSP00000273130:E519K;ENSP00000407279:E403K	ENSP00000273130:E519K	E	-	1	0	DYNC1LI1	32543312	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.401000	0.59716	2.753000	0.94483	0.585000	0.79938	GAA	.	.		0.398	DYNC1LI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253250.1	NM_016141		T	32568308	C	T	32568308	3	4	162	1	0	0	0	0	1	0	0	0	4846	864	30	3	20	3	DYNC1LI1	3	32568308	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10		32568308	165454122	33	24683										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41268766	41268766	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gaggacctatacttacgaaaAactactgtggaccacaagca	8	10	0	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr3:41268766A>T	ENST00000349496.5	+	7	1284	c.1004A>T	c.(1003-1005)aAa>aTa	p.K335I	CTNNB1_ENST00000396185.3_Missense_Mutation_p.K335I|CTNNB1_ENST00000405570.1_Missense_Mutation_p.K335I|CTNNB1_ENST00000453024.1_Missense_Mutation_p.K328I|CTNNB1_ENST00000396183.3_Missense_Mutation_p.K335I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	335					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.K335I(8)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACTTACGAAAAACTACTGTGG	0.383		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.K335I	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,colon,carcinoma,-1,11	CTNNB1	4904	.	8	Substitution - Missense(8)	liver(7)|kidney(1)	c.A1004T						.						110	108	109					3																	41268766		2203	4300	6503	SO:0001583	missense	1499	exon7	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACGAAAAACTACT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1004A>T	chr3.hg19:g.41268766A>T	ENSP00000344456:p.Lys335Ile	110.0	0.0		104.0	41.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.040885	0.93685	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.82148	0.4974	M	0.89287	3.02	0.80722	D	1	D;D	0.71674	0.995;0.998	D;D	0.75484	0.97;0.986	D	0.85830	0.1391	10	0.72032	D	0.01	-3.7939	15.5934	0.76558	1.0:0.0:0.0:0.0	.	263;335	B4DSW9;P35222	.;CTNB1_HUMAN	I	335;335;335;328;335	ENSP00000385604:K335I;ENSP00000379486:K335I;ENSP00000344456:K335I;ENSP00000411226:K328I;ENSP00000379488:K335I	ENSP00000344456:K335I	K	+	2	0	CTNNB1	41243770	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	9.339000	0.96797	2.094000	0.63399	0.482000	0.46254	AAA	.	.		0.383	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41268766	A	T	41268766	3	4	162	1	0	0	0	0	1	0	0	0	4018	14	1	4	1026	4	CTNNB1	3	41268766	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	8700458	41268766	156753664	34	24684										
CD200R1	131450	hgsc.bcm.edu	37	chr3	112693693	112693693	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cctaggttagcagttctccaAgggcagagcatttctgtttt	10	9	2	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr3:112693693A>T	ENST00000471858.1	-	1	244	c.12T>A	c.(10-12)ccT>ccA	p.P4P	CD200R1_ENST00000295863.4_Silent_p.P4P|CD200R1_ENST00000308611.3_Silent_p.P4P|CD200R1_ENST00000440122.2_Silent_p.P4P|CD200R1_ENST00000490004.1_Silent_p.P4P	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	4					regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						CAGTTCTCCAAGGGCAGAGCA	0.468																																					p.P4P		Atlas-SNP	.											.	CD200R1	91	.	0			c.T12A						.						207	178	188					3																	112693693		2203	4300	6503	SO:0001819	synonymous_variant	131450	exon1			TCTCCAAGGGCAG	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"Immunoglobulin superfamily / C2-set domain containing"	24235	protein-coding gene	gene with protein product		607546	"MOX2 receptor"	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.12T>A	chr3.hg19:g.112693693A>T		84.0	0.0		84.0	30.0	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Silent	SNP	ENST00000471858.1	hg19	CCDS2970.1																																																																																			.	.		0.468	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806		T	112693693	A	T	112693693	2	4	162	1	0	0	0	0	0	0	0	1	2983	59	3	4		4	CD200R1	3	112693693	Silent	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	71424927	112693693	85328737	35	24685										
MRPL47	57129	hgsc.bcm.edu	37	chr3	179311574	179311574	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	agatgattcttccaaagatgTctcttctccaagcaccaggt	7	11	3	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr3:179311574T>A	ENST00000476781.1	-	5	541	c.512A>T	c.(511-513)gAc>gTc	p.D171V	MRPL47_ENST00000392659.2_Missense_Mutation_p.D61V|MRPL47_ENST00000259038.2_Missense_Mutation_p.D151V	NM_020409.2	NP_065142.2	Q9HD33	RM47_HUMAN	mitochondrial ribosomal protein L47	171					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|stomach(1)	11	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			TCCAAAGATGTCTCTTCTCCA	0.428																																					p.D171V		Atlas-SNP	.											.	MRPL47	31	.	0			c.A512T						.						140	142	142					3																	179311574		2203	4300	6503	SO:0001583	missense	57129	exon5			AAGATGTCTCTTC	AF285120	CCDS3232.1, CCDS3233.1	3q26.33	2012-11-14			ENSG00000136522	ENSG00000136522		"Mitochondrial ribosomal proteins / large subunits"	16652	protein-coding gene	gene with protein product	"nasopharyngeal carcinoma metastasis-related 1"	611852				11551941	Standard	NM_177988		Approved	CGI-204, NCM1	uc003fjz.3	Q9HD33	OTTHUMG00000157784	ENST00000476781.1:c.512A>T	chr3.hg19:g.179311574T>A	ENSP00000417602:p.Asp171Val	76.0	0.0		73.0	28.0	NM_020409	Q6XRG1|Q8N5D1	Missense_Mutation	SNP	ENST00000476781.1	hg19	CCDS3232.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.144660	0.77888	.	.	ENSG00000136522	ENST00000476781;ENST00000259038;ENST00000392659	T;T;T	0.48201	1.28;1.35;0.82	5.95	5.95	0.96441	.	0.316986	0.38272	N	0.001749	T	0.67618	0.2912	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.72982	0.979;0.968	T	0.70565	-0.4837	10	0.87932	D	0	-15.2394	16.4116	0.83717	0.0:0.0:0.0:1.0	.	151;171	Q9HD33-2;Q9HD33	.;RM47_HUMAN	V	171;151;61	ENSP00000417602:D171V;ENSP00000259038:D151V;ENSP00000376427:D61V	ENSP00000259038:D151V	D	-	2	0	MRPL47	180794268	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	6.263000	0.72521	2.276000	0.75962	0.528000	0.53228	GAC	.	.		0.428	MRPL47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349623.1	NM_020409		A	179311574	T	A	179311574	3	1	162	1	0	0	0	0	1	0	0	0	9820	1667	58	4	252	4	MRPL47	3	179311574	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	66617881	179311574	18710856	36	24686										
EVC2	132884	hgsc.bcm.edu	37	chr4	5642462	5642462	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ttggggtgagaggtggccacTgctggtgagatttttcagca	16	6	1	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr4:5642462T>A	ENST00000344408.5	-	10	1302	c.1249A>T	c.(1249-1251)Agt>Tgt	p.S417C	EVC2_ENST00000310917.2_Missense_Mutation_p.S337C|EVC2_ENST00000344938.1_Missense_Mutation_p.S417C	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	417					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						aggtggccactgctggtgaga	0.453																																					p.S417C		Atlas-SNP	.											.	EVC2	202	.	0			c.A1249T						.						100	99	100					4																	5642462		2203	4300	6503	SO:0001583	missense	132884	exon10			GGCCACTGCTGGT	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1249A>T	chr4.hg19:g.5642462T>A	ENSP00000342144:p.Ser417Cys	89.0	0.0		76.0	25.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	T	11.46	1.646443	0.29246	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.78595	-1.19;-1.19;-1.19	4.25	-2.84	0.05751	.	0.537818	0.19199	N	0.120234	T	0.76076	0.3937	L	0.56769	1.78	0.09310	N	1	D	0.69078	0.997	P	0.60173	0.87	T	0.65672	-0.6111	10	0.56958	D	0.05	3.2052	1.3344	0.02142	0.136:0.2377:0.1401:0.4862	.	417	Q86UK5	LBN_HUMAN	C	417;337;417	ENSP00000339954:S417C;ENSP00000311683:S337C;ENSP00000342144:S417C	ENSP00000311683:S337C	S	-	1	0	EVC2	5693363	0.000000	0.05858	0.004000	0.12327	0.051000	0.14879	-0.774000	0.04684	-0.455000	0.07054	0.482000	0.46254	AGT	.	.		0.453	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		A	5642462	T	A	5642462	3	1	162	1	0	0	0	0	1	0	0	0	5288	1580	55	4	2729	4	EVC2	4	5642462	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10		5642462	185511814	37	24687										
ALB	213	hgsc.bcm.edu	37	chr4	74277801	74277801	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	atcttaccaaagtccacacgGaatgctgccatggagatctg	9	11	2	1	rs78340021|rs36067576		TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr4:74277801G>A	ENST00000503124.1	+	5	559	c.352G>A	c.(352-354)Gaa>Aaa	p.E118K	ALB_ENST00000401494.3_Missense_Mutation_p.E153K|ALB_ENST00000295897.4_Missense_Mutation_p.E268K|ALB_ENST00000509063.1_Missense_Mutation_p.E268K|ALB_ENST00000415165.2_Missense_Mutation_p.E76K|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.V265fs*8(2)		NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGTCCACACGGAATGCTGCCA	0.453																																					p.E268K		Atlas-SNP	.											.	ALB	132	.	2	Deletion - Frameshift(2)	liver(2)	c.G802A	GRCh37	CM050168	ALB	M	rs36067576	.						201	182	189					4																	74277801		2203	4300	6503	SO:0001583	missense	213	exon7			CACACGGAATGCT	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.352G>A	chr4.hg19:g.74277801G>A	ENSP00000421027:p.Glu118Lys	105.0	0.0		89.0	31.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.180770|5.180770	0.94846|0.94846	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202|ENST00000511370	T;T;T;T;T|.	0.71698|.	-0.59;-0.59;-0.59;-0.59;-0.59|.	6.02|6.02	6.02|6.02	0.97574|0.97574	Serum albumin-like (1);Serum albumin, N-terminal (3);|.	0.109676|.	0.64402|.	D|.	0.000010|.	T|T	0.78426|0.78426	0.4281|0.4281	M|M	0.77486|0.77486	2.375|2.375	0.51767|0.51767	D|D	0.999939|0.999939	D;D;D;D;D|.	0.89917|.	1.0;0.975;0.997;0.993;0.996|.	D;P;D;P;D|.	0.76575|.	0.988;0.832;0.95;0.902;0.942|.	T|T	0.76798|0.76798	-0.2826|-0.2826	10|5	0.87932|.	D|.	0|.	-42.9847|-42.9847	19.1045|19.1045	0.93287|0.93287	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	153;76;118;268;268|.	B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768|.	.;.;.;.;ALBU_HUMAN|.	K|E	268;76;118;268;153;277|112	ENSP00000295897:E268K;ENSP00000401820:E76K;ENSP00000421027:E118K;ENSP00000422784:E268K;ENSP00000384695:E153K|.	ENSP00000295897:E268K|.	E|G	+|+	1|2	0|0	ALB|ALB	74496665|74496665	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.755000|0.755000	0.42902|0.42902	4.321000|4.321000	0.59209|0.59209	2.865000|2.865000	0.98341|0.98341	0.655000|0.655000	0.94253|0.94253	GAA|GGA	.	.		0.453	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		A	74277801	G	A	74277801	3	1	162	1	0	0	0	0	1	0	0	0	486	1175	41	3	828	3	ALB	4	74277801	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	68635339	74277801	116876475	38	24688										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79328978	79328978	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	caggagccccagcccagagcGactccttccgcttcgaggta	11	16	0	1	rs371136161		TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr4:79328978G>A	ENST00000325942.6	+	31	4731	c.4291G>A	c.(4291-4293)Gac>Aac	p.D1431N	FRAS1_ENST00000264895.6_Missense_Mutation_p.D1431N	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1431					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AGCCCAGAGCGACTCCTTCCG	0.502																																					p.D1431N		Atlas-SNP	.											.	FRAS1	779	.	0			c.G4291A						.	G	ASN/ASP,ASN/ASP	0,4172		0,0,2086	59	67	64		4291,4291	5.7	1	4		64	2,8434		0,2,4216	no	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	23,23	0,2,6302	AA,AG,GG		0.0237,0.0,0.0159	probably-damaging,probably-damaging	1431/1977,1431/4013	79328978	2,12606	2086	4218	6304	SO:0001583	missense	80144	exon31			CAGAGCGACTCCT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.4291G>A	chr4.hg19:g.79328978G>A	ENSP00000326330:p.Asp1431Asn	150.0	0.0		188.0	66.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.619240	0.87460	0.0	2.37E-4	ENSG00000138759	ENST00000325942;ENST00000264895	T;T	0.48522	0.81;0.81	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.72252	0.3437	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.65443	0.935;0.932	T	0.76052	-0.3100	10	0.66056	D	0.02	.	18.7528	0.91821	0.0:0.0:1.0:0.0	.	1431;1431	E9PHH6;A2RRR8	.;.	N	1431	ENSP00000326330:D1431N;ENSP00000264895:D1431N	ENSP00000264895:D1431N	D	+	1	0	FRAS1	79548002	1.000000	0.71417	0.995000	0.50966	0.865000	0.49528	8.884000	0.92432	2.671000	0.90904	0.585000	0.79938	GAC	.	.		0.502	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			A	79328978	G	A	79328978	3	1	162	1	0	0	0	0	1	0	0	0	6050	1058	37	1	4413	1	FRAS1	4	79328978	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	5051177	79328978	111825298	39	24689										
PLAC8	51316	hgsc.bcm.edu	37	chr4	84026085	84026085	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gtcctgtagagagtcctcatTgcgacgcttgttccacacag	10	12	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr4:84026085T>C	ENST00000509973.1	-	2	159	c.36A>G	c.(34-36)gcA>gcG	p.A12A	PLAC8_ENST00000515389.1_Intron|PLAC8_ENST00000505406.1_Silent_p.A69A|PLAC8_ENST00000411416.2_Silent_p.A69A|PLAC8_ENST00000311507.4_Silent_p.A69A|PLAC8_ENST00000426923.2_Silent_p.A69A			Q9UHV8	PP13_HUMAN	placenta-specific 8	0	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|phospholipid metabolic process (GO:0006644)		carbohydrate binding (GO:0030246)|lysophospholipase activity (GO:0004622)			large_intestine(2)|lung(3)|ovary(1)	6		Hepatocellular(203;0.114)				GAGTCCTCATTGCGACGCTTG	0.443																																					p.A69A		Atlas-SNP	.											.	PLAC8	17	.	0			c.A207G						.						121	111	114					4																	84026085		2203	4300	6503	SO:0001819	synonymous_variant	51316	exon3			CCTCATTGCGACG	AF208846	CCDS3601.1	4q21.22	2006-05-20			ENSG00000145287	ENSG00000145287			19254	protein-coding gene	gene with protein product		607515				12758124, 12384430	Standard	NM_016619		Approved	onzin, C15	uc003hoe.3	Q9NZF1	OTTHUMG00000130294	ENST00000509973.1:c.36A>G	chr4.hg19:g.84026085T>C		228.0	0.0		217.0	83.0	NM_001130716	C5HZ15	Silent	SNP	ENST00000509973.1	hg19																																																																																				.	.		0.443	PLAC8-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363078.1	NM_016619		C	84026085	T	C	84026085	2	2	162	1	0	0	0	0	0	0	0	1	12024	1799	63	2		2	PLAC8	4	84026085	Silent	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	4697107	84026085	107128191	40	24690										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85781608	85781608	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tatacagtttctcttcttgtTccttctgagtcatgtgccgg	8	10	4	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr4:85781608T>A	ENST00000295888.4	-	4	544	c.137A>T	c.(136-138)gAa>gTa	p.E46V	WDFY3_ENST00000322366.6_Missense_Mutation_p.E46V	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	46					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CTCTTCTTGTTCCTTCTGAGT	0.547																																					p.E46V		Atlas-SNP	.											.	WDFY3	314	.	0			c.A137T						.						150	137	142					4																	85781608		2203	4300	6503	SO:0001583	missense	23001	exon4			TCTTGTTCCTTCT	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.137A>T	chr4.hg19:g.85781608T>A	ENSP00000295888:p.Glu46Val	94.0	0.0		104.0	35.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	T	35	5.495060	0.96339	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000509172	T;T	0.70045	-0.45;-0.45	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.80423	0.4620	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.73380	0.98;0.854	T	0.82544	-0.0404	10	0.87932	D	0	.	16.0204	0.80478	0.0:0.0:0.0:1.0	.	46;46	E2QRK8;Q8IZQ1	.;WDFY3_HUMAN	V	46	ENSP00000318466:E46V;ENSP00000295888:E46V	ENSP00000295888:E46V	E	-	2	0	WDFY3	86000632	1.000000	0.71417	0.992000	0.48379	0.992000	0.81027	7.806000	0.86020	2.174000	0.68829	0.533000	0.62120	GAA	.	.		0.547	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85781608	T	A	85781608	3	1	162	1	0	0	0	0	1	0	0	0	17285	1783	62	4	10746	4	WDFY3	4	85781608	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	1755523	85781608	105372668	41	24691										
GYPB	2994	hgsc.bcm.edu	37	chr4	144920597	144920597	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	acgatggacaagttgtcccgTttctcctataaagcaaaatt	7	9	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr4:144920597T>A	ENST00000502664.1	-	3	193	c.142A>T	c.(142-144)Acg>Tcg	p.T48S	GYPB_ENST00000283126.7_Missense_Mutation_p.T48S|GYPB_ENST00000510196.2_5'UTR|GYPB_ENST00000429670.2_Missense_Mutation_p.T48S|GYPB_ENST00000513128.1_Missense_Mutation_p.T15S|RP11-673E1.4_ENST00000506982.1_RNA	NM_002100.4	NP_002091	P06028	GLPB_HUMAN	glycophorin B (MNS blood group)	48			T -> M (in S antigen and Mit antigen; dbSNP:rs7683365). {ECO:0000269|PubMed:11239234}.			integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|skin(1)	4	all_hematologic(180;0.158)					AGTTGTCCCGTTTCTCCTATA	0.323																																					p.T48S		Atlas-SNP	.											.	GYPB	17	.	0			c.A142T						.						47	51	50					4																	144920597		2182	4299	6481	SO:0001583	missense	2994	exon3			GTCCCGTTTCTCC		CCDS54809.1	4q31.21	2014-09-17	2006-02-23			ENSG00000250361		"CD molecules", "Blood group antigens"	4703	protein-coding gene	gene with protein product		111740	"glycophorin B (includes Ss blood group)", "glycophorin B (Ss blood group)"	MNS			Standard	NM_002100		Approved	GPB, SS, CD235b		P06028		ENST00000502664.1:c.142A>T	chr4.hg19:g.144920597T>A	ENSP00000427690:p.Thr48Ser	423.0	0.0		439.0	181.0	NM_002100	B8Q174|E2QBW7|Q0VAF4|Q58HE9|Q58HF0|Q58HF1|Q9UCH7	Missense_Mutation	SNP	ENST00000502664.1	hg19	CCDS54809.1	.	.	.	.	.	.	.	.	.	.	t	0.972	-0.699786	0.03279	.	.	ENSG00000250361	ENST00000283126;ENST00000502664;ENST00000513128;ENST00000429670	T;T;T;T	0.14266	2.52;2.52;2.52;3.15	1.85	-3.71	0.04424	.	1.054030	0.07555	N	0.916052	T	0.05044	0.0135	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.41016	-0.9532	9	0.12430	T	0.62	.	1.0137	0.01502	0.19:0.145:0.3852:0.2797	.	48	E2QBW7	.	S	48;48;15;48	ENSP00000283126:T48S;ENSP00000427690:T48S;ENSP00000425244:T15S;ENSP00000394200:T48S	ENSP00000283126:T48S	T	-	1	0	GYPB	145140047	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.151000	0.03175	-1.420000	0.02009	-1.667000	0.00748	ACG	.	.		0.323	GYPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364791.1	NM_002100		A	144920597	T	A	144920597	3	1	162	1	0	0	0	0	1	0	0	0	6918	1725	60	4	145	4	GYPB	4	144920597	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	59138989	144920597	46233679	42	24692										
NR3C2	4306	hgsc.bcm.edu	37	chr4	149357529	149357529	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	agagtcagacataaatgatcTcaagggcgtgttcacacaac	9	9	3	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr4:149357529T>A	ENST00000358102.3	-	2	846	c.484A>T	c.(484-486)Aga>Tga	p.R162*	NR3C2_ENST00000355292.3_Nonsense_Mutation_p.R162*|NR3C2_ENST00000512865.1_Nonsense_Mutation_p.R162*|NR3C2_ENST00000344721.4_Nonsense_Mutation_p.R162*|NR3C2_ENST00000511528.1_Nonsense_Mutation_p.R162*	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	162	Modulating.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	ATAAATGATCTCAAGGGCGTG	0.463																																					p.R162X	Melanoma(27;428 957 40335 51025 51111)	Atlas-SNP	.											.	NR3C2	94	.	0			c.A484T						.						104	103	104					4																	149357529		2203	4300	6503	SO:0001587	stop_gained	4306	exon2			ATGATCTCAAGGG	M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.484A>T	chr4.hg19:g.149357529T>A	ENSP00000350815:p.Arg162*	46.0	0.0		51.0	14.0	NM_001166104	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Nonsense_Mutation	SNP	ENST00000358102.3	hg19	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	T	37	6.128488	0.97310	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000544252;ENST00000342437;ENST00000511528	.	.	.	5.56	-0.276	0.12902	.	0.265869	0.35838	N	0.002953	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1596	0.81693	0.0:0.0:0.5715:0.4285	.	.	.	.	X	162	.	.	R	-	1	2	NR3C2	149576979	0.998000	0.40836	0.684000	0.30055	0.990000	0.78478	0.671000	0.25172	-0.235000	0.09767	0.383000	0.25322	AGA	.	.		0.463	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			A	149357529	T	A	149357529	4	1	162	1	0	0	0	0	0	1	0	0	10640	1559	54	4	2502	4	NR3C2	4	149357529	Nonsense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	4436932	149357529	41796747	43	24693										
LRBA	987	hgsc.bcm.edu	37	chr4	151935691	151935691	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgatggggagccctggtttcAgagacaatgcacccccttca	11	12	2	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr4:151935691A>G	ENST00000357115.3	-	2	347	c.104T>C	c.(103-105)cTg>cCg	p.L35P	LRBA_ENST00000535741.1_Missense_Mutation_p.L35P|LRBA_ENST00000507224.1_Missense_Mutation_p.L35P|LRBA_ENST00000510413.1_Missense_Mutation_p.L35P	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	35						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					CCCTGGTTTCAGAGACAATGC	0.522																																					p.L35P		Atlas-SNP	.											.	LRBA	253	.	0			c.T104C						.						63	55	58					4																	151935691		2203	4300	6503	SO:0001583	missense	987	exon2			GGTTTCAGAGACA	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.104T>C	chr4.hg19:g.151935691A>G	ENSP00000349629:p.Leu35Pro	148.0	0.0		167.0	64.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.408210	0.83340	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.63744	0.37;0.52;0.37;-0.06	5.24	5.24	0.73138	.	0.540003	0.16201	N	0.224916	T	0.74726	0.3754	L	0.53249	1.67	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.99	D;D;P	0.78314	0.991;0.951;0.885	T	0.75246	-0.3385	10	0.62326	D	0.03	.	13.3454	0.60571	1.0:0.0:0.0:0.0	.	35;35;35	P50851;Q6P1X2;P50851-2	LRBA_HUMAN;.;.	P	35	ENSP00000446299:L35P;ENSP00000421552:L35P;ENSP00000349629:L35P;ENSP00000422180:L35P	ENSP00000349629:L35P	L	-	2	0	LRBA	152155141	1.000000	0.71417	0.980000	0.43619	0.841000	0.47740	6.272000	0.72575	1.988000	0.58038	0.454000	0.30748	CTG	.	.		0.522	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			G	151935691	A	G	151935691	3	3	162	1	0	0	0	0	1	0	0	0	8940	188	7	2	8715	2	LRBA	4	151935691	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	2578162	151935691	39218585	44	24694										
MTNR1A	4543	hgsc.bcm.edu	37	chr4	187454913	187454913	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gtttccatttaaccctatcgGccacgtcgttagagctgtcc	8	13	0	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr4:187454913G>T	ENST00000307161.5	-	2	1184	c.983C>A	c.(982-984)gCc>gAc	p.A328D	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	328					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	AACCCTATCGGCCACGTCGTT	0.463																																					p.A328D		Atlas-SNP	.											.	MTNR1A	46	.	0			c.C983A						.						134	131	132					4																	187454913		2203	4300	6503	SO:0001583	missense	4543	exon2			CTATCGGCCACGT		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"GPCR / Class A : Melatonin receptors"	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.983C>A	chr4.hg19:g.187454913G>T	ENSP00000302811:p.Ala328Asp	155.0	0.0		138.0	12.0	NM_005958	A0AVC5|B0M0L2	Missense_Mutation	SNP	ENST00000307161.5	hg19	CCDS3848.1	.	.	.	.	.	.	.	.	.	.	G	3.400	-0.122501	0.06795	.	.	ENSG00000168412	ENST00000307161	T	0.71934	-0.61	4.66	1.78	0.24846	.	0.416861	0.26971	N	0.021562	T	0.57154	0.2034	M	0.65975	2.015	0.26810	N	0.969029	B	0.20550	0.046	B	0.20184	0.028	T	0.37502	-0.9703	10	0.12430	T	0.62	-1.1541	0.9476	0.01369	0.2233:0.1312:0.3768:0.2687	.	328	P48039	MTR1A_HUMAN	D	328	ENSP00000302811:A328D	ENSP00000302811:A328D	A	-	2	0	MTNR1A	187691907	0.608000	0.26966	0.005000	0.12908	0.016000	0.09150	0.581000	0.23819	0.097000	0.17492	0.655000	0.94253	GCC	.	.		0.463	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1			T	187454913	G	T	187454913	3	4	162	1	0	0	0	0	1	0	0	0	9960	1203	42	3	73	3	MTNR1A	4	187454913	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	35519222	187454913	3699363	45	24695										
BASP1	10409	hgsc.bcm.edu	37	chr5	17275577	17275577	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gccaaggaggaggccccgaaGgcggagcccgagaagacgga	18	11	0	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr5:17275577G>A	ENST00000322611.3	+	2	512	c.252G>A	c.(250-252)aaG>aaA	p.K84K		NM_001271606.1|NM_006317.3	NP_001258535.1|NP_006308.3	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein 1	84					diaphragm development (GO:0060539)|glomerular visceral epithelial cell differentiation (GO:0072112)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|metanephric mesenchyme development (GO:0072075)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of heart growth (GO:0060421)|positive regulation of metanephric ureteric bud development (GO:2001076)|substantia nigra development (GO:0021762)|thorax and anterior abdomen determination (GO:0007356)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(8)	9						AGGCCCCGAAGGCGGAGCCCG	0.756																																					p.K84K		Atlas-SNP	.											.	BASP1	29	.	0			c.G252A						.						11	16	15					5																	17275577		2007	3903	5910	SO:0001819	synonymous_variant	10409	exon2			CCCGAAGGCGGAG	AF039656	CCDS3888.1	5p15.1	2010-12-03			ENSG00000176788	ENSG00000176788			957	protein-coding gene	gene with protein product		605940				9310187, 9749536	Standard	NM_001271606		Approved	NAP-22, NAP22, CAP23, CAP-23	uc031siz.1	P80723	OTTHUMG00000131061	ENST00000322611.3:c.252G>A	chr5.hg19:g.17275577G>A		101.0	0.0		107.0	38.0	NM_006317	B4DJA8|D3DTD5|O43596|Q5U0S0|Q9BWA5	Silent	SNP	ENST00000322611.3	hg19	CCDS3888.1																																																																																			.	.		0.756	BASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253716.2			A	17275577	G	A	17275577	2	1	162	1	0	0	0	0	0	0	0	1	1317	991	35	3		3	BASP1	5	17275577	Silent	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10		17275577	163639683	46	24696										
HCN1	348980	hgsc.bcm.edu	37	chr5	45303784	45303785	+	Frame_Shift_Ins	INS	-	-	T													0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	accgtgttgaatgaaatacaINStttttttacccacggctcct							TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr5:45303784_45303785insT	ENST00000303230.4	-	6	1591_1592	c.1534_1535insA	c.(1534-1536)atgfs	p.M512fs		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	512					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.M512fs*17(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						AATGAAATACATTTTTTTACCC	0.401																																					p.M512fs		Atlas-INDEL	.											.,1	HCN1	298	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1535_1536insA						.																																			SO:0001589	frameshift_variant	348980	exon6			.	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1535dupA	chr5.hg19:g.45303791_45303791dupT	ENSP00000307342:p.Met512fs	115.0	0.0		129.0	39.0	NM_021072		Frame_Shift_Ins	INS	ENST00000303230.4	hg19	CCDS3952.1																																																																																			.	.		0.401	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		T	45303785	-	T	45303784	7	5	162	1	0	1	1	0	0	0	0	0	7005	217	8	0	1149	0	HCN1	5	45303784	Frame_Shift_Ins	INS	-	TCGA-DD-AACK-01A-11D-A40R-10	28028207	45303784	135611476	47	24697										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128994333	128994333	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gttggctgtgatggtttattAgggtctcttgcaagagaaga	14	4	1	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr5:128994333A>C	ENST00000274487.4	+	15	2455	c.2310A>C	c.(2308-2310)ttA>ttC	p.L770F	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	770	Cys-rich.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		ATGGTTTATTAGGGTCTCTTG	0.378																																					p.L770F		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.A2310C						.						176	173	174					5																	128994333		2203	4300	6503	SO:0001583	missense	171019	exon15			TTTATTAGGGTCT	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.2310A>C	chr5.hg19:g.128994333A>C	ENSP00000274487:p.Leu770Phe	77.0	0.0		75.0	23.0	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.038989	0.55003	.	.	ENSG00000145808	ENST00000274487	T	0.69306	-0.39	3.89	0.284	0.15701	.	0.114263	0.33327	N	0.005030	T	0.64692	0.2621	L	0.58510	1.815	0.41536	D	0.988481	D	0.56968	0.978	P	0.50754	0.649	T	0.61431	-0.7064	9	.	.	.	.	8.3034	0.32027	0.6485:0.0:0.3515:0.0	.	770	Q8TE59	ATS19_HUMAN	F	770	ENSP00000274487:L770F	.	L	+	3	2	ADAMTS19	129022232	0.988000	0.35896	0.998000	0.56505	0.987000	0.75469	0.277000	0.18734	0.046000	0.15833	-0.263000	0.10527	TTA	.	.		0.378	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		C	128994333	A	C	128994333	3	2	162	1	0	0	0	0	1	0	0	0	264	417	15	5	2368	5	ADAMTS19	5	128994333	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	83690549	128994333	51920927	48	24698										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148406144	148406144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ccctgactcacctggcggtaTttaggttccgataaagctgc	10	12	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr5:148406144T>C	ENST00000515425.1	-	12	3145	c.3044A>G	c.(3043-3045)aAt>aGt	p.N1015S	SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000394358.2_3'UTR|SH3TC2_ENST00000538184.1_Missense_Mutation_p.N562S|SH3TC2_ENST00000512049.1_Missense_Mutation_p.N1008S	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1015					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGGCGGTATTTAGGTTCCG	0.547																																					p.N1015S		Atlas-SNP	.											.	SH3TC2	178	.	0			c.A3044G						.						83	89	87					5																	148406144		2203	4300	6503	SO:0001583	missense	79628	exon12			GCGGTATTTAGGT	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.3044A>G	chr5.hg19:g.148406144T>C	ENSP00000423660:p.Asn1015Ser	124.0	0.0		109.0	33.0	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	T	9.446	1.089388	0.20390	.	.	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049	T;T;T	0.80566	-1.39;-0.97;-0.97	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.67031	0.2850	L	0.40543	1.245	0.80722	D	1	P;P;P	0.41188	0.495;0.741;0.495	B;B;B	0.29598	0.104;0.104;0.104	T	0.67906	-0.5549	10	0.33141	T	0.24	-22.2996	10.2038	0.43101	0.0:0.083:0.0:0.917	.	1008;1015;1015	Q14CC0;E9PDF1;Q8TF17	.;.;S3TC2_HUMAN	S	562;1015;1008	ENSP00000441427:N562S;ENSP00000423660:N1015S;ENSP00000421860:N1008S	ENSP00000425627:N1015S	N	-	2	0	SH3TC2	148386337	1.000000	0.71417	0.948000	0.38648	0.006000	0.05464	3.440000	0.52886	2.254000	0.74563	0.482000	0.46254	AAT	.	.		0.547	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		C	148406144	T	C	148406144	3	2	162	1	0	0	0	0	1	0	0	0	14277	1493	52	2	846	2	SH3TC2	5	148406144	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	19411811	148406144	32509116	49	24699										
PNPLA1	285848	hgsc.bcm.edu	37	chr6	36269664	36269664	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tttatcttaattcttcctccAagagagtgattttcccccgg	6	11	2	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr6:36269664A>T	ENST00000394571.2	+	6	802	c.802A>T	c.(802-804)Aag>Tag	p.K268*	PNPLA1_ENST00000388715.3_Nonsense_Mutation_p.K173*|PNPLA1_ENST00000312917.5_Nonsense_Mutation_p.K182*	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	268					lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						TTCTTCCTCCAAGAGAGTGAT	0.498											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K268X		Atlas-SNP	.											.	PNPLA1	92	.	0			c.A802T						.						82	85	84					6																	36269664		2203	4300	6503	SO:0001587	stop_gained	285848	exon6			TCCTCCAAGAGAG		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"Patatin-like phospholipase domain containing"	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.802A>T	chr6.hg19:g.36269664A>T	ENSP00000378072:p.Lys268*	76.0	0.0	861	80.0	22.0	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Nonsense_Mutation	SNP	ENST00000394571.2	hg19	CCDS54997.1	.	.	.	.	.	.	.	.	.	.	A	36	5.767684	0.96914	.	.	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	.	.	.	5.61	5.61	0.85477	.	0.000000	0.52532	D	0.000075	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.2608	12.1977	0.54307	1.0:0.0:0.0:0.0	.	.	.	.	X	173;182;269;268	.	ENSP00000321116:K182X	K	+	1	0	PNPLA1	36377642	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.247000	0.58750	2.136000	0.66102	0.459000	0.35465	AAG	.	.		0.498	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676		T	36269664	A	T	36269664	4	4	162	1	0	0	0	0	0	1	0	0	12173	131	5	4	851	4	PNPLA1	6	36269664	Nonsense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10		36269664	134845403	50	24700										
FAM135A	57579	hgsc.bcm.edu	37	chr6	71185406	71185406	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	aatgaattttctattatcctTggatctacacttcacagatg	5	8	3	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr6:71185406T>A	ENST00000418814.2	+	7	952	c.338T>A	c.(337-339)tTg>tAg	p.L113*	FAM135A_ENST00000457062.2_Nonsense_Mutation_p.L70*|FAM135A_ENST00000370479.3_Nonsense_Mutation_p.L70*|FAM135A_ENST00000505769.1_Nonsense_Mutation_p.L113*|FAM135A_ENST00000505868.1_Nonsense_Mutation_p.L113*|FAM135A_ENST00000361499.3_Nonsense_Mutation_p.L113*	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	113										breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						CTATTATCCTTGGATCTACAC	0.284																																					p.L113X		Atlas-SNP	.											.	FAM135A	181	.	0			c.T338A						.						60	65	63					6																	71185406		2201	4292	6493	SO:0001587	stop_gained	57579	exon5			TATCCTTGGATCT	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"KIAA1411"	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.338T>A	chr6.hg19:g.71185406T>A	ENSP00000410768:p.Leu113*	130.0	0.0		105.0	41.0	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Nonsense_Mutation	SNP	ENST00000418814.2	hg19	CCDS55028.1	.	.	.	.	.	.	.	.	.	.	T	38	7.185762	0.98121	.	.	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000515323;ENST00000457062;ENST00000361499;ENST00000505868	.	.	.	5.67	5.67	0.87782	.	0.077054	0.56097	D	0.000031	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.2002	0.82067	0.0:0.0:0.0:1.0	.	.	.	.	X	113;70;113;113;70;113;113	.	ENSP00000194672:L113X	L	+	2	0	FAM135A	71242127	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.595000	0.82710	2.285000	0.76669	0.528000	0.53228	TTG	.	.		0.284	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		A	71185406	T	A	71185406	4	1	162	1	0	0	0	0	0	1	0	0	5453	1821	63	4	352	4	FAM135A	6	71185406	Nonsense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	34915742	71185406	99929661	51	24701										
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74228303	74228303	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cgggtttgagaacaccagtcTccactcggccaacaggaaca	10	13	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr6:74228303T>A	ENST00000316292.9	-	5	1794	c.803A>T	c.(802-804)gAg>gTg	p.E268V	EEF1A1_ENST00000309268.6_Missense_Mutation_p.E268V|EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000331523.2_Missense_Mutation_p.E268V	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	268					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						AACACCAGTCTCCACTCGGCC	0.413											OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.E268V		Atlas-SNP	.											.	EEF1A1	56	.	0			c.A803T						.						71	72	72					6																	74228303		2133	4269	6402	SO:0001583	missense	1915	exon6			CCAGTCTCCACTC	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.803A>T	chr6.hg19:g.74228303T>A	ENSP00000339063:p.Glu268Val	280.0	0.0	1151	317.0	98.0	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.296290	0.81025	.	.	ENSG00000156508	ENST00000316292;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.64803	-0.12;-0.12;-0.12	4.71	4.71	0.59529	Translation elongation factor EFTu/EF1A, domain 2 (2);Translation elongation/initiation factor/Ribosomal, beta-barrel (2);	0.126928	0.50627	U	0.000107	D	0.86793	0.6018	H	0.99650	4.68	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.92591	0.6083	10	0.87932	D	0	.	14.5361	0.67960	0.0:0.0:0.0:1.0	.	268;268;268;268	P68104;Q53HR5;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;.;EF1A3_HUMAN	V	268;268;268;247	ENSP00000339063:E268V;ENSP00000339053:E268V;ENSP00000330054:E268V	ENSP00000339053:E268V	E	-	2	0	EEF1A1	74285024	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.654000	0.83653	1.883000	0.54544	0.454000	0.30748	GAG	.	.		0.413	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		A	74228303	T	A	74228303	3	1	162	1	0	0	0	0	1	0	0	0	4925	1551	54	4	597	4	EEF1A1	6	74228303	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	3042897	74228303	96886764	52	24702										
PHIP	55023	hgsc.bcm.edu	37	chr6	79679863	79679863	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	taatcccacttcatactttaTgccaactattttcataagtt	2	10	2	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr6:79679863T>C	ENST00000275034.4	-	26	3192	c.3025A>G	c.(3025-3027)Ata>Gta	p.I1009V	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1009	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TCATACTTTATGCCAACTATT	0.363																																					p.I1009V		Atlas-SNP	.											.	PHIP	177	.	0			c.A3025G						.						118	119	118					6																	79679863		2203	4300	6503	SO:0001583	missense	55023	exon26			ACTTTATGCCAAC	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.3025A>G	chr6.hg19:g.79679863T>C	ENSP00000275034:p.Ile1009Val	74.0	0.0		62.0	22.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.269135	0.80469	.	.	ENSG00000146247	ENST00000275034	T	0.39406	1.08	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.49474	0.1559	M	0.62209	1.925	0.80722	D	1	P;P	0.48640	0.913;0.913	P;P	0.61592	0.891;0.891	T	0.47262	-0.9131	9	.	.	.	-20.8541	14.7826	0.69776	0.0:0.0:0.0:1.0	.	1009;1009	A7J992;Q8WWQ0	.;PHIP_HUMAN	V	1009	ENSP00000275034:I1009V	.	I	-	1	0	PHIP	79736582	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.094000	0.63399	0.455000	0.32223	ATA	.	.		0.363	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			C	79679863	T	C	79679863	3	2	162	1	0	0	0	0	1	0	0	0	11851	1464	51	2	2500	2	PHIP	6	79679863	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	5451560	79679863	91435204	53	24703										
FBXL4	26235	hgsc.bcm.edu	37	chr6	99353398	99353398	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gagactgtagaaattccagaGaagtgtcatctagttttgcc	10	7	2	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr6:99353398G>A	ENST00000369244.2	-	6	1435	c.1007C>T	c.(1006-1008)tCt>tTt	p.S336F	FBXL4_ENST00000229971.1_Missense_Mutation_p.S336F	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	336					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		AAATTCCAGAGAAGTGTCATC	0.448																																					p.S336F		Atlas-SNP	.											.	FBXL4	54	.	0			c.C1007T						.						190	174	179					6																	99353398		2203	4300	6503	SO:0001583	missense	26235	exon5			TCCAGAGAAGTGT	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"F-boxes / Leucine-rich repeats"	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.1007C>T	chr6.hg19:g.99353398G>A	ENSP00000358247:p.Ser336Phe	133.0	0.0		107.0	31.0	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	hg19	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.773871	0.49786	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.18338	2.22;2.22	5.43	5.43	0.79202	.	0.102077	0.64402	D	0.000001	T	0.16642	0.0400	M	0.71036	2.16	0.80722	D	1	P	0.45348	0.856	P	0.44477	0.451	T	0.01767	-1.1278	10	0.30078	T	0.28	.	17.412	0.87488	0.0:0.0:1.0:0.0	.	336	Q9UKA2	FBXL4_HUMAN	F	336	ENSP00000358247:S336F;ENSP00000229971:S336F	ENSP00000229971:S336F	S	-	2	0	FBXL4	99460119	1.000000	0.71417	0.136000	0.22124	0.428000	0.31595	9.476000	0.97823	2.543000	0.85770	0.591000	0.81541	TCT	.	.		0.448	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			A	99353398	G	A	99353398	3	1	162	1	0	0	0	0	1	0	0	0	5729	942	33	3	878	3	FBXL4	6	99353398	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	19673535	99353398	71761669	54	24704										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129813106	129813106	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	caaaacctgacagttgaacaGcctatcgaagttaaaaagct	7	9	0	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr6:129813106G>A	ENST00000421865.2	+	57	8008	c.7959G>A	c.(7957-7959)caG>caA	p.Q2653Q	LAMA2_ENST00000498257.1_3'UTR	NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2653	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CAGTTGAACAGCCTATCGAAG	0.373																																					p.Q2653Q		Atlas-SNP	.											.	LAMA2	481	.	0			c.G7959A						.						65	67	67					6																	129813106		2203	4300	6503	SO:0001819	synonymous_variant	3908	exon57			TGAACAGCCTATC	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.7959G>A	chr6.hg19:g.129813106G>A		111.0	0.0		112.0	41.0	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	hg19	CCDS5138.1																																																																																			.	.		0.373	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129813106	G	A	129813106	2	1	162	1	0	0	0	0	0	0	0	1	8615	962	34	3		3	LAMA2	6	129813106	Silent	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	30459708	129813106	41301961	55	24705										
SNX8	29886	hgsc.bcm.edu	37	chr7	2309216	2309216	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tggccctggtagccagcttaCagttcaggaattcgtccccg	11	13	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr7:2309216C>T	ENST00000222990.3	-	5	641	c.599G>A	c.(598-600)tGt>tAt	p.C200Y		NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	200					early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)	early endosome membrane (GO:0031901)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(2)|skin(3)	26		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		AGCCAGCTTACAGTTCAGGAA	0.388																																					p.C200Y		Atlas-SNP	.											.	SNX8	46	.	0			c.G599A						.						79	69	72					7																	2309216		2203	4300	6503	SO:0001583	missense	29886	exon5			AGCTTACAGTTCA	AF121858	CCDS5331.1	7p22.3	2010-08-05			ENSG00000106266	ENSG00000106266		"Sorting nexins"	14972	protein-coding gene	gene with protein product		614905					Standard	NM_013321		Approved	Mvp1	uc003slw.3	Q9Y5X2	OTTHUMG00000151512	ENST00000222990.3:c.599G>A	chr7.hg19:g.2309216C>T	ENSP00000222990:p.Cys200Tyr	39.0	0.0		40.0	16.0	NM_013321	A4D207|Q96I67	Missense_Mutation	SNP	ENST00000222990.3	hg19	CCDS5331.1	.	.	.	.	.	.	.	.	.	.	C	9.033	0.987765	0.18966	.	.	ENSG00000106266	ENST00000222990;ENST00000435060;ENST00000457286;ENST00000435336	.	.	.	3.64	3.64	0.41730	.	0.130437	0.53938	D	0.000051	T	0.42291	0.1196	L	0.36672	1.1	0.45621	D	0.998559	B	0.15473	0.013	B	0.10450	0.005	T	0.32929	-0.9888	9	0.02654	T	1	.	13.8704	0.63615	0.0:1.0:0.0:0.0	.	200	Q9Y5X2	SNX8_HUMAN	Y	200;186;147;147	.	ENSP00000222990:C200Y	C	-	2	0	SNX8	2275742	1.000000	0.71417	0.973000	0.42090	0.703000	0.40648	4.827000	0.62723	1.735000	0.51646	0.462000	0.41574	TGT	.	.		0.388	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322949.2			T	2309216	C	T	2309216	3	4	162	1	0	0	0	0	1	0	0	0	14923	478	17	3	826	3	SNX8	7	2309216	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10		2309216	156829447	56	24706										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5385411	5385411	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cgtcctcctcctcgagctccTcctcctcgtcctcctcctcc	4	24	0	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr7:5385411T>A	ENST00000430969.1	-	18	5849	c.5501A>T	c.(5500-5502)gAg>gTg	p.E1834V	TNRC18_ENST00000399537.4_Missense_Mutation_p.E1834V	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1834	Poly-Glu.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		ctcgagctcctcctcctcgtc	0.706																																					p.E1834V		Atlas-SNP	.											.	TNRC18	311	.	0			c.A5501T						.						4	4	4					7																	5385411		1410	3314	4724	SO:0001583	missense	84629	exon18			AGCTCCTCCTCCT	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.5501A>T	chr7.hg19:g.5385411T>A	ENSP00000395538:p.Glu1834Val	56.0	0.0		59.0	28.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	.	11.84	1.759032	0.31137	.	.	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544	T;T	0.12774	2.65;2.65	5.17	3.7	0.42460	.	1.029360	0.07800	N	0.956285	T	0.12518	0.0304	L	0.36672	1.1	0.21719	N	0.999571	B	0.24186	0.099	B	0.19391	0.025	T	0.36601	-0.9741	10	0.32370	T	0.25	.	8.8881	0.35416	0.2489:0.0:0.0:0.7511	.	1834	O15417	TNC18_HUMAN	V	1834;1834;889	ENSP00000382452:E1834V;ENSP00000395538:E1834V	ENSP00000382452:E1834V	E	-	2	0	TNRC18	5351937	0.696000	0.27757	0.334000	0.25495	0.938000	0.57974	2.898000	0.48672	0.514000	0.28300	0.523000	0.50628	GAG	.	.		0.706	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5385411	T	A	5385411	3	1	162	1	0	0	0	0	1	0	0	0	16354	1551	54	4	3457	4	TNRC18	7	5385411	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	3076195	5385411	153753252	57	24707										
CCT6A	908	hgsc.bcm.edu	37	chr7	56125786	56125786	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cttgtaacgtgtcattagagTatgagaaaacgtaagtttat	9	4	1	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr7:56125786T>C	ENST00000275603.4	+	6	934	c.715T>C	c.(715-717)Tat>Cat	p.Y239H	CCT6A_ENST00000335503.3_Missense_Mutation_p.Y194H|SNORA15_ENST00000384439.1_RNA|SNORA22_ENST00000383876.1_RNA|CCT6A_ENST00000540286.1_Missense_Mutation_p.Y208H	NM_001762.3	NP_001753.1	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A (zeta 1)	239					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|cervix(2)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	15	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GTCATTAGAGTATGAGAAAAC	0.418																																					p.Y239H		Atlas-SNP	.											.	CCT6A	44	.	0			c.T715C						.						67	59	62					7																	56125786		2203	4300	6503	SO:0001583	missense	908	exon6			TTAGAGTATGAGA	M94083	CCDS5523.1, CCDS34640.1	7p11.2	2011-09-02			ENSG00000146731	ENSG00000146731		"Heat Shock Proteins / Chaperonins"	1620	protein-coding gene	gene with protein product		104613		CCT6		1352881, 8034610	Standard	NM_001762		Approved	TTCP20, TCPZ, Cctz, HTR3, TCP20	uc003trl.1	P40227	OTTHUMG00000022842	ENST00000275603.4:c.715T>C	chr7.hg19:g.56125786T>C	ENSP00000275603:p.Tyr239His	69.0	0.0		82.0	33.0	NM_001762	A6NCD2|Q3KP28|Q75LP4|Q96S46	Missense_Mutation	SNP	ENST00000275603.4	hg19	CCDS5523.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.511151	0.64522	.	.	ENSG00000146731	ENST00000275603;ENST00000335503;ENST00000540286;ENST00000539340	T;T;T	0.68903	-0.36;-0.36;-0.36	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.86802	0.6020	H	0.95328	3.655	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.997	D;D;D	0.75484	0.986;0.981;0.947	D	0.90640	0.4574	10	0.87932	D	0	-14.8046	14.7035	0.69171	0.0:0.0:0.0:1.0	.	208;194;239	B4DPJ8;A6NCD2;P40227	.;.;TCPZ_HUMAN	H	239;194;208;97	ENSP00000275603:Y239H;ENSP00000352019:Y194H;ENSP00000438488:Y208H	ENSP00000275603:Y239H	Y	+	1	0	CCT6A	56093280	1.000000	0.71417	0.991000	0.47740	0.281000	0.26958	7.243000	0.78219	2.151000	0.67156	0.397000	0.26171	TAT	.	.		0.418	CCT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251526.2	NM_001762		C	56125786	T	C	56125786	3	2	162	1	0	0	0	0	1	0	0	0	2959	1638	57	2	737	2	CCT6A	7	56125786	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	50740375	56125786	103012877	58	24708										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	71130560	71130560	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tacaagtctcatgtgtacatAgcgtggaacctgccgctgga	11	10	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr7:71130560A>T	ENST00000333538.5	+	7	1879	c.1245A>T	c.(1243-1245)atA>atT	p.I415I	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	415					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ATGTGTACATAGCGTGGAACC	0.458																																					p.I415I		Atlas-SNP	.											.	WBSCR17	208	.	0			c.A1245T						.						91	74	80					7																	71130560		2203	4300	6503	SO:0001819	synonymous_variant	64409	exon7			GTACATAGCGTGG	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1245A>T	chr7.hg19:g.71130560A>T		78.0	0.0		66.0	26.0	NM_022479	Q8NFV9|Q9NTA8	Silent	SNP	ENST00000333538.5	hg19	CCDS5540.1																																																																																			.	.		0.458	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		T	71130560	A	T	71130560	2	4	162	1	0	0	0	0	0	0	0	1	17279	410	15	4		4	WBSCR17	7	71130560	Silent	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	15004774	71130560	88008103	59	24709										
AKR1D1	6718	hgsc.bcm.edu	37	chr7	137761312	137761312	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	atacctctaagtgatggaaaCagcattcccatcatcggact	7	11	2	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr7:137761312C>A	ENST00000242375.3	+	1	90	c.48C>A	c.(46-48)aaC>aaA	p.N16K	AKR1D1_ENST00000411726.2_Missense_Mutation_p.N16K|AKR1D1_ENST00000468877.2_Intron|AKR1D1_ENST00000432161.1_Missense_Mutation_p.N16K	NM_005989.3	NP_005980.1	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1	16					androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|C21-steroid hormone metabolic process (GO:0008207)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|steroid binding (GO:0005496)			endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	23					Azelaic Acid(DB00548)|Finasteride(DB01216)	GTGATGGAAACAGCATTCCCA	0.423																																					p.N16K		Atlas-SNP	.											.	AKR1D1	52	.	0			c.C48A						.						235	184	201					7																	137761312		2203	4300	6503	SO:0001583	missense	6718	exon1			TGGAAACAGCATT	Z28339	CCDS5846.1, CCDS55169.1, CCDS55170.1	7q32-q33	2012-12-04	2012-12-04		ENSG00000122787	ENSG00000122787	1.3.99.6	"Aldo-keto reductases"	388	protein-coding gene	gene with protein product	"delta 4-3-ketosteroid-5-beta-reductase"	604741	"aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5-beta-reductase)"	SRD5B1		7508385, 10343119	Standard	NM_005989		Approved		uc003vtz.3	P51857	OTTHUMG00000155787	ENST00000242375.3:c.48C>A	chr7.hg19:g.137761312C>A	ENSP00000242375:p.Asn16Lys	86.0	0.0		91.0	33.0	NM_001190907	A1L4P6|A8K060|B4DPN3|B4DPN8	Missense_Mutation	SNP	ENST00000242375.3	hg19	CCDS5846.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278729	0.59758	.	.	ENSG00000122787	ENST00000432161;ENST00000411726;ENST00000242375;ENST00000438242	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	4.92	1.16	0.20824	NADP-dependent oxidoreductase domain (2);	0.102971	0.64402	D	0.000005	T	0.34687	0.0906	L	0.38649	1.16	0.42479	D	0.99285	P;P;B	0.50272	0.862;0.933;0.17	B;B;B	0.43478	0.421;0.319;0.061	T	0.10894	-1.0610	10	0.56958	D	0.05	.	6.4969	0.22148	0.0:0.6097:0.0:0.3903	.	16;16;16	B4DPN8;B4DPN3;P51857	.;.;AK1D1_HUMAN	K	16	ENSP00000389197:N16K;ENSP00000402374:N16K;ENSP00000242375:N16K;ENSP00000397042:N16K	ENSP00000242375:N16K	N	+	3	2	AKR1D1	137411852	0.996000	0.38824	0.998000	0.56505	0.992000	0.81027	0.036000	0.13819	0.380000	0.24823	-0.145000	0.13849	AAC	.	.		0.423	AKR1D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341637.1	NM_005989		A	137761312	C	A	137761312	3	1	162	1	0	0	0	0	1	0	0	0	473	477	17	3	50	3	AKR1D1	7	137761312	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	66630752	137761312	21377351	60	24710										
SSPO	23145	hgsc.bcm.edu	37	chr7	149493829	149493829	+	RNA	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gtgttgctgcctgagggcacTggcaggtatactgtggccgg	17	9	0	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr7:149493829T>A	ENST00000378016.2	+	0	6825							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTGAGGGCACTGGCAGGTATA	0.657																																					p.T2275T		Atlas-SNP	.											.	.	.	.	0			c.T6825A						.						94	96	95					7																	149493829		2142	4234	6376			23145	exon45			GGGCACTGGCAGG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149493829T>A		78.0	0.0		71.0	33.0	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149493829	T	A	149493829	1	1	162	0	1	0	0	0	0	0	0	0	15204	1567	55	4		4	SSPO	7	149493829	RNA	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	11732517	149493829	9644834	61	24711										
BAG4	9530	hgsc.bcm.edu	37	chr8	38065143	38065143	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cctggttatactcagaccagTtactccacagaagttccaag	7	12	1	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr8:38065143T>C	ENST00000287322.4	+	3	763	c.492T>C	c.(490-492)agT>agC	p.S164S	BAG4_ENST00000432471.2_Silent_p.S128S|BAG4_ENST00000521282.1_3'UTR	NM_004874.3	NP_004865.1	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	164					cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to tumor necrosis factor (GO:0071356)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA modification (GO:0090367)|negative regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:2001145)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein localization to plasma membrane (GO:0072659)|ruffle assembly (GO:0097178)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	11	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				CTCAGACCAGTTACTCCACAG	0.507																																					p.S164S		Atlas-SNP	.											.	BAG4	32	.	0			c.T492C						.						97	90	92					8																	38065143		2203	4300	6503	SO:0001819	synonymous_variant	9530	exon3			GACCAGTTACTCC	AF095194	CCDS6104.1, CCDS56533.1	8p11.23	2008-08-07			ENSG00000156735	ENSG00000156735			940	protein-coding gene	gene with protein product	"silencer of death domains"	603884				9873016, 9915703	Standard	NM_004874		Approved	SODD	uc003xky.2	O95429	OTTHUMG00000164064	ENST00000287322.4:c.492T>C	chr8.hg19:g.38065143T>C		109.0	0.0		89.0	43.0	NM_004874	B4E217|O95818	Silent	SNP	ENST00000287322.4	hg19	CCDS6104.1																																																																																			.	.		0.507	BAG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377038.2	NM_004874		C	38065143	T	C	38065143	2	2	162	1	0	0	0	0	0	0	0	1	1289	1722	60	2		2	BAG4	8	38065143	Silent	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10		38065143	108298879	62	24712										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52323892	52323892	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgctcaaaaatctcccctgcTcttgccatttccacaatcag	4	15	4	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr8:52323892T>G	ENST00000356297.4	-	16	2080	c.1980A>C	c.(1978-1980)agA>agC	p.R660S	PXDNL_ENST00000543296.1_Missense_Mutation_p.R660S	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	660					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TCTCCCCTGCTCTTGCCATTT	0.507																																					p.R660S		Atlas-SNP	.											.	PXDNL	414	.	0			c.A1980C						.						60	60	60					8																	52323892		1964	4163	6127	SO:0001583	missense	137902	exon16			CCCTGCTCTTGCC		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1980A>C	chr8.hg19:g.52323892T>G	ENSP00000348645:p.Arg660Ser	115.0	0.0		116.0	55.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	T	12.13	1.846314	0.32606	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.69306	-0.39;-0.35	4.46	4.46	0.54185	.	.	.	.	.	D	0.82332	0.5014	M	0.85630	2.765	0.26127	N	0.980466	D	0.89917	1.0	D	0.79784	0.993	T	0.74191	-0.3745	9	0.87932	D	0	.	11.6895	0.51508	0.0:0.0:0.0:1.0	.	660	A1KZ92	PXDNL_HUMAN	S	660	ENSP00000348645:R660S;ENSP00000444865:R660S	ENSP00000348645:R660S	R	-	3	2	PXDNL	52486445	0.054000	0.20591	0.008000	0.14137	0.005000	0.04900	-0.659000	0.05323	1.645000	0.50612	0.533000	0.62120	AGA	.	.		0.507	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		G	52323892	T	G	52323892	3	3	162	1	0	0	0	0	1	0	0	0	12863	1548	54	5	2443	5	PXDNL	8	52323892	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	14258749	52323892	94040130	63	24713										
VLDLR	7436	hgsc.bcm.edu	37	chr9	2643403	2643403	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gtccctggagcagtgtggccGtcagccagtcatacacacca	11	14	2	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr9:2643403G>A	ENST00000382100.3	+	5	1048	c.692G>A	c.(691-693)cGt>cAt	p.R231H	VLDLR_ENST00000382099.2_Missense_Mutation_p.R231H|RP11-125B21.2_ENST00000599229.1_RNA	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	231	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		CAGTGTGGCCGTCAGCCAGTC	0.582																																					p.R231H		Atlas-SNP	.											VLDLR,NS,carcinoma,0,2	VLDLR	68	.	0			c.G692A						.						47	41	43					9																	2643403		2203	4300	6503	SO:0001583	missense	7436	exon5			GTGGCCGTCAGCC		CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"Low density lipoprotein receptors"	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.692G>A	chr9.hg19:g.2643403G>A	ENSP00000371532:p.Arg231His	86.0	0.0		82.0	31.0	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	Missense_Mutation	SNP	ENST00000382100.3	hg19	CCDS6446.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.349753	0.61183	.	.	ENSG00000147852	ENST00000382100;ENST00000382099;ENST00000382092	D;D	0.90844	-2.74;-2.74	5.5	4.6	0.57074	.	0.117180	0.39274	N	0.001411	D	0.85305	0.5666	L	0.35542	1.07	0.58432	D	0.999999	B;B;B	0.13594	0.008;0.005;0.003	B;B;B	0.08055	0.003;0.002;0.002	T	0.80968	-0.1145	10	0.36615	T	0.2	.	14.3127	0.66426	0.0707:0.0:0.9292:0.0	.	231;231;231	P98155-2;Q5VVF5;P98155	.;.;VLDLR_HUMAN	H	231;231;110	ENSP00000371532:R231H;ENSP00000371531:R231H	ENSP00000371524:R110H	R	+	2	0	VLDLR	2633403	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.265000	0.65519	1.547000	0.49401	0.655000	0.94253	CGT	.	.		0.582	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383		A	2643403	G	A	2643403	3	1	162	1	0	0	0	0	1	0	0	0	17189	1145	40	1	710	1	VLDLR	9	2643403	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10		2643403	138570028	64	24714										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21971035	21971035	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cgggcagacggccccaggcaTcgcgcacgtccagccgcgcc	14	19	0	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr9:21971035T>C	ENST00000304494.5	-	2	593	c.323A>G	c.(322-324)gAt>gGt	p.D108G	CDKN2A_ENST00000579122.1_Missense_Mutation_p.D108G|CDKN2A_ENST00000578845.2_Missense_Mutation_p.D57G|CDKN2A_ENST00000494262.1_Missense_Mutation_p.D57G|CDKN2A_ENST00000497750.1_Missense_Mutation_p.D57G|CDKN2A_ENST00000530628.2_Silent_p.R122R|CDKN2A_ENST00000579755.1_Silent_p.R122R|CDKN2A_ENST00000361570.3_Silent_p.R163R|CDKN2A_ENST00000498628.2_Missense_Mutation_p.D57G|CDKN2A_ENST00000498124.1_Missense_Mutation_p.D108G|CDKN2A_ENST00000479692.2_Missense_Mutation_p.D57G|CDKN2A_ENST00000446177.1_Missense_Mutation_p.D108G|RP11-145E5.5_ENST00000404796.2_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	108			D -> H (in a bladder tumor).|D -> Y (in a head and neck tumor).		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(44)|p.D108G(2)|p.H83fs*2(2)|p.D105fs*8(1)|p.0(1)|p.A68fs*3(1)|p.R163R(1)|p.R107fs*33(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GCCCCAGGCATCGCGCACGTC	0.741		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.D108G		Atlas-SNP	.											CDKN2A_ENST00000498124,bladder,carcinoma,-1,5	CDKN2A	4810	.	1368	Whole gene deletion(1316)|Unknown(44)|Deletion - Frameshift(5)|Substitution - Missense(2)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(283)|skin(174)|central_nervous_system(167)|lung(148)|urinary_tract(91)|bone(74)|soft_tissue(57)|pleura(51)|oesophagus(51)|upper_aerodigestive_tract(49)|ovary(36)|kidney(32)|pancreas(32)|breast(32)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(9)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.A323G						.						17	19	18					9																	21971035		2198	4292	6490	SO:0001583	missense	1029	exon2			CAGGCATCGCGCA	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.323A>G	chr9.hg19:g.21971035T>C	ENSP00000307101:p.Asp108Gly	127.0	0.0		123.0	41.0	NM_000077	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	hg19	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.715925	0.89112	.	.	ENSG00000147889	ENST00000304494;ENST00000446177	D;D	0.93953	-3.32;-3.32	5.93	5.93	0.95920	Ankyrin repeat-containing domain (4);	.	.	.	.	D	0.96775	0.8947	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.97240	0.9890	8	0.72032	D	0.01	-14.8146	15.3697	0.74554	0.0:0.0:0.0:1.0	.	108	P42771	CD2A1_HUMAN	G	108	ENSP00000307101:D108G;ENSP00000394932:D108G	ENSP00000307101:D108G	D	-	2	0	CDKN2A	21961035	1.000000	0.71417	0.974000	0.42286	0.662000	0.39071	7.037000	0.76531	2.265000	0.75225	0.533000	0.62120	GAT	.	.		0.741	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		C	21971035	T	C	21971035	3	2	162	1	0	0	0	0	1	0	0	0	3163	1435	50	2	155	2	CDKN2A	9	21971035	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	19327632	21971035	119242396	65	24715										
CREB3	57704	hgsc.bcm.edu	37	chr9	35736083	35736083	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gaggaaactccaggccatggTgattgagatatcaaacaaaa	10	7	1	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr9:35736083T>C	ENST00000378103.3	-	0	3611				CREB3_ENST00000486056.1_3'UTR|CREB3_ENST00000353704.2_Missense_Mutation_p.V217A|GBA2_ENST00000467252.1_5'Flank	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGGCCATGGTGATTGAGATA	0.517											OREG0019176	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V217A		Atlas-SNP	.											.	CREB3	24	.	0			c.T650C						.						154	136	142					9																	35736083		2203	4300	6503	SO:0001628	intergenic_variant	10488	exon7			CCATGGTGATTGA	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		chr9.hg19:g.35736083T>C		81.0	0.0	857	79.0	30.0	NM_006368	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	ENST00000378103.3	hg19	CCDS6589.1	.	.	.	.	.	.	.	.	.	.	T	9.581	1.123676	0.20959	.	.	ENSG00000107175	ENST00000353704	T	0.70631	-0.5	5.41	3.02	0.34903	.	0.264850	0.36268	N	0.002690	T	0.71978	0.3404	M	0.85630	2.765	0.40994	D	0.984871	P;B	0.38617	0.64;0.176	B;B	0.40602	0.334;0.054	T	0.71337	-0.4623	10	0.87932	D	0	.	7.045	0.25040	0.1324:0.0729:0.0:0.7947	.	241;217	O43889;O43889-2	CREB3_HUMAN;.	A	217	ENSP00000342136:V217A	ENSP00000342136:V217A	V	+	2	0	CREB3	35726083	1.000000	0.71417	0.650000	0.29550	0.012000	0.07955	3.606000	0.54095	0.351000	0.24027	-0.410000	0.06199	GTG	.	.		0.517	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		C	35736083	T	C	35736083	1	2	162	0	1	0	0	0	0	0	0	0	3857	1696	59	2		2	CREB3	9	35736083	IGR	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	13765048	35736083	105477348	66	24716										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79325451	79325451	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ggctcaaatttctttcagagTtatctctgggactgtcttgt	9	8	5	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr9:79325451T>A	ENST00000376718.3	-	8	1862	c.1739A>T	c.(1738-1740)aAc>aTc	p.N580I	PRUNE2_ENST00000428286.1_Missense_Mutation_p.N221I	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	580					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TCTTTCAGAGTTATCTCTGGG	0.443																																					p.N580I		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A1739T						.						57	51	53					9																	79325451		1568	3582	5150	SO:0001583	missense	158471	exon8			TCAGAGTTATCTC	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.1739A>T	chr9.hg19:g.79325451T>A	ENSP00000365908:p.Asn580Ile	103.0	0.0		72.0	26.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	T	7.208	0.594751	0.13875	.	.	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.42513	0.97;0.98	5.71	3.12	0.35913	.	0.495429	0.18752	N	0.132156	T	0.29783	0.0744	L	0.51422	1.61	0.09310	N	0.999994	P	0.35077	0.483	B	0.30251	0.113	T	0.10753	-1.0616	10	0.24483	T	0.36	-12.4268	6.0619	0.19842	0.251:0.0865:0.0:0.6625	.	580	Q8WUY3	PRUN2_HUMAN	I	580;221;579	ENSP00000365908:N580I;ENSP00000397425:N221I	ENSP00000365908:N580I	N	-	2	0	PRUNE2	78515271	0.008000	0.16893	0.852000	0.33557	0.799000	0.45148	1.057000	0.30492	1.010000	0.39314	0.533000	0.62120	AAC	.	.		0.443	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79325451	T	A	79325451	3	1	162	1	0	0	0	0	1	0	0	0	12653	1725	60	4	7575	4	PRUNE2	9	79325451	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	43589368	79325451	61887980	67	24717										
RAD23B	5887	hgsc.bcm.edu	37	chr9	110081131	110081131	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgagagccagtttcaacaacCctgacagagcagtggagtat	11	9	1	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr9:110081131C>G	ENST00000358015.3	+	6	1003	c.652C>G	c.(652-654)Cct>Gct	p.P218A	RAD23B_ENST00000416373.2_Missense_Mutation_p.P146A	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	218	UBA 1. {ECO:0000255|PROSITE- ProRule:PRU00212}.				DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						TTTCAACAACCCTGACAGAGC	0.383								Direct reversal of damage;Nucleotide excision repair (NER)																													p.P218A		Atlas-SNP	.											.	RAD23B	31	.	0			c.C652G						.						117	111	113					9																	110081131		2203	4300	6503	SO:0001583	missense	5887	exon6			AACAACCCTGACA		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"XP-C repair complementing protein", "XP-C repair complementing complex 58 kDa"	600062	"RAD23 (S. cerevisiae) homolog B"			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.652C>G	chr9.hg19:g.110081131C>G	ENSP00000350708:p.Pro218Ala	80.0	0.0		97.0	25.0	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	hg19	CCDS6769.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.648312	0.87958	.	.	ENSG00000119318	ENST00000358015;ENST00000374678;ENST00000416373	T;T	0.23950	1.88;1.88	4.9	4.9	0.64082	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.55577	0.1929	M	0.80616	2.505	0.80722	D	1	D;D;D	0.89917	0.999;0.987;1.0	D;D;D	0.87578	0.998;0.951;0.998	T	0.62450	-0.6852	10	0.87932	D	0	-20.0749	18.4398	0.90662	0.0:1.0:0.0:0.0	.	197;218;218	B7Z4W4;B4DEA3;P54727	.;.;RD23B_HUMAN	A	218;146;146	ENSP00000350708:P218A;ENSP00000405623:P146A	ENSP00000350708:P218A	P	+	1	0	RAD23B	109120952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.459000	0.80802	2.417000	0.82017	0.561000	0.74099	CCT	.	.		0.383	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874		G	110081131	C	G	110081131	3	3	162	1	0	0	0	0	1	0	0	0	12998	623	22	4	674	4	RAD23B	9	110081131	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	30755680	110081131	31132300	68	24718										
ENTPD2	954	hgsc.bcm.edu	37	chr9	139943427	139943427	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tcacgccgccgaaggcgcgcTcgtcgaagccgtagccgcga	14	16	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr9:139943427T>A	ENST00000355097.2	-	8	1297	c.1250A>T	c.(1249-1251)gAg>gTg	p.E417V	ENTPD2_ENST00000312665.5_Missense_Mutation_p.E394V|NPDC1_ENST00000488145.1_5'Flank|NPDC1_ENST00000371601.4_5'Flank|ENTPD2_ENST00000460614.1_5'UTR	NM_001246.3|NM_203468.2	NP_001237.1|NP_982293.1	Q9Y5L3	ENTP2_HUMAN	ectonucleoside triphosphate diphosphohydrolase 2	417					G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			endometrium(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(3)	12	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GAAGGCGCGCTCGTCGAAGCC	0.736																																					p.E417V		Atlas-SNP	.											.	ENTPD2	30	.	0			c.A1250T						.						2	2	2					9																	139943427		1517	3185	4702	SO:0001583	missense	954	exon8			GCGCGCTCGTCGA	U91510	CCDS7025.1, CCDS7026.1	9q34	2008-07-21			ENSG00000054179	ENSG00000054179			3364	protein-coding gene	gene with protein product	"CD39-like-1", "ecto-ATPase"	602012		CD39L1		9271669	Standard	NM_203468		Approved	NTPDase-2	uc004ckw.2	Q9Y5L3	OTTHUMG00000020953	ENST00000355097.2:c.1250A>T	chr9.hg19:g.139943427T>A	ENSP00000347213:p.Glu417Val	98.0	0.0		92.0	20.0	NM_203468	O15464|Q5SPY6|Q5SPY7	Missense_Mutation	SNP	ENST00000355097.2	hg19	CCDS7026.1	.	.	.	.	.	.	.	.	.	.	T	15.14	2.746056	0.49151	.	.	ENSG00000054179	ENST00000355097;ENST00000312665	T;T	0.13089	2.8;2.62	3.65	3.65	0.41850	.	0.411454	0.27891	N	0.017424	T	0.32496	0.0831	M	0.77406	2.37	0.41415	D	0.987767	D;D;D	0.71674	0.998;0.996;0.996	D;D;D	0.67231	0.95;0.941;0.941	T	0.06716	-1.0811	10	0.56958	D	0.05	-41.9107	8.4598	0.32921	0.0:0.1008:0.0:0.8992	.	394;417;417	Q9Y5L3-2;Q9Y5L3;Q5SPY7	.;ENTP2_HUMAN;.	V	417;394	ENSP00000347213:E417V;ENSP00000312494:E394V	ENSP00000312494:E394V	E	-	2	0	ENTPD2	139063248	0.005000	0.15991	0.809000	0.32408	0.012000	0.07955	1.606000	0.36826	1.644000	0.50603	0.368000	0.22195	GAG	.	.		0.736	ENTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055169.1	NM_203468		A	139943427	T	A	139943427	3	1	162	1	0	0	0	0	1	0	0	0	5141	1551	54	4	245	4	ENTPD2	9	139943427	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	29862296	139943427	1270004	69	24719										
GATA3	2625	hgsc.bcm.edu	37	chr10	8097825	8097825	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tactacggaaactcggtcagGgccacggtgcagaggtaccc	13	12	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr10:8097825G>A	ENST00000346208.3	+	2	662	c.207G>A	c.(205-207)agG>agA	p.R69R	GATA3-AS1_ENST00000355358.1_lincRNA|RP11-379F12.3_ENST00000458727.1_lincRNA|RP11-379F12.4_ENST00000418270.1_lincRNA|GATA3_ENST00000379328.3_Silent_p.R69R			P23771	GATA3_HUMAN	GATA binding protein 3	69					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						ACTCGGTCAGGGCCACGGTGC	0.697			"F, N, S"		breast		"HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"																														p.R69R		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.G207A						.						30	26	27					10																	8097825		2196	4290	6486	SO:0001819	synonymous_variant	2625	exon2			GGTCAGGGCCACG	X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"GATA zinc finger domain containing"	4172	protein-coding gene	gene with protein product		131320	"GATA-binding protein 3"			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.207G>A	chr10.hg19:g.8097825G>A		248.0	0.0		227.0	92.0	NM_002051	Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	hg19	CCDS7083.1																																																																																			.	.		0.697	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		A	8097825	G	A	8097825	2	1	162	1	0	0	0	0	0	0	0	1	6263	1223	43	3		3	GATA3	10	8097825	Silent	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10		8097825	127436922	70	24720										
SLC39A12	221074	hgsc.bcm.edu	37	chr10	18270244	18270244	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	atgttttcctcacacagaccTgcttctctgctaggcagctg	8	13	2	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr10:18270244T>A	ENST00000377369.2	+	6	1201	c.928T>A	c.(928-930)Tgc>Agc	p.C310S	SLC39A12_ENST00000539911.1_Missense_Mutation_p.C176S|SLC39A12_ENST00000377374.4_Missense_Mutation_p.C310S|SLC39A12_ENST00000377371.3_Missense_Mutation_p.C310S	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	310					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						CACACAGACCTGCTTCTCTGC	0.423																																					p.C310S		Atlas-SNP	.											.	SLC39A12	181	.	0			c.T928A						.						90	88	89					10																	18270244		2203	4300	6503	SO:0001583	missense	221074	exon6			CAGACCTGCTTCT		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"Solute carriers"	20860	protein-coding gene	gene with protein product		608734	"solute carrier family 39 (metal ion transporter), member 12"			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.928T>A	chr10.hg19:g.18270244T>A	ENSP00000366586:p.Cys310Ser	113.0	0.0		116.0	41.0	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Missense_Mutation	SNP	ENST00000377369.2	hg19	CCDS44362.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.328580	0.81690	.	.	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219	D;D;D;D	0.95690	-3.47;-3.78;-3.42;-3.15	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.97739	0.9258	M	0.82517	2.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.98588	1.0653	10	0.87932	D	0	-13.5218	15.8497	0.78921	0.0:0.0:0.0:1.0	.	310;310;310	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	S	310;310;310;176;230	ENSP00000366586:C310S;ENSP00000366591:C310S;ENSP00000366588:C310S;ENSP00000440445:C176S	ENSP00000366586:C310S	C	+	1	0	SLC39A12	18310250	1.000000	0.71417	0.998000	0.56505	0.796000	0.44982	7.303000	0.78871	2.155000	0.67459	0.533000	0.62120	TGC	.	.		0.423	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725		A	18270244	T	A	18270244	3	1	162	1	0	0	0	0	1	0	0	0	14630	1580	55	4	946	4	SLC39A12	10	18270244	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	10172419	18270244	117264503	71	24721										
MPP7	143098	hgsc.bcm.edu	37	chr10	28491163	28491163	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tggctatccacatgtggctgCagctgggctggcagagcagc	15	11	0	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr10:28491163C>A	ENST00000375732.1	-	3	334	c.75G>T	c.(73-75)ctG>ctT	p.L25L	MPP7_ENST00000540098.1_Silent_p.L25L|MPP7_ENST00000445954.2_Intron|MPP7_ENST00000375719.3_Silent_p.L25L|MPP7_ENST00000481244.1_5'UTR|MPP7_ENST00000337532.5_Silent_p.L25L			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	25	L27 1. {ECO:0000255|PROSITE- ProRule:PRU00365}.				establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						CATGTGGCTGCAGCTGGGCTG	0.433																																					p.L25L		Atlas-SNP	.											.	MPP7	60	.	0			c.G75T						.						62	58	60					10																	28491163		2203	4300	6503	SO:0001819	synonymous_variant	143098	exon5			TGGCTGCAGCTGG	BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.75G>T	chr10.hg19:g.28491163C>A		119.0	0.0		140.0	47.0	NM_173496	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Silent	SNP	ENST00000375732.1	hg19	CCDS7158.1																																																																																			.	.		0.433	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		A	28491163	C	A	28491163	2	1	162	1	0	0	0	0	0	0	0	1	9748	697	25	3		3	MPP7	10	28491163	Silent	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	10220919	28491163	107043584	72	24722										
CSTF2T	23283	hgsc.bcm.edu	37	chr10	53457589	53457589	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgatcaaagctgccttctccTgatcctgtggagtgacctgg	11	11	2	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr10:53457589T>A	ENST00000331173.4	-	1	1766	c.1721A>T	c.(1720-1722)cAg>cTg	p.Q574L	PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron|PRKG1_ENST00000373980.4_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	574					mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		TGCCTTCTCCTGATCCTGTGG	0.517																																					p.Q574L		Atlas-SNP	.											.	CSTF2T	64	.	0			c.A1721T						.						124	102	110					10																	53457589		2203	4300	6503	SO:0001583	missense	23283	exon1			TTCTCCTGATCCT	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"RNA binding motif (RRM) containing"	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.1721A>T	chr10.hg19:g.53457589T>A	ENSP00000332444:p.Gln574Leu	101.0	0.0		103.0	37.0	NM_015235	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Missense_Mutation	SNP	ENST00000331173.4	hg19	CCDS7245.1	.	.	.	.	.	.	.	.	.	.	T	11.96	1.795326	0.31777	.	.	ENSG00000177613	ENST00000331173	T	0.23754	1.89	4.65	3.53	0.40419	.	0.227106	0.44097	D	0.000496	T	0.24509	0.0594	L	0.59436	1.845	0.39225	D	0.963573	B	0.14438	0.01	B	0.17433	0.018	T	0.19418	-1.0306	10	0.87932	D	0	-9.4223	8.2905	0.31954	0.0:0.096:0.0:0.904	.	574	Q9H0L4	CSTFT_HUMAN	L	574	ENSP00000332444:Q574L	ENSP00000332444:Q574L	Q	-	2	0	CSTF2T	53127595	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.110000	0.64622	2.102000	0.63906	0.533000	0.62120	CAG	.	.		0.517	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235		A	53457589	T	A	53457589	3	1	162	1	0	0	0	0	1	0	0	0	3987	1580	55	4	133	4	CSTF2T	10	53457589	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	24966426	53457589	82077158	73	24723										
CNGA4	1262	hgsc.bcm.edu	37	chr11	6261883	6261883	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	acccagatcatgcactggtgAagaagtacatgaagctgcag	11	9	1	4			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr11:6261883A>T	ENST00000379936.2	+	4	974	c.859A>T	c.(859-861)Aag>Tag	p.K287*	CNGA4_ENST00000533426.1_Nonsense_Mutation_p.K56*	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	287					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCACTGGTGAAGAAGTACAT	0.547																																					p.K287X		Atlas-SNP	.											.	CNGA4	96	.	0			c.A859T						.						99	88	92					11																	6261883		2201	4296	6497	SO:0001587	stop_gained	1262	exon4			CTGGTGAAGAAGT	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2152	protein-coding gene	gene with protein product		609472	"cyclic nucleotide gated channel beta 2"	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.859A>T	chr11.hg19:g.6261883A>T	ENSP00000369268:p.Lys287*	129.0	0.0		141.0	50.0	NM_001037329		Nonsense_Mutation	SNP	ENST00000379936.2	hg19	CCDS31408.1	.	.	.	.	.	.	.	.	.	.	A	37	6.296064	0.97449	.	.	ENSG00000132259	ENST00000533426;ENST00000379936	.	.	.	5.3	5.3	0.74995	.	0.090520	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.1129	0.48243	0.8455:0.1545:0.0:0.0	.	.	.	.	X	56;287	.	ENSP00000369268:K287X	K	+	1	0	CNGA4	6218459	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.028000	0.57246	2.133000	0.65898	0.459000	0.35465	AAG	.	.		0.547	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329		T	6261883	A	T	6261883	4	4	162	1	0	0	0	0	0	1	0	0	3601	247	9	4	873	4	CNGA4	11	6261883	Nonsense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10		6261883	128744633	74	24724										
OR4A15	81328	hgsc.bcm.edu	37	chr11	55135453	55135453	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	caccttcagaagaacacatgAaaaataagaacaatgtgact	6	8	1	5			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr11:55135453A>T	ENST00000314706.3	+	1	94	c.94A>T	c.(94-96)Aaa>Taa	p.K32*		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	32						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						AGAACACATGAAAAATAAGAA	0.388																																					p.K32X		Atlas-SNP	.											.	OR4A15	161	.	0			c.A94T						.						64	60	62					11																	55135453		2201	4296	6497	SO:0001587	stop_gained	81328	exon1			CACATGAAAAATA	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"GPCR / Class A : Olfactory receptors"	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.94A>T	chr11.hg19:g.55135453A>T	ENSP00000325065:p.Lys32*	114.0	0.0		109.0	44.0	NM_001005275	Q6IFL4|Q96R65	Nonsense_Mutation	SNP	ENST00000314706.3	hg19	CCDS31500.1	.	.	.	.	.	.	.	.	.	.	a	13.55	2.270661	0.40194	.	.	ENSG00000181958	ENST00000314706	.	.	.	3.48	2.54	0.30619	.	1.993750	0.03854	U	0.272736	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	6.6947	0.23193	0.1355:0.0:0.8645:0.0	.	.	.	.	X	32	.	ENSP00000325065:K32X	K	+	1	0	OR4A15	54892029	0.712000	0.27916	0.122000	0.21767	0.015000	0.08874	0.762000	0.26503	0.677000	0.31305	-0.342000	0.07992	AAA	.	.		0.388	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		T	55135453	A	T	55135453	4	4	162	1	0	0	0	0	0	1	0	0	11049	247	9	4	96	4	OR4A15	11	55135453	Nonsense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	48873570	55135453	79871063	75	24725										
SYT7	9066	hgsc.bcm.edu	37	chr11	61295635	61295635	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgcaaccctcgtgggcctcaTcctcctcggagcctggggag	13	15	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr11:61295635T>C	ENST00000263846.4	-	5	701	c.374A>G	c.(373-375)gAt>gGt	p.D125G	SYT7_ENST00000539008.1_Missense_Mutation_p.D408G|SYT7_ENST00000535826.1_Missense_Mutation_p.D244G|SYT7_ENST00000542836.1_Missense_Mutation_p.D169G|SYT7_ENST00000542670.1_Missense_Mutation_p.D333G|SYT7_ENST00000540677.1_Missense_Mutation_p.D200G|SYT7_ENST00000540831.1_5'UTR	NM_004200.3	NP_004191.2	O43581	SYT7_HUMAN	synaptotagmin VII	125					exocytosis (GO:0006887)|plasma membrane repair (GO:0001778)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			kidney(2)|large_intestine(3)|lung(4)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						GTGGGCCTCATCCTCCTCGGA	0.642																																					p.D200G		Atlas-SNP	.											.	SYT7	39	.	0			c.A599G						.						41	48	46					11																	61295635		2201	4299	6500	SO:0001583	missense	9066	exon6			GCCTCATCCTCCT	AF038535	CCDS31577.1, CCDS58139.1, CCDS73298.1	11q12-q13.1	2013-01-21			ENSG00000011347	ENSG00000011347		"Synaptotagmins"	11514	protein-coding gene	gene with protein product		604146	"prostate cancer associated protein 7"	PCANAP7		9615227	Standard	NM_001252065		Approved	IPCA-7, SYT-VII, MGC150517	uc009ynr.3	O43581	OTTHUMG00000168199	ENST00000263846.4:c.374A>G	chr11.hg19:g.61295635T>C	ENSP00000263846:p.Asp125Gly	51.0	0.0		36.0	14.0	NM_001252065	F5GZU9|Q08AH6	Missense_Mutation	SNP	ENST00000263846.4	hg19	CCDS31577.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.373484	0.82573	.	.	ENSG00000011347	ENST00000263846;ENST00000540677;ENST00000539008;ENST00000542836;ENST00000542670;ENST00000535826;ENST00000545053	T;T;T;T;T;T;T	0.56444	0.46;0.48;0.61;0.5;0.49;0.49;1.84	4.42	4.42	0.53409	.	0.090510	0.85682	D	0.000000	T	0.41627	0.1167	L	0.34521	1.04	0.80722	D	1	B;B	0.25955	0.138;0.067	B;B	0.21151	0.033;0.013	T	0.34079	-0.9843	10	0.40728	T	0.16	.	14.047	0.64710	0.0:0.0:0.0:1.0	.	200;125	F5GZU9;O43581	.;SYT7_HUMAN	G	125;200;408;169;333;244;125	ENSP00000263846:D125G;ENSP00000444201:D200G;ENSP00000439694:D408G;ENSP00000444568:D169G;ENSP00000444019:D333G;ENSP00000437720:D244G;ENSP00000443576:D125G	ENSP00000263846:D125G	D	-	2	0	SYT7	61052211	1.000000	0.71417	0.999000	0.59377	0.894000	0.52154	5.893000	0.69798	1.951000	0.56629	0.533000	0.62120	GAT	.	.		0.642	SYT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398733.1	NM_004200		C	61295635	T	C	61295635	3	2	162	1	0	0	0	0	1	0	0	0	15494	1435	50	2	857	2	SYT7	11	61295635	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	6160182	61295635	73710881	76	24726										
SLC22A8	9376	hgsc.bcm.edu	37	chr11	62763192	62763192	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ttaccaggccagggaaagacAgaaggtcatgcggcgcagca	14	10	1	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr11:62763192A>T	ENST00000336232.2	-	7	1120	c.985T>A	c.(985-987)Tgt>Agt	p.C329S	SLC22A8_ENST00000542795.1_5'Flank|SLC22A8_ENST00000535878.1_Missense_Mutation_p.C206S|SLC22A8_ENST00000430500.2_Missense_Mutation_p.C329S|SLC22A8_ENST00000545207.1_Missense_Mutation_p.C238S|SLC22A8_ENST00000311438.8_Missense_Mutation_p.C329S	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8	329					glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	AGGGAAAGACAGAAGGTCATG	0.587																																					p.C329S		Atlas-SNP	.											.	SLC22A8	60	.	0			c.T985A						.						144	130	134					11																	62763192		2201	4298	6499	SO:0001583	missense	9376	exon7			AAAGACAGAAGGT	AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"Solute carriers"	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.985T>A	chr11.hg19:g.62763192A>T	ENSP00000337335:p.Cys329Ser	85.0	0.0		77.0	44.0	NM_001184732	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Missense_Mutation	SNP	ENST00000336232.2	hg19	CCDS8042.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.269079	0.80469	.	.	ENSG00000149452	ENST00000336232;ENST00000540631;ENST00000545207;ENST00000535878;ENST00000311438;ENST00000430500	T;T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73;-0.73	5.34	5.34	0.76211	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.120557	0.64402	D	0.000010	T	0.79197	0.4405	M	0.66378	2.025	0.47511	D	0.999443	P;P	0.50272	0.918;0.933	P;P	0.58391	0.749;0.838	T	0.80944	-0.1156	10	0.62326	D	0.03	.	11.7357	0.51763	1.0:0.0:0.0:0.0	.	329;329	Q8TCC7-2;Q8TCC7	.;S22A8_HUMAN	S	329;315;238;206;329;329	ENSP00000337335:C329S;ENSP00000441658:C238S;ENSP00000443368:C206S;ENSP00000311463:C329S;ENSP00000398548:C329S	ENSP00000311463:C329S	C	-	1	0	SLC22A8	62519768	1.000000	0.71417	0.985000	0.45067	0.969000	0.65631	5.477000	0.66799	2.023000	0.59567	0.454000	0.30748	TGT	.	.		0.587	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254		T	62763192	A	T	62763192	3	4	162	1	0	0	0	0	1	0	0	0	14475	188	7	4	663	4	SLC22A8	11	62763192	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	1467557	62763192	72243324	77	24727										
INTS4	92105	hgsc.bcm.edu	37	chr11	77632432	77632432	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gactgtctcggaggtaggcaTagtgcctgaaggtgtgatct	15	7	2	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr11:77632432T>A	ENST00000534064.1	-	14	1752	c.1718A>T	c.(1717-1719)tAt>tTt	p.Y573F	INTS4_ENST00000525931.1_5'Flank	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	573					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			GAGGTAGGCATAGTGCCTGAA	0.413																																					p.Y573F		Atlas-SNP	.											.	INTS4	89	.	0			c.A1718T						.						145	125	132					11																	77632432		2200	4292	6492	SO:0001583	missense	92105	exon14			TAGGCATAGTGCC	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.1718A>T	chr11.hg19:g.77632432T>A	ENSP00000434466:p.Tyr573Phe	334.0	0.0		334.0	119.0	NM_033547	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	hg19	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.764159	0.89932	.	.	ENSG00000149262	ENST00000534064;ENST00000354849	D	0.86097	-2.07	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	D	0.91372	0.7278	M	0.79475	2.455	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	D	0.91927	0.5552	10	0.52906	T	0.07	-14.6043	14.1606	0.65443	0.0:0.0:0.0:1.0	.	573	Q96HW7	INT4_HUMAN	F	573;424	ENSP00000434466:Y573F	ENSP00000346913:Y424F	Y	-	2	0	INTS4	77310080	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.195000	0.77798	1.926000	0.55796	0.477000	0.44152	TAT	.	.		0.413	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		A	77632432	T	A	77632432	3	1	162	1	0	0	0	0	1	0	0	0	7789	1406	49	4	1213	4	INTS4	11	77632432	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	14869240	77632432	57374084	78	24728										
FLI1	2313	hgsc.bcm.edu	37	chr11	128680398	128680398	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	aattcctcctggagctgctcTccgacagcgccaacgccagc	9	17	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr11:128680398T>A	ENST00000527786.2	+	9	1363	c.874T>A	c.(874-876)Tcc>Acc	p.S292T	FLI1_ENST00000344954.6_Missense_Mutation_p.S259T|FLI1_ENST00000534087.2_Missense_Mutation_p.S259T|FLI1_ENST00000281428.8_Missense_Mutation_p.S226T|FLI1_ENST00000525560.1_Missense_Mutation_p.S99T	NM_001271010.1|NM_002017.4	NP_001257939.1|NP_002008.2	Q01543	FLI1_HUMAN	Fli-1 proto-oncogene, ETS transcription factor	292					blood circulation (GO:0008015)|cell differentiation (GO:0030154)|hemostasis (GO:0007599)|megakaryocyte development (GO:0035855)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/FLI1(2569)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(2)	31	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		GGAGCTGCTCTCCGACAGCGC	0.632			T	EWSR1	Ewing sarcoma																																p.S292T		Atlas-SNP	.		Dom	yes		11	11q24	2313	Friend leukemia virus integration 1		M	.	FLI1	72	.	0			c.T874A						.						17	19	18					11																	128680398		2175	4293	6468	SO:0001583	missense	2313	exon9			CTGCTCTCCGACA	M98833	CCDS44768.1, CCDS53725.1, CCDS59230.1, CCDS59231.1	11q24.1-q24.3	2014-09-17	2013-08-07		ENSG00000151702	ENSG00000151702			3749	protein-coding gene	gene with protein product		193067	"Friend leukemia virus integration 1"			1765382	Standard	NM_001167681		Approved	SIC-1, EWSR2	uc010sbu.2	Q01543	OTTHUMG00000165792	ENST00000527786.2:c.874T>A	chr11.hg19:g.128680398T>A	ENSP00000433488:p.Ser292Thr	76.0	0.0		84.0	24.0	NM_002017	B2R8H2|B4DFV4|B4DTC6|G3V183|Q14319|Q92480|Q9UE07	Missense_Mutation	SNP	ENST00000527786.2	hg19	CCDS44768.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.117864	0.77323	.	.	ENSG00000151702	ENST00000525560;ENST00000344954;ENST00000429175;ENST00000534087;ENST00000281428	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	5.63	5.63	0.86233	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.106359	0.64402	D	0.000003	T	0.31702	0.0805	N	0.21324	0.655	0.80722	D	1	P;P;P	0.50943	0.887;0.927;0.94	P;P;D	0.63597	0.874;0.842;0.916	T	0.05115	-1.0905	10	0.46703	T	0.11	.	15.8302	0.78743	0.0:0.0:0.0:1.0	.	292;99;226	Q01543;B4DFV4;Q01543-2	FLI1_HUMAN;.;.	T	99;259;292;259;226	ENSP00000437124:S99T;ENSP00000339627:S259T;ENSP00000399985:S292T;ENSP00000432950:S259T;ENSP00000281428:S226T	ENSP00000281428:S226T	S	+	1	0	FLI1	128185608	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	8.040000	0.89188	2.145000	0.66743	0.477000	0.44152	TCC	.	.		0.632	FLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386226.2	NM_002017		A	128680398	T	A	128680398	3	1	162	1	0	0	0	0	1	0	0	0	5932	1551	54	4	908	4	FLI1	11	128680398	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	51047966	128680398	6326118	79	24729										
NCAPD2	9918	hgsc.bcm.edu	37	chr12	6640135	6640135	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	agcctcagacaatgactttgTcacaccagagccccgccgta	8	15	2	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr12:6640135T>C	ENST00000315579.5	+	31	4812	c.4013T>C	c.(4012-4014)gTc>gCc	p.V1338A	RP5-940J5.3_ENST00000537921.1_RNA|NCAPD2_ENST00000545962.1_Missense_Mutation_p.V1293A|GAPDH_ENST00000229239.5_5'Flank	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1338					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						AATGACTTTGTCACACCAGAG	0.473																																					p.V1338A		Atlas-SNP	.											.	NCAPD2	99	.	0			c.T4013C						.						67	78	74					12																	6640135		2203	4300	6503	SO:0001583	missense	9918	exon31			ACTTTGTCACACC	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"chromosome condensation related SMC associated protein 1"	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.4013T>C	chr12.hg19:g.6640135T>C	ENSP00000325017:p.Val1338Ala	101.0	0.0		109.0	43.0	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	hg19	CCDS8548.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223363	0.39300	.	.	ENSG00000010292	ENST00000315579;ENST00000545962	T;T	0.17370	2.55;2.28	5.1	1.41	0.22369	.	0.140303	0.47852	N	0.000215	T	0.06645	0.0170	N	0.08118	0	0.40423	D	0.979862	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.35549	-0.9784	10	0.10902	T	0.67	-12.2539	7.699	0.28611	0.0:0.2425:0.0:0.7575	.	1293;1338	F5GZJ1;Q15021	.;CND1_HUMAN	A	1338;1293	ENSP00000325017:V1338A;ENSP00000444417:V1293A	ENSP00000325017:V1338A	V	+	2	0	NCAPD2	6510396	0.995000	0.38212	0.153000	0.22517	0.417000	0.31264	1.921000	0.40035	0.074000	0.16767	-0.411000	0.06167	GTC	.	.		0.473	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		C	6640135	T	C	6640135	3	2	162	1	0	0	0	0	1	0	0	0	10214	1667	58	2	4131	2	NCAPD2	12	6640135	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10		6640135	127211760	80	24730										
CLEC1A	51267	hgsc.bcm.edu	37	chr12	10224016	10224016	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cttctctcacagacacaacgCttcaattctttgcagtcctt	4	14	4	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr12:10224016C>T	ENST00000315330.4	-	6	821	c.759G>A	c.(757-759)aaG>aaA	p.K253K	CLEC1A_ENST00000457018.2_Silent_p.K220K|CLEC1A_ENST00000420265.2_Silent_p.K161K	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	253	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						AGACACAACGCTTCAATTCTT	0.483																																					p.K253K		Atlas-SNP	.											.	CLEC1A	48	.	0			c.G759A						.						202	180	187					12																	10224016		2203	4300	6503	SO:0001819	synonymous_variant	51267	exon6			ACAACGCTTCAAT	AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"C-type lectin domain containing"	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.759G>A	chr12.hg19:g.10224016C>T		89.0	0.0		84.0	6.0	NM_016511	Q8IUW7|Q9NZH3	Silent	SNP	ENST00000315330.4	hg19	CCDS8612.1																																																																																			.	.		0.483	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511		T	10224016	C	T	10224016	2	4	162	1	0	0	0	0	0	0	0	1	3507	796	28	3		3	CLEC1A	12	10224016	Silent	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	3583881	10224016	123627879	81	24731										
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42860019	42860019	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tatgttccccacaggtttcaCagtactccgcatagagagac	8	12	1	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr12:42860019C>G	ENST00000455697.1	-	6	1037	c.752G>C	c.(751-753)tGt>tCt	p.C251S	PRICKLE1_ENST00000552240.1_Missense_Mutation_p.C251S|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.C251S|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.C251S|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.C251S	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	251	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		ACAGGTTTCACAGTACTCCGC	0.502																																					p.C251S		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.G752C						.						75	75	75					12																	42860019		2203	4300	6503	SO:0001583	missense	144165	exon6			GTTTCACAGTACT	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.752G>C	chr12.hg19:g.42860019C>G	ENSP00000401060:p.Cys251Ser	124.0	0.0		131.0	44.0	NM_001144882	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	hg19	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.873294	0.91664	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	D;D;D;D;D	0.99311	-5.73;-5.73;-5.73;-5.73;-5.73	4.98	4.98	0.66077	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.99750	0.9900	H	0.99555	4.625	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96840	0.9617	10	0.66056	D	0.02	-3.4384	18.6235	0.91330	0.0:1.0:0.0:0.0	.	251	Q96MT3	PRIC1_HUMAN	S	251	ENSP00000401060:C251S;ENSP00000398947:C251S;ENSP00000448359:C251S;ENSP00000345064:C251S;ENSP00000449819:C251S	ENSP00000345064:C251S	C	-	2	0	PRICKLE1	41146286	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	7.776000	0.85560	2.484000	0.83849	0.561000	0.74099	TGT	.	.		0.502	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			G	42860019	C	G	42860019	3	3	162	1	0	0	0	0	1	0	0	0	12498	478	17	4	1755	4	PRICKLE1	12	42860019	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	32636003	42860019	90991876	82	24732										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48393717	48393717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	acaaccactggcagtggcgaGgtcagttgggcagatggggc	17	9	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr12:48393717G>A	ENST00000380518.3	-	2	441	c.277C>T	c.(277-279)Ctc>Ttc	p.L93F	COL2A1_ENST00000337299.6_Intron	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	93					axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	GCAGTGGCGAGGTCAGTTGGG	0.493																																					p.L93F		Atlas-SNP	.											.	COL2A1	368	.	0			c.C277T						.						72	79	76					12																	48393717		2063	4206	6269	SO:0001583	missense	1280	exon2			TGGCGAGGTCAGT	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.277C>T	chr12.hg19:g.48393717G>A	ENSP00000369889:p.Leu93Phe	150.0	0.0		114.0	34.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	G	13.51	2.257381	0.39896	.	.	ENSG00000139219	ENST00000380518	D	0.89939	-2.59	4.66	4.66	0.58398	.	0.485117	0.19947	N	0.102515	D	0.82637	0.5080	N	0.25957	0.775	0.80722	D	1	B	0.19583	0.037	B	0.17433	0.018	T	0.77043	-0.2734	10	0.23891	T	0.37	.	16.8676	0.86033	0.0:0.0:1.0:0.0	.	93	P02458	CO2A1_HUMAN	F	93	ENSP00000369889:L93F	ENSP00000369889:L93F	L	-	1	0	COL2A1	46679984	0.972000	0.33761	1.000000	0.80357	0.996000	0.88848	2.122000	0.41987	2.584000	0.87258	0.563000	0.77884	CTC	.	.		0.493	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		A	48393717	G	A	48393717	3	1	162	1	0	0	0	0	1	0	0	0	3689	1000	35	3	4398	3	COL2A1	12	48393717	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	5533698	48393717	85458178	83	24733										
SMARCD1	6602	hgsc.bcm.edu	37	chr12	50492775	50492775	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	agcaagccctgggaatccggAatacatagggcctctcccac	10	14	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr12:50492775A>G	ENST00000394963.4	+	13	1938	c.1540A>G	c.(1540-1542)Aat>Gat	p.N514D	SMARCD1_ENST00000548573.1_Missense_Mutation_p.N312D|SMARCD1_ENST00000381513.4_Missense_Mutation_p.N473D	NM_003076.4	NP_003067.3			SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1											NS(1)|breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	18						GGGAATCCGGAATACATAGGG	0.507																																					p.N514D		Atlas-SNP	.											.	SMARCD1	37	.	0			c.A1540G						.						107	104	105					12																	50492775		2203	4300	6503	SO:0001583	missense	6602	exon13			ATCCGGAATACAT	U66617	CCDS8797.2, CCDS8798.2	12q13-q14	2008-08-05			ENSG00000066117	ENSG00000066117			11106	protein-coding gene	gene with protein product		601735				8804307, 9693044, 12917342	Standard	NM_003076		Approved	BAF60A, Rsc6p, CRACD1	uc001rvx.4	Q96GM5	OTTHUMG00000150194	ENST00000394963.4:c.1540A>G	chr12.hg19:g.50492775A>G	ENSP00000378414:p.Asn514Asp	66.0	0.0		58.0	22.0	NM_003076		Missense_Mutation	SNP	ENST00000394963.4	hg19	CCDS8797.2	.	.	.	.	.	.	.	.	.	.	A	18.50	3.637649	0.67130	.	.	ENSG00000066117	ENST00000394963;ENST00000381513;ENST00000542914;ENST00000548573	T;T	0.48836	0.8;0.9	5.65	4.48	0.54585	.	0.050225	0.85682	D	0.000000	T	0.56949	0.2020	M	0.83692	2.655	0.80722	D	1	P;P;P	0.48640	0.712;0.913;0.743	P;P;B	0.47044	0.535;0.535;0.334	T	0.59637	-0.7417	10	0.33940	T	0.23	-10.5949	12.9701	0.58508	0.8648:0.1352:0.0:0.0	.	312;473;514	F8VRQ4;Q96GM5-2;Q96GM5	.;.;SMRD1_HUMAN	D	514;473;290;312	ENSP00000378414:N514D;ENSP00000370924:N473D	ENSP00000370924:N473D	N	+	1	0	SMARCD1	48779042	1.000000	0.71417	0.991000	0.47740	0.977000	0.68977	7.485000	0.81204	1.050000	0.40346	0.482000	0.46254	AAT	.	.		0.507	SMARCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316759.2	NM_003076		G	50492775	A	G	50492775	3	3	162	1	0	0	0	0	1	0	0	0	14792	246	9	2	1590	2	SMARCD1	12	50492775	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	2099058	50492775	83359120	84	24734										
IRAK3	11213	hgsc.bcm.edu	37	chr12	66638917	66638917	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgatggagaagagaggcctgGattcatgtctctcatttcta	11	7	4	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr12:66638917G>A	ENST00000261233.4	+	11	1610	c.1189G>A	c.(1189-1191)Gat>Aat	p.D397N	IRAK3_ENST00000457197.2_Missense_Mutation_p.D336N	NM_007199.2	NP_009130.2			interleukin-1 receptor-associated kinase 3											breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(28;0.0203)		GAGAGGCCTGGATTCATGTCT	0.478																																					p.D397N		Atlas-SNP	.											.	IRAK3	75	.	0			c.G1189A						.						93	95	95					12																	66638917		2203	4300	6503	SO:0001583	missense	11213	exon11			GGCCTGGATTCAT	AF113136	CCDS8975.1, CCDS44937.1	12q13.13	2008-05-02			ENSG00000090376	ENSG00000090376			17020	protein-coding gene	gene with protein product		604459				10383454	Standard	NM_001142523		Approved	IRAK-M	uc001sth.3	Q9Y616	OTTHUMG00000169002	ENST00000261233.4:c.1189G>A	chr12.hg19:g.66638917G>A	ENSP00000261233:p.Asp397Asn	110.0	0.0		136.0	69.0	NM_007199		Missense_Mutation	SNP	ENST00000261233.4	hg19	CCDS8975.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.764261	0.49574	.	.	ENSG00000090376	ENST00000261233;ENST00000457197	T;T	0.66815	-0.23;-0.23	5.89	4.06	0.47325	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.312643	0.31566	N	0.007435	T	0.56645	0.1999	L	0.49640	1.575	0.25990	N	0.982258	B;B	0.20671	0.047;0.028	B;B	0.20955	0.032;0.027	T	0.45891	-0.9230	9	.	.	.	-5.7203	8.4694	0.32975	0.0817:0.1535:0.7647:0.0	.	336;397	Q9Y616-2;Q9Y616	.;IRAK3_HUMAN	N	397;336	ENSP00000261233:D397N;ENSP00000409852:D336N	.	D	+	1	0	IRAK3	64925184	0.986000	0.35501	0.140000	0.22221	0.173000	0.22820	1.350000	0.34010	0.822000	0.34565	-0.305000	0.09177	GAT	.	.		0.478	IRAK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401908.1			A	66638917	G	A	66638917	3	1	162	1	0	0	0	0	1	0	0	0	7833	1174	41	3	1231	3	IRAK3	12	66638917	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	16146142	66638917	67212978	85	24735										
ATXN2	6311	hgsc.bcm.edu	37	chr12	111902504	111902504	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ggcttgtctccttgttgtatGgtaatttgggacatgctgaa	12	6	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr12:111902504G>T	ENST00000377617.3	-	21	3493	c.3332C>A	c.(3331-3333)cCa>cAa	p.P1111Q	ATXN2_ENST00000542287.2_Missense_Mutation_p.P846Q|ATXN2_ENST00000550104.1_3'UTR|ATXN2_ENST00000535949.1_Intron|ATXN2_ENST00000608853.1_Missense_Mutation_p.P951Q|ATXN2_ENST00000389153.4_Missense_Mutation_p.P848Q	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	1111					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						CTTGTTGTATGGTAATTTGGG	0.323																																					p.P1111Q		Atlas-SNP	.											.	ATXN2	99	.	0			c.C3332A						.						141	146	144					12																	111902504		2203	4300	6503	SO:0001583	missense	6311	exon21			TTGTATGGTAATT	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.3332C>A	chr12.hg19:g.111902504G>T	ENSP00000366843:p.Pro1111Gln	70.0	0.0		91.0	4.0	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Missense_Mutation	SNP	ENST00000377617.3	hg19	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.148222	0.78001	.	.	ENSG00000204842	ENST00000389154;ENST00000389153;ENST00000377617;ENST00000542287;ENST00000550844	T	0.69685	-0.42	5.74	5.74	0.90152	.	0.152147	0.46442	D	0.000300	T	0.75657	0.3879	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.999	D;P;D	0.85130	0.997;0.836;0.994	T	0.72697	-0.4215	10	0.38643	T	0.18	-8.7208	18.4783	0.90800	0.0:0.0:1.0:0.0	.	1111;846;848	Q99700;F8VQP2;F8WB06	ATX2_HUMAN;.;.	Q	166;848;1111;846;36	ENSP00000366843:P1111Q	ENSP00000366843:P1111Q	P	-	2	0	ATXN2	110386887	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.013000	0.70776	2.873000	0.98535	0.563000	0.77884	CCA	.	.		0.323	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		T	111902504	G	T	111902504	3	4	162	1	0	0	0	0	1	0	0	0	1211	1348	47	3	629	3	ATXN2	12	111902504	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	45263587	111902504	21949391	86	24736										
TCTN2	79867	hgsc.bcm.edu	37	chr12	124192255	124192255	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ccagaatatgcaaagcctatAgttagacaaccacctggctt	7	11	0	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr12:124192255A>T	ENST00000303372.5	+	18	2217	c.2089A>T	c.(2089-2091)Agt>Tgt	p.S697C	RP11-338K17.8_ENST00000538837.1_lincRNA|TCTN2_ENST00000426174.2_Missense_Mutation_p.S696C	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	697					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		CAAAGCCTATAGTTAGACAAC	0.483																																					p.S697C		Atlas-SNP	.											.	TCTN2	50	.	0			c.A2089T						.						143	124	131					12																	124192255		2203	4300	6503	SO:0001583	missense	79867	exon18			GCCTATAGTTAGA	AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"Tectonic proteins"	25774	protein-coding gene	gene with protein product	"Meckel syndrome, type 8"	613846	"chromosome 12 open reading frame 38"	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.2089A>T	chr12.hg19:g.124192255A>T	ENSP00000304941:p.Ser697Cys	74.0	0.0		82.0	39.0	NM_024809	A8K7Y8|B3KPW5|Q9H966	Missense_Mutation	SNP	ENST00000303372.5	hg19	CCDS9253.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.483430	0.44147	.	.	ENSG00000168778	ENST00000426174;ENST00000303372	D;D	0.84298	-1.83;-1.83	4.46	-1.11	0.09840	.	0.461184	0.16889	U	0.195373	T	0.71846	0.3388	L	0.40543	1.245	0.09310	N	1	D;D	0.54047	0.964;0.964	B;B	0.40702	0.338;0.338	T	0.66168	-0.5991	10	0.66056	D	0.02	.	0.9967	0.01469	0.5084:0.1591:0.1793:0.1533	.	696;697	A8K7Y8;Q96GX1	.;TECT2_HUMAN	C	696;697	ENSP00000395171:S696C;ENSP00000304941:S697C	ENSP00000304941:S697C	S	+	1	0	TCTN2	122758208	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.138000	0.16016	-0.403000	0.07622	-0.361000	0.07541	AGT	.	.		0.483	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809		T	124192255	A	T	124192255	3	4	162	1	0	0	0	0	1	0	0	0	15738	420	15	4	2159	4	TCTN2	12	124192255	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	12289751	124192255	9659640	87	24737										
SUCLA2	8803	hgsc.bcm.edu	37	chr13	48517535	48517540	+	In_Frame_Del	DEL	CATGTG	CATGTG	-													0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	caactgaaatttcacatccaCatgtgcttgcttcgctaagg							TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	CATGTG	CATGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr13:48517535_48517540delCATGTG	ENST00000378654.3	-	11	1414_1419	c.1358_1363delCACATG	c.(1357-1365)gcacatgtg>gtg	p.AH453del	SUCLA2_ENST00000543413.1_In_Frame_Del_p.AH395del|SUCLA2_ENST00000534875.1_In_Frame_Del_p.AH395del|SUCLA2_ENST00000544100.1_In_Frame_Del_p.AH319del	NM_003850.2	NP_003841.1	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	453					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|succinyl-CoA pathway (GO:0006781)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(4)	15		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)	TTCACATCCACATGTGCTTGCTTCGC	0.369																																					p.453_455del		Atlas-INDEL	.											.	SUCLA2	40	.	0			c.1359_1364del						.																																			SO:0001651	inframe_deletion	8803	exon11			.	AF058953	CCDS9406.1	13q12.2-q13.3	2010-04-16			ENSG00000136143	ENSG00000136143	6.2.1.5		11448	protein-coding gene	gene with protein product		603921				9765291	Standard	NM_003850		Approved		uc001vbs.3	Q9P2R7	OTTHUMG00000016889	ENST00000378654.3:c.1358_1363delCACATG	chr13.hg19:g.48517535_48517540delCATGTG	ENSP00000367923:p.Ala453_His454del	188.0	0.0		158.0	35.0	NM_003850	B2RDE7|O95194|Q5T9Q4|Q5T9Q6|Q9NV21|Q9NVP7	In_Frame_Del	DEL	ENST00000378654.3	hg19	CCDS9406.1																																																																																			.	.		0.369	SUCLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044852.1			-	48517540	CATGTG	-	48517535	7	5	162	1	0	1	0	1	0	0	0	0	15378	478	17	0	32	0	SUCLA2	13	48517535	In_Frame_Del	DEL	CATGTG	TCGA-DD-AACK-01A-11D-A40R-10		48517535	66652343	88	24738										
ARHGEF7	8874	hgsc.bcm.edu	37	chr13	111926288	111926288	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cgctgctcaaagagctcgagAgacacatggaggtactgcgc	13	11	1	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr13:111926288A>T	ENST00000375741.2	+	11	1514	c.1264A>T	c.(1264-1266)Aga>Tga	p.R422*	ARHGEF7_ENST00000370623.3_Nonsense_Mutation_p.R329*|ARHGEF7_ENST00000375736.4_Nonsense_Mutation_p.R244*|ARHGEF7_ENST00000426073.2_Nonsense_Mutation_p.R244*|ARHGEF7_ENST00000478679.1_Nonsense_Mutation_p.R166*|ARHGEF7_ENST00000375723.1_Nonsense_Mutation_p.R244*|ARHGEF7_ENST00000483189.1_3'UTR|ARHGEF7_ENST00000218789.5_Nonsense_Mutation_p.R244*|ARHGEF7_ENST00000375737.5_Nonsense_Mutation_p.R319*|ARHGEF7_ENST00000544132.1_Intron|ARHGEF7_ENST00000317133.5_Nonsense_Mutation_p.R401*|ARHGEF7_ENST00000375739.2_Nonsense_Mutation_p.R372*	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	422	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			AGAGCTCGAGAGACACATGGA	0.498																																					p.R422X		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.A1264T						.						69	60	63					13																	111926288		2203	4300	6503	SO:0001587	stop_gained	8874	exon11			CTCGAGAGACACA	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.1264A>T	chr13.hg19:g.111926288A>T	ENSP00000364893:p.Arg422*	79.0	0.0		77.0	19.0	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Nonsense_Mutation	SNP	ENST00000375741.2	hg19	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	A	38	6.921280	0.97936	.	.	ENSG00000102606	ENST00000317133;ENST00000375741;ENST00000375739;ENST00000370623;ENST00000545635;ENST00000466143;ENST00000218789;ENST00000375736;ENST00000426073;ENST00000375737;ENST00000375723;ENST00000478679	.	.	.	4.87	2.18	0.27775	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.3829	0.49768	0.5561:0.4439:0.0:0.0	.	.	.	.	X	401;422;372;329;399;244;244;244;244;319;244;166	.	ENSP00000218789:R244X	R	+	1	2	ARHGEF7	110724289	1.000000	0.71417	0.986000	0.45419	0.958000	0.62258	2.243000	0.43115	0.669000	0.31146	0.477000	0.44152	AGA	.	.		0.498	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511		T	111926288	A	T	111926288	4	4	162	1	0	0	0	0	0	1	0	0	911	296	11	4	1306	4	ARHGEF7	13	111926288	Nonsense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	63408753	111926288	3243590	89	24739										
MYH7	4625	hgsc.bcm.edu	37	chr14	23900980	23900980	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gcaggcctaccttgcccgggCtctggtccttcttgctgcgg	13	15	2	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr14:23900980C>T	ENST00000355349.3	-	7	791	c.629G>A	c.(628-630)aGc>aAc	p.S210N		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	210	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CTTGCCCGGGCTCTGGTCCTT	0.597																																					p.S210N		Atlas-SNP	.											.	MYH7	349	.	0			c.G629A						.						103	94	97					14																	23900980		2203	4300	6503	SO:0001583	missense	4625	exon7			CCCGGGCTCTGGT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.629G>A	chr14.hg19:g.23900980C>T	ENSP00000347507:p.Ser210Asn	60.0	0.0		69.0	24.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.504108	0.00992	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.95137	-3.62	3.12	-1.69	0.08186	Myosin head, motor domain (2);	.	.	.	.	D	0.88647	0.6493	L	0.33753	1.03	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.75563	-0.3274	9	0.35671	T	0.21	.	8.6915	0.34269	0.0:0.2308:0.2876:0.4815	.	210	P12883	MYH7_HUMAN	N	210	ENSP00000347507:S210N	ENSP00000347507:S210N	S	-	2	0	MYH7	22970820	0.001000	0.12720	0.038000	0.18304	0.057000	0.15508	0.000000	0.12993	-0.488000	0.06726	-0.786000	0.03341	AGC	.	.		0.597	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23900980	C	T	23900980	3	4	162	1	0	0	0	0	1	0	0	0	10048	797	28	3	5314	3	MYH7	14	23900980	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10		23900980	83448560	90	24740										
INSM2	84684	hgsc.bcm.edu	37	chr14	36003923	36003923	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tcctgctccgtggcgccagcAgccgcaccgaccccggggga	14	18	0	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr14:36003923A>T	ENST00000307169.3	+	1	676	c.465A>T	c.(463-465)gcA>gcT	p.A155A		NM_032594.3	NP_115983.3	Q96T92	INSM2_HUMAN	insulinoma-associated 2	155					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	10	Breast(36;0.122)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(9;2.16e-07)|Lung(238;2.63e-07)|Epithelial(34;0.00145)|all cancers(34;0.00452)	GBM - Glioblastoma multiforme(112;0.0223)		TGGCGCCAGCAGCCGCACCGA	0.756																																					p.A155A		Atlas-SNP	.											.	INSM2	39	.	0			c.A465T						.						2	2	2					14																	36003923		1229	2805	4034	SO:0001819	synonymous_variant	84684	exon1			GCCAGCAGCCGCA	AF260323	CCDS9657.1	14q13.1	2013-01-08			ENSG00000168348	ENSG00000168348		"Zinc fingers, C2H2-type"	17539	protein-coding gene	gene with protein product	"mlt 1"	614027					Standard	NM_032594		Approved	IA-6	uc001wth.1	Q96T92	OTTHUMG00000140223	ENST00000307169.3:c.465A>T	chr14.hg19:g.36003923A>T		30.0	0.0		29.0	8.0	NM_032594	A1L432|J9Y024|Q8N8K7|Q96Q84	Silent	SNP	ENST00000307169.3	hg19	CCDS9657.1																																																																																			.	.		0.756	INSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276686.1			T	36003923	A	T	36003923	2	4	162	1	0	0	0	0	0	0	0	1	7781	175	7	4		4	INSM2	14	36003923	Silent	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	12102943	36003923	71345617	91	24741										
PELI2	57161	hgsc.bcm.edu	37	chr14	56757106	56757106	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cccagcccggggtctggcgcGagatctctgtctgtggagat	15	12	3	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr14:56757106G>A	ENST00000267460.4	+	5	914	c.628G>A	c.(628-630)Gag>Aag	p.E210K		NM_021255.2	NP_067078.1	Q9HAT8	PELI2_HUMAN	pellino E3 ubiquitin protein ligase family member 2	210					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein phosphorylation (GO:0001934)|protein ubiquitination (GO:0016567)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)	ligase activity (GO:0016874)			kidney(6)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	22						GGTCTGGCGCGAGATCTCTGT	0.587																																					p.E210K		Atlas-SNP	.											PELI2,NS,carcinoma,-2,1	PELI2	55	.	0			c.G628A						.						105	109	107					14																	56757106		2203	4300	6503	SO:0001583	missense	57161	exon5			TGGCGCGAGATCT	AF302502	CCDS9726.1	14q21	2012-02-23	2012-02-23		ENSG00000139946	ENSG00000139946		"Pellino homologs"	8828	protein-coding gene	gene with protein product		614798	"pellino (Drosophila) homolog 2", "pellino homolog 2 (Drosophila)"			11306823, 12860405	Standard	XM_006720211		Approved		uc001xch.3	Q9HAT8	OTTHUMG00000152336	ENST00000267460.4:c.628G>A	chr14.hg19:g.56757106G>A	ENSP00000267460:p.Glu210Lys	81.0	1.0		75.0	27.0	NM_021255	B2RDY5	Missense_Mutation	SNP	ENST00000267460.4	hg19	CCDS9726.1	.	.	.	.	.	.	.	.	.	.	G	37	6.315957	0.97467	.	.	ENSG00000139946	ENST00000267460	T	0.59772	0.24	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.81880	0.4916	M	0.89601	3.045	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.84626	0.0687	10	0.87932	D	0	-34.1072	20.1634	0.98142	0.0:0.0:1.0:0.0	.	210	Q9HAT8	PELI2_HUMAN	K	210	ENSP00000267460:E210K	ENSP00000267460:E210K	E	+	1	0	PELI2	55826859	1.000000	0.71417	0.972000	0.41901	0.991000	0.79684	9.869000	0.99810	2.773000	0.95371	0.655000	0.94253	GAG	.	.		0.587	PELI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276925.1			A	56757106	G	A	56757106	3	1	162	1	0	0	0	0	1	0	0	0	11731	1059	37	1	646	1	PELI2	14	56757106	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	20753183	56757106	50592434	92	24742										
KIAA0317	9870	hgsc.bcm.edu	37	chr14	75139861	75139861	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gagctccacaggaggttgaaTgccatcatccaccaccagtg	10	13	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr14:75139861T>A	ENST00000356357.4	-	10	1734	c.1219A>T	c.(1219-1221)Att>Ttt	p.I407F	AREL1_ENST00000557401.1_5'UTR	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	407					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GGAGGTTGAATGCCATCATCC	0.448																																					p.I407F		Atlas-SNP	.											.	KIAA0317	68	.	0			c.A1219T						.						107	106	107					14																	75139861		1943	4135	6078	SO:0001583	missense	9870	exon10			GTTGAATGCCATC	AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"KIAA0317"	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.1219A>T	chr14.hg19:g.75139861T>A	ENSP00000348714:p.Ile407Phe	103.0	0.0		98.0	39.0	NM_001039479	B4E2C7|Q7LDY1|Q8IYY9	Missense_Mutation	SNP	ENST00000356357.4	hg19	CCDS41971.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.326482	0.41197	.	.	ENSG00000119682	ENST00000356357;ENST00000543377;ENST00000556202	T;T	0.50277	0.75;0.75	6.17	6.17	0.99709	.	0.045801	0.85682	D	0.000000	T	0.40398	0.1115	L	0.29908	0.895	0.80722	D	1	P;B	0.46512	0.879;0.01	P;B	0.47864	0.559;0.004	T	0.19289	-1.0310	10	0.08599	T	0.76	.	12.6398	0.56702	0.0:0.0:0.1377:0.8623	.	407;407	O15033-2;O15033	.;K0317_HUMAN	F	407;246;246	ENSP00000348714:I407F;ENSP00000452101:I246F	ENSP00000348714:I407F	I	-	1	0	KIAA0317	74209614	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.873000	0.69644	2.371000	0.80710	0.533000	0.62120	ATT	.	.		0.448	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821		A	75139861	T	A	75139861	3	1	162	1	0	0	0	0	1	0	0	0	8176	1464	51	4	1296	4	KIAA0317	14	75139861	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	18382755	75139861	32209679	93	24743										
NRXN3	9369	hgsc.bcm.edu	37	chr14	79432393	79432393	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	atggtgggagaccatacccgTttggagttccacaacattga	11	9	0	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr14:79432393T>G	ENST00000554719.1	+	9	1793	c.1302T>G	c.(1300-1302)cgT>cgG	p.R434R	NRXN3_ENST00000335750.5_Silent_p.R434R	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	203					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		ACCATACCCGTTTGGAGTTCC	0.423																																					p.R434R		Atlas-SNP	.											.	NRXN3	342	.	0			c.T1302G						.						97	90	92					14																	79432393		2203	4300	6503	SO:0001819	synonymous_variant	9369	exon9			TACCCGTTTGGAG	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.1302T>G	chr14.hg19:g.79432393T>G		66.0	0.0		68.0	22.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Silent	SNP	ENST00000554719.1	hg19	CCDS9870.1																																																																																			.	.		0.423	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250		G	79432393	T	G	79432393	2	3	162	1	0	0	0	0	0	0	0	1	10676	1712	60	5		5	NRXN3	14	79432393	Silent	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	4292532	79432393	27917147	94	24744										
GPR68	8111	hgsc.bcm.edu	37	chr14	91701172	91701172	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cacgtactgcagccagaaggGcagcgagcagatgtagaaga	14	9	0	4			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr14:91701172G>T	ENST00000531499.2	-	2	562	c.223C>A	c.(223-225)Ccc>Acc	p.P75T	GPR68_ENST00000238699.3_Missense_Mutation_p.P85T|GPR68_ENST00000529300.1_5'Flank|GPR68_ENST00000535815.1_Missense_Mutation_p.P75T			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	75					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		AGCCAGAAGGGCAGCGAGCAG	0.602																																					p.P75T		Atlas-SNP	.											.	GPR68	32	.	0			c.C223A						.						60	56	57					14																	91701172		2203	4300	6503	SO:0001583	missense	8111	exon2			AGAAGGGCAGCGA	U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"GPCR / Class A : Orphans"	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.223C>A	chr14.hg19:g.91701172G>T	ENSP00000434045:p.Pro75Thr	87.0	0.0		87.0	38.0	NM_001177676	Q13334|Q4VBB4|Q6IX34	Missense_Mutation	SNP	ENST00000531499.2	hg19	CCDS9894.2	.	.	.	.	.	.	.	.	.	.	G	23.8	4.461116	0.84317	.	.	ENSG00000119714	ENST00000531499;ENST00000238699;ENST00000535815;ENST00000529102	T;T;T;T	0.73047	-0.71;-0.71;-0.71;-0.71	5.56	5.56	0.83823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.88555	0.6468	M	0.92604	3.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90847	0.4728	10	0.87932	D	0	.	19.5343	0.95242	0.0:0.0:1.0:0.0	.	75;75	Q6NWR5;Q15743	.;OGR1_HUMAN	T	75;85;75;75	ENSP00000434045:P75T;ENSP00000238699:P85T;ENSP00000440797:P75T;ENSP00000432740:P75T	ENSP00000238699:P85T	P	-	1	0	GPR68	90770925	1.000000	0.71417	0.978000	0.43139	0.776000	0.43924	9.869000	0.99810	2.601000	0.87937	0.655000	0.94253	CCC	.	.		0.602	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2			T	91701172	G	T	91701172	3	4	162	1	0	0	0	0	1	0	0	0	6715	1203	42	3	878	3	GPR68	14	91701172	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	12268779	91701172	15648368	95	24745										
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32928129	32928129	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	aaagaaaggtacatttacatActactgttagagttttacct	6	6	0	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr15:32928129A>G	ENST00000361627.3	+	11	2205				ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.Y499C|ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.Y471C|ARHGAP11A_ENST00000543522.1_Intron|ARHGAP11A_ENST00000565905.1_Intron	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A						regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		ACATTTACATACTACTGTTAG	0.274																																					p.Y499C	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.A1496G						.						60	60	60					15																	32928129		2201	4299	6500	SO:0001627	intron_variant	9824	exon11			TTACATACTACTG	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1483+13A>G	chr15.hg19:g.32928129A>G		165.0	0.0		191.0	58.0	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	hg19	CCDS10028.1																																																																																			.	.		0.274	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		G	32928129	A	G	32928129	1	3	162	0	1	0	0	0	0	0	0	0	863	391	14	2		2	ARHGAP11A	15	32928129	Intron	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10		32928129	69603263	96	24746										
UACA	55075	hgsc.bcm.edu	37	chr15	70959550	70959550	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gtacagaagagttcttttgaTtctccaacaattgatgcagt	8	7	2	4			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr15:70959550T>G	ENST00000322954.6	-	16	3658	c.3473A>C	c.(3472-3474)aAt>aCt	p.N1158T	UACA_ENST00000560441.1_Missense_Mutation_p.N1143T|UACA_ENST00000539319.1_Missense_Mutation_p.N1049T|UACA_ENST00000379983.2_Missense_Mutation_p.N1145T	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1158					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						GTTCTTTTGATTCTCCAACAA	0.393																																					p.N1158T		Atlas-SNP	.											.	UACA	235	.	0			c.A3473C						.						169	169	169					15																	70959550		2199	4298	6497	SO:0001583	missense	55075	exon16			TTTTGATTCTCCA	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.3473A>C	chr15.hg19:g.70959550T>G	ENSP00000314556:p.Asn1158Thr	81.0	0.0		58.0	25.0	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	hg19	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	T	7.643	0.681369	0.14907	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000539319	T;T;T	0.33865	1.39;1.41;1.88	5.66	5.66	0.87406	.	0.357899	0.27100	N	0.020934	T	0.37348	0.1000	L	0.55103	1.725	0.09310	N	1	P;B;P;P	0.40398	0.529;0.394;0.536;0.716	B;B;B;B	0.39840	0.228;0.114;0.114;0.311	T	0.31052	-0.9957	10	0.32370	T	0.25	-21.1466	15.9023	0.79387	0.0:0.0:0.0:1.0	.	1049;1158;1158;1145	F5H2B9;B7ZKM6;Q9BZF9;G3XAG2	.;.;UACA_HUMAN;.	T	1158;1145;1049	ENSP00000314556:N1158T;ENSP00000369319:N1145T;ENSP00000438667:N1049T	ENSP00000314556:N1158T	N	-	2	0	UACA	68746604	0.000000	0.05858	0.964000	0.40570	0.036000	0.12997	0.072000	0.14617	2.153000	0.67306	0.533000	0.62120	AAT	.	.		0.393	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			G	70959550	T	G	70959550	3	3	162	1	0	0	0	0	1	0	0	0	16839	1493	52	5	793	5	UACA	15	70959550	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	38031421	70959550	31571842	97	24747										
NGRN	51335	hgsc.bcm.edu	37	chr15	90808975	90808984	+	Frame_Shift_Del	DEL	GGGCGCGTTT	GGGCGCGTTT	-													0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ccctgagtctcttgctgggcGggcgcgtttgcgccgccgtc							TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	GGGCGCGTTT	GGGCGCGTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr15:90808975_90808984delGGGCGCGTTT	ENST00000379095.3	+	1	39_48	c.31_40delGGGCGCGTTT	c.(31-42)gggcgcgtttgcfs	p.GRVC11fs	RP11-697E2.6_ENST00000561573.1_Intron|NGRN_ENST00000331497.3_3'UTR	NM_001033088.1	NP_001028260.2	Q9NPE2	NGRN_HUMAN	neugrin, neurite outgrowth associated	11					neuron differentiation (GO:0030182)	extracellular region (GO:0005576)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)			CTTGCTGGGCGGGCGCGTTTGCGCCGCCGT	0.676																																					p.10_13del		Atlas-INDEL	.											.	NGRN	27	.	0			c.30_39del						.																																			SO:0001589	frameshift_variant	51335	exon1			.	AB029315	CCDS32329.1	15q26.1	2008-02-05			ENSG00000182768	ENSG00000182768			18077	protein-coding gene	gene with protein product						11118320	Standard	NR_028052		Approved	DSC92	uc002bpf.1	Q9NPE2	OTTHUMG00000149807	ENST00000379095.3:c.31_40delGGGCGCGTTT	chr15.hg19:g.90808975_90808984delGGGCGCGTTT	ENSP00000368389:p.Gly11fs	49.0	0.0		54.0	11.0	NM_001033088	B2R6M8|Q4V9L7|Q9HBL4	Frame_Shift_Del	DEL	ENST00000379095.3	hg19	CCDS32329.1																																																																																			.	.		0.676	NGRN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313418.1			-	90808984	GGGCGCGTTT	-	90808975	7	5	162	1	0	1	0	1	0	0	0	0	10408	1116	39	0	33	0	NGRN	15	90808975	Frame_Shift_Del	DEL	GGGCGCGTTT	TCGA-DD-AACK-01A-11D-A40R-10	19849425	90808975	11722417	98	24748										
ZNF646	9726	hgsc.bcm.edu	37	chr16	31090546	31090546	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ggctgctgtggtcagacctaCgatgacctggggagcctgga	16	10	1	2	rs140492151		TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr16:31090546C>T	ENST00000394979.2	+	1	3324	c.2901C>T	c.(2899-2901)taC>taT	p.Y967Y	ZNF646_ENST00000300850.5_Silent_p.Y967Y			O15015	ZN646_HUMAN	zinc finger protein 646	967					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						GTCAGACCTACGATGACCTGG	0.607																																					p.Y967Y		Atlas-SNP	.											.	ZNF646	133	.	0			c.C2901T						.	C		0,4394		0,0,2197	86	75	79		2901	-4.4	1	16	dbSNP_134	79	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF646	NM_014699.3		0,1,6496	TT,TC,CC		0.0116,0.0,0.0077		967/1833	31090546	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			GACCTACGATGAC	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.2901C>T	chr16.hg19:g.31090546C>T		103.0	0.0		63.0	22.0	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	hg19																																																																																				.	C|1.000;T|0.000		0.607	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		T	31090546	C	T	31090546	2	4	162	1	0	0	0	0	0	0	0	1	18077	547	19	1		1	ZNF646	16	31090546	Silent	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10		31090546	59264207	99	24749										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7637534	7637534	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	actggaggggcacacggtccTctacatccctgcagaggcca	12	14	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr17:7637534T>A	ENST00000572933.1	+	6	2122	c.662T>A	c.(661-663)cTc>cAc	p.L221H	DNAH2_ENST00000082259.3_Missense_Mutation_p.L221H|DNAH2_ENST00000389173.2_Missense_Mutation_p.L221H|DNAH2_ENST00000570791.1_Missense_Mutation_p.L221H			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	221	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CACACGGTCCTCTACATCCCT	0.532																																					p.L221H		Atlas-SNP	.											.	DNAH2	498	.	0			c.T662A						.						92	77	82					17																	7637534		2203	4300	6503	SO:0001583	missense	146754	exon5			CGGTCCTCTACAT	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.662T>A	chr17.hg19:g.7637534T>A	ENSP00000458355:p.Leu221His	142.0	0.0		156.0	56.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.418614	0.83559	.	.	ENSG00000183914	ENST00000360606;ENST00000389173;ENST00000082259	T;T	0.38560	1.13;1.19	5.24	5.24	0.73138	.	0.955765	0.08632	N	0.916895	T	0.69922	0.3165	M	0.84326	2.69	0.47511	D	0.999445	D;D	0.89917	0.999;1.0	D;D	0.91635	0.921;0.999	T	0.64554	-0.6380	10	0.87932	D	0	.	14.1209	0.65186	0.0:0.0:0.0:1.0	.	221;221	Q9P225;Q9P225-3	DYH2_HUMAN;.	H	221	ENSP00000373825:L221H;ENSP00000082259:L221H	ENSP00000082259:L221H	L	+	2	0	DNAH2	7578259	1.000000	0.71417	0.999000	0.59377	0.959000	0.62525	6.690000	0.74567	2.004000	0.58718	0.374000	0.22700	CTC	.	.		0.532	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7637534	T	A	7637534	3	1	162	1	0	0	0	0	1	0	0	0	4604	1551	54	4	680	4	DNAH2	17	7637534	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10		7637534	73557676	100	24750										
TAF15	8148	hgsc.bcm.edu	37	chr17	34171663	34171663	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gtggagacagaagtgggggtGgctatggtggggacagaggc	22	4	0	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr17:34171663G>A	ENST00000588240.1	+	15	1475	c.1360G>A	c.(1360-1362)Ggc>Agc	p.G454S	TAF15_ENST00000592237.1_Intron|TAF15_ENST00000311979.3_Missense_Mutation_p.G451S	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		aagtgggggtggctatggtgg	0.622			T	"TEC, CHN1, ZNF384"	"extraskeletal myxoid chondrosarcomas, ALL"																																p.G454S		Atlas-SNP	.		Dom	yes		17	17q11.1-q11.2	8148	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"		"L, M"	.	TAF15	46	.	0			c.G1360A						.						20	21	20					17																	34171663		2200	4297	6497	SO:0001583	missense	8148	exon15			GGGGGTGGCTATG	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"RNA binding motif (RRM) containing"	11547	protein-coding gene	gene with protein product		601574	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1360G>A	chr17.hg19:g.34171663G>A	ENSP00000466950:p.Gly454Ser	89.0	0.0		72.0	23.0	NM_139215	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000588240.1	hg19	CCDS32623.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.887249	0.52014	.	.	ENSG00000172660	ENST00000311979;ENST00000536077	D	0.94280	-3.39	5.06	4.09	0.47781	.	.	.	.	.	D	0.87334	0.6151	N	0.22421	0.69	0.27235	N	0.95928	B;B	0.09022	0.001;0.002	B;B	0.10450	0.002;0.005	T	0.80086	-0.1529	9	0.87932	D	0	-0.2947	7.8671	0.29543	0.1881:0.0:0.8119:0.0	.	454;451	Q92804;Q92804-2	RBP56_HUMAN;.	S	454;257	ENSP00000309558:G454S	ENSP00000309558:G454S	G	+	1	0	TAF15	31195776	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.402000	0.73260	1.152000	0.42452	0.585000	0.79938	GGC	.	.		0.622	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215		A	34171663	G	A	34171663	3	1	162	1	0	0	0	0	1	0	0	0	15533	1348	47	3	1418	3	TAF15	17	34171663	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	26534129	34171663	47023547	101	24751										
KRT10	3858	hgsc.bcm.edu	37	chr17	38975889	38975889	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tttcagctcgaatctgttgcAactgttcttccagagcggat	9	10	3	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr17:38975889A>T	ENST00000269576.5	-	6	1262	c.1253T>A	c.(1252-1254)tTg>tAg	p.L418*	TMEM99_ENST00000301665.3_Intron|TMEM99_ENST00000496847.1_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	418	Coil 2.|Gly-rich.|Rod.				cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				AATCTGTTGCAACTGTTCTTC	0.483																																					p.L418X		Atlas-SNP	.											.	KRT10	56	.	0			c.T1253A						.						128	123	124					17																	38975889		2203	4300	6503	SO:0001587	stop_gained	3858	exon6			TGTTGCAACTGTT	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1253T>A	chr17.hg19:g.38975889A>T	ENSP00000269576:p.Leu418*	152.0	0.0		136.0	59.0	NM_000421	Q14664|Q8N175	Nonsense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	A	38	6.680169	0.97755	.	.	ENSG00000186395	ENST00000269576	.	.	.	5.6	5.6	0.85130	.	0.000000	0.29080	N	0.013219	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7953	0.78404	1.0:0.0:0.0:0.0	.	.	.	.	X	418	.	ENSP00000269576:L418X	L	-	2	0	KRT10	36229415	0.992000	0.36948	0.999000	0.59377	0.888000	0.51559	8.907000	0.92634	2.151000	0.67156	0.533000	0.62120	TTG	.	.		0.483	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		T	38975889	A	T	38975889	4	4	162	1	0	0	0	0	0	1	0	0	8457	131	5	4	513	4	KRT10	17	38975889	Nonsense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	4804226	38975889	42219321	102	24752										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901119	51901119	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	catcaccgtcccctcggacaAtgtggttatggtgcatgagt	11	11	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr17:51901119A>T	ENST00000268919.4	+	1	881	c.725A>T	c.(724-726)aAt>aTt	p.N242I		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	242	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CCCTCGGACAATGTGGTTATG	0.547																																					p.N242I		Atlas-SNP	.											.	KIF2B	254	.	0			c.A725T						.						124	102	109					17																	51901119		2203	4300	6503	SO:0001583	missense	84643	exon1			CGGACAATGTGGT	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.725A>T	chr17.hg19:g.51901119A>T	ENSP00000268919:p.Asn242Ile	146.0	0.0		104.0	32.0	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	hg19	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	A	16.48	3.136156	0.56936	.	.	ENSG00000141200	ENST00000268919	T	0.18960	2.18	5.63	4.56	0.56223	Kinesin, motor domain (4);	0.285603	0.26485	N	0.024105	T	0.26231	0.0640	M	0.74647	2.275	0.20764	N	0.999851	B	0.18461	0.028	B	0.25759	0.063	T	0.19484	-1.0304	10	0.46703	T	0.11	.	9.6414	0.39842	0.8542:0.0:0.1458:0.0	.	242	Q8N4N8	KIF2B_HUMAN	I	242	ENSP00000268919:N242I	ENSP00000268919:N242I	N	+	2	0	KIF2B	49256118	0.489000	0.26004	0.022000	0.16811	0.955000	0.61496	2.078000	0.41567	1.072000	0.40860	0.533000	0.62120	AAT	.	.		0.547	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51901119	A	T	51901119	3	4	162	1	0	0	0	0	1	0	0	0	8307	101	4	4	727	4	KIF2B	17	51901119	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	12925230	51901119	29294091	103	24753										
CARD14	79092	hgsc.bcm.edu	37	chr17	78176201	78176201	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ggatactgccgcgcacggcaCcatccccaactactccaggt	9	17	0	0	rs371296759		TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr17:78176201C>G	ENST00000573882.1	+	17	2737	c.2201C>G	c.(2200-2202)aCc>aGc	p.T734S	RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000573935.1_RNA|CARD14_ENST00000570421.1_Missense_Mutation_p.T734S|RP11-334C17.5_ENST00000570309.1_RNA|RP11-334C17.5_ENST00000576824.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA|CARD14_ENST00000392434.2_3'UTR|CARD14_ENST00000344227.2_Missense_Mutation_p.T734S			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	734					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			GCGCACGGCACCATCCCCAAC	0.647																																					p.T734S		Atlas-SNP	.											.	CARD14	98	.	0			c.C2201G						.						47	37	40					17																	78176201		2203	4300	6503	SO:0001583	missense	79092	exon15			ACGGCACCATCCC	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"psoriasis susceptibility 2"	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2201C>G	chr17.hg19:g.78176201C>G	ENSP00000458715:p.Thr734Ser	63.0	0.0		59.0	12.0	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	hg19	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	C	10.25	1.298728	0.23650	.	.	ENSG00000141527	ENST00000344227	T	0.04706	3.57	4.64	3.66	0.41972	.	0.368348	0.29830	N	0.011087	T	0.07052	0.0179	M	0.71581	2.175	0.80722	D	1	B	0.30406	0.278	B	0.27887	0.084	T	0.09707	-1.0662	10	0.62326	D	0.03	-21.8755	7.6124	0.28137	0.0:0.7401:0.1685:0.0914	.	734	Q9BXL6	CAR14_HUMAN	S	734	ENSP00000344549:T734S	ENSP00000344549:T734S	T	+	2	0	CARD14	75790796	0.997000	0.39634	0.981000	0.43875	0.263000	0.26337	1.851000	0.39338	0.920000	0.36970	0.462000	0.41574	ACC	.	.		0.647	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1			G	78176201	C	G	78176201	3	3	162	1	0	0	0	0	1	0	0	0	2648	507	18	4	2420	4	CARD14	17	78176201	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	26275082	78176201	3019009	104	24754										
C17orf70	80233	hgsc.bcm.edu	37	chr17	79514592	79514592	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ggtgctggtggtgcaggagaTgggtctggggcccgtgccgc	21	9	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr17:79514592T>C	ENST00000327787.8	-	5	1562	c.1516A>G	c.(1516-1518)Atc>Gtc	p.I506V	C17orf70_ENST00000425898.2_Missense_Mutation_p.I155V|C17orf70_ENST00000537152.1_Missense_Mutation_p.I355V			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	506					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GTGCAGGAGATGGGTCTGGGG	0.612																																					p.I506V		Atlas-SNP	.											.	C17orf70	79	.	0			c.A1516G						.						99	89	92					17																	79514592		2203	4300	6503	SO:0001583	missense	80233	exon5			AGGAGATGGGTCT	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"Fanconi anemia-associated protein, 100kDa"	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.1516A>G	chr17.hg19:g.79514592T>C	ENSP00000333283:p.Ile506Val	57.0	0.0		54.0	14.0	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Missense_Mutation	SNP	ENST00000327787.8	hg19	CCDS32765.2	.	.	.	.	.	.	.	.	.	.	T	7.517	0.655955	0.14580	.	.	ENSG00000185504	ENST00000327787;ENST00000425898;ENST00000537152	T;T;T	0.34859	1.34;1.34;1.34	4.24	0.824	0.18818	.	0.161496	0.41712	N	0.000827	T	0.27629	0.0679	L	0.49640	1.575	0.36352	D	0.860178	B;B	0.27316	0.006;0.175	B;B	0.26969	0.028;0.075	T	0.11991	-1.0565	10	0.33940	T	0.23	.	7.4203	0.27067	0.0:0.3853:0.0:0.6147	.	506;155	Q0VG06;E7EVV8	FP100_HUMAN;.	V	506;155;355	ENSP00000333283:I506V;ENSP00000399674:I155V;ENSP00000440151:I355V	ENSP00000333283:I506V	I	-	1	0	C17orf70	77125045	0.998000	0.40836	0.319000	0.25293	0.483000	0.33249	0.478000	0.22212	-0.046000	0.13446	0.379000	0.24179	ATC	.	.		0.612	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161		C	79514592	T	C	79514592	3	2	162	1	0	0	0	0	1	0	0	0	1879	1464	51	2	1149	2	C17orf70	17	79514592	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	1338391	79514592	1680618	105	24755										
MOCOS	55034	hgsc.bcm.edu	37	chr18	33779681	33779681	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ccacaccaccgcagaagactAcactgtgatcttcactgccg	7	16	2	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr18:33779681A>T	ENST00000261326.5	+	4	356	c.335A>T	c.(334-336)tAc>tTc	p.Y112F		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GCAGAAGACTACACTGTGATC	0.602																																					p.Y112F		Atlas-SNP	.											.	MOCOS	84	.	0			c.A335T						.						76	73	74					18																	33779681		2203	4300	6503	SO:0001583	missense	55034	exon4			AAGACTACACTGT	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.335A>T	chr18.hg19:g.33779681A>T	ENSP00000261326:p.Tyr112Phe	90.0	0.0		79.0	31.0	NM_017947		Missense_Mutation	SNP	ENST00000261326.5	hg19	CCDS11919.1	.	.	.	.	.	.	.	.	.	.	A	18.88	3.718169	0.68844	.	.	ENSG00000075643	ENST00000261326	D	0.87029	-2.2	5.38	5.38	0.77491	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	D	0.91043	0.7182	L	0.58925	1.835	0.49582	D	0.999803	D	0.76494	0.999	D	0.70935	0.971	D	0.89846	0.4006	10	0.33940	T	0.23	-21.3111	13.6318	0.62200	1.0:0.0:0.0:0.0	.	112	Q96EN8	MOCOS_HUMAN	F	112	ENSP00000261326:Y112F	ENSP00000261326:Y112F	Y	+	2	0	MOCOS	32033679	1.000000	0.71417	0.993000	0.49108	0.215000	0.24574	9.142000	0.94618	2.176000	0.68965	0.383000	0.25322	TAC	.	.		0.602	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			T	33779681	A	T	33779681	3	4	162	1	0	0	0	0	1	0	0	0	9698	391	14	4	349	4	MOCOS	18	33779681	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10		33779681	44297567	106	24756										
MC4R	4160	hgsc.bcm.edu	37	chr18	58038792	58038792	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	aagagatgtagaatattaagTggaggaagaatggggcccag	15	3	0	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr18:58038792T>A	ENST00000299766.3	-	1	1209	c.791A>T	c.(790-792)cAc>cTc	p.H264L		NM_005912.2	NP_005903.2	P32245	MC4R_HUMAN	melanocortin 4 receptor	264					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|diet induced thermogenesis (GO:0002024)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|insulin secretion (GO:0030073)|negative regulation of feeding behavior (GO:2000252)|positive regulation of bone resorption (GO:0045780)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of grooming behavior (GO:2000821)|response to insulin (GO:0032868)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(73;0.0946)				GAATATTAAGTGGAGGAAGAA	0.448																																					p.H264L		Atlas-SNP	.											.	MC4R	49	.	0			c.A791T						.						100	90	94					18																	58038792		2203	4300	6503	SO:0001583	missense	4160	exon1			ATTAAGTGGAGGA	AY236539	CCDS11976.1	18q22	2012-08-10			ENSG00000166603	ENSG00000166603		"GPCR / Class A : Melanocortin receptors"	6932	protein-coding gene	gene with protein product		155541				7949735, 9763669	Standard	NM_005912		Approved		uc002lie.1	P32245	OTTHUMG00000132766	ENST00000299766.3:c.791A>T	chr18.hg19:g.58038792T>A	ENSP00000299766:p.His264Leu	132.0	0.0		167.0	69.0	NM_005912	B2RAC3|Q16317|Q3MIJ6	Missense_Mutation	SNP	ENST00000299766.3	hg19	CCDS11976.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.245346	0.80024	.	.	ENSG00000166603	ENST00000299766	T	0.69175	-0.38	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.78941	0.4363	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80854	-0.1196	10	0.87932	D	0	.	14.1876	0.65617	0.0:0.0:0.0:1.0	.	264	P32245	MC4R_HUMAN	L	264	ENSP00000299766:H264L	ENSP00000299766:H264L	H	-	2	0	MC4R	56189772	1.000000	0.71417	0.911000	0.35937	0.957000	0.61999	8.040000	0.89188	2.238000	0.73509	0.533000	0.62120	CAC	.	.		0.448	MC4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256139.1	NM_005912		A	58038792	T	A	58038792	3	1	162	1	0	0	0	0	1	0	0	0	9375	1696	59	4	211	4	MC4R	18	58038792	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	24259111	58038792	20038456	107	24757										
MED16	10025	hgsc.bcm.edu	37	chr19	868161	868161	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ggggtcctgggagagtggtgTgtggactgcgggcccagctg	21	8	0	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr19:868161T>A	ENST00000589119.1	-	15	2573	c.2574A>T	c.(2572-2574)acA>acT	p.T858T	MED16_ENST00000395808.3_3'UTR|MED16_ENST00000269814.4_3'UTR|MED16_ENST00000325464.1_Silent_p.T858T|MED16_ENST00000312090.6_3'UTR			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	858					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGAGTGGTGTGTGGACTGCG	0.687																																					p.T858T		Atlas-SNP	.											.	MED16	61	.	0			c.A2574T						.						40	38	39					19																	868161		2196	4297	6493	SO:0001819	synonymous_variant	10025	exon16			GTGGTGTGTGGAC	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"WD repeat domain containing"	17556	protein-coding gene	gene with protein product		604062	"thyroid hormone receptor associated protein 5"	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.2574A>T	chr19.hg19:g.868161T>A		61.0	0.0		39.0	14.0	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	hg19	CCDS12047.1																																																																																			.	.		0.687	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481		A	868161	T	A	868161	2	1	162	1	0	0	0	0	0	0	0	1	9443	1683	59	4		4	MED16	19	868161	Silent	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10		868161	58260822	108	24758										
MUC16	94025	hgsc.bcm.edu	37	chr19	9049962	9049962	+	Missense_Mutation	SNP	T	T	A													0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tctattgaaaacagatggggTtgtcctgggaagagctgtgc							TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr19:9049962T>A	ENST00000397910.4	-	5	31872	c.31669A>T	c.(31669-31671)Acc>Tcc	p.T10557S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10559	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ACAGATGGGGTTGTCCTGGGA	0.488																																					p.T10557S		Atlas-SNP	.											.	MUC16	4315	.	0			c.A31669T						.						223	204	210					19																	9049962		1933	4131	6064	SO:0001583	missense	94025	exon5			ATGGGGTTGTCCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31669A>T	chr19.hg19:g.9049962T>A	ENSP00000381008:p.Thr10557Ser	170.0	0.0		199.0	78.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	8.565	0.878694	0.17395	.	.	ENSG00000181143	ENST00000397910	T	0.02369	4.32	3.08	2.03	0.26663	.	.	.	.	.	T	0.02888	0.0086	L	0.52573	1.65	.	.	.	P	0.36282	0.546	B	0.28784	0.094	T	0.26430	-1.0103	8	0.87932	D	0	.	5.285	0.15696	0.0:0.1368:0.0:0.8632	.	10557	B5ME49	.	S	10557	ENSP00000381008:T10557S	ENSP00000381008:T10557S	T	-	1	0	MUC16	8910962	0.021000	0.18746	0.018000	0.16275	0.073000	0.16967	0.387000	0.20718	0.537000	0.28751	0.248000	0.18094	ACC	.	.		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9049962	T	A	9049962	3	1	162	1	0	0	0	0	1	0	0	0	9982	1725	60	4	12174	4	MUC16	19	9049962	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	8181801	9049962	50079021	109	24759	114	2								
MUC16	94025	hgsc.bcm.edu	37	chr19	9049967	9049967	+	Missense_Mutation	SNP	C	C	A													0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgaaaacagatggggttgtcCtgggaagagctgtgctggtt							TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr19:9049967C>A	ENST00000397910.4	-	5	31867	c.31664G>T	c.(31663-31665)aGg>aTg	p.R10555M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10557	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGGGTTGTCCTGGGAAGAGC	0.483																																					p.R10555M		Atlas-SNP	.											.	MUC16	4315	.	0			c.G31664T						.						230	210	216					19																	9049967		1932	4135	6067	SO:0001583	missense	94025	exon5			GTTGTCCTGGGAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31664G>T	chr19.hg19:g.9049967C>A	ENSP00000381008:p.Arg10555Met	174.0	0.0		197.0	74.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	6.633	0.485205	0.12641	.	.	ENSG00000181143	ENST00000397910	T	0.02974	4.09	3.08	-1.69	0.08186	.	.	.	.	.	T	0.02083	0.0065	L	0.27053	0.805	.	.	.	P	0.37573	0.6	B	0.36885	0.235	T	0.42207	-0.9465	8	0.87932	D	0	.	2.75	0.05277	0.2197:0.3987:0.0:0.3816	.	10555	B5ME49	.	M	10555	ENSP00000381008:R10555M	ENSP00000381008:R10555M	R	-	2	0	MUC16	8910967	0.000000	0.05858	0.012000	0.15200	0.062000	0.15995	-0.334000	0.07883	-0.257000	0.09459	0.298000	0.19748	AGG	.	.		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9049967	C	A	9049967	3	1	162	1	0	0	0	0	1	0	0	0	9982	681	24	3	12179	3	MUC16	19	9049967	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	5	9049967	50079016	110	24760	114	2								
ICAM1	3383	hgsc.bcm.edu	37	chr19	10395559	10395559	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gcttgggggaacccattgccCgagctcaagtgtctaaagga	13	10	2	0	rs556280231		TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr19:10395559C>T	ENST00000264832.3	+	6	1606	c.1281C>T	c.(1279-1281)ccC>ccT	p.P427P	ICAM4_ENST00000393717.2_5'Flank|CTD-2369P2.8_ENST00000589379.1_RNA|ICAM1_ENST00000423829.2_Silent_p.P205P|CTD-2369P2.5_ENST00000592893.1_RNA|ICAM4_ENST00000380770.3_5'Flank|ICAM4_ENST00000340992.4_5'Flank	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	427	Ig-like C2-type 5.				adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	ACCCATTGCCCGAGCTCAAGT	0.582													C|||	1	0.000199681	8e-04	0	5008	,	,		18051	0		0	False		,,,				2504	0				p.P427P		Atlas-SNP	.											.	ICAM1	32	.	0			c.C1281T						.						52	53	53					19																	10395559		2203	4300	6503	SO:0001819	synonymous_variant	3383	exon6			ATTGCCCGAGCTC		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	5344	protein-coding gene	gene with protein product	"human rhinovirus receptor"	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.1281C>T	chr19.hg19:g.10395559C>T		107.0	0.0		90.0	25.0	NM_000201	B2R6M3|Q5NKV7|Q96B50	Silent	SNP	ENST00000264832.3	hg19	CCDS12231.1																																																																																			.	.		0.582	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1			T	10395559	C	T	10395559	2	4	162	1	0	0	0	0	0	0	0	1	7488	639	23	1		1	ICAM1	19	10395559	Silent	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	1345592	10395559	48733424	111	24761										
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927688	23927688	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	acatatgtacgatttctctcCaatatgaattcttttatgtt	4	7	2	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr19:23927688C>A	ENST00000402377.3	-	4	805	c.664G>T	c.(664-666)Gga>Tga	p.G222*	ZNF681_ENST00000395385.3_Nonsense_Mutation_p.G153*	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	222					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				GATTTCTCTCCAATATGAATT	0.308																																					p.G222X		Atlas-SNP	.											.	ZNF681	76	.	0			c.G664T						.						43	43	43					19																	23927688		2203	4299	6502	SO:0001587	stop_gained	148213	exon4			TCTCTCCAATATG	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.664G>T	chr19.hg19:g.23927688C>A	ENSP00000384000:p.Gly222*	64.0	0.0		61.0	20.0	NM_138286	B3KVF7	Nonsense_Mutation	SNP	ENST00000402377.3	hg19	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	9.979	1.227542	0.22542	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	.	.	.	1.62	1.62	0.23740	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	8.7414	0.34560	0.0:1.0:0.0:0.0	.	.	.	.	X	222;153	.	ENSP00000378783:G153X	G	-	1	0	ZNF681	23719528	0.007000	0.16637	0.004000	0.12327	0.003000	0.03518	2.402000	0.44521	0.870000	0.35726	0.453000	0.30009	GGA	.	.		0.308	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		A	23927688	C	A	23927688	4	1	162	1	0	0	0	0	0	1	0	0	18103	603	21	3	1277	3	ZNF681	19	23927688	Nonsense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	13532129	23927688	35201295	112	24762										
DMKN	93099	hgsc.bcm.edu	37	chr19	35993746	35993746	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tcctacctcccagagtcggcTgaagtagaggagggctcggg	15	11	0	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr19:35993746T>A	ENST00000339686.3	-	10	1353	c.1177A>T	c.(1177-1179)Agc>Tgc	p.S393C	DMKN_ENST00000408915.2_5'Flank|DMKN_ENST00000472252.2_Missense_Mutation_p.S40C|DMKN_ENST00000602781.1_Missense_Mutation_p.S106C|DMKN_ENST00000429837.1_Missense_Mutation_p.S352C|DMKN_ENST00000467637.1_Missense_Mutation_p.S118C|DMKN_ENST00000443640.1_Missense_Mutation_p.S156C|DMKN_ENST00000492341.2_Missense_Mutation_p.S40C|DMKN_ENST00000480502.1_Intron|DMKN_ENST00000436012.1_Missense_Mutation_p.S89C|DMKN_ENST00000462126.1_5'UTR|DMKN_ENST00000419602.1_Missense_Mutation_p.S382C|DMKN_ENST00000402589.2_Missense_Mutation_p.S106C|DMKN_ENST00000414866.2_Missense_Mutation_p.S106C	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	393						extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CAGAGTCGGCTGAAGTAGAGG	0.637																																					p.S393C		Atlas-SNP	.											.	DMKN	116	.	0			c.A1177T						.						33	37	36					19																	35993746		2203	4300	6503	SO:0001583	missense	93099	exon10			GTCGGCTGAAGTA	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.1177A>T	chr19.hg19:g.35993746T>A	ENSP00000342012:p.Ser393Cys	143.0	0.0		140.0	44.0	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	hg19	CCDS12463.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.94|16.94	3.259441|3.259441	0.59321|0.59321	.|.	.|.	ENSG00000161249|ENSG00000161249	ENST00000434389|ENST00000402589;ENST00000339686;ENST00000436012;ENST00000414866;ENST00000429837;ENST00000419602;ENST00000443640	.|T;T;T;T;T;T;T	.|0.34859	.|1.34;1.34;1.34;1.34;1.34;1.34;1.34	5.85|5.85	1.1|1.1	0.20463|0.20463	.|.	.|0.869080	.|0.09885	.|N	.|0.743095	T|T	0.52175|0.52175	0.1718|0.1718	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	.|B;B;D;B;B;B;D;D;B;B;B	.|0.76494	.|0.063;0.023;0.997;0.006;0.01;0.01;0.999;0.999;0.063;0.01;0.023	.|B;B;P;B;B;B;D;D;B;B;B	.|0.72075	.|0.026;0.015;0.847;0.007;0.01;0.01;0.912;0.976;0.026;0.01;0.015	T|T	0.47761|0.47761	-0.9092|-0.9092	5|10	.|0.62326	.|D	.|0.03	-0.3348|-0.3348	8.3368|8.3368	0.32219|0.32219	0.1139:0.0:0.55:0.3361|0.1139:0.0:0.55:0.3361	.|.	.|89;40;49;49;69;87;382;352;393;106;156	.|B4E3D1;B7ZB10;Q6E0U4-12;Q6E0U4-11;Q6E0U4-10;Q6E0U4-9;C9J4P6;Q6E0U4-4;Q6E0U4;Q6E0U4-8;C9IYI1	.|.;.;.;.;.;.;.;.;DMKN_HUMAN;.;.	L|C	103|106;393;89;106;352;382;156	.|ENSP00000384509:S106C;ENSP00000342012:S393C;ENSP00000412075:S89C;ENSP00000392222:S106C;ENSP00000405503:S352C;ENSP00000391036:S382C;ENSP00000406864:S156C	.|ENSP00000342012:S393C	Q|S	-|-	2|1	0|0	DMKN|DMKN	40685586|40685586	0.941000|0.941000	0.31946|0.31946	0.803000|0.803000	0.32268|0.32268	0.870000|0.870000	0.49936|0.49936	0.633000|0.633000	0.24598|0.24598	0.184000|0.184000	0.20083|0.20083	-0.619000|-0.619000	0.04042|0.04042	CAG|AGC	.	.		0.637	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		A	35993746	T	A	35993746	3	1	162	1	0	0	0	0	1	0	0	0	4584	1580	55	4	408	4	DMKN	19	35993746	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	12066058	35993746	23135237	113	24763										
B9D2	80776	hgsc.bcm.edu	37	chr19	41860749	41860749	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	agcagctgcggcccaccaccCacgaaagcccgtgccaactg	10	18	0	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr19:41860749C>A	ENST00000243578.3	-	4	603	c.384G>T	c.(382-384)gtG>gtT	p.V128V	TGFB1_ENST00000221930.5_5'Flank|TMEM91_ENST00000604123.1_Intron|TMEM91_ENST00000539627.1_Intron|CTC-435M10.3_ENST00000604424.1_Intron	NM_030578.3	NP_085055.2	Q9BPU9	B9D2_HUMAN	B9 protein domain 2	128					cilium assembly (GO:0042384)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)	gamma-tubulin binding (GO:0043015)			large_intestine(1)|ovary(1)	2						GCCCACCACCCACGAAAGCCC	0.672																																					p.V128V		Atlas-SNP	.											.	B9D2	9	.	0			c.G384T						.						61	55	57					19																	41860749		2203	4299	6502	SO:0001819	synonymous_variant	80776	exon4			ACCACCCACGAAA	BC004157	CCDS12579.1	19q13.2	2014-01-28				ENSG00000123810			28636	protein-coding gene	gene with protein product		611951				21763481	Standard	NM_030578		Approved	MGC4093, MKS10	uc002oqj.2	Q9BPU9		ENST00000243578.3:c.384G>T	chr19.hg19:g.41860749C>A		100.0	0.0		99.0	30.0	NM_030578		Silent	SNP	ENST00000243578.3	hg19	CCDS12579.1																																																																																			.	.		0.672	B9D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463489.1	NM_030578		A	41860749	C	A	41860749	2	1	162	1	0	0	0	0	0	0	0	1	1278	581	21	3		3	B9D2	19	41860749	Silent	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	5867003	41860749	17268234	114	24764										
IL4I1	259307	hgsc.bcm.edu	37	chr19	50393835	50393835	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cgcgcgcggcagcaggtcccAgccacccacgatgcggctgt	14	17	0	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr19:50393835A>T	ENST00000391826.2	-	8	938	c.796T>A	c.(796-798)Tgg>Agg	p.W266R	MIR4750_ENST00000584564.1_RNA|IL4I1_ENST00000341114.3_Missense_Mutation_p.W288R|IL4I1_ENST00000595948.1_Missense_Mutation_p.W288R	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	266						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	AGCAGGTCCCAGCCACCCACG	0.736																																					p.W288R		Atlas-SNP	.											.	IL4I1	50	.	0			c.T862A						.						7	8	8					19																	50393835		2171	4242	6413	SO:0001583	missense	259307	exon10			GGTCCCAGCCACC	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.796T>A	chr19.hg19:g.50393835A>T	ENSP00000375702:p.Trp266Arg	35.0	0.0		30.0	11.0	NM_172374	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Missense_Mutation	SNP	ENST00000391826.2	hg19	CCDS12787.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107392	0.77096	.	.	ENSG00000104951	ENST00000341114;ENST00000391826	T;T	0.09255	3.0;3.0	4.24	4.24	0.50183	Amine oxidase (1);	0.543501	0.19465	N	0.113611	T	0.19525	0.0469	L	0.57536	1.79	0.33508	D	0.590823	D;D;D	0.55172	0.962;0.97;0.97	P;P;P	0.53450	0.605;0.726;0.726	T	0.20207	-1.0282	10	0.51188	T	0.08	-12.6054	9.634	0.39795	1.0:0.0:0.0:0.0	.	288;288;266	Q96RQ9-2;Q1WMJ3;Q96RQ9	.;.;OXLA_HUMAN	R	288;266	ENSP00000342557:W288R;ENSP00000375702:W266R	ENSP00000342557:W288R	W	-	1	0	IL4I1	55085647	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.360000	0.34125	1.787000	0.52448	0.358000	0.22013	TGG	.	.		0.736	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			T	50393835	A	T	50393835	3	4	162	1	0	0	0	0	1	0	0	0	7706	188	7	4	911	4	IL4I1	19	50393835	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	8533086	50393835	8735148	115	24765										
PRKCG	5582	hgsc.bcm.edu	37	chr19	54409615	54409615	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cgcctgggctcagggcctgaTggggaacctaccatccgtgc	14	14	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr19:54409615T>A	ENST00000263431.3	+	17	2091	c.1809T>A	c.(1807-1809)gaT>gaA	p.D603E	PRKCG_ENST00000542049.1_Missense_Mutation_p.D454E|PRKCG_ENST00000540413.1_Missense_Mutation_p.D603E|CACNG7_ENST00000391767.1_5'Flank	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	603	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	CAGGGCCTGATGGGGAACCTA	0.592																																					p.D603E		Atlas-SNP	.											.	PRKCG	246	.	0			c.T1809A						.						50	38	42					19																	54409615		2182	4251	6433	SO:0001583	missense	5582	exon17			GCCTGATGGGGAA	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.1809T>A	chr19.hg19:g.54409615T>A	ENSP00000263431:p.Asp603Glu	79.0	0.0		76.0	26.0	NM_002739	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	hg19	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	T	6.192	0.403597	0.11754	.	.	ENSG00000126583	ENST00000540413;ENST00000263431;ENST00000542049	T;T;T	0.52983	0.64;0.64;1.87	3.89	-1.34	0.09143	Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.21227	0.0511	N	0.12746	0.255	0.36304	D	0.857192	B;B;B	0.12630	0.006;0.0;0.0	B;B;B	0.15870	0.014;0.0;0.0	T	0.41998	-0.9477	9	0.02654	T	1	.	8.5494	0.33442	0.0:0.475:0.0:0.525	.	454;603;603	B7Z8Q0;F5H5C4;P05129	.;.;KPCG_HUMAN	E	603;603;454	ENSP00000443493:D603E;ENSP00000263431:D603E;ENSP00000438090:D454E	ENSP00000263431:D603E	D	+	3	2	PRKCG	59101427	0.000000	0.05858	0.963000	0.40424	0.986000	0.74619	-4.656000	0.00202	-0.469000	0.06911	0.454000	0.30748	GAT	.	.		0.592	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		A	54409615	T	A	54409615	3	1	162	1	0	0	0	0	1	0	0	0	12524	1461	51	4	1875	4	PRKCG	19	54409615	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	4015780	54409615	4719368	116	24766										
ZNF416	55659	hgsc.bcm.edu	37	chr19	58084830	58084830	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gtccatgtcactttccaaggGtttctctgcactatgatgct	8	11	2	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr19:58084830G>C	ENST00000196489.3	-	4	664	c.442C>G	c.(442-444)Ccc>Gcc	p.P148A		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	148					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		CTTTCCAAGGGTTTCTCTGCA	0.517																																					p.P148A		Atlas-SNP	.											.	ZNF416	50	.	0			c.C442G						.						103	87	92					19																	58084830		2203	4300	6503	SO:0001583	missense	55659	exon4			CCAAGGGTTTCTC	BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"Zinc fingers, C2H2-type", "-"	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.442C>G	chr19.hg19:g.58084830G>C	ENSP00000196489:p.Pro148Ala	113.0	0.0		114.0	44.0	NM_017879	Q9NWW8	Missense_Mutation	SNP	ENST00000196489.3	hg19	CCDS12954.1	.	.	.	.	.	.	.	.	.	.	G	0.052	-1.248520	0.01469	.	.	ENSG00000083817	ENST00000196489;ENST00000359489;ENST00000428052	T	0.07216	3.21	1.85	-3.69	0.04450	.	.	.	.	.	T	0.09069	0.0224	M	0.76938	2.355	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.37502	-0.9703	9	0.38643	T	0.18	.	2.7052	0.05160	0.4665:0.0:0.3164:0.2172	.	148	Q9BWM5	ZN416_HUMAN	A	148;134;128	ENSP00000196489:P148A	ENSP00000196489:P148A	P	-	1	0	ZNF416	62776642	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.272000	0.18644	-0.932000	0.03742	-1.087000	0.02190	CCC	.	.		0.517	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879		C	58084830	G	C	58084830	3	2	162	1	0	0	0	0	1	0	0	0	17908	1261	44	4	1346	4	ZNF416	19	58084830	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	3675215	58084830	1044153	117	24767										
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47602054	47602054	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	agaatttgtctcagccctgcGgacattcctagaaggtttcc	9	11	1	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr20:47602054G>C	ENST00000371917.4	+	16	2180	c.2180G>C	c.(2179-2181)cGg>cCg	p.R727P		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	727	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TCAGCCCTGCGGACATTCCTA	0.473																																					p.R727P	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.G2180C						.						115	100	105					20																	47602054		2203	4300	6503	SO:0001583	missense	10564	exon16			CCCTGCGGACATT	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.2180G>C	chr20.hg19:g.47602054G>C	ENSP00000360985:p.Arg727Pro	198.0	0.0		178.0	71.0	NM_006420	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	G	34	5.392717	0.96009	.	.	ENSG00000124198	ENST00000538445;ENST00000371917	T	0.71817	-0.6	6.03	6.03	0.97812	SEC7-like, alpha orthogonal bundle (1);Armadillo-type fold (1);SEC7-like (4);	0.000000	0.85682	D	0.000000	D	0.92417	0.7593	H	0.99689	4.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95106	0.8234	10	0.87932	D	0	.	20.5568	0.99304	0.0:0.0:1.0:0.0	.	727	Q9Y6D5	BIG2_HUMAN	P	727	ENSP00000360985:R727P	ENSP00000360985:R727P	R	+	2	0	ARFGEF2	47035461	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.869000	0.99810	2.861000	0.98227	0.655000	0.94253	CGG	.	.		0.473	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		C	47602054	G	C	47602054	3	2	162	1	0	0	0	0	1	0	0	0	853	1116	39	4	2242	4	ARFGEF2	20	47602054	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10		47602054	15423466	118	24768										
CDH4	1002	hgsc.bcm.edu	37	chr20	60485571	60485571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cccactctccaaactggaatGccgtttaccgcatcatcagt	6	15	3	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr20:60485571G>A	ENST00000360469.5	+	9	1370	c.1282G>A	c.(1282-1284)Gcc>Acc	p.A428T	CDH4_ENST00000543233.1_Missense_Mutation_p.A354T	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	428	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			AAACTGGAATGCCGTTTACCG	0.597																																					p.A428T		Atlas-SNP	.											.	CDH4	172	.	0			c.G1282A						.						128	96	107					20																	60485571		2203	4300	6503	SO:0001583	missense	1002	exon9			TGGAATGCCGTTT	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.1282G>A	chr20.hg19:g.60485571G>A	ENSP00000353656:p.Ala428Thr	132.0	0.0		138.0	51.0	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	hg19	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	g	19.16	3.773754	0.69992	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.54279	0.58;0.58	4.66	4.66	0.58398	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	M	0.73753	2.245	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74390	-0.3681	9	.	.	.	.	17.1368	0.86742	0.0:0.0:1.0:0.0	.	428	P55283	CADH4_HUMAN	T	428;336;354	ENSP00000353656:A428T;ENSP00000443301:A354T	.	A	+	1	0	CDH4	59918966	1.000000	0.71417	0.442000	0.26870	0.153000	0.21895	9.189000	0.94928	2.145000	0.66743	0.556000	0.70494	GCC	.	.		0.597	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		A	60485571	G	A	60485571	3	1	162	1	0	0	0	0	1	0	0	0	3114	1319	46	3	1316	3	CDH4	20	60485571	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	12883517	60485571	2539949	119	24769										
OLIG2	10215	hgsc.bcm.edu	37	chr21	34400111	34400111	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gtcggctatgggcgccggcaGcctgccgcgcctcacctccg	14	18	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr21:34400111G>T	ENST00000333337.3	+	1	1869	c.941G>T	c.(940-942)aGc>aTc	p.S314I	OLIG2_ENST00000382357.3_Missense_Mutation_p.S314I|AP000282.2_ENST00000420356.1_RNA|AP000282.2_ENST00000454622.1_RNA			Q13516	OLIG2_HUMAN	oligodendrocyte lineage transcription factor 2	314					myelination (GO:0042552)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate commitment (GO:0048663)|positive regulation of oligodendrocyte differentiation (GO:0048714)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|thalamus development (GO:0021794)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(1)|central_nervous_system(2)	3						GGCGCCGGCAGCCTGCCGCGC	0.756			T	TRA@	T-ALL																																p.S314I		Atlas-SNP	.		Dom	yes		21	21q22.11	10215	oligodendrocyte lineage transcription factor 2 (BHLHB1)		L	.	OLIG2	22	.	0			c.G941T						.						1	1	1					21																	34400111		561	1185	1746	SO:0001583	missense	10215	exon2			CCGGCAGCCTGCC	U48250	CCDS13620.1	21q22.11	2013-05-21	2001-12-04	2001-12-07	ENSG00000205927	ENSG00000205927		"Basic helix-loop-helix proteins"	9398	protein-coding gene	gene with protein product	"oligodendrocyte-specific bHLH transcription factor 2", "protein kinase C binding protein 2", "human protein kinase C-binding protein RACK17", "basic domain, helix-loop-helix protein, class B, 1"	606386	"protein kinase C binding protein 2"	PRKCBP2, BHLHB1		11526205	Standard	NM_005806		Approved	RACK17, OLIGO2, bHLHe19	uc002yqx.2	Q13516	OTTHUMG00000065032	ENST00000333337.3:c.941G>T	chr21.hg19:g.34400111G>T	ENSP00000331040:p.Ser314Ile	16.0	0.0		22.0	6.0	NM_005806	B3KRF3|Q05BP9|Q49AL3|Q86X04|Q9NZ14	Missense_Mutation	SNP	ENST00000333337.3	hg19	CCDS13620.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.740437	0.49045	.	.	ENSG00000205927	ENST00000382357;ENST00000333337	T;T	0.70749	-0.51;-0.51	3.75	0.682	0.17992	.	0.301943	0.28778	U	0.014164	T	0.49304	0.1549	N	0.22421	0.69	0.30335	N	0.786272	B	0.15141	0.012	B	0.11329	0.006	T	0.41016	-0.9532	10	0.72032	D	0.01	.	3.1794	0.06579	0.1003:0.3381:0.4003:0.1613	.	314	Q13516	OLIG2_HUMAN	I	314	ENSP00000371794:S314I;ENSP00000331040:S314I	ENSP00000331040:S314I	S	+	2	0	OLIG2	33321981	1.000000	0.71417	0.990000	0.47175	0.993000	0.82548	0.600000	0.24104	-0.069000	0.12931	0.455000	0.32223	AGC	.	.		0.756	OLIG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139663.1	NM_005806		T	34400111	G	T	34400111	3	4	162	1	0	0	0	0	1	0	0	0	10870	971	34	3	943	3	OLIG2	21	34400111	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10		34400111	13729784	120	24770										
IL10RB	3588	hgsc.bcm.edu	37	chr21	34655403	34655403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ttgtctccattactagtttcAaattactccccagtatgact	4	11	2	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr21:34655403A>G	ENST00000290200.2	+	5	611	c.503A>G	c.(502-504)cAa>cGa	p.Q168R	AP000295.9_ENST00000433395.2_Missense_Mutation_p.K296E	NM_000628.4	NP_000619.3	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta	168	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	14						TACTAGTTTCAAATTACTCCC	0.398																																					p.Q168R	Melanoma(67;315 1275 21667 21943 44564)	Atlas-SNP	.											.	IL10RB	37	.	0			c.A503G						.						115	105	108					21																	34655403		2203	4300	6503	SO:0001583	missense	3588	exon5			AGTTTCAAATTAC	U08988	CCDS13623.1	21q22.11	2014-09-17			ENSG00000243646	ENSG00000243646		"Interleukins and interleukin receptors", "CD molecules"	5965	protein-coding gene	gene with protein product		123889		CRFB4, D21S58, D21S66		8314576, 9312047	Standard	NM_000628		Approved	CRF2-4, CDW210B, IL-10R2		Q08334	OTTHUMG00000065128	ENST00000290200.2:c.503A>G	chr21.hg19:g.34655403A>G	ENSP00000290200:p.Gln168Arg	95.0	0.0		89.0	38.0	NM_000628	Q9BUU4	Missense_Mutation	SNP	ENST00000290200.2	hg19	CCDS13623.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.91|10.91	1.484773|1.484773	0.26598|0.26598	.|.	.|.	ENSG00000249624|ENSG00000243646	ENST00000433395|ENST00000290200;ENST00000539894	.|T	.|0.28666	.|1.6	5.27|5.27	4.18|4.18	0.49190|0.49190	.|Fibronectin, type III (2);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	.|0.626286	.|0.16259	.|N	.|0.222354	T|T	0.27900|0.27900	0.0687|0.0687	L|L	0.51422|0.51422	1.61|1.61	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.22746	.|0.074;0.035;0.035;0.035	.|B;B;B;B	.|0.27076	.|0.076;0.038;0.055;0.046	T|T	0.20706|0.20706	-1.0267|-1.0267	5|10	.|0.27082	.|T	.|0.32	-0.6922|-0.6922	8.8031|8.8031	0.34920|0.34920	0.7553:0.2447:0.0:0.0|0.7553:0.2447:0.0:0.0	.|.	.|170;168;168;168	.|Q6ZVU9;Q08334;B4DSX5;F5H766	.|.;I10R2_HUMAN;.;.	E|R	296|168	.|ENSP00000290200:Q168R	.|ENSP00000290200:Q168R	K|Q	+|+	1|2	0|0	AP000295.9|IL10RB	33577273|33577273	0.000000|0.000000	0.05858|0.05858	0.007000|0.007000	0.13788|0.13788	0.100000|0.100000	0.18952|0.18952	0.280000|0.280000	0.18790|0.18790	0.942000|0.942000	0.37525|0.37525	0.459000|0.459000	0.35465|0.35465	AAA|CAA	.	.		0.398	IL10RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139831.3			G	34655403	A	G	34655403	3	3	162	1	0	0	0	0	1	0	0	0	7630	130	5	2	521	2	IL10RB	21	34655403	Missense_Mutation	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	255292	34655403	13474492	121	24771										
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38877655	38877655	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	aaacaggaggacctggtgggCgacgtgctggggagtcaggt	19	7	1	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr21:38877655C>T	ENST00000398960.2	+	9	1384	c.1309C>T	c.(1309-1311)Cga>Tga	p.R437*	DYRK1A_ENST00000455387.2_Nonsense_Mutation_p.R209*|DYRK1A_ENST00000451934.1_Nonsense_Mutation_p.R437*|DYRK1A_ENST00000398956.2_Nonsense_Mutation_p.R437*|DYRK1A_ENST00000321219.8_Nonsense_Mutation_p.R437*|DYRK1A_ENST00000338785.3_Nonsense_Mutation_p.R437*|DYRK1A_ENST00000339659.4_Nonsense_Mutation_p.R428*	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	437	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACCTGGTGGGCGACGTGCTGG	0.463																																					p.R437X	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											DYRK1A,caecum,carcinoma,0,1	DYRK1A	85	.	0			c.C1309T						.						87	83	84					21																	38877655		2203	4300	6503	SO:0001587	stop_gained	1859	exon9			GGTGGGCGACGTG	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.1309C>T	chr21.hg19:g.38877655C>T	ENSP00000381932:p.Arg437*	135.0	0.0		85.0	34.0	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Nonsense_Mutation	SNP	ENST00000398960.2	hg19	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	C	50	17.038654	0.99878	.	.	ENSG00000157540	ENST00000338785;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956;ENST00000455387	.	.	.	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.115	0.97926	0.0:1.0:0.0:0.0	.	.	.	.	X	437;428;437;437;437;437;209	.	ENSP00000319032:R437X	R	+	1	2	DYRK1A	37799525	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	7.757000	0.85209	2.761000	0.94854	0.650000	0.86243	CGA	.	.		0.463	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		T	38877655	C	T	38877655	4	4	162	1	0	0	0	0	0	1	0	0	4856	760	27	1	1343	1	DYRK1A	21	38877655	Nonsense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	4222252	38877655	9252240	122	24772										
ITGB2	3689	hgsc.bcm.edu	37	chr21	46311901	46311901	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	ctgtggccgtgaccttcaccTggaaggtgatctgcagggca	14	11	2	2			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr21:46311901T>A	ENST00000397850.2	-	12	1687	c.1235A>T	c.(1234-1236)cAg>cTg	p.Q412L	ITGB2_ENST00000397854.3_Missense_Mutation_p.Q355L|ITGB2_ENST00000397852.1_Missense_Mutation_p.Q412L|ITGB2_ENST00000302347.5_Missense_Mutation_p.Q412L|ITGB2_ENST00000355153.4_Missense_Mutation_p.Q412L|ITGB2_ENST00000397857.1_Missense_Mutation_p.Q412L			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	412					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	GACCTTCACCTGGAAGGTGAT	0.647																																					p.Q412L		Atlas-SNP	.											.	ITGB2	107	.	0			c.A1235T						.						66	50	55					21																	46311901		2200	4300	6500	SO:0001583	missense	3689	exon11			TTCACCTGGAAGG	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.1235A>T	chr21.hg19:g.46311901T>A	ENSP00000380948:p.Gln412Leu	37.0	0.0		44.0	21.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	hg19	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.613725	0.28712	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347;ENST00000545414	T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	5.54	3.17	0.36434	Integrin beta subunit, N-terminal (2);	.	.	.	.	T	0.57007	0.2024	L	0.58583	1.82	0.30247	N	0.79444	B;B	0.19445	0.036;0.007	B;B	0.10450	0.005;0.002	T	0.53143	-0.8480	9	0.46703	T	0.11	.	10.6348	0.45558	0.0:0.1485:0.0:0.8515	.	355;412	A8MYE6;P05107	.;ITB2_HUMAN	L	412;412;355;412;412;412;355	ENSP00000380950:Q412L;ENSP00000380955:Q412L;ENSP00000380952:Q355L;ENSP00000347279:Q412L;ENSP00000380948:Q412L;ENSP00000303242:Q412L	ENSP00000303242:Q412L	Q	-	2	0	ITGB2	45136329	0.956000	0.32656	1.000000	0.80357	0.849000	0.48306	0.085000	0.14912	0.077000	0.16863	-1.139000	0.01908	CAG	.	.		0.647	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		A	46311901	T	A	46311901	3	1	162	1	0	0	0	0	1	0	0	0	7903	1580	55	4	1098	4	ITGB2	21	46311901	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10	7434246	46311901	1817994	123	24773										
RASD2	23551	hgsc.bcm.edu	37	chr22	35948024	35948024	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgacctcaagtacatcaaggCcaaggtccttcgggaaggcc	11	12	2	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr22:35948024C>A	ENST00000216127.4	+	3	1388	c.746C>A	c.(745-747)gCc>gAc	p.A249D		NM_014310.3	NP_055125.2	Q96D21	RHES_HUMAN	RASD family, member 2	249					locomotory behavior (GO:0007626)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein sumoylation (GO:0033235)|regulation of cAMP-mediated signaling (GO:0043949)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission, dopaminergic (GO:0001963)	plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	13						TACATCAAGGCCAAGGTCCTT	0.647																																					p.A249D		Atlas-SNP	.											.	RASD2	34	.	0			c.C746A						.						56	54	55					22																	35948024		2203	4300	6503	SO:0001583	missense	23551	exon3			TCAAGGCCAAGGT	AF279143	CCDS13916.1	22q13.1	2014-05-09			ENSG00000100302	ENSG00000100302			18229	protein-coding gene	gene with protein product	"tumor endothelial marker 2", "Ras homolog enriched in striatum"	612842				10947988, 10467249, 14724584	Standard	NM_014310		Approved	TEM2, Rhes, MGC:4834	uc003anx.3	Q96D21	OTTHUMG00000150607	ENST00000216127.4:c.746C>A	chr22.hg19:g.35948024C>A	ENSP00000216127:p.Ala249Asp	21.0	0.0		21.0	8.0	NM_014310	O95520|Q5THY8	Missense_Mutation	SNP	ENST00000216127.4	hg19	CCDS13916.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.592338	0.46214	.	.	ENSG00000100302	ENST00000216127	T	0.70986	-0.53	5.68	5.68	0.88126	.	0.158364	0.56097	D	0.000032	T	0.61350	0.2340	N	0.24115	0.695	0.40944	D	0.984498	B	0.19935	0.04	B	0.23150	0.044	T	0.55095	-0.8194	10	0.30078	T	0.28	.	19.8575	0.96767	0.0:1.0:0.0:0.0	.	249	Q96D21	RHES_HUMAN	D	249	ENSP00000216127:A249D	ENSP00000216127:A249D	A	+	2	0	RASD2	34277970	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.887000	0.69751	2.705000	0.92388	0.556000	0.70494	GCC	.	.		0.647	RASD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319063.1	NM_014310		A	35948024	C	A	35948024	3	1	162	1	0	0	0	0	1	0	0	0	13082	739	26	3	752	3	RASD2	22	35948024	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10		35948024	15356542	124	24774										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40069972	40069972	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tgggtctcgcccgcagtgctGaagctgttgaagatggccac	14	11	1	3			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr22:40069972G>T	ENST00000402142.3	+	29	4788	c.4788G>T	c.(4786-4788)ctG>ctT	p.L1596L	CACNA1I_ENST00000400164.3_Silent_p.L1561L|CACNA1I_ENST00000404898.1_Silent_p.L1561L|CACNA1I_ENST00000407673.1_Silent_p.L1561L|CACNA1I_ENST00000336649.4_Silent_p.L1602L|CACNA1I_ENST00000401624.1_Silent_p.L1596L	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1596					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	CCGCAGTGCTGAAGCTGTTGA	0.622																																					p.L1596L		Atlas-SNP	.											.	CACNA1I	264	.	0			c.G4788T						.						49	54	53					22																	40069972		2108	4217	6325	SO:0001819	synonymous_variant	8911	exon29			AGTGCTGAAGCTG	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.4788G>T	chr22.hg19:g.40069972G>T		50.0	0.0		39.0	10.0	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Silent	SNP	ENST00000402142.3	hg19	CCDS46710.1																																																																																			.	.		0.622	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		T	40069972	G	T	40069972	2	4	162	1	0	0	0	0	0	0	0	1	2548	1277	45	3		3	CACNA1I	22	40069972	Silent	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	4121948	40069972	11234594	125	24775										
PRR5	55615	hgsc.bcm.edu	37	chr22	45132780	45132780	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	aggcggagggcgcggcggccGgcggtaccagcatccgcagg	20	13	0	0	rs376477477		TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr22:45132780G>T	ENST00000336985.6	+	8	1097	c.820G>T	c.(820-822)Ggc>Tgc	p.G274C	PRR5_ENST00000006251.7_Missense_Mutation_p.G265C|ARHGAP8_ENST00000389773.5_Intron|PRR5_ENST00000477331.1_3'UTR|PRR5-ARHGAP8_ENST00000352766.7_Intron|PRR5_ENST00000403581.1_Missense_Mutation_p.G297C|PRR5-ARHGAP8_ENST00000361473.5_Intron|ARHGAP8_ENST00000517296.3_Intron	NM_181333.3	NP_851850.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	274					cell cycle (GO:0007049)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)	TORC2 complex (GO:0031932)				central_nervous_system(1)|endometrium(2)|lung(6)|prostate(1)|skin(1)	11		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		CGCGGCGGCCGGCGGTACCAG	0.706																																					p.G297C		Atlas-SNP	.											.	PRR5	75	.	0			c.G889T						.						17	21	20					22																	45132780		2177	4263	6440	SO:0001583	missense	55615	exon10			GCGGCCGGCGGTA	AF177331	CCDS14058.1, CCDS14059.1, CCDS56232.1, CCDS74875.1	22q13.3	2011-02-10			ENSG00000186654	ENSG00000186654			31682	protein-coding gene	gene with protein product	"protein observed with Rictor-1"	609406				15718101, 17599906	Standard	NM_001017528		Approved	PP610, FLJ20185k, Protor-1		P85299	OTTHUMG00000150460	ENST00000336985.6:c.820G>T	chr22.hg19:g.45132780G>T	ENSP00000337464:p.Gly274Cys	113.0	0.0		86.0	23.0	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000336985.6	hg19	CCDS14058.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.582069	0.46006	.	.	ENSG00000186654	ENST00000432186;ENST00000006251;ENST00000404016;ENST00000403581;ENST00000336985	T;T;T;T	0.32753	1.44;1.47;1.45;1.47	5.41	-0.997	0.10215	.	.	.	.	.	T	0.42177	0.1191	L	0.53249	1.67	0.09310	N	1	D;D;D;D;D	0.76494	0.975;0.999;0.998;0.983;0.983	P;P;P;P;P	0.61800	0.648;0.894;0.841;0.775;0.775	T	0.32851	-0.9891	9	0.59425	D	0.04	.	9.048	0.36358	0.568:0.0:0.432:0.0	.	238;297;173;274;274	B1AHF5;B1AHF6;P85299-2;P85299;A8K699	.;.;.;PRR5_HUMAN;.	C	265;265;238;297;274	ENSP00000400925:G265C;ENSP00000006251:G265C;ENSP00000384848:G297C;ENSP00000337464:G274C	ENSP00000006251:G265C	G	+	1	0	PRR5	43511444	0.933000	0.31639	0.001000	0.08648	0.177000	0.22998	2.330000	0.43885	0.015000	0.14971	0.313000	0.20887	GGC	.	.		0.706	PRR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318200.2	NM_001017528		T	45132780	G	T	45132780	3	4	162	1	0	0	0	0	1	0	0	0	12612	1116	39	1	850	1	PRR5	22	45132780	Missense_Mutation	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	5062808	45132780	6171786	126	24776										
MAPK11	5600	hgsc.bcm.edu	37	chr22	50706332	50706332	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	cgactggaaggggcgcgacaGcttcttcaccgccaccttct	11	15	3	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chr22:50706332G>A	ENST00000330651.6	-	2	263	c.163C>T	c.(163-165)Ctg>Ttg	p.L55L	MAPK11_ENST00000495277.1_5'UTR|MAPK11_ENST00000449719.2_5'UTR	NM_002751.5	NP_002742.3	Q15759	MK11_HUMAN	mitogen-activated protein kinase 11	55	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|lung(4)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Regorafenib(DB08896)	GGGCGCGACAGCTTCTTCACC	0.716																																					p.L55L	GBM(9;634 739 50668)	Atlas-SNP	.											.	MAPK11	23	.	0			c.C163T						.						11	11	11					22																	50706332		2175	4276	6451	SO:0001819	synonymous_variant	5600	exon2			GCGACAGCTTCTT	Y14440	CCDS14090.1	22q13.33	2011-06-09			ENSG00000185386	ENSG00000185386	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6873	protein-coding gene	gene with protein product		602898		PRKM11		9218798	Standard	NM_002751		Approved	p38-2, p38Beta, SAPK2	uc003bkr.3	Q15759	OTTHUMG00000150226	ENST00000330651.6:c.163C>T	chr22.hg19:g.50706332G>A		126.0	0.0		123.0	46.0	NM_002751	A8K730|B0LPG1|B7Z630|E7ETQ1|L7RT27|O00284|O15472|Q2XNF2	Silent	SNP	ENST00000330651.6	hg19	CCDS14090.1																																																																																			.	.		0.716	MAPK11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316900.1			A	50706332	G	A	50706332	2	1	162	1	0	0	0	0	0	0	0	1	9282	962	34	3		3	MAPK11	22	50706332	Silent	SNP	G	TCGA-DD-AACK-01A-11D-A40R-10	5573552	50706332	598234	127	24777										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53561499	53561499	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	gaatagagttggactggtacTtgtggtattcagtgttggat	14	3	1	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chrX:53561499T>A	ENST00000342160.3	-	81	13266	c.12809A>T	c.(12808-12810)aAg>aTg	p.K4270M	HUWE1_ENST00000262854.6_Missense_Mutation_p.K4270M			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	4270	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						GGACTGGTACTTGTGGTATTC	0.473																																					p.K4270M		Atlas-SNP	.											.	HUWE1	724	.	0			c.A12809T						.						235	169	191					X																	53561499		2203	4300	6503	SO:0001583	missense	10075	exon82			TGGTACTTGTGGT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.12809A>T	chrX.hg19:g.53561499T>A	ENSP00000340648:p.Lys4270Met	75.0	0.0		79.0	55.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.34|12.34	1.908266|1.908266	0.33721|0.33721	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000342160;ENST00000262854|ENST00000427052;ENST00000426907	T;T|.	0.44482|.	0.92;0.92|.	5.36|5.36	5.36|5.36	0.76844|0.76844	HECT (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76941|0.76941	0.4058|0.4058	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	D;D|.	0.61080|.	0.989;0.986|.	D;D|.	0.77557|.	0.99;0.983|.	T|T	0.79249|0.79249	-0.1881|-0.1881	10|5	0.87932|.	D|.	0|.	.|.	13.5296|13.5296	0.61615|0.61615	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	4270;4254|.	Q7Z6Z7;Q7Z6Z7-2|.	HUWE1_HUMAN;.|.	M|H	4270|3303;1092	ENSP00000340648:K4270M;ENSP00000262854:K4270M|.	ENSP00000262854:K4270M|.	K|Q	-|-	2|3	0|2	HUWE1|HUWE1	53578224|53578224	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.410000|7.410000	0.80065|0.80065	1.907000|1.907000	0.55213|0.55213	0.486000|0.486000	0.48141|0.48141	AAG|CAA	.	.		0.473	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		A	53561499	T	A	53561499	3	1	162	1	0	0	0	0	1	0	0	0	7470	1609	56	4	327	4	HUWE1	23	53561499	Missense_Mutation	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10		53561499	101709061	128	24778										
GJB1	2705	hgsc.bcm.edu	37	chrX	70443636	70443637	+	In_Frame_Ins	INS	-	-	TCATCT													0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tggccgagtatggctctcggINStcatcttcatcttcagaatc							TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chrX:70443636_70443637insTCATCT	ENST00000374022.3	+	2	174_175	c.79_80insTCATCT	c.(79-81)gtc>gTCATCTtc	p.31_32insIF	GJB1_ENST00000361726.6_In_Frame_Ins_p.31_32insIF|GJB1_ENST00000374029.1_In_Frame_Ins_p.31_32insIF	NM_001097642.2	NP_001091111.1	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa	31					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)|purine ribonucleotide transport (GO:0015868)|transport (GO:0006810)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(1)	10	Renal(35;0.156)					ATGGCTCTCGGTCATCTTCATC	0.53																																					p.V27delinsVIF		Atlas-INDEL	.											.	GJB1	21	.	0			c.79_80insTCATCT						.																																			SO:0001652	inframe_insertion	2705	exon2			.	X04325	CCDS14408.1	Xq13.1	2014-09-17	2007-01-16		ENSG00000169562	ENSG00000169562		"Ion channels / Gap junction proteins (connexins)"	4283	protein-coding gene	gene with protein product	"Charcot-Marie-Tooth neuropathy, X-linked", "connexin 32"	304040	"gap junction protein, beta 1, 32kD (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)", "gap junction protein, beta 1, 32kDa (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)", "gap junction protein, beta 1, 32kDa (connexin 32)"	CMTX1, CMTX		1319395	Standard	NM_000166		Approved	CX32	uc004dzf.3	P08034	OTTHUMG00000021797	ENST00000374022.3:c.86_91dupTCATCT	chrX.hg19:g.70443637_70443642dupTCATCT	ENSP00000363134:p.Ile30_Phe31dup	50.0	0.0		45.0	20.0	NM_001097642	B2R8R2|D3DVV2|Q5U0S4	In_Frame_Ins	INS	ENST00000374022.3	hg19	CCDS14408.1																																																																																			.	.		0.53	GJB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057133.1	NM_000166		TCATCT	70443637	-	TCATCT	70443636	7	5	162	1	0	1	1	0	0	0	0	0	6415	1261	44	0	81	0	GJB1	23	70443636	In_Frame_Ins	INS	-	TCGA-DD-AACK-01A-11D-A40R-10	16882137	70443636	84826924	129	24779										
RAB33A	9363	hgsc.bcm.edu	37	chrX	129318331	129318331	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	agcattactaccgcaacgtaCatgccgtggtcttcgtctat	8	12	2	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chrX:129318331C>A	ENST00000257017.4	+	2	745	c.331C>A	c.(331-333)Cat>Aat	p.H111N		NM_004794.2	NP_004785.1	Q14088	RB33A_HUMAN	RAB33A, member RAS oncogene family	111					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(5)	11						CCGCAACGTACATGCCGTGGT	0.498																																					p.H111N		Atlas-SNP	.											.	RAB33A	24	.	0			c.C331A						.						163	124	137					X																	129318331		2203	4300	6503	SO:0001583	missense	9363	exon2			AACGTACATGCCG	D14889	CCDS14621.1	Xq26	2008-02-05			ENSG00000134594	ENSG00000134594		"RAB, member RAS oncogene"	9773	protein-coding gene	gene with protein product		300333				7688322, 9512502	Standard	NM_004794		Approved	RabS10	uc004evl.3	Q14088	OTTHUMG00000022391	ENST00000257017.4:c.331C>A	chrX.hg19:g.129318331C>A	ENSP00000257017:p.His111Asn	88.0	0.0		59.0	48.0	NM_004794	Q5JUZ6|Q92465	Missense_Mutation	SNP	ENST00000257017.4	hg19	CCDS14621.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.623769	0.66901	.	.	ENSG00000134594	ENST00000257017	T	0.79845	-1.31	4.71	4.71	0.59529	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.79793	0.4507	N	0.21282	0.65	0.80722	D	1	P	0.36789	0.57	P	0.48921	0.595	T	0.82723	-0.0316	10	0.72032	D	0.01	-10.8948	17.2062	0.86918	0.0:1.0:0.0:0.0	.	111	Q14088	RB33A_HUMAN	N	111	ENSP00000257017:H111N	ENSP00000257017:H111N	H	+	1	0	RAB33A	129146012	1.000000	0.71417	0.999000	0.59377	0.920000	0.55202	7.776000	0.85560	2.072000	0.62099	0.429000	0.28392	CAT	.	.		0.498	RAB33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058246.1	NM_004794		A	129318331	C	A	129318331	3	1	162	1	0	0	0	0	1	0	0	0	12937	478	17	3	337	3	RAB33A	23	129318331	Missense_Mutation	SNP	C	TCGA-DD-AACK-01A-11D-A40R-10	58874695	129318331	25952229	130	24780										
FRMD7	90167	hgsc.bcm.edu	37	chrX	131212800	131212800	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	acagggtccatataaataaaAgggaaagaggaactgctttg	11	5	0	1			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chrX:131212800A>G	ENST00000298542.4	-	12	1420	c.1245T>C	c.(1243-1245)ccT>ccC	p.P415P	FRMD7_ENST00000370879.1_Silent_p.P295P|FRMD7_ENST00000464296.1_Silent_p.P400P	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	415					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					TATAAATAAAAGGGAAAGAGG	0.453																																					p.P415P		Atlas-SNP	.											.	FRMD7	69	.	0			c.T1245C						.						151	141	144					X																	131212800		2203	4300	6503	SO:0001819	synonymous_variant	90167	exon12			AATAAAAGGGAAA	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"nystagmus 1, congenital"	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1245T>C	chrX.hg19:g.131212800A>G		106.0	0.0		95.0	4.0	NM_194277	C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	hg19	CCDS35397.1																																																																																			.	.		0.453	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		G	131212800	A	G	131212800	2	3	162	1	0	0	0	0	0	0	0	1	6063	59	3	2		2	FRMD7	23	131212800	Silent	SNP	A	TCGA-DD-AACK-01A-11D-A40R-10	1894469	131212800	24057760	131	24781										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	4924912	4924912	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.684530955239239	0.862001943634597	0.62064139941691	1	1	0	tcttcttcctcttctctctcTcctcttcttttggtcagtgt	4	14	8	0			TCGA-DD-AACK-01A-11D-A40R-10	TCGA-DD-AACK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1606e906-2e7b-4b31-a047-f6669a5f5db0	20530127-b977-4fd9-bd3e-d983efbe98cd	g.chrY:4924912T>A	ENST00000362095.5	+	1	782	c.48T>A	c.(46-48)tcT>tcA	p.S16S	PCDH11Y_ENST00000215473.6_Silent_p.S16S|PCDH11Y_ENST00000333703.4_Intron	NM_032972.2	NP_116754.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	16					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CTTCTCTCTCTCCTCTTCTTT	0.388																																					p.S16S		Atlas-SNP	.											.	PCDH11Y	163	.	0			c.T48A						.																																			SO:0001819	synonymous_variant	83259	exon1			TCTCTCTCCTCTT	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000362095.5:c.48T>A	chrY.hg19:g.4924912T>A		155.0	0.0		174.0	112.0	NM_032972	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Silent	SNP	ENST00000362095.5	hg19	CCDS14777.1																																																																																			.	.		0.388	PCDH11Y-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000084980.1	NM_032973		A	4924912	T	A	4924912	2	1	162	1	0	0	0	0	0	0	0	1	11518	1538	54	4		4	PCDH11Y	24	4924912	Silent	SNP	T	TCGA-DD-AACK-01A-11D-A40R-10		4924912	54448654	132	24782										
SKI	6497	hgsc.bcm.edu	37	chr1	2236002	2236002	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaagctcagcgcagccctgcAggccaagcgcagcctccacc	11	18	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:2236002A>T	ENST00000378536.4	+	5	1817	c.1745A>T	c.(1744-1746)cAg>cTg	p.Q582L		NM_003036.3	NP_003027.1	P12755	SKI_HUMAN	SKI proto-oncogene	582					anterior/posterior axis specification (GO:0009948)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|gene expression (GO:0010467)|lens morphogenesis in camera-type eye (GO:0002089)|myelination in peripheral nervous system (GO:0022011)|myotube differentiation (GO:0014902)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neural tube closure (GO:0001843)|nose morphogenesis (GO:0043585)|olfactory bulb development (GO:0021772)|palate development (GO:0060021)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|retina development in camera-type eye (GO:0060041)|skeletal muscle fiber development (GO:0048741)|SMAD protein signal transduction (GO:0060395)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase inhibitor activity (GO:0046811)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|repressing transcription factor binding (GO:0070491)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(2)|lung(5)|prostate(1)|stomach(1)	10	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)		GCAGCCCTGCAGGCCAAGCGC	0.652																																					p.Q582L	Ovarian(177;144 1678 13697 20086 27838 40755)	Atlas-SNP	.											.	SKI	33	.	0			c.A1745T						.						21	15	17					1																	2236002		2175	4268	6443	SO:0001583	missense	6497	exon5			CCCTGCAGGCCAA	X15218	CCDS39.1	1p36.33	2014-06-25	2014-06-25		ENSG00000157933	ENSG00000157933		"SKI transcriptional corepressors"	10896	protein-coding gene	gene with protein product		164780	"v-ski avian sarcoma viral oncogene homolog"			2762147	Standard	NM_003036		Approved		uc001aja.4	P12755	OTTHUMG00000001407	ENST00000378536.4:c.1745A>T	chr1.hg19:g.2236002A>T	ENSP00000367797:p.Gln582Leu	67.0	0.0		83.0	14.0	NM_003036	Q5SYT7	Missense_Mutation	SNP	ENST00000378536.4	hg19	CCDS39.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.959431	0.74016	.	.	ENSG00000157933	ENST00000378536	D	0.96491	-4.03	4.37	4.37	0.52481	.	0.000000	0.85682	D	0.000000	D	0.97387	0.9145	M	0.71581	2.175	0.46096	D	0.998868	D	0.60160	0.987	D	0.67725	0.953	D	0.97887	1.0295	10	0.87932	D	0	-21.6274	12.8803	0.58014	1.0:0.0:0.0:0.0	.	582	P12755	SKI_HUMAN	L	582	ENSP00000367797:Q582L	ENSP00000367797:Q582L	Q	+	2	0	SKI	2225862	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.457000	0.73505	1.823000	0.53134	0.459000	0.35465	CAG	.	.		0.652	SKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004070.1	NM_003036		T	2236002	A	T	2236002	3	4	163	1	0	0	0	0	1	0	0	0	14372	188	7	4	1763	4	SKI	1	2236002	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		2236002	247014619	1	24783										
SLC45A1	50651	hgsc.bcm.edu	37	chr1	8384424	8384424	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cagcagcaccccgccgggagAtgccctcttccccagcgtgg	12	18	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:8384424A>T	ENST00000471889.1	+	2	420	c.35A>T	c.(34-36)gAt>gTt	p.D12V	SLC45A1_ENST00000377479.2_Missense_Mutation_p.D46V|SLC45A1_ENST00000289877.8_Missense_Mutation_p.D12V			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	12					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(2)	33	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		CCGCCGGGAGATGCCCTCTTC	0.667																																					p.D12V		Atlas-SNP	.											.	SLC45A1	85	.	0			c.A35T						.						44	52	49					1																	8384424		2203	4298	6501	SO:0001583	missense	50651	exon1			CGGGAGATGCCCT	AF118274	CCDS30577.1	1p36.23	2014-01-28	2005-10-04	2005-10-04	ENSG00000162426	ENSG00000162426		"Solute carriers"	17939	protein-coding gene	gene with protein product	"H+/sugar symporter"	605763	"deleted in neuroblastoma 5"	DNB5		10729226	Standard	XM_005263467		Approved		uc001apb.3	Q9Y2W3	OTTHUMG00000000503	ENST00000471889.1:c.35A>T	chr1.hg19:g.8384424A>T	ENSP00000418096:p.Asp12Val	82.0	0.0		79.0	19.0	NM_001080397	Q5VY46|Q5VY49	Missense_Mutation	SNP	ENST00000471889.1	hg19	CCDS30577.1	.	.	.	.	.	.	.	.	.	.	A	9.349	1.064929	0.20067	.	.	ENSG00000162426	ENST00000471889;ENST00000377479;ENST00000289877	T;T;T	0.20881	2.04;2.09;2.04	4.32	4.32	0.51571	.	0.380726	0.26780	N	0.022534	T	0.15435	0.0372	L	0.27053	0.805	0.58432	D	0.999999	B	0.27559	0.181	B	0.28011	0.085	T	0.05852	-1.0860	10	0.59425	D	0.04	-15.6051	9.9293	0.41512	0.8153:0.1847:0.0:0.0	.	12	Q9Y2W3	S45A1_HUMAN	V	12;46;12	ENSP00000418096:D12V;ENSP00000366699:D46V;ENSP00000289877:D12V	ENSP00000289877:D12V	D	+	2	0	SLC45A1	8307011	1.000000	0.71417	0.930000	0.37139	0.050000	0.14768	6.453000	0.73488	1.732000	0.51606	0.482000	0.46254	GAT	.	.		0.667	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5			T	8384424	A	T	8384424	3	4	163	1	0	0	0	0	1	0	0	0	14655	333	12	4	37	4	SLC45A1	1	8384424	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	6148422	8384424	240866197	2	24784										
EXOSC10	5394	hgsc.bcm.edu	37	chr1	11142771	11142771	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctccaatcagccagctgataTtgcttgtttgagtccacgtt	8	11	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:11142771T>C	ENST00000376936.4	-	10	1303	c.1254A>G	c.(1252-1254)caA>caG	p.Q418Q	EXOSC10_ENST00000485606.1_5'Flank|EXOSC10_ENST00000304457.7_Silent_p.Q418Q|EXOSC10_ENST00000544779.1_Silent_p.Q418Q	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	418					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		CCAGCTGATATTGCTTGTTTG	0.463																																					p.Q418Q	Colon(179;105 1987 14326 27364 29542)	Atlas-SNP	.											.	EXOSC10	59	.	0			c.A1254G						.						194	176	182					1																	11142771		2203	4300	6503	SO:0001819	synonymous_variant	5394	exon10			CTGATATTGCTTG	BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 2 (100kD)"	605960	"polymyositis/scleroderma autoantigen 2, 100kDa"	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.1254A>G	chr1.hg19:g.11142771T>C		101.0	0.0		122.0	22.0	NM_001001998	B1AKQ0|B1AKQ1|Q15158	Silent	SNP	ENST00000376936.4	hg19	CCDS30584.1																																																																																			.	.		0.463	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998		C	11142771	T	C	11142771	2	2	163	1	0	0	0	0	0	0	0	1	5316	1490	52	2		2	EXOSC10	1	11142771	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	2758347	11142771	238107850	3	24785										
NBPF3	84224	hgsc.bcm.edu	37	chr1	21799874	21799874	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	atcccacctggctcatcaggGaggtgcagaaggctgaagaa	13	10	2	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:21799874G>T	ENST00000318249.5	+	7	1086	c.736G>T	c.(736-738)Gag>Tag	p.E246*	NBPF3_ENST00000342104.5_Splice_Site_p.E246*|NBPF3_ENST00000454000.2_Splice_Site_p.E176*|NBPF3_ENST00000318220.6_Splice_Site_p.E190*	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	246	NBPF 1. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCTCATCAGGGAGGTGCAGAA	0.522																																					p.L246F		Atlas-SNP	.											.	NBPF3	55	.	0			c.C736T						.						131	129	130					1																	21799874		2203	4300	6503	SO:0001630	splice_region_variant	84224	exon7			ATCAGGGAGGTGC	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"neuroblastoma breakpoint family"	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.735-1G>T	chr1.hg19:g.21799874G>T		90.0	0.0		133.0	39.0	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Missense_Mutation	SNP	ENST00000318249.5	hg19	CCDS216.1	.	.	.	.	.	.	.	.	.	.	.	36	5.890999	0.97074	.	.	ENSG00000142794	ENST00000454000;ENST00000318220;ENST00000318249;ENST00000417552;ENST00000342104;ENST00000434838	.	.	.	0.9	0.9	0.19278	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	5.1902	0.15205	0.0:0.0:1.0:0.0	.	.	.	.	X	176;190;246;190;246;190	.	ENSP00000316739:E190X	E	+	1	0	NBPF3	21672461	0.456000	0.25744	0.001000	0.08648	0.029000	0.11900	0.257000	0.18369	0.810000	0.34279	0.184000	0.17185	GAG	.	.		0.522	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	Nonsense_Mutation	T	21799874	G	T	21799874	5	4	163	1	0	0	0	0	0	0	1	0	10206	1188	41	3	758	3	NBPF3	1	21799874	Splice_Site	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	10657103	21799874	227450747	4	24786										
CLSPN	63967	hgsc.bcm.edu	37	chr1	36226433	36226433	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cctgttgtctgctcagaaccTttactatggtgatcactgtt	8	10	3	2	rs78526448		TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:36226433T>A	ENST00000318121.3	-	8	1146	c.1089A>T	c.(1087-1089)aaA>aaT	p.K363N	CLSPN_ENST00000251195.5_Missense_Mutation_p.K363N|CLSPN_ENST00000520551.1_Missense_Mutation_p.K363N|CLSPN_ENST00000373220.3_Missense_Mutation_p.K363N	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	363					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GCTCAGAACCTTTACTATGGT	0.383																																					p.K363N		Atlas-SNP	.											.	CLSPN	248	.	0			c.A1089T						.						92	93	93					1																	36226433		2201	4299	6500	SO:0001583	missense	63967	exon8			AGAACCTTTACTA	AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"claspin homolog (Xenopus laevis)"			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.1089A>T	chr1.hg19:g.36226433T>A	ENSP00000312995:p.Lys363Asn	34.0	0.0		40.0	7.0	NM_001190481	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	hg19	CCDS396.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.578559	0.46006	.	.	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551;ENST00000544356	T;T;T;T	0.26067	1.76;1.76;1.81;1.82	5.51	3.08	0.35506	.	0.572927	0.20109	N	0.099056	T	0.27384	0.0672	L	0.57536	1.79	0.09310	N	1	P;P	0.52316	0.763;0.952	B;P	0.46659	0.387;0.523	T	0.09862	-1.0655	10	0.48119	T	0.1	-16.7277	6.6832	0.23131	0.0:0.0781:0.1537:0.7682	.	363;363	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	N	363	ENSP00000251195:K363N;ENSP00000312995:K363N;ENSP00000362317:K363N;ENSP00000428848:K363N	ENSP00000251195:K363N	K	-	3	2	CLSPN	35999020	0.064000	0.20934	0.918000	0.36340	0.397000	0.30659	1.359000	0.34113	0.928000	0.37168	0.482000	0.46254	AAA	.	.		0.383	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111		A	36226433	T	A	36226433	3	1	163	1	0	0	0	0	1	0	0	0	3562	1606	56	4	3002	4	CLSPN	1	36226433	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	14426559	36226433	213024188	5	24787										
MSH4	4438	hgsc.bcm.edu	37	chr1	76378494	76378494	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gatccagacagtttacgaatAtatttaagtaacctcaagaa	6	7	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:76378494A>G	ENST00000263187.3	+	20	2837	c.2733A>G	c.(2731-2733)atA>atG	p.I911M		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	911					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						GTTTACGAATATATTTAAGTA	0.378								Mismatch excision repair (MMR)																													p.I911M		Atlas-SNP	.											.	MSH4	147	.	0			c.A2733G						.						53	56	55					1																	76378494		2203	4300	6503	SO:0001583	missense	4438	exon20			ACGAATATATTTA	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.2733A>G	chr1.hg19:g.76378494A>G	ENSP00000263187:p.Ile911Met	149.0	0.0		156.0	34.0	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	hg19	CCDS670.1	.	.	.	.	.	.	.	.	.	.	A	10.55	1.382745	0.25031	.	.	ENSG00000057468	ENST00000263187	D	0.87179	-2.22	5.22	-2.95	0.05564	.	0.652627	0.16419	N	0.215234	T	0.47414	0.1444	N	0.04508	-0.205	0.09310	N	0.999993	B	0.02656	0.0	B	0.04013	0.001	T	0.50566	-0.8813	10	0.42905	T	0.14	-15.5076	6.0029	0.19531	0.5169:0.2278:0.2553:0.0	.	911	O15457	MSH4_HUMAN	M	911	ENSP00000263187:I911M	ENSP00000263187:I911M	I	+	3	3	MSH4	76151082	0.644000	0.27277	0.359000	0.25824	0.867000	0.49689	0.056000	0.14256	-0.151000	0.11176	0.383000	0.25322	ATA	.	.		0.378	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		G	76378494	A	G	76378494	3	3	163	1	0	0	0	0	1	0	0	0	9881	439	16	2	2811	2	MSH4	1	76378494	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	40152061	76378494	172872127	6	24788										
LPHN2	23266	hgsc.bcm.edu	37	chr1	82456641	82456641	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aagaagacctctctccctccAggaggagtgagaatgaggac	12	10	1	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:82456641A>T	ENST00000370728.1	+	25	4837	c.4192A>T	c.(4192-4194)Agg>Tgg	p.R1398W	LPHN2_ENST00000370727.1_Missense_Mutation_p.R1370W|LPHN2_ENST00000359929.3_Missense_Mutation_p.R1342W|LPHN2_ENST00000271029.4_Missense_Mutation_p.R1370W|LPHN2_ENST00000319517.6_Missense_Mutation_p.R1342W|LPHN2_ENST00000370730.1_Missense_Mutation_p.R1355W|LPHN2_ENST00000394879.1_Missense_Mutation_p.R1400W|LPHN2_ENST00000370713.1_3'UTR|LPHN2_ENST00000370723.1_Missense_Mutation_p.R1400W|LPHN2_ENST00000335786.5_Missense_Mutation_p.R1355W|LPHN2_ENST00000370721.1_Missense_Mutation_p.R1323W|LPHN2_ENST00000370717.2_Missense_Mutation_p.R1413W|LPHN2_ENST00000370725.1_Missense_Mutation_p.R1413W|LPHN2_ENST00000370715.1_3'UTR|LPHN2_ENST00000469377.2_3'UTR			O95490	LPHN2_HUMAN	latrophilin 2	1398					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		CTCTCCCTCCAGGAGGAGTGA	0.498																																					p.R1342W		Atlas-SNP	.											.	LPHN2	464	.	0			c.A4024T						.						74	70	71					1																	82456641		2203	4300	6503	SO:0001583	missense	23266	exon20			CCCTCCAGGAGGA	AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"-", "GPCR / Class B : Orphans"	18582	protein-coding gene	gene with protein product		607018	"latrophilin 1"	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.4192A>T	chr1.hg19:g.82456641A>T	ENSP00000359763:p.Arg1398Trp	99.0	0.0		98.0	18.0	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.99|16.99	3.274967|3.274967	0.59649|0.59649	.|.	.|.	ENSG00000117114|ENSG00000117114	ENST00000402328|ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786	.|T;T;T;T;T;T;T;T;T;T;T;T	.|0.70045	.|-0.42;-0.45;-0.43;-0.38;-0.39;-0.34;-0.39;-0.39;-0.39;-0.34;-0.38;-0.43	5.15|5.15	-4.79|-4.79	0.03200|0.03200	.|.	.|0.207171	.|0.39615	.|N	.|0.001305	T|T	0.58963|0.58963	0.2159|0.2159	L|L	0.29908|0.29908	0.895|0.895	0.37418|0.37418	D|D	0.913513|0.913513	.|D;D	.|0.65815	.|0.995;0.992	.|P;P	.|0.60173	.|0.87;0.868	T|T	0.70346|0.70346	-0.4897|-0.4897	5|10	.|0.72032	.|D	.|0.01	.|.	20.2633|20.2633	0.98458|0.98458	0.2505:0.7495:0.0:0.0|0.2505:0.7495:0.0:0.0	.|.	.|1342;322	.|O95490-2;B3KVU1	.|.;.	L|W	409|1323;1398;1355;1370;1413;1400;1342;1342;1413;1400;1370;1355	.|ENSP00000359756:R1323W;ENSP00000359763:R1398W;ENSP00000359765:R1355W;ENSP00000359762:R1370W;ENSP00000359760:R1413W;ENSP00000359758:R1400W;ENSP00000353006:R1342W;ENSP00000322270:R1342W;ENSP00000359752:R1413W;ENSP00000378344:R1400W;ENSP00000271029:R1370W;ENSP00000337306:R1355W	.|ENSP00000271029:R1370W	Q|R	+|+	2|1	0|2	LPHN2|LPHN2	82229229|82229229	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.997000|0.997000	0.91878|0.91878	1.551000|1.551000	0.36233|0.36233	-0.309000|-0.309000	0.08779|0.08779	0.459000|0.459000	0.35465|0.35465	CAG|AGG	.	.		0.498	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		T	82456641	A	T	82456641	3	4	163	1	0	0	0	0	1	0	0	0	8925	179	7	4	4098	4	LPHN2	1	82456641	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	6078147	82456641	166793980	7	24789										
RPAP2	79871	hgsc.bcm.edu	37	chr1	92846304	92846304	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaccccaattcttggcattcAgaaacattctcaggaaggta	8	10	3	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:92846304A>T	ENST00000610020.1	+	12	1821	c.1712A>T	c.(1711-1713)cAg>cTg	p.Q571L		NM_024813.2	NP_079089.2	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	571					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|snRNA transcription (GO:0009301)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleolus (GO:0005730)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	22		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		CTTGGCATTCAGAAACATTCT	0.383																																					p.Q571L		Atlas-SNP	.											.	RPAP2	48	.	0			c.A1712T						.						131	134	133					1																	92846304		2203	4300	6503	SO:0001583	missense	79871	exon12			GCATTCAGAAACA	AK023212	CCDS740.1	1p22.1	2014-01-28	2007-07-26	2007-07-26	ENSG00000122484	ENSG00000122484			25791	protein-coding gene	gene with protein product		611476	"chromosome 1 open reading frame 82"	C1orf82		17643375	Standard	NM_024813		Approved	FLJ13150	uc001dot.2	Q8IXW5	OTTHUMG00000010288	ENST00000610020.1:c.1712A>T	chr1.hg19:g.92846304A>T	ENSP00000476948:p.Gln571Leu	65.0	0.0		67.0	13.0	NM_024813	C9JKB5|Q49AS7|Q9H8Y2	Missense_Mutation	SNP	ENST00000610020.1	hg19	CCDS740.1	.	.	.	.	.	.	.	.	.	.	A	8.959	0.970214	0.18659	.	.	ENSG00000122484	ENST00000370343	.	.	.	5.71	4.57	0.56435	.	0.500596	0.21383	N	0.075440	T	0.08846	0.0219	N	0.17082	0.46	0.26685	N	0.971467	P	0.41313	0.745	B	0.38803	0.282	T	0.06041	-1.0849	8	0.02654	T	1	-1.7658	10.1167	0.42596	0.8317:0.1683:0.0:0.0	.	571	Q8IXW5	RPAP2_HUMAN	L	571	.	ENSP00000359368:Q571L	Q	+	2	0	RPAP2	92618892	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.249000	0.32839	1.079000	0.41038	-0.323000	0.08544	CAG	.	.		0.383	RPAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028368.2	NM_024813		T	92846304	A	T	92846304	3	4	163	1	0	0	0	0	1	0	0	0	13557	188	7	4	1758	4	RPAP2	1	92846304	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	10389663	92846304	156404317	8	24790										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117127378	117127378	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	atggcagctgtaggtcccgcTgtcctgcacagccacgttct	11	14	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:117127378T>A	ENST00000369486.3	-	9	3502	c.2737A>T	c.(2737-2739)Agc>Tgc	p.S913C	IGSF3_ENST00000369483.1_Missense_Mutation_p.S933C|IGSF3_ENST00000318837.6_Missense_Mutation_p.S933C	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	913	Ig-like C2-type 7.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		TAGGTCCCGCTGTCCTGCACA	0.612																																					p.S933C		Atlas-SNP	.											.	IGSF3	294	.	0			c.A2797T						.						52	49	50					1																	117127378		2203	4300	6503	SO:0001583	missense	3321	exon10			TCCCGCTGTCCTG	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.2737A>T	chr1.hg19:g.117127378T>A	ENSP00000358498:p.Ser913Cys	76.0	0.0		102.0	28.0	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	T	15.04	2.716048	0.48622	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.70986	-0.53;-0.53;-0.53	4.8	4.8	0.61643	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.366291	0.26851	N	0.022179	T	0.73079	0.3541	L	0.52573	1.65	0.38385	D	0.945251	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.68192	0.927;0.934;0.956	T	0.77827	-0.2443	10	0.87932	D	0	-30.3136	12.3806	0.55305	0.0:0.0:0.0:1.0	.	933;913;933	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	C	913;933;933	ENSP00000358498:S913C;ENSP00000358495:S933C;ENSP00000321184:S933C	ENSP00000321184:S933C	S	-	1	0	IGSF3	116928901	0.999000	0.42202	0.998000	0.56505	0.635000	0.38103	1.604000	0.36804	2.017000	0.59298	0.533000	0.62120	AGC	.	.		0.612	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		A	117127378	T	A	117127378	3	1	163	1	0	0	0	0	1	0	0	0	7610	1580	55	4	859	4	IGSF3	1	117127378	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	24281074	117127378	132123243	9	24791										
CGN	57530	hgsc.bcm.edu	37	chr1	151501990	151501990	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaacagaacctccagctacaAaagaccctccagcaactgcg	7	15	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:151501990A>G	ENST00000271636.7	+	11	2194	c.2061A>G	c.(2059-2061)caA>caG	p.Q687Q	SNORA44_ENST00000517031.1_RNA	NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	681	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			TCCAGCTACAAAAGACCCTCC	0.627																																					p.Q687Q		Atlas-SNP	.											.	CGN	106	.	0			c.A2061G						.						35	32	33					1																	151501990		2203	4300	6503	SO:0001819	synonymous_variant	57530	exon11			GCTACAAAAGACC	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.2061A>G	chr1.hg19:g.151501990A>G		166.0	0.0		250.0	94.0	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Silent	SNP	ENST00000271636.7	hg19	CCDS999.1																																																																																			.	.		0.627	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		G	151501990	A	G	151501990	2	3	163	1	0	0	0	0	0	0	0	1	3305	11	1	2		2	CGN	1	151501990	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	34374612	151501990	97748631	10	24792										
FLG	2312	hgsc.bcm.edu	37	chr1	152281864	152281864	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctgagtgtccagaactatctAccgattgctcatagtgggat	10	9	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:152281864A>T	ENST00000368799.1	-	3	5533	c.5498T>A	c.(5497-5499)gTa>gAa	p.V1833E	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1833	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGAACTATCTACCGATTGCTC	0.572									Ichthyosis																												p.V1833E		Atlas-SNP	.											.	FLG	900	.	0			c.T5498A						.						360	351	354					1																	152281864		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTATCTACCGATT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5498T>A	chr1.hg19:g.152281864A>T	ENSP00000357789:p.Val1833Glu	84.0	0.0		116.0	31.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	A	9.540	1.113176	0.20795	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01629	4.72	3.76	-7.53	0.01336	.	.	.	.	.	T	0.00552	0.0018	M	0.76838	2.35	0.09310	N	1	P	0.49185	0.92	B	0.41036	0.346	T	0.49244	-0.8960	9	0.05525	T	0.97	0.1171	4.7315	0.12966	0.3865:0.1327:0.4018:0.0791	.	1833	P20930	FILA_HUMAN	E	1833;68	ENSP00000357789:V1833E	ENSP00000271820:V68E	V	-	2	0	FLG	150548488	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.185000	0.03073	-2.402000	0.00577	-0.262000	0.10625	GTA	.	.		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152281864	A	T	152281864	3	4	163	1	0	0	0	0	1	0	0	0	5930	391	14	4	6691	4	FLG	1	152281864	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	779874	152281864	96968757	11	24793										
S100A7A	338324	hgsc.bcm.edu	37	chr1	153391627	153391627	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttttctcttcacaggacaaaAagggcatacattacctcgcc	6	12	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:153391627A>T	ENST00000368729.4	+	3	205	c.148A>T	c.(148-150)Aag>Tag	p.K50*	S100A7A_ENST00000368728.2_Nonsense_Mutation_p.K50*|S100A7A_ENST00000329256.2_Nonsense_Mutation_p.K50*	NM_176823.3	NP_789793.1	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7A	50	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein self-association (GO:0043621)			cervix(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	12	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			ACAGGACAAAAAGGGCATACA	0.408																																					p.K50X		Atlas-SNP	.											.	S100A7A	24	.	0			c.A148T						.						85	78	81					1																	153391627		2203	4300	6503	SO:0001587	stop_gained	338324	exon3			GACAAAAAGGGCA	AY189118	CCDS30872.1	1q22	2013-01-10	2006-09-11	2006-09-11	ENSG00000184330	ENSG00000184330		"S100 calcium binding proteins", "EF-hand domain containing"	21657	protein-coding gene	gene with protein product			"S100 calcium binding protein A15", "S100 calcium binding protein A7-like 1"	S100A15, S100A7L1		11230159	Standard	NM_176823		Approved	S100A7f	uc001fbt.1	Q86SG5	OTTHUMG00000013122	ENST00000368729.4:c.148A>T	chr1.hg19:g.153391627A>T	ENSP00000357718:p.Lys50*	226.0	0.0		337.0	122.0	NM_176823	D3DV38|Q5SY69	Nonsense_Mutation	SNP	ENST00000368729.4	hg19	CCDS30872.1	.	.	.	.	.	.	.	.	.	.	.	13.28	2.191419	0.38707	.	.	ENSG00000184330	ENST00000368729;ENST00000368728;ENST00000329256	.	.	.	1.72	1.72	0.24424	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4906	0.16774	1.0:0.0:0.0:0.0	.	.	.	.	X	50	.	ENSP00000329008:K50X	K	+	1	0	S100A7A	151658251	0.006000	0.16342	0.005000	0.12908	0.232000	0.25224	2.396000	0.44468	1.019000	0.39547	0.383000	0.25322	AAG	.	.		0.408	S100A7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036786.2	NM_176823		T	153391627	A	T	153391627	4	4	163	1	0	0	0	0	0	1	0	0	13799	15	1	4	154	4	S100A7A	1	153391627	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1109763	153391627	95858994	12	24794										
THBS3	7059	hgsc.bcm.edu	37	chr1	155165894	155165894	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccccagaatccgccacaagcTggggtccctcatagagcttc	9	16	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:155165894T>A	ENST00000368378.3	-	22	2716	c.2696A>T	c.(2695-2697)cAg>cTg	p.Q899L	RP11-263K19.4_ENST00000454348.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA|THBS3_ENST00000541576.1_Missense_Mutation_p.Q296L|THBS3_ENST00000541990.1_Missense_Mutation_p.Q428L|MIR92B_ENST00000607575.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000457183.2_Missense_Mutation_p.Q779L	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	899	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CGCCACAAGCTGGGGTCCCTC	0.547																																					p.Q899L		Atlas-SNP	.											.	THBS3	70	.	0			c.A2696T						.						97	104	102					1																	155165894		2203	4300	6503	SO:0001583	missense	7059	exon22			ACAAGCTGGGGTC	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.2696A>T	chr1.hg19:g.155165894T>A	ENSP00000357362:p.Gln899Leu	69.0	0.0		131.0	16.0	NM_007112	B1AVR8|B4DQ20|Q8WV34	Missense_Mutation	SNP	ENST00000368378.3	hg19	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.616820	0.46736	.	.	ENSG00000169231	ENST00000368378;ENST00000541576;ENST00000457183;ENST00000541990	D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63	3.5	3.5	0.40072	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.534600	0.17581	N	0.169134	D	0.87180	0.6113	L	0.29908	0.895	0.80722	D	1	B;B;B;B	0.33345	0.409;0.131;0.066;0.409	B;B;B;B	0.38755	0.281;0.103;0.103;0.158	D	0.87378	0.2355	10	0.52906	T	0.07	-12.0819	10.6152	0.45445	0.0:0.0:0.0:1.0	.	779;899;899;899	B4DQ20;Q53FK6;Q2HIZ0;P49746	.;.;.;TSP3_HUMAN	L	899;296;779;428	ENSP00000357362:Q899L;ENSP00000444792:Q296L;ENSP00000392207:Q779L;ENSP00000437353:Q428L	ENSP00000357362:Q899L	Q	-	2	0	THBS3	153432518	0.001000	0.12720	1.000000	0.80357	0.989000	0.77384	1.123000	0.31308	1.842000	0.53543	0.402000	0.26972	CAG	.	.		0.547	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		A	155165894	T	A	155165894	3	1	163	1	0	0	0	0	1	0	0	0	15870	1580	55	4	182	4	THBS3	1	155165894	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	1774267	155165894	94084727	13	24795										
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161023128	161023128	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tggattgtacccgcacctccAtgaaggccgctgtcccattg	10	14	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:161023128A>T	ENST00000368013.3	-	6	904	c.584T>A	c.(583-585)aTg>aAg	p.M195K	ARHGAP30_ENST00000368015.1_Missense_Mutation_p.M18K|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.M195K	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	195	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CCGCACCTCCATGAAGGCCGC	0.567																																					p.M195K		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.T584A						.						144	107	120					1																	161023128		2203	4300	6503	SO:0001583	missense	257106	exon6			ACCTCCATGAAGG	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"Rho GTPase activating proteins"	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.584T>A	chr1.hg19:g.161023128A>T	ENSP00000356992:p.Met195Lys	79.0	0.0		119.0	46.0	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	hg19	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	A	17.82	3.482658	0.63962	.	.	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.34472	2.81;2.81;1.36	5.54	5.54	0.83059	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.047007	0.85682	D	0.000000	T	0.25531	0.0621	L	0.48935	1.535	0.48696	D	0.999693	B;B	0.28584	0.138;0.216	B;B	0.36845	0.168;0.234	T	0.15867	-1.0422	10	0.66056	D	0.02	.	13.6974	0.62589	1.0:0.0:0.0:0.0	.	195;195	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	K	195;195;47;18	ENSP00000356995:M195K;ENSP00000356992:M195K;ENSP00000356994:M18K	ENSP00000356992:M195K	M	-	2	0	ARHGAP30	159289752	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.687000	0.74552	2.117000	0.64856	0.529000	0.55759	ATG	.	.		0.567	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		T	161023128	A	T	161023128	3	4	163	1	0	0	0	0	1	0	0	0	879	217	8	4	2749	4	ARHGAP30	1	161023128	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	5857234	161023128	88227493	14	24796										
OLFML2B	25903	hgsc.bcm.edu	37	chr1	161968003	161968003	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcggtccgagcgttcaggtcGcttgtcacagcagtgctgtg	15	11	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:161968003G>A	ENST00000294794.3	-	6	1509	c.1086C>T	c.(1084-1086)agC>agT	p.S362S	OLFML2B_ENST00000367940.2_Silent_p.S363S	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	362					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			CGTTCAGGTCGCTTGTCACAG	0.617																																					p.S362S		Atlas-SNP	.											.	OLFML2B	114	.	0			c.C1086T						.						134	134	134					1																	161968003		2203	4300	6503	SO:0001819	synonymous_variant	25903	exon6			CAGGTCGCTTGTC	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.1086C>T	chr1.hg19:g.161968003G>A		111.0	0.0		135.0	24.0	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Silent	SNP	ENST00000294794.3	hg19	CCDS1236.1																																																																																			.	.		0.617	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		A	161968003	G	A	161968003	2	1	163	1	0	0	0	0	0	0	0	1	10867	1078	38	1		1	OLFML2B	1	161968003	Silent	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	944875	161968003	87282618	15	24797										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200974470	200974470	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgcacatgcgcatctggcacAggtggatggtgaagatggcg	16	8	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:200974470A>T	ENST00000422435.2	-	5	1014	c.698T>A	c.(697-699)cTg>cAg	p.L233Q	KIF21B_ENST00000461742.2_Missense_Mutation_p.L233Q|KIF21B_ENST00000332129.2_Missense_Mutation_p.L233Q|KIF21B_ENST00000360529.5_Missense_Mutation_p.L233Q	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	233	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CATCTGGCACAGGTGGATGGT	0.652																																					p.L233Q		Atlas-SNP	.											.	KIF21B	208	.	0			c.T698A						.						92	81	85					1																	200974470		2203	4300	6503	SO:0001583	missense	23046	exon5			TGGCACAGGTGGA	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.698T>A	chr1.hg19:g.200974470A>T	ENSP00000411831:p.Leu233Gln	43.0	0.0		58.0	21.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	hg19	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.724370	0.89298	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37	5.17	5.17	0.71159	Kinesin, motor domain (5);	0.079373	0.52532	D	0.000072	D	0.90041	0.6890	M	0.82716	2.605	0.80722	D	1	D;D;P;D	0.89917	1.0;1.0;0.809;1.0	D;D;P;D	0.91635	0.999;0.999;0.814;0.999	D	0.91649	0.5333	10	0.87932	D	0	.	15.0047	0.71501	1.0:0.0:0.0:0.0	.	233;233;233;233	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	Q	233	ENSP00000328494:L233Q;ENSP00000353724:L233Q;ENSP00000433808:L233Q;ENSP00000411831:L233Q	ENSP00000328494:L233Q	L	-	2	0	KIF21B	199241093	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.845000	0.92153	1.946000	0.56461	0.533000	0.62120	CTG	.	.		0.652	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		T	200974470	A	T	200974470	3	4	163	1	0	0	0	0	1	0	0	0	8298	188	7	4	4296	4	KIF21B	1	200974470	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	39006467	200974470	48276151	16	24798										
NFASC	23114	hgsc.bcm.edu	37	chr1	204923314	204923314	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cactgctccccactctccacAgcttccactggacacgaaac	5	19	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:204923314A>T	ENST00000401399.1	+	5	414		c.e5-1		NFASC_ENST00000539706.1_Splice_Site|NFASC_ENST00000404907.1_Splice_Site|NFASC_ENST00000338586.6_Splice_Site|NFASC_ENST00000404076.1_Splice_Site|NFASC_ENST00000403080.1_Splice_Site|NFASC_ENST00000367172.4_Splice_Site|NFASC_ENST00000367169.4_Splice_Site|NFASC_ENST00000339876.6_Splice_Site|NFASC_ENST00000367170.4_Splice_Site|NFASC_ENST00000360049.4_Splice_Site|NFASC_ENST00000513543.1_Splice_Site|NFASC_ENST00000367171.4_Splice_Site|NFASC_ENST00000338515.6_Splice_Site			O94856	NFASC_HUMAN	neurofascin						axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CACTCTCCACAGCTTCCACTG	0.582																																					.		Atlas-SNP	.											.	NFASC	396	.	0			c.198-2A>T						.						45	41	42					1																	204923314		2203	4300	6503	SO:0001630	splice_region_variant	23114	exon5			CTCCACAGCTTCC	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.216-1A>T	chr1.hg19:g.204923314A>T		72.0	0.0		86.0	23.0	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Splice_Site	SNP	ENST00000401399.1	hg19	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.220034	0.79464	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000505079;ENST00000404907;ENST00000513543;ENST00000430393;ENST00000367173	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0284	0.71687	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NFASC	203189937	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	6.876000	0.75556	2.036000	0.60181	0.533000	0.62120	.	.	.		0.582	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	Intron	T	204923314	A	T	204923314	5	4	163	1	0	0	0	0	0	0	1	0	10368	202	7	4	228	4	NFASC	1	204923314	Splice_Site	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	3948844	204923314	44327307	17	24799										
TGFB2	7042	hgsc.bcm.edu	37	chr1	218609331	218609331	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggtattgatggcacctccacAtataccagtggtgatcagaa	10	9	1	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:218609331A>T	ENST00000366930.4	+	5	1241	c.774A>T	c.(772-774)acA>acT	p.T258T	TGFB2_ENST00000366929.4_Silent_p.T286T|TGFB2_ENST00000479322.1_3'UTR	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	258					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		GCACCTCCACATATACCAGTG	0.373																																					p.T286T		Atlas-SNP	.											.	TGFB2	102	.	0			c.A858T						.						82	86	85					1																	218609331		2203	4300	6503	SO:0001819	synonymous_variant	7042	exon6			CTCCACATATACC	M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.774A>T	chr1.hg19:g.218609331A>T		100.0	0.0		193.0	28.0	NM_001135599	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Silent	SNP	ENST00000366930.4	hg19	CCDS1521.1																																																																																			.	.		0.373	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		T	218609331	A	T	218609331	2	4	163	1	0	0	0	0	0	0	0	1	15833	204	8	4		4	TGFB2	1	218609331	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	13686017	218609331	30641290	18	24800										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228520596	228520596	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	atgacactgcagcagatgccAcggagtcctcatcctacttc	8	14	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:228520596A>T	ENST00000422127.1	+	57	15732	c.15688A>T	c.(15688-15690)Acg>Tcg	p.T5230S	OBSCN_ENST00000284548.11_Missense_Mutation_p.T5230S|OBSCN_ENST00000366709.4_Missense_Mutation_p.T2349S|OBSCN_ENST00000570156.2_Missense_Mutation_p.T6187S|OBSCN_ENST00000366707.4_Missense_Mutation_p.T2864S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5230					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGCAGATGCCACGGAGTCCTC	0.612																																					p.T6187S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A18559T						.						87	90	89					1																	228520596		2119	4227	6346	SO:0001583	missense	84033	exon68			GATGCCACGGAGT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15688A>T	chr1.hg19:g.228520596A>T	ENSP00000409493:p.Thr5230Ser	99.0	0.0		94.0	16.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	31	5.085053	0.94100	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.63417	0.42;-0.04;0.0;0.47	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.66934	0.2840	L	0.29908	0.895	0.48185	D	0.999601	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.60860	-0.7179	10	0.12103	T	0.63	.	15.4727	0.75453	1.0:0.0:0.0:0.0	.	5230;5230	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	5230;5230;2864;2349	ENSP00000284548:T5230S;ENSP00000409493:T5230S;ENSP00000355668:T2864S;ENSP00000355670:T2349S	ENSP00000284548:T5230S	T	+	1	0	OBSCN	226587219	1.000000	0.71417	0.985000	0.45067	0.685000	0.39939	8.463000	0.90377	2.240000	0.73641	0.533000	0.62120	ACG	.	.		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228520596	A	T	228520596	3	4	163	1	0	0	0	0	1	0	0	0	10821	159	6	4	15910	4	OBSCN	1	228520596	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	9911265	228520596	20730025	19	24801										
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458280	248458280	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaccaggagcattaacacacAgcagatgtacatggcgtttt	10	9	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr1:248458280A>T	ENST00000317996.1	-	1	600	c.601T>A	c.(601-603)Tgt>Agt	p.C201S		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	201						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			ATTAACACACAGCAGATGTAC	0.542																																					p.C201S		Atlas-SNP	.											.	OR2T12	113	.	0			c.T601A						.						48	39	42					1																	248458280		2202	4296	6498	SO:0001583	missense	127064	exon1			ACACACAGCAGAT	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.601T>A	chr1.hg19:g.248458280A>T	ENSP00000324583:p.Cys201Ser	441.0	0.0		529.0	177.0	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	hg19	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	a	13.78	2.337893	0.41398	.	.	ENSG00000177201	ENST00000317996	T	0.34667	1.35	1.55	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38436	U	0.001687	T	0.34048	0.0884	N	0.16201	0.385	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.05649	-1.0872	10	0.45353	T	0.12	.	4.556	0.12136	0.7143:0.0:0.0:0.2857	.	201	Q8NG77	O2T12_HUMAN	S	201	ENSP00000324583:C201S	ENSP00000324583:C201S	C	-	1	0	OR2T12	246524903	0.000000	0.05858	0.124000	0.21820	0.369000	0.29798	-2.464000	0.00996	0.540000	0.28808	0.147000	0.16070	TGT	.	.		0.542	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		T	248458280	A	T	248458280	3	4	163	1	0	0	0	0	1	0	0	0	11028	188	7	4	364	4	OR2T12	1	248458280	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	19937684	248458280	792341	20	24802										
NTSR2	23620	hgsc.bcm.edu	37	chr2	11798756	11798756	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gttttctgaaggaggaggacAcggcgttgtagagaagagga	17	4	1	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:11798756A>T	ENST00000306928.5	-	4	1116	c.1082T>A	c.(1081-1083)gTg>gAg	p.V361E		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	361					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	GGAGGAGGACACGGCGTTGTA	0.542																																					p.V361E		Atlas-SNP	.											.	NTSR2	36	.	0			c.T1082A						.						93	93	93					2																	11798756		2203	4300	6503	SO:0001583	missense	23620	exon4			GAGGACACGGCGT	Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"GPCR / Class A : Neurotensin receptors"	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.1082T>A	chr2.hg19:g.11798756A>T	ENSP00000303686:p.Val361Glu	66.0	0.0		112.0	27.0	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Missense_Mutation	SNP	ENST00000306928.5	hg19	CCDS1681.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.225312	0.39300	.	.	ENSG00000169006	ENST00000306928	T	0.38560	1.13	4.31	1.8	0.24995	.	1.479790	0.04388	N	0.361983	T	0.35770	0.0943	L	0.32530	0.975	0.26333	N	0.977492	B	0.22909	0.077	B	0.26517	0.07	T	0.36817	-0.9732	10	0.66056	D	0.02	-2.9716	7.0514	0.25075	0.7764:0.0:0.2236:0.0	.	361	O95665	NTR2_HUMAN	E	361	ENSP00000303686:V361E	ENSP00000303686:V361E	V	-	2	0	NTSR2	11716207	0.978000	0.34361	0.279000	0.24732	0.099000	0.18886	5.099000	0.64554	0.236000	0.21180	-0.417000	0.06048	GTG	.	.		0.542	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1			T	11798756	A	T	11798756	3	4	163	1	0	0	0	0	1	0	0	0	10720	159	6	4	154	4	NTSR2	2	11798756	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		11798756	231400617	21	24803										
DPYSL5	56896	hgsc.bcm.edu	37	chr2	27121452	27121452	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcacccacgaggctgacgtcTacatcgagaatggcatcatc	10	13	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:27121452T>A	ENST00000288699.6	+	2	243	c.85T>A	c.(85-87)Tac>Aac	p.Y29N	DPYSL5_ENST00000401478.1_Missense_Mutation_p.Y29N	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	29					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)|signal transduction (GO:0007165)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			breast(1)|endometrium(5)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCTGACGTCTACATCGAGAA	0.572																																					p.Y29N		Atlas-SNP	.											.	DPYSL5	69	.	0			c.T85A						.						154	127	136					2																	27121452		2203	4300	6503	SO:0001583	missense	56896	exon2			GACGTCTACATCG	AF264015	CCDS1730.1	2p23.3	2008-02-05			ENSG00000157851	ENSG00000157851			20637	protein-coding gene	gene with protein product		608383				10851247, 11034345	Standard	NM_020134		Approved	CRMP5, Ulip6, CRMP-5, CRAM	uc002rhu.4	Q9BPU6	OTTHUMG00000097071	ENST00000288699.6:c.85T>A	chr2.hg19:g.27121452T>A	ENSP00000288699:p.Tyr29Asn	219.0	0.0		208.0	38.0	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Missense_Mutation	SNP	ENST00000288699.6	hg19	CCDS1730.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.409471	0.83340	.	.	ENSG00000157851	ENST00000450961;ENST00000288699;ENST00000401478;ENST00000431402;ENST00000434719	T;D;D;T;T	0.85773	-1.09;-2.03;-2.03;-1.09;-1.09	4.61	4.61	0.57282	Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.92694	0.7678	M	0.88906	2.99	0.51767	D	0.999938	D	0.71674	0.998	D	0.71656	0.974	D	0.93866	0.7158	10	0.72032	D	0.01	-20.6452	13.2923	0.60278	0.0:0.0:0.0:1.0	.	29	Q9BPU6	DPYL5_HUMAN	N	29	ENSP00000407174:Y29N;ENSP00000288699:Y29N;ENSP00000385549:Y29N;ENSP00000399581:Y29N;ENSP00000413075:Y29N	ENSP00000288699:Y29N	Y	+	1	0	DPYSL5	26974956	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.555000	0.82223	1.854000	0.53819	0.459000	0.35465	TAC	.	.		0.572	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134		A	27121452	T	A	27121452	3	1	163	1	0	0	0	0	1	0	0	0	4752	1522	53	4	87	4	DPYSL5	2	27121452	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	15322696	27121452	216077921	22	24804										
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44187687	44187687	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gttgtatacttacaaaatgaTaatacaaagtctaagttccc	5	7	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:44187687T>A	ENST00000260665.7	-	13	1632	c.1575A>T	c.(1573-1575)ttA>ttT	p.L525F	LRPPRC_ENST00000409946.1_Missense_Mutation_p.L525F	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	525					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TACAAAATGATAATACAAAGT	0.373																																					p.L525F		Atlas-SNP	.											.	LRPPRC	105	.	0			c.A1575T						.						134	128	130					2																	44187687		2203	4300	6503	SO:0001583	missense	10128	exon13			AAATGATAATACA	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1575A>T	chr2.hg19:g.44187687T>A	ENSP00000260665:p.Leu525Phe	52.0	0.0		71.0	12.0	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	hg19	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	T	8.325	0.825086	0.16678	.	.	ENSG00000138095	ENST00000465633;ENST00000260665;ENST00000409946	T;T	0.59906	0.39;0.23	4.93	1.11	0.20524	.	0.491609	0.21147	N	0.079392	T	0.44953	0.1318	M	0.75447	2.3	0.80722	D	1	B;B	0.22746	0.074;0.06	B;B	0.18871	0.023;0.011	T	0.19418	-1.0306	10	0.12103	T	0.63	-5.6491	0.6772	0.00869	0.166:0.2007:0.2972:0.336	.	425;525	F5H4J6;P42704	.;LPPRC_HUMAN	F	425;525;525	ENSP00000260665:L525F;ENSP00000386234:L525F	ENSP00000260665:L525F	L	-	3	2	LRPPRC	44041191	0.992000	0.36948	0.927000	0.36925	0.549000	0.35272	0.002000	0.13061	0.031000	0.15407	0.482000	0.46254	TTA	.	.		0.373	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		A	44187687	T	A	44187687	3	1	163	1	0	0	0	0	1	0	0	0	8974	1403	49	4	2713	4	LRPPRC	2	44187687	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	17066235	44187687	199011686	23	24805										
TSPYL6	388951	hgsc.bcm.edu	37	chr2	54483166	54483166	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acgattggctccaagcggccAtcaaacatatctgccattac	7	13	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:54483166A>G	ENST00000317802.7	-	1	243	c.123T>C	c.(121-123)gaT>gaC	p.D41D	ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000606865.1_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	41					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						CCAAGCGGCCATCAAACATAT	0.607																																					p.D41D		Atlas-SNP	.											.	TSPYL6	54	.	0			c.T123C						.						82	93	90					2																	54483166		1954	4137	6091	SO:0001819	synonymous_variant	388951	exon1			GCGGCCATCAAAC	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.123T>C	chr2.hg19:g.54483166A>G		93.0	0.0		82.0	18.0	NM_001003937	Q6NUJ3	Silent	SNP	ENST00000317802.7	hg19	CCDS42682.1																																																																																			.	.		0.607	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494		G	54483166	A	G	54483166	2	3	163	1	0	0	0	0	0	0	0	1	16678	214	8	2		2	TSPYL6	2	54483166	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	10295479	54483166	188716207	24	24806										
LMAN2L	81562	hgsc.bcm.edu	37	chr2	97373021	97373021	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agcgctttcggctctgttccTgccatttgttgtagagtatg	11	9	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:97373021T>A	ENST00000264963.4	-	8	1041	c.1019A>T	c.(1018-1020)cAg>cTg	p.Q340L	LMAN2L_ENST00000534882.1_Missense_Mutation_p.Q195L|LMAN2L_ENST00000426463.2_Missense_Mutation_p.Q206L|LMAN2L_ENST00000537039.1_Missense_Mutation_p.Q202L|FER1L5_ENST00000457909.1_RNA|LMAN2L_ENST00000377079.4_Missense_Mutation_p.Q351L	NM_030805.3	NP_110432.1	Q9H0V9	LMA2L_HUMAN	lectin, mannose-binding 2-like	340					ER to Golgi vesicle-mediated transport (GO:0006888)|protein folding (GO:0006457)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|lung(2)|skin(1)|urinary_tract(1)	7						GCTCTGTTCCTGCCATTTGTT	0.527																																					p.Q351L		Atlas-SNP	.											.	LMAN2L	27	.	0			c.A1052T						.						89	71	77					2																	97373021		2203	4300	6503	SO:0001583	missense	81562	exon9			TGTTCCTGCCATT	AL136617	CCDS2023.1, CCDS46365.1	2q11.1	2008-02-05			ENSG00000114988	ENSG00000114988			19263	protein-coding gene	gene with protein product		609552				12609988	Standard	NM_001142292		Approved	DKFZp564L2423, VIPL	uc002swv.3	Q9H0V9	OTTHUMG00000130453	ENST00000264963.4:c.1019A>T	chr2.hg19:g.97373021T>A	ENSP00000264963:p.Gln340Leu	164.0	0.0		169.0	39.0	NM_001142292	B4DSH3|D3DXH6|Q53GV3|Q53S67|Q63HN6|Q8NBQ6|Q9BQ14	Missense_Mutation	SNP	ENST00000264963.4	hg19	CCDS2023.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.583117	0.65992	.	.	ENSG00000114988	ENST00000264963;ENST00000377079;ENST00000426463;ENST00000537039;ENST00000534882	T;T;T;T;T	0.79352	0.75;0.74;-1.26;-1.21;-1.25	5.58	5.58	0.84498	.	0.241636	0.42548	D	0.000695	T	0.78868	0.4351	M	0.72479	2.2	0.52099	D	0.999942	B;B;B;B;P	0.36683	0.167;0.282;0.167;0.138;0.565	B;B;B;B;B	0.38562	0.045;0.103;0.045;0.071;0.276	T	0.81313	-0.0989	10	0.72032	D	0.01	.	15.0359	0.71748	0.0:0.0:0.0:1.0	.	195;213;206;351;340	B4DVH1;B4DI83;B4DSH3;Q9H0V9-2;Q9H0V9	.;.;.;.;LMA2L_HUMAN	L	340;351;206;202;195	ENSP00000264963:Q340L;ENSP00000366280:Q351L;ENSP00000396391:Q206L;ENSP00000441701:Q202L;ENSP00000438501:Q195L	ENSP00000264963:Q340L	Q	-	2	0	LMAN2L	96736748	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.902000	0.69869	2.246000	0.74042	0.533000	0.62120	CAG	.	.		0.527	LMAN2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252844.1	NM_030805		A	97373021	T	A	97373021	3	1	163	1	0	0	0	0	1	0	0	0	8848	1580	55	4	31	4	LMAN2L	2	97373021	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	42889855	97373021	145826352	25	24807										
CHST10	9486	hgsc.bcm.edu	37	chr2	101023082	101023082	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgatgaacttgctagccaccAtgaacatgaaaatcacccaa	6	11	1	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:101023082A>G	ENST00000264249.3	-	3	441	c.56T>C	c.(55-57)aTg>aCg	p.M19T	CHST10_ENST00000542617.1_Missense_Mutation_p.M67T|CHST10_ENST00000409701.1_Missense_Mutation_p.M19T|CHST10_ENST00000485085.1_5'Flank	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	19					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						GCTAGCCACCATGAACATGAA	0.473																																					p.M19T		Atlas-SNP	.											.	CHST10	42	.	0			c.T56C						.						290	273	279					2																	101023082		2203	4300	6503	SO:0001583	missense	9486	exon3			GCCACCATGAACA	BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"Sulfotransferases, membrane-bound"	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.56T>C	chr2.hg19:g.101023082A>G	ENSP00000264249:p.Met19Thr	98.0	0.0		127.0	37.0	NM_004854	Q53T18	Missense_Mutation	SNP	ENST00000264249.3	hg19	CCDS2047.1	.	.	.	.	.	.	.	.	.	.	A	17.04	3.287216	0.59867	.	.	ENSG00000115526	ENST00000264249;ENST00000542617;ENST00000409701;ENST00000409046;ENST00000420858;ENST00000448989;ENST00000421474;ENST00000418201;ENST00000435960	T;T;T;T;T;T;T;T;T	0.72394	-0.56;-0.65;-0.56;0.73;0.67;0.45;0.32;0.11;-0.25	5.18	5.18	0.71444	.	0.041188	0.85682	D	0.000000	T	0.58836	0.2150	L	0.29908	0.895	0.80722	D	1	P	0.38922	0.651	B	0.33521	0.165	T	0.64901	-0.6298	10	0.59425	D	0.04	-45.4345	15.3465	0.74343	1.0:0.0:0.0:0.0	.	19	O43529	CHSTA_HUMAN	T	19;67;19;19;19;67;19;19;19	ENSP00000264249:M19T;ENSP00000438869:M67T;ENSP00000387309:M19T;ENSP00000387121:M19T;ENSP00000405922:M19T;ENSP00000387977:M67T;ENSP00000407525:M19T;ENSP00000416831:M19T;ENSP00000395643:M19T	ENSP00000264249:M19T	M	-	2	0	CHST10	100389514	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.877000	0.87225	2.084000	0.62774	0.533000	0.62120	ATG	.	.		0.473	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854		G	101023082	A	G	101023082	3	3	163	1	0	0	0	0	1	0	0	0	3400	217	8	2	1034	2	CHST10	2	101023082	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	3650061	101023082	142176291	26	24808										
RIF1	55183	hgsc.bcm.edu	37	chr2	152298453	152298453	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tacaattaaaggacttcctcAgaaagtattaggttcaccag	7	8	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:152298453A>T	ENST00000243326.5	+	15	2165	c.1682A>T	c.(1681-1683)cAg>cTg	p.Q561L	RIF1_ENST00000433166.2_3'UTR|RIF1_ENST00000453091.2_Missense_Mutation_p.Q561L|RIF1_ENST00000444746.2_Missense_Mutation_p.Q561L|RIF1_ENST00000428287.2_Missense_Mutation_p.Q561L|RIF1_ENST00000430328.2_Missense_Mutation_p.Q561L			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		GGACTTCCTCAGAAAGTATTA	0.299																																					p.Q561L		Atlas-SNP	.											.	RIF1	244	.	0			c.A1682T						.						61	63	63					2																	152298453		2202	4284	6486	SO:0001583	missense	55183	exon16			TTCCTCAGAAAGT	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.1682A>T	chr2.hg19:g.152298453A>T	ENSP00000243326:p.Gln561Leu	336.0	0.0		429.0	108.0	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	hg19	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.953541	0.53293	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.4	4.22	0.49857	.	0.242707	0.42964	D	0.000632	T	0.60818	0.2298	L	0.54323	1.7	0.80722	D	1	P;P	0.44627	0.839;0.804	B;P	0.44394	0.205;0.448	T	0.62353	-0.6872	10	0.59425	D	0.04	-0.1278	12.0171	0.53319	0.6644:0.3355:0.0:0.0	.	561;561	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	L	561	ENSP00000390181:Q561L;ENSP00000414615:Q561L;ENSP00000415691:Q561L;ENSP00000243326:Q561L;ENSP00000416123:Q561L	ENSP00000243326:Q561L	Q	+	2	0	RIF1	152006699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.740000	0.55082	0.858000	0.35431	0.528000	0.53228	CAG	.	.		0.299	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			T	152298453	A	T	152298453	3	4	163	1	0	0	0	0	1	0	0	0	13374	188	7	4	1740	4	RIF1	2	152298453	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	51275371	152298453	90900920	27	24809										
TANC1	85461	hgsc.bcm.edu	37	chr2	160086384	160086384	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggtcccagccatcctcatctGtcccttcctcatacatccga	5	18	3	0	rs370179463		TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:160086384G>T	ENST00000263635.6	+	27	4684	c.4447G>T	c.(4447-4449)Gtc>Ttc	p.V1483F	TANC1_ENST00000454300.1_Missense_Mutation_p.V1377F	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1483					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						ATCCTCATCTGTCCCTTCCTC	0.522																																					p.V1483F		Atlas-SNP	.											.	TANC1	157	.	0			c.G4447T						.						97	103	101					2																	160086384		1995	4158	6153	SO:0001583	missense	85461	exon27			TCATCTGTCCCTT	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4447G>T	chr2.hg19:g.160086384G>T	ENSP00000263635:p.Val1483Phe	116.0	0.0		149.0	37.0	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	hg19	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	G	6.542	0.468302	0.12461	.	.	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.69806	-0.43;-0.43	5.52	3.72	0.42706	.	1.299240	0.04737	N	0.422150	T	0.52693	0.1750	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35871	-0.9771	9	.	.	.	.	6.7065	0.23254	0.213:0.1282:0.6588:0.0	.	1483	Q9C0D5	TANC1_HUMAN	F	1377;1483	ENSP00000396339:V1377F;ENSP00000263635:V1483F	.	V	+	1	0	TANC1	159794630	0.000000	0.05858	0.002000	0.10522	0.646000	0.38490	0.490000	0.22403	0.688000	0.31529	0.655000	0.94253	GTC	.	.		0.522	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			T	160086384	G	T	160086384	3	4	163	1	0	0	0	0	1	0	0	0	15559	1377	48	3	4550	3	TANC1	2	160086384	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	7787931	160086384	83112989	28	24810										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160873149	160873149	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgacatcctgattcagcatcAgagaggacatggcctgcttt	10	10	2	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:160873149A>T	ENST00000283243.7	-	9	1733	c.1527T>A	c.(1525-1527)tcT>tcA	p.S509S	PLA2R1_ENST00000392771.1_Silent_p.S509S	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	509					cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						ATTCAGCATCAGAGAGGACAT	0.373																																					p.S509S		Atlas-SNP	.											.	PLA2R1	153	.	0			c.T1527A						.						166	158	161					2																	160873149		2203	4300	6503	SO:0001819	synonymous_variant	22925	exon9			AGCATCAGAGAGG	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.1527T>A	chr2.hg19:g.160873149A>T		87.0	0.0		100.0	20.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	hg19	CCDS33309.1																																																																																			.	.		0.373	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			T	160873149	A	T	160873149	2	4	163	1	0	0	0	0	0	0	0	1	12019	175	7	4		4	PLA2R1	2	160873149	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	786765	160873149	82326224	29	24811										
SCN3A	6328	hgsc.bcm.edu	37	chr2	165987869	165987869	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agccttcttggaaatagtaaTaaggatccatggcaatgatc	9	7	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:165987869T>G	ENST00000360093.3	-	16	2941	c.2450A>C	c.(2449-2451)tAt>tCt	p.Y817S	SCN3A_ENST00000409101.3_Missense_Mutation_p.Y768S|SCN3A_ENST00000283254.7_Missense_Mutation_p.Y817S	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	817					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GAAATAGTAATAAGGATCCAT	0.388																																					p.Y817S		Atlas-SNP	.											.	SCN3A	544	.	0			c.A2450C						.						106	107	107					2																	165987869		2203	4300	6503	SO:0001583	missense	6328	exon16			TAGTAATAAGGAT	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.2450A>C	chr2.hg19:g.165987869T>G	ENSP00000353206:p.Tyr817Ser	248.0	0.0		295.0	71.0	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	hg19		.	.	.	.	.	.	.	.	.	.	T	25.7	4.664383	0.88251	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4	5.82	5.82	0.92795	Ion transport (1);	0.000000	0.52532	D	0.000074	D	0.98172	0.9396	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.87578	0.989;0.997;0.994;0.994;0.998	D	0.99327	1.0908	10	0.87932	D	0	.	16.1758	0.81851	0.0:0.0:0.0:1.0	.	817;768;768;768;817	Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3	SCN3A_HUMAN;.;.;.;.	S	817;817;768;768	ENSP00000353206:Y817S;ENSP00000283254:Y817S;ENSP00000386726:Y768S;ENSP00000403348:Y768S	ENSP00000283254:Y817S	Y	-	2	0	SCN3A	165696115	1.000000	0.71417	0.997000	0.53966	0.914000	0.54420	6.100000	0.71473	2.225000	0.72522	0.477000	0.44152	TAT	.	.		0.388	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		G	165987869	T	G	165987869	3	3	163	1	0	0	0	0	1	0	0	0	13933	1406	49	5	3604	5	SCN3A	2	165987869	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	5114720	165987869	77211504	30	24812										
GAD1	2571	hgsc.bcm.edu	37	chr2	171705847	171705847	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggaagcaccgccataaactcAacggcatagaaaggtaacgg	11	10	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:171705847A>T	ENST00000358196.3	+	12	1721	c.1171A>T	c.(1171-1173)Aac>Tac	p.N391Y		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	391					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CCATAAACTCAACGGCATAGA	0.572																																					p.N391Y		Atlas-SNP	.											.	GAD1	79	.	0			c.A1171T						.						83	72	76					2																	171705847		2203	4300	6503	SO:0001583	missense	2571	exon12			AAACTCAACGGCA		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1171A>T	chr2.hg19:g.171705847A>T	ENSP00000350928:p.Asn391Tyr	39.0	0.0		46.0	14.0	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	hg19	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	A	16.01	2.999986	0.54147	.	.	ENSG00000128683	ENST00000358196	T	0.38722	1.12	5.76	5.76	0.90799	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.301820	0.46442	D	0.000290	T	0.55449	0.1921	M	0.71036	2.16	0.80722	D	1	P	0.44139	0.827	P	0.53722	0.733	T	0.59674	-0.7410	10	0.72032	D	0.01	-10.8918	10.4299	0.44400	0.9277:0.0:0.0723:0.0	.	391	Q99259	DCE1_HUMAN	Y	391	ENSP00000350928:N391Y	ENSP00000350928:N391Y	N	+	1	0	GAD1	171414093	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.416000	0.52707	2.186000	0.69663	0.533000	0.62120	AAC	.	.		0.572	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			T	171705847	A	T	171705847	3	4	163	1	0	0	0	0	1	0	0	0	6187	130	5	4	1254	4	GAD1	2	171705847	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	5717978	171705847	71493526	31	24813										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178528616	178528616	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gatacaaaggcatgcagatgCtatcaatccactccagttgc	8	11	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:178528616C>T	ENST00000286063.6	-	19	2941	c.2624G>A	c.(2623-2625)aGc>aAc	p.S875N	PDE11A_ENST00000449286.2_Missense_Mutation_p.S517N|PDE11A_ENST00000358450.4_Missense_Mutation_p.S625N|PDE11A_ENST00000450799.2_Missense_Mutation_p.S66N|PDE11A_ENST00000409504.1_Missense_Mutation_p.S517N|PDE11A_ENST00000389683.3_Missense_Mutation_p.S431N	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	875	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)	p.S875N(1)|p.S625N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	CATGCAGATGCTATCAATCCA	0.448									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.S875N		Atlas-SNP	.											PDE11A_ENST00000358450,caecum,carcinoma,0,2	PDE11A	283	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2624A						.						121	103	109					2																	178528616		2203	4300	6503	SO:0001583	missense	50940	exon19	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	CAGATGCTATCAA	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2624G>A	chr2.hg19:g.178528616C>T	ENSP00000286063:p.Ser875Asn	72.0	0.0		70.0	19.0	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	hg19	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	C	15.77	2.932868	0.52866	.	.	ENSG00000128655	ENST00000286063;ENST00000358450;ENST00000450799;ENST00000409504;ENST00000389683;ENST00000449286	T;T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04;-1.04	6.07	6.07	0.98685	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.078860	0.85682	D	0.000000	T	0.60077	0.2241	N	0.08118	0	0.33734	D	0.618544	B;B	0.09022	0.001;0.002	B;B	0.09377	0.003;0.004	T	0.63107	-0.6711	10	0.30854	T	0.27	.	13.8057	0.63230	0.0:0.9305:0.0:0.0695	.	625;875	Q9HCR9-2;Q9HCR9	.;PDE11_HUMAN	N	875;625;66;517;431;517	ENSP00000286063:S875N;ENSP00000351232:S625N;ENSP00000387964:S66N;ENSP00000386539:S517N;ENSP00000374333:S431N;ENSP00000390599:S517N	ENSP00000286063:S875N	S	-	2	0	PDE11A	178236862	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.863000	0.56016	2.885000	0.99019	0.655000	0.94253	AGC	.	.		0.448	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			T	178528616	C	T	178528616	3	4	163	1	0	0	0	0	1	0	0	0	11640	797	28	3	185	3	PDE11A	2	178528616	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	6822769	178528616	64670757	32	24814										
CWC22	57703	hgsc.bcm.edu	37	chr2	180835257	180835257	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tagctttgtacttctcttcaTtctccataaaattaggatcc	4	10	3	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:180835257T>A	ENST00000410053.3	-	11	1480	c.1181A>T	c.(1180-1182)aAt>aTt	p.N394I	CWC22_ENST00000295749.6_Missense_Mutation_p.N394I	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	394					mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						CTTCTCTTCATTCTCCATAAA	0.249																																					p.N394I		Atlas-SNP	.											.	CWC22	62	.	0			c.A1181T						.						26	23	24					2																	180835257		1570	3628	5198	SO:0001583	missense	57703	exon11			TCTTCATTCTCCA		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"functional spliceosome-associated protein b"	615186	"CWC22 spliceosome-associated protein homolog (S. cerevisiae)"			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.1181A>T	chr2.hg19:g.180835257T>A	ENSP00000387006:p.Asn394Ile	218.0	0.0		251.0	52.0	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	hg19	CCDS46465.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.635371	0.87760	.	.	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.26518	1.99;1.99;1.73	6.16	6.16	0.99307	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.60728	0.2291	M	0.91972	3.26	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.69800	-0.5047	10	0.87932	D	0	-33.9824	15.9872	0.80168	0.0:0.0:0.0:1.0	.	394	Q9HCG8	CWC22_HUMAN	I	394	ENSP00000387006:N394I;ENSP00000295749:N394I;ENSP00000384159:N394I	ENSP00000295749:N394I	N	-	2	0	CWC22	180543502	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.631000	0.83237	2.367000	0.80283	0.528000	0.53228	AAT	.	.		0.249	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943		A	180835257	T	A	180835257	3	1	163	1	0	0	0	0	1	0	0	0	4070	1493	52	4	1585	4	CWC22	2	180835257	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	2306641	180835257	62364116	33	24815										
FRZB	2487	hgsc.bcm.edu	37	chr2	183699694	183699694	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaagcttcatatcccagcgcTgtgaaatttaaaatagaaaa	7	7	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:183699694T>A	ENST00000295113.4	-	6	1471		c.e6-2			NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein						brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			ATCCCAGCGCTGTGAAATTTA	0.418																																					.		Atlas-SNP	.											.	FRZB	42	.	0			c.862-2A>T						.						73	71	72					2																	183699694		2203	4300	6503	SO:0001630	splice_region_variant	2487	exon7			CAGCGCTGTGAAA	U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"Secreted frizzled-related proteins"	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.862-2A>T	chr2.hg19:g.183699694T>A		66.0	0.0		73.0	30.0	NM_001463	O00181|Q99686	Splice_Site	SNP	ENST00000295113.4	hg19	CCDS2286.1	.	.	.	.	.	.	.	.	.	.	T	18.60	3.658416	0.67586	.	.	ENSG00000162998	ENST00000295113	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7981	0.78428	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FRZB	183407939	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.505000	0.66981	2.140000	0.66376	0.528000	0.53228	.	.	.		0.418	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463	Intron	A	183699694	T	A	183699694	5	1	163	1	0	0	0	0	0	0	1	0	6073	1594	55	4	121	4	FRZB	2	183699694	Splice_Site	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	2864437	183699694	59499679	34	24816										
CCDC150	284992	hgsc.bcm.edu	37	chr2	197540923	197540923	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	caaaacttattgctggatgcAgcccatgccagtatcacaaa	7	11	1	0	rs367679012		TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:197540923A>T	ENST00000389175.4	+	11	1329	c.1194A>T	c.(1192-1194)gcA>gcT	p.A398A	CCDC150_ENST00000423093.2_Silent_p.A66A|CCDC150_ENST00000472405.2_3'UTR|CCDC150_ENST00000272831.7_Silent_p.A66A	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	398										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						TGCTGGATGCAGCCCATGCCA	0.393																																					p.A398A		Atlas-SNP	.											.	CCDC150	96	.	0			c.A1194T						.						135	135	135					2																	197540923		1921	4137	6058	SO:0001819	synonymous_variant	284992	exon11			GGATGCAGCCCAT		CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.1194A>T	chr2.hg19:g.197540923A>T		214.0	0.0		253.0	65.0	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Silent	SNP	ENST00000389175.4	hg19	CCDS46478.1																																																																																			.	.		0.393	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539		T	197540923	A	T	197540923	2	4	163	1	0	0	0	0	0	0	0	1	2787	175	7	4		4	CCDC150	2	197540923	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	13841229	197540923	45658450	35	24817										
MAP2	4133	hgsc.bcm.edu	37	chr2	210560487	210560487	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgtccagatggaatttattcAggggccaaaagaagaaagca	11	6	1	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:210560487A>T	ENST00000360351.4	+	7	4099	c.3593A>T	c.(3592-3594)cAg>cTg	p.Q1198L	MAP2_ENST00000447185.1_Missense_Mutation_p.Q1194L|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1198					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	GAATTTATTCAGGGGCCAAAA	0.463																																					p.Q1198L	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											MAP2,NS,carcinoma,0,1	MAP2	372	.	0			c.A3593T						.						56	56	56					2																	210560487		2203	4300	6503	SO:0001583	missense	4133	exon7			TTATTCAGGGGCC		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.3593A>T	chr2.hg19:g.210560487A>T	ENSP00000353508:p.Gln1198Leu	111.0	0.0		131.0	32.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	hg19	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	A	5.827	0.336906	0.11013	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.23147	1.92;1.92	5.76	4.58	0.56647	MAP2/Tau projection (1);	0.250035	0.29342	N	0.012430	T	0.27559	0.0677	L	0.54323	1.7	0.29457	N	0.858069	P;P	0.39717	0.634;0.684	B;B	0.40199	0.215;0.322	T	0.10314	-1.0635	10	0.41790	T	0.15	-6.1799	12.4616	0.55734	0.669:0.331:0.0:0.0	.	1194;1198	P11137-3;P11137	.;MAP2_HUMAN	L	1198;1194	ENSP00000353508:Q1198L;ENSP00000392164:Q1194L	ENSP00000353508:Q1198L	Q	+	2	0	MAP2	210268732	1.000000	0.71417	0.894000	0.35097	0.098000	0.18820	4.119000	0.57891	0.989000	0.38761	0.528000	0.53228	CAG	.	.		0.463	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		T	210560487	A	T	210560487	3	4	163	1	0	0	0	0	1	0	0	0	9244	188	7	4	3607	4	MAP2	2	210560487	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	13019564	210560487	32638886	36	24818										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215840627	215840627	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggcagtggtaacaaagacgaTggggaggataacctgagcaa	15	6	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:215840627T>A	ENST00000272895.7	-	34	5482	c.5263A>T	c.(5263-5265)Atc>Ttc	p.I1755F	ABCA12_ENST00000389661.4_Missense_Mutation_p.I1437F	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1755					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ACAAAGACGATGGGGAGGATA	0.493																																					p.I1755F	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.A5263T						.						179	164	169					2																	215840627		2203	4300	6503	SO:0001583	missense	26154	exon34			AGACGATGGGGAG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5263A>T	chr2.hg19:g.215840627T>A	ENSP00000272895:p.Ile1755Phe	136.0	0.0		199.0	61.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.640960	0.67244	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.90069	-2.61;-2.61	5.73	1.65	0.23941	.	0.244500	0.32357	N	0.006207	D	0.82549	0.5061	L	0.29908	0.895	0.80722	D	1	B;P	0.36048	0.25;0.534	B;B	0.44224	0.388;0.444	T	0.76547	-0.2919	10	0.56958	D	0.05	.	3.5686	0.07909	0.1825:0.4047:0.0:0.4129	.	1755;1437	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	F	1755;1437	ENSP00000272895:I1755F;ENSP00000374312:I1437F	ENSP00000272895:I1755F	I	-	1	0	ABCA12	215548872	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.164000	0.42387	0.507000	0.28148	0.533000	0.62120	ATC	.	.		0.493	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		A	215840627	T	A	215840627	3	1	163	1	0	0	0	0	1	0	0	0	30	1464	51	4	2604	4	ABCA12	2	215840627	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	5280140	215840627	27358746	37	24819										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222365815	222365815	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcacgaggtggctccttcccAgacagagtagctgtggggtg	16	10	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr2:222365815A>T	ENST00000281821.2	-	4	942	c.901T>A	c.(901-903)Tgg>Agg	p.W301R	EPHA4_ENST00000409854.1_Missense_Mutation_p.W301R|EPHA4_ENST00000409938.1_Missense_Mutation_p.W301R|EPHA4_ENST00000392071.4_Missense_Mutation_p.W250R	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	301	Cys-rich.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GCTCCTTCCCAGACAGAGTAG	0.527																																					p.W301R		Atlas-SNP	.											.	EPHA4	263	.	0			c.T901A						.						109	95	100					2																	222365815		2203	4300	6503	SO:0001583	missense	2043	exon4			CTTCCCAGACAGA	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.901T>A	chr2.hg19:g.222365815A>T	ENSP00000281821:p.Trp301Arg	55.0	0.0		66.0	10.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	A	11.10	1.539029	0.27475	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071	T;T;T;T	0.62232	0.04;0.04;0.04;0.04	6.07	6.07	0.98685	.	0.061060	0.85682	D	0.000000	T	0.28699	0.0711	N	0.00483	-1.445	0.41004	D	0.984953	B	0.02656	0.0	B	0.01281	0.0	T	0.30937	-0.9961	10	0.30078	T	0.28	.	10.8883	0.46981	0.9305:0.0:0.0695:0.0	.	301	P54764	EPHA4_HUMAN	R	301;301;301;250	ENSP00000281821:W301R;ENSP00000386276:W301R;ENSP00000386829:W301R;ENSP00000375923:W250R	ENSP00000281821:W301R	W	-	1	0	EPHA4	222074059	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.690000	0.54713	2.326000	0.78906	0.533000	0.62120	TGG	.	.		0.527	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222365815	A	T	222365815	3	4	163	1	0	0	0	0	1	0	0	0	5171	188	7	4	2115	4	EPHA4	2	222365815	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	6525188	222365815	20833558	38	24820										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4726008	4726008	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcatgaaagcaccagcagctAcaactacagagtggtcaaag	10	10	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:4726008A>T	ENST00000443694.2	+	26	3497	c.3497A>T	c.(3496-3498)tAc>tTc	p.Y1166F	ITPR1_ENST00000456211.2_Missense_Mutation_p.Y1157F|ITPR1_ENST00000354582.6_Missense_Mutation_p.Y1181F|ITPR1_ENST00000302640.8_Missense_Mutation_p.Y1166F|ITPR1_ENST00000357086.4_Missense_Mutation_p.Y1172F|ITPR1_ENST00000423119.2_Missense_Mutation_p.Y1172F|ITPR1_ENST00000544951.1_Intron			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1181					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	ACCAGCAGCTACAACTACAGA	0.423																																					p.Y1172F		Atlas-SNP	.											.	ITPR1	659	.	0			c.A3515T						.						136	151	146					3																	4726008		1946	4127	6073	SO:0001583	missense	3708	exon29			GCAGCTACAACTA	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.3497A>T	chr3.hg19:g.4726008A>T	ENSP00000401671:p.Tyr1166Phe	64.0	0.0		119.0	19.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	14.01	2.408966	0.42715	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.89196	-2.48;-2.48;-2.48;-2.48;-2.48;-2.48	5.05	5.05	0.67936	.	0.061520	0.64402	D	0.000003	D	0.84220	0.5424	L	0.51422	1.61	0.80722	D	1	B;B	0.34372	0.318;0.451	B;B	0.32677	0.127;0.15	T	0.81464	-0.0921	10	0.10111	T	0.7	.	15.1175	0.72413	1.0:0.0:0.0:0.0	.	1181;1172	Q14643;G5E9P1	ITPR1_HUMAN;.	F	1181;1166;1181;1172;1172;1157;1166	ENSP00000306253:Y1166F;ENSP00000346595:Y1181F;ENSP00000405934:Y1172F;ENSP00000349597:Y1172F;ENSP00000397885:Y1157F;ENSP00000401671:Y1166F	ENSP00000306253:Y1166F	Y	+	2	0	ITPR1	4701008	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.825000	0.92029	2.017000	0.59298	0.455000	0.32223	TAC	.	.		0.423	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4726008	A	T	4726008	3	4	163	1	0	0	0	0	1	0	0	0	7929	391	14	4	3648	4	ITPR1	3	4726008	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		4726008	193296422	39	24821										
BRPF1	7862	hgsc.bcm.edu	37	chr3	9784748	9784748	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aggacttcaacctcatcgtcAgcaactgcctcaagtataac	6	13	4	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:9784748A>T	ENST00000457855.1	+	6	2115	c.2104A>T	c.(2104-2106)Agc>Tgc	p.S702C	BRPF1_ENST00000424362.1_Missense_Mutation_p.S702C|BRPF1_ENST00000302054.3_Missense_Mutation_p.S702C|BRPF1_ENST00000433861.2_Missense_Mutation_p.S702C|BRPF1_ENST00000383829.2_Missense_Mutation_p.S708C			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	702	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.|Interaction with MEAF6 and ING5.|Required for RUNX1 and RUNX2 transcriptional activation.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					CCTCATCGTCAGCAACTGCCT	0.537																																					p.S708C		Atlas-SNP	.											.	BRPF1	104	.	0			c.A2122T						.						97	83	88					3																	9784748		2203	4300	6503	SO:0001583	missense	7862	exon7			ATCGTCAGCAACT	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"peregrin", "bromodomain-containing protein, 140kD"	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.2104A>T	chr3.hg19:g.9784748A>T	ENSP00000410210:p.Ser702Cys	135.0	0.0		172.0	52.0	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	hg19	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	A	17.25	3.341200	0.60963	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39	5.69	5.69	0.88448	Bromodomain (6);Bromodomain, conserved site (1);	0.189311	0.64402	D	0.000016	T	0.65026	0.2652	M	0.93507	3.425	0.40109	D	0.97646	D;P;P;P	0.56746	0.977;0.496;0.627;0.678	P;B;B;P	0.56127	0.792;0.396;0.396;0.532	T	0.76394	-0.2975	10	0.62326	D	0.03	.	15.9481	0.79809	1.0:0.0:0.0:0.0	.	702;702;708;702	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	C	702;702;708;702;702	ENSP00000402485:S702C;ENSP00000398863:S702C;ENSP00000373340:S708C;ENSP00000306297:S702C;ENSP00000410210:S702C	ENSP00000306297:S702C	S	+	1	0	BRPF1	9759748	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.238000	0.65366	2.153000	0.67306	0.533000	0.62120	AGC	.	.		0.537	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		T	9784748	A	T	9784748	3	4	163	1	0	0	0	0	1	0	0	0	1522	188	7	4	2144	4	BRPF1	3	9784748	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	5058740	9784748	188237682	40	24822										
ZNF619	285267	hgsc.bcm.edu	37	chr3	40529425	40529425	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgcaagtttcatccagcatcAgaagtggcatactaggaaga	10	8	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:40529425A>T	ENST00000314686.5	+	6	1781	c.1376A>T	c.(1375-1377)cAg>cTg	p.Q459L	ZNF619_ENST00000429348.2_Missense_Mutation_p.Q475L|ZNF619_ENST00000522736.1_Missense_Mutation_p.Q466L|ZNF619_ENST00000456778.1_Missense_Mutation_p.Q431L|ZNF619_ENST00000432264.2_Missense_Mutation_p.Q475L|ZNF619_ENST00000447116.2_Missense_Mutation_p.Q515L|ZNF619_ENST00000520737.1_3'UTR|ZNF619_ENST00000521353.1_Missense_Mutation_p.Q515L			Q8N2I2	ZN619_HUMAN	zinc finger protein 619	459					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		ATCCAGCATCAGAAGTGGCAT	0.507																																					p.Q515L		Atlas-SNP	.											.	ZNF619	57	.	0			c.A1544T						.						117	94	102					3																	40529425		2203	4300	6503	SO:0001583	missense	285267	exon6			AGCATCAGAAGTG	AK075245	CCDS46801.1, CCDS46802.1, CCDS46803.1	3p21.33	2013-01-08			ENSG00000177873	ENSG00000177873		"Zinc fingers, C2H2-type", "-"	26910	protein-coding gene	gene with protein product							Standard	NM_001145083		Approved	FLJ90764	uc011azb.2	Q8N2I2	OTTHUMG00000131391	ENST00000314686.5:c.1376A>T	chr3.hg19:g.40529425A>T	ENSP00000322529:p.Gln459Leu	83.0	0.0		105.0	39.0	NM_001145082	B4E271|C9JRN5|D4PHA2|E9PCD9	Missense_Mutation	SNP	ENST00000314686.5	hg19		.	.	.	.	.	.	.	.	.	.	A	15.37	2.814170	0.50527	.	.	ENSG00000177873	ENST00000314686;ENST00000447116;ENST00000429348;ENST00000456778;ENST00000442066;ENST00000522736;ENST00000521353;ENST00000432264	T;T;T;T;T;T;T	0.06294	3.32;3.32;3.32;3.32;3.32;3.32;3.32	2.3	2.3	0.28687	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10035	0.0246	L	0.29908	0.895	0.25467	N	0.987865	D;B;B;B;B;D	0.69078	0.997;0.235;0.235;0.393;0.235;0.98	P;B;B;B;B;P	0.56700	0.804;0.049;0.049;0.095;0.049;0.471	T	0.20438	-1.0275	9	0.62326	D	0.03	.	8.1652	0.31222	1.0:0.0:0.0:0.0	.	431;475;515;417;466;459	B4E271;C9JRN5;E9PCD9;B7Z9B3;Q17RW3;Q8N2I2	.;.;.;.;.;ZN619_HUMAN	L	459;515;475;431;96;466;515;475	ENSP00000322529:Q459L;ENSP00000411132:Q515L;ENSP00000398024:Q475L;ENSP00000397232:Q431L;ENSP00000428004:Q466L;ENSP00000430705:Q515L;ENSP00000388710:Q475L	ENSP00000322529:Q459L	Q	+	2	0	ZNF619	40504429	0.909000	0.30893	0.837000	0.33122	0.876000	0.50452	1.489000	0.35562	1.071000	0.40834	0.379000	0.24179	CAG	.	.		0.507	ZNF619-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000254180.2	NM_173656		T	40529425	A	T	40529425	3	4	163	1	0	0	0	0	1	0	0	0	18058	188	7	4	1584	4	ZNF619	3	40529425	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	30744677	40529425	157493005	41	24823										
NEK4	6787	hgsc.bcm.edu	37	chr3	52794925	52794925	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggcttggattgagagtcaccAtttttaatgttatttttgga	10	4	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:52794925A>G	ENST00000233027.5	-	6	1051	c.849T>C	c.(847-849)aaT>aaC	p.N283N	NEK4_ENST00000535191.1_Silent_p.N194N|NEK4_ENST00000383721.4_Silent_p.N283N	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	283					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		GAGAGTCACCATTTTTAATGT	0.373																																					p.N283N		Atlas-SNP	.											.	NEK4	51	.	0			c.T849C						.						88	95	92					3																	52794925		2203	4300	6503	SO:0001819	synonymous_variant	6787	exon6			GTCACCATTTTTA	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"serine/threonine protein kinase-2"	601959	"serine/threonine kinase 2", "NIMA (never in mitosis gene a)-related kinase 4"	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.849T>C	chr3.hg19:g.52794925A>G		61.0	0.0		75.0	20.0	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Silent	SNP	ENST00000233027.5	hg19	CCDS2863.1																																																																																			.	.		0.373	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157		G	52794925	A	G	52794925	2	3	163	1	0	0	0	0	0	0	0	1	10335	214	8	2		2	NEK4	3	52794925	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	12265500	52794925	145227505	42	24824										
CCDC52	152185	hgsc.bcm.edu	37	chr3	113218394	113218394	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agttcccagtgtactaatgcTctattcttcgatttgtgtat	7	8	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:113218394T>A	ENST00000295872.4	-	4	442	c.183A>T	c.(181-183)agA>agT	p.R61S		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	61					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						GTACTAATGCTCTATTCTTCG	0.358																																					p.R61S		Atlas-SNP	.											.	SPICE1	130	.	0			c.A183T						.						99	91	94					3																	113218394		2203	4300	6503	SO:0001583	missense	152185	exon4			TAATGCTCTATTC	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.183A>T	chr3.hg19:g.113218394T>A	ENSP00000295872:p.Arg61Ser	74.0	0.0		103.0	43.0	NM_144718	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	hg19	CCDS2973.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.910635	0.72983	.	.	ENSG00000163611	ENST00000295872;ENST00000495812;ENST00000480527	T	0.33438	1.41	6.03	4.88	0.63580	.	0.116162	0.64402	D	0.000008	T	0.51176	0.1659	M	0.67953	2.075	0.40944	D	0.984496	D;D	0.76494	0.974;0.999	P;D	0.83275	0.647;0.996	T	0.54193	-0.8330	10	0.72032	D	0.01	-19.1278	10.0131	0.41999	0.0:0.0772:0.0:0.9228	.	73;61	B4DJN7;Q8N0Z3	.;SPICE_HUMAN	S	61	ENSP00000295872:R61S	ENSP00000295872:R61S	R	-	3	2	SPICE1	114701084	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	1.172000	0.31908	1.100000	0.41517	0.455000	0.32223	AGA	.	.		0.358	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		A	113218394	T	A	113218394	3	1	163	1	0	0	0	0	1	0	0	0	2824	1548	54	4	2444	4	CCDC52	3	113218394	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	60423469	113218394	84804036	43	24825										
ARHGAP31	57514	hgsc.bcm.edu	37	chr3	119133709	119133709	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctccagcagctgtgctaatcTtgaaacagagaggaattctg	10	9	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:119133709T>A	ENST00000264245.4	+	12	3465	c.2933T>A	c.(2932-2934)cTt>cAt	p.L978H		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	978					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						TGTGCTAATCTTGAAACAGAG	0.537																																					p.L978H	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.T2933A						.						93	92	92					3																	119133709		1909	4126	6035	SO:0001583	missense	57514	exon12			CTAATCTTGAAAC		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.2933T>A	chr3.hg19:g.119133709T>A	ENSP00000264245:p.Leu978His	66.0	0.0		107.0	32.0	NM_020754	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	hg19	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	T	9.904	1.207740	0.22205	.	.	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.09445	2.98	4.74	3.51	0.40186	.	0.298369	0.24301	N	0.039734	T	0.18593	0.0446	L	0.34521	1.04	0.09310	N	1	D	0.76494	0.999	D	0.85130	0.997	T	0.01587	-1.1318	10	0.87932	D	0	.	7.1066	0.25366	0.1298:0.0:0.249:0.6213	.	978	Q2M1Z3	RHG31_HUMAN	H	978	ENSP00000264245:L978H	ENSP00000264245:L978H	L	+	2	0	ARHGAP31	120616399	0.004000	0.15560	0.277000	0.24703	0.398000	0.30690	0.365000	0.20348	1.979000	0.57680	0.379000	0.24179	CTT	.	.		0.537	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			A	119133709	T	A	119133709	3	1	163	1	0	0	0	0	1	0	0	0	880	1609	56	4	2979	4	ARHGAP31	3	119133709	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	5915315	119133709	78888721	44	24826										
TMEM39A	55254	hgsc.bcm.edu	37	chr3	119156670	119156670	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggagttgaagagaacctcctTgattctgtggttgaaatctg	12	6	2	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:119156670T>A	ENST00000319172.5	-	6	1276	c.856A>T	c.(856-858)Aag>Tag	p.K286*	TMEM39A_ENST00000486159.1_5'Flank	NM_018266.1	NP_060736.1	Q9NV64	TM39A_HUMAN	transmembrane protein 39A	286						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	13				GBM - Glioblastoma multiforme(114;0.244)		AGAACCTCCTTGATTCTGTGG	0.443																																					p.K286X		Atlas-SNP	.											.	TMEM39A	36	.	0			c.A856T						.						137	118	124					3																	119156670		2203	4300	6503	SO:0001587	stop_gained	55254	exon6			CCTCCTTGATTCT	BC021277	CCDS2987.1	3q13.33	2005-01-10			ENSG00000176142	ENSG00000176142			25600	protein-coding gene	gene with protein product						12477932	Standard	NM_018266		Approved	FLJ10902	uc003eck.2	Q9NV64	OTTHUMG00000159361	ENST00000319172.5:c.856A>T	chr3.hg19:g.119156670T>A	ENSP00000326063:p.Lys286*	107.0	0.0		173.0	36.0	NM_018266	D3DN80|Q53FN4|Q53GI1|Q6PKB5	Nonsense_Mutation	SNP	ENST00000319172.5	hg19	CCDS2987.1	.	.	.	.	.	.	.	.	.	.	T	39	7.906291	0.98554	.	.	ENSG00000176142	ENST00000319172;ENST00000491685	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.6791	14.7932	0.69857	0.0:0.0:0.0:1.0	.	.	.	.	X	286;132	.	ENSP00000326063:K286X	K	-	1	0	TMEM39A	120639360	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.974000	0.70465	2.090000	0.63153	0.528000	0.53228	AAG	.	.		0.443	TMEM39A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354941.3	NM_018266		A	119156670	T	A	119156670	4	1	163	1	0	0	0	0	0	1	0	0	16176	1821	63	4	626	4	TMEM39A	3	119156670	Nonsense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	22961	119156670	78865760	45	24827										
POLQ	10721	hgsc.bcm.edu	37	chr3	121208682	121208682	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aaacttctgctcatcttttcTgaattgaaattcaaaggtgc	6	8	5	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:121208682T>A	ENST00000264233.5	-	16	3224	c.3096A>T	c.(3094-3096)tcA>tcT	p.S1032S		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1032					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TCATCTTTTCTGAATTGAAAT	0.423								DNA polymerases (catalytic subunits)																													p.S1032S	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A3096T						.						66	74	72					3																	121208682		2202	4300	6502	SO:0001819	synonymous_variant	10721	exon16			CTTTTCTGAATTG	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.3096A>T	chr3.hg19:g.121208682T>A		57.0	0.0		89.0	15.0	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.423	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121208682	T	A	121208682	2	1	163	1	0	0	0	0	0	0	0	1	12217	1567	55	4		4	POLQ	3	121208682	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	2052012	121208682	76813748	46	24828										
NEK11	79858	hgsc.bcm.edu	37	chr3	130871532	130871543	+	In_Frame_Del	DEL	TTACCTTGATGA	TTACCTTGATGA	-													0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	atcgaaattttaaaaatcccTtaccttgatgagcagctaca							TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	TTACCTTGATGA	TTACCTTGATGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:130871532_130871543delTTACCTTGATGA	ENST00000383366.4	+	9	1148_1159	c.855_866delTTACCTTGATGA	c.(853-867)ccttaccttgatgag>ccg	p.YLDE286del	NEK11_ENST00000429253.2_In_Frame_Del_p.YLDE286del|NEK11_ENST00000356918.4_In_Frame_Del_p.YLDE286del|NEK11_ENST00000510769.1_Intron|NEK11_ENST00000508196.1_In_Frame_Del_p.YLDE286del|NEK11_ENST00000426022.2_3'UTR|NEK11_ENST00000507910.1_In_Frame_Del_p.YLDE286del|NEK11_ENST00000510688.1_In_Frame_Del_p.YLDE286del|NEK11_ENST00000511262.1_In_Frame_Del_p.YLDE286del|NEK11_ENST00000412440.2_In_Frame_Del_p.YLDE138del	NM_024800.4	NP_079076.3			NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						TAAAAATCCCTTACCTTGATGAGCAGCTACAG	0.335																																					p.285_289del		Atlas-INDEL	.											.	NEK11	76	.	0			c.854_865del						.																																			SO:0001651	inframe_deletion	79858	exon9			.	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"NIMA (never in mitosis gene a)- related kinase 11"				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000383366.4:c.855_866delTTACCTTGATGA	chr3.hg19:g.130871532_130871543delTTACCTTGATGA	ENSP00000372857:p.Tyr286_Glu289del	173.0	0.0		207.0	28.0	NM_024800		In_Frame_Del	DEL	ENST00000383366.4	hg19	CCDS3069.1																																																																																			.	.		0.335	NEK11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356755.1	NM_024800		-	130871543	TTACCTTGATGA	-	130871532	7	5	163	1	0	1	0	1	0	0	0	0	10332	1596	56	0	881	0	NEK11	3	130871532	In_Frame_Del	DEL	TTACCTTGATGA	TCGA-DD-AACL-01A-11D-A40R-10	9662850	130871532	67150898	47	24829										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151171236	151171236	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tcacaggtccatgggtttccAtgcaggtaaaggctgtctag	12	9	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:151171236A>T	ENST00000282466.3	-	3	650	c.651T>A	c.(649-651)caT>caA	p.H217Q		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	217					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ATGGGTTTCCATGCAGGTAAA	0.418																																					p.H217Q		Atlas-SNP	.											.	IGSF10	279	.	0			c.T651A						.						106	106	106					3																	151171236		2203	4300	6503	SO:0001583	missense	285313	exon3			GTTTCCATGCAGG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.651T>A	chr3.hg19:g.151171236A>T	ENSP00000282466:p.His217Gln	148.0	0.0		177.0	32.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	A	18.55	3.648957	0.67358	.	.	ENSG00000152580	ENST00000282466	T	0.51817	0.69	5.1	-3.11	0.05299	.	0.000000	0.47455	D	0.000230	T	0.51890	0.1701	L	0.38692	1.165	0.33480	D	0.587312	D	0.89917	1.0	D	0.71414	0.973	T	0.60276	-0.7295	10	0.87932	D	0	.	12.5991	0.56487	0.5541:0.0:0.4459:0.0	.	217	Q6WRI0	IGS10_HUMAN	Q	217	ENSP00000282466:H217Q	ENSP00000282466:H217Q	H	-	3	2	IGSF10	152653926	0.887000	0.30362	0.954000	0.39281	0.951000	0.60555	0.174000	0.16743	-0.907000	0.03862	-0.256000	0.11100	CAT	.	.		0.418	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		T	151171236	A	T	151171236	3	4	163	1	0	0	0	0	1	0	0	0	7606	214	8	4	7284	4	IGSF10	3	151171236	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	20299704	151171236	46851194	48	24830										
PLCH1	23007	hgsc.bcm.edu	37	chr3	155198967	155198967	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtggagtggcgattcactgcAggggtgggtgctgagggttt	20	5	1	1	rs201081912	byFrequency	TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:155198967A>T	ENST00000340059.7	-	23	4871	c.4872T>A	c.(4870-4872)ccT>ccA	p.P1624P	PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000334686.6_Silent_p.P1586P|PLCH1_ENST00000414191.1_Silent_p.P1586P|PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000460012.1_Silent_p.P1586P	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1624					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GATTCACTGCAGGGGTGGGTG	0.582																																					p.P1624P		Atlas-SNP	.											.	PLCH1	406	.	0			c.T4872A						.						101	103	102					3																	155198967		2203	4300	6503	SO:0001819	synonymous_variant	23007	exon23			CACTGCAGGGGTG	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.4872T>A	chr3.hg19:g.155198967A>T		117.0	0.0		163.0	62.0	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Silent	SNP	ENST00000340059.7	hg19	CCDS46939.1																																																																																			.	A|0.999;G|0.001		0.582	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		T	155198967	A	T	155198967	2	4	163	1	0	0	0	0	0	0	0	1	12046	175	7	4		4	PLCH1	3	155198967	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	4027731	155198967	42823463	49	24831										
GMPS	8833	hgsc.bcm.edu	37	chr3	155640020	155640020	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tatgtgctgaagaaccttatAtttgtaaggactttcctgaa	8	6	0	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:155640020A>G	ENST00000496455.2	+	11	1698	c.1363A>G	c.(1363-1365)Att>Gtt	p.I455V	GMPS_ENST00000295920.7_Missense_Mutation_p.I356V	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase	455					glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|GMP synthase (glutamine-hydrolyzing) activity (GO:0003922)|GMP synthase activity (GO:0003921)|pyrophosphatase activity (GO:0016462)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamine(DB00130)	AGAACCTTATATTTGTAAGGA	0.289			T	MLL	AML																																p.I455V	Ovarian(153;896 1876 4149 15499 28134)	Atlas-SNP	.		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	.	GMPS	70	.	0			c.A1363G						.						34	32	33					3																	155640020		1799	4056	5855	SO:0001583	missense	8833	exon11			CCTTATATTTGTA	U10860	CCDS46941.1	3q25.31	2013-06-18	2013-06-18		ENSG00000163655	ENSG00000163655	6.3.5.2		4378	protein-coding gene	gene with protein product	"GMP synthase"	600358	"guanine monphosphate synthetase"			8089153, 9195163	Standard	NM_003875		Approved		uc003faq.3	P49915	OTTHUMG00000158551	ENST00000496455.2:c.1363A>G	chr3.hg19:g.155640020A>G	ENSP00000419851:p.Ile455Val	357.0	0.0		539.0	179.0	NM_003875	A8K639|B4DXV7|F8W720	Missense_Mutation	SNP	ENST00000496455.2	hg19	CCDS46941.1	.	.	.	.	.	.	.	.	.	.	A	11.02	1.516799	0.27123	.	.	ENSG00000163655	ENST00000496455;ENST00000295920;ENST00000537975;ENST00000541628	.	.	.	5.78	4.65	0.58169	.	0.372923	0.27331	N	0.019854	T	0.28466	0.0704	N	0.16567	0.415	0.42271	D	0.99205	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.19386	-1.0307	9	0.14656	T	0.56	-9.6857	3.3371	0.07105	0.6703:0.0:0.3297:0.0	.	356;455	F8W720;P49915	.;GUAA_HUMAN	V	455;356;404;455	.	ENSP00000295920:I356V	I	+	1	0	GMPS	157122714	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.783000	0.55409	2.191000	0.70037	0.528000	0.53228	ATT	.	.		0.289	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351260.2			G	155640020	A	G	155640020	3	3	163	1	0	0	0	0	1	0	0	0	6506	449	16	2	1405	2	GMPS	3	155640020	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	441053	155640020	42382410	50	24832										
OPA1	4976	hgsc.bcm.edu	37	chr3	193353249	193353249	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aacgattagaaaaggagaacAaagaattgagaaaattagta	9	2	0	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:193353249A>T	ENST00000392438.3	+	7	955	c.721A>T	c.(721-723)Aaa>Taa	p.K241*	OPA1_ENST00000361908.3_Nonsense_Mutation_p.K278*|OPA1_ENST00000361828.2_Nonsense_Mutation_p.K259*|OPA1_ENST00000361150.2_Nonsense_Mutation_p.K242*|OPA1_ENST00000361510.2_Nonsense_Mutation_p.K296*|OPA1_ENST00000361715.2_Nonsense_Mutation_p.K260*	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	241					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		AAAGGAGAACAAAGAATTGAG	0.284																																					p.K296X		Atlas-SNP	.											.	OPA1	79	.	0			c.A886T						.						93	105	101					3																	193353249		2202	4297	6499	SO:0001587	stop_gained	4976	exon9			GAGAACAAAGAAT	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.721A>T	chr3.hg19:g.193353249A>T	ENSP00000376233:p.Lys241*	230.0	0.0		340.0	89.0	NM_130837	D3DNW4	Nonsense_Mutation	SNP	ENST00000392438.3	hg19	CCDS43186.1	.	.	.	.	.	.	.	.	.	.	A	39	7.583455	0.98371	.	.	ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361715;ENST00000361828;ENST00000361150	.	.	.	5.72	5.72	0.89469	.	0.125406	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.946	15.2015	0.73142	1.0:0.0:0.0:0.0	.	.	.	.	X	278;241;296;260;259;242	.	ENSP00000354781:K242X	K	+	1	0	OPA1	194835943	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.310000	0.96267	2.174000	0.68829	0.533000	0.62120	AAA	.	.		0.284	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		T	193353249	A	T	193353249	4	4	163	1	0	0	0	0	0	1	0	0	10880	131	5	4	920	4	OPA1	3	193353249	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	37713229	193353249	4669181	51	24833										
UBXN7	26043	hgsc.bcm.edu	37	chr3	196096315	196096315	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tccgtgggtccaatatggaaAcataggggaaatcccctaac	10	10	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:196096315A>G	ENST00000296328.4	-	7	757	c.683T>C	c.(682-684)gTt>gCt	p.V228A	UBXN7_ENST00000535858.1_Missense_Mutation_p.V80A|UBXN7_ENST00000428095.1_Missense_Mutation_p.V66A	NM_015562.1	NP_056377.1	O94888	UBXN7_HUMAN	UBX domain protein 7	228						Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|nucleus (GO:0005634)	transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						CAATATGGAAACATAGGGGAA	0.333																																					p.V228A		Atlas-SNP	.											.	UBXN7	43	.	0			c.T683C						.						93	91	92					3																	196096315		1822	4087	5909	SO:0001583	missense	26043	exon7			ATGGAAACATAGG	AB018337	CCDS43191.1	3q29	2012-07-06	2008-07-25	2008-07-25	ENSG00000163960	ENSG00000163960		"UBX domain containing"	29119	protein-coding gene	gene with protein product			"UBX domain containing 7"	UBXD7		9872452, 22537386	Standard	NM_015562		Approved	KIAA0794	uc003fwm.4	O94888	OTTHUMG00000155639	ENST00000296328.4:c.683T>C	chr3.hg19:g.196096315A>G	ENSP00000296328:p.Val228Ala	54.0	0.0		94.0	20.0	NM_015562	D3DXB3|Q6ZP77|Q86X20|Q8N327	Missense_Mutation	SNP	ENST00000296328.4	hg19	CCDS43191.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.183091	0.78677	.	.	ENSG00000163960	ENST00000296328;ENST00000428095;ENST00000535858	T;T;T	0.46819	0.86;0.86;0.86	5.45	5.45	0.79879	UAS (1);	0.053561	0.85682	D	0.000000	T	0.58438	0.2122	M	0.79614	2.46	0.58432	D	0.999996	B	0.25563	0.129	B	0.37387	0.248	T	0.61816	-0.6985	10	0.72032	D	0.01	-15.1313	15.6711	0.77274	1.0:0.0:0.0:0.0	.	228	O94888	UBXN7_HUMAN	A	228;66;80	ENSP00000296328:V228A;ENSP00000397256:V66A;ENSP00000440716:V80A	ENSP00000296328:V228A	V	-	2	0	UBXN7	197580712	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.874000	0.92363	2.285000	0.76669	0.477000	0.44152	GTT	.	.		0.333	UBXN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340938.2	XM_087353		G	196096315	A	G	196096315	3	3	163	1	0	0	0	0	1	0	0	0	16933	43	2	2	806	2	UBXN7	3	196096315	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	2743066	196096315	1926115	52	24834										
FBXO45	200933	hgsc.bcm.edu	37	chr3	196296086	196296086	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cacggcgatgagaacagcgaGgtgtggcggagcctgtgcgc	18	10	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:196296086G>C	ENST00000311630.6	+	1	528	c.231G>C	c.(229-231)gaG>gaC	p.E77D	WDR53_ENST00000433160.1_5'Flank|WDR53_ENST00000429115.1_5'Flank|FBXO45_ENST00000440469.1_Intron|WDR53_ENST00000332629.5_5'Flank	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	77	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		AGAACAGCGAGGTGTGGCGGA	0.647																																					p.E77D		Atlas-SNP	.											.	FBXO45	18	.	0			c.G231C						.						9	13	12					3																	196296086		2133	4262	6395	SO:0001583	missense	200933	exon1			CAGCGAGGTGTGG	AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013		"F-boxes /  "other""	29148	protein-coding gene	gene with protein product		609112					Standard	NM_001105573		Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.231G>C	chr3.hg19:g.196296086G>C	ENSP00000310332:p.Glu77Asp	59.0	0.0		84.0	19.0	NM_001105573	A6NF90|D3DXB5	Missense_Mutation	SNP	ENST00000311630.6	hg19	CCDS46985.1	.	.	.	.	.	.	.	.	.	.	g	13.08	2.131818	0.37630	.	.	ENSG00000174013	ENST00000311630	T	0.45276	0.9	5.17	5.17	0.71159	Concanavalin A-like lectin/glucanase (1);F-box domain, cyclin-like (2);	0.000000	0.85682	D	0.000000	T	0.22859	0.0552	N	0.12471	0.22	0.58432	D	0.999997	B	0.09022	0.002	B	0.10450	0.005	T	0.09143	-1.0688	10	0.08381	T	0.77	-7.3865	12.1856	0.54236	0.0781:0.0:0.9219:0.0	.	77	P0C2W1	FBSP1_HUMAN	D	77	ENSP00000310332:E77D	ENSP00000310332:E77D	E	+	3	2	FBXO45	197780483	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.794000	0.69067	2.427000	0.82271	0.533000	0.62120	GAG	.	.		0.647	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2			C	196296086	G	C	196296086	3	2	163	1	0	0	0	0	1	0	0	0	5762	991	35	4	233	4	FBXO45	3	196296086	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	199771	196296086	1726344	53	24835										
IQCG	84223	hgsc.bcm.edu	37	chr3	197640825	197640825	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gggcaatctgcagctcggtaTtggttttcatgtagcgattc	12	8	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr3:197640825T>A	ENST00000265239.6	-	8	1239	c.815A>T	c.(814-816)aAt>aTt	p.N272I	IQCG_ENST00000455191.1_Missense_Mutation_p.N272I|IQCG_ENST00000453254.1_Missense_Mutation_p.N272I	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	272						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		CAGCTCGGTATTGGTTTTCAT	0.443																																					p.N272I		Atlas-SNP	.											.	IQCG	44	.	0			c.A815T						.						366	342	350					3																	197640825		2203	4300	6503	SO:0001583	missense	84223	exon8			TCGGTATTGGTTT	AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 9"	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.815A>T	chr3.hg19:g.197640825T>A	ENSP00000265239:p.Asn272Ile	114.0	0.0		127.0	34.0	NM_032263	Q9BST2|Q9HAG8	Missense_Mutation	SNP	ENST00000265239.6	hg19	CCDS3331.1	.	.	.	.	.	.	.	.	.	.	T	9.511	1.105764	0.20632	.	.	ENSG00000114473	ENST00000265239;ENST00000455191;ENST00000453254	T;T;T	0.47528	0.84;0.84;0.97	5.92	3.53	0.40419	.	0.201209	0.42294	N	0.000736	T	0.38532	0.1044	L	0.56769	1.78	0.09310	N	0.999999	P;B	0.40332	0.713;0.141	B;B	0.36845	0.234;0.04	T	0.28299	-1.0048	10	0.39692	T	0.17	-21.1296	6.8248	0.23876	0.1365:0.0739:0.0:0.7896	.	272;272	C9JKX8;Q9H095	.;IQCG_HUMAN	I	272	ENSP00000265239:N272I;ENSP00000407736:N272I;ENSP00000389897:N272I	ENSP00000265239:N272I	N	-	2	0	IQCG	199125222	0.890000	0.30428	0.096000	0.21009	0.416000	0.31233	1.529000	0.35996	1.038000	0.40049	0.519000	0.50382	AAT	.	.		0.443	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263		A	197640825	T	A	197640825	3	1	163	1	0	0	0	0	1	0	0	0	7819	1493	52	4	536	4	IQCG	3	197640825	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	1344739	197640825	381605	54	24836										
OTOP1	133060	hgsc.bcm.edu	37	chr4	4228281	4228281	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cgtaccacagcatccacagcAgctgcagcagcatgagcgcc	10	16	0	1	rs111245977|rs75328065		TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:4228281A>T	ENST00000296358.4	-	1	335	c.311T>A	c.(310-312)cTg>cAg	p.L104Q		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	104					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.L104_W106delLLW(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CATCCACAGCAGCTGCAGCAG	0.721																																					p.L104Q		Atlas-SNP	.											.	OTOP1	118	.	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.T311A						.						10	11	11					4																	4228281		2088	4090	6178	SO:0001583	missense	133060	exon1			CACAGCAGCTGCA	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.311T>A	chr4.hg19:g.4228281A>T	ENSP00000296358:p.Leu104Gln	39.0	0.0		44.0	11.0	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	hg19	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.403491	0.83230	.	.	ENSG00000163982	ENST00000296358	T	0.11385	2.78	3.55	3.55	0.40652	.	0.088508	0.47455	U	0.000238	T	0.17492	0.0420	L	0.34521	1.04	0.54753	D	0.999988	D	0.58620	0.983	P	0.58660	0.843	T	0.01390	-1.1367	10	0.59425	D	0.04	.	12.2771	0.54741	1.0:0.0:0.0:0.0	.	104	Q7RTM1	OTOP1_HUMAN	Q	104	ENSP00000296358:L104Q	ENSP00000296358:L104Q	L	-	2	0	OTOP1	4279182	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.287000	0.78681	1.490000	0.48466	0.352000	0.21897	CTG	.	.		0.721	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		T	4228281	A	T	4228281	3	4	163	1	0	0	0	0	1	0	0	0	11314	188	7	4	1551	4	OTOP1	4	4228281	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		4228281	186925995	55	24837										
ATP10D	57205	hgsc.bcm.edu	37	chr4	47548881	47548881	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgctttcagtagccccattgTaagtatgaatgcatgactag	9	8	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:47548881T>C	ENST00000273859.3	+	10	1904		c.e10+2		ATP10D_ENST00000504445.1_Missense_Mutation_p.V531A	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D						cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						AGCCCCATTGTAAGTATGAAT	0.438																																					.		Atlas-SNP	.											.	ATP10D	168	.	0			c.1635+2T>C						.						45	46	46					4																	47548881		2203	4300	6503	SO:0001630	splice_region_variant	57205	exon10			CCATTGTAAGTAT	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.1635+2T>C	chr4.hg19:g.47548881T>C		76.0	0.0		88.0	10.0	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Splice_Site	SNP	ENST00000273859.3	hg19	CCDS3476.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.81|15.81	2.943060|2.943060	0.53079|0.53079	.|.	.|.	ENSG00000145246|ENSG00000145246	ENST00000273859|ENST00000504445	.|T	.|0.03065	.|4.06	5.02|5.02	5.02|5.02	0.67125|0.67125	.|.	.|.	.|.	.|.	.|.	.|T	.|0.15912	.|0.0383	.|.	.|.	.|.	0.30792|0.30792	N|N	0.740796|0.740796	.|D	.|0.76494	.|0.999	.|D	.|0.78314	.|0.991	.|T	.|0.01045	.|-1.1470	.|7	.|.	.|.	.|.	.|.	14.0599|14.0599	0.64793|0.64793	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|531	.|Q6PEW3	.|.	.|A	-1|531	.|ENSP00000420909:V531A	.|.	.|V	+|+	.|2	.|0	ATP10D|ATP10D	47243638|47243638	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.535000|0.535000	0.34838|0.34838	7.310000|7.310000	0.78947|0.78947	2.113000|2.113000	0.64589|0.64589	0.402000|0.402000	0.26972|0.26972	.|GTA	.	.		0.438	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	Intron	C	47548881	T	C	47548881	5	2	163	1	0	0	0	0	0	0	1	0	1118	1652	57	2	1671	2	ATP10D	4	47548881	Splice_Site	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	43320600	47548881	143605395	56	24838										
UGT2B15	7367	hgsc.bcm.edu	37	chr4	69434019	69434019	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tttactggcattgacaagaaTagaagccgaagatgtcaaca	9	7	1	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:69434019T>A	ENST00000317746.2	-	1	226	c.184A>T	c.(184-186)Att>Ttt	p.I62F		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	62					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	TTGACAAGAATAGAAGCCGAA	0.358																																					p.I62F	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											.	UGT2B17	34	.	0			c.A184T						.						129	131	130					4																	69434019		2091	3964	6055	SO:0001583	missense	7367	exon1			CAAGAATAGAAGC	U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"UDP glucuronosyltransferases"	12547	protein-coding gene	gene with protein product		601903	"UDP glycosyltransferase 2 family, polypeptide B17"			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.184A>T	chr4.hg19:g.69434019T>A	ENSP00000320401:p.Ile62Phe	203.0	0.0		219.0	103.0	NM_001077		Missense_Mutation	SNP	ENST00000317746.2	hg19	CCDS3523.1	.	.	.	.	.	.	.	.	.	.	t	6.938	0.542774	0.13250	.	.	ENSG00000197888	ENST00000317746	T	0.60920	0.15	2.66	-5.33	0.02713	.	0.257987	0.29692	U	0.011453	T	0.40272	0.1110	L	0.35854	1.095	0.09310	N	1	.	.	.	.	.	.	T	0.35226	-0.9797	8	0.36615	T	0.2	.	5.1473	0.14991	0.154:0.4519:0.0:0.3941	.	.	.	.	F	62	ENSP00000320401:I62F	ENSP00000320401:I62F	I	-	1	0	UGT2B17	69116614	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.169000	0.03120	-1.056000	0.03205	0.409000	0.27619	ATT	.	.		0.358	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077		A	69434019	T	A	69434019	3	1	163	1	0	0	0	0	1	0	0	0	16973	1406	49	4	1432	4	UGT2B15	4	69434019	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	21885138	69434019	121720257	57	24839										
DSPP	1834	hgsc.bcm.edu	37	chr4	88536436	88536436	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agcgatagcagtgacagcagCaacagcagtgacagcagtga	13	9	0	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:88536436C>T	ENST00000282478.7	+	4	2655	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	DSPP_ENST00000399271.1_Silent_p.S874S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	874	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagcaacagcagtg	0.502																																					p.S874S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2622T						.						70	85	79					4																	88536436		1641	2936	4577	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCAACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2622C>T	chr4.hg19:g.88536436C>T		205.0	0.0		188.0	19.0	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.502	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88536436	C	T	88536436	2	4	163	1	0	0	0	0	0	0	0	1	4784	709	25	3		3	DSPP	4	88536436	Silent	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	19102417	88536436	102617840	58	24840										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90857648	90857648	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aatgcttctacaagtgtgtcAgaactgaatgctaccatccc	7	11	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:90857648A>T	ENST00000394980.1	+	7	3136	c.2817A>T	c.(2815-2817)tcA>tcT	p.S939S	MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000508372.1_Silent_p.S681S|MMRN1_ENST00000264790.2_Silent_p.S939S			Q13201	MMRN1_HUMAN	multimerin 1	939					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		CAAGTGTGTCAGAACTGAATG	0.358																																					p.S939S		Atlas-SNP	.											.	MMRN1	174	.	0			c.A2817T						.						72	71	72					4																	90857648		2203	4299	6502	SO:0001819	synonymous_variant	22915	exon6			TGTGTCAGAACTG	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.2817A>T	chr4.hg19:g.90857648A>T		95.0	0.0		81.0	15.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Silent	SNP	ENST00000394980.1	hg19	CCDS3635.1																																																																																			.	.		0.358	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		T	90857648	A	T	90857648	2	4	163	1	0	0	0	0	0	0	0	1	9679	175	7	4		4	MMRN1	4	90857648	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	2321212	90857648	100296628	59	24841										
EGF	1950	hgsc.bcm.edu	37	chr4	110882063	110882063	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tggaatcatggctgtactctTgggtgtaaaaacacccctgg	11	9	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:110882063T>A	ENST00000265171.5	+	7	1552	c.1107T>A	c.(1105-1107)ctT>ctA	p.L369L	EGF_ENST00000509793.1_Silent_p.L327L|EGF_ENST00000503392.1_Silent_p.L369L	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	369	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	GCTGTACTCTTGGGTGTAAAA	0.393																																					p.L369L		Atlas-SNP	.											.	EGF	113	.	0			c.T1107A						.						254	224	234					4																	110882063		2203	4300	6503	SO:0001819	synonymous_variant	1950	exon7			TACTCTTGGGTGT	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.1107T>A	chr4.hg19:g.110882063T>A		116.0	0.0		108.0	30.0	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Silent	SNP	ENST00000265171.5	hg19	CCDS3689.1																																																																																			.	.		0.393	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			A	110882063	T	A	110882063	2	1	163	1	0	0	0	0	0	0	0	1	4964	1799	63	4		4	EGF	4	110882063	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	20024415	110882063	80272213	60	24842										
MYOZ2	51778	hgsc.bcm.edu	37	chr4	120072181	120072181	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaaaatttccagtatcaatcTagagcacaaataaatgtagg	7	6	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:120072181T>A	ENST00000307128.5	+	3	444	c.231T>A	c.(229-231)tcT>tcA	p.S77S		NM_016599.4	NP_057683.1			myozenin 2											endometrium(1)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						AGTATCAATCTAGAGCACAAA	0.338																																					p.S77S		Atlas-SNP	.											.	MYOZ2	34	.	0			c.T231A						.						87	84	85					4																	120072181		2203	4300	6503	SO:0001819	synonymous_variant	51778	exon3			TCAATCTAGAGCA	AF249873	CCDS3711.1	4q26-q27	2014-09-17	2002-01-07	2002-01-11	ENSG00000172399	ENSG00000172399			1330	protein-coding gene	gene with protein product		605602	"chromosome 4 open reading frame 5"	C4orf5		8619474, 9110174	Standard	NM_016599		Approved	CS-1	uc003icp.4	Q9NPC6	OTTHUMG00000132968	ENST00000307128.5:c.231T>A	chr4.hg19:g.120072181T>A		95.0	0.0		77.0	14.0	NM_016599		Silent	SNP	ENST00000307128.5	hg19	CCDS3711.1																																																																																			.	.		0.338	MYOZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256526.2			A	120072181	T	A	120072181	2	1	163	1	0	0	0	0	0	0	0	1	10105	1509	53	4		4	MYOZ2	4	120072181	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	9190118	120072181	71082095	61	24843										
BBS7	55212	hgsc.bcm.edu	37	chr4	122789150	122789150	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cagtaccttttgtgtagctcTgtgtcttgaggcaggaatta	11	7	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:122789150T>A	ENST00000264499.4	-	2	271	c.88A>T	c.(88-90)Aga>Tga	p.R30*	RP11-63B13.1_ENST00000567769.1_lincRNA|BBS7_ENST00000506636.1_Nonsense_Mutation_p.R30*	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	30					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						TGTGTAGCTCTGTGTCTTGAG	0.373									Bardet-Biedl syndrome																												p.R30X		Atlas-SNP	.											.	BBS7	61	.	0			c.A88T						.						163	154	157					4																	122789150		2203	4300	6503	SO:0001587	stop_gained	55212	exon2	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TAGCTCTGTGTCT	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.88A>T	chr4.hg19:g.122789150T>A	ENSP00000264499:p.Arg30*	80.0	0.0		89.0	27.0	NM_018190	Q4W5P8|Q8N581|Q9NVI4	Nonsense_Mutation	SNP	ENST00000264499.4	hg19	CCDS3724.1	.	.	.	.	.	.	.	.	.	.	T	37	6.436395	0.97564	.	.	ENSG00000138686	ENST00000264499;ENST00000506636	.	.	.	5.56	4.35	0.52113	.	0.197163	0.53938	D	0.000055	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-6.7128	11.5063	0.50468	0.0:0.0:0.2858:0.7142	.	.	.	.	X	30	.	ENSP00000264499:R30X	R	-	1	2	BBS7	123008600	1.000000	0.71417	0.324000	0.25361	0.905000	0.53344	4.325000	0.59234	0.902000	0.36520	0.533000	0.62120	AGA	.	.		0.373	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256716.1			A	122789150	T	A	122789150	4	1	163	1	0	0	0	0	0	1	0	0	1341	1588	55	4	2136	4	BBS7	4	122789150	Nonsense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	2716969	122789150	68365126	62	24844										
PCDH18	54510	hgsc.bcm.edu	37	chr4	138442493	138442493	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccttcctgcgctccagggagTtggaccgatccacctcactg	10	16	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:138442493T>A	ENST00000344876.4	-	4	3484	c.3098A>T	c.(3097-3099)aAc>aTc	p.N1033I	PCDH18_ENST00000507846.1_Missense_Mutation_p.N812I|PCDH18_ENST00000511115.1_Missense_Mutation_p.N213I|PCDH18_ENST00000510305.1_Missense_Mutation_p.N244I|PCDH18_ENST00000412923.2_Missense_Mutation_p.N1032I	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	1033	Interaction with DAB1. {ECO:0000250}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					CTCCAGGGAGTTGGACCGATC	0.562																																					p.N1033I		Atlas-SNP	.											.	PCDH18	229	.	0			c.A3098T						.						61	58	59					4																	138442493		2203	4300	6503	SO:0001583	missense	54510	exon4			AGGGAGTTGGACC	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.3098A>T	chr4.hg19:g.138442493T>A	ENSP00000355082:p.Asn1033Ile	98.0	0.0		97.0	30.0	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	hg19	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	T	11.58	1.679730	0.29783	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846;ENST00000510305;ENST00000511115	T;T;T;T;T	0.54071	0.68;0.69;0.59;1.5;1.51	4.77	2.36	0.29203	.	0.000000	0.46758	D	0.000265	T	0.35393	0.0930	N	0.22421	0.69	0.37443	D	0.914523	P;B;B;B	0.36249	0.545;0.309;0.231;0.309	B;B;B;B	0.36289	0.221;0.109;0.159;0.109	T	0.37888	-0.9686	10	0.72032	D	0.01	.	7.8874	0.29659	0.0:0.2394:0.0:0.7606	.	213;812;1032;1033	B4DLR6;D6RIG4;Q9HCL0-2;Q9HCL0	.;.;.;PCD18_HUMAN	I	1033;1032;812;244;213	ENSP00000355082:N1033I;ENSP00000390688:N1032I;ENSP00000425903:N812I;ENSP00000424269:N244I;ENSP00000425647:N213I	ENSP00000355082:N1033I	N	-	2	0	PCDH18	138661943	1.000000	0.71417	0.988000	0.46212	0.896000	0.52359	1.184000	0.32053	0.682000	0.31407	0.482000	0.46254	AAC	.	.		0.562	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		A	138442493	T	A	138442493	3	1	163	1	0	0	0	0	1	0	0	0	11522	1725	60	4	313	4	PCDH18	4	138442493	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	15653343	138442493	52711783	63	24845										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155156629	155156629	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cacagggaccacctcgttacTgcagtcgtcagttttctgga	10	12	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:155156629T>A	ENST00000357232.4	-	25	7809	c.7810A>T	c.(7810-7812)Agt>Tgt	p.S2604C		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2604					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ACCTCGTTACTGCAGTCGTCA	0.458																																					p.S2604C		Atlas-SNP	.											.	DCHS2	594	.	0			c.A7810T						.						124	125	125					4																	155156629		2203	4300	6503	SO:0001583	missense	54798	exon25			CGTTACTGCAGTC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.7810A>T	chr4.hg19:g.155156629T>A	ENSP00000349768:p.Ser2604Cys	80.0	0.0		62.0	20.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	10.43	1.348529	0.24426	.	.	ENSG00000197410	ENST00000357232	T	0.55588	0.51	5.82	-2.84	0.05751	.	1.239470	0.05135	N	0.493223	T	0.41604	0.1166	N	0.22421	0.69	0.09310	N	1	D	0.56287	0.975	B	0.43103	0.408	T	0.51980	-0.8636	10	0.51188	T	0.08	.	13.3492	0.60593	0.0:0.5699:0.0:0.4301	.	2604	Q6V1P9	PCD23_HUMAN	C	2604	ENSP00000349768:S2604C	ENSP00000349768:S2604C	S	-	1	0	DCHS2	155376079	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.569000	0.05902	-0.337000	0.08426	0.383000	0.25322	AGT	.	.		0.458	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155156629	T	A	155156629	3	1	163	1	0	0	0	0	1	0	0	0	4290	1580	55	4	944	4	DCHS2	4	155156629	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	16714136	155156629	35997647	64	24846										
ANP32C	55016	hgsc.bcm.edu	37	chr4	165118291	165118291	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tcctcctcttcaccttcctcCtcctcctcctcgccctcctc	1	25	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr4:165118291C>A	ENST00000503008.1	-	2	864				MARCH1_ENST00000514618.1_Intron|MARCH1_ENST00000508725.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				caccttcctcctcctcctcct	0.552																																					p.E191D		Atlas-SNP	.											.	ANP32C	59	.	0			c.G573T						.						175	137	150					4																	165118291		2203	4300	6503	SO:0001627	intron_variant	23520	exon1			TTCCTCCTCCTCC	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	26077	protein-coding gene	gene with protein product		613331	"membrane-associated ring finger (C3HC4) 1"			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-85477G>T	chr4.hg19:g.165118291C>A		71.0	0.0		72.0	25.0	NM_012403	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	hg19	CCDS54814.1																																																																																			.	.		0.552	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923		A	165118291	C	A	165118291	1	1	163	0	1	0	0	0	0	0	0	0	707	680	24	3		3	ANP32C	4	165118291	Intron	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	9961662	165118291	26035985	65	24847										
ADCY2	108	hgsc.bcm.edu	37	chr5	7707845	7707845	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tcacatttcttctgtcacccTggagcacttgaatggcgctt	8	12	4	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:7707845T>A	ENST00000338316.4	+	9	1384	c.1295T>A	c.(1294-1296)cTg>cAg	p.L432Q	ADCY2_ENST00000537121.1_Missense_Mutation_p.L252Q|RP11-711G10.1_ENST00000514105.2_RNA	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	432					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						TCTGTCACCCTGGAGCACTTG	0.398																																					p.L432Q		Atlas-SNP	.											.	ADCY2	337	.	0			c.T1295A						.						122	121	121					5																	7707845		2203	4300	6503	SO:0001583	missense	108	exon9			TCACCCTGGAGCA	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1295T>A	chr5.hg19:g.7707845T>A	ENSP00000342952:p.Leu432Gln	97.0	0.0		118.0	24.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	T	31	5.095374	0.94197	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	D;D	0.85411	-1.98;-1.98	5.85	5.85	0.93711	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.000000	0.64402	D	0.000002	D	0.91277	0.7250	M	0.64567	1.98	0.49299	D	0.999772	D;D	0.89917	1.0;0.995	D;D	0.91635	0.999;0.991	D	0.92078	0.5670	10	0.87932	D	0	.	16.2378	0.82389	0.0:0.0:0.0:1.0	.	252;432	B7Z2C1;Q08462	.;ADCY2_HUMAN	Q	432;283;252	ENSP00000342952:L432Q;ENSP00000444803:L252Q	ENSP00000342952:L432Q	L	+	2	0	ADCY2	7760845	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.704000	0.84595	2.228000	0.72767	0.528000	0.53228	CTG	.	.		0.398	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7707845	T	A	7707845	3	1	163	1	0	0	0	0	1	0	0	0	294	1580	55	4	1329	4	ADCY2	5	7707845	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10		7707845	173207415	66	24848										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11385034	11385034	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tggtgctgtaggacttggccAggcggctgggcgactgcttg	18	9	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:11385034A>T	ENST00000304623.8	-	7	1109	c.920T>A	c.(919-921)cTg>cAg	p.L307Q	CTNND2_ENST00000458100.2_Intron|CTNND2_ENST00000503622.1_Intron|CTNND2_ENST00000511377.1_Missense_Mutation_p.L216Q|CTNND2_ENST00000359640.2_Missense_Mutation_p.L307Q|CTNND2_ENST00000495388.2_5'Flank	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	307					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GGACTTGGCCAGGCGGCTGGG	0.746																																					p.L307Q		Atlas-SNP	.											.	CTNND2	289	.	0			c.T920A						.						46	53	51					5																	11385034		2194	4296	6490	SO:0001583	missense	1501	exon7			TTGGCCAGGCGGC	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.920T>A	chr5.hg19:g.11385034A>T	ENSP00000307134:p.Leu307Gln	24.0	0.0		39.0	6.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.378929	0.82682	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377	T;T;T	0.79352	-1.19;-1.26;-1.16	3.61	3.61	0.41365	.	0.472817	0.15959	U	0.236371	T	0.81866	0.4913	L	0.40543	1.245	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.78455	-0.2197	10	0.35671	T	0.21	-4.8029	11.8549	0.52431	1.0:0.0:0.0:0.0	.	307	Q9UQB3	CTND2_HUMAN	Q	307;307;216	ENSP00000307134:L307Q;ENSP00000352661:L307Q;ENSP00000426510:L216Q	ENSP00000307134:L307Q	L	-	2	0	CTNND2	11438034	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.016000	0.64041	1.249000	0.43950	0.379000	0.24179	CTG	.	.		0.746	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		T	11385034	A	T	11385034	3	4	163	1	0	0	0	0	1	0	0	0	4022	188	7	4	2821	4	CTNND2	5	11385034	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	3677189	11385034	169530226	67	24849										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13716756	13716756	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cagtgactctgcctccatatTgaatctctcctatcatgtag	6	12	3	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:13716756T>A	ENST00000265104.4	-	74	12853	c.12749A>T	c.(12748-12750)cAa>cTa	p.Q4250L		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4250					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GCCTCCATATTGAATCTCTCC	0.383									Kartagener syndrome																												p.Q4250L		Atlas-SNP	.											.	DNAH5	868	.	0			c.A12749T						.						101	87	92					5																	13716756		2203	4300	6503	SO:0001583	missense	1767	exon74	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCATATTGAATCT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12749A>T	chr5.hg19:g.13716756T>A	ENSP00000265104:p.Gln4250Leu	64.0	0.0		86.0	24.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.056780	0.76074	.	.	ENSG00000039139	ENST00000265104	T	0.07216	3.21	5.53	5.53	0.82687	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.28234	0.0697	M	0.89658	3.05	0.80722	D	1	P	0.51057	0.941	P	0.51742	0.678	T	0.20907	-1.0261	10	0.72032	D	0.01	.	15.682	0.77376	0.0:0.0:0.0:1.0	.	4250	Q8TE73	DYH5_HUMAN	L	4250	ENSP00000265104:Q4250L	ENSP00000265104:Q4250L	Q	-	2	0	DNAH5	13769756	1.000000	0.71417	0.844000	0.33320	0.427000	0.31564	8.020000	0.88740	2.112000	0.64535	0.528000	0.53228	CAA	.	.		0.383	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13716756	T	A	13716756	3	1	163	1	0	0	0	0	1	0	0	0	4606	1812	63	4	1149	4	DNAH5	5	13716756	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	2331722	13716756	167198504	68	24850										
CDH18	1016	hgsc.bcm.edu	37	chr5	19483513	19483513	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	caggtccgcacacgcccatcTctctcgcatgcacaaaccct	6	19	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:19483513T>G	ENST00000507958.1	-	14	2769	c.1779A>C	c.(1777-1779)agA>agC	p.R593S	CDH18_ENST00000502796.1_Missense_Mutation_p.E557A|CDH18_ENST00000382275.1_Missense_Mutation_p.R593S|CDH18_ENST00000274170.4_Missense_Mutation_p.R593S|CDH18_ENST00000506372.1_Missense_Mutation_p.E558A			Q13634	CAD18_HUMAN	cadherin 18, type 2	593	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CACGCCCATCTCTCTCGCATG	0.522																																					p.R593S		Atlas-SNP	.											.	CDH18	561	.	0			c.A1779C						.						82	71	74					5																	19483513		2203	4300	6503	SO:0001583	missense	1016	exon12			CCCATCTCTCTCG	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1779A>C	chr5.hg19:g.19483513T>G	ENSP00000425093:p.Arg593Ser	133.0	0.0		171.0	43.0	NM_004934	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.260|6.260	0.416029|0.416029	0.11870|0.11870	.|.	.|.	ENSG00000145526|ENSG00000145526	ENST00000506372;ENST00000502796;ENST00000515257|ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170	T;T;T|T;T;T	0.60040|0.56444	0.22;0.22;0.54|0.46;0.46;0.46	5.54|5.54	4.39|4.39	0.52855|0.52855	.|Cadherin (2);	.|0.052910	.|0.64402	.|D	.|0.000001	T|T	0.29389|0.29389	0.0732|0.0732	N|N	0.10760|0.10760	0.04|0.04	0.49299|0.49299	D|D	0.999777|0.999777	B|B	0.02656|0.11235	0.0|0.004	B|B	0.01281|0.10450	0.0|0.005	T|T	0.06041|0.06041	-1.0849|-1.0849	8|9	.|.	.|.	.|.	.|.	9.9917|9.9917	0.41874|0.41874	0.0:0.0796:0.0:0.9204|0.0:0.0796:0.0:0.9204	.|.	557|593	B4DHG6|Q13634	.|CAD18_HUMAN	A|S	558;557;424|593	ENSP00000424931:E558A;ENSP00000422138:E557A;ENSP00000427383:E424A|ENSP00000371710:R593S;ENSP00000425093:R593S;ENSP00000274170:R593S	.|.	E|R	-|-	2|3	0|2	CDH18|CDH18	19519270|19519270	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	1.310000|1.310000	0.33551|0.33551	0.962000|0.962000	0.38057|0.38057	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.522	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		G	19483513	T	G	19483513	3	3	163	1	0	0	0	0	1	0	0	0	3105	1551	54	5	601	5	CDH18	5	19483513	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	5766757	19483513	161431747	69	24851										
CDH6	1004	hgsc.bcm.edu	37	chr5	31322954	31322954	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgctgtttgcagctctgaggCggcagcgaaaaaaagagcct	13	9	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:31322954C>T	ENST00000265071.2	+	12	2177	c.1912C>T	c.(1912-1914)Cgg>Tgg	p.R638W		NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	638					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AGCTCTGAGGCGGCAGCGAAA	0.458																																					p.R638W		Atlas-SNP	.											.	CDH6	175	.	0			c.C1912T						.						77	78	78					5																	31322954		2203	4300	6503	SO:0001583	missense	1004	exon12			CTGAGGCGGCAGC	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"Cadherins / Major cadherins"	1765	protein-coding gene	gene with protein product	"K-Cadherin"	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.1912C>T	chr5.hg19:g.31322954C>T	ENSP00000265071:p.Arg638Trp	73.0	0.0		114.0	27.0	NM_004932	A8K5H5|Q9BWS0	Missense_Mutation	SNP	ENST00000265071.2	hg19	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.950394	0.73787	.	.	ENSG00000113361	ENST00000265071	T	0.80033	-1.33	5.42	4.54	0.55810	Cadherin, cytoplasmic domain (1);	0.050614	0.85682	D	0.000000	D	0.92110	0.7499	M	0.93808	3.46	0.54753	D	0.999984	D	0.89917	1.0	D	0.91635	0.999	D	0.94208	0.7456	10	0.87932	D	0	.	15.7166	0.77672	0.138:0.862:0.0:0.0	.	638	P55285	CADH6_HUMAN	W	638	ENSP00000265071:R638W	ENSP00000265071:R638W	R	+	1	2	CDH6	31358711	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.766000	0.38491	1.387000	0.46486	0.591000	0.81541	CGG	.	.		0.458	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		T	31322954	C	T	31322954	3	4	163	1	0	0	0	0	1	0	0	0	3116	759	27	1	1954	1	CDH6	5	31322954	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	11839441	31322954	149592306	70	24852										
RNASEN	29102	hgsc.bcm.edu	37	chr5	31472271	31472271	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggcaatctcctcctcaggcaCcagggctttgctgcacctta	9	15	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:31472271C>G	ENST00000511367.2	-	16	2384	c.2140G>C	c.(2140-2142)Gtg>Ctg	p.V714L	DROSHA_ENST00000442743.1_Missense_Mutation_p.V677L|DROSHA_ENST00000513349.1_Missense_Mutation_p.V677L|DROSHA_ENST00000344624.3_Missense_Mutation_p.V714L	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	714	Necessary for interaction with DGCR8 and pri-miRNA processing activity.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						TCCTCAGGCACCAGGGCTTTG	0.517																																					p.V714L		Atlas-SNP	.											.	DROSHA	130	.	0			c.G2140C						.						128	126	126					5																	31472271		2041	4191	6232	SO:0001583	missense	29102	exon16			CAGGCACCAGGGC	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"drosha, ribonuclease type III", "drosha, double-stranded RNA-specific endoribonuclease"	608828	"ribonuclease type III, nuclear"	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.2140G>C	chr5.hg19:g.31472271C>G	ENSP00000425979:p.Val714Leu	136.0	0.0		184.0	42.0	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	hg19	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.300245	0.81136	.	.	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188	T;T;T;T	0.52057	1.29;1.29;0.68;0.68	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.52208	0.1720	M	0.71581	2.175	0.80722	D	1	P;B	0.42357	0.777;0.131	B;B	0.38803	0.282;0.119	T	0.60403	-0.7270	10	0.72032	D	0.01	-20.8766	19.7815	0.96417	0.0:1.0:0.0:0.0	.	677;714	E7EMP9;Q9NRR4	.;RNC_HUMAN	L	714;714;677;677;639;670	ENSP00000425979:V714L;ENSP00000339845:V714L;ENSP00000409335:V677L;ENSP00000424161:V677L	ENSP00000265075:V639L	V	-	1	0	DROSHA	31508028	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.352000	0.79404	2.746000	0.94184	0.655000	0.94253	GTG	.	.		0.517	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		G	31472271	C	G	31472271	3	3	163	1	0	0	0	0	1	0	0	0	13432	507	18	4	2064	4	RNASEN	5	31472271	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	149317	31472271	149442989	71	24853										
NIPBL	25836	hgsc.bcm.edu	37	chr5	37049313	37049313	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tatctcaaacaggtgcttgaGgcattttttcacacccagtc	7	11	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:37049313G>A	ENST00000282516.8	+	40	7363	c.6864G>A	c.(6862-6864)gaG>gaA	p.E2288E	NIPBL_ENST00000448238.2_Silent_p.E2288E	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2288					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			AGGTGCTTGAGGCATTTTTTC	0.413																																					p.E2288E		Atlas-SNP	.											.	NIPBL	513	.	0			c.G6864A						.						220	209	213					5																	37049313		2203	4300	6503	SO:0001819	synonymous_variant	25836	exon40			GCTTGAGGCATTT	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.6864G>A	chr5.hg19:g.37049313G>A		92.0	0.0		136.0	30.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.		0.413	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		A	37049313	G	A	37049313	2	1	163	1	0	0	0	0	0	0	0	1	10437	991	35	3		3	NIPBL	5	37049313	Silent	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	5577042	37049313	143865947	72	24854										
MOCS2	4338	hgsc.bcm.edu	37	chr5	52404403	52404403	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gctgcaacgcttttatttctTgaggcacagaaatggtctct	9	9	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:52404403T>A	ENST00000361377.4	-	2	130	c.89A>T	c.(88-90)cAa>cTa	p.Q30L	MOCS2_ENST00000527216.1_Missense_Mutation_p.Q25L|CTD-2366F13.1_ENST00000502171.2_RNA|MOCS2_ENST00000450852.3_Missense_Mutation_p.Q30L|MOCS2_ENST00000396954.3_5'UTR|MOCS2_ENST00000584946.1_Missense_Mutation_p.Q30L|CTD-2366F13.1_ENST00000512301.1_RNA|MOCS2_ENST00000510818.2_Missense_Mutation_p.Q30L|MOCS2_ENST00000508922.1_Missense_Mutation_p.Q30L|CTD-2366F13.1_ENST00000499459.2_RNA|MOCS2_ENST00000582677.1_Missense_Mutation_p.Q30L					molybdenum cofactor synthesis 2											endometrium(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(810;3.08e-05)|Breast(144;0.0848)				TTTTATTTCTTGAGGCACAGA	0.343																																					p.Q30L		Atlas-SNP	.											.	MOCS2	28	.	0			c.A89T						.						125	112	116					5																	52404403		1849	4108	5957	SO:0001583	missense	4338	exon2			ATTTCTTGAGGCA	AF117815	CCDS3958.1, CCDS47205.1	5q11	2008-02-05			ENSG00000164172	ENSG00000164172			7193	protein-coding gene	gene with protein product		603708				10053004, 9889283	Standard	NM_004531		Approved	MOCO1	uc003joz.3	O96007	OTTHUMG00000096981	ENST00000361377.4:c.89A>T	chr5.hg19:g.52404403T>A	ENSP00000355160:p.Gln30Leu	51.0	0.0		87.0	20.0	NM_176806		Missense_Mutation	SNP	ENST00000361377.4	hg19	CCDS47205.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.435026	0.43224	.	.	ENSG00000164172	ENST00000361377;ENST00000510818;ENST00000450852;ENST00000508922	T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16	5.86	5.86	0.93980	Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp (1);Beta-grasp fold, ferredoxin-type (1);	.	.	.	.	T	0.73984	0.3657	.	.	.	0.28643	N	0.907059	D	0.61697	0.99	D	0.64042	0.921	T	0.68014	-0.5521	8	0.27082	T	0.32	.	15.9403	0.79747	0.0:0.0:0.0:1.0	.	30	O96033	MOC2A_HUMAN	L	30	ENSP00000355160:Q30L;ENSP00000424267:Q30L;ENSP00000411022:Q30L;ENSP00000426274:Q30L	ENSP00000355160:Q30L	Q	-	2	0	MOCS2	52440160	1.000000	0.71417	0.997000	0.53966	0.970000	0.65996	1.466000	0.35310	2.240000	0.73641	0.533000	0.62120	CAA	.	.		0.343	MOCS2-004	KNOWN	alternative_3_UTR|NMD_exception|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000367796.3	NM_183418		A	52404403	T	A	52404403	3	1	163	1	0	0	0	0	1	0	0	0	9700	1812	63	4	688	4	MOCS2	5	52404403	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	15355090	52404403	128510857	73	24855										
IPO11	51194	hgsc.bcm.edu	37	chr5	61833050	61833050	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tttcagacatacgcagtaggTctatgccagtccttttgtga	9	9	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:61833050T>G	ENST00000325324.6	+	24	2353	c.2184T>G	c.(2182-2184)ggT>ggG	p.G728G	KIF2A_ENST00000509663.2_3'UTR|IPO11_ENST00000409296.3_Silent_p.G768G	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	728					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		ACGCAGTAGGTCTATGCCAGT	0.284																																					p.G768G		Atlas-SNP	.											.	IPO11	76	.	0			c.T2304G						.						77	85	82					5																	61833050		2203	4298	6501	SO:0001819	synonymous_variant	51194	exon24			AGTAGGTCTATGC	AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"Importins"	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.2184T>G	chr5.hg19:g.61833050T>G		172.0	0.0		198.0	40.0	NM_001134779	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	Silent	SNP	ENST00000325324.6	hg19	CCDS34167.1																																																																																			.	.		0.284	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338		G	61833050	T	G	61833050	2	3	163	1	0	0	0	0	0	0	0	1	7802	1654	58	5		5	IPO11	5	61833050	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	9428647	61833050	119082210	74	24856										
ELL2	22936	hgsc.bcm.edu	37	chr5	95249476	95249476	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaaagatatctatacaaaccTacatatggtccaccgggttt	7	9	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:95249476T>A	ENST00000237853.4	-	4	829	c.480A>T	c.(478-480)gtA>gtT	p.V160V	ELL2_ENST00000431061.2_Intron|ELL2_ENST00000506628.1_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	160					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		TATACAAACCTACATATGGTC	0.398																																					p.V160V		Atlas-SNP	.											.	ELL2	63	.	0			c.A480T						.						159	163	161					5																	95249476		2203	4300	6503	SO:0001630	splice_region_variant	22936	exon4			CAAACCTACATAT	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.481+1A>T	chr5.hg19:g.95249476T>A		77.0	0.0		71.0	20.0	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	hg19	CCDS4080.1																																																																																			.	.		0.398	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	Silent	A	95249476	T	A	95249476	5	1	163	1	0	0	0	0	0	0	1	0	5065	1536	53	4	1478	4	ELL2	5	95249476	Splice_Site	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	33416426	95249476	85665784	75	24857										
PPP2CA	5515	hgsc.bcm.edu	37	chr5	133534792	133534792	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cttacaaagagtattttagaGtatcgtcaagttccatgatt	7	6	1	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:133534792G>T	ENST00000481195.1	-	6	1122	c.842C>A	c.(841-843)aCt>aAt	p.T281N	CTD-2410N18.5_ENST00000519718.1_Intron	NM_002715.2	NP_002706.1	P67775	PP2AA_HUMAN	protein phosphatase 2, catalytic subunit, alpha isozyme	281					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|meiotic nuclear division (GO:0007126)|mesoderm development (GO:0007498)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein dephosphorylation (GO:0006470)|protein heterotrimerization (GO:0070208)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of protein autophosphorylation (GO:0031952)|regulation of protein catabolic process (GO:0042176)|regulation of receptor activity (GO:0010469)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein phosphatase type 2A complex (GO:0000159)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|skin(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Vitamin E(DB00163)	GTATTTTAGAGTATCGTCAAG	0.363																																					p.T281N		Atlas-SNP	.											.	PPP2CA	29	.	0			c.C842A						.						109	98	102					5																	133534792		2203	4300	6503	SO:0001583	missense	5515	exon6			TTTAGAGTATCGT		CCDS4173.1	5q31.1	2013-01-24	2010-03-05		ENSG00000113575	ENSG00000113575	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9299	protein-coding gene	gene with protein product	"protein phosphatase 2A catalytic subunit, alpha isoform"	176915	"protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform"			8383590	Standard	NM_002715		Approved	PP2Calpha		P67775	OTTHUMG00000129119	ENST00000481195.1:c.842C>A	chr5.hg19:g.133534792G>T	ENSP00000418447:p.Thr281Asn	65.0	0.0		85.0	18.0	NM_002715	P05323|P13197	Missense_Mutation	SNP	ENST00000481195.1	hg19	CCDS4173.1	.	.	.	.	.	.	.	.	.	.	G	9.952	1.220389	0.22457	.	.	ENSG00000113575	ENST00000481195	T	0.04275	3.66	5.56	5.56	0.83823	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);	0.000000	0.85682	D	0.000000	T	0.01835	0.0058	N	0.00605	-1.335	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46652	-0.9176	10	0.02654	T	1	-10.847	19.5159	0.95165	0.0:0.0:1.0:0.0	.	281	P67775	PP2AA_HUMAN	N	281	ENSP00000418447:T281N	ENSP00000418447:T281N	T	-	2	0	PPP2CA	133562691	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.464000	0.97655	2.621000	0.88768	0.655000	0.94253	ACT	.	.		0.363	PPP2CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251165.1	NM_002715		T	133534792	G	T	133534792	3	4	163	1	0	0	0	0	1	0	0	0	12392	1029	36	3	95	3	PPP2CA	5	133534792	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	38285316	133534792	47380468	76	24858										
SAR1B	51128	hgsc.bcm.edu	37	chr5	133945262	133945262	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tttcagttatttaacttacaTcaagttcttcttttgactct	3	8	5	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:133945262T>G	ENST00000402673.2	-	5	625	c.347A>C	c.(346-348)gAt>gCt	p.D116A	SAR1B_ENST00000507419.1_Splice_Site_p.D48A|SAR1B_ENST00000502539.1_Splice_Site_p.D48A|SAR1B_ENST00000509937.1_Splice_Site_p.D48A|SAR1B_ENST00000439578.1_Splice_Site_p.D116A	NM_016103.3	NP_057187.1	Q9Y6B6	SAR1B_HUMAN	secretion associated, Ras related GTPase 1B	116					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|GTP catabolic process (GO:0006184)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			kidney(2)|lung(2)|urinary_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTAACTTACATCAAGTTCTTC	0.403																																					p.D116A		Atlas-SNP	.											.	SAR1B	19	.	0			c.A347C						.						108	96	101					5																	133945262		2203	4300	6503	SO:0001630	splice_region_variant	51128	exon6			CTTACATCAAGTT	AF092130	CCDS4177.1	5q31.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000152700	ENSG00000152700			10535	protein-coding gene	gene with protein product		607690	"SAR1a gene homolog (S. cerevisiae) 2", "SAR1a gene homolog 2 (S. cerevisiae)", "SAR1 homolog B (S. cerevisiae)"	SARA2			Standard	NM_001033503		Approved		uc003kzr.3	Q9Y6B6	OTTHUMG00000129114	ENST00000402673.2:c.348+1A>C	chr5.hg19:g.133945262T>G		67.0	0.0		107.0	21.0	NM_001033503	D3DQA4|Q567T4	Missense_Mutation	SNP	ENST00000402673.2	hg19	CCDS4177.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.857878	0.91433	.	.	ENSG00000152700	ENST00000394992;ENST00000402673;ENST00000507419;ENST00000502539;ENST00000439578;ENST00000509937;ENST00000509730;ENST00000505758	T;T;T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01;0.01;0.01	5.46	5.46	0.80206	Small GTP-binding protein domain (1);	0.094859	0.64402	D	0.000001	T	0.66257	0.2771	M	0.76838	2.35	0.80722	D	1	B	0.17268	0.021	B	0.23275	0.045	T	0.66416	-0.5929	10	0.66056	D	0.02	-18.9555	15.8338	0.78782	0.0:0.0:0.0:1.0	.	116	Q9Y6B6	SAR1B_HUMAN	A	48;116;48;48;116;48;48;116	ENSP00000385432:D116A;ENSP00000425339:D48A;ENSP00000426335:D48A;ENSP00000404997:D116A;ENSP00000424673:D48A;ENSP00000423197:D48A;ENSP00000425466:D116A	ENSP00000378443:D48A	D	-	2	0	SAR1B	133973161	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.242000	0.72376	2.205000	0.71048	0.482000	0.46254	GAT	.	.		0.403	SAR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251158.2	NM_016103	Missense_Mutation	G	133945262	T	G	133945262	5	3	163	1	0	0	0	0	0	0	1	0	13855	1449	50	5	261	5	SAR1B	5	133945262	Splice_Site	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	410470	133945262	46969998	77	24859										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135651458	135651458	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcattgcatagataacttccTgtaatcgttctaacagaata	6	8	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:135651458T>A	ENST00000513104.1	-	3	1072	c.790A>T	c.(790-792)Agg>Tgg	p.R264W	TRPC7_ENST00000355180.3_Intron|TRPC7_ENST00000426057.2_Intron|TRPC7-AS2_ENST00000513958.1_RNA	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	264					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GATAACTTCCTGTAATCGTTC	0.478																																					p.R264W		Atlas-SNP	.											.	TRPC7	126	.	0			c.A790T						.						59	60	59					5																	135651458		2053	4223	6276	SO:0001583	missense	57113	exon3			ACTTCCTGTAATC	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.790A>T	chr5.hg19:g.135651458T>A	ENSP00000426070:p.Arg264Trp	100.0	0.0		89.0	24.0	NM_020389	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	hg19	CCDS47267.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.6|22.6	4.309628|4.309628	0.81247|0.81247	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000502753|ENST00000513104;ENST00000265193	.|T	.|0.64803	.|-0.12	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.62270|0.62270	0.2414|0.2414	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	D|D	1|1	.|B;B	.|0.22541	.|0.032;0.071	.|B;B	.|0.25987	.|0.041;0.065	T|T	0.62072|0.62072	-0.6931|-0.6931	5|10	.|0.72032	.|D	.|0.01	-23.9142|-23.9142	16.0238|16.0238	0.80522|0.80522	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|264;264	.|Q70T25;Q9HCX4	.|.;TRPC7_HUMAN	L|W	263|264	.|ENSP00000426070:R264W	.|ENSP00000265193:R264W	Q|R	-|-	2|1	0|2	TRPC7|TRPC7	135679357|135679357	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.991000|0.991000	0.29654|0.29654	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	CAG|AGG	.	.		0.478	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135651458	T	A	135651458	3	1	163	1	0	0	0	0	1	0	0	0	16599	1579	55	4	1838	4	TRPC7	5	135651458	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	1706196	135651458	45263802	78	24860										
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140165998	140165998	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	atcccggaggaagccaaacaCggcaccttcgttggccgcgt	12	14	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:140165998C>A	ENST00000504120.2	+	1	123	c.123C>A	c.(121-123)caC>caA	p.H41Q	PCDHA1_ENST00000394633.3_Missense_Mutation_p.H41Q|PCDHA1_ENST00000378133.3_Missense_Mutation_p.H41Q	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	41	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGCCAAACACGGCACCTTCG	0.657																																					p.H41Q		Atlas-SNP	.											.	PCDHA1	387	.	0			c.C123A						.						48	55	53					5																	140165998		2203	4300	6503	SO:0001583	missense	56147	exon1			CAAACACGGCACC	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"Cadherins / Protocadherins : Clustered"	8663	other	complex locus constituent	"KIAA0345-like 13"	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.123C>A	chr5.hg19:g.140165998C>A	ENSP00000420840:p.His41Gln	93.0	0.0		117.0	22.0	NM_031411	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	hg19	CCDS54913.1	.	.	.	.	.	.	.	.	.	.	c	14.44	2.535543	0.45176	.	.	ENSG00000204970	ENST00000504120;ENST00000394633;ENST00000378133	T;T;T	0.26373	1.74;1.74;1.74	4.53	4.53	0.55603	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	0.000000	0.45361	U	0.000361	T	0.50120	0.1597	M	0.82517	2.595	0.31959	N	0.608694	D;D;D	0.58620	0.983;0.983;0.971	P;D;P	0.64144	0.793;0.922;0.746	T	0.63739	-0.6569	10	0.72032	D	0.01	.	12.1585	0.54091	0.0:0.9156:0.0:0.0844	.	41;41;41	Q9Y5I3;Q9Y5I3-2;Q9Y5I3-3	PCDA1_HUMAN;.;.	Q	41	ENSP00000420840:H41Q;ENSP00000378129:H41Q;ENSP00000367373:H41Q	ENSP00000367373:H41Q	H	+	3	2	PCDHA1	140146182	0.000000	0.05858	1.000000	0.80357	0.545000	0.35147	-0.429000	0.06982	2.246000	0.74042	0.650000	0.86243	CAC	.	.		0.657	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		A	140165998	C	A	140165998	3	1	163	1	0	0	0	0	1	0	0	0	11528	535	19	1	125	1	PCDHA1	5	140165998	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	4514540	140165998	40749262	79	24861										
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140175983	140175983	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgccacatcttcacggtgtcAgcgtgggatgcggacgcgca	14	12	3	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:140175983A>T	ENST00000526136.1	+	1	1434	c.1434A>T	c.(1432-1434)tcA>tcT	p.S478S	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Silent_p.S478S|PCDHA2_ENST00000378132.1_Silent_p.S478S|PCDHA1_ENST00000504120.2_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	478	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCACGGTGTCAGCGTGGGATG	0.652																																					p.S478S		Atlas-SNP	.											.	PCDHA2	404	.	0			c.A1434T						.						72	76	74					5																	140175983		2203	4300	6503	SO:0001819	synonymous_variant	56146	exon1			GGTGTCAGCGTGG	AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"Cadherins / Protocadherins : Clustered"	8668	other	complex locus constituent	"KIAA0345-like 12"	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.1434A>T	chr5.hg19:g.140175983A>T		175.0	0.0		185.0	36.0	NM_031495	O75287|Q9BTV3	Silent	SNP	ENST00000526136.1	hg19	CCDS54914.1																																																																																			.	.		0.652	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		T	140175983	A	T	140175983	2	4	163	1	0	0	0	0	0	0	0	1	11533	175	7	4		4	PCDHA2	5	140175983	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	9985	140175983	40739277	80	24862										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140208516	140208516	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aatggggcaatttcatattcTtttaatagccttgttgcagc	8	7	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:140208516T>A	ENST00000529310.1	+	1	954	c.840T>A	c.(838-840)tcT>tcA	p.S280S	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Silent_p.S280S|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	280	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCATATTCTTTTAATAGCC	0.388																																					p.S280S		Atlas-SNP	.											.	PCDHA6	442	.	0			c.T840A						.						108	108	108					5																	140208516		2203	4300	6503	SO:0001819	synonymous_variant	56142	exon1			ATATTCTTTTAAT	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.840T>A	chr5.hg19:g.140208516T>A		353.0	0.0		478.0	112.0	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	hg19	CCDS47281.1																																																																																			.	.		0.388	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		A	140208516	T	A	140208516	2	1	163	1	0	0	0	0	0	0	0	1	11537	1596	56	4		4	PCDHA6	5	140208516	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	32533	140208516	40706744	81	24863										
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140515388	140515388	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	caaactgatctgcagctcacAgatataaatgaccatgcccc	6	13	2	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:140515388A>T	ENST00000231134.5	+	1	589	c.372A>T	c.(370-372)acA>acT	p.T124T		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	124	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGCAGCTCACAGATATAAATG	0.478																																					p.T124T		Atlas-SNP	.											.	PCDHB5	184	.	0			c.A372T						.						65	72	70					5																	140515388		2203	4300	6503	SO:0001819	synonymous_variant	26167	exon1			GCTCACAGATATA	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.372A>T	chr5.hg19:g.140515388A>T		126.0	0.0		147.0	37.0	NM_015669	Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	hg19	CCDS4247.1																																																																																			.	.		0.478	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		T	140515388	A	T	140515388	2	4	163	1	0	0	0	0	0	0	0	1	11554	175	7	4		4	PCDHB5	5	140515388	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	306872	140515388	40399872	82	24864										
PCDHB6	56130	hgsc.bcm.edu	37	chr5	140530514	140530514	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cgccccggtcagggacctccGagattcagatccaggttttg	12	13	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:140530514G>A	ENST00000231136.1	+	1	676	c.676G>A	c.(676-678)Gag>Aag	p.E226K	PCDHB6_ENST00000543635.1_Missense_Mutation_p.E90K	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	226	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGGACCTCCGAGATTCAGAT	0.592																																					p.E226K		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G676A						.						42	46	45					5																	140530514		2203	4300	6503	SO:0001583	missense	56130	exon1			ACCTCCGAGATTC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.676G>A	chr5.hg19:g.140530514G>A	ENSP00000231136:p.Glu226Lys	116.0	0.0		143.0	30.0	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	hg19	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	G	1.555	-0.538242	0.04082	.	.	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.01767	4.65;4.65	4.85	-3.64	0.04515	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01092	0.0036	L	0.28014	0.82	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.49072	-0.8977	9	0.07325	T	0.83	.	3.3639	0.07197	0.4685:0.1528:0.2881:0.0906	.	226	Q9Y5E3	PCDB6_HUMAN	K	90;226;11	ENSP00000438466:E90K;ENSP00000231136:E226K	ENSP00000231136:E226K	E	+	1	0	PCDHB6	140510698	0.000000	0.05858	0.001000	0.08648	0.337000	0.28794	-1.859000	0.01657	-0.369000	0.08028	0.561000	0.74099	GAG	.	.		0.592	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		A	140530514	G	A	140530514	3	1	163	1	0	0	0	0	1	0	0	0	11555	1059	37	1	678	1	PCDHB6	5	140530514	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	15126	140530514	40384746	83	24865										
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140773294	140773294	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tggggaaatatcaatagcaaAaagtctagattatgaagaat	9	3	2	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:140773294A>T	ENST00000398604.2	+	1	914	c.914A>T	c.(913-915)aAa>aTa	p.K305I	PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	305	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAATAGCAAAAAGTCTAGAT	0.373																																					p.K305I		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.A914T						.						95	101	99					5																	140773294		1817	4081	5898	SO:0001583	missense	9708	exon1			TAGCAAAAAGTCT	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.914A>T	chr5.hg19:g.140773294A>T	ENSP00000381605:p.Lys305Ile	191.0	0.0		260.0	54.0	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	hg19	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	14.59	2.580299	0.46006	.	.	ENSG00000253767	ENST00000398604	T	0.57436	0.4	5.41	-2.51	0.06365	Cadherin (4);Cadherin-like (1);	0.271764	0.18119	U	0.151118	T	0.60222	0.2252	M	0.76574	2.34	0.09310	N	1	P;P	0.44690	0.841;0.809	P;B	0.51550	0.673;0.35	T	0.62215	-0.6901	10	0.66056	D	0.02	.	13.3165	0.60409	0.4132:0.0:0.5868:0.0	.	305;305	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	I	305	ENSP00000381605:K305I	ENSP00000381605:K305I	K	+	2	0	PCDHGA8	140753478	0.000000	0.05858	0.017000	0.16124	0.963000	0.63663	0.288000	0.18939	-0.189000	0.10482	0.533000	0.62120	AAA	.	.		0.373	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		T	140773294	A	T	140773294	3	4	163	1	0	0	0	0	1	0	0	0	11569	14	1	4	916	4	PCDHGA8	5	140773294	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	242780	140773294	40141966	84	24866										
FAT2	2196	hgsc.bcm.edu	37	chr5	150905451	150905451	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cttggtgattcgaaacgagtAgggggggccattctctggag	16	7	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:150905451A>T	ENST00000261800.5	-	17	10396	c.10384T>A	c.(10384-10386)Tac>Aac	p.Y3462N		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3462	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CGAAACGAGTAGGGGGGGCCA	0.582																																					p.Y3462N		Atlas-SNP	.											.,2	FAT2	465	.	0			c.T10384A						.						58	54	55					5																	150905451		2203	4300	6503	SO:0001583	missense	2196	exon17			ACGAGTAGGGGGG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10384T>A	chr5.hg19:g.150905451A>T	ENSP00000261800:p.Tyr3462Asn	51.0	0.0		73.0	14.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.3|23.3	4.397548|4.397548	0.83120|0.83120	.|.	.|.	ENSG00000086570|ENSG00000086570	ENST00000520200|ENST00000261800	.|T	.|0.60920	.|0.15	5.09|5.09	5.09|5.09	0.68999|0.68999	.|Cadherin (4);Cadherin-like (1);	.|0.214974	.|0.33075	.|N	.|0.005319	T|T	0.74581|0.74581	0.3735|0.3735	M|M	0.71296|0.71296	2.17|2.17	0.54753|0.54753	D|D	0.999985|0.999985	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.76071	.|0.987;0.98	T|T	0.78028|0.78028	-0.2364|-0.2364	5|10	.|0.72032	.|D	.|0.01	.|.	15.1694|15.1694	0.72858|0.72858	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|3462;653	.|Q9NYQ8;E9PDJ8	.|FAT2_HUMAN;.	Q|N	320|3462	.|ENSP00000261800:Y3462N	.|ENSP00000261800:Y3462N	L|Y	-|-	2|1	0|0	FAT2|FAT2	150885644|150885644	1.000000|1.000000	0.71417|0.71417	0.845000|0.845000	0.33349|0.33349	0.803000|0.803000	0.45373|0.45373	8.832000|8.832000	0.92079|0.92079	2.046000|2.046000	0.60703|0.60703	0.445000|0.445000	0.29226|0.29226	CTA|TAC	.	.		0.582	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150905451	A	T	150905451	3	4	163	1	0	0	0	0	1	0	0	0	5698	420	15	4	2693	4	FAT2	5	150905451	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	10132157	150905451	30009809	85	24867										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169482326	169482326	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cagatatccagtgcttcactGtccagcctgtcttggatgaa	9	11	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr5:169482326G>A	ENST00000256935.8	+	42	4311	c.4231G>A	c.(4231-4233)Gtc>Atc	p.V1411I	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Missense_Mutation_p.V472I|DOCK2_ENST00000520908.1_Missense_Mutation_p.V903I	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1411	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTGCTTCACTGTCCAGCCTGT	0.473																																					p.V1411I		Atlas-SNP	.											.	DOCK2	389	.	0			c.G4231A						.						87	84	85					5																	169482326		2203	4300	6503	SO:0001583	missense	1794	exon42			TTCACTGTCCAGC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4231G>A	chr5.hg19:g.169482326G>A	ENSP00000256935:p.Val1411Ile	75.0	0.0		96.0	24.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	34	5.396535	0.96009	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.19669	2.9;2.4;2.13	5.07	5.07	0.68467	.	0.066924	0.64402	D	0.000015	T	0.45696	0.1355	M	0.83012	2.62	0.52501	D	0.999958	B;P	0.48834	0.035;0.916	B;P	0.54664	0.039;0.758	T	0.50825	-0.8782	10	0.54805	T	0.06	.	18.4485	0.90695	0.0:0.0:1.0:0.0	.	903;1411	E7ERW7;Q92608	.;DOCK2_HUMAN	I	1411;903;472	ENSP00000256935:V1411I;ENSP00000429283:V903I;ENSP00000438827:V472I	ENSP00000256935:V1411I	V	+	1	0	DOCK2	169414904	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.864000	0.99589	2.343000	0.79666	0.655000	0.94253	GTC	.	.		0.473	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169482326	G	A	169482326	3	1	163	1	0	0	0	0	1	0	0	0	4689	1377	48	3	4397	3	DOCK2	5	169482326	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	18576875	169482326	11432934	86	24868										
LY86	9450	hgsc.bcm.edu	37	chr6	6589096	6589096	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggcttggaagtgctctaccaGagttgcggtaagcccttgca	13	10	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:6589096G>C	ENST00000379953.2	+	2	481	c.129G>C	c.(127-129)caG>caC	p.Q43H	LY86-AS1_ENST00000429345.1_RNA|LY86-AS1_ENST00000435641.1_RNA|LY86-AS1_ENST00000447858.1_RNA|LY86_ENST00000230568.4_Missense_Mutation_p.Q43H			O95711	LY86_HUMAN	lymphocyte antigen 86	43					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				large_intestine(2)|lung(6)	8	Ovarian(93;0.0377)					TGCTCTACCAGAGTTGCGGTA	0.582																																					p.Q43H		Atlas-SNP	.											.	LY86	18	.	0			c.G129C						.						79	75	76					6																	6589096		2203	4300	6503	SO:0001583	missense	9450	exon1			CTACCAGAGTTGC	AF057178	CCDS4498.1	6p24.3	2010-07-08			ENSG00000112799	ENSG00000112799			16837	protein-coding gene	gene with protein product		605241				9763566	Standard	NM_004271		Approved	MD-1, dJ80N2.1	uc003mwy.1	O95711	OTTHUMG00000014190	ENST00000379953.2:c.129G>C	chr6.hg19:g.6589096G>C	ENSP00000369286:p.Gln43His	49.0	0.0		65.0	9.0	NM_004271	Q9UQC4	Missense_Mutation	SNP	ENST00000379953.2	hg19	CCDS4498.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.597521	0.66332	.	.	ENSG00000112799	ENST00000379953;ENST00000230568	T;T	0.52057	0.68;0.68	5.3	5.3	0.74995	MD-2-related lipid-recognition (2);Immunoglobulin E-set (1);	0.486350	0.17954	N	0.156407	T	0.52933	0.1765	L	0.59436	1.845	0.38078	D	0.93657	D	0.63880	0.993	P	0.59825	0.864	T	0.57051	-0.7877	10	0.66056	D	0.02	-1.9443	14.4667	0.67490	0.0:0.0:1.0:0.0	.	43	O95711	LY86_HUMAN	H	43	ENSP00000369286:Q43H;ENSP00000230568:Q43H	ENSP00000230568:Q43H	Q	+	3	2	LY86	6534095	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	4.189000	0.58358	2.478000	0.83669	0.491000	0.48974	CAG	.	.		0.582	LY86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039762.2			C	6589096	G	C	6589096	3	2	163	1	0	0	0	0	1	0	0	0	9109	933	33	4	131	4	LY86	6	6589096	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10		6589096	164525971	87	24869										
HIST1H4C	8364	hgsc.bcm.edu	37	chr6	26104224	26104224	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcttggggaagggtggtgctAagcgccatcgtaaggtgctc	17	8	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:26104224A>T	ENST00000377803.2	+	1	121	c.49A>T	c.(49-51)Aag>Tag	p.K17*		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	17					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7						GGGTGGTGCTAAGCGCCATCG	0.537																																					p.K17X		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.A49T						.						64	64	64					6																	26104224		2203	4300	6503	SO:0001587	stop_gained	8364	exon1			GGTGCTAAGCGCC	X60486	CCDS4583.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000197061	ENSG00000197061		"Histones / Replication-dependent"	4787	protein-coding gene	gene with protein product		602827	"H4 histone family, member G", "histone 1, H4c"	H4FG		9119399, 12408966	Standard	NM_003542		Approved	H4/g, dJ221C16.1	uc003ngi.3	P62805	OTTHUMG00000014429	ENST00000377803.2:c.49A>T	chr6.hg19:g.26104224A>T	ENSP00000367034:p.Lys17*	92.0	0.0		72.0	18.0	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Nonsense_Mutation	SNP	ENST00000377803.2	hg19	CCDS4583.1	.	.	.	.	.	.	.	.	.	.	.	17.49	3.401834	0.62288	.	.	ENSG00000197061	ENST00000377803	.	.	.	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.5543	0.61751	1.0:0.0:0.0:0.0	.	.	.	.	X	17	.	ENSP00000367034:K17X	K	+	1	0	HIST1H4C	26212203	1.000000	0.71417	0.997000	0.53966	0.049000	0.14656	9.125000	0.94402	2.052000	0.61016	0.459000	0.35465	AAG	.	.		0.537	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542		T	26104224	A	T	26104224	4	4	163	1	0	0	0	0	0	1	0	0	7176	363	13	4	51	4	HIST1H4C	6	26104224	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	19515128	26104224	145010843	88	24870										
HIST1H2BL	8340	hgsc.bcm.edu	37	chr6	27775503	27775503	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgacgaaggagttcatgattCccatggccttagaagagatg	12	7	1	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:27775503C>A	ENST00000377401.2	-	1	206	c.182G>T	c.(181-183)gGa>gTa	p.G61V	HIST1H3H_ENST00000369163.2_5'Flank|HIST1H2AI_ENST00000358739.3_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	61					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						GTTCATGATTCCCATGGCCTT	0.587																																					p.G61V		Atlas-SNP	.											.	HIST1H2BL	48	.	0			c.G182T						.						198	187	191					6																	27775503		2203	4300	6503	SO:0001583	missense	8340	exon1			ATGATTCCCATGG	Z83740	CCDS4625.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000185130	ENSG00000185130		"Histones / Replication-dependent"	4748	protein-coding gene	gene with protein product		602800	"H2B histone family, member C", "histone 1, H2bl"	H2BFC		9439656, 12408966	Standard	NM_003519		Approved	H2B/c, dJ97D16.4	uc003njl.3	Q99880	OTTHUMG00000014485	ENST00000377401.2:c.182G>T	chr6.hg19:g.27775503C>A	ENSP00000366618:p.Gly61Val	119.0	0.0		142.0	27.0	NM_003519	B2R5A3|Q52LW9	Missense_Mutation	SNP	ENST00000377401.2	hg19	CCDS4625.1	.	.	.	.	.	.	.	.	.	.	.	18.15	3.560481	0.65538	.	.	ENSG00000185130	ENST00000377401	T	0.21543	2.0	4.35	4.35	0.52113	Histone-fold (2);Histone core (1);	.	.	.	.	T	0.43743	0.1261	M	0.88377	2.95	0.58432	D	0.999999	P	0.44877	0.845	P	0.60173	0.87	T	0.51849	-0.8653	9	0.66056	D	0.02	.	16.7577	0.85504	0.0:1.0:0.0:0.0	.	61	Q99880	H2B1L_HUMAN	V	61	ENSP00000366618:G61V	ENSP00000366618:G61V	G	-	2	0	HIST1H2BL	27883482	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.429000	0.66495	2.335000	0.79485	0.655000	0.94253	GGA	.	.		0.587	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519		A	27775503	C	A	27775503	3	1	163	1	0	0	0	0	1	0	0	0	7160	855	30	3	202	3	HIST1H2BL	6	27775503	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	1671279	27775503	143339564	89	24871										
OR2H1	26716	hgsc.bcm.edu	37	chr6	29429803	29429803	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gctggtcaacctctggggccCaaagaagaccatcagcttcc	10	14	3	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:29429803C>A	ENST00000377136.1	+	4	722	c.257C>A	c.(256-258)cCa>cAa	p.P86Q	OR2H1_ENST00000377133.1_Missense_Mutation_p.P86Q|OR2H1_ENST00000396792.2_Missense_Mutation_p.P86Q|OR2H1_ENST00000442615.1_Missense_Mutation_p.P86Q|OR2H1_ENST00000473369.1_3'UTR|OR2H1_ENST00000377132.1_Missense_Mutation_p.P86Q			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						CTCTGGGGCCCAAAGAAGACC	0.537																																					p.P86Q		Atlas-SNP	.											.	OR2H1	38	.	0			c.C257A						.						96	97	96					6																	29429803		1511	2709	4220	SO:0001583	missense	26716	exon3			GGGGCCCAAAGAA	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"GPCR / Class A : Olfactory receptors"	8252	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily H, member 8"	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.257C>A	chr6.hg19:g.29429803C>A	ENSP00000366340:p.Pro86Gln	80.0	0.0		74.0	18.0	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	hg19	CCDS4660.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.267445	0.40095	.	.	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.01902	4.57;4.57;4.57;4.57;4.57	2.74	2.74	0.32292	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40302	N	0.001139	T	0.01421	0.0046	N	0.10837	0.055	0.09310	N	1	D	0.71674	0.998	D	0.67725	0.953	T	0.53781	-0.8390	10	0.51188	T	0.08	.	7.4508	0.27237	0.1808:0.6417:0.1775:0.0	.	86	Q9GZK4	OR2H1_HUMAN	Q	86	ENSP00000366340:P86Q;ENSP00000366337:P86Q;ENSP00000393254:P86Q;ENSP00000366336:P86Q;ENSP00000380010:P86Q	ENSP00000366336:P86Q	P	+	2	0	OR2H1	29537782	0.000000	0.05858	0.831000	0.32960	0.993000	0.82548	-1.904000	0.01593	1.847000	0.53656	0.603000	0.83216	CCA	.	.		0.537	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			A	29429803	C	A	29429803	3	1	163	1	0	0	0	0	1	0	0	0	11010	594	21	3	259	3	OR2H1	6	29429803	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	1654300	29429803	141685264	90	24872										
GABBR1	2550	hgsc.bcm.edu	37	chr6	29574219	29574219	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	atgctccagctggggcagaaTagagacgtcaatatcttcct	10	10	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:29574219T>A	ENST00000377034.4	-	19	2595	c.2260A>T	c.(2260-2262)Att>Ttt	p.I754F	GABBR1_ENST00000377016.4_Missense_Mutation_p.I692F|GABBR1_ENST00000376977.3_3'UTR|GABBR1_ENST00000355973.3_Missense_Mutation_p.I637F|GABBR1_ENST00000377012.4_Missense_Mutation_p.I637F	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	754					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	TGGGGCAGAATAGAGACGTCA	0.527																																					p.I754F		Atlas-SNP	.											.	GABBR1	95	.	0			c.A2260T						.						206	199	202					6																	29574219		1511	2709	4220	SO:0001583	missense	2550	exon19			GCAGAATAGAGAC	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.2260A>T	chr6.hg19:g.29574219T>A	ENSP00000366233:p.Ile754Phe	76.0	0.0		89.0	21.0	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	hg19	CCDS4663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.55|19.55	3.847941|3.847941	0.71603|0.71603	.|.	.|.	ENSG00000204681|ENSG00000204681	ENST00000355973;ENST00000377016;ENST00000377012;ENST00000377034|ENST00000485026	D;D;D;D|.	0.87809|.	-2.3;-2.3;-2.3;-2.3|.	4.3|4.3	4.3|4.3	0.51218|0.51218	GPCR, family 3, C-terminal (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.60715|0.60715	0.2290|0.2290	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	P;P;B|.	0.50369|.	0.813;0.934;0.317|.	P;P;B|.	0.52909|.	0.576;0.713;0.224|.	T|T	0.62501|0.62501	-0.6841|-0.6841	10|5	0.59425|.	D|.	0.04|.	-4.5873|-4.5873	12.0438|12.0438	0.53469|0.53469	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	692;754;637|.	Q9UBS5-3;Q9UBS5;Q5SUJ9|.	.;GABR1_HUMAN;.|.	F|F	637;692;637;754|134	ENSP00000348248:I637F;ENSP00000366215:I692F;ENSP00000366211:I637F;ENSP00000366233:I754F|.	ENSP00000348248:I637F|.	I|Y	-|-	1|2	0|0	GABBR1|GABBR1	29682198|29682198	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.986000|0.986000	0.74619|0.74619	7.355000|7.355000	0.79434|0.79434	1.872000|1.872000	0.54250|0.54250	0.533000|0.533000	0.62120|0.62120	ATT|TAT	.	.		0.527	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			A	29574219	T	A	29574219	3	1	163	1	0	0	0	0	1	0	0	0	6163	1406	49	4	645	4	GABBR1	6	29574219	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	144416	29574219	141540848	91	24873										
GABBR1	2550	hgsc.bcm.edu	37	chr6	29574242	29574242	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agacgtcaatatcttccttaGgttcctccttggcaaatgtc	7	11	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:29574242G>A	ENST00000377034.4	-	19	2572	c.2237C>T	c.(2236-2238)cCt>cTt	p.P746L	GABBR1_ENST00000377016.4_Missense_Mutation_p.P684L|GABBR1_ENST00000376977.3_3'UTR|GABBR1_ENST00000355973.3_Missense_Mutation_p.P629L|GABBR1_ENST00000377012.4_Missense_Mutation_p.P629L	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	746					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	ATCTTCCTTAGGTTCCTCCTT	0.522																																					p.P746L		Atlas-SNP	.											.	GABBR1	95	.	0			c.C2237T						.						172	163	167					6																	29574242		1511	2709	4220	SO:0001583	missense	2550	exon19			TCCTTAGGTTCCT	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.2237C>T	chr6.hg19:g.29574242G>A	ENSP00000366233:p.Pro746Leu	77.0	0.0		89.0	18.0	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	hg19	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	G	19.96	3.923601	0.73213	.	.	ENSG00000204681	ENST00000355973;ENST00000377016;ENST00000377012;ENST00000377034	D;D;D;T	0.84442	-1.85;-1.74;-1.85;-0.61	4.59	4.59	0.56863	GPCR, family 3, C-terminal (2);	0.123004	0.56097	D	0.000036	D	0.83059	0.5172	M	0.61703	1.905	0.80722	D	1	P;P;B	0.43231	0.554;0.801;0.117	B;P;B	0.46629	0.373;0.522;0.268	D	0.86234	0.1639	10	0.72032	D	0.01	-10.4866	15.268	0.73678	0.0:0.0:1.0:0.0	.	684;746;629	Q9UBS5-3;Q9UBS5;Q5SUJ9	.;GABR1_HUMAN;.	L	629;684;629;746	ENSP00000348248:P629L;ENSP00000366215:P684L;ENSP00000366211:P629L;ENSP00000366233:P746L	ENSP00000348248:P629L	P	-	2	0	GABBR1	29682221	1.000000	0.71417	0.980000	0.43619	0.831000	0.47069	7.290000	0.78711	2.239000	0.73571	0.563000	0.77884	CCT	.	.		0.522	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			A	29574242	G	A	29574242	3	1	163	1	0	0	0	0	1	0	0	0	6163	1000	35	3	668	3	GABBR1	6	29574242	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	23	29574242	141540825	92	24874										
GRM4	2914	hgsc.bcm.edu	37	chr6	34003952	34003952	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	caggtgccaaggtcgggctcAgcgatcatgaggaaggtggt	17	8	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:34003952A>T	ENST00000538487.2	-	9	2378	c.1935T>A	c.(1933-1935)gcT>gcA	p.A645A	GRM4_ENST00000374181.4_Silent_p.A645A|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000535756.1_Silent_p.A512A|GRM4_ENST00000374177.3_Silent_p.A529A|GRM4_ENST00000455714.2_Silent_p.A505A|GRM4_ENST00000609222.1_Silent_p.A512A|GRM4_ENST00000544773.2_Silent_p.A476A	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	645					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GGTCGGGCTCAGCGATCATGA	0.602																																					p.A645A		Atlas-SNP	.											.	GRM4	317	.	0			c.T1935A						.						100	87	92					6																	34003952		2203	4300	6503	SO:0001819	synonymous_variant	2914	exon9			GGGCTCAGCGATC	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.1935T>A	chr6.hg19:g.34003952A>T		74.0	0.0		82.0	18.0	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Silent	SNP	ENST00000538487.2	hg19	CCDS4787.1																																																																																			.	.		0.602	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			T	34003952	A	T	34003952	2	4	163	1	0	0	0	0	0	0	0	1	6808	175	7	4		4	GRM4	6	34003952	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	4429710	34003952	137111115	93	24875										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38749117	38749117	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tctgggtgaggcagctctatCgccggataagtgagcccatc	13	11	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:38749117C>T	ENST00000359357.3	+	14	1830	c.1576C>T	c.(1576-1578)Cgc>Tgc	p.R526C	DNAH8_ENST00000449981.2_Missense_Mutation_p.R743C|DNAH8_ENST00000441566.1_Missense_Mutation_p.R526C			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	526					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GCAGCTCTATCGCCGGATAAG	0.368																																					p.R743C		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C2227T						.						61	63	62					6																	38749117		2203	4300	6503	SO:0001583	missense	1769	exon16			CTCTATCGCCGGA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.1576C>T	chr6.hg19:g.38749117C>T	ENSP00000352312:p.Arg526Cys	192.0	0.0		240.0	65.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	C	19.69	3.873768	0.72180	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.57907	0.37;0.37;0.37	5.66	3.78	0.43462	Dynein heavy chain, domain-1 (1);	0.061470	0.64402	D	0.000011	T	0.52565	0.1742	M	0.64997	1.995	0.53005	D	0.999967	D	0.76494	0.999	D	0.64877	0.93	T	0.57394	-0.7819	10	0.54805	T	0.06	.	6.9773	0.24683	0.2611:0.6526:0.0:0.0863	.	526	Q96JB1	DYH8_HUMAN	C	731;731;526;526	ENSP00000333363:R731C;ENSP00000352312:R526C;ENSP00000402294:R526C	ENSP00000333363:R731C	R	+	1	0	DNAH8	38857095	0.999000	0.42202	0.984000	0.44739	0.998000	0.95712	2.292000	0.43549	1.401000	0.46761	0.543000	0.68304	CGC	.	.		0.368	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38749117	C	T	38749117	3	4	163	1	0	0	0	0	1	0	0	0	4609	884	31	1	1622	1	DNAH8	6	38749117	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	4745165	38749117	132365950	94	24876										
TREML2	79865	hgsc.bcm.edu	37	chr6	41162396	41162396	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctgtagcctgtcttggaggcAggtctggtggaggctaagag	17	7	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:41162396A>T	ENST00000483722.1	-	3	737	c.552T>A	c.(550-552)ccT>ccA	p.P184P		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	184					T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCTTGGAGGCAGGTCTGGTGG	0.602																																					p.P184P		Atlas-SNP	.											.	TREML2	41	.	0			c.T552A						.						127	94	105					6																	41162396		2203	4300	6503	SO:0001819	synonymous_variant	79865	exon3			GGAGGCAGGTCTG	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"Immunoglobulin superfamily / V-set domain containing"	21092	protein-coding gene	gene with protein product	"TREM-like transcript 2"	609715	"chromosome 6 open reading frame 76"	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.552T>A	chr6.hg19:g.41162396A>T		124.0	0.0		138.0	30.0	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Silent	SNP	ENST00000483722.1	hg19	CCDS4853.2																																																																																			.	.		0.602	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807		T	41162396	A	T	41162396	2	4	163	1	0	0	0	0	0	0	0	1	16488	175	7	4		4	TREML2	6	41162396	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	2413279	41162396	129952671	95	24877										
NCR2	9436	hgsc.bcm.edu	37	chr6	41309624	41309624	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgcctcccactgcaggagccAgacaagcccctgagtctcca	9	17	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:41309624A>T	ENST00000373089.5	+	3	575	c.487A>T	c.(487-489)Aga>Tga	p.R163*	NCR2_ENST00000373083.4_Nonsense_Mutation_p.R163*|NCR2_ENST00000373086.3_Nonsense_Mutation_p.R163*	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	163					cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	14	Ovarian(28;0.0327)|Colorectal(47;0.196)					TGCAGGAGCCAGACAAGCCCC	0.642																																					p.R163X		Atlas-SNP	.											.	NCR2	44	.	0			c.A487T						.						92	85	88					6																	41309624		2203	4300	6503	SO:0001587	stop_gained	9436	exon3			GGAGCCAGACAAG	AJ225109	CCDS4855.1, CCDS56428.1, CCDS56429.1	6p21.1	2013-01-11	2002-11-13	2002-11-15	ENSG00000096264	ENSG00000096264		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	6732	protein-coding gene	gene with protein product		604531	"lymphocyte antigen 95 (activating NK-receptor; NK-p44)"	LY95		10049942	Standard	NM_004828		Approved	NK-p44, CD336	uc003oqh.2	O95944	OTTHUMG00000014678	ENST00000373089.5:c.487A>T	chr6.hg19:g.41309624A>T	ENSP00000362181:p.Arg163*	44.0	0.0		81.0	19.0	NM_004828	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Nonsense_Mutation	SNP	ENST00000373089.5	hg19	CCDS4855.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.805501	0.50315	.	.	ENSG00000096264	ENST00000373083;ENST00000373089;ENST00000373086	.	.	.	1.78	0.582	0.17412	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.6097	0.08055	0.7885:0.0:0.2115:0.0	.	.	.	.	X	163	.	ENSP00000362175:R163X	R	+	1	2	NCR2	41417602	0.001000	0.12720	0.007000	0.13788	0.007000	0.05969	0.754000	0.26390	0.163000	0.19507	0.383000	0.25322	AGA	.	.		0.642	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3			T	41309624	A	T	41309624	4	4	163	1	0	0	0	0	0	1	0	0	10247	180	7	4	497	4	NCR2	6	41309624	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	147228	41309624	129805443	96	24878										
KLC4	89953	hgsc.bcm.edu	37	chr6	43038459	43038459	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acgaatcatccagatgtggcAaaacagctgaacaacctggc	9	11	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:43038459A>T	ENST00000394056.2	+	9	1506	c.1011A>T	c.(1009-1011)gcA>gcT	p.A337A	KLC4_ENST00000259708.3_Silent_p.A355A|KLC4_ENST00000453940.2_Silent_p.A260A|KLC4_ENST00000479388.1_Silent_p.A337A|KLC4_ENST00000347162.5_Silent_p.A337A|KLC4_ENST00000394058.1_Silent_p.A337A			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	337						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			CAGATGTGGCAAAACAGCTGA	0.527																																					p.A355A		Atlas-SNP	.											.	KLC4	89	.	0			c.A1065T						.						90	80	83					6																	43038459		2203	4300	6503	SO:0001819	synonymous_variant	89953	exon8			TGTGGCAAAACAG	AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"Tetratricopeptide (TTC) repeat domain containing"	21624	protein-coding gene	gene with protein product			"kinesin-like 8"	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.1011A>T	chr6.hg19:g.43038459A>T		141.0	0.0		154.0	37.0	NM_201523	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Silent	SNP	ENST00000394056.2	hg19	CCDS4883.1																																																																																			.	.		0.527	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		T	43038459	A	T	43038459	2	4	163	1	0	0	0	0	0	0	0	1	8345	117	5	4		4	KLC4	6	43038459	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1728835	43038459	128076608	97	24879										
TDRD6	221400	hgsc.bcm.edu	37	chr6	46661686	46661686	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccatgtgtactgaggacatgAgaaagtcaagttgtgtagaa	12	5	1	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:46661686A>T	ENST00000316081.6	+	1	5821	c.5821A>T	c.(5821-5823)Aga>Tga	p.R1941*	TDRD6_ENST00000544460.1_Nonsense_Mutation_p.R1941*	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1941					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			TGAGGACATGAGAAAGTCAAG	0.413																																					p.R1941X		Atlas-SNP	.											.	TDRD6	205	.	0			c.A5821T						.						159	152	154					6																	46661686		2203	4300	6503	SO:0001587	stop_gained	221400	exon1			GACATGAGAAAGT	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.5821A>T	chr6.hg19:g.46661686A>T	ENSP00000346065:p.Arg1941*	156.0	0.0		237.0	60.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Nonsense_Mutation	SNP	ENST00000316081.6	hg19	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	A	44	11.056824	0.99509	.	.	ENSG00000180113	ENST00000544460;ENST00000316081;ENST00000371334	.	.	.	5.56	0.0233	0.14136	.	0.433239	0.22340	N	0.061352	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.0756	9.2958	0.37815	0.6595:0.0:0.3405:0.0	.	.	.	.	X	1941;1941;2	.	ENSP00000346065:R1941X	R	+	1	2	TDRD6	46769645	0.002000	0.14202	0.000000	0.03702	0.019000	0.09904	0.237000	0.17985	0.084000	0.17077	-0.379000	0.06801	AGA	.	.		0.413	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		T	46661686	A	T	46661686	4	4	163	1	0	0	0	0	0	1	0	0	15749	296	11	4	5823	4	TDRD6	6	46661686	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	3623227	46661686	124453381	98	24880										
IL17F	112744	hgsc.bcm.edu	37	chr6	52103728	52103728	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agaaaggcaagccccaatatCgacagcagcaagtacttgac	9	11	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:52103728C>T	ENST00000336123.4	-	2	161	c.54G>A	c.(52-54)tcG>tcA	p.S18S		NM_052872.3	NP_443104.1	Q96PD4	IL17F_HUMAN	interleukin 17F	18					cartilage development (GO:0051216)|cytokine biosynthetic process (GO:0042089)|inflammatory response (GO:0006954)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045423)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of interleukin-8 biosynthetic process (GO:0045414)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine binding (GO:0019955)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)	14	Lung NSC(77;0.116)					GCCCCAATATCGACAGCAGCA	0.512																																					p.S18S		Atlas-SNP	.											.	IL17F	28	.	0			c.G54A						.						54	57	56					6																	52103728		2203	4300	6503	SO:0001819	synonymous_variant	112744	exon2			CAATATCGACAGC	AF384857	CCDS4938.1	6p12	2014-09-17			ENSG00000112116	ENSG00000112116		"Interleukins and interleukin receptors"	16404	protein-coding gene	gene with protein product		606496				11591732, 11591768	Standard	NM_052872		Approved	IL-17F, ML-1, ML1	uc003pam.1	Q96PD4	OTTHUMG00000014845	ENST00000336123.4:c.54G>A	chr6.hg19:g.52103728C>T		105.0	0.0		129.0	25.0	NM_052872	Q6NSI0|Q7Z6P4|Q96PI8|Q9NUE6	Silent	SNP	ENST00000336123.4	hg19	CCDS4938.1																																																																																			.	.		0.512	IL17F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040901.3	NM_052872		T	52103728	C	T	52103728	2	4	163	1	0	0	0	0	0	0	0	1	7647	871	31	1		1	IL17F	6	52103728	Silent	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	5442042	52103728	119011339	99	24881										
COL9A1	1297	hgsc.bcm.edu	37	chr6	70942395	70942395	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccaggagggccggggggaccAggagggccaggccttccagg	20	12	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:70942395A>T	ENST00000357250.6	-	36	2552	c.2394T>A	c.(2392-2394)ccT>ccA	p.P798P	COL9A1_ENST00000370499.4_Silent_p.P555P|RP1-149L1.1_ENST00000522264.1_RNA|COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000320755.7_Silent_p.P555P	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	798	Collagen-like 9.|Triple-helical region (COL1).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						CGGGGGGACCAGGAGGGCCAG	0.572																																					p.P798P		Atlas-SNP	.											.	COL9A1	228	.	0			c.T2394A						.						36	41	39					6																	70942395		2203	4300	6503	SO:0001819	synonymous_variant	1297	exon36			GGGACCAGGAGGG		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.2394T>A	chr6.hg19:g.70942395A>T		268.0	0.0		323.0	67.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Silent	SNP	ENST00000357250.6	hg19	CCDS4971.1																																																																																			.	.		0.572	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			T	70942395	A	T	70942395	2	4	163	1	0	0	0	0	0	0	0	1	3709	175	7	4		4	COL9A1	6	70942395	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	18838667	70942395	100172672	100	24882										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72968769	72968769	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctcccgaagtccagttgatcAtagaaccagagatgtggata	10	9	1	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:72968769A>T	ENST00000521978.1	+	18	3008	c.3008A>T	c.(3007-3009)cAt>cTt	p.H1003L	RIMS1_ENST00000538414.1_5'UTR|RIMS1_ENST00000518273.1_Missense_Mutation_p.H1003L|RIMS1_ENST00000522291.1_Missense_Mutation_p.H1002L|RIMS1_ENST00000523963.1_Missense_Mutation_p.H477L|RIMS1_ENST00000517827.1_Missense_Mutation_p.H462L|RIMS1_ENST00000517960.1_Missense_Mutation_p.H1002L|RIMS1_ENST00000520567.1_Missense_Mutation_p.H1002L|RIMS1_ENST00000401910.3_Missense_Mutation_p.H476L|RIMS1_ENST00000264839.7_Missense_Mutation_p.H1003L|RIMS1_ENST00000491071.2_Missense_Mutation_p.H1003L|RIMS1_ENST00000348717.5_Missense_Mutation_p.H1002L|RIMS1_ENST00000425662.2_Missense_Mutation_p.H396L	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1003					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				CCAGTTGATCATAGAACCAGA	0.348																																					p.H1003L		Atlas-SNP	.											.	RIMS1	278	.	0			c.A3008T						.						119	119	119					6																	72968769		1920	4124	6044	SO:0001583	missense	22999	exon18			TTGATCATAGAAC	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.3008A>T	chr6.hg19:g.72968769A>T	ENSP00000428417:p.His1003Leu	89.0	0.0		99.0	22.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.88|10.88	1.475676|1.475676	0.26511|0.26511	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420|ENST00000522211	T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.18502|.	2.49;2.64;2.59;2.65;2.67;2.64;2.57;2.62;2.64;2.66;2.67;2.41;2.67;2.21|.	5.71|5.71	3.23|3.23	0.37069|0.37069	.|.	0.482718|.	0.20514|.	N|.	0.090827|.	T|T	0.26085|0.26085	0.0636|0.0636	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	B;B;B;B;B;B;P;B;B;B;B;B|.	0.52842|.	0.0;0.0;0.004;0.0;0.0;0.021;0.956;0.035;0.002;0.02;0.007;0.0|.	B;B;B;B;B;B;B;B;B;B;B;B|.	0.44224|.	0.001;0.0;0.002;0.0;0.001;0.012;0.444;0.008;0.001;0.028;0.002;0.0|.	T|T	0.09796|0.09796	-1.0658|-1.0658	10|5	0.11794|.	T|.	0.64|.	-6.5828|-6.5828	4.4541|4.4541	0.11635|0.11635	0.656:0.0:0.2101:0.1339|0.656:0.0:0.2101:0.1339	.|.	462;477;1003;462;476;1002;255;1003;1002;256;1003;1003|.	B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5|.	.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN|.	L|L	1003;1003;1003;1002;1003;1002;1003;1002;1003;1002;1002;1003;476;477;396;396;462;228|94	ENSP00000430101:H1003L;ENSP00000275037:H1002L;ENSP00000264839:H1003L;ENSP00000429959:H1002L;ENSP00000430408:H1003L;ENSP00000430502:H1002L;ENSP00000430932:H1002L;ENSP00000428417:H1003L;ENSP00000385649:H476L;ENSP00000428328:H477L;ENSP00000411235:H396L;ENSP00000389503:H396L;ENSP00000428367:H462L;ENSP00000359448:H228L|.	ENSP00000264839:H1003L|.	H|I	+|+	2|1	0|0	RIMS1|RIMS1	73025490|73025490	1.000000|1.000000	0.71417|0.71417	0.969000|0.969000	0.41365|0.41365	0.268000|0.268000	0.26511|0.26511	2.055000|2.055000	0.41345|0.41345	1.005000|1.005000	0.39183|0.39183	-0.371000|-0.371000	0.07208|0.07208	CAT|ATA	.	.		0.348	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			T	72968769	A	T	72968769	3	4	163	1	0	0	0	0	1	0	0	0	13382	217	8	4	3241	4	RIMS1	6	72968769	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	2026374	72968769	98146298	101	24883										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75893246	75893246	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaccctatttggtgaaatttCaaaactttttacaagaactt	5	7	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:75893246C>A	ENST00000322507.8	-	10	1720	c.1411G>T	c.(1411-1413)Gaa>Taa	p.E471*	COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Nonsense_Mutation_p.E471*|COL12A1_ENST00000483888.2_Nonsense_Mutation_p.E471*	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	471	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						GGTGAAATTTCAAAACTTTTT	0.353																																					p.E471X		Atlas-SNP	.											.	COL12A1	385	.	0			c.G1411T						.						64	61	62					6																	75893246		1820	4074	5894	SO:0001587	stop_gained	1303	exon10			AAATTTCAAAACT	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.1411G>T	chr6.hg19:g.75893246C>A	ENSP00000325146:p.Glu471*	254.0	0.0		311.0	75.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Nonsense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	37	6.583815	0.97684	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	.	.	.	5.49	5.49	0.81192	.	0.237476	0.36374	N	0.002627	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	19.7404	0.96228	0.0:1.0:0.0:0.0	.	.	.	.	X	471	.	ENSP00000325146:E471X	E	-	1	0	COL12A1	75949966	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.776000	0.85560	2.734000	0.93682	0.655000	0.94253	GAA	.	.		0.353	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75893246	C	A	75893246	4	1	163	1	0	0	0	0	0	1	0	0	3671	835	29	3	8008	3	COL12A1	6	75893246	Nonsense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	2924477	75893246	95221821	102	24884										
HTR1E	3354	hgsc.bcm.edu	37	chr6	87725224	87725224	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agaagctccaccagcctgccAactacctaatctgttctctg	6	15	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:87725224A>T	ENST00000305344.5	+	2	875	c.172A>T	c.(172-174)Aac>Tac	p.N58Y		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	58					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	CCAGCCTGCCAACTACCTAAT	0.547																																					p.N58Y		Atlas-SNP	.											.	HTR1E	89	.	0			c.A172T						.						172	134	147					6																	87725224		2203	4300	6503	SO:0001583	missense	3354	exon2			CCTGCCAACTACC		CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5291	protein-coding gene	gene with protein product		182132	"5-hydroxytryptamine (serotonin) receptor 1E"			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.172A>T	chr6.hg19:g.87725224A>T	ENSP00000307766:p.Asn58Tyr	123.0	0.0		152.0	30.0	NM_000865	E1P503|Q9P1Y1	Missense_Mutation	SNP	ENST00000305344.5	hg19	CCDS5006.1	.	.	.	.	.	.	.	.	.	.	A	18.51	3.639580	0.67244	.	.	ENSG00000168830	ENST00000305344;ENST00000369584	T;T	0.37058	1.22;1.22	4.4	4.4	0.53042	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000005	T	0.60090	0.2242	M	0.91612	3.225	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	T	0.71388	-0.4608	10	0.72032	D	0.01	.	13.8983	0.63787	1.0:0.0:0.0:0.0	.	58	P28566	5HT1E_HUMAN	Y	58	ENSP00000307766:N58Y;ENSP00000358597:N58Y	ENSP00000307766:N58Y	N	+	1	0	HTR1E	87781943	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.677000	0.91203	1.746000	0.51805	0.416000	0.27883	AAC	.	.		0.547	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2	NM_000865		T	87725224	A	T	87725224	3	4	163	1	0	0	0	0	1	0	0	0	7448	130	5	4	174	4	HTR1E	6	87725224	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	11831978	87725224	83389843	103	24885										
RNGTT	8732	hgsc.bcm.edu	37	chr6	89600237	89600237	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtaccatctgctttccagctTactttgtatggcttcaggtc	8	11	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:89600237T>A	ENST00000369485.4	-	8	1059	c.873A>T	c.(871-873)gtA>gtT	p.V291V	RNGTT_ENST00000369475.3_Silent_p.V291V|RNGTT_ENST00000265607.6_Silent_p.V291V|RNGTT_ENST00000538899.1_Silent_p.V231V	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	291	GTase.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA processing (GO:0006396)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|mRNA guanylyltransferase activity (GO:0004484)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA guanylyltransferase activity (GO:0008192)|triphosphatase activity (GO:0050355)			endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	21		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		CTTTCCAGCTTACTTTGTATG	0.343																																					p.V291V		Atlas-SNP	.											.	RNGTT	52	.	0			c.A873T						.						105	94	98					6																	89600237		2203	4300	6503	SO:0001819	synonymous_variant	8732	exon8			CCAGCTTACTTTG	AF025654	CCDS5017.1	6q16	2011-06-09			ENSG00000111880	ENSG00000111880	2.7.7.50	"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	10073	protein-coding gene	gene with protein product		603512				9828141, 9512541	Standard	NM_001286428		Approved	HCE, HCE1, hCAP	uc003pmr.2	O60942	OTTHUMG00000015190	ENST00000369485.4:c.873A>T	chr6.hg19:g.89600237T>A		61.0	0.0		77.0	21.0	NM_003800	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	Silent	SNP	ENST00000369485.4	hg19	CCDS5017.1																																																																																			.	.		0.343	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041469.1			A	89600237	T	A	89600237	2	1	163	1	0	0	0	0	0	0	0	1	13518	1741	61	4		4	RNGTT	6	89600237	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	1875013	89600237	81514830	104	24886										
SFRS18	25957	hgsc.bcm.edu	37	chr6	99849420	99849420	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cacatcaccgtctgcttctcTtgcttctagtagtgataaac	6	12	4	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:99849420T>A	ENST00000369239.5	-	12	1618	c.1414A>T	c.(1414-1416)Aga>Tga	p.R472*	PNISR_ENST00000438806.1_Nonsense_Mutation_p.R472*	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	472						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						TCTGCTTCTCTTGCTTCTAGT	0.323																																					p.R472X		Atlas-SNP	.											.	PNISR	74	.	0			c.A1414T						.						106	110	109					6																	99849420		2203	4300	6503	SO:0001587	stop_gained	25957	exon11			CTTCTCTTGCTTC	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 111", "splicing factor, arginine/serine-rich 18"	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.1414A>T	chr6.hg19:g.99849420T>A	ENSP00000358242:p.Arg472*	86.0	0.0		70.0	13.0	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Nonsense_Mutation	SNP	ENST00000369239.5	hg19	CCDS5043.1	.	.	.	.	.	.	.	.	.	.	T	37	6.077775	0.97262	.	.	ENSG00000132424	ENST00000369239;ENST00000438806	.	.	.	5.46	5.46	0.80206	.	0.184779	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	.	15.83	0.78743	0.0:0.0:0.0:1.0	.	.	.	.	X	472	.	ENSP00000358242:R472X	R	-	1	2	PNISR	99956141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.018000	0.76406	2.203000	0.70933	0.472000	0.43445	AGA	.	.		0.323	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870		A	99849420	T	A	99849420	4	1	163	1	0	0	0	0	0	1	0	0	14189	1617	56	4	1007	4	SFRS18	6	99849420	Nonsense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	10249183	99849420	71265647	105	24887										
DSE	29940	hgsc.bcm.edu	37	chr6	116757981	116757981	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgctgagattttcagataagAgacagactgaggaggccatt	12	6	1	5			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:116757981A>T	ENST00000331677.3	+	7	2794	c.2350A>T	c.(2350-2352)Aga>Tga	p.R784*	DSE_ENST00000537543.1_Nonsense_Mutation_p.R803*|DSE_ENST00000359564.2_Nonsense_Mutation_p.R784*|DSE_ENST00000452085.3_Nonsense_Mutation_p.R784*			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	784					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		TTCAGATAAGAGACAGACTGA	0.483																																					p.R784X		Atlas-SNP	.											.	DSE	98	.	0			c.A2350T						.						73	76	75					6																	116757981		2203	4300	6503	SO:0001587	stop_gained	29940	exon6			GATAAGAGACAGA	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"squamous cell carcinoma antigen recognized by T cells 2"	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.2350A>T	chr6.hg19:g.116757981A>T	ENSP00000332151:p.Arg784*	130.0	0.0		153.0	33.0	NM_001080976	Q5R3K6	Nonsense_Mutation	SNP	ENST00000331677.3	hg19	CCDS5107.1	.	.	.	.	.	.	.	.	.	.	A	39	7.312940	0.98203	.	.	ENSG00000111817	ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	.	.	.	6.16	4.94	0.65067	.	0.045192	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.7989	13.2493	0.60041	0.8678:0.1322:0.0:0.0	.	.	.	.	X	784;803;784;784	.	ENSP00000332151:R784X	R	+	1	2	DSE	116864674	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	7.040000	0.76551	2.367000	0.80283	0.528000	0.53228	AGA	.	.		0.483	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352		T	116757981	A	T	116757981	4	4	163	1	0	0	0	0	0	1	0	0	4776	296	11	4	2368	4	DSE	6	116757981	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	16908561	116757981	54357086	106	24888										
CTGF	1490	hgsc.bcm.edu	37	chr6	132270673	132270673	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cttgataggcttggagatttTgggagtacggatgcactttt	13	5	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:132270673T>A	ENST00000367976.3	-	5	981	c.781A>T	c.(781-783)Aaa>Taa	p.K261*	RP11-69I8.3_ENST00000435287.1_RNA	NM_001901.2	NP_001892	P29279	CTGF_HUMAN	connective tissue growth factor	261	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.|Heparin-binding.				angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|chondrocyte proliferation (GO:0035988)|cytosolic calcium ion transport (GO:0060401)|DNA replication (GO:0006260)|epidermis development (GO:0008544)|extracellular matrix constituent secretion (GO:0070278)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of gene expression (GO:0010629)|organ senescence (GO:0010260)|ossification (GO:0001503)|positive regulation of cardiac muscle contraction (GO:0060452)|positive regulation of cell activation (GO:0050867)|positive regulation of cell death (GO:0010942)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G0 to G1 transition (GO:0070318)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|regulation of cell growth (GO:0001558)|regulation of chondrocyte differentiation (GO:0032330)|response to amino acid (GO:0043200)|response to anoxia (GO:0034059)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to glucose (GO:0009749)|response to mineralocorticoid (GO:0051385)|response to peptide hormone (GO:0043434)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell cortex (GO:0005938)|cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|insulin-like growth factor binding (GO:0005520)			breast(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	13	Breast(56;0.0602)			GBM - Glioblastoma multiforme(226;0.015)|OV - Ovarian serous cystadenocarcinoma(155;0.0169)		TTGGAGATTTTGGGAGTACGG	0.458																																					p.K261X	Esophageal Squamous(127;510 1660 12817 24400 38449)	Atlas-SNP	.											.	CTGF	36	.	0			c.A781T						.						243	253	250					6																	132270673		2203	4300	6503	SO:0001587	stop_gained	1490	exon5			AGATTTTGGGAGT	X78947	CCDS5151.1	6q23.2	2008-02-05			ENSG00000118523	ENSG00000118523			2500	protein-coding gene	gene with protein product		121009				1654338	Standard	NM_001901		Approved	IGFBP8, CCN2	uc003qcz.3	P29279	OTTHUMG00000015573	ENST00000367976.3:c.781A>T	chr6.hg19:g.132270673T>A	ENSP00000356954:p.Lys261*	83.0	0.0		92.0	19.0	NM_001901	E1P578|Q6LCY0|Q96A79|Q96QX2|Q9UDL6	Nonsense_Mutation	SNP	ENST00000367976.3	hg19	CCDS5151.1	.	.	.	.	.	.	.	.	.	.	T	37	6.508108	0.97624	.	.	ENSG00000118523	ENST00000367976	.	.	.	5.64	5.64	0.86602	.	0.096735	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1617	0.81721	0.0:0.0:0.0:1.0	.	.	.	.	X	261	.	ENSP00000356954:K261X	K	-	1	0	CTGF	132312366	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.035000	0.57297	2.275000	0.75901	0.528000	0.53228	AAA	.	.		0.458	CTGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042239.2	NM_001901		A	132270673	T	A	132270673	4	1	163	1	0	0	0	0	0	1	0	0	4010	1821	63	4	272	4	CTGF	6	132270673	Nonsense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	15512692	132270673	38844394	107	24889										
TAGAP	117289	hgsc.bcm.edu	37	chr6	159459160	159459160	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccatacctgaactgtcagtgTgctccagggagtcatcagaa	10	11	3	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:159459160T>A	ENST00000367066.3	-	9	1215	c.884A>T	c.(883-885)cAc>cTc	p.H295L	TAGAP_ENST00000326965.6_Missense_Mutation_p.H117L|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	295					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		ACTGTCAGTGTGCTCCAGGGA	0.418																																					p.H295L		Atlas-SNP	.											.	TAGAP	75	.	0			c.A884T						.						142	130	134					6																	159459160		2203	4300	6503	SO:0001583	missense	117289	exon9			TCAGTGTGCTCCA	AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.884A>T	chr6.hg19:g.159459160T>A	ENSP00000356033:p.His295Leu	85.0	0.0		106.0	20.0	NM_054114	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	hg19	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.549849	0.45383	.	.	ENSG00000164691	ENST00000367066;ENST00000326965	T;T	0.19532	2.14;2.37	6.17	6.17	0.99709	.	0.209190	0.42821	D	0.000660	T	0.13200	0.0320	L	0.59436	1.845	0.80722	D	1	B	0.30824	0.296	B	0.23419	0.046	T	0.01729	-1.1286	10	0.45353	T	0.12	-38.3706	16.4837	0.84171	0.0:0.0:0.0:1.0	.	295	Q8N103	TAGAP_HUMAN	L	295;117	ENSP00000356033:H295L;ENSP00000322650:H117L	ENSP00000322650:H117L	H	-	2	0	TAGAP	159379148	1.000000	0.71417	0.997000	0.53966	0.207000	0.24258	2.898000	0.48672	2.371000	0.80710	0.533000	0.62120	CAC	.	.		0.418	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		A	159459160	T	A	159459160	3	1	163	1	0	0	0	0	1	0	0	0	15552	1696	59	4	1319	4	TAGAP	6	159459160	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	27188487	159459160	11655907	108	24890										
C6orf118	168090	hgsc.bcm.edu	37	chr6	165715248	165715248	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgcctctggacccggcctccTggtagcacagcaccttcaag	10	16	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr6:165715248T>A	ENST00000230301.8	-	2	583	c.563A>T	c.(562-564)cAg>cTg	p.Q188L	C6orf118_ENST00000543069.1_Missense_Mutation_p.Q84L	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	188										breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		CCCGGCCTCCTGGTAGCACAG	0.637																																					p.Q188L		Atlas-SNP	.											.	C6orf118	116	.	0			c.A563T						.						41	45	44					6																	165715248		2203	4300	6503	SO:0001583	missense	168090	exon2			GCCTCCTGGTAGC		CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.563A>T	chr6.hg19:g.165715248T>A	ENSP00000230301:p.Gln188Leu	89.0	0.0		72.0	19.0	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	hg19	CCDS5288.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.891640	0.33442	.	.	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.12774	2.65;2.65	4.76	-4.35	0.03656	.	1.202810	0.05844	N	0.619937	T	0.03390	0.0098	L	0.44542	1.39	0.09310	N	1	P	0.38370	0.628	B	0.33254	0.16	T	0.31447	-0.9943	10	0.42905	T	0.14	.	8.6853	0.34234	0.0:0.5359:0.1436:0.3206	.	188	Q5T5N4	CF118_HUMAN	L	188;84	ENSP00000230301:Q188L;ENSP00000439288:Q84L	ENSP00000230301:Q188L	Q	-	2	0	C6orf118	165635238	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.839000	0.04368	-1.037000	0.03283	0.459000	0.35465	CAG	.	.		0.637	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980		A	165715248	T	A	165715248	3	1	163	1	0	0	0	0	1	0	0	0	2325	1580	55	4	878	4	C6orf118	6	165715248	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	6256088	165715248	5399819	109	24891										
SDK1	221935	hgsc.bcm.edu	37	chr7	3658710	3658710	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gttttgttttttaatatttcAgatgatgttgctccatattt	6	4	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:3658710A>T	ENST00000404826.2	+	2	437		c.e2-1		SDK1_ENST00000389531.3_Splice_Site	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1						cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TTAATATTTCAGATGATGTTG	0.383																																					.		Atlas-SNP	.											.	SDK1	361	.	0			c.299-2A>T						.						28	22	24					7																	3658710		2202	4299	6501	SO:0001630	splice_region_variant	221935	exon2			TATTTCAGATGAT	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.299-1A>T	chr7.hg19:g.3658710A>T		142.0	0.0		125.0	30.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Splice_Site	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	A	13.31	2.198762	0.38806	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0546	0.80788	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SDK1	3625236	1.000000	0.71417	0.996000	0.52242	0.376000	0.30014	8.688000	0.91260	2.191000	0.70037	0.528000	0.53228	.	.	.		0.383	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	Intron	T	3658710	A	T	3658710	5	4	163	1	0	0	0	0	0	0	1	0	13983	202	7	4	303	4	SDK1	7	3658710	Splice_Site	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		3658710	155479953	110	24892										
KLHL7	55975	hgsc.bcm.edu	37	chr7	23164366	23164366	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aagatgctgaacctgatattAttgaacaactggtggaattt	9	5	0	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:23164366A>T	ENST00000339077.5	+	3	526	c.283A>T	c.(283-285)Att>Ttt	p.I95F	KLHL7_ENST00000542558.1_Intron|KLHL7_ENST00000545771.1_Missense_Mutation_p.I73F|KLHL7_ENST00000410047.1_Missense_Mutation_p.I73F|KLHL7_ENST00000539124.1_Missense_Mutation_p.I19F|KLHL7_ENST00000479288.1_Intron|KLHL7_ENST00000322275.5_Missense_Mutation_p.I95F|KLHL7_ENST00000545443.1_Missense_Mutation_p.I73F|KLHL7_ENST00000409689.1_Missense_Mutation_p.I47F|KLHL7_ENST00000322231.7_Missense_Mutation_p.I73F	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	95	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ACCTGATATTATTGAACAACT	0.348																																					p.I95F		Atlas-SNP	.											.	KLHL7	102	.	0			c.A283T						.						123	116	118					7																	23164366		2203	4300	6503	SO:0001583	missense	55975	exon3			GATATTATTGAAC		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"Kelch-like", "BTB/POZ domain containing"	15646	protein-coding gene	gene with protein product	"retinitis pigmentosa 42"	611119	"kelch-like 7 (Drosophila)"			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.283A>T	chr7.hg19:g.23164366A>T	ENSP00000343273:p.Ile95Phe	86.0	0.0		84.0	33.0	NM_001172428	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Missense_Mutation	SNP	ENST00000339077.5	hg19	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.121105	0.77436	.	.	ENSG00000122550	ENST00000536369;ENST00000322231;ENST00000339077;ENST00000322275;ENST00000539124;ENST00000409689;ENST00000410047;ENST00000545771;ENST00000545443	T;T;T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17	5.77	5.77	0.91146	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.55481	0.1923	N	0.02876	-0.465	0.80722	D	1	D;P;P;D;D	0.76494	0.999;0.802;0.867;0.999;0.999	D;B;B;D;D	0.80764	0.994;0.337;0.354;0.994;0.994	T	0.70396	-0.4883	10	0.87932	D	0	.	16.383	0.83481	1.0:0.0:0.0:0.0	.	73;95;73;95;73	F5GYE2;Q8IXQ5;Q8IXQ5-2;Q8IXQ5-3;Q8IXQ5-4	.;KLHL7_HUMAN;.;.;.	F	95;73;95;95;19;47;73;73;73	ENSP00000322958:I73F;ENSP00000343273:I95F;ENSP00000323270:I95F;ENSP00000441136:I19F;ENSP00000386263:I47F;ENSP00000386999:I73F;ENSP00000446445:I73F;ENSP00000442366:I73F	ENSP00000322958:I73F	I	+	1	0	KLHL7	23130891	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.414000	0.90238	2.326000	0.78906	0.533000	0.62120	ATT	.	.		0.348	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846		T	23164366	A	T	23164366	3	4	163	1	0	0	0	0	1	0	0	0	8403	449	16	4	293	4	KLHL7	7	23164366	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	19505656	23164366	135974297	111	24893										
HOXA10	3206	hgsc.bcm.edu	37	chr7	27211677	27211677	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cgctctcgagtaaggtacatAttgaacagaaactccttctc	7	11	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:27211677A>G	ENST00000283921.4	-	2	1073	c.1074T>C	c.(1072-1074)aaT>aaC	p.N358N	HOXA10_ENST00000396344.4_Silent_p.N42N|RP1-170O19.20_ENST00000465941.1_Intron|MIR196B_ENST00000384852.1_RNA|HOXA-AS4_ENST00000519694.1_RNA|HOXA9_ENST00000497089.1_5'Flank|HOXA10_ENST00000521421.1_5'UTR|HOXA-AS4_ENST00000523790.1_RNA|RP1-170O19.20_ENST00000470747.4_Intron|HOXA-AS4_ENST00000519935.1_RNA	NM_018951.3	NP_061824.3	P31260	HXA10_HUMAN	homeobox A10	358					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|male gonad development (GO:0008584)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	9						TAAGGTACATATTGAACAGAA	0.532																																					p.N358N		Atlas-SNP	.											.	HOXA10	55	.	0			c.T1074C						.						115	110	112					7																	27211677		2203	4300	6503	SO:0001819	synonymous_variant	3206	exon2			GTACATATTGAAC		CCDS5410.2	7p15.2	2011-06-20	2005-12-22		ENSG00000253293	ENSG00000253293		"Homeoboxes / ANTP class : HOXL subclass"	5100	protein-coding gene	gene with protein product		142957	"homeo box A10"	HOX1H, HOX1		1973146, 1358459	Standard	NR_037939		Approved		uc011jzm.2	P31260	OTTHUMG00000023436	ENST00000283921.4:c.1074T>C	chr7.hg19:g.27211677A>G		124.0	0.0		146.0	38.0	NM_018951	O43370|O43605|Q15949|Q504T1	Silent	SNP	ENST00000283921.4	hg19	CCDS5410.2																																																																																			.	.		0.532	HOXA10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358724.2			G	27211677	A	G	27211677	2	3	163	1	0	0	0	0	0	0	0	1	7298	446	16	2		2	HOXA10	7	27211677	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	4047311	27211677	131926986	112	24894										
NPSR1	387129	hgsc.bcm.edu	37	chr7	34889208	34889208	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cacaggattccagaatgacgTtccgggagagaactgagagg	14	8	0	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:34889208T>G	ENST00000360581.1	+	9	1185	c.1057T>G	c.(1057-1059)Ttc>Gtc	p.F353V	NPSR1_ENST00000359791.1_Intron|NPSR1_ENST00000531252.1_Intron|NPSR1_ENST00000381542.1_Missense_Mutation_p.F287V|NPSR1_ENST00000381539.3_Missense_Mutation_p.V386G	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	353						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)	p.F353I(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	CAGAATGACGTTCCGGGAGAG	0.468																																					p.F353V		Atlas-SNP	.											NPSR1,NS,carcinoma,0,1	NPSR1	134	.	1	Substitution - Missense(1)	lung(1)	c.T1057G						.						134	125	128					7																	34889208		2203	4300	6503	SO:0001583	missense	387129	exon9			ATGACGTTCCGGG	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"GPCR / Class A : Neuropeptide receptors : S"	23631	protein-coding gene	gene with protein product		608595	"G protein-coupled receptor 154"	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.1057T>G	chr7.hg19:g.34889208T>G	ENSP00000353788:p.Phe353Val	145.0	0.0		144.0	36.0	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	hg19	CCDS5444.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.43|11.43	1.635227|1.635227	0.29068|0.29068	.|.	.|.	ENSG00000187258|ENSG00000187258	ENST00000360581;ENST00000381542;ENST00000334481|ENST00000381539	T;T|T	0.36340|0.73789	1.26;1.26|-0.78	5.24|5.24	2.84|2.84	0.33178|0.33178	.|.	.|4.249060	.|0.00166	.|N	.|0.000016	T|T	0.63022|0.63022	0.2476|0.2476	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	B;B|B	0.19706|0.21905	0.038;0.009|0.062	B;B|B	0.21708|0.18561	0.036;0.004|0.022	T|T	0.45101|0.45101	-0.9284|-0.9284	9|10	0.17369|0.35671	T|T	0.5|0.21	7.4597|7.4597	2.8287|2.8287	0.05492|0.05492	0.1455:0.078:0.1518:0.6248|0.1455:0.078:0.1518:0.6248	.|.	287;353|386	Q6W5P4-2;Q6W5P4|Q6W5P4-3	.;NPSR1_HUMAN|.	V|G	353;287;156|386	ENSP00000353788:F353V;ENSP00000370953:F287V|ENSP00000370950:V386G	ENSP00000334093:F156V|ENSP00000370950:V386G	F|V	+|+	1|2	0|0	NPSR1|NPSR1	34855733|34855733	0.002000|0.002000	0.14202|0.14202	0.001000|0.001000	0.08648|0.08648	0.337000|0.337000	0.28794|0.28794	1.264000|1.264000	0.33015|0.33015	0.443000|0.443000	0.26582|0.26582	0.454000|0.454000	0.30748|0.30748	TTC|GTT	.	.		0.468	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173		G	34889208	T	G	34889208	3	3	163	1	0	0	0	0	1	0	0	0	10609	1725	60	5	1091	5	NPSR1	7	34889208	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	7677531	34889208	124249455	113	24895										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48550698	48550698	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agctcttttacttggtttccGtctgcctgtgtgttgccgtt	10	10	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:48550698G>C	ENST00000435803.1	+	51	13567	c.13543G>C	c.(13543-13545)Gtc>Ctc	p.V4515L	ABCA13_ENST00000544596.1_Missense_Mutation_p.V245L	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4515					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTTGGTTTCCGTCTGCCTGTG	0.433																																					p.V4515L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G13543C						.						107	104	105					7																	48550698		1919	4124	6043	SO:0001583	missense	154664	exon51			GTTTCCGTCTGCC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.13543G>C	chr7.hg19:g.48550698G>C	ENSP00000411096:p.Val4515Leu	62.0	0.0		79.0	18.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.095348|4.095348	0.76870|0.76870	.|.	.|.	ENSG00000179869|ENSG00000179869	ENST00000435451|ENST00000435803;ENST00000411975;ENST00000544596	.|T;T;T	.|0.78246	.|-1.16;-1.16;-1.16	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	.|0.000000	.|0.43260	.|D	.|0.000584	D|D	0.85647|0.85647	0.5745|0.5745	L|L	0.60067|0.60067	1.865|1.865	0.43617|0.43617	D|D	0.995995|0.995995	.|D;D;D	.|0.89917	.|0.961;0.999;1.0	.|P;D;D	.|0.74023	.|0.814;0.978;0.982	D|D	0.86504|0.86504	0.1805|0.1805	5|10	.|0.62326	.|D	.|0.03	.|.	16.1838|16.1838	0.81934|0.81934	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|245;2217;4515	.|F5H7B7;Q86UQ4-3;Q86UQ4	.|.;.;ABCAD_HUMAN	P|L	35|4515;288;245	.|ENSP00000411096:V4515L;ENSP00000391042:V288L;ENSP00000442634:V245L	.|ENSP00000391042:V288L	R|V	+|+	2|1	0|0	ABCA13|ABCA13	48521244|48521244	0.957000|0.957000	0.32711|0.32711	0.996000|0.996000	0.52242|0.52242	0.913000|0.913000	0.54294|0.54294	3.561000|3.561000	0.53770|0.53770	2.535000|2.535000	0.85469|0.85469	0.563000|0.563000	0.77884|0.77884	CGT|GTC	.	.		0.433	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48550698	G	C	48550698	3	2	163	1	0	0	0	0	1	0	0	0	31	1145	40	4	13574	4	ABCA13	7	48550698	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	13661490	48550698	110587965	114	24896										
COBL	23242	hgsc.bcm.edu	37	chr7	51095925	51095925	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtagacaacttcctgtgtggGccaatgacctcccccctagg	10	14	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:51095925G>C	ENST00000265136.7	-	10	3033	c.2868C>G	c.(2866-2868)ggC>ggG	p.G956G	COBL_ENST00000395542.2_Silent_p.G1038G	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	956					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TCCTGTGTGGGCCAATGACCT	0.567																																					p.G956G	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C2868G						.						73	68	70					7																	51095925		2203	4300	6503	SO:0001819	synonymous_variant	23242	exon10			GTGTGGGCCAATG	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.2868C>G	chr7.hg19:g.51095925G>C		108.0	0.0		135.0	25.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	hg19	CCDS34637.1																																																																																			.	.		0.567	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		C	51095925	G	C	51095925	2	2	163	1	0	0	0	0	0	0	0	1	3655	1190	42	4		4	COBL	7	51095925	Silent	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	2545227	51095925	108042738	115	24897										
ZNF107	51427	hgsc.bcm.edu	37	chr7	64167010	64167010	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acttcaaatgtaaagaatgtAgcaaatcattttgcgtgctt	7	6	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:64167010A>T	ENST00000395391.1	+	4	1703	c.328A>T	c.(328-330)Agc>Tgc	p.S110C	ZNF107_ENST00000344930.3_Missense_Mutation_p.S110C|ZNF107_ENST00000423627.1_Missense_Mutation_p.S110C			Q9UII5	ZN107_HUMAN	zinc finger protein 107	110					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				TAAAGAATGTAGCAAATCATT	0.308																																					p.S110C		Atlas-SNP	.											.	ZNF107	107	.	0			c.A328T						.						31	31	31					7																	64167010		2201	4300	6501	SO:0001583	missense	51427	exon7			GAATGTAGCAAAT	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"Zinc fingers, C2H2-type"	12887	protein-coding gene	gene with protein product		603989	"zinc finger protein 588", "zinc finger protein 107 (Y8)"	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.328A>T	chr7.hg19:g.64167010A>T	ENSP00000378789:p.Ser110Cys	151.0	0.0		178.0	29.0	NM_016220		Missense_Mutation	SNP	ENST00000395391.1	hg19	CCDS5527.1	.	.	.	.	.	.	.	.	.	.	.	13.44	2.236636	0.39498	.	.	ENSG00000196247	ENST00000541526;ENST00000344930;ENST00000423627;ENST00000395391	T;T;T	0.30714	1.52;1.52;1.52	0.916	-1.83	0.07833	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32102	0.0818	L	0.35341	1.055	0.21604	N	0.999622	D	0.58268	0.982	P	0.61275	0.886	T	0.17018	-1.0383	8	.	.	.	.	4.0134	0.09632	0.5373:0.0:0.4627:0.0	.	110	Q9UII5	ZN107_HUMAN	C	110	ENSP00000343443:S110C;ENSP00000400037:S110C;ENSP00000378789:S110C	.	S	+	1	0	ZNF107	63804445	0.998000	0.40836	0.127000	0.21898	0.126000	0.20510	1.464000	0.35288	-0.721000	0.04929	-0.718000	0.03613	AGC	.	.		0.308	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		T	64167010	A	T	64167010	3	4	163	1	0	0	0	0	1	0	0	0	17730	420	15	4	334	4	ZNF107	7	64167010	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	13071085	64167010	94971653	116	24898										
LAT2	7462	hgsc.bcm.edu	37	chr7	73639059	73639059	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cgtgaatggggaggtggcagCcacagaagcctagggcagac	17	9	0	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:73639059C>A	ENST00000460943.1	+	13	1608	c.719C>A	c.(718-720)gCc>gAc	p.A240D	LAT2_ENST00000344995.5_Missense_Mutation_p.A240D|LAT2_ENST00000275635.7_Missense_Mutation_p.A240D|LAT2_ENST00000398475.1_Missense_Mutation_p.A240D	NM_032464.2	NP_115853.2	Q9UHI5	LAT2_HUMAN	linker for activation of T cells family, member 2	0					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6					L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	GAGGTGGCAGCCACAGAAGCC	0.622																																					p.A240D		Atlas-SNP	.											.	LAT2	24	.	0			c.C719A						.						21	25	23					7																	73639059		2011	4181	6192	SO:0001583	missense	7462	exon13			TGGCAGCCACAGA	AF257135	CCDS5566.2	7q11.23	2011-11-01	2005-04-26	2005-04-26	ENSG00000086730	ENSG00000086730			12749	protein-coding gene	gene with protein product	"linker for activation of B cells", "non-T cell activation linker", "linker for activation of T cells, transmembrane adaptor 2"	605719	"Williams-Beuren syndrome chromosome region 5"	WBSCR15, WBSCR5		8812460, 12514734	Standard	NM_032464		Approved	WSCR5, HSPC046, LAB, NTAL	uc003uai.3	Q9GZY6	OTTHUMG00000130151	ENST00000460943.1:c.719C>A	chr7.hg19:g.73639059C>A	ENSP00000420494:p.Ala240Asp	56.0	0.0		85.0	23.0	NM_032464	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000460943.1	hg19	CCDS5566.2	.	.	.	.	.	.	.	.	.	.	c	14.18	2.458036	0.43634	.	.	ENSG00000086730	ENST00000344995;ENST00000460943;ENST00000398475;ENST00000275635	.	.	.	3.31	0.407	0.16371	.	2.940010	0.00958	N	0.003078	T	0.38214	0.1032	L	0.29908	0.895	0.09310	N	1	P	0.48503	0.911	P	0.52481	0.7	T	0.16988	-1.0384	9	0.72032	D	0.01	-0.9253	3.613	0.08067	0.0:0.5464:0.2096:0.244	.	240	Q9GZY6	NTAL_HUMAN	D	240	.	ENSP00000275635:A240D	A	+	2	0	LAT2	73276995	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.132000	0.15891	0.068000	0.16574	-0.451000	0.05528	GCC	.	.		0.622	LAT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277062.1			A	73639059	C	A	73639059	3	1	163	1	0	0	0	0	1	0	0	0	8654	739	26	3	761	3	LAT2	7	73639059	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	9472049	73639059	85499604	117	24899										
PTPN12	5782	hgsc.bcm.edu	37	chr7	77256052	77256052	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaaggggatgctaaagaagaAatactgcagccaccggaacc	12	9	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:77256052A>C	ENST00000248594.6	+	13	1328	c.1056A>C	c.(1054-1056)gaA>gaC	p.E352D	PTPN12_ENST00000415482.2_Missense_Mutation_p.E233D|PTPN12_ENST00000435495.2_Missense_Mutation_p.E222D	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	352	Interaction with TGFB1I1. {ECO:0000250}.				protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						CTAAAGAAGAAATACTGCAGC	0.428																																					p.E352D		Atlas-SNP	.											.	PTPN12	83	.	0			c.A1056C						.						83	79	80					7																	77256052		2203	4300	6503	SO:0001583	missense	5782	exon13			AGAAGAAATACTG		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.1056A>C	chr7.hg19:g.77256052A>C	ENSP00000248594:p.Glu352Asp	76.0	0.0		93.0	25.0	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	hg19	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.520142	0.64747	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.32515	1.45;1.45;1.45	6.17	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.49423	0.1556	L	0.55103	1.725	0.47994	D	0.999561	D	0.89917	1.0	D	0.80764	0.994	T	0.47761	-0.9092	10	0.59425	D	0.04	.	12.5474	0.56208	0.9349:0.0:0.0651:0.0	.	352	Q05209	PTN12_HUMAN	D	352;233;233;222	ENSP00000248594:E352D;ENSP00000392429:E233D;ENSP00000397991:E222D	ENSP00000248594:E352D	E	+	3	2	PTPN12	77093988	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.885000	0.56182	1.119000	0.41883	0.533000	0.62120	GAA	.	.		0.428	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			C	77256052	A	C	77256052	3	2	163	1	0	0	0	0	1	0	0	0	12794	11	1	5	1106	5	PTPN12	7	77256052	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	3616993	77256052	81882611	118	24900										
GNAT3	346562	hgsc.bcm.edu	37	chr7	80117908	80117908	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtcatggctttcacaatagcTaggatggattgcaatgtatt	10	6	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:80117908T>A	ENST00000398291.3	-	3	339	c.246A>T	c.(244-246)ctA>ctT	p.L82L	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	82					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						TCACAATAGCTAGGATGGATT	0.363																																					p.L82L		Atlas-SNP	.											.	GNAT3	65	.	0			c.A246T						.						129	115	119					7																	80117908		1899	4112	6011	SO:0001819	synonymous_variant	346562	exon3			AATAGCTAGGATG		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.246A>T	chr7.hg19:g.80117908T>A		72.0	0.0		80.0	18.0	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Silent	SNP	ENST00000398291.3	hg19	CCDS47625.1																																																																																			.	.		0.363	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370		A	80117908	T	A	80117908	2	1	163	1	0	0	0	0	0	0	0	1	6521	1509	53	4		4	GNAT3	7	80117908	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	2861856	80117908	79020755	119	24901										
HGF	3082	hgsc.bcm.edu	37	chr7	81331975	81331975	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gctactcggacaaaaataccAggacgatttggaatggcaca	10	9	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:81331975A>T	ENST00000222390.5	-	18	2335	c.2109T>A	c.(2107-2109)ccT>ccA	p.P703P	HGF_ENST00000457544.2_Silent_p.P698P	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	703	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						CAAAAATACCAGGACGATTTG	0.403																																					p.P703P		Atlas-SNP	.											.	HGF	171	.	0			c.T2109A						.						133	126	128					7																	81331975		2203	4299	6502	SO:0001819	synonymous_variant	3082	exon18			AATACCAGGACGA		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.2109T>A	chr7.hg19:g.81331975A>T		280.0	0.0		357.0	78.0	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Silent	SNP	ENST00000222390.5	hg19	CCDS5597.1																																																																																			.	.		0.403	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		T	81331975	A	T	81331975	2	4	163	1	0	0	0	0	0	0	0	1	7094	175	7	4		4	HGF	7	81331975	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1214067	81331975	77806688	120	24902										
PCLO	27445	hgsc.bcm.edu	37	chr7	82595396	82595396	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggggttggctttttttcttcTaggagtggctttttttcttc	11	6	3	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:82595396T>A	ENST00000333891.9	-	4	4045	c.3708A>T	c.(3706-3708)ctA>ctT	p.L1236L	PCLO_ENST00000423517.2_Silent_p.L1236L	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTTTTTCTTCTAGGAGTGGCT	0.388																																					p.L1236L		Atlas-SNP	.											.	PCLO	1506	.	0			c.A3708T						.						229	222	224					7																	82595396		1801	4074	5875	SO:0001819	synonymous_variant	27445	exon4			TTCTTCTAGGAGT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.3708A>T	chr7.hg19:g.82595396T>A		127.0	0.0		179.0	41.0	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.388	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82595396	T	A	82595396	2	1	163	1	0	0	0	0	0	0	0	1	11592	1509	53	4		4	PCLO	7	82595396	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	1263421	82595396	76543267	121	24903										
GRM3	2913	hgsc.bcm.edu	37	chr7	86394697	86394698	+	Frame_Shift_Ins	INS	-	-	C													0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttgtttgctattgatgaaatINScaacaaagatgattacttgc							TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:86394697_86394698insC	ENST00000361669.2	+	2	1335_1336	c.236_237insC	c.(235-240)atcaacfs	p.N80fs	GRM3_ENST00000536043.1_Intron|GRM3_ENST00000439827.1_Frame_Shift_Ins_p.N80fs|GRM3_ENST00000546348.1_Intron|GRM3_ENST00000394720.2_Frame_Shift_Ins_p.N78fs	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	80					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					ATTGATGAAATCAACAAAGATG	0.426																																					p.I79fs	GBM(52;969 1098 3139 52280)	Atlas-INDEL	.											.	GRM3	237	.	0			c.236_237insC						.																																			SO:0001589	frameshift_variant	2913	exon2			.		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.237dupC	chr7.hg19:g.86394698_86394698dupC	ENSP00000355316:p.Asn80fs	85.0	0.0		118.0	31.0	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Frame_Shift_Ins	INS	ENST00000361669.2	hg19	CCDS5600.1																																																																																			.	.		0.426	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			C	86394698	-	C	86394697	7	5	163	1	0	1	1	0	0	0	0	0	6807	1435	50	0	238	0	GRM3	7	86394697	Frame_Shift_Ins	INS	-	TCGA-DD-AACL-01A-11D-A40R-10	3799301	86394697	72743966	122	24904										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94053728	94053728	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cctggctcgagaggtgaacgTggtctaccaggtgttgctgg	16	9	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:94053728T>C	ENST00000297268.6	+	41	3117	c.2646T>C	c.(2644-2646)cgT>cgC	p.R882R		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	882					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GAGGTGAACGTGGTCTACCAG	0.473										HNSCC(75;0.22)																											p.R882R		Atlas-SNP	.											.	COL1A2	240	.	0			c.T2646C						.						159	148	152					7																	94053728		2203	4300	6503	SO:0001819	synonymous_variant	1278	exon41			TGAACGTGGTCTA	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.2646T>C	chr7.hg19:g.94053728T>C		72.0	0.0		95.0	18.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	hg19	CCDS34682.1																																																																																			.	.		0.473	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		C	94053728	T	C	94053728	2	2	163	1	0	0	0	0	0	0	0	1	3680	1683	59	2		2	COL1A2	7	94053728	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	7659031	94053728	65084935	123	24905										
LHFPL3	375612	hgsc.bcm.edu	37	chr7	103969251	103969251	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cccggagccgccgccgctgcCgccgccgccgccgccgcgat	14	23	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:103969251C>T	ENST00000535008.1	+	1	148	c.24C>T	c.(22-24)gcC>gcT	p.A8A	LHFPL3_ENST00000424859.1_5'UTR|LHFPL3_ENST00000543266.1_Silent_p.A8A|LHFPL3_ENST00000401970.2_5'UTR			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	8						integral component of membrane (GO:0016021)		p.A8A(1)		kidney(1)|large_intestine(2)|lung(6)	9						ccgccgctgccgccgccgccg	0.721																																					p.A8A		Atlas-SNP	.											LHFPL3,NS,carcinoma,0,1	LHFPL3	24	.	1	Substitution - coding silent(1)	kidney(1)	c.C24T						.						11	14	13					7																	103969251		1949	4092	6041	SO:0001819	synonymous_variant	375612	exon1			CGCTGCCGCCGCC	AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416			6589	protein-coding gene	gene with protein product		609719	"lipoma HMGIC fusion partner-like 4"	LHFPL4		10329012	Standard	NM_199000		Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000535008.1:c.24C>T	chr7.hg19:g.103969251C>T		31.0	1.0		45.0	2.0	NM_199000	A1L383|A4D0Q5	Silent	SNP	ENST00000535008.1	hg19																																																																																				.	.		0.721	LHFPL3-201	KNOWN	basic	protein_coding	protein_coding		NM_199000		T	103969251	C	T	103969251	2	4	163	1	0	0	0	0	0	0	0	1	8775	639	23	1		1	LHFPL3	7	103969251	Silent	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	9915523	103969251	55169412	124	24906										
CDHR3	222256	hgsc.bcm.edu	37	chr7	105653379	105653379	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agttctgctttgatgatgacAgtgaggcaccaaacaacaga	10	8	1	5			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:105653379A>T	ENST00000317716.9	+	9	1206	c.1126A>T	c.(1126-1128)Agt>Tgt	p.S376C	CDHR3_ENST00000478080.1_Missense_Mutation_p.S288C|CDHR3_ENST00000343407.5_Missense_Mutation_p.S93C|CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000542731.1_Missense_Mutation_p.S376C|CDHR3_ENST00000541203.1_3'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	376	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						TGATGATGACAGTGAGGCACC	0.478																																					p.S376C		Atlas-SNP	.											.	CDHR3	153	.	0			c.A1126T						.						233	222	225					7																	105653379		2009	4199	6208	SO:0001583	missense	222256	exon9			GATGACAGTGAGG	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"Cadherins / Cadherin-related"	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1126A>T	chr7.hg19:g.105653379A>T	ENSP00000325954:p.Ser376Cys	99.0	0.0		135.0	37.0	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	hg19	CCDS47684.1	.	.	.	.	.	.	.	.	.	.	A	18.22	3.575601	0.65878	.	.	ENSG00000128536	ENST00000542731;ENST00000343407;ENST00000317716;ENST00000478080;ENST00000466045	T;T;T;T;T	0.61859	0.21;0.41;0.21;0.07;0.41	5.23	1.4	0.22301	Cadherin (3);Cadherin-like (1);	0.327119	0.28958	N	0.013592	T	0.53658	0.1810	L	0.57536	1.79	0.30839	N	0.735842	P;D;P;P	0.61080	0.904;0.989;0.947;0.947	P;P;P;P	0.50192	0.634;0.608;0.527;0.527	T	0.58148	-0.7687	10	0.87932	D	0	-8.7428	2.9229	0.05774	0.4106:0.2503:0.3391:0.0	.	93;363;376;288	Q6ZTQ4-2;B3KYA0;Q6ZTQ4;B7Z8X2	.;.;CDHR3_HUMAN;.	C	376;93;376;288;134	ENSP00000439766:S376C;ENSP00000341510:S93C;ENSP00000325954:S376C;ENSP00000417771:S288C;ENSP00000419017:S134C	ENSP00000325954:S376C	S	+	1	0	CDHR3	105440615	0.912000	0.30974	0.992000	0.48379	0.922000	0.55478	1.126000	0.31344	0.295000	0.22570	-0.514000	0.04452	AGT	.	.		0.478	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		T	105653379	A	T	105653379	3	4	163	1	0	0	0	0	1	0	0	0	3122	188	7	4	1160	4	CDHR3	7	105653379	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1684128	105653379	53485284	125	24907										
WNT2	7472	hgsc.bcm.edu	37	chr7	116960675	116960675	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cctgtccagggtgttgcaatTccagcggtgctggcggaact	14	11	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:116960675T>A	ENST00000265441.3	-	2	555	c.256A>T	c.(256-258)Aat>Tat	p.N86Y	AC002465.2_ENST00000436097.1_RNA	NM_003391.2	NP_003382.1	P09544	WNT2_HUMAN	wingless-type MMTV integration site family member 2	86					atrial cardiac muscle tissue morphogenesis (GO:0055009)|canonical Wnt signaling pathway (GO:0060070)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|iris morphogenesis (GO:0061072)|labyrinthine layer blood vessel development (GO:0060716)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|lung induction (GO:0060492)|mammary gland epithelium development (GO:0061180)|neuron differentiation (GO:0030182)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(2)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|ovary(3)|prostate(1)|skin(2)	31	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		GTGTTGCAATTCCAGCGGTGC	0.587																																					p.N86Y		Atlas-SNP	.											.	WNT2	56	.	0			c.A256T						.						80	62	68					7																	116960675		2203	4300	6503	SO:0001583	missense	7472	exon2			TGCAATTCCAGCG	X07876	CCDS5771.1	7q31	2013-02-28			ENSG00000105989	ENSG00000105989		"Wingless-type MMTV integration sites", "Endogenous ligands"	12780	protein-coding gene	gene with protein product	"secreted growth factor"	147870		INT1L1		2971536	Standard	NM_003391		Approved	IRP	uc003viz.3	P09544	OTTHUMG00000023428	ENST00000265441.3:c.256A>T	chr7.hg19:g.116960675T>A	ENSP00000265441:p.Asn86Tyr	63.0	0.0		91.0	20.0	NM_003391	A4D0V1|Q75N05|Q9UDP9	Missense_Mutation	SNP	ENST00000265441.3	hg19	CCDS5771.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.234526	0.79800	.	.	ENSG00000105989	ENST00000265441;ENST00000491214	D;D	0.83837	-1.77;-1.77	5.28	5.28	0.74379	.	0.045054	0.85682	D	0.000000	D	0.94079	0.8102	H	0.98769	4.325	0.52501	D	0.999954	D	0.89917	1.0	D	0.81914	0.995	D	0.94839	0.8003	10	0.87932	D	0	.	9.166	0.37052	0.0:0.0903:0.0:0.9097	.	86	P09544	WNT2_HUMAN	Y	86	ENSP00000265441:N86Y;ENSP00000419466:N86Y	ENSP00000265441:N86Y	N	-	1	0	WNT2	116747911	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.014000	0.49590	2.105000	0.64084	0.533000	0.62120	AAT	.	.		0.587	WNT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059749.3	NM_003391		A	116960675	T	A	116960675	3	1	163	1	0	0	0	0	1	0	0	0	17401	1783	62	4	842	4	WNT2	7	116960675	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	11307296	116960675	42177988	126	24908										
NDUFA5	4698	hgsc.bcm.edu	37	chr7	123190558	123190558	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccagcttctcatttgtaatcTgttctgtatactttctatat	4	9	4	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:123190558T>A	ENST00000355749.2	-	3	608	c.149A>T	c.(148-150)cAg>cTg	p.Q50L	NDUFA5_ENST00000471770.1_Missense_Mutation_p.Q50L|NDUFA5_ENST00000467117.1_5'UTR	NM_001282419.1|NM_005000.2	NP_001269348.1|NP_004991.1	Q16718	NDUA5_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5	50					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			large_intestine(1)|urinary_tract(1)	2						ATTTGTAATCTGTTCTGTATA	0.328																																					p.Q50L		Atlas-SNP	.											.	NDUFA5	6	.	0			c.A149T						.						112	119	117					7																	123190558		2203	4299	6502	SO:0001583	missense	4698	exon3			GTAATCTGTTCTG		CCDS5788.1, CCDS64760.1, CCDS75655.1, CCDS75656.1	7q31.33	2013-06-19	2013-06-19		ENSG00000128609	ENSG00000128609		"Mitochondrial respiratory chain complex / Complex I"	7688	protein-coding gene	gene with protein product	"complex I 13kDa subunit B", "ubiquinone reductase", "type I dehydrogenase", "NADH-ubiquinone oxidoreductase 13 kDa-B subunit"	601677	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5 (13kD, B13)", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDa"			9763677, 9021153	Standard	XM_005250371		Approved	B13, NUFM, CI-13KD-B, UQOR13, CI-13kB	uc003vks.3	Q16718	OTTHUMG00000157348	ENST00000355749.2:c.149A>T	chr7.hg19:g.123190558T>A	ENSP00000347988:p.Gln50Leu	46.0	0.0		76.0	19.0	NM_005000	B2RD98|Q5H9R2|Q6IRX7	Missense_Mutation	SNP	ENST00000355749.2	hg19	CCDS5788.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.409625	0.83340	.	.	ENSG00000128609	ENST00000471770;ENST00000355749;ENST00000470123	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	T	0.76793	0.4037	M	0.78049	2.395	0.80722	D	1	D	0.57257	0.979	P	0.60886	0.88	T	0.78615	-0.2135	8	0.49607	T	0.09	.	14.9406	0.70992	0.0:0.0:0.0:1.0	.	50	Q16718	NDUA5_HUMAN	L	50;50;60	.	ENSP00000347988:Q50L	Q	-	2	0	NDUFA5	122977794	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.448000	0.60027	2.220000	0.72140	0.533000	0.62120	CAG	.	.		0.328	NDUFA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348533.1	NM_005000		A	123190558	T	A	123190558	3	1	163	1	0	0	0	0	1	0	0	0	10277	1580	55	4	213	4	NDUFA5	7	123190558	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	6229883	123190558	35948105	127	24909										
METTL2B	55798	hgsc.bcm.edu	37	chr7	128141930	128141930	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aatgtaccgggtttggattcAgtgcaaatactgcaagcccc	10	10	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:128141930A>T	ENST00000262432.8	+	9	1134	c.1097A>T	c.(1096-1098)cAg>cTg	p.Q366L	METTL2B_ENST00000480046.1_Missense_Mutation_p.Q301L	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	366					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GTTTGGATTCAGTGCAAATAC	0.502																																					p.Q366L		Atlas-SNP	.											.	METTL2B	34	.	0			c.A1097T						.						154	157	156					7																	128141930		2203	4300	6503	SO:0001583	missense	55798	exon9			GGATTCAGTGCAA	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"methyltransferase like 2"	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.1097A>T	chr7.hg19:g.128141930A>T	ENSP00000262432:p.Gln366Leu	126.0	0.0		194.0	36.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	hg19	CCDS5803.2	.	.	.	.	.	.	.	.	.	.	A	20.6	4.022651	0.75275	.	.	ENSG00000165055	ENST00000262432;ENST00000480046	T;T	0.03717	3.83;3.83	3.44	3.44	0.39384	.	0.000000	0.85682	D	0.000000	T	0.21550	0.0519	H	0.94886	3.595	0.80722	D	1	D;D	0.64830	0.994;0.99	D;P	0.63877	0.919;0.847	T	0.05178	-1.0901	10	0.87932	D	0	-0.129	10.1503	0.42788	1.0:0.0:0.0:0.0	.	301;366	Q6P1Q9-2;Q6P1Q9	.;MTL2B_HUMAN	L	366;301	ENSP00000262432:Q366L;ENSP00000418402:Q301L	ENSP00000262432:Q366L	Q	+	2	0	METTL2B	127929166	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	8.496000	0.90485	1.548000	0.49413	0.164000	0.16699	CAG	.	.		0.502	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396		T	128141930	A	T	128141930	3	4	163	1	0	0	0	0	1	0	0	0	9509	188	7	4	1131	4	METTL2B	7	128141930	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	4951372	128141930	30996733	128	24910										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131833393	131833393	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agatcatccttgccccacttCcttgtcgccactctgccaaa	5	17	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:131833393C>T	ENST00000359827.3	-	26	5635	c.4673G>A	c.(4672-4674)gGa>gAa	p.G1558E	PLXNA4_ENST00000321063.4_Missense_Mutation_p.G1558E			Q9HCM2	PLXA4_HUMAN	plexin A4	1558					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TGCCCCACTTCCTTGTCGCCA	0.547																																					p.G1558E		Atlas-SNP	.											.	PLXNA4	873	.	0			c.G4673A						.						124	122	122					7																	131833393		2150	4285	6435	SO:0001583	missense	91584	exon26			CCACTTCCTTGTC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.4673G>A	chr7.hg19:g.131833393C>T	ENSP00000352882:p.Gly1558Glu	53.0	0.0		42.0	8.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.943076	0.73672	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.13196	2.61;2.61	4.62	4.62	0.57501	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.217226	0.48286	D	0.000197	T	0.35248	0.0925	M	0.80982	2.52	0.58432	D	0.999997	D	0.62365	0.991	D	0.64237	0.923	T	0.09530	-1.0670	10	0.54805	T	0.06	.	12.1193	0.53883	0.0:0.6759:0.3241:0.0	.	1558	Q9HCM2	PLXA4_HUMAN	E	1558	ENSP00000323194:G1558E;ENSP00000352882:G1558E	ENSP00000323194:G1558E	G	-	2	0	PLXNA4	131483933	0.972000	0.33761	1.000000	0.80357	0.985000	0.73830	1.945000	0.40273	2.401000	0.81631	0.561000	0.74099	GGA	.	.		0.547	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131833393	C	T	131833393	3	4	163	1	0	0	0	0	1	0	0	0	12131	855	30	3	1039	3	PLXNA4	7	131833393	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	3691463	131833393	27305270	129	24911										
EXOC4	60412	hgsc.bcm.edu	37	chr7	133749242	133749242	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	atctgcgagcaggctgccatCaagcaagccaccaaggacaa	10	13	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:133749242C>A	ENST00000253861.4	+	18	2915	c.2886C>A	c.(2884-2886)atC>atA	p.I962I	EXOC4_ENST00000539845.1_Silent_p.I861I|EXOC4_ENST00000545148.1_Silent_p.I572I|EXOC4_ENST00000541309.1_Silent_p.I250I	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	962					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				AGGCTGCCATCAAGCAAGCCA	0.572																																					p.I962I		Atlas-SNP	.											.	EXOC4	118	.	0			c.C2886A						.						87	78	81					7																	133749242		2203	4300	6503	SO:0001819	synonymous_variant	60412	exon18			TGCCATCAAGCAA	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"SEC8-like 1 (S. cerevisiae)"	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2886C>A	chr7.hg19:g.133749242C>A		32.0	0.0		32.0	8.0	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	hg19	CCDS5829.1																																																																																			.	.		0.572	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		A	133749242	C	A	133749242	2	1	163	1	0	0	0	0	0	0	0	1	5308	816	29	3		3	EXOC4	7	133749242	Silent	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	1915849	133749242	25389421	130	24912										
WDR91	29062	hgsc.bcm.edu	37	chr7	134894482	134894482	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	catacacctgcattaactgcTgcagctggtccacaatctta	6	13	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:134894482T>A	ENST00000354475.4	-	2	180	c.149A>T	c.(148-150)cAg>cTg	p.Q50L	WDR91_ENST00000485942.1_5'Flank|WDR91_ENST00000423565.1_Missense_Mutation_p.Q15L|WDR91_ENST00000344400.5_Missense_Mutation_p.Q50L	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	50										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						CATTAACTGCTGCAGCTGGTC	0.502																																					p.Q50L		Atlas-SNP	.											.	WDR91	82	.	0			c.A149T						.						93	93	93					7																	134894482		2203	4300	6503	SO:0001583	missense	29062	exon2			AACTGCTGCAGCT	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.149A>T	chr7.hg19:g.134894482T>A	ENSP00000346466:p.Gln50Leu	74.0	0.0		98.0	24.0	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	hg19	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	T	6.376	0.437569	0.12104	.	.	ENSG00000105875	ENST00000344400;ENST00000354475;ENST00000423565	T;T;T	0.61742	1.63;0.08;0.68	6.04	6.04	0.98038	.	0.055875	0.64402	D	0.000001	T	0.39332	0.1074	L	0.28694	0.88	0.58432	D	0.999999	B	0.13145	0.007	B	0.06405	0.002	T	0.28235	-1.0050	10	0.02654	T	1	-5.3735	10.3312	0.43823	0.2528:0.0:0.0:0.7472	.	50	A4D1P6	WDR91_HUMAN	L	50;50;15	ENSP00000340877:Q50L;ENSP00000346466:Q50L;ENSP00000392555:Q15L	ENSP00000340877:Q50L	Q	-	2	0	WDR91	134545022	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.954000	0.49113	2.317000	0.78254	0.459000	0.35465	CAG	.	.		0.502	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		A	134894482	T	A	134894482	3	1	163	1	0	0	0	0	1	0	0	0	17353	1580	55	4	2150	4	WDR91	7	134894482	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	1145240	134894482	24244181	131	24913										
TRYX3	136541	hgsc.bcm.edu	37	chr7	141952124	141952124	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aacatcggctctcaaaacacAtccatccgcaaaagacagga	6	13	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr7:141952124A>T	ENST00000552471.1	-	5	962	c.643T>A	c.(643-645)Tgt>Agt	p.C215S	PRSS58_ENST00000547058.2_Missense_Mutation_p.C215S			Q8IYP2	PRS58_HUMAN	protease, serine, 58	215	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	19						CTCAAAACACATCCATCCGCA	0.408																																					p.C215S		Atlas-SNP	.											.	PRSS58	41	.	0			c.T643A						.						61	65	64					7																	141952124		2203	4300	6503	SO:0001583	missense	136541	exon6			AAACACATCCATC		CCDS5871.1	7q34	2012-10-03			ENSG00000258223	ENSG00000258223	3.4.21.4	"Serine peptidases / Serine peptidases"	39125	protein-coding gene	gene with protein product	"trypsin X3"						Standard	NM_001001317		Approved	TRYX3	uc003vxc.4	Q8IYP2	OTTHUMG00000158565	ENST00000552471.1:c.643T>A	chr7.hg19:g.141952124A>T	ENSP00000446916:p.Cys215Ser	131.0	0.0		149.0	42.0	NM_001001317	B3KVJ6|D3DXD2	Missense_Mutation	SNP	ENST00000552471.1	hg19	CCDS5871.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.571396	0.86542	.	.	ENSG00000258223	ENST00000547058;ENST00000552471	D;D	0.86627	-2.15;-2.15	5.24	5.24	0.73138	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.92061	0.7484	M	0.88512	2.96	0.53005	D	0.99996	P	0.48162	0.906	P	0.53593	0.73	D	0.93167	0.6563	9	0.87932	D	0	.	11.4549	0.50176	1.0:0.0:0.0:0.0	.	215	Q8IYP2	PRS58_HUMAN	S	215	ENSP00000447588:C215S;ENSP00000446916:C215S	ENSP00000307206:C215S	C	-	1	0	PRSS58	141598602	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	6.520000	0.73773	2.199000	0.70637	0.533000	0.62120	TGT	.	.		0.408	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317		T	141952124	A	T	141952124	3	4	163	1	0	0	0	0	1	0	0	0	16619	217	8	4	86	4	TRYX3	7	141952124	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	7057642	141952124	17186539	132	24914										
MCPH1	79648	hgsc.bcm.edu	37	chr8	6266840	6266840	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtgtggtcatccaatggaacAgaaaattattcaaagacatt	8	6	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:6266840A>T	ENST00000344683.5	+	2	139	c.63A>T	c.(61-63)acA>acT	p.T21T	MCPH1_ENST00000519480.1_Silent_p.T21T|RP11-115C21.2_ENST00000523225.1_RNA|RP11-115C21.2_ENST00000500118.2_RNA|RP11-115C21.2_ENST00000606853.1_RNA|MCPH1_ENST00000522905.1_Silent_p.T21T	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	21	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		CCAATGGAACAGAAAATTATT	0.378																																					p.T21T	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.A63T						.						160	150	153					8																	6266840		1882	4113	5995	SO:0001819	synonymous_variant	79648	exon2			TGGAACAGAAAAT	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.63A>T	chr8.hg19:g.6266840A>T		74.0	0.0		102.0	17.0	NM_001172575	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	hg19	CCDS43689.1																																																																																			.	.		0.378	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		T	6266840	A	T	6266840	2	4	163	1	0	0	0	0	0	0	0	1	9407	175	7	4		4	MCPH1	8	6266840	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		6266840	140097182	133	24915										
PTK2B	2185	hgsc.bcm.edu	37	chr8	27294711	27294711	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tggacaacaaggagaagttcAtgagcgaggcaggtagggac	16	6	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:27294711A>G	ENST00000397501.1	+	21	2222	c.1414A>G	c.(1414-1416)Atg>Gtg	p.M472V	PTK2B_ENST00000346049.5_Missense_Mutation_p.M472V|PTK2B_ENST00000544172.1_Missense_Mutation_p.M472V|PTK2B_ENST00000338238.4_Missense_Mutation_p.M472V|PTK2B_ENST00000517339.1_Missense_Mutation_p.M472V|PTK2B_ENST00000397497.4_Missense_Mutation_p.M218V|PTK2B_ENST00000420218.2_Missense_Mutation_p.M472V	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	472	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	GGAGAAGTTCATGAGCGAGGC	0.537																																					p.M472V		Atlas-SNP	.											.	PTK2B	304	.	0			c.A1414G						.						121	111	114					8																	27294711		2203	4300	6503	SO:0001583	missense	2185	exon21			AAGTTCATGAGCG	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"protein tyrosine kinase 2 beta", "PTK2B protein tyrosine kinase 2 beta"	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.1414A>G	chr8.hg19:g.27294711A>G	ENSP00000380638:p.Met472Val	85.0	0.0		83.0	21.0	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Missense_Mutation	SNP	ENST00000397501.1	hg19	CCDS6057.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.238444	0.39598	.	.	ENSG00000120899	ENST00000397501;ENST00000539100;ENST00000338238;ENST00000544172;ENST00000346049;ENST00000420218;ENST00000517339;ENST00000397497	D;D;D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62;-1.62;-1.62	5.47	1.67	0.24075	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.156962	0.64402	D	0.000001	T	0.59797	0.2220	N	0.04669	-0.19	0.49582	D	0.9998	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.0	T	0.47586	-0.9106	10	0.62326	D	0.03	.	3.6008	0.08024	0.6562:0.1373:0.0749:0.1315	.	218;472;472	E9PBI4;Q14289-2;Q14289	.;.;FAK2_HUMAN	V	472;477;472;472;472;472;472;218	ENSP00000380638:M472V;ENSP00000342242:M472V;ENSP00000440926:M472V;ENSP00000332816:M472V;ENSP00000391995:M472V;ENSP00000427931:M472V;ENSP00000380634:M218V	ENSP00000342242:M472V	M	+	1	0	PTK2B	27350628	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	2.459000	0.45023	0.113000	0.18004	0.528000	0.53228	ATG	.	.		0.537	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103		G	27294711	A	G	27294711	3	3	163	1	0	0	0	0	1	0	0	0	12776	217	8	2	1472	2	PTK2B	8	27294711	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	21027871	27294711	119069311	134	24916										
EXTL3	2137	hgsc.bcm.edu	37	chr8	28574021	28574021	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acaaggagctcatggcccagAaccagcccaagctgtccctg	10	15	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:28574021A>T	ENST00000220562.4	+	3	1347	c.445A>T	c.(445-447)Aac>Tac	p.N149Y	EXTL3_ENST00000523149.1_Intron|EXTL3_ENST00000519886.1_Intron	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	149					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)			biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		CATGGCCCAGAACCAGCCCAA	0.607																																					p.N149Y		Atlas-SNP	.											.	EXTL3	83	.	0			c.A445T						.						50	45	47					8																	28574021		2203	4300	6503	SO:0001583	missense	2137	exon3			GCCCAGAACCAGC	U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"Exostosin glycosyltransferase family"	3518	protein-coding gene	gene with protein product	"REG receptor", "glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"	605744	"exostoses (multiple)-like 3"			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.445A>T	chr8.hg19:g.28574021A>T	ENSP00000220562:p.Asn149Tyr	57.0	0.0		66.0	16.0	NM_001440	D3DST8|O00225|Q53XT3	Missense_Mutation	SNP	ENST00000220562.4	hg19	CCDS6070.1	.	.	.	.	.	.	.	.	.	.	A	17.82	3.482091	0.63849	.	.	ENSG00000012232	ENST00000220562	D	0.96427	-4.01	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.96830	0.8965	L	0.52573	1.65	0.80722	D	1	D	0.71674	0.998	D	0.64506	0.926	D	0.96486	0.9360	9	.	.	.	-24.3	14.7977	0.69889	1.0:0.0:0.0:0.0	.	149	O43909	EXTL3_HUMAN	Y	149	ENSP00000220562:N149Y	.	N	+	1	0	EXTL3	28629940	1.000000	0.71417	0.995000	0.50966	0.864000	0.49448	9.339000	0.96797	1.903000	0.55091	0.397000	0.26171	AAC	.	.		0.607	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440		T	28574021	A	T	28574021	3	4	163	1	0	0	0	0	1	0	0	0	5329	246	9	4	447	4	EXTL3	8	28574021	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1279310	28574021	117790001	135	24917										
DUSP4	1846	hgsc.bcm.edu	37	chr8	29195843	29195843	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	accaggagctgatgtcggccTtgtggttatcttccactggg	13	10	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:29195843T>A	ENST00000240100.2	-	3	1144	c.755A>T	c.(754-756)aAg>aTg	p.K252M	DUSP4_ENST00000240101.2_Missense_Mutation_p.K161M	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	252	Tyrosine-protein phosphatase.				endoderm formation (GO:0001706)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein dephosphorylation (GO:0006470)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			endometrium(1)|large_intestine(1)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		GATGTCGGCCTTGTGGTTATC	0.557																																					p.K252M		Atlas-SNP	.											.	DUSP4	58	.	0			c.A755T						.						184	154	164					8																	29195843		2203	4300	6503	SO:0001583	missense	1846	exon3			TCGGCCTTGTGGT	U21108	CCDS6072.1, CCDS6073.1	8p12-p11	2011-06-09			ENSG00000120875	ENSG00000120875		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3070	protein-coding gene	gene with protein product	"VH1 homologous phosphatase 2", "MAP kinase phosphatase 2"	602747				7535768, 9205128	Standard	NM_001394		Approved	HVH2, MKP-2, TYP	uc003xhm.3	Q13115	OTTHUMG00000133395	ENST00000240100.2:c.755A>T	chr8.hg19:g.29195843T>A	ENSP00000240100:p.Lys252Met	107.0	0.0		115.0	19.0	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Missense_Mutation	SNP	ENST00000240100.2	hg19	CCDS6072.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.294922	0.60086	.	.	ENSG00000120875	ENST00000240100;ENST00000240101	D;D	0.86097	-2.07;-2.07	4.93	4.93	0.64822	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.86360	0.5914	N	0.25890	0.77	0.80722	D	1	D;B	0.76494	0.999;0.03	D;B	0.79784	0.993;0.074	D	0.85404	0.1133	10	0.34782	T	0.22	.	13.1578	0.59527	0.0:0.0:0.0:1.0	.	252;161	Q13115;G5E930	DUS4_HUMAN;.	M	252;161	ENSP00000240100:K252M;ENSP00000240101:K161M	ENSP00000240100:K252M	K	-	2	0	DUSP4	29251762	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	6.074000	0.71253	2.143000	0.66587	0.460000	0.39030	AAG	.	.		0.557	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394		A	29195843	T	A	29195843	3	1	163	1	0	0	0	0	1	0	0	0	4829	1609	56	4	437	4	DUSP4	8	29195843	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	621822	29195843	117168179	136	24918										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36768468	36768468	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggatgtgcactttattctggAgacctccatgcggccaacat	10	11	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:36768468A>T	ENST00000399881.3	+	22	2389	c.2352A>T	c.(2350-2352)ggA>ggT	p.G784G		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	784					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TTTATTCTGGAGACCTCCATG	0.522																																					p.G784G		Atlas-SNP	.											.	KCNU1	359	.	0			c.A2352T						.						89	93	92					8																	36768468		2000	4173	6173	SO:0001819	synonymous_variant	157855	exon22			TTCTGGAGACCTC	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2352A>T	chr8.hg19:g.36768468A>T		32.0	0.0		38.0	13.0	NM_001031836		Silent	SNP	ENST00000399881.3	hg19	CCDS55220.1																																																																																			.	.		0.522	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		T	36768468	A	T	36768468	2	4	163	1	0	0	0	0	0	0	0	1	8102	291	11	4		4	KCNU1	8	36768468	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	7572625	36768468	109595554	137	24919										
ST18	9705	hgsc.bcm.edu	37	chr8	53044593	53044593	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agggacaatgtggtagctctTgtttgttcagtttccaggag	13	6	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:53044593T>A	ENST00000276480.7	-	22	3274	c.2591A>T	c.(2590-2592)cAa>cTa	p.Q864L		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	864					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TGGTAGCTCTTGTTTGTTCAG	0.493																																					p.Q864L		Atlas-SNP	.											.	ST18	212	.	0			c.A2591T						.						155	137	143					8																	53044593		2203	4300	6503	SO:0001583	missense	9705	exon22			AGCTCTTGTTTGT	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2591A>T	chr8.hg19:g.53044593T>A	ENSP00000276480:p.Gln864Leu	114.0	0.0		135.0	34.0	NM_014682	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	hg19	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.132554	0.77662	.	.	ENSG00000147488	ENST00000276480	T	0.44881	0.91	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.60495	0.2273	M	0.62723	1.935	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.57394	-0.7819	10	0.29301	T	0.29	-17.8825	15.4931	0.75629	0.0:0.0:0.0:1.0	.	864	O60284	ST18_HUMAN	L	864	ENSP00000276480:Q864L	ENSP00000276480:Q864L	Q	-	2	0	ST18	53207146	1.000000	0.71417	0.949000	0.38748	0.951000	0.60555	6.099000	0.71466	2.103000	0.63969	0.482000	0.46254	CAA	.	.		0.493	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			A	53044593	T	A	53044593	3	1	163	1	0	0	0	0	1	0	0	0	15227	1812	63	4	572	4	ST18	8	53044593	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	16276125	53044593	93319429	138	24920										
SULF1	23213	hgsc.bcm.edu	37	chr8	70501222	70501222	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttcaggactacttcacagacTtaatcactaacgagagcatt	6	10	3	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:70501222T>A	ENST00000260128.4	+	8	1297	c.580T>A	c.(580-582)Tta>Ata	p.L194I	SULF1_ENST00000402687.4_Missense_Mutation_p.L194I|SULF1_ENST00000419716.3_Missense_Mutation_p.L194I|SULF1_ENST00000458141.2_Missense_Mutation_p.L194I	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	194					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			CTTCACAGACTTAATCACTAA	0.418																																					p.L194I		Atlas-SNP	.											.	SULF1	153	.	0			c.T580A						.						87	83	84					8																	70501222		2203	4300	6503	SO:0001583	missense	23213	exon8			ACAGACTTAATCA	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.580T>A	chr8.hg19:g.70501222T>A	ENSP00000260128:p.Leu194Ile	141.0	0.0		157.0	28.0	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	hg19	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	T	15.15	2.749362	0.49257	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98	5.54	5.54	0.83059	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.96087	0.8725	L	0.39467	1.215	0.58432	D	0.999999	B	0.29212	0.237	B	0.33846	0.171	D	0.94592	0.7788	10	0.54805	T	0.06	.	10.6705	0.45755	0.0:0.0807:0.0:0.9193	.	194	Q8IWU6	SULF1_HUMAN	I	194	ENSP00000403040:L194I;ENSP00000260128:L194I;ENSP00000385704:L194I;ENSP00000390315:L194I	ENSP00000260128:L194I	L	+	1	2	SULF1	70663776	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.338000	0.52128	2.231000	0.72958	0.533000	0.62120	TTA	.	.		0.418	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		A	70501222	T	A	70501222	3	1	163	1	0	0	0	0	1	0	0	0	15385	1606	56	4	594	4	SULF1	8	70501222	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	17456629	70501222	75862800	139	24921										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110439372	110439372	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gagaagcacctgcggaaagcAgaatcttctacaggttccct	10	11	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:110439372A>T	ENST00000378402.5	+	25	3091	c.2987A>T	c.(2986-2988)cAg>cTg	p.Q996L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	996					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TGCGGAAAGCAGAATCTTCTA	0.483										HNSCC(38;0.096)																											p.Q996L		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A2987T						.						44	47	46					8																	110439372		1865	4110	5975	SO:0001583	missense	93035	exon25			GAAAGCAGAATCT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.2987A>T	chr8.hg19:g.110439372A>T	ENSP00000367655:p.Gln996Leu	103.0	0.0		84.0	25.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.078200	0.76528	.	.	ENSG00000205038	ENST00000378402	D	0.86164	-2.08	5.45	5.45	0.79879	.	0.000000	0.64402	D	0.000001	D	0.89602	0.6762	L	0.43923	1.385	0.31919	N	0.613629	D	0.89917	1.0	D	0.71184	0.972	D	0.89490	0.3756	10	0.38643	T	0.18	.	11.9127	0.52747	1.0:0.0:0.0:0.0	.	996	Q86WI1	PKHL1_HUMAN	L	996	ENSP00000367655:Q996L	ENSP00000367655:Q996L	Q	+	2	0	PKHD1L1	110508548	1.000000	0.71417	0.978000	0.43139	0.909000	0.53808	4.985000	0.63845	2.066000	0.61787	0.482000	0.46254	CAG	.	.		0.483	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110439372	A	T	110439372	3	4	163	1	0	0	0	0	1	0	0	0	11981	188	7	4	3085	4	PKHD1L1	8	110439372	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	39938150	110439372	35924650	140	24922										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113585883	113585884	+	Missense_Mutation	DNP	AA	AA	TT													0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cgttttatcttttccatcatAaatctgcaaaatatatttat							TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:113585883_113585884AA>TT	ENST00000297405.5	-	24	4132_4133	c.3888_3889TT>AA	c.(3886-3891)atTTat>atAAat	p.Y1297N	CSMD3_ENST00000352409.3_Missense_Mutation_p.Y1297N|CSMD3_ENST00000455883.2_Missense_Mutation_p.Y1193N|CSMD3_ENST00000343508.3_Missense_Mutation_p.Y1257N	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1297	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTTCCATCATAAATCTGCaaaa	0.317										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.Y1297N|p.I1296I		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T3889A|c.T3888A						.																																			SO:0001583	missense	114788	exon24			CATCATAAATCTG|ATCATAAATCTGC	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3888_3889delinsTT	chr8.hg19:g.113585883_113585884delinsTT	ENSP00000297405:p.Tyr1297Asn	56.0	0.0		81.0|80.0	12.0	NM_198123	Q96PZ3	Missense_Mutation|Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.317	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		TT	113585884	AA	TT	113585883	3	4	163	1	0	0	0	0	1	0	0	0	3948	362	13	4	7426	4	CSMD3	8	113585883	Missense_Mutation	DNP	AA	TCGA-DD-AACL-01A-11D-A40R-10	3146511	113585883	32778139	141	24923										
TAF2	6873	hgsc.bcm.edu	37	chr8	120809963	120809963	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agcctcatcaatgaagacagTcttaaaacaggagtatgggt	10	7	3	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:120809963T>A	ENST00000378164.2	-	7	1214	c.916A>T	c.(916-918)Act>Tct	p.T306S		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	306					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			ATGAAGACAGTCTTAAAACAG	0.353																																					p.T306S		Atlas-SNP	.											.	TAF2	204	.	0			c.A916T						.						115	109	111					8																	120809963		2203	4300	6503	SO:0001583	missense	6873	exon7			AGACAGTCTTAAA	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.916A>T	chr8.hg19:g.120809963T>A	ENSP00000367406:p.Thr306Ser	67.0	0.0		108.0	37.0	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	hg19	CCDS34937.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.21|18.21	3.573165|3.573165	0.65765|0.65765	.|.	.|.	ENSG00000064313|ENSG00000064313	ENST00000523904|ENST00000378164	.|T	.|0.04706	.|3.57	6.07|6.07	6.07|6.07	0.98685|0.98685	.|Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	.|0.049676	.|0.85682	.|N	.|0.000000	T|T	0.06280|0.06280	0.0162|0.0162	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	.|P	.|0.42993	.|0.797	.|B	.|0.43052	.|0.406	T|T	0.39820|0.39820	-0.9595|-0.9595	5|10	.|0.52906	.|T	.|0.07	-15.5069|-15.5069	16.6407|16.6407	0.85098|0.85098	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|306	.|Q6P1X5	.|TAF2_HUMAN	S|S	36|306	.|ENSP00000367406:T306S	.|ENSP00000367406:T306S	R|T	-|-	3|1	2|0	TAF2|TAF2	120879144|120879144	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.997000|7.997000	0.88414|0.88414	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	AGA|ACT	.	.		0.353	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		A	120809963	T	A	120809963	3	1	163	1	0	0	0	0	1	0	0	0	15539	1667	58	4	2763	4	TAF2	8	120809963	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	7224080	120809963	25554059	142	24924										
GSDMC	56169	hgsc.bcm.edu	37	chr8	130774950	130774950	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agtcagcgccttcttcttcaCtctgagactctctccttggc	7	15	6	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:130774950C>G	ENST00000276708.4	-	5	1479	c.598G>C	c.(598-600)Gtg>Ctg	p.V200L		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	200						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						TTCTTCTTCACTCTGAGACTC	0.463																																					p.V200L		Atlas-SNP	.											.	GSDMC	71	.	0			c.G598C						.						201	179	187					8																	130774950		2203	4300	6503	SO:0001583	missense	56169	exon5			TCTTCACTCTGAG	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"melanoma-derived leucine zipper, extra-nuclear factor"	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.598G>C	chr8.hg19:g.130774950C>G	ENSP00000276708:p.Val200Leu	41.0	0.0		79.0	11.0	NM_031415	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	hg19	CCDS6360.1	.	.	.	.	.	.	.	.	.	.	C	8.629	0.893315	0.17613	.	.	ENSG00000147697	ENST00000276708	T	0.22539	1.95	4.13	-3.91	0.04168	.	1.622190	0.03789	N	0.262515	T	0.14787	0.0357	L	0.27053	0.805	0.09310	N	1	P	0.49559	0.925	B	0.40864	0.342	T	0.34551	-0.9824	10	0.28530	T	0.3	.	10.6398	0.45586	0.0:0.3687:0.0:0.6313	.	200	Q9BYG8	GSDMC_HUMAN	L	200	ENSP00000276708:V200L	ENSP00000276708:V200L	V	-	1	0	GSDMC	130844132	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.558000	0.05978	-0.868000	0.04058	-0.658000	0.03865	GTG	.	.		0.463	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1			G	130774950	C	G	130774950	3	3	163	1	0	0	0	0	1	0	0	0	6827	565	20	4	968	4	GSDMC	8	130774950	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	9964987	130774950	15589072	143	24925										
ADCY8	114	hgsc.bcm.edu	37	chr8	131896933	131896933	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttgttaatttcctcaggcccAgactggacatgcaaagcttg	9	10	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:131896933A>T	ENST00000286355.5	-	8	4078	c.1986T>A	c.(1984-1986)tcT>tcA	p.S662S	ADCY8_ENST00000377928.3_Silent_p.S662S	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	662					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CCTCAGGCCCAGACTGGACAT	0.433										HNSCC(32;0.087)																											p.S662S		Atlas-SNP	.											.	ADCY8	291	.	0			c.T1986A						.						153	146	148					8																	131896933		2203	4300	6503	SO:0001819	synonymous_variant	114	exon8			AGGCCCAGACTGG	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1986T>A	chr8.hg19:g.131896933A>T		118.0	0.0		153.0	23.0	NM_001115		Silent	SNP	ENST00000286355.5	hg19	CCDS6363.1																																																																																			.	.		0.433	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			T	131896933	A	T	131896933	2	4	163	1	0	0	0	0	0	0	0	1	300	175	7	4		4	ADCY8	8	131896933	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1121983	131896933	14467089	144	24926										
GLI4	2738	hgsc.bcm.edu	37	chr8	144358897	144358897	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acacgggcgagaagcccttcGcgtgtggcgcctgcggcaag	16	13	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr8:144358897G>T	ENST00000523522.1	+	3	1093	c.1054G>T	c.(1054-1056)Gcg>Tcg	p.A352S	GLI4_ENST00000523812.1_3'UTR|GLI4_ENST00000340042.1_Missense_Mutation_p.A352S			P10075	GLI4_HUMAN	GLI family zinc finger 4	352					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(1)|lung(5)	9	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			GAAGCCCTTCGCGTGTGGCGC	0.711																																					p.A352S		Atlas-SNP	.											.	GLI4	28	.	0			c.G1054T						.						10	12	11					8																	144358897		2195	4280	6475	SO:0001583	missense	2738	exon4			CCCTTCGCGTGTG		CCDS6398.1	8q24.3	2013-01-08	2009-03-05		ENSG00000250571	ENSG00000250571		"Zinc fingers, C2H2-type"	4320	protein-coding gene	gene with protein product		165280	"GLI-Kruppel family member GLI4", "glioma-associated oncogene family zinc finger 4"			2850480	Standard	NM_138465		Approved	HKR4, ZNF928	uc003yxx.3	P10075	OTTHUMG00000164952	ENST00000523522.1:c.1054G>T	chr8.hg19:g.144358897G>T	ENSP00000430987:p.Ala352Ser	87.0	0.0		86.0	25.0	NM_138465	Q96CK9	Missense_Mutation	SNP	ENST00000523522.1	hg19	CCDS6398.1	.	.	.	.	.	.	.	.	.	.	G	5.610	0.297317	0.10622	.	.	ENSG00000250571	ENST00000340042;ENST00000523522	T;T	0.17854	2.25;2.25	3.92	-1.47	0.08772	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04952	0.0133	N	0.02169	-0.655	0.09310	N	1	B	0.14438	0.01	B	0.16289	0.015	T	0.37502	-0.9703	9	0.27785	T	0.31	.	2.9903	0.05981	0.3997:0.0:0.276:0.3243	.	352	P10075	GLI4_HUMAN	S	352	ENSP00000345024:A352S;ENSP00000430987:A352S	ENSP00000345024:A352S	A	+	1	0	GLI4	144430272	0.000000	0.05858	0.013000	0.15412	0.026000	0.11368	-1.963000	0.01513	-0.651000	0.05415	0.563000	0.77884	GCG	.	.		0.711	GLI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381128.2			T	144358897	G	T	144358897	3	4	163	1	0	0	0	0	1	0	0	0	6448	1087	38	1	1064	1	GLI4	8	144358897	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	12461964	144358897	2005125	145	24927										
SLC24A2	25769	hgsc.bcm.edu	37	chr9	19786279	19786279	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gttgctgtgagcgataaataCccctatgagagatgtgaaaa	11	6	0	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr9:19786279C>A	ENST00000341998.2	-	1	647	c.586G>T	c.(586-588)Gta>Tta	p.V196L	SLC24A2_ENST00000286344.3_Missense_Mutation_p.V196L	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	196					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		GCGATAAATACCCCTATGAGA	0.468																																					p.V196L		Atlas-SNP	.											.	SLC24A2	93	.	0			c.G586T						.						82	81	81					9																	19786279		2203	4300	6503	SO:0001583	missense	25769	exon1			TAAATACCCCTAT	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"Solute carriers"	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.586G>T	chr9.hg19:g.19786279C>A	ENSP00000344801:p.Val196Leu	49.0	0.0		86.0	17.0	NM_001193288	B7ZLL8|Q9NTN5|Q9NZQ4	Missense_Mutation	SNP	ENST00000341998.2	hg19	CCDS6493.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.553177	0.86127	.	.	ENSG00000155886	ENST00000341998;ENST00000286344	T;T	0.63255	-0.03;-0.03	5.76	5.76	0.90799	Sodium/calcium exchanger membrane region (1);	0.057766	0.64402	D	0.000002	T	0.76271	0.3964	L	0.59967	1.855	0.80722	D	1	P;D	0.71674	0.87;0.998	P;D	0.66084	0.612;0.941	T	0.73474	-0.3971	9	.	.	.	.	19.967	0.97274	0.0:1.0:0.0:0.0	.	196;196	Q9UI40-2;Q9UI40	.;NCKX2_HUMAN	L	196	ENSP00000344801:V196L;ENSP00000286344:V196L	.	V	-	1	0	SLC24A2	19776279	1.000000	0.71417	0.997000	0.53966	0.959000	0.62525	7.814000	0.86154	2.714000	0.92807	0.655000	0.94253	GTA	.	.		0.468	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344		A	19786279	C	A	19786279	3	1	163	1	0	0	0	0	1	0	0	0	14481	507	18	3	1439	3	SLC24A2	9	19786279	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10		19786279	121427152	146	24928										
UBAP2	55833	hgsc.bcm.edu	37	chr9	33927030	33927030	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cgggacctacgaggtactggTtgtgcagcaggggaggcacc	17	10	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr9:33927030T>C	ENST00000379238.1	-	21	2537	c.2420A>G	c.(2419-2421)aAc>aGc	p.N807S	UBAP2_ENST00000360802.1_Missense_Mutation_p.N807S|UBAP2_ENST00000449054.1_Missense_Mutation_p.N807S|UBAP2_ENST00000379239.4_Missense_Mutation_p.N540S|UBAP2_ENST00000379235.1_Missense_Mutation_p.N46S|UBAP2_ENST00000539807.1_Missense_Mutation_p.N562S					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		GAGGTACTGGTTGTGCAGCAG	0.592																																					p.N807S		Atlas-SNP	.											.	UBAP2	82	.	0			c.A2420G						.						49	51	50					9																	33927030		2203	4300	6503	SO:0001583	missense	55833	exon21			TACTGGTTGTGCA	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.2420A>G	chr9.hg19:g.33927030T>C	ENSP00000368540:p.Asn807Ser	52.0	0.0		40.0	12.0	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	hg19	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	T	17.03	3.284675	0.59867	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379235;ENST00000379239;ENST00000539807;ENST00000351580	T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93	6.17	3.82	0.43975	.	0.039579	0.85682	N	0.000000	T	0.34308	0.0893	L	0.49350	1.555	0.80722	D	1	B;B;B;B;B	0.25235	0.121;0.121;0.121;0.121;0.074	B;B;B;B;B	0.23419	0.029;0.046;0.046;0.029;0.013	T	0.07849	-1.0751	10	0.31617	T	0.26	-15.1683	8.4862	0.33074	0.0:0.1673:0.0:0.8327	.	732;562;540;716;807	F5H4D5;F5H2U4;A6NCA8;F5H2C8;Q5T6F2	.;.;.;.;UBAP2_HUMAN	S	807;807;807;716;46;540;562;243	ENSP00000368540:N807S;ENSP00000416932:N807S;ENSP00000354039:N807S;ENSP00000368537:N46S;ENSP00000368541:N540S;ENSP00000439329:N562S	ENSP00000259602:N243S	N	-	2	0	UBAP2	33917030	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.758000	0.62220	0.552000	0.29026	0.533000	0.62120	AAC	.	.		0.592	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		C	33927030	T	C	33927030	3	2	163	1	0	0	0	0	1	0	0	0	16852	1725	60	2	975	2	UBAP2	9	33927030	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	14140751	33927030	107286401	147	24929										
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88247600	88247600	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgtacaccataaggcctttcTaaaataggctctttgaatgg	8	8	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr9:88247600T>A	ENST00000357081.3	-	14	2136	c.1992A>T	c.(1990-1992)ttA>ttT	p.L664F	AGTPBP1_ENST00000376109.3_Missense_Mutation_p.L676F|AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000432218.1_Missense_Mutation_p.L502F|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.L624F			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	664					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						AAGGCCTTTCTAAAATAGGCT	0.378																																					p.L624F		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.A1872T						.						54	55	55					9																	88247600		2203	4300	6503	SO:0001583	missense	23287	exon14			CCTTTCTAAAATA	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.1992A>T	chr9.hg19:g.88247600T>A	ENSP00000349592:p.Leu664Phe	84.0	0.0		124.0	30.0	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	hg19		.	.	.	.	.	.	.	.	.	.	T	18.02	3.529970	0.64860	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218	T;T;T;T	0.53206	2.06;2.06;2.04;0.63	6.03	-0.142	0.13448	.	0.065519	0.64402	D	0.000006	T	0.59662	0.2210	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	0.961;0.983;1.0;0.979	P;P;D;P	0.87578	0.808;0.762;0.998;0.864	T	0.56086	-0.8037	10	0.22109	T	0.4	-11.7842	8.102	0.30863	0.1452:0.5828:0.0:0.2719	.	676;664;502;624	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	F	664;624;676;502	ENSP00000349592:L664F;ENSP00000365251:L624F;ENSP00000365277:L676F;ENSP00000402804:L502F	ENSP00000349592:L664F	L	-	3	2	AGTPBP1	87437420	0.998000	0.40836	0.998000	0.56505	0.813000	0.45954	0.410000	0.21098	-0.037000	0.13646	-0.256000	0.11100	TTA	.	.		0.378	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		A	88247600	T	A	88247600	3	1	163	1	0	0	0	0	1	0	0	0	400	1519	53	4	1740	4	AGTPBP1	9	88247600	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	54320570	88247600	52965831	148	24930										
ROR2	4920	hgsc.bcm.edu	37	chr9	94486744	94486744	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctcccacaggaccacaccgtAggaccagatgtctgagtcga	10	14	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr9:94486744A>T	ENST00000375708.3	-	9	2230	c.2032T>A	c.(2032-2034)Tac>Aac	p.Y678N	ROR2_ENST00000375715.1_Missense_Mutation_p.Y538N|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	678	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						ACCACACCGTAGGACCAGATG	0.592																																					p.Y678N		Atlas-SNP	.											.	ROR2	167	.	0			c.T2032A						.						74	61	65					9																	94486744		2203	4300	6503	SO:0001583	missense	4920	exon9			CACCGTAGGACCA	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.2032T>A	chr9.hg19:g.94486744A>T	ENSP00000364860:p.Tyr678Asn	64.0	0.0		74.0	17.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	hg19	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.124611	0.56613	.	.	ENSG00000169071	ENST00000375715;ENST00000375708	D;D	0.86097	-2.07;-2.07	4.86	4.86	0.63082	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38381	N	0.001703	D	0.93769	0.8008	M	0.92219	3.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.989	D	0.95200	0.8316	10	0.87932	D	0	.	14.6483	0.68777	1.0:0.0:0.0:0.0	.	678;538	Q01974;B1APY4	ROR2_HUMAN;.	N	538;678	ENSP00000364867:Y538N;ENSP00000364860:Y678N	ENSP00000364860:Y678N	Y	-	1	0	ROR2	93526565	1.000000	0.71417	1.000000	0.80357	0.421000	0.31385	7.242000	0.78210	2.044000	0.60594	0.459000	0.35465	TAC	.	.		0.592	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			T	94486744	A	T	94486744	3	4	163	1	0	0	0	0	1	0	0	0	13542	420	15	4	803	4	ROR2	9	94486744	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	6239144	94486744	46726687	149	24931										
ROR2	4920	hgsc.bcm.edu	37	chr9	94495465	94495465	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttggcagcgtcggggctctcAggcatgggcagcgcctcaca	15	13	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr9:94495465A>T	ENST00000375708.3	-	6	1074	c.876T>A	c.(874-876)ccT>ccA	p.P292P	ROR2_ENST00000375715.1_Silent_p.P152P|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	292	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CGGGGCTCTCAGGCATGGGCA	0.701																																					p.P292P		Atlas-SNP	.											.	ROR2	167	.	0			c.T876A						.						25	23	24					9																	94495465		2200	4298	6498	SO:0001819	synonymous_variant	4920	exon6			GCTCTCAGGCATG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.876T>A	chr9.hg19:g.94495465A>T		88.0	0.0		104.0	27.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	hg19	CCDS6691.1																																																																																			.	.		0.701	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			T	94495465	A	T	94495465	2	4	163	1	0	0	0	0	0	0	0	1	13542	175	7	4		4	ROR2	9	94495465	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	8721	94495465	46717966	150	24932										
OR1J1	347168	hgsc.bcm.edu	37	chr9	125240200	125240200	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acgctgctctggttctcaggGctcatgtttatatcagctgg	11	10	4	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr9:125240200G>T	ENST00000259357.2	-	1	35	c.6C>A	c.(4-6)agC>agA	p.S2R	RP11-542K23.9_ENST00000412262.2_RNA	NM_001004451.1	NP_001004451.1	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J, member 1	2						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	16						GGTTCTCAGGGCTCATGTTTA	0.502																																					p.S2R		Atlas-SNP	.											.	OR1J1	46	.	0			c.C6A						.						80	84	83					9																	125240200		2203	4300	6503	SO:0001583	missense	347168	exon1			CTCAGGGCTCATG	AL353767	CCDS35120.1	9q33.2	2013-09-20			ENSG00000136834	ENSG00000136834		"GPCR / Class A : Olfactory receptors"	8208	protein-coding gene	gene with protein product							Standard	NM_001004451		Approved	hg32	uc011lyu.2	Q8NGS3	OTTHUMG00000020603	ENST00000259357.2:c.6C>A	chr9.hg19:g.125240200G>T	ENSP00000259357:p.Ser2Arg	88.0	0.0		121.0	24.0	NM_001004451	A3KFL8|Q6IF10|Q96R88	Missense_Mutation	SNP	ENST00000259357.2	hg19	CCDS35120.1	.	.	.	.	.	.	.	.	.	.	G	0.024	-1.390446	0.01185	.	.	ENSG00000136834	ENST00000259357	T	0.00580	6.43	4.06	-1.53	0.08611	.	0.708561	0.13409	N	0.390017	T	0.00271	0.0008	N	0.02275	-0.615	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41805	-0.9488	10	0.40728	T	0.16	.	1.558	0.02589	0.1534:0.3449:0.3101:0.1916	.	2	Q8NGS3	OR1J1_HUMAN	R	2	ENSP00000259357:S2R	ENSP00000259357:S2R	S	-	3	2	OR1J1	124280021	0.000000	0.05858	0.008000	0.14137	0.103000	0.19146	-1.891000	0.01611	-0.255000	0.09486	-0.717000	0.03617	AGC	.	.		0.502	OR1J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053931.1			T	125240200	G	T	125240200	3	4	163	1	0	0	0	0	1	0	0	0	10968	1194	42	3	965	3	OR1J1	9	125240200	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	30744735	125240200	15973231	151	24933										
RALGDS	5900	hgsc.bcm.edu	37	chr9	135977865	135977865	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccttggccaggcccttactcGctccagcgcttgacaatggc	10	16	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr9:135977865G>A	ENST00000372050.3	-	14	2028	c.2007C>T	c.(2005-2007)agC>agT	p.S669S	RALGDS_ENST00000372047.3_Silent_p.S657S|RALGDS_ENST00000393160.3_Silent_p.S614S|RALGDS_ENST00000372062.3_Silent_p.S640S|RALGDS_ENST00000469972.1_5'UTR|RALGDS_ENST00000542690.1_Silent_p.S740S|RALGDS_ENST00000393157.3_Silent_p.S668S	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	669					neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		GCCCTTACTCGCTCCAGCGCT	0.627			T	CIITA	"PMBL, Hodgkin Lymphona, "																																p.S669S	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.C2007T						.						79	72	74					9																	135977865		2203	4300	6503	SO:0001819	synonymous_variant	5900	exon14			TTACTCGCTCCAG	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.2007C>T	chr9.hg19:g.135977865G>A		28.0	0.0		26.0	4.0	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	hg19	CCDS6959.1																																																																																			.	.		0.627	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266		A	135977865	G	A	135977865	2	1	163	1	0	0	0	0	0	0	0	1	13031	1078	38	1		1	RALGDS	9	135977865	Silent	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	10737665	135977865	5235566	152	24934										
PTER	9317	hgsc.bcm.edu	37	chr10	16547129	16547129	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccaactcggcccagatattgAcatgcctgatgataacaaaa	7	11	0	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:16547129A>G	ENST00000378000.1	+	5	1055	c.809A>G	c.(808-810)gAc>gGc	p.D270G	PTER_ENST00000535784.2_Missense_Mutation_p.D270G|PTER_ENST00000298942.3_Missense_Mutation_p.D270G|PTER_ENST00000423462.2_Intron	NM_001001484.2|NM_001261838.1|NM_030664.4	NP_001001484.1|NP_001248767.1|NP_109589.2	Q96BW5	PTER_HUMAN	phosphotriesterase related	270					catabolic process (GO:0009056)|epithelial cell differentiation (GO:0030855)	extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)	15						CCAGATATTGACATGCCTGAT	0.398																																					p.D270G	Ovarian(2;46 150 15648 38137 47908)	Atlas-SNP	.											.	PTER	40	.	0			c.A809G						.						153	149	150					10																	16547129		2203	4300	6503	SO:0001583	missense	9317	exon5			ATATTGACATGCC	BC015092	CCDS7111.1, CCDS58070.1, CCDS73070.1	10p12	2003-11-05			ENSG00000165983	ENSG00000165983			9590	protein-coding gene	gene with protein product		604446				9925913	Standard	NM_001001484		Approved		uc001ioi.2	Q96BW5	OTTHUMG00000017737	ENST00000378000.1:c.809A>G	chr10.hg19:g.16547129A>G	ENSP00000367239:p.Asp270Gly	85.0	0.0		108.0	26.0	NM_030664	B0YJ77|B3KTF5|D3DRU0|Q9BY46	Missense_Mutation	SNP	ENST00000378000.1	hg19	CCDS7111.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.753566	0.69648	.	.	ENSG00000165983	ENST00000343656;ENST00000535784;ENST00000378000;ENST00000298942	T;T;T	0.46451	0.87;0.87;0.87	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.59115	0.2170	M	0.80746	2.51	0.80722	D	1	P	0.36535	0.557	P	0.49637	0.617	T	0.58064	-0.7702	10	0.29301	T	0.29	-30.4121	15.2599	0.73613	1.0:0.0:0.0:0.0	.	270	Q96BW5	PTER_HUMAN	G	270	ENSP00000439485:D270G;ENSP00000367239:D270G;ENSP00000298942:D270G	ENSP00000298942:D270G	D	+	2	0	PTER	16587135	1.000000	0.71417	1.000000	0.80357	0.689000	0.40095	8.640000	0.91028	2.078000	0.62432	0.454000	0.30748	GAC	.	.		0.398	PTER-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047001.2	NM_030664		G	16547129	A	G	16547129	3	3	163	1	0	0	0	0	1	0	0	0	12751	275	10	2	819	2	PTER	10	16547129	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		16547129	118987618	153	24935										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27306542	27306542	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agttctaccatattcctttcTatatgacttctcaggttgat	5	9	3	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:27306542T>A	ENST00000376087.4	-	30	4560	c.4395A>T	c.(4393-4395)atA>atT	p.I1465I	ANKRD26_ENST00000436985.2_Silent_p.I1481I|ANKRD26_ENST00000376070.3_Silent_p.I1022I	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1464					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TATTCCTTTCTATATGACTTC	0.323																																					p.I1465I		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A4395T						.						133	120	124					10																	27306542		1826	4082	5908	SO:0001819	synonymous_variant	22852	exon30			CCTTTCTATATGA	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.4395A>T	chr10.hg19:g.27306542T>A		74.0	0.0		133.0	33.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Silent	SNP	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.323	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			A	27306542	T	A	27306542	2	1	163	1	0	0	0	0	0	0	0	1	654	1512	53	4		4	ANKRD26	10	27306542	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	10759413	27306542	108228205	154	24936										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27337852	27337852	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tcatcagtagcaccatcatgTatgtttgctgatacttccat	6	10	3	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:27337852T>A	ENST00000376087.4	-	17	1857	c.1692A>T	c.(1690-1692)atA>atT	p.I564I	ANKRD26_ENST00000436985.2_Silent_p.I580I|ANKRD26_ENST00000376070.3_Silent_p.I121I	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	564					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						caccatcatGTATGTTTGCTG	0.328																																					p.I564I		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A1692T						.						157	148	151					10																	27337852		1943	4150	6093	SO:0001819	synonymous_variant	22852	exon17			ATCATGTATGTTT	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.1692A>T	chr10.hg19:g.27337852T>A		53.0	0.0		76.0	20.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Silent	SNP	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.328	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			A	27337852	T	A	27337852	2	1	163	1	0	0	0	0	0	0	0	1	654	1628	57	4		4	ANKRD26	10	27337852	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	31310	27337852	108196895	155	24937										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72434384	72434384	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cacagactttcggggacgctTcctctcccacgtggtgtctg	11	14	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:72434384T>A	ENST00000373207.1	+	2	155	c.155T>A	c.(154-156)tTc>tAc	p.F52Y	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.F52Y	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	52					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CGGGGACGCTTCCTCTCCCAC	0.587																																					p.F52Y		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.T155A						.						69	64	65					10																	72434384		2203	4300	6503	SO:0001583	missense	140766	exon2			GACGCTTCCTCTC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.155T>A	chr10.hg19:g.72434384T>A	ENSP00000362303:p.Phe52Tyr	35.0	0.0		35.0	10.0	NM_080722	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	hg19	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.175293	0.38413	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.64085	-0.08;-0.06	4.95	4.95	0.65309	Peptidase M12B, propeptide (1);	0.074832	0.56097	D	0.000027	T	0.50034	0.1592	L	0.34521	1.04	0.31554	N	0.658421	B;B	0.30326	0.276;0.083	B;B	0.36092	0.217;0.156	T	0.53641	-0.8410	10	0.15952	T	0.53	.	9.7286	0.40348	0.1545:0.0:0.0:0.8455	.	52;52	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	Y	52	ENSP00000362304:F52Y;ENSP00000362303:F52Y	ENSP00000362303:F52Y	F	+	2	0	ADAMTS14	72104390	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.719000	0.61937	1.878000	0.54408	0.397000	0.26171	TTC	.	.		0.587	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		A	72434384	T	A	72434384	3	1	163	1	0	0	0	0	1	0	0	0	259	1783	62	4	161	4	ADAMTS14	10	72434384	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	45096532	72434384	63100363	156	24938										
KIAA0913	23053	hgsc.bcm.edu	37	chr10	75551724	75551724	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcggctcttccccggcttccGgccagcggtggaggcctgct	15	16	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:75551724G>T	ENST00000605216.1	+	10	1644	c.1427G>T	c.(1426-1428)cGg>cTg	p.R476L	ZSWIM8_ENST00000604729.1_Missense_Mutation_p.R476L|ZSWIM8_ENST00000603114.1_Missense_Mutation_p.R476L|ZSWIM8_ENST00000398706.2_Missense_Mutation_p.R476L|ZSWIM8_ENST00000604524.1_Missense_Mutation_p.R476L	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	476							zinc ion binding (GO:0008270)										CCCGGCTTCCGGCCAGCGGTG	0.617																																					p.R476L		Atlas-SNP	.											.	.	.	.	0			c.G1427T						.						8	10	9					10																	75551724		1793	3840	5633	SO:0001583	missense	23053	exon10			GCTTCCGGCCAGC	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"Zinc fingers, SWIM-type"	23528	protein-coding gene	gene with protein product			"KIAA0913"	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.1427G>T	chr10.hg19:g.75551724G>T	ENSP00000474748:p.Arg476Leu	90.0	0.0		139.0	29.0	NM_001242488	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Missense_Mutation	SNP	ENST00000605216.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.41	3.381691	0.61845	.	.	ENSG00000214655	ENST00000398706	T	0.73363	-0.74	5.55	5.55	0.83447	.	0.127555	0.30752	U	0.008941	T	0.43411	0.1246	N	0.02539	-0.55	0.38515	D	0.948583	P;P;P	0.38455	0.632;0.491;0.632	B;B;B	0.32211	0.142;0.142;0.142	T	0.51364	-0.8715	10	0.37606	T	0.19	-7.746	6.7079	0.23260	0.1984:0.0:0.8016:0.0	.	476;476;476	A7E2V4;A7E2V4-5;A7E2V4-4	K0913_HUMAN;.;.	L	476	ENSP00000381693:R476L	ENSP00000381693:R476L	R	+	2	0	KIAA0913	75221730	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.338000	0.79269	2.894000	0.99253	0.655000	0.94253	CGG	.	.		0.617	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		T	75551724	G	T	75551724	3	4	163	1	0	0	0	0	1	0	0	0	8209	1116	39	1	1465	1	KIAA0913	10	75551724	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	3117340	75551724	59983023	157	24939										
KCNMA1	3778	hgsc.bcm.edu	37	chr10	79397295	79397295	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggaggaggaggacgcgtctaGgctgagatggttcgcgtgga	20	6	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:79397295G>A	ENST00000286628.8	-	1	105	c.106C>T	c.(106-108)Cta>Tta	p.L36L	KCNMA1_ENST00000404857.1_Silent_p.L36L|KCNMA1_ENST00000406533.3_Silent_p.L36L|KCNMA1_ENST00000354353.5_Silent_p.L36L|KCNMA1_ENST00000480683.1_Silent_p.L36L|KCNMA1_ENST00000372440.1_Silent_p.L36L|KCNMA1_ENST00000404771.3_Silent_p.L36L|KCNMA1_ENST00000372443.1_Silent_p.L36L|KCNMA1_ENST00000481070.1_Silent_p.L36L|KCNMA1_ENST00000286627.5_Silent_p.L36L	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	36					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	gaCGCGTCTAGGCTGAGATGG	0.637																																					p.L36L		Atlas-SNP	.											.	KCNMA1	370	.	0			c.C106T						.						18	16	17					10																	79397295		2201	4291	6492	SO:0001819	synonymous_variant	3778	exon1			CGTCTAGGCTGAG	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.106C>T	chr10.hg19:g.79397295G>A		247.0	0.0		352.0	79.0	NM_001161352	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Silent	SNP	ENST00000286628.8	hg19		.	.	.	.	.	.	.	.	.	.	G	11.23	1.576066	0.28092	.	.	ENSG00000156113	ENST00000372421	.	.	.	3.54	3.54	0.40534	.	.	.	.	.	T	0.59238	0.2179	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56980	-0.7889	4	.	.	.	-1.6146	9.1609	0.37021	0.0:0.0:0.7643:0.2357	.	.	.	.	L	24	.	.	P	-	2	0	KCNMA1	79067301	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.938000	0.56583	1.915000	0.55452	0.455000	0.32223	CCT	.	.		0.637	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247		A	79397295	G	A	79397295	2	1	163	1	0	0	0	0	0	0	0	1	8082	991	35	3		3	KCNMA1	10	79397295	Silent	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	3845571	79397295	56137452	158	24940										
OPN4	94233	hgsc.bcm.edu	37	chr10	88414684	88414684	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cttccatccatcagtcccacAgtaagcctgggcgagcatgt	9	14	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:88414684A>C	ENST00000241891.5	+	1	311	c.144A>C	c.(142-144)acA>acC	p.T48T	OPN4_ENST00000372071.2_Splice_Site_p.T48T	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	48					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						TCAGTCCCACAGTAAGCCTGG	0.627																																					p.T48T		Atlas-SNP	.											.	OPN4	61	.	0			c.A144C						.						55	49	51					10																	88414684		2203	4300	6503	SO:0001630	splice_region_variant	94233	exon1			TCCCACAGTAAGC	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"GPCR / Class A : Opsin receptors"	14449	protein-coding gene	gene with protein product	"melanopsin"	606665	"opsin 4 (melanopsin)"			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.144+1A>C	chr10.hg19:g.88414684A>C		45.0	0.0		61.0	13.0	NM_033282	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Silent	SNP	ENST00000241891.5	hg19	CCDS7376.1																																																																																			.	.		0.627	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	Silent	C	88414684	A	C	88414684	5	2	163	1	0	0	0	0	0	0	1	0	10891	202	7	5	146	5	OPN4	10	88414684	Splice_Site	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	9017389	88414684	47120063	159	24941										
IDE	3416	hgsc.bcm.edu	37	chr10	94267964	94267964	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acaagagtattaacccagccTgcaacattcaaaggaaatca	6	10	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:94267964T>A	ENST00000265986.6	-	8	1117		c.e8-2			NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme						beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TAACCCAGCCTGCAACATTCA	0.363																																					.		Atlas-SNP	.											.	IDE	77	.	0			c.1061-2A>T						.						127	135	132					10																	94267964		2203	4300	6503	SO:0001630	splice_region_variant	3416	exon9			CCAGCCTGCAACA	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.1061-2A>T	chr10.hg19:g.94267964T>A		211.0	0.0		283.0	57.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Splice_Site	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.390257	0.82902	.	.	ENSG00000119912	ENST00000265986	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4411	0.75184	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	IDE	94257944	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.857000	0.86963	2.114000	0.64651	0.455000	0.32223	.	.	.		0.363	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969	Intron	A	94267964	T	A	94267964	5	1	163	1	0	0	0	0	0	0	1	0	7502	1594	55	4	2072	4	IDE	10	94267964	Splice_Site	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	5853280	94267964	41266783	160	24942										
NOC3L	64318	hgsc.bcm.edu	37	chr10	96116932	96116932	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	accagtttattagactcaccTggcttctccctagtctgtgg	8	12	3	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:96116932T>A	ENST00000371361.3	-	4	607	c.507A>T	c.(505-507)ccA>ccT	p.P169P	NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000371350.1_Splice_Site_p.P169P	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	169					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				TAGACTCACCTGGCTTCTCCC	0.338																																					p.P169P		Atlas-SNP	.											.	NOC3L	67	.	0			c.A507T						.						134	129	131					10																	96116932		2203	4300	6503	SO:0001630	splice_region_variant	64318	exon4			CTCACCTGGCTTC	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.508+1A>T	chr10.hg19:g.96116932T>A		87.0	0.0		132.0	24.0	NM_022451	Q9H5M6|Q9H9D8	Silent	SNP	ENST00000371361.3	hg19	CCDS7433.1																																																																																			.	.		0.338	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451	Silent	A	96116932	T	A	96116932	5	1	163	1	0	0	0	0	0	0	1	0	10523	1594	55	4	1967	4	NOC3L	10	96116932	Splice_Site	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	1848968	96116932	39417815	161	24943										
BTRC	8945	hgsc.bcm.edu	37	chr10	103296339	103296339	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggtgcatgtttacgagtgttAgaaggccatgaggaattggt	15	4	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:103296339A>T	ENST00000370187.3	+	12	1624	c.1506A>T	c.(1504-1506)ttA>ttT	p.L502F	BTRC_ENST00000393441.4_Missense_Mutation_p.L461F|BTRC_ENST00000493877.1_3'UTR|BTRC_ENST00000408038.2_Missense_Mutation_p.L466F	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	502					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		TACGAGTGTTAGAAGGCCATG	0.398																																					p.L502F		Atlas-SNP	.											.	BTRC	64	.	0			c.A1506T						.						251	237	242					10																	103296339		2203	4300	6503	SO:0001583	missense	8945	exon12			AGTGTTAGAAGGC	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.1506A>T	chr10.hg19:g.103296339A>T	ENSP00000359206:p.Leu502Phe	96.0	0.0		111.0	21.0	NM_033637	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	hg19	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.293073	0.80914	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038	T;T;T	0.63744	-0.06;-0.06;-0.06	5.69	-1.46	0.08800	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000018	T	0.67505	0.2900	L	0.39147	1.195	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	1.0;0.961;1.0	T	0.66540	-0.5898	10	0.54805	T	0.06	-8.213	13.2336	0.59957	0.3825:0.0:0.6175:0.0	.	476;466;502	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	F	502;461;466	ENSP00000359206:L502F;ENSP00000377088:L461F;ENSP00000385339:L466F	ENSP00000359206:L502F	L	+	3	2	BTRC	103286329	1.000000	0.71417	0.973000	0.42090	0.997000	0.91878	0.889000	0.28282	-0.145000	0.11294	0.529000	0.55759	TTA	.	.		0.398	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		T	103296339	A	T	103296339	3	4	163	1	0	0	0	0	1	0	0	0	1571	417	15	4	1552	4	BTRC	10	103296339	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	7179407	103296339	32238408	162	24944										
C10orf84	63877	hgsc.bcm.edu	37	chr10	120070409	120070409	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttttggtttcccatctcttcTttgcttcaaacctaaaagga	5	10	3	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:120070409T>C	ENST00000369183.4	-	9	921	c.662A>G	c.(661-663)aAg>aGg	p.K221R	FAM204A_ENST00000469758.1_5'UTR|FAM204A_ENST00000369172.4_Missense_Mutation_p.K221R	NM_022063.2	NP_071346.1	Q9H8W3	F204A_HUMAN	family with sequence similarity 204, member A	221										kidney(1)|large_intestine(5)|lung(4)|ovary(1)	11						CCATCTCTTCTTTGCTTCAAA	0.323																																					p.K221R		Atlas-SNP	.											.	FAM204A	20	.	0			c.A662G						.						119	108	112					10																	120070409		2203	4300	6503	SO:0001583	missense	63877	exon8			CTCTTCTTTGCTT	AK023250	CCDS7605.1	10q26.12	2011-06-01	2011-06-01	2011-06-01	ENSG00000165669	ENSG00000165669			25794	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 84"	C10orf84		12477932	Standard	NM_022063		Approved	FLJ13188, bA319I23.1	uc010qss.1	Q9H8W3	OTTHUMG00000019131	ENST00000369183.4:c.662A>G	chr10.hg19:g.120070409T>C	ENSP00000358183:p.Lys221Arg	38.0	0.0		56.0	11.0	NM_001134672	D3DRC6|Q5T373|Q9H5V5	Missense_Mutation	SNP	ENST00000369183.4	hg19	CCDS7605.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.676304	0.88445	.	.	ENSG00000165669	ENST00000369183;ENST00000369172	.	.	.	6.08	6.08	0.98989	.	0.040549	0.85682	D	0.000000	T	0.67896	0.2942	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.68988	-0.5264	9	0.52906	T	0.07	-21.6781	16.643	0.85134	0.0:0.0:0.0:1.0	.	221	Q9H8W3	F204A_HUMAN	R	221	.	ENSP00000358170:K221R	K	-	2	0	FAM204A	120060399	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.483000	0.81158	2.330000	0.79161	0.533000	0.62120	AAG	.	.		0.323	FAM204A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050596.2	NM_022063		C	120070409	T	C	120070409	3	2	163	1	0	0	0	0	1	0	0	0	1623	1609	56	2	43	2	C10orf84	10	120070409	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	16774070	120070409	15464338	163	24945										
RGS10	6001	hgsc.bcm.edu	37	chr10	121275042	121275042	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tggtcctggagtttctggaaCatcagagggtgcggttcttc	14	8	3	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:121275042C>T	ENST00000369101.3	-	3	381	c.354G>A	c.(352-354)atG>atA	p.M118I	RGS10_ENST00000369103.2_Missense_Mutation_p.M126I|RGS10_ENST00000469575.1_Intron|RGS10_ENST00000392865.1_Missense_Mutation_p.M112I			O43665	RGS10_HUMAN	regulator of G-protein signaling 10	118	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(2)|large_intestine(1)|lung(3)	6		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00105)|GBM - Glioblastoma multiforme(135;0.195)		GTTTCTGGAACATCAGAGGGT	0.512																																					p.M126I		Atlas-SNP	.											.	RGS10	14	.	0			c.G378A						.						173	145	155					10																	121275042		2203	4300	6503	SO:0001583	missense	6001	exon4			CTGGAACATCAGA	AF045229	CCDS31294.1, CCDS41572.1	10q25	2007-08-14	2007-08-14		ENSG00000148908	ENSG00000148908		"Regulators of G-protein signaling"	9992	protein-coding gene	gene with protein product		602856	"regulator of G-protein signalling 10"			8774883	Standard	NM_002925		Approved		uc001leg.3	O43665	OTTHUMG00000019150	ENST00000369101.3:c.354G>A	chr10.hg19:g.121275042C>T	ENSP00000358097:p.Met118Ile	119.0	0.0		153.0	38.0	NM_001005339	A8K408|B1AMR8|Q6IAZ6|Q96GN0	Missense_Mutation	SNP	ENST00000369101.3	hg19		.	.	.	.	.	.	.	.	.	.	C	26.1	4.707212	0.89018	.	.	ENSG00000148908	ENST00000392865;ENST00000369103;ENST00000369101	T;T;T	0.01787	4.64;4.64;4.64	5.35	5.35	0.76521	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.05547	0.0146	L	0.31752	0.955	0.58432	D	0.999998	P;P;P	0.52577	0.954;0.889;0.909	D;D;D	0.70716	0.966;0.95;0.97	T	0.64385	-0.6420	10	0.16896	T	0.51	-9.6124	18.6828	0.91553	0.0:1.0:0.0:0.0	.	126;112;118	O43665-3;O43665-2;O43665	.;.;RGS10_HUMAN	I	112;126;118	ENSP00000376605:M112I;ENSP00000358099:M126I;ENSP00000358097:M118I	ENSP00000358097:M118I	M	-	3	0	RGS10	121265032	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	6.344000	0.72991	2.492000	0.84095	0.455000	0.32223	ATG	.	.		0.512	RGS10-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050655.1	NM_002925		T	121275042	C	T	121275042	3	4	163	1	0	0	0	0	1	0	0	0	13308	478	17	3	175	3	RGS10	10	121275042	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	1204633	121275042	14259705	164	24946										
WDR11	55717	hgsc.bcm.edu	37	chr10	122650234	122650234	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	attcactcttgaaggttcagAtggtgagcagtttaagaagt	11	5	3	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:122650234A>C	ENST00000263461.6	+	19	2596	c.2350A>C	c.(2350-2352)Atg>Ctg	p.M784L	WDR11_ENST00000604509.1_Intron	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						GAAGGTTCAGATGGTGAGCAG	0.418																																					p.M784L		Atlas-SNP	.											.	WDR11	95	.	0			c.A2350C						.						234	211	219					10																	122650234		2203	4300	6503	SO:0001583	missense	55717	exon19			GTTCAGATGGTGA	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.2350A>C	chr10.hg19:g.122650234A>C	ENSP00000263461:p.Met784Leu	77.0	0.0		93.0	15.0	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	hg19	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	A	12.83	2.055125	0.36277	.	.	ENSG00000120008	ENST00000263461	D	0.90069	-2.61	5.79	5.79	0.91817	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84719	0.5534	N	0.05441	-0.05	0.80722	D	1	P;P;B;B	0.40970	0.734;0.734;0.015;0.025	P;P;B;B	0.50825	0.651;0.651;0.01;0.008	D	0.84070	0.0379	10	0.23891	T	0.37	-35.6176	16.1354	0.81481	1.0:0.0:0.0:0.0	.	784;784;75;313	Q9BZH6;B2RCJ6;Q9NWV7;Q659C9	WDR11_HUMAN;.;.;.	L	784	ENSP00000263461:M784L	ENSP00000263461:M784L	M	+	1	0	WDR11	122640224	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.792000	0.91856	2.207000	0.71202	0.533000	0.62120	ATG	.	.		0.418	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			C	122650234	A	C	122650234	3	2	163	1	0	0	0	0	1	0	0	0	17288	333	12	5	2424	5	WDR11	10	122650234	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1375192	122650234	12884513	165	24947										
STK32C	282974	hgsc.bcm.edu	37	chr10	134022595	134022595	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	catcgaggcagtcttgaagaTagtcattctcctgtggatgg	12	8	3	2	rs374006685		TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr10:134022595T>C	ENST00000368622.1	-	11	1292	c.911A>G	c.(910-912)tAt>tGt	p.Y304C	STK32C_ENST00000368625.4_Missense_Mutation_p.Y434C					serine/threonine kinase 32C											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|ovary(2)|skin(1)	23		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		GTCTTGAAGATAGTCATTCTC	0.567																																					p.Y421C		Atlas-SNP	.											.	STK32C	61	.	0			c.A1262G						.	T	CYS/TYR	1,4403	2.1+/-5.4	0,1,2201	218	170	186		1262	4	1	10		186	0,8596		0,0,4298	no	missense	STK32C	NM_173575.2	194	0,1,6499	CC,CT,TT		0.0,0.0227,0.0077	possibly-damaging	421/487	134022595	1,12999	2202	4298	6500	SO:0001583	missense	282974	exon11			TGAAGATAGTCAT	AK057849	CCDS7666.1	10q26.3	2004-07-22			ENSG00000165752	ENSG00000165752			21332	protein-coding gene	gene with protein product							Standard	NM_173575		Approved	PKE, MGC23665, YANK3	uc001lle.1	Q86UX6	OTTHUMG00000019285	ENST00000368622.1:c.911A>G	chr10.hg19:g.134022595T>C	ENSP00000357611:p.Tyr304Cys	77.0	0.0		95.0	22.0	NM_173575		Missense_Mutation	SNP	ENST00000368622.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.11	2.140345	0.37825	2.27E-4	0.0	ENSG00000165752	ENST00000368622;ENST00000298630;ENST00000368625	T;T;T	0.68479	-0.33;-0.2;-0.26	4.04	4.04	0.47022	.	0.000000	0.53938	U	0.000057	T	0.75664	0.3880	L	0.54323	1.7	0.52501	D	0.999954	D;D;D	0.89917	0.998;0.998;1.0	D;P;D	0.87578	0.912;0.865;0.998	T	0.74794	-0.3544	10	0.39692	T	0.17	.	11.7648	0.51924	0.0:0.0:0.0:1.0	.	434;421;304	B7Z7J1;Q86UX6;Q86UX6-2	.;ST32C_HUMAN;.	C	304;421;434	ENSP00000357611:Y304C;ENSP00000298630:Y421C;ENSP00000357614:Y434C	ENSP00000298630:Y421C	Y	-	2	0	STK32C	133872585	1.000000	0.71417	0.997000	0.53966	0.066000	0.16364	4.304000	0.59104	1.720000	0.51447	0.529000	0.55759	TAT	.	.		0.567	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575		C	134022595	T	C	134022595	3	2	163	1	0	0	0	0	1	0	0	0	15314	1406	49	2	206	2	STK32C	10	134022595	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	11372361	134022595	1512152	166	24948										
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	379652	379652	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cgccccgagctctgccggccActgcgcctggcctggcgcca	13	20	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:379652A>T	ENST00000329962.6	+	15	2439	c.2439A>T	c.(2437-2439)ccA>ccT	p.P813P		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	813					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCTGCCGGCCACTGCGCCTGG	0.721																																					p.P813P		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.A2439T						.						5	6	6					11																	379652		1954	4009	5963	SO:0001819	synonymous_variant	338707	exon15			CCGGCCACTGCGC	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"Beta 4-glycosyltransferases"	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2439A>T	chr11.hg19:g.379652A>T		55.0	0.0		75.0	19.0	NM_178537	Q96LV2	Silent	SNP	ENST00000329962.6	hg19	CCDS7694.1																																																																																			.	.		0.721	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		T	379652	A	T	379652	2	4	163	1	0	0	0	0	0	0	0	1	1269	146	6	4		4	B4GALNT4	11	379652	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		379652	134626864	167	24949										
OR51E1	143503	hgsc.bcm.edu	37	chr11	4674516	4674516	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgtgtgctgtgttcatattcTatgtacctttcattggattg	9	6	3	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:4674516T>A	ENST00000396952.5	+	2	1410	c.760T>A	c.(760-762)Tat>Aat	p.Y254N	OR51E1_ENST00000530215.1_Intron	NM_152430.3	NP_689643.2	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|skin(1)|stomach(2)	30		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;7.37e-14)|GBM - Glioblastoma multiforme(2;2.85e-05)|BRCA - Breast invasive adenocarcinoma(625;0.00222)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTTCATATTCTATGTACCTTT	0.493																																					p.Y254N		Atlas-SNP	.											.	OR51E1	67	.	0			c.T760A						.						235	224	228					11																	4674516		2201	4298	6499	SO:0001583	missense	143503	exon2			ATATTCTATGTAC	AY775731	CCDS31358.2	11p15.4	2012-08-22	2004-11-03	2004-11-06	ENSG00000180785	ENSG00000180785		"GPCR / Class A : Olfactory receptors"	15194	protein-coding gene	gene with protein product		611267	"olfactory receptor, family 51, subfamily E, member 1 pseudogene"	OR51E1P, OR52A3P, GPR164			Standard	NM_152430		Approved	GPR136	uc001lzi.4	Q8TCB6	OTTHUMG00000157024	ENST00000396952.5:c.760T>A	chr11.hg19:g.4674516T>A	ENSP00000380155:p.Tyr254Asn	52.0	0.0		63.0	19.0	NM_152430	A8KAM6|Q5S4P5|Q66X57|Q6IF93	Missense_Mutation	SNP	ENST00000396952.5	hg19	CCDS31358.2	.	.	.	.	.	.	.	.	.	.	T	20.4	3.983493	0.74474	.	.	ENSG00000180785	ENST00000396952	T	0.72394	-0.65	4.89	4.89	0.63831	GPCR, rhodopsin-like superfamily (1);	0.130327	0.35262	N	0.003328	D	0.90109	0.6910	H	0.98951	4.38	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.93626	0.6952	10	0.87932	D	0	.	13.7621	0.62973	0.0:0.0:0.0:1.0	.	253	Q8TCB6	O51E1_HUMAN	N	254	ENSP00000380155:Y254N	ENSP00000380155:Y254N	Y	+	1	0	OR51E1	4631092	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	4.106000	0.57804	2.188000	0.69820	0.533000	0.62120	TAT	.	.		0.493	OR51E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347136.2	NM_152430		A	4674516	T	A	4674516	3	1	163	1	0	0	0	0	1	0	0	0	11103	1522	53	4	762	4	OR51E1	11	4674516	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	4294864	4674516	130332000	168	24950										
FAR1	84188	hgsc.bcm.edu	37	chr11	13721881	13721881	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tagctttttgacagattgagAgatgaaaatccagattttag	9	4	0	6			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:13721881A>T	ENST00000354817.3	+	3	351	c.207A>T	c.(205-207)agA>agT	p.R69S		NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	69					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)|wax biosynthetic process (GO:0010025)	integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13						ACAGATTGAGAGATGAAAATC	0.343																																					p.R69S		Atlas-SNP	.											.	FAR1	40	.	0			c.A207T						.						54	57	56					11																	13721881		2200	4293	6493	SO:0001583	missense	84188	exon3			ATTGAGAGATGAA	AK026381	CCDS7813.1	11p15.2	2011-09-14	2008-06-06	2008-06-06	ENSG00000197601	ENSG00000197601	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	26222	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 1"		"male sterility domain containing 2"	MLSTD2		15220348, 15220349, 19027726	Standard	NM_032228		Approved	FLJ22728, SDR10E1	uc001mld.3	Q8WVX9	OTTHUMG00000165743	ENST00000354817.3:c.207A>T	chr11.hg19:g.13721881A>T	ENSP00000346874:p.Arg69Ser	229.0	0.0		322.0	71.0	NM_032228	D3DQW8|Q5CZA3	Missense_Mutation	SNP	ENST00000354817.3	hg19	CCDS7813.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.557581	0.86231	.	.	ENSG00000197601	ENST00000354817;ENST00000532701;ENST00000355107	T;T	0.40225	1.04;1.04	5.6	5.6	0.85130	Male sterility, NAD-binding (1);	0.096756	0.64402	D	0.000001	T	0.66694	0.2815	M	0.89414	3.03	0.80722	D	1	P;P	0.44478	0.741;0.836	P;P	0.56216	0.72;0.794	T	0.73088	-0.4093	10	0.72032	D	0.01	-11.7547	15.723	0.77728	1.0:0.0:0.0:0.0	.	69;69	E7ETC1;Q8WVX9	.;FACR1_HUMAN	S	69	ENSP00000346874:R69S;ENSP00000437111:R69S	ENSP00000346874:R69S	R	+	3	2	FAR1	13678457	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.666000	0.37460	2.252000	0.74401	0.533000	0.62120	AGA	.	.		0.343	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228		T	13721881	A	T	13721881	3	4	163	1	0	0	0	0	1	0	0	0	5682	301	11	4	213	4	FAR1	11	13721881	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	9047365	13721881	121284635	169	24951										
MRGPRX1	259249	hgsc.bcm.edu	37	chr11	18955672	18955672	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aggaggaagaccagtactgtGagcaggatggtcacgtacag	15	7	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:18955672G>T	ENST00000302797.3	-	1	884	c.660C>A	c.(658-660)ctC>ctA	p.L220L	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'Flank	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	220					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CCAGTACTGTGAGCAGGATGG	0.507																																					p.L220L		Atlas-SNP	.											.	MRGPRX1	84	.	0			c.C660A						.						98	82	87					11																	18955672		2194	4285	6479	SO:0001819	synonymous_variant	259249	exon1			TACTGTGAGCAGG		CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"GPCR / Class A : Orphans"	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.660C>A	chr11.hg19:g.18955672G>T		62.0	0.0		70.0	9.0	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Silent	SNP	ENST00000302797.3	hg19	CCDS7846.1																																																																																			.	.		0.507	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199		T	18955672	G	T	18955672	2	4	163	1	0	0	0	0	0	0	0	1	9775	1277	45	3		3	MRGPRX1	11	18955672	Silent	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	5233791	18955672	116050844	170	24952										
CD44	960	hgsc.bcm.edu	37	chr11	35223290	35223290	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acaccctcccctcattcaccAtgagcatcatgaggaagaag	7	14	3	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:35223290A>T	ENST00000428726.2	+	9	1232	c.1109A>T	c.(1108-1110)cAt>cTt	p.H370L	CD44_ENST00000434472.2_Intron|CD44_ENST00000433892.2_Intron|CD44_ENST00000360158.4_Intron|CD44_ENST00000526669.2_Intron|CD44_ENST00000415148.2_Missense_Mutation_p.H327L|CD44_ENST00000263398.6_Intron|CD44_ENST00000433354.2_Missense_Mutation_p.H371L|CD44_ENST00000278386.6_Intron|CD44_ENST00000449691.2_Missense_Mutation_p.H370L|CD44_ENST00000352818.4_Intron|CD44_ENST00000437706.2_Missense_Mutation_p.H370L	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	370	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	CTCATTCACCATGAGCATCAT	0.458																																					p.H370L		Atlas-SNP	.											.	CD44	48	.	0			c.A1109T						.						160	132	142					11																	35223290		2202	4298	6500	SO:0001583	missense	960	exon9			TTCACCATGAGCA	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"CD molecules", "Blood group antigens", "Proteoglycans / Cell surface : Other"	1681	protein-coding gene	gene with protein product	"hematopoietic cell E- and L-selectin ligand", "chondroitin sulfate proteoglycan 8"	107269	"CD44 antigen (homing function and Indian blood group system)"	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.1109A>T	chr11.hg19:g.35223290A>T	ENSP00000398632:p.His370Leu	91.0	0.0		131.0	31.0	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Missense_Mutation	SNP	ENST00000428726.2	hg19	CCDS7897.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.669701	0.29693	.	.	ENSG00000026508	ENST00000415148;ENST00000433354;ENST00000449691;ENST00000437706;ENST00000428726;ENST00000528672	T;T;T;T;T;T	0.29917	2.92;2.89;1.94;2.89;2.91;1.55	5.3	0.277	0.15668	.	0.821686	0.10860	N	0.626240	T	0.26991	0.0661	M	0.62723	1.935	0.19300	N	0.999976	B;B	0.18968	0.032;0.019	B;B	0.18561	0.022;0.01	T	0.30563	-0.9974	10	0.48119	T	0.1	-18.6779	4.2355	0.10623	0.561:0.1688:0.2702:0.0	.	327;370	P16070-4;P16070	.;CD44_HUMAN	L	327;371;370;370;370;22	ENSP00000389830:H327L;ENSP00000414567:H371L;ENSP00000391008:H370L;ENSP00000403990:H370L;ENSP00000398632:H370L;ENSP00000431860:H22L	ENSP00000389830:H327L	H	+	2	0	CD44	35179866	0.125000	0.22332	0.297000	0.24988	0.005000	0.04900	-0.035000	0.12205	0.014000	0.14944	-0.441000	0.05720	CAT	.	.		0.458	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610		T	35223290	A	T	35223290	3	4	163	1	0	0	0	0	1	0	0	0	3019	217	8	4	1143	4	CD44	11	35223290	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	16267618	35223290	99783226	171	24953										
RAG1	5896	hgsc.bcm.edu	37	chr11	36595110	36595110	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cattgttaaaagcccaccctAagttttcaaagaaatttcac	4	10	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:36595110A>T	ENST00000299440.5	+	2	368	c.256A>T	c.(256-258)Aag>Tag	p.K86*		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	86	Interaction with importin alpha-1.				adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				AGCCCACCCTAAGTTTTCAAA	0.488									Familial Hemophagocytic Lymphohistiocytosis																												p.K86X	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.A256T	GRCh37	CD982919	RAG1	D		.						78	85	82					11																	36595110		2202	4298	6500	SO:0001587	stop_gained	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CACCCTAAGTTTT	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.256A>T	chr11.hg19:g.36595110A>T	ENSP00000299440:p.Lys86*	151.0	0.0		149.0	40.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Nonsense_Mutation	SNP	ENST00000299440.5	hg19	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.799495	0.70567	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	.	.	.	6.14	6.14	0.99180	.	0.241604	0.41712	D	0.000838	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	12.1018	0.53788	0.7491:0.2509:0.0:0.0	.	.	.	.	X	86	.	ENSP00000299440:K86X	K	+	1	0	RAG1	36551686	0.991000	0.36638	0.822000	0.32727	0.519000	0.34347	3.003000	0.49505	2.367000	0.80283	0.529000	0.55759	AAG	.	.		0.488	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		T	36595110	A	T	36595110	4	4	163	1	0	0	0	0	0	1	0	0	13018	363	13	4	258	4	RAG1	11	36595110	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1371820	36595110	98411406	172	24954										
RAG2	5897	hgsc.bcm.edu	37	chr11	36615073	36615073	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	atgtcctcctaaaatatagaTggtgtcatttttggcaatag	8	6	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:36615073T>A	ENST00000311485.3	-	2	807	c.646A>T	c.(646-648)Atc>Ttc	p.I216F	C11orf74_ENST00000347206.4_5'Flank|C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000446510.2_5'Flank|C11orf74_ENST00000334307.5_5'Flank|RAG2_ENST00000528428.1_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	216					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				AAAATATAGATGGTGTCATTT	0.428									Familial Hemophagocytic Lymphohistiocytosis																												p.I216F		Atlas-SNP	.											.	RAG2	92	.	0			c.A646T						.						91	93	92					11																	36615073		2202	4298	6500	SO:0001583	missense	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TATAGATGGTGTC	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.646A>T	chr11.hg19:g.36615073T>A	ENSP00000308620:p.Ile216Phe	54.0	0.0		86.0	12.0	NM_001243785	A8K9E9|Q8TBL4	Missense_Mutation	SNP	ENST00000311485.3	hg19	CCDS7903.1	.	.	.	.	.	.	.	.	.	.	T	12.76	2.033200	0.35893	.	.	ENSG00000175097	ENST00000311485	T	0.77098	-1.07	5.7	-4.54	0.03452	Galactose oxidase/kelch, beta-propeller (1);Kelch-type beta propeller (1);	0.382274	0.27100	N	0.020921	T	0.78272	0.4257	M	0.80847	2.515	0.30621	N	0.758531	P	0.40619	0.724	P	0.45610	0.487	T	0.78375	-0.2228	10	0.87932	D	0	-0.0801	12.0096	0.53280	0.0:0.5675:0.1115:0.321	.	216	P55895	RAG2_HUMAN	F	216	ENSP00000308620:I216F	ENSP00000308620:I216F	I	-	1	0	RAG2	36571649	0.001000	0.12720	0.904000	0.35570	0.504000	0.33889	-0.198000	0.09505	-0.899000	0.03901	-0.256000	0.11100	ATC	.	.		0.428	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536		A	36615073	T	A	36615073	3	1	163	1	0	0	0	0	1	0	0	0	13020	1464	51	4	941	4	RAG2	11	36615073	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	19963	36615073	98391443	173	24955										
CKAP5	9793	hgsc.bcm.edu	37	chr11	46819392	46819392	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aaaagggctttagcaagctcTttggcagggtagaagcagtg	14	6	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:46819392T>A	ENST00000529230.1	-	11	1347	c.1301A>T	c.(1300-1302)aAg>aTg	p.K434M	CKAP5_ENST00000312055.5_Missense_Mutation_p.K434M|CKAP5_ENST00000415402.1_Missense_Mutation_p.K434M|CKAP5_ENST00000532321.1_5'Flank|CKAP5_ENST00000354558.3_Missense_Mutation_p.K434M			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	434					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						TAGCAAGCTCTTTGGCAGGGT	0.408																																					p.K434M	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.A1301T						.						144	145	144					11																	46819392		2201	4299	6500	SO:0001583	missense	9793	exon11			AAGCTCTTTGGCA		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.1301A>T	chr11.hg19:g.46819392T>A	ENSP00000432768:p.Lys434Met	213.0	0.0		280.0	53.0	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	hg19	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.006193	0.93287	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.52	5.52	0.82312	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81413	0.4817	M	0.76170	2.325	0.80722	D	1	D;D;D	0.89917	0.992;0.997;1.0	D;D;D	0.79108	0.983;0.989;0.992	D	0.83749	0.0208	10	0.72032	D	0.01	-7.0972	15.6381	0.76970	0.0:0.0:0.0:1.0	.	434;434;434	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	M	434	ENSP00000432768:K434M;ENSP00000395302:K434M;ENSP00000310227:K434M;ENSP00000346566:K434M	ENSP00000310227:K434M	K	-	2	0	CKAP5	46775968	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.280000	0.72626	2.102000	0.63906	0.528000	0.53228	AAG	.	.		0.408	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		A	46819392	T	A	46819392	3	1	163	1	0	0	0	0	1	0	0	0	3447	1609	56	4	4933	4	CKAP5	11	46819392	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	10204319	46819392	88187124	174	24956										
FNBP4	23360	hgsc.bcm.edu	37	chr11	47744591	47744591	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttgggagctggtggtggtggAggaggaggaggaggaggtgg	26	1	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:47744591A>T	ENST00000263773.5	-	15	2754	c.2742T>A	c.(2740-2742)ccT>ccA	p.P914P		NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	914	Pro-rich.					nucleus (GO:0005634)		p.P914P(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						gtggtggtggaggaggaggag	0.463																																					p.P914P		Atlas-SNP	.											FNBP4,NS,carcinoma,0,1	FNBP4	99	.	1	Substitution - coding silent(1)	endometrium(1)	c.T2742A						.						15	15	15					11																	47744591		1997	4159	6156	SO:0001819	synonymous_variant	23360	exon15			TGGTGGAGGAGGA	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.2742T>A	chr11.hg19:g.47744591A>T		46.0	0.0		34.0	4.0	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Silent	SNP	ENST00000263773.5	hg19	CCDS41644.1																																																																																			.	.		0.463	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			T	47744591	A	T	47744591	2	4	163	1	0	0	0	0	0	0	0	1	5975	291	11	4		4	FNBP4	11	47744591	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	925199	47744591	87261925	175	24957										
OR5D13	390142	hgsc.bcm.edu	37	chr11	55541071	55541071	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	catgataataatcatcagacTcaattcaaaactccatacaa	2	10	4	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:55541071T>A	ENST00000361760.1	+	1	158	c.158T>A	c.(157-159)cTc>cAc	p.L53H		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				ATCATCAGACTCAATTCAAAA	0.403																																					p.L53H		Atlas-SNP	.											.	OR5D13	96	.	0			c.T158A						.						175	162	166					11																	55541071		2200	4296	6496	SO:0001583	missense	390142	exon1			TCAGACTCAATTC	BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"GPCR / Class A : Olfactory receptors"	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.158T>A	chr11.hg19:g.55541071T>A	ENSP00000354800:p.Leu53His	138.0	0.0		121.0	35.0	NM_001001967	Q6IF68|Q6IFC9	Missense_Mutation	SNP	ENST00000361760.1	hg19	CCDS31507.1	.	.	.	.	.	.	.	.	.	.	T	12.74	2.029479	0.35797	.	.	ENSG00000198877	ENST00000361760	T	0.03065	4.06	3.52	2.26	0.28386	GPCR, rhodopsin-like superfamily (1);	1.214740	0.06546	U	0.744161	T	0.09335	0.0230	M	0.83384	2.64	0.09310	N	1	P	0.40376	0.715	B	0.42653	0.394	T	0.33317	-0.9873	10	0.87932	D	0	-10.5256	5.291	0.15727	0.1695:0.0:0.1734:0.6571	.	53	Q8NGL4	OR5DD_HUMAN	H	53	ENSP00000354800:L53H	ENSP00000354800:L53H	L	+	2	0	OR5D13	55297647	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.905000	0.04075	1.626000	0.50381	0.398000	0.26397	CTC	.	.		0.403	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967		A	55541071	T	A	55541071	3	1	163	1	0	0	0	0	1	0	0	0	11163	1551	54	4	160	4	OR5D13	11	55541071	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	7796480	55541071	79465445	176	24958										
OR5T2	219464	hgsc.bcm.edu	37	chr11	56000215	56000215	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcagccaagagaaagcattcTgtggttccaaaactacaagc	9	10	1	1	rs369632317		TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:56000215T>A	ENST00000313264.4	-	1	522	c.447A>T	c.(445-447)acA>acT	p.T149T		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	149						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					GAAAGCATTCTGTGGTTCCAA	0.418																																					p.T149T		Atlas-SNP	.											.	OR5T2	107	.	0			c.A447T						.						173	150	158					11																	56000215		2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			GCATTCTGTGGTT	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.447A>T	chr11.hg19:g.56000215T>A		93.0	0.0		102.0	27.0	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	hg19	CCDS31523.1																																																																																			.	.		0.418	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		A	56000215	T	A	56000215	2	1	163	1	0	0	0	0	0	0	0	1	11191	1567	55	4		4	OR5T2	11	56000215	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	459144	56000215	79006301	177	24959										
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57076311	57076311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aggactgcagactgcccctgGggccatgtttctcagcccaa	11	14	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:57076311G>A	ENST00000532437.1	-	5	4185	c.3874C>T	c.(3874-3876)Cca>Tca	p.P1292S	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.P1292S|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1292	Acidic.|Gly-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				ACTGCCCCTGGGGCCATGTTT	0.582																																					p.P1292S		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.C3874T						.						100	104	103					11																	57076311		2201	4296	6497	SO:0001583	missense	85456	exon6			CCCCTGGGGCCAT	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.3874C>T	chr11.hg19:g.57076311G>A	ENSP00000437271:p.Pro1292Ser	45.0	0.0		40.0	6.0	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	hg19	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	G	1.957	-0.439753	0.04636	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.27890	1.64;1.64	4.56	-0.763	0.11030	.	0.648565	0.13545	N	0.379893	T	0.21145	0.0509	L	0.51422	1.61	0.09310	N	1	B	0.16396	0.017	B	0.15052	0.012	T	0.30446	-0.9978	10	0.62326	D	0.03	-4.8043	0.7367	0.00967	0.2932:0.1859:0.3598:0.1611	.	1292	Q9C0C2	TB182_HUMAN	S	1292	ENSP00000350990:P1292S;ENSP00000437271:P1292S	ENSP00000350990:P1292S	P	-	1	0	TNKS1BP1	56832887	0.000000	0.05858	0.002000	0.10522	0.046000	0.14306	-0.430000	0.06973	-0.194000	0.10399	-0.361000	0.07541	CCA	.	.		0.582	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		A	57076311	G	A	57076311	3	1	163	1	0	0	0	0	1	0	0	0	16335	1232	43	3	1339	3	TNKS1BP1	11	57076311	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	1076096	57076311	77930205	178	24960										
DTX4	23220	hgsc.bcm.edu	37	chr11	58940270	58940270	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agtccatgaaccagttccgcCaagacacgggtgagccagcc	11	14	0	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:58940270C>G	ENST00000227451.3	+	1	306	c.202C>G	c.(202-204)Caa>Gaa	p.Q68E	DTX4_ENST00000532982.1_Intron	NM_015177.1	NP_055992.1	Q9Y2E6	DTX4_HUMAN	deltex 4, E3 ubiquitin ligase	68	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				innate immune response (GO:0045087)|Notch signaling pathway (GO:0007219)|positive regulation of type I interferon production (GO:0032481)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	20		all_epithelial(135;0.125)				CCAGTTCCGCCAAGACACGGG	0.711																																					p.Q68E		Atlas-SNP	.											.	DTX4	84	.	0			c.C202G						.						14	17	16					11																	58940270		2182	4285	6467	SO:0001583	missense	23220	exon1			TTCCGCCAAGACA	AB023154	CCDS44612.1	11q12.2	2014-01-28	2014-01-28		ENSG00000110042	ENSG00000110042		"RING-type (C3HC4) zinc fingers"	29151	protein-coding gene	gene with protein product			"deltex 4 homolog (Drosophila)", "deltex homolog 4 (Drosophila)"			10231032, 22388039	Standard	NM_015177		Approved	KIAA0937, RNF155	uc001nns.2	Q9Y2E6	OTTHUMG00000167336	ENST00000227451.3:c.202C>G	chr11.hg19:g.58940270C>G	ENSP00000227451:p.Gln68Glu	106.0	0.0		127.0	33.0	NM_015177	Q0VF38	Missense_Mutation	SNP	ENST00000227451.3	hg19	CCDS44612.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.340849	0.60963	.	.	ENSG00000110042	ENST00000227451	T	0.40225	1.04	4.07	3.14	0.36123	WWE domain (2);WWE domain, subgroup (1);	.	.	.	.	T	0.36991	0.0987	L	0.33792	1.035	0.48975	D	0.999735	P	0.35033	0.481	B	0.42030	0.373	T	0.11743	-1.0575	9	0.30854	T	0.27	.	12.6732	0.56878	0.1672:0.8328:0.0:0.0	.	68	Q9Y2E6	DTX4_HUMAN	E	68	ENSP00000227451:Q68E	ENSP00000227451:Q68E	Q	+	1	0	DTX4	58696846	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.946000	0.75953	0.962000	0.38057	0.655000	0.94253	CAA	.	.		0.711	DTX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394228.1	XM_166213		G	58940270	C	G	58940270	3	3	163	1	0	0	0	0	1	0	0	0	4799	595	21	4	204	4	DTX4	11	58940270	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	1863959	58940270	76066246	179	24961										
MS4A3	932	hgsc.bcm.edu	37	chr11	59828780	59828780	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tatcagaaagcaaaattacaAgttcttggggtaagtcagcc	9	7	3	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:59828780A>C	ENST00000278865.3	+	2	220	c.147A>C	c.(145-147)caA>caC	p.Q49H	MS4A3_ENST00000395032.2_Intron|MS4A3_ENST00000358152.2_Missense_Mutation_p.Q49H|MS4A3_ENST00000534744.1_Missense_Mutation_p.Q49H|MS4A3_ENST00000526199.1_3'UTR	NM_006138.4	NP_006129.4	Q96HJ5	MS4A3_HUMAN	membrane-spanning 4-domains, subfamily A, member 3 (hematopoietic cell-specific)	49						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(4)|kidney(2)|lung(9)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		all_epithelial(135;0.245)				CAAAATTACAAGTTCTTGGGG	0.433																																					p.Q49H		Atlas-SNP	.											.	MS4A3	47	.	0			c.A147C						.						107	102	104					11																	59828780		2201	4295	6496	SO:0001583	missense	932	exon2			ATTACAAGTTCTT	L35848	CCDS31567.1, CCDS31568.1, CCDS41651.1	11q12-q13.1	2008-03-25				ENSG00000149516			7317	protein-coding gene	gene with protein product		606498		CD20L		7524084	Standard	NM_006138		Approved	HTM4	uc001nom.3	Q96HJ5		ENST00000278865.3:c.147A>C	chr11.hg19:g.59828780A>C	ENSP00000278865:p.Gln49His	70.0	0.0		89.0	16.0	NM_001031809	A8MTP8|Q8NHW2	Missense_Mutation	SNP	ENST00000278865.3	hg19	CCDS31567.1	.	.	.	.	.	.	.	.	.	.	A	10.17	1.277820	0.23307	.	.	ENSG00000149516	ENST00000358152;ENST00000278865;ENST00000534744	T;T;T	0.38722	1.12;3.07;1.12	4.21	0.678	0.17969	.	0.391986	0.25944	N	0.027291	T	0.43897	0.1268	L	0.29908	0.895	0.09310	N	1	D;D	0.89917	1.0;0.999	D;D	0.70935	0.971;0.936	T	0.19128	-1.0315	10	0.87932	D	0	-9.0683	5.822	0.18532	0.6552:0.0:0.3448:0.0	.	49;49	Q96HJ5-2;Q96HJ5	.;MS4A3_HUMAN	H	49	ENSP00000350872:Q49H;ENSP00000278865:Q49H;ENSP00000434117:Q49H	ENSP00000278865:Q49H	Q	+	3	2	MS4A3	59585356	0.000000	0.05858	0.275000	0.24674	0.054000	0.15201	-0.488000	0.06497	0.263000	0.21812	0.460000	0.39030	CAA	.	.		0.433	MS4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394417.1			C	59828780	A	C	59828780	3	2	163	1	0	0	0	0	1	0	0	0	9870	69	3	5	149	5	MS4A3	11	59828780	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	888510	59828780	75177736	180	24962										
MS4A14	84689	hgsc.bcm.edu	37	chr11	60170383	60170383	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tcatttttaaactatctttcAgggtcaaggtgtcacgggca	9	8	5	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:60170383A>T	ENST00000300187.6	+	4	595		c.e4-1		MS4A14_ENST00000531787.1_Splice_Site|MS4A14_ENST00000531783.1_Splice_Site|MS4A14_ENST00000395005.2_Splice_Site|MS4A14_ENST00000395001.1_Splice_Site	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14							integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						ACTATCTTTCAGGGTCAAGGT	0.353																																					.		Atlas-SNP	.											.	MS4A14	120	.	0			c.319-2A>T						.						179	168	172					11																	60170383		2203	4300	6503	SO:0001630	splice_region_variant	84689	exon4			TCTTTCAGGGTCA	AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"membrane-spanning 4-domains, subfamily A, member 16"	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.319-1A>T	chr11.hg19:g.60170383A>T		54.0	0.0		87.0	15.0	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Splice_Site	SNP	ENST00000300187.6	hg19	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	A	8.253	0.809407	0.16537	.	.	ENSG00000166928	ENST00000300187;ENST00000395005;ENST00000526375;ENST00000531783;ENST00000534688	.	.	.	4.45	4.45	0.53987	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.4078	0.44274	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MS4A14	59926959	1.000000	0.71417	0.986000	0.45419	0.021000	0.10359	3.397000	0.52572	2.223000	0.72356	0.528000	0.53228	.	.	.		0.353	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		Intron	T	60170383	A	T	60170383	5	4	163	1	0	0	0	0	0	0	1	0	9867	202	7	4	331	4	MS4A14	11	60170383	Splice_Site	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	341603	60170383	74836133	181	24963										
HRASLS5	117245	hgsc.bcm.edu	37	chr11	63235905	63235905	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tagccaattcgaaaaatctcAatcaggtctccaggtctggg	9	10	4	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:63235905A>T	ENST00000301790.4	-	4	567	c.408T>A	c.(406-408)atT>atA	p.I136I	HRASLS5_ENST00000539221.1_Silent_p.I136I|HRASLS5_ENST00000540857.1_Silent_p.I126I			Q96KN8	HRSL5_HUMAN	HRAS-like suppressor family, member 5	136							transferase activity, transferring acyl groups (GO:0016746)			endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	14						GAAAAATCTCAATCAGGTCTC	0.423																																					p.I136I		Atlas-SNP	.											.	HRASLS5	28	.	0			c.T408A						.						128	125	126					11																	63235905		2201	4298	6499	SO:0001819	synonymous_variant	117245	exon4			AATCTCAATCAGG	AJ416558	CCDS8044.1, CCDS53646.1, CCDS53647.1	11q13.2	2006-08-16			ENSG00000168004	ENSG00000168004			24978	protein-coding gene	gene with protein product		611474					Standard	NM_001146729		Approved	HRLP5	uc001nwy.2	Q96KN8	OTTHUMG00000167806	ENST00000301790.4:c.408T>A	chr11.hg19:g.63235905A>T		46.0	0.0		80.0	9.0	NM_001146728	B7X6T1|F5GZ87|F5H4Y9	Silent	SNP	ENST00000301790.4	hg19	CCDS8044.1																																																																																			.	.		0.423	HRASLS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396375.1	NM_054108		T	63235905	A	T	63235905	2	4	163	1	0	0	0	0	0	0	0	1	7360	126	5	4		4	HRASLS5	11	63235905	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	3065522	63235905	71770611	182	24964										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73066957	73066957	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cgctgtctgacctcatgatcAagcctgtgcagcggatccca	10	14	3	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:73066957A>T	ENST00000263674.3	+	5	3972	c.3622A>T	c.(3622-3624)Aag>Tag	p.K1208*	AP002761.1_ENST00000582555.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1208	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CCTCATGATCAAGCCTGTGCA	0.572																																					p.K1208X		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.A3622T						.						153	142	146					11																	73066957		2200	4293	6493	SO:0001587	stop_gained	9828	exon5			ATGATCAAGCCTG	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.3622A>T	chr11.hg19:g.73066957A>T	ENSP00000263674:p.Lys1208*	59.0	0.0		76.0	15.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Nonsense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	A	46	12.552663	0.99677	.	.	ENSG00000110237	ENST00000263674	.	.	.	5.68	5.68	0.88126	.	0.047372	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.1042	14.7721	0.69688	1.0:0.0:0.0:0.0	.	.	.	.	X	1208	.	ENSP00000263674:K1208X	K	+	1	0	ARHGEF17	72744605	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.170000	0.68504	0.460000	0.39030	AAG	.	.		0.572	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		T	73066957	A	T	73066957	4	4	163	1	0	0	0	0	0	1	0	0	900	131	5	4	3640	4	ARHGEF17	11	73066957	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	9831052	73066957	61939559	183	24965										
NAALAD2	10003	hgsc.bcm.edu	37	chr11	89911262	89911262	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	taagaaacatgatcaacaatTgacagaccatggagtatcat	7	7	2	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:89911262T>A	ENST00000534061.1	+	16	2065	c.1835T>A	c.(1834-1836)tTg>tAg	p.L612*	NAALAD2_ENST00000321955.4_Nonsense_Mutation_p.L579*|NAALAD2_ENST00000375944.3_Intron	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	612					neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GATCAACAATTGACAGACCAT	0.308																																					p.L612X		Atlas-SNP	.											.	NAALAD2	113	.	0			c.T1835A						.						88	93	91					11																	89911262		2201	4296	6497	SO:0001587	stop_gained	10003	exon16			AACAATTGACAGA	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1835T>A	chr11.hg19:g.89911262T>A	ENSP00000432481:p.Leu612*	123.0	0.0		127.0	26.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Nonsense_Mutation	SNP	ENST00000534061.1	hg19	CCDS8288.1	.	.	.	.	.	.	.	.	.	.	T	39	7.586059	0.98374	.	.	ENSG00000077616	ENST00000534061;ENST00000321955	.	.	.	5.63	4.49	0.54785	.	0.425440	0.21786	N	0.069125	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.2761	12.9185	0.58218	0.0:0.0:0.1357:0.8643	.	.	.	.	X	612;579	.	.	L	+	2	0	NAALAD2	89550910	0.877000	0.30153	0.002000	0.10522	0.838000	0.47535	4.510000	0.60455	0.956000	0.37904	0.524000	0.50904	TTG	.	.		0.308	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		A	89911262	T	A	89911262	4	1	163	1	0	0	0	0	0	1	0	0	10137	1821	63	4	1897	4	NAALAD2	11	89911262	Nonsense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	16844305	89911262	45095254	184	24966										
MMP20	9313	hgsc.bcm.edu	37	chr11	102479781	102479781	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggtctgtggaatgggccaggCccagggcatggccaaattca	15	10	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:102479781C>A	ENST00000260228.2	-	5	710	c.698G>T	c.(697-699)gGc>gTc	p.G233V	MMP20_ENST00000544938.1_5'Flank|RP11-817J15.2_ENST00000544115.1_RNA|RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	240					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	ATGGGCCAGGCCCAGGGCATG	0.428																																					p.G233V		Atlas-SNP	.											.	MMP20	52	.	0			c.G698T						.						102	96	98					11																	102479781		2203	4299	6502	SO:0001583	missense	9313	exon5			GCCAGGCCCAGGG	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"enamelysin"	604629	"matrix metalloproteinase 20 (enamelysin)"			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.698G>T	chr11.hg19:g.102479781C>A	ENSP00000260228:p.Gly233Val	92.0	0.0		109.0	29.0	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	hg19	CCDS8318.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.885304	0.91814	.	.	ENSG00000137674	ENST00000260228	D	0.91894	-2.93	5.38	5.38	0.77491	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98160	0.9392	H	0.99498	4.595	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99372	1.0920	10	0.87932	D	0	.	18.9412	0.92605	0.0:1.0:0.0:0.0	.	233	O60882	MMP20_HUMAN	V	233	ENSP00000260228:G233V	ENSP00000260228:G233V	G	-	2	0	MMP20	101984991	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.376000	0.79658	2.793000	0.96121	0.655000	0.94253	GGC	.	.		0.428	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1			A	102479781	C	A	102479781	3	1	163	1	0	0	0	0	1	0	0	0	9668	739	26	3	777	3	MMP20	11	102479781	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	12568519	102479781	32526735	185	24967										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105768993	105768993	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tcttttgtattaatttttatAgggattcaaggatatttctc	6	4	3	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:105768993A>T	ENST00000530497.1	+	6	726		c.e6-1		GRIA4_ENST00000282499.5_Splice_Site|GRIA4_ENST00000428631.2_Splice_Site|GRIA4_ENST00000393127.2_Splice_Site|GRIA4_ENST00000525187.1_Splice_Site|GRIA4_ENST00000393125.2_Splice_Site			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4						glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		TAATTTTTATAGGGATTCAAG	0.279																																					.		Atlas-SNP	.											.	GRIA4	380	.	0			c.727-2A>T						.						33	37	35					11																	105768993		2201	4294	6495	SO:0001630	splice_region_variant	2893	exon7			TTTTATAGGGATT	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.727-1A>T	chr11.hg19:g.105768993A>T		130.0	0.0		165.0	35.0	NM_001077243	Q86XE8	Splice_Site	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.079267	0.76528	.	.	ENSG00000152578	ENST00000393125;ENST00000282499;ENST00000393127;ENST00000428631;ENST00000530497;ENST00000525187	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0037	0.80327	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GRIA4	105274203	1.000000	0.71417	0.997000	0.53966	0.818000	0.46254	8.926000	0.92839	2.184000	0.69523	0.533000	0.62120	.	.	.		0.279	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1		Intron	T	105768993	A	T	105768993	5	4	163	1	0	0	0	0	0	0	1	0	6779	434	15	4	747	4	GRIA4	11	105768993	Splice_Site	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	3289212	105768993	29237523	186	24968										
ANKK1	255239	hgsc.bcm.edu	37	chr11	113270966	113270966	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccactctgggtggttctaagCcaggagccgagatggaaatt	13	9	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:113270966C>A	ENST00000303941.3	+	8	2369	c.2275C>A	c.(2275-2277)Cca>Aca	p.P759T		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	759							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TGGTTCTAAGCCAGGAGCCGA	0.587																																					p.P759T		Atlas-SNP	.											.	ANKK1	83	.	0			c.C2275A						.						7	9	8					11																	113270966		1783	3859	5642	SO:0001583	missense	255239	exon8			TCTAAGCCAGGAG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"Ankyrin repeat domain containing"	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.2275C>A	chr11.hg19:g.113270966C>A	ENSP00000306678:p.Pro759Thr	99.0	0.0		98.0	26.0	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	hg19	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	C	10.74	1.436234	0.25813	.	.	ENSG00000170209	ENST00000303941	T	0.74737	-0.87	4.94	0.403	0.16350	Ankyrin repeat-containing domain (1);	0.242926	0.20916	U	0.083367	T	0.52058	0.1711	N	0.19112	0.55	0.09310	N	1	B	0.23377	0.084	B	0.20767	0.031	T	0.44544	-0.9321	10	0.66056	D	0.02	-0.3747	2.9286	0.05792	0.1968:0.4703:0.0:0.333	.	759	Q8NFD2	ANKK1_HUMAN	T	759	ENSP00000306678:P759T	ENSP00000306678:P759T	P	+	1	0	ANKK1	112776176	0.006000	0.16342	0.006000	0.13384	0.003000	0.03518	0.198000	0.17217	0.516000	0.28340	-0.290000	0.09829	CCA	.	.		0.587	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		A	113270966	C	A	113270966	3	1	163	1	0	0	0	0	1	0	0	0	631	739	26	3	2305	3	ANKK1	11	113270966	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	7501973	113270966	21735550	187	24969										
DRD2	1813	hgsc.bcm.edu	37	chr11	113295219	113295219	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cagccatgcacaccagcacgTtgccgaagacgatgacagcg	11	14	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:113295219T>A	ENST00000362072.3	-	2	499	c.155A>T	c.(154-156)aAc>aTc	p.N52I	DRD2_ENST00000346454.3_Missense_Mutation_p.N52I|DRD2_ENST00000535984.1_5'UTR|DRD2_ENST00000542968.1_Missense_Mutation_p.N52I|DRD2_ENST00000355319.2_Missense_Mutation_p.N52I|DRD2_ENST00000538967.1_Missense_Mutation_p.N52I|DRD2_ENST00000544518.1_Missense_Mutation_p.N52I	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	52					activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CACCAGCACGTTGCCGAAGAC	0.622																																					p.N52I		Atlas-SNP	.											.	DRD2	98	.	0			c.A155T						.						246	185	206					11																	113295219		2201	4296	6497	SO:0001583	missense	1813	exon2			AGCACGTTGCCGA	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.155A>T	chr11.hg19:g.113295219T>A	ENSP00000354859:p.Asn52Ile	98.0	0.0		85.0	17.0	NM_016574	Q9NZR3|Q9UPA9	Missense_Mutation	SNP	ENST00000362072.3	hg19	CCDS8361.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.030105	0.93575	.	.	ENSG00000149295	ENST00000355319;ENST00000346454;ENST00000362072;ENST00000544518;ENST00000542968;ENST00000538967;ENST00000543292	D;D;D;D;D;D;D	0.96619	-4.07;-4.07;-4.07;-4.07;-4.07;-4.07;-4.07	5.52	5.52	0.82312	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.99118	0.9696	H	0.99732	4.735	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98740	1.0716	10	0.87932	D	0	.	15.6343	0.76937	0.0:0.0:0.0:1.0	.	52;52;52;52	F8VUV1;P14416-3;P14416-2;P14416	.;.;.;DRD2_HUMAN	I	52	ENSP00000347474:N52I;ENSP00000278597:N52I;ENSP00000354859:N52I;ENSP00000441068:N52I;ENSP00000442172:N52I;ENSP00000438215:N52I;ENSP00000438419:N52I	ENSP00000278597:N52I	N	-	2	0	DRD2	112800429	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.979000	0.88103	2.091000	0.63221	0.459000	0.35465	AAC	.	.		0.622	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		A	113295219	T	A	113295219	3	1	163	1	0	0	0	0	1	0	0	0	4759	1725	60	4	1204	4	DRD2	11	113295219	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	24253	113295219	21711297	188	24970										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117299320	117299320	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aaggtggctgtggaggcggcAgcgggggcccctgggtgggg	24	8	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:117299320A>T	ENST00000321322.6	-	33	6067	c.6066T>A	c.(6064-6066)gcT>gcA	p.A2022A	DSCAML1_ENST00000527706.1_Silent_p.A1752A	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1962					axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		TGGAGGCGGCAGCGGGGGCCC	0.721																																					p.A2022A		Atlas-SNP	.											.	DSCAML1	286	.	0			c.T6066A						.						11	13	12					11																	117299320		2190	4281	6471	SO:0001819	synonymous_variant	57453	exon33			GGCGGCAGCGGGG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.6066T>A	chr11.hg19:g.117299320A>T		79.0	0.0		128.0	24.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	hg19	CCDS8384.1																																																																																			.	.		0.721	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117299320	A	T	117299320	2	4	163	1	0	0	0	0	0	0	0	1	4771	175	7	4		4	DSCAML1	11	117299320	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	4004101	117299320	17707196	189	24971										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117375751	117375751	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttgggttgcaccacaaatcgAgggggcactgcagaaagagg	15	8	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:117375751A>T	ENST00000321322.6	-	10	2251	c.2250T>A	c.(2248-2250)ccT>ccA	p.P750P	DSCAML1_ENST00000527706.1_Silent_p.P480P	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	690	Ig-like C2-type 8.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CCACAAATCGAGGGGGCACTG	0.562																																					p.P750P		Atlas-SNP	.											.	DSCAML1	286	.	0			c.T2250A						.						93	82	86					11																	117375751		2201	4296	6497	SO:0001819	synonymous_variant	57453	exon10			AAATCGAGGGGGC		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2250T>A	chr11.hg19:g.117375751A>T		66.0	0.0		70.0	10.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	hg19	CCDS8384.1																																																																																			.	.		0.562	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117375751	A	T	117375751	2	4	163	1	0	0	0	0	0	0	0	1	4771	291	11	4		4	DSCAML1	11	117375751	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	76431	117375751	17630765	190	24972										
FOXR1	283150	hgsc.bcm.edu	37	chr11	118851924	118851924	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tccttttcttacagatgtgaTgcccttcctctttgatcttt	5	11	3	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr11:118851924T>A	ENST00000317011.3	+	6	1082	c.857T>A	c.(856-858)aTg>aAg	p.M286K		NM_181721.2	NP_859072.1	Q6PIV2	FOXR1_HUMAN	forkhead box R1	286					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		ACAGATGTGATGCCCTTCCTC	0.448																																					p.M286K		Atlas-SNP	.											.	FOXR1	30	.	0			c.T857A						.						257	240	246					11																	118851924		2200	4295	6495	SO:0001583	missense	283150	exon6			ATGTGATGCCCTT	AB094092	CCDS31688.1	11q23.3	2008-02-05			ENSG00000176302	ENSG00000176302		"Forkhead boxes"	29980	protein-coding gene	gene with protein product		615755				15067358	Standard	XM_005271514		Approved	DLNB13, FOXN5	uc001pui.3	Q6PIV2	OTTHUMG00000166347	ENST00000317011.3:c.857T>A	chr11.hg19:g.118851924T>A	ENSP00000314806:p.Met286Lys	129.0	0.0		119.0	21.0	NM_181721	B0YJ15|Q08AS8|Q86UT9|Q8IXX2	Missense_Mutation	SNP	ENST00000317011.3	hg19	CCDS31688.1	.	.	.	.	.	.	.	.	.	.	T	16.12	3.032635	0.54790	.	.	ENSG00000176302	ENST00000317011	D	0.95171	-3.63	5.59	5.59	0.84812	.	0.226336	0.45126	D	0.000387	D	0.91181	0.7222	N	0.25647	0.755	0.42761	D	0.993808	P	0.48911	0.917	P	0.46049	0.502	D	0.91854	0.5494	10	0.56958	D	0.05	.	12.4511	0.55677	0.0:0.0:0.0:1.0	.	286	Q6PIV2	FOXR1_HUMAN	K	286	ENSP00000314806:M286K	ENSP00000314806:M286K	M	+	2	0	FOXR1	118357134	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.013000	0.57138	2.254000	0.74563	0.533000	0.62120	ATG	.	.		0.448	FOXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389312.1	NM_181721		A	118851924	T	A	118851924	3	1	163	1	0	0	0	0	1	0	0	0	6039	1464	51	4	879	4	FOXR1	11	118851924	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	1476173	118851924	16154592	191	24973										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2800241	2800241	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tggcgccctcttaccctttgTgaactgcagggacgcggggc	14	13	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:2800241T>A	ENST00000347598.4	+	49	6437	c.6437T>A	c.(6436-6438)gTg>gAg	p.V2146E	CACNA1C_ENST00000399629.1_Missense_Mutation_p.V2115E|CACNA1C_ENST00000399638.1_Missense_Mutation_p.V2126E|CACNA1C_ENST00000399617.1_Missense_Mutation_p.V2133E|CACNA1C_ENST00000335762.5_Missense_Mutation_p.V2123E|CACNA1C_ENST00000399637.1_Missense_Mutation_p.V2117E|CACNA1C_ENST00000344100.3_Missense_Mutation_p.V2139E|CACNA1C_ENST00000399595.1_Missense_Mutation_p.V2106E|CACNA1C_ENST00000399606.1_Missense_Mutation_p.V2118E|CACNA1C_ENST00000399641.1_Missense_Mutation_p.V2098E|CACNA1C_ENST00000399634.1_Missense_Mutation_p.V2169E|CACNA1C_ENST00000399644.1_Missense_Mutation_p.V2098E|CACNA1C_ENST00000399597.1_Missense_Mutation_p.V2098E|CACNA1C_ENST00000399621.1_Missense_Mutation_p.V2117E|CACNA1C_ENST00000399603.1_Missense_Mutation_p.V2098E|CACNA1C_ENST00000402845.3_Missense_Mutation_p.V2117E|CACNA1C-AS1_ENST00000541673.1_RNA|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399649.1_Missense_Mutation_p.V2104E|CACNA1C_ENST00000406454.3_Missense_Mutation_p.V2169E|CACNA1C-AS1_ENST00000544517.1_RNA|CACNA1C_ENST00000399601.1_Missense_Mutation_p.V2098E|CACNA1C_ENST00000399655.1_Missense_Mutation_p.V2098E|CACNA1C_ENST00000327702.7_Missense_Mutation_p.V2133E|CACNA1C_ENST00000399591.1_Missense_Mutation_p.V2106E	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	2181					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TTACCCTTTGTGAACTGCAGG	0.692																																					p.V2181E		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.T6542A						.						13	16	15					12																	2800241		1901	4090	5991	SO:0001583	missense	775	exon50			CCTTTGTGAACTG	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.6437T>A	chr12.hg19:g.2800241T>A	ENSP00000266376:p.Val2146Glu	117.0	0.0		143.0	30.0	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.620520	0.46736	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2	4.49	2.11	0.27256	.	0.462954	0.21481	N	0.073824	T	0.40956	0.1138	N	0.25647	0.755	0.24399	N	0.994716	B;P;B;B;B;B;B;B;B;B;B;B;B;P;B;P;B;B;B;B;B;P;B;B;B	0.37663	0.167;0.546;0.13;0.046;0.374;0.328;0.145;0.374;0.214;0.082;0.328;0.007;0.066;0.604;0.016;0.469;0.066;0.321;0.328;0.029;0.145;0.515;0.328;0.277;0.007	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.36845	0.066;0.234;0.055;0.028;0.156;0.116;0.079;0.156;0.139;0.034;0.116;0.015;0.036;0.156;0.007;0.075;0.036;0.075;0.116;0.047;0.079;0.156;0.116;0.079;0.015	T	0.27502	-1.0072	10	0.59425	D	0.04	.	8.1687	0.31241	0.0:0.3378:0.0:0.6622	.	789;2139;2095;2181;2133;2117;2098;2115;2126;2098;2118;2098;2129;2146;2098;2133;2169;2106;2104;2106;2087;2117;2117;2098;2098	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	E	2123;2098;2098;2126;2098;2117;2117;2106;2098;2146;2118;2098;2139;2115;2133;2104;2117;2098;2169;2133;2169;2106;1999	ENSP00000336982:V2123E;ENSP00000382563:V2098E;ENSP00000382552:V2098E;ENSP00000382547:V2126E;ENSP00000382506:V2098E;ENSP00000382530:V2117E;ENSP00000382546:V2117E;ENSP00000382500:V2106E;ENSP00000382549:V2098E;ENSP00000266376:V2146E;ENSP00000382515:V2118E;ENSP00000382510:V2098E;ENSP00000341092:V2139E;ENSP00000382537:V2115E;ENSP00000329877:V2133E;ENSP00000382557:V2104E;ENSP00000385724:V2117E;ENSP00000382512:V2098E;ENSP00000382542:V2169E;ENSP00000382526:V2133E;ENSP00000385896:V2169E;ENSP00000382504:V2106E	ENSP00000323129:V1999E	V	+	2	0	CACNA1C	2670502	0.988000	0.35896	0.938000	0.37757	0.984000	0.73092	1.181000	0.32017	0.346000	0.23899	-0.353000	0.07706	GTG	.	.		0.692	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		A	2800241	T	A	2800241	3	1	163	1	0	0	0	0	1	0	0	0	2542	1696	59	4	7188	4	CACNA1C	12	2800241	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10		2800241	131051654	192	24974										
MFAP5	8076	hgsc.bcm.edu	37	chr12	8813492	8813492	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	attgacccccaggggtatccAgtctatagcaaaggaagaga	11	9	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:8813492A>T	ENST00000359478.2	-	3	248	c.61T>A	c.(61-63)Tgg>Agg	p.W21R	MFAP5_ENST00000543369.1_Intron|MFAP5_ENST00000433590.2_Missense_Mutation_p.W21R|MFAP5_ENST00000535336.1_Missense_Mutation_p.W21R|MFAP5_ENST00000396549.2_Missense_Mutation_p.W21R|MFAP5_ENST00000538107.1_5'UTR|MFAP5_ENST00000540087.1_Missense_Mutation_p.W21R	NM_003480.2	NP_003471.1	Q13361	MFAP5_HUMAN	microfibrillar associated protein 5	21					extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|skin(1)	13	Lung SC(5;0.184)					AGGGGTATCCAGTCTATAGCA	0.428																																					p.W21R		Atlas-SNP	.											.	MFAP5	34	.	0			c.T61A						.						88	89	89					12																	8813492		2203	4300	6503	SO:0001583	missense	8076	exon3			GTATCCAGTCTAT	AK124368	CCDS8595.1, CCDS73437.1	12p13.1-p12.3	2004-04-05				ENSG00000197614			29673	protein-coding gene	gene with protein product		601103				9792630, 8557636	Standard	XM_005253485		Approved	MAGP2, MP25	uc001qut.1	Q13361		ENST00000359478.2:c.61T>A	chr12.hg19:g.8813492A>T	ENSP00000352455:p.Trp21Arg	135.0	0.0		149.0	31.0	NM_003480	B0AZL6|D3DUV1|Q7Z490	Missense_Mutation	SNP	ENST00000359478.2	hg19	CCDS8595.1	.	.	.	.	.	.	.	.	.	.	A	6.246	0.413525	0.11812	.	.	ENSG00000197614	ENST00000359478;ENST00000433590;ENST00000396549;ENST00000535336;ENST00000540087;ENST00000544889	.	.	.	4.81	2.43	0.29744	.	0.142496	0.34178	N	0.004199	T	0.29914	0.0748	L	0.38838	1.175	0.26858	N	0.968011	B;B;B	0.24258	0.014;0.1;0.1	B;B;B	0.26202	0.025;0.067;0.067	T	0.19289	-1.0310	9	0.48119	T	0.1	-6.3481	6.5106	0.22220	0.8067:0.0:0.1933:0.0	.	21;21;21	B3KW70;Q13361;Q7Z490	.;MFAP5_HUMAN;.	R	21	.	ENSP00000352455:W21R	W	-	1	0	MFAP5	8704759	0.936000	0.31750	0.438000	0.26821	0.038000	0.13279	1.918000	0.40006	0.417000	0.25871	0.533000	0.62120	TGG	.	.		0.428	MFAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400656.2	NM_003480		T	8813492	A	T	8813492	3	4	163	1	0	0	0	0	1	0	0	0	9527	188	7	4	492	4	MFAP5	12	8813492	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	6013251	8813492	125038403	193	24975										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41374784	41374784	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtggcacttacttggagccgTggttcagacaatcatagtcc	11	10	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:41374784T>A	ENST00000551295.2	+	16	1995	c.1878T>A	c.(1876-1878)cgT>cgA	p.R626R	CNTN1_ENST00000347616.1_Silent_p.R626R|CNTN1_ENST00000348761.2_Silent_p.R615R	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	626	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				CTTGGAGCCGTGGTTCAGACA	0.428																																					p.R626R		Atlas-SNP	.											.	CNTN1	207	.	0			c.T1878A						.						133	135	135					12																	41374784		2203	4300	6503	SO:0001819	synonymous_variant	1272	exon16			GAGCCGTGGTTCA	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1878T>A	chr12.hg19:g.41374784T>A		71.0	0.0		77.0	17.0	NM_001843	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Silent	SNP	ENST00000551295.2	hg19	CCDS8737.1																																																																																			.	.		0.428	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		A	41374784	T	A	41374784	2	1	163	1	0	0	0	0	0	0	0	1	3642	1683	59	4		4	CNTN1	12	41374784	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	32561292	41374784	92477111	194	24976										
KRT81	3887	hgsc.bcm.edu	37	chr12	52680125	52680125	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gccgcaggaaccccctccgcAggtggtgttcaattggccgc	13	15	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:52680125A>T	ENST00000327741.5	-	9	1500	c.1432T>A	c.(1432-1434)Tgc>Agc	p.C478S	KRT86_ENST00000544024.1_Intron|KRT86_ENST00000423955.2_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	478	Tail.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCCCCTCCGCAGGTGGTGTTC	0.662																																					p.C478S		Atlas-SNP	.											.	KRT81	46	.	0			c.T1432A						.						27	25	25					12																	52680125		2162	4230	6392	SO:0001583	missense	3887	exon9			CTCCGCAGGTGGT	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"-", "Intermediate filaments type II, keratins (basic)"	6458	protein-coding gene	gene with protein product	"hard keratin type II 1"	602153	"keratin, hair, basic, 1"	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.1432T>A	chr12.hg19:g.52680125A>T	ENSP00000369349:p.Cys478Ser	136.0	0.0		128.0	26.0	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Missense_Mutation	SNP	ENST00000327741.5	hg19	CCDS31805.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.700306	0.30142	.	.	ENSG00000205426	ENST00000327741	T	0.80653	-1.4	3.0	3.0	0.34707	.	.	.	.	.	T	0.66386	0.2784	N	0.22421	0.69	0.09310	N	1	B	0.27853	0.191	B	0.25759	0.063	T	0.53711	-0.8400	9	0.29301	T	0.29	.	8.8019	0.34914	1.0:0.0:0.0:0.0	.	478	Q14533	KRT81_HUMAN	S	478	ENSP00000369349:C478S	ENSP00000369349:C478S	C	-	1	0	KRT81	50966392	0.014000	0.17966	0.004000	0.12327	0.011000	0.07611	0.717000	0.25851	1.150000	0.42419	0.379000	0.24179	TGC	.	.		0.662	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281		T	52680125	A	T	52680125	3	4	163	1	0	0	0	0	1	0	0	0	8504	188	7	4	89	4	KRT81	12	52680125	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	11305341	52680125	81171770	195	24977										
KRT6A	3853	hgsc.bcm.edu	37	chr12	52883809	52883809	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tctcctgcttggtgttgcgcAggtcgtccccatgtctgcct	11	14	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:52883809A>T	ENST00000330722.6	-	6	1189	c.1121T>A	c.(1120-1122)cTg>cAg	p.L374Q		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	374	Coil 2.|Rod.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		GGTGTTGCGCAGGTCGTCCCC	0.562																																					p.L374Q		Atlas-SNP	.											.	KRT6A	89	.	0			c.T1121A						.						107	85	93					12																	52883809		2202	4279	6481	SO:0001583	missense	3853	exon6			TTGCGCAGGTCGT	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"-", "Intermediate filaments type II, keratins (basic)"	6443	protein-coding gene	gene with protein product		148041	"keratin 6C", "keratin 6D"	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.1121T>A	chr12.hg19:g.52883809A>T	ENSP00000369317:p.Leu374Gln	106.0	0.0		106.0	21.0	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Missense_Mutation	SNP	ENST00000330722.6	hg19	CCDS41786.1	.	.	.	.	.	.	.	.	.	.	a	28.5	4.922238	0.92319	.	.	ENSG00000205420	ENST00000330722;ENST00000452121	D	0.81908	-1.55	5.3	5.3	0.74995	Filament (1);	0.000000	0.46442	D	0.000283	D	0.93923	0.8055	H	0.96518	3.835	0.52099	D	0.99994	D	0.89917	1.0	D	0.91635	0.999	D	0.95755	0.8795	10	0.87932	D	0	.	15.5563	0.76196	1.0:0.0:0.0:0.0	.	374	P02538	K2C6A_HUMAN	Q	374;330	ENSP00000369317:L374Q	ENSP00000369317:L374Q	L	-	2	0	KRT6A	51170076	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.197000	0.94985	2.148000	0.66965	0.459000	0.35465	CTG	.	.		0.562	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		T	52883809	A	T	52883809	3	4	163	1	0	0	0	0	1	0	0	0	8489	188	7	4	589	4	KRT6A	12	52883809	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	203684	52883809	80968086	196	24978										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58127876	58127876	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cgaagggaactcagctgcccAtggagacggctcacagcctg	13	13	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:58127876A>T	ENST00000547588.1	-	5	1481	c.1482T>A	c.(1480-1482)caT>caA	p.H494Q	AGAP2_ENST00000257897.3_Missense_Mutation_p.H158Q	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	494	G domain.				axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						TCAGCTGCCCATGGAGACGGC	0.597																																					p.H494Q		Atlas-SNP	.											.	AGAP2	167	.	0			c.T1482A						.						62	50	54					12																	58127876		2203	4300	6503	SO:0001583	missense	116986	exon5			CTGCCCATGGAGA	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.1482T>A	chr12.hg19:g.58127876A>T	ENSP00000449241:p.His494Gln	69.0	0.0		62.0	14.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	hg19	CCDS44932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.5|20.5	3.998442|3.998442	0.74818|0.74818	.|.	.|.	ENSG00000135439|ENSG00000135439	ENST00000257897;ENST00000547588|ENST00000328568	T;T|.	0.21932|.	1.98;1.98|.	5.43|5.43	-3.88|-3.88	0.04205|0.04205	Mitochondrial Rho-like (1);|.	0.088804|.	0.46442|.	D|.	0.000293|.	T|T	0.57125|0.57125	0.2032|0.2032	L|L	0.49350|0.49350	1.555|1.555	0.39558|0.39558	D|D	0.969081|0.969081	D;D;D|.	0.57571|.	0.98;0.972;0.978|.	P;P;P|.	0.56751|.	0.527;0.705;0.805|.	T|T	0.58476|0.58476	-0.7630|-0.7630	10|5	0.87932|.	D|.	0|.	.|.	14.0267|14.0267	0.64590|0.64590	0.429:0.0:0.571:0.0|0.429:0.0:0.571:0.0	.|.	158;494;494|.	Q99490-2;F8VVT9;Q99490|.	.;.;AGAP2_HUMAN|.	Q|R	158;494|358	ENSP00000257897:H158Q;ENSP00000449241:H494Q|.	ENSP00000257897:H158Q|.	H|W	-|-	3|1	2|0	AGAP2|AGAP2	56414143|56414143	0.156000|0.156000	0.22821|0.22821	0.975000|0.975000	0.42487|0.42487	0.975000|0.975000	0.68041|0.68041	0.406000|0.406000	0.21032|0.21032	-0.647000|-0.647000	0.05444|0.05444	-0.379000|-0.379000	0.06801|0.06801	CAT|TGG	.	.		0.597	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		T	58127876	A	T	58127876	3	4	163	1	0	0	0	0	1	0	0	0	368	214	8	4	2156	4	AGAP2	12	58127876	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	5244067	58127876	75724019	197	24979										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70965670	70965670	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgtagtaacagtgacactgtAcaaccgtccagggactagct	10	10	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:70965670A>T	ENST00000261266.5	-	10	2415	c.2386T>A	c.(2386-2388)Tac>Aac	p.Y796N	PTPRB_ENST00000538708.1_Missense_Mutation_p.Y796N|PTPRB_ENST00000551525.1_Missense_Mutation_p.Y1013N|PTPRB_ENST00000550857.1_Missense_Mutation_p.Y706N|PTPRB_ENST00000550358.1_Missense_Mutation_p.Y926N|PTPRB_ENST00000334414.6_Missense_Mutation_p.Y1014N|PTPRB_ENST00000451516.2_Missense_Mutation_p.Y706N	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	796	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			GTGACACTGTACAACCGTCCA	0.383																																					p.Y1014N		Atlas-SNP	.											.	PTPRB	676	.	0			c.T3040A						.						194	191	192					12																	70965670		1905	4132	6037	SO:0001583	missense	5787	exon12			CACTGTACAACCG	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.2386T>A	chr12.hg19:g.70965670A>T	ENSP00000261266:p.Tyr796Asn	92.0	0.0		112.0	20.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.367254	0.82463	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	D;D;D;D;D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49	6.17	6.17	0.99709	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94918	0.8357	M	0.85630	2.765	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;0.999;0.999	D;D;D;D;D;D;D	0.87578	0.997;0.998;0.998;0.987;0.997;0.997;0.997	D	0.95421	0.8507	10	0.87932	D	0	.	15.3933	0.74767	1.0:0.0:0.0:0.0	.	706;796;893;1013;1014;796;926	P23467-2;F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;PTPRB_HUMAN;.	N	1014;706;926;796;706;796;1013;893	ENSP00000334928:Y1014N;ENSP00000393028:Y706N;ENSP00000448058:Y926N;ENSP00000438927:Y796N;ENSP00000447302:Y706N;ENSP00000261266:Y796N;ENSP00000448349:Y1013N;ENSP00000446982:Y893N	ENSP00000261266:Y796N	Y	-	1	0	PTPRB	69251937	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.809000	0.91944	2.371000	0.80710	0.533000	0.62120	TAC	.	.		0.383	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70965670	A	T	70965670	3	4	163	1	0	0	0	0	1	0	0	0	12811	391	14	4	3699	4	PTPRB	12	70965670	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	12837794	70965670	62886225	198	24980										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70989857	70989857	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccattggtataaactgaaaaAgaacgttttcctccagaaac	6	9	0	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:70989857A>T	ENST00000261266.5	-	3	605	c.576T>A	c.(574-576)tcT>tcA	p.S192S	PTPRB_ENST00000538708.1_Silent_p.S192S|PTPRB_ENST00000551525.1_Silent_p.S409S|PTPRB_ENST00000550857.1_Silent_p.S192S|PTPRB_ENST00000550358.1_Silent_p.S410S|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Silent_p.S410S|PTPRB_ENST00000451516.2_Silent_p.S192S	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	192	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			AAACTGAAAAAGAACGTTTTC	0.323																																					p.S410S		Atlas-SNP	.											.	PTPRB	676	.	0			c.T1230A						.						46	44	44					12																	70989857		1828	4085	5913	SO:0001819	synonymous_variant	5787	exon5			TGAAAAAGAACGT	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.576T>A	chr12.hg19:g.70989857A>T		96.0	0.0		105.0	20.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.323	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70989857	A	T	70989857	2	4	163	1	0	0	0	0	0	0	0	1	12811	59	3	4		4	PTPRB	12	70989857	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	24187	70989857	62862038	199	24981										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85466707	85466707	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tattccttctttctggaagaAaaacttgttgacaatgcagg	8	7	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:85466707A>G	ENST00000393217.2	+	11	2779	c.2718A>G	c.(2716-2718)gaA>gaG	p.E906E		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	906										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		TTCTGGAAGAAAAACTTGTTG	0.388																																					p.E906E		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A2718G						.						68	59	62					12																	85466707		2203	4300	6503	SO:0001819	synonymous_variant	84125	exon11			GGAAGAAAAACTT	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.2718A>G	chr12.hg19:g.85466707A>G		74.0	0.0		121.0	26.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Silent	SNP	ENST00000393217.2	hg19	CCDS41816.1																																																																																			.	.		0.388	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		G	85466707	A	G	85466707	2	3	163	1	0	0	0	0	0	0	0	1	9038	11	1	2		2	LRRIQ1	12	85466707	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	14476850	85466707	48385188	200	24982										
KERA	11081	hgsc.bcm.edu	37	chr12	91449375	91449375	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acattaaaataattttctggTattccttcaatggaattgtt	5	5	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:91449375T>A	ENST00000266719.3	-	2	931	c.684A>T	c.(682-684)atA>atT	p.I228I		NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan	228					carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						AATTTTCTGGTATTCCTTCAA	0.383																																					p.I228I		Atlas-SNP	.											.	KERA	62	.	0			c.A684T						.						112	112	112					12																	91449375		2203	4299	6502	SO:0001819	synonymous_variant	11081	exon2			TTCTGGTATTCCT	AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6309	protein-coding gene	gene with protein product	"keratocan proteoglycan"	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.684A>T	chr12.hg19:g.91449375T>A		103.0	0.0		109.0	33.0	NM_007035		Silent	SNP	ENST00000266719.3	hg19	CCDS9037.1																																																																																			.	.		0.383	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035		A	91449375	T	A	91449375	2	1	163	1	0	0	0	0	0	0	0	1	8152	1628	57	4		4	KERA	12	91449375	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	5982668	91449375	42402520	201	24983										
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100453136	100453136	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aagatttggggaagctggtaTatgttttactaaaaaaatca	9	3	1	1	rs538548609		TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:100453136T>A	ENST00000279907.7	-	14	2131	c.1919A>T	c.(1918-1920)tAt>tTt	p.Y640F	UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.Y290F	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	640										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						GAAGCTGGTATATGTTTTACT	0.333																																					p.Y640F		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.A1919T						.						45	50	48					12																	100453136		2202	4298	6500	SO:0001583	missense	23074	exon14			CTGGTATATGTTT		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.1919A>T	chr12.hg19:g.100453136T>A	ENSP00000279907:p.Tyr640Phe	85.0	0.0		129.0	26.0	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	hg19	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	T	7.262	0.605358	0.14002	.	.	ENSG00000111647	ENST00000279907;ENST00000545232	T;T	0.09538	2.99;2.97	5.56	4.42	0.53409	.	0.184331	0.46145	D	0.000310	T	0.04452	0.0122	N	0.04043	-0.29	0.80722	D	1	B	0.17038	0.02	B	0.16722	0.016	T	0.41270	-0.9518	10	0.25751	T	0.34	-15.1681	5.3052	0.15799	0.2614:0.0822:0.0:0.6563	.	640	A0JNW5	UH1BL_HUMAN	F	640;290	ENSP00000279907:Y640F;ENSP00000444824:Y290F	ENSP00000279907:Y640F	Y	-	2	0	UHRF1BP1L	98977267	1.000000	0.71417	0.759000	0.31340	0.996000	0.88848	4.264000	0.58859	0.961000	0.38030	0.528000	0.53228	TAT	.	.		0.333	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		A	100453136	T	A	100453136	3	1	163	1	0	0	0	0	1	0	0	0	16984	1406	49	4	2507	4	UHRF1BP1L	12	100453136	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	9003761	100453136	33398759	202	24984										
SLC17A8	246213	hgsc.bcm.edu	37	chr12	100813686	100813686	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tctttgcttctggggagaaaCaggagtgggctgacccagag	15	8	2	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:100813686C>G	ENST00000323346.5	+	12	1832	c.1519C>G	c.(1519-1521)Cag>Gag	p.Q507E	SLC17A8_ENST00000392989.3_Missense_Mutation_p.Q457E|SLC17A8_ENST00000552697.1_3'UTR	NM_001145288.1|NM_139319.2	NP_001138760.1|NP_647480.1	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 8	507					ion transport (GO:0006811)|neurotransmitter transport (GO:0006836)|sensory perception of sound (GO:0007605)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	44						TGGGGAGAAACAGGAGTGGGC	0.473																																					p.Q507E		Atlas-SNP	.											.	SLC17A8	89	.	0			c.C1519G						.						68	74	72					12																	100813686		2203	4300	6503	SO:0001583	missense	246213	exon12			GAGAAACAGGAGT	AJ459241	CCDS9077.1, CCDS44957.1	12q23.1	2013-07-18	2013-07-18		ENSG00000179520	ENSG00000179520		"Solute carriers"	20151	protein-coding gene	gene with protein product	"vesicular glutamate transporter 3"	607557	"deafness, autosomal dominant 25", "solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"	DFNA25		12151341	Standard	NM_139319		Approved	VGLUT3	uc010svi.2	Q8NDX2	OTTHUMG00000170358	ENST00000323346.5:c.1519C>G	chr12.hg19:g.100813686C>G	ENSP00000316909:p.Gln507Glu	38.0	0.0		52.0	9.0	NM_139319	B3KXZ6|B7ZKV4|Q17RQ8	Missense_Mutation	SNP	ENST00000323346.5	hg19	CCDS9077.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.778828	0.90195	.	.	ENSG00000179520	ENST00000323346;ENST00000392989	T;T	0.75477	-0.43;-0.94	5.18	5.18	0.71444	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.87237	0.6127	M	0.81802	2.56	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.78314	0.983;0.991	D	0.88585	0.3139	10	0.72032	D	0.01	.	19.0814	0.93185	0.0:1.0:0.0:0.0	.	507;457	Q8NDX2;Q8NDX2-2	VGLU3_HUMAN;.	E	507;457	ENSP00000316909:Q507E;ENSP00000376715:Q457E	ENSP00000316909:Q507E	Q	+	1	0	SLC17A8	99337817	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.767000	0.85331	2.579000	0.87056	0.591000	0.81541	CAG	.	.		0.473	SLC17A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408673.2	NM_139319		G	100813686	C	G	100813686	3	3	163	1	0	0	0	0	1	0	0	0	14438	479	17	4	1565	4	SLC17A8	12	100813686	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	360550	100813686	33038209	203	24985										
UTP20	27340	hgsc.bcm.edu	37	chr12	101711258	101711258	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	actttctttccacggtagcaAtgagtattacccagcagatc	7	11	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:101711258A>G	ENST00000261637.4	+	22	2729	c.2555A>G	c.(2554-2556)aAt>aGt	p.N852S		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	852					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CACGGTAGCAATGAGTATTAC	0.478																																					p.N852S		Atlas-SNP	.											.	UTP20	222	.	0			c.A2555G						.						62	63	63					12																	101711258		2203	4300	6503	SO:0001583	missense	27340	exon22			GTAGCAATGAGTA	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.2555A>G	chr12.hg19:g.101711258A>G	ENSP00000261637:p.Asn852Ser	77.0	0.0		94.0	25.0	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	hg19	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	A	18.80	3.700633	0.68501	.	.	ENSG00000120800	ENST00000261637	T	0.62941	-0.01	5.36	5.36	0.76844	Armadillo-type fold (1);	0.046249	0.85682	D	0.000000	T	0.68339	0.2990	L	0.52011	1.625	0.80722	D	1	D	0.69078	0.997	P	0.61397	0.888	T	0.64089	-0.6489	10	0.07990	T	0.79	-18.9427	15.3488	0.74368	1.0:0.0:0.0:0.0	.	852	O75691	UTP20_HUMAN	S	852	ENSP00000261637:N852S	ENSP00000261637:N852S	N	+	2	0	UTP20	100235389	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	8.203000	0.89739	2.037000	0.60232	0.482000	0.46254	AAT	.	.		0.478	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		G	101711258	A	G	101711258	3	3	163	1	0	0	0	0	1	0	0	0	17114	101	4	2	2641	2	UTP20	12	101711258	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	897572	101711258	32140637	204	24986										
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105540256	105540256	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gatgttttagaaattatgagAaacattcatatatttgtgtc	7	3	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:105540256A>T	ENST00000332180.5	+	23	2448	c.2361A>T	c.(2359-2361)agA>agT	p.R787S		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						AAATTATGAGAAACATTCATA	0.279																																					p.R787S		Atlas-SNP	.											.	KIAA1033	83	.	0			c.A2361T						.						93	89	90					12																	105540256		1786	4058	5844	SO:0001583	missense	23325	exon23			TATGAGAAACATT	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.2361A>T	chr12.hg19:g.105540256A>T	ENSP00000328062:p.Arg787Ser	241.0	0.0		282.0	55.0	NM_015275		Missense_Mutation	SNP	ENST00000332180.5	hg19	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.459986	0.84317	.	.	ENSG00000136051	ENST00000332180	T	0.54071	0.59	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.76744	0.4030	M	0.87900	2.915	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.81348	-0.0973	10	0.87932	D	0	.	16.0952	0.81114	1.0:0.0:0.0:0.0	.	788;787	B7ZKT9;Q2M389	.;WASH7_HUMAN	S	787	ENSP00000328062:R787S	ENSP00000328062:R787S	R	+	3	2	KIAA1033	104064386	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.849000	0.62882	2.209000	0.71365	0.477000	0.44152	AGA	.	.		0.279	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		T	105540256	A	T	105540256	3	4	163	1	0	0	0	0	1	0	0	0	8215	243	9	4	2451	4	KIAA1033	12	105540256	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	3828998	105540256	28311639	205	24987										
SSH1	54434	hgsc.bcm.edu	37	chr12	109186287	109186287	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agtccggaaccttgctggggCtgtctggccggcctgtgcac	15	13	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:109186287C>T	ENST00000326495.5	-	14	1761	c.1668G>A	c.(1666-1668)caG>caA	p.Q556Q	SSH1_ENST00000551165.1_Silent_p.Q556Q|SSH1_ENST00000326470.5_Silent_p.Q567Q|SSH1_ENST00000360239.3_Silent_p.Q244Q	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	556					actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTTGCTGGGGCTGTCTGGCCG	0.592																																					p.Q567Q		Atlas-SNP	.											.	SSH1	144	.	0			c.G1701A						.						92	98	96					12																	109186287		2203	4300	6503	SO:0001819	synonymous_variant	54434	exon13			CTGGGGCTGTCTG	BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30579	protein-coding gene	gene with protein product		606778	"slingshot homolog 1 (Drosophila)"			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.1668G>A	chr12.hg19:g.109186287C>T		60.0	0.0		73.0	13.0	NM_001161331	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Silent	SNP	ENST00000326495.5	hg19	CCDS9121.1																																																																																			.	.		0.592	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984		T	109186287	C	T	109186287	2	4	163	1	0	0	0	0	0	0	0	1	15199	796	28	3		3	SSH1	12	109186287	Silent	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	3646031	109186287	24665608	206	24988										
UBE3B	89910	hgsc.bcm.edu	37	chr12	109968392	109968392	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtggtttccatggaagtcacAgagtcatcatctggctctgg	12	9	5	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:109968392A>T	ENST00000342494.3	+	26	3446	c.2851A>T	c.(2851-2853)Aga>Tga	p.R951*	UBE3B_ENST00000535089.1_Nonsense_Mutation_p.R38*|UBE3B_ENST00000434735.2_Nonsense_Mutation_p.R951*	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	951	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						TGGAAGTCACAGAGTCATCAT	0.478																																					p.R951X		Atlas-SNP	.											.	UBE3B	116	.	0			c.A2851T						.						156	140	146					12																	109968392		2203	4300	6503	SO:0001587	stop_gained	89910	exon26			AGTCACAGAGTCA	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.2851A>T	chr12.hg19:g.109968392A>T	ENSP00000340596:p.Arg951*	50.0	0.0		58.0	18.0	NM_130466	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Nonsense_Mutation	SNP	ENST00000342494.3	hg19	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	A	51	17.716017	0.99892	.	.	ENSG00000151148	ENST00000434735;ENST00000342494;ENST00000538070;ENST00000535089	.	.	.	5.56	2.98	0.34508	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.9151	12.2106	0.54377	0.5814:0.4186:0.0:0.0	.	.	.	.	X	951;951;246;38	.	ENSP00000340596:R951X	R	+	1	2	UBE3B	108452775	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.459000	0.45023	0.911000	0.36747	0.533000	0.62120	AGA	.	.		0.478	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		T	109968392	A	T	109968392	4	4	163	1	0	0	0	0	0	1	0	0	16895	180	7	4	2945	4	UBE3B	12	109968392	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	782105	109968392	23883503	207	24989										
CCDC60	160777	hgsc.bcm.edu	37	chr12	119978503	119978503	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tcaacatacccattgggcccTacagcgccctgaggtaggct	10	14	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:119978503T>A	ENST00000327554.2	+	14	2101	c.1636T>A	c.(1636-1638)Tac>Aac	p.Y546N	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	546										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CATTGGGCCCTACAGCGCCCT	0.537																																					p.Y546N		Atlas-SNP	.											.	CCDC60	84	.	0			c.T1636A						.						102	94	97					12																	119978503		2203	4300	6503	SO:0001583	missense	160777	exon14			GGGCCCTACAGCG	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.1636T>A	chr12.hg19:g.119978503T>A	ENSP00000333374:p.Tyr546Asn	58.0	0.0		45.0	8.0	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	hg19	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	T	9.388	1.074744	0.20227	.	.	ENSG00000183273	ENST00000327554	T	0.22539	1.95	5.4	2.13	0.27403	.	1.076280	0.07121	N	0.843947	T	0.13670	0.0331	N	0.22421	0.69	0.09310	N	1	B	0.25904	0.137	B	0.21917	0.037	T	0.36744	-0.9735	9	.	.	.	-1.5606	6.6445	0.22927	0.0:0.6164:0.0:0.3836	.	546	Q8IWA6	CCD60_HUMAN	N	546	ENSP00000333374:Y546N	.	Y	+	1	0	CCDC60	118462886	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	0.070000	0.14573	0.221000	0.20879	0.533000	0.62120	TAC	.	.		0.537	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		A	119978503	T	A	119978503	3	1	163	1	0	0	0	0	1	0	0	0	2833	1522	53	4	1690	4	CCDC60	12	119978503	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	10010111	119978503	13873392	208	24990										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124284917	124284917	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agcaagaaatgttgctctccAggaagacaaattccttaggt	9	8	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:124284917A>T	ENST00000409039.3	+	14	2115	c.2090A>T	c.(2089-2091)cAg>cTg	p.Q697L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	697	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GTTGCTCTCCAGGAAGACAAA	0.378																																					p.Q697L		Atlas-SNP	.											.	DNAH10	888	.	0			c.A2090T						.						49	51	50					12																	124284917		2203	4300	6503	SO:0001583	missense	196385	exon14			CTCTCCAGGAAGA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.2090A>T	chr12.hg19:g.124284917A>T	ENSP00000386770:p.Gln697Leu	140.0	0.0		167.0	31.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	23.4	4.406878	0.83230	.	.	ENSG00000197653	ENST00000409039	T	0.57907	0.37	5.53	5.53	0.82687	Dynein heavy chain, domain-1 (1);	0.215065	0.28047	N	0.016809	T	0.71643	0.3364	M	0.84511	2.7	0.58432	D	0.999993	B;B;P	0.36535	0.206;0.376;0.557	B;P;P	0.51777	0.244;0.452;0.679	T	0.72609	-0.4241	10	0.42905	T	0.14	.	15.7102	0.77620	1.0:0.0:0.0:0.0	.	697;572;697	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	L	697	ENSP00000386770:Q697L	ENSP00000386770:Q697L	Q	+	2	0	DNAH10	122850870	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	8.850000	0.92190	2.112000	0.64535	0.529000	0.55759	CAG	.	.		0.378	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124284917	A	T	124284917	3	4	163	1	0	0	0	0	1	0	0	0	4600	188	7	4	2144	4	DNAH10	12	124284917	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	4306414	124284917	9566978	209	24991										
CCDC92	80212	hgsc.bcm.edu	37	chr12	124427948	124427948	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtgcagccccttgagcgtgcTggcatgctcccgctgaagga	14	13	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:124427948T>A	ENST00000238156.3	-	3	481	c.127A>T	c.(127-129)Agc>Tgc	p.S43C	CCDC92_ENST00000545891.1_Missense_Mutation_p.S26C|CCDC92_ENST00000545135.1_Missense_Mutation_p.S26C|CCDC92_ENST00000544798.1_5'UTR	NM_025140.1	NP_079416.1	Q53HC0	CCD92_HUMAN	coiled-coil domain containing 92	43						centriole (GO:0005814)				large_intestine(5)|lung(2)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.0002)|OV - Ovarian serous cystadenocarcinoma(86;0.000222)|all cancers(50;0.00129)|BRCA - Breast invasive adenocarcinoma(302;0.242)		TTGAGCGTGCTGGCATGCTCC	0.652																																					p.S43C		Atlas-SNP	.											.	CCDC92	18	.	0			c.A127T						.						117	104	109					12																	124427948		2203	4300	6503	SO:0001583	missense	80212	exon3			GCGTGCTGGCATG	AK026124	CCDS9256.1	12q24.31	2011-09-02			ENSG00000119242	ENSG00000119242			29563	protein-coding gene	gene with protein product	"limkain beta 2"					12477932	Standard	NM_025140		Approved	FLJ22471	uc001ufw.1	Q53HC0	OTTHUMG00000168725	ENST00000238156.3:c.127A>T	chr12.hg19:g.124427948T>A	ENSP00000238156:p.Ser43Cys	37.0	0.0		28.0	7.0	NM_025140	B3KNQ0|Q9H697	Missense_Mutation	SNP	ENST00000238156.3	hg19	CCDS9256.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.570022	0.86542	.	.	ENSG00000119242	ENST00000238156;ENST00000545135;ENST00000545891;ENST00000539761;ENST00000535556;ENST00000539551	T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89	5.49	3.13	0.36017	.	0.451063	0.29260	N	0.012671	T	0.45538	0.1347	L	0.57536	1.79	0.27955	N	0.936988	D	0.55800	0.973	P	0.50192	0.634	T	0.40739	-0.9547	10	0.62326	D	0.03	-21.813	8.9374	0.35708	0.0:0.2111:0.0:0.7889	.	43	Q53HC0	CCD92_HUMAN	C	43;26;26;43;26;43	ENSP00000238156:S43C;ENSP00000439526:S26C;ENSP00000440024:S26C;ENSP00000439441:S43C;ENSP00000438281:S26C;ENSP00000442369:S43C	ENSP00000238156:S43C	S	-	1	0	CCDC92	122993901	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.376000	0.44292	0.384000	0.24942	0.459000	0.35465	AGC	.	.		0.652	CCDC92-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400780.2	NM_025140		A	124427948	T	A	124427948	3	1	163	1	0	0	0	0	1	0	0	0	2873	1580	55	4	880	4	CCDC92	12	124427948	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	143031	124427948	9423947	210	24992										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126138935	126138935	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaggagtgcacaaccatgatAgacaggggcctgcagttcga	14	9	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr12:126138935A>T	ENST00000299308.3	+	9	2924	c.2916A>T	c.(2914-2916)atA>atT	p.I972I	TMEM132B_ENST00000535886.1_Silent_p.I484I	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	972						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CAACCATGATAGACAGGGGCC	0.498																																					p.I972I		Atlas-SNP	.											.	TMEM132B	207	.	0			c.A2916T						.						62	59	60					12																	126138935		1894	4114	6008	SO:0001819	synonymous_variant	114795	exon9			CATGATAGACAGG	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.2916A>T	chr12.hg19:g.126138935A>T		62.0	0.0		119.0	40.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	hg19	CCDS41859.1																																																																																			.	.		0.498	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		T	126138935	A	T	126138935	2	4	163	1	0	0	0	0	0	0	0	1	16061	410	15	4		4	TMEM132B	12	126138935	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1710987	126138935	7712960	211	24993										
RNF17	56163	hgsc.bcm.edu	37	chr13	25374648	25374648	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttagcacaaccatgctcattGaaagacattgttccacagaa	6	10	1	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr13:25374648G>T	ENST00000255324.5	+	13	1786	c.1734G>T	c.(1732-1734)ttG>ttT	p.L578F	RNF17_ENST00000255325.6_Missense_Mutation_p.L578F|RNF17_ENST00000381921.1_Missense_Mutation_p.L578F	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	578					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		CATGCTCATTGAAAGACATTG	0.343																																					p.L578F		Atlas-SNP	.											.	RNF17	259	.	0			c.G1734T						.						121	117	119					13																	25374648		2203	4300	6503	SO:0001583	missense	56163	exon13			CTCATTGAAAGAC	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.1734G>T	chr13.hg19:g.25374648G>T	ENSP00000255324:p.Leu578Phe	35.0	0.0		37.0	11.0	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	hg19	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	G	16.02	3.003656	0.54254	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000255325	T;T;T	0.24538	1.85;1.85;1.85	4.44	2.71	0.32032	.	0.574441	0.14662	N	0.305886	T	0.45115	0.1326	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.30851	-0.9964	10	0.87932	D	0	.	7.5753	0.27933	0.2729:0.0:0.7271:0.0	.	578;578	B7Z7S1;Q9BXT8	.;RNF17_HUMAN	F	578;578;437;579	ENSP00000255324:L578F;ENSP00000371346:L578F;ENSP00000255325:L579F	ENSP00000255324:L578F	L	+	3	2	RNF17	24272648	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	2.487000	0.45268	0.623000	0.30267	0.462000	0.41574	TTG	.	.		0.343	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		T	25374648	G	T	25374648	3	4	163	1	0	0	0	0	1	0	0	0	13476	1281	45	3	1784	3	RNF17	13	25374648	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10		25374648	89795230	212	24994										
CPB2	1361	hgsc.bcm.edu	37	chr13	46627758	46627758	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aatcaggggcattaaacattCctaatgacatgccaagctat	7	9	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr13:46627758C>A	ENST00000181383.4	-	11	1279	c.1263G>T	c.(1261-1263)agG>agT	p.R421S	CPB2_ENST00000439329.3_3'UTR|CPB2-AS1_ENST00000606991.1_RNA|ZC3H13_ENST00000282007.3_5'Flank|CPB2-AS1_ENST00000606351.1_RNA|ZC3H13_ENST00000242848.4_5'Flank|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606243.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	421					blood coagulation (GO:0007596)|cellular response to glucose stimulus (GO:0071333)|fibrinolysis (GO:0042730)|liver regeneration (GO:0097421)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of plasminogen activation (GO:0010757)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to heat (GO:0009408)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(3)|liver(1)|lung(9)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		ATTAAACATTCCTAATGACAT	0.383																																					p.R421S		Atlas-SNP	.											.	CPB2	60	.	0			c.G1263T						.						81	85	83					13																	46627758		2203	4300	6503	SO:0001583	missense	1361	exon11			AACATTCCTAATG	M75106	CCDS9401.1, CCDS73568.1	13q14.11	2012-02-10	2007-02-21		ENSG00000080618	ENSG00000080618			2300	protein-coding gene	gene with protein product	"thrombin-activatable fibrinolysis inhibitor", "carboxypeptidase U", "plasma carboxypeptidase B", "carboxypeptidase R"	603101	"carboxypeptidase B2 (plasma, carboxypeptidase U)"			1939207, 1427879	Standard	NM_001278541		Approved	CPU, PCPB, TAFI	uc001vaw.3	Q96IY4	OTTHUMG00000016867	ENST00000181383.4:c.1263G>T	chr13.hg19:g.46627758C>A	ENSP00000181383:p.Arg421Ser	163.0	0.0		138.0	39.0	NM_001872	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Missense_Mutation	SNP	ENST00000181383.4	hg19	CCDS9401.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957491	0.53400	.	.	ENSG00000080618	ENST00000181383	T	0.30448	1.53	5.84	-0.436	0.12275	.	0.450845	0.27000	N	0.021429	T	0.13670	0.0331	N	0.16602	0.42	0.24278	N	0.995216	D	0.53885	0.963	B	0.39465	0.3	T	0.22556	-1.0213	10	0.59425	D	0.04	.	5.1158	0.14833	0.1653:0.2735:0.0:0.5612	.	421	Q96IY4	CBPB2_HUMAN	S	421	ENSP00000181383:R421S	ENSP00000181383:R421S	R	-	3	2	CPB2	45525759	0.001000	0.12720	0.206000	0.23566	0.990000	0.78478	-0.125000	0.10579	0.122000	0.18314	0.561000	0.74099	AGG	.	.		0.383	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872		A	46627758	C	A	46627758	3	1	163	1	0	0	0	0	1	0	0	0	3799	854	30	3	12	3	CPB2	13	46627758	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	21253110	46627758	68542120	213	24995										
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84453857	84453857	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggtctccgccaacccagtgcTgtttttactgtgcgaagtta	10	11	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr13:84453857T>A	ENST00000377084.2	-	1	2671	c.1786A>T	c.(1786-1788)Agc>Tgc	p.S596C		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	596					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		AACCCAGTGCTGTTTTTACTG	0.542																																					p.S596C		Atlas-SNP	.											.	SLITRK1	196	.	0			c.A1786T						.						100	87	92					13																	84453857		2203	4300	6503	SO:0001583	missense	114798	exon1			CAGTGCTGTTTTT	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1786A>T	chr13.hg19:g.84453857T>A	ENSP00000366288:p.Ser596Cys	100.0	0.0		94.0	24.0	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	hg19	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.520453	0.64747	.	.	ENSG00000178235	ENST00000377084	T	0.60299	0.2	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.54191	0.1843	L	0.52573	1.65	0.58432	D	0.999997	B	0.28324	0.207	B	0.29716	0.106	T	0.56117	-0.8032	10	0.56958	D	0.05	-17.8047	14.5694	0.68202	0.0:0.0:0.0:1.0	.	596	Q96PX8	SLIK1_HUMAN	C	596	ENSP00000366288:S596C	ENSP00000366288:S596C	S	-	1	0	SLITRK1	83351858	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.059000	0.57470	2.187000	0.69744	0.533000	0.62120	AGC	.	.		0.542	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84453857	T	A	84453857	3	1	163	1	0	0	0	0	1	0	0	0	14757	1580	55	4	308	4	SLITRK1	13	84453857	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	37826099	84453857	30716021	214	24996										
FGF14	2259	hgsc.bcm.edu	37	chr13	103053956	103053956	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cagcttagacaccctgagaaAgaagagatccttgtggttgc	11	9	0	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr13:103053956A>G	ENST00000376131.4	-	1	168	c.73T>C	c.(73-75)Ttt>Ctt	p.F25L	RP11-811P12.3_ENST00000418923.2_RNA	NM_175929.2	NP_787125.1	Q92915	FGF14_HUMAN	fibroblast growth factor 14	0					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cell-cell signaling (GO:0007267)|JNK cascade (GO:0007254)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)	29	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ACCCTGAGAAAGAAGAGATCC	0.413																																					p.F25L		Atlas-SNP	.											.	FGF14	86	.	0			c.T73C						.						77	73	75					13																	103053956		2203	4300	6503	SO:0001583	missense	2259	exon1			TGAGAAAGAAGAG		CCDS9500.1, CCDS9501.1	13q34	2008-02-05			ENSG00000102466	ENSG00000102466			3671	protein-coding gene	gene with protein product		601515				8790420, 17236779	Standard	NM_175929		Approved	FHF4, SCA27	uc001vpf.2	Q92915	OTTHUMG00000017303	ENST00000376131.4:c.73T>C	chr13.hg19:g.103053956A>G	ENSP00000365301:p.Phe25Leu	91.0	0.0		106.0	8.0	NM_175929	Q86YN7|Q96QX6	Missense_Mutation	SNP	ENST00000376131.4	hg19	CCDS9500.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.320950	0.41096	.	.	ENSG00000102466	ENST00000376131	T	0.78481	-1.18	4.73	4.73	0.59995	.	1.151740	0.06111	N	0.667184	T	0.66228	0.2768	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49744	-0.8907	8	.	.	.	.	8.9819	0.35970	0.9173:0.0:0.0827:0.0	.	25	Q92915-2	.	L	25	ENSP00000365301:F25L	.	F	-	1	0	FGF14	101851957	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.994000	0.76251	1.984000	0.57885	0.533000	0.62120	TTT	.	.		0.413	FGF14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045680.5			G	103053956	A	G	103053956	3	3	163	1	0	0	0	0	1	0	0	0	5851	72	3	2	902	2	FGF14	13	103053956	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	18600099	103053956	12115922	215	24997										
OR11H4	390442	hgsc.bcm.edu	37	chr14	20711318	20711318	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	actgggaacaactgaatgtcTctttctggcagtaatggctt	10	8	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr14:20711318T>A	ENST00000315409.2	+	1	421	c.368T>A	c.(367-369)cTc>cAc	p.L123H		NM_001004479.1	NP_001004479.1	Q8NGC9	O11H4_HUMAN	olfactory receptor, family 11, subfamily H, member 4	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	29	all_cancers(95;0.000888)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0146)		ACTGAATGTCTCTTTCTGGCA	0.468																																					p.L123H		Atlas-SNP	.											.	OR11H4	63	.	0			c.T368A						.						115	116	116					14																	20711318		2203	4300	6503	SO:0001583	missense	390442	exon1			AATGTCTCTTTCT		CCDS32034.1	14q11.2	2013-09-24			ENSG00000176198	ENSG00000176198		"GPCR / Class A : Olfactory receptors"	15347	protein-coding gene	gene with protein product							Standard	NM_001004479		Approved		uc010tld.2	Q8NGC9	OTTHUMG00000170852	ENST00000315409.2:c.368T>A	chr14.hg19:g.20711318T>A	ENSP00000318997:p.Leu123His	92.0	0.0		76.0	23.0	NM_001004479	B2RNQ4|Q6IF07	Missense_Mutation	SNP	ENST00000315409.2	hg19	CCDS32034.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.674083	0.47781	.	.	ENSG00000176198	ENST00000315409	T	0.01422	4.91	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.143965	0.29995	N	0.010667	T	0.05914	0.0154	M	0.80508	2.5	0.09310	N	1	D	0.58620	0.983	P	0.57846	0.828	T	0.10451	-1.0629	10	0.87932	D	0	-9.9763	8.5198	0.33268	0.0:0.0:0.1961:0.8039	.	123	Q8NGC9	O11H4_HUMAN	H	123	ENSP00000318997:L123H	ENSP00000318997:L123H	L	+	2	0	OR11H4	19781158	0.000000	0.05858	0.991000	0.47740	0.997000	0.91878	0.642000	0.24735	1.993000	0.58246	0.528000	0.53228	CTC	.	.		0.468	OR11H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410678.1			A	20711318	T	A	20711318	3	1	163	1	0	0	0	0	1	0	0	0	10937	1551	54	4	370	4	OR11H4	14	20711318	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10		20711318	86638222	216	24998										
EDDM3A	10876	hgsc.bcm.edu	37	chr14	21215986	21215986	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttcagcgtgcatgcatcaatGagaaggggagcgaccgatat	13	8	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr14:21215986G>A	ENST00000326842.2	+	2	374	c.247G>A	c.(247-249)Gag>Aag	p.E83K		NM_006683.4	NP_006674.2	Q14507	EP3A_HUMAN	epididymal protein 3A	83					sperm displacement (GO:0007321)	extracellular space (GO:0005615)				breast(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						ATGCATCAATGAGAAGGGGAG	0.443																																					p.E83K		Atlas-SNP	.											.	EDDM3A	15	.	0			c.G247A						.						99	95	96					14																	21215986		2203	4300	6503	SO:0001583	missense	10876	exon2			ATCAATGAGAAGG	X76383	CCDS9556.1	14q11.1	2010-03-19	2010-01-27	2010-01-27	ENSG00000181562	ENSG00000181562			16978	protein-coding gene	gene with protein product		611580	"family with sequence similarity 12, member A"	FAM12A		7514008	Standard	NM_006683		Approved	HE3-ALPHA	uc001vyc.3	Q14507	OTTHUMG00000029581	ENST00000326842.2:c.247G>A	chr14.hg19:g.21215986G>A	ENSP00000315098:p.Glu83Lys	91.0	0.0		94.0	24.0	NM_006683	Q4KN33	Missense_Mutation	SNP	ENST00000326842.2	hg19	CCDS9556.1	.	.	.	.	.	.	.	.	.	.	G	6.445	0.450319	0.12223	.	.	ENSG00000181562	ENST00000326842	T	0.72505	-0.66	1.21	-0.646	0.11472	Ribonuclease A, domain (2);	.	.	.	.	T	0.48295	0.1492	L	0.36672	1.1	0.09310	N	1	B	0.32245	0.361	B	0.27500	0.08	T	0.31558	-0.9939	9	0.08381	T	0.77	.	3.4827	0.07609	0.5337:0.0:0.4663:0.0	.	83	Q14507	EP3A_HUMAN	K	83	ENSP00000315098:E83K	ENSP00000315098:E83K	E	+	1	0	EDDM3A	20285826	0.005000	0.15991	0.001000	0.08648	0.226000	0.24999	0.787000	0.26858	-0.204000	0.10235	0.313000	0.20887	GAG	.	.		0.443	EDDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073742.3			A	21215986	G	A	21215986	3	1	163	1	0	0	0	0	1	0	0	0	4911	1291	45	3	249	3	EDDM3A	14	21215986	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	504668	21215986	86133554	217	24999										
EFS	10278	hgsc.bcm.edu	37	chr14	23828142	23828142	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tcccctgtgcaggcctgatcCgggggcctagatccctgagc	13	15	0	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr14:23828142C>T	ENST00000216733.3	-	5	1801	c.1194G>A	c.(1192-1194)ccG>ccA	p.P398P	RP11-124D2.3_ENST00000554010.1_RNA|EFS_ENST00000429593.2_Silent_p.P229P|EFS_ENST00000351354.3_Silent_p.P305P	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	398					cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		AGGCCTGATCCGGGGGCCTAG	0.672																																					p.P398P		Atlas-SNP	.											.	EFS	37	.	0			c.G1194A						.						45	47	46					14																	23828142		2203	4300	6503	SO:0001819	synonymous_variant	10278	exon5			CTGATCCGGGGGC	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"Cas scaffolding proteins"	16898	protein-coding gene	gene with protein product	"Cas scaffolding protein family member 3"	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.1194G>A	chr14.hg19:g.23828142C>T		59.0	0.0		69.0	11.0	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Silent	SNP	ENST00000216733.3	hg19	CCDS9595.1																																																																																			.	.		0.672	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2			T	23828142	C	T	23828142	2	4	163	1	0	0	0	0	0	0	0	1	4961	639	23	1		1	EFS	14	23828142	Silent	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	2612156	23828142	83521398	218	25000										
FANCM	57697	hgsc.bcm.edu	37	chr14	45645010	45645010	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgctaagggtactgcacttgAgaatttgcttttcttaccct	8	9	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr14:45645010A>T	ENST00000267430.5	+	14	3138	c.3053A>T	c.(3052-3054)gAg>gTg	p.E1018V	FANCM_ENST00000542564.2_Missense_Mutation_p.E992V	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1018					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						ACTGCACTTGAGAATTTGCTT	0.398								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.E1018V		Atlas-SNP	.											.	FANCM	225	.	0			c.A3053T						.						46	43	44					14																	45645010		2203	4296	6499	SO:0001583	missense	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CACTTGAGAATTT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.3053A>T	chr14.hg19:g.45645010A>T	ENSP00000267430:p.Glu1018Val	105.0	0.0		94.0	24.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	8.151	0.787412	0.16258	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.19669	2.72;2.73;2.13	4.87	4.87	0.63330	.	1.383380	0.04051	N	0.304812	T	0.24774	0.0601	L	0.44542	1.39	0.09310	N	1	P;P	0.41041	0.671;0.736	B;B	0.38803	0.188;0.282	T	0.30736	-0.9968	10	0.39692	T	0.17	.	12.693	0.56985	1.0:0.0:0.0:0.0	.	992;1018	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	V	1018;992;534	ENSP00000267430:E1018V;ENSP00000442493:E992V;ENSP00000452033:E534V	ENSP00000267430:E1018V	E	+	2	0	FANCM	44714760	0.047000	0.20315	0.002000	0.10522	0.094000	0.18550	3.014000	0.49590	1.947000	0.56498	0.482000	0.46254	GAG	.	.		0.398	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45645010	A	T	45645010	3	4	163	1	0	0	0	0	1	0	0	0	5679	304	11	4	3107	4	FANCM	14	45645010	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	21816868	45645010	61704530	219	25001										
PLEK2	26499	hgsc.bcm.edu	37	chr14	67864480	67864480	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccgacccccctcaagcttgtAgtacaccagcgtgttctgcc	8	17	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr14:67864480A>T	ENST00000216446.4	-	2	246	c.106T>A	c.(106-108)Tac>Aac	p.Y36N	PLEK2_ENST00000557388.1_5'UTR	NM_016445.1	NP_057529.1	Q9NYT0	PLEK2_HUMAN	pleckstrin 2	36	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.L33fs*8(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	15				all cancers(60;0.000728)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.00953)		TCAAGCTTGTAGTACACCAGC	0.597																																					p.Y36N		Atlas-SNP	.											.	PLEK2	23	.	1	Deletion - Frameshift(1)	prostate(1)	c.T106A						.						56	47	50					14																	67864480		2203	4300	6503	SO:0001583	missense	26499	exon2			GCTTGTAGTACAC	AF228603	CCDS9782.1	14q23.3	2014-08-12			ENSG00000100558	ENSG00000100558		"Pleckstrin homology (PH) domain containing"	19238	protein-coding gene	gene with protein product		608007				11911883, 17658464	Standard	NM_016445		Approved		uc001xjh.1	Q9NYT0	OTTHUMG00000171247	ENST00000216446.4:c.106T>A	chr14.hg19:g.67864480A>T	ENSP00000216446:p.Tyr36Asn	103.0	0.0		91.0	19.0	NM_016445	Q96JT0	Missense_Mutation	SNP	ENST00000216446.4	hg19	CCDS9782.1	.	.	.	.	.	.	.	.	.	.	A	32	5.112601	0.94339	.	.	ENSG00000100558	ENST00000216446	T	0.79352	-1.26	5.6	5.6	0.85130	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.176500	0.52532	D	0.000078	D	0.90776	0.7104	H	0.95470	3.675	0.58432	D	0.999998	D	0.69078	0.997	D	0.64877	0.93	D	0.93336	0.6705	10	0.87932	D	0	-27.6637	14.6491	0.68784	1.0:0.0:0.0:0.0	.	36	Q9NYT0	PLEK2_HUMAN	N	36	ENSP00000216446:Y36N	ENSP00000216446:Y36N	Y	-	1	0	PLEK2	66934233	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.930000	0.92872	2.254000	0.74563	0.460000	0.39030	TAC	.	.		0.597	PLEK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412547.2			T	67864480	A	T	67864480	3	4	163	1	0	0	0	0	1	0	0	0	12063	420	15	4	987	4	PLEK2	14	67864480	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	22219470	67864480	39485060	220	25002										
EML5	161436	hgsc.bcm.edu	37	chr14	89105158	89105158	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aatacagaaacatacctactTggccagttgccactatgttg	7	10	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr14:89105158T>A	ENST00000380664.5	-	30	4306	c.4307A>T	c.(4306-4308)cAa>cTa	p.Q1436L	EML5_ENST00000554922.1_Missense_Mutation_p.Q1444L|EML5_ENST00000352093.5_Missense_Mutation_p.Q1398L			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1436						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CATACCTACTTGGCCAGTTGC	0.303																																					p.Q1444L		Atlas-SNP	.											.	EML5	141	.	0			c.A4331T						.						73	64	67					14																	89105158		1810	4066	5876	SO:0001583	missense	161436	exon31			CCTACTTGGCCAG	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.4307A>T	chr14.hg19:g.89105158T>A	ENSP00000370039:p.Gln1436Leu	59.0	0.0		86.0	16.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.694837	0.88830	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.04917	3.61;3.53;3.61	5.38	5.38	0.77491	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.30417	0.0764	M	0.87381	2.88	0.58432	D	0.999994	D;D	0.76494	0.999;0.995	D;D	0.91635	0.999;0.992	T	0.13629	-1.0502	10	0.87932	D	0	-13.7652	15.3849	0.74691	0.0:0.0:0.0:1.0	.	1444;1436	Q05BV3-5;Q05BV3	.;EMAL5_HUMAN	L	1444;1398;1436	ENSP00000451998:Q1444L;ENSP00000298315:Q1398L;ENSP00000370039:Q1436L	ENSP00000298315:Q1398L	Q	-	2	0	EML5	88174911	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.049000	0.60858	0.482000	0.46254	CAA	.	.		0.303	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			A	89105158	T	A	89105158	3	1	163	1	0	0	0	0	1	0	0	0	5102	1812	63	4	1654	4	EML5	14	89105158	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	21240678	89105158	18244382	221	25003										
FBLN5	10516	hgsc.bcm.edu	37	chr14	92403334	92403334	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	atctggtatccaaagcggcaTataagaggcctggagatcgt	12	8	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr14:92403334T>A	ENST00000342058.4	-	4	929	c.336A>T	c.(334-336)atA>atT	p.I112I	FBLN5_ENST00000267620.10_Silent_p.I153I|FBLN5_ENST00000556154.1_Silent_p.I117I	NM_006329.3	NP_006320.2	Q9UBX5	FBLN5_HUMAN	fibulin 5	112					cell-matrix adhesion (GO:0007160)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|protein localization to cell surface (GO:0034394)|regulation of cell growth (GO:0001558)|regulation of removal of superoxide radicals (GO:2000121)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	28		all_cancers(154;0.0722)				CAAAGCGGCATATAAGAGGCC	0.552																																					p.I112I		Atlas-SNP	.											.	FBLN5	60	.	0			c.A336T						.						133	129	130					14																	92403334		2203	4300	6503	SO:0001819	synonymous_variant	10516	exon4			GCGGCATATAAGA	AJ133490	CCDS9898.1	14q31	2014-09-17				ENSG00000140092		"Fibulins"	3602	protein-coding gene	gene with protein product		604580				10640802	Standard	NM_006329		Approved	EVEC, UP50, DANCE, ARMD3	uc001xzx.4	Q9UBX5		ENST00000342058.4:c.336A>T	chr14.hg19:g.92403334T>A		98.0	0.0		137.0	28.0	NM_006329	O75966|Q6IAL4|Q6UWA3	Silent	SNP	ENST00000342058.4	hg19	CCDS9898.1																																																																																			.	.		0.552	FBLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411787.1			A	92403334	T	A	92403334	2	1	163	1	0	0	0	0	0	0	0	1	5708	1396	49	4		4	FBLN5	14	92403334	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	3298176	92403334	14946206	222	25004										
C14orf153	84334	hgsc.bcm.edu	37	chr14	104029339	104029339	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gagccagggggcgtggggccAtggtggtcttgcgggcgggg	24	8	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr14:104029339A>T	ENST00000409074.2	+	1	41	c.40A>T	c.(40-42)Atg>Ttg	p.M14L	BAG5_ENST00000445922.2_5'Flank|APOPT1_ENST00000556253.2_Start_Codon_SNP_p.M1L|RP11-894P9.2_ENST00000556332.1_RNA|RP11-73M18.2_ENST00000472726.2_Missense_Mutation_p.M14L|APOPT1_ENST00000247618.4_Start_Codon_SNP_p.M1L|BAG5_ENST00000299204.4_5'Flank|BAG5_ENST00000337322.4_5'Flank	NM_032374.3	NP_115750.2	Q96IL0	APOP1_HUMAN	apoptogenic 1, mitochondrial	14					intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)	mitochondrion (GO:0005739)											GCGTGGGGCCATGGTGGTCTT	0.751																																					p.M14L		Atlas-SNP	.											.	.	.	.	0			c.A40T						.						6	9	8					14																	104029339		2121	4179	6300	SO:0001583	missense	84334	exon1			GGGGCCATGGTGG	BC007412	CCDS9983.2	14q32.33	2012-06-28	2012-06-28	2011-09-07	ENSG00000256053	ENSG00000256053			20492	protein-coding gene	gene with protein product	"apoptogenic protein 1"		"chromosome 14 open reading frame 153", "apoptogenic 1"	C14orf153		16782708, 18977203	Standard	NM_032374		Approved	MGC2562, APOP-1		Q96IL0	OTTHUMG00000153929	ENST00000409074.2:c.40A>T	chr14.hg19:g.104029339A>T	ENSP00000386485:p.Met14Leu	22.0	0.0		42.0	8.0	NM_032374	Q53G28	Missense_Mutation	SNP	ENST00000409074.2	hg19	CCDS9983.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.92|11.92	1.782100|1.782100	0.31502|0.31502	.|.	.|.	ENSG00000256053|ENSG00000256053;ENSG00000256500;ENSG00000256500	ENST00000440963|ENST00000409074;ENST00000472726;ENST00000247618	.|T;T;T	.|0.68025	.|1.56;-0.3;1.62	4.22|4.22	1.36|1.36	0.22044|0.22044	.|.	.|0.578247	.|0.16155	.|N	.|0.227056	T|T	0.53449|0.53449	0.1797|0.1797	L|L	0.51422|0.51422	1.61|1.61	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.0;0.001	T|T	0.43861|0.43861	-0.9365|-0.9365	5|10	.|0.41790	.|T	.|0.15	.|.	4.2324|4.2324	0.10610|0.10610	0.6617:0.2092:0.1291:0.0|0.6617:0.2092:0.1291:0.0	.|.	.|14;14	.|E7EVH7;Q96IL0	.|.;APOP1_HUMAN	L|L	13|14;14;1	.|ENSP00000386485:M14L;ENSP00000439065:M14L;ENSP00000247618:M1L	.|ENSP00000247618:M1L	H|M	+|+	2|1	0|0	C14orf153|C14orf153;RP11-73M18.2	103099092|103099092	0.621000|0.621000	0.27077|0.27077	0.113000|0.113000	0.21522|0.21522	0.010000|0.010000	0.07245|0.07245	0.841000|0.841000	0.27613|0.27613	0.472000|0.472000	0.27344|0.27344	0.533000|0.533000	0.62120|0.62120	CAT|ATG	.	.		0.751	APOPT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333060.2	NM_032374		T	104029339	A	T	104029339	3	4	163	1	0	0	0	0	1	0	0	0	1755	217	8	4	42	4	C14orf153	14	104029339	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	11626005	104029339	3320201	223	25005										
WDR76	79968	hgsc.bcm.edu	37	chr15	44120478	44120478	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aaagtaacaagctacaacccAagagaacggcagatgcgatg	10	9	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr15:44120478A>T	ENST00000263795.6	+	2	446	c.376A>T	c.(376-378)Aag>Tag	p.K126*	WDR76_ENST00000381246.2_Nonsense_Mutation_p.K62*	NM_001167941.1|NM_024908.3	NP_001161413.1|NP_079184.2	Q9H967	WDR76_HUMAN	WD repeat domain 76	126										breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)	20		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)		GCTACAACCCAAGAGAACGGC	0.423																																					p.K126X		Atlas-SNP	.											.	WDR76	34	.	0			c.A376T						.						88	82	84					15																	44120478		2198	4298	6496	SO:0001587	stop_gained	79968	exon2			CAACCCAAGAGAA	AK023035	CCDS10106.1, CCDS53938.1	15q15.3	2013-01-09			ENSG00000092470	ENSG00000092470		"WD repeat domain containing"	25773	protein-coding gene	gene with protein product						12860291	Standard	NM_024908		Approved	FLJ12973	uc001zti.2	Q9H967	OTTHUMG00000060143	ENST00000263795.6:c.376A>T	chr15.hg19:g.44120478A>T	ENSP00000263795:p.Lys126*	108.0	0.0		89.0	31.0	NM_024908	A0MNP5|Q05CI4	Nonsense_Mutation	SNP	ENST00000263795.6	hg19	CCDS10106.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.272769	0.80580	.	.	ENSG00000092470	ENST00000263795;ENST00000381246;ENST00000452115	.	.	.	4.14	1.82	0.25136	.	0.522997	0.18547	N	0.138014	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.9066	3.888	0.09107	0.6669:0.2198:0.1133:0.0	.	.	.	.	X	126;62;62	.	ENSP00000263795:K126X	K	+	1	0	WDR76	41907770	0.018000	0.18449	0.212000	0.23672	0.003000	0.03518	0.127000	0.15790	0.732000	0.32470	0.460000	0.39030	AAG	.	.		0.423	WDR76-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133482.2	NM_024908		T	44120478	A	T	44120478	4	4	163	1	0	0	0	0	0	1	0	0	17341	131	5	4	382	4	WDR76	15	44120478	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		44120478	58410914	224	25006										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54919024	54919024	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tttgtatttttaatccacacAgcattctcggaaaggaaaat	6	7	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr15:54919024A>T	ENST00000260323.11	+	32	6359		c.e32-1		UNC13C_ENST00000545554.1_Splice_Site|UNC13C_ENST00000537900.1_Splice_Site|UNC13C_ENST00000539562.2_Splice_Site	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)						exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TAATCCACACAGCATTCTCGG	0.373																																					.		Atlas-SNP	.											.	UNC13C	674	.	0			c.6360-2A>T						.						38	34	35					15																	54919024		1817	4070	5887	SO:0001630	splice_region_variant	440279	exon31			CCACACAGCATTC	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.6360-1A>T	chr15.hg19:g.54919024A>T		44.0	0.0		55.0	17.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Splice_Site	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	A	18.95	3.731167	0.69189	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900;ENST00000539562	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2361	0.73432	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UNC13C	52706316	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	9.228000	0.95250	2.193000	0.70182	0.477000	0.44152	.	.	.		0.373	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	Intron	T	54919024	A	T	54919024	5	4	163	1	0	0	0	0	0	0	1	0	17001	202	7	4	6480	4	UNC13C	15	54919024	Splice_Site	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	10798546	54919024	47612368	225	25007										
TSC2	7249	hgsc.bcm.edu	37	chr16	2104375	2104375	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccaacgaagaccttcacgaaAggctggaggttttcaaggcc	11	11	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr16:2104375A>T	ENST00000219476.3	+	5	1045	c.415A>T	c.(415-417)Agg>Tgg	p.R139W	TSC2_ENST00000439673.2_Missense_Mutation_p.R102W|TSC2_ENST00000382538.6_Missense_Mutation_p.R90W|TSC2_ENST00000350773.4_Missense_Mutation_p.R139W|TSC2_ENST00000401874.2_Missense_Mutation_p.R139W|TSC2_ENST00000568454.1_Missense_Mutation_p.R150W|TSC2_ENST00000353929.4_Missense_Mutation_p.R139W	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	139	Required for interaction with TSC1.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CCTTCACGAAAGGCTGGAGGT	0.532			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.R139W		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.A415T	GRCh37	CD993486	TSC2	D	rs137854010	.						93	89	90					16																	2104375		2198	4300	6498	SO:0001583	missense	7249	exon5	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CACGAAAGGCTGG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.415A>T	chr16.hg19:g.2104375A>T	ENSP00000219476:p.Arg139Trp	84.0	0.0		79.0	25.0	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	.	14.89	2.669578	0.47677	.	.	ENSG00000103197	ENST00000219476;ENST00000432909;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773;ENST00000445113	T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06	4.97	2.65	0.31530	Armadillo-like helical (1);Armadillo-type fold (1);Tuberin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.86117	0.5856	M	0.72118	2.19	0.58432	D	0.999997	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.996;0.997;1.0;0.997	D	0.86016	0.1504	10	0.87932	D	0	-17.8573	13.5344	0.61639	0.3943:0.6057:0.0:0.0	.	90;102;139;139;139	B4DIL8;P49815-6;P49815-4;P49815-5;P49815	.;.;.;.;TSC2_HUMAN	W	139;90;139;139;102;90;139;150	ENSP00000219476:R139W;ENSP00000384468:R139W;ENSP00000248099:R139W;ENSP00000399232:R102W;ENSP00000371978:R90W;ENSP00000344383:R139W	ENSP00000219476:R139W	R	+	1	2	TSC2	2044376	0.898000	0.30612	0.741000	0.31004	0.468000	0.32798	1.956000	0.40382	0.231000	0.21079	0.379000	0.24179	AGG	.	.		0.532	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		T	2104375	A	T	2104375	3	4	163	1	0	0	0	0	1	0	0	0	16621	63	3	4	429	4	TSC2	16	2104375	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		2104375	88250378	226	25008										
COG7	91949	hgsc.bcm.edu	37	chr16	23436070	23436070	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tggcaggaaggaatgtttacGtaggtgggggagcagtgcca	18	5	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr16:23436070G>A	ENST00000307149.5	-	7	1194	c.1009C>T	c.(1009-1011)Cat>Tat	p.H337Y		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	337					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		GAATGTTTACGTAGGTGGGGG	0.552																																					p.H337Y		Atlas-SNP	.											.	COG7	62	.	0			c.C1009T						.						95	102	100					16																	23436070		2197	4300	6497	SO:0001630	splice_region_variant	91949	exon7			GTTTACGTAGGTG	AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"Components of oligomeric golgi complex"	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1009+1C>T	chr16.hg19:g.23436070G>A		112.0	0.0		92.0	27.0	NM_153603	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	hg19	CCDS10610.1	.	.	.	.	.	.	.	.	.	.	G	0.429	-0.904390	0.02453	.	.	ENSG00000168434	ENST00000307149	T	0.41758	0.99	5.31	-0.321	0.12717	.	0.595355	0.18401	N	0.142353	T	0.13670	0.0331	N	0.03608	-0.345	0.33088	D	0.537524	B	0.02656	0.0	B	0.01281	0.0	T	0.14090	-1.0485	9	.	.	.	-0.4271	2.2485	0.04037	0.1404:0.3242:0.2924:0.243	.	337	P83436	COG7_HUMAN	Y	337	ENSP00000305442:H337Y	.	H	-	1	0	COG7	23343571	0.365000	0.25006	0.036000	0.18154	0.493000	0.33554	0.819000	0.27308	-0.268000	0.09312	-0.216000	0.12614	CAT	.	.		0.552	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1		Missense_Mutation	A	23436070	G	A	23436070	5	1	163	1	0	0	0	0	0	0	1	0	3665	1159	40	1	1347	1	COG7	16	23436070	Splice_Site	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	21331695	23436070	66918683	227	25009										
MYLK3	91807	hgsc.bcm.edu	37	chr16	46781875	46781875	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	atgtggggaaccccatcagcCccgcccgggcccggtgcccg	14	18	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr16:46781875C>T	ENST00000394809.4	-	1	346	c.231G>A	c.(229-231)ggG>ggA	p.G77G	MYLK3_ENST00000536476.1_Intron	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	77					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				CCCCATCAGCCCCGCCCGGGC	0.692																																					p.G77G		Atlas-SNP	.											.	MYLK3	82	.	0			c.G231A						.						20	23	22					16																	46781875		2201	4295	6496	SO:0001819	synonymous_variant	91807	exon1			ATCAGCCCCGCCC	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.231G>A	chr16.hg19:g.46781875C>T		57.0	0.0		59.0	16.0	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Silent	SNP	ENST00000394809.4	hg19	CCDS10723.2																																																																																			.	.		0.692	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		T	46781875	C	T	46781875	2	4	163	1	0	0	0	0	0	0	0	1	10067	610	22	3		3	MYLK3	16	46781875	Silent	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	23345805	46781875	43572878	228	25010										
TP53	7157	hgsc.bcm.edu	37	chr17	7577569	7577569	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcccatgcaggaactgttacAcatgtagttgtagtggatgg	13	7	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:7577569A>G	ENST00000269305.4	-	7	901	c.712T>C	c.(712-714)Tgt>Cgt	p.C238R	TP53_ENST00000445888.2_Missense_Mutation_p.C238R|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.C238R|TP53_ENST00000420246.2_Missense_Mutation_p.C238R|TP53_ENST00000359597.4_Missense_Mutation_p.C238R|TP53_ENST00000455263.2_Missense_Mutation_p.C238R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	238	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C238R(14)|p.C238S(12)|p.0?(8)|p.?(5)|p.C238G(4)|p.M237_N239delMCN(4)|p.C238fs*21(1)|p.C238fs*2(1)|p.M144_N146delMCN(1)|p.C238del(1)|p.Y236_M243delYMCNSSCM(1)|p.C145G(1)|p.V225fs*23(1)|p.M237_C238insX(1)|p.H233fs*6(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)|p.M237fs*1(1)|p.C238fs*9(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GAACTGTTACACATGTAGTTG	0.567		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.C238R	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,colon,carcinoma,0,2	TP53	33396	.	60	Substitution - Missense(31)|Deletion - In frame(9)|Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(5)|Insertion - Frameshift(1)|Insertion - In frame(1)	ovary(11)|liver(7)|biliary_tract(6)|bone(5)|upper_aerodigestive_tract(4)|large_intestine(4)|stomach(3)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|lung(2)|skin(2)|prostate(2)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|oesophagus(1)|pancreas(1)	c.T712C	GRCh37	CM025271|CM056070	TP53	M		.						131	103	112					17																	7577569		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TGTTACACATGTA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.712T>C	chr17.hg19:g.7577569A>G	ENSP00000269305:p.Cys238Arg	85.0	0.0		63.0	27.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.062565	0.76187	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99964	-9.96;-9.96;-9.96;-9.96;-9.96;-9.96;-9.96;-9.96	4.09	4.09	0.47781	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99971	0.9990	M	0.92970	3.365	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.95386	0.8477	10	0.87932	D	0	-18.536	11.6823	0.51466	1.0:0.0:0.0:0.0	.	238;238;145;238;238;238	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	R	238;238;238;238;238;238;227;145;106;145	ENSP00000410739:C238R;ENSP00000352610:C238R;ENSP00000269305:C238R;ENSP00000398846:C238R;ENSP00000391127:C238R;ENSP00000391478:C238R;ENSP00000425104:C106R;ENSP00000423862:C145R	ENSP00000269305:C238R	C	-	1	0	TP53	7518294	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.021000	0.93673	2.074000	0.62210	0.379000	0.24179	TGT	.	.		0.567	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7577569	A	G	7577569	3	3	163	1	0	0	0	0	1	0	0	0	16396	159	6	2	578	2	TP53	17	7577569	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		7577569	73617641	229	25011										
FOXN1	8456	hgsc.bcm.edu	37	chr17	26861766	26861766	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gagacaagagagaaaagctgGgctccccactcctgggctgt	13	11	0	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:26861766G>C	ENST00000226247.2	+	7	1206	c.1177G>C	c.(1177-1179)Ggc>Cgc	p.G393R	FOXN1_ENST00000579795.1_Missense_Mutation_p.G393R	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	393					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					AGAAAAGCTGGGCTCCCCACT	0.632																																					p.G393R		Atlas-SNP	.											.	FOXN1	51	.	0			c.G1177C						.						15	18	17					17																	26861766		2203	4299	6502	SO:0001583	missense	8456	exon7			AAGCTGGGCTCCC	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"Forkhead boxes"	12765	protein-coding gene	gene with protein product		600838	"winged-helix nude", "Rowett nude"	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.1177G>C	chr17.hg19:g.26861766G>C	ENSP00000226247:p.Gly393Arg	112.0	0.0		126.0	25.0	NM_003593	B2R9Q7|O15352	Missense_Mutation	SNP	ENST00000226247.2	hg19	CCDS11232.1	.	.	.	.	.	.	.	.	.	.	G	0.719	-0.784166	0.02907	.	.	ENSG00000109101	ENST00000226247	D	0.92699	-3.09	4.25	2.12	0.27331	.	0.200206	0.32987	N	0.005409	T	0.71022	0.3291	N	0.01352	-0.895	0.28908	N	0.89288	B	0.02656	0.0	B	0.01281	0.0	T	0.62982	-0.6738	10	0.10377	T	0.69	.	4.5257	0.11980	0.3129:0.2452:0.4419:0.0	.	393	O15353	FOXN1_HUMAN	R	393	ENSP00000226247:G393R	ENSP00000226247:G393R	G	+	1	0	FOXN1	23885893	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	2.530000	0.45641	1.006000	0.39211	0.561000	0.74099	GGC	.	.		0.632	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1			C	26861766	G	C	26861766	3	2	163	1	0	0	0	0	1	0	0	0	6027	1232	43	4	1203	4	FOXN1	17	26861766	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	19284197	26861766	54333444	230	25012										
PIGS	94005	hgsc.bcm.edu	37	chr17	26888503	26888503	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtcctctggaaggtggtcagCcagagcagcagcaagcacat	13	11	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:26888503C>T	ENST00000308360.7	-	6	988	c.613G>A	c.(613-615)Gct>Act	p.A205T	PIGS_ENST00000543734.1_Missense_Mutation_p.A144T|PIGS_ENST00000395346.2_Missense_Mutation_p.A197T|PIGS_ENST00000465444.1_5'UTR	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	205					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					AGGTGGTCAGCCAGAGCAGCA	0.592																																					p.A205T		Atlas-SNP	.											PIGS,NS,carcinoma,0,1	PIGS	42	.	0			c.G613A						.						83	67	72					17																	26888503		2203	4300	6503	SO:0001583	missense	94005	exon6			GGTCAGCCAGAGC		CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"Phosphatidylinositol glycan anchor biosynthesis"	14937	protein-coding gene	gene with protein product	"GPI transamidase subunit"	610271	"phosphatidylinositol glycan, class S"				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.613G>A	chr17.hg19:g.26888503C>T	ENSP00000309430:p.Ala205Thr	60.0	0.0		64.0	18.0	NM_033198	Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	hg19	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.084781	0.36758	.	.	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.47869	0.84;0.83;0.88	5.68	4.71	0.59529	.	0.253846	0.46442	D	0.000281	T	0.38453	0.1041	L	0.28115	0.83	0.29611	N	0.846957	B;B	0.33022	0.394;0.342	B;B	0.40256	0.324;0.217	T	0.30966	-0.9960	10	0.14252	T	0.57	-7.461	13.424	0.61015	0.3922:0.6078:0.0:0.0	.	205;197	Q96S52;Q96S52-2	PIGS_HUMAN;.	T	197;205;144	ENSP00000378755:A197T;ENSP00000309430:A205T;ENSP00000438447:A144T	ENSP00000309430:A205T	A	-	1	0	PIGS	23912630	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.525000	0.35953	1.388000	0.46506	0.655000	0.94253	GCT	.	.		0.592	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198		T	26888503	C	T	26888503	3	4	163	1	0	0	0	0	1	0	0	0	11907	739	26	3	1082	3	PIGS	17	26888503	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	26737	26888503	54306707	231	25013										
SLC6A4	6532	hgsc.bcm.edu	37	chr17	28548654	28548654	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cccctccattctggtaacatAtgtaggggaagcgccagaca	10	12	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:28548654A>T	ENST00000401766.2	-	2	835	c.323T>A	c.(322-324)aTa>aAa	p.I108K	SLC6A4_ENST00000261707.3_Missense_Mutation_p.I108K			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	108					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	CTGGTAACATATGTAGGGGAA	0.592																																					p.I108K		Atlas-SNP	.											.	SLC6A4	60	.	0			c.T323A						.						123	116	118					17																	28548654		2203	4300	6503	SO:0001583	missense	6532	exon3			TAACATATGTAGG	L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"Solute carriers"	11050	protein-coding gene	gene with protein product	"serotonin transporter 1"	182138	"solute carrier family 6 (neurotransmitter transporter, serotonin), member 4", "5-hydroxytryptamine (serotonin) transporter", "obsessive-compulsive disorder 1"	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.323T>A	chr17.hg19:g.28548654A>T	ENSP00000385822:p.Ile108Lys	70.0	0.0		61.0	17.0	NM_001045	Q5EE02	Missense_Mutation	SNP	ENST00000401766.2	hg19	CCDS11256.1	.	.	.	.	.	.	.	.	.	.	A	31	5.064677	0.93898	.	.	ENSG00000108576	ENST00000394821;ENST00000401766;ENST00000261707	T;T;T	0.74947	-0.89;-0.88;-0.88	5.85	5.85	0.93711	.	0.040304	0.85682	D	0.000000	D	0.86053	0.5841	M	0.78801	2.425	0.80722	D	1	D	0.54772	0.968	D	0.70935	0.971	D	0.87699	0.2559	10	0.87932	D	0	.	15.4155	0.74962	1.0:0.0:0.0:0.0	.	108	P31645	SC6A4_HUMAN	K	150;108;108	ENSP00000378298:I150K;ENSP00000385822:I108K;ENSP00000261707:I108K	ENSP00000261707:I108K	I	-	2	0	SLC6A4	25572780	1.000000	0.71417	0.991000	0.47740	0.968000	0.65278	9.318000	0.96334	2.234000	0.73211	0.533000	0.62120	ATA	.	.		0.592	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045		T	28548654	A	T	28548654	3	4	163	1	0	0	0	0	1	0	0	0	14701	449	16	4	1621	4	SLC6A4	17	28548654	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1660151	28548654	52646556	232	25014										
SPACA3	124912	hgsc.bcm.edu	37	chr17	31322727	31322727	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cggataccggggatacagccTggctgactgtgagaacccct	13	12	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:31322727T>A	ENST00000269053.3	+	2	405	c.335T>A	c.(334-336)cTg>cAg	p.L112Q	SPACA3_ENST00000394638.1_Intron|SPACA3_ENST00000394637.2_3'UTR|SPACA3_ENST00000580599.1_Missense_Mutation_p.L43Q	NM_173847.3	NP_776246.1	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	112					cell wall macromolecule catabolic process (GO:0016998)|defense response to Gram-positive bacterium (GO:0050830)|monocyte activation (GO:0042117)|peptidoglycan catabolic process (GO:0009253)|positive regulation of macrophage activation (GO:0043032)|positive regulation of phagocytosis (GO:0050766)|response to virus (GO:0009615)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|secretory granule (GO:0030141)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(9;0.193)			GGATACAGCCTGGCTGACTGT	0.607																																					p.L112Q		Atlas-SNP	.											.	SPACA3	35	.	0			c.T335A						.						74	50	58					17																	31322727		2203	4300	6503	SO:0001583	missense	124912	exon2			ACAGCCTGGCTGA	AF216311, AF099029	CCDS11275.1	17q12	2014-07-23			ENSG00000141316	ENSG00000141316			16260	protein-coding gene	gene with protein product	"cancer/testis antigen 54", "sperm lyzozyme-like acrosomal protein 1"	612749				12606493	Standard	NM_173847		Approved	ALLP17, SLLP1, LYC3, LYZL3, CT54	uc002hhs.1	Q8IXA5	OTTHUMG00000132886	ENST00000269053.3:c.335T>A	chr17.hg19:g.31322727T>A	ENSP00000269053:p.Leu112Gln	80.0	0.0		119.0	26.0	NM_173847	Q7Z4Y5	Missense_Mutation	SNP	ENST00000269053.3	hg19	CCDS11275.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	16.35|16.35	3.098594|3.098594	0.56183|0.56183	.|.	.|.	ENSG00000141316|ENSG00000141316	ENST00000269053;ENST00000394637|ENST00000411740	T|.	0.78126|.	-1.15|.	3.94|3.94	3.94|3.94	0.45596|0.45596	Lysozyme-like domain (1);|.	0.384395|.	0.21511|.	N|.	0.073362|.	T|T	0.76572|0.76572	0.4006|0.4006	M|M	0.87900|0.87900	2.915|2.915	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	T|T	0.79654|0.79654	-0.1713|-0.1713	10|6	0.87932|0.87932	D|D	0|0	-8.2128|-8.2128	9.49|9.49	0.38953|0.38953	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	112|.	Q8IXA5|.	SACA3_HUMAN|.	Q|R	112;113|13	ENSP00000269053:L112Q|.	ENSP00000269053:L112Q|ENSP00000392807:W13R	L|W	+|+	2|1	0|0	SPACA3|SPACA3	28346840|28346840	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.492000|0.492000	0.33523|0.33523	4.986000|4.986000	0.63851|0.63851	2.510000|2.510000	0.84645|0.84645	0.443000|0.443000	0.29094|0.29094	CTG|TGG	.	.		0.607	SPACA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256380.1	NM_173847		A	31322727	T	A	31322727	3	1	163	1	0	0	0	0	1	0	0	0	14988	1580	55	4	341	4	SPACA3	17	31322727	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	2774073	31322727	49872483	233	25015										
FNDC8	54752	hgsc.bcm.edu	37	chr17	33454263	33454263	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aaaatgaggacctggcgctcGgcccctgcccatgcccatcg	11	16	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:33454263G>T	ENST00000158009.5	+	2	527	c.412G>T	c.(412-414)Ggc>Tgc	p.G138C		NM_017559.2	NP_060029.1	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	138						nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	11		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)		CCTGGCGCTCGGCCCCTGCCC	0.587																																					p.G138C		Atlas-SNP	.											.	FNDC8	28	.	0			c.G412T						.						106	114	111					17																	33454263		2203	4300	6503	SO:0001583	missense	54752	exon2			GCGCTCGGCCCCT	BC024002	CCDS11290.1	17q12	2013-02-11			ENSG00000073598	ENSG00000073598		"Fibronectin type III domain containing"	25286	protein-coding gene	gene with protein product						12477932	Standard	XM_005257993		Approved	DKFZp434H2215	uc002hix.3	Q8TC99	OTTHUMG00000132932	ENST00000158009.5:c.412G>T	chr17.hg19:g.33454263G>T	ENSP00000158009:p.Gly138Cys	64.0	0.0		115.0	17.0	NM_017559	B2R9G6|Q9UFC2	Missense_Mutation	SNP	ENST00000158009.5	hg19	CCDS11290.1	.	.	.	.	.	.	.	.	.	.	G	8.013	0.757960	0.15846	.	.	ENSG00000073598	ENST00000158009	T	0.32515	1.45	5.38	3.19	0.36642	.	.	.	.	.	T	0.15478	0.0373	N	0.08118	0	0.24912	N	0.992031	B	0.06786	0.001	B	0.04013	0.001	T	0.19451	-1.0305	9	0.66056	D	0.02	.	6.0482	0.19772	0.1573:0.0:0.1814:0.6612	.	138	Q8TC99	FNDC8_HUMAN	C	138	ENSP00000158009:G138C	ENSP00000158009:G138C	G	+	1	0	FNDC8	30478376	0.941000	0.31946	0.929000	0.37066	0.001000	0.01503	1.310000	0.33551	0.496000	0.27904	-1.104000	0.02111	GGC	.	.		0.587	FNDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256459.2	NM_017559		T	33454263	G	T	33454263	3	4	163	1	0	0	0	0	1	0	0	0	5982	1116	39	1	418	1	FNDC8	17	33454263	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	2131536	33454263	47740947	234	25016										
KRTAP9-9	81870	hgsc.bcm.edu	37	chr17	39411680	39411680	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gctgtcagcctacctgctgcAggaccacctgctggaagccc	11	16	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:39411680A>T	ENST00000394008.1	+	1	45	c.43A>T	c.(43-45)Agg>Tgg	p.R15W		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	15	14 X 5 AA repeats of C-C-[RQVGE]- [SPSTNQ]-[TASL].					keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			TACCTGCTGCAGGACCACCTG	0.607																																					p.R15W		Atlas-SNP	.											.	KRTAP9-9	24	.	0			c.A43T						.																																			SO:0001583	missense	81870	exon1			TGCTGCAGGACCA	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"Keratin associated proteins"	16773	protein-coding gene	gene with protein product			"keratin associated protein 9-5"	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.43A>T	chr17.hg19:g.39411680A>T	ENSP00000377576:p.Arg15Trp	62.0	0.0		58.0	16.0	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	hg19	CCDS54127.1	.	.	.	.	.	.	.	.	.	.	.	10.60	1.394937	0.25205	.	.	ENSG00000198083	ENST00000394008	T	0.00873	5.59	0.589	0.589	0.17452	.	.	.	.	.	T	0.02304	0.0071	L	0.38175	1.15	0.24849	N	0.992417	D	0.69078	0.997	D	0.69307	0.963	T	0.51309	-0.8722	8	0.72032	D	0.01	.	.	.	.	.	20	Q9BYP9	KRA99_HUMAN	W	15	ENSP00000377576:R15W	ENSP00000377576:R15W	R	+	1	2	KRTAP9-9	36665206	0.847000	0.29606	0.979000	0.43373	0.805000	0.45488	0.126000	0.15769	0.507000	0.28148	0.374000	0.22700	AGG	.	.		0.607	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975		T	39411680	A	T	39411680	3	4	163	1	0	0	0	0	1	0	0	0	8586	179	7	4	45	4	KRTAP9-9	17	39411680	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	5957417	39411680	41783530	235	25017										
KRT33B	3884	hgsc.bcm.edu	37	chr17	39525975	39525975	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcagctggtgcggcagctcaGgctgggcaggcagaagttgt	18	9	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:39525975G>T	ENST00000251646.3	-	1	77	c.28C>A	c.(28-30)Ctg>Atg	p.L10M		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	10	Head.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				CGGCAGCTCAGGCTGGGCAGG	0.617																																					p.L10M		Atlas-SNP	.											.	KRT33B	46	.	0			c.C28A						.						18	20	20					17																	39525975		2199	4292	6491	SO:0001583	missense	3884	exon1			AGCTCAGGCTGGG	X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"-", "Intermediate filaments type I, keratins (acidic)"	6451	protein-coding gene	gene with protein product	"hard keratin type I 3II"	602762	"keratin, hair, acidic, 3B"	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.28C>A	chr17.hg19:g.39525975G>T	ENSP00000251646:p.Leu10Met	145.0	0.0		150.0	33.0	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	hg19	CCDS11389.1	.	.	.	.	.	.	.	.	.	.	g	9.460	1.092875	0.20471	.	.	ENSG00000131738	ENST00000251646	D	0.82619	-1.63	4.44	-4.99	0.03010	.	1.361320	0.04724	N	0.419971	T	0.73860	0.3641	L	0.47016	1.485	0.09310	N	1	B	0.19817	0.039	B	0.22386	0.039	T	0.58880	-0.7558	10	0.51188	T	0.08	.	3.4962	0.07655	0.3533:0.0:0.2401:0.4066	.	10	Q14525	KT33B_HUMAN	M	10	ENSP00000251646:L10M	ENSP00000251646:L10M	L	-	1	2	KRT33B	36779501	0.000000	0.05858	0.032000	0.17829	0.827000	0.46813	-2.497000	0.00969	-0.593000	0.05844	-0.157000	0.13467	CTG	.	.		0.617	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279		T	39525975	G	T	39525975	3	4	163	1	0	0	0	0	1	0	0	0	8479	991	35	3	1214	3	KRT33B	17	39525975	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	114295	39525975	41669235	236	25018										
DHX8	1659	hgsc.bcm.edu	37	chr17	41582192	41582192	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	actgaaggagcaattggtccAggtgagaagacttttatgat	12	5	0	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:41582192A>T	ENST00000262415.3	+	12	1799	c.1727A>T	c.(1726-1728)cAg>cTg	p.Q576L	DHX8_ENST00000540306.1_Splice_Site_p.Q576L	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	576	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		CAATTGGTCCAGGTGAGAAGA	0.443																																					p.Q576L	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.A1727T						.						72	69	70					17																	41582192		2203	4300	6503	SO:0001630	splice_region_variant	1659	exon12			TGGTCCAGGTGAG	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"DEAH-boxes"	2749	protein-coding gene	gene with protein product		600396	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.1728+1A>T	chr17.hg19:g.41582192A>T		103.0	0.0		160.0	29.0	NM_004941		Missense_Mutation	SNP	ENST00000262415.3	hg19	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.494548	0.85069	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.06449	3.3;3.3	4.95	4.95	0.65309	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.21801	0.0525	M	0.85777	2.775	0.80722	D	1	P;P	0.50528	0.936;0.797	P;P	0.53954	0.738;0.491	T	0.01819	-1.1267	10	0.72032	D	0.01	.	13.8026	0.63212	1.0:0.0:0.0:0.0	.	576;576	F5H658;Q14562	.;DHX8_HUMAN	L	576	ENSP00000437886:Q576L;ENSP00000262415:Q576L	ENSP00000262415:Q576L	Q	+	2	0	DHX8	38937718	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.237000	0.95368	1.855000	0.53841	0.454000	0.30748	CAG	.	.		0.443	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1		Missense_Mutation	T	41582192	A	T	41582192	5	4	163	1	0	0	0	0	0	0	1	0	4517	202	7	4	1773	4	DHX8	17	41582192	Splice_Site	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	2056217	41582192	39613018	237	25019										
ASB16	92591	hgsc.bcm.edu	37	chr17	42249420	42249420	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tttgctctccctagggttctGggtgctgacccccaagacca	10	14	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:42249420G>C	ENST00000293414.1	+	2	392	c.308G>C	c.(307-309)tGg>tCg	p.W103S		NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	103					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CTAGGGTTCTGGGTGCTGACC	0.607																																					p.W103S		Atlas-SNP	.											.	ASB16	34	.	0			c.G308C						.						36	32	33					17																	42249420		2203	4300	6503	SO:0001583	missense	92591	exon2			GGTTCTGGGTGCT	AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"Ankyrin repeat domain containing"	19768	protein-coding gene	gene with protein product		615056	"ankyrin repeat and SOCS box-containing 16"			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.308G>C	chr17.hg19:g.42249420G>C	ENSP00000293414:p.Trp103Ser	35.0	0.0		50.0	12.0	NM_080863	B2RBC0|Q8WXK0	Missense_Mutation	SNP	ENST00000293414.1	hg19	CCDS11478.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.544241	0.86022	.	.	ENSG00000161664	ENST00000293414	T	0.50813	0.73	5.55	5.55	0.83447	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.60753	0.2293	L	0.39898	1.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51020	-0.8758	10	0.26408	T	0.33	-19.1143	18.4386	0.90656	0.0:0.0:1.0:0.0	.	103	Q96NS5	ASB16_HUMAN	S	103	ENSP00000293414:W103S	ENSP00000293414:W103S	W	+	2	0	ASB16	39604946	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.721000	0.74728	2.894000	0.99253	0.655000	0.94253	TGG	.	.		0.607	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1			C	42249420	G	C	42249420	3	2	163	1	0	0	0	0	1	0	0	0	1020	1357	47	4	314	4	ASB16	17	42249420	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	667228	42249420	38945790	238	25020										
SLC4A1	6521	hgsc.bcm.edu	37	chr17	42327879	42327879	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccgaccttcctcctcatcaaAggttgccttggcatcatcag	7	15	4	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:42327879A>T	ENST00000262418.6	-	20	2838	c.2683T>A	c.(2683-2685)Ttt>Att	p.F895I	AC003102.1_ENST00000399246.2_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	895	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		TCCTCATCAAAGGTTGCCTTG	0.627																																					p.F895I		Atlas-SNP	.											.	SLC4A1	104	.	0			c.T2683A						.						112	75	88					17																	42327879		2203	4300	6503	SO:0001583	missense	6521	exon20			CATCAAAGGTTGC		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"CD molecules", "Blood group antigens", "Solute carriers"	11027	protein-coding gene	gene with protein product	"Froese blood group", "Swann blood group", "Wright blood group"	109270	"Waldner blood group", "erythrocyte membrane protein band 3", "Diego blood group", "solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)", "solute carrier family 4 (anion exchanger), member 1"	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.2683T>A	chr17.hg19:g.42327879A>T	ENSP00000262418:p.Phe895Ile	62.0	0.0		53.0	12.0	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	hg19	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.169256	0.38315	.	.	ENSG00000004939	ENST00000262418	T	0.74002	-0.8	4.66	2.37	0.29283	.	0.543240	0.20261	N	0.095871	T	0.69205	0.3085	M	0.74647	2.275	0.46927	D	0.999254	B	0.23249	0.082	B	0.25884	0.064	T	0.63310	-0.6666	10	0.49607	T	0.09	.	4.5964	0.12332	0.6607:0.1661:0.1732:0.0	.	895	P02730	B3AT_HUMAN	I	895	ENSP00000262418:F895I	ENSP00000262418:F895I	F	-	1	0	SLC4A1	39683405	0.979000	0.34478	0.084000	0.20598	0.323000	0.28346	2.848000	0.48278	0.369000	0.24510	0.459000	0.35465	TTT	.	.		0.627	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		T	42327879	A	T	42327879	3	4	163	1	0	0	0	0	1	0	0	0	14665	72	3	4	56	4	SLC4A1	17	42327879	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	78459	42327879	38867331	239	25021										
SLC4A1	6521	hgsc.bcm.edu	37	chr17	42335828	42335828	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcttggcagggctggactgaTagcgccttcgaagtagctcc	14	11	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:42335828T>A	ENST00000262418.6	-	10	1195	c.1040A>T	c.(1039-1041)tAt>tTt	p.Y347F	SLC4A1_ENST00000471005.1_5'Flank|AC003043.1_ENST00000597382.1_Intron	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	347	Dimerization arm.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GCTGGACTGATAGCGCCTTCG	0.632																																					p.Y347F		Atlas-SNP	.											SLC4A1,NS,neuroblastoma,0,1	SLC4A1	104	.	0			c.A1040T						.						105	109	107					17																	42335828		2203	4300	6503	SO:0001583	missense	6521	exon10			GACTGATAGCGCC		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"CD molecules", "Blood group antigens", "Solute carriers"	11027	protein-coding gene	gene with protein product	"Froese blood group", "Swann blood group", "Wright blood group"	109270	"Waldner blood group", "erythrocyte membrane protein band 3", "Diego blood group", "solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)", "solute carrier family 4 (anion exchanger), member 1"	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.1040A>T	chr17.hg19:g.42335828T>A	ENSP00000262418:p.Tyr347Phe	96.0	0.0		129.0	31.0	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	hg19	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	N	3.348	-0.133095	0.06711	.	.	ENSG00000004939	ENST00000262418	T	0.79554	-1.28	4.68	4.68	0.58851	Bicarbonate transporter, cytoplasmic (1);Phosphotransferase/anion transporter (1);	0.618725	0.15933	N	0.237572	D	0.83995	0.5375	M	0.67953	2.075	0.36133	D	0.846262	D;B	0.56968	0.978;0.001	P;B	0.56612	0.802;0.011	T	0.82625	-0.0365	10	0.11485	T	0.65	.	13.2439	0.60012	0.0:0.0:0.0:1.0	.	347;347	E2RVJ0;P02730	.;B3AT_HUMAN	F	347	ENSP00000262418:Y347F	ENSP00000262418:Y347F	Y	-	2	0	SLC4A1	39691354	0.992000	0.36948	0.552000	0.28243	0.058000	0.15608	2.729000	0.47327	1.963000	0.57068	0.255000	0.18592	TAT	.	.		0.632	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		A	42335828	T	A	42335828	3	1	163	1	0	0	0	0	1	0	0	0	14665	1406	49	4	1739	4	SLC4A1	17	42335828	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	7949	42335828	38859382	240	25022										
KCNH6	81033	hgsc.bcm.edu	37	chr17	61623092	61623092	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tcctcagaacaggaacagccTgaggggctctggccacccct	11	15	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:61623092T>A	ENST00000583023.1	+	14	2825	c.2814T>A	c.(2812-2814)ccT>ccA	p.P938P	KCNH6_ENST00000456941.2_Silent_p.P849P|KCNH6_ENST00000581784.1_Silent_p.P849P|KCNH6_ENST00000314672.5_Silent_p.P902P	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	938					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	AGGAACAGCCTGAGGGGCTCT	0.577																																					p.P938P		Atlas-SNP	.											.	KCNH6	122	.	0			c.T2814A						.						111	101	104					17																	61623092		2203	4300	6503	SO:0001819	synonymous_variant	81033	exon14			ACAGCCTGAGGGG	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2814T>A	chr17.hg19:g.61623092T>A		89.0	0.0		66.0	13.0	NM_030779	Q9BRD7	Silent	SNP	ENST00000583023.1	hg19	CCDS11638.1																																																																																			.	.		0.577	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		A	61623092	T	A	61623092	2	1	163	1	0	0	0	0	0	0	0	1	8045	1567	55	4		4	KCNH6	17	61623092	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	19287264	61623092	19572118	241	25023										
HELZ	9931	hgsc.bcm.edu	37	chr17	65186459	65186459	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcaccatacctacagattccTtgttctaaaaatctaagtag	5	10	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:65186459T>A	ENST00000358691.5	-	10	736	c.570A>T	c.(568-570)caA>caT	p.Q190H	HELZ_ENST00000580168.1_Missense_Mutation_p.Q190H|HELZ_ENST00000580662.1_5'UTR	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	190						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TACAGATTCCTTGTTCTAAAA	0.368																																					p.Q190H		Atlas-SNP	.											.	HELZ	160	.	0			c.A570T						.						109	99	102					17																	65186459		1840	4087	5927	SO:0001583	missense	9931	exon10			GATTCCTTGTTCT	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.570A>T	chr17.hg19:g.65186459T>A	ENSP00000351524:p.Gln190His	82.0	0.0		142.0	27.0	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	T	10.61	1.397691	0.25205	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	T;T	0.41400	1.0;1.0	5.38	5.38	0.77491	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.56761	0.2007	L	0.56769	1.78	0.58432	D	0.999998	D;D	0.71674	0.997;0.998	D;D	0.68765	0.96;0.955	T	0.59408	-0.7460	10	0.62326	D	0.03	-11.9044	9.8451	0.41021	0.0:0.0764:0.0:0.9236	.	190;190	B7ZLW2;P42694	.;HELZ_HUMAN	H	190	ENSP00000351524:Q190H;ENSP00000411144:Q190H	ENSP00000351524:Q190H	Q	-	3	2	HELZ	62616921	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.948000	0.49066	2.047000	0.60756	0.533000	0.62120	CAA	.	.		0.368	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65186459	T	A	65186459	3	1	163	1	0	0	0	0	1	0	0	0	7058	1606	56	4	5354	4	HELZ	17	65186459	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	3563367	65186459	16008751	242	25024										
KCNJ2	3759	hgsc.bcm.edu	37	chr17	68171897	68171897	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aaatccagaattacttctgaAggggagtatatccctctgga	9	8	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:68171897A>T	ENST00000243457.3	+	2	1100	c.717A>T	c.(715-717)gaA>gaT	p.E239D	KCNJ2_ENST00000535240.1_Missense_Mutation_p.E239D	NM_000891.2	NP_000882.1	P63252	KCNJ2_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 2	239					cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|magnesium ion transport (GO:0015693)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of resting membrane potential (GO:0060075)|regulation of skeletal muscle contraction via regulation of action potential (GO:0014861)|relaxation of cardiac muscle (GO:0055119)|relaxation of skeletal muscle (GO:0090076)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of membrane (GO:0031224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(13)|skin(1)|urinary_tract(1)	25	Breast(10;1.64e-08)					TTACTTCTGAAGGGGAGTATA	0.453																																					p.E239D		Atlas-SNP	.											.	KCNJ2	74	.	0			c.A717T						.						92	93	93					17																	68171897		2203	4300	6503	SO:0001583	missense	3759	exon2			TTCTGAAGGGGAG	AF011904	CCDS11688.1	17q24.3	2014-09-17				ENSG00000123700		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6263	protein-coding gene	gene with protein product		600681				7696590, 11240146, 16382105	Standard	NM_000891		Approved	Kir2.1, IRK1, LQT7	uc002jir.3	P63252		ENST00000243457.3:c.717A>T	chr17.hg19:g.68171897A>T	ENSP00000243457:p.Glu239Asp	55.0	0.0		91.0	18.0	NM_000891	O15110|P48049	Missense_Mutation	SNP	ENST00000243457.3	hg19	CCDS11688.1	.	.	.	.	.	.	.	.	.	.	A	13.65	2.301047	0.40694	.	.	ENSG00000123700	ENST00000535240;ENST00000243457	D;D	0.96522	-4.04;-4.04	5.86	2.5	0.30297	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.97807	0.9280	M	0.86805	2.84	0.50467	D	0.999872	D	0.65815	0.995	D	0.91635	0.999	D	0.96680	0.9503	9	.	.	.	.	9.5361	0.39224	0.8021:0.0:0.1979:0.0	.	239	P63252	IRK2_HUMAN	D	239	ENSP00000441848:E239D;ENSP00000243457:E239D	.	E	+	3	2	KCNJ2	65683492	1.000000	0.71417	0.982000	0.44146	0.520000	0.34377	2.928000	0.48908	0.153000	0.19213	-0.250000	0.11733	GAA	.	.		0.453	KCNJ2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450889.1	NM_000891		T	68171897	A	T	68171897	3	4	163	1	0	0	0	0	1	0	0	0	8060	69	3	4	719	4	KCNJ2	17	68171897	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	2985438	68171897	13023313	243	25025										
LLGL2	3993	hgsc.bcm.edu	37	chr17	73566301	73566301	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	accagccatggctttggcctCtttgaccaccagcagcggcg	11	15	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:73566301C>T	ENST00000392550.3	+	15	1956	c.1839C>T	c.(1837-1839)ctC>ctT	p.L613L	LLGL2_ENST00000167462.5_Silent_p.L613L|LLGL2_ENST00000577200.1_Silent_p.L613L	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	613					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			GCTTTGGCCTCTTTGACCACC	0.672																																					p.L613L		Atlas-SNP	.											.	LLGL2	155	.	0			c.C1839T						.						17	16	17					17																	73566301		2196	4297	6493	SO:0001819	synonymous_variant	3993	exon15			TGGCCTCTTTGAC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"WD repeat domain containing"	6629	protein-coding gene	gene with protein product			"lethal giant larvae (Drosophila) homolog 2"				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1839C>T	chr17.hg19:g.73566301C>T		64.0	0.0		63.0	21.0	NM_004524	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	hg19	CCDS32733.1																																																																																			.	.		0.672	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		T	73566301	C	T	73566301	2	4	163	1	0	0	0	0	0	0	0	1	8843	900	32	3		3	LLGL2	17	73566301	Silent	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	5394404	73566301	7628909	244	25026										
EXOC7	23265	hgsc.bcm.edu	37	chr17	74087274	74087274	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttttcccatctagaccatgcTgggaatactgtttcagaagg	9	9	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr17:74087274T>A	ENST00000335146.7	-	7	904	c.851A>T	c.(850-852)cAg>cTg	p.Q284L	EXOC7_ENST00000607838.1_Missense_Mutation_p.Q284L|EXOC7_ENST00000411744.2_Intron|EXOC7_ENST00000332065.5_Intron|EXOC7_ENST00000467929.2_Missense_Mutation_p.Q243L|EXOC7_ENST00000589210.1_Missense_Mutation_p.Q284L|EXOC7_ENST00000405575.4_Missense_Mutation_p.Q284L			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	284					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			TAGACCATGCTGGGAATACTG	0.512																																					p.Q284L		Atlas-SNP	.											.	EXOC7	47	.	0			c.A851T						.						211	176	188					17																	74087274		2203	4300	6503	SO:0001583	missense	23265	exon7			CCATGCTGGGAAT	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.851A>T	chr17.hg19:g.74087274T>A	ENSP00000334100:p.Gln284Leu	106.0	0.0		87.0	27.0	NM_001013839	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.042241	0.55003	.	.	ENSG00000182473	ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372	.	.	.	5.81	4.72	0.59763	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.39937	0.1097	L	0.34521	1.04	0.80722	D	1	B;B;P;B;B	0.37276	0.002;0.065;0.589;0.142;0.029	B;B;B;B;B	0.33392	0.025;0.01;0.163;0.098;0.017	T	0.16247	-1.0409	9	0.33940	T	0.23	-29.392	13.1099	0.59267	0.0:0.0:0.134:0.866	.	284;243;243;284;284	Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-1	.;.;.;EXOC7_HUMAN;.	L	284;284;284;243	.	ENSP00000334100:Q284L	Q	-	2	0	EXOC7	71598869	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.503000	0.81632	1.000000	0.39049	-0.313000	0.08912	CAG	.	.		0.512	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		A	74087274	T	A	74087274	3	1	163	1	0	0	0	0	1	0	0	0	5312	1580	55	4	1412	4	EXOC7	17	74087274	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	520973	74087274	7107936	245	25027										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2784472	2784472	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttaaaattacacactgtcctAcactgctgaccagagatgga	7	10	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr18:2784472A>T	ENST00000320876.6	+	45	5910	c.5572A>T	c.(5572-5574)Aca>Tca	p.T1858S	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.T1858S	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1858					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						ACACTGTCCTACACTGCTGAC	0.368																																					p.T1858S		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A5572T						.						38	37	38					18																	2784472		1826	4082	5908	SO:0001583	missense	23347	exon45			TGTCCTACACTGC	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.5572A>T	chr18.hg19:g.2784472A>T	ENSP00000326603:p.Thr1858Ser	144.0	0.0		170.0	36.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.843766	0.91197	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	D;D	0.85702	-2.02;-2.02	5.29	5.29	0.74685	SMCs flexible hinge (1);	0.000000	0.85682	D	0.000000	D	0.91092	0.7196	M	0.65498	2.005	0.41310	D	0.9871	D	0.69078	0.997	D	0.75020	0.985	D	0.92240	0.5800	10	0.72032	D	0.01	-19.449	15.2314	0.73390	1.0:0.0:0.0:0.0	.	1858	A6NHR9	SMHD1_HUMAN	S	1858	ENSP00000326603:T1858S;ENSP00000261598:T1858S	ENSP00000261598:T1858S	T	+	1	0	SMCHD1	2774472	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.213000	0.89758	1.985000	0.57927	0.482000	0.46254	ACA	.	.		0.368	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2784472	A	T	2784472	3	4	163	1	0	0	0	0	1	0	0	0	14803	391	14	4	5750	4	SMCHD1	18	2784472	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		2784472	75292776	246	25028										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21422660	21422660	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cagattgagtttgacatctcAgagcctgaagtggccgcaac	11	10	1	5			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr18:21422660A>T	ENST00000313654.9	+	29	3790	c.3549A>T	c.(3547-3549)tcA>tcT	p.S1183S	LAMA3_ENST00000399516.3_Silent_p.S1183S	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1183	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TTGACATCTCAGAGCCTGAAG	0.547																																					p.S1183S		Atlas-SNP	.											.	LAMA3	397	.	0			c.A3549T						.						127	139	135					18																	21422660		2015	4186	6201	SO:0001819	synonymous_variant	3909	exon29			CATCTCAGAGCCT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3549A>T	chr18.hg19:g.21422660A>T		142.0	0.0		129.0	33.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.		0.547	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21422660	A	T	21422660	2	4	163	1	0	0	0	0	0	0	0	1	8616	175	7	4		4	LAMA3	18	21422660	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	18638188	21422660	56654588	247	25029										
KLHL14	57565	hgsc.bcm.edu	37	chr18	30350114	30350114	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	accgtgtccagggacagggtCacgttggccgtgtagaggta	16	9	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr18:30350114C>T	ENST00000359358.4	-	2	879	c.441G>A	c.(439-441)gtG>gtA	p.V147V	AC012123.1_ENST00000426194.1_Intron|KLHL14_ENST00000358095.4_Silent_p.V147V	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	147	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						GGGACAGGGTCACGTTGGCCG	0.637																																					p.V147V		Atlas-SNP	.											.	KLHL14	92	.	0			c.G441A						.						99	95	96					18																	30350114		2203	4300	6503	SO:0001819	synonymous_variant	57565	exon2			CAGGGTCACGTTG	AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"Kelch-like", "BTB/POZ domain containing"	29266	protein-coding gene	gene with protein product	"printor"	613772	"kelch-like 14 (Drosophila)"			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.441G>A	chr18.hg19:g.30350114C>T		157.0	0.0		217.0	45.0	NM_020805	A6NNW1|B4DHA0|Q8WU41	Silent	SNP	ENST00000359358.4	hg19	CCDS32813.1																																																																																			.	.		0.637	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1			T	30350114	C	T	30350114	2	4	163	1	0	0	0	0	0	0	0	1	8379	813	29	3		3	KLHL14	18	30350114	Silent	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	8927454	30350114	47727134	248	25030										
ZBTB7C	201501	hgsc.bcm.edu	37	chr18	45566767	45566767	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cctgtcggggatgttggcctTggggtacaggttctccctta	14	10	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr18:45566767T>A	ENST00000588982.1	-	3	1213	c.712A>T	c.(712-714)Aag>Tag	p.K238*	ZBTB7C_ENST00000586438.1_Nonsense_Mutation_p.K238*|ZBTB7C_ENST00000590800.1_Nonsense_Mutation_p.K238*|ZBTB7C_ENST00000535628.2_Nonsense_Mutation_p.K238*|ZBTB7C_ENST00000332053.2_Nonsense_Mutation_p.K238*			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	238							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						ATGTTGGCCTTGGGGTACAGG	0.612																																					p.K238X		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.A712T						.						43	46	45					18																	45566767		2203	4300	6503	SO:0001587	stop_gained	201501	exon2			TGGCCTTGGGGTA	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	31700	protein-coding gene	gene with protein product			"zinc finger and BTB domain containing 36"	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.712A>T	chr18.hg19:g.45566767T>A	ENSP00000468782:p.Lys238*	70.0	0.0		87.0	17.0	NM_001039360	O73453	Nonsense_Mutation	SNP	ENST00000588982.1	hg19	CCDS32830.1	.	.	.	.	.	.	.	.	.	.	T	37	6.206122	0.97376	.	.	ENSG00000184828	ENST00000535628;ENST00000332053	.	.	.	5.25	5.25	0.73442	.	0.114755	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.1156	0.72397	0.0:0.0:0.0:1.0	.	.	.	.	X	238	.	ENSP00000328732:K238X	K	-	1	0	ZBTB7C	43820765	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.099000	0.64554	1.975000	0.57531	0.402000	0.26972	AAG	.	.		0.612	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360		A	45566767	T	A	45566767	4	1	163	1	0	0	0	0	0	1	0	0	17570	1821	63	4	1155	4	ZBTB7C	18	45566767	Nonsense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	15216653	45566767	32510481	249	25031										
ZNF532	55205	hgsc.bcm.edu	37	chr18	56651265	56651265	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gttcaggcctccccgaggagCaatcactcaaccactgaaaa	8	14	3	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr18:56651265C>T	ENST00000336078.4	+	11	4249	c.3473C>T	c.(3472-3474)gCa>gTa	p.A1158V	ZNF532_ENST00000589288.1_Missense_Mutation_p.A1158V|ZNF532_ENST00000591083.1_Missense_Mutation_p.A1158V|ZNF532_ENST00000591230.1_Missense_Mutation_p.A1158V|ZNF532_ENST00000591808.1_Missense_Mutation_p.A1158V|ZNF532_ENST00000588956.1_3'UTR	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	1158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						CCCCGAGGAGCAATCACTCAA	0.483																																					p.A1158V		Atlas-SNP	.											.	ZNF532	108	.	0			c.C3473T						.						73	74	74					18																	56651265		2203	4300	6503	SO:0001583	missense	55205	exon11			GAGGAGCAATCAC	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.3473C>T	chr18.hg19:g.56651265C>T	ENSP00000338217:p.Ala1158Val	269.0	0.0		285.0	50.0	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	hg19	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.624289	0.66901	.	.	ENSG00000074657	ENST00000336078	T	0.01665	4.7	5.84	5.84	0.93424	.	0.185708	0.46758	D	0.000267	T	0.08088	0.0202	L	0.49778	1.585	0.44834	D	0.997845	D;P	0.63880	0.993;0.736	D;B	0.68192	0.956;0.118	T	0.32640	-0.9899	10	0.34782	T	0.22	-0.1438	19.7382	0.96215	0.0:1.0:0.0:0.0	.	1158;1158	B3KXW2;Q9HCE3	.;ZN532_HUMAN	V	1158	ENSP00000338217:A1158V	ENSP00000338217:A1158V	A	+	2	0	ZNF532	54802245	1.000000	0.71417	0.517000	0.27799	0.667000	0.39255	7.347000	0.79356	2.769000	0.95229	0.561000	0.74099	GCA	.	.		0.483	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		T	56651265	C	T	56651265	3	4	163	1	0	0	0	0	1	0	0	0	17987	710	25	3	3503	3	ZNF532	18	56651265	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	11084498	56651265	21425983	250	25032										
CDH20	28316	hgsc.bcm.edu	37	chr18	59217403	59217403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cccagaggcctacatgctccCagtcagtttgagccggggcg	13	14	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr18:59217403C>T	ENST00000262717.4	+	11	2239	c.1841C>T	c.(1840-1842)cCa>cTa	p.P614L	CDH20_ENST00000538374.1_Missense_Mutation_p.P614L|CDH20_ENST00000536675.2_Missense_Mutation_p.P614L			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	614					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				TACATGCTCCCAGTCAGTTTG	0.602																																					p.P614L		Atlas-SNP	.											.	CDH20	117	.	0			c.C1841T						.						77	59	65					18																	59217403		2203	4300	6503	SO:0001583	missense	28316	exon10			TGCTCCCAGTCAG	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1841C>T	chr18.hg19:g.59217403C>T	ENSP00000262717:p.Pro614Leu	73.0	0.0		67.0	9.0	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	hg19	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.449307	0.84101	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.57595	0.39;0.39;0.39	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.65428	0.2690	M	0.79123	2.44	0.80722	D	1	B	0.28820	0.224	B	0.38500	0.275	T	0.65199	-0.6226	10	0.72032	D	0.01	.	20.3539	0.98825	0.0:1.0:0.0:0.0	.	614	Q9HBT6	CAD20_HUMAN	L	614	ENSP00000444767:P614L;ENSP00000442226:P614L;ENSP00000262717:P614L	ENSP00000262717:P614L	P	+	2	0	CDH20	57368383	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.087000	0.71362	2.826000	0.97356	0.655000	0.94253	CCA	.	.		0.602	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		T	59217403	C	T	59217403	3	4	163	1	0	0	0	0	1	0	0	0	3108	594	21	3	1879	3	CDH20	18	59217403	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	2566138	59217403	18859845	251	25033										
CDH19	28513	hgsc.bcm.edu	37	chr18	64172081	64172081	+	Missense_Mutation	SNP	T	T	A													0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctgcactgcagaaccaaacaTgcatgctaatcttttaaagc							TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr18:64172081T>A	ENST00000262150.2	-	12	2579	c.2287A>T	c.(2287-2289)Atg>Ttg	p.M763L		NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	3179	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				GAACCAAACATGCATGCTAAT	0.388																																					p.M763L		Atlas-SNP	.											.	CDH19	141	.	0			c.A2287T						.						79	71	74					18																	64172081		2203	4300	6503	SO:0001583	missense	28513	exon12			CAAACATGCATGC	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"Cadherins / Major cadherins"	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000262150.2:c.2287A>T	chr18.hg19:g.64172081T>A	ENSP00000262150:p.Met763Leu	94.0	0.0		96.0	16.0	NM_021153	O15098	Missense_Mutation	SNP	ENST00000262150.2	hg19	CCDS11994.1	.	.	.	.	.	.	.	.	.	.	T	1.362	-0.588385	0.03799	.	.	ENSG00000071991	ENST00000262150	T	0.74315	-0.83	4.99	3.73	0.42828	Cadherin, cytoplasmic domain (1);	0.170310	0.52532	D	0.000061	T	0.51534	0.1680	N	0.16708	0.43	0.80722	D	1	B	0.15141	0.012	B	0.18263	0.021	T	0.45716	-0.9242	10	0.05436	T	0.98	.	9.2923	0.37793	0.3398:0.0:0.0:0.6602	.	763	Q9H159	CAD19_HUMAN	L	763	ENSP00000262150:M763L	ENSP00000262150:M763L	M	-	1	0	CDH19	62323061	0.992000	0.36948	0.967000	0.41034	0.643000	0.38383	1.197000	0.32211	1.992000	0.58205	0.482000	0.46254	ATG	.	.		0.388	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153		A	64172081	T	A	64172081	3	1	163	1	0	0	0	0	1	0	0	0	3106	1464	51	4	35	4	CDH19	18	64172081	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	4954678	64172081	13905167	252	25034	115	2								
CDH19	28513	hgsc.bcm.edu	37	chr18	64172083	64172083	+	Missense_Mutation	SNP	C	C	A													0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcactgcagaaccaaacatgCatgctaatcttttaaagcga							TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr18:64172083C>A	ENST00000262150.2	-	12	2577	c.2285G>T	c.(2284-2286)tGc>tTc	p.C762F		NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	3178	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				ACCAAACATGCATGCTAATCT	0.383																																					p.C762F		Atlas-SNP	.											.	CDH19	141	.	0			c.G2285T						.						80	72	75					18																	64172083		2203	4300	6503	SO:0001583	missense	28513	exon12			AACATGCATGCTA	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"Cadherins / Major cadherins"	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000262150.2:c.2285G>T	chr18.hg19:g.64172083C>A	ENSP00000262150:p.Cys762Phe	94.0	0.0		96.0	16.0	NM_021153	O15098	Missense_Mutation	SNP	ENST00000262150.2	hg19	CCDS11994.1	.	.	.	.	.	.	.	.	.	.	C	9.704	1.155376	0.21454	.	.	ENSG00000071991	ENST00000262150	T	0.76060	-0.99	4.99	2.18	0.27775	Cadherin, cytoplasmic domain (1);	0.718048	0.14317	N	0.327316	T	0.53786	0.1818	N	0.08118	0	0.09310	N	1	B	0.21821	0.061	B	0.21917	0.037	T	0.49283	-0.8956	10	0.87932	D	0	.	8.8185	0.35011	0.0:0.7053:0.0:0.2947	.	762	Q9H159	CAD19_HUMAN	F	762	ENSP00000262150:C762F	ENSP00000262150:C762F	C	-	2	0	CDH19	62323063	0.258000	0.24033	0.541000	0.28102	0.714000	0.41099	0.346000	0.19997	0.214000	0.20742	0.591000	0.81541	TGC	.	.		0.383	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153		A	64172083	C	A	64172083	3	1	163	1	0	0	0	0	1	0	0	0	3106	710	25	3	37	3	CDH19	18	64172083	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	2	64172083	13905165	253	25035	115	2								
ZNF407	55628	hgsc.bcm.edu	37	chr18	72345386	72345386	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgaaggccatataggtgtgcAattacaagagcattcctatc	9	8	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr18:72345386A>T	ENST00000299687.5	+	1	2411	c.2411A>T	c.(2410-2412)cAa>cTa	p.Q804L	ZNF407_ENST00000577538.1_Missense_Mutation_p.Q804L|ZNF407_ENST00000582337.1_Missense_Mutation_p.Q804L|ZNF407_ENST00000309902.6_Missense_Mutation_p.Q804L	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	804					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		ATAGGTGTGCAATTACAAGAG	0.408																																					p.Q804L		Atlas-SNP	.											.	ZNF407	231	.	0			c.A2411T						.						174	172	173					18																	72345386		1974	4161	6135	SO:0001583	missense	55628	exon1			GTGTGCAATTACA	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.2411A>T	chr18.hg19:g.72345386A>T	ENSP00000299687:p.Gln804Leu	73.0	0.0		83.0	16.0	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.601339	0.28534	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.10288	2.89;3.32	5.65	1.65	0.23941	.	.	.	.	.	T	0.07908	0.0198	L	0.34521	1.04	0.09310	N	1	P;P;P	0.37276	0.589;0.589;0.454	B;B;B	0.33454	0.164;0.164;0.053	T	0.27673	-1.0067	9	0.72032	D	0.01	.	6.4437	0.21865	0.5695:0.2947:0.1358:0.0	.	804;804;804	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	L	804	ENSP00000299687:Q804L;ENSP00000310359:Q804L	ENSP00000299687:Q804L	Q	+	2	0	ZNF407	70474374	0.000000	0.05858	0.000000	0.03702	0.857000	0.48899	0.171000	0.16685	-2.091000	0.00858	-0.379000	0.06801	CAA	.	.		0.408	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72345386	A	T	72345386	3	4	163	1	0	0	0	0	1	0	0	0	17902	130	5	4	2413	4	ZNF407	18	72345386	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	8173303	72345386	5731862	254	25036										
NFIC	4782	hgsc.bcm.edu	37	chr19	3382056	3382056	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctgtctccggcaggcggacaAggtgtggcggctggacctgg	18	11	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:3382056A>T	ENST00000443272.2	+	2	428	c.377A>T	c.(376-378)aAg>aTg	p.K126M	NFIC_ENST00000586919.1_Missense_Mutation_p.K117M|NFIC_ENST00000590282.1_Missense_Mutation_p.K126M|NFIC_ENST00000395111.3_Missense_Mutation_p.K117M|NFIC_ENST00000346156.5_Missense_Mutation_p.K117M|NFIC_ENST00000341919.3_Missense_Mutation_p.K126M|NFIC_ENST00000589123.1_Missense_Mutation_p.K117M	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	126					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		CAGGCGGACAAGGTGTGGCGG	0.667																																					p.K126M		Atlas-SNP	.											.	NFIC	36	.	0			c.A377T						.						75	80	78					19																	3382056		2203	4298	6501	SO:0001583	missense	4782	exon2			CGGACAAGGTGTG	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.377A>T	chr19.hg19:g.3382056A>T	ENSP00000396843:p.Lys126Met	93.0	0.0		88.0	35.0	NM_001245004	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	hg19	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.060452	0.76074	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T	0.80738	-1.41;-1.41;-1.41	3.88	3.88	0.44766	MAD homology 1, Dwarfin-type (2);CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.88097	0.6345	M	0.75777	2.31	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.998;0.998	D	0.89139	0.3515	10	0.87932	D	0	.	11.8626	0.52476	1.0:0.0:0.0:0.0	.	126;126;117;126;117	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	M	117;117;117;126;126;126	ENSP00000378543:K117M;ENSP00000301935:K117M;ENSP00000342194:K126M	ENSP00000269778:K126M	K	+	2	0	NFIC	3333056	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.967000	0.93402	1.533000	0.49186	0.383000	0.25322	AAG	.	.		0.667	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597		T	3382056	A	T	3382056	3	4	163	1	0	0	0	0	1	0	0	0	10381	72	3	4	390	4	NFIC	19	3382056	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		3382056	55746927	255	25037										
C19orf59	199675	hgsc.bcm.edu	37	chr19	7743420	7743420	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaagagagacagaagagaggCtgggattccgttcagcagag	16	6	1	5			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:7743420C>A	ENST00000333598.3	+	5	871	c.417C>A	c.(415-417)ggC>ggA	p.G139G	C19orf59_ENST00000597445.1_Silent_p.G96G|TRAPPC5_ENST00000317378.5_5'Flank|CTD-3214H19.16_ENST00000597959.1_Missense_Mutation_p.L12M|TRAPPC5_ENST00000596148.1_5'Flank|TRAPPC5_ENST00000426877.2_5'Flank	NM_174918.2	NP_777578.2	Q8IX19	MCEM1_HUMAN		139						integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|skin(1)|stomach(1)	5						AGAAGAGAGGCTGGGATTCCG	0.532											OREG0025208	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G139G		Atlas-SNP	.											.	C19orf59	15	.	0			c.C417A						.						133	126	128					19																	7743420		2203	4300	6503	SO:0001819	synonymous_variant	199675	exon5			GAGAGGCTGGGAT																												ENST00000333598.3:c.417C>A	chr19.hg19:g.7743420C>A		94.0	0.0	644	104.0	31.0	NM_174918	Q8IX20	Silent	SNP	ENST00000333598.3	hg19	CCDS12183.1																																																																																			.	.		0.532	C19orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461248.1			A	7743420	C	A	7743420	2	1	163	1	0	0	0	0	0	0	0	1	1942	784	28	3		3	C19orf59	19	7743420	Silent	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	4361364	7743420	51385563	256	25038										
OR7E24	26648	hgsc.bcm.edu	37	chr19	9361792	9361792	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acacagagccacagaatctcAcaggtgtctcagaattcctc	7	13	2	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:9361792A>T	ENST00000456448.1	+	1	187	c.73A>T	c.(73-75)Aca>Tca	p.T25S		NM_001079935.1	NP_001073404.1	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E, member 24	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)	16						ACAGAATCTCACAGGTGTCTC	0.493																																					p.T25S		Atlas-SNP	.											.	OR7E24	48	.	0			c.A73T						.						36	38	37					19																	9361792		2114	4244	6358	SO:0001583	missense	26648	exon1			AATCTCACAGGTG	Y10529	CCDS45955.1	19p13.2	2012-08-09	2004-03-04	2004-03-05		ENSG00000237521		"GPCR / Class A : Olfactory receptors"	8396	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily E, member 24 pseudogene"	OR7E24P		9268701	Standard	NM_001079935		Approved	OR19-8, HSHT2, OR7E24Q	uc002mlb.1	Q6IFN5		ENST00000456448.1:c.73A>T	chr19.hg19:g.9361792A>T	ENSP00000387523:p.Thr25Ser	36.0	0.0		43.0	9.0	NM_001079935	B9EJD9|Q9UPJ1	Missense_Mutation	SNP	ENST00000456448.1	hg19	CCDS45955.1	.	.	.	.	.	.	.	.	.	.	a	11.71	1.719833	0.30503	.	.	ENSG00000237521	ENST00000456448	T	0.36878	1.23	2.39	2.39	0.29439	.	.	.	.	.	T	0.25232	0.0613	N	0.21448	0.665	0.09310	N	1	B	0.25563	0.129	B	0.27076	0.076	T	0.22243	-1.0222	9	0.51188	T	0.08	.	9.2996	0.37838	1.0:0.0:0.0:0.0	.	25	Q6IFN5	O7E24_HUMAN	S	25	ENSP00000387523:T25S	ENSP00000387523:T25S	T	+	1	0	OR7E24	9222792	.	.	0.004000	0.12327	0.030000	0.12068	.	.	1.112000	0.41740	0.358000	0.22013	ACA	.	.		0.493	OR7E24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449006.1			T	9361792	A	T	9361792	3	4	163	1	0	0	0	0	1	0	0	0	11230	159	6	4	75	4	OR7E24	19	9361792	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1618372	9361792	49767191	257	25039										
CD97	976	hgsc.bcm.edu	37	chr19	14507927	14507927	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccggacaaaacccgtgccacAgctccacccactgcctcaac	6	20	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:14507927A>T	ENST00000242786.5	+	6	597	c.517A>T	c.(517-519)Agc>Tgc	p.S173C	CD97_ENST00000587728.1_Intron|CD97_ENST00000358600.3_Intron|CD97_ENST00000357355.3_Intron	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	173	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CCCGTGCCACAGCTCCACCCA	0.617																																					p.S173C		Atlas-SNP	.											.	CD97	86	.	0			c.A517T						.						106	96	99					19																	14507927		2203	4300	6503	SO:0001583	missense	976	exon6			TGCCACAGCTCCA		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.517A>T	chr19.hg19:g.14507927A>T	ENSP00000242786:p.Ser173Cys	97.0	0.0		72.0	21.0	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Missense_Mutation	SNP	ENST00000242786.5	hg19	CCDS32929.1	.	.	.	.	.	.	.	.	.	.	a	16.82	3.228517	0.58777	.	.	ENSG00000123146	ENST00000242786	D	0.88741	-2.42	3.53	0.187	0.15109	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.85906	0.5806	L	0.27053	0.805	0.09310	N	1	P	0.52316	0.952	P	0.58520	0.84	T	0.74677	-0.3585	9	0.56958	D	0.05	.	3.2061	0.06666	0.5129:0.2351:0.2521:0.0	.	173	P48960	CD97_HUMAN	C	173	ENSP00000242786:S173C	ENSP00000242786:S173C	S	+	1	0	CD97	14368927	0.252000	0.23972	0.083000	0.20561	0.415000	0.31203	0.607000	0.24209	-0.032000	0.13758	0.454000	0.30748	AGC	.	.		0.617	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		T	14507927	A	T	14507927	3	4	163	1	0	0	0	0	1	0	0	0	3051	188	7	4	539	4	CD97	19	14507927	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	5146135	14507927	44621056	258	25040										
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15794357	15794357	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctcagtgcccttgtagagaaAagaagccagcatatcctcca	8	12	1	2	rs376069087		TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:15794357A>G	ENST00000550308.1	+	7	1082	c.702A>G	c.(700-702)aaA>aaG	p.K234K	CYP4F12_ENST00000324632.10_Silent_p.K234K	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	234					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	TTGTAGAGAAAAGAAGCCAGC	0.537																																					p.K234K		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A702G						.						73	74	74					19																	15794357		2202	4300	6502	SO:0001819	synonymous_variant	66002	exon7			AGAGAAAAGAAGC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"Cytochrome P450s"	18857	protein-coding gene	gene with protein product		611485	"cytochrome P450, subfamily IVF, polypeptide 12"			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.702A>G	chr19.hg19:g.15794357A>G		53.0	0.0		107.0	23.0	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	hg19	CCDS42517.1																																																																																			.	.		0.537	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			G	15794357	A	G	15794357	2	3	163	1	0	0	0	0	0	0	0	1	4189	11	1	2		2	CYP4F12	19	15794357	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1286430	15794357	43334626	259	25041										
GLT25D1	79709	hgsc.bcm.edu	37	chr19	17678227	17678227	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttctgcagtttgtagatgcgGacaacctgatcctcaaccct	8	12	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:17678227G>C	ENST00000252599.4	+	4	622	c.502G>C	c.(502-504)Gac>Cac	p.D168H	COLGALT1_ENST00000601354.1_3'UTR	NM_024656.2	NP_078932.2	Q8NBJ5	GT251_HUMAN	collagen beta(1-O)galactosyltransferase 1	168					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	procollagen galactosyltransferase activity (GO:0050211)										TGTAGATGCGGACAACCTGAT	0.587																																					p.D168H		Atlas-SNP	.											.	.	.	.	0			c.G502C						.						114	93	100					19																	17678227		2203	4300	6503	SO:0001583	missense	79709	exon4			GATGCGGACAACC	AK075541	CCDS12363.1	19p13.11	2013-02-27	2013-02-27	2013-02-27	ENSG00000130309	ENSG00000130309			26182	protein-coding gene	gene with protein product			"glycosyltransferase 25 domain containing 1"	GLT25D1		19075007	Standard	NM_024656		Approved	FLJ22329	uc002nhc.1	Q8NBJ5		ENST00000252599.4:c.502G>C	chr19.hg19:g.17678227G>C	ENSP00000252599:p.Asp168His	45.0	0.0		91.0	16.0	NM_024656	Q8NC64	Missense_Mutation	SNP	ENST00000252599.4	hg19	CCDS12363.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.717403	0.48622	.	.	ENSG00000130309	ENST00000252599	D	0.98090	-4.71	4.5	4.5	0.54988	.	0.000000	0.85682	D	0.000000	D	0.98927	0.9636	M	0.93062	3.375	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99589	1.0975	10	0.87932	D	0	-14.0629	14.6789	0.69001	0.0:0.0:1.0:0.0	.	168	Q8NBJ5	GT251_HUMAN	H	168	ENSP00000252599:D168H	ENSP00000252599:D168H	D	+	1	0	GLT25D1	17539227	1.000000	0.71417	0.831000	0.32960	0.023000	0.10783	9.428000	0.97476	2.070000	0.61991	0.491000	0.48974	GAC	.	.		0.587	COLGALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464216.1	NM_024656		C	17678227	G	C	17678227	3	2	163	1	0	0	0	0	1	0	0	0	6474	1174	41	4	516	4	GLT25D1	19	17678227	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	1883870	17678227	41450756	260	25042										
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19766889	19766889	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggcccgtggtggctttctgtGgggggatgtgctgcaccacc	17	11	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:19766889G>A	ENST00000357324.6	-	8	1213	c.1187C>T	c.(1186-1188)cCa>cTa	p.P396L	ATP13A1_ENST00000496082.1_5'Flank|ATP13A1_ENST00000291503.5_Missense_Mutation_p.P278L	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	396						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GGCTTTCTGTGGGGGGATGTG	0.637																																					p.P396L	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.C1187T						.						68	65	66					19																	19766889		2203	4300	6503	SO:0001583	missense	57130	exon8			TTCTGTGGGGGGA	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"ATPases / P-type"	24215	protein-coding gene	gene with protein product	"cation transporting ATPase"		"ATPase type 13A"	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.1187C>T	chr19.hg19:g.19766889G>A	ENSP00000349877:p.Pro396Leu	32.0	0.0		39.0	7.0	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Missense_Mutation	SNP	ENST00000357324.6	hg19	CCDS32970.2	.	.	.	.	.	.	.	.	.	.	G	17.61	3.431237	0.62844	.	.	ENSG00000105726	ENST00000291503;ENST00000357324	D;D	0.90504	-2.68;-2.68	4.47	4.47	0.54385	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.91164	0.7217	M	0.82056	2.57	0.80722	D	1	B;B	0.22080	0.064;0.044	B;B	0.29716	0.106;0.049	D	0.89697	0.3902	10	0.44086	T	0.13	-10.7803	14.9828	0.71324	0.0:0.0:1.0:0.0	.	396;278	Q9HD20;Q9HD20-2	AT131_HUMAN;.	L	278;396	ENSP00000291503:P278L;ENSP00000349877:P396L	ENSP00000291503:P278L	P	-	2	0	ATP13A1	19627889	1.000000	0.71417	0.558000	0.28319	0.278000	0.26855	9.209000	0.95087	2.193000	0.70182	0.491000	0.48974	CCA	.	.		0.637	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		A	19766889	G	A	19766889	3	1	163	1	0	0	0	0	1	0	0	0	1123	1348	47	3	2503	3	ATP13A1	19	19766889	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	2088662	19766889	39362094	261	25043										
ZFP14	57677	hgsc.bcm.edu	37	chr19	36832052	36832052	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctccttacattcatagggttTctcaccggtgtgaagtttgt	9	9	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:36832052T>A	ENST00000270001.7	-	5	791	c.676A>T	c.(676-678)Aaa>Taa	p.K226*		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	226					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					TCATAGGGTTTCTCACCGGTG	0.428																																					p.K226X		Atlas-SNP	.											.	ZFP14	68	.	0			c.A676T						.						104	96	99					19																	36832052		2203	4300	6503	SO:0001587	stop_gained	57677	exon5			AGGGTTTCTCACC	AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"Zinc fingers, C2H2-type", "-"	29312	protein-coding gene	gene with protein product			"zinc finger protein 14 homolog (mouse)"			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.676A>T	chr19.hg19:g.36832052T>A	ENSP00000270001:p.Lys226*	57.0	0.0		72.0	21.0	NM_020917	A7MD23	Nonsense_Mutation	SNP	ENST00000270001.7	hg19	CCDS33002.1	.	.	.	.	.	.	.	.	.	.	t	27.2	4.808752	0.90707	.	.	ENSG00000142065	ENST00000270001;ENST00000392172	.	.	.	4.07	4.07	0.47477	.	0.000000	0.48286	D	0.000192	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.4234	0.55532	0.0:0.0:0.0:1.0	.	.	.	.	X	226	.	ENSP00000270001:K226X	K	-	1	0	ZFP14	41523892	0.997000	0.39634	1.000000	0.80357	0.989000	0.77384	3.798000	0.55522	1.831000	0.53308	0.448000	0.29417	AAA	.	.		0.428	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		A	36832052	T	A	36832052	4	1	163	1	0	0	0	0	0	1	0	0	17654	1792	62	4	929	4	ZFP14	19	36832052	Nonsense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	17065163	36832052	22296931	262	25044										
GGN	199720	hgsc.bcm.edu	37	chr19	38877316	38877316	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gctttctgtcgggggtgaggCgggtgtggccagagcaggag	21	7	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:38877316C>T	ENST00000334928.6	-	3	718	c.586G>A	c.(586-588)Gcc>Acc	p.A196T	AC005789.9_ENST00000585411.1_RNA|SPRED3_ENST00000587013.1_5'Flank|SPRED3_ENST00000586301.1_5'Flank|GGN_ENST00000591809.1_Intron	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	196	Interaction with GGNBP1. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GGGGGTGAGGCGGGTGTGGCC	0.692																																					p.A196T		Atlas-SNP	.											.	GGN	50	.	0			c.G586A						.						10	13	12					19																	38877316		2149	4227	6376	SO:0001583	missense	199720	exon3			GTGAGGCGGGTGT	AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.586G>A	chr19.hg19:g.38877316C>T	ENSP00000334940:p.Ala196Thr	76.0	0.0		78.0	20.0	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Missense_Mutation	SNP	ENST00000334928.6	hg19	CCDS12516.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.459|8.459	0.854812|0.854812	0.17106|0.17106	.|.	.|.	ENSG00000179168|ENSG00000179168	ENST00000392116|ENST00000334928	.|.	.|.	.|.	3.58|3.58	-3.68|-3.68	0.04463|0.04463	.|.	.|0.355912	.|0.20324	.|N	.|0.094573	.|T	.|0.13200	.|0.0320	N|N	0.17082|0.17082	0.46|0.46	0.09310|0.09310	N|N	1|1	.|B;B	.|0.12630	.|0.006;0.006	.|B;B	.|0.09377	.|0.004;0.004	.|T	.|0.10451	.|-1.0629	.|9	.|0.22109	.|T	.|0.4	.|-5.3675	0.3497|0.3497	0.00347|0.00347	0.3358:0.2765:0.1654:0.2222|0.3358:0.2765:0.1654:0.2222	.|.	.|113;196	.|Q86UU5-2;Q86UU5	.|.;GGN_HUMAN	.|T	-1|196	.|.	.|ENSP00000334940:A196T	.|A	-|-	.|1	.|0	GGN|GGN	43569156|43569156	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.186000|0.186000	0.23388|0.23388	-0.932000|-0.932000	0.03963|0.03963	-0.303000|-0.303000	0.08856|0.08856	-0.448000|-0.448000	0.05591|0.05591	.|GCC	.	.		0.692	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		T	38877316	C	T	38877316	3	4	163	1	0	0	0	0	1	0	0	0	6366	768	27	1	1380	1	GGN	19	38877316	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	2045264	38877316	20251667	263	25045										
DLL3	10683	hgsc.bcm.edu	37	chr19	39998581	39998581	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acgccccttttccccccgctAcacactgggcgcgctgggca	10	19	0	0	rs199745659		TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:39998581A>T	ENST00000205143.4	+	8	1792	c.1785A>T	c.(1783-1785)ctA>ctT	p.L595L	DLL3_ENST00000356433.5_Intron	NM_016941.3	NP_058637.1	Q9NYJ7	DLL3_HUMAN	delta-like 3 (Drosophila)	595					compartment pattern specification (GO:0007386)|negative regulation of neurogenesis (GO:0050768)|Notch signaling pathway (GO:0007219)|paraxial mesoderm development (GO:0048339)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)	integral component of membrane (GO:0016021)	Notch binding (GO:0005112)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)	19	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TCCCCCCGCTACACACTGGGC	0.532																																					p.L595L		Atlas-SNP	.											.	DLL3	47	.	0			c.A1785T						.						60	51	54					19																	39998581		2203	4300	6503	SO:0001819	synonymous_variant	10683	exon8			CCCGCTACACACT	AF241373	CCDS12537.1, CCDS12538.1	19q13.2	2008-05-14	2001-12-03			ENSG00000090932			2909	protein-coding gene	gene with protein product		602768	"delta (Drosophila)-like 3"			10364530, 10742114	Standard	NM_203486		Approved	SCDO1	uc002olx.2	Q9NYJ7		ENST00000205143.4:c.1785A>T	chr19.hg19:g.39998581A>T		77.0	0.0		94.0	15.0	NM_016941	E9PFG2|Q8NBS4	Silent	SNP	ENST00000205143.4	hg19	CCDS12538.1																																																																																			.	A|0.999;G|0.001		0.532	DLL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464958.1			T	39998581	A	T	39998581	2	4	163	1	0	0	0	0	0	0	0	1	4569	378	14	4		4	DLL3	19	39998581	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1121265	39998581	19130402	264	25046										
CEACAM4	1089	hgsc.bcm.edu	37	chr19	42132079	42132079	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gggtgatgttttggaacagcAgggatccattggggtatact	15	5	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:42132079A>T	ENST00000221954.2	-	2	430	c.320T>A	c.(319-321)cTg>cAg	p.L107Q	CEACAM4_ENST00000600925.1_Missense_Mutation_p.L107Q	NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	107	Ig-like V-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						TTGGAACAGCAGGGATCCATT	0.512																																					p.L107Q		Atlas-SNP	.											.	CEACAM4	42	.	0			c.T320A						.						204	181	188					19																	42132079		2203	4300	6503	SO:0001583	missense	1089	exon2			AACAGCAGGGATC	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"Immunoglobulin superfamily / V-set domain containing"	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.320T>A	chr19.hg19:g.42132079A>T	ENSP00000221954:p.Leu107Gln	120.0	0.0		162.0	39.0	NM_001817	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	hg19	CCDS33033.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.046558	0.36085	.	.	ENSG00000105352	ENST00000221954	T	0.09630	2.96	1.76	1.76	0.24704	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.39358	0.1075	H	0.95645	3.7	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.12682	-1.0538	9	0.87932	D	0	.	5.5316	0.16987	1.0:0.0:0.0:0.0	.	107;107	E7EMX3;O75871	.;CEAM4_HUMAN	Q	107	ENSP00000221954:L107Q	ENSP00000221954:L107Q	L	-	2	0	CEACAM4	46823919	0.289000	0.24334	0.031000	0.17742	0.038000	0.13279	0.282000	0.18829	1.053000	0.40415	0.172000	0.16884	CTG	.	.		0.512	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817		T	42132079	A	T	42132079	3	4	163	1	0	0	0	0	1	0	0	0	3196	188	7	4	438	4	CEACAM4	19	42132079	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	2133498	42132079	16996904	265	25047										
ZNF226	7769	hgsc.bcm.edu	37	chr19	44676286	44676286	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctgtggccttcacggaggagGaattggggctgctgggccct	17	10	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:44676286G>T	ENST00000590089.1	+	5	428	c.61G>T	c.(61-63)Gaa>Taa	p.E21*	ZNF226_ENST00000589160.1_Nonsense_Mutation_p.E21*|ZNF226_ENST00000413984.2_Nonsense_Mutation_p.E21*|ZNF226_ENST00000588742.1_Nonsense_Mutation_p.E21*|ZNF226_ENST00000588795.1_Nonsense_Mutation_p.E21*|ZNF226_ENST00000300823.6_Nonsense_Mutation_p.E21*|ZNF226_ENST00000337433.5_Nonsense_Mutation_p.E21*|ZNF226_ENST00000588883.1_Nonsense_Mutation_p.E21*|ZNF226_ENST00000454662.2_Nonsense_Mutation_p.E21*			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	21	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)						Prostate(69;0.0352)|all_neural(266;0.202)				CACGGAGGAGGAATTGGGGCT	0.537																																					p.E21X	Pancreas(115;581 1665 13228 19278 50070)	Atlas-SNP	.											.	.	.	.	0			c.G61T						.						155	155	155					19																	44676286		2203	4300	6503	SO:0001587	stop_gained	7769	exon4			GAGGAGGAATTGG	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"Zinc fingers, C2H2-type", "-"	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.61G>T	chr19.hg19:g.44676286G>T	ENSP00000465121:p.Glu21*	74.0	0.0		74.0	12.0	NM_015919	Q8WWE6|Q96TE6|Q9NS44	Nonsense_Mutation	SNP	ENST00000590089.1	hg19	CCDS46102.1	.	.	.	.	.	.	.	.	.	.	G	35	5.483631	0.96307	.	.	ENSG00000167380	ENST00000300823;ENST00000337433;ENST00000413984;ENST00000454662	.	.	.	4.32	4.32	0.51571	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.7373	0.69424	0.0:0.0:1.0:0.0	.	.	.	.	X	21	.	ENSP00000300823:E21X	E	+	1	0	ZNF226	49368126	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	3.457000	0.53007	2.417000	0.82017	0.650000	0.86243	GAA	.	.		0.537	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1			T	44676286	G	T	44676286	4	4	163	1	0	0	0	0	0	1	0	0	17795	1175	41	3	67	3	ZNF226	19	44676286	Nonsense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	2544207	44676286	14452697	266	25048										
CBLC	23624	hgsc.bcm.edu	37	chr19	45303670	45303670	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gggaactcccctccagctgcGctgggaccccaggaccctgc	12	18	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:45303670G>T	ENST00000270279.3	+	10	1458	c.1395G>T	c.(1393-1395)gcG>gcT	p.A465A	CBLC_ENST00000341505.4_Silent_p.A419A	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	465	Interaction with RET.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				CTCCAGCTGCGCTGGGACCCC	0.622			M		AML						OREG0025543	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A465A		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.G1395T						.						50	52	51					19																	45303670		2203	4300	6503	SO:0001819	synonymous_variant	23624	exon10			AGCTGCGCTGGGA	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"RING-type (C3HC4) zinc fingers"	15961	protein-coding gene	gene with protein product		608453	"Cas-Br-M (murine) ectropic retroviral transforming sequence c", "Cas-Br-M (murine) ecotropic retroviral transforming sequence c"			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.1395G>T	chr19.hg19:g.45303670G>T		161.0	0.0	930	165.0	30.0	NM_012116	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Silent	SNP	ENST00000270279.3	hg19	CCDS12643.1																																																																																			.	.		0.622	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116		T	45303670	G	T	45303670	2	4	163	1	0	0	0	0	0	0	0	1	2704	1074	38	1		1	CBLC	19	45303670	Silent	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	627384	45303670	13825313	267	25049										
MYBPC2	4606	hgsc.bcm.edu	37	chr19	50962198	50962198	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cacccaagatccggcttcccCgccatctccgccagacctac	6	21	1	2	rs202035202		TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:50962198C>A	ENST00000357701.5	+	22	2581	c.2530C>A	c.(2530-2532)Cgc>Agc	p.R844S		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	844	Ig-like C2-type 6.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		CCGGCTTCCCCGCCATCTCCG	0.682																																					p.R844S		Atlas-SNP	.											.	MYBPC2	103	.	0			c.C2530A						.						21	27	25					19																	50962198		2013	4220	6233	SO:0001583	missense	4606	exon22			CTTCCCCGCCATC		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7550	protein-coding gene	gene with protein product	"fast-type muscle myosin-binding-protein C"	160793	"myosin-binding protein C, fast-type"			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.2530C>A	chr19.hg19:g.50962198C>A	ENSP00000350332:p.Arg844Ser	104.0	0.0		106.0	31.0	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	hg19	CCDS46152.1	.	.	.	.	.	.	.	.	.	.	c	23.3	4.398585	0.83120	.	.	ENSG00000086967	ENST00000357701	T	0.56444	0.46	4.01	2.88	0.33553	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.36167	U	0.002743	T	0.74876	0.3774	M	0.93939	3.475	0.45914	D	0.998752	P	0.41008	0.735	D	0.63793	0.918	T	0.75578	-0.3269	10	0.12103	T	0.63	.	12.4097	0.55459	0.1677:0.8323:0.0:0.0	.	844	Q14324	MYPC2_HUMAN	S	844	ENSP00000350332:R844S	ENSP00000350332:R844S	R	+	1	0	MYBPC2	55654010	1.000000	0.71417	0.996000	0.52242	0.967000	0.64934	5.209000	0.65208	1.967000	0.57214	0.457000	0.33378	CGC	.	.		0.682	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533		A	50962198	C	A	50962198	3	1	163	1	0	0	0	0	1	0	0	0	10021	652	23	1	2616	1	MYBPC2	19	50962198	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	5658528	50962198	8166785	268	25050										
SYT3	84258	hgsc.bcm.edu	37	chr19	51129240	51129240	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cggccgtggggaggtagcagAgtgagaagttgagctcccca	17	9	0	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:51129240A>T	ENST00000338916.4	-	5	1949	c.1316T>A	c.(1315-1317)cTc>cAc	p.L439H	SYT3_ENST00000544769.1_Missense_Mutation_p.L439H|SYT3_ENST00000600079.1_Missense_Mutation_p.L439H|SYT3_ENST00000593901.1_Missense_Mutation_p.L439H	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	439	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		GAGGTAGCAGAGTGAGAAGTT	0.557																																					p.L439H		Atlas-SNP	.											.	SYT3	85	.	0			c.T1316A						.						106	92	97					19																	51129240		2203	4300	6503	SO:0001583	missense	84258	exon5			TAGCAGAGTGAGA	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.1316T>A	chr19.hg19:g.51129240A>T	ENSP00000340914:p.Leu439His	102.0	0.0		121.0	23.0	NM_032298	Q8N5Z1|Q8N640	Missense_Mutation	SNP	ENST00000338916.4	hg19	CCDS12798.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.331634	0.81690	.	.	ENSG00000213023	ENST00000338916;ENST00000544769	T;T	0.75704	-0.96;-0.96	4.13	4.13	0.48395	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.47852	U	0.000217	D	0.89976	0.6871	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.92600	0.6090	10	0.87932	D	0	.	12.4368	0.55604	1.0:0.0:0.0:0.0	.	439	Q9BQG1	SYT3_HUMAN	H	439	ENSP00000340914:L439H;ENSP00000438883:L439H	ENSP00000340914:L439H	L	-	2	0	SYT3	55821052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.980000	0.93460	1.662000	0.50781	0.454000	0.30748	CTC	.	.		0.557	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		T	51129240	A	T	51129240	3	4	163	1	0	0	0	0	1	0	0	0	15490	304	11	4	472	4	SYT3	19	51129240	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	167042	51129240	7999743	269	25051										
KLK6	5653	hgsc.bcm.edu	37	chr19	51470458	51470458	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gggcagctgtgaggacccacAgtggatggataaggacccca	15	10	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:51470458A>T	ENST00000376851.3	-	3	603	c.164T>A	c.(163-165)cTg>cAg	p.L55Q	CTB-147C22.9_ENST00000594512.1_RNA|KLK6_ENST00000310157.2_Missense_Mutation_p.L55Q|KLK6_ENST00000424910.2_Intron|KLK6_ENST00000594641.1_Missense_Mutation_p.L55Q|KLK6_ENST00000376853.4_Missense_Mutation_p.L55Q|KLK6_ENST00000391808.1_5'UTR	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	55	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		GAGGACCCACAGTGGATGGAT	0.552																																					p.L55Q		Atlas-SNP	.											.	KLK6	35	.	0			c.T164A						.						110	99	103					19																	51470458		2203	4300	6503	SO:0001583	missense	5653	exon3			ACCCACAGTGGAT	U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"Kallikreins", "Serine peptidases / Serine peptidases"	6367	protein-coding gene	gene with protein product		602652	"protease, serine, 18", "kallikrein 6 (neurosin, zyme)"	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.164T>A	chr19.hg19:g.51470458A>T	ENSP00000366047:p.Leu55Gln	92.0	0.0		135.0	27.0	NM_001012964	A6NJA1|A8MW09|Q6H301	Missense_Mutation	SNP	ENST00000376851.3	hg19	CCDS12811.1	.	.	.	.	.	.	.	.	.	.	A	0.759	-0.769808	0.02974	.	.	ENSG00000167755	ENST00000310157;ENST00000376851;ENST00000376853	D;D;D	0.87571	-2.27;-2.27;-2.27	4.31	1.91	0.25777	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.643386	0.11908	N	0.517954	T	0.59252	0.2180	N	0.00389	-1.56	0.51767	D	0.999936	B;B	0.21905	0.062;0.003	B;B	0.27262	0.078;0.001	T	0.56092	-0.8036	10	0.02654	T	1	.	9.1095	0.36718	0.2317:0.0:0.0:0.7683	.	55;55	E7ETY0;Q92876	.;KLK6_HUMAN	Q	55	ENSP00000309148:L55Q;ENSP00000366047:L55Q;ENSP00000366049:L55Q	ENSP00000309148:L55Q	L	-	2	0	KLK6	56162270	0.001000	0.12720	0.450000	0.26969	0.918000	0.54935	0.787000	0.26858	0.128000	0.18479	0.454000	0.30748	CTG	.	.		0.552	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774		T	51470458	A	T	51470458	3	4	163	1	0	0	0	0	1	0	0	0	8417	188	7	4	586	4	KLK6	19	51470458	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	341218	51470458	7658525	270	25052										
HAS1	3036	hgsc.bcm.edu	37	chr19	52222631	52222631	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gataggctccggcgcccaccGcgcccgccgccgcgggttcc	14	20	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:52222631G>A	ENST00000222115.1	-	2	564	c.530C>T	c.(529-531)gCg>gTg	p.A177V	HAS1_ENST00000594621.1_Missense_Mutation_p.A31V|HAS1_ENST00000540069.2_Missense_Mutation_p.A176V|HAS1_ENST00000601714.1_Missense_Mutation_p.A184V	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	177					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		ggcgcccaccgcgcccgccgc	0.711																																					p.A177V	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.C530T						.						7	8	8					19																	52222631		2116	4090	6206	SO:0001583	missense	3036	exon2			CCCACCGCGCCCG	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.530C>T	chr19.hg19:g.52222631G>A	ENSP00000222115:p.Ala177Val	106.0	0.0		107.0	25.0	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	hg19	CCDS12838.1	.	.	.	.	.	.	.	.	.	.	.	11.16	1.557107	0.27827	.	.	ENSG00000105509	ENST00000540069;ENST00000222115;ENST00000376737;ENST00000376738	T;T	0.31769	1.48;1.48	3.83	-0.101	0.13618	.	1.113020	0.07042	N	0.830345	T	0.11580	0.0282	N	0.08118	0	0.20926	N	0.999825	P;B;P	0.42692	0.564;0.429;0.787	B;B;B	0.32677	0.061;0.028;0.15	T	0.14337	-1.0476	10	0.30854	T	0.27	-9.6168	4.1606	0.10282	0.1009:0.1538:0.5885:0.1569	.	176;177;176	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	V	176;177;31;31	ENSP00000445021:A176V;ENSP00000222115:A177V	ENSP00000222115:A177V	A	-	2	0	HAS1	56914443	0.000000	0.05858	0.053000	0.19242	0.756000	0.42949	-0.079000	0.11357	0.202000	0.20498	0.423000	0.28283	GCG	.	.		0.711	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		A	52222631	G	A	52222631	3	1	163	1	0	0	0	0	1	0	0	0	6970	1087	38	1	1222	1	HAS1	19	52222631	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	752173	52222631	6906352	271	25053										
ZNF880	400713	hgsc.bcm.edu	37	chr19	52888535	52888535	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	caaacctggcaaatcatcacAgaatccatactggagagaaa	7	10	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:52888535A>T	ENST00000422689.2	+	4	1717	c.1702A>T	c.(1702-1704)Aga>Tga	p.R568*		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	568					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						AAATCATCACAGAATCCATAC	0.383																																					p.R568X		Atlas-SNP	.											.	ZNF880	45	.	0			c.A1702T						.						73	66	68					19																	52888535		692	1591	2283	SO:0001587	stop_gained	400713	exon4			CATCACAGAATCC	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"Zinc fingers, C2H2-type", "-"	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1702A>T	chr19.hg19:g.52888535A>T	ENSP00000406318:p.Arg568*	163.0	0.0		177.0	39.0	NM_001145434	B4DNA6	Nonsense_Mutation	SNP	ENST00000422689.2	hg19	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	C	11.29	1.596041	0.28445	.	.	ENSG00000221923	ENST00000422689	.	.	.	1.79	1.79	0.24919	.	.	.	.	.	.	.	.	.	.	.	0.25643	N	0.986184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3334	0.32200	1.0:0.0:0.0:0.0	.	.	.	.	X	568	.	.	R	+	1	2	ZNF880	57580347	0.000000	0.05858	0.001000	0.08648	0.039000	0.13416	-1.373000	0.02568	0.798000	0.33994	0.363000	0.22086	AGA	.	.		0.383	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434		T	52888535	A	T	52888535	4	4	163	1	0	0	0	0	0	1	0	0	18212	180	7	4	1716	4	ZNF880	19	52888535	Nonsense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	665904	52888535	6240448	272	25054										
LENG8	114823	hgsc.bcm.edu	37	chr19	54965762	54965762	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cagctccagccacacagcacAgccaggcggggcccgccacg	12	19	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:54965762A>T	ENST00000326764.5	+	6	1059	c.580A>T	c.(580-582)Agc>Tgc	p.S194C	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	157										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		CACACAGCACAGCCAGGCGGG	0.672																																					p.S194C		Atlas-SNP	.											.	LENG8	73	.	0			c.A580T						.						14	14	14					19																	54965762		2186	4277	6463	SO:0001583	missense	114823	exon6			CAGCACAGCCAGG	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.580A>T	chr19.hg19:g.54965762A>T	ENSP00000318374:p.Ser194Cys	119.0	0.0		144.0	22.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	hg19	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	A	19.46	3.831047	0.71258	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000439657;ENST00000376526;ENST00000431846	T;T;T;T	0.52754	1.34;0.65;1.3;1.31	5.38	3.19	0.36642	.	0.336327	0.32093	N	0.006595	T	0.48732	0.1516	L	0.40543	1.245	0.80722	D	1	P;D	0.60575	0.896;0.988	P;P	0.56514	0.591;0.8	T	0.43782	-0.9370	10	0.49607	T	0.09	-22.7198	8.0119	0.30357	0.8152:0.0:0.1848:0.0	.	194;157	Q96PV6-2;F8W9Q9	.;.	C	194;157;194;157;194	ENSP00000318374:S194C;ENSP00000399507:S194C;ENSP00000365709:S157C;ENSP00000388053:S194C	ENSP00000301196:S157C	S	+	1	0	LENG8	59657574	0.996000	0.38824	1.000000	0.80357	0.990000	0.78478	0.988000	0.29616	0.985000	0.38656	0.533000	0.62120	AGC	.	.		0.672	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		T	54965762	A	T	54965762	3	4	163	1	0	0	0	0	1	0	0	0	8733	188	7	4	598	4	LENG8	19	54965762	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	2077227	54965762	4163221	273	25055										
NLRP13	126204	hgsc.bcm.edu	37	chr19	56413554	56413554	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcttgcaagcgggtgctgccAgctggcaaaaccagagcctg	14	12	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:56413554A>T	ENST00000342929.3	-	9	2635	c.2636T>A	c.(2635-2637)cTg>cAg	p.L879Q	NLRP13_ENST00000588751.1_Missense_Mutation_p.L879Q	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	879							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		GGGTGCTGCCAGCTGGCAAAA	0.597																																					p.L879Q		Atlas-SNP	.											.	NLRP13	220	.	0			c.T2636A						.						60	49	52					19																	56413554		2203	4300	6503	SO:0001583	missense	126204	exon9			GCTGCCAGCTGGC	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2636T>A	chr19.hg19:g.56413554A>T	ENSP00000343891:p.Leu879Gln	43.0	0.0		39.0	7.0	NM_176810	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	hg19	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	A	13.32	2.201602	0.38905	.	.	ENSG00000173572	ENST00000342929	T	0.62364	0.03	2.52	2.52	0.30459	.	.	.	.	.	T	0.80401	0.4616	M	0.91140	3.18	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66642	-0.5872	9	0.87932	D	0	.	7.2153	0.25957	1.0:0.0:0.0:0.0	.	879	Q86W25	NAL13_HUMAN	Q	879	ENSP00000343891:L879Q	ENSP00000343891:L879Q	L	-	2	0	NLRP13	61105366	0.149000	0.22717	0.058000	0.19502	0.202000	0.24057	3.926000	0.56491	1.137000	0.42214	0.383000	0.25322	CTG	.	.		0.597	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		T	56413554	A	T	56413554	3	4	163	1	0	0	0	0	1	0	0	0	10484	188	7	4	505	4	NLRP13	19	56413554	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1447792	56413554	2715429	274	25056										
NLRP5	126206	hgsc.bcm.edu	37	chr19	56520164	56520164	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgtcttccaggacattcaccAgaagatcctgaagcaacgat	8	11	2	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:56520164A>T	ENST00000390649.3	+	3	453	c.453A>T	c.(451-453)ccA>ccT	p.P151P		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	151					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GACATTCACCAGAAGATCCTG	0.463																																					p.P151P		Atlas-SNP	.											.	NLRP5	217	.	0			c.A453T						.						64	61	62					19																	56520164		1913	4133	6046	SO:0001819	synonymous_variant	126206	exon3			TTCACCAGAAGAT	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.453A>T	chr19.hg19:g.56520164A>T		78.0	0.0		105.0	21.0	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	hg19	CCDS12938.1																																																																																			.	.		0.463	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		T	56520164	A	T	56520164	2	4	163	1	0	0	0	0	0	0	0	1	10489	175	7	4		4	NLRP5	19	56520164	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	106610	56520164	2608819	275	25057										
ZNF835	90485	hgsc.bcm.edu	37	chr19	57176467	57176467	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cacggcctctggctctggacAgctttcctggttttcctgca	10	14	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:57176467A>T	ENST00000537055.2	-	2	331	c.100T>A	c.(100-102)Tgt>Agt	p.C34S		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	34					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						GGCTCTGGACAGCTTTCCTGG	0.597																																					p.C34S		Atlas-SNP	.											.	ZNF835	106	.	0			c.T100A						.						75	80	79					19																	57176467		1989	4164	6153	SO:0001583	missense	90485	exon2			CTGGACAGCTTTC	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.100T>A	chr19.hg19:g.57176467A>T	ENSP00000444747:p.Cys34Ser	81.0	0.0		80.0	10.0	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	hg19	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	A	1.362	-0.588359	0.03799	.	.	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.05580	3.42	2.59	-3.39	0.04868	.	.	.	.	.	T	0.03011	0.0089	N	0.24115	0.695	0.09310	N	1	B	0.15473	0.013	B	0.09377	0.004	T	0.46911	-0.9157	9	0.21540	T	0.41	.	0.3145	0.00293	0.2899:0.1935:0.1361:0.3804	.	56	Q9Y2P0	ZN835_HUMAN	S	56;34	ENSP00000444747:C34S	ENSP00000341756:C56S	C	-	1	0	ZNF835	61868279	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.333000	0.07894	-0.577000	0.05967	-0.441000	0.05720	TGT	.	.		0.597	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		T	57176467	A	T	57176467	3	4	163	1	0	0	0	0	1	0	0	0	18201	188	7	4	1515	4	ZNF835	19	57176467	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	656303	57176467	1952516	276	25058										
ZNF135	7694	hgsc.bcm.edu	37	chr19	58571397	58571397	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cctggggtgcgcgtctccacAgacccggtgagaatctcggc	14	14	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr19:58571397A>T	ENST00000313434.5	+	2	128	c.27A>T	c.(25-27)acA>acT	p.T9T	ZNF135_ENST00000511556.1_Silent_p.T9T|ZNF135_ENST00000439855.2_Silent_p.T9T|ZNF135_ENST00000506786.1_5'UTR|ZNF135_ENST00000359978.6_Intron|ZNF135_ENST00000401053.4_Intron	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	9					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		GCGTCTCCACAGACCCGGTGA	0.701																																					p.T9T		Atlas-SNP	.											.	ZNF135	159	.	0			c.A27T						.						81	66	71					19																	58571397		2203	4300	6503	SO:0001819	synonymous_variant	7694	exon2			CTCCACAGACCCG	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"Zinc fingers, C2H2-type", "-"	12919	protein-coding gene	gene with protein product		604077	"zinc finger protein 61", "zinc finger protein 135 (clone pHZ-17)"	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.27A>T	chr19.hg19:g.58571397A>T		53.0	0.0		65.0	16.0	NM_003436	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Silent	SNP	ENST00000313434.5	hg19																																																																																				.	.		0.701	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		T	58571397	A	T	58571397	2	4	163	1	0	0	0	0	0	0	0	1	17740	175	7	4		4	ZNF135	19	58571397	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1394930	58571397	557586	277	25059										
ADAM33	80332	hgsc.bcm.edu	37	chr20	3652923	3652923	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaggtgcccgtgcaaaactcAgggaggtcacagtcacccat	12	12	3	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr20:3652923A>T	ENST00000356518.2	-	14	1696	c.1455T>A	c.(1453-1455)ccT>ccA	p.P485P	ADAM33_ENST00000350009.2_Silent_p.P485P|ADAM33_ENST00000379861.4_Silent_p.P485P|ADAM33_ENST00000466620.1_5'UTR	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	485	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|skin(3)	29						TGCAAAACTCAGGGAGGTCAC	0.657																																					p.P485P		Atlas-SNP	.											.	ADAM33	76	.	0			c.T1455A						.						70	68	69					20																	3652923		2203	4300	6503	SO:0001819	synonymous_variant	80332	exon14			AAACTCAGGGAGG	AL117415, AB055891	CCDS13058.1, CCDS63219.1	20p13	2010-04-06	2005-08-18		ENSG00000149451	ENSG00000149451		"ADAM metallopeptidase domain containing"	15478	protein-coding gene	gene with protein product		607114	"a disintegrin and metalloproteinase domain 33", "chromosome 20 open reading frame 153"	C20orf153		11814695	Standard	XM_005260843		Approved	DKFZp434K0521, dJ964F7.1	uc002wit.3	Q9BZ11	OTTHUMG00000031758	ENST00000356518.2:c.1455T>A	chr20.hg19:g.3652923A>T		94.0	0.0		119.0	29.0	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Silent	SNP	ENST00000356518.2	hg19	CCDS13058.1																																																																																			.	.		0.657	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220		T	3652923	A	T	3652923	2	4	163	1	0	0	0	0	0	0	0	1	250	175	7	4		4	ADAM33	20	3652923	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		3652923	59372597	278	25060										
FERMT1	55612	hgsc.bcm.edu	37	chr20	6064810	6064810	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cctccaggatccgggcggccAgctgaacagaaacagacatc	11	14	0	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr20:6064810A>T	ENST00000217289.4	-	13	2383	c.1595T>A	c.(1594-1596)cTg>cAg	p.L532Q	FERMT1_ENST00000478194.1_5'UTR|FERMT1_ENST00000536936.1_Splice_Site_p.L275Q	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	532	FERM.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						CCGGGCGGCCAGCTGAACAGA	0.572																																					p.L532Q		Atlas-SNP	.											.	FERMT1	106	.	0			c.T1595A						.						38	29	32					20																	6064810		2203	4300	6503	SO:0001630	splice_region_variant	55612	exon13			GCGGCCAGCTGAA	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"Fermitins", "Pleckstrin homology (PH) domain containing"	15889	protein-coding gene	gene with protein product	"kindlin-1", "kinderlin"	607900	"chromosome 20 open reading frame 42", "fermitin family homolog 1 (Drosophila)"	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1594-1T>A	chr20.hg19:g.6064810A>T		33.0	0.0		41.0	11.0	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Missense_Mutation	SNP	ENST00000217289.4	hg19	CCDS13098.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.433421	0.83776	.	.	ENSG00000101311	ENST00000217289;ENST00000536936;ENST00000339538	T;T	0.81415	-1.49;-1.49	4.68	4.68	0.58851	Band 4.1 domain (1);FERM central domain (2);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.075318	0.53938	D	0.000041	D	0.88385	0.6422	M	0.72118	2.19	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.89877	0.4027	10	0.87932	D	0	-0.0175	14.4531	0.67399	1.0:0.0:0.0:0.0	.	532	Q9BQL6	FERM1_HUMAN	Q	532;275;532	ENSP00000217289:L532Q;ENSP00000441063:L275Q	ENSP00000217289:L532Q	L	-	2	0	FERMT1	6012810	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	9.220000	0.95180	1.869000	0.54173	0.459000	0.35465	CTG	.	.		0.572	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	Missense_Mutation	T	6064810	A	T	6064810	5	4	163	1	0	0	0	0	0	0	1	0	5825	202	7	4	450	4	FERMT1	20	6064810	Splice_Site	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	2411887	6064810	56960710	279	25061										
SEC23B	10483	hgsc.bcm.edu	37	chr20	18534971	18534971	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcaccactggatgatgctcaAgaaattctgcaagcacgctt	9	11	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr20:18534971A>T	ENST00000336714.3	+	18	2517	c.2085A>T	c.(2083-2085)caA>caT	p.Q695H	SEC23B_ENST00000262544.2_Missense_Mutation_p.Q695H|SEC23B_ENST00000377475.3_Missense_Mutation_p.Q695H|SEC23B_ENST00000377465.1_Missense_Mutation_p.Q695H	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	695					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						ATGATGCTCAAGAAATTCTGC	0.522																																					p.Q695H		Atlas-SNP	.											.	SEC23B	70	.	0			c.A2085T						.						167	135	146					20																	18534971		2203	4300	6503	SO:0001583	missense	10483	exon18			TGCTCAAGAAATT	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"Sec23 (S. cerevisiae) homolog B", "congenital dyserythropoietic anemia, type II"	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.2085A>T	chr20.hg19:g.18534971A>T	ENSP00000338844:p.Gln695His	80.0	0.0		85.0	19.0	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	hg19	CCDS13137.1	.	.	.	.	.	.	.	.	.	.	A	18.35	3.604778	0.66445	.	.	ENSG00000101310	ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465;ENST00000422877	D;D;D;D;D	0.94138	-3.36;-3.36;-3.36;-3.36;-3.36	4.69	-1.33	0.09172	Gelsolin domain (1);	0.103484	0.64402	D	0.000002	D	0.92424	0.7595	M	0.75085	2.285	0.58432	D	0.999999	P;P	0.37015	0.542;0.578	B;B	0.43018	0.309;0.405	D	0.89226	0.3574	10	0.72032	D	0.01	-14.3883	10.9766	0.47469	0.3191:0.0:0.6809:0.0	.	677;695	B4DJW8;Q15437	.;SC23B_HUMAN	H	695;695;695;695;174	ENSP00000338844:Q695H;ENSP00000262544:Q695H;ENSP00000366695:Q695H;ENSP00000366685:Q695H;ENSP00000409882:Q174H	ENSP00000262544:Q695H	Q	+	3	2	SEC23B	18482971	0.991000	0.36638	0.984000	0.44739	0.988000	0.76386	0.237000	0.17985	-0.136000	0.11475	-0.250000	0.11733	CAA	.	.		0.522	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			T	18534971	A	T	18534971	3	4	163	1	0	0	0	0	1	0	0	0	14007	69	3	4	2151	4	SEC23B	20	18534971	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	12470161	18534971	44490549	280	25062										
RALGAPA2	57186	hgsc.bcm.edu	37	chr20	20601245	20601245	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tgaactacttttcttgttacAgctatctcacaggaaggcaa	7	9	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr20:20601245A>T	ENST00000202677.7	-	11	1270	c.1263T>A	c.(1261-1263)gcT>gcA	p.A421A		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	421					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						TTCTTGTTACAGCTATCTCAC	0.423																																					p.A421A		Atlas-SNP	.											.	RALGAPA2	274	.	0			c.T1263A						.						67	64	65					20																	20601245		1857	4116	5973	SO:0001819	synonymous_variant	57186	exon11			TGTTACAGCTATC	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.1263T>A	chr20.hg19:g.20601245A>T		102.0	0.0		101.0	25.0	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Silent	SNP	ENST00000202677.7	hg19	CCDS46584.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.535094	0.27475	.	.	ENSG00000188559	ENST00000430436	.	.	.	5.5	1.72	0.24424	.	.	.	.	.	T	0.52677	0.1749	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45323	-0.9269	4	.	.	.	.	5.9768	0.19385	0.739:0.0:0.1391:0.1219	.	.	.	.	Q	238	.	.	L	-	2	0	RALGAPA2	20549245	0.908000	0.30866	1.000000	0.80357	0.995000	0.86356	0.236000	0.17967	0.922000	0.37019	0.482000	0.46254	CTG	.	.		0.423	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		T	20601245	A	T	20601245	2	4	163	1	0	0	0	0	0	0	0	1	13029	175	7	4		4	RALGAPA2	20	20601245	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	2066274	20601245	42424275	281	25063										
ID1	3397	hgsc.bcm.edu	37	chr20	30193298	30193298	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gaggtggtgcgctgtctgtcTgagcagagcgtggccatctc	16	10	3	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr20:30193298T>C	ENST00000376112.3	+	1	213	c.108T>C	c.(106-108)tcT>tcC	p.S36S	ID1_ENST00000376105.3_Silent_p.S36S|MIR3193_ENST00000578262.1_RNA	NM_002165.3	NP_002156.2	P41134	ID1_HUMAN	inhibitor of DNA binding 1, dominant negative helix-loop-helix protein	36					angiogenesis (GO:0001525)|blood vessel endothelial cell migration (GO:0043534)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|collagen metabolic process (GO:0032963)|endothelial cell morphogenesis (GO:0001886)|heart development (GO:0007507)|lung morphogenesis (GO:0060425)|lung vasculature development (GO:0060426)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein destabilization (GO:0031648)|regulation of angiogenesis (GO:0045765)|regulation of MAPK cascade (GO:0043408)|response to antibiotic (GO:0046677)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|ovary(1)|pancreas(1)	4	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			GCTGTCTGTCTGAGCAGAGCG	0.731																																					p.S36S	NSCLC(123;1618 1779 21803 28680 33854)	Atlas-SNP	.											.	ID1	12	.	0			c.T108C						.						11	12	12					20																	30193298		2168	4186	6354	SO:0001819	synonymous_variant	3397	exon1			TCTGTCTGAGCAG		CCDS13185.1, CCDS13186.1	20q11	2013-05-21			ENSG00000125968	ENSG00000125968		"Basic helix-loop-helix proteins"	5360	protein-coding gene	gene with protein product	"DNA-binding protein inhibitor ID-1"	600349				8294468	Standard	NM_002165		Approved	dJ857M17.1.2, bHLHb24	uc002wwg.2	P41134	OTTHUMG00000032181	ENST00000376112.3:c.108T>C	chr20.hg19:g.30193298T>C		76.0	0.0		76.0	20.0	NM_002165	A8K537|E1P5L4|O00651|O00652|Q16371|Q16377|Q5TE66|Q5TE67|Q969Z7|Q9H0Z5|Q9H109	Silent	SNP	ENST00000376112.3	hg19	CCDS13185.1																																																																																			.	.		0.731	ID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078550.1	NM_002165		C	30193298	T	C	30193298	2	2	163	1	0	0	0	0	0	0	0	1	7498	1567	55	2		2	ID1	20	30193298	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	9592053	30193298	32832222	282	25064										
R3HDML	140902	hgsc.bcm.edu	37	chr20	42966048	42966048	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtacccacctgccgccaacaTggaatacatggtgagtcccc	9	15	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr20:42966048T>A	ENST00000217043.2	+	1	423	c.251T>A	c.(250-252)aTg>aAg	p.M84K		NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	84	SCP.					extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)	21		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			GCCGCCAACATGGAATACATG	0.582																																					p.M84K		Atlas-SNP	.											.	R3HDML	33	.	0			c.T251A						.						53	51	51					20																	42966048		2203	4300	6503	SO:0001583	missense	140902	exon1			CCAACATGGAATA	BC107048	CCDS13329.1	20q13.12	2007-04-26	2005-09-02		ENSG00000101074	ENSG00000101074			16249	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing-like"				Standard	NM_178491		Approved	dJ881L22.3	uc002xls.2	Q9H3Y0	OTTHUMG00000032524	ENST00000217043.2:c.251T>A	chr20.hg19:g.42966048T>A	ENSP00000217043:p.Met84Lys	108.0	0.0		130.0	34.0	NM_178491		Missense_Mutation	SNP	ENST00000217043.2	hg19	CCDS13329.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.852875	0.71719	.	.	ENSG00000101074	ENST00000217043	T	0.22336	1.96	5.18	5.18	0.71444	CAP domain (3);	0.000000	0.85682	D	0.000000	T	0.65913	0.2737	H	0.99261	4.49	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81810	-0.0762	10	0.87932	D	0	.	15.0238	0.71653	0.0:0.0:0.0:1.0	.	84	Q9H3Y0	CRSPL_HUMAN	K	84	ENSP00000217043:M84K	ENSP00000217043:M84K	M	+	2	0	R3HDML	42399462	1.000000	0.71417	1.000000	0.80357	0.528000	0.34623	5.389000	0.66255	1.958000	0.56883	0.317000	0.21355	ATG	.	.		0.582	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491		A	42966048	T	A	42966048	3	1	163	1	0	0	0	0	1	0	0	0	12904	1464	51	4	253	4	R3HDML	20	42966048	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	12772750	42966048	20059472	283	25065										
WISP2	8839	hgsc.bcm.edu	37	chr20	43355869	43355869	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ccagaaccgcttctgccgacTggagacccagcgccgcctgt	11	17	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr20:43355869T>A	ENST00000372868.2	+	5	1017	c.674T>A	c.(673-675)cTg>cAg	p.L225Q	WISP2_ENST00000471629.1_3'UTR|WISP2_ENST00000190983.4_Missense_Mutation_p.L225Q|WISP2_ENST00000372865.4_Missense_Mutation_p.W143R|RP11-445H22.4_ENST00000427598.1_RNA|RP11-445H22.4_ENST00000445420.1_RNA|RP11-445H22.4_ENST00000427303.1_RNA			O76076	WISP2_HUMAN	WNT1 inducible signaling pathway protein 2	225	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				skin(1)	1		Myeloproliferative disorder(115;0.0122)				TTCTGCCGACTGGAGACCCAG	0.682																																					p.L225Q		Atlas-SNP	.											.	WISP2	28	.	0			c.T674A						.						34	36	35					20																	43355869		2203	4299	6502	SO:0001583	missense	8839	exon4			GCCGACTGGAGAC	AF100780	CCDS13336.1	20q13.12	2007-05-14			ENSG00000064205	ENSG00000064205			12770	protein-coding gene	gene with protein product		603399				9843955	Standard	NM_003881		Approved	CT58, CTGF-L, CCN5	uc002xmp.3	O76076	OTTHUMG00000033071	ENST00000372868.2:c.674T>A	chr20.hg19:g.43355869T>A	ENSP00000361959:p.Leu225Gln	48.0	0.0		31.0	7.0	NM_003881	B2R9N4|E1P612|Q6PEG3	Missense_Mutation	SNP	ENST00000372868.2	hg19	CCDS13336.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.69|17.69	3.451746|3.451746	0.63290|0.63290	.|.	.|.	ENSG00000064205|ENSG00000064205	ENST00000372868;ENST00000190983|ENST00000372865	T;T|T	0.55930|0.63417	0.49;0.49|-0.04	4.05|4.05	4.05|4.05	0.47172|0.47172	.|.	0.000000|.	0.64402|.	D|.	0.000004|.	T|T	0.73598|0.73598	0.3607|0.3607	L|L	0.58354|0.58354	1.805|1.805	0.58432|0.58432	D|D	0.999998|0.999998	D|D	0.89917|0.76494	1.0|0.999	D|D	0.87578|0.68765	0.998|0.96	T|T	0.77054|0.77054	-0.2730|-0.2730	10|9	0.51188|0.87932	T|D	0.08|0	-21.0299|-21.0299	13.1748|13.1748	0.59619|0.59619	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	225|143	O76076|Q6PEG3	WISP2_HUMAN|.	Q|R	225|143	ENSP00000361959:L225Q;ENSP00000190983:L225Q|ENSP00000361956:W143R	ENSP00000190983:L225Q|ENSP00000361956:W143R	L|W	+|+	2|1	0|0	WISP2|WISP2	42789283|42789283	1.000000|1.000000	0.71417|0.71417	0.948000|0.948000	0.38648|0.38648	0.336000|0.336000	0.28762|0.28762	7.752000|7.752000	0.85141|0.85141	1.700000|1.700000	0.51204|0.51204	0.459000|0.459000	0.35465|0.35465	CTG|TGG	.	.		0.682	WISP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127824.1	NM_003881		A	43355869	T	A	43355869	3	1	163	1	0	0	0	0	1	0	0	0	17388	1580	55	4	688	4	WISP2	20	43355869	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	389821	43355869	19669651	284	25066										
SEMG1	6406	hgsc.bcm.edu	37	chr20	43836884	43836884	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tatcccaaagcagtatttatAgccaaactgaagagaaagca	7	8	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr20:43836884A>T	ENST00000372781.3	+	2	1003	c.946A>T	c.(946-948)Agc>Tgc	p.S316C	SEMG1_ENST00000244069.6_Intron	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	316	2 X 60 AA tandem repeats, type 1.|Repeat-rich region. {ECO:0000250}.				insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				CAGTATTTATAGCCAAACTGA	0.378																																					p.S316C		Atlas-SNP	.											.	SEMG1	71	.	0			c.A946T						.						72	68	70					20																	43836884		2203	4300	6503	SO:0001583	missense	6406	exon2			ATTTATAGCCAAA		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"semen coagulating protein", "cancer/testis antigen 103"	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.946A>T	chr20.hg19:g.43836884A>T	ENSP00000361867:p.Ser316Cys	305.0	0.0		427.0	98.0	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	hg19	CCDS13345.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.673529	0.29693	.	.	ENSG00000124233	ENST00000372781	T	0.06933	3.24	1.69	0.403	0.16350	.	.	.	.	.	T	0.14098	0.0341	L	0.50333	1.59	0.09310	N	1	D;D	0.63880	0.992;0.993	P;P	0.57425	0.82;0.815	T	0.14783	-1.0460	9	0.62326	D	0.03	.	4.2989	0.10915	0.6399:0.3601:0.0:0.0	.	316;316	P04279;E7EPD3	SEMG1_HUMAN;.	C	316	ENSP00000361867:S316C	ENSP00000361867:S316C	S	+	1	0	SEMG1	43270298	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.004000	0.13106	0.078000	0.16900	0.455000	0.32223	AGC	.	.		0.378	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007		T	43836884	A	T	43836884	3	4	163	1	0	0	0	0	1	0	0	0	14059	420	15	4	952	4	SEMG1	20	43836884	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	481015	43836884	19188636	285	25067										
PARD6B	84612	hgsc.bcm.edu	37	chr20	49366413	49366413	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tacggcacggagaaacccctAggattctacatccgggatgg	12	11	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr20:49366413A>T	ENST00000371610.2	+	3	750	c.507A>T	c.(505-507)ctA>ctT	p.L169L	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	169	Interaction with PARD3 and CDC42. {ECO:0000250}.|PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						AGAAACCCCTAGGATTCTACA	0.488																																					p.L169L		Atlas-SNP	.											.	PARD6B	31	.	0			c.A507T						.						70	67	68					20																	49366413		2203	4300	6503	SO:0001819	synonymous_variant	84612	exon3			ACCCCTAGGATTC	AB044555	CCDS33485.1	20q13.13	2013-08-28	2013-08-28		ENSG00000124171	ENSG00000124171			16245	protein-coding gene	gene with protein product		608975	"par-6 (partitioning defective 6, C.elegans) homolog beta", "par-6 partitioning defective 6 homolog beta (C. elegans)"			11260256	Standard	NM_032521		Approved	PAR-6B	uc002xvo.3	Q9BYG5	OTTHUMG00000032732	ENST00000371610.2:c.507A>T	chr20.hg19:g.49366413A>T		158.0	0.0		195.0	52.0	NM_032521	A2A2A7|Q9Y510	Silent	SNP	ENST00000371610.2	hg19	CCDS33485.1																																																																																			.	.		0.488	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		T	49366413	A	T	49366413	2	4	163	1	0	0	0	0	0	0	0	1	11455	407	15	4		4	PARD6B	20	49366413	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	5529529	49366413	13659107	286	25068										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19666925	19666925	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aacatatttacttacatttaTggttacactgtaaccgaatc	4	8	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr21:19666925T>A	ENST00000284885.3	-	20	2339	c.2306A>T	c.(2305-2307)cAt>cTt	p.H769L		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	769	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CTTACATTTATGGTTACACTG	0.289																																					p.H769L		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A2306T						.						79	82	81					21																	19666925		2203	4297	6500	SO:0001583	missense	5651	exon20			CATTTATGGTTAC		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.2306A>T	chr21.hg19:g.19666925T>A	ENSP00000284885:p.His769Leu	271.0	0.0		348.0	80.0	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	hg19	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	T	6.401	0.442068	0.12164	.	.	ENSG00000154646	ENST00000284885	T	0.27256	1.68	5.42	1.72	0.24424	Speract/scavenger receptor (2);Speract/scavenger receptor-related (1);	0.460627	0.24625	N	0.036927	T	0.20373	0.0490	L	0.60455	1.87	0.34294	D	0.683583	B	0.25351	0.124	B	0.27500	0.08	T	0.12785	-1.0534	9	.	.	.	.	3.245	0.06794	0.138:0.0766:0.1442:0.6411	.	769	P98073	ENTK_HUMAN	L	769	ENSP00000284885:H769L	.	H	-	2	0	TMPRSS15	18588796	0.047000	0.20315	0.863000	0.33907	0.123000	0.20343	0.043000	0.13971	0.137000	0.18759	-1.204000	0.01649	CAT	.	.		0.289	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		A	19666925	T	A	19666925	3	1	163	1	0	0	0	0	1	0	0	0	16261	1464	51	4	777	4	TMPRSS15	21	19666925	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10		19666925	28462970	287	25069										
RNF160	26046	hgsc.bcm.edu	37	chr21	30341864	30341864	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	taaaacgtaagcattcaaaaAaagcagatattactgccgag	7	7	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr21:30341864A>C	ENST00000361371.5	-	9	1314	c.1235T>G	c.(1234-1236)tTt>tGt	p.F412C	LTN1_ENST00000389194.2_Missense_Mutation_p.F458C|LTN1_ENST00000389195.2_Missense_Mutation_p.F458C			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	412					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						GCATTCAAAAAAAGCAGATAT	0.353																																					p.F458C		Atlas-SNP	.											.	LTN1	141	.	0			c.T1373G						.						96	96	96					21																	30341864		2202	4300	6502	SO:0001583	missense	26046	exon9			TCAAAAAAAGCAG	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"RING-type (C3HC4) zinc fingers"	13082	protein-coding gene	gene with protein product	"listerin"	613083	"chromosome 21 open reading frame 98", "zinc finger protein 294", "ring finger protein 160"	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1235T>G	chr21.hg19:g.30341864A>C	ENSP00000354977:p.Phe412Cys	71.0	0.0		81.0	18.0	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	hg19		.	.	.	.	.	.	.	.	.	.	A	16.13	3.034638	0.54896	.	.	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000446611;ENST00000389195	T;T;T	0.65178	3.61;3.61;-0.14	4.91	3.76	0.43208	Armadillo-type fold (1);	0.195954	0.45867	D	0.000322	T	0.64461	0.2600	L	0.42245	1.32	0.41031	D	0.98515	D	0.71674	0.998	P	0.57324	0.818	T	0.65573	-0.6135	10	0.62326	D	0.03	.	8.5886	0.33672	0.911:0.0:0.089:0.0	.	412	O94822	LTN1_HUMAN	C	458;412;414;458	ENSP00000373846:F458C;ENSP00000354977:F412C;ENSP00000373847:F458C	ENSP00000354977:F412C	F	-	2	0	LTN1	29263735	1.000000	0.71417	0.999000	0.59377	0.556000	0.35491	5.623000	0.67757	1.013000	0.39391	-0.256000	0.11100	TTT	.	.		0.353	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		C	30341864	A	C	30341864	3	2	163	1	0	0	0	0	1	0	0	0	13470	14	1	5	4153	5	RNF160	21	30341864	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	10674939	30341864	17788031	288	25070										
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26707784	26707784	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acatccagaatgggaacttcActacatccgacccgacctat	6	14	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr22:26707784A>T	ENST00000248933.6	+	8	1827	c.1732A>T	c.(1732-1734)Act>Tct	p.T578S	SEZ6L_ENST00000343706.4_Missense_Mutation_p.T578S|SEZ6L_ENST00000529632.2_Missense_Mutation_p.T578S|SEZ6L_ENST00000360929.3_Missense_Mutation_p.T578S|SEZ6L_ENST00000404234.3_Missense_Mutation_p.T578S|SEZ6L_ENST00000403121.1_Missense_Mutation_p.T351S|SEZ6L_ENST00000402979.1_Missense_Mutation_p.T351S			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	578	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						TGGGAACTTCACTACATCCGA	0.552																																					p.T578S		Atlas-SNP	.											.	SEZ6L	174	.	0			c.A1732T						.						222	212	216					22																	26707784		2203	4300	6503	SO:0001583	missense	23544	exon8			AACTTCACTACAT	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1732A>T	chr22.hg19:g.26707784A>T	ENSP00000248933:p.Thr578Ser	130.0	0.0		120.0	33.0	NM_021115	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	hg19	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	A	10.42	1.345602	0.24426	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.83	3.77	0.43336	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000019	T	0.48909	0.1526	N	0.16201	0.385	0.80722	D	1	P;P;B;P;P;P;P	0.52170	0.951;0.624;0.128;0.791;0.812;0.624;0.624	P;B;B;B;P;B;B	0.50754	0.649;0.329;0.099;0.332;0.481;0.329;0.329	T	0.32877	-0.9890	10	0.13853	T	0.58	.	10.1055	0.42530	0.85:0.0:0.0:0.15	.	578;578;351;578;578;578;578	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	S	578;578;578;578;578;351;351	ENSP00000384772:T578S;ENSP00000437037:T578S;ENSP00000354185:T578S;ENSP00000248933:T578S;ENSP00000342661:T578S;ENSP00000384838:T351S;ENSP00000384733:T351S	ENSP00000248933:T578S	T	+	1	0	SEZ6L	25037784	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	5.400000	0.66320	0.825000	0.34637	0.460000	0.39030	ACT	.	.		0.552	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			T	26707784	A	T	26707784	3	4	163	1	0	0	0	0	1	0	0	0	14158	159	6	4	1762	4	SEZ6L	22	26707784	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10		26707784	24596782	289	25071										
SLC5A1	6523	hgsc.bcm.edu	37	chr22	32480985	32480985	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ctgatgcccatgttcatcatGgtgatgccaggaatgatcag	11	9	3	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr22:32480985G>A	ENST00000266088.4	+	9	1234	c.984G>A	c.(982-984)atG>atA	p.M328I	SLC5A1_ENST00000543737.1_Missense_Mutation_p.M201I	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	328					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	TGTTCATCATGGTGATGCCAG	0.488																																					p.M328I		Atlas-SNP	.											.	SLC5A1	80	.	0			c.G984A						.						192	157	169					22																	32480985		2203	4300	6503	SO:0001583	missense	6523	exon9			CATCATGGTGATG		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"Solute carriers"	11036	protein-coding gene	gene with protein product	"sodium/glucose cotransporter 1"	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.984G>A	chr22.hg19:g.32480985G>A	ENSP00000266088:p.Met328Ile	79.0	0.0		94.0	20.0	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Missense_Mutation	SNP	ENST00000266088.4	hg19	CCDS13902.1	.	.	.	.	.	.	.	.	.	.	G	3.998	-0.003210	0.07773	.	.	ENSG00000100170	ENST00000266088;ENST00000543737	D;D	0.86769	-2.17;-2.17	4.92	-2.79	0.05841	.	0.119935	0.85682	N	0.000000	T	0.70360	0.3215	L	0.31578	0.945	0.46654	D	0.999147	B	0.10296	0.003	B	0.17722	0.019	T	0.47560	-0.9108	10	0.13108	T	0.6	.	2.1713	0.03850	0.376:0.1174:0.3866:0.12	.	328	P13866	SC5A1_HUMAN	I	328;201	ENSP00000266088:M328I;ENSP00000444898:M201I	ENSP00000266088:M328I	M	+	3	0	SLC5A1	30810985	1.000000	0.71417	0.896000	0.35187	0.033000	0.12548	2.773000	0.47686	-0.590000	0.05866	-1.057000	0.02308	ATG	.	.		0.488	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343		A	32480985	G	A	32480985	3	1	163	1	0	0	0	0	1	0	0	0	14676	1348	47	3	1018	3	SLC5A1	22	32480985	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	5773201	32480985	18823581	290	25072										
TOMM22	56993	hgsc.bcm.edu	37	chr22	39078326	39078326	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acccgcgtctactccaccacAgctagatgagaccctgtcgg	9	16	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr22:39078326A>T	ENST00000216034.4	+	2	148		c.e2-1		RP3-508I15.9_ENST00000444381.1_RNA|RP3-508I15.9_ENST00000412067.1_RNA|RP3-508I15.9_ENST00000431924.2_RNA	NM_020243.4	NP_064628.1	Q9NS69	TOM22_HUMAN	translocase of outer mitochondrial membrane 22 homolog (yeast)						cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			large_intestine(1)|lung(2)	3	Melanoma(58;0.04)					ACTCCACCACAGCTAGATGAG	0.627																																					.		Atlas-SNP	.											.	TOMM22	10	.	0			c.118-2A>T						.						35	37	37					22																	39078326		2203	4300	6503	SO:0001630	splice_region_variant	56993	exon2			CACCACAGCTAGA	AB040119	CCDS13975.1	22q12-q13	2010-07-29			ENSG00000100216	ENSG00000100216			18002	protein-coding gene	gene with protein product		607046				10982837, 10900208	Standard	NM_020243		Approved	TOM22	uc003awe.3	Q9NS69	OTTHUMG00000150991	ENST00000216034.4:c.118-1A>T	chr22.hg19:g.39078326A>T		74.0	0.0		57.0	13.0	NM_020243		Splice_Site	SNP	ENST00000216034.4	hg19	CCDS13975.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.476747	0.84640	.	.	ENSG00000100216	ENST00000216034	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4157	0.74966	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TOMM22	37408272	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	8.367000	0.90113	2.037000	0.60232	0.460000	0.39030	.	.	.		0.627	TOMM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320842.1		Intron	T	39078326	A	T	39078326	5	4	163	1	0	0	0	0	0	0	1	0	16371	202	7	4	122	4	TOMM22	22	39078326	Splice_Site	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	6597341	39078326	12226240	291	25073										
TNRC6B	23112	hgsc.bcm.edu	37	chr22	40708618	40708618	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acagccacatctcccattgtAgatactgaccaccaactgct	5	15	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chr22:40708618A>T	ENST00000454349.2	+	18	4756	c.4545A>T	c.(4543-4545)gtA>gtT	p.V1515V	TNRC6B_ENST00000402203.1_Silent_p.V711V|TNRC6B_ENST00000301923.9_Silent_p.V711V|TNRC6B_ENST00000335727.9_Silent_p.V1405V	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	1515	Silencing domain; interaction with CNOT1 and PAN3.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						CTCCCATTGTAGATACTGACC	0.483																																					p.V1515V		Atlas-SNP	.											.	TNRC6B	195	.	0			c.A4545T						.						155	149	151					22																	40708618		2020	4188	6208	SO:0001819	synonymous_variant	23112	exon18			CATTGTAGATACT	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.4545A>T	chr22.hg19:g.40708618A>T		68.0	0.0		82.0	18.0	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Silent	SNP	ENST00000454349.2	hg19	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	A	10.49	1.365661	0.24684	.	.	ENSG00000100354	ENST00000446273	.	.	.	5.01	3.96	0.45880	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.9606	11.8066	0.52158	0.8406:0.1594:0.0:0.0	.	.	.	.	L	1201	.	.	X	+	2	0	TNRC6B	39038564	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.314000	0.43743	0.758000	0.33059	-0.331000	0.08364	TAG	.	.		0.483	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				T	40708618	A	T	40708618	2	4	163	1	0	0	0	0	0	0	0	1	16356	407	15	4		4	TNRC6B	22	40708618	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	1630292	40708618	10595948	292	25074										
CLCN4	1183	hgsc.bcm.edu	37	chrX	10166045	10166045	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cgctgctgtttgcatttttgGctgtctccctggtgcgtgta	12	10	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:10166045G>C	ENST00000380833.4	+	6	890	c.499G>C	c.(499-501)Gct>Cct	p.A167P	CLCN4_ENST00000421085.2_Missense_Mutation_p.A73P|CLCN4_ENST00000380829.1_Missense_Mutation_p.A167P	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	167					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TGCATTTTTGGCTGTCTCCCT	0.433																																					p.A167P	Melanoma(74;1050 1296 1576 30544 38374)	Atlas-SNP	.											.	CLCN4	84	.	0			c.G499C						.						289	238	255					X																	10166045		2203	4300	6503	SO:0001583	missense	1183	exon6			TTTTTGGCTGTCT	X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"Ion channels / Chloride channels : Voltage-sensitive"	2022	protein-coding gene	gene with protein product		302910	"chloride channel 4"			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.499G>C	chrX.hg19:g.10166045G>C	ENSP00000370213:p.Ala167Pro	99.0	0.0		141.0	34.0	NM_001830	A1L3U1|B7Z5Z4|Q9UBU1	Missense_Mutation	SNP	ENST00000380833.4	hg19	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	G	32	5.143757	0.94603	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000421085	D;D;D	0.95412	-3.7;-3.7;-3.7	5.4	5.4	0.78164	Chloride channel, core (2);	0.101975	0.64402	D	0.000003	D	0.98353	0.9453	M	0.93808	3.46	0.80722	D	1	D	0.71674	0.998	D	0.81914	0.995	D	0.99643	1.0989	10	0.87932	D	0	-20.2161	17.8837	0.88848	0.0:0.0:1.0:0.0	.	167	P51793	CLCN4_HUMAN	P	167;167;73	ENSP00000370213:A167P;ENSP00000370209:A167P;ENSP00000405754:A73P	ENSP00000370209:A167P	A	+	1	0	CLCN4	10126045	1.000000	0.71417	0.528000	0.27938	0.981000	0.71138	9.667000	0.98616	2.264000	0.75181	0.544000	0.68410	GCT	.	.		0.433	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1			C	10166045	G	C	10166045	3	2	163	1	0	0	0	0	1	0	0	0	3467	1203	42	4	513	4	CLCN4	23	10166045	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10		10166045	145104515	293	25075										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12735864	12735864	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tcctcgcacgccctggctgcTaggccagcaaccgacctccc	9	20	0	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:12735864T>A	ENST00000380682.1	+	16	3425	c.2919T>A	c.(2917-2919)gcT>gcA	p.A973A		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	973					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						CCCTGGCTGCTAGGCCAGCAA	0.602																																					p.A973A		Atlas-SNP	.											.	FRMPD4	214	.	0			c.T2919A						.						57	58	58					X																	12735864		2203	4300	6503	SO:0001819	synonymous_variant	9758	exon16			GGCTGCTAGGCCA	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.2919T>A	chrX.hg19:g.12735864T>A		204.0	0.0		234.0	65.0	NM_014728	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	hg19	CCDS35201.1																																																																																			.	.		0.602	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		A	12735864	T	A	12735864	2	1	163	1	0	0	0	0	0	0	0	1	6067	1509	53	4		4	FRMPD4	23	12735864	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	2569819	12735864	142534696	294	25076										
CDKL5	6792	hgsc.bcm.edu	37	chrX	18606148	18606148	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gcttagcgatggacagccttTatttcctggagaaagtgaaa	11	7	0	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:18606148T>C	ENST00000379989.3	+	10	914	c.629T>C	c.(628-630)tTa>tCa	p.L210S	CDKL5_ENST00000379996.3_Missense_Mutation_p.L210S	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	210	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					GGACAGCCTTTATTTCCTGGA	0.443																																					p.L210S		Atlas-SNP	.											.	CDKL5	124	.	0			c.T629C						.						222	217	219					X																	18606148		2203	4300	6503	SO:0001583	missense	6792	exon9			AGCCTTTATTTCC	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"Cyclin-dependent kinases"	11411	protein-coding gene	gene with protein product		300203	"serine/threonine kinase 9"	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.629T>C	chrX.hg19:g.18606148T>C	ENSP00000369325:p.Leu210Ser	187.0	0.0		225.0	53.0	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	hg19	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.620277	0.87460	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.67171	-0.25;-0.25	6.1	6.1	0.99115	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.86347	0.5911	M	0.93939	3.475	0.53005	D	0.999963	D	0.76494	0.999	D	0.77557	0.99	D	0.89845	0.4005	10	0.87932	D	0	-12.2514	15.5648	0.76281	0.0:0.0:0.0:1.0	.	210	O76039	CDKL5_HUMAN	S	210	ENSP00000369332:L210S;ENSP00000369325:L210S	ENSP00000369325:L210S	L	+	2	0	CDKL5	18516069	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.695000	0.84257	2.060000	0.61445	0.481000	0.45027	TTA	.	.		0.443	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159		C	18606148	T	C	18606148	3	2	163	1	0	0	0	0	1	0	0	0	3159	1764	61	2	659	2	CDKL5	23	18606148	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	5870284	18606148	136664412	295	25077										
MAGEB3	4114	hgsc.bcm.edu	37	chrX	30254845	30254845	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	caagtgcccaacagtaatccTgcacgctatgaattcctgtg	8	12	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:30254845T>A	ENST00000361644.2	+	5	1541	c.804T>A	c.(802-804)ccT>ccA	p.P268P		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	268	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						ACAGTAATCCTGCACGCTATG	0.488																																					p.P268P		Atlas-SNP	.											.	MAGEB3	54	.	0			c.T804A						.						86	74	78					X																	30254845		2202	4300	6502	SO:0001819	synonymous_variant	4114	exon5			TAATCCTGCACGC	AK057441	CCDS14220.1	Xp21.3	2009-03-17			ENSG00000198798	ENSG00000198798			6810	protein-coding gene	gene with protein product	"cancer/testis antigen family 3, member 5"	300152				9441743	Standard	NM_002365		Approved	CT3.5	uc004dca.2	O15480	OTTHUMG00000021320	ENST00000361644.2:c.804T>A	chrX.hg19:g.30254845T>A		252.0	0.0		346.0	84.0	NM_002365	A0AVE4|B3KQ52|O75861	Silent	SNP	ENST00000361644.2	hg19	CCDS14220.1																																																																																			.	.		0.488	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2	NM_002365		A	30254845	T	A	30254845	2	1	163	1	0	0	0	0	0	0	0	1	9186	1567	55	4		4	MAGEB3	23	30254845	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	11648697	30254845	125015715	296	25078										
PRRG1	5638	hgsc.bcm.edu	37	chrX	37285109	37285109	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttagttttcctcacgggagaAaaagccaattccatattaaa	6	8	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:37285109A>G	ENST00000542554.1	+	4	299	c.27A>G	c.(25-27)gaA>gaG	p.E9E	PRRG1_ENST00000463135.1_Silent_p.E9E|PRRG1_ENST00000378628.4_Silent_p.E9E|TM4SF2_ENST00000465127.1_Silent_p.E9E|PRRG1_ENST00000449135.2_Silent_p.E9E|PRRG1_ENST00000543642.1_Silent_p.E9E|PRRG1_ENST00000491253.1_Intron	NM_001173489.1	NP_001166960.1	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1	9						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	15						TCACGGGAGAAAAAGCCAATT	0.348																																					p.E9E		Atlas-SNP	.											.	PRRG1	42	.	0			c.A27G						.						45	44	44					X																	37285109		2202	4300	6502	SO:0001819	synonymous_variant	5638	exon3			GGGAGAAAAAGCC	AF009242	CCDS14239.1, CCDS55397.1	Xp21.1	2010-08-13	2004-05-27		ENSG00000130962	ENSG00000130962			9469	protein-coding gene	gene with protein product		604428	"proline-rich Gla (G-carboxyglutamic acid) polypeptide 1"			9256434	Standard	NM_000950		Approved	PRGP1	uc004ddo.3	O14668	OTTHUMG00000021360	ENST00000542554.1:c.27A>G	chrX.hg19:g.37285109A>G		549.0	0.0		677.0	151.0	NM_001173490	B2R7A3|C9JXL7|D3DWA9|Q5JT66	Silent	SNP	ENST00000542554.1	hg19	CCDS14239.1																																																																																			.	.		0.348	PRRG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056228.2	NM_000950		G	37285109	A	G	37285109	2	3	163	1	0	0	0	0	0	0	0	1	12617	11	1	2		2	PRRG1	23	37285109	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	7030264	37285109	117985451	297	25079										
RPGR	6103	hgsc.bcm.edu	37	chrX	38145017	38145017	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	gtactcctctccatcctgccTttcattctcttcttcgcctg	4	17	4	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:38145017T>A	ENST00000339363.3	-	14	2688				TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000378505.2_Missense_Mutation_p.R1079W|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						CCATCCTGCCTTTCATTCTCT	0.413																																					p.R1079W		Atlas-SNP	.											.	RPGR	175	.	0			c.A3235T						.						409	328	355					X																	38145017		2202	4300	6502	SO:0001627	intron_variant	6103	exon15			CCTGCCTTTCATT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"retinitis pigmentosa 15", "cone dystrophy 1 (X-linked)"	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+1329A>T	chrX.hg19:g.38145017T>A		86.0	0.0		115.0	20.0	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	hg19		.	.	.	.	.	.	.	.	.	.	t	10.73	1.432423	0.25813	.	.	ENSG00000156313	ENST00000378505	T	0.02579	4.24	2.84	0.237	0.15475	.	1.292120	0.05640	U	0.583284	T	0.04815	0.0130	L	0.48642	1.525	0.34659	D	0.722529	D	0.62365	0.991	P	0.46389	0.515	T	0.46679	-0.9174	10	0.87932	D	0	.	5.9165	0.19057	0.0:0.3952:0.0:0.6048	.	1079	E9PE28	.	W	1079	ENSP00000367766:R1079W	ENSP00000367766:R1079W	R	-	1	2	RPGR	38029961	0.005000	0.15991	0.023000	0.16930	0.544000	0.35116	0.950000	0.29122	0.147000	0.19030	0.278000	0.19347	AGG	.	.		0.413	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		A	38145017	T	A	38145017	1	1	163	0	1	0	0	0	0	0	0	0	13563	1608	56	4		4	RPGR	23	38145017	Intron	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	859908	38145017	117125543	298	25080										
MAOB	4129	hgsc.bcm.edu	37	chrX	43656381	43656381	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	tggatgggtacctgtcctccAtttgttgtcgagatgattct	11	8	1	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:43656381A>T	ENST00000378069.4	-	6	756	c.609T>A	c.(607-609)aaT>aaA	p.N203K	MAOB_ENST00000538942.1_Missense_Mutation_p.N187K|MAOB_ENST00000536181.1_Missense_Mutation_p.N187K|MAOB_ENST00000487544.1_5'Flank	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	203					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	CCTGTCCTCCATTTGTTGTCG	0.473																																					p.N203K		Atlas-SNP	.											.	MAOB	52	.	0			c.T609A						.						127	112	117					X																	43656381		2203	4300	6503	SO:0001583	missense	4129	exon6			TCCTCCATTTGTT		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.609T>A	chrX.hg19:g.43656381A>T	ENSP00000367309:p.Asn203Lys	68.0	0.0		88.0	22.0	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.570033	0.45798	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	D;D;D	0.92397	-3.03;-3.03;-3.03	5.45	4.3	0.51218	Amine oxidase (1);	0.000000	0.85682	D	0.000000	D	0.95294	0.8473	M	0.85373	2.75	0.80722	D	1	D;D	0.89917	0.975;1.0	P;D	0.85130	0.778;0.997	D	0.93049	0.6464	10	0.23891	T	0.37	-19.6609	9.2353	0.37461	0.8459:0.0:0.1541:0.0	.	187;203	B7Z5H3;P27338	.;AOFB_HUMAN	K	203;187;187	ENSP00000367309:N203K;ENSP00000441613:N187K;ENSP00000442240:N187K	ENSP00000367309:N203K	N	-	3	2	MAOB	43541325	1.000000	0.71417	1.000000	0.80357	0.271000	0.26615	1.002000	0.29796	0.726000	0.32339	0.441000	0.28932	AAT	.	.		0.473	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		T	43656381	A	T	43656381	3	4	163	1	0	0	0	0	1	0	0	0	9235	214	8	4	993	4	MAOB	23	43656381	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	5511364	43656381	111614179	299	25081										
SSX1	6756	hgsc.bcm.edu	37	chrX	48123234	48123234	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aagatcatgcccaagaagccAgcagaggacgaaaatgattc	10	9	1	4			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:48123234A>T	ENST00000376919.3	+	6	484	c.348A>T	c.(346-348)ccA>ccT	p.P116P		NM_001278691.1|NM_005635.2	NP_001265620.1|NP_005626.1	Q16384	SSX1_HUMAN	synovial sarcoma, X breakpoint 1	116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)		SS18/SSX1(1169)|SS18L1/SSX1(2)	endometrium(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9						CCAAGAAGCCAGCAGAGGACG	0.428			T	SS18	synovial sarcoma																																p.P116P	Esophageal Squamous(175;994 1982 2214 6527 18857)	Atlas-SNP	.		Dom	yes		X	Xp11.23-p11.22	6756	"synovial sarcoma, X breakpoint 1"		M	.	SSX1	27	.	0			c.A348T						.						182	173	176					X																	48123234		2203	4299	6502	SO:0001819	synonymous_variant	6756	exon6			GAAGCCAGCAGAG	BC001003	CCDS14290.1	Xp11.23	2009-03-12			ENSG00000126752	ENSG00000126752			11335	protein-coding gene	gene with protein product	"cancer/testis antigen family 5, member 1"	312820				7655467	Standard	NM_005635		Approved	CT5.1	uc004djb.1	Q16384	OTTHUMG00000021488	ENST00000376919.3:c.348A>T	chrX.hg19:g.48123234A>T		444.0	0.0		518.0	110.0	NM_005635	A3KN76|Q08AJ2|Q5JQ64	Silent	SNP	ENST00000376919.3	hg19	CCDS14290.1																																																																																			.	.		0.428	SSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056485.1	NM_005635		T	48123234	A	T	48123234	2	4	163	1	0	0	0	0	0	0	0	1	15218	175	7	4		4	SSX1	23	48123234	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	4466853	48123234	107147326	300	25082										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53619443	53619443	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cctcttctcctcgagaccccTccttctccttgcttagtctc	4	19	4	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:53619443T>A	ENST00000342160.3	-	32	4344	c.3887A>T	c.(3886-3888)gAg>gTg	p.E1296V	HUWE1_ENST00000262854.6_Missense_Mutation_p.E1296V|HUWE1_ENST00000218328.8_Missense_Mutation_p.E1296V			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	1296					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TCGAGACCCCTCCTTCTCCTT	0.542																																					p.E1296V		Atlas-SNP	.											.	HUWE1	724	.	0			c.A3887T						.						236	186	203					X																	53619443		2203	4300	6503	SO:0001583	missense	10075	exon33			GACCCCTCCTTCT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.3887A>T	chrX.hg19:g.53619443T>A	ENSP00000340648:p.Glu1296Val	66.0	0.0		62.0	12.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.171325	0.57584	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328	T;T;T	0.49720	1.11;1.11;0.77	5.88	5.88	0.94601	UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.37376	0.1001	L	0.28115	0.83	0.80722	D	1	B;B	0.29432	0.192;0.244	B;B	0.28991	0.061;0.097	T	0.21042	-1.0257	10	0.45353	T	0.12	.	14.1505	0.65381	0.0:0.0:0.0:1.0	.	1296;1296	Q7Z6Z7;Q7Z6Z7-2	HUWE1_HUMAN;.	V	1296	ENSP00000340648:E1296V;ENSP00000262854:E1296V;ENSP00000218328:E1296V	ENSP00000218328:E1296V	E	-	2	0	HUWE1	53636168	1.000000	0.71417	0.996000	0.52242	0.811000	0.45836	7.286000	0.78671	1.987000	0.57996	0.486000	0.48141	GAG	.	.		0.542	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		A	53619443	T	A	53619443	3	1	163	1	0	0	0	0	1	0	0	0	7470	1551	54	4	9445	4	HUWE1	23	53619443	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	5496209	53619443	101651117	301	25083										
TRO	7216	hgsc.bcm.edu	37	chrX	54956640	54956640	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	accagcctctgctttggcagTgcatctaatactaacctatg	7	12	2	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:54956640T>C	ENST00000173898.7	+	12	3595	c.3483T>C	c.(3481-3483)agT>agC	p.S1161S	TRO_ENST00000399736.1_Intron|TRO_ENST00000319167.8_Intron|TRO_ENST00000375022.4_Intron|TRO_ENST00000375041.2_Silent_p.S764S|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000420798.2_Silent_p.S692S	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	1161	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						GCTTTGGCAGTGCATCTAATA	0.552																																					p.S1161S		Atlas-SNP	.											.	TRO	246	.	0			c.T3483C						.						78	76	76					X																	54956640		2012	4166	6178	SO:0001819	synonymous_variant	7216	exon12			TGGCAGTGCATCT	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.3483T>C	chrX.hg19:g.54956640T>C		101.0	0.0		93.0	28.0	NM_001039705	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Silent	SNP	ENST00000173898.7	hg19	CCDS43959.1																																																																																			.	.		0.552	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		C	54956640	T	C	54956640	2	2	163	1	0	0	0	0	0	0	0	1	16589	1693	59	2		2	TRO	23	54956640	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	1337197	54956640	100313920	302	25084										
TEX11	56159	hgsc.bcm.edu	37	chrX	69749740	69749740	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ggttaaggaaacgcaaggccAggccacaccacttttcagca	10	12	1	0			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:69749740A>C	ENST00000395889.2	-	30	2830	c.2675T>G	c.(2674-2676)cTg>cGg	p.L892R	TEX11_ENST00000374320.2_Missense_Mutation_p.L567R|TEX11_ENST00000374333.2_Missense_Mutation_p.L877R|TEX11_ENST00000344304.3_Missense_Mutation_p.L892R	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	892					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					ACGCAAGGCCAGGCCACACCA	0.502																																					p.L892R		Atlas-SNP	.											.	TEX11	132	.	0			c.T2675G						.						125	90	102					X																	69749740		2203	4300	6503	SO:0001583	missense	56159	exon30			AAGGCCAGGCCAC	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.2675T>G	chrX.hg19:g.69749740A>C	ENSP00000379226:p.Leu892Arg	76.0	0.0		89.0	18.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	hg19	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.782625	0.31502	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	T;T;T;T	0.52057	1.28;1.29;0.68;1.29	4.33	4.33	0.51752	.	0.103897	0.38959	U	0.001513	T	0.58963	0.2159	L	0.52573	1.65	0.09310	N	1	D;D	0.71674	0.998;0.997	D;D	0.73708	0.981;0.957	T	0.49872	-0.8893	9	.	.	.	-1.0835	10.4751	0.44659	1.0:0.0:0.0:0.0	.	877;892	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	R	877;892;567;892	ENSP00000363453:L877R;ENSP00000379226:L892R;ENSP00000363440:L567R;ENSP00000340995:L892R	.	L	-	2	0	TEX11	69666465	0.994000	0.37717	0.001000	0.08648	0.156000	0.22039	7.469000	0.80959	1.592000	0.50018	0.407000	0.27541	CTG	.	.		0.502	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			C	69749740	A	C	69749740	3	2	163	1	0	0	0	0	1	0	0	0	15789	188	7	5	155	5	TEX11	23	69749740	Missense_Mutation	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	14793100	69749740	85520820	303	25085										
TEX11	56159	hgsc.bcm.edu	37	chrX	69964041	69964041	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ttctggcccagtagatttctTatccatcttcccaatatcat	4	12	4	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:69964041T>C	ENST00000395889.2	-	11	921	c.766A>G	c.(766-768)Aag>Gag	p.K256E	TEX11_ENST00000374333.2_Missense_Mutation_p.K241E|TEX11_ENST00000344304.3_Missense_Mutation_p.K256E	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	256					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					GTAGATTTCTTATCCATCTTC	0.234																																					p.K256E		Atlas-SNP	.											.	TEX11	132	.	0			c.A766G						.						45	39	41					X																	69964041		2203	4289	6492	SO:0001583	missense	56159	exon11			ATTTCTTATCCAT	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.766A>G	chrX.hg19:g.69964041T>C	ENSP00000379226:p.Lys256Glu	454.0	0.0		627.0	121.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	hg19	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.495590	0.44352	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000344304	T;T;T	0.62498	0.02;0.02;0.02	3.66	-0.173	0.13322	Tetratricopeptide-like helical (1);	0.486384	0.20341	N	0.094226	T	0.51975	0.1706	L	0.40543	1.245	0.09310	N	1	P;P	0.48089	0.884;0.905	B;P	0.47941	0.426;0.562	T	0.45848	-0.9233	9	.	.	.	0.1503	5.9338	0.19154	0.0:0.3521:0.0:0.6479	.	241;256	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	E	241;256;256	ENSP00000363453:K241E;ENSP00000379226:K256E;ENSP00000340995:K256E	.	K	-	1	0	TEX11	69880766	0.790000	0.28787	0.006000	0.13384	0.395000	0.30598	1.087000	0.30865	-0.331000	0.08501	-0.456000	0.05471	AAG	.	.		0.234	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			C	69964041	T	C	69964041	3	2	163	1	0	0	0	0	1	0	0	0	15789	1763	61	2	2140	2	TEX11	23	69964041	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	214301	69964041	85306519	304	25086										
IL2RG	3561	hgsc.bcm.edu	37	chrX	70330769	70330769	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	ataatgcagagtgaggttggTaggctggggctcagagctgc	17	6	1	3			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:70330769T>A	ENST00000374202.2	-	2	338	c.247A>T	c.(247-249)Acc>Tcc	p.T83S	IL2RG_ENST00000456850.2_Intron|IL2RG_ENST00000374188.3_5'Flank	NM_000206.2	NP_000197.1	P31785	IL2RG_HUMAN	interleukin 2 receptor, gamma	83					immune response (GO:0006955)|interleukin-2-mediated signaling pathway (GO:0038110)|interleukin-4-mediated signaling pathway (GO:0035771)|interleukin-7-mediated signaling pathway (GO:0038111)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|interleukin-2 binding (GO:0019976)			breast(1)|endometrium(3)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	15	Renal(35;0.156)				Aldesleukin(DB00041)|Denileukin diftitox(DB00004)	GTGAGGTTGGTAGGCTGGGGC	0.522									Severe Combined Immunodeficiency, X-linked																												p.T83S		Atlas-SNP	.											.	IL2RG	96	.	0			c.A247T						.						75	55	62					X																	70330769		2203	4300	6503	SO:0001583	missense	3561	exon2	Familial Cancer Database	Agammaglobulinemia, Swiss Type	GGTTGGTAGGCTG	D11086	CCDS14406.1	Xq13	2014-09-17	2010-06-24		ENSG00000147168	ENSG00000147168		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6010	protein-coding gene	gene with protein product		308380	"severe combined immunodeficiency", "combined immunodeficiency, X-linked"	SCIDX1, IMD4, CIDX		1631559, 7883965	Standard	NM_000206		Approved	CD132	uc004dyw.2	P31785	OTTHUMG00000021787	ENST00000374202.2:c.247A>T	chrX.hg19:g.70330769T>A	ENSP00000363318:p.Thr83Ser	149.0	0.0		171.0	42.0	NM_000206	Q5FC12	Missense_Mutation	SNP	ENST00000374202.2	hg19	CCDS14406.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.247801	0.39697	.	.	ENSG00000147168	ENST00000374202;ENST00000374191;ENST00000464642;ENST00000487883;ENST00000473378	D;D;D;D	0.97906	-4.6;-4.6;-4.6;-4.6	5.43	5.43	0.79202	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.597865	0.18482	N	0.139913	D	0.95815	0.8638	M	0.69823	2.125	0.80722	D	1	B	0.22080	0.064	B	0.21917	0.037	D	0.92475	0.5988	10	0.30078	T	0.28	-2.9811	6.3582	0.21412	0.0:0.1111:0.0:0.8889	.	83	P31785	IL2RG_HUMAN	S	83;83;39;71;62	ENSP00000363318:T83S;ENSP00000425233:T39S;ENSP00000423966:T71S;ENSP00000423601:T62S	ENSP00000363306:T83S	T	-	1	0	IL2RG	70247494	0.975000	0.34042	0.998000	0.56505	0.866000	0.49608	1.836000	0.39191	2.006000	0.58801	0.486000	0.48141	ACC	.	.		0.522	IL2RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057102.2			A	70330769	T	A	70330769	3	1	163	1	0	0	0	0	1	0	0	0	7697	1638	57	4	890	4	IL2RG	23	70330769	Missense_Mutation	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	366728	70330769	84939791	305	25087										
CXCR3	2833	hgsc.bcm.edu	37	chrX	70836820	70836820	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agccaggcaggtgagggtcaCgcgggccgggggcccccggc	20	14	1	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:70836820C>T	ENST00000373693.3	-	2	569	c.502G>A	c.(502-504)Gtg>Atg	p.V168M	CXCR3_ENST00000373691.4_Missense_Mutation_p.V215M	NM_001504.1	NP_001495.1	P49682	CXCR3_HUMAN	chemokine (C-X-C motif) receptor 3	168					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|calcium-mediated signaling (GO:0019722)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|chemokine (C-C motif) ligand 11 production (GO:0071954)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of leukocyte migration (GO:0002685)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|chemokine binding (GO:0019956)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(2)|lung(3)|ovary(2)	10	Renal(35;0.156)					GTGAGGGTCAcgcgggccggg	0.657																																					p.V215M		Atlas-SNP	.											.	CXCR3	57	.	0			c.G643A						.						25	27	27					X																	70836820		2192	4287	6479	SO:0001583	missense	2833	exon2			GGGTCACGCGGGC	U32674	CCDS14416.1, CCDS48135.1	Xq13	2012-08-08	2002-08-22	2002-08-23	ENSG00000186810	ENSG00000186810		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	4540	protein-coding gene	gene with protein product		300574	"G protein-coupled receptor 9"	GPR9		8666380, 9064356	Standard	NM_001142797		Approved	CKR-L2, CMKAR3, IP10-R, MigR, CD183	uc011mpx.2	P49682	OTTHUMG00000033326	ENST00000373693.3:c.502G>A	chrX.hg19:g.70836820C>T	ENSP00000362797:p.Val168Met	248.0	0.0		254.0	61.0	NM_001142797	B2R982|O15185|Q7Z710|Q9P2T4|Q9P2T5	Missense_Mutation	SNP	ENST00000373693.3	hg19	CCDS14416.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.926058	0.34002	.	.	ENSG00000186810	ENST00000373691;ENST00000373693;ENST00000373687	T;T	0.39056	1.1;1.1	5.34	5.34	0.76211	GPCR, rhodopsin-like superfamily (1);	0.071575	0.53938	D	0.000045	T	0.54481	0.1861	L	0.46947	1.48	0.37781	D	0.927028	D;D	0.89917	1.0;1.0	D;D	0.83275	0.962;0.996	T	0.57940	-0.7724	10	0.46703	T	0.11	.	10.2579	0.43408	0.1966:0.8034:0.0:0.0	.	215;168	P49682-2;P49682	.;CXCR3_HUMAN	M	215;168;168	ENSP00000362795:V215M;ENSP00000362797:V168M	ENSP00000362791:V168M	V	-	1	0	CXCR3	70753545	0.000000	0.05858	0.653000	0.29593	0.010000	0.07245	0.235000	0.17948	2.472000	0.83506	0.538000	0.68166	GTG	.	.		0.657	CXCR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144141.1			T	70836820	C	T	70836820	3	4	163	1	0	0	0	0	1	0	0	0	4094	536	19	1	608	1	CXCR3	23	70836820	Missense_Mutation	SNP	C	TCGA-DD-AACL-01A-11D-A40R-10	506051	70836820	84433740	306	25088										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91132904	91132904	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	cccttaaccagcaatgtcacAgtctttgtaagcattattga	6	10	2	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:91132904A>T	ENST00000373094.1	+	2	2510	c.1665A>T	c.(1663-1665)acA>acT	p.T555T	PCDH11X_ENST00000504220.2_Silent_p.T555T|PCDH11X_ENST00000406881.1_Silent_p.T555T|PCDH11X_ENST00000395337.2_Silent_p.T555T|PCDH11X_ENST00000373097.1_Silent_p.T555T|PCDH11X_ENST00000361655.2_Silent_p.T555T|PCDH11X_ENST00000298274.8_Silent_p.T555T|PCDH11X_ENST00000361724.1_Silent_p.T555T|PCDH11X_ENST00000373088.1_Silent_p.T555T	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	555	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						GCAATGTCACAGTCTTTGTAA	0.378																																					p.T555T	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.A1665T						.						81	78	79					X																	91132904		2202	4298	6500	SO:0001819	synonymous_variant	27328	exon2			TGTCACAGTCTTT	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.1665A>T	chrX.hg19:g.91132904A>T		268.0	0.0		324.0	86.0	NM_001168363	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Silent	SNP	ENST00000373094.1	hg19	CCDS14461.1																																																																																			.	.		0.378	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		T	91132904	A	T	91132904	2	4	163	1	0	0	0	0	0	0	0	1	11517	175	7	4		4	PCDH11X	23	91132904	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	20296084	91132904	64137656	307	25089										
DCX	1641	hgsc.bcm.edu	37	chrX	110644314	110644314	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	acttgctcaaaagagtgggcTgtcttcttgttcagaagcac	10	9	4	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:110644314T>A	ENST00000338081.3	-	3	1023	c.852A>T	c.(850-852)acA>acT	p.T284T	DCX_ENST00000356915.2_Silent_p.T203T|DCX_ENST00000488120.1_Silent_p.T203T|DCX_ENST00000356220.3_Silent_p.T203T|DCX_ENST00000496551.1_5'UTR|DCX_ENST00000371993.2_Silent_p.T203T	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	284	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.		T -> A (in SBHX). {ECO:0000269|PubMed:11175293}.|T -> R (in LISX1 and SBHX). {ECO:0000269|PubMed:11175293, ECO:0000269|PubMed:9489700}.		axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						AAGAGTGGGCTGTCTTCTTGT	0.517																																					p.T284T		Atlas-SNP	.											.	DCX	158	.	0			c.A852T						.						124	112	116					X																	110644314		2203	4300	6503	SO:0001819	synonymous_variant	1641	exon3			GTGGGCTGTCTTC	AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"doublecortex"	300121	"doublecortex; lissencephaly, X-linked (doublecortin)"			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.852A>T	chrX.hg19:g.110644314T>A		114.0	0.0		137.0	28.0	NM_000555	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Silent	SNP	ENST00000338081.3	hg19	CCDS14556.1	.	.	.	.	.	.	.	.	.	.	T	10.30	1.311170	0.23821	.	.	ENSG00000077279	ENST00000358070	.	.	.	4.74	-2.91	0.05631	.	.	.	.	.	T	0.36082	0.0954	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33727	-0.9857	4	.	.	.	.	0.0629	0.00016	0.3002:0.2271:0.1777:0.295	.	.	.	.	L	276	.	.	Q	-	2	0	DCX	110530970	0.000000	0.05858	0.989000	0.46669	0.991000	0.79684	-2.222000	0.01215	-0.372000	0.07992	0.486000	0.48141	CAG	.	.		0.517	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153		A	110644314	T	A	110644314	2	1	163	1	0	0	0	0	0	0	0	1	4320	1567	55	4		4	DCX	23	110644314	Silent	SNP	T	TCGA-DD-AACL-01A-11D-A40R-10	19511410	110644314	44626246	308	25090										
ZNF75D	7626	hgsc.bcm.edu	37	chrX	134425482	134425482	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	agggctaacatctgttgatcAtgcacagctgtgggtagaaa	12	7	2	2			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:134425482A>G	ENST00000370766.3	-	5	3321	c.612T>C	c.(610-612)caT>caC	p.H204H	ZNF75D_ENST00000370764.1_Intron|ZNF75D_ENST00000494295.1_Intron	NM_007131.3	NP_009062.2	P51815	ZN75D_HUMAN	zinc finger protein 75D	204					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						TCTGTTGATCATGCACAGCTG	0.408																																					p.H204H		Atlas-SNP	.											.	ZNF75D	65	.	0			c.T612C						.						110	86	94					X																	134425482		2203	4300	6503	SO:0001819	synonymous_variant	7626	exon4			TTGATCATGCACA	S43109	CCDS14648.1, CCDS55503.1	Xq26	2013-01-09	2008-06-11	2008-06-11	ENSG00000186376	ENSG00000186376		"Zinc fingers, C2H2-type", "-", "-", "-"	13145	protein-coding gene	gene with protein product		314997	"zinc finger protein 75 (D8C6)"	ZNF82, ZNF75		1505955	Standard	XM_005262469		Approved	ZKSCAN24, D8C6, ZSCAN28	uc004eyo.3	P51815	OTTHUMG00000022482	ENST00000370766.3:c.612T>C	chrX.hg19:g.134425482A>G		133.0	0.0		180.0	45.0	NM_007131	A6NK62|B3KRI7|Q5JPG0|Q6LDE0	Silent	SNP	ENST00000370766.3	hg19	CCDS14648.1																																																																																			.	.		0.408	ZNF75D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058415.1	NM_007131		G	134425482	A	G	134425482	2	3	163	1	0	0	0	0	0	0	0	1	18149	214	8	2		2	ZNF75D	23	134425482	Silent	SNP	A	TCGA-DD-AACL-01A-11D-A40R-10	23781168	134425482	20845078	309	25091										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153042749	153042749	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0129449838187702	4	1	0.691339307469475	0.619324796274738	0.719215892448083	0.569230769230769	1	0	aggagccagaaggggccaagGtgcggtgcagcagcctgcgg	19	10	0	1			TCGA-DD-AACL-01A-11D-A40R-10	TCGA-DD-AACL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2b9cdb07-82ec-42bb-9de0-6329a096b64a	799314ef-97a0-4db6-ac6c-f820a0294be9	g.chrX:153042749G>T	ENST00000361971.5	+	30	5128	c.5014G>T	c.(5014-5016)Gtg>Ttg	p.V1672L	SRPK3_ENST00000489426.1_5'UTR|PLXNB3_ENST00000538776.1_Missense_Mutation_p.V1325L|PLXNB3_ENST00000538966.1_Missense_Mutation_p.V1695L|PLXNB3_ENST00000485980.1_3'UTR	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1672					axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					AGGGGCCAAGGTGCGGTGCAG	0.657																																					p.V1695L		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G5083T						.						38	26	30					X																	153042749		2191	4292	6483	SO:0001583	missense	5365	exon31			GCCAAGGTGCGGT	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.5014G>T	chrX.hg19:g.153042749G>T	ENSP00000355378:p.Val1672Leu	110.0	0.0		156.0	29.0	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	7.481	0.648744	0.14516	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776	T;T;T	0.11277	2.79;2.79;2.79	4.99	4.12	0.48240	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.552403	0.20624	N	0.088718	T	0.05823	0.0152	N	0.08118	0	0.80722	D	1	B;B;B	0.20368	0.044;0.035;0.044	B;B;B	0.29524	0.065;0.062;0.103	T	0.37911	-0.9685	10	0.28530	T	0.3	.	6.7321	0.23388	0.1189:0.4766:0.4045:0.0	.	1325;1695;1672	B7Z3H9;F5H773;Q9ULL4	.;.;PLXB3_HUMAN	L	1695;1672;1325	ENSP00000442736:V1695L;ENSP00000355378:V1672L;ENSP00000445569:V1325L	ENSP00000355378:V1672L	V	+	1	0	PLXNB3	152695943	1.000000	0.71417	0.043000	0.18650	0.064000	0.16182	3.604000	0.54081	0.995000	0.38917	0.529000	0.55759	GTG	.	.		0.657	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			T	153042749	G	T	153042749	3	4	163	1	0	0	0	0	1	0	0	0	12134	1261	44	3	5246	3	PLXNB3	23	153042749	Missense_Mutation	SNP	G	TCGA-DD-AACL-01A-11D-A40R-10	18617267	153042749	2227811	310	25092										
PADI3	51702	hgsc.bcm.edu	37	chr1	17586148	17586148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	atctacatctctcccaacatGgagaggggccgggagcgtgc	13	12	2	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr1:17586148G>A	ENST00000375460.3	+	2	208	c.168G>A	c.(166-168)atG>atA	p.M56I		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	56					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CTCCCAACATGGAGAGGGGCC	0.592																																					p.M56I		Atlas-SNP	.											.	PADI3	81	.	0			c.G168A						.						79	77	78					1																	17586148		2203	4300	6503	SO:0001583	missense	51702	exon2			CAACATGGAGAGG	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"Peptidyl arginine deiminases"	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.168G>A	chr1.hg19:g.17586148G>A	ENSP00000364609:p.Met56Ile	178.0	0.0		177.0	66.0	NM_016233	Q58EY7|Q70SX5	Missense_Mutation	SNP	ENST00000375460.3	hg19	CCDS179.1	.	.	.	.	.	.	.	.	.	.	G	1.357	-0.589924	0.03799	.	.	ENSG00000142619	ENST00000375460	T	0.07216	3.21	5.2	3.26	0.37387	Cupredoxin (1);Protein-arginine deiminase (PAD) N-terminal (1);	0.863636	0.10280	N	0.693602	T	0.06142	0.0159	N	0.22421	0.69	0.09310	N	1	B	0.11235	0.004	B	0.15870	0.014	T	0.45116	-0.9283	10	0.22109	T	0.4	-9.4176	7.5265	0.27658	0.0869:0.3131:0.6:0.0	.	56	Q9ULW8	PADI3_HUMAN	I	56	ENSP00000364609:M56I	ENSP00000364609:M56I	M	+	3	0	PADI3	17458735	0.002000	0.14202	0.224000	0.23877	0.052000	0.14988	1.142000	0.31540	0.536000	0.28733	0.563000	0.77884	ATG	.	.		0.592	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1			A	17586148	G	A	17586148	3	1	164	1	0	0	0	0	1	0	0	0	11388	1348	47	3	174	3	PADI3	1	17586148	Missense_Mutation	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10		17586148	231664473	1	25093										
SF3B4	10262	hgsc.bcm.edu	37	chr1	149895819	149895819	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ttccaggtggtggtcggggcGgtggctggcccccagagcct	18	12	0	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr1:149895819G>C	ENST00000271628.8	-	5	1585	c.1001C>G	c.(1000-1002)cCg>cGg	p.P334R		NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	334					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)	17	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			TGGTCGGGGCGGTGGCTGGCC	0.612																																					p.P334R		Atlas-SNP	.											.	SF3B4	37	.	0			c.C1001G						.						11	13	13					1																	149895819		2193	4291	6484	SO:0001583	missense	10262	exon5			CGGGGCGGTGGCT	L35013	CCDS72900.1	1q21.2	2013-02-12	2002-08-29		ENSG00000143368	ENSG00000143368		"RNA binding motif (RRM) containing"	10771	protein-coding gene	gene with protein product		605593	"splicing factor 3b, subunit 4, 49kD"			7958871	Standard	NM_005850		Approved	SAP49, SF3b49, Hsh49	uc001etk.2	Q15427	OTTHUMG00000012208	ENST00000271628.8:c.1001C>G	chr1.hg19:g.149895819G>C	ENSP00000271628:p.Pro334Arg	206.0	0.0		245.0	67.0	NM_005850	Q5SZ63	Missense_Mutation	SNP	ENST00000271628.8	hg19	CCDS941.1	.	.	.	.	.	.	.	.	.	.	G	13.25	2.181125	0.38511	.	.	ENSG00000143368	ENST00000271628	T	0.26067	1.76	5.1	5.1	0.69264	.	0.327890	0.35585	N	0.003112	T	0.18882	0.0453	M	0.64997	1.995	0.51482	D	0.999927	P	0.35033	0.481	B	0.32090	0.14	T	0.05162	-1.0902	10	0.66056	D	0.02	.	17.2581	0.87063	0.0:0.0:1.0:0.0	.	334	Q15427	SF3B4_HUMAN	R	334	ENSP00000271628:P334R	ENSP00000271628:P334R	P	-	2	0	SF3B4	148162443	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	8.396000	0.90190	2.653000	0.90120	0.650000	0.86243	CCG	.	.		0.612	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033753.1	NM_005850		C	149895819	G	C	149895819	3	2	164	1	0	0	0	0	1	0	0	0	14168	1116	39	4	281	4	SF3B4	1	149895819	Missense_Mutation	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10	132309671	149895819	99354802	2	25094										
CD247	919	hgsc.bcm.edu	37	chr1	167407853	167407853	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ggccacgtctcttgtccaaaAcatcgtactcctctcttcgt	6	15	2	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr1:167407853A>G	ENST00000362089.5	-	4	326	c.254T>C	c.(253-255)gTt>gCt	p.V85A	CD247_ENST00000483825.1_5'UTR|CD247_ENST00000392122.3_Missense_Mutation_p.V85A			P20963	CD3Z_HUMAN	CD247 molecule	85	ITAM 1. {ECO:0000255|PROSITE- ProRule:PRU00379}.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)	6			LUSC - Lung squamous cell carcinoma(543;0.236)		Muromonab(DB00075)	CTTGTCCAAAACATCGTACTC	0.552																																					p.V85A	Ovarian(192;1815 2869 36877 43334)	Atlas-SNP	.											.	CD247	25	.	0			c.T254C						.						149	141	144					1																	167407853		2203	4300	6503	SO:0001583	missense	919	exon4			TCCAAAACATCGT	BC025703	CCDS1260.1, CCDS1261.1	1q24.2	2014-09-17	2006-03-28	2006-03-09	ENSG00000198821	ENSG00000198821		"CD molecules"	1677	protein-coding gene	gene with protein product		186780	"CD3z antigen, zeta polypeptide (TiT3 complex)", "CD247 antigen"	CD3Z		2974162	Standard	NM_198053		Approved	CD3H, CD3Q	uc001gei.4	P20963	OTTHUMG00000034593	ENST00000362089.5:c.254T>C	chr1.hg19:g.167407853A>G	ENSP00000354782:p.Val85Ala	119.0	0.0		145.0	38.0	NM_198053	B1AK49|Q5VX13|Q8TAX4	Missense_Mutation	SNP	ENST00000362089.5	hg19	CCDS1261.1	.	.	.	.	.	.	.	.	.	.	A	10.06	1.245866	0.22796	.	.	ENSG00000198821	ENST00000392122;ENST00000362089	T;T	0.42513	0.97;0.97	4.52	4.52	0.55395	.	0.595996	0.12974	U	0.423873	T	0.25344	0.0616	L	0.50333	1.59	0.33143	D	0.544638	P;B;B	0.40000	0.698;0.079;0.097	P;B;B	0.46659	0.523;0.046;0.076	T	0.05338	-1.0891	9	0.07813	T	0.8	.	11.3298	0.49468	1.0:0.0:0.0:0.0	.	85;85;85	Q6KAV0;P20963-3;P20963	.;.;CD3Z_HUMAN	A	85	ENSP00000375969:V85A;ENSP00000354782:V85A	ENSP00000354782:V85A	V	-	2	0	CD247	165674477	0.056000	0.20664	0.012000	0.15200	0.971000	0.66376	2.808000	0.47963	1.885000	0.54596	0.460000	0.39030	GTT	.	.		0.552	CD247-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083707.1	NM_198053		G	167407853	A	G	167407853	3	3	164	1	0	0	0	0	1	0	0	0	2990	43	2	2	260	2	CD247	1	167407853	Missense_Mutation	SNP	A	TCGA-DD-AACM-01A-11D-A40R-10	17512034	167407853	81842768	3	25095										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54786000	54786000	+	Intron	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	cttacaactacaaccagctgGaaggcagattcaagcagctg	9	11	1	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr2:54786000G>A	ENST00000356805.4	+	2	429				SPTBN1_ENST00000333896.5_Missense_Mutation_p.E29K	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1						actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CAACCAGCTGGAAGGCAGATT	0.587																																					p.E29K		Atlas-SNP	.											.	SPTBN1	378	.	0			c.G85A						.						67	70	69					2																	54786000		2203	4300	6503	SO:0001627	intron_variant	6711	exon1			CAGCTGGAAGGCA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.148+32297G>A	chr2.hg19:g.54786000G>A		574.0	0.0		525.0	150.0	NM_178313	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.079815	0.76528	.	.	ENSG00000115306	ENST00000333896	D	0.95447	-3.71	5.42	5.42	0.78866	.	.	.	.	.	D	0.93973	0.8070	.	.	.	0.33083	D	0.536881	B	0.21606	0.058	B	0.22601	0.04	D	0.93773	0.7077	8	0.87932	D	0	.	19.2114	0.93757	0.0:0.0:1.0:0.0	.	29	Q01082-3	.	K	29	ENSP00000334156:E29K	ENSP00000334156:E29K	E	+	1	0	SPTBN1	54639504	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.843000	0.75384	2.537000	0.85549	0.561000	0.74099	GAA	.	.		0.587	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			A	54786000	G	A	54786000	1	1	164	0	1	0	0	0	0	0	0	0	15134	1175	41	3		3	SPTBN1	2	54786000	Intron	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10		54786000	188413373	4	25096										
FER1L5	90342	hgsc.bcm.edu	37	chr2	97354959	97354959	+	RNA	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ccctcccctagtatgagaatCaggccaagtataaagaccag	8	12	1	2			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr2:97354959C>A	ENST00000457909.1	+	0	830							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						GTATGAGAATCAGGCCAAGTA	0.607																																					p.Q786K		Atlas-SNP	.											.	FER1L5	113	.	0			c.C2356A						.						49	53	51					2																	97354959		692	1591	2283			90342	exon24			GAGAATCAGGCCA	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		chr2.hg19:g.97354959C>A		285.0	0.0		237.0	75.0	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.69	2.312189	0.40895	.	.	ENSG00000214272	ENST00000414152;ENST00000436930	.	.	.	4.83	0.546	0.17196	.	.	.	.	.	T	0.62011	0.2393	M	0.82823	2.61	.	.	.	D	0.54397	0.966	B	0.41860	0.368	T	0.78360	-0.2234	7	0.87932	D	0	-14.2635	16.9881	0.86346	0.0:0.4294:0.5706:0.0	.	786	A0AVI2	FR1L5_HUMAN	K	786;776	.	ENSP00000444148:Q786K	Q	+	1	0	FER1L5	96718686	1.000000	0.71417	0.996000	0.52242	0.917000	0.54804	2.464000	0.45067	-0.017000	0.14103	0.551000	0.68910	CAG	.	.		0.607	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		A	97354959	C	A	97354959	1	1	164	0	1	0	0	0	0	0	0	0	5822	827	29	3		3	FER1L5	2	97354959	RNA	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	42568959	97354959	145844414	5	25097										
PDCL3	79031	hgsc.bcm.edu	37	chr2	101192856	101192856	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gaatctggagcaattatgacAgacctggaggaaaaccctaa	10	8	1	2			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr2:101192856A>G	ENST00000264254.6	+	6	996	c.618A>G	c.(616-618)acA>acG	p.T206T	snoU13_ENST00000458824.1_RNA	NM_024065.4	NP_076970.1	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	206	Thioredoxin fold. {ECO:0000250}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|protein folding (GO:0006457)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|viral process (GO:0016032)	cytoplasm (GO:0005737)	protein binding involved in protein folding (GO:0044183)			endometrium(3)|large_intestine(2)|liver(1)|lung(6)	12						CAATTATGACAGACCTGGAGG	0.498																																					p.T206T		Atlas-SNP	.											.	PDCL3	27	.	0			c.A618G						.						100	90	93					2																	101192856		2203	4300	6503	SO:0001819	synonymous_variant	79031	exon6			TATGACAGACCTG	AF267853	CCDS33261.1	2q12	2008-02-05			ENSG00000115539	ENSG00000115539			28860	protein-coding gene	gene with protein product		611678					Standard	NM_024065		Approved	VIAF1	uc002tao.2	Q9H2J4	OTTHUMG00000153141	ENST00000264254.6:c.618A>G	chr2.hg19:g.101192856A>G		77.0	0.0		83.0	12.0	NM_024065	B2RA00|Q53S68	Silent	SNP	ENST00000264254.6	hg19	CCDS33261.1																																																																																			.	.		0.498	PDCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329734.1	NM_024065		G	101192856	A	G	101192856	2	3	164	1	0	0	0	0	0	0	0	1	11637	175	7	2		2	PDCL3	2	101192856	Silent	SNP	A	TCGA-DD-AACM-01A-11D-A40R-10	3837897	101192856	142006517	6	25098										
TMEM43	79188	hgsc.bcm.edu	37	chr3	14174384	14174384	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	agacactgaatggaggtcagAaatcatcaacagcaaaaact	8	8	3	3			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr3:14174384A>G	ENST00000306077.4	+	6	715	c.461A>G	c.(460-462)gAa>gGa	p.E154G	RP11-434D12.1_ENST00000608606.1_5'Flank	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	154					nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						TGGAGGTCAGAAATCATCAAC	0.567																																					p.E154G		Atlas-SNP	.											.	TMEM43	33	.	0			c.A461G						.						88	90	90					3																	14174384		2203	4300	6503	SO:0001583	missense	79188	exon6			GGTCAGAAATCAT	BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"arrhythmogenic right ventricular dysplasia 5"	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.461A>G	chr3.hg19:g.14174384A>G	ENSP00000303992:p.Glu154Gly	183.0	0.0		185.0	54.0	NM_024334	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	hg19	CCDS2618.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.628012	0.87560	.	.	ENSG00000170876	ENST00000306077	T	0.37752	1.18	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.20861	0.0502	N	0.04018	-0.295	0.80722	D	1	P;P	0.51147	0.942;0.557	B;B	0.43728	0.419;0.429	T	0.08391	-1.0724	10	0.23891	T	0.37	-12.4724	14.8499	0.70289	1.0:0.0:0.0:0.0	.	84;154	Q8TEP9;Q9BTV4	.;TMM43_HUMAN	G	154	ENSP00000303992:E154G	ENSP00000303992:E154G	E	+	2	0	TMEM43	14149385	1.000000	0.71417	0.949000	0.38748	0.942000	0.58702	8.962000	0.93254	1.900000	0.55004	0.482000	0.46254	GAA	.	.		0.567	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334		G	14174384	A	G	14174384	3	3	164	1	0	0	0	0	1	0	0	0	16182	246	9	2	483	2	TMEM43	3	14174384	Missense_Mutation	SNP	A	TCGA-DD-AACM-01A-11D-A40R-10		14174384	183848046	7	25099										
ITIH4	3700	hgsc.bcm.edu	37	chr3	52847499	52847499	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	cccctcctggtaatccagccTgcgctctctgaaatggaaag	9	14	1	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr3:52847499T>G	ENST00000266041.4	-	24	2827	c.2731A>C	c.(2731-2733)Agg>Cgg	p.R911R	ITIH4_ENST00000406595.1_Silent_p.R881R|ITIH4_ENST00000485816.1_Silent_p.R916R|ITIH4_ENST00000346281.5_Silent_p.R895R|RP5-966M1.6_ENST00000468472.1_3'UTR	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	911					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		TAATCCAGCCTGCGCTCTCTG	0.567																																					p.R911R		Atlas-SNP	.											.	ITIH4	74	.	0			c.A2731C						.						61	68	66					3																	52847499		2203	4300	6503	SO:0001819	synonymous_variant	3700	exon24			CCAGCCTGCGCTC	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"plasma Kallikrein-sensitive glycoprotein"	600564	"inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.2731A>C	chr3.hg19:g.52847499T>G		207.0	0.0		172.0	56.0	NM_002218	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Silent	SNP	ENST00000266041.4	hg19	CCDS2865.1	.	.	.	.	.	.	.	.	.	.	T	1.323	-0.598868	0.03744	.	.	ENSG00000055955	ENST00000441637	.	.	.	4.3	3.12	0.35913	.	.	.	.	.	T	0.56746	0.2006	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51725	-0.8669	4	.	.	.	-9.7437	7.9988	0.30284	0.0:0.0:0.2074:0.7926	.	.	.	.	P	699	.	.	Q	-	2	0	ITIH4	52822539	0.982000	0.34865	0.985000	0.45067	0.154000	0.21943	1.289000	0.33307	0.957000	0.37930	0.459000	0.35465	CAG	.	.		0.567	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218		G	52847499	T	G	52847499	2	3	164	1	0	0	0	0	0	0	0	1	7915	1579	55	5		5	ITIH4	3	52847499	Silent	SNP	T	TCGA-DD-AACM-01A-11D-A40R-10	38673115	52847499	145174931	8	25100										
ABHD10	55347	hgsc.bcm.edu	37	chr3	111705759	111705759	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ttttattttattttatttttAgattcttgttggatctagcc	5	4	2	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr3:111705759A>G	ENST00000273359.3	+	4	465		c.e4-1		ABHD10_ENST00000534857.1_Splice_Site|ABHD10_ENST00000494817.1_Splice_Site	NM_018394.2	NP_060864.1	Q9NUJ1	ABHDA_HUMAN	abhydrolase domain containing 10						glucuronoside catabolic process (GO:0019391)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			large_intestine(2)|lung(7)|skin(1)	10						ttttattttTAGATTCTTGTT	0.328																																					.		Atlas-SNP	.											.	ABHD10	20	.	0			c.439-2A>G						.						55	56	56					3																	111705759		2203	4300	6503	SO:0001630	splice_region_variant	55347	exon4			ATTTTTAGATTCT	AL713726	CCDS2963.1, CCDS63718.1	3q13.2	2012-03-26			ENSG00000144827	ENSG00000144827		"Abhydrolase domain containing"	25656	protein-coding gene	gene with protein product						22294686	Standard	NM_018394		Approved	FLJ11342	uc003dyk.5	Q9NUJ1	OTTHUMG00000159280	ENST00000273359.3:c.439-1A>G	chr3.hg19:g.111705759A>G		35.0	0.0		25.0	7.0	NM_001272069	B7Z6A8|C9IZX5|D3DN63|Q8TCF9	Splice_Site	SNP	ENST00000273359.3	hg19	CCDS2963.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.335067	0.41398	.	.	ENSG00000144827	ENST00000273359;ENST00000494817	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2058	0.73177	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ABHD10	113188449	1.000000	0.71417	0.995000	0.50966	0.235000	0.25334	8.613000	0.90913	2.243000	0.73865	0.482000	0.46254	.	.	.		0.328	ABHD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354326.1	NM_018394	Intron	G	111705759	A	G	111705759	5	3	164	1	0	0	0	0	0	0	1	0	74	434	15	2	451	2	ABHD10	3	111705759	Splice_Site	SNP	A	TCGA-DD-AACM-01A-11D-A40R-10	58858260	111705759	86316671	9	25101										
CPNE4	131034	hgsc.bcm.edu	37	chr3	131388547	131388547	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ggcggtctgggtctccgctgCatagagaatttacagatact	12	9	2	2			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr3:131388547C>T	ENST00000512055.1	-	11	2779	c.653G>A	c.(652-654)tGc>tAc	p.C218Y	CPNE4_ENST00000511604.1_Missense_Mutation_p.C218Y|CPNE4_ENST00000429747.1_Missense_Mutation_p.C218Y|CPNE4_ENST00000512332.1_Missense_Mutation_p.C236Y|CPNE4_ENST00000502818.1_Missense_Mutation_p.C236Y			Q96A23	CPNE4_HUMAN	copine IV	218	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						GTCTCCGCTGCATAGAGAATT	0.388																																					p.C218Y		Atlas-SNP	.											.	CPNE4	112	.	0			c.G653A						.						93	104	100					3																	131388547		2203	4300	6503	SO:0001583	missense	131034	exon7			CCGCTGCATAGAG	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.653G>A	chr3.hg19:g.131388547C>T	ENSP00000421705:p.Cys218Tyr	69.0	0.0		51.0	13.0	NM_130808	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	hg19	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	C	19.33	3.807756	0.70797	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818	T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07	5.66	5.66	0.87406	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.75361	0.3839	H	0.95260	3.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82655	-0.0350	10	0.72032	D	0.01	-20.9926	16.6772	0.85282	0.0:1.0:0.0:0.0	.	236;218	Q96A23-2;Q96A23	.;CPNE4_HUMAN	Y	218;218;236;218;236	ENSP00000421705:C218Y;ENSP00000411904:C218Y;ENSP00000424853:C236Y;ENSP00000423811:C218Y;ENSP00000421646:C236Y	ENSP00000411904:C218Y	C	-	2	0	CPNE4	132871237	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.719000	0.68462	2.675000	0.91044	0.655000	0.94253	TGC	.	.		0.388	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808		T	131388547	C	T	131388547	3	4	164	1	0	0	0	0	1	0	0	0	3816	710	25	3	1060	3	CPNE4	3	131388547	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	19682788	131388547	66633883	10	25102										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916726	178916726	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	agtgactttagaatgcctccGtgaggctacattaataacca	8	9	0	3			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr3:178916726G>A	ENST00000263967.3	+	2	270	c.113G>A	c.(112-114)cGt>cAt	p.R38H		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	38	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.		R -> H (in CRC; likely involved in disease pathogenesis; shows an increase in lipid kinase activity; may disrupt the interaction between the PI3K-ABD domain and the N-terminal lobe of PI3K/PI4K kinase domain possibly affecting the conformation of the kinase domain).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.R38H(10)|p.R38L(2)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GAATGCCTCCGTGAGGCTACA	0.393		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.R38H	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,caecum,carcinoma,+1,16	PIK3CA	8460	.	12	Substitution - Missense(12)	endometrium(7)|large_intestine(3)|lung(2)	c.G113A						.						76	74	75					3																	178916726		1838	4082	5920	SO:0001583	missense	5290	exon2			GCCTCCGTGAGGC		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.113G>A	chr3.hg19:g.178916726G>A	ENSP00000263967:p.Arg38His	217.0	0.0		170.0	51.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.755529	0.89843	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	T;T	0.73681	-0.77;-0.77	5.44	5.44	0.79542	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	D	0.84875	0.5569	M	0.64170	1.965	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.83898	0.0288	9	.	.	.	-9.214	19.2635	0.93977	0.0:0.0:1.0:0.0	.	38	P42336	PK3CA_HUMAN	H	38	ENSP00000263967:R38H;ENSP00000417479:R38H	.	R	+	2	0	PIK3CA	180399420	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.409000	0.97331	2.547000	0.85894	0.555000	0.69702	CGT	.	.		0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178916726	G	A	178916726	3	1	164	1	0	0	0	0	1	0	0	0	11922	1145	40	1	115	1	PIK3CA	3	178916726	Missense_Mutation	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10	47528179	178916726	19105704	11	25103										
YIPF7	285525	hgsc.bcm.edu	37	chr4	44631421	44631421	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gcttcctgtgacacattaccAgaagcaaggtggctcccagg	11	12	0	2			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr4:44631421A>G	ENST00000332990.5	-	4	513	c.497T>C	c.(496-498)cTg>cCg	p.L166P	YIPF7_ENST00000415895.4_Splice_Site_p.L142P	NM_182592.2	NP_872398.2	Q8N8F6	YIPF7_HUMAN	Yip1 domain family, member 7	166						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(1)	12						ACACATTACCAGAAGCAAGGT	0.443																																					p.L166P		Atlas-SNP	.											.	YIPF7	33	.	0			c.T497C						.						64	71	69					4																	44631421		1906	4114	6020	SO:0001630	splice_region_variant	285525	exon4			ATTACCAGAAGCA	AK096895	CCDS54766.1	4p13	2008-08-07			ENSG00000177752	ENSG00000177752		"Yip1 domain family"	26825	protein-coding gene	gene with protein product							Standard	NM_182592		Approved	FLJ39576, FinGER9	uc021xnx.1	Q8N8F6	OTTHUMG00000160467	ENST00000332990.5:c.498+1T>C	chr4.hg19:g.44631421A>G		87.0	0.0		346.0	18.0	NM_182592	Q3SY21|Q3SY22	Missense_Mutation	SNP	ENST00000332990.5	hg19	CCDS54766.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914571	0.72983	.	.	ENSG00000177752	ENST00000332990	T	0.47177	0.85	5.31	5.31	0.75309	Yip1 domain (1);	0.134012	0.49305	D	0.000152	T	0.72922	0.3521	M	0.89030	3	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.78846	-0.2043	10	0.72032	D	0.01	-5.5962	14.5846	0.68315	1.0:0.0:0.0:0.0	.	166	Q8N8F6	YIPF7_HUMAN	P	166	ENSP00000332772:L166P	ENSP00000332772:L166P	L	-	2	0	YIPF7	44326178	1.000000	0.71417	1.000000	0.80357	0.698000	0.40448	9.077000	0.94016	2.217000	0.71921	0.477000	0.44152	CTG	.	.		0.443	YIPF7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_182592	Missense_Mutation	G	44631421	A	G	44631421	5	3	164	1	0	0	0	0	0	0	1	0	17498	202	7	2	357	2	YIPF7	4	44631421	Splice_Site	SNP	A	TCGA-DD-AACM-01A-11D-A40R-10		44631421	146522855	12	25104										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123275094	123275094	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	caataaccaagataacaaggCgtcgccatgaaaatccaccc	6	13	0	2			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr4:123275094C>T	ENST00000264501.4	+	82	14600	c.14227C>T	c.(14227-14229)Cgt>Tgt	p.R4743C	KIAA1109_ENST00000388738.3_Missense_Mutation_p.R4743C			Q2LD37	K1109_HUMAN	KIAA1109	4743					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R4743C(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GATAACAAGGCGTCGCCATGA	0.393																																					p.R4743C		Atlas-SNP	.											KIAA1109,colon,carcinoma,0,3	KIAA1109	424	.	1	Substitution - Missense(1)	large_intestine(1)	c.C14227T						.						94	90	92					4																	123275094		1868	4116	5984	SO:0001583	missense	84162	exon80			ACAAGGCGTCGCC	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.14227C>T	chr4.hg19:g.123275094C>T	ENSP00000264501:p.Arg4743Cys	281.0	0.0		160.0	65.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.283300	0.80803	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707;ENST00000431755	T;T;T	0.57436	0.4;0.4;0.4	6.04	6.04	0.98038	Fragile site-associated protein, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.65249	0.2673	L	0.44542	1.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.64918	-0.6294	10	0.62326	D	0.03	.	13.9184	0.63916	0.2654:0.7345:0.0:0.0	.	4742;4743	Q2LD37-4;Q2LD37	.;K1109_HUMAN	C	4743;4743;1412;344	ENSP00000264501:R4743C;ENSP00000373390:R4743C;ENSP00000410874:R1412C	ENSP00000264501:R4743C	R	+	1	0	KIAA1109	123494544	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.834000	0.55798	2.876000	0.98609	0.650000	0.86243	CGT	.	.		0.393	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123275094	C	T	123275094	3	4	164	1	0	0	0	0	1	0	0	0	8217	768	27	1	14545	1	KIAA1109	4	123275094	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	78643673	123275094	67879182	13	25105										
ELMOD2	255520	hgsc.bcm.edu	37	chr4	141464674	141464674	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gcttactgaagagtgaagctTtgaagtttcatctctataac	8	7	2	4			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr4:141464674T>C	ENST00000323570.3	+	8	802	c.670T>C	c.(670-672)Ttg>Ctg	p.L224L		NM_153702.3	NP_714913.1	Q8IZ81	ELMD2_HUMAN	ELMO/CED-12 domain containing 2	224	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				defense response to virus (GO:0051607)|phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)|regulation of defense response to virus (GO:0050688)	cytoskeleton (GO:0005856)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	7	all_hematologic(180;0.162)					GAGTGAAGCTTTGAAGTTTCA	0.338																																					p.L224L		Atlas-SNP	.											.	ELMOD2	16	.	0			c.T670C						.						108	108	108					4																	141464674		2203	4293	6496	SO:0001819	synonymous_variant	255520	exon8			GAAGCTTTGAAGT	BX648349	CCDS3752.1	4q31.1	2006-10-24	2006-01-20		ENSG00000179387	ENSG00000179387			28111	protein-coding gene	gene with protein product		610196	"ELMO domain containing 2"			16773575	Standard	NM_153702		Approved	MGC10084	uc003iik.3	Q8IZ81	OTTHUMG00000133417	ENST00000323570.3:c.670T>C	chr4.hg19:g.141464674T>C		48.0	0.0		37.0	16.0	NM_153702	B2R712|D3DNZ0	Silent	SNP	ENST00000323570.3	hg19	CCDS3752.1																																																																																			.	.		0.338	ELMOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257277.2	NM_153702		C	141464674	T	C	141464674	2	2	164	1	0	0	0	0	0	0	0	1	5071	1838	64	2		2	ELMOD2	4	141464674	Silent	SNP	T	TCGA-DD-AACM-01A-11D-A40R-10	18189580	141464674	49689602	14	25106										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183721165	183721165	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	cagtccaccacggtggtgaaCggcaggacgcgcaggttcgc	15	13	0	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr4:183721165C>T	ENST00000511685.1	+	28	7884	c.7761C>T	c.(7759-7761)aaC>aaT	p.N2587N	TENM3_ENST00000406950.2_Silent_p.N2587N			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2587					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CGGTGGTGAACGGCAGGACGC	0.692																																					p.N2587N		Atlas-SNP	.											.	.	.	.	0			c.C7761T						.						20	25	24					4																	183721165		2180	4264	6444	SO:0001819	synonymous_variant	55714	exon27			GGTGAACGGCAGG	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.7761C>T	chr4.hg19:g.183721165C>T		184.0	0.0		90.0	33.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.		0.692	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183721165	C	T	183721165	2	4	164	1	0	0	0	0	0	0	0	1	10845	535	19	1		1	ODZ3	4	183721165	Silent	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	42256491	183721165	7433111	15	25107										
ATG12	9140	hgsc.bcm.edu	37	chr5	115177201	115177201	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	cgtaagtccttcccctccagCagcaattgaagtaggaagct	9	12	0	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr5:115177201C>A	ENST00000509910.1	-	1	354	c.49G>T	c.(49-51)Gct>Tct	p.A17S	ATG12_ENST00000509598.1_5'Flank|AP3S1_ENST00000316788.7_5'UTR|ATG12_ENST00000500945.2_Missense_Mutation_p.A17S|ATG12_ENST00000274459.4_Missense_Mutation_p.A64S			O94817	ATG12_HUMAN	autophagy related 12	17					autophagic vacuole assembly (GO:0000045)|C-terminal protein lipidation (GO:0006501)|cellular response to nitrogen starvation (GO:0006995)|innate immune response (GO:0045087)|mitochondrion degradation (GO:0000422)|negative regulation of type I interferon production (GO:0032480)|nucleophagy (GO:0044804)	Atg12-Atg5-Atg16 complex (GO:0034274)|pre-autophagosomal structure membrane (GO:0034045)	Atg8 ligase activity (GO:0019776)			endometrium(2)|kidney(1)|lung(1)|prostate(1)	5		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;7.59e-08)|Epithelial(69;7.05e-07)|all cancers(49;3.11e-05)		TCCCCTCCAGCAGCAATTGAA	0.607																																					p.A17S		Atlas-SNP	.											.	ATG12	14	.	0			c.G49T						.						76	83	81					5																	115177201		2202	4300	6502	SO:0001583	missense	9140	exon1			CTCCAGCAGCAAT	AB017507	CCDS4122.1, CCDS4122.2, CCDS64222.1	5q21-q22	2014-02-12	2012-06-06	2005-09-11	ENSG00000145782	ENSG00000145782			588	protein-coding gene	gene with protein product	"APG12 autophagy 12-like"	609608	"Apg12 (autophagy 12, S. cerevisiae)-like", "APG12 autophagy 12-like (S. cerevisiae)", "ATG12 autophagy related 12 homolog (S. cerevisiae)"	APG12L		9852036	Standard	NM_004707		Approved	APG12	uc003krh.3	O94817	OTTHUMG00000128889	ENST00000509910.1:c.49G>T	chr5.hg19:g.115177201C>A	ENSP00000425107:p.Ala17Ser	143.0	0.0		129.0	33.0	NM_004707	Q6PJV2	Missense_Mutation	SNP	ENST00000509910.1	hg19	CCDS4122.2	.	.	.	.	.	.	.	.	.	.	C	14.05	2.420345	0.42918	.	.	ENSG00000145782	ENST00000274459;ENST00000509910;ENST00000500945	.	.	.	4.88	2.06	0.26882	.	0.938134	0.08865	N	0.882410	T	0.35158	0.0922	L	0.57536	1.79	0.21220	N	0.999759	P;B	0.37061	0.58;0.18	B;B	0.34722	0.188;0.037	T	0.18023	-1.0350	9	0.13853	T	0.58	-22.4913	8.0103	0.30349	0.0:0.6119:0.3035:0.0845	.	17;64	O94817;C1IDX9	ATG12_HUMAN;.	S	64;17;17	.	ENSP00000274459:A64S	A	-	1	0	ATG12	115205100	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.365000	0.20348	0.114000	0.18032	-0.176000	0.13171	GCT	.	.		0.607	ATG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250851.3	NM_004707		A	115177201	C	A	115177201	3	1	164	1	0	0	0	0	1	0	0	0	1090	710	25	3	389	3	ATG12	5	115177201	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10		115177201	65738059	16	25108										
HAND1	9421	hgsc.bcm.edu	37	chr5	153857205	153857205	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ggtgtcggccggcacgttggGgatgcactcgcgcaactccg	16	13	0	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr5:153857205G>C	ENST00000231121.2	-	1	619	c.364C>G	c.(364-366)Ccc>Gcc	p.P122A		NM_004821.2	NP_004812.1	O96004	HAND1_HUMAN	heart and neural crest derivatives expressed 1	122	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				angiogenesis (GO:0001525)|blastocyst development (GO:0001824)|cardiac left ventricle formation (GO:0003218)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cartilage morphogenesis (GO:0060536)|embryonic heart tube development (GO:0035050)|embryonic heart tube formation (GO:0003144)|heart development (GO:0007507)|heart looping (GO:0001947)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)|trophoblast giant cell differentiation (GO:0060707)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			GGCACGTTGGGGATGCACTCG	0.617																																					p.P122A		Atlas-SNP	.											.	HAND1	21	.	0			c.C364G						.						149	122	131					5																	153857205		2203	4300	6503	SO:0001583	missense	9421	exon1			CGTTGGGGATGCA	AF061756	CCDS4327.1	5q33	2013-05-21			ENSG00000113196	ENSG00000113196		"Basic helix-loop-helix proteins"	4807	protein-coding gene	gene with protein product		602406				9337404, 9931445	Standard	NM_004821		Approved	eHand, Thing1, Hxt, bHLHa27	uc003lvn.3	O96004	OTTHUMG00000130193	ENST00000231121.2:c.364C>G	chr5.hg19:g.153857205G>C	ENSP00000231121:p.Pro122Ala	92.0	0.0		84.0	25.0	NM_004821		Missense_Mutation	SNP	ENST00000231121.2	hg19	CCDS4327.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.721626	0.89298	.	.	ENSG00000113196	ENST00000231121	D	0.97328	-4.34	5.11	5.11	0.69529	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.98960	0.9646	H	0.96365	3.81	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99517	1.0957	10	0.87932	D	0	-24.9243	16.0319	0.80585	0.0:0.0:1.0:0.0	.	122	O96004	HAND1_HUMAN	A	122	ENSP00000231121:P122A	ENSP00000231121:P122A	P	-	1	0	HAND1	153837398	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.612000	0.98347	2.367000	0.80283	0.462000	0.41574	CCC	.	.		0.617	HAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252511.1	NM_004821		C	153857205	G	C	153857205	3	2	164	1	0	0	0	0	1	0	0	0	6958	1232	43	4	291	4	HAND1	5	153857205	Missense_Mutation	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10	38680004	153857205	27058055	17	25109										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168180048	168180048	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ggacagcagtctcaccgaacTcaggccggcaaaggtgtcat	12	12	3	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr5:168180048T>A	ENST00000519560.1	-	18	2304	c.1885A>T	c.(1885-1887)Agt>Tgt	p.S629C	SLIT3_ENST00000332966.8_Missense_Mutation_p.S629C|SLIT3_ENST00000404867.3_Missense_Mutation_p.S629C	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	629					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTCACCGAACTCAGGCCGGCA	0.547																																					p.S629C	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.A1885T						.						141	99	113					5																	168180048		2203	4300	6503	SO:0001583	missense	6586	exon18			CCGAACTCAGGCC	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.1885A>T	chr5.hg19:g.168180048T>A	ENSP00000430333:p.Ser629Cys	157.0	0.0		121.0	43.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	hg19	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.629850	0.67015	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.60040	0.22;0.22;0.22	5.34	5.34	0.76211	.	0.153798	0.64402	D	0.000001	T	0.69931	0.3166	M	0.88979	2.995	0.80722	D	1	P	0.40578	0.722	P	0.44359	0.447	T	0.76462	-0.2950	10	0.62326	D	0.03	.	15.3207	0.74120	0.0:0.0:0.0:1.0	.	629	O75094	SLIT3_HUMAN	C	629	ENSP00000430333:S629C;ENSP00000332164:S629C;ENSP00000384890:S629C	ENSP00000332164:S629C	S	-	1	0	SLIT3	168112626	1.000000	0.71417	0.986000	0.45419	0.973000	0.67179	5.159000	0.64923	2.031000	0.59945	0.533000	0.62120	AGT	.	.		0.547	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		A	168180048	T	A	168180048	3	1	164	1	0	0	0	0	1	0	0	0	14756	1551	54	4	2762	4	SLIT3	5	168180048	Missense_Mutation	SNP	T	TCGA-DD-AACM-01A-11D-A40R-10	14322843	168180048	12735212	18	25110										
FGFR4	2264	hgsc.bcm.edu	37	chr5	176520342	176520342	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	tggcccgacaggtactgggcGcatcccccacctcacatgtg	11	16	1	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr5:176520342G>A	ENST00000292408.4	+	9	1496				FGFR4_ENST00000292410.3_Missense_Mutation_p.R356H|FGFR4_ENST00000393637.1_Missense_Mutation_p.R356H|FGFR4_ENST00000502906.1_Intron|FGFR4_ENST00000393648.2_Intron	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4						alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	GGTACTGGGCGCATCCCCCAC	0.662										TSP Lung(9;0.080)																											p.R356H		Atlas-SNP	.											FGFR4_ENST00000292408,caecum,carcinoma,0,2	FGFR4	174	.	0			c.G1067A						.						72	76	74					5																	176520342		2203	4300	6503	SO:0001627	intron_variant	2264	exon8			CTGGGCGCATCCC	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1251+10G>A	chr5.hg19:g.176520342G>A		115.0	0.0		94.0	4.0	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	G	3.996	-0.003484	0.07773	.	.	ENSG00000160867	ENST00000292410;ENST00000393637	T;T	0.78816	-1.21;-1.21	4.01	-1.99	0.07457	.	.	.	.	.	T	0.58949	0.2158	.	.	.	0.09310	N	1	B	0.30914	0.3	B	0.25140	0.058	T	0.42882	-0.9425	8	0.33940	T	0.23	.	5.2551	0.15542	0.0:0.46:0.1558:0.3842	.	356	P22455-2	.	H	356	ENSP00000292410:R356H;ENSP00000377254:R356H	ENSP00000292410:R356H	R	+	2	0	FGFR4	176452948	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.917000	0.04025	-0.329000	0.08527	-0.311000	0.09066	CGC	.	.		0.662	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			A	176520342	G	A	176520342	1	1	164	0	1	0	0	0	0	0	0	0	5876	1087	38	1		1	FGFR4	5	176520342	Intron	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10	8340294	176520342	4394918	19	25111										
GABBR1	2550	hgsc.bcm.edu	37	chr6	29599329	29599329	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	cacctggtcccgagtcaggcCccggtacctgatgccccctt	10	18	1	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr6:29599329C>T	ENST00000377034.4	-	3	468	c.133G>A	c.(133-135)Ggc>Agc	p.G45S	GABBR1_ENST00000377016.4_Missense_Mutation_p.G45S|GABBR1_ENST00000376977.3_Missense_Mutation_p.G45S	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	45	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	CGAGTCAGGCCCCGGTACCTG	0.597																																					p.G45S		Atlas-SNP	.											.	GABBR1	95	.	0			c.G133A						.						80	86	84					6																	29599329		2203	4300	6503	SO:0001583	missense	2550	exon3			TCAGGCCCCGGTA	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.133G>A	chr6.hg19:g.29599329C>T	ENSP00000366233:p.Gly45Ser	134.0	0.0		149.0	6.0	NM_021904	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	hg19	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.367941	0.82463	.	.	ENSG00000204681	ENST00000376977;ENST00000377016;ENST00000377034;ENST00000462632;ENST00000476670	T;D;T;T;T	0.94497	-0.93;-3.44;-0.4;1.48;0.86	4.48	4.48	0.54585	Complement control module (1);Sushi/SCR/CCP (1);	0.133753	0.49305	D	0.000144	D	0.93265	0.7854	N	0.19112	0.55	0.41362	D	0.987431	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.998	D	0.95178	0.8296	10	0.87932	D	0	-2.4707	14.7347	0.69406	0.0:1.0:0.0:0.0	.	45;45;45	Q9UBS5-5;Q9UBS5-3;Q9UBS5	.;.;GABR1_HUMAN	S	45;45;45;45;50	ENSP00000366176:G45S;ENSP00000366215:G45S;ENSP00000366233:G45S;ENSP00000419755:G45S;ENSP00000417332:G50S	ENSP00000366176:G45S	G	-	1	0	GABBR1	29707308	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.024000	0.49674	2.062000	0.61559	0.449000	0.29647	GGC	.	.		0.597	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			T	29599329	C	T	29599329	3	4	164	1	0	0	0	0	1	0	0	0	6163	623	22	3	2981	3	GABBR1	6	29599329	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10		29599329	141515738	20	25112										
COL19A1	1310	hgsc.bcm.edu	37	chr6	70890211	70890211	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	tttgccttgccagggaaaacCtggtgccccagggcctccag	12	14	0	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr6:70890211C>T	ENST00000322773.4	+	43	2777	c.2675C>T	c.(2674-2676)cCt>cTt	p.P892L	COL19A1_ENST00000393344.1_Missense_Mutation_p.P514L	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	892	Collagen-like 9.|Triple-helical region 5 (COL5).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						CAGGGAAAACCTGGTGCCCCA	0.473																																					p.P892L		Atlas-SNP	.											.	COL19A1	232	.	0			c.C2675T						.						116	132	127					6																	70890211		2203	4300	6503	SO:0001583	missense	1310	exon43			GAAAACCTGGTGC		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.2675C>T	chr6.hg19:g.70890211C>T	ENSP00000316030:p.Pro892Leu	121.0	0.0		111.0	38.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	hg19	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.694043	0.30052	.	.	ENSG00000082293	ENST00000322773;ENST00000393344	D;D	0.95554	-3.74;-3.74	5.54	5.54	0.83059	.	0.068176	0.56097	D	0.000026	D	0.96562	0.8878	M	0.83118	2.625	0.58432	D	0.999995	D	0.58268	0.982	P	0.57620	0.824	D	0.96278	0.9204	10	0.52906	T	0.07	.	13.4928	0.61407	0.1559:0.8441:0.0:0.0	.	892	Q14993	COJA1_HUMAN	L	892;514	ENSP00000316030:P892L;ENSP00000377013:P514L	ENSP00000316030:P892L	P	+	2	0	COL19A1	70946932	0.995000	0.38212	0.861000	0.33841	0.008000	0.06430	3.308000	0.51896	2.601000	0.87937	0.585000	0.79938	CCT	.	.		0.473	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			T	70890211	C	T	70890211	3	4	164	1	0	0	0	0	1	0	0	0	3678	681	24	3	2841	3	COL19A1	6	70890211	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	41290882	70890211	100224856	21	25113										
TRDN	10345	hgsc.bcm.edu	37	chr6	123868487	123868487	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	aaggtgaaaacaactaacctTtttttctcaagggaggctca	8	8	2	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr6:123868487T>G	ENST00000398178.3	-	4	443	c.422A>C	c.(421-423)aAa>aCa	p.K141T	TRDN_ENST00000542443.1_Missense_Mutation_p.K141T|TRDN_ENST00000334268.4_Missense_Mutation_p.K141T|TRDN_ENST00000546248.1_Missense_Mutation_p.K141T	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	141					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		CAACTAACCTTTTTTTCTCAA	0.249																																					p.K141T		Atlas-SNP	.											.	TRDN	88	.	0			c.A422C						.						13	12	12					6																	123868487		1701	3839	5540	SO:0001583	missense	10345	exon4			TAACCTTTTTTTC	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.422A>C	chr6.hg19:g.123868487T>G	ENSP00000381240:p.Lys141Thr	626.0	0.0		464.0	138.0	NM_001256022	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	hg19	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.385488	0.42308	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268;ENST00000542014;ENST00000543022;ENST00000546248;ENST00000333613;ENST00000542443;ENST00000265491	T;T;T;T	0.65732	0.21;0.21;0.21;-0.17	5.73	4.52	0.55395	Aspartyl beta-hydroxylase/Triadin domain (1);	0.370469	0.27031	N	0.021264	T	0.66954	0.2842	M	0.75447	2.3	0.80722	D	1	B;P;P;P;D	0.67145	0.073;0.885;0.951;0.951;0.996	B;B;P;P;D	0.67900	0.053;0.389;0.807;0.807;0.954	T	0.72523	-0.4267	10	0.87932	D	0	-8.7326	6.1972	0.20555	0.0:0.0826:0.1627:0.7547	.	141;141;141;141;141	F5H6E3;F5H2W7;Q5SWK9;Q8IVK2;Q13061	.;.;.;.;TRDN_HUMAN	T	141;141;141;141;141;141;46;141;46	ENSP00000381240:K141T;ENSP00000333984:K141T;ENSP00000439281:K141T;ENSP00000437684:K141T	ENSP00000265491:K46T	K	-	2	0	TRDN	123910186	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	1.572000	0.36461	2.196000	0.70406	0.524000	0.50904	AAA	.	.		0.249	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	123868487	T	G	123868487	3	3	164	1	0	0	0	0	1	0	0	0	16483	1841	64	5	1919	5	TRDN	6	123868487	Missense_Mutation	SNP	T	TCGA-DD-AACM-01A-11D-A40R-10	52978276	123868487	47246580	22	25114										
ECT2L	345930	hgsc.bcm.edu	37	chr6	139164328	139164328	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gagagacaaagagaaaagtgCctgaggaaaagaatttggga	14	3	0	4			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr6:139164328C>T	ENST00000423192.1	+	5	716	c.555C>T	c.(553-555)tgC>tgT	p.C185C	ECT2L_ENST00000541398.1_Silent_p.C116C|ECT2L_ENST00000367682.2_Silent_p.C185C			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	185							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						GAGAAAAGTGCCTGAGGAAAA	0.403			"N, Splice, Mis"		ETP ALL																																p.C185C		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.C555T						.						116	117	116					6																	139164328		1863	4095	5958	SO:0001819	synonymous_variant	345930	exon5			AAAGTGCCTGAGG		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.555C>T	chr6.hg19:g.139164328C>T		143.0	0.0		123.0	40.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Silent	SNP	ENST00000423192.1	hg19	CCDS43508.1																																																																																			.	.		0.403	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		T	139164328	C	T	139164328	2	4	164	1	0	0	0	0	0	0	0	1	4904	747	26	3		3	ECT2L	6	139164328	Silent	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	15295841	139164328	31950739	23	25115										
TAGAP	117289	hgsc.bcm.edu	37	chr6	159456896	159456896	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	tggcatattggaattggtcaGcctcaaagaccggctggcta	12	9	2	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr6:159456896G>A	ENST00000367066.3	-	10	2490	c.2159C>T	c.(2158-2160)gCt>gTt	p.A720V	RP1-111C20.4_ENST00000607391.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA|TAGAP_ENST00000326965.6_Missense_Mutation_p.A542V|RP1-111C20.4_ENST00000606466.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	720					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		GAATTGGTCAGCCTCAAAGAC	0.517																																					p.A720V		Atlas-SNP	.											.	TAGAP	75	.	0			c.C2159T						.						69	63	65					6																	159456896		2203	4300	6503	SO:0001583	missense	117289	exon10			TGGTCAGCCTCAA	AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.2159C>T	chr6.hg19:g.159456896G>A	ENSP00000356033:p.Ala720Val	88.0	0.0		62.0	16.0	NM_054114	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	hg19	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	G	1.822	-0.471899	0.04445	.	.	ENSG00000164691	ENST00000367066;ENST00000326965	T;T	0.15718	2.4;2.66	5.95	0.439	0.16567	.	0.530211	0.19672	N	0.108739	T	0.03053	0.0090	N	0.26130	0.795	0.80722	D	1	B	0.09022	0.002	B	0.12156	0.007	T	0.34428	-0.9829	10	0.11794	T	0.64	-4.1843	8.0603	0.30629	0.6241:0.0:0.3759:0.0	.	720	Q8N103	TAGAP_HUMAN	V	720;542	ENSP00000356033:A720V;ENSP00000322650:A542V	ENSP00000322650:A542V	A	-	2	0	TAGAP	159376884	0.736000	0.28164	0.339000	0.25562	0.076000	0.17211	1.171000	0.31896	0.125000	0.18397	-0.136000	0.14681	GCT	.	.		0.517	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		A	159456896	G	A	159456896	3	1	164	1	0	0	0	0	1	0	0	0	15552	971	34	3	40	3	TAGAP	6	159456896	Missense_Mutation	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10	20292568	159456896	11658171	24	25116										
CSGALNACT1	55790	hgsc.bcm.edu	37	chr8	19315958	19315958	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	tgaaattctgcatgaactgcCggaacttgtccacccttttt	7	11	1	2	rs35454485		TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr8:19315958C>T	ENST00000454498.2	-	5	1843	c.830G>A	c.(829-831)cGg>cAg	p.R277Q	CSGALNACT1_ENST00000518542.1_5'UTR|CSGALNACT1_ENST00000311540.4_Missense_Mutation_p.R277Q|CSGALNACT1_ENST00000332246.6_Missense_Mutation_p.R277Q|CSGALNACT1_ENST00000544602.1_Missense_Mutation_p.R277Q|CSGALNACT1_ENST00000522854.1_Missense_Mutation_p.R277Q	NM_001130518.1	NP_001123990.1	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 1	277					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|endochondral ossification (GO:0001958)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|heparin biosynthetic process (GO:0030210)|nervous system development (GO:0007399)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|UDP-glucuronate metabolic process (GO:0046398)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|intracellular (GO:0005622)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|glucuronosyltransferase activity (GO:0015020)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)|peptidoglycan glycosyltransferase activity (GO:0008955)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				Colorectal(111;0.182)		CATGAACTGCCGGAACTTGTC	0.448																																					p.R277Q		Atlas-SNP	.											.	CSGALNACT1	72	.	0			c.G830A						.						312	295	301					8																	19315958		2203	4300	6503	SO:0001583	missense	55790	exon5			AACTGCCGGAACT	AK002126	CCDS6010.1	8p21.3	2013-02-19				ENSG00000147408		"Beta 4-glycosyltransferases"	24290	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase"					17145758, 12446672	Standard	NM_018371		Approved	CSGalNAcT-1, FLJ11264, ChGn	uc011kyo.2	Q8TDX6		ENST00000454498.2:c.830G>A	chr8.hg19:g.19315958C>T	ENSP00000411816:p.Arg277Gln	207.0	0.0		140.0	58.0	NM_018371	B2RBE4|Q6P9G6|Q8IUF9|Q9NSQ7|Q9NUM9	Missense_Mutation	SNP	ENST00000454498.2	hg19	CCDS6010.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.079119	0.36662	.	.	ENSG00000147408	ENST00000454498;ENST00000332246;ENST00000311540;ENST00000522854;ENST00000544602	T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29	5.61	3.83	0.44106	.	0.317587	0.35772	N	0.003000	T	0.19685	0.0473	N	0.25485	0.75	0.38096	D	0.937101	B	0.31655	0.334	B	0.25291	0.059	T	0.08027	-1.0742	10	0.10111	T	0.7	-32.1472	8.8171	0.35002	0.0:0.7685:0.0:0.2315	rs35454485	277	Q8TDX6	CGAT1_HUMAN	Q	277	ENSP00000411816:R277Q;ENSP00000330805:R277Q;ENSP00000310891:R277Q;ENSP00000429809:R277Q;ENSP00000442155:R277Q	ENSP00000310891:R277Q	R	-	2	0	CSGALNACT1	19360238	0.996000	0.38824	1.000000	0.80357	0.986000	0.74619	1.875000	0.39578	0.862000	0.35528	-0.140000	0.14226	CGG	.	C|0.987;T|0.013		0.448	CSGALNACT1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375204.1	NM_018371		T	19315958	C	T	19315958	3	4	164	1	0	0	0	0	1	0	0	0	3940	652	23	1	792	1	CSGALNACT1	8	19315958	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10		19315958	127048064	25	25117										
SNX30	401548	hgsc.bcm.edu	37	chr9	115567201	115567201	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	agttgatgatcccaagaagcAtgtgtgtacaatggagactt	11	6	0	4			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr9:115567201A>T	ENST00000374232.3	+	2	466	c.302A>T	c.(301-303)cAt>cTt	p.H101L		NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	101	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						CCCAAGAAGCATGTGTGTACA	0.448																																					p.H101L		Atlas-SNP	.											.	SNX30	32	.	0			c.A302T						.						211	190	197					9																	115567201		1965	4165	6130	SO:0001583	missense	401548	exon2			AGAAGCATGTGTG	AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158		"Sorting nexins"	23685	protein-coding gene	gene with protein product							Standard	NM_001012994		Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.302A>T	chr9.hg19:g.115567201A>T	ENSP00000363349:p.His101Leu	91.0	0.0		79.0	30.0	NM_001012994		Missense_Mutation	SNP	ENST00000374232.3	hg19	CCDS43865.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.458659	0.84317	.	.	ENSG00000148158	ENST00000374232	T	0.39592	1.07	5.33	5.33	0.75918	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.60392	0.2265	M	0.73753	2.245	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.59920	-0.7363	10	0.07813	T	0.8	.	15.308	0.74008	1.0:0.0:0.0:0.0	.	101	Q5VWJ9	SNX30_HUMAN	L	101	ENSP00000363349:H101L	ENSP00000363349:H101L	H	+	2	0	SNX30	114607022	1.000000	0.71417	0.998000	0.56505	0.804000	0.45430	8.885000	0.92439	2.017000	0.59298	0.460000	0.39030	CAT	.	.		0.448	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053700.1			T	115567201	A	T	115567201	3	4	164	1	0	0	0	0	1	0	0	0	14915	217	8	4	308	4	SNX30	9	115567201	Missense_Mutation	SNP	A	TCGA-DD-AACM-01A-11D-A40R-10		115567201	25646230	26	25118										
USP54	159195	hgsc.bcm.edu	37	chr10	75276875	75276875	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	acttttaaagtcaatgaagtTttgaggctttggccttggag	11	5	1	2			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr10:75276875T>G	ENST00000339859.4	-	19	3409	c.3309A>C	c.(3307-3309)aaA>aaC	p.K1103N	RP11-137L10.6_ENST00000595069.1_RNA|RP11-137L10.6_ENST00000600206.1_RNA|USP54_ENST00000408019.1_Missense_Mutation_p.K1103N|USP54_ENST00000394811.2_Missense_Mutation_p.K191N|RP11-137L10.6_ENST00000597958.1_RNA|RP11-137L10.6_ENST00000593790.1_RNA|USP54_ENST00000497106.1_5'UTR|USP54_ENST00000422491.2_Missense_Mutation_p.K285N|USP54_ENST00000428547.1_Missense_Mutation_p.K953N			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1103					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					TCAATGAAGTTTTGAGGCTTT	0.498																																					p.K1103N	Colon(195;880 2046 8854 25025 38456)	Atlas-SNP	.											.	USP54	178	.	0			c.A3309C						.						95	96	96					10																	75276875		2203	4300	6503	SO:0001583	missense	159195	exon18			TGAAGTTTTGAGG	AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"Ubiquitin-specific peptidases"	23513	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 29", "ubiquitin specific protease 54"	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.3309A>C	chr10.hg19:g.75276875T>G	ENSP00000345216:p.Lys1103Asn	76.0	0.0		112.0	26.0	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Missense_Mutation	SNP	ENST00000339859.4	hg19	CCDS7329.2	.	.	.	.	.	.	.	.	.	.	T	14.18	2.459443	0.43736	.	.	ENSG00000166348	ENST00000339859;ENST00000408019;ENST00000428547;ENST00000394811;ENST00000422491	T;T;T;T;T	0.24908	1.87;1.87;1.86;1.83;1.84	5.83	2.18	0.27775	.	.	.	.	.	T	0.16214	0.0390	N	0.24115	0.695	0.80722	D	1	P;B	0.49090	0.919;0.361	B;B	0.42422	0.387;0.036	T	0.02925	-1.1093	9	0.49607	T	0.09	-2.894	6.9605	0.24595	0.0:0.4399:0.0:0.5601	.	285;1103	E7EW90;Q70EL1	.;UBP54_HUMAN	N	1103;1103;953;191;285	ENSP00000345216:K1103N;ENSP00000386080:K1103N;ENSP00000408714:K953N;ENSP00000378290:K191N;ENSP00000407368:K285N	ENSP00000345216:K1103N	K	-	3	2	USP54	74946881	1.000000	0.71417	0.814000	0.32528	0.992000	0.81027	0.799000	0.27028	0.436000	0.26393	0.533000	0.62120	AAA	.	.		0.498	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		G	75276875	T	G	75276875	3	3	164	1	0	0	0	0	1	0	0	0	17100	1838	64	5	1765	5	USP54	10	75276875	Missense_Mutation	SNP	T	TCGA-DD-AACM-01A-11D-A40R-10		75276875	60257872	27	25119										
SEC24C	9632	hgsc.bcm.edu	37	chr10	75519919	75519919	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	cccagcgatctgccccatcaCaggcctccagcttcacaccc	6	21	3	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr10:75519919C>T	ENST00000339365.2	+	6	787	c.625C>T	c.(625-627)Cag>Tag	p.Q209*	SEC24C_ENST00000345254.4_Nonsense_Mutation_p.Q209*|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000411652.2_Nonsense_Mutation_p.Q67*|SEC24C_ENST00000546025.1_Nonsense_Mutation_p.Q67*|SEC24C_ENST00000540668.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	209					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					TGCCCCATCACAGGCCTCCAG	0.627																																					p.Q209X		Atlas-SNP	.											.	SEC24C	86	.	0			c.C625T						.						91	92	92					10																	75519919		2203	4299	6502	SO:0001587	stop_gained	9632	exon5			CCATCACAGGCCT	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"SEC24 (S. cerevisiae) related gene family, member C", "SEC24 family, member C (S. cerevisiae)"			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.625C>T	chr10.hg19:g.75519919C>T	ENSP00000343405:p.Gln209*	78.0	0.0		102.0	25.0	NM_198597	B4DZT4|Q8WV25	Nonsense_Mutation	SNP	ENST00000339365.2	hg19	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.578913	0.86645	.	.	ENSG00000176986	ENST00000546025;ENST00000345254;ENST00000339365;ENST00000411652	.	.	.	5.63	4.73	0.59995	.	0.322570	0.36740	N	0.002423	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-1.0912	14.329	0.66541	0.0:0.9281:0.0:0.0719	.	.	.	.	X	67;209;209;67	.	ENSP00000343405:Q209X	Q	+	1	0	SEC24C	75189925	0.974000	0.33945	0.965000	0.40720	0.850000	0.48378	2.441000	0.44864	1.523000	0.49018	0.561000	0.74099	CAG	.	.		0.627	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			T	75519919	C	T	75519919	4	4	164	1	0	0	0	0	0	1	0	0	14011	479	17	3	639	3	SEC24C	10	75519919	Nonsense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	243044	75519919	60014828	28	25120										
MKI67	4288	hgsc.bcm.edu	37	chr10	129901847	129901847	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ttcacctgctggttctttgtCtgcatccgtggtttcccctg	9	13	3	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr10:129901847C>G	ENST00000368654.3	-	13	8632	c.8257G>C	c.(8257-8259)Gac>Cac	p.D2753H	MKI67_ENST00000368653.3_Missense_Mutation_p.D2393H	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2753	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGTTCTTTGTCTGCATCCGTG	0.488																																					p.D2753H		Atlas-SNP	.											.	MKI67	363	.	0			c.G8257C						.						160	141	147					10																	129901847		2203	4300	6503	SO:0001583	missense	4288	exon13			CTTTGTCTGCATC	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.8257G>C	chr10.hg19:g.129901847C>G	ENSP00000357643:p.Asp2753His	105.0	0.0		55.0	26.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	C	1.348	-0.592300	0.03799	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02103	4.45;4.45	3.24	-1.69	0.08186	.	.	.	.	.	T	0.01940	0.0061	L	0.28274	0.84	0.09310	N	1	B;B;B	0.25272	0.004;0.043;0.122	B;B;B	0.26416	0.003;0.019;0.069	T	0.44757	-0.9307	9	0.45353	T	0.12	.	7.5951	0.28044	0.1157:0.5875:0.2968:0.0	.	2752;2393;2753	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	H	2753;2393;2752	ENSP00000357643:D2753H;ENSP00000357642:D2393H	ENSP00000357642:D2393H	D	-	1	0	MKI67	129791837	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.112000	0.10791	-0.492000	0.06687	-0.211000	0.12701	GAC	.	.		0.488	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		G	129901847	C	G	129901847	3	3	164	1	0	0	0	0	1	0	0	0	9607	913	32	4	1525	4	MKI67	10	129901847	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	54381928	129901847	5632900	29	25121										
OR9G4	283189	hgsc.bcm.edu	37	chr11	56510313	56510313	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gagaataaccttcatgtttgTggttgtatagtctgtgttgc	11	5	2	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr11:56510313T>C	ENST00000302957.3	-	1	974	c.975A>G	c.(973-975)ccA>ccG	p.P325P		NM_001005284.1	NP_001005284.1	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G, member 4	325						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						TTCATGTTTGTGGTTGTATAG	0.368																																					p.P325P		Atlas-SNP	.											.	OR9G4	73	.	0			c.A975G						.						184	162	170					11																	56510313		2201	4296	6497	SO:0001819	synonymous_variant	283189	exon1			TGTTTGTGGTTGT	BK004400	CCDS31537.1	11q11	2012-08-09			ENSG00000172457	ENSG00000172457		"GPCR / Class A : Olfactory receptors"	15322	protein-coding gene	gene with protein product							Standard	NM_001005284		Approved		uc010rjo.2	Q8NGQ1	OTTHUMG00000166932	ENST00000302957.3:c.975A>G	chr11.hg19:g.56510313T>C		86.0	0.0		75.0	18.0	NM_001005284	Q6IF62|Q96RA9	Silent	SNP	ENST00000302957.3	hg19	CCDS31537.1																																																																																			.	.		0.368	OR9G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391945.1	NM_001005284		C	56510313	T	C	56510313	2	2	164	1	0	0	0	0	0	0	0	1	11260	1683	59	2		2	OR9G4	11	56510313	Silent	SNP	T	TCGA-DD-AACM-01A-11D-A40R-10		56510313	78496203	30	25122										
LPXN	80829	hgsc.bcm.edu	37	chr11	58345512	58345512	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	cggaagacgagatcaataatGtagacatgaacgctggctag	12	7	1	4			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr11:58345512G>A	ENST00000316059.6	+	0	0				LPXN_ENST00000528954.1_Missense_Mutation_p.T3I|LPXN_ENST00000528489.1_5'UTR|ZFP91-CNTF_ENST00000389919.4_5'Flank|LPXN_ENST00000395074.2_5'Flank	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein						activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				gatcaataatgtagacatgaa	0.557																																					p.T3I		Atlas-SNP	.											.	LPXN	55	.	0			c.C8T						.						48	46	46					11																	58345512		692	1591	2283	SO:0001631	upstream_gene_variant	9404	exon1			AATAATGTAGACA	AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"Zinc fingers, C2H2-type"	14983	protein-coding gene	gene with protein product			"zinc finger protein homologous to Zfp91 in mouse", "zinc finger protein 91 homolog (mouse)"			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391		chr11.hg19:g.58345512G>A	Exception_encountered	194.0	0.0		178.0	46.0	NM_001143995	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Missense_Mutation	SNP	ENST00000316059.6	hg19	CCDS31553.1	.	.	.	.	.	.	.	.	.	.	G	11.04	1.521171	0.27211	.	.	ENSG00000110031	ENST00000528954	T	0.29655	1.56	3.89	2.96	0.34315	.	.	.	.	.	T	0.16642	0.0400	N	0.08118	0	0.24849	N	0.99241	B	0.19583	0.037	B	0.17098	0.017	T	0.18023	-1.0350	9	0.72032	D	0.01	.	8.9831	0.35977	0.0:0.0:0.7799:0.2201	.	3	B4DV71	.	I	3	ENSP00000431284:T3I	ENSP00000431284:T3I	T	-	2	0	LPXN	58102088	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.998000	0.29744	1.211000	0.43351	0.561000	0.74099	ACA	.	.		0.557	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023		A	58345512	G	A	58345512	1	1	164	0	1	0	0	0	0	0	0	0	8938	1377	48	3		3	LPXN	11	58345512	5'Flank	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10	1835199	58345512	76661004	31	25123										
C11orf48	79081	hgsc.bcm.edu	37	chr11	62437490	62437493	+	Frame_Shift_Del	DEL	GGCA	GGCA	-													0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	catcctccttgcttctccctGgcacaagggccatggtggtg							TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	GGCA	GGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr11:62437490_62437493delGGCA	ENST00000431002.2	-	1	1744_1747	c.11_14delTGCC	c.(10-15)gtgccafs	p.VP4fs	C11orf48_ENST00000532208.1_Frame_Shift_Del_p.VP4fs|C11orf48_ENST00000354588.3_Frame_Shift_Del_p.VP4fs|C11orf83_ENST00000531323.1_5'Flank|C11orf83_ENST00000377953.3_5'Flank			Q9BQE6	CK048_HUMAN	chromosome 11 open reading frame 48	4										endometrium(1)|lung(5)|urinary_tract(1)	7						GCTTCTCCCTGGCACAAGGGCCAT	0.529																																					p.4_5del		Atlas-INDEL	.											.	C11orf48	18	.	0			c.12_15del						.																																			SO:0001589	frameshift_variant	79081	exon2			.	BC001434	CCDS8028.1	11q12.3	2014-02-12			ENSG00000162194	ENSG00000162194			28351	protein-coding gene	gene with protein product						12477932	Standard	NM_024099		Approved	MGC2477	uc001nuf.3	Q9BQE6	OTTHUMG00000167588	ENST00000431002.2:c.11_14delTGCC	chr11.hg19:g.62437490_62437493delGGCA	ENSP00000416856:p.Val4fs	76.0	0.0		62.0	18.0	NM_024099	Q96NA4	Frame_Shift_Del	DEL	ENST00000431002.2	hg19																																																																																				.	.		0.529	C11orf48-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000395233.1	NM_024099		-	62437493	GGCA	-	62437490	7	5	164	1	0	1	0	1	0	0	0	0	1646	1348	47	0	801	0	C11orf48	11	62437490	Frame_Shift_Del	DEL	GGCA	TCGA-DD-AACM-01A-11D-A40R-10	4091978	62437490	72569026	32	25124										
GDPD5	81544	hgsc.bcm.edu	37	chr11	75146556	75146556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	acagacatgtcttcagctaaCgcccactccgctctatgagg	8	14	3	2	rs551593132	byFrequency	TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr11:75146556C>T	ENST00000336898.3	-	17	2651	c.1814G>A	c.(1813-1815)cGt>cAt	p.R605H	GDPD5_ENST00000533784.1_Missense_Mutation_p.R486H|GDPD5_ENST00000376282.3_Missense_Mutation_p.R486H|GDPD5_ENST00000529721.1_Missense_Mutation_p.R605H|GDPD5_ENST00000443276.2_3'UTR|GDPD5_ENST00000533805.1_Missense_Mutation_p.R360H|GDPD5_ENST00000526177.1_Missense_Mutation_p.R467H	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	605					cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						CTTCAGCTAACGCCCACTCCG	0.592													C|||	4	0.000798722	0	0	5008	,	,		19386	0		0	False		,,,				2504	0.0041				p.R605H		Atlas-SNP	.											.	GDPD5	49	.	0			c.G1814A						.						66	59	61					11																	75146556		2200	4293	6493	SO:0001583	missense	81544	exon17			AGCTAACGCCCAC	AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.1814G>A	chr11.hg19:g.75146556C>T	ENSP00000337972:p.Arg605His	45.0	0.0		32.0	5.0	NM_030792	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Missense_Mutation	SNP	ENST00000336898.3	hg19	CCDS8238.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.008051	0.75046	.	.	ENSG00000158555	ENST00000526177;ENST00000533784;ENST00000529721;ENST00000336898;ENST00000533805;ENST00000376282	T;T;T;T;T;T	0.16597	2.33;2.34;2.36;2.36;2.35;2.34	4.74	-1.98	0.07480	.	0.602094	0.15213	N	0.274342	T	0.06962	0.0177	N	0.08118	0	0.22266	N	0.999243	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.24941	-1.0146	10	0.87932	D	0	.	5.0714	0.14609	0.0:0.3104:0.1639:0.5257	.	486;605	Q8WTR4-2;Q8WTR4	.;GDPD5_HUMAN	H	467;486;605;605;360;486	ENSP00000434050:R467H;ENSP00000437049:R486H;ENSP00000433214:R605H;ENSP00000337972:R605H;ENSP00000435196:R360H;ENSP00000365459:R486H	ENSP00000337972:R605H	R	-	2	0	GDPD5	74824204	0.012000	0.17670	0.748000	0.31131	0.982000	0.71751	-0.589000	0.05767	-0.220000	0.09988	0.655000	0.94253	CGT	.	.		0.592	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792		T	75146556	C	T	75146556	3	4	164	1	0	0	0	0	1	0	0	0	6335	536	19	1	7	1	GDPD5	11	75146556	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	12709066	75146556	59859960	33	25125										
CADM1	23705	hgsc.bcm.edu	37	chr11	115047195	115047195	+	Nonstop_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ttgaaacaaaaaggctgatcTagatgaagtactctttcttt	7	6	3	4			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr11:115047195T>A	ENST00000452722.3	-	10	1348	c.1328A>T	c.(1327-1329)tAg>tTg	p.*443L	CADM1_ENST00000537058.1_Nonstop_Mutation_p.*454L|CADM1_ENST00000537140.1_Intron|CADM1_ENST00000542447.2_Nonstop_Mutation_p.*415L|CADM1_ENST00000536727.1_Nonstop_Mutation_p.*444L|CADM1_ENST00000331581.6_Nonstop_Mutation_p.*472L	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		AAGGCTGATCTAGATGAAGTA	0.418																																					p.X443L		Atlas-SNP	.											.	CADM1	74	.	0			c.A1328T						.						260	240	247					11																	115047195		2201	4296	6497	SO:0001578	stop_lost	23705	exon10			CTGATCTAGATGA	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5951	protein-coding gene	gene with protein product	"nectin-like 2"	605686	"tumor suppressor in lung cancer 1", "immunoglobulin superfamily, member 4"	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.1328A>T	chr11.hg19:g.115047195T>A		115.0	0.0		109.0	30.0	NM_014333		Missense_Mutation	SNP	ENST00000452722.3	hg19	CCDS8373.1	.	.	.	.	.	.	.	.	.	.	T	14.68	2.609213	0.46527	.	.	ENSG00000182985	ENST00000542447;ENST00000452722;ENST00000537058;ENST00000536727;ENST00000404468;ENST00000331581;ENST00000541325	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5185	0.75846	0.0:0.0:0.0:1.0	.	.	.	.	L	415;443;454;444;374;472;128	.	.	X	-	2	0	CADM1	114552405	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.526000	0.60566	2.246000	0.74042	0.533000	0.62120	TAG	.	.		0.418	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		A	115047195	T	A	115047195	4	1	164	1	0	0	0	0	0	0	0	0	2568	1535	53	4	4	4	CADM1	11	115047195	Nonstop_Mutation	SNP	T	TCGA-DD-AACM-01A-11D-A40R-10	39900639	115047195	19959321	34	25126										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117375644	117375644	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gggccaggggcttacccttgGcatgcttccacatgaccttg	12	13	0	1	rs147991561		TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr11:117375644G>A	ENST00000321322.6	-	10	2358	c.2357C>T	c.(2356-2358)gCc>gTc	p.A786V	DSCAML1_ENST00000527706.1_Missense_Mutation_p.A516V	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	726					axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.A786V(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CTTACCCTTGGCATGCTTCCA	0.592																																					p.A786V		Atlas-SNP	.											DSCAML1,arm,malignant_melanoma,+1,1	DSCAML1	286	.	1	Substitution - Missense(1)	skin(1)	c.C2357T						.						63	59	60					11																	117375644		2201	4296	6497	SO:0001583	missense	57453	exon10			CCCTTGGCATGCT		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2357C>T	chr11.hg19:g.117375644G>A	ENSP00000315465:p.Ala786Val	70.0	0.0		61.0	15.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.990913	0.93106	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.67865	-0.29;-0.29	4.42	4.42	0.53409	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72070	0.3415	L	0.39085	1.19	0.80722	D	1	D	0.54207	0.965	P	0.59221	0.854	T	0.76334	-0.2997	9	0.87932	D	0	.	16.8247	0.85927	0.0:0.0:1.0:0.0	.	726	Q8TD84	DSCL1_HUMAN	V	516;786;493	ENSP00000434335:A516V;ENSP00000315465:A786V	ENSP00000315465:A786V	A	-	2	0	DSCAML1	116880854	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	9.540000	0.98080	2.289000	0.77006	0.305000	0.20034	GCC	.	.		0.592	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		A	117375644	G	A	117375644	3	1	164	1	0	0	0	0	1	0	0	0	4771	1203	42	3	4080	3	DSCAML1	11	117375644	Missense_Mutation	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10	2328449	117375644	17630872	35	25127										
LRP1	4035	hgsc.bcm.edu	37	chr12	57586981	57586981	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gtgaattcctcttgccgagcAcaagatgagtttgagtgtgc	12	8	1	4			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr12:57586981A>G	ENST00000243077.3	+	46	8044	c.7578A>G	c.(7576-7578)gcA>gcG	p.A2526A	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2526	LDL-receptor class A 11. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CTTGCCGAGCACAAGATGAGT	0.627																																					p.A2526A		Atlas-SNP	.											.	LRP1	428	.	0			c.A7578G						.						77	62	67					12																	57586981		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon46			CCGAGCACAAGAT	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.7578A>G	chr12.hg19:g.57586981A>G		62.0	0.0		66.0	13.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.627	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		G	57586981	A	G	57586981	2	3	164	1	0	0	0	0	0	0	0	1	8960	146	6	2		2	LRP1	12	57586981	Silent	SNP	A	TCGA-DD-AACM-01A-11D-A40R-10		57586981	76264914	36	25128										
FAM71C	196472	hgsc.bcm.edu	37	chr12	100041989	100041989	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	tgctaccgtattacacggccCaaagcagccccgcaatgggc	10	15	0	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr12:100041989C>T	ENST00000324341.1	+	1	459	c.37C>T	c.(37-39)Caa>Taa	p.Q13*	ANKS1B_ENST00000547776.2_Intron|ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	13										breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		TTACACGGCCCAAAGCAGCCC	0.498																																					p.Q13X		Atlas-SNP	.											.	FAM71C	48	.	0			c.C37T						.						66	65	65					12																	100041989		2203	4300	6503	SO:0001587	stop_gained	196472	exon1			ACGGCCCAAAGCA		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.37C>T	chr12.hg19:g.100041989C>T	ENSP00000315247:p.Gln13*	102.0	0.0		97.0	30.0	NM_153364	B2R6Y6	Nonsense_Mutation	SNP	ENST00000324341.1	hg19	CCDS9072.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.603009	0.87157	.	.	ENSG00000180219	ENST00000324341	.	.	.	3.94	-6.34	0.01982	.	1.291070	0.05656	N	0.586079	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.3648	4.4746	0.11729	0.3071:0.1549:0.4565:0.0815	.	.	.	.	X	13	.	.	Q	+	1	0	FAM71C	98566120	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-2.263000	0.01174	-1.468000	0.01892	-1.497000	0.00963	CAA	.	.		0.498	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364		T	100041989	C	T	100041989	4	4	164	1	0	0	0	0	0	1	0	0	5617	595	21	3	39	3	FAM71C	12	100041989	Nonsense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	42455008	100041989	33809906	37	25129										
DHX37	57647	hgsc.bcm.edu	37	chr12	125451681	125451681	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ctctttaccttgtggccgggCtctggagggtgggaaagcct	15	10	2	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr12:125451681C>A	ENST00000308736.2	-	11	1590	c.1492G>T	c.(1492-1494)Gcc>Tcc	p.A498S	DHX37_ENST00000544745.1_Missense_Mutation_p.A285S	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	498	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		TGTGGCCGGGCTCTGGAGGGT	0.662																																					p.A498S		Atlas-SNP	.											.	DHX37	114	.	0			c.G1492T						.						48	38	41					12																	125451681		2203	4300	6503	SO:0001583	missense	57647	exon11			GCCGGGCTCTGGA	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.1492G>T	chr12.hg19:g.125451681C>A	ENSP00000311135:p.Ala498Ser	53.0	0.0		63.0	17.0	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	hg19	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	C	2.698	-0.271599	0.05716	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.13538	2.58;2.58	4.43	-1.92	0.07618	Helicase, C-terminal (1);	1.034950	0.07576	N	0.919411	T	0.05227	0.0139	N	0.12182	0.205	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.43097	-0.9412	10	0.11794	T	0.64	-22.1249	1.0184	0.01513	0.3778:0.292:0.1726:0.1577	.	498	Q8IY37	DHX37_HUMAN	S	498;285	ENSP00000311135:A498S;ENSP00000439009:A285S	ENSP00000311135:A498S	A	-	1	0	DHX37	124017634	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	0.043000	0.13971	-0.174000	0.10743	-0.152000	0.13540	GCC	.	.		0.662	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		A	125451681	C	A	125451681	3	1	164	1	0	0	0	0	1	0	0	0	4512	797	28	3	2049	3	DHX37	12	125451681	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	25409692	125451681	8400214	38	25130										
FSCB	84075	hgsc.bcm.edu	37	chr14	44975143	44975143	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ttcagctgatggaggcagaaTttcagccagaagctctacag	11	9	3	3			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr14:44975143T>C	ENST00000340446.4	-	1	1339	c.1048A>G	c.(1048-1050)Att>Gtt	p.I350V	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	350	Pro-rich.					sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		GGAGGCAGAATTTCAGCCAGA	0.512																																					p.I350V		Atlas-SNP	.											.	FSCB	173	.	0			c.A1048G						.						73	85	81					14																	44975143		2203	4300	6503	SO:0001583	missense	84075	exon1			GCAGAATTTCAGC	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"chromosome 14 open reading frame 155"	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.1048A>G	chr14.hg19:g.44975143T>C	ENSP00000344579:p.Ile350Val	135.0	0.0		123.0	35.0	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	hg19	CCDS9679.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.700276	0.00725	.	.	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.12039	2.72	4.13	-8.26	0.01021	.	.	.	.	.	T	0.07052	0.0179	N	0.19112	0.55	0.09310	N	1	B	0.18741	0.03	B	0.17433	0.018	T	0.32666	-0.9898	9	0.25106	T	0.35	.	9.8942	0.41309	0.0:0.4712:0.3222:0.2066	.	350	Q5H9T9	FSCB_HUMAN	V	350	ENSP00000344579:I350V	ENSP00000344579:I350V	I	-	1	0	FSCB	44044893	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-5.784000	0.00098	-3.134000	0.00235	-0.548000	0.04221	ATT	.	.		0.512	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		C	44975143	T	C	44975143	3	2	164	1	0	0	0	0	1	0	0	0	6074	1493	52	2	1433	2	FSCB	14	44975143	Missense_Mutation	SNP	T	TCGA-DD-AACM-01A-11D-A40R-10		44975143	62374397	39	25131										
MLH3	27030	hgsc.bcm.edu	37	chr14	75485660	75485678	+	Frame_Shift_Del	DEL	GGCCATCATTAAACTTAAT	GGCCATCATTAAACTTAAT	-													0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gcaactttcctgtaagctcaGgccatcattaaacttaatgg					rs61752724|rs142590981		TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	GGCCATCATTAAACTTAAT	GGCCATCATTAAACTTAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr14:75485660_75485678delGGCCATCATTAAACTTAAT	ENST00000556740.1	-	11	4131_4149	c.4096_4114delATTAAGTTTAATGATGGCC	c.(4096-4116)attaagtttaatgatggcctgfs	p.IKFNDGL1366fs	MLH3_ENST00000355774.2_Frame_Shift_Del_p.IKFNDGL1366fs|MLH3_ENST00000238662.7_Frame_Shift_Del_p.IKFNDGL1342fs|MLH3_ENST00000380968.2_Frame_Shift_Del_p.IKFNDGL304fs|MLH3_ENST00000556257.1_Frame_Shift_Del_p.IKFNDGL1188fs|RNU6-689P_ENST00000384197.1_RNA			Q9UHC1	MLH3_HUMAN	mutL homolog 3	1366					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TGTAAGCTCAGGCCATCATTAAACTTAATGGCCCCTAAA	0.452								Mismatch excision repair (MMR)																													p.1366_1372del		Atlas-INDEL	.											.	MLH3	200	.	0			c.4097_4115del						.																																			SO:0001589	frameshift_variant	27030	exon12			.	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.4096_4114delATTAAGTTTAATGATGGCC	chr14.hg19:g.75485660_75485678delGGCCATCATTAAACTTAAT	ENSP00000452316:p.Ile1366fs	77.0	0.0		85.0	16.0	NM_001040108	P49751|Q56DK9|Q9P292|Q9UHC0	Frame_Shift_Del	DEL	ENST00000556740.1	hg19	CCDS32123.1																																																																																			.	.		0.452	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		-	75485678	GGCCATCATTAAACTTAAT	-	75485660	7	5	164	1	0	1	0	1	0	0	0	0	9627	991	35	0	255	0	MLH3	14	75485660	Frame_Shift_Del	DEL	GGCCATCATTAAACTTAAT	TCGA-DD-AACM-01A-11D-A40R-10	30510517	75485660	31863880	40	25132										
HERC2	8924	hgsc.bcm.edu	37	chr15	28501325	28501325	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	actctgcagcacggcctgggCggccgactgcacggtgctca	14	15	2	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr15:28501325C>A	ENST00000261609.7	-	18	2764	c.2656G>T	c.(2656-2658)Gcc>Tcc	p.A886S		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		ACGGCCTGGGCGGCCGACTGC	0.701																																					p.A886S		Atlas-SNP	.											HERC2,NS,carcinoma,0,1	HERC2	501	.	0			c.G2656T						.						14	16	15					15																	28501325		2168	4223	6391	SO:0001583	missense	8924	exon18			CCTGGGCGGCCGA	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.2656G>T	chr15.hg19:g.28501325C>A	ENSP00000261609:p.Ala886Ser	27.0	0.0		30.0	6.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.537435	0.85917	.	.	ENSG00000128731	ENST00000261609	T	0.52754	0.65	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.70298	0.3208	M	0.79475	2.455	0.80722	D	1	D	0.63880	0.993	D	0.69479	0.964	T	0.73212	-0.4054	10	0.59425	D	0.04	.	19.0185	0.92903	0.0:1.0:0.0:0.0	.	886	O95714	HERC2_HUMAN	S	886	ENSP00000261609:A886S	ENSP00000261609:A886S	A	-	1	0	HERC2	26174920	1.000000	0.71417	0.803000	0.32268	0.439000	0.31926	6.048000	0.71046	2.500000	0.84329	0.539000	0.68188	GCC	.	.		0.701	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28501325	C	A	28501325	3	1	164	1	0	0	0	0	1	0	0	0	7067	768	27	1	12152	1	HERC2	15	28501325	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10		28501325	74030067	41	25133										
TP53	7157	hgsc.bcm.edu	37	chr17	7576854	7576860	+	Splice_Site	DEL	TGAAGGG	TGAAGGG	-													0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	aggtcccaagacttagtaccTgaagggtgaaatattctcca							TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	TGAAGGG	TGAAGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr17:7576854_7576860delTGAAGGG	ENST00000269305.4	-	9	1175_1181	c.986_992delCCCTTCA	c.(985-993)acccttcag>ag	p.TLQ329fs	TP53_ENST00000420246.2_Splice_Site_p.TLQ329fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Splice_Site_p.TLQ329fs|TP53_ENST00000359597.4_Splice_Site_p.TLQ329fs|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Splice_Site_p.TLQ329fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	329	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		T -> I (in a sporadic cancer; somatic mutation).|T -> S (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q331*(23)|p.0?(8)|p.Q331fs*6(3)|p.Q331P(3)|p.T329I(3)|p.L330H(3)|p.T329T(2)|p.Q331fs*14(1)|p.?(1)|p.L330P(1)|p.Q331R(1)|p.L330fs*15(1)|p.L330R(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACTTAGTACCTGAAGGGTGAAATATTC	0.444		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.329_331del	Pancreas(47;798 1329 9957 10801)	Atlas-INDEL	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,0,3	TP53	33396	.	51	Substitution - Nonsense(23)|Substitution - Missense(12)|Whole gene deletion(8)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Substitution - coding silent(2)|Unknown(1)	skin(6)|lung(6)|large_intestine(5)|urinary_tract(5)|ovary(5)|upper_aerodigestive_tract(4)|oesophagus(4)|bone(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|endometrium(2)|breast(2)|liver(2)|stomach(1)|prostate(1)	c.987_993del						.																																			SO:0001630	splice_region_variant	7157	exon9	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.993+1CCCTTCA>-	chr17.hg19:g.7576854_7576860delTGAAGGG		162.0	0.0		51.0	20.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.444	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Frame_Shift_Del	-	7576860	TGAAGGG	-	7576854	8	5	164	1	0	1	0	1	0	0	1	0	16396	1594	55	0	290	0	TP53	17	7576854	Splice_Site	DEL	TGAAGGG	TCGA-DD-AACM-01A-11D-A40R-10		7576854	73618356	42	25134										
FBXW10	10517	hgsc.bcm.edu	37	chr17	18654340	18654340	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	ggaagagcatgcgtgtgaaaCatccgaagtggaagctgaga	15	6	0	3			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr17:18654340C>A	ENST00000395665.4	+	5	1317	c.1096C>A	c.(1096-1098)Cat>Aat	p.H366N	FBXW10_ENST00000395667.1_Missense_Mutation_p.H366N|FBXW10_ENST00000301938.4_Missense_Mutation_p.H366N|FBXW10_ENST00000308799.4_Missense_Mutation_p.H395N			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	366										NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GCGTGTGAAACATCCGAAGTG	0.478																																					p.H366N		Atlas-SNP	.											.	FBXW10	82	.	0			c.C1096A						.						193	186	189					17																	18654340		2203	4300	6503	SO:0001583	missense	10517	exon5			GTGAAACATCCGA	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"F-boxes / WD-40 domains", "WD repeat domain containing"	1211	protein-coding gene	gene with protein product		611679	"chromosome 17 open reading frame 1A", "F-box and WD-40 domain protein 10"	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.1096C>A	chr17.hg19:g.18654340C>A	ENSP00000379025:p.His366Asn	102.0	0.0		60.0	23.0	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	hg19	CCDS11199.3	.	.	.	.	.	.	.	.	.	.	C	0	-2.809061	0.00074	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	2.73	0.408	0.16377	F-box domain, Skp2-like (1);	0.597736	0.13615	N	0.374861	T	0.04003	0.0112	N	0.00707	-1.245	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.40327	-0.9569	10	0.07644	T	0.81	.	2.5763	0.04807	0.4417:0.2823:0.276:0.0	.	366;395;366;366	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	N	366;395;366;366	ENSP00000379026:H366N;ENSP00000310382:H395N;ENSP00000306937:H366N;ENSP00000379025:H366N	ENSP00000306937:H366N	H	+	1	0	FBXW10	18595065	0.130000	0.22417	0.406000	0.26421	0.367000	0.29736	0.394000	0.20834	0.264000	0.21851	-0.750000	0.03501	CAT	.	.		0.478	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456		A	18654340	C	A	18654340	3	1	164	1	0	0	0	0	1	0	0	0	5771	478	17	3	1114	3	FBXW10	17	18654340	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	11077486	18654340	62540870	43	25135										
USP22	23326	hgsc.bcm.edu	37	chr17	20919117	20919117	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gcgatgaggaactcgtgggcGtcctgctgctcgtagcctgc	15	12	0	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr17:20919117G>A	ENST00000261497.4	-	6	989	c.786C>T	c.(784-786)gaC>gaT	p.D262D	USP22_ENST00000537526.2_Silent_p.D250D|USP22_ENST00000455117.2_Intron	NM_015276.1	NP_056091.1	Q9UPT9	UBP22_HUMAN	ubiquitin specific peptidase 22	262	USP.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|embryo development (GO:0009790)|histone deubiquitination (GO:0016578)|histone H4 acetylation (GO:0043967)|histone ubiquitination (GO:0016574)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deubiquitination (GO:0016579)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	SAGA complex (GO:0000124)	enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|transcription coactivator activity (GO:0003713)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	15						ACTCGTGGGCGTCCTGCTGCT	0.627																																					p.D262D		Atlas-SNP	.											.	USP22	45	.	0			c.C786T						.						51	61	57					17																	20919117		2052	4184	6236	SO:0001819	synonymous_variant	23326	exon6			GTGGGCGTCCTGC	AB028986	CCDS42285.1	17p11.2	2006-11-24	2005-08-08		ENSG00000124422	ENSG00000124422		"Ubiquitin-specific peptidases"	12621	protein-coding gene	gene with protein product		612116	"ubiquitin specific protease 22", "ubiquitin specific peptidase 3-like"	USP3L		12838346	Standard	NM_015276		Approved	KIAA1063	uc002gym.4	Q9UPT9	OTTHUMG00000133621	ENST00000261497.4:c.786C>T	chr17.hg19:g.20919117G>A		107.0	0.0		59.0	26.0	NM_015276	A0JNS3|Q2NLE2|Q6MZY4|Q8TBS8|Q96IW5	Silent	SNP	ENST00000261497.4	hg19	CCDS42285.1																																																																																			.	.		0.627	USP22-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444169.1			A	20919117	G	A	20919117	2	1	164	1	0	0	0	0	0	0	0	1	17069	1136	40	1		1	USP22	17	20919117	Silent	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10	2264777	20919117	60276093	44	25136										
DHRS7B	25979	hgsc.bcm.edu	37	chr17	21075458	21075458	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gggtgcgcgggaaggcctacCtgcggaatgctgtggtggtg	20	8	0	0	rs115639276		TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr17:21075458C>G	ENST00000395511.3	+	2	468	c.148C>G	c.(148-150)Ctg>Gtg	p.L50V	DHRS7B_ENST00000579303.1_Missense_Mutation_p.L35V	NM_015510.4	NP_056325.2	Q6IAN0	DRS7B_HUMAN	dehydrogenase/reductase (SDR family) member 7B	50						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|pancreas(2)	7						GAAGGCCTACCTGCGGAATGC	0.672																																					p.L50V		Atlas-SNP	.											.	DHRS7B	27	.	0			c.C148G						.						34	32	32					17																	21075458		2203	4300	6503	SO:0001583	missense	25979	exon2			GCCTACCTGCGGA	BC004126	CCDS11215.1	17p12	2011-09-20				ENSG00000109016		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	24547	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 32C, member 1"					10810093, 11230166, 19027726	Standard	NM_015510		Approved	DKFZp566O084, MGC8916, CGI-93, SDR32C1	uc002gyo.3	Q6IAN0		ENST00000395511.3:c.148C>G	chr17.hg19:g.21075458C>G	ENSP00000378887:p.Leu50Val	148.0	0.0		99.0	43.0	NM_015510	B5MEF4|Q6UX59|Q9BTF9|Q9UFM6|Q9Y3A1	Missense_Mutation	SNP	ENST00000395511.3	hg19	CCDS11215.1	.	.	.	.	.	.	.	.	.	.	C	9.087	1.000787	0.19121	.	.	ENSG00000109016	ENST00000395511;ENST00000346603	T	0.58797	0.31	5.41	-3.28	0.05033	.	0.416255	0.26275	N	0.025309	T	0.36580	0.0972	L	0.34521	1.04	0.80722	D	1	B	0.10296	0.003	B	0.09377	0.004	T	0.02676	-1.1125	10	0.48119	T	0.1	.	5.5244	0.16951	0.3673:0.3821:0.1893:0.0613	.	50	Q6IAN0	DRS7B_HUMAN	V	50	ENSP00000378887:L50V	ENSP00000320352:L50V	L	+	1	2	DHRS7B	21016050	0.046000	0.20272	0.104000	0.21259	0.451000	0.32288	-0.484000	0.06528	-0.171000	0.10797	-0.137000	0.14449	CTG	.	C|0.995;T|0.005		0.672	DHRS7B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444066.3	NM_015510		G	21075458	C	G	21075458	3	3	164	1	0	0	0	0	1	0	0	0	4498	680	24	4	154	4	DHRS7B	17	21075458	Missense_Mutation	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	156341	21075458	60119752	45	25137										
NF1	4763	hgsc.bcm.edu	37	chr17	29657472	29657483	+	In_Frame_Del	DEL	CGTTAGAATTTT	CGTTAGAATTTT	-													0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	agccaatgagccacacctcaCgttagaatttttggaagagt					rs137854565		TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	CGTTAGAATTTT	CGTTAGAATTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr17:29657472_29657483delCGTTAGAATTTT	ENST00000358273.4	+	39	6151_6162	c.5768_5779delCGTTAGAATTTT	c.(5767-5781)acgttagaatttttg>atg	p.1923_1927TLEFL>M	NF1_ENST00000356175.3_In_Frame_Del_p.1902_1906TLEFL>M|NF1_ENST00000581113.2_3'UTR	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1923					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CCACACCTCACGTTAGAATTTTTGGAAGAGTG	0.354			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.1923_1926del		Atlas-INDEL	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.5767_5778del	GRCh37	CD086562	NF1	D		.																																			SO:0001651	inframe_deletion	4763	exon39	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	.		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.5768_5779delCGTTAGAATTTT	chr17.hg19:g.29657472_29657483delCGTTAGAATTTT	ENSP00000351015:p.Thr1923_Leu1927delinsMet	100.0	0.0		87.0	17.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	In_Frame_Del	DEL	ENST00000358273.4	hg19	CCDS42292.1																																																																																			.	.		0.354	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		-	29657483	CGTTAGAATTTT	-	29657472	7	5	164	1	0	1	0	1	0	0	0	0	10365	536	19	0	5983	0	NF1	17	29657472	In_Frame_Del	DEL	CGTTAGAATTTT	TCGA-DD-AACM-01A-11D-A40R-10	8582014	29657472	51537738	46	25138										
CA10	56934	hgsc.bcm.edu	37	chr17	49710849	49710849	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	aaacccacctctatactgaaGcttctgggctcggttgtttg	9	11	2	1	rs375126312		TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr17:49710849G>A	ENST00000285273.4	-	9	2063	c.952C>T	c.(952-954)Ctt>Ttt	p.L318F	CA10_ENST00000571918.1_5'Flank|CA10_ENST00000340813.6_Missense_Mutation_p.L324F|CA10_ENST00000442502.2_Missense_Mutation_p.L318F|CA10_ENST00000451037.2_Missense_Mutation_p.L318F|CA10_ENST00000570565.1_Missense_Mutation_p.L243F	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	318					brain development (GO:0007420)					cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	CTATACTGAAGCTTCTGGGCT	0.502																																					p.L318F		Atlas-SNP	.											.	CA10	84	.	0			c.C952T						.	G	PHE/LEU,PHE/LEU,PHE/LEU	0,4406		0,0,2203	124	113	117		952,952,952	5.4	1	17		117	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	CA10	NM_001082533.1,NM_001082534.1,NM_020178.4	22,22,22	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	318/329,318/329,318/329	49710849	1,13005	2203	4300	6503	SO:0001583	missense	56934	exon9			ACTGAAGCTTCTG	AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"Carbonic anhydrases"	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.952C>T	chr17.hg19:g.49710849G>A	ENSP00000285273:p.Leu318Phe	153.0	0.0		125.0	41.0	NM_001082534	B2R7J0|B4DGL6	Missense_Mutation	SNP	ENST00000285273.4	hg19	CCDS32684.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.672754	0.88445	0.0	1.16E-4	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	T;T;T;T	0.71103	-0.5;-0.5;-0.5;-0.54	5.44	5.44	0.79542	.	0.000000	0.64402	D	0.000001	T	0.62756	0.2454	L	0.29908	0.895	0.80722	D	1	B;B;P	0.36483	0.267;0.267;0.555	B;B;B	0.36719	0.058;0.058;0.231	T	0.63919	-0.6528	10	0.42905	T	0.14	.	18.2623	0.90039	0.0:0.0:1.0:0.0	.	318;324;243	Q9NS85;Q68D28;B4DGL6	CAH10_HUMAN;.;.	F	318;318;318;324	ENSP00000390666:L318F;ENSP00000285273:L318F;ENSP00000405388:L318F;ENSP00000340363:L324F	ENSP00000285273:L318F	L	-	1	0	CA10	47065848	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.583000	0.74053	2.558000	0.86282	0.655000	0.94253	CTT	.	.		0.502	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178		A	49710849	G	A	49710849	3	1	164	1	0	0	0	0	1	0	0	0	2513	971	34	3	42	3	CA10	17	49710849	Missense_Mutation	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10	20053377	49710849	31484361	47	25139										
BPTF	2186	hgsc.bcm.edu	37	chr17	65905802	65905802	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	attctgaaaaagatgaggtaAaaggttcagatgctgcaaaa	10	4	2	4			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr17:65905802A>G	ENST00000321892.4	+	12	3356	c.3295A>G	c.(3295-3297)Aaa>Gaa	p.K1099E	BPTF_ENST00000424123.3_Missense_Mutation_p.K960E|BPTF_ENST00000306378.6_Missense_Mutation_p.K973E|BPTF_ENST00000335221.5_Missense_Mutation_p.K1099E			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1099					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AGATGAGGTAAAAGGTTCAGA	0.363																																					p.K1099E		Atlas-SNP	.											.	BPTF	415	.	0			c.A3295G						.						58	57	57					17																	65905802		2203	4300	6503	SO:0001583	missense	2186	exon12			GAGGTAAAAGGTT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.3295A>G	chr17.hg19:g.65905802A>G	ENSP00000315454:p.Lys1099Glu	227.0	0.0		201.0	51.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	A	12.48	1.950761	0.34471	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	T;T;T	0.61859	0.07;0.07;0.11	6.07	5.0	0.66597	.	.	.	.	.	T	0.41789	0.1174	N	0.19112	0.55	0.20307	N	0.999911	B;B	0.24920	0.01;0.114	B;B	0.24394	0.009;0.053	T	0.28170	-1.0052	9	0.56958	D	0.05	-3.8014	8.167	0.31233	0.9133:0.0:0.0867:0.0	.	973;1099	Q12830-2;Q12830-4	.;.	E	973;1099;1099	ENSP00000307208:K973E;ENSP00000334351:K1099E;ENSP00000315454:K1099E	ENSP00000307208:K973E	K	+	1	0	BPTF	63336264	1.000000	0.71417	0.589000	0.28718	0.968000	0.65278	2.991000	0.49409	2.326000	0.78906	0.533000	0.62120	AAA	.	.		0.363	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65905802	A	G	65905802	3	3	164	1	0	0	0	0	1	0	0	0	1497	15	1	2	3341	2	BPTF	17	65905802	Missense_Mutation	SNP	A	TCGA-DD-AACM-01A-11D-A40R-10	16194953	65905802	15289408	48	25140										
SDK2	54549	hgsc.bcm.edu	37	chr17	71361407	71361407	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gtccactcaccatccacgggGctgcagggctcgtacaccag	11	16	1	0			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr17:71361407G>A	ENST00000392650.3	-	38	5295	c.5295C>T	c.(5293-5295)agC>agT	p.S1765S	SDK2_ENST00000388726.3_Silent_p.S1746S|SDK2_ENST00000410094.1_5'UTR	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1765	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CATCCACGGGGCTGCAGGGCT	0.612																																					p.S1765S		Atlas-SNP	.											.	SDK2	219	.	0			c.C5295T						.						27	26	26					17																	71361407		2203	4300	6503	SO:0001819	synonymous_variant	54549	exon38			CACGGGGCTGCAG	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.5295C>T	chr17.hg19:g.71361407G>A		64.0	0.0		41.0	21.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	hg19	CCDS45769.1																																																																																			.	.		0.612	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		A	71361407	G	A	71361407	2	1	164	1	0	0	0	0	0	0	0	1	13984	1194	42	3		3	SDK2	17	71361407	Silent	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10	5455605	71361407	9833803	49	25141										
PPP5C	5536	hgsc.bcm.edu	37	chr19	46891672	46891672	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	cgctccccaccagggcccatGtgtgacctgctctggtcaga	11	16	2	2			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr19:46891672G>A	ENST00000012443.4	+	10	1246	c.1143G>A	c.(1141-1143)atG>atA	p.M381I	PPP5C_ENST00000391919.1_Missense_Mutation_p.M253I|AC007193.8_ENST00000598616.1_RNA	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	381	Catalytic.				cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		CAGGGCCCATGTGTGACCTGC	0.672																																					p.M381I		Atlas-SNP	.											.	PPP5C	44	.	0			c.G1143A						.						56	52	53					19																	46891672		2203	4300	6503	SO:0001583	missense	5536	exon10			GCCCATGTGTGAC		CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "Tetratricopeptide (TTC) repeat domain containing"	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.1143G>A	chr19.hg19:g.46891672G>A	ENSP00000012443:p.Met381Ile	90.0	0.0		99.0	35.0	NM_006247	Q16722|Q53XV2	Missense_Mutation	SNP	ENST00000012443.4	hg19	CCDS12684.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.278012	0.59758	.	.	ENSG00000011485	ENST00000012443;ENST00000451918;ENST00000391919	T;T	0.05199	3.48;3.48	4.8	3.68	0.42216	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.041386	0.85682	D	0.000000	T	0.17916	0.0430	M	0.78285	2.405	0.80722	D	1	P;B	0.48640	0.913;0.18	P;B	0.54499	0.754;0.128	T	0.00557	-1.1672	10	0.49607	T	0.09	-25.508	12.1384	0.53984	0.0:0.1745:0.8255:0.0	.	381;381	B2R6R6;P53041	.;PPP5_HUMAN	I	381;368;253	ENSP00000012443:M381I;ENSP00000375786:M253I	ENSP00000012443:M381I	M	+	3	0	PPP5C	51583512	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	7.143000	0.77348	2.211000	0.71520	0.491000	0.48974	ATG	.	.		0.672	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		A	46891672	G	A	46891672	3	1	164	1	0	0	0	0	1	0	0	0	12418	1377	48	3	1181	3	PPP5C	19	46891672	Missense_Mutation	SNP	G	TCGA-DD-AACM-01A-11D-A40R-10		46891672	12237311	50	25142										
SIGLEC14	100049587	hgsc.bcm.edu	37	chr19	52147072	52147072	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gacaggtgctgggagcccagCggatgctgaacccggcaggt	17	11	0	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr19:52147072C>T	ENST00000360844.6	-	5	1013	c.972G>A	c.(970-972)ccG>ccA	p.P324P	SIGLEC5_ENST00000534261.2_Intron|SIGLEC5_ENST00000599649.1_Intron|SIGLEC5_ENST00000429354.3_Intron|SIGLEC5_ENST00000222107.4_Intron	NM_001098612.1	NP_001092082.1	Q08ET2	SIG14_HUMAN	sialic acid binding Ig-like lectin 14	324	Ig-like C2-type 2.				cell adhesion (GO:0007155)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	29		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000965)|OV - Ovarian serous cystadenocarcinoma(262;0.0195)		GGGAGCCCAGCGGATGCTGAA	0.577																																					p.P324P		Atlas-SNP	.											.	SIGLEC14	46	.	0			c.G972A						.						47	53	51					19																	52147072		1803	4039	5842	SO:0001819	synonymous_variant	100049587	exon5			GCCCAGCGGATGC	AY854038	CCDS42604.1	19q13.41	2013-01-29			ENSG00000254415	ENSG00000254415		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	32926	protein-coding gene	gene with protein product						17012248	Standard	NM_001098612		Approved		uc002pxf.4	Q08ET2	OTTHUMG00000165511	ENST00000360844.6:c.972G>A	chr19.hg19:g.52147072C>T		115.0	0.0		125.0	34.0	NM_001098612	Q6UXG0	Silent	SNP	ENST00000360844.6	hg19	CCDS42604.1																																																																																			.	.		0.577	SIGLEC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466899.2	NM_001098612		T	52147072	C	T	52147072	2	4	164	1	0	0	0	0	0	0	0	1	14324	755	27	1		1	SIGLEC14	19	52147072	Silent	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	5255400	52147072	6981911	51	25143										
ZFP28	140612	hgsc.bcm.edu	37	chr19	57065248	57065248	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	gcaagagccaattactcataAcaaaaccctctctaaggaaa	5	11	2	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr19:57065248A>T	ENST00000301318.3	+	8	1165	c.1094A>T	c.(1093-1095)aAc>aTc	p.N365I	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	365					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		ATTACTCATAACAAAACCCTC	0.378																																					p.N365I	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.A1094T						.						82	76	78					19																	57065248		2203	4300	6503	SO:0001583	missense	140612	exon8			CTCATAACAAAAC		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.1094A>T	chr19.hg19:g.57065248A>T	ENSP00000301318:p.Asn365Ile	165.0	0.0		179.0	91.0	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	hg19	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	A	3.378	-0.126951	0.06795	.	.	ENSG00000196867	ENST00000301318	T	0.05139	3.49	4.96	2.86	0.33363	.	0.554792	0.16498	N	0.211799	T	0.04770	0.0129	N	0.26130	0.795	0.19775	N	0.999959	P	0.45283	0.855	B	0.38327	0.271	T	0.34800	-0.9814	10	0.62326	D	0.03	.	7.8401	0.29393	0.8255:0.0:0.1745:0.0	.	365	Q8NHY6	ZFP28_HUMAN	I	365	ENSP00000301318:N365I	ENSP00000301318:N365I	N	+	2	0	ZFP28	61757060	0.000000	0.05858	0.002000	0.10522	0.020000	0.10135	0.571000	0.23669	0.372000	0.24591	0.533000	0.62120	AAC	.	.		0.378	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		T	57065248	A	T	57065248	3	4	164	1	0	0	0	0	1	0	0	0	17657	43	2	4	1124	4	ZFP28	19	57065248	Missense_Mutation	SNP	A	TCGA-DD-AACM-01A-11D-A40R-10	4918176	57065248	2063735	52	25144										
SLC5A4	6527	hgsc.bcm.edu	37	chr22	32620469	32620469	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	cattagaccccagaatgctcCctgcaaaagaagcaagaaga	8	11	0	5			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr22:32620469C>A	ENST00000266086.4	-	13	1461	c.1450G>T	c.(1450-1452)Gga>Tga	p.G484*	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	484					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CAGAATGCTCCCTGCAAAAGA	0.408																																					p.G484X		Atlas-SNP	.											.	SLC5A4	82	.	0			c.G1450T						.						45	40	41					22																	32620469		2203	4300	6503	SO:0001630	splice_region_variant	6527	exon13			ATGCTCCCTGCAA	U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"Solute carriers"	11039	protein-coding gene	gene with protein product			"solute carrier family 5 (low affinity glucose cotransporter), member 4"			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.1450-1G>T	chr22.hg19:g.32620469C>A		125.0	0.0		114.0	35.0	NM_014227	O15279	Nonsense_Mutation	SNP	ENST00000266086.4	hg19	CCDS13903.1	.	.	.	.	.	.	.	.	.	.	C	32	5.118820	0.94385	.	.	ENSG00000100191	ENST00000266086	.	.	.	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.4815	0.75530	0.0:1.0:0.0:0.0	.	.	.	.	X	484	.	ENSP00000266086:G484X	G	-	1	0	SLC5A4	30950469	1.000000	0.71417	1.000000	0.80357	0.473000	0.32948	7.463000	0.80869	2.507000	0.84556	0.643000	0.83706	GGA	.	.		0.408	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227	Nonsense_Mutation	A	32620469	C	A	32620469	5	1	164	1	0	0	0	0	0	0	1	0	14682	637	22	3	541	3	SLC5A4	22	32620469	Splice_Site	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10		32620469	18684097	53	25145										
APOBEC3B	9582	hgsc.bcm.edu	37	chr22	39387543	39387543	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	agactgcgcatcttcgctgcCcgcatctatgattacgaccc	8	15	2	2			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chr22:39387543C>G	ENST00000333467.3	+	6	975	c.930C>G	c.(928-930)gcC>gcG	p.A310A	APOBEC3B_ENST00000407298.3_Silent_p.A285A|APOBEC3B_ENST00000402182.3_Silent_p.A310A|APOBEC3B-AS1_ENST00000513758.2_RNA	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	310					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|negative regulation of transposition (GO:0010529)	nucleus (GO:0005634)	deoxycytidine deaminase activity (GO:0047844)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	13	Melanoma(58;0.04)					TCTTCGCTGCCCGCATCTATG	0.572																																					p.A310A		Atlas-SNP	.											.	APOBEC3B	32	.	0			c.C930G						.						126	123	124					22																	39387543		2199	4282	6481	SO:0001819	synonymous_variant	9582	exon6			CGCTGCCCGCATC	AK024854	CCDS13982.1, CCDS58807.1	22q13.1-q13.2	2008-05-15			ENSG00000179750	ENSG00000179750		"Apolipoprotein B mRNA editing enzymes"	17352	protein-coding gene	gene with protein product	"phorbolin 3"	607110				11863358, 10469298	Standard	NM_004900		Approved	PHRBNL, FLJ21201	uc003awo.2	Q9UH17	OTTHUMG00000151085	ENST00000333467.3:c.930C>G	chr22.hg19:g.39387543C>G		205.0	0.0		183.0	37.0	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	hg19	CCDS13982.1																																																																																			.	.		0.572	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900		G	39387543	C	G	39387543	2	3	164	1	0	0	0	0	0	0	0	1	790	610	22	4		4	APOBEC3B	22	39387543	Silent	SNP	C	TCGA-DD-AACM-01A-11D-A40R-10	6767074	39387543	11917023	54	25146										
MAOB	4129	hgsc.bcm.edu	37	chrX	43634423	43634423	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0181818181818182	1	1	0.277777777777778	1.5	0	1	1	0	tagcatgcttttactctaccTtccatattgagtcaggatcc	6	11	2	1			TCGA-DD-AACM-01A-11D-A40R-10	TCGA-DD-AACM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f581ac9-bc00-4c25-8727-7069d737912e	c758de19-378a-4db8-b408-599509d3864c	g.chrX:43634423T>A	ENST00000378069.4	-	12	1381	c.1234A>T	c.(1234-1236)Agg>Tgg	p.R412W	MAOB_ENST00000538942.1_Intron|MAOB_ENST00000536181.1_Splice_Site_p.R396W	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	412					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	TTACTCTACCTTCCATATTGA	0.448																																					p.R412W		Atlas-SNP	.											.	MAOB	52	.	0			c.A1234T						.						42	39	40					X																	43634423		2203	4300	6503	SO:0001630	splice_region_variant	4129	exon12			TCTACCTTCCATA		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.1235+1A>T	chrX.hg19:g.43634423T>A		45.0	0.0		45.0	27.0	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.905092	0.92035	.	.	ENSG00000069535	ENST00000378069;ENST00000536181	D;D	0.92348	-3.02;-3.02	5.96	5.96	0.96718	Amine oxidase (1);	0.044283	0.85682	D	0.000000	D	0.96071	0.8720	M	0.84683	2.71	0.80722	D	1	D	0.76494	0.999	D	0.69479	0.964	D	0.96501	0.9371	10	0.72032	D	0.01	-6.3778	14.2661	0.66118	0.0:0.0:0.0:1.0	.	412	P27338	AOFB_HUMAN	W	412;396	ENSP00000367309:R412W;ENSP00000441613:R396W	ENSP00000367309:R412W	R	-	1	2	MAOB	43519367	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.422000	0.66453	2.015000	0.59207	0.486000	0.48141	AGG	.	.		0.448	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898	Missense_Mutation	A	43634423	T	A	43634423	5	1	164	1	0	0	0	0	0	0	1	0	9235	1623	56	4	344	4	MAOB	23	43634423	Splice_Site	SNP	T	TCGA-DD-AACM-01A-11D-A40R-10		43634423	111636137	55	25147										
TAS1R1	80835	hgsc.bcm.edu	37	chr1	6630983	6630983	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	ccacaggtcttgtagcttcaAtgagcatggctaccacctct	8	13	3	1	rs373171619		TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr1:6630983A>T	ENST00000333172.6	+	2	399	c.206A>T	c.(205-207)aAt>aTt	p.N69I	TAS1R1_ENST00000351136.3_Missense_Mutation_p.N69I|TAS1R1_ENST00000328191.4_Missense_Mutation_p.N69I	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	69					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		TGTAGCTTCAATGAGCATGGC	0.567																																					p.N69I		Atlas-SNP	.											.	TAS1R1	76	.	0			c.A206T						.						112	101	105					1																	6630983		2203	4300	6503	SO:0001583	missense	80835	exon2			GCTTCAATGAGCA		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14448	protein-coding gene	gene with protein product		606225	"G protein-coupled receptor 70"	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.206A>T	chr1.hg19:g.6630983A>T	ENSP00000331867:p.Asn69Ile	62.0	0.0		60.0	5.0	NM_177540	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Missense_Mutation	SNP	ENST00000333172.6	hg19	CCDS81.1	.	.	.	.	.	.	.	.	.	.	A	6.915	0.538504	0.13250	.	.	ENSG00000173662	ENST00000333172;ENST00000328191;ENST00000351136	D;D;D	0.86497	-2.13;-2.13;-2.13	5.08	3.95	0.45737	.	0.105784	0.64402	D	0.000008	D	0.89529	0.6741	L	0.54323	1.7	0.44523	D	0.997475	D;D;D;D	0.89917	1.0;0.997;0.989;0.997	D;D;P;D	0.79784	0.993;0.964;0.885;0.94	D	0.87319	0.2317	10	0.54805	T	0.06	.	5.5356	0.17009	0.7371:0.172:0.0908:0.0	.	69;69;69;69	Q7RTX1-3;Q7RTX1-4;Q7RTX1-2;Q7RTX1	.;.;.;TS1R1_HUMAN	I	69	ENSP00000331867:N69I;ENSP00000327705:N69I;ENSP00000312558:N69I	ENSP00000327705:N69I	N	+	2	0	TAS1R1	6553570	0.846000	0.29590	0.862000	0.33874	0.221000	0.24807	1.677000	0.37576	0.745000	0.32763	0.528000	0.53228	AAT	.	.		0.567	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			T	6630983	A	T	6630983	3	4	165	1	0	0	0	0	1	0	0	0	15577	101	4	4	212	4	TAS1R1	1	6630983	Missense_Mutation	SNP	A	TCGA-DD-AACN-01A-11D-A40R-10		6630983	242619638	1	25148										
GIPC2	54810	hgsc.bcm.edu	37	chr1	78601371	78601371	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gagactttgcgttcccagacGaatttgtctttgatgtttgg	11	7	1	3	rs138793126		TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr1:78601371G>T	ENST00000370759.3	+	6	1085	c.892G>T	c.(892-894)Gaa>Taa	p.E298*		NM_017655.4	NP_060125.4	Q8TF65	GIPC2_HUMAN	GIPC PDZ domain containing family, member 2	298						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)	20						GTTCCCAGACGAATTTGTCTT	0.423																																					p.E298X		Atlas-SNP	.											GIPC2,NS,carcinoma,0,1	GIPC2	37	.	0			c.G892T						.						111	98	103					1																	78601371		2203	4300	6503	SO:0001587	stop_gained	54810	exon6			CCAGACGAATTTG	AB073737	CCDS685.1	1p31.1	2010-05-28			ENSG00000137960	ENSG00000137960			18177	protein-coding gene	gene with protein product	"semaphorin cytoplasmic domain associated protein 2"					11836570	Standard	NM_017655		Approved	FLJ20075, SEMCAP-2	uc001dik.3	Q8TF65	OTTHUMG00000041145	ENST00000370759.3:c.892G>T	chr1.hg19:g.78601371G>T	ENSP00000359795:p.Glu298*	101.0	0.0		71.0	3.0	NM_017655	Q8IYD3|Q9NXS7	Nonsense_Mutation	SNP	ENST00000370759.3	hg19	CCDS685.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.303818	0.81136	.	.	ENSG00000137960	ENST00000370759	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-10.7864	19.85	0.96736	0.0:0.0:1.0:0.0	.	.	.	.	X	298	.	ENSP00000359795:E298X	E	+	1	0	GIPC2	78373959	1.000000	0.71417	1.000000	0.80357	0.065000	0.16274	9.447000	0.97595	2.771000	0.95319	0.650000	0.86243	GAA	.	G|1.000;A|0.000		0.423	GIPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098629.1	NM_017655		T	78601371	G	T	78601371	4	4	165	1	0	0	0	0	0	1	0	0	6401	1059	37	1	914	1	GIPC2	1	78601371	Nonsense_Mutation	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10	71970388	78601371	170649250	2	25149										
TCHH	7062	hgsc.bcm.edu	37	chr1	152084224	152084224	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gcctctcctcctcctcgagcTtcagccaacgttcgcgcctc	7	20	2	0			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr1:152084224T>C	ENST00000368804.1	-	2	1468	c.1469A>G	c.(1468-1470)aAg>aGg	p.K490R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	490	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCTCGAGCTTCAGCCAACG	0.672																																					p.K490R		Atlas-SNP	.											.	TCHH	275	.	0			c.A1469G						.						65	71	69					1																	152084224		2109	4224	6333	SO:0001583	missense	7062	exon3			TCGAGCTTCAGCC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1469A>G	chr1.hg19:g.152084224T>C	ENSP00000357794:p.Lys490Arg	28.0	0.0		64.0	5.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	t	8.419	0.845945	0.16963	.	.	ENSG00000159450	ENST00000368804	T	0.04654	3.58	2.98	-5.97	0.02227	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.09590	T	0.72	.	5.0277	0.14393	0.1398:0.4054:0.0:0.4548	.	490	Q07283	TRHY_HUMAN	R	490	ENSP00000357794:K490R	ENSP00000357794:K490R	K	-	2	0	TCHH	150350848	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.247000	0.00266	-1.053000	0.03218	-1.396000	0.01147	AAG	.	.		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084224	T	C	152084224	3	2	165	1	0	0	0	0	1	0	0	0	15715	1609	56	2	4366	2	TCHH	1	152084224	Missense_Mutation	SNP	T	TCGA-DD-AACN-01A-11D-A40R-10	73482853	152084224	97166397	3	25150										
TDRD10	126668	hgsc.bcm.edu	37	chr1	154516919	154516919	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gagcagcagccctacctggaGggctccaccgttatgcgcgg	14	14	0	0			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr1:154516919G>A	ENST00000368480.3	+	10	808	c.723G>A	c.(721-723)gaG>gaA	p.E241E	TDRD10_ENST00000368482.4_Silent_p.E241E|TDRD10_ENST00000479937.1_3'UTR			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	241	Tudor.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			CCTACCTGGAGGGCTCCACCG	0.632																																					p.E241E		Atlas-SNP	.											.	TDRD10	48	.	0			c.G723A						.						35	31	32					1																	154516919		2203	4300	6503	SO:0001819	synonymous_variant	126668	exon10			CCTGGAGGGCTCC	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"Tudor domain containing", "RNA binding motif (RRM) containing"	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.723G>A	chr1.hg19:g.154516919G>A		252.0	0.0		339.0	44.0	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Silent	SNP	ENST00000368480.3	hg19	CCDS41406.1																																																																																			.	.		0.632	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499		A	154516919	G	A	154516919	2	1	165	1	0	0	0	0	0	0	0	1	15746	991	35	3		3	TDRD10	1	154516919	Silent	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10	2432695	154516919	94733702	4	25151										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196394993	196394993	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gatacctactttgctctcaaTaggtcttgatctttaagggc	8	9	3	1			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr1:196394993T>C	ENST00000294725.9	-	11	2025	c.1110A>G	c.(1108-1110)ctA>ctG	p.L370L	KCNT2_ENST00000609185.1_Silent_p.L370L|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000451324.2_Intron|KCNT2_ENST00000367431.4_Silent_p.L370L|KCNT2_ENST00000367433.5_Silent_p.L370L			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	370					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						TTGCTCTCAATAGGTCTTGAT	0.403																																					p.L370L		Atlas-SNP	.											KCNT2,colon,carcinoma,0,1	KCNT2	243	.	0			c.A1110G						.						175	160	165					1																	196394993		2203	4300	6503	SO:0001819	synonymous_variant	343450	exon11			TCTCAATAGGTCT	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.1110A>G	chr1.hg19:g.196394993T>C		133.0	0.0		214.0	59.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	hg19	CCDS1384.1																																																																																			.	.		0.403	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		C	196394993	T	C	196394993	2	2	165	1	0	0	0	0	0	0	0	1	8101	1393	49	2		2	KCNT2	1	196394993	Silent	SNP	T	TCGA-DD-AACN-01A-11D-A40R-10	41878074	196394993	52855628	5	25152										
CRB1	23418	hgsc.bcm.edu	37	chr1	197390426	197390426	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	caaccacactttcatttgagGgcgatggcttcctgtgggtc	11	11	1	1			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr1:197390426G>T	ENST00000367400.3	+	6	1603	c.1468G>T	c.(1468-1470)Ggc>Tgc	p.G490C	CRB1_ENST00000543483.1_Missense_Mutation_p.G189C|CRB1_ENST00000367397.1_5'UTR|CRB1_ENST00000538660.1_Missense_Mutation_p.G490C|CRB1_ENST00000544212.1_5'UTR|CRB1_ENST00000476483.1_3'UTR|CRB1_ENST00000535699.1_Missense_Mutation_p.G421C|CRB1_ENST00000367399.2_Missense_Mutation_p.G378C	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	490	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TTCATTTGAGGGCGATGGCTT	0.517																																					p.G490C		Atlas-SNP	.											.	CRB1	284	.	0			c.G1468T						.						106	95	99					1																	197390426		2203	4300	6503	SO:0001583	missense	23418	exon6			TTTGAGGGCGATG		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.1468G>T	chr1.hg19:g.197390426G>T	ENSP00000356370:p.Gly490Cys	84.0	0.0		144.0	22.0	NM_001257966	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	hg19	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.810482	0.32053	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400;ENST00000367399;ENST00000543483;ENST00000367401	D;D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81;-1.81	5.82	3.94	0.45596	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	D	0.91168	0.7218	M	0.78916	2.43	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0	D;D;D;D;D	0.74348	0.942;0.981;0.974;0.983;0.953	D	0.90763	0.4666	9	0.56958	D	0.05	.	12.1515	0.54051	0.1271:0.0:0.8729:0.0	.	490;421;378;139;490	B7Z5T2;F5H0L2;P82279-3;P82279-4;P82279	.;.;.;.;CRUM1_HUMAN	C	421;490;490;378;189;139	ENSP00000438786:G421C;ENSP00000438091:G490C;ENSP00000356370:G490C;ENSP00000356369:G378C;ENSP00000439579:G189C	ENSP00000356369:G378C	G	+	1	0	CRB1	195657049	1.000000	0.71417	0.015000	0.15790	0.003000	0.03518	3.934000	0.56553	0.782000	0.33613	0.650000	0.86243	GGC	.	.		0.517	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		T	197390426	G	T	197390426	3	4	165	1	0	0	0	0	1	0	0	0	3850	1232	43	3	1490	3	CRB1	1	197390426	Missense_Mutation	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10	995433	197390426	51860195	6	25153										
LAMB3	3914	hgsc.bcm.edu	37	chr1	209807908	209807908	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	ggtggaggtgcagtcggcagCcaggtactggtacactcgcc	16	11	0	0			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr1:209807908C>T	ENST00000356082.4	-	6	582	c.448G>A	c.(448-450)Gct>Act	p.A150T	LAMB3_ENST00000391911.1_Missense_Mutation_p.A150T|LAMB3_ENST00000367030.3_Missense_Mutation_p.A150T	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	150	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		CAGTCGGCAGCCAGGTACTGG	0.652																																					p.A150T		Atlas-SNP	.											.	LAMB3	136	.	0			c.G448A						.						64	56	59					1																	209807908		2203	4300	6503	SO:0001583	missense	3914	exon6			CGGCAGCCAGGTA	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.448G>A	chr1.hg19:g.209807908C>T	ENSP00000348384:p.Ala150Thr	104.0	0.0		196.0	123.0	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	hg19	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.307411	0.81247	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030;ENST00000415782	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	4.57	4.57	0.56435	Laminin, N-terminal (3);	0.000000	0.85682	D	0.000000	D	0.90652	0.7068	M	0.91406	3.205	0.58432	D	0.999995	D	0.76494	0.999	D	0.68765	0.96	D	0.92418	0.5943	10	0.87932	D	0	.	13.1427	0.59444	0.1604:0.8396:0.0:0.0	.	150	Q13751	LAMB3_HUMAN	T	150	ENSP00000375778:A150T;ENSP00000348384:A150T;ENSP00000355997:A150T;ENSP00000388960:A150T	ENSP00000348384:A150T	A	-	1	0	LAMB3	207874531	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	2.423000	0.44705	2.381000	0.81170	0.558000	0.71614	GCT	.	.		0.652	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		T	209807908	C	T	209807908	3	4	165	1	0	0	0	0	1	0	0	0	8621	739	26	3	3142	3	LAMB3	1	209807908	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10	12417482	209807908	39442713	7	25154										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131520231	131520231	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	acccgtcagaccctggggggCggcgaagcaaagccttcctc	13	15	1	1			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr2:131520231C>T	ENST00000423981.1	+	2	696	c.586C>T	c.(586-588)Cgg>Tgg	p.R196W	AMER3_ENST00000321420.4_Missense_Mutation_p.R196W	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	196					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										CCCTGGGGGGCGGCGAAGCAA	0.672																																					p.R196W		Atlas-SNP	.											.	.	.	.	0			c.C586T						.						25	32	29					2																	131520231		2200	4284	6484	SO:0001583	missense	205147	exon2			GGGGGGCGGCGAA	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.586C>T	chr2.hg19:g.131520231C>T	ENSP00000392700:p.Arg196Trp	61.0	0.0		58.0	13.0	NM_152698	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	hg19	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	C	10.67	1.415480	0.25552	.	.	ENSG00000178171	ENST00000321420;ENST00000423981	T;T	0.54279	0.58;0.58	5.21	0.769	0.18492	.	1.448950	0.03947	N	0.287921	T	0.52517	0.1739	N	0.24115	0.695	0.09310	N	1	D	0.69078	0.997	P	0.54815	0.761	T	0.47560	-0.9108	10	0.72032	D	0.01	.	8.3373	0.32221	0.4865:0.3968:0.1168:0.0	.	196	Q8N944	F123C_HUMAN	W	196	ENSP00000314914:R196W;ENSP00000392700:R196W	ENSP00000314914:R196W	R	+	1	2	FAM123C	131236701	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.044000	0.13992	0.009000	0.14813	-0.314000	0.08810	CGG	.	.		0.672	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		T	131520231	C	T	131520231	3	4	165	1	0	0	0	0	1	0	0	0	5429	759	27	1	588	1	FAM123C	2	131520231	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10		131520231	111679142	8	25155										
P2RY12	64805	hgsc.bcm.edu	37	chr3	151056067	151056067	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	acttgacagatgtaatttacTatttcatgccagactagacc	6	9	1	4			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr3:151056067T>C	ENST00000302632.3	-	3	866	c.567A>G	c.(565-567)atA>atG	p.I189M	MED12L_ENST00000474524.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron	NM_022788.4|NM_176876.2	NP_073625.1|NP_795345.1	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y, G-protein coupled, 12	189					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell projection organization (GO:0030030)|G-protein coupled purinergic nucleotide receptor signaling pathway (GO:0035589)|G-protein coupled receptor signaling pathway (GO:0007186)|hemostasis (GO:0007599)|negative regulation of cell differentiation (GO:0045596)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of GTPase activity (GO:0043547)|positive regulation of ion transport (GO:0043270)|potassium ion transmembrane transport (GO:0071805)|protein kinase B signaling (GO:0043491)|regulation of calcium ion transport (GO:0051924)	basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	ADP receptor activity (GO:0001621)|G-protein coupled adenosine receptor activity (GO:0001609)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	17			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Prasugrel(DB06209)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Treprostinil(DB00374)	TGTAATTTACTATTTCATGCC	0.358																																					p.I189M		Atlas-SNP	.											.	P2RY12	36	.	0			c.A567G						.						88	87	87					3																	151056067		2203	4300	6503	SO:0001583	missense	64805	exon3			ATTTACTATTTCA	AJ320495	CCDS3159.1	3q24-q25	2014-09-17			ENSG00000169313	ENSG00000169313		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	18124	protein-coding gene	gene with protein product		600515				11502873, 11104774	Standard	NM_022788		Approved	P2Y12, SP1999, HORK3	uc003eyw.1	Q9H244	OTTHUMG00000159863	ENST00000302632.3:c.567A>G	chr3.hg19:g.151056067T>C	ENSP00000307259:p.Ile189Met	103.0	0.0		95.0	18.0	NM_022788	D3DNJ5|Q546J7	Missense_Mutation	SNP	ENST00000302632.3	hg19	CCDS3159.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.076140	0.36662	.	.	ENSG00000169313	ENST00000302632	T	0.73469	-0.75	5.42	-3.77	0.04346	GPCR, rhodopsin-like superfamily (1);	0.266926	0.42172	D	0.000758	T	0.59542	0.2201	L	0.57536	1.79	0.33964	D	0.645931	B	0.14438	0.01	B	0.22386	0.039	T	0.40117	-0.9580	10	0.33141	T	0.24	-18.7762	2.695	0.05132	0.2655:0.0802:0.3979:0.2564	.	189	Q9H244	P2Y12_HUMAN	M	189	ENSP00000307259:I189M	ENSP00000307259:I189M	I	-	3	3	P2RY12	152538757	0.688000	0.27680	0.996000	0.52242	0.993000	0.82548	-0.138000	0.10374	-0.171000	0.10797	0.533000	0.62120	ATA	.	.		0.358	P2RY12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357796.1			C	151056067	T	C	151056067	3	2	165	1	0	0	0	0	1	0	0	0	11358	1512	53	2	465	2	P2RY12	3	151056067	Missense_Mutation	SNP	T	TCGA-DD-AACN-01A-11D-A40R-10		151056067	46966363	9	25156										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6037770	6037770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	ggccctcgctcagcgcctcaCcggccctccgccccggctcc	10	24	2	0			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr4:6037770C>T	ENST00000409021.3	-	19	2689	c.2240G>A	c.(2239-2241)gGt>gAt	p.G747D	JAKMIP1_ENST00000409371.3_Missense_Mutation_p.G562D	NM_001099433.1	NP_001092903.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	103					cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CAGCGCCTCACCGGCCCTCCG	0.642																																					p.G747D		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.G2240A						.						10	13	12					4																	6037770		2067	4128	6195	SO:0001583	missense	152789	exon19			GCCTCACCGGCCC	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000409021.3:c.2240G>A	chr4.hg19:g.6037770C>T	ENSP00000386711:p.Gly747Asp	143.0	0.0		116.0	30.0	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000409021.3	hg19	CCDS47005.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.048128	0.36181	.	.	ENSG00000152969	ENST00000409021;ENST00000409371	T;T	0.30714	1.94;1.52	4.79	4.79	0.61399	.	0.116804	0.31071	U	0.008301	T	0.22859	0.0552	.	.	.	0.80722	D	1	B;B	0.25609	0.02;0.13	B;B	0.32533	0.05;0.147	T	0.05666	-1.0871	9	0.13470	T	0.59	.	12.6993	0.57022	0.0:0.8344:0.1656:0.0	.	562;747	Q96N16-5;Q96N16-2	.;.	D	747;562	ENSP00000386711:G747D;ENSP00000387042:G562D	ENSP00000386711:G747D	G	-	2	0	JAKMIP1	6088671	0.999000	0.42202	0.927000	0.36925	0.457000	0.32468	3.058000	0.49939	2.219000	0.72066	0.436000	0.28706	GGT	.	.		0.642	JAKMIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329747.1	NM_144720		T	6037770	C	T	6037770	3	4	165	1	0	0	0	0	1	0	0	0	7949	507	18	3	267	3	JAKMIP1	4	6037770	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10		6037770	185116506	10	25157										
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42524292	42524292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	cgctctctgaaatctcagccAcagcaaaacataaagttctt	5	12	3	1			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr4:42524292A>G	ENST00000381668.5	-	22	2063	c.1832T>C	c.(1831-1833)gTg>gCg	p.V611A	ATP8A1_ENST00000264449.10_Missense_Mutation_p.V596A	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	611					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	AATCTCAGCCACAGCAAAACA	0.418																																					p.V611A		Atlas-SNP	.											.	ATP8A1	206	.	0			c.T1832C						.						70	66	67					4																	42524292		2203	4300	6503	SO:0001583	missense	10396	exon22			TCAGCCACAGCAA	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1832T>C	chr4.hg19:g.42524292A>G	ENSP00000371084:p.Val611Ala	83.0	0.0		90.0	13.0	NM_006095	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	hg19	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.848875	0.32699	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.67345	-0.26;-0.26	5.54	5.54	0.83059	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.69584	0.3127	L	0.33137	0.985	0.80722	D	1	B;B	0.32862	0.387;0.037	P;B	0.48089	0.566;0.055	T	0.70597	-0.4828	10	0.51188	T	0.08	.	15.9755	0.80060	1.0:0.0:0.0:0.0	.	596;611	Q32M35;Q9Y2Q0	.;AT8A1_HUMAN	A	611;596	ENSP00000371084:V611A;ENSP00000264449:V596A	ENSP00000264449:V596A	V	-	2	0	ATP8A1	42219049	1.000000	0.71417	1.000000	0.80357	0.117000	0.20001	8.196000	0.89725	2.219000	0.72066	0.528000	0.53228	GTG	.	.		0.418	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		G	42524292	A	G	42524292	3	3	165	1	0	0	0	0	1	0	0	0	1192	159	6	2	1726	2	ATP8A1	4	42524292	Missense_Mutation	SNP	A	TCGA-DD-AACN-01A-11D-A40R-10	36486522	42524292	148629984	11	25158										
KIT	3815	hgsc.bcm.edu	37	chr4	55569979	55569979	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	actatcagttcagcgagagtTaatgattctggagtgttcat	10	6	4	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr4:55569979T>C	ENST00000288135.5	+	5	943	c.846T>C	c.(844-846)gtT>gtC	p.V282V		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	282	Ig-like C2-type 3.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGCGAGAGTTAATGATTCTG	0.398		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.V282V		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT	7396	.	0			c.T846C						.						152	150	150					4																	55569979		2203	4300	6503	SO:0001819	synonymous_variant	3815	exon5	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	GAGAGTTAATGAT	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.846T>C	chr4.hg19:g.55569979T>C		222.0	0.0		139.0	87.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	hg19	CCDS3496.1																																																																																			.	.		0.398	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			C	55569979	T	C	55569979	2	2	165	1	0	0	0	0	0	0	0	1	8338	1741	61	2		2	KIT	4	55569979	Silent	SNP	T	TCGA-DD-AACN-01A-11D-A40R-10	13045687	55569979	135584297	12	25159										
ALB	213	hgsc.bcm.edu	37	chr4	74272457	74272457	+	Frame_Shift_Del	DEL	T	T	-													0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	tgtgttgctgatgagtcagcTgaaaattgtgacaaatcact							TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr4:74272457delT	ENST00000503124.1	+	2	218	c.11delT	c.(10-12)ctgfs	p.L4fs	ALB_ENST00000295897.4_Frame_Shift_Del_p.A83fs|ALB_ENST00000401494.3_Intron|ALB_ENST00000415165.2_Intron|ALB_ENST00000509063.1_Frame_Shift_Del_p.A83fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATGAGTCAGCTGAAAATTGTG	0.328																																					p.A83fs		Atlas-INDEL	.											.	ALB	132	.	0			c.248delC						.						100	93	95					4																	74272457		2203	4300	6503	SO:0001589	frameshift_variant	213	exon3			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.11delT	chr4.hg19:g.74272457delT	ENSP00000421027:p.Leu4fs	68.0	0.0		41.0	21.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.328	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74272457	T	-	74272457	7	5	165	1	0	1	0	1	0	0	0	0	486	1567	55	0	259	0	ALB	4	74272457	Frame_Shift_Del	DEL	T	TCGA-DD-AACN-01A-11D-A40R-10	18702478	74272457	116881819	13	25160	116	2								
ALB	213	hgsc.bcm.edu	37	chr4	74272458	74272458	+	Missense_Mutation	SNP	G	G	C													0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gtgttgctgatgagtcagctGaaaattgtgacaaatcactt					rs77050410		TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr4:74272458G>C	ENST00000295897.4	+	3	339	c.250G>C	c.(250-252)Gaa>Caa	p.E84Q	ALB_ENST00000503124.1_Silent_p.L4L|ALB_ENST00000401494.3_Intron|ALB_ENST00000415165.2_Intron|ALB_ENST00000509063.1_Missense_Mutation_p.E84Q	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGAGTCAGCTGAAAATTGTGA	0.323																																					p.E84Q		Atlas-SNP	.											.,1	ALB	132	.	0			c.G250C	GRCh37	CM900420	ALB	M	rs77050410	.						98	92	94					4																	74272458		2203	4300	6503	SO:0001583	missense	213	exon3			TCAGCTGAAAATT	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.250G>C	chr4.hg19:g.74272458G>C	ENSP00000295897:p.Glu84Gln	65.0	0.0		18.0	0.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000295897.4	hg19	CCDS3555.1	.	.	.	.	.	.	.	.	.	.	G	9.932	1.215120	0.22373	.	.	ENSG00000163631	ENST00000441319;ENST00000295897;ENST00000329326;ENST00000509063;ENST00000430202	T;T;T	0.73789	-0.78;-0.78;-0.78	5.44	2.6	0.31112	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.861933	0.09632	N	0.776156	T	0.71005	0.3289	L	0.47716	1.5	0.09310	N	0.999999	B;B	0.14438	0.01;0.005	B;B	0.18561	0.01;0.022	T	0.57734	-0.7760	10	0.36615	T	0.2	-1.6974	16.7573	0.85503	0.0:0.6476:0.3524:0.0	.	84;84	A6NBZ8;P02768	.;ALBU_HUMAN	Q	86;84;84;84;93	ENSP00000392541:E86Q;ENSP00000295897:E84Q;ENSP00000422784:E84Q	ENSP00000295897:E84Q	E	+	1	0	ALB	74491322	0.001000	0.12720	0.002000	0.10522	0.995000	0.86356	1.001000	0.29783	0.340000	0.23745	0.650000	0.86243	GAA	.	.		0.323	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477		C	74272458	G	C	74272458	3	2	165	1	0	0	0	0	1	0	0	0	486	1291	45	4	260	4	ALB	4	74272458	Missense_Mutation	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10	1	74272458	116881818	14	25161	116	2								
UNC5C	8633	hgsc.bcm.edu	37	chr4	96141175	96141175	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gttcacaggctgaaagccccCattgagtgccgaagagtcaa	11	11	2	3			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr4:96141175C>T	ENST00000453304.1	-	8	1609	c.1261G>A	c.(1261-1263)Ggg>Agg	p.G421R	UNC5C_ENST00000506749.1_Missense_Mutation_p.G440R	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	421					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		TGAAAGCCCCCATTGAGTGCC	0.443																																					p.G421R		Atlas-SNP	.											.	UNC5C	141	.	0			c.G1261A						.						140	128	132					4																	96141175		2203	4300	6503	SO:0001583	missense	8633	exon8			AGCCCCCATTGAG	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"Immunoglobulin superfamily / I-set domain containing"	12569	protein-coding gene	gene with protein product		603610	"unc5 (C.elegans homolog) c"			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.1261G>A	chr4.hg19:g.96141175C>T	ENSP00000406022:p.Gly421Arg	318.0	0.0		190.0	95.0	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	hg19	CCDS3643.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.022802	0.93462	.	.	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796;ENST00000506749	T;T;T	0.61627	0.48;0.17;0.09	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.80369	0.4610	M	0.85859	2.78	0.80722	D	1	D;D;D	0.89917	0.996;1.0;1.0	D;D;D	0.91635	0.918;0.999;0.999	T	0.82532	-0.0410	10	0.87932	D	0	.	19.9179	0.97070	0.0:1.0:0.0:0.0	.	421;440;421	A8K385;E0CX15;O95185	.;.;UNC5C_HUMAN	R	421;380;440;440	ENSP00000406022:G421R;ENSP00000426924:G440R;ENSP00000426153:G440R	ENSP00000328673:G380R	G	-	1	0	UNC5C	96360198	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	7.818000	0.86416	2.723000	0.93209	0.655000	0.94253	GGG	.	.		0.443	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		T	96141175	C	T	96141175	3	4	165	1	0	0	0	0	1	0	0	0	17008	594	21	3	1570	3	UNC5C	4	96141175	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10	21868717	96141175	95013101	15	25162										
CCT5	22948	hgsc.bcm.edu	37	chr5	10250466	10250466	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	ttgcaccatggcgtccatggGgaccctcgccttcgatgaat	11	13	0	1			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr5:10250466G>T	ENST00000280326.4	+	1	434	c.14G>T	c.(13-15)gGg>gTg	p.G5V	CCT5_ENST00000506600.1_5'Flank|FAM173B_ENST00000280330.8_5'Flank|FAM173B_ENST00000511437.1_5'Flank|CTD-2256P15.1_ENST00000509915.1_RNA|CCT5_ENST00000515390.1_Missense_Mutation_p.G5V|FAM173B_ENST00000510052.1_5'Flank|CCT5_ENST00000515676.1_5'Flank|CCT5_ENST00000503026.1_Intron|FAM173B_ENST00000510047.1_5'Flank	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	5					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						GCGTCCATGGGGACCCTCGCC	0.577																																					p.G5V		Atlas-SNP	.											.	CCT5	49	.	0			c.G14T						.						80	59	66					5																	10250466		2203	4300	6503	SO:0001583	missense	22948	exon1			CCATGGGGACCCT	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"Heat Shock Proteins / Chaperonins"	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.14G>T	chr5.hg19:g.10250466G>T	ENSP00000280326:p.Gly5Val	172.0	0.0		142.0	49.0	NM_012073	A8JZY8|A8K2X8|B4DYD8	Missense_Mutation	SNP	ENST00000280326.4	hg19	CCDS3877.1	.	.	.	.	.	.	.	.	.	.	G	38	7.023384	0.98010	.	.	ENSG00000150753	ENST00000280326;ENST00000515390;ENST00000440011	T;T	0.56941	0.43;2.52	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.71195	0.3311	M	0.64997	1.995	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;0.982;0.982	D;D;P;P	0.80764	0.994;0.911;0.743;0.743	T	0.73269	-0.4036	10	0.72032	D	0.01	-25.754	18.3542	0.90351	0.0:0.0:1.0:0.0	.	5;3;5;5	E7ENZ3;Q9BU08;A8K2X8;P48643	.;.;.;TCPE_HUMAN	V	5	ENSP00000280326:G5V;ENSP00000426923:G5V	ENSP00000280326:G5V	G	+	2	0	CCT5	10303466	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.737000	0.91562	2.565000	0.86533	0.650000	0.86243	GGG	.	.		0.577	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2			T	10250466	G	T	10250466	3	4	165	1	0	0	0	0	1	0	0	0	2958	1232	43	3	16	3	CCT5	5	10250466	Missense_Mutation	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10		10250466	170664794	16	25163										
FAM134B	54463	hgsc.bcm.edu	37	chr5	16477816	16477816	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gtatccttctgaaaggttgaAggtcccattatcagtccagg	10	9	2	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr5:16477816A>T	ENST00000306320.9	-	8	1041	c.955T>A	c.(955-957)Ttc>Atc	p.F319I	FAM134B_ENST00000399793.2_Missense_Mutation_p.F178I	NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	319					sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						GAAAGGTTGAAGGTCCCATTA	0.388																																					p.F319I		Atlas-SNP	.											.	FAM134B	72	.	0			c.T955A						.						89	83	85					5																	16477816		1841	4090	5931	SO:0001583	missense	54463	exon8			GGTTGAAGGTCCC	BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153			25964	protein-coding gene	gene with protein product		613114				19838196, 24327336	Standard	NM_001034850		Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.955T>A	chr5.hg19:g.16477816A>T	ENSP00000304642:p.Phe319Ile	171.0	0.0		146.0	31.0	NM_001034850	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	Missense_Mutation	SNP	ENST00000306320.9	hg19	CCDS43304.1	.	.	.	.	.	.	.	.	.	.	A	34	5.320351	0.95682	.	.	ENSG00000154153	ENST00000399793;ENST00000306320	T;T	0.69806	-0.11;-0.43	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	D	0.82513	0.5053	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.991;0.996	D	0.84628	0.0688	10	0.87932	D	0	-17.8941	16.5494	0.84464	1.0:0.0:0.0:0.0	.	319;178	Q9H6L5;Q9H6L5-2	F134B_HUMAN;.	I	178;319	ENSP00000382691:F178I;ENSP00000304642:F319I	ENSP00000304642:F319I	F	-	1	0	FAM134B	16530816	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.637000	0.91014	2.299000	0.77371	0.528000	0.53228	TTC	.	.		0.388	FAM134B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366090.1	NM_001034850		T	16477816	A	T	16477816	3	4	165	1	0	0	0	0	1	0	0	0	5451	72	3	4	546	4	FAM134B	5	16477816	Missense_Mutation	SNP	A	TCGA-DD-AACN-01A-11D-A40R-10	6227350	16477816	164437444	17	25164										
ITGA2	3673	hgsc.bcm.edu	37	chr5	52367816	52367816	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	atttgcgtgtggacatcagtCtggaaaaccctggcactagc	11	10	2	0			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr5:52367816C>A	ENST00000296585.5	+	18	2427	c.2284C>A	c.(2284-2286)Ctg>Atg	p.L762M		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	762					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				GGACATCAGTCTGGAAAACCC	0.473																																					p.L762M		Atlas-SNP	.											.	ITGA2	211	.	0			c.C2284A						.						166	147	153					5																	52367816		2203	4300	6503	SO:0001583	missense	3673	exon18			ATCAGTCTGGAAA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2284C>A	chr5.hg19:g.52367816C>A	ENSP00000296585:p.Leu762Met	115.0	0.0		103.0	23.0	NM_002203	Q14595	Missense_Mutation	SNP	ENST00000296585.5	hg19	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.868437	0.51588	.	.	ENSG00000164171	ENST00000296585	T	0.58506	0.33	5.03	2.31	0.28768	Integrin alpha-2 (1);	0.272680	0.30890	N	0.008669	T	0.64962	0.2646	L	0.55481	1.735	0.09310	N	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.994;0.989	T	0.52555	-0.8560	10	0.66056	D	0.02	.	5.2632	0.15586	0.0:0.5272:0.1571:0.3158	.	762;762	E7ESP4;P17301	.;ITA2_HUMAN	M	762	ENSP00000296585:L762M	ENSP00000296585:L762M	L	+	1	2	ITGA2	52403573	0.959000	0.32827	0.991000	0.47740	0.893000	0.52053	1.922000	0.40045	0.759000	0.33084	0.467000	0.42956	CTG	.	.		0.473	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		A	52367816	C	A	52367816	3	1	165	1	0	0	0	0	1	0	0	0	7884	912	32	3	2354	3	ITGA2	5	52367816	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10	35890000	52367816	128547444	18	25165										
REEP5	7905	hgsc.bcm.edu	37	chr5	112238198	112238198	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	tatcatcttctttgttgggaCtctctatagctttaattctg	6	8	5	0			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr5:112238198C>T	ENST00000379638.4	-	3	578	c.230G>A	c.(229-231)aGt>aAt	p.S77N	REEP5_ENST00000474542.2_5'UTR|REEP5_ENST00000513339.1_Missense_Mutation_p.S77N|REEP5_ENST00000504247.1_Intron|REEP5_ENST00000545426.1_Missense_Mutation_p.S77N	NM_005669.4	NP_005660.4	Q00765	REEP5_HUMAN	receptor accessory protein 5	77						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		Epithelial(69;1.3e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.26e-08)|all cancers(49;3.56e-07)|Colorectal(14;0.00778)|COAD - Colon adenocarcinoma(37;0.013)		TTTGTTGGGACTCTCTATAGC	0.378																																					p.S77N		Atlas-SNP	.											.	REEP5	12	.	0			c.G230A						.						141	141	141					5																	112238198		2202	4300	6502	SO:0001583	missense	7905	exon3			TTGGGACTCTCTA	BC000232	CCDS4109.2	5q22-q23	2008-02-05	2006-02-07	2006-02-07	ENSG00000129625	ENSG00000129625		"Receptor accessory proteins"	30077	protein-coding gene	gene with protein product	"deleted in polyposis 1", "polyposis locus protein 1", "polyposis coli region hypothetical protein DP1"	125265	"chromosome 5 open reading frame 18"	C5orf18		16271481, 15550249	Standard	NM_005669		Approved	DP1, TB2, D5S346	uc003kqe.1	Q00765	OTTHUMG00000128807	ENST00000379638.4:c.230G>A	chr5.hg19:g.112238198C>T	ENSP00000368959:p.Ser77Asn	114.0	0.0		133.0	22.0	NM_005669	B7Z681|D3DT04|Q04198|Q5QGT0|Q9BWH9	Missense_Mutation	SNP	ENST00000379638.4	hg19	CCDS4109.2	.	.	.	.	.	.	.	.	.	.	C	32	5.112205	0.94339	.	.	ENSG00000129625	ENST00000379638;ENST00000513339;ENST00000545426;ENST00000261482	D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.96592	0.8888	M	0.72576	2.205	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.887	D;D;P	0.87578	0.995;0.998;0.775	D	0.96636	0.9470	10	0.87932	D	0	-26.8718	19.9036	0.96999	0.0:1.0:0.0:0.0	.	77;50;77	B7Z510;B7Z2A3;Q00765	.;.;REEP5_HUMAN	N	77;77;77;68	ENSP00000368959:S77N;ENSP00000425901:S77N;ENSP00000442940:S77N;ENSP00000261482:S68N	ENSP00000261482:S68N	S	-	2	0	REEP5	112266097	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.794000	0.85869	2.706000	0.92434	0.655000	0.94253	AGT	.	.		0.378	REEP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250739.2	NM_005669		T	112238198	C	T	112238198	3	4	165	1	0	0	0	0	1	0	0	0	13223	565	20	3	351	3	REEP5	5	112238198	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10	59870382	112238198	68677062	19	25166										
PRSS16	10279	hgsc.bcm.edu	37	chr6	27223091	27223091	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	agccagattaagggtgaagtCtgaatctcataccctttcca	8	10	2	3			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr6:27223091C>A	ENST00000230582.3	+	12	1557	c.1542C>A	c.(1540-1542)gtC>gtA	p.V514V	PRSS16_ENST00000377456.2_3'UTR|PRSS16_ENST00000421826.2_Silent_p.V257V	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	514					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						AGGGTGAAGTCTGAATCTCAT	0.463																																					p.V514V	NSCLC(178;1118 2105 17078 23587 44429)	Atlas-SNP	.											.	PRSS16	66	.	0			c.C1542A						.						83	68	73					6																	27223091		2203	4300	6503	SO:0001819	synonymous_variant	10279	exon12			TGAAGTCTGAATC	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"Serine peptidases / Serine peptidases"	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1542C>A	chr6.hg19:g.27223091C>A		119.0	0.0		178.0	52.0	NM_005865	O75416	Silent	SNP	ENST00000230582.3	hg19	CCDS4623.1																																																																																			.	.		0.463	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2			A	27223091	C	A	27223091	2	1	165	1	0	0	0	0	0	0	0	1	12628	900	32	3		3	PRSS16	6	27223091	Silent	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10		27223091	143891976	20	25167										
TMEM30A	55754	hgsc.bcm.edu	37	chr6	75974997	75974997	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	actatcatctcgagatttcaCgtaacgacgatggttttgat	8	8	3	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr6:75974997C>T	ENST00000230461.6	-	3	732	c.403G>A	c.(403-405)Gtg>Atg	p.V135M	TMEM30A_ENST00000475111.2_Missense_Mutation_p.V99M|TMEM30A_ENST00000370050.5_Missense_Mutation_p.V16M	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	135					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CGAGATTTCACGTAACGACGA	0.294																																					p.V135M		Atlas-SNP	.											.	TMEM30A	40	.	0			c.G403A						.						77	75	76					6																	75974997		2203	4298	6501	SO:0001583	missense	55754	exon3			ATTTCACGTAACG	AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"chromosome 6 open reading frame 67"	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.403G>A	chr6.hg19:g.75974997C>T	ENSP00000230461:p.Val135Met	67.0	0.0		84.0	57.0	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Missense_Mutation	SNP	ENST00000230461.6	hg19	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.522822	0.85600	.	.	ENSG00000112697	ENST00000230461;ENST00000545449;ENST00000370050;ENST00000475111;ENST00000518161	.	.	.	6.02	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.64538	0.2607	M	0.84326	2.69	0.80722	D	1	P;P	0.48407	0.89;0.91	P;P	0.48795	0.454;0.59	T	0.70554	-0.4840	9	0.49607	T	0.09	.	15.4073	0.74890	0.0:0.9335:0.0:0.0665	.	99;135	Q9NV96-2;Q9NV96	.;CC50A_HUMAN	M	135;119;16;99;16	.	ENSP00000230461:V135M	V	-	1	0	TMEM30A	76031717	1.000000	0.71417	0.997000	0.53966	0.949000	0.60115	7.719000	0.84751	1.551000	0.49450	0.650000	0.86243	GTG	.	.		0.294	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247		T	75974997	C	T	75974997	3	4	165	1	0	0	0	0	1	0	0	0	16168	536	19	1	702	1	TMEM30A	6	75974997	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10	48751906	75974997	95140070	21	25168										
ADAM18	8749	hgsc.bcm.edu	37	chr8	39467002	39467002	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gcctttctatactgtttttcAgatgcattgccattaccaag	6	10	2	1			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr8:39467002A>T	ENST00000265707.5	+	5	312		c.e5-1		ADAM18_ENST00000379866.1_Splice_Site|ADAM18_ENST00000541111.1_Splice_Site|ADAM18_ENST00000520772.1_Splice_Site	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			ACTGTTTTTCAGATGCATTGC	0.299																																					.		Atlas-SNP	.											.	ADAM18	169	.	0			c.268-2A>T						.						85	81	82					8																	39467002		2203	4298	6501	SO:0001630	splice_region_variant	8749	exon5			TTTTTCAGATGCA	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.268-1A>T	chr8.hg19:g.39467002A>T		48.0	0.0		70.0	42.0	NM_001190956	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Splice_Site	SNP	ENST00000265707.5	hg19	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	A	8.779	0.927871	0.18056	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000520772;ENST00000522198	.	.	.	4.89	3.75	0.43078	.	.	.	.	.	.	.	.	.	.	.	0.44728	D	0.997722	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.6969	0.23203	0.897:0.0:0.103:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADAM18	39586159	0.973000	0.33851	0.896000	0.35187	0.253000	0.25986	4.186000	0.58337	2.168000	0.68352	0.528000	0.53228	.	.	.		0.299	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	Intron	T	39467002	A	T	39467002	5	4	165	1	0	0	0	0	0	0	1	0	239	202	7	4	284	4	ADAM18	8	39467002	Splice_Site	SNP	A	TCGA-DD-AACN-01A-11D-A40R-10		39467002	106897020	22	25169										
PRKDC	5591	hgsc.bcm.edu	37	chr8	48846651	48846651	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	tcagattcagactcagggccCtggccagaaagacagcatga	11	11	3	5			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr8:48846651C>T	ENST00000523565.1	-	15	1554		c.e15-1		PRKDC_ENST00000338368.3_Splice_Site|PRKDC_ENST00000314191.2_Splice_Site			P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide						B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	ACTCAGGGCCCTGGCCAGAAA	0.473								Non-homologous end-joining																													.	Esophageal Squamous(79;1091 1253 12329 31680 40677)	Atlas-SNP	.											PRKDC,bladder,carcinoma,0,2	PRKDC	394	.	0			c.1498-1G>A						.						117	111	113					8																	48846651		1894	4106	6000	SO:0001630	splice_region_variant	5591	exon16			AGGGCCCTGGCCA		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000523565.1:c.11955-1G>A	chr8.hg19:g.48846651C>T		48.0	0.0		86.0	62.0	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Splice_Site	SNP	ENST00000523565.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.34	1.908506	0.33721	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	.	.	.	4.14	4.14	0.48551	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.3222	0.21225	0.0:0.808:0.0:0.192	.	.	.	.	.	-1	.	.	.	-	.	.	PRKDC	49009204	0.982000	0.34865	0.662000	0.29724	0.036000	0.12997	1.609000	0.36858	2.583000	0.87209	0.557000	0.71058	.	.	.		0.473	PRKDC-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000377896.1	NM_001081640	Intron	T	48846651	C	T	48846651	5	4	165	1	0	0	0	0	0	0	1	0	12533	695	24	3	11176	3	PRKDC	8	48846651	Splice_Site	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10	9379649	48846651	97517371	23	25170										
EFR3A	23167	hgsc.bcm.edu	37	chr8	133008691	133008691	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gaagaaaaagcattgtggacAccgtatccattcaggtggat	11	7	1	1			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr8:133008691A>G	ENST00000254624.5	+	19	2329	c.2104A>G	c.(2104-2106)Acc>Gcc	p.T702A	EFR3A_ENST00000519656.1_Missense_Mutation_p.T666A|EFR3A_ENST00000334503.4_Missense_Mutation_p.T702A	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	702						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			CATTGTGGACACCGTATCCAT	0.328																																					p.T702A		Atlas-SNP	.											.	EFR3A	96	.	0			c.A2104G						.						94	92	93					8																	133008691		2203	4299	6502	SO:0001583	missense	23167	exon19			GTGGACACCGTAT	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.2104A>G	chr8.hg19:g.133008691A>G	ENSP00000254624:p.Thr702Ala	70.0	0.0		78.0	47.0	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Missense_Mutation	SNP	ENST00000254624.5	hg19	CCDS34942.2	.	.	.	.	.	.	.	.	.	.	A	23.2	4.391569	0.83011	.	.	ENSG00000132294	ENST00000254624;ENST00000407309;ENST00000377917;ENST00000334503;ENST00000519656	T;T;T	0.32272	1.46;1.46;1.46	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.32912	0.0845	L	0.47716	1.5	0.80722	D	1	B	0.32338	0.365	B	0.35470	0.203	T	0.07520	-1.0768	10	0.52906	T	0.07	-14.8991	15.7938	0.78394	1.0:0.0:0.0:0.0	.	702	Q14156	EFR3A_HUMAN	A	702;81;658;702;666	ENSP00000254624:T702A;ENSP00000334769:T702A;ENSP00000428086:T666A	ENSP00000254624:T702A	T	+	1	0	EFR3A	133077873	1.000000	0.71417	0.997000	0.53966	0.976000	0.68499	8.622000	0.90953	2.322000	0.78497	0.528000	0.53228	ACC	.	.		0.328	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		G	133008691	A	G	133008691	3	3	165	1	0	0	0	0	1	0	0	0	4960	159	6	2	2178	2	EFR3A	8	133008691	Missense_Mutation	SNP	A	TCGA-DD-AACN-01A-11D-A40R-10	84162040	133008691	13355331	24	25171										
RPL8	6132	hgsc.bcm.edu	37	chr8	146016689	146016689	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	agctctgttggctgaggagaTaaccttcttggagccggagg	15	8	2	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr8:146016689T>A	ENST00000262584.3	-	4	704	c.472A>T	c.(472-474)Atc>Ttc	p.I158F	RPL8_ENST00000528957.1_Missense_Mutation_p.I158F|RPL8_ENST00000394920.2_Missense_Mutation_p.I158F|RPL8_ENST00000527914.1_Missense_Mutation_p.I49F|RPL8_ENST00000529163.1_5'UTR	NM_000973.3	NP_000964.1	P62917	RL8_HUMAN	ribosomal protein L8	158					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			kidney(12)|lung(7)|prostate(1)	20	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.191)		GCTGAGGAGATAACCTTCTTG	0.577																																					p.I158F		Atlas-SNP	.											.	RPL8	29	.	0			c.A472T						.						76	69	71					8																	146016689		2203	4300	6503	SO:0001583	missense	6132	exon4			AGGAGATAACCTT	Z28407	CCDS6433.1	8q24.3	2011-04-06			ENSG00000161016	ENSG00000161016		"L ribosomal proteins"	10368	protein-coding gene	gene with protein product		604177				7506540, 9582194	Standard	NM_033301		Approved	L8	uc003zec.3	P62917	OTTHUMG00000165249	ENST00000262584.3:c.472A>T	chr8.hg19:g.146016689T>A	ENSP00000262584:p.Ile158Phe	73.0	0.0		116.0	21.0	NM_033301	A8K094|D3DWN2|P25120|Q567Q7|Q969V7|Q9BWQ9	Missense_Mutation	SNP	ENST00000262584.3	hg19	CCDS6433.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.568049	0.86439	.	.	ENSG00000161016	ENST00000394920;ENST00000527914;ENST00000262584;ENST00000528957;ENST00000534813;ENST00000533397;ENST00000532702	T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92	5.21	5.21	0.72293	Translation protein SH3-like (1);Translation protein SH3-like, subgroup (1);Ribosomal protein L2, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.45617	0.1351	M	0.62088	1.915	0.80722	D	1	B;B	0.24092	0.009;0.097	B;B	0.35353	0.066;0.201	T	0.37267	-0.9713	10	0.28530	T	0.3	.	13.3852	0.60791	0.0:0.0:0.0:1.0	.	158;122	P62917;E9PIZ3	RL8_HUMAN;.	F	158;49;158;158;122;137;158	ENSP00000378378:I158F;ENSP00000436460:I49F;ENSP00000262584:I158F;ENSP00000433464:I158F;ENSP00000435313:I137F;ENSP00000434535:I158F	ENSP00000262584:I158F	I	-	1	0	RPL8	145987493	1.000000	0.71417	0.995000	0.50966	0.911000	0.54048	4.024000	0.57218	2.103000	0.63969	0.456000	0.33151	ATC	.	.		0.577	RPL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382948.1	NM_000973		A	146016689	T	A	146016689	3	1	165	1	0	0	0	0	1	0	0	0	13617	1406	49	4	313	4	RPL8	8	146016689	Missense_Mutation	SNP	T	TCGA-DD-AACN-01A-11D-A40R-10	13007998	146016689	347333	25	25172										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8341939	8341939	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	tttattctttctaacatggcAtctatgacgatgaagcaacc	6	9	3	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr9:8341939A>G	ENST00000381196.4	-	37	5244	c.4701T>C	c.(4699-4701)gaT>gaC	p.D1567D	PTPRD_ENST00000397606.3_Silent_p.D1160D|PTPRD_ENST00000540109.1_Silent_p.D1567D|PTPRD_ENST00000356435.5_Silent_p.D1567D|PTPRD_ENST00000397611.3_Silent_p.D1157D|PTPRD_ENST00000537002.1_Silent_p.D1157D|PTPRD_ENST00000360074.4_Silent_p.D1554D|PTPRD_ENST00000358503.5_Silent_p.D1545D|PTPRD_ENST00000397617.3_Silent_p.D1160D|PTPRD_ENST00000486161.1_Silent_p.D1160D|PTPRD_ENST00000355233.5_Silent_p.D1161D	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1567	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CTAACATGGCATCTATGACGA	0.373										TSP Lung(15;0.13)																											p.D1567D		Atlas-SNP	.											.	PTPRD	1348	.	0			c.T4701C						.						79	79	79					9																	8341939		2203	4300	6503	SO:0001819	synonymous_variant	5789	exon40			CATGGCATCTATG	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.4701T>C	chr9.hg19:g.8341939A>G		79.0	0.0		85.0	36.0	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	hg19	CCDS43786.1																																																																																			.	.		0.373	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			G	8341939	A	G	8341939	2	3	165	1	0	0	0	0	0	0	0	1	12814	214	8	2		2	PTPRD	9	8341939	Silent	SNP	A	TCGA-DD-AACN-01A-11D-A40R-10		8341939	132871492	26	25173										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138662763	138662763	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	aagagcatcctgctgaacccGgggccccggcacatcctggc	12	16	0	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr9:138662763G>T	ENST00000263604.3	+	18	1773	c.1773G>T	c.(1771-1773)ccG>ccT	p.P591P	KCNT1_ENST00000371757.2_Silent_p.P610P|KCNT1_ENST00000488444.2_Silent_p.P591P|KCNT1_ENST00000486577.2_Silent_p.P571P|KCNT1_ENST00000490355.2_Silent_p.P591P|KCNT1_ENST00000491806.2_Silent_p.P577P|KCNT1_ENST00000487664.1_Silent_p.P565P|KCNT1_ENST00000298480.5_Silent_p.P610P			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	591	RCK N-terminal.				potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		TGCTGAACCCGGGGCCCCGGC	0.612																																					p.P610P		Atlas-SNP	.											.	KCNT1	139	.	0			c.G1830T						.						46	41	42					9																	138662763		2202	4300	6502	SO:0001819	synonymous_variant	57582	exon18			GAACCCGGGGCCC	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.1773G>T	chr9.hg19:g.138662763G>T		209.0	0.0		203.0	41.0	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Silent	SNP	ENST00000263604.3	hg19																																																																																				.	.		0.612	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		T	138662763	G	T	138662763	2	4	165	1	0	0	0	0	0	0	0	1	8100	1103	39	1		1	KCNT1	9	138662763	Silent	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10	130320824	138662763	2550668	27	25174										
C10orf47	254427	hgsc.bcm.edu	37	chr10	11912001	11912001	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	ccttccccgccgcgggggacGccggcgagggggccccaggg	19	17	0	0			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr10:11912001G>A	ENST00000277570.5	+	4	1058	c.904G>A	c.(904-906)Gcc>Acc	p.A302T	PROSER2_ENST00000379200.1_Missense_Mutation_p.A106T|PROSER2-AS1_ENST00000453242.1_RNA|PROSER2-AS1_ENST00000445498.1_RNA	NM_153256.3	NP_694988.3	Q86WR7	PRSR2_HUMAN	proline and serine rich 2	302																	cgcgggggacgccggcgaggg	0.806																																					p.A302T		Atlas-SNP	.											.	.	.	.	0			c.G904A						.						1	1	1					10																	11912001		349	861	1210	SO:0001583	missense	254427	exon4			GGGGACGCCGGCG	BC017269	CCDS7085.1	10p14	2014-02-19	2014-02-19	2012-12-05	ENSG00000148426	ENSG00000148426			23728	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 47", "proline and serine-rich protein 2"	C10orf47		12477932	Standard	NM_153256		Approved	MGC35403	uc001ikx.3	Q86WR7	OTTHUMG00000017673	ENST00000277570.5:c.904G>A	chr10.hg19:g.11912001G>A	ENSP00000277570:p.Ala302Thr	19.0	0.0		27.0	15.0	NM_153256	D3DRR8|Q5W0J9|Q5W0K0|Q5W0K1|Q5W0K2|Q6PJC8|Q8N317	Missense_Mutation	SNP	ENST00000277570.5	hg19	CCDS7085.1	.	.	.	.	.	.	.	.	.	.	G	6.708	0.499271	0.12762	.	.	ENSG00000148426	ENST00000277570;ENST00000379200	T;T	0.39592	1.07;1.08	4.49	-8.98	0.00754	.	2.037870	0.02223	N	0.064156	T	0.18718	0.0449	N	0.04880	-0.145	0.09310	N	1	B	0.16396	0.017	B	0.09377	0.004	T	0.25363	-1.0134	10	0.87932	D	0	1.8777	4.961	0.14066	0.1296:0.353:0.4103:0.1071	.	302	Q86WR7	CJ047_HUMAN	T	302;106	ENSP00000277570:A302T;ENSP00000368498:A106T	ENSP00000277570:A302T	A	+	1	0	C10orf47	11952007	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.568000	0.05909	-2.283000	0.00672	0.305000	0.20034	GCC	.	.		0.806	PROSER2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090189.2	NM_153256		A	11912001	G	A	11912001	3	1	165	1	0	0	0	0	1	0	0	0	1607	1087	38	1	914	1	C10orf47	10	11912001	Missense_Mutation	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10		11912001	123622746	28	25175										
ABTB2	25841	hgsc.bcm.edu	37	chr11	34180864	34180864	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	tgaaaaatgtggtacttcatGtcgctgatctcgatggtctt	10	7	3	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr11:34180864G>T	ENST00000435224.2	-	14	3100	c.2676C>A	c.(2674-2676)gaC>gaA	p.D892E	ABTB2_ENST00000298992.2_Missense_Mutation_p.D706E	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	892	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				GGTACTTCATGTCGCTGATCT	0.527																																					p.D892E		Atlas-SNP	.											.	ABTB2	101	.	0			c.C2676A						.						306	205	239					11																	34180864		2202	4298	6500	SO:0001583	missense	25841	exon14			CTTCATGTCGCTG	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.2676C>A	chr11.hg19:g.34180864G>T	ENSP00000410157:p.Asp892Glu	73.0	0.0		92.0	4.0	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Missense_Mutation	SNP	ENST00000435224.2	hg19	CCDS7890.2	.	.	.	.	.	.	.	.	.	.	G	18.60	3.658268	0.67586	.	.	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.26957	1.7;1.7	5.32	4.39	0.52855	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.104848	0.64402	D	0.000006	T	0.25232	0.0613	M	0.64997	1.995	0.48571	D	0.999678	B	0.31256	0.316	B	0.32342	0.144	T	0.07102	-1.0790	10	0.52906	T	0.07	-8.5818	7.0064	0.24838	0.299:0.0:0.701:0.0	.	706	Q8N961	ABTB2_HUMAN	E	892;706	ENSP00000410157:D892E;ENSP00000298992:D706E	ENSP00000298992:D706E	D	-	3	2	ABTB2	34137440	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	0.942000	0.29017	1.340000	0.45581	0.655000	0.94253	GAC	.	.		0.527	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804		T	34180864	G	T	34180864	3	4	165	1	0	0	0	0	1	0	0	0	103	1368	48	3	417	3	ABTB2	11	34180864	Missense_Mutation	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10		34180864	100825652	29	25176										
PACSIN3	29763	hgsc.bcm.edu	37	chr11	47201777	47201777	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	agcgttccacccgttcctgcAgtttgcgcagctgctcctgg	11	15	0	0			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr11:47201777A>T	ENST00000539589.1	-	6	905	c.563T>A	c.(562-564)cTg>cAg	p.L188Q	PACSIN3_ENST00000298838.6_Missense_Mutation_p.L188Q	NM_001184975.1	NP_001171904.1	Q9UKS6	PACN3_HUMAN	protein kinase C and casein kinase substrate in neurons 3	188	F-BAR domain. {ECO:0000250}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endocytosis (GO:0045806)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium channel inhibitor activity (GO:0019855)|cytoskeletal protein binding (GO:0008092)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)	11						CCGTTCCTGCAGTTTGCGCAG	0.642											OREG0020952	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L188Q		Atlas-SNP	.											.	PACSIN3	28	.	0			c.T563A						.						106	90	96					11																	47201777		2201	4298	6499	SO:0001583	missense	29763	exon6			TCCTGCAGTTTGC	AF130979	CCDS31481.1	11p12-p11	2008-02-05				ENSG00000165912			8572	protein-coding gene	gene with protein product	"syndapin III"	606513				10531379	Standard	NM_016223		Approved	SDPIII	uc001ndx.3	Q9UKS6		ENST00000539589.1:c.563T>A	chr11.hg19:g.47201777A>T	ENSP00000440945:p.Leu188Gln	35.0	0.0	945	33.0	16.0	NM_016223	A6NH84|Q9H331|Q9NWV9	Missense_Mutation	SNP	ENST00000539589.1	hg19	CCDS31481.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	31|31	5.085343|5.085343	0.94100|0.94100	.|.	.|.	ENSG00000165912|ENSG00000165912	ENST00000415232|ENST00000298838;ENST00000539589;ENST00000528462	.|T;T;T	.|0.44482	.|0.92;0.92;0.92	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|0.174164	.|0.52532	.|D	.|0.000078	T|T	0.43478|0.43478	0.1249|0.1249	M|M	0.76727|0.76727	2.345|2.345	0.50632|0.50632	D|D	0.99988|0.99988	.|P	.|0.51240	.|0.943	.|B	.|0.37267	.|0.245	T|T	0.55431|0.55431	-0.8142|-0.8142	6|10	0.52906|0.66056	T|D	0.07|0.02	-15.5803|-15.5803	15.6266|15.6266	0.76863|0.76863	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|188	.|Q9UKS6	.|PACN3_HUMAN	S|Q	187|188	.|ENSP00000298838:L188Q;ENSP00000440945:L188Q;ENSP00000437252:L188Q	ENSP00000405352:C187S|ENSP00000298838:L188Q	C|L	-|-	1|2	0|0	PACSIN3|PACSIN3	47158353|47158353	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	7.519000|7.519000	0.81809|0.81809	2.109000|2.109000	0.64355|0.64355	0.459000|0.459000	0.35465|0.35465	TGC|CTG	.	.		0.642	PACSIN3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391632.1	NM_016223		T	47201777	A	T	47201777	3	4	165	1	0	0	0	0	1	0	0	0	11385	188	7	4	735	4	PACSIN3	11	47201777	Missense_Mutation	SNP	A	TCGA-DD-AACN-01A-11D-A40R-10	13020913	47201777	87804739	30	25177										
TYR	7299	hgsc.bcm.edu	37	chr11	89028410	89028410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gatggtaggggccgtcctcaCtgccctgctggcagggcttg	16	12	1	0	rs543973275|rs61754399		TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr11:89028410C>T	ENST00000263321.5	+	5	1968	c.1466C>T	c.(1465-1467)aCt>aTt	p.T489I		NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	489					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	GCCGTCCTCACTGCCCTGCTG	0.537																																					p.T489I		Atlas-SNP	.											TYR,NS,carcinoma,0,1	TYR	130	.	0			c.C1466T						.						47	49	48					11																	89028410		2201	4299	6500	SO:0001583	missense	7299	exon5			TCCTCACTGCCCT	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"oculocutaneous albinism IA"	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.1466C>T	chr11.hg19:g.89028410C>T	ENSP00000263321:p.Thr489Ile	192.0	0.0		194.0	32.0	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	hg19	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	C	7.314	0.615527	0.14129	.	.	ENSG00000077498	ENST00000263321	D	0.99143	-5.48	5.02	4.11	0.48088	.	0.352939	0.32671	N	0.005800	D	0.96393	0.8823	L	0.36672	1.1	0.09310	N	1	B	0.28713	0.22	B	0.26864	0.074	D	0.91333	0.5091	9	.	.	.	.	9.7404	0.40416	0.0:0.8295:0.0:0.1705	.	489	P14679	TYRO_HUMAN	I	489	ENSP00000263321:T489I	.	T	+	2	0	TYR	88668058	0.013000	0.17824	0.002000	0.10522	0.218000	0.24690	2.557000	0.45871	1.247000	0.43917	0.455000	0.32223	ACT	.	.		0.537	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		T	89028410	C	T	89028410	3	4	165	1	0	0	0	0	1	0	0	0	16828	565	20	3	1484	3	TYR	11	89028410	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10	41826633	89028410	45978106	31	25178										
POU2F3	25833	hgsc.bcm.edu	37	chr11	120175898	120175898	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	ccaagaccttcaagcagaggCgcattaagctgggcttcaca	10	12	2	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr11:120175898C>T	ENST00000543440.2	+	7	754	c.604C>T	c.(604-606)Cgc>Tgc	p.R202C	POU2F3_ENST00000260264.4_Missense_Mutation_p.R204C	NM_014352.3	NP_055167.2	Q9UKI9	PO2F3_HUMAN	POU class 2 homeobox 3	202	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|negative regulation by host of viral transcription (GO:0043922)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)	17		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)		CAAGCAGAGGCGCATTAAGCT	0.557																																					p.R204C		Atlas-SNP	.											.	POU2F3	44	.	0			c.C610T						.						78	83	81					11																	120175898		2203	4299	6502	SO:0001583	missense	25833	exon7			CAGAGGCGCATTA	AF133895	CCDS8431.1, CCDS58190.1	11q23.3	2011-06-20	2007-07-13		ENSG00000137709	ENSG00000137709		"Homeoboxes / POU class"	19864	protein-coding gene	gene with protein product		607394	"POU domain class 2, transcription factor 3"			10473598	Standard	NM_014352		Approved	OCT11, PLA-1, Skn-1a, Epoc-1	uc021qrk.1	Q9UKI9	OTTHUMG00000166140	ENST00000543440.2:c.604C>T	chr11.hg19:g.120175898C>T	ENSP00000441687:p.Arg202Cys	113.0	0.0		136.0	12.0	NM_001244682	A8K7H8|B4DY07|F5GWW6|Q3MIY3|Q9UKR7|Q9Y504	Missense_Mutation	SNP	ENST00000543440.2	hg19	CCDS8431.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.672501	0.88348	.	.	ENSG00000137709	ENST00000543440;ENST00000260264;ENST00000533620	D;D;D	0.90197	-2.63;-2.63;-2.63	6.16	6.16	0.99307	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.85682	D	0.000000	D	0.95903	0.8666	M	0.88512	2.96	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95948	0.8952	10	0.87932	D	0	.	14.6998	0.69147	0.2551:0.7448:0.0:0.0	.	156;202	E9PIN6;Q9UKI9	.;PO2F3_HUMAN	C	204;202;156	ENSP00000441687:R204C;ENSP00000260264:R202C;ENSP00000435738:R156C	ENSP00000260264:R202C	R	+	1	0	POU2F3	119681108	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.833000	0.62766	2.937000	0.99478	0.650000	0.86243	CGC	.	.		0.557	POU2F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388039.2			T	120175898	C	T	120175898	3	4	165	1	0	0	0	0	1	0	0	0	12282	768	27	1	630	1	POU2F3	11	120175898	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10	31147488	120175898	14830618	32	25179										
WSB2	55884	hgsc.bcm.edu	37	chr12	118480654	118480654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	cacttcccataccgtgtttaTtcaggtcccagatgcgaaga	8	12	1	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr12:118480654T>C	ENST00000315436.3	-	4	692	c.551A>G	c.(550-552)aAt>aGt	p.N184S	WSB2_ENST00000536738.1_5'UTR|WSB2_ENST00000544233.1_Intron|WSB2_ENST00000441406.2_Missense_Mutation_p.N201S|WSB2_ENST00000542304.1_5'UTR|WSB2_ENST00000535496.1_Missense_Mutation_p.N186S	NM_001278557.1|NM_018639.3	NP_001265486.1|NP_061109.1	Q9NYS7	WSB2_HUMAN	WD repeat and SOCS box containing 2	184					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACCGTGTTTATTCAGGTCCCA	0.453																																					p.N184S		Atlas-SNP	.											.	WSB2	32	.	0			c.A551G						.						151	152	152					12																	118480654		2203	4300	6503	SO:0001583	missense	55884	exon4			TGTTTATTCAGGT	AF038187	CCDS9186.1, CCDS61251.1, CCDS61252.1	12q24.23	2013-01-09	2011-01-25		ENSG00000176871	ENSG00000176871		"WD repeat domain containing"	19222	protein-coding gene	gene with protein product			"WD repeat and SOCS box-containing 2"			12076535	Standard	NM_018639		Approved	SBA2, MGC10210	uc001twr.2	Q9NYS7	OTTHUMG00000168885	ENST00000315436.3:c.551A>G	chr12.hg19:g.118480654T>C	ENSP00000319474:p.Asn184Ser	76.0	0.0		56.0	14.0	NM_018639	B4DIE6|B4DPV6|Q9NRX9	Missense_Mutation	SNP	ENST00000315436.3	hg19	CCDS9186.1	.	.	.	.	.	.	.	.	.	.	T	11.78	1.741379	0.30865	.	.	ENSG00000176871	ENST00000315436;ENST00000441406;ENST00000535496;ENST00000537945	T;T;T;T	0.01287	5.05;5.05;5.05;5.05	5.75	5.75	0.90469	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.219434	0.31809	N	0.007032	T	0.01092	0.0036	N	0.13327	0.33	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.61058	-0.7139	10	0.14252	T	0.57	-24.1683	10.0893	0.42436	0.0:0.0781:0.0:0.9219	.	184	Q9NYS7	WSB2_HUMAN	S	184;201;186;186	ENSP00000319474:N184S;ENSP00000409131:N201S;ENSP00000439450:N186S;ENSP00000440386:N186S	ENSP00000319474:N184S	N	-	2	0	WSB2	116965037	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.360000	0.52299	2.202000	0.70862	0.524000	0.50904	AAT	.	.		0.453	WSB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401515.1	NM_018639		C	118480654	T	C	118480654	3	2	165	1	0	0	0	0	1	0	0	0	17420	1493	52	2	687	2	WSB2	12	118480654	Missense_Mutation	SNP	T	TCGA-DD-AACN-01A-11D-A40R-10		118480654	15371241	33	25180										
C13orf34	79866	hgsc.bcm.edu	37	chr13	73327942	73327942	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gtgaagttgagagtaaatctCaagcatttaatatgaaggta	10	3	1	3			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr13:73327942C>G	ENST00000390667.5	+	11	1694	c.1597C>G	c.(1597-1599)Caa>Gaa	p.Q533E	BORA_ENST00000377815.3_Missense_Mutation_p.Q463E	NM_024808.2	NP_079084.2	Q6PGQ7	BORA_HUMAN	bora, aurora kinase A activator	533					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of mitosis (GO:0007088)|regulation of mitotic spindle organization (GO:0060236)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)	protein kinase binding (GO:0019901)										GAGTAAATCTCAAGCATTTAA	0.294																																					p.Q533E		Atlas-SNP	.											.	.	.	.	0			c.C1597G						.						77	75	76					13																	73327942		1821	4082	5903	SO:0001583	missense	79866	exon11			AAATCTCAAGCAT	BC025367	CCDS9446.1, CCDS66560.1, CCDS9446.2, CCDS73583.1	13q22.1	2013-08-13	2011-08-09	2011-08-09	ENSG00000136122	ENSG00000136122			24724	protein-coding gene	gene with protein product		610510	"chromosome 13 open reading frame 34"	C13orf34		16890155, 18378770, 18566290, 19487276	Standard	NM_001286746		Approved	FLJ22624	uc001viv.1	Q6PGQ7	OTTHUMG00000017068	ENST00000390667.5:c.1597C>G	chr13.hg19:g.73327942C>G	ENSP00000375082:p.Gln533Glu	326.0	0.0		204.0	118.0	NM_024808	B4DQ30|Q5W0P3|Q5W0P4|Q86YC6|Q96IW9|Q9H640	Missense_Mutation	SNP	ENST00000390667.5	hg19	CCDS9446.1	.	.	.	.	.	.	.	.	.	.	C	7.494	0.651318	0.14516	.	.	ENSG00000136122	ENST00000377815;ENST00000390667	T;T	0.35789	1.29;1.32	5.51	3.72	0.42706	.	0.580975	0.19008	N	0.125162	T	0.34803	0.0910	L	0.58101	1.795	0.29893	N	0.825024	B;B;B;B	0.33549	0.417;0.287;0.287;0.287	B;B;B;B	0.31101	0.085;0.079;0.124;0.079	T	0.34229	-0.9837	10	0.72032	D	0.01	1.2477	12.5995	0.56489	0.1326:0.7402:0.1273:0.0	.	463;533;593;533	B4DQ30;A8K631;B5LMG6;Q6PGQ7	.;.;.;BORA_HUMAN	E	463;533	ENSP00000367046:Q463E;ENSP00000375082:Q533E	ENSP00000367046:Q463E	Q	+	1	0	BORA	72225943	0.996000	0.38824	0.308000	0.25141	0.042000	0.13812	0.944000	0.29043	0.745000	0.32763	0.655000	0.94253	CAA	.	.		0.294	BORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045245.3	NM_024808		G	73327942	C	G	73327942	3	3	165	1	0	0	0	0	1	0	0	0	1730	827	29	4	1635	4	C13orf34	13	73327942	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10		73327942	41841936	34	25181										
C16orf78	123970	hgsc.bcm.edu	37	chr16	49407994	49407994	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	caggggaagaagaaacaagcTcccgaggtgggtaccatcca	13	10	0	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr16:49407994T>A	ENST00000299191.3	+	1	261	c.144T>A	c.(142-144)gcT>gcA	p.A48A		NM_144602.2	NP_653203.1	Q8WTQ4	CP078_HUMAN	chromosome 16 open reading frame 78	48						nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(1)	22						AGAAACAAGCTCCCGAGGTGG	0.502																																					p.A48A		Atlas-SNP	.											.	C16orf78	57	.	0			c.T144A						.						66	64	64					16																	49407994		2199	4300	6499	SO:0001819	synonymous_variant	123970	exon1			ACAAGCTCCCGAG	BC021181	CCDS10738.1	16q12.1	2008-02-05			ENSG00000166152	ENSG00000166152			28479	protein-coding gene	gene with protein product						12477932	Standard	NM_144602		Approved	MGC33367	uc002efr.3	Q8WTQ4	OTTHUMG00000133149	ENST00000299191.3:c.144T>A	chr16.hg19:g.49407994T>A		82.0	0.0		60.0	37.0	NM_144602		Silent	SNP	ENST00000299191.3	hg19	CCDS10738.1																																																																																			.	.		0.502	C16orf78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256846.1	NM_144602		A	49407994	T	A	49407994	2	1	165	1	0	0	0	0	0	0	0	1	1837	1538	54	4		4	C16orf78	16	49407994	Silent	SNP	T	TCGA-DD-AACN-01A-11D-A40R-10		49407994	40946759	35	25182										
BRD7	29117	hgsc.bcm.edu	37	chr16	50368752	50368752	+	Frame_Shift_Del	DEL	T	T	-													0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	tccatctttctgctttcgagTtttctgcaagtcagccatga							TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr16:50368752delT	ENST00000394688.3	-	7	916	c.757delA	c.(757-759)actfs	p.T253fs	BRD7_ENST00000394689.2_Frame_Shift_Del_p.T253fs			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	253					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				TGCTTTCGAGTTTTCTGCAAG	0.453																																					p.T253fs		Atlas-INDEL	.											.	BRD7	61	.	0			c.758delC						.						98	96	97					16																	50368752		2198	4297	6495	SO:0001589	frameshift_variant	29117	exon7			.	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"bromodomain-containing 7"			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.757delA	chr16.hg19:g.50368752delT	ENSP00000378180:p.Thr253fs	117.0	0.0		56.0	30.0	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Frame_Shift_Del	DEL	ENST00000394688.3	hg19	CCDS10742.1																																																																																			.	.		0.453	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		-	50368752	T	-	50368752	7	5	165	1	0	1	0	1	0	0	0	0	1507	1725	60	0	1245	0	BRD7	16	50368752	Frame_Shift_Del	DEL	T	TCGA-DD-AACN-01A-11D-A40R-10	960758	50368752	39986001	36	25183										
LCAT	3931	hgsc.bcm.edu	37	chr16	67974099	67974099	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	agatgtaggtgcggggcgtgGgcaggcccacgccgtaaaga	18	9	0	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr16:67974099G>A	ENST00000264005.5	-	6	1060	c.1031C>T	c.(1030-1032)cCc>cTc	p.P344L		NM_000229.1	NP_000220.1	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase	344					cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of high-density lipoprotein particle assembly (GO:0090107)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	apolipoprotein A-I binding (GO:0034186)|phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607)			cervix(4)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)		GCGGGGCGTGGGCAGGCCCAC	0.612																																					p.P344L		Atlas-SNP	.											.	LCAT	31	.	0			c.C1031T						.						75	85	81					16																	67974099		2198	4300	6498	SO:0001583	missense	3931	exon6			GGCGTGGGCAGGC		CCDS10854.1	16q22.1	2012-10-02			ENSG00000213398	ENSG00000213398	2.3.1.43		6522	protein-coding gene	gene with protein product		606967					Standard	NM_000229		Approved		uc002euy.1	P04180	OTTHUMG00000137551	ENST00000264005.5:c.1031C>T	chr16.hg19:g.67974099G>A	ENSP00000264005:p.Pro344Leu	109.0	0.0		69.0	22.0	NM_000229	Q53XQ3	Missense_Mutation	SNP	ENST00000264005.5	hg19	CCDS10854.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.459532	0.43736	.	.	ENSG00000213398	ENST00000264005	D	0.96856	-4.15	5.61	5.61	0.85477	.	0.000000	0.64402	U	0.000001	D	0.95847	0.8648	M	0.85299	2.745	0.49389	D	0.999784	B	0.12630	0.006	B	0.12837	0.008	D	0.93302	0.6677	10	0.62326	D	0.03	-19.4667	12.142	0.54002	0.0:0.0:0.829:0.171	.	344	P04180	LCAT_HUMAN	L	344	ENSP00000264005:P344L	ENSP00000264005:P344L	P	-	2	0	LCAT	66531600	1.000000	0.71417	0.999000	0.59377	0.671000	0.39405	5.571000	0.67404	2.639000	0.89480	0.555000	0.69702	CCC	.	.		0.612	LCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268885.3			A	67974099	G	A	67974099	3	1	165	1	0	0	0	0	1	0	0	0	8667	1232	43	3	295	3	LCAT	16	67974099	Missense_Mutation	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10	17605347	67974099	22380654	37	25184										
SNTB2	6645	hgsc.bcm.edu	37	chr16	69318053	69318053	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	ggcattgagatgcatctcttCagggtggagacacatcggga	14	8	2	2			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr16:69318053C>T	ENST00000336278.4	+	5	1289	c.1251C>T	c.(1249-1251)ttC>ttT	p.F417F		NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)	417	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|microtubule (GO:0005874)|protein complex (GO:0043234)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		TGCATCTCTTCAGGGTGGAGA	0.532																																					p.F417F	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-SNP	.											.	SNTB2	22	.	0			c.C1251T						.						154	140	145					16																	69318053		2198	4300	6498	SO:0001819	synonymous_variant	6645	exon5			TCTCTTCAGGGTG	U40572	CCDS10873.1	16q22.1	2008-05-14	2002-08-29		ENSG00000168807	ENSG00000168807			11169	protein-coding gene	gene with protein product		600027	"syntrophin, beta 2 (dystrophin-associated protein A1, 59kD, basic component 2)"	SNT2B2, SNTL, D16S2531E		8576247, 8183929	Standard	NM_006750		Approved	EST25263, SNT3	uc002ewu.3	Q13425	OTTHUMG00000137567	ENST00000336278.4:c.1251C>T	chr16.hg19:g.69318053C>T		117.0	0.0		70.0	19.0	NM_006750	Q9BY09	Silent	SNP	ENST00000336278.4	hg19	CCDS10873.1																																																																																			.	.		0.532	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1			T	69318053	C	T	69318053	2	4	165	1	0	0	0	0	0	0	0	1	14888	825	29	3		3	SNTB2	16	69318053	Silent	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10	1343954	69318053	21036700	38	25185										
KRT10	3858	hgsc.bcm.edu	37	chr17	38975319	38975319	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gccggaactgccgccgtggcCgccgccgtggccgccgccgg	17	19	0	0			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr17:38975319C>T	ENST00000269576.5	-	7	1477	c.1468G>A	c.(1468-1470)Ggc>Agc	p.G490S	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ccgccgtggccgccgccgtgg	0.791																																					p.G490S		Atlas-SNP	.											.	KRT10	56	.	0			c.G1468A						.																																			SO:0001583	missense	3858	exon7			CGTGGCCGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1468G>A	chr17.hg19:g.38975319C>T	ENSP00000269576:p.Gly490Ser	20.0	0.0		58.0	11.0	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546565	0.86022	.	.	ENSG00000186395	ENST00000269576	D	0.96587	-4.06	4.38	4.38	0.52667	.	0.845686	0.09879	N	0.743932	D	0.94778	0.8314	N	0.08118	0	0.27860	N	0.940431	D	0.89917	1.0	D	0.76071	0.987	D	0.87790	0.2618	10	0.18710	T	0.47	.	12.7512	0.57310	0.0:1.0:0.0:0.0	.	490	P13645	K1C10_HUMAN	S	490	ENSP00000269576:G490S	ENSP00000269576:G490S	G	-	1	0	KRT10	36228845	0.019000	0.18553	0.876000	0.34364	0.184000	0.23303	0.448000	0.21726	2.739000	0.93911	0.603000	0.83216	GGC	.	.		0.791	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		T	38975319	C	T	38975319	3	4	165	1	0	0	0	0	1	0	0	0	8457	652	23	1	294	1	KRT10	17	38975319	Missense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10		38975319	42219891	39	25186										
KRT40	125115	hgsc.bcm.edu	37	chr17	39134528	39134528	+	Frame_Shift_Del	DEL	G	G	-													0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	tgctcgaggtgcatgtggtcGaacatgggctacaggaaagc					rs16968862	byFrequency	TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr17:39134528delG	ENST00000398486.2	-	9	1377	c.1217delC	c.(1216-1218)tcgfs	p.S406fs	AC004231.2_ENST00000418393.1_RNA|KRT40_ENST00000377755.4_Frame_Shift_Del_p.S406fs	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	406	Tail.		S -> L (in dbSNP:rs16968862).			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				GCATGTGGTCGAACATGGGCT	0.438																																					p.S406fs		Atlas-INDEL	.											.	KRT40	27	.	0			c.1218delG						.						100	110	107					17																	39134528		1933	4144	6077	SO:0001589	frameshift_variant	125115	exon9			.	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"-", "Intermediate filaments type I, keratins (acidic)"	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.1217delC	chr17.hg19:g.39134528delG	ENSP00000381500:p.Ser406fs	102.0	0.0		111.0	15.0	NM_182497	Q6IFU5	Frame_Shift_Del	DEL	ENST00000398486.2	hg19	CCDS42320.1																																																																																			.	.		0.438	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497		-	39134528	G	-	39134528	7	5	165	1	0	1	0	1	0	0	0	0	8487	1059	37	0	82	0	KRT40	17	39134528	Frame_Shift_Del	DEL	G	TCGA-DD-AACN-01A-11D-A40R-10	159209	39134528	42060682	40	25187										
ARMC7	79637	hgsc.bcm.edu	37	chr17	73106617	73106617	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	cttatgaccccagcaactacGagtatctgcggcagctgcag	10	13	1	1	rs141301558		TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr17:73106617G>A	ENST00000245543.1	+	2	453	c.151G>A	c.(151-153)Gag>Aag	p.E51K	ARMC7_ENST00000581078.1_Missense_Mutation_p.E51K|ARMC7_ENST00000584947.1_Missense_Mutation_p.E51K|ARMC7_ENST00000582136.1_Missense_Mutation_p.E51K	NM_024585.2	NP_078861.1	Q9H6L4	ARMC7_HUMAN	armadillo repeat containing 7	51						cytoplasm (GO:0005737)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|pancreas(3)	9	all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)			CAGCAACTACGAGTATCTGCG	0.597																																					p.E51K		Atlas-SNP	.											.	ARMC7	14	.	0			c.G151A						.						86	82	83					17																	73106617		2203	4300	6503	SO:0001583	missense	79637	exon2			AACTACGAGTATC	AK025813	CCDS11714.1	17q25	2013-02-14				ENSG00000125449		"Armadillo repeat containing"	26168	protein-coding gene	gene with protein product						12477932	Standard	NM_024585		Approved	FLJ22160	uc002jmw.1	Q9H6L4		ENST00000245543.1:c.151G>A	chr17.hg19:g.73106617G>A	ENSP00000245543:p.Glu51Lys	108.0	0.0		133.0	24.0	NM_024585	B4DVA4	Missense_Mutation	SNP	ENST00000245543.1	hg19	CCDS11714.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.876175	0.51801	.	.	ENSG00000125449	ENST00000245543	T	0.53640	0.61	6.07	1.69	0.24217	Armadillo-like helical (1);Armadillo-type fold (1);	0.479354	0.23316	N	0.049502	T	0.30947	0.0781	L	0.34521	1.04	0.29223	N	0.873825	B;B	0.22346	0.068;0.025	B;B	0.13407	0.009;0.004	T	0.24083	-1.0170	10	0.11485	T	0.65	.	10.8369	0.46692	0.0996:0.2367:0.6018:0.062	.	51;51	B4DVA4;Q9H6L4	.;ARMC7_HUMAN	K	51	ENSP00000245543:E51K	ENSP00000245543:E51K	E	+	1	0	ARMC7	70618212	0.998000	0.40836	0.997000	0.53966	0.927000	0.56198	0.888000	0.28268	0.111000	0.17947	-0.165000	0.13383	GAG	.	G|1.000;C|0.000		0.597	ARMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445846.1	NM_024585		A	73106617	G	A	73106617	3	1	165	1	0	0	0	0	1	0	0	0	956	1059	37	1	157	1	ARMC7	17	73106617	Missense_Mutation	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10	33972089	73106617	8088593	41	25188										
MATK	4145	hgsc.bcm.edu	37	chr19	3783153	3783153	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	gctcctcctcggccgacttgGtcccgtgtttccgctttggt	11	15	0	0			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr19:3783153G>C	ENST00000310132.6	-	7	1045	c.647C>G	c.(646-648)aCc>aGc	p.T216S	MATK_ENST00000395040.2_Missense_Mutation_p.T175S|MATK_ENST00000585778.1_Missense_Mutation_p.T216S|MATK_ENST00000395045.2_Missense_Mutation_p.T217S	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	216					cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCCGACTTGGTCCCGTGTTT	0.652																																					p.T217S		Atlas-SNP	.											.	MATK	108	.	0			c.C650G						.						131	97	109					19																	3783153		2203	4300	6503	SO:0001583	missense	4145	exon7			GACTTGGTCCCGT	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"SH2 domain containing"	6906	protein-coding gene	gene with protein product	"Csk-homologous kinase", "tyrosine-protein kinase CTK", "protein kinase HYL", "hematopoietic consensus tyrosine-lacking kinase", "tyrosylprotein kinase", "hydroxyaryl-protein kinase", "Csk-type protein tyrosine kinase", "HYL tyrosine kinase", "tyrosine kinase MATK", "leukocyte carboxyl-terminal src kinase related"	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.647C>G	chr19.hg19:g.3783153G>C	ENSP00000308734:p.Thr216Ser	73.0	0.0		79.0	11.0	NM_002378	B3KNZ9|Q9NST8	Missense_Mutation	SNP	ENST00000310132.6	hg19	CCDS12114.1	.	.	.	.	.	.	.	.	.	.	G	8.738	0.918267	0.17982	.	.	ENSG00000007264	ENST00000395045;ENST00000310132;ENST00000395040	T;T;T	0.73363	-0.74;-0.74;-0.72	4.71	4.71	0.59529	.	0.387226	0.25651	N	0.029220	T	0.63046	0.2478	L	0.48642	1.525	0.20403	N	0.999906	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.12837	0.007;0.008;0.007	T	0.45249	-0.9274	10	0.15952	T	0.53	-23.4139	8.3547	0.32323	0.1144:0.0:0.8856:0.0	.	216;217;216	F1T0G6;B3KNZ9;P42679	.;.;MATK_HUMAN	S	217;216;175	ENSP00000378485:T217S;ENSP00000308734:T216S;ENSP00000378481:T175S	ENSP00000308734:T216S	T	-	2	0	MATK	3734153	1.000000	0.71417	0.312000	0.25196	0.045000	0.14185	4.694000	0.61760	2.159000	0.67721	0.561000	0.74099	ACC	.	.		0.652	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355		C	3783153	G	C	3783153	3	2	165	1	0	0	0	0	1	0	0	0	9341	1261	44	4	908	4	MATK	19	3783153	Missense_Mutation	SNP	G	TCGA-DD-AACN-01A-11D-A40R-10		3783153	55345830	42	25189										
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13915863	13915863	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.831417624521073	3.74137931034483	0.467672413793103	1	1	0	accagctgcagaagttcgtgCagtacctcatcagcgcccat	9	14	2	1			TCGA-DD-AACN-01A-11D-A40R-10	TCGA-DD-AACN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4fcf6ef-eba4-47be-8457-574686f0add0	1d70749b-f7ee-4419-9978-ef6792e52e18	g.chr19:13915863C>T	ENST00000254323.2	+	3	802	c.613C>T	c.(613-615)Cag>Tag	p.Q205*	ZSWIM4_ENST00000440752.2_5'Flank	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	205							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			GAAGTTCGTGCAGTACCTCAT	0.617											OREG0025298	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q205X		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.C613T						.						54	46	49					19																	13915863		2203	4300	6503	SO:0001587	stop_gained	65249	exon3			TTCGTGCAGTACC	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.613C>T	chr19.hg19:g.13915863C>T	ENSP00000254323:p.Gln205*	47.0	0.0	691	31.0	5.0	NM_023072		Nonsense_Mutation	SNP	ENST00000254323.2	hg19	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	C	39	7.524704	0.98339	.	.	ENSG00000132003	ENST00000254323	.	.	.	4.81	4.81	0.61882	.	0.109676	0.39083	N	0.001469	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-17.006	15.3756	0.74602	0.0:1.0:0.0:0.0	.	.	.	.	X	205	.	ENSP00000254323:Q205X	Q	+	1	0	ZSWIM4	13776863	1.000000	0.71417	1.000000	0.80357	0.281000	0.26958	7.565000	0.82337	2.226000	0.72624	0.561000	0.74099	CAG	.	.		0.617	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		T	13915863	C	T	13915863	4	4	165	1	0	0	0	0	0	1	0	0	18258	711	25	3	623	3	ZSWIM4	19	13915863	Nonsense_Mutation	SNP	C	TCGA-DD-AACN-01A-11D-A40R-10	10132710	13915863	45213120	43	25190										
PHTF1	10745	hgsc.bcm.edu	37	chr1	114254606	114254606	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	tattgattttctattcttaaCttcacaaccattgtcacttg	3	9	4	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:114254606C>A	ENST00000369604.1	-	9	1396	c.913G>T	c.(913-915)Gtt>Ttt	p.V305F	PHTF1_ENST00000357783.2_Missense_Mutation_p.V305F|PHTF1_ENST00000393357.2_Missense_Mutation_p.V305F|PHTF1_ENST00000447664.2_3'UTR|PHTF1_ENST00000369596.2_Missense_Mutation_p.V252F|PHTF1_ENST00000369600.1_Missense_Mutation_p.V252F|PHTF1_ENST00000369598.1_Missense_Mutation_p.V260F|PHTF1_ENST00000474926.1_5'UTR			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	305					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTATTCTTAACTTCACAACCA	0.378																																					p.V305F		Atlas-SNP	.											.	PHTF1	69	.	0			c.G913T						.						124	118	120					1																	114254606		2203	4300	6503	SO:0001583	missense	10745	exon8			TCTTAACTTCACA	AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.913G>T	chr1.hg19:g.114254606C>A	ENSP00000358617:p.Val305Phe	106.0	0.0		108.0	62.0	NM_006608	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Missense_Mutation	SNP	ENST00000369604.1	hg19	CCDS861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.27|11.27	1.588763|1.588763	0.28357|0.28357	.|.	.|.	ENSG00000116793|ENSG00000116793	ENST00000412670|ENST00000369597;ENST00000393357;ENST00000369596;ENST00000369598;ENST00000369600;ENST00000369604;ENST00000357783	.|.	.|.	.|.	5.72|5.72	0.704|0.704	0.18121|0.18121	.|.	.|0.572283	.|0.18251	.|N	.|0.146927	T|T	0.08582|0.08582	0.0213|0.0213	N|N	0.14661|0.14661	0.345|0.345	0.24930|0.24930	N|N	0.991922|0.991922	.|B;B;B	.|0.10296	.|0.0;0.003;0.0	.|B;B;B	.|0.08055	.|0.0;0.003;0.002	T|T	0.26503|0.26503	-1.0101|-1.0101	5|9	.|0.49607	.|T	.|0.09	-7.6242|-7.6242	5.5222|5.5222	0.16939|0.16939	0.127:0.4715:0.0:0.4015|0.127:0.4715:0.0:0.4015	.|.	.|305;60;305	.|Q9UMS5;Q5TCR1;Q9UMS5-2	.|PHTF1_HUMAN;.;.	N|F	60|260;305;252;260;252;305;305	.|.	.|ENSP00000350428:V305F	K|V	-|-	3|1	2|0	PHTF1|PHTF1	114056129|114056129	0.841000|0.841000	0.29509|0.29509	0.989000|0.989000	0.46669|0.46669	0.748000|0.748000	0.42578|0.42578	0.063000|0.063000	0.14410|0.14410	0.363000|0.363000	0.24346|0.24346	0.460000|0.460000	0.39030|0.39030	AAG|GTT	.	.		0.378	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608		A	114254606	C	A	114254606	3	1	166	1	0	0	0	0	1	0	0	0	11871	565	20	3	1419	3	PHTF1	1	114254606	Missense_Mutation	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10		114254606	134996015	1	25191										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179609571	179609571	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	tgttctttggcttgggtgagAccagtagaggtatgtttgct	14	5	1	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:179609571A>G	ENST00000367614.1	+	11	2150	c.1791A>G	c.(1789-1791)agA>agG	p.R597R	TDRD5_ENST00000294848.8_Silent_p.R597R|TDRD5_ENST00000444136.1_Silent_p.R597R	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	597					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						CTTGGGTGAGACCAGTAGAGG	0.408																																					p.R597R		Atlas-SNP	.											.	TDRD5	149	.	0			c.A1791G						.						192	157	169					1																	179609571		2203	4300	6503	SO:0001819	synonymous_variant	163589	exon11			GGTGAGACCAGTA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1791A>G	chr1.hg19:g.179609571A>G		64.0	0.0		72.0	20.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.		0.408	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		G	179609571	A	G	179609571	2	3	166	1	0	0	0	0	0	0	0	1	15748	272	10	2		2	TDRD5	1	179609571	Silent	SNP	A	TCGA-DD-AACO-01A-11D-A40R-10	65354965	179609571	69641050	2	25192										
PTGS2	5743	hgsc.bcm.edu	37	chr1	186647479	186647479	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ggttagagaaggcttcccagCttttgtagccatagtcagca	11	9	1	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:186647479C>G	ENST00000367468.5	-	4	507	c.371G>C	c.(370-372)aGc>aCc	p.S124T	PTGS2_ENST00000490885.2_5'UTR|RP5-973M2.2_ENST00000608917.1_lincRNA	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	124					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	GGCTTCCCAGCTTTTGTAGCC	0.408																																					p.S124T		Atlas-SNP	.											.	PTGS2	144	.	0			c.G371C						.						82	73	76					1																	186647479		2203	4300	6503	SO:0001583	missense	5743	exon4			TCCCAGCTTTTGT	D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.371G>C	chr1.hg19:g.186647479C>G	ENSP00000356438:p.Ser124Thr	140.0	0.0		161.0	12.0	NM_000963	A8K802|Q16876	Missense_Mutation	SNP	ENST00000367468.5	hg19	CCDS1371.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.828035	0.50845	.	.	ENSG00000073756	ENST00000367468	T	0.18657	2.2	5.52	3.66	0.41972	.	0.156380	0.64402	D	0.000001	T	0.19167	0.0460	L	0.56340	1.77	0.47476	D	0.999436	B	0.12630	0.006	B	0.23018	0.043	T	0.04781	-1.0927	10	0.20519	T	0.43	-13.0003	8.9337	0.35686	0.0:0.7395:0.123:0.1375	.	124	P35354	PGH2_HUMAN	T	124	ENSP00000356438:S124T	ENSP00000356438:S124T	S	-	2	0	PTGS2	184914102	0.644000	0.27277	1.000000	0.80357	0.976000	0.68499	-0.111000	0.10807	0.698000	0.31739	-0.136000	0.14681	AGC	.	.		0.408	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963		G	186647479	C	G	186647479	3	3	166	1	0	0	0	0	1	0	0	0	12769	797	28	4	1471	4	PTGS2	1	186647479	Missense_Mutation	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	7037908	186647479	62603142	3	25193										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200946498	200946498	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	tcccctgagatcacctggccCgaggacctgcccatcggaga	11	16	1	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:200946498C>A	ENST00000422435.2	-	31	4483	c.4167G>T	c.(4165-4167)tcG>tcT	p.S1389S	KIF21B_ENST00000332129.2_Silent_p.S1376S|KIF21B_ENST00000360529.5_Silent_p.S1376S|KIF21B_ENST00000461742.2_Silent_p.S1389S	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1389					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TCACCTGGCCCGAGGACCTGC	0.562																																					p.S1389S		Atlas-SNP	.											.	KIF21B	208	.	0			c.G4167T						.						85	81	82					1																	200946498		2203	4300	6503	SO:0001819	synonymous_variant	23046	exon31			CTGGCCCGAGGAC	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.4167G>T	chr1.hg19:g.200946498C>A		111.0	0.0		96.0	52.0	NM_001252102	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	.		0.562	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200946498	C	A	200946498	2	1	166	1	0	0	0	0	0	0	0	1	8298	639	23	1		1	KIF21B	1	200946498	Silent	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	14299019	200946498	48304123	4	25194										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201017755	201017755	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	gcggaccagggcaaagagtgTggcattgaaggtgactgtgc	17	7	0	3			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:201017755T>A	ENST00000362061.3	-	36	4622	c.4396A>T	c.(4396-4398)Aca>Tca	p.T1466S	CACNA1S_ENST00000367338.3_Missense_Mutation_p.T1447S	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1466					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GCAAAGAGTGTGGCATTGAAG	0.607																																					p.T1466S		Atlas-SNP	.											.	CACNA1S	249	.	0			c.A4396T						.						139	108	119					1																	201017755		2203	4300	6503	SO:0001583	missense	779	exon36			AGAGTGTGGCATT	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.4396A>T	chr1.hg19:g.201017755T>A	ENSP00000355192:p.Thr1466Ser	47.0	0.0		50.0	29.0	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	31	5.065373	0.93898	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	T;T	0.09255	3.0;3.0	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.41190	0.1148	M	0.89904	3.07	0.58432	D	0.999993	D	0.76494	0.999	D	0.83275	0.996	T	0.51996	-0.8634	10	0.87932	D	0	.	15.2557	0.73582	0.0:0.0:0.0:1.0	.	1466	Q13698	CAC1S_HUMAN	S	1466;1447	ENSP00000355192:T1466S;ENSP00000356307:T1447S	ENSP00000355192:T1466S	T	-	1	0	CACNA1S	199284378	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	7.965000	0.87945	2.060000	0.61445	0.455000	0.32223	ACA	.	.		0.607	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201017755	T	A	201017755	3	1	166	1	0	0	0	0	1	0	0	0	2549	1696	59	4	1261	4	CACNA1S	1	201017755	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10	71257	201017755	48232866	5	25195										
EXO1	9156	hgsc.bcm.edu	37	chr1	242035468	242035468	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ctgacctggtaaatggacctActaacaaaaagagtgtaagc	9	8	0	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:242035468A>G	ENST00000366548.3	+	12	1995	c.1402A>G	c.(1402-1404)Act>Gct	p.T468A	EXO1_ENST00000518483.1_Missense_Mutation_p.T468A|EXO1_ENST00000348581.5_Missense_Mutation_p.T468A	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	468	Interaction with MLH1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			AAATGGACCTACTAACAAAAA	0.378								Editing and processing nucleases																													p.T468A		Atlas-SNP	.											.	EXO1	103	.	0			c.A1402G						.						82	82	82					1																	242035468		2203	4300	6503	SO:0001583	missense	9156	exon12			GGACCTACTAACA	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1402A>G	chr1.hg19:g.242035468A>G	ENSP00000355506:p.Thr468Ala	329.0	0.0		381.0	130.0	NM_130398	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	hg19	CCDS1620.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.837237	0.00579	.	.	ENSG00000174371	ENST00000366548;ENST00000348581;ENST00000518483	T;T;T	0.31769	1.48;1.48;1.48	5.85	-0.853	0.10709	.	1.139940	0.06337	N	0.707193	T	0.12902	0.0313	N	0.05383	-0.06	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.29397	-1.0013	10	0.08381	T	0.77	-21.1506	5.8209	0.18526	0.3839:0.0:0.4283:0.1877	.	467;468;468	A8K5H6;Q9UQ84-4;Q9UQ84	.;.;EXO1_HUMAN	A	468	ENSP00000355506:T468A;ENSP00000311873:T468A;ENSP00000430251:T468A	ENSP00000311873:T468A	T	+	1	0	EXO1	240102091	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.178000	0.09782	0.141000	0.18875	-0.280000	0.10049	ACT	.	.		0.378	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027		G	242035468	A	G	242035468	3	3	166	1	0	0	0	0	1	0	0	0	5302	391	14	2	1436	2	EXO1	1	242035468	Missense_Mutation	SNP	A	TCGA-DD-AACO-01A-11D-A40R-10	41017713	242035468	7215153	6	25196										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207172701	207172701	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	aaaccatatgtacttggaagTtaagaacagccaatatagtt	7	6	0	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr2:207172701T>C	ENST00000374423.3	+	5	3835	c.3449T>C	c.(3448-3450)gTt>gCt	p.V1150A		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1150							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						TACTTGGAAGTTAAGAACAGC	0.378																																					p.V1150A		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T3449C						.						75	72	73					2																	207172701		1855	4096	5951	SO:0001583	missense	57683	exon5			TGGAAGTTAAGAA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.3449T>C	chr2.hg19:g.207172701T>C	ENSP00000363545:p.Val1150Ala	124.0	0.0		124.0	50.0	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	T	8.634	0.894421	0.17613	.	.	ENSG00000204186	ENST00000374423	T	0.41758	0.99	4.25	0.388	0.16264	.	.	.	.	.	T	0.20495	0.0493	N	0.14661	0.345	0.09310	N	1	B	0.17268	0.021	B	0.15052	0.012	T	0.22243	-1.0222	9	0.21540	T	0.41	.	3.968	0.09441	0.5866:0.0:0.1134:0.2999	.	1150	Q9HCK1	ZDBF2_HUMAN	A	1150	ENSP00000363545:V1150A	ENSP00000363545:V1150A	V	+	2	0	ZDBF2	206880946	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.194000	0.17135	0.057000	0.16193	0.528000	0.53228	GTT	.	.		0.378	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		C	207172701	T	C	207172701	3	2	166	1	0	0	0	0	1	0	0	0	17614	1725	60	2	3459	2	ZDBF2	2	207172701	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10		207172701	36026672	7	25197										
DGKD	8527	hgsc.bcm.edu	37	chr2	234360641	234360641	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ggaatgtctggttccttaccCggtggctcagtcatcagtcg	12	11	4	0	rs375913920		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr2:234360641C>T	ENST00000264057.2	+	18	2211	c.2199C>T	c.(2197-2199)ccC>ccT	p.P733P	DGKD_ENST00000409813.3_Silent_p.P689P	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	733					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	GTTCCTTACCCGGTGGCTCAG	0.498													C|||	1	0.000199681	8e-04	0	5008	,	,		17823	0		0	False		,,,				2504	0				p.P733P		Atlas-SNP	.											.	DGKD	106	.	0			c.C2199T						.	C	,	3,4403	6.2+/-15.9	0,3,2200	127	118	121		2067,2199	-9.6	0.1	2		121	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DGKD	NM_003648.2,NM_152879.2	,	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	,	689/1171,733/1215	234360641	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	8527	exon18			CTTACCCGGTGGC	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2199C>T	chr2.hg19:g.234360641C>T		59.0	0.0		65.0	26.0	NM_152879	Q14158|Q6PK55|Q8NG53	Silent	SNP	ENST00000264057.2	hg19	CCDS2504.1																																																																																			.	.		0.498	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234360641	C	T	234360641	2	4	166	1	0	0	0	0	0	0	0	1	4469	639	23	1		1	DGKD	2	234360641	Silent	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	27187940	234360641	8838732	8	25198										
ZFYVE20	64145	hgsc.bcm.edu	37	chr3	15115634	15115634	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ttccctgccactgcttcctcCtcctcgtcctcttcctcgaa	4	20	1	0			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr3:15115634C>A	ENST00000253699.3	-	14	2623	c.2010G>T	c.(2008-2010)gaG>gaT	p.E670D	ZFYVE20_ENST00000476527.2_Missense_Mutation_p.E670D	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	670	Necessary for the interaction with EHD1.|Necessary for the interaction with RAB5A.|Poly-Glu.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						CTGCTTCCTCCTCCTCGTCCT	0.562																																					p.E670D		Atlas-SNP	.											.	ZFYVE20	61	.	0			c.G2010T						.						144	148	146					3																	15115634		2203	4300	6503	SO:0001583	missense	64145	exon14			TTCCTCCTCCTCG	AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"Zinc fingers, FYVE domain containing"	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.2010G>T	chr3.hg19:g.15115634C>A	ENSP00000253699:p.Glu670Asp	70.0	0.0		48.0	22.0	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Missense_Mutation	SNP	ENST00000253699.3	hg19	CCDS2623.1	.	.	.	.	.	.	.	.	.	.	C	3.450	-0.112244	0.06881	.	.	ENSG00000131381	ENST00000253699;ENST00000476527	T;T	0.54071	0.59;0.59	5.02	-3.86	0.04230	.	0.312584	0.33290	N	0.005077	T	0.23249	0.0562	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.07501	-1.0769	10	0.19147	T	0.46	-5.8485	0.7989	0.01072	0.2115:0.1569:0.1957:0.4359	.	670	Q9H1K0	RBNS5_HUMAN	D	670	ENSP00000253699:E670D;ENSP00000422551:E670D	ENSP00000253699:E670D	E	-	3	2	ZFYVE20	15090638	0.002000	0.14202	0.001000	0.08648	0.009000	0.06853	-0.282000	0.08445	-0.575000	0.05982	0.591000	0.81541	GAG	.	.		0.562	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		A	15115634	C	A	15115634	3	1	166	1	0	0	0	0	1	0	0	0	17681	680	24	3	348	3	ZFYVE20	3	15115634	Missense_Mutation	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10		15115634	182906796	9	25199										
ALDH1L1	10840	hgsc.bcm.edu	37	chr3	125856710	125856710	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	cctcgcagcttcctcactaaCagctggatgaagtccccaaa	7	15	1	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr3:125856710C>A	ENST00000393434.2	-	10	1519	c.1170G>T	c.(1168-1170)ctG>ctT	p.L390L	ALDH1L1_ENST00000393431.2_Silent_p.L390L|ALDH1L1_ENST00000452905.2_Silent_p.L289L|ALDH1L1_ENST00000273450.3_Silent_p.L400L|ALDH1L1_ENST00000472186.1_Silent_p.L390L	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	390	Acyl carrier. {ECO:0000255|PROSITE- ProRule:PRU00258}.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	TCCTCACTAACAGCTGGATGA	0.582																																					p.L400L		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.G1200T						.						137	101	113					3																	125856710		2203	4300	6503	SO:0001819	synonymous_variant	10840	exon10			CACTAACAGCTGG	AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"Aldehyde dehydrogenases"	3978	protein-coding gene	gene with protein product	"cytosolic 10-formyltetrahydrofolate dehydrogenase"	600249	"formyltetrahydrofolate dehydrogenase"	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.1170G>T	chr3.hg19:g.125856710C>A		113.0	0.0		107.0	36.0	NM_001270364	B4DG36|E9PBX3|Q68CS1	Silent	SNP	ENST00000393434.2	hg19	CCDS3034.1																																																																																			.	.		0.582	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		A	125856710	C	A	125856710	2	1	166	1	0	0	0	0	0	0	0	1	494	465	17	3		3	ALDH1L1	3	125856710	Silent	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	110741076	125856710	72165720	10	25200										
SLC9A9	285195	hgsc.bcm.edu	37	chr3	142987725	142987725	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	agatttacttaccccataggCttgaggactggtaagcagcc	10	10	0	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr3:142987725C>A	ENST00000316549.6	-	15	1910	c.1702G>T	c.(1702-1704)Gcc>Tcc	p.A568S		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	568					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)			breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						ACCCCATAGGCTTGAGGACTG	0.493																																					p.A568S		Atlas-SNP	.											SLC9A9,NS,carcinoma,0,1	SLC9A9	117	.	0			c.G1702T						.						144	139	141					3																	142987725		2203	4300	6503	SO:0001583	missense	285195	exon15			CATAGGCTTGAGG	AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"Solute carriers"	20653	protein-coding gene	gene with protein product		608396	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 9", "solute carrier family 9 (sodium/hydrogen exchanger), member 9"			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.1702G>T	chr3.hg19:g.142987725C>A	ENSP00000320246:p.Ala568Ser	113.0	0.0		87.0	41.0	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Missense_Mutation	SNP	ENST00000316549.6	hg19	CCDS33872.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600024	0.87055	.	.	ENSG00000181804	ENST00000316549	T	0.57595	0.39	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000001	T	0.71796	0.3382	M	0.78637	2.42	0.47276	D	0.999378	D	0.63880	0.993	D	0.72625	0.978	T	0.66212	-0.5980	10	0.10902	T	0.67	.	19.6526	0.95823	0.0:1.0:0.0:0.0	.	568	Q8IVB4	SL9A9_HUMAN	S	568	ENSP00000320246:A568S	ENSP00000320246:A568S	A	-	1	0	SLC9A9	144470415	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.634000	0.67833	2.641000	0.89580	0.655000	0.94253	GCC	.	.		0.493	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653		A	142987725	C	A	142987725	3	1	166	1	0	0	0	0	1	0	0	0	14736	797	28	3	243	3	SLC9A9	3	142987725	Missense_Mutation	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	17131015	142987725	55034705	11	25201										
PLSCR1	5359	hgsc.bcm.edu	37	chr3	146234856	146234856	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	tcaaggtctaaagggaactgGattccaaagttatcagcgtc	10	8	3	0	rs377240309		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr3:146234856G>T	ENST00000342435.4	-	8	1247	c.837C>A	c.(835-837)atC>atA	p.I279I	PLSCR1_ENST00000484560.1_5'UTR|PLSCR1_ENST00000448205.1_5'UTR|PLSCR1_ENST00000487389.1_Silent_p.I272I|PLSCR1_ENST00000448787.2_Silent_p.I198I	NM_021105.2	NP_066928.1	O15162	PLS1_HUMAN	phospholipid scramblase 1	279					acute-phase response (GO:0006953)|apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|negative regulation of viral genome replication (GO:0045071)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid scrambling (GO:0017121)|platelet activation (GO:0030168)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of gene expression (GO:0010628)|positive regulation of innate immune response (GO:0045089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|regulation of mast cell activation (GO:0033003)|response to interferon-beta (GO:0035456)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|epidermal growth factor receptor binding (GO:0005154)|phospholipid scramblase activity (GO:0017128)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15						AAGGGAACTGGATTCCAAAGT	0.368																																					p.I279I		Atlas-SNP	.											.	PLSCR1	35	.	0			c.C837A						.						126	120	122					3																	146234856		2203	4300	6503	SO:0001819	synonymous_variant	5359	exon8			GAACTGGATTCCA	AF098642	CCDS3135.1	3q23	2004-02-27			ENSG00000188313	ENSG00000188313			9092	protein-coding gene	gene with protein product		604170				9218461	Standard	NM_021105		Approved	MMTRA1B	uc003evx.4	O15162	OTTHUMG00000159427	ENST00000342435.4:c.837C>A	chr3.hg19:g.146234856G>T		167.0	0.0		169.0	32.0	NM_021105	B2R8H8|B4DTE8	Silent	SNP	ENST00000342435.4	hg19	CCDS3135.1	.	.	.	.	.	.	.	.	.	.	.	9.900	1.206612	0.22205	.	.	ENSG00000188313	ENST00000483300	.	.	.	4.84	0.891	0.19224	.	.	.	.	.	T	0.53498	0.1800	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42515	-0.9447	4	.	.	.	.	6.5816	0.22598	0.2178:0.0:0.6543:0.1279	.	.	.	.	Y	146	.	.	S	-	2	0	PLSCR1	147717546	1.000000	0.71417	0.951000	0.38953	0.988000	0.76386	0.690000	0.25451	0.183000	0.20059	0.555000	0.69702	TCC	.	.		0.368	PLSCR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355257.2	NM_021105		T	146234856	G	T	146234856	2	4	166	1	0	0	0	0	0	0	0	1	12118	1164	41	3		3	PLSCR1	3	146234856	Silent	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10	3247131	146234856	51787574	12	25202										
MFSD1	64747	hgsc.bcm.edu	37	chr3	158531837	158531837	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	tctgctggtcacacaaccctCgggatcacacttatgattgg	9	12	3	1	rs147447476		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr3:158531837C>T	ENST00000264266.8	+	7	695	c.633C>T	c.(631-633)ctC>ctT	p.L211L	MFSD1_ENST00000415822.2_Silent_p.L260L|MFSD1_ENST00000392813.4_Silent_p.L221L			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	211					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ACACAACCCTCGGGATCACAC	0.453																																					p.L260L	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											MFSD1_ENST00000415822,right_lower_lobe,carcinoma,0,2	MFSD1	88	.	0			c.C780T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	175	137	150		663,780	-2.8	0.9	3	dbSNP_134	150	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MFSD1	NM_001167903.1,NM_022736.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	221/476,260/515	158531837	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	64747	exon7			AACCCTCGGGATC	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.633C>T	chr3.hg19:g.158531837C>T		73.0	0.0		55.0	33.0	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Silent	SNP	ENST00000264266.8	hg19																																																																																				.	C|1.000;T|0.000		0.453	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		T	158531837	C	T	158531837	2	4	166	1	0	0	0	0	0	0	0	1	9536	871	31	1		1	MFSD1	3	158531837	Silent	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	12296981	158531837	39490593	13	25203										
ZCCHC4	29063	hgsc.bcm.edu	37	chr4	25314444	25314444	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	gcgggaagatggcggcctccAggaatgggtttgaagccgtg	18	8	0	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr4:25314444A>C	ENST00000302874.4	+	1	37	c.13A>C	c.(13-15)Agg>Cgg	p.R5R	ZCCHC4_ENST00000505451.1_3'UTR	NM_024936.2	NP_079212.2	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	5							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)	9		Breast(46;0.0503)				GGCGGCCTCCAGGAATGGGTT	0.662											OREG0016141	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R5R		Atlas-SNP	.											.	ZCCHC4	34	.	0			c.A13C						.						81	97	92					4																	25314444		1985	4154	6139	SO:0001819	synonymous_variant	29063	exon1			GCCTCCAGGAATG	AF161537	CCDS43218.1	4p15.31	2014-02-18			ENSG00000168228	ENSG00000168228		"Zinc fingers, CCHC domain containing"	22917	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 4"	611792				11042152	Standard	NM_024936		Approved	HSPC052, FLJ23024, ZGRF4	uc003grl.4	Q9H5U6	OTTHUMG00000160563	ENST00000302874.4:c.13A>C	chr4.hg19:g.25314444A>C		55.0	0.0	778	44.0	19.0	NM_024936	B2RXF6|B4DRD8|B7ZW20|Q5IW78|Q96AN7	Silent	SNP	ENST00000302874.4	hg19	CCDS43218.1																																																																																			.	.		0.662	ZCCHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361151.1			C	25314444	A	C	25314444	2	2	166	1	0	0	0	0	0	0	0	1	17605	179	7	5		5	ZCCHC4	4	25314444	Silent	SNP	A	TCGA-DD-AACO-01A-11D-A40R-10		25314444	165839832	14	25204										
ALB	213	hgsc.bcm.edu	37	chr4	74272435	74272440	+	De_novo_Start_InFrame	DEL	CATGTG	CATGTG	-													0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	agtaactgaatttgcaaaaaCatgtgttgctgatgagtcag					rs75152012		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	CATGTG	CATGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr4:74272435_74272440delCATGTG	ENST00000503124.1	+	0	196_201				ALB_ENST00000401494.3_Intron|ALB_ENST00000415165.2_Intron|ALB_ENST00000295897.4_In_Frame_Del_p.76_78TCV>I|ALB_ENST00000509063.1_In_Frame_Del_p.76_78TCV>I			Q8TES7	FBF1_HUMAN	albumin						apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTGCAAAAACATGTGTTGCTGATGA	0.35																																					p.76_77del		Atlas-INDEL	.											.	ALB	132	.	0			c.226_231del	GRCh37	CD023226	ALB	D	rs75152012	.																																					213	exon3			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919		chr4.hg19:g.74272435_74272440delCATGTG		42.0	0.0		44.0	13.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	In_Frame_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.35	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74272440	CATGTG	-	74272435	6	5	166	1	0	1	0	1	0	0	0	0	486	478	17	0		0	ALB	4	74272435	De_novo_Start_InFrame	DEL	CATGTG	TCGA-DD-AACO-01A-11D-A40R-10	48957991	74272435	116881841	15	25205										
ALB	213	hgsc.bcm.edu	37	chr4	74286007	74286007	+	Frame_Shift_Del	DEL	G	G	-													0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ctgcaagtcaagctgccttaGgcttataacatcacatttaa							TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr4:74286007delG	ENST00000503124.1	+	12	1579	c.1372delG	c.(1372-1374)ggcfs	p.G458fs	ALB_ENST00000401494.3_Frame_Shift_Del_p.G493fs|ALB_ENST00000415165.2_Frame_Shift_Del_p.G416fs|ALB_ENST00000295897.4_Frame_Shift_Del_p.G608fs|ALB_ENST00000509063.1_Intron|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGCTGCCTTAGGCTTATAACA	0.279																																					p.L607fs		Atlas-INDEL	.											.	ALB	132	.	0			c.1821delA						.						89	85	87					4																	74286007		2201	4300	6501	SO:0001589	frameshift_variant	213	exon14			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1372delG	chr4.hg19:g.74286007delG	ENSP00000421027:p.Gly458fs	155.0	0.0		134.0	70.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.279	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74286007	G	-	74286007	7	5	166	1	0	1	0	1	0	0	0	0	486	1000	35	0	1876	0	ALB	4	74286007	Frame_Shift_Del	DEL	G	TCGA-DD-AACO-01A-11D-A40R-10	13572	74286007	116868269	16	25206										
CCNO	10309	hgsc.bcm.edu	37	chr5	54529209	54529209	+	Frame_Shift_Del	DEL	G	G	-													0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	agtctcccgggagcgggcacGggttcaggggatgcagcggc							TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr5:54529209delG	ENST00000282572.4	-	1	299	c.143delC	c.(142-144)ccgfs	p.P48fs	RP11-506H20.1_ENST00000506435.1_RNA	NM_021147.3	NP_066970.3	P22674	CCNO_HUMAN	cyclin O	48					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cell cycle (GO:0007049)|cell division (GO:0051301)|cilium assembly (GO:0042384)|depyrimidination (GO:0045008)|DNA repair (GO:0006281)|embryo development (GO:0009790)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	uracil DNA N-glycosylase activity (GO:0004844)			endometrium(1)|lung(3)|skin(1)	5		Lung NSC(810;4.08e-05)|Breast(144;0.0735)|Prostate(74;0.183)	LUSC - Lung squamous cell carcinoma(15;0.142)|Lung(15;0.161)			GAGCGGGCACGGGTTCAGGGG	0.711																																					p.P48fs		Atlas-INDEL	.											.	CCNO	17	.	0			c.144delG						.																																			SO:0001589	frameshift_variant	10309	exon1			.	M87499	CCDS34157.1	5q11.2	2010-11-15	2007-07-26	2007-07-26	ENSG00000152669	ENSG00000152669			18576	protein-coding gene	gene with protein product		607752	"cyclin U"	CCNU			Standard	NR_125346		Approved	UDG2, FLJ22422, UNG2	uc003jpw.3	P22674	OTTHUMG00000162598	ENST00000282572.4:c.143delC	chr5.hg19:g.54529209delG	ENSP00000282572:p.Pro48fs	143.0	0.0		136.0	56.0	NM_021147	A8K1W5|Q0P6J2|Q9H6B0|Q9UMD5	Frame_Shift_Del	DEL	ENST00000282572.4	hg19	CCDS34157.1																																																																																			.	.		0.711	CCNO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369707.1	NM_021147		-	54529209	G	-	54529209	7	5	166	1	0	1	0	1	0	0	0	0	2935	1116	39	0	921	0	CCNO	5	54529209	Frame_Shift_Del	DEL	G	TCGA-DD-AACO-01A-11D-A40R-10		54529209	126386051	17	25207										
PDLIM4	8572	hgsc.bcm.edu	37	chr5	131606786	131606786	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	gcatgtgtctccaccccccaGgtagcacagagatgccttcg	10	15	1	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr5:131606786G>T	ENST00000253754.3	+	4	570	c.506G>T	c.(505-507)aGc>aTc	p.S169I	PDLIM4_ENST00000484620.1_3'UTR|PDLIM4_ENST00000379018.3_Splice_Site_p.S169I|P4HA2_ENST00000471826.1_Intron	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	169							zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|urinary_tract(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCACCCCCCAGGTAGCACAGA	0.587																																					p.S169I		Atlas-SNP	.											.	PDLIM4	22	.	0			c.G506T						.						124	122	123					5																	131606786		2203	4300	6503	SO:0001630	splice_region_variant	8572	exon4			CCCCCAGGTAGCA	AF153882	CCDS4152.1, CCDS47261.1	5q31.1	2008-02-05			ENSG00000131435	ENSG00000131435			16501	protein-coding gene	gene with protein product		603422				9573374	Standard	NM_001131027		Approved	RIL	uc003kwn.3	P50479	OTTHUMG00000059645	ENST00000253754.3:c.506+1G>T	chr5.hg19:g.131606786G>T		98.0	0.0		99.0	4.0	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Missense_Mutation	SNP	ENST00000253754.3	hg19	CCDS4152.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.930457	0.73327	.	.	ENSG00000131435	ENST00000253754;ENST00000379018;ENST00000418373	T;T;T	0.48522	2.58;1.91;0.81	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.67674	0.2918	M	0.68952	2.095	0.80722	D	1	D;D;B	0.89917	1.0;1.0;0.293	D;D;B	0.97110	1.0;0.997;0.095	T	0.69636	-0.5092	10	0.72032	D	0.01	-31.8443	16.2992	0.82801	0.0:0.0:1.0:0.0	.	169;110;169	P50479-2;C9J542;P50479	.;.;PDLI4_HUMAN	I	169;169;110	ENSP00000253754:S169I;ENSP00000368303:S169I;ENSP00000411753:S110I	ENSP00000253754:S169I	S	+	2	0	PDLIM4	131634685	1.000000	0.71417	1.000000	0.80357	0.624000	0.37722	5.142000	0.64820	2.631000	0.89168	0.455000	0.32223	AGC	.	.		0.587	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687	Missense_Mutation	T	131606786	G	T	131606786	5	4	166	1	0	0	0	0	0	0	1	0	11691	1014	35	3	520	3	PDLIM4	5	131606786	Splice_Site	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10	77077577	131606786	49308474	18	25208										
UNC5A	90249	hgsc.bcm.edu	37	chr5	176306745	176306745	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	tctcagcttctttgcctccaAgcccagccccacagccatga	6	18	2	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr5:176306745A>T	ENST00000329542.4	+	15	2661	c.2387A>T	c.(2386-2388)aAg>aTg	p.K796M	UNC5A_ENST00000261961.3_Missense_Mutation_p.K756M	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	796	Death.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTTGCCTCCAAGCCCAGCCCC	0.697																																					p.K796M		Atlas-SNP	.											.	UNC5A	76	.	0			c.A2387T						.						44	47	46					5																	176306745		2203	4300	6503	SO:0001583	missense	90249	exon15			CCTCCAAGCCCAG	AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"Immunoglobulin superfamily / I-set domain containing"	12567	protein-coding gene	gene with protein product		607869	"unc5 (C.elegans homolog) a"				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.2387A>T	chr5.hg19:g.176306745A>T	ENSP00000332737:p.Lys796Met	85.0	0.0		73.0	13.0	NM_133369	B2RXE6|Q8TF26|Q96GP4	Missense_Mutation	SNP	ENST00000329542.4	hg19	CCDS34299.1	.	.	.	.	.	.	.	.	.	.	A	19.55	3.848309	0.71603	.	.	ENSG00000113763	ENST00000329542;ENST00000261961	D;D	0.86164	-2.08;-2.08	4.51	4.51	0.55191	Death (2);DEATH-like (2);	0.000000	0.85682	D	0.000000	D	0.93000	0.7772	M	0.80746	2.51	0.53688	D	0.999972	D	0.89917	1.0	D	0.81914	0.995	D	0.93934	0.7217	10	0.87932	D	0	-31.7076	13.66	0.62361	1.0:0.0:0.0:0.0	.	796	Q6ZN44	UNC5A_HUMAN	M	796;756	ENSP00000332737:K796M;ENSP00000261961:K756M	ENSP00000261961:K756M	K	+	2	0	UNC5A	176239351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.664000	0.91139	1.898000	0.54952	0.383000	0.25322	AAG	.	.		0.697	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300		T	176306745	A	T	176306745	3	4	166	1	0	0	0	0	1	0	0	0	17006	72	3	4	2445	4	UNC5A	5	176306745	Missense_Mutation	SNP	A	TCGA-DD-AACO-01A-11D-A40R-10	44699959	176306745	4608515	19	25209										
C5orf45	51149	hgsc.bcm.edu	37	chr5	179274998	179274998	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ctgagtggcagctctgaaacTtgtccctgtagtagatttaa	10	8	1	3			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr5:179274998T>G	ENST00000292586.6	-	3	285	c.195A>C	c.(193-195)caA>caC	p.Q65H	C5orf45_ENST00000518235.1_Missense_Mutation_p.Q65H|RN7SKP150_ENST00000410516.1_RNA|C5orf45_ENST00000376931.2_Intron|C5orf45_ENST00000520698.1_Intron|C5orf45_ENST00000403396.2_Missense_Mutation_p.Q107H|C5orf45_ENST00000518219.1_Missense_Mutation_p.Q65H|Y_RNA_ENST00000516393.1_RNA|C5orf45_ENST00000523084.1_Intron|C5orf45_ENST00000521333.1_Missense_Mutation_p.Q65H	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	65										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						GCTCTGAAACTTGTCCCTGTA	0.418																																					p.Q65H		Atlas-SNP	.											.	C5orf45	23	.	0			c.A195C						.						117	112	114					5																	179274998		2203	4300	6503	SO:0001583	missense	51149	exon3			TGAAACTTGTCCC		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"truncated calcium binding protein"						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.195A>C	chr5.hg19:g.179274998T>G	ENSP00000292586:p.Gln65His	105.0	0.0		81.0	32.0	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	hg19	CCDS34319.1	.	.	.	.	.	.	.	.	.	.	T	9.433	1.086065	0.20390	.	.	ENSG00000161010	ENST00000403396;ENST00000518235;ENST00000518219;ENST00000292586;ENST00000521333	T;T;T;T;T	0.23552	1.9;3.07;3.07;3.07;3.07	4.1	-2.01	0.07410	.	0.199418	0.31113	N	0.008234	T	0.38401	0.1039	M	0.71581	2.175	0.09310	N	0.999995	D;P;B	0.69078	0.997;0.662;0.385	D;B;B	0.70935	0.971;0.278;0.106	T	0.19418	-1.0306	10	0.66056	D	0.02	-6.5747	4.3111	0.10971	0.1636:0.3382:0.0:0.4981	.	65;65;107	B7Z1T6;Q6NTE8;Q6NTE8-2	.;CE045_HUMAN;.	H	107;65;65;65;65	ENSP00000384599:Q107H;ENSP00000430298:Q65H;ENSP00000428460:Q65H;ENSP00000292586:Q65H;ENSP00000429651:Q65H	ENSP00000292586:Q65H	Q	-	3	2	C5orf45	179207604	0.046000	0.20272	0.012000	0.15200	0.027000	0.11550	-0.031000	0.12287	-0.453000	0.07076	-2.065000	0.00396	CAA	.	.		0.418	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175		G	179274998	T	G	179274998	3	3	166	1	0	0	0	0	1	0	0	0	2306	1606	56	5	856	5	C5orf45	5	179274998	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10	2968253	179274998	1640262	20	25210										
DAXX	1616	hgsc.bcm.edu	37	chr6	33289254	33289254	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	gcagaactccgccgaggccaAaaacagagagtgggcacgtt	13	11	0	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr6:33289254A>C	ENST00000374542.5	-	3	502	c.298T>G	c.(298-300)Ttg>Gtg	p.L100V	DAXX_ENST00000266000.6_Missense_Mutation_p.L100V|DAXX_ENST00000477162.1_Intron|DAXX_ENST00000414083.2_Missense_Mutation_p.L25V	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	100	Necessary for interaction with USP7 and ATRX.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						GCCGAGGCCAAAAACAGAGAG	0.547			"Mis, F, N"		Pancreatic neuroendocrine tumors. Paediatric GBM																																p.L112V		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.T334G						.						69	75	73					6																	33289254		2203	4300	6503	SO:0001583	missense	1616	exon3			AGGCCAAAAACAG	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"death-associated protein 6"			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.298T>G	chr6.hg19:g.33289254A>C	ENSP00000363668:p.Leu100Val	79.0	0.0		83.0	33.0	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Missense_Mutation	SNP	ENST00000374542.5	hg19	CCDS4776.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.247371	0.59103	.	.	ENSG00000204209	ENST00000266000;ENST00000374542;ENST00000414083;ENST00000446403;ENST00000453407	.	.	.	5.11	0.0611	0.14339	Armadillo-like helical (1);	0.000000	0.64402	D	0.000001	T	0.51584	0.1683	L	0.44542	1.39	0.43412	D	0.995552	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.996;0.999;0.999	T	0.53272	-0.8462	9	0.49607	T	0.09	-6.2462	8.4696	0.32977	0.6545:0.0:0.3455:0.0	.	112;100;100	B4E1C1;B2R7M0;Q9UER7	.;.;DAXX_HUMAN	V	100;100;25;100;100	.	ENSP00000266000:L100V	L	-	1	2	DAXX	33397232	0.998000	0.40836	0.963000	0.40424	0.974000	0.67602	0.370000	0.20433	0.115000	0.18071	0.443000	0.29094	TTG	.	.		0.547	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			C	33289254	A	C	33289254	3	2	166	1	0	0	0	0	1	0	0	0	4245	11	1	5	1948	5	DAXX	6	33289254	Missense_Mutation	SNP	A	TCGA-DD-AACO-01A-11D-A40R-10		33289254	137825813	21	25211										
PRSS35	167681	hgsc.bcm.edu	37	chr6	84233828	84233828	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	agagggtaccagagagcatcTgcgggagagagcgaagggtg	19	6	1	3			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr6:84233828T>G	ENST00000369700.3	+	2	845	c.668T>G	c.(667-669)cTg>cGg	p.L223R	PRSS35_ENST00000536636.1_Missense_Mutation_p.L223R	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	223	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		AGAGAGCATCTGCGGGAGAGA	0.527																																					p.L223R		Atlas-SNP	.											.	PRSS35	60	.	0			c.T668G						.						58	67	64					6																	84233828		2203	4300	6503	SO:0001583	missense	167681	exon2			AGCATCTGCGGGA	BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"Serine peptidases / Serine peptidases"	21387	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 158"	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.668T>G	chr6.hg19:g.84233828T>G	ENSP00000358714:p.Leu223Arg	161.0	0.0		156.0	34.0	NM_153362	A8K7B3|Q9BQP6	Missense_Mutation	SNP	ENST00000369700.3	hg19	CCDS4999.1	.	.	.	.	.	.	.	.	.	.	T	0.038	-1.295115	0.01375	.	.	ENSG00000146250	ENST00000536636;ENST00000369700	T;T	0.42900	0.96;0.96	5.65	-0.0528	0.13820	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.840251	0.10503	N	0.667053	T	0.07458	0.0188	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36383	-0.9750	10	0.30078	T	0.28	-1.6262	5.01	0.14308	0.0:0.2526:0.2715:0.476	.	223	Q8N3Z0	PRS35_HUMAN	R	223	ENSP00000440870:L223R;ENSP00000358714:L223R	ENSP00000358714:L223R	L	+	2	0	PRSS35	84290547	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.266000	0.08631	0.055000	0.16094	0.379000	0.24179	CTG	.	.		0.527	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362		G	84233828	T	G	84233828	3	3	166	1	0	0	0	0	1	0	0	0	12636	1580	55	5	670	5	PRSS35	6	84233828	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10	50944574	84233828	86881239	22	25212										
FERD3L	222894	hgsc.bcm.edu	37	chr7	19184898	19184898	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	cccgggtgcgaagtcgcagaGgagagggcgtctcggggagg	21	9	1	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr7:19184898G>A	ENST00000275461.3	-	1	146	c.88C>T	c.(88-90)Ctc>Ttc	p.L30F	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	30					cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L30F(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						AAGTCGCAGAGGAGAGGGCGT	0.672																																					p.L30F		Atlas-SNP	.											FERD3L,scalp,carcinoma,0,1	FERD3L	63	.	1	Substitution - Missense(1)	skin(1)	c.C88T						.						37	36	36					7																	19184898		2201	4300	6501	SO:0001583	missense	222894	exon1			CGCAGAGGAGAGG	AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"Basic helix-loop-helix proteins"	16660	protein-coding gene	gene with protein product			"Fer3-like (Drosophila)"			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.88C>T	chr7.hg19:g.19184898G>A	ENSP00000275461:p.Leu30Phe	41.0	0.0		32.0	11.0	NM_152898	Q495K0	Missense_Mutation	SNP	ENST00000275461.3	hg19	CCDS5368.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.188341	0.57909	.	.	ENSG00000146618	ENST00000275461	D	0.96802	-4.13	5.39	4.51	0.55191	.	0.325996	0.22051	N	0.065313	D	0.89860	0.6837	L	0.27053	0.805	0.25955	N	0.982706	B	0.18461	0.028	B	0.13407	0.009	T	0.76719	-0.2856	10	0.10111	T	0.7	-3.247	5.2416	0.15475	0.2375:0.1656:0.5968:0.0	.	30	Q96RJ6	FER3L_HUMAN	F	30	ENSP00000275461:L30F	ENSP00000275461:L30F	L	-	1	0	FERD3L	19151423	0.998000	0.40836	0.987000	0.45799	0.833000	0.47200	1.910000	0.39927	1.274000	0.44362	0.650000	0.86243	CTC	.	.		0.672	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1			A	19184898	G	A	19184898	3	1	166	1	0	0	0	0	1	0	0	0	5824	1000	35	3	416	3	FERD3L	7	19184898	Missense_Mutation	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10		19184898	139953765	23	25213										
IGF2BP3	10643	hgsc.bcm.edu	37	chr7	23509595	23509595	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ttgagggcccagctctcgtcCgggcagtccacgaacgcgta	13	14	1	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr7:23509595C>T	ENST00000258729.3	-	1	491	c.135G>A	c.(133-135)ccG>ccA	p.P45P	IGF2BP3_ENST00000491719.1_5'Flank	NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	45	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						AGCTCTCGTCCGGGCAGTCCA	0.697																																					p.P45P		Atlas-SNP	.											.	IGF2BP3	71	.	0			c.G135A						.						40	46	44					7																	23509595		2203	4300	6503	SO:0001819	synonymous_variant	10643	exon1			CTCGTCCGGGCAG	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"RNA binding motif (RRM) containing"	28868	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 3", "cancer/testis antigen 98"	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.135G>A	chr7.hg19:g.23509595C>T		48.0	0.0		51.0	13.0	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Silent	SNP	ENST00000258729.3	hg19	CCDS5382.1																																																																																			.	.		0.697	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547		T	23509595	C	T	23509595	2	4	166	1	0	0	0	0	0	0	0	1	7584	639	23	1		1	IGF2BP3	7	23509595	Silent	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	4324697	23509595	135629068	24	25214										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48313643	48313643	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	tcacatataaattgtgtcaaTatttacttgaaagatgtaac	5	5	2	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr7:48313643T>G	ENST00000435803.1	+	17	4404	c.4380T>G	c.(4378-4380)aaT>aaG	p.N1460K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1460					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATTGTGTCAATATTTACTTGA	0.249																																					p.N1460K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T4380G						.						27	30	29					7																	48313643		1787	4029	5816	SO:0001583	missense	154664	exon17			TGTCAATATTTAC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4380T>G	chr7.hg19:g.48313643T>G	ENSP00000411096:p.Asn1460Lys	116.0	0.0		127.0	49.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	9.564	1.119347	0.20877	.	.	ENSG00000179869	ENST00000435803	D	0.86030	-2.06	5.44	1.67	0.24075	.	0.425529	0.20048	N	0.100369	D	0.85999	0.5828	M	0.62723	1.935	0.09310	N	1	D	0.63880	0.993	P	0.53954	0.738	T	0.77032	-0.2738	9	.	.	.	.	8.8855	0.35400	0.0:0.3008:0.0:0.6992	.	1460	Q86UQ4	ABCAD_HUMAN	K	1460	ENSP00000411096:N1460K	.	N	+	3	2	ABCA13	48284189	0.047000	0.20315	0.200000	0.23457	0.219000	0.24729	0.652000	0.24888	0.099000	0.17552	-0.400000	0.06385	AAT	.	.		0.249	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48313643	T	G	48313643	3	3	166	1	0	0	0	0	1	0	0	0	31	1403	49	5	4275	5	ABCA13	7	48313643	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10	24804048	48313643	110825020	25	25215										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91652251	91652251	+	Frame_Shift_Del	DEL	A	A	-													0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	acagttgaaagaaactgaacAaaactatgaggcagagatcc					rs548801776		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr7:91652251delA	ENST00000359028.2	+	15	4337	c.4112delA	c.(4111-4113)caafs	p.Q1371fs	AKAP9_ENST00000358100.2_Frame_Shift_Del_p.Q1371fs|AKAP9_ENST00000356239.3_Frame_Shift_Del_p.Q1359fs			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1371					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAAACTGAACAAAACTATGAG	0.393			T	BRAF	papillary thyroid																																p.Q1359fs		Atlas-INDEL	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.4075delC						.						98	91	93					7																	91652251		2203	4300	6503	SO:0001589	frameshift_variant	10142	exon14			.	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.4112delA	chr7.hg19:g.91652251delA	ENSP00000351922:p.Gln1371fs	108.0	0.0		78.0	16.0	NM_147185	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Frame_Shift_Del	DEL	ENST00000359028.2	hg19																																																																																				.	.		0.393	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		-	91652251	A	-	91652251	7	5	166	1	0	1	0	1	0	0	0	0	459	130	5	0	4130	0	AKAP9	7	91652251	Frame_Shift_Del	DEL	A	TCGA-DD-AACO-01A-11D-A40R-10	43338608	91652251	67486412	26	25216										
LETM2	137994	hgsc.bcm.edu	37	chr8	38257839	38257839	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	aaagttggaactagcaaaatTtcttcaagaaaccatgacag	7	7	2	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr8:38257839T>A	ENST00000379957.4	+	5	822	c.695T>A	c.(694-696)tTt>tAt	p.F232Y	LETM2_ENST00000524874.1_Missense_Mutation_p.F184Y|LETM2_ENST00000527710.1_Missense_Mutation_p.F18Y|LETM2_ENST00000297720.5_Missense_Mutation_p.F137Y|LETM2_ENST00000523983.2_Missense_Mutation_p.F185Y|RP11-350N15.3_ENST00000533301.1_RNA	NM_001199659.1	NP_001186588.1	Q2VYF4	LETM2_HUMAN	leucine zipper-EF-hand containing transmembrane protein 2	232	LETM1.					integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.F137C(1)		NS(1)|large_intestine(1)|lung(3)|prostate(2)	7	all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202)	all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175)	Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114)			CTAGCAAAATTTCTTCAAGAA	0.398																																					p.F185Y		Atlas-SNP	.											LETM2,rectum,carcinoma,0,1	LETM2	57	.	1	Substitution - Missense(1)	large_intestine(1)	c.T554A						.						78	70	73					8																	38257839		2203	4300	6503	SO:0001583	missense	137994	exon5			CAAAATTTCTTCA	AK058138	CCDS6106.1, CCDS56534.1, CCDS69466.1, CCDS75731.1	8p12	2013-01-11						"EF-hand domain containing"	14648	protein-coding gene	gene with protein product						11549311	Standard	NM_001286821		Approved	FLJ25409	uc003xlm.2	Q2VYF4		ENST00000379957.4:c.695T>A	chr8.hg19:g.38257839T>A	ENSP00000369291:p.Phe232Tyr	66.0	0.0		40.0	12.0	NM_001199659	A6NMG3|Q8NCR2|Q96LL1	Missense_Mutation	SNP	ENST00000379957.4	hg19		.	.	.	.	.	.	.	.	.	.	T	33	5.207499	0.95033	.	.	ENSG00000165046	ENST00000297720;ENST00000524874;ENST00000379957;ENST00000523983;ENST00000527710	T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72	5.77	5.77	0.91146	LETM1-like (1);	0.000000	0.85682	D	0.000000	T	0.71896	0.3394	M	0.83312	2.635	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.76680	-0.2870	10	0.87932	D	0	-15.1134	16.0892	0.81080	0.0:0.0:0.0:1.0	.	29;232;184	B7Z7T4;Q2VYF4;E9PMA4	.;LETM2_HUMAN;.	Y	137;184;232;185;18	ENSP00000297720:F137Y;ENSP00000431211:F184Y;ENSP00000369291:F232Y;ENSP00000428765:F185Y;ENSP00000434867:F18Y	ENSP00000297720:F137Y	F	+	2	0	LETM2	38376996	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.584000	0.82572	2.208000	0.71279	0.454000	0.30748	TTT	.	.		0.398	LETM2-013	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000381816.1	NM_144652		A	38257839	T	A	38257839	3	1	166	1	0	0	0	0	1	0	0	0	8744	1841	64	4	416	4	LETM2	8	38257839	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10		38257839	108106183	27	25217										
ADAM18	8749	hgsc.bcm.edu	37	chr8	39468133	39468133	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	agcatataatttatcaaatgAaaaataatgatccaaatgta	4	4	1	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr8:39468133A>G	ENST00000265707.5	+	6	475	c.430A>G	c.(430-432)Aaa>Gaa	p.K144E	ADAM18_ENST00000379866.1_Missense_Mutation_p.K144E|ADAM18_ENST00000520772.1_Missense_Mutation_p.K144E|ADAM18_ENST00000541111.1_Intron	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	144					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TTATCAAATGAAAAATAATGA	0.328																																					p.K144E		Atlas-SNP	.											.	ADAM18	169	.	0			c.A430G						.						48	50	49					8																	39468133		2203	4298	6501	SO:0001583	missense	8749	exon6			CAAATGAAAAATA	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.430A>G	chr8.hg19:g.39468133A>G	ENSP00000265707:p.Lys144Glu	444.0	1.0		308.0	142.0	NM_001190956	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	hg19	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.858578	0.51376	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000520772;ENST00000522198	T;T;T	0.11495	5.35;4.95;2.77	5.25	5.25	0.73442	.	0.123619	0.37219	N	0.002183	T	0.07818	0.0196	N	0.08118	0	0.80722	D	1	P;P;B	0.45634	0.863;0.784;0.217	P;B;B	0.49528	0.614;0.41;0.109	T	0.38286	-0.9668	10	0.07990	T	0.79	.	11.4678	0.50249	1.0:0.0:0.0:0.0	.	144;144;144	Q9Y3Q7-2;Q9Y3Q7;Q6IRW9	.;ADA18_HUMAN;.	E	144;144;144;100	ENSP00000265707:K144E;ENSP00000369195:K144E;ENSP00000429908:K144E	ENSP00000265707:K144E	K	+	1	0	ADAM18	39587290	0.996000	0.38824	0.986000	0.45419	0.146000	0.21551	1.900000	0.39828	2.206000	0.71126	0.533000	0.62120	AAA	.	.		0.328	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		G	39468133	A	G	39468133	3	3	166	1	0	0	0	0	1	0	0	0	239	247	9	2	452	2	ADAM18	8	39468133	Missense_Mutation	SNP	A	TCGA-DD-AACO-01A-11D-A40R-10	1210294	39468133	106895889	28	25218										
ODF1	4956	hgsc.bcm.edu	37	chr8	103573034	103573042	+	In_Frame_Del	DEL	CCCGTGCAG	CCCGTGCAG	-													0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	aacccctgcagcccctgcaaCccgtgcagcccatatgatcc					rs143802899|rs199994329|rs568456031|rs372688769|rs59109601|rs377699584|rs11992195|rs62523273|rs386728348|rs58232162	byFrequency	TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	CCCGTGCAG	CCCGTGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr8:103573034_103573042delCCCGTGCAG	ENST00000285402.3	+	2	831_839	c.675_683delCCCGTGCAG	c.(673-684)aacccgtgcagc>aac	p.PCS226del	ODF1_ENST00000518835.1_In_Frame_Del_p.PCS19del	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	226	C-X-P repeat region.		Missing. {ECO:0000269|PubMed:8111388}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.C218_P226delCNPCSPCNP(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			gcccctgcaacccgtgcagcccATATGAT	0.541																																					p.225_228del		Atlas-INDEL	.											ODF1,NS,carcinoma,0,1	ODF1	55	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.674_682del						.																																			SO:0001651	inframe_deletion	4956	exon2			.	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"Heat shock proteins / HSPB"	8113	protein-coding gene	gene with protein product	"cancer/testis antigen 133"	182878	"outer dense fibre of sperm tails 1"			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.675_683delCCCGTGCAG	chr8.hg19:g.103573034_103573042delCCCGTGCAG	ENSP00000285402:p.Pro226_Ser228del	46.0	0.0		47.0	10.0	NM_024410	Q3SX72	In_Frame_Del	DEL	ENST00000285402.3	hg19	CCDS6293.1																																																																																			.	.		0.541	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1			-	103573042	CCCGTGCAG	-	103573034	7	5	166	1	0	1	0	1	0	0	0	0	10835	506	18	0	681	0	ODF1	8	103573034	In_Frame_Del	DEL	CCCGTGCAG	TCGA-DD-AACO-01A-11D-A40R-10	64104901	103573034	42790988	29	25219										
DENND3	22898	hgsc.bcm.edu	37	chr8	142151392	142151392	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	gcgtggtctccaggtttcccTattacaactccctcaaggac	8	14	2	0			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr8:142151392T>C	ENST00000262585.2	+	4	630	c.352T>C	c.(352-354)Tat>Cat	p.Y118H	DENND3_ENST00000519811.1_Missense_Mutation_p.Y198H|DENND3_ENST00000424248.1_Missense_Mutation_p.Y118H|DENND3_ENST00000518347.1_Missense_Mutation_p.Y198H	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	118	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			CAGGTTTCCCTATTACAACTC	0.587																																					p.Y118H		Atlas-SNP	.											.	DENND3	127	.	0			c.T352C						.						146	119	128					8																	142151392		2203	4300	6503	SO:0001583	missense	22898	exon4			TTTCCCTATTACA	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.352T>C	chr8.hg19:g.142151392T>C	ENSP00000262585:p.Tyr118His	51.0	0.0		73.0	8.0	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	hg19	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.1|20.1	3.940896|3.940896	0.73557|0.73557	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000518668|ENST00000518347;ENST00000262585;ENST00000424248;ENST00000519811;ENST00000523058;ENST00000518249	.|T;T;T;T	.|0.11495	.|2.77;2.77;2.77;2.77	5.24|5.24	5.24|5.24	0.73138|0.73138	.|DENN (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.34366|0.34366	0.0895|0.0895	M|M	0.78049|0.78049	2.395|2.395	0.51767|0.51767	D|D	0.999936|0.999936	.|D;D;D	.|0.89917	.|1.0;1.0;0.999	.|D;D;D	.|0.97110	.|1.0;1.0;0.996	T|T	0.07770|0.07770	-1.0755|-1.0755	5|9	.|.	.|.	.|.	-13.0908|-13.0908	15.15|15.15	0.72689|0.72689	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|198;118;198	.|E9PF32;A2RUS2;E5RIR7	.|.;DEND3_HUMAN;.	P|H	174|198;118;118;198;198;31	.|ENSP00000262585:Y118H;ENSP00000410594:Y118H;ENSP00000428714:Y198H;ENSP00000430786:Y198H	.|.	L|Y	+|+	2|1	0|0	DENND3|DENND3	142220574|142220574	1.000000|1.000000	0.71417|0.71417	0.467000|0.467000	0.27180|0.27180	0.540000|0.540000	0.34992|0.34992	6.209000|6.209000	0.72171|0.72171	1.972000|1.972000	0.57404|0.57404	0.533000|0.533000	0.62120|0.62120	CTA|TAT	.	.		0.587	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		C	142151392	T	C	142151392	3	2	166	1	0	0	0	0	1	0	0	0	4434	1522	53	2	362	2	DENND3	8	142151392	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10	38578358	142151392	4212630	30	25220										
CCIN	881	hgsc.bcm.edu	37	chr9	36170372	36170372	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ggtggccagaaggcccacggCcagttcaatgatggagtgtt	15	9	1	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr9:36170372C>T	ENST00000335119.2	+	1	984	c.873C>T	c.(871-873)ggC>ggT	p.G291G		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	291					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			AGGCCCACGGCCAGTTCAATG	0.582																																					p.G291G		Atlas-SNP	.											.	CCIN	56	.	0			c.C873T						.						75	71	72					9																	36170372		2203	4300	6503	SO:0001819	synonymous_variant	881	exon1			CCACGGCCAGTTC	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"BTB/POZ domain containing"	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.873C>T	chr9.hg19:g.36170372C>T		56.0	0.0		35.0	19.0	NM_005893	Q9BXG7	Silent	SNP	ENST00000335119.2	hg19	CCDS6599.1																																																																																			.	.		0.582	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893		T	36170372	C	T	36170372	2	4	166	1	0	0	0	0	0	0	0	1	2880	726	26	3		3	CCIN	9	36170372	Silent	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10		36170372	105043059	31	25221										
ANK3	288	hgsc.bcm.edu	37	chr10	61828727	61828727	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	tggtggtggtagtggtggtaGtggtggtggtggtggcagtg	24	1	0	0	rs368539157		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr10:61828727G>A	ENST00000280772.2	-	37	12103	c.11912C>T	c.(11911-11913)aCt>aTt	p.T3971I	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3971	Thr-rich.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						agtggtggtagtggtggtggt	0.468																																					p.T3971I		Atlas-SNP	.											.,2	ANK3	703	.	0			c.C11912T						.						78	86	83					10																	61828727		2202	4300	6502	SO:0001583	missense	288	exon37			GTGGTAGTGGTGG	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11912C>T	chr10.hg19:g.61828727G>A	ENSP00000280772:p.Thr3971Ile	62.0	1.0		52.0	4.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	1.592	-0.528734	0.04112	.	.	ENSG00000151150	ENST00000280772	T	0.42513	0.97	3.29	3.29	0.37713	.	0.251972	0.20684	U	0.087593	T	0.20495	0.0493	N	0.08118	0	0.80722	D	1	P	0.49783	0.928	B	0.39119	0.291	T	0.03296	-1.1051	10	0.39692	T	0.17	.	10.3334	0.43835	0.0:0.0:1.0:0.0	.	3971	Q12955	ANK3_HUMAN	I	3971	ENSP00000280772:T3971I	ENSP00000280772:T3971I	T	-	2	0	ANK3	61498733	1.000000	0.71417	1.000000	0.80357	0.165000	0.22458	2.153000	0.42282	2.149000	0.67028	0.563000	0.77884	ACT	.	.		0.468	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61828727	G	A	61828727	3	1	166	1	0	0	0	0	1	0	0	0	622	1029	36	3	1562	3	ANK3	10	61828727	Missense_Mutation	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10		61828727	73706020	32	25222										
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72326463	72326463	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	agcagagctgcagcctcgagCcctctgcccccgaggacttg	12	16	1	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr10:72326463C>T	ENST00000263563.6	+	20	2813	c.2545C>T	c.(2545-2547)Ccc>Tcc	p.P849S		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	849						cytosol (GO:0005829)											CAGCCTCGAGCCCTCTGCCCC	0.687																																					p.P849S		Atlas-SNP	.											.	.	.	.	0			c.C2545T						.						26	26	26					10																	72326463		2201	4299	6500	SO:0001583	missense	27143	exon20			CTCGAGCCCTCTG	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"paladin", "KIAA1274"	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.2545C>T	chr10.hg19:g.72326463C>T	ENSP00000263563:p.Pro849Ser	26.0	0.0		13.0	7.0	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	hg19	CCDS31215.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.15|17.15	3.316980|3.316980	0.60524|0.60524	.|.	.|.	ENSG00000107719|ENSG00000107719	ENST00000426268|ENST00000263563;ENST00000373214	.|T	.|0.32988	.|1.43	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	.|0.064498	.|0.64402	.|D	.|0.000006	T|T	0.51805|0.51805	0.1696|0.1696	M|M	0.66939|0.66939	2.045|2.045	0.52099|0.52099	D|D	0.999945|0.999945	.|D	.|0.61080	.|0.989	.|D	.|0.66084	.|0.941	T|T	0.54146|0.54146	-0.8337|-0.8337	5|10	.|0.72032	.|D	.|0.01	-10.2785|-10.2785	14.1938|14.1938	0.65656|0.65656	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|849	.|Q9ULE6	.|PALD_HUMAN	V|S	229|849;825	.|ENSP00000263563:P849S	.|ENSP00000263563:P849S	A|P	+|+	2|1	0|0	KIAA1274|KIAA1274	71996469|71996469	0.281000|0.281000	0.24258|0.24258	0.971000|0.971000	0.41717|0.41717	0.081000|0.081000	0.17604|0.17604	0.696000|0.696000	0.25541|0.25541	2.415000|2.415000	0.81967|0.81967	0.491000|0.491000	0.48974|0.48974	GCC|CCC	.	.		0.687	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		T	72326463	C	T	72326463	3	4	166	1	0	0	0	0	1	0	0	0	8229	739	26	3	2619	3	KIAA1274	10	72326463	Missense_Mutation	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	10497736	72326463	63208284	33	25223										
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249530	71249530	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	agctgctgcaagccctgctgTtcccagtccagctgctgtaa	10	14	0	0	rs532438179|rs369043826	byFrequency	TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr11:71249530T>C	ENST00000398534.3	+	1	460	c.429T>C	c.(427-429)tgT>tgC	p.C143C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	143	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						AGCCCTGCTGTTCCCAGTCCA	0.612																																					p.C143C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.T429C						.						146	159	155					11																	71249530		2200	4294	6494	SO:0001819	synonymous_variant	57830	exon1			CTGCTGTTCCCAG	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"Keratin associated proteins"	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.429T>C	chr11.hg19:g.71249530T>C		79.0	0.0		99.0	15.0	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	hg19	CCDS41683.1																																																																																			.	.		0.612	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046		C	71249530	T	C	71249530	2	2	166	1	0	0	0	0	0	0	0	1	8576	1731	60	2		2	KRTAP5-8	11	71249530	Silent	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10		71249530	63756986	34	25224										
EFCAB4B	84766	hgsc.bcm.edu	37	chr12	3788188	3788188	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	tcccctctggacagatacacCttctcttcatggcgctgggc	9	15	3	1	rs3803135	byFrequency	TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr12:3788188C>A	ENST00000252322.1	-	6	885	c.417G>T	c.(415-417)aaG>aaT	p.K139N	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.K139N|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.K139N	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		139					activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			ACAGATACACCTTCTCTTCAT	0.557																																					p.K139N		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.G417T						.						188	152	164					12																	3788188		2203	4300	6503	SO:0001583	missense	84766	exon6			ATACACCTTCTCT																												ENST00000252322.1:c.417G>T	chr12.hg19:g.3788188C>A	ENSP00000252322:p.Lys139Asn	88.0	0.0		49.0	18.0	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	hg19	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	C	5.197	0.221924	0.09863	.	.	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.61980	0.06;2.5;2.51	4.9	2.65	0.31530	EF-hand-like domain (1);	0.350601	0.31041	N	0.008369	T	0.55049	0.1896	M	0.75447	2.3	0.36095	P	0.156231	B;B;B	0.12013	0.004;0.005;0.003	B;B;B	0.10450	0.005;0.003;0.003	T	0.55768	-0.8089	9	0.18276	T	0.48	-21.8852	7.1665	0.25693	0.0:0.7457:0.0:0.2543	.	139;139;139	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	N	139	ENSP00000409382:K139N;ENSP00000412496:K139N;ENSP00000252322:K139N	ENSP00000252322:K139N	K	-	3	2	EFCAB4B	3658449	0.995000	0.38212	0.988000	0.46212	0.279000	0.26890	0.436000	0.21526	1.026000	0.39733	0.561000	0.74099	AAG	.	C|0.862;T|0.138		0.557	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1			A	3788188	C	A	3788188	3	1	166	1	0	0	0	0	1	0	0	0	4939	680	24	3	2030	3	EFCAB4B	12	3788188	Missense_Mutation	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10		3788188	130063707	35	25225										
SOX5	6660	hgsc.bcm.edu	37	chr12	24048957	24048957	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ggctggtcgcttggaagacaTcctggaaggaacaaaagagg	15	7	0	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr12:24048957T>C	ENST00000451604.2	-	2	141	c.40A>G	c.(40-42)Atg>Gtg	p.M14V	SOX5_ENST00000541847.1_Splice_Site_p.M4V|SOX5_ENST00000546136.1_Start_Codon_SNP_p.M1V|SOX5_ENST00000545921.1_Splice_Site_p.M4V|SOX5_ENST00000541536.1_Start_Codon_SNP_p.M1V|SOX5_ENST00000537393.1_Splice_Site_p.M14V|SOX5_ENST00000309359.1_Splice_Site_p.M1V|SOX5_ENST00000441133.2_Splice_Site_p.M14V|SOX5_ENST00000381381.2_Splice_Site_p.M1V			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	14					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						TTGGAAGACATCCTGGAAGGA	0.473																																					p.M14V		Atlas-SNP	.											.	SOX5	134	.	0			c.A40G						.						107	105	106					12																	24048957		2203	4300	6503	SO:0001630	splice_region_variant	6660	exon2			AAGACATCCTGGA	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"SRY (sex determining region Y)-boxes"	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.39-1A>G	chr12.hg19:g.24048957T>C		48.0	0.0		45.0	17.0	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	hg19	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	T	15.95	2.983197	0.53827	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921;ENST00000541847;ENST00000441133;ENST00000538083	D;D;D;D;D;D;D	0.98602	-4.81;-4.81;-4.89;-4.83;-5.02;-4.89;-4.81	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.98842	0.9609	M	0.77103	2.36	0.80722	D	1	P;D;B;D	0.61080	0.811;0.989;0.219;0.98	P;D;P;D	0.75484	0.828;0.986;0.455;0.968	D	0.99861	1.1083	10	0.87932	D	0	.	16.2948	0.82765	0.0:0.0:0.0:1.0	.	14;14;1;14	G3V0H1;F5H0I3;P35711-4;P35711	.;.;.;SOX5_HUMAN	V	1;1;1;14;1;14;1;4;4;14;1	ENSP00000437487:M1V;ENSP00000308927:M1V;ENSP00000370788:M1V;ENSP00000398273:M14V;ENSP00000439832:M14V;ENSP00000441973:M1V;ENSP00000443520:M4V	ENSP00000308927:M1V	M	-	1	0	SOX5	23940224	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.378000	0.79679	2.253000	0.74438	0.455000	0.32223	ATG	.	.		0.473	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940	Missense_Mutation	C	24048957	T	C	24048957	5	2	166	1	0	0	0	0	0	0	1	0	14969	1449	50	2	2317	2	SOX5	12	24048957	Splice_Site	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10	20260769	24048957	109802938	36	25226										
IL31	386653	hgsc.bcm.edu	37	chr12	122657036	122657036	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ctctgaaaactgttgagaaaTagtcaggatgaagcgtttac	10	6	2	3			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr12:122657036T>C	ENST00000377035.1	-	3	444	c.418A>G	c.(418-420)Att>Gtt	p.I140V		NM_001014336.1	NP_001014358.1	Q6EBC2	IL31_HUMAN	interleukin 31	140					immune system process (GO:0002376)	extracellular space (GO:0005615)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;6.93e-05)|Breast(359;0.0544)		OV - Ovarian serous cystadenocarcinoma(86;3.27e-29)|Epithelial(86;4.86e-27)|BRCA - Breast invasive adenocarcinoma(302;0.223)		TGTTGAGAAATAGTCAGGATG	0.448																																					p.I140V		Atlas-SNP	.											.	IL31	23	.	0			c.A418G						.						175	160	165					12																	122657036		2203	4300	6503	SO:0001583	missense	386653	exon3			GAGAAATAGTCAG	AY499343	CCDS31919.1	12q24.31	2011-07-21			ENSG00000204671	ENSG00000204671		"Interleukins and interleukin receptors"	19372	protein-coding gene	gene with protein product		609509				15184896	Standard	NM_001014336		Approved	IL-31	uc001ubv.3	Q6EBC2	OTTHUMG00000168916	ENST00000377035.1:c.418A>G	chr12.hg19:g.122657036T>C	ENSP00000366234:p.Ile140Val	102.0	0.0		72.0	26.0	NM_001014336	A2RUQ1	Missense_Mutation	SNP	ENST00000377035.1	hg19	CCDS31919.1	.	.	.	.	.	.	.	.	.	.	T	7.013	0.557194	0.13436	.	.	ENSG00000204671	ENST00000377035	.	.	.	4.18	-8.36	0.00980	.	1.491180	0.04518	N	0.384050	T	0.21631	0.0521	N	0.14661	0.345	0.09310	N	1	B	0.13145	0.007	B	0.15052	0.012	T	0.23119	-1.0197	9	0.13853	T	0.58	-2.3243	9.5938	0.39563	0.1742:0.6206:0.0878:0.1173	.	140	Q6EBC2	IL31_HUMAN	V	140	.	ENSP00000366234:I140V	I	-	1	0	IL31	121222989	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.865000	0.01649	-3.932000	0.00090	-0.371000	0.07208	ATT	.	.		0.448	IL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401594.1	NM_001014336		C	122657036	T	C	122657036	3	2	166	1	0	0	0	0	1	0	0	0	7699	1406	49	2	80	2	IL31	12	122657036	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10	98608079	122657036	11194859	37	25227										
DACH1	1602	hgsc.bcm.edu	37	chr13	72440337	72440337	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ccccctcagatccaccatttTgcactcattattctgagggg	7	14	3	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr13:72440337T>C	ENST00000359684.2	-	1	570	c.571A>G	c.(571-573)Aaa>Gaa	p.K191E	DACH1_ENST00000354591.4_Missense_Mutation_p.K191E|DACH1_ENST00000313174.7_Missense_Mutation_p.K191E|DACH1_ENST00000305425.4_Missense_Mutation_p.K191E			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	191	DACHbox-N.|Interaction with SIX6 and HDAC3. {ECO:0000250}.				cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		TCCACCATTTTGCACTCATTA	0.602																																					p.K191E		Atlas-SNP	.											.	DACH1	123	.	0			c.A571G						.						39	42	41					13																	72440337		1956	4147	6103	SO:0001583	missense	1602	exon1			CCATTTTGCACTC	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.571A>G	chr13.hg19:g.72440337T>C	ENSP00000352712:p.Lys191Glu	89.0	0.0		48.0	35.0	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Missense_Mutation	SNP	ENST00000359684.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.25	3.340931	0.60963	.	.	ENSG00000165659	ENST00000305425;ENST00000313174;ENST00000354591;ENST00000359684;ENST00000377826	D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63	3.9	3.9	0.45041	.	0.275476	0.33875	U	0.004472	D	0.84347	0.5452	L	0.61218	1.895	0.54753	D	0.999985	P;P;P	0.52061	0.827;0.827;0.95	B;B;P	0.49999	0.271;0.271;0.628	D	0.86050	0.1525	10	0.87932	D	0	-6.9207	12.3897	0.55352	0.0:0.0:0.0:1.0	.	189;189;189	Q9UI36-4;Q9UI36-3;Q9UI36-2	.;.;.	E	191	ENSP00000304994:K191E;ENSP00000318506:K191E;ENSP00000346604:K191E;ENSP00000352712:K191E	ENSP00000304994:K191E	K	-	1	0	DACH1	71338338	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.498000	0.66931	1.396000	0.46663	0.254000	0.18369	AAA	.	.		0.602	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		C	72440337	T	C	72440337	3	2	166	1	0	0	0	0	1	0	0	0	4222	1821	63	2	1599	2	DACH1	13	72440337	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10		72440337	42729541	38	25228										
PSMB11	122706	hgsc.bcm.edu	37	chr14	23512059	23512059	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	acgccctggctcgctgcgccGtggcccacgccacccaccgt	11	21	0	0	rs368929459		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr14:23512059G>A	ENST00000408907.2	+	1	684	c.625G>A	c.(625-627)Gtg>Atg	p.V209M		NM_001099780.1	NP_001093250.1	A5LHX3	PSB11_HUMAN	proteasome (prosome, macropain) subunit, beta type, 11	209					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|kidney(2)|lung(4)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00643)		TCGCTGCGCCGTGGCCCACGC	0.627																																					p.V209M		Atlas-SNP	.											.	PSMB11	40	.	0			c.G625A						.	G	MET/VAL	0,4238		0,0,2119	40	42	41		625	4.1	0.4	14		41	2,8484		0,2,4241	no	missense	PSMB11	NM_001099780.1	21	0,2,6360	AA,AG,GG		0.0236,0.0,0.0157	probably-damaging	209/301	23512059	2,12722	2119	4243	6362	SO:0001583	missense	122706	exon1			TGCGCCGTGGCCC		CCDS41923.1	14q11.2	2008-01-31				ENSG00000222028			31963	protein-coding gene	gene with protein product		611137				17540904	Standard	NM_001099780		Approved	beta5t	uc010ake.1	A5LHX3		ENST00000408907.2:c.625G>A	chr14.hg19:g.23512059G>A	ENSP00000386212:p.Val209Met	48.0	0.0		35.0	20.0	NM_001099780		Missense_Mutation	SNP	ENST00000408907.2	hg19	CCDS41923.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.232866	0.39498	0.0	2.36E-4	ENSG00000222028	ENST00000408907	T	0.23552	1.9	5.02	4.13	0.48395	.	0.000000	0.85682	D	0.000000	T	0.52613	0.1745	M	0.83692	2.655	0.37205	D	0.904548	D	0.89917	1.0	D	0.97110	1.0	T	0.65005	-0.6273	10	0.87932	D	0	-12.6072	12.3151	0.54951	0.0833:0.0:0.9167:0.0	.	209	A5LHX3	PSB11_HUMAN	M	209	ENSP00000386212:V209M	ENSP00000386212:V209M	V	+	1	0	PSMB11	22581899	1.000000	0.71417	0.362000	0.25862	0.002000	0.02628	3.680000	0.54641	1.135000	0.42183	-0.136000	0.14681	GTG	.	.		0.627	PSMB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408294.1	NM_001099780		A	23512059	G	A	23512059	3	1	166	1	0	0	0	0	1	0	0	0	12688	1145	40	1	627	1	PSMB11	14	23512059	Missense_Mutation	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10		23512059	83837481	39	25229										
STON2	85439	hgsc.bcm.edu	37	chr14	81744593	81744593	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	acaatgagggaatctctttgGcttttgcccgtggtactgga	12	8	1	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr14:81744593G>T	ENST00000267540.2	-	4	1262	c.1062C>A	c.(1060-1062)agC>agA	p.S354R	STON2_ENST00000556280.1_5'Flank|STON2_ENST00000555447.1_Missense_Mutation_p.S354R	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	354					hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		AATCTCTTTGGCTTTTGCCCG	0.468																																					p.S354R		Atlas-SNP	.											.	STON2	94	.	0			c.C1062A						.						115	119	118					14																	81744593		2203	4300	6503	SO:0001583	missense	85439	exon6			TCTTTGGCTTTTG	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"stoned B homolog 2 (Drosophila)"	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.1062C>A	chr14.hg19:g.81744593G>T	ENSP00000267540:p.Ser354Arg	121.0	0.0		96.0	5.0	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	hg19	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.349891	0.24426	.	.	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.12465	2.68;2.69	6.17	4.36	0.52297	.	0.145674	0.64402	D	0.000006	T	0.14614	0.0353	L	0.57536	1.79	0.34730	D	0.729635	B;B	0.18461	0.016;0.028	B;B	0.17433	0.005;0.018	T	0.11060	-1.0603	10	0.25106	T	0.35	-24.6284	11.0372	0.47808	0.1977:0.0:0.8023:0.0	.	354;354	Q8WXE9;G3V2T7	STON2_HUMAN;.	R	354;366;354	ENSP00000450857:S354R;ENSP00000267540:S354R	ENSP00000267540:S354R	S	-	3	2	STON2	80814346	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	4.432000	0.59922	0.943000	0.37553	0.655000	0.94253	AGC	.	.		0.468	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104		T	81744593	G	T	81744593	3	4	166	1	0	0	0	0	1	0	0	0	15333	1194	42	3	1661	3	STON2	14	81744593	Missense_Mutation	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10	58232534	81744593	25604947	40	25230										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96779699	96779699	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	cacagctccaaagatgaacaTgaaaagttgtaaatgaagtt	8	6	0	4			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr14:96779699T>C	ENST00000359933.4	-	24	4609	c.3716A>G	c.(3715-3717)cAt>cGt	p.H1239R	ATG2B_ENST00000261834.5_5'Flank	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1239					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AAGATGAACATGAAAAGTTGT	0.279																																					p.H1239R		Atlas-SNP	.											.	ATG2B	169	.	0			c.A3716G						.						57	58	58					14																	96779699		2203	4297	6500	SO:0001583	missense	55102	exon24			TGAACATGAAAAG	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.3716A>G	chr14.hg19:g.96779699T>C	ENSP00000353010:p.His1239Arg	387.0	0.0		367.0	143.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	T	25.1	4.600303	0.87055	.	.	ENSG00000066739	ENST00000359933	T	0.20332	2.08	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.48169	0.1485	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.48801	-0.9003	10	0.59425	D	0.04	.	16.0133	0.80420	0.0:0.0:0.0:1.0	.	1239	Q96BY7	ATG2B_HUMAN	R	1239	ENSP00000353010:H1239R	ENSP00000353010:H1239R	H	-	2	0	ATG2B	95849452	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.424000	0.80242	2.179000	0.69175	0.533000	0.62120	CAT	.	.		0.279	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		C	96779699	T	C	96779699	3	2	166	1	0	0	0	0	1	0	0	0	1094	1464	51	2	2596	2	ATG2B	14	96779699	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10	15035106	96779699	10569841	41	25231										
FRMD5	84978	hgsc.bcm.edu	37	chr15	44194417	44194418	+	Frame_Shift_Ins	INS	-	-	T													0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	tatgtttccaatgtctgtgcINSttttcttaagaagttcagct							TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr15:44194417_44194418insT	ENST00000417257.1	-	7	770_771	c.594_595insA	c.(592-597)aaagcafs	p.A199fs	FRMD5_ENST00000484674.1_Frame_Shift_Ins_p.A110fs|FRMD5_ENST00000402883.1_Frame_Shift_Ins_p.A199fs	NM_032892.3	NP_116281.2	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5	199	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		AATGTCTGTGCTTTTCTTAAGA	0.465																																					p.A199fs		Atlas-INDEL	.											.	FRMD5	45	.	0			c.595_596insA						.																																			SO:0001589	frameshift_variant	84978	exon7			.	BC007796	CCDS10107.2, CCDS73715.1, CCDS73716.1	15q15.3	2005-08-09			ENSG00000171877	ENSG00000171877			28214	protein-coding gene	gene with protein product							Standard	XM_005254729		Approved	MGC14161	uc001ztl.3	Q7Z6J6	OTTHUMG00000060475	ENST00000417257.1:c.595dupA	chr15.hg19:g.44194421_44194421dupT	ENSP00000403067:p.Ala199fs	65.0	0.0		48.0	23.0	NM_032892	Q8NBG4	Frame_Shift_Ins	INS	ENST00000417257.1	hg19	CCDS10107.2																																																																																			.	.		0.465	FRMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133879.1	NM_032892		T	44194418	-	T	44194417	7	5	166	1	0	1	1	0	0	0	0	0	6061	797	28	0	1149	0	FRMD5	15	44194417	Frame_Shift_Ins	INS	-	TCGA-DD-AACO-01A-11D-A40R-10		44194417	58336975	42	25232										
EIF3J	8669	hgsc.bcm.edu	37	chr15	44849749	44849749	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	cttcaagagatgactttacaGagtttggaaagttactaaaa	8	5	1	3			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr15:44849749G>T	ENST00000261868.5	+	6	610	c.472G>T	c.(472-474)Gag>Tag	p.E158*	EIF3J_ENST00000424492.3_Nonsense_Mutation_p.E109*|EIF3J_ENST00000535391.1_Intron|RP11-151N17.1_ENST00000558006.1_RNA	NM_003758.2	NP_003749.2			eukaryotic translation initiation factor 3, subunit J											endometrium(1)|large_intestine(5)|liver(2)|skin(1)	9		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)		TGACTTTACAGAGTTTGGAAA	0.333																																					p.E158X		Atlas-SNP	.											.	EIF3J	29	.	0			c.G472T						.						70	76	74					15																	44849749		2198	4296	6494	SO:0001587	stop_gained	8669	exon6			TTTACAGAGTTTG	U97670	CCDS10111.1, CCDS61612.1, CCDS61613.1	15q21.1	2014-05-13	2007-07-27	2007-07-27	ENSG00000104131	ENSG00000104131			3270	protein-coding gene	gene with protein product		603910	"eukaryotic translation initiation factor 3, subunit 1 alpha, 35kDa"	EIF3S1		9822659	Standard	NM_001284335		Approved	eIF3-p35, eIF3-alpha, eIF3j	uc001ztv.3	O75822	OTTHUMG00000131158	ENST00000261868.5:c.472G>T	chr15.hg19:g.44849749G>T	ENSP00000261868:p.Glu158*	66.0	0.0		77.0	27.0	NM_003758		Nonsense_Mutation	SNP	ENST00000261868.5	hg19	CCDS10111.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.591824|5.591824	0.96590|0.96590	.|.	.|.	ENSG00000104131|ENSG00000104131	ENST00000261868;ENST00000424492|ENST00000536248	.|.	.|.	.|.	5.77|5.77	3.89|3.89	0.44902|0.44902	.|.	0.097124|.	0.64402|.	D|.	0.000001|.	.|T	.|0.62441	.|0.2428	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.58951	.|-0.7545	.|4	0.25106|.	T|.	0.35|.	.|.	11.564|11.564	0.50794|0.50794	0.0672:0.1254:0.8074:0.0|0.0672:0.1254:0.8074:0.0	.|.	.|.	.|.	.|.	X|I	158;109|36	.|.	ENSP00000261868:E158X|.	E|R	+|+	1|2	0|0	EIF3J|EIF3J	42637041|42637041	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	7.611000|7.611000	0.82962|0.82962	0.779000|0.779000	0.33543|0.33543	0.555000|0.555000	0.69702|0.69702	GAG|AGA	.	.		0.333	EIF3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253850.1	NM_003758		T	44849749	G	T	44849749	4	4	166	1	0	0	0	0	0	1	0	0	5022	943	33	3	494	3	EIF3J	15	44849749	Nonsense_Mutation	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10	655332	44849749	57681643	43	25233										
ADAD2	161931	hgsc.bcm.edu	37	chr16	84228736	84228736	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	agcgccggctttgacctcctGttggacgagcgctcgccata	12	14	0	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr16:84228736G>T	ENST00000315906.5	+	4	721	c.669G>T	c.(667-669)ctG>ctT	p.L223L	ADAD2_ENST00000268624.3_Silent_p.L295L|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	223					RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						TTGACCTCCTGTTGGACGAGC	0.672																																					p.L295L		Atlas-SNP	.											.	ADAD2	46	.	0			c.G885T						.						38	39	39					16																	84228736		2200	4300	6500	SO:0001819	synonymous_variant	161931	exon5			CCTCCTGTTGGAC	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.669G>T	chr16.hg19:g.84228736G>T		125.0	0.0		56.0	37.0	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	hg19	CCDS45536.1																																																																																			.	.		0.672	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		T	84228736	G	T	84228736	2	4	166	1	0	0	0	0	0	0	0	1	232	1364	48	3		3	ADAD2	16	84228736	Silent	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10		84228736	6126017	44	25234										
KRT10	3858	hgsc.bcm.edu	37	chr17	38975317	38975317	+	Silent	SNP	G	G	A													0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ccgccggaactgccgccgtgGccgccgccgtggccgccgcc							TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr17:38975317G>A	ENST00000269576.5	-	7	1479	c.1470C>T	c.(1468-1470)ggC>ggT	p.G490G	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				tgccgccgtggccgccgccgt	0.796																																					p.G490G		Atlas-SNP	.											.	KRT10	56	.	0			c.C1470T						.																																			SO:0001819	synonymous_variant	3858	exon7			GCCGTGGCCGCCG	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1470C>T	chr17.hg19:g.38975317G>A		27.0	0.0		77.0	9.0	NM_000421	Q14664|Q8N175	Silent	SNP	ENST00000269576.5	hg19	CCDS11377.1																																																																																			.	.		0.796	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		A	38975317	G	A	38975317	2	1	166	1	0	0	0	0	0	0	0	1	8457	1190	42	3		3	KRT10	17	38975317	Silent	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10		38975317	42219893	45	25235	117	2								
KRT10	3858	hgsc.bcm.edu	37	chr17	38975319	38975319	+	Missense_Mutation	SNP	C	C	T													0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	gccggaactgccgccgtggcCgccgccgtggccgccgccgg							TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr17:38975319C>T	ENST00000269576.5	-	7	1477	c.1468G>A	c.(1468-1470)Ggc>Agc	p.G490S	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ccgccgtggccgccgccgtgg	0.791																																					p.G490S		Atlas-SNP	.											.	KRT10	56	.	0			c.G1468A						.																																			SO:0001583	missense	3858	exon7			CGTGGCCGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1468G>A	chr17.hg19:g.38975319C>T	ENSP00000269576:p.Gly490Ser	27.0	0.0		74.0	8.0	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546565	0.86022	.	.	ENSG00000186395	ENST00000269576	D	0.96587	-4.06	4.38	4.38	0.52667	.	0.845686	0.09879	N	0.743932	D	0.94778	0.8314	N	0.08118	0	0.27860	N	0.940431	D	0.89917	1.0	D	0.76071	0.987	D	0.87790	0.2618	10	0.18710	T	0.47	.	12.7512	0.57310	0.0:1.0:0.0:0.0	.	490	P13645	K1C10_HUMAN	S	490	ENSP00000269576:G490S	ENSP00000269576:G490S	G	-	1	0	KRT10	36228845	0.019000	0.18553	0.876000	0.34364	0.184000	0.23303	0.448000	0.21726	2.739000	0.93911	0.603000	0.83216	GGC	.	.		0.791	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		T	38975319	C	T	38975319	3	4	166	1	0	0	0	0	1	0	0	0	8457	652	23	1	294	1	KRT10	17	38975319	Missense_Mutation	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	2	38975319	42219891	46	25236	117	2								
UBTF	7343	hgsc.bcm.edu	37	chr17	42289011	42289011	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	gataggcgtccttctccttcTgggacagcagcttccactgc	10	14	2	0			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr17:42289011T>G	ENST00000302904.4	-	10	1502	c.1010A>C	c.(1009-1011)cAg>cCg	p.Q337P	UBTF_ENST00000343638.5_Missense_Mutation_p.Q300P|UBTF_ENST00000527034.1_Missense_Mutation_p.Q300P|UBTF_ENST00000393606.3_Missense_Mutation_p.Q300P|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000526094.1_Missense_Mutation_p.Q300P|UBTF_ENST00000436088.1_Missense_Mutation_p.Q337P|UBTF_ENST00000533177.1_Missense_Mutation_p.Q300P|UBTF_ENST00000529383.1_Missense_Mutation_p.Q337P			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	337					chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CTTCTCCTTCTGGGACAGCAG	0.577																																					p.Q337P		Atlas-SNP	.											.	UBTF	65	.	0			c.A1010C						.						103	98	100					17																	42289011		2203	4300	6503	SO:0001583	missense	7343	exon10			TCCTTCTGGGACA	BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.1010A>C	chr17.hg19:g.42289011T>G	ENSP00000302640:p.Gln337Pro	26.0	0.0		23.0	8.0	NM_014233	A8K6R8	Missense_Mutation	SNP	ENST00000302904.4	hg19	CCDS11480.1	.	.	.	.	.	.	.	.	.	.	t	19.89	3.911255	0.72983	.	.	ENSG00000108312	ENST00000343638;ENST00000302904;ENST00000527034;ENST00000533177;ENST00000436088;ENST00000393606;ENST00000526094;ENST00000529383	T;T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01;1.01	4.4	4.4	0.53042	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	T	0.47303	0.1438	N	0.17312	0.475	0.80722	D	1	D;D;D	0.76494	0.99;0.994;0.999	D;D;D	0.91635	0.999;0.941;0.999	T	0.51301	-0.8723	10	0.51188	T	0.08	-38.8703	13.4552	0.61195	0.0:0.0:0.0:1.0	.	300;300;337	E9PKP7;P17480-2;P17480	.;.;UBF1_HUMAN	P	300;337;300;300;337;300;300;337	ENSP00000345297:Q300P;ENSP00000302640:Q337P;ENSP00000431539:Q300P;ENSP00000437180:Q300P;ENSP00000390669:Q337P;ENSP00000377231:Q300P;ENSP00000432925:Q300P;ENSP00000435708:Q337P	ENSP00000302640:Q337P	Q	-	2	0	UBTF	39644537	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.768000	0.85345	1.858000	0.53909	0.402000	0.26972	CAG	.	.		0.577	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233		G	42289011	T	G	42289011	3	3	166	1	0	0	0	0	1	0	0	0	16924	1580	55	5	1332	5	UBTF	17	42289011	Missense_Mutation	SNP	T	TCGA-DD-AACO-01A-11D-A40R-10	3313692	42289011	38906199	47	25237										
MUC16	94025	hgsc.bcm.edu	37	chr19	9076110	9076110	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	cacttgtaatgtgccctataGagaagggcaactgtgaggta	12	7	0	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr19:9076110G>C	ENST00000397910.4	-	3	11539	c.11336C>G	c.(11335-11337)tCt>tGt	p.S3779C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3780	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGCCCTATAGAGAAGGGCAA	0.527																																					p.S3779C		Atlas-SNP	.											.	MUC16	4315	.	0			c.C11336G						.						151	147	148					19																	9076110		2049	4206	6255	SO:0001583	missense	94025	exon3			CCTATAGAGAAGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11336C>G	chr19.hg19:g.9076110G>C	ENSP00000381008:p.Ser3779Cys	83.0	0.0		49.0	32.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	1.751	-0.489244	0.04352	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	1.93	0.801	0.18679	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	.	.	.	D	0.71674	0.998	D	0.69307	0.963	T	0.43909	-0.9362	8	0.87932	D	0	.	4.0161	0.09644	0.246:0.0:0.754:0.0	.	3779	B5ME49	.	C	3779	ENSP00000381008:S3779C	ENSP00000381008:S3779C	S	-	2	0	MUC16	8937110	0.001000	0.12720	0.001000	0.08648	0.021000	0.10359	0.729000	0.26028	0.313000	0.23062	0.313000	0.20887	TCT	.	.		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9076110	G	C	9076110	3	2	166	1	0	0	0	0	1	0	0	0	9982	942	33	4	32515	4	MUC16	19	9076110	Missense_Mutation	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10		9076110	50052873	48	25238										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10600016	10600019	+	Frame_Shift_Del	DEL	ATAG	ATAG	-													0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	ccatcatagcccccagcagcAtagatacagttgtgcaggac							TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	ATAG	ATAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr19:10600016_10600019delATAG	ENST00000171111.5	-	5	2104_2107	c.1557_1560delCTAT	c.(1555-1560)atctatfs	p.IY519fs	KEAP1_ENST00000393623.2_Frame_Shift_Del_p.IY519fs|CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000588024.1_5'Flank	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	519					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CCCCAGCAGCATAGATACAGTTGT	0.583																																					p.520_521del		Atlas-INDEL	.											.	KEAP1	182	.	0			c.1558_1561del						.																																			SO:0001589	frameshift_variant	9817	exon5			.	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1557_1560delCTAT	chr19.hg19:g.10600016_10600019delATAG	ENSP00000171111:p.Ile519fs	131.0	0.0		67.0	40.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Frame_Shift_Del	DEL	ENST00000171111.5	hg19	CCDS12239.1																																																																																			.	.		0.583	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		-	10600019	ATAG	-	10600016	7	5	166	1	0	1	0	1	0	0	0	0	8150	224	8	0	322	0	KEAP1	19	10600016	Frame_Shift_Del	DEL	ATAG	TCGA-DD-AACO-01A-11D-A40R-10	1523906	10600016	48528967	49	25239										
DPF1	8193	hgsc.bcm.edu	37	chr19	38703032	38703032	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	agacccgcccagctggcaccCtgggggcacgggcaccagaa	14	16	0	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr19:38703032C>T	ENST00000420980.2	-	10	987		c.e10-1		DPF1_ENST00000412732.1_Intron|DPF1_ENST00000416611.1_Splice_Site|DPF1_ENST00000414789.1_Intron|DPF1_ENST00000456296.1_Intron|DPF1_ENST00000355526.4_Intron	NM_004647.2	NP_004638.2	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1						apoptotic process (GO:0006915)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AGCTGGCACCCTGGGGGCACG	0.667																																					.		Atlas-SNP	.											.	DPF1	54	.	0			c.961-1G>A						.						7	7	7					19																	38703032		2059	4010	6069	SO:0001630	splice_region_variant	8193	exon11			GGCACCCTGGGGG	U43843	CCDS33008.2, CCDS46064.1, CCDS46065.1	19q13.12	2013-01-28			ENSG00000011332	ENSG00000011332		"Zinc fingers, PHD-type"	20225	protein-coding gene	gene with protein product		601670				8812431	Standard	XM_005259288		Approved	neuro-d4, NEUD4, BAF45b	uc002ohm.3	Q92782	OTTHUMG00000157164	ENST00000420980.2:c.961-1G>A	chr19.hg19:g.38703032C>T		81.0	0.0		109.0	38.0	NM_004647	B3KSY8|Q08AJ0	Splice_Site	SNP	ENST00000420980.2	hg19	CCDS33008.2	.	.	.	.	.	.	.	.	.	.	C	14.88	2.668539	0.47677	.	.	ENSG00000011332	ENST00000420980;ENST00000416611	.	.	.	4.01	1.71	0.24356	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7924	0.18367	0.1899:0.7045:0.0:0.1055	.	.	.	.	.	-1	.	.	.	-	.	.	DPF1	43394872	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.960000	0.40422	0.882000	0.36016	0.579000	0.79373	.	.	.		0.667	DPF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347721.1		Intron	T	38703032	C	T	38703032	5	4	166	1	0	0	0	0	0	0	1	0	4718	695	24	3	190	3	DPF1	19	38703032	Splice_Site	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	28103016	38703032	20425951	50	25240										
TULP2	7288	hgsc.bcm.edu	37	chr19	49399799	49399816	+	Splice_Site	DEL	TTCAAACAGCCGCCGCTG	TTCAAACAGCCGCCGCTG	-													0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	cgcttctgtcgctgcttcttTtcaaacagccgccgctgggg					rs375021981|rs575577268		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	TTCAAACAGCCGCCGCTG	TTCAAACAGCCGCCGCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr19:49399799_49399816delTTCAAACAGCCGCCGCTG	ENST00000221399.3	-	4	229_243	c.85_99delCAGCGGCGGCTGTTTGAA	c.(85-99)cagcggcggctgtttdel	p.QRRLF29del		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	29					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		GCTGCTTCTTTTCAAACAGCCGCCGCTGGGGAGATGGG	0.628																																					p.29_34del		Atlas-INDEL	.											.	TULP2	60	.	0			c.85_100del						.																																			SO:0001630	splice_region_variant	7288	exon4			.	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"cancer/testis antigen 65"	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.85-1CAGCGGCGGCTGTTTGAA>-	chr19.hg19:g.49399799_49399816delTTCAAACAGCCGCCGCTG		36.0	0.0		30.0	10.0	NM_003323	Q8TC50	Frame_Shift_Del	DEL	ENST00000221399.3	hg19	CCDS12739.1																																																																																			.	.		0.628	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	In_Frame_Del	-	49399816	TTCAAACAGCCGCCGCTG	-	49399799	8	5	166	1	0	1	0	1	0	0	1	0	16789	1838	64	0	1503	0	TULP2	19	49399799	Splice_Site	DEL	TTCAAACAGCCGCCGCTG	TCGA-DD-AACO-01A-11D-A40R-10	10696767	49399799	9729184	51	25241										
TNNC2	7125	hgsc.bcm.edu	37	chr20	44451995	44451995	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	actgtccactccttactgcaCgccctccatcatcttcagga	5	17	3	0			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr20:44451995C>G	ENST00000372555.3	-	6	567	c.475G>C	c.(475-477)Gtg>Ctg	p.V159L	TNNC2_ENST00000372557.1_Missense_Mutation_p.V144L	NM_003279.2	NP_003270.1	P02585	TNNC2_HUMAN	troponin C type 2 (fast)	159	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				muscle filament sliding (GO:0030049)|regulation of muscle contraction (GO:0006937)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(115;0.0122)			Felodipine(DB01023)	CCTTACTGCACGCCCTCCATC	0.652																																					p.V159L		Atlas-SNP	.											.	TNNC2	12	.	0			c.G475C						.						77	51	60					20																	44451995		2203	4299	6502	SO:0001583	missense	7125	exon6			ACTGCACGCCCTC		CCDS13375.1	20q12-q13.11	2013-01-10	2005-09-12		ENSG00000101470	ENSG00000101470		"EF-hand domain containing"	11944	protein-coding gene	gene with protein product		191039	"troponin C2, fast"			2373703	Standard	NM_003279		Approved		uc002xpr.3	P02585	OTTHUMG00000032623	ENST00000372555.3:c.475G>C	chr20.hg19:g.44451995C>G	ENSP00000361636:p.Val159Leu	38.0	0.0		39.0	21.0	NM_003279	Q6FH92	Missense_Mutation	SNP	ENST00000372555.3	hg19	CCDS13375.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.094030	0.56075	.	.	ENSG00000101470	ENST00000372557;ENST00000372555	T;T	0.75589	-0.95;-0.85	4.92	3.97	0.46021	.	0.000000	0.85682	D	0.000000	T	0.55353	0.1915	N	0.05467	-0.045	0.51767	D	0.999932	P	0.35612	0.512	B	0.37091	0.241	T	0.60342	-0.7282	10	0.87932	D	0	-40.8879	9.9765	0.41786	0.1553:0.6944:0.1502:0.0	.	159	P02585	TNNC2_HUMAN	L	144;159	ENSP00000361638:V144L;ENSP00000361636:V159L	ENSP00000361636:V159L	V	-	1	0	TNNC2	43885402	1.000000	0.71417	0.996000	0.52242	0.809000	0.45718	4.403000	0.59729	1.055000	0.40461	0.491000	0.48974	GTG	.	.		0.652	TNNC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079524.3	NM_003279		G	44451995	C	G	44451995	3	3	166	1	0	0	0	0	1	0	0	0	16340	536	19	4	11	4	TNNC2	20	44451995	Missense_Mutation	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10		44451995	18573525	52	25242										
SGSM1	129049	hgsc.bcm.edu	37	chr22	25308673	25308673	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	gaaccagaacttcccccacgGaggcgccatggacacgcact	10	16	0	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr22:25308673G>A	ENST00000400359.4	+	23	3054	c.3047G>A	c.(3046-3048)gGa>gAa	p.G1016E	SGSM1_ENST00000400358.4_Missense_Mutation_p.G961E	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	1016	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						TTCCCCCACGGAGGCGCCATG	0.507																																					p.G1016E		Atlas-SNP	.											.	SGSM1	150	.	0			c.G3047A						.						82	83	83					22																	25308673		2155	4277	6432	SO:0001583	missense	129049	exon23			CCCACGGAGGCGC	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"Small G protein signaling modulators"	29410	protein-coding gene	gene with protein product		611417	"RUN and TBC1 domain containing 2"	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.3047G>A	chr22.hg19:g.25308673G>A	ENSP00000383212:p.Gly1016Glu	95.0	0.0		85.0	11.0	NM_001039948	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	hg19	CCDS46674.1	.	.	.	.	.	.	.	.	.	.	g	31	5.062794	0.93898	.	.	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.10477	2.87;2.87	5.3	5.3	0.74995	Rab-GAP/TBC domain (5);	0.000000	0.85682	D	0.000000	T	0.33089	0.0851	M	0.67700	2.07	0.80722	D	1	B;B;D;D	0.89917	0.335;0.176;0.971;1.0	B;B;P;D	0.97110	0.31;0.437;0.861;1.0	T	0.00797	-1.1562	10	0.46703	T	0.11	-16.8961	18.3333	0.90277	0.0:0.0:1.0:0.0	.	961;1016;1033;1016	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	E	1016;961;1016	ENSP00000383211:G961E;ENSP00000383212:G1016E	ENSP00000383211:G961E	G	+	2	0	SGSM1	23638673	1.000000	0.71417	0.978000	0.43139	0.991000	0.79684	9.779000	0.99018	2.663000	0.90544	0.655000	0.94253	GGA	.	.		0.507	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318		A	25308673	G	A	25308673	3	1	166	1	0	0	0	0	1	0	0	0	14237	1174	41	3	3137	3	SGSM1	22	25308673	Missense_Mutation	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10		25308673	25995893	53	25243										
RBM10	8241	hgsc.bcm.edu	37	chrX	47030582	47030582	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	gaggaggaggaggaggaggaGgatgaggaggaggaggagaa	25	0	0	2			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chrX:47030582G>T	ENST00000377604.3	+	4	1099	c.357G>T	c.(355-357)gaG>gaT	p.E119D	RBM10_ENST00000345781.6_Intron|RBM10_ENST00000329236.7_Intron	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	119	Poly-Glu.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						aggaggaggaggatgaggagg	0.662																																					p.E184D	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.G552T						.						20	19	19					X																	47030582		2202	4294	6496	SO:0001583	missense	8241	exon4			GGAGGAGGATGAG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.357G>T	chrX.hg19:g.47030582G>T	ENSP00000366829:p.Glu119Asp	52.0	0.0		52.0	4.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	G	7.514	0.655267	0.14580	.	.	ENSG00000182872	ENST00000377604	T	0.11169	2.8	3.1	1.15	0.20763	Nucleotide-binding, alpha-beta plait (1);	0.859005	0.09469	N	0.797951	T	0.04815	0.0130	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38628	-0.9652	10	0.11182	T	0.66	-1.7872	6.9396	0.24486	0.0:0.0:0.4873:0.5127	.	184;119;119	Q7Z3D7;P98175-2;P98175	.;.;RBM10_HUMAN	D	119	ENSP00000366829:E119D	ENSP00000366829:E119D	E	+	3	2	RBM10	46915526	1.000000	0.71417	0.776000	0.31678	0.914000	0.54420	0.961000	0.29267	0.165000	0.19558	0.502000	0.49764	GAG	.	.		0.662	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		T	47030582	G	T	47030582	3	4	166	1	0	0	0	0	1	0	0	0	13126	991	35	3	367	3	RBM10	23	47030582	Missense_Mutation	SNP	G	TCGA-DD-AACO-01A-11D-A40R-10		47030582	108239978	54	25244										
IRAK1	3654	hgsc.bcm.edu	37	chrX	153277357	153277357	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.652173913043478	2.82608695652174	0	1	1	0	gggcccctgcctgtcctgttCcaggcccaagcctacagaag	11	16	0	1			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chrX:153277357C>A	ENST00000369980.3	-	14	2259	c.2092G>T	c.(2092-2094)Gaa>Taa	p.E698*	IRAK1_ENST00000369974.2_Nonsense_Mutation_p.E619*|IRAK1_ENST00000429936.2_Nonsense_Mutation_p.E694*|IRAK1_ENST00000393682.1_Nonsense_Mutation_p.E679*|IRAK1_ENST00000393687.2_Nonsense_Mutation_p.E668*|IRAK1_ENST00000477274.1_Intron	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	698					activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTGTCCTGTTCCAGGCCCAAG	0.567																																					p.E698X		Atlas-SNP	.											.	IRAK1	107	.	0			c.G2092T						.						61	62	62					X																	153277357		2203	4300	6503	SO:0001587	stop_gained	3654	exon14			CCTGTTCCAGGCC	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.2092G>T	chrX.hg19:g.153277357C>A	ENSP00000358997:p.Glu698*	19.0	0.0		24.0	16.0	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Nonsense_Mutation	SNP	ENST00000369980.3	hg19	CCDS14740.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	c|c|c	39|39|39	7.303695|7.303695|7.303695	0.98200|0.98200|0.98200	.|.|.	.|.|.	ENSG00000184216|ENSG00000184216|ENSG00000184216	ENST00000369980;ENST00000369974;ENST00000393682;ENST00000393687;ENST00000429936|ENST00000444254|ENST00000455690;ENST00000437278	.|.|.	.|.|.	.|.|.	5.63|5.63|5.63	4.75|4.75|4.75	0.60458|0.60458|0.60458	.|.|.	0.959084|.|.	0.08611|.|.	N|.|.	0.920017|.|.	.|T|T	.|0.60983|0.60983	.|0.2311|0.2311	.|.|.	.|.|.	.|.|.	0.35444|0.35444|0.35444	D|D|D	0.795096|0.795096|0.795096	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.67662|0.67662	.|-0.5613|-0.5613	.|4|4	0.51188|.|.	T|.|.	0.08|.|.	0.3674|0.3674|0.3674	11.4292|11.4292|11.4292	0.50029|0.50029|0.50029	0.0:0.8225:0.1775:0.0|0.0:0.8225:0.1775:0.0|0.0:0.8225:0.1775:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|V|C	698;619;679;668;694|203|147;261	.|.|.	ENSP00000358991:E619X|.|.	E|G|W	-|-|-	1|2|3	0|0|0	IRAK1|IRAK1|IRAK1	152930551|152930551|152930551	0.006000|0.006000|0.006000	0.16342|0.16342|0.16342	0.005000|0.005000|0.005000	0.12908|0.12908|0.12908	0.989000|0.989000|0.989000	0.77384|0.77384|0.77384	2.036000|2.036000|2.036000	0.41165|0.41165|0.41165	1.125000|1.125000|1.125000	0.41998|0.41998|0.41998	0.525000|0.525000|0.525000	0.51046|0.51046|0.51046	GAA|GGA|TGG	.	.		0.567	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3			A	153277357	C	A	153277357	4	1	166	1	0	0	0	0	0	1	0	0	7830	864	30	3	50	3	IRAK1	23	153277357	Nonsense_Mutation	SNP	C	TCGA-DD-AACO-01A-11D-A40R-10	106246775	153277357	1993203	55	25245										
ZBTB17	7709	hgsc.bcm.edu	37	chr1	16271291	16271291	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cccccgtgtggatgcggatgTgccgcttgaagttccccgtg	14	13	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:16271291T>G	ENST00000375743.4	-	8	1203	c.971A>C	c.(970-972)cAc>cCc	p.H324P	ZBTB17_ENST00000537142.1_Missense_Mutation_p.H242P|ZBTB17_ENST00000448462.2_Missense_Mutation_p.H261P|ZBTB17_ENST00000479282.1_5'Flank|ZBTB17_ENST00000375733.2_Missense_Mutation_p.H324P	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17	324					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|ectoderm development (GO:0007398)|endoplasmic reticulum unfolded protein response (GO:0030968)|gastrulation with mouth forming second (GO:0001702)|negative regulation of cell cycle (GO:0045786)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)	15		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		GATGCGGATGTGCCGCTTGAA	0.672																																					p.H324P		Atlas-SNP	.											.	ZBTB17	45	.	0			c.A971C						.						42	41	42					1																	16271291		2202	4300	6502	SO:0001583	missense	7709	exon8			CGGATGTGCCGCT	U20647	CCDS165.1, CCDS55576.1, CCDS72712.1	1p36.13	2013-01-08	2004-07-16	2004-07-16	ENSG00000116809	ENSG00000116809		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12936	protein-coding gene	gene with protein product		604084	"zinc finger protein 151 (pHZ-67)", "zinc finger protein 60"	ZNF151, ZNF60			Standard	NM_003443		Approved	MIZ1, pHZ-67	uc001axl.4	Q13105	OTTHUMG00000009377	ENST00000375743.4:c.971A>C	chr1.hg19:g.16271291T>G	ENSP00000364895:p.His324Pro	72.0	0.0		53.0	6.0	NM_003443	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Missense_Mutation	SNP	ENST00000375743.4	hg19	CCDS165.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.499630	0.85176	.	.	ENSG00000116809	ENST00000375743;ENST00000375733;ENST00000444654;ENST00000537142;ENST00000448462	D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18	5.33	4.19	0.49359	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.94644	0.8273	H	0.94698	3.57	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.997;0.999;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.993;0.996;0.998;0.977	D	0.95333	0.8431	10	0.87932	D	0	.	11.2715	0.49142	0.0:0.0732:0.0:0.9268	.	248;261;324;242;324	B4DYU5;E7EPQ4;Q13105-2;F5H411;Q13105	.;.;.;.;ZBT17_HUMAN	P	324;324;243;242;261	ENSP00000364895:H324P;ENSP00000364885:H324P;ENSP00000438529:H242P;ENSP00000391002:H261P	ENSP00000364885:H324P	H	-	2	0	ZBTB17	16143878	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.170000	0.71920	2.009000	0.58944	0.459000	0.35465	CAC	.	.		0.672	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443		G	16271291	T	G	16271291	3	3	167	1	0	0	0	0	1	0	0	0	17542	1696	59	5	1476	5	ZBTB17	1	16271291	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10		16271291	232979330	1	25246										
PIGV	55650	hgsc.bcm.edu	37	chr1	27124181	27124200	+	Frame_Shift_Del	DEL	CCCCACCAGGACAAAAGGTC	CCCCACCAGGACAAAAGGTC	-													0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gaagcctcttgcagaggactCcccaccaggacaaaaggtcc					rs370891890		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	CCCCACCAGGACAAAAGGTC	CCCCACCAGGACAAAAGGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:27124181_27124200delCCCCACCAGGACAAAAGGTC	ENST00000374145.1	+	4	2010_2029	c.1328_1347delCCCCACCAGGACAAAAGGTC	c.(1327-1347)tccccaccaggacaaaaggtcfs	p.SPPGQKV443fs	PIGV_ENST00000078527.4_Frame_Shift_Del_p.SPPGQKV443fs|PIGV_ENST00000449950.2_Frame_Shift_Del_p.SPPGQKV215fs	NM_001202554.1	NP_001189483.1	Q9NUD9	PIGV_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class V	443					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	14		all_cancers(24;3.93e-26)|all_epithelial(13;3.96e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.26e-54)|Epithelial(14;2.85e-53)|OV - Ovarian serous cystadenocarcinoma(117;1.91e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000504)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.0222)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		GCAGAGGACTCCCCACCAGGACAAAAGGTCCCCAGAAATC	0.486																																					p.443_449del		Atlas-INDEL	.											.	PIGV	47	.	0			c.1327_1346del						.																																			SO:0001589	frameshift_variant	55650	exon4			.	AK000484	CCDS287.1	1p36.11	2013-02-26	2006-06-28		ENSG00000060642	ENSG00000060642		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	26031	protein-coding gene	gene with protein product	"GPI mannosyltransferase 2", "dol-P-Man dependent GPI mannosyltransferase"	610274	"phosphatidylinositol glycan, class V"			15623507	Standard	NM_017837		Approved	FLJ20477	uc001bmz.3	Q9NUD9	OTTHUMG00000004005	ENST00000374145.1:c.1328_1347delCCCCACCAGGACAAAAGGTC	chr1.hg19:g.27124181_27124200delCCCCACCAGGACAAAAGGTC	ENSP00000363260:p.Ser443fs	118.0	0.0		80.0	14.0	NM_001202554	D3DPL2|Q5JYG7|Q5JYG8|Q5JYG9|Q9NX26	Frame_Shift_Del	DEL	ENST00000374145.1	hg19	CCDS287.1																																																																																			.	.		0.486	PIGV-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011441.1	NM_017837		-	27124200	CCCCACCAGGACAAAAGGTC	-	27124181	7	5	167	1	0	1	0	1	0	0	0	0	11910	855	30	0	1338	0	PIGV	1	27124181	Frame_Shift_Del	DEL	CCCCACCAGGACAAAAGGTC	TCGA-DD-AACP-01A-11D-A40R-10	10852890	27124181	222126440	2	25247										
EIF2C3	192669	hgsc.bcm.edu	37	chr1	36479616	36479616	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gtgggctatcgcttgttttgCcacacagaggcagtgcagag	14	9	0	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:36479616C>A	ENST00000373191.4	+	11	1722	c.1373C>A	c.(1372-1374)gCc>gAc	p.A458D	RP4-665N4.8_ENST00000479395.2_RNA|RP4-665N4.8_ENST00000466576.2_RNA|AGO3_ENST00000246314.6_Missense_Mutation_p.A224D	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	458					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										GCTTGTTTTGCCACACAGAGG	0.418																																					p.A458D		Atlas-SNP	.											.	.	.	.	0			c.C1373A						.						162	153	156					1																	36479616		2203	4300	6503	SO:0001583	missense	192669	exon11			GTTTTGCCACACA	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"Argonaute/PIWI family"	18421	protein-coding gene	gene with protein product	"argonaute 3"	607355	"eukaryotic translation initiation factor 2C, 3"	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.1373C>A	chr1.hg19:g.36479616C>A	ENSP00000362287:p.Ala458Asp	396.0	0.0		318.0	137.0	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	hg19	CCDS399.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.324380	0.81580	.	.	ENSG00000126070	ENST00000373191;ENST00000246314	T;T	0.06294	3.32;3.32	5.65	5.65	0.86999	.	0.048537	0.85682	D	0.000000	T	0.13500	0.0327	M	0.75150	2.29	0.80722	D	1	B	0.12630	0.006	B	0.18263	0.021	T	0.02411	-1.1163	10	0.48119	T	0.1	-7.2302	19.7916	0.96461	0.0:1.0:0.0:0.0	.	458	Q9H9G7	AGO3_HUMAN	D	458;224	ENSP00000362287:A458D;ENSP00000246314:A224D	ENSP00000246314:A224D	A	+	2	0	EIF2C3	36252203	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.810000	0.86072	2.685000	0.91497	0.650000	0.86243	GCC	.	.		0.418	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852		A	36479616	C	A	36479616	3	1	167	1	0	0	0	0	1	0	0	0	5009	739	26	3	1415	3	EIF2C3	1	36479616	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	9355435	36479616	212771005	3	25248										
PCSK9	255738	hgsc.bcm.edu	37	chr1	55527163	55527163	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gaggccagcatccacgcttcCtgctgccatgccccaggtct	10	17	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:55527163C>G	ENST00000302118.5	+	11	2087	c.1797C>G	c.(1795-1797)tcC>tcG	p.S599S	PCSK9_ENST00000490692.1_3'UTR|PCSK9_ENST00000543384.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	599	C-terminal domain.				apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						TCCACGCTTCCTGCTGCCATG	0.667																																					p.S599S	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.C1797G						.						29	26	27					1																	55527163		2198	4299	6497	SO:0001819	synonymous_variant	255738	exon11			CGCTTCCTGCTGC	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"hypercholesterolemia, autosomal dominant 3"	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1797C>G	chr1.hg19:g.55527163C>G		387.0	0.0		304.0	113.0	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Silent	SNP	ENST00000302118.5	hg19	CCDS603.1																																																																																			.	.		0.667	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		G	55527163	C	G	55527163	2	3	167	1	0	0	0	0	0	0	0	1	11615	668	24	4		4	PCSK9	1	55527163	Silent	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	19047547	55527163	193723458	4	25249										
HFM1	164045	hgsc.bcm.edu	37	chr1	91781372	91781372	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	atcagaaatttcacacttacGtaatcttgtgcagataaact	5	8	3	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:91781372G>A	ENST00000370425.3	-	28	3238	c.3140C>T	c.(3139-3141)aCg>aTg	p.T1047M	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Splice_Site_p.T726M|HFM1_ENST00000294696.5_Splice_Site_p.T279M	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1047	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.T1047M(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TCACACTTACGTAATCTTGTG	0.313																																					p.T1047M		Atlas-SNP	.											HFM1,caecum,carcinoma,0,1	HFM1	188	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3140T						.						66	64	64					1																	91781372		2201	4299	6500	SO:0001630	splice_region_variant	164045	exon28			ACTTACGTAATCT	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.3140+1C>T	chr1.hg19:g.91781372G>A		154.0	0.0		115.0	47.0	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	hg19	CCDS30769.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	5.133|5.133	0.210150|0.210150	0.09757|0.09757	.|.	.|.	ENSG00000162669|ENSG00000162669	ENST00000430465|ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	.|T;T;T	.|0.62232	.|0.04;0.04;0.04	5.25|5.25	4.12|4.12	0.48240|0.48240	.|Sec63 domain (2);	.|0.765588	.|0.12875	.|N	.|0.431977	T|T	0.11281|0.11281	0.0275|0.0275	N|N	0.00855|0.00855	-1.145|-1.145	0.25714|0.25714	N|N	0.985443|0.985443	.|B;B;B	.|0.14012	.|0.009;0.0;0.005	.|B;B;B	.|0.09377	.|0.001;0.002;0.004	T|T	0.31971|0.31971	-0.9924|-0.9924	5|9	.|.	.|.	.|.	.|.	11.1879|11.1879	0.48669|0.48669	0.9269:0.0:0.0731:0.0|0.9269:0.0:0.0731:0.0	.|.	.|726;258;1047	.|A6NGI5;B1B0B5;A2PYH4	.|.;.;HFM1_HUMAN	W|M	259|1047;279;726;731	.|ENSP00000359454:T1047M;ENSP00000294696:T279M;ENSP00000359453:T726M	.|.	R|T	-|-	1|2	2|0	HFM1|HFM1	91553960|91553960	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.100000|0.100000	0.18952|0.18952	3.507000|3.507000	0.53371|0.53371	0.832000|0.832000	0.34804|0.34804	-0.606000|-0.606000	0.04082|0.04082	CGG|ACG	.	.		0.313	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	Missense_Mutation	A	91781372	G	A	91781372	5	1	167	1	0	0	0	0	0	0	1	0	7092	1159	40	1	1215	1	HFM1	1	91781372	Splice_Site	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	36254209	91781372	157469249	5	25250										
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95310943	95310943	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgctcccttcctgctgttccAgccactgtggacatttgcca	8	15	0	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:95310943A>T	ENST00000271227.6	+	9	1097	c.995A>T	c.(994-996)cAg>cTg	p.Q332L	SLC44A3_ENST00000527077.1_Missense_Mutation_p.Q264L|SLC44A3_ENST00000446120.2_Missense_Mutation_p.Q296L|SLC44A3_ENST00000467909.1_Missense_Mutation_p.Q284L|SLC44A3_ENST00000530397.1_3'UTR|RP11-465K1.2_ENST00000422162.1_RNA|SLC44A3_ENST00000529450.1_Missense_Mutation_p.Q300L|SLC44A3_ENST00000532427.1_Missense_Mutation_p.Q252L	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	332					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	CTGCTGTTCCAGCCACTGTGG	0.483																																					p.Q332L		Atlas-SNP	.											.	SLC44A3	109	.	0			c.A995T						.						121	125	124					1																	95310943		2203	4300	6503	SO:0001583	missense	126969	exon9			TGTTCCAGCCACT	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"Solute carriers"	28689	protein-coding gene	gene with protein product			"solute carrier family, member 3"			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.995A>T	chr1.hg19:g.95310943A>T	ENSP00000271227:p.Gln332Leu	49.0	0.0		47.0	14.0	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	hg19	CCDS44176.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.412535	0.42817	.	.	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427	T;T;T;T;T;T	0.18960	2.18;2.18;2.18;2.18;2.18;2.18	5.86	3.49	0.39957	.	0.208139	0.33916	N	0.004433	T	0.30355	0.0762	M	0.73372	2.23	0.41018	D	0.985056	D;D;D;D;D	0.89917	0.997;0.982;0.997;0.998;1.0	D;D;D;D;D	0.85130	0.973;0.914;0.994;0.982;0.997	T	0.04467	-1.0949	10	0.46703	T	0.11	-5.0002	11.0309	0.47772	0.7527:0.0:0.0:0.2473	.	252;296;264;300;332	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	L	296;332;264;300;284;252	ENSP00000389143:Q296L;ENSP00000271227:Q332L;ENSP00000433641:Q264L;ENSP00000431836:Q300L;ENSP00000432789:Q284L;ENSP00000436661:Q252L	ENSP00000271227:Q332L	Q	+	2	0	SLC44A3	95083531	1.000000	0.71417	0.861000	0.33841	0.087000	0.18053	7.659000	0.83766	0.446000	0.26666	-1.412000	0.01120	CAG	.	.		0.483	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		T	95310943	A	T	95310943	3	4	167	1	0	0	0	0	1	0	0	0	14652	188	7	4	1029	4	SLC44A3	1	95310943	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	3529571	95310943	153939678	6	25251										
STXBP3	6814	hgsc.bcm.edu	37	chr1	109321972	109321972	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tcctgtgtccactgtcctgcAtgaactgacctttcaggcaa	8	13	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:109321972A>G	ENST00000370008.3	+	9	799	c.749A>G	c.(748-750)cAt>cGt	p.H250R	STXBP3_ENST00000485167.1_3'UTR	NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	250	Mediates interaction with DOC2B. {ECO:0000250}.				blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		ACTGTCCTGCATGAACTGACC	0.373																																					p.H250R		Atlas-SNP	.											.	STXBP3	44	.	0			c.A749G						.						207	196	199					1																	109321972		2203	4300	6503	SO:0001583	missense	6814	exon9			TCCTGCATGAACT	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.749A>G	chr1.hg19:g.109321972A>G	ENSP00000359025:p.His250Arg	123.0	0.0		69.0	24.0	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	hg19	CCDS790.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.787090	0.90367	.	.	ENSG00000116266	ENST00000370008	T	0.80566	-1.39	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.90229	0.6945	M	0.90369	3.11	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92316	0.5862	10	0.87932	D	0	-19.3411	15.7572	0.78043	1.0:0.0:0.0:0.0	.	250	O00186	STXB3_HUMAN	R	250	ENSP00000359025:H250R	ENSP00000359025:H250R	H	+	2	0	STXBP3	109123495	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.283000	0.95860	2.199000	0.70637	0.533000	0.62120	CAT	.	.		0.373	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		G	109321972	A	G	109321972	3	3	167	1	0	0	0	0	1	0	0	0	15369	217	8	2	783	2	STXBP3	1	109321972	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	14011029	109321972	139928649	7	25252										
HIPK1	204851	hgsc.bcm.edu	37	chr1	114514596	114514596	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggtaagtgctatgggctactGccttctgtttgggccctgca	13	10	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:114514596G>A	ENST00000369558.1	+	15	3376				HIPK1_ENST00000340480.4_Intron|HIPK1_ENST00000369561.4_Intron|HIPK1_ENST00000369555.2_Intron|HIPK1_ENST00000369553.1_Intron|HIPK1_ENST00000369554.2_Intron|HIPK1_ENST00000426820.2_Intron|HIPK1_ENST00000406344.1_Intron|HIPK1_ENST00000369559.4_Missense_Mutation_p.C1055Y			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1						anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATGGGCTACTGCCTTCTGTTT	0.517																																					p.C1055Y		Atlas-SNP	.											HIPK1,NS,carcinoma,0,1	HIPK1	195	.	0			c.G3164A						.						193	160	171					1																	114514596		2203	4300	6503	SO:0001627	intron_variant	204851	exon15			GCTACTGCCTTCT	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.3144+20G>A	chr1.hg19:g.114514596G>A		123.0	0.0		127.0	32.0	NM_152696	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Missense_Mutation	SNP	ENST00000369558.1	hg19	CCDS867.1	.	.	.	.	.	.	.	.	.	.	G	8.659	0.900152	0.17686	.	.	ENSG00000163349	ENST00000369559	T	0.46451	0.87	5.89	4.97	0.65823	.	.	.	.	.	T	0.10981	0.0268	N	0.08118	0	0.80722	D	1	B	0.31351	0.32	B	0.31812	0.136	T	0.11324	-1.0592	8	.	.	.	.	12.8971	0.58106	0.0796:0.0:0.9204:0.0	.	1055	Q86Z02-2	.	Y	1055	ENSP00000358572:C1055Y	.	C	+	2	0	HIPK1	114316119	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	4.289000	0.59013	1.474000	0.48178	0.563000	0.77884	TGC	.	.		0.517	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		A	114514596	G	A	114514596	1	1	167	0	1	0	0	0	0	0	0	0	7125	1319	46	3		3	HIPK1	1	114514596	Intron	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	5192624	114514596	134736025	8	25253										
SYCP1	6847	hgsc.bcm.edu	37	chr1	115487586	115487586	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aaatagctgaaatggtagcaCttatggaaaaacataaggta	9	4	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:115487586C>T	ENST00000369522.3	+	25	2377	c.2137C>T	c.(2137-2139)Ctt>Ttt	p.L713F	SYCP1_ENST00000369518.1_Missense_Mutation_p.L713F	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	713					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATGGTAGCACTTATGGAAAA	0.274																																					p.L713F		Atlas-SNP	.											.	SYCP1	149	.	0			c.C2137T						.						37	37	37					1																	115487586		2200	4282	6482	SO:0001583	missense	6847	exon25			GTAGCACTTATGG	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2137C>T	chr1.hg19:g.115487586C>T	ENSP00000358535:p.Leu713Phe	468.0	0.0		499.0	31.0	NM_003176	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	hg19	CCDS879.1	.	.	.	.	.	.	.	.	.	.	C	18.71	3.682764	0.68157	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.58797	0.31;0.31;0.31	4.91	4.91	0.64330	.	0.000000	0.64402	D	0.000001	T	0.67711	0.2922	M	0.74258	2.255	0.49051	D	0.99974	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.999	T	0.71817	-0.4478	10	0.62326	D	0.03	-4.8495	11.2611	0.49083	0.0:0.9149:0.0:0.0851	.	713;713	B7ZLS9;Q15431	.;SYCP1_HUMAN	F	713	ENSP00000358535:L713F;ENSP00000410011:L713F;ENSP00000358531:L713F	ENSP00000358531:L713F	L	+	1	0	SYCP1	115289109	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.788000	0.55446	2.268000	0.75426	0.650000	0.86243	CTT	.	.		0.274	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		T	115487586	C	T	115487586	3	4	167	1	0	0	0	0	1	0	0	0	15446	565	20	3	2231	3	SYCP1	1	115487586	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	972990	115487586	133763035	9	25254										
ZNF687	57592	hgsc.bcm.edu	37	chr1	151261604	151261604	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tcagtggtgtttgggggtgtGaactccatcaagtcccacat	12	9	2	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:151261604G>A	ENST00000368879.2	+	4	2426	c.2328G>A	c.(2326-2328)gtG>gtA	p.V776V		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	776					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TTGGGGGTGTGAACTCCATCA	0.617																																					p.V776V		Atlas-SNP	.											.	ZNF687	94	.	0			c.G2328A						.						106	92	96					1																	151261604		2203	4300	6503	SO:0001819	synonymous_variant	57592	exon4			GGGTGTGAACTCC		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.2328G>A	chr1.hg19:g.151261604G>A		78.0	0.0		137.0	7.0	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Silent	SNP	ENST00000368879.2	hg19																																																																																				.	.		0.617	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		A	151261604	G	A	151261604	2	1	167	1	0	0	0	0	0	0	0	1	18107	1277	45	3		3	ZNF687	1	151261604	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	35774018	151261604	97989017	10	25255										
OR10R2	343406	hgsc.bcm.edu	37	chr1	158450591	158450591	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	actccattactaaaccccatGgtttatagcctcagaaacaa	4	12	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:158450591G>C	ENST00000368152.1	+	1	924	c.924G>C	c.(922-924)atG>atC	p.M308I	RP11-144L1.4_ENST00000426251.1_RNA|RP11-144L1.4_ENST00000419738.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	308						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					TAAACCCCATGGTTTATAGCC	0.393																																					p.M308I		Atlas-SNP	.											.	OR10R2	81	.	0			c.G924C						.						108	99	102					1																	158450591		2203	4300	6503	SO:0001583	missense	343406	exon1			CCCCATGGTTTAT	AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"GPCR / Class A : Olfactory receptors"	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.924G>C	chr1.hg19:g.158450591G>C	ENSP00000357134:p.Met308Ile	227.0	0.0		298.0	57.0	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	hg19	CCDS30898.1	.	.	.	.	.	.	.	.	.	.	g	1.742	-0.491558	0.04322	.	.	ENSG00000198965	ENST00000368152	T	0.28255	1.62	4.2	3.26	0.37387	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.02888	0.0086	N	0.01624	-0.795	0.22378	N	0.999155	B	0.06786	0.001	B	0.06405	0.002	T	0.44390	-0.9331	9	0.14252	T	0.57	.	5.3635	0.16101	0.1014:0.0:0.5898:0.3089	.	308	Q8NGX6	O10R2_HUMAN	I	308	ENSP00000357134:M308I	ENSP00000357134:M308I	M	+	3	0	OR10R2	156717215	0.038000	0.19896	0.996000	0.52242	0.390000	0.30446	-0.553000	0.06012	2.135000	0.66039	0.655000	0.94253	ATG	.	.		0.393	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472		C	158450591	G	C	158450591	3	2	167	1	0	0	0	0	1	0	0	0	10926	1348	47	4	926	4	OR10R2	1	158450591	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	7188987	158450591	90800030	11	25256										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158622440	158622440	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gcccgatccaagagggagcgGtatctggatggagaattggg	17	7	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:158622440G>A	ENST00000368147.4	-	23	3372	c.3192C>T	c.(3190-3192)taC>taT	p.Y1064Y		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1064					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGAGGGAGCGGTATCTGGATG	0.423																																					p.Y1064Y		Atlas-SNP	.											.	SPTA1	720	.	0			c.C3192T						.						78	72	74					1																	158622440		1854	4099	5953	SO:0001819	synonymous_variant	6708	exon23			GGAGCGGTATCTG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3192C>T	chr1.hg19:g.158622440G>A		102.0	0.0		99.0	17.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.		0.423	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158622440	G	A	158622440	2	1	167	1	0	0	0	0	0	0	0	1	15131	1256	44	3		3	SPTA1	1	158622440	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	171849	158622440	90628181	12	25257										
CD55	1604	hgsc.bcm.edu	37	chr1	207498067	207498067	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	acttgccttcagaatttaaaAtggtccacagcagtcgaatt	7	9	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:207498067A>G	ENST00000367064.3	+	3	708	c.450A>G	c.(448-450)aaA>aaG	p.K150K	CD55_ENST00000367065.5_Silent_p.K150K|CD55_ENST00000367063.2_Silent_p.K150K|CD55_ENST00000367062.4_Silent_p.K150K|CD55_ENST00000465534.1_3'UTR|CD55_ENST00000391920.4_Silent_p.K150K|CD55_ENST00000391921.4_Intron|CD55_ENST00000367067.4_Missense_Mutation_p.M122V|CD55_ENST00000314754.8_Silent_p.K150K	NM_000574.3	NP_000565.1	P08174	DAF_HUMAN	CD55 molecule, decay accelerating factor for complement (Cromer blood group)	150	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				CD4-positive, alpha-beta T cell cytokine production (GO:0035743)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|maternal process involved in parturition (GO:0060137)|negative regulation of complement activation (GO:0045916)|positive regulation of CD4-positive, alpha-beta T cell activation (GO:2000516)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of complement activation (GO:0030449)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|respiratory burst (GO:0045730)|response to peptide hormone (GO:0043434)|response to virus (GO:0009615)|spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	enzyme inhibitor activity (GO:0004857)|lipid binding (GO:0008289)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16					Chloramphenicol(DB00446)	AGAATTTAAAATGGTCCACAG	0.368																																					p.K150K		Atlas-SNP	.											.	CD55	55	.	0			c.A450G						.						80	82	81					1																	207498067		2203	4300	6503	SO:0001819	synonymous_variant	1604	exon3			TTTAAAATGGTCC	BC001288	CCDS31006.1, CCDS44307.1, CCDS73022.1	1q32	2014-09-17	2006-03-28	2006-02-23	ENSG00000196352	ENSG00000196352		"CD molecules", "Blood group antigens"	2665	protein-coding gene	gene with protein product		125240	"decay accelerating factor for complement (CD55, Cromer blood group system)"	DAF			Standard	XM_005273077		Approved	CR, TC, CROM	uc001hfr.4	P08174	OTTHUMG00000036255	ENST00000367064.3:c.450A>G	chr1.hg19:g.207498067A>G		115.0	0.0		179.0	108.0	NM_001114752	B1AP14|D3DT83|D3DT84|E7ER69|P09679|P78361|Q14UF2|Q14UF3|Q14UF4|Q14UF5|Q14UF6	Silent	SNP	ENST00000367064.3	hg19	CCDS31006.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.006|0.006	-2.104425|-2.104425	0.00356|0.00356	.|.	.|.	ENSG00000196352|ENSG00000196352	ENST00000367067|ENST00000343420	T|.	0.03152|.	4.03|.	6.16|6.16	0.0513|0.0513	0.14297|0.14297	.|.	.|.	.|.	.|.	.|.	T|T	0.34542|0.34542	0.0901|0.0901	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.30851|0.30851	-0.9964|-0.9964	6|4	0.02654|.	T|.	1|.	.|.	9.5294|9.5294	0.39185|0.39185	0.5446:0.0:0.4554:0.0|0.5446:0.0:0.4554:0.0	.|.	.|.	.|.	.|.	V|S	122|160	ENSP00000356034:M122V|.	ENSP00000356034:M122V|.	M|N	+|+	1|2	0|0	CD55|CD55	205564690|205564690	0.000000|0.000000	0.05858|0.05858	0.130000|0.130000	0.21974|0.21974	0.015000|0.015000	0.08874|0.08874	-1.065000|-1.065000	0.03458|0.03458	0.030000|0.030000	0.15379|0.15379	-0.263000|-0.263000	0.10527|0.10527	ATG|AAT	.	.		0.368	CD55-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088208.2	NM_000574		G	207498067	A	G	207498067	2	3	167	1	0	0	0	0	0	0	0	1	3026	98	4	2		2	CD55	1	207498067	Silent	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	48875627	207498067	41752554	13	25258										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208202219	208202219	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gggatgtccttggcatagagCagcttgttggagggggagtc	18	6	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:208202219C>A	ENST00000367033.3	-	30	6151	c.5394G>T	c.(5392-5394)ctG>ctT	p.L1798L	PLXNA2_ENST00000483048.1_5'UTR	NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1798					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TGGCATAGAGCAGCTTGTTGG	0.612																																					p.L1798L		Atlas-SNP	.											.	PLXNA2	178	.	0			c.G5394T						.						106	103	104					1																	208202219		2203	4300	6503	SO:0001819	synonymous_variant	5362	exon30			ATAGAGCAGCTTG	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.5394G>T	chr1.hg19:g.208202219C>A		106.0	0.0		131.0	33.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	hg19	CCDS31013.1																																																																																			.	.		0.612	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		A	208202219	C	A	208202219	2	1	167	1	0	0	0	0	0	0	0	1	12129	697	25	3		3	PLXNA2	1	208202219	Silent	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	704152	208202219	41048402	14	25259										
FAM71A	149647	hgsc.bcm.edu	37	chr1	212798986	212798986	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	caaacccactaatgtgctcaAtgcatccatccccaaaacat	3	15	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:212798986A>G	ENST00000294829.3	+	1	1198	c.767A>G	c.(766-768)aAt>aGt	p.N256S	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	256						nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		AATGTGCTCAATGCATCCATC	0.547																																					p.N256S		Atlas-SNP	.											.	FAM71A	87	.	0			c.A767G						.						101	109	106					1																	212798986		2203	4300	6503	SO:0001583	missense	149647	exon1			TGCTCAATGCATC		CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.767A>G	chr1.hg19:g.212798986A>G	ENSP00000294829:p.Asn256Ser	53.0	0.0		87.0	17.0	NM_153606	Q5VTZ1	Missense_Mutation	SNP	ENST00000294829.3	hg19	CCDS1507.1	.	.	.	.	.	.	.	.	.	.	A	6.126	0.391525	0.11581	.	.	ENSG00000162771	ENST00000294829;ENST00000545975	T	0.03272	3.99	4.02	-0.867	0.10655	.	.	.	.	.	T	0.01765	0.0056	N	0.12182	0.205	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.47407	-0.9120	9	0.02654	T	1	1.6651	7.5677	0.27890	0.4329:0.0:0.5671:0.0	.	256	Q8IYT1	FA71A_HUMAN	S	256;31	ENSP00000294829:N256S	ENSP00000294829:N256S	N	+	2	0	FAM71A	210865609	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.163000	0.09997	-0.038000	0.13624	0.460000	0.39030	AAT	.	.		0.547	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606		G	212798986	A	G	212798986	3	3	167	1	0	0	0	0	1	0	0	0	5615	101	4	2	769	2	FAM71A	1	212798986	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	4596767	212798986	36451635	15	25260										
USH2A	7399	hgsc.bcm.edu	37	chr1	216420462	216420462	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgcccagagtgaggattgcaGaatttgttcactgagccatg	12	8	1	4	rs61747101		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:216420462G>A	ENST00000307340.3	-	13	2660	c.2274C>T	c.(2272-2274)ttC>ttT	p.F758F	USH2A_ENST00000366943.2_Silent_p.F758F|USH2A_ENST00000366942.3_Silent_p.F758F	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	758	Laminin EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GAGGATTGCAGAATTTGTTCA	0.428										HNSCC(13;0.011)																											p.F758F		Atlas-SNP	.											.	USH2A	1168	.	0			c.C2274T						.						111	114	113					1																	216420462		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon13			ATTGCAGAATTTG	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.2274C>T	chr1.hg19:g.216420462G>A		125.0	0.0		138.0	11.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	G|0.024;C|0.976		0.428	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216420462	G	A	216420462	2	1	167	1	0	0	0	0	0	0	0	1	17051	933	33	3		3	USH2A	1	216420462	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	3621476	216420462	32830159	16	25261										
EPRS	2058	hgsc.bcm.edu	37	chr1	220160734	220160734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aaggagttcttgaacagctaTatctacttgatcctttagtt	7	7	2	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:220160734T>C	ENST00000366923.3	-	20	3057	c.2788A>G	c.(2788-2790)Ata>Gta	p.I930V	snoU13_ENST00000459217.1_RNA	NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	930	3 X 57 AA approximate repeats.|WHEP-TRS 3.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	TGAACAGCTATATCTACTTGA	0.378																																					p.I930V		Atlas-SNP	.											.	EPRS	140	.	0			c.A2788G						.						62	62	62					1																	220160734		2203	4300	6503	SO:0001583	missense	2058	exon20			CAGCTATATCTAC	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.2788A>G	chr1.hg19:g.220160734T>C	ENSP00000355890:p.Ile930Val	67.0	0.0		79.0	13.0	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Missense_Mutation	SNP	ENST00000366923.3	hg19	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	T	17.89	3.499650	0.64298	.	.	ENSG00000136628	ENST00000366923;ENST00000536921;ENST00000435048	T	0.28666	1.6	5.9	-11.8	0.00035	WHEP-TRS (3);S15/NS1, RNA-binding (2);	1.680160	0.02731	N	0.115118	T	0.10937	0.0267	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.18840	-1.0324	10	0.28530	T	0.3	1.6487	11.3	0.49300	0.0814:0.6065:0.2348:0.0773	.	954;937;930	E7EMN0;Q3KQZ8;P07814	.;.;SYEP_HUMAN	V	930;937;954	ENSP00000355890:I930V	ENSP00000355890:I930V	I	-	1	0	EPRS	218227357	0.000000	0.05858	0.000000	0.03702	0.893000	0.52053	-1.045000	0.03528	-2.716000	0.00391	0.460000	0.39030	ATA	.	.		0.378	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		C	220160734	T	C	220160734	3	2	167	1	0	0	0	0	1	0	0	0	5193	1406	49	2	1802	2	EPRS	1	220160734	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	3740272	220160734	29089887	17	25262										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245809448	245809448	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggaggtcgcagccgcctgcaTctcattgatctcggcagctg	13	13	2	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:245809448T>A	ENST00000407071.2	+	10	2564	c.2124T>A	c.(2122-2124)caT>caA	p.H708Q	KIF26B_ENST00000366518.4_Missense_Mutation_p.H327Q	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	708	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GCCGCCTGCATCTCATTGATC	0.498																																					p.H708Q		Atlas-SNP	.											.	KIF26B	343	.	0			c.T2124A						.						64	65	64					1																	245809448		1955	4160	6115	SO:0001583	missense	55083	exon10			CCTGCATCTCATT	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2124T>A	chr1.hg19:g.245809448T>A	ENSP00000385545:p.His708Gln	72.0	0.0		85.0	6.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392018	0.62066	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.74315	-0.83;-0.83	5.78	0.597	0.17504	Kinesin, motor domain (5);	.	.	.	.	D	0.83912	0.5357	M	0.80616	2.505	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.998	T	0.82827	-0.0265	9	0.66056	D	0.02	.	10.1192	0.42609	0.0:0.5936:0.0:0.4064	.	327;708	B7WPD9;Q2KJY2	.;KI26B_HUMAN	Q	708;327;324	ENSP00000385545:H708Q;ENSP00000355475:H327Q	ENSP00000355475:H327Q	H	+	3	2	KIF26B	243876071	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.559000	0.36320	0.192000	0.20272	0.454000	0.30748	CAT	.	.		0.498	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245809448	T	A	245809448	3	1	167	1	0	0	0	0	1	0	0	0	8304	1432	50	4	2162	4	KIF26B	1	245809448	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	25648714	245809448	3441173	18	25263										
OR2T3	343173	hgsc.bcm.edu	37	chr1	248636988	248636988	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgttcttctacctgaccctgGctggagctgaggttttcctc	10	12	2	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr1:248636988G>A	ENST00000359594.2	+	1	362	c.337G>A	c.(337-339)Gct>Act	p.A113T		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCTGACCCTGGCTGGAGCTGA	0.552																																					p.A113T		Atlas-SNP	.											.	OR2T3	79	.	0			c.G337A						.						122	112	115					1																	248636988		2195	4298	6493	SO:0001583	missense	343173	exon1			ACCCTGGCTGGAG		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"GPCR / Class A : Olfactory receptors"	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.337G>A	chr1.hg19:g.248636988G>A	ENSP00000352604:p.Ala113Thr	374.0	0.0		525.0	91.0	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	hg19	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	g	9.761	1.170098	0.21621	.	.	ENSG00000196539	ENST00000359594	T	0.02050	4.48	2.65	-3.07	0.05363	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.02649	0.0080	L	0.49126	1.545	0.09310	N	1	B	0.23442	0.085	B	0.20955	0.032	T	0.31888	-0.9927	9	0.42905	T	0.14	.	9.407	0.38469	0.1806:0.0:0.8194:0.0	.	113	Q8NH03	OR2T3_HUMAN	T	113	ENSP00000352604:A113T	ENSP00000352604:A113T	A	+	1	0	OR2T3	246703611	0.000000	0.05858	0.000000	0.03702	0.675000	0.39556	-2.090000	0.01356	-1.215000	0.02610	0.186000	0.17326	GCT	.	.		0.552	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495		A	248636988	G	A	248636988	3	1	167	1	0	0	0	0	1	0	0	0	11032	1203	42	3	339	3	OR2T3	1	248636988	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	2827540	248636988	613633	19	25264										
TPO	7173	hgsc.bcm.edu	37	chr2	1480955	1480955	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggaccaaggcgcgctctttgGgaacctgtccacggccaacc	12	15	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr2:1480955G>C	ENST00000345913.4	+	8	1008	c.917G>C	c.(916-918)gGg>gCg	p.G306A	TPO_ENST00000346956.3_Missense_Mutation_p.G306A|TPO_ENST00000329066.4_Missense_Mutation_p.G306A|TPO_ENST00000382201.3_Missense_Mutation_p.G306A|TPO_ENST00000497517.2_Intron|TPO_ENST00000337415.3_Missense_Mutation_p.G306A|TPO_ENST00000382198.1_Intron|TPO_ENST00000349624.3_Intron	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	306					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GCGCTCTTTGGGAACCTGTCC	0.711																																					p.G306A		Atlas-SNP	.											.	TPO	224	.	0			c.G917C						.						17	17	17					2																	1480955		2201	4294	6495	SO:0001583	missense	7173	exon8			TCTTTGGGAACCT		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.917G>C	chr2.hg19:g.1480955G>C	ENSP00000318820:p.Gly306Ala	698.0	0.0		708.0	123.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.489787	0.44249	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000329066;ENST00000382201;ENST00000422464	T;T;T;T;T;T	0.68903	-0.33;-0.35;-0.31;-0.35;-0.29;-0.36	4.99	3.13	0.36017	.	0.480118	0.23606	N	0.046382	T	0.76912	0.4054	M	0.77103	2.36	0.80722	D	1	D;D;D	0.69078	0.996;0.996;0.997	P;P;P	0.61132	0.877;0.816;0.884	T	0.78247	-0.2278	10	0.66056	D	0.02	-31.9024	9.7654	0.40557	0.0771:0.1421:0.7808:0.0	.	306;306;306	P07202-4;P07202-2;P07202	.;.;PERT_HUMAN	A	306;306;306;306;306;235	ENSP00000337263:G306A;ENSP00000318820:G306A;ENSP00000263886:G306A;ENSP00000329869:G306A;ENSP00000371636:G306A;ENSP00000405788:G235A	ENSP00000329869:G306A	G	+	2	0	TPO	1459962	0.109000	0.22037	0.911000	0.35937	0.015000	0.08874	0.234000	0.17930	1.057000	0.40506	0.460000	0.39030	GGG	.	.		0.711	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		C	1480955	G	C	1480955	3	2	167	1	0	0	0	0	1	0	0	0	16425	1232	43	4	943	4	TPO	2	1480955	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10		1480955	241718418	20	25265										
GREB1	9687	hgsc.bcm.edu	37	chr2	11750992	11750992	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gcccctgcggccacgggctcAtggtcctgctgcgggtgccc	15	17	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr2:11750992A>T	ENST00000381486.2	+	18	3145	c.2845A>T	c.(2845-2847)Atg>Ttg	p.M949L	GREB1_ENST00000396123.1_5'Flank|GREB1_ENST00000234142.5_Missense_Mutation_p.M949L	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	949						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CCACGGGCTCATGGTCCTGCT	0.677																																					p.M949L	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.A2845T						.						27	31	30					2																	11750992		2063	4191	6254	SO:0001583	missense	9687	exon18			GGGCTCATGGTCC		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.2845A>T	chr2.hg19:g.11750992A>T	ENSP00000370896:p.Met949Leu	205.0	0.0		235.0	10.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	A	34	5.401334	0.96030	.	.	ENSG00000196208	ENST00000381486;ENST00000234142	T;T	0.48201	0.82;0.82	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.67429	0.2892	M	0.76170	2.325	0.80722	D	1	P	0.48407	0.91	D	0.62955	0.909	T	0.71384	-0.4609	10	0.72032	D	0.01	-19.5302	15.2741	0.73728	1.0:0.0:0.0:0.0	.	949	Q4ZG55	GREB1_HUMAN	L	949	ENSP00000370896:M949L;ENSP00000234142:M949L	ENSP00000234142:M949L	M	+	1	0	GREB1	11668443	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.825000	0.92029	2.006000	0.58801	0.460000	0.39030	ATG	.	.		0.677	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		T	11750992	A	T	11750992	3	4	167	1	0	0	0	0	1	0	0	0	6769	217	8	4	3019	4	GREB1	2	11750992	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	10270037	11750992	231448381	21	25266										
LPIN1	23175	hgsc.bcm.edu	37	chr2	11911614	11911614	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agaggcctggaccccagcacGccagcccaagtgatcgctcc	11	17	0	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr2:11911614G>A	ENST00000256720.2	+	4	498	c.405G>A	c.(403-405)acG>acA	p.T135T	LPIN1_ENST00000425416.2_Silent_p.T141T|LPIN1_ENST00000396098.1_Silent_p.T141T|LPIN1_ENST00000396099.1_Silent_p.T141T|LPIN1_ENST00000449576.2_Silent_p.T184T	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	135					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		ACCCCAGCACGCCAGCCCAAG	0.567																																					p.T184T		Atlas-SNP	.											LPIN1,colon,carcinoma,+1,1	LPIN1	99	.	0			c.G552A						.						55	56	55					2																	11911614		2203	4300	6503	SO:0001819	synonymous_variant	23175	exon5			CAGCACGCCAGCC	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.405G>A	chr2.hg19:g.11911614G>A		141.0	0.0		165.0	43.0	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	hg19	CCDS1682.1																																																																																			.	.		0.567	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		A	11911614	G	A	11911614	2	1	167	1	0	0	0	0	0	0	0	1	8927	1074	38	1		1	LPIN1	2	11911614	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	160622	11911614	231287759	22	25267										
WDR35	57539	hgsc.bcm.edu	37	chr2	20135328	20135328	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cattcagctaagcgttcctgGttccgtccttgtacataata	7	11	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr2:20135328G>C	ENST00000345530.3	-	22	2599	c.2484C>G	c.(2482-2484)aaC>aaG	p.N828K	WDR35_ENST00000416055.2_Missense_Mutation_p.N393K|WDR35_ENST00000281405.4_Missense_Mutation_p.N817K	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	828					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCGTTCCTGGTTCCGTCCTT	0.353																																					p.N828K		Atlas-SNP	.											.	WDR35	92	.	0			c.C2484G						.						103	98	99					2																	20135328		2203	4300	6503	SO:0001583	missense	57539	exon22			TTCCTGGTTCCGT	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"WD repeat domain containing", "Intraflagellar transport homologs"	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.2484C>G	chr2.hg19:g.20135328G>C	ENSP00000314444:p.Asn828Lys	79.0	0.0		72.0	19.0	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	hg19	CCDS33152.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053258	0.75960	.	.	ENSG00000118965	ENST00000345530;ENST00000281405;ENST00000416055;ENST00000453014	T;T;T;D	0.87334	-0.2;-0.19;-0.79;-2.24	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.93239	0.7846	M	0.88031	2.925	0.80722	D	1	D;D;D;D	0.69078	0.957;0.997;0.996;0.992	P;D;D;D	0.79784	0.791;0.993;0.916;0.922	D	0.92362	0.5898	10	0.34782	T	0.22	-20.488	10.8993	0.47043	0.087:0.0:0.913:0.0	.	828;817;828;393	F8WB94;Q9P2L0-2;Q9P2L0;B3KR94	.;.;WDR35_HUMAN;.	K	828;817;393;363	ENSP00000314444:N828K;ENSP00000281405:N817K;ENSP00000399159:N393K;ENSP00000404409:N363K	ENSP00000281405:N817K	N	-	3	2	WDR35	19998809	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.773000	0.62331	2.415000	0.81967	0.491000	0.48974	AAC	.	.		0.353	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779		C	20135328	G	C	20135328	3	2	167	1	0	0	0	0	1	0	0	0	17304	1252	44	4	1089	4	WDR35	2	20135328	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	8223714	20135328	223064045	23	25268										
CCDC85A	114800	hgsc.bcm.edu	37	chr2	56419881	56419881	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aagggtgcaggctgcgcaggCagccgctgctccatcgacag	15	13	0	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr2:56419881C>A	ENST00000407595.2	+	2	1048	c.546C>A	c.(544-546)ggC>ggA	p.G182G	RP11-482H16.1_ENST00000607540.1_RNA	NM_001080433.1	NP_001073902.1	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	182										breast(6)|cervix(2)|endometrium(5)|kidney(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)	38			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GCTGCGCAGGCAGCCGCTGCT	0.617																																					p.G182G		Atlas-SNP	.											.	CCDC85A	70	.	0			c.C546A						.						24	32	29					2																	56419881		2113	4234	6347	SO:0001819	synonymous_variant	114800	exon2			CGCAGGCAGCCGC	AB067499	CCDS46290.1	2p16.1	2006-03-29			ENSG00000055813	ENSG00000055813			29400	protein-coding gene	gene with protein product						11572484	Standard	NM_001080433		Approved	KIAA1912	uc002rzn.3	Q96PX6	OTTHUMG00000152033	ENST00000407595.2:c.546C>A	chr2.hg19:g.56419881C>A		202.0	0.0		190.0	56.0	NM_001080433		Silent	SNP	ENST00000407595.2	hg19	CCDS46290.1																																																																																			.	.		0.617	CCDC85A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324993.1			A	56419881	C	A	56419881	2	1	167	1	0	0	0	0	0	0	0	1	2861	697	25	3		3	CCDC85A	2	56419881	Silent	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	36284553	56419881	186779492	24	25269										
TTN	7273	hgsc.bcm.edu	37	chr2	179637884	179637884	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	attttctcccgcgtaaaatgTgtattttccttcatcatctt	4	10	4	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr2:179637884T>G	ENST00000591111.1	-	33	8031	c.7807A>C	c.(7807-7809)Aca>Cca	p.T2603P	TTN_ENST00000460472.2_Missense_Mutation_p.T2557P|TTN_ENST00000342992.6_Missense_Mutation_p.T2603P|TTN_ENST00000360870.5_Missense_Mutation_p.T2603P|TTN_ENST00000589042.1_Missense_Mutation_p.T2603P|TTN_ENST00000359218.5_Missense_Mutation_p.T2557P|TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T2557P|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12926					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCGTAAAATGTGTATTTTCCT	0.308																																					p.T2603P		Atlas-SNP	.											.	TTN	18412	.	0			c.A7807C						.						53	55	54					2																	179637884		2203	4299	6502	SO:0001583	missense	7273	exon33			AAAATGTGTATTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.7807A>C	chr2.hg19:g.179637884T>G	ENSP00000465570:p.Thr2603Pro	178.0	0.0		178.0	118.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.04	1.817957	0.32145	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	5.59	4.45	0.53987	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.58949	0.2158	M	0.84511	2.7	0.23351	N	0.997859	B;B;B;B;P	0.49559	0.171;0.171;0.427;0.171;0.925	B;B;B;B;P	0.48840	0.283;0.283;0.283;0.283;0.592	T	0.56805	-0.7918	9	0.87932	D	0	.	8.6559	0.34062	0.0:0.1703:0.0:0.8297	.	2557;2557;2557;2603;2603	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	P	2603;2557;2557;2557;2557;2603	ENSP00000343764:T2603P;ENSP00000434586:T2557P;ENSP00000340554:T2557P;ENSP00000352154:T2557P;ENSP00000354117:T2603P	ENSP00000340554:T2557P	T	-	1	0	TTN	179346129	1.000000	0.71417	0.997000	0.53966	0.942000	0.58702	2.631000	0.46502	0.971000	0.38288	0.528000	0.53228	ACA	.	.		0.308	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179637884	T	G	179637884	3	3	167	1	0	0	0	0	1	0	0	0	16750	1696	59	5	103501	5	TTN	2	179637884	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	123218003	179637884	63561489	25	25270										
SPATS2L	26010	hgsc.bcm.edu	37	chr2	201305388	201305388	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ttaggcccaaatattgagaaAtcagtgaaggatttgcaacg	10	6	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr2:201305388A>T	ENST00000358677.5	+	8	916	c.669A>T	c.(667-669)aaA>aaT	p.K223N	SPATS2L_ENST00000409988.3_Missense_Mutation_p.K223N|SPATS2L_ENST00000409755.3_Missense_Mutation_p.K253N|SPATS2L_ENST00000409151.1_Missense_Mutation_p.K231N|SPATS2L_ENST00000409718.1_Missense_Mutation_p.K223N|SPATS2L_ENST00000360760.5_Missense_Mutation_p.K154N|SPATS2L_ENST00000451764.2_Missense_Mutation_p.K223N|SPATS2L_ENST00000409140.3_Missense_Mutation_p.K223N|SPATS2L_ENST00000409385.1_Missense_Mutation_p.K163N	NM_001282735.1|NM_001282743.1|NM_001282744.1|NM_015535.2	NP_001269664.1|NP_001269672.1|NP_001269673.1|NP_056350.2	Q9NUQ6	SPS2L_HUMAN	spermatogenesis associated, serine-rich 2-like	223						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	10						ATATTGAGAAATCAGTGAAGG	0.358																																					p.K223N		Atlas-SNP	.											.	SPATS2L	88	.	0			c.A669T						.						77	73	75					2																	201305388		1877	4111	5988	SO:0001583	missense	26010	exon8			TGAGAAATCAGTG	AF193059	CCDS46483.1, CCDS46484.1, CCDS74621.1, CCDS74622.1	2q33.1	2009-06-12			ENSG00000196141	ENSG00000196141			24574	protein-coding gene	gene with protein product	"DNA polymerase transactivated protein 6"	613817				11230166	Standard	NM_001100422		Approved	DNAPTP6	uc002uvr.4	Q9NUQ6	OTTHUMG00000154589	ENST00000358677.5:c.669A>T	chr2.hg19:g.201305388A>T	ENSP00000351503:p.Lys223Asn	100.0	0.0		102.0	22.0	NM_001100423	A8K381|B4DRE6|B4DT67|B7WNZ7|Q53T22|Q8WV53|Q8WYG1|Q9NTW4	Missense_Mutation	SNP	ENST00000358677.5	hg19	CCDS46483.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.88|19.88	3.908517|3.908517	0.72868|0.72868	.|.	.|.	ENSG00000196141|ENSG00000196141	ENST00000409718;ENST00000358677;ENST00000409988;ENST00000409385;ENST00000451764;ENST00000360760;ENST00000453663;ENST00000409140;ENST00000409397;ENST00000409755;ENST00000409151;ENST00000449647;ENST00000438761|ENST00000366118	.|.	.|.	.|.	6.03|6.03	3.68|3.68	0.42216|0.42216	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|T	0.61664|0.61664	0.2365|0.2365	M|M	0.64170|0.64170	1.965|1.965	0.42936|0.42936	D|D	0.994332|0.994332	D;D;D|.	0.89917|.	1.0;0.999;1.0|.	D;D;D|.	0.87578|.	0.998;0.973;0.995|.	T|T	0.57556|0.57556	-0.7791|-0.7791	9|5	0.87932|.	D|.	0|.	-26.0019|-26.0019	8.9601|8.9601	0.35842|0.35842	0.7304:0.0:0.2696:0.0|0.7304:0.0:0.2696:0.0	.|.	253;154;223|.	B4DT67;Q9NUQ6-2;Q9NUQ6|.	.;.;SPS2L_HUMAN|.	N|I	223;223;223;163;223;154;154;223;154;253;231;154;149|6	.|.	ENSP00000351503:K223N|.	K|N	+|+	3|2	2|0	SPATS2L|SPATS2L	201013633|201013633	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.290000|1.290000	0.33319|0.33319	0.536000|0.536000	0.28733|0.28733	0.533000|0.533000	0.62120|0.62120	AAA|AAT	.	.		0.358	SPATS2L-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336208.3	NM_015535		T	201305388	A	T	201305388	3	4	167	1	0	0	0	0	1	0	0	0	15035	98	4	4	691	4	SPATS2L	2	201305388	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	21667504	201305388	41893985	26	25271										
STK11IP	114790	hgsc.bcm.edu	37	chr2	220480870	220480870	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgggaggagctgttttccatCggactccggacagtgatcca	13	10	0	1	rs373252328	byFrequency	TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr2:220480870C>T	ENST00000456909.1	+	25	3312	c.3222C>T	c.(3220-3222)atC>atT	p.I1074I	STK11IP_ENST00000295641.10_Silent_p.I1085I			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	1085					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGTTTTCCATCGGACTCCGGA	0.622													C|||	6	0.00119808	0.0038	0	5008	,	,		18227	0.001		0	False		,,,				2504	0				p.I1085I		Atlas-SNP	.											.	STK11IP	152	.	0			c.C3255T						.	C		2,4318		0,2,2158	42	48	46		3255	-2.7	1	2		46	0,8548		0,0,4274	no	coding-synonymous	STK11IP	NM_052902.2		0,2,6432	TT,TC,CC		0.0,0.0463,0.0155		1085/1100	220480870	2,12866	2160	4274	6434	SO:0001819	synonymous_variant	114790	exon25			TTCCATCGGACTC	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"LKB1 interacting protein"	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.3222C>T	chr2.hg19:g.220480870C>T		121.0	0.0		121.0	28.0	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Silent	SNP	ENST00000456909.1	hg19																																																																																				.	.		0.622	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		T	220480870	C	T	220480870	2	4	167	1	0	0	0	0	0	0	0	1	15303	874	31	1		1	STK11IP	2	220480870	Silent	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	19175482	220480870	22718503	27	25272										
UBE2F	140739	hgsc.bcm.edu	37	chr2	238925260	238925260	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tttgaaactgaagttcccgaTgcgtacaacatggtggtgag	12	7	0	3	rs139771082		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr2:238925260T>C	ENST00000272930.4	+	5	461	c.267T>C	c.(265-267)gaT>gaC	p.D89D	UBE2F_ENST00000414443.1_Silent_p.D57D|UBE2F_ENST00000409633.1_Silent_p.D89D|UBE2F-SCLY_ENST00000449191.1_Silent_p.D89D|UBE2F_ENST00000409953.1_Silent_p.D65D|UBE2F_ENST00000409332.1_Silent_p.D67D	NM_001278305.1|NM_080678.2	NP_001265234.1|NP_542409.1	Q969M7	UBE2F_HUMAN	ubiquitin-conjugating enzyme E2F (putative)	89					protein neddylation (GO:0045116)		ATP binding (GO:0005524)|NEDD8 ligase activity (GO:0019788)			endometrium(1)|large_intestine(1)	2		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;6.7e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|Kidney(56;3.53e-09)|KIRC - Kidney renal clear cell carcinoma(57;9.79e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000136)|Lung(119;0.0126)|LUSC - Lung squamous cell carcinoma(224;0.0301)		AAGTTCCCGATGCGTACAACA	0.463																																					p.D89D		Atlas-SNP	.											.	UBE2F	11	.	0			c.T267C						.	T		0,4406		0,0,2203	139	143	142		267	-0.9	0.9	2	dbSNP_134	142	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	UBE2F	NM_080678.2		0,1,6502	CC,CT,TT		0.0116,0.0,0.0077		89/186	238925260	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	140739	exon5			TCCCGATGCGTAC	BC010549	CCDS2523.1, CCDS63175.1, CCDS63176.1, CCDS63177.1	2q37.3	2008-02-05	2005-12-15		ENSG00000184182	ENSG00000184182		"Ubiquitin-conjugating enzymes E2"	12480	protein-coding gene	gene with protein product	"NEDD8 conjugating enzyme"					12477932	Standard	NM_080678		Approved	NCE2	uc031rrz.1	Q969M7	OTTHUMG00000133341	ENST00000272930.4:c.267T>C	chr2.hg19:g.238925260T>C		94.0	0.0		79.0	19.0	NM_080678	A8K1Z8|B4DDT9|B4DFI1|B4DMK3|B4DZU2|B8ZZG2|C9J212|H9KVB9	Silent	SNP	ENST00000272930.4	hg19	CCDS2523.1																																																																																			.	T|1.000;C|0.000		0.463	UBE2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257171.2	NM_080678		C	238925260	T	C	238925260	2	2	167	1	0	0	0	0	0	0	0	1	16870	1461	51	2		2	UBE2F	2	238925260	Silent	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	18444390	238925260	4274113	28	25273										
IL17RE	132014	hgsc.bcm.edu	37	chr3	9955676	9955676	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cagtgtcactagacctcatcAttcccttcctgaggccaggg	9	14	3	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:9955676A>G	ENST00000383814.3	+	13	1369	c.1264A>G	c.(1264-1266)Att>Gtt	p.I422V	IL17RE_ENST00000454190.2_Missense_Mutation_p.I422V|IL17RE_ENST00000421412.1_Missense_Mutation_p.I455V|IL17RE_ENST00000295980.3_Missense_Mutation_p.I422V	NM_153480.1	NP_705613.1	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E	422					inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(11)|skin(1)	21				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		AGACCTCATCATTCCCTTCCT	0.577																																					p.I462V		Atlas-SNP	.											.	IL17RE	62	.	0			c.A1384G						.						148	141	143					3																	9955676		2203	4300	6503	SO:0001583	missense	132014	exon14			CTCATCATTCCCT	AF458069	CCDS2589.1, CCDS54552.1	3p25.3	2008-02-05			ENSG00000163701	ENSG00000163701		"Interleukins and interleukin receptors"	18439	protein-coding gene	gene with protein product		614995					Standard	NM_153480		Approved	FLJ23658	uc003btu.3	Q8NFR9	OTTHUMG00000128649	ENST00000383814.3:c.1264A>G	chr3.hg19:g.9955676A>G	ENSP00000373325:p.Ile422Val	95.0	0.0		122.0	63.0	NM_153483	B2RB34|B2RNR1|B9EH65|Q6P532|Q8N8H7|Q8N8H8|Q8TEC2	Missense_Mutation	SNP	ENST00000383814.3	hg19	CCDS2589.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.569411	0.28003	.	.	ENSG00000163701	ENST00000421412;ENST00000295980;ENST00000383814;ENST00000454190;ENST00000441648	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.32	1.39	0.22231	.	0.292675	0.28442	N	0.015335	T	0.06735	0.0172	N	0.17082	0.46	0.26253	N	0.978693	B;B	0.24721	0.11;0.006	B;B	0.20184	0.028;0.004	T	0.26710	-1.0095	10	0.44086	T	0.13	-3.4751	4.3306	0.11062	0.6412:0.1685:0.1903:0.0	.	422;422	Q8NFR9-3;Q8NFR9	.;I17RE_HUMAN	V	455;422;422;422;305	ENSP00000404916:I455V;ENSP00000295980:I422V;ENSP00000373325:I422V;ENSP00000388086:I422V	ENSP00000295980:I422V	I	+	1	0	IL17RE	9930676	1.000000	0.71417	0.958000	0.39756	0.781000	0.44180	0.725000	0.25970	0.084000	0.17077	0.459000	0.35465	ATT	.	.		0.577	IL17RE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250529.1	NM_153480		G	9955676	A	G	9955676	3	3	167	1	0	0	0	0	1	0	0	0	7652	217	8	2	1314	2	IL17RE	3	9955676	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10		9955676	188066754	29	25274										
DYNC1LI1	51143	hgsc.bcm.edu	37	chr3	32570073	32570073	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gttgaagaaatttgccagaaCgccttcacttgtagctccag	9	10	1	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:32570073C>A	ENST00000273130.4	-	12	1430	c.1327G>T	c.(1327-1329)Gtt>Ttt	p.V443F	DYNC1LI1_ENST00000432458.2_Missense_Mutation_p.V327F	NM_016141.3	NP_057225.2	Q9Y6G9	DC1L1_HUMAN	dynein, cytoplasmic 1, light intermediate chain 1	443					microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(1)|lung(3)|ovary(1)	7						TTTGCCAGAACGCCTTCACTT	0.413																																					p.V443F		Atlas-SNP	.											.	DYNC1LI1	23	.	0			c.G1327T						.						66	67	66					3																	32570073		2203	4300	6503	SO:0001583	missense	51143	exon12			CCAGAACGCCTTC	AF078849	CCDS2654.1	3p23	2013-01-18	2005-11-25	2005-11-25	ENSG00000144635	ENSG00000144635		"Cytoplasmic dyneins"	18745	protein-coding gene	gene with protein product		615890	"dynein, cytoplasmic, light intermediate polypeptide 1"	DNCLI1		16260502	Standard	NM_016141		Approved		uc003cfb.4	Q9Y6G9	OTTHUMG00000130750	ENST00000273130.4:c.1327G>T	chr3.hg19:g.32570073C>A	ENSP00000273130:p.Val443Phe	130.0	0.0		146.0	91.0	NM_016141	A2RRG7|Q53HC8|Q53HK7	Missense_Mutation	SNP	ENST00000273130.4	hg19	CCDS2654.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.432592	0.83776	.	.	ENSG00000144635	ENST00000273130;ENST00000432458	T;T	0.29917	1.55;1.55	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.63379	0.2506	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.67612	-0.5626	10	0.87932	D	0	-15.1813	19.975	0.97300	0.0:1.0:0.0:0.0	.	327;443	E9PHI6;Q9Y6G9	.;DC1L1_HUMAN	F	443;327	ENSP00000273130:V443F;ENSP00000407279:V327F	ENSP00000273130:V443F	V	-	1	0	DYNC1LI1	32545077	1.000000	0.71417	0.979000	0.43373	0.504000	0.33889	7.635000	0.83286	2.724000	0.93272	0.585000	0.79938	GTT	.	.		0.413	DYNC1LI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253250.1	NM_016141		A	32570073	C	A	32570073	3	1	167	1	0	0	0	0	1	0	0	0	4846	536	19	1	252	1	DYNC1LI1	3	32570073	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	22614397	32570073	165452357	30	25275										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	C													0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gcagcaacagtcttacctggActctggaatccattctggtg					rs121913396|rs121913416		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:41266098A>C	ENST00000349496.5	+	3	375	c.95A>C	c.(94-96)gAc>gCc	p.D32A	CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32A|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32A|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95C						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>C	chr3.hg19:g.41266098A>C	ENSP00000344456:p.Asp32Ala	148.0	1.0		161.0	10.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.218742	0.79464	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	M	0.79614	2.46	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	T	0.73949	-0.3821	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	A	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25A;ENSP00000385604:D32A;ENSP00000412219:D32A;ENSP00000379486:D32A;ENSP00000344456:D32A;ENSP00000411226:D25A;ENSP00000379488:D32A;ENSP00000409302:D32A;ENSP00000401599:D32A	ENSP00000344456:D32A	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266098	A	C	41266098	3	2	167	1	0	0	0	0	1	0	0	0	4018	275	10	5	101	5	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	8696025	41266098	156756332	31	25276	118	2								
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266101	41266101	+	Missense_Mutation	SNP	C	C	A													0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gcaacagtcttacctggactCtggaatccattctggtgcca					rs121913416|rs121913400		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:41266101C>A	ENST00000349496.5	+	3	378	c.98C>A	c.(97-99)tCt>tAt	p.S33Y	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33Y|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33Y|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26Y|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33Y	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33Y	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,359	CTNNB1	4904	.	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98A						.						92	77	82					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>A	chr3.hg19:g.41266101C>A	ENSP00000344456:p.Ser33Tyr	148.0	0.0		160.0	22.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.449496	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	Y	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26Y;ENSP00000385604:S33Y;ENSP00000412219:S33Y;ENSP00000379486:S33Y;ENSP00000344456:S33Y;ENSP00000411226:S26Y;ENSP00000379488:S33Y;ENSP00000409302:S33Y;ENSP00000401599:S33Y	ENSP00000344456:S33Y	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266101	C	A	41266101	3	1	167	1	0	0	0	0	1	0	0	0	4018	913	32	3	104	3	CTNNB1	3	41266101	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	3	41266101	156756329	32	25277	118	2								
MST1R	4486	hgsc.bcm.edu	37	chr3	49928959	49928959	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cattcgggtggttcaggccaCgcatgagcagcccctctcgc	12	15	2	1	rs140250708		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:49928959C>T	ENST00000296474.3	-	16	3434	c.3407G>A	c.(3406-3408)cGt>cAt	p.R1136H	MST1R_ENST00000344206.4_Missense_Mutation_p.R1087H	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	1136	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		GTTCAGGCCACGCATGAGCAG	0.607																																					p.R1136H		Atlas-SNP	.											.	MST1R	205	.	0			c.G3407A						.	C	HIS/ARG	1,4405		0,1,2202	96	88	91		3407	4.2	0.9	3	dbSNP_134	91	0,8600		0,0,4300	no	missense	MST1R	NM_002447.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	1136/1401	49928959	1,13005	2203	4300	6503	SO:0001583	missense	4486	exon16			AGGCCACGCATGA	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.3407G>A	chr3.hg19:g.49928959C>T	ENSP00000296474:p.Arg1136His	187.0	0.0		228.0	12.0	NM_002447	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	hg19	CCDS2807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	22.7|22.7	4.319341|4.319341	0.81469|0.81469	2.27E-4|2.27E-4	0.0|0.0	ENSG00000164078|ENSG00000164078	ENST00000296474;ENST00000344206|ENST00000434765;ENST00000440292	D;D|.	0.83250|.	-1.7;-1.7|.	5.08|5.08	4.21|4.21	0.49690|0.49690	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);|.	0.143218|.	0.56097|.	N|.	0.000034|.	T|T	0.36441|0.36441	0.0967|0.0967	N|N	0.17379|0.17379	0.485|0.485	0.42428|0.42428	D|D	0.992669|0.992669	P|.	0.52061|.	0.95|.	P|.	0.49012|.	0.598|.	T|T	0.15321|0.15321	-1.0441|-1.0441	10|5	0.87932|.	D|.	0|.	-13.1317|-13.1317	5.7738|5.7738	0.18267|0.18267	0.0:0.6801:0.0:0.3199|0.0:0.6801:0.0:0.3199	.|.	1136|.	Q04912|.	RON_HUMAN|.	H|M	1136;1087|114;157	ENSP00000296474:R1136H;ENSP00000341325:R1087H|.	ENSP00000296474:R1136H|.	R|V	-|-	2|1	0|0	MST1R|MST1R	49903963|49903963	1.000000|1.000000	0.71417|0.71417	0.872000|0.872000	0.34217|0.34217	0.935000|0.935000	0.57460|0.57460	5.844000|5.844000	0.69430|0.69430	1.408000|1.408000	0.46895|0.46895	0.632000|0.632000	0.83419|0.83419	CGT|GTG	.	C|1.000;T|0.000		0.607	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			T	49928959	C	T	49928959	3	4	167	1	0	0	0	0	1	0	0	0	9900	536	19	1	815	1	MST1R	3	49928959	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	8662858	49928959	148093471	33	25278										
CADPS	8618	hgsc.bcm.edu	37	chr3	62648033	62648033	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tagacgtccatccagctctcGtctgatctgggctgcttgct	10	13	3	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:62648033G>A	ENST00000383710.4	-	4	1274	c.925C>T	c.(925-927)Cga>Tga	p.R309*	CADPS_ENST00000283269.9_Nonsense_Mutation_p.R309*|CADPS_ENST00000357948.3_Nonsense_Mutation_p.R309*|CADPS_ENST00000490353.2_Nonsense_Mutation_p.R309*	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	309					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TCCAGCTCTCGTCTGATCTGG	0.493																																					p.R309X		Atlas-SNP	.											.	CADPS	387	.	0			c.C925T						.						165	136	146					3																	62648033		2203	4300	6503	SO:0001587	stop_gained	8618	exon4			GCTCTCGTCTGAT	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.925C>T	chr3.hg19:g.62648033G>A	ENSP00000373215:p.Arg309*	61.0	0.0		65.0	34.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Nonsense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	G	40	8.385425	0.98789	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000490353	.	.	.	5.54	3.67	0.42095	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4533	0.61184	0.0:0.0:0.7136:0.2864	.	.	.	.	X	309	.	ENSP00000283269:R309X	R	-	1	2	CADPS	62623073	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.924000	0.48876	0.643000	0.30638	0.655000	0.94253	CGA	.	.		0.493	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		A	62648033	G	A	62648033	4	1	167	1	0	0	0	0	0	1	0	0	2572	1153	40	1	3317	1	CADPS	3	62648033	Nonsense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	12719074	62648033	135374397	34	25279										
HHLA2	11148	hgsc.bcm.edu	37	chr3	108076940	108076940	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggatcttaatctttcagacaGtggggaatatttatgcaata	9	5	3	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:108076940G>A	ENST00000357759.5	+	6	1349	c.935G>A	c.(934-936)aGt>aAt	p.S312N	HHLA2_ENST00000489514.2_Missense_Mutation_p.S312N|HHLA2_ENST00000491820.1_Missense_Mutation_p.S312N|HHLA2_ENST00000467562.1_Missense_Mutation_p.S248N|HHLA2_ENST00000467761.1_Missense_Mutation_p.S312N	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	312	Ig-like V-type 2.				positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						CTTTCAGACAGTGGGGAATAT	0.353																																					p.S312N		Atlas-SNP	.											.	HHLA2	95	.	0			c.G935A						.						109	107	107					3																	108076940		1851	4086	5937	SO:0001583	missense	11148	exon6			CAGACAGTGGGGA	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.935G>A	chr3.hg19:g.108076940G>A	ENSP00000350402:p.Ser312Asn	118.0	0.0		89.0	50.0	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Missense_Mutation	SNP	ENST00000357759.5	hg19	CCDS46883.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.848160	0.32699	.	.	ENSG00000114455	ENST00000491820;ENST00000467562;ENST00000357759;ENST00000467761;ENST00000489514	T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47	5.06	1.64	0.23874	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.192281	0.25783	N	0.028326	T	0.50343	0.1610	L	0.27053	0.805	0.21675	N	0.999598	B;B;B	0.31256	0.316;0.316;0.316	B;B;B	0.32022	0.139;0.139;0.139	T	0.29212	-1.0019	10	0.22706	T	0.39	-15.1011	5.6397	0.17557	0.414:0.0:0.586:0.0	.	248;312;312	B4DKN2;C9J7D0;Q9UM44	.;.;HHLA2_HUMAN	N	312;248;312;312;312	ENSP00000418284:S312N;ENSP00000418345:S248N;ENSP00000350402:S312N;ENSP00000419207:S312N;ENSP00000417856:S312N	ENSP00000350402:S312N	S	+	2	0	HHLA2	109559630	0.951000	0.32395	0.966000	0.40874	0.432000	0.31715	-0.119000	0.10676	0.590000	0.29694	0.650000	0.86243	AGT	.	.		0.353	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072		A	108076940	G	A	108076940	3	1	167	1	0	0	0	0	1	0	0	0	7104	1029	36	3	949	3	HHLA2	3	108076940	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	45428907	108076940	89945490	35	25280										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121410144	121410144	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gcatcatgatgaagatgcttTaattctttcttcagtttatc	6	7	4	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:121410144T>C	ENST00000340645.5	-	14	8177	c.8052A>G	c.(8050-8052)ttA>ttG	p.L2684L	GOLGB1_ENST00000393667.3_Silent_p.L2689L	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2684					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		GAAGATGCTTTAATTCTTTCT	0.393																																					p.L2689L		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A8067G						.						223	225	225					3																	121410144		2203	4300	6503	SO:0001819	synonymous_variant	2804	exon14			ATGCTTTAATTCT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.8052A>G	chr3.hg19:g.121410144T>C		72.0	0.0		75.0	24.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Silent	SNP	ENST00000340645.5	hg19	CCDS3004.1																																																																																			.	.		0.393	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121410144	T	C	121410144	2	2	167	1	0	0	0	0	0	0	0	1	6573	1751	61	2		2	GOLGB1	3	121410144	Silent	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	13333204	121410144	76612286	36	25281										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121417563	121417563	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctcaccctccatctgtttcaTttctttctggtcaaggacct	5	14	6	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:121417563T>C	ENST00000340645.5	-	13	1917	c.1792A>G	c.(1792-1794)Atg>Gtg	p.M598V	GOLGB1_ENST00000393667.3_Missense_Mutation_p.M603V	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	598					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		ATCTGTTTCATTTCTTTCTGG	0.403																																					p.M603V		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A1807G						.						90	93	92					3																	121417563		2203	4299	6502	SO:0001583	missense	2804	exon13			GTTTCATTTCTTT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.1792A>G	chr3.hg19:g.121417563T>C	ENSP00000341848:p.Met598Val	139.0	0.0		126.0	34.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	7.353	0.623191	0.14193	.	.	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235	T;T;T	0.19669	2.71;2.71;2.13	5.32	-1.33	0.09172	.	0.469306	0.20838	N	0.084751	T	0.09335	0.0230	N	0.17674	0.51	0.26262	N	0.978568	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.001;0.002;0.001;0.001;0.001	T	0.18808	-1.0325	10	0.28530	T	0.3	.	3.3626	0.07192	0.27:0.2274:0.0:0.5025	.	523;562;603;603;598	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789	.;.;.;.;GOGB1_HUMAN	V	598;603;562;410	ENSP00000341848:M598V;ENSP00000377275:M603V;ENSP00000418231:M562V	ENSP00000341848:M598V	M	-	1	0	GOLGB1	122900253	0.000000	0.05858	0.121000	0.21740	0.956000	0.61745	-0.556000	0.05992	-0.364000	0.08088	0.533000	0.62120	ATG	.	.		0.403	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121417563	T	C	121417563	3	2	167	1	0	0	0	0	1	0	0	0	6573	1493	52	2	8027	2	GOLGB1	3	121417563	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	7419	121417563	76604867	37	25282										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130098644	130098644	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tggtcacccacagaccatcaGatgatgaggtgcatgatgct	11	10	2	5			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:130098644G>T	ENST00000432398.2	+	4	1545	c.1051G>T	c.(1051-1053)Gat>Tat	p.D351Y	COL6A5_ENST00000265379.6_Missense_Mutation_p.D351Y	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	351	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						CAGACCATCAGATGATGAGGT	0.488																																					p.D351Y		Atlas-SNP	.											.	COL6A5	205	.	0			c.G1051T						.						127	110	115					3																	130098644		692	1591	2283	SO:0001583	missense	256076	exon4			CCATCAGATGATG	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.1051G>T	chr3.hg19:g.130098644G>T	ENSP00000390895:p.Asp351Tyr	184.0	0.0		227.0	64.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.	.	.	.	.	.	.	.	.	.	G	10.75	1.439338	0.25900	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.78816	-1.21;-1.21	5.34	3.56	0.40772	.	.	.	.	.	T	0.75436	0.3849	N	0.24115	0.695	0.09310	N	1	D	0.57571	0.98	P	0.58721	0.844	T	0.63985	-0.6513	9	0.59425	D	0.04	.	8.3447	0.32266	0.2459:0.0:0.7541:0.0	.	351	A8TX70-2	.	Y	351	ENSP00000390895:D351Y;ENSP00000265379:D351Y	ENSP00000265379:D351Y	D	+	1	0	COL6A5	131581334	0.000000	0.05858	0.001000	0.08648	0.797000	0.45037	0.619000	0.24388	0.641000	0.30601	0.455000	0.32223	GAT	.	.		0.488	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		T	130098644	G	T	130098644	3	4	167	1	0	0	0	0	1	0	0	0	3704	942	33	3	1061	3	COL6A5	3	130098644	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	8681081	130098644	67923786	38	25283										
COPB2	9276	hgsc.bcm.edu	37	chr3	139096979	139096979	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgggtgtgtccttcaaacacTtgtgagcaagaccatttttt	9	8	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:139096979T>C	ENST00000333188.5	-	5	589	c.408A>G	c.(406-408)caA>caG	p.Q136Q	COPB2_ENST00000510491.1_5'Flank|COPB2_ENST00000507777.1_Silent_p.Q107Q	NM_004766.2	NP_004757.1	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta prime)	136					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	24						CTTCAAACACTTGTGAGCAAG	0.393																																					p.Q136Q		Atlas-SNP	.											.	COPB2	80	.	0			c.A408G						.						252	230	238					3																	139096979		2203	4300	6503	SO:0001819	synonymous_variant	9276	exon5			AAACACTTGTGAG	BC000326	CCDS3108.1	3q23	2013-01-10			ENSG00000184432	ENSG00000184432		"WD repeat domain containing"	2232	protein-coding gene	gene with protein product		606990				9858824	Standard	NM_004766		Approved	beta'-COP, betaprime-COP	uc003etf.4	P35606	OTTHUMG00000159959	ENST00000333188.5:c.408A>G	chr3.hg19:g.139096979T>C		128.0	0.0		142.0	28.0	NM_004766	B4DZI8	Silent	SNP	ENST00000333188.5	hg19	CCDS3108.1																																																																																			.	.		0.393	COPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358495.2	NM_004766		C	139096979	T	C	139096979	2	2	167	1	0	0	0	0	0	0	0	1	3731	1606	56	2		2	COPB2	3	139096979	Silent	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	8998335	139096979	58925451	39	25284										
SI	6476	hgsc.bcm.edu	37	chr3	164783108	164783108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tttccaggataaatcatgacGaaatctcttatgaacttgtt	6	7	2	2	rs200745562		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:164783108G>A	ENST00000264382.3	-	7	810	c.748C>T	c.(748-750)Cgt>Tgt	p.R250C		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	250	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.R250C(2)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	AAATCATGACGAAATCTCTTA	0.343										HNSCC(35;0.089)																											p.R250C		Atlas-SNP	.											SI,colon,carcinoma,0,2	SI	500	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.C748T						.						76	75	75					3																	164783108		2203	4300	6503	SO:0001583	missense	6476	exon7			CATGACGAAATCT	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.748C>T	chr3.hg19:g.164783108G>A	ENSP00000264382:p.Arg250Cys	291.0	0.0		239.0	88.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	hg19	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035583	0.75617	.	.	ENSG00000090402	ENST00000264382	D	0.90955	-2.76	5.9	5.9	0.94986	Glycoside hydrolase-type carbohydrate-binding (1);	0.105792	0.64402	D	0.000003	D	0.97049	0.9036	H	0.97540	4.025	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	D	0.97789	1.0237	10	0.72032	D	0.01	.	14.5224	0.67859	0.0:0.0:0.7337:0.2663	.	250	P14410	SUIS_HUMAN	C	250	ENSP00000264382:R250C	ENSP00000264382:R250C	R	-	1	0	SI	166265802	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.105000	0.57797	2.788000	0.95919	0.650000	0.86243	CGT	.	.		0.343	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		A	164783108	G	A	164783108	3	1	167	1	0	0	0	0	1	0	0	0	14312	1058	37	1	4903	1	SI	3	164783108	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	25686129	164783108	33239322	40	25285										
SPATA16	83893	hgsc.bcm.edu	37	chr3	172834953	172834953	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctgctgccaaggcgtatttcTtttgtctatagcaagagctg	10	9	2	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr3:172834953T>C	ENST00000351008.3	-	2	752	c.569A>G	c.(568-570)aAg>aGg	p.K190R		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	190					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			GGCGTATTTCTTTTGTCTATA	0.408																																					p.K190R		Atlas-SNP	.											.	SPATA16	111	.	0			c.A569G						.						145	142	143					3																	172834953		2203	4300	6503	SO:0001583	missense	83893	exon2			TATTTCTTTTGTC	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.569A>G	chr3.hg19:g.172834953T>C	ENSP00000341765:p.Lys190Arg	112.0	0.0		117.0	63.0	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	hg19	CCDS3221.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.181172	0.78677	.	.	ENSG00000144962	ENST00000351008	T	0.77877	-1.13	5.7	5.7	0.88788	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000008	T	0.81880	0.4916	L	0.29908	0.895	0.33536	D	0.594221	D	0.89917	1.0	D	0.85130	0.997	D	0.87240	0.2266	10	0.87932	D	0	-18.3896	14.1991	0.65690	0.0:0.0:0.0:1.0	.	190	Q9BXB7	SPT16_HUMAN	R	190	ENSP00000341765:K190R	ENSP00000341765:K190R	K	-	2	0	SPATA16	174317647	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.714000	0.68422	2.162000	0.67917	0.528000	0.53228	AAG	.	.		0.408	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955		C	172834953	T	C	172834953	3	2	167	1	0	0	0	0	1	0	0	0	15016	1609	56	2	1180	2	SPATA16	3	172834953	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	8051845	172834953	25187477	41	25286										
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15589442	15589442	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ttttttctttttgtcagcaaTttcttgatctcctggcaggg	8	8	4	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr4:15589442T>C	ENST00000503292.1	+	33	4249	c.4069T>C	c.(4069-4071)Ttt>Ctt	p.F1357L	CC2D2A_ENST00000424120.1_Missense_Mutation_p.F1357L|CC2D2A_ENST00000389652.5_Missense_Mutation_p.F1249L|CC2D2A_ENST00000413206.1_Missense_Mutation_p.F1357L	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	1357					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						TTGTCAGCAATTTCTTGATCT	0.388																																					p.F1357L		Atlas-SNP	.											.,2	CC2D2A	158	.	0			c.T4069C						.						72	66	68					4																	15589442		1852	4099	5951	SO:0001583	missense	57545	exon33			CAGCAATTTCTTG	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.4069T>C	chr4.hg19:g.15589442T>C	ENSP00000421809:p.Phe1357Leu	37.0	0.0		33.0	15.0	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Missense_Mutation	SNP	ENST00000503292.1	hg19	CCDS47026.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.485738	0.84854	.	.	ENSG00000048342	ENST00000424120;ENST00000413206;ENST00000426932;ENST00000510333;ENST00000503292;ENST00000389652	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	5.8	5.8	0.92144	.	0.103416	0.64402	D	0.000002	D	0.84584	0.5504	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;0.964	D;P	0.91635	0.999;0.83	D	0.85048	0.0927	10	0.44086	T	0.13	.	16.1498	0.81605	0.0:0.0:0.0:1.0	.	1357;1249	Q9P2K1;Q9P2K1-2	C2D2A_HUMAN;.	L	1357;1357;1249;1249;1357;1249	ENSP00000403465:F1357L;ENSP00000398391:F1357L;ENSP00000421809:F1357L;ENSP00000374303:F1249L	ENSP00000374303:F1249L	F	+	1	0	CC2D2A	15198540	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	8.040000	0.89188	2.218000	0.71995	0.377000	0.23210	TTT	.	.		0.388	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		C	15589442	T	C	15589442	3	2	167	1	0	0	0	0	1	0	0	0	2730	1493	52	2	4394	2	CC2D2A	4	15589442	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10		15589442	175564834	42	25287										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30921954	30921954	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aactatgaaaggaccacgccGgatggcagtgttggtgaggc	15	8	0	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr4:30921954G>T	ENST00000543491.1	+	2	3354	c.3354G>T	c.(3352-3354)ccG>ccT	p.P1118P	PCDH7_ENST00000509925.1_3'UTR			O60245	PCDH7_HUMAN	protocadherin 7	0					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						GGACCACGCCGGATGGCAGTG	0.527																																					p.P1118P		Atlas-SNP	.											.	PCDH7	215	.	0			c.G3354T						.						68	73	71					4																	30921954		2185	4291	6476	SO:0001819	synonymous_variant	5099	exon2			CACGCCGGATGGC	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000543491.1:c.3354G>T	chr4.hg19:g.30921954G>T		90.0	0.0		82.0	31.0	NM_032457	O60246|O60247|Q4W5C4	Silent	SNP	ENST00000543491.1	hg19	CCDS54753.1	.	.	.	.	.	.	.	.	.	.	G	8.324	0.825034	0.16678	.	.	ENSG00000169851	ENST00000511884	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4661	0.61254	0.0709:0.0:0.9291:0.0	.	.	.	.	X	808	.	.	G	+	1	0	PCDH7	30531052	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	4.477000	0.60223	2.788000	0.95919	0.650000	0.86243	GGA	.	.		0.527	PCDH7-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032457, NM_002589		T	30921954	G	T	30921954	2	4	167	1	0	0	0	0	0	0	0	1	11525	1103	39	1		1	PCDH7	4	30921954	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	15332512	30921954	160232322	43	25288										
PPAT	5471	hgsc.bcm.edu	37	chr4	57261616	57261616	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	atttccattttcttggatcaTaatatcgtgctttttctctt	4	8	3	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr4:57261616T>G	ENST00000264220.2	-	11	1593	c.1456A>C	c.(1456-1458)Atg>Ctg	p.M486L	RP11-646I6.6_ENST00000602749.1_lincRNA	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	486					'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	TCTTGGATCATAATATCGTGC	0.363																																					p.M486L		Atlas-SNP	.											.	PPAT	41	.	0			c.A1456C						.						105	100	102					4																	57261616		2203	4300	6503	SO:0001583	missense	5471	exon11			GGATCATAATATC		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.1456A>C	chr4.hg19:g.57261616T>G	ENSP00000264220:p.Met486Leu	275.0	0.0		192.0	66.0	NM_002703		Missense_Mutation	SNP	ENST00000264220.2	hg19	CCDS3505.1	.	.	.	.	.	.	.	.	.	.	T	0.183	-1.060553	0.01950	.	.	ENSG00000128059	ENST00000264220	.	.	.	4.68	-0.779	0.10973	.	1.077110	0.07182	N	0.854195	T	0.26304	0.0642	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24693	-1.0153	9	0.23891	T	0.37	0.0837	7.4708	0.27347	0.0:0.3997:0.0:0.6003	.	486	Q06203	PUR1_HUMAN	L	486	.	ENSP00000264220:M486L	M	-	1	0	PPAT	56956373	0.100000	0.21855	0.009000	0.14445	0.191000	0.23601	-0.231000	0.09069	-0.044000	0.13491	-0.263000	0.10527	ATG	.	.		0.363	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		G	57261616	T	G	57261616	3	3	167	1	0	0	0	0	1	0	0	0	12311	1406	49	5	101	5	PPAT	4	57261616	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	26339662	57261616	133892660	44	25289										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62845284	62845284	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tttcattgtgtttccagcacAgtgatgcggtccatgacctc	9	11	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr4:62845284A>G	ENST00000514591.1	+	17	2934	c.2605A>G	c.(2605-2607)Agt>Ggt	p.S869G	LPHN3_ENST00000512091.2_Missense_Mutation_p.S869G|LPHN3_ENST00000509896.1_Missense_Mutation_p.S937G|LPHN3_ENST00000504896.1_Missense_Mutation_p.S869G|LPHN3_ENST00000508693.1_Missense_Mutation_p.S937G|LPHN3_ENST00000514996.1_Missense_Mutation_p.S869G|LPHN3_ENST00000506720.1_Missense_Mutation_p.S937G|LPHN3_ENST00000508946.1_Missense_Mutation_p.S869G|LPHN3_ENST00000506746.1_Missense_Mutation_p.S937G|LPHN3_ENST00000514157.1_Missense_Mutation_p.S869G|LPHN3_ENST00000545650.1_Missense_Mutation_p.S869G|LPHN3_ENST00000507164.1_Missense_Mutation_p.S937G|LPHN3_ENST00000506700.1_Missense_Mutation_p.S869G|LPHN3_ENST00000511324.1_Missense_Mutation_p.S937G|LPHN3_ENST00000507625.1_Missense_Mutation_p.S937G			Q9HAR2	LPHN3_HUMAN	latrophilin 3	856					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						TTTCCAGCACAGTGATGCGGT	0.408																																					p.S869G		Atlas-SNP	.											.	LPHN3	800	.	0			c.A2605G						.						260	248	252					4																	62845284		1952	4157	6109	SO:0001583	missense	23284	exon15			CAGCACAGTGATG	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.2605A>G	chr4.hg19:g.62845284A>G	ENSP00000422533:p.Ser869Gly	124.0	0.0		104.0	39.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.864|8.864	0.947569|0.947569	0.18356|0.18356	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000502815|ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.71934	.|-0.59;-0.59;-0.61;-0.6;-0.58;-0.59;-0.59;-0.6;-0.58;-0.58;-0.59;-0.59;-0.59;-0.58;-0.57	5.5|5.5	4.32|4.32	0.51571|0.51571	.|.	.|0.292182	.|0.38778	.|N	.|0.001574	T|T	0.46870|0.46870	0.1415|0.1415	N|N	0.12853|0.12853	0.265|0.265	0.32366|0.32366	N|N	0.556455|0.556455	.|B;B;B	.|0.06786	.|0.001;0.001;0.001	.|B;B;B	.|0.04013	.|0.001;0.001;0.001	T|T	0.45308|0.45308	-0.9270|-0.9270	5|10	.|0.24483	.|T	.|0.36	.|.	5.4275|5.4275	0.16433|0.16433	0.6991:0.1483:0.1527:0.0|0.6991:0.1483:0.1527:0.0	.|.	.|869;856;869	.|E9PE04;Q9HAR2;Q9HAR2-2	.|.;LPHN3_HUMAN;.	R|G	326|869;869;937;937;869;869;856;869;937;937;937;869;869;869;937;937;869	.|ENSP00000423388:S869G;ENSP00000422533:S869G;ENSP00000423787:S937G;ENSP00000425033:S937G;ENSP00000424120:S869G;ENSP00000439831:S869G;ENSP00000421476:S937G;ENSP00000424030:S937G;ENSP00000421372:S937G;ENSP00000425201:S869G;ENSP00000423434:S869G;ENSP00000421627:S869G;ENSP00000420931:S937G;ENSP00000425884:S937G;ENSP00000424258:S869G	.|ENSP00000280009:S869G	Q|S	+|+	2|1	0|0	LPHN3|LPHN3	62527879|62527879	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.876000|0.876000	0.50452|0.50452	1.872000|1.872000	0.39549|0.39549	0.918000|0.918000	0.36919|0.36919	0.383000|0.383000	0.25322|0.25322	CAG|AGT	.	.		0.408	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			G	62845284	A	G	62845284	3	3	167	1	0	0	0	0	1	0	0	0	8926	188	7	2	2663	2	LPHN3	4	62845284	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	5583668	62845284	128308992	45	25290										
UGT2B4	7363	hgsc.bcm.edu	37	chr4	70361015	70361018	+	Frame_Shift_Del	DEL	ACAG	ACAG	-													0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aggcacataggaaggagggaAcagaagtcctccactatgct							TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	ACAG	ACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr4:70361015_70361018delACAG	ENST00000305107.6	-	1	608_611	c.562_565delCTGT	c.(562-567)ctgttcfs	p.LF188fs	UGT2B4_ENST00000381096.3_Frame_Shift_Del_p.LF52fs|UGT2B4_ENST00000506580.1_Intron|UGT2B4_ENST00000512583.1_Frame_Shift_Del_p.LF188fs	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	188					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	GAAGGAGGGAACAGAAGTCCTCCA	0.426																																					p.188_189del		Atlas-INDEL	.											.	UGT2B4	105	.	0			c.563_566del						.																																			SO:0001589	frameshift_variant	7363	exon1			.	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"UDP glucuronosyltransferases"	12553	protein-coding gene	gene with protein product		600067	"UDP glycosyltransferase 2 family, polypeptide B4"			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.562_565delCTGT	chr4.hg19:g.70361015_70361018delACAG	ENSP00000305221:p.Leu188fs	170.0	0.0		126.0	42.0	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Frame_Shift_Del	DEL	ENST00000305107.6	hg19	CCDS43234.1																																																																																			.	.		0.426	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139		-	70361018	ACAG	-	70361015	7	5	167	1	0	1	0	1	0	0	0	0	16976	43	2	0	1045	0	UGT2B4	4	70361015	Frame_Shift_Del	DEL	ACAG	TCGA-DD-AACP-01A-11D-A40R-10	7515731	70361015	120793261	46	25291										
ARHGAP24	83478	hgsc.bcm.edu	37	chr4	86916340	86916340	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ccaaatggctatgtgaccctGagggataacaagcagaaaga	11	8	0	4			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr4:86916340G>C	ENST00000395184.1	+	9	1999	c.1533G>C	c.(1531-1533)ctG>ctC	p.L511L	ARHGAP24_ENST00000264343.4_Silent_p.L418L|ARHGAP24_ENST00000395183.2_Silent_p.L416L	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	511					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		ATGTGACCCTGAGGGATAACA	0.488																																					p.L511L		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.G1533C						.						122	111	115					4																	86916340		2203	4300	6503	SO:0001819	synonymous_variant	83478	exon9			GACCCTGAGGGAT	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.1533G>C	chr4.hg19:g.86916340G>C		135.0	0.0		100.0	42.0	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Silent	SNP	ENST00000395184.1	hg19	CCDS34025.1																																																																																			.	.		0.488	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		C	86916340	G	C	86916340	2	2	167	1	0	0	0	0	0	0	0	1	873	1277	45	4		4	ARHGAP24	4	86916340	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	16555325	86916340	104237936	47	25292										
GAB1	2549	hgsc.bcm.edu	37	chr4	144359564	144359564	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gacagacatcaaagctagacActattccagatattcctcca	5	12	1	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr4:144359564A>T	ENST00000262994.4	+	4	1308	c.1006A>T	c.(1006-1008)Act>Tct	p.T336S	GAB1_ENST00000262995.4_Missense_Mutation_p.T336S|GAB1_ENST00000505913.1_Missense_Mutation_p.T233S	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	336					activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					AAAGCTAGACACTATTCCAGA	0.473																																					p.T336S		Atlas-SNP	.											.	GAB1	80	.	0			c.A1006T						.						147	122	131					4																	144359564		2203	4300	6503	SO:0001583	missense	2549	exon4			CTAGACACTATTC	U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"Pleckstrin homology (PH) domain containing"	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.1006A>T	chr4.hg19:g.144359564A>T	ENSP00000262994:p.Thr336Ser	102.0	0.0		79.0	44.0	NM_207123	A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	ENST00000262994.4	hg19	CCDS3759.1	.	.	.	.	.	.	.	.	.	.	A	9.958	1.222107	0.22457	.	.	ENSG00000109458	ENST00000262995;ENST00000262994;ENST00000505913	T;T;T	0.16897	2.31;2.31;2.31	5.8	-5.18	0.02840	.	0.700955	0.15342	N	0.267467	T	0.05227	0.0139	N	0.16903	0.455	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.38607	-0.9653	10	0.08381	T	0.77	-0.7723	0.6661	0.00851	0.3476:0.1057:0.2393:0.3075	.	336;336	Q13480;Q13480-2	GAB1_HUMAN;.	S	336;336;233	ENSP00000262995:T336S;ENSP00000262994:T336S;ENSP00000424554:T233S	ENSP00000262994:T336S	T	+	1	0	GAB1	144579014	0.994000	0.37717	0.074000	0.20217	0.476000	0.33039	0.684000	0.25364	-0.797000	0.04450	-0.290000	0.09829	ACT	.	.		0.473	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039		T	144359564	A	T	144359564	3	4	167	1	0	0	0	0	1	0	0	0	6156	159	6	4	1020	4	GAB1	4	144359564	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	57443224	144359564	46794712	48	25293										
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109065183	109065183	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tttcaaagtggtgggatattAtagatattcagaagaaggat	11	2	2	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr5:109065183A>G	ENST00000261483.4	+	4	1728	c.676A>G	c.(676-678)Ata>Gta	p.I226V		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	226					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		GTGGGATATTATAGATATTCA	0.303																																					p.I226V		Atlas-SNP	.											.	MAN2A1	136	.	0			c.A676G						.						97	100	99					5																	109065183		2202	4300	6502	SO:0001583	missense	4124	exon4			GATATTATAGATA		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.676A>G	chr5.hg19:g.109065183A>G	ENSP00000261483:p.Ile226Val	97.0	0.0		108.0	32.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	A	17.08	3.297623	0.60086	.	.	ENSG00000112893	ENST00000261483	T	0.21932	1.98	5.83	5.83	0.93111	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.000000	0.85682	D	0.000000	T	0.29321	0.0730	L	0.46157	1.445	0.53688	D	0.999975	B	0.33379	0.41	P	0.45276	0.475	T	0.04229	-1.0967	10	0.17369	T	0.5	-23.5895	16.1982	0.82046	1.0:0.0:0.0:0.0	.	226	Q16706	MA2A1_HUMAN	V	226	ENSP00000261483:I226V	ENSP00000261483:I226V	I	+	1	0	MAN2A1	109093082	1.000000	0.71417	0.988000	0.46212	0.993000	0.82548	3.722000	0.54948	2.226000	0.72624	0.533000	0.62120	ATA	.	.		0.303	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			G	109065183	A	G	109065183	3	3	167	1	0	0	0	0	1	0	0	0	9223	449	16	2	690	2	MAN2A1	5	109065183	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10		109065183	71850077	49	25294										
KCNN2	3781	hgsc.bcm.edu	37	chr5	113798873	113798873	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gtggaaaaggagtctgcttaCttactggaattatggtaagt	12	4	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr5:113798873C>G	ENST00000512097.3	+	5	2147	c.1129C>G	c.(1129-1131)Ctt>Gtt	p.L377V	KCNN2_ENST00000264773.3_Missense_Mutation_p.L377V|KCNN2_ENST00000507750.1_3'UTR|KCNN2_ENST00000503706.1_Missense_Mutation_p.L29V			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	377					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	AGTCTGCTTACTTACTGGAAT	0.388																																					p.L377V		Atlas-SNP	.											.	KCNN2	144	.	0			c.C1129G						.						256	217	230					5																	113798873		2202	4300	6502	SO:0001583	missense	3781	exon4			TGCTTACTTACTG	AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.1129C>G	chr5.hg19:g.113798873C>G	ENSP00000427120:p.Leu377Val	106.0	0.0		98.0	19.0	NM_021614	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Missense_Mutation	SNP	ENST00000512097.3	hg19	CCDS4114.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.180657	0.57800	.	.	ENSG00000080709	ENST00000512097;ENST00000264773;ENST00000503706	T;T;T	0.27890	1.64;1.64;1.64	5.63	5.63	0.86233	Ion transport 2 (1);	0.000000	0.85682	D	0.000000	T	0.42494	0.1205	L	0.48877	1.53	0.80722	D	1	P	0.45474	0.859	P	0.51777	0.679	T	0.03403	-1.1040	10	0.31617	T	0.26	-2.5274	19.2915	0.94102	0.0:1.0:0.0:0.0	.	377	Q9H2S1	KCNN2_HUMAN	V	377;377;29	ENSP00000427120:L377V;ENSP00000264773:L377V;ENSP00000421439:L29V	ENSP00000264773:L377V	L	+	1	0	KCNN2	113826772	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.684000	0.84104	2.658000	0.90341	0.561000	0.74099	CTT	.	.		0.388	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614		G	113798873	C	G	113798873	3	3	167	1	0	0	0	0	1	0	0	0	8088	565	20	4	1143	4	KCNN2	5	113798873	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	4733690	113798873	67116387	50	25295										
PSD2	84249	hgsc.bcm.edu	37	chr5	139218319	139218319	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gctccatgaagaagttctgtCggcccctgctgccctcctgc	10	16	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr5:139218319C>T	ENST00000274710.3	+	13	2135	c.1930C>T	c.(1930-1932)Cgg>Tgg	p.R644W		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	644					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGTTCTGTCGGCCCCTGCT	0.617																																					p.R644W		Atlas-SNP	.											.	PSD2	88	.	0			c.C1930T						.						56	53	54					5																	139218319		2203	4300	6503	SO:0001583	missense	84249	exon13			TTCTGTCGGCCCC	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1930C>T	chr5.hg19:g.139218319C>T	ENSP00000274710:p.Arg644Trp	134.0	0.0		161.0	32.0	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150491	0.78001	.	.	ENSG00000146005	ENST00000274710	T	0.80566	-1.39	5.06	4.14	0.48551	.	0.000000	0.85682	D	0.000000	D	0.89832	0.6829	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	D	0.91268	0.5042	10	0.87932	D	0	.	13.3135	0.60394	0.2704:0.7296:0.0:0.0	.	644	Q9BQI7	PSD2_HUMAN	W	644	ENSP00000274710:R644W	ENSP00000274710:R644W	R	+	1	2	PSD2	139198503	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.851000	0.48302	2.514000	0.84764	0.561000	0.74099	CGG	.	.		0.617	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139218319	C	T	139218319	3	4	167	1	0	0	0	0	1	0	0	0	12659	875	31	1	1976	1	PSD2	5	139218319	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	25419446	139218319	41696941	51	25296										
PCDHGA9	56107	hgsc.bcm.edu	37	chr5	140783284	140783284	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gttaaagtccttgagaacgtGcccccaggcacctggctgct	11	13	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr5:140783284G>T	ENST00000573521.1	+	1	765	c.765G>T	c.(763-765)gtG>gtT	p.V255V	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	255	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGAGAACGTGCCCCCAGGCA	0.473																																					p.V255V		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.G765T						.						48	53	51					5																	140783284		1935	4128	6063	SO:0001819	synonymous_variant	56107	exon1			GAACGTGCCCCCA	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.765G>T	chr5.hg19:g.140783284G>T		170.0	0.0		172.0	110.0	NM_032089	A2RU65|Q9Y5C9	Silent	SNP	ENST00000573521.1	hg19	CCDS58981.1																																																																																			.	.		0.473	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921		T	140783284	G	T	140783284	2	4	167	1	0	0	0	0	0	0	0	1	11570	1306	46	3		3	PCDHGA9	5	140783284	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	1564965	140783284	40131976	52	25297										
WWC1	23286	hgsc.bcm.edu	37	chr5	167826554	167826554	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gctgcagttcaaagagcgtgGctttcagaccctgaagaagt	12	9	2	4			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr5:167826554G>A	ENST00000265293.4	+	5	1074	c.572G>A	c.(571-573)gGc>gAc	p.G191D	WWC1_ENST00000521089.1_Missense_Mutation_p.G191D	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	191					cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		AAAGAGCGTGGCTTTCAGACC	0.582																																					p.G191D		Atlas-SNP	.											.	WWC1	98	.	0			c.G572A						.						99	88	92					5																	167826554		2203	4300	6503	SO:0001583	missense	23286	exon5			AGCGTGGCTTTCA	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.572G>A	chr5.hg19:g.167826554G>A	ENSP00000265293:p.Gly191Asp	251.0	0.0		246.0	52.0	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	hg19	CCDS4366.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.0|25.0	4.588451|4.588451	0.86851|0.86851	.|.	.|.	ENSG00000113645|ENSG00000113645	ENST00000265293;ENST00000521089|ENST00000393895	T;T|.	0.42900|.	1.02;0.96|.	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	0.068675|.	0.64402|.	D|.	0.000019|.	T|.	0.78984|.	0.4370|.	M|M	0.85197|0.85197	2.74|2.74	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;0.999|.	T|.	0.81366|.	-0.0965|.	10|.	0.56958|.	D|.	0.05|.	.|.	15.7065|15.7065	0.77588|0.77588	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	191;97;191|.	Q8IX03-2;B3KX05;Q8IX03|.	.;.;KIBRA_HUMAN|.	D|X	191|152	ENSP00000265293:G191D;ENSP00000427772:G191D|.	ENSP00000265293:G191D|.	G|W	+|+	2|3	0|0	WWC1|WWC1	167759132|167759132	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	8.115000|8.115000	0.89572|0.89572	2.415000|2.415000	0.81967|0.81967	0.563000|0.563000	0.77884|0.77884	GGC|TGG	.	.		0.582	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		A	167826554	G	A	167826554	3	1	167	1	0	0	0	0	1	0	0	0	17426	1203	42	3	590	3	WWC1	5	167826554	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	27043270	167826554	13088706	53	25298										
C6orf27	80737	hgsc.bcm.edu	37	chr6	31736938	31736938	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	caagatctcacgccgagctcGaccctgaacccttgatgtat	8	14	1	3	rs369133546		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr6:31736938G>A	ENST00000375688.4	-	10	1560	c.1360C>T	c.(1360-1362)Cga>Tga	p.R454*	VWA7_ENST00000447450.1_Nonsense_Mutation_p.R454*|VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000375686.3_Nonsense_Mutation_p.R454*			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	454	VWFA.					extracellular region (GO:0005576)											CGCCGAGCTCGACCCTGAACC	0.517																																					p.R454X		Atlas-SNP	.											.	.	.	.	0			c.C1360T						.	G	stop/ARG	0,3022		0,0,1511	156	111	127		1360	3.8	0	6		127	1,5417		0,1,2708	no	stop-gained	C6orf27	NM_025258.2		0,1,4219	AA,AG,GG		0.0185,0.0,0.0118		454/892	31736938	1,8439	1511	2709	4220	SO:0001587	stop_gained	80737	exon10			GAGCTCGACCCTG		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"chromosome 6 open reading frame 27"	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.1360C>T	chr6.hg19:g.31736938G>A	ENSP00000364840:p.Arg454*	58.0	0.0		86.0	17.0	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Nonsense_Mutation	SNP	ENST00000375688.4	hg19	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	G	33	5.216607	0.95104	0.0	1.85E-4	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	.	.	.	5.65	3.8	0.43715	.	0.132928	0.48286	D	0.000196	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.9585	7.0767	0.25209	0.0811:0.0:0.6286:0.2904	.	.	.	.	X	454	.	ENSP00000364838:R454X	R	-	1	2	C6orf27	31844917	0.104000	0.21937	0.046000	0.18839	0.108000	0.19459	1.079000	0.30766	1.388000	0.46506	0.462000	0.41574	CGA	.	.		0.517	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		A	31736938	G	A	31736938	4	1	167	1	0	0	0	0	0	1	0	0	2364	1066	37	1	1346	1	C6orf27	6	31736938	Nonsense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10		31736938	139378129	54	25299										
GUCA1A	2978	hgsc.bcm.edu	37	chr6	42147077	42147077	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggaccttacccgcatcgtgcGcaggctccagaatggcgagc	13	14	0	1	rs558249974		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr6:42147077G>A	ENST00000394237.1	+	6	1518	c.542G>A	c.(541-543)cGc>cAc	p.R181H	GUCA1A_ENST00000053469.4_Missense_Mutation_p.R181H|GUCA1A_ENST00000372958.1_Missense_Mutation_p.R181H|GUCA1A_ENST00000541991.1_Missense_Mutation_p.R181H			P43080	GUC1A_HUMAN	guanylate cyclase activator 1A (retina)	181					phototransduction, visible light (GO:0007603)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;5.54e-05)|Epithelial(12;0.000167)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CGCATCGTGCGCAGGCTCCAG	0.642																																					p.R181H		Atlas-SNP	.											.	GUCA1A	18	.	0			c.G542A						.						30	28	29					6																	42147077		2203	4300	6503	SO:0001583	missense	2978	exon6			TCGTGCGCAGGCT		CCDS4864.1	6p21.1	2013-06-06			ENSG00000048545	ENSG00000048545		"EF-hand domain containing"	4678	protein-coding gene	gene with protein product	"cone dystrophy 3"	600364	"chromosome 6 open reading frame 131"	GUCA, GUCA1, C6orf131		9425234	Standard	NM_000409		Approved	GCAP, GCAP1, COD3, dJ139D8.6, CORD14	uc003orx.3	P43080	OTTHUMG00000014696	ENST00000394237.1:c.542G>A	chr6.hg19:g.42147077G>A	ENSP00000377784:p.Arg181His	216.0	0.0		329.0	21.0	NM_000409	B3KWT4|Q7Z6T1|Q9NU14	Missense_Mutation	SNP	ENST00000394237.1	hg19	CCDS4864.1	.	.	.	.	.	.	.	.	.	.	G	13.43	2.235085	0.39498	.	.	ENSG00000048545	ENST00000541991;ENST00000372965;ENST00000053469;ENST00000394237;ENST00000372958	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	4.34	3.46	0.39613	.	0.877024	0.10146	N	0.710186	T	0.18676	0.0448	N	0.08118	0	0.30242	N	0.794948	B	0.16802	0.019	B	0.04013	0.001	T	0.09037	-1.0693	10	0.33940	T	0.23	.	6.1165	0.20130	0.104:0.1939:0.7022:0.0	.	181	P43080	GUC1A_HUMAN	H	181;185;181;181;181	ENSP00000437476:R181H;ENSP00000053469:R181H;ENSP00000377784:R181H;ENSP00000362049:R181H	ENSP00000053469:R181H	R	+	2	0	GUCA1A	42255055	0.406000	0.25344	0.982000	0.44146	0.942000	0.58702	1.283000	0.33237	0.811000	0.34303	0.561000	0.74099	CGC	.	.		0.642	GUCA1A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316582.1			A	42147077	G	A	42147077	3	1	167	1	0	0	0	0	1	0	0	0	6897	1087	38	1	556	1	GUCA1A	6	42147077	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	10410139	42147077	128967990	55	25300										
RIMS1	22999	hgsc.bcm.edu	37	chr6	73102465	73102465	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgattttcttgatggattggGaccagcccagcttgttggcc	12	9	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr6:73102465G>A	ENST00000521978.1	+	31	4571	c.4571G>A	c.(4570-4572)gGa>gAa	p.G1524E	RIMS1_ENST00000401910.3_Missense_Mutation_p.G844E|RIMS1_ENST00000522291.1_Missense_Mutation_p.G1123E|RIMS1_ENST00000425662.2_Missense_Mutation_p.G592E|RIMS1_ENST00000431478.2_3'UTR|RIMS1_ENST00000523963.1_Missense_Mutation_p.G649E|RIMS1_ENST00000520567.1_Missense_Mutation_p.G1174E|RIMS1_ENST00000538414.1_Missense_Mutation_p.G330E|RIMS1_ENST00000348717.5_Missense_Mutation_p.G1307E|RIMS1_ENST00000491071.2_Missense_Mutation_p.G1347E|RIMS1_ENST00000517960.1_Missense_Mutation_p.G1307E|RIMS1_ENST00000518273.1_Missense_Mutation_p.G1203E|RIMS1_ENST00000414192.2_Missense_Mutation_p.G51E|RIMS1_ENST00000517827.1_Missense_Mutation_p.G658E|RIMS1_ENST00000264839.7_Missense_Mutation_p.G1373E	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1524					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GATGGATTGGGACCAGCCCAG	0.403																																					p.G1524E		Atlas-SNP	.											.	RIMS1	278	.	0			c.G4571A						.						97	92	94					6																	73102465		1844	4107	5951	SO:0001583	missense	22999	exon31			GATTGGGACCAGC	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.4571G>A	chr6.hg19:g.73102465G>A	ENSP00000428417:p.Gly1524Glu	118.0	0.0		87.0	6.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.203102|5.203102	0.95033|0.95033	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000522211|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420;ENST00000538414;ENST00000414192	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.81247	.|-1.42;1.34;1.26;1.35;1.84;1.9;1.91;1.15;1.22;1.86;1.63;-1.47;1.61;1.08;1.36;1.95	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.000000	.|0.64402	.|D	.|0.000008	D|D	0.90160|0.90160	0.6925|0.6925	M|M	0.84683|0.84683	2.71|2.71	0.80722|0.80722	D|D	1|1	.|D;D;D;P;D;D;D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.898;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;P;D;D;D;D;D;D;D;D;D	.|0.97110	.|0.999;0.999;0.999;0.874;1.0;1.0;0.999;1.0;0.999;1.0;0.997;1.0;0.997	D|D	0.91174|0.91174	0.4971|0.4971	5|10	.|0.87932	.|D	.|0	-18.708|-18.708	19.3783|19.3783	0.94521|0.94521	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|148;330;658;649;1373;844;1123;427;1203;1307;600;1347;1524	.|B7Z6K9;B7Z7W2;B7Z3S3;E9PHF5;E9PHR1;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5	.|.;.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN	N|E	442|1347;1373;1347;1307;1203;1123;1373;1307;1203;1174;1123;1524;844;649;592;689;658;572;330;51	.|ENSP00000430101:G1347E;ENSP00000275037:G1307E;ENSP00000264839:G1373E;ENSP00000429959:G1307E;ENSP00000430408:G1203E;ENSP00000430502:G1174E;ENSP00000430932:G1123E;ENSP00000428417:G1524E;ENSP00000385649:G844E;ENSP00000428328:G649E;ENSP00000411235:G592E;ENSP00000389503:G689E;ENSP00000428367:G658E;ENSP00000359448:G572E;ENSP00000439730:G330E;ENSP00000402273:G51E	.|ENSP00000264839:G1373E	D|G	+|+	1|2	0|0	RIMS1|RIMS1	73159186|73159186	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.869000|9.869000	0.99810|0.99810	2.582000|2.582000	0.87167|0.87167	0.591000|0.591000	0.81541|0.81541	GAC|GGA	.	.		0.403	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			A	73102465	G	A	73102465	3	1	167	1	0	0	0	0	1	0	0	0	13382	1174	41	3	4856	3	RIMS1	6	73102465	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	30955388	73102465	98012602	56	25301										
ENPP3	5169	hgsc.bcm.edu	37	chr6	131996239	131996239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gatgtggctgacagcaatgtAtcaaggtttaaaagccgcta	11	7	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr6:131996239A>G	ENST00000414305.1	+	10	1110	c.782A>G	c.(781-783)tAt>tGt	p.Y261C	ENPP3_ENST00000543135.1_Missense_Mutation_p.Y227C|ENPP3_ENST00000358229.5_Missense_Mutation_p.Y261C|ENPP3_ENST00000427148.2_3'UTR|ENPP3_ENST00000357639.3_Missense_Mutation_p.Y261C			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	261	Phosphodiesterase.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		ACAGCAATGTATCAAGGTTTA	0.403																																					p.Y261C		Atlas-SNP	.											.	ENPP3	117	.	0			c.A782G						.						92	89	90					6																	131996239		2203	4300	6503	SO:0001583	missense	5169	exon9			CAATGTATCAAGG	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.782A>G	chr6.hg19:g.131996239A>G	ENSP00000406261:p.Tyr261Cys	121.0	0.0		81.0	22.0	NM_005021	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	hg19	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.650063	0.67472	.	.	ENSG00000154269	ENST00000414305;ENST00000357639;ENST00000543135;ENST00000358229	T;T;T;T	0.72394	-0.65;-0.65;-0.65;-0.65	5.52	5.52	0.82312	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.203901	0.34178	N	0.004181	T	0.78464	0.4287	M	0.76002	2.32	0.80722	D	1	D	0.64830	0.994	D	0.64687	0.928	T	0.80946	-0.1155	10	0.54805	T	0.06	-11.3445	14.6197	0.68574	1.0:0.0:0.0:0.0	.	261	O14638	ENPP3_HUMAN	C	261;261;227;261	ENSP00000406261:Y261C;ENSP00000350265:Y261C;ENSP00000440810:Y227C;ENSP00000350964:Y261C	ENSP00000350265:Y261C	Y	+	2	0	ENPP3	132037932	1.000000	0.71417	0.998000	0.56505	0.880000	0.50808	2.789000	0.47813	2.090000	0.63153	0.363000	0.22086	TAT	.	.		0.403	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2			G	131996239	A	G	131996239	3	3	167	1	0	0	0	0	1	0	0	0	5133	449	16	2	816	2	ENPP3	6	131996239	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	58893774	131996239	39118828	57	25302										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152749436	152749436	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gctgtagagccgcagcctccTgaacacaggaatctctgttc	10	13	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr6:152749436T>C	ENST00000367255.5	-	37	5481	c.4880A>G	c.(4879-4881)cAg>cGg	p.Q1627R	SYNE1_ENST00000448038.1_Missense_Mutation_p.Q1634R|SYNE1_ENST00000341594.5_Missense_Mutation_p.Q1697R|SYNE1_ENST00000265368.4_Missense_Mutation_p.Q1627R|SYNE1_ENST00000423061.1_Missense_Mutation_p.Q1634R|SYNE1_ENST00000367253.4_Missense_Mutation_p.Q1627R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1627					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CGCAGCCTCCTGAACACAGGA	0.577										HNSCC(10;0.0054)																											p.Q1634R		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A4901G						.						130	130	130					6																	152749436		2203	4300	6503	SO:0001583	missense	23345	exon37			GCCTCCTGAACAC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.4880A>G	chr6.hg19:g.152749436T>C	ENSP00000356224:p.Gln1627Arg	35.0	0.0		26.0	7.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	9.522	1.108625	0.20714	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253	T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68	5.87	4.71	0.59529	.	0.000000	0.56097	D	0.000028	T	0.22898	0.0553	L	0.47716	1.5	0.80722	D	1	P;B;B;B;B	0.38922	0.651;0.013;0.002;0.013;0.01	B;B;B;B;B	0.33521	0.165;0.003;0.007;0.003;0.005	T	0.03773	-1.1005	10	0.34782	T	0.22	.	11.8976	0.52665	0.0:0.0678:0.0:0.9322	.	1610;1627;1627;1627;1634	B3W695;Q8NF91;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.	R	1627;1634;1627;1634;1697;1627	ENSP00000356224:Q1627R;ENSP00000396024:Q1634R;ENSP00000265368:Q1627R;ENSP00000390975:Q1634R;ENSP00000341887:Q1697R;ENSP00000356222:Q1627R	ENSP00000265368:Q1627R	Q	-	2	0	SYNE1	152791129	1.000000	0.71417	0.906000	0.35671	0.194000	0.23727	3.625000	0.54238	1.057000	0.40506	0.533000	0.62120	CAG	.	.		0.577	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152749436	T	C	152749436	3	2	167	1	0	0	0	0	1	0	0	0	15460	1580	55	2	22026	2	SYNE1	6	152749436	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	20753197	152749436	18365631	58	25303										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152804308	152804308	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cctctctcagggccacctccGctctgtacagccaggcacct	8	19	3	0	rs150409035		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr6:152804308G>T	ENST00000367255.5	-	14	1863	c.1262C>A	c.(1261-1263)gCg>gAg	p.A421E	SYNE1_ENST00000448038.1_Missense_Mutation_p.A428E|SYNE1_ENST00000367248.3_Missense_Mutation_p.A411E|SYNE1_ENST00000466159.2_Missense_Mutation_p.A421E|SYNE1_ENST00000341594.5_Missense_Mutation_p.A421E|SYNE1_ENST00000265368.4_Missense_Mutation_p.A421E|SYNE1_ENST00000423061.1_Missense_Mutation_p.A428E|SYNE1_ENST00000413186.2_Missense_Mutation_p.A421E|SYNE1_ENST00000367253.4_Missense_Mutation_p.A421E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	421					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GGCCACCTCCGCTCTGTACAG	0.448										HNSCC(10;0.0054)																											p.A428E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C1283A						.						178	172	174					6																	152804308		2203	4300	6503	SO:0001583	missense	23345	exon14			ACCTCCGCTCTGT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.1262C>A	chr6.hg19:g.152804308G>T	ENSP00000356224:p.Ala421Glu	68.0	0.0		60.0	25.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	26.9	4.781188	0.90282	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000466159;ENST00000537750	T;T;T;T;T;D;D;D;D;D	0.92545	0.01;0.0;-0.08;-0.0;0.36;-2.81;-2.81;-2.91;-3.04;-3.06	5.87	5.87	0.94306	.	0.109437	0.40385	N	0.001104	D	0.94778	0.8314	M	0.76328	2.33	0.80722	D	1	D;D;D;D;D	0.71674	0.996;0.996;0.998;0.996;0.998	P;D;D;D;D	0.68765	0.88;0.912;0.922;0.912;0.96	D	0.91152	0.4954	10	0.17832	T	0.49	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	404;421;421;421;428	B3W695;Q8NF91;F5H4Q0;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.	E	421;428;421;428;421;421;411;421;421;404	ENSP00000356224:A421E;ENSP00000396024:A428E;ENSP00000265368:A421E;ENSP00000390975:A428E;ENSP00000341887:A421E;ENSP00000356222:A421E;ENSP00000356217:A411E;ENSP00000414510:A421E;ENSP00000446021:A421E;ENSP00000441264:A404E	ENSP00000265368:A421E	A	-	2	0	SYNE1	152846001	1.000000	0.71417	0.988000	0.46212	0.921000	0.55340	7.472000	0.80996	2.941000	0.99782	0.655000	0.94253	GCG	.	G|1.000;A|0.000		0.448	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152804308	G	T	152804308	3	4	167	1	0	0	0	0	1	0	0	0	15460	1087	38	1	25736	1	SYNE1	6	152804308	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	54872	152804308	18310759	59	25304										
PDE10A	10846	hgsc.bcm.edu	37	chr6	165844911	165844911	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aaacaccccaaagactcaccTgcacctgatgtattgctact	5	14	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr6:165844911T>C	ENST00000366882.1	-	9	867	c.713A>G	c.(712-714)cAg>cGg	p.Q238R	PDE10A_ENST00000539869.2_Splice_Site_p.Q248R|PDE10A_ENST00000354448.4_Splice_Site_p.Q238R			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	238					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	AAGACTCACCTGCACCTGATG	0.418																																					p.Q248R	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											.	PDE10A	154	.	0			c.A743G						.						115	119	117					6																	165844911		2203	4300	6503	SO:0001630	splice_region_variant	10846	exon8			CTCACCTGCACCT	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.714+1A>G	chr6.hg19:g.165844911T>C		324.0	0.0		216.0	53.0	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.40	3.819705	0.71028	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.67345	-0.26;-0.26	5.5	5.5	0.81552	GAF (1);	0.000000	0.85682	D	0.000000	T	0.38108	0.1028	L	0.34521	1.04	0.54753	D	0.999981	P;B	0.37781	0.608;0.187	B;B	0.30401	0.115;0.052	T	0.38693	-0.9649	10	0.23891	T	0.37	.	15.6089	0.76699	0.0:0.0:0.0:1.0	.	248;238	Q9ULW9;Q9Y233	.;PDE10_HUMAN	R	238;266;248;238;237	ENSP00000355847:Q238R;ENSP00000346435:Q238R	ENSP00000341187:Q248R	Q	-	2	0	PDE10A	165764901	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.727000	0.84838	2.082000	0.62665	0.528000	0.53228	CAG	.	.		0.418	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1		Missense_Mutation	C	165844911	T	C	165844911	5	2	167	1	0	0	0	0	0	0	1	0	11639	1594	55	2	1686	2	PDE10A	6	165844911	Splice_Site	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	13040603	165844911	5270156	60	25305										
ANLN	54443	hgsc.bcm.edu	37	chr7	36445824	36445824	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agctcactcttctcaccaatGccatcagaggaaaaggctgc	8	13	4	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr7:36445824G>A	ENST00000265748.2	+	4	743	c.522G>A	c.(520-522)atG>atA	p.M174I	ANLN_ENST00000396068.2_Missense_Mutation_p.M174I	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	174	Nuclear localization.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						TCTCACCAATGCCATCAGAGG	0.458																																					p.M174I		Atlas-SNP	.											.	ANLN	101	.	0			c.G522A						.						77	78	78					7																	36445824		2203	4300	6503	SO:0001583	missense	54443	exon4			ACCAATGCCATCA	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.522G>A	chr7.hg19:g.36445824G>A	ENSP00000265748:p.Met174Ile	72.0	0.0		103.0	40.0	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	hg19	CCDS5447.1	.	.	.	.	.	.	.	.	.	.	G	8.675	0.903794	0.17760	.	.	ENSG00000011426	ENST00000265748;ENST00000396068;ENST00000424865	T;T;T	0.29655	2.77;2.75;1.56	5.34	5.34	0.76211	.	0.915503	0.09662	N	0.772375	T	0.29556	0.0737	L	0.47716	1.5	0.26719	N	0.970824	B;B;B;B	0.12013	0.005;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.001;0.002;0.001	T	0.06881	-1.0802	10	0.49607	T	0.09	1.1445	9.966	0.41725	0.0:0.1875:0.6822:0.1303	.	51;174;174;174	B4DSL6;A8K5D9;Q9NQW6-2;Q9NQW6	.;.;.;ANLN_HUMAN	I	174;174;152	ENSP00000265748:M174I;ENSP00000379380:M174I;ENSP00000404979:M152I	ENSP00000265748:M174I	M	+	3	0	ANLN	36412349	0.995000	0.38212	0.545000	0.28153	0.084000	0.17831	1.122000	0.31295	2.657000	0.90304	0.557000	0.71058	ATG	.	.		0.458	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		A	36445824	G	A	36445824	3	1	167	1	0	0	0	0	1	0	0	0	694	1319	46	3	536	3	ANLN	7	36445824	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10		36445824	122692839	61	25306										
ZNF273	10793	hgsc.bcm.edu	37	chr7	64363699	64363699	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctcgtcttcactgctctatgTcctctgctcctagaggtcca	7	15	4	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr7:64363699T>C	ENST00000476120.1	+	1	75	c.4T>C	c.(4-6)Tcc>Ccc	p.S2P	ZNF273_ENST00000545510.1_5'UTR|ZNF273_ENST00000319636.5_5'UTR|ZNF273_ENST00000527278.1_Intron	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				CTGCTCTATGTCCTCTGCTCC	0.597																																					p.S2P	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-SNP	.											.	ZNF273	45	.	0			c.T4C						.						54	55	55					7																	64363699		2203	4300	6503	SO:0001583	missense	10793	exon1			TCTATGTCCTCTG	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"Zinc fingers, C2H2-type", "-"	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.4T>C	chr7.hg19:g.64363699T>C	ENSP00000418719:p.Ser2Pro	39.0	0.0		54.0	8.0	NM_021148	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	hg19	CCDS5528.2	.	.	.	.	.	.	.	.	.	.	.	6.748	0.506806	0.12883	.	.	ENSG00000198039	ENST00000476120	T	0.07021	3.23	0.158	0.158	0.14942	.	.	.	.	.	T	0.04137	0.0115	N	0.08118	0	0.20307	N	0.999917	B	0.02656	0.0	B	0.01281	0.0	T	0.39643	-0.9604	8	0.87932	D	0	.	.	.	.	.	2	Q14593	ZN273_HUMAN	P	2	ENSP00000418719:S2P	ENSP00000433382:S2P	S	+	1	0	ZNF273	64001134	0.001000	0.12720	0.006000	0.13384	0.006000	0.05464	0.429000	0.21412	0.175000	0.19841	0.172000	0.16884	TCC	.	.		0.597	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1			C	64363699	T	C	64363699	3	2	167	1	0	0	0	0	1	0	0	0	17823	1667	58	2	6	2	ZNF273	7	64363699	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	27917875	64363699	94774964	62	25307										
NPTX2	4885	hgsc.bcm.edu	37	chr7	98254264	98254264	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctttaagtcaccagatgcgtTcaaggtgtccctcccactcc	7	15	2	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr7:98254264T>C	ENST00000265634.3	+	3	839	c.674T>C	c.(673-675)tTc>tCc	p.F225S		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	225					synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			CCAGATGCGTTCAAGGTGTCC	0.602																																					p.F225S		Atlas-SNP	.											.	NPTX2	45	.	0			c.T674C						.						239	193	209					7																	98254264		2203	4300	6503	SO:0001583	missense	4885	exon3			ATGCGTTCAAGGT		CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"apexin"	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.674T>C	chr7.hg19:g.98254264T>C	ENSP00000265634:p.Phe225Ser	49.0	0.0		76.0	17.0	NM_002523	A4D267|Q86XV7|Q96G70	Missense_Mutation	SNP	ENST00000265634.3	hg19	CCDS5657.1	.	.	.	.	.	.	.	.	.	.	T	19.17	3.775834	0.70107	.	.	ENSG00000106236	ENST00000265634	T	0.13901	2.55	5.57	5.57	0.84162	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.46756	0.1409	M	0.92367	3.3	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.58047	-0.7705	10	0.54805	T	0.06	-15.6153	14.9047	0.70709	0.0:0.0:0.0:1.0	.	225	P47972	NPTX2_HUMAN	S	225	ENSP00000265634:F225S	ENSP00000265634:F225S	F	+	2	0	NPTX2	98092200	1.000000	0.71417	0.992000	0.48379	0.240000	0.25518	6.248000	0.72418	2.116000	0.64780	0.459000	0.35465	TTC	.	.		0.602	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523		C	98254264	T	C	98254264	3	2	167	1	0	0	0	0	1	0	0	0	10612	1783	62	2	684	2	NPTX2	7	98254264	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	33890565	98254264	60884399	63	25308										
GIGYF1	64599	hgsc.bcm.edu	37	chr7	100284400	100284400	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cgctgtctgagcgggcgtgcTccttccttgggccagcccct	13	16	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr7:100284400T>C	ENST00000275732.5	-	7	1775	c.566A>G	c.(565-567)gAg>gGg	p.E189G	GIGYF1_ENST00000471340.2_Intron	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	189					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					GCGGGCGTGCTCCTTCCTTGG	0.662																																					p.E189G		Atlas-SNP	.											.	GIGYF1	113	.	0			c.A566G						.						41	40	41					7																	100284400		2202	4300	6502	SO:0001583	missense	64599	exon7			GCGTGCTCCTTCC	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"GYF domain containing 1"	612064	"PERQ amino acid rich, with GYF domain 1"	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.566A>G	chr7.hg19:g.100284400T>C	ENSP00000275732:p.Glu189Gly	137.0	0.0		211.0	14.0	NM_022574	Q6Y7W7|Q8WZ38	Missense_Mutation	SNP	ENST00000275732.5	hg19	CCDS34708.1	.	.	.	.	.	.	.	.	.	.	.	27.7	4.857550	0.91433	.	.	ENSG00000146830	ENST00000275732	D	0.84944	-1.92	4.96	4.96	0.65561	.	0.122413	0.53938	D	0.000048	D	0.83353	0.5236	L	0.52759	1.655	0.58432	D	0.999998	P	0.52463	0.953	P	0.47603	0.551	T	0.81645	-0.0839	10	0.28530	T	0.3	-21.7271	12.6263	0.56632	0.0:0.0:0.0:1.0	.	189	O75420	PERQ1_HUMAN	G	189	ENSP00000275732:E189G	ENSP00000275732:E189G	E	-	2	0	GIGYF1	100122336	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	6.994000	0.76251	2.079000	0.62486	0.460000	0.39030	GAG	.	.		0.662	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		C	100284400	T	C	100284400	3	2	167	1	0	0	0	0	1	0	0	0	6385	1551	54	2	2613	2	GIGYF1	7	100284400	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	2030136	100284400	58854263	64	25309										
RELN	5649	hgsc.bcm.edu	37	chr7	103126731	103126731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agtctccatgggcgtaggggGccagctgcccacagccactt	13	14	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr7:103126731G>A	ENST00000428762.1	-	61	10055	c.9896C>T	c.(9895-9897)gCc>gTc	p.A3299V	RELN_ENST00000343529.5_Missense_Mutation_p.A3299V|RELN_ENST00000473945.1_5'Flank|CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000424685.2_Missense_Mutation_p.A3299V|RN7SKP86_ENST00000410454.1_RNA	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	3299					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GGCGTAGGGGGCCAGCTGCCC	0.517																																					p.A3299V	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C9896T						.						91	89	89					7																	103126731		2203	4300	6503	SO:0001583	missense	5649	exon61			TAGGGGGCCAGCT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.9896C>T	chr7.hg19:g.103126731G>A	ENSP00000392423:p.Ala3299Val	155.0	0.0		235.0	39.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.093733	0.76870	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000424828;ENST00000448171	T;T;T	0.23348	1.91;1.91;1.91	6.06	6.06	0.98353	.	0.279422	0.36066	N	0.002814	T	0.25754	0.0627	L	0.34521	1.04	0.44373	D	0.997273	B;B	0.16603	0.001;0.018	B;B	0.18871	0.023;0.017	T	0.01988	-1.1234	10	0.42905	T	0.14	.	20.6243	0.99512	0.0:0.0:1.0:0.0	.	3299;3299	P78509-2;P78509	.;RELN_HUMAN	V	3299;3299;3299;816;3299	ENSP00000392423:A3299V;ENSP00000345694:A3299V;ENSP00000388446:A3299V	ENSP00000345694:A3299V	A	-	2	0	RELN	102913967	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.649000	0.83500	2.879000	0.98667	0.650000	0.86243	GCC	.	.		0.517	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		A	103126731	G	A	103126731	3	1	167	1	0	0	0	0	1	0	0	0	13235	1203	42	3	506	3	RELN	7	103126731	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	2842331	103126731	56011932	65	25310										
LAMB1	3912	hgsc.bcm.edu	37	chr7	107569615	107569615	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cttccagagcttcctttaccAtatctgcagtgactttaaca	5	12	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr7:107569615A>G	ENST00000222399.6	-	31	5011	c.4781T>C	c.(4780-4782)aTg>aCg	p.M1594T	LAMB1_ENST00000393561.1_Missense_Mutation_p.M1618T|LAMB1_ENST00000474380.1_5'Flank	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1594	Domain I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						TTCCTTTACCATATCTGCAGT	0.398																																					p.M1594T		Atlas-SNP	.											LAMB1,NS,carcinoma,0,1	LAMB1	185	.	0			c.T4781C						.						199	182	188					7																	107569615		2203	4300	6503	SO:0001583	missense	3912	exon31			TTTACCATATCTG	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.4781T>C	chr7.hg19:g.107569615A>G	ENSP00000222399:p.Met1594Thr	74.0	1.0		107.0	22.0	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	hg19	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	A	6.349	0.432520	0.12045	.	.	ENSG00000091136	ENST00000393561;ENST00000222399	T;T	0.77098	-1.07;-1.07	5.96	2.37	0.29283	Prefoldin (1);	.	.	.	.	T	0.63271	0.2497	L	0.37630	1.12	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.09377	0.001;0.004;0.0	T	0.49523	-0.8931	9	0.14252	T	0.57	.	8.237	0.31631	0.6956:0.0:0.3044:0.0	.	1594;1618;891	P07942;G3XAI2;Q8TAS6	LAMB1_HUMAN;.;.	T	1618;1594	ENSP00000377191:M1618T;ENSP00000222399:M1594T	ENSP00000222399:M1594T	M	-	2	0	LAMB1	107356851	0.691000	0.27709	1.000000	0.80357	0.994000	0.84299	0.124000	0.15728	0.498000	0.27948	-0.274000	0.10170	ATG	.	.		0.398	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		G	107569615	A	G	107569615	3	3	167	1	0	0	0	0	1	0	0	0	8619	217	8	2	595	2	LAMB1	7	107569615	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	4442884	107569615	51569048	66	25311										
AASS	10157	hgsc.bcm.edu	37	chr7	121716604	121716604	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctgctttaattcgctccaatAttggtccatagatctccttt	5	11	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr7:121716604A>C	ENST00000393376.1	-	23	2815	c.2720T>G	c.(2719-2721)aTa>aGa	p.I907R	AASS_ENST00000473553.1_5'UTR|AASS_ENST00000417368.2_Missense_Mutation_p.I907R			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	907	Saccharopine dehydrogenase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TCGCTCCAATATTGGTCCATA	0.353																																					p.I907R		Atlas-SNP	.											.	AASS	123	.	0			c.T2720G						.						117	118	118					7																	121716604		2203	4300	6503	SO:0001583	missense	10157	exon24			TCCAATATTGGTC	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.2720T>G	chr7.hg19:g.121716604A>C	ENSP00000377040:p.Ile907Arg	87.0	0.0		124.0	24.0	NM_005763	O95462	Missense_Mutation	SNP	ENST00000393376.1	hg19	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.135008	0.77662	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	T;T	0.44482	0.92;0.92	5.7	5.7	0.88788	.	0.146897	0.64402	D	0.000007	T	0.63815	0.2543	M	0.88570	2.965	0.58432	D	0.999999	P	0.41265	0.744	P	0.50378	0.639	T	0.70791	-0.4776	10	0.87932	D	0	-22.6427	15.6246	0.76845	1.0:0.0:0.0:0.0	.	907	Q9UDR5	AASS_HUMAN	R	907	ENSP00000377040:I907R;ENSP00000403768:I907R	ENSP00000377040:I907R	I	-	2	0	AASS	121503840	1.000000	0.71417	0.993000	0.49108	0.938000	0.57974	6.229000	0.72294	2.171000	0.68590	0.482000	0.46254	ATA	.	.		0.353	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		C	121716604	A	C	121716604	3	2	167	1	0	0	0	0	1	0	0	0	24	449	16	5	64	5	AASS	7	121716604	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	14146989	121716604	37422059	67	25312										
KCNH2	3757	hgsc.bcm.edu	37	chr7	150647095	150647095	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cacgtggggctcctctccatGgccccgcttggagggcctga	14	15	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr7:150647095G>A	ENST00000262186.5	-	9	2800				KCNH2_ENST00000392968.2_Intron|KCNH2_ENST00000430723.3_Silent_p.A853A|KCNH2_ENST00000330883.4_Intron	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2						cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	TCCTCTCCATGGCCCCGCTTG	0.577																																					p.A853A	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.C2559T						.						25	36	32					7																	150647095		1173	2206	3379	SO:0001627	intron_variant	3757	exon9			CTCCATGGCCCCG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.2398+160C>T	chr7.hg19:g.150647095G>A		86.0	0.0		148.0	6.0	NM_172056	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	hg19	CCDS5910.1																																																																																			.	.		0.577	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		A	150647095	G	A	150647095	1	1	167	0	1	0	0	0	0	0	0	0	8041	1335	47	3		3	KCNH2	7	150647095	Intron	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	28930491	150647095	8491568	68	25313										
UBE3C	9690	hgsc.bcm.edu	37	chr7	156974230	156974230	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agggtattataggtctctatAtttgttgattaacagcaagc	9	5	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr7:156974230A>G	ENST00000348165.5	+	7	995	c.635A>G	c.(634-636)tAt>tGt	p.Y212C	UBE3C_ENST00000389103.4_Missense_Mutation_p.Y169C	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	212					protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		AGGTCTCTATATTTGTTGATT	0.289																																					p.Y212C		Atlas-SNP	.											.	UBE3C	124	.	0			c.A635G						.						69	70	70					7																	156974230		2203	4300	6503	SO:0001583	missense	9690	exon7			CTCTATATTTGTT	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.635A>G	chr7.hg19:g.156974230A>G	ENSP00000309198:p.Tyr212Cys	107.0	0.0		184.0	29.0	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	hg19	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	A	16.66	3.186345	0.57909	.	.	ENSG00000009335	ENST00000348165;ENST00000389103	T	0.43294	0.95	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.61350	0.2340	M	0.65975	2.015	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.99	P;D;P	0.71870	0.887;0.975;0.784	T	0.63501	-0.6623	10	0.49607	T	0.09	-8.8462	14.6399	0.68717	1.0:0.0:0.0:0.0	.	212;212;169	Q15386;Q15386-2;Q15386-3	UBE3C_HUMAN;.;.	C	212;169	ENSP00000309198:Y212C	ENSP00000309198:Y212C	Y	+	2	0	UBE3C	156666991	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.358000	0.90090	1.870000	0.54199	0.455000	0.32223	TAT	.	.		0.289	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		G	156974230	A	G	156974230	3	3	167	1	0	0	0	0	1	0	0	0	16896	449	16	2	661	2	UBE3C	7	156974230	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	6327135	156974230	2164433	69	25314										
PCM1	5108	hgsc.bcm.edu	37	chr8	17823507	17823507	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	atgctttcaatcttgtgttaGgtggaagaacaattgccctt	9	7	2	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr8:17823507G>T	ENST00000519253.1	+	19	3106		c.e19-1		PCM1_ENST00000325083.8_Splice_Site|PCM1_ENST00000524226.1_Splice_Site			Q15154	PCM1_HUMAN	pericentriolar material 1						centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TCTTGTGTTAGGTGGAAGAAC	0.373			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																.		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.2856-1G>T						.						68	63	64					8																	17823507		1868	4101	5969	SO:0001630	splice_region_variant	5108	exon19			GTGTTAGGTGGAA		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.2856-1G>T	chr8.hg19:g.17823507G>T		125.0	0.0		89.0	28.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Splice_Site	SNP	ENST00000519253.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.53	3.411791	0.62399	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5471	0.99284	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PCM1	17867787	1.000000	0.71417	0.998000	0.56505	0.834000	0.47266	7.573000	0.82421	2.941000	0.99782	0.655000	0.94253	.	.	.		0.373	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	Intron	T	17823507	G	T	17823507	5	4	167	1	0	0	0	0	0	0	1	0	11593	1014	35	3	2921	3	PCM1	8	17823507	Splice_Site	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10		17823507	128540515	70	25315										
WRN	7486	hgsc.bcm.edu	37	chr8	31004928	31004928	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctaggcagaaacatgccaatAaaatggatgttcccccagct	8	11	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr8:31004928A>G	ENST00000298139.5	+	30	3757	c.3508A>G	c.(3508-3510)Aaa>Gaa	p.K1170E		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	1170	HRDC. {ECO:0000255|PROSITE- ProRule:PRU00328}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		ACATGCCAATAAAATGGATGT	0.343			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.K1170E	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"L, E, M, O"	.	WRN	116	.	0			c.A3508G						.						100	101	101					8																	31004928		2203	4300	6503	SO:0001583	missense	7486	exon30	Familial Cancer Database	WS, Adult Progeria	GCCAATAAAATGG		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"Werner syndrome"			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.3508A>G	chr8.hg19:g.31004928A>G	ENSP00000298139:p.Lys1170Glu	235.0	0.0		136.0	39.0	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	hg19	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	A	0.047	-1.264149	0.01433	.	.	ENSG00000165392	ENST00000298139	T	0.39056	1.1	5.17	-3.96	0.04106	HRDC-like (1);Helicase/RNase D C-terminal, HRDC domain (3);	0.892395	0.09812	N	0.752635	T	0.15435	0.0372	N	0.04820	-0.15	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.37454	-0.9705	10	0.02654	T	1	-2.0254	8.9677	0.35887	0.2321:0.1526:0.6154:0.0	.	580;1170	Q59F09;Q14191	.;WRN_HUMAN	E	1170	ENSP00000298139:K1170E	ENSP00000298139:K1170E	K	+	1	0	WRN	31124470	0.301000	0.24444	0.005000	0.12908	0.371000	0.29859	0.623000	0.24447	-0.512000	0.06505	-0.256000	0.11100	AAA	.	.		0.343	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			G	31004928	A	G	31004928	3	3	167	1	0	0	0	0	1	0	0	0	17417	363	13	2	3622	2	WRN	8	31004928	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	13181421	31004928	115359094	71	25316										
C8orf86	389649	hgsc.bcm.edu	37	chr8	38386128	38386128	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tctaatcaactcctcagctgGgaggagtcccttccccaggg	10	14	3	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr8:38386128G>A	ENST00000358138.1	-	1	52	c.28C>T	c.(28-30)Cca>Tca	p.P10S	C8orf86_ENST00000437935.2_Missense_Mutation_p.P10S	NM_207412.1	NP_997295.1	Q6ZUL3	CH086_HUMAN	chromosome 8 open reading frame 86	10										breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	5						TCCTCAGCTGGGAGGAGTCCC	0.547																																					p.P10S		Atlas-SNP	.											.	C8orf86	17	.	0			c.C28T						.						53	50	51					8																	38386128		2203	4300	6503	SO:0001583	missense	389649	exon1			CAGCTGGGAGGAG	BC137511	CCDS6108.1	8p12-p11.23	2009-03-03			ENSG00000196166	ENSG00000196166			33774	protein-coding gene	gene with protein product							Standard	NM_207412		Approved	FLJ43582	uc003xlx.1	Q6ZUL3	OTTHUMG00000163992	ENST00000358138.1:c.28C>T	chr8.hg19:g.38386128G>A	ENSP00000350856:p.Pro10Ser	37.0	0.0		45.0	13.0	NM_207412	A4QPB7	Missense_Mutation	SNP	ENST00000358138.1	hg19	CCDS6108.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.664995	0.29604	.	.	ENSG00000196166	ENST00000358138;ENST00000437935	T;T	0.58060	0.44;0.36	4.67	-9.34	0.00636	.	.	.	.	.	T	0.23806	0.0576	N	0.08118	0	0.09310	N	1	B	0.22983	0.078	B	0.22386	0.039	T	0.33929	-0.9849	9	0.87932	D	0	.	4.2211	0.10558	0.0915:0.2837:0.4466:0.1782	.	10	Q6ZUL3	CH086_HUMAN	S	10	ENSP00000350856:P10S;ENSP00000389615:P10S	ENSP00000350856:P10S	P	-	1	0	C8orf86	38505285	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.205000	0.03014	-1.818000	0.01218	-0.868000	0.02995	CCA	.	.		0.547	C8orf86-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376668.1	NM_207412		A	38386128	G	A	38386128	3	1	167	1	0	0	0	0	1	0	0	0	2444	1232	43	3	655	3	C8orf86	8	38386128	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	7381200	38386128	107977894	72	25317										
PRKDC	5591	hgsc.bcm.edu	37	chr8	48767935	48767935	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	acttcatctttagggaccccCtgaaaaggtacagaaattct	7	10	3	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr8:48767935C>T	ENST00000523565.1	-	50	6665		c.e50-1		PRKDC_ENST00000314191.2_Splice_Site|PRKDC_ENST00000338368.3_Splice_Site			P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide						B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	TAGGGACCCCCTGAAAAGGTA	0.343								Non-homologous end-joining																													.	Esophageal Squamous(79;1091 1253 12329 31680 40677)	Atlas-SNP	.											.	PRKDC	394	.	0			c.6609-1G>A						.						41	36	38					8																	48767935		1818	4073	5891	SO:0001630	splice_region_variant	5591	exon51			GACCCCCTGAAAA		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000523565.1:c.6844-1G>A	chr8.hg19:g.48767935C>T		82.0	0.0		58.0	25.0	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Splice_Site	SNP	ENST00000523565.1	hg19		.	.	.	.	.	.	.	.	.	.	C	19.26	3.793479	0.70452	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.771	0.88493	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRKDC	48930488	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	7.403000	0.79983	2.521000	0.84997	0.650000	0.86243	.	.	.		0.343	PRKDC-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000377896.1	NM_001081640	Intron	T	48767935	C	T	48767935	5	4	167	1	0	0	0	0	0	0	1	0	12533	695	24	3	5925	3	PRKDC	8	48767935	Splice_Site	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	10381807	48767935	97596087	73	25318										
RBM12B	389677	hgsc.bcm.edu	37	chr8	94748356	94748356	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgatgtcccagatcctggacGccctcttcctacacgatcag	8	15	2	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr8:94748356G>A	ENST00000399300.2	-	3	496	c.283C>T	c.(283-285)Cgt>Tgt	p.R95C	RBM12B_ENST00000517700.1_Missense_Mutation_p.R95C|RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	95							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			GATCCTGGACGCCCTCTTCCT	0.408																																					p.R95C		Atlas-SNP	.											.	RBM12B	78	.	0			c.C283T						.						182	174	177					8																	94748356		1865	4089	5954	SO:0001583	missense	389677	exon3			CTGGACGCCCTCT		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.283C>T	chr8.hg19:g.94748356G>A	ENSP00000382239:p.Arg95Cys	99.0	0.0		149.0	9.0	NM_203390	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	hg19	CCDS43755.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.600308	0.46423	.	.	ENSG00000183808	ENST00000399300;ENST00000517700;ENST00000519109;ENST00000518597;ENST00000520560	T;T;T;T;T	0.17370	2.84;2.89;2.28;2.3;2.34	5.51	4.62	0.57501	.	0.000000	0.47093	D	0.000246	T	0.18215	0.0437	N	0.24115	0.695	0.38891	D	0.957122	D	0.69078	0.997	P	0.50440	0.641	T	0.03684	-1.1013	10	0.72032	D	0.01	-12.0673	12.7592	0.57354	0.0:0.0:0.5289:0.4711	.	95	Q8IXT5	RB12B_HUMAN	C	95	ENSP00000382239:R95C;ENSP00000427729:R95C;ENSP00000430474:R95C;ENSP00000428269:R95C;ENSP00000429807:R95C	ENSP00000382239:R95C	R	-	1	0	RBM12B	94817532	0.706000	0.27856	1.000000	0.80357	0.970000	0.65996	1.067000	0.30616	1.269000	0.44280	0.655000	0.94253	CGT	.	.		0.408	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		A	94748356	G	A	94748356	3	1	167	1	0	0	0	0	1	0	0	0	13129	1087	38	1	2726	1	RBM12B	8	94748356	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	45980421	94748356	51615666	74	25319										
ZNF16	7564	hgsc.bcm.edu	37	chr8	146156959	146156959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgccacaatcattacactcaTaaggcttctctccagtgtgg	7	12	3	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr8:146156959T>C	ENST00000276816.4	-	4	1400	c.1214A>G	c.(1213-1215)tAt>tGt	p.Y405C	ZNF16_ENST00000394909.2_Missense_Mutation_p.Y405C	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	405					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to sodium dodecyl sulfate (GO:0072707)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell cycle phase transition (GO:1901989)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of kinase activity (GO:0033674)|positive regulation of megakaryocyte differentiation (GO:0045654)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|lung(9)|ovary(5)|prostate(1)|skin(1)|urinary_tract(1)	29	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)		ATTACACTCATAAGGCTTCTC	0.527																																					p.Y405C		Atlas-SNP	.											.	ZNF16	80	.	0			c.A1214G						.						97	92	93					8																	146156959		2203	4300	6503	SO:0001583	missense	7564	exon3			CACTCATAAGGCT	X52340	CCDS6437.1	8q24	2013-01-08	2006-05-10		ENSG00000170631	ENSG00000170631		"Zinc fingers, C2H2-type"	12947	protein-coding gene	gene with protein product		601262	"zinc finger protein 16 (KOX 9)"				Standard	NM_006958		Approved	KOX9	uc003zeu.3	P17020	OTTHUMG00000165253	ENST00000276816.4:c.1214A>G	chr8.hg19:g.146156959T>C	ENSP00000276816:p.Tyr405Cys	140.0	0.0		173.0	44.0	NM_006958	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Missense_Mutation	SNP	ENST00000276816.4	hg19	CCDS6437.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.673816	0.47781	.	.	ENSG00000170631	ENST00000276816;ENST00000394909	T;T	0.25414	1.8;1.8	3.88	3.88	0.44766	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.53367	0.1792	M	0.85462	2.755	0.09310	N	0.999995	D	0.89917	1.0	D	0.74023	0.982	T	0.45512	-0.9256	9	0.87932	D	0	.	11.8081	0.52167	0.0:0.0:0.0:1.0	.	405	P17020	ZNF16_HUMAN	C	405	ENSP00000276816:Y405C;ENSP00000378369:Y405C	ENSP00000276816:Y405C	Y	-	2	0	ZNF16	146127763	0.000000	0.05858	0.327000	0.25402	0.935000	0.57460	0.263000	0.18478	1.615000	0.50252	0.379000	0.24179	TAT	.	.		0.527	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958		C	146156959	T	C	146156959	3	2	167	1	0	0	0	0	1	0	0	0	17753	1406	49	2	838	2	ZNF16	8	146156959	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	51408603	146156959	207063	75	25320										
PDCD1LG2	80380	hgsc.bcm.edu	37	chr9	5535017	5535017	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	taatcatctatggggtcgccTgggactacaagtacctgact	10	10	2	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:5535017T>A	ENST00000397747.3	+	3	576	c.328T>A	c.(328-330)Tgg>Agg	p.W110R	PDCD1LG2_ENST00000397745.2_Missense_Mutation_p.W110R	NM_025239.3	NP_079515.2	Q9BQ51	PD1L2_HUMAN	programmed cell death 1 ligand 2	110	Ig-like V-type.				immune response (GO:0006955)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(2)|lung(4)|prostate(2)	8	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000767)|Lung(218;0.112)		TGGGGTCGCCTGGGACTACAA	0.512																																					p.W110R		Atlas-SNP	.											.	PDCD1LG2	16	.	0			c.T328A						.						62	56	58					9																	5535017		2203	4300	6503	SO:0001583	missense	80380	exon3			GTCGCCTGGGACT	AF344424	CCDS6465.1	9p24.2	2014-01-30			ENSG00000197646	ENSG00000197646		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	18731	protein-coding gene	gene with protein product	"B7 dendritic cell molecule"	605723				11224527	Standard	NM_025239		Approved	PD-L2, Btdc, PDL2, bA574F11.2, CD273, B7-DC	uc003zjg.4	Q9BQ51	OTTHUMG00000019504	ENST00000397747.3:c.328T>A	chr9.hg19:g.5535017T>A	ENSP00000380855:p.Trp110Arg	35.0	0.0		27.0	13.0	NM_025239	Q14CN8|Q5T7Z6|Q6JXL8|Q6JXL9	Missense_Mutation	SNP	ENST00000397747.3	hg19	CCDS6465.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.154811	0.57259	.	.	ENSG00000197646	ENST00000397745;ENST00000397747	T;T	0.02395	4.31;4.31	5.19	2.78	0.32641	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.408346	0.18771	N	0.131612	T	0.09202	0.0227	L	0.50919	1.6	0.28850	N	0.896102	D;D;D;D;D	0.89917	0.996;0.999;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.924;0.955;0.996;0.999;0.955	T	0.03423	-1.1038	10	0.45353	T	0.12	-0.1939	9.1241	0.36805	0.0:0.0:0.3931:0.6069	.	99;110;110;110;110	Q2LC89;A4GW21;Q9BQ51-3;Q9BQ51-2;Q9BQ51	.;.;.;.;PD1L2_HUMAN	R	110	ENSP00000380853:W110R;ENSP00000380855:W110R	ENSP00000380853:W110R	W	+	1	0	PDCD1LG2	5525017	0.997000	0.39634	0.996000	0.52242	0.811000	0.45836	1.220000	0.32491	0.984000	0.38629	0.459000	0.35465	TGG	.	.		0.512	PDCD1LG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051634.1	NM_025239		A	5535017	T	A	5535017	3	1	167	1	0	0	0	0	1	0	0	0	11627	1580	55	4	334	4	PDCD1LG2	9	5535017	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10		5535017	135678414	76	25321										
CNTLN	54875	hgsc.bcm.edu	37	chr9	17394652	17394652	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ccctcttaaaacagcaacaaGaagatacagagaccagagaa	7	10	1	4			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:17394652G>C	ENST00000380647.3	+	15	2284	c.2200G>C	c.(2200-2202)Gaa>Caa	p.E734Q	CNTLN_ENST00000262360.5_Missense_Mutation_p.E734Q|CNTLN_ENST00000425824.1_Missense_Mutation_p.E734Q			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	734					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		ACAGCAACAAGAAGATACAGA	0.308																																					p.E734Q		Atlas-SNP	.											.	CNTLN	128	.	0			c.G2200C						.						66	62	63					9																	17394652		1799	4071	5870	SO:0001583	missense	54875	exon15			CAACAAGAAGATA	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.2200G>C	chr9.hg19:g.17394652G>C	ENSP00000370021:p.Glu734Gln	283.0	0.0		263.0	19.0	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	hg19	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	G	10.02	1.237395	0.22711	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.20069	2.1;2.1;2.36	5.37	5.37	0.77165	.	.	.	.	.	T	0.37210	0.0995	L	0.60455	1.87	0.32444	N	0.546271	D;D;D	0.71674	0.998;0.962;0.962	D;P;P	0.65684	0.937;0.764;0.764	T	0.30001	-0.9993	9	0.18710	T	0.47	.	12.1299	0.53936	0.0796:0.0:0.9204:0.0	.	734;734;734	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	Q	734	ENSP00000370021:E734Q;ENSP00000392798:E734Q;ENSP00000262360:E734Q	ENSP00000262360:E734Q	E	+	1	0	CNTLN	17384652	1.000000	0.71417	1.000000	0.80357	0.505000	0.33919	2.779000	0.47734	2.511000	0.84671	0.650000	0.86243	GAA	.	.		0.308	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		C	17394652	G	C	17394652	3	2	167	1	0	0	0	0	1	0	0	0	3641	943	33	4	2288	4	CNTLN	9	17394652	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	11859635	17394652	123818779	77	25322										
TLN1	7094	hgsc.bcm.edu	37	chr9	35717322	35717322	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cccctcgcaacagttgcccaTcctctgtagctgcctgggag	10	16	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:35717322T>A	ENST00000314888.9	-	19	2632	c.2279A>T	c.(2278-2280)gAt>gTt	p.D760V	TLN1_ENST00000540444.1_Missense_Mutation_p.D760V	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	760					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGTTGCCCATCCTCTGTAGC	0.612																																					p.D760V		Atlas-SNP	.											.	TLN1	185	.	0			c.A2279T						.						73	70	71					9																	35717322		2203	4300	6503	SO:0001583	missense	7094	exon19			TGCCCATCCTCTG	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.2279A>T	chr9.hg19:g.35717322T>A	ENSP00000316029:p.Asp760Val	57.0	0.0		45.0	22.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.803632	0.90623	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.72615	-0.66;-0.67	5.6	5.6	0.85130	.	0.048591	0.85682	D	0.000000	T	0.71787	0.3381	M	0.81341	2.54	0.80722	D	1	P	0.43633	0.813	B	0.36567	0.228	T	0.78362	-0.2233	10	0.87932	D	0	-16.0705	15.7766	0.78224	0.0:0.0:0.0:1.0	.	760	Q9Y490	TLN1_HUMAN	V	760	ENSP00000316029:D760V;ENSP00000442981:D760V	ENSP00000316029:D760V	D	-	2	0	TLN1	35707322	1.000000	0.71417	0.984000	0.44739	0.998000	0.95712	6.269000	0.72558	2.143000	0.66587	0.459000	0.35465	GAT	.	.		0.612	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35717322	T	A	35717322	3	1	167	1	0	0	0	0	1	0	0	0	15962	1435	50	4	5502	4	TLN1	9	35717322	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	18322670	35717322	105496109	78	25323										
C9orf128	392307	hgsc.bcm.edu	37	chr9	35819298	35819298	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggtcaaaggtggcccgtctcTtgagccagaactcacccacc	10	15	3	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:35819298T>G	ENST00000423537.2	-	5	1216	c.947A>C	c.(946-948)aAg>aCg	p.K316T	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	316										endometrium(2)|kidney(1)|lung(4)	7						GGCCCGTCTCTTGAGCCAGAA	0.597																																					p.K316T		Atlas-SNP	.											.	FAM221B	38	.	0			c.A947C						.						202	200	200					9																	35819298		692	1591	2283	SO:0001583	missense	392307	exon5			CGTCTCTTGAGCC	BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 128"	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.947A>C	chr9.hg19:g.35819298T>G	ENSP00000415299:p.Lys316Thr	118.0	0.0		125.0	18.0	NM_001012446	Q5TCW2	Missense_Mutation	SNP	ENST00000423537.2	hg19	CCDS43799.2	.	.	.	.	.	.	.	.	.	.	T	11.97	1.798257	0.31777	.	.	ENSG00000204930	ENST00000423537	T	0.15603	2.41	5.1	-4.36	0.03645	.	.	.	.	.	T	0.08802	0.0218	L	0.27053	0.805	0.22317	N	0.999203	B	0.12630	0.006	B	0.12837	0.008	T	0.34378	-0.9831	9	0.33141	T	0.24	-1.8824	3.2101	0.06680	0.1292:0.441:0.1599:0.2698	.	316	A6H8Z2	CI128_HUMAN	T	316	ENSP00000415299:K316T	ENSP00000415299:K316T	K	-	2	0	C9orf128	35809298	0.950000	0.32346	0.810000	0.32431	0.972000	0.66771	-0.013000	0.12678	-0.929000	0.03757	-1.386000	0.01163	AAG	.	.		0.597	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1	NM_001012446		G	35819298	T	G	35819298	3	3	167	1	0	0	0	0	1	0	0	0	2457	1609	56	5	273	5	C9orf128	9	35819298	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	101976	35819298	105394133	79	25324										
GKAP1	80318	hgsc.bcm.edu	37	chr9	86421241	86421241	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tttgcttcactctgttgctgTtccttcttttttcttctttt	4	10	5	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:86421241T>C	ENST00000376371.2	-	3	592	c.192A>G	c.(190-192)gaA>gaG	p.E64E	GKAP1_ENST00000376365.3_Silent_p.E64E	NM_025211.3	NP_079487.2	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1	64					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)	14						TCTGTTGCTGttccttctttt	0.378																																					p.E64E		Atlas-SNP	.											.	GKAP1	27	.	0			c.A192G						.						141	131	135					9																	86421241		2145	4173	6318	SO:0001819	synonymous_variant	80318	exon3			TTGCTGTTCCTTC	BC014476	CCDS35049.1, CCDS47988.1	9q22.1	2008-02-05			ENSG00000165113	ENSG00000165113			17496	protein-coding gene	gene with protein product	"cGMP-dependent protein kinase anchoring protein 42kDa"	611356					Standard	NM_025211		Approved	GKAP42, FKSG21	uc004amy.3	Q5VSY0	OTTHUMG00000020106	ENST00000376371.2:c.192A>G	chr9.hg19:g.86421241T>C		37.0	0.0		35.0	11.0	NM_025211	Q96LI0|Q9BYI1|Q9BYI2|Q9H225	Silent	SNP	ENST00000376371.2	hg19	CCDS35049.1																																																																																			.	.		0.378	GKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052839.2	NM_025211		C	86421241	T	C	86421241	2	2	167	1	0	0	0	0	0	0	0	1	6431	1722	60	2		2	GKAP1	9	86421241	Silent	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	50601943	86421241	54792190	80	25325										
ROR2	4920	hgsc.bcm.edu	37	chr9	94486330	94486330	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gttgacggggacgtagagctGcggcgggggcaccatgggtc	20	9	0	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:94486330G>A	ENST00000375708.3	-	9	2644	c.2446C>T	c.(2446-2448)Cag>Tag	p.Q816*	ROR2_ENST00000375715.1_Intron|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	816	Pro-rich.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						ACGTAGAGCTGCGGCGGGGGC	0.672																																					p.Q816X		Atlas-SNP	.											.	ROR2	167	.	0			c.C2446T						.						38	47	44					9																	94486330		2203	4298	6501	SO:0001587	stop_gained	4920	exon9			AGAGCTGCGGCGG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.2446C>T	chr9.hg19:g.94486330G>A	ENSP00000364860:p.Gln816*	39.0	0.0		33.0	12.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Nonsense_Mutation	SNP	ENST00000375708.3	hg19	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	G	37	6.626304	0.97718	.	.	ENSG00000169071	ENST00000375708	.	.	.	4.52	4.52	0.55395	.	0.000000	0.39909	N	0.001222	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	17.4667	0.87634	0.0:0.0:1.0:0.0	.	.	.	.	X	816	.	ENSP00000364860:Q816X	Q	-	1	0	ROR2	93526151	1.000000	0.71417	0.997000	0.53966	0.574000	0.36063	9.548000	0.98103	2.345000	0.79718	0.462000	0.41574	CAG	.	.		0.672	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			A	94486330	G	A	94486330	4	1	167	1	0	0	0	0	0	1	0	0	13542	1328	46	3	389	3	ROR2	9	94486330	Nonsense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	8065089	94486330	46727101	81	25326										
DNAJC25	548645	hgsc.bcm.edu	37	chr9	114411923	114411923	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	catcataaagaacattataaAaagtaaaatagatataaagg	5	3	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:114411923A>C	ENST00000313525.3	+	3	736	c.680A>C	c.(679-681)aAa>aCa	p.K227T	DNAJC25_ENST00000556107.1_Intron|DNAJC25-GNG10_ENST00000374294.3_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	227						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						AACATTATAAAAAGTAAAATA	0.358																																					p.K227T		Atlas-SNP	.											.	DNAJC25	20	.	0			c.A680C						.						36	37	37					9																	114411923		1804	4058	5862	SO:0001583	missense	548645	exon3			TTATAAAAAGTAA		CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"Heat shock proteins / DNAJ (HSP40)"	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.680A>C	chr9.hg19:g.114411923A>C	ENSP00000320650:p.Lys227Thr	182.0	0.0		170.0	77.0	NM_001015882	Q5QTD8|Q96BN9	Missense_Mutation	SNP	ENST00000313525.3	hg19	CCDS43862.1	.	.	.	.	.	.	.	.	.	.	A	16.84	3.234024	0.58886	.	.	ENSG00000059769	ENST00000313525	T	0.46451	0.87	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.62307	0.2417	M	0.61703	1.905	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.62859	-0.6765	10	0.54805	T	0.06	-22.6788	15.3933	0.74767	1.0:0.0:0.0:0.0	.	227	Q9H1X3	DJC25_HUMAN	T	227	ENSP00000320650:K227T	ENSP00000320650:K227T	K	+	2	0	DNAJC25	113451744	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.888000	0.92464	2.371000	0.80710	0.533000	0.62120	AAA	.	.		0.358	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882		C	114411923	A	C	114411923	3	2	167	1	0	0	0	0	1	0	0	0	4645	14	1	5	690	5	DNAJC25	9	114411923	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	19925593	114411923	26801508	82	25327										
SLC46A2	57864	hgsc.bcm.edu	37	chr9	115652456	115652456	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgaggatgaggcgcacagagCggcggccctcggaggagccc	18	12	0	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:115652456C>T	ENST00000374228.4	-	1	737	c.506G>A	c.(505-507)cGc>cAc	p.R169H		NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	169					negative regulation of T cell apoptotic process (GO:0070233)|regulation of T cell differentiation (GO:0045580)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(1)	18						GCGCACAGAGCGGCGGCCCTC	0.672																																					p.R169H		Atlas-SNP	.											.	SLC46A2	30	.	0			c.G506A						.						17	22	20					9																	115652456		2201	4299	6500	SO:0001583	missense	57864	exon1			ACAGAGCGGCGGC	AF242557	CCDS6786.1	9q32	2013-05-22	2007-03-29	2007-03-29	ENSG00000119457	ENSG00000119457		"Solute carriers"	16055	protein-coding gene	gene with protein product		608956	"thymic stromal co-transporter"	TSCOT		10978518, 12826694	Standard	NM_033051		Approved	Ly110	uc004bgk.3	Q9BY10	OTTHUMG00000020513	ENST00000374228.4:c.506G>A	chr9.hg19:g.115652456C>T	ENSP00000363345:p.Arg169His	137.0	0.0		123.0	8.0	NM_033051	B1ALK1|Q86VT0|Q96NE2	Missense_Mutation	SNP	ENST00000374228.4	hg19	CCDS6786.1	.	.	.	.	.	.	.	.	.	.	C	33	5.256549	0.95336	.	.	ENSG00000119457	ENST00000374228	T	0.68765	-0.35	5.54	5.54	0.83059	Major facilitator superfamily domain, general substrate transporter (1);	0.095337	0.85682	D	0.000000	T	0.81088	0.4750	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82269	-0.0541	10	0.87932	D	0	-24.48	19.1516	0.93491	0.0:1.0:0.0:0.0	.	169	Q9BY10	TSCOT_HUMAN	H	169	ENSP00000363345:R169H	ENSP00000363345:R169H	R	-	2	0	SLC46A2	114692277	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.888000	0.69758	2.621000	0.88768	0.549000	0.68633	CGC	.	.		0.672	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051		T	115652456	C	T	115652456	3	4	167	1	0	0	0	0	1	0	0	0	14660	768	27	1	937	1	SLC46A2	9	115652456	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	1240533	115652456	25560975	83	25328										
CERCAM	51148	hgsc.bcm.edu	37	chr9	131186523	131186523	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggactcccagacctactactCcaacttctggtgtgggatca	9	13	2	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:131186523C>A	ENST00000372838.4	+	4	931	c.533C>A	c.(532-534)tCc>tAc	p.S178Y	CERCAM_ENST00000372842.1_Missense_Mutation_p.S100Y	NM_016174.4	NP_057258.3	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule	178					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|leukocyte cell-cell adhesion (GO:0007159)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|pancreas(2)	20						ACCTACTACTCCAACTTCTGG	0.607																																					p.S178Y		Atlas-SNP	.											.	CERCAM	104	.	0			c.C533A						.						88	99	95					9																	131186523		2203	4300	6503	SO:0001583	missense	51148	exon4			ACTACTCCAACTT	AB040935	CCDS6901.2, CCDS69675.1	9q34.13	2008-02-05	2007-10-17	2007-10-17	ENSG00000167123	ENSG00000167123			23723	protein-coding gene	gene with protein product	"glycosyltransferase 25 domain containing 3"		"cerebral cell adhesion molecule"	CEECAM1		10608765	Standard	NM_016174		Approved	GLT25D3, CerCAM	uc004buz.4	Q5T4B2	OTTHUMG00000020747	ENST00000372838.4:c.533C>A	chr9.hg19:g.131186523C>A	ENSP00000361929:p.Ser178Tyr	96.0	0.0		91.0	30.0	NM_016174	A7MD00|C4AMA2|Q0VDF3|Q2VPJ4|Q4KMP2|Q5T4B1|Q8N107|Q96EZ5|Q9P226|Q9UMW5	Missense_Mutation	SNP	ENST00000372838.4	hg19	CCDS6901.2	.	.	.	.	.	.	.	.	.	.	C	33	5.255502	0.95336	.	.	ENSG00000167123	ENST00000372842;ENST00000447915;ENST00000420512;ENST00000372838;ENST00000413863	T;T;T	0.26067	1.76;1.76;1.76	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.57975	0.2090	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.67741	-0.5592	10	0.87932	D	0	-10.4709	16.1793	0.81889	0.0:1.0:0.0:0.0	.	178	Q5T4B2	GT253_HUMAN	Y	100;100;100;178;131	ENSP00000361933:S100Y;ENSP00000416676:S100Y;ENSP00000361929:S178Y	ENSP00000361929:S178Y	S	+	2	0	CERCAM	130226344	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.609000	0.82925	2.385000	0.81259	0.467000	0.42956	TCC	.	.		0.607	CERCAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054435.2	NM_016174		A	131186523	C	A	131186523	3	1	167	1	0	0	0	0	1	0	0	0	3268	855	30	3	547	3	CERCAM	9	131186523	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	15534067	131186523	10026908	84	25329										
FAM73B	84895	hgsc.bcm.edu	37	chr9	131832663	131832663	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctggggtacctgggggtgccCgcggccagcagcgcaggcgt	19	13	0	0	rs375061896		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:131832663C>T	ENST00000358369.4	+	16	1939	c.1713C>T	c.(1711-1713)ccC>ccT	p.P571P	FAM73B_ENST00000277475.5_3'UTR|FAM73B_ENST00000406926.2_3'UTR	NM_032809.2	NP_116198.2	Q7L4E1	FA73B_HUMAN	family with sequence similarity 73, member B	571					bone development (GO:0060348)	integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)	13						TGGGGGTGCCCGCGGCCAGCA	0.697																																					p.P571P		Atlas-SNP	.											.	FAM73B	37	.	0			c.C1713T						.																																			SO:0001819	synonymous_variant	84895	exon16			GGTGCCCGCGGCC	AK074127	CCDS6917.1	9q34.13	2008-02-05	2005-08-11	2005-08-11	ENSG00000148343	ENSG00000148343			23621	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 54"	C9orf54			Standard	NM_032809		Approved	FLJ14596, FLJ00199	uc004bxa.3	Q7L4E1	OTTHUMG00000020770	ENST00000358369.4:c.1713C>T	chr9.hg19:g.131832663C>T		155.0	0.0		134.0	12.0	NM_032809	Q8NBM3|Q8TEJ6|Q969E6	Silent	SNP	ENST00000358369.4	hg19	CCDS6917.1																																																																																			.	.		0.697	FAM73B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054542.7	NM_032809		T	131832663	C	T	131832663	2	4	167	1	0	0	0	0	0	0	0	1	5626	639	23	1		1	FAM73B	9	131832663	Silent	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	646140	131832663	9380768	85	25330										
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139395186	139395186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgtctggttgtgcaggctggCgccctggtagatgaagtcgg	17	8	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr9:139395186C>T	ENST00000277541.6	-	31	5827	c.5752G>A	c.(5752-5754)Gcc>Acc	p.A1918T		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1918					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A1919T(1)|p.A1918T(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGCAGGCTGGCGCCCTGGTAG	0.692			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.A1918T		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	NOTCH1_ENST00000277541,NS,carcinoma,0,2	NOTCH1	1980	.	2	Substitution - Missense(2)	endometrium(2)	c.G5752A						.						61	75	71					9																	139395186		2144	4268	6412	SO:0001583	missense	4851	exon31			GGCTGGCGCCCTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5752G>A	chr9.hg19:g.139395186C>T	ENSP00000277541:p.Ala1918Thr	52.0	0.0		69.0	18.0	NM_017617	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	hg19	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.661939	0.88251	.	.	ENSG00000148400	ENST00000277541	T	0.60672	0.17	4.62	4.62	0.57501	Ankyrin repeat-containing domain (3);	0.053761	0.64402	D	0.000001	T	0.65069	0.2656	M	0.84082	2.675	0.80722	D	1	D	0.62365	0.991	B	0.43916	0.436	T	0.75720	-0.3219	10	0.87932	D	0	.	16.9775	0.86317	0.0:1.0:0.0:0.0	.	1918	P46531	NOTC1_HUMAN	T	1918	ENSP00000277541:A1918T	ENSP00000277541:A1918T	A	-	1	0	NOTCH1	138515007	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	7.578000	0.82498	2.317000	0.78254	0.549000	0.68633	GCC	.	.		0.692	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		T	139395186	C	T	139395186	3	4	167	1	0	0	0	0	1	0	0	0	10556	768	27	1	1931	1	NOTCH1	9	139395186	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	7562523	139395186	1818245	86	25331										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27342285	27342285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tcactcccttccctttcttgCtcttcttctgatgctacttc	3	16	5	1	rs138423863	byFrequency	TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr10:27342285C>A	ENST00000376087.4	-	16	1764	c.1599G>T	c.(1597-1599)gaG>gaT	p.E533D	ANKRD26_ENST00000436985.2_Missense_Mutation_p.E549D|ANKRD26_ENST00000376070.3_5'Flank	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	533					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CCCTTTCTTGCTCTTCTTCTG	0.294																																					p.E533D		Atlas-SNP	.											.	ANKRD26	179	.	0			c.G1599T						.						177	170	172					10																	27342285		1798	4062	5860	SO:0001583	missense	22852	exon16			TTCTTGCTCTTCT	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.1599G>T	chr10.hg19:g.27342285C>A	ENSP00000365255:p.Glu533Asp	71.0	0.0		70.0	22.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	hg19	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	C	10.64	1.405899	0.25378	.	.	ENSG00000107890	ENST00000376087;ENST00000436985	T;T	0.36699	4.12;1.24	3.33	-2.02	0.07388	.	2.522110	0.03352	U	0.196392	T	0.29491	0.0735	L	0.52573	1.65	0.38414	D	0.946015	B;B;B	0.30851	0.297;0.197;0.034	B;B;B	0.27170	0.077;0.035;0.015	T	0.19418	-1.0306	10	0.56958	D	0.05	.	2.9844	0.05963	0.2385:0.3747:0.0:0.3868	.	533;533;549	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	D	533;549	ENSP00000365255:E533D;ENSP00000405112:E549D	ENSP00000365255:E533D	E	-	3	2	ANKRD26	27382291	0.836000	0.29430	0.014000	0.15608	0.035000	0.12851	-0.381000	0.07417	-0.394000	0.07727	0.484000	0.47621	GAG	.	.		0.294	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			A	27342285	C	A	27342285	3	1	167	1	0	0	0	0	1	0	0	0	654	796	28	3	3609	3	ANKRD26	10	27342285	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10		27342285	108192462	87	25332										
NOC3L	64318	hgsc.bcm.edu	37	chr10	96116942	96116942	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tagactcacctggcttctccCtagtctgtgggattatacca	8	12	3	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr10:96116942C>T	ENST00000371361.3	-	4	597	c.497G>A	c.(496-498)aGg>aAg	p.R166K	NOC3L_ENST00000371350.1_Missense_Mutation_p.R166K|NOC3L_ENST00000463649.1_5'UTR	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	166					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				TGGCTTCTCCCTAGTCTGTGG	0.323																																					p.R166K		Atlas-SNP	.											.	NOC3L	67	.	0			c.G497A						.						133	129	130					10																	96116942		2203	4300	6503	SO:0001583	missense	64318	exon4			TTCTCCCTAGTCT	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.497G>A	chr10.hg19:g.96116942C>T	ENSP00000360412:p.Arg166Lys	101.0	0.0		113.0	21.0	NM_022451	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	hg19	CCDS7433.1	.	.	.	.	.	.	.	.	.	.	C	8.350	0.830640	0.16820	.	.	ENSG00000173145	ENST00000371361;ENST00000371350	T;T	0.11930	2.73;2.73	5.18	5.18	0.71444	.	0.137834	0.64402	D	0.000006	T	0.07863	0.0197	N	0.19112	0.55	0.36518	D	0.87	B	0.28233	0.204	B	0.26310	0.068	T	0.09292	-1.0681	10	0.05721	T	0.95	-2.0234	12.2812	0.54765	0.2846:0.7154:0.0:0.0	.	166	Q8WTT2	NOC3L_HUMAN	K	166	ENSP00000360412:R166K;ENSP00000360401:R166K	ENSP00000360401:R166K	R	-	2	0	NOC3L	96106932	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.252000	0.72447	2.569000	0.86673	0.561000	0.74099	AGG	.	.		0.323	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451		T	96116942	C	T	96116942	3	4	167	1	0	0	0	0	1	0	0	0	10523	681	24	3	1977	3	NOC3L	10	96116942	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	68774657	96116942	39417805	88	25333										
NEURL	9148	hgsc.bcm.edu	37	chr10	105344941	105344941	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctcgcagccgctttggatgcTcttcggcctgcacgggacca	12	15	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr10:105344941T>A	ENST00000369780.4	+	4	1707	c.1298T>A	c.(1297-1299)cTc>cAc	p.L433H	NEURL_ENST00000369777.2_Missense_Mutation_p.L416H	NM_004210.4	NP_004201.3	O76050	NEUL1_HUMAN		433	NHR 2. {ECO:0000255|PROSITE- ProRule:PRU00400}.				brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Notch signaling pathway (GO:0045746)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse maturation (GO:0090129)|protein monoubiquitination (GO:0006513)|skeletal muscle tissue development (GO:0007519)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|translation factor activity, non-nucleic acid binding (GO:0045183)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	17				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)		CTTTGGATGCTCTTCGGCCTG	0.697																																					p.L433H		Atlas-SNP	.											.	NEURL	38	.	0			c.T1298A						.						8	9	9					10																	105344941		2088	4133	6221	SO:0001583	missense	9148	exon4			GGATGCTCTTCGG																												ENST00000369780.4:c.1298T>A	chr10.hg19:g.105344941T>A	ENSP00000358795:p.Leu433His	46.0	0.0		48.0	5.0	NM_004210	Q5TDR2|Q5TDR3|Q8TAN0|Q9H463	Missense_Mutation	SNP	ENST00000369780.4	hg19	CCDS7551.1	.	.	.	.	.	.	.	.	.	.	T	18.56	3.650112	0.67472	.	.	ENSG00000107954	ENST00000369780;ENST00000369777	.	.	.	4.82	4.82	0.62117	NEUZ (1);	0.107189	0.64402	D	0.000004	T	0.68531	0.3011	L	0.61218	1.895	0.45837	D	0.998707	D	0.69078	0.997	P	0.57283	0.817	T	0.73275	-0.4034	9	0.87932	D	0	-0.341	14.3726	0.66852	0.0:0.0:0.0:1.0	.	433	O76050	NEU1A_HUMAN	H	433;416	.	ENSP00000358792:L416H	L	+	2	0	NEURL	105334931	1.000000	0.71417	1.000000	0.80357	0.385000	0.30292	8.040000	0.89188	1.804000	0.52760	0.260000	0.18958	CTC	.	.		0.697	NEURL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050170.1			A	105344941	T	A	105344941	3	1	167	1	0	0	0	0	1	0	0	0	10354	1551	54	4	1312	4	NEURL	10	105344941	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	9227999	105344941	30189806	89	25334										
PNLIP	5406	hgsc.bcm.edu	37	chr10	118306864	118306864	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gatgactccccatggtcaggAattacggaaagacccctcca	9	13	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr10:118306864A>T	ENST00000369221.2	+	3	133	c.105A>T	c.(103-105)ggA>ggT	p.G35G	PNLIP_ENST00000470562.1_3'UTR	NM_000936.2	NP_000927.1	P16233	LIPP_HUMAN	pancreatic lipase	35					intestinal cholesterol absorption (GO:0030299)|lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|triglyceride lipase activity (GO:0004806)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	43				all cancers(201;0.0131)	Glycerol Phenylbutyrate(DB08909)|Orlistat(DB01083)	CATGGTCAGGAATTACGGAAA	0.433																																					p.G35G		Atlas-SNP	.											.	PNLIP	166	.	0			c.A105T						.						93	90	91					10																	118306864		2203	4300	6503	SO:0001819	synonymous_variant	5406	exon3			GTCAGGAATTACG	BC014309	CCDS7594.1	10q25.3	2012-07-31			ENSG00000175535	ENSG00000175535	3.1.1.3		9155	protein-coding gene	gene with protein product		246600				1783385	Standard	NM_000936		Approved	PL	uc001lcm.3	P16233	OTTHUMG00000019103	ENST00000369221.2:c.105A>T	chr10.hg19:g.118306864A>T		123.0	0.0		128.0	39.0	NM_000936	Q5VSQ2	Silent	SNP	ENST00000369221.2	hg19	CCDS7594.1																																																																																			.	.		0.433	PNLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050524.1	NM_000936		T	118306864	A	T	118306864	2	4	167	1	0	0	0	0	0	0	0	1	12158	233	9	4		4	PNLIP	10	118306864	Silent	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	12961923	118306864	17227883	90	25335										
KCNA4	3739	hgsc.bcm.edu	37	chr11	30033588	30033588	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aatactcattgcgcaaagggTcaaagtactgagtcctcttt	8	9	3	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr11:30033588T>A	ENST00000328224.6	-	2	1871	c.638A>T	c.(637-639)gAc>gTc	p.D213V	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	213					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	GCGCAAAGGGTCAAAGTACTG	0.463																																					p.D213V		Atlas-SNP	.											.	KCNA4	158	.	0			c.A638T						.						69	65	66					11																	30033588		1872	4106	5978	SO:0001583	missense	3739	exon2			AAAGGGTCAAAGT	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.638A>T	chr11.hg19:g.30033588T>A	ENSP00000328511:p.Asp213Val	62.0	0.0		51.0	35.0	NM_002233		Missense_Mutation	SNP	ENST00000328224.6	hg19	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.644769	0.67358	.	.	ENSG00000182255	ENST00000328224	T	0.78003	-1.14	4.81	4.81	0.61882	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.052911	0.64402	D	0.000001	D	0.89444	0.6717	M	0.91717	3.235	0.80722	D	1	D	0.69078	0.997	D	0.65987	0.94	D	0.91931	0.5555	10	0.87932	D	0	.	14.382	0.66916	0.0:0.0:0.0:1.0	.	213	P22459	KCNA4_HUMAN	V	213	ENSP00000328511:D213V	ENSP00000328511:D213V	D	-	2	0	KCNA4	29990164	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.008000	0.88588	1.808000	0.52836	0.459000	0.35465	GAC	.	.		0.463	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		A	30033588	T	A	30033588	3	1	167	1	0	0	0	0	1	0	0	0	8014	1667	58	4	1327	4	KCNA4	11	30033588	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10		30033588	104972928	91	25336										
WT1	7490	hgsc.bcm.edu	37	chr11	32450064	32450064	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cagcgagccctgctggcccaTgggatcctcatgcttgaatg	12	13	1	1	rs142653301		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr11:32450064T>G	ENST00000379079.2	-	2	385	c.112A>C	c.(112-114)Atg>Ctg	p.M38L	WT1_ENST00000332351.3_Missense_Mutation_p.M250L|WT1_ENST00000448076.3_Missense_Mutation_p.M250L|WT1_ENST00000530998.1_Missense_Mutation_p.M38L	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	182	Pro-rich.				adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.?(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			TGCTGGCCCATGGGATCCTCA	0.612			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																												p.M250L		Atlas-SNP	.	yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	.	WT1	744	.	1	Unknown(1)	kidney(1)	c.A748C						.						87	67	74					11																	32450064		2202	4299	6501	SO:0001583	missense	7490	exon2	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	GGCCCATGGGATC		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.112A>C	chr11.hg19:g.32450064T>G	ENSP00000368370:p.Met38Leu	81.0	0.0		72.0	28.0	NM_024424	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000379079.2	hg19	CCDS55751.1	.	.	.	.	.	.	.	.	.	.	T	11.61	1.691120	0.30052	.	.	ENSG00000184937	ENST00000379079;ENST00000332351;ENST00000530998;ENST00000452863;ENST00000448076;ENST00000527775	T;T;T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43;-1.43;-1.43	5.62	5.62	0.85841	Wilm&apos (1);s tumour protein, N-terminal (1);	0.344892	0.24899	U	0.034714	T	0.60741	0.2292	N	0.04018	-0.295	0.32431	N	0.54802	B;B;B;B;B	0.06786	0.001;0.0;0.001;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.0;0.0	T	0.61505	-0.7049	10	0.18276	T	0.48	.	12.9355	0.58311	0.0:0.0:0.2044:0.7956	.	255;182;255;38;38	P19544-8;P19544;P19544-7;B3KSA5;P19544-6	.;WT1_HUMAN;.;.;.	L	38;250;38;250;250;1	ENSP00000368370:M38L;ENSP00000331327:M250L;ENSP00000435307:M38L;ENSP00000415516:M250L;ENSP00000413452:M250L;ENSP00000435351:M1L	ENSP00000331327:M250L	M	-	1	0	WT1	32406640	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.663000	0.46774	2.279000	0.76181	0.459000	0.35465	ATG	.	T|1.000;C|0.000		0.612	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378		G	32450064	T	G	32450064	3	3	167	1	0	0	0	0	1	0	0	0	17423	1464	51	5	841	5	WT1	11	32450064	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	2416476	32450064	102556452	92	25337										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33572682	33572682	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctgtggtgatcgaaatgctgGgtgtgtatggagtcagcaac	15	6	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr11:33572682G>A	ENST00000321505.4	+	4	2887	c.2707G>A	c.(2707-2709)Ggt>Agt	p.G903S	KIAA1549L_ENST00000265654.5_Missense_Mutation_p.G909S|KIAA1549L_ENST00000389726.3_Missense_Mutation_p.G909S			Q6ZVL6	K154L_HUMAN	KIAA1549-like	903						integral component of membrane (GO:0016021)											CGAAATGCTGGGTGTGTATGG	0.493																																					p.G903S		Atlas-SNP	.											.	.	.	.	0			c.G2707A						.						206	206	206					11																	33572682		2171	4270	6441	SO:0001583	missense	25758	exon4			ATGCTGGGTGTGT	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.2707G>A	chr11.hg19:g.33572682G>A	ENSP00000315295:p.Gly903Ser	129.0	0.0		119.0	98.0	NM_012194	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	hg19	CCDS44565.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.245|8.245	0.807768|0.807768	0.16467|0.16467	.|.	.|.	ENSG00000110427|ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000265654;ENST00000536568|ENST00000526400	.|.	.|.	.|.	6.06|6.06	2.94|2.94	0.34122|0.34122	.|.	0.721236|.	0.14787|.	N|.	0.298422|.	T|.	0.24044|.	0.0582|.	N|N	0.24115|0.24115	0.695|0.695	0.28889|0.28889	N|N	0.893961|0.893961	P;D|.	0.61697|.	0.842;0.99|.	B;P|.	0.61003|.	0.236;0.882|.	T|.	0.14783|.	-1.0460|.	9|.	0.32370|.	T|.	0.25|.	-9.2274|-9.2274	5.3107|5.3107	0.15829|0.15829	0.1989:0.2808:0.5202:0.0|0.1989:0.2808:0.5202:0.0	.|.	909;909|.	E9PAT2;Q6ZVL6-2|.	.;.|.	S|X	903;909;909;742|300	.|.	ENSP00000265654:G909S|.	G|W	+|+	1|3	0|0	C11orf41|C11orf41	33529258|33529258	0.021000|0.021000	0.18746|0.18746	0.993000|0.993000	0.49108|0.49108	0.716000|0.716000	0.41182|0.41182	0.819000|0.819000	0.27308|0.27308	1.569000|1.569000	0.49696|0.49696	0.655000|0.655000	0.94253|0.94253	GGT|TGG	.	.		0.493	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33572682	G	A	33572682	3	1	167	1	0	0	0	0	1	0	0	0	1642	1232	43	3	2739	3	C11orf41	11	33572682	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	1122618	33572682	101433834	93	25338										
PLCB3	5331	hgsc.bcm.edu	37	chr11	64032516	64032517	+	Frame_Shift_Ins	INS	-	-	C													0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ccccagcccactggatgcctINSccccccgccggccccctggc							TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr11:64032516_64032517insC	ENST00000540288.1	+	23	2849_2850	c.2746_2747insC	c.(2746-2748)tccfs	p.S916fs	PLCB3_ENST00000325234.5_Frame_Shift_Ins_p.S849fs|PLCB3_ENST00000279230.6_Frame_Shift_Ins_p.S916fs	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	916					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						ACTGGATGCCTCCCCCCGCCGG	0.703																																					p.S916fs		Atlas-INDEL	.											.	PLCB3	103	.	0			c.2746_2747insC						.																																			SO:0001589	frameshift_variant	5331	exon23			.	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.2752dupC	chr11.hg19:g.64032522_64032522dupC	ENSP00000443631:p.Ser916fs	194.0	0.0		178.0	11.0	NM_000932	A5PKZ6|G5E960|Q8N1A4	Frame_Shift_Ins	INS	ENST00000540288.1	hg19	CCDS8064.1																																																																																			.	.		0.703	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1			C	64032517	-	C	64032516	7	5	167	1	0	1	1	0	0	0	0	0	12038	1551	54	0	2836	0	PLCB3	11	64032516	Frame_Shift_Ins	INS	-	TCGA-DD-AACP-01A-11D-A40R-10	30459834	64032516	70974000	94	25339										
RPS6KB2	6199	hgsc.bcm.edu	37	chr11	67200655	67200655	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctgtggactggtggagcctgGgggccctgatgtacgacatg	17	9	0	1	rs536646745		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr11:67200655G>A	ENST00000312629.5	+	9	811	c.766G>A	c.(766-768)Ggg>Agg	p.G256R	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	256	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			GTGGAGCCTGGGGGCCCTGAT	0.682																																					p.G256R		Atlas-SNP	.											.	RPS6KB2	92	.	0			c.G766A						.						17	19	19					11																	67200655		1955	4125	6080	SO:0001583	missense	6199	exon9			AGCCTGGGGGCCC	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"ribosomal protein S6 kinase, 70kD, polypeptide 2"			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.766G>A	chr11.hg19:g.67200655G>A	ENSP00000308413:p.Gly256Arg	76.0	0.0		39.0	13.0	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	hg19	CCDS41677.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.891680	0.91889	.	.	ENSG00000175634	ENST00000312629	T	0.76578	-1.03	4.88	4.88	0.63580	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93926	0.8056	H	0.99752	4.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96819	0.9602	10	0.87932	D	0	.	17.8166	0.88637	0.0:0.0:1.0:0.0	.	256;256	Q9BRS0;Q9UBS0	.;KS6B2_HUMAN	R	256	ENSP00000308413:G256R	ENSP00000308413:G256R	G	+	1	0	RPS6KB2	66957231	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.942000	0.92970	2.521000	0.84997	0.561000	0.74099	GGG	.	.		0.682	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952		A	67200655	G	A	67200655	3	1	167	1	0	0	0	0	1	0	0	0	13672	1232	43	3	800	3	RPS6KB2	11	67200655	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	3168139	67200655	67805861	95	25340										
XRRA1	143570	hgsc.bcm.edu	37	chr11	74563036	74563036	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggtttgcgggcactatacctCgtgtatgggccaccagaggg	15	10	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr11:74563036C>T	ENST00000340360.6	-	13	1569	c.1238G>A	c.(1237-1239)cGa>cAa	p.R413Q	XRRA1_ENST00000527087.1_Intron|XRRA1_ENST00000321448.8_Missense_Mutation_p.R138Q	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1									p.R413L(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						CACTATACCTCGTGTATGGGC	0.547																																					p.R413Q		Atlas-SNP	.											XRRA1,NS,carcinoma,0,1	XRRA1	46	.	1	Substitution - Missense(1)	prostate(1)	c.G1238A						.						116	115	115					11																	74563036		1996	4165	6161	SO:0001583	missense	143570	exon13			ATACCTCGTGTAT	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1238G>A	chr11.hg19:g.74563036C>T	ENSP00000339918:p.Arg413Gln	107.0	0.0		87.0	36.0	NM_182969		Missense_Mutation	SNP	ENST00000340360.6	hg19	CCDS44680.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.893170	0.91889	.	.	ENSG00000166435	ENST00000340360;ENST00000321448;ENST00000344880;ENST00000398418	T;T	0.52526	0.66;1.42	6.07	3.9	0.45041	.	.	.	.	.	T	0.45836	0.1362	M	0.63428	1.95	0.80722	D	1	D;P;P	0.58970	0.984;0.576;0.777	P;B;B	0.44860	0.462;0.113;0.159	T	0.45804	-0.9236	9	0.42905	T	0.14	-16.5361	9.5643	0.39389	0.0:0.8189:0.0:0.1811	.	413;357;399	Q6P2D8;Q6P2D8-4;Q6P2D8-3	XRRA1_HUMAN;.;.	Q	413;138;399;357	ENSP00000339918:R413Q;ENSP00000319303:R138Q	ENSP00000319303:R138Q	R	-	2	0	XRRA1	74240684	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	2.431000	0.44775	1.582000	0.49881	0.585000	0.79938	CGA	.	.		0.547	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969		T	74563036	C	T	74563036	3	4	167	1	0	0	0	0	1	0	0	0	17476	884	31	1	1168	1	XRRA1	11	74563036	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	7362381	74563036	60443480	96	25341										
DLG2	1740	hgsc.bcm.edu	37	chr11	83177808	83177808	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	caatgggatagagctgggcaActtgtaaccgcttgatagca	12	8	0	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr11:83177808A>G	ENST00000532653.1	-	21	2605	c.2303T>C	c.(2302-2304)gTt>gCt	p.V768A	DLG2_ENST00000404783.3_Missense_Mutation_p.V264A|DLG2_ENST00000398309.2_Missense_Mutation_p.V786A|DLG2_ENST00000524982.1_Missense_Mutation_p.V782A|DLG2_ENST00000280241.8_Missense_Mutation_p.V825A|DLG2_ENST00000543673.1_Missense_Mutation_p.V891A|DLG2_ENST00000376104.2_Missense_Mutation_p.V891A|DLG2_ENST00000426717.2_Missense_Mutation_p.V250A|DLG2_ENST00000537455.1_Missense_Mutation_p.V536A|DLG2_ENST00000531015.1_Missense_Mutation_p.V753A|DLG2_ENST00000330014.6_Missense_Mutation_p.V707A|DLG2_ENST00000418306.2_Missense_Mutation_p.V665A|DLG2_ENST00000376106.3_Missense_Mutation_p.V250A			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	482					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				GAGCTGGGCAACTTGTAACCG	0.443																																					p.V891A		Atlas-SNP	.											.	DLG2	448	.	0			c.T2672C						.						146	143	144					11																	83177808		1882	4104	5986	SO:0001583	missense	1740	exon26			TGGGCAACTTGTA	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.2303T>C	chr11.hg19:g.83177808A>G	ENSP00000435849:p.Val768Ala	78.0	0.0		66.0	21.0	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.02	1.813343	0.32053	.	.	ENSG00000150672	ENST00000398309;ENST00000426717;ENST00000376104;ENST00000418306;ENST00000543673;ENST00000280241;ENST00000404783;ENST00000330014;ENST00000537455;ENST00000376106;ENST00000524982;ENST00000532653;ENST00000546021;ENST00000531015;ENST00000457267	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08;1.08;1.08;1.08;1.08;1.08;1.08;1.08;1.08;1.08	5.84	5.84	0.93424	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.000000	0.64402	D	0.000013	T	0.35566	0.0936	L	0.28458	0.855	0.58432	D	0.999996	P;B;B;B;B;B;B;B	0.46784	0.884;0.001;0.0;0.0;0.0;0.001;0.132;0.001	P;B;B;B;B;B;B;B	0.45660	0.489;0.011;0.002;0.005;0.008;0.004;0.101;0.003	T	0.09037	-1.0693	9	.	.	.	.	11.2836	0.49210	0.9295:0.0:0.0705:0.0	.	753;768;782;707;264;891;786;665	E9PIW2;B7Z2T4;E9PN83;B7Z264;B5MCC5;Q15700-2;Q15700;Q15700-3	.;.;.;.;.;.;DLG2_HUMAN;.	A	786;250;891;665;891;825;264;707;536;250;782;768;891;753;138	ENSP00000381355:V786A;ENSP00000393049:V250A;ENSP00000365272:V891A;ENSP00000402275:V665A;ENSP00000441994:V891A;ENSP00000280241:V825A;ENSP00000385113:V264A;ENSP00000381353:V707A;ENSP00000443248:V536A;ENSP00000365274:V250A;ENSP00000432894:V782A;ENSP00000435849:V768A;ENSP00000433848:V753A;ENSP00000409133:V138A	.	V	-	2	0	DLG2	82855456	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.898000	0.63238	2.219000	0.72066	0.528000	0.53228	GTT	.	.		0.443	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		G	83177808	A	G	83177808	3	3	167	1	0	0	0	0	1	0	0	0	4557	43	2	2	267	2	DLG2	11	83177808	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	8614772	83177808	51828708	97	25342										
C11orf87	399947	hgsc.bcm.edu	37	chr11	109294946	109294946	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ccttttgcaaacggtggtacTgtcctgatcgtctagcccct	9	13	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr11:109294946T>A	ENST00000327419.6	+	2	990	c.587T>A	c.(586-588)cTg>cAg	p.L196Q	RP11-708B6.2_ENST00000532929.1_RNA|RP11-708B6.2_ENST00000532992.1_RNA	NM_207645.3	NP_997528.2	Q6NUJ2	CK087_HUMAN	chromosome 11 open reading frame 87	196						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17						ACGGTGGTACTGTCCTGATCG	0.577																																					p.L196Q		Atlas-SNP	.											.	C11orf87	37	.	0			c.T587A						.						33	32	32					11																	109294946		2201	4298	6499	SO:0001583	missense	399947	exon2			TGGTACTGTCCTG	AB096240, BC035798	CCDS31672.1	11q22.3	2013-12-13	2013-12-13	2013-12-13	ENSG00000185742	ENSG00000185742			33788	protein-coding gene	gene with protein product	"neuronal integral membrane protein 1"					12477932	Standard	NM_207645		Approved	LOH11CR1A, LOC399947, NEURIM1	uc010rwb.2	Q6NUJ2		ENST00000327419.6:c.587T>A	chr11.hg19:g.109294946T>A	ENSP00000331581:p.Leu196Gln	86.0	0.0		57.0	20.0	NM_207645	B4E169	Missense_Mutation	SNP	ENST00000327419.6	hg19	CCDS31672.1	.	.	.	.	.	.	.	.	.	.	T	16.30	3.083311	0.55861	.	.	ENSG00000185742	ENST00000327419	.	.	.	3.8	3.8	0.43715	.	0.316142	0.16595	U	0.207620	T	0.57227	0.2039	N	0.19112	0.55	0.40562	D	0.981223	D	0.76494	0.999	D	0.85130	0.997	T	0.62854	-0.6766	9	0.87932	D	0	-0.1988	12.3675	0.55236	0.0:0.0:0.0:1.0	.	196	Q6NUJ2	CK087_HUMAN	Q	196	.	ENSP00000331581:L196Q	L	+	2	0	C11orf87	108800156	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.016000	0.64041	1.956000	0.56807	0.533000	0.62120	CTG	.	.		0.577	C11orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390403.1	NM_207645		A	109294946	T	A	109294946	3	1	167	1	0	0	0	0	1	0	0	0	1671	1580	55	4	589	4	C11orf87	11	109294946	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	26117138	109294946	25711570	98	25343										
TECTA	7007	hgsc.bcm.edu	37	chr11	121016430	121016430	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tcggagcatgcagaacagcaCctatggtctgtgtggccgct	13	11	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr11:121016430C>T	ENST00000392793.1	+	12	3981	c.3710C>T	c.(3709-3711)aCc>aTc	p.T1237I	TECTA_ENST00000478058.1_3'UTR|TECTA_ENST00000264037.2_Missense_Mutation_p.T1237I			O75443	TECTA_HUMAN	tectorin alpha	1237	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CAGAACAGCACCTATGGTCTG	0.542																																					p.T1237I		Atlas-SNP	.											.	TECTA	329	.	0			c.C3710T						.						154	124	134					11																	121016430		2203	4299	6502	SO:0001583	missense	7007	exon11			ACAGCACCTATGG	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.3710C>T	chr11.hg19:g.121016430C>T	ENSP00000376543:p.Thr1237Ile	243.0	0.0		179.0	57.0	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.463297	0.63513	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.67698	-0.28;-0.28	5.76	4.85	0.62838	von Willebrand factor, type D domain (3);	0.127800	0.53938	D	0.000042	T	0.66896	0.2836	M	0.73217	2.22	0.47659	D	0.999484	B	0.30193	0.272	B	0.34385	0.181	T	0.64765	-0.6330	10	0.32370	T	0.25	.	14.2129	0.65776	0.0:0.9285:0.0:0.0715	.	1237	O75443	TECTA_HUMAN	I	1237	ENSP00000376543:T1237I;ENSP00000264037:T1237I	ENSP00000264037:T1237I	T	+	2	0	TECTA	120521640	0.995000	0.38212	0.702000	0.30337	0.963000	0.63663	4.939000	0.63526	2.721000	0.93114	0.591000	0.81541	ACC	.	.		0.542	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		T	121016430	C	T	121016430	3	4	167	1	0	0	0	0	1	0	0	0	15762	507	18	3	3752	3	TECTA	11	121016430	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	11721484	121016430	13990086	99	25344										
OR10S1	219873	hgsc.bcm.edu	37	chr11	123847992	123847992	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gttgacagatagccagatagCggtcataggccatgactgtg	13	8	1	4	rs199683540		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr11:123847992C>A	ENST00000531945.1	-	1	496	c.407G>T	c.(406-408)cGc>cTc	p.R136L		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		AGCCAGATAGCGGTCATAGGC	0.542																																					p.R136L		Atlas-SNP	.											.	OR10S1	78	.	0			c.G407T						.						100	83	88					11																	123847992		2202	4299	6501	SO:0001583	missense	219873	exon1			AGATAGCGGTCAT	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"GPCR / Class A : Olfactory receptors"	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.407G>T	chr11.hg19:g.123847992C>A	ENSP00000431914:p.Arg136Leu	74.0	0.0		60.0	52.0	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	hg19	CCDS31701.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.283685	0.80803	.	.	ENSG00000196248	ENST00000531945	T	0.77358	-1.09	4.74	3.84	0.44239	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38720	U	0.001587	D	0.91446	0.7300	H	0.97340	3.985	0.44834	D	0.997848	D	0.89917	1.0	D	0.72075	0.976	D	0.93549	0.6885	10	0.87932	D	0	-16.9097	12.6678	0.56851	0.0:0.9191:0.0:0.0809	.	136	Q8NGN2	O10S1_HUMAN	L	136	ENSP00000431914:R136L	ENSP00000431914:R136L	R	-	2	0	OR10S1	123353202	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	7.306000	0.78905	1.253000	0.44018	0.573000	0.79308	CGC	.	.		0.542	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474		A	123847992	C	A	123847992	3	1	167	1	0	0	0	0	1	0	0	0	10927	768	27	1	592	1	OR10S1	11	123847992	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	2831562	123847992	11158524	100	25345										
FAM90A1	55138	hgsc.bcm.edu	37	chr12	8376148	8376148	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gagccttcctctgcgggtctTgtggcctgcagaacagaaaa	12	11	2	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr12:8376148T>A	ENST00000538603.1	-	6	887	c.329A>T	c.(328-330)cAa>cTa	p.Q110L	FAM90A1_ENST00000307435.6_Missense_Mutation_p.Q110L	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	110							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		CTGCGGGTCTTGTGGCCTGCA	0.542																																					p.Q110L		Atlas-SNP	.											.	FAM90A1	68	.	0			c.A329T						.						32	31	32					12																	8376148		2201	4297	6498	SO:0001583	missense	55138	exon6			GGGTCTTGTGGCC	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.329A>T	chr12.hg19:g.8376148T>A	ENSP00000445418:p.Gln110Leu	35.0	0.0		47.0	18.0	NM_018088	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	hg19	CCDS31738.1	.	.	.	.	.	.	.	.	.	.	.	9.054	0.992835	0.18966	.	.	ENSG00000171847	ENST00000307435;ENST00000538603	T;T	0.13778	2.56;2.56	1.06	1.06	0.20224	.	.	.	.	.	T	0.09379	0.0231	L	0.38175	1.15	0.09310	N	1	B	0.29766	0.256	B	0.26310	0.068	T	0.29181	-1.0020	9	0.44086	T	0.13	-13.0793	4.2802	0.10829	0.0:0.0:0.0:1.0	.	110	Q86YD7	F90A1_HUMAN	L	110	ENSP00000307798:Q110L;ENSP00000445418:Q110L	ENSP00000307798:Q110L	Q	-	2	0	FAM90A1	8267415	0.011000	0.17503	0.031000	0.17742	0.072000	0.16883	0.260000	0.18424	0.721000	0.32231	0.172000	0.16884	CAA	.	.		0.542	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088		A	8376148	T	A	8376148	3	1	167	1	0	0	0	0	1	0	0	0	5658	1812	63	4	1073	4	FAM90A1	12	8376148	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10		8376148	125475747	101	25346										
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14794100	14794100	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gatcccatagctgtacacatCtcctttctgagagatgttgg	9	10	2	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr12:14794100C>G	ENST00000261170.3	-	18	2120	c.1984G>C	c.(1984-1986)Gat>Cat	p.D662H		NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	662	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	CTGTACACATCTCCTTTCTGA	0.493																																					p.D662H		Atlas-SNP	.											.	GUCY2C	126	.	0			c.G1984C						.						140	112	121					12																	14794100		2203	4300	6503	SO:0001583	missense	2984	exon18			ACACATCTCCTTT		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.1984G>C	chr12.hg19:g.14794100C>G	ENSP00000261170:p.Asp662His	87.0	0.0		80.0	8.0	NM_004963	B2RMY6	Missense_Mutation	SNP	ENST00000261170.3	hg19	CCDS8664.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.883343	0.72410	.	.	ENSG00000070019	ENST00000261170	D	0.88896	-2.44	5.34	5.34	0.76211	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.96574	0.8882	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97744	1.0210	10	0.87932	D	0	.	19.0276	0.92939	0.0:1.0:0.0:0.0	.	662	P25092	GUC2C_HUMAN	H	662	ENSP00000261170:D662H	ENSP00000261170:D662H	D	-	1	0	GUCY2C	14685367	1.000000	0.71417	0.977000	0.42913	0.351000	0.29236	7.773000	0.85462	2.495000	0.84180	0.655000	0.94253	GAT	.	.		0.493	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			G	14794100	C	G	14794100	3	3	167	1	0	0	0	0	1	0	0	0	6905	913	32	4	1277	4	GUCY2C	12	14794100	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	6417952	14794100	119057795	102	25347										
DDX11	1663	hgsc.bcm.edu	37	chr12	31247737	31247737	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tctcttccagagccagatcgAcaacatcaacctgttcaagg	7	13	3	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr12:31247737A>G	ENST00000407793.2	+	14	1714	c.1463A>G	c.(1462-1464)gAc>gGc	p.D488G	DDX11_ENST00000542838.1_Missense_Mutation_p.D488G|DDX11_ENST00000539673.1_3'UTR|DDX11_ENST00000545668.1_Missense_Mutation_p.D488G|DDX11_ENST00000350437.4_Missense_Mutation_p.D488G|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000228264.6_Missense_Mutation_p.D462G	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	488					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					AGCCAGATCGACAACATCAAC	0.483										Multiple Myeloma(12;0.14)																											p.D488G		Atlas-SNP	.											.	DDX11	188	.	0			c.A1463G						.						51	52	52					12																	31247737		2203	4297	6500	SO:0001583	missense	1663	exon14			AGATCGACAACAT	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1463A>G	chr12.hg19:g.31247737A>G	ENSP00000384703:p.Asp488Gly	241.0	1.0		268.0	133.0	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	hg19	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.528808	0.64860	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000404673;ENST00000228264;ENST00000545668;ENST00000350437	T;T;T;T;T	0.56611	0.45;0.45;0.45;0.45;0.45	3.23	3.23	0.37069	.	0.000000	0.85682	D	0.000000	T	0.73976	0.3656	M	0.90483	3.12	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.999;0.999	T	0.77635	-0.2514	10	0.72032	D	0.01	.	9.5852	0.39512	1.0:0.0:0.0:0.0	.	462;488;488;488	Q96FC9-3;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	G	488;488;213;462;488;488	ENSP00000443426:D488G;ENSP00000384703:D488G;ENSP00000228264:D462G;ENSP00000440402:D488G;ENSP00000309965:D488G	ENSP00000228264:D462G	D	+	2	0	DDX11	31139004	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	7.902000	0.87389	1.335000	0.45486	0.414000	0.27820	GAC	.	.		0.483	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		G	31247737	A	G	31247737	3	3	167	1	0	0	0	0	1	0	0	0	4345	275	10	2	1513	2	DDX11	12	31247737	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	16453637	31247737	102604158	103	25348										
INHBE	83729	hgsc.bcm.edu	37	chr12	57850290	57850290	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gccgggccaggaggaggaccCccacctgtgagcctgcgacc	15	16	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr12:57850290C>A	ENST00000266646.2	+	2	928	c.712C>A	c.(712-714)Ccc>Acc	p.P238T	INHBE_ENST00000551553.1_3'UTR	NM_031479.3	NP_113667.1	P58166	INHBE_HUMAN	inhibin, beta E	238					growth (GO:0040007)	extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	15						GAGGAGGACCCCCACCTGTGA	0.622											OREG0021944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P238T	GBM(191;1808 2166 15720 36624 50371)	Atlas-SNP	.											.	INHBE	38	.	0			c.C712A						.						77	89	85					12																	57850290		2203	4300	6503	SO:0001583	missense	83729	exon2			AGGACCCCCACCT		CCDS8939.1	12q13.2	2008-02-05				ENSG00000139269			24029	protein-coding gene	gene with protein product		612031				12242034	Standard	NM_031479		Approved	activin, MGC4638	uc001snw.3	P58166		ENST00000266646.2:c.712C>A	chr12.hg19:g.57850290C>A	ENSP00000266646:p.Pro238Thr	120.0	0.0	1026	132.0	6.0	NM_031479		Missense_Mutation	SNP	ENST00000266646.2	hg19	CCDS8939.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.855354	0.51376	.	.	ENSG00000139269	ENST00000547970;ENST00000266646	D;T	0.81908	-1.55;-1.26	4.79	4.79	0.61399	Transforming growth factor-beta, C-terminal (1);	0.187302	0.44097	D	0.000493	T	0.79149	0.4397	L	0.45581	1.43	0.40541	D	0.98102	B	0.19706	0.038	B	0.24394	0.053	T	0.74150	-0.3758	10	0.25106	T	0.35	-1.5374	17.1522	0.86781	0.0:1.0:0.0:0.0	.	238	P58166	INHBE_HUMAN	T	183;238	ENSP00000450212:P183T;ENSP00000266646:P238T	ENSP00000266646:P238T	P	+	1	0	INHBE	56136557	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.340000	0.65958	2.653000	0.90120	0.655000	0.94253	CCC	.	.		0.622	INHBE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406773.1	NM_031479		A	57850290	C	A	57850290	3	1	167	1	0	0	0	0	1	0	0	0	7753	623	22	3	718	3	INHBE	12	57850290	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	26602553	57850290	76001605	104	25349										
MARS	4141	hgsc.bcm.edu	37	chr12	57910274	57910274	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gacaagaacgaggttgctgcGgaggtggcgaaactcttgga	16	7	1	1	rs373439522		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr12:57910274G>A	ENST00000262027.5	+	21	2747	c.2613G>A	c.(2611-2613)gcG>gcA	p.A871A	RN7SL312P_ENST00000582079.1_RNA|MIR616_ENST00000385293.1_RNA	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	871	WHEP-TRS.				gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	AGGTTGCTGCGGAGGTGGCGA	0.483																																					p.A871A		Atlas-SNP	.											.	MARS	84	.	0			c.G2613A						.	G		0,4406		0,0,2203	66	64	65		2613	-10.9	0.9	12		65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MARS	NM_004990.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		871/901	57910274	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4141	exon21			TGCTGCGGAGGTG	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.2613G>A	chr12.hg19:g.57910274G>A		244.0	0.0		302.0	76.0	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Silent	SNP	ENST00000262027.5	hg19	CCDS8942.1																																																																																			.	.		0.483	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		A	57910274	G	A	57910274	2	1	167	1	0	0	0	0	0	0	0	1	9325	1103	39	1		1	MARS	12	57910274	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	59984	57910274	75941621	105	25350										
CMKLR1	1240	hgsc.bcm.edu	37	chr12	108686420	108686420	+	Frame_Shift_Del	DEL	A	A	-													0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tcttgcacatggctgtcccgAaaacccagtggtagtccatg							TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr12:108686420delA	ENST00000312143.7	-	3	683	c.320delT	c.(319-321)ttcfs	p.F107fs	CMKLR1_ENST00000397688.2_Frame_Shift_Del_p.F105fs|CMKLR1_ENST00000412676.1_Frame_Shift_Del_p.F107fs|CMKLR1_ENST00000550402.1_Frame_Shift_Del_p.F107fs|CMKLR1_ENST00000552995.1_Frame_Shift_Del_p.F105fs	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	107					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)	p.F105S(2)		endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						GGCTGTCCCGAAAACCCAGTG	0.517																																					p.F107fs		Atlas-INDEL	.											.	CMKLR1	67	.	2	Substitution - Missense(2)	lung(2)	c.321delC						.						134	140	138					12																	108686420		2130	4228	6358	SO:0001589	frameshift_variant	1240	exon3			.	U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"GPCR / Class A : Resolvin receptors"	2121	protein-coding gene	gene with protein product	"resolvin E1 receptor", "chemerin receptor"	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.320delT	chr12.hg19:g.108686420delA	ENSP00000311733:p.Phe107fs	215.0	0.0		256.0	50.0	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Frame_Shift_Del	DEL	ENST00000312143.7	hg19	CCDS44965.1																																																																																			.	.		0.517	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1			-	108686420	A	-	108686420	7	5	167	1	0	1	0	1	0	0	0	0	3581	246	9	0	805	0	CMKLR1	12	108686420	Frame_Shift_Del	DEL	A	TCGA-DD-AACP-01A-11D-A40R-10	50776146	108686420	25165475	106	25351										
TMEM119	338773	hgsc.bcm.edu	37	chr12	108985575	108985575	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ccctccaccatcctggctccGtccccaccgcccagtgcagc	7	23	0	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr12:108985575G>A	ENST00000392806.3	-	2	753	c.585C>T	c.(583-585)gaC>gaT	p.D195D		NM_181724.2	NP_859075.2	Q4V9L6	TM119_HUMAN	transmembrane protein 119	195					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(3)|ovary(1)|skin(1)	7						TCCTGGCTCCGTCCCCACCGC	0.682																																					p.D195D		Atlas-SNP	.											.	TMEM119	31	.	0			c.C585T						.						41	34	36					12																	108985575		2203	4300	6503	SO:0001819	synonymous_variant	338773	exon2			GGCTCCGTCCCCA	AK075501	CCDS9119.1	12q23.3	2014-02-12				ENSG00000183160			27884	protein-coding gene	gene with protein product						12975309	Standard	NM_181724		Approved		uc001tng.3	Q4V9L6		ENST00000392806.3:c.585C>T	chr12.hg19:g.108985575G>A		47.0	0.0		50.0	26.0	NM_181724	Q6UXE5|Q8N2F5	Silent	SNP	ENST00000392806.3	hg19	CCDS9119.1																																																																																			.	.		0.682	TMEM119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403900.1	NM_181724		A	108985575	G	A	108985575	2	1	167	1	0	0	0	0	0	0	0	1	16047	1136	40	1		1	TMEM119	12	108985575	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	299155	108985575	24866320	107	25352										
CDK8	1024	hgsc.bcm.edu	37	chr13	26911779	26911779	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tcggcatgtagagaaatagcAgtaagtgaagttctttttat	10	4	1	2	rs371097459		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr13:26911779A>T	ENST00000381527.3	+	2	707	c.204A>T	c.(202-204)gcA>gcT	p.A68A	CDK8_ENST00000536792.1_Splice_Site_p.A68A	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	68	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		GAGAAATAGCAGTAAGTGAAG	0.299																																					p.A68A		Atlas-SNP	.											.	CDK8	61	.	0			c.A204T						.						89	101	97					13																	26911779		2203	4291	6494	SO:0001630	splice_region_variant	1024	exon2			AATAGCAGTAAGT	X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"Cyclin-dependent kinases"	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.204+1A>T	chr13.hg19:g.26911779A>T		228.0	0.0		132.0	109.0	NM_001260	Q5VUF3|Q6ISB5	Silent	SNP	ENST00000381527.3	hg19	CCDS9317.1																																																																																			.	.		0.299	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1		Silent	T	26911779	A	T	26911779	5	4	167	1	0	0	0	0	0	0	1	0	3152	202	7	4	210	4	CDK8	13	26911779	Splice_Site	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10		26911779	88258099	108	25353										
NBEA	26960	hgsc.bcm.edu	37	chr13	36046629	36046629	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ccacgacagaaatctacttcGaggtagatgaggatgattct	10	8	2	4			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr13:36046629G>A	ENST00000400445.3	+	41	7075	c.6541G>A	c.(6541-6543)Gag>Aag	p.E2181K	NBEA_ENST00000540320.1_Missense_Mutation_p.E2181K|NBEA_ENST00000379939.2_Missense_Mutation_p.E2178K|NBEA_ENST00000310336.4_Missense_Mutation_p.E2181K	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2181					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AATCTACTTCGAGGTAGATGA	0.527																																					p.E2181K		Atlas-SNP	.											NBEA,colon,carcinoma,0,1	NBEA	340	.	0			c.G6541A						.						87	87	87					13																	36046629		1987	4170	6157	SO:0001583	missense	26960	exon41			TACTTCGAGGTAG	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.6541G>A	chr13.hg19:g.36046629G>A	ENSP00000383295:p.Glu2181Lys	89.0	0.0		69.0	22.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	36	5.800512	0.96960	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	5.51	5.51	0.81932	PH-BEACH domain (1);	0.000000	0.85682	D	0.000000	T	0.50120	0.1597	M	0.80183	2.485	0.80722	D	1	P;P	0.46912	0.664;0.886	B;B	0.34824	0.085;0.19	T	0.59736	-0.7398	10	0.39692	T	0.17	.	19.4328	0.94778	0.0:0.0:1.0:0.0	.	2181;2178	Q8NFP9;Q5T321	NBEA_HUMAN;.	K	2181;2181;2178;2181;808	ENSP00000440951:E2181K;ENSP00000383295:E2181K;ENSP00000369271:E2178K;ENSP00000308534:E2181K	ENSP00000308534:E2181K	E	+	1	0	NBEA	34944629	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.584000	0.87258	0.563000	0.77884	GAG	.	.		0.527	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	36046629	G	A	36046629	3	1	167	1	0	0	0	0	1	0	0	0	10196	1059	37	1	6703	1	NBEA	13	36046629	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	9134850	36046629	79123249	109	25354										
EBPL	84650	hgsc.bcm.edu	37	chr13	50265487	50265487	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggcgcaggcccagggcgcagCccgccgccagcagcgcggcg	18	18	0	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr13:50265487C>G	ENST00000242827.6	-	1	124	c.74G>C	c.(73-75)gGc>gCc	p.G25A	EBPL_ENST00000378270.5_Missense_Mutation_p.G25A|EBPL_ENST00000378272.5_Missense_Mutation_p.G25A|EBPL_ENST00000378268.1_Missense_Mutation_p.G25A|EBPL_ENST00000378282.5_Missense_Mutation_p.G25A|EBPL_ENST00000495963.2_5'UTR|EBPL_ENST00000378284.2_Missense_Mutation_p.G25A	NM_032565.3	NP_115954.1	Q9BY08	EBPL_HUMAN	emopamil binding protein-like	25					sterol metabolic process (GO:0016125)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholestenol delta-isomerase activity (GO:0047750)			endometrium(8)|kidney(6)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		cagggcgcagcccgccgccAG	0.761																																					p.G25A	NSCLC(39;857 1083 36109 42364 51411)	Atlas-SNP	.											.	EBPL	44	.	0			c.G74C						.						3	3	3					13																	50265487		1532	3209	4741	SO:0001583	missense	84650	exon1			GCGCAGCCCGCCG	AF243433	CCDS9420.1, CCDS61334.1	13q12-q13	2008-02-05			ENSG00000123179	ENSG00000123179			18061	protein-coding gene	gene with protein product							Standard	NM_032565		Approved	EBRP	uc001vdg.3	Q9BY08	OTTHUMG00000016920	ENST00000242827.6:c.74G>C	chr13.hg19:g.50265487C>G	ENSP00000242827:p.Gly25Ala	41.0	0.0		27.0	6.0	NM_032565	A6NJ59|Q569H7|Q5JVN2|Q5JVN3|Q5JVN4|Q5JVN5|Q5JVN6	Missense_Mutation	SNP	ENST00000242827.6	hg19	CCDS9420.1	.	.	.	.	.	.	.	.	.	.	C	10.96	1.499296	0.26861	.	.	ENSG00000123179	ENST00000378272;ENST00000378284;ENST00000242827;ENST00000378274;ENST00000378270;ENST00000378282;ENST00000378268	D;D;D;D	0.97430	-4.38;-4.38;-4.38;-4.38	3.7	3.7	0.42460	.	0.060996	0.64402	D	0.000006	D	0.93756	0.8004	N	0.11000	0.08	0.51233	D	0.999914	D;D	0.63046	0.989;0.992	P;P	0.56960	0.711;0.81	D	0.91042	0.4872	10	0.02654	T	1	-0.628	14.6852	0.69044	0.0:1.0:0.0:0.0	.	25;25	Q9BY08-2;Q9BY08	.;EBPL_HUMAN	A	25	ENSP00000367521:G25A;ENSP00000242827:G25A;ENSP00000367531:G25A;ENSP00000367516:G25A	ENSP00000242827:G25A	G	-	2	0	EBPL	49163488	0.994000	0.37717	0.080000	0.20451	0.226000	0.24999	2.378000	0.44309	2.072000	0.62099	0.543000	0.68304	GGC	.	.		0.761	EBPL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044932.2	NM_032565		G	50265487	C	G	50265487	3	3	167	1	0	0	0	0	1	0	0	0	4889	739	26	4	562	4	EBPL	13	50265487	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	14218858	50265487	64904391	110	25355										
RNASEH2B	79621	hgsc.bcm.edu	37	chr13	51504867	51504867	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggatcctctatttctgcttcTccactacctcataaaggctg	6	13	4	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr13:51504867T>G	ENST00000336617.3	+	4	692	c.293T>G	c.(292-294)cTc>cGc	p.L98R	RNASEH2B_ENST00000495244.2_3'UTR|RNASEH2B_ENST00000422660.1_Missense_Mutation_p.L98R	NM_024570.3	NP_078846.2	Q5TBB1	RNH2B_HUMAN	ribonuclease H2, subunit B	98					in utero embryonic development (GO:0001701)|negative regulation of gene expression (GO:0010629)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of DNA damage checkpoint (GO:2000001)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|ribonucleotide metabolic process (GO:0009259)|RNA catabolic process (GO:0006401)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)	RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(2)|liver(1)|lung(1)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(7;1.03e-07)|Breast(56;0.00122)|Lung NSC(96;0.00143)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;9e-08)		TTTCTGCTTCTCCACTACCTC	0.433																																					p.L98R		Atlas-SNP	.											.	RNASEH2B	26	.	0			c.T293G						.						213	208	209					13																	51504867		2203	4300	6503	SO:0001583	missense	79621	exon4			TGCTTCTCCACTA	AK021774	CCDS9425.1, CCDS45047.1	13q14.3	2014-09-17	2006-08-17	2006-08-17	ENSG00000136104	ENSG00000136104			25671	protein-coding gene	gene with protein product		610326	"deleted in lymphocytic leukemia 8", "Aicardi-Goutieres syndrome 2"	DLEU8, AGS2		16845400	Standard	NM_001142279		Approved	FLJ11712	uc001vfa.4	Q5TBB1	OTTHUMG00000016937	ENST00000336617.3:c.293T>G	chr13.hg19:g.51504867T>G	ENSP00000337623:p.Leu98Arg	59.0	0.0		51.0	7.0	NM_024570	G3XAJ1|Q05DR2|Q6PK48|Q9HAF7	Missense_Mutation	SNP	ENST00000336617.3	hg19	CCDS9425.1	.	.	.	.	.	.	.	.	.	.	T	16.38	3.105734	0.56291	.	.	ENSG00000136104	ENST00000336617;ENST00000539292;ENST00000422660	D;D	0.97731	-4.51;-4.51	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.98823	0.9603	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99667	1.0995	10	0.66056	D	0.02	-8.2014	13.4138	0.60958	0.0:0.0:0.0:1.0	.	98;98	G3XAJ1;Q5TBB1	.;RNH2B_HUMAN	R	98	ENSP00000337623:L98R;ENSP00000389877:L98R	ENSP00000337623:L98R	L	+	2	0	RNASEH2B	50402868	1.000000	0.71417	0.971000	0.41717	0.350000	0.29205	4.871000	0.63042	2.095000	0.63458	0.533000	0.62120	CTC	.	.		0.433	RNASEH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045006.3	NM_024570		G	51504867	T	G	51504867	3	3	167	1	0	0	0	0	1	0	0	0	13428	1551	54	5	307	5	RNASEH2B	13	51504867	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	1239380	51504867	63665011	111	25356										
UGGT2	55757	hgsc.bcm.edu	37	chr13	96579477	96579477	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	attattttacctgatgtagaTattaaattgaggtactgctg	8	4	0	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr13:96579477T>C	ENST00000376747.3	-	18	2161	c.2091A>G	c.(2089-2091)atA>atG	p.I697M		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	697					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						CTGATGTAGATATTAAATTGA	0.284																																					p.I697M		Atlas-SNP	.											.	UGGT2	127	.	0			c.A2091G						.						65	68	67					13																	96579477		2202	4293	6495	SO:0001583	missense	55757	exon18			TGTAGATATTAAA	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.2091A>G	chr13.hg19:g.96579477T>C	ENSP00000365938:p.Ile697Met	276.0	0.0		203.0	159.0	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	hg19	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	T	13.63	2.294716	0.40594	.	.	ENSG00000102595	ENST00000376747	T	0.08370	3.1	5.95	0.596	0.17496	.	0.199911	0.52532	N	0.000061	T	0.08670	0.0215	M	0.74881	2.28	0.80722	D	1	B	0.34399	0.452	B	0.35312	0.2	T	0.19257	-1.0311	10	0.35671	T	0.21	-17.0339	1.1521	0.01788	0.2427:0.134:0.1263:0.497	.	697	Q9NYU1	UGGG2_HUMAN	M	697	ENSP00000365938:I697M	ENSP00000365938:I697M	I	-	3	3	UGGT2	95377478	0.996000	0.38824	0.972000	0.41901	0.988000	0.76386	0.223000	0.17719	-0.096000	0.12329	-0.274000	0.10170	ATA	.	.		0.284	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		C	96579477	T	C	96579477	3	2	167	1	0	0	0	0	1	0	0	0	16957	1396	49	2	2547	2	UGGT2	13	96579477	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	45074610	96579477	18590401	112	25357										
PARP2	10038	hgsc.bcm.edu	37	chr14	20820473	20820473	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aaggtgcctggaaaatatgaTatgctacagatggactatgc	11	6	0	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr14:20820473T>C	ENST00000250416.5	+	7	633	c.606T>C	c.(604-606)gaT>gaC	p.D202D	PARP2_ENST00000527915.1_Silent_p.D202D|PARP2_ENST00000429687.3_Silent_p.D189D	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	202					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		GAAAATATGATATGCTACAGA	0.343								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.D202D		Atlas-SNP	.											.	PARP2	92	.	0			c.T606C						.						108	98	101					14																	20820473		1845	4097	5942	SO:0001819	synonymous_variant	10038	exon7			ATATGATATGCTA	AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484		"Poly (ADP-ribose) polymerases"	272	protein-coding gene	gene with protein product		607725	"ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2", "poly (ADP-ribose) polymerase family, member 2"	ADPRTL2		10329013, 18353725	Standard	NM_005484		Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000250416.5:c.606T>C	chr14.hg19:g.20820473T>C		139.0	0.0		138.0	29.0	NM_005484	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Silent	SNP	ENST00000250416.5	hg19	CCDS41910.1																																																																																			.	.		0.343	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2			C	20820473	T	C	20820473	2	2	167	1	0	0	0	0	0	0	0	1	11470	1403	49	2		2	PARP2	14	20820473	Silent	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10		20820473	86529067	113	25358										
DHRS4L1	728635	hgsc.bcm.edu	37	chr14	24517955	24517955	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agaccttggccatagagctgGccccaaggaacattagggtg	13	10	0	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr14:24517955G>A	ENST00000558293.1	+	0	603					NR_102693.1																						CATAGAGCTGGCCCCAAGGAA	0.512																																					p.A204T		Atlas-SNP	.											.	.	.	.	0			c.G610A						.						164	163	164					14																	24517955		2203	4300	6503			728635	exon8			GAGCTGGCCCCAA																													chr14.hg19:g.24517955G>A		647.0	0.0		771.0	153.0	NM_001082488		Missense_Mutation	SNP	ENST00000558293.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.15	1.270983	0.23221	.	.	ENSG00000225766	ENST00000397065	.	.	.	4.67	4.67	0.58626	NAD(P)-binding domain (1);	.	.	.	.	T	0.79997	0.4543	M	0.93594	3.435	0.45747	D	0.998640	D	0.57571	0.98	P	0.58660	0.843	D	0.87790	0.2618	7	0.87932	D	0	.	10.1886	0.43013	0.0:0.0:0.8016:0.1984	.	204	P0CG22	DR4L1_HUMAN	T	204	.	ENSP00000380255:A204T	A	+	1	0	AL136295.1	23587795	1.000000	0.71417	0.451000	0.26982	0.210000	0.24377	2.410000	0.44592	2.418000	0.82041	0.400000	0.26472	GCC	.	.		0.512	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1			A	24517955	G	A	24517955	1	1	167	0	1	0	0	0	0	0	0	0	4495	1203	42	3		3	DHRS4L1	14	24517955	RNA	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	3697482	24517955	82831585	114	25359										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31647288	31647288	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aagttcaactacaaccaaacGattacaaagtgcttttatag	5	8	1	0	rs377423641		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr14:31647288G>A	ENST00000399332.1	-	3	801	c.313C>T	c.(313-315)Cgt>Tgt	p.R105C	HECTD1_ENST00000553700.1_Missense_Mutation_p.R105C	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	105					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		ACAACCAAACGATTACAAAGT	0.413																																					p.R105C		Atlas-SNP	.											.	HECTD1	159	.	0			c.C313T						.						175	172	173					14																	31647288		1894	4131	6025	SO:0001583	missense	25831	exon3			CCAAACGATTACA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.313C>T	chr14.hg19:g.31647288G>A	ENSP00000382269:p.Arg105Cys	122.0	0.0		143.0	7.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.698510	0.88830	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000556224	T;T;T	0.64991	-0.13;-0.13;-0.13	5.57	5.57	0.84162	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65460	0.2693	M	0.82630	2.6	0.80722	D	1	D	0.61697	0.99	B	0.40659	0.336	T	0.74645	-0.3596	10	0.87932	D	0	-9.8804	14.3921	0.66986	0.0:0.0:0.8523:0.1477	.	105	Q9ULT8	HECD1_HUMAN	C	105	ENSP00000450697:R105C;ENSP00000382269:R105C;ENSP00000452015:R105C	ENSP00000261312:R105C	R	-	1	0	HECTD1	30717039	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.158000	0.71851	2.624000	0.88883	0.484000	0.47621	CGT	.	.		0.413	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			A	31647288	G	A	31647288	3	1	167	1	0	0	0	0	1	0	0	0	7048	1058	37	1	7683	1	HECTD1	14	31647288	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	7129333	31647288	75702252	115	25360										
L2HGDH	79944	hgsc.bcm.edu	37	chr14	50760900	50760900	+	Frame_Shift_Del	DEL	T	T	-													0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tcaggcccgggacaccattcTggaggcctttctcatatagg							TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr14:50760900delT	ENST00000267436.4	-	4	870	c.473delA	c.(472-474)cagfs	p.Q158fs	L2HGDH_ENST00000555610.1_Frame_Shift_Del_p.Q158fs|L2HGDH_ENST00000421284.3_Frame_Shift_Del_p.Q158fs|L2HGDH_ENST00000261699.4_Frame_Shift_Del_p.Q158fs|L2HGDH_ENST00000555423.1_Frame_Shift_Del_p.Q158fs			Q9H9P8	L2HDH_HUMAN	L-2-hydroxyglutarate dehydrogenase	158					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2-hydroxyglutarate dehydrogenase activity (GO:0047545)			kidney(1)|large_intestine(4)|lung(3)|ovary(2)	10	all_epithelial(31;0.000599)|Breast(41;0.0102)					GACACCATTCTGGAGGCCTTT	0.418																																					p.Q158fs		Atlas-INDEL	.											.	L2HGDH	33	.	0			c.474delG						.						96	92	93					14																	50760900		2203	4300	6503	SO:0001589	frameshift_variant	79944	exon4			.		CCDS9698.1	14q22.1	2006-04-28	2005-05-25	2005-05-25	ENSG00000087299	ENSG00000087299	1.1.99.2		20499	protein-coding gene	gene with protein product	"2-hydroxyglutarate dehydrogenase"	609584	"chromosome 14 open reading frame 160"	C14orf160		16005139	Standard	NM_024884		Approved	FLJ12618	uc001wxu.3	Q9H9P8	OTTHUMG00000140289	ENST00000267436.4:c.473delA	chr14.hg19:g.50760900delT	ENSP00000267436:p.Gln158fs	59.0	0.0		68.0	14.0	NM_024884	Q9BRR1	Frame_Shift_Del	DEL	ENST00000267436.4	hg19	CCDS9698.1																																																																																			.	.		0.418	L2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276870.2	NM_024884		-	50760900	T	-	50760900	7	5	167	1	0	1	0	1	0	0	0	0	8599	1580	55	0	946	0	L2HGDH	14	50760900	Frame_Shift_Del	DEL	T	TCGA-DD-AACP-01A-11D-A40R-10	19113612	50760900	56588640	116	25361										
SIX6	4990	hgsc.bcm.edu	37	chr14	60976223	60976223	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cctgggtcgcttcctctggtCgctgcccgtggcccctgcgg	14	17	1	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr14:60976223C>T	ENST00000327720.5	+	1	555	c.107C>T	c.(106-108)tCg>tTg	p.S36L		NM_007374.2	NP_031400.2	O95475	SIX6_HUMAN	SIX homeobox 6	36					organ morphogenesis (GO:0009887)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)	11				OV - Ovarian serous cystadenocarcinoma(108;0.088)		TTCCTCTGGTCGCTGCCCGTG	0.647																																					p.S36L		Atlas-SNP	.											.	SIX6	27	.	0			c.C107T						.						40	46	44					14																	60976223		2203	4299	6502	SO:0001583	missense	4990	exon1			TCTGGTCGCTGCC	AF141651	CCDS9747.1	14q23.1	2011-06-20	2007-07-13		ENSG00000184302	ENSG00000184302		"Homeoboxes / SINE class"	10892	protein-coding gene	gene with protein product		606326	"sine oculis homeobox (Drosophila) homolog 6", "sine oculis homeobox homolog 6 (Drosophila)"	OPTX2		10512683	Standard	NM_007374		Approved	Six9	uc001xfa.4	O95475	OTTHUMG00000152339	ENST00000327720.5:c.107C>T	chr14.hg19:g.60976223C>T	ENSP00000328596:p.Ser36Leu	1246.0	2.0		1321.0	397.0	NM_007374	Q6NT42|Q9P1X8	Missense_Mutation	SNP	ENST00000327720.5	hg19	CCDS9747.1	.	.	.	.	.	.	.	.	.	.	C	36	5.722062	0.96839	.	.	ENSG00000184302	ENST00000327720	D	0.97378	-4.36	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.98972	0.9650	H	0.96777	3.88	0.80722	D	1	D	0.76494	0.999	D	0.63033	0.91	D	0.99312	1.0904	10	0.87932	D	0	.	18.891	0.92403	0.0:1.0:0.0:0.0	.	36	O95475	SIX6_HUMAN	L	36	ENSP00000328596:S36L	ENSP00000328596:S36L	S	+	2	0	SIX6	60045976	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.623000	0.83113	2.941000	0.99782	0.655000	0.94253	TCG	.	.		0.647	SIX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276952.2			T	60976223	C	T	60976223	3	4	167	1	0	0	0	0	1	0	0	0	14366	893	31	1	109	1	SIX6	14	60976223	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	10215323	60976223	46373317	117	25362										
SIX4	51804	hgsc.bcm.edu	37	chr14	61180534	61180534	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cagtagatttgcttgccaccGgtgcagacattggttggcta	12	9	0	2	rs374417781		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr14:61180534G>A	ENST00000216513.4	-	3	1996	c.1937C>T	c.(1936-1938)cCg>cTg	p.P646L		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	646					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		GCTTGCCACCGGTGCAGACAT	0.453																																					p.P646L		Atlas-SNP	.											.	SIX4	69	.	0			c.C1937T						.	G	LEU/PRO	2,4404	4.2+/-10.8	0,2,2201	119	97	104		1937	5.4	1	14		104	1,8599	1.2+/-3.3	0,1,4299	no	missense	SIX4	NM_017420.4	98	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	possibly-damaging	646/782	61180534	3,13003	2203	4300	6503	SO:0001583	missense	51804	exon3			GCCACCGGTGCAG	AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"Homeoboxes / SINE class"	10890	protein-coding gene	gene with protein product		606342	"sine oculis homeobox (Drosophila) homolog 4", "sine oculis homeobox homolog 4 (Drosophila)"			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.1937C>T	chr14.hg19:g.61180534G>A	ENSP00000216513:p.Pro646Leu	107.0	0.0		97.0	4.0	NM_017420	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	hg19	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	G	17.02	3.281504	0.59758	4.54E-4	1.16E-4	ENSG00000100625	ENST00000216513;ENST00000554079	D;T	0.92249	-3.0;0.65	5.41	5.41	0.78517	.	0.453038	0.24050	N	0.042006	D	0.93210	0.7837	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94344	0.7573	10	0.87932	D	0	.	19.5632	0.95380	0.0:0.0:1.0:0.0	.	646	Q9UIU6	SIX4_HUMAN	L	646;319	ENSP00000216513:P646L;ENSP00000451537:P319L	ENSP00000216513:P646L	P	-	2	0	SIX4	60250287	1.000000	0.71417	1.000000	0.80357	0.582000	0.36321	6.722000	0.74735	2.710000	0.92621	0.655000	0.94253	CCG	.	.		0.453	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			A	61180534	G	A	61180534	3	1	167	1	0	0	0	0	1	0	0	0	14364	1116	39	1	412	1	SIX4	14	61180534	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	204311	61180534	46169006	118	25363										
WDR89	112840	hgsc.bcm.edu	37	chr14	64065604	64065604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctttgtaaaggtcttctctaTagctccaggtttccaaagta	7	9	2	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr14:64065604T>C	ENST00000394942.2	-	2	1145	c.1057A>G	c.(1057-1059)Ata>Gta	p.I353V	CTD-2302E22.2_ENST00000553983.1_lincRNA|WDR89_ENST00000267522.3_Missense_Mutation_p.I353V	NM_001008726.2|NM_001258272.1|NM_080666.3	NP_001008726.1|NP_001245201.1|NP_542397.1	Q96FK6	WDR89_HUMAN	WD repeat domain 89	353										endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.00543)|all cancers(60;0.0181)|BRCA - Breast invasive adenocarcinoma(234;0.101)		GTCTTCTCTATAGCTCCAGGT	0.393																																					p.I353V		Atlas-SNP	.											.	WDR89	22	.	0			c.A1057G						.						122	114	116					14																	64065604		2203	4300	6503	SO:0001583	missense	112840	exon3			TCTCTATAGCTCC	AF115513	CCDS9759.1	14q23.2	2013-01-09		2006-07-07	ENSG00000140006	ENSG00000140006		"WD repeat domain containing"	20489	protein-coding gene	gene with protein product				C14orf150			Standard	NM_080666		Approved	MGC9907	uc001xgi.4	Q96FK6	OTTHUMG00000140340	ENST00000394942.2:c.1057A>G	chr14.hg19:g.64065604T>C	ENSP00000378399:p.Ile353Val	68.0	0.0		82.0	10.0	NM_080666		Missense_Mutation	SNP	ENST00000394942.2	hg19	CCDS9759.1	.	.	.	.	.	.	.	.	.	.	T	4.931	0.172957	0.09391	.	.	ENSG00000140006	ENST00000394942;ENST00000267522	T;T	0.65364	-0.15;-0.15	5.65	-6.68	0.01778	WD40-repeat-containing domain (1);	1.194700	0.05653	N	0.585591	T	0.31009	0.0783	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26849	-1.0091	10	0.12766	T	0.61	.	8.4453	0.32838	0.1043:0.6051:0.1062:0.1844	.	353	Q96FK6	WDR89_HUMAN	V	353	ENSP00000378399:I353V;ENSP00000267522:I353V	ENSP00000267522:I353V	I	-	1	0	WDR89	63135357	0.000000	0.05858	0.321000	0.25320	0.762000	0.43233	-0.373000	0.07494	-1.363000	0.02164	-1.039000	0.02377	ATA	.	.		0.393	WDR89-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411879.2	NM_080666		C	64065604	T	C	64065604	3	2	167	1	0	0	0	0	1	0	0	0	17351	1406	49	2	110	2	WDR89	14	64065604	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	2885070	64065604	43283936	119	25364										
BATF	10538	hgsc.bcm.edu	37	chr14	75989066	75989066	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cagtgactccagcttcagccGctctcctccccctggcaaac	7	19	2	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr14:75989066G>A	ENST00000286639.6	+	1	299	c.41G>A	c.(40-42)cGc>cAc	p.R14H	BATF_ENST00000555795.1_Intron|BATF_ENST00000555504.1_Missense_Mutation_p.R14H	NM_006399.3	NP_006390.1	Q16520	BATF_HUMAN	basic leucine zipper transcription factor, ATF-like	14					cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hematopoietic stem cell differentiation (GO:0060218)|isotype switching (GO:0045190)|lymphoid progenitor cell differentiation (GO:0002320)|myeloid dendritic cell differentiation (GO:0043011)|T-helper 17 cell differentiation (GO:0072539)|T-helper 17 cell lineage commitment (GO:0072540)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|ovary(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.028)		AGCTTCAGCCGCTCTCCTCCC	0.582																																					p.R14H		Atlas-SNP	.											.	BATF	12	.	0			c.G41A						.						81	74	76					14																	75989066		2203	4300	6503	SO:0001583	missense	10538	exon1			TCAGCCGCTCTCC	AF016898	CCDS9843.1	14q24	2013-01-10				ENSG00000156127		"basic leucine zipper proteins"	958	protein-coding gene	gene with protein product	"activating transcription factor B", "SF-HT-activated gene 2"	612476				8570175, 8630063	Standard	NM_006399		Approved	B-ATF, SFA-2, BATF1	uc001xrr.3	Q16520		ENST00000286639.6:c.41G>A	chr14.hg19:g.75989066G>A	ENSP00000286639:p.Arg14His	63.0	0.0		60.0	6.0	NM_006399		Missense_Mutation	SNP	ENST00000286639.6	hg19	CCDS9843.1	.	.	.	.	.	.	.	.	.	.	G	15.96	2.986688	0.53934	.	.	ENSG00000156127	ENST00000286639;ENST00000555504	T	0.77877	-1.13	4.92	4.92	0.64577	.	0.132608	0.50627	D	0.000116	T	0.51822	0.1697	N	0.08118	0	0.36008	D	0.837863	P	0.36789	0.57	B	0.17098	0.017	T	0.64786	-0.6325	10	0.51188	T	0.08	-16.2395	9.6678	0.39994	0.1251:0.0:0.8749:0.0	.	14	Q16520	BATF_HUMAN	H	14	ENSP00000286639:R14H	ENSP00000286639:R14H	R	+	2	0	BATF	75058819	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.801000	0.62532	2.715000	0.92844	0.655000	0.94253	CGC	.	.		0.582	BATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413669.1	NM_006399		A	75989066	G	A	75989066	3	1	167	1	0	0	0	0	1	0	0	0	1325	1087	38	1	43	1	BATF	14	75989066	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	11923462	75989066	31360474	120	25365										
NRXN3	9369	hgsc.bcm.edu	37	chr14	79746796	79746796	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tcgccggggtctcactctcaGcacgagcaccatttccatgg	10	15	2	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr14:79746796G>A	ENST00000557594.1	+	1	1115	c.162G>A	c.(160-162)caG>caA	p.Q54Q	NRXN3_ENST00000428277.2_Silent_p.Q54Q|NRXN3_ENST00000554719.1_Intron|NRXN3_ENST00000335750.5_Intron|NRXN3_ENST00000281127.7_Silent_p.Q54Q	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3	54					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		CTCACTCTCAGCACGAGCACC	0.527																																					p.Q54Q		Atlas-SNP	.											.	NRXN3	342	.	0			c.G162A						.						210	182	192					14																	79746796		2203	4300	6503	SO:0001819	synonymous_variant	9369	exon1			CTCTCAGCACGAG	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000557594.1:c.162G>A	chr14.hg19:g.79746796G>A		87.0	0.0		75.0	40.0	NM_138970	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Silent	SNP	ENST00000557594.1	hg19																																																																																				.	.		0.527	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250		A	79746796	G	A	79746796	2	1	167	1	0	0	0	0	0	0	0	1	10676	962	34	3		3	NRXN3	14	79746796	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	3757730	79746796	27602744	121	25366										
TRPM7	54822	hgsc.bcm.edu	37	chr15	50884532	50884532	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agatcaccttgaggaagagaGgagctaagtgtatttacaac	11	6	1	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr15:50884532G>A	ENST00000313478.7	-	26	4181	c.3900C>T	c.(3898-3900)tcC>tcT	p.S1300S	TRPM7_ENST00000560955.1_Silent_p.S1300S	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1300					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		GAGGAAGAGAGGAGCTAAGTG	0.353																																					p.S1300S		Atlas-SNP	.											.	TRPM7	145	.	0			c.C3900T						.						136	119	124					15																	50884532		1849	4085	5934	SO:0001819	synonymous_variant	54822	exon26			AAGAGAGGAGCTA	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.3900C>T	chr15.hg19:g.50884532G>A		119.0	0.0		156.0	38.0	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Silent	SNP	ENST00000313478.7	hg19	CCDS42035.1																																																																																			.	.		0.353	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		A	50884532	G	A	50884532	2	1	167	1	0	0	0	0	0	0	0	1	16606	987	35	3		3	TRPM7	15	50884532	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10		50884532	51646860	122	25367										
ADAM10	102	hgsc.bcm.edu	37	chr15	58936148	58936148	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aagtctgtggtctggtaaatTgtatcaatcgctttaacatg	9	6	3	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr15:58936148T>A	ENST00000260408.3	-	7	1208	c.765A>T	c.(763-765)acA>acT	p.T255T	ADAM10_ENST00000561288.1_Intron|ADAM10_ENST00000402627.1_Intron|ADAM10_ENST00000396140.2_Intron	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	255	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		TCTGGTAAATTGTATCAATCG	0.308																																					p.T255T		Atlas-SNP	.											.	ADAM10	59	.	0			c.A765T						.						116	116	116					15																	58936148		2192	4292	6484	SO:0001819	synonymous_variant	102	exon7			GTAAATTGTATCA	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"ADAM metallopeptidase domain containing", "CD molecules"	188	protein-coding gene	gene with protein product		602192	"a disintegrin and metalloproteinase domain 10"			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.765A>T	chr15.hg19:g.58936148T>A		98.0	0.0		99.0	10.0	NM_001110	B4DU28|Q10742|Q92650	Silent	SNP	ENST00000260408.3	hg19	CCDS10167.1																																																																																			.	.		0.308	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110		A	58936148	T	A	58936148	2	1	167	1	0	0	0	0	0	0	0	1	234	1799	63	4		4	ADAM10	15	58936148	Silent	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	8051616	58936148	43595244	123	25368										
SLC24A1	9187	hgsc.bcm.edu	37	chr15	65943145	65943145	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gaagaggaggaggaggaggaGgaagaggaggagaagggaaa	23	0	0	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr15:65943145G>A	ENST00000261892.6	+	7	2945	c.2658G>A	c.(2656-2658)gaG>gaA	p.E886E	SLC24A1_ENST00000544319.2_Silent_p.E772E|SLC24A1_ENST00000339868.6_Silent_p.E868E|SLC24A1_ENST00000449142.2_3'UTR|SLC24A1_ENST00000546330.1_Silent_p.E868E|SLC24A1_ENST00000537259.1_Silent_p.E868E|SLC24A1_ENST00000399033.4_Silent_p.E886E	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	886	Poly-Glu.				calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						aggaggaggaggaagaggagg	0.567																																					p.E886E		Atlas-SNP	.											.	SLC24A1	58	.	0			c.G2658A						.						44	49	48					15																	65943145		2194	4289	6483	SO:0001819	synonymous_variant	9187	exon7			GGAGGAGGAAGAG	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"Solute carriers"	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.2658G>A	chr15.hg19:g.65943145G>A		100.0	0.0		125.0	5.0	NM_004727	O43485|O75184|Q17RM9	Silent	SNP	ENST00000261892.6	hg19	CCDS45284.1																																																																																			.	.		0.567	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727		A	65943145	G	A	65943145	2	1	167	1	0	0	0	0	0	0	0	1	14480	991	35	3		3	SLC24A1	15	65943145	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	7006997	65943145	36588247	124	25369										
GOLGA6B	55889	hgsc.bcm.edu	37	chr15	72955008	72955008	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aggctgtggaagaaggaggaGaggctacaaaagcaggagga	18	4	0	2	rs199550549	byFrequency	TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr15:72955008G>C	ENST00000421285.3	+	11	1263	c.1263G>C	c.(1261-1263)gaG>gaC	p.E421D	RN7SL853P_ENST00000477951.2_RNA	NM_018652.4	NP_061122.4	A6NDN3	GOG6B_HUMAN	golgin A6 family, member B	421						Golgi apparatus (GO:0005794)		p.E421D(1)		NS(1)|breast(1)|endometrium(1)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	16						AGAAGGAGGAGAGGCTACAAA	0.587																																					p.E421D		Atlas-SNP	.											GOLGA6B,NS,malignant_melanoma,0,1	GOLGA6B	30	.	1	Substitution - Missense(1)	NS(1)	c.G1263C						.						1	1	1					15																	72955008		108	305	413	SO:0001583	missense	55889	exon11			GGAGGAGAGGCTA		CCDS10245.2	15q24.1	2011-10-25	2010-02-12		ENSG00000215186	ENSG00000215186			32205	protein-coding gene	gene with protein product			"golgi autoantigen, golgin subfamily a, 6B"				Standard	XM_006720604		Approved		uc010uks.1	A6NDN3	OTTHUMG00000133511	ENST00000421285.3:c.1263G>C	chr15.hg19:g.72955008G>C	ENSP00000408132:p.Glu421Asp	88.0	0.0		107.0	5.0	NM_018652	A8MYY7	Missense_Mutation	SNP	ENST00000421285.3	hg19	CCDS10245.2	.	.	.	.	.	.	.	.	.	.	.	3.065	-0.192360	0.06259	.	.	ENSG00000215186	ENST00000421285	T	0.07444	3.19	.	.	.	.	.	.	.	.	T	0.06962	0.0177	L	0.47190	1.495	0.22888	N	0.99861	P	0.49961	0.93	B	0.40444	0.329	T	0.30208	-0.9986	8	0.62326	D	0.03	.	2.6645	0.05037	0.4931:0.0:0.5069:0.0	.	421	A6NDN3	GOG6B_HUMAN	D	421	ENSP00000408132:E421D	ENSP00000408132:E421D	E	+	3	2	GOLGA6B	70742062	0.998000	0.40836	0.134000	0.22075	0.265000	0.26407	0.636000	0.24644	0.088000	0.17205	0.089000	0.15464	GAG	.	G|1.000;|0.000		0.587	GOLGA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257474.4	NM_018652		C	72955008	G	C	72955008	3	2	167	1	0	0	0	0	1	0	0	0	6566	933	33	4	1305	4	GOLGA6B	15	72955008	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	7011863	72955008	29576384	125	25370										
NPTN	27020	hgsc.bcm.edu	37	chr15	73889554	73889554	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ttacggtgacacggcgcttcCgagcaccgtcccacagctgt	11	15	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr15:73889554C>A	ENST00000345330.4	-	2	445	c.248G>T	c.(247-249)cGg>cTg	p.R83L	NPTN_ENST00000287226.8_Missense_Mutation_p.R83L|NPTN_ENST00000564551.1_Intron|NPTN_ENST00000562924.1_Intron|NPTN_ENST00000351217.6_Intron|NPTN_ENST00000542234.1_Intron|NPTN_ENST00000545878.1_Missense_Mutation_p.R83L|NPTN_ENST00000563691.1_Missense_Mutation_p.R83L	NM_001161363.1|NM_012428.3	NP_001154835.1|NP_036560.1	Q9Y639	NPTN_HUMAN	neuroplastin	83	Ig-like 1.				homophilic cell adhesion (GO:0007156)|long-term synaptic potentiation (GO:0060291)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein phosphorylation (GO:0001934)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)	cell adhesion molecule binding (GO:0050839)|type 1 fibroblast growth factor receptor binding (GO:0005105)			breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	13						ACGGCGCTTCCGAGCACCGTC	0.602																																					p.R83L	Pancreas(101;1519 1568 9459 19537 41286)|Esophageal Squamous(143;1278 1787 35254 36835 44843)	Atlas-SNP	.											.	NPTN	35	.	0			c.G248T						.						117	97	104					15																	73889554		2198	4297	6495	SO:0001583	missense	27020	exon2			CGCTTCCGAGCAC	AF035287	CCDS10249.1, CCDS10250.1, CCDS58379.1, CCDS58380.1	15q24.1	2013-01-29	2006-02-22	2006-02-22	ENSG00000156642	ENSG00000156642		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17867	protein-coding gene	gene with protein product		612820	"stromal cell derived factor receptor 1"	SDFR1		8619474, 9110174	Standard	NM_012428		Approved	SDR1, GP55, GP65, np65, np55	uc002avs.3	Q9Y639	OTTHUMG00000137586	ENST00000345330.4:c.248G>T	chr15.hg19:g.73889554C>A	ENSP00000290401:p.Arg83Leu	155.0	0.0		213.0	47.0	NM_001161363	B2RAL7|B7Z4D3|B7ZLL2|Q17R52|Q59EJ9|Q6NVX7|Q9Y640	Missense_Mutation	SNP	ENST00000345330.4	hg19	CCDS10249.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.778437	0.90195	.	.	ENSG00000156642	ENST00000345330;ENST00000545878;ENST00000287226	T;T;T	0.68181	-0.31;-0.31;-0.31	5.61	5.61	0.85477	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.79656	0.4483	L	0.49256	1.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.79938	-0.1592	10	0.72032	D	0.01	.	20.0018	0.97417	0.0:1.0:0.0:0.0	.	83;83	Q9Y639-5;Q9Y639	.;NPTN_HUMAN	L	83	ENSP00000290401:R83L;ENSP00000444548:R83L;ENSP00000287226:R83L	ENSP00000287226:R83L	R	-	2	0	NPTN	71676607	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.684000	0.84104	2.793000	0.96121	0.655000	0.94253	CGG	.	.		0.602	NPTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268980.1	NM_012428		A	73889554	C	A	73889554	3	1	167	1	0	0	0	0	1	0	0	0	10610	652	23	1	976	1	NPTN	15	73889554	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	934546	73889554	28641838	126	25371										
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79090369	79090369	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gcctgacgcttgtacaccacAtggggctgggcgtggccagg	16	12	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr15:79090369A>G	ENST00000388820.4	-	3	753	c.543T>C	c.(541-543)caT>caC	p.H181H	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	181					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						TGTACACCACATGGGGCTGGG	0.622																																					p.H181H		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.T543C						.						62	63	62					15																	79090369		2196	4293	6489	SO:0001819	synonymous_variant	11173	exon3			CACCACATGGGGC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.543T>C	chr15.hg19:g.79090369A>G		41.0	0.0		66.0	16.0	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	hg19	CCDS32303.1																																																																																			.	.		0.622	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		G	79090369	A	G	79090369	2	3	167	1	0	0	0	0	0	0	0	1	271	214	8	2		2	ADAMTS7	15	79090369	Silent	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	5200815	79090369	23441023	127	25372										
SCNN1G	6340	hgsc.bcm.edu	37	chr16	23200752	23200752	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gagaccagagaggccctgaaGtccctgtatggctttccaga	12	11	0	4			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr16:23200752G>A	ENST00000300061.2	+	3	521	c.378G>A	c.(376-378)aaG>aaA	p.K126K		NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	126					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	AGGCCCTGAAGTCCCTGTATG	0.607																																					p.K126K		Atlas-SNP	.											.	SCNN1G	82	.	0			c.G378A						.						77	84	81					16																	23200752		2197	4300	6497	SO:0001819	synonymous_variant	6340	exon3			CCTGAAGTCCCTG	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.378G>A	chr16.hg19:g.23200752G>A		104.0	0.0		78.0	68.0	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Silent	SNP	ENST00000300061.2	hg19	CCDS10608.1																																																																																			.	.		0.607	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		A	23200752	G	A	23200752	2	1	167	1	0	0	0	0	0	0	0	1	13945	1020	36	3		3	SCNN1G	16	23200752	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10		23200752	67154001	128	25373										
SCNN1G	6340	hgsc.bcm.edu	37	chr16	23223412	23223412	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agaaatgtgggtgtgcccagTacagccagcctctacctcct	10	13	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr16:23223412T>A	ENST00000300061.2	+	8	1377	c.1234T>A	c.(1234-1236)Tac>Aac	p.Y412N	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	412					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	GTGTGCCCAGTACAGCCAGCC	0.547																																					p.Y412N		Atlas-SNP	.											.	SCNN1G	82	.	0			c.T1234A						.						126	99	108					16																	23223412		2197	4300	6497	SO:0001583	missense	6340	exon8			GCCCAGTACAGCC	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.1234T>A	chr16.hg19:g.23223412T>A	ENSP00000300061:p.Tyr412Asn	67.0	0.0		49.0	42.0	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Missense_Mutation	SNP	ENST00000300061.2	hg19	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.451107	0.84209	.	.	ENSG00000166828	ENST00000300061	T	0.64438	-0.1	5.72	5.72	0.89469	.	0.412831	0.25538	N	0.029984	T	0.80768	0.4686	M	0.83774	2.66	0.50313	D	0.999865	D	0.89917	1.0	D	0.97110	1.0	D	0.83573	0.0113	10	0.72032	D	0.01	-5.3756	15.1903	0.73038	0.0:0.0:0.0:1.0	.	412	P51170	SCNNG_HUMAN	N	412	ENSP00000300061:Y412N	ENSP00000300061:Y412N	Y	+	1	0	SCNN1G	23130913	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.911000	0.69939	2.185000	0.69588	0.459000	0.35465	TAC	.	.		0.547	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		A	23223412	T	A	23223412	3	1	167	1	0	0	0	0	1	0	0	0	13945	1638	57	4	1260	4	SCNN1G	16	23223412	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	22660	23223412	67131341	129	25374										
CDH11	1009	hgsc.bcm.edu	37	chr16	65005962	65005962	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gactttggcttcctgatgccGattgtctgggaagacagaat	12	8	1	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr16:65005962G>T	ENST00000268603.4	-	10	2011	c.1396C>A	c.(1396-1398)Cgg>Agg	p.R466R	CDH11_ENST00000566827.1_Silent_p.R340R|CDH11_ENST00000394156.3_Silent_p.R466R	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	466	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TCCTGATGCCGATTGTCTGGG	0.478			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.R466R		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	CDH11,NS,carcinoma,0,1	CDH11	260	.	0			c.C1396A						.						86	75	79					16																	65005962		2203	4300	6503	SO:0001819	synonymous_variant	1009	exon10			GATGCCGATTGTC	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1396C>A	chr16.hg19:g.65005962G>T		158.0	0.0		93.0	71.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	hg19	CCDS10803.1																																																																																			.	.		0.478	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		T	65005962	G	T	65005962	2	4	167	1	0	0	0	0	0	0	0	1	3099	1057	37	1		1	CDH11	16	65005962	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	41782550	65005962	25348791	130	25375										
DYNC1LI2	1783	hgsc.bcm.edu	37	chr16	66776358	66776358	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cacacttccgttccagctccCtcattttttctggtggaatt	6	13	2	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr16:66776358C>T	ENST00000258198.2	-	4	718	c.512G>A	c.(511-513)aGg>aAg	p.R171K	DYNC1LI2_ENST00000443351.2_Intron|DYNC1LI2_ENST00000379482.2_Missense_Mutation_p.R171K|DYNC1LI2_ENST00000440564.2_Missense_Mutation_p.R132K	NM_006141.2	NP_006132.1	O43237	DC1L2_HUMAN	dynein, cytoplasmic 1, light intermediate chain 2	171					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|centrosome localization (GO:0051642)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based movement (GO:0007018)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			central_nervous_system(3)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(4)|stomach(1)	15		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0907)|Epithelial(162;0.212)		TTCCAGCTCCCTCATTTTTTC	0.388																																					p.R171K		Atlas-SNP	.											.	DYNC1LI2	37	.	0			c.G512A						.						99	101	101					16																	66776358		2200	4300	6500	SO:0001583	missense	1783	exon4			AGCTCCCTCATTT	AF035812	CCDS10818.1, CCDS67049.1	16q22.1	2008-02-05	2005-11-25	2005-11-25	ENSG00000135720	ENSG00000135720		"Cytoplasmic dyneins"	2966	protein-coding gene	gene with protein product		611406	"dynein, cytoplasmic, light intermediate polypeptide 2"	DNCLI2		16260502	Standard	NM_006141		Approved		uc002eqb.1	O43237	OTTHUMG00000137523	ENST00000258198.2:c.512G>A	chr16.hg19:g.66776358C>T	ENSP00000258198:p.Arg171Lys	76.0	0.0		53.0	21.0	NM_006141	A8K6V1|B4DZP4|Q8TAT3	Missense_Mutation	SNP	ENST00000258198.2	hg19	CCDS10818.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.117435	0.37339	.	.	ENSG00000135720	ENST00000258198;ENST00000379482;ENST00000440564	T;T;T	0.17213	2.29;2.29;2.29	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.24122	0.0584	N	0.13352	0.335	0.80722	D	1	D;B;B	0.63046	0.992;0.003;0.019	D;B;B	0.76071	0.987;0.01;0.074	T	0.05937	-1.0855	10	0.10111	T	0.7	-1.7346	19.0071	0.92856	0.0:1.0:0.0:0.0	.	132;171;171	B4E2E0;B4DHD8;O43237	.;.;DC1L2_HUMAN	K	171;171;132	ENSP00000258198:R171K;ENSP00000368795:R171K;ENSP00000408566:R132K	ENSP00000258198:R171K	R	-	2	0	DYNC1LI2	65333859	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.786000	0.62425	2.793000	0.96121	0.563000	0.77884	AGG	.	.		0.388	DYNC1LI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268846.1	NM_006141		T	66776358	C	T	66776358	3	4	167	1	0	0	0	0	1	0	0	0	4847	681	24	3	1006	3	DYNC1LI2	16	66776358	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	1770396	66776358	23578395	131	25376										
AARS	16	hgsc.bcm.edu	37	chr16	70304225	70304225	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cttttcttgggaagaggtttCagaatgccatcagcttccct	9	10	3	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr16:70304225C>A	ENST00000261772.8	-	6	833	c.690G>T	c.(688-690)ctG>ctT	p.L230L		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		GAAGAGGTTTCAGAATGCCAT	0.468																																					p.L230L		Atlas-SNP	.											.	AARS	62	.	0			c.G690T						.						162	132	142					16																	70304225		2198	4300	6498	SO:0001819	synonymous_variant	16	exon6			AGGTTTCAGAATG	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.690G>T	chr16.hg19:g.70304225C>A		94.0	0.0		90.0	69.0	NM_001605		Silent	SNP	ENST00000261772.8	hg19	CCDS32474.1																																																																																			.	.		0.468	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		A	70304225	C	A	70304225	2	1	167	1	0	0	0	0	0	0	0	1	19	813	29	3		3	AARS	16	70304225	Silent	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	3527867	70304225	20050528	132	25377										
SF3B3	23450	hgsc.bcm.edu	37	chr16	70588395	70588395	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tctttcgtgaatgccaccctAgtgttgtccattggagaaac	9	10	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr16:70588395A>G	ENST00000302516.5	+	12	1660	c.1449A>G	c.(1447-1449)ctA>ctG	p.L483L		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	483					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				ATGCCACCCTAGTGTTGTCCA	0.443																																					p.L483L		Atlas-SNP	.											.	SF3B3	99	.	0			c.A1449G						.						174	153	160					16																	70588395		2198	4300	6498	SO:0001819	synonymous_variant	23450	exon12			CACCCTAGTGTTG	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.1449A>G	chr16.hg19:g.70588395A>G		100.0	0.0		84.0	11.0	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Silent	SNP	ENST00000302516.5	hg19	CCDS10894.1																																																																																			.	.		0.443	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		G	70588395	A	G	70588395	2	3	167	1	0	0	0	0	0	0	0	1	14167	407	15	2		2	SF3B3	16	70588395	Silent	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	284170	70588395	19766358	133	25378										
KLHL36	79786	hgsc.bcm.edu	37	chr16	84691009	84691009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gctgtgtgtctacctgagcaGcagcgaggtgcagcgggagt	17	9	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr16:84691009G>A	ENST00000564996.1	+	3	737	c.596G>A	c.(595-597)aGc>aAc	p.S199N	KLHL36_ENST00000258157.5_Missense_Mutation_p.S199N	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	199	BACK.				protein ubiquitination (GO:0016567)					endometrium(3)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						TACCTGAGCAGCAGCGAGGTG	0.642																																					p.S199N		Atlas-SNP	.											.	KLHL36	51	.	0			c.G596A						.						41	35	37					16																	84691009		2199	4300	6499	SO:0001583	missense	79786	exon3			TGAGCAGCAGCGA	AK022605	CCDS10948.1	16q24.1	2013-02-22	2013-02-22	2008-07-07	ENSG00000135686	ENSG00000135686		"Kelch-like", "BTB/POZ domain containing"	17844	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 44", "kelch-like 36 (Drosophila)"	C16orf44			Standard	NM_024731		Approved	FLJ12543	uc002fig.3	Q8N4N3	OTTHUMG00000137642	ENST00000564996.1:c.596G>A	chr16.hg19:g.84691009G>A	ENSP00000456743:p.Ser199Asn	47.0	0.0		24.0	11.0	NM_024731	Q8N5G6|Q9H9U6	Missense_Mutation	SNP	ENST00000564996.1	hg19	CCDS10948.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.453358	0.84209	.	.	ENSG00000135686	ENST00000325279;ENST00000258157	T	0.70749	-0.51	5.42	5.42	0.78866	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	D	0.85239	0.5651	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.86468	0.1783	10	0.59425	D	0.04	.	18.2083	0.89861	0.0:0.0:1.0:0.0	.	199;199	Q8N4N3-2;Q8N4N3	.;KLH36_HUMAN	N	199	ENSP00000258157:S199N	ENSP00000258157:S199N	S	+	2	0	KLHL36	83248510	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	6.550000	0.73905	2.516000	0.84829	0.563000	0.77884	AGC	.	.		0.642	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2			A	84691009	G	A	84691009	3	1	167	1	0	0	0	0	1	0	0	0	8398	971	34	3	602	3	KLHL36	16	84691009	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	14102614	84691009	5663744	134	25379										
MYO1C	4641	hgsc.bcm.edu	37	chr17	1371776	1371776	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ttgaagatctcactagccacGgccttctgctgcagctgagg	11	12	2	3	rs374091489		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr17:1371776G>C	ENST00000575158.1	-	26	2696	c.2520C>G	c.(2518-2520)gcC>gcG	p.A840A	MYO1C_ENST00000359786.5_Silent_p.A875A|MYO1C_ENST00000438665.2_Silent_p.A856A|MYO1C_ENST00000361007.2_Silent_p.A840A|MYO1C_ENST00000545534.2_Silent_p.A851A			Q12965	MYO1E_HUMAN	myosin IC	720	Myosin tail. {ECO:0000255}.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CACTAGCCACGGCCTTCTGCT	0.587																																					p.A875A		Atlas-SNP	.											.	MYO1C	57	.	0			c.C2625G						.						103	89	94					17																	1371776		2203	4300	6503	SO:0001819	synonymous_variant	4641	exon26			AGCCACGGCCTTC	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"Myosins / Myosin superfamily : Class I"	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.2520C>G	chr17.hg19:g.1371776G>C		50.0	0.0		60.0	8.0	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	hg19	CCDS11003.1																																																																																			.	.		0.587	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2			C	1371776	G	C	1371776	2	2	167	1	0	0	0	0	0	0	0	1	10079	1103	39	4		4	MYO1C	17	1371776	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10		1371776	79823434	135	25380										
SGSM2	9905	hgsc.bcm.edu	37	chr17	2276666	2276666	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aggtaccagcaggtgttggcAgagtggaaggcctgcgaggt	18	7	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr17:2276666A>G	ENST00000426855.2	+	16	1999	c.1824A>G	c.(1822-1824)gcA>gcG	p.A608A	SGSM2_ENST00000574563.1_Silent_p.A608A|RP1-59D14.5_ENST00000574290.1_RNA|SGSM2_ENST00000268989.3_Silent_p.A653A	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	608	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		AGGTGTTGGCAGAGTGGAAGG	0.657																																					p.A653A		Atlas-SNP	.											.	SGSM2	60	.	0			c.A1959G						.						122	92	102					17																	2276666		2203	4300	6503	SO:0001819	synonymous_variant	9905	exon17			GTTGGCAGAGTGG	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"Small G protein signaling modulators"	29026	protein-coding gene	gene with protein product		611418	"RUN and TBC1 domain containing 1"	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.1824A>G	chr17.hg19:g.2276666A>G		53.0	0.0		56.0	17.0	NM_014853	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Silent	SNP	ENST00000426855.2	hg19	CCDS45570.1																																																																																			.	.		0.657	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853		G	2276666	A	G	2276666	2	3	167	1	0	0	0	0	0	0	0	1	14238	175	7	2		2	SGSM2	17	2276666	Silent	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	904890	2276666	78918544	136	25381										
MYH4	4622	hgsc.bcm.edu	37	chr17	10363528	10363528	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agtcatgtttacctgctgcaCagtctggcctttggttacga	10	10	2	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr17:10363528C>G	ENST00000255381.2	-	13	1368	c.1258G>C	c.(1258-1260)Gtg>Ctg	p.V420L	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	420	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						ACCTGCTGCACAGTCTGGCCT	0.413																																					p.V420L		Atlas-SNP	.											.	MYH4	349	.	0			c.G1258C						.						123	113	116					17																	10363528		2203	4300	6503	SO:0001583	missense	4622	exon13			GCTGCACAGTCTG		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.1258G>C	chr17.hg19:g.10363528C>G	ENSP00000255381:p.Val420Leu	134.0	0.0		124.0	9.0	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.131563	0.77662	.	.	ENSG00000141048	ENST00000255381	T	0.71817	-0.6	5.56	5.56	0.83823	Myosin head, motor domain (2);	0.000000	0.33813	U	0.004538	T	0.73713	0.3622	M	0.75777	2.31	0.80722	D	1	B	0.02656	0.0	B	0.15052	0.012	T	0.69781	-0.5052	10	0.52906	T	0.07	.	19.8925	0.96935	0.0:1.0:0.0:0.0	.	420	Q9Y623	MYH4_HUMAN	L	420	ENSP00000255381:V420L	ENSP00000255381:V420L	V	-	1	0	MYH4	10304253	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	6.019000	0.70818	2.787000	0.95880	0.650000	0.86243	GTG	.	.		0.413	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		G	10363528	C	G	10363528	3	3	167	1	0	0	0	0	1	0	0	0	10046	478	17	4	4673	4	MYH4	17	10363528	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	8086862	10363528	70831682	137	25382										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27419423	27419423	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gtcttcgatctccacctccaTtgctttccgtgctttcacgg	7	15	3	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr17:27419423T>C	ENST00000527372.1	-	34	5305	c.5125A>G	c.(5125-5127)Atg>Gtg	p.M1709V	MYO18A_ENST00000533112.1_Missense_Mutation_p.M1672V|MYO18A_ENST00000354329.4_Missense_Mutation_p.M1709V|TIAF1_ENST00000408971.2_5'Flank|MYO18A_ENST00000529578.1_5'Flank|MYO18A_ENST00000531253.1_Missense_Mutation_p.M1709V	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1709					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			TCCACCTCCATTGCTTTCCGT	0.622																																					p.M1709V	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.A5125G						.						50	56	54					17																	27419423		2203	4298	6501	SO:0001583	missense	399687	exon34			CCTCCATTGCTTT	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.5125A>G	chr17.hg19:g.27419423T>C	ENSP00000437073:p.Met1709Val	36.0	0.0		43.0	11.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	T	18.71	3.682274	0.68042	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000529799;ENST00000540575;ENST00000458428	T;D;T;T	0.87571	-0.95;-2.27;-0.95;-0.95	5.2	5.2	0.72013	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.92374	0.7580	M	0.70595	2.14	0.37321	D	0.909576	D;D;D;P	0.58268	0.982;0.982;0.982;0.728	D;D;D;P	0.68943	0.961;0.961;0.961;0.501	D	0.94376	0.7600	10	0.62326	D	0.03	.	15.0435	0.71811	0.0:0.0:0.0:1.0	.	1312;1672;1709;1709	F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;MY18A_HUMAN	V	1709;1672;1672;1709;1709;605;605;1312	ENSP00000346291:M1709V;ENSP00000435932:M1672V;ENSP00000434228:M1709V;ENSP00000437073:M1709V	ENSP00000346291:M1709V	M	-	1	0	MYO18A	24443549	1.000000	0.71417	0.946000	0.38457	0.985000	0.73830	7.463000	0.80869	2.104000	0.64026	0.482000	0.46254	ATG	.	.		0.622	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		C	27419423	T	C	27419423	3	2	167	1	0	0	0	0	1	0	0	0	10074	1493	52	2	1075	2	MYO18A	17	27419423	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	17055895	27419423	53775787	138	25383										
GGNBP2	79893	hgsc.bcm.edu	37	chr17	34916707	34916707	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	atacgcacaagccaaaacctTtggggtaagtagaattgaat	9	7	0	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr17:34916707T>C	ENST00000304718.4	+	5	839	c.523T>C	c.(523-525)Ttg>Ctg	p.L175L		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	175					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		GCCAAAACCTTTGGGGTAAGT	0.318																																					p.L175L		Atlas-SNP	.											.	GGNBP2	72	.	0			c.T523C						.						73	74	74					17																	34916707		2203	4298	6501	SO:0001819	synonymous_variant	79893	exon5			AAACCTTTGGGGT	AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.523T>C	chr17.hg19:g.34916707T>C		123.0	0.0		109.0	34.0	NM_024835	B2RPK7|Q96T90|Q9GZR8|Q9H767	Silent	SNP	ENST00000304718.4	hg19	CCDS11314.1																																																																																			.	.		0.318	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		C	34916707	T	C	34916707	2	2	167	1	0	0	0	0	0	0	0	1	6367	1838	64	2		2	GGNBP2	17	34916707	Silent	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	7497284	34916707	46278503	139	25384										
TUBG2	27175	hgsc.bcm.edu	37	chr17	40817531	40817531	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agccctgaaccggattgccaCagaccgcctgcacatccaga	9	16	0	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr17:40817531C>T	ENST00000251412.7	+	7	843	c.644C>T	c.(643-645)aCa>aTa	p.T215I	PLEKHH3_ENST00000456950.2_5'Flank	NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	215					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		CGGATTGCCACAGACCGCCTG	0.562																																					p.T215I		Atlas-SNP	.											.	TUBG2	43	.	0			c.C644T						.						181	173	176					17																	40817531		2203	4300	6503	SO:0001583	missense	27175	exon7			TTGCCACAGACCG	AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"Tubulins"	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.644C>T	chr17.hg19:g.40817531C>T	ENSP00000251412:p.Thr215Ile	140.0	0.0		114.0	38.0	NM_016437	A6NDI4|Q32NB2	Missense_Mutation	SNP	ENST00000251412.7	hg19	CCDS32658.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.611222	0.66558	.	.	ENSG00000037042	ENST00000251412	T	0.70164	-0.46	4.55	4.55	0.56014	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	T	0.70919	0.3279	M	0.76574	2.34	0.80722	D	1	B	0.25105	0.118	B	0.32149	0.141	T	0.73335	-0.4015	10	0.62326	D	0.03	-10.1674	17.6915	0.88269	0.0:1.0:0.0:0.0	.	215	Q9NRH3	TBG2_HUMAN	I	215	ENSP00000251412:T215I	ENSP00000251412:T215I	T	+	2	0	TUBG2	38071057	1.000000	0.71417	0.999000	0.59377	0.801000	0.45260	7.674000	0.83992	2.246000	0.74042	0.561000	0.74099	ACA	.	.		0.562	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437		T	40817531	C	T	40817531	3	4	167	1	0	0	0	0	1	0	0	0	16780	478	17	3	670	3	TUBG2	17	40817531	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	5900824	40817531	40377679	140	25385										
NBR1	4077	hgsc.bcm.edu	37	chr17	41347008	41347008	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgtcctttgagctgttggatAtaaacattgttcaagagttg	10	5	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr17:41347008A>G	ENST00000422280.1	+	14	2161	c.1702A>G	c.(1702-1704)Ata>Gta	p.I568V	NBR1_ENST00000590996.1_Missense_Mutation_p.I568V|NBR1_ENST00000589872.1_Missense_Mutation_p.I568V|NBR1_ENST00000341165.6_Missense_Mutation_p.I568V|NBR1_ENST00000389312.4_Missense_Mutation_p.I568V|NBR1_ENST00000542611.1_Missense_Mutation_p.I547V	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	568	ATG8 family protein-binding.				macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		GCTGTTGGATATAAACATTGT	0.438																																					p.I568V		Atlas-SNP	.											.	NBR1	55	.	0			c.A1702G						.						114	112	113					17																	41347008		1929	4118	6047	SO:0001583	missense	4077	exon14			TTGGATATAAACA	X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.1702A>G	chr17.hg19:g.41347008A>G	ENSP00000411250:p.Ile568Val	299.0	0.0		325.0	22.0	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	hg19	CCDS45694.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.412723	0.83340	.	.	ENSG00000188554	ENST00000422280;ENST00000542611;ENST00000341165;ENST00000389312;ENST00000389311	T;T;T;T	0.57595	0.96;0.39;0.96;0.96	5.75	5.75	0.90469	.	.	.	.	.	T	0.70150	0.3191	L	0.61387	1.9	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.80764	0.994;0.976;0.994	T	0.71922	-0.4446	9	0.56958	D	0.05	-9.5175	16.0539	0.80782	1.0:0.0:0.0:0.0	.	547;568;568	B7Z5R6;Q14596-2;Q14596	.;.;NBR1_HUMAN	V	568;547;568;568;568	ENSP00000411250:I568V;ENSP00000437545:I547V;ENSP00000343479:I568V;ENSP00000373963:I568V	ENSP00000343479:I568V	I	+	1	0	NBR1	38600534	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.940000	0.75917	2.193000	0.70182	0.533000	0.62120	ATA	.	.		0.438	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		G	41347008	A	G	41347008	3	3	167	1	0	0	0	0	1	0	0	0	10209	449	16	2	1752	2	NBR1	17	41347008	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	529477	41347008	39848202	141	25386										
FMNL1	752	hgsc.bcm.edu	37	chr17	43310645	43310645	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tacgggagctggagacctccCtgaggaccaaccacattggg	13	12	0	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr17:43310645C>A	ENST00000331495.3	+	4	718	c.382C>A	c.(382-384)Ctg>Atg	p.L128M	FMNL1_ENST00000592006.1_3'UTR|FMNL1_ENST00000328118.3_Missense_Mutation_p.L128M	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	128	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						GGAGACCTCCCTGAGGACCAA	0.617																																					p.L128M	GBM(164;1247 1997 8702 11086 51972)	Atlas-SNP	.											.	FMNL1	78	.	0			c.C382A						.						65	57	60					17																	43310645		2194	4285	6479	SO:0001583	missense	752	exon4			ACCTCCCTGAGGA	AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"formin-like"	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.382C>A	chr17.hg19:g.43310645C>A	ENSP00000329219:p.Leu128Met	83.0	0.0		72.0	24.0	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Missense_Mutation	SNP	ENST00000331495.3	hg19	CCDS11497.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.549235	0.45383	.	.	ENSG00000184922	ENST00000328118;ENST00000331495	D;D	0.96365	-3.99;-3.99	4.2	3.23	0.37069	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.270223	0.31020	N	0.008402	D	0.98077	0.9366	M	0.92169	3.28	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.91635	0.998;0.999	D	0.97757	1.0218	10	0.87932	D	0	.	7.8429	0.29408	0.0:0.8066:0.0:0.1934	.	128;128	O95466-2;O95466	.;FMNL_HUMAN	M	128	ENSP00000327442:L128M;ENSP00000329219:L128M	ENSP00000327442:L128M	L	+	1	2	FMNL1	40666428	0.180000	0.23148	1.000000	0.80357	0.935000	0.57460	0.585000	0.23879	1.121000	0.41925	0.561000	0.74099	CTG	.	.		0.617	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892		A	43310645	C	A	43310645	3	1	167	1	0	0	0	0	1	0	0	0	5959	680	24	3	396	3	FMNL1	17	43310645	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	1963637	43310645	37884565	142	25387										
TEX2	55852	hgsc.bcm.edu	37	chr17	62291064	62291064	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgaggcactggatgagaggaTgggagacttagaaggagagg	19	3	0	5			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr17:62291064T>A	ENST00000583097.1	-	2	686	c.514A>T	c.(514-516)Atc>Ttc	p.I172F	TEX2_ENST00000584379.1_Missense_Mutation_p.I172F|TEX2_ENST00000258991.3_Missense_Mutation_p.I172F			Q8IWB9	TEX2_HUMAN	testis expressed 2	172					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		GATGAGAGGATGGGAGACTTA	0.542																																					p.I172F		Atlas-SNP	.											.	TEX2	89	.	0			c.A514T						.						58	51	53					17																	62291064		2203	4300	6503	SO:0001583	missense	55852	exon2			AGAGGATGGGAGA	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"transmembrane protein 96"		"testis expressed sequence 2"			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.514A>T	chr17.hg19:g.62291064T>A	ENSP00000462665:p.Ile172Phe	76.0	0.0		94.0	9.0	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	hg19		.	.	.	.	.	.	.	.	.	.	T	1.514	-0.548822	0.04024	.	.	ENSG00000136478	ENST00000258991	T	0.51325	0.71	5.82	-1.21	0.09524	.	0.563539	0.19645	N	0.109343	T	0.23611	0.0571	N	0.08118	0	0.19775	N	0.999957	B;B	0.26258	0.145;0.09	B;B	0.25759	0.063;0.029	T	0.14364	-1.0475	10	0.33940	T	0.23	-2.9811	10.2567	0.43401	0.0:0.5806:0.0:0.4194	.	172;172	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	F	172	ENSP00000258991:I172F	ENSP00000258991:I172F	I	-	1	0	TEX2	59644796	0.076000	0.21285	0.003000	0.11579	0.156000	0.22039	0.065000	0.14466	-0.429000	0.07329	-0.899000	0.02877	ATC	.	.		0.542	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		A	62291064	T	A	62291064	3	1	167	1	0	0	0	0	1	0	0	0	15796	1464	51	4	2934	4	TEX2	17	62291064	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	18980419	62291064	18904146	143	25388										
BAIAP2	10458	hgsc.bcm.edu	37	chr17	79077867	79077867	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ctcctactccaacacactccCcgtgcgcaagagcgtgaccc	7	19	0	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr17:79077867C>T	ENST00000321300.6	+	9	1118	c.1025C>T	c.(1024-1026)cCc>cTc	p.P342L	BAIAP2_ENST00000575245.1_Missense_Mutation_p.P375L|BAIAP2_ENST00000575712.1_Missense_Mutation_p.P342L|BAIAP2_ENST00000416299.2_Missense_Mutation_p.P205L|BAIAP2_ENST00000435091.3_Missense_Mutation_p.P342L|BAIAP2_ENST00000392411.3_Missense_Mutation_p.P264L|BAIAP2_ENST00000321280.7_Missense_Mutation_p.P342L|BAIAP2_ENST00000428708.2_Missense_Mutation_p.P342L	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	342					actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			AACACACTCCCCGTGCGCAAG	0.627																																					p.P342L		Atlas-SNP	.											.	BAIAP2	74	.	0			c.C1025T						.						88	93	91					17																	79077867		2203	4300	6503	SO:0001583	missense	10458	exon9			CACTCCCCGTGCG	AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.1025C>T	chr17.hg19:g.79077867C>T	ENSP00000316338:p.Pro342Leu	204.0	0.0		222.0	66.0	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Missense_Mutation	SNP	ENST00000321300.6	hg19	CCDS11775.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.009412	0.75046	.	.	ENSG00000175866	ENST00000321300;ENST00000428708;ENST00000435091;ENST00000321280;ENST00000392411;ENST00000416299	T;T;T;T;T;T	0.35973	1.75;1.78;1.31;1.31;1.76;1.28	4.55	4.55	0.56014	.	0.053328	0.85682	D	0.000000	T	0.58177	0.2104	M	0.65498	2.005	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.998;1.0;1.0;1.0;0.996;1.0	D;D;D;D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.928;0.999;0.999;0.999;0.929;0.999	T	0.55891	-0.8069	10	0.32370	T	0.25	-16.0987	17.4893	0.87699	0.0:1.0:0.0:0.0	.	205;264;343;342;342;342;342;342;342	B4DWA1;F8W878;B3KPV9;Q9UQB8;Q9UQB8-2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-6;Q9UQB8-4	.;.;.;BAIP2_HUMAN;.;.;.;.;.	L	342;342;342;342;264;205	ENSP00000316338:P342L;ENSP00000401022:P342L;ENSP00000413069:P342L;ENSP00000315685:P342L;ENSP00000376211:P264L;ENSP00000391837:P205L	ENSP00000315685:P342L	P	+	2	0	BAIAP2	76692462	1.000000	0.71417	0.989000	0.46669	0.470000	0.32858	6.938000	0.75904	2.361000	0.80049	0.462000	0.41574	CCC	.	.		0.627	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1			T	79077867	C	T	79077867	3	4	167	1	0	0	0	0	1	0	0	0	1301	623	22	3	1059	3	BAIAP2	17	79077867	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	16786803	79077867	2117343	144	25389										
DSG1	1828	hgsc.bcm.edu	37	chr18	28934321	28934321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	taatgactgtttgctcatatAtgacatcgaaggtgtaggtt	10	5	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr18:28934321A>G	ENST00000257192.4	+	15	2374	c.2162A>G	c.(2161-2163)tAt>tGt	p.Y721C	RP11-534N16.1_ENST00000578119.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|DSG1_ENST00000462981.2_Missense_Mutation_p.Y80C	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	721					apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			TTGCTCATATATGACATCGAA	0.428																																					p.Y721C		Atlas-SNP	.											.	DSG1	176	.	0			c.A2162G						.						130	127	128					18																	28934321		2203	4300	6503	SO:0001583	missense	1828	exon15			TCATATATGACAT	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"Cadherins / Major cadherins"	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.2162A>G	chr18.hg19:g.28934321A>G	ENSP00000257192:p.Tyr721Cys	89.0	0.0		62.0	23.0	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	hg19	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	A	15.05	2.718160	0.48622	.	.	ENSG00000134760	ENST00000257192	D	0.87809	-2.3	6.04	6.04	0.98038	Cadherin, cytoplasmic domain (1);	0.000000	0.64402	D	0.000011	D	0.94368	0.8189	M	0.87456	2.885	0.53688	D	0.999973	D	0.89917	1.0	D	0.97110	1.0	D	0.95067	0.8201	10	0.87932	D	0	.	16.5885	0.84745	1.0:0.0:0.0:0.0	.	721	Q02413	DSG1_HUMAN	C	721	ENSP00000257192:Y721C	ENSP00000257192:Y721C	Y	+	2	0	DSG1	27188319	1.000000	0.71417	0.996000	0.52242	0.973000	0.67179	7.223000	0.78033	2.317000	0.78254	0.460000	0.39030	TAT	.	.		0.428	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		G	28934321	A	G	28934321	3	3	167	1	0	0	0	0	1	0	0	0	4778	449	16	2	2220	2	DSG1	18	28934321	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10		28934321	49142927	145	25390										
PIGN	23556	hgsc.bcm.edu	37	chr18	59777111	59777111	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggcagtggcaacaaaccataTacataatatgtccagggaca	9	9	0	0	rs373958969		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr18:59777111T>C	ENST00000357637.5	-	17	1945	c.1530A>G	c.(1528-1530)gtA>gtG	p.V510V	PIGN_ENST00000400334.3_Silent_p.V510V	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	510					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				ACAAACCATATACATAATATG	0.388																																					p.V510V		Atlas-SNP	.											.	PIGN	62	.	0			c.A1530G						.	T	,	1,3797		0,1,1898	152	147	149		1530,1530	-4.8	0.2	18		149	0,8238		0,0,4119	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	0,1,6017	CC,CT,TT		0.0,0.0263,0.0083	,	510/932,510/932	59777111	1,12035	1899	4119	6018	SO:0001819	synonymous_variant	23556	exon17			ACCATATACATAA	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.1530A>G	chr18.hg19:g.59777111T>C		240.0	1.0		180.0	138.0	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	hg19	CCDS45879.1																																																																																			.	.		0.388	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		C	59777111	T	C	59777111	2	2	167	1	0	0	0	0	0	0	0	1	11902	1393	49	2		2	PIGN	18	59777111	Silent	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	30842790	59777111	18300137	146	25391										
NETO1	81832	hgsc.bcm.edu	37	chr18	70526062	70526062	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tttttaagtacttacttaccAggtgtgaaattgtatcgagc	8	6	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr18:70526062A>T	ENST00000327305.6	-	4	1125	c.468T>A	c.(466-468)ccT>ccA	p.P156P	NETO1_ENST00000299430.2_Splice_Site_p.P155P|NETO1_ENST00000583169.1_Splice_Site_p.P156P|NETO1_ENST00000397929.1_Splice_Site_p.P155P|NETO1_ENST00000580049.1_5'UTR	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	156					memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		CTTACTTACCAGGTGTGAAAT	0.318																																					p.P156P		Atlas-SNP	.											.	NETO1	178	.	0			c.T468A						.						44	47	46					18																	70526062		2197	4296	6493	SO:0001630	splice_region_variant	81832	exon4			CTTACCAGGTGTG	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.469+1T>A	chr18.hg19:g.70526062A>T		151.0	0.0		112.0	47.0	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Silent	SNP	ENST00000327305.6	hg19	CCDS12000.1																																																																																			.	.		0.318	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999	Silent	T	70526062	A	T	70526062	5	4	167	1	0	0	0	0	0	0	1	0	10348	202	7	4	1170	4	NETO1	18	70526062	Splice_Site	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	10748951	70526062	7551186	147	25392										
MUC16	94025	hgsc.bcm.edu	37	chr19	9038082	9038082	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agaggagcttcctacctgtgGagctggggatggaggatgtg	18	6	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:9038082G>T	ENST00000397910.4	-	8	36397	c.36194C>A	c.(36193-36195)tCc>tAc	p.S12065Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12067	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCTACCTGTGGAGCTGGGGAT	0.498																																					p.S12065Y		Atlas-SNP	.											.	MUC16	4315	.	0			c.C36194A						.						51	53	52					19																	9038082		1948	4126	6074	SO:0001583	missense	94025	exon8			CCTGTGGAGCTGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.36194C>A	chr19.hg19:g.9038082G>T	ENSP00000381008:p.Ser12065Tyr	181.0	0.0		133.0	118.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	G	9.253	1.041272	0.19669	.	.	ENSG00000181143	ENST00000397910	T	0.02236	4.38	2.44	0.27	0.15635	.	.	.	.	.	T	0.06826	0.0174	M	0.70275	2.135	.	.	.	D	0.58268	0.982	P	0.59825	0.864	T	0.18209	-1.0344	8	0.87932	D	0	.	4.3176	0.11000	0.3487:0.0:0.6513:0.0	.	12065	B5ME49	.	Y	12065	ENSP00000381008:S12065Y	ENSP00000381008:S12065Y	S	-	2	0	MUC16	8899082	0.018000	0.18449	0.023000	0.16930	0.046000	0.14306	0.396000	0.20867	0.138000	0.18790	0.411000	0.27672	TCC	.	.		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9038082	G	T	9038082	3	4	167	1	0	0	0	0	1	0	0	0	9982	1174	41	3	7637	3	MUC16	19	9038082	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10		9038082	50090901	148	25393										
ZNF763	284390	hgsc.bcm.edu	37	chr19	12089204	12089204	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cctaagaaagccttcagataTcacccctcctttagaacaca	4	14	2	3	rs372060440		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:12089204T>G	ENST00000358987.3	+	4	592	c.465T>G	c.(463-465)taT>taG	p.Y155*	ZNF763_ENST00000538752.1_Nonsense_Mutation_p.Y175*|ZNF763_ENST00000343949.5_Nonsense_Mutation_p.Y158*|ZNF763_ENST00000592625.1_3'UTR|ZNF763_ENST00000590798.1_Nonsense_Mutation_p.Y175*|ZNF763_ENST00000545530.1_Nonsense_Mutation_p.Y33*			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	155					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						CCTTCAGATATCACCCCTCCT	0.418																																					p.Y158X		Atlas-SNP	.											.	ZNF763	31	.	0			c.T474G						.						131	134	133					19																	12089204		2196	4300	6496	SO:0001587	stop_gained	284390	exon4			CAGATATCACCCC	AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"Zinc fingers, C2H2-type", "-"	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.465T>G	chr19.hg19:g.12089204T>G	ENSP00000402017:p.Tyr155*	157.0	0.0		132.0	8.0	NM_001012753	B3KRU3|B4DRE7	Nonsense_Mutation	SNP	ENST00000358987.3	hg19		.	.	.	.	.	.	.	.	.	.	t	13.50	2.256868	0.39896	.	.	ENSG00000197054	ENST00000538752;ENST00000343949;ENST00000545530;ENST00000358987	.	.	.	1.68	0.601	0.17529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.0482	0.06160	0.0:0.2707:0.0:0.7293	.	.	.	.	X	175;158;33;155	.	ENSP00000369774:Y158X	Y	+	3	2	ZNF763	11950204	0.000000	0.05858	0.002000	0.10522	0.060000	0.15804	0.026000	0.13599	0.753000	0.32945	0.164000	0.16699	TAT	.	.		0.418	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753		G	12089204	T	G	12089204	4	3	167	1	0	0	0	0	0	1	0	0	18152	1442	50	5	488	5	ZNF763	19	12089204	Nonsense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	3051122	12089204	47039779	149	25394										
BRD4	23476	hgsc.bcm.edu	37	chr19	15350628	15350628	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggaccacggaggcagcacgcAgctcctgggatggcacaggc	16	13	0	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:15350628A>G	ENST00000263377.2	-	16	3508	c.3287T>C	c.(3286-3288)cTg>cCg	p.L1096P		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1096	C-terminal (CTD) region.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			GGCAGCACGCAGCTCCTGGGA	0.672			T	C15orf55	lethal midline carcinoma of young people																																p.L1096P		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.T3287C						.						48	49	49					19																	15350628		2203	4300	6503	SO:0001583	missense	23476	exon16			GCACGCAGCTCCT	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.3287T>C	chr19.hg19:g.15350628A>G	ENSP00000263377:p.Leu1096Pro	58.0	0.0		43.0	35.0	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	hg19	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	A	11.35	1.611850	0.28712	.	.	ENSG00000141867	ENST00000263377	T	0.33438	1.41	4.62	4.62	0.57501	.	0.000000	0.39834	N	0.001257	T	0.34658	0.0905	N	0.22421	0.69	0.80722	D	1	D	0.64830	0.994	P	0.56343	0.796	T	0.21793	-1.0235	10	0.87932	D	0	-5.7885	13.0172	0.58764	1.0:0.0:0.0:0.0	.	1096	O60885	BRD4_HUMAN	P	1096	ENSP00000263377:L1096P	ENSP00000263377:L1096P	L	-	2	0	BRD4	15211628	1.000000	0.71417	0.917000	0.36280	0.858000	0.48976	3.909000	0.56363	1.701000	0.51217	0.459000	0.35465	CTG	.	.		0.672	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		G	15350628	A	G	15350628	3	3	167	1	0	0	0	0	1	0	0	0	1506	188	7	2	821	2	BRD4	19	15350628	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	3261424	15350628	43778355	150	25395										
UNC13A	23025	hgsc.bcm.edu	37	chr19	17759295	17759295	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ttctcgtggcacttgacaccGcactcggtgcagcgcatgcc	11	15	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:17759295G>A	ENST00000519716.2	-	16	1760	c.1761C>T	c.(1759-1761)tgC>tgT	p.C587C	UNC13A_ENST00000551649.1_Silent_p.C587C|UNC13A_ENST00000252773.7_Silent_p.C587C|UNC13A_ENST00000428389.2_Silent_p.C675C|UNC13A_ENST00000550896.1_Silent_p.C585C|UNC13A_ENST00000552293.1_Silent_p.C587C	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	587					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						ACTTGACACCGCACTCGGTGC	0.677																																					p.C587C		Atlas-SNP	.											UNC13A_ENST00000519716,NS,carcinoma,0,2	UNC13A	299	.	0			c.C1761T						.						68	72	71					19																	17759295		2201	4300	6501	SO:0001819	synonymous_variant	23025	exon15			GACACCGCACTCG	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.1761C>T	chr19.hg19:g.17759295G>A		37.0	0.0		38.0	34.0	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	hg19	CCDS46013.2																																																																																			.	.		0.677	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17759295	G	A	17759295	2	1	167	1	0	0	0	0	0	0	0	1	16999	1079	38	1		1	UNC13A	19	17759295	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	2408667	17759295	41369688	151	25396										
GPATCH1	55094	hgsc.bcm.edu	37	chr19	33579137	33579137	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggggcctttagtggaggtttCtctgctggatacttcaatac	12	8	2	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:33579137C>T	ENST00000170564.2	+	2	485	c.171C>T	c.(169-171)ttC>ttT	p.F57F		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	57					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					GTGGAGGTTTCTCTGCTGGAT	0.383																																					p.F57F	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											GPATCH1,bladder,carcinoma,0,1	GPATCH1	79	.	0			c.C171T						.						102	106	105					19																	33579137		2203	4300	6503	SO:0001819	synonymous_variant	55094	exon2			AGGTTTCTCTGCT	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"G patch domain containing"	24658	protein-coding gene	gene with protein product	"evolutionarily conserved G patch domain containing"			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.171C>T	chr19.hg19:g.33579137C>T		77.0	0.0		87.0	9.0	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	hg19	CCDS12428.1																																																																																			.	.		0.383	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		T	33579137	C	T	33579137	2	4	167	1	0	0	0	0	0	0	0	1	6598	912	32	3		3	GPATCH1	19	33579137	Silent	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	15819842	33579137	25549846	152	25397										
ZNF30	90075	hgsc.bcm.edu	37	chr19	35435284	35435284	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tcagagtgcacgtacatctcAcacagcatcggaaaattcat	7	11	3	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:35435284A>G	ENST00000601142.1	+	5	1651	c.1414A>G	c.(1414-1416)Aca>Gca	p.T472A	ZNF30_ENST00000426813.2_Missense_Mutation_p.T391A|ZNF30_ENST00000303586.7_Missense_Mutation_p.T473A|ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000439785.1_Missense_Mutation_p.T473A			P17039	ZNF30_HUMAN	zinc finger protein 30	472					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		CGTACATCTCACACAGCATCG	0.438																																					p.T473A		Atlas-SNP	.											.	ZNF30	44	.	0			c.A1417G						.						72	75	74					19																	35435284		2202	4300	6502	SO:0001583	missense	90075	exon5			CATCTCACACAGC	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"Zinc fingers, C2H2-type", "-"	13090	protein-coding gene	gene with protein product			"zinc finger protein 30 (KOX 28)"				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.1414A>G	chr19.hg19:g.35435284A>G	ENSP00000469954:p.Thr472Ala	106.0	0.0		126.0	46.0	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	hg19	CCDS46045.1	.	.	.	.	.	.	.	.	.	.	a	0.013	-1.626963	0.00813	.	.	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813;ENST00000342559	T;T	0.07216	3.21;3.21	2.25	-4.49	0.03504	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03477	0.0100	N	0.17723	0.515	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.45190	-0.9278	9	0.08599	T	0.76	.	2.9778	0.05943	0.3482:0.0:0.3275:0.3243	.	473;472	P17039-2;P17039	.;ZNF30_HUMAN	A	473;472;391;181	ENSP00000403441:T473A;ENSP00000416457:T391A	ENSP00000303889:T472A	T	+	1	0	ZNF30	40127124	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.841000	0.27613	-2.025000	0.00935	-1.488000	0.00978	ACA	.	.		0.438	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325		G	35435284	A	G	35435284	3	3	167	1	0	0	0	0	1	0	0	0	17845	159	6	2	1431	2	ZNF30	19	35435284	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	1856147	35435284	23693699	153	25398										
ZNF30	90075	hgsc.bcm.edu	37	chr19	35435313	35435313	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cggaaaattcatactgatgtAaagccctatgaatgtaagga	9	6	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:35435313A>G	ENST00000601142.1	+	5	1680	c.1443A>G	c.(1441-1443)gtA>gtG	p.V481V	ZNF30_ENST00000426813.2_Silent_p.V400V|ZNF30_ENST00000303586.7_Silent_p.V482V|ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000439785.1_Silent_p.V482V			P17039	ZNF30_HUMAN	zinc finger protein 30	481					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		ATACTGATGTAAAGCCCTATG	0.438																																					p.V482V		Atlas-SNP	.											.	ZNF30	44	.	0			c.A1446G						.						77	82	81					19																	35435313		2202	4300	6502	SO:0001819	synonymous_variant	90075	exon5			TGATGTAAAGCCC	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"Zinc fingers, C2H2-type", "-"	13090	protein-coding gene	gene with protein product			"zinc finger protein 30 (KOX 28)"				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.1443A>G	chr19.hg19:g.35435313A>G		101.0	0.0		130.0	45.0	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Silent	SNP	ENST00000601142.1	hg19	CCDS46045.1																																																																																			.	.		0.438	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325		G	35435313	A	G	35435313	2	3	167	1	0	0	0	0	0	0	0	1	17845	349	13	2		2	ZNF30	19	35435313	Silent	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	29	35435313	23693670	154	25399										
PSG7	5676	hgsc.bcm.edu	37	chr19	43430643	43430643	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgccaccatatcggtcccgtAtttcacattgatagggtcct	8	12	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:43430643A>G	ENST00000406070.2	-	0	1031				PSG7_ENST00000446844.3_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)						female pregnancy (GO:0007565)	extracellular region (GO:0005576)							Prostate(69;0.00682)				TCGGTCCCGTATTTCACATTG	0.517																																					p.I190T		Atlas-SNP	.											.	.	.	.	0			c.T569C						.						131	120	124					19																	43430643		2201	4296	6497			5676	exon3			TCCCGTATTTCAC			19q13.2	2013-01-29	2010-02-26		ENSG00000221878	ENSG00000221878		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9524	protein-coding gene	gene with protein product		176396	"pregnancy specific beta-1-glycoprotein 7"				Standard	NM_002783		Approved		uc010xwl.2	Q13046	OTTHUMG00000151125		chr19.hg19:g.43430643A>G		73.0	0.0		109.0	52.0	NM_001206650	Q15232	Missense_Mutation	SNP	ENST00000406070.2	hg19																																																																																				.	.		0.517	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	NM_001206650		G	43430643	A	G	43430643	1	3	167	0	1	0	0	0	0	0	0	0	12672	449	16	2		2	PSG7	19	43430643	RNA	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	7995330	43430643	15698340	155	25400										
ZNF155	7711	hgsc.bcm.edu	37	chr19	44500765	44500765	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gcacttaatgttcatcgtaaAttacacacaggagagaaacc	7	9	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:44500765A>G	ENST00000270014.2	+	5	884	c.756A>G	c.(754-756)aaA>aaG	p.K252K	RP11-15A1.7_ENST00000589021.1_RNA|ZNF155_ENST00000407951.2_Silent_p.K263K|RP11-15A1.7_ENST00000586860.1_RNA|ZNF155_ENST00000590615.1_Silent_p.K252K	NM_001260487.1|NM_198089.2	NP_001247416|NP_932355	Q12901	ZN155_HUMAN	zinc finger protein 155	252					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	15		Prostate(69;0.0352)				TTCATCGTAAATTACACACAG	0.428																																					p.K263K	NSCLC(61;554 1277 20909 42067 42312)	Atlas-SNP	.											.	ZNF155	30	.	0			c.A789G						.						127	126	127					19																	44500765		2203	4300	6503	SO:0001819	synonymous_variant	7711	exon6			TCGTAAATTACAC	U09852	CCDS12634.1, CCDS58668.1	19q13.2-q13.32	2013-01-08	2006-08-22			ENSG00000204920		"Zinc fingers, C2H2-type", "-"	12940	protein-coding gene	gene with protein product		604086	"zinc finger protein 155 (pHZ-96)"			7557990	Standard	NM_001260486		Approved	pHZ-96	uc010xwt.2	Q12901		ENST00000270014.2:c.756A>G	chr19.hg19:g.44500765A>G		121.0	0.0		183.0	37.0	NM_001260488	A2BDE6|B2RB63|B4DM95|J3KQ08|Q6AZZ8|Q9UIE1|Q9UK14	Silent	SNP	ENST00000270014.2	hg19	CCDS12634.1	.	.	.	.	.	.	.	.	.	.	A	2.320	-0.355877	0.05138	.	.	ENSG00000204920	ENST00000425747	.	.	.	2.59	-1.27	0.09347	.	.	.	.	.	T	0.17959	0.0431	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23013	-1.0200	5	0.23302	T	0.38	.	0.7484	0.00986	0.4572:0.1667:0.2122:0.1638	.	.	.	.	S	126	.	ENSP00000401576:N126S	N	+	2	0	ZNF155	49192605	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.402000	0.02499	-0.579000	0.05952	0.379000	0.24179	AAT	.	.		0.428	ZNF155-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460074.1	NM_003445		G	44500765	A	G	44500765	2	3	167	1	0	0	0	0	0	0	0	1	17751	98	4	2		2	ZNF155	19	44500765	Silent	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	1070122	44500765	14628218	156	25401										
SNRNP70	6625	hgsc.bcm.edu	37	chr19	49604657	49604657	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgccccacagatacacatggTctacagtaagcggtcaggaa	10	11	2	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:49604657T>G	ENST00000598441.1	+	7	628	c.404T>G	c.(403-405)gTc>gGc	p.V135G	SNRNP70_ENST00000221448.5_Missense_Mutation_p.V135G			P08621	RU17_HUMAN	small nuclear ribonucleoprotein 70kDa (U1)	135	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	12						ATACACATGGTCTACAGTAAG	0.637																																					p.V135G		Atlas-SNP	.											.	SNRNP70	30	.	0			c.T404G						.						124	81	95					19																	49604657		2203	4300	6503	SO:0001583	missense	6625	exon7			ACATGGTCTACAG		CCDS12756.1, CCDS74417.1	19q13.3	2013-02-12	2008-10-29	2008-10-29		ENSG00000104852		"RNA binding motif (RRM) containing"	11150	protein-coding gene	gene with protein product		180740	"small nuclear ribonucleoprotein 70kDa (RNP antigen)"	RNPU1Z, RPU1, SNRP70			Standard	XM_005259177		Approved	U1-70K, Snp1	uc021uxh.1	P08621		ENST00000598441.1:c.404T>G	chr19.hg19:g.49604657T>G	ENSP00000472998:p.Val135Gly	70.0	0.0		114.0	7.0	NM_003089	B3KUA3|P78493|P78494|Q15364|Q15686|Q15687|Q15689|Q99377|Q9UE45|Q9UE46|Q9UE47|Q9UE48|Q9UFQ6	Missense_Mutation	SNP	ENST00000598441.1	hg19	CCDS12756.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.977889	0.74360	.	.	ENSG00000104852	ENST00000221448;ENST00000401730	T;T	0.19806	2.12;2.12	4.95	4.95	0.65309	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.46112	0.1376	M	0.77616	2.38	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.67725	0.953;0.917	T	0.50996	-0.8761	10	0.87932	D	0	-19.3167	13.9272	0.63970	0.0:0.0:0.0:1.0	.	135;135	P08621;P08621-2	RU17_HUMAN;.	G	135	ENSP00000221448:V135G;ENSP00000385077:V135G	ENSP00000221448:V135G	V	+	2	0	SNRNP70	54296469	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.535000	0.82014	2.000000	0.58554	0.533000	0.62120	GTC	.	.		0.637	SNRNP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466266.1	NM_003089		G	49604657	T	G	49604657	3	3	167	1	0	0	0	0	1	0	0	0	14873	1667	58	5	426	5	SNRNP70	19	49604657	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	5103892	49604657	9524326	157	25402										
PTPRH	5794	hgsc.bcm.edu	37	chr19	55715250	55715250	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggtccaaggccatccacggtGactctggtgtctgttgtgtt	13	10	2	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr19:55715250G>A	ENST00000376350.3	-	5	808	c.786C>T	c.(784-786)gtC>gtT	p.V262V	PTPRH_ENST00000263434.5_Intron|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	262	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CATCCACGGTGACTCTGGTGT	0.537																																					p.V262V		Atlas-SNP	.											.	PTPRH	139	.	0			c.C786T						.						227	195	206					19																	55715250		2203	4300	6503	SO:0001819	synonymous_variant	5794	exon5			CACGGTGACTCTG		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.786C>T	chr19.hg19:g.55715250G>A		120.0	0.0		164.0	31.0	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Silent	SNP	ENST00000376350.3	hg19	CCDS33110.1																																																																																			.	.		0.537	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			A	55715250	G	A	55715250	2	1	167	1	0	0	0	0	0	0	0	1	12818	1277	45	3		3	PTPRH	19	55715250	Silent	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	6110593	55715250	3413733	158	25403										
PLCB1	23236	hgsc.bcm.edu	37	chr20	8705358	8705358	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	aatgtctaatctggtgaactAtattcagccagtcaagtttg	8	7	4	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr20:8705358A>G	ENST00000338037.6	+	16	1664	c.1637A>G	c.(1636-1638)tAt>tGt	p.Y546C	PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378641.3_Missense_Mutation_p.Y546C|PLCB1_ENST00000378637.2_Missense_Mutation_p.Y546C	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	546	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						CTGGTGAACTATATTCAGCCA	0.363																																					p.V546G		Atlas-SNP	.											.	PLCB1	394	.	0			c.T1637G						.						70	75	73					20																	8705358		2203	4300	6503	SO:0001583	missense	23236	exon16			TGAACTATATTCA	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.1637A>G	chr20.hg19:g.8705358A>G	ENSP00000338185:p.Tyr546Cys	82.0	0.0		118.0	46.0	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	hg19	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.174884	0.78564	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.77098	-1.07;-1.07;-1.07	5.22	5.22	0.72569	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.063541	0.64402	D	0.000004	D	0.92760	0.7698	H	0.98682	4.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95491	0.8569	10	0.87932	D	0	.	15.4026	0.74852	1.0:0.0:0.0:0.0	.	546;546	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	C	546;546;546;466;466	ENSP00000367908:Y546C;ENSP00000338185:Y546C;ENSP00000367904:Y546C	ENSP00000338185:Y546C	Y	+	2	0	PLCB1	8653358	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.339000	0.96797	2.095000	0.63458	0.460000	0.39030	TAT	.	.		0.363	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			G	8705358	A	G	8705358	3	3	167	1	0	0	0	0	1	0	0	0	12036	449	16	2	1699	2	PLCB1	20	8705358	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10		8705358	54320162	159	25404										
CYP24A1	1591	hgsc.bcm.edu	37	chr20	52773780	52773780	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cagggtgcctgagtgtagcaTctcaacaggctcattgtctg	12	10	3	1	rs77167734		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr20:52773780T>G	ENST00000216862.3	-	11	1876	c.1483A>C	c.(1483-1485)Atg>Ctg	p.M495L	CYP24A1_ENST00000395954.3_Missense_Mutation_p.M353L|CYP24A1_ENST00000460643.1_5'UTR|CYP24A1_ENST00000395955.3_Missense_Mutation_p.M429L	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	495					osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin D receptor signaling pathway (GO:0070561)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity (GO:0030342)|25-hydroxycholecalciferol-24-hydroxylase activity (GO:0008403)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Corticotropin(DB01285)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	GAGTGTAGCATCTCAACAGGC	0.522																																					p.M495L		Atlas-SNP	.											.	CYP24A1	75	.	0			c.A1483C						.						80	67	72					20																	52773780		2203	4300	6503	SO:0001583	missense	1591	exon11			GTAGCATCTCAAC	U60669	CCDS33491.1, CCDS46616.1	20q13.2-q13.3	2003-02-28	2003-02-14	2003-02-28	ENSG00000019186	ENSG00000019186		"Cytochrome P450s"	2602	protein-coding gene	gene with protein product		126065	"cytochrome P450, subfamily XXIV (vitamin D 24-hydroxylase)"	CYP24			Standard	NM_000782		Approved	CP24, P450-CC24	uc002xwv.2	Q07973	OTTHUMG00000032773	ENST00000216862.3:c.1483A>C	chr20.hg19:g.52773780T>G	ENSP00000216862:p.Met495Leu	99.0	0.0		189.0	10.0	NM_000782	Q15807|Q32ML3|Q5I2W7	Missense_Mutation	SNP	ENST00000216862.3	hg19	CCDS33491.1	.	.	.	.	.	.	.	.	.	.	t	9.157	1.017805	0.19355	.	.	ENSG00000019186	ENST00000216862;ENST00000395955;ENST00000395954	T;T;T	0.67523	-0.27;5.18;-0.27	5.53	5.53	0.82687	.	0.366494	0.35151	N	0.003407	T	0.51787	0.1695	N	0.17594	0.5	0.24752	N	0.99297	B;B;B	0.12630	0.006;0.002;0.0	B;B;B	0.12156	0.001;0.007;0.007	T	0.44345	-0.9334	10	0.37606	T	0.19	-18.0223	14.8619	0.70387	0.0:0.0:0.0:1.0	.	429;495;353	Q32ML3;Q07973;Q5I2W7	.;CP24A_HUMAN;.	L	495;429;353	ENSP00000216862:M495L;ENSP00000379285:M429L;ENSP00000379284:M353L	ENSP00000216862:M495L	M	-	1	0	CYP24A1	52207187	0.828000	0.29307	1.000000	0.80357	0.041000	0.13682	1.949000	0.40313	2.094000	0.63399	0.524000	0.50904	ATG	.	.		0.522	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2			G	52773780	T	G	52773780	3	3	167	1	0	0	0	0	1	0	0	0	4156	1435	50	5	65	5	CYP24A1	20	52773780	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	44068422	52773780	10251740	160	25405										
PRIC285	85441	hgsc.bcm.edu	37	chr20	62196516	62196516	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agatcttggtcacggagccaTtgatggggaccatgatgcgc	14	9	2	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr20:62196516T>C	ENST00000467148.1	-	8	3728	c.3659A>G	c.(3658-3660)aAt>aGt	p.N1220S	HELZ2_ENST00000427522.2_Missense_Mutation_p.N651S	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1220					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CACGGAGCCATTGATGGGGAC	0.652																																					p.N1220S		Atlas-SNP	.											.	.	.	.	0			c.A3659G						.						28	24	26					20																	62196516		2181	4293	6474	SO:0001583	missense	85441	exon9			GAGCCATTGATGG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.3659A>G	chr20.hg19:g.62196516T>C	ENSP00000417401:p.Asn1220Ser	130.0	0.0		179.0	10.0	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.322541	0.41096	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.21734	1.99;1.99	4.77	4.77	0.60923	.	0.604046	0.16540	N	0.209980	T	0.20414	0.0491	L	0.46157	1.445	0.20074	N	0.999934	P;P	0.42692	0.488;0.787	B;B	0.36567	0.114;0.228	T	0.11446	-1.0587	10	0.62326	D	0.03	-15.513	14.2869	0.66251	0.0:0.0:0.0:1.0	.	1220;651	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	S	651;1220	ENSP00000393257:N651S;ENSP00000417401:N1220S	ENSP00000393257:N651S	N	-	2	0	RP4-697K14.7	61666960	0.999000	0.42202	0.244000	0.24202	0.937000	0.57800	4.365000	0.59486	1.782000	0.52362	0.397000	0.26171	AAT	.	.		0.652	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		C	62196516	T	C	62196516	3	2	167	1	0	0	0	0	1	0	0	0	12497	1493	52	2	4338	2	PRIC285	20	62196516	Missense_Mutation	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10	9422736	62196516	829004	161	25406										
TMPRSS6	164656	hgsc.bcm.edu	37	chr22	37485802	37485802	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gaggacctggccctggcccaCgtagctgtagcggtaacaac	13	13	0	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chr22:37485802C>T	ENST00000346753.3	-	7	795	c.679G>A	c.(679-681)Gtg>Atg	p.V227M	TMPRSS6_ENST00000406856.1_Missense_Mutation_p.V218M|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.V218M|TMPRSS6_ENST00000381792.2_Missense_Mutation_p.V218M|TMPRSS6_ENST00000442782.2_Missense_Mutation_p.V227M	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	227	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						CCCTGGCCCACGTAGCTGTAG	0.667																																					p.V227M		Atlas-SNP	.											.	TMPRSS6	99	.	0			c.G679A						.						17	19	18					22																	37485802		2201	4297	6498	SO:0001583	missense	164656	exon7			GGCCCACGTAGCT	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"Serine peptidases / Transmembrane"	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.679G>A	chr22.hg19:g.37485802C>T	ENSP00000334962:p.Val227Met	219.0	0.0		256.0	70.0	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	hg19	CCDS13941.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.679863	0.47886	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856;ENST00000442782	D;D;D;D;T	0.91945	-2.94;-2.94;-2.94;-2.94;-0.95	4.28	2.11	0.27256	CUB (1);	0.165070	0.38720	N	0.001594	D	0.91171	0.7219	L	0.29908	0.895	0.41722	D	0.989516	D;D;D	0.76494	0.999;0.993;0.987	D;P;P	0.67382	0.951;0.759;0.579	D	0.88453	0.3050	10	0.33940	T	0.23	.	9.9163	0.41436	0.0:0.7605:0.0:0.2395	.	227;218;227	Q8IU80-2;Q8IU80-5;Q8IU80	.;.;TMPS6_HUMAN	M	218;227;218;218;227	ENSP00000371211:V218M;ENSP00000334962:V227M;ENSP00000385453:V218M;ENSP00000384964:V218M;ENSP00000397691:V227M	ENSP00000334962:V227M	V	-	1	0	TMPRSS6	35815748	0.984000	0.35163	1.000000	0.80357	0.808000	0.45660	2.573000	0.46007	0.910000	0.36722	-0.463000	0.05309	GTG	.	.		0.667	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609		T	37485802	C	T	37485802	3	4	167	1	0	0	0	0	1	0	0	0	16266	536	19	1	1804	1	TMPRSS6	22	37485802	Missense_Mutation	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10		37485802	13818764	162	25407										
BEND2	139105	hgsc.bcm.edu	37	chrX	18189191	18189191	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	agattgccatagacgttactTtggaccaggacatcttttgt	9	8	1	2			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chrX:18189191T>C	ENST00000380033.4	-	13	2247	c.2115A>G	c.(2113-2115)caA>caG	p.Q705Q	BEND2_ENST00000380030.3_Silent_p.Q614Q	NM_153346.4	NP_699177.2	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	705	BEN 2. {ECO:0000255|PROSITE- ProRule:PRU00784}.									NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(11)|liver(1)|lung(21)|ovary(3)|prostate(1)	49						AGACGTTACTTTGGACCAGGA	0.438																																					p.Q705Q		Atlas-SNP	.											.	BEND2	108	.	0			c.A2115G						.						218	189	199					X																	18189191		2203	4300	6503	SO:0001819	synonymous_variant	139105	exon13			GTTACTTTGGACC	AK128155	CCDS14184.1, CCDS55375.1	Xp22.22	2012-11-22	2008-10-03	2008-10-03	ENSG00000177324	ENSG00000177324		"BEN domain containing"	28509	protein-coding gene	gene with protein product			"chromosome X open reading frame 20"	CXorf20		12477932	Standard	NM_153346		Approved	MGC33653	uc004cyj.4	Q8NDZ0	OTTHUMG00000021211	ENST00000380033.4:c.2115A>G	chrX.hg19:g.18189191T>C		107.0	0.0		94.0	7.0	NM_153346	E9PFY2|Q4V9S2|Q5JXE5	Silent	SNP	ENST00000380033.4	hg19	CCDS14184.1																																																																																			.	.		0.438	BEND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055940.1	NM_153346		C	18189191	T	C	18189191	2	2	167	1	0	0	0	0	0	0	0	1	1398	1838	64	2		2	BEND2	23	18189191	Silent	SNP	T	TCGA-DD-AACP-01A-11D-A40R-10		18189191	137081369	163	25408										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20187519	20187519	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	catattaaagaatctacttaCatcctttagagtgataatgt	5	6	1	3			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chrX:20187519C>T	ENST00000379565.3	-	16	1651		c.e16+1		RPS6KA3_ENST00000540702.1_Splice_Site|RPS6KA3_ENST00000479809.1_Splice_Site|RPS6KA3_ENST00000544447.1_Splice_Site|RPS6KA3_ENST00000379548.4_Splice_Site	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3						axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	AATCTACTTACATCCTTTAGA	0.318																																					.		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.1443+1G>A						.						154	149	151					X																	20187519		2203	4300	6503	SO:0001630	splice_region_variant	6197	exon17			TACTTACATCCTT	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1443+1G>A	chrX.hg19:g.20187519C>T		64.0	0.0		38.0	20.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Splice_Site	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520373	0.85495	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4385	0.90654	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RPS6KA3	20097440	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.715000	0.84713	2.382000	0.81193	0.600000	0.82982	.	.	.		0.318	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586	Intron	T	20187519	C	T	20187519	5	4	167	1	0	0	0	0	0	0	1	0	13667	492	17	3	806	3	RPS6KA3	23	20187519	Splice_Site	SNP	C	TCGA-DD-AACP-01A-11D-A40R-10	1998328	20187519	135083041	164	25409										
EFHC2	80258	hgsc.bcm.edu	37	chrX	44035625	44035625	+	Frame_Shift_Del	DEL	T	T	-													0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgtctttggtgggtaatacaTtttttctgcattaaaacaac							TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chrX:44035625delT	ENST00000420999.1	-	13	2038	c.1955delA	c.(1954-1956)aatfs	p.N652fs	EFHC2_ENST00000343571.3_5'UTR	NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	652							calcium ion binding (GO:0005509)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						GGGTAATACATTTTTTCTGCA	0.308																																					p.N652fs		Atlas-INDEL	.											.	EFHC2	81	.	0			c.1956delT						.						124	104	111					X																	44035625		1823	4079	5902	SO:0001589	frameshift_variant	80258	exon13			.	AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"EF-hand domain containing"	26233	protein-coding gene	gene with protein product		300817	"mental retardation, X-linked 74"	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.1955delA	chrX.hg19:g.44035625delT	ENSP00000404232:p.Asn652fs	59.0	0.0		99.0	34.0	NM_025184	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Frame_Shift_Del	DEL	ENST00000420999.1	hg19	CCDS55405.1																																																																																			.	.		0.308	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184		-	44035625	T	-	44035625	7	5	167	1	0	1	0	1	0	0	0	0	4949	1493	52	0	306	0	EFHC2	23	44035625	Frame_Shift_Del	DEL	T	TCGA-DD-AACP-01A-11D-A40R-10	23848106	44035625	111234935	165	25410										
FAM155B	27112	hgsc.bcm.edu	37	chrX	68748901	68748901	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	cagcaggaatgccagcgctgGgtgccctgcaagcaatactg	13	12	0	0			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chrX:68748901G>T	ENST00000252338.4	+	2	969	c.927G>T	c.(925-927)tgG>tgT	p.W309C		NM_015686.2	NP_056501.2	O75949	F155B_HUMAN	family with sequence similarity 155, member B	309						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)	16						GCCAGCGCTGGGTGCCCTGCA	0.582																																					p.W309C		Atlas-SNP	.											.	FAM155B	44	.	0			c.G927T						.						57	44	49					X																	68748901		2203	4300	6503	SO:0001583	missense	27112	exon2			GCGCTGGGTGCCC	AF087142	CCDS35317.1	Xq13.1	2008-04-15	2008-04-15	2008-04-15	ENSG00000130054	ENSG00000130054			30701	protein-coding gene	gene with protein product			"transmembrane protein 28", "chromosome X open reading frame 63"	TMEM28, CXorf63			Standard	NM_015686		Approved	TED	uc004dxk.3	O75949	OTTHUMG00000021756	ENST00000252338.4:c.927G>T	chrX.hg19:g.68748901G>T	ENSP00000252338:p.Trp309Cys	128.0	1.0		136.0	117.0	NM_015686	B1ALV6|B9EGK1|D3DVU1	Missense_Mutation	SNP	ENST00000252338.4	hg19	CCDS35317.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.180620	0.57800	.	.	ENSG00000130054	ENST00000252338	T	0.11604	2.76	5.31	5.31	0.75309	.	0.189003	0.37348	N	0.002134	T	0.14270	0.0345	N	0.14661	0.345	0.58432	D	0.999999	D	0.69078	0.997	P	0.60236	0.871	T	0.04976	-1.0914	10	0.62326	D	0.03	-6.6114	11.2167	0.48830	0.0:0.1808:0.8192:0.0	.	309	O75949-2	.	C	309	ENSP00000252338:W309C	ENSP00000252338:W309C	W	+	3	0	FAM155B	68665626	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.310000	0.59141	2.207000	0.71202	0.523000	0.50628	TGG	.	.		0.582	FAM155B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057037.1	NM_015686		T	68748901	G	T	68748901	3	4	167	1	0	0	0	0	1	0	0	0	5471	1241	43	3	933	3	FAM155B	23	68748901	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	24713276	68748901	86521659	166	25411										
ACRC	93953	hgsc.bcm.edu	37	chrX	70811974	70811974	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tctcttttatttttgcagttAcatccttaatgttcagtcaa	4	8	3	0	rs36115715		TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chrX:70811974A>G	ENST00000373695.1	+	2	599	c.62A>G	c.(61-63)tAc>tGc	p.Y21C	ACRC_ENST00000373696.3_Missense_Mutation_p.Y21C			Q96QF7	ACRC_HUMAN	acidic repeat containing	21						nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1)	54	Renal(35;0.156)					TTTTGCAGTTACATCCTTAAT	0.373																																					p.Y21C		Atlas-SNP	.											.	ACRC	110	.	0			c.A62G						.						206	168	181					X																	70811974		2203	4299	6502	SO:0001583	missense	93953	exon3			GCAGTTACATCCT	AJ311392	CCDS35326.1	Xq13.1	2010-08-05			ENSG00000147174	ENSG00000147174			15805	protein-coding gene	gene with protein product		300369					Standard	NM_052957		Approved		uc004eae.2	Q96QF7	OTTHUMG00000033327	ENST00000373695.1:c.62A>G	chrX.hg19:g.70811974A>G	ENSP00000362799:p.Tyr21Cys	237.0	0.0		285.0	25.0	NM_052957	B9EG62	Missense_Mutation	SNP	ENST00000373695.1	hg19	CCDS35326.1	.	.	.	.	.	.	.	.	.	.	A	3.429	-0.116547	0.06838	.	.	ENSG00000147174	ENST00000373696;ENST00000373695	T;T	0.38722	1.12;1.12	2.49	-4.98	0.03019	.	.	.	.	.	T	0.20088	0.0483	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.13629	-1.0502	9	0.87932	D	0	.	2.998	0.06004	0.2061:0.1561:0.4825:0.1554	rs36115715	21	Q96QF7	ACRC_HUMAN	C	21	ENSP00000362800:Y21C;ENSP00000362799:Y21C	ENSP00000362799:Y21C	Y	+	2	0	ACRC	70728699	0.001000	0.12720	0.000000	0.03702	0.035000	0.12851	-0.876000	0.04201	-2.515000	0.00501	-2.143000	0.00337	TAC	.	.		0.373	ACRC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081856.1			G	70811974	A	G	70811974	3	3	167	1	0	0	0	0	1	0	0	0	171	391	14	2	68	2	ACRC	23	70811974	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	2063073	70811974	84458586	167	25412										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73963968	73963968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	gcctaagcaagtccgacttgGctgcatgagacagtccccat	10	13	0	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chrX:73963968G>A	ENST00000055682.6	-	3	1035	c.424C>T	c.(424-426)Cca>Tca	p.P142S		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	142					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						GTCCGACTTGGCTGCATGAGA	0.483																																					p.P142S		Atlas-SNP	.											.	KIAA2022	262	.	0			c.C424T						.						87	77	80					X																	73963968		2203	4300	6503	SO:0001583	missense	340533	exon3			GACTTGGCTGCAT		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.424C>T	chrX.hg19:g.73963968G>A	ENSP00000055682:p.Pro142Ser	69.0	0.0		122.0	6.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.689597	0.68271	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.36157	1.27;1.27	6.08	6.08	0.98989	.	0.431758	0.26692	N	0.022986	T	0.52419	0.1733	L	0.36672	1.1	0.54753	D	0.999989	D	0.76494	0.999	D	0.67382	0.951	T	0.51100	-0.8748	10	0.66056	D	0.02	-9.8297	19.5098	0.95137	0.0:0.0:1.0:0.0	.	142	Q5QGS0	K2022_HUMAN	S	142	ENSP00000362567:P142S;ENSP00000055682:P142S	ENSP00000055682:P142S	P	-	1	0	KIAA2022	73880693	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.476000	0.97823	2.562000	0.86427	0.600000	0.82982	CCA	.	.		0.483	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		A	73963968	G	A	73963968	3	1	167	1	0	0	0	0	1	0	0	0	8278	1203	42	3	4134	3	KIAA2022	23	73963968	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	3151994	73963968	81306592	168	25413										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91132817	91132817	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ggcatgctgactgtagtgaaGaaactagatagagaaaaaga	12	4	0	6			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chrX:91132817G>T	ENST00000373094.1	+	2	2423	c.1578G>T	c.(1576-1578)aaG>aaT	p.K526N	PCDH11X_ENST00000504220.2_Missense_Mutation_p.K526N|PCDH11X_ENST00000298274.8_Missense_Mutation_p.K526N|PCDH11X_ENST00000373088.1_Missense_Mutation_p.K526N|PCDH11X_ENST00000361655.2_Missense_Mutation_p.K526N|PCDH11X_ENST00000395337.2_Missense_Mutation_p.K526N|PCDH11X_ENST00000406881.1_Missense_Mutation_p.K526N|PCDH11X_ENST00000373097.1_Missense_Mutation_p.K526N|PCDH11X_ENST00000361724.1_Missense_Mutation_p.K526N	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	526	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						CTGTAGTGAAGAAACTAGATA	0.433																																					p.K526N	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.G1578T						.						61	57	58					X																	91132817		2203	4300	6503	SO:0001583	missense	27328	exon2			AGTGAAGAAACTA	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.1578G>T	chrX.hg19:g.91132817G>T	ENSP00000362186:p.Lys526Asn	192.0	0.0		206.0	18.0	NM_001168363	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	hg19	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	G	3.054	-0.194801	0.06259	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42	5.38	2.1	0.27182	Cadherin (4);Cadherin-like (1);	0.216100	0.46145	N	0.000312	T	0.38904	0.1058	L	0.42529	1.33	0.36950	D	0.892834	B;B;B;B;B;B;B;B	0.17038	0.016;0.003;0.016;0.016;0.016;0.02;0.009;0.009	B;B;B;B;B;B;B;B	0.20384	0.012;0.007;0.017;0.017;0.017;0.029;0.012;0.012	T	0.24297	-1.0164	10	0.33940	T	0.23	.	5.445	0.16529	0.2542:0.0:0.5833:0.1625	.	526;526;526;526;526;526;526;526	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	N	526	ENSP00000378746:K526N;ENSP00000362186:K526N;ENSP00000362189:K526N;ENSP00000355040:K526N;ENSP00000362180:K526N;ENSP00000423762:K526N;ENSP00000355105:K526N;ENSP00000384758:K526N;ENSP00000298274:K526N	ENSP00000298274:K526N	K	+	3	2	PCDH11X	91019473	1.000000	0.71417	1.000000	0.80357	0.545000	0.35147	0.924000	0.28777	0.443000	0.26582	0.544000	0.68410	AAG	.	.		0.433	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		T	91132817	G	T	91132817	3	4	167	1	0	0	0	0	1	0	0	0	11517	933	33	3	1584	3	PCDH11X	23	91132817	Missense_Mutation	SNP	G	TCGA-DD-AACP-01A-11D-A40R-10	17168849	91132817	64137743	169	25414										
MCF2	4168	hgsc.bcm.edu	37	chrX	138729064	138729064	+	Splice_Site	DEL	T	T	-													0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	ttgtcctttccccggccaccTacaacaatagaaaaataatc							TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chrX:138729064delT	ENST00000519895.1	-	3	191		c.e3-2		MCF2_ENST00000370578.4_Splice_Site|MCF2_ENST00000520602.1_Splice_Site|MCF2_ENST00000414978.1_Splice_Site	NM_001171876.1	NP_001165347.1	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence						apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					CCCGGCCACCTACAACAATAG	0.333																																					.		Atlas-INDEL	.											.	MCF2	432	.	0			c.26-1A>-						.						49	41	43					X																	138729064		1822	4071	5893	SO:0001630	splice_region_variant	4168	exon4			.		CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"Rho guanine nucleotide exchange factors"	6940	protein-coding gene	gene with protein product	"Oncogene MCF2 (oncogene DBL)"	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000519895.1:c.26-2A>-	chrX.hg19:g.138729064delT		285.0	0.0		377.0	34.0	NM_001171876	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Splice_Site	DEL	ENST00000519895.1	hg19	CCDS55517.1																																																																																			.	.		0.333	MCF2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377602.1	NM_005369	Intron	-	138729064	T	-	138729064	8	5	167	1	0	1	0	1	0	0	1	0	9387	1536	53	0	3172	0	MCF2	23	138729064	Splice_Site	DEL	T	TCGA-DD-AACP-01A-11D-A40R-10	47596247	138729064	16541496	170	25415										
LDOC1	23641	hgsc.bcm.edu	37	chrX	140271004	140271004	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0470588235294118	8	1	0.900277374190992	2.51327433628319	0.548350764279968	1	1	0	tgtaagacgccgtctgcacgAtaaactcggggagccgggag	15	10	1	1			TCGA-DD-AACP-01A-11D-A40R-10	TCGA-DD-AACP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1a97e7e-0519-436d-940f-2e59ec5f7a59	4d93e7d7-d828-4696-a682-754d76c9bb04	g.chrX:140271004A>G	ENST00000370526.2	-	1	306	c.203T>C	c.(202-204)aTc>aCc	p.I68T	LDOC1_ENST00000460721.1_Intron	NM_012317.2	NP_036449.1	O95751	LDOC1_HUMAN	leucine zipper, down-regulated in cancer 1	68					negative regulation of cell proliferation (GO:0008285)	nucleus (GO:0005634)				endometrium(6)|large_intestine(1)|lung(6)|ovary(1)	14	Acute lymphoblastic leukemia(192;7.65e-05)					CGTCTGCACGATAAACTCGGG	0.622																																					p.I68T		Atlas-SNP	.											.	LDOC1	26	.	0			c.T203C						.						67	58	61					X																	140271004		2203	4300	6503	SO:0001583	missense	23641	exon1			TGCACGATAAACT	AB019527	CCDS14672.1	Xq27	2008-02-05			ENSG00000182195	ENSG00000182195			6548	protein-coding gene	gene with protein product		300402		BCUR1		10403563, 15716091, 16093683	Standard	NM_012317		Approved	Mar7, Mart7	uc004fbj.3	O95751	OTTHUMG00000022558	ENST00000370526.2:c.203T>C	chrX.hg19:g.140271004A>G	ENSP00000359557:p.Ile68Thr	63.0	0.0		87.0	11.0	NM_012317	Q6IAR6	Missense_Mutation	SNP	ENST00000370526.2	hg19	CCDS14672.1	.	.	.	.	.	.	.	.	.	.	.	14.85	2.657614	0.47467	.	.	ENSG00000182195	ENST00000370526	T	0.31247	1.5	3.67	3.67	0.42095	.	0.286062	0.24449	N	0.038425	T	0.40767	0.1130	L	0.55213	1.73	0.25260	N	0.989604	D	0.58268	0.982	P	0.57324	0.818	T	0.17167	-1.0378	10	0.87932	D	0	-5.0147	7.8896	0.29669	1.0:0.0:0.0:0.0	.	68	O95751	LDOC1_HUMAN	T	68	ENSP00000359557:I68T	ENSP00000359557:I68T	I	-	2	0	LDOC1	140098670	1.000000	0.71417	0.998000	0.56505	0.922000	0.55478	3.499000	0.53310	1.678000	0.50952	0.237000	0.17872	ATC	.	.		0.622	LDOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058592.1	NM_012317		G	140271004	A	G	140271004	3	3	167	1	0	0	0	0	1	0	0	0	8718	333	12	2	241	2	LDOC1	23	140271004	Missense_Mutation	SNP	A	TCGA-DD-AACP-01A-11D-A40R-10	1541940	140271004	14999556	171	25416										
CHD5	26038	hgsc.bcm.edu	37	chr1	6211179	6211179	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggcactgtggatgctggcgcTgtcgaagtccgactcctccc	13	14	0	0	rs140594423		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:6211179T>A	ENST00000262450.3	-	7	1006	c.907A>T	c.(907-909)Agc>Tgc	p.S303C	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		ATGCTGGCGCTGTCGAAGTCC	0.607																																					p.S303C		Atlas-SNP	.											.	CHD5	267	.	0			c.A907T						.						99	86	90					1																	6211179		2203	4300	6503	SO:0001583	missense	26038	exon7			TGGCGCTGTCGAA	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.907A>T	chr1.hg19:g.6211179T>A	ENSP00000262450:p.Ser303Cys	44.0	0.0		26.0	8.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	hg19	CCDS57.1	.	.	.	.	.	.	.	.	.	.	t	18.78	3.697786	0.68386	.	.	ENSG00000116254	ENST00000262450	D	0.91351	-2.83	4.0	2.87	0.33458	.	0.221134	0.37761	U	0.001955	D	0.84428	0.5470	L	0.47716	1.5	0.80722	D	1	B	0.32918	0.39	B	0.25506	0.061	T	0.80455	-0.1375	10	0.59425	D	0.04	-6.8704	8.9636	0.35863	0.0:0.0898:0.0:0.9102	.	303	Q8TDI0	CHD5_HUMAN	C	303	ENSP00000262450:S303C	ENSP00000262450:S303C	S	-	1	0	CHD5	6133766	1.000000	0.71417	0.862000	0.33874	0.949000	0.60115	4.459000	0.60102	0.562000	0.29204	0.375000	0.23000	AGC	.	T|1.000;G|0.000		0.607	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		A	6211179	T	A	6211179	3	1	168	1	0	0	0	0	1	0	0	0	3330	1580	55	4	5097	4	CHD5	1	6211179	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10		6211179	243039442	1	25417										
ZBTB48	3104	hgsc.bcm.edu	37	chr1	6641168	6641168	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tccccagggatcaggagcccAgaggcagtcatagtcctcag	12	13	3	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:6641168A>T	ENST00000377674.4	+	2	657	c.499A>T	c.(499-501)Aga>Tga	p.R167*		NM_001278647.1|NM_001278648.1|NM_005341.2	NP_001265576.1|NP_001265577.1|NP_005332.1	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	167					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		TCAGGAGCCCAGAGGCAGTCA	0.597																																					p.R167X	Esophageal Squamous(125;1449 1657 4031 29866 49542)	Atlas-SNP	.											.	ZBTB48	33	.	0			c.A499T						.						44	49	47					1																	6641168		2202	4300	6502	SO:0001587	stop_gained	3104	exon2			GAGCCCAGAGGCA	BC013573	CCDS84.1	1p36.3	2013-01-08	2006-09-20	2006-09-20	ENSG00000204859	ENSG00000204859		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	4930	protein-coding gene	gene with protein product		165270	"GLI-Kruppel family member HKR3"	HKR3		2850480, 8661141	Standard	NM_001278647		Approved	ZNF855	uc001anx.3	P10074	OTTHUMG00000001438	ENST00000377674.4:c.499A>T	chr1.hg19:g.6641168A>T	ENSP00000366902:p.Arg167*	95.0	0.0		77.0	33.0	NM_005341	Q5SY19	Nonsense_Mutation	SNP	ENST00000377674.4	hg19	CCDS84.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.961527	0.92791	.	.	ENSG00000204859	ENST00000319084;ENST00000435905;ENST00000377674	.	.	.	5.5	-2.94	0.05581	.	1.203510	0.05511	N	0.560217	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-0.1369	1.7132	0.02896	0.3068:0.1516:0.3758:0.1658	.	.	.	.	X	167	.	ENSP00000313416:R167X	R	+	1	2	ZBTB48	6563755	0.000000	0.05858	0.001000	0.08648	0.934000	0.57294	-0.438000	0.06905	-0.135000	0.11495	0.533000	0.62120	AGA	.	.		0.597	ZBTB48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004193.1	NM_005341		T	6641168	A	T	6641168	4	4	168	1	0	0	0	0	0	1	0	0	17564	180	7	4	501	4	ZBTB48	1	6641168	Nonsense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	429989	6641168	242609453	2	25418										
MASP2	10747	hgsc.bcm.edu	37	chr1	11087660	11087686	+	In_Frame_Del	DEL	CCTCCATATATACGCCCTCCTGTTGTG	CCTCCATATATACGCCCTCCTGTTGTG	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	caccaggttttgccttttgcCctccatatatacgccctcct					rs571956287|rs376909147		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	CCTCCATATATACGCCCTCCTGTTGTG	CCTCCATATATACGCCCTCCTGTTGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:11087660_11087686delCCTCCATATATACGCCCTCCTGTTGTG	ENST00000400897.3	-	11	1332_1358	c.1317_1343delCACAACAGGAGGGCGTATATATGGAGG	c.(1315-1344)cgcacaacaggagggcgtatatatggaggg>cgg	p.TTGGRIYGG440del	RP4-635E18.8_ENST00000607145.1_RNA	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	440					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		TGCCTTTTGCCCTCCATATATACGCCCTCCTGTTGTGCGGGCTGATA	0.441																																					p.440_448del	GBM(35;611 746 20780 22741 36496)	Atlas-INDEL	.											.	MASP2	71	.	0			c.1318_1344del						.																																			SO:0001651	inframe_deletion	10747	exon11			.	X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"mannan-binding lectin serine protease 2", "mannan-binding lectin serine peptidase 1 pseudogene 1", "mannan-binding lectin serine protease 1 pseudogene 1"	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.1317_1343delCACAACAGGAGGGCGTATATATGGAGG	chr1.hg19:g.11087660_11087686delCCTCCATATATACGCCCTCCTGTTGTG	ENSP00000383690:p.Thr440_Gly448del	146.0	0.0		85.0	19.0	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	In_Frame_Del	DEL	ENST00000400897.3	hg19	CCDS123.1																																																																																			.	.		0.441	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610		-	11087686	CCTCCATATATACGCCCTCCTGTTGTG	-	11087660	7	5	168	1	0	1	0	1	0	0	0	0	9332	623	22	0	721	0	MASP2	1	11087660	In_Frame_Del	DEL	CCTCCATATATACGCCCTCCTGTTGTG	TCGA-DD-AACQ-01A-11D-A40R-10	4446492	11087660	238162961	3	25419										
MTOR	2475	hgsc.bcm.edu	37	chr1	11301649	11301649	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgggctccagcagctccttgAtatcctgctggatgcctggc	12	13	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:11301649A>T	ENST00000361445.4	-	10	1578	c.1502T>A	c.(1501-1503)aTc>aAc	p.I501N		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	501	Interaction with NBN.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CAGCTCCTTGATATCCTGCTG	0.577											OREG0013097	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I501N		Atlas-SNP	.											.	MTOR	327	.	0			c.T1502A						.						80	71	74					1																	11301649		2203	4300	6503	SO:0001583	missense	2475	exon10			TCCTTGATATCCT	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.1502T>A	chr1.hg19:g.11301649A>T	ENSP00000354558:p.Ile501Asn	65.0	0.0	671	80.0	25.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	A	18.76	3.692141	0.68271	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.68479	-0.33	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (2);	0.057436	0.64402	D	0.000001	T	0.69052	0.3068	M	0.62723	1.935	0.80722	D	1	P	0.43094	0.799	B	0.43575	0.424	T	0.73855	-0.3851	10	0.87932	D	0	-7.3906	15.9756	0.80060	1.0:0.0:0.0:0.0	.	501	P42345	MTOR_HUMAN	N	501	ENSP00000354558:I501N	ENSP00000354558:I501N	I	-	2	0	MTOR	11224236	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	8.830000	0.92063	2.171000	0.68590	0.533000	0.62120	ATC	.	.		0.577	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		T	11301649	A	T	11301649	3	4	168	1	0	0	0	0	1	0	0	0	9963	333	12	4	6343	4	MTOR	1	11301649	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	213989	11301649	237948972	4	25420										
CROCC	9696	hgsc.bcm.edu	37	chr1	17280852	17280852	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agccggcaggagcaggaccgGgtagggcaggctgggcagct	20	10	0	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:17280852G>T	ENST00000375541.5	+	22	3390	c.3321G>T	c.(3319-3321)cgG>cgT	p.R1107R	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		AGCAGGACCGGGTAGGGCAGG	0.652																																					p.R1107R		Atlas-SNP	.											.	CROCC	185	.	0			c.G3321T						.						30	33	32					1																	17280852		2202	4298	6500	SO:0001630	splice_region_variant	9696	exon22			GGACCGGGTAGGG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.3321+1G>T	chr1.hg19:g.17280852G>T		148.0	0.0		102.0	47.0	NM_014675		Silent	SNP	ENST00000375541.5	hg19	CCDS30616.1																																																																																			.	.		0.652	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	Silent	T	17280852	G	T	17280852	5	4	168	1	0	0	0	0	0	0	1	0	3895	1246	43	3	3407	3	CROCC	1	17280852	Splice_Site	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	5979203	17280852	231969769	5	25421										
ARHGEF10L	55160	hgsc.bcm.edu	37	chr1	17975106	17975106	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggacaagaagagcaaagcccCattctggtgcccgatcctgg	12	12	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:17975106C>G	ENST00000361221.3	+	22	2489	c.2330C>G	c.(2329-2331)cCa>cGa	p.P777R	ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.P738R|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.P480R|ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.P772R|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.P738R|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.P550R	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	777						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		AGCAAAGCCCCATTCTGGTGC	0.617																																					p.P777R		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.C2330G						.						81	75	77					1																	17975106		2203	4300	6503	SO:0001583	missense	55160	exon22			AAGCCCCATTCTG	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.2330C>G	chr1.hg19:g.17975106C>G	ENSP00000355060:p.Pro777Arg	137.0	0.0		142.0	12.0	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	hg19	CCDS182.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.373329	0.61624	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415;ENST00000375408;ENST00000457829;ENST00000167825	T;T;T;T;T;T	0.58940	0.54;0.57;0.36;0.57;0.3;2.55	4.95	4.95	0.65309	.	0.339865	0.30830	N	0.008788	T	0.62478	0.2431	M	0.75264	2.295	0.53005	D	0.999969	B;B;P;B;B;P;P	0.43701	0.093;0.151;0.674;0.012;0.151;0.815;0.583	B;B;B;B;B;B;B	0.42692	0.042;0.091;0.395;0.013;0.091;0.395;0.222	T	0.66156	-0.5994	10	0.40728	T	0.16	-21.1273	17.0971	0.86638	0.0:1.0:0.0:0.0	.	550;772;480;538;733;738;777	Q5VXI4;Q9HCE6-5;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;.;ARGAL_HUMAN	R	777;738;772;738;550;550;480	ENSP00000355060:P777R;ENSP00000399401:P738R;ENSP00000394621:P772R;ENSP00000364564:P738R;ENSP00000364557:P550R;ENSP00000167825:P480R	ENSP00000167825:P480R	P	+	2	0	ARHGEF10L	17847693	0.950000	0.32346	0.984000	0.44739	0.996000	0.88848	2.047000	0.41269	2.443000	0.82685	0.591000	0.81541	CCA	.	.		0.617	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		G	17975106	C	G	17975106	3	3	168	1	0	0	0	0	1	0	0	0	895	594	21	4	2412	4	ARHGEF10L	1	17975106	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	694254	17975106	231275515	6	25422										
IL28RA	163702	hgsc.bcm.edu	37	chr1	24486039	24486039	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	actgaacgtgtagatggttcTggcactgaggcagtggtgtt	15	6	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:24486039T>A	ENST00000327535.1	-	5	607	c.595A>T	c.(595-597)Aga>Tga	p.R199*	IFNLR1_ENST00000374421.3_Nonsense_Mutation_p.R199*|IFNLR1_ENST00000327575.2_Nonsense_Mutation_p.R199*|IFNLR1_ENST00000374419.1_Nonsense_Mutation_p.R116*	NM_170743.3|NM_173064.2	NP_734464.1|NP_775087.1	Q8IU57	INLR1_HUMAN	interferon, lambda receptor 1	199					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mucosal immune response (GO:0002385)|negative regulation of cell proliferation (GO:0008285)|regulation of defense response to virus by host (GO:0050691)|response to type III interferon (GO:0034342)	integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)											TAGATGGTTCTGGCACTGAGG	0.537																																					p.R199X		Atlas-SNP	.											.	.	.	.	0			c.A595T						.						127	113	118					1																	24486039		2203	4300	6503	SO:0001587	stop_gained	163702	exon5			TGGTTCTGGCACT	AY129153	CCDS248.1, CCDS249.1, CCDS250.1	1p36.11	2012-11-27	2012-11-26	2012-11-26	ENSG00000185436	ENSG00000185436		"Interferons"	18584	protein-coding gene	gene with protein product	"interferon lambda receptor 1"	607404	"interleukin 28 receptor, alpha", "interleukin 28 receptor, alpha (interferon, lambda receptor)"	IL28RA			Standard	NM_173064		Approved	CRF2/12, IFNLR, IL-28R1	uc001bis.3	Q8IU57	OTTHUMG00000003036	ENST00000327535.1:c.595A>T	chr1.hg19:g.24486039T>A	ENSP00000327824:p.Arg199*	198.0	0.0		137.0	50.0	NM_170743	Q5VTX5|Q5VTX7|Q5VTX8|Q6ZML8|Q8IV66|Q8IZI7|Q8IZI8	Nonsense_Mutation	SNP	ENST00000327535.1	hg19	CCDS248.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.041983	0.93685	.	.	ENSG00000185436	ENST00000327535;ENST00000327575;ENST00000374421;ENST00000374419	.	.	.	5.89	4.72	0.59763	.	0.394001	0.30419	N	0.009667	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.9947	10.2521	0.43375	0.0:0.0:0.1648:0.8352	.	.	.	.	X	199;199;199;116	.	ENSP00000327824:R199X	R	-	1	2	IL28RA	24358626	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	2.113000	0.41902	2.254000	0.74563	0.459000	0.35465	AGA	.	.		0.537	IFNLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008402.1	NM_170743		A	24486039	T	A	24486039	4	1	168	1	0	0	0	0	0	1	0	0	7693	1588	55	4	979	4	IL28RA	1	24486039	Nonsense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	6510933	24486039	224764582	7	25423										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32149574	32149574	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cacgcccttcagtcctggggGcccttgaactcctggtagac	11	15	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:32149574G>A	ENST00000373672.3	-	33	2830	c.2314C>T	c.(2314-2316)Ccc>Tcc	p.P772S	COL16A1_ENST00000373668.3_Missense_Mutation_p.P772S|COL16A1_ENST00000271069.6_Missense_Mutation_p.P771S	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	772	Triple-helical region 5 (COL5) with 3 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		AGTCCTGGGGGCCCTTGAACT	0.627																																					p.P772S	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.C2314T						.						49	54	52					1																	32149574		1938	4126	6064	SO:0001583	missense	1307	exon33			CTGGGGGCCCTTG	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.2314C>T	chr1.hg19:g.32149574G>A	ENSP00000362776:p.Pro772Ser	357.0	0.0		285.0	106.0	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	G	18.90	3.721636	0.68959	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668	D;D;D	0.97665	-4.48;-4.48;-4.48	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.97942	0.9323	M	0.71920	2.185	0.45139	D	0.998154	D;D;D	0.89917	1.0;0.982;0.99	D;P;P	0.75484	0.986;0.778;0.889	D	0.97165	0.9840	10	0.31617	T	0.26	.	15.881	0.79205	0.0:0.0:1.0:0.0	.	772;772;772	A6NCT7;Q07092;Q07092-2	.;COGA1_HUMAN;.	S	772;771;772	ENSP00000362776:P772S;ENSP00000271069:P771S;ENSP00000362772:P772S	ENSP00000271069:P771S	P	-	1	0	COL16A1	31922161	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	4.890000	0.63178	2.664000	0.90586	0.491000	0.48974	CCC	.	.		0.627	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		A	32149574	G	A	32149574	3	1	168	1	0	0	0	0	1	0	0	0	3675	1203	42	3	2656	3	COL16A1	1	32149574	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	7663535	32149574	217101047	8	25424										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35884117	35884117	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggggtggagatggcagagaaTactgacaatccactaagatg	14	6	0	4			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:35884117T>C	ENST00000314607.6	+	29	4463	c.4383T>C	c.(4381-4383)aaT>aaC	p.N1461N	ZMYM4_ENST00000373297.2_Silent_p.N1372N	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	1461					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TGGCAGAGAATACTGACAATC	0.418																																					p.N1461N		Atlas-SNP	.											.	ZMYM4	143	.	0			c.T4383C						.						144	130	135					1																	35884117		2203	4300	6503	SO:0001819	synonymous_variant	9202	exon29			AGAGAATACTGAC	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.4383T>C	chr1.hg19:g.35884117T>C		134.0	0.0		120.0	62.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Silent	SNP	ENST00000314607.6	hg19	CCDS389.1	.	.	.	.	.	.	.	.	.	.	T	9.932	1.215030	0.22373	.	.	ENSG00000146463	ENST00000457946	.	.	.	5.84	1.1	0.20463	.	.	.	.	.	T	0.58424	0.2121	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51988	-0.8635	4	.	.	.	-17.0879	10.1377	0.42717	0.0:0.4986:0.0:0.5014	.	.	.	.	H	1120	.	.	Y	+	1	0	ZMYM4	35656704	0.941000	0.31946	1.000000	0.80357	0.998000	0.95712	0.083000	0.14871	0.154000	0.19237	0.528000	0.53228	TAC	.	.		0.418	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		C	35884117	T	C	35884117	2	2	168	1	0	0	0	0	0	0	0	1	17717	1403	49	2		2	ZMYM4	1	35884117	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	3734543	35884117	213366504	9	25425										
RIMS3	9783	hgsc.bcm.edu	37	chr1	41094561	41094561	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cacaggtcttcttggtcatcTttgtcttcttcttggccaag	8	11	7	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:41094561T>A	ENST00000372684.3	-	7	1104	c.635A>T	c.(634-636)aAg>aTg	p.K212M	RIMS3_ENST00000372683.1_Missense_Mutation_p.K212M	NM_014747.2	NP_055562.2	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3	212	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			CTTGGTCATCTTTGTCTTCTT	0.552																																					p.K212M		Atlas-SNP	.											.	RIMS3	44	.	0			c.A635T						.						171	156	162					1																	41094561		2203	4300	6503	SO:0001583	missense	9783	exon7			GTCATCTTTGTCT	BC003103	CCDS30687.1	1p34.2	2013-09-19			ENSG00000117016	ENSG00000117016			21292	protein-coding gene	gene with protein product		611600				12620390, 10748113	Standard	NM_014747		Approved	RIM3, NIM3	uc001cfu.1	Q9UJD0	OTTHUMG00000007453	ENST00000372684.3:c.635A>T	chr1.hg19:g.41094561T>A	ENSP00000361769:p.Lys212Met	77.0	0.0		62.0	26.0	NM_014747	D3DPV8|Q92511|X5D7U7	Missense_Mutation	SNP	ENST00000372684.3	hg19	CCDS30687.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.140833	0.56936	.	.	ENSG00000117016	ENST00000372684;ENST00000372683	D;D	0.81739	-1.53;-1.53	4.92	2.56	0.30785	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.127164	0.64402	D	0.000001	D	0.87939	0.6304	M	0.88310	2.945	0.54753	D	0.999988	D	0.71674	0.998	D	0.68621	0.959	D	0.85953	0.1465	10	0.56958	D	0.05	-17.9447	5.2343	0.15439	0.0:0.3145:0.0:0.6855	.	212	Q9UJD0	RIMS3_HUMAN	M	212	ENSP00000361769:K212M;ENSP00000361768:K212M	ENSP00000361768:K212M	K	-	2	0	RIMS3	40867148	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.704000	0.47118	0.899000	0.36444	0.402000	0.26972	AAG	.	.		0.552	RIMS3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019585.1	NM_014747		A	41094561	T	A	41094561	3	1	168	1	0	0	0	0	1	0	0	0	13384	1609	56	4	299	4	RIMS3	1	41094561	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	5210444	41094561	208156060	10	25426										
EIF2B3	8891	hgsc.bcm.edu	37	chr1	45340421	45340421	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctatcttttatgagacaggaTgagccaatgactgagcgctt	10	8	1	4			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:45340421T>A	ENST00000360403.2	-	10	1257	c.1131A>T	c.(1129-1131)tcA>tcT	p.S377S	EIF2B3_ENST00000372183.3_Silent_p.S377S	NM_001261418.1|NM_020365.4	NP_001248347.1|NP_065098.1	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa	377					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|positive regulation of GTPase activity (GO:0043547)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	guanyl-nucleotide exchange factor activity (GO:0005085)|nucleotidyltransferase activity (GO:0016779)|translation initiation factor activity (GO:0003743)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	17	Acute lymphoblastic leukemia(166;0.155)					TGAGACAGGATGAGCCAATGA	0.453																																					p.S377S	Colon(26;357 658 2581 11857 12657)	Atlas-SNP	.											.	EIF2B3	43	.	0			c.A1131T						.						198	185	190					1																	45340421		2203	4300	6503	SO:0001819	synonymous_variant	8891	exon10			ACAGGATGAGCCA	AF257077	CCDS517.1, CCDS53313.1, CCDS72775.1	1p34.1	2008-02-05	2002-08-29		ENSG00000070785	ENSG00000070785			3259	protein-coding gene	gene with protein product		606273	"eukaryotic translation initiation factor 2B, subunit 3 (gamma, 58kD)"			10900014	Standard	NM_020365		Approved	EIF2Bgamma, EIF-2B	uc001cmt.3	Q9NR50	OTTHUMG00000008585	ENST00000360403.2:c.1131A>T	chr1.hg19:g.45340421T>A		111.0	0.0		89.0	45.0	NM_020365	B2RBH8|D3DPZ2|Q5QP89|Q5QP90|Q8NDB5|Q8WV57|Q9H850	Silent	SNP	ENST00000360403.2	hg19	CCDS517.1	.	.	.	.	.	.	.	.	.	.	T	9.105	1.005200	0.19199	.	.	ENSG00000070785	ENST00000439363	.	.	.	5.52	1.77	0.24775	.	.	.	.	.	T	0.68403	0.2997	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66352	-0.5945	4	.	.	.	-4.2574	14.4673	0.67492	0.0:0.0:0.7069:0.2931	.	.	.	.	L	198	.	.	H	-	2	0	EIF2B3	45113008	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	1.573000	0.36472	0.343000	0.23821	0.533000	0.62120	CAT	.	.		0.453	EIF2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023724.1	NM_020365		A	45340421	T	A	45340421	2	1	168	1	0	0	0	0	0	0	0	1	5004	1451	51	4		4	EIF2B3	1	45340421	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	4245860	45340421	203910200	11	25427										
KANK4	163782	hgsc.bcm.edu	37	chr1	62740090	62740090	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctggaggctcagctccctccTggaccagctctggaatccga	11	15	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:62740090T>A	ENST00000371153.4	-	3	1064	c.686A>T	c.(685-687)cAg>cTg	p.Q229L	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	229	Pro-rich.					cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						AGCTCCCTCCTGGACCAGCTC	0.552																																					p.Q229L		Atlas-SNP	.											.	KANK4	135	.	0			c.A686T						.						45	42	43					1																	62740090		2203	4300	6503	SO:0001583	missense	163782	exon3			CCCTCCTGGACCA	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	27263	protein-coding gene	gene with protein product		614612	"ankyrin repeat domain 38"	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.686A>T	chr1.hg19:g.62740090T>A	ENSP00000360195:p.Gln229Leu	201.0	0.0		159.0	63.0	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	hg19	CCDS620.1	.	.	.	.	.	.	.	.	.	.	T	9.235	1.036841	0.19669	.	.	ENSG00000132854	ENST00000371153	T	0.49432	0.78	4.66	-9.32	0.00643	.	1.898770	0.02928	N	0.138859	T	0.33498	0.0865	L	0.50333	1.59	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.09618	-1.0666	10	0.30078	T	0.28	1.3173	3.7557	0.08585	0.1816:0.1312:0.1067:0.5804	.	229	Q5T7N3	KANK4_HUMAN	L	229	ENSP00000360195:Q229L	ENSP00000360195:Q229L	Q	-	2	0	KANK4	62512678	0.000000	0.05858	0.004000	0.12327	0.011000	0.07611	-3.183000	0.00568	-2.054000	0.00900	-0.468000	0.05107	CAG	.	.		0.552	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		A	62740090	T	A	62740090	3	1	168	1	0	0	0	0	1	0	0	0	7988	1580	55	4	2333	4	KANK4	1	62740090	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	17399669	62740090	186510531	12	25428										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70503923	70503923	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gtgatactttcactgacaacTggactgatggctcgcattat	9	9	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:70503923T>C	ENST00000035383.5	+	19	2332	c.2302T>C	c.(2302-2304)Tgg>Cgg	p.W768R	LRRC7_ENST00000310961.5_Missense_Mutation_p.W773R|LRRC7_ENST00000415775.2_Missense_Mutation_p.W52R	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	768						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CACTGACAACTGGACTGATGG	0.498																																					p.W768R		Atlas-SNP	.											.	LRRC7	400	.	0			c.T2302C						.						153	142	146					1																	70503923		2203	4300	6503	SO:0001583	missense	57554	exon19			GACAACTGGACTG		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2302T>C	chr1.hg19:g.70503923T>C	ENSP00000035383:p.Trp768Arg	160.0	0.0		144.0	55.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	hg19	CCDS645.1	.	.	.	.	.	.	.	.	.	.	T	11.72	1.721745	0.30503	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.60548	0.18;0.3;1.41	5.58	4.44	0.53790	.	0.134555	0.53938	D	0.000047	T	0.57888	0.2084	L	0.47716	1.5	0.47862	D	0.999531	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.998;0.996	T	0.60717	-0.7208	10	0.46703	T	0.11	.	11.2231	0.48866	0.1373:0.0:0.0:0.8627	.	52;768;768	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	R	773;768;52;591	ENSP00000309245:W773R;ENSP00000035383:W768R;ENSP00000394867:W52R	ENSP00000035383:W768R	W	+	1	0	LRRC7	70276511	1.000000	0.71417	1.000000	0.80357	0.207000	0.24258	7.643000	0.83403	0.933000	0.37291	-0.691000	0.03719	TGG	.	.		0.498	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		C	70503923	T	C	70503923	3	2	168	1	0	0	0	0	1	0	0	0	9029	1580	55	2	2376	2	LRRC7	1	70503923	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	7763833	70503923	178746698	13	25429										
RWDD3	25950	hgsc.bcm.edu	37	chr1	95712212	95712212	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	aagtacagacagaacacaaaAggtataatttagtactattg	7	5	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:95712212A>T	ENST00000370202.4	+	3	764	c.688A>T	c.(688-690)Agg>Tgg	p.R230W	RP11-57H12.5_ENST00000444665.1_RNA|RP11-57H12.5_ENST00000598739.1_RNA|RWDD3_ENST00000495272.1_3'UTR|RWDD3_ENST00000263893.6_Intron	NM_001199682.1|NM_015485.4	NP_001186611.1|NP_056300	Q9Y3V2	RWDD3_HUMAN	RWD domain containing 3	230					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of hypoxia-inducible factor-1alpha signaling pathway (GO:1902073)|positive regulation of protein sumoylation (GO:0033235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(1)|large_intestine(2)|lung(6)|ovary(1)	10		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)		AGAACACAAAAGGTATAATTT	0.333																																					p.R230W		Atlas-SNP	.											.	RWDD3	24	.	0			c.A688T						.						101	93	96					1																	95712212		1836	4082	5918	SO:0001630	splice_region_variant	25950	exon3			CACAAAAGGTATA	BC010936	CCDS41357.1, CCDS44177.1	1p22.1	2012-12-07			ENSG00000122481	ENSG00000122481			21393	protein-coding gene	gene with protein product		615875				11230166	Standard	NM_015485		Approved	DKFZP566K023	uc009wdu.3	Q9Y3V2	OTTHUMG00000010910	ENST00000370202.4:c.689+1A>T	chr1.hg19:g.95712212A>T		275.0	0.0		228.0	96.0	NM_015485	A6NP44|A8K9F0|C9J9L7|C9JI45|Q08AJ7|Q6FID3|Q9BX35	Missense_Mutation	SNP	ENST00000370202.4	hg19	CCDS41357.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.118277	0.77323	.	.	ENSG00000122481	ENST00000370202	T	0.34859	1.34	5.88	5.88	0.94601	.	0.100748	0.64402	D	0.000002	T	0.52370	0.1730	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.57619	-0.7780	10	0.72032	D	0.01	-14.0317	16.3015	0.82820	1.0:0.0:0.0:0.0	.	230	Q9Y3V2	RWDD3_HUMAN	W	230	ENSP00000359221:R230W	ENSP00000359221:R230W	R	+	1	2	RWDD3	95484800	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.049000	0.76613	2.239000	0.73571	0.533000	0.62120	AGG	.	.		0.333	RWDD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030078.1	NM_015485	Missense_Mutation	T	95712212	A	T	95712212	5	4	168	1	0	0	0	0	0	0	1	0	13772	86	3	4	713	4	RWDD3	1	95712212	Splice_Site	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	25208289	95712212	153538409	14	25430										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109812061	109812061	+	Frame_Shift_Del	DEL	G	G	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	atcagagtccccaaacgcccGatcatcaacacacccgtggt					rs368719508		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:109812061delG	ENST00000271332.3	+	21	6889	c.6828delG	c.(6826-6828)ccgfs	p.P2276fs		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2276					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CCAAACGCCCGATCATCAACA	0.632																																					p.P2276fs	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-INDEL	.											.	CELSR2	228	.	0			c.6827delC						.						57	47	50					1																	109812061		2203	4300	6503	SO:0001589	frameshift_variant	1952	exon21			.	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.6828delG	chr1.hg19:g.109812061delG	ENSP00000271332:p.Pro2276fs	62.0	0.0		43.0	21.0	NM_001408	Q5T2Y7|Q92566	Frame_Shift_Del	DEL	ENST00000271332.3	hg19	CCDS796.1																																																																																			.	.		0.632	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		-	109812061	G	-	109812061	7	5	168	1	0	1	0	1	0	0	0	0	3224	1045	37	0	6910	0	CELSR2	1	109812061	Frame_Shift_Del	DEL	G	TCGA-DD-AACQ-01A-11D-A40R-10	14099849	109812061	139438560	15	25431										
MYBPHL	343263	hgsc.bcm.edu	37	chr1	109839480	109839480	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcactggttttcagcaaagaCacggaaggcataggagttgc	13	8	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:109839480C>T	ENST00000357155.1	-	5	704	c.655G>A	c.(655-657)Gtc>Atc	p.V219I	MYBPHL_ENST00000477962.1_Intron	NM_001010985.2|NM_001265613.1	NP_001010985.2|NP_001252542.1	A2RUH7	MBPHL_HUMAN	myosin binding protein H-like	219	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.									central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(2)	14		all_lung(203;0.00519)|all_epithelial(167;0.00575)|Lung NSC(277;0.00822)		Colorectal(144;0.0306)|Lung(183;0.0681)|COAD - Colon adenocarcinoma(174;0.117)|Epithelial(280;0.197)|all cancers(265;0.225)		TCAGCAAAGACACGGAAGGCA	0.572																																					p.V219I		Atlas-SNP	.											.	MYBPHL	28	.	0			c.G655A						.						148	115	127					1																	109839480		2203	4300	6503	SO:0001583	missense	343263	exon5			CAAAGACACGGAA	AK129834	CCDS30793.1	1p13	2013-02-11			ENSG00000221986	ENSG00000221986		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	30434	protein-coding gene	gene with protein product							Standard	NM_001010985		Approved		uc001dxk.1	A2RUH7	OTTHUMG00000012002	ENST00000357155.1:c.655G>A	chr1.hg19:g.109839480C>T	ENSP00000349678:p.Val219Ile	105.0	0.0		116.0	55.0	NM_001010985	B7ZME5|Q5T2Z7	Missense_Mutation	SNP	ENST00000357155.1	hg19	CCDS30793.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.473577	0.63737	.	.	ENSG00000221986	ENST00000357155	T	0.70749	-0.51	5.01	3.08	0.35506	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60996	0.2312	L	0.57130	1.785	0.44067	D	0.996816	B;B	0.32040	0.353;0.102	B;P	0.45037	0.42;0.467	T	0.62959	-0.6743	9	0.39692	T	0.17	.	8.4167	0.32676	0.1538:0.7618:0.0:0.0844	.	196;219	B7ZME5;A2RUH7	.;MBPHL_HUMAN	I	219	ENSP00000349678:V219I	ENSP00000349678:V219I	V	-	1	0	MYBPHL	109641003	0.997000	0.39634	0.945000	0.38365	0.641000	0.38312	3.609000	0.54117	1.335000	0.45486	0.561000	0.74099	GTC	.	.		0.572	MYBPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033197.1	NM_001010985		T	109839480	C	T	109839480	3	4	168	1	0	0	0	0	1	0	0	0	10024	478	17	3	425	3	MYBPHL	1	109839480	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	27419	109839480	139411141	16	25432										
EPS8L3	79574	hgsc.bcm.edu	37	chr1	110294361	110294361	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gaatgtagccgctccgtcccGcctcattcttcaccagccac	7	18	3	0	rs549152937		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:110294361G>T	ENST00000361965.4	-	16	1584	c.1478C>A	c.(1477-1479)gCg>gAg	p.A493E	RP4-735C1.4_ENST00000431955.1_RNA|EPS8L3_ENST00000369805.3_Missense_Mutation_p.A494E|EPS8L3_ENST00000361852.4_Missense_Mutation_p.A463E	NM_133181.3	NP_573444.2	Q8TE67	ES8L3_HUMAN	EPS8-like 3	493	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	32		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		GCTCCGTCCCGCCTCATTCTT	0.642																																					p.A494E		Atlas-SNP	.											EPS8L3,colon,carcinoma,0,1	EPS8L3	73	.	0			c.C1481A						.						58	58	58					1																	110294361		2203	4300	6503	SO:0001583	missense	79574	exon16			CGTCCCGCCTCAT	AK025175	CCDS813.1, CCDS814.1, CCDS815.1	1p13.2	2008-02-05			ENSG00000198758	ENSG00000198758			21297	protein-coding gene	gene with protein product		614989				12620401	Standard	NM_139053		Approved	FLJ21522, MGC16817	uc001dyq.2	Q8TE67	OTTHUMG00000011651	ENST00000361965.4:c.1478C>A	chr1.hg19:g.110294361G>T	ENSP00000355255:p.Ala493Glu	61.0	0.0		52.0	18.0	NM_139053	A8K833|Q5T8Q6|Q5T8Q7|Q5T8Q8|Q96E47|Q9H719	Missense_Mutation	SNP	ENST00000361965.4	hg19	CCDS814.1	.	.	.	.	.	.	.	.	.	.	G	0.275	-0.990054	0.02162	.	.	ENSG00000198758	ENST00000361852;ENST00000369805;ENST00000361965	T;T;T	0.28895	1.59;1.59;1.59	5.72	-3.51	0.04696	Src homology-3 domain (4);	0.754711	0.12846	N	0.434366	T	0.04363	0.0120	N	0.16903	0.455	0.09310	N	1	B;B;B	0.19706	0.038;0.001;0.002	B;B;B	0.17433	0.018;0.008;0.011	T	0.38607	-0.9653	10	0.27082	T	0.32	0.1163	4.5647	0.12177	0.2599:0.0:0.2154:0.5247	.	463;493;494	Q8TE67-2;Q8TE67;Q8TE67-3	.;ES8L3_HUMAN;.	E	463;494;493	ENSP00000354551:A463E;ENSP00000358820:A494E;ENSP00000355255:A493E	ENSP00000354551:A463E	A	-	2	0	EPS8L3	110095884	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.374000	0.02566	-0.586000	0.05898	0.655000	0.94253	GCG	.	.		0.642	EPS8L3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032234.1	NM_024526		T	110294361	G	T	110294361	3	4	168	1	0	0	0	0	1	0	0	0	5199	1087	38	1	319	1	EPS8L3	1	110294361	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	454881	110294361	138956260	17	25433										
SYT6	148281	hgsc.bcm.edu	37	chr1	114646329	114646329	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agggagaacatgatctctccCaagtccacgctttcctgcaa	8	13	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:114646329C>T	ENST00000610222.1	-	4	1232	c.1086G>A	c.(1084-1086)ttG>ttA	p.L362L	SYT6_ENST00000393296.1_Silent_p.L362L|SYT6_ENST00000369547.1_Silent_p.L277L|SYT6_ENST00000609117.1_Silent_p.L277L|SYT6_ENST00000607941.1_Silent_p.L277L			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	362					acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGATCTCTCCCAAGTCCACGC	0.567																																					p.L277L		Atlas-SNP	.											.	SYT6	66	.	0			c.G831A						.						106	74	84					1																	114646329		2203	4300	6503	SO:0001819	synonymous_variant	148281	exon4			CTCTCCCAAGTCC		CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"Synaptotagmins"	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.1086G>A	chr1.hg19:g.114646329C>T		62.0	0.0		66.0	27.0	NM_205848	B1AMB8|B3KPK1	Silent	SNP	ENST00000610222.1	hg19																																																																																				.	.		0.567	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848		T	114646329	C	T	114646329	2	4	168	1	0	0	0	0	0	0	0	1	15493	593	21	3		3	SYT6	1	114646329	Silent	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	4351968	114646329	134604292	18	25434										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118539254	118539254	+	Frame_Shift_Del	DEL	T	T	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	caccatagatttgctgatgaTtcttttcaaggtgcatagag							TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:118539254delT	ENST00000336338.5	-	33	4954	c.4889delA	c.(4888-4890)aatfs	p.N1630fs		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1630						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TTGCTGATGATTCTTTTCAAG	0.323																																					p.N1630fs		Atlas-INDEL	.											.	SPAG17	263	.	0			c.4890delT						.						98	98	98					1																	118539254		2203	4300	6503	SO:0001589	frameshift_variant	200162	exon33			.		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4889delA	chr1.hg19:g.118539254delT	ENSP00000337804:p.Asn1630fs	186.0	0.0		191.0	91.0	NM_206996	Q8NAZ1|Q9NT21	Frame_Shift_Del	DEL	ENST00000336338.5	hg19	CCDS899.1																																																																																			.	.		0.323	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		-	118539254	T	-	118539254	7	5	168	1	0	1	0	1	0	0	0	0	14994	1493	52	0	1846	0	SPAG17	1	118539254	Frame_Shift_Del	DEL	T	TCGA-DD-AACQ-01A-11D-A40R-10	3892925	118539254	130711367	19	25435										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118558796	118558796	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ccattgatgactgacttttgTgactttttcctgtgaagttc	8	8	0	5			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:118558796T>G	ENST00000336338.5	-	29	4144	c.4079A>C	c.(4078-4080)cAc>cCc	p.H1360P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1360						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CTGACTTTTGTGACTTTTTCC	0.383																																					p.H1360P		Atlas-SNP	.											.	SPAG17	263	.	0			c.A4079C						.						119	116	117					1																	118558796		2203	4300	6503	SO:0001583	missense	200162	exon29			CTTTTGTGACTTT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4079A>C	chr1.hg19:g.118558796T>G	ENSP00000337804:p.His1360Pro	131.0	0.0		108.0	49.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	T	11.73	1.724939	0.30593	.	.	ENSG00000155761	ENST00000336338	T	0.18810	2.19	4.72	1.97	0.26223	.	1.067670	0.07204	N	0.858010	T	0.07728	0.0194	L	0.51422	1.61	0.29640	N	0.844751	B	0.11235	0.004	B	0.08055	0.003	T	0.24404	-1.0161	10	0.34782	T	0.22	.	5.844	0.18652	0.1627:0.0:0.1683:0.6691	.	1360	Q6Q759	SPG17_HUMAN	P	1360	ENSP00000337804:H1360P	ENSP00000337804:H1360P	H	-	2	0	SPAG17	118360319	1.000000	0.71417	1.000000	0.80357	0.559000	0.35586	1.369000	0.34227	1.780000	0.52325	0.377000	0.23210	CAC	.	.		0.383	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		G	118558796	T	G	118558796	3	3	168	1	0	0	0	0	1	0	0	0	14994	1696	59	5	2672	5	SPAG17	1	118558796	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	19542	118558796	130691825	20	25436										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144930752	144930752	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gggccaggcttggctccaggTaggctggatttcactggaat	15	9	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:144930752T>A	ENST00000369354.3	-	6	826				PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000479408.2_Intron|PDE4DIP_ENST00000529945.1_Silent_p.L319L|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000313431.9_Silent_p.L319L|PDE4DIP_ENST00000369351.3_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein						cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGGCTCCAGGTAGGCTGGATT	0.493			T	PDGFRB	MPD																																p.L319L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A957T						.						107	113	111					1																	144930752		2203	4300	6503	SO:0001627	intron_variant	9659	exon1			TCCAGGTAGGCTG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.637-6931A>T	chr1.hg19:g.144930752T>A		222.0	0.0		262.0	41.0	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	hg19	CCDS30824.1																																																																																			.	.		0.493	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		A	144930752	T	A	144930752	1	1	168	0	1	0	0	0	0	0	0	0	11652	1625	57	4		4	PDE4DIP	1	144930752	Intron	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	26371956	144930752	104319869	21	25437										
CTSS	1520	hgsc.bcm.edu	37	chr1	150722488	150722488	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	attttattttttaccacttcTgtagaggaagaaagaaggat	8	4	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:150722488T>A	ENST00000368985.3	-	6	1047	c.787A>T	c.(787-789)Aga>Tga	p.R263*	CTSS_ENST00000448301.2_Nonsense_Mutation_p.R213*|CTSS_ENST00000480760.1_Intron	NM_001199739.1|NM_004079.4	NP_001186668.1|NP_004070.3	P25774	CATS_HUMAN	cathepsin S	263					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|basement membrane disassembly (GO:0034769)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of inflammatory response (GO:0050729)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	15	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)			TTACCACTTCTGTAGAGGAAG	0.398																																					p.R263X		Atlas-SNP	.											.	CTSS	31	.	0			c.A787T						.						55	50	51					1																	150722488		2203	4300	6503	SO:0001587	stop_gained	1520	exon6			CACTTCTGTAGAG	M90696	CCDS968.1, CCDS55634.1	1q21	2008-02-05			ENSG00000163131	ENSG00000163131	3.4.22.27	"Cathepsins"	2545	protein-coding gene	gene with protein product		116845				1373132	Standard	NM_001199739		Approved		uc001evn.3	P25774	OTTHUMG00000035010	ENST00000368985.3:c.787A>T	chr1.hg19:g.150722488T>A	ENSP00000357981:p.Arg263*	81.0	0.0		84.0	34.0	NM_004079	B4DWC9|D3DV05|Q5T5I0|Q6FHS5|Q9BUG3	Nonsense_Mutation	SNP	ENST00000368985.3	hg19	CCDS968.1	.	.	.	.	.	.	.	.	.	.	T	37	6.618515	0.97709	.	.	ENSG00000163131	ENST00000448301;ENST00000368985	.	.	.	5.71	3.3	0.37823	.	0.711059	0.13758	N	0.364789	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	12.3463	0.55122	0.0:0.0:0.4018:0.5982	.	.	.	.	X	213;263	.	ENSP00000357981:R263X	R	-	1	2	CTSS	148989112	0.984000	0.35163	0.502000	0.27614	0.963000	0.63663	1.993000	0.40747	0.386000	0.24997	0.482000	0.46254	AGA	.	.		0.398	CTSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084737.1	NM_004079		A	150722488	T	A	150722488	4	1	168	1	0	0	0	0	0	1	0	0	4043	1588	55	4	220	4	CTSS	1	150722488	Nonsense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	5791736	150722488	98528133	22	25438										
PGLYRP3	114771	hgsc.bcm.edu	37	chr1	153276487	153276487	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcagggctgggactgctgccTtaaagaggaggacagggagc	18	8	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:153276487T>G	ENST00000290722.1	-	4	429		c.e4-2			NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3						defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GACTGCTGCCTTAAAGAGGAG	0.512																																					.		Atlas-SNP	.											.	PGLYRP3	55	.	0			c.377-2A>C						.						44	46	46					1																	153276487		2203	4300	6503	SO:0001630	splice_region_variant	114771	exon5			GCTGCCTTAAAGA	AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I alpha precursor"	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.377-2A>C	chr1.hg19:g.153276487T>G		45.0	0.0		92.0	35.0	NM_052891	A1A4U8|Q5SY65	Splice_Site	SNP	ENST00000290722.1	hg19	CCDS1035.1	.	.	.	.	.	.	.	.	.	.	T	14.44	2.537007	0.45176	.	.	ENSG00000159527	ENST00000290722	.	.	.	4.15	4.15	0.48705	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.743	0.40429	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PGLYRP3	151543111	0.967000	0.33354	0.686000	0.30086	0.757000	0.42996	3.141000	0.50593	1.878000	0.54408	0.528000	0.53228	.	.	.		0.512	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891	Intron	G	153276487	T	G	153276487	5	3	168	1	0	0	0	0	0	0	1	0	11804	1623	56	5	666	5	PGLYRP3	1	153276487	Splice_Site	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	2553999	153276487	95974134	23	25439										
IL6R	3570	hgsc.bcm.edu	37	chr1	154407475	154407475	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ttttcccacagtgcagcctgAtccgcctgccaacatcacag	7	16	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:154407475A>T	ENST00000368485.3	+	5	1087	c.650A>T	c.(649-651)gAt>gTt	p.D217V	IL6R_ENST00000344086.4_Missense_Mutation_p.D217V	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	217	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)		IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	GTGCAGCCTGATCCGCCTGCC	0.562																																					p.D217V		Atlas-SNP	.											.	IL6R	47	.	0			c.A650T						.						46	42	43					1																	154407475		2203	4300	6503	SO:0001583	missense	3570	exon5			AGCCTGATCCGCC	X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.650A>T	chr1.hg19:g.154407475A>T	ENSP00000357470:p.Asp217Val	79.0	0.0		99.0	34.0	NM_000565	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Missense_Mutation	SNP	ENST00000368485.3	hg19	CCDS1067.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.71|15.71	2.914137|2.914137	0.52546|0.52546	.|.	.|.	ENSG00000160712|ENSG00000160712	ENST00000368485;ENST00000344086|ENST00000476006;ENST00000515190	T;T|.	0.26660|.	1.88;1.72|.	5.19|5.19	5.19|5.19	0.71726|0.71726	Long hematopoietin receptor, soluble alpha chain, conserved site (1);Fibronectin, type III (3);Immunoglobulin-like fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71995|0.71995	0.3406|0.3406	M|M	0.87758|0.87758	2.905|2.905	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.999|.	T|T	0.77078|0.77078	-0.2721|-0.2721	10|5	0.62326|.	D|.	0.03|.	-48.9129|-48.9129	11.3582|11.3582	0.49627|0.49627	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	217;217|.	P08887-2;P08887|.	.;IL6RA_HUMAN|.	V|F	217|140;20	ENSP00000357470:D217V;ENSP00000340589:D217V|.	ENSP00000340589:D217V|.	D|I	+|+	2|1	0|0	IL6R|IL6R	152674099|152674099	0.997000|0.997000	0.39634|0.39634	0.913000|0.913000	0.36048|0.36048	0.272000|0.272000	0.26649|0.26649	4.072000|4.072000	0.57563|0.57563	2.183000|2.183000	0.69458|0.69458	0.533000|0.533000	0.62120|0.62120	GAT|ATC	.	.		0.562	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565		T	154407475	A	T	154407475	3	4	168	1	0	0	0	0	1	0	0	0	7711	333	12	4	668	4	IL6R	1	154407475	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	1130988	154407475	94843146	24	25440										
NES	10763	hgsc.bcm.edu	37	chr1	156640210	156640210	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cctgctcgctctctactttcCccagggcttcagccctcccc	6	21	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:156640210C>A	ENST00000368223.3	-	4	3902	c.3770G>T	c.(3769-3771)gGg>gTg	p.G1257V		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1257	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTCTACTTTCCCCAGGGCTTC	0.647																																					p.G1257V		Atlas-SNP	.											.	NES	196	.	0			c.G3770T						.						83	94	90					1																	156640210		2203	4300	6503	SO:0001583	missense	10763	exon4			ACTTTCCCCAGGG	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3770G>T	chr1.hg19:g.156640210C>A	ENSP00000357206:p.Gly1257Val	44.0	0.0		56.0	21.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.117725	0.37339	.	.	ENSG00000132688	ENST00000368223	D	0.85955	-2.05	4.3	-1.8	0.07907	.	0.546292	0.13841	N	0.359032	T	0.67173	0.2865	L	0.53249	1.67	0.20307	N	0.999912	D	0.54964	0.969	B	0.41135	0.348	T	0.63752	-0.6566	10	0.72032	D	0.01	.	8.8667	0.35291	0.0:0.2922:0.0:0.7078	.	1257	P48681	NEST_HUMAN	V	1257	ENSP00000357206:G1257V	ENSP00000357206:G1257V	G	-	2	0	NES	154906834	0.000000	0.05858	0.000000	0.03702	0.565000	0.35776	-3.521000	0.00443	-0.199000	0.10317	0.557000	0.71058	GGG	.	.		0.647	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		A	156640210	C	A	156640210	3	1	168	1	0	0	0	0	1	0	0	0	10346	623	22	3	1099	3	NES	1	156640210	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	2232735	156640210	92610411	25	25441										
NTRK1	4914	hgsc.bcm.edu	37	chr1	156838010	156838010	+	Silent	SNP	G	G	A													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctgcagtgtcatgggcaaggGcccctggcccacatgcccaa							TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:156838010G>A	ENST00000524377.1	+	5	584	c.543G>A	c.(541-543)ggG>ggA	p.G181G	NTRK1_ENST00000358660.3_Silent_p.G181G|NTRK1_ENST00000368196.3_Silent_p.G181G|NTRK1_ENST00000392302.2_Silent_p.G151G	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	181	LRRCT.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	ATGGGCAAGGGCCCCTGGCCC	0.652			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.G181G		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1	287	.	0			c.G543A	GRCh37	CD060633	NTRK1	D		.						49	46	47					1																	156838010		2203	4300	6503	SO:0001819	synonymous_variant	4914	exon5			GCAAGGGCCCCTG	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.543G>A	chr1.hg19:g.156838010G>A		40.0	0.0		60.0	11.0	NM_001012331	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Silent	SNP	ENST00000524377.1	hg19	CCDS1161.1																																																																																			.	.		0.652	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		A	156838010	G	A	156838010	2	1	168	1	0	0	0	0	0	0	0	1	10715	1190	42	3		3	NTRK1	1	156838010	Silent	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	197800	156838010	92412611	26	25442	119	2								
NTRK1	4914	hgsc.bcm.edu	37	chr1	156838011	156838011	+	Frame_Shift_Del	DEL	C	C	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgcagtgtcatgggcaagggCccctggcccacatgcccaat							TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:156838011delC	ENST00000524377.1	+	5	585	c.544delC	c.(544-546)cccfs	p.P182fs	NTRK1_ENST00000358660.3_Frame_Shift_Del_p.P182fs|NTRK1_ENST00000368196.3_Frame_Shift_Del_p.P182fs|NTRK1_ENST00000392302.2_Frame_Shift_Del_p.P152fs	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	182	LRRCT.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	TGGGCAAGGGCCCCTGGCCCA	0.652			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.G181fs		Atlas-INDEL	.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1	287	.	0			c.543delG						.						48	46	47					1																	156838011		2203	4300	6503	SO:0001589	frameshift_variant	4914	exon5			.	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.544delC	chr1.hg19:g.156838011delC	ENSP00000431418:p.Pro182fs	38.0	0.0		59.0	11.0	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Frame_Shift_Del	DEL	ENST00000524377.1	hg19	CCDS1161.1																																																																																			.	.		0.652	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		-	156838011	C	-	156838011	7	5	168	1	0	1	0	1	0	0	0	0	10715	739	26	0	692	0	NTRK1	1	156838011	Frame_Shift_Del	DEL	C	TCGA-DD-AACQ-01A-11D-A40R-10	1	156838011	92412610	27	25443	119	2								
CADM3	57863	hgsc.bcm.edu	37	chr1	159166681	159166681	+	Splice_Site	DEL	C	C	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgatttgtctgcctcgacagCccccagcagtacctatggga					rs149370954		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:159166681delC	ENST00000368125.4	+	7	940	c.783delC	c.(781-783)gtc>gt	p.V261fs	CTA-134P22.2_ENST00000415675.2_RNA|CADM3_ENST00000368124.4_Splice_Site_p.V295fs|CADM3_ENST00000497636.1_3'UTR	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	261	Ig-like C2-type 2.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					GCCTCGACAGCCCCCAGCAGT	0.517																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.						70	67	68					1																	159166681		2203	4300	6503	SO:0001630	splice_region_variant	0	.			.	AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17601	protein-coding gene	gene with protein product	"nectin-like 1"	609743	"immunoglobulin superfamily, member 4B"	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.783-1C>-	chr1.hg19:g.159166681delC		130.0	0.0		180.0	56.0	.	Q8IZQ9|Q9NVJ5|Q9UJP1	RNA	DEL	ENST00000368125.4	hg19	CCDS44251.1																																																																																			.	.		0.517	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189	Frame_Shift_Del	-	159166681	C	-	159166681	8	5	168	1	0	1	0	1	0	0	1	0	2570	753	26	0	915	0	CADM3	1	159166681	Splice_Site	DEL	C	TCGA-DD-AACQ-01A-11D-A40R-10	2328670	159166681	90083940	28	25444										
PBX1	5087	hgsc.bcm.edu	37	chr1	164768945	164768945	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgccattccaggcctgcaacGagttcaccacccacgtgatg	9	15	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:164768945G>A	ENST00000420696.2	+	4	708	c.520G>A	c.(520-522)Gag>Aag	p.E174K	PBX1_ENST00000540246.1_Missense_Mutation_p.E69K|PBX1_ENST00000540236.1_Missense_Mutation_p.E174K|PBX1_ENST00000560641.1_Missense_Mutation_p.E69K|PBX1_ENST00000367897.1_Missense_Mutation_p.E174K|PBX1_ENST00000559240.1_Missense_Mutation_p.E174K|PBX1_ENST00000401534.1_Missense_Mutation_p.E174K	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	174					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						GGCCTGCAACGAGTTCACCAC	0.547			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.E174K		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	PBX1_ENST00000420696,NS,carcinoma,0,1	PBX1	60	.	0			c.G520A						.						82	77	79					1																	164768945		2203	4300	6503	SO:0001583	missense	5087	exon4			TGCAACGAGTTCA	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"Homeoboxes / TALE class"	8632	protein-coding gene	gene with protein product		176310	"pre-B-cell leukemia transcription factor 1"				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.520G>A	chr1.hg19:g.164768945G>A	ENSP00000405890:p.Glu174Lys	169.0	0.0		174.0	44.0	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	hg19	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	G	36	5.831450	0.97003	.	.	ENSG00000185630	ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35	5.76	5.76	0.90799	PBX (1);	0.000000	0.85682	D	0.000000	T	0.48259	0.1490	M	0.81802	2.56	0.80722	D	1	P;P;P;P;P	0.46784	0.884;0.884;0.859;0.884;0.884	P;P;P;P;P	0.50970	0.603;0.655;0.468;0.655;0.603	T	0.50516	-0.8819	10	0.54805	T	0.06	-18.188	19.571	0.95419	0.0:0.0:1.0:0.0	.	69;174;174;174;174	B7Z774;A8K5V0;F5H4U9;P40424;Q53YC7	.;.;.;PBX1_HUMAN;.	K	174;174;174;174;69	ENSP00000405890:E174K;ENSP00000356872:E174K;ENSP00000439943:E174K;ENSP00000384856:E174K;ENSP00000440869:E69K	ENSP00000356872:E174K	E	+	1	0	PBX1	163035569	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	9.338000	0.96553	2.713000	0.92767	0.655000	0.94253	GAG	.	.		0.547	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		A	164768945	G	A	164768945	3	1	168	1	0	0	0	0	1	0	0	0	11501	1059	37	1	534	1	PBX1	1	164768945	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	5602264	164768945	84481676	29	25445										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171556150	171556150	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cttattttctaggttacagtAcctttaccagcatcgcagct	6	11	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:171556150A>G	ENST00000338920.4	+	31	7989	c.7752A>G	c.(7750-7752)gtA>gtG	p.V2584V	PRRC2C_ENST00000367742.3_Silent_p.V2586V|PRRC2C_ENST00000392078.3_Silent_p.V2586V|PRRC2C_ENST00000426496.2_Silent_p.V2519V	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2584	Gln-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AGGTTACAGTACCTTTACCAG	0.388																																					p.V2584V		Atlas-SNP	.											.	.	.	.	0			c.A7752G						.						78	68	71					1																	171556150		2203	4300	6503	SO:0001819	synonymous_variant	23215	exon31			TACAGTACCTTTA	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.7752A>G	chr1.hg19:g.171556150A>G		92.0	0.0		98.0	4.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	A	10.07	1.250613	0.22880	.	.	ENSG00000117523	ENST00000495585	.	.	.	5.24	-1.75	0.08031	.	.	.	.	.	T	0.35422	0.0931	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35126	-0.9801	4	.	.	.	.	6.7391	0.23424	0.4998:0.3663:0.1339:0.0	.	.	.	.	C	1067	.	.	Y	+	2	0	PRRC2C	169822774	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	1.385000	0.34408	-0.225000	0.09913	0.377000	0.23210	TAC	.	.		0.388	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		G	171556150	A	G	171556150	2	3	168	1	0	0	0	0	0	0	0	1	1321	378	14	2		2	BAT2L2	1	171556150	Silent	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	6787205	171556150	77694471	30	25446										
METTL13	51603	hgsc.bcm.edu	37	chr1	171761248	171761248	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ccaaagtcctgcattgatgcTgtggagatcgatccctccat	9	12	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:171761248T>A	ENST00000361735.3	+	6	1832	c.1566T>A	c.(1564-1566)gcT>gcA	p.A522A	METTL13_ENST00000466643.1_3'UTR|METTL13_ENST00000362019.3_Silent_p.A436A|METTL13_ENST00000458517.1_Silent_p.A521A|METTL13_ENST00000367737.5_Silent_p.A366A	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	522							methyltransferase activity (GO:0008168)			breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						GCATTGATGCTGTGGAGATCG	0.542																																					p.A522A		Atlas-SNP	.											.	METTL13	67	.	0			c.T1566A						.						152	134	140					1																	171761248		2203	4300	6503	SO:0001819	synonymous_variant	51603	exon6			TGATGCTGTGGAG	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"KIAA0859"	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.1566T>A	chr1.hg19:g.171761248T>A		102.0	0.0		118.0	24.0	NM_015935	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Silent	SNP	ENST00000361735.3	hg19	CCDS1299.1																																																																																			.	.		0.542	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955		A	171761248	T	A	171761248	2	1	168	1	0	0	0	0	0	0	0	1	9506	1567	55	4		4	METTL13	1	171761248	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	205098	171761248	77489373	31	25447										
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180885579	180885579	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cccaagagtggtcatcccccAagaaaccccaatgcagacga	8	15	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:180885579A>G	ENST00000367588.4	+	2	395	c.340A>G	c.(340-342)Aag>Gag	p.K114E		NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	114										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						GTCATCCCCCAAGAAACCCCA	0.577																																					p.K114E		Atlas-SNP	.											.	KIAA1614	75	.	0			c.A340G						.						83	90	88					1																	180885579		2022	4173	6195	SO:0001583	missense	57710	exon2			TCCCCCAAGAAAC	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.340A>G	chr1.hg19:g.180885579A>G	ENSP00000356560:p.Lys114Glu	103.0	0.0		168.0	51.0	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	hg19	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.500804	0.64298	.	.	ENSG00000135835	ENST00000367588	T	0.05319	3.46	5.08	3.94	0.45596	.	0.393782	0.18631	N	0.135581	T	0.07279	0.0184	N	0.24115	0.695	0.23758	N	0.99693	D	0.55605	0.972	P	0.49752	0.621	T	0.33369	-0.9871	9	0.31617	T	0.26	-11.7207	10.0316	0.42103	0.8305:0.1695:0.0:0.0	.	114	Q5VZ46	K1614_HUMAN	E	114	ENSP00000356560:K114E	ENSP00000356560:K114E	K	+	1	0	KIAA1614	179152202	0.986000	0.35501	0.002000	0.10522	0.212000	0.24457	2.892000	0.48625	0.934000	0.37316	0.533000	0.62120	AAG	.	.		0.577	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		G	180885579	A	G	180885579	3	3	168	1	0	0	0	0	1	0	0	0	8257	131	5	2	346	2	KIAA1614	1	180885579	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	9124331	180885579	68365042	32	25448										
ZNF648	127665	hgsc.bcm.edu	37	chr1	182025741	182025741	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gggcctctcgccagtgtggaTgcgctggtggcgcacgaggc	18	12	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:182025741T>A	ENST00000339948.3	-	2	1612	c.1405A>T	c.(1405-1407)Atc>Ttc	p.I469F		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	469					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						CCAGTGTGGATGCGCTGGTGG	0.672																																					p.I469F	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											.	ZNF648	111	.	0			c.A1405T						.						38	35	36					1																	182025741		2202	4300	6502	SO:0001583	missense	127665	exon2			TGTGGATGCGCTG	AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"Zinc fingers, C2H2-type"	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.1405A>T	chr1.hg19:g.182025741T>A	ENSP00000344129:p.Ile469Phe	89.0	0.0		125.0	35.0	NM_001009992	B2RP16	Missense_Mutation	SNP	ENST00000339948.3	hg19	CCDS30952.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.645448	0.67358	.	.	ENSG00000179930	ENST00000339948	T	0.18338	2.22	2.77	2.77	0.32553	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22704	0.0548	M	0.79011	2.435	0.43494	D	0.995732	P	0.38745	0.645	B	0.39379	0.298	T	0.09335	-1.0679	9	0.87932	D	0	.	9.3398	0.38074	0.0:0.0:0.0:1.0	.	469	Q5T619	ZN648_HUMAN	F	469	ENSP00000344129:I469F	ENSP00000344129:I469F	I	-	1	0	ZNF648	180292364	0.000000	0.05858	1.000000	0.80357	0.999000	0.98932	0.336000	0.19823	1.501000	0.48654	0.533000	0.62120	ATC	.	.		0.672	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		A	182025741	T	A	182025741	3	1	168	1	0	0	0	0	1	0	0	0	18078	1464	51	4	305	4	ZNF648	1	182025741	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	1140162	182025741	67224880	33	25449										
LAMC2	3918	hgsc.bcm.edu	37	chr1	183209229	183209229	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cagcagatggagccttggccAtggaaaagggactggcctct	14	10	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:183209229A>T	ENST00000264144.4	+	21	3189	c.3124A>T	c.(3124-3126)Atg>Ttg	p.M1042L	LAMC2_ENST00000461729.1_3'UTR|LAMC2_ENST00000493293.1_Missense_Mutation_p.M1042L	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	1042	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						AGCCTTGGCCATGGAAAAGGG	0.517																																					p.M1042L		Atlas-SNP	.											.	LAMC2	113	.	0			c.A3124T						.						131	129	129					1																	183209229		2203	4300	6503	SO:0001583	missense	3918	exon21			TTGGCCATGGAAA	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.3124A>T	chr1.hg19:g.183209229A>T	ENSP00000264144:p.Met1042Leu	116.0	0.0		157.0	45.0	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	hg19	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	A	5.460	0.269973	0.10349	.	.	ENSG00000058085	ENST00000493293;ENST00000264144	T;T	0.76316	2.96;-1.01	5.69	2.21	0.28008	.	0.336181	0.28933	N	0.013671	T	0.56046	0.1959	N	0.12887	0.27	0.27131	N	0.961906	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33574	-0.9863	10	0.02654	T	1	.	14.4065	0.67086	0.2705:0.7295:0.0:0.0	.	1042;1042;1042	Q2M1N2;Q13753;Q13753-2	.;LAMC2_HUMAN;.	L	1042	ENSP00000432063:M1042L;ENSP00000264144:M1042L	ENSP00000264144:M1042L	M	+	1	0	LAMC2	181475852	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.825000	0.39081	0.446000	0.26666	0.528000	0.53228	ATG	.	.		0.517	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		T	183209229	A	T	183209229	3	4	168	1	0	0	0	0	1	0	0	0	8624	217	8	4	3206	4	LAMC2	1	183209229	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	1183488	183209229	66041392	34	25450										
CFHR5	81494	hgsc.bcm.edu	37	chr1	196965322	196965322	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gaatatggacagagcttcctAtgtgtgttggtgagaaaaca	12	5	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:196965322A>T	ENST00000256785.4	+	6	1070	c.961A>T	c.(961-963)Atg>Ttg	p.M321L	CFHR5_ENST00000367414.5_Missense_Mutation_p.M345L			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	321	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)				NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						AGAGCTTCCTATGTGTGTTGG	0.308																																					p.M321L		Atlas-SNP	.											.	CFHR5	150	.	0			c.A961T						.						115	117	116					1																	196965322		2203	4300	6503	SO:0001583	missense	81494	exon6			CTTCCTATGTGTG	AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"Complement system"	24668	protein-coding gene	gene with protein product	"factor H related protein 5"	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.961A>T	chr1.hg19:g.196965322A>T	ENSP00000256785:p.Met321Leu	86.0	0.0		104.0	35.0	NM_030787	Q2NKK2	Missense_Mutation	SNP	ENST00000256785.4	hg19	CCDS1387.1	.	.	.	.	.	.	.	.	.	.	A	5.542	0.284920	0.10513	.	.	ENSG00000134389	ENST00000367414;ENST00000256785	T;T	0.63096	-0.02;-0.02	3.13	-6.25	0.02039	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.32704	0.0838	N	0.04090	-0.28	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22382	-1.0218	9	0.28530	T	0.3	.	9.1476	0.36942	0.1722:0.6646:0.1632:0.0	.	321	Q9BXR6	FHR5_HUMAN	L	345;321	ENSP00000356384:M345L;ENSP00000256785:M321L	ENSP00000256785:M321L	M	+	1	0	CFHR5	195231945	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.500000	0.00967	-2.539000	0.00486	-0.788000	0.03338	ATG	.	.		0.308	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787		T	196965322	A	T	196965322	3	4	168	1	0	0	0	0	1	0	0	0	3290	449	16	4	983	4	CFHR5	1	196965322	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	13756093	196965322	52285299	35	25451										
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204226522	204226522	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cctcatcacataggcagcagGgtcagcatagatgtcctcac	9	13	4	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:204226522G>A	ENST00000272203.3	-	9	1799	c.1483C>T	c.(1483-1485)Cct>Tct	p.P495S	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.P515S	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	495										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			TAGGCAGCAGGGTCAGCATAG	0.622																																					p.P495S		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.C1483T						.																																			SO:0001583	missense	22874	exon9			CAGCAGGGTCAGC	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.1483C>T	chr1.hg19:g.204226522G>A	ENSP00000272203:p.Pro495Ser	141.0	0.0		118.0	42.0	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	hg19	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.073708	0.76415	.	.	ENSG00000143850	ENST00000272203;ENST00000414478;ENST00000450705;ENST00000543129;ENST00000454206;ENST00000367191;ENST00000430806;ENST00000538441	T;T	0.10960	2.82;3.28	5.4	4.49	0.54785	.	0.899571	0.09859	N	0.746463	T	0.26412	0.0645	M	0.77313	2.365	0.58432	D	0.99999	P;B;P;D;P;P;P;B	0.55172	0.562;0.421;0.952;0.97;0.749;0.481;0.713;0.191	B;B;P;P;B;B;P;B	0.49829	0.275;0.254;0.623;0.558;0.242;0.22;0.589;0.09	T	0.05178	-1.0901	10	0.48119	T	0.1	-12.9424	15.5838	0.76465	0.0:0.0:0.8612:0.1388	.	29;29;29;29;515;29;29;495	A5XEJ5;A5XEJ7;A5XEJ6;A5XEJ8;Q5VTI5;A5XEJ3;A5XEJ2;Q9Y2H5	.;.;.;.;.;.;.;PKHA6_HUMAN	S	495;515;29;29;29;29;29;29	ENSP00000272203:P495S;ENSP00000402046:P515S	ENSP00000272203:P495S	P	-	1	0	PLEKHA6	202493145	1.000000	0.71417	0.956000	0.39512	0.942000	0.58702	6.895000	0.75660	1.402000	0.46780	0.655000	0.94253	CCT	.	.		0.622	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		A	204226522	G	A	204226522	3	1	168	1	0	0	0	0	1	0	0	0	12069	1232	43	3	1719	3	PLEKHA6	1	204226522	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	7261200	204226522	45024099	36	25452										
AVPR1B	553	hgsc.bcm.edu	37	chr1	206225342	206225342	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggctcccttcttcagtgtccAgatgtggtccgtgtgggaca	13	11	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:206225342A>T	ENST00000367126.4	+	1	1367	c.902A>T	c.(901-903)cAg>cTg	p.Q301L	RP11-38J22.3_ENST00000425896.1_RNA	NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	301					activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)|skin(2)	20			BRCA - Breast invasive adenocarcinoma(75;0.0312)		Desmopressin(DB00035)|Terlipressin(DB02638)|Vasopressin(DB00067)	TTCAGTGTCCAGATGTGGTCC	0.547																																					p.Q301L		Atlas-SNP	.											.	AVPR1B	47	.	0			c.A902T						.						87	80	82					1																	206225342		2203	4300	6503	SO:0001583	missense	553	exon1			GTGTCCAGATGTG	D31833	CCDS73015.1	1q32	2014-05-06			ENSG00000198049	ENSG00000198049		"GPCR / Class A : Vasopressin and oxytocin receptors"	896	protein-coding gene	gene with protein product		600264		AVPR3		7929452, 8586456	Standard	NM_000707		Approved		uc001hds.2	P47901	OTTHUMG00000184377	ENST00000367126.4:c.902A>T	chr1.hg19:g.206225342A>T	ENSP00000356094:p.Gln301Leu	66.0	0.0		91.0	19.0	NM_000707	B0M0J6|Q5TZ00	Missense_Mutation	SNP	ENST00000367126.4	hg19	CCDS30994.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.062038	0.76187	.	.	ENSG00000198049	ENST00000367126	T	0.34667	1.35	5.34	5.34	0.76211	GPCR, rhodopsin-like superfamily (1);	0.081511	0.52532	D	0.000069	T	0.59810	0.2221	M	0.71871	2.18	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.64037	-0.6501	10	0.72032	D	0.01	-24.8691	14.9914	0.71390	1.0:0.0:0.0:0.0	.	301	P47901	V1BR_HUMAN	L	301	ENSP00000356094:Q301L	ENSP00000356094:Q301L	Q	+	2	0	AVPR1B	204391965	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	9.339000	0.96797	2.023000	0.59567	0.379000	0.24179	CAG	.	.		0.547	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707		T	206225342	A	T	206225342	3	4	168	1	0	0	0	0	1	0	0	0	1232	188	7	4	904	4	AVPR1B	1	206225342	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	1998820	206225342	43025279	37	25453										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228482634	228482634	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggacagatacagcctgaggcAggatgggaccagatgtgagc	16	8	0	4			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:228482634A>T	ENST00000422127.1	+	43	11593	c.11549A>T	c.(11548-11550)cAg>cTg	p.Q3850L	OBSCN_ENST00000570156.2_Missense_Mutation_p.Q4279L|OBSCN_ENST00000359599.6_Missense_Mutation_p.Q2697L|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000284548.11_Missense_Mutation_p.Q3850L|OBSCN_ENST00000366707.4_Missense_Mutation_p.Q969L|OBSCN_ENST00000366709.4_Missense_Mutation_p.Q969L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3850	Ig-like 39.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGCCTGAGGCAGGATGGGACC	0.632																																					p.Q4279L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A12836T						.						136	139	138					1																	228482634		2109	4205	6314	SO:0001583	missense	84033	exon48			TGAGGCAGGATGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11549A>T	chr1.hg19:g.228482634A>T	ENSP00000409493:p.Gln3850Leu	262.0	0.0		304.0	93.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	19.73	3.882841	0.72410	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.1	3.96	0.45880	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.074400	0.56097	D	0.000040	T	0.69682	0.3138	L	0.46670	1.46	0.44155	D	0.996956	P;P	0.52577	0.931;0.954	P;P	0.56648	0.803;0.598	T	0.65685	-0.6108	10	0.28530	T	0.3	.	12.2184	0.54420	0.8575:0.1425:0.0:0.0	.	3850;3850	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	L	3850;3850;969;969;2697	ENSP00000284548:Q3850L;ENSP00000409493:Q3850L;ENSP00000355668:Q969L;ENSP00000355670:Q969L;ENSP00000352613:Q2697L	ENSP00000284548:Q3850L	Q	+	2	0	OBSCN	226549257	0.990000	0.36364	0.988000	0.46212	0.285000	0.27093	2.452000	0.44961	0.946000	0.37632	0.383000	0.25322	CAG	.	.		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228482634	A	T	228482634	3	4	168	1	0	0	0	0	1	0	0	0	10821	188	7	4	11715	4	OBSCN	1	228482634	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	22257292	228482634	20767987	38	25454										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245851010	245851010	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggcaccccgccctccaaggcTaccctggaggggaaggtggc	15	15	0	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:245851010T>A	ENST00000407071.2	+	12	5165	c.4725T>A	c.(4723-4725)gcT>gcA	p.A1575A	KIF26B_ENST00000366518.4_Silent_p.A1194A	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1575					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			CCTCCAAGGCTACCCTGGAGG	0.667																																					p.A1575A		Atlas-SNP	.											.	KIF26B	343	.	0			c.T4725A						.						11	14	13					1																	245851010		1940	4118	6058	SO:0001819	synonymous_variant	55083	exon12			CAAGGCTACCCTG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.4725T>A	chr1.hg19:g.245851010T>A		182.0	0.0		218.0	62.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	.		0.667	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245851010	T	A	245851010	2	1	168	1	0	0	0	0	0	0	0	1	8304	1509	53	4		4	KIF26B	1	245851010	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	17368376	245851010	3399611	39	25455										
OR13G1	441933	hgsc.bcm.edu	37	chr1	247835424	247835424	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ttgcatgttgaaactactagTgtttcagaaatgcaaacacc	7	8	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:247835424T>A	ENST00000359688.2	-	1	941	c.920A>T	c.(919-921)cAc>cTc	p.H307L	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	307						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			AAACTACTAGTGTTTCAGAAA	0.413																																					p.H307L		Atlas-SNP	.											.	OR13G1	78	.	0			c.A920T						.						88	97	94					1																	247835424		2203	4300	6503	SO:0001583	missense	441933	exon1			TACTAGTGTTTCA	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"GPCR / Class A : Olfactory receptors"	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.920A>T	chr1.hg19:g.247835424T>A	ENSP00000352717:p.His307Leu	65.0	0.0		110.0	24.0	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	hg19	CCDS31094.1	.	.	.	.	.	.	.	.	.	.	T	12.51	1.959548	0.34565	.	.	ENSG00000197437	ENST00000359688	T	0.09255	3.0	3.84	-2.56	0.06268	.	1.814060	0.03308	N	0.190104	T	0.04907	0.0132	N	0.08118	0	0.09310	N	1	B	0.30511	0.282	B	0.21546	0.035	T	0.30327	-0.9982	10	0.38643	T	0.18	.	4.2864	0.10857	0.1837:0.4442:0.0:0.372	.	307	Q8NGZ3	O13G1_HUMAN	L	307	ENSP00000352717:H307L	ENSP00000352717:H307L	H	-	2	0	OR13G1	245902047	0.000000	0.05858	0.007000	0.13788	0.228000	0.25075	-2.741000	0.00798	-0.395000	0.07715	0.533000	0.62120	CAC	.	.		0.413	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487		A	247835424	T	A	247835424	3	1	168	1	0	0	0	0	1	0	0	0	10951	1696	59	4	7	4	OR13G1	1	247835424	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	1984414	247835424	1415197	40	25456										
OR2T11	127077	hgsc.bcm.edu	37	chr1	248789949	248789949	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gccacagtaagggacattcaTggtgatgggagtgagcagaa	15	6	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr1:248789949T>A	ENST00000330803.2	-	1	542	c.481A>T	c.(481-483)Atg>Ttg	p.M161L		NM_001001964.1	NP_001001964.1	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T, member 11 (gene/pseudogene)	161						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(5)|lung(20)|skin(2)	28	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGGACATTCATGGTGATGGGA	0.517																																					p.M161L		Atlas-SNP	.											.	OR2T11	64	.	0			c.A481T						.						53	60	58					1																	248789949		2049	4233	6282	SO:0001583	missense	127077	exon1			CATTCATGGTGAT	BK004476	CCDS31122.1	1q44	2013-10-10	2013-10-10		ENSG00000183130	ENSG00000183130		"GPCR / Class A : Olfactory receptors"	19574	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily T, member 11"				Standard	NM_001001964		Approved	OR2T11Q	uc001ier.1	Q8NH01	OTTHUMG00000040384	ENST00000330803.2:c.481A>T	chr1.hg19:g.248789949T>A	ENSP00000328934:p.Met161Leu	63.0	0.0		150.0	59.0	NM_001001964	Q6IEY6	Missense_Mutation	SNP	ENST00000330803.2	hg19	CCDS31122.1	.	.	.	.	.	.	.	.	.	.	.	6.404	0.442747	0.12164	.	.	ENSG00000183130	ENST00000330803	T	0.00024	8.98	4.38	3.18	0.36537	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000057	T	0.00109	0.0003	N	0.04820	-0.15	0.09310	N	1	D	0.56521	0.976	P	0.57283	0.817	T	0.57791	-0.7750	10	0.07644	T	0.81	.	8.5357	0.33362	0.2719:0.0:0.0:0.7281	.	161	Q8NH01	O2T11_HUMAN	L	161	ENSP00000328934:M161L	ENSP00000328934:M161L	M	-	1	0	OR2T11	246856572	0.000000	0.05858	1.000000	0.80357	0.416000	0.31233	-0.368000	0.07543	1.820000	0.53075	0.533000	0.62120	ATG	.	.		0.517	OR2T11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097134.1	NM_001001964		A	248789949	T	A	248789949	3	1	168	1	0	0	0	0	1	0	0	0	11027	1464	51	4	473	4	OR2T11	1	248789949	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	954525	248789949	460672	41	25457										
ASAP2	8853	hgsc.bcm.edu	37	chr2	9520899	9520899	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	caggagagactccgctggacAttgccaagcgcctcaagcac	11	14	1	1	rs542556113		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:9520899A>T	ENST00000281419.3	+	20	2318	c.1978A>T	c.(1978-1980)Att>Ttt	p.I660F	ASAP2_ENST00000315273.4_Missense_Mutation_p.I660F	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	660					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						TCCGCTGGACATTGCCAAGCG	0.572																																					p.I660F		Atlas-SNP	.											.	ASAP2	91	.	0			c.A1978T						.						97	103	101					2																	9520899		2203	4300	6503	SO:0001583	missense	8853	exon20			CTGGACATTGCCA	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1978A>T	chr2.hg19:g.9520899A>T	ENSP00000281419:p.Ile660Phe	40.0	0.0		42.0	24.0	NM_001135191	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	hg19	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	A	33	5.220086	0.95139	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.60171	0.22;0.21	5.5	5.5	0.81552	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.74921	0.3780	M	0.71206	2.165	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.81914	0.887;0.995	T	0.77595	-0.2529	10	0.62326	D	0.03	.	15.6129	0.76740	1.0:0.0:0.0:0.0	.	660;660	O43150-2;O43150	.;ASAP2_HUMAN	F	660	ENSP00000281419:I660F;ENSP00000316404:I660F	ENSP00000281419:I660F	I	+	1	0	ASAP2	9438350	1.000000	0.71417	0.999000	0.59377	0.946000	0.59487	9.180000	0.94867	2.089000	0.63090	0.528000	0.53228	ATT	.	.		0.572	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		T	9520899	A	T	9520899	3	4	168	1	0	0	0	0	1	0	0	0	1011	217	8	4	2056	4	ASAP2	2	9520899	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10		9520899	233678474	42	25458										
C2orf16	84226	hgsc.bcm.edu	37	chr2	27804758	27804758	+	Missense_Mutation	SNP	A	A	C													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgcagtccctctgagagaagAcatcgcagtccctctgagag					rs200680705	byFrequency	TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:27804758A>C	ENST00000408964.2	+	1	5370	c.5319A>C	c.(5317-5319)agA>agC	p.R1773S	ZNF512_ENST00000355467.4_5'Flank|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000379717.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1773	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CTGAGAGAAGACATCGCAGTC	0.527													a|||	15	0.00299521	0.0023	0	5008	,	,		22319	0.001		0.001	False		,,,				2504	0.0102				p.R1773S		Atlas-SNP	.											C2orf16_ENST00000408964,NS,carcinoma,0,2	C2orf16	357	.	0			c.A5319C						.						201	204	203					2																	27804758		1930	4131	6061	SO:0001583	missense	84226	exon1			GAGAAGACATCGC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.5319A>C	chr2.hg19:g.27804758A>C	ENSP00000386190:p.Arg1773Ser	103.0	1.0		72.0	15.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	hg19	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	a	0.251	-1.006368	0.02112	.	.	ENSG00000221843	ENST00000408964	T	0.04917	3.53	0.158	-0.317	0.12736	.	.	.	.	.	T	0.01627	0.0052	N	0.01640	-0.785	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42155	-0.9468	8	0.07175	T	0.84	.	.	.	.	.	1773	Q68DN1	CB016_HUMAN	S	1773	ENSP00000386190:R1773S	ENSP00000386190:R1773S	R	+	3	2	C2orf16	27658262	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-9.976000	0.00008	-1.184000	0.02720	-1.203000	0.01651	AGA	.	.		0.527	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		C	27804758	A	C	27804758	3	2	168	1	0	0	0	0	1	0	0	0	2159	272	10	5	5321	5	C2orf16	2	27804758	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	18283859	27804758	215394615	43	25459	120	2								
C2orf16	84226	hgsc.bcm.edu	37	chr2	27804762	27804762	+	Missense_Mutation	SNP	C	C	T													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gtccctctgagagaagacatCgcagtccctctgagagaaga					rs572973586	byFrequency	TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:27804762C>T	ENST00000408964.2	+	1	5374	c.5323C>T	c.(5323-5325)Cgc>Tgc	p.R1775C	ZNF512_ENST00000355467.4_5'Flank|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000379717.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1775	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GAGAAGACATCGCAGTCCCTC	0.527													C|||	7	0.00139776	8e-04	0	5008	,	,		21123	0.001		0	False		,,,				2504	0.0051				p.R1775C		Atlas-SNP	.											C2orf16_ENST00000408964,NS,carcinoma,0,4	C2orf16	357	.	0			c.C5323T						.						199	203	201					2																	27804762		1937	4131	6068	SO:0001583	missense	84226	exon1			AGACATCGCAGTC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.5323C>T	chr2.hg19:g.27804762C>T	ENSP00000386190:p.Arg1775Cys	102.0	0.0		77.0	19.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	hg19	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	C	9.837	1.189997	0.21954	.	.	ENSG00000221843	ENST00000408964	T	0.05717	3.4	3.4	-1.73	0.08081	.	.	.	.	.	T	0.05181	0.0138	L	0.46157	1.445	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.41980	-0.9478	9	0.45353	T	0.12	.	1.5182	0.02510	0.2773:0.4095:0.1356:0.1777	.	1775	Q68DN1	CB016_HUMAN	C	1775	ENSP00000386190:R1775C	ENSP00000386190:R1775C	R	+	1	0	C2orf16	27658266	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.612000	0.02061	-0.413000	0.07507	-0.567000	0.04161	CGC	.	.		0.527	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		T	27804762	C	T	27804762	3	4	168	1	0	0	0	0	1	0	0	0	2159	884	31	1	5325	1	C2orf16	2	27804762	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	4	27804762	215394611	44	25460	120	2								
TTC27	55622	hgsc.bcm.edu	37	chr2	33007745	33007745	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctatatccgattaaaacaaaAgtaagtacatcagacaaata	4	7	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:33007745A>T	ENST00000317907.4	+	15	2063	c.1832A>T	c.(1831-1833)aAa>aTa	p.K611I		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	611										breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						TTAAAACAAAAGTAAGTACAT	0.303																																					p.K611I		Atlas-SNP	.											.	TTC27	71	.	0			c.A1832T						.						60	60	60					2																	33007745		2201	4292	6493	SO:0001630	splice_region_variant	55622	exon15			AACAAAAGTAAGT	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1832+1A>T	chr2.hg19:g.33007745A>T		398.0	0.0		289.0	119.0	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	hg19	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	a	29.7	5.026563	0.93518	.	.	ENSG00000018699	ENST00000317907	T	0.59638	0.25	5.9	5.9	0.94986	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.72787	0.3504	M	0.65677	2.01	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	T	0.69083	-0.5239	10	0.22109	T	0.4	-18.5157	16.336	0.83060	1.0:0.0:0.0:0.0	.	611	Q6P3X3	TTC27_HUMAN	I	611	ENSP00000313953:K611I	ENSP00000313953:K611I	K	+	2	0	TTC27	32861249	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.269000	0.95684	2.252000	0.74401	0.529000	0.55759	AAA	.	.		0.303	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735	Missense_Mutation	T	33007745	A	T	33007745	5	4	168	1	0	0	0	0	0	0	1	0	16710	86	3	4	1890	4	TTC27	2	33007745	Splice_Site	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	5202983	33007745	210191628	45	25461										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37255261	37255261	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggtatcatcatccatctcatCtttcttttcagcttcttcat	3	12	8	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:37255261C>G	ENST00000233099.5	-	24	3753	c.3658G>C	c.(3658-3660)Gat>Cat	p.D1220H	HEATR5B_ENST00000354531.2_Missense_Mutation_p.D1220H	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1220						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TCCATCTCATCTTTCTTTTCA	0.398																																					p.D1220H		Atlas-SNP	.											.	HEATR5B	185	.	0			c.G3658C						.						92	97	96					2																	37255261		2203	4300	6503	SO:0001583	missense	54497	exon24			TCTCATCTTTCTT	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.3658G>C	chr2.hg19:g.37255261C>G	ENSP00000233099:p.Asp1220His	291.0	0.0		245.0	94.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.186055	0.57909	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.54479	0.57;0.57	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	M	0.66939	2.045	0.80722	D	1	P	0.35959	0.53	B	0.35813	0.211	T	0.58358	-0.7650	10	0.40728	T	0.16	-18.5623	17.7328	0.88383	0.0:1.0:0.0:0.0	.	1220	Q9P2D3	HTR5B_HUMAN	H	1220	ENSP00000233099:D1220H;ENSP00000346531:D1220H	ENSP00000233099:D1220H	D	-	1	0	HEATR5B	37108765	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.686000	0.84128	2.259000	0.74868	0.467000	0.42956	GAT	.	.		0.398	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		G	37255261	C	G	37255261	3	3	168	1	0	0	0	0	1	0	0	0	7041	913	32	4	2609	4	HEATR5B	2	37255261	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	4247516	37255261	205944112	46	25462										
SULT6B1	391365	hgsc.bcm.edu	37	chr2	37415605	37415605	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cgcactttggataagatgctAgcacgatgtcatcatgtctg	10	9	3	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:37415605A>T	ENST00000535679.1	-	1	178	c.179T>A	c.(178-180)cTa>cAa	p.L60Q	SULT6B1_ENST00000379149.2_Missense_Mutation_p.L60Q|SULT6B1_ENST00000407963.1_Missense_Mutation_p.L22Q|SULT6B1_ENST00000260637.3_Missense_Mutation_p.L22Q			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	60						cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				ATAAGATGCTAGCACGATGTC	0.468																																					p.L22Q		Atlas-SNP	.											.	SULT6B1	46	.	0			c.T65A						.						233	197	209					2																	37415605		2203	4300	6503	SO:0001583	missense	391365	exon1			GATGCTAGCACGA	AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"Sulfotransferases, cytosolic"	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.179T>A	chr2.hg19:g.37415605A>T	ENSP00000444081:p.Leu60Gln	141.0	0.0		92.0	41.0	NM_001032377	B2RTS7	Missense_Mutation	SNP	ENST00000535679.1	hg19		.	.	.	.	.	.	.	.	.	.	A	18.00	3.524388	0.64747	.	.	ENSG00000138068	ENST00000535679;ENST00000379149;ENST00000260637;ENST00000407963	D;T;D;D	0.85861	-2.04;2.51;-2.04;-2.04	4.39	4.39	0.52855	Sulfotransferase domain (1);	0.000000	0.64402	D	0.000005	D	0.91700	0.7376	M	0.83384	2.64	0.53688	D	0.999972	D	0.76494	0.999	D	0.74674	0.984	D	0.92596	0.6087	10	0.87932	D	0	.	11.6066	0.51035	1.0:0.0:0.0:0.0	.	60	Q6IMI4	ST6B1_HUMAN	Q	60;60;22;22	ENSP00000444081:L60Q;ENSP00000368444:L60Q;ENSP00000260637:L22Q;ENSP00000384950:L22Q	ENSP00000260637:L22Q	L	-	2	0	SULT6B1	37269109	0.982000	0.34865	0.884000	0.34674	0.709000	0.40893	5.664000	0.68045	1.846000	0.53633	0.533000	0.62120	CTA	.	.		0.468	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377		T	37415605	A	T	37415605	3	4	168	1	0	0	0	0	1	0	0	0	15399	420	15	4	760	4	SULT6B1	2	37415605	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	160344	37415605	205783768	47	25463										
CD207	50489	hgsc.bcm.edu	37	chr2	71058314	71058314	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgttcccagcattgttgggcTcacctggaatccagaaccta	9	12	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:71058314T>A	ENST00000410009.3	-	6	899	c.854A>T	c.(853-855)gAg>gTg	p.E285V		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	285	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						ATTGTTGGGCTCACCTGGAAT	0.418																																					p.E285V		Atlas-SNP	.											.	CD207	47	.	0			c.A854T						.						126	115	119					2																	71058314		1905	4129	6034	SO:0001583	missense	50489	exon6			TTGGGCTCACCTG	AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"C-type lectin domain containing", "CD molecules"	17935	protein-coding gene	gene with protein product		604862	"CD207 antigen, langerin"			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.854A>T	chr2.hg19:g.71058314T>A	ENSP00000386378:p.Glu285Val	99.0	0.0		92.0	27.0	NM_015717		Missense_Mutation	SNP	ENST00000410009.3	hg19		.	.	.	.	.	.	.	.	.	.	T	15.39	2.818627	0.50633	.	.	ENSG00000116031	ENST00000410009	T	0.21543	2.0	3.87	3.87	0.44632	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.52532	D	0.000062	T	0.58850	0.2151	H	0.98199	4.17	0.39040	D	0.960115	D	0.89917	1.0	D	0.87578	0.998	T	0.72151	-0.4377	10	0.87932	D	0	.	9.3545	0.38157	0.0:0.0:0.0:1.0	.	285	Q9UJ71	CLC4K_HUMAN	V	285	ENSP00000386378:E285V	ENSP00000386378:E285V	E	-	2	0	CD207	70911822	0.998000	0.40836	1.000000	0.80357	0.547000	0.35210	3.626000	0.54245	1.978000	0.57642	0.523000	0.50628	GAG	.	.		0.418	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717		A	71058314	T	A	71058314	3	1	168	1	0	0	0	0	1	0	0	0	2985	1551	54	4	136	4	CD207	2	71058314	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	33642709	71058314	172141059	48	25464										
GGCX	2677	hgsc.bcm.edu	37	chr2	85780558	85780558	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggggcagtaggacaccagctTccgaggccactcaggggagc	16	12	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:85780558T>A	ENST00000233838.4	-	8	1032	c.952A>T	c.(952-954)Aag>Tag	p.K318*	GGCX_ENST00000430215.3_Nonsense_Mutation_p.K261*|GGCX_ENST00000473665.1_5'UTR	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	318					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	GACACCAGCTTCCGAGGCCAC	0.552																																					p.K318X		Atlas-SNP	.											.	GGCX	44	.	0			c.A952T						.						65	74	71					2																	85780558		2203	4300	6503	SO:0001587	stop_gained	2677	exon8			CCAGCTTCCGAGG		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"vitamin K-dependent gamma-carboxylase"	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.952A>T	chr2.hg19:g.85780558T>A	ENSP00000233838:p.Lys318*	288.0	0.0		219.0	86.0	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Nonsense_Mutation	SNP	ENST00000233838.4	hg19	CCDS1978.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.947706	0.92593	.	.	ENSG00000115486	ENST00000233838;ENST00000430215	.	.	.	5.64	4.41	0.53225	.	0.240008	0.46758	D	0.000276	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.9945	10.5883	0.45296	0.0:0.0:0.1614:0.8386	.	.	.	.	X	318;261	.	ENSP00000233838:K318X	K	-	1	0	GGCX	85634069	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	1.597000	0.36729	2.147000	0.66899	0.533000	0.62120	AAG	.	.		0.552	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		A	85780558	T	A	85780558	4	1	168	1	0	0	0	0	0	1	0	0	6364	1792	62	4	1356	4	GGCX	2	85780558	Nonsense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	14722244	85780558	157418815	49	25465										
DPP10	57628	hgsc.bcm.edu	37	chr2	116257157	116257157	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tagaaacaaatgctaccacaTtattattggaaaacacaact	4	8	0	1	rs139947044		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:116257157T>C	ENST00000410059.1	+	4	823	c.343T>C	c.(343-345)Tta>Cta	p.L115L	DPP10_ENST00000488208.1_3'UTR|DPP10_ENST00000409163.1_Silent_p.L65L|DPP10_ENST00000393147.2_Silent_p.L119L|DPP10_ENST00000310323.8_Silent_p.L108L	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	115						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						TGCTACCACATTATTATTGGA	0.299																																					p.L119L		Atlas-SNP	.											.	DPP10	415	.	0			c.T355C						.	T	,,,,	0,4406		0,0,2203	113	110	111		322,355,193,331,343	4.2	1	2	dbSNP_134	111	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DPP10	NM_001004360.3,NM_001178034.1,NM_001178036.1,NM_001178037.1,NM_020868.3	,,,,	0,1,6501	CC,CT,TT		0.0116,0.0,0.0077	,,,,	108/790,119/801,65/747,111/793,115/797	116257157	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	57628	exon4			ACCACATTATTAT	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.343T>C	chr2.hg19:g.116257157T>C		297.0	0.0		261.0	112.0	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Silent	SNP	ENST00000410059.1	hg19	CCDS46400.1																																																																																			.	T|1.000;C|0.000		0.299	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		C	116257157	T	C	116257157	2	2	168	1	0	0	0	0	0	0	0	1	4729	1490	52	2		2	DPP10	2	116257157	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	30476599	116257157	126942216	50	25466										
KYNU	8942	hgsc.bcm.edu	37	chr2	143718311	143718311	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tggacagcactttaatattcCtgccatcacaaaagctggac	7	11	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:143718311C>T	ENST00000264170.4	+	8	959	c.701C>T	c.(700-702)cCt>cTt	p.P234L	KYNU_ENST00000375773.2_Missense_Mutation_p.P234L|KYNU_ENST00000409512.1_Missense_Mutation_p.P234L	NM_003937.2	NP_003928.1			kynureninase											large_intestine(10)|liver(1)|lung(18)|prostate(3)|skin(4)	36				BRCA - Breast invasive adenocarcinoma(221;0.072)		TTTAATATTCCTGCCATCACA	0.418																																					p.P234L		Atlas-SNP	.											.	KYNU	110	.	0			c.C701T						.						135	131	132					2																	143718311		2203	4300	6503	SO:0001583	missense	8942	exon9			ATATTCCTGCCAT	U57721	CCDS2183.1, CCDS33299.1	2q22.2	2010-11-23	2010-11-23		ENSG00000115919	ENSG00000115919	3.7.1.3		6469	protein-coding gene	gene with protein product	"L-kynurenine hydrolase"	605197	"kynureninase (L-kynurenine hydrolase)"			8706755, 9180257	Standard	NM_001199241		Approved		uc002tvl.3	Q16719	OTTHUMG00000131829	ENST00000264170.4:c.701C>T	chr2.hg19:g.143718311C>T	ENSP00000264170:p.Pro234Leu	91.0	0.0		98.0	44.0	NM_001199241		Missense_Mutation	SNP	ENST00000264170.4	hg19	CCDS2183.1	.	.	.	.	.	.	.	.	.	.	C	15.77	2.931862	0.52866	.	.	ENSG00000115919	ENST00000264170;ENST00000375773;ENST00000409512	T;T;T	0.55413	0.52;0.52;0.52	5.35	4.46	0.54185	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.124843	0.56097	D	0.000035	T	0.54854	0.1884	M	0.78916	2.43	0.80722	D	1	B;B	0.29835	0.258;0.069	B;B	0.31390	0.129;0.03	T	0.56288	-0.8004	10	0.40728	T	0.16	.	13.2071	0.59803	0.2896:0.7104:0.0:0.0	.	234;234	Q16719;Q9BVW3	KYNU_HUMAN;.	L	234	ENSP00000264170:P234L;ENSP00000364928:P234L;ENSP00000386731:P234L	ENSP00000264170:P234L	P	+	2	0	KYNU	143434781	0.157000	0.22836	0.991000	0.47740	0.826000	0.46750	1.644000	0.37228	1.369000	0.46134	0.644000	0.83932	CCT	.	.		0.418	KYNU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254772.1	NM_001032998		T	143718311	C	T	143718311	3	4	168	1	0	0	0	0	1	0	0	0	8596	681	24	3	727	3	KYNU	2	143718311	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	27461154	143718311	99481062	51	25467										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160884730	160884730	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ttaaaataaaaacgcttaccAactatttcatgatcaatgtg	4	7	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:160884730A>T	ENST00000283243.7	-	6	1304	c.1098T>A	c.(1096-1098)gtT>gtA	p.V366V	PLA2R1_ENST00000392771.1_Splice_Site_p.V366V	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	366					cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						AACGCTTACCAACTATTTCAT	0.318																																					p.V366V		Atlas-SNP	.											.	PLA2R1	153	.	0			c.T1098A						.						99	109	105					2																	160884730		2203	4300	6503	SO:0001630	splice_region_variant	22925	exon6			CTTACCAACTATT	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.1099+1T>A	chr2.hg19:g.160884730A>T		377.0	0.0		303.0	135.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	hg19	CCDS33309.1																																																																																			.	.		0.318	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		Silent	T	160884730	A	T	160884730	5	4	168	1	0	0	0	0	0	0	1	0	12019	144	5	4	3401	4	PLA2R1	2	160884730	Splice_Site	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	17166419	160884730	82314643	52	25468										
SLC38A11	151258	hgsc.bcm.edu	37	chr2	165793884	165793884	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gtggacccagtgaaattgccCttgccattacaattccaaga	8	11	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:165793884C>T	ENST00000409149.3	-	6	716	c.425G>A	c.(424-426)aGg>aAg	p.R142K	SLC38A11_ENST00000303735.4_Missense_Mutation_p.R120K|SLC38A11_ENST00000409058.1_Missense_Mutation_p.R173K|SLC38A11_ENST00000409662.1_Missense_Mutation_p.R142K|SLC38A11_ENST00000493887.1_5'UTR	NM_001199148.1	NP_001186077.1	Q08AI6	S38AB_HUMAN	solute carrier family 38, member 11	142					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15						TGAAATTGCCCTTGCCATTAC	0.363																																					p.R142K		Atlas-SNP	.											.	SLC38A11	41	.	0			c.G425A						.						129	129	129					2																	165793884		2203	4300	6503	SO:0001583	missense	151258	exon6			ATTGCCCTTGCCA		CCDS2224.1, CCDS56142.1	2q24.3	2013-05-22			ENSG00000169507	ENSG00000169507		"Solute carriers"	26836	protein-coding gene	gene with protein product							Standard	NM_173512		Approved	FLJ39822, AVT2	uc002ucw.2	Q08AI6	OTTHUMG00000132144	ENST00000409149.3:c.425G>A	chr2.hg19:g.165793884C>T	ENSP00000386272:p.Arg142Lys	106.0	0.0		91.0	13.0	NM_001199148	B4DF99|Q8N887	Missense_Mutation	SNP	ENST00000409149.3	hg19	CCDS56142.1	.	.	.	.	.	.	.	.	.	.	C	13.18	2.158833	0.38119	.	.	ENSG00000169507	ENST00000303735;ENST00000409149;ENST00000409058;ENST00000409662;ENST00000424914	T;T;T;T	0.02197	4.4;4.4;4.4;4.4	4.92	4.04	0.47022	.	0.043794	0.85682	D	0.000000	T	0.06826	0.0174	M	0.71920	2.185	0.46416	D	0.999039	P;P	0.52061	0.95;0.938	P;P	0.58266	0.836;0.664	T	0.32214	-0.9915	10	0.02654	T	1	-3.0994	12.583	0.56401	0.0:0.9171:0.0:0.0829	.	142;120	Q08AI6;Q08AI6-2	S38AB_HUMAN;.	K	120;142;173;142;17	ENSP00000306178:R120K;ENSP00000386272:R142K;ENSP00000387345:R173K;ENSP00000386774:R142K	ENSP00000306178:R120K	R	-	2	0	SLC38A11	165502130	0.983000	0.35010	0.266000	0.24541	0.006000	0.05464	4.096000	0.57734	1.213000	0.43380	0.555000	0.69702	AGG	.	.		0.363	SLC38A11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333390.1	NM_173512		T	165793884	C	T	165793884	3	4	168	1	0	0	0	0	1	0	0	0	14618	681	24	3	819	3	SLC38A11	2	165793884	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	4909154	165793884	77405489	53	25469										
TTC21B	79809	hgsc.bcm.edu	37	chr2	166781090	166781090	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ttcacttttgctattaggaaGactgtttgcagaagacctgg	10	7	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:166781090G>C	ENST00000243344.7	-	12	1622	c.1485C>G	c.(1483-1485)gtC>gtG	p.V495V		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	495					forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)				breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						CTATTAGGAAGACTGTTTGCA	0.383																																					p.V495V		Atlas-SNP	.											.	TTC21B	130	.	0			c.C1485G						.						47	49	48					2																	166781090		2203	4300	6503	SO:0001819	synonymous_variant	79809	exon12			TAGGAAGACTGTT	AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"Tetratricopeptide (TTC) repeat domain containing", "Intraflagellar transport homologs"	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.1485C>G	chr2.hg19:g.166781090G>C		447.0	0.0		321.0	14.0	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Silent	SNP	ENST00000243344.7	hg19	CCDS33315.1																																																																																			.	.		0.383	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753		C	166781090	G	C	166781090	2	2	168	1	0	0	0	0	0	0	0	1	16703	929	33	4		4	TTC21B	2	166781090	Silent	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	987206	166781090	76418283	54	25470										
LRP2	4036	hgsc.bcm.edu	37	chr2	170062841	170062841	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcacctggagtgcacttaccTgaagcaatgacagttggagt	12	9	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:170062841T>A	ENST00000263816.3	-	39	7674	c.7389A>T	c.(7387-7389)tcA>tcT	p.S2463S		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2463					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TGCACTTACCTGAAGCAATGA	0.448																																					p.S2463S		Atlas-SNP	.											.	LRP2	751	.	0			c.A7389T						.						57	60	59					2																	170062841		2203	4300	6503	SO:0001630	splice_region_variant	4036	exon39			CTTACCTGAAGCA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.7390+1A>T	chr2.hg19:g.170062841T>A		80.0	0.0		68.0	33.0	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.		0.448	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	Silent	A	170062841	T	A	170062841	5	1	168	1	0	0	0	0	0	0	1	0	8965	1594	55	4	6742	4	LRP2	2	170062841	Splice_Site	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	3281751	170062841	73136532	55	25471										
TTN	7273	hgsc.bcm.edu	37	chr2	179428033	179428033	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	catccgcagcagcttctttgAcctctacaacatagccttta	5	14	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:179428033A>T	ENST00000591111.1	-	276	78127	c.77903T>A	c.(77902-77904)gTc>gAc	p.V25968D	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V25041D|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V27609D|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V18544D|TTN_ENST00000359218.5_Missense_Mutation_p.V18669D|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V18736D|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25968	Fibronectin type-III 89. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGCTTCTTTGACCTCTACAAC	0.453																																					p.V27609D		Atlas-SNP	.											.	TTN	18412	.	0			c.T82826A						.						79	79	79					2																	179428033		2042	4216	6258	SO:0001583	missense	7273	exon326			TCTTTGACCTCTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.77903T>A	chr2.hg19:g.179428033A>T	ENSP00000465570:p.Val25968Asp	129.0	0.0		108.0	35.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.62	2.290134	0.40494	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.74	0.687	0.18020	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50222	0.1603	L	0.56199	1.76	0.28016	N	0.934721	B;B;B;B	0.24576	0.055;0.055;0.055;0.106	B;B;B;B	0.28385	0.048;0.048;0.089;0.089	T	0.51068	-0.8752	9	0.87932	D	0	.	6.6545	0.22981	0.6286:0.1164:0.255:0.0	.	18544;18669;18736;25968	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	25041;18544;18736;18669;18542	ENSP00000343764:V25041D;ENSP00000434586:V18544D;ENSP00000340554:V18736D;ENSP00000352154:V18669D	ENSP00000340554:V18736D	V	-	2	0	TTN	179136279	0.978000	0.34361	0.956000	0.39512	0.936000	0.57629	1.718000	0.38001	0.096000	0.17463	0.460000	0.39030	GTC	.	.		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179428033	A	T	179428033	3	4	168	1	0	0	0	0	1	0	0	0	16750	275	10	4	25301	4	TTN	2	179428033	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	9365192	179428033	63771340	56	25472										
TTN	7273	hgsc.bcm.edu	37	chr2	179436145	179436145	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gaggaccaggaactttgaatGgatattgggctacagtaggc	14	6	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:179436145G>A	ENST00000591111.1	-	276	70015	c.69791C>T	c.(69790-69792)cCa>cTa	p.P23264L	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P22337L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P24905L|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P15840L|TTN_ENST00000359218.5_Missense_Mutation_p.P15965L|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P16032L|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23264	Fibronectin type-III 68. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AACTTTGAATGGATATTGGGC	0.458																																					p.P24905L		Atlas-SNP	.											.	TTN	18412	.	0			c.C74714T						.						110	100	103					2																	179436145		1926	4144	6070	SO:0001583	missense	7273	exon326			TTGAATGGATATT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.69791C>T	chr2.hg19:g.179436145G>A	ENSP00000465570:p.Pro23264Leu	115.0	0.0		96.0	31.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.95	2.090381	0.36855	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.39	4.5	0.54988	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.62672	0.2447	M	0.83603	2.65	0.80722	D	1	D;D;D;D	0.59767	0.986;0.986;0.986;0.974	P;P;P;P	0.50970	0.655;0.655;0.655;0.563	T	0.72074	-0.4400	9	0.87932	D	0	.	15.9687	0.79995	0.0:0.0:0.8645:0.1355	.	15840;15965;16032;23264	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	22337;15840;16032;15965;15838	ENSP00000343764:P22337L;ENSP00000434586:P15840L;ENSP00000340554:P16032L;ENSP00000352154:P15965L	ENSP00000340554:P16032L	P	-	2	0	TTN	179144391	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.751000	0.98889	1.384000	0.46424	0.650000	0.86243	CCA	.	.		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179436145	G	A	179436145	3	1	168	1	0	0	0	0	1	0	0	0	16750	1348	47	3	33413	3	TTN	2	179436145	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	8112	179436145	63763228	57	25473										
TTN	7273	hgsc.bcm.edu	37	chr2	179605680	179605680	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggctttagcaatatgctcatAagatagttgctggttttctt	9	6	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:179605680A>T	ENST00000591111.1	-	46	11553	c.11329T>A	c.(11329-11331)Tat>Aat	p.Y3777N	TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.Y4094N|TTN_ENST00000460472.2_Missense_Mutation_p.Y3731N|TTN_ENST00000359218.5_Missense_Mutation_p.Y3856N|TTN_ENST00000342175.6_Missense_Mutation_p.Y3923N			Q8WZ42	TITIN_HUMAN	titin	33949					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATATGCTCATAAGATAGTTGC	0.413																																					p.Y4094N		Atlas-SNP	.											.	TTN	18412	.	0			c.T12280A						.						98	96	96					2																	179605680		1874	4101	5975	SO:0001583	missense	7273	exon48			GCTCATAAGATAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.11329T>A	chr2.hg19:g.179605680A>T	ENSP00000465570:p.Tyr3777Asn	90.0	0.0		76.0	28.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	4.395	0.072873	0.08436	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.60299	0.26;0.21;0.2	4.5	2.0	0.26442	.	.	.	.	.	T	0.41581	0.1165	L	0.27053	0.805	0.20403	N	0.999903	B;B;B	0.12013	0.005;0.005;0.005	B;B;B	0.14023	0.005;0.005;0.01	T	0.36089	-0.9762	9	0.87932	D	0	.	6.0807	0.19940	0.6611:0.1735:0.1655:0.0	.	3731;3856;3923	D3DPF9;E7EQE6;E7ET18	.;.;.	N	3731;3923;3856;3731	ENSP00000434586:Y3731N;ENSP00000340554:Y3923N;ENSP00000352154:Y3856N	ENSP00000340554:Y3923N	Y	-	1	0	TTN	179313925	0.154000	0.22792	0.267000	0.24556	0.137000	0.21094	0.544000	0.23253	0.277000	0.22141	0.533000	0.62120	TAT	.	.		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179605680	A	T	179605680	3	4	168	1	0	0	0	0	1	0	0	0	16750	362	13	4	92509	4	TTN	2	179605680	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	169535	179605680	63593693	58	25474										
PARD3B	117583	hgsc.bcm.edu	37	chr2	205912302	205912302	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cacctctcactttgtcttccAggcactccactgctggtgag	8	15	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:205912302A>T	ENST00000406610.2	+	4	601		c.e4-1		PARD3B_ENST00000462231.1_Splice_Site|PARD3B_ENST00000351153.1_Splice_Site|PARD3B_ENST00000349953.3_Splice_Site|PARD3B_ENST00000358768.2_Splice_Site	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta						cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		TTTGTCTTCCAGGCACTCCAC	0.512																																					.		Atlas-SNP	.											.	PARD3B	314	.	0			c.395-2A>T						.						35	36	36					2																	205912302		1859	3913	5772	SO:0001630	splice_region_variant	117583	exon4			TCTTCCAGGCACT	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19", "par-3 partitioning defective 3 homolog B (C. elegans)"	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.395-1A>T	chr2.hg19:g.205912302A>T		72.0	0.0		48.0	24.0	NM_057177	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Splice_Site	SNP	ENST00000406610.2	hg19		.	.	.	.	.	.	.	.	.	.	A	18.37	3.610226	0.66558	.	.	ENSG00000116117	ENST00000406610;ENST00000358768;ENST00000351153;ENST00000349953	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5891	0.61948	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PARD3B	205620547	1.000000	0.71417	0.993000	0.49108	0.822000	0.46500	5.600000	0.67599	2.220000	0.72140	0.533000	0.62120	.	.	.		0.512	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	Intron	T	205912302	A	T	205912302	5	4	168	1	0	0	0	0	0	0	1	0	11453	202	7	4	407	4	PARD3B	2	205912302	Splice_Site	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	26306622	205912302	37287071	59	25475										
GLB1L	79411	hgsc.bcm.edu	37	chr2	220104515	220104515	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	accaatggcccatggggttcAtacttccgaagcagggtaaa	11	10	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:220104515A>T	ENST00000295759.7	-	8	1075	c.762T>A	c.(760-762)taT>taA	p.Y254*	GLB1L_ENST00000356283.3_Nonsense_Mutation_p.Y164*|GLB1L_ENST00000497855.1_5'UTR|GLB1L_ENST00000409640.1_Nonsense_Mutation_p.Y164*|GLB1L_ENST00000392089.2_Nonsense_Mutation_p.Y254*			Q6UWU2	GLB1L_HUMAN	galactosidase, beta 1-like	254					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559)		Epithelial(149;1.3e-11)|all cancers(144;2.07e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CATGGGGTTCATACTTCCGAA	0.493																																					p.Y254X		Atlas-SNP	.											.	GLB1L	52	.	0			c.T762A						.						90	92	91					2																	220104515		2203	4300	6503	SO:0001587	stop_gained	79411	exon8			GGGTTCATACTTC		CCDS2437.1, CCDS74657.1	2q36.1	2008-02-05			ENSG00000163521	ENSG00000163521			28129	protein-coding gene	gene with protein product						12975309	Standard	XM_005246850		Approved	MGC10771	uc002vkm.3	Q6UWU2	OTTHUMG00000133133	ENST00000295759.7:c.762T>A	chr2.hg19:g.220104515A>T	ENSP00000295759:p.Tyr254*	214.0	0.0		186.0	87.0	NM_024506	Q96DR0	Nonsense_Mutation	SNP	ENST00000295759.7	hg19	CCDS2437.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.969675	0.74246	.	.	ENSG00000163521	ENST00000295759;ENST00000409640;ENST00000392089;ENST00000356283	.	.	.	5.64	3.22	0.36961	.	0.177191	0.50627	D	0.000104	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.7038	7.1368	0.25533	0.7434:0.1239:0.1327:0.0	.	.	.	.	X	254;164;254;164	.	ENSP00000295759:Y254X	Y	-	3	2	GLB1L	219812759	0.996000	0.38824	1.000000	0.80357	0.903000	0.53119	0.567000	0.23608	0.534000	0.28695	0.528000	0.53228	TAT	.	.		0.493	GLB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256822.2	NM_024506		T	220104515	A	T	220104515	4	4	168	1	0	0	0	0	0	1	0	0	6436	224	8	4	1242	4	GLB1L	2	220104515	Nonsense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	14192213	220104515	23094858	60	25476										
SPEG	10290	hgsc.bcm.edu	37	chr2	220344852	220344852	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agagccccgtgtctggagtcActgacatctggtaaggctgg	14	10	3	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:220344852A>T	ENST00000312358.7	+	25	5464	c.5332A>T	c.(5332-5334)Act>Tct	p.T1778S	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1778	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GTCTGGAGTCACTGACATCTG	0.617																																					p.T1778S		Atlas-SNP	.											.	SPEG	272	.	0			c.A5332T						.						61	65	63					2																	220344852		2068	4206	6274	SO:0001583	missense	10290	exon25			GGAGTCACTGACA	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.5332A>T	chr2.hg19:g.220344852A>T	ENSP00000311684:p.Thr1778Ser	60.0	0.0		37.0	16.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	a	16.87	3.243199	0.58995	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.35236	1.32	4.36	4.36	0.52297	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.40728	N	0.001021	T	0.34890	0.0913	N	0.12637	0.245	0.80722	D	1	P	0.36683	0.565	P	0.49953	0.627	T	0.39396	-0.9616	10	0.54805	T	0.06	.	14.0438	0.64693	1.0:0.0:0.0:0.0	.	1778	Q15772	SPEG_HUMAN	S	1778	ENSP00000311684:T1778S	ENSP00000265327:T1778S	T	+	1	0	SPEG	220053096	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.829000	0.62737	1.962000	0.57031	0.492000	0.49549	ACT	.	.		0.617	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220344852	A	T	220344852	3	4	168	1	0	0	0	0	1	0	0	0	15051	159	6	4	5442	4	SPEG	2	220344852	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	240337	220344852	22854521	61	25477										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220501121	220501121	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctgggagctcagccgctgctTgtggttggcttctctgggcc	15	12	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:220501121T>A	ENST00000358055.3	+	15	2801	c.2289T>A	c.(2287-2289)ctT>ctA	p.L763L	SLC4A3_ENST00000373762.3_Silent_p.L790L|SLC4A3_ENST00000373760.2_Silent_p.L763L|SLC4A3_ENST00000273063.6_Silent_p.L790L|SLC4A3_ENST00000317151.3_Silent_p.L763L			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	763	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCCGCTGCTTGTGGTTGGCT	0.617																																					p.L790L		Atlas-SNP	.											.	SLC4A3	144	.	0			c.T2370A						.						81	75	77					2																	220501121		2203	4299	6502	SO:0001819	synonymous_variant	6508	exon15			GCTGCTTGTGGTT		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2289T>A	chr2.hg19:g.220501121T>A		47.0	0.0		36.0	14.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Silent	SNP	ENST00000358055.3	hg19	CCDS2445.1																																																																																			.	.		0.617	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		A	220501121	T	A	220501121	2	1	168	1	0	0	0	0	0	0	0	1	14670	1799	63	4		4	SLC4A3	2	220501121	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	156269	220501121	22698252	62	25478										
DGKD	8527	hgsc.bcm.edu	37	chr2	234296973	234296973	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	atcaaaaaggagatactttaAgcttcgagggcgaacgcttt	10	7	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr2:234296973A>T	ENST00000264057.2	+	2	239	c.227A>T	c.(226-228)aAg>aTg	p.K76M	DGKD_ENST00000489613.1_3'UTR|DGKD_ENST00000409813.3_Missense_Mutation_p.K32M|AC019221.4_ENST00000442524.1_RNA	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	76	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	AGATACTTTAAGCTTCGAGGG	0.478																																					p.K76M		Atlas-SNP	.											.	DGKD	106	.	0			c.A227T						.						125	120	122					2																	234296973		2203	4300	6503	SO:0001583	missense	8527	exon2			ACTTTAAGCTTCG	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.227A>T	chr2.hg19:g.234296973A>T	ENSP00000264057:p.Lys76Met	333.0	0.0		212.0	91.0	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	hg19	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.458088	0.84317	.	.	ENSG00000077044	ENST00000264057;ENST00000447484;ENST00000409813	T;T;T	0.75154	-0.91;-0.91;-0.91	5.29	5.29	0.74685	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.069907	0.56097	D	0.000034	D	0.82531	0.5057	L	0.48986	1.54	0.52501	D	0.99995	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.83505	0.0077	10	0.56958	D	0.05	.	14.9114	0.70761	1.0:0.0:0.0:0.0	.	32;76	Q16760-2;Q16760	.;DGKD_HUMAN	M	76;46;32	ENSP00000264057:K76M;ENSP00000395530:K46M;ENSP00000386455:K32M	ENSP00000264057:K76M	K	+	2	0	DGKD	233961712	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	6.700000	0.74619	2.311000	0.77944	0.533000	0.62120	AAG	.	.		0.478	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234296973	A	T	234296973	3	4	168	1	0	0	0	0	1	0	0	0	4469	72	3	4	257	4	DGKD	2	234296973	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	13795852	234296973	8902400	63	25479										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4558209	4558209	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgtctagcttcctacatattGgagacatttgttctctgtac	7	9	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:4558209G>T	ENST00000443694.2	+	1	34	c.34G>T	c.(34-36)Gga>Tga	p.G12*	ITPR1_ENST00000357086.4_Nonsense_Mutation_p.G12*|ITPR1_ENST00000302640.8_Nonsense_Mutation_p.G12*|ITPR1_ENST00000456211.2_Nonsense_Mutation_p.G12*|ITPR1_ENST00000544951.1_Nonsense_Mutation_p.G12*|ITPR1_ENST00000354582.6_Nonsense_Mutation_p.G12*|ITPR1_ENST00000423119.2_Nonsense_Mutation_p.G12*			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	12					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	CCTACATATTGGAGACATTTG	0.378																																					p.G12X		Atlas-SNP	.											.	ITPR1	659	.	0			c.G34T						.						194	182	186					3																	4558209		1885	4105	5990	SO:0001587	stop_gained	3708	exon3			CATATTGGAGACA	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.34G>T	chr3.hg19:g.4558209G>T	ENSP00000401671:p.Gly12*	127.0	0.0		109.0	5.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Nonsense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	39	7.627581	0.98399	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.3298	0.90264	0.0:0.0:1.0:0.0	.	.	.	.	X	12	.	ENSP00000306253:G12X	G	+	1	0	ITPR1	4533209	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	8.929000	0.92859	2.602000	0.87976	0.591000	0.81541	GGA	.	.		0.378	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4558209	G	T	4558209	4	4	168	1	0	0	0	0	0	1	0	0	7929	1349	47	3	36	3	ITPR1	3	4558209	Nonsense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10		4558209	193464221	64	25480										
LHFPL4	375323	hgsc.bcm.edu	37	chr3	9547751	9547751	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agggcgttgaggatgccgatGatggccaggatgtatgccca	16	8	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:9547751G>C	ENST00000287585.6	-	3	828	c.543C>G	c.(541-543)atC>atG	p.I181M		NM_198560.2	NP_940962.1	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 4	194						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(3)|skin(1)	10	Medulloblastoma(99;0.227)					GGATGCCGATGATGGCCAGGA	0.612																																					p.I181M		Atlas-SNP	.											.	LHFPL4	34	.	0			c.C543G						.						172	132	146					3																	9547751		2203	4300	6503	SO:0001583	missense	375323	exon3			GCCGATGATGGCC	AY278320	CCDS33691.1	3p25.3	2006-06-13			ENSG00000156959	ENSG00000156959			29568	protein-coding gene	gene with protein product		610240				15905332	Standard	NM_198560		Approved		uc003bry.3	Q7Z7J7	OTTHUMG00000155066	ENST00000287585.6:c.543C>G	chr3.hg19:g.9547751G>C	ENSP00000287585:p.Ile181Met	174.0	0.0		129.0	10.0	NM_198560	A1L383|A4D0Q5	Missense_Mutation	SNP	ENST00000287585.6	hg19	CCDS33691.1	.	.	.	.	.	.	.	.	.	.	G	18.36	3.607769	0.66558	.	.	ENSG00000156959	ENST00000287585	T	0.74209	-0.82	5.5	3.67	0.42095	.	0.000000	0.64402	U	0.000002	T	0.78780	0.4337	M	0.70903	2.155	0.54753	D	0.999987	P	0.44429	0.835	P	0.53518	0.728	T	0.76631	-0.2888	10	0.54805	T	0.06	-10.1601	6.9409	0.24492	0.1459:0.0:0.7126:0.1414	.	181	Q7Z7J7	LHPL4_HUMAN	M	181	ENSP00000287585:I181M	ENSP00000287585:I181M	I	-	3	3	LHFPL4	9522751	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.203000	0.58453	0.662000	0.31006	0.591000	0.81541	ATC	.	.		0.612	LHFPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338298.1	NM_198560		C	9547751	G	C	9547751	3	2	168	1	0	0	0	0	1	0	0	0	8776	1280	45	4	208	4	LHFPL4	3	9547751	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	4989542	9547751	188474679	65	25481										
HRH1	3269	hgsc.bcm.edu	37	chr3	11300933	11300933	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctgtacatcgtcagcctctcGgtggcggacttgatcgtggg	14	11	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:11300933G>A	ENST00000397056.1	+	3	401	c.210G>A	c.(208-210)tcG>tcA	p.S70S	HRH1_ENST00000431010.2_Silent_p.S70S|HRH1_ENST00000438284.2_Silent_p.S70S	NM_000861.3|NM_001098211.1	NP_000852.1|NP_001091681.1	P35367	HRH1_HUMAN	histamine receptor H1	70					cellular response to histamine (GO:0071420)|eosinophil chemotaxis (GO:0048245)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|inositol phosphate-mediated signaling (GO:0048016)|memory (GO:0007613)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|regulation of vascular permeability (GO:0043114)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|histamine receptor activity (GO:0004969)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25					Aceprometazine(DB01615)|Alcaftadine(DB06766)|Alimemazine(DB01246)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Antazoline(DB08799)|Aripiprazole(DB01238)|Asenapine(DB06216)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzatropine(DB00245)|Bepotastine(DB04890)|Betahistine(DB06698)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlorcyclizine(DB08936)|Chloropyramine(DB08800)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clemastine(DB00283)|Clofedanol(DB04837)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Dimetindene(DB08801)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Escitalopram(DB01175)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Iloperidone(DB04946)|Imipramine(DB00458)|Isothipendyl(DB08802)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Loxapine(DB00408)|Maprotiline(DB00934)|Meclizine(DB00737)|Mepyramine(DB06691)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Paliperidone(DB01267)|Phenindamine(DB01619)|Pheniramine(DB01620)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	TCAGCCTCTCGGTGGCGGACT	0.582																																					p.S70S		Atlas-SNP	.											.	HRH1	58	.	0			c.G210A						.						151	118	129					3																	11300933		2203	4300	6503	SO:0001819	synonymous_variant	3269	exon3			CCTCTCGGTGGCG		CCDS2604.1	3p25	2012-11-12			ENSG00000196639	ENSG00000196639		"GPCR / Class A : Histamine receptors"	5182	protein-coding gene	gene with protein product		600167				8003029	Standard	NM_001098211		Approved		uc010hds.3	P35367	OTTHUMG00000129719	ENST00000397056.1:c.210G>A	chr3.hg19:g.11300933G>A		110.0	0.0		97.0	37.0	NM_000861	A8K047|Q6P9E5	Silent	SNP	ENST00000397056.1	hg19	CCDS2604.1																																																																																			.	.		0.582	HRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251928.2			A	11300933	G	A	11300933	2	1	168	1	0	0	0	0	0	0	0	1	7364	1103	39	1		1	HRH1	3	11300933	Silent	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	1753182	11300933	186721497	66	25482										
RFTN1	23180	hgsc.bcm.edu	37	chr3	16450985	16450985	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cattgtgaagatcagttttcTgagatctgaagagaaagaaa	10	4	3	6			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:16450985T>A	ENST00000334133.4	-	4	610	c.338A>T	c.(337-339)cAg>cTg	p.Q113L	RFTN1_ENST00000432519.1_Missense_Mutation_p.Q77L	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	113					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						ATCAGTTTTCTGAGATCTGAA	0.423																																					p.Q113L		Atlas-SNP	.											.	RFTN1	79	.	0			c.A338T						.						106	102	103					3																	16450985		2203	4300	6503	SO:0001583	missense	23180	exon4			GTTTTCTGAGATC	D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"raft-linking protein"					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.338A>T	chr3.hg19:g.16450985T>A	ENSP00000334153:p.Gln113Leu	81.0	0.0		73.0	34.0	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Missense_Mutation	SNP	ENST00000334133.4	hg19	CCDS33712.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.121714	0.37436	.	.	ENSG00000131378	ENST00000432519;ENST00000334133;ENST00000451036;ENST00000449415;ENST00000441460;ENST00000431547	T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5	5.63	5.63	0.86233	.	0.242616	0.42294	D	0.000727	T	0.30166	0.0756	M	0.64997	1.995	0.37333	D	0.910046	B;B	0.28082	0.2;0.11	B;B	0.21360	0.034;0.018	T	0.20706	-1.0267	10	0.32370	T	0.25	-24.212	12.2288	0.54476	0.0:0.0:0.0:1.0	.	77;113	G3XAJ6;Q14699	.;RFTN1_HUMAN	L	77;113;113;113;113;113	ENSP00000403926:Q77L;ENSP00000334153:Q113L;ENSP00000403997:Q113L;ENSP00000409427:Q113L;ENSP00000388718:Q113L;ENSP00000393216:Q113L	ENSP00000334153:Q113L	Q	-	2	0	RFTN1	16425989	1.000000	0.71417	1.000000	0.80357	0.459000	0.32528	1.299000	0.33424	2.145000	0.66743	0.533000	0.62120	CAG	.	.		0.423	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150		A	16450985	T	A	16450985	3	1	168	1	0	0	0	0	1	0	0	0	13273	1580	55	4	1426	4	RFTN1	3	16450985	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	5150052	16450985	181571445	67	25483										
MYD88	30	hgsc.bcm.edu	37	chr3	38180513	38180513	+	5'Flank	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgctgctggagctgggacccAgcattggtgaggacgtcccc	15	12	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:38180513A>T	ENST00000333167.8	-	0	0				MYD88_ENST00000443433.2_Missense_Mutation_p.S121C|ACAA1_ENST00000301810.7_5'Flank|MYD88_ENST00000417037.2_Missense_Mutation_p.S121C|MYD88_ENST00000495303.1_Missense_Mutation_p.S121C|ACAA1_ENST00000544624.1_5'Flank|MYD88_ENST00000396334.3_Missense_Mutation_p.S121C|ACAA1_ENST00000450296.1_5'Flank|ACAA1_ENST00000444607.2_5'Flank|MYD88_ENST00000424893.1_Missense_Mutation_p.S121C	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1						alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		GCTGGGACCCAGCATTGGTGA	0.667																																					p.S121C		Atlas-SNP	.											.	MYD88	900	.	0			c.A361T						.																																			SO:0001631	upstream_gene_variant	4615	exon1			GGACCCAGCATTG	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"peroxisomal 3-oxoacyl-Coenzyme A thiolase"	604054	"acetyl-Coenzyme A acyltransferase 1"				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087		chr3.hg19:g.38180513A>T	Exception_encountered	49.0	0.0		41.0	16.0	NM_002468	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	hg19	CCDS2673.1	.	.	.	.	.	.	.	.	.	.	A	18.51	3.640234	0.67244	.	.	ENSG00000172936	ENST00000417037;ENST00000396334;ENST00000424893;ENST00000495303;ENST00000443433;ENST00000421571;ENST00000421516;ENST00000415158	T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24	4.15	1.72	0.24424	Death (2);DEATH-like (2);	0.443565	0.24881	N	0.034852	T	0.65091	0.2658	L	0.60455	1.87	0.21020	N	0.999802	D;D;D;D;D;P	0.89917	0.98;1.0;1.0;0.984;0.999;0.939	P;D;D;P;D;P	0.75484	0.846;0.968;0.986;0.855;0.961;0.598	T	0.52578	-0.8557	10	0.38643	T	0.18	-4.7723	5.6047	0.17373	0.5562:0.3522:0.0917:0.0	.	108;121;121;108;108;97	Q99836-2;B4DQ60;B4DQ72;Q99836;B4DU08;B4E3D6	.;.;.;MYD88_HUMAN;.;.	C	121;121;121;121;121;108;120;97	ENSP00000401399:S121C;ENSP00000379625:S121C;ENSP00000389979:S121C;ENSP00000417848:S121C;ENSP00000390565:S121C;ENSP00000391753:S120C	ENSP00000379625:S121C	S	+	1	0	MYD88	38155517	0.006000	0.16342	0.454000	0.27019	0.992000	0.81027	0.040000	0.13905	0.253000	0.21552	0.459000	0.35465	AGC	.	.		0.667	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		T	38180513	A	T	38180513	1	4	168	0	1	0	0	0	0	0	0	0	10032	188	7	4		4	MYD88	3	38180513	5'Flank	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	21729528	38180513	159841917	68	25484										
CSPG5	10675	hgsc.bcm.edu	37	chr3	47614356	47614356	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgtgccagatgtagtcctgcGtgttgcacctgcagcagcga	13	11	0	1	rs371926119		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:47614356G>A	ENST00000383738.2	-	3	3300	c.1202C>T	c.(1201-1203)aCg>aTg	p.T401M	CSPG5_ENST00000264723.4_Missense_Mutation_p.T401M|CSPG5_ENST00000456150.1_Missense_Mutation_p.T263M	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	401	EGF-like.				axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GTAGTCCTGCGTGTTGCACCT	0.632																																					p.T401M		Atlas-SNP	.											.	CSPG5	46	.	0			c.C1202T						.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	71	63	66		788,1202,1202,788,1202	4.8	1	3		66	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	CSPG5	NM_001206942.1,NM_001206943.1,NM_001206944.1,NM_001206945.1,NM_006574.3	81,81,81,81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	263/402,401/567,401/478,263/429,401/540	47614356	1,13005	2203	4300	6503	SO:0001583	missense	10675	exon3			TCCTGCGTGTTGC	AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.1202C>T	chr3.hg19:g.47614356G>A	ENSP00000373244:p.Thr401Met	180.0	0.0		113.0	48.0	NM_006574	Q71M39|Q71M40	Missense_Mutation	SNP	ENST00000383738.2	hg19	CCDS56253.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.151697	0.78001	0.0	1.16E-4	ENSG00000114646	ENST00000456150;ENST00000383738;ENST00000264723	T;T;T	0.25749	1.82;1.78;1.78	4.81	4.81	0.61882	Epidermal growth factor-like (1);	0.148962	0.47093	D	0.000246	T	0.36276	0.0961	N	0.22421	0.69	0.35794	D	0.822622	D;D	0.89917	0.999;1.0	P;D	0.70487	0.908;0.969	T	0.45659	-0.9246	10	0.56958	D	0.05	-11.5546	15.4314	0.75102	0.0:0.0:1.0:0.0	.	401;401	O95196;O95196-2	CSPG5_HUMAN;.	M	263;401;401	ENSP00000392096:T263M;ENSP00000373244:T401M;ENSP00000264723:T401M	ENSP00000264723:T401M	T	-	2	0	CSPG5	47589360	1.000000	0.71417	0.987000	0.45799	0.973000	0.67179	5.246000	0.65411	2.501000	0.84356	0.561000	0.74099	ACG	.	.		0.632	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574		A	47614356	G	A	47614356	3	1	168	1	0	0	0	0	1	0	0	0	3963	1145	40	1	429	1	CSPG5	3	47614356	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	9433843	47614356	150408074	69	25485										
DHX30	22907	hgsc.bcm.edu	37	chr3	47889323	47889323	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gccatattccagcagcctccAgttggggtgcgcaagattgt	12	11	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:47889323A>G	ENST00000445061.1	+	14	2570	c.2163A>G	c.(2161-2163)ccA>ccG	p.P721P	DHX30_ENST00000457607.1_Silent_p.P749P|DHX30_ENST00000348968.4_Silent_p.P693P|MIR1226_ENST00000408658.1_RNA|DHX30_ENST00000446256.2_Silent_p.P682P	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	721	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		AGCAGCCTCCAGTTGGGGTGC	0.527																																					p.P721P		Atlas-SNP	.											.	DHX30	101	.	0			c.A2163G						.						111	88	96					3																	47889323		2203	4300	6503	SO:0001819	synonymous_variant	22907	exon14			GCCTCCAGTTGGG	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.2163A>G	chr3.hg19:g.47889323A>G		184.0	0.0		110.0	43.0	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Silent	SNP	ENST00000445061.1	hg19	CCDS2759.1																																																																																			.	.		0.527	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		G	47889323	A	G	47889323	2	3	168	1	0	0	0	0	0	0	0	1	4506	175	7	2		2	DHX30	3	47889323	Silent	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	274967	47889323	150133107	70	25486										
IL17RD	54756	hgsc.bcm.edu	37	chr3	57135384	57135384	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tcttcatctaaatgtgaataTatattttctaaattggaaaa	4	4	4	1	rs143634778		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:57135384T>A	ENST00000296318.7	-	11	1075	c.987A>T	c.(985-987)atA>atT	p.I329I	IL17RD_ENST00000463523.1_Silent_p.I185I|IL17RD_ENST00000427856.2_Silent_p.I305I|IL17RD_ENST00000320057.5_Silent_p.I185I	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	329					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		AATGTGAATATATATTTTCTA	0.413																																					p.I329I		Atlas-SNP	.											.	IL17RD	93	.	0			c.A987T						.						27	30	29					3																	57135384		2202	4300	6502	SO:0001819	synonymous_variant	54756	exon11			TGAATATATATTT	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.987A>T	chr3.hg19:g.57135384T>A		62.0	0.0		57.0	21.0	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Silent	SNP	ENST00000296318.7	hg19	CCDS2880.2																																																																																			.	T|1.000;C|0.000		0.413	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		A	57135384	T	A	57135384	2	1	168	1	0	0	0	0	0	0	0	1	7651	1396	49	4		4	IL17RD	3	57135384	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	9246061	57135384	140887046	71	25487										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108407715	108407715	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cttgtgtgatctgtcatgagAatctgtctccagaaaatctt	8	8	5	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:108407715A>T	ENST00000361582.3	+	31	3690	c.3460A>T	c.(3460-3462)Aat>Tat	p.N1154Y	DZIP3_ENST00000463306.1_Missense_Mutation_p.N1154Y	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	1154					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						CTGTCATGAGAATCTGTCTCC	0.363																																					p.N1154Y		Atlas-SNP	.											.	DZIP3	111	.	0			c.A3460T						.						111	106	108					3																	108407715		2203	4300	6503	SO:0001583	missense	9666	exon31			CATGAGAATCTGT	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.3460A>T	chr3.hg19:g.108407715A>T	ENSP00000355028:p.Asn1154Tyr	347.0	0.0		272.0	126.0	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	hg19	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	A	18.78	3.695970	0.68386	.	.	ENSG00000198919	ENST00000361582;ENST00000463306	T;T	0.42900	0.96;0.96	5.36	5.36	0.76844	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.000000	0.64402	D	0.000016	T	0.49575	0.1565	N	0.25485	0.75	0.36437	D	0.865234	D;D	0.71674	0.998;0.998	D;D	0.85130	0.997;0.994	T	0.57688	-0.7768	10	0.48119	T	0.1	-25.206	11.6796	0.51451	1.0:0.0:0.0:0.0	.	772;1154	D3DN61;Q86Y13	.;DZIP3_HUMAN	Y	1154	ENSP00000355028:N1154Y;ENSP00000419981:N1154Y	ENSP00000355028:N1154Y	N	+	1	0	DZIP3	109890405	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.571000	0.45990	2.246000	0.74042	0.533000	0.62120	AAT	.	.		0.363	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		T	108407715	A	T	108407715	3	4	168	1	0	0	0	0	1	0	0	0	4867	246	9	4	3578	4	DZIP3	3	108407715	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	51272331	108407715	89614715	72	25488										
MYLK	4638	hgsc.bcm.edu	37	chr3	123419013	123419013	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gaacatcttgcagcttctgcTtgaaggctggggctgtcccc	12	12	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:123419013T>A	ENST00000475616.1	-	15	3301	c.3302A>T	c.(3301-3303)aAg>aTg	p.K1101M	MYLK_ENST00000346322.5_Missense_Mutation_p.K1032M|MYLK_ENST00000360772.3_Missense_Mutation_p.K1101M|MYLK_ENST00000510775.1_5'Flank|MYLK_ENST00000359169.1_Missense_Mutation_p.K1101M|MYLK_ENST00000360304.3_Missense_Mutation_p.K1101M			Q15746	MYLK_HUMAN	myosin light chain kinase	1101	Actin-binding (calcium/calmodulin- insensitive). {ECO:0000250}.|Ig-like C2-type 7.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CAGCTTCTGCTTGAAGGCTGG	0.532																																					p.K1101M		Atlas-SNP	.											.	MYLK	224	.	0			c.A3302T						.						116	116	116					3																	123419013		2203	4300	6503	SO:0001583	missense	4638	exon18			TTCTGCTTGAAGG	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7590	protein-coding gene	gene with protein product	"smooth muscle myosin light chain kinase"	600922	"myosin, light polypeptide kinase"			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.3302A>T	chr3.hg19:g.123419013T>A	ENSP00000418335:p.Lys1101Met	71.0	0.0		38.0	20.0	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	hg19	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	T	7.309	0.614676	0.14129	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	5.76	-3.31	0.04988	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.28732	0.0712	L	0.31157	0.91	0.58432	D	0.999999	B;B;B;B;B;B	0.27117	0.004;0.014;0.168;0.021;0.046;0.006	B;B;B;B;B;B	0.26094	0.017;0.017;0.066;0.046;0.045;0.029	T	0.12477	-1.0546	9	0.45353	T	0.12	.	13.1922	0.59717	0.0969:0.0:0.7089:0.1942	.	1101;179;1032;1101;1032;1101	Q15746-6;Q15746-7;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;.;MYLK_HUMAN	M	1101;1101;1101;1032;1101	ENSP00000354004:K1101M;ENSP00000353452:K1101M;ENSP00000352088:K1101M;ENSP00000320622:K1032M;ENSP00000418335:K1101M	ENSP00000320622:K1032M	K	-	2	0	MYLK	124901703	0.997000	0.39634	0.974000	0.42286	0.029000	0.11900	1.169000	0.31871	-0.182000	0.10602	0.454000	0.30748	AAG	.	.		0.532	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		A	123419013	T	A	123419013	3	1	168	1	0	0	0	0	1	0	0	0	10065	1609	56	4	2510	4	MYLK	3	123419013	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	15011298	123419013	74603417	73	25489										
RPN1	6184	hgsc.bcm.edu	37	chr3	128356921	128356921	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gccccaggatcaagagcaacTgggagcttgactgtgaagaa	13	9	1	4			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:128356921T>A	ENST00000296255.3	-	3	402	c.354A>T	c.(352-354)ccA>ccT	p.P118P	RPN1_ENST00000497289.1_5'UTR	NM_002950.3	NP_002941.1	P04843	RPN1_HUMAN	ribophorin I	118					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|stomach(2)	13				GBM - Glioblastoma multiforme(114;0.189)		CAAGAGCAACTGGGAGCTTGA	0.458			T	EVI1	AML																																p.P118P		Atlas-SNP	.		Dom	yes		3	3q21.3-q25.2	6184	ribophorin I		L	.	RPN1	39	.	0			c.A354T						.						85	77	79					3																	128356921		2203	4300	6503	SO:0001819	synonymous_variant	6184	exon3			AGCAACTGGGAGC		CCDS3051.1	3q21.3	2013-03-06			ENSG00000163902	ENSG00000163902			10381	protein-coding gene	gene with protein product	"oligosaccharyltransferase 1 homolog (S. cerevisiae)", "oligosaccharyltransferase complex subunit (non-catalytic)"	180470					Standard	NM_002950		Approved	OST1	uc003ekr.1	P04843	OTTHUMG00000159691	ENST00000296255.3:c.354A>T	chr3.hg19:g.128356921T>A		112.0	0.0		84.0	43.0	NM_002950	B2R5Z0|D3DNB6|Q68DT1	Silent	SNP	ENST00000296255.3	hg19	CCDS3051.1																																																																																			.	.		0.458	RPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356934.2	NM_002950		A	128356921	T	A	128356921	2	1	168	1	0	0	0	0	0	0	0	1	13622	1567	55	4		4	RPN1	3	128356921	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	4937908	128356921	69665509	74	25490										
ATR	545	hgsc.bcm.edu	37	chr3	142268433	142268433	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctctacgattgacatttaatTgttttcctaaagttcgaatg	6	7	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:142268433T>A	ENST00000350721.4	-	15	3180	c.3059A>T	c.(3058-3060)cAa>cTa	p.Q1020L	ATR_ENST00000383101.3_Missense_Mutation_p.Q956L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1020					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GACATTTAATTGTTTTCCTAA	0.358								Other conserved DNA damage response genes																													p.Q1020L		Atlas-SNP	.											.	ATR	285	.	0			c.A3059T						.						49	51	50					3																	142268433		2199	4299	6498	SO:0001583	missense	545	exon15			TTTAATTGTTTTC	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.3059A>T	chr3.hg19:g.142268433T>A	ENSP00000343741:p.Gln1020Leu	478.0	0.0		389.0	176.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	T	11.82	1.751559	0.31046	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.55930	0.49;0.49	5.59	5.59	0.84812	Armadillo-like helical (1);Armadillo-type fold (1);	0.122584	0.56097	D	0.000034	T	0.36468	0.0968	N	0.19112	0.55	0.58432	D	0.999999	B	0.18863	0.031	B	0.13407	0.009	T	0.20075	-1.0286	10	0.13108	T	0.6	-16.7171	14.3368	0.66595	0.0:0.0:0.0:1.0	.	1020	Q13535	ATR_HUMAN	L	1020;956	ENSP00000343741:Q1020L;ENSP00000372581:Q956L	ENSP00000343741:Q1020L	Q	-	2	0	ATR	143751123	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.523000	0.81856	2.129000	0.65627	0.533000	0.62120	CAA	.	.		0.358	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142268433	T	A	142268433	3	1	168	1	0	0	0	0	1	0	0	0	1204	1812	63	4	5007	4	ATR	3	142268433	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	13911512	142268433	55753997	75	25491										
CPB1	1360	hgsc.bcm.edu	37	chr3	148558490	148558490	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cagggtactgataagcaaccTgagaaatgtggtggaggctc	14	7	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:148558490T>A	ENST00000491148.1	+	5	624	c.290T>A	c.(289-291)cTg>cAg	p.L97Q	CPB1_ENST00000282957.4_Missense_Mutation_p.L97Q			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	97						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			ATAAGCAACCTGAGAAATGTG	0.458																																					p.L97Q		Atlas-SNP	.											.	CPB1	74	.	0			c.T290A						.						150	153	152					3																	148558490		2203	4300	6503	SO:0001583	missense	1360	exon4			GCAACCTGAGAAA	AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase B", "tissue carboxypeptidase B", "protaminase"	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.290T>A	chr3.hg19:g.148558490T>A	ENSP00000417222:p.Leu97Gln	168.0	0.0		153.0	65.0	NM_001871	O60834|Q53XJ0|Q96BQ8	Missense_Mutation	SNP	ENST00000491148.1	hg19	CCDS33874.1	.	.	.	.	.	.	.	.	.	.	T	14.00	2.405243	0.42613	.	.	ENSG00000153002	ENST00000491148;ENST00000462345;ENST00000282957;ENST00000468341	T;T;T;T	0.21191	2.02;2.02;2.02;2.02	5.15	5.15	0.70609	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.157745	0.43747	D	0.000522	T	0.49098	0.1537	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.55698	-0.8100	10	0.87932	D	0	.	15.0077	0.71524	0.0:0.0:0.0:1.0	.	97	P15086	CBPB1_HUMAN	Q	97	ENSP00000417222:L97Q;ENSP00000417117:L97Q;ENSP00000282957:L97Q;ENSP00000419427:L97Q	ENSP00000282957:L97Q	L	+	2	0	CPB1	150041180	1.000000	0.71417	0.977000	0.42913	0.093000	0.18481	7.422000	0.80217	1.934000	0.56057	0.533000	0.62120	CTG	.	.		0.458	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871		A	148558490	T	A	148558490	3	1	168	1	0	0	0	0	1	0	0	0	3798	1580	55	4	304	4	CPB1	3	148558490	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	6290057	148558490	49463940	76	25492										
LAMP3	27074	hgsc.bcm.edu	37	chr3	182871558	182871558	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gaacctgataaattccagtcTtgactgacgatggctgaggt	11	8	1	4			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr3:182871558T>A	ENST00000265598.3	-	2	926	c.671A>T	c.(670-672)aAg>aTg	p.K224M	LAMP3_ENST00000466939.1_Missense_Mutation_p.K200M	NM_014398.3	NP_055213.2	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	224					cell proliferation (GO:0008283)|immune system process (GO:0002376)	alveolar lamellar body membrane (GO:0097233)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(2)	28	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			AATTCCAGTCTTGACTGACGA	0.547																																					p.K224M		Atlas-SNP	.											.	LAMP3	48	.	0			c.A671T						.						106	100	102					3																	182871558		2203	4300	6503	SO:0001583	missense	27074	exon2			CCAGTCTTGACTG	AB013924	CCDS3242.1	3q26.3-q27	2011-11-24			ENSG00000078081	ENSG00000078081		"CD molecules"	14582	protein-coding gene	gene with protein product		605883				9721848	Standard	NM_014398		Approved	LAMP, TSC403, DC-LAMP, DCLAMP, CD208	uc003flh.4	Q9UQV4	OTTHUMG00000158387	ENST00000265598.3:c.671A>T	chr3.hg19:g.182871558T>A	ENSP00000265598:p.Lys224Met	122.0	0.0		125.0	52.0	NM_014398	D3DNS4|O94781|Q8NEC8	Missense_Mutation	SNP	ENST00000265598.3	hg19	CCDS3242.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.125473	0.56721	.	.	ENSG00000078081	ENST00000265598;ENST00000466939	T;T	0.34472	1.36;1.36	5.81	1.96	0.26148	.	0.496664	0.20344	N	0.094173	T	0.50480	0.1618	M	0.70595	2.14	0.09310	N	1	D	0.76494	0.999	D	0.70716	0.97	T	0.33420	-0.9869	10	0.66056	D	0.02	-5.1605	4.398	0.11372	0.0:0.173:0.1687:0.6582	.	224	Q9UQV4	LAMP3_HUMAN	M	224;200	ENSP00000265598:K224M;ENSP00000418912:K200M	ENSP00000265598:K224M	K	-	2	0	LAMP3	184354252	0.429000	0.25530	0.415000	0.26534	0.029000	0.11900	0.656000	0.24948	0.468000	0.27243	-0.256000	0.11100	AAG	.	.		0.547	LAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350863.1			A	182871558	T	A	182871558	3	1	168	1	0	0	0	0	1	0	0	0	8628	1609	56	4	599	4	LAMP3	3	182871558	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	34313068	182871558	15150872	77	25493										
EVC2	132884	hgsc.bcm.edu	37	chr4	5570231	5570231	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tctcagctgcgtggtccacaTgtctctcggtggccgaatcc	11	14	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr4:5570231T>A	ENST00000344408.5	-	20	3550	c.3497A>T	c.(3496-3498)cAt>cTt	p.H1166L	EVC2_ENST00000344938.1_Missense_Mutation_p.H1166L|EVC2_ENST00000310917.2_Missense_Mutation_p.H1086L	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	1166					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						GTGGTCCACATGTCTCTCGGT	0.701																																					p.H1166L		Atlas-SNP	.											.	EVC2	202	.	0			c.A3497T						.						25	25	25					4																	5570231		2200	4298	6498	SO:0001583	missense	132884	exon20			TCCACATGTCTCT	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.3497A>T	chr4.hg19:g.5570231T>A	ENSP00000342144:p.His1166Leu	81.0	0.0		81.0	40.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	T	9.678	1.148655	0.21288	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74632	-0.85;-0.85;-0.86	5.0	5.0	0.66597	.	0.701841	0.14452	N	0.318727	T	0.61098	0.2320	L	0.27053	0.805	0.18873	N	0.999984	B	0.29716	0.255	B	0.22152	0.038	T	0.56312	-0.8000	10	0.54805	T	0.06	-15.7781	11.0918	0.48121	0.0:0.0:0.0:1.0	.	1166	Q86UK5	LBN_HUMAN	L	1166;1086;1166	ENSP00000339954:H1166L;ENSP00000311683:H1086L;ENSP00000342144:H1166L	ENSP00000311683:H1086L	H	-	2	0	EVC2	5621132	0.632000	0.27172	0.049000	0.19019	0.003000	0.03518	2.239000	0.43079	1.886000	0.54624	0.334000	0.21626	CAT	.	.		0.701	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		A	5570231	T	A	5570231	3	1	168	1	0	0	0	0	1	0	0	0	5288	1464	51	4	441	4	EVC2	4	5570231	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10		5570231	185584045	78	25494										
CRMP1	1400	hgsc.bcm.edu	37	chr4	5868428	5868428	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cctccaggtagacgtcagcaTaaagggattggtcatcgttg	12	9	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr4:5868428T>A	ENST00000397890.2	-	2	309	c.95A>T	c.(94-96)tAt>tTt	p.Y32F	CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000324989.7_Missense_Mutation_p.Y146F|CRMP1_ENST00000512574.1_Missense_Mutation_p.Y30F	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	32					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		GACGTCAGCATAAAGGGATTG	0.483																																					p.Y146F		Atlas-SNP	.											.	CRMP1	118	.	0			c.A437T						.						153	132	139					4																	5868428		2203	4300	6503	SO:0001583	missense	1400	exon2			TCAGCATAAAGGG	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.95A>T	chr4.hg19:g.5868428T>A	ENSP00000380987:p.Tyr32Phe	118.0	0.0		115.0	48.0	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	hg19	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.649880	0.29336	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	D;D;D	0.85339	-1.97;-1.95;-1.95	3.96	3.96	0.45880	Metal-dependent hydrolase, composite domain (1);	0.000000	0.64402	D	0.000001	T	0.79793	0.4507	L	0.52823	1.66	0.46981	D	0.999273	B;B;B	0.25312	0.002;0.027;0.123	B;B;B	0.26693	0.014;0.012;0.072	T	0.73023	-0.4113	10	0.11794	T	0.64	-12.1897	12.1777	0.54194	0.0:0.0:0.0:1.0	.	146;30;32	A0EJG6;E9PD68;Q14194	.;.;DPYL1_HUMAN	F	146;32;32;30	ENSP00000321606:Y146F;ENSP00000380987:Y32F;ENSP00000425742:Y30F	ENSP00000321606:Y146F	Y	-	2	0	CRMP1	5919329	1.000000	0.71417	0.972000	0.41901	0.942000	0.58702	3.518000	0.53451	1.659000	0.50751	0.460000	0.39030	TAT	.	.		0.483	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		A	5868428	T	A	5868428	3	1	168	1	0	0	0	0	1	0	0	0	3892	1406	49	4	1675	4	CRMP1	4	5868428	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	298197	5868428	185285848	79	25495										
CHRNA9	55584	hgsc.bcm.edu	37	chr4	40351387	40351387	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	catgactgtatttcagctaaTggtggcagaaatcatgccgg	11	8	2	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr4:40351387T>C	ENST00000310169.2	+	4	993	c.854T>C	c.(853-855)aTg>aCg	p.M285T		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	285					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|inner ear morphogenesis (GO:0042472)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine-activated cation-selective channel activity (GO:0004889)|calcium channel activity (GO:0005262)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(4)|stomach(1)	33					Galantamine(DB00674)|Nicotine(DB00184)	TTTCAGCTAATGGTGGCAGAA	0.522																																					p.M285T	Esophageal Squamous(115;1297 1602 22235 25158 43327)	Atlas-SNP	.											.	CHRNA9	53	.	0			c.T854C						.						91	97	95					4																	40351387		2203	4300	6503	SO:0001583	missense	55584	exon4			AGCTAATGGTGGC	AF227732	CCDS3459.1	4p14	2012-02-11	2012-02-07		ENSG00000174343	ENSG00000174343		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	14079	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 9 (neuronal)"	605116	"cholinergic receptor, nicotinic, alpha polypeptide 9"				Standard	NM_017581		Approved	NACHRA9	uc003gva.2	Q9UGM1	OTTHUMG00000099375	ENST00000310169.2:c.854T>C	chr4.hg19:g.40351387T>C	ENSP00000312663:p.Met285Thr	202.0	0.0		157.0	54.0	NM_017581	Q14CY7|Q4W5A2|Q9NYV2	Missense_Mutation	SNP	ENST00000310169.2	hg19	CCDS3459.1	.	.	.	.	.	.	.	.	.	.	T	15.31	2.794675	0.50102	.	.	ENSG00000174343	ENST00000310169	D	0.85013	-1.93	5.6	5.6	0.85130	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.90683	0.7077	M	0.74467	2.265	0.80722	D	1	P	0.52316	0.952	P	0.57846	0.828	D	0.91834	0.5478	10	0.87932	D	0	.	15.7833	0.78281	0.0:0.0:0.0:1.0	.	285	Q9UGM1	ACHA9_HUMAN	T	285	ENSP00000312663:M285T	ENSP00000312663:M285T	M	+	2	0	CHRNA9	40046144	1.000000	0.71417	0.997000	0.53966	0.820000	0.46376	8.040000	0.89188	2.133000	0.65898	0.459000	0.35465	ATG	.	.		0.522	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1			C	40351387	T	C	40351387	3	2	168	1	0	0	0	0	1	0	0	0	3391	1464	51	2	868	2	CHRNA9	4	40351387	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	34482959	40351387	150802889	80	25496										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55127497	55127497	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agtgcctcggcggcccacacAgggttgtacacttgctatta	11	12	0	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr4:55127497A>T	ENST00000257290.5	+	3	616	c.285A>T	c.(283-285)acA>acT	p.T95T	PDGFRA_ENST00000508170.1_Silent_p.T95T|FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	95	Ig-like C2-type 1.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	CGGCCCACACAGGGTTGTACA	0.498			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.T95T	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	.	PDGFRA	1583	.	0			c.A285T						.						183	188	187					4																	55127497		2203	4300	6503	SO:0001819	synonymous_variant	5156	exon3	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	CCACACAGGGTTG	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.285A>T	chr4.hg19:g.55127497A>T		114.0	0.0		116.0	51.0	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	hg19	CCDS3495.1																																																																																			.	.		0.498	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		T	55127497	A	T	55127497	2	4	168	1	0	0	0	0	0	0	0	1	11670	175	7	4		4	PDGFRA	4	55127497	Silent	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	14776110	55127497	136026779	81	25497										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85678264	85678264	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	aaaatgacaagcatctcggtTaatctccctgaccgtcgatc	7	12	2	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr4:85678264T>A	ENST00000295888.4	-	33	5646	c.5239A>T	c.(5239-5241)Aac>Tac	p.N1747Y	WDFY3_ENST00000322366.6_Missense_Mutation_p.N1747Y	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1747					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GCATCTCGGTTAATCTCCCTG	0.448																																					p.N1747Y		Atlas-SNP	.											.	WDFY3	314	.	0			c.A5239T						.						139	130	133					4																	85678264		2203	4300	6503	SO:0001583	missense	23001	exon33			CTCGGTTAATCTC	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.5239A>T	chr4.hg19:g.85678264T>A	ENSP00000295888:p.Asn1747Tyr	218.0	0.0		165.0	76.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.683762	0.88639	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.66460	-0.2;-0.21	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.79197	0.4405	M	0.63843	1.955	0.80722	D	1	D	0.71674	0.998	D	0.64776	0.929	T	0.80876	-0.1186	10	0.72032	D	0.01	.	16.5582	0.84512	0.0:0.0:0.0:1.0	.	1747	Q8IZQ1	WDFY3_HUMAN	Y	1747	ENSP00000318466:N1747Y;ENSP00000295888:N1747Y	ENSP00000295888:N1747Y	N	-	1	0	WDFY3	85897288	1.000000	0.71417	1.000000	0.80357	0.734000	0.41952	8.040000	0.89188	2.308000	0.77769	0.533000	0.62120	AAC	.	.		0.448	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85678264	T	A	85678264	3	1	168	1	0	0	0	0	1	0	0	0	17285	1754	61	4	5485	4	WDFY3	4	85678264	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	30550767	85678264	105476012	82	25498										
PRSS12	8492	hgsc.bcm.edu	37	chr4	119256640	119256640	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ttttttaccatgggaaaagcTacacgtgacagcagctgcca	9	10	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr4:119256640T>A	ENST00000296498.3	-	3	1090	c.808A>T	c.(808-810)Agc>Tgc	p.S270C		NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	270	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						TGGGAAAAGCTACACGTGACA	0.388																																					p.S270C		Atlas-SNP	.											.	PRSS12	71	.	0			c.A808T						.						112	109	110					4																	119256640		2203	4300	6503	SO:0001583	missense	8492	exon3			AAAAGCTACACGT	AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"Serine peptidases / Serine peptidases"	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.808A>T	chr4.hg19:g.119256640T>A	ENSP00000296498:p.Ser270Cys	107.0	0.0		93.0	44.0	NM_003619	Q9UP16	Missense_Mutation	SNP	ENST00000296498.3	hg19	CCDS3709.1	.	.	.	.	.	.	.	.	.	.	T	17.91	3.505528	0.64410	.	.	ENSG00000164099	ENST00000296498	T	0.33865	1.39	5.96	4.79	0.61399	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.414871	0.30695	N	0.009078	T	0.49321	0.1550	M	0.93678	3.445	0.36671	D	0.878483	B	0.15930	0.015	B	0.16289	0.015	T	0.58103	-0.7695	10	0.66056	D	0.02	.	10.5696	0.45192	0.0:0.0723:0.0:0.9277	.	270	P56730	NETR_HUMAN	C	270	ENSP00000296498:S270C	ENSP00000296498:S270C	S	-	1	0	PRSS12	119476088	1.000000	0.71417	0.087000	0.20705	0.653000	0.38743	4.792000	0.62467	1.094000	0.41399	0.528000	0.53228	AGC	.	.		0.388	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2			A	119256640	T	A	119256640	3	1	168	1	0	0	0	0	1	0	0	0	12627	1522	53	4	1863	4	PRSS12	4	119256640	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	33578376	119256640	71897636	83	25499										
GUCY1A3	2982	hgsc.bcm.edu	37	chr4	156634263	156634263	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ttcataggttatggacctcaAaggccaaatgatctacattg	8	8	3	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr4:156634263A>T	ENST00000296518.7	+	7	1309	c.1100A>T	c.(1099-1101)aAa>aTa	p.K367I	GUCY1A3_ENST00000455639.2_Missense_Mutation_p.K367I|GUCY1A3_ENST00000513574.1_Missense_Mutation_p.K367I|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.K367I|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.K367I|GUCY1A3_ENST00000393832.3_Missense_Mutation_p.K109I|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.K367I			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	367					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		ATGGACCTCAAAGGCCAAATG	0.408																																					p.K367I		Atlas-SNP	.											.	GUCY1A3	133	.	0			c.A1100T						.						66	63	64					4																	156634263		2203	4300	6503	SO:0001583	missense	2982	exon7			ACCTCAAAGGCCA		CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.1100A>T	chr4.hg19:g.156634263A>T	ENSP00000296518:p.Lys367Ile	84.0	0.0		57.0	47.0	NM_001130687	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	hg19	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.619832	0.87460	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	D;D;D;D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.33;-3.33;-3.33;-3.33	6.03	6.03	0.97812	Haem NO binding associated (1);	0.000000	0.64402	D	0.000002	D	0.97526	0.9190	M	0.92923	3.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98400	1.0567	10	0.87932	D	0	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	367;367	B3KU69;Q02108	.;GCYA3_HUMAN	I	367;367;367;367;109;367;367	ENSP00000424361:K367I;ENSP00000421493:K367I;ENSP00000426968:K367I;ENSP00000412201:K367I;ENSP00000377418:K109I;ENSP00000296518:K367I;ENSP00000426040:K367I	ENSP00000296518:K367I	K	+	2	0	GUCY1A3	156853713	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.930000	0.92872	2.308000	0.77769	0.533000	0.62120	AAA	.	.		0.408	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			T	156634263	A	T	156634263	3	4	168	1	0	0	0	0	1	0	0	0	6903	14	1	4	1133	4	GUCY1A3	4	156634263	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	37377623	156634263	34520013	84	25500										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13737537	13737537	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggtaaagcaagttatcttctAgttccttcatccttcttttg	6	9	4	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr5:13737537A>T	ENST00000265104.4	-	66	11383	c.11279T>A	c.(11278-11280)cTa>cAa	p.L3760Q		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3760	AAA 5. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GTTATCTTCTAGTTCCTTCAT	0.398									Kartagener syndrome																												p.L3760Q		Atlas-SNP	.											.	DNAH5	868	.	0			c.T11279A						.						187	167	174					5																	13737537		2203	4300	6503	SO:0001583	missense	1767	exon66	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TCTTCTAGTTCCT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.11279T>A	chr5.hg19:g.13737537A>T	ENSP00000265104:p.Leu3760Gln	89.0	0.0		79.0	31.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	17.93	3.508454	0.64410	.	.	ENSG00000039139	ENST00000265104	T	0.70869	-0.52	5.68	5.68	0.88126	.	0.000000	0.64402	D	0.000001	D	0.89245	0.6660	H	0.96398	3.815	0.54753	D	0.99998	D	0.89917	1.0	D	0.97110	1.0	D	0.92603	0.6093	10	0.87932	D	0	.	15.9332	0.79683	1.0:0.0:0.0:0.0	.	3760	Q8TE73	DYH5_HUMAN	Q	3760	ENSP00000265104:L3760Q	ENSP00000265104:L3760Q	L	-	2	0	DNAH5	13790537	1.000000	0.71417	0.519000	0.27824	0.673000	0.39480	7.025000	0.76449	2.172000	0.68678	0.533000	0.62120	CTA	.	.		0.398	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13737537	A	T	13737537	3	4	168	1	0	0	0	0	1	0	0	0	4606	420	15	4	2651	4	DNAH5	5	13737537	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10		13737537	167177723	85	25501										
MYO10	4651	hgsc.bcm.edu	37	chr5	16779678	16779678	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	acttccctaaaggattcctgGtcactgattgtcttgtcttc	7	11	3	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr5:16779678G>C	ENST00000513610.1	-	9	1360	c.906C>G	c.(904-906)gaC>gaG	p.D302E		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	302	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						AGGATTCCTGGTCACTGATTG	0.323																																					p.D302E		Atlas-SNP	.											.	MYO10	198	.	0			c.C906G						.						100	92	95					5																	16779678		1821	4079	5900	SO:0001583	missense	4651	exon9			TTCCTGGTCACTG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.906C>G	chr5.hg19:g.16779678G>C	ENSP00000421280:p.Asp302Glu	302.0	1.0		197.0	84.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	hg19	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.975879	0.74360	.	.	ENSG00000145555	ENST00000513610;ENST00000513882	D;D	0.93307	-3.2;-3.2	5.91	2.75	0.32379	Myosin head, motor domain (2);	.	.	.	.	D	0.96620	0.8897	M	0.87381	2.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96735	0.9542	9	0.87932	D	0	.	13.0328	0.58851	0.2543:0.0:0.7457:0.0	.	302	Q9HD67	MYO10_HUMAN	E	302;313	ENSP00000421280:D302E;ENSP00000421309:D313E	ENSP00000421280:D302E	D	-	3	2	MYO10	16832678	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.474000	0.45154	0.848000	0.35191	0.655000	0.94253	GAC	.	.		0.323	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		C	16779678	G	C	16779678	3	2	168	1	0	0	0	0	1	0	0	0	10071	1252	44	4	5402	4	MYO10	5	16779678	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	3042141	16779678	164135582	86	25502										
MYO10	4651	hgsc.bcm.edu	37	chr5	16779718	16779718	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctacacatccagactgattcAagtagtggtagttttctggc	9	9	2	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr5:16779718A>T	ENST00000513610.1	-	9	1320	c.866T>A	c.(865-867)tTg>tAg	p.L289*		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	289	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						AGACTGATTCAAGTAGTGGTA	0.338																																					p.L289X		Atlas-SNP	.											.	MYO10	198	.	0			c.T866A						.						90	83	85					5																	16779718		1831	4071	5902	SO:0001587	stop_gained	4651	exon9			TGATTCAAGTAGT	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.866T>A	chr5.hg19:g.16779718A>T	ENSP00000421280:p.Leu289*	292.0	0.0		216.0	100.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Nonsense_Mutation	SNP	ENST00000513610.1	hg19	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	A	41	8.879256	0.98988	.	.	ENSG00000145555	ENST00000513610;ENST00000513882	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.3436	0.83110	1.0:0.0:0.0:0.0	.	.	.	.	X	289;300	.	ENSP00000421280:L289X	L	-	2	0	MYO10	16832718	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.619000	0.90938	2.269000	0.75478	0.533000	0.62120	TTG	.	.		0.338	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16779718	A	T	16779718	4	4	168	1	0	0	0	0	0	1	0	0	10071	131	5	4	5442	4	MYO10	5	16779718	Nonsense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	40	16779718	164135542	87	25503										
RAB3C	115827	hgsc.bcm.edu	37	chr5	58120945	58120945	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gtgtgacatggaagacgagcGggtcatctcaactgagcgag	15	8	2	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr5:58120945G>T	ENST00000282878.4	+	4	621	c.452G>T	c.(451-453)cGg>cTg	p.R151L		NM_138453.2	NP_612462.1	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family	151					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)	21		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		GAAGACGAGCGGGTCATCTCA	0.363																																					p.R151L		Atlas-SNP	.											.	RAB3C	47	.	0			c.G452T						.						101	91	94					5																	58120945		2203	4300	6503	SO:0001583	missense	115827	exon4			ACGAGCGGGTCAT	AY026936	CCDS3976.1	5q13	2008-02-05			ENSG00000152932	ENSG00000152932		"RAB, member RAS oncogene"	30269	protein-coding gene	gene with protein product		612829				12296628	Standard	NM_138453		Approved		uc003jrp.3	Q96E17	OTTHUMG00000097053	ENST00000282878.4:c.452G>T	chr5.hg19:g.58120945G>T	ENSP00000282878:p.Arg151Leu	455.0	0.0		349.0	142.0	NM_138453		Missense_Mutation	SNP	ENST00000282878.4	hg19	CCDS3976.1	.	.	.	.	.	.	.	.	.	.	G	36	5.631140	0.96682	.	.	ENSG00000152932	ENST00000282878	T	0.80304	-1.36	6.16	6.16	0.99307	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000018	D	0.93154	0.7820	H	0.94345	3.525	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	D	0.93783	0.7085	10	0.87932	D	0	-22.0607	20.8598	0.99761	0.0:0.0:1.0:0.0	.	151	Q96E17	RAB3C_HUMAN	L	151	ENSP00000282878:R151L	ENSP00000282878:R151L	R	+	2	0	RAB3C	58156702	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.832000	0.99423	2.937000	0.99478	0.650000	0.86243	CGG	.	.		0.363	RAB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214156.2	NM_138453		T	58120945	G	T	58120945	3	4	168	1	0	0	0	0	1	0	0	0	12948	1116	39	1	466	1	RAB3C	5	58120945	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	41341227	58120945	122794315	88	25504										
LOC153328	153328	hgsc.bcm.edu	37	chr5	135188296	135188296	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tccttccccctcgccagcatTgccgtctacaactccgtggt	7	18	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr5:135188296T>A	ENST00000420621.1	+	4	379	c.207T>A	c.(205-207)atT>atA	p.I69I	SLC25A48_ENST00000412661.2_Silent_p.I69I|SLC25A48_ENST00000274513.5_Silent_p.I69I|SLC25A48_ENST00000433282.2_Silent_p.I15I|SLC25A48_ENST00000425402.1_Intron			Q6ZT89	S2548_HUMAN	solute carrier family 25, member 48	69					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						TCGCCAGCATTGCCGTCTACA	0.632																																					p.I69I		Atlas-SNP	.											.	SLC25A48	37	.	0			c.T207A						.						132	141	138					5																	135188296		2039	4200	6239	SO:0001819	synonymous_variant	153328	exon4			CAGCATTGCCGTC		CCDS43366.2	5q31.1	2013-05-22			ENSG00000145832	ENSG00000145832		"Solute carriers"	30451	protein-coding gene	gene with protein product	"HCC-down-regulated mitochondrial carrier protein"					15322095, 19303656	Standard	NM_145282		Approved	FLJ44862, HDMCP	uc003lba.3	Q6ZT89	OTTHUMG00000157007	ENST00000420621.1:c.207T>A	chr5.hg19:g.135188296T>A		72.0	0.0		81.0	30.0	NM_145282	Q8TAV9	Silent	SNP	ENST00000420621.1	hg19																																																																																				.	.		0.632	SLC25A48-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_145282		A	135188296	T	A	135188296	2	1	168	1	0	0	0	0	0	0	0	1	8880	1800	63	4		4	LOC153328	5	135188296	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	77067351	135188296	45726964	89	25505										
PCDHGB1	56104	hgsc.bcm.edu	37	chr5	140730033	140730033	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	aaaactgcgggttagtgcagAggattatttcaacgttagtt	11	5	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr5:140730033A>T	ENST00000523390.1	+	1	206	c.206A>T	c.(205-207)gAg>gTg	p.E69V	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	69	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTAGTGCAGAGGATTATTTC	0.512											OREG0016856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E69V		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.A206T						.						92	90	91					5																	140730033		1874	4098	5972	SO:0001583	missense	56104	exon1			GTGCAGAGGATTA	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"Cadherins / Protocadherins : Clustered"	8708	other	protocadherin	"protocadherin gamma subfamily B, 1, isoform 2"	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.206A>T	chr5.hg19:g.140730033A>T	ENSP00000429273:p.Glu69Val	156.0	0.0	1658	125.0	58.0	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	hg19	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	17.15	3.316617	0.60524	.	.	ENSG00000254221	ENST00000523390	T	0.39406	1.08	5.52	5.52	0.82312	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.60379	0.2264	L	0.56340	1.77	0.26105	N	0.980769	D;D	0.69078	0.997;0.972	D;P	0.71184	0.972;0.824	T	0.55579	-0.8119	9	0.59425	D	0.04	.	15.6173	0.76778	1.0:0.0:0.0:0.0	.	69;69	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	V	69	ENSP00000429273:E69V	ENSP00000429273:E69V	E	+	2	0	PCDHGB1	140710217	0.052000	0.20516	0.968000	0.41197	0.987000	0.75469	3.049000	0.49869	2.225000	0.72522	0.460000	0.39030	GAG	.	.		0.512	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922		T	140730033	A	T	140730033	3	4	168	1	0	0	0	0	1	0	0	0	11571	304	11	4	208	4	PCDHGB1	5	140730033	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	5541737	140730033	40185227	90	25506										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141038013	141038013	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ccgcatctccagtacctggtTagtcagctcctcagcagtca	8	15	4	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr5:141038013T>A	ENST00000239440.4	-	25	3510	c.3445A>T	c.(3445-3447)Aac>Tac	p.N1149Y	ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000513878.1_Missense_Mutation_p.N811Y|ARAP3_ENST00000508305.1_Missense_Mutation_p.N980Y	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1149	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						AGTACCTGGTTAGTCAGCTCC	0.577																																					p.N1149Y		Atlas-SNP	.											.	ARAP3	139	.	0			c.A3445T						.						137	106	116					5																	141038013		2203	4300	6503	SO:0001583	missense	64411	exon25			CCTGGTTAGTCAG	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3445A>T	chr5.hg19:g.141038013T>A	ENSP00000239440:p.Asn1149Tyr	124.0	0.0		104.0	44.0	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	hg19	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.902169	0.72754	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.75050	-0.9;-0.9;-0.9	5.97	5.97	0.96955	Ras-association (2);	0.000000	0.85682	D	0.000000	D	0.82462	0.5042	M	0.71581	2.175	0.58432	D	0.999991	D;D;D	0.89917	0.983;1.0;1.0	D;D;D	0.97110	0.937;0.998;1.0	T	0.79232	-0.1888	10	0.05525	T	0.97	.	14.6802	0.69012	0.0:0.0:0.0:1.0	.	811;980;1149	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	Y	980;1149;811	ENSP00000421826:N980Y;ENSP00000239440:N1149Y;ENSP00000421468:N811Y	ENSP00000239440:N1149Y	N	-	1	0	ARAP3	141018197	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.165000	0.77544	2.288000	0.76882	0.533000	0.62120	AAC	.	.		0.577	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		A	141038013	T	A	141038013	3	1	168	1	0	0	0	0	1	0	0	0	840	1754	61	4	1225	4	ARAP3	5	141038013	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	307980	141038013	39877247	91	25507										
HMMR	3161	hgsc.bcm.edu	37	chr5	162917465	162917465	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	caaaacttcaagaggaattgAataaagttctaggtatcaaa	7	5	3	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr5:162917465A>T	ENST00000358715.3	+	17	2065	c.2029A>T	c.(2029-2031)Aat>Tat	p.N677Y	HMMR_ENST00000393915.4_Missense_Mutation_p.N678Y|RP11-80G7.1_ENST00000521666.1_RNA|HMMR_ENST00000432118.2_Missense_Mutation_p.N591Y|RP11-80G7.1_ENST00000514724.2_RNA|HMMR_ENST00000353866.3_Missense_Mutation_p.N662Y			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	677					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	AGAGGAATTGAATAAAGTTCT	0.328																																					p.N678Y		Atlas-SNP	.											.	HMMR	64	.	0			c.A2032T						.						66	72	70					5																	162917465		2203	4299	6502	SO:0001583	missense	3161	exon17			GAATTGAATAAAG	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"CD molecules"	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.2029A>T	chr5.hg19:g.162917465A>T	ENSP00000351554:p.Asn677Tyr	446.0	0.0		379.0	155.0	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	hg19	CCDS4362.1	.	.	.	.	.	.	.	.	.	.	A	12.36	1.913293	0.33815	.	.	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.08546	3.08;3.08;3.08;3.08;3.08	5.97	3.6	0.41247	.	0.233245	0.49916	D	0.000134	T	0.15998	0.0385	L	0.47716	1.5	0.25786	N	0.984678	B;D;B;B	0.67145	0.091;0.996;0.218;0.218	B;D;B;B	0.65874	0.039;0.939;0.055;0.055	T	0.06023	-1.0850	10	0.41790	T	0.15	-18.2886	5.6777	0.17757	0.7221:0.0:0.1445:0.1334	.	591;678;662;677	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	Y	563;662;678;654;591;677	ENSP00000400527:N563Y;ENSP00000185942:N662Y;ENSP00000377492:N678Y;ENSP00000402673:N591Y;ENSP00000351554:N677Y	ENSP00000185942:N662Y	N	+	1	0	HMMR	162850043	0.888000	0.30383	1.000000	0.80357	0.973000	0.67179	0.554000	0.23407	0.519000	0.28406	0.528000	0.53228	AAT	.	.		0.328	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484		T	162917465	A	T	162917465	3	4	168	1	0	0	0	0	1	0	0	0	7251	246	9	4	2098	4	HMMR	5	162917465	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	21879452	162917465	17997795	92	25508										
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178553054	178553054	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcggatggctttgggcttcgAgagggcggcacagaagccac	17	10	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr5:178553054A>T	ENST00000251582.7	-	18	2796	c.2695T>A	c.(2695-2697)Tcg>Acg	p.S899T		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	899	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		TTGGGCTTCGAGAGGGCGGCA	0.642																																					p.S899T		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.T2695A						.						82	81	81					5																	178553054		2203	4300	6503	SO:0001583	missense	9509	exon18			GCTTCGAGAGGGC	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.2695T>A	chr5.hg19:g.178553054A>T	ENSP00000251582:p.Ser899Thr	60.0	0.0		32.0	11.0	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	hg19	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	A	4.793	0.147376	0.09134	.	.	ENSG00000087116	ENST00000251582	T	0.52295	0.67	4.8	-4.0	0.04057	.	1.987270	0.02787	N	0.121612	T	0.20210	0.0486	N	0.04787	-0.16	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.07443	-1.0772	10	0.12103	T	0.63	.	1.7135	0.02896	0.2127:0.161:0.3918:0.2345	.	899	O95450	ATS2_HUMAN	T	899	ENSP00000251582:S899T	ENSP00000251582:S899T	S	-	1	0	ADAMTS2	178485660	0.002000	0.14202	0.000000	0.03702	0.201000	0.24016	-0.040000	0.12104	-0.825000	0.04290	-0.648000	0.03929	TCG	.	.		0.642	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		T	178553054	A	T	178553054	3	4	168	1	0	0	0	0	1	0	0	0	265	304	11	4	960	4	ADAMTS2	5	178553054	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	15635589	178553054	2362206	93	25509										
CDYL	9425	hgsc.bcm.edu	37	chr6	4937882	4937882	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctcagcgccgttggcagcgtCttctgttgtggacttgactt	12	11	3	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr6:4937882C>G	ENST00000328908.5	+	6	1325	c.1194C>G	c.(1192-1194)gtC>gtG	p.V398V	CDYL_ENST00000449732.2_Silent_p.V212V|CDYL_ENST00000472453.1_3'UTR|CDYL_ENST00000343762.5_Silent_p.V212V|CDYL_ENST00000397588.3_Silent_p.V344V			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	398					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		TTGGCAGCGTCTTCTGTTGTG	0.468																																					p.V344V		Atlas-SNP	.											.	CDYL	74	.	0			c.C1032G						.						98	94	95					6																	4937882		2203	4300	6503	SO:0001819	synonymous_variant	9425	exon4			CAGCGTCTTCTGT	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"CDY-like, autosomal", "testis-specific chromodomain Y-like protein"	603778	"chromodomain protein, Y chromosome-like"			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.1194C>G	chr6.hg19:g.4937882C>G		153.0	0.0		214.0	128.0	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Silent	SNP	ENST00000328908.5	hg19																																																																																				.	.		0.468	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		G	4937882	C	G	4937882	2	3	168	1	0	0	0	0	0	0	0	1	3187	900	32	4		4	CDYL	6	4937882	Silent	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10		4937882	166177185	94	25510										
RPP40	10799	hgsc.bcm.edu	37	chr6	4996253	4996253	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gtgattgtacacaaataagcTtttgccaccactgtgcttgg	9	9	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr6:4996253T>A	ENST00000380051.2	-	7	869	c.825A>T	c.(823-825)aaA>aaT	p.K275N	RPP40_ENST00000319533.5_Missense_Mutation_p.K252N|RPP40_ENST00000464646.1_Missense_Mutation_p.K215N	NM_006638.2	NP_006629.2	O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	275					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			NS(1)|breast(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	14	Ovarian(93;0.11)	all_hematologic(90;0.0895)				ACAAATAAGCTTTTGCCACCA	0.383																																					p.K275N		Atlas-SNP	.											.	RPP40	36	.	0			c.A825T						.						92	93	93					6																	4996253		2203	4300	6503	SO:0001583	missense	10799	exon7			ATAAGCTTTTGCC	U94317	CCDS34333.1, CCDS69040.1, CCDS75391.1	6p25.1	2012-05-21	2007-06-26	2004-03-19	ENSG00000124787	ENSG00000124787			20992	protein-coding gene	gene with protein product		606117	"ribonuclease P1", "ribonuclease P 40kDa subunit"	RNASEP1		9630247	Standard	NM_006638		Approved	bA428J1.3	uc003mwl.3	O75818	OTTHUMG00000014168	ENST00000380051.2:c.825A>T	chr6.hg19:g.4996253T>A	ENSP00000369391:p.Lys275Asn	154.0	0.0		214.0	52.0	NM_006638	Q5VX97|Q8WVK8	Missense_Mutation	SNP	ENST00000380051.2	hg19	CCDS34333.1	.	.	.	.	.	.	.	.	.	.	T	11.81	1.749992	0.30955	.	.	ENSG00000124787	ENST00000380051;ENST00000319533;ENST00000464646	T;T;T	0.42900	0.96;0.96;0.96	5.16	-1.38	0.09027	.	0.649635	0.16882	N	0.195646	T	0.11537	0.0281	L	0.46157	1.445	0.21604	N	0.999629	P;B	0.35272	0.493;0.408	B;B	0.37833	0.167;0.259	T	0.24368	-1.0162	10	0.21014	T	0.42	-5.7164	1.6421	0.02754	0.1346:0.308:0.1393:0.4181	.	252;275	O75818-2;O75818	.;RPP40_HUMAN	N	275;252;215	ENSP00000369391:K275N;ENSP00000317998:K252N;ENSP00000419431:K215N	ENSP00000317998:K252N	K	-	3	2	RPP40	4941252	0.046000	0.20272	0.005000	0.12908	0.812000	0.45895	0.069000	0.14552	-0.238000	0.09724	-0.313000	0.08912	AAA	.	.		0.383	RPP40-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039733.2	NM_006638		A	4996253	T	A	4996253	3	1	168	1	0	0	0	0	1	0	0	0	13629	1606	56	4	274	4	RPP40	6	4996253	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	58371	4996253	166118814	95	25511										
PHACTR1	221692	hgsc.bcm.edu	37	chr6	13053698	13053698	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gtaagtttgccaacctgggaAggattttcaagccttggaaa	11	7	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr6:13053698A>T	ENST00000379350.1	+	4	481	c.352A>T	c.(352-354)Agg>Tgg	p.R118W	PHACTR1_ENST00000332995.7_Missense_Mutation_p.R118W|PHACTR1_ENST00000457702.2_De_novo_Start_InFrame|PHACTR1_ENST00000379345.2_De_novo_Start_InFrame|PHACTR1_ENST00000482982.1_3'UTR			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	118					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			CAACCTGGGAAGGATTTTCAA	0.502																																					p.R118W		Atlas-SNP	.											.	PHACTR1	94	.	0			c.A352T						.						50	49	50					6																	13053698		1939	4143	6082	SO:0001583	missense	221692	exon5			CTGGGAAGGATTT	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"Phosphatase and actin regulators"	20990	protein-coding gene	gene with protein product		608723	"RPEL repeat containing 1"	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379350.1:c.352A>T	chr6.hg19:g.13053698A>T	ENSP00000368655:p.Arg118Trp	180.0	0.0		236.0	67.0	NM_030948	A8K1V2|Q3MJ93|Q5JSJ2	Missense_Mutation	SNP	ENST00000379350.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.2|24.2	4.505195|4.505195	0.85282|0.85282	.|.	.|.	ENSG00000112137|ENSG00000112137	ENST00000406205|ENST00000379350;ENST00000332995;ENST00000432934;ENST00000434977	.|T;T	.|0.49720	.|0.77;0.84	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|0.108141	.|0.64402	.|D	.|0.000016	T|T	0.54791|0.54791	0.1880|0.1880	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.999;0.999	.|D;D;D	.|0.81914	.|0.993;0.99;0.995	T|T	0.60188|0.60188	-0.7312|-0.7312	5|10	.|0.87932	.|D	.|0	-14.8727|-14.8727	15.4022|15.4022	0.74849|0.74849	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|118;118;118	.|E7ESR5;Q9C0D0;Q9C0D0-2	.|.;PHAR1_HUMAN;.	M|W	153|118;118;118;4	.|ENSP00000368655:R118W;ENSP00000329880:R118W	.|ENSP00000329880:R118W	K|R	+|+	2|1	0|2	PHACTR1|PHACTR1	13161684|13161684	0.998000|0.998000	0.40836|0.40836	0.959000|0.959000	0.39883|0.39883	0.996000|0.996000	0.88848|0.88848	3.764000|3.764000	0.55264|0.55264	2.242000|2.242000	0.73789|0.73789	0.496000|0.496000	0.49642|0.49642	AAG|AGG	.	.		0.502	PHACTR1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039876.1	XM_166420		T	13053698	A	T	13053698	3	4	168	1	0	0	0	0	1	0	0	0	11818	63	3	4	362	4	PHACTR1	6	13053698	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	8057445	13053698	158061369	96	25512										
NUP153	9972	hgsc.bcm.edu	37	chr6	17616802	17616802	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tggttaaatggaaagcccccCgagcctgaaggctgggctga	14	10	0	2	rs563893774	byFrequency	TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr6:17616802C>A	ENST00000262077.2	-	21	4298	c.4299G>T	c.(4297-4299)tcG>tcT	p.S1433S	NUP153_ENST00000537253.1_Silent_p.S1464S|RNU6-190P_ENST00000384154.1_RNA	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	1433					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			GAAAGCCCCCCGAGCCTGAAG	0.448																																					p.S1433S		Atlas-SNP	.											.	NUP153	116	.	0			c.G4299T						.						69	68	68					6																	17616802		2203	4300	6503	SO:0001819	synonymous_variant	9972	exon21			GCCCCCCGAGCCT	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"nucleoporin 153kD"			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.4299G>T	chr6.hg19:g.17616802C>A		111.0	0.0		94.0	34.0	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Silent	SNP	ENST00000262077.2	hg19	CCDS4541.1																																																																																			.	.		0.448	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			A	17616802	C	A	17616802	2	1	168	1	0	0	0	0	0	0	0	1	10764	639	23	1		1	NUP153	6	17616802	Silent	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	4563104	17616802	153498265	97	25513										
PPP1R11	6992	hgsc.bcm.edu	37	chr6	30035217	30035217	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcaggggctgggctgagcgaGaccgtcactgagacaacggt	17	10	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr6:30035217G>T	ENST00000376772.3	+	1	353	c.30G>T	c.(28-30)gaG>gaT	p.E10D	PPP1R11_ENST00000376763.1_5'Flank|PPP1R11_ENST00000376769.2_5'UTR|PPP1R11_ENST00000376773.1_Intron|PPP1R11_ENST00000376758.1_5'Flank|PPP1R11_ENST00000376765.2_5'Flank	NM_021959.2	NP_068778.1	O60927	PP1RB_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 11	10						cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)			lung(2)|ovary(1)|prostate(1)|skin(2)	6						GGCTGAGCGAGACCGTCACTG	0.632																																					p.E10D	Pancreas(185;1767 3918 43793)	Atlas-SNP	.											.	PPP1R11	10	.	0			c.G30T						.						57	55	56					6																	30035217		2203	4300	6503	SO:0001583	missense	6992	exon1			GAGCGAGACCGTC	X81003	CCDS4671.1	6p21.3	2012-04-17			ENSG00000204619	ENSG00000204619		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9285	protein-coding gene	gene with protein product		606670		TCTE5		9843442, 8781118	Standard	NM_021959		Approved	HCGV, Tctex5, HCG-V	uc003npb.3	O60927	OTTHUMG00000031260	ENST00000376772.3:c.30G>T	chr6.hg19:g.30035217G>T	ENSP00000365963:p.Glu10Asp	235.0	0.0		182.0	85.0	NM_021959		Missense_Mutation	SNP	ENST00000376772.3	hg19	CCDS4671.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.580058	0.65992	.	.	ENSG00000204619	ENST00000376772	.	.	.	5.15	4.28	0.50868	.	0.115123	0.64402	D	0.000020	T	0.17789	0.0427	L	0.27053	0.805	0.80722	D	1	P	0.34662	0.462	B	0.27887	0.084	T	0.05937	-1.0855	9	0.24483	T	0.36	-0.2413	9.3427	0.38089	0.0964:0.0:0.9036:0.0	.	10	O60927	PP1RB_HUMAN	D	10	.	ENSP00000365963:E10D	E	+	3	2	PPP1R11	30143196	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.622000	0.54217	1.395000	0.46643	0.643000	0.83706	GAG	.	.		0.632	PPP1R11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076557.3	NM_021959		T	30035217	G	T	30035217	3	4	168	1	0	0	0	0	1	0	0	0	12365	933	33	3	32	3	PPP1R11	6	30035217	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	12418415	30035217	141079850	98	25514										
SFTA2	389376	hgsc.bcm.edu	37	chr6	30899302	30899302	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	catggtgttgagatcttgcaTggtggagggtgacgctggtc	17	6	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr6:30899302T>C	ENST00000359086.3	-	3	278	c.200A>G	c.(199-201)cAt>cGt	p.H67R	Y_RNA_ENST00000516952.1_RNA	NM_205854.2	NP_995326.1	Q6UW10	SFTA2_HUMAN	surfactant associated 2	67						extracellular region (GO:0005576)				lung(2)	2						AGATCTTGCATGGTGGAGGGT	0.577																																					p.H67R		Atlas-SNP	.											.	SFTA2	6	.	0			c.A200G						.						116	85	96					6																	30899302		1508	2709	4217	SO:0001583	missense	389376	exon3			CTTGCATGGTGGA	AY102070	CCDS4691.1	6p21.3	2008-08-26	2008-08-26	2008-08-26	ENSG00000196260	ENSG00000196260			18386	protein-coding gene	gene with protein product			"surfactant associated protein G"	SFTPG			Standard	NM_205854		Approved		uc003nsf.3	Q6UW10	OTTHUMG00000031183	ENST00000359086.3:c.200A>G	chr6.hg19:g.30899302T>C	ENSP00000351989:p.His67Arg	119.0	0.0		92.0	31.0	NM_205854	A2ABK7|A2ACH1|B7ZCJ7	Missense_Mutation	SNP	ENST00000359086.3	hg19	CCDS4691.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.240857	0.39598	.	.	ENSG00000196260	ENST00000359086	T	0.46819	0.86	4.45	-1.22	0.09494	.	.	.	.	.	T	0.12944	0.0314	.	.	.	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.29119	-1.0022	8	0.56958	D	0.05	.	3.3092	0.07011	0.1764:0.3166:0.0:0.507	.	67	Q6UW10	SFTA2_HUMAN	R	67	ENSP00000351989:H67R	ENSP00000351989:H67R	H	-	2	0	SFTA2	31007281	0.006000	0.16342	0.014000	0.15608	0.634000	0.38068	-0.187000	0.09656	0.140000	0.18849	0.383000	0.25322	CAT	.	.		0.577	SFTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076360.2	NM_205854		C	30899302	T	C	30899302	3	2	168	1	0	0	0	0	1	0	0	0	14202	1464	51	2	40	2	SFTA2	6	30899302	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	864085	30899302	140215765	99	25515										
LCA5	167691	hgsc.bcm.edu	37	chr6	80196733	80196733	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctagtcagtcatctcagtgcTacttcttcaatttcatcttc	4	12	7	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr6:80196733T>A	ENST00000392959.1	-	9	2693	c.2082A>T	c.(2080-2082)gtA>gtT	p.V694V	LCA5_ENST00000369846.4_Silent_p.V694V	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	694					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		ATCTCAGTGCTACTTCTTCAA	0.289																																					p.V694V		Atlas-SNP	.											.	LCA5	71	.	0			c.A2082T						.						41	45	43					6																	80196733		2203	4298	6501	SO:0001819	synonymous_variant	167691	exon8			CAGTGCTACTTCT		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.2082A>T	chr6.hg19:g.80196733T>A		52.0	0.0		68.0	28.0	NM_001122769	E1P542|Q9BWX7	Silent	SNP	ENST00000392959.1	hg19	CCDS4990.1																																																																																			.	.		0.289	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		A	80196733	T	A	80196733	2	1	168	1	0	0	0	0	0	0	0	1	8665	1509	53	4		4	LCA5	6	80196733	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	49297431	80196733	90918334	100	25516										
BEND3	57673	hgsc.bcm.edu	37	chr6	107390113	107390113	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgcaagccccggaatggttgTactgcagccggaggttctcg	14	11	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr6:107390113T>A	ENST00000369042.1	-	4	2472	c.2282A>T	c.(2281-2283)tAc>tTc	p.Y761F	BEND3_ENST00000429433.2_Missense_Mutation_p.Y761F			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	761	BEN 4. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						GGAATGGTTGTACTGCAGCCG	0.632																																					p.Y761F		Atlas-SNP	.											.	BEND3	70	.	0			c.A2282T						.						50	52	51					6																	107390113		2203	4300	6503	SO:0001583	missense	57673	exon5			TGGTTGTACTGCA	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"BEN domain containing"	23040	protein-coding gene	gene with protein product			"KIAA1553"	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.2282A>T	chr6.hg19:g.107390113T>A	ENSP00000358038:p.Tyr761Phe	168.0	0.0		103.0	43.0	NM_001080450	A2RRH2|Q9HCL9	Missense_Mutation	SNP	ENST00000369042.1	hg19	CCDS34507.1	.	.	.	.	.	.	.	.	.	.	T	16.28	3.078890	0.55753	.	.	ENSG00000178409	ENST00000369042;ENST00000429433	T;T	0.49139	0.79;0.79	5.32	4.13	0.48395	BEN domain (2);	0.302382	0.32386	N	0.006165	T	0.27832	0.0685	N	0.20685	0.6	0.48236	D	0.999619	P	0.43662	0.814	P	0.49477	0.612	T	0.08700	-1.0709	10	0.41790	T	0.15	-0.007	12.2563	0.54625	0.0:0.0:0.1424:0.8576	.	761	Q5T5X7	BEND3_HUMAN	F	761	ENSP00000358038:Y761F;ENSP00000411268:Y761F	ENSP00000358038:Y761F	Y	-	2	0	BEND3	107496806	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.649000	0.83500	0.825000	0.34637	0.374000	0.22700	TAC	.	.		0.632	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913		A	107390113	T	A	107390113	3	1	168	1	0	0	0	0	1	0	0	0	1399	1638	57	4	208	4	BEND3	6	107390113	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	27193380	107390113	63724954	101	25517										
TAAR1	134864	hgsc.bcm.edu	37	chr6	132966654	132966654	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tcttcagcgcctttgaagttTagctccagaaagatcattcc	7	11	3	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr6:132966654T>A	ENST00000275216.1	-	1	488	c.489A>T	c.(487-489)ctA>ctT	p.L163L		NM_138327.1	NP_612200.1	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	163					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)	18	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)|Dextroamphetamine(DB01576)|Methamphetamine(DB01577)|Propylhexedrine(DB06714)	CTTTGAAGTTTAGCTCCAGAA	0.383																																					p.L163L		Atlas-SNP	.											.	TAAR1	41	.	0			c.A489T						.						65	68	67					6																	132966654		2202	4299	6501	SO:0001819	synonymous_variant	134864	exon1			GAAGTTTAGCTCC	AY180374	CCDS5158.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146399	ENSG00000146399		"GPCR / Class A : Trace amine associated receptors"	17734	protein-coding gene	gene with protein product		609333	"trace amine receptor 1"	TRAR1		11459929, 15718104	Standard	NM_138327		Approved	TAR1, TA1	uc003qdm.1	Q96RJ0	OTTHUMG00000015583	ENST00000275216.1:c.489A>T	chr6.hg19:g.132966654T>A		111.0	0.0		110.0	49.0	NM_138327	Q2M1W5|Q3MIH8|Q5VUQ1	Silent	SNP	ENST00000275216.1	hg19	CCDS5158.1																																																																																			.	.		0.383	TAAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042259.1	NM_138327		A	132966654	T	A	132966654	2	1	168	1	0	0	0	0	0	0	0	1	15504	1741	61	4		4	TAAR1	6	132966654	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	25576541	132966654	38148413	102	25518										
MAD1L1	8379	hgsc.bcm.edu	37	chr7	2020106	2020106	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	acctgagcgtgtccgcctccTccctggagaacaggaagctc	11	15	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr7:2020106T>A	ENST00000406869.1	-	15	2044	c.1487A>T	c.(1486-1488)gAg>gTg	p.E496V	MAD1L1_ENST00000402746.1_Missense_Mutation_p.E404V|MAD1L1_ENST00000399654.2_Missense_Mutation_p.E496V|MAD1L1_ENST00000265854.7_Missense_Mutation_p.E496V			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	496	Necessary for interaction with NEK2.				mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GTCCGCCTCCTCCCTGGAGAA	0.617																																					p.E496V		Atlas-SNP	.											.	MAD1L1	81	.	0			c.A1487T						.						31	34	33					7																	2020106		2024	4165	6189	SO:0001583	missense	8379	exon15			GCCTCCTCCCTGG	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.1487A>T	chr7.hg19:g.2020106T>A	ENSP00000385334:p.Glu496Val	62.0	0.0		66.0	25.0	NM_003550	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	hg19	CCDS43539.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.326960	0.41197	.	.	ENSG00000002822	ENST00000402746;ENST00000399654;ENST00000406869;ENST00000442131;ENST00000265854;ENST00000450235;ENST00000438959	T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06	5.09	5.09	0.68999	.	0.048976	0.85682	D	0.000000	T	0.57286	0.2043	M	0.66939	2.045	0.46542	D	0.999093	D;D;D	0.89917	1.0;0.996;0.995	D;D;P	0.71414	0.973;0.93;0.904	T	0.59815	-0.7383	10	0.54805	T	0.06	-34.8095	7.57	0.27902	0.0:0.0963:0.0:0.9037	.	495;404;496	A4D218;B3KR41;Q9Y6D9	.;.;MD1L1_HUMAN	V	404;496;496;47;496;47;163	ENSP00000384155:E404V;ENSP00000382562:E496V;ENSP00000385334:E496V;ENSP00000265854:E496V;ENSP00000394886:E47V;ENSP00000414877:E163V	ENSP00000265854:E496V	E	-	2	0	MAD1L1	1986632	1.000000	0.71417	0.994000	0.49952	0.140000	0.21249	2.512000	0.45485	1.918000	0.55548	0.533000	0.62120	GAG	.	.		0.617	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		A	2020106	T	A	2020106	3	1	168	1	0	0	0	0	1	0	0	0	9156	1551	54	4	689	4	MAD1L1	7	2020106	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10		2020106	157118557	103	25519										
AQP1	358	hgsc.bcm.edu	37	chr7	30961780	30961780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctactaccgaccggaggcgcCgtgaccttggtggctcagcc	13	15	1	1	rs546847577		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr7:30961780C>T	ENST00000311813.4	+	2	539	c.484C>T	c.(484-486)Cgt>Tgt	p.R162C	AQP1_ENST00000409899.1_Missense_Mutation_p.R47C|AQP1_ENST00000482461.1_3'UTR|AQP1_ENST00000434909.2_Missense_Mutation_p.R222C|AQP1_ENST00000441328.2_Missense_Mutation_p.R79C|AQP1_ENST00000509504.1_Missense_Mutation_p.R339C|AQP1_ENST00000409611.1_Missense_Mutation_p.R111C	NM_198098.2	NP_932766.1	P29972	AQP1_HUMAN	aquaporin 1 (Colton blood group)	162	Poly-Arg.				ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|camera-type eye morphogenesis (GO:0048593)|carbon dioxide transmembrane transport (GO:0035378)|carbon dioxide transport (GO:0015670)|cation transmembrane transport (GO:0098655)|cell volume homeostasis (GO:0006884)|cellular homeostasis (GO:0019725)|cellular hyperosmotic response (GO:0071474)|cellular response to cAMP (GO:0071320)|cellular response to copper ion (GO:0071280)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to inorganic substance (GO:0071241)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mercury ion (GO:0071288)|cellular response to nitric oxide (GO:0071732)|cellular response to retinoic acid (GO:0071300)|cellular response to salt stress (GO:0071472)|cellular response to stress (GO:0033554)|cellular response to UV (GO:0034644)|cerebrospinal fluid secretion (GO:0033326)|cGMP biosynthetic process (GO:0006182)|corticotropin secretion (GO:0051458)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|glomerular filtration (GO:0003094)|glycerol transport (GO:0015793)|hyperosmotic salinity response (GO:0042538)|lateral ventricle development (GO:0021670)|lipid digestion (GO:0044241)|maintenance of symbiont-containing vacuole by host (GO:0085018)|metanephric descending thin limb development (GO:0072220)|metanephric glomerulus vasculature development (GO:0072239)|metanephric proximal convoluted tubule segment 2 development (GO:0072232)|metanephric proximal straight tubule development (GO:0072230)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|nitric oxide transport (GO:0030185)|odontogenesis (GO:0042476)|pancreatic juice secretion (GO:0030157)|positive regulation of angiogenesis (GO:0045766)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of saliva secretion (GO:0046878)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|renal water absorption (GO:0070295)|renal water transport (GO:0003097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|secretory granule organization (GO:0033363)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)|transepithelial water transport (GO:0035377)|transmembrane transport (GO:0055085)|water transport (GO:0006833)|wound healing (GO:0042060)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|symbiont-containing vacuole (GO:0020003)	ammonium transmembrane transporter activity (GO:0008519)|carbon dioxide transmembrane transporter activity (GO:0035379)|glycerol transmembrane transporter activity (GO:0015168)|intracellular cGMP activated cation channel activity (GO:0005223)|nitric oxide transmembrane transporter activity (GO:0030184)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)|transmembrane transporter activity (GO:0022857)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			kidney(1)|large_intestine(2)|lung(9)	12		Melanoma(862;0.16)			Acetazolamide(DB00819)	CCGGAGGCGCCGTGACCTTGG	0.662													C|||	1	0.000199681	0	0	5008	,	,		14392	0		0	False		,,,				2504	0.001				p.R162C		Atlas-SNP	.											.	AQP1	38	.	0			c.C484T						.						69	62	65					7																	30961780		2203	4300	6503	SO:0001583	missense	358	exon2			AGGCGCCGTGACC	M77829	CCDS5431.1, CCDS55096.1, CCDS55097.1, CCDS55098.1	7p14	2014-07-19	2014-01-02		ENSG00000240583	ENSG00000240583		"Ion channels / Aquaporins", "Blood group antigens"	633	protein-coding gene	gene with protein product		107776	"Colton blood group", "aquaporin 1 (channel-forming integral protein, 28kDa)", "aquaporin 1 (channel-forming integral protein, 28kDa, CO blood group)", "aquaporin 1"	CO		1722319, 3166547	Standard	NM_198098		Approved	CHIP28		P29972	OTTHUMG00000023944	ENST00000311813.4:c.484C>T	chr7.hg19:g.30961780C>T	ENSP00000311165:p.Arg162Cys	41.0	0.0		59.0	30.0	NM_198098	B5BU39|E7EM69|E9PC21|F5GY19|Q8TBI5|Q8TDC1	Missense_Mutation	SNP	ENST00000311813.4	hg19	CCDS5431.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.413597	0.62511	.	.	ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000250424	ENST00000434909;ENST00000265298;ENST00000311813;ENST00000413400;ENST00000441328;ENST00000409899;ENST00000409611;ENST00000509504	D;D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23;-3.23	5.45	3.53	0.40419	Aquaporin-like (2);	0.281854	0.41605	D	0.000853	D	0.94647	0.8274	M	0.79011	2.435	0.58432	D	0.999999	D;D;B;D	0.89917	1.0;0.999;0.097;0.997	P;P;B;P	0.60068	0.868;0.825;0.051;0.526	D	0.93508	0.6850	10	0.59425	D	0.04	5.1726	5.7696	0.18245	0.3066:0.6014:0.0:0.092	.	222;111;47;162	B4E220;E7EM69;E9PC21;P29972	.;.;.;AQP1_HUMAN	C	222;67;162;147;79;47;111;339	ENSP00000395059:R222C;ENSP00000311165:R162C;ENSP00000405698:R79C;ENSP00000386712:R47C;ENSP00000387178:R111C;ENSP00000421315:R339C	ENSP00000265298:R67C	R	+	1	0	RP5-877J2.1;AQP1	30928305	0.025000	0.19082	0.987000	0.45799	0.485000	0.33311	1.438000	0.35002	1.309000	0.44985	0.561000	0.74099	CGT	.	.		0.662	AQP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215002.3	NM_000385		T	30961780	C	T	30961780	3	4	168	1	0	0	0	0	1	0	0	0	821	652	23	1	747	1	AQP1	7	30961780	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	28941674	30961780	128176883	104	25520										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81589122	81589122	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgaatattaagttggtgttcAtaagcttttctccatgaaag	8	5	2	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr7:81589122A>T	ENST00000356253.5	-	37	3281	c.3026T>A	c.(3025-3027)aTg>aAg	p.M1009K	CACNA2D1_ENST00000535308.1_Missense_Mutation_p.M209K|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.M997K			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	1009					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GTTGGTGTTCATAAGCTTTTC	0.343																																					p.M997K		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.T2990A						.						84	76	78					7																	81589122		2203	4300	6503	SO:0001583	missense	781	exon37			GTGTTCATAAGCT	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.3026T>A	chr7.hg19:g.81589122A>T	ENSP00000348589:p.Met1009Lys	59.0	0.0		54.0	22.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	hg19		.	.	.	.	.	.	.	.	.	.	A	11.75	1.732247	0.30684	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000535308	T;T;T	0.50548	0.74;0.74;0.74	5.46	5.46	0.80206	.	0.157946	0.56097	D	0.000025	T	0.38188	0.1031	L	0.44542	1.39	0.29956	N	0.819778	B;B	0.32010	0.351;0.002	B;B	0.32465	0.146;0.012	T	0.42766	-0.9432	10	0.38643	T	0.18	-20.2195	8.2288	0.31587	0.8805:0.0:0.1195:0.0	.	209;997	B7Z658;P54289-2	.;.	K	997;1016;1009;209	ENSP00000349320:M997K;ENSP00000348589:M1009K;ENSP00000443124:M209K	ENSP00000284088:M1016K	M	-	2	0	CACNA2D1	81427058	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	4.868000	0.63021	2.067000	0.61834	0.528000	0.53228	ATG	.	.		0.343	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				T	81589122	A	T	81589122	3	4	168	1	0	0	0	0	1	0	0	0	2550	217	8	4	297	4	CACNA2D1	7	81589122	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	50627342	81589122	77549541	105	25521										
SAMD9	54809	hgsc.bcm.edu	37	chr7	92734072	92734072	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tttgaccactccattgatgtTagactcaggatcaaactcca	6	11	2	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr7:92734072T>C	ENST00000379958.2	-	3	1608	c.1339A>G	c.(1339-1341)Aac>Gac	p.N447D		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	447						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			CCATTGATGTTAGACTCAGGA	0.373																																					p.N447D		Atlas-SNP	.											.	SAMD9	239	.	0			c.A1339G						.						49	47	48					7																	92734072		2203	4300	6503	SO:0001583	missense	54809	exon2			TGATGTTAGACTC	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1339A>G	chr7.hg19:g.92734072T>C	ENSP00000369292:p.Asn447Asp	87.0	0.0		72.0	31.0	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	hg19	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.535544	0.00942	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.13538	2.58;2.58	4.38	1.32	0.21799	.	2.427720	0.02851	N	0.129091	T	0.07234	0.0183	N	0.08118	0	0.19300	N	0.999976	B	0.02656	0.0	B	0.04013	0.001	T	0.30765	-0.9967	10	0.12103	T	0.63	2.5682	6.1562	0.20338	0.1505:0.6686:0.0:0.1809	.	447	Q5K651	SAMD9_HUMAN	D	447	ENSP00000369292:N447D;ENSP00000414529:N447D	ENSP00000369292:N447D	N	-	1	0	SAMD9	92572008	0.000000	0.05858	0.414000	0.26521	0.141000	0.21300	0.742000	0.26216	0.594000	0.29761	-0.237000	0.12165	AAC	.	.		0.373	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		C	92734072	T	C	92734072	3	2	168	1	0	0	0	0	1	0	0	0	13841	1754	61	2	3434	2	SAMD9	7	92734072	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	11144950	92734072	66404591	106	25522										
STAG3	10734	hgsc.bcm.edu	37	chr7	99798553	99798553	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agccagctagtagatttgctGactgaccgcttccagcagga	11	11	0	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr7:99798553G>C	ENST00000426455.1	+	19	2429	c.2022G>C	c.(2020-2022)ctG>ctC	p.L674L	STAG3_ENST00000394018.2_Silent_p.L616L|STAG3_ENST00000317296.5_Silent_p.L674L|STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000436886.2_3'UTR|GATS_ENST00000543273.1_RNA	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	674					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TAGATTTGCTGACTGACCGCT	0.587																																					p.L674L		Atlas-SNP	.											.	STAG3	121	.	0			c.G2022C						.						43	40	41					7																	99798553		2203	4300	6503	SO:0001819	synonymous_variant	10734	exon19			TTTGCTGACTGAC	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2022G>C	chr7.hg19:g.99798553G>C		146.0	0.0		138.0	24.0	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Silent	SNP	ENST00000426455.1	hg19	CCDS34703.1																																																																																			.	.		0.587	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		C	99798553	G	C	99798553	2	2	168	1	0	0	0	0	0	0	0	1	15259	1277	45	4		4	STAG3	7	99798553	Silent	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	7064481	99798553	59340110	107	25523										
MET	4233	hgsc.bcm.edu	37	chr7	116423438	116423438	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	taaagaatactatagtgtacAcaacaaaacaggtgcaaagc	7	7	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr7:116423438A>T	ENST00000318493.6	+	19	3954	c.3767A>T	c.(3766-3768)cAc>cTc	p.H1256L	MET_ENST00000539704.1_Missense_Mutation_p.H108L|MET_ENST00000397752.3_Missense_Mutation_p.H1238L			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TATAGTGTACACAACAAAACA	0.388			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.H1256L		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A3767T						.						97	94	95					7																	116423438		1869	4100	5969	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GTGTACACAACAA	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3767A>T	chr7.hg19:g.116423438A>T	ENSP00000317272:p.His1256Leu	128.0	0.0		139.0	58.0	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	A	17.12	3.309531	0.60414	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	D;D;D	0.81996	-1.56;-1.56;-1.56	5.46	5.46	0.80206	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84543	0.5495	N	0.17723	0.515	0.80722	D	1	D;D	0.76494	0.992;0.999	D;D	0.77004	0.923;0.989	D	0.85197	0.1013	10	0.40728	T	0.16	.	15.824	0.78683	1.0:0.0:0.0:0.0	.	1256;1238	P08581-2;P08581	.;MET_HUMAN	L	1238;1256;108	ENSP00000380860:H1238L;ENSP00000317272:H1256L;ENSP00000445020:H108L	ENSP00000317272:H1256L	H	+	2	0	MET	116210674	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.287000	0.95975	2.197000	0.70478	0.460000	0.39030	CAC	.	.		0.388	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116423438	A	T	116423438	3	4	168	1	0	0	0	0	1	0	0	0	9494	159	6	4	3837	4	MET	7	116423438	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	16624885	116423438	42715225	108	25524										
LEP	3952	hgsc.bcm.edu	37	chr7	127894673	127894673	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctaagagctgccacttgcccTgggccagtggcctggagacc	13	14	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr7:127894673T>A	ENST00000308868.4	+	3	412	c.361T>A	c.(361-363)Tgg>Agg	p.W121R		NM_000230.2	NP_000221.1	P41159	LEP_HUMAN	leptin	121					adipose tissue development (GO:0060612)|adult feeding behavior (GO:0008343)|bile acid metabolic process (GO:0008206)|bone mineralization involved in bone maturation (GO:0035630)|cellular response to L-ascorbic acid (GO:0071298)|cellular response to retinoic acid (GO:0071300)|central nervous system neuron development (GO:0021954)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|eating behavior (GO:0042755)|energy reserve metabolic process (GO:0006112)|fatty acid beta-oxidation (GO:0006635)|female pregnancy (GO:0007565)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process (GO:0006114)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|leptin-mediated signaling pathway (GO:0033210)|leukocyte tethering or rolling (GO:0050901)|negative regulation of apoptotic process (GO:0043066)|negative regulation of appetite (GO:0032099)|negative regulation of cartilage development (GO:0061037)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of glutamine transport (GO:2000486)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vasoconstriction (GO:0045906)|ovulation from ovarian follicle (GO:0001542)|placenta development (GO:0001890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of developmental growth (GO:0048639)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of ion transport (GO:0043270)|positive regulation of luteinizing hormone secretion (GO:0033686)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of blood pressure (GO:0008217)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis (GO:0006111)|regulation of insulin secretion (GO:0050796)|regulation of intestinal cholesterol absorption (GO:0030300)|regulation of lipoprotein lipid oxidation (GO:0060587)|regulation of steroid biosynthetic process (GO:0050810)|response to dietary excess (GO:0002021)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to vitamin E (GO:0033197)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)				endometrium(1)|large_intestine(2)|lung(5)	8						CCACTTGCCCTGGGCCAGTGG	0.592																																					p.W121R		Atlas-SNP	.											.	LEP	17	.	0			c.T361A						.						53	53	53					7																	127894673		2203	4300	6503	SO:0001583	missense	3952	exon3			TTGCCCTGGGCCA		CCDS5800.1	7q31	2008-03-06	2008-03-06		ENSG00000174697	ENSG00000174697			6553	protein-coding gene	gene with protein product		164160	"leptin (murine obesity homolog)", "leptin (obesity homolog, mouse)"	OBS, OB		1686014, 16932309	Standard	NM_000230		Approved		uc003vml.2	P41159	OTTHUMG00000157564	ENST00000308868.4:c.361T>A	chr7.hg19:g.127894673T>A	ENSP00000312652:p.Trp121Arg	77.0	0.0		50.0	27.0	NM_000230	O15158|Q56A88	Missense_Mutation	SNP	ENST00000308868.4	hg19	CCDS5800.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.802444	0.00611	.	.	ENSG00000174697	ENST00000308868	T	0.60920	0.15	5.76	-0.77	0.11005	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.927150	0.02354	N	0.076215	T	0.21227	0.0511	N	0.00960	-1.095	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30090	-0.9990	10	0.07030	T	0.85	-13.3965	0.5856	0.00719	0.2844:0.3457:0.1353:0.2346	.	121;121	A4D0Y8;P41159	.;LEP_HUMAN	R	121	ENSP00000312652:W121R	ENSP00000312652:W121R	W	+	1	0	LEP	127681909	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.110000	0.15437	0.014000	0.14944	-0.250000	0.11733	TGG	.	.		0.592	LEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349174.1			A	127894673	T	A	127894673	3	1	168	1	0	0	0	0	1	0	0	0	8736	1580	55	4	367	4	LEP	7	127894673	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	11471235	127894673	31243990	109	25525										
SSPO	23145	hgsc.bcm.edu	37	chr7	149488699	149488699	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgggccctggggccagggccGgagccgccgctgctccccac	16	18	0	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr7:149488699G>T	ENST00000378016.2	+	0	5150							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGCCAGGGCCGGAGCCGCCGC	0.731																																					p.R1717L		Atlas-SNP	.											.	.	.	.	0			c.G5150T						.						3	5	4					7																	149488699		1622	3649	5271			23145	exon34			AGGGCCGGAGCCG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149488699G>T		64.0	0.0		52.0	27.0	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.731	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149488699	G	T	149488699	1	4	168	0	1	0	0	0	0	0	0	0	15204	1116	39	1		1	SSPO	7	149488699	RNA	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	21594026	149488699	9649964	110	25526										
ADRB3	155	hgsc.bcm.edu	37	chr8	37821737	37821737	+	Nonstop_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgcttcttgtccttcaggccTaagaaactccccaagaagcc	7	14	2	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr8:37821737T>A	ENST00000345060.3	-	2	1721	c.1226A>T	c.(1225-1227)tAg>tTg	p.*409L	ADRB3_ENST00000520341.1_5'UTR	NM_000025.2	NP_000016.1	P13945	ADRB3_HUMAN	adrenoceptor beta 3	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|aging (GO:0007568)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|diet induced thermogenesis (GO:0002024)|eating behavior (GO:0042755)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|generation of precursor metabolites and energy (GO:0006091)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of MAPK cascade (GO:0043410)|response to antibiotic (GO:0046677)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta-adrenergic receptor activity (GO:0004939)|beta3-adrenergic receptor activity (GO:0015052)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)	9	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)		Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Bethanidine(DB00217)|Bopindolol(DB08807)|Bupranolol(DB08808)|Clenbuterol(DB01407)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Isoprenaline(DB01064)|Mephentermine(DB01365)|Mirabegron(DB08893)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Propranolol(DB00571)|Trimipramine(DB00726)	CCTTCAGGCCTAAGAAACTCC	0.502																																					p.X409L		Atlas-SNP	.											.	ADRB3	27	.	0			c.A1226T						.						73	73	73					8																	37821737		2203	4300	6503	SO:0001578	stop_lost	155	exon2			CAGGCCTAAGAAA	AY487247	CCDS6099.1	8p12	2012-08-08	2012-05-09			ENSG00000188778		"GPCR / Class A : Adrenoceptors : beta"	288	protein-coding gene	gene with protein product		109691	"adrenergic, beta-3-, receptor"			7898940, 15123695	Standard	NM_000025		Approved		uc003xkr.2	P13945		ENST00000345060.3:c.1226A>T	chr8.hg19:g.37821737T>A		128.0	0.0		58.0	45.0	NM_000025	Q4JFT4	Missense_Mutation	SNP	ENST00000345060.3	hg19	CCDS6099.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.673404	0.29693	.	.	ENSG00000188778	ENST00000345060	.	.	.	3.43	2.22	0.28083	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.9253	0.24412	0.0:0.0:0.2343:0.7657	.	.	.	.	L	409	.	.	X	-	2	0	ADRB3	37940894	0.004000	0.15560	0.009000	0.14445	0.930000	0.56654	0.360000	0.20250	0.656000	0.30886	0.482000	0.46254	TAG	.	.		0.502	ADRB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376826.1	NM_000025		A	37821737	T	A	37821737	4	1	168	1	0	0	0	0	0	0	0	0	342	1535	53	4	4	4	ADRB3	8	37821737	Nonstop_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10		37821737	108542285	111	25527										
CHRNB3	1142	hgsc.bcm.edu	37	chr8	42587110	42587110	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agggacggcgtgtactcctaTccctttatcacgtattcctt	8	12	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr8:42587110T>C	ENST00000289957.2	+	5	788	c.660T>C	c.(658-660)taT>taC	p.Y220Y		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	220					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	TGTACTCCTATCCCTTTATCA	0.473																																					p.Y220Y		Atlas-SNP	.											.	CHRNB3	74	.	0			c.T660C						.						104	106	105					8																	42587110		2203	4300	6503	SO:0001819	synonymous_variant	1142	exon5			CTCCTATCCCTTT	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.660T>C	chr8.hg19:g.42587110T>C		102.0	0.0		84.0	38.0	NM_000749	Q15827	Silent	SNP	ENST00000289957.2	hg19	CCDS6134.1																																																																																			.	.		0.473	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			C	42587110	T	C	42587110	2	2	168	1	0	0	0	0	0	0	0	1	3394	1442	50	2		2	CHRNB3	8	42587110	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	4765373	42587110	103776912	112	25528										
XKR4	114786	hgsc.bcm.edu	37	chr8	56436483	56436483	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agcaccctacggtccatctcCaacaaccgcagtgttgtcag	8	15	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr8:56436483C>A	ENST00000327381.6	+	3	1750	c.1650C>A	c.(1648-1650)tcC>tcA	p.S550S	RP11-628E19.2_ENST00000522918.1_RNA	NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	550						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GGTCCATCTCCAACAACCGCA	0.592																																					p.S550S		Atlas-SNP	.											.	XKR4	104	.	0			c.C1650A						.						66	67	67					8																	56436483		2203	4300	6503	SO:0001819	synonymous_variant	114786	exon3			CATCTCCAACAAC	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 4"				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.1650C>A	chr8.hg19:g.56436483C>A		99.0	0.0		77.0	35.0	NM_052898	Q96PZ8	Silent	SNP	ENST00000327381.6	hg19	CCDS34893.1																																																																																			.	.		0.592	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		A	56436483	C	A	56436483	2	1	168	1	0	0	0	0	0	0	0	1	17448	581	21	3		3	XKR4	8	56436483	Silent	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	13849373	56436483	89927539	113	25529										
ADHFE1	137872	hgsc.bcm.edu	37	chr8	67356642	67356642	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	atatggagcagcagttacaaAggaagtaggaatggcaagta	13	4	0	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr8:67356642A>T	ENST00000396623.3	+	4	216	c.185A>T	c.(184-186)aAg>aTg	p.K62M	ADHFE1_ENST00000415254.1_Missense_Mutation_p.K14M|ADHFE1_ENST00000496501.1_Intron|ADHFE1_ENST00000379385.4_Missense_Mutation_p.K62M	NM_144650.2	NP_653251.2	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	62					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|molecular hydrogen transport (GO:0015993)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacid-oxoacid transhydrogenase activity (GO:0047988)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	29		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			GCAGTTACAAAGGAAGTAGGA	0.378																																					p.K62M		Atlas-SNP	.											.	ADHFE1	83	.	0			c.A185T						.						100	98	99					8																	67356642		2203	4300	6503	SO:0001583	missense	137872	exon4			TTACAAAGGAAGT	AK056992	CCDS6190.2	8q12.3	2013-05-21			ENSG00000147576	ENSG00000147576	1.1.99.24	"Alcohol dehydrogenases"	16354	protein-coding gene	gene with protein product	"hydroxyacid-oxoacid transhydrogenase"	611083				12592711	Standard	NM_144650		Approved	ADHFe1, FLJ32430	uc003xwb.4	Q8IWW8	OTTHUMG00000150215	ENST00000396623.3:c.185A>T	chr8.hg19:g.67356642A>T	ENSP00000379865:p.Lys62Met	175.0	0.0		213.0	50.0	NM_144650	B4DTJ8|Q49A19|Q68CI7|Q6P2B6|Q96MF9	Missense_Mutation	SNP	ENST00000396623.3	hg19	CCDS6190.2	.	.	.	.	.	.	.	.	.	.	A	20.3	3.972577	0.74246	.	.	ENSG00000147576	ENST00000379385;ENST00000396623;ENST00000415254	T;T;T	0.46451	0.87;0.87;0.87	5.79	5.79	0.91817	Alcohol dehydrogenase, iron-type (1);	0.131924	0.64402	D	0.000002	T	0.64832	0.2634	M	0.79614	2.46	0.38529	D	0.948937	P	0.48834	0.916	P	0.61874	0.895	T	0.70310	-0.4907	10	0.62326	D	0.03	-11.3699	16.4237	0.83790	1.0:0.0:0.0:0.0	.	62	Q8IWW8	HOT_HUMAN	M	62;62;14	ENSP00000368695:K62M;ENSP00000379865:K62M;ENSP00000407115:K14M	ENSP00000368695:K62M	K	+	2	0	ADHFE1	67519196	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.519000	0.53458	2.338000	0.79540	0.533000	0.62120	AAG	.	.		0.378	ADHFE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316867.3	NM_144650		T	67356642	A	T	67356642	3	4	168	1	0	0	0	0	1	0	0	0	314	72	3	4	199	4	ADHFE1	8	67356642	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	10920159	67356642	79007380	114	25530										
EYA1	2138	hgsc.bcm.edu	37	chr8	72129021	72129021	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tccacaccgccccgtacaccAgttgccaaacataagttagc	6	16	0	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr8:72129021A>T	ENST00000340726.3	-	14	1905	c.1266T>A	c.(1264-1266)acT>acA	p.T422T	EYA1_ENST00000388742.4_Silent_p.T422T|EYA1_ENST00000303824.7_Silent_p.T416T|EYA1_ENST00000388743.2_Silent_p.T421T|EYA1_ENST00000388740.3_Silent_p.T389T|EYA1_ENST00000419131.1_Silent_p.T387T|EYA1_ENST00000388741.2_Silent_p.T388T	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	422					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			CCCGTACACCAGTTGCCAAAC	0.453																																					p.T422T		Atlas-SNP	.											.	EYA1	108	.	0			c.T1266A						.						146	132	137					8																	72129021		2203	4300	6503	SO:0001819	synonymous_variant	2138	exon14			TACACCAGTTGCC	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"Protein tyrosine phosphatases / Asp-based PTPs"	3519	protein-coding gene	gene with protein product		601653	"eyes absent (Drosophila) homolog 1", "eyes absent homolog 1 (Drosophila)"	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.1266T>A	chr8.hg19:g.72129021A>T		164.0	0.0		210.0	62.0	NM_000503	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Silent	SNP	ENST00000340726.3	hg19	CCDS34906.1																																																																																			.	.		0.453	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		T	72129021	A	T	72129021	2	4	168	1	0	0	0	0	0	0	0	1	5330	175	7	4		4	EYA1	8	72129021	Silent	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	4772379	72129021	74235001	115	25531										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125107154	125107154	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cagatgagacagtggagtctTatgaacacctggccctcaag	11	10	2	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr8:125107154T>C	ENST00000522917.1	+	35	4776	c.4570T>C	c.(4570-4572)Tat>Cat	p.Y1524H	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.Y1524H	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1524						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AGTGGAGTCTTATGAACACCT	0.483																																					p.Y1524H		Atlas-SNP	.											.	FER1L6	268	.	0			c.T4570C						.						97	90	92					8																	125107154		1899	4123	6022	SO:0001583	missense	654463	exon35			GAGTCTTATGAAC	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.4570T>C	chr8.hg19:g.125107154T>C	ENSP00000428280:p.Tyr1524His	147.0	0.0		101.0	39.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.274150	0.40194	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.61040	0.14;0.14	5.52	4.37	0.52481	.	0.000000	0.85682	U	0.000000	T	0.63780	0.2540	L	0.37897	1.145	0.40272	D	0.978291	D	0.89917	1.0	D	0.91635	0.999	T	0.59994	-0.7349	10	0.25106	T	0.35	-17.7278	11.3575	0.49623	0.0:0.0709:0.0:0.9291	.	1524	Q2WGJ9	FR1L6_HUMAN	H	1524	ENSP00000428280:Y1524H;ENSP00000381982:Y1524H	ENSP00000381982:Y1524H	Y	+	1	0	FER1L6	125176335	0.822000	0.29219	0.449000	0.26957	0.707000	0.40811	1.162000	0.31786	1.044000	0.40200	0.450000	0.29827	TAT	.	.		0.483	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		C	125107154	T	C	125107154	3	2	168	1	0	0	0	0	1	0	0	0	5823	1754	61	2	4704	2	FER1L6	8	125107154	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	52978133	125107154	21256868	116	25532										
FAM135B	51059	hgsc.bcm.edu	37	chr8	139323154	139323154	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	accttcaaggtcactcggatCtggtaatacctaagaaaaga	8	9	3	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr8:139323154C>G	ENST00000395297.1	-	3	257	c.87G>C	c.(85-87)caG>caC	p.Q29H		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	29										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TCACTCGGATCTGGTAATACC	0.478										HNSCC(54;0.14)																											p.Q29H		Atlas-SNP	.											.	FAM135B	423	.	0			c.G87C						.						74	71	72					8																	139323154		1920	4130	6050	SO:0001583	missense	51059	exon3			TCGGATCTGGTAA	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.87G>C	chr8.hg19:g.139323154C>G	ENSP00000378710:p.Gln29His	56.0	0.0		58.0	21.0	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	hg19	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631368	0.46944	.	.	ENSG00000147724	ENST00000395297;ENST00000160713;ENST00000520380	T	0.19938	2.11	5.01	2.16	0.27623	.	0.000000	0.52532	U	0.000072	T	0.15955	0.0384	L	0.46157	1.445	0.35994	D	0.836923	B	0.21821	0.061	B	0.23150	0.044	T	0.09640	-1.0665	10	0.51188	T	0.08	-3.9002	4.493	0.11822	0.0:0.6158:0.1867:0.1975	.	29	Q49AJ0	F135B_HUMAN	H	29	ENSP00000378710:Q29H	ENSP00000160713:Q29H	Q	-	3	2	FAM135B	139392336	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.892000	0.28322	0.783000	0.33636	0.591000	0.81541	CAG	.	.		0.478	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		G	139323154	C	G	139323154	3	3	168	1	0	0	0	0	1	0	0	0	5454	912	32	4	4205	4	FAM135B	8	139323154	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	14216000	139323154	7040868	117	25533										
C8orf31	286122	hgsc.bcm.edu	37	chr8	144126142	144126142	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gggagacacagaccccatccAggaaggggcacgagaccacg	14	13	0	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr8:144126142A>T	ENST00000395172.1	+	4	615	c.263A>T	c.(262-264)cAg>cTg	p.Q88L	C8orf31_ENST00000517653.1_3'UTR	NM_173687.2	NP_775958.1	Q8N9H6	CH031_HUMAN	chromosome 8 open reading frame 31	88										breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10	all_cancers(97;1.89e-10)|all_epithelial(106;8.73e-09)|Lung NSC(106;0.000161)|all_lung(105;0.000447)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GACCCCATCCAGGAAGGGGCA	0.632																																					p.Q88L		Atlas-SNP	.											.	C8orf31	18	.	0			c.A263T						.						77	69	72					8																	144126142		2203	4300	6503	SO:0001583	missense	286122	exon4			CCATCCAGGAAGG		CCDS6395.1	8q24.3	2012-04-11			ENSG00000177335	ENSG00000177335			26731	protein-coding gene	gene with protein product							Standard	NM_173687		Approved	FLJ37131	uc003yxp.1	Q8N9H6	OTTHUMG00000164771	ENST00000395172.1:c.263A>T	chr8.hg19:g.144126142A>T	ENSP00000378601:p.Gln88Leu	76.0	0.0		55.0	22.0	NM_173687	Q6GMU7	Missense_Mutation	SNP	ENST00000395172.1	hg19	CCDS6395.1	.	.	.	.	.	.	.	.	.	.	a	3.573	-0.087163	0.07097	.	.	ENSG00000177335	ENST00000395172	T	0.52754	0.65	1.77	0.837	0.18896	.	.	.	.	.	T	0.23572	0.0570	N	0.08118	0	0.09310	N	1	B	0.24186	0.099	B	0.17098	0.017	T	0.18713	-1.0328	9	0.87932	D	0	.	3.9384	0.09316	0.2469:0.0:0.7531:0.0	.	88	Q8N9H6	CH031_HUMAN	L	88	ENSP00000378601:Q88L	ENSP00000378601:Q88L	Q	+	2	0	C8orf31	144197517	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.377000	0.20552	0.296000	0.22592	-0.537000	0.04273	CAG	.	.		0.632	C8orf31-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380167.1	NM_173687		T	144126142	A	T	144126142	3	4	168	1	0	0	0	0	1	0	0	0	2422	188	7	4	273	4	C8orf31	8	144126142	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	4802988	144126142	2237880	118	25534										
TSTA3	7264	hgsc.bcm.edu	37	chr8	144696547	144696547	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cacgtggccatcctcgatgtTgaagttgtcgtggggcccga	14	11	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr8:144696547T>A	ENST00000425753.2	-	6	644	c.541A>T	c.(541-543)Aac>Tac	p.N181Y	TSTA3_ENST00000529064.1_Missense_Mutation_p.N181Y	NM_003313.3	NP_003304.1	Q13630	FCL_HUMAN	tissue specific transplantation antigen P35B	181					'de novo' GDP-L-fucose biosynthetic process (GO:0042351)|cytolysis (GO:0019835)|GDP-mannose metabolic process (GO:0019673)|leukocyte cell-cell adhesion (GO:0007159)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	coenzyme binding (GO:0050662)|electron carrier activity (GO:0009055)|GDP-4-dehydro-D-rhamnose reductase activity (GO:0042356)|GDP-L-fucose synthase activity (GO:0050577)|isomerase activity (GO:0016853)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			TCCTCGATGTTGAAGTTGTCG	0.647																																					p.N181Y		Atlas-SNP	.											.	TSTA3	23	.	0			c.A541T						.						142	126	131					8																	144696547		2203	4300	6503	SO:0001583	missense	7264	exon6			CGATGTTGAAGTT	U58766	CCDS6408.1	8q24.3	2012-02-22			ENSG00000104522	ENSG00000104522	1.1.1.271	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	12390	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 4E, member 1", "GDP-L-fucose synthase"	137020				7803801, 1348494, 19027726	Standard	NM_003313		Approved	FX, P35B, SDR4E1	uc003yzb.2	Q13630	OTTHUMG00000165159	ENST00000425753.2:c.541A>T	chr8.hg19:g.144696547T>A	ENSP00000398803:p.Asn181Tyr	97.0	0.0		65.0	25.0	NM_003313	B2R8Y7|D3DWK5|Q567Q9|Q9UDG7	Missense_Mutation	SNP	ENST00000425753.2	hg19	CCDS6408.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.211323	0.79240	.	.	ENSG00000104522	ENST00000529064;ENST00000425753;ENST00000529048;ENST00000533817	D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27	4.85	4.85	0.62838	NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1);	0.131866	0.64402	D	0.000002	D	0.96534	0.8869	M	0.90145	3.09	0.80722	D	1	B	0.33777	0.425	P	0.50934	0.654	D	0.97081	0.9784	10	0.72032	D	0.01	-28.8401	13.2624	0.60113	0.0:0.0:0.0:1.0	.	181	Q13630	FCL_HUMAN	Y	181	ENSP00000435386:N181Y;ENSP00000398803:N181Y;ENSP00000431587:N181Y;ENSP00000437012:N181Y	ENSP00000398803:N181Y	N	-	1	0	TSTA3	144767690	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.203000	0.58453	1.816000	0.52996	0.482000	0.46254	AAC	.	.		0.647	TSTA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382263.1	NM_003313		A	144696547	T	A	144696547	3	1	168	1	0	0	0	0	1	0	0	0	16689	1812	63	4	448	4	TSTA3	8	144696547	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	570405	144696547	1667475	119	25535										
DOCK8	81704	hgsc.bcm.edu	37	chr9	439312	439312	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cctgtcacctgacgaggatgGggtgtgcgcaggccagtact	15	11	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr9:439312G>T	ENST00000453981.1	+	40	5259	c.5147G>T	c.(5146-5148)gGg>gTg	p.G1716V	DOCK8_ENST00000469391.1_Missense_Mutation_p.G1616V|DOCK8_ENST00000432829.2_Missense_Mutation_p.G1648V|DOCK8_ENST00000382329.1_Missense_Mutation_p.G1183V			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1716	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		GACGAGGATGGGGTGTGCGCA	0.587																																					p.G1716V		Atlas-SNP	.											.	DOCK8	401	.	0			c.G5147T						.						88	81	83					9																	439312		2203	4300	6503	SO:0001583	missense	81704	exon40			AGGATGGGGTGTG	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.5147G>T	chr9.hg19:g.439312G>T	ENSP00000408464:p.Gly1716Val	115.0	0.0		90.0	40.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	21.1	4.103563	0.76983	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.20332	2.31;2.31;2.3;2.08	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.55242	0.1908	M	0.88906	2.99	0.80722	D	1	D;P;D	0.89917	1.0;0.937;1.0	D;P;D	0.85130	0.997;0.704;0.996	T	0.64322	-0.6435	10	0.87932	D	0	.	18.6173	0.91306	0.0:0.0:1.0:0.0	.	1616;1183;1716	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	V	1716;1684;1648;1616;1183	ENSP00000408464:G1716V;ENSP00000394888:G1648V;ENSP00000419438:G1616V;ENSP00000371766:G1183V	ENSP00000287364:G1684V	G	+	2	0	DOCK8	429312	1.000000	0.71417	0.944000	0.38274	0.519000	0.34347	9.150000	0.94667	2.624000	0.88883	0.655000	0.94253	GGG	.	.		0.587	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		T	439312	G	T	439312	3	4	168	1	0	0	0	0	1	0	0	0	4695	1232	43	3	5305	3	DOCK8	9	439312	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10		439312	140774119	120	25536										
CEP78	84131	hgsc.bcm.edu	37	chr9	80851282	80851282	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gggccatgatcgactccgtgAagctgcgccgcgacagcgcg	15	14	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr9:80851282A>T	ENST00000424347.2	+	1	305	c.16A>T	c.(16-18)Aag>Tag	p.K6*	CEP78_ENST00000376597.4_Nonsense_Mutation_p.K6*|CEP78_ENST00000415759.2_Nonsense_Mutation_p.K6*|CEP78_ENST00000277082.5_Nonsense_Mutation_p.K6*|CEP78_ENST00000376598.2_Nonsense_Mutation_p.K6*			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	6					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						CGACTCCGTGAAGCTGCGCCG	0.731																																					p.K6X		Atlas-SNP	.											.	CEP78	79	.	0			c.A16T						.						5	6	6					9																	80851282		1873	4019	5892	SO:0001587	stop_gained	84131	exon1			TCCGTGAAGCTGC	BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 81"	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.16A>T	chr9.hg19:g.80851282A>T	ENSP00000411284:p.Lys6*	55.0	0.0		33.0	17.0	NM_001098802	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Nonsense_Mutation	SNP	ENST00000424347.2	hg19		.	.	.	.	.	.	.	.	.	.	a	34	5.319128	0.95682	.	.	ENSG00000148019	ENST00000424347;ENST00000415085;ENST00000415759;ENST00000376597;ENST00000277082;ENST00000376598	.	.	.	4.95	2.39	0.29439	.	0.162995	0.39687	N	0.001292	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.8776	9.743	0.40429	0.6657:0.3343:0.0:0.0	.	.	.	.	X	6	.	ENSP00000277082:K6X	K	+	1	0	CEP78	80041102	1.000000	0.71417	0.999000	0.59377	0.307000	0.27823	1.727000	0.38095	0.678000	0.31325	0.524000	0.50904	AAG	.	.		0.731	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991		T	80851282	A	T	80851282	4	4	168	1	0	0	0	0	0	1	0	0	3264	247	9	4	18	4	CEP78	9	80851282	Nonsense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	80411970	80851282	60362149	121	25537										
NDUFA8	4702	hgsc.bcm.edu	37	chr9	124906563	124906563	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggctgccatgtgtggcaggcTgcagatctccctcgatctca	12	13	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr9:124906563T>A	ENST00000373768.3	-	4	617	c.476A>T	c.(475-477)cAg>cTg	p.Q159L	NDUFA8_ENST00000537618.1_Intron	NM_014222.2	NP_055037.1	P51970	NDUA8_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8, 19kDa	159					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|protein complex binding (GO:0032403)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)	9						TGTGGCAGGCTGCAGATCTCC	0.532																																					p.Q159L		Atlas-SNP	.											.	NDUFA8	20	.	0			c.A476T						.						90	78	82					9																	124906563		2203	4300	6503	SO:0001583	missense	4702	exon4			GCAGGCTGCAGAT	AF044953	CCDS6835.1	9q33.2	2011-07-04	2002-08-29		ENSG00000119421	ENSG00000119421		"Mitochondrial respiratory chain complex / Complex I"	7692	protein-coding gene	gene with protein product	"complex I PGIV subunit"	603359	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8 (19kD, PGIV)"			9763677	Standard	NM_014222		Approved	PGIV, MGC793	uc004blv.3	P51970	OTTHUMG00000020598	ENST00000373768.3:c.476A>T	chr9.hg19:g.124906563T>A	ENSP00000362873:p.Gln159Leu	129.0	0.0		105.0	48.0	NM_014222	B1AM93|Q9Y6N0	Missense_Mutation	SNP	ENST00000373768.3	hg19	CCDS6835.1	.	.	.	.	.	.	.	.	.	.	T	10.75	1.437251	0.25900	.	.	ENSG00000119421	ENST00000373768	D	0.82803	-1.65	5.67	5.67	0.87782	.	0.138391	0.64402	D	0.000003	T	0.73552	0.3601	N	0.24115	0.695	0.80722	D	1	B	0.11235	0.004	B	0.13407	0.009	T	0.68588	-0.5369	10	0.38643	T	0.18	-23.6897	13.876	0.63653	0.0:0.0:0.0:1.0	.	159	P51970	NDUA8_HUMAN	L	159	ENSP00000362873:Q159L	ENSP00000362873:Q159L	Q	-	2	0	NDUFA8	123946384	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	7.483000	0.81158	2.163000	0.67991	0.459000	0.35465	CAG	.	.		0.532	NDUFA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053909.1	NM_014222		A	124906563	T	A	124906563	3	1	168	1	0	0	0	0	1	0	0	0	10280	1580	55	4	46	4	NDUFA8	9	124906563	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	44055281	124906563	16306868	122	25538										
OR1J1	347168	hgsc.bcm.edu	37	chr9	125240003	125240003	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	atgaaaaggagatgtcagtgAgggccaagtggctaaggaag	16	4	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr9:125240003A>T	ENST00000259357.2	-	1	232	c.203T>A	c.(202-204)cTc>cAc	p.L68H	RP11-542K23.9_ENST00000412262.2_RNA	NM_001004451.1	NP_001004451.1	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J, member 1	68						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	16						GATGTCAGTGAGGGCCAAGTG	0.507																																					p.L68H		Atlas-SNP	.											.	OR1J1	46	.	0			c.T203A						.						227	174	192					9																	125240003		2203	4300	6503	SO:0001583	missense	347168	exon1			TCAGTGAGGGCCA	AL353767	CCDS35120.1	9q33.2	2013-09-20			ENSG00000136834	ENSG00000136834		"GPCR / Class A : Olfactory receptors"	8208	protein-coding gene	gene with protein product							Standard	NM_001004451		Approved	hg32	uc011lyu.2	Q8NGS3	OTTHUMG00000020603	ENST00000259357.2:c.203T>A	chr9.hg19:g.125240003A>T	ENSP00000259357:p.Leu68His	147.0	0.0		120.0	42.0	NM_001004451	A3KFL8|Q6IF10|Q96R88	Missense_Mutation	SNP	ENST00000259357.2	hg19	CCDS35120.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.776677	0.49786	.	.	ENSG00000136834	ENST00000259357	T	0.00532	6.75	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.670270	0.14363	N	0.324301	T	0.02418	0.0074	M	0.89840	3.065	0.23089	N	0.998314	D	0.71674	0.998	D	0.64687	0.928	T	0.24190	-1.0167	10	0.87932	D	0	.	9.6494	0.39888	0.8248:0.1752:0.0:0.0	.	68	Q8NGS3	OR1J1_HUMAN	H	68	ENSP00000259357:L68H	ENSP00000259357:L68H	L	-	2	0	OR1J1	124279824	0.866000	0.29940	0.968000	0.41197	0.666000	0.39218	7.032000	0.76498	1.953000	0.56701	0.327000	0.21459	CTC	.	.		0.507	OR1J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053931.1			T	125240003	A	T	125240003	3	4	168	1	0	0	0	0	1	0	0	0	10968	304	11	4	768	4	OR1J1	9	125240003	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	333440	125240003	15973428	123	25539										
EGFL7	51162	hgsc.bcm.edu	37	chr9	139566450	139566450	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agcatgggctcccggaccccGgcagcctcctggtgcactcc	12	18	0	0	rs370929489		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr9:139566450G>C	ENST00000371699.1	+	9	1620	c.709G>C	c.(709-711)Ggc>Cgc	p.G237R	EGFL7_ENST00000406555.3_Missense_Mutation_p.G237R|EGFL7_ENST00000371698.3_Missense_Mutation_p.G237R|MIR126_ENST00000362291.1_RNA|EGFL7_ENST00000308874.7_Missense_Mutation_p.G237R			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	237					angiogenesis (GO:0001525)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|negative regulation of cell migration (GO:0030336)|negative regulation of Notch signaling pathway (GO:0045746)|positive regulation of endothelial cell proliferation (GO:0001938)|vasculogenesis (GO:0001570)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)			kidney(2)|ovary(1)|prostate(2)|urinary_tract(1)	6	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		CCCGGACCCCGGCAGCCTCCT	0.672											OREG0019619	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G237R		Atlas-SNP	.											.	EGFL7	11	.	0			c.G709C						.						8	9	8					9																	139566450		1977	3880	5857	SO:0001583	missense	51162	exon10			GACCCCGGCAGCC	AF186111	CCDS7002.1	9q34.3	2008-02-05			ENSG00000172889	ENSG00000172889			20594	protein-coding gene	gene with protein product		608582					Standard	NM_016215		Approved	ZNEU1	uc004cih.3	Q9UHF1	OTTHUMG00000020938	ENST00000371699.1:c.709G>C	chr9.hg19:g.139566450G>C	ENSP00000360764:p.Gly237Arg	74.0	0.0	1649	60.0	29.0	NM_016215	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	ENST00000371699.1	hg19	CCDS7002.1	.	.	.	.	.	.	.	.	.	.	G	7.864	0.726797	0.15439	.	.	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74	4.15	-2.2	0.06994	.	1.027160	0.07759	N	0.949732	T	0.69061	0.3069	L	0.36672	1.1	0.22112	N	0.999356	P	0.39847	0.691	B	0.31495	0.131	T	0.54609	-0.8268	10	0.20519	T	0.43	-7.2998	9.4632	0.38798	0.7719:0.0:0.2281:0.0	.	237	Q9UHF1	EGFL7_HUMAN	R	237	ENSP00000360764:G237R;ENSP00000307843:G237R;ENSP00000385639:G237R;ENSP00000360763:G237R	ENSP00000307843:G237R	G	+	1	0	EGFL7	138686271	0.158000	0.22850	0.062000	0.19696	0.007000	0.05969	0.431000	0.21444	-0.334000	0.08463	-0.224000	0.12420	GGC	.	.		0.672	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215		C	139566450	G	C	139566450	3	2	168	1	0	0	0	0	1	0	0	0	4966	1116	39	4	735	4	EGFL7	9	139566450	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	14326447	139566450	1646981	124	25540										
AKR1C1	1645	hgsc.bcm.edu	37	chr10	5005646	5005646	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tagtgacagaaatggattcgAaatatcagtgtgtgaagctg	12	4	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr10:5005646A>G	ENST00000380872.4	+	1	202	c.10A>G	c.(10-12)Aaa>Gaa	p.K4E	AKR1C1_ENST00000477661.1_3'UTR|U8_ENST00000459095.1_RNA|AKR1C1_ENST00000380859.1_5'Flank|AKR1C1_ENST00000434459.2_Missense_Mutation_p.K4E	NM_001353.5	NP_001344.2	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	4					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|cholesterol homeostasis (GO:0042632)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|intestinal cholesterol absorption (GO:0030299)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|progesterone metabolic process (GO:0042448)|protein homooligomerization (GO:0051260)|response to organophosphorus (GO:0046683)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase (B-specific) activity (GO:0047042)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|indanol dehydrogenase activity (GO:0047718)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(2)|ovary(3)|prostate(1)	13					Acetylsalicylic acid(DB00945)|Salicylic acid(DB00936)	AATGGATTCGAAATATCAGTG	0.468																																					p.K4E	Colon(130;2054 2316 13360 15380)	Atlas-SNP	.											.	AKR1C1	39	.	0			c.A10G						.						202	176	185					10																	5005646		2203	4300	6503	SO:0001583	missense	1645	exon1			GATTCGAAATATC	D26124	CCDS7061.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000187134	ENSG00000187134	1.3.1.20, 1.1.1.149, 1.1.1.112	"Aldo-keto reductases"	384	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase"	600449	"aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)"	DDH1		8011662	Standard	NM_001353		Approved	DDH, MBAB, DD1, HAKRC		Q04828	OTTHUMG00000017580	ENST00000380872.4:c.10A>G	chr10.hg19:g.5005646A>G	ENSP00000370254:p.Lys4Glu	138.0	0.0		89.0	42.0	NM_001353	P52896|Q5SR15|Q7M4N2|Q9UCX2	Missense_Mutation	SNP	ENST00000380872.4	hg19	CCDS7061.1	.	.	.	.	.	.	.	.	.	.	A	13.55	2.270324	0.40194	.	.	ENSG00000187134	ENST00000434459;ENST00000380872	T;T	0.27104	1.69;1.69	2.46	2.46	0.29980	.	0.590465	0.15121	N	0.279371	T	0.19046	0.0457	L	0.39898	1.24	0.09310	N	1	B;B;B	0.21381	0.055;0.007;0.004	B;B;B	0.17098	0.017;0.013;0.004	T	0.15093	-1.0449	10	0.49607	T	0.09	.	6.7142	0.23294	1.0:0.0:0.0:0.0	.	4;4;4	B4E0M1;Q2XPP3;Q04828	.;.;AK1C1_HUMAN	E	4	ENSP00000412248:K4E;ENSP00000370254:K4E	ENSP00000370254:K4E	K	+	1	0	AKR1C1	4995646	0.045000	0.20229	0.031000	0.17742	0.212000	0.24457	1.049000	0.30392	1.131000	0.42111	0.254000	0.18369	AAA	.	.		0.468	AKR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046523.2	NM_001353		G	5005646	A	G	5005646	3	3	168	1	0	0	0	0	1	0	0	0	469	247	9	2	12	2	AKR1C1	10	5005646	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10		5005646	130529101	125	25541										
ZNF248	57209	hgsc.bcm.edu	37	chr10	38121875	38121875	+	Frame_Shift_Del	DEL	G	G	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	catgagtcacatattttataGggataatttcttaaagaaac							TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr10:38121875delG	ENST00000395867.3	-	6	958	c.408delC	c.(406-408)cccfs	p.P136fs	ZNF248_ENST00000374648.3_Intron|AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000494133.1_Intron|ZNF248_ENST00000357328.4_Frame_Shift_Del_p.P136fs	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						ATATTTTATAGGGATAATTTC	0.318																																					p.Y137fs		Atlas-INDEL	.											.	ZNF248	61	.	0			c.409delT						.						54	55	55					10																	38121875		2202	4298	6500	SO:0001589	frameshift_variant	57209	exon6			.	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"Zinc fingers, C2H2-type", "-"	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.408delC	chr10.hg19:g.38121875delG	ENSP00000379208:p.Pro136fs	199.0	0.0		153.0	63.0	NM_021045	Q8NDV8|Q9UMP3	Frame_Shift_Del	DEL	ENST00000395867.3	hg19	CCDS7194.1																																																																																			.	.		0.318	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		-	38121875	G	-	38121875	7	5	168	1	0	1	0	1	0	0	0	0	17808	987	35	0	1335	0	ZNF248	10	38121875	Frame_Shift_Del	DEL	G	TCGA-DD-AACQ-01A-11D-A40R-10	33116229	38121875	97412872	126	25542										
RASSF4	83937	hgsc.bcm.edu	37	chr10	45480272	45480272	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctcatgcagggcccctggagGaggcagaggaggccccccag	16	14	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr10:45480272G>A	ENST00000340258.5	+	6	498	c.385G>A	c.(385-387)Gag>Aag	p.E129K	RASSF4_ENST00000472561.1_3'UTR|RASSF4_ENST00000334940.6_Missense_Mutation_p.E138K|RASSF4_ENST00000374417.2_Missense_Mutation_p.G98E	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	294	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						GCCCCTGGAGGAGGCAGAGGA	0.657																																					p.E129K		Atlas-SNP	.											.	RASSF4	33	.	0			c.G385A						.						77	91	86					10																	45480272		2203	4300	6503	SO:0001583	missense	83937	exon6			CTGGAGGAGGCAG	BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.385G>A	chr10.hg19:g.45480272G>A	ENSP00000339692:p.Glu129Lys	137.0	0.0		65.0	15.0	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000340258.5	hg19	CCDS7208.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.75|16.75	3.209060|3.209060	0.58343|0.58343	.|.	.|.	ENSG00000107551|ENSG00000107551	ENST00000334940;ENST00000340258;ENST00000374411|ENST00000374417	T;T|T	0.14766|0.30714	2.48;2.49|1.52	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.866984|.	0.10347|.	N|.	0.685596|.	T|T	0.33294|0.33294	0.0858|0.0858	L|L	0.52573|0.52573	1.65|1.65	0.34110|0.34110	D|D	0.662865|0.662865	B;B;B|.	0.28258|.	0.134;0.205;0.009|.	B;B;B|.	0.22753|.	0.041;0.021;0.004|.	T|T	0.16689|0.16689	-1.0394|-1.0394	10|7	0.12766|0.02654	T|T	0.61|1	-29.5222|-29.5222	15.9221|15.9221	0.79583|0.79583	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	138;220;129|.	Q9H2L5-2;Q59FL4;Q9H2L5|.	.;.;RASF4_HUMAN|.	K|E	138;129;220|98	ENSP00000334543:E138K;ENSP00000339692:E129K|ENSP00000363538:G98E	ENSP00000334543:E138K|ENSP00000363538:G98E	E|G	+|+	1|2	0|0	RASSF4|RASSF4	44800278|44800278	1.000000|1.000000	0.71417|0.71417	0.612000|0.612000	0.29024|0.29024	0.591000|0.591000	0.36615|0.36615	7.248000|7.248000	0.78268|0.78268	2.832000|2.832000	0.97577|0.97577	0.655000|0.655000	0.94253|0.94253	GAG|GGA	.	.		0.657	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023		A	45480272	G	A	45480272	3	1	168	1	0	0	0	0	1	0	0	0	13103	1175	41	3	403	3	RASSF4	10	45480272	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	7358397	45480272	90054475	127	25543										
SLK	9748	hgsc.bcm.edu	37	chr10	105762701	105762701	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agaaattaattaataagcccAtggtgggtcctgaggctggt	12	6	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr10:105762701A>T	ENST00000369755.3	+	9	2310	c.1765A>T	c.(1765-1767)Atg>Ttg	p.M589L	SLK_ENST00000335753.4_Missense_Mutation_p.M589L	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	589	Glu-rich.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TAATAAGCCCATGGTGGGTCC	0.393																																					p.M589L	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.A1765T						.						39	42	41					10																	105762701		2203	4300	6503	SO:0001583	missense	9748	exon9			AAGCCCATGGTGG		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.1765A>T	chr10.hg19:g.105762701A>T	ENSP00000358770:p.Met589Leu	110.0	0.0		49.0	34.0	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	hg19	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	2.780	-0.253637	0.05829	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.66815	-0.23;-0.23	5.78	-6.95	0.01628	Protein kinase-like domain (1);	2.135570	0.01677	N	0.025939	T	0.41119	0.1145	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.13308	-1.0514	10	0.30854	T	0.27	.	1.6036	0.02679	0.2273:0.2771:0.3112:0.1845	.	589;589	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	L	589	ENSP00000336824:M589L;ENSP00000358770:M589L	ENSP00000336824:M589L	M	+	1	0	SLK	105752691	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	0.247000	0.18179	-0.778000	0.04566	-0.375000	0.07067	ATG	.	.		0.393	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		T	105762701	A	T	105762701	3	4	168	1	0	0	0	0	1	0	0	0	14763	217	8	4	1799	4	SLK	10	105762701	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	60282429	105762701	29772046	128	25544										
MUC6	4588	hgsc.bcm.edu	37	chr11	1013919	1013919	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctggcagcggaaatgcaggcGccctcacagcgggttaccgt	14	13	1	0	rs372205312		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr11:1013919G>T	ENST00000421673.2	-	32	7172	c.7122C>A	c.(7120-7122)ggC>ggA	p.G2374G		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2374	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AAATGCAGGCGCCCTCACAGC	0.657																																					p.G2374G		Atlas-SNP	.											.	MUC6	408	.	0			c.C7122A						.						24	30	28					11																	1013919		2133	4236	6369	SO:0001819	synonymous_variant	4588	exon32			GCAGGCGCCCTCA	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.7122C>A	chr11.hg19:g.1013919G>T		37.0	0.0		45.0	16.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	hg19	CCDS44513.1																																																																																			.	.		0.657	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		T	1013919	G	T	1013919	2	4	168	1	0	0	0	0	0	0	0	1	9989	1074	38	1		1	MUC6	11	1013919	Silent	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10		1013919	133992597	129	25545										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6651648	6651648	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gggccgtcggcgtccgacgcGcggaaagtgtacagcgctgc	17	13	0	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr11:6651648G>A	ENST00000299441.3	-	10	4788	c.4377C>T	c.(4375-4377)cgC>cgT	p.R1459R	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1459	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CGTCCGACGCGCGGAAAGTGT	0.746																																					p.R1459R		Atlas-SNP	.											.	DCHS1	277	.	0			c.C4377T						.						1	2	2					11																	6651648		1268	2783	4051	SO:0001819	synonymous_variant	8642	exon10			CGACGCGCGGAAA	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.4377C>T	chr11.hg19:g.6651648G>A		1.0	0.0		9.0	7.0	NM_003737	O15098	Silent	SNP	ENST00000299441.3	hg19	CCDS7771.1																																																																																			.	.		0.746	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6651648	G	A	6651648	2	1	168	1	0	0	0	0	0	0	0	1	4289	1074	38	1		1	DCHS1	11	6651648	Silent	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	5637729	6651648	128354868	130	25546										
DGKZ	8525	hgsc.bcm.edu	37	chr11	46394022	46394022	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctctggtatctcaatccccgAcaagtcttcgacctgagcca	7	15	3	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr11:46394022A>T	ENST00000454345.1	+	12	1661	c.1536A>T	c.(1534-1536)cgA>cgT	p.R512R	DGKZ_ENST00000532868.2_Silent_p.R328R|DGKZ_ENST00000456247.2_Silent_p.R323R|DGKZ_ENST00000527911.1_Silent_p.R324R|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000528615.1_Silent_p.R102R|DGKZ_ENST00000318201.8_Silent_p.R301R|DGKZ_ENST00000343674.6_Silent_p.R340R|DGKZ_ENST00000395574.3_Silent_p.R290R|DGKZ_ENST00000421244.2_Silent_p.R324R	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	512	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.|Mediates interaction with RASGRP1.				blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		TCAATCCCCGACAAGTCTTCG	0.582																																					p.R512R		Atlas-SNP	.											.	DGKZ	199	.	0			c.A1536T						.						91	76	81					11																	46394022		2202	4298	6500	SO:0001819	synonymous_variant	8525	exon12			TCCCCGACAAGTC	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"diacylglycerol kinase, zeta 104kDa"			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.1536A>T	chr11.hg19:g.46394022A>T		115.0	0.0		93.0	26.0	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Silent	SNP	ENST00000454345.1	hg19	CCDS41640.1																																																																																			.	.		0.582	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540		T	46394022	A	T	46394022	2	4	168	1	0	0	0	0	0	0	0	1	4476	262	10	4		4	DGKZ	11	46394022	Silent	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	39742374	46394022	88612494	131	25547										
SLC22A10	387775	hgsc.bcm.edu	37	chr11	63057748	63057748	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ttaatccctcatatactgctAgagaactttgctgcagccat	6	11	1	1	rs537943997		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr11:63057748A>G	ENST00000332793.6	+	1	113	c.111A>G	c.(109-111)ctA>ctG	p.L37L	SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000526800.1_5'Flank|SLC22A10_ENST00000544661.1_Splice_Site	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	37						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	ATATACTGCTAGAGAACTTTG	0.443																																					p.L37L		Atlas-SNP	.											.	SLC22A10	79	.	0			c.A111G						.						93	97	95					11																	63057748		2156	4291	6447	SO:0001819	synonymous_variant	387775	exon1			ACTGCTAGAGAAC	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.111A>G	chr11.hg19:g.63057748A>G		139.0	0.0		121.0	63.0	NM_001039752	Q68CJ0	Silent	SNP	ENST00000332793.6	hg19	CCDS41661.1																																																																																			.	.		0.443	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		G	63057748	A	G	63057748	2	3	168	1	0	0	0	0	0	0	0	1	14456	407	15	2		2	SLC22A10	11	63057748	Silent	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	16663726	63057748	71948768	132	25548										
NARS2	79731	hgsc.bcm.edu	37	chr11	78147774	78147774	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	taacatctttgatattgtcaAcacccaagatgcactgcagg	7	10	2	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr11:78147774A>G	ENST00000281038.5	-	14	1751	c.1376T>C	c.(1375-1377)gTt>gCt	p.V459A	NARS2_ENST00000528850.1_Missense_Mutation_p.V232A|RP11-452H21.1_ENST00000534168.1_RNA	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	459					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	GATATTGTCAACACCCAAGAT	0.448																																					p.V459A		Atlas-SNP	.											.	NARS2	62	.	0			c.T1376C						.						230	226	228					11																	78147774		2200	4292	6492	SO:0001583	missense	79731	exon14			TTGTCAACACCCA	BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"Aminoacyl tRNA synthetases / Class II"	26274	protein-coding gene	gene with protein product	"asparagine tRNA ligase 2, mitochondrial (putative)"	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.1376T>C	chr11.hg19:g.78147774A>G	ENSP00000281038:p.Val459Ala	388.0	1.0		316.0	129.0	NM_024678	G3V178	Missense_Mutation	SNP	ENST00000281038.5	hg19	CCDS8261.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.051574	0.75960	.	.	ENSG00000137513	ENST00000281038;ENST00000528850	T;T	0.77358	-1.09;-1.09	5.92	5.92	0.95590	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.249658	0.39985	N	0.001201	T	0.75221	0.3820	L	0.48877	1.53	0.80722	D	1	B	0.19817	0.039	B	0.25987	0.065	T	0.72481	-0.4280	10	0.87932	D	0	-5.5204	16.3678	0.83341	1.0:0.0:0.0:0.0	.	459	Q96I59	SYNM_HUMAN	A	459;232	ENSP00000281038:V459A;ENSP00000432635:V232A	ENSP00000281038:V459A	V	-	2	0	NARS2	77825422	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.962000	0.93254	2.254000	0.74563	0.528000	0.53228	GTT	.	.		0.448	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		G	78147774	A	G	78147774	3	3	168	1	0	0	0	0	1	0	0	0	10180	43	2	2	61	2	NARS2	11	78147774	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	15090026	78147774	56858742	133	25549										
SLC35F2	54733	hgsc.bcm.edu	37	chr11	107682490	107682490	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggatgtacttccaccattttCttttcaagattactaaaagg	6	8	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr11:107682490C>G	ENST00000525815.1	-	3	737	c.317G>C	c.(316-318)aGa>aCa	p.R106T	SLC35F2_ENST00000265836.7_5'UTR|SLC35F2_ENST00000375682.4_Missense_Mutation_p.R59T|SLC35F2_ENST00000429869.1_Missense_Mutation_p.R106T|SLC35F2_ENST00000525071.1_Missense_Mutation_p.R106T	NM_017515.4	NP_059985.2	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2	106					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		CCACCATTTTCTTTTCAAGAT	0.388																																					p.R106T		Atlas-SNP	.											.	SLC35F2	29	.	0			c.G317C						.						194	179	184					11																	107682490		1859	4093	5952	SO:0001583	missense	54733	exon3			CATTTTCTTTTCA		CCDS41709.1	11q22.3	2013-05-22			ENSG00000110660	ENSG00000110660		"Solute carriers"	23615	protein-coding gene	gene with protein product						9119394	Standard	NM_017515		Approved	FLJ13018	uc001pjq.3	Q8IXU6	OTTHUMG00000166366	ENST00000525815.1:c.317G>C	chr11.hg19:g.107682490C>G	ENSP00000436785:p.Arg106Thr	116.0	0.0		64.0	18.0	NM_017515	Q14963|Q5JPA8|Q6ZRQ3|Q9H947	Missense_Mutation	SNP	ENST00000525815.1	hg19	CCDS41709.1	.	.	.	.	.	.	.	.	.	.	C	7.806	0.714773	0.15306	.	.	ENSG00000110660	ENST00000525815;ENST00000525071;ENST00000375682;ENST00000429869	.	.	.	5.32	1.26	0.21427	.	0.498346	0.22814	N	0.055311	T	0.36826	0.0981	N	0.17872	0.535	0.43777	D	0.996306	B;B	0.17038	0.02;0.006	B;B	0.28305	0.088;0.038	T	0.05099	-1.0906	9	0.15952	T	0.53	.	7.0634	0.25139	0.0:0.4223:0.0:0.5777	.	106;106	E9PJD1;Q8IXU6	.;S35F2_HUMAN	T	106;106;59;106	.	ENSP00000364834:R59T	R	-	2	0	SLC35F2	107187700	0.070000	0.21116	0.998000	0.56505	0.953000	0.61014	-0.184000	0.09698	0.598000	0.29829	0.555000	0.69702	AGA	.	.		0.388	SLC35F2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389417.1	NM_017515		G	107682490	C	G	107682490	3	3	168	1	0	0	0	0	1	0	0	0	14604	913	32	4	831	4	SLC35F2	11	107682490	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	29534716	107682490	27324026	134	25550										
UBE4A	9354	hgsc.bcm.edu	37	chr11	118245934	118245934	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gaacgaaaaattaaaaatgtAcacatgagaggtaggagaga	11	3	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr11:118245934A>T	ENST00000431736.2	+	9	1533	c.1461A>T	c.(1459-1461)gtA>gtT	p.V487V	UBE4A_ENST00000252108.3_Silent_p.V480V					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		TTAAAAATGTACACATGAGAG	0.433																																					p.V487V		Atlas-SNP	.											.	UBE4A	97	.	0			c.A1461T						.						49	46	47					11																	118245934		2200	4296	6496	SO:0001819	synonymous_variant	9354	exon9			AAATGTACACATG	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"U-box domain containing"	12499	protein-coding gene	gene with protein product		603753	"ubiquitination factor E4A (homologous to yeast UFD2)", "ubiquitination factor E4A (UFD2 homolog, yeast)"			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.1461A>T	chr11.hg19:g.118245934A>T		70.0	0.0		64.0	31.0	NM_004788		Silent	SNP	ENST00000431736.2	hg19	CCDS8396.1																																																																																			.	.		0.433	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		T	118245934	A	T	118245934	2	4	168	1	0	0	0	0	0	0	0	1	16897	378	14	4		4	UBE4A	11	118245934	Silent	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	10563444	118245934	16760582	135	25551										
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126326329	126326329	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cactggctgtggctccaccgAgaggttgaccagtggagggt	16	10	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr11:126326329A>T	ENST00000525144.2	-	7	1012	c.763T>A	c.(763-765)Tcg>Acg	p.S255T	KIRREL3_ENST00000529097.2_Missense_Mutation_p.S255T|KIRREL3_ENST00000525704.2_Missense_Mutation_p.S255T	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	255	Ig-like C2-type 3.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		GGCTCCACCGAGAGGTTGACC	0.587																																					p.S255T		Atlas-SNP	.											.	KIRREL3	183	.	0			c.T763A						.						36	41	39					11																	126326329		2039	4194	6233	SO:0001583	missense	84623	exon7			CCACCGAGAGGTT	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.763T>A	chr11.hg19:g.126326329A>T	ENSP00000435466:p.Ser255Thr	72.0	0.0		70.0	25.0	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Missense_Mutation	SNP	ENST00000525144.2	hg19	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	A	12.00	1.807274	0.31961	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000525704	T;T;T	0.12361	2.69;2.69;2.69	5.48	5.48	0.80851	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.28034	0.0691	L	0.58101	1.795	0.80722	D	1	B;B;D	0.55605	0.035;0.001;0.972	B;B;P	0.60415	0.019;0.01;0.874	T	0.01245	-1.1407	10	0.66056	D	0.02	.	10.0738	0.42349	0.8502:0.0:0.0:0.1498	.	255;255;255	Q8IZU9-2;E9PRX9;Q8IZU9	.;.;KIRR3_HUMAN	T	255	ENSP00000435466:S255T;ENSP00000434081:S255T;ENSP00000435094:S255T	ENSP00000435466:S255T	S	-	1	0	KIRREL3	125831539	1.000000	0.71417	0.988000	0.46212	0.010000	0.07245	6.953000	0.75995	2.087000	0.62958	0.445000	0.29226	TCG	.	.		0.587	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		T	126326329	A	T	126326329	3	4	168	1	0	0	0	0	1	0	0	0	8335	304	11	4	1724	4	KIRREL3	11	126326329	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	8080395	126326329	8680187	136	25552										
ACAD8	27034	hgsc.bcm.edu	37	chr11	134127071	134127071	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gatgtgggcgggtctgggctGtcacgtcttgatacctctgt	15	9	4	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr11:134127071G>T	ENST00000281182.4	+	3	406	c.300G>T	c.(298-300)ctG>ctT	p.L100L	ACAD8_ENST00000524547.1_Intron|ACAD8_ENST00000537423.1_Silent_p.L23L|ACAD8_ENST00000543332.1_Intron|ACAD8_ENST00000374752.4_Intron	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	100					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	GGTCTGGGCTGTCACGTCTTG	0.527																																					p.L100L	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.G300T						.						120	106	111					11																	134127071		2201	4297	6498	SO:0001819	synonymous_variant	27034	exon3			TGGGCTGTCACGT	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"acyl-Coenzyme A dehydrogenase family, member 8"			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.300G>T	chr11.hg19:g.134127071G>T		100.0	0.0		73.0	33.0	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Silent	SNP	ENST00000281182.4	hg19	CCDS8498.1																																																																																			.	.		0.527	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384		T	134127071	G	T	134127071	2	4	168	1	0	0	0	0	0	0	0	1	110	1364	48	3		3	ACAD8	11	134127071	Silent	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	7800742	134127071	879445	137	25553										
B3GAT1	27087	hgsc.bcm.edu	37	chr11	134253922	134253922	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgcaccgggcggctgtaggtGggcgtcaccacgtggatggt	18	10	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr11:134253922G>T	ENST00000524765.1	-	3	4817	c.273C>A	c.(271-273)ccC>ccA	p.P91P	B3GAT1_ENST00000392580.1_Silent_p.P91P|B3GAT1_ENST00000537389.1_Silent_p.P104P|B3GAT1_ENST00000312527.4_Silent_p.P91P|B3GAT1_ENST00000531510.1_5'UTR			Q9P2W7	B3GA1_HUMAN	beta-1,3-glucuronyltransferase 1	91					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|metal ion binding (GO:0046872)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.127)	all_cancers(12;1.39e-23)|all_epithelial(12;7.17e-17)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|Medulloblastoma(222;0.0125)|all_neural(223;0.0137)|Esophageal squamous(93;0.0559)		Epithelial(10;2.58e-11)|all cancers(11;5.75e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.000879)|Lung(977;0.0864)		GGCTGTAGGTGGGCGTCACCA	0.692																																					p.P91P		Atlas-SNP	.											.	B3GAT1	49	.	0			c.C273A						.						37	26	30					11																	134253922		2200	4294	6494	SO:0001819	synonymous_variant	27087	exon3			GTAGGTGGGCGTC	AB029396	CCDS8500.1	11q25	2014-07-08	2014-07-08		ENSG00000109956	ENSG00000109956	2.4.1.135	"CD molecules", "Beta-1,3-glucuronyltransferases"	921	protein-coding gene	gene with protein product	"galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1", "glucuronosyltransferase P"	151290	"CD57 antigen"	CD57, LEU7			Standard	XM_005271506		Approved	GlcAT-P, HNK-1, NK-1	uc001qhq.3	Q9P2W7	OTTHUMG00000167180	ENST00000524765.1:c.273C>A	chr11.hg19:g.134253922G>T		123.0	0.0		119.0	56.0	NM_054025	Q96FS7	Silent	SNP	ENST00000524765.1	hg19	CCDS8500.1																																																																																			.	.		0.692	B3GAT1-002	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393639.1	NM_018644		T	134253922	G	T	134253922	2	4	168	1	0	0	0	0	0	0	0	1	1253	1335	47	3		3	B3GAT1	11	134253922	Silent	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	126851	134253922	752594	138	25554										
VWF	7450	hgsc.bcm.edu	37	chr12	6091140	6091140	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gggtggggacactcttttgcActcctccttcctgcaggctg	12	13	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:6091140A>C	ENST00000261405.5	-	42	7353	c.7099T>G	c.(7099-7101)Tgc>Ggc	p.C2367G		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2367					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	ACTCTTTTGCACTCCTCCTTC	0.592																																					p.C2367G		Atlas-SNP	.											.	VWF	338	.	0			c.T7099G						.						54	49	50					12																	6091140		2203	4300	6503	SO:0001583	missense	7450	exon42			TTTTGCACTCCTC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.7099T>G	chr12.hg19:g.6091140A>C	ENSP00000261405:p.Cys2367Gly	68.0	0.0		66.0	25.0	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	hg19	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.513203	0.64522	.	.	ENSG00000110799	ENST00000261405	D	0.87809	-2.3	4.83	4.83	0.62350	.	0.000000	0.44483	D	0.000460	D	0.93334	0.7875	M	0.83953	2.67	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.94084	0.7347	10	0.66056	D	0.02	.	13.7391	0.62836	1.0:0.0:0.0:0.0	.	2367	P04275	VWF_HUMAN	G	2367	ENSP00000261405:C2367G	ENSP00000261405:C2367G	C	-	1	0	VWF	5961401	1.000000	0.71417	0.926000	0.36857	0.718000	0.41266	7.962000	0.87912	2.027000	0.59764	0.454000	0.30748	TGC	.	.		0.592	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		C	6091140	A	C	6091140	3	2	168	1	0	0	0	0	1	0	0	0	17261	159	6	5	1386	5	VWF	12	6091140	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10		6091140	127760755	139	25555										
NCAPD2	9918	hgsc.bcm.edu	37	chr12	6618958	6618958	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tactatctacagcattttgcAgtaagtgaaacacccaactg	6	10	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:6618958A>T	ENST00000315579.5	+	3	1002	c.203A>T	c.(202-204)cAt>cTt	p.H68L	NCAPD2_ENST00000545962.1_Splice_Site_p.M43L|SCARNA10_ENST00000459255.1_RNA	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	68	Interactions with SMC2 and SMC4.				mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						AGCATTTTGCAGTAAGTGAAA	0.418																																					p.H68L		Atlas-SNP	.											.	NCAPD2	99	.	0			c.A203T						.						127	124	125					12																	6618958		2203	4300	6503	SO:0001630	splice_region_variant	9918	exon3			TTTTGCAGTAAGT	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"chromosome condensation related SMC associated protein 1"	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.203+1A>T	chr12.hg19:g.6618958A>T		84.0	0.0		58.0	16.0	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	hg19	CCDS8548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.36|14.36	2.513248|2.513248	0.44660|0.44660	.|.	.|.	ENSG00000010292|ENSG00000010292	ENST00000315579;ENST00000539714;ENST00000382457;ENST00000535602|ENST00000545962	T;T;T|T	0.44083|0.15603	2.56;0.93;1.0|2.41	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.256767|.	0.45867|.	D|.	0.000326|.	T|T	0.18173|0.18173	0.0436|0.0436	L|L	0.54323|0.54323	1.7|1.7	0.21147|0.21147	N|N	0.999772|0.999772	B;B|B	0.33022|0.06786	0.394;0.384|0.001	B;B|B	0.27608|0.01281	0.055;0.081|0.0	T|T	0.11299|0.11299	-1.0593|-1.0593	10|8	0.33940|.	T|.	0.23|.	-8.4094|-8.4094	11.422|11.422	0.49987|0.49987	0.9274:0.0:0.0726:0.0|0.9274:0.0:0.0726:0.0	.|.	68;68|43	B3KY03;Q15021|F5GZJ1	.;CND1_HUMAN|.	L|L	68|43	ENSP00000325017:H68L;ENSP00000444377:H68L;ENSP00000371895:H68L|ENSP00000444417:M43L	ENSP00000325017:H68L|.	H|M	+|+	2|1	0|0	NCAPD2|NCAPD2	6489219|6489219	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.890000|0.890000	0.51754|0.51754	5.103000|5.103000	0.64578|0.64578	2.059000|2.059000	0.61396|0.61396	0.454000|0.454000	0.30748|0.30748	CAT|ATG	.	.		0.418	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	Missense_Mutation	T	6618958	A	T	6618958	5	4	168	1	0	0	0	0	0	0	1	0	10214	202	7	4	209	4	NCAPD2	12	6618958	Splice_Site	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	527818	6618958	127232937	140	25556										
CLEC12B	387837	hgsc.bcm.edu	37	chr12	10167985	10167985	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agaactccaccctagtgaagAtagacagtttggaagaaaag	10	7	0	5			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:10167985A>G	ENST00000338896.5	+	4	672	c.544A>G	c.(544-546)Ata>Gta	p.I182V	RP11-133L14.5_ENST00000544225.1_RNA|CLEC1B_ENST00000428126.2_5'Flank|CLEC12B_ENST00000396502.1_Missense_Mutation_p.I182V	NM_001129998.1	NP_001123470.1	Q2HXU8	CL12B_HUMAN	C-type lectin domain family 12, member B	182	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|large_intestine(2)|lung(5)	9						CCTAGTGAAGATAGACAGTTT	0.358																																					p.I182V		Atlas-SNP	.											.	CLEC12B	25	.	0			c.A544G						.						93	97	96					12																	10167985		2203	4300	6503	SO:0001583	missense	387837	exon4			GTGAAGATAGACA	AK128243	CCDS8610.1, CCDS44830.1	12p13.2	2010-08-17			ENSG00000256660	ENSG00000256660		"C-type lectin domain containing"	31966	protein-coding gene	gene with protein product						17562706	Standard	NM_205852		Approved		uc001qwz.2	Q2HXU8	OTTHUMG00000168397	ENST00000338896.5:c.544A>G	chr12.hg19:g.10167985A>G	ENSP00000344563:p.Ile182Val	120.0	0.0		111.0	48.0	NM_001129998	Q6UWF2|Q6ZRG0	Missense_Mutation	SNP	ENST00000338896.5	hg19	CCDS44830.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.099443	0.56183	.	.	ENSG00000256660	ENST00000396502;ENST00000338896	T;T	0.23147	1.92;1.92	4.55	3.41	0.39046	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.087960	0.48286	N	0.000196	T	0.25717	0.0626	M	0.67517	2.055	0.30009	N	0.81538	B;B	0.14012	0.009;0.008	B;B	0.15870	0.008;0.014	T	0.22941	-1.0202	10	0.87932	D	0	.	7.1812	0.25774	0.8946:0.0:0.1054:0.0	.	182;182	Q2HXU8;Q2HXU8-2	CL12B_HUMAN;.	V	182	ENSP00000379759:I182V;ENSP00000344563:I182V	ENSP00000344563:I182V	I	+	1	0	CLEC12B	10059252	0.997000	0.39634	1.000000	0.80357	0.936000	0.57629	2.395000	0.44459	0.872000	0.35775	0.402000	0.26972	ATA	.	.		0.358	CLEC12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399554.2	NM_205852		G	10167985	A	G	10167985	3	3	168	1	0	0	0	0	1	0	0	0	3500	333	12	2	558	2	CLEC12B	12	10167985	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	3549027	10167985	123683910	141	25557										
RAPGEF3	10411	hgsc.bcm.edu	37	chr12	48143536	48143536	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gggctcaccttgccatgggtCaccacgttgacagatccctt	10	14	2	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:48143536C>G	ENST00000449771.2	-	9	970	c.882G>C	c.(880-882)gtG>gtC	p.V294V	RAPGEF3_ENST00000549151.1_Silent_p.V252V|RAPGEF3_ENST00000171000.4_Silent_p.V252V|RAPGEF3_ENST00000395358.3_Silent_p.V294V|RAPGEF3_ENST00000548919.1_Silent_p.V252V|RAPGEF3_ENST00000549347.1_5'Flank|RAPGEF3_ENST00000389212.3_Silent_p.V294V|RAPGEF3_ENST00000405493.2_Silent_p.V252V			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	294					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		TGCCATGGGTCACCACGTTGA	0.592																																					p.V294V		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.G882C						.						119	100	106					12																	48143536		2203	4300	6503	SO:0001819	synonymous_variant	10411	exon9			ATGGGTCACCACG	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"exchange protein directly activated by cAMP 1"	606057	"RAP guanine-nucleotide-exchange factor (GEF) 3"			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.882G>C	chr12.hg19:g.48143536C>G		91.0	0.0		55.0	6.0	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Silent	SNP	ENST00000449771.2	hg19	CCDS41775.1																																																																																			.	.		0.592	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		G	48143536	C	G	48143536	2	3	168	1	0	0	0	0	0	0	0	1	13060	813	29	4		4	RAPGEF3	12	48143536	Silent	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	37975551	48143536	85708359	142	25558										
MLL2	8085	hgsc.bcm.edu	37	chr12	49440559	49440559	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	caacgccagcccttgagcagCatcaccttggtgatctgggg	12	13	2	2	rs200353763		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:49440559C>A	ENST00000301067.7	-	15	4250	c.4251G>T	c.(4249-4251)atG>atT	p.M1417I		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1417	Cys-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CCTTGAGCAGCATCACCTTGG	0.498																																					p.M1417I		Atlas-SNP	.											.	MLL2	1173	.	0			c.G4251T						.						36	39	38					12																	49440559		2041	4164	6205	SO:0001583	missense	8085	exon15			GAGCAGCATCACC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.4251G>T	chr12.hg19:g.49440559C>A	ENSP00000301067:p.Met1417Ile	117.0	0.0		74.0	28.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	14.25	2.480756	0.44044	.	.	ENSG00000167548	ENST00000301067	D	0.86956	-2.19	4.87	4.87	0.63330	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.44688	D	0.000436	T	0.75729	0.3889	N	0.00841	-1.15	0.45015	D	0.99803	D	0.53312	0.959	P	0.49922	0.626	D	0.85834	0.1393	10	0.87932	D	0	.	16.8011	0.85614	0.0:1.0:0.0:0.0	.	1417	O14686	MLL2_HUMAN	I	1417	ENSP00000301067:M1417I	ENSP00000301067:M1417I	M	-	3	0	MLL2	47726826	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.716000	0.84723	2.252000	0.74401	0.561000	0.74099	ATG	.	C|1.000;T|0.000		0.498	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49440559	C	A	49440559	3	1	168	1	0	0	0	0	1	0	0	0	9630	710	25	3	12522	3	MLL2	12	49440559	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	1297023	49440559	84411336	143	25559										
KRT71	112802	hgsc.bcm.edu	37	chr12	52946681	52946681	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tccactcttcccgctgccacTggccacattgaggctccgga	9	17	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:52946681T>A	ENST00000267119.5	-	1	250	c.181A>T	c.(181-183)Agt>Tgt	p.S61C		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	61	Gly-rich.|Head.				hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		CCGCTGCCACTGGCCACATTG	0.662																																					p.S61C		Atlas-SNP	.											.	KRT71	70	.	0			c.A181T						.						63	72	69					12																	52946681		2203	4300	6503	SO:0001583	missense	112802	exon1			TGCCACTGGCCAC	AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"-", "Intermediate filaments type II, keratins (basic)"	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.181A>T	chr12.hg19:g.52946681T>A	ENSP00000267119:p.Ser61Cys	89.0	0.0		67.0	34.0	NM_033448	B3KVC1|Q3SY85|Q96DU2	Missense_Mutation	SNP	ENST00000267119.5	hg19	CCDS8831.1	.	.	.	.	.	.	.	.	.	.	T	9.707	1.156124	0.21454	.	.	ENSG00000139648	ENST00000267119	T	0.75704	-0.96	4.77	-2.75	0.05914	.	0.761041	0.11346	N	0.573481	T	0.68174	0.2972	M	0.74258	2.255	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.57033	-0.7880	10	0.38643	T	0.18	.	7.5183	0.27614	0.1403:0.4891:0.0:0.3706	.	61	Q3SY84	K2C71_HUMAN	C	61	ENSP00000267119:S61C	ENSP00000267119:S61C	S	-	1	0	KRT71	51232948	0.000000	0.05858	0.098000	0.21074	0.813000	0.45954	-0.726000	0.04936	-0.575000	0.05982	0.459000	0.35465	AGT	.	.		0.662	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448		A	52946681	T	A	52946681	3	1	168	1	0	0	0	0	1	0	0	0	8493	1580	55	4	1426	4	KRT71	12	52946681	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	3506122	52946681	80905214	144	25560										
PPM1H	57460	hgsc.bcm.edu	37	chr12	63328291	63328291	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctctgcgtagccagtggcccAgggcagccgccgagtctcct	13	16	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:63328291A>T	ENST00000228705.6	-	1	526	c.226T>A	c.(226-228)Tgg>Agg	p.W76R	Y_RNA_ENST00000516851.1_RNA	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	76							phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		CCAGTGGCCCAGGGCAGCCGC	0.697																																					p.W76R		Atlas-SNP	.											.	PPM1H	42	.	0			c.T226A						.						4	7	6					12																	63328291		1893	3939	5832	SO:0001583	missense	57460	exon1			TGGCCCAGGGCAG	AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	18583	protein-coding gene	gene with protein product	"neurite extension-related protein phosphatase related to PP2C"		"ras homolog gene family, member C like 1", "protein phosphatase 1H (PP2C domain containing)"	ARHCL1			Standard	NM_020700		Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.226T>A	chr12.hg19:g.63328291A>T	ENSP00000228705:p.Trp76Arg	119.0	0.0		90.0	40.0	NM_020700	B1Q2A9|B2RXG4|Q6PI86	Missense_Mutation	SNP	ENST00000228705.6	hg19	CCDS44934.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.230240	0.79688	.	.	ENSG00000111110	ENST00000228705	T	0.44083	0.93	3.45	3.45	0.39498	Protein phosphatase 2C-like (3);	0.000000	0.85682	D	0.000000	T	0.60728	0.2291	M	0.74467	2.265	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.62817	-0.6774	9	.	.	.	8.2293	11.1814	0.48631	1.0:0.0:0.0:0.0	.	76	Q9ULR3	PPM1H_HUMAN	R	76	ENSP00000228705:W76R	.	W	-	1	0	PPM1H	61614558	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.059000	0.71133	1.571000	0.49722	0.459000	0.35465	TGG	.	.		0.697	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700		T	63328291	A	T	63328291	3	4	168	1	0	0	0	0	1	0	0	0	12353	188	7	4	1358	4	PPM1H	12	63328291	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	10381610	63328291	70523604	145	25561										
EEA1	8411	hgsc.bcm.edu	37	chr12	93170694	93170694	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	attgtcttcggcccactttcTattcaacgcttgtgtatgtt	7	10	3	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:93170694T>A	ENST00000322349.8	-	28	4303	c.4039A>T	c.(4039-4041)Aga>Tga	p.R1347*		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	1347					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						GCCCACTTTCTATTCAACGCT	0.333																																					p.R1347X		Atlas-SNP	.											.	EEA1	104	.	0			c.A4039T						.						219	210	213					12																	93170694		2203	4300	6503	SO:0001587	stop_gained	8411	exon28			ACTTTCTATTCAA	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.4039A>T	chr12.hg19:g.93170694T>A	ENSP00000317955:p.Arg1347*	84.0	0.0		85.0	42.0	NM_003566	Q14221	Nonsense_Mutation	SNP	ENST00000322349.8	hg19	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	T	45	11.459250	0.99564	.	.	ENSG00000102189	ENST00000322349	.	.	.	5.48	5.48	0.80851	.	0.000000	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5639	0.76273	0.0:0.0:0.0:1.0	.	.	.	.	X	1347	.	ENSP00000317955:R1347X	R	-	1	2	EEA1	91694825	1.000000	0.71417	0.993000	0.49108	0.923000	0.55619	4.697000	0.61782	2.070000	0.61991	0.528000	0.53228	AGA	.	.		0.333	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		A	93170694	T	A	93170694	4	1	168	1	0	0	0	0	0	1	0	0	4923	1530	53	4	204	4	EEA1	12	93170694	Nonsense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	29842403	93170694	40681201	146	25562										
UTP20	27340	hgsc.bcm.edu	37	chr12	101745844	101745844	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gttttacagcatgaaaatatAaccactgctgccacagagat	7	9	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:101745844A>T	ENST00000261637.4	+	39	5070	c.4896A>T	c.(4894-4896)atA>atT	p.I1632I		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1632					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						ATGAAAATATAACCACTGCTG	0.338																																					p.I1632I		Atlas-SNP	.											.	UTP20	222	.	0			c.A4896T						.						105	103	104					12																	101745844		2203	4300	6503	SO:0001819	synonymous_variant	27340	exon39			AAATATAACCACT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.4896A>T	chr12.hg19:g.101745844A>T		116.0	0.0		101.0	35.0	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	hg19	CCDS9081.1																																																																																			.	.		0.338	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101745844	A	T	101745844	2	4	168	1	0	0	0	0	0	0	0	1	17114	352	13	4		4	UTP20	12	101745844	Silent	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	8575150	101745844	32106051	147	25563										
CAMKK2	10645	hgsc.bcm.edu	37	chr12	121691155	121691155	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgcccacggtgttggagaggAgcgcgtcactgcccttgaat	14	11	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:121691155A>T	ENST00000324774.5	-	10	1856	c.1028T>A	c.(1027-1029)cTc>cAc	p.L343H	CAMKK2_ENST00000392474.2_Missense_Mutation_p.L343H|CAMKK2_ENST00000347034.2_Missense_Mutation_p.L343H|CAMKK2_ENST00000446440.2_Missense_Mutation_p.L343H|CAMKK2_ENST00000337174.3_Missense_Mutation_p.L343H|CAMKK2_ENST00000402834.4_Missense_Mutation_p.L343H|CAMKK2_ENST00000545538.1_Missense_Mutation_p.L130H|CAMKK2_ENST00000535524.1_5'UTR|CAMKK2_ENST00000392473.2_Missense_Mutation_p.L343H|CAMKK2_ENST00000538733.1_Missense_Mutation_p.L343H|CAMKK2_ENST00000412367.2_Missense_Mutation_p.L343H|CAMKK2_ENST00000404169.3_Missense_Mutation_p.L343H	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	343	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTTGGAGAGGAGCGCGTCACT	0.577																																					p.L343H		Atlas-SNP	.											.	CAMKK2	87	.	0			c.T1028A						.						227	159	182					12																	121691155		2203	4300	6503	SO:0001583	missense	10645	exon10			GAGAGGAGCGCGT	AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.1028T>A	chr12.hg19:g.121691155A>T	ENSP00000312741:p.Leu343His	130.0	0.0		93.0	40.0	NM_153500	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Missense_Mutation	SNP	ENST00000324774.5	hg19	CCDS9216.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.263682	0.80358	.	.	ENSG00000110931	ENST00000392474;ENST00000347034;ENST00000538733;ENST00000337174;ENST00000324774;ENST00000545538;ENST00000412367;ENST00000404169;ENST00000360452;ENST00000446440;ENST00000392473	T;T;T;T;T;T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15	5.35	5.35	0.76521	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.067242	0.64402	D	0.000017	T	0.70622	0.3245	L	0.41906	1.305	0.58432	D	0.999993	P;D;D;P;B;D;D;D	0.71674	0.942;0.984;0.984;0.889;0.354;0.998;0.996;0.984	P;P;P;P;B;D;D;P	0.67382	0.831;0.881;0.881;0.721;0.283;0.951;0.95;0.831	T	0.73033	-0.4110	10	0.59425	D	0.04	-1.329	14.5272	0.67897	1.0:0.0:0.0:0.0	.	343;343;343;130;343;343;343;343	Q96RR4-6;Q96RR4-2;Q96RR4-7;F5GZ00;Q96RR4-5;Q96RR4-4;Q96RR4;Q96RR4-3	.;.;.;.;.;.;KKCC2_HUMAN;.	H	343;343;343;343;343;130;343;343;326;343;343	ENSP00000376266:L343H;ENSP00000321230:L343H;ENSP00000445944:L343H;ENSP00000336634:L343H;ENSP00000312741:L343H;ENSP00000441352:L130H;ENSP00000388368:L343H;ENSP00000384600:L343H;ENSP00000388273:L343H;ENSP00000376265:L343H	ENSP00000312741:L343H	L	-	2	0	CAMKK2	120175538	1.000000	0.71417	0.728000	0.30774	0.755000	0.42902	7.041000	0.76558	2.033000	0.60031	0.533000	0.62120	CTC	.	.		0.577	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226		T	121691155	A	T	121691155	3	4	168	1	0	0	0	0	1	0	0	0	2609	304	11	4	780	4	CAMKK2	12	121691155	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	19945311	121691155	12160740	148	25564										
PUS1	80324	hgsc.bcm.edu	37	chr12	132428101	132428101	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	caggtgcccagtcccctggaAggcagtgaaggggacggaga	17	10	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr12:132428101A>T	ENST00000376649.3	+	6	1754	c.1254A>T	c.(1252-1254)gaA>gaT	p.E418D	PUS1_ENST00000535067.1_Missense_Mutation_p.E125D|PUS1_ENST00000440818.2_Missense_Mutation_p.E390D|PUS1_ENST00000443358.2_Missense_Mutation_p.E390D|PUS1_ENST00000542167.2_Missense_Mutation_p.E365D	NM_025215.5	NP_079491.2	Q9Y606	TRUA_HUMAN	pseudouridylate synthase 1	418					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|tRNA pseudouridine synthesis (GO:0031119)	mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)|pseudouridylate synthase activity (GO:0004730)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	11	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.05e-08)|Epithelial(86;2.51e-07)|all cancers(50;2.94e-07)		GTCCCCTGGAAGGCAGTGAAG	0.607																																					p.E418D	Esophageal Squamous(102;671 2009 17384 45666)	Atlas-SNP	.											.	PUS1	47	.	0			c.A1254T						.						112	100	104					12																	132428101		2203	4300	6503	SO:0001583	missense	80324	exon6			CCTGGAAGGCAGT	AF116238	CCDS9275.2, CCDS31928.1	12q24	2004-05-17			ENSG00000177192	ENSG00000177192			15508	protein-coding gene	gene with protein product		608109				10094309	Standard	NM_001002019		Approved		uc001ujf.3	Q9Y606	OTTHUMG00000128507	ENST00000376649.3:c.1254A>T	chr12.hg19:g.132428101A>T	ENSP00000365837:p.Glu418Asp	60.0	0.0		47.0	23.0	NM_025215	A8K877|B3KQC1|Q8WYT2|Q9BU44	Missense_Mutation	SNP	ENST00000376649.3	hg19	CCDS9275.2	.	.	.	.	.	.	.	.	.	.	A	0.079	-1.188014	0.01607	.	.	ENSG00000177192	ENST00000443358;ENST00000376649;ENST00000440818;ENST00000542167;ENST00000535067	T;T;T;T;T	0.57752	0.55;0.54;0.55;0.53;0.38	2.67	-5.35	0.02697	.	1.298410	0.05470	N	0.552951	T	0.33789	0.0875	L	0.41236	1.265	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.003	T	0.14008	-1.0488	10	0.18710	T	0.47	-19.5947	1.5947	0.02661	0.1895:0.2965:0.3669:0.1471	.	365;418	F5H1S9;Q9Y606	.;TRUA_HUMAN	D	390;418;390;365;125	ENSP00000392451:E390D;ENSP00000365837:E418D;ENSP00000400032:E390D;ENSP00000438948:E365D;ENSP00000443969:E125D	ENSP00000365837:E418D	E	+	3	2	PUS1	130994054	0.003000	0.15002	0.049000	0.19019	0.091000	0.18340	-0.614000	0.05604	-1.693000	0.01427	-0.408000	0.06270	GAA	.	.		0.607	PUS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250313.2	NM_025215		T	132428101	A	T	132428101	3	4	168	1	0	0	0	0	1	0	0	0	12845	69	3	4	1276	4	PUS1	12	132428101	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	10736946	132428101	1423794	149	25565										
NUDT15	55270	hgsc.bcm.edu	37	chr13	48611949	48611949	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tcggagtcgtggtgaccagcTgcaagcatccgcgttgcgtc	14	12	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr13:48611949T>G	ENST00000258662.2	+	1	247	c.67T>G	c.(67-69)Tgc>Ggc	p.C23G	SUCLA2_ENST00000543413.1_5'UTR	NM_018283.1	NP_060753.1	Q9NV35	NUD15_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 15	23	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				dGTP catabolic process (GO:0006203)|GTP catabolic process (GO:0006184)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity (GO:0035539)|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity (GO:0008413)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	7		all_cancers(8;3.75e-25)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|all_hematologic(8;0.000219)|Lung NSC(96;0.000226)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;4.83e-07)		GGTGACCAGCTGCAAGCATCC	0.682											OREG0022405	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C23G		Atlas-SNP	.											.	NUDT15	12	.	0			c.T67G						.						34	33	33					13																	48611949		2199	4296	6495	SO:0001583	missense	55270	exon1			ACCAGCTGCAAGC		CCDS9407.1	13q14.12	2006-04-12			ENSG00000136159	ENSG00000136159		"Nudix motif containing"	23063	protein-coding gene	gene with protein product		615792				12767940	Standard	NM_018283		Approved	MTH2, FLJ10956	uc001vbw.1	Q9NV35	OTTHUMG00000016890	ENST00000258662.2:c.67T>G	chr13.hg19:g.48611949T>G	ENSP00000258662:p.Cys23Gly	217.0	0.0	955	103.0	91.0	NM_018283	A2RUR6|Q32Q27|Q6P2C9	Missense_Mutation	SNP	ENST00000258662.2	hg19	CCDS9407.1	.	.	.	.	.	.	.	.	.	.	T	7.572	0.666850	0.14710	.	.	ENSG00000136159	ENST00000258662	T	0.06528	3.29	5.57	-11.1	0.00147	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.689450	0.16148	N	0.227381	T	0.00936	0.0031	N	0.00317	-1.655	0.19945	N	0.999941	B	0.02656	0.0	B	0.01281	0.0	T	0.37009	-0.9724	10	0.23302	T	0.38	-15.4805	3.3734	0.07229	0.6162:0.1188:0.082:0.183	.	23	Q9NV35	NUD15_HUMAN	G	23	ENSP00000258662:C23G	ENSP00000258662:C23G	C	+	1	0	NUDT15	47509950	0.000000	0.05858	0.006000	0.13384	0.128000	0.20619	-2.545000	0.00933	-1.890000	0.01111	0.533000	0.62120	TGC	.	.		0.682	NUDT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044862.3	NM_018283		G	48611949	T	G	48611949	3	3	168	1	0	0	0	0	1	0	0	0	10740	1580	55	5	69	5	NUDT15	13	48611949	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10		48611949	66557929	150	25566										
ZNF828	283489	hgsc.bcm.edu	37	chr13	115090611	115090611	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cactatccccagagatccgtAgtccagcaggatctccagag	9	14	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr13:115090611A>T	ENST00000361283.1	+	3	1603	c.1294A>T	c.(1294-1296)Agt>Tgt	p.S432C		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	432	Mediates interaction with MAD2L2.|Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										AGAGATCCGTAGTCCAGCAGG	0.527																																					p.S432C		Atlas-SNP	.											.	.	.	.	0			c.A1294T						.						77	86	83					13																	115090611		2203	4300	6503	SO:0001583	missense	283489	exon3			ATCCGTAGTCCAG	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"Zinc fingers, C2H2-type"	20311	protein-coding gene	gene with protein product	"chromosome alignment-maintaining phosphoprotein"		"chromosome 13 open reading frame 8", "zinc finger protein 828"	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.1294A>T	chr13.hg19:g.115090611A>T	ENSP00000354730:p.Ser432Cys	119.0	0.0		110.0	32.0	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	SNP	ENST00000361283.1	hg19	CCDS9545.1	.	.	.	.	.	.	.	.	.	.	A	16.67	3.187300	0.57909	.	.	ENSG00000198824	ENST00000361283	T	0.01287	5.05	5.92	5.92	0.95590	.	0.284783	0.30260	N	0.010029	T	0.04137	0.0115	L	0.40543	1.245	0.40909	D	0.984213	D	0.65815	0.995	P	0.58873	0.847	T	0.61397	-0.7071	9	.	.	.	-9.8501	14.5878	0.68339	1.0:0.0:0.0:0.0	.	432	Q96JM3	ZN828_HUMAN	C	432	ENSP00000354730:S432C	.	S	+	1	0	ZNF828	114108713	0.668000	0.27493	0.666000	0.29783	0.879000	0.50718	3.734000	0.55037	2.260000	0.74910	0.528000	0.53228	AGT	.	.		0.527	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		T	115090611	A	T	115090611	3	4	168	1	0	0	0	0	1	0	0	0	18196	420	15	4	1296	4	ZNF828	13	115090611	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	66478662	115090611	79267	151	25567										
IRF9	10379	hgsc.bcm.edu	37	chr14	24634149	24634150	+	Missense_Mutation	DNP	GC	GC	TT													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcgtggagctcttcagaaccGcctacttctgcagaggtgag							TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr14:24634149_24634150GC>TT	ENST00000396864.3	+	7	1263_1264	c.976_977GC>TT	c.(976-978)GCc>TTc	p.A326F	RP11-468E2.4_ENST00000558468.1_3'UTR|IRF9_ENST00000557894.1_Missense_Mutation_p.A224F	NM_006084.4	NP_006075.3	Q00978	IRF9_HUMAN	interferon regulatory factor 9	326					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(265;0.00853)		CTTCAGAACCGCCTACTTCTGC	0.619																																					p.A326S|p.A326V		Atlas-SNP	.											.	IRF9	33	.	0			c.G976T|c.C977T						.																																			SO:0001583	missense	10379	exon7			AGAACCGCCTACT|GAACCGCCTACTT	M87503	CCDS9615.1	14q11.2	2007-07-06	2007-07-06	2007-07-06	ENSG00000213928	ENSG00000213928			6131	protein-coding gene	gene with protein product		147574	"interferon-stimulated transcription factor 3, gamma (48kD)", "interferon-stimulated transcription factor 3, gamma 48kDa"	ISGF3G		1630447, 10199920	Standard	NM_006084		Approved		uc001wmq.3	Q00978	OTTHUMG00000028799	Exception_encountered	chr14.hg19:g.24634149_24634150delinsTT	ENSP00000380073:p.Ala326Phe	44.0|42.0	0.0		39.0|38.0	16.0	NM_006084	D3DS61	Missense_Mutation	SNP	ENST00000396864.3	hg19	CCDS9615.1																																																																																			.	.		0.619	IRF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071927.2			TT	24634150	GC	TT	24634149	3	4	168	1	0	0	0	0	1	0	0	0	7846	1087	38	1	998	1	IRF9	14	24634149	Missense_Mutation	DNP	GC	TCGA-DD-AACQ-01A-11D-A40R-10		24634149	82715391	152	25568										
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58965625	58965627	+	In_Frame_Del	DEL	TGG	TGG	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tgtcactaatacacagtcttTggatcaacaatgtgatccta							TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr14:58965625_58965627delTGG	ENST00000556134.1	+	28	4344_4346	c.4070_4072delTGG	c.(4069-4074)ttggat>tat	p.1357_1358LD>Y	KIAA0586_ENST00000423743.3_In_Frame_Del_p.1328_1329LD>Y|KIAA0586_ENST00000261244.5_In_Frame_Del_p.1296_1297LD>Y|KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000354386.6_In_Frame_Del_p.1425_1426LD>Y	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	1357					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						ACACAGTCTTTGGATCAACAATG	0.404																																					p.1425_1425del		Atlas-INDEL	.											.	KIAA0586	180	.	0			c.4273_4275del						.																																			SO:0001651	inframe_deletion	9786	exon29			.	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.4070_4072delTGG	chr14.hg19:g.58965625_58965627delTGG	ENSP00000452351:p.Leu1357_Asp1358delinsTyr	104.0	0.0		103.0	31.0	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	In_Frame_Del	DEL	ENST00000556134.1	hg19	CCDS58321.1																																																																																			.	.		0.404	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		-	58965627	TGG	-	58965625	7	5	168	1	0	1	0	1	0	0	0	0	8195	1821	63	0	3989	0	KIAA0586	14	58965625	In_Frame_Del	DEL	TGG	TCGA-DD-AACQ-01A-11D-A40R-10	34331476	58965625	48383915	153	25569	121	2								
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58965630	58965631	+	Frame_Shift_Del	DEL	CA	CA	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctaatacacagtctttggatCaacaatgtgatcctaaacca							TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr14:58965630_58965631delCA	ENST00000556134.1	+	28	4349_4350	c.4075_4076delCA	c.(4075-4077)caafs	p.Q1360fs	KIAA0586_ENST00000423743.3_Frame_Shift_Del_p.Q1331fs|KIAA0586_ENST00000261244.5_Frame_Shift_Del_p.Q1299fs|KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000354386.6_Frame_Shift_Del_p.Q1428fs	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	1360					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GTCTTTGGATCAACAATGTGAT	0.406																																					p.1426_1427del		Atlas-INDEL	.											.	KIAA0586	180	.	0			c.4278_4279del						.																																			SO:0001589	frameshift_variant	9786	exon29			.	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.4075_4076delCA	chr14.hg19:g.58965630_58965631delCA	ENSP00000452351:p.Gln1360fs	102.0	0.0		101.0	31.0	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Frame_Shift_Del	DEL	ENST00000556134.1	hg19	CCDS58321.1																																																																																			.	.		0.406	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		-	58965631	CA	-	58965630	7	5	168	1	0	1	0	1	0	0	0	0	8195	827	29	0	3994	0	KIAA0586	14	58965630	Frame_Shift_Del	DEL	CA	TCGA-DD-AACQ-01A-11D-A40R-10	5	58965630	48383910	154	25570	121	2								
ITPK1	3705	hgsc.bcm.edu	37	chr14	93424588	93424588	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cttgagtgagggcctctggaCcacggtgtaggactcgccaa	14	11	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr14:93424588C>A	ENST00000267615.6	-	8	801	c.628G>T	c.(628-630)Gtc>Ttc	p.V210F	ITPK1_ENST00000556603.2_Missense_Mutation_p.V210F|ITPK1_ENST00000354313.3_Missense_Mutation_p.V210F|ITPK1_ENST00000555495.1_Missense_Mutation_p.V91F|ITPK1_ENST00000556954.1_5'UTR			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	210	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		GGCCTCTGGACCACGGTGTAG	0.582																																					p.V210F		Atlas-SNP	.											.	ITPK1	53	.	0			c.G628T						.						185	150	162					14																	93424588		2203	4300	6503	SO:0001583	missense	3705	exon8			TCTGGACCACGGT	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.628G>T	chr14.hg19:g.93424588C>A	ENSP00000267615:p.Val210Phe	110.0	0.0		101.0	58.0	NM_001142593	Q9BTL6|Q9H2E7	Missense_Mutation	SNP	ENST00000267615.6	hg19	CCDS9907.1	.	.	.	.	.	.	.	.	.	.	C	36	5.599892	0.96614	.	.	ENSG00000100605	ENST00000354313;ENST00000405174;ENST00000556603;ENST00000555495;ENST00000267615;ENST00000311458;ENST00000554999;ENST00000556185	T	0.09445	2.98	5.22	5.22	0.72569	ATP-grasp fold (1);	0.058605	0.64402	D	0.000002	T	0.35740	0.0942	M	0.89095	3.005	0.80722	D	1	D;D	0.67145	0.993;0.996	P;P	0.57548	0.778;0.823	T	0.33854	-0.9852	10	0.41790	T	0.15	-16.5851	18.8139	0.92070	0.0:1.0:0.0:0.0	.	210;210	Q13572;Q13572-2	ITPK1_HUMAN;.	F	210;240;210;91;210;210;168;228	ENSP00000346272:V210F	ENSP00000267615:V210F	V	-	1	0	ITPK1	92494341	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.665000	0.83852	2.432000	0.82394	0.655000	0.94253	GTC	.	.		0.582	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		A	93424588	C	A	93424588	3	1	168	1	0	0	0	0	1	0	0	0	7925	507	18	3	680	3	ITPK1	14	93424588	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	34458958	93424588	13924952	155	25571										
HHIPL1	84439	hgsc.bcm.edu	37	chr14	100138668	100138668	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tggcaggcgggcaccacctgGcaaatgtcagatccagcctg	13	13	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr14:100138668G>C	ENST00000330710.5	+	8	1843	c.1745G>C	c.(1744-1746)gGc>gCc	p.G582A		NM_001127258.1	NP_001120730.1	Q96JK4	HIPL1_HUMAN	HHIP-like 1	582					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|skin(2)	15		Melanoma(154;0.128)				GCACCACCTGGCAAATGTCAG	0.562																																					p.G582A		Atlas-SNP	.											.	HHIPL1	86	.	0			c.G1745C						.						64	67	66					14																	100138668		692	1591	2283	SO:0001583	missense	84439	exon8			CACCTGGCAAATG	AB058725	CCDS9953.1, CCDS45162.1	14q32	2008-01-16	2008-01-16	2008-01-16		ENSG00000182218			19710	protein-coding gene	gene with protein product			"KIAA1822"	KIAA1822			Standard	NM_032425		Approved		uc010avs.3	Q96JK4		ENST00000330710.5:c.1745G>C	chr14.hg19:g.100138668G>C	ENSP00000330601:p.Gly582Ala	123.0	0.0		117.0	8.0	NM_001127258	A2RUF8|B2RN09|Q6UXX2	Missense_Mutation	SNP	ENST00000330710.5	hg19	CCDS45162.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.868313	0.91587	.	.	ENSG00000182218	ENST00000330710	T	0.01335	5.0	5.28	5.28	0.74379	Six-bladed beta-propeller, TolB-like (1);	.	.	.	.	T	0.08403	0.0209	M	0.75615	2.305	0.80722	D	1	D	0.71674	0.998	D	0.66979	0.948	T	0.07347	-1.0777	9	0.44086	T	0.13	.	18.9509	0.92641	0.0:0.0:1.0:0.0	.	582	Q96JK4	HIPL1_HUMAN	A	582	ENSP00000330601:G582A	ENSP00000330601:G582A	G	+	2	0	HHIPL1	99208421	1.000000	0.71417	0.996000	0.52242	0.979000	0.70002	7.344000	0.79328	2.477000	0.83638	0.645000	0.84053	GGC	.	.		0.562	HHIPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413811.1	XM_041566		C	100138668	G	C	100138668	3	2	168	1	0	0	0	0	1	0	0	0	7102	1203	42	4	1876	4	HHIPL1	14	100138668	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	6714080	100138668	7210872	156	25572										
JAG2	3714	hgsc.bcm.edu	37	chr14	105609964	105609964	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctgtcaggcaggtccctggcAgggctgaaggactgcggcaa	16	11	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr14:105609964A>T	ENST00000331782.3	-	25	3499	c.3096T>A	c.(3094-3096)ccT>ccA	p.P1032P	JAG2_ENST00000347004.2_Silent_p.P994P	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	1032					auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		GGTCCCTGGCAGGGCTGAAGG	0.682																																					p.P1032P		Atlas-SNP	.											.	JAG2	69	.	0			c.T3096A						.						45	44	44					14																	105609964		2202	4298	6500	SO:0001819	synonymous_variant	3714	exon25			CCTGGCAGGGCTG	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.3096T>A	chr14.hg19:g.105609964A>T		53.0	0.0		51.0	22.0	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	hg19	CCDS9998.1																																																																																			.	.		0.682	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			T	105609964	A	T	105609964	2	4	168	1	0	0	0	0	0	0	0	1	7944	175	7	4		4	JAG2	14	105609964	Silent	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	5471296	105609964	1739576	157	25573										
PACS2	23241	hgsc.bcm.edu	37	chr14	105849223	105849223	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggacgtccaggcggccttcaGcaccatcgtctcacggatac	11	15	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr14:105849223G>T	ENST00000325438.8	+	15	2090	c.1586G>T	c.(1585-1587)aGc>aTc	p.S529I	PACS2_ENST00000547217.1_Missense_Mutation_p.S499I|PACS2_ENST00000447393.1_Missense_Mutation_p.S533I|PACS2_ENST00000551743.1_5'Flank|PACS2_ENST00000458164.2_Missense_Mutation_p.S533I|PACS2_ENST00000430725.2_Missense_Mutation_p.S454I			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	529					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to plasma membrane (GO:0072661)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)				endometrium(2)|kidney(2)|lung(7)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	21		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		GCGGCCTTCAGCACCATCGTC	0.632																																					p.S533I		Atlas-SNP	.											.	PACS2	75	.	0			c.G1598T						.						80	70	73					14																	105849223		2202	4300	6502	SO:0001583	missense	23241	exon15			CCTTCAGCACCAT	AB011174	CCDS32168.1, CCDS45178.1, CCDS45178.2, CCDS58339.1	14q32	2005-02-15	2005-02-15	2005-02-15		ENSG00000179364			23794	protein-coding gene	gene with protein product		610423	"phosphofurin acidic cluster sorting protein 1-like"	PACS1L		15692567	Standard	NM_001100913		Approved	KIAA0602	uc001yqu.3	Q86VP3	OTTHUMG00000170450	ENST00000325438.8:c.1586G>T	chr14.hg19:g.105849223G>T	ENSP00000321834:p.Ser529Ile	35.0	0.0		29.0	13.0	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Missense_Mutation	SNP	ENST00000325438.8	hg19	CCDS32168.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.885520	0.33255	.	.	ENSG00000179364	ENST00000430725;ENST00000325438;ENST00000458164;ENST00000447393;ENST00000547217	T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77	4.52	4.52	0.55395	.	0.050976	0.85682	D	0.000000	T	0.40297	0.1111	L	0.41824	1.3	0.49299	D	0.999771	B;B;B;B	0.24618	0.054;0.022;0.107;0.006	B;B;B;B	0.30716	0.114;0.047;0.119;0.006	T	0.38457	-0.9660	10	0.56958	D	0.05	-28.1887	9.9605	0.41693	0.0969:0.0:0.9031:0.0	.	533;533;529;530	E9PB38;Q86VP3-2;Q86VP3;Q86VP3-3	.;.;PACS2_HUMAN;.	I	454;529;533;533;499	ENSP00000393524:S454I;ENSP00000321834:S529I;ENSP00000399732:S533I;ENSP00000393559:S533I;ENSP00000449525:S499I	ENSP00000321834:S529I	S	+	2	0	PACS2	104920268	1.000000	0.71417	1.000000	0.80357	0.545000	0.35147	2.475000	0.45162	2.210000	0.71456	0.462000	0.41574	AGC	.	.		0.632	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355		T	105849223	G	T	105849223	3	4	168	1	0	0	0	0	1	0	0	0	11382	971	34	3	1656	3	PACS2	14	105849223	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	239259	105849223	1500317	158	25574										
MTA1	9112	hgsc.bcm.edu	37	chr14	105931455	105931455	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggcgcggctgcccgaagcctCccagagcccgctggtgctga	15	16	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr14:105931455C>T	ENST00000331320.7	+	16	1773	c.1559C>T	c.(1558-1560)tCc>tTc	p.S520F	MTA1_ENST00000405646.1_Missense_Mutation_p.S503F|MTA1_ENST00000435036.2_Missense_Mutation_p.S56F|MTA1_ENST00000406191.1_Missense_Mutation_p.S520F|RP11-521B24.5_ENST00000552675.1_RNA	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	520					circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		CCCGAAGCCTCCCAGAGCCCG	0.711																																					p.S520F		Atlas-SNP	.											.	MTA1	61	.	0			c.C1559T						.						8	12	11					14																	105931455		1712	3151	4863	SO:0001583	missense	9112	exon16			AAGCCTCCCAGAG	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"GATA zinc finger domain containing"	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.1559C>T	chr14.hg19:g.105931455C>T	ENSP00000333633:p.Ser520Phe	119.0	0.0		100.0	37.0	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	17.31	3.358316	0.61403	.	.	ENSG00000182979	ENST00000414153;ENST00000331320;ENST00000406191;ENST00000405646;ENST00000434050;ENST00000435036	T;T;T;T;T	0.48522	1.42;1.42;1.42;1.43;0.81	5.38	5.38	0.77491	.	0.112601	0.64402	D	0.000006	T	0.51635	0.1686	M	0.69823	2.125	0.58432	D	0.999994	B;B	0.17465	0.004;0.022	B;B	0.17979	0.01;0.02	T	0.52162	-0.8612	10	0.62326	D	0.03	-27.0519	17.6815	0.88245	0.0:1.0:0.0:0.0	.	312;520	Q59FW1;Q13330	.;MTA1_HUMAN	F	429;520;520;503;312;56	ENSP00000333633:S520F;ENSP00000385702:S520F;ENSP00000384180:S503F;ENSP00000394106:S312F;ENSP00000389425:S56F	ENSP00000333633:S520F	S	+	2	0	MTA1	105002500	0.212000	0.23540	0.896000	0.35187	0.696000	0.40369	4.283000	0.58977	2.518000	0.84900	0.561000	0.74099	TCC	.	.		0.711	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			T	105931455	C	T	105931455	3	4	168	1	0	0	0	0	1	0	0	0	9917	855	30	3	1621	3	MTA1	14	105931455	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	82232	105931455	1418085	159	25575										
HERC2	8924	hgsc.bcm.edu	37	chr15	28474355	28474355	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	actcaccaagctctttaaatTtggcactggcatccatcaaa	5	12	3	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr15:28474355T>C	ENST00000261609.7	-	34	5366	c.5258A>G	c.(5257-5259)aAa>aGa	p.K1753R		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CTCTTTAAATTTGGCACTGGC	0.378																																					p.K1753R		Atlas-SNP	.											.	HERC2	501	.	0			c.A5258G						.						111	123	119					15																	28474355		2203	4300	6503	SO:0001583	missense	8924	exon34			TTAAATTTGGCAC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.5258A>G	chr15.hg19:g.28474355T>C	ENSP00000261609:p.Lys1753Arg	339.0	0.0		245.0	100.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	T	8.291	0.817701	0.16607	.	.	ENSG00000128731	ENST00000261609	T	0.38887	1.11	4.41	-0.914	0.10497	.	0.627123	0.16621	N	0.206467	T	0.24586	0.0596	L	0.27053	0.805	0.29395	N	0.862372	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	10	0.16420	T	0.52	.	10.2316	0.43258	0.0:0.546:0.0:0.454	.	1753	O95714	HERC2_HUMAN	R	1753	ENSP00000261609:K1753R	ENSP00000261609:K1753R	K	-	2	0	HERC2	26147950	0.976000	0.34144	0.969000	0.41365	0.995000	0.86356	0.467000	0.22035	-0.060000	0.13132	0.454000	0.30748	AAA	.	.		0.378	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		C	28474355	T	C	28474355	3	2	168	1	0	0	0	0	1	0	0	0	7067	1841	64	2	9486	2	HERC2	15	28474355	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10		28474355	74057037	160	25576										
GREM1	26585	hgsc.bcm.edu	37	chr15	33022899	33022899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tcctttctttagtatgagccGcacagcctacacggtgggag	11	11	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr15:33022899G>A	ENST00000300177.4	+	2	197	c.8G>A	c.(7-9)cGc>cAc	p.R3H	GREM1_ENST00000322805.4_Missense_Mutation_p.R3H|GREM1_ENST00000560677.1_Missense_Mutation_p.R3H|GREM1_ENST00000560830.1_Missense_Mutation_p.R3H	NM_001191322.1|NM_001191323.1|NM_013372.6	NP_001178251.1|NP_001178252.1|NP_037504.1	O60565	GREM1_HUMAN	gremlin 1, DAN family BMP antagonist	3					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell morphogenesis (GO:0000902)|collagen fibril organization (GO:0030199)|determination of dorsal identity (GO:0048263)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of bone mineralization (GO:0030502)|negative regulation of bone mineralization involved in bone maturation (GO:1900158)|negative regulation of bone remodeling (GO:0046851)|negative regulation of bone trabecula formation (GO:1900155)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine autophosphorylation (GO:1900086)|positive regulation of receptor activity (GO:2000273)|positive regulation of receptor internalization (GO:0002092)|positive regulation of telomerase activity (GO:0051973)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|regulation of epithelial to mesenchymal transition (GO:0010717)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|receptor agonist activity (GO:0048018)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)	10		all_lung(180;1.49e-09)		all cancers(64;2.97e-18)|Epithelial(43;3.15e-12)|GBM - Glioblastoma multiforme(186;2.32e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0107)		AGTATGAGCCGCACAGCCTAC	0.498																																					p.R3H		Atlas-SNP	.											.	GREM1	18	.	0			c.G8A						.						22	25	24					15																	33022899		2147	4212	6359	SO:0001583	missense	26585	exon2			TGAGCCGCACAGC		CCDS10029.1, CCDS53927.1	15q13.3	2014-02-07	2013-02-26	2004-05-07	ENSG00000166923	ENSG00000166923			2001	protein-coding gene	gene with protein product		603054	"cysteine knot superfamily 1, BMP antagonist 1", "gremlin 1, cysteine knot superfamily, homolog (Xenopus laevis)", "gremlin 1", "colorectal adenoma and carcinoma 1"	CKTSF1B1, CRAC1		9660951, 10026205, 22561515	Standard	NM_013372		Approved	DRM, gremlin, DAND2, HMPS	uc001zhe.2	O60565	OTTHUMG00000129319	ENST00000300177.4:c.8G>A	chr15.hg19:g.33022899G>A	ENSP00000300177:p.Arg3His	170.0	0.0		133.0	49.0	NM_001191322	Q52LV3|Q8N914|Q8N936	Missense_Mutation	SNP	ENST00000300177.4	hg19	CCDS10029.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.182110	0.78677	.	.	ENSG00000166923	ENST00000300177;ENST00000322805	T;T	0.35421	1.4;1.31	5.25	5.25	0.73442	.	0.245861	0.42294	D	0.000739	T	0.51143	0.1657	L	0.39898	1.24	0.48571	D	0.99967	D;P;P	0.69078	0.997;0.878;0.774	D;B;B	0.64237	0.923;0.074;0.161	T	0.47045	-0.9147	10	0.52906	T	0.07	-26.7977	19.0472	0.93027	0.0:0.0:1.0:0.0	.	3;3;3	O60565-2;O60565;B3KTR9	.;GREM1_HUMAN;.	H	3	ENSP00000300177:R3H;ENSP00000323101:R3H	ENSP00000300177:R3H	R	+	2	0	GREM1	30810191	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	8.576000	0.90770	2.749000	0.94314	0.655000	0.94253	CGC	.	.		0.498	GREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251455.2	NM_013372		A	33022899	G	A	33022899	3	1	168	1	0	0	0	0	1	0	0	0	6770	1087	38	1	10	1	GREM1	15	33022899	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	4548544	33022899	69508493	161	25577										
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43724680	43724680	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ccttctttctggtcttctagCacatctgtcaccattgcctc	5	15	6	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr15:43724680C>G	ENST00000263801.3	-	17	3624	c.3372G>C	c.(3370-3372)gtG>gtC	p.V1124V	TP53BP1_ENST00000382044.4_Silent_p.V1129V|TP53BP1_ENST00000450115.2_Silent_p.V1129V|TP53BP1_ENST00000382039.3_Silent_p.V1129V	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1124					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GGTCTTCTAGCACATCTGTCA	0.473								Other conserved DNA damage response genes																													p.V1129V		Atlas-SNP	.											.	TP53BP1	157	.	0			c.G3387C						.						136	126	129					15																	43724680		2201	4298	6499	SO:0001819	synonymous_variant	7158	exon17			TTCTAGCACATCT	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.3372G>C	chr15.hg19:g.43724680C>G		108.0	0.0		76.0	27.0	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	hg19	CCDS10096.1																																																																																			.	.		0.473	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			G	43724680	C	G	43724680	2	3	168	1	0	0	0	0	0	0	0	1	16398	697	25	4		4	TP53BP1	15	43724680	Silent	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	10701781	43724680	58806712	162	25578										
ANXA2	302	hgsc.bcm.edu	37	chr15	60678246	60678246	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	catcaccctccaagctgagcTtgcacaggatttcgtgaaca	8	13	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr15:60678246T>A	ENST00000396024.3	-	3	188	c.29A>T	c.(28-30)aAg>aTg	p.K10M	ANXA2_ENST00000332680.4_Missense_Mutation_p.K28M|ANXA2_ENST00000451270.2_Missense_Mutation_p.K10M|ANXA2_ENST00000421017.2_Missense_Mutation_p.K10M|ANXA2_ENST00000557937.1_5'UTR	NM_001136015.2	NP_001129487.1	P07355	ANXA2_HUMAN	annexin A2	10	S100A10-binding site. {ECO:0000255}.				angiogenesis (GO:0001525)|body fluid secretion (GO:0007589)|cellular response to acid chemical (GO:0071229)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|membrane budding (GO:0006900)|membrane raft assembly (GO:0001765)|negative regulation of catalytic activity (GO:0043086)|osteoclast development (GO:0036035)|positive regulation of binding (GO:0051099)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vesicle fusion (GO:0031340)|protein heterotetramerization (GO:0051290)|protein targeting to plasma membrane (GO:0072661)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell surface (GO:0009986)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|late endosome membrane (GO:0031902)|lipid particle (GO:0005811)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)|midbody (GO:0030496)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|sarcolemma (GO:0042383)|Schmidt-Lanterman incisure (GO:0043220)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phospholipase A2 inhibitor activity (GO:0019834)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			kidney(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9					Tenecteplase(DB00031)	CAAGCTGAGCTTGCACAGGAT	0.373																																					p.K28M		Atlas-SNP	.											.	ANXA2	28	.	0			c.A83T						.						76	70	72					15																	60678246		2203	4300	6503	SO:0001583	missense	302	exon2			CTGAGCTTGCACA	D00017	CCDS10175.1, CCDS32256.1	15q22.2	2012-10-02			ENSG00000182718	ENSG00000182718		"Annexins"	537	protein-coding gene	gene with protein product	"annexin II"	151740		ANX2, ANX2L4, CAL1H, LPC2D		7961821	Standard	NM_001136015		Approved	LIP2	uc002agm.3	P07355	OTTHUMG00000132763	ENST00000396024.3:c.29A>T	chr15.hg19:g.60678246T>A	ENSP00000379342:p.Lys10Met	525.0	0.0		403.0	187.0	NM_001002858	Q567R4|Q6N0B3|Q8TBV2|Q96DD5|Q9UDH8	Missense_Mutation	SNP	ENST00000396024.3	hg19	CCDS10175.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.065152	0.76187	.	.	ENSG00000182718	ENST00000396024;ENST00000332680;ENST00000421017;ENST00000451270	T;T;T;T	0.02177	4.45;4.41;4.45;4.45	5.64	5.64	0.86602	.	0.067843	0.64402	U	0.000017	T	0.04363	0.0120	N	0.08118	0	0.47949	D	0.999552	D;D;D	0.76494	0.994;0.999;0.976	D;D;P	0.79784	0.94;0.993;0.72	T	0.62329	-0.6877	10	0.51188	T	0.08	.	12.2636	0.54665	0.0:0.0:0.0:1.0	.	10;28;10	B4DNH8;P07355-2;P07355	.;.;ANXA2_HUMAN	M	10;28;10;10	ENSP00000379342:K10M;ENSP00000346032:K28M;ENSP00000411352:K10M;ENSP00000387545:K10M	ENSP00000346032:K28M	K	-	2	0	ANXA2	58465538	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.328000	0.59253	2.160000	0.67779	0.528000	0.53228	AAG	.	.		0.373	ANXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256135.1	NM_001002857		A	60678246	T	A	60678246	3	1	168	1	0	0	0	0	1	0	0	0	718	1609	56	4	1038	4	ANXA2	15	60678246	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	16953566	60678246	41853146	163	25579										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62212341	62212341	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ttgacttgaaggtaccatgcTggcatactccagttccaaat	8	10	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr15:62212341T>A	ENST00000261517.5	-	57	7475	c.7402A>T	c.(7402-7404)Agc>Tgc	p.S2468C	VPS13C_ENST00000249837.3_Missense_Mutation_p.S2425C|VPS13C_ENST00000395898.3_Missense_Mutation_p.S2425C|VPS13C_ENST00000395896.4_Missense_Mutation_p.S2468C	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						GGTACCATGCTGGCATACTCC	0.418																																					p.S2468C		Atlas-SNP	.											.	VPS13C	506	.	0			c.A7402T						.						107	105	106					15																	62212341		2203	4300	6503	SO:0001583	missense	54832	exon57			CCATGCTGGCATA	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.7402A>T	chr15.hg19:g.62212341T>A	ENSP00000261517:p.Ser2468Cys	128.0	0.0		126.0	45.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	10.86	1.470734	0.26423	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.46819	0.86;0.86;1.03	5.56	1.9	0.25705	.	0.660369	0.16388	N	0.216566	T	0.38612	0.1047	L	0.44542	1.39	0.09310	N	1	P;P;P;P	0.47604	0.606;0.738;0.898;0.836	P;B;P;B	0.45474	0.482;0.413;0.482;0.289	T	0.25745	-1.0123	10	0.56958	D	0.05	.	3.59	0.07985	0.1613:0.3049:0.0:0.5338	.	2425;2468;2425;2468	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	C	2425;2468;2468;2468	ENSP00000249837:S2425C;ENSP00000261517:S2468C;ENSP00000379233:S2468C	ENSP00000249837:S2425C	S	-	1	0	VPS13C	59999633	0.000000	0.05858	0.162000	0.22713	0.498000	0.33706	0.414000	0.21164	0.061000	0.16311	0.528000	0.53228	AGC	.	.		0.418	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62212341	T	A	62212341	3	1	168	1	0	0	0	0	1	0	0	0	17206	1580	55	4	4003	4	VPS13C	15	62212341	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	1534095	62212341	40319051	164	25580										
LACTB	114294	hgsc.bcm.edu	37	chr15	63419550	63419550	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	attttcatgtttttacaattAggtttctgtcacaacaagat	5	6	3	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr15:63419550A>T	ENST00000261893.4	+	4	687		c.e4-1		RPS27L_ENST00000559763.1_Intron|LACTB_ENST00000413507.2_Splice_Site	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta							cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						TTTTACAATTAGGTTTCTGTC	0.303																																					.	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											.	LACTB	29	.	0			c.616-2A>T						.						50	57	55					15																	63419550		2202	4290	6492	SO:0001630	splice_region_variant	114294	exon4			ACAATTAGGTTTC	AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"Mitochondrial ribosomal proteins / large subunits"	16468	protein-coding gene	gene with protein product		608440	"mitochondrial ribosomal protein L56"	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.616-1A>T	chr15.hg19:g.63419550A>T		214.0	0.0		198.0	81.0	NM_171846	P83096	Splice_Site	SNP	ENST00000261893.4	hg19	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.128033	0.77549	.	.	ENSG00000103642	ENST00000261893;ENST00000413507	.	.	.	6.01	6.01	0.97437	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7096	0.77615	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LACTB	61206603	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.339000	0.90041	2.307000	0.77673	0.528000	0.53228	.	.	.		0.303	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857	Intron	T	63419550	A	T	63419550	5	4	168	1	0	0	0	0	0	0	1	0	8606	434	15	4	628	4	LACTB	15	63419550	Splice_Site	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	1207209	63419550	39111842	165	25581										
KIAA1024	23251	hgsc.bcm.edu	37	chr15	79749293	79749293	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gaggattttcacaatttgatGgcagtgtcccccagtttggt	11	8	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr15:79749293G>A	ENST00000305428.3	+	2	879	c.804G>A	c.(802-804)atG>atA	p.M268I		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	268						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						ACAATTTGATGGCAGTGTCCC	0.493																																					p.M268I		Atlas-SNP	.											.	KIAA1024	146	.	0			c.G804A						.						85	96	92					15																	79749293		2196	4293	6489	SO:0001583	missense	23251	exon2			TTTGATGGCAGTG	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.804G>A	chr15.hg19:g.79749293G>A	ENSP00000307461:p.Met268Ile	141.0	0.0		132.0	54.0	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	hg19	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.741227	0.00675	.	.	ENSG00000169330	ENST00000305428	T	0.30981	1.51	5.29	2.09	0.27110	.	0.355735	0.34088	N	0.004274	T	0.11623	0.0283	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17745	-1.0359	9	.	.	.	.	3.8649	0.09012	0.0835:0.1928:0.4761:0.2476	.	268	Q9UPX6	K1024_HUMAN	I	268	ENSP00000307461:M268I	.	M	+	3	0	KIAA1024	77536348	0.947000	0.32204	0.064000	0.19789	0.257000	0.26127	1.101000	0.31037	1.156000	0.42514	0.591000	0.81541	ATG	.	.		0.493	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		A	79749293	G	A	79749293	3	1	168	1	0	0	0	0	1	0	0	0	8214	1348	47	3	806	3	KIAA1024	15	79749293	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	16329743	79749293	22782099	166	25582										
FLYWCH1	84256	hgsc.bcm.edu	37	chr16	2983205	2983205	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tacacgagtcgttcctctacAagcgggagaaggctgtcggg	14	10	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:2983205A>C	ENST00000253928.9	+	5	1276	c.871A>C	c.(871-873)Aag>Cag	p.K291Q	FLYWCH1_ENST00000416288.2_Missense_Mutation_p.K290Q|FLYWCH1_ENST00000399667.2_Missense_Mutation_p.K291Q			Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1	291						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|lung(3)	4						GTTCCTCTACAAGCGGGAGAA	0.657																																					p.K290Q		Atlas-SNP	.											.	FLYWCH1	27	.	0			c.A868C						.						37	40	39					16																	2983205		2048	4174	6222	SO:0001583	missense	84256	exon5			CTCTACAAGCGGG	AL136585	CCDS45390.1	16p13.3	2013-01-10	2007-06-21	2007-06-21	ENSG00000059122	ENSG00000059122		"Zinc fingers"	25404	protein-coding gene	gene with protein product						11230166, 10997877	Standard	XM_006720959		Approved	DKFZp761A132	uc002csc.3	Q4VC44		ENST00000253928.9:c.871A>C	chr16.hg19:g.2983205A>C	ENSP00000253928:p.Lys291Gln	46.0	0.0		42.0	10.0	NM_020912	D3DUA1|Q6ZSQ1|Q8WV62|Q9BQG6|Q9BUS5|Q9HCM0	Missense_Mutation	SNP	ENST00000253928.9	hg19		.	.	.	.	.	.	.	.	.	.	A	17.45	3.393250	0.62066	.	.	ENSG00000059122	ENST00000399667;ENST00000253928;ENST00000416288	.	.	.	4.04	4.04	0.47022	Zinc finger, FLYWCH-type (1);	.	.	.	.	T	0.54711	0.1875	L	0.48642	1.525	0.26490	N	0.974959	D;D	0.76494	0.999;0.996	D;D	0.81914	0.995;0.923	T	0.41270	-0.9518	8	0.54805	T	0.06	.	9.9533	0.41651	1.0:0.0:0.0:0.0	.	291;290	Q4VC44;Q4VC44-2	FWCH1_HUMAN;.	Q	291;291;290	.	ENSP00000253928:K291Q	K	+	1	0	FLYWCH1	2923206	1.000000	0.71417	1.000000	0.80357	0.603000	0.37013	2.665000	0.46791	1.791000	0.52520	0.459000	0.35465	AAG	.	.		0.657	FLYWCH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000436479.1	NM_032296		C	2983205	A	C	2983205	3	2	168	1	0	0	0	0	1	0	0	0	5955	131	5	5	878	5	FLYWCH1	16	2983205	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10		2983205	87371548	167	25583										
BTBD12	84464	hgsc.bcm.edu	37	chr16	3634809	3634809	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcaccggcgtctccataatgGaatactgtggcatcggcgtt	12	11	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:3634809G>C	ENST00000294008.3	-	13	5340	c.4700C>G	c.(4699-4701)tCc>tGc	p.S1567C	RP11-461A8.1_ENST00000573982.1_lincRNA	NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1567	Interaction with MUS81.|Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CTCCATAATGGAATACTGTGG	0.493								Direct reversal of damage																													p.S1567C		Atlas-SNP	.											.	SLX4	173	.	0			c.C4700G						.						174	162	166					16																	3634809		2197	4300	6497	SO:0001583	missense	84464	exon13			ATAATGGAATACT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.4700C>G	chr16.hg19:g.3634809G>C	ENSP00000294008:p.Ser1567Cys	125.0	0.0		95.0	47.0	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	hg19	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	G	26.2	4.711836	0.89112	.	.	ENSG00000188827	ENST00000294008	T	0.01538	4.79	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.11196	0.0273	M	0.77820	2.39	0.47094	D	0.999316	D	0.89917	1.0	D	0.91635	0.999	T	0.00046	-1.2214	10	0.87932	D	0	.	16.8496	0.85990	0.0:0.0:1.0:0.0	.	1567	Q8IY92	SLX4_HUMAN	C	1567	ENSP00000294008:S1567C	ENSP00000294008:S1567C	S	-	2	0	SLX4	3574810	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.904000	0.87408	2.723000	0.93209	0.655000	0.94253	TCC	.	.		0.493	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		C	3634809	G	C	3634809	3	2	168	1	0	0	0	0	1	0	0	0	1542	1174	41	4	816	4	BTBD12	16	3634809	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	651604	3634809	86719944	168	25584										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3807812	3807812	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	aaaaacttaaaactgtacctTgcgtccacagcaatatccaa	4	11	0	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:3807812T>A	ENST00000262367.5	-	18	4416	c.3607A>T	c.(3607-3609)Aag>Tag	p.K1203*	CREBBP_ENST00000382070.3_Nonsense_Mutation_p.K1165*	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1203	Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		AACTGTACCTTGCGTCCACAG	0.453			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.K1203X		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.A3607T						.						76	68	71					16																	3807812		2197	4300	6497	SO:0001587	stop_gained	1387	exon18			GTACCTTGCGTCC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.3607A>T	chr16.hg19:g.3807812T>A	ENSP00000262367:p.Lys1203*	33.0	0.0		48.0	19.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Nonsense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	T	50	16.370891	0.99861	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.0443	15.7654	0.78123	0.0:0.0:0.0:1.0	.	.	.	.	X	1203;1233;1165	.	ENSP00000262367:K1203X	K	-	1	0	CREBBP	3747813	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.932000	0.87634	2.127000	0.65507	0.477000	0.44152	AAG	.	.		0.453	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3807812	T	A	3807812	4	1	168	1	0	0	0	0	0	1	0	0	3863	1821	63	4	3777	4	CREBBP	16	3807812	Nonsense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	173003	3807812	86546941	169	25585										
ADCY9	115	hgsc.bcm.edu	37	chr16	4057436	4057436	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tccctgatgacgctgtccccTgtcccctagggcctgaggac	11	16	0	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:4057436T>A	ENST00000294016.3	-	3	2355	c.1817A>T	c.(1816-1818)cAg>cTg	p.Q606L	ADCY9_ENST00000571889.1_5'UTR	NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	606					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CGCTGTCCCCTGTCCCCTAGG	0.498																																					p.Q606L		Atlas-SNP	.											.	ADCY9	151	.	0			c.A1817T						.						110	97	101					16																	4057436		2197	4300	6497	SO:0001583	missense	115	exon3			GTCCCCTGTCCCC	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.1817A>T	chr16.hg19:g.4057436T>A	ENSP00000294016:p.Gln606Leu	44.0	0.0		29.0	12.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	hg19	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.643046	0.47153	.	.	ENSG00000162104	ENST00000294016	D	0.82984	-1.67	5.55	3.29	0.37713	.	0.348949	0.32416	N	0.006140	T	0.72415	0.3457	L	0.44542	1.39	0.43628	D	0.99601	B	0.26672	0.156	B	0.19666	0.026	T	0.63506	-0.6622	10	0.36615	T	0.2	.	5.9302	0.19134	0.0:0.0853:0.1664:0.7483	.	606	O60503	ADCY9_HUMAN	L	606	ENSP00000294016:Q606L	ENSP00000294016:Q606L	Q	-	2	0	ADCY9	3997437	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.903000	0.39858	0.476000	0.27440	0.523000	0.50628	CAG	.	.		0.498	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			A	4057436	T	A	4057436	3	1	168	1	0	0	0	0	1	0	0	0	301	1580	55	4	2280	4	ADCY9	16	4057436	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	249624	4057436	86297317	170	25586										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21086768	21086768	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcggttgcagtgagactcacAgtgtccctgtatttcacgaa	11	10	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:21086768A>T	ENST00000261383.3	-	21	3083	c.3084T>A	c.(3082-3084)acT>acA	p.T1028T	DNAH3_ENST00000415178.1_Splice_Site_p.T1028T	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1028	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TGAGACTCACAGTGTCCCTGT	0.448																																					p.T1028T		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T3084A						.						122	108	113					16																	21086768		2201	4300	6501	SO:0001630	splice_region_variant	55567	exon21			ACTCACAGTGTCC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.3084+1T>A	chr16.hg19:g.21086768A>T		260.0	0.0		220.0	105.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	hg19	CCDS10594.1																																																																																			.	.		0.448	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	Silent	T	21086768	A	T	21086768	5	4	168	1	0	0	0	0	0	0	1	0	4605	202	7	4	9433	4	DNAH3	16	21086768	Splice_Site	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	17029332	21086768	69267985	171	25587										
TAOK2	9344	hgsc.bcm.edu	37	chr16	29990374	29990374	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggcctggcatatctgcactcCcacaacatgatccataggta	8	13	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:29990374C>T	ENST00000308893.4	+	6	1475	c.432C>T	c.(430-432)tcC>tcT	p.S144S	TAOK2_ENST00000416441.2_5'Flank|TAOK2_ENST00000543033.1_Silent_p.S144S|TAOK2_ENST00000279394.3_Silent_p.S144S	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	144	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						ATCTGCACTCCCACAACATGA	0.577																																					p.S144S		Atlas-SNP	.											.	TAOK2	142	.	0			c.C432T						.						83	79	80					16																	29990374		2197	4300	6497	SO:0001819	synonymous_variant	9344	exon6			GCACTCCCACAAC	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.432C>T	chr16.hg19:g.29990374C>T		101.0	0.0		81.0	38.0	NM_004783	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Silent	SNP	ENST00000308893.4	hg19	CCDS10663.1																																																																																			.	.		0.577	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151		T	29990374	C	T	29990374	2	4	168	1	0	0	0	0	0	0	0	1	15563	610	22	3		3	TAOK2	16	29990374	Silent	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	8903606	29990374	60364379	172	25588										
LONP2	83752	hgsc.bcm.edu	37	chr16	48368263	48368263	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cttgggcccccgatgtatgaAatggaggtgattcattcttt	11	8	2	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:48368263A>C	ENST00000285737.4	+	12	2025	c.1932A>C	c.(1930-1932)gaA>gaC	p.E644D	LONP2_ENST00000535754.1_Missense_Mutation_p.E600D	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						CGATGTATGAAATGGAGGTGA	0.473																																					p.E644D		Atlas-SNP	.											.	LONP2	63	.	0			c.A1932C						.						137	132	134					16																	48368263		2200	4300	6500	SO:0001583	missense	83752	exon12			GTATGAAATGGAG	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.1932A>C	chr16.hg19:g.48368263A>C	ENSP00000285737:p.Glu644Asp	130.0	0.0		62.0	46.0	NM_031490		Missense_Mutation	SNP	ENST00000285737.4	hg19	CCDS10734.1	.	.	.	.	.	.	.	.	.	.	A	6.440	0.449304	0.12223	.	.	ENSG00000102910	ENST00000285737;ENST00000544734;ENST00000535754;ENST00000416006	T;T	0.30182	1.54;1.54	5.76	-1.05	0.10036	Peptidase S16, Lon C-terminal (1);	0.095518	0.64402	D	0.000001	T	0.07908	0.0198	N	0.02697	-0.525	0.32081	N	0.593103	B;B	0.12630	0.006;0.006	B;B	0.15484	0.013;0.013	T	0.32455	-0.9906	10	0.06365	T	0.9	-26.0722	3.3072	0.07003	0.3951:0.116:0.3765:0.1124	.	600;644	B7ZKL7;Q86WA8	.;LONP2_HUMAN	D	644;373;600;600	ENSP00000285737:E644D;ENSP00000445426:E600D	ENSP00000285737:E644D	E	+	3	2	LONP2	46925764	0.990000	0.36364	0.979000	0.43373	0.967000	0.64934	0.307000	0.19296	-0.372000	0.07992	-0.256000	0.11100	GAA	.	.		0.473	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		C	48368263	A	C	48368263	3	2	168	1	0	0	0	0	1	0	0	0	8902	11	1	5	1978	5	LONP2	16	48368263	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	18377889	48368263	41986490	173	25589										
CDH8	1006	hgsc.bcm.edu	37	chr16	61689606	61689606	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ttgaatccattatgctttgcCaaaatactgagggaattatc	7	7	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:61689606C>T	ENST00000577390.1	-	11	2628	c.1674G>A	c.(1672-1674)ttG>ttA	p.L558L	CDH8_ENST00000577730.1_Silent_p.L558L|CDH8_ENST00000299345.6_Silent_p.L558L	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	558	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		TATGCTTTGCCAAAATACTGA	0.348																																					p.L558L		Atlas-SNP	.											.	CDH8	273	.	0			c.G1674A						.						87	84	85					16																	61689606		2203	4300	6503	SO:0001819	synonymous_variant	1006	exon11			CTTTGCCAAAATA	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1674G>A	chr16.hg19:g.61689606C>T		177.0	0.0		78.0	57.0	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	hg19	CCDS10802.1																																																																																			.	.		0.348	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		T	61689606	C	T	61689606	2	4	168	1	0	0	0	0	0	0	0	1	3118	593	21	3		3	CDH8	16	61689606	Silent	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	13321343	61689606	28665147	174	25590										
AGRP	181	hgsc.bcm.edu	37	chr16	67517219	67517219	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	caggccttctgatgccctccAtgggggccaagcccatctgg	12	15	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:67517219A>T	ENST00000290953.2	-	2	382	c.83T>A	c.(82-84)aTg>aAg	p.M28K	ATP6V0D1_ENST00000290949.3_5'Flank|ATP6V0D1_ENST00000540149.1_5'Flank|RP11-297D21.4_ENST00000602596.1_RNA	NM_001138.1	NP_001129.1	O00253	AGRP_HUMAN	agouti related neuropeptide	28					adult feeding behavior (GO:0008343)|eating behavior (GO:0042755)|feeding behavior (GO:0007631)|hormone-mediated signaling pathway (GO:0009755)|maternal process involved in female pregnancy (GO:0060135)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of feeding behavior (GO:2000253)|regulation of feeding behavior (GO:0060259)|response to insulin (GO:0032868)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)	neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			endometrium(1)	1		Acute lymphoblastic leukemia(13;0.00263)|all_hematologic(13;0.0274)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0717)|Epithelial(162;0.16)		GATGCCCTCCATGGGGGCCAA	0.672																																					p.M28K		Atlas-SNP	.											.	AGRP	8	.	0			c.T83A						.						21	21	21					16																	67517219		2198	4299	6497	SO:0001583	missense	181	exon2			CCCTCCATGGGGG	U88063	CCDS10839.1	16q22	2014-07-15	2014-07-15		ENSG00000159723	ENSG00000159723		"Endogenous ligands"	330	protein-coding gene	gene with protein product		602311	"agouti (mouse) related protein", "agouti related protein homolog (mouse)"			9119224, 9311920	Standard	NM_001138		Approved	Agrt, ART, ASIP2	uc002etg.1	O00253	OTTHUMG00000137509	ENST00000290953.2:c.83T>A	chr16.hg19:g.67517219A>T	ENSP00000290953:p.Met28Lys	137.0	0.0		51.0	39.0	NM_001138	O15459|Q2TBD9	Missense_Mutation	SNP	ENST00000290953.2	hg19	CCDS10839.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.979494	0.34942	.	.	ENSG00000159723	ENST00000290953	T	0.40225	1.04	5.67	3.05	0.35203	.	0.773311	0.12205	N	0.489835	T	0.19846	0.0477	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.22312	-1.0220	10	0.18276	T	0.48	-9.3363	6.1218	0.20157	0.762:0.0:0.0894:0.1485	.	28	O00253	AGRP_HUMAN	K	28	ENSP00000290953:M28K	ENSP00000290953:M28K	M	-	2	0	AGRP	66074720	0.316000	0.24580	0.753000	0.31225	0.846000	0.48090	0.901000	0.28445	0.941000	0.37499	0.460000	0.39030	ATG	.	.		0.672	AGRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268828.1			T	67517219	A	T	67517219	3	4	168	1	0	0	0	0	1	0	0	0	398	217	8	4	327	4	AGRP	16	67517219	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	5827613	67517219	22837534	175	25591										
IL34	146433	hgsc.bcm.edu	37	chr16	70690996	70690996	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cctgcaggaggtggagacgcTgctgctgaatgtccagcagg	16	10	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:70690996T>A	ENST00000288098.2	+	4	757	c.374T>A	c.(373-375)cTg>cAg	p.L125Q	IL34_ENST00000429149.2_Missense_Mutation_p.L125Q|IL34_ENST00000566361.1_Missense_Mutation_p.L100Q	NM_001172772.1	NP_001166243.1	Q6ZMJ4	IL34_HUMAN	interleukin 34	125					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	extracellular space (GO:0005615)	macrophage colony-stimulating factor receptor binding (GO:0005157)			breast(1)|central_nervous_system(1)|kidney(9)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(2)	17						GTGGAGACGCTGCTGCTGAAT	0.602																																					p.L125Q		Atlas-SNP	.											.	IL34	26	.	0			c.T374A						.						114	80	91					16																	70690996		2198	4300	6498	SO:0001583	missense	146433	exon5			AGACGCTGCTGCT	BC029804	CCDS10895.1	16q22.1	2008-08-01	2008-06-04	2008-06-04	ENSG00000157368	ENSG00000157368		"Interleukins and interleukin receptors"	28529	protein-coding gene	gene with protein product		612081	"chromosome 16 open reading frame 77"	C16orf77		18467591	Standard	NM_152456		Approved	MGC34647, IL-34	uc002ezh.2	Q6ZMJ4	OTTHUMG00000137581	ENST00000288098.2:c.374T>A	chr16.hg19:g.70690996T>A	ENSP00000288098:p.Leu125Gln	43.0	0.0		22.0	18.0	NM_152456	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	Missense_Mutation	SNP	ENST00000288098.2	hg19	CCDS10895.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.461608	0.84317	.	.	ENSG00000157368	ENST00000429149;ENST00000288098	T;T	0.62941	-0.01;-0.01	5.18	5.18	0.71444	.	0.000000	0.56097	D	0.000030	T	0.71195	0.3311	M	0.78637	2.42	0.40811	D	0.983424	P;P	0.50943	0.94;0.94	P;P	0.54100	0.742;0.742	T	0.76146	-0.3066	10	0.87932	D	0	-19.628	8.5084	0.33201	0.1726:0.0:0.0:0.8274	.	124;125	Q6ZMJ4-2;Q6ZMJ4	.;IL34_HUMAN	Q	125	ENSP00000397863:L125Q;ENSP00000288098:L125Q	ENSP00000288098:L125Q	L	+	2	0	IL34	69248497	0.987000	0.35691	0.940000	0.37924	0.463000	0.32649	1.912000	0.39946	1.956000	0.56807	0.402000	0.26972	CTG	.	.		0.602	IL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268971.3	NM_152456		A	70690996	T	A	70690996	3	1	168	1	0	0	0	0	1	0	0	0	7703	1580	55	4	388	4	IL34	16	70690996	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	3173777	70690996	19663757	176	25592										
LRRC50	123872	hgsc.bcm.edu	37	chr16	84203529	84203529	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcggaaggcaaggaggagccTcccggggacagagaaacaag	17	9	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr16:84203529T>A	ENST00000378553.5	+	8	1219	c.1095T>A	c.(1093-1095)ccT>ccA	p.P365P	DNAAF1_ENST00000563818.1_3'UTR|DNAAF1_ENST00000334315.5_Silent_p.P365P	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	365					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						AGGAGGAGCCTCCCGGGGACA	0.532																																					p.P365P		Atlas-SNP	.											.	DNAAF1	81	.	0			c.T1095A						.						70	75	73					16																	84203529		2200	4300	6500	SO:0001819	synonymous_variant	123872	exon8			GGAGCCTCCCGGG	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"outer row dynein assembly 7 homolog (Chlamydomonas)"	613190	"leucine rich repeat containing 50"	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1095T>A	chr16.hg19:g.84203529T>A		130.0	0.0		58.0	44.0	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Silent	SNP	ENST00000378553.5	hg19	CCDS10943.2																																																																																			.	.		0.532	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452		A	84203529	T	A	84203529	2	1	168	1	0	0	0	0	0	0	0	1	9018	1538	54	4		4	LRRC50	16	84203529	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	13512533	84203529	6151224	177	25593										
NXN	64359	hgsc.bcm.edu	37	chr17	722716	722716	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cggttgaggcgcgaccgccgGgcctcatccgtgtaggggac	17	13	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:722716G>C	ENST00000336868.3	-	5	874	c.783C>G	c.(781-783)gcC>gcG	p.A261A	NXN_ENST00000538650.1_Silent_p.A12A|NXN_ENST00000575801.1_Silent_p.A153A|NXN_ENST00000537628.2_Silent_p.A12A	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	261	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		GCGACCGCCGGGCCTCATCCG	0.642																																					p.A261A		Atlas-SNP	.											.	NXN	32	.	0			c.C783G						.						64	63	63					17																	722716		2203	4300	6503	SO:0001819	synonymous_variant	64359	exon5			CCGCCGGGCCTCA		CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693			18008	protein-coding gene	gene with protein product		612895					Standard	NM_022463		Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.783C>G	chr17.hg19:g.722716G>C		106.0	0.0		52.0	42.0	NM_022463	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	Silent	SNP	ENST00000336868.3	hg19	CCDS10998.1																																																																																			.	.		0.642	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206669.1			C	722716	G	C	722716	2	2	168	1	0	0	0	0	0	0	0	1	10796	1219	43	4		4	NXN	17	722716	Silent	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10		722716	80472494	178	25594										
TP53	7157	hgsc.bcm.edu	37	chr17	7577595	7577598	+	Frame_Shift_Del	DEL	CAGT	CAGT	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agttgtagtggatggtggtaCagtcagagccaacctaggag							TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	CAGT	CAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:7577595_7577598delCAGT	ENST00000269305.4	-	7	872_875	c.683_686delACTG	c.(682-687)gactgtfs	p.DC228fs	TP53_ENST00000413465.2_Frame_Shift_Del_p.DC228fs|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000359597.4_Frame_Shift_Del_p.DC228fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.DC228fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.DC228fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.DC228fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	228	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		D -> A (in sporadic cancers; somatic mutation).|D -> E (in sporadic cancers; somatic mutation).|D -> G (in sporadic cancers; somatic mutation).|D -> H (in sporadic cancers; somatic mutation).|D -> N (in sporadic cancers; somatic mutation).|D -> P (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|D -> V (in sporadic cancers; somatic mutation).|D -> Y (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C229fs*10(14)|p.0?(8)|p.D228E(5)|p.?(5)|p.D228G(4)|p.C229fs*1(4)|p.D228D(3)|p.C229F(3)|p.D228V(2)|p.C229_H233delCTTIH(2)|p.C229S(2)|p.C229R(2)|p.C229Y(2)|p.D228A(2)|p.V225fs*23(1)|p.C136fs*10(1)|p.D228fs*12(1)|p.D228fs*11(1)|p.C229_I232del(1)|p.S227_I232delSDCTTI(1)|p.C136fs*1(1)|p.C136F(1)|p.G226_D228delGSD(1)|p.C229fs*18(1)|p.C229G(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGTGGTACAGTCAGAGCCAAC	0.525		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.228_229del	Pancreas(47;798 1329 9957 10801)	Atlas-INDEL	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,bile_duct,carcinoma,-1,1	TP53	33396	.	69	Substitution - Missense(24)|Deletion - Frameshift(19)|Whole gene deletion(8)|Deletion - In frame(5)|Unknown(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Complex - frameshift(1)	biliary_tract(13)|ovary(12)|breast(8)|oesophagus(6)|upper_aerodigestive_tract(5)|bone(5)|haematopoietic_and_lymphoid_tissue(3)|skin(3)|stomach(2)|central_nervous_system(2)|large_intestine(2)|urinary_tract(2)|prostate(2)|genital_tract(1)|lung(1)|pancreas(1)|liver(1)	c.684_687del						.																																			SO:0001589	frameshift_variant	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.683_686delACTG	chr17.hg19:g.7577595_7577598delCAGT	ENSP00000269305:p.Asp228fs	92.0	0.0		32.0	21.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.525	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7577598	CAGT	-	7577595	7	5	168	1	0	1	0	1	0	0	0	0	16396	478	17	0	604	0	TP53	17	7577595	Frame_Shift_Del	DEL	CAGT	TCGA-DD-AACQ-01A-11D-A40R-10	6854879	7577595	73617615	179	25595										
SDF2	6388	hgsc.bcm.edu	37	chr17	26982447	26982447	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tcttcccccgtatcctccagTaactgttgctgtcatccaca	5	16	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:26982447T>A	ENST00000247020.4	-	2	504	c.206A>T	c.(205-207)tAc>tTc	p.Y69F	SDF2_ENST00000592250.1_5'UTR	NM_006923.3	NP_008854.2	Q99470	SDF2_HUMAN	stromal cell-derived factor 2	69	MIR 1. {ECO:0000255|PROSITE- ProRule:PRU00131}.				protein glycosylation (GO:0006486)|protein O-linked mannosylation (GO:0035269)	extracellular space (GO:0005615)|membrane (GO:0016020)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Lung NSC(42;0.00431)					TATCCTCCAGTAACTGTTGCT	0.537																																					p.Y69F		Atlas-SNP	.											.	SDF2	17	.	0			c.A206T						.						201	181	188					17																	26982447		2203	4300	6503	SO:0001583	missense	6388	exon2			CTCCAGTAACTGT	BC001406	CCDS11238.1	17q11.2	2004-02-16			ENSG00000132581	ENSG00000132581			10675	protein-coding gene	gene with protein product		602934				8918255	Standard	NR_045585		Approved		uc002hbw.3	Q99470	OTTHUMG00000132681	ENST00000247020.4:c.206A>T	chr17.hg19:g.26982447T>A	ENSP00000247020:p.Tyr69Phe	132.0	0.0		123.0	58.0	NM_006923	Q9BQ79	Missense_Mutation	SNP	ENST00000247020.4	hg19	CCDS11238.1	.	.	.	.	.	.	.	.	.	.	T	33	5.194512	0.94960	.	.	ENSG00000132581	ENST00000247020	D	0.86230	-2.09	5.95	5.95	0.96441	MIR motif (2);MIR (2);	0.000000	0.85682	D	0.000000	D	0.91994	0.7464	M	0.83118	2.625	0.58432	D	0.999999	P	0.48407	0.91	P	0.53912	0.737	D	0.91681	0.5358	10	0.40728	T	0.16	-16.3264	16.0893	0.81082	0.0:0.0:0.0:1.0	.	69	Q99470	SDF2_HUMAN	F	69	ENSP00000247020:Y69F	ENSP00000247020:Y69F	Y	-	2	0	SDF2	24006574	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.688000	0.84153	2.279000	0.76181	0.533000	0.62120	TAC	.	.		0.537	SDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255965.2	NM_006923		A	26982447	T	A	26982447	3	1	168	1	0	0	0	0	1	0	0	0	13975	1638	57	4	437	4	SDF2	17	26982447	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	19404852	26982447	54212763	180	25596										
CCDC55	84081	hgsc.bcm.edu	37	chr17	28507943	28507943	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tagcatgtttggatgtaaccAagcagaaagatctcagtgga	11	6	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:28507943A>T	ENST00000247026.5	+	6	589	c.526A>T	c.(526-528)Aag>Tag	p.K176*	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	176					developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						GGATGTAACCAAGCAGAAAGA	0.373																																					p.K176X		Atlas-SNP	.											.	NSRP1	49	.	0			c.A526T						.						138	137	137					17																	28507943		2203	4300	6503	SO:0001587	stop_gained	84081	exon6			GTAACCAAGCAGA	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"coiled-coil domain containing 55"	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.526A>T	chr17.hg19:g.28507943A>T	ENSP00000247026:p.Lys176*	100.0	0.0		81.0	32.0	NM_032141	Q6FI71	Nonsense_Mutation	SNP	ENST00000247026.5	hg19	CCDS11255.1	.	.	.	.	.	.	.	.	.	.	A	19.95	3.922258	0.73213	.	.	ENSG00000126653	ENST00000247026;ENST00000540900;ENST00000394826	.	.	.	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.0647	14.104	0.65075	1.0:0.0:0.0:0.0	.	.	.	.	X	176;107;122	.	ENSP00000247026:K176X	K	+	1	0	NSRP1	25532069	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	8.850000	0.92190	1.918000	0.55548	0.533000	0.62120	AAG	.	.		0.373	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141		T	28507943	A	T	28507943	4	4	168	1	0	0	0	0	0	1	0	0	2827	131	5	4	548	4	CCDC55	17	28507943	Nonsense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	1525496	28507943	52687267	181	25597										
C17orf79	55352	hgsc.bcm.edu	37	chr17	30179202	30179202	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tcctgtttcaaagaccatctTggaataatagggtatcagtg	9	7	3	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:30179202T>A	ENST00000302362.6	-	4	648	c.511A>T	c.(511-513)Aag>Tag	p.K171*	COPRS_ENST00000378634.2_Nonsense_Mutation_p.K159*	NM_018405.3	NP_060875.2	Q9NQ92	COPRS_HUMAN	coordinator of PRMT5, differentiation stimulator	171					histone H4-R3 methylation (GO:0043985)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone binding (GO:0042393)										AAGACCATCTTGGAATAATAG	0.507																																					p.K171X		Atlas-SNP	.											.	.	.	.	0			c.A511T						.						131	114	120					17																	30179202		2203	4300	6503	SO:0001587	stop_gained	55352	exon4			CCATCTTGGAATA	AJ272196	CCDS11268.1	17q11.2	2012-11-16	2012-11-16	2012-11-16	ENSG00000172301	ENSG00000172301			28848	protein-coding gene	gene with protein product	"cooperator of PRMT5"		"chromosome 17 open reading frame 79"	C17orf79		10843809, 18404153	Standard	NM_018405		Approved	TTP1, HSA272196, COPR5	uc002hgp.3	Q9NQ92	OTTHUMG00000132812	ENST00000302362.6:c.511A>T	chr17.hg19:g.30179202T>A	ENSP00000304327:p.Lys171*	157.0	0.0		140.0	54.0	NM_018405	A6NP14|E1P656|Q96EF5|Q96P75	Nonsense_Mutation	SNP	ENST00000302362.6	hg19	CCDS11268.1	.	.	.	.	.	.	.	.	.	.	T	36	5.761698	0.96906	.	.	ENSG00000172301	ENST00000302362;ENST00000378634	.	.	.	5.02	5.02	0.67125	.	0.000000	0.53938	D	0.000055	.	.	.	.	.	.	0.50313	D	0.999863	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.5963	11.1531	0.48471	0.0:0.0:0.0:1.0	.	.	.	.	X	171;159	.	ENSP00000304327:K171X	K	-	1	0	C17orf79	27203315	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.371000	0.52379	1.877000	0.54381	0.533000	0.62120	AAG	.	.		0.507	COPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256257.2	NM_018405		A	30179202	T	A	30179202	4	1	168	1	0	0	0	0	0	1	0	0	1886	1821	63	4	47	4	C17orf79	17	30179202	Nonsense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	1671259	30179202	51016008	182	25598										
FNDC8	54752	hgsc.bcm.edu	37	chr17	33456507	33456507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	agctcctgttacaggaggtgGccaagacacaggagaatgag	14	8	0	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:33456507G>A	ENST00000158009.5	+	3	767	c.652G>A	c.(652-654)Gcc>Acc	p.A218T	NLE1_ENST00000586869.1_3'UTR	NM_017559.2	NP_060029.1	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	218	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	11		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)		ACAGGAGGTGGCCAAGACACA	0.527																																					p.A218T		Atlas-SNP	.											.	FNDC8	28	.	0			c.G652A						.						109	101	104					17																	33456507		2203	4300	6503	SO:0001583	missense	54752	exon3			GAGGTGGCCAAGA	BC024002	CCDS11290.1	17q12	2013-02-11			ENSG00000073598	ENSG00000073598		"Fibronectin type III domain containing"	25286	protein-coding gene	gene with protein product						12477932	Standard	XM_005257993		Approved	DKFZp434H2215	uc002hix.3	Q8TC99	OTTHUMG00000132932	ENST00000158009.5:c.652G>A	chr17.hg19:g.33456507G>A	ENSP00000158009:p.Ala218Thr	101.0	0.0		99.0	4.0	NM_017559	B2R9G6|Q9UFC2	Missense_Mutation	SNP	ENST00000158009.5	hg19	CCDS11290.1	.	.	.	.	.	.	.	.	.	.	G	5.984	0.365550	0.11352	.	.	ENSG00000073598	ENST00000158009	T	0.39056	1.1	5.24	-3.49	0.04724	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.335090	0.04914	N	0.453661	T	0.20414	0.0491	N	0.08118	0	0.09310	N	0.999999	B	0.14012	0.009	B	0.15052	0.012	T	0.16070	-1.0415	10	0.23302	T	0.38	-0.9997	6.4561	0.21930	0.5289:0.1327:0.3384:0.0	.	218	Q8TC99	FNDC8_HUMAN	T	218	ENSP00000158009:A218T	ENSP00000158009:A218T	A	+	1	0	FNDC8	30480620	0.418000	0.25440	0.000000	0.03702	0.004000	0.04260	0.040000	0.13905	-0.849000	0.04158	-1.263000	0.01449	GCC	.	.		0.527	FNDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256459.2	NM_017559		A	33456507	G	A	33456507	3	1	168	1	0	0	0	0	1	0	0	0	5982	1203	42	3	662	3	FNDC8	17	33456507	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	3277305	33456507	47738703	183	25599										
GAST	2520	hgsc.bcm.edu	37	chr17	39871711	39871711	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcagcgactgtgtgtgtatgTgctgatctttgcactggctc	13	9	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:39871711T>C	ENST00000329402.3	+	2	90	c.23T>C	c.(22-24)gTg>gCg	p.V8A	RNA5SP442_ENST00000365050.1_RNA|JUP_ENST00000540235.1_Intron	NM_000805.4	NP_000796.1	P01350	GAST_HUMAN	gastrin	8					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7		Breast(137;0.000307)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			TGTGTGTATGTGCTGATCTTT	0.597																																					p.V8A		Atlas-SNP	.											.	GAST	13	.	0			c.T23C						.						274	270	271					17																	39871711		2203	4300	6503	SO:0001583	missense	2520	exon2			TGTATGTGCTGAT		CCDS11404.1	17q21.2	2013-02-26	2005-06-14	2005-06-14	ENSG00000184502	ENSG00000184502		"Endogenous ligands"	4164	protein-coding gene	gene with protein product	"preprogastrin"	137250		GAS			Standard	NM_000805		Approved		uc002hxl.3	P01350	OTTHUMG00000133496	ENST00000329402.3:c.23T>C	chr17.hg19:g.39871711T>C	ENSP00000331358:p.Val8Ala	45.0	0.0		36.0	19.0	NM_000805	P78463|P78464	Missense_Mutation	SNP	ENST00000329402.3	hg19	CCDS11404.1	.	.	.	.	.	.	.	.	.	.	T	7.413	0.635168	0.14322	.	.	ENSG00000184502	ENST00000329402	T	0.29655	1.56	4.41	-4.9	0.03094	Gastrin/cholecystokinin peptide hormone (1);	1.513610	0.03922	N	0.283756	T	0.32882	0.0844	M	0.67953	2.075	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31308	-0.9948	10	0.33940	T	0.23	-0.1986	13.0563	0.58982	0.0:0.6478:0.0:0.3522	.	8	P01350	GAST_HUMAN	A	8	ENSP00000331358:V8A	ENSP00000331358:V8A	V	+	2	0	GAST	37125237	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.762000	0.00785	-1.504000	0.01810	-2.033000	0.00422	GTG	.	.		0.597	GAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257409.1			C	39871711	T	C	39871711	3	2	168	1	0	0	0	0	1	0	0	0	6260	1696	59	2	25	2	GAST	17	39871711	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	6415204	39871711	41323499	184	25600										
ATXN7L3	79089	hgsc.bcm.edu	37	chr17	42271987	42271987	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ccggctgatcagggcctggcTgtcagtcatgtcaaagctgt	13	11	4	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:42271987T>A	ENST00000587989.1	+	0	1969				ATXN7L3_ENST00000593073.1_5'UTR|ATXN7L3_ENST00000389384.4_Missense_Mutation_p.S265C|ATXN7L3_ENST00000454077.2_Missense_Mutation_p.S272C			Q71RG4	TMUB2_HUMAN	transmembrane and ubiquitin-like domain containing 2							integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(3)	8		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		AGGGCCTGGCTGTCAGTCATG	0.542																																					p.S272C		Atlas-SNP	.											.	ATXN7L3	31	.	0			c.A814T						.						45	48	47					17																	42271987		1970	4156	6126	SO:0001628	intergenic_variant	56970	exon11			CCTGGCTGTCAGT		CCDS11479.1, CCDS54134.1	17q21	2006-06-27				ENSG00000168591			28459	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_177441		Approved	MGC3123	uc002ifo.3	Q71RG4			chr17.hg19:g.42271987T>A		59.0	0.0		42.0	14.0	NM_020218	B3KU81|Q8NDI2|Q9BPZ5|Q9HAG3	Missense_Mutation	SNP	ENST00000587989.1	hg19	CCDS54134.1	.	.	.	.	.	.	.	.	.	.	T	16.22	3.063041	0.55432	.	.	ENSG00000087152	ENST00000454077;ENST00000389384;ENST00000541672	.	.	.	5.05	2.86	0.33363	.	0.108957	0.64402	D	0.000007	T	0.39937	0.1097	N	0.14661	0.345	0.38280	D	0.942413	D;D	0.61697	0.983;0.99	P;P	0.55824	0.615;0.785	T	0.36578	-0.9742	9	0.49607	T	0.09	.	7.2608	0.26201	0.0:0.2526:0.0:0.7474	.	265;272	Q14CW9;Q14CW9-2	AT7L3_HUMAN;.	C	272;265;47	.	ENSP00000374035:S265C	S	-	1	0	ATXN7L3	39627513	1.000000	0.71417	0.996000	0.52242	0.736000	0.42039	1.776000	0.38594	0.428000	0.26173	-0.250000	0.11733	AGC	.	.		0.542	TMUB2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457711.1	NM_177441		A	42271987	T	A	42271987	1	1	168	0	1	0	0	0	0	0	0	0	1218	1580	55	4		4	ATXN7L3	17	42271987	IGR	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	2400276	42271987	38923223	185	25601										
COL1A1	1277	hgsc.bcm.edu	37	chr17	48263006	48263006	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cttgccccaggctccggtgtGactctggggtggggcggaga	18	11	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:48263006G>C	ENST00000225964.5	-	51	4370	c.4252C>G	c.(4252-4254)Cac>Gac	p.H1418D		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	1418	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	GCTCCGGTGTGACTCTGGGGT	0.617			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.H1418D		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1	158	.	0			c.C4252G						.						70	61	64					17																	48263006		2203	4300	6503	SO:0001583	missense	1277	exon51			CGGTGTGACTCTG	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.4252C>G	chr17.hg19:g.48263006G>C	ENSP00000225964:p.His1418Asp	89.0	0.0		66.0	12.0	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Missense_Mutation	SNP	ENST00000225964.5	hg19	CCDS11561.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.753554	0.49362	.	.	ENSG00000108821	ENST00000225964	T	0.72942	-0.7	4.49	4.49	0.54785	Fibrillar collagen, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.86159	0.5866	M	0.89287	3.02	0.80722	D	1	D	0.62365	0.991	D	0.78314	0.991	D	0.89206	0.3561	10	0.87932	D	0	.	16.098	0.81144	0.0:0.0:1.0:0.0	.	1418	P02452	CO1A1_HUMAN	D	1418	ENSP00000225964:H1418D	ENSP00000225964:H1418D	H	-	1	0	COL1A1	45618005	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.720000	0.84759	2.333000	0.79357	0.313000	0.20887	CAC	.	.		0.617	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			C	48263006	G	C	48263006	3	2	168	1	0	0	0	0	1	0	0	0	3679	1290	45	4	146	4	COL1A1	17	48263006	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	5991019	48263006	32932204	186	25602										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48653340	48653340	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggagatccaggacagggatgCcaatgggtcccgccggctca	15	12	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:48653340C>G	ENST00000359106.5	+	8	1577	c.1577C>G	c.(1576-1578)gCc>gGc	p.A526G	CACNA1G_ENST00000358244.5_Missense_Mutation_p.A526G|CACNA1G_ENST00000510366.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000507510.2_Missense_Mutation_p.A526G|CACNA1G_ENST00000429973.2_Missense_Mutation_p.A526G|CACNA1G_ENST00000514181.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000505165.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000515411.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000442258.2_Missense_Mutation_p.A526G|CACNA1G_ENST00000503485.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000360761.4_Missense_Mutation_p.A526G|CACNA1G_ENST00000515765.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000510115.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000352832.5_Missense_Mutation_p.A526G|CACNA1G_ENST00000416767.4_Missense_Mutation_p.A526G|CACNA1G_ENST00000512389.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000513689.2_Missense_Mutation_p.A526G|CACNA1G_ENST00000514079.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000515165.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000513964.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000507896.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000514717.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000507336.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000354983.4_Missense_Mutation_p.A526G|CACNA1G_ENST00000502264.1_Missense_Mutation_p.A526G|CACNA1G_ENST00000507609.1_Missense_Mutation_p.A526G	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	526					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GACAGGGATGCCAATGGGTCC	0.692																																					p.A526G		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C1577G						.						11	19	16					17																	48653340		1942	4094	6036	SO:0001583	missense	8913	exon8			GGGATGCCAATGG	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.1577C>G	chr17.hg19:g.48653340C>G	ENSP00000352011:p.Ala526Gly	97.0	0.0		88.0	7.0	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	c	15.81	2.944535	0.53079	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96774	-3.98;-3.98;-4.12;-3.93;-3.98;-3.99;-4.0;-4.08;-4.05;-4.06;-4.07;-3.94;-3.95;-4.02;-3.96;-3.93;-4.0;-3.96;-3.94;-4.0;-3.98;-3.95;-3.99;-3.94;-4.0;-4.0	5.42	5.42	0.78866	.	0.615791	0.17391	N	0.175909	D	0.97052	0.9037	L	0.42245	1.32	0.44825	D	0.997837	D;B;P;D;B;D;D;B;D;B;B;P;B;B;D;B;D;P;B;B;D;B;B;B;B;D	0.76494	0.995;0.001;0.875;0.992;0.354;0.99;0.996;0.227;0.989;0.002;0.007;0.486;0.001;0.349;0.998;0.001;0.997;0.763;0.354;0.349;0.994;0.354;0.349;0.001;0.231;0.999	D;B;B;D;B;P;D;B;P;B;B;B;B;B;D;B;D;B;B;B;D;B;B;B;B;D	0.77004	0.978;0.005;0.377;0.989;0.146;0.625;0.986;0.101;0.868;0.004;0.006;0.333;0.005;0.108;0.986;0.001;0.91;0.21;0.146;0.079;0.97;0.138;0.114;0.001;0.039;0.958	D	0.95557	0.8626	10	0.22109	T	0.4	.	19.2315	0.93842	0.0:1.0:0.0:0.0	.	526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526;526	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	G	526	ENSP00000353990:A526G;ENSP00000339302:A526G;ENSP00000392390:A526G;ENSP00000347078:A526G;ENSP00000409759:A526G;ENSP00000425522:A526G;ENSP00000426261:A526G;ENSP00000425451:A526G;ENSP00000422407:A526G;ENSP00000426814:A526G;ENSP00000427238:A526G;ENSP00000423112:A526G;ENSP00000420918:A526G;ENSP00000426172:A526G;ENSP00000423045:A526G;ENSP00000427173:A526G;ENSP00000426098:A526G;ENSP00000425698:A526G;ENSP00000426232:A526G;ENSP00000423317:A526G;ENSP00000350979:A526G;ENSP00000352011:A526G;ENSP00000414388:A526G;ENSP00000423155:A526G;ENSP00000422268:A526G;ENSP00000421518:A526G	ENSP00000339302:A526G	A	+	2	0	CACNA1G	46008339	0.991000	0.36638	0.996000	0.52242	0.923000	0.55619	5.315000	0.65810	2.552000	0.86080	0.655000	0.94253	GCC	.	.		0.692	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		G	48653340	C	G	48653340	3	3	168	1	0	0	0	0	1	0	0	0	2546	739	26	4	1607	4	CACNA1G	17	48653340	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	390334	48653340	32541870	187	25603										
MFSD11	79157	hgsc.bcm.edu	37	chr17	74737121	74737121	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ttgtaggacctcaactctctAtgtttgccagtggtttattt	8	8	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:74737121A>C	ENST00000588460.1	+	3	2277	c.235A>C	c.(235-237)Atg>Ctg	p.M79L	MFSD11_ENST00000593181.1_Missense_Mutation_p.M79L|MFSD11_ENST00000590514.1_Missense_Mutation_p.M79L|MFSD11_ENST00000355954.3_Missense_Mutation_p.M79L|MFSD11_ENST00000336509.4_Missense_Mutation_p.M79L|MFSD11_ENST00000586622.1_Missense_Mutation_p.M79L	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	79						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						TCAACTCTCTATGTTTGCCAG	0.373																																					p.M79L		Atlas-SNP	.											.	MFSD11	47	.	0			c.A235C						.						224	207	213					17																	74737121		2203	4300	6503	SO:0001583	missense	79157	exon4			CTCTCTATGTTTG	BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.235A>C	chr17.hg19:g.74737121A>C	ENSP00000464932:p.Met79Leu	87.0	0.0		59.0	29.0	NM_001242536	O43442|Q9NXI5	Missense_Mutation	SNP	ENST00000588460.1	hg19	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	A	17.60	3.430840	0.62844	.	.	ENSG00000092931	ENST00000336509;ENST00000355954	T;T	0.76968	-1.06;-1.06	5.8	5.8	0.92144	Major facilitator superfamily domain, general substrate transporter (1);	0.071084	0.85682	D	0.000000	T	0.70064	0.3181	L	0.31526	0.94	0.80722	D	1	B;B	0.18741	0.03;0.024	B;B	0.26517	0.012;0.07	T	0.64689	-0.6348	10	0.31617	T	0.26	-31.2459	16.1429	0.81539	1.0:0.0:0.0:0.0	.	79;79	O43934-2;O43934	.;MFS11_HUMAN	L	79	ENSP00000337240:M79L;ENSP00000348225:M79L	ENSP00000337240:M79L	M	+	1	0	MFSD11	72248716	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	5.757000	0.68766	2.209000	0.71365	0.460000	0.39030	ATG	.	.		0.373	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311		C	74737121	A	C	74737121	3	2	168	1	0	0	0	0	1	0	0	0	9538	449	16	5	245	5	MFSD11	17	74737121	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	26083781	74737121	6458089	188	25604										
AZI1	22994	hgsc.bcm.edu	37	chr17	79167868	79167868	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctccgcctcgtgcaggctctTgagcctccgcacttcctgct	9	18	1	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr17:79167868T>A	ENST00000269392.4	-	18	2435	c.2188A>T	c.(2188-2190)Aag>Tag	p.K730*	AZI1_ENST00000374782.3_Nonsense_Mutation_p.K727*|AZI1_ENST00000450824.2_Nonsense_Mutation_p.K727*|AZI1_ENST00000575907.1_Nonsense_Mutation_p.K730*	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		730					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TGCAGGCTCTTGAGCCTCCGC	0.682																																					p.K727X		Atlas-SNP	.											.	AZI1	145	.	0			c.A2179T						.						16	18	17					17																	79167868		2192	4298	6490	SO:0001587	stop_gained	22994	exon18			GGCTCTTGAGCCT																												ENST00000269392.4:c.2188A>T	chr17.hg19:g.79167868T>A	ENSP00000269392:p.Lys730*	157.0	0.0		133.0	6.0	NM_014984	A6NHI8|B2RN11|Q96F50	Nonsense_Mutation	SNP	ENST00000269392.4	hg19		.	.	.	.	.	.	.	.	.	.	T	20.8	4.049475	0.75846	.	.	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	.	.	.	3.66	-0.274	0.12910	.	0.194661	0.41712	D	0.000823	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.1238	11.0905	0.48113	0.0:0.0:0.4607:0.5393	.	.	.	.	X	727;727;730	.	ENSP00000269392:K730X	K	-	1	0	AZI1	76782463	0.978000	0.34361	0.013000	0.15412	0.352000	0.29268	1.079000	0.30766	-0.303000	0.08856	-0.460000	0.05396	AAG	.	.		0.682	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			A	79167868	T	A	79167868	4	1	168	1	0	0	0	0	0	1	0	0	1240	1821	63	4	1099	4	AZI1	17	79167868	Nonsense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	4430747	79167868	2027342	189	25605										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2762178	2762178	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cacctacaccagctgtttcaAatgttcgctcagttgccagt	7	13	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr18:2762178A>T	ENST00000320876.6	+	36	4848	c.4510A>T	c.(4510-4512)Aat>Tat	p.N1504Y	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.N1504Y	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1504					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AGCTGTTTCAAATGTTCGCTC	0.383																																					p.N1504Y		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A4510T						.						174	164	167					18																	2762178		1859	4098	5957	SO:0001583	missense	23347	exon36			GTTTCAAATGTTC	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.4510A>T	chr18.hg19:g.2762178A>T	ENSP00000326603:p.Asn1504Tyr	177.0	0.0		181.0	51.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.850996	0.71719	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.26957	1.7;1.71	5.34	5.34	0.76211	.	0.100087	0.64402	D	0.000003	T	0.47488	0.1448	L	0.58669	1.825	0.41222	D	0.98651	D	0.71674	0.998	D	0.80764	0.994	T	0.45352	-0.9267	10	0.52906	T	0.07	-26.9511	15.3144	0.74062	1.0:0.0:0.0:0.0	.	1504	A6NHR9	SMHD1_HUMAN	Y	1504	ENSP00000326603:N1504Y;ENSP00000261598:N1504Y	ENSP00000261598:N1504Y	N	+	1	0	SMCHD1	2752178	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.702000	0.74628	2.016000	0.59253	0.528000	0.53228	AAT	.	.		0.383	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2762178	A	T	2762178	3	4	168	1	0	0	0	0	1	0	0	0	14803	14	1	4	4652	4	SMCHD1	18	2762178	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10		2762178	75315070	190	25606										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31319940	31319940	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	caattccagaacttgcttctActgaaatgataaaagttaaa	5	7	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr18:31319940A>G	ENST00000269197.5	+	11	2572	c.2572A>G	c.(2572-2574)Act>Gct	p.T858A		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	858					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						ACTTGCTTCTACTGAAATGAT	0.388																																					p.T858A		Atlas-SNP	.											.	ASXL3	405	.	0			c.A2572G						.						72	72	72					18																	31319940		1864	4104	5968	SO:0001583	missense	80816	exon11			GCTTCTACTGAAA	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.2572A>G	chr18.hg19:g.31319940A>G	ENSP00000269197:p.Thr858Ala	115.0	0.0		101.0	45.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	A	0.023	-1.401316	0.01165	.	.	ENSG00000141431	ENST00000269197	T	0.13778	2.56	6.04	-2.73	0.05950	.	1.744750	0.02847	N	0.128633	T	0.08492	0.0211	N	0.19112	0.55	0.19775	N	0.999952	B	0.02656	0.0	B	0.01281	0.0	T	0.27739	-1.0065	10	0.23302	T	0.38	.	4.9813	0.14166	0.2835:0.3593:0.2894:0.0678	.	858	Q9C0F0	ASXL3_HUMAN	A	858	ENSP00000269197:T858A	ENSP00000269197:T858A	T	+	1	0	ASXL3	29573938	0.982000	0.34865	0.581000	0.28614	0.071000	0.16799	0.216000	0.17585	-1.366000	0.02155	-1.450000	0.01041	ACT	.	.		0.388	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			G	31319940	A	G	31319940	3	3	168	1	0	0	0	0	1	0	0	0	1068	391	14	2	2614	2	ASXL3	18	31319940	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	28557762	31319940	46757308	191	25607										
ZNF396	252884	hgsc.bcm.edu	37	chr18	32953553	32953553	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcaatcatgtccttccttcgTccaaaaaagatctaaaaaca	4	11	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr18:32953553T>C	ENST00000589332.1	-	3	560	c.429A>G	c.(427-429)ggA>ggG	p.G143G	ZNF396_ENST00000586687.1_Silent_p.G143G|ZNF396_ENST00000306346.1_Silent_p.G143G			Q96N95	ZN396_HUMAN	zinc finger protein 396	143					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)	7						CCTTCCTTCGTCCAAAAAAGA	0.433																																					p.G143G		Atlas-SNP	.											.	ZNF396	28	.	0			c.A429G						.						81	72	75					18																	32953553		2203	4300	6503	SO:0001819	synonymous_variant	252884	exon3			CCTTCGTCCAAAA	AK055775	CCDS11913.1	18p12	2013-01-09			ENSG00000186496	ENSG00000186496		"-", "Zinc fingers, C2H2-type"	18824	protein-coding gene	gene with protein product		609600					Standard	NM_145756		Approved	ZSCAN14, FLJ31213	uc010xcf.1	Q96N95	OTTHUMG00000132562	ENST00000589332.1:c.429A>G	chr18.hg19:g.32953553T>C		73.0	0.0		72.0	4.0	NM_145756	A1L3V0|Q8NF98|Q8TD80	Silent	SNP	ENST00000589332.1	hg19																																																																																				.	.		0.433	ZNF396-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255766.1	NM_145756		C	32953553	T	C	32953553	2	2	168	1	0	0	0	0	0	0	0	1	17897	1654	58	2		2	ZNF396	18	32953553	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	1633613	32953553	45123695	192	25608										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43497668	43497668	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cattcttcagaaggtaatacTggcaagggtaaaataaaggc	10	6	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr18:43497668T>A	ENST00000282041.5	-	17	3249	c.3215A>T	c.(3214-3216)cAg>cTg	p.Q1072L	EPG5_ENST00000585906.1_5'Flank	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1072					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						AAGGTAATACTGGCAAGGGTA	0.428																																					p.Q1072L		Atlas-SNP	.											EPG5,NS,carcinoma,0,1	EPG5	199	.	0			c.A3215T						.						172	159	163					18																	43497668		1880	4118	5998	SO:0001583	missense	57724	exon17			TAATACTGGCAAG	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.3215A>T	chr18.hg19:g.43497668T>A	ENSP00000282041:p.Gln1072Leu	196.0	0.0		174.0	72.0	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	T	15.74	2.924156	0.52653	.	.	ENSG00000152223	ENST00000282041	T	0.10573	2.86	5.4	5.4	0.78164	.	1.079280	0.06987	N	0.820984	T	0.27419	0.0673	L	0.59436	1.845	0.46954	D	0.999262	D;D	0.56035	0.974;0.974	P;P	0.53861	0.736;0.736	T	0.00422	-1.1749	10	0.54805	T	0.06	-15.201	15.712	0.77635	0.0:0.0:0.0:1.0	.	1072;1072	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	L	1072	ENSP00000282041:Q1072L	ENSP00000282041:Q1072L	Q	-	2	0	EPG5	41751666	1.000000	0.71417	1.000000	0.80357	0.375000	0.29983	3.489000	0.53237	2.178000	0.69098	0.533000	0.62120	CAG	.	.		0.428	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		A	43497668	T	A	43497668	3	1	168	1	0	0	0	0	1	0	0	0	8258	1580	55	4	4636	4	KIAA1632	18	43497668	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	10544115	43497668	34579580	193	25609										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610421	10610421	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggatgaggccagcaccacctTgtgggccatgaactgggcgg	16	11	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr19:10610421T>A	ENST00000171111.5	-	2	836	c.289A>T	c.(289-291)Aag>Tag	p.K97*	KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Nonsense_Mutation_p.K97*	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	97	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	AGCACCACCTTGTGGGCCATG	0.612																																					p.K97X		Atlas-SNP	.											.	KEAP1	182	.	0			c.A289T						.						81	64	70					19																	10610421		2203	4300	6503	SO:0001587	stop_gained	9817	exon2			CCACCTTGTGGGC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.289A>T	chr19.hg19:g.10610421T>A	ENSP00000171111:p.Lys97*	90.0	0.0		48.0	36.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Nonsense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	T	37	6.132171	0.97310	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	.	.	.	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.0934	0.53739	0.0:0.0:0.0:1.0	.	.	.	.	X	97	.	ENSP00000171111:K97X	K	-	1	0	KEAP1	10471421	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	3.331000	0.52075	1.756000	0.51951	0.379000	0.24179	AAG	.	.		0.612	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		A	10610421	T	A	10610421	4	1	168	1	0	0	0	0	0	1	0	0	8150	1821	63	4	1605	4	KEAP1	19	10610421	Nonsense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10		10610421	48518562	194	25610										
YIPF2	78992	hgsc.bcm.edu	37	chr19	11034009	11034009	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ggcaaggtaggggacagcgcGatgtttgagggcagagatgt	19	5	0	2	rs151256467	byFrequency	TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr19:11034009G>C	ENST00000586748.1	-	9	1081	c.909C>G	c.(907-909)atC>atG	p.I303M	YIPF2_ENST00000590329.1_Missense_Mutation_p.I264M|YIPF2_ENST00000253031.2_Missense_Mutation_p.I303M			Q9BWQ6	YIPF2_HUMAN	Yip1 domain family, member 2	303						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				cervix(1)|endometrium(1)|lung(3)|ovary(2)	7						GGGACAGCGCGATGTTTGAGG	0.627																																					p.I303M		Atlas-SNP	.											YIPF2,bladder,carcinoma,0,1	YIPF2	13	.	0			c.C909G						.						158	154	155					19																	11034009		2203	4300	6503	SO:0001583	missense	78992	exon9			CAGCGCGATGTTT	BC013014	CCDS12251.1	19p13.2	2008-02-05				ENSG00000130733		"Yip1 domain family"	28476	protein-coding gene	gene with protein product						12477932	Standard	NM_024029		Approved	MGC3262, FinGER2	uc002mqc.3	Q9BWQ6		ENST00000586748.1:c.909C>G	chr19.hg19:g.11034009G>C	ENSP00000466055:p.Ile303Met	108.0	0.0		65.0	34.0	NM_024029		Missense_Mutation	SNP	ENST00000586748.1	hg19	CCDS12251.1	.	.	.	.	.	.	.	.	.	.	G	8.286	0.816577	0.16607	.	.	ENSG00000130733	ENST00000253031	.	.	.	4.48	-8.95	0.00765	.	4.078650	0.00397	N	0.000042	T	0.17619	0.0423	N	0.22421	0.69	0.09310	N	1	B	0.29716	0.255	B	0.20384	0.029	T	0.06534	-1.0821	9	0.29301	T	0.29	-21.9981	4.0341	0.09722	0.0909:0.3705:0.3725:0.1662	.	303	Q9BWQ6	YIPF2_HUMAN	M	303	.	ENSP00000253031:I303M	I	-	3	3	YIPF2	10895009	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.927000	0.00690	-2.032000	0.00926	-0.271000	0.10264	ATC	.	G|1.000;A|0.000		0.627	YIPF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453045.1	NM_024029		C	11034009	G	C	11034009	3	2	168	1	0	0	0	0	1	0	0	0	17493	1048	37	4	45	4	YIPF2	19	11034009	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	423588	11034009	48094974	195	25611										
RFX1	5989	hgsc.bcm.edu	37	chr19	14104453	14104453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cgtactgcttctggccacccGgtggctgtgcctggggctgg	16	13	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr19:14104453G>A	ENST00000254325.4	-	2	437	c.203C>T	c.(202-204)cCg>cTg	p.P68L		NM_002918.4	NP_002909.4	P22670	RFX1_HUMAN	regulatory factor X, 1 (influences HLA class II expression)	68					immune response (GO:0006955)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)			CTGGCCACCCGGTggctgtgc	0.706																																					p.P68L		Atlas-SNP	.											.	RFX1	63	.	0			c.C203T						.						23	19	20					19																	14104453		2201	4298	6499	SO:0001583	missense	5989	exon2			CCACCCGGTGGCT		CCDS12301.1	19p13.1	2008-07-17				ENSG00000132005			9982	protein-coding gene	gene with protein product	"trans-acting regulatory factor 1", "enhancer factor C", "MHC class II regulatory factor RFX"	600006				1505960, 8289803	Standard	NM_002918		Approved	EF-C	uc002mxv.3	P22670		ENST00000254325.4:c.203C>T	chr19.hg19:g.14104453G>A	ENSP00000254325:p.Pro68Leu	123.0	0.0		105.0	7.0	NM_002918		Missense_Mutation	SNP	ENST00000254325.4	hg19	CCDS12301.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382794	0.82792	.	.	ENSG00000132005	ENST00000254325	T	0.65178	-0.14	5.17	5.17	0.71159	.	0.379500	0.22255	N	0.062499	T	0.52158	0.1717	L	0.27053	0.805	0.41730	D	0.989554	D	0.54207	0.965	B	0.42087	0.375	T	0.60510	-0.7249	10	0.66056	D	0.02	-24.3835	15.9534	0.79861	0.0:0.0:1.0:0.0	.	68	P22670	RFX1_HUMAN	L	68	ENSP00000254325:P68L	ENSP00000254325:P68L	P	-	2	0	RFX1	13965453	0.943000	0.32029	0.860000	0.33809	0.979000	0.70002	2.812000	0.47994	2.578000	0.87016	0.650000	0.86243	CCG	.	.		0.706	RFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458510.1	NM_002918		A	14104453	G	A	14104453	3	1	168	1	0	0	0	0	1	0	0	0	13277	1116	39	1	2816	1	RFX1	19	14104453	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	3070444	14104453	45024530	196	25612										
SYDE1	85360	hgsc.bcm.edu	37	chr19	15221086	15221086	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctcctgcgcgccctggtgctTgcgtgggaccctggcgtgag	16	14	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr19:15221086T>A	ENST00000342784.2	+	3	1033	c.1002T>A	c.(1000-1002)ctT>ctA	p.L334L	SYDE1_ENST00000600440.1_Silent_p.L267L|SYDE1_ENST00000600252.1_5'UTR	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	334					activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)			endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						CCCTGGTGCTTGCGTGGGACC	0.716																																					p.L334L		Atlas-SNP	.											.	SYDE1	44	.	0			c.T1002A						.						6	9	8					19																	15221086		1927	3674	5601	SO:0001819	synonymous_variant	85360	exon3			GGTGCTTGCGTGG	BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.1002T>A	chr19.hg19:g.15221086T>A		46.0	0.0		51.0	16.0	NM_033025	Q7L2I8|Q8N6J2|Q9H8K4	Silent	SNP	ENST00000342784.2	hg19	CCDS12324.1																																																																																			.	.		0.716	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025		A	15221086	T	A	15221086	2	1	168	1	0	0	0	0	0	0	0	1	15450	1799	63	4		4	SYDE1	19	15221086	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	1116633	15221086	43907897	197	25613										
RYR1	6261	hgsc.bcm.edu	37	chr19	38973749	38973749	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ccagtttgagctggggaagcAgaaggtacaagtgcagtgat	15	6	0	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr19:38973749A>T	ENST00000359596.3	+	32	4703	c.4703A>T	c.(4702-4704)cAg>cTg	p.Q1568L	RYR1_ENST00000360985.3_Missense_Mutation_p.Q1568L|RYR1_ENST00000355481.4_Missense_Mutation_p.Q1568L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1568	6 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTGGGGAAGCAGAAGGTACAA	0.602																																					p.Q1568L		Atlas-SNP	.											.	RYR1	708	.	0			c.A4703T						.						136	104	115					19																	38973749		2203	4300	6503	SO:0001583	missense	6261	exon32			GGAAGCAGAAGGT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.4703A>T	chr19.hg19:g.38973749A>T	ENSP00000352608:p.Gln1568Leu	85.0	0.0		78.0	35.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	A	10.76	1.442264	0.25987	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.68624	-0.34;-0.34;-0.34	4.33	2.07	0.26955	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.350892	0.21765	U	0.069444	T	0.24236	0.0587	N	0.00170	-1.935	0.31756	N	0.633958	B;B	0.09022	0.002;0.002	B;B	0.12156	0.001;0.007	T	0.25433	-1.0132	10	0.16420	T	0.52	.	9.1032	0.36681	0.3038:0.0:0.0:0.6962	.	1568;1568	P21817-2;P21817	.;RYR1_HUMAN	L	1568	ENSP00000352608:Q1568L;ENSP00000347667:Q1568L;ENSP00000354254:Q1568L	ENSP00000347667:Q1568L	Q	+	2	0	RYR1	43665589	1.000000	0.71417	0.997000	0.53966	0.854000	0.48673	4.262000	0.58847	0.181000	0.19994	0.379000	0.24179	CAG	.	.		0.602	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38973749	A	T	38973749	3	4	168	1	0	0	0	0	1	0	0	0	13783	188	7	4	4829	4	RYR1	19	38973749	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	23752663	38973749	20155234	198	25614										
DEDD2	162989	hgsc.bcm.edu	37	chr19	42713986	42713986	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gccgctgccgcttggttgggGgggagcctgaggggaaaaaa	19	8	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr19:42713986G>A	ENST00000595337.1	-	4	542	c.455C>T	c.(454-456)cCc>cTc	p.P152L	DEDD2_ENST00000598727.1_Missense_Mutation_p.P152L|DEDD2_ENST00000596251.1_Missense_Mutation_p.P152L|DEDD2_ENST00000593804.1_5'UTR|DEDD2_ENST00000336034.4_Missense_Mutation_p.P147L	NM_001270614.1	NP_001257543.1	Q8WXF8	DEDD2_HUMAN	death effector domain containing 2	152					apoptotic nuclear changes (GO:0030262)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|RNA processing (GO:0006396)|rRNA catabolic process (GO:0016075)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|large_intestine(1)|ovary(1)|prostate(2)	5		Prostate(69;0.0704)				CTTGGTTGGGGGGGAGCCTGA	0.657																																					p.P152L		Atlas-SNP	.											.	DEDD2	16	.	0			c.C455T						.						14	17	16					19																	42713986		1976	3972	5948	SO:0001583	missense	162989	exon4			GTTGGGGGGGAGC	AY125488	CCDS12597.1, CCDS59391.1	19q13.31	2008-02-05				ENSG00000160570			24450	protein-coding gene	gene with protein product						11965497, 12235123	Standard	NM_133328		Approved	FLAME-3	uc031rkv.1	Q8WXF8		ENST00000595337.1:c.455C>T	chr19.hg19:g.42713986G>A	ENSP00000470082:p.Pro152Leu	111.0	0.0		96.0	37.0	NM_133328	Q8NBR2|Q8NES1|Q8TAA8|Q96D35	Missense_Mutation	SNP	ENST00000595337.1	hg19	CCDS12597.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.895665	0.52121	.	.	ENSG00000160570	ENST00000336034	.	.	.	3.81	3.81	0.43845	.	0.521378	0.20537	N	0.090382	T	0.22551	0.0544	N	0.08118	0	0.28696	N	0.904337	P;P	0.44659	0.84;0.753	P;B	0.47206	0.541;0.339	T	0.03493	-1.1031	9	0.20519	T	0.43	-23.0781	9.6457	0.39865	0.0:0.2132:0.7868:0.0	.	147;152	Q8WXF8-2;Q8WXF8	.;DEDD2_HUMAN	L	152	.	ENSP00000336972:P152L	P	-	2	0	DEDD2	47405826	0.321000	0.24625	0.876000	0.34364	0.763000	0.43281	0.743000	0.26231	2.426000	0.82243	0.467000	0.42956	CCC	.	.		0.657	DEDD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463508.1	NM_133328		A	42713986	G	A	42713986	3	1	168	1	0	0	0	0	1	0	0	0	4387	1232	43	3	533	3	DEDD2	19	42713986	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	3740237	42713986	16414997	199	25615										
EXOC3L2	90332	hgsc.bcm.edu	37	chr19	45731442	45731442	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cctcacacacatcctgggccAggctgctgggctggtcctcc	11	17	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr19:45731442A>T	ENST00000252482.3	-	2	200	c.173T>A	c.(172-174)cTg>cAg	p.L58Q	EXOC3L2_ENST00000413988.1_Missense_Mutation_p.L58Q			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	58					exocytosis (GO:0006887)	exocyst (GO:0000145)				endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		ATCCTGGGCCAGGCTGCTGGG	0.657																																					p.L58Q		Atlas-SNP	.											.	EXOC3L2	30	.	0			c.T173A						.						108	109	109					19																	45731442		2203	4300	6503	SO:0001583	missense	90332	exon3			TGGGCCAGGCTGC	AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.173T>A	chr19.hg19:g.45731442A>T	ENSP00000252482:p.Leu58Gln	125.0	0.0		85.0	34.0	NM_138568	Q8N9W2|Q96GV2	Missense_Mutation	SNP	ENST00000252482.3	hg19	CCDS12657.1	.	.	.	.	.	.	.	.	.	.	A	17.64	3.439540	0.63067	.	.	ENSG00000130201	ENST00000252482;ENST00000413988	T;T	0.07688	3.17;3.17	4.89	4.89	0.63831	.	0.000000	0.53938	D	0.000057	T	0.23846	0.0577	M	0.64997	1.995	0.33454	D	0.584075	D	0.89917	1.0	D	0.97110	1.0	T	0.26360	-1.0105	10	0.52906	T	0.07	.	10.8643	0.46844	1.0:0.0:0.0:0.0	.	58	Q2M3D2	EX3L2_HUMAN	Q	58	ENSP00000252482:L58Q;ENSP00000400713:L58Q	ENSP00000252482:L58Q	L	-	2	0	EXOC3L2	50423282	1.000000	0.71417	0.998000	0.56505	0.642000	0.38348	4.999000	0.63934	1.836000	0.53414	0.254000	0.18369	CTG	.	.		0.657	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568		T	45731442	A	T	45731442	3	4	168	1	0	0	0	0	1	0	0	0	5307	188	7	4	1088	4	EXOC3L2	19	45731442	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	3017456	45731442	13397541	200	25616										
DKKL1	27120	hgsc.bcm.edu	37	chr19	49868854	49868854	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctaccacaaagaggagaaccAggagcaccagctggggaaca	12	11	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr19:49868854A>T	ENST00000221498.2	+	3	677	c.272A>T	c.(271-273)cAg>cTg	p.Q91L	DKKL1_ENST00000594268.1_Intron	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	91					anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		GAGGAGAACCAGGAGCACCAG	0.607																																					p.Q91L		Atlas-SNP	.											.	DKKL1	23	.	0			c.A272T						.						91	82	85					19																	49868854		2203	4300	6503	SO:0001583	missense	27120	exon3			AGAACCAGGAGCA	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"cancer/testis antigen 34", "soggy"	605418	"dickkopf-like 1 (soggy)"			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.272A>T	chr19.hg19:g.49868854A>T	ENSP00000221498:p.Gln91Leu	88.0	0.0		78.0	38.0	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	hg19	CCDS12762.1	.	.	.	.	.	.	.	.	.	.	A	19.22	3.785406	0.70337	.	.	ENSG00000104901	ENST00000221498	T	0.12361	2.69	4.85	2.59	0.31030	.	0.000000	0.38959	N	0.001517	T	0.10208	0.0250	L	0.46157	1.445	0.31441	N	0.671943	P	0.40731	0.728	B	0.36186	0.219	T	0.11690	-1.0577	10	0.59425	D	0.04	-23.8153	4.6736	0.12701	0.7059:0.193:0.1012:0.0	.	91	Q9UK85	DKKL1_HUMAN	L	91	ENSP00000221498:Q91L	ENSP00000221498:Q91L	Q	+	2	0	DKKL1	54560666	0.987000	0.35691	1.000000	0.80357	0.990000	0.78478	0.615000	0.24329	0.808000	0.34231	0.459000	0.35465	CAG	.	.		0.607	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419		T	49868854	A	T	49868854	3	4	168	1	0	0	0	0	1	0	0	0	4550	188	7	4	282	4	DKKL1	19	49868854	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	4137412	49868854	9260129	201	25617										
CCDC155	147872	hgsc.bcm.edu	37	chr19	49901341	49901341	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cagcggagcatggagacagcTgaggaggggtcagcacgcct	17	10	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr19:49901341T>A	ENST00000447857.3	+	7	775	c.570T>A	c.(568-570)gcT>gcA	p.A190A		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	190						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						TGGAGACAGCTGAGGAGGGGT	0.632																																					p.A190A		Atlas-SNP	.											.	CCDC155	46	.	0			c.T570A						.						52	56	55					19																	49901341		2103	4223	6326	SO:0001819	synonymous_variant	147872	exon7			GACAGCTGAGGAG		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.570T>A	chr19.hg19:g.49901341T>A		151.0	0.0		116.0	51.0	NM_144688	Q96MC3	Silent	SNP	ENST00000447857.3	hg19	CCDS46140.1																																																																																			.	.		0.632	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688		A	49901341	T	A	49901341	2	1	168	1	0	0	0	0	0	0	0	1	2790	1567	55	4		4	CCDC155	19	49901341	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	32487	49901341	9227642	202	25618										
SIGLEC11	114132	hgsc.bcm.edu	37	chr19	50463581	50463581	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	caggagaaagaaggggctggAcatttcttgaaagcccagtt	13	7	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr19:50463581A>T	ENST00000447370.2	-	3	648	c.558T>A	c.(556-558)tgT>tgA	p.C186*	CTC-326K19.6_ENST00000451973.1_5'Flank|SIGLEC11_ENST00000426971.2_Nonsense_Mutation_p.C186*	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	186	Ig-like C2-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		AAGGGGCTGGACATTTCTTGA	0.597																																					p.C186X		Atlas-SNP	.											.	SIGLEC11	70	.	0			c.T558A						.						13	21	18					19																	50463581		1979	4239	6218	SO:0001587	stop_gained	114132	exon3			GGCTGGACATTTC	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.558T>A	chr19.hg19:g.50463581A>T	ENSP00000412361:p.Cys186*	263.0	0.0		267.0	59.0	NM_052884		Nonsense_Mutation	SNP	ENST00000447370.2	hg19	CCDS12790.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.78|17.78	3.473476|3.473476	0.63737|0.63737	.|.	.|.	ENSG00000161640|ENSG00000161640	ENST00000447370;ENST00000458019|ENST00000426971	.|.	.|.	.|.	3.28|3.28	-6.57|-6.57	0.01842|0.01842	.|.	0.226724|.	0.32055|.	N|.	0.006647|.	.|T	.|0.16981	.|0.0408	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.21827	.|-1.0234	.|3	.|.	.|.	.|.	.|.	2.4926|2.4926	0.04614|0.04614	0.1868:0.2968:0.3908:0.1255|0.1868:0.2968:0.3908:0.1255	.|.	.|.	.|.	.|.	X|D	186|176	.|.	.|.	C|V	-|-	3|2	2|0	SIGLEC11|SIGLEC11	55155393|55155393	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.077000|0.077000	0.17291|0.17291	-0.596000|-0.596000	0.05720|0.05720	-1.620000|-1.620000	0.01564|0.01564	0.459000|0.459000	0.35465|0.35465	TGT|GTC	.	.		0.597	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		T	50463581	A	T	50463581	4	4	168	1	0	0	0	0	0	1	0	0	14322	273	10	4	1574	4	SIGLEC11	19	50463581	Nonsense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	562240	50463581	8665402	203	25619										
DEFB129	140881	hgsc.bcm.edu	37	chr20	210384	210384	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	catactgccaacaccatcacTggagctagaggaagcagaag	10	11	1	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr20:210384T>A	ENST00000246105.4	+	2	555	c.524T>A	c.(523-525)cTg>cAg	p.L175Q		NM_080831.3	NP_543021.1	Q9H1M3	DB129_HUMAN	defensin, beta 129	175					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|stomach(1)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			ACACCATCACTGGAGCTAGAG	0.448																																					p.L175Q		Atlas-SNP	.											.	DEFB129	24	.	0			c.T524A						.						88	81	83					20																	210384		2203	4300	6503	SO:0001583	missense	140881	exon2			CATCACTGGAGCT	AY358186	CCDS12992.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125903	ENSG00000125903		"Defensins, beta"	16218	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 87"	C20orf87		11854508	Standard	NM_080831		Approved	bA530N10.3, DEFB-29	uc002wda.3	Q9H1M3	OTTHUMG00000031618	ENST00000246105.4:c.524T>A	chr20.hg19:g.210384T>A	ENSP00000246105:p.Leu175Gln	52.0	0.0		36.0	12.0	NM_080831	Q8NES7	Missense_Mutation	SNP	ENST00000246105.4	hg19	CCDS12992.1	.	.	.	.	.	.	.	.	.	.	T	15.00	2.703131	0.48412	.	.	ENSG00000125903	ENST00000246105	T	0.55234	0.53	4.39	-2.5	0.06384	.	2.100700	0.03031	N	0.152128	T	0.36248	0.0960	N	0.14661	0.345	0.09310	N	1	P	0.50617	0.937	B	0.43478	0.421	T	0.35525	-0.9785	10	0.87932	D	0	-0.0153	5.4593	0.16607	0.0:0.2882:0.4099:0.302	.	175	Q9H1M3	DB129_HUMAN	Q	175	ENSP00000246105:L175Q	ENSP00000246105:L175Q	L	+	2	0	DEFB129	158384	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.895000	0.04118	-0.445000	0.07159	-0.371000	0.07208	CTG	.	.		0.448	DEFB129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077430.2	NM_080831		A	210384	T	A	210384	3	1	168	1	0	0	0	0	1	0	0	0	4417	1580	55	4	530	4	DEFB129	20	210384	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10		210384	62815136	204	25620										
PAK7	57144	hgsc.bcm.edu	37	chr20	9560941	9560941	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cctggacctctgccgcatggTgggctgagggcttgtctgat	15	11	2	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr20:9560941T>A	ENST00000378429.3	-	5	1387	c.841A>T	c.(841-843)Acc>Tcc	p.T281S	PAK7_ENST00000378423.1_Missense_Mutation_p.T281S|RP5-986I17.2_ENST00000428769.1_RNA|PAK7_ENST00000353224.5_Missense_Mutation_p.T281S	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	281	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TGCCGCATGGTGGGCTGAGGG	0.552																																					p.T281S		Atlas-SNP	.											.	PAK7	194	.	0			c.A841T						.						172	149	157					20																	9560941		2203	4300	6503	SO:0001583	missense	57144	exon4			GCATGGTGGGCTG	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.841A>T	chr20.hg19:g.9560941T>A	ENSP00000367686:p.Thr281Ser	153.0	0.0		156.0	69.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	T	0.535	-0.856332	0.02630	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.29397	1.57;1.57;1.57	5.6	0.192	0.15134	.	0.313678	0.38436	N	0.001690	T	0.12433	0.0302	N	0.04508	-0.205	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.19148	0.024;0.002	T	0.31081	-0.9956	9	.	.	.	.	10.7354	0.46122	0.0:0.562:0.0:0.438	.	281;281	B0AZM9;Q9P286	.;PAK7_HUMAN	S	281;281;281;229	ENSP00000367686:T281S;ENSP00000322957:T281S;ENSP00000367679:T281S	.	T	-	1	0	PAK7	9508941	0.095000	0.21747	0.020000	0.16555	0.006000	0.05464	0.612000	0.24283	-0.191000	0.10448	-1.728000	0.00702	ACC	.	.		0.552	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			A	9560941	T	A	9560941	3	1	168	1	0	0	0	0	1	0	0	0	11414	1696	59	4	1346	4	PAK7	20	9560941	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	9350557	9560941	53464579	205	25621										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20071622	20071622	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tcatgctgttgtgtgtgaggTcagtgactgattcatgtggg	15	5	3	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr20:20071622T>A	ENST00000245957.5	+	7	775		c.e7+2		C20orf26_ENST00000451767.2_Splice_Site|C20orf26_ENST00000389656.3_Splice_Site|C20orf26_ENST00000377309.2_Splice_Site|C20orf26_ENST00000377306.1_Splice_Site	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN												NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		GTGTGTGAGGTCAGTGACTGA	0.493																																					.		Atlas-SNP	.											.	C20orf26	188	.	0			c.699+2T>A						.						180	154	163					20																	20071622		2203	4300	6503	SO:0001630	splice_region_variant	26074	exon7			GTGAGGTCAGTGA																												ENST00000245957.5:c.699+2T>A	chr20.hg19:g.20071622T>A		118.0	0.0		95.0	40.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Splice_Site	SNP	ENST00000245957.5	hg19	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	T	17.69	3.450777	0.63290	.	.	ENSG00000089101	ENST00000340348;ENST00000343997;ENST00000389655;ENST00000245957;ENST00000377306;ENST00000451767;ENST00000472660	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6148	0.76756	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	C20orf26	20019622	1.000000	0.71417	0.981000	0.43875	0.689000	0.40095	6.128000	0.71650	2.086000	0.62901	0.533000	0.62120	.	.	.		0.493	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		Intron	A	20071622	T	A	20071622	5	1	168	1	0	0	0	0	0	0	1	0	2108	1681	58	4	723	4	C20orf26	20	20071622	Splice_Site	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	10510681	20071622	42953898	206	25622										
CEP250	11190	hgsc.bcm.edu	37	chr20	34091356	34091356	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gaagggcccaagtaaagcacAgcgcgggagcctagagcaca	14	11	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr20:34091356A>T	ENST00000397527.1	+	30	5879	c.5159A>T	c.(5158-5160)cAg>cTg	p.Q1720L	CEP250_ENST00000342580.4_Missense_Mutation_p.Q1664L	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1720	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AGTAAAGCACAGCGCGGGAGC	0.567																																					p.Q1720L		Atlas-SNP	.											.	CEP250	141	.	0			c.A5159T						.						107	102	104					20																	34091356		2203	4300	6503	SO:0001583	missense	11190	exon30			AAGCACAGCGCGG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.5159A>T	chr20.hg19:g.34091356A>T	ENSP00000380661:p.Gln1720Leu	141.0	0.0		113.0	41.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	A	0.078	-1.188487	0.01607	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.36340	3.25;3.22;1.26	4.66	4.66	0.58398	.	0.113936	0.38663	N	0.001617	T	0.22975	0.0555	N	0.20986	0.625	0.25662	N	0.986	B	0.22683	0.073	B	0.22880	0.042	T	0.11966	-1.0566	10	0.26408	T	0.33	.	9.2305	0.37434	0.7972:0.0:0.0:0.2028	.	1720	Q9BV73	CP250_HUMAN	L	1720;1664;208	ENSP00000380661:Q1720L;ENSP00000341541:Q1664L;ENSP00000395992:Q208L	ENSP00000341541:Q1664L	Q	+	2	0	CEP250	33554770	0.995000	0.38212	0.988000	0.46212	0.585000	0.36419	2.348000	0.44045	1.968000	0.57251	0.374000	0.22700	CAG	.	.		0.567	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34091356	A	T	34091356	3	4	168	1	0	0	0	0	1	0	0	0	3254	188	7	4	5265	4	CEP250	20	34091356	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	14019734	34091356	28934164	207	25623										
ARFGAP1	55738	hgsc.bcm.edu	37	chr20	61916216	61916216	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cacgtgacttcccttcctacAggcgtccgagctgggccaca	10	16	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr20:61916216A>T	ENST00000370283.4	+	10	857		c.e10-1		ARFGAP1_ENST00000519604.1_Splice_Site|ARFGAP1_ENST00000547204.1_Splice_Site|ARFGAP1_ENST00000519273.2_Splice_Site|ARFGAP1_ENST00000370275.4_Splice_Site|MIR4326_ENST00000582203.1_RNA|ARFGAP1_ENST00000518794.2_3'UTR|ARFGAP1_ENST00000353546.3_Splice_Site	NM_018209.2	NP_060679.1	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating protein 1						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPI coating of Golgi vesicle (GO:0048205)|endoplasmic reticulum unfolded protein response (GO:0030968)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cytosol (GO:0005829)|Golgi-associated vesicle membrane (GO:0030660)|synapse (GO:0045202)	ARF GTPase activator activity (GO:0008060)|GTPase activator activity (GO:0005096)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)	13	all_cancers(38;1.59e-09)					CCCTTCCTACAGGCGTCCGAG	0.647																																					.		Atlas-SNP	.											.	ARFGAP1	38	.	0			c.718-2A>T						.						81	63	69					20																	61916216		2203	4299	6502	SO:0001630	splice_region_variant	55738	exon10			TCCTACAGGCGTC	AK001629	CCDS13515.1, CCDS13516.1, CCDS63326.1, CCDS63327.1, CCDS63328.1	20q13.33	2009-11-30	2002-08-20	2002-08-23	ENSG00000101199	ENSG00000101199		"ADP-ribosylation factor GTPase activating proteins"	15852	protein-coding gene	gene with protein product		608377	"ADP-ribosylation factor 1 GTPase activating protein"	ARF1GAP		11210549	Standard	NM_018209		Approved	FLJ10767, bA261N11.3	uc002yel.3	Q8N6T3	OTTHUMG00000032965	ENST00000370283.4:c.718-1A>T	chr20.hg19:g.61916216A>T		47.0	0.0		66.0	22.0	NM_018209	B7Z3U0|B7Z8H8|B7ZBI3|E1P5I9|E7EV62|Q6PK71|Q96KC4|Q96T02|Q9NSU3|Q9NVF6|Q9UIL0	Splice_Site	SNP	ENST00000370283.4	hg19	CCDS13515.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.783751	0.31593	.	.	ENSG00000101199	ENST00000370283;ENST00000547204;ENST00000549047;ENST00000519604;ENST00000519273;ENST00000370275;ENST00000518601;ENST00000353546;ENST00000522403	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.258	0.60089	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARFGAP1	61386661	1.000000	0.71417	0.990000	0.47175	0.106000	0.19336	5.494000	0.66905	1.961000	0.56991	0.379000	0.24179	.	.	.		0.647	ARFGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080134.3	NM_018209	Intron	T	61916216	A	T	61916216	5	4	168	1	0	0	0	0	0	0	1	0	849	202	7	4	784	4	ARFGAP1	20	61916216	Splice_Site	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	27824860	61916216	1109304	208	25624										
COL20A1	57642	hgsc.bcm.edu	37	chr20	61943819	61943819	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gccacgctggggcctctctcTtcctccaccacctacactgt	7	19	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr20:61943819T>A	ENST00000358894.6	+	15	1951	c.1851T>A	c.(1849-1851)tcT>tcA	p.S617S	COL20A1_ENST00000422202.1_Silent_p.S624S|COL20A1_ENST00000326996.6_Silent_p.S617S|COL20A1_ENST00000435874.1_Silent_p.S624S	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	617	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GGCCTCTCTCTTCCTCCACCA	0.672																																					p.S617S		Atlas-SNP	.											.	COL20A1	137	.	0			c.T1851A						.						39	46	44					20																	61943819		2198	4297	6495	SO:0001819	synonymous_variant	57642	exon15			TCTCTCTTCCTCC	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.1851T>A	chr20.hg19:g.61943819T>A		48.0	0.0		56.0	19.0	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Silent	SNP	ENST00000358894.6	hg19	CCDS46628.1																																																																																			.	.		0.672	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		A	61943819	T	A	61943819	2	1	168	1	0	0	0	0	0	0	0	1	3681	1596	56	4		4	COL20A1	20	61943819	Silent	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	27603	61943819	1081701	209	25625										
COL20A1	57642	hgsc.bcm.edu	37	chr20	61948029	61948038	+	Frame_Shift_Del	DEL	GACAAGACGG	GACAAGACGG	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctcttcaaggacgcccagctGacaagacgggtcaggtgtga							TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	GACAAGACGG	GACAAGACGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr20:61948029_61948038delGACAAGACGG	ENST00000358894.6	+	21	2749_2758	c.2649_2658delGACAAGACGG	c.(2647-2658)ctgacaagacggfs	p.LTRR883fs	COL20A1_ENST00000422202.1_Frame_Shift_Del_p.LTRR890fs|COL20A1_ENST00000326996.6_Frame_Shift_Del_p.LTRR883fs|COL20A1_ENST00000435874.1_Frame_Shift_Del_p.LTRR890fs	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	883	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					ACGCCCAGCTGACAAGACGGGTCAGGTGTG	0.667																																					p.883_886del		Atlas-INDEL	.											.	COL20A1	137	.	0			c.2648_2657del						.																																			SO:0001589	frameshift_variant	57642	exon21			.	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.2649_2658delGACAAGACGG	chr20.hg19:g.61948029_61948038delGACAAGACGG	ENSP00000351767:p.Leu883fs	29.0	0.0		49.0	13.0	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Frame_Shift_Del	DEL	ENST00000358894.6	hg19	CCDS46628.1																																																																																			.	.		0.667	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		-	61948038	GACAAGACGG	-	61948029	7	5	168	1	0	1	0	1	0	0	0	0	3681	1277	45	0	2727	0	COL20A1	20	61948029	Frame_Shift_Del	DEL	GACAAGACGG	TCGA-DD-AACQ-01A-11D-A40R-10	4210	61948029	1077491	210	25626										
TCEA2	6919	hgsc.bcm.edu	37	chr20	62701907	62701907	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	aaggaggccatccgagagcaCcagatggcccgcactggcgg	15	13	0	2			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr20:62701907C>T	ENST00000343484.5	+	8	907	c.738C>T	c.(736-738)caC>caT	p.H246H	TCEA2_ENST00000465111.1_3'UTR|TCEA2_ENST00000361317.2_Silent_p.H219H|TCEA2_ENST00000395053.3_3'UTR	NM_003195.4	NP_003186.1	Q15560	TCEA2_HUMAN	transcription elongation factor A (SII), 2	246	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				DNA-templated transcription, elongation (GO:0006354)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)	centrosome (GO:0005813)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)	12	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)					TCCGAGAGCACCAGATGGCCC	0.627																																					p.H246H		Atlas-SNP	.											.	TCEA2	22	.	0			c.C738T						.						48	49	49					20																	62701907		2203	4300	6503	SO:0001819	synonymous_variant	6919	exon8			AGAGCACCAGATG	U86749	CCDS13553.1, CCDS13554.1	20q13.33	2011-01-25			ENSG00000171703	ENSG00000171703			11614	protein-coding gene	gene with protein product		604784				9441762, 8566795	Standard	NM_003195		Approved	TFIIS	uc021wgq.1	Q15560	OTTHUMG00000033026	ENST00000343484.5:c.738C>T	chr20.hg19:g.62701907C>T		233.0	0.0		230.0	70.0	NM_003195	B3KNM1|Q8TD37|Q8TD38	Silent	SNP	ENST00000343484.5	hg19	CCDS13553.1																																																																																			.	.		0.627	TCEA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080277.2	NM_198723		T	62701907	C	T	62701907	2	4	168	1	0	0	0	0	0	0	0	1	15683	506	18	3		3	TCEA2	20	62701907	Silent	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	753878	62701907	323613	211	25627										
SLC7A4	6545	hgsc.bcm.edu	37	chr22	21384217	21384217	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ctccagggctgtacccatccAagaagcccaggtagggcctc	11	15	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr22:21384217A>T	ENST00000382932.2	-	3	1473	c.1406T>A	c.(1405-1407)tTg>tAg	p.L469*	AC002472.11_ENST00000450652.1_RNA|SLC7A4_ENST00000403586.1_Nonsense_Mutation_p.L469*	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	469					basic amino acid transport (GO:0015802)|cellular amino acid metabolic process (GO:0006520)|transport (GO:0006810)	integral component of membrane (GO:0016021)	basic amino acid transmembrane transporter activity (GO:0015174)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GTACCCATCCAAGAAGCCCAG	0.612																																					p.L469X		Atlas-SNP	.											.	SLC7A4	50	.	0			c.T1406A						.						44	38	40					22																	21384217		2203	4300	6503	SO:0001587	stop_gained	6545	exon3			CCATCCAAGAAGC	AJ000730	CCDS33608.1	22q11.21	2013-07-19	2013-07-19		ENSG00000099960	ENSG00000099960		"Solute carriers"	11062	protein-coding gene	gene with protein product		603752	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 4", "solute carrier family 7 (orphan transporter), member 4"			9598310, 11665818	Standard	NM_004173		Approved	HCAT3, CAT-4, VH	uc002zud.3	O43246	OTTHUMG00000150896	ENST00000382932.2:c.1406T>A	chr22.hg19:g.21384217A>T	ENSP00000372390:p.Leu469*	93.0	0.0		81.0	29.0	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Nonsense_Mutation	SNP	ENST00000382932.2	hg19	CCDS33608.1	.	.	.	.	.	.	.	.	.	.	A	37	6.443640	0.97572	.	.	ENSG00000099960	ENST00000403586;ENST00000382932	.	.	.	5.46	5.46	0.80206	.	0.074728	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7984	0.63186	1.0:0.0:0.0:0.0	.	.	.	.	X	469	.	ENSP00000372390:L469X	L	-	2	0	SLC7A4	19714217	1.000000	0.71417	0.982000	0.44146	0.693000	0.40251	8.800000	0.91900	2.203000	0.70933	0.459000	0.35465	TTG	.	.		0.612	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173		T	21384217	A	T	21384217	4	4	168	1	0	0	0	0	0	1	0	0	14714	131	5	4	513	4	SLC7A4	22	21384217	Nonsense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10		21384217	29920349	212	25628										
ADORA2A	135	hgsc.bcm.edu	37	chr22	24836866	24836878	+	Frame_Shift_Del	DEL	GCCGGGGGAGCGG	GCCGGGGGAGCGG	-													0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cagatggagagccagcctctGccgggggagcgggcacggtc					rs200674969|rs199725333		TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	GCCGGGGGAGCGG	GCCGGGGGAGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr22:24836866_24836878delGCCGGGGGAGCGG	ENST00000337539.7	+	3	1107_1119	c.648_660delGCCGGGGGAGCGG	c.(646-660)ctgccgggggagcggfs	p.LPGER216fs	ADORA2A-AS1_ENST00000326341.4_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A_ENST00000496497.1_3'UTR|ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000427813.2_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	216					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)	p.R220W(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	GCCAGCCTCTGCCGGGGGAGCGGGCACGGTCCA	0.615																																					p.216_220del		Atlas-INDEL	.											.	ADORA2A	44	.	1	Substitution - Missense(1)	endometrium(1)	c.647_659del						.																																			SO:0001589	frameshift_variant	135	exon3			.	X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"GPCR / Class A : Adenosine receptors"	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.648_660delGCCGGGGGAGCGG	chr22.hg19:g.24836866_24836878delGCCGGGGGAGCGG	ENSP00000336630:p.Leu216fs	74.0	0.0		43.0	15.0	NM_000675	B2R7E0	Frame_Shift_Del	DEL	ENST00000337539.7	hg19	CCDS13826.1																																																																																			.	.		0.615	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675		-	24836878	GCCGGGGGAGCGG	-	24836866	7	5	168	1	0	1	0	1	0	0	0	0	327	1306	46	0	654	0	ADORA2A	22	24836866	Frame_Shift_Del	DEL	GCCGGGGGAGCGG	TCGA-DD-AACQ-01A-11D-A40R-10	3452649	24836866	26467700	213	25629										
CSF2RB	1439	hgsc.bcm.edu	37	chr22	37333867	37333867	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cctccctggagtccgggggaGgccctgcccctcctgctctt	12	18	1	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr22:37333867G>T	ENST00000403662.3	+	14	2239	c.2017G>T	c.(2017-2019)Ggc>Tgc	p.G673C	CSF2RB_ENST00000536485.1_Missense_Mutation_p.G620C|CSF2RB_ENST00000406230.1_Missense_Mutation_p.G679C|CSF2RB_ENST00000262825.5_Missense_Mutation_p.G679C			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	673					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GTCCGGGGGAGGCCCTGCCCC	0.677																																					p.G673C		Atlas-SNP	.											.	CSF2RB	104	.	0			c.G2017T						.						21	24	23					22																	37333867		2203	4295	6498	SO:0001583	missense	1439	exon14			GGGGGAGGCCCTG	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"CD molecules", "Fibronectin type III domain containing"	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.2017G>T	chr22.hg19:g.37333867G>T	ENSP00000384053:p.Gly673Cys	63.0	0.0		53.0	26.0	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	hg19	CCDS13936.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.134739	0.37728	.	.	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.92048	-2.45;-2.96;-2.96;-2.96	4.79	-2.85	0.05734	.	1.881320	0.02481	N	0.088509	D	0.91710	0.7379	L	0.47716	1.5	0.09310	N	1	D;D	0.61697	0.988;0.99	P;P	0.55161	0.77;0.594	T	0.82008	-0.0670	10	0.87932	D	0	-1.1415	4.9664	0.14093	0.3549:0.2746:0.3706:0.0	.	679;673	P32927-2;P32927	.;IL3RB_HUMAN	C	673;673;679;679;620	ENSP00000384053:G673C;ENSP00000262825:G679C;ENSP00000385271:G679C;ENSP00000440003:G620C	ENSP00000262825:G679C	G	+	1	0	CSF2RB	35663813	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.143000	0.16115	-0.328000	0.08539	-0.312000	0.09012	GGC	.	.		0.677	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395		T	37333867	G	T	37333867	3	4	168	1	0	0	0	0	1	0	0	0	3937	1000	35	3	2067	3	CSF2RB	22	37333867	Missense_Mutation	SNP	G	TCGA-DD-AACQ-01A-11D-A40R-10	12497001	37333867	13970699	214	25630										
LMF2	91289	hgsc.bcm.edu	37	chr22	50943406	50943406	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	tcccgggctccacgtaggagTacggcacctggagacaggtg	15	12	0	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chr22:50943406T>A	ENST00000474879.2	-	10	1277	c.1262A>T	c.(1261-1263)tAc>tTc	p.Y421F	LMF2_ENST00000216080.5_Missense_Mutation_p.Y396F|LMF2_ENST00000505981.1_5'Flank|LMF2_ENST00000380796.3_Intron	NM_033200.2	NP_149977.2	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	421						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|cervix(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CACGTAGGAGTACGGCACCTG	0.687																																					p.Y421F		Atlas-SNP	.											.	LMF2	40	.	0			c.A1262T						.						24	27	26					22																	50943406		2199	4294	6493	SO:0001583	missense	91289	exon10			TAGGAGTACGGCA	BC002942	CCDS14093.1, CCDS14093.2	22q13.33	2008-02-04	2007-11-29	2007-11-29	ENSG00000100258	ENSG00000100258			25096	protein-coding gene	gene with protein product			"transmembrane protein 153", "transmembrane protein 112B"	TMEM153, TMEM112B		12477932	Standard	NM_033200		Approved		uc003blp.2	Q9BU23	OTTHUMG00000150206	ENST00000474879.2:c.1262A>T	chr22.hg19:g.50943406T>A	ENSP00000424381:p.Tyr421Phe	147.0	0.0		105.0	36.0	NM_033200	A6NEZ0|Q13392|Q6ZNR2|Q8WU74|Q96C62	Missense_Mutation	SNP	ENST00000474879.2	hg19	CCDS14093.2	.	.	.	.	.	.	.	.	.	.	T	16.00	2.997406	0.54147	.	.	ENSG00000100258	ENST00000474879;ENST00000216080	T;T	0.21734	1.99;1.99	4.84	4.84	0.62591	.	0.073989	0.56097	D	0.000028	T	0.15825	0.0381	L	0.28115	0.83	0.80722	D	1	B;B	0.16802	0.003;0.019	B;B	0.18871	0.018;0.023	T	0.04333	-1.0959	10	0.37606	T	0.19	-0.2525	12.365	0.55224	0.0:0.0:0.0:1.0	.	421;396	Q9BU23;Q9BU23-2	LMF2_HUMAN;.	F	421;396	ENSP00000424381:Y421F;ENSP00000216080:Y396F	ENSP00000216080:Y396F	Y	-	2	0	LMF2	49290272	1.000000	0.71417	0.993000	0.49108	0.918000	0.54935	4.096000	0.57734	1.805000	0.52779	0.528000	0.53228	TAC	.	.		0.687	LMF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316833.2	NM_033200		A	50943406	T	A	50943406	3	1	168	1	0	0	0	0	1	0	0	0	8855	1638	57	4	881	4	LMF2	22	50943406	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	13609539	50943406	361160	215	25631										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3241470	3241470	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	gcaacattggtctctggttcTttttccgaatgcttccagag	9	10	2	1			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chrX:3241470T>A	ENST00000217939.6	-	5	2410	c.2256A>T	c.(2254-2256)aaA>aaT	p.K752N		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	752						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TCTCTGGTTCTTTTTCCGAAT	0.443																																					p.K752N		Atlas-SNP	.											.	MXRA5	815	.	0			c.A2256T						.						107	91	96					X																	3241470		2203	4300	6503	SO:0001583	missense	25878	exon5			TGGTTCTTTTTCC	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2256A>T	chrX.hg19:g.3241470T>A	ENSP00000217939:p.Lys752Asn	65.0	0.0		62.0	51.0	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	t	11.97	1.796657	0.31777	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.66638	-0.22	3.63	-1.63	0.08345	.	0.354042	0.20155	U	0.098076	T	0.44603	0.1301	N	0.24115	0.695	0.09310	N	1	P	0.43477	0.808	B	0.36567	0.228	T	0.43829	-0.9367	10	0.56958	D	0.05	.	9.3214	0.37966	0.0:0.2632:0.0:0.7368	.	752	Q9NR99	MXRA5_HUMAN	N	752	ENSP00000217939:K752N	ENSP00000217939:K752N	K	-	3	2	MXRA5	3251470	0.000000	0.05858	0.002000	0.10522	0.110000	0.19582	-0.018000	0.12568	-0.316000	0.08690	0.430000	0.28490	AAA	.	.		0.443	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3241470	T	A	3241470	3	1	168	1	0	0	0	0	1	0	0	0	10012	1606	56	4	6242	4	MXRA5	23	3241470	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10		3241470	152029090	216	25632										
GPM6B	2824	hgsc.bcm.edu	37	chrX	13803759	13803759	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	acacctcgctcagcaaggcaTggtcactggcgttggtggag	14	11	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chrX:13803759T>A	ENST00000356942.5	-	2	671	c.230A>T	c.(229-231)cAt>cTt	p.H77L	GPM6B_ENST00000454189.2_Missense_Mutation_p.H58L|GPM6B_ENST00000316715.4_Missense_Mutation_p.H117L|GPM6B_ENST00000493677.1_Missense_Mutation_p.H91L|GPM6B_ENST00000398361.3_5'UTR|GPM6B_ENST00000355135.2_Missense_Mutation_p.H117L	NM_005278.3	NP_005269.1	Q13491	GPM6B_HUMAN	glycoprotein M6B	77					cell differentiation (GO:0030154)|extracellular matrix assembly (GO:0085029)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of serotonin uptake (GO:0051612)|nervous system development (GO:0007399)|ossification (GO:0001503)|positive regulation of bone mineralization (GO:0030501)|protein transport (GO:0015031)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of focal adhesion assembly (GO:0051893)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|ovary(1)|pancreas(1)	6						CAGCAAGGCATGGTCACTGGC	0.567																																					p.H117L		Atlas-SNP	.											.	GPM6B	46	.	0			c.A350T						.						80	71	74					X																	13803759		2203	4300	6503	SO:0001583	missense	2824	exon3			AAGGCATGGTCAC		CCDS14158.1, CCDS35206.1, CCDS35207.1, CCDS48084.1	Xp22.2	2010-08-03			ENSG00000046653	ENSG00000046653			4461	protein-coding gene	gene with protein product		300051				8661015	Standard	NM_001001995		Approved	M6B, MGC17150, MGC54284	uc004cvw.3	Q13491	OTTHUMG00000021162	ENST00000356942.5:c.230A>T	chrX.hg19:g.13803759T>A	ENSP00000349420:p.His77Leu	250.0	0.0		216.0	191.0	NM_001001995	O76077|Q86X43|Q8N956	Missense_Mutation	SNP	ENST00000356942.5	hg19	CCDS14158.1	.	.	.	.	.	.	.	.	.	.	T	17.62	3.435475	0.62955	.	.	ENSG00000046653	ENST00000316715;ENST00000454189;ENST00000493677;ENST00000355135;ENST00000356942;ENST00000475307	D;D;D;D;D;D	0.99158	-5.5;-5.5;-5.5;-5.5;-5.5;-5.5	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.97961	0.9329	M	0.63428	1.95	0.80722	D	1	B;B;P;P;B;B	0.38395	0.009;0.123;0.629;0.58;0.011;0.019	B;B;B;B;B;B	0.40982	0.022;0.117;0.345;0.228;0.015;0.034	D	0.98824	1.0748	10	0.23302	T	0.38	-15.127	15.1934	0.73063	0.0:0.0:0.0:1.0	.	91;58;77;117;69;117	B7Z613;Q13491-2;Q13491;Q13491-3;Q59FD5;Q8N956	.;.;GPM6B_HUMAN;.;.;.	L	117;58;91;117;77;77	ENSP00000316861:H117L;ENSP00000389915:H58L;ENSP00000419904:H91L;ENSP00000347258:H117L;ENSP00000349420:H77L;ENSP00000418594:H77L	ENSP00000316861:H117L	H	-	2	0	GPM6B	13713680	1.000000	0.71417	0.973000	0.42090	0.994000	0.84299	7.557000	0.82243	1.971000	0.57363	0.486000	0.48141	CAT	.	.		0.567	GPM6B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055822.1	NM_001001995		A	13803759	T	A	13803759	3	1	168	1	0	0	0	0	1	0	0	0	6624	1464	51	4	745	4	GPM6B	23	13803759	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	10562289	13803759	141466801	217	25633										
GRPR	2925	hgsc.bcm.edu	37	chrX	16170727	16170727	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	acccctccgtggccacctttAgcctcatcaatggaaacatc	6	16	2	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chrX:16170727A>T	ENST00000380289.2	+	3	1512	c.1114A>T	c.(1114-1116)Agc>Tgc	p.S372C	RP11-431J24.2_ENST00000454712.2_RNA|RP11-431J24.2_ENST00000422438.1_RNA|RP11-431J24.2_ENST00000435789.1_RNA	NM_005314.2	NP_005305.1	P30550	GRPR_HUMAN	gastrin-releasing peptide receptor	372					cell proliferation (GO:0008283)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cell proliferation (GO:0042127)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)|G-protein coupled peptide receptor activity (GO:0008528)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(3)|stomach(1)|upper_aerodigestive_tract(3)	25	Hepatocellular(33;0.183)					GGCCACCTTTAGCCTCATCAA	0.537																																					p.S372C		Atlas-SNP	.											.	GRPR	51	.	0			c.A1114T						.						167	155	159					X																	16170727		2203	4300	6503	SO:0001583	missense	2925	exon3			ACCTTTAGCCTCA		CCDS14174.1	Xp22.2	2014-02-21			ENSG00000126010	ENSG00000126010		"GPCR / Class A : Bombesin receptors"	4609	protein-coding gene	gene with protein product	"bombesin receptor 2"	305670					Standard	NM_005314		Approved	BB2	uc004cxj.3	P30550	OTTHUMG00000021189	ENST00000380289.2:c.1114A>T	chrX.hg19:g.16170727A>T	ENSP00000369643:p.Ser372Cys	83.0	0.0		68.0	53.0	NM_005314	B2R910	Missense_Mutation	SNP	ENST00000380289.2	hg19	CCDS14174.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.9|26.9	4.782386|4.782386	0.90282|0.90282	.|.	.|.	ENSG00000126010|ENSG00000126010	ENST00000380289|ENST00000535371	T|.	0.67171|.	-0.25|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.329161|.	0.34853|.	N|.	0.003635|.	T|.	0.73783|.	0.3631|.	M|M	0.74258|0.74258	2.255|2.255	0.54753|0.54753	D|D	0.999984|0.999984	D|.	0.69078|.	0.997|.	P|.	0.56865|.	0.808|.	T|.	0.74589|.	-0.3615|.	10|.	0.72032|.	D|.	0.01|.	-28.3464|-28.3464	13.9157|13.9157	0.63895|0.63895	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	372|.	P30550|.	GRPR_HUMAN|.	C|L	372|160	ENSP00000369643:S372C|.	ENSP00000369643:S372C|.	S|X	+|+	1|2	0|0	GRPR|GRPR	16080648|16080648	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	5.560000|5.560000	0.67332|0.67332	1.883000|1.883000	0.54544|0.54544	0.486000|0.486000	0.48141|0.48141	AGC|TAG	.	.		0.537	GRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055901.1	NM_005314		T	16170727	A	T	16170727	3	4	168	1	0	0	0	0	1	0	0	0	6817	420	15	4	1124	4	GRPR	23	16170727	Missense_Mutation	SNP	A	TCGA-DD-AACQ-01A-11D-A40R-10	2366968	16170727	139099833	218	25634										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128059	83128059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	cccatcttaaaaaagcagaaTataaaaagtccaaagatgaa	5	7	1	3			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chrX:83128059T>C	ENST00000329312.4	+	4	380	c.343T>C	c.(343-345)Tat>Cat	p.Y115H		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	115					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						AAAAGCAGAATATAAAAAGTC	0.368																																					p.Y115H		Atlas-SNP	.											.	CYLC1	272	.	0			c.T343C						.						32	30	31					X																	83128059		2197	4291	6488	SO:0001583	missense	1538	exon4			GCAGAATATAAAA	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.343T>C	chrX.hg19:g.83128059T>C	ENSP00000331556:p.Tyr115His	326.0	1.0		256.0	221.0	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	hg19	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	t	2.934	-0.220312	0.06061	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.43294	0.95	4.53	-4.11	0.03928	.	.	.	.	.	T	0.23886	0.0578	L	0.29908	0.895	0.09310	N	1	P;P	0.45957	0.869;0.869	B;B	0.42361	0.385;0.385	T	0.19943	-1.0290	9	0.15066	T	0.55	0.8047	4.8281	0.13427	0.3768:0.0:0.3547:0.2685	.	115;115	P35663;F5H4V5	CYLC1_HUMAN;.	H	115	ENSP00000331556:Y115H	ENSP00000331556:Y115H	Y	+	1	0	CYLC1	83014715	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.784000	0.01769	-0.991000	0.03476	0.486000	0.48141	TAT	.	.		0.368	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		C	83128059	T	C	83128059	3	2	168	1	0	0	0	0	1	0	0	0	4143	1406	49	2	357	2	CYLC1	23	83128059	Missense_Mutation	SNP	T	TCGA-DD-AACQ-01A-11D-A40R-10	66957332	83128059	72142501	219	25635										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153128941	153128941	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0414746543778802	9	1	1.83619744058501	4.08043875685558	0	0.000119075970469159	0.00972331562456005	0	ccccggctcacctgtactcgCcgaaggtctcatctttcatc	7	17	4	0			TCGA-DD-AACQ-01A-11D-A40R-10	TCGA-DD-AACQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5ad554e-26df-4b28-bf84-a689d77c2602	90e3ca3e-5517-4d7e-a1da-204704c66280	g.chrX:153128941C>A	ENST00000370060.1	-	27	3710	c.3521G>T	c.(3520-3522)gGc>gTc	p.G1174V	L1CAM_ENST00000543994.1_Missense_Mutation_p.G1176V|L1CAM_ENST00000538883.1_Missense_Mutation_p.G1176V|L1CAM_ENST00000361699.4_Missense_Mutation_p.G1174V|L1CAM_ENST00000370057.3_Missense_Mutation_p.G1174V|L1CAM_ENST00000361981.3_Missense_Mutation_p.G1169V|L1CAM_ENST00000370055.1_Missense_Mutation_p.G1169V	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	1174					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCTGTACTCGCCGAAGGTCTC	0.612																																					p.G1174V		Atlas-SNP	.											.	L1CAM	189	.	0			c.G3521T						.						62	58	59					X																	153128941		2203	4300	6503	SO:0001583	missense	3897	exon26			TACTCGCCGAAGG	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.3521G>T	chrX.hg19:g.153128941C>A	ENSP00000359077:p.Gly1174Val	143.0	0.0		122.0	105.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	hg19	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.144047	0.77888	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000370058;ENST00000361699	D;D;D;D;D;D;D;D	0.86627	-2.15;-2.15;-2.15;-2.15;-2.15;-2.15;-2.15;-2.15	4.57	4.57	0.56435	.	0.000000	0.56097	D	0.000038	D	0.92753	0.7696	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.80764	0.986;0.994;0.99	D	0.93459	0.6809	10	0.59425	D	0.04	.	15.6115	0.76721	0.0:1.0:0.0:0.0	.	1169;1174;1174	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	V	1174;1176;1174;1176;1169;1169;74;1174	ENSP00000359077:G1174V;ENSP00000438430:G1176V;ENSP00000359074:G1174V;ENSP00000439645:G1176V;ENSP00000354712:G1169V;ENSP00000359072:G1169V;ENSP00000359075:G74V;ENSP00000355380:G1174V	ENSP00000355380:G1174V	G	-	2	0	L1CAM	152782135	1.000000	0.71417	0.991000	0.47740	0.766000	0.43426	4.520000	0.60524	2.015000	0.59207	0.529000	0.55759	GGC	.	.		0.612	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		A	153128941	C	A	153128941	3	1	168	1	0	0	0	0	1	0	0	0	8597	739	26	3	264	3	L1CAM	23	153128941	Missense_Mutation	SNP	C	TCGA-DD-AACQ-01A-11D-A40R-10	70000882	153128941	2141619	220	25636										
KIAA0090	23065	hgsc.bcm.edu	37	chr1	19571434	19571434	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	cgggaatttaatgctgcaatCacattcttctctgtggctac	8	10	3	0			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr1:19571434C>A	ENST00000477853.1	-	2	228	c.186G>T	c.(184-186)gtG>gtT	p.V62V	EMC1_ENST00000356068.2_Silent_p.V62V|EMC1_ENST00000375199.3_Silent_p.V62V|EMC1_ENST00000375208.3_Silent_p.V62V	NM_001271427.1|NM_001271428.1|NM_015047.2	NP_001258356.1|NP_001258357.1|NP_055862.1	Q8N766	EMC1_HUMAN	ER membrane protein complex subunit 1	62						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											ATGCTGCAATCACATTCTTCT	0.458																																					p.V62V		Atlas-SNP	.											.	.	.	.	0			c.G186T						.						143	147	146					1																	19571434		2203	4300	6503	SO:0001819	synonymous_variant	23065	exon2			TGCAATCACATTC		CCDS190.1, CCDS59190.1, CCDS59191.1	1p36.13	2012-05-23	2012-05-23	2012-05-23	ENSG00000127463	ENSG00000127463			28957	protein-coding gene	gene with protein product			"KIAA0090"	KIAA0090		22119785	Standard	NM_015047		Approved		uc001bbo.4	Q8N766	OTTHUMG00000002497	ENST00000477853.1:c.186G>T	chr1.hg19:g.19571434C>A		255.0	0.0		255.0	109.0	NM_001271427	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Silent	SNP	ENST00000477853.1	hg19	CCDS190.1																																																																																			.	.		0.458	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047		A	19571434	C	A	19571434	2	1	169	1	0	0	0	0	0	0	0	1	8162	813	29	3		3	KIAA0090	1	19571434	Silent	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10		19571434	229679187	1	25637										
NBPF3	84224	hgsc.bcm.edu	37	chr1	21799392	21799392	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	aggaggctgagaaagtacagGaattatatgcccccaggtaa	12	7	0	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr1:21799392G>C	ENST00000318249.5	+	6	1068	c.718G>C	c.(718-720)Gaa>Caa	p.E240Q	NBPF3_ENST00000454000.2_Missense_Mutation_p.E170Q|NBPF3_ENST00000342104.5_Missense_Mutation_p.E240Q|NBPF3_ENST00000318220.6_Missense_Mutation_p.E184Q	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	240	NBPF 1. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GAAAGTACAGGAATTATATGC	0.413																																					p.K240Q		Atlas-SNP	.											.	NBPF3	55	.	0			c.A718C						.						135	145	142					1																	21799392		2203	4300	6503	SO:0001583	missense	84224	exon6			GTACAGGAATTAT	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"neuroblastoma breakpoint family"	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.718G>C	chr1.hg19:g.21799392G>C	ENSP00000316782:p.Glu240Gln	110.0	0.0		93.0	10.0	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Missense_Mutation	SNP	ENST00000318249.5	hg19	CCDS216.1	.	.	.	.	.	.	.	.	.	.	.	3.732	-0.055366	0.07362	.	.	ENSG00000142794	ENST00000454000;ENST00000318220;ENST00000318249;ENST00000417552;ENST00000342104;ENST00000434838	T;T;T;T;T	0.08546	3.08;3.08;3.08;3.08;3.08	0.716	0.716	0.18191	DUF1220 (2);	.	.	.	.	T	0.21590	0.0520	M	0.69823	2.125	0.09310	N	1	P;D;P	0.71674	0.863;0.998;0.642	P;D;B	0.65987	0.696;0.94;0.265	T	0.05273	-1.0895	8	0.45353	T	0.12	.	.	.	.	.	170;240;240	B4DSP2;Q9H094-3;Q9H094	.;.;NBPF3_HUMAN	Q	170;184;240;184;240;184	ENSP00000415711:E170Q;ENSP00000316739:E184Q;ENSP00000316782:E240Q;ENSP00000340336:E240Q;ENSP00000391865:E184Q	ENSP00000316739:E184Q	E	+	1	0	NBPF3	21671979	0.012000	0.17670	0.002000	0.10522	0.013000	0.08279	0.231000	0.17872	0.682000	0.31407	0.184000	0.17185	GAA	.	.		0.413	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264		C	21799392	G	C	21799392	3	2	169	1	0	0	0	0	1	0	0	0	10206	1175	41	4	736	4	NBPF3	1	21799392	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	2227958	21799392	227451229	2	25638										
RBBP4	5928	hgsc.bcm.edu	37	chr1	33145241	33145241	+	Splice_Site	SNP	G	G	A													0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tttttcttgtttttgggcagGcagagaacatttataatgat							TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr1:33145241G>A	ENST00000373493.5	+	12	1372	c.1213G>A	c.(1213-1215)Gca>Aca	p.A405T	RBBP4_ENST00000414241.3_Splice_Site_p.A404T|RBBP4_ENST00000458695.2_Splice_Site_p.A370T|RBBP4_ENST00000373485.1_Intron|RBBP4_ENST00000544435.1_Splice_Site_p.A153T	NM_001135255.1|NM_005610.2	NP_001128727.1|NP_005601.1	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4	405					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin assembly (GO:0031497)|chromatin remodeling (GO:0006338)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|nucleosome assembly (GO:0006334)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|NURF complex (GO:0016589)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				TTTTGGGCAGGCAGAGAACAT	0.388																																					p.A405T		Atlas-SNP	.											.	RBBP4	38	.	0			c.G1213A						.						118	117	118					1																	33145241		2203	4300	6503	SO:0001630	splice_region_variant	5928	exon12			GGGCAGGCAGAGA	BC053904	CCDS366.1, CCDS44105.1, CCDS44106.1	1p35.1	2014-07-17	2001-11-28		ENSG00000162521	ENSG00000162521		"WD repeat domain containing"	9887	protein-coding gene	gene with protein product		602923	"retinoblastoma-binding protein 4"			8350924, 14609955, 17531812	Standard	NM_005610		Approved	RbAp48, NURF55, lin-53	uc001bvr.3	Q09028	OTTHUMG00000007998	ENST00000373493.5:c.1213-1G>A	chr1.hg19:g.33145241G>A		54.0	0.0		67.0	29.0	NM_005610	B2R6G9|B4DRH0|D3DPQ3|P31149|Q53H02|Q96BV9	Missense_Mutation	SNP	ENST00000373493.5	hg19	CCDS366.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.48|18.48	3.633258|3.633258	0.67015|0.67015	.|.	.|.	ENSG00000162521|ENSG00000162521	ENST00000414241;ENST00000373493;ENST00000544435;ENST00000458695|ENST00000463378	T;T;T;T|.	0.65364|.	-0.15;-0.15;-0.15;-0.15|.	5.3|5.3	5.3|5.3	0.74995|0.74995	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.047823|.	0.85682|.	D|.	0.000000|.	T|T	0.74489|0.74489	0.3723|0.3723	M|M	0.67700|0.67700	2.07|2.07	0.80722|0.80722	D|D	1|1	B;B|.	0.29378|.	0.087;0.243|.	B;B|.	0.30646|.	0.118;0.087|.	T|T	0.72934|0.72934	-0.4141|-0.4141	10|5	0.48119|.	T|.	0.1|.	.|.	18.3208|18.3208	0.90238|0.90238	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	404;405|.	Q09028-2;Q09028|.	.;RBBP4_HUMAN|.	T|D	404;405;153;370|205	ENSP00000398242:A404T;ENSP00000362592:A405T;ENSP00000442384:A153T;ENSP00000396057:A370T|.	ENSP00000362592:A405T|.	A|G	+|+	1|2	0|0	RBBP4|RBBP4	32917828|32917828	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	8.928000|8.928000	0.92853|0.92853	2.646000|2.646000	0.89796|0.89796	0.557000|0.557000	0.71058|0.71058	GCA|GGC	.	.		0.388	RBBP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021957.3	NM_005610	Missense_Mutation	A	33145241	G	A	33145241	5	1	169	1	0	0	0	0	0	0	1	0	13116	1217	42	3	1259	3	RBBP4	1	33145241	Splice_Site	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	11345849	33145241	216105380	3	25639	122	2								
RBBP4	5928	hgsc.bcm.edu	37	chr1	33145248	33145248	+	Missense_Mutation	SNP	A	A	T													0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tgtttttgggcaggcagagaAcatttataatgatgaagacc							TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr1:33145248A>T	ENST00000373493.5	+	12	1379	c.1220A>T	c.(1219-1221)aAc>aTc	p.N407I	RBBP4_ENST00000414241.3_Missense_Mutation_p.N406I|RBBP4_ENST00000458695.2_Missense_Mutation_p.N372I|RBBP4_ENST00000373485.1_Intron|RBBP4_ENST00000544435.1_Missense_Mutation_p.N155I	NM_001135255.1|NM_005610.2	NP_001128727.1|NP_005601.1	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4	407					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin assembly (GO:0031497)|chromatin remodeling (GO:0006338)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|nucleosome assembly (GO:0006334)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|NURF complex (GO:0016589)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				CAGGCAGAGAACATTTATAAT	0.388																																					p.N407I		Atlas-SNP	.											.	RBBP4	38	.	0			c.A1220T						.						119	118	118					1																	33145248		2203	4300	6503	SO:0001583	missense	5928	exon12			CAGAGAACATTTA	BC053904	CCDS366.1, CCDS44105.1, CCDS44106.1	1p35.1	2014-07-17	2001-11-28		ENSG00000162521	ENSG00000162521		"WD repeat domain containing"	9887	protein-coding gene	gene with protein product		602923	"retinoblastoma-binding protein 4"			8350924, 14609955, 17531812	Standard	NM_005610		Approved	RbAp48, NURF55, lin-53	uc001bvr.3	Q09028	OTTHUMG00000007998	ENST00000373493.5:c.1220A>T	chr1.hg19:g.33145248A>T	ENSP00000362592:p.Asn407Ile	53.0	0.0		71.0	29.0	NM_005610	B2R6G9|B4DRH0|D3DPQ3|P31149|Q53H02|Q96BV9	Missense_Mutation	SNP	ENST00000373493.5	hg19	CCDS366.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	14.22|14.22|14.22	2.470740|2.470740|2.470740	0.43942|0.43942|0.43942	.|.|.	.|.|.	ENSG00000162521|ENSG00000162521|ENSG00000162521	ENST00000463378|ENST00000414241;ENST00000373493;ENST00000544435;ENST00000458695|ENST00000482190	.|T;T;T;T|T	.|0.66638|0.71341	.|-0.22;-0.22;-0.22;-0.22|-0.56	5.3|5.3|5.3	5.3|5.3|5.3	0.74995|0.74995|0.74995	.|WD40-repeat-containing domain (1);|.	.|0.127086|.	.|0.64402|.	.|D|.	.|0.000001|.	T|T|T	0.80884|0.80884|0.80884	0.4709|0.4709|0.4709	M|M|M	0.76727|0.76727|0.76727	2.345|2.345|2.345	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|B;B|.	.|0.16166|.	.|0.016;0.002|.	.|B;B|.	.|0.18263|.	.|0.021;0.009|.	T|T|T	0.82641|0.82641|0.82641	-0.0357|-0.0357|-0.0357	5|10|7	.|0.46703|0.56958	.|T|D	.|0.11|0.05	.|.|.	14.7313|14.7313|14.7313	0.69383|0.69383|0.69383	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|406;407|.	.|Q09028-2;Q09028|.	.|.;RBBP4_HUMAN|.	D|I|S	207|406;407;155;372|147	.|ENSP00000398242:N406I;ENSP00000362592:N407I;ENSP00000442384:N155I;ENSP00000396057:N372I|ENSP00000436565:T147S	.|ENSP00000362592:N407I|ENSP00000436565:T147S	E|N|T	+|+|+	3|2|1	2|0|0	RBBP4|RBBP4|RBBP4	32917835|32917835|32917835	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.995000|0.995000|0.995000	0.86356|0.86356|0.86356	8.716000|8.716000|8.716000	0.91420|0.91420|0.91420	2.137000|2.137000|2.137000	0.66172|0.66172|0.66172	0.455000|0.455000|0.455000	0.32223|0.32223|0.32223	GAA|AAC|ACA	.	.		0.388	RBBP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021957.3	NM_005610		T	33145248	A	T	33145248	3	4	169	1	0	0	0	0	1	0	0	0	13116	43	2	4	1266	4	RBBP4	1	33145248	Missense_Mutation	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10	7	33145248	216105373	4	25640	122	2								
LRRC7	57554	hgsc.bcm.edu	37	chr1	70504162	70504162	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ccttggcagaattggaccagAacccctagtccgtttgaaga	10	11	0	4			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr1:70504162A>G	ENST00000035383.5	+	19	2571	c.2541A>G	c.(2539-2541)agA>agG	p.R847R	LRRC7_ENST00000310961.5_Silent_p.R852R|LRRC7_ENST00000415775.2_Silent_p.R131R	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	847						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						ATTGGACCAGAACCCCTAGTC	0.483																																					p.R847R		Atlas-SNP	.											.	LRRC7	400	.	0			c.A2541G						.						72	82	78					1																	70504162		2203	4300	6503	SO:0001819	synonymous_variant	57554	exon19			GACCAGAACCCCT		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2541A>G	chr1.hg19:g.70504162A>G		228.0	0.0		215.0	97.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Silent	SNP	ENST00000035383.5	hg19	CCDS645.1																																																																																			.	.		0.483	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		G	70504162	A	G	70504162	2	3	169	1	0	0	0	0	0	0	0	1	9029	243	9	2		2	LRRC7	1	70504162	Silent	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10	37358914	70504162	178746459	5	25641										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158648305	158648305	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tttgcttagactgaattaagGgtaggtcaggatggttttcc	12	5	1	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr1:158648305G>C	ENST00000368147.4	-	6	878	c.698C>G	c.(697-699)cCc>cGc	p.P233R		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	233					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CTGAATTAAGGGTAGGTCAGG	0.393																																					p.P233R		Atlas-SNP	.											.	SPTA1	720	.	0			c.C698G						.						68	64	65					1																	158648305		1871	4099	5970	SO:0001583	missense	6708	exon6			ATTAAGGGTAGGT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.698C>G	chr1.hg19:g.158648305G>C	ENSP00000357129:p.Pro233Arg	68.0	0.0		123.0	61.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.775274	0.49786	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.53640	0.61;0.61	4.66	3.67	0.42095	.	0.271170	0.19816	N	0.105426	T	0.25344	0.0616	L	0.47716	1.5	0.19575	N	0.999968	B	0.30973	0.302	B	0.35770	0.21	T	0.04621	-1.0938	10	0.33940	T	0.23	.	10.0707	0.42330	0.0:0.0:0.6683:0.3317	.	233	P02549	SPTA1_HUMAN	R	233	ENSP00000357130:P233R;ENSP00000357129:P233R	ENSP00000357129:P233R	P	-	2	0	SPTA1	156914929	0.920000	0.31207	0.024000	0.17045	0.024000	0.10985	3.265000	0.51561	2.572000	0.86782	0.650000	0.86243	CCC	.	.		0.393	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158648305	G	C	158648305	3	2	169	1	0	0	0	0	1	0	0	0	15131	1232	43	4	6749	4	SPTA1	1	158648305	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	88144143	158648305	90602316	6	25642										
GORAB	92344	hgsc.bcm.edu	37	chr1	170511631	170511636	+	Splice_Site	DEL	GGCAAG	GGCAAG	-													0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tatgctttttttgccccctaGgcaagaaaaatctcgttggg							TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	GGCAAG	GGCAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr1:170511631_170511636delGGCAAG	ENST00000367763.3	+	3	514_519	c.494_499delGGCAAG	c.(493-501)tggcaagaa>taa	p.165_167WQE>*	GORAB_ENST00000367762.1_Splice_Site_p.165_167WQE>*	NM_152281.2	NP_689494.2	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	165						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|liver(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	17						TTGCCCCCTAGGCAAGAAAAATCTCG	0.369																																					p.165_166del		Atlas-INDEL	.											.	GORAB	41	.	0			c.495_498del						.																																			SO:0001630	splice_region_variant	92344	exon3			.	AK021814	CCDS1289.1, CCDS53428.1	1q24.2	2009-02-13	2009-02-13	2009-02-13	ENSG00000120370	ENSG00000120370			25676	protein-coding gene	gene with protein product	"gerodermia osteodysplastica"	607983	"SCY1-like 1 binding protein 1"	SCYL1BP1		12783284, 15781263, 18997784	Standard	NM_152281		Approved	FLJ11752, NTKL-BP1, GO	uc001gha.2	Q5T7V8	OTTHUMG00000035228	ENST00000367763.3:c.495-1GGCAAG>-	chr1.hg19:g.170511631_170511636delGGCAAG		244.0	0.0		524.0	68.0	NM_152281	Q49A22|Q6P1P9|Q9HAE6|Q9Y350	Frame_Shift_Del	DEL	ENST00000367763.3	hg19	CCDS1289.1																																																																																			.	.		0.369	GORAB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085226.1	NM_152281	In_Frame_Del	-	170511636	GGCAAG	-	170511631	8	5	169	1	0	1	0	1	0	0	1	0	6582	1014	35	0	504	0	GORAB	1	170511631	Splice_Site	DEL	GGCAAG	TCGA-DD-AACS-01A-11D-A40R-10	11863326	170511631	78738990	7	25643										
PFKFB2	5208	hgsc.bcm.edu	37	chr1	207228111	207228111	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	acaacaacagctatgaaaccAaaaccccaaatcttcgaatg	4	12	1	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr1:207228111A>G	ENST00000367080.3	+	2	173	c.49A>G	c.(49-51)Aaa>Gaa	p.K17E	YOD1_ENST00000367084.1_5'Flank|PFKFB2_ENST00000545806.1_5'UTR|PFKFB2_ENST00000411990.2_5'UTR|YOD1_ENST00000391927.1_5'Flank|PFKFB2_ENST00000367079.2_Missense_Mutation_p.K17E	NM_006212.2	NP_006203.2	O60825	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	17	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose catabolic process (GO:0006007)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|lactate metabolic process (GO:0006089)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|protein kinase binding (GO:0019901)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	20	Prostate(682;0.19)					CTATGAAACCAAAACCCCAAA	0.423																																					p.K17E		Atlas-SNP	.											.	PFKFB2	70	.	0			c.A49G						.						62	57	59					1																	207228111		2203	4300	6503	SO:0001583	missense	5208	exon2			GAAACCAAAACCC		CCDS31003.1, CCDS31004.1	1q31-q32.2	2012-07-13			ENSG00000123836	ENSG00000123836	2.7.1.105, 3.1.3.46		8873	protein-coding gene	gene with protein product		171835					Standard	XM_005273162		Approved		uc001hfg.3	O60825	OTTHUMG00000036033	ENST00000367080.3:c.49A>G	chr1.hg19:g.207228111A>G	ENSP00000356047:p.Lys17Glu	71.0	0.0		165.0	40.0	NM_001018053	O60824|Q5VVQ3|Q5VVQ4|Q9H3P1	Missense_Mutation	SNP	ENST00000367080.3	hg19	CCDS31004.1	.	.	.	.	.	.	.	.	.	.	A	3.716	-0.058595	0.07317	.	.	ENSG00000123836	ENST00000367080;ENST00000367079	.	.	.	4.49	3.34	0.38264	.	0.641392	0.16258	N	0.222373	T	0.17916	0.0430	N	0.19112	0.55	0.19300	N	0.99998	B;B	0.24258	0.1;0.019	B;B	0.19148	0.024;0.017	T	0.28902	-1.0029	9	0.02654	T	1	.	8.1168	0.30948	0.784:0.216:0.0:0.0	.	17;17	Q5VVQ3;O60825	.;F262_HUMAN	E	17	.	ENSP00000356046:K17E	K	+	1	0	PFKFB2	205294734	0.206000	0.23470	0.003000	0.11579	0.138000	0.21146	1.848000	0.39309	0.675000	0.31264	0.533000	0.62120	AAA	.	.		0.423	PFKFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087838.1			G	207228111	A	G	207228111	3	3	169	1	0	0	0	0	1	0	0	0	11770	131	5	2	51	2	PFKFB2	1	207228111	Missense_Mutation	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10	36716480	207228111	42022510	8	25644										
RD3	343035	hgsc.bcm.edu	37	chr1	211654728	211654728	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	gacagccgggatggggcctcGttccaccgaagccatgagat	14	12	0	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr1:211654728G>A	ENST00000367002.4	-	2	1193	c.30C>T	c.(28-30)aaC>aaT	p.N10N	RD3_ENST00000484910.1_Intron	NM_001164688.1|NM_183059.2	NP_001158160.1|NP_898882.1	Q7Z3Z2	RD3_HUMAN	retinal degeneration 3	10					response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)			p.N10N(1)		central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10				OV - Ovarian serous cystadenocarcinoma(81;0.00284)|all cancers(67;0.0279)|Epithelial(68;0.0689)		ATGGGGCCTCGTTCCACCGAA	0.607																																					p.N10N		Atlas-SNP	.											RD3,colon,carcinoma,0,3	RD3	26	.	1	Substitution - coding silent(1)	ovary(1)	c.C30T						.						44	44	44					1																	211654728		2203	4300	6503	SO:0001819	synonymous_variant	343035	exon2			GGCCTCGTTCCAC	AY191519	CCDS1498.1	1q32.3	2008-02-05	2006-11-13	2006-11-13	ENSG00000198570	ENSG00000198570			19689	protein-coding gene	gene with protein product		180040	"chromosome 1 open reading frame 36"	C1orf36		12914764	Standard	NM_183059		Approved	LCA12	uc001hin.2	Q7Z3Z2	OTTHUMG00000037002	ENST00000367002.4:c.30C>T	chr1.hg19:g.211654728G>A		85.0	0.0		158.0	43.0	NM_183059	A8K595	Silent	SNP	ENST00000367002.4	hg19	CCDS1498.1																																																																																			.	.		0.607	RD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089837.1	NM_183059		A	211654728	G	A	211654728	2	1	169	1	0	0	0	0	0	0	0	1	13202	1136	40	1		1	RD3	1	211654728	Silent	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	4426617	211654728	37595893	9	25645										
OR2M2	391194	hgsc.bcm.edu	37	chr1	248343509	248343509	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ctcatggacctcatgctcatCtgcaccaccgtacccaagat	6	16	4	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr1:248343509C>G	ENST00000359682.2	+	1	222	c.222C>G	c.(220-222)atC>atG	p.I74M		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	74						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TCATGCTCATCTGCACCACCG	0.498																																					p.I74M		Atlas-SNP	.											.	OR2M2	149	.	0			c.C222G						.						265	256	259					1																	248343509		2203	4297	6500	SO:0001583	missense	391194	exon1			GCTCATCTGCACC	AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"GPCR / Class A : Olfactory receptors"	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.222C>G	chr1.hg19:g.248343509C>G	ENSP00000352710:p.Ile74Met	158.0	0.0		360.0	85.0	NM_001004688	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	hg19	CCDS31106.1	.	.	.	.	.	.	.	.	.	.	c	6.199	0.404892	0.11754	.	.	ENSG00000198601	ENST00000359682	T	0.00433	7.43	2.03	-0.513	0.11962	GPCR, rhodopsin-like superfamily (1);	0.585147	0.12867	U	0.432637	T	0.00468	0.0015	M	0.85945	2.785	0.09310	N	1	B	0.28439	0.212	B	0.31869	0.137	T	0.41106	-0.9527	10	0.87932	D	0	.	2.7369	0.05242	0.3915:0.3667:0.0:0.2418	.	74	Q96R28	OR2M2_HUMAN	M	74	ENSP00000352710:I74M	ENSP00000352710:I74M	I	+	3	3	OR2M2	246410132	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.865000	0.04250	-0.276000	0.09206	0.454000	0.30748	ATC	.	.		0.498	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688		G	248343509	C	G	248343509	3	3	169	1	0	0	0	0	1	0	0	0	11019	903	32	4	224	4	OR2M2	1	248343509	Missense_Mutation	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10	36688781	248343509	907112	10	25646										
VWA3B	200403	hgsc.bcm.edu	37	chr2	98852884	98852884	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ttgctggctgaggagtggctGgatgacaaatcgtcagaaaa	14	6	1	3			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr2:98852884G>T	ENST00000477737.1	+	18	2664	c.2460G>T	c.(2458-2460)ctG>ctT	p.L820L		NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	820										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AGGAGTGGCTGGATGACAAAT	0.433																																					p.L820L		Atlas-SNP	.											.	VWA3B	138	.	0			c.G2460T						.						112	121	118					2																	98852884		1936	4151	6087	SO:0001819	synonymous_variant	200403	exon18			GTGGCTGGATGAC	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.2460G>T	chr2.hg19:g.98852884G>T		163.0	0.0		162.0	63.0	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Silent	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	G	1.749	-0.489817	0.04352	.	.	ENSG00000168658	ENST00000473149	.	.	.	4.48	-3.27	0.05048	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.7091	0.02888	0.2591:0.2582:0.3516:0.131	.	.	.	.	X	231	.	.	G	+	1	0	VWA3B	98219316	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.470000	0.06639	-0.870000	0.04047	-3.009000	0.00075	GGA	.	.		0.433	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		T	98852884	G	T	98852884	2	4	169	1	0	0	0	0	0	0	0	1	17256	1335	47	3		3	VWA3B	2	98852884	Silent	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10		98852884	144346489	11	25647										
SCRN3	79634	hgsc.bcm.edu	37	chr2	175292534	175292534	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ttcaaaacaagcatcttgatGtggagaaaattgttaatctc	7	6	3	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr2:175292534G>T	ENST00000272732.6	+	8	1268	c.1186G>T	c.(1186-1188)Gtg>Ttg	p.V396L	SCRN3_ENST00000409673.3_Missense_Mutation_p.V389L|SCRN3_ENST00000548921.1_3'UTR	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	396							dipeptidase activity (GO:0016805)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			GCATCTTGATGTGGAGAAAAT	0.323																																					p.V396L		Atlas-SNP	.											.	SCRN3	76	.	0			c.G1186T						.						84	83	83					2																	175292534		2203	4296	6499	SO:0001583	missense	79634	exon8			CTTGATGTGGAGA	AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.1186G>T	chr2.hg19:g.175292534G>T	ENSP00000272732:p.Val396Leu	342.0	0.0		398.0	208.0	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Missense_Mutation	SNP	ENST00000272732.6	hg19	CCDS2258.1	.	.	.	.	.	.	.	.	.	.	G	6.742	0.505792	0.12822	.	.	ENSG00000144306	ENST00000409673;ENST00000272732	T;T	0.07800	3.16;3.16	5.63	3.36	0.38483	.	0.957919	0.08717	N	0.904091	T	0.04952	0.0133	N	0.08118	0	0.09310	N	1	B;B	0.12013	0.005;0.002	B;B	0.04013	0.001;0.001	T	0.46205	-0.9208	10	0.15499	T	0.54	-0.0209	10.8016	0.46491	0.2274:0.0:0.7726:0.0	.	389;396	B4DI11;Q0VDG4	.;SCRN3_HUMAN	L	389;396	ENSP00000387142:V389L;ENSP00000272732:V396L	ENSP00000272732:V396L	V	+	1	0	SCRN3	175000780	0.006000	0.16342	0.944000	0.38274	0.943000	0.58893	0.299000	0.19138	0.463000	0.27118	0.655000	0.94253	GTG	.	.		0.323	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583		T	175292534	G	T	175292534	3	4	169	1	0	0	0	0	1	0	0	0	13955	1377	48	3	1212	3	SCRN3	2	175292534	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	76439650	175292534	67906839	12	25648										
GNAT1	2779	hgsc.bcm.edu	37	chr3	50232232	50232232	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	gaggacgccggcaactacatCaaggtgcagttcctcgagct	12	12	1	0			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr3:50232232C>A	ENST00000433068.1	+	8	953	c.897C>A	c.(895-897)atC>atA	p.I299I	GNAT1_ENST00000232461.3_Silent_p.I299I	NM_000172.3	NP_000163.2	P11488	GNAT1_HUMAN	guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1	299					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell proliferation (GO:0008283)|cellular response to electrical stimulus (GO:0071257)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|phototransduction, visible light (GO:0007603)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to light intensity (GO:0009642)|response to light stimulus (GO:0009416)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	acyl binding (GO:0000035)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GCAACTACATCAAGGTGCAGT	0.627											OREG0015580	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I299I		Atlas-SNP	.											.	GNAT1	39	.	0			c.C897A						.						76	64	68					3																	50232232		2203	4300	6503	SO:0001819	synonymous_variant	2779	exon8			CTACATCAAGGTG		CCDS2812.1	3p21	2014-01-28			ENSG00000114349	ENSG00000114349			4393	protein-coding gene	gene with protein product		139330					Standard	NM_000172		Approved	CSNBAD3	uc003cyl.2	P11488	OTTHUMG00000156808	ENST00000433068.1:c.897C>A	chr3.hg19:g.50232232C>A		90.0	0.0	968	91.0	45.0	NM_144499	Q4VBN2	Silent	SNP	ENST00000433068.1	hg19	CCDS2812.1																																																																																			.	.		0.627	GNAT1-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345957.1	NM_000172		A	50232232	C	A	50232232	2	1	169	1	0	0	0	0	0	0	0	1	6519	816	29	3		3	GNAT1	3	50232232	Silent	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10		50232232	147790198	13	25649										
SEMA3G	56920	hgsc.bcm.edu	37	chr3	52472194	52472194	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	cagctgggccacacccagccGagagcccacgtatagcattt	10	15	0	1	rs371791154		TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr3:52472194G>T	ENST00000231721.2	-	14	1530	c.1531C>A	c.(1531-1533)Cgg>Agg	p.R511R		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	511	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R511W(1)		kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		ACACCCAGCCGAGAGCCCACG	0.647																																					p.R511R		Atlas-SNP	.											SEMA3G,NS,carcinoma,0,1	SEMA3G	58	.	1	Substitution - Missense(1)	lung(1)	c.C1531A						.						24	27	26					3																	52472194		2203	4299	6502	SO:0001819	synonymous_variant	56920	exon14			CCAGCCGAGAGCC		CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.1531C>A	chr3.hg19:g.52472194G>T		138.0	0.0		138.0	55.0	NM_020163	Q7L9D9|Q9H7Q3	Silent	SNP	ENST00000231721.2	hg19	CCDS2856.1																																																																																			.	.		0.647	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163		T	52472194	G	T	52472194	2	4	169	1	0	0	0	0	0	0	0	1	14045	1057	37	1		1	SEMA3G	3	52472194	Silent	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	2239962	52472194	145550236	14	25650										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121416741	121416741	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	catttttgttatttcaagttCcttctgtgaaagagcctggg	9	7	2	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr3:121416741C>T	ENST00000340645.5	-	13	2739	c.2614G>A	c.(2614-2616)Gaa>Aaa	p.E872K	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E877K	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	872					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		ATTTCAAGTTCCTTCTGTGAA	0.433																																					p.E877K		Atlas-SNP	.											.	GOLGB1	319	.	0			c.G2629A						.						139	146	144					3																	121416741		2203	4299	6502	SO:0001583	missense	2804	exon13			CAAGTTCCTTCTG	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.2614G>A	chr3.hg19:g.121416741C>T	ENSP00000341848:p.Glu872Lys	83.0	0.0		107.0	62.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.868893	0.51588	.	.	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235	T;T;T	0.29142	2.18;2.18;1.58	5.35	5.35	0.76521	.	0.103582	0.44285	D	0.000475	T	0.47507	0.1449	L	0.60455	1.87	0.42961	D	0.994402	D;D;D;D;D	0.71674	0.998;0.998;0.998;0.998;0.998	D;D;D;D;D	0.80764	0.986;0.991;0.994;0.991;0.915	T	0.22591	-1.0212	10	0.10902	T	0.67	.	14.4328	0.67261	0.0:1.0:0.0:0.0	.	797;836;877;877;872	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789	.;.;.;.;GOGB1_HUMAN	K	872;877;836;684	ENSP00000341848:E872K;ENSP00000377275:E877K;ENSP00000418231:E836K	ENSP00000341848:E872K	E	-	1	0	GOLGB1	122899431	0.008000	0.16893	1.000000	0.80357	0.987000	0.75469	0.011000	0.13264	2.780000	0.95670	0.655000	0.94253	GAA	.	.		0.433	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		T	121416741	C	T	121416741	3	4	169	1	0	0	0	0	1	0	0	0	6573	864	30	3	7205	3	GOLGB1	3	121416741	Missense_Mutation	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10	68944547	121416741	76605689	15	25651										
EPHB3	2049	hgsc.bcm.edu	37	chr3	184298884	184298884	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	caggcccaaattctcccagaTtgtcaataccctggacaagc	7	14	2	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr3:184298884T>A	ENST00000330394.2	+	14	3115	c.2663T>A	c.(2662-2664)aTt>aAt	p.I888N	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	888	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TTCTCCCAGATTGTCAATACC	0.602																																					p.I888N		Atlas-SNP	.											.	EPHB3	114	.	0			c.T2663A						.						83	92	89					3																	184298884		2203	4300	6503	SO:0001583	missense	2049	exon14			CCCAGATTGTCAA	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3394	protein-coding gene	gene with protein product		601839	"EphB3"	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.2663T>A	chr3.hg19:g.184298884T>A	ENSP00000332118:p.Ile888Asn	73.0	0.0		102.0	59.0	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.381227	0.61845	.	.	ENSG00000182580	ENST00000330394	D	0.85339	-1.97	3.99	3.99	0.46301	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94725	0.8298	H	0.97440	4.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95985	0.8981	10	0.87932	D	0	.	12.786	0.57504	0.0:0.0:0.0:1.0	.	888	P54753	EPHB3_HUMAN	N	888	ENSP00000332118:I888N	ENSP00000332118:I888N	I	+	2	0	EPHB3	185781578	1.000000	0.71417	0.992000	0.48379	0.986000	0.74619	8.032000	0.88838	1.779000	0.52309	0.448000	0.29417	ATT	.	.		0.602	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		A	184298884	T	A	184298884	3	1	169	1	0	0	0	0	1	0	0	0	5178	1493	52	4	2717	4	EPHB3	3	184298884	Missense_Mutation	SNP	T	TCGA-DD-AACS-01A-11D-A40R-10	62882143	184298884	13723546	16	25652										
CRMP1	1400	hgsc.bcm.edu	37	chr4	5853138	5853138	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	gagtgtgagggacctacctgGctgtcggacatttggtagac	15	8	0	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr4:5853138G>A	ENST00000397890.2	-	5	751	c.537C>T	c.(535-537)agC>agT	p.S179S	CRMP1_ENST00000512574.1_Silent_p.S177S|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000324989.7_Silent_p.S293S	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	179					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		GACCTACCTGGCTGTCGGACA	0.483																																					p.S293S		Atlas-SNP	.											.	CRMP1	118	.	0			c.C879T						.						209	191	197					4																	5853138		2203	4300	6503	SO:0001819	synonymous_variant	1400	exon5			TACCTGGCTGTCG	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.537C>T	chr4.hg19:g.5853138G>A		95.0	0.0		104.0	45.0	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Silent	SNP	ENST00000397890.2	hg19	CCDS43207.1																																																																																			.	.		0.483	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		A	5853138	G	A	5853138	2	1	169	1	0	0	0	0	0	0	0	1	3892	1194	42	3		3	CRMP1	4	5853138	Silent	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10		5853138	185301138	17	25653										
DCAF4L1	285429	hgsc.bcm.edu	37	chr4	41984060	41984060	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tctggcgagtaccaacagcgAccagctcttcgtagtgaacc	10	13	2	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr4:41984060A>T	ENST00000333141.5	+	1	348	c.251A>T	c.(250-252)gAc>gTc	p.D84V		NM_001029955.3	NP_001025126.2	Q3SXM0	DC4L1_HUMAN	DDB1 and CUL4 associated factor 4-like 1	84										breast(1)|endometrium(5)|kidney(6)|large_intestine(11)|lung(12)|prostate(1)|skin(1)	37						ACCAACAGCGACCAGCTCTTC	0.537																																					p.D84V		Atlas-SNP	.											.	DCAF4L1	70	.	0			c.A251T						.						90	78	82					4																	41984060		2203	4300	6503	SO:0001583	missense	285429	exon1			ACAGCGACCAGCT	BC035027	CCDS33978.1	4p13	2013-01-09	2009-07-17	2009-07-17		ENSG00000182308		"WD repeat domain containing"	27723	protein-coding gene	gene with protein product			"WD repeat domain 21B"	WDR21B			Standard	NM_001029955		Approved		uc003gwk.2	Q3SXM0		ENST00000333141.5:c.251A>T	chr4.hg19:g.41984060A>T	ENSP00000327796:p.Asp84Val	138.0	0.0		172.0	80.0	NM_001029955	B3KVI3|Q3ZCW8|Q499Y5|Q9UFI0	Missense_Mutation	SNP	ENST00000333141.5	hg19	CCDS33978.1	.	.	.	.	.	.	.	.	.	.	A	17.83	3.484912	0.63962	.	.	ENSG00000182308	ENST00000333141	T	0.42900	0.96	0.688	0.688	0.18027	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.224065	0.53938	D	0.000056	T	0.31606	0.0802	L	0.57536	1.79	0.58432	D	0.99999	P	0.37233	0.588	B	0.26864	0.074	T	0.29941	-0.9995	9	0.87932	D	0	.	.	.	.	.	84	Q3SXM0	DC4L1_HUMAN	V	84	ENSP00000327796:D84V	ENSP00000327796:D84V	D	+	2	0	DCAF4L1	41678817	1.000000	0.71417	0.536000	0.28039	0.507000	0.33981	4.771000	0.62318	0.530000	0.28619	0.260000	0.18958	GAC	.	.		0.537	DCAF4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360958.1	NM_001029955		T	41984060	A	T	41984060	3	4	169	1	0	0	0	0	1	0	0	0	4273	275	10	4	253	4	DCAF4L1	4	41984060	Missense_Mutation	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10	36130922	41984060	149170216	18	25654										
PRDM5	11107	hgsc.bcm.edu	37	chr4	121706177	121706177	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	atgtattagcaggtgtctctGtaaagaaaatggggtccgga	13	5	1	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr4:121706177G>C	ENST00000264808.3	-	11	1498	c.1258C>G	c.(1258-1260)Cag>Gag	p.Q420E	PRDM5_ENST00000515109.1_Missense_Mutation_p.Q389E|PRDM5_ENST00000428209.2_Missense_Mutation_p.Q389E	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	420					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						AGGTGTCTCTGTAAAGAAAAT	0.398																																					p.Q420E		Atlas-SNP	.											.	PRDM5	76	.	0			c.C1258G						.						97	90	92					4																	121706177		2203	4300	6503	SO:0001583	missense	11107	exon11			GTCTCTGTAAAGA	AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"Zinc fingers, C2H2-type"	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.1258C>G	chr4.hg19:g.121706177G>C	ENSP00000264808:p.Gln420Glu	45.0	0.0		36.0	21.0	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Missense_Mutation	SNP	ENST00000264808.3	hg19	CCDS3716.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.123623	0.37436	.	.	ENSG00000138738	ENST00000264808;ENST00000515109;ENST00000428209	T;T;T	0.18016	2.24;2.24;2.24	5.31	4.46	0.54185	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.054557	0.85682	D	0.000000	T	0.11707	0.0285	N	0.21194	0.64	0.80722	D	1	B;P;B	0.38395	0.037;0.629;0.037	B;B;B	0.34242	0.062;0.178;0.038	T	0.11060	-1.0603	10	0.22109	T	0.4	-13.3319	15.3865	0.74706	0.0:0.0:0.8597:0.1403	.	389;389;420	Q0VAI9;Q9NQX1-2;Q9NQX1	.;.;PRDM5_HUMAN	E	420;389;389	ENSP00000264808:Q420E;ENSP00000422309:Q389E;ENSP00000404832:Q389E	ENSP00000264808:Q420E	Q	-	1	0	PRDM5	121925627	1.000000	0.71417	0.975000	0.42487	0.943000	0.58893	9.578000	0.98200	1.225000	0.43566	0.591000	0.81541	CAG	.	.		0.398	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2			C	121706177	G	C	121706177	3	2	169	1	0	0	0	0	1	0	0	0	12472	1386	48	4	658	4	PRDM5	4	121706177	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	79722117	121706177	69448099	19	25655										
TRIML1	339976	hgsc.bcm.edu	37	chr4	189061721	189061721	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tgaatcttttgcgtgtaaggAgaaaggaagctcaggctgta	13	5	2	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr4:189061721A>G	ENST00000332517.3	+	2	588	c.448A>G	c.(448-450)Aga>Gga	p.R150G	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	150					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		GCGTGTAAGGAGAAAGGAAGC	0.468																																					p.R150G	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											.	TRIML1	126	.	0			c.A448G						.						166	156	159					4																	189061721		2203	4300	6503	SO:0001583	missense	339976	exon2			GTAAGGAGAAAGG	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"RING-type (C3HC4) zinc fingers"	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.448A>G	chr4.hg19:g.189061721A>G	ENSP00000327738:p.Arg150Gly	113.0	0.0		67.0	63.0	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	hg19	CCDS3851.1	.	.	.	.	.	.	.	.	.	.	A	6.708	0.499399	0.12762	.	.	ENSG00000184108	ENST00000332517	T	0.63417	-0.04	4.74	4.74	0.60224	.	1.271710	0.05378	N	0.536602	T	0.54663	0.1872	L	0.36672	1.1	0.09310	N	1	B	0.19817	0.039	B	0.14578	0.011	T	0.35624	-0.9781	10	0.23891	T	0.37	-15.2049	11.2026	0.48749	1.0:0.0:0.0:0.0	.	150	Q8N9V2	TRIML_HUMAN	G	150	ENSP00000327738:R150G	ENSP00000327738:R150G	R	+	1	2	TRIML1	189298715	0.000000	0.05858	0.165000	0.22776	0.004000	0.04260	0.768000	0.26590	2.075000	0.62263	0.533000	0.62120	AGA	.	.		0.468	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556		G	189061721	A	G	189061721	3	3	169	1	0	0	0	0	1	0	0	0	16565	296	11	2	454	2	TRIML1	4	189061721	Missense_Mutation	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10	67355544	189061721	2092555	20	25656										
TMED9	54732	hgsc.bcm.edu	37	chr5	177021211	177021211	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	attgctgctaaagacaagttGagtgagttgcagctacgagt	12	6	0	3			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr5:177021211G>A	ENST00000332598.6	+	4	540	c.483G>A	c.(481-483)ttG>ttA	p.L161L		NM_017510.4	NP_059980.2	Q9BVK6	TMED9_HUMAN	transmembrane emp24 protein transport domain containing 9	161					COPI coating of Golgi vesicle (GO:0048205)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network transport vesicle (GO:0030140)	syntaxin binding (GO:0019905)			endometrium(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(2)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGACAAGTTGAGTGAGTTGC	0.512																																					p.L161L		Atlas-SNP	.											.	TMED9	18	.	0			c.G483A						.						110	97	101					5																	177021211		2203	4300	6503	SO:0001819	synonymous_variant	54732	exon4			CAAGTTGAGTGAG	AF441399	CCDS4428.1	5q35.3	2008-02-05			ENSG00000184840	ENSG00000184840			24878	protein-coding gene	gene with protein product						12477932	Standard	NM_017510		Approved	HSGP25L2G	uc003mhx.3	Q9BVK6	OTTHUMG00000130859	ENST00000332598.6:c.483G>A	chr5.hg19:g.177021211G>A		199.0	0.0		214.0	95.0	NM_017510	Q14437|Q8WZ61	Silent	SNP	ENST00000332598.6	hg19	CCDS4428.1																																																																																			.	.		0.512	TMED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253433.1	NM_017510		A	177021211	G	A	177021211	2	1	169	1	0	0	0	0	0	0	0	1	16027	1281	45	3		3	TMED9	5	177021211	Silent	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10		177021211	3894049	21	25657										
OR2W1	26692	hgsc.bcm.edu	37	chr6	29012190	29012190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ttgcaggtacatgtagataaTagttccatagaacatagaca	8	6	0	3			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr6:29012190T>C	ENST00000377175.1	-	1	827	c.763A>G	c.(763-765)Att>Gtt	p.I255V		NM_030903.3	NP_112165.1	Q9Y3N9	OR2W1_HUMAN	olfactory receptor, family 2, subfamily W, member 1	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|skin(1)	23						ATGTAGATAATAGTTCCATAG	0.463																																					p.I255V		Atlas-SNP	.											.	OR2W1	36	.	0			c.A763G						.						150	131	138					6																	29012190		1511	2709	4220	SO:0001583	missense	26692	exon1			AGATAATAGTTCC	AL035402	CCDS4656.1	6p22.1	2012-08-09			ENSG00000204704	ENSG00000204704		"GPCR / Class A : Olfactory receptors"	8281	protein-coding gene	gene with protein product							Standard	NM_030903		Approved	hs6M1-15	uc003nlw.2	Q9Y3N9	OTTHUMG00000031048	ENST00000377175.1:c.763A>G	chr6.hg19:g.29012190T>C	ENSP00000366380:p.Ile255Val	168.0	0.0		200.0	98.0	NM_030903	B0S7Y5|Q5JNZ1|Q6IEU0|Q96R17|Q9GZL0|Q9GZL1	Missense_Mutation	SNP	ENST00000377175.1	hg19	CCDS4656.1	.	.	.	.	.	.	.	.	.	.	T	8.625	0.892289	0.17613	.	.	ENSG00000204704	ENST00000377175	T	0.00115	8.71	4.79	0.724	0.18236	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000092	T	0.00012	0.0000	N	0.11845	0.185	0.31829	N	0.624996	B	0.10296	0.003	B	0.14023	0.01	T	0.01626	-1.1309	10	0.10111	T	0.7	.	5.1656	0.15084	0.0:0.179:0.2302:0.5908	.	255	Q9Y3N9	OR2W1_HUMAN	V	255	ENSP00000366380:I255V	ENSP00000366380:I255V	I	-	1	0	OR2W1	29120169	0.000000	0.05858	0.998000	0.56505	0.991000	0.79684	-1.988000	0.01482	0.190000	0.20209	0.482000	0.46254	ATT	.	.		0.463	OR2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076053.2			C	29012190	T	C	29012190	3	2	169	1	0	0	0	0	1	0	0	0	11041	1406	49	2	203	2	OR2W1	6	29012190	Missense_Mutation	SNP	T	TCGA-DD-AACS-01A-11D-A40R-10		29012190	142102877	22	25658										
MTRF1L	54516	hgsc.bcm.edu	37	chr6	153316444	153316444	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tttcttctgagggaaccaaaAgtaagataatctgtaaatat	7	5	3	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr6:153316444A>C	ENST00000367233.5	-	3	349	c.350T>G	c.(349-351)cTt>cGt	p.L117R	MTRF1L_ENST00000367231.5_Missense_Mutation_p.L117R|MTRF1L_ENST00000464135.1_Intron|MTRF1L_ENST00000367230.1_Missense_Mutation_p.L117R	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	117						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		GGGAACCAAAAGTAAGATAAT	0.294																																					p.L117R		Atlas-SNP	.											.	MTRF1L	21	.	0			c.T350G						.						24	24	24					6																	153316444		2192	4293	6485	SO:0001583	missense	54516	exon3			ACCAAAAGTAAGA	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.350T>G	chr6.hg19:g.153316444A>C	ENSP00000356202:p.Leu117Arg	134.0	0.0		174.0	71.0	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Missense_Mutation	SNP	ENST00000367233.5	hg19	CCDS5243.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.526299	0.44969	.	.	ENSG00000112031	ENST00000367233;ENST00000367231;ENST00000367230;ENST00000414771	T;T;T;T	0.50813	0.73;0.73;0.73;2.65	5.43	5.43	0.79202	Peptide chain release factor (2);	0.061987	0.64402	D	0.000004	T	0.63803	0.2542	M	0.86420	2.815	0.50632	D	0.999885	D;D;D;D	0.76494	0.998;0.997;0.999;0.998	D;D;D;D	0.71656	0.964;0.949;0.967;0.974	T	0.72017	-0.4417	10	0.87932	D	0	-19.4498	11.2595	0.49074	0.8632:0.0:0.0:0.1368	.	117;117;117;117	B4DMX1;Q9UGC7-2;Q9UGC7-4;Q9UGC7	.;.;.;RF1ML_HUMAN	R	117;117;117;4	ENSP00000356202:L117R;ENSP00000356200:L117R;ENSP00000356199:L117R;ENSP00000414383:L4R	ENSP00000356199:L117R	L	-	2	0	MTRF1L	153358137	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.526000	0.53509	2.062000	0.61559	0.477000	0.44152	CTT	.	.		0.294	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041		C	153316444	A	C	153316444	3	2	169	1	0	0	0	0	1	0	0	0	9969	72	3	5	812	5	MTRF1L	6	153316444	Missense_Mutation	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10	124304254	153316444	17798623	23	25659										
ZNF716	441234	hgsc.bcm.edu	37	chr7	57529237	57529237	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	actctacacatgtgaagaatGtgggaaagcctttaccttct	8	9	2	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr7:57529237G>T	ENST00000420713.1	+	4	1182	c.1070G>T	c.(1069-1071)tGt>tTt	p.C357F		NM_001159279.1	NP_001152751.1	A6NP11	ZN716_HUMAN	zinc finger protein 716	357					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|lung(20)|ovary(2)	24						TGTGAAGAATGTGGGAAAGCC	0.398																																					p.C357F		Atlas-SNP	.											.	ZNF716	207	.	0			c.G1070T						.						68	69	69					7																	57529237		692	1591	2283	SO:0001583	missense	441234	exon4			AAGAATGTGGGAA	AK131575	CCDS55112.1	7p11.1	2013-01-08			ENSG00000182111	ENSG00000182111		"Zinc fingers, C2H2-type", "-"	32458	protein-coding gene	gene with protein product							Standard	NM_001159279		Approved	FLJ46189	uc011kdi.1	A6NP11	OTTHUMG00000156689	ENST00000420713.1:c.1070G>T	chr7.hg19:g.57529237G>T	ENSP00000394248:p.Cys357Phe	134.0	0.0		172.0	76.0	NM_001159279		Missense_Mutation	SNP	ENST00000420713.1	hg19	CCDS55112.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.840559	0.32513	.	.	ENSG00000182111	ENST00000420713;ENST00000418732	D	0.85861	-2.04	0.109	0.109	0.14578	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.92459	0.7606	H	0.94264	3.515	0.37001	D	0.895288	D	0.69078	0.997	D	0.79108	0.992	D	0.90456	0.4442	9	0.87932	D	0	.	5.9913	0.19465	6.0E-4:0.0:0.9994:0.0	.	345	A6NP11	ZN716_HUMAN	F	357;345	ENSP00000394248:C357F	ENSP00000387687:C345F	C	+	2	0	ZNF716	57533179	1.000000	0.71417	0.009000	0.14445	0.009000	0.06853	4.919000	0.63383	0.181000	0.19994	0.184000	0.17185	TGT	.	.		0.398	ZNF716-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345309.1	NM_001159279		T	57529237	G	T	57529237	3	4	169	1	0	0	0	0	1	0	0	0	18134	1377	48	3	1084	3	ZNF716	7	57529237	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10		57529237	101609426	24	25660										
TECPR1	25851	hgsc.bcm.edu	37	chr7	97863048	97863048	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ttccacggtatcttctgcggTcctgccagcccccaggcctg	10	17	2	0			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr7:97863048T>C	ENST00000447648.2	-	11	1656	c.1357A>G	c.(1357-1359)Acc>Gcc	p.T453A	TECPR1_ENST00000542604.1_Missense_Mutation_p.T383A|TECPR1_ENST00000379795.3_Missense_Mutation_p.T453A			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	453					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TCTTCTGCGGTCCTGCCAGCC	0.672																																					p.T453A		Atlas-SNP	.											.	TECPR1	77	.	0			c.A1357G						.						20	25	23					7																	97863048		2027	4176	6203	SO:0001583	missense	25851	exon11			CTGCGGTCCTGCC		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.1357A>G	chr7.hg19:g.97863048T>C	ENSP00000404923:p.Thr453Ala	113.0	0.0		162.0	54.0	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Missense_Mutation	SNP	ENST00000447648.2	hg19	CCDS47648.1	.	.	.	.	.	.	.	.	.	.	T	1.890	-0.455758	0.04540	.	.	ENSG00000205356	ENST00000447648;ENST00000379795;ENST00000542604	T;T;T	0.29655	1.56;1.57;1.57	4.14	-0.212	0.13169	.	1.622620	0.03237	N	0.179720	T	0.19127	0.0459	N	0.22421	0.69	0.09310	N	1	B;B	0.20671	0.047;0.001	B;B	0.18263	0.021;0.002	T	0.16600	-1.0397	10	0.07482	T	0.82	-5.2761	7.7384	0.28827	0.0:0.0835:0.3161:0.6004	.	383;453	F5GX57;Q7Z6L1	.;TCPR1_HUMAN	A	453;453;383	ENSP00000404923:T453A;ENSP00000369121:T453A;ENSP00000441121:T383A	ENSP00000369121:T453A	T	-	1	0	TECPR1	97700984	0.001000	0.12720	0.018000	0.16275	0.018000	0.09664	0.805000	0.27112	0.111000	0.17947	0.379000	0.24179	ACC	.	.		0.672	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395		C	97863048	T	C	97863048	3	2	169	1	0	0	0	0	1	0	0	0	15758	1667	58	2	2204	2	TECPR1	7	97863048	Missense_Mutation	SNP	T	TCGA-DD-AACS-01A-11D-A40R-10	40333811	97863048	61275615	25	25661										
NEIL2	252969	hgsc.bcm.edu	37	chr8	11637363	11637363	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	agatgctgggaggtggctgcGtgtcagctttggtttgtttg	17	5	1	1	rs147360797		TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr8:11637363G>A	ENST00000284503.6	+	3	994	c.395G>A	c.(394-396)cGt>cAt	p.R132H	NEIL2_ENST00000436750.3_Missense_Mutation_p.R132H|NEIL2_ENST00000403422.3_Missense_Mutation_p.R71H|NEIL2_ENST00000455213.2_Missense_Mutation_p.R132H|NEIL2_ENST00000528323.1_Intron	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	132					base-excision repair (GO:0006284)|nucleotide-excision repair (GO:0006289)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		AGGTGGCTGCGTGTCAGCTTT	0.577								Base excision repair (BER), DNA glycosylases																													p.R132H		Atlas-SNP	.											.	NEIL2	14	.	0			c.G395A						.	G	HIS/ARG,HIS/ARG,,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	87	84	85		395,212,,395	2.4	0.4	8	dbSNP_134	85	0,8600		0,0,4300	no	missense,missense,intron,missense	NEIL2	NM_001135746.1,NM_001135747.1,NM_001135748.1,NM_145043.2	29,29,,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,,probably-damaging	132/333,71/272,,132/333	11637363	1,13005	2203	4300	6503	SO:0001583	missense	252969	exon3			GGCTGCGTGTCAG	AK056206	CCDS5984.1, CCDS47802.1, CCDS47803.1	8p23.1	2010-04-27	2010-04-27		ENSG00000154328	ENSG00000154328			18956	protein-coding gene	gene with protein product		608933	"nei like 2 (E. coli)"			12097317, 17686777	Standard	NM_145043		Approved	NEH2, FLJ31644, MGC2832, MGC4505	uc003wue.2	Q969S2	OTTHUMG00000090753	ENST00000284503.6:c.395G>A	chr8.hg19:g.11637363G>A	ENSP00000284503:p.Arg132His	81.0	0.0		49.0	39.0	NM_001135746	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Missense_Mutation	SNP	ENST00000284503.6	hg19	CCDS5984.1	.	.	.	.	.	.	.	.	.	.	G	8.671	0.902754	0.17760	2.27E-4	0.0	ENSG00000154328	ENST00000530433;ENST00000455213;ENST00000403422;ENST00000436750;ENST00000284503;ENST00000382309	T;T;T;T	0.13778	2.56;3.25;2.56;2.56	4.72	2.44	0.29823	DNA glycosylase/AP lyase, catalytic domain (2);	0.328143	0.30911	N	0.008628	T	0.10508	0.0257	L	0.43152	1.355	0.23831	N	0.99672	B	0.18863	0.031	B	0.12837	0.008	T	0.20306	-1.0279	10	0.62326	D	0.03	-13.0699	4.8675	0.13616	0.5972:0.0:0.4028:0.0	.	132	Q969S2	NEIL2_HUMAN	H	132;132;71;132;132;117	ENSP00000397538:R132H;ENSP00000384070:R71H;ENSP00000394023:R132H;ENSP00000284503:R132H	ENSP00000284503:R132H	R	+	2	0	NEIL2	11674772	0.981000	0.34729	0.407000	0.26434	0.009000	0.06853	3.069000	0.50026	0.957000	0.37930	-0.367000	0.07326	CGT	.	G|1.000;A|0.000		0.577	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043		A	11637363	G	A	11637363	3	1	169	1	0	0	0	0	1	0	0	0	10328	1145	40	1	406	1	NEIL2	8	11637363	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10		11637363	134726659	26	25662										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110477316	110477316	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ctttgaccgtcccaactgtgTagctttgggagtgacatcca	10	11	0	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr8:110477316T>A	ENST00000378402.5	+	49	8359	c.8255T>A	c.(8254-8256)gTa>gAa	p.V2752E		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2752					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CCCAACTGTGTAGCTTTGGGA	0.473										HNSCC(38;0.096)																											p.V2752E		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T8255A						.						151	149	150					8																	110477316		1925	4135	6060	SO:0001583	missense	93035	exon49			ACTGTGTAGCTTT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.8255T>A	chr8.hg19:g.110477316T>A	ENSP00000367655:p.Val2752Glu	158.0	0.0		265.0	77.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	T	14.20	2.464112	0.43736	.	.	ENSG00000205038	ENST00000378402	D	0.87179	-2.22	5.83	0.678	0.17969	.	0.208381	0.40818	N	0.001001	T	0.80412	0.4618	L	0.52573	1.65	0.31124	N	0.708562	B	0.28933	0.228	B	0.23716	0.048	T	0.75539	-0.3282	10	0.66056	D	0.02	.	8.5466	0.33426	0.0:0.4415:0.0:0.5585	.	2752	Q86WI1	PKHL1_HUMAN	E	2752	ENSP00000367655:V2752E	ENSP00000367655:V2752E	V	+	2	0	PKHD1L1	110546492	0.990000	0.36364	0.999000	0.59377	0.993000	0.82548	0.409000	0.21082	0.095000	0.17434	-0.376000	0.06991	GTA	.	.		0.473	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110477316	T	A	110477316	3	1	169	1	0	0	0	0	1	0	0	0	11981	1638	57	4	8449	4	PKHD1L1	8	110477316	Missense_Mutation	SNP	T	TCGA-DD-AACS-01A-11D-A40R-10	98839953	110477316	35886706	27	25663										
KLF9	687	hgsc.bcm.edu	37	chr9	73028153	73028153	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	gtcaccgtgctccttggtcaCctcgcgctcaggtagtcgca	11	15	3	0			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr9:73028153C>T	ENST00000377126.2	-	1	1387	c.127G>A	c.(127-129)Gtg>Atg	p.V43M		NM_001206.2	NP_001197.1	Q13886	KLF9_HUMAN	Kruppel-like factor 9	43					cellular response to thyroid hormone stimulus (GO:0097067)|embryo implantation (GO:0007566)|progesterone receptor signaling pathway (GO:0050847)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1)	9						TCCTTGGTCACCTCGCGCTCA	0.632																																					p.V43M		Atlas-SNP	.											.	KLF9	16	.	0			c.G127A						.						50	40	43					9																	73028153		2203	4300	6503	SO:0001583	missense	687	exon1			TGGTCACCTCGCG	BC069431	CCDS6633.1	9q21.11	2013-01-08	2004-11-29	2004-12-01	ENSG00000119138	ENSG00000119138		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	1123	protein-coding gene	gene with protein product		602902	"basic transcription element binding protein 1"	BTEB1		1356762	Standard	NM_001206		Approved		uc004aht.3	Q13886	OTTHUMG00000019991	ENST00000377126.2:c.127G>A	chr9.hg19:g.73028153C>T	ENSP00000366330:p.Val43Met	68.0	0.0		60.0	25.0	NM_001206	B2R943|Q16196	Missense_Mutation	SNP	ENST00000377126.2	hg19	CCDS6633.1	.	.	.	.	.	.	.	.	.	.	C	13.74	2.326636	0.41197	.	.	ENSG00000119138	ENST00000377126	T	0.04917	3.53	4.85	4.85	0.62838	.	0.596324	0.14987	N	0.286898	T	0.04770	0.0129	N	0.14661	0.345	0.27395	N	0.955014	B	0.26845	0.161	B	0.24541	0.054	T	0.34229	-0.9837	10	0.32370	T	0.25	.	12.6348	0.56677	0.0:0.833:0.167:0.0	.	43	Q13886	KLF9_HUMAN	M	43	ENSP00000366330:V43M	ENSP00000366330:V43M	V	-	1	0	KLF9	72217973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.279000	0.43435	2.250000	0.74265	0.557000	0.71058	GTG	.	.		0.632	KLF9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052602.1	NM_001206		T	73028153	C	T	73028153	3	4	169	1	0	0	0	0	1	0	0	0	8362	507	18	3	615	3	KLF9	9	73028153	Missense_Mutation	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10		73028153	68185278	28	25664										
ARID5B	84159	hgsc.bcm.edu	37	chr10	63852733	63852733	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ctttagctgctataaatcctCaagctgcctttccatcttcc	4	14	2	0			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr10:63852733C>G	ENST00000279873.7	+	10	3921	c.3511C>G	c.(3511-3513)Caa>Gaa	p.Q1171E	ARID5B_ENST00000309334.5_Missense_Mutation_p.Q928E	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	1171					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					TATAAATCCTCAAGCTGCCTT	0.517																																					p.Q1171E		Atlas-SNP	.											.	ARID5B	125	.	0			c.C3511G						.						115	119	118					10																	63852733		2203	4300	6503	SO:0001583	missense	84159	exon10			AATCCTCAAGCTG	M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.3511C>G	chr10.hg19:g.63852733C>G	ENSP00000279873:p.Gln1171Glu	45.0	0.0		66.0	34.0	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	hg19	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.624031	0.66901	.	.	ENSG00000150347	ENST00000279873;ENST00000309334	T;T	0.60548	0.25;0.18	5.87	5.87	0.94306	.	0.051979	0.85682	D	0.000000	T	0.67813	0.2933	M	0.65975	2.015	0.54753	D	0.999984	D	0.60160	0.987	P	0.49887	0.625	T	0.71203	-0.4662	10	0.87932	D	0	-17.7233	20.2033	0.98269	0.0:1.0:0.0:0.0	.	1171	Q14865	ARI5B_HUMAN	E	1171;928	ENSP00000279873:Q1171E;ENSP00000308862:Q928E	ENSP00000279873:Q1171E	Q	+	1	0	ARID5B	63522739	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.400000	0.52594	2.779000	0.95612	0.655000	0.94253	CAA	.	.		0.517	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		G	63852733	C	G	63852733	3	3	169	1	0	0	0	0	1	0	0	0	922	827	29	4	3549	4	ARID5B	10	63852733	Missense_Mutation	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10		63852733	71682014	29	25665										
DNA2	1763	hgsc.bcm.edu	37	chr10	70192255	70192255	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	aacaaagttgattctggaagGaccgacaagtttctaaaaca	8	7	2	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr10:70192255G>A	ENST00000358410.3	-	11	1709	c.1659C>T	c.(1657-1659)gtC>gtT	p.V553V	DNA2_ENST00000399179.2_Silent_p.V553V|DNA2_ENST00000399180.2_Silent_p.V639V	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	553	Helicase activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						ATTCTGGAAGGACCGACAAGT	0.333																																					p.V553V		Atlas-SNP	.											.	DNA2	76	.	0			c.C1659T						.						26	24	25					10																	70192255		1829	4071	5900	SO:0001819	synonymous_variant	1763	exon11			TGGAAGGACCGAC	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"DNA2 DNA replication helicase 2-like (yeast)", "DNA replication helicase 2 homolog (yeast)"	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.1659C>T	chr10.hg19:g.70192255G>A		328.0	0.0		346.0	135.0	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	hg19																																																																																				.	.		0.333	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			A	70192255	G	A	70192255	2	1	169	1	0	0	0	0	0	0	0	1	4598	1161	41	3		3	DNA2	10	70192255	Silent	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	6339522	70192255	65342492	30	25666										
DUSP13	51207	hgsc.bcm.edu	37	chr10	76867822	76867822	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ggcactgatgtcaaaatcagGgaggtcgtgggctggcaccc	15	10	2	1	rs201419297		TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr10:76867822G>T	ENST00000372702.3	-	2	358	c.295C>A	c.(295-297)Cct>Act	p.P99T	DUSP13_ENST00000491677.2_5'UTR|DUSP13_ENST00000607131.1_Intron|DUSP13_ENST00000607009.1_5'UTR|DUSP13_ENST00000372700.3_Intron			Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	108					meiotic nuclear division (GO:0007126)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	8	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					TCAAAATCAGGGAGGTCGTGG	0.622																																					p.P99T	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											.	DUSP13	82	.	0			c.C295A						.						42	51	48					10																	76867822		2058	4185	6243	SO:0001583	missense	51207	exon2			AATCAGGGAGGTC	AB027004	CCDS7346.1, CCDS31224.1, CCDS53542.1	10q23.1	2013-10-25			ENSG00000079393	ENSG00000079393		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	19681	protein-coding gene	gene with protein product		613191				10585869	Standard	XM_005269883		Approved	BEDP, TMDP, FLJ32450, DUSP13A, DUSP13B	uc001jwu.3	Q6B8I1	OTTHUMG00000018516	ENST00000372702.3:c.295C>A	chr10.hg19:g.76867822G>T	ENSP00000361787:p.Pro99Thr	119.0	0.0		142.0	58.0	NM_001007271	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Missense_Mutation	SNP	ENST00000372702.3	hg19	CCDS53542.1	.	.	.	.	.	.	.	.	.	.	G	30	5.050143	0.93740	.	.	ENSG00000079393	ENST00000372702	D	0.84660	-1.88	5.35	5.35	0.76521	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	.	.	.	.	D	0.92639	0.7661	M	0.83483	2.645	0.80722	D	1	D	0.67145	0.996	D	0.70935	0.971	D	0.92597	0.6088	9	0.52906	T	0.07	.	17.983	0.89147	0.0:0.0:1.0:0.0	.	99	Q6B8I1	MDSP_HUMAN	T	99	ENSP00000361787:P99T	ENSP00000361787:P99T	P	-	1	0	DUSP13	76537828	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.900000	0.92551	2.781000	0.95711	0.655000	0.94253	CCT	.	G|0.998;A|0.002		0.622	DUSP13-012	KNOWN	NMD_exception|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401503.3			T	76867822	G	T	76867822	3	4	169	1	0	0	0	0	1	0	0	0	4815	1232	43	3	1175	3	DUSP13	10	76867822	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	6675567	76867822	58666925	31	25667										
CD81	975	hgsc.bcm.edu	37	chr11	2416745	2416745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ctgtggtgaagaccttccacGagacggtgcggccccggggg	17	12	0	3	rs538164293		TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr11:2416745G>A	ENST00000263645.5	+	5	710	c.454G>A	c.(454-456)Gag>Aag	p.E152K	CD81_ENST00000524805.1_3'UTR|CD81_ENST00000492627.1_Missense_Mutation_p.E81K|CD81_ENST00000481687.1_Missense_Mutation_p.E158K|CD81_ENST00000381036.3_Missense_Mutation_p.E190K|CD81_ENST00000526072.1_Missense_Mutation_p.E81K	NM_004356.3	NP_004347.1	P60033	CD81_HUMAN	CD81 molecule	152					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of 1-phosphatidylinositol 4-kinase activity (GO:0043128)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization (GO:0008104)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of immune response (GO:0050776)|viral entry into host cell (GO:0046718)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	MHC class II protein complex binding (GO:0023026)			endometrium(1)|lung(3)|skin(1)	5		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000338)|LUSC - Lung squamous cell carcinoma(625;0.191)		GACCTTCCACGAGACGGTGCG	0.657													G|||	1	0.000199681	0	0	5008	,	,		13972	0		0.001	False		,,,				2504	0				p.E152K		Atlas-SNP	.											.	CD81	11	.	0			c.G454A						.						64	61	62					11																	2416745		2201	4298	6499	SO:0001583	missense	975	exon5			TTCCACGAGACGG		CCDS7734.1, CCDS73240.1	11p15.5	2014-09-17	2006-03-28		ENSG00000110651	ENSG00000110651		"CD molecules", "Tetraspanins"	1701	protein-coding gene	gene with protein product		186845	"CD81 antigen (target of antiproliferative antibody 1)"	TAPA1		1650385	Standard	XM_005253260		Approved	TAPA-1, TSPAN28	uc001lwf.1	P60033	OTTHUMG00000009892	ENST00000263645.5:c.454G>A	chr11.hg19:g.2416745G>A	ENSP00000263645:p.Glu152Lys	108.0	0.0		116.0	58.0	NM_004356	P18582|Q5U0J6	Missense_Mutation	SNP	ENST00000263645.5	hg19	CCDS7734.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184139	0.38609	.	.	ENSG00000110651	ENST00000475945;ENST00000263645;ENST00000533417;ENST00000492627;ENST00000527343;ENST00000381036;ENST00000492252;ENST00000526072;ENST00000481687	T;T;D;T;T;T;T;T;T	0.86562	-1.26;-1.26;-2.14;-1.26;-1.26;-1.26;-1.26;-1.26;-1.26	3.65	3.65	0.41850	Tetraspanin, EC2 domain (1);CD81 extracellular domain (1);	0.118955	0.56097	D	0.000036	T	0.72969	0.3527	N	0.16903	0.455	0.80722	D	1	P;P	0.47545	0.897;0.811	B;B	0.39339	0.297;0.109	T	0.71328	-0.4626	10	0.11485	T	0.65	.	11.05	0.47880	0.0:0.0:1.0:0.0	.	190;152	A6NMH8;P60033	.;CD81_HUMAN	K	81;152;147;81;141;190;145;81;158	ENSP00000433178:E81K;ENSP00000263645:E152K;ENSP00000435633:E147K;ENSP00000437242:E81K;ENSP00000433767:E141K;ENSP00000370424:E190K;ENSP00000432249:E145K;ENSP00000431780:E81K;ENSP00000432033:E158K	ENSP00000263645:E152K	E	+	1	0	CD81	2373321	1.000000	0.71417	0.997000	0.53966	0.689000	0.40095	3.620000	0.54203	2.060000	0.61445	0.561000	0.74099	GAG	.	.		0.657	CD81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027357.4	NM_004356		A	2416745	G	A	2416745	3	1	169	1	0	0	0	0	1	0	0	0	3041	1059	37	1	472	1	CD81	11	2416745	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10		2416745	132589771	32	25668										
IPO7	10527	hgsc.bcm.edu	37	chr11	9452513	9452513	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tatgggaattctgaatacaaTtgatacacttcttagtgtag	8	5	2	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr11:9452513T>G	ENST00000379719.3	+	16	1986	c.1844T>G	c.(1843-1845)aTt>aGt	p.I615S	CTD-2371O3.2_ENST00000531111.1_RNA|SNORA23_ENST00000365128.1_RNA	NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	615					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		CTGAATACAATTGATACACTT	0.373																																					p.I615S		Atlas-SNP	.											.	IPO7	72	.	0			c.T1844G						.						98	90	92					11																	9452513		2201	4295	6496	SO:0001583	missense	10527	exon16			ATACAATTGATAC	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.1844T>G	chr11.hg19:g.9452513T>G	ENSP00000369042:p.Ile615Ser	95.0	0.0		78.0	31.0	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	hg19	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.699270	0.88830	.	.	ENSG00000205339	ENST00000379719	T	0.71698	-0.59	5.53	5.53	0.82687	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85062	0.5611	M	0.85197	2.74	0.80722	D	1	D	0.69078	0.997	D	0.68765	0.96	D	0.87609	0.2502	10	0.72032	D	0.01	.	15.6512	0.77095	0.0:0.0:0.0:1.0	.	615	O95373	IPO7_HUMAN	S	615	ENSP00000369042:I615S	ENSP00000369042:I615S	I	+	2	0	IPO7	9409089	1.000000	0.71417	0.717000	0.30585	0.996000	0.88848	8.040000	0.89188	2.113000	0.64589	0.528000	0.53228	ATT	.	.		0.373	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		G	9452513	T	G	9452513	3	3	169	1	0	0	0	0	1	0	0	0	7806	1493	52	5	1906	5	IPO7	11	9452513	Missense_Mutation	SNP	T	TCGA-DD-AACS-01A-11D-A40R-10	7035768	9452513	125554003	33	25669										
LRRC4C	57689	hgsc.bcm.edu	37	chr11	40137427	40137427	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	atacaaaagctccattcgggAtggtagtaagacgattgtca	10	7	1	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr11:40137427A>G	ENST00000278198.2	-	2	2379	c.416T>C	c.(415-417)aTc>aCc	p.I139T	LRRC4C_ENST00000530763.1_Missense_Mutation_p.I139T|LRRC4C_ENST00000527150.1_Missense_Mutation_p.I139T|LRRC4C_ENST00000528697.1_Missense_Mutation_p.I139T			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	139					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TCCATTCGGGATGGTAGTAAG	0.428																																					p.I139T		Atlas-SNP	.											.	LRRC4C	190	.	0			c.T416C						.						69	71	70					11																	40137427		2203	4300	6503	SO:0001583	missense	57689	exon7			TTCGGGATGGTAG	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.416T>C	chr11.hg19:g.40137427A>G	ENSP00000278198:p.Ile139Thr	107.0	0.0		123.0	45.0	NM_001258419	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	hg19	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	A	15.96	2.988134	0.53934	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	D;D;D;D	0.94723	-3.5;-3.5;-3.5;-3.5	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.97876	0.9302	M	0.94101	3.495	0.80722	D	1	D	0.64830	0.994	D	0.71184	0.972	D	0.98911	1.0780	10	0.87932	D	0	.	15.3632	0.74499	1.0:0.0:0.0:0.0	.	139	Q9HCJ2	LRC4C_HUMAN	T	139	ENSP00000278198:I139T;ENSP00000436976:I139T;ENSP00000437132:I139T;ENSP00000434761:I139T	ENSP00000278198:I139T	I	-	2	0	LRRC4C	40094003	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.287000	0.95975	2.222000	0.72286	0.528000	0.53228	ATC	.	.		0.428	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		G	40137427	A	G	40137427	3	3	169	1	0	0	0	0	1	0	0	0	9017	333	12	2	1510	2	LRRC4C	11	40137427	Missense_Mutation	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10	30684914	40137427	94869089	34	25670										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78387281	78387281	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	accaggttgaggccgttgtcGatgggcagcgtgacattcct	14	10	0	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr11:78387281G>A	ENST00000278550.7	-	30	5874	c.5412C>T	c.(5410-5412)atC>atT	p.I1804I		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1804					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										GGCCGTTGTCGATGGGCAGCG	0.672																																					p.I1804I		Atlas-SNP	.											.	.	.	.	0			c.C5412T						.						23	28	26					11																	78387281		2132	4230	6362	SO:0001819	synonymous_variant	26011	exon30			GTTGTCGATGGGC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5412C>T	chr11.hg19:g.78387281G>A		67.0	0.0		71.0	29.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	hg19	CCDS44688.1																																																																																			.	.		0.672	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78387281	G	A	78387281	2	1	169	1	0	0	0	0	0	0	0	1	10846	1048	37	1		1	ODZ4	11	78387281	Silent	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	38249854	78387281	56619235	35	25671										
SPSB2	84727	hgsc.bcm.edu	37	chr12	6981831	6981831	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tgaatagcccctcttaccccGggccccatcagtgctctggg	10	16	3	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr12:6981831G>A	ENST00000524270.1	-	2	421	c.235C>T	c.(235-237)Cgg>Tgg	p.R79W	LRRC23_ENST00000433346.1_5'Flank|SPSB2_ENST00000523102.1_Missense_Mutation_p.R79W|SPSB2_ENST00000519357.1_Missense_Mutation_p.R79W|RPL13P5_ENST00000412023.1_RNA	NM_032641.3	NP_116030.1	Q99619	SPSB2_HUMAN	splA/ryanodine receptor domain and SOCS box containing 2	79	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				kidney(2)|lung(2)|upper_aerodigestive_tract(1)	5						CTCTTACCCCGGGCCCCATCA	0.647											OREG0021639	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R79W		Atlas-SNP	.											.	SPSB2	11	.	0			c.C235T						.						39	47	44					12																	6981831		2201	4300	6501	SO:0001583	missense	84727	exon2			TACCCCGGGCCCC	AF403027	CCDS8567.1	12p13.31	2008-02-05				ENSG00000111671			29522	protein-coding gene	gene with protein product		611658				8723724, 12076535	Standard	NM_001146316		Approved	GRCC9, SSB-2	uc001qrl.3	Q99619		ENST00000524270.1:c.235C>T	chr12.hg19:g.6981831G>A	ENSP00000428338:p.Arg79Trp	72.0	0.0	638	71.0	29.0	NM_032641	B7Z4W1|D3DUT0	Missense_Mutation	SNP	ENST00000524270.1	hg19	CCDS8567.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.056372	0.36277	.	.	ENSG00000111671	ENST00000523102;ENST00000524270;ENST00000519357;ENST00000432205	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	3.84	2.94	0.34122	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.000000	0.64402	D	0.000010	T	0.82121	0.4968	H	0.94183	3.505	0.41234	D	0.986593	D;B	0.89917	1.0;0.446	D;B	0.97110	1.0;0.034	D	0.84307	0.0508	10	0.87932	D	0	.	9.362	0.38201	0.1086:0.0:0.8914:0.0	.	79;79	B7Z4W1;Q99619	.;SPSB2_HUMAN	W	79	ENSP00000430872:R79W;ENSP00000428338:R79W;ENSP00000431037:R79W;ENSP00000428458:R79W	ENSP00000428458:R79W	R	-	1	2	SPSB2	6852092	1.000000	0.71417	0.896000	0.35187	0.025000	0.11179	2.132000	0.42083	0.947000	0.37659	-0.251000	0.11542	CGG	.	.		0.647	SPSB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375721.1	NM_032641		A	6981831	G	A	6981831	3	1	169	1	0	0	0	0	1	0	0	0	15128	1115	39	1	564	1	SPSB2	12	6981831	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10		6981831	126870064	36	25672										
CUX2	23316	hgsc.bcm.edu	37	chr12	111744831	111744831	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ggacgtgcagcacctccagaGctcactgcaggagctggagg	15	12	1	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr12:111744831G>A	ENST00000261726.6	+	11	1119	c.965G>A	c.(964-966)aGc>aAc	p.S322N		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	322					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						CACCTCCAGAGCTCACTGCAG	0.662																																					p.S322N		Atlas-SNP	.											.	CUX2	145	.	0			c.G965A						.						34	39	37					12																	111744831		2005	4174	6179	SO:0001583	missense	23316	exon11			TCCAGAGCTCACT	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.965G>A	chr12.hg19:g.111744831G>A	ENSP00000261726:p.Ser322Asn	57.0	0.0		65.0	24.0	NM_015267	A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	hg19	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	G	5.674	0.308957	0.10733	.	.	ENSG00000111249	ENST00000261726	T	0.44083	0.93	5.3	-2.0	0.07433	.	0.453060	0.26485	N	0.024102	T	0.13157	0.0319	N	0.02357	-0.585	0.20074	N	0.999939	B	0.02656	0.0	B	0.01281	0.0	T	0.27262	-1.0079	10	0.13853	T	0.58	-7.4032	7.2769	0.26290	0.4924:0.1193:0.3883:0.0	.	322	O14529	CUX2_HUMAN	N	322	ENSP00000261726:S322N	ENSP00000261726:S322N	S	+	2	0	CUX2	110229214	0.998000	0.40836	0.326000	0.25389	0.398000	0.30690	0.543000	0.23237	-0.647000	0.05444	-0.366000	0.07423	AGC	.	.		0.662	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		A	111744831	G	A	111744831	3	1	169	1	0	0	0	0	1	0	0	0	4067	971	34	3	1007	3	CUX2	12	111744831	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	104763000	111744831	22107064	37	25673										
RPH3A	22895	hgsc.bcm.edu	37	chr12	113303258	113303258	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	gaaaacatgaggaagaacgtGgctggagatggggtgaaccg	17	5	0	4			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr12:113303258G>A	ENST00000389385.4	+	6	767	c.270G>A	c.(268-270)gtG>gtA	p.V90V	RPH3A_ENST00000420983.2_Silent_p.V90V|RPH3A_ENST00000543106.2_Silent_p.V90V|RPH3A_ENST00000551052.1_Silent_p.V86V|RPH3A_ENST00000415485.3_Silent_p.V90V|RPH3A_ENST00000447659.2_Silent_p.V41V|RPH3A_ENST00000548866.1_Silent_p.V41V	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	90	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		GGAAGAACGTGGCTGGAGATG	0.532																																					p.V90V		Atlas-SNP	.											.	RPH3A	98	.	0			c.G270A						.						208	182	191					12																	113303258		2203	4300	6503	SO:0001819	synonymous_variant	22895	exon6			GAACGTGGCTGGA	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.270G>A	chr12.hg19:g.113303258G>A		113.0	0.0		97.0	40.0	NM_001143854	B7Z3C3|Q96AE0	Silent	SNP	ENST00000389385.4	hg19	CCDS44979.1																																																																																			.	.		0.532	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		A	113303258	G	A	113303258	2	1	169	1	0	0	0	0	0	0	0	1	13566	1335	47	3		3	RPH3A	12	113303258	Silent	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	1558427	113303258	20548637	38	25674										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124343733	124343733	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	aaatgttcgagaccatgttaAcccgccacacgacgatggtg	10	11	0	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr12:124343733A>T	ENST00000409039.3	+	37	6338	c.6313A>T	c.(6313-6315)Acc>Tcc	p.T2105S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2105	AAA 2. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GACCATGTTAACCCGCCACAC	0.512																																					p.T2105S		Atlas-SNP	.											.	DNAH10	888	.	0			c.A6313T						.						34	36	36					12																	124343733		1895	4114	6009	SO:0001583	missense	196385	exon37			ATGTTAACCCGCC	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.6313A>T	chr12.hg19:g.124343733A>T	ENSP00000386770:p.Thr2105Ser	63.0	0.0		127.0	12.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	21.6	4.166405	0.78339	.	.	ENSG00000197653	ENST00000409039	T	0.38722	1.12	5.4	4.25	0.50352	ATPase, AAA+ type, core (1);	0.000000	0.64402	U	0.000005	T	0.54870	0.1885	M	0.65677	2.01	0.44207	D	0.997035	D	0.56035	0.974	P	0.57911	0.829	T	0.53683	-0.8404	10	0.44086	T	0.13	.	11.1109	0.48232	0.9275:0.0:0.0725:0.0	.	2105	Q8IVF4	DYH10_HUMAN	S	2105	ENSP00000386770:T2105S	ENSP00000386770:T2105S	T	+	1	0	DNAH10	122909686	1.000000	0.71417	0.292000	0.24919	0.885000	0.51271	9.238000	0.95380	0.894000	0.36317	0.456000	0.33151	ACC	.	.		0.512	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124343733	A	T	124343733	3	4	169	1	0	0	0	0	1	0	0	0	4600	43	2	4	6459	4	DNAH10	12	124343733	Missense_Mutation	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10	11040475	124343733	9508162	39	25675										
FOXG1	2290	hgsc.bcm.edu	37	chr14	29237712	29237712	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	aacccctgctccgtcaacctGctcgcgggccagaccagtta	9	17	1	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr14:29237712G>A	ENST00000313071.4	+	1	1426	c.1227G>A	c.(1225-1227)ctG>ctA	p.L409L	FOXG1_ENST00000382535.3_Silent_p.L409L	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	409					aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		CCGTCAACCTGCTCGCGGGCC	0.687																																					p.L409L		Atlas-SNP	.											FOXG1,caecum,carcinoma,0,1	FOXG1	92	.	0			c.G1227A						.						50	41	44					14																	29237712		2203	4300	6503	SO:0001819	synonymous_variant	2290	exon1			CAACCTGCTCGCG		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.1227G>A	chr14.hg19:g.29237712G>A		95.0	0.0		88.0	32.0	NM_005249	A6NFY2|P55315|Q14488|Q86XT7	Silent	SNP	ENST00000313071.4	hg19	CCDS9636.1																																																																																			.	.		0.687	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			A	29237712	G	A	29237712	2	1	169	1	0	0	0	0	0	0	0	1	6015	1306	46	3		3	FOXG1	14	29237712	Silent	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10		29237712	78111828	40	25676										
SIP1	8487	hgsc.bcm.edu	37	chr14	39601242	39601244	+	In_Frame_Del	DEL	AAG	AAG	-													0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tcactgattcggcagcttgcAagaaggtgctctgaagtgag							TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr14:39601242_39601244delAAG	ENST00000308317.6	+	8	797_799	c.714_716delAAG	c.(712-717)gcaaga>gca	p.R240del	GEMIN2_ENST00000250379.8_In_Frame_Del_p.R225del|GEMIN2_ENST00000396249.2_In_Frame_Del_p.R240del	NM_003616.2	NP_003607.1	O14893	GEMI2_HUMAN	gem (nuclear organelle) associated protein 2	240					gene expression (GO:0010467)|mRNA processing (GO:0006397)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)											GGCAGCTTGCAAGAAGGTGCTCT	0.384																																					p.238_239del		Atlas-INDEL	.											.	.	.	.	0			c.713_715del						.																																			SO:0001651	inframe_deletion	8487	exon8			.	AF027150	CCDS9669.1, CCDS32068.1, CCDS41946.1	14q21.1	2011-08-04	2011-08-04	2011-08-04	ENSG00000092208	ENSG00000092208			10884	protein-coding gene	gene with protein product		602595	"survival of motor neuron protein interacting protein 1"	SIP1		9323130, 9323129, 11121410	Standard	NM_003616		Approved		uc001wuq.3	O14893	OTTHUMG00000028816	ENST00000308317.6:c.714_716delAAG	chr14.hg19:g.39601245_39601247delAAG	ENSP00000308533:p.Arg240del	46.0	0.0		48.0	17.0	NM_003616	B2R9W8|Q2M3B3|Q9H4F5|Q9NS77|Q9NS78|Q9NS79	In_Frame_Del	DEL	ENST00000308317.6	hg19	CCDS9669.1																																																																																			.	.		0.384	GEMIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276730.2			-	39601244	AAG	-	39601242	7	5	169	1	0	1	0	1	0	0	0	0	14342	117	5	0	744	0	SIP1	14	39601242	In_Frame_Del	DEL	AAG	TCGA-DD-AACS-01A-11D-A40R-10	10363530	39601242	67748298	41	25677										
PSMC6	5706	hgsc.bcm.edu	37	chr14	53194276	53194276	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	aggaagacttcatgaaagcaGtcagaaaagtggctgattct	11	6	3	4			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr14:53194276G>T	ENST00000606149.1	+	14	1127	c.1111G>T	c.(1111-1113)Gtc>Ttc	p.V371F	PSMC6_ENST00000445930.2_Missense_Mutation_p.V385F|STYX_ENST00000442123.2_5'Flank|PSMC6_ENST00000557557.1_3'UTR|STYX_ENST00000354586.4_5'Flank	NM_002806.3	NP_002797.3	P62333	PRS10_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 6	371					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein binding, bridging (GO:0030674)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	19	Breast(41;0.176)					CATGAAAGCAGTCAGAAAAGT	0.373																																					p.V385F		Atlas-SNP	.											.	PSMC6	71	.	0			c.G1153T						.						71	70	70					14																	53194276		2203	4300	6503	SO:0001583	missense	5706	exon14			AAAGCAGTCAGAA		CCDS9710.2	14q22.1	2010-04-21			ENSG00000100519	ENSG00000100519		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9553	protein-coding gene	gene with protein product		602708				8674546, 9473509	Standard	NM_002806		Approved	p42	uc010tqx.2	P62333	OTTHUMG00000152333	ENST00000606149.1:c.1111G>T	chr14.hg19:g.53194276G>T	ENSP00000475721:p.Val371Phe	136.0	0.0		100.0	68.0	NM_002806	B2R975|P49719|Q6IBU3|Q92524	Missense_Mutation	SNP	ENST00000606149.1	hg19		.	.	.	.	.	.	.	.	.	.	G	26.8	4.767923	0.90020	.	.	ENSG00000100519	ENST00000445930	D	0.94966	-3.57	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.96128	0.8738	L	0.53617	1.68	0.80722	D	1	D	0.61080	0.989	P	0.61800	0.894	D	0.96450	0.9333	10	0.87932	D	0	.	19.3235	0.94252	0.0:0.0:1.0:0.0	.	371	P62333	PRS10_HUMAN	F	385	ENSP00000401802:V385F	ENSP00000401802:V385F	V	+	1	0	PSMC6	52264026	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.385000	0.97223	2.627000	0.88993	0.650000	0.86243	GTC	.	.		0.373	PSMC6-018	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470741.1	NM_002806		T	53194276	G	T	53194276	3	4	169	1	0	0	0	0	1	0	0	0	12703	1029	36	3	1207	3	PSMC6	14	53194276	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	13593034	53194276	54155264	42	25678										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63483654	63483654	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	aatccacaatctgggcatttCccagtaagaaacttgattct	6	10	2	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr14:63483654C>T	ENST00000322893.7	-	2	360	c.92G>A	c.(91-93)gGa>gAa	p.G31E	KCNH5_ENST00000420622.2_Missense_Mutation_p.G31E|KCNH5_ENST00000394964.2_5'UTR|KCNH5_ENST00000394968.1_5'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	31	PAS.				potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CTGGGCATTTCCCAGTAAGAA	0.368																																					p.G31E		Atlas-SNP	.											.	KCNH5	320	.	0			c.G92A						.						86	81	82					14																	63483654		2203	4299	6502	SO:0001583	missense	27133	exon2			GCATTTCCCAGTA	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.92G>A	chr14.hg19:g.63483654C>T	ENSP00000321427:p.Gly31Glu	91.0	0.0		46.0	37.0	NM_172375	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	hg19	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.860679	0.91433	.	.	ENSG00000140015	ENST00000322893;ENST00000420622	D;D	0.99032	-5.35;-5.13	5.29	5.29	0.74685	PAS (1);	0.000000	0.85682	D	0.000000	D	0.99184	0.9717	M	0.69523	2.12	0.80722	D	1	D;D	0.89917	0.975;1.0	P;D	0.81914	0.875;0.995	D	0.99863	1.1086	10	0.87932	D	0	.	18.928	0.92553	0.0:1.0:0.0:0.0	.	31;31	Q8NCM2-2;Q8NCM2	.;KCNH5_HUMAN	E	31	ENSP00000321427:G31E;ENSP00000395439:G31E	ENSP00000321427:G31E	G	-	2	0	KCNH5	62553407	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.482000	0.83794	0.591000	0.81541	GGA	.	.		0.368	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		T	63483654	C	T	63483654	3	4	169	1	0	0	0	0	1	0	0	0	8044	855	30	3	2948	3	KCNH5	14	63483654	Missense_Mutation	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10	10289378	63483654	43865886	43	25679										
TECPR2	9895	hgsc.bcm.edu	37	chr14	102918935	102918935	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	gagctgccccacgggcatgcActggaccaggctggacctct	13	15	1	0			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr14:102918935A>G	ENST00000359520.7	+	16	3837	c.3611A>G	c.(3610-3612)cAc>cGc	p.H1204R	TECPR2_ENST00000558678.1_Missense_Mutation_p.H1204R	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	1204					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						ACGGGCATGCACTGGACCAGG	0.652																																					p.H1204R		Atlas-SNP	.											.	TECPR2	114	.	0			c.A3611G						.						16	13	14					14																	102918935		2194	4287	6481	SO:0001583	missense	9895	exon16			GCATGCACTGGAC	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"KIAA0329"	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.3611A>G	chr14.hg19:g.102918935A>G	ENSP00000352510:p.His1204Arg	113.0	0.0		55.0	37.0	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	hg19	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.459539	0.84317	.	.	ENSG00000196663	ENST00000359520	T	0.14516	2.5	5.83	5.83	0.93111	.	0.052058	0.85682	D	0.000000	T	0.21801	0.0525	N	0.17082	0.46	0.58432	D	0.999998	D;D;D	0.71674	0.996;0.996;0.998	D;D;D	0.67548	0.924;0.93;0.952	T	0.06092	-1.0846	10	0.37606	T	0.19	.	16.2009	0.82078	1.0:0.0:0.0:0.0	.	387;1204;1204	B4DSD3;A5PKY3;O15040	.;.;TCPR2_HUMAN	R	1204	ENSP00000352510:H1204R	ENSP00000352510:H1204R	H	+	2	0	TECPR2	101988688	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.879000	0.92398	2.235000	0.73313	0.533000	0.62120	CAC	.	.		0.652	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		G	102918935	A	G	102918935	3	3	169	1	0	0	0	0	1	0	0	0	15759	159	6	2	3669	2	TECPR2	14	102918935	Missense_Mutation	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10	39435281	102918935	4430605	44	25680										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42145951	42145951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ggcaggcctccgtctgtagcCgtgccacctccttctccata	9	17	2	0	rs548461931	byFrequency	TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr15:42145951C>T	ENST00000320955.6	-	58	10036	c.9809G>A	c.(9808-9810)cGg>cAg	p.R3270Q	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3270					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CGTCTGTAGCCGTGCCACCTC	0.657													C|||	2	0.000399361	0	0	5008	,	,		17352	0		0	False		,,,				2504	0.002				p.R3235Q		Atlas-SNP	.											SPTBN5,colon,carcinoma,0,1	SPTBN5	171	.	0			c.G9704A						.						28	32	31					15																	42145951		2034	4164	6198	SO:0001583	missense	51332	exon58			TGTAGCCGTGCCA	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.9809G>A	chr15.hg19:g.42145951C>T	ENSP00000317790:p.Arg3270Gln	30.0	0.0		32.0	16.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	13.84	2.356035	0.41700	.	.	ENSG00000137877	ENST00000320955	T	0.47528	0.84	4.5	-1.04	0.10068	.	0.218004	0.27482	N	0.019171	T	0.24812	0.0602	N	0.16790	0.44	0.09310	N	1	B	0.33000	0.393	B	0.27608	0.081	T	0.10291	-1.0636	10	0.52906	T	0.07	.	8.3695	0.32406	0.0:0.5803:0.0:0.4197	.	3270	Q9NRC6	SPTN5_HUMAN	Q	3270	ENSP00000317790:R3270Q	ENSP00000317790:R3270Q	R	-	2	0	SPTBN5	39933243	0.000000	0.05858	0.000000	0.03702	0.292000	0.27327	-0.719000	0.04974	-0.426000	0.07360	0.313000	0.20887	CGG	.	.		0.657	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		T	42145951	C	T	42145951	3	4	169	1	0	0	0	0	1	0	0	0	15137	652	23	1	1259	1	SPTBN5	15	42145951	Missense_Mutation	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10		42145951	60385441	45	25681										
ABCA3	21	hgsc.bcm.edu	37	chr16	2336731	2336731	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tggcagcctgcagggcgctcCggggctgggggaagttggag	21	9	0	0	rs565777051		TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr16:2336731C>T	ENST00000301732.5	-	22	3942	c.3242G>A	c.(3241-3243)cGg>cAg	p.R1081Q	ABCA3_ENST00000382381.3_Missense_Mutation_p.R1023Q	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1081					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	CAGGGCGCTCCGGGGCTGGGG	0.652													C|||	1	0.000199681	8e-04	0	5008	,	,		18733	0		0	False		,,,				2504	0				p.R1081Q		Atlas-SNP	.											.	ABCA3	176	.	0			c.G3242A						.						76	81	80					16																	2336731		2198	4300	6498	SO:0001583	missense	21	exon22			GCGCTCCGGGGCT	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.3242G>A	chr16.hg19:g.2336731C>T	ENSP00000301732:p.Arg1081Gln	68.0	0.0		138.0	28.0	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	hg19	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.045894	0.36085	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.86956	-2.19	4.26	4.26	0.50523	.	0.059441	0.64402	N	0.000003	T	0.77980	0.4212	L	0.34521	1.04	0.80722	D	1	P;B	0.35628	0.513;0.02	B;B	0.26416	0.069;0.017	T	0.76383	-0.2979	10	0.18276	T	0.48	.	15.8306	0.78745	0.0:1.0:0.0:0.0	.	1085;1081	Q4LE27;Q99758	.;ABCA3_HUMAN	Q	1081;1085	ENSP00000301732:R1081Q	ENSP00000301732:R1081Q	R	-	2	0	ABCA3	2276732	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.260000	0.78391	2.388000	0.81334	0.555000	0.69702	CGG	.	.		0.652	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		T	2336731	C	T	2336731	3	4	169	1	0	0	0	0	1	0	0	0	33	652	23	1	1920	1	ABCA3	16	2336731	Missense_Mutation	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10		2336731	88018022	46	25682										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2819139	2819139	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tcctcctcctcctcctcctcCtcttcttcctcctcctcttc	0	24	3	0			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr16:2819139C>T	ENST00000301740.8	+	12	8424	c.7875C>T	c.(7873-7875)tcC>tcT	p.S2625S	SRRM2_ENST00000574593.1_3'UTR|AC092117.2_ENST00000581119.1_RNA	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2625	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						cctcctcctcctcttcttcct	0.592																																					p.S2625S		Atlas-SNP	.											.	SRRM2	263	.	0			c.C7875T						.						141	121	128					16																	2819139		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon12			CTCCTCCTCTTCT	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.7875C>T	chr16.hg19:g.2819139C>T		54.0	0.0		108.0	7.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.		0.592	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2819139	C	T	2819139	2	4	169	1	0	0	0	0	0	0	0	1	15184	668	24	3		3	SRRM2	16	2819139	Silent	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10	482408	2819139	87535614	47	25683										
RBL2	5934	hgsc.bcm.edu	37	chr16	53488620	53488620	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ttttatctgttgggaatttaGatgagcggatatttcttgga	11	3	2	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr16:53488620G>C	ENST00000262133.6	+	8	1182	c.1045G>C	c.(1045-1047)Gat>Cat	p.D349H	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Missense_Mutation_p.D133H	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	349					chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TGGGAATTTAGATGAGCGGAT	0.428																																					p.D349H		Atlas-SNP	.											.	RBL2	115	.	0			c.G1045C						.						137	134	135					16																	53488620		2198	4300	6498	SO:0001583	missense	5934	exon8			AATTTAGATGAGC	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.1045G>C	chr16.hg19:g.53488620G>C	ENSP00000262133:p.Asp349His	98.0	0.0		69.0	62.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	hg19	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.837443	0.50951	.	.	ENSG00000103479	ENST00000262133;ENST00000544405;ENST00000379935;ENST00000544545	D;D;D	0.98313	-4.86;-4.23;-3.57	5.5	4.55	0.56014	.	0.048907	0.85682	D	0.000000	D	0.98957	0.9645	M	0.87827	2.91	0.58432	D	0.999997	D;D;D;D	0.89917	0.991;1.0;1.0;1.0	P;D;D;D	0.97110	0.707;0.999;1.0;0.998	D	0.99612	1.0981	10	0.87932	D	0	-20.3931	14.4673	0.67492	0.071:0.0:0.929:0.0	.	133;349;59;349	B7Z913;Q8NE70;E9PG04;Q08999	.;.;.;RBL2_HUMAN	H	349;275;59;133	ENSP00000262133:D349H;ENSP00000443744:D275H;ENSP00000444685:D133H	ENSP00000262133:D349H	D	+	1	0	RBL2	52046121	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	9.636000	0.98440	1.324000	0.45282	-0.300000	0.09419	GAT	.	.		0.428	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		C	53488620	G	C	53488620	3	2	169	1	0	0	0	0	1	0	0	0	13125	942	33	4	1075	4	RBL2	16	53488620	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	50669481	53488620	36866133	48	25684										
TP53	7157	hgsc.bcm.edu	37	chr17	7578554	7578554	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	cttgttgagggcaggggagtActgtaggaagaggaaggaga	19	3	0	3			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr17:7578554A>T	ENST00000269305.4	-	5	565	c.376T>A	c.(376-378)Tac>Aac	p.Y126N	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Splice_Site_p.Y126N|TP53_ENST00000413465.2_Splice_Site_p.Y126N|TP53_ENST00000359597.4_Splice_Site_p.Y126N|TP53_ENST00000445888.2_Splice_Site_p.Y126N|TP53_ENST00000420246.2_Splice_Site_p.Y126N	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	126	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> G (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y126D(9)|p.0?(8)|p.Y126N(6)|p.Y126_K132delYSPALNK(6)|p.Y126_N131delYSPALN(3)|p.Y33D(2)|p.V73fs*9(1)|p.?(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)|p.Y126fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAGGGGAGTACTGTAGGAAG	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y126N	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	40	Substitution - Missense(17)|Deletion - In frame(9)|Whole gene deletion(8)|Deletion - Frameshift(4)|Insertion - In frame(1)|Unknown(1)	central_nervous_system(6)|haematopoietic_and_lymphoid_tissue(6)|upper_aerodigestive_tract(4)|large_intestine(4)|lung(4)|prostate(4)|bone(4)|breast(3)|ovary(2)|stomach(1)|liver(1)|oesophagus(1)	c.T376A	GRCh37	CI004819	TP53	I		.						42	43	43					17																	7578554		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGGAGTACTGTAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.376-1T>A	chr17.hg19:g.7578554A>T		54.0	0.0		51.0	47.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.639687	0.87760	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D;D	0.99869	-7.33;-7.33;-7.33;-7.33;-7.33;-7.33;-7.33;-7.33;-7.33	5.48	5.48	0.80851	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99869	0.9938	M	0.90483	3.12	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.998;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.999;0.999;1.0;0.961;1.0;1.0;1.0	D	0.96375	0.9277	10	0.87932	D	0	-28.2517	13.8301	0.63375	1.0:0.0:0.0:0.0	.	87;126;126;33;126;126;126	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	N	126;126;126;126;126;126;115;33;33;126;126	ENSP00000410739:Y126N;ENSP00000352610:Y126N;ENSP00000269305:Y126N;ENSP00000398846:Y126N;ENSP00000391127:Y126N;ENSP00000391478:Y126N;ENSP00000423862:Y33N;ENSP00000424104:Y126N;ENSP00000426252:Y126N	ENSP00000269305:Y126N	Y	-	1	0	TP53	7519279	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	9.240000	0.95396	2.206000	0.71126	0.533000	0.62120	TAC	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Missense_Mutation	T	7578554	A	T	7578554	5	4	169	1	0	0	0	0	0	0	1	0	16396	405	14	4	922	4	TP53	17	7578554	Splice_Site	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10		7578554	73616656	49	25685										
MPRIP	23164	hgsc.bcm.edu	37	chr17	17061859	17061859	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	ccctgagcagaagaggagccGcgcacgggagcggaggcgag	19	11	0	3			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr17:17061859G>A	ENST00000341712.4	+	14	1589	c.1589G>A	c.(1588-1590)cGc>cAc	p.R530H	MPRIP_ENST00000395804.3_Missense_Mutation_p.R530H|MPRIP_ENST00000395811.5_Missense_Mutation_p.R530H|MPRIP_ENST00000444976.1_Missense_Mutation_p.R492H			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	530						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						AAGAGGAGCCGCGCACGGGAG	0.647																																					p.R530H		Atlas-SNP	.											.	MPRIP	87	.	0			c.G1589A						.						16	19	18					17																	17061859		2201	4294	6495	SO:0001583	missense	23164	exon14			GGAGCCGCGCACG	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"Pleckstrin homology (PH) domain containing"	30321	protein-coding gene	gene with protein product	"Rho interacting protein 3"	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.1589G>A	chr17.hg19:g.17061859G>A	ENSP00000342379:p.Arg530His	100.0	0.0		114.0	66.0	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	hg19	CCDS32578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.57|18.57	3.651700|3.651700	0.67472|0.67472	.|.	.|.	ENSG00000133030|ENSG00000133030	ENST00000423885|ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	.|T;T;T;T	.|0.29917	.|1.55;1.87;1.86;1.86	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	.|.	.|.	.|.	.|.	T|T	0.36635|0.36635	0.0974|0.0974	M|M	0.80183|0.80183	2.485|2.485	0.58432|0.58432	D|D	0.999998|0.999998	.|P;P	.|0.48998	.|0.796;0.918	.|B;B	.|0.33042	.|0.119;0.157	T|T	0.53542|0.53542	-0.8424|-0.8424	5|9	.|0.87932	.|D	.|0	.|.	19.6557|19.6557	0.95837|0.95837	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|530;530	.|Q6WCQ1-2;Q6WCQ1	.|.;MPRIP_HUMAN	T|H	17|492;530;530;530	.|ENSP00000400189:R492H;ENSP00000379156:R530H;ENSP00000379149:R530H;ENSP00000342379:R530H	.|ENSP00000342379:R530H	A|R	+|+	1|2	0|0	MPRIP|MPRIP	17002584|17002584	1.000000|1.000000	0.71417|0.71417	0.965000|0.965000	0.40720|0.40720	0.554000|0.554000	0.35429|0.35429	9.134000|9.134000	0.94467|0.94467	2.657000|2.657000	0.90304|0.90304	0.563000|0.563000	0.77884|0.77884	GCG|CGC	.	.		0.647	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		A	17061859	G	A	17061859	3	1	169	1	0	0	0	0	1	0	0	0	9752	1087	38	1	1643	1	MPRIP	17	17061859	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	9483305	17061859	64133351	50	25686										
KRTAP4-3	85290	hgsc.bcm.edu	37	chr17	39324355	39324355	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	gcagcagctggggcggcagcAgctctcctggccgagacctt	15	14	1	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr17:39324355A>T	ENST00000391356.2	-	1	69	c.70T>A	c.(70-72)Tgc>Agc	p.C24S		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	24					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GGGCGGCAGCAGCTCTCCTGG	0.637																																					p.C24S		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.T70A						.						27	31	30					17																	39324355		2196	4298	6494	SO:0001583	missense	85290	exon1			GGCAGCAGCTCTC	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"Keratin associated proteins"	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.70T>A	chr17.hg19:g.39324355A>T	ENSP00000375151:p.Cys24Ser	117.0	0.0		160.0	17.0	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	hg19	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	12.63	1.996334	0.35226	.	.	ENSG00000196156	ENST00000391356	T	0.04406	3.63	5.15	5.15	0.70609	.	.	.	.	.	T	0.22627	0.0546	M	0.82323	2.585	0.43703	D	0.996168	D	0.89917	1.0	D	0.83275	0.996	T	0.00724	-1.1593	9	0.49607	T	0.09	.	13.2133	0.59839	1.0:0.0:0.0:0.0	.	24	Q9BYR4	KRA43_HUMAN	S	24	ENSP00000375151:C24S	ENSP00000375151:C24S	C	-	1	0	KRTAP4-3	36577881	0.767000	0.28508	0.753000	0.31225	0.100000	0.18952	1.312000	0.33574	2.039000	0.60335	0.533000	0.62120	TGC	.	.		0.637	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1			T	39324355	A	T	39324355	3	4	169	1	0	0	0	0	1	0	0	0	8561	188	7	4	521	4	KRTAP4-3	17	39324355	Missense_Mutation	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10	22262496	39324355	41870855	51	25687										
C17orf57	124989	hgsc.bcm.edu	37	chr17	45507195	45507195	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	cttttgcagctacacagataCtcttagctactacccaaatt	4	12	1	1			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr17:45507195C>G	ENST00000331493.2	+	24	2917	c.2506C>G	c.(2506-2508)Ctc>Gtc	p.L836V	EFCAB13_ENST00000517484.1_Missense_Mutation_p.L740V	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	836						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TACACAGATACTCTTAGCTAC	0.373																																					p.L836V		Atlas-SNP	.											.	.	.	.	0			c.C2506G						.						188	172	177					17																	45507195		2203	4300	6503	SO:0001583	missense	124989	exon24			CAGATACTCTTAG	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.2506C>G	chr17.hg19:g.45507195C>G	ENSP00000332111:p.Leu836Val	87.0	0.0		108.0	9.0	NM_152347	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	hg19	CCDS11512.1	.	.	.	.	.	.	.	.	.	.	.	9.430	1.085247	0.20390	.	.	ENSG00000178852	ENST00000331493;ENST00000517484	T;D	0.81908	1.73;-1.55	2.56	1.59	0.23543	.	1.021530	0.07849	N	0.964366	T	0.70684	0.3252	L	0.27053	0.805	0.24730	N	0.9931	P;P	0.50156	0.932;0.865	B;B	0.42112	0.3;0.376	T	0.59500	-0.7443	10	0.23302	T	0.38	-2.6706	5.3245	0.15898	0.0:0.836:0.0:0.164	.	836;740	Q8IY85;G3V128	CQ057_HUMAN;.	V	836;740	ENSP00000332111:L836V;ENSP00000430048:L740V	ENSP00000332111:L836V	L	+	1	0	C17orf57	42862194	0.999000	0.42202	0.890000	0.34922	0.253000	0.25986	0.694000	0.25512	0.663000	0.31027	0.187000	0.17357	CTC	.	.		0.373	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		G	45507195	C	G	45507195	3	3	169	1	0	0	0	0	1	0	0	0	1867	565	20	4	2588	4	C17orf57	17	45507195	Missense_Mutation	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10	6182840	45507195	35688015	52	25688										
BSG	682	hgsc.bcm.edu	37	chr19	580781	580781	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	gatcactgactctgaggacaAggtgagaagccaaggaggct	14	8	2	3			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr19:580781A>G	ENST00000333511.3	+	5	861	c.791A>G	c.(790-792)aAg>aGg	p.K264R	BSG_ENST00000353555.4_Splice_Site_p.K148R|BSG_ENST00000346916.4_Splice_Site_p.K84R|BSG_ENST00000545507.2_Splice_Site_p.K55R	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	264	Ig-like V-type.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCTGAGGACAAGGTGAGAAGC	0.627																																					p.K264R		Atlas-SNP	.											.	BSG	48	.	0			c.A791G						.						48	49	49					19																	580781		2200	4299	6499	SO:0001630	splice_region_variant	682	exon5			AGGACAAGGTGAG	L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1116	protein-coding gene	gene with protein product	"Ok blood group"	109480	"basigin"	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.792+1A>G	chr19.hg19:g.580781A>G		64.0	0.0		94.0	6.0	NM_001728	A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Missense_Mutation	SNP	ENST00000333511.3	hg19	CCDS12033.1	.	.	.	.	.	.	.	.	.	.	A	11.50	1.656638	0.29425	.	.	ENSG00000172270	ENST00000346916;ENST00000545507;ENST00000333511;ENST00000353555	T;T;T	0.67523	-0.27;-0.27;-0.27	3.6	3.6	0.41247	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.720750	0.01835	N	0.034952	T	0.45577	0.1349	N	0.02765	-0.5	0.18873	N	0.999986	B;B;B;B;B	0.15719	0.005;0.014;0.006;0.014;0.0	B;B;B;B;B	0.15052	0.007;0.012;0.012;0.012;0.0	T	0.37174	-0.9717	10	0.16420	T	0.52	-25.4539	10.4328	0.44417	1.0:0.0:0.0:0.0	.	148;264;148;264;84	P35613-2;B4DNE1;Q54A51;P35613;A6NJW1	.;.;.;BASI_HUMAN;.	R	84;55;264;148	ENSP00000344707:K84R;ENSP00000333769:K264R;ENSP00000343809:K148R	ENSP00000333769:K264R	K	+	2	0	BSG	531781	0.450000	0.25697	0.418000	0.26571	0.087000	0.18053	1.155000	0.31700	1.409000	0.46915	0.379000	0.24179	AAG	.	.		0.627	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728	Missense_Mutation	G	580781	A	G	580781	5	3	169	1	0	0	0	0	0	0	1	0	1531	86	3	2	845	2	BSG	19	580781	Splice_Site	SNP	A	TCGA-DD-AACS-01A-11D-A40R-10		580781	58548202	53	25689										
C19orf26	255057	hgsc.bcm.edu	37	chr19	1235018	1235018	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	accggcgacccttgtcctgcGtcttgcggctctgctcaaac	10	16	3	0			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr19:1235018G>A	ENST00000382477.2	-	5	693	c.419C>T	c.(418-420)aCg>aTg	p.T140M	C19orf26_ENST00000590083.1_Missense_Mutation_p.T146M|C19orf26_ENST00000215376.6_Missense_Mutation_p.T140M			Q8N350	DOS_HUMAN	chromosome 19 open reading frame 26	140						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTGTCCTGCGTCTTGCGGCT	0.701										HNSCC(14;0.022)																											p.T146M		Atlas-SNP	.											.	C19orf26	31	.	0			c.C437T						.						22	25	24					19																	1235018		2196	4296	6492	SO:0001583	missense	255057	exon5			TCCTGCGTCTTGC	BC028156	CCDS12057.1, CCDS12057.2	19p13.3	2012-10-24			ENSG00000099625	ENSG00000099625			28617	protein-coding gene	gene with protein product	"downstream of STK11"					12477932	Standard	NM_152769		Approved	MGC40084, DOS	uc002lrm.3	Q8N350	OTTHUMG00000180141	ENST00000382477.2:c.419C>T	chr19.hg19:g.1235018G>A	ENSP00000371917:p.Thr140Met	73.0	0.0		84.0	35.0	NM_152769	O43385	Missense_Mutation	SNP	ENST00000382477.2	hg19		.	.	.	.	.	.	.	.	.	.	G	13.67	2.306661	0.40795	.	.	ENSG00000099625	ENST00000382477;ENST00000215376	.	.	.	3.64	3.64	0.41730	.	0.659654	0.14689	N	0.304255	T	0.19685	0.0473	N	0.19112	0.55	0.22446	N	0.999095	P	0.50710	0.938	B	0.41723	0.365	T	0.07462	-1.0771	9	0.72032	D	0.01	.	8.4625	0.32936	0.1115:0.0:0.8885:0.0	.	140	Q8N350-2	.	M	140	.	ENSP00000215376:T140M	T	-	2	0	C19orf26	1186018	0.997000	0.39634	0.107000	0.21349	0.095000	0.18619	4.848000	0.62874	2.026000	0.59711	0.561000	0.74099	ACG	.	.		0.701	C19orf26-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_152769		A	1235018	G	A	1235018	3	1	169	1	0	0	0	0	1	0	0	0	1918	1145	40	1	944	1	C19orf26	19	1235018	Missense_Mutation	SNP	G	TCGA-DD-AACS-01A-11D-A40R-10	654237	1235018	57893965	54	25690										
SIGLEC10	89790	hgsc.bcm.edu	37	chr19	51920435	51920435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	4	1	1.07680835197614	3.1150527325024	0.363422818791946	0.545454545454546	1	0	tgactcatcctgcatctgcgCgtctctgatcaccaaggagc	9	14	4	2			TCGA-DD-AACS-01A-11D-A40R-10	TCGA-DD-AACS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8d9f3207-beef-4207-90c3-219a58374551	957b73a6-e2d4-4b9b-b4c1-b4a9baa467c7	g.chr19:51920435C>T	ENST00000339313.5	-	2	438	c.322G>A	c.(322-324)Gcg>Acg	p.A108T	SIGLEC10_ENST00000432469.2_Missense_Mutation_p.A108T|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.A108T|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.A108T|SIGLEC10_ENST00000525998.1_Missense_Mutation_p.A108T|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.A108T|CTD-2616J11.2_ENST00000532688.1_RNA|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.A108T|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.A108T|SIGLEC10_ENST00000442846.3_Missense_Mutation_p.A108T			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	108	Ig-like V-type.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		TGCATCTGCGCGTCTCTGATC	0.517																																					p.A108T		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.G322A						.						69	69	69					19																	51920435		2203	4300	6503	SO:0001583	missense	89790	exon2			TCTGCGCGTCTCT	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15620	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 10 Ig-like lectin 7", "siglec-like gene 2"	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.322G>A	chr19.hg19:g.51920435C>T	ENSP00000345243:p.Ala108Thr	126.0	0.0		148.0	57.0	NM_001171161	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	hg19	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	19.60	3.857497	0.71834	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000442846;ENST00000356298;ENST00000441969;ENST00000525998;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000530476	T;T;T;T;T;T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17	4.92	4.92	0.64577	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.610455	0.15571	N	0.255453	T	0.78046	0.4222	M	0.80422	2.495	0.09310	N	1	D;D;D;P;D;D;D	0.89917	0.99;0.999;0.999;0.873;1.0;0.998;0.995	P;D;P;B;D;P;D	0.69142	0.831;0.962;0.872;0.319;0.928;0.823;0.961	T	0.68938	-0.5277	10	0.32370	T	0.25	.	13.6027	0.62029	0.0:1.0:0.0:0.0	.	108;108;108;108;108;108;108	C9JM10;E9PL79;C9JJ33;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;.;SIG10_HUMAN	T	108;108;108;108;108;108;108;108;108;75	ENSP00000342389:A108T;ENSP00000396742:A108T;ENSP00000395475:A108T;ENSP00000348646:A108T;ENSP00000408387:A108T;ENSP00000431444:A108T;ENSP00000389132:A108T;ENSP00000414324:A108T;ENSP00000345243:A108T;ENSP00000433838:A75T	ENSP00000345243:A108T	A	-	1	0	SIGLEC10	56612247	0.005000	0.15991	0.008000	0.14137	0.012000	0.07955	2.222000	0.42926	2.272000	0.75746	0.313000	0.20887	GCG	.	.		0.517	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		T	51920435	C	T	51920435	3	4	169	1	0	0	0	0	1	0	0	0	14321	768	27	1	1811	1	SIGLEC10	19	51920435	Missense_Mutation	SNP	C	TCGA-DD-AACS-01A-11D-A40R-10	50685417	51920435	7208548	55	25691										
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1887238	1887238	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tagctgctgctcagagaagcTggtggcggctttgtcataca	13	9	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:1887238T>A								TMEM52 (36526 upstream) : C1orf222 (32324 downstream)																							TCAGAGAAGCTGGTGGCGGCT	0.562																																					p.S690C		Atlas-SNP	.											.	KIAA1751	92	.	0			c.A2068T						.						46	50	48					1																	1887238		2063	4214	6277	SO:0001628	intergenic_variant	85452	exon18			AGAAGCTGGTGGC																													chr1.hg19:g.1887238T>A		49.0	0.0		71.0	17.0	NM_001080484		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	T	12.74	2.029075	0.35797	.	.	ENSG00000142609	ENST00000270720;ENST00000461752	.	.	.	3.07	1.94	0.25998	.	1.211860	0.05999	N	0.647351	T	0.58148	0.2102	M	0.62723	1.935	0.09310	N	0.999999	D;D	0.89917	1.0;0.999	D;D	0.70935	0.971;0.947	T	0.31888	-0.9927	9	0.72032	D	0.01	-6.2328	4.8553	0.13555	0.0:0.1448:0.0:0.8552	.	690;690	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	C	690;137	.	ENSP00000270720:S690C	S	-	1	0	C1orf222	1877098	0.000000	0.05858	0.011000	0.14972	0.006000	0.05464	-0.108000	0.10857	0.579000	0.29504	0.460000	0.39030	AGC	.	.	0	0.562									A	1887238	T	A	1887238	1	1	170	0	1	0	0	0	0	0	0	0	8265	1580	55	4		4	KIAA1751	1	1887238	IGR	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10		1887238	247363383	1	25692										
THAP3	90326	hgsc.bcm.edu	37	chr1	6685353	6685353	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aagcagctcaccttccaccgGtaagaggcggggacccgggg	15	13	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:6685353G>T	ENST00000054650.4	+	2	232		c.e2+1		THAP3_ENST00000484676.1_Splice_Site|THAP3_ENST00000377627.3_Splice_Site|THAP3_ENST00000307896.6_Splice_Site	NM_001195753.1	NP_001182682.1	Q8WTV1	THAP3_HUMAN	THAP domain containing, apoptosis associated protein 3								DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|large_intestine(1)|prostate(1)	4	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		CCTTCCACCGGTAAGAGGCGG	0.751																																					.		Atlas-SNP	.											.	THAP3	43	.	0			c.74+1G>T						.						2	3	3					1																	6685353		1725	3599	5324	SO:0001630	splice_region_variant	90326	exon2			CCACCGGTAAGAG	BC022081	CCDS86.1, CCDS55572.1, CCDS55573.1	1p36.1	2013-01-25			ENSG00000041988	ENSG00000041988		"THAP (C2CH-type zinc finger) domain containing"	20855	protein-coding gene	gene with protein product		612532				12575992	Standard	NM_138350		Approved		uc001aod.3	Q8WTV1	OTTHUMG00000001440	ENST00000054650.4:c.74+1G>T	chr1.hg19:g.6685353G>T		75.0	0.0		56.0	23.0	NM_001195753	Q569K1|Q5TH66|Q5TH67|Q8N8T6|Q9BSC7|Q9Y3H2|Q9Y3H3	Splice_Site	SNP	ENST00000054650.4	hg19	CCDS55572.1	.	.	.	.	.	.	.	.	.	.	G	13.23	2.176447	0.38413	.	.	ENSG00000041988	ENST00000054650;ENST00000307896;ENST00000377627	.	.	.	3.3	3.3	0.37823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.7702	0.51953	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	THAP3	6607940	1.000000	0.71417	0.999000	0.59377	0.450000	0.32258	3.509000	0.53386	1.838000	0.53458	0.313000	0.20887	.	.	.		0.751	THAP3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004203.1	NM_138350	Intron	T	6685353	G	T	6685353	5	4	170	1	0	0	0	0	0	0	1	0	15860	1275	44	3	77	3	THAP3	1	6685353	Splice_Site	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	4798115	6685353	242565268	2	25693										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32163575	32163575	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cacaggcctcatgggtcgtcGgggccccagaggctgggagg	18	12	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:32163575G>A	ENST00000373672.3	-	6	1105	c.589C>T	c.(589-591)Cga>Tga	p.R197*	COL16A1_ENST00000271069.6_Nonsense_Mutation_p.R197*|COL16A1_ENST00000373668.3_Nonsense_Mutation_p.R197*	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	197	Laminin G-like.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		ATGGGTCGTCGGGGCCCCAGA	0.617																																					p.R197X	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.C589T						.						31	37	35					1																	32163575		2036	4195	6231	SO:0001587	stop_gained	1307	exon6			GTCGTCGGGGCCC	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.589C>T	chr1.hg19:g.32163575G>A	ENSP00000362776:p.Arg197*	170.0	0.0		166.0	14.0	NM_001856	Q16593|Q59F89|Q71RG9	Nonsense_Mutation	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	G	37	6.079774	0.97267	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668	.	.	.	5.14	-0.0938	0.13647	.	0.236988	0.33161	N	0.005206	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.3637	0.16101	0.3626:0.0:0.5129:0.1244	.	.	.	.	X	197	.	ENSP00000271069:R197X	R	-	1	2	COL16A1	31936162	0.938000	0.31826	0.891000	0.34965	0.144000	0.21451	-0.084000	0.11268	-0.182000	0.10602	-1.010000	0.02471	CGA	.	.		0.617	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		A	32163575	G	A	32163575	4	1	170	1	0	0	0	0	0	1	0	0	3675	1124	39	1	4489	1	COL16A1	1	32163575	Nonsense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	25478222	32163575	217087046	3	25694										
MFSD2A	84879	hgsc.bcm.edu	37	chr1	40431684	40431684	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gcaccacctcacacagggaaAcggtgaggccctgggcaggg	15	13	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:40431684A>G	ENST00000372809.5	+	6	894	c.751A>G	c.(751-753)Acg>Gcg	p.T251A	MFSD2A_ENST00000480630.1_3'UTR|MFSD2A_ENST00000420632.2_Missense_Mutation_p.T82A|MFSD2A_ENST00000372811.5_Missense_Mutation_p.T238A	NM_001136493.1	NP_001129965.1	Q8NA29	NLS1_HUMAN	major facilitator superfamily domain containing 2A	251					establishment of blood-brain barrier (GO:0060856)|fatty acid transport (GO:0015908)|lipid transport across blood brain barrier (GO:1990379)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phospholipid transporter activity (GO:0005548)|symporter activity (GO:0015293)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						ACACAGGGAAACGGTGAGGCC	0.493																																					p.T251A		Atlas-SNP	.											.	MFSD2A	53	.	0			c.A751G						.						76	60	66					1																	40431684		2203	4300	6503	SO:0001583	missense	84879	exon6			AGGGAAACGGTGA	AK093223	CCDS446.1, CCDS44118.1, CCDS72762.1	1p34.2	2009-09-08	2009-09-08	2009-09-08	ENSG00000168389	ENSG00000168389			25897	protein-coding gene	gene with protein product		614397	"major facilitator superfamily domain containing 2"	MFSD2		18694395	Standard	XM_005271285		Approved	FLJ14490	uc001cev.3	Q8NA29	OTTHUMG00000009293	ENST00000372809.5:c.751A>G	chr1.hg19:g.40431684A>G	ENSP00000361895:p.Thr251Ala	141.0	0.0		143.0	38.0	NM_001136493	A8K675|Q6UWU5|Q96F59|Q9BRC8	Missense_Mutation	SNP	ENST00000372809.5	hg19	CCDS44118.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.567694	0.28003	.	.	ENSG00000168389	ENST00000372811;ENST00000420632;ENST00000434861;ENST00000372809	.	.	.	5.94	5.94	0.96194	Major facilitator superfamily domain, general substrate transporter (1);	0.139570	0.64402	D	0.000004	T	0.45677	0.1354	N	0.25286	0.73	0.54753	D	0.999985	P;B;B	0.42735	0.788;0.237;0.346	P;B;B	0.48425	0.577;0.297;0.204	T	0.32134	-0.9918	9	0.07030	T	0.85	-15.9514	15.5763	0.76392	1.0:0.0:0.0:0.0	.	201;251;238	B4DNN7;Q8NA29;Q8NA29-2	.;MFS2A_HUMAN;.	A	238;82;236;251	.	ENSP00000361895:T251A	T	+	1	0	MFSD2A	40204271	1.000000	0.71417	0.980000	0.43619	0.502000	0.33828	5.543000	0.67225	2.272000	0.75746	0.460000	0.39030	ACG	.	.		0.493	MFSD2A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025756.1	NM_032793		G	40431684	A	G	40431684	3	3	170	1	0	0	0	0	1	0	0	0	9539	43	2	2	773	2	MFSD2A	1	40431684	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	8268109	40431684	208818937	4	25695										
FOXD3	27022	hgsc.bcm.edu	37	chr1	63789072	63789072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ttggcggcgaggagggcggcGcgagcggcggcgggcctggc	24	11	0	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:63789072G>A	ENST00000371116.2	+	1	343	c.343G>A	c.(343-345)Gcg>Acg	p.A115T	RP4-792G4.2_ENST00000427268.1_RNA|RP4-792G4.2_ENST00000431294.1_RNA|RP4-792G4.2_ENST00000418244.1_RNA|RP4-792G4.2_ENST00000426393.1_RNA|RP4-792G4.2_ENST00000449386.1_RNA	NM_012183.2	NP_036315.1	Q9UJU5	FOXD3_HUMAN	forkhead box D3	115					embryonic placenta development (GO:0001892)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|trophectodermal cell differentiation (GO:0001829)	nuclear chromatin (GO:0000790)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|lung(2)|upper_aerodigestive_tract(1)	5						ggagggcggcgcgagcggcgg	0.776																																					p.A115T	Pancreas(68;276 1750 11966 31252)	Atlas-SNP	.											.	FOXD3	15	.	0			c.G343A						.						3	5	4					1																	63789072		1389	2838	4227	SO:0001583	missense	27022	exon1			GGCGGCGCGAGCG	AF197560	CCDS624.1	1p31.3	2008-04-10			ENSG00000187140	ENSG00000187140		"Forkhead boxes"	3804	protein-coding gene	gene with protein product		611539				8499623	Standard	NM_012183		Approved	Genesis, HFH2	uc001dax.2	Q9UJU5	OTTHUMG00000009141	ENST00000371116.2:c.343G>A	chr1.hg19:g.63789072G>A	ENSP00000360157:p.Ala115Thr	49.0	0.0		50.0	4.0	NM_012183	Q9BYM2|Q9UDD1	Missense_Mutation	SNP	ENST00000371116.2	hg19	CCDS624.1	.	.	.	.	.	.	.	.	.	.	G	1.327	-0.597791	0.03771	.	.	ENSG00000187140	ENST00000371116	D	0.82433	-1.61	2.69	2.69	0.31865	.	1.680140	0.03823	U	0.267807	T	0.44201	0.1282	N	0.08118	0	0.20489	N	0.999891	B	0.28636	0.218	B	0.12156	0.007	T	0.47341	-0.9125	10	0.11485	T	0.65	.	9.0375	0.36296	0.0:0.0:1.0:0.0	.	115	Q9UJU5	FOXD3_HUMAN	T	115	ENSP00000360157:A115T	ENSP00000360157:A115T	A	+	1	0	FOXD3	63561660	0.002000	0.14202	0.339000	0.25562	0.010000	0.07245	0.260000	0.18424	1.811000	0.52892	0.404000	0.27445	GCG	.	.		0.776	FOXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025331.1			A	63789072	G	A	63789072	3	1	170	1	0	0	0	0	1	0	0	0	6006	1087	38	1	345	1	FOXD3	1	63789072	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	23357388	63789072	185461549	5	25696										
PTPN22	26191	hgsc.bcm.edu	37	chr1	114372603	114372603	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	caagaaagaaggactctagaGttctttctgggagaggaggt	14	5	3	4			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:114372603G>C	ENST00000359785.5	-	17	2237	c.2102C>G	c.(2101-2103)aCt>aGt	p.T701S	RP5-1073O3.2_ENST00000448199.1_RNA|PTPN22_ENST00000528414.1_Missense_Mutation_p.T646S|PTPN22_ENST00000538253.1_Missense_Mutation_p.T457S|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000525799.1_Missense_Mutation_p.T574S|PTPN22_ENST00000420377.2_Missense_Mutation_p.T701S	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	701					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGACTCTAGAGTTCTTTCTGG	0.338																																					p.T701S		Atlas-SNP	.											.	PTPN22	90	.	0			c.C2102G						.						65	68	67					1																	114372603		2202	4300	6502	SO:0001583	missense	26191	exon17			TCTAGAGTTCTTT	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.2102C>G	chr1.hg19:g.114372603G>C	ENSP00000352833:p.Thr701Ser	211.0	0.0		228.0	49.0	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	hg19	CCDS863.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.594024	0.86953	.	.	ENSG00000134242	ENST00000359785;ENST00000528414;ENST00000538253;ENST00000420377;ENST00000525799	T;T;T;T;T	0.59364	2.71;2.32;0.27;3.04;2.3	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000002	T	0.74596	0.3737	M	0.80183	2.485	0.51012	D	0.999903	D;D;D;D;D	0.89917	1.0;0.999;1.0;0.999;1.0	D;D;D;D;D	0.91635	0.996;0.994;0.999;0.994;0.998	T	0.76675	-0.2872	10	0.87932	D	0	.	17.4736	0.87653	0.0:0.0:1.0:0.0	.	457;574;701;646;701	F5H2S8;E9PPI1;E9PMT0;E9PLD8;Q9Y2R2	.;.;.;.;PTN22_HUMAN	S	701;646;457;701;574	ENSP00000352833:T701S;ENSP00000435176:T646S;ENSP00000439372:T457S;ENSP00000388229:T701S;ENSP00000432674:T574S	ENSP00000352833:T701S	T	-	2	0	PTPN22	114174126	1.000000	0.71417	0.970000	0.41538	0.998000	0.95712	5.598000	0.67585	2.861000	0.98227	0.655000	0.94253	ACT	.	.		0.338	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		C	114372603	G	C	114372603	3	2	170	1	0	0	0	0	1	0	0	0	12802	1029	36	4	341	4	PTPN22	1	114372603	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	50583531	114372603	134878018	6	25697										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117122106	117122106	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgggcagccactcctccacaTggcaggagtaattgcctgta	11	12	0	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:117122106T>A	ENST00000369486.3	-	10	4007	c.3242A>T	c.(3241-3243)cAt>cTt	p.H1081L	IGSF3_ENST00000369483.1_Missense_Mutation_p.H1101L|IGSF3_ENST00000318837.6_Missense_Mutation_p.H1101L	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1081	Ig-like C2-type 8.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		CTCCTCCACATGGCAGGAGTA	0.602																																					p.H1101L		Atlas-SNP	.											.	IGSF3	294	.	0			c.A3302T						.						51	54	53					1																	117122106		2203	4300	6503	SO:0001583	missense	3321	exon11			TCCACATGGCAGG	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3242A>T	chr1.hg19:g.117122106T>A	ENSP00000358498:p.His1081Leu	103.0	0.0		92.0	24.0	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	T	8.657	0.899739	0.17686	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.20463	2.07;2.07;2.07	4.67	-0.198	0.13224	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.433417	0.25878	N	0.027717	T	0.02012	0.0063	N	0.02916	-0.46	0.22240	N	0.99927	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45920	-0.9228	10	0.23891	T	0.37	-13.554	8.1574	0.31178	0.0:0.4353:0.0:0.5647	.	1081;1101	O75054;A6NJZ6	IGSF3_HUMAN;.	L	1081;1101;1101	ENSP00000358498:H1081L;ENSP00000358495:H1101L;ENSP00000321184:H1101L	ENSP00000321184:H1101L	H	-	2	0	IGSF3	116923629	0.005000	0.15991	0.186000	0.23195	0.793000	0.44817	0.019000	0.13444	-0.221000	0.09973	-0.414000	0.06135	CAT	.	.		0.602	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		A	117122106	T	A	117122106	3	1	170	1	0	0	0	0	1	0	0	0	7610	1464	51	4	350	4	IGSF3	1	117122106	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	2749503	117122106	132128515	7	25698										
SSR2	6746	hgsc.bcm.edu	37	chr1	155989929	155989929	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gcttgagtgacagcaaatagAgccaacaccacaaatgacag	9	10	0	4			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:155989929A>C	ENST00000295702.4	-	2	101	c.30T>G	c.(28-30)gcT>gcG	p.A10A	SSR2_ENST00000480567.1_Silent_p.A10A|SSR2_ENST00000529008.1_Silent_p.A10A|SSR2_ENST00000496742.1_Silent_p.A10A	NM_003145.3	NP_003136.1	P43308	SSRB_HUMAN	signal sequence receptor, beta (translocon-associated protein beta)	10					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|stomach(1)	10	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CAGCAAATAGAGCCAACACCA	0.473																																					p.A10A		Atlas-SNP	.											.	SSR2	20	.	0			c.T30G						.						98	90	92					1																	155989929		2203	4300	6503	SO:0001819	synonymous_variant	6746	exon2			AAATAGAGCCAAC	BC000341	CCDS1126.1	1q21-q23	2008-02-05			ENSG00000163479	ENSG00000163479			11324	protein-coding gene	gene with protein product		600867				7789174	Standard	NM_003145		Approved	TLAP, TRAPB	uc001fmx.3	P43308	OTTHUMG00000017456	ENST00000295702.4:c.30T>G	chr1.hg19:g.155989929A>C		100.0	0.0		178.0	27.0	NM_003145	B2R9K9|D3DVA7|Q53HI0|Q5VY95|Q5VY96|Q6IB31|Q9BWE4	Silent	SNP	ENST00000295702.4	hg19	CCDS1126.1																																																																																			.	.		0.473	SSR2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046172.2	NM_003145		C	155989929	A	C	155989929	2	2	170	1	0	0	0	0	0	0	0	1	15206	291	11	5		5	SSR2	1	155989929	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	38867823	155989929	93260692	8	25699										
C1orf61	10485	hgsc.bcm.edu	37	chr1	156384479	156384479	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tccgtggtgctggatgtggcTctatcgtccacacggaggaa	14	10	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:156384479T>A	ENST00000368243.1	-	4	254	c.138A>T	c.(136-138)agA>agT	p.R46S		NM_006365.1	NP_006356.1	Q13536	CROC4_HUMAN	chromosome 1 open reading frame 61	46						nucleus (GO:0005634)				large_intestine(2)|lung(2)|skin(1)	5	Hepatocellular(266;0.158)					TGGATGTGGCTCTATCGTCCA	0.577																																					p.R46S		Atlas-SNP	.											.	C1orf61	15	.	0			c.A138T						.						37	36	36					1																	156384479		2203	4300	6503	SO:0001583	missense	10485	exon4			TGTGGCTCTATCG		CCDS1142.1	1q22	2014-03-17			ENSG00000125462	ENSG00000125462			30780	protein-coding gene	gene with protein product	"contingent replication of cDNA-4", "transcriptional activator of the c fos promoter"					10995546, 23012322	Standard	XM_005244832		Approved	CROC4	uc001fou.1	Q13536	OTTHUMG00000031022	ENST00000368243.1:c.138A>T	chr1.hg19:g.156384479T>A	ENSP00000357226:p.Arg46Ser	79.0	0.0		123.0	14.0	NM_006365	B1ALL5|B1ALL8	Missense_Mutation	SNP	ENST00000368243.1	hg19	CCDS1142.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.01|15.01	2.706096|2.706096	0.48412|0.48412	.|.	.|.	ENSG00000125462|ENSG00000125462	ENST00000368242|ENST00000310027;ENST00000368243;ENST00000357975	.|.	.|.	.|.	4.08|4.08	0.224|0.224	0.15297|0.15297	.|.	.|.	.|.	.|.	.|.	T|T	0.07863|0.07863	0.0197|0.0197	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	.|P	.|0.42908	.|0.793	.|B	.|0.42163	.|0.378	T|T	0.15378|0.15378	-1.0439|-1.0439	5|8	.|0.87932	.|D	.|0	-0.5088|-0.5088	3.23|3.23	0.06745|0.06745	0.0:0.245:0.2151:0.5399|0.0:0.245:0.2151:0.5399	.|.	.|46	.|Q13536	.|CROC4_HUMAN	V|S	78|60;46;59	.|.	.|ENSP00000310651:R60S	E|R	-|-	2|3	0|2	C1orf61|C1orf61	154651103|154651103	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.251000|0.251000	0.25915|0.25915	-0.184000|-0.184000	0.09698|0.09698	-0.054000|-0.054000	0.13266|0.13266	0.459000|0.459000	0.35465|0.35465	GAG|AGA	.	.		0.577	C1orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075988.1	NM_006365		A	156384479	T	A	156384479	3	1	170	1	0	0	0	0	1	0	0	0	2054	1548	54	4	348	4	C1orf61	1	156384479	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	394550	156384479	92866142	9	25700										
FCRLB	127943	hgsc.bcm.edu	37	chr1	161697120	161697120	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gtaataggccgctttccttcAgaaagcccccggtgtccaga	10	13	1	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:161697120A>T	ENST00000367948.2	+	8	1164	c.949A>T	c.(949-951)Aga>Tga	p.R317*	FCRLB_ENST00000495397.1_3'UTR|FCRLB_ENST00000367944.3_3'UTR|FCRLB_ENST00000367946.3_Silent_p.S268S|FCRLB_ENST00000392158.1_Nonsense_Mutation_p.R317*|FCRLB_ENST00000367945.1_Silent_p.S261S|FCRLB_ENST00000336830.5_3'UTR			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	317					negative regulation of immune response (GO:0050777)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|skin(1)	17	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			GCTTTCCTTCAGAAAGCCCCC	0.677																																					p.R317X		Atlas-SNP	.											.	FCRLB	35	.	0			c.A949T						.						20	22	21					1																	161697120		2203	4299	6502	SO:0001587	stop_gained	127943	exon6			TCCTTCAGAAAGC	AY670683	CCDS30927.1, CCDS72962.1, CCDS72963.1, CCDS72964.1, CCDS72965.1	1q23.3	2013-01-11	2006-09-26	2006-09-26	ENSG00000162746	ENSG00000162746		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26431	protein-coding gene	gene with protein product		609251	"Fc receptor-like and mucin-like 2"	FCRLM2		15676285	Standard	NM_001288829		Approved	FLJ31052, FCRL2, FREB-2, FCRLY	uc001gbi.3	Q6BAA4	OTTHUMG00000133629	ENST00000367948.2:c.949A>T	chr1.hg19:g.161697120A>T	ENSP00000356925:p.Arg317*	127.0	0.0		251.0	163.0	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Nonsense_Mutation	SNP	ENST00000367948.2	hg19	CCDS30927.1	.	.	.	.	.	.	.	.	.	.	A	31	5.084735	0.94100	.	.	ENSG00000162746	ENST00000367948;ENST00000392158	.	.	.	4.27	-3.58	0.04597	.	0.000000	0.44483	D	0.000452	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3996	0.67034	0.2551:0.7449:0.0:0.0	.	.	.	.	X	317	.	ENSP00000356925:R317X	R	+	1	2	FCRLB	159963744	0.960000	0.32886	0.143000	0.22291	0.441000	0.31987	-0.205000	0.09411	-0.919000	0.03803	-0.548000	0.04221	AGA	.	.		0.677	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378		T	161697120	A	T	161697120	4	4	170	1	0	0	0	0	0	1	0	0	5809	180	7	4	971	4	FCRLB	1	161697120	Nonsense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	5312641	161697120	87553501	10	25701										
KIFAP3	22920	hgsc.bcm.edu	37	chr1	170001030	170001030	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgcttaggaattcatacctcGtaatagctgttcctgtttta	7	8	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:170001030G>A	ENST00000361580.2	-	8	1065	c.838C>T	c.(838-840)Cga>Tga	p.R280*	KIFAP3_ENST00000367765.1_Nonsense_Mutation_p.R240*|KIFAP3_ENST00000367767.1_Nonsense_Mutation_p.R236*|KIFAP3_ENST00000538366.1_Nonsense_Mutation_p.R202*	NM_014970.3	NP_055785.2	Q92845	KIFA3_HUMAN	kinesin-associated protein 3	280					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|membrane organization (GO:0061024)|microtubule-based movement (GO:0007018)|microtubule-based process (GO:0007017)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of calcium-dependent cell-cell adhesion (GO:0046587)|protein complex assembly (GO:0006461)|protein localization (GO:0008104)|signal transduction (GO:0007165)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule cytoskeleton (GO:0015630)	kinesin binding (GO:0019894)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|prostate(2)|skin(3)|urinary_tract(2)	35	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TTCATACCTCGTAATAGCTGT	0.348																																					p.R280X		Atlas-SNP	.											.	KIFAP3	102	.	0			c.C838T						.						180	187	184					1																	170001030		2202	4298	6500	SO:0001587	stop_gained	22920	exon8			TACCTCGTAATAG	U59919	CCDS1288.1, CCDS55659.1, CCDS55660.1, CCDS55661.1	1q24.2	2012-09-20			ENSG00000075945	ENSG00000075945			17060	protein-coding gene	gene with protein product	"Smg GDS"	601836				8900189	Standard	NM_014970		Approved	SMAP, KAP3, FLA3, KAP-1	uc001ggv.3	Q92845	OTTHUMG00000035947	ENST00000361580.2:c.838C>T	chr1.hg19:g.170001030G>A	ENSP00000354560:p.Arg280*	93.0	0.0		180.0	113.0	NM_014970	B1AKU4|B1AKU5|B2RDL1|B7Z8A3|F5H591|Q8NHU7|Q9H416	Nonsense_Mutation	SNP	ENST00000361580.2	hg19	CCDS1288.1	.	.	.	.	.	.	.	.	.	.	G	38	7.243945	0.98161	.	.	ENSG00000075945	ENST00000361580;ENST00000367765;ENST00000367767;ENST00000538366	.	.	.	5.59	-1.65	0.08291	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4215	0.90592	0.0:0.0:0.2762:0.7238	.	.	.	.	X	280;240;236;202	.	.	R	-	1	2	KIFAP3	168267654	0.999000	0.42202	0.770000	0.31555	0.989000	0.77384	0.455000	0.21843	-0.615000	0.05679	-0.314000	0.08810	CGA	.	.		0.348	KIFAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087568.1	NM_014970		A	170001030	G	A	170001030	4	1	170	1	0	0	0	0	0	1	0	0	8320	1153	40	1	1592	1	KIFAP3	1	170001030	Nonsense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	8303910	170001030	79249591	11	25702										
FMO3	2328	hgsc.bcm.edu	37	chr1	171061808	171061809	+	Frame_Shift_Ins	INS	-	-	A													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cacaggttaccatggggaagINSaaagtggccatcattggagc							TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:171061808_171061809insA	ENST00000367755.4	+	2	120_121	c.9_10insA	c.(10-12)aaafs	p.K4fs	FMO3_ENST00000392085.2_Frame_Shift_Ins_p.K4fs|FMO3_ENST00000542847.1_5'UTR|FMO3_ENST00000534514.1_3'UTR|FMO3_ENST00000538429.1_Frame_Shift_Ins_p.K4fs	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	4					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CCATGGGGAAGAAAGTGGCCAT	0.455																																					p.K3fs		Atlas-INDEL	.											.	FMO3	73	.	0			c.9_10insA						.																																			SO:0001589	frameshift_variant	2328	exon2			.	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.12dupA	chr1.hg19:g.171061811_171061811dupA	ENSP00000356729:p.Lys4fs	124.0	0.0		231.0	17.0	NM_001002294	B2R816|Q14854|Q8N5N5	Frame_Shift_Ins	INS	ENST00000367755.4	hg19	CCDS1292.1																																																																																			.	.		0.455	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		A	171061809	-	A	171061808	7	5	170	1	0	1	1	0	0	0	0	0	5964	933	33	0	11	0	FMO3	1	171061808	Frame_Shift_Ins	INS	-	TCGA-DD-AACT-01A-11D-A40R-10	1060778	171061808	78188813	12	25703										
FMO1	2326	hgsc.bcm.edu	37	chr1	171236812	171236812	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgtgccaaattctcaattccTggaatatctcaaaatgtatg	6	8	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:171236812T>A	ENST00000354841.4	+	2	394	c.263T>A	c.(262-264)cTg>cAg	p.L88Q	FMO1_ENST00000367750.3_Missense_Mutation_p.L88Q|FMO1_ENST00000469112.1_3'UTR|FMO1_ENST00000402921.2_Intron	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	88					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	TCTCAATTCCTGGAATATCTC	0.373																																					p.L88Q		Atlas-SNP	.											.	FMO1	79	.	0			c.T263A						.						124	119	120					1																	171236812		2203	4300	6503	SO:0001583	missense	2326	exon3			AATTCCTGGAATA	M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.263T>A	chr1.hg19:g.171236812T>A	ENSP00000346901:p.Leu88Gln	90.0	0.0		152.0	90.0	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Missense_Mutation	SNP	ENST00000354841.4	hg19	CCDS1294.1	.	.	.	.	.	.	.	.	.	.	T	15.15	2.748444	0.49257	.	.	ENSG00000010932	ENST00000367750;ENST00000433267;ENST00000354841	T;T;T	0.56275	0.47;0.47;0.47	5.68	5.68	0.88126	.	0.185488	0.46442	D	0.000286	T	0.64238	0.2580	M	0.73962	2.25	0.80722	D	1	P;D	0.89917	0.661;1.0	P;D	0.76575	0.686;0.988	T	0.64529	-0.6386	10	0.34782	T	0.22	-15.5341	14.9131	0.70773	0.0:0.0:0.0:1.0	.	88;88	B2RCG5;Q01740	.;FMO1_HUMAN	Q	88	ENSP00000356724:L88Q;ENSP00000406982:L88Q;ENSP00000346901:L88Q	ENSP00000346901:L88Q	L	+	2	0	FMO1	169503436	1.000000	0.71417	0.888000	0.34837	0.905000	0.53344	7.697000	0.84279	2.144000	0.66660	0.533000	0.62120	CTG	.	.		0.373	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021		A	171236812	T	A	171236812	3	1	170	1	0	0	0	0	1	0	0	0	5962	1580	55	4	269	4	FMO1	1	171236812	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	175004	171236812	78013809	13	25704										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181767884	181767884	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ccaacgggcactatcggcggCggaggcgcggggggcctggg	21	12	0	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:181767884C>T	ENST00000367573.2	+	48	6856	c.6856C>T	c.(6856-6858)Cgg>Tgg	p.R2286W	CACNA1E_ENST00000367570.1_Missense_Mutation_p.R2243W|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R2267W|CACNA1E_ENST00000358338.5_Missense_Mutation_p.R2175W|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R2224W|CACNA1E_ENST00000367567.4_Missense_Mutation_p.R1850W|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R2237W	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2286	Poly-Arg.				calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.R2243W(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CTATCGGCGGCGGAGGCGCGG	0.647																																					p.R2286W		Atlas-SNP	.											CACNA1E,NS,carcinoma,0,1	CACNA1E	778	.	1	Substitution - Missense(1)	breast(1)	c.C6856T						.						13	16	15					1																	181767884		1950	4138	6088	SO:0001583	missense	777	exon48			CGGCGGCGGAGGC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6856C>T	chr1.hg19:g.181767884C>T	ENSP00000356545:p.Arg2286Trp	69.0	0.0		104.0	24.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103731	0.76983	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96459	-3.95;-3.95;-3.96;-3.95;-4.02;-3.97;-3.96	5.59	4.63	0.57726	.	0.379952	0.26975	N	0.021551	D	0.96510	0.8861	L	0.36672	1.1	0.52099	D	0.999942	D;D	0.89917	1.0;1.0	D;D	0.79108	0.978;0.992	D	0.96368	0.9271	10	0.62326	D	0.03	.	13.7614	0.62968	0.2537:0.7462:0.0:0.0	.	2224;2243	Q15878-2;Q15878-3	.;.	W	2243;2224;2237;2175;1850;2267;2286	ENSP00000356542:R2243W;ENSP00000434814:R2224W;ENSP00000350183:R2237W;ENSP00000351101:R2175W;ENSP00000356539:R1850W;ENSP00000353222:R2267W;ENSP00000356545:R2286W	ENSP00000350183:R2237W	R	+	1	2	CACNA1E	180034507	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	0.866000	0.27954	2.622000	0.88805	0.563000	0.77884	CGG	.	.		0.647	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181767884	C	T	181767884	3	4	170	1	0	0	0	0	1	0	0	0	2544	759	27	1	6913	1	CACNA1E	1	181767884	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	10531072	181767884	67482737	14	25705										
PRG4	10216	hgsc.bcm.edu	37	chr1	186266079	186266079	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gtgattcagcaagtttcatcTcaaggtagcttaaccatcga	8	9	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:186266079T>G	ENST00000445192.2	+	2	117	c.72T>G	c.(70-72)tcT>tcG	p.S24S	PRG4_ENST00000367483.4_Silent_p.S24S|PRG4_ENST00000367484.3_Silent_p.S24S|PRG4_ENST00000367486.3_Silent_p.S24S|PRG4_ENST00000367485.4_Silent_p.S24S	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	24					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						AAGTTTCATCTCAAGGTAGCT	0.343																																					p.S24S		Atlas-SNP	.											.	PRG4	259	.	0			c.T72G						.						195	147	163					1																	186266079		2203	4300	6503	SO:0001819	synonymous_variant	10216	exon2			TTCATCTCAAGGT	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.72T>G	chr1.hg19:g.186266079T>G		91.0	0.0		133.0	69.0	NM_001127708	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	hg19	CCDS1369.1																																																																																			.	.		0.343	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		G	186266079	T	G	186266079	2	3	170	1	0	0	0	0	0	0	0	1	12493	1538	54	5		5	PRG4	1	186266079	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	4498195	186266079	62984542	15	25706										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208212331	208212331	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggttgacgcagttcaggatcTacaagtaggggacagagggt	16	6	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:208212331T>A	ENST00000367033.3	-	25	5258		c.e25-2			NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2						axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GTTCAGGATCTACAAGTAGGG	0.493																																					.		Atlas-SNP	.											.	PLXNA2	178	.	0			c.4501-2A>T						.						111	98	102					1																	208212331		2203	4300	6503	SO:0001630	splice_region_variant	5362	exon26			AGGATCTACAAGT	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.4501-2A>T	chr1.hg19:g.208212331T>A		92.0	0.0		201.0	34.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Splice_Site	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	T	15.23	2.772714	0.49680	.	.	ENSG00000076356	ENST00000367033	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8538	0.78960	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PLXNA2	206278954	1.000000	0.71417	0.920000	0.36463	0.370000	0.29829	3.903000	0.56318	2.141000	0.66446	0.528000	0.53228	.	.	.		0.493	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	Intron	A	208212331	T	A	208212331	5	1	170	1	0	0	0	0	0	0	1	0	12129	1536	53	4	1217	4	PLXNA2	1	208212331	Splice_Site	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	21946252	208212331	41038290	16	25707										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214538000	214538000	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tggtatggcgacggaccgacTggatctcctccaagtaggct	13	11	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:214538000T>C	ENST00000366956.5	-	18	3484	c.3290A>G	c.(3289-3291)cAg>cGg	p.Q1097R	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	1097	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		ACGGACCGACTGGATCTCCTC	0.587																																					p.Q1097R	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											.	PTPN14	168	.	0			c.A3290G						.						98	85	90					1																	214538000		2203	4300	6503	SO:0001583	missense	5784	exon18			ACCGACTGGATCT	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.3290A>G	chr1.hg19:g.214538000T>C	ENSP00000355923:p.Gln1097Arg	92.0	0.0		189.0	83.0	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.625592	0.66901	.	.	ENSG00000152104	ENST00000366956	D	0.82344	-1.6	5.7	5.7	0.88788	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.061995	0.64402	D	0.000002	T	0.60945	0.2308	N	0.04245	-0.25	0.80722	D	1	B	0.21071	0.051	B	0.17433	0.018	T	0.59606	-0.7423	10	0.06099	T	0.92	.	10.329	0.43812	0.0:0.0731:0.0:0.9269	.	1097	Q15678	PTN14_HUMAN	R	1097	ENSP00000355923:Q1097R	ENSP00000355923:Q1097R	Q	-	2	0	PTPN14	212604623	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.203000	0.72137	2.170000	0.68504	0.533000	0.62120	CAG	.	.		0.587	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		C	214538000	T	C	214538000	3	2	170	1	0	0	0	0	1	0	0	0	12796	1580	55	2	281	2	PTPN14	1	214538000	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	6325669	214538000	34712621	17	25708										
CENPF	1063	hgsc.bcm.edu	37	chr1	214815369	214815370	+	Frame_Shift_Del	DEL	GA	GA	-													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aacttcaggaaagtgagaagGagaaggagtgcctgcagcat					rs199690817		TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:214815369_214815370delGA	ENST00000366955.3	+	12	3856_3857	c.3688_3689delGA	c.(3688-3690)gagfs	p.E1230fs		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AAGTGAGAAGGAGAAGGAGTGC	0.371																																					p.1229_1230del	Colon(80;575 1284 11000 14801 43496)	Atlas-INDEL	.											.	CENPF	321	.	0			c.3687_3688del						.																																			SO:0001589	frameshift_variant	1063	exon12			.	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.3688_3689delGA	chr1.hg19:g.214815371_214815372delGA	ENSP00000355922:p.Glu1230fs	372.0	0.0		797.0	369.0	NM_016343	Q13171|Q13246|Q5VVM7	Frame_Shift_Del	DEL	ENST00000366955.3	hg19	CCDS31023.1																																																																																			.	.		0.371	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		-	214815370	GA	-	214815369	7	5	170	1	0	1	0	1	0	0	0	0	3233	1175	41	0	3730	0	CENPF	1	214815369	Frame_Shift_Del	DEL	GA	TCGA-DD-AACT-01A-11D-A40R-10	277369	214815369	34435252	18	25709										
NUP133	55746	hgsc.bcm.edu	37	chr1	229584906	229584906	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gagctttgcaaaggatttccAgttttagatcatttatattt	7	5	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:229584906A>G	ENST00000261396.3	-	24	3303	c.3212T>C	c.(3211-3213)cTg>cCg	p.L1071P	NUP133_ENST00000485119.1_5'UTR|NUP133_ENST00000537506.1_Missense_Mutation_p.L1055P	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	1071					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				AAGGATTTCCAGTTTTAGATC	0.353																																					p.L1071P		Atlas-SNP	.											.	NUP133	111	.	0			c.T3212C						.						87	85	86					1																	229584906		2203	4300	6503	SO:0001583	missense	55746	exon24			ATTTCCAGTTTTA		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.3212T>C	chr1.hg19:g.229584906A>G	ENSP00000261396:p.Leu1071Pro	55.0	0.0		96.0	45.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	hg19	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	A	17.38	3.375993	0.61735	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.28666	1.6;1.62;1.61	6.04	6.04	0.98038	Nucleoporin, Nup133/Nup155-like, C-terminal (1);	0.118214	0.64402	D	0.000016	T	0.54334	0.1852	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.50482	-0.8823	10	0.23891	T	0.37	-0.2002	15.1596	0.72771	1.0:0.0:0.0:0.0	.	1071	Q8WUM0	NU133_HUMAN	P	1000;1071;1000;1055	ENSP00000261396:L1071P;ENSP00000355640:L1000P;ENSP00000443496:L1055P	ENSP00000261396:L1071P	L	-	2	0	NUP133	227651529	1.000000	0.71417	0.998000	0.56505	0.678000	0.39670	5.432000	0.66514	2.317000	0.78254	0.460000	0.39030	CTG	.	.		0.353	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		G	229584906	A	G	229584906	3	3	170	1	0	0	0	0	1	0	0	0	10763	188	7	2	270	2	NUP133	1	229584906	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	14769537	229584906	19665715	19	25710										
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458135	248458135	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	taaaaatgccagctccataaAagagtcccaccacagccaca	5	14	0	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr1:248458135A>G	ENST00000317996.1	-	1	745	c.746T>C	c.(745-747)tTt>tCt	p.F249S		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	249						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			AGCTCCATAAAAGAGTCCCAC	0.493																																					p.F249S		Atlas-SNP	.											.	OR2T12	113	.	0			c.T746C						.						83	83	83					1																	248458135		2203	4298	6501	SO:0001583	missense	127064	exon1			CCATAAAAGAGTC	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.746T>C	chr1.hg19:g.248458135A>G	ENSP00000324583:p.Phe249Ser	169.0	0.0		305.0	30.0	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	hg19	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	a	15.08	2.727038	0.48833	.	.	ENSG00000177201	ENST00000317996	T	0.00297	8.23	1.55	-0.0962	0.13637	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36234	U	0.002714	T	0.00496	0.0016	M	0.82056	2.57	0.09310	N	1	D	0.64830	0.994	D	0.71656	0.974	T	0.46803	-0.9165	10	0.72032	D	0.01	.	5.3308	0.15932	0.5475:0.0:0.0:0.4525	.	249	Q8NG77	O2T12_HUMAN	S	249	ENSP00000324583:F249S	ENSP00000324583:F249S	F	-	2	0	OR2T12	246524758	0.000000	0.05858	0.515000	0.27774	0.456000	0.32438	-1.448000	0.02394	0.540000	0.28808	0.147000	0.16070	TTT	.	.		0.493	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		G	248458135	A	G	248458135	3	3	170	1	0	0	0	0	1	0	0	0	11028	14	1	2	219	2	OR2T12	1	248458135	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	18873229	248458135	792486	20	25711										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1920989	1920989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggacttactttctggagggaCcctatctttgtgcgggcatc	12	10	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:1920989C>T	ENST00000399161.2	-	11	2353	c.1606G>A	c.(1606-1608)Gtc>Atc	p.V536I	MYT1L_ENST00000428368.2_Missense_Mutation_p.V534I	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	536					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TCTGGAGGGACCCTATCTTTG	0.567																																					p.V534I		Atlas-SNP	.											.	MYT1L	241	.	0			c.G1600A						.						193	202	199					2																	1920989		2070	4186	6256	SO:0001583	missense	23040	exon11			GAGGGACCCTATC	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.1606G>A	chr2.hg19:g.1920989C>T	ENSP00000382114:p.Val536Ile	90.0	0.0		101.0	24.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	C	22.7	4.323937	0.81580	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.48522	0.81;0.82	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.56572	0.1994	N	0.25426	0.745	0.80722	D	1	D;P	0.65815	0.995;0.839	D;P	0.74674	0.984;0.863	T	0.46373	-0.9196	10	0.18710	T	0.47	-43.7854	19.8984	0.96975	0.0:1.0:0.0:0.0	.	536;534	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	I	536;482;534	ENSP00000382114:V536I;ENSP00000396103:V534I	ENSP00000295067:V482I	V	-	1	0	MYT1L	1899996	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.011000	0.70760	2.713000	0.92767	0.655000	0.94253	GTC	.	.		0.567	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		T	1920989	C	T	1920989	3	4	170	1	0	0	0	0	1	0	0	0	10116	507	18	3	2014	3	MYT1L	2	1920989	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10		1920989	241278384	21	25712										
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43939487	43939487	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	acccactttccctgcagcctGagggcaaacccaccatgaag	8	16	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:43939487G>A	ENST00000282406.4	+	15	2535	c.2425G>A	c.(2425-2427)Gag>Aag	p.E809K		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	809					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CCTGCAGCCTGAGGGCAAACC	0.488																																					p.E809K		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.G2425A						.						92	83	86					2																	43939487		2203	4300	6503	SO:0001583	missense	130271	exon15			CAGCCTGAGGGCA	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.2425G>A	chr2.hg19:g.43939487G>A	ENSP00000282406:p.Glu809Lys	86.0	0.0		102.0	21.0	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.775744	0.70107	.	.	ENSG00000152527	ENST00000282406	T	0.21543	2.0	4.93	4.93	0.64822	Pleckstrin homology-type (1);	0.220226	0.44285	D	0.000462	T	0.19446	0.0467	L	0.38175	1.15	0.52099	D	0.99994	B;B	0.30361	0.016;0.277	B;B	0.23852	0.007;0.049	T	0.03077	-1.1075	10	0.49607	T	0.09	-5.5497	18.1513	0.89675	0.0:0.0:1.0:0.0	.	809;246	Q8IVE3;Q8IVE3-2	PKHH2_HUMAN;.	K	809	ENSP00000282406:E809K	ENSP00000282406:E809K	E	+	1	0	PLEKHH2	43792991	1.000000	0.71417	0.999000	0.59377	0.857000	0.48899	9.298000	0.96132	2.275000	0.75901	0.460000	0.39030	GAG	.	.		0.488	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		A	43939487	G	A	43939487	3	1	170	1	0	0	0	0	1	0	0	0	12086	1291	45	3	2479	3	PLEKHH2	2	43939487	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	42018498	43939487	199259886	22	25713										
PREPL	9581	hgsc.bcm.edu	37	chr2	44559599	44559599	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgaagattataagacctaccTtgcttttggcttctagacgt	8	8	1	4			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:44559599T>G	ENST00000409936.1	-	9	1789	c.1352A>C	c.(1351-1353)aAg>aCg	p.K451T	PREPL_ENST00000378511.3_Splice_Site_p.K389T|PREPL_ENST00000410081.1_Splice_Site_p.K451T|PREPL_ENST00000409272.1_Splice_Site_p.K451T|PREPL_ENST00000409411.1_Splice_Site_p.K362T|PREPL_ENST00000260648.6_Splice_Site_p.K451T|PREPL_ENST00000409957.1_Splice_Site_p.K362T|PREPL_ENST00000378520.3_Intron|PREPL_ENST00000541738.1_Splice_Site_p.K362T	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	451						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				AAGACCTACCTTGCTTTTGGC	0.428																																					p.K451T		Atlas-SNP	.											.	PREPL	69	.	0			c.A1352C						.						128	112	117					2																	44559599		2203	4300	6503	SO:0001630	splice_region_variant	9581	exon9			CCTACCTTGCTTT	AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.1353+1A>C	chr2.hg19:g.44559599T>G		94.0	0.0		94.0	32.0	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Missense_Mutation	SNP	ENST00000409936.1	hg19	CCDS33190.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.213818	0.79352	.	.	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378511	.	.	.	5.55	5.55	0.83447	.	0.222358	0.46442	D	0.000281	T	0.75539	0.3863	M	0.65498	2.005	0.58432	D	0.999999	D;D	0.67145	0.996;0.972	D;P	0.75484	0.986;0.786	T	0.71981	-0.4428	9	0.18276	T	0.48	-7.9121	15.6846	0.77400	0.0:0.0:0.0:1.0	.	389;451	Q4J6C6-3;Q4J6C6	.;PPCEL_HUMAN	T	362;362;362;451;451;451;451;389	.	ENSP00000260648:K451T	K	-	2	0	PREPL	44413103	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	4.441000	0.59981	2.111000	0.64477	0.454000	0.30748	AAG	.	.		0.428	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036	Missense_Mutation	G	44559599	T	G	44559599	5	3	170	1	0	0	0	0	0	0	1	0	12487	1623	56	5	859	5	PREPL	2	44559599	Splice_Site	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	620112	44559599	198639774	23	25714										
LHCGR	3973	hgsc.bcm.edu	37	chr2	48915582	48915582	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggtgagggtgtagacagaaaGttcacttgcgaatacagtga	14	5	1	4			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:48915582G>T	ENST00000294954.7	-	11	1375	c.1354C>A	c.(1354-1356)Ctt>Att	p.L452I	STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000344775.3_Missense_Mutation_p.L390I|LHCGR_ENST00000403273.1_3'UTR|LHCGR_ENST00000405626.1_Missense_Mutation_p.L425I|LHCGR_ENST00000401907.1_Intron	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	452					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	TAGACAGAAAGTTCACTTGCG	0.483																																					p.L452I		Atlas-SNP	.											.	LHCGR	154	.	0			c.C1354A						.						119	97	105					2																	48915582		2203	4300	6503	SO:0001583	missense	3973	exon11			CAGAAAGTTCACT		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"GPCR / Class A : Gonadotropin and TSH receptors"	6585	protein-coding gene	gene with protein product		152790	"hypergonadotropic hypogonadism"	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.1354C>A	chr2.hg19:g.48915582G>T	ENSP00000294954:p.Leu452Ile	97.0	0.0		103.0	28.0	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	hg19	CCDS1842.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.997316	0.74818	.	.	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000405626	D;D;D	0.85629	-2.01;-2.01;-2.01	5.91	5.91	0.95273	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.94751	0.8306	M	0.93283	3.4	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.95372	0.8465	9	.	.	.	.	19.2938	0.94114	0.0:0.0:1.0:0.0	.	452	P22888	LSHR_HUMAN	I	390;452;425	ENSP00000344301:L390I;ENSP00000294954:L452I;ENSP00000386033:L425I	.	L	-	1	0	LHCGR	48769086	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.749000	0.68704	2.791000	0.96007	0.655000	0.94253	CTT	.	.		0.483	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3		T	48915582	G	T	48915582	3	4	170	1	0	0	0	0	1	0	0	0	8771	1029	36	3	749	3	LHCGR	2	48915582	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	4355983	48915582	194283791	24	25715										
EIF2AK3	9451	hgsc.bcm.edu	37	chr2	88887518	88887518	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	accatatggatactgcaagaTtgaaagtgcaccattactat	7	8	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:88887518T>C	ENST00000303236.3	-	8	1712	c.1411A>G	c.(1411-1413)Atc>Gtc	p.I471V	EIF2AK3_ENST00000419748.1_Missense_Mutation_p.I320V	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	471					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						TACTGCAAGATTGAAAGTGCA	0.294																																					p.I471V	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.A1411G						.						49	53	51					2																	88887518		2203	4288	6491	SO:0001583	missense	9451	exon8			GCAAGATTGAAAG	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.1411A>G	chr2.hg19:g.88887518T>C	ENSP00000307235:p.Ile471Val	785.0	0.0		797.0	188.0	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Missense_Mutation	SNP	ENST00000303236.3	hg19	CCDS33241.1	.	.	.	.	.	.	.	.	.	.	T	1.005	-0.689850	0.03328	.	.	ENSG00000172071	ENST00000419748;ENST00000303236;ENST00000535951;ENST00000415570	T;T;T	0.46063	0.88;0.88;0.88	5.82	4.67	0.58626	.	0.208574	0.49916	N	0.000125	T	0.16642	0.0400	N	0.04724	-0.175	0.37195	D	0.904104	B	0.14012	0.009	B	0.14578	0.011	T	0.17623	-1.0363	10	0.02654	T	1	-17.5937	6.2817	0.21011	0.0:0.2905:0.0:0.7095	.	471	Q9NZJ5	E2AK3_HUMAN	V	320;471;320;350	ENSP00000408325:I320V;ENSP00000307235:I471V;ENSP00000412076:I350V	ENSP00000307235:I471V	I	-	1	0	EIF2AK3	88668633	0.981000	0.34729	0.999000	0.59377	0.977000	0.68977	2.152000	0.42272	1.042000	0.40150	0.455000	0.32223	ATC	.	.		0.294	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		C	88887518	T	C	88887518	3	2	170	1	0	0	0	0	1	0	0	0	5000	1493	52	2	1979	2	EIF2AK3	2	88887518	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	39971936	88887518	154311855	25	25716										
RGPD4	285190	hgsc.bcm.edu	37	chr2	108453058	108453058	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	caacttttaattttttttagAagtcaacgagaggattctat	6	5	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:108453058A>C	ENST00000408999.3	+	2	150	c.73A>C	c.(73-75)Aag>Cag	p.K25Q	RGPD4_ENST00000354986.4_Splice_Site_p.K25Q	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	25					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						TTTTTTTTAGAAGTCAACGAG	0.254																																					p.K25Q		Atlas-SNP	.											.	RGPD4	112	.	0			c.A73C						.																																			SO:0001630	splice_region_variant	285190	exon2			TTTTAGAAGTCAA	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.73-1A>C	chr2.hg19:g.108453058A>C		288.0	0.0		300.0	85.0	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	hg19	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	a	7.825	0.718676	0.15372	.	.	ENSG00000196862	ENST00000354986;ENST00000408999	T;T	0.46451	0.87;0.87	2.35	2.35	0.29111	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.37652	0.1011	L	0.54323	1.7	0.32246	N	0.572059	P	0.41978	0.767	B	0.41036	0.346	T	0.48468	-0.9033	8	.	.	.	-11.4122	9.2374	0.37475	1.0:0.0:0.0:0.0	.	25	Q7Z3J3	RGPD4_HUMAN	Q	25	ENSP00000347081:K25Q;ENSP00000386810:K25Q	.	K	+	1	0	RGPD4	107819490	1.000000	0.71417	1.000000	0.80357	0.070000	0.16714	7.091000	0.76923	1.080000	0.41073	0.155000	0.16302	AAG	.	.		0.254	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	Missense_Mutation	C	108453058	A	C	108453058	5	2	170	1	0	0	0	0	0	0	1	0	13303	260	9	5	79	5	RGPD4	2	108453058	Splice_Site	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	19565540	108453058	134746315	26	25717										
CCDC74B	91409	hgsc.bcm.edu	37	chr2	130897154	130897154	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	caccgagcgatgcaggcgccGtttctgcattgcctgcagcc	12	15	1	0	rs546767071		TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:130897154G>T	ENST00000310463.6	-	8	1254	c.1117C>A	c.(1117-1119)Cgg>Agg	p.R373R	CCDC74B_ENST00000392984.3_Silent_p.R475R|MED15P9_ENST00000427638.1_RNA|CCDC74B_ENST00000409943.3_Silent_p.R307R	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	373										endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					TGCAGGCGCCGTTTCTGCATT	0.602																																					p.R373R		Atlas-SNP	.											.	CCDC74B	27	.	0			c.C1117A						.						42	42	42					2																	130897154		2201	4300	6501	SO:0001819	synonymous_variant	91409	exon8			GGCGCCGTTTCTG		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.1117C>A	chr2.hg19:g.130897154G>T		186.0	0.0		167.0	44.0	NM_207310	Q6NW18	Silent	SNP	ENST00000310463.6	hg19	CCDS2155.1																																																																																			.	.		0.602	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310		T	130897154	G	T	130897154	2	4	170	1	0	0	0	0	0	0	0	1	2850	1144	40	1		1	CCDC74B	2	130897154	Silent	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	22444096	130897154	112302219	27	25718										
GALNT3	2591	hgsc.bcm.edu	37	chr2	166615986	166615986	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ttgttgaattcaaacgtgttCagatctatggatgcaatatc	8	6	3	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:166615986C>T	ENST00000392701.3	-	5	1708	c.933G>A	c.(931-933)ctG>ctA	p.L311L	GALNT3_ENST00000409882.1_Silent_p.L49L	NM_004482.3	NP_004473.2	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	311					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(1)	20						CAAACGTGTTCAGATCTATGG	0.448																																					p.L311L		Atlas-SNP	.											.	GALNT3	65	.	0			c.G933A						.						90	88	89					2																	166615986		2203	4300	6503	SO:0001819	synonymous_variant	2591	exon5			CGTGTTCAGATCT		CCDS2226.1	2q24-q31	2014-03-13	2014-03-13		ENSG00000115339	ENSG00000115339	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4125	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 3"	601756	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)"			9592121, 15133511	Standard	NM_004482		Approved	GalNAc-T3, HHS, HFTC	uc010fph.1	Q14435	OTTHUMG00000132157	ENST00000392701.3:c.933G>A	chr2.hg19:g.166615986C>T		128.0	0.0		135.0	31.0	NM_004482	Q53TG9|Q7Z476	Silent	SNP	ENST00000392701.3	hg19	CCDS2226.1																																																																																			.	.		0.448	GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255205.2	NM_004482		T	166615986	C	T	166615986	2	4	170	1	0	0	0	0	0	0	0	1	6222	813	29	3		3	GALNT3	2	166615986	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	35718832	166615986	76583387	28	25719										
TTN	7273	hgsc.bcm.edu	37	chr2	179610419	179610419	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	taagcttgttataaacaggtTatggaaccctgtgccacttt	8	8	0	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:179610419T>A	ENST00000591111.1	-	46	10585				TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.N5570Y			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATAAACAGGTTATGGAACCCT	0.438																																					p.N5570Y		Atlas-SNP	.											.	TTN	18412	.	0			c.A16708T						.						114	110	111					2																	179610419		2203	4299	6502	SO:0001627	intron_variant	7273	exon46			ACAGGTTATGGAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-3771A>T	chr2.hg19:g.179610419T>A		123.0	0.0		108.0	31.0	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.20	2.762018	0.49468	.	.	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.67171	-0.25	6.17	6.17	0.99709	.	.	.	.	.	T	0.69895	0.3162	N	0.21373	0.66	0.80722	D	1	D	0.76494	0.999	D	0.69479	0.964	T	0.72924	-0.4144	9	0.59425	D	0.04	.	12.6398	0.56702	0.0:0.0:0.1377:0.8623	.	5570	Q8WZ42-6	.	Y	5570;851	ENSP00000354117:N5570Y	ENSP00000304714:N851Y	N	-	1	0	TTN	179318664	1.000000	0.71417	0.997000	0.53966	0.646000	0.38490	4.772000	0.62324	2.371000	0.80710	0.533000	0.62120	AAC	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179610419	T	A	179610419	1	1	170	0	1	0	0	0	0	0	0	0	16750	1754	61	4		4	TTN	2	179610419	Intron	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	12994433	179610419	63588954	29	25720										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185801445	185801445	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tacagttcttcagtggccatCagaaatgctggtttatacaa	8	8	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:185801445C>G	ENST00000302277.6	+	4	1916	c.1322C>G	c.(1321-1323)tCa>tGa	p.S441*		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	441							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						CAGTGGCCATCAGAAATGCTG	0.328																																					p.S441X		Atlas-SNP	.											.	ZNF804A	322	.	0			c.C1322G						.						112	117	115					2																	185801445		2203	4299	6502	SO:0001587	stop_gained	91752	exon4			GGCCATCAGAAAT	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.1322C>G	chr2.hg19:g.185801445C>G	ENSP00000303252:p.Ser441*	323.0	0.0		308.0	85.0	NM_194250	A7E253|Q6ZN26	Nonsense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	C	43	10.062489	0.99329	.	.	ENSG00000170396	ENST00000302277	.	.	.	5.6	5.6	0.85130	.	0.289408	0.25019	N	0.033770	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-11.9591	18.5921	0.91217	0.0:1.0:0.0:0.0	.	.	.	.	X	441	.	ENSP00000303252:S441X	S	+	2	0	ZNF804A	185509690	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.294000	0.78760	2.642000	0.89623	0.591000	0.81541	TCA	.	.		0.328	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		G	185801445	C	G	185801445	4	3	170	1	0	0	0	0	0	1	0	0	18185	838	29	4	1336	4	ZNF804A	2	185801445	Nonsense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	6191026	185801445	57397928	30	25721										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220424039	220424039	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gagcagcaggtagcaccaggCggcagcgtggcccatccctc	14	15	0	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:220424039C>T	ENST00000404537.1	-	9	3190	c.3134G>A	c.(3133-3135)cGc>cAc	p.R1045H	OBSL1_ENST00000603926.1_Missense_Mutation_p.R1045H|OBSL1_ENST00000265318.4_Missense_Mutation_p.R1045H|OBSL1_ENST00000373876.1_Missense_Mutation_p.R1045H|OBSL1_ENST00000265317.5_Missense_Mutation_p.R36H|RP11-256I23.2_ENST00000597192.1_RNA	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1045	Ig-like 8.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		TAGCACCAGGCGGCAGCGTGG	0.632																																					p.R1045H		Atlas-SNP	.											.	OBSL1	120	.	0			c.G3134A						.						120	133	128					2																	220424039		2191	4281	6472	SO:0001583	missense	23363	exon9			ACCAGGCGGCAGC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.3134G>A	chr2.hg19:g.220424039C>T	ENSP00000385636:p.Arg1045His	114.0	0.0		127.0	18.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	hg19	CCDS46520.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.3|25.3	4.622685|4.622685	0.87460|0.87460	.|.	.|.	ENSG00000124006|ENSG00000124006	ENST00000456147|ENST00000265318;ENST00000404537;ENST00000373876;ENST00000265317	.|T;T;T;T	.|0.42513	.|3.51;3.51;3.51;0.97	4.34|4.34	4.34|4.34	0.51931|0.51931	.|Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|.	.|.	.|.	.|.	T|T	0.65565|0.65565	0.2703|0.2703	M|M	0.82823|0.82823	2.61|2.61	0.50632|0.50632	D|D	0.99988|0.99988	.|D;D;D;D	.|0.89917	.|0.976;1.0;1.0;1.0	.|P;D;D;D	.|0.97110	.|0.756;0.999;0.999;1.0	T|T	0.65059|0.65059	-0.6260|-0.6260	5|9	.|0.19147	.|T	.|0.46	.|.	17.0511|17.0511	0.86519|0.86519	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|36;1046;1045;36	.|B7Z5P5;A4KVA4;O75147;E7ER99	.|.;.;OBSL1_HUMAN;.	T|H	39|1045;1045;1045;36	.|ENSP00000265318:R1045H;ENSP00000385636:R1045H;ENSP00000362983:R1045H;ENSP00000265317:R36H	.|ENSP00000265317:R36H	A|R	-|-	1|2	0|0	OBSL1|OBSL1	220132283|220132283	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	3.085000|3.085000	0.50151|0.50151	2.256000|2.256000	0.74724|0.74724	0.491000|0.491000	0.48974|0.48974	GCC|CGC	.	.		0.632	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			T	220424039	C	T	220424039	3	4	170	1	0	0	0	0	1	0	0	0	10822	768	27	1	2631	1	OBSL1	2	220424039	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	34622594	220424039	22775334	31	25722										
FAM124B	79843	hgsc.bcm.edu	37	chr2	225244553	225244553	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cctgggttcagaatttatgaTggtcaagccggtgtcaacat	11	8	3	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:225244553T>A	ENST00000409685.3	-	2	1370	c.1105A>T	c.(1105-1107)Atc>Ttc	p.I369F	FAM124B_ENST00000389874.3_3'UTR	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	369										endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		GAATTTATGATGGTCAAGCCG	0.512																																					p.I369F		Atlas-SNP	.											.	FAM124B	71	.	0			c.A1105T						.						20	24	22					2																	225244553		692	1591	2283	SO:0001583	missense	79843	exon2			TTATGATGGTCAA	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.1105A>T	chr2.hg19:g.225244553T>A	ENSP00000386895:p.Ile369Phe	127.0	0.0		129.0	44.0	NM_001122779	A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	hg19	CCDS46527.1	.	.	.	.	.	.	.	.	.	.	T	9.827	1.187474	0.21870	.	.	ENSG00000124019	ENST00000409685	T	0.36520	1.25	5.9	-3.1	0.05315	.	.	.	.	.	T	0.20820	0.0501	N	0.14661	0.345	0.09310	N	1	P	0.37276	0.589	B	0.35971	0.215	T	0.13656	-1.0501	9	0.72032	D	0.01	-0.6236	11.7601	0.51898	0.0:0.3807:0.0:0.6193	.	369	Q9H5Z6	F124B_HUMAN	F	369	ENSP00000386895:I369F	ENSP00000386895:I369F	I	-	1	0	FAM124B	224952797	0.004000	0.15560	0.000000	0.03702	0.005000	0.04900	-0.100000	0.10990	-1.073000	0.03137	-0.427000	0.05922	ATC	.	.		0.512	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		A	225244553	T	A	225244553	3	1	170	1	0	0	0	0	1	0	0	0	5431	1464	51	4	266	4	FAM124B	2	225244553	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	4820514	225244553	17954820	32	25723										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228855727	228855727	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	acatgataccttttcaattcTgttttcctgagatttcttaa	4	8	3	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:228855727T>C	ENST00000392056.3	-	11	4994	c.4948A>G	c.(4948-4950)Aga>Gga	p.R1650G	SPHKAP_ENST00000344657.5_Missense_Mutation_p.R1621G	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1650						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TTTTCAATTCTGTTTTCCTGA	0.458																																					p.R1650G		Atlas-SNP	.											.	SPHKAP	750	.	0			c.A4948G						.						79	78	78					2																	228855727		2203	4300	6503	SO:0001583	missense	80309	exon11			CAATTCTGTTTTC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4948A>G	chr2.hg19:g.228855727T>C	ENSP00000375909:p.Arg1650Gly	64.0	0.0		57.0	17.0	NM_001142644	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	hg19	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	T	19.05	3.751148	0.69533	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.06528	3.29;3.29	6.17	1.0	0.19881	A-kinase anchor 110kDa, C-terminal (1);	0.237565	0.47093	D	0.000245	T	0.16041	0.0386	L	0.60455	1.87	0.36432	D	0.864966	B;D	0.65815	0.265;0.995	B;D	0.68483	0.11;0.958	T	0.02933	-1.1092	10	0.66056	D	0.02	.	8.5385	0.33377	0.0:0.0652:0.3776:0.5572	.	1650;1621	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	G	1650;1621	ENSP00000375909:R1650G;ENSP00000339886:R1621G	ENSP00000339886:R1621G	R	-	1	2	SPHKAP	228563971	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.434000	0.44802	0.153000	0.19213	0.533000	0.62120	AGA	.	.		0.458	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		C	228855727	T	C	228855727	3	2	170	1	0	0	0	0	1	0	0	0	15063	1588	55	2	162	2	SPHKAP	2	228855727	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	3611174	228855727	14343646	33	25724										
ILKAP	80895	hgsc.bcm.edu	37	chr2	239079292	239079292	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gggcgtcggctgcggacttcCcttcccgggtctggatcttt	14	13	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr2:239079292C>G	ENST00000254654.3	-	12	1239	c.1064G>C	c.(1063-1065)gGg>gCg	p.G355A		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	355	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)		TGCGGACTTCCCTTCCCGGGT	0.602																																					p.G355A		Atlas-SNP	.											.	ILKAP	42	.	0			c.G1064C						.						38	39	38					2																	239079292		2203	4300	6503	SO:0001583	missense	80895	exon12			GACTTCCCTTCCC	AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	15566	protein-coding gene	gene with protein product			"integrin-linked kinase-associated serine/threonine phosphatase 2C"				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.1064G>C	chr2.hg19:g.239079292C>G	ENSP00000254654:p.Gly355Ala	218.0	0.0		235.0	65.0	NM_030768	B3KM39	Missense_Mutation	SNP	ENST00000254654.3	hg19	CCDS2526.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.471267	0.43942	.	.	ENSG00000132323	ENST00000254654	T	0.23552	1.9	5.69	5.69	0.88448	Protein phosphatase 2C-like (5);	0.048255	0.85682	D	0.000000	T	0.28400	0.0702	L	0.60904	1.88	0.80722	D	1	B	0.23442	0.085	B	0.27076	0.076	T	0.03157	-1.1066	10	0.24483	T	0.36	-28.543	14.8304	0.70142	0.0:0.8553:0.1447:0.0	.	355	Q9H0C8	ILKAP_HUMAN	A	355	ENSP00000254654:G355A	ENSP00000254654:G355A	G	-	2	0	ILKAP	238744031	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	2.450000	0.44943	2.688000	0.91661	0.563000	0.77884	GGG	.	.		0.602	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768		G	239079292	C	G	239079292	3	3	170	1	0	0	0	0	1	0	0	0	7723	623	22	4	118	4	ILKAP	2	239079292	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	10223565	239079292	4120081	34	25725										
CMTM6	54918	hgsc.bcm.edu	37	chr3	32544113	32544113	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gactcaccagctgcaagcccTtgagaacgcgccggagcaat	11	14	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:32544113T>A	ENST00000205636.3	-	1	787	c.125A>T	c.(124-126)aAg>aTg	p.K42M		NM_017801.2	NP_060271.1	Q9NX76	CKLF6_HUMAN	CKLF-like MARVEL transmembrane domain containing 6	42	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(1)	2						CTGCAAGCCCTTGAGAACGCG	0.721																																					p.K42M		Atlas-SNP	.											.	CMTM6	5	.	0			c.A125T						.						7	10	9					3																	32544113		2156	4235	6391	SO:0001583	missense	54918	exon1			AAGCCCTTGAGAA	AK000403	CCDS2653.1	3p22.2	2006-08-25	2005-11-08	2005-11-08	ENSG00000091317	ENSG00000091317			19177	protein-coding gene	gene with protein product		607889	"chemokine-like factor super family 6", "chemokine-like factor superfamily 6"	CKLFSF6			Standard	NM_017801		Approved	FLJ20396	uc003cfa.1	Q9NX76	OTTHUMG00000130747	ENST00000205636.3:c.125A>T	chr3.hg19:g.32544113T>A	ENSP00000205636:p.Lys42Met	103.0	0.0		162.0	57.0	NM_017801	Q6IAC4	Missense_Mutation	SNP	ENST00000205636.3	hg19	CCDS2653.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.016499	0.93404	.	.	ENSG00000091317	ENST00000205636	T	0.32515	1.45	4.64	4.64	0.57946	Marvel (1);MARVEL-like domain (1);	0.050416	0.85682	D	0.000000	T	0.53174	0.1780	M	0.75264	2.295	0.34775	D	0.734139	D	0.89917	1.0	D	0.91635	0.999	T	0.67719	-0.5598	10	0.66056	D	0.02	.	11.0323	0.47781	0.0:0.0:0.0:1.0	.	42	Q9NX76	CKLF6_HUMAN	M	42	ENSP00000205636:K42M	ENSP00000205636:K42M	K	-	2	0	CMTM6	32519117	0.984000	0.35163	0.136000	0.22124	0.689000	0.40095	3.236000	0.51336	2.032000	0.59987	0.383000	0.25322	AAG	.	.		0.721	CMTM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253247.1			A	32544113	T	A	32544113	3	1	170	1	0	0	0	0	1	0	0	0	3589	1609	56	4	442	4	CMTM6	3	32544113	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10		32544113	165478317	35	25726										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38157966	38157966	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	atccgcctggattgggagacCtatgttccagaagacaagga	12	9	0	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:38157966C>T	ENST00000308059.6	+	28	3900	c.3879C>T	c.(3877-3879)acC>acT	p.T1293T	DLEC1_ENST00000452631.2_Silent_p.T1296T|DLEC1_ENST00000346219.3_Silent_p.T1293T					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		ATTGGGAGACCTATGTTCCAG	0.612																																					p.T1293T		Atlas-SNP	.											.	DLEC1	278	.	0			c.C3879T						.						39	40	40					3																	38157966		1963	4174	6137	SO:0001819	synonymous_variant	9940	exon28			GGAGACCTATGTT	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.3879C>T	chr3.hg19:g.38157966C>T		59.0	0.0		67.0	19.0	NM_007337		Silent	SNP	ENST00000308059.6	hg19	CCDS2672.2																																																																																			.	.		0.612	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38157966	C	T	38157966	2	4	170	1	0	0	0	0	0	0	0	1	4554	668	24	3		3	DLEC1	3	38157966	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	5613853	38157966	159864464	36	25727										
ULK4	54986	hgsc.bcm.edu	37	chr3	41977412	41977412	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gaggttttcatcttgagcaaTaactgtttttaaggaaccac	8	7	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:41977412T>G	ENST00000301831.4	-	4	721	c.259A>C	c.(259-261)Att>Ctt	p.I87L	ULK4_ENST00000420927.1_Missense_Mutation_p.I87L	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	87	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TCTTGAGCAATAACTGTTTTT	0.418																																					p.I87L		Atlas-SNP	.											.	ULK4	150	.	0			c.A259C						.						114	110	112					3																	41977412		1911	4155	6066	SO:0001583	missense	54986	exon4			GAGCAATAACTGT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.259A>C	chr3.hg19:g.41977412T>G	ENSP00000301831:p.Ile87Leu	70.0	0.0		90.0	27.0	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	hg19	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	T	13.90	2.376492	0.42105	.	.	ENSG00000168038	ENST00000301831;ENST00000420927	T;T	0.62788	0.0;0.0	5.86	5.86	0.93980	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.095687	0.64402	D	0.000001	T	0.33411	0.0862	N	0.01779	-0.725	0.80722	D	1	B;B	0.34147	0.127;0.438	B;B	0.34652	0.133;0.187	T	0.48387	-0.9040	10	0.02654	T	1	.	15.2278	0.73364	0.0:0.0:0.0:1.0	.	87;87	B4E2M4;Q96C45	.;ULK4_HUMAN	L	87	ENSP00000301831:I87L;ENSP00000412187:I87L	ENSP00000301831:I87L	I	-	1	0	ULK4	41952416	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	3.582000	0.53921	2.241000	0.73720	0.533000	0.62120	ATT	.	.		0.418	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		G	41977412	T	G	41977412	3	3	170	1	0	0	0	0	1	0	0	0	16993	1406	49	5	3704	5	ULK4	3	41977412	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	3819446	41977412	156045018	37	25728										
TGM4	7047	hgsc.bcm.edu	37	chr3	44938212	44938212	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ccaaaatagtttgagaaaaaTgtcctggactgctgcatttc	8	8	0	1	rs142027211		TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:44938212T>A	ENST00000296125.4	+	6	629	c.561T>A	c.(559-561)aaT>aaA	p.N187K	RP11-272D20.2_ENST00000427258.1_RNA	NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	187					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	TTGAGAAAAATGTCCTGGACT	0.483																																					p.N187K		Atlas-SNP	.											.	TGM4	82	.	0			c.T561A						.	T	LYS/ASN	1,4405	4.2+/-10.8	0,1,2202	103	102	102		561	-3.3	0	3	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	no	missense	TGM4	NM_003241.3	94	0,2,6501	AA,AT,TT		0.0116,0.0227,0.0154	benign	187/685	44938212	2,13004	2203	4300	6503	SO:0001583	missense	7047	exon6			GAAAAATGTCCTG	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"Transglutaminases"	11780	protein-coding gene	gene with protein product		600585	"transglutaminase 4 (prostate)"			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.561T>A	chr3.hg19:g.44938212T>A	ENSP00000296125:p.Asn187Lys	86.0	0.0		92.0	21.0	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	hg19	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	T	9.221	1.033352	0.19590	2.27E-4	1.16E-4	ENSG00000163810	ENST00000296125	D	0.88741	-2.42	2.43	-3.3	0.05003	.	3.097460	0.02523	U	0.092773	T	0.81302	0.4794	L	0.33624	1.015	0.09310	N	1	B	0.19073	0.033	B	0.19148	0.024	T	0.64364	-0.6425	10	0.41790	T	0.15	.	3.8373	0.08899	0.401:0.1563:0.0:0.4427	.	187	P49221	TGM4_HUMAN	K	187	ENSP00000296125:N187K	ENSP00000296125:N187K	N	+	3	2	TGM4	44913216	0.000000	0.05858	0.002000	0.10522	0.406000	0.30931	-2.574000	0.00911	-0.655000	0.05387	-0.456000	0.05471	AAT	.	T|1.000;A|0.000		0.483	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		A	44938212	T	A	44938212	3	1	170	1	0	0	0	0	1	0	0	0	15847	1461	51	4	583	4	TGM4	3	44938212	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	2960800	44938212	153084218	38	25729										
NME6	10201	hgsc.bcm.edu	37	chr3	48336594	48336595	+	Frame_Shift_Del	DEL	GT	GT	-													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gggtggtgttgcgggtgtcaGtgaggccgaaactcccacgg					rs368964694		TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:48336594_48336595delGT	ENST00000452211.1	-	6	601_602	c.364_365delAC	c.(364-366)actfs	p.T122fs	NME6_ENST00000435684.1_Frame_Shift_Del_p.L109fs|NME6_ENST00000450160.1_Frame_Shift_Del_p.L109fs|NME6_ENST00000415644.1_Intron|NME6_ENST00000442597.1_Frame_Shift_Del_p.T122fs|NME6_ENST00000421967.1_Frame_Shift_Del_p.T130fs|NME6_ENST00000447314.1_Frame_Shift_Del_p.T77fs|ZNF589_ENST00000412564.1_Intron|NME6_ENST00000426689.2_Frame_Shift_Del_p.T122fs|NME6_ENST00000444069.1_5'UTR|NME6_ENST00000415053.1_Frame_Shift_Del_p.T122fs|NME6_ENST00000451657.1_Frame_Shift_Del_p.L109fs|NME6_ENST00000426723.1_Intron			O75414	NDK6_HUMAN	NME/NM23 nucleoside diphosphate kinase 6	122					apoptotic process (GO:0006915)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|negative regulation of cell growth (GO:0030308)|negative regulation of mitosis (GO:0045839)|UTP biosynthetic process (GO:0006228)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			breast(1)|large_intestine(5)	6				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		GCGGGTGTCAGTGAGGCCGAAA	0.589																																					p.130_130del		Atlas-INDEL	.											.	NME6	14	.	0			c.389_390del						.																																			SO:0001589	frameshift_variant	10201	exon5			.	AF051941	CCDS2763.1	3p21.31	2012-05-18	2012-05-18		ENSG00000172113	ENSG00000172113			20567	protein-coding gene	gene with protein product		608294	"non-metastatic cells 6, protein expressed in (nucleoside-diphosphate kinase)"			10453732, 19852809	Standard	NM_005793		Approved	NM23-H6, IPIA-ALPHA	uc003cso.3	O75414	OTTHUMG00000133531	ENST00000452211.1:c.364_365delAC	chr3.hg19:g.48336594_48336595delGT	ENSP00000392352:p.Thr122fs	114.0	0.0		107.0	35.0	NM_005793	B4DGW7|B4DM99|Q53HM5|Q96E73|Q9BQ63	Frame_Shift_Del	DEL	ENST00000452211.1	hg19																																																																																				.	.		0.589	NME6-005	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000346107.1	NM_005793		-	48336595	GT	-	48336594	7	5	170	1	0	1	0	1	0	0	0	0	10504	1029	36	0	203	0	NME6	3	48336594	Frame_Shift_Del	DEL	GT	TCGA-DD-AACT-01A-11D-A40R-10	3398382	48336594	149685836	39	25730										
RBM5	10181	hgsc.bcm.edu	37	chr3	50137458	50137458	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cgaaggccctcagcctgcggAtgtgaggctgatgaagagga	16	9	1	4			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:50137458A>C	ENST00000347869.3	+	5	558	c.383A>C	c.(382-384)gAt>gCt	p.D128A	RBM5_ENST00000469838.1_Missense_Mutation_p.D128A	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	128	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CAGCCTGCGGATGTGAGGCTG	0.453																																					p.D128A		Atlas-SNP	.											.	RBM5	76	.	0			c.A383C						.						116	94	102					3																	50137458		2203	4300	6503	SO:0001583	missense	10181	exon5			CTGCGGATGTGAG	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"G patch domain containing", "RNA binding motif (RRM) containing"	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.383A>C	chr3.hg19:g.50137458A>C	ENSP00000343054:p.Asp128Ala	116.0	0.0		102.0	31.0	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Missense_Mutation	SNP	ENST00000347869.3	hg19	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.963597	0.74016	.	.	ENSG00000003756	ENST00000347869;ENST00000469838;ENST00000441305;ENST00000543047;ENST00000539538	T;T;T	0.46063	3.04;0.88;0.88	5.86	5.86	0.93980	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.050258	0.85682	D	0.000000	T	0.55081	0.1898	L	0.37800	1.135	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.998;0.996	T	0.50939	-0.8768	9	.	.	.	-19.9812	16.2479	0.82454	1.0:0.0:0.0:0.0	.	128;128	P52756;E1CJT4	RBM5_HUMAN;.	A	128;128;128;127;127	ENSP00000343054:D128A;ENSP00000419534:D128A;ENSP00000390711:D128A	.	D	+	2	0	RBM5	50112462	1.000000	0.71417	0.929000	0.37066	0.997000	0.91878	8.923000	0.92808	2.241000	0.73720	0.533000	0.62120	GAT	.	.		0.453	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		C	50137458	A	C	50137458	3	2	170	1	0	0	0	0	1	0	0	0	13158	333	12	5	397	5	RBM5	3	50137458	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	1800864	50137458	147884972	40	25731										
RBM5	10181	hgsc.bcm.edu	37	chr3	50143082	50143082	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gtcaataacatccgcctcatAaaagacaaacagacccagca	5	13	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:50143082A>G	ENST00000347869.3	+	10	970	c.795A>G	c.(793-795)atA>atG	p.I265M		NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	265	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TCCGCCTCATAAAAGACAAAC	0.463																																					p.I265M		Atlas-SNP	.											.	RBM5	76	.	0			c.A795G						.						110	100	103					3																	50143082		2203	4300	6503	SO:0001583	missense	10181	exon10			CCTCATAAAAGAC	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"G patch domain containing", "RNA binding motif (RRM) containing"	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.795A>G	chr3.hg19:g.50143082A>G	ENSP00000343054:p.Ile265Met	115.0	0.0		128.0	34.0	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Missense_Mutation	SNP	ENST00000347869.3	hg19	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.350056	0.82132	.	.	ENSG00000003756	ENST00000347869;ENST00000543047	T	0.07908	3.15	6.16	0.562	0.17290	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.20210	0.0486	L	0.52905	1.665	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	T	0.00191	-1.1936	10	0.41790	T	0.15	-16.7755	12.1742	0.54176	0.2604:0.6382:0.0:0.1014	.	265	P52756	RBM5_HUMAN	M	265;264	ENSP00000343054:I265M	ENSP00000343054:I265M	I	+	3	3	RBM5	50118086	0.997000	0.39634	0.999000	0.59377	0.997000	0.91878	0.759000	0.26461	0.144000	0.18951	0.528000	0.53228	ATA	.	.		0.463	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		G	50143082	A	G	50143082	3	3	170	1	0	0	0	0	1	0	0	0	13158	352	13	2	829	2	RBM5	3	50143082	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	5624	50143082	147879348	41	25732										
SLMAP	7871	hgsc.bcm.edu	37	chr3	57882301	57882301	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gagtccaagcaaggaaaaaaGcagtgacgacactacaggtg	12	8	0	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:57882301G>C	ENST00000428312.1	+	14	1467	c.1373G>C	c.(1372-1374)aGc>aCc	p.S458T	SLMAP_ENST00000472546.1_3'UTR|SLMAP_ENST00000442599.2_5'UTR|SLMAP_ENST00000495364.1_5'UTR|SLMAP_ENST00000449503.2_Missense_Mutation_p.S420T|SLMAP_ENST00000383718.3_Missense_Mutation_p.S454T|SLMAP_ENST00000295952.3_Missense_Mutation_p.S441T|SLMAP_ENST00000295951.3_Missense_Mutation_p.S441T|SLMAP_ENST00000416870.1_5'UTR|SLMAP_ENST00000494088.1_5'UTR			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	458					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)				endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		AAGGAAAAAAGCAGTGACGAC	0.343																																					p.S441T		Atlas-SNP	.											.	SLMAP	46	.	0			c.G1322C						.						57	62	60					3																	57882301		2202	4300	6502	SO:0001583	missense	7871	exon13			AAAAAAGCAGTGA	AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"Sarcolemmal-associated protein"	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.1373G>C	chr3.hg19:g.57882301G>C	ENSP00000398661:p.Ser458Thr	360.0	0.0		417.0	127.0	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Missense_Mutation	SNP	ENST00000428312.1	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	18.57|18.57|18.57	3.652420|3.652420|3.652420	0.67472|0.67472|0.67472	.|.|.	.|.|.	ENSG00000163681|ENSG00000163681|ENSG00000163681	ENST00000417128|ENST00000416658;ENST00000438794|ENST00000295951;ENST00000295952;ENST00000383718;ENST00000428312;ENST00000449503;ENST00000537224;ENST00000465203	.|T;T|T;T;T;T;T	.|0.58060|0.55413	.|0.73;0.36|1.21;1.21;0.52;1.17;1.33	6.08|6.08|6.08	6.08|6.08|6.08	0.98989|0.98989|0.98989	.|.|.	.|.|0.000000	.|.|0.85682	.|.|D	.|.|0.000000	T|T|T	0.70500|0.70500|0.70500	0.3231|0.3231|0.3231	M|M|M	0.68952|0.68952|0.68952	2.095|2.095|2.095	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D;D;D	.|.|0.76494	.|.|0.988;0.999;0.999;0.996;0.988	.|.|D;D;D;D;D	.|.|0.83275	.|.|0.992;0.996;0.991;0.99;0.992	T|T|T	0.61008|0.61008|0.61008	-0.7149|-0.7149|-0.7149	5|7|10	.|0.40728|0.10902	.|T|T	.|0.16|0.67	-6.3822|-6.3822|-6.3822	20.6721|20.6721|20.6721	0.99693|0.99693|0.99693	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|.|52;420;458;441;454	.|.|Q14BN4-4;Q14BN4-2;Q14BN4;Q14BN4-3;Q14BN4-6	.|.|.;.;SLMAP_HUMAN;.;.	P|N|T	42|65;36|441;441;454;458;420;52;165	.|ENSP00000389978:K65N;ENSP00000391886:K36N|ENSP00000295951:S441T;ENSP00000295952:S441T;ENSP00000373224:S454T;ENSP00000398661:S458T;ENSP00000412945:S420T	.|ENSP00000389978:K65N|ENSP00000295951:S441T	A|K|S	+|+|+	1|3|2	0|2|0	SLMAP|SLMAP|SLMAP	57857341|57857341|57857341	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.989000|0.989000|0.989000	0.77384|0.77384|0.77384	7.781000|7.781000|7.781000	0.85668|0.85668|0.85668	2.894000|2.894000|2.894000	0.99253|0.99253|0.99253	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GCA|AAG|AGC	.	.		0.343	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159		C	57882301	G	C	57882301	3	2	170	1	0	0	0	0	1	0	0	0	14764	971	34	4	1372	4	SLMAP	3	57882301	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	7739219	57882301	140140129	42	25733										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78649366	78649366	+	Frame_Shift_Del	DEL	C	C	-													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cttgttctctttgtctgcttCctgatcctcttgatgacatt							TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:78649366delC	ENST00000464233.1	-	30	4951	c.4838delG	c.(4837-4839)ggafs	p.G1613fs	ROBO1_ENST00000436010.2_Frame_Shift_Del_p.G1574fs|ROBO1_ENST00000466906.1_5'UTR|ROBO1_ENST00000467549.1_Frame_Shift_Del_p.G1513fs|ROBO1_ENST00000495273.1_Frame_Shift_Del_p.G1568fs	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1613					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TTGTCTGCTTCCTGATCCTCT	0.378																																					p.G1613fs		Atlas-INDEL	.											.	ROBO1	833	.	0			c.4839delA						.						176	162	166					3																	78649366		1888	4105	5993	SO:0001589	frameshift_variant	6091	exon30			.	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.4838delG	chr3.hg19:g.78649366delC	ENSP00000420321:p.Gly1613fs	188.0	0.0		228.0	56.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Frame_Shift_Del	DEL	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.		0.378	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		-	78649366	C	-	78649366	7	5	170	1	0	1	0	1	0	0	0	0	13528	855	30	0	125	0	ROBO1	3	78649366	Frame_Shift_Del	DEL	C	TCGA-DD-AACT-01A-11D-A40R-10	20767065	78649366	119373064	43	25734										
EPHA6	285220	hgsc.bcm.edu	37	chr3	96945199	96945199	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	acatacatggaagcaacttcTgtctgtcagtgtgaaaaggg	11	7	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:96945199T>G	ENST00000389672.5	+	4	1244	c.1206T>G	c.(1204-1206)tcT>tcG	p.S402S	EPHA6_ENST00000470610.2_Silent_p.S402S	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	308	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						AAGCAACTTCTGTCTGTCAGT	0.383																																					p.S402S		Atlas-SNP	.											.	EPHA6	439	.	0			c.T1206G						.						159	152	154					3																	96945199		1845	4088	5933	SO:0001819	synonymous_variant	285220	exon4			AACTTCTGTCTGT	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.1206T>G	chr3.hg19:g.96945199T>G		126.0	0.0		111.0	27.0	NM_001080448	D6RAL5	Silent	SNP	ENST00000389672.5	hg19	CCDS46876.1																																																																																			.	.		0.383	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		G	96945199	T	G	96945199	2	3	170	1	0	0	0	0	0	0	0	1	5173	1567	55	5		5	EPHA6	3	96945199	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	18295833	96945199	101077231	44	25735										
OR5AC2	81050	hgsc.bcm.edu	37	chr3	97806627	97806627	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cgcactaatgatatttatttTtggtgcttttatacaaatac	5	6	0	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:97806627T>C	ENST00000358642.2	+	1	611	c.611T>C	c.(610-612)tTt>tCt	p.F204S		NM_054106.1	NP_473447.1	Q9NZP5	O5AC2_HUMAN	olfactory receptor, family 5, subfamily AC, member 2	204					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	28						ATATTTATTTTTGGTGCTTTT	0.303																																					p.F204S		Atlas-SNP	.											.	OR5AC2	64	.	0			c.T611C						.						39	41	41					3																	97806627		2203	4299	6502	SO:0001583	missense	81050	exon1			TTATTTTTGGTGC	AF179759	CCDS33796.1	3q11.2	2013-09-23			ENSG00000196578	ENSG00000196578		"GPCR / Class A : Olfactory receptors"	15431	protein-coding gene	gene with protein product							Standard	NM_054106		Approved	HSA1	uc011bgs.2	Q9NZP5	OTTHUMG00000160083	ENST00000358642.2:c.611T>C	chr3.hg19:g.97806627T>C	ENSP00000351466:p.Phe204Ser	67.0	0.0		94.0	25.0	NM_054106		Missense_Mutation	SNP	ENST00000358642.2	hg19	CCDS33796.1	.	.	.	.	.	.	.	.	.	.	T	13.86	2.362749	0.41902	.	.	ENSG00000196578	ENST00000358642	T	0.00183	8.6	4.51	3.35	0.38373	GPCR, rhodopsin-like superfamily (1);	0.207171	0.23844	U	0.044008	T	0.00178	0.0005	L	0.37850	1.14	0.09310	N	1	B	0.27700	0.186	B	0.36186	0.219	T	0.25433	-1.0132	10	0.62326	D	0.03	-16.4108	8.2278	0.31579	0.0:0.0964:0.0:0.9036	.	204	Q9NZP5	O5AC2_HUMAN	S	204	ENSP00000351466:F204S	ENSP00000351466:F204S	F	+	2	0	OR5AC2	99289317	0.003000	0.15002	0.017000	0.16124	0.110000	0.19582	0.714000	0.25808	0.785000	0.33685	0.481000	0.45027	TTT	.	.		0.303	OR5AC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359116.1			C	97806627	T	C	97806627	3	2	170	1	0	0	0	0	1	0	0	0	11150	1841	64	2	613	2	OR5AC2	3	97806627	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	861428	97806627	100215803	45	25736										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113379342	113379342	+	Frame_Shift_Del	DEL	T	T	-													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aacaagaaagagtccaaccaTtgtccaaagggtttcccgaa							TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:113379342delT	ENST00000478658.1	-	5	1204	c.1187delA	c.(1186-1188)aatfs	p.N396fs	KIAA2018_ENST00000316407.4_Frame_Shift_Del_p.N396fs|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	396						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						AGTCCAACCATTGTCCAAAGG	0.443																																					p.N396fs		Atlas-INDEL	.											.	KIAA2018	180	.	0			c.1188delT						.						90	84	86					3																	113379342		1925	4116	6041	SO:0001589	frameshift_variant	205717	exon7			.	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.1187delA	chr3.hg19:g.113379342delT	ENSP00000420721:p.Asn396fs	55.0	0.0		61.0	19.0	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Frame_Shift_Del	DEL	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.		0.443	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		-	113379342	T	-	113379342	7	5	170	1	0	1	0	1	0	0	0	0	8277	1493	52	0	5554	0	KIAA2018	3	113379342	Frame_Shift_Del	DEL	T	TCGA-DD-AACT-01A-11D-A40R-10	15572715	113379342	84643088	46	25737										
UPK1B	7348	hgsc.bcm.edu	37	chr3	118906777	118906777	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctcttctgcctgtctgttctAggcattgtaggcatcatgaa	9	10	5	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:118906777A>G	ENST00000264234.3	+	3	374	c.225A>G	c.(223-225)ctA>ctG	p.L75L	UPK1B_ENST00000497685.1_5'UTR|UPK1B_ENST00000460625.1_Silent_p.L75L	NM_006952.3	NP_008883.2	O75841	UPK1B_HUMAN	uroplakin 1B	75					epithelial cell differentiation (GO:0030855)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	structural molecule activity (GO:0005198)			breast(1)|endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)	14				GBM - Glioblastoma multiforme(114;0.222)		TGTCTGTTCTAGGCATTGTAG	0.498																																					p.L75L		Atlas-SNP	.											.	UPK1B	27	.	0			c.A225G						.						137	122	127					3																	118906777		2203	4300	6503	SO:0001819	synonymous_variant	7348	exon3			TGTTCTAGGCATT	AF082888	CCDS2985.1	3q13.32	2013-02-14			ENSG00000114638	ENSG00000114638		"Tetraspanins"	12578	protein-coding gene	gene with protein product		602380		UPK1		9935153, 9846985	Standard	NM_006952		Approved	TSPAN20	uc003ecc.3	O75841	OTTHUMG00000159354	ENST00000264234.3:c.225A>G	chr3.hg19:g.118906777A>G		120.0	0.0		115.0	35.0	NM_006952	O60753|Q9UIM2|Q9UNX6	Silent	SNP	ENST00000264234.3	hg19	CCDS2985.1																																																																																			.	.		0.498	UPK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354883.2			G	118906777	A	G	118906777	2	3	170	1	0	0	0	0	0	0	0	1	17023	407	15	2		2	UPK1B	3	118906777	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	5527435	118906777	79115653	47	25738										
KALRN	8997	hgsc.bcm.edu	37	chr3	124207122	124207122	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gaggtgatgctcagtgtcccAaagaaagccaatgatgccat	11	9	1	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:124207122A>G	ENST00000240874.3	+	29	4507	c.4350A>G	c.(4348-4350)ccA>ccG	p.P1450P	KALRN_ENST00000460856.1_Silent_p.P1441P|KALRN_ENST00000360013.3_Silent_p.P1450P	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1450	DH 1. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TCAGTGTCCCAAAGAAAGCCA	0.512																																					p.P1450P		Atlas-SNP	.											.	KALRN	556	.	0			c.A4350G						.						136	105	116					3																	124207122		2203	4300	6503	SO:0001819	synonymous_variant	8997	exon29			TGTCCCAAAGAAA	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4350A>G	chr3.hg19:g.124207122A>G		128.0	0.0		105.0	23.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	hg19	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	A	10.12	1.263994	0.23136	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.14	1.66	0.24008	.	.	.	.	.	T	0.59649	0.2209	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53486	-0.8432	4	.	.	.	.	11.1575	0.48497	0.3371:0.5892:0.0737:0.0	.	.	.	.	R	1419	.	.	Q	+	2	0	KALRN	125689812	0.192000	0.23301	1.000000	0.80357	0.998000	0.95712	-0.345000	0.07770	0.149000	0.19098	0.533000	0.62120	CAA	.	.		0.512	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		G	124207122	A	G	124207122	2	3	170	1	0	0	0	0	0	0	0	1	7984	117	5	2		2	KALRN	3	124207122	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	5300345	124207122	73815308	48	25739										
CCDC37	348807	hgsc.bcm.edu	37	chr3	126137512	126137512	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggagacgctggcgaccaaagAggaggccaggctggagcggg	20	9	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:126137512A>T	ENST00000352312.1	+	7	644	c.545A>T	c.(544-546)gAg>gTg	p.E182V	CCDC37_ENST00000505024.1_Missense_Mutation_p.E183V|CCDC37_ENST00000393425.1_Missense_Mutation_p.E183V	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	182										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		GCGACCAAAGAGGAGGCCAGG	0.652																																					p.E182V		Atlas-SNP	.											.	CCDC37	69	.	0			c.A545T						.						33	36	35					3																	126137512		2197	4293	6490	SO:0001583	missense	348807	exon7			CCAAAGAGGAGGC	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.545A>T	chr3.hg19:g.126137512A>T	ENSP00000344749:p.Glu182Val	86.0	0.0		77.0	22.0	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Missense_Mutation	SNP	ENST00000352312.1	hg19	CCDS3037.1	.	.	.	.	.	.	.	.	.	.	A	16.63	3.177307	0.57692	.	.	ENSG00000163885	ENST00000352312;ENST00000393425;ENST00000505024	T;T;T	0.18338	2.22;2.22;2.22	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.44664	0.1304	M	0.85542	2.76	0.58432	D	0.999998	D;D	0.76494	0.999;0.999	D;D	0.75484	0.976;0.986	T	0.48736	-0.9009	10	0.54805	T	0.06	-32.4345	12.4869	0.55879	1.0:0.0:0.0:0.0	.	183;182	Q494V2-2;Q494V2	.;CCD37_HUMAN	V	182;183;183	ENSP00000344749:E182V;ENSP00000377076:E183V;ENSP00000423046:E183V	ENSP00000344749:E182V	E	+	2	0	CCDC37	127620202	1.000000	0.71417	0.796000	0.32109	0.093000	0.18481	7.773000	0.85462	1.845000	0.53610	0.402000	0.26972	GAG	.	.		0.652	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		T	126137512	A	T	126137512	3	4	170	1	0	0	0	0	1	0	0	0	2811	304	11	4	567	4	CCDC37	3	126137512	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	1930390	126137512	71884918	49	25740										
GATA2	2624	hgsc.bcm.edu	37	chr3	128205213	128205213	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tggcctccggtcaggcgggcTgcgggcaaagagagagagga	19	9	1	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:128205213T>A	ENST00000341105.2	-	3	561		c.e3-2		RP11-475N22.4_ENST00000473958.1_RNA|RP11-475N22.4_ENST00000464242.1_RNA|GATA2_ENST00000430265.2_Splice_Site|GATA2_ENST00000487848.1_Splice_Site|RP11-475N22.4_ENST00000468377.1_RNA	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2						blood coagulation (GO:0007596)|cell differentiation in hindbrain (GO:0021533)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|definitive hemopoiesis (GO:0060216)|embryonic placenta development (GO:0001892)|eosinophil fate commitment (GO:0035854)|GABAergic neuron differentiation (GO:0097154)|homeostasis of number of cells within a tissue (GO:0048873)|inner ear morphogenesis (GO:0042472)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of phagocytosis (GO:0050766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of forebrain neuron differentiation (GO:2000977)|regulation of histone acetylation (GO:0035065)|semicircular canal development (GO:0060872)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|ventral spinal cord interneuron differentiation (GO:0021514)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(58)|kidney(2)|large_intestine(3)|lung(9)|prostate(3)|skin(1)|urinary_tract(1)	79				GBM - Glioblastoma multiforme(114;0.173)		TCAGGCGGGCTGCGGGCAAAG	0.642			Mis		AML(CML blast transformation)																																.		Atlas-SNP	.		Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	.	GATA2	122	.	0			c.230-2A>T						.						10	14	12					3																	128205213		2144	4208	6352	SO:0001630	splice_region_variant	2624	exon5			GCGGGCTGCGGGC	AF169253	CCDS3049.1, CCDS46903.1	3q21	2014-09-17	2001-11-28		ENSG00000179348	ENSG00000179348		"GATA zinc finger domain containing"	4171	protein-coding gene	gene with protein product		137295	"GATA-binding protein 2"			1714909	Standard	NM_032638		Approved	NFE1B	uc003eko.2	P23769	OTTHUMG00000159689	ENST00000341105.2:c.230-2A>T	chr3.hg19:g.128205213T>A		51.0	0.0		42.0	17.0	NM_001145661	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Splice_Site	SNP	ENST00000341105.2	hg19	CCDS3049.1	.	.	.	.	.	.	.	.	.	.	T	16.90	3.249196	0.59103	.	.	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848;ENST00000492608	.	.	.	4.63	3.37	0.38596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5582	0.45129	0.0:0.0:0.1621:0.8379	.	.	.	.	.	-1	.	.	.	-	.	.	GATA2	129687903	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	3.853000	0.55941	1.702000	0.51228	0.247000	0.18012	.	.	.		0.642	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638	Intron	A	128205213	T	A	128205213	5	1	170	1	0	0	0	0	0	0	1	0	6262	1594	55	4	1230	4	GATA2	3	128205213	Splice_Site	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	2067701	128205213	69817217	50	25741										
PRR23A	729627	hgsc.bcm.edu	37	chr3	138724450	138724450	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggggacaggctccagaaggcGgaattccgggtcgaagaagg	18	8	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:138724450G>A	ENST00000383163.2	-	1	660	c.661C>T	c.(661-663)Cgc>Tgc	p.R221C	MRPS22_ENST00000495075.1_5'Flank	NM_001134659.1	NP_001128131.1	A6NEV1	PR23A_HUMAN	proline rich 23A	221	Pro-rich.									endometrium(3)|kidney(1)|lung(7)	11						TCCAGAAGGCGGAATTCCGGG	0.682																																					p.R221C		Atlas-SNP	.											.	PRR23A	35	.	0			c.C661T						.						34	40	38					3																	138724450		692	1591	2283	SO:0001583	missense	729627	exon1			GAAGGCGGAATTC		CCDS46923.1	3q22.3	2014-06-03				ENSG00000206260			37172	protein-coding gene	gene with protein product							Standard	NM_001134659		Approved		uc011bms.2	A6NEV1		ENST00000383163.2:c.661C>T	chr3.hg19:g.138724450G>A	ENSP00000372649:p.Arg221Cys	206.0	0.0		228.0	55.0	NM_001134659		Missense_Mutation	SNP	ENST00000383163.2	hg19	CCDS46923.1	.	.	.	.	.	.	.	.	.	.	G	13.92	2.379666	0.42207	.	.	ENSG00000206260	ENST00000383163	.	.	.	3.23	-0.918	0.10482	.	0.965081	0.08521	N	0.933459	T	0.12987	0.0315	N	0.08118	0	0.09310	N	1	P	0.40970	0.734	B	0.38921	0.285	T	0.12578	-1.0542	9	0.72032	D	0.01	.	0.6688	0.00855	0.2363:0.1892:0.3812:0.1934	.	221	A6NEV1	PR23A_HUMAN	C	221	.	ENSP00000372649:R221C	R	-	1	0	PRR23A	140207140	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.035000	0.13797	-0.204000	0.10235	0.591000	0.81541	CGC	.	.		0.682	PRR23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361503.1	NM_001134659		A	138724450	G	A	138724450	3	1	170	1	0	0	0	0	1	0	0	0	12606	1116	39	1	143	1	PRR23A	3	138724450	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	10519237	138724450	59297980	51	25742										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916869	178916869	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gggaagaattttttgatgaaAcaagacgactttgtgacctt	10	5	0	5			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr3:178916869A>T	ENST00000263967.3	+	2	413	c.256A>T	c.(256-258)Aca>Tca	p.T86S		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	86	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTTTGATGAAACAAGACGACT	0.368		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.T86S	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	.	PIK3CA	8460	.	0			c.A256T						.						108	103	105					3																	178916869		1821	4082	5903	SO:0001583	missense	5290	exon2			GATGAAACAAGAC		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.256A>T	chr3.hg19:g.178916869A>T	ENSP00000263967:p.Thr86Ser	271.0	0.0		285.0	77.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.418975	0.42918	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	T;T	0.73152	-0.72;-0.72	5.44	5.44	0.79542	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	T	0.49795	0.1578	N	0.04880	-0.145	0.80722	D	1	B	0.10296	0.003	B	0.12837	0.008	T	0.46952	-0.9154	9	.	.	.	-9.8977	15.4956	0.75646	1.0:0.0:0.0:0.0	.	86	P42336	PK3CA_HUMAN	S	86	ENSP00000263967:T86S;ENSP00000417479:T86S	.	T	+	1	0	PIK3CA	180399563	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.800000	0.69108	2.059000	0.61396	0.454000	0.30748	ACA	.	.		0.368	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178916869	A	T	178916869	3	4	170	1	0	0	0	0	1	0	0	0	11922	43	2	4	258	4	PIK3CA	3	178916869	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	40192419	178916869	19105561	52	25743										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6027974	6027974	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	atcaaggccacagaatgaatGctagtgagaaaaacaaaaaa	8	6	1	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr4:6027974G>A	ENST00000409021.3	-	21	2926	c.2477C>T	c.(2476-2478)gCa>gTa	p.A826V	JAKMIP1_ENST00000409371.3_Missense_Mutation_p.A641V	NM_001099433.1	NP_001092903.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	0					cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						Cagaatgaatgctagtgagaa	0.338																																					p.A826V		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.C2477T						.						50	48	48					4																	6027974		950	2098	3048	SO:0001583	missense	152789	exon21			ATGAATGCTAGTG	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000409021.3:c.2477C>T	chr4.hg19:g.6027974G>A	ENSP00000386711:p.Ala826Val	560.0	1.0		550.0	152.0	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000409021.3	hg19	CCDS47005.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.852313	0.51270	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000425341	T;T	0.39592	1.51;1.07	5.07	5.07	0.68467	.	0.000000	0.51477	U	0.000098	T	0.63105	0.2483	.	.	.	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.70935	0.971;0.971	T	0.66586	-0.5886	9	0.62326	D	0.03	.	13.9656	0.64207	0.0:0.0:1.0:0.0	.	641;826	Q96N16-5;Q96N16-2	.;.	V	826;641;564	ENSP00000386711:A826V;ENSP00000387042:A641V	ENSP00000386711:A826V	A	-	2	0	JAKMIP1	6078875	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.041000	0.64196	2.364000	0.80123	0.655000	0.94253	GCA	.	.		0.338	JAKMIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329747.1	NM_144720		A	6027974	G	A	6027974	3	1	170	1	0	0	0	0	1	0	0	0	7949	1319	46	3	22	3	JAKMIP1	4	6027974	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10		6027974	185126302	53	25744										
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15529075	15529075	+	Frame_Shift_Del	DEL	A	A	-													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgctttccttggcaggctgtAaaatacgttcacagtagtca							TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr4:15529075delA	ENST00000503292.1	+	13	1335	c.1155delA	c.(1153-1155)gtafs	p.V385fs	CC2D2A_ENST00000389652.5_Frame_Shift_Del_p.V336fs|CC2D2A_ENST00000424120.1_Frame_Shift_Del_p.V385fs|CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000413206.1_Frame_Shift_Del_p.V385fs	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	385					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						GGCAGGCTGTAAAATACGTTC	0.408																																					p.V385fs		Atlas-INDEL	.											.	CC2D2A	158	.	0			c.1154delT						.						73	71	72					4																	15529075		1892	4117	6009	SO:0001589	frameshift_variant	57545	exon13			.	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.1155delA	chr4.hg19:g.15529075delA	ENSP00000421809:p.Val385fs	50.0	0.0		58.0	11.0	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Frame_Shift_Del	DEL	ENST00000503292.1	hg19	CCDS47026.1																																																																																			.	.		0.408	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		-	15529075	A	-	15529075	7	5	170	1	0	1	0	1	0	0	0	0	2730	349	13	0	1400	0	CC2D2A	4	15529075	Frame_Shift_Del	DEL	A	TCGA-DD-AACT-01A-11D-A40R-10	9501101	15529075	175625201	54	25745										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55143655	55143655	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aaagttgcagtgaagatgctAaaacgtaagtgctccttcct	9	8	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr4:55143655A>G	ENST00000257290.5	+	13	2218	c.1887A>G	c.(1885-1887)ctA>ctG	p.L629L	FIP1L1_ENST00000507166.1_Silent_p.L389L	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	629	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	TGAAGATGCTAAAACGTAAGT	0.463			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.L629L	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	.	PDGFRA	1583	.	0			c.A1887G						.						112	112	112					4																	55143655		2203	4300	6503	SO:0001819	synonymous_variant	5156	exon13	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	GATGCTAAAACGT	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1887A>G	chr4.hg19:g.55143655A>G		146.0	0.0		137.0	35.0	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	hg19	CCDS3495.1																																																																																			.	.		0.463	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		G	55143655	A	G	55143655	2	3	170	1	0	0	0	0	0	0	0	1	11670	349	13	2		2	PDGFRA	4	55143655	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	39614580	55143655	136010621	55	25746										
AGPAT9	84803	hgsc.bcm.edu	37	chr4	84516038	84516038	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cttgatgggaattattcagaGagctatggtcaaggcttgtc	12	6	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr4:84516038G>T	ENST00000395226.2	+	8	997	c.779G>T	c.(778-780)aGa>aTa	p.R260I	AGPAT9_ENST00000264409.4_Missense_Mutation_p.R260I	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	260					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				ATTATTCAGAGAGCTATGGTC	0.428																																					p.R260I		Atlas-SNP	.											.	AGPAT9	41	.	0			c.G779T						.						164	165	165					4																	84516038		2203	4300	6503	SO:0001583	missense	84803	exon8			TTCAGAGAGCTAT	AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	28157	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, theta"	610958	"1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.779G>T	chr4.hg19:g.84516038G>T	ENSP00000378651:p.Arg260Ile	74.0	0.0		78.0	22.0	NM_001256421	Q68CJ4|Q6GPI6|Q96NA3	Missense_Mutation	SNP	ENST00000395226.2	hg19	CCDS3606.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577796	0.86645	.	.	ENSG00000138678	ENST00000395226;ENST00000264409	D;D	0.97505	-4.41;-4.41	5.81	4.03	0.46877	Phospholipid/glycerol acyltransferase (2);	0.041875	0.85682	D	0.000000	D	0.96990	0.9017	M	0.84433	2.695	0.80722	D	1	P	0.50710	0.938	P	0.47299	0.543	D	0.96704	0.9520	10	0.72032	D	0.01	-23.3819	11.1526	0.48469	0.0665:0.0:0.8055:0.128	.	260	Q53EU6	GPAT3_HUMAN	I	260	ENSP00000378651:R260I;ENSP00000264409:R260I	ENSP00000264409:R260I	R	+	2	0	AGPAT9	84735062	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	8.006000	0.88564	1.456000	0.47831	-0.140000	0.14226	AGA	.	.		0.428	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717		T	84516038	G	T	84516038	3	4	170	1	0	0	0	0	1	0	0	0	392	942	33	3	805	3	AGPAT9	4	84516038	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	29372383	84516038	106638238	56	25747										
EMCN	51705	hgsc.bcm.edu	37	chr4	101386642	101386642	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gtgtaacacttgttactgttAcgtttgaaatgatggagtca	10	5	1	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr4:101386642A>G	ENST00000296420.4	-	4	492	c.314T>C	c.(313-315)gTa>gCa	p.V105A	EMCN_ENST00000305864.3_Missense_Mutation_p.V105A|EMCN_ENST00000502327.1_5'UTR|EMCN_ENST00000511970.1_Missense_Mutation_p.V105A	NM_001159694.1|NM_016242.3	NP_001153166.1|NP_057326.2	Q9ULC0	MUCEN_HUMAN	endomucin	105	Thr-rich.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)		TGTTACTGTTACGTTTGAAAT	0.368																																					p.V105A		Atlas-SNP	.											.	EMCN	37	.	0			c.T314C						.						193	169	177					4																	101386642		2203	4300	6503	SO:0001583	missense	51705	exon4			ACTGTTACGTTTG	AF205940	CCDS3655.1, CCDS54782.1	4q22.1	2008-02-05			ENSG00000164035	ENSG00000164035		"Mucins"	16041	protein-coding gene	gene with protein product		608350				11418125, 11594763	Standard	NM_016242		Approved	MUC14	uc003hvr.3	Q9ULC0	OTTHUMG00000131051	ENST00000296420.4:c.314T>C	chr4.hg19:g.101386642A>G	ENSP00000296420:p.Val105Ala	99.0	0.0		108.0	34.0	NM_001159694	A8K716|B4E347|Q8NEY5|Q8WWE7|Q9NRM8	Missense_Mutation	SNP	ENST00000296420.4	hg19	CCDS3655.1	.	.	.	.	.	.	.	.	.	.	A	4.875	0.162698	0.09287	.	.	ENSG00000164035	ENST00000296420;ENST00000305864;ENST00000506300;ENST00000511970;ENST00000502569	.	.	.	3.93	-5.87	0.02297	.	5.984870	0.00541	N	0.000223	T	0.14787	0.0357	N	0.08118	0	0.09310	N	1	B;B;B	0.11235	0.003;0.004;0.004	B;B;B	0.09377	0.002;0.004;0.004	T	0.09100	-1.0690	9	0.19590	T	0.45	0.1434	1.6265	0.02724	0.3609:0.1092:0.3722:0.1576	.	105;105;105	Q9ULC0-2;B4E347;Q9ULC0	.;.;MUCEN_HUMAN	A	105;105;32;105;105	.	ENSP00000296420:V105A	V	-	2	0	EMCN	101605665	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.616000	0.05591	-1.489000	0.01844	-0.290000	0.09829	GTA	.	.		0.368	EMCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253699.2	NM_016242		G	101386642	A	G	101386642	3	3	170	1	0	0	0	0	1	0	0	0	5088	391	14	2	503	2	EMCN	4	101386642	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	16870604	101386642	89767634	57	25748										
MAML3	55534	hgsc.bcm.edu	37	chr4	140640793	140640793	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tggtgccttgctgccccgggAgcgatggcatcatctgccga	14	13	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr4:140640793A>T	ENST00000509479.2	-	5	3957	c.3101T>A	c.(3100-3102)cTc>cAc	p.L1034H	MGST2_ENST00000515137.1_Intron	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					CTGCCCCGGGAGCGATGGCAT	0.647																																					p.L1030H		Atlas-SNP	.											.	MAML3	192	.	0			c.T3089A						.						30	32	31					4																	140640793		2172	4284	6456	SO:0001583	missense	55534	exon6			CCCGGGAGCGATG	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.3101T>A	chr4.hg19:g.140640793A>T	ENSP00000421180:p.Leu1034His	43.0	0.0		48.0	10.0	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	hg19	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.778402	0.70107	.	.	ENSG00000196782	ENST00000509479;ENST00000538400	T	0.29655	1.56	4.88	4.88	0.63580	.	0.172368	0.37955	N	0.001877	T	0.56411	0.1983	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	T	0.61623	-0.7025	10	0.59425	D	0.04	.	14.79	0.69833	1.0:0.0:0.0:0.0	.	1034;1030	E7EVW8;Q96JK9	.;MAML3_HUMAN	H	1034;341	ENSP00000421180:L1034H	ENSP00000421180:L1034H	L	-	2	0	MAML3	140860243	1.000000	0.71417	0.278000	0.24718	0.944000	0.59088	7.489000	0.81451	1.944000	0.56390	0.482000	0.46254	CTC	.	.		0.647	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140640793	A	T	140640793	3	4	170	1	0	0	0	0	1	0	0	0	9216	304	11	4	319	4	MAML3	4	140640793	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	39254151	140640793	50513483	58	25749										
SCOC	60592	hgsc.bcm.edu	37	chr4	141294779	141294779	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	acggcgcacgttctgtgggcGgagtgggcggagctgccggg	21	10	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr4:141294779G>A	ENST00000608372.1	+	1	116	c.89G>A	c.(88-90)cGg>cAg	p.R30Q	SCOC_ENST00000502535.1_5'Flank|SCOC_ENST00000394203.3_Intron|SCOC_ENST00000338517.4_Intron|RP11-425I13.3_ENST00000608178.1_RNA|SCOC_ENST00000394205.3_Intron|SCOC_ENST00000510586.1_5'Flank|RP11-425I13.3_ENST00000609616.1_RNA|RP11-425I13.3_ENST00000512692.2_RNA|SCOC_ENST00000506322.1_Intron|SCOC_ENST00000512749.1_Intron|SCOC_ENST00000394201.4_5'Flank|SCOC_ENST00000506597.1_Missense_Mutation_p.R30Q			Q9UIL1	SCOC_HUMAN	short coiled-coil protein	30				GRSG -> HEGR (in Ref. 5; AAK01707 and 6; AAP97732). {ECO:0000305}.	positive regulation of macroautophagy (GO:0016239)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5	all_hematologic(180;0.162)					TTCTGTGGGCGGAGTGGGCGG	0.677																																					p.R30Q		Atlas-SNP	.											.	SCOC	11	.	0			c.G89A						.						69	75	74					4																	141294779		692	1591	2283	SO:0001583	missense	60592	exon1			GTGGGCGGAGTGG	AK027797	CCDS3750.1, CCDS54806.1, CCDS54807.1	4q28.3	2014-05-22	2003-03-19		ENSG00000153130	ENSG00000153130			20335	protein-coding gene	gene with protein product			"short coiled coil protein"			11303027	Standard	NM_032547		Approved	HRIHFB2072, SCOCO	uc011che.1	Q9UIL1	OTTHUMG00000133416	ENST00000608372.1:c.89G>A	chr4.hg19:g.141294779G>A	ENSP00000477352:p.Arg30Gln	67.0	0.0		61.0	14.0	NM_001153484	B7WPH7|D3DNY7|E9PB65|Q6P5T9|Q7L2Y0|Q7Z4P2|Q96JY9|Q9BZB2	Missense_Mutation	SNP	ENST00000608372.1	hg19	CCDS54806.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.421336	0.62622	.	.	ENSG00000153130	ENST00000394201;ENST00000506597	.	.	.	4.87	2.11	0.27256	.	.	.	.	.	T	0.23210	0.0561	N	0.08118	0	0.35762	D	0.820256	B;B	0.24882	0.113;0.064	B;B	0.13407	0.009;0.004	T	0.10042	-1.0647	8	0.44086	T	0.13	-23.5909	5.7114	0.17937	0.0928:0.0:0.5614:0.3458	.	30;30	E9PB65;Q9UIL1	.;SCOC_HUMAN	Q	30	.	ENSP00000377751:R30Q	R	+	2	0	SCOC	141514229	0.105000	0.21958	0.180000	0.23079	0.766000	0.43426	0.476000	0.22180	0.172000	0.19760	0.563000	0.77884	CGG	.	.		0.677	SCOC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257274.2			A	141294779	G	A	141294779	3	1	170	1	0	0	0	0	1	0	0	0	13948	1116	39	1	165	1	SCOC	4	141294779	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	653986	141294779	49859497	59	25750										
FBXO8	26269	hgsc.bcm.edu	37	chr4	175162348	175162348	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cgaatcatccaggataccctTggacataaagtagttcactc	7	11	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr4:175162348T>A	ENST00000393674.2	-	4	1340	c.478A>T	c.(478-480)Aag>Tag	p.K160*	FBXO8_ENST00000503293.1_Nonsense_Mutation_p.K119*	NM_012180.2	NP_036312.2	Q9NRD0	FBX8_HUMAN	F-box protein 8	160	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell junction (GO:0030054)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|urinary_tract(1)	14		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)		AGGATACCCTTGGACATAAAG	0.333																																					p.K160X		Atlas-SNP	.											.	FBXO8	34	.	0			c.A478T						.						106	102	103					4																	175162348		2203	4297	6500	SO:0001587	stop_gained	26269	exon4			TACCCTTGGACAT	AF174596	CCDS3820.1	4q34.1	2008-02-05	2004-06-15			ENSG00000164117		"F-boxes /  "other""	13587	protein-coding gene	gene with protein product		605649	"F-box only protein 8"			10531035, 10531037	Standard	NM_012180		Approved	FBX8, FBS	uc003itp.3	Q9NRD0		ENST00000393674.2:c.478A>T	chr4.hg19:g.175162348T>A	ENSP00000377280:p.Lys160*	107.0	0.0		97.0	29.0	NM_012180	B2RB40|D3DP41|G5E9Z0|Q6UWN4|Q8IWE1|Q9NRP5|Q9UKC4	Nonsense_Mutation	SNP	ENST00000393674.2	hg19	CCDS3820.1	.	.	.	.	.	.	.	.	.	.	T	43	10.123001	0.99342	.	.	ENSG00000164117	ENST00000393674;ENST00000503293;ENST00000296517;ENST00000513696	.	.	.	5.39	5.39	0.77823	.	0.103453	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7605	0.78076	0.0:0.0:0.0:1.0	.	.	.	.	X	160;119;73;160	.	ENSP00000296517:K73X	K	-	1	0	FBXO8	175398923	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.328000	0.79160	2.171000	0.68590	0.529000	0.55759	AAG	.	.		0.333	FBXO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362085.2	NM_012180		A	175162348	T	A	175162348	4	1	170	1	0	0	0	0	0	1	0	0	5769	1821	63	4	493	4	FBXO8	4	175162348	Nonsense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	33867569	175162348	15991928	60	25751										
IRX4	50805	hgsc.bcm.edu	37	chr5	1879844	1879844	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	atgatcttctcgcccttggtGgggtaggggttcttgcggtg	16	8	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:1879844G>A	ENST00000505790.1	-	5	966	c.510C>T	c.(508-510)ccC>ccT	p.P170P	IRX4_ENST00000231357.2_Silent_p.P170P|IRX4_ENST00000505938.1_5'UTR|IRX4_ENST00000513692.1_Silent_p.P170P	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	170					establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		CGCCCTTGGTGGGGTAGGGGT	0.637																																					p.P170P		Atlas-SNP	.											.	IRX4	45	.	0			c.C510T						.						178	132	147					5																	1879844		2203	4300	6503	SO:0001819	synonymous_variant	50805	exon4			CTTGGTGGGGTAG	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"Homeoboxes / TALE class"	6129	protein-coding gene	gene with protein product		606199	"iroquois homeobox protein 4"			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.510C>T	chr5.hg19:g.1879844G>A		107.0	0.0		104.0	7.0	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Silent	SNP	ENST00000505790.1	hg19	CCDS3867.1																																																																																			.	.		0.637	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358		A	1879844	G	A	1879844	2	1	170	1	0	0	0	0	0	0	0	1	7855	1335	47	3		3	IRX4	5	1879844	Silent	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10		1879844	179035416	61	25752										
ZNF622	90441	hgsc.bcm.edu	37	chr5	16463667	16463667	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aaactgtggtctttggtcatGtgagccacattcttcatcag	9	9	5	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:16463667G>A	ENST00000308683.2	-	2	936	c.810C>T	c.(808-810)caC>caT	p.H270H		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	270					intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of kinase activity (GO:0033674)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						CTTTGGTCATGTGAGCCACAT	0.418																																					p.H270H		Atlas-SNP	.											.	ZNF622	49	.	0			c.C810T						.						137	138	137					5																	16463667		2203	4300	6503	SO:0001819	synonymous_variant	90441	exon2			GGTCATGTGAGCC	AY046059	CCDS3886.1	5p15.1	2012-10-05			ENSG00000173545	ENSG00000173545			30958	protein-coding gene	gene with protein product		608694				11802789, 12645566	Standard	NM_033414		Approved	MGC2485, MGC17552, ZPR9	uc003jfq.3	Q969S3	OTTHUMG00000090567	ENST00000308683.2:c.810C>T	chr5.hg19:g.16463667G>A		146.0	0.0		166.0	48.0	NM_033414		Silent	SNP	ENST00000308683.2	hg19	CCDS3886.1																																																																																			.	.		0.418	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414		A	16463667	G	A	16463667	2	1	170	1	0	0	0	0	0	0	0	1	18061	1368	48	3		3	ZNF622	5	16463667	Silent	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	14583823	16463667	164451593	62	25753										
NNT	23530	hgsc.bcm.edu	37	chr5	43702725	43702725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ttttgttttattatatagatActgatttggtccttgtaatt	6	3	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:43702725A>G	ENST00000264663.5	+	21	3219	c.2998A>G	c.(2998-3000)Act>Gct	p.T1000A	NNT_ENST00000344920.4_Missense_Mutation_p.T1000A|NNT_ENST00000512996.2_Missense_Mutation_p.T869A	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	1000					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					TTATATAGATACTGATTTGGT	0.313																																					p.T1000A		Atlas-SNP	.											.	NNT	92	.	0			c.A2998G						.						46	44	45					5																	43702725		2203	4300	6503	SO:0001583	missense	23530	exon21			ATAGATACTGATT	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.2998A>G	chr5.hg19:g.43702725A>G	ENSP00000264663:p.Thr1000Ala	44.0	0.0		55.0	8.0	NM_182977	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	hg19	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.372833	0.82573	.	.	ENSG00000112992	ENST00000542759;ENST00000264663;ENST00000344920;ENST00000512996	D;D;D	0.85013	-1.93;-1.93;-1.93	5.75	5.75	0.90469	.	0.099034	0.64402	D	0.000002	D	0.90539	0.7035	M	0.67569	2.06	0.80722	D	1	P	0.51449	0.945	P	0.62435	0.902	D	0.90186	0.4246	10	0.44086	T	0.13	-24.7307	15.7357	0.77842	1.0:0.0:0.0:0.0	.	1000	Q13423	NNTM_HUMAN	A	515;1000;1000;869	ENSP00000264663:T1000A;ENSP00000343873:T1000A;ENSP00000426343:T869A	ENSP00000264663:T1000A	T	+	1	0	NNT	43738482	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.962000	0.93254	2.195000	0.70347	0.533000	0.62120	ACT	.	.		0.313	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		G	43702725	A	G	43702725	3	3	170	1	0	0	0	0	1	0	0	0	10519	391	14	2	3076	2	NNT	5	43702725	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	27239058	43702725	137212535	63	25754										
GPR98	84059	hgsc.bcm.edu	37	chr5	89943496	89943496	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	atttttgaggttggaagtagAcagcagagcatatccatatt	10	5	0	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:89943496A>G	ENST00000405460.2	+	17	3300	c.3204A>G	c.(3202-3204)agA>agG	p.R1068R		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1068	Calx-beta 8. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTGGAAGTAGACAGCAGAGCA	0.398																																					p.R1068R		Atlas-SNP	.											.	GPR98	605	.	0			c.A3204G						.						147	142	144					5																	89943496		1883	4109	5992	SO:0001819	synonymous_variant	84059	exon17			AAGTAGACAGCAG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.3204A>G	chr5.hg19:g.89943496A>G		140.0	0.0		125.0	38.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	5.523	0.281429	0.10458	.	.	ENSG00000164199	ENST00000504142	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	T	0.71710	0.3372	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71174	-0.4670	4	.	.	.	.	15.5764	0.76392	1.0:0.0:0.0:0.0	.	.	.	.	A	657	.	.	T	+	1	0	GPR98	89979252	1.000000	0.71417	1.000000	0.80357	0.392000	0.30506	3.251000	0.51453	2.082000	0.62665	0.528000	0.53228	ACA	.	.		0.398	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	89943496	A	G	89943496	2	3	170	1	0	0	0	0	0	0	0	1	6730	272	10	2		2	GPR98	5	89943496	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	46240771	89943496	90971764	64	25755										
GIN1	54826	hgsc.bcm.edu	37	chr5	102432254	102432254	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cagatatttaccttgttcacTggattctcttatgtagggct	8	8	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:102432254T>A	ENST00000399004.2	-	7	1379	c.1285A>T	c.(1285-1287)Agt>Tgt	p.S429C	GIN1_ENST00000508629.1_Intron	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	429					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		CCTTGTTCACTGGATTCTCTT	0.378																																					p.S429C		Atlas-SNP	.											.	GIN1	53	.	0			c.A1285T						.						164	154	157					5																	102432254		1857	4095	5952	SO:0001583	missense	54826	exon7			GTTCACTGGATTC	BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"gypsy integrase 1", "Ty3/Gypsy integrase 1"		"zinc finger, H2C2 domain containing"	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.1285A>T	chr5.hg19:g.102432254T>A	ENSP00000381970:p.Ser429Cys	119.0	0.0		121.0	34.0	NM_017676	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Missense_Mutation	SNP	ENST00000399004.2	hg19	CCDS43349.1	.	.	.	.	.	.	.	.	.	.	T	8.596	0.885773	0.17540	.	.	ENSG00000145723	ENST00000399004	T	0.19938	2.11	5.77	2.13	0.27403	.	0.528262	0.15667	U	0.250600	T	0.11707	0.0285	N	0.14661	0.345	0.09310	N	1	P	0.40660	0.726	B	0.40101	0.319	T	0.12708	-1.0537	10	0.72032	D	0.01	-16.1771	5.15	0.15005	0.0:0.283:0.1487:0.5683	.	429	Q9NXP7	GIN1_HUMAN	C	429	ENSP00000381970:S429C	ENSP00000381970:S429C	S	-	1	0	GIN1	102460153	0.073000	0.21202	0.976000	0.42696	0.259000	0.26198	0.307000	0.19296	0.462000	0.27095	-0.256000	0.11100	AGT	.	.		0.378	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		A	102432254	T	A	102432254	3	1	170	1	0	0	0	0	1	0	0	0	6394	1580	55	4	291	4	GIN1	5	102432254	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	12488758	102432254	78483006	65	25756										
AQPEP	206338	hgsc.bcm.edu	37	chr5	115336354	115336354	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tctatggaggcattttcaaaTggtaattgtcctactttctg	8	7	3	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:115336354T>C	ENST00000357872.4	+	9	1770	c.1646T>C	c.(1645-1647)aTg>aCg	p.M549T	AQPEP_ENST00000395528.2_Splice_Site_p.M66T	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		549						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CATTTTCAAATGGTAATTGTC	0.368																																					p.M549T		Atlas-SNP	.											.	.	.	.	0			c.T1646C						.						96	95	96					5																	115336354		2202	4300	6502	SO:0001630	splice_region_variant	0	exon9			TTCAAATGGTAAT																												ENST00000357872.4:c.1647+1T>C	chr5.hg19:g.115336354T>C		97.0	0.0		99.0	27.0	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	hg19	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	T	10.94	1.493909	0.26774	.	.	ENSG00000172901	ENST00000395528;ENST00000357872;ENST00000379578	T;T	0.04275	3.66;3.66	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.07098	0.0180	L	0.28776	0.89	0.43292	D	0.995279	D	0.54207	0.965	P	0.50049	0.629	T	0.42050	-0.9474	10	0.36615	T	0.2	.	11.1922	0.48691	0.1376:0.0:0.0:0.8624	.	549	Q6Q4G3	AMPQ_HUMAN	T	66;549;538	ENSP00000378899:M66T;ENSP00000350541:M549T	ENSP00000350541:M549T	M	+	2	0	AC010282.1	115364253	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.939000	0.40213	2.371000	0.80710	0.533000	0.62120	ATG	.	.		0.368	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		Missense_Mutation	C	115336354	T	C	115336354	5	2	170	1	0	0	0	0	0	0	1	0	834	1478	51	2	1680	2	AQPEP	5	115336354	Splice_Site	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	12904100	115336354	65578906	66	25757										
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140589674	140589674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgctaaaatcttcggtaaatAattactacactttggaaaca	5	7	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:140589674A>G	ENST00000239450.2	+	1	1384	c.1195A>G	c.(1195-1197)Aat>Gat	p.N399D	PCDHB12_ENST00000541609.1_Missense_Mutation_p.N62D	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	399	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTCGGTAAATAATTACTACAC	0.488																																					p.N399D		Atlas-SNP	.											.	PCDHB12	179	.	0			c.A1195G						.						63	66	65					5																	140589674		2203	4300	6503	SO:0001583	missense	56124	exon1			GTAAATAATTACT	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1195A>G	chr5.hg19:g.140589674A>G	ENSP00000239450:p.Asn399Asp	156.0	0.0		190.0	46.0	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	hg19	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.729554	0.48833	.	.	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.47177	0.85;0.85	3.87	3.87	0.44632	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.66665	0.2812	M	0.91406	3.205	0.35734	D	0.818144	P	0.39551	0.678	P	0.49387	0.609	T	0.79274	-0.1871	9	0.62326	D	0.03	.	12.6328	0.56667	1.0:0.0:0.0:0.0	.	399	Q9Y5F1	PCDBC_HUMAN	D	62;399;19	ENSP00000440199:N62D;ENSP00000239450:N399D	ENSP00000239450:N399D	N	+	1	0	PCDHB12	140569858	0.102000	0.21896	0.775000	0.31657	0.174000	0.22865	1.756000	0.38390	1.518000	0.48934	0.402000	0.26972	AAT	.	.		0.488	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		G	140589674	A	G	140589674	3	3	170	1	0	0	0	0	1	0	0	0	11546	362	13	2	1197	2	PCDHB12	5	140589674	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	25253320	140589674	40325586	67	25758										
LARS	51520	hgsc.bcm.edu	37	chr5	145512586	145512586	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	atacctgcatctgccatggcTtccacaaagttggcatcttc	7	13	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:145512586T>A	ENST00000394434.2	-	23	2437	c.2271A>T	c.(2269-2271)gaA>gaT	p.E757D	LARS_ENST00000510191.1_Missense_Mutation_p.E703D|LARS_ENST00000274562.9_Missense_Mutation_p.E730D|LARS_ENST00000545646.1_Missense_Mutation_p.E711D	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	757					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	CTGCCATGGCTTCCACAAAGT	0.463																																					p.E757D		Atlas-SNP	.											.	LARS	100	.	0			c.A2271T						.						99	89	92					5																	145512586		2203	4300	6503	SO:0001583	missense	51520	exon23			CATGGCTTCCACA	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"Aminoacyl tRNA synthetases / Class I"	6512	protein-coding gene	gene with protein product	"leucine tRNA ligase 1, cytoplasmic"	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.2271A>T	chr5.hg19:g.145512586T>A	ENSP00000377954:p.Glu757Asp	142.0	0.0		121.0	38.0	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Missense_Mutation	SNP	ENST00000394434.2	hg19	CCDS34265.1	.	.	.	.	.	.	.	.	.	.	T	17.26	3.343682	0.61073	.	.	ENSG00000133706	ENST00000394434;ENST00000539715;ENST00000545646;ENST00000540713;ENST00000510191;ENST00000274562	T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.88220	0.6378	M	0.83692	2.655	0.58432	D	0.999999	B;D;B	0.67145	0.023;0.996;0.344	B;D;B	0.76071	0.024;0.987;0.099	D	0.87771	0.2605	10	0.34782	T	0.22	-25.1828	15.6849	0.77402	0.0:0.0:0.0:1.0	.	730;711;757	B4DER1;F5H698;Q9P2J5	.;.;SYLC_HUMAN	D	757;66;711;66;703;730	ENSP00000377954:E757D;ENSP00000437791:E711D;ENSP00000426005:E703D;ENSP00000274562:E730D	ENSP00000274562:E730D	E	-	3	2	LARS	145492779	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	6.087000	0.71362	2.103000	0.63969	0.529000	0.55759	GAA	.	.		0.463	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		A	145512586	T	A	145512586	3	1	170	1	0	0	0	0	1	0	0	0	8643	1606	56	4	1299	4	LARS	5	145512586	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	4922912	145512586	35402674	68	25759										
WWC1	23286	hgsc.bcm.edu	37	chr5	167833201	167833201	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tttcccattaactgtctcctAgaatcgataagaaaatgtct	5	9	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:167833201A>T	ENST00000265293.4	+	6	1092		c.e6-1		WWC1_ENST00000521089.1_Splice_Site	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1						cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		ACTGTCTCCTAGAATCGATAA	0.478																																					.		Atlas-SNP	.											.	WWC1	98	.	0			c.591-2A>T						.						123	111	115					5																	167833201		2203	4300	6503	SO:0001630	splice_region_variant	23286	exon6			TCTCCTAGAATCG	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.591-1A>T	chr5.hg19:g.167833201A>T		104.0	0.0		122.0	45.0	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Splice_Site	SNP	ENST00000265293.4	hg19	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.059775	0.76074	.	.	ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000393895	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5264	0.75910	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WWC1	167765779	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.251000	0.95483	2.078000	0.62432	0.459000	0.35465	.	.	.		0.478	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	Intron	T	167833201	A	T	167833201	5	4	170	1	0	0	0	0	0	0	1	0	17426	434	15	4	611	4	WWC1	5	167833201	Splice_Site	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	22320615	167833201	13082059	69	25760										
PANK3	79646	hgsc.bcm.edu	37	chr5	167986088	167986088	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ccttttgaccagtaatccagTgcatatgccaaaagtttcat	6	10	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:167986088T>G	ENST00000239231.6	-	6	1327	c.1011A>C	c.(1009-1011)gcA>gcC	p.A337A	MIR103A1_ENST00000362165.1_RNA|PANK3_ENST00000520504.1_5'UTR	NM_024594.3	NP_078870.1	Q9H999	PANK3_HUMAN	pantothenate kinase 3	337					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			NS(1)|cervix(2)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	Renal(175;0.000159)|Lung NSC(126;0.0441)|all_lung(126;0.0909)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0989)|OV - Ovarian serous cystadenocarcinoma(192;0.147)|Epithelial(171;0.188)		AGTAATCCAGTGCATATGCCA	0.308																																					p.A337A		Atlas-SNP	.											.	PANK3	39	.	0			c.A1011C						.						108	105	106					5																	167986088		2202	4300	6502	SO:0001819	synonymous_variant	79646	exon6			ATCCAGTGCATAT	AK022961	CCDS4368.1	5q35.1	2008-02-05			ENSG00000120137	ENSG00000120137			19365	protein-coding gene	gene with protein product		606161				11479594	Standard	NM_024594		Approved	FLJ12899	uc003lzz.2	Q9H999	OTTHUMG00000130410	ENST00000239231.6:c.1011A>C	chr5.hg19:g.167986088T>G		115.0	0.0		108.0	28.0	NM_024594	D3DQL1|Q53FJ9|Q7RTX4	Silent	SNP	ENST00000239231.6	hg19	CCDS4368.1																																																																																			.	.		0.308	PANK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252793.2	NM_024594		G	167986088	T	G	167986088	2	3	170	1	0	0	0	0	0	0	0	1	11427	1683	59	5		5	PANK3	5	167986088	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	152887	167986088	12929172	70	25761										
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178541174	178541174	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tcaatgtcgttgtgcttcccAggcggtggctctatcctgcc	11	13	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr5:178541174A>T	ENST00000251582.7	-	22	3431	c.3330T>A	c.(3328-3330)ccT>ccA	p.P1110P		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	1110					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		TGTGCTTCCCAGGCGGTGGCT	0.592																																					p.P1110P		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.T3330A						.						179	135	150					5																	178541174		2203	4300	6503	SO:0001819	synonymous_variant	9509	exon22			CTTCCCAGGCGGT	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.3330T>A	chr5.hg19:g.178541174A>T		135.0	0.0		294.0	54.0	NM_014244		Silent	SNP	ENST00000251582.7	hg19	CCDS4444.1																																																																																			.	.		0.592	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		T	178541174	A	T	178541174	2	4	170	1	0	0	0	0	0	0	0	1	265	175	7	4		4	ADAMTS2	5	178541174	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	10555086	178541174	2374086	71	25762										
STK19	8859	hgsc.bcm.edu	37	chr6	31940408	31940408	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	atctgcccagggtcggcgcgCgcggctgtctcagaactcat	13	14	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr6:31940408C>T	ENST00000375333.2	+	3	494	c.441C>T	c.(439-441)cgC>cgT	p.R147R	DXO_ENST00000375349.3_5'Flank|DXO_ENST00000478221.1_5'Flank|DXO_ENST00000337523.5_5'Flank|DXO_ENST00000375356.3_5'Flank|STK19_ENST00000463823.1_Intron|STK19_ENST00000375331.2_Silent_p.R147R	NM_032454.1	NP_115830.1	P49842	STK19_HUMAN	serine/threonine kinase 19	147					protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			skin(5)|upper_aerodigestive_tract(2)	7						GGTCGGCGCGCGCGGCTGTCT	0.652																																					p.R147R		Atlas-SNP	.											.	STK19	33	.	0			c.C441T						.						56	66	62					6																	31940408		2203	4299	6502	SO:0001819	synonymous_variant	8859	exon3			GGCGCGCGCGGCT	X77474	CCDS4733.1, CCDS34417.1	6p21.33	2011-09-15			ENSG00000204344	ENSG00000204344			11398	protein-coding gene	gene with protein product		604977				8012361, 9812991	Standard	NM_032454		Approved	D6S60, G11, RP1	uc003nyv.3	P49842	OTTHUMG00000166424	ENST00000375333.2:c.441C>T	chr6.hg19:g.31940408C>T		93.0	0.0		108.0	21.0	NM_032454	A6NF95|A6NFW8|B0QZR5|Q13159|Q31617|Q5JP77|Q5ST72|Q5ST75	Silent	SNP	ENST00000375333.2	hg19	CCDS4733.1																																																																																			.	.		0.652	STK19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076484.3			T	31940408	C	T	31940408	2	4	170	1	0	0	0	0	0	0	0	1	15307	755	27	1		1	STK19	6	31940408	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10		31940408	139174659	72	25763										
HLA-DOB	3112	hgsc.bcm.edu	37	chr6	32782304	32782304	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	atcccctggatagaagcctgTcacagagcagtgcagcagat	11	11	1	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr6:32782304T>A	ENST00000438763.2	-	3	532	c.436A>T	c.(436-438)Aca>Tca	p.T146S	TAP2_ENST00000452392.2_Missense_Mutation_p.T753S	NM_002120.3	NP_002111.1	P13765	DOB_HUMAN	major histocompatibility complex, class II, DO beta	146	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	9						TAGAAGCCTGTCACAGAGCAG	0.537																																					p.T146S		Atlas-SNP	.											.	HLA-DOB	17	.	0			c.A436T						.						197	200	199					6																	32782304		1511	2709	4220	SO:0001583	missense	3112	exon3			AGCCTGTCACAGA		CCDS4754.1	6p21.3	2013-01-11			ENSG00000241106	ENSG00000241106		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4937	protein-coding gene	gene with protein product		600629					Standard	NM_002120		Approved			P13765	OTTHUMG00000031213	ENST00000438763.2:c.436A>T	chr6.hg19:g.32782304T>A	ENSP00000390020:p.Thr146Ser	139.0	0.0		165.0	27.0	NM_002120	B0V0Y0|Q29746|Q29825|Q6FHC2	Missense_Mutation	SNP	ENST00000438763.2	hg19	CCDS4754.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.2|20.2	3.952157|3.952157	0.73787|0.73787	.|.	.|.	ENSG00000241106|ENSG00000241106;ENSG00000204267;ENSG00000250264	ENST00000447394|ENST00000438763;ENST00000556934;ENST00000452392	.|T;T	.|0.03004	.|4.08;4.08	3.96|3.96	3.96|3.96	0.45880|0.45880	.|Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	.|0.366720	.|0.31177	.|N	.|0.008106	T|T	0.01905|0.01905	0.0060|0.0060	L|L	0.41710|0.41710	1.295|1.295	0.31948|0.31948	N|N	0.610026|0.610026	.|D;P;B	.|0.56746	.|0.977;0.626;0.425	.|P;B;B	.|0.52424	.|0.698;0.253;0.144	T|T	0.42344|0.42344	-0.9457|-0.9457	5|10	.|0.10902	.|T	.|0.67	-52.6371|-52.6371	6.1596|6.1596	0.20356|0.20356	0.0:0.1101:0.0:0.8899|0.0:0.1101:0.0:0.8899	.|.	.|146;753;146	.|B7Z742;E7ENX8;P13765	.|.;.;DOB_HUMAN	V|S	129|146;753;753	.|ENSP00000390020:T146S;ENSP00000391806:T753S	.|ENSP00000390020:T146S	D|T	-|-	2|1	0|0	HLA-DOB|XXbac-BPG246D15.9;TAP2;HLA-DOB	32890282|32890282	0.721000|0.721000	0.28007|0.28007	0.981000|0.981000	0.43875|0.43875	0.929000|0.929000	0.56500|0.56500	1.462000|1.462000	0.35266|0.35266	2.019000|2.019000	0.59389|0.59389	0.523000|0.523000	0.50628|0.50628	GAC|ACA	.	.		0.537	HLA-DOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076439.1	NM_002120		A	32782304	T	A	32782304	3	1	170	1	0	0	0	0	1	0	0	0	7210	1667	58	4	401	4	HLA-DOB	6	32782304	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	841896	32782304	138332763	73	25764										
FTSJD2	23070	hgsc.bcm.edu	37	chr6	37411922	37411922	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	taatagcgtctcccagaagcTtatggtatgtcagcgcttgg	11	9	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr6:37411922T>A	ENST00000373451.4	+	3	445	c.281T>A	c.(280-282)cTt>cAt	p.L94H		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	94	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)										TCCCAGAAGCTTATGGTATGT	0.438																																					p.L94H		Atlas-SNP	.											.	FTSJD2	64	.	0			c.T281A						.						129	123	125					6																	37411922		2203	4300	6503	SO:0001583	missense	23070	exon3			AGAAGCTTATGGT	BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"G patch domain containing"	21077	protein-coding gene	gene with protein product			"KIAA0082", "FtsJ methyltransferase domain containing 2"	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.281T>A	chr6.hg19:g.37411922T>A	ENSP00000362550:p.Leu94His	55.0	0.0		77.0	23.0	NM_015050	A8K949|Q14670|Q96FJ9	Missense_Mutation	SNP	ENST00000373451.4	hg19	CCDS4835.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.703253	0.88924	.	.	ENSG00000137200	ENST00000373451;ENST00000455891;ENST00000373427	T;T	0.38887	1.11;1.11	5.82	5.82	0.92795	D111/G-patch (3);	0.060697	0.64402	D	0.000002	T	0.60676	0.2287	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.81914	0.995;0.963	T	0.66929	-0.5799	9	.	.	.	-16.8521	13.9171	0.63905	0.0:0.0:0.0:1.0	.	94;94	Q5T7F5;Q8N1G2	.;MTR1_HUMAN	H	94	ENSP00000362550:L94H;ENSP00000414233:L94H	.	L	+	2	0	FTSJD2	37519900	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.901000	0.75693	2.229000	0.72834	0.397000	0.26171	CTT	.	.		0.438	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050		A	37411922	T	A	37411922	3	1	170	1	0	0	0	0	1	0	0	0	6099	1609	56	4	287	4	FTSJD2	6	37411922	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	4629618	37411922	133703145	74	25765										
TTBK1	84630	hgsc.bcm.edu	37	chr6	43250465	43250465	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cctgtgtatgccccttgcagGtgttctccgtggcgccccca	11	16	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr6:43250465G>A	ENST00000259750.4	+	14	2070	c.1987G>A	c.(1987-1989)Gtg>Atg	p.V663M		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	663					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			CCCCTTGCAGGTGTTCTCCGT	0.607																																					p.V663M		Atlas-SNP	.											TTBK1,NS,carcinoma,0,1	TTBK1	124	.	0			c.G1987A						.						72	80	77					6																	43250465		2203	4300	6503	SO:0001630	splice_region_variant	84630	exon14			TTGCAGGTGTTCT	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.1987-1G>A	chr6.hg19:g.43250465G>A		56.0	0.0		89.0	26.0	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	hg19	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.853587	0.51270	.	.	ENSG00000146216	ENST00000259750	T	0.27104	1.69	4.27	2.44	0.29823	.	0.105307	0.38217	N	0.001776	T	0.09818	0.0241	L	0.29908	0.895	0.80722	D	1	P	0.52316	0.952	P	0.45881	0.496	T	0.06752	-1.0809	9	.	.	.	.	8.612	0.33808	0.1966:0.0:0.8034:0.0	.	663	Q5TCY1	TTBK1_HUMAN	M	663	ENSP00000259750:V663M	.	V	+	1	0	TTBK1	43358443	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	3.562000	0.53777	0.774000	0.33427	0.555000	0.69702	GTG	.	.		0.607	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		Missense_Mutation	A	43250465	G	A	43250465	5	1	170	1	0	0	0	0	0	0	1	0	16691	1275	44	3	2037	3	TTBK1	6	43250465	Splice_Site	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	5838543	43250465	127864602	75	25766										
RUNX2	860	hgsc.bcm.edu	37	chr6	45390466	45390466	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cagcagcagcagcagcagcaAcagcagcagcagcagcagga	13	13	0	0	rs575896136	byFrequency	TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr6:45390466A>G	ENST00000371438.1	+	2	553	c.195A>G	c.(193-195)caA>caG	p.Q65Q	RUNX2_ENST00000576263.1_Silent_p.Q65Q|RUNX2_ENST00000371432.3_Silent_p.Q51Q|RUNX2_ENST00000465038.2_Silent_p.Q65Q|RUNX2_ENST00000352853.5_Silent_p.Q133Q|RUNX2_ENST00000359524.5_Silent_p.Q51Q|RUNX2_ENST00000541979.1_Silent_p.Q133Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371436.6_Silent_p.Q65Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	65	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcaacagcagcagc	0.731													A|||	8	0.00159744	0.0023	0	5008	,	,		7675	0.002		0	False		,,,				2504	0.0031				p.Q65Q		Atlas-SNP	.											.	RUNX2	128	.	0			c.A195G						.						10	15	14					6																	45390466		1452	3071	4523	SO:0001819	synonymous_variant	860	exon3			GCAGCAACAGCAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.195A>G	chr6.hg19:g.45390466A>G		67.0	0.0		69.0	4.0	NM_001024630	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	hg19	CCDS43467.2																																																																																			.	.		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390466	A	G	45390466	2	3	170	1	0	0	0	0	0	0	0	1	13763	40	2	2		2	RUNX2	6	45390466	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	2140001	45390466	125724601	76	25767										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51613247	51613247	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tattagtgacagtataggccTgaccctctaaatctatgcca	7	10	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr6:51613247T>A	ENST00000371117.3	-	58	9442	c.9167A>T	c.(9166-9168)cAg>cTg	p.Q3056L	PKHD1_ENST00000340994.4_Missense_Mutation_p.Q3056L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3056					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGTATAGGCCTGACCCTCTAA	0.493																																					p.Q3056L		Atlas-SNP	.											.	PKHD1	927	.	0			c.A9167T						.						106	95	99					6																	51613247		2203	4300	6503	SO:0001583	missense	5314	exon58			TAGGCCTGACCCT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.9167A>T	chr6.hg19:g.51613247T>A	ENSP00000360158:p.Gln3056Leu	57.0	0.0		64.0	20.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.301049	0.60195	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.80738	-1.41;-1.29	5.86	5.86	0.93980	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.414937	0.25156	N	0.032706	T	0.71953	0.3401	M	0.66939	2.045	0.35596	D	0.807473	P;B;P	0.39920	0.695;0.43;0.485	B;B;B	0.39339	0.297;0.142;0.297	T	0.74532	-0.3634	10	0.31617	T	0.26	.	15.448	0.75248	0.0:0.0:0.0:1.0	.	3056;3056;3056	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	L	3056	ENSP00000360158:Q3056L;ENSP00000341097:Q3056L	ENSP00000341097:Q3056L	Q	-	2	0	PKHD1	51721206	0.806000	0.28996	0.968000	0.41197	0.964000	0.63967	3.735000	0.55044	2.240000	0.73641	0.533000	0.62120	CAG	.	.		0.493	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51613247	T	A	51613247	3	1	170	1	0	0	0	0	1	0	0	0	11980	1580	55	4	3136	4	PKHD1	6	51613247	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	6222781	51613247	119501820	77	25768										
GOPC	57120	hgsc.bcm.edu	37	chr6	117884420	117884420	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctggagatatggtcaatttaAtaagattttttatgatacag	8	3	1	3	rs139949957	byFrequency	TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr6:117884420A>G	ENST00000368498.2	-	9	1461	c.1386T>C	c.(1384-1386)taT>taC	p.Y462Y	DCBLD1_ENST00000296955.8_Intron|GOPC_ENST00000535237.1_Silent_p.Y462Y|GOPC_ENST00000467125.1_Intron|GOPC_ENST00000052569.6_Silent_p.Y454Y	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	462					apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)		GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		GGTCAATTTAATAAGATTTTT	0.413			O	ROS1	glioblastoma																																p.Y462Y		Atlas-SNP	.		Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	.	GOPC	29	.	0			c.T1386C						.						106	109	108					6																	117884420		2203	4300	6503	SO:0001819	synonymous_variant	57120	exon9			AATTTAATAAGAT	AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.1386T>C	chr6.hg19:g.117884420A>G		38.0	0.0		43.0	18.0	NM_020399	A6NM30|Q59FS4|Q969U8	Silent	SNP	ENST00000368498.2	hg19	CCDS5117.1																																																																																			.	.		0.413	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399		G	117884420	A	G	117884420	2	3	170	1	0	0	0	0	0	0	0	1	6581	108	4	2		2	GOPC	6	117884420	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	66271173	117884420	53230647	78	25769										
KATNA1	11104	hgsc.bcm.edu	37	chr6	149959640	149959640	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agtttcccagcaatgcatatTcacgagccaattttacattc	5	11	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr6:149959640T>A	ENST00000335647.5	-	1	88	c.44A>T	c.(43-45)gAa>gTa	p.E15V	KATNA1_ENST00000367411.2_Missense_Mutation_p.E15V|KATNA1_ENST00000335643.8_Missense_Mutation_p.E15V					katanin p60 (ATPase containing) subunit A 1											endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	12		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		CAATGCATATTCACGAGCCAA	0.358																																					p.E15V		Atlas-SNP	.											.	KATNA1	34	.	0			c.A44T						.						171	176	175					6																	149959640		2203	4300	6503	SO:0001583	missense	11104	exon2			GCATATTCACGAG	AF056022	CCDS5217.1, CCDS56456.1	6q24.3	2011-01-25	2011-01-25		ENSG00000186625	ENSG00000186625		"ATPases / AAA-type"	6216	protein-coding gene	gene with protein product		606696	"katanin p60 (ATPase-containing) subunit A 1"			9658175	Standard	NM_007044		Approved		uc003qms.3	O75449	OTTHUMG00000015787	ENST00000335647.5:c.44A>T	chr6.hg19:g.149959640T>A	ENSP00000335106:p.Glu15Val	104.0	0.0		140.0	57.0	NM_007044		Missense_Mutation	SNP	ENST00000335647.5	hg19	CCDS5217.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.841510	0.91197	.	.	ENSG00000186625	ENST00000335647;ENST00000335643;ENST00000367411;ENST00000444282;ENST00000420200	T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.53738	0.1815	M	0.78049	2.395	0.80722	D	1	D;D;D	0.76494	0.992;0.999;0.998	D;D;D	0.80764	0.955;0.994;0.973	T	0.57039	-0.7879	9	.	.	.	.	16.1166	0.81309	0.0:0.0:0.0:1.0	.	15;15;15	A8K7S5;O75449-2;O75449	.;.;KTNA1_HUMAN	V	15	ENSP00000335106:E15V;ENSP00000335180:E15V;ENSP00000356381:E15V;ENSP00000390322:E15V;ENSP00000398993:E15V	.	E	-	2	0	KATNA1	150001333	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.692000	0.84203	2.204000	0.70986	0.529000	0.55759	GAA	.	.		0.358	KATNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042641.2	NM_007044		A	149959640	T	A	149959640	3	1	170	1	0	0	0	0	1	0	0	0	7993	1783	62	4	1471	4	KATNA1	6	149959640	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	32075220	149959640	21155427	79	25770										
POLM	27434	hgsc.bcm.edu	37	chr7	44119332	44119332	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gctgcctcggccagtatctcCagagcctcctgcagggaggg	14	14	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr7:44119332C>G	ENST00000242248.5	-	4	581	c.480G>C	c.(478-480)ctG>ctC	p.L160L	POLM_ENST00000492971.1_5'Flank|POLM_ENST00000335195.6_Silent_p.L160L|POLM_ENST00000395831.3_Silent_p.L160L	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	160					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(3)|skin(2)	22						CCAGTATCTCCAGAGCCTCCT	0.657								DNA polymerases (catalytic subunits)																													p.L160L		Atlas-SNP	.											.	POLM	50	.	0			c.G480C						.						34	37	36					7																	44119332		2203	4300	6503	SO:0001819	synonymous_variant	27434	exon4			TATCTCCAGAGCC	AF176097	CCDS34625.1, CCDS64635.1, CCDS64636.1	7p13	2012-05-18			ENSG00000122678	ENSG00000122678		"DNA polymerases"	9185	protein-coding gene	gene with protein product	"Pol iota"	606344				10982892	Standard	XM_005249708		Approved	Tdt-N	uc003tjt.3	Q9NP87	OTTHUMG00000155353	ENST00000242248.5:c.480G>C	chr7.hg19:g.44119332C>G		36.0	0.0		42.0	23.0	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Silent	SNP	ENST00000242248.5	hg19	CCDS34625.1																																																																																			.	.		0.657	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284		G	44119332	C	G	44119332	2	3	170	1	0	0	0	0	0	0	0	1	12215	581	21	4		4	POLM	7	44119332	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10		44119332	115019331	80	25771										
PTPN12	5782	hgsc.bcm.edu	37	chr7	77236577	77236577	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gctgtggaagaacaggtgccAtttgtgccatagattatacg	12	7	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr7:77236577A>G	ENST00000248594.6	+	9	993	c.721A>G	c.(721-723)Att>Gtt	p.I241V	PTPN12_ENST00000415482.2_Missense_Mutation_p.I122V|PTPN12_ENST00000435495.2_Missense_Mutation_p.I111V	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	241	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						AACAGGTGCCATTTGTGCCAT	0.294																																					p.I241V		Atlas-SNP	.											.	PTPN12	83	.	0			c.A721G						.						110	115	113					7																	77236577		2203	4299	6502	SO:0001583	missense	5782	exon9			GGTGCCATTTGTG		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.721A>G	chr7.hg19:g.77236577A>G	ENSP00000248594:p.Ile241Val	163.0	0.0		195.0	41.0	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	hg19	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.986388	0.74589	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;D;D	0.83075	2.81;-1.68;-1.68	5.68	5.68	0.88126	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.87589	0.6215	L	0.44542	1.39	0.53688	D	0.999979	D	0.62365	0.991	D	0.67382	0.951	D	0.88735	0.3239	10	0.72032	D	0.01	.	15.9283	0.79639	1.0:0.0:0.0:0.0	.	241	Q05209	PTN12_HUMAN	V	241;122;122;111	ENSP00000248594:I241V;ENSP00000392429:I122V;ENSP00000397991:I111V	ENSP00000248594:I241V	I	+	1	0	PTPN12	77074513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.074000	0.76791	2.170000	0.68504	0.460000	0.39030	ATT	.	.		0.294	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			G	77236577	A	G	77236577	3	3	170	1	0	0	0	0	1	0	0	0	12794	217	8	2	755	2	PTPN12	7	77236577	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	33117245	77236577	81902086	81	25772										
SGCE	8910	hgsc.bcm.edu	37	chr7	94252667	94252667	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cattatattaattatcaaatTatgccttgcagtctcaaagg	5	7	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr7:94252667T>A	ENST00000265735.7	-	4	543	c.433A>T	c.(433-435)Aat>Tat	p.N145Y	SGCE_ENST00000428696.2_Missense_Mutation_p.N145Y|SGCE_ENST00000445866.2_Missense_Mutation_p.N145Y|SGCE_ENST00000447873.1_Missense_Mutation_p.N145Y|SGCE_ENST00000415788.2_Missense_Mutation_p.N181Y|SGCE_ENST00000437425.2_Missense_Mutation_p.N104Y	NM_003919.2	NP_003910.1	O43556	SGCE_HUMAN	sarcoglycan, epsilon	145					cell-matrix adhesion (GO:0007160)|muscle organ development (GO:0007517)	cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|dystrophin-associated glycoprotein complex (GO:0016010)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	14	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			ATTATCAAATTATGCCTTGCA	0.274																																					p.N145Y		Atlas-SNP	.											.	SGCE	68	.	0			c.A433T						.						40	41	40					7																	94252667		2202	4285	6487	SO:0001583	missense	8910	exon4			TCAAATTATGCCT	AF036364	CCDS5637.1, CCDS47642.1, CCDS47643.1, CCDS75634.1	7q21.3	2014-09-17			ENSG00000127990	ENSG00000127990			10808	protein-coding gene	gene with protein product		604149		DYT11		9475163, 9405466	Standard	NM_001099401		Approved		uc003unn.2	O43556	OTTHUMG00000022828	ENST00000265735.7:c.433A>T	chr7.hg19:g.94252667T>A	ENSP00000265735:p.Asn145Tyr	239.0	0.0		314.0	77.0	NM_001099401	B2R8N2|D6W5Q8|E9PF60|G5E9K6|Q6L8P0|Q75MH8|Q8NFG8|Q8WW28	Missense_Mutation	SNP	ENST00000265735.7	hg19	CCDS5637.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.118880	0.77323	.	.	ENSG00000127990	ENST00000265735;ENST00000445866;ENST00000437425;ENST00000447873;ENST00000428696;ENST00000415788	D;D;D;D;D;D	0.97710	-4.5;-4.5;-4.5;-4.5;-4.5;-4.5	5.35	5.35	0.76521	Dystroglycan-type cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.97353	0.9134	L	0.44542	1.39	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.997;0.991;0.997;0.999	D;D;D;P;D	0.87578	0.994;0.996;0.926;0.879;0.998	D	0.95540	0.8611	10	0.02654	T	1	-26.2513	15.631	0.76908	0.0:0.0:0.0:1.0	.	181;104;145;145;145	B7Z2R4;E9PEH6;E9PF60;G5E9K6;O43556	.;.;.;.;SGCE_HUMAN	Y	145;145;104;145;145;181	ENSP00000265735:N145Y;ENSP00000398930:N145Y;ENSP00000394061:N104Y;ENSP00000388734:N145Y;ENSP00000397536:N145Y;ENSP00000405313:N181Y	ENSP00000265735:N145Y	N	-	1	0	SGCE	94090603	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.499000	0.81566	2.161000	0.67846	0.528000	0.53228	AAT	.	.		0.274	SGCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255251.2			A	94252667	T	A	94252667	3	1	170	1	0	0	0	0	1	0	0	0	14217	1754	61	4	1064	4	SGCE	7	94252667	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	17016090	94252667	64885996	82	25773										
ACHE	43	hgsc.bcm.edu	37	chr7	100490380	100490380	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gactcgttgtctttgctgaaGcctggggccccgtaaaccag	12	12	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr7:100490380G>A	ENST00000412389.1	-	2	1283	c.1128C>T	c.(1126-1128)ggC>ggT	p.G376G	ACHE_ENST00000428317.1_Silent_p.G376G|ACHE_ENST00000302913.4_Silent_p.G376G|ACHE_ENST00000411582.1_Silent_p.G376G|ACHE_ENST00000419336.2_Intron|ACHE_ENST00000241069.5_Silent_p.G376G			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	376					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	CTTTGCTGAAGCCTGGGGCCC	0.647																																					p.G376G		Atlas-SNP	.											.	ACHE	80	.	0			c.C1128T						.						22	25	24					7																	100490380		2203	4299	6502	SO:0001819	synonymous_variant	43	exon3			GCTGAAGCCTGGG		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"Blood group antigens"	108	protein-coding gene	gene with protein product	"Yt blood group"	100740	"acetylcholinesterase (YT blood group)", "acetylcholinesterase (Yt blood group)", "acetylcholinesterase"	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1128C>T	chr7.hg19:g.100490380G>A		70.0	0.0		67.0	24.0	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Silent	SNP	ENST00000412389.1	hg19	CCDS5709.1																																																																																			.	.		0.647	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831		A	100490380	G	A	100490380	2	1	170	1	0	0	0	0	0	0	0	1	141	958	34	3		3	ACHE	7	100490380	Silent	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	6237713	100490380	58648283	83	25774										
KCNH2	3757	hgsc.bcm.edu	37	chr7	150671846	150671846	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctttgcgctcctcggcgcccAgcagtgcctgcgcgatctgc	12	17	1	0	rs199473495		TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr7:150671846A>G	ENST00000262186.5	-	2	661	c.260T>C	c.(259-261)cTg>cCg	p.L87P	KCNH2_ENST00000430723.3_Missense_Mutation_p.L87P	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	87					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	CTCGGCGCCCAGCAGTGCCTG	0.721																																					p.L87P	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.T260C	GRCh37	CM022800	KCNH2	M		.						11	11	11					7																	150671846		2179	4235	6414	SO:0001583	missense	3757	exon2			GCGCCCAGCAGTG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.260T>C	chr7.hg19:g.150671846A>G	ENSP00000262186:p.Leu87Pro	168.0	0.0		213.0	88.0	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	hg19	CCDS5910.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.052130	0.75960	.	.	ENSG00000055118	ENST00000262186;ENST00000430723	D;D	0.99591	-6.24;-6.24	4.44	4.44	0.53790	PAS (2);PAS fold (1);	0.478913	0.16060	N	0.231507	D	0.99585	0.9850	M	0.86420	2.815	0.80722	D	1	D;P	0.76494	0.999;0.913	D;D	0.79108	0.992;0.935	D	0.98260	1.0498	10	0.66056	D	0.02	.	11.6624	0.51354	1.0:0.0:0.0:0.0	.	87;87	G5E9I0;Q12809	.;KCNH2_HUMAN	P	87	ENSP00000262186:L87P;ENSP00000387657:L87P	ENSP00000262186:L87P	L	-	2	0	KCNH2	150302779	1.000000	0.71417	1.000000	0.80357	0.277000	0.26821	7.223000	0.78033	1.630000	0.50440	0.391000	0.25812	CTG	.	.		0.721	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		G	150671846	A	G	150671846	3	3	170	1	0	0	0	0	1	0	0	0	8041	188	7	2	3656	2	KCNH2	7	150671846	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	50181466	150671846	8466817	84	25775										
VIPR2	7434	hgsc.bcm.edu	37	chr7	158823365	158823365	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cgcgggagccgcggtggaacTgcagggcgccctccgagccg	18	15	0	0	rs184356169	byFrequency	TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr7:158823365T>A	ENST00000262178.2	-	13	1444	c.1259A>T	c.(1258-1260)cAg>cTg	p.Q420L	VIPR2_ENST00000402066.1_Missense_Mutation_p.Q561L|VIPR2_ENST00000377633.3_Missense_Mutation_p.Q404L	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	420					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		GCGGTGGAACTGCAGGGCGCC	0.697																																					p.Q420L	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.A1259T						.						15	18	17					7																	158823365		2161	4243	6404	SO:0001583	missense	7434	exon13			TGGAACTGCAGGG	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12695	protein-coding gene	gene with protein product	"VIP and PACAP receptor 2"	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.1259A>T	chr7.hg19:g.158823365T>A	ENSP00000262178:p.Gln420Leu	181.0	0.0		206.0	82.0	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Missense_Mutation	SNP	ENST00000262178.2	hg19	CCDS5950.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.393065	0.83011	.	.	ENSG00000106018	ENST00000262178;ENST00000377633;ENST00000402066	T;T;T	0.45668	0.96;0.92;0.89	5.01	3.84	0.44239	.	0.144241	0.31809	N	0.007036	T	0.51466	0.1676	M	0.82323	2.585	0.80722	D	1	D	0.56287	0.975	P	0.47744	0.556	T	0.56968	-0.7891	10	0.66056	D	0.02	.	10.1269	0.42654	0.0:0.0:0.1687:0.8313	.	420	P41587	VIPR2_HUMAN	L	420;404;561	ENSP00000262178:Q420L;ENSP00000366860:Q404L;ENSP00000384497:Q561L	ENSP00000262178:Q420L	Q	-	2	0	VIPR2	158516126	0.993000	0.37304	0.750000	0.31169	0.527000	0.34593	2.300000	0.43620	0.737000	0.32582	0.397000	0.26171	CAG	.	T|0.999;G|0.001		0.697	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382		A	158823365	T	A	158823365	3	1	170	1	0	0	0	0	1	0	0	0	17185	1580	55	4	61	4	VIPR2	7	158823365	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	8151519	158823365	315298	85	25776										
CHRNA2	1135	hgsc.bcm.edu	37	chr8	27320996	27320996	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gatgagcgggatgaccagcgAggtggacgggatgatctcag	18	7	1	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr8:27320996A>T	ENST00000520933.2	-	5	1117	c.964T>A	c.(964-966)Tcg>Acg	p.S322T	CHRNA2_ENST00000407991.1_Missense_Mutation_p.S322T|CHRNA2_ENST00000240132.2_Missense_Mutation_p.S307T			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	322					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	ATGACCAGCGAGGTGGACGGG	0.587																																					p.S322T		Atlas-SNP	.											.	CHRNA2	48	.	0			c.T964A						.						187	140	156					8																	27320996		2203	4300	6503	SO:0001583	missense	1135	exon6			CCAGCGAGGTGGA	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1956	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 2 (neuronal)"	118502	"cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.964T>A	chr8.hg19:g.27320996A>T	ENSP00000429616:p.Ser322Thr	148.0	0.0		175.0	34.0	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	hg19	CCDS6059.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.606131	0.87157	.	.	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132	D;D;D	0.93189	-3.18;-3.18;-3.18	4.88	4.88	0.63580	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.97685	0.9241	H	0.96861	3.895	0.58432	D	0.999998	D;D	0.76494	0.999;0.999	D;D	0.87578	0.995;0.998	D	0.98521	1.0623	10	0.87932	D	0	.	12.4689	0.55775	1.0:0.0:0.0:0.0	.	307;322	B4DK19;Q15822	.;ACHA2_HUMAN	T	322;322;307	ENSP00000385026:S322T;ENSP00000429616:S322T;ENSP00000240132:S307T	ENSP00000240132:S307T	S	-	1	0	CHRNA2	27376913	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.139000	0.94554	2.048000	0.60808	0.459000	0.35465	TCG	.	.		0.587	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4			T	27320996	A	T	27320996	3	4	170	1	0	0	0	0	1	0	0	0	3385	304	11	4	633	4	CHRNA2	8	27320996	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10		27320996	119043026	86	25777										
FGFR1	2260	hgsc.bcm.edu	37	chr8	38271457	38271457	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tggttggaggtcaaggccacGatgcggtccaggtcttccac	14	11	2	0	rs369782405		TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr8:38271457G>A	ENST00000447712.2	-	17	3212	c.2271C>T	c.(2269-2271)atC>atT	p.I757I	FGFR1_ENST00000335922.5_Silent_p.I747I|FGFR1_ENST00000326324.6_Silent_p.I666I|FGFR1_ENST00000397091.5_Silent_p.I755I|FGFR1_ENST00000397113.2_Silent_p.I755I|FGFR1_ENST00000397103.1_Silent_p.I668I|FGFR1_ENST00000532791.1_Silent_p.I755I|FGFR1_ENST00000356207.5_Silent_p.I668I|FGFR1_ENST00000425967.3_Silent_p.I788I|FGFR1_ENST00000341462.5_Silent_p.I757I|FGFR1_ENST00000397108.4_Silent_p.I755I	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	757	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)		FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TCAAGGCCACGATGCGGTCCA	0.642		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"																														p.I788I	Melanoma(146;1153 1840 21453 21841 43625)	Atlas-SNP	.		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	Q7Z2S2_HUMAN,NS,carcinoma,0,4	FGFR1	284	.	0			c.C2364T						.						51	58	56					8																	38271457		2203	4300	6503	SO:0001819	synonymous_variant	2260	exon18			GGCCACGATGCGG	M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.2271C>T	chr8.hg19:g.38271457G>A		91.0	0.0		120.0	45.0	NM_001174067	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Silent	SNP	ENST00000447712.2	hg19	CCDS6107.2																																																																																			.	.		0.642	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	38271457	G	A	38271457	2	1	170	1	0	0	0	0	0	0	0	1	5871	1048	37	1		1	FGFR1	8	38271457	Silent	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	10950461	38271457	108092565	87	25778										
OXR1	55074	hgsc.bcm.edu	37	chr8	107751706	107751706	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	attactacaagggaagacatAaattcaaagcaggttgctac	8	7	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr8:107751706A>T	ENST00000442977.2	+	12	2160	c.2061A>T	c.(2059-2061)atA>atT	p.I687I	OXR1_ENST00000521592.1_5'UTR|OXR1_ENST00000452423.2_Intron|OXR1_ENST00000312046.6_Silent_p.I652I|OXR1_ENST00000445937.1_Silent_p.I659I|OXR1_ENST00000517566.2_Silent_p.I686I|OXR1_ENST00000531443.1_Silent_p.I659I|OXR1_ENST00000449762.2_Silent_p.I29I|OXR1_ENST00000297447.6_Silent_p.I56I	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	687					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			GGGAAGACATAAATTCAAAGC	0.358																																					p.I687I		Atlas-SNP	.											.	OXR1	190	.	0			c.A2061T						.						97	95	96					8																	107751706		2203	4300	6503	SO:0001819	synonymous_variant	55074	exon12			AGACATAAATTCA	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 3"	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.2061A>T	chr8.hg19:g.107751706A>T		95.0	0.0		151.0	26.0	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	hg19	CCDS56548.1																																																																																			.	.		0.358	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		T	107751706	A	T	107751706	2	4	170	1	0	0	0	0	0	0	0	1	11343	352	13	4		4	OXR1	8	107751706	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	69480249	107751706	38612316	88	25779										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124383232	124383232	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgtacatattaagattgctcTaaaaatgtttaaataaaagc	5	4	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr8:124383232T>A	ENST00000287394.5	-	6	747		c.e6-2		ATAD2_ENST00000521903.1_Splice_Site|ATAD2_ENST00000534257.1_5'Flank	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2						ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AAGATTGCTCTAAAAATGTTT	0.284																																					.		Atlas-SNP	.											.	ATAD2	160	.	0			c.640-2A>T						.						100	91	94					8																	124383232		2203	4299	6502	SO:0001630	splice_region_variant	29028	exon7			TTGCTCTAAAAAT	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.640-2A>T	chr8.hg19:g.124383232T>A		57.0	0.0		121.0	62.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Splice_Site	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	T	17.49	3.403703	0.62288	.	.	ENSG00000156802	ENST00000287394	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8434	0.63453	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATAD2	124452413	1.000000	0.71417	0.996000	0.52242	0.884000	0.51177	4.866000	0.63005	1.925000	0.55765	0.397000	0.26171	.	.	.		0.284	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109	Intron	A	124383232	T	A	124383232	5	1	170	1	0	0	0	0	0	0	1	0	1071	1536	53	4	3626	4	ATAD2	8	124383232	Splice_Site	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	16631526	124383232	21980790	89	25780										
MAFA	389692	hgsc.bcm.edu	37	chr8	144512455	144512455	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctggcggcaggcggtggcagAagcgctcggcctcgggaggc	20	12	0	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr8:144512455A>T	ENST00000333480.2	-	1	121	c.122T>A	c.(121-123)tTc>tAc	p.F41Y	MAFA_ENST00000528185.1_5'Flank	NM_201589.3	NP_963883.2	Q8NHW3	MAFA_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog A	41					insulin secretion (GO:0030073)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|lung(1)|upper_aerodigestive_tract(2)	4	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.237)			GCGGTGGCAGAAGCGCTCGGC	0.706										HNSCC(29;0.082)																											p.F41Y		Atlas-SNP	.											.	MAFA	9	.	0			c.T122A						.						21	18	19					8																	144512455		2143	4226	6369	SO:0001583	missense	389692	exon1			TGGCAGAAGCGCT	AY083269	CCDS34955.1	8q24.3	2013-07-09	2013-07-09			ENSG00000182759			23145	protein-coding gene	gene with protein product		610303					Standard	NM_201589		Approved	RIPE3b1, hMafA	uc003yyc.2	Q8NHW3		ENST00000333480.2:c.122T>A	chr8.hg19:g.144512455A>T	ENSP00000328364:p.Phe41Tyr	41.0	0.0		62.0	12.0	NM_201589		Missense_Mutation	SNP	ENST00000333480.2	hg19	CCDS34955.1	.	.	.	.	.	.	.	.	.	.	a	3.511	-0.099778	0.07010	.	.	ENSG00000182759	ENST00000333480	D	0.98207	-4.79	3.27	3.27	0.37495	.	0.117810	0.35615	U	0.003094	D	0.91205	0.7229	N	0.03608	-0.345	0.23724	N	0.997011	B	0.02656	0.0	B	0.01281	0.0	T	0.79198	-0.1902	10	0.02654	T	1	.	11.6314	0.51178	1.0:0.0:0.0:0.0	.	41	Q8NHW3	MAFA_HUMAN	Y	41	ENSP00000328364:F41Y	ENSP00000328364:F41Y	F	-	2	0	MAFA	144583598	0.794000	0.28838	0.999000	0.59377	0.695000	0.40330	0.293000	0.19029	1.129000	0.42072	0.335000	0.21663	TTC	.	.		0.706	MAFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381511.2	NM_201589		T	144512455	A	T	144512455	3	4	170	1	0	0	0	0	1	0	0	0	9166	246	9	4	943	4	MAFA	8	144512455	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	20129223	144512455	1851567	90	25781										
CPSF1	29894	hgsc.bcm.edu	37	chr8	145623168	145623168	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gccgggaatgagggggcctaCatggtgcagcgggggcttgt	20	8	0	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr8:145623168C>T	ENST00000349769.3	-	20	2168		c.e20+1		MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			AGGGGGCCTACATGGTGCAGC	0.677																																					.	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.2073+1G>A						.						50	53	52					8																	145623168		2202	4298	6500	SO:0001630	splice_region_variant	29894	exon21			GGCCTACATGGTG	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.2073+1G>A	chr8.hg19:g.145623168C>T		53.0	0.0		82.0	14.0	NM_013291	Q96AF0	Splice_Site	SNP	ENST00000349769.3	hg19	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.280339	0.59758	.	.	ENSG00000071894	ENST00000349769	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1116	0.72362	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CPSF1	145593976	1.000000	0.71417	0.994000	0.49952	0.639000	0.38242	5.948000	0.70249	2.644000	0.89710	0.491000	0.48974	.	.	.		0.677	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	Intron	T	145623168	C	T	145623168	5	4	170	1	0	0	0	0	0	0	1	0	3826	492	17	3	2333	3	CPSF1	8	145623168	Splice_Site	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	1110713	145623168	740854	91	25782										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2115820	2115820	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agcatattgaccccccaaacAggatctgcaggcccaagacc	8	15	1	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr9:2115820A>T	ENST00000382203.1	+	25	3665		c.e25-1		SMARCA2_ENST00000357248.2_Splice_Site|SMARCA2_ENST00000349721.2_Splice_Site|SMARCA2_ENST00000382194.1_Splice_Site			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2						aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		CCCCCCAAACAGGATCTGCAG	0.557																																					.		Atlas-SNP	.											.	SMARCA2	313	.	0			c.3457-2A>T						.						23	22	22					9																	2115820		2203	4300	6503	SO:0001630	splice_region_variant	6595	exon25			CCAAACAGGATCT	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.3457-1A>T	chr9.hg19:g.2115820A>T		318.0	0.0		321.0	106.0	NM_003070	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Splice_Site	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.480929	0.84747	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000382203;ENST00000382194	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9124	0.79482	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMARCA2	2105820	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	9.339000	0.96797	2.164000	0.68074	0.460000	0.39030	.	.	.		0.557	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	Intron	T	2115820	A	T	2115820	5	4	170	1	0	0	0	0	0	0	1	0	14784	202	7	4	3549	4	SMARCA2	9	2115820	Splice_Site	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10		2115820	139097611	92	25783										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8527349	8527349	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agaactaagcacttaccaatAgattctggagatttaaatac	6	7	1	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr9:8527349A>G	ENST00000381196.4	-	13	1089	c.546T>C	c.(544-546)tcT>tcC	p.S182S	PTPRD_ENST00000356435.5_Silent_p.S182S|PTPRD_ENST00000355233.5_Silent_p.S182S|PTPRD_ENST00000486161.1_Silent_p.S182S|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000360074.4_Intron|PTPRD_ENST00000540109.1_Silent_p.S182S|PTPRD_ENST00000358503.5_Intron|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000397606.3_Silent_p.S182S|PTPRD_ENST00000397611.3_Intron	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	182	Ig-like C2-type 2.|Interaction with IL1RAPL1. {ECO:0000250}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		ACTTACCAATAGATTCTGGAG	0.284										TSP Lung(15;0.13)																											p.S182S		Atlas-SNP	.											.	PTPRD	1348	.	0			c.T546C						.						47	47	47					9																	8527349		1780	4056	5836	SO:0001819	synonymous_variant	5789	exon5			ACCAATAGATTCT	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.546T>C	chr9.hg19:g.8527349A>G		791.0	0.0		807.0	38.0	NM_130392	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	hg19	CCDS43786.1																																																																																			.	.		0.284	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			G	8527349	A	G	8527349	2	3	170	1	0	0	0	0	0	0	0	1	12814	407	15	2		2	PTPRD	9	8527349	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	6411529	8527349	132686082	93	25784										
C9orf93	203238	hgsc.bcm.edu	37	chr9	15744565	15744565	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctttgtcaactgtagaggaaAagaagcaagaggaagccaag	12	6	1	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr9:15744565A>T	ENST00000380701.3	+	17	2672	c.2344A>T	c.(2344-2346)Aag>Tag	p.K782*	CCDC171_ENST00000297641.3_Nonsense_Mutation_p.K782*	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	782																	TGTAGAGGAAAAGAAGCAAGA	0.403																																					p.K782X		Atlas-SNP	.											.	.	.	.	0			c.A2344T						.						96	100	98					9																	15744565		2203	4300	6503	SO:0001587	stop_gained	203238	exon17			GAGGAAAAGAAGC	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.2344A>T	chr9.hg19:g.15744565A>T	ENSP00000370077:p.Lys782*	188.0	0.0		198.0	60.0	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Nonsense_Mutation	SNP	ENST00000380701.3	hg19	CCDS6481.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	45|45	11.754129|11.754129	0.99599|0.99599	.|.	.|.	ENSG00000164989|ENSG00000164989	ENST00000449575|ENST00000297641;ENST00000380689;ENST00000380701	.|.	.|.	.|.	5.46|5.46	4.32|4.32	0.51571|0.51571	.|.	0.053840|0.053840	0.64402|0.64402	D|D	0.000001|0.000001	T|.	0.32255|.	0.0823|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.16778|.	-1.0391|.	5|.	.|0.02654	.|T	.|1	-20.4428|-20.4428	11.0391|11.0391	0.47820|0.47820	0.927:0.0:0.0729:0.0|0.927:0.0:0.0729:0.0	.|.	.|.	.|.	.|.	N|X	21|782;49;782	.|.	.|ENSP00000297641:K782X	K|K	+|+	3|1	2|0	C9orf93|C9orf93	15734565|15734565	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	2.886000|2.886000	0.48578|0.48578	2.206000|2.206000	0.71126|0.71126	0.383000|0.383000	0.25322|0.25322	AAA|AAG	.	.		0.403	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		T	15744565	A	T	15744565	4	4	170	1	0	0	0	0	0	1	0	0	2508	15	1	4	2406	4	C9orf93	9	15744565	Nonsense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	7217216	15744565	125468866	94	25785										
RASEF	158158	hgsc.bcm.edu	37	chr9	85615446	85615446	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gtctaagacggaagccacatCttctaaaccaaatgtctctt	6	11	4	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr9:85615446C>A	ENST00000376447.3	-	11	1737	c.1477G>T	c.(1477-1479)Gat>Tat	p.D493Y		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	493					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(4)|liver(1)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						GAAGCCACATCTTCTAAACCA	0.408																																					p.D493Y		Atlas-SNP	.											.	RASEF	69	.	0			c.G1477T						.						65	68	67					9																	85615446		2203	4300	6503	SO:0001583	missense	158158	exon11			CCACATCTTCTAA	AK056176	CCDS6662.1	9q21.33	2014-05-09	2004-06-11	2004-06-16	ENSG00000165105	ENSG00000165105		"EF-hand domain containing", "RAB, member RAS oncogene"	26464	protein-coding gene	gene with protein product		611344	"RAB45, member RAS oncogene family"	RAB45		17448446	Standard	NM_152573		Approved	FLJ31614	uc004amo.2	Q8IZ41	OTTHUMG00000020100	ENST00000376447.3:c.1477G>T	chr9.hg19:g.85615446C>A	ENSP00000365630:p.Asp493Tyr	115.0	0.0		92.0	26.0	NM_152573	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	hg19	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	C	5.279	0.236901	0.10023	.	.	ENSG00000165105	ENST00000376447	T	0.61627	0.09	5.36	2.06	0.26882	.	0.971791	0.08483	N	0.939182	T	0.42494	0.1205	L	0.34521	1.04	0.09310	N	1	P	0.39624	0.681	B	0.33750	0.169	T	0.28996	-1.0026	10	0.54805	T	0.06	.	6.9155	0.24357	0.0:0.5756:0.0:0.4244	.	493	Q8IZ41	RASEF_HUMAN	Y	493	ENSP00000365630:D493Y	ENSP00000365630:D493Y	D	-	1	0	RASEF	84805266	0.001000	0.12720	0.003000	0.11579	0.139000	0.21198	1.052000	0.30429	0.638000	0.30545	0.462000	0.41574	GAT	.	.		0.408	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		A	85615446	C	A	85615446	3	1	170	1	0	0	0	0	1	0	0	0	13083	913	32	3	773	3	RASEF	9	85615446	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	69870881	85615446	55597985	95	25786										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138646978	138646978	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tcttcccagggctcctattcTgtgggtggagagaaagatga	13	8	2	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr9:138646978T>C	ENST00000263604.3	+	6	446	c.446T>C	c.(445-447)cTg>cCg	p.L149P	KCNT1_ENST00000371757.2_Missense_Mutation_p.L168P|KCNT1_ENST00000491806.2_Missense_Mutation_p.L135P|KCNT1_ENST00000490355.2_Missense_Mutation_p.L149P|KCNT1_ENST00000487664.1_Missense_Mutation_p.L120P|KCNT1_ENST00000488444.2_Missense_Mutation_p.L149P|KCNT1_ENST00000486577.2_Missense_Mutation_p.L129P|KCNT1_ENST00000298480.5_Missense_Mutation_p.L168P			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	149					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		GCTCCTATTCTGTGGGTGGAG	0.612																																					p.L168P		Atlas-SNP	.											.	KCNT1	139	.	0			c.T503C						.						113	90	98					9																	138646978		2203	4300	6503	SO:0001583	missense	57582	exon6			CTATTCTGTGGGT	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.446T>C	chr9.hg19:g.138646978T>C	ENSP00000263604:p.Leu149Pro	63.0	0.0		42.0	12.0	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	.	13.90	2.374324	0.42105	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000473941;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;D;T	0.97731	1.57;1.56;1.56;-4.51;1.56	3.11	3.11	0.35812	.	0.170470	0.40064	U	0.001196	D	0.97439	0.9162	L	0.60455	1.87	0.80722	D	1	P;D	0.55385	0.951;0.971	P;P	0.58331	0.707;0.837	D	0.97079	0.9783	10	0.72032	D	0.01	-14.7654	10.4513	0.44524	0.0:0.0:0.0:1.0	.	168;120	B9EGP2;G5E9V0	.;.	P	120;168;168;115;129;135;149;149;149	ENSP00000417851:L120P;ENSP00000298480:L168P;ENSP00000360822:L168P;ENSP00000420764:L115P;ENSP00000263604:L149P	ENSP00000263604:L149P	L	+	2	0	KCNT1	137786799	1.000000	0.71417	0.984000	0.44739	0.222000	0.24845	7.288000	0.78691	1.194000	0.43101	0.260000	0.18958	CTG	.	.		0.612	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		C	138646978	T	C	138646978	3	2	170	1	0	0	0	0	1	0	0	0	8100	1580	55	2	525	2	KCNT1	9	138646978	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	53031532	138646978	2566453	96	25787										
MCM10	55388	hgsc.bcm.edu	37	chr10	13243528	13243528	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aagtgccgtgtcgtgacatgCaagacggtgggtgaaggtgg	18	6	0	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:13243528C>A	ENST00000484800.2	+	17	2452	c.2349C>A	c.(2347-2349)tgC>tgA	p.C783*	MCM10_ENST00000378694.1_Nonsense_Mutation_p.C782*|MCM10_ENST00000378714.3_Nonsense_Mutation_p.C782*			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	783	Zinc finger-like 2. {ECO:0000250}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						TCGTGACATGCAAGACGGTGG	0.537																																					p.C783X		Atlas-SNP	.											MCM10_ENST00000361282,lower_third,carcinoma,0,1	MCM10	76	.	0			c.C2349A						.						55	44	48					10																	13243528		2203	4300	6503	SO:0001587	stop_gained	55388	exon17			GACATGCAAGACG	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.2349C>A	chr10.hg19:g.13243528C>A	ENSP00000418268:p.Cys783*	70.0	0.0		67.0	15.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Nonsense_Mutation	SNP	ENST00000484800.2	hg19	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	C	39	7.654588	0.98415	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	.	.	.	5.27	3.43	0.39272	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.2155	8.8525	0.35208	0.0:0.7782:0.0:0.2218	.	.	.	.	X	782;783;783;782	.	ENSP00000354945:C783X	C	+	3	2	MCM10	13283534	0.959000	0.32827	1.000000	0.80357	0.841000	0.47740	0.113000	0.15499	0.629000	0.30376	0.655000	0.94253	TGC	.	.		0.537	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		A	13243528	C	A	13243528	4	1	170	1	0	0	0	0	0	1	0	0	9394	718	25	3	2411	3	MCM10	10	13243528	Nonsense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10		13243528	122291219	97	25788										
COMMD3	23412	hgsc.bcm.edu	37	chr10	22605412	22605412	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gatccccgctccttcgactcCaacgccttcacgcttctcct	5	20	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:22605412C>T	ENST00000376836.3	+	1	510	c.66C>T	c.(64-66)tcC>tcT	p.S22S	COMMD3-BMI1_ENST00000602390.1_Silent_p.S22S|COMMD3-BMI1_ENST00000463409.2_3'UTR	NM_012071.3	NP_036203.1	Q9UBI1	COMD3_HUMAN	COMM domain containing 3	22										kidney(2)|lung(2)|ovary(1)	5						CCTTCGACTCCAACGCCTTCA	0.647																																					p.S22S		Atlas-SNP	.											.	.	.	.	0			c.C66T						.						57	36	43					10																	22605412		2039	4007	6046	SO:0001819	synonymous_variant	0	exon1			CGACTCCAACGCC	AY542159	CCDS7137.1	10p12.2	2012-09-20	2004-02-13	2004-02-18	ENSG00000148444	ENSG00000148444			23332	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 8"	C10orf8		11042152, 15799966	Standard	NM_012071		Approved	BUP		Q9UBI1	OTTHUMG00000017806	ENST00000376836.3:c.66C>T	chr10.hg19:g.22605412C>T		100.0	0.0		116.0	30.0	NM_001204062	D3DRU7|Q5T8Y9	Silent	SNP	ENST00000376836.3	hg19	CCDS7137.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.488413	0.84854	.	.	ENSG00000148444	ENST00000456711;ENST00000444869	.	.	.	5.07	3.21	0.36854	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.1886	5.7432	0.18106	0.0:0.5277:0.3075:0.1648	.	.	.	.	X	23;22	.	.	Q	+	1	0	COMMD3	22645418	0.976000	0.34144	0.999000	0.59377	0.938000	0.57974	0.693000	0.25497	0.831000	0.34780	-0.150000	0.13652	CAA	.	.		0.647	COMMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047159.1	NM_012071		T	22605412	C	T	22605412	2	4	170	1	0	0	0	0	0	0	0	1	3719	581	21	3		3	COMMD3	10	22605412	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	9361884	22605412	112929335	98	25789										
ZEB1	6935	hgsc.bcm.edu	37	chr10	31816120	31816120	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gatgacagggctgaaagtcaAgcaagcagcttaggacaaaa	12	7	1	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:31816120A>T	ENST00000320985.10	+	9	3413	c.3303A>T	c.(3301-3303)caA>caT	p.Q1101H	ZEB1_ENST00000446923.2_Missense_Mutation_p.Q1085H|ZEB1_ENST00000560721.2_Missense_Mutation_p.Q1081H|ZEB1_ENST00000361642.5_Missense_Mutation_p.Q1102H|ZEB1_ENST00000542815.3_Missense_Mutation_p.Q1034H			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	1101	Glu-rich (acidic).				cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				CTGAAAGTCAAGCAAGCAGCT	0.418																																					p.Q1102H	Ovarian(40;423 959 14296 36701 49589)	Atlas-SNP	.											.	ZEB1	173	.	0			c.A3306T						.						125	120	121					10																	31816120		2203	4300	6503	SO:0001583	missense	6935	exon9			AAGTCAAGCAAGC	AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.3303A>T	chr10.hg19:g.31816120A>T	ENSP00000319248:p.Gln1101His	53.0	0.0		66.0	17.0	NM_001174096	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	hg19	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291919	0.40594	.	.	ENSG00000148516	ENST00000542879;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000541037;ENST00000543514;ENST00000446923	T;T;T;T;T	0.12672	2.97;2.67;2.71;2.66;2.71	5.27	-4.43	0.03568	.	20.999700	0.00166	N	0.000000	T	0.13884	0.0336	L	0.47716	1.5	0.09310	N	1	B;B;B;B;B	0.26935	0.164;0.102;0.102;0.102;0.102	B;B;B;B;B	0.30401	0.115;0.054;0.054;0.054;0.054	T	0.30621	-0.9972	10	0.52906	T	0.07	-0.0954	5.9924	0.19474	0.4537:0.2356:0.3106:0.0	.	1034;1085;1081;1102;1101	F5H4I8;E9PCM7;Q5VZ84;Q2KJ05;P37275	.;.;.;.;ZEB1_HUMAN	H	883;1102;1096;1034;1101;1081;620;992;1085	ENSP00000444282:Q883H;ENSP00000354487:Q1102H;ENSP00000444891:Q1034H;ENSP00000319248:Q1101H;ENSP00000391612:Q1085H	ENSP00000319248:Q1101H	Q	+	3	2	ZEB1	31856126	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.201000	0.09464	-1.180000	0.02734	-0.269000	0.10298	CAA	.	.		0.418	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		T	31816120	A	T	31816120	3	4	170	1	0	0	0	0	1	0	0	0	17638	69	3	4	3351	4	ZEB1	10	31816120	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	9210708	31816120	103718627	99	25790										
ZNF365	22891	hgsc.bcm.edu	37	chr10	64148324	64148324	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctggctttgtccgtgatctcAgcgggcacgtggtgagtcac	14	11	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:64148324A>T	ENST00000395254.3	+	3	1193	c.913A>T	c.(913-915)Agc>Tgc	p.S305C	ZNF365_ENST00000410046.3_Missense_Mutation_p.S305C|ZNF365_ENST00000395255.3_Missense_Mutation_p.S305C|ZNF365_ENST00000466727.1_3'UTR	NM_014951.2	NP_055766.2	Q70YC4	TALAN_HUMAN	zinc finger protein 365	0										breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					CCGTGATCTCAGCGGGCACGT	0.562																																					p.S305C		Atlas-SNP	.											.	ZNF365	174	.	0			c.A913T						.						39	40	40					10																	64148324		2203	4300	6503	SO:0001583	missense	22891	exon3			GATCTCAGCGGGC	AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395254.3:c.913A>T	chr10.hg19:g.64148324A>T	ENSP00000378674:p.Ser305Cys	42.0	0.0		59.0	12.0	NM_014951		Missense_Mutation	SNP	ENST00000395254.3	hg19	CCDS31209.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.112581	0.77210	.	.	ENSG00000138311	ENST00000395254;ENST00000395255;ENST00000410046	T	0.48201	0.82	5.58	3.2	0.36748	.	32.444400	0.00166	N	0.000000	T	0.64549	0.2608	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.76494	0.999;0.997;0.994;0.994	P;P;P;P	0.60236	0.871;0.847;0.77;0.847	T	0.37314	-0.9711	10	0.66056	D	0.02	-11.3536	7.6218	0.28189	0.7876:0.1407:0.0717:0.0	.	305;305;305;320	Q70YC5-3;Q70YC5-2;Q70YC5;Q70YC5-4	.;.;ZN365_HUMAN;.	C	305	ENSP00000378674:S305C	ENSP00000378674:S305C	S	+	1	0	ZNF365	63818330	0.601000	0.26907	0.034000	0.17996	0.200000	0.23975	2.655000	0.46707	0.463000	0.27118	0.533000	0.62120	AGC	.	.		0.562	ZNF365-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048238.2	NM_014951		T	64148324	A	T	64148324	3	4	170	1	0	0	0	0	1	0	0	0	17884	188	7	4	919	4	ZNF365	10	64148324	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	32332204	64148324	71386423	100	25791										
TET1	80312	hgsc.bcm.edu	37	chr10	70446431	70446431	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agaataactcaacaacaacaAacaacagtaagccttcgtca	4	11	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:70446431A>T	ENST00000373644.4	+	11	5580	c.5371A>T	c.(5371-5373)Aac>Tac	p.N1791Y		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1791					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						AACAACAACAAACAACAGTAA	0.453																																					p.N1791Y		Atlas-SNP	.											.	TET1	255	.	0			c.A5371T						.						82	75	77					10																	70446431		2203	4300	6503	SO:0001583	missense	80312	exon11			ACAACAAACAACA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.5371A>T	chr10.hg19:g.70446431A>T	ENSP00000362748:p.Asn1791Tyr	124.0	0.0		143.0	49.0	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	A	14.42	2.531045	0.45073	.	.	ENSG00000138336	ENST00000373644	T	0.07216	3.21	4.75	0.527	0.17084	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	3.439290	0.00628	N	0.000471	T	0.12050	0.0293	L	0.40543	1.245	0.09310	N	1	P	0.41393	0.748	P	0.45037	0.467	T	0.42732	-0.9434	10	0.14252	T	0.57	.	11.652	0.51295	0.5714:0.4286:0.0:0.0	.	1791	Q8NFU7	TET1_HUMAN	Y	1791	ENSP00000362748:N1791Y	ENSP00000362748:N1791Y	N	+	1	0	TET1	70116437	0.005000	0.15991	0.001000	0.08648	0.020000	0.10135	2.083000	0.41615	0.237000	0.21200	0.372000	0.22366	AAC	.	.		0.453	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		T	70446431	A	T	70446431	3	4	170	1	0	0	0	0	1	0	0	0	15784	14	1	4	5409	4	TET1	10	70446431	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	6298107	70446431	65088316	101	25792										
PRF1	5551	hgsc.bcm.edu	37	chr10	72358753	72358753	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cccttccagggccagctcgcAggtgcgcagggcagtgaggg	17	13	0	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:72358753A>T	ENST00000441259.1	-	3	884	c.724T>A	c.(724-726)Tgc>Agc	p.C242S	PRF1_ENST00000373209.2_Missense_Mutation_p.C242S	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	242	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						GCCAGCTCGCAGGTGCGCAGG	0.647			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.C242S		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.T724A						.						81	64	70					10																	72358753		2203	4300	6503	SO:0001583	missense	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCTCGCAGGTGCG	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"Perforin", "perforin 1 (preforming protein)"	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.724T>A	chr10.hg19:g.72358753A>T	ENSP00000398568:p.Cys242Ser	110.0	0.0		83.0	22.0	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	hg19	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	A	19.09	3.760150	0.69763	.	.	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.82526	-1.62;-1.62	5.83	5.83	0.93111	Membrane attack complex component/perforin (MACPF) domain (3);	0.000000	0.85682	D	0.000000	D	0.90597	0.7052	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.89171	0.3537	10	0.23891	T	0.37	-41.7881	14.1426	0.65329	1.0:0.0:0.0:0.0	.	242	P14222	PERF_HUMAN	S	242	ENSP00000362305:C242S;ENSP00000398568:C242S	ENSP00000316746:C242S	C	-	1	0	PRF1	72028759	1.000000	0.71417	0.996000	0.52242	0.237000	0.25408	7.989000	0.88205	2.212000	0.71576	0.533000	0.62120	TGC	.	.		0.647	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		T	72358753	A	T	72358753	3	4	170	1	0	0	0	0	1	0	0	0	12490	188	7	4	947	4	PRF1	10	72358753	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	1912322	72358753	63175994	102	25793										
IFIT3	3437	hgsc.bcm.edu	37	chr10	91099326	91099326	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgaagctagtggaaataaagAgatgattgaagcactaaagc	11	4	0	4			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:91099326A>T	ENST00000371818.4	+	2	1094	c.914A>T	c.(913-915)gAg>gTg	p.E305V	IFIT3_ENST00000371811.4_Missense_Mutation_p.E305V|LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001549.4	NP_001540.2	O14879	IFIT3_HUMAN	interferon-induced protein with tetratricopeptide repeats 3	305					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)|urinary_tract(1)	15						GGAAATAAAGAGATGATTGAA	0.418																																					p.E305V		Atlas-SNP	.											.	IFIT3	36	.	0			c.A914T						.						81	73	76					10																	91099326		2203	4300	6503	SO:0001583	missense	3437	exon2			ATAAAGAGATGAT	U52513	CCDS7402.1, CCDS31241.1	10q23.31	2014-05-22	2004-07-16	2004-07-16	ENSG00000119917	ENSG00000119917		"Tetratricopeptide (TTC) repeat domain containing"	5411	protein-coding gene	gene with protein product		604650	"interferon-induced protein with tetratricopeptide repeats 4"	IFIT4		9828129, 9391139	Standard	NM_001031683		Approved	ISG60, RIG-G, CIG-49, IFI60, GARG-49, IRG2	uc001kgg.3	O14879	OTTHUMG00000018708	ENST00000371818.4:c.914A>T	chr10.hg19:g.91099326A>T	ENSP00000360883:p.Glu305Val	116.0	0.0		111.0	31.0	NM_001549	Q99634|Q9BSK7	Missense_Mutation	SNP	ENST00000371818.4	hg19	CCDS7402.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.093991	0.56075	.	.	ENSG00000119917	ENST00000371818;ENST00000371811;ENST00000543062	T;T	0.14516	2.5;2.5	4.28	4.28	0.50868	Tetratricopeptide-like helical (1);	0.650217	0.13988	N	0.349033	T	0.31606	0.0802	M	0.80746	2.51	0.09310	N	1	D	0.59767	0.986	P	0.58391	0.838	T	0.11991	-1.0565	10	0.56958	D	0.05	-2.7629	8.291	0.31958	0.9102:0.0:0.0898:0.0	.	305	O14879	IFIT3_HUMAN	V	305;305;126	ENSP00000360883:E305V;ENSP00000360876:E305V	ENSP00000360876:E305V	E	+	2	0	IFIT3	91089306	0.868000	0.29978	0.069000	0.20011	0.276000	0.26787	2.400000	0.44504	2.167000	0.68274	0.529000	0.55759	GAG	.	.		0.418	IFIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049294.1	NM_001549		T	91099326	A	T	91099326	3	4	170	1	0	0	0	0	1	0	0	0	7533	304	11	4	929	4	IFIT3	10	91099326	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	18740573	91099326	44435421	103	25794										
BTAF1	9044	hgsc.bcm.edu	37	chr10	93699802	93699802	+	Frame_Shift_Del	DEL	C	C	-													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aaaatgtacctgagtggaatCcagtgccgagaaccagacaa							TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:93699802delC	ENST00000265990.6	+	3	540	c.232delC	c.(232-234)ccafs	p.P78fs		NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	78					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				TGAGTGGAATCCAGTGCCGAG	0.353																																					p.N77fs		Atlas-INDEL	.											.	BTAF1	148	.	0			c.231delT						.						64	65	65					10																	93699802		2203	4300	6503	SO:0001589	frameshift_variant	9044	exon3			.	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.232delC	chr10.hg19:g.93699802delC	ENSP00000265990:p.Pro78fs	162.0	0.0		202.0	57.0	NM_003972	B4E0W6|O43578	Frame_Shift_Del	DEL	ENST00000265990.6	hg19	CCDS7419.1																																																																																			.	.		0.353	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		-	93699802	C	-	93699802	7	5	170	1	0	1	0	1	0	0	0	0	1538	855	30	0	242	0	BTAF1	10	93699802	Frame_Shift_Del	DEL	C	TCGA-DD-AACT-01A-11D-A40R-10	2600476	93699802	41834945	104	25795										
GPR120	338557	hgsc.bcm.edu	37	chr10	95338925	95338931	+	Frame_Shift_Del	DEL	CACCTCC	CACCTCC	-													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ccccattacagacctcggaaCacctcctggatgcaagagct							TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	CACCTCC	CACCTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:95338925_95338931delCACCTCC	ENST00000371483.4	+	3	762_768	c.706_712delCACCTCC	c.(706-714)cacctcctgfs	p.HLL236fs	FFAR4_ENST00000371481.4_Intron|FFAR4_ENST00000604414.1_Intron	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	236					hormone secretion (GO:0046879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of inflammatory response (GO:0050728)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of glucose transport (GO:0010827)	endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fatty acid binding (GO:0005504)|taste receptor activity (GO:0008527)										GACCTCGGAACACCTCCTGGATGCAAG	0.483																																					p.235_237del		Atlas-INDEL	.											.	.	.	.	0			c.705_711del						.																																			SO:0001589	frameshift_variant	338557	exon3			.		CCDS31248.1, CCDS55720.1	10q23.33	2012-11-16	2012-11-16	2012-11-16	ENSG00000186188	ENSG00000186188		"GPCR / Class A : Fatty acid receptors"	19061	protein-coding gene	gene with protein product		609044	"G protein-coupled receptor 129", "G protein-coupled receptor 120", "omega-3 fatty acid receptor 1"	GPR129, GPR120, O3FAR1		20471368, 19723586, 15619630, 20813258	Standard	NM_181745		Approved	PGR4	uc010qnt.2	Q5NUL3	OTTHUMG00000034409	ENST00000371483.4:c.706_712delCACCTCC	chr10.hg19:g.95338925_95338931delCACCTCC	ENSP00000360538:p.His236fs	76.0	0.0		79.0	16.0	NM_181745	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Frame_Shift_Del	DEL	ENST00000371483.4	hg19	CCDS31248.1																																																																																			.	.		0.483	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745		-	95338931	CACCTCC	-	95338925	7	5	170	1	0	1	0	1	0	0	0	0	6644	478	17	0	716	0	GPR120	10	95338925	Frame_Shift_Del	DEL	CACCTCC	TCGA-DD-AACT-01A-11D-A40R-10	1639123	95338925	40195822	105	25796										
OPALIN	93377	hgsc.bcm.edu	37	chr10	98111161	98111161	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tttcccacctgtgacaggagAggacgtctgtatggaaaaag	12	8	1	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:98111161A>T	ENST00000371172.3	-	3	451	c.46T>A	c.(46-48)Tct>Act	p.S16T	OPALIN_ENST00000393870.2_Intron|OPALIN_ENST00000419479.1_Missense_Mutation_p.S6T|OPALIN_ENST00000393871.1_Intron|OPALIN_ENST00000536387.1_Missense_Mutation_p.S6T	NM_001284326.1|NM_001284327.1|NM_033207.3	NP_001271255.1|NP_001271256.1|NP_149984.1	Q96PE5	OPALI_HUMAN	oligodendrocytic myelin paranodal and inner loop protein	16						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(5)|prostate(2)	9						GTGACAGGAGAGGACGTCTGT	0.333																																					p.S16T		Atlas-SNP	.											.	OPALIN	31	.	0			c.T46A						.						82	85	84					10																	98111161		2203	4300	6503	SO:0001583	missense	93377	exon3			CAGGAGAGGACGT	AF367761	CCDS7448.1, CCDS41556.1, CCDS44466.1, CCDS60602.1, CCDS73172.1, CCDS73173.1	10q23-q24	2010-11-23	2008-05-01	2008-05-01	ENSG00000197430	ENSG00000197430			20707	protein-coding gene	gene with protein product			"transmembrane protein 10"	TMEM10		11814680, 17442045	Standard	NM_001284324		Approved	TMP10, HTMP10	uc001kmj.3	Q96PE5	OTTHUMG00000018831	ENST00000371172.3:c.46T>A	chr10.hg19:g.98111161A>T	ENSP00000360214:p.Ser16Thr	606.0	0.0		677.0	210.0	NM_033207	A8MX69|A8MYG4|B4DK96|B4DKH0|Q5W102	Missense_Mutation	SNP	ENST00000371172.3	hg19	CCDS7448.1	.	.	.	.	.	.	.	.	.	.	A	0.740	-0.776602	0.02951	.	.	ENSG00000197430	ENST00000371172;ENST00000419479;ENST00000536387	.	.	.	3.74	2.58	0.30949	.	0.139556	0.33691	N	0.004655	T	0.27866	0.0686	L	0.34521	1.04	0.29869	N	0.82698	B;P	0.37330	0.361;0.59	B;B	0.34652	0.187;0.187	T	0.21075	-1.0256	9	0.59425	D	0.04	-7.0333	7.209	0.25923	0.7719:0.2281:0.0:0.0	.	16;6	Q96PE5;B4DK96	OPALI_HUMAN;.	T	16;6;6	.	ENSP00000360214:S16T	S	-	1	0	OPALIN	98101151	1.000000	0.71417	0.999000	0.59377	0.097000	0.18754	0.854000	0.27791	0.776000	0.33473	-0.313000	0.08912	TCT	.	.		0.333	OPALIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049606.1	NM_033207		T	98111161	A	T	98111161	3	4	170	1	0	0	0	0	1	0	0	0	10882	304	11	4	395	4	OPALIN	10	98111161	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	2772236	98111161	37423586	106	25797										
C10orf12	26148	hgsc.bcm.edu	37	chr10	98741566	98741566	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gatgatatcaacctccatcaAgacagctcggaaaagtaaaa	7	9	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:98741566A>T	ENST00000286067.2	+	1	526	c.419A>T	c.(418-420)aAg>aTg	p.K140M		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	140										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		ACCTCCATCAAGACAGCTCGG	0.443																																					p.K140M		Atlas-SNP	.											.	C10orf12	94	.	0			c.A419T						.						95	93	94					10																	98741566		2203	4300	6503	SO:0001583	missense	26148	exon1			CCATCAAGACAGC	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.419A>T	chr10.hg19:g.98741566A>T	ENSP00000286067:p.Lys140Met	124.0	0.0		148.0	37.0	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	hg19	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	A	14.45	2.539571	0.45176	.	.	ENSG00000155640	ENST00000286067	T	0.13420	2.59	5.95	5.95	0.96441	.	0.286982	0.24456	N	0.038373	T	0.22898	0.0553	N	0.24115	0.695	0.33017	D	0.52829	D	0.89917	1.0	D	0.76575	0.988	T	0.25710	-1.0124	10	0.87932	D	0	-15.792	10.9937	0.47563	0.9224:0.0:0.0776:0.0	.	140	Q8N655	CJ012_HUMAN	M	140	ENSP00000286067:K140M	ENSP00000286067:K140M	K	+	2	0	C10orf12	98731556	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	4.297000	0.59061	2.277000	0.76020	0.533000	0.62120	AAG	.	.		0.443	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		T	98741566	A	T	98741566	3	4	170	1	0	0	0	0	1	0	0	0	1591	72	3	4	421	4	C10orf12	10	98741566	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	630405	98741566	36793181	107	25798										
ZDHHC16	84287	hgsc.bcm.edu	37	chr10	99213301	99213301	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aaccagcctggctaaacaatTgtgtgggccactataaccat	8	11	0	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:99213301T>A	ENST00000370854.3	+	6	760	c.571T>A	c.(571-573)Tgt>Agt	p.C191S	ZDHHC16_ENST00000495735.1_3'UTR|ZDHHC16_ENST00000345745.5_Missense_Mutation_p.C126S|ZDHHC16_ENST00000370842.2_Missense_Mutation_p.C191S|ZDHHC16_ENST00000370846.4_Intron|ZDHHC16_ENST00000353979.3_Intron|ZDHHC16_ENST00000352634.4_Missense_Mutation_p.C191S|ZDHHC16_ENST00000393760.1_Missense_Mutation_p.C191S	NM_032327.2	NP_115703.2	Q969W1	ZDH16_HUMAN	zinc finger, DHHC-type containing 16	191					apoptotic process (GO:0006915)|protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			kidney(4)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	14		Colorectal(252;0.0846)		Epithelial(162;5.81e-10)|all cancers(201;4.19e-08)		GCTAAACAATTGTGTGGGCCA	0.483																																					p.C191S		Atlas-SNP	.											.	ZDHHC16	25	.	0			c.T571A						.						270	238	249					10																	99213301		2203	4300	6503	SO:0001583	missense	84287	exon7			AACAATTGTGTGG	AF258563	CCDS7460.1, CCDS7461.1, CCDS7462.1, CCDS7463.1, CCDS73176.1	10q24.1	2008-05-02			ENSG00000171307	ENSG00000171307		"Zinc fingers, DHHC-type"	20714	protein-coding gene	gene with protein product						12021275	Standard	NM_198043		Approved	APH2	uc001knk.3	Q969W1	OTTHUMG00000018847	ENST00000370854.3:c.571T>A	chr10.hg19:g.99213301T>A	ENSP00000359891:p.Cys191Ser	69.0	0.0		73.0	30.0	NM_198046	D3DR52|D3DR53|D3DR54|Q5JTG7|Q5JTH0|Q8N4Z6|Q8WY84|Q9BSV3	Missense_Mutation	SNP	ENST00000370854.3	hg19	CCDS7460.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.470758	0.84533	.	.	ENSG00000171307	ENST00000370854;ENST00000393760;ENST00000414567;ENST00000352634;ENST00000370842;ENST00000345745;ENST00000433086	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.95	5.95	0.96441	Zinc finger, DHHC-type, palmitoyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.78368	0.4272	H	0.97940	4.11	0.80722	D	1	D;D;D;D;D;D	0.89917	0.993;1.0;0.997;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.952;0.998;0.994;0.997;0.993;0.996	D	0.86731	0.1948	10	0.87932	D	0	-4.0762	16.397	0.83610	0.0:0.0:0.0:1.0	.	191;126;166;126;191;191	B4DNL2;E9PCL9;B1AMU1;Q969W1-4;Q969W1-2;Q969W1	.;.;.;.;.;ZDH16_HUMAN	S	191;191;191;191;191;126;126	ENSP00000359891:C191S;ENSP00000377357:C191S;ENSP00000400719:C191S;ENSP00000345383:C191S;ENSP00000359879:C191S;ENSP00000304487:C126S;ENSP00000398532:C126S	ENSP00000304487:C126S	C	+	1	0	ZDHHC16	99203291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.275000	0.75901	0.459000	0.35465	TGT	.	.		0.483	ZDHHC16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049658.2	NM_032327		A	99213301	T	A	99213301	3	1	170	1	0	0	0	0	1	0	0	0	17621	1812	63	4	589	4	ZDHHC16	10	99213301	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	471735	99213301	36321446	108	25799										
SEC31B	25956	hgsc.bcm.edu	37	chr10	102250575	102250575	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	taagggctaggatgggaaggTgccaagggcatcgctggtga	18	6	0	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:102250575T>A	ENST00000370345.3	-	20	2635	c.2538A>T	c.(2536-2538)gcA>gcT	p.A846A		NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	846	Pro-rich.				protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GATGGGAAGGTGCCAAGGGCA	0.542																																					p.A846A		Atlas-SNP	.											.	SEC31B	84	.	0			c.A2538T						.						65	57	60					10																	102250575		2203	4300	6503	SO:0001819	synonymous_variant	25956	exon20			GGAAGGTGCCAAG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.2538A>T	chr10.hg19:g.102250575T>A		81.0	0.0		72.0	28.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	ENST00000370345.3	hg19	CCDS7495.1																																																																																			.	.		0.542	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		A	102250575	T	A	102250575	2	1	170	1	0	0	0	0	0	0	0	1	14014	1683	59	4		4	SEC31B	10	102250575	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	3037274	102250575	33284172	109	25800										
GBF1	8729	hgsc.bcm.edu	37	chr10	104018779	104018779	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cgaaatgcccgatggagcacCcatacaccactggtaagtgg	11	12	0	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr10:104018779C>A	ENST00000369983.3	+	2	344	c.84C>A	c.(82-84)acC>acA	p.T28T	AL160011.1_ENST00000516180.2_RNA	NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	28					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GATGGAGCACCCATACACCAC	0.413																																					p.T28T		Atlas-SNP	.											.	GBF1	142	.	0			c.C84A						.						98	106	103					10																	104018779		2203	4300	6503	SO:0001819	synonymous_variant	8729	exon2			GAGCACCCATACA	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.84C>A	chr10.hg19:g.104018779C>A		158.0	0.0		138.0	36.0	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Silent	SNP	ENST00000369983.3	hg19	CCDS7533.1																																																																																			.	.		0.413	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			A	104018779	C	A	104018779	2	1	170	1	0	0	0	0	0	0	0	1	6279	610	22	3		3	GBF1	10	104018779	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	1768204	104018779	31515968	110	25801										
OR56A5	0	hgsc.bcm.edu	37	chr11	5989217	5989217	+	IGR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gatgtgtcctgcacagtatcTgagtcgagaagaaagtatgg	13	6	1	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:5989217T>G								OR56A3 (19626 upstream) : OR52L1 (17904 downstream)																							GCACAGTATCTGAGTCGAGAA	0.448																																					p.R170R		Atlas-SNP	.											.	.	.	.	0			c.A508C						.						97	81	86					11																	5989217		692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			AGTATCTGAGTCG																													chr11.hg19:g.5989217T>G		79.0	0.0		73.0	21.0	NM_001146033		Silent	SNP		hg19																																																																																				.	.	0	0.448									G	5989217	T	G	5989217	1	3	170	0	1	0	0	0	0	0	0	0	11145	1588	55	5		5	OR56A5	11	5989217	IGR	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10		5989217	129017299	111	25802										
CD44	960	hgsc.bcm.edu	37	chr11	35219675	35219675	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gtcaccacaacaggtacgtcTtcaaataccatctcagcagg	7	13	4	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:35219675T>A	ENST00000428726.2	+	7	927	c.804T>A	c.(802-804)tcT>tcA	p.S268S	CD44_ENST00000437706.2_Silent_p.S268S|CD44_ENST00000433892.2_Intron|CD44_ENST00000434472.2_Intron|CD44_ENST00000526669.2_Intron|CD44_ENST00000433354.2_Silent_p.S268S|CD44_ENST00000528922.1_3'UTR|CD44_ENST00000360158.4_Intron|CD44_ENST00000278386.6_Intron|CD44_ENST00000449691.2_Silent_p.S268S|CD44_ENST00000352818.4_Intron|CD44_ENST00000415148.2_Silent_p.S225S|CD44_ENST00000263398.6_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	268	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	CAGGTACGTCTTCAAATACCA	0.448																																					p.S268S		Atlas-SNP	.											.	CD44	48	.	0			c.T804A						.						75	68	71					11																	35219675		2202	4298	6500	SO:0001819	synonymous_variant	960	exon7			TACGTCTTCAAAT	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"CD molecules", "Blood group antigens", "Proteoglycans / Cell surface : Other"	1681	protein-coding gene	gene with protein product	"hematopoietic cell E- and L-selectin ligand", "chondroitin sulfate proteoglycan 8"	107269	"CD44 antigen (homing function and Indian blood group system)"	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.804T>A	chr11.hg19:g.35219675T>A		115.0	0.0		120.0	34.0	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	hg19	CCDS7897.1	.	.	.	.	.	.	.	.	.	.	T	10.43	1.349180	0.24426	.	.	ENSG00000026508	ENST00000525685	.	.	.	5.33	2.65	0.31530	.	.	.	.	.	T	0.46521	0.1397	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35525	-0.9785	4	.	.	.	-7.8408	3.5136	0.07717	0.0:0.1456:0.2427:0.6117	.	.	.	.	H	136	.	.	L	+	2	0	CD44	35176251	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	0.484000	0.22308	0.948000	0.37687	0.459000	0.35465	CTT	.	.		0.448	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610		A	35219675	T	A	35219675	2	1	170	1	0	0	0	0	0	0	0	1	3019	1596	56	4		4	CD44	11	35219675	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	29230458	35219675	99786841	112	25803										
NUP160	23279	hgsc.bcm.edu	37	chr11	47823484	47823484	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gacaaaaacattccagagccTggagaaataaaatataaaat	6	6	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:47823484T>C	ENST00000378460.2	-	23	2822		c.e23-2		NUP160_ENST00000528071.1_Splice_Site|NUP160_ENST00000530326.1_Splice_Site|RNA5SP340_ENST00000517132.1_RNA	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						TTCCAGAGCCTGGAGAAATAA	0.418																																					.		Atlas-SNP	.											.	NUP160	116	.	0			c.2776-2A>G						.						55	51	52					11																	47823484		2201	4298	6499	SO:0001630	splice_region_variant	23279	exon24			AGAGCCTGGAGAA	D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"nucleoporin 160kD"			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.2776-2A>G	chr11.hg19:g.47823484T>C		101.0	0.0		107.0	36.0	NM_015231	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Splice_Site	SNP	ENST00000378460.2	hg19	CCDS31484.1	.	.	.	.	.	.	.	.	.	.	T	15.51	2.854404	0.51270	.	.	ENSG00000030066	ENST00000378460;ENST00000530326;ENST00000528071	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6385	0.62235	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NUP160	47780060	1.000000	0.71417	0.982000	0.44146	0.402000	0.30811	6.835000	0.75344	2.158000	0.67659	0.454000	0.30748	.	.	.		0.418	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231	Intron	C	47823484	T	C	47823484	5	2	170	1	0	0	0	0	0	0	1	0	10766	1594	55	2	1592	2	NUP160	11	47823484	Splice_Site	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	12603809	47823484	87183032	113	25804										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62290643	62290643	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ccttcaggtttaaatcaatgTcaggcatcgatattttggga	9	7	3	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:62290643T>A	ENST00000378024.4	-	5	11520	c.11246A>T	c.(11245-11247)gAc>gTc	p.D3749V	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3749					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TAAATCAATGTCAGGCATCGA	0.463																																					p.D3749V		Atlas-SNP	.											.	AHNAK	532	.	0			c.A11246T						.						123	126	125					11																	62290643		2202	4299	6501	SO:0001583	missense	79026	exon5			TCAATGTCAGGCA	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11246A>T	chr11.hg19:g.62290643T>A	ENSP00000367263:p.Asp3749Val	104.0	0.0		76.0	18.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	15.67	2.901762	0.52227	.	.	ENSG00000124942	ENST00000378024	T	0.01414	4.92	5.05	5.05	0.67936	.	0.167110	0.27936	N	0.017250	T	0.15262	0.0368	H	0.97732	4.065	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.12293	-1.0553	10	0.42905	T	0.14	-12.515	14.4851	0.67611	0.0:0.0:0.0:1.0	.	3749	Q09666	AHNK_HUMAN	V	3749	ENSP00000367263:D3749V	ENSP00000367263:D3749V	D	-	2	0	AHNAK	62047219	1.000000	0.71417	0.565000	0.28409	0.191000	0.23601	7.999000	0.88496	1.905000	0.55150	0.472000	0.43445	GAC	.	.		0.463	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62290643	T	A	62290643	3	1	170	1	0	0	0	0	1	0	0	0	414	1667	58	4	6546	4	AHNAK	11	62290643	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	14467159	62290643	72715873	114	25805										
MAP4K2	5871	hgsc.bcm.edu	37	chr11	64563810	64563810	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggaacctgttgctgtagcctCcgctgctcaaacaggcctgg	12	13	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:64563810C>A	ENST00000294066.2	-	24	1777	c.1686G>T	c.(1684-1686)cgG>cgT	p.R562R	MAP4K2_ENST00000377350.3_Silent_p.R554R	NM_004579.3	NP_004570.2	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase kinase 2	562	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JUN kinase activity (GO:0007257)|immune response (GO:0006955)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|positive regulation of JNK cascade (GO:0046330)|protein phosphorylation (GO:0006468)|vesicle targeting (GO:0006903)	Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(1)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(2)	8						GCTGTAGCCTCCGCTGCTCAA	0.637																																					p.R562R		Atlas-SNP	.											.	MAP4K2	83	.	0			c.G1686T						.						91	92	91					11																	64563810		2201	4297	6498	SO:0001819	synonymous_variant	5871	exon24			TAGCCTCCGCTGC	BC047865	CCDS8082.1	11q13.1	2011-06-09			ENSG00000168067	ENSG00000168067		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6864	protein-coding gene	gene with protein product		603166		RAB8IP		7515885	Standard	NM_004579		Approved	GCK, BL44	uc001obh.3	Q12851	OTTHUMG00000045328	ENST00000294066.2:c.1686G>T	chr11.hg19:g.64563810C>A		105.0	0.0		101.0	25.0	NM_004579	Q86VU3	Silent	SNP	ENST00000294066.2	hg19	CCDS8082.1																																																																																			.	.		0.637	MAP4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105239.1	NM_004579		A	64563810	C	A	64563810	2	1	170	1	0	0	0	0	0	0	0	1	9269	842	30	3		3	MAP4K2	11	64563810	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	2273167	64563810	70442706	115	25806										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65349553	65349553	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gggaggctgggagtcaggacCagggatgaggctccctcagg	19	9	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:65349553C>T	ENST00000309295.4	+	9	1675	c.1410C>T	c.(1408-1410)acC>acT	p.T470T		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	470						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GAGTCAGGACCAGGGATGAGG	0.687																																					p.T470T		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.C1410T						.						25	30	28					11																	65349553		1919	4093	6012	SO:0001819	synonymous_variant	254102	exon9			CAGGACCAGGGAT	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.1410C>T	chr11.hg19:g.65349553C>T		133.0	0.0		155.0	37.0	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	hg19	CCDS44649.1																																																																																			.	.		0.687	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		T	65349553	C	T	65349553	2	4	170	1	0	0	0	0	0	0	0	1	4978	581	21	3		3	EHBP1L1	11	65349553	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	785743	65349553	69656963	116	25807										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66466555	66466555	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gtcttgattcttcttgtgccTggaacgacaccctcttgtga	9	11	4	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:66466555T>A	ENST00000533211.1	-	19	4108		c.e19-2		SPTBN2_ENST00000529997.1_Splice_Site|SPTBN2_ENST00000309996.2_Splice_Site			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2						actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						TTCTTGTGCCTGGAACGACAC	0.522																																					.		Atlas-SNP	.											.	SPTBN2	188	.	0			c.3777-2A>T						.						72	68	70					11																	66466555		2200	4295	6495	SO:0001630	splice_region_variant	6712	exon19			TGTGCCTGGAACG	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.3777-2A>T	chr11.hg19:g.66466555T>A		107.0	0.0		96.0	28.0	NM_006946	O14872|O14873	Splice_Site	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	T	13.73	2.325617	0.41197	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	.	.	.	4.7	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3076	0.60362	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SPTBN2	66223131	1.000000	0.71417	0.974000	0.42286	0.274000	0.26718	7.753000	0.85153	1.977000	0.57605	0.533000	0.62120	.	.	.		0.522	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	Intron	A	66466555	T	A	66466555	5	1	170	1	0	0	0	0	0	0	1	0	15135	1594	55	4	3477	4	SPTBN2	11	66466555	Splice_Site	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	1117002	66466555	68539961	117	25808										
FGF19	9965	hgsc.bcm.edu	37	chr11	69518447	69518447	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ccccgcgcgcagtccacgacGccgtcggcacggatgcgcag	14	18	0	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:69518447G>T	ENST00000294312.3	-	1	963	c.198C>A	c.(196-198)ggC>ggA	p.G66G		NM_005117.2	NP_005108.1	O95750	FGF19_HUMAN	fibroblast growth factor 19	66					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of bile acid biosynthetic process (GO:0070858)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of JNK cascade (GO:0046330)	extracellular region (GO:0005576)	fibroblast growth factor receptor binding (GO:0005104)			large_intestine(2)|lung(2)|skin(2)	6	all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;3.05e-56)|all cancers(3;2.69e-50)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)			AGTCCACGACGCCGTCGGCAC	0.776																																					p.G66G		Atlas-SNP	.											.	FGF19	11	.	0			c.C198A						.						3	6	5					11																	69518447		1478	2685	4163	SO:0001819	synonymous_variant	9965	exon1			CACGACGCCGTCG	AB018122	CCDS8193.1	11q13.1	2008-02-01			ENSG00000162344	ENSG00000162344			3675	protein-coding gene	gene with protein product		603891				9931477, 10525310	Standard	NM_005117		Approved		uc001opf.3	O95750	OTTHUMG00000167886	ENST00000294312.3:c.198C>A	chr11.hg19:g.69518447G>T		45.0	0.0		29.0	14.0	NM_005117		Silent	SNP	ENST00000294312.3	hg19	CCDS8193.1																																																																																			.	.		0.776	FGF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396833.1	NM_005117		T	69518447	G	T	69518447	2	4	170	1	0	0	0	0	0	0	0	1	5855	1074	38	1		1	FGF19	11	69518447	Silent	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	3051892	69518447	65488069	118	25809										
PAK1	5058	hgsc.bcm.edu	37	chr11	77070041	77070041	+	Missense_Mutation	SNP	T	T	A													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aactggtggcactgcaggagTctcagacacagccttcacat							TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:77070041T>A	ENST00000356341.3	-	6	1030	c.499A>T	c.(499-501)Act>Tct	p.T167S	PAK1_ENST00000278568.4_Missense_Mutation_p.T167S|PAK1_ENST00000530617.1_Missense_Mutation_p.T167S|PAK1_ENST00000528203.1_Missense_Mutation_p.T69S|PAK1_ENST00000525542.1_5'Flank	NM_002576.4	NP_002567.3	Q13153	PAK1_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 1	167	Interaction with CRIPAK.				actin cytoskeleton reorganization (GO:0031532)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to insulin stimulus (GO:0032869)|dendrite development (GO:0016358)|exocytosis (GO:0006887)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor clustering (GO:0043113)|response to hypoxia (GO:0001666)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|wound healing (GO:0042060)	axon (GO:0030424)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|Z disc (GO:0030018)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1)	29	all_cancers(14;1.75e-18)					ACTGCAGGAGTCTCAGACACA	0.493																																					p.T167S		Atlas-SNP	.											.	PAK1	89	.	0			c.A499T						.						75	65	69					11																	77070041		2200	4292	6492	SO:0001583	missense	5058	exon6			CAGGAGTCTCAGA	U51120	CCDS8250.1, CCDS44687.1	11q13-q14	2008-06-17	2008-06-17						8590	protein-coding gene	gene with protein product	"STE20 homolog, yeast"	602590	"p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)", "p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)"			8805275, 9533029	Standard	NM_002576		Approved		uc001oyg.4	Q13153		ENST00000356341.3:c.499A>T	chr11.hg19:g.77070041T>A	ENSP00000348696:p.Thr167Ser	58.0	0.0		49.0	10.0	NM_001128620	O75561|Q13567|Q32M53|Q32M54|Q86W79	Missense_Mutation	SNP	ENST00000356341.3	hg19	CCDS8250.1	.	.	.	.	.	.	.	.	.	.	T	8.747	0.920266	0.17982	.	.	ENSG00000149269	ENST00000356341;ENST00000530617;ENST00000278568;ENST00000528203	T;T;T;T	0.70869	-0.48;-0.51;-0.51;-0.52	5.74	4.62	0.57501	.	0.283555	0.44902	D	0.000412	T	0.55847	0.1946	L	0.42245	1.32	0.39732	D	0.971621	B;B;B;B	0.22276	0.067;0.0;0.0;0.001	B;B;B;B	0.19946	0.027;0.001;0.001;0.008	T	0.46119	-0.9214	10	0.08381	T	0.77	.	7.3244	0.26547	0.0:0.0733:0.1449:0.7818	.	69;167;167;167	E9PM17;B3KNX7;Q13153;Q13153-2	.;.;PAK1_HUMAN;.	S	167;167;167;69	ENSP00000348696:T167S;ENSP00000433423:T167S;ENSP00000278568:T167S;ENSP00000433211:T69S	ENSP00000278568:T167S	T	-	1	0	PAK1	76747689	1.000000	0.71417	0.987000	0.45799	0.995000	0.86356	2.701000	0.47094	1.003000	0.39130	0.454000	0.30748	ACT	.	.		0.493	PAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382083.2	NM_002576		A	77070041	T	A	77070041	3	1	170	1	0	0	0	0	1	0	0	0	11408	1667	58	4	1231	4	PAK1	11	77070041	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	7551594	77070041	57936475	119	25810	123	2								
PAK1	5058	hgsc.bcm.edu	37	chr11	77070043	77070043	+	Missense_Mutation	SNP	T	T	A													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctggtggcactgcaggagtcTcagacacagccttcacattc							TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:77070043T>A	ENST00000356341.3	-	6	1028	c.497A>T	c.(496-498)gAg>gTg	p.E166V	PAK1_ENST00000278568.4_Missense_Mutation_p.E166V|PAK1_ENST00000530617.1_Missense_Mutation_p.E166V|PAK1_ENST00000528203.1_Missense_Mutation_p.E68V|PAK1_ENST00000525542.1_5'Flank	NM_002576.4	NP_002567.3	Q13153	PAK1_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 1	166	Interaction with CRIPAK.				actin cytoskeleton reorganization (GO:0031532)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to insulin stimulus (GO:0032869)|dendrite development (GO:0016358)|exocytosis (GO:0006887)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor clustering (GO:0043113)|response to hypoxia (GO:0001666)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|wound healing (GO:0042060)	axon (GO:0030424)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|Z disc (GO:0030018)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1)	29	all_cancers(14;1.75e-18)					TGCAGGAGTCTCAGACACAGC	0.493																																					p.E166V		Atlas-SNP	.											.	PAK1	89	.	0			c.A497T						.						75	64	68					11																	77070043		2200	4292	6492	SO:0001583	missense	5058	exon6			GGAGTCTCAGACA	U51120	CCDS8250.1, CCDS44687.1	11q13-q14	2008-06-17	2008-06-17						8590	protein-coding gene	gene with protein product	"STE20 homolog, yeast"	602590	"p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)", "p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)"			8805275, 9533029	Standard	NM_002576		Approved		uc001oyg.4	Q13153		ENST00000356341.3:c.497A>T	chr11.hg19:g.77070043T>A	ENSP00000348696:p.Glu166Val	58.0	0.0		46.0	10.0	NM_001128620	O75561|Q13567|Q32M53|Q32M54|Q86W79	Missense_Mutation	SNP	ENST00000356341.3	hg19	CCDS8250.1	.	.	.	.	.	.	.	.	.	.	T	18.07	3.542063	0.65198	.	.	ENSG00000149269	ENST00000356341;ENST00000530617;ENST00000278568;ENST00000528203	T;T;T;T	0.72167	-0.59;-0.62;-0.62;-0.63	5.74	5.74	0.90152	.	0.088361	0.85682	D	0.000000	T	0.72277	0.3440	M	0.73598	2.24	0.80722	D	1	P;B;B;B	0.45348	0.856;0.001;0.004;0.272	B;B;B;B	0.41299	0.353;0.005;0.036;0.192	T	0.76176	-0.3055	10	0.51188	T	0.08	.	15.7037	0.77560	0.0:0.0:0.0:1.0	.	68;166;166;166	E9PM17;B3KNX7;Q13153;Q13153-2	.;.;PAK1_HUMAN;.	V	166;166;166;68	ENSP00000348696:E166V;ENSP00000433423:E166V;ENSP00000278568:E166V;ENSP00000433211:E68V	ENSP00000278568:E166V	E	-	2	0	PAK1	76747691	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.181000	0.77682	2.173000	0.68751	0.454000	0.30748	GAG	.	.		0.493	PAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382083.2	NM_002576		A	77070043	T	A	77070043	3	1	170	1	0	0	0	0	1	0	0	0	11408	1551	54	4	1233	4	PAK1	11	77070043	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	2	77070043	57936473	120	25811	123	2								
FAT3	120114	hgsc.bcm.edu	37	chr11	92600067	92600067	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggatgacagctacgtggagcGgcgccgggcgcccctctact	15	14	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:92600067G>A	ENST00000298047.6	+	21	11836	c.11819G>A	c.(11818-11820)cGg>cAg	p.R3940Q	FAT3_ENST00000525166.1_Missense_Mutation_p.R3790Q|FAT3_ENST00000409404.2_Missense_Mutation_p.R3940Q|FAT3_ENST00000533797.1_Missense_Mutation_p.R275Q			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3940	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TACGTGGAGCGGCGCCGGGCG	0.622										TCGA Ovarian(4;0.039)																											p.R3940Q		Atlas-SNP	.											.	FAT3	1822	.	0			c.G11819A						.						31	35	34					11																	92600067		1941	4120	6061	SO:0001583	missense	120114	exon21			TGGAGCGGCGCCG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.11819G>A	chr11.hg19:g.92600067G>A	ENSP00000298047:p.Arg3940Gln	72.0	0.0		62.0	22.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	29.4	5.001270	0.93227	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.74	5.74	0.90152	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.82365	0.5021	L	0.31752	0.955	0.80722	D	1	D;B	0.89917	1.0;0.175	D;B	0.70227	0.968;0.053	T	0.79885	-0.1614	9	0.32370	T	0.25	.	19.9226	0.97093	0.0:0.0:1.0:0.0	.	3940;3940	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	Q	3940;3940;3790;275	ENSP00000298047:R3940Q;ENSP00000387040:R3940Q;ENSP00000432586:R3790Q;ENSP00000436399:R275Q	ENSP00000298047:R3940Q	R	+	2	0	FAT3	92239715	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.190000	0.77755	2.720000	0.93068	0.561000	0.74099	CGG	.	.		0.622	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92600067	G	A	92600067	3	1	170	1	0	0	0	0	1	0	0	0	5699	1116	39	1	11901	1	FAT3	11	92600067	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	15530024	92600067	42406449	121	25812										
MMP20	9313	hgsc.bcm.edu	37	chr11	102495988	102495988	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gcaactagggagggggctgcAgtggaaaacttcaaagccat	14	8	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:102495988A>G	ENST00000260228.2	-	1	75	c.63T>C	c.(61-63)acT>acC	p.T21T	RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	0					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	AGGGGGCTGCAGTGGAAAACT	0.537																																					p.T21T		Atlas-SNP	.											.	MMP20	52	.	0			c.T63C						.						117	96	103					11																	102495988		2203	4299	6502	SO:0001819	synonymous_variant	9313	exon1			GGCTGCAGTGGAA	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"enamelysin"	604629	"matrix metalloproteinase 20 (enamelysin)"			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.63T>C	chr11.hg19:g.102495988A>G		104.0	0.0		75.0	24.0	NM_004771	D3DUA8|Q9H3Q0	Silent	SNP	ENST00000260228.2	hg19	CCDS8318.1																																																																																			.	.		0.537	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1			G	102495988	A	G	102495988	2	3	170	1	0	0	0	0	0	0	0	1	9668	175	7	2		2	MMP20	11	102495988	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	9895921	102495988	32510528	122	25813										
LAYN	143903	hgsc.bcm.edu	37	chr11	111430883	111430883	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	atctggccctctcctcaccaGggaaacagcccggacctaga	9	16	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr11:111430883G>T	ENST00000375615.3	+	8	1034	c.849G>T	c.(847-849)caG>caT	p.Q283H	LAYN_ENST00000533265.1_3'UTR|LAYN_ENST00000375614.2_Missense_Mutation_p.Q275H|LAYN_ENST00000525126.1_3'UTR|LAYN_ENST00000436913.2_Missense_Mutation_p.Q130H	NM_001258390.1	NP_001245319.1	Q6UX15	LAYN_HUMAN	layilin	283						cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|ruffle (GO:0001726)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|skin(1)	14		all_cancers(61;9.06e-10)|all_epithelial(67;1.34e-05)|Melanoma(852;1.74e-05)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.086)		Epithelial(105;1.5e-06)|BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|all cancers(92;2.45e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0476)	Hyaluronan(DB08818)	CTCCTCACCAGGGAAACAGCC	0.498																																					p.Q283H	Ovarian(17;551 586 12136 22082 22900)	Atlas-SNP	.											.	LAYN	35	.	0			c.G849T						.						70	73	72					11																	111430883		2201	4297	6498	SO:0001583	missense	143903	exon8			TCACCAGGGAAAC		CCDS31676.1, CCDS58178.1, CCDS58179.1	11q23.1	2006-02-09			ENSG00000204381	ENSG00000204381			29471	protein-coding gene	gene with protein product						15913605	Standard	NM_001258390		Approved	FLJ30977, FLJ31092	uc001plr.2	Q6UX15	OTTHUMG00000166721	ENST00000375615.3:c.849G>T	chr11.hg19:g.111430883G>T	ENSP00000364765:p.Gln283His	163.0	0.0		146.0	42.0	NM_001258390	A6NJB0|B4DJU0|Q8TAY8|Q96NC5|Q96NF3	Missense_Mutation	SNP	ENST00000375615.3	hg19	CCDS58178.1	.	.	.	.	.	.	.	.	.	.	G	8.107	0.777981	0.16120	.	.	ENSG00000204381	ENST00000375614;ENST00000375615;ENST00000436913;ENST00000541011	T;T	0.05580	3.83;3.42	5.5	-8.81	0.00813	.	0.974275	0.08406	N	0.950621	T	0.03871	0.0109	N	0.22421	0.69	0.09310	N	1	B;B;B	0.11235	0.003;0.003;0.004	B;B;B	0.12156	0.004;0.002;0.007	T	0.41770	-0.9490	10	0.36615	T	0.2	0.7953	10.0405	0.42155	0.2507:0.5082:0.2412:0.0	.	130;283;275	B4DJU0;Q6UX15;Q6UX15-2	.;LAYN_HUMAN;.	H	275;283;130;238	ENSP00000364764:Q275H;ENSP00000364765:Q283H	ENSP00000364764:Q275H	Q	+	3	2	LAYN	110936093	0.000000	0.05858	0.000000	0.03702	0.305000	0.27757	-0.865000	0.04250	-1.876000	0.01131	-0.294000	0.09567	CAG	.	.		0.498	LAYN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391187.1	NM_178834		T	111430883	G	T	111430883	3	4	170	1	0	0	0	0	1	0	0	0	8658	991	35	3	851	3	LAYN	11	111430883	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	8934895	111430883	23575633	123	25814										
ERC1	23085	hgsc.bcm.edu	37	chr12	1137264	1137264	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	atacaatctttaaatgctgcCtatgccacctctggccctat	5	13	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr12:1137264C>T	ENST00000397203.2	+	2	601	c.195C>T	c.(193-195)gcC>gcT	p.A65A	ERC1_ENST00000360905.4_Silent_p.A65A|ERC1_ENST00000355446.5_Silent_p.A65A|ERC1_ENST00000546231.2_Silent_p.A65A|ERC1_ENST00000543086.3_Silent_p.A65A|ERC1_ENST00000589028.1_Silent_p.A65A			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	65					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			TAAATGCTGCCTATGCCACCT	0.493																																					p.A65A		Atlas-SNP	.											.	ERC1	95	.	0			c.C195T						.						90	92	91					12																	1137264		2203	4300	6503	SO:0001819	synonymous_variant	23085	exon2			TGCTGCCTATGCC	AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"RAB6 interacting protein 2"	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.195C>T	chr12.hg19:g.1137264C>T		70.0	0.0		82.0	26.0	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Silent	SNP	ENST00000397203.2	hg19	CCDS8508.1																																																																																			.	.		0.493	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		T	1137264	C	T	1137264	2	4	170	1	0	0	0	0	0	0	0	1	5212	668	24	3		3	ERC1	12	1137264	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10		1137264	132714631	124	25815										
DBX2	440097	hgsc.bcm.edu	37	chr12	45417596	45417596	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gagcctttctctggtcctcaGaaaagacagctcttcttaaa	7	11	4	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr12:45417596G>A	ENST00000332700.6	-	3	752	c.581C>T	c.(580-582)tCt>tTt	p.S194F		NM_001004329.2	NP_001004329.2	Q6ZNG2	DBX2_HUMAN	developing brain homeobox 2	194					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	22	Lung SC(27;0.192)	Lung NSC(34;0.142)		GBM - Glioblastoma multiforme(48;0.0515)		CTGGTCCTCAGAAAAGACAGC	0.443																																					p.S194F		Atlas-SNP	.											.	DBX2	45	.	0			c.C581T						.						109	111	110					12																	45417596		2203	4300	6503	SO:0001583	missense	440097	exon3			TCCTCAGAAAAGA		CCDS31781.1	12q12	2011-06-20				ENSG00000185610		"Homeoboxes / ANTP class : NKL subclass"	33186	protein-coding gene	gene with protein product						11239429	Standard	NM_001004329		Approved	FLJ16139	uc001rok.1	Q6ZNG2	OTTHUMG00000169559	ENST00000332700.6:c.581C>T	chr12.hg19:g.45417596G>A	ENSP00000331470:p.Ser194Phe	80.0	0.0		70.0	18.0	NM_001004329		Missense_Mutation	SNP	ENST00000332700.6	hg19	CCDS31781.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.979819	0.92982	.	.	ENSG00000185610	ENST00000332700	D	0.96802	-4.13	5.49	5.49	0.81192	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000013	D	0.98645	0.9546	M	0.92923	3.36	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99517	1.0957	10	0.87932	D	0	-16.9304	19.3677	0.94471	0.0:0.0:1.0:0.0	.	194	Q6ZNG2	DBX2_HUMAN	F	194	ENSP00000331470:S194F	ENSP00000331470:S194F	S	-	2	0	DBX2	43703863	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.807000	0.99171	2.582000	0.87167	0.655000	0.94253	TCT	.	.		0.443	DBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404810.1	NM_001004329		A	45417596	G	A	45417596	3	1	170	1	0	0	0	0	1	0	0	0	4262	942	33	3	446	3	DBX2	12	45417596	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	44280332	45417596	88434299	125	25816										
TENC1	23371	hgsc.bcm.edu	37	chr12	53454679	53454679	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggagtccagggggccactcaGatggcgccagtcctcggagc	16	13	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr12:53454679G>T	ENST00000314250.6	+	20	3279	c.2989G>T	c.(2989-2991)Gat>Tat	p.D997Y	TENC1_ENST00000314276.3_Missense_Mutation_p.D1007Y|TENC1_ENST00000546602.1_Missense_Mutation_p.D900Y|TENC1_ENST00000549700.1_Missense_Mutation_p.D932Y|TENC1_ENST00000552570.1_Missense_Mutation_p.D997Y|TENC1_ENST00000451358.1_Missense_Mutation_p.D987Y|TENC1_ENST00000379902.3_Missense_Mutation_p.D873Y	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	997	Pro-rich.				cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						GGGCCACTCAGATGGCGCCAG	0.697																																					p.D1007Y		Atlas-SNP	.											.	TENC1	148	.	0			c.G3019T						.						18	20	19					12																	53454679		2198	4298	6496	SO:0001583	missense	23371	exon20			CACTCAGATGGCG	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	19737	protein-coding gene	gene with protein product	"tensin 2"	607717	"tensin like C1 domain-containing phosphatase"				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.2989G>T	chr12.hg19:g.53454679G>T	ENSP00000319684:p.Asp997Tyr	89.0	0.0		105.0	29.0	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Missense_Mutation	SNP	ENST00000314250.6	hg19	CCDS8843.1	.	.	.	.	.	.	.	.	.	.	G	7.511	0.654653	0.14580	.	.	ENSG00000111077	ENST00000379902;ENST00000314276;ENST00000314250;ENST00000451358;ENST00000546602;ENST00000552570;ENST00000549700	D;D;D;D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42;-3.39;-3.42;-3.41	4.45	3.54	0.40534	.	0.825543	0.10800	N	0.632769	D	0.88043	0.6331	N	0.14661	0.345	0.25593	N	0.986679	P;P;P;P	0.37276	0.589;0.589;0.454;0.589	B;B;B;B	0.37888	0.192;0.192;0.133;0.26	T	0.80564	-0.1326	10	0.44086	T	0.13	-2.1879	7.6828	0.28524	0.1184:0.0:0.8816:0.0	.	997;900;997;1007	Q63HR2-6;Q63HR2-2;Q63HR2;Q63HR2-4	.;.;TENC1_HUMAN;.	Y	873;1007;997;987;900;997;932	ENSP00000369232:D873Y;ENSP00000319756:D1007Y;ENSP00000319684:D997Y;ENSP00000393362:D987Y;ENSP00000449363:D900Y;ENSP00000447021:D997Y;ENSP00000449361:D932Y	ENSP00000319684:D997Y	D	+	1	0	TENC1	51740946	0.021000	0.18746	0.312000	0.25196	0.082000	0.17680	2.016000	0.40971	1.206000	0.43276	0.561000	0.74099	GAT	.	.		0.697	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754		T	53454679	G	T	53454679	3	4	170	1	0	0	0	0	1	0	0	0	15773	942	33	3	3176	3	TENC1	12	53454679	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	8037083	53454679	80397216	126	25817										
SPRYD3	84926	hgsc.bcm.edu	37	chr12	53460128	53460128	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctgccctcatgctccggctcTatctcttccccatcctcttc	4	20	4	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr12:53460128T>A	ENST00000301463.4	-	10	1250	c.1164A>T	c.(1162-1164)atA>atT	p.I388I	SPRYD3_ENST00000547837.1_Silent_p.I425I	NM_032840.2	NP_116229.1	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3	388	Glu-rich.									central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						GCTCCGGCTCTATctcttccc	0.582											OREG0021856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I388I		Atlas-SNP	.											.	SPRYD3	29	.	0			c.A1164T						.						306	237	261					12																	53460128		2203	4300	6503	SO:0001819	synonymous_variant	84926	exon10			CGGCTCTATCTCT	AK074694	CCDS8845.1	12q13.13	2006-11-29		2006-02-02		ENSG00000167778			25920	protein-coding gene	gene with protein product						14702039	Standard	NM_032840		Approved	FLJ14800	uc001sbt.2	Q8NCJ5	OTTHUMG00000170101	ENST00000301463.4:c.1164A>T	chr12.hg19:g.53460128T>A		82.0	0.0	992	94.0	28.0	NM_032840	B9EG99|Q96SK5	Silent	SNP	ENST00000301463.4	hg19	CCDS8845.1																																																																																			.	.		0.582	SPRYD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407264.1	NM_032840		A	53460128	T	A	53460128	2	1	170	1	0	0	0	0	0	0	0	1	15124	1512	53	4		4	SPRYD3	12	53460128	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	5449	53460128	80391767	127	25818										
RARG	5916	hgsc.bcm.edu	37	chr12	53608001	53608001	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ccccagatccagctgcacgcGgtggtctgcactggagttct	12	14	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr12:53608001G>A	ENST00000425354.2	-	7	1142	c.655C>T	c.(655-657)Cgc>Tgc	p.R219C	RARG_ENST00000327550.3_Missense_Mutation_p.R147C|RARG_ENST00000394426.1_Missense_Mutation_p.R219C|RARG_ENST00000543726.1_Missense_Mutation_p.R197C|RARG_ENST00000338561.5_Missense_Mutation_p.R208C|RARG_ENST00000543762.1_5'UTR	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	219	Ligand-binding.				anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R219C(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	AGCTGCACGCGGTGGTCTGCA	0.567																																					p.R219C		Atlas-SNP	.											RARG,colon,carcinoma,0,1	RARG	53	.	1	Substitution - Missense(1)	large_intestine(1)	c.C655T						.						77	67	70					12																	53608001		2203	4300	6503	SO:0001583	missense	5916	exon7			GCACGCGGTGGTC	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"Nuclear hormone receptors"	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.655C>T	chr12.hg19:g.53608001G>A	ENSP00000388510:p.Arg219Cys	93.0	0.0		83.0	17.0	NM_000966	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Missense_Mutation	SNP	ENST00000425354.2	hg19	CCDS8850.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.464891	0.63513	.	.	ENSG00000172819	ENST00000425354;ENST00000394426;ENST00000327550;ENST00000338561;ENST00000543726;ENST00000550265	T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23	5.37	5.37	0.77165	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	T	0.61110	0.2321	M	0.83603	2.65	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;P	0.81914	0.986;0.985;0.995;0.817	T	0.64398	-0.6417	10	0.59425	D	0.04	.	11.8888	0.52618	0.0:0.0:0.7219:0.2781	.	256;197;219;208	F8VR45;B7Z4F1;P13631;F1D8P1	.;.;RARG_HUMAN;.	C	219;219;147;208;197;256	ENSP00000388510:R219C;ENSP00000377947:R219C;ENSP00000332695:R147C;ENSP00000343698:R208C;ENSP00000444335:R197C	ENSP00000332695:R147C	R	-	1	0	RARG	51894268	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.445000	0.44899	2.688000	0.91661	0.563000	0.77884	CGC	.	.		0.567	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966		A	53608001	G	A	53608001	3	1	170	1	0	0	0	0	1	0	0	0	13069	1116	39	1	725	1	RARG	12	53608001	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	147873	53608001	80243894	128	25819										
CALCOCO1	57658	hgsc.bcm.edu	37	chr12	54105826	54105826	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctcagcaggaaagcgctcctTacagataggacactccttcc	8	14	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr12:54105826T>A	ENST00000550804.1	-	15	2038	c.1978A>T	c.(1978-1980)Aag>Tag	p.K660*	CALCOCO1_ENST00000262059.4_Nonsense_Mutation_p.K659*|CALCOCO1_ENST00000548263.1_3'UTR|CALCOCO1_ENST00000430117.2_Nonsense_Mutation_p.K575*			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	660	C-terminal AD (CTNNB1 binding site). {ECO:0000250}.			K -> E (in Ref. 7; CAG38598). {ECO:0000305}.	intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						AAGCGCTCCTTACAGATAGGA	0.547																																					p.K660X		Atlas-SNP	.											.	CALCOCO1	50	.	0			c.A1978T						.						145	127	133					12																	54105826		2203	4300	6503	SO:0001587	stop_gained	57658	exon15			GCTCCTTACAGAT	AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"coiled-coil leucine zipper coactivator 1", "inorganic pyrophosphatase activator"					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.1978A>T	chr12.hg19:g.54105826T>A	ENSP00000449960:p.Lys660*	170.0	0.0		160.0	45.0	NM_020898	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Nonsense_Mutation	SNP	ENST00000550804.1	hg19	CCDS8864.1	.	.	.	.	.	.	.	.	.	.	t	37	6.342693	0.97489	.	.	ENSG00000012822	ENST00000342760;ENST00000430117;ENST00000262059;ENST00000413257;ENST00000550804	.	.	.	4.26	4.26	0.50523	.	0.207171	0.24431	N	0.038596	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-23.0702	8.0675	0.30669	0.0:0.0:0.2057:0.7943	.	.	.	.	X	361;575;659;598;660	.	ENSP00000262059:K659X	K	-	1	0	CALCOCO1	52392093	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.821000	0.39041	1.933000	0.56026	0.375000	0.23000	AAG	.	.		0.547	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898		A	54105826	T	A	54105826	4	1	170	1	0	0	0	0	0	1	0	0	2579	1763	61	4	101	4	CALCOCO1	12	54105826	Nonsense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	497825	54105826	79746069	129	25820										
LRP1	4035	hgsc.bcm.edu	37	chr12	57589063	57589063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tccccctacagaaggcaagaCgtgcggcccctcctccttct	8	18	1	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr12:57589063C>T	ENST00000243077.3	+	52	8784	c.8318C>T	c.(8317-8319)aCg>aTg	p.T2773M	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2773	LDL-receptor class A 17. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GAAGGCAAGACGTGCGGCCCC	0.627																																					p.T2773M		Atlas-SNP	.											.	LRP1	428	.	0			c.C8318T						.						117	123	121					12																	57589063		2203	4300	6503	SO:0001583	missense	4035	exon52			GCAAGACGTGCGG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.8318C>T	chr12.hg19:g.57589063C>T	ENSP00000243077:p.Thr2773Met	53.0	0.0		51.0	15.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966717	0.74131	.	.	ENSG00000123384	ENST00000243077	D	0.96073	-3.9	4.82	4.82	0.62117	.	0.000000	0.64402	D	0.000001	D	0.97411	0.9153	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97764	1.0222	10	0.59425	D	0.04	.	16.8286	0.85938	0.0:1.0:0.0:0.0	.	2773	Q07954	LRP1_HUMAN	M	2773	ENSP00000243077:T2773M	ENSP00000243077:T2773M	T	+	2	0	LRP1	55875330	1.000000	0.71417	0.992000	0.48379	0.939000	0.58152	4.736000	0.62059	2.493000	0.84123	0.462000	0.41574	ACG	.	.		0.627	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57589063	C	T	57589063	3	4	170	1	0	0	0	0	1	0	0	0	8960	536	19	1	8524	1	LRP1	12	57589063	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	3483237	57589063	76262832	130	25821										
NOS1	4842	hgsc.bcm.edu	37	chr12	117657990	117657990	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agccatggtgacgtccccacAgacgtatatgtggccccctt	10	14	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr12:117657990A>T	ENST00000338101.4	-	27	4166	c.4162T>A	c.(4162-4164)Tgt>Agt	p.C1388S	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.C1354S			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		ACGTCCCCACAGACGTATATG	0.597																																					p.C1388S	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.T4162A						.						142	153	150					12																	117657990		2199	4299	6498	SO:0001583	missense	4842	exon28			CCCCACAGACGTA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.4162T>A	chr12.hg19:g.117657990A>T	ENSP00000337459:p.Cys1388Ser	50.0	0.0		42.0	16.0	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.399238	0.83120	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000338101	D;D	0.91295	-2.82;-2.82	4.44	3.27	0.37495	Oxidoreductase FAD/NAD(P)-binding (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.000000	0.85682	D	0.000000	D	0.93805	0.8019	M	0.87328	2.875	0.80722	D	1	P	0.43938	0.822	P	0.52793	0.709	D	0.93514	0.6855	10	0.87932	D	0	-17.9165	11.2674	0.49118	0.8471:0.1528:0.0:0.0	.	1354	P29475	NOS1_HUMAN	S	1249;1354;1388	ENSP00000320758:C1354S;ENSP00000337459:C1388S	ENSP00000320758:C1354S	C	-	1	0	NOS1	116142373	1.000000	0.71417	0.627000	0.29227	0.926000	0.56050	7.282000	0.78630	0.712000	0.32039	0.459000	0.35465	TGT	.	.		0.597	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			T	117657990	A	T	117657990	3	4	170	1	0	0	0	0	1	0	0	0	10550	188	7	4	256	4	NOS1	12	117657990	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	60068927	117657990	16193905	131	25822										
SACS	26278	hgsc.bcm.edu	37	chr13	23929324	23929324	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ccagctctctccattttatgCtcctgcggttatcagtaagg	8	12	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr13:23929324C>T	ENST00000382292.3	-	7	1700	c.1427G>A	c.(1426-1428)aGc>aAc	p.S476N	SACS_ENST00000476776.1_5'Flank|SACS_ENST00000402364.1_5'UTR|SACS_ENST00000382298.3_Missense_Mutation_p.S476N			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	476					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CCATTTTATGCTCCTGCGGTT	0.483																																					p.S476N		Atlas-SNP	.											.	SACS	871	.	0			c.G1427A						.						58	57	58					13																	23929324		2203	4300	6503	SO:0001583	missense	26278	exon8			TTTATGCTCCTGC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.1427G>A	chr13.hg19:g.23929324C>T	ENSP00000371729:p.Ser476Asn	64.0	0.0		53.0	17.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	28.9	4.962941	0.92791	.	.	ENSG00000151835	ENST00000382292;ENST00000382298;ENST00000423156	T;T;T	0.18657	2.2;2.2;2.2	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.38746	0.1052	L	0.36672	1.1	0.54753	D	0.999987	D;P;P	0.76494	0.999;0.729;0.638	D;B;P	0.71414	0.973;0.413;0.613	T	0.02365	-1.1170	10	0.44086	T	0.13	.	19.9404	0.97159	0.0:1.0:0.0:0.0	.	375;263;476	B2REB1;E9PAL4;Q9NZJ4	.;.;SACS_HUMAN	N	476;476;100	ENSP00000371729:S476N;ENSP00000371735:S476N;ENSP00000390925:S100N	ENSP00000371729:S476N	S	-	2	0	SACS	22827324	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.764000	0.85297	2.788000	0.95919	0.555000	0.69702	AGC	.	.		0.483	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23929324	C	T	23929324	3	4	170	1	0	0	0	0	1	0	0	0	13819	797	28	3	12324	3	SACS	13	23929324	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10		23929324	91240554	132	25823										
PDS5B	23047	hgsc.bcm.edu	37	chr13	33333788	33333788	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tttcagtaacaccaaaaattAtctgcctcctgaaatgaaat	4	9	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr13:33333788A>G	ENST00000315596.10	+	29	3518	c.3332A>G	c.(3331-3333)tAt>tGt	p.Y1111C		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	1111					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		ACCAAAAATTATCTGCCTCCT	0.313																																					p.Y1111C		Atlas-SNP	.											.	PDS5B	141	.	0			c.A3332G						.						75	70	71					13																	33333788		1801	4058	5859	SO:0001583	missense	23047	exon29			AAAATTATCTGCC	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"androgen-induced proliferation inhibitor"	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.3332A>G	chr13.hg19:g.33333788A>G	ENSP00000313851:p.Tyr1111Cys	102.0	0.0		103.0	28.0	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	hg19	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.312817	0.81358	.	.	ENSG00000083642	ENST00000315596;ENST00000421084;ENST00000447833	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.77831	0.4189	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.78450	-0.2199	9	0.46703	T	0.11	-21.814	15.5627	0.76262	1.0:0.0:0.0:0.0	.	1111	Q9NTI5	PDS5B_HUMAN	C	1111;1111;65	.	ENSP00000313851:Y1111C	Y	+	2	0	PDS5B	32231788	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.887000	0.92456	2.153000	0.67306	0.528000	0.53228	TAT	.	.		0.313	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		G	33333788	A	G	33333788	3	3	170	1	0	0	0	0	1	0	0	0	11701	449	16	2	3442	2	PDS5B	13	33333788	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	9404464	33333788	81836090	133	25824										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77672195	77672195	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gaaggaagcaaacacagctcTggcacattcggccacagaag	11	11	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr13:77672195T>A	ENST00000544440.2	-	56	8997	c.8980A>T	c.(8980-8982)Aga>Tga	p.R2994*	MYCBP2_ENST00000482517.1_5'Flank|MYCBP2_ENST00000357337.6_Nonsense_Mutation_p.R2994*|MYCBP2_ENST00000407578.2_Nonsense_Mutation_p.R3032*|MYCBP2-AS1_ENST00000593933.1_RNA					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		AACACAGCTCTGGCACATTCG	0.443																																					p.R3032X		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A9094T						.						78	75	76					13																	77672195		2203	4300	6503	SO:0001587	stop_gained	23077	exon56			CAGCTCTGGCACA	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.8980A>T	chr13.hg19:g.77672195T>A	ENSP00000444596:p.Arg2994*	64.0	0.0		115.0	30.0	NM_015057		Nonsense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	T	48	14.860176	0.99813	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	.	.	.	5.57	-1.86	0.07760	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	21.0492	0.99944	0.0:0.0:0.7593:0.2407	.	.	.	.	X	2994;3032;2994	.	ENSP00000349892:R2994X	R	-	1	2	MYCBP2	76570196	1.000000	0.71417	0.986000	0.45419	0.947000	0.59692	1.020000	0.30027	-0.540000	0.06265	0.482000	0.46254	AGA	.	.		0.443	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		A	77672195	T	A	77672195	4	1	170	1	0	0	0	0	0	1	0	0	10027	1588	55	4	5054	4	MYCBP2	13	77672195	Nonsense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	44338407	77672195	37497683	134	25825										
DAOA	267012	hgsc.bcm.edu	37	chr13	106119492	106119492	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aactctctaaactctattggTatgttactctttatctttat	3	8	4	0	rs148297571	byFrequency	TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr13:106119492T>C	ENST00000375936.3	+	2	179		c.e2+2		DAOA-AS1_ENST00000448407.1_RNA|DAOA_ENST00000329625.5_Splice_Site	NM_001161812.1|NM_172370.3	NP_001155284.1|NP_758958.3	P59103	DAOA_HUMAN	D-amino acid oxidase activator						negative regulation of D-amino-acid oxidase activity (GO:1900758)|positive regulation of catalytic activity (GO:0043085)	Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	13	Lung NSC(43;0.01)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					ACTCTATTGGTATGTTACTCT	0.289																																					.		Atlas-SNP	.											.	DAOA	26	.	0			c.133+2T>C						.						69	66	67					13																	106119492		1790	4063	5853	SO:0001630	splice_region_variant	267012	exon2			TATTGGTATGTTA	AY138547	CCDS41905.1, CCDS53880.1, CCDS59242.1	13q33.2	2011-08-01			ENSG00000182346	ENSG00000182346			21191	protein-coding gene	gene with protein product	"G72 transcript"	607408				12364586, 15057823	Standard	NM_001161814		Approved	G72	uc010tjg.2	P59103	OTTHUMG00000041333	ENST00000375936.3:c.133+2T>C	chr13.hg19:g.106119492T>C		62.0	0.0		78.0	10.0	NM_172370	A6NKG7|Q0VAE6|Q5VX59|Q86Y17|Q8IWM4	Splice_Site	SNP	ENST00000375936.3	hg19	CCDS41905.1	.	.	.	.	.	.	.	.	.	.	T	1.982	-0.433970	0.04669	.	.	ENSG00000182346	ENST00000375936	.	.	.	3.19	0.607	0.17564	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999986	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.3622	0.04310	0.2417:0.1378:0.0:0.6205	.	.	.	.	.	-1	.	.	.	+	.	.	DAOA	104917493	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	0.961000	0.29267	0.122000	0.18314	0.455000	0.32223	.	.	T|0.994;A|0.006		0.289	DAOA-005	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099040.2	NM_172370	Intron	C	106119492	T	C	106119492	5	2	170	1	0	0	0	0	0	0	1	0	4234	1652	57	2	141	2	DAOA	13	106119492	Splice_Site	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	28447297	106119492	9050386	135	25826										
FANCM	57697	hgsc.bcm.edu	37	chr14	45645056	45645056	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gagcatttacgaagtgataaAtgcacctgtttgctgtcaca	9	8	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr14:45645056A>G	ENST00000267430.5	+	14	3184	c.3099A>G	c.(3097-3099)aaA>aaG	p.K1033K	FANCM_ENST00000542564.2_Silent_p.K1007K	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1033					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						GAAGTGATAAATGCACCTGTT	0.363								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.K1033K		Atlas-SNP	.											.	FANCM	225	.	0			c.A3099G						.						39	34	36					14																	45645056		2203	4298	6501	SO:0001819	synonymous_variant	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGATAAATGCACC	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.3099A>G	chr14.hg19:g.45645056A>G		156.0	0.0		151.0	48.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Silent	SNP	ENST00000267430.5	hg19	CCDS32070.1																																																																																			.	.		0.363	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45645056	A	G	45645056	2	3	170	1	0	0	0	0	0	0	0	1	5679	98	4	2		2	FANCM	14	45645056	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10		45645056	61704484	136	25827										
COQ6	51004	hgsc.bcm.edu	37	chr14	74417192	74417192	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgggcgctgccatggcctgtGccttgggtaagcccttctcc	13	14	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr14:74417192G>A	ENST00000334571.2	+	1	197	c.157G>A	c.(157-159)Gcc>Acc	p.A53T	FAM161B_ENST00000286544.3_5'Flank|COQ6_ENST00000555552.1_3'UTR|COQ6_ENST00000394026.4_Intron|COQ6_ENST00000554920.1_Missense_Mutation_p.A53T|FAM161B_ENST00000534936.1_5'Flank|COQ6_ENST00000238709.4_Intron	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	53					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		CATGGCCTGTGCCTTGGGTAA	0.657																																					p.A53T		Atlas-SNP	.											.	COQ6	27	.	0			c.G157A						.						32	27	29					14																	74417192		2202	4297	6499	SO:0001583	missense	51004	exon1			GCCTGTGCCTTGG	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"coenzyme Q6 homolog (yeast)", "coenzyme Q6 homolog, monooxygenase (yeast)", "coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.157G>A	chr14.hg19:g.74417192G>A	ENSP00000333946:p.Ala53Thr	79.0	0.0		95.0	26.0	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Missense_Mutation	SNP	ENST00000334571.2	hg19	CCDS9823.1	.	.	.	.	.	.	.	.	.	.	G	32	5.184132	0.94885	.	.	ENSG00000119723	ENST00000334571;ENST00000556300;ENST00000554920;ENST00000545052	T	0.48201	0.82	5.01	5.01	0.66863	Aromatic-ring hydroxylase-like (1);	0.052943	0.85682	D	0.000000	T	0.67316	0.2880	M	0.65498	2.005	0.80722	D	1	D;P	0.65815	0.995;0.952	D;P	0.66847	0.947;0.703	T	0.70234	-0.4928	10	0.72032	D	0.01	-2.6135	18.5698	0.91130	0.0:0.0:1.0:0.0	.	53;53	B7Z357;Q9Y2Z9	.;COQ6_HUMAN	T	53	ENSP00000333946:A53T	ENSP00000333946:A53T	A	+	1	0	COQ6	73486945	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.548000	0.67255	2.615000	0.88500	0.650000	0.86243	GCC	.	.		0.657	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1			A	74417192	G	A	74417192	3	1	170	1	0	0	0	0	1	0	0	0	3751	1319	46	3	159	3	COQ6	14	74417192	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	28772136	74417192	32932348	137	25828										
PROX2	283571	hgsc.bcm.edu	37	chr14	75329266	75329266	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aaaggcagtgcctccatgacAgcatgcaggcctctctgttc	10	13	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr14:75329266A>T	ENST00000445876.1	-	1	1271	c.1272T>A	c.(1270-1272)gcT>gcA	p.A424A	PROX2_ENST00000556084.2_Intron|PROX2_ENST00000556489.2_Silent_p.A424A			Q3B8N5	PROX2_HUMAN	prospero homeobox 2	424					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(3)	6			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)		CCTCCATGACAGCATGCAGGC	0.512																																					p.A424A		Atlas-SNP	.											.	PROX2	44	.	0			c.T1272A						.						92	93	93					14																	75329266		2014	4176	6190	SO:0001819	synonymous_variant	283571	exon1			CATGACAGCATGC		CCDS45136.1, CCDS45136.2, CCDS73663.1	14q24.3	2012-10-02			ENSG00000119608	ENSG00000119608		"Homeoboxes / PROS class"	26715	protein-coding gene	gene with protein product		615094					Standard	NM_001080408		Approved	FLJ36749	uc031qpi.1	Q3B8N5	OTTHUMG00000171481	ENST00000445876.1:c.1272T>A	chr14.hg19:g.75329266A>T		49.0	0.0		61.0	20.0	NM_001243007	C9J5W1|Q8N9Q3	Silent	SNP	ENST00000445876.1	hg19	CCDS45136.2																																																																																			.	.		0.512	PROX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	75329266	A	T	75329266	2	4	170	1	0	0	0	0	0	0	0	1	12573	175	7	4		4	PROX2	14	75329266	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	912074	75329266	32020274	138	25829										
RPS6KA5	9252	hgsc.bcm.edu	37	chr14	91340125	91340125	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tttaagccttttgtttggatCtactgtgagaagtcctttgg	10	6	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr14:91340125C>A	ENST00000261991.3	-	16	2184	c.2011G>T	c.(2011-2013)Gat>Tat	p.D671Y	RPS6KA5_ENST00000536315.2_Missense_Mutation_p.D592Y	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	671	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		TTGTTTGGATCTACTGTGAGA	0.353																																					p.D671Y		Atlas-SNP	.											.	RPS6KA5	135	.	0			c.G2011T						.						219	216	217					14																	91340125		2203	4300	6503	SO:0001583	missense	9252	exon16			TTGGATCTACTGT	AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"ribosomal protein S6 kinase, 90kD, polypeptide 5"			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.2011G>T	chr14.hg19:g.91340125C>A	ENSP00000261991:p.Asp671Tyr	38.0	0.0		59.0	15.0	NM_004755	O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	hg19	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.488128	0.84854	.	.	ENSG00000100784	ENST00000261991;ENST00000536315	T;T	0.58506	0.33;0.33	5.44	5.44	0.79542	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.82476	0.5045	M	0.92122	3.275	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.86682	0.1917	10	0.87932	D	0	.	19.2862	0.94072	0.0:1.0:0.0:0.0	.	671	O75582	KS6A5_HUMAN	Y	671;592	ENSP00000261991:D671Y;ENSP00000442803:D592Y	ENSP00000261991:D671Y	D	-	1	0	RPS6KA5	90409878	1.000000	0.71417	0.992000	0.48379	0.954000	0.61252	7.794000	0.85869	2.553000	0.86117	0.650000	0.86243	GAT	.	.		0.353	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		A	91340125	C	A	91340125	3	1	170	1	0	0	0	0	1	0	0	0	13669	913	32	3	405	3	RPS6KA5	14	91340125	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	16010859	91340125	16009415	139	25830										
DICER1	23405	hgsc.bcm.edu	37	chr14	95590842	95590842	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agtgctcttcacatagtgcaTgtattttccttaggaaagtg	9	7	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr14:95590842T>A	ENST00000526495.1	-	10	1358	c.1067A>T	c.(1066-1068)cAt>cTt	p.H356L	DICER1_ENST00000527414.1_Missense_Mutation_p.H356L|DICER1_ENST00000343455.3_Missense_Mutation_p.H356L|DICER1_ENST00000541352.1_Missense_Mutation_p.H356L|DICER1_ENST00000393063.1_Missense_Mutation_p.H356L			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	356	Required for interaction with PRKRA and TARBP2.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		ACATAGTGCATGTATTTTCCT	0.373			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.H356L		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.A1067T						.						136	137	136					14																	95590842		2203	4300	6503	SO:0001583	missense	23405	exon9	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	AGTGCATGTATTT	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.1067A>T	chr14.hg19:g.95590842T>A	ENSP00000437256:p.His356Leu	146.0	0.0		145.0	42.0	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	hg19	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.457908	0.84317	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000541352	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.49847	0.1581	L	0.56769	1.78	0.80722	D	1	D	0.56035	0.974	P	0.51742	0.678	T	0.41787	-0.9489	10	0.20046	T	0.44	-27.1109	15.6811	0.77371	0.0:0.0:0.0:1.0	.	356	Q9UPY3	DICER_HUMAN	L	356	ENSP00000343745:H356L;ENSP00000437256:H356L;ENSP00000376783:H356L;ENSP00000435681:H356L;ENSP00000444719:H356L	ENSP00000343745:H356L	H	-	2	0	DICER1	94660595	1.000000	0.71417	0.761000	0.31378	0.997000	0.91878	7.471000	0.80985	2.106000	0.64143	0.477000	0.44152	CAT	.	.		0.373	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			A	95590842	T	A	95590842	3	1	170	1	0	0	0	0	1	0	0	0	4523	1464	51	4	4781	4	DICER1	14	95590842	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	4250717	95590842	11758698	140	25831										
TECPR2	9895	hgsc.bcm.edu	37	chr14	102898383	102898383	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cccctgtcacagagattcaaCgccatcagctcagaggactt	8	14	4	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr14:102898383C>T	ENST00000359520.7	+	8	1561	c.1335C>T	c.(1333-1335)aaC>aaT	p.N445N	TECPR2_ENST00000558678.1_Silent_p.N445N	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	445					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						AGAGATTCAACGCCATCAGCT	0.592																																					p.N445N		Atlas-SNP	.											.	TECPR2	114	.	0			c.C1335T						.						17	18	17					14																	102898383		2082	4102	6184	SO:0001819	synonymous_variant	9895	exon8			ATTCAACGCCATC	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"KIAA0329"	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.1335C>T	chr14.hg19:g.102898383C>T		93.0	0.0		80.0	21.0	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Silent	SNP	ENST00000359520.7	hg19	CCDS32162.1																																																																																			.	.		0.592	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		T	102898383	C	T	102898383	2	4	170	1	0	0	0	0	0	0	0	1	15759	535	19	1		1	TECPR2	14	102898383	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	7307541	102898383	4451157	141	25832										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24921184	24921184	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gttccgccggaacgcccgtcGcaggccttcagcagccagca	12	17	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr15:24921184G>A	ENST00000329468.2	+	1	644	c.170G>A	c.(169-171)cGc>cAc	p.R57H		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	57					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											AACGCCCGTCGCAGGCCTTCA	0.746																																					p.R57H		Atlas-SNP	.											C15orf2,caecum,carcinoma,0,2	.	.	.	0			c.G170A						.						15	19	17					15																	24921184		2167	4254	6421	SO:0001583	missense	23742	exon1			CCCGTCGCAGGCC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.170G>A	chr15.hg19:g.24921184G>A	ENSP00000333735:p.Arg57His	136.0	0.0		134.0	39.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	15.11	2.735211	0.48939	.	.	ENSG00000185823	ENST00000329468	T	0.07216	3.21	2.17	1.23	0.21249	.	.	.	.	.	T	0.09113	0.0225	L	0.34521	1.04	0.09310	N	1	D	0.69078	0.997	P	0.53518	0.728	T	0.28586	-1.0039	9	0.17369	T	0.5	.	4.5859	0.12282	0.1955:0.0:0.8045:0.0	.	57	Q9NZP6	CO002_HUMAN	H	57	ENSP00000333735:R57H	ENSP00000333735:R57H	R	+	2	0	C15orf2	22472277	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.074000	0.14662	0.465000	0.27167	0.484000	0.47621	CGC	.	.		0.746	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24921184	G	A	24921184	3	1	170	1	0	0	0	0	1	0	0	0	1786	1087	38	1	172	1	C15orf2	15	24921184	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10		24921184	77610208	142	25833										
C15orf55	256646	hgsc.bcm.edu	37	chr15	34646775	34646775	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctgtgaaggagtatgttgacAtcatggaatggctggtgggg	17	4	1	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr15:34646775A>T	ENST00000333756.4	+	5	1275	c.1120A>T	c.(1120-1122)Atc>Ttc	p.I374F	NUTM1_ENST00000537011.1_Missense_Mutation_p.I402F|NUTM1_ENST00000438749.3_Missense_Mutation_p.I392F	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	374						cytoplasm (GO:0005737)|nucleus (GO:0005634)											GTATGTTGACATCATGGAATG	0.587																																					p.I374F		Atlas-SNP	.											.	C15orf55	110	.	0			c.A1120T						.						122	119	120					15																	34646775		2201	4298	6499	SO:0001583	missense	256646	exon5			GTTGACATCATGG	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"nuclear protein in testis"	608963	"chromosome 15 open reading frame 55"	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.1120A>T	chr15.hg19:g.34646775A>T	ENSP00000329448:p.Ile374Phe	146.0	0.0		179.0	58.0	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	hg19	CCDS32190.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.434087	0.62955	.	.	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000354999;ENST00000333756	T;T;T	0.16073	2.37;2.38;2.38	5.32	4.19	0.49359	Nuclear Testis protein, C-terminal (1);	0.000000	0.56097	D	0.000039	T	0.41166	0.1147	M	0.83483	2.645	0.39550	D	0.968951	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.995;0.992;0.997	T	0.43426	-0.9392	10	0.87932	D	0	.	8.5691	0.33558	0.9111:0.0:0.0889:0.0	.	392;402;374	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	F	402;392;243;374	ENSP00000444896:I402F;ENSP00000407031:I392F;ENSP00000329448:I374F	ENSP00000329448:I374F	I	+	1	0	C15orf55	32434067	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	4.911000	0.63328	2.133000	0.65898	0.482000	0.46254	ATC	.	.		0.587	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		T	34646775	A	T	34646775	3	4	170	1	0	0	0	0	1	0	0	0	1805	217	8	4	1138	4	C15orf55	15	34646775	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	9725591	34646775	67884617	143	25834										
LTK	4058	hgsc.bcm.edu	37	chr15	41804112	41804112	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	catccatcgccgcgtgctctTcaacggctcgagactccccg	9	18	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr15:41804112T>A	ENST00000263800.6	-	5	656	c.560A>T	c.(559-561)gAa>gTa	p.E187V	LTK_ENST00000453182.2_Missense_Mutation_p.E187V|LTK_ENST00000561619.1_Intron|LTK_ENST00000355166.5_Missense_Mutation_p.E187V	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	187					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CGCGTGCTCTTCAACGGCTCG	0.746										TSP Lung(18;0.14)																											p.E187V		Atlas-SNP	.											.	LTK	117	.	0			c.A560T						.						3	4	4					15																	41804112		1796	3749	5545	SO:0001583	missense	4058	exon5			TGCTCTTCAACGG	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.560A>T	chr15.hg19:g.41804112T>A	ENSP00000263800:p.Glu187Val	76.0	0.0		81.0	24.0	NM_001135685	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.755498	0.69648	.	.	ENSG00000062524	ENST00000360087;ENST00000355166;ENST00000263800;ENST00000453182	T;T;T	0.47177	0.85;0.85;0.85	3.38	2.24	0.28232	.	0.481200	0.15183	U	0.275992	T	0.60327	0.2260	M	0.67397	2.05	0.26839	N	0.968425	D;D;P	0.63046	0.992;0.989;0.553	D;P;B	0.65443	0.935;0.893;0.259	T	0.49661	-0.8916	10	0.56958	D	0.05	.	7.4895	0.27454	0.0:0.1091:0.0:0.8909	.	187;187;187	E9PFX4;P29376-4;P29376	.;.;LTK_HUMAN	V	187	ENSP00000347293:E187V;ENSP00000263800:E187V;ENSP00000392196:E187V	ENSP00000263800:E187V	E	-	2	0	LTK	39591404	0.291000	0.24352	0.260000	0.24451	0.044000	0.14063	0.249000	0.18216	0.385000	0.24970	-0.441000	0.05720	GAA	.	.		0.746	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			A	41804112	T	A	41804112	3	1	170	1	0	0	0	0	1	0	0	0	9089	1783	62	4	2098	4	LTK	15	41804112	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	7157337	41804112	60727280	144	25835										
DUOX1	53905	hgsc.bcm.edu	37	chr15	45426494	45426494	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctgagaaaccgcacagtgttGggggtcttctttggtgagaa	14	7	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr15:45426494G>A	ENST00000321429.4	+	5	701	c.294G>A	c.(292-294)ttG>ttA	p.L98L	DUOX1_ENST00000389037.3_Silent_p.L98L	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	98	Peroxidase-like; mediates peroxidase activity.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GCACAGTGTTGGGGGTCTTCT	0.602																																					p.L98L		Atlas-SNP	.											.	DUOX1	125	.	0			c.G294A						.						38	43	42					15																	45426494		2198	4298	6496	SO:0001819	synonymous_variant	53905	exon5			AGTGTTGGGGGTC	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.294G>A	chr15.hg19:g.45426494G>A		139.0	0.0		136.0	48.0	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	hg19	CCDS32221.1																																																																																			.	.		0.602	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		A	45426494	G	A	45426494	2	1	170	1	0	0	0	0	0	0	0	1	4802	1339	47	3		3	DUOX1	15	45426494	Silent	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	3622382	45426494	57104898	145	25836										
SHF	90525	hgsc.bcm.edu	37	chr15	45464477	45464477	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gccgccccttctcctcccggCcaggtgacaggcagctcttc	10	19	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr15:45464477C>G	ENST00000290894.8	-	6	1327	c.833G>C	c.(832-834)gGc>gCc	p.G278A	SHF_ENST00000318390.6_Missense_Mutation_p.G288A|SHF_ENST00000560734.1_Intron|SHF_ENST00000458022.2_Missense_Mutation_p.G94A|SHF_ENST00000560540.1_Missense_Mutation_p.G296A|SHF_ENST00000561091.1_5'Flank|RP11-519G16.2_ENST00000560034.1_RNA|SHF_ENST00000560471.1_Missense_Mutation_p.G343A	NM_138356.2	NP_612365			Src homology 2 domain containing F											endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		CTCCTCCCGGCCAGGTGACAG	0.607																																					p.G278A		Atlas-SNP	.											.	SHF	27	.	0			c.G833C						.						35	41	39					15																	45464477		2198	4298	6496	SO:0001583	missense	90525	exon6			TCCCGGCCAGGTG	BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"SH2 domain containing"	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000290894.8:c.833G>C	chr15.hg19:g.45464477C>G	ENSP00000290894:p.Gly278Ala	60.0	0.0		53.0	17.0	NM_138356		Missense_Mutation	SNP	ENST00000290894.8	hg19	CCDS10120.2	.	.	.	.	.	.	.	.	.	.	C	10.03	1.240036	0.22711	.	.	ENSG00000138606	ENST00000290894;ENST00000361989;ENST00000318390;ENST00000458022;ENST00000413198	T;T;T	0.32023	1.47;1.47;1.47	3.91	3.91	0.45181	.	0.760658	0.13439	N	0.387802	T	0.26738	0.0654	L	0.31926	0.97	0.32589	N	0.527461	P;B;B;B	0.47677	0.899;0.0;0.014;0.001	P;B;B;B	0.47528	0.549;0.002;0.032;0.004	T	0.05131	-1.0904	10	0.12766	T	0.61	-13.252	9.9553	0.41663	0.0:0.792:0.208:0.0	.	141;221;288;278	Q8N9I8;E7EWB7;F8W6K9;Q7M4L6	.;.;.;SHF_HUMAN	A	278;278;288;94;221	ENSP00000290894:G278A;ENSP00000315978:G288A;ENSP00000411530:G94A	ENSP00000290894:G278A	G	-	2	0	SHF	43251769	0.990000	0.36364	1.000000	0.80357	0.996000	0.88848	2.265000	0.43311	1.904000	0.55121	0.563000	0.77884	GGC	.	.		0.607	SHF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254141.2	NM_138356		G	45464477	C	G	45464477	3	3	170	1	0	0	0	0	1	0	0	0	14292	739	26	4	450	4	SHF	15	45464477	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	37983	45464477	57066915	146	25837										
TLN2	83660	hgsc.bcm.edu	37	chr15	63089561	63089561	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gctcgcagaagtggtcaagcTgggggcagccagcctgggct	17	11	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr15:63089561T>A	ENST00000561311.1	+	47	6424	c.6194T>A	c.(6193-6195)cTg>cAg	p.L2065Q	TLN2_ENST00000306829.6_Missense_Mutation_p.L2065Q			Q9Y4G6	TLN2_HUMAN	talin 2	2065					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						GTGGTCAAGCTGGGGGCAGCC	0.662																																					p.L2065Q		Atlas-SNP	.											.	TLN2	253	.	0			c.T6194A						.						32	35	34					15																	63089561		2202	4300	6502	SO:0001583	missense	83660	exon45			TCAAGCTGGGGGC	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.6194T>A	chr15.hg19:g.63089561T>A	ENSP00000453508:p.Leu2065Gln	108.0	0.0		124.0	39.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.535519	0.85812	.	.	ENSG00000171914	ENST00000306829	T	0.13307	2.6	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.29288	0.0729	L	0.57536	1.79	0.58432	D	0.999997	D	0.71674	0.998	P	0.62089	0.898	T	0.03852	-1.0998	10	0.13853	T	0.58	-13.024	16.3483	0.83171	0.0:0.0:0.0:1.0	.	2065	Q9Y4G6	TLN2_HUMAN	Q	2065	ENSP00000303476:L2065Q	ENSP00000303476:L2065Q	L	+	2	0	TLN2	60876614	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.997000	0.88414	2.254000	0.74563	0.533000	0.62120	CTG	.	.		0.662	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63089561	T	A	63089561	3	1	170	1	0	0	0	0	1	0	0	0	15963	1580	55	4	6372	4	TLN2	15	63089561	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	17625084	63089561	39441831	147	25838										
PIF1	80119	hgsc.bcm.edu	37	chr15	65113605	65113605	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgtcaaacaggtctgcctccAccattgagatctcgtcaatg	8	12	4	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr15:65113605A>T	ENST00000268043.4	-	5	1026	c.932T>A	c.(931-933)gTg>gAg	p.V311E	PIF1_ENST00000333425.6_Missense_Mutation_p.V311E|PIF1_ENST00000559239.1_Missense_Mutation_p.V311E					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						GTCTGCCTCCACCATTGAGAT	0.612																																					p.V311E		Atlas-SNP	.											.	PIF1	43	.	0			c.T932A						.						96	94	95					15																	65113605		2202	4299	6501	SO:0001583	missense	80119	exon5			GCCTCCACCATTG	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"chromosome 15 open reading frame 20", "PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.932T>A	chr15.hg19:g.65113605A>T	ENSP00000268043:p.Val311Glu	195.0	0.0		171.0	40.0	NM_025049		Missense_Mutation	SNP	ENST00000268043.4	hg19	CCDS10195.2	.	.	.	.	.	.	.	.	.	.	A	24.7	4.557026	0.86231	.	.	ENSG00000140451	ENST00000268043;ENST00000333425	T;T	0.57273	0.41;0.41	5.97	4.82	0.62117	.	0.053557	0.64402	D	0.000001	T	0.79890	0.4524	H	0.96460	3.825	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.84310	0.0510	10	0.87932	D	0	-26.6362	11.4094	0.49917	0.8485:0.1515:0.0:0.0	.	311	Q9H611	PIF1_HUMAN	E	311	ENSP00000268043:V311E;ENSP00000328174:V311E	ENSP00000268043:V311E	V	-	2	0	PIF1	62900658	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.920000	0.75799	1.035000	0.39972	0.533000	0.62120	GTG	.	.		0.612	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049		T	65113605	A	T	65113605	3	4	170	1	0	0	0	0	1	0	0	0	11892	159	6	4	1029	4	PIF1	15	65113605	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	2024044	65113605	37417787	148	25839										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75968374	75968374	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cgggcagcattgtaaggctcAgtggcaaagtccagggaggc	16	9	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr15:75968374A>C	ENST00000308508.5	-	10	6578	c.6486T>G	c.(6484-6486)acT>acG	p.T2162T	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	2162	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						TGTAAGGCTCAGTGGCAAAGT	0.701																																					p.T2162T		Atlas-SNP	.											.	CSPG4	175	.	0			c.T6486G						.						16	15	16					15																	75968374		2185	4277	6462	SO:0001819	synonymous_variant	1464	exon10			AGGCTCAGTGGCA	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.6486T>G	chr15.hg19:g.75968374A>C		18.0	0.0		27.0	9.0	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	hg19	CCDS10284.1																																																																																			.	.		0.701	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		C	75968374	A	C	75968374	2	2	170	1	0	0	0	0	0	0	0	1	3962	175	7	5		5	CSPG4	15	75968374	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	10854769	75968374	26563018	149	25840										
ABHD2	11057	hgsc.bcm.edu	37	chr15	89659582	89659582	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aatgccatgctggagactccCgaactcccagccgtgtttga	10	13	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr15:89659582C>T	ENST00000352732.5	+	3	544	c.24C>T	c.(22-24)ccC>ccT	p.P8P	ABHD2_ENST00000355100.3_Silent_p.P8P|ABHD2_ENST00000565973.1_Silent_p.P8P	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	8					negative regulation of cell migration (GO:0030336)|response to wounding (GO:0009611)	integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)	p.P8P(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|soft_tissue(1)	23	Lung NSC(78;0.0472)|all_lung(78;0.089)					TGGAGACTCCCGAACTCCCAG	0.577																																					p.P8P	Colon(11;252 417 24570 33239 41878)	Atlas-SNP	.											.	ABHD2	55	.	1	Substitution - coding silent(1)	lung(1)	c.C24T						.						107	94	98					15																	89659582		2200	4299	6499	SO:0001819	synonymous_variant	11057	exon7			GACTCCCGAACTC	X12433	CCDS10348.1	15q26.1	2006-10-06			ENSG00000140526	ENSG00000140526		"Abhydrolase domain containing"	18717	protein-coding gene	gene with protein product		612196					Standard	NM_152924		Approved	LABH2	uc002bnk.2	P08910	OTTHUMG00000148684	ENST00000352732.5:c.24C>T	chr15.hg19:g.89659582C>T		93.0	0.0		109.0	25.0	NM_007011	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Silent	SNP	ENST00000352732.5	hg19	CCDS10348.1																																																																																			.	.		0.577	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2			T	89659582	C	T	89659582	2	4	170	1	0	0	0	0	0	0	0	1	82	639	23	1		1	ABHD2	15	89659582	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	13691208	89659582	12871810	150	25841										
CASKIN1	57524	hgsc.bcm.edu	37	chr16	2235014	2235014	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cggactcagagacggacttcTgggaaagcaccgttgccagg	14	11	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr16:2235014T>A	ENST00000343516.6	-	13	1354	c.1262A>T	c.(1261-1263)cAg>cTg	p.Q421L	CASKIN1_ENST00000564289.1_5'UTR	NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	421	CASK-binding. {ECO:0000250}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|liver(1)|lung(7)|ovary(4)|prostate(5)|skin(3)	28						GACGGACTTCTGGGAAAGCAC	0.667																																					p.Q421L		Atlas-SNP	.											.	CASKIN1	130	.	0			c.A1262T						.						41	55	51					16																	2235014		1942	4135	6077	SO:0001583	missense	57524	exon13			GACTTCTGGGAAA	AF451977	CCDS42103.1	16p13.3	2013-01-10				ENSG00000167971		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20879	protein-coding gene	gene with protein product		612184				12040031	Standard	NM_020764		Approved	KIAA1306, ANKS5A	uc010bsg.1	Q8WXD9		ENST00000343516.6:c.1262A>T	chr16.hg19:g.2235014T>A	ENSP00000345436:p.Gln421Leu	94.0	0.0		113.0	52.0	NM_020764	Q9P2P0	Missense_Mutation	SNP	ENST00000343516.6	hg19	CCDS42103.1	.	.	.	.	.	.	.	.	.	.	T	9.285	1.049204	0.19827	.	.	ENSG00000167971	ENST00000343516;ENST00000382453	T	0.68765	-0.35	4.91	3.82	0.43975	.	.	.	.	.	T	0.57533	0.2060	L	0.58101	1.795	0.54753	D	0.999984	B	0.24258	0.1	B	0.14023	0.01	T	0.55121	-0.8190	9	0.30078	T	0.28	-26.4998	8.3321	0.32193	0.0:0.1583:0.0:0.8417	.	421	Q8WXD9	CSKI1_HUMAN	L	421;250	ENSP00000345436:Q421L	ENSP00000345436:Q421L	Q	-	2	0	CASKIN1	2175015	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	0.727000	0.25999	1.829000	0.53265	0.454000	0.30748	CAG	.	.		0.667	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764		A	2235014	T	A	2235014	3	1	170	1	0	0	0	0	1	0	0	0	2668	1580	55	4	3065	4	CASKIN1	16	2235014	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10		2235014	88119739	151	25842										
NOMO3	408050	hgsc.bcm.edu	37	chr16	16356983	16356983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gctgacgttgaaaccccagaCatttcctcttactgtgaccg	8	13	1	4			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr16:16356983C>T	ENST00000399336.4	+	13	1620	c.1448C>T	c.(1447-1449)aCa>aTa	p.T483I	NOMO3_ENST00000263012.6_Missense_Mutation_p.T483I|NOMO3_ENST00000538468.1_Missense_Mutation_p.T316I	NM_001004067.3	NP_001004067.1	P69849	NOMO3_HUMAN	NODAL modulator 3	483						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	8				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		AAACCCCAGACATTTCCTCTT	0.502																																					p.T483I		Atlas-SNP	.											.	NOMO3	23	.	0			c.C1448T						.						117	149	138					16																	16356983		2061	4295	6356	SO:0001583	missense	408050	exon13			CCCAGACATTTCC	AK125530	CCDS42123.1	16p13	2004-11-24				ENSG00000103226			25242	protein-coding gene	gene with protein product		609159				15257293	Standard	NM_001004067		Approved		uc002deq.3	P69849	OTTHUMG00000170525	ENST00000399336.4:c.1448C>T	chr16.hg19:g.16356983C>T	ENSP00000382274:p.Thr483Ile	137.0	0.0		159.0	65.0	NM_001004067		Missense_Mutation	SNP	ENST00000399336.4	hg19	CCDS42123.1	.	.	.	.	.	.	.	.	.	.	.	8.973	0.973374	0.18736	.	.	ENSG00000103226	ENST00000263012;ENST00000399336;ENST00000538468	T;T;T	0.14516	2.5;2.5;2.5	4.31	-5.12	0.02893	.	1.094200	0.06932	N	0.811328	T	0.09905	0.0243	L	0.27053	0.805	0.09310	N	1	B;B;B	0.15141	0.012;0.009;0.007	B;B;B	0.18561	0.022;0.009;0.013	T	0.39165	-0.9627	10	0.40728	T	0.16	0.1932	12.0743	0.53634	0.0:0.3491:0.0:0.6509	.	316;483;483	F5H826;P69849;Q5JPE7-2	.;NOMO3_HUMAN;.	I	483;483;316	ENSP00000263012:T483I;ENSP00000382274:T483I;ENSP00000443768:T316I	ENSP00000263012:T483I	T	+	2	0	NOMO3	16264484	0.000000	0.05858	0.000000	0.03702	0.909000	0.53808	-0.491000	0.06474	-0.832000	0.04251	-0.720000	0.03607	ACA	.	.		0.502	NOMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409528.13	NM_001004067		T	16356983	C	T	16356983	3	4	170	1	0	0	0	0	1	0	0	0	10542	478	17	3	1498	3	NOMO3	16	16356983	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	14121969	16356983	73997770	152	25843										
PRKCB	5579	hgsc.bcm.edu	37	chr16	24105573	24105573	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gaatgacttcatgggatcttTgtcctttgggatttctgaac	10	7	3	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr16:24105573T>C	ENST00000321728.7	+	7	951	c.776T>C	c.(775-777)tTg>tCg	p.L259S	PRKCB_ENST00000303531.7_Missense_Mutation_p.L259S|PRKCB_ENST00000482000.1_3'UTR	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	259	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	ATGGGATCTTTGTCCTTTGGG	0.448																																					p.L259S		Atlas-SNP	.											.	PRKCB	383	.	0			c.T776C						.						164	148	153					16																	24105573		2197	4300	6497	SO:0001583	missense	5579	exon7			GATCTTTGTCCTT	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"protein kinase C, beta 1"	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.776T>C	chr16.hg19:g.24105573T>C	ENSP00000318315:p.Leu259Ser	159.0	0.0		201.0	92.0	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	hg19	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628472	0.67015	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	T;T	0.70164	-0.46;-0.46	5.52	5.52	0.82312	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.079948	0.52532	D	0.000073	T	0.65770	0.2723	L	0.43923	1.385	0.80722	D	1	B;B	0.31318	0.272;0.319	B;B	0.39935	0.209;0.314	T	0.66976	-0.5787	10	0.54805	T	0.06	.	14.8443	0.70249	0.0:0.0:0.0:1.0	.	259;259	P05771-2;P05771	.;KPCB_HUMAN	S	259	ENSP00000318315:L259S;ENSP00000305355:L259S	ENSP00000305355:L259S	L	+	2	0	PRKCB	24013074	1.000000	0.71417	0.965000	0.40720	0.934000	0.57294	7.692000	0.84203	2.088000	0.63022	0.533000	0.62120	TTG	.	.		0.448	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		C	24105573	T	C	24105573	3	2	170	1	0	0	0	0	1	0	0	0	12520	1821	63	2	802	2	PRKCB	16	24105573	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	7748590	24105573	66249180	153	25844										
ITGAM	3684	hgsc.bcm.edu	37	chr16	31336309	31336309	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agaagaattgtggcaatgacAacatctgccaggatgacctc	10	9	1	4			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr16:31336309A>T	ENST00000287497.8	+	19	2395	c.2320A>T	c.(2320-2322)Aac>Tac	p.N774Y	ITGAM_ENST00000544665.3_Missense_Mutation_p.N775Y			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	774					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						TGGCAATGACAACATCTGCCA	0.393																																					p.N775Y		Atlas-SNP	.											.	ITGAM	137	.	0			c.A2323T						.						77	71	73					16																	31336309		1904	4127	6031	SO:0001583	missense	3684	exon19			AATGACAACATCT	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2320A>T	chr16.hg19:g.31336309A>T	ENSP00000287497:p.Asn774Tyr	46.0	0.0		70.0	28.0	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	hg19	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.609792	0.28623	.	.	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.57273	0.41;0.41	4.94	2.67	0.31697	Integrin alpha-2 (1);	.	.	.	.	T	0.41558	0.1164	L	0.34521	1.04	0.21184	N	0.999763	B;B;B	0.27013	0.166;0.166;0.166	B;B;B	0.35182	0.197;0.197;0.197	T	0.41980	-0.9478	9	0.54805	T	0.06	.	3.8459	0.08934	0.5652:0.18:0.2548:0.0	.	180;774;774	B3KXM6;Q4VAK1;P11215	.;.;ITAM_HUMAN	Y	775;774	ENSP00000441691:N775Y;ENSP00000287497:N774Y	ENSP00000287497:N774Y	N	+	1	0	ITGAM	31243810	0.049000	0.20398	0.319000	0.25293	0.913000	0.54294	0.785000	0.26830	0.367000	0.24454	0.533000	0.62120	AAC	.	.		0.393	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		T	31336309	A	T	31336309	3	4	170	1	0	0	0	0	1	0	0	0	7896	130	5	4	2397	4	ITGAM	16	31336309	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	7230736	31336309	59018444	154	25845										
NOD2	64127	hgsc.bcm.edu	37	chr16	50746089	50746089	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gcaggaggagcggctggctcGgaaggctgcacgtggcctga	19	10	0	1	rs375713299		TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr16:50746089G>T	ENST00000300589.2	+	4	2372	c.2267G>T	c.(2266-2268)cGg>cTg	p.R756L	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	756					activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CGGCTGGCTCGGAAGGCTGCA	0.632																																					p.R756L		Atlas-SNP	.											NOD2,caecum,carcinoma,0,1	NOD2	118	.	0			c.G2267T						.						78	56	63					16																	50746089		2198	4300	6498	SO:0001583	missense	64127	exon4			TGGCTCGGAAGGC	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"Nucleotide-binding domain and leucine rich repeat containing"	5331	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2", "NOD-like receptor C2", "NLR family, CARD domain containing 2"	605956	"caspase recruitment domain family, member 15"	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.2267G>T	chr16.hg19:g.50746089G>T	ENSP00000300589:p.Arg756Leu	57.0	0.0		98.0	20.0	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	hg19	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	G	6.635	0.485603	0.12641	.	.	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.70399	-0.48	5.47	-0.00388	0.14024	.	0.576361	0.16535	N	0.210192	T	0.68137	0.2968	M	0.77103	2.36	0.09310	N	1	P;P;P	0.42973	0.796;0.795;0.796	B;B;B	0.40982	0.264;0.345;0.252	T	0.61720	-0.7005	10	0.72032	D	0.01	.	8.972	0.35912	0.4753:0.0:0.5247:0.0	.	540;729;756	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	L	729;756	ENSP00000300589:R756L	ENSP00000300589:R756L	R	+	2	0	NOD2	49303590	0.279000	0.24239	0.007000	0.13788	0.015000	0.08874	0.639000	0.24690	-0.201000	0.10284	0.561000	0.74099	CGG	.	.		0.632	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		T	50746089	G	T	50746089	3	4	170	1	0	0	0	0	1	0	0	0	10526	1116	39	1	2281	1	NOD2	16	50746089	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	19409780	50746089	39608664	155	25846										
SALL1	6299	hgsc.bcm.edu	37	chr16	51175130	51175130	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	catattgggagaagagccgcTgttggatggaatgatggtgt	16	4	0	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr16:51175130T>A	ENST00000251020.4	-	2	1036	c.1003A>T	c.(1003-1005)Agc>Tgc	p.S335C	SALL1_ENST00000440970.1_Missense_Mutation_p.S238C|SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	335					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GAAGAGCCGCTGTTGGATGGA	0.547																																					p.S335C	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.A1003T						.						110	114	113					16																	51175130		2198	4300	6498	SO:0001583	missense	6299	exon2			AGCCGCTGTTGGA	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.1003A>T	chr16.hg19:g.51175130T>A	ENSP00000251020:p.Ser335Cys	59.0	0.0		82.0	27.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	T	10.40	1.338625	0.24253	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.08458	3.09;3.11	4.39	2.06	0.26882	.	0.132053	0.64402	D	0.000001	T	0.05318	0.0141	N	0.19112	0.55	0.42144	D	0.991525	P	0.39131	0.661	B	0.36186	0.219	T	0.44862	-0.9300	10	0.56958	D	0.05	-4.4151	8.703	0.34338	0.0:0.1601:0.0:0.8399	.	335	Q9NSC2	SALL1_HUMAN	C	335;238;299	ENSP00000251020:S335C;ENSP00000407914:S238C	ENSP00000251020:S335C	S	-	1	0	SALL1	49732631	1.000000	0.71417	0.555000	0.28281	0.967000	0.64934	3.179000	0.50887	0.206000	0.20587	0.260000	0.18958	AGC	.	.		0.547	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51175130	T	A	51175130	3	1	170	1	0	0	0	0	1	0	0	0	13825	1580	55	4	2979	4	SALL1	16	51175130	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	429041	51175130	39179623	156	25847										
BBS2	583	hgsc.bcm.edu	37	chr16	56545111	56545111	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cttcatgattgaaaccttgcAgagcacaattgccaccaata	6	11	1	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr16:56545111A>T	ENST00000245157.5	-	3	851	c.431T>A	c.(430-432)cTg>cAg	p.L144Q	BBS2_ENST00000561951.1_5'UTR|BBS2_ENST00000568104.1_Missense_Mutation_p.L144Q	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	144					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						GAAACCTTGCAGAGCACAATT	0.388									Bardet-Biedl syndrome																												p.L144Q		Atlas-SNP	.											.	BBS2	67	.	0			c.T431A						.						125	109	115					16																	56545111		2198	4300	6498	SO:0001583	missense	583	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CCTTGCAGAGCAC	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.431T>A	chr16.hg19:g.56545111A>T	ENSP00000245157:p.Leu144Gln	51.0	0.0		77.0	37.0	NM_031885	Q96CM0|Q96SN9	Missense_Mutation	SNP	ENST00000245157.5	hg19	CCDS32451.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.785484	0.90282	.	.	ENSG00000125124	ENST00000245157	D	0.84589	-1.87	5.9	5.9	0.94986	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.91862	0.7424	M	0.76002	2.32	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.70935	0.971;0.971	D	0.92605	0.6094	10	0.72032	D	0.01	-10.1552	16.3294	0.83004	1.0:0.0:0.0:0.0	.	144;144	A8K0N9;Q9BXC9	.;BBS2_HUMAN	Q	144	ENSP00000245157:L144Q	ENSP00000245157:L144Q	L	-	2	0	BBS2	55102612	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	9.186000	0.94906	2.259000	0.74868	0.523000	0.50628	CTG	.	.		0.388	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		T	56545111	A	T	56545111	3	4	170	1	0	0	0	0	1	0	0	0	1338	188	7	4	1794	4	BBS2	16	56545111	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	5369981	56545111	33809642	157	25848										
KATNB1	10300	hgsc.bcm.edu	37	chr16	57785926	57785926	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cctgtcaacgtggtcgagttTcaccccaacgagtacctcct	8	15	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr16:57785926T>G	ENST00000379661.3	+	8	983	c.591T>G	c.(589-591)ttT>ttG	p.F197L		NM_005886.2	NP_005877.2			katanin p80 (WD repeat containing) subunit B 1											cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_neural(199;0.223)				TGGTCGAGTTTCACCCCAACG	0.617																																					p.F197L		Atlas-SNP	.											.	KATNB1	35	.	0			c.T591G						.						95	60	72					16																	57785926		2198	4300	6498	SO:0001583	missense	10300	exon8			CGAGTTTCACCCC	AF052432	CCDS10788.1	16q12.2	2013-01-09	2003-03-13		ENSG00000140854	ENSG00000140854		"WD repeat domain containing"	6217	protein-coding gene	gene with protein product		602703	"katanin p80 (WD40-containing) subunit B 1"			9568719	Standard	XM_006721121		Approved		uc002eml.1	Q9BVA0	OTTHUMG00000133467	ENST00000379661.3:c.591T>G	chr16.hg19:g.57785926T>G	ENSP00000368982:p.Phe197Leu	69.0	0.0		105.0	46.0	NM_005886		Missense_Mutation	SNP	ENST00000379661.3	hg19	CCDS10788.1	.	.	.	.	.	.	.	.	.	.	T	18.10	3.548718	0.65311	.	.	ENSG00000140854	ENST00000379661	T	0.67171	-0.25	5.34	0.197	0.15164	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.048698	0.85682	N	0.000000	T	0.52256	0.1723	L	0.45137	1.4	0.58432	D	0.999995	B	0.06786	0.001	B	0.12156	0.007	T	0.42965	-0.9420	10	0.87932	D	0	9.2791	5.9544	0.19265	0.0:0.335:0.1345:0.5305	.	197	Q9BVA0	KTNB1_HUMAN	L	197	ENSP00000368982:F197L	ENSP00000368982:F197L	F	+	3	2	KATNB1	56343427	0.986000	0.35501	0.998000	0.56505	0.985000	0.73830	0.167000	0.16602	0.018000	0.15052	0.459000	0.35465	TTT	.	.		0.617	KATNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257343.3			G	57785926	T	G	57785926	3	3	170	1	0	0	0	0	1	0	0	0	7996	1780	62	5	617	5	KATNB1	16	57785926	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	1240815	57785926	32568827	158	25849										
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88643896	88643896	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggcctcctcagtcaccagggAgctggatgagcatgagctag	14	11	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr16:88643896A>T	ENST00000301011.5	+	2	565	c.365A>T	c.(364-366)gAg>gTg	p.E122V	ZC3H18_ENST00000452588.2_Missense_Mutation_p.E122V	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	122						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		GTCACCAGGGAGCTGGATGAG	0.647																																					p.E122V	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.A365T						.						42	40	41					16																	88643896		2195	4299	6494	SO:0001583	missense	124245	exon2			CCAGGGAGCTGGA	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.365A>T	chr16.hg19:g.88643896A>T	ENSP00000301011:p.Glu122Val	58.0	0.0		82.0	21.0	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	hg19	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.761772	0.49468	.	.	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588	T;T	0.35789	1.3;1.29	5.43	5.43	0.79202	.	0.161156	0.53938	D	0.000041	T	0.46946	0.1419	L	0.54323	1.7	0.54753	D	0.99998	P;P	0.48589	0.912;0.912	P;P	0.51742	0.678;0.678	T	0.40664	-0.9551	10	0.45353	T	0.12	-20.4026	15.4961	0.75653	1.0:0.0:0.0:0.0	.	122;122	E7ERS3;Q86VM9	.;ZCH18_HUMAN	V	122	ENSP00000301011:E122V;ENSP00000416951:E122V	ENSP00000289509:E122V	E	+	2	0	ZC3H18	87171397	1.000000	0.71417	0.996000	0.52242	0.232000	0.25224	8.576000	0.90770	2.072000	0.62099	0.459000	0.35465	GAG	.	.		0.647	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		T	88643896	A	T	88643896	3	4	170	1	0	0	0	0	1	0	0	0	17583	304	11	4	367	4	ZC3H18	16	88643896	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	30857970	88643896	1710857	159	25850										
SMYD4	114826	hgsc.bcm.edu	37	chr17	1703349	1703349	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ctgtctgcacagtgcagaaaCacagagagcacagaggaatt	11	9	1	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:1703349C>A	ENST00000305513.7	-	5	1506	c.1339G>T	c.(1339-1341)Gtt>Ttt	p.V447F		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	447	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						AGTGCAGAAACACAGAGAGCA	0.448																																					p.V447F		Atlas-SNP	.											.	SMYD4	50	.	0			c.G1339T						.						91	82	85					17																	1703349		2203	4300	6503	SO:0001583	missense	114826	exon5			CAGAAACACAGAG	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"Zinc fingers, MYND-type"	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.1339G>T	chr17.hg19:g.1703349C>A	ENSP00000304360:p.Val447Phe	95.0	0.0		80.0	25.0	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	hg19	CCDS11013.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.593960	0.66219	.	.	ENSG00000186532	ENST00000305513	T	0.13657	2.57	6.03	0.692	0.18050	SET domain (2);	0.547815	0.21608	N	0.071838	T	0.31544	0.0800	M	0.78049	2.395	0.21355	N	0.999711	D	0.60575	0.988	D	0.63113	0.911	T	0.08472	-1.0720	10	0.56958	D	0.05	-4.9941	11.2161	0.48827	0.0:0.6409:0.0:0.3591	.	447	Q8IYR2	SMYD4_HUMAN	F	447	ENSP00000304360:V447F	ENSP00000304360:V447F	V	-	1	0	SMYD4	1650099	0.452000	0.25713	0.627000	0.29227	0.931000	0.56810	0.144000	0.16135	0.161000	0.19458	0.655000	0.94253	GTT	.	.		0.448	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082		A	1703349	C	A	1703349	3	1	170	1	0	0	0	0	1	0	0	0	14839	478	17	3	1103	3	SMYD4	17	1703349	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10		1703349	79491861	160	25851										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7681450	7681450	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gcaatttcagtataattatgAgtacttgggtaactcgggcc	10	7	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:7681450A>T	ENST00000572933.1	+	34	6763	c.5303A>T	c.(5302-5304)gAg>gTg	p.E1768V	DNAH2_ENST00000389173.2_Missense_Mutation_p.E1768V			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1768	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TATAATTATGAGTACTTGGGT	0.552																																					p.E1768V		Atlas-SNP	.											.	DNAH2	498	.	0			c.A5303T						.						90	86	87					17																	7681450		2203	4300	6503	SO:0001583	missense	146754	exon33			ATTATGAGTACTT	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.5303A>T	chr17.hg19:g.7681450A>T	ENSP00000458355:p.Glu1768Val	72.0	0.0		80.0	18.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.762857	0.89932	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.14516	2.5	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.55417	0.1919	H	0.98612	4.28	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73733	-0.3890	10	0.87932	D	0	.	14.7836	0.69784	1.0:0.0:0.0:0.0	.	1768	Q9P225	DYH2_HUMAN	V	1768	ENSP00000373825:E1768V	ENSP00000353818:E1768V	E	+	2	0	DNAH2	7622175	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	8.968000	0.93407	2.322000	0.78497	0.528000	0.53228	GAG	.	.		0.552	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7681450	A	T	7681450	3	4	170	1	0	0	0	0	1	0	0	0	4604	304	11	4	5433	4	DNAH2	17	7681450	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	5978101	7681450	73513760	161	25852										
MYH8	4626	hgsc.bcm.edu	37	chr17	10314242	10314242	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tctcgttggtgaagttgatgCacagctgctccaggctgtta	12	9	1	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:10314242C>A	ENST00000403437.2	-	15	1533	c.1439G>T	c.(1438-1440)tGc>tTc	p.C480F	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	480	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GAAGTTGATGCACAGCTGCTC	0.378									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.C480F		Atlas-SNP	.											.	MYH8	346	.	0			c.G1439T						.						138	120	126					17																	10314242		2203	4300	6503	SO:0001583	missense	4626	exon15	Familial Cancer Database	Carney Complex Variant	TTGATGCACAGCT		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.1439G>T	chr17.hg19:g.10314242C>A	ENSP00000384330:p.Cys480Phe	96.0	0.0		112.0	31.0	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	hg19	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.453777	0.84209	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.75154	-0.91	5.02	5.02	0.67125	Myosin head, motor domain (3);	0.000000	0.45867	U	0.000323	D	0.89818	0.6825	M	0.93939	3.475	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	D	0.92335	0.5877	10	0.87932	D	0	.	18.5246	0.90967	0.0:1.0:0.0:0.0	.	480	P13535	MYH8_HUMAN	F	480	ENSP00000384330:C480F	ENSP00000252173:C480F	C	-	2	0	MYH8	10254967	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.609000	0.82925	2.621000	0.88768	0.655000	0.94253	TGC	.	.		0.378	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		A	10314242	C	A	10314242	3	1	170	1	0	0	0	0	1	0	0	0	10050	710	25	3	4478	3	MYH8	17	10314242	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	2632792	10314242	70880968	162	25853										
GPR179	440435	hgsc.bcm.edu	37	chr17	36485868	36485868	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tggcaagccctgttttacctGctctctcagctttccgttcc	7	15	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:36485868G>A	ENST00000342292.4	-	11	3604	c.3584C>T	c.(3583-3585)gCa>gTa	p.A1195V	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1195					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TGTTTTACCTGCTCTCTCAGC	0.542																																					p.A1195V		Atlas-SNP	.											.	GPR179	170	.	0			c.C3584T						.						225	229	228					17																	36485868		2085	4208	6293	SO:0001583	missense	440435	exon11			TTACCTGCTCTCT		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.3584C>T	chr17.hg19:g.36485868G>A	ENSP00000345060:p.Ala1195Val	93.0	0.0		95.0	29.0	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	G	8.953	0.968733	0.18659	.	.	ENSG00000188888	ENST00000342292	T	0.52983	0.64	5.03	-0.498	0.12019	.	0.966593	0.08512	N	0.934781	T	0.27900	0.0687	N	0.17082	0.46	0.09310	N	1	B	0.18461	0.028	B	0.16722	0.016	T	0.22836	-1.0205	10	0.49607	T	0.09	-0.0154	3.936	0.09305	0.2327:0.0:0.4839:0.2834	.	1195	Q6PRD1	GP179_HUMAN	V	1195	ENSP00000345060:A1195V	ENSP00000345060:A1195V	A	-	2	0	GPR179	33739394	0.000000	0.05858	0.000000	0.03702	0.417000	0.31264	0.010000	0.13242	-0.175000	0.10725	0.462000	0.41574	GCA	.	.		0.542	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36485868	G	A	36485868	3	1	170	1	0	0	0	0	1	0	0	0	6682	1319	46	3	3523	3	GPR179	17	36485868	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	26171626	36485868	44709342	163	25854										
MED24	9862	hgsc.bcm.edu	37	chr17	38183205	38183205	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggtggtcagggttcaggatcTtgccctcctcaggcatgcag	14	11	4	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:38183205T>A	ENST00000394128.2	-	17	1694	c.1613A>T	c.(1612-1614)aAg>aTg	p.K538M	MED24_ENST00000501516.3_Missense_Mutation_p.K557M|MED24_ENST00000356271.3_Missense_Mutation_p.K525M|MED24_ENST00000394126.1_Missense_Mutation_p.K563M|MED24_ENST00000394127.2_Missense_Mutation_p.K525M|SNORD124_ENST00000459577.1_RNA	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	538					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					GTTCAGGATCTTGCCCTCCTC	0.607											OREG0024386	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K538M		Atlas-SNP	.											.	MED24	89	.	0			c.A1613T						.						55	51	53					17																	38183205		2203	4300	6503	SO:0001583	missense	9862	exon17			AGGATCTTGCCCT	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1613A>T	chr17.hg19:g.38183205T>A	ENSP00000377686:p.Lys538Met	124.0	0.0	876	138.0	43.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	hg19	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.926399	0.34002	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000431269	T;T;T	0.57436	0.4;0.4;0.4	4.5	3.41	0.39046	Mediator complex, subunit Med24, N-terminal (1);	0.047359	0.85682	D	0.000000	T	0.61850	0.2380	M	0.63843	1.955	0.58432	D	0.999999	D;D;D;D;D;D	0.69078	0.997;0.995;0.995;0.995;0.996;0.995	D;P;P;P;P;P	0.63113	0.911;0.847;0.847;0.847;0.905;0.847	T	0.61695	-0.7010	10	0.72032	D	0.01	-15.9486	6.0967	0.20025	0.0:0.0822:0.1654:0.7524	.	479;488;448;525;538;480	B4DSQ6;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;MED24_HUMAN;.	M	538;538;538;488;525;480;448	ENSP00000377686:K538M;ENSP00000443344:K488M;ENSP00000377685:K525M	ENSP00000348610:K538M	K	-	2	0	MED24	35436731	1.000000	0.71417	0.996000	0.52242	0.926000	0.56050	6.092000	0.71414	0.738000	0.32606	-0.313000	0.08912	AAG	.	.		0.607	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		A	38183205	T	A	38183205	3	1	170	1	0	0	0	0	1	0	0	0	9451	1609	56	4	1396	4	MED24	17	38183205	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	1697337	38183205	43012005	164	25855										
TOP2A	7153	hgsc.bcm.edu	37	chr17	38557137	38557137	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ttctccatccatcaaacgccTgatgttatttacaatttcac	3	12	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:38557137T>A	ENST00000423485.1	-	21	2787	c.2629A>T	c.(2629-2631)Agg>Tgg	p.R877W		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	877					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	ATCAAACGCCTGATGTTATTT	0.408																																					p.R877W		Atlas-SNP	.											.	TOP2A	124	.	0			c.A2629T						.						258	248	251					17																	38557137		1909	4126	6035	SO:0001583	missense	7153	exon21			AACGCCTGATGTT		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.2629A>T	chr17.hg19:g.38557137T>A	ENSP00000411532:p.Arg877Trp	109.0	0.0		96.0	16.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	hg19	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	T	17.15	3.314874	0.60524	.	.	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.25912	1.77	5.21	4.1	0.47936	DNA topoisomerase, type IIA, subunit A/C-terminal (2);DNA topoisomerase, type IIA, subunit A/ C-terminal, alpha-beta (1);DNA topoisomerase, type IIA, central (1);	0.097636	0.64402	D	0.000003	T	0.46870	0.1415	M	0.82923	2.615	0.48632	D	0.999684	D	0.56035	0.974	P	0.61874	0.895	T	0.46345	-0.9198	10	0.87932	D	0	.	7.0162	0.24889	0.0:0.0811:0.3787:0.5402	.	877	P11388	TOP2A_HUMAN	W	877;957;900;913	ENSP00000411532:R877W	ENSP00000269577:R957W	R	-	1	2	TOP2A	35810663	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	2.168000	0.42424	0.887000	0.36136	0.383000	0.25322	AGG	.	.		0.408	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			A	38557137	T	A	38557137	3	1	170	1	0	0	0	0	1	0	0	0	16380	1579	55	4	2026	4	TOP2A	17	38557137	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	373932	38557137	42638073	165	25856										
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305778	39305779	+	In_Frame_Ins	INS	-	-	AGCAGCTGGGGCGGC													0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cctgcagcaggtggtctggcINSagcagcaggggcggcagcag							TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:39305778_39305779insAGCAGCTGGGGCGGC	ENST00000343246.4	-	1	275_276	c.241_242insGCCGCCCCAGCTGCT	c.(241-243)tgc>tGCCGCCCCAGCTGCTgc	p.81_81C>CRPSCC		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	81	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ggtggtctggcagcagcagggg	0.653																																					p.C81delinsCRPSCC		Atlas-INDEL	.											.	KRTAP4-5	34	.	0			c.242_243insGCCGCCCCAGCTGCT						.																																			SO:0001652	inframe_insertion	85289	exon1			.	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.241_242insGCCGCCCCAGCTGCT	chr17.hg19:g.39305778_39305779insAGCAGCTGGGGCGGC	Exception_encountered	45.0	0.0		61.0	37.0	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	hg19	CCDS32650.1																																																																																			.	.		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			AGCAGCTGGGGCGGC	39305779	-	AGCAGCTGGGGCGGC	39305778	7	5	170	1	0	1	1	0	0	0	0	0	8563	710	25	0	307	0	KRTAP4-5	17	39305778	In_Frame_Ins	INS	-	TCGA-DD-AACT-01A-11D-A40R-10	748641	39305778	41889432	166	25857										
STAT3	6774	hgsc.bcm.edu	37	chr17	40474482	40474482	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgttcagctgctgctttgtgTatggttccacggactggatc	12	9	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:40474482T>A	ENST00000264657.5	-	21	2231	c.1919A>T	c.(1918-1920)tAc>tTc	p.Y640F	STAT3_ENST00000404395.3_Missense_Mutation_p.Y640F|STAT3_ENST00000389272.3_Missense_Mutation_p.Y542F|STAT3_ENST00000588969.1_Missense_Mutation_p.Y640F|STAT3_ENST00000585517.1_Missense_Mutation_p.Y640F	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	640	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		CTGCTTTGTGTATGGTTCCAC	0.463									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.Y640F		Atlas-SNP	.											STAT3,NS,lymphoid_neoplasm,0,46	STAT3	268	.	0			c.A1919T						.						243	213	223					17																	40474482		2203	4300	6503	SO:0001583	missense	6774	exon21	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	TTTGTGTATGGTT	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610		"SH2 domain containing"	11364	protein-coding gene	gene with protein product		102582				7512451	Standard	NM_139276		Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.1919A>T	chr17.hg19:g.40474482T>A	ENSP00000264657:p.Tyr640Phe	136.0	0.0		134.0	37.0	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	hg19	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.813449	0.70912	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.89196	-2.48;-2.48;-2.48	4.64	4.64	0.57946	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.87120	0.6098	N	0.16016	0.355	0.80722	D	1	D;D;D	0.59357	0.982;0.985;0.985	D;D;D	0.78314	0.984;0.991;0.991	T	0.82589	-0.0382	10	0.06891	T	0.86	-37.3581	14.2314	0.65895	0.0:0.0:0.0:1.0	.	640;640;640	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	F	640;542;640	ENSP00000264657:Y640F;ENSP00000373923:Y542F;ENSP00000384943:Y640F	ENSP00000264657:Y640F	Y	-	2	0	STAT3	37728008	1.000000	0.71417	0.964000	0.40570	0.715000	0.41141	7.868000	0.87116	1.953000	0.56701	0.460000	0.39030	TAC	.	.		0.463	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		A	40474482	T	A	40474482	3	1	170	1	0	0	0	0	1	0	0	0	15281	1638	57	4	409	4	STAT3	17	40474482	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	1168704	40474482	40720728	167	25858										
COL1A1	1277	hgsc.bcm.edu	37	chr17	48276663	48276663	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	caggctgtccagggatgccaTctcggccaggggggcctgcg	17	13	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:48276663T>A	ENST00000225964.5	-	5	513	c.395A>T	c.(394-396)gAt>gTt	p.D132V		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	132					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	AGGGATGCCATCTCGGCCAGG	0.741			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.D132V		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1	158	.	0			c.A395T						.						2	3	3					17																	48276663		1658	3560	5218	SO:0001583	missense	1277	exon5			ATGCCATCTCGGC	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.395A>T	chr17.hg19:g.48276663T>A	ENSP00000225964:p.Asp132Val	174.0	0.0		178.0	34.0	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Missense_Mutation	SNP	ENST00000225964.5	hg19	CCDS11561.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.429419	0.83776	.	.	ENSG00000108821	ENST00000225964	D	0.93307	-3.2	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.95370	0.8497	L	0.54908	1.71	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.94999	0.8141	10	0.44086	T	0.13	.	14.3852	0.66940	0.0:0.0:0.0:1.0	.	132	P02452	CO1A1_HUMAN	V	132	ENSP00000225964:D132V	ENSP00000225964:D132V	D	-	2	0	COL1A1	45631662	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.266000	0.78452	2.037000	0.60232	0.459000	0.35465	GAT	.	.		0.741	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			A	48276663	T	A	48276663	3	1	170	1	0	0	0	0	1	0	0	0	3679	1435	50	4	4187	4	COL1A1	17	48276663	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	7802181	48276663	32918547	168	25859										
TEX2	55852	hgsc.bcm.edu	37	chr17	62290645	62290645	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggcctatggctgccactttcTtcccctataattttactaag	6	12	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:62290645T>A	ENST00000583097.1	-	2	1105	c.933A>T	c.(931-933)gaA>gaT	p.E311D	TEX2_ENST00000258991.3_Missense_Mutation_p.E311D|TEX2_ENST00000584379.1_Missense_Mutation_p.E311D			Q8IWB9	TEX2_HUMAN	testis expressed 2	311					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TGCCACTTTCTTCCCCTATAA	0.423																																					p.E311D		Atlas-SNP	.											.	TEX2	89	.	0			c.A933T						.						45	48	47					17																	62290645		2203	4300	6503	SO:0001583	missense	55852	exon2			ACTTTCTTCCCCT	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"transmembrane protein 96"		"testis expressed sequence 2"			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.933A>T	chr17.hg19:g.62290645T>A	ENSP00000462665:p.Glu311Asp	73.0	0.0		75.0	14.0	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	hg19		.	.	.	.	.	.	.	.	.	.	T	8.850	0.944323	0.18356	.	.	ENSG00000136478	ENST00000258991	T	0.44881	0.91	6.03	-3.07	0.05363	.	0.112860	0.64402	D	0.000004	T	0.19127	0.0459	N	0.14661	0.345	0.29597	N	0.847959	B;B	0.19445	0.036;0.021	B;B	0.24541	0.054;0.024	T	0.07404	-1.0774	10	0.30854	T	0.27	-22.5236	5.6553	0.17639	0.139:0.5082:0.1037:0.2491	.	311;311	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	D	311	ENSP00000258991:E311D	ENSP00000258991:E311D	E	-	3	2	TEX2	59644377	0.043000	0.20138	0.911000	0.35937	0.901000	0.52897	-0.683000	0.05179	-0.536000	0.06298	-0.250000	0.11733	GAA	.	.		0.423	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		A	62290645	T	A	62290645	3	1	170	1	0	0	0	0	1	0	0	0	15796	1606	56	4	2515	4	TEX2	17	62290645	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	14013982	62290645	18904565	169	25860										
ABCA9	10350	hgsc.bcm.edu	37	chr17	66988376	66988376	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tcatttctaggcatcgcagaAtgaaaagaaaaatgagaaaa	8	5	2	4			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:66988376A>C	ENST00000340001.4	-	28	3867	c.3656T>G	c.(3655-3657)aTt>aGt	p.I1219S	ABCA9_ENST00000370732.2_Missense_Mutation_p.I1219S|ABCA9_ENST00000453985.2_Missense_Mutation_p.I1181S	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1219					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					GCATCGCAGAATGAAAAGAAA	0.318																																					p.I1219S		Atlas-SNP	.											.	ABCA9	192	.	0			c.T3656G						.						57	51	53					17																	66988376		2203	4299	6502	SO:0001583	missense	10350	exon28			CGCAGAATGAAAA	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.3656T>G	chr17.hg19:g.66988376A>C	ENSP00000342216:p.Ile1219Ser	190.0	0.0		217.0	53.0	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	hg19	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	A	10.64	1.406150	0.25378	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732	D;D	0.89050	-2.46;-2.46	5.26	3.0	0.34707	.	1.196280	0.06335	N	0.706852	D	0.90324	0.6973	L	0.57536	1.79	0.09310	N	1	P;B	0.40909	0.732;0.161	P;B	0.48677	0.586;0.314	T	0.78420	-0.2211	10	0.54805	T	0.06	.	8.6598	0.34086	0.8416:0.0:0.1584:0.0	.	1219;1219	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	S	1219;1164;1219	ENSP00000342216:I1219S;ENSP00000359767:I1219S	ENSP00000342216:I1219S	I	-	2	0	ABCA9	64499971	0.022000	0.18835	0.589000	0.28718	0.230000	0.25150	2.971000	0.49248	0.814000	0.34374	0.482000	0.46254	ATT	.	.		0.318	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		C	66988376	A	C	66988376	3	2	170	1	0	0	0	0	1	0	0	0	39	101	4	5	1266	5	ABCA9	17	66988376	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	4697731	66988376	14206834	170	25861										
COG1	9382	hgsc.bcm.edu	37	chr17	71197661	71197661	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agatacgcagatgcggggacCgtgcaggagatgctgcggac	17	9	0	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr17:71197661C>G	ENST00000299886.4	+	7	1775	c.1695C>G	c.(1693-1695)acC>acG	p.T565T		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	565					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			ATGCGGGGACCGTGCAGGAGA	0.577																																					p.T565T		Atlas-SNP	.											.	COG1	46	.	0			c.C1695G						.						95	82	86					17																	71197661		2203	4300	6503	SO:0001819	synonymous_variant	9382	exon7			GGGGACCGTGCAG		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"Components of oligomeric golgi complex"	6545	protein-coding gene	gene with protein product		606973	"low density lipoprotein receptor defect B complementing"	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1695C>G	chr17.hg19:g.71197661C>G		80.0	0.0		81.0	25.0	NM_018714	Q9NPV9|Q9P2G6	Silent	SNP	ENST00000299886.4	hg19	CCDS11692.1																																																																																			.	.		0.577	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			G	71197661	C	G	71197661	2	3	170	1	0	0	0	0	0	0	0	1	3659	639	23	4		4	COG1	17	71197661	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	4209285	71197661	9997549	171	25862										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3215130	3215130	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cggcggagcgtttcttctccCgctggtagtgactcacggtg	14	12	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr18:3215130C>T	ENST00000356443.4	-	2	425	c.92G>A	c.(91-93)cGg>cAg	p.R31Q	MYOM1_ENST00000261606.7_Missense_Mutation_p.R31Q|MYOM1_ENST00000400569.3_Missense_Mutation_p.R31Q|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	31					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.R31L(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TTTCTTCTCCCGCTGGTAGTG	0.642																																					p.R31Q		Atlas-SNP	.											MYOM1,NS,carcinoma,0,1	MYOM1	192	.	1	Substitution - Missense(1)	ovary(1)	c.G92A						.						53	58	56					18																	3215130		2089	4235	6324	SO:0001583	missense	8736	exon2			TTCTCCCGCTGGT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.92G>A	chr18.hg19:g.3215130C>T	ENSP00000348821:p.Arg31Gln	80.0	0.0		74.0	25.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	0.978	-0.697845	0.03279	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.39997	1.17;1.18;1.05	5.67	4.52	0.55395	.	0.516121	0.20942	N	0.082914	T	0.15089	0.0364	N	0.01874	-0.695	0.21897	N	0.999483	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24584	-1.0156	10	0.02654	T	1	.	10.6635	0.45717	0.0:0.0763:0.0:0.9237	.	31;31	P52179-2;P52179	.;MYOM1_HUMAN	Q	31	ENSP00000348821:R31Q;ENSP00000383413:R31Q;ENSP00000261606:R31Q	ENSP00000261606:R31Q	R	-	2	0	MYOM1	3205130	1.000000	0.71417	1.000000	0.80357	0.450000	0.32258	4.038000	0.57318	0.989000	0.38761	-0.238000	0.12139	CGG	.	.		0.642	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3215130	C	T	3215130	3	4	170	1	0	0	0	0	1	0	0	0	10100	652	23	1	5113	1	MYOM1	18	3215130	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10		3215130	74862118	172	25863										
PTPRM	5797	hgsc.bcm.edu	37	chr18	7926575	7926575	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tctttatgtagccaggactcCtcacttcctgcggattcaga	8	12	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr18:7926575C>T	ENST00000332175.8	+	5	1594	c.557C>T	c.(556-558)cCt>cTt	p.P186L	PTPRM_ENST00000400053.4_Missense_Mutation_p.P124L|PTPRM_ENST00000400060.4_Missense_Mutation_p.P186L|PTPRM_ENST00000580170.1_Missense_Mutation_p.P186L	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	186	Ig-like C2-type.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GCCAGGACTCCTCACTTCCTG	0.433																																					p.P186L		Atlas-SNP	.											.	PTPRM	185	.	0			c.C557T						.						80	73	75					18																	7926575		2203	4300	6503	SO:0001583	missense	5797	exon5			GGACTCCTCACTT	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.557C>T	chr18.hg19:g.7926575C>T	ENSP00000331418:p.Pro186Leu	74.0	0.0		64.0	16.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.527336	0.85706	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053	T;T;T	0.54279	0.75;0.7;0.58	5.72	5.72	0.89469	Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.73118	0.3546	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.74478	-0.3652	10	0.87932	D	0	.	19.8788	0.96888	0.0:1.0:0.0:0.0	.	186;186	A7MBN1;P28827	.;PTPRM_HUMAN	L	186;186;124	ENSP00000331418:P186L;ENSP00000382933:P186L;ENSP00000382927:P124L	ENSP00000331418:P186L	P	+	2	0	PTPRM	7916575	1.000000	0.71417	1.000000	0.80357	0.737000	0.42083	6.709000	0.74665	2.704000	0.92352	0.563000	0.77884	CCT	.	.		0.433	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	7926575	C	T	7926575	3	4	170	1	0	0	0	0	1	0	0	0	12821	681	24	3	575	3	PTPRM	18	7926575	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	4711445	7926575	70150673	173	25864										
ANKRD30B	374860	hgsc.bcm.edu	37	chr18	14842894	14842894	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ataaatctcttttgctttttAgagtctcctgaaaagccttc	5	9	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr18:14842894A>G	ENST00000358984.4	+	32	2902		c.e32-1			NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B											breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						TTTGCTTTTTAGAGTCTCCTG	0.299																																					.		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.2723-2A>G						.						165	126	138					18																	14842894		692	1590	2282	SO:0001630	splice_region_variant	374860	exon32			CTTTTTAGAGTCT	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"Ankyrin repeat domain containing"	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.2723-1A>G	chr18.hg19:g.14842894A>G		454.0	0.0		482.0	85.0	NM_001145029	B4DGP1|F8WAG3|Q4G175	Splice_Site	SNP	ENST00000358984.4	hg19	CCDS54182.1	.	.	.	.	.	.	.	.	.	.	a	1.119	-0.655948	0.03480	.	.	ENSG00000180777	ENST00000358984;ENST00000320584;ENST00000277669	.	.	.	2.27	2.27	0.28462	.	.	.	.	.	.	.	.	.	.	.	0.49299	D	0.999771	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.4285	0.21784	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ANKRD30B	14832894	1.000000	0.71417	0.240000	0.24138	0.021000	0.10359	3.104000	0.50306	1.064000	0.40671	0.367000	0.22151	.	.	.		0.299	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	Intron	G	14842894	A	G	14842894	5	3	170	1	0	0	0	0	0	0	1	0	659	434	15	2	2847	2	ANKRD30B	18	14842894	Splice_Site	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	6916319	14842894	63234354	174	25865										
GATA6	2627	hgsc.bcm.edu	37	chr18	19751506	19751506	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gctgtggtccagccgcggcgCcaagctgagccccttcgcac	13	17	0	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr18:19751506C>G	ENST00000269216.3	+	2	678	c.401C>G	c.(400-402)gCc>gGc	p.A134G	GATA6_ENST00000581694.1_Missense_Mutation_p.A134G|GATA6-AS1_ENST00000583490.1_lincRNA	NM_005257.4	NP_005248.2	Q92908	GATA6_HUMAN	GATA binding protein 6	134					blood coagulation (GO:0007596)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cellular response to BMP stimulus (GO:0071773)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to hypoxia (GO:0071456)|Clara cell differentiation (GO:0060486)|endodermal cell fate determination (GO:0007493)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|liver development (GO:0001889)|lung saccule development (GO:0060430)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta1 production (GO:0032911)|negative regulation of transforming growth factor beta2 production (GO:0032912)|organ formation (GO:0048645)|outflow tract septum morphogenesis (GO:0003148)|pancreatic A cell differentiation (GO:0003310)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to growth factor (GO:0070848)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)|tube morphogenesis (GO:0035239)|type B pancreatic cell differentiation (GO:0003309)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	18	all_cancers(21;0.00271)|all_epithelial(16;7.31e-05)|Ovarian(2;0.116)|Lung NSC(20;0.123)|all_lung(20;0.246)		STAD - Stomach adenocarcinoma(5;0.106)			AGCCGCGGCGCCAAGCTGAGC	0.716																																					p.A134G	Colon(8;48 282 46199 46856)|Melanoma(177;170 2725 12489 26999)	Atlas-SNP	.											.	GATA6	35	.	0			c.C401G						.						14	19	17					18																	19751506		2142	4222	6364	SO:0001583	missense	2627	exon2			GCGGCGCCAAGCT	U66075	CCDS11872.1	18q11-q12	2013-01-25	2001-11-28		ENSG00000141448	ENSG00000141448		"GATA zinc finger domain containing"	4174	protein-coding gene	gene with protein product		601656	"GATA-binding protein 6"			8975704	Standard	XM_005258248		Approved		uc002ktt.2	Q92908	OTTHUMG00000131767	ENST00000269216.3:c.401C>G	chr18.hg19:g.19751506C>G	ENSP00000269216:p.Ala134Gly	1248.0	0.0		1043.0	281.0	NM_005257	B0YJ17|P78327	Missense_Mutation	SNP	ENST00000269216.3	hg19	CCDS11872.1	.	.	.	.	.	.	.	.	.	.	c	17.38	3.374194	0.61735	.	.	ENSG00000141448	ENST00000269216	D	0.98135	-4.74	3.3	3.3	0.37823	.	1.034180	0.07690	N	0.938563	D	0.93926	0.8056	N	0.19112	0.55	0.36202	D	0.850782	P	0.37525	0.598	B	0.31751	0.135	D	0.89800	0.3974	10	0.30854	T	0.27	-17.452	14.3936	0.66996	0.0:1.0:0.0:0.0	.	134	Q92908	GATA6_HUMAN	G	134	ENSP00000269216:A134G	ENSP00000269216:A134G	A	+	2	0	GATA6	18005504	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.665000	0.46791	1.667000	0.50832	0.450000	0.29827	GCC	.	.		0.716	GATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254696.1	NM_005257		G	19751506	C	G	19751506	3	3	170	1	0	0	0	0	1	0	0	0	6266	739	26	4	403	4	GATA6	18	19751506	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	4908612	19751506	58325742	175	25866										
PIAS2	9063	hgsc.bcm.edu	37	chr18	44400939	44400939	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gatattggcgtatggtggaaTggtactgagtagtctgttaa	14	3	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr18:44400939T>C	ENST00000585916.1	-	12	1604	c.1605A>G	c.(1603-1605)ccA>ccG	p.P535P	PIAS2_ENST00000545673.1_Silent_p.P245P|PIAS2_ENST00000324794.7_Silent_p.P535P	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	535					androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						TATGGTGGAATGGTACTGAGT	0.398																																					p.P535P		Atlas-SNP	.											.	PIAS2	85	.	0			c.A1605G						.						217	188	198					18																	44400939		2203	4300	6503	SO:0001819	synonymous_variant	9063	exon12			GTGGAATGGTACT	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"Zinc fingers, MIZ-type"	17311	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 4"	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.1605A>G	chr18.hg19:g.44400939T>C		146.0	0.0		115.0	31.0	NM_173206	O75927|Q96BT5|Q96KE3	Silent	SNP	ENST00000585916.1	hg19	CCDS32824.1																																																																																			.	.		0.398	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671		C	44400939	T	C	44400939	2	2	170	1	0	0	0	0	0	0	0	1	11885	1451	51	2		2	PIAS2	18	44400939	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	24649433	44400939	33676309	176	25867										
S1PR4	8698	hgsc.bcm.edu	37	chr19	3179175	3179175	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agggcctgctcttcaccgccCtggccgcctccaccttcagc	9	20	3	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:3179175C>T	ENST00000246115.3	+	1	440	c.385C>T	c.(385-387)Ctg>Ttg	p.L129L	S1PR4_ENST00000591346.1_Intron	NM_003775.3	NP_003766.1	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4	129					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			breast(1)|kidney(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13						CTTCACCGCCCTGGCCGCCTC	0.721																																					p.L129L	GBM(82;318 1638 33279 49708)	Atlas-SNP	.											.	S1PR4	31	.	0			c.C385T						.						33	35	35					19																	3179175		2178	4257	6435	SO:0001819	synonymous_variant	8698	exon1			ACCGCCCTGGCCG	AJ000479	CCDS12105.1	19p13.3	2012-08-08	2008-04-30	2008-04-30		ENSG00000125910		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3170	protein-coding gene	gene with protein product		603751	"endothelial differentiation, G-protein-coupled receptor 6", "endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 6"	EDG6		9790765	Standard	NM_003775		Approved		uc002lxg.3	O95977		ENST00000246115.3:c.385C>T	chr19.hg19:g.3179175C>T		125.0	0.0		157.0	29.0	NM_003775	D6W612	Silent	SNP	ENST00000246115.3	hg19	CCDS12105.1																																																																																			.	.		0.721	S1PR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452517.1	NM_003775		T	3179175	C	T	3179175	2	4	170	1	0	0	0	0	0	0	0	1	13811	680	24	3		3	S1PR4	19	3179175	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10		3179175	55949808	177	25868										
PTPRS	5802	hgsc.bcm.edu	37	chr19	5244417	5244417	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	taggacacaggatctgggttGcccgagtcccacgtgatggt	14	10	1	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:5244417G>A	ENST00000587303.1	-	10	1164	c.1065C>T	c.(1063-1065)ggC>ggT	p.G355G	PTPRS_ENST00000262963.6_Silent_p.G351G|PTPRS_ENST00000372412.4_Silent_p.G356G|PTPRS_ENST00000588012.1_Silent_p.G342G|PTPRS_ENST00000592099.1_Silent_p.G342G|PTPRS_ENST00000348075.2_Silent_p.G342G|PTPRS_ENST00000353284.2_Silent_p.G342G|PTPRS_ENST00000357368.4_Silent_p.G355G|PTPRS_ENST00000588552.1_5'UTR			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	355	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GATCTGGGTTGCCCGAGTCCC	0.547																																					p.G355G		Atlas-SNP	.											.	PTPRS	169	.	0			c.C1065T						.						127	115	119					19																	5244417		2203	4300	6503	SO:0001819	synonymous_variant	5802	exon11			TGGGTTGCCCGAG	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.1065C>T	chr19.hg19:g.5244417G>A		113.0	0.0		131.0	54.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	hg19	CCDS45930.1																																																																																			.	.		0.547	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			A	5244417	G	A	5244417	2	1	170	1	0	0	0	0	0	0	0	1	12826	1306	46	3		3	PTPRS	19	5244417	Silent	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	2065242	5244417	53884566	178	25869										
MUC16	94025	hgsc.bcm.edu	37	chr19	9068492	9068492	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gggtctgagtcaggtgagacAgtaaaatagaattcatttgg	13	4	3	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:9068492A>T	ENST00000397910.4	-	3	19157	c.18954T>A	c.(18952-18954)acT>acA	p.T6318T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6320	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGGTGAGACAGTAAAATAGA	0.463																																					p.T6318T		Atlas-SNP	.											.	MUC16	4315	.	0			c.T18954A						.						177	167	170					19																	9068492		1992	4176	6168	SO:0001819	synonymous_variant	94025	exon3			TGAGACAGTAAAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.18954T>A	chr19.hg19:g.9068492A>T		88.0	0.0		134.0	53.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9068492	A	T	9068492	2	4	170	1	0	0	0	0	0	0	0	1	9982	175	7	4		4	MUC16	19	9068492	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	3824075	9068492	50060491	179	25870										
OR1M1	125963	hgsc.bcm.edu	37	chr19	9204033	9204033	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cttctgcatgtacctggtcaTggtcgtggggaacctgctca	12	11	3	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:9204033T>A	ENST00000429566.3	+	1	179	c.113T>A	c.(112-114)aTg>aAg	p.M38K		NM_001004456.1	NP_001004456.1	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M, member 1	38						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|large_intestine(3)|lung(17)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						TACCTGGTCATGGTCGTGGGG	0.527																																					p.M38K		Atlas-SNP	.											.	OR1M1	52	.	0			c.T113A						.						130	105	113					19																	9204033		2203	4300	6503	SO:0001583	missense	125963	exon1			TGGTCATGGTCGT		CCDS32896.1	19p13.2	2013-09-20			ENSG00000170929	ENSG00000170929		"GPCR / Class A : Olfactory receptors"	8220	protein-coding gene	gene with protein product							Standard	NM_001004456		Approved	OR19-6	uc010xkj.2	Q8NGA1	OTTHUMG00000179930	ENST00000429566.3:c.113T>A	chr19.hg19:g.9204033T>A	ENSP00000401966:p.Met38Lys	73.0	0.0		94.0	15.0	NM_001004456	B9EHA6|Q6IFJ3|Q96R91	Missense_Mutation	SNP	ENST00000429566.3	hg19	CCDS32896.1	.	.	.	.	.	.	.	.	.	.	c	10.98	1.503730	0.26949	.	.	ENSG00000170929	ENST00000305465;ENST00000429566	T	0.00509	6.91	3.49	2.43	0.29744	.	0.718575	0.12863	N	0.432985	T	0.00384	0.0012	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46925	-0.9156	10	0.87932	D	0	.	8.6652	0.34116	0.0:0.8024:0.0:0.1976	.	38	Q8NGA1	OR1M1_HUMAN	K	41;38	ENSP00000401966:M38K	ENSP00000303195:M41K	M	+	2	0	OR1M1	9065033	0.715000	0.27946	0.002000	0.10522	0.000000	0.00434	2.370000	0.44240	0.295000	0.22570	-0.511000	0.04467	ATG	.	.		0.527	OR1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448993.1			A	9204033	T	A	9204033	3	1	170	1	0	0	0	0	1	0	0	0	10977	1464	51	4	115	4	OR1M1	19	9204033	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	135541	9204033	49924950	180	25871										
PODNL1	79883	hgsc.bcm.edu	37	chr19	14047181	14047181	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cctccctctgccccctcaccTtcggaggagatgaggttgtt	10	15	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:14047181T>C	ENST00000339560.5	-	3	612	c.339A>G	c.(337-339)gaA>gaG	p.E113E	PODNL1_ENST00000254320.3_Splice_Site_p.K53R|PODNL1_ENST00000538517.2_Splice_Site_p.E111E|PODNL1_ENST00000538371.2_Splice_Site_p.E111E	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	113	Leu-rich.					proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			CCCCCTCACCTTCGGAGGAGA	0.647																																					p.E113E		Atlas-SNP	.											.	PODNL1	27	.	0			c.A339G						.						154	135	141					19																	14047181		2203	4300	6503	SO:0001630	splice_region_variant	79883	exon3			CTCACCTTCGGAG	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.340+1A>G	chr19.hg19:g.14047181T>C		66.0	0.0		71.0	23.0	NM_024825	B7Z564|Q9H5G9	Silent	SNP	ENST00000339560.5	hg19	CCDS12300.1	.	.	.	.	.	.	.	.	.	.	t	11.33	1.607520	0.28623	.	.	ENSG00000132000	ENST00000545071;ENST00000254320	T	0.38401	1.14	4.64	2.49	0.30216	.	.	.	.	.	T	0.21841	0.0526	.	.	.	0.80722	D	1	B	0.12013	0.005	B	0.15052	0.012	T	0.04991	-1.0913	8	0.22706	T	0.39	.	7.2974	0.26401	0.0:0.7819:0.0:0.2181	.	53	B7Z3M0	.	R	53	ENSP00000254320:K53R	ENSP00000254320:K53R	K	-	2	0	PODNL1	13908181	0.597000	0.26874	0.995000	0.50966	0.404000	0.30871	-0.136000	0.10405	0.930000	0.37217	-0.433000	0.05886	AAG	.	.		0.647	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825	Silent	C	14047181	T	C	14047181	5	2	170	1	0	0	0	0	0	0	1	0	12188	1623	56	2	1223	2	PODNL1	19	14047181	Splice_Site	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	4843148	14047181	45081802	181	25872										
JAK3	3718	hgsc.bcm.edu	37	chr19	17954263	17954263	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cttgcgtagcccgaagcggtGgcacttctccagcccaaacc	10	16	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:17954263G>T	ENST00000527670.1	-	3	375	c.346C>A	c.(346-348)Cac>Aac	p.H116N	JAK3_ENST00000458235.1_Missense_Mutation_p.H116N|JAK3_ENST00000526008.1_5'UTR|JAK3_ENST00000534444.1_Missense_Mutation_p.H116N			P52333	JAK3_HUMAN	Janus kinase 3	116	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with cytokine/interferon/growth hormone receptors. {ECO:0000250}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	CCGAAGCGGTGGCACTTCTCC	0.562		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.H116N		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	JAK3	341	.	0			c.C346A						.						25	22	23					19																	17954263		2201	4297	6498	SO:0001583	missense	3718	exon4			AGCGGTGGCACTT	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.346C>A	chr19.hg19:g.17954263G>T	ENSP00000432511:p.His116Asn	170.0	0.0		227.0	49.0	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	hg19	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.486848	0.44249	.	.	ENSG00000105639	ENST00000458235;ENST00000428406;ENST00000527670;ENST00000534444	T;T;T	0.70869	-0.52;-0.52;-0.52	4.78	3.51	0.40186	Band 4.1 domain (1);FERM domain (1);	0.204238	0.45126	D	0.000400	T	0.59074	0.2167	L	0.47716	1.5	0.29632	N	0.845346	P;P;B	0.51933	0.949;0.696;0.432	B;B;B	0.43301	0.415;0.32;0.093	T	0.60551	-0.7241	10	0.42905	T	0.14	-42.9992	4.9412	0.13967	0.2664:0.0:0.7336:0.0	.	116;116;116	B4DK43;P52333-2;P52333	.;.;JAK3_HUMAN	N	116	ENSP00000391676:H116N;ENSP00000432511:H116N;ENSP00000436421:H116N	ENSP00000413248:H116N	H	-	1	0	JAK3	17815263	0.999000	0.42202	0.952000	0.39060	0.732000	0.41865	3.433000	0.52834	2.386000	0.81285	0.485000	0.47835	CAC	.	.		0.562	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		T	17954263	G	T	17954263	3	4	170	1	0	0	0	0	1	0	0	0	7948	1348	47	3	3112	3	JAK3	19	17954263	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	3907082	17954263	41174720	182	25873										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36351548	36351548	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ccgtgggtagcgccaaccgcAgtactgcgctggatgtgctg	15	12	0	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:36351548A>C	ENST00000360202.5	+	7	1105	c.907A>C	c.(907-909)Agt>Cgt	p.S303R	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Missense_Mutation_p.S303R|KIRREL2_ENST00000347900.6_Missense_Mutation_p.S253R|KIRREL2_ENST00000262625.7_Missense_Mutation_p.S303R	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	303	Ig-like C2-type 3.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CGCCAACCGCAGTACTGCGCT	0.682																																					p.S303R		Atlas-SNP	.											.	KIRREL2	170	.	0			c.A907C						.						61	68	66					19																	36351548		2203	4300	6503	SO:0001583	missense	84063	exon7			AACCGCAGTACTG	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.907A>C	chr19.hg19:g.36351548A>C	ENSP00000353331:p.Ser303Arg	61.0	0.0		71.0	31.0	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	hg19	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	a	24.6	4.548749	0.86127	.	.	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.18016	2.24;2.24;2.24	3.99	3.99	0.46301	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.49916	D	0.000126	T	0.39172	0.1068	M	0.84683	2.71	0.48830	D	0.999711	P;P;P;D;P	0.53462	0.942;0.928;0.901;0.96;0.928	P;P;P;P;P	0.60012	0.867;0.79;0.743;0.626;0.626	T	0.37197	-0.9716	10	0.87932	D	0	-20.8176	9.5376	0.39231	1.0:0.0:0.0:0.0	.	303;283;303;253;303	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	R	303;253;303;283	ENSP00000262625:S303R;ENSP00000345067:S253R;ENSP00000353331:S303R	ENSP00000262625:S303R	S	+	1	0	KIRREL2	41043388	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	8.067000	0.89488	1.831000	0.53308	0.365000	0.22127	AGT	.	.		0.682	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		C	36351548	A	C	36351548	3	2	170	1	0	0	0	0	1	0	0	0	8334	188	7	5	933	5	KIRREL2	19	36351548	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	18397285	36351548	22777435	183	25874										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41025770	41025770	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gggcccctgcccaacagcctAgaagaggcggacgcgctgct	14	15	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:41025770A>T	ENST00000352632.3	+	16	3452	c.3366A>T	c.(3364-3366)ctA>ctT	p.L1122L	SPTBN4_ENST00000344104.3_Silent_p.L1122L|SPTBN4_ENST00000598249.1_Silent_p.L1122L|SPTBN4_ENST00000595535.1_Silent_p.L1122L|SPTBN4_ENST00000338932.3_Silent_p.L1122L			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1122					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CCAACAGCCTAGAAGAGGCGG	0.711																																					p.L1122L		Atlas-SNP	.											.	SPTBN4	213	.	0			c.A3366T						.						3	3	3					19																	41025770		1591	3203	4794	SO:0001819	synonymous_variant	57731	exon16			CAGCCTAGAAGAG	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.3366A>T	chr19.hg19:g.41025770A>T		28.0	0.0		38.0	9.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	hg19	CCDS12559.1																																																																																			.	.		0.711	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			T	41025770	A	T	41025770	2	4	170	1	0	0	0	0	0	0	0	1	15136	407	15	4		4	SPTBN4	19	41025770	Silent	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	4674222	41025770	18103213	184	25875										
HNRNPUL1	11100	hgsc.bcm.edu	37	chr19	41808816	41808816	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ccgtggcggcttccagaaccGagggggaggcagcggtggag	20	10	0	1	rs147281768		TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:41808816G>A	ENST00000392006.3	+	12	2107	c.1934G>A	c.(1933-1935)cGa>cAa	p.R645Q	HNRNPUL1_ENST00000378215.4_Missense_Mutation_p.R531Q|HNRNPUL1_ENST00000352456.3_Missense_Mutation_p.R545Q|HNRNPUL1_ENST00000602130.1_Missense_Mutation_p.R645Q|HNRNPUL1_ENST00000595018.1_Missense_Mutation_p.R545Q|HNRNPUL1_ENST00000263367.3_Missense_Mutation_p.R556Q|HNRNPUL1_ENST00000593587.1_Missense_Mutation_p.R545Q	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	645	5 X 3 AA repeats of R-G-G.|Gly-rich.|Necessary for interaction with TP53.|Necessary for transcription repression.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						TTCCAGAACCGAGGGGGAGGC	0.647													G|||	1	0.000199681	0	0	5008	,	,		14965	0		0.001	False		,,,				2504	0				p.R645Q		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.G1934A						.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	35	41	39		1934,1634	5.3	1	19	dbSNP_134	39	2,8596	2.2+/-6.3	0,2,4297	no	missense,missense	HNRNPUL1	NM_007040.3,NM_144732.2	43,43	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	645/857,545/757	41808816	2,13002	2203	4299	6502	SO:0001583	missense	11100	exon12			AGAACCGAGGGGG	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"E1B 55kDa associated protein 5"	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.1934G>A	chr19.hg19:g.41808816G>A	ENSP00000375863:p.Arg645Gln	185.0	0.0		247.0	44.0	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Missense_Mutation	SNP	ENST00000392006.3	hg19	CCDS12576.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.492286	0.84962	0.0	2.33E-4	ENSG00000105323	ENST00000352456;ENST00000392006;ENST00000378215;ENST00000263367	D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.85639	0.5743	N	0.24115	0.695	0.47547	D	0.99945	D;D;D;D;D;D;D	0.89917	0.98;0.993;0.996;1.0;0.996;0.993;0.996	P;P;P;D;P;P;P	0.76575	0.449;0.546;0.806;0.988;0.806;0.644;0.734	D	0.85884	0.1424	10	0.44086	T	0.13	-7.3539	18.1981	0.89829	0.0:0.0:1.0:0.0	.	556;545;645;169;531;645;545	B7Z4B8;A8K3W4;Q9BUJ2-2;Q9BUJ2-5;Q9BUJ2-3;Q9BUJ2;Q9BUJ2-4	.;.;.;.;.;HNRL1_HUMAN;.	Q	545;645;531;556	ENSP00000340857:R545Q;ENSP00000375863:R645Q;ENSP00000367460:R531Q;ENSP00000263367:R556Q	ENSP00000263367:R556Q	R	+	2	0	HNRNPUL1	46500656	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	8.522000	0.90573	2.659000	0.90383	0.655000	0.94253	CGA	.	G|1.000;A|0.000		0.647	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040		A	41808816	G	A	41808816	3	1	170	1	0	0	0	0	1	0	0	0	7283	1058	37	1	1980	1	HNRNPUL1	19	41808816	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	783046	41808816	17320167	185	25876										
IRGQ	126298	hgsc.bcm.edu	37	chr19	44096203	44096203	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gggcaggctcagggggtgccAgcacagcctcagcatcagcc	15	14	3	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:44096203A>T	ENST00000602269.1	-	2	2032	c.1847T>A	c.(1846-1848)cTg>cAg	p.L616Q	IRGQ_ENST00000601520.1_Intron|IRGQ_ENST00000422989.1_Missense_Mutation_p.L616Q|L34079.2_ENST00000594374.1_Intron			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	616	Ala-rich.									endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				AGGGGGTGCCAGCACAGCCTC	0.667																																					p.L616Q		Atlas-SNP	.											.	IRGQ	40	.	0			c.T1847A						.						74	85	82					19																	44096203		2201	4294	6495	SO:0001583	missense	126298	exon3			GGTGCCAGCACAG	AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"immunity-related GTPase family, Q1"	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.1847T>A	chr19.hg19:g.44096203A>T	ENSP00000472250:p.Leu616Gln	116.0	0.0		166.0	34.0	NM_001007561	B2RNP3	Missense_Mutation	SNP	ENST00000602269.1	hg19	CCDS33040.1	.	.	.	.	.	.	.	.	.	.	A	15.27	2.782907	0.49891	.	.	ENSG00000167378	ENST00000422989	T	0.59224	0.28	4.9	4.9	0.64082	.	0.101452	0.39544	N	0.001324	T	0.69602	0.3129	L	0.53249	1.67	0.34845	D	0.741081	D	0.89917	1.0	D	0.91635	0.999	T	0.78753	-0.2081	10	0.87932	D	0	-11.5777	11.1101	0.48228	1.0:0.0:0.0:0.0	.	616	Q8WZA9	IRGQ_HUMAN	Q	616	ENSP00000387535:L616Q	ENSP00000387535:L616Q	L	-	2	0	IRGQ	48788043	1.000000	0.71417	1.000000	0.80357	0.300000	0.27592	4.277000	0.58939	2.185000	0.69588	0.533000	0.62120	CTG	.	.		0.667	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561		T	44096203	A	T	44096203	3	4	170	1	0	0	0	0	1	0	0	0	7848	188	7	4	28	4	IRGQ	19	44096203	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	2287387	44096203	15032780	186	25877										
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305829	48305829	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gattgggccacggaatgggcCtgggatctggactgggcctg	18	9	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:48305829C>T	ENST00000322175.3	-	2	594	c.439G>A	c.(439-441)Ggc>Agc	p.G147S	TPRX1_ENST00000535759.1_Missense_Mutation_p.G244S|TPRX1_ENST00000543508.1_Missense_Mutation_p.G147S	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	147	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		cggaatgggcctgggatctgg	0.642																																					p.G147S	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.G439A						.						21	18	19					19																	48305829		1961	3844	5805	SO:0001583	missense	284355	exon2			ATGGGCCTGGGAT		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"Homeoboxes / PRD class"	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.439G>A	chr19.hg19:g.48305829C>T	ENSP00000323455:p.Gly147Ser	146.0	0.0		198.0	36.0	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	hg19	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	c	2.004	-0.428714	0.04701	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.40225	1.04;1.04;1.04	0.383	0.383	0.16239	.	.	.	.	.	T	0.17238	0.0414	N	0.03608	-0.345	0.09310	N	1	P	0.43314	0.803	B	0.41946	0.371	T	0.11817	-1.0572	8	0.09590	T	0.72	.	.	.	.	.	147	Q8N7U7	TPRX1_HUMAN	S	147;244;147	ENSP00000323455:G147S;ENSP00000438832:G244S;ENSP00000438712:G147S	ENSP00000323455:G147S	G	-	1	0	TPRX1	52997641	0.000000	0.05858	0.028000	0.17463	0.028000	0.11728	-0.232000	0.09055	0.423000	0.26033	0.423000	0.28283	GGC	.	.		0.642	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		T	48305829	C	T	48305829	3	4	170	1	0	0	0	0	1	0	0	0	16437	681	24	3	800	3	TPRX1	19	48305829	Missense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	4209626	48305829	10823154	187	25878										
ZNF615	284370	hgsc.bcm.edu	37	chr19	52496688	52496688	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgactcttctcagtgaagccTtttccacactcattgcaaat	5	12	3	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:52496688T>C	ENST00000602063.1	-	6	1990	c.1641A>G	c.(1639-1641)aaA>aaG	p.K547K	ZNF615_ENST00000376716.5_Silent_p.K547K|ZNF615_ENST00000391795.3_Silent_p.K552K|ZNF615_ENST00000594083.1_Silent_p.K558K|ZNF615_ENST00000598071.1_Silent_p.K558K			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	547					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		CAGTGAAGCCTTTTCCACACT	0.448																																					p.K558K		Atlas-SNP	.											.	ZNF615	111	.	0			c.A1674G						.						117	103	108					19																	52496688		2203	4300	6503	SO:0001819	synonymous_variant	284370	exon7			GAAGCCTTTTCCA	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.1641A>G	chr19.hg19:g.52496688T>C		80.0	0.0		97.0	4.0	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Silent	SNP	ENST00000602063.1	hg19	CCDS12846.1																																																																																			.	.		0.448	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		C	52496688	T	C	52496688	2	2	170	1	0	0	0	0	0	0	0	1	18055	1606	56	2		2	ZNF615	19	52496688	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	4190859	52496688	6632295	188	25879										
ZNF808	388558	hgsc.bcm.edu	37	chr19	53050791	53050791	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ttgactttcagggatgtggcTatagaattctcattggcaga	11	6	2	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:53050791T>C	ENST00000359798.4	+	4	270	c.90T>C	c.(88-90)gcT>gcC	p.A30A		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	30	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		GGGATGTGGCTATAGAATTCT	0.438																																					p.A30A		Atlas-SNP	.											.	ZNF808	81	.	0			c.T90C						.						122	129	127					19																	53050791		2203	4300	6503	SO:0001819	synonymous_variant	388558	exon4			TGTGGCTATAGAA	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.90T>C	chr19.hg19:g.53050791T>C		83.0	0.0		118.0	22.0	NM_001039886	Q68CN7	Silent	SNP	ENST00000359798.4	hg19	CCDS46167.1																																																																																			.	.		0.438	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		C	53050791	T	C	53050791	2	2	170	1	0	0	0	0	0	0	0	1	18188	1509	53	2		2	ZNF808	19	53050791	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	554103	53050791	6078192	189	25880										
VN1R2	317701	hgsc.bcm.edu	37	chr19	53762581	53762581	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	cagagccatccaaagcatccTtgcattggtgagcacctttg	9	12	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr19:53762581T>A	ENST00000341702.3	+	1	1037	c.953T>A	c.(952-954)cTt>cAt	p.L318H	VN1R2_ENST00000598458.1_3'UTR	NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	318					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		CAAAGCATCCTTGCATTGGTG	0.453																																					p.L318H		Atlas-SNP	.											.	VN1R2	71	.	0			c.T953A						.						231	202	212					19																	53762581		2203	4300	6503	SO:0001583	missense	317701	exon1			GCATCCTTGCATT	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.953T>A	chr19.hg19:g.53762581T>A	ENSP00000351244:p.Leu318His	161.0	0.0		133.0	51.0	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	hg19	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.126336	0.56721	.	.	ENSG00000196131	ENST00000341702	T	0.14640	2.49	2.93	2.93	0.34026	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.45994	0.1370	H	0.94658	3.565	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.32322	-0.9911	9	0.87932	D	0	.	9.7491	0.40464	0.0:0.0:0.0:1.0	.	318	Q8NFZ6	VN1R2_HUMAN	H	318	ENSP00000351244:L318H	ENSP00000351244:L318H	L	+	2	0	VN1R2	58454393	0.018000	0.18449	0.080000	0.20451	0.436000	0.31835	2.713000	0.47194	1.615000	0.50252	0.481000	0.45027	CTT	.	.		0.453	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		A	53762581	T	A	53762581	3	1	170	1	0	0	0	0	1	0	0	0	17194	1609	56	4	955	4	VN1R2	19	53762581	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	711790	53762581	5366402	190	25881										
SIRPB1	10326	hgsc.bcm.edu	37	chr20	1551730	1551730	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gctcacctggcaggtgacgtTtgcctggttctctgccctca	11	14	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr20:1551730T>C	ENST00000381605.4	-	4	869	c.805A>G	c.(805-807)Aac>Gac	p.N269D	SIRPB1_ENST00000262929.5_Intron|SIRPB1_ENST00000381603.3_Intron|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	269	Ig-like C1-type 2.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CAGGTGACGTTTGCCTGGTTC	0.542																																					p.N269D		Atlas-SNP	.											.	SIRPB1	83	.	0			c.A805G						.						95	88	90					20																	1551730		2203	4300	6503	SO:0001583	missense	10326	exon4			TGACGTTTGCCTG	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.805A>G	chr20.hg19:g.1551730T>C	ENSP00000371018:p.Asn269Asp	146.0	0.0		195.0	80.0	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	hg19	CCDS13019.1	.	.	.	.	.	.	.	.	.	.	.	14.56	2.573313	0.45902	.	.	ENSG00000101307	ENST00000381605	T	0.00612	6.22	2.39	2.39	0.29439	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.455016	0.21297	N	0.076865	T	0.02230	0.0069	M	0.80422	2.495	0.19775	N	0.999959	D	0.57571	0.98	P	0.60789	0.879	T	0.31530	-0.9940	10	0.52906	T	0.07	.	6.5862	0.22622	0.0:0.0:0.0:1.0	.	269	O00241	SIRB1_HUMAN	D	269	ENSP00000371018:N269D	ENSP00000371018:N269D	N	-	1	0	SIRPB1	1499730	0.013000	0.17824	0.082000	0.20525	0.027000	0.11550	1.809000	0.38922	1.095000	0.41419	0.260000	0.18958	AAC	.	.		0.542	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		C	1551730	T	C	1551730	3	2	170	1	0	0	0	0	1	0	0	0	14348	1841	64	2	399	2	SIRPB1	20	1551730	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10		1551730	61473790	191	25882										
CEP250	11190	hgsc.bcm.edu	37	chr20	34092199	34092199	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggaggccagcactgcaacccTgcaagcctccctggatgcct	11	16	0	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr20:34092199T>A	ENST00000397527.1	+	30	6722	c.6002T>A	c.(6001-6003)cTg>cAg	p.L2001Q	CEP250_ENST00000342580.4_Missense_Mutation_p.L1945Q	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	2001	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			ACTGCAACCCTGCAAGCCTCC	0.612																																					p.L2001Q		Atlas-SNP	.											.	CEP250	141	.	0			c.T6002A						.						18	20	19					20																	34092199		2198	4298	6496	SO:0001583	missense	11190	exon30			CAACCCTGCAAGC	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.6002T>A	chr20.hg19:g.34092199T>A	ENSP00000380661:p.Leu2001Gln	77.0	0.0		89.0	39.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	T	12.59	1.984543	0.35036	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.50001	2.76;2.74;0.76	5.08	5.08	0.68730	.	0.261790	0.25487	N	0.030338	T	0.62696	0.2449	L	0.49126	1.545	0.37119	D	0.900729	D	0.89917	1.0	D	0.91635	0.999	T	0.67562	-0.5639	10	0.46703	T	0.11	.	14.6713	0.68945	0.0:0.0:0.0:1.0	.	2001	Q9BV73	CP250_HUMAN	Q	2001;1945;489	ENSP00000380661:L2001Q;ENSP00000341541:L1945Q;ENSP00000395992:L489Q	ENSP00000341541:L1945Q	L	+	2	0	CEP250	33555613	0.994000	0.37717	0.870000	0.34147	0.064000	0.16182	2.321000	0.43805	2.127000	0.65507	0.533000	0.62120	CTG	.	.		0.612	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		A	34092199	T	A	34092199	3	1	170	1	0	0	0	0	1	0	0	0	3254	1580	55	4	6108	4	CEP250	20	34092199	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	32540469	34092199	28933321	192	25883										
KIAA0406	9675	hgsc.bcm.edu	37	chr20	36642114	36642114	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tcactcacagcttgtagtcgTgtctgcagatgctccacatt	8	12	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr20:36642114T>A	ENST00000373448.2	-	3	343	c.105A>T	c.(103-105)acA>acT	p.T35T	TTI1_ENST00000487362.1_5'UTR|TTI1_ENST00000373447.3_Silent_p.T35T|TTI1_ENST00000449821.1_Silent_p.T35T	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	35					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						CTTGTAGTCGTGTCTGCAGAT	0.512																																					p.T35T		Atlas-SNP	.											.	TTI1	104	.	0			c.A105T						.						141	117	125					20																	36642114		2203	4300	6503	SO:0001819	synonymous_variant	9675	exon3			TAGTCGTGTCTGC	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"	614425	"KIAA0406", "Tel2 interacting protein 1 homolog (S. pombe)"	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.105A>T	chr20.hg19:g.36642114T>A		85.0	0.0		117.0	57.0	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Silent	SNP	ENST00000373448.2	hg19	CCDS13300.1																																																																																			.	.		0.512	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657		A	36642114	T	A	36642114	2	1	170	1	0	0	0	0	0	0	0	1	8182	1683	59	4		4	KIAA0406	20	36642114	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	2549915	36642114	26383406	193	25884										
SYS1	90196	hgsc.bcm.edu	37	chr20	43995718	43995718	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	catgcggacggagctcaaggAgatacccctcaactcagccc	10	15	3	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr20:43995718A>T	ENST00000243918.5	+	4	725	c.434A>T	c.(433-435)gAg>gTg	p.E145V	SYS1_ENST00000414310.1_Missense_Mutation_p.E124V|SYS1_ENST00000372727.1_Missense_Mutation_p.E145V|SYS1_ENST00000479779.1_3'UTR|SYS1-DBNDD2_ENST00000452133.1_Intron|SYS1-DBNDD2_ENST00000475242.1_Intron|SYS1_ENST00000426004.1_Intron	NM_033542.3	NP_291020.1	Q8N2H4	SYS1_HUMAN	Sys1 golgi trafficking protein	145					protein transport (GO:0015031)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|large_intestine(2)|prostate(1)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				GAGCTCAAGGAGATACCCCTC	0.582																																					p.E145V		Atlas-SNP	.											.	SYS1	15	.	0			c.A434T						.						116	112	113					20																	43995718		2203	4300	6503	SO:0001583	missense	90196	exon5			TCAAGGAGATACC	AL021578	CCDS13351.1, CCDS56192.1	20q13.12	2014-05-07	2014-05-07	2006-11-06	ENSG00000204070	ENSG00000204070			16162	protein-coding gene	gene with protein product		612979	"chromosome 20 open reading frame 169", "SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)"	C20orf169		15077113	Standard	NM_001197129		Approved	dJ453C12.4	uc002xnv.3	Q8N2H4	OTTHUMG00000032579	ENST00000243918.5:c.434A>T	chr20.hg19:g.43995718A>T	ENSP00000243918:p.Glu145Val	117.0	0.0		136.0	52.0	NM_001197129	C9JFB3|E1P620|Q5QPU7|Q96SD8|Q9BQZ2|Q9BQZ4|Q9H1F7	Missense_Mutation	SNP	ENST00000243918.5	hg19	CCDS13351.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.644275	0.87859	.	.	ENSG00000204070	ENST00000372727;ENST00000414310;ENST00000243918	.	.	.	6.17	6.17	0.99709	.	0.054549	0.64402	D	0.000001	T	0.67401	0.2889	M	0.76170	2.325	0.58432	D	0.999996	P	0.34864	0.473	B	0.38106	0.265	T	0.70077	-0.4971	9	0.66056	D	0.02	-0.1171	16.0034	0.80327	1.0:0.0:0.0:0.0	.	145	Q8N2H4	SYS1_HUMAN	V	145;124;145	.	ENSP00000243918:E145V	E	+	2	0	SYS1	43429132	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.080000	0.71299	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.582	SYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079453.2	NM_033542		T	43995718	A	T	43995718	3	4	170	1	0	0	0	0	1	0	0	0	15479	304	11	4	444	4	SYS1	20	43995718	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	7353604	43995718	19029802	194	25885										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44665420	44665420	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	catgagtgcaattgcaacgaAtggtgttgtgcctggtaggt	14	6	0	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr20:44665420A>G	ENST00000454036.2	+	5	585	c.536A>G	c.(535-537)aAt>aGt	p.N179S	SLC12A5_ENST00000243964.3_Missense_Mutation_p.N156S|SLC12A5_ENST00000608944.1_Missense_Mutation_p.N105S|SLC12A5_ENST00000372315.1_Missense_Mutation_p.N156S	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	179					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	ATTGCAACGAATGGTGTTGTG	0.607																																					p.N179S		Atlas-SNP	.											.	SLC12A5	181	.	0			c.A536G						.						156	116	130					20																	44665420		2203	4300	6503	SO:0001583	missense	57468	exon5			CAACGAATGGTGT	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.536A>G	chr20.hg19:g.44665420A>G	ENSP00000387694:p.Asn179Ser	96.0	0.0		143.0	22.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	hg19	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.761230	0.49468	.	.	ENSG00000124140	ENST00000454036;ENST00000372315;ENST00000539566;ENST00000243964	D;D;D;D	0.98849	-5.18;-5.18;-5.18;-5.18	4.65	4.65	0.58169	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99245	0.9737	M	0.92219	3.285	0.80722	D	1	D;D;D	0.89917	0.997;0.999;1.0	D;D;D	0.81914	0.98;0.991;0.995	D	0.99063	1.0831	10	0.87932	D	0	.	13.416	0.60968	1.0:0.0:0.0:0.0	.	179;156;156	Q9H2X9;Q9H2X9-2;A8K143	S12A5_HUMAN;.;.	S	179;156;156;156	ENSP00000387694:N179S;ENSP00000361389:N156S;ENSP00000446091:N156S;ENSP00000243964:N156S	ENSP00000243964:N156S	N	+	2	0	SLC12A5	44098827	1.000000	0.71417	0.996000	0.52242	0.040000	0.13550	9.006000	0.93592	1.953000	0.56701	0.460000	0.39030	AAT	.	.		0.607	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			G	44665420	A	G	44665420	3	3	170	1	0	0	0	0	1	0	0	0	14401	101	4	2	610	2	SLC12A5	20	44665420	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	669702	44665420	18360100	195	25886										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58441392	58441392	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	taaagactgtgaatctttttCaaaattctccagctcctcta	4	10	4	2	rs377589640		TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr20:58441392C>A	ENST00000357552.3	-	41	4501	c.4276G>T	c.(4276-4278)Gaa>Taa	p.E1426*	SYCP2_ENST00000371001.2_Nonsense_Mutation_p.E1426*			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	1426					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)	p.E1426K(1)		NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			GAATCTTTTTCAAAATTCTCC	0.234																																					p.E1426X		Atlas-SNP	.											SYCP2,NS,carcinoma,0,1	SYCP2	204	.	1	Substitution - Missense(1)	lung(1)	c.G4276T						.						30	35	33					20																	58441392		2120	4219	6339	SO:0001587	stop_gained	10388	exon40			CTTTTTCAAAATT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.4276G>T	chr20.hg19:g.58441392C>A	ENSP00000350162:p.Glu1426*	310.0	1.0		464.0	96.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Nonsense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.221123	0.79464	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000412613	.	.	.	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-17.1811	14.3627	0.66785	0.0:0.8522:0.1478:0.0	.	.	.	.	X	1426;1426;112	.	ENSP00000350162:E1426X	E	-	1	0	SYCP2	57874787	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.360000	0.52299	2.735000	0.93741	0.557000	0.71058	GAA	.	.		0.234	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		A	58441392	C	A	58441392	4	1	170	1	0	0	0	0	0	1	0	0	15447	835	29	3	336	3	SYCP2	20	58441392	Nonsense_Mutation	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	13775972	58441392	4584128	196	25887										
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62595237	62595237	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggcttccccgcgctcatggaTggccctctgccactgctctt	10	17	3	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr20:62595237T>C	ENST00000450537.1	-	9	1570	c.1510A>G	c.(1510-1512)Atc>Gtc	p.I504V	ZNF512B_ENST00000217130.3_Missense_Mutation_p.I504V|ZNF512B_ENST00000369888.1_Missense_Mutation_p.I504V			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	504					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CGCTCATGGATGGCCCTCTGC	0.637																																					p.I504V		Atlas-SNP	.											.	ZNF512B	72	.	0			c.A1510G						.						52	53	53					20																	62595237		2202	4298	6500	SO:0001583	missense	57473	exon9			CATGGATGGCCCT	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.1510A>G	chr20.hg19:g.62595237T>C	ENSP00000393795:p.Ile504Val	40.0	0.0		54.0	13.0	NM_020713	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	hg19	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	T	8.421	0.846335	0.16963	.	.	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.30448	1.53;1.53;1.53	4.62	1.95	0.26073	.	0.060400	0.64402	D	0.000004	T	0.44891	0.1315	M	0.64404	1.975	0.37675	D	0.923278	P	0.51240	0.943	D	0.66716	0.946	T	0.42531	-0.9446	10	0.45353	T	0.12	-13.3647	6.9432	0.24504	0.0:0.0902:0.2862:0.6236	.	504	Q96KM6	Z512B_HUMAN	V	504	ENSP00000358904:I504V;ENSP00000393795:I504V;ENSP00000217130:I504V	ENSP00000217130:I504V	I	-	1	0	ZNF512B	62065681	1.000000	0.71417	0.996000	0.52242	0.055000	0.15305	2.884000	0.48562	0.581000	0.29539	0.383000	0.25322	ATC	.	.		0.637	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		C	62595237	T	C	62595237	3	2	170	1	0	0	0	0	1	0	0	0	17972	1464	51	2	1204	2	ZNF512B	20	62595237	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	4153845	62595237	430283	197	25888										
TPTE	7179	hgsc.bcm.edu	37	chr21	10921957	10921957	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgcagttgaacatatttcagAggcaataaggaaggcacaaa	10	6	1	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr21:10921957A>G	ENST00000361285.4	-	18	1395	c.1066T>C	c.(1066-1068)Tct>Cct	p.S356P	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Missense_Mutation_p.S338P|TPTE_ENST00000342420.5_Missense_Mutation_p.S318P	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	356	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CATATTTCAGAGGCAATAAGG	0.343																																					p.S356P		Atlas-SNP	.											.	TPTE	513	.	0			c.T1066C						.						142	121	128					21																	10921957		2203	4299	6502	SO:0001583	missense	7179	exon18			TTTCAGAGGCAAT	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1066T>C	chr21.hg19:g.10921957A>G	ENSP00000355208:p.Ser356Pro	570.0	0.0		577.0	63.0	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	11.74	1.730269	0.30684	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.86297	-2.1;-2.1;-2.1	2.26	-0.715	0.11215	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.279979	0.44483	D	0.000445	D	0.91851	0.7421	M	0.93375	3.41	0.18873	N	0.999983	D;D;D	0.58970	0.984;0.964;0.97	P;P;P	0.59761	0.847;0.786;0.863	D	0.84323	0.0517	10	0.66056	D	0.02	-5.384	4.9133	0.13833	0.5101:0.0:0.0:0.4899	.	318;338;356	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	P	338;356;318	ENSP00000298232:S338P;ENSP00000355208:S356P;ENSP00000344441:S318P	ENSP00000298232:S338P	S	-	1	0	TPTE	9943828	0.017000	0.18338	0.015000	0.15790	0.010000	0.07245	-0.469000	0.06648	-0.275000	0.09219	0.102000	0.15555	TCT	.	.		0.343	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			G	10921957	A	G	10921957	3	3	170	1	0	0	0	0	1	0	0	0	16445	304	11	2	617	2	TPTE	21	10921957	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10		10921957	37207938	198	25889										
KRTAP13-4	284827	hgsc.bcm.edu	37	chr21	31802679	31802679	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aggctcctaccccagcagccTggtctacagcactgccctct	8	18	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr21:31802679T>A	ENST00000334068.2	+	1	108	c.86T>A	c.(85-87)cTg>cAg	p.L29Q		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	29						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						CCCAGCAGCCTGGTCTACAGC	0.602																																					p.L29Q	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.T86A						.						87	88	88					21																	31802679		2203	4300	6503	SO:0001583	missense	284827	exon1			GCAGCCTGGTCTA	AP001708	CCDS13592.1	21q22.1	2006-03-13			ENSG00000186971	ENSG00000186971		"Keratin associated proteins"	18926	protein-coding gene	gene with protein product						12359730	Standard	NM_181600		Approved	KAP13.4	uc011acw.2	Q3LI77	OTTHUMG00000057770	ENST00000334068.2:c.86T>A	chr21.hg19:g.31802679T>A	ENSP00000334834:p.Leu29Gln	114.0	0.0		118.0	40.0	NM_181600	A2RRL3	Missense_Mutation	SNP	ENST00000334068.2	hg19	CCDS13592.1	.	.	.	.	.	.	.	.	.	.	-	10.73	1.433548	0.25813	.	.	ENSG00000186971	ENST00000334068	T	0.04083	3.71	4.64	3.48	0.39840	.	0.000000	0.36234	N	0.002717	T	0.12220	0.0297	M	0.83223	2.63	0.23936	N	0.996413	P	0.52061	0.95	P	0.49502	0.613	T	0.07927	-1.0747	10	0.56958	D	0.05	.	8.2291	0.31587	0.1777:0.0:0.0:0.8223	.	29	Q3LI77	KR134_HUMAN	Q	29	ENSP00000334834:L29Q	ENSP00000334834:L29Q	L	+	2	0	KRTAP13-4	30724550	0.987000	0.35691	0.987000	0.45799	0.173000	0.22820	1.149000	0.31626	0.900000	0.36469	-0.280000	0.10049	CTG	.	.		0.602	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1			A	31802679	T	A	31802679	3	1	170	1	0	0	0	0	1	0	0	0	8534	1580	55	4	88	4	KRTAP13-4	21	31802679	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	20880722	31802679	16327216	199	25890										
TMPRSS2	7113	hgsc.bcm.edu	37	chr21	42845270	42845270	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	acttttccacgcagtgggcgGctgtcacgatccactcgggg	13	13	1	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr21:42845270G>A	ENST00000332149.5	-	9	1015	c.881C>T	c.(880-882)gCc>gTc	p.A294V	TMPRSS2_ENST00000398585.3_Missense_Mutation_p.A331V|TMPRSS2_ENST00000458356.1_Missense_Mutation_p.A294V	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	294	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)		TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				GCAGTGGGCGGCTGTCACGAT	0.692			T	"ERG, ETV1, ETV4, ETV5"	prostate																																p.A331V		Atlas-SNP	.		Dom	yes		21	21q22.3	7113	"transmembrane protease, serine 2"		E	.	TMPRSS2	148	.	0			c.C992T						.						17	16	16					21																	42845270		2177	4277	6454	SO:0001583	missense	7113	exon9			TGGGCGGCTGTCA	U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"Serine peptidases / Transmembrane"	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.881C>T	chr21.hg19:g.42845270G>A	ENSP00000330330:p.Ala294Val	108.0	0.0		115.0	36.0	NM_001135099	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Missense_Mutation	SNP	ENST00000332149.5	hg19	CCDS33564.1	.	.	.	.	.	.	.	.	.	.	G	17.63	3.436731	0.62955	.	.	ENSG00000184012	ENST00000332149;ENST00000398585;ENST00000458356;ENST00000454499	D;D;D;D	0.95238	-3.65;-3.65;-3.65;-3.65	5.31	5.31	0.75309	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.64402	D	0.000002	D	0.97445	0.9164	M	0.86953	2.85	0.51482	D	0.999928	D;D	0.76494	0.999;0.997	D;D	0.79108	0.992;0.992	D	0.97805	1.0247	10	0.56958	D	0.05	.	16.4733	0.84124	0.0:0.0:1.0:0.0	.	331;294	F8WES1;O15393	.;TMPS2_HUMAN	V	294;331;294;294	ENSP00000330330:A294V;ENSP00000381588:A331V;ENSP00000391216:A294V;ENSP00000389006:A294V	ENSP00000330330:A294V	A	-	2	0	TMPRSS2	41767140	1.000000	0.71417	0.296000	0.24974	0.126000	0.20510	7.106000	0.77039	2.476000	0.83614	0.650000	0.86243	GCC	.	.		0.692	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1			A	42845270	G	A	42845270	3	1	170	1	0	0	0	0	1	0	0	0	16262	1203	42	3	621	3	TMPRSS2	21	42845270	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	11042591	42845270	5284625	200	25891										
COL6A2	1292	hgsc.bcm.edu	37	chr21	47535813	47535813	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agggcaacatgggtgagccgGgagagcctggccagaaggga	19	8	0	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr21:47535813G>A	ENST00000300527.4	+	6	933	c.829G>A	c.(829-831)Gga>Aga	p.G277R	COL6A2_ENST00000397763.1_Missense_Mutation_p.G277R|COL6A2_ENST00000310645.5_Missense_Mutation_p.G277R|COL6A2_ENST00000357838.4_Missense_Mutation_p.G277R|COL6A2_ENST00000409416.1_Missense_Mutation_p.G277R	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	277	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		GGGTGAGCCGGGAGAGCCTGG	0.657																																					p.G277R		Atlas-SNP	.											.	COL6A2	351	.	0			c.G829A						.						63	56	59					21																	47535813		2201	4299	6500	SO:0001583	missense	1292	exon6			GAGCCGGGAGAGC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"Collagens"	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.829G>A	chr21.hg19:g.47535813G>A	ENSP00000300527:p.Gly277Arg	68.0	0.0		79.0	20.0	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	hg19	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.062627	0.55432	.	.	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763	D;D;D;D;D	0.99353	-5.77;-5.77;-5.77;-5.77;-5.77	3.98	3.98	0.46160	.	0.060364	0.64402	D	0.000003	D	0.99603	0.9856	H	0.96048	3.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.995;0.998;0.967	D	0.97535	1.0082	10	0.87932	D	0	-1.4171	16.5135	0.84293	0.0:0.0:1.0:0.0	.	277;277;277	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	R	277	ENSP00000300527:G277R;ENSP00000350497:G277R;ENSP00000312529:G277R;ENSP00000387115:G277R;ENSP00000380870:G277R	ENSP00000300527:G277R	G	+	1	0	COL6A2	46360241	1.000000	0.71417	0.956000	0.39512	0.758000	0.43043	5.682000	0.68182	1.956000	0.56807	0.555000	0.69702	GGA	.	.		0.657	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			A	47535813	G	A	47535813	3	1	170	1	0	0	0	0	1	0	0	0	3702	1233	43	3	847	3	COL6A2	21	47535813	Missense_Mutation	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	4690543	47535813	594082	201	25892										
CYTSA	23384	hgsc.bcm.edu	37	chr22	24807640	24807640	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	atacatatctccctgcccacAttccatatcaagaactgaac	3	14	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr22:24807640A>T	ENST00000314328.9	+	15	3457	c.3172A>T	c.(3172-3174)Att>Ttt	p.I1058F	SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|SPECC1L_ENST00000437398.1_Missense_Mutation_p.I1058F|SPECC1L_ENST00000541492.1_Intron	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	1058	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						CCCTGCCCACATTCCATATCA	0.532																																					p.I1058F		Atlas-SNP	.											.	SPECC1L	85	.	0			c.A3172T						.						115	98	103					22																	24807640		2203	4300	6503	SO:0001583	missense	23384	exon14			GCCCACATTCCAT	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"cytokinesis and spindle organization A", "cytospin A"	614140	"SPECC1-like"			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.3172A>T	chr22.hg19:g.24807640A>T	ENSP00000325785:p.Ile1058Phe	66.0	0.0		60.0	19.0	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	hg19	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.629030	0.87560	.	.	ENSG00000100014	ENST00000437398;ENST00000314328	D;D	0.95656	-3.77;-3.77	5.84	5.84	0.93424	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.96346	0.8808	L	0.42008	1.315	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.95740	0.8782	10	0.35671	T	0.21	-22.215	15.3856	0.74699	1.0:0.0:0.0:0.0	.	1058	Q69YQ0	CYTSA_HUMAN	F	1058	ENSP00000393363:I1058F;ENSP00000325785:I1058F	ENSP00000325785:I1058F	I	+	1	0	SPECC1L	23137640	1.000000	0.71417	0.998000	0.56505	0.760000	0.43138	8.631000	0.90991	2.234000	0.73211	0.459000	0.35465	ATT	.	.		0.532	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		T	24807640	A	T	24807640	3	4	170	1	0	0	0	0	1	0	0	0	4211	217	8	4	3222	4	CYTSA	22	24807640	Missense_Mutation	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10		24807640	26496926	202	25893										
ADRBK2	157	hgsc.bcm.edu	37	chr22	26083502	26083502	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	taaattctgaatctgattccAgggggcgatttgcactacca	9	9	2	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chr22:26083502A>C	ENST00000324198.6	+	11	1018		c.e11-1			NM_005160.3	NP_005151.2	P35626	ARBK2_HUMAN	adrenergic, beta, receptor kinase 2						receptor internalization (GO:0031623)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)		ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|skin(3)|stomach(2)	32					Adenosine triphosphate(DB00171)	ATCTGATTCCAGGGGGCGATT	0.403																																					.		Atlas-SNP	.											.	ADRBK2	78	.	0			c.827-2A>C						.						106	89	95					22																	26083502		2203	4300	6503	SO:0001630	splice_region_variant	157	exon11			GATTCCAGGGGGC	X69117	CCDS13832.1	22q11	2013-01-10			ENSG00000100077	ENSG00000100077		"Pleckstrin homology (PH) domain containing"	290	protein-coding gene	gene with protein product		109636				7695743	Standard	NM_005160		Approved	GRK3, BARK2	uc003abx.4	P35626	OTTHUMG00000150280	ENST00000324198.6:c.827-1A>C	chr22.hg19:g.26083502A>C		68.0	0.0		75.0	22.0	NM_005160	Q9UGW9	Splice_Site	SNP	ENST00000324198.6	hg19	CCDS13832.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.710931	0.30322	.	.	ENSG00000100077	ENST00000324198;ENST00000545323	.	.	.	4.71	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8081	0.63246	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADRBK2	24413502	1.000000	0.71417	0.999000	0.59377	0.110000	0.19582	8.100000	0.89544	2.105000	0.64084	0.528000	0.53228	.	.	.		0.403	ADRBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317296.4	NM_005160	Intron	C	26083502	A	C	26083502	5	2	170	1	0	0	0	0	0	0	1	0	344	202	7	5	867	5	ADRBK2	22	26083502	Splice_Site	SNP	A	TCGA-DD-AACT-01A-11D-A40R-10	1275862	26083502	25221064	203	25894										
RPGR	6103	hgsc.bcm.edu	37	chrX	38182690	38182690	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gttcatctccacatgaaagaTgtacagggacatcattttta	7	8	3	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chrX:38182690T>C	ENST00000339363.3	-	2	283	c.116A>G	c.(115-117)cAt>cGt	p.H39R	RPGR_ENST00000318842.7_Missense_Mutation_p.H39R|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Missense_Mutation_p.H39R|RPGR_ENST00000338898.3_Missense_Mutation_p.H39R|RPGR_ENST00000378505.2_Missense_Mutation_p.H39R|RPGR_ENST00000342811.3_Missense_Mutation_p.H39R			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	39					cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						ACATGAAAGATGTACAGGGAC	0.323																																					p.H39R		Atlas-SNP	.											.	RPGR	175	.	0			c.A116G						.						52	46	48					X																	38182690		2201	4298	6499	SO:0001583	missense	6103	exon2			GAAAGATGTACAG	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"retinitis pigmentosa 15", "cone dystrophy 1 (X-linked)"	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.116A>G	chrX.hg19:g.38182690T>C	ENSP00000343671:p.His39Arg	769.0	0.0		551.0	245.0	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	hg19		.	.	.	.	.	.	.	.	.	.	T	3.418	-0.118851	0.06838	.	.	ENSG00000156313	ENST00000339363;ENST00000309513;ENST00000338898;ENST00000318842;ENST00000342811;ENST00000378505	T;T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32;-1.32	5.6	-6.54	0.01860	.	1.355820	0.04617	U	0.401283	T	0.59404	0.2191	N	0.17872	0.535	0.09310	N	1	B;B	0.16603	0.018;0.01	B;B	0.19148	0.024;0.018	T	0.45071	-0.9286	10	0.23302	T	0.38	.	0.8369	0.01142	0.2216:0.305:0.2236:0.2498	.	39;39	E9PE28;Q92834-2	.;.	R	39	ENSP00000343671:H39R;ENSP00000308783:H39R;ENSP00000340208:H39R;ENSP00000322219:H39R;ENSP00000339531:H39R;ENSP00000367766:H39R	ENSP00000308783:H39R	H	-	2	0	RPGR	38067634	0.000000	0.05858	0.000000	0.03702	0.214000	0.24535	-0.145000	0.10265	-1.885000	0.01118	0.417000	0.27973	CAT	.	.		0.323	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		C	38182690	T	C	38182690	3	2	170	1	0	0	0	0	1	0	0	0	13563	1464	51	2	3957	2	RPGR	23	38182690	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10		38182690	117087870	204	25895										
KCND1	3750	hgsc.bcm.edu	37	chrX	48826085	48826085	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	accacattggcgatgaccgaCacggcgatgaagaagccggt	13	11	0	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chrX:48826085C>T	ENST00000218176.3	-	1	1891	c.594G>A	c.(592-594)gtG>gtA	p.V198V	KCND1_ENST00000376477.1_5'Flank	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	198					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	CGATGACCGACACGGCGATGA	0.632																																					p.V198V		Atlas-SNP	.											.	KCND1	63	.	0			c.G594A						.						18	16	17					X																	48826085		2199	4298	6497	SO:0001819	synonymous_variant	3750	exon1			GACCGACACGGCG	AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.594G>A	chrX.hg19:g.48826085C>T		127.0	0.0		107.0	41.0	NM_004979	A6NEF1|B2RCG0|O75671	Silent	SNP	ENST00000218176.3	hg19	CCDS14314.1																																																																																			.	.		0.632	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979		T	48826085	C	T	48826085	2	4	170	1	0	0	0	0	0	0	0	1	8027	465	17	3		3	KCND1	23	48826085	Silent	SNP	C	TCGA-DD-AACT-01A-11D-A40R-10	10643395	48826085	106444475	205	25896										
ARHGEF9	23229	hgsc.bcm.edu	37	chrX	62926291	62926291	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	tgtccgttctgcacatcgctGggcccctcctccacctcatc	7	19	2	0			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chrX:62926291G>A	ENST00000253401.6	-	3	1028	c.228C>T	c.(226-228)ccC>ccT	p.P76P	ARHGEF9_ENST00000374872.1_Silent_p.P55P|ARHGEF9_ENST00000437457.2_Silent_p.P23P|ARHGEF9_ENST00000495564.1_5'UTR|ARHGEF9_ENST00000374878.1_Silent_p.P74P|ARHGEF9_ENST00000374870.4_5'UTR	NM_015185.2	NP_056000.1	O43307	ARHG9_HUMAN	Cdc42 guanine nucleotide exchange factor (GEF) 9	76					apoptotic signaling pathway (GO:0097190)|ion transmembrane transport (GO:0034220)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|skin(1)	35						GCACATCGCTGGGCCCCTCCT	0.557																																					p.P76P		Atlas-SNP	.											.	ARHGEF9	117	.	0			c.C228T						.						69	51	57					X																	62926291		2203	4300	6503	SO:0001819	synonymous_variant	23229	exon3			ATCGCTGGGCCCC	AB007884	CCDS35315.1, CCDS55429.1, CCDS55430.1	Xq11.1	2013-01-10			ENSG00000131089	ENSG00000131089		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14561	protein-coding gene	gene with protein product	"collybistin"	300429				10559246, 9455477	Standard	NM_015185		Approved	KIAA0424, PEM-2	uc011mot.2	O43307	OTTHUMG00000021700	ENST00000253401.6:c.228C>T	chrX.hg19:g.62926291G>A		65.0	0.0		39.0	14.0	NM_015185	A8K1S8|B4DHC7|F8W7P8|Q5JSL6	Silent	SNP	ENST00000253401.6	hg19	CCDS35315.1																																																																																			.	.		0.557	ARHGEF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056937.1			A	62926291	G	A	62926291	2	1	170	1	0	0	0	0	0	0	0	1	912	1335	47	3		3	ARHGEF9	23	62926291	Silent	SNP	G	TCGA-DD-AACT-01A-11D-A40R-10	14100206	62926291	92344269	206	25897										
AWAT2	158835	hgsc.bcm.edu	37	chrX	69269752	69269752	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	agcaaagacatccagggcagTcttgaggtccttcttagagg	12	9	2	3			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chrX:69269752T>A	ENST00000276101.3	-	1	36	c.31A>T	c.(31-33)Act>Tct	p.T11S		NM_001002254.1	NP_001002254.1	Q6E213	AWAT2_HUMAN	acyl-CoA wax alcohol acyltransferase 2	11					wax biosynthetic process (GO:0010025)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(3)|lung(2)|ovary(1)	9						TCCAGGGCAGTCTTGAGGTCC	0.552																																					p.T11S	NSCLC(80;1334 1436 9350 24214 26427)	Atlas-SNP	.											.	AWAT2	36	.	0			c.A31T						.						146	103	118					X																	69269752		2203	4300	6503	SO:0001583	missense	158835	exon1			GGGCAGTCTTGAG	BC063698	CCDS35320.1	Xq13.1	2009-02-23	2009-02-23	2009-02-23	ENSG00000147160	ENSG00000147160			23251	protein-coding gene	gene with protein product	"multifunctional O-acyltransferase"	300925	"diacylglycerol O-acyltransferase 2-like 4"	DGAT2L4		14970677, 16106050, 15671038	Standard	NM_001002254		Approved	MFAT	uc004dxt.1	Q6E213	OTTHUMG00000021763	ENST00000276101.3:c.31A>T	chrX.hg19:g.69269752T>A	ENSP00000421172:p.Thr11Ser	405.0	0.0		358.0	130.0	NM_001002254	Q6IEE3|Q6P437	Missense_Mutation	SNP	ENST00000276101.3	hg19	CCDS35320.1	.	.	.	.	.	.	.	.	.	.	T	0.065	-1.214724	0.01555	.	.	ENSG00000147160	ENST00000276101	T	0.11277	2.79	4.0	1.6	0.23607	.	0.752361	0.11823	N	0.525975	T	0.05135	0.0137	N	0.08118	0	0.09310	N	1	B	0.16396	0.017	B	0.09377	0.004	T	0.38134	-0.9675	10	0.51188	T	0.08	.	4.9677	0.14098	0.0:0.2646:0.0:0.7354	.	11	Q6E213	AWAT2_HUMAN	S	11	ENSP00000421172:T11S	ENSP00000421172:T11S	T	-	1	0	AWAT2	69186477	0.175000	0.23083	0.023000	0.16930	0.094000	0.18550	0.110000	0.15437	0.128000	0.18479	0.356000	0.21956	ACT	.	.		0.552	AWAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358738.1	NM_001002254		A	69269752	T	A	69269752	3	1	170	1	0	0	0	0	1	0	0	0	1235	1667	58	4	998	4	AWAT2	23	69269752	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	6343461	69269752	86000808	207	25898										
ZMAT1	84460	hgsc.bcm.edu	37	chrX	101139286	101139286	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	ggtaactggctttccactggTgaaatatggtatggtcgttg	13	6	0	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chrX:101139286T>A	ENST00000372782.3	-	7	1160	c.1113A>T	c.(1111-1113)tcA>tcT	p.S371S	ZMAT1_ENST00000458570.1_Silent_p.S200S|ZMAT1_ENST00000494068.1_5'UTR|ZMAT1_ENST00000540921.1_Silent_p.S371S	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	371						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						TTTCCACTGGTGAAATATGGT	0.423																																					p.S371S		Atlas-SNP	.											.	ZMAT1	143	.	0			c.A1113T						.						178	160	166					X																	101139286		2203	4300	6503	SO:0001819	synonymous_variant	84460	exon7			CACTGGTGAAATA	Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"Zinc fingers, matrin-type"	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.1113A>T	chrX.hg19:g.101139286T>A		176.0	0.0		145.0	52.0	NM_001011657	Q8NDS3|Q96JN6	Silent	SNP	ENST00000372782.3	hg19	CCDS35348.1																																																																																			.	.		0.423	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1			A	101139286	T	A	101139286	2	1	170	1	0	0	0	0	0	0	0	1	17706	1683	59	4		4	ZMAT1	23	101139286	Silent	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	31869534	101139286	54131274	208	25899										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107867495	107867495	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	gagtttcagggccaaaaggtTatcagggtttgcctggagac	14	7	2	1			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chrX:107867495T>A	ENST00000361603.2	+	34	3191	c.2947T>A	c.(2947-2949)Tat>Aat	p.Y983N	COL4A5_ENST00000328300.6_Missense_Mutation_p.Y983N	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	983	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GCCAAAAGGTTATCAGGGTTT	0.458									Alport syndrome with Diffuse Leiomyomatosis																												p.Y983N		Atlas-SNP	.											.	COL4A5	262	.	0			c.T2947A						.						104	82	89					X																	107867495		2203	4300	6503	SO:0001583	missense	1287	exon34	Familial Cancer Database		AAAGGTTATCAGG	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.2947T>A	chrX.hg19:g.107867495T>A	ENSP00000354505:p.Tyr983Asn	156.0	0.0		110.0	34.0	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	hg19	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.692822	0.30052	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.89810	-2.57;-2.57	5.5	1.71	0.24356	.	0.657110	0.15722	N	0.247857	T	0.70692	0.3253	N	0.02916	-0.46	0.09310	N	1	B;B;B	0.24043	0.095;0.096;0.095	B;B;B	0.28465	0.062;0.09;0.062	T	0.59606	-0.7423	10	0.20519	T	0.43	.	5.2906	0.15725	0.0:0.1513:0.2744:0.5744	.	983;591;983	E7EVY4;Q49AM6;P29400	.;.;CO4A5_HUMAN	N	983	ENSP00000331902:Y983N;ENSP00000354505:Y983N	ENSP00000331902:Y983N	Y	+	1	0	COL4A5	107754151	0.960000	0.32886	0.833000	0.33012	0.488000	0.33401	1.027000	0.30115	0.227000	0.20999	-0.496000	0.04628	TAT	.	.		0.458	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			A	107867495	T	A	107867495	3	1	170	1	0	0	0	0	1	0	0	0	3696	1754	61	4	3081	4	COL4A5	23	107867495	Missense_Mutation	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	6728209	107867495	47403065	209	25900										
AIFM1	9131	hgsc.bcm.edu	37	chrX	129289157	129289157	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0191387559808612	4	1	0.594787725935267	0.966530054644809	0.527198211624441	0.576470588235294	1	0	aactcctgccccagtgactgTtgctcctacaattaagaagt	7	12	0	2			TCGA-DD-AACT-01A-11D-A40R-10	TCGA-DD-AACT-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9f7c9ce7-623f-4bd3-be0d-2c55d8e86fcf	52619546-0765-495f-b30e-c05fc98e8c92	g.chrX:129289157T>C	ENST00000287295.3	-	2	480				AIFM1_ENST00000346424.2_Intron|AIFM1_ENST00000319908.3_Missense_Mutation_p.T71A|AIFM1_ENST00000535724.1_Intron	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	CCAGTGACTGTTGCTCCTACA	0.443																																					p.T71A		Atlas-SNP	.											.	AIFM1	75	.	0			c.A211G						.						154	143	147					X																	129289157		2203	4300	6503	SO:0001627	intron_variant	9131	exon2			TGACTGTTGCTCC	AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"programmed cell death 8 (apoptosis-inducing factor)", "neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.249+1277A>G	chrX.hg19:g.129289157T>C		317.0	0.0		268.0	13.0	NM_145812	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Missense_Mutation	SNP	ENST00000287295.3	hg19	CCDS14618.1	.	.	.	.	.	.	.	.	.	.	T	6.223	0.409231	0.11812	.	.	ENSG00000156709	ENST00000319908	T	0.40225	1.04	4.42	2.03	0.26663	.	.	.	.	.	T	0.21347	0.0514	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.07751	-1.0756	8	0.09338	T	0.73	.	7.9019	0.29740	0.0:0.2317:0.0:0.7683	.	71	O95831-3	.	A	71	ENSP00000315122:T71A	ENSP00000315122:T71A	T	-	1	0	AIFM1	129116838	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	0.523000	0.22925	0.204000	0.20548	0.417000	0.27973	ACA	.	.		0.443	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2			C	129289157	T	C	129289157	1	2	170	0	1	0	0	0	0	0	0	0	426	1725	60	2		2	AIFM1	23	129289157	Intron	SNP	T	TCGA-DD-AACT-01A-11D-A40R-10	21421662	129289157	25981403	210	25901										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22163367	22163367	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tgaaccaacggagctgggtaCcccggtcgctgggcacagca	14	13	0	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr1:22163367C>T	ENST00000374695.3	-	75	10362	c.10283G>A	c.(10282-10284)gGt>gAt	p.G3428D		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3428	Ig-like C2-type 20.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GAGCTGGGTACCCCGGTCGCT	0.672																																					p.G3428D		Atlas-SNP	.											.	HSPG2	311	.	0			c.G10283A						.						36	32	34					1																	22163367		2192	4292	6484	SO:0001583	missense	3339	exon75			TGGGTACCCCGGT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.10283G>A	chr1.hg19:g.22163367C>T	ENSP00000363827:p.Gly3428Asp	1385.0	0.0		1480.0	559.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	7.364	0.625391	0.14257	.	.	ENSG00000142798	ENST00000374695	T	0.64618	-0.11	4.59	1.72	0.24424	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.178548	0.26959	N	0.021621	T	0.41050	0.1142	N	0.05280	-0.08	0.30668	N	0.753705	B;P	0.41978	0.004;0.767	B;P	0.44946	0.029;0.465	T	0.43686	-0.9376	10	0.29301	T	0.29	.	8.6094	0.33793	0.0:0.7449:0.0:0.2551	.	1368;3428	Q59EG0;P98160	.;PGBM_HUMAN	D	3428	ENSP00000363827:G3428D	ENSP00000363827:G3428D	G	-	2	0	HSPG2	22035954	0.995000	0.38212	0.829000	0.32907	0.934000	0.57294	1.152000	0.31663	0.197000	0.20387	0.655000	0.94253	GGT	.	.		0.672	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		T	22163367	C	T	22163367	3	4	171	1	0	0	0	0	1	0	0	0	7439	507	18	3	2984	3	HSPG2	1	22163367	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10		22163367	227087254	1	25902										
SERBP1	26135	hgsc.bcm.edu	37	chr1	67885696	67885696	+	Missense_Mutation	SNP	T	T	C													0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	caaaacttaattttacctctTcactctttgatttatgaaga							TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr1:67885696T>C	ENST00000370995.2	-	6	1077	c.992A>G	c.(991-993)gAa>gGa	p.E331G	SERBP1_ENST00000484880.1_5'UTR|RNU6-387P_ENST00000411331.1_RNA|SERBP1_ENST00000361219.6_Missense_Mutation_p.E316G|SERBP1_ENST00000370994.4_Missense_Mutation_p.E310G|SERBP1_ENST00000370990.5_Missense_Mutation_p.E325G			Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1	331					regulation of apoptotic process (GO:0042981)|regulation of mRNA stability (GO:0043488)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	13						TTTTACCTCTTCACTCTTTGA	0.323																																					p.E331G		Atlas-SNP	.											.	SERBP1	31	.	0			c.A992G						.						77	77	77					1																	67885696		2203	4300	6503	SO:0001583	missense	26135	exon6			ACCTCTTCACTCT	AF151813	CCDS639.1, CCDS30746.1, CCDS30747.1, CCDS30748.1	1p31	2009-12-17			ENSG00000142864	ENSG00000142864			17860	protein-coding gene	gene with protein product		607378				11001948, 10810093, 18440126, 17698176	Standard	NM_001018067		Approved	PAI-RBP1, DKFZP564M2423, CGI-55, HABP4L, PAIRBP1, CHD3IP	uc001ddv.3	Q8NC51	OTTHUMG00000009372	ENST00000370995.2:c.992A>G	chr1.hg19:g.67885696T>C	ENSP00000360034:p.Glu331Gly	377.0	0.0		220.0	131.0	NM_001018067	Q5VU19|Q5VU20|Q5VU22|Q8WUH0|Q96SE2|Q9BTY3|Q9BUM4|Q9Y367|Q9Y4S3	Missense_Mutation	SNP	ENST00000370995.2	hg19	CCDS30746.1	.	.	.	.	.	.	.	.	.	.	T	16.12	3.031913	0.54790	.	.	ENSG00000142864	ENST00000370994;ENST00000370995;ENST00000361219;ENST00000370990	.	.	.	5.45	5.45	0.79879	.	0.089542	0.85682	D	0.000000	T	0.50326	0.1609	L	0.27053	0.805	0.54753	D	0.999987	B;D;B;B	0.67145	0.023;0.996;0.137;0.028	B;P;B;B	0.62649	0.007;0.905;0.061;0.048	T	0.49370	-0.8947	9	0.24483	T	0.36	-3.9322	15.5093	0.75766	0.0:0.0:0.0:1.0	.	373;388;316;331	D3DQ69;D3DQ70;Q8NC51-3;Q8NC51	.;.;.;PAIRB_HUMAN	G	310;331;316;325	.	ENSP00000354591:E316G	E	-	2	0	SERBP1	67658284	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.101000	0.71479	2.064000	0.61679	0.377000	0.23210	GAA	.	.		0.323	SERBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025984.2	NM_001018067		C	67885696	T	C	67885696	3	2	171	1	0	0	0	0	1	0	0	0	14090	1783	62	2	246	2	SERBP1	1	67885696	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	45722329	67885696	181364925	2	25903	124	2								
SERBP1	26135	hgsc.bcm.edu	37	chr1	67885701	67885701	+	Missense_Mutation	SNP	C	C	G													0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cttaattttacctcttcactCtttgatttatgaagaacaaa							TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr1:67885701C>G	ENST00000370995.2	-	6	1072	c.987G>C	c.(985-987)aaG>aaC	p.K329N	SERBP1_ENST00000484880.1_5'UTR|RNU6-387P_ENST00000411331.1_RNA|SERBP1_ENST00000361219.6_Missense_Mutation_p.K314N|SERBP1_ENST00000370994.4_Missense_Mutation_p.K308N|SERBP1_ENST00000370990.5_Missense_Mutation_p.K323N			Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1	329					regulation of apoptotic process (GO:0042981)|regulation of mRNA stability (GO:0043488)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	13						CCTCTTCACTCTTTGATTTAT	0.313																																					p.K329N		Atlas-SNP	.											.	SERBP1	31	.	0			c.G987C						.						76	76	76					1																	67885701		2203	4300	6503	SO:0001583	missense	26135	exon6			TTCACTCTTTGAT	AF151813	CCDS639.1, CCDS30746.1, CCDS30747.1, CCDS30748.1	1p31	2009-12-17			ENSG00000142864	ENSG00000142864			17860	protein-coding gene	gene with protein product		607378				11001948, 10810093, 18440126, 17698176	Standard	NM_001018067		Approved	PAI-RBP1, DKFZP564M2423, CGI-55, HABP4L, PAIRBP1, CHD3IP	uc001ddv.3	Q8NC51	OTTHUMG00000009372	ENST00000370995.2:c.987G>C	chr1.hg19:g.67885701C>G	ENSP00000360034:p.Lys329Asn	383.0	0.0		226.0	137.0	NM_001018067	Q5VU19|Q5VU20|Q5VU22|Q8WUH0|Q96SE2|Q9BTY3|Q9BUM4|Q9Y367|Q9Y4S3	Missense_Mutation	SNP	ENST00000370995.2	hg19	CCDS30746.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.829690	0.71258	.	.	ENSG00000142864	ENST00000370994;ENST00000370995;ENST00000361219;ENST00000370990	.	.	.	5.45	0.366	0.16136	.	0.000000	0.85682	D	0.000000	T	0.67785	0.2930	M	0.80746	2.51	0.58432	D	0.999999	D;D;D;D	0.89917	0.981;1.0;1.0;0.999	D;D;D;D	0.85130	0.966;0.996;0.987;0.997	T	0.69355	-0.5167	9	0.56958	D	0.05	-8.5192	9.1115	0.36730	0.0:0.6351:0.0:0.3649	.	371;386;314;329	D3DQ69;D3DQ70;Q8NC51-3;Q8NC51	.;.;.;PAIRB_HUMAN	N	308;329;314;323	.	ENSP00000354591:K314N	K	-	3	2	SERBP1	67658289	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	2.684000	0.46951	0.021000	0.15133	0.460000	0.39030	AAG	.	.		0.313	SERBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025984.2	NM_001018067		G	67885701	C	G	67885701	3	3	171	1	0	0	0	0	1	0	0	0	14090	912	32	4	251	4	SERBP1	1	67885701	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	5	67885701	181364920	3	25904	124	2								
KPRP	448834	hgsc.bcm.edu	37	chr1	152733603	152733603	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gttccatacccaggagacctAggctgtcatgagtctagtcc	10	12	2	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr1:152733603A>T	ENST00000606109.1	+	1	1567	c.1539A>T	c.(1537-1539)ctA>ctT	p.L513L	KPRP_ENST00000368773.1_Silent_p.L513L			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	513						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAGGAGACCTAGGCTGTCATG	0.647																																					p.L513L		Atlas-SNP	.											.	KPRP	152	.	0			c.A1539T						.						59	60	59					1																	152733603		2203	4300	6503	SO:0001819	synonymous_variant	448834	exon2			AGACCTAGGCTGT	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1539A>T	chr1.hg19:g.152733603A>T		106.0	0.0		128.0	39.0	NM_001025231		Silent	SNP	ENST00000606109.1	hg19	CCDS30862.1																																																																																			.	.		0.647	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		T	152733603	A	T	152733603	2	4	171	1	0	0	0	0	0	0	0	1	8445	407	15	4		4	KPRP	1	152733603	Silent	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	84847902	152733603	96517018	4	25905										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181705462	181705462	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cttgaaggaggcagagatcaGagaggatgaggaggaggtgg	20	3	1	4			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr1:181705462G>T	ENST00000367573.2	+	22	3314	c.3314G>T	c.(3313-3315)aGa>aTa	p.R1105I	CACNA1E_ENST00000357570.5_Missense_Mutation_p.R1056I|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R1086I|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R1086I|CACNA1E_ENST00000367567.4_Missense_Mutation_p.R712I|CACNA1E_ENST00000358338.5_Missense_Mutation_p.R1037I|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R1105I	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1105					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GCAGAGATCAGAgaggatgag	0.502																																					p.R1105I		Atlas-SNP	.											.	CACNA1E	778	.	0			c.G3314T						.						81	100	94					1																	181705462		2131	4237	6368	SO:0001583	missense	777	exon22			AGATCAGAGAGGA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3314G>T	chr1.hg19:g.181705462G>T	ENSP00000356545:p.Arg1105Ile	178.0	0.0		165.0	58.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.182825	0.38511	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96200	-3.89;-3.89;-3.88;-3.89;-3.94;-3.88;-3.88	5.28	2.98	0.34508	.	0.875561	0.10070	N	0.719890	D	0.88647	0.6493	N	0.08118	0	0.29883	N	0.825884	B;B;B	0.22683	0.073;0.0;0.021	B;B;B	0.19946	0.027;0.0;0.027	T	0.81927	-0.0709	10	0.59425	D	0.04	.	8.3613	0.32361	0.8306:0.0:0.1694:0.0	.	1086;1105;1105	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	I	1105;1086;1056;1037;712;1086;1105	ENSP00000356542:R1105I;ENSP00000434814:R1086I;ENSP00000350183:R1056I;ENSP00000351101:R1037I;ENSP00000356539:R712I;ENSP00000353222:R1086I;ENSP00000356545:R1105I	ENSP00000350183:R1056I	R	+	2	0	CACNA1E	179972085	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	3.423000	0.52756	0.337000	0.23665	-0.378000	0.06908	AGA	.	.		0.502	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181705462	G	T	181705462	3	4	171	1	0	0	0	0	1	0	0	0	2544	942	33	3	3400	3	CACNA1E	1	181705462	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	28971859	181705462	67545159	5	25906										
PM20D1	148811	hgsc.bcm.edu	37	chr1	205811830	205811830	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tgccagttgctgcaatacagTcaccactgtcccgcttccaa	7	15	1	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr1:205811830T>A	ENST00000367136.4	-	7	921	c.877A>T	c.(877-879)Act>Tct	p.T293S	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	293					negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			TGCAATACAGTCACCACTGTC	0.443																																					p.T293S		Atlas-SNP	.											.	PM20D1	56	.	0			c.A877T						.						128	117	121					1																	205811830		2203	4300	6503	SO:0001583	missense	148811	exon7			ATACAGTCACCAC		CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.877A>T	chr1.hg19:g.205811830T>A	ENSP00000356104:p.Thr293Ser	40.0	0.0		44.0	13.0	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	hg19	CCDS1460.1	.	.	.	.	.	.	.	.	.	.	T	3.399	-0.122560	0.06795	.	.	ENSG00000162877	ENST00000367136	T	0.06449	3.3	5.7	3.37	0.38596	Peptidase M20, dimerisation (2);	1.034310	0.07497	N	0.906621	T	0.04137	0.0115	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.17098	0.017	T	0.47249	-0.9132	10	0.08381	T	0.77	.	4.69	0.12776	0.1297:0.2139:0.0:0.6564	.	293	Q6GTS8	P20D1_HUMAN	S	293	ENSP00000356104:T293S	ENSP00000356104:T293S	T	-	1	0	PM20D1	204078453	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.343000	0.19944	0.978000	0.38470	-0.421000	0.06004	ACT	.	.		0.443	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491		A	205811830	T	A	205811830	3	1	171	1	0	0	0	0	1	0	0	0	12137	1667	58	4	659	4	PM20D1	1	205811830	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	24106368	205811830	43438791	6	25907										
OR2T11	127077	hgsc.bcm.edu	37	chr1	248790047	248790047	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ggttcatcaggactgggtatCtcagagggttacagacagcc	13	9	3	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr1:248790047C>G	ENST00000330803.2	-	1	444	c.383G>C	c.(382-384)aGa>aCa	p.R128T		NM_001001964.1	NP_001001964.1	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T, member 11 (gene/pseudogene)	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(5)|lung(20)|skin(2)	28	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GACTGGGTATCTCAGAGGGTT	0.547																																					p.R128T		Atlas-SNP	.											.	OR2T11	64	.	0			c.G383C						.						53	59	57					1																	248790047		2052	4234	6286	SO:0001583	missense	127077	exon1			GGGTATCTCAGAG	BK004476	CCDS31122.1	1q44	2013-10-10	2013-10-10		ENSG00000183130	ENSG00000183130		"GPCR / Class A : Olfactory receptors"	19574	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily T, member 11"				Standard	NM_001001964		Approved	OR2T11Q	uc001ier.1	Q8NH01	OTTHUMG00000040384	ENST00000330803.2:c.383G>C	chr1.hg19:g.248790047C>G	ENSP00000328934:p.Arg128Thr	169.0	0.0		182.0	69.0	NM_001001964	Q6IEY6	Missense_Mutation	SNP	ENST00000330803.2	hg19	CCDS31122.1	.	.	.	.	.	.	.	.	.	.	.	13.28	2.190363	0.38707	.	.	ENSG00000183130	ENST00000330803	T	0.00882	5.58	4.38	2.33	0.28932	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000172	T	0.01800	0.0057	M	0.84082	2.675	0.25920	N	0.983127	D	0.52996	0.957	B	0.43867	0.434	T	0.41858	-0.9485	10	0.87932	D	0	.	4.3372	0.11092	0.1623:0.5906:0.1574:0.0897	.	128	Q8NH01	O2T11_HUMAN	T	128	ENSP00000328934:R128T	ENSP00000328934:R128T	R	-	2	0	OR2T11	246856670	0.001000	0.12720	0.256000	0.24389	0.380000	0.30137	0.127000	0.15790	0.994000	0.38892	0.655000	0.94253	AGA	.	.		0.547	OR2T11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097134.1	NM_001001964		G	248790047	C	G	248790047	3	3	171	1	0	0	0	0	1	0	0	0	11027	913	32	4	571	4	OR2T11	1	248790047	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	42978217	248790047	460574	7	25908										
NTSR2	23620	hgsc.bcm.edu	37	chr2	11798694	11798695	+	Missense_Mutation	DNP	GG	GG	AT													0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cgggggtaaccgcttcatggGgtggtgctctccacacaggg					rs77419493	byFrequency	TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:11798694_11798695GG>AT	ENST00000306928.5	-	4	1177_1178	c.1143_1144CC>AT	c.(1141-1146)caCCcc>caATcc	p.381_382HP>QS		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	381					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	CGCTTCATGGGGTGGTGCTCTC	0.564																																					p.P382S|p.H381Q		Atlas-SNP	.											.	NTSR2	36	.	0			c.C1144T|c.C1143A						.																																			SO:0001583	missense	23620	exon4			TCATGGGGTGGTG|CATGGGGTGGTGC	Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"GPCR / Class A : Neurotensin receptors"	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.1143_1144delinsAT	chr2.hg19:g.11798694_11798695delinsAT	ENSP00000303686:p.H381_P382delinsQS	96.0|95.0	0.0		92.0	20.0|21.0	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Missense_Mutation	SNP	ENST00000306928.5	hg19	CCDS1681.1																																																																																			.	G|0.997;T|0.003|.		0.564	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1			AT	11798695	GG	AT	11798694	3	1	171	1	0	0	0	0	1	0	0	0	10720	1232	43	3	92	3	NTSR2	2	11798694	Missense_Mutation	DNP	GG	TCGA-DD-AACU-01A-11D-A40R-10		11798694	231400679	8	25909										
FAM84A	151354	hgsc.bcm.edu	37	chr2	14774464	14774464	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ccgcgctgccagcgctctgcGaacccggcgacctgctggag	14	17	1	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:14774464G>T	ENST00000295092.2	+	2	649	c.361G>T	c.(361-363)Gaa>Taa	p.E121*	AC011897.1_ENST00000581929.1_5'Flank|FAM84A_ENST00000331243.4_Nonsense_Mutation_p.E121*	NM_145175.2	NP_660158.2	Q96KN4	FA84A_HUMAN	family with sequence similarity 84, member A	121										endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(1;0.00969)			AGCGCTCTGCGAACCCGGCGA	0.716																																					p.E121X		Atlas-SNP	.											.	FAM84A	23	.	0			c.G361T						.						6	7	7					2																	14774464		2100	4142	6242	SO:0001587	stop_gained	151354	exon2			CTCTGCGAACCCG	AJ417080, BC026346	CCDS1684.1	2p24.3	2005-08-09			ENSG00000162981	ENSG00000162981			20743	protein-coding gene	gene with protein product	"neurological/sensory 1"	611234				14702039	Standard	NM_145175		Approved	NSE1, FLJ35392	uc002rbz.2	Q96KN4	OTTHUMG00000119093	ENST00000295092.2:c.361G>T	chr2.hg19:g.14774464G>T	ENSP00000295092:p.Glu121*	83.0	0.0		96.0	4.0	NM_145175	A6NP76|Q86UZ2|Q8NAH7|Q8TAM5	Nonsense_Mutation	SNP	ENST00000295092.2	hg19	CCDS1684.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	41|41	8.948052|8.948052	0.99014|0.99014	.|.	.|.	ENSG00000162981|ENSG00000162981	ENST00000295092;ENST00000331243;ENST00000359969|ENST00000540701	.|.	.|.	.|.	4.96|4.96	4.02|4.02	0.46733|0.46733	.|.	0.221076|.	0.45606|.	D|.	0.000359|.	.|T	.|0.59595	.|0.2205	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.63721	.|-0.6573	.|5	0.02654|0.87932	T|D	1|0	-16.6579|-16.6579	4.4396|4.4396	0.11568|0.11568	0.1898:0.3018:0.5084:0.0|0.1898:0.3018:0.5084:0.0	.|.	.|.	.|.	.|.	X|L	121|28	.|.	ENSP00000295092:E121X|ENSP00000443261:R28L	E|R	+|+	1|2	0|0	FAM84A|FAM84A	14691915|14691915	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.957000|0.957000	0.61999|0.61999	3.511000|3.511000	0.53400|0.53400	2.426000|2.426000	0.82243|0.82243	0.655000|0.655000	0.94253|0.94253	GAA|CGA	.	.		0.716	FAM84A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239308.2	NM_145175		T	14774464	G	T	14774464	4	4	171	1	0	0	0	0	0	1	0	0	5649	1059	37	1	363	1	FAM84A	2	14774464	Nonsense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	2975770	14774464	228424909	9	25910										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50463932	50463932	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gcaaaaagtacttactatatGcagttctaggtagtcaccca	7	9	2	0	rs377333818		TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:50463932G>T	ENST00000406316.2	-	18	5017	c.3541C>A	c.(3541-3543)Cat>Aat	p.H1181N	NRXN1_ENST00000402717.3_Missense_Mutation_p.H1173N|NRXN1_ENST00000405472.3_Missense_Mutation_p.H1173N|NRXN1_ENST00000404971.1_Missense_Mutation_p.H1221N|NRXN1_ENST00000342183.5_Missense_Mutation_p.H146N|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000406859.3_Missense_Mutation_p.H1181N|NRXN1_ENST00000401669.2_Missense_Mutation_p.H1181N|NRXN1_ENST00000401710.1_Missense_Mutation_p.H199N	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1181	Laminin G-like 6. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.H1181N(1)|p.H1221N(1)|p.H1222N(1)|p.H146N(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CTTACTATATGCAGTTCTAGG	0.398																																					p.H1221N		Atlas-SNP	.											NRXN1_ENST00000536085,colon,carcinoma,+2,8	NRXN1	1118	.	4	Substitution - Missense(4)	lung(4)	c.C3661A						.	G	ASN/HIS,ASN/HIS,ASN/HIS	0,4406		0,0,2203	95	86	89		3661,3541,436	5.7	1	2		89	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	NRXN1	NM_001135659.1,NM_004801.4,NM_138735.2	68,68,68	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	1221/1548,1181/1478,146/443	50463932	1,13005	2203	4300	6503	SO:0001583	missense	9378	exon19			CTATATGCAGTTC	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3541C>A	chr2.hg19:g.50463932G>T	ENSP00000384311:p.His1181Asn	147.0	0.0		151.0	75.0	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964205	0.74131	0.0	1.16E-4	ENSG00000179915	ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	5.68	5.68	0.88126	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.187162	0.34411	U	0.003987	D	0.88872	0.6555	M	0.82517	2.595	0.44289	D	0.997153	P;P;P;P	0.47910	0.734;0.683;0.88;0.902	P;P;P;P	0.61397	0.648;0.798;0.716;0.888	D	0.89430	0.3716	10	0.72032	D	0.01	.	19.7969	0.96490	0.0:0.0:1.0:0.0	.	1221;146;1181;1173	Q9ULB1-3;P58400;F8WB18;A7E294	.;NRX1B_HUMAN;.;.	N	146;100;199;1221;1181;1173;1181;1222;1173;1181	ENSP00000341184:H146N;ENSP00000385580:H199N;ENSP00000385142:H1221N;ENSP00000384311:H1181N;ENSP00000434015:H1173N;ENSP00000385017:H1181N;ENSP00000385434:H1173N;ENSP00000385681:H1181N	ENSP00000341184:H146N	H	-	1	0	NRXN1	50317436	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.653000	0.98506	2.679000	0.91253	0.650000	0.86243	CAT	.	.		0.398	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50463932	G	T	50463932	3	4	171	1	0	0	0	0	1	0	0	0	10674	1319	46	3	1006	3	NRXN1	2	50463932	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	35689468	50463932	192735441	10	25911										
UGP2	7360	hgsc.bcm.edu	37	chr2	64112930	64112930	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ctgggtgccacagtggatctGtatattcttaatcatctaat	8	8	4	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:64112930G>A	ENST00000337130.5	+	6	1259	c.783G>A	c.(781-783)ctG>ctA	p.L261L	UGP2_ENST00000487469.1_3'UTR|UGP2_ENST00000467648.2_Silent_p.L250L|UGP2_ENST00000394417.2_Silent_p.L250L|ACA59_ENST00000515966.1_RNA|UGP2_ENST00000445915.2_Silent_p.L270L	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	261					carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)			endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						CAGTGGATCTGTATATTCTTA	0.378																																					p.L261L		Atlas-SNP	.											.	UGP2	38	.	0			c.G783A						.						110	111	111					2																	64112930		2203	4300	6503	SO:0001819	synonymous_variant	7360	exon6			GGATCTGTATATT		CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"UDP-glucose pyrophosphorylase 1"	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.783G>A	chr2.hg19:g.64112930G>A		152.0	0.0		121.0	20.0	NM_006759	Q07131|Q0P6K2|Q86Y81|Q9BU15	Silent	SNP	ENST00000337130.5	hg19	CCDS1875.1																																																																																			.	.		0.378	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759		A	64112930	G	A	64112930	2	1	171	1	0	0	0	0	0	0	0	1	16958	1364	48	3		3	UGP2	2	64112930	Silent	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	13648998	64112930	179086443	11	25912										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80816462	80816462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aactaccgcaggaggagaagGcaaaaatagctgagcaggtg	14	7	0	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:80816462G>A	ENST00000402739.4	+	14	2046	c.2041G>A	c.(2041-2043)Gca>Aca	p.A681T	AC008067.2_ENST00000595478.1_RNA|CTNNA2_ENST00000540488.1_Missense_Mutation_p.A681T|CTNNA2_ENST00000496558.1_Missense_Mutation_p.A681T|AC008067.2_ENST00000430876.1_RNA|CTNNA2_ENST00000343114.3_Missense_Mutation_p.A360T|AC008067.2_ENST00000596887.1_RNA|CTNNA2_ENST00000541047.1_Missense_Mutation_p.A681T|AC008067.2_ENST00000609950.1_RNA|CTNNA2_ENST00000466387.1_Missense_Mutation_p.A681T|CTNNA2_ENST00000361291.4_Missense_Mutation_p.A715T	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	681					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GGAGGAGAAGGCAAAAATAGC	0.493																																					p.A681T		Atlas-SNP	.											.	CTNNA2	462	.	0			c.G2041A						.						83	90	88					2																	80816462		2192	4299	6491	SO:0001583	missense	1496	exon15			GAGAAGGCAAAAA		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.2041G>A	chr2.hg19:g.80816462G>A	ENSP00000384638:p.Ala681Thr	327.0	0.0		274.0	66.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	G	23.4	4.408328	0.83340	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488;ENST00000343114	T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.76	5.76	0.90799	.	0.055163	0.64402	D	0.000001	T	0.57198	0.2037	M	0.64997	1.995	0.80722	D	1	B;D;P;P	0.60160	0.312;0.987;0.93;0.93	B;P;P;P	0.62298	0.236;0.9;0.548;0.548	T	0.51252	-0.8729	9	.	.	.	.	19.9813	0.97326	0.0:0.0:1.0:0.0	.	313;681;681;681	F6KRI5;P26232;P26232-3;P26232-2	.;CTNA2_HUMAN;.;.	T	681;681;715;681;681;681;360	ENSP00000418191:A681T;ENSP00000419295:A681T;ENSP00000355398:A715T;ENSP00000384638:A681T;ENSP00000444675:A681T;ENSP00000441705:A681T;ENSP00000341500:A360T	.	A	+	1	0	CTNNA2	80669973	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.623000	0.98386	2.726000	0.93360	0.655000	0.94253	GCA	.	.		0.493	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		A	80816462	G	A	80816462	3	1	171	1	0	0	0	0	1	0	0	0	4015	1203	42	3	1887	3	CTNNA2	2	80816462	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	16703532	80816462	162382911	12	25913										
FAHD2A	51011	hgsc.bcm.edu	37	chr2	96072725	96072725	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ttgccagtcctaccacggtcGgaggtaaccttcctggctcc	10	15	0	0	rs544140833		TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:96072725G>A	ENST00000233379.4	+	3	435	c.282G>A	c.(280-282)tcG>tcA	p.S94S	FAHD2A_ENST00000447036.1_Silent_p.S94S	NM_016044.2	NP_057128.2	Q96GK7	FAH2A_HUMAN	fumarylacetoacetate hydrolase domain containing 2A	94							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	8						TACCACGGTCGGAGGTAACCT	0.597													g|||	1	0.000199681	0	0	5008	,	,		19592	0		0.001	False		,,,				2504	0				p.S94S		Atlas-SNP	.											.	FAHD2A	25	.	0			c.G282A						.						91	72	79					2																	96072725		2203	4300	6503	SO:0001819	synonymous_variant	51011	exon3			ACGGTCGGAGGTA	AF151863	CCDS2014.1	2q11.2	2008-02-05			ENSG00000115042	ENSG00000115042			24252	protein-coding gene	gene with protein product							Standard	NM_016044		Approved	CGI-105	uc002sur.3	Q96GK7	OTTHUMG00000130397	ENST00000233379.4:c.282G>A	chr2.hg19:g.96072725G>A		415.0	0.0		343.0	146.0	NM_016044	Q9Y3B0	Silent	SNP	ENST00000233379.4	hg19	CCDS2014.1																																																																																			.	.		0.597	FAHD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252778.1	NM_016044		A	96072725	G	A	96072725	2	1	171	1	0	0	0	0	0	0	0	1	5378	1103	39	1		1	FAHD2A	2	96072725	Silent	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	15256263	96072725	147126648	13	25914										
ST6GAL2	84620	hgsc.bcm.edu	37	chr2	107459494	107459494	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cccccgctgagacctacctaTttcctcgcccaaggaagagt	8	16	0	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:107459494T>A	ENST00000409382.3	-	2	1550	c.940A>T	c.(940-942)Ata>Tta	p.I314L	ST6GAL2_ENST00000361686.4_Missense_Mutation_p.I314L|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000409087.3_Missense_Mutation_p.I314L	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	314					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						GACCTACCTATTTCCTCGCCC	0.672																																					p.I314L		Atlas-SNP	.											.	ST6GAL2	159	.	0			c.A940T						.						10	11	11					2																	107459494		1702	3682	5384	SO:0001583	missense	84620	exon2			TACCTATTTCCTC	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"sialyltransferase 2 (monosialoganglioside sialyltransferase)"	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.940A>T	chr2.hg19:g.107459494T>A	ENSP00000386942:p.Ile314Leu	173.0	0.0		182.0	45.0	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	hg19	CCDS2073.1	.	.	.	.	.	.	.	.	.	.	T	19.64	3.865360	0.71949	.	.	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.60920	0.15;0.15;0.15	4.92	4.92	0.64577	.	0.049037	0.85682	D	0.000000	T	0.69913	0.3164	M	0.85859	2.78	0.80722	D	1	B;P	0.41450	0.278;0.75	B;P	0.47827	0.163;0.558	T	0.75847	-0.3173	10	0.66056	D	0.02	.	14.0703	0.64856	0.0:0.0:0.0:1.0	.	314;314	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	L	314	ENSP00000355273:I314L;ENSP00000386942:I314L;ENSP00000387332:I314L	ENSP00000355273:I314L	I	-	1	0	ST6GAL2	106825926	1.000000	0.71417	0.992000	0.48379	0.946000	0.59487	7.603000	0.82811	1.971000	0.57363	0.533000	0.62120	ATA	.	.		0.672	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		A	107459494	T	A	107459494	3	1	171	1	0	0	0	0	1	0	0	0	15237	1493	52	4	756	4	ST6GAL2	2	107459494	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	11386769	107459494	135739879	14	25915										
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113082111	113082111	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	actgttctccaggttcatcaTaccagcaaagtcctggtgaa	8	11	3	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:113082111T>C	ENST00000409871.1	+	10	2124	c.1723T>C	c.(1723-1725)Tac>Cac	p.Y575H	ZC3H6_ENST00000343936.4_Missense_Mutation_p.Y575H	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	575							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						AGGTTCATCATACCAGCAAAG	0.458																																					p.Y575H		Atlas-SNP	.											.	ZC3H6	93	.	0			c.T1723C						.						33	32	32					2																	113082111		1906	4118	6024	SO:0001583	missense	376940	exon10			TCATCATACCAGC	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.1723T>C	chr2.hg19:g.113082111T>C	ENSP00000386764:p.Tyr575His	219.0	0.0		211.0	64.0	NM_198581	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	hg19	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	T	10.24	1.296737	0.23650	.	.	ENSG00000188177	ENST00000409871;ENST00000343936;ENST00000542974	T;T	0.14640	2.49;2.49	5.75	2.03	0.26663	.	0.559074	0.20388	N	0.093310	T	0.07369	0.0186	N	0.12961	0.28	0.22541	N	0.99901	B	0.15141	0.012	B	0.11329	0.006	T	0.37911	-0.9685	10	0.21014	T	0.42	-1.6765	9.8002	0.40759	0.0:0.1229:0.0:0.8771	.	575	P61129	ZC3H6_HUMAN	H	575;575;552	ENSP00000386764:Y575H;ENSP00000340298:Y575H	ENSP00000340298:Y575H	Y	+	1	0	ZC3H6	112798582	0.991000	0.36638	0.158000	0.22627	0.997000	0.91878	2.456000	0.44997	0.555000	0.29079	0.482000	0.46254	TAC	.	.		0.458	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		C	113082111	T	C	113082111	3	2	171	1	0	0	0	0	1	0	0	0	17586	1406	49	2	1761	2	ZC3H6	2	113082111	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	5622617	113082111	130117262	15	25916										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196636524	196636524	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cctcatggcagcctcgatgtCgaagttgtttggaagtttgc	12	9	1	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:196636524C>T	ENST00000312428.6	-	61	11393	c.11293G>A	c.(11293-11295)Gac>Aac	p.D3765N	DNAH7_ENST00000409063.1_Missense_Mutation_p.D248N	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3765					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GCCTCGATGTCGAAGTTGTTT	0.453																																					p.D3765N		Atlas-SNP	.											DNAH7,colon,carcinoma,0,1	DNAH7	512	.	0			c.G11293A						.						267	247	254					2																	196636524		2017	4165	6182	SO:0001583	missense	56171	exon61			CGATGTCGAAGTT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.11293G>A	chr2.hg19:g.196636524C>T	ENSP00000311273:p.Asp3765Asn	141.0	0.0		136.0	39.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.970047	0.53614	.	.	ENSG00000118997	ENST00000312428;ENST00000409063	T;T	0.08720	3.06;3.06	5.08	4.19	0.49359	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.13157	0.0319	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	P	0.55923	0.787	T	0.10870	-1.0611	10	0.25106	T	0.35	.	10.154	0.42812	0.0:0.7873:0.1366:0.0761	.	3765	Q8WXX0	DYH7_HUMAN	N	3765;248	ENSP00000311273:D3765N;ENSP00000386912:D248N	ENSP00000311273:D3765N	D	-	1	0	DNAH7	196344769	1.000000	0.71417	0.861000	0.33841	0.360000	0.29518	1.993000	0.40747	1.352000	0.45808	0.655000	0.94253	GAC	.	.		0.453	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196636524	C	T	196636524	3	4	171	1	0	0	0	0	1	0	0	0	4608	884	31	1	801	1	DNAH7	2	196636524	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	83554413	196636524	46562849	16	25917										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196912120	196912120	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ctaaagttttctcgttctttAtgtggagatttgccctttga	8	7	2	2	rs372676468		TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:196912120A>T	ENST00000312428.6	-	5	454	c.354T>A	c.(352-354)caT>caA	p.H118Q	DNAH7_ENST00000410072.1_Missense_Mutation_p.H118Q	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	118	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CTCGTTCTTTATGTGGAGATT	0.383																																					p.H118Q		Atlas-SNP	.											.	DNAH7	512	.	0			c.T354A						.						177	172	174					2																	196912120		1835	4079	5914	SO:0001583	missense	56171	exon5			TTCTTTATGTGGA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.354T>A	chr2.hg19:g.196912120A>T	ENSP00000311273:p.His118Gln	132.0	0.0		104.0	33.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	A	6.070	0.381236	0.11466	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446;ENST00000427816	T;T	0.21031	2.03;2.92	5.2	-0.0772	0.13720	.	0.801655	0.11396	N	0.568365	T	0.09069	0.0224	N	0.08118	0	0.22240	N	0.999265	B	0.06786	0.001	B	0.04013	0.001	T	0.40136	-0.9579	10	0.18276	T	0.48	.	7.6939	0.28583	0.5473:0.0:0.4527:0.0	.	118	Q8WXX0	DYH7_HUMAN	Q	118;118;118;93	ENSP00000311273:H118Q;ENSP00000386260:H118Q	ENSP00000311273:H118Q	H	-	3	2	DNAH7	196620365	0.432000	0.25554	0.933000	0.37362	0.120000	0.20174	-0.487000	0.06505	-0.156000	0.11079	-0.353000	0.07706	CAT	.	.		0.383	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196912120	A	T	196912120	3	4	171	1	0	0	0	0	1	0	0	0	4608	446	16	4	11964	4	DNAH7	2	196912120	Missense_Mutation	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	275596	196912120	46287253	17	25918										
GMPPA	29926	hgsc.bcm.edu	37	chr2	220370997	220370997	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	agcacacgtgtgttctgcatAgcatcgtgggctgggggagc	16	9	1	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:220370997A>T	ENST00000358215.3	+	12	1384	c.1015A>T	c.(1015-1017)Agc>Tgc	p.S339C	GMPPA_ENST00000373917.3_Missense_Mutation_p.S392C|GMPPA_ENST00000373908.1_Missense_Mutation_p.S339C|GMPPA_ENST00000313597.5_Missense_Mutation_p.S339C|GMPPA_ENST00000341142.3_Missense_Mutation_p.S339C|AC053503.11_ENST00000429882.1_RNA	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	339				S -> C (in Ref. 1; AAD38517). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		TGTTCTGCATAGCATCGTGGG	0.637																																					p.S339C		Atlas-SNP	.											.	GMPPA	50	.	0			c.A1015T						.						85	82	83					2																	220370997		2203	4300	6503	SO:0001583	missense	29926	exon12			CTGCATAGCATCG	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.1015A>T	chr2.hg19:g.220370997A>T	ENSP00000350949:p.Ser339Cys	66.0	0.0		46.0	11.0	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Missense_Mutation	SNP	ENST00000358215.3	hg19	CCDS2441.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.987926	0.74589	.	.	ENSG00000144591	ENST00000313597;ENST00000373917;ENST00000358215;ENST00000373908;ENST00000341142	D;D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45;-3.45	4.48	4.48	0.54585	.	0.199434	0.51477	D	0.000096	D	0.93000	0.7772	L	0.54863	1.705	0.58432	D	0.999999	B;P	0.40107	0.397;0.703	B;B	0.42827	0.399;0.369	D	0.92386	0.5917	10	0.42905	T	0.14	-8.7512	13.4827	0.61345	1.0:0.0:0.0:0.0	.	392;339	Q96IJ6-2;Q96IJ6	.;GMPPA_HUMAN	C	339;392;339;339;339	ENSP00000315925:S339C;ENSP00000363027:S392C;ENSP00000350949:S339C;ENSP00000363016:S339C;ENSP00000340760:S339C	ENSP00000315925:S339C	S	+	1	0	GMPPA	220079241	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.890000	0.69774	1.656000	0.50722	0.451000	0.29950	AGC	.	.		0.637	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335		T	220370997	A	T	220370997	3	4	171	1	0	0	0	0	1	0	0	0	6502	420	15	4	1057	4	GMPPA	2	220370997	Missense_Mutation	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	23458877	220370997	22828376	18	25919										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220500393	220500393	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cagcagccccttgttcccccAgaactgtctttggagttggg	11	13	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:220500393A>T	ENST00000358055.3	+	14	2484		c.e14-1		SLC4A3_ENST00000373762.3_Splice_Site|SLC4A3_ENST00000273063.6_Splice_Site|SLC4A3_ENST00000317151.3_Splice_Site|SLC4A3_ENST00000373760.2_Splice_Site			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3						bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTGTTCCCCCAGAACTGTCTT	0.637																																					.		Atlas-SNP	.											.	SLC4A3	144	.	0			c.1973-2A>T						.						19	21	20					2																	220500393		2202	4298	6500	SO:0001630	splice_region_variant	6508	exon14			TCCCCCAGAACTG		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1973-1A>T	chr2.hg19:g.220500393A>T		90.0	0.0		63.0	20.0	NM_005070	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Splice_Site	SNP	ENST00000358055.3	hg19	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	A	12.91	2.078226	0.36662	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.0188	0.36186	0.8356:0.0:0.0:0.1644	.	.	.	.	.	-1	.	.	.	+	.	.	SLC4A3	220208637	0.164000	0.22935	0.998000	0.56505	0.469000	0.32828	1.646000	0.37249	1.838000	0.53458	0.523000	0.50628	.	.	.		0.637	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070	Intron	T	220500393	A	T	220500393	5	4	171	1	0	0	0	0	0	0	1	0	14670	202	7	4	2102	4	SLC4A3	2	220500393	Splice_Site	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	129396	220500393	22698980	19	25920										
ECEL1	9427	hgsc.bcm.edu	37	chr2	233346334	233346334	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ggttccctgagcggtcatacTggccccctgtgggcagtgca	14	13	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr2:233346334T>A	ENST00000304546.1	-	14	2081	c.1871A>T	c.(1870-1872)cAg>cTg	p.Q624L	ECEL1_ENST00000409941.1_Missense_Mutation_p.Q622L	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	624					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		GCGGTCATACTGGCCCCCTGT	0.647																																					p.Q624L		Atlas-SNP	.											.	ECEL1	73	.	0			c.A1871T						.						53	52	52					2																	233346334		2203	4300	6503	SO:0001583	missense	9427	exon14			TCATACTGGCCCC	Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.1871A>T	chr2.hg19:g.233346334T>A	ENSP00000302051:p.Gln624Leu	60.0	0.0		50.0	15.0	NM_004826	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Missense_Mutation	SNP	ENST00000304546.1	hg19	CCDS2493.1	.	.	.	.	.	.	.	.	.	.	T	16.59	3.165497	0.57476	.	.	ENSG00000171551	ENST00000411860;ENST00000304546;ENST00000409941	D;D;D	0.91237	-2.81;-2.81;-2.81	5.48	4.29	0.51040	Peptidase M13, neprilysin, C-terminal (1);Metallopeptidase, catalytic domain (1);	0.057579	0.64402	N	0.000001	D	0.87313	0.6146	L	0.27975	0.815	0.58432	D	0.999998	B;P	0.36354	0.098;0.549	B;B	0.43623	0.019;0.425	D	0.86992	0.2111	10	0.87932	D	0	-10.3714	12.7306	0.57195	0.0:0.0:0.1374:0.8626	.	622;624	O95672-2;O95672	.;ECEL1_HUMAN	L	39;624;622	ENSP00000412683:Q39L;ENSP00000302051:Q624L;ENSP00000386333:Q622L	ENSP00000302051:Q624L	Q	-	2	0	ECEL1	233054578	1.000000	0.71417	0.984000	0.44739	0.965000	0.64279	6.240000	0.72363	0.988000	0.38734	0.456000	0.33151	CAG	.	.		0.647	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		A	233346334	T	A	233346334	3	1	171	1	0	0	0	0	1	0	0	0	4893	1580	55	4	476	4	ECEL1	2	233346334	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	12845941	233346334	9853039	20	25921										
C3orf24	115795	hgsc.bcm.edu	37	chr3	10145989	10145989	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	catacagcaagaggatagagCgcagcatctgtttgcacata	10	9	1	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr3:10145989C>A	ENST00000450660.2	-	2	686	c.470G>T	c.(469-471)cGc>cTc	p.R157L	FANCD2OS_ENST00000524279.1_Missense_Mutation_p.R157L	NM_001164839.1	NP_001158311.1	Q96PS1	FACOS_HUMAN	FANCD2 opposite strand	157								p.R157H(1)									GAGGATAGAGCGCAGCATCTG	0.473																																					p.R157L		Atlas-SNP	.											C3orf24,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	endometrium(1)	c.G470T						.						126	114	118					3																	10145989		2203	4300	6503	SO:0001583	missense	115795	exon2			ATAGAGCGCAGCA	AF230334	CCDS2596.1	3p25.3	2012-11-12	2012-11-12	2012-11-12	ENSG00000163705	ENSG00000163705			28623	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 24"	C3orf24		12477932	Standard	NM_001164839		Approved	MGC40179	uc003buz.3	Q96PS1	OTTHUMG00000128669	ENST00000450660.2:c.470G>T	chr3.hg19:g.10145989C>A	ENSP00000429608:p.Arg157Leu	73.0	0.0		80.0	4.0	NM_001164839		Missense_Mutation	SNP	ENST00000450660.2	hg19	CCDS2596.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.398215	0.83120	.	.	ENSG00000163705	ENST00000524279;ENST00000450660	.	.	.	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000001	T	0.47040	0.1424	L	0.29908	0.895	0.49798	D	0.999828	B	0.29862	0.259	B	0.20384	0.029	T	0.49735	-0.8908	9	0.87932	D	0	.	16.9439	0.86225	0.0:1.0:0.0:0.0	.	157	Q96PS1	CC024_HUMAN	L	157	.	ENSP00000429608:R157L	R	-	2	0	C3orf24	10120989	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.683000	0.61679	2.608000	0.88229	0.650000	0.86243	CGC	.	.		0.473	FANCD2OS-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339891.2	NM_173472		A	10145989	C	A	10145989	3	1	171	1	0	0	0	0	1	0	0	0	2219	768	27	1	67	1	C3orf24	3	10145989	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10		10145989	187876441	21	25922										
CAND2	23066	hgsc.bcm.edu	37	chr3	12857490	12857490	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aggcagcctggccgagcataTgcctgtgctggtatcaggta	14	10	1	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr3:12857490T>C	ENST00000456430.2	+	9	1465	c.1424T>C	c.(1423-1425)aTg>aCg	p.M475T	CAND2_ENST00000295989.5_Missense_Mutation_p.M382T	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	475					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GCCGAGCATATGCCTGTGCTG	0.627																																					p.M475T	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.T1424C						.						58	63	61					3																	12857490		2036	4187	6223	SO:0001583	missense	23066	exon9			AGCATATGCCTGT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1424T>C	chr3.hg19:g.12857490T>C	ENSP00000387641:p.Met475Thr	154.0	0.0		164.0	11.0	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	T	9.993	1.231341	0.22626	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.64260	-0.09;-0.09	5.12	5.12	0.69794	Armadillo-like helical (1);Armadillo-type fold (1);	0.106956	0.64402	D	0.000013	T	0.53029	0.1771	L	0.38175	1.15	0.80722	D	1	B;B	0.29378	0.243;0.119	B;B	0.30716	0.119;0.069	T	0.54016	-0.8356	10	0.45353	T	0.12	-39.4142	12.9041	0.58141	0.0:0.0:0.0:1.0	.	475;382	O75155;O75155-2	CAND2_HUMAN;.	T	382;475	ENSP00000295989:M382T;ENSP00000387641:M475T	ENSP00000295989:M382T	M	+	2	0	CAND2	12832490	1.000000	0.71417	0.999000	0.59377	0.301000	0.27625	6.202000	0.72131	1.941000	0.56285	0.459000	0.35465	ATG	.	.		0.627	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		C	12857490	T	C	12857490	3	2	171	1	0	0	0	0	1	0	0	0	2618	1464	51	2	1458	2	CAND2	3	12857490	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	2711501	12857490	185164940	22	25923										
ZCWPW2	152098	hgsc.bcm.edu	37	chr3	28476731	28476731	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gatcatggataaaggcaacaTtcgttggacattatagtatc	9	6	1	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr3:28476731T>A	ENST00000383768.2	+	4	651	c.463T>A	c.(463-465)Ttc>Atc	p.F155I	ZCWPW2_ENST00000421010.1_Missense_Mutation_p.F155I			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	155	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.						zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						AAAGGCAACATTCGTTGGACA	0.328																																					p.F155I		Atlas-SNP	.											.	ZCWPW2	49	.	0			c.T463A						.						105	109	108					3																	28476731		2203	4300	6503	SO:0001583	missense	152098	exon3			GCAACATTCGTTG	BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.463T>A	chr3.hg19:g.28476731T>A	ENSP00000373278:p.Phe155Ile	378.0	0.0		429.0	162.0	NM_001040432		Missense_Mutation	SNP	ENST00000383768.2	hg19	CCDS33723.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.60|13.60	2.284127|2.284127	0.40394|0.40394	.|.	.|.	ENSG00000206559|ENSG00000206559	ENST00000383768;ENST00000421010|ENST00000428875;ENST00000419130	T;T|.	0.70631|.	-0.5;-0.5|.	6.06|6.06	3.47|3.47	0.39725|0.39725	PWWP (1);|.	0.310063|.	0.28653|.	N|.	0.014596|.	T|T	0.45935|0.45935	0.1367|0.1367	L|L	0.60455|0.60455	1.87|1.87	0.09310|0.09310	N|N	0.999994|0.999994	P|.	0.51147|.	0.942|.	P|.	0.49999|.	0.628|.	T|T	0.29822|0.29822	-0.9999|-0.9999	10|5	0.22706|.	T|.	0.39|.	-16.9379|-16.9379	8.8751|8.8751	0.35340|0.35340	0.2372:0.0:0.0:0.7628|0.2372:0.0:0.0:0.7628	.|.	155|.	Q504Y3|.	ZCPW2_HUMAN|.	I|N	155|138;6	ENSP00000373278:F155I;ENSP00000412386:F155I|.	ENSP00000373278:F155I|.	F|I	+|+	1|2	0|0	ZCWPW2|ZCWPW2	28451735|28451735	0.744000|0.744000	0.28250|0.28250	0.901000|0.901000	0.35422|0.35422	0.649000|0.649000	0.38597|0.38597	0.534000|0.534000	0.23098|0.23098	2.322000|2.322000	0.78497|0.78497	0.528000|0.528000	0.53228|0.53228	TTC|ATT	.	.		0.328	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384		A	28476731	T	A	28476731	3	1	171	1	0	0	0	0	1	0	0	0	17613	1493	52	4	469	4	ZCWPW2	3	28476731	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	15619241	28476731	169545699	23	25924										
EPM2AIP1	9852	hgsc.bcm.edu	37	chr3	37033938	37033938	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	atgatgagtcaggttgattaTggtcagaagatcttcttgca	11	5	4	5			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr3:37033938T>C	ENST00000322716.5	-	1	857	c.631A>G	c.(631-633)Ata>Gta	p.I211V	MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000539477.1_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	211					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						AGGTTGATTATGGTCAGAAGA	0.517																																					p.I211V		Atlas-SNP	.											.	EPM2AIP1	47	.	0			c.A631G						.						81	83	82					3																	37033938		2011	4178	6189	SO:0001583	missense	9852	exon1			TGATTATGGTCAG	AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.631A>G	chr3.hg19:g.37033938T>C	ENSP00000406027:p.Ile211Val	96.0	0.0		146.0	59.0	NM_014805	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	hg19	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	T	10.69	1.421105	0.25639	.	.	ENSG00000178567	ENST00000322716	T	0.12361	2.69	5.09	1.31	0.21738	.	.	.	.	.	T	0.05364	0.0142	N	0.14661	0.345	0.26550	N	0.973932	B	0.06786	0.001	B	0.06405	0.002	T	0.43048	-0.9415	9	0.02654	T	1	-4.925	3.3868	0.07274	0.0:0.2789:0.2028:0.5183	.	211	Q7L775	EPMIP_HUMAN	V	211	ENSP00000406027:I211V	ENSP00000406027:I211V	I	-	1	0	EPM2AIP1	37008942	0.956000	0.32656	0.919000	0.36401	0.673000	0.39480	-0.099000	0.11007	0.389000	0.25086	0.455000	0.32223	ATA	.	.		0.517	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805		C	37033938	T	C	37033938	3	2	171	1	0	0	0	0	1	0	0	0	5186	1464	51	2	1196	2	EPM2AIP1	3	37033938	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	8557207	37033938	160988492	24	25925										
ACAD9	28976	hgsc.bcm.edu	37	chr3	128621398	128621398	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tccctgttctccctgcaggtGgccatgaacatcctcaacag	8	15	2	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr3:128621398G>C	ENST00000308982.7	+	9	966	c.885G>C	c.(883-885)gtG>gtC	p.V295V	ACAD9_ENST00000511526.1_3'UTR	NM_014049.4	NP_054768.2	Q9H845	ACAD9_HUMAN	acyl-CoA dehydrogenase family, member 9	295						dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	30						CCCTGCAGGTGGCCATGAACA	0.602																																					p.V295V		Atlas-SNP	.											.	ACAD9	51	.	0			c.G885C						.						99	95	97					3																	128621398		2203	4300	6503	SO:0001819	synonymous_variant	28976	exon9			GCAGGTGGCCATG	AF078854	CCDS3053.1	3q21.3	2013-05-24	2010-04-30		ENSG00000177646	ENSG00000177646		"Mitochondrial respiratory chain complex assembly factors"	21497	protein-coding gene	gene with protein product		611103	"acyl-Coenzyme A dehydrogenase family, member 9"			12359260, 21057504, 20816094	Standard	NM_014049		Approved	NPD002, MGC14452	uc003ela.4	Q9H845	OTTHUMG00000159942	ENST00000308982.7:c.885G>C	chr3.hg19:g.128621398G>C		104.0	0.0		122.0	34.0	NM_014049	D3DNB8|Q8WXX3	Silent	SNP	ENST00000308982.7	hg19	CCDS3053.1																																																																																			.	.		0.602	ACAD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358405.1	NM_014049		C	128621398	G	C	128621398	2	2	171	1	0	0	0	0	0	0	0	1	111	1335	47	4		4	ACAD9	3	128621398	Silent	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	91587460	128621398	69401032	25	25926										
CHRD	8646	hgsc.bcm.edu	37	chr3	184101425	184101425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ctggactccagccaggaggaCacacggtgagggctccaggt	15	12	0	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr3:184101425C>T	ENST00000204604.1	+	12	1681	c.1435C>T	c.(1435-1437)Cac>Tac	p.H479Y	CHRD_ENST00000545352.1_Missense_Mutation_p.H109Y|CHRD_ENST00000348986.3_Intron|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000450923.1_Missense_Mutation_p.H479Y	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	479	CHRD 3. {ECO:0000255|PROSITE- ProRule:PRU00230}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GCCAGGAGGACACACGGTGAG	0.607																																					p.H479Y		Atlas-SNP	.											.	CHRD	149	.	0			c.C1435T						.						60	50	54					3																	184101425		2203	4300	6503	SO:0001583	missense	8646	exon12			GGAGGACACACGG	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.1435C>T	chr3.hg19:g.184101425C>T	ENSP00000204604:p.His479Tyr	112.0	0.0		95.0	38.0	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	hg19	CCDS3266.1	.	.	.	.	.	.	.	.	.	.	C	0.946	-0.708073	0.03230	.	.	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000545352;ENST00000342610	T;T;T	0.42513	0.97;0.97;0.97	4.27	3.39	0.38822	CHRD (3);	0.712995	0.13515	N	0.382185	T	0.25680	0.0625	N	0.14661	0.345	0.23559	N	0.997414	B;B;B	0.20550	0.004;0.016;0.046	B;B;B	0.20384	0.009;0.029;0.029	T	0.19647	-1.0299	10	0.66056	D	0.02	-2.4332	7.4132	0.27029	0.0:0.7936:0.0:0.2064	.	109;479;479	B7Z6F4;E7ESX1;Q9H2X0	.;.;CHRD_HUMAN	Y	479;479;109;192	ENSP00000204604:H479Y;ENSP00000408972:H479Y;ENSP00000442948:H109Y	ENSP00000204604:H479Y	H	+	1	0	CHRD	185584119	0.950000	0.32346	0.703000	0.30354	0.097000	0.18754	0.104000	0.15313	0.904000	0.36572	0.313000	0.20887	CAC	.	.		0.607	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		T	184101425	C	T	184101425	3	4	171	1	0	0	0	0	1	0	0	0	3374	478	17	3	1481	3	CHRD	3	184101425	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	55480027	184101425	13921005	26	25927										
HTT	3064	hgsc.bcm.edu	37	chr4	3131687	3131687	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	acaaccagtatttgggcctgCagattggacagccccaggat	11	11	0	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr4:3131687C>T	ENST00000355072.5	+	13	1925	c.1780C>T	c.(1780-1782)Cag>Tag	p.Q594*		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	594					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TTTGGGCCTGCAGATTGGACA	0.512																																					p.Q594X		Atlas-SNP	.											.	HTT	221	.	0			c.C1780T						.						95	92	93					4																	3131687		1899	4137	6036	SO:0001587	stop_gained	3064	exon13			GGCCTGCAGATTG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1780C>T	chr4.hg19:g.3131687C>T	ENSP00000347184:p.Gln594*	103.0	0.0		80.0	41.0	NM_002111	Q9UQB7	Nonsense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	C	40	8.340561	0.98767	.	.	ENSG00000197386	ENST00000355072	.	.	.	4.5	4.5	0.54988	.	0.056009	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	17.5696	0.87931	0.0:1.0:0.0:0.0	.	.	.	.	X	594	.	ENSP00000347184:Q594X	Q	+	1	0	HTT	3101485	1.000000	0.71417	0.386000	0.26170	0.266000	0.26442	6.585000	0.74062	2.224000	0.72417	0.561000	0.74099	CAG	.	.		0.512	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3131687	C	T	3131687	4	4	171	1	0	0	0	0	0	1	0	0	7466	711	25	3	1830	3	HTT	4	3131687	Nonsense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10		3131687	188022589	27	25928										
NKX3-2	579	hgsc.bcm.edu	37	chr4	13544068	13544068	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ctgccggcccgctgccgcccCcgccgccggccccgctgcac	12	25	0	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr4:13544068C>A	ENST00000382438.5	-	2	1186	c.551G>T	c.(550-552)gGg>gTg	p.G184V		NM_001189.3	NP_001180.1	P78367	NKX32_HUMAN	NK3 homeobox 2	184	Poly-Gly.				determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|intestinal epithelial cell development (GO:0060576)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|organ formation (GO:0048645)|pancreas development (GO:0031016)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|spleen development (GO:0048536)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(1)|lung(4)|prostate(1)	7						gctgccgcccccgccgccggc	0.771																																					p.G184V		Atlas-SNP	.											.	NKX3-2	15	.	0			c.G551T						.						4	5	5					4																	13544068		1294	2994	4288	SO:0001583	missense	579	exon2			CCGCCCCCGCCGC	AF009801	CCDS3410.1	4p16.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000109705	ENSG00000109705		"Homeoboxes / ANTP class : NKL subclass"	951	protein-coding gene	gene with protein product		602183	"bagpipe homeobox homolog 1 (Drosophila)"	BAPX1		9344671	Standard	NM_001189		Approved	NKX3B, NKX3.2	uc003gmx.2	P78367	OTTHUMG00000090657	ENST00000382438.5:c.551G>T	chr4.hg19:g.13544068C>A	ENSP00000371875:p.Gly184Val	812.0	2.0		498.0	313.0	NM_001189	Q2M2I7	Missense_Mutation	SNP	ENST00000382438.5	hg19	CCDS3410.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.739871	0.69304	.	.	ENSG00000109705	ENST00000382438	D	0.92397	-3.03	4.43	2.54	0.30619	.	0.593374	0.14127	N	0.339626	T	0.81725	0.4883	N	0.14661	0.345	0.09310	N	0.999999	B	0.26512	0.151	B	0.29716	0.106	T	0.67669	-0.5611	10	0.13108	T	0.6	.	6.8785	0.24160	0.0:0.7143:0.1815:0.1042	.	184	P78367	NKX32_HUMAN	V	184	ENSP00000371875:G184V	ENSP00000371875:G184V	G	-	2	0	NKX3-2	13153166	0.002000	0.14202	0.240000	0.24138	0.169000	0.22640	0.675000	0.25232	2.200000	0.70718	0.561000	0.74099	GGG	.	.		0.771	NKX3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207317.3			A	13544068	C	A	13544068	3	1	171	1	0	0	0	0	1	0	0	0	10465	623	22	3	454	3	NKX3-2	4	13544068	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	10412381	13544068	177610208	28	25929										
FAM172A	83989	hgsc.bcm.edu	37	chr5	93294536	93294536	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ccactgtccagatcttcattTataataagtcttctagccca	4	12	4	1	rs375944243		TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr5:93294536T>A	ENST00000395965.3	-	6	655	c.513A>T	c.(511-513)atA>atT	p.I171I	FAM172A_ENST00000505869.1_Intron|FAM172A_ENST00000509163.1_Silent_p.I125I|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000504768.2_5'UTR	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	171						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						GATCTTCATTTATAATAAGTC	0.388																																					p.I171I		Atlas-SNP	.											.	FAM172A	38	.	0			c.A513T						.						129	127	127					5																	93294536		2203	4300	6503	SO:0001819	synonymous_variant	83989	exon6			TTCATTTATAATA		CCDS4069.1, CCDS54879.1, CCDS54880.1	5q15	2008-06-16	2008-06-16	2008-06-16	ENSG00000113391	ENSG00000113391			25365	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 21"	C5orf21		11230166	Standard	NM_032042		Approved	DKFZP564D172	uc010jbd.3	Q8WUF8	OTTHUMG00000131329	ENST00000395965.3:c.513A>T	chr5.hg19:g.93294536T>A		202.0	0.0		251.0	92.0	NM_032042	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	Silent	SNP	ENST00000395965.3	hg19	CCDS4069.1																																																																																			.	.		0.388	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254100.3	NM_032042		A	93294536	T	A	93294536	2	1	171	1	0	0	0	0	0	0	0	1	5497	1744	61	4		4	FAM172A	5	93294536	Silent	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10		93294536	87620724	29	25930										
PPIP5K2	23262	hgsc.bcm.edu	37	chr5	102515808	102515808	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gttgatcgagctgtgatattGtttaaaccaatggtatcaga	10	5	1	3			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr5:102515808G>C	ENST00000358359.3	+	24	3350	c.2841G>C	c.(2839-2841)ttG>ttC	p.L947F	PPIP5K2_ENST00000414217.1_Missense_Mutation_p.L947F|PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000321521.9_Missense_Mutation_p.L947F	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	947					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						CTGTGATATTGTTTAAACCAA	0.363																																					p.L947F		Atlas-SNP	.											.	PPIP5K2	98	.	0			c.G2841C						.						101	98	99					5																	102515808		2203	4299	6502	SO:0001583	missense	23262	exon23			GATATTGTTTAAA	AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"histidine acid phosphatase domain containing 1"	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.2841G>C	chr5.hg19:g.102515808G>C	ENSP00000351126:p.Leu947Phe	164.0	0.0		193.0	8.0	NM_015216	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	hg19		.	.	.	.	.	.	.	.	.	.	G	13.51	2.259784	0.39995	.	.	ENSG00000145725	ENST00000321521;ENST00000358359;ENST00000451606;ENST00000414217;ENST00000509597	T;T;T;T	0.24908	2.44;2.44;2.44;1.83	5.98	0.299	0.15771	.	0.254773	0.31123	N	0.008214	T	0.16085	0.0387	L	0.29908	0.895	0.32040	N	0.598291	P;P;B	0.37158	0.585;0.488;0.245	B;B;B	0.38378	0.211;0.272;0.092	T	0.12682	-1.0538	10	0.54805	T	0.06	.	5.7754	0.18277	0.3164:0.0:0.5098:0.1738	.	962;947;947	E9PGM8;O43314-2;O43314	.;.;VIP2_HUMAN	F	947;947;962;947;221	ENSP00000313070:L947F;ENSP00000351126:L947F;ENSP00000416016:L947F;ENSP00000424948:L221F	ENSP00000313070:L947F	L	+	3	2	PPIP5K2	102543707	0.995000	0.38212	0.787000	0.31911	0.991000	0.79684	0.315000	0.19451	0.100000	0.17581	0.591000	0.81541	TTG	.	.		0.363	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		C	102515808	G	C	102515808	3	2	171	1	0	0	0	0	1	0	0	0	12345	1368	48	4	2931	4	PPIP5K2	5	102515808	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	9221272	102515808	78399452	30	25931										
PCDHB13	56123	hgsc.bcm.edu	37	chr5	140594106	140594106	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tctccagtatttctggacaaAcaaatgttggtgaaagtatc	8	7	2	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr5:140594106A>G	ENST00000341948.4	+	1	598	c.411A>G	c.(409-411)aaA>aaG	p.K137K		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	137					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTCTGGACAAACAAATGTTGG	0.428																																					p.K137K		Atlas-SNP	.											.	PCDHB13	142	.	0			c.A411G						.						42	43	43					5																	140594106		2203	4298	6501	SO:0001819	synonymous_variant	56123	exon1			GGACAAACAAATG	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"Cadherins / Protocadherins : Clustered"	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.411A>G	chr5.hg19:g.140594106A>G		649.0	0.0		698.0	209.0	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	hg19	CCDS4255.1																																																																																			.	.		0.428	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		G	140594106	A	G	140594106	2	3	171	1	0	0	0	0	0	0	0	1	11547	40	2	2		2	PCDHB13	5	140594106	Silent	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	38078298	140594106	40321154	31	25932										
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140712001	140712001	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tggcgcccctctccgcagagCccggctacctggtgaccaag	12	17	1	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr5:140712001C>A	ENST00000517417.1	+	1	1750	c.1750C>A	c.(1750-1752)Ccc>Acc	p.P584T	PCDHGA1_ENST00000378105.3_Missense_Mutation_p.P584T	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	584	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCGCAGAGCCCGGCTACCT	0.667																																					p.P584T		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.C1750A						.						58	70	66					5																	140712001		2202	4300	6502	SO:0001583	missense	56114	exon1			GCAGAGCCCGGCT	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1750C>A	chr5.hg19:g.140712001C>A	ENSP00000431083:p.Pro584Thr	89.0	0.0		108.0	35.0	NM_018912	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	hg19	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.723413	0.30503	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.60797	0.16;0.16	3.92	3.92	0.45320	Cadherin (3);Cadherin-like (1);	0.142955	0.32204	N	0.006423	T	0.72724	0.3496	M	0.74546	2.27	0.23320	N	0.997912	D;D	0.56746	0.971;0.977	P;P	0.62560	0.844;0.904	T	0.66795	-0.5833	10	0.87932	D	0	.	15.2338	0.73413	0.0:1.0:0.0:0.0	.	584;584	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	T	584	ENSP00000431083:P584T;ENSP00000367345:P584T	ENSP00000367345:P584T	P	+	1	0	PCDHGA1	140692185	0.000000	0.05858	0.876000	0.34364	0.185000	0.23345	0.280000	0.18790	2.186000	0.69663	0.557000	0.71058	CCC	.	.		0.667	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		A	140712001	C	A	140712001	3	1	171	1	0	0	0	0	1	0	0	0	11559	739	26	3	1752	3	PCDHGA1	5	140712001	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	117895	140712001	40203259	32	25933										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141335502	141335502	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gtgggcttcatttccactgcGgatgctgtagaggggctctc	14	10	2	1	rs370147049		TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr5:141335502G>A	ENST00000231484.3	-	1	3125	c.1915C>T	c.(1915-1917)Cgc>Tgc	p.R639C	AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	639	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCCACTGCGGATGCTGTAG	0.562																																					p.R639C		Atlas-SNP	.											.	PCDH12	133	.	0			c.C1915T						.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	75	68	71		1915	1.5	0	5		71	0,8600		0,0,4300	no	missense	PCDH12	NM_016580.2	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	639/1185	141335502	1,13005	2203	4300	6503	SO:0001583	missense	51294	exon1			CACTGCGGATGCT	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.1915C>T	chr5.hg19:g.141335502G>A	ENSP00000231484:p.Arg639Cys	72.0	0.0		67.0	25.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	G	6.237	0.411843	0.11812	2.27E-4	0.0	ENSG00000113555	ENST00000231484	T	0.52057	0.68	5.38	1.55	0.23275	Cadherin (4);Cadherin-like (1);	0.691899	0.14591	N	0.310280	T	0.46698	0.1406	M	0.73217	2.22	0.09310	N	1	D	0.59767	0.986	P	0.48901	0.594	T	0.38564	-0.9655	10	0.42905	T	0.14	.	2.1559	0.03811	0.1573:0.2769:0.4083:0.1576	.	639	Q9NPG4	PCD12_HUMAN	C	639	ENSP00000231484:R639C	ENSP00000231484:R639C	R	-	1	0	PCDH12	141315686	0.000000	0.05858	0.015000	0.15790	0.050000	0.14768	-0.159000	0.10056	0.091000	0.17302	-0.892000	0.02923	CGC	.	.		0.562	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141335502	G	A	141335502	3	1	171	1	0	0	0	0	1	0	0	0	11519	1116	39	1	1655	1	PCDH12	5	141335502	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	623501	141335502	39579758	33	25934										
PPARGC1B	133522	hgsc.bcm.edu	37	chr5	149216515	149216515	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gggtcagccccacttgctctGaccactgcccctaccagagc	9	18	2	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr5:149216515G>A	ENST00000309241.5	+	8	2529	c.2497G>A	c.(2497-2499)Gac>Aac	p.D833N	PPARGC1B_ENST00000403750.1_Missense_Mutation_p.D769N|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.D794N|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.D833N	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	833					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CACTTGCTCTGACCACTGCCC	0.632																																					p.D833N		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.G2497A						.						74	73	73					5																	149216515		2203	4300	6503	SO:0001583	missense	133522	exon8			TGCTCTGACCACT	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"RNA binding motif (RRM) containing"	30022	protein-coding gene	gene with protein product		608886	"peroxisome proliferative activated receptor, gamma, coactivator 1, beta"			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.2497G>A	chr5.hg19:g.149216515G>A	ENSP00000312649:p.Asp833Asn	73.0	0.0		89.0	14.0	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	hg19	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.957452	0.53400	.	.	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.08193	3.13;3.12;3.13;3.13	5.6	4.72	0.59763	.	0.489617	0.21568	N	0.072449	T	0.10895	0.0266	L	0.46157	1.445	0.35262	D	0.779719	P;D;P;P;D	0.56521	0.921;0.976;0.921;0.872;0.96	P;P;P;B;P	0.49140	0.601;0.6;0.601;0.396;0.497	T	0.09314	-1.0680	10	0.31617	T	0.26	-27.8118	7.6871	0.28546	0.1351:0.1978:0.667:0.0	.	812;812;794;833;833	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	N	794;833;833;769	ENSP00000353638:D794N;ENSP00000377855:D833N;ENSP00000312649:D833N;ENSP00000384403:D769N	ENSP00000312649:D833N	D	+	1	0	PPARGC1B	149196708	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	1.534000	0.36051	2.641000	0.89580	0.462000	0.41574	GAC	.	.		0.632	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		A	149216515	G	A	149216515	3	1	171	1	0	0	0	0	1	0	0	0	12310	1290	45	3	2534	3	PPARGC1B	5	149216515	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	7881013	149216515	31698745	34	25935										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169230174	169230174	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aagtactgcgttgaattgctCaacagcatcttggaagtcct	9	9	2	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr5:169230174C>T	ENST00000256935.8	+	26	2747	c.2667C>T	c.(2665-2667)ctC>ctT	p.L889L	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000520908.1_Silent_p.L381L	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	889					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTGAATTGCTCAACAGCATCT	0.488																																					p.L889L		Atlas-SNP	.											.	DOCK2	389	.	0			c.C2667T						.						147	123	131					5																	169230174		2203	4300	6503	SO:0001819	synonymous_variant	1794	exon26			ATTGCTCAACAGC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2667C>T	chr5.hg19:g.169230174C>T		148.0	0.0		204.0	73.0	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	hg19	CCDS4371.1																																																																																			.	.		0.488	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169230174	C	T	169230174	2	4	171	1	0	0	0	0	0	0	0	1	4689	813	29	3		3	DOCK2	5	169230174	Silent	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	20013659	169230174	11685086	35	25936										
HK3	3101	hgsc.bcm.edu	37	chr5	176314451	176314451	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	acactcaggccaggtccttaCcgctgccgtcaggggtggcc	13	15	2	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr5:176314451C>T	ENST00000292432.5	-	11	1692		c.e11+1			NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)						carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGGTCCTTACCGCTGCCGTC	0.672																																					.		Atlas-SNP	.											.	HK3	210	.	0			c.1600+1G>A						.						32	36	35					5																	176314451		2203	4300	6503	SO:0001630	splice_region_variant	3101	exon12			TCCTTACCGCTGC		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1600+1G>A	chr5.hg19:g.176314451C>T		75.0	0.0		75.0	30.0	NM_002115	Q8N1E7	Splice_Site	SNP	ENST00000292432.5	hg19	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	C	10.39	1.337347	0.24253	.	.	ENSG00000160883	ENST00000292432	.	.	.	3.78	3.78	0.43462	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.585	0.61926	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HK3	176247057	1.000000	0.71417	0.959000	0.39883	0.037000	0.13140	5.571000	0.67404	1.936000	0.56123	0.462000	0.41574	.	.	.		0.672	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		Intron	T	176314451	C	T	176314451	5	4	171	1	0	0	0	0	0	0	1	0	7201	521	18	3	1206	3	HK3	5	176314451	Splice_Site	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	7084277	176314451	4600809	36	25937										
IRF4	3662	hgsc.bcm.edu	37	chr6	405053	405053	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ctcaccacggccgctccctgCcaagattccaggtgactcta	8	17	2	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr6:405053C>A	ENST00000380956.4	+	8	1261	c.1135C>A	c.(1135-1137)Cca>Aca	p.P379T		NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	379					cytokine-mediated signaling pathway (GO:0019221)|defense response to protozoan (GO:0042832)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of DNA binding (GO:0043388)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of interleukin-13 biosynthetic process (GO:0045368)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of T-helper cell differentiation (GO:0045622)|T cell activation (GO:0042110)|T-helper 17 cell lineage commitment (GO:0072540)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear nucleosome (GO:0000788)|nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		CCGCTCCCTGCCAAGATTCCA	0.512			T	IGH@	MM																																p.P379T		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.C1135A						.						81	78	79					6																	405053		2203	4300	6503	SO:0001583	missense	3662	exon8			TCCCTGCCAAGAT	U52682	CCDS4469.1	6p25-p23	2008-08-29			ENSG00000137265	ENSG00000137265			6119	protein-coding gene	gene with protein product		601900		MUM1		8921401, 18417578	Standard	NM_002460		Approved	LSIRF	uc003msz.4	Q15306	OTTHUMG00000016294	ENST00000380956.4:c.1135C>A	chr6.hg19:g.405053C>A	ENSP00000370343:p.Pro379Thr	48.0	0.0		60.0	15.0	NM_002460	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	hg19	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.178474	0.78564	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.99186	-5.53	5.71	5.71	0.89125	SMAD domain-like (1);SMAD/FHA domain (1);Interferon regulatory factor-3 (1);	0.102956	0.64402	D	0.000002	D	0.99423	0.9796	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	D	0.99208	1.0875	10	0.87932	D	0	-15.2749	19.8773	0.96884	0.0:1.0:0.0:0.0	.	378;379	Q15306-2;Q15306	.;IRF4_HUMAN	T	379;408	ENSP00000370343:P379T	ENSP00000370343:P379T	P	+	1	0	IRF4	350053	1.000000	0.71417	0.922000	0.36590	0.862000	0.49288	4.555000	0.60767	2.686000	0.91538	0.650000	0.86243	CCA	.	.		0.512	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			A	405053	C	A	405053	3	1	171	1	0	0	0	0	1	0	0	0	7841	739	26	3	1161	3	IRF4	6	405053	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10		405053	170710014	37	25938										
TDP2	51567	hgsc.bcm.edu	37	chr6	24666984	24666984	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ccactgcggcatcgcagcttGcgaccgaggcaaactccaca	10	16	0	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr6:24666984G>A	ENST00000378198.4	-	1	277	c.107C>T	c.(106-108)gCa>gTa	p.A36V	ACOT13_ENST00000537591.1_5'Flank|ACOT13_ENST00000230048.4_5'Flank|TDP2_ENST00000545995.1_Missense_Mutation_p.A66V|TDP2_ENST00000341060.3_5'Flank			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	36					cell surface receptor signaling pathway (GO:0007166)|double-strand break repair (GO:0006302)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|PML body (GO:0016605)	5'-tyrosyl-DNA phosphodiesterase activity (GO:0070260)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)|tyrosyl-RNA phosphodiesterase activity (GO:0036317)			kidney(2)|large_intestine(1)|lung(5)|ovary(1)	9						ATCGCAGCTTGCGACCGAGGC	0.622								Direct reversal of damage																													p.A36V		Atlas-SNP	.											.	TDP2	29	.	0			c.C107T						.						170	185	180					6																	24666984		2203	4300	6503	SO:0001583	missense	51567	exon1			CAGCTTGCGACCG	AJ269473	CCDS4557.1	6p22.3-p22.1	2010-05-07	2010-05-07	2010-05-07	ENSG00000111802	ENSG00000111802	3.1.4.-		17768	protein-coding gene	gene with protein product		605764	"TRAF and TNF receptor associated protein"	TTRAP		11478795	Standard	NM_016614		Approved		uc003nej.3	O95551	OTTHUMG00000014360	ENST00000378198.4:c.107C>T	chr6.hg19:g.24666984G>A	ENSP00000367440:p.Ala36Val	119.0	0.0		104.0	45.0	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Missense_Mutation	SNP	ENST00000378198.4	hg19	CCDS4557.1	.	.	.	.	.	.	.	.	.	.	G	16.46	3.129052	0.56721	.	.	ENSG00000111802	ENST00000378198;ENST00000545995;ENST00000545780	T;T	0.26373	1.79;1.74	5.09	3.25	0.37280	UBA-like (1);	0.361881	0.32273	N	0.006333	T	0.14098	0.0341	M	0.62723	1.935	0.09310	N	1	P;P	0.49090	0.919;0.536	B;B	0.40825	0.341;0.114	T	0.02813	-1.1107	10	0.66056	D	0.02	-19.1299	13.3712	0.60713	0.0:0.3008:0.6992:0.0	.	66;36	O95551-2;O95551	.;TYDP2_HUMAN	V	36;66;36	ENSP00000367440:A36V;ENSP00000437637:A66V	ENSP00000367440:A36V	A	-	2	0	TDP2	24774963	0.992000	0.36948	0.006000	0.13384	0.276000	0.26787	4.478000	0.60230	0.673000	0.31224	0.655000	0.94253	GCA	.	.		0.622	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1			A	24666984	G	A	24666984	3	1	171	1	0	0	0	0	1	0	0	0	15744	1319	46	3	1009	3	TDP2	6	24666984	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	24261931	24666984	146448083	38	25939										
TINAG	27283	hgsc.bcm.edu	37	chr6	54214615	54214615	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tgggcgaggaaaacggcatgCcacgaagccatgtcccaaca	12	12	0	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr6:54214615C>T	ENST00000259782.4	+	7	1097	c.1001C>T	c.(1000-1002)gCc>gTc	p.A334V		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	334					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			AAACGGCATGCCACGAAGCCA	0.458																																					p.A334V		Atlas-SNP	.											.	TINAG	102	.	0			c.C1001T						.						152	138	143					6																	54214615		2203	4300	6503	SO:0001583	missense	27283	exon7			GGCATGCCACGAA	AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.1001C>T	chr6.hg19:g.54214615C>T	ENSP00000259782:p.Ala334Val	160.0	0.0		173.0	73.0	NM_014464	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	hg19	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993207	0.93167	.	.	ENSG00000137251	ENST00000339741;ENST00000259782;ENST00000370865	D	0.83914	-1.78	5.87	5.87	0.94306	Peptidase C1A, papain C-terminal (2);	0.078533	0.56097	D	0.000039	D	0.85379	0.5683	L	0.43554	1.36	0.80722	D	1	D	0.67145	0.996	D	0.65443	0.935	D	0.85139	0.0979	10	0.51188	T	0.08	.	17.7085	0.88315	0.0:1.0:0.0:0.0	.	334	Q9UJW2	TINAG_HUMAN	V	193;334;13	ENSP00000259782:A334V	ENSP00000259782:A334V	A	+	2	0	TINAG	54322574	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.209000	0.72171	2.785000	0.95823	0.591000	0.81541	GCC	.	.		0.458	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		T	54214615	C	T	54214615	3	4	171	1	0	0	0	0	1	0	0	0	15936	739	26	3	1027	3	TINAG	6	54214615	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	29547631	54214615	116900452	39	25940										
COL19A1	1310	hgsc.bcm.edu	37	chr6	70733546	70733546	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aaggagaaaaaggagatccaGctctggctggccttaatgga	13	7	1	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr6:70733546G>T	ENST00000322773.4	+	12	1156	c.1054G>T	c.(1054-1056)Gct>Tct	p.A352S		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	352	Collagen-like 2.		A -> G (in dbSNP:rs2273426).		cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						AGGAGATCCAGCTCTGGCTGG	0.308																																					p.A352S		Atlas-SNP	.											.	COL19A1	232	.	0			c.G1054T						.						90	88	88					6																	70733546		2203	4300	6503	SO:0001583	missense	1310	exon12			GATCCAGCTCTGG		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.1054G>T	chr6.hg19:g.70733546G>T	ENSP00000316030:p.Ala352Ser	122.0	0.0		104.0	28.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	hg19	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596159	0.46318	.	.	ENSG00000082293	ENST00000322773	D	0.93189	-3.18	5.5	5.5	0.81552	.	0.068567	0.64402	D	0.000018	D	0.84588	0.5505	N	0.16368	0.405	0.80722	D	1	B	0.02656	0.0	B	0.11329	0.006	T	0.81061	-0.1103	10	0.87932	D	0	.	18.3978	0.90504	0.0:0.0:1.0:0.0	.	352	Q14993	COJA1_HUMAN	S	352	ENSP00000316030:A352S	ENSP00000316030:A352S	A	+	1	0	COL19A1	70790267	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	5.835000	0.69368	2.588000	0.87417	0.655000	0.94253	GCT	.	.		0.308	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			T	70733546	G	T	70733546	3	4	171	1	0	0	0	0	1	0	0	0	3678	971	34	3	1096	3	COL19A1	6	70733546	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	16518931	70733546	100381521	40	25941										
KLHL32	114792	hgsc.bcm.edu	37	chr6	97533088	97533088	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gagaaggcagtgatcgatttCttagtgaaacatctctctga	10	7	3	4			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr6:97533088C>G	ENST00000369261.4	+	6	861	c.498C>G	c.(496-498)ttC>ttG	p.F166L	KLHL32_ENST00000539200.1_Missense_Mutation_p.F97L|KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000536676.1_Missense_Mutation_p.F130L	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	166										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		TGATCGATTTCTTAGTGAAAC	0.458																																					p.F166L		Atlas-SNP	.											.	KLHL32	85	.	0			c.C498G						.						111	111	111					6																	97533088		2203	4300	6503	SO:0001583	missense	114792	exon6			CGATTTCTTAGTG	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"Kelch-like", "BTB/POZ domain containing"	21221	protein-coding gene	gene with protein product			"BTB and kelch domain containing 5", "KIAA1900", "kelch-like 32 (Drosophila)"	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.498C>G	chr6.hg19:g.97533088C>G	ENSP00000358265:p.Phe166Leu	103.0	0.0		79.0	7.0	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	hg19	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.084587	0.76642	.	.	ENSG00000186231	ENST00000369255;ENST00000369261;ENST00000536676;ENST00000539200;ENST00000447886	T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51	6.01	5.04	0.67666	BTB/Kelch-associated (2);	0.048141	0.85682	D	0.000000	T	0.72851	0.3512	L	0.50993	1.605	0.80722	D	1	D;D;P;D	0.67145	0.996;0.992;0.941;0.977	D;D;P;P	0.76071	0.966;0.987;0.756;0.891	T	0.73332	-0.4016	10	0.51188	T	0.08	.	10.1864	0.43000	0.0:0.8274:0.0:0.1726	.	97;130;166;166	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	L	92;166;130;97;62	ENSP00000358265:F166L;ENSP00000440382:F130L;ENSP00000441527:F97L;ENSP00000389310:F62L	ENSP00000358259:F92L	F	+	3	2	KLHL32	97639809	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.950000	0.49081	2.850000	0.98022	0.655000	0.94253	TTC	.	.		0.458	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		G	97533088	C	G	97533088	3	3	171	1	0	0	0	0	1	0	0	0	8395	912	32	4	516	4	KLHL32	6	97533088	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	26799542	97533088	73581979	41	25942										
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117150058	117150058	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tttcatgaatagcaaacaaaCctccaattatgatatgtccc	4	10	1	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr6:117150058C>T	ENST00000310357.3	-	1	140	c.119G>A	c.(118-120)gGt>gAt	p.G40D	GPRC6A_ENST00000368549.3_Missense_Mutation_p.G40D|GPRC6A_ENST00000530250.1_Missense_Mutation_p.G40D	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	40					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		AGCAAACAAACCTCCAATTAT	0.438																																					p.G40D		Atlas-SNP	.											.	GPRC6A	152	.	0			c.G119A						.						91	90	90					6																	117150058		2203	4300	6503	SO:0001583	missense	222545	exon1			AACAAACCTCCAA	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.119G>A	chr6.hg19:g.117150058C>T	ENSP00000309493:p.Gly40Asp	180.0	0.0		138.0	32.0	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	hg19	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068392	0.76301	.	.	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.87491	-2.26;-2.26;-2.26	5.18	5.18	0.71444	.	0.071607	0.53938	D	0.000044	D	0.83188	0.5200	N	0.08118	0	0.27843	N	0.94101	D;D;D	0.89917	1.0;0.973;1.0	D;P;D	0.97110	1.0;0.71;0.991	T	0.81568	-0.0873	10	0.87932	D	0	.	17.0749	0.86583	0.0:1.0:0.0:0.0	.	40;40;40	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	D	40	ENSP00000309493:G40D;ENSP00000357537:G40D;ENSP00000433465:G40D	ENSP00000309493:G40D	G	-	2	0	GPRC6A	117256751	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	2.918000	0.48829	2.713000	0.92767	0.655000	0.94253	GGT	.	.		0.438	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			T	117150058	C	T	117150058	3	4	171	1	0	0	0	0	1	0	0	0	6737	507	18	3	2685	3	GPRC6A	6	117150058	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	19616970	117150058	53965009	42	25943										
RP9	6100	hgsc.bcm.edu	37	chr7	33134956	33134956	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ttctttcttcttctttttctTgtgtttctctttaccttcag	3	10	7	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr7:33134956T>A	ENST00000297157.3	-	6	573	c.556A>T	c.(556-558)Aag>Tag	p.K186*		NM_203288.1	NP_976033.1	Q8TA86	RP9_HUMAN	retinitis pigmentosa 9 (autosomal dominant)	186	Lys-rich.				cognition (GO:0050890)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|signal recognition particle receptor complex (GO:0005785)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|urinary_tract(1)	7			GBM - Glioblastoma multiforme(11;0.0403)			ttctttttcttGTGTTTCTCT	0.363																																					p.K186X		Atlas-SNP	.											.	RP9	19	.	0			c.A556T						.						29	31	31					7																	33134956		2199	4297	6496	SO:0001587	stop_gained	6100	exon6			TTTTCTTGTGTTT	AX016710	CCDS5440.1	7p14.3	2014-01-28			ENSG00000164610	ENSG00000164610			10288	protein-coding gene	gene with protein product	"Pim-1 kinase associated protein"	607331				8513323	Standard	NM_203288		Approved	PAP-1	uc003tdm.3	Q8TA86	OTTHUMG00000152988	ENST00000297157.3:c.556A>T	chr7.hg19:g.33134956T>A	ENSP00000297157:p.Lys186*	378.0	0.0		430.0	147.0	NM_203288		Nonsense_Mutation	SNP	ENST00000297157.3	hg19	CCDS5440.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.247961	0.59103	.	.	ENSG00000164610	ENST00000297157;ENST00000448915	.	.	.	3.17	1.95	0.26073	.	0.606531	0.17070	N	0.188214	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.6438	9.5011	0.39017	0.0:0.0:0.1789:0.8211	.	.	.	.	X	186;152	.	ENSP00000297157:K186X	K	-	1	0	RP9	33101481	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.558000	0.45879	0.545000	0.28902	0.460000	0.39030	AAG	.	.		0.363	RP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328914.1	NM_203288		A	33134956	T	A	33134956	4	1	171	1	0	0	0	0	0	1	0	0	13550	1821	63	4	113	4	RP9	7	33134956	Nonsense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10		33134956	126003707	43	25944										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48315128	48315128	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aagcaagttgctttgcaaatCatagaaaaacttaaaaatgt	6	5	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr7:48315128C>T	ENST00000435803.1	+	17	5889	c.5865C>T	c.(5863-5865)atC>atT	p.I1955I		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1955					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTTTGCAAATCATAGAAAAAC	0.318																																					p.I1955I		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C5865T						.						64	63	63					7																	48315128		1818	4080	5898	SO:0001819	synonymous_variant	154664	exon17			GCAAATCATAGAA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.5865C>T	chr7.hg19:g.48315128C>T		154.0	0.0		223.0	32.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.318	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48315128	C	T	48315128	2	4	171	1	0	0	0	0	0	0	0	1	31	816	29	3		3	ABCA13	7	48315128	Silent	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	15180172	48315128	110823535	44	25945										
PCLO	27445	hgsc.bcm.edu	37	chr7	82582848	82582848	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tagtacatattcttgtaacaGgtaatccattacttctcaga	5	8	2	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr7:82582848G>T	ENST00000333891.9	-	5	7758	c.7421C>A	c.(7420-7422)cCt>cAt	p.P2474H	PCLO_ENST00000423517.2_Missense_Mutation_p.P2474H|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCTTGTAACAGGTAATCCATT	0.433																																					p.P2474H		Atlas-SNP	.											.	PCLO	1506	.	0			c.C7421A						.						126	125	125					7																	82582848		1954	4150	6104	SO:0001583	missense	27445	exon5			GTAACAGGTAATC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.7421C>A	chr7.hg19:g.82582848G>T	ENSP00000334319:p.Pro2474His	97.0	0.0		123.0	45.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	1.769	-0.484819	0.04352	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17370	2.28;2.28	4.52	3.56	0.40772	.	.	.	.	.	T	0.13927	0.0337	L	0.27053	0.805	0.80722	D	1	B;B	0.27498	0.18;0.18	B;B	0.29176	0.099;0.099	T	0.11251	-1.0595	9	0.87932	D	0	.	12.8149	0.57658	0.0:0.0:0.8355:0.1645	.	2474;2474	Q9Y6V0-5;Q9Y6V0-6	.;.	H	2405;2474;2474	ENSP00000334319:P2474H;ENSP00000388393:P2474H	ENSP00000334319:P2474H	P	-	2	0	PCLO	82420784	1.000000	0.71417	0.794000	0.32065	0.110000	0.19582	4.445000	0.60007	2.057000	0.61298	0.484000	0.47621	CCT	.	.		0.433	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82582848	G	T	82582848	3	4	171	1	0	0	0	0	1	0	0	0	11592	1000	35	3	8108	3	PCLO	7	82582848	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	34267720	82582848	76555815	45	25946										
PCLO	27445	hgsc.bcm.edu	37	chr7	82764321	82764321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gggttcttccttcttttgtaCggggtcaacttgtttttgac	10	8	3	1	rs547726879		TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr7:82764321C>T	ENST00000333891.9	-	3	2882	c.2545G>A	c.(2545-2547)Gta>Ata	p.V849I	PCLO_ENST00000423517.2_Missense_Mutation_p.V849I	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTCTTTTGTACGGGGTCAACT	0.453													C|||	1	0.000199681	0	0.0014	5008	,	,		18191	0		0	False		,,,				2504	0				p.V849I		Atlas-SNP	.											Q9Y6V0-3,colon,carcinoma,0,3	PCLO	1506	.	0			c.G2545A						.						152	154	154					7																	82764321		1926	4131	6057	SO:0001583	missense	27445	exon3			TTTGTACGGGGTC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.2545G>A	chr7.hg19:g.82764321C>T	ENSP00000334319:p.Val849Ile	184.0	0.0		192.0	72.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	9.769	1.172127	0.21704	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16073	2.37;2.37	5.98	2.05	0.26809	.	.	.	.	.	T	0.12518	0.0304	L	0.31294	0.92	0.80722	D	1	B;B	0.19331	0.035;0.035	B;B	0.11329	0.006;0.006	T	0.07424	-1.0773	9	0.87932	D	0	.	9.565	0.39394	0.0:0.7049:0.0:0.2951	.	849;849	Q9Y6V0-5;Q9Y6V0-6	.;.	I	795;849;849	ENSP00000334319:V849I;ENSP00000388393:V849I	ENSP00000334319:V849I	V	-	1	0	PCLO	82602257	0.001000	0.12720	0.490000	0.27465	0.843000	0.47879	-0.414000	0.07114	0.092000	0.17331	0.655000	0.94253	GTA	.	.		0.453	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82764321	C	T	82764321	3	4	171	1	0	0	0	0	1	0	0	0	11592	536	19	1	12992	1	PCLO	7	82764321	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	181473	82764321	76374342	46	25947										
FZD3	7976	hgsc.bcm.edu	37	chr8	28385158	28385158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	catgctttttatgatactctAtttttttactatggctggca	6	7	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr8:28385158A>G	ENST00000240093.3	+	5	1359	c.881A>G	c.(880-882)tAt>tGt	p.Y294C	RNA5SP259_ENST00000365541.1_RNA|FZD3_ENST00000537916.1_Missense_Mutation_p.Y294C	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	294					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		ATGATACTCTATTTTTTTACT	0.418																																					p.Y294C		Atlas-SNP	.											.,1	FZD3	65	.	0			c.A881G						.						82	83	83					8																	28385158		2203	4300	6503	SO:0001583	missense	7976	exon5			TACTCTATTTTTT	AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"GPCR / Class F : Frizzled receptors"	4041	protein-coding gene	gene with protein product		606143	"frizzled (Drosophila) homolog 3", "frizzled homolog 3 (Drosophila)", "frizzled 3, seven transmembrane spanning receptor", "frizzled family receptor 3"			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.881A>G	chr8.hg19:g.28385158A>G	ENSP00000240093:p.Tyr294Cys	104.0	0.0		78.0	51.0	NM_017412	A8K615	Missense_Mutation	SNP	ENST00000240093.3	hg19	CCDS6069.1	.	.	.	.	.	.	.	.	.	.	A	16.99	3.272938	0.59649	.	.	ENSG00000104290	ENST00000537916;ENST00000240093	D;D	0.90004	-2.6;-2.6	5.0	5.0	0.66597	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	D	0.95799	0.8633	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96795	0.9585	10	0.87932	D	0	.	13.525	0.61591	1.0:0.0:0.0:0.0	.	294	Q9NPG1	FZD3_HUMAN	C	294	ENSP00000437489:Y294C;ENSP00000240093:Y294C	ENSP00000240093:Y294C	Y	+	2	0	FZD3	28441077	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	1.871000	0.54225	0.460000	0.39030	TAT	.	.		0.418	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866		G	28385158	A	G	28385158	3	3	171	1	0	0	0	0	1	0	0	0	6139	449	16	2	891	2	FZD3	8	28385158	Missense_Mutation	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10		28385158	117978864	47	25948										
ASH2L	9070	hgsc.bcm.edu	37	chr8	37978484	37978484	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ctgctcagcgccttccccctCatggctacccattggaacac	7	18	2	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr8:37978484C>T	ENST00000343823.6	+	10	1291	c.982C>T	c.(982-984)Cat>Tat	p.H328Y	ASH2L_ENST00000428278.2_Missense_Mutation_p.H234Y|RP11-90P5.4_ENST00000519081.1_RNA|ASH2L_ENST00000250635.7_Missense_Mutation_p.H234Y|RP11-90P5.5_ENST00000476186.2_RNA|ASH2L_ENST00000545394.1_Missense_Mutation_p.H189Y|ASH2L_ENST00000521652.1_Missense_Mutation_p.H234Y	NM_004674.4	NP_004665.2	Q9UBL3	ASH2L_HUMAN	ash2 (absent, small, or homeotic)-like (Drosophila)	328					cellular response to DNA damage stimulus (GO:0006974)|hemopoiesis (GO:0030097)|histone H3-K4 methylation (GO:0051568)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)	19	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)				CCTTCCCCCTCATGGCTACCC	0.473											OREG0018719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H328Y		Atlas-SNP	.											.	ASH2L	62	.	0			c.C982T						.						148	138	142					8																	37978484		2203	4300	6503	SO:0001583	missense	9070	exon10			CCCCCTCATGGCT	AF056717	CCDS6101.1, CCDS47840.1, CCDS59100.1, CCDS64872.1	8p11.2	2013-01-28	2001-11-28		ENSG00000129691	ENSG00000129691		"Zinc fingers, PHD-type"	744	protein-coding gene	gene with protein product		604782	"ash2 (absent, small, or homeotic, Drosophila, homolog)-like"	ASH2L1		10393421	Standard	NM_004674		Approved	ASH2L2, ASH2, Bre2	uc003xkt.5	Q9UBL3	OTTHUMG00000164016	ENST00000343823.6:c.982C>T	chr8.hg19:g.37978484C>T	ENSP00000340896:p.His328Tyr	103.0	0.0	874	183.0	38.0	NM_004674	A8K7C3|D3DSW9|O60659|O60660|Q96B62	Missense_Mutation	SNP	ENST00000343823.6	hg19	CCDS6101.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.744954	0.49151	.	.	ENSG00000129691	ENST00000343823;ENST00000250635;ENST00000545394;ENST00000428278;ENST00000521652	T;T;T;T;T	0.78126	-0.18;-1.15;-1.13;-1.14;-1.15	5.62	5.62	0.85841	.	0.090622	0.85682	D	0.000000	D	0.83760	0.5324	L	0.52905	1.665	0.80722	D	1	D;P	0.58620	0.983;0.596	P;B	0.56916	0.809;0.201	T	0.82802	-0.0277	10	0.44086	T	0.13	.	19.6764	0.95936	0.0:1.0:0.0:0.0	.	234;328	Q9UBL3-2;Q9UBL3	.;ASH2L_HUMAN	Y	328;234;189;234;234	ENSP00000340896:H328Y;ENSP00000250635:H234Y;ENSP00000443606:H189Y;ENSP00000395310:H234Y;ENSP00000430259:H234Y	ENSP00000250635:H234Y	H	+	1	0	ASH2L	38097641	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.764000	0.85297	2.660000	0.90430	0.655000	0.94253	CAT	.	.		0.473	ASH2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376749.4	NM_004674		T	37978484	C	T	37978484	3	4	171	1	0	0	0	0	1	0	0	0	1042	826	29	3	1020	3	ASH2L	8	37978484	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	9593326	37978484	108385538	48	25949										
ADAM9	8754	hgsc.bcm.edu	37	chr8	38913107	38913107	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tttcactagttccttccaggAggtactttatgccgaggaaa	9	9	1	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr8:38913107A>T	ENST00000487273.2	+	14	1485	c.1407A>T	c.(1405-1407)ggA>ggT	p.G469G		NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	469	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			TCCTTCCAGGAGGTACTTTAT	0.358																																					p.G469G		Atlas-SNP	.											.	ADAM9	66	.	0			c.A1407T						.						135	133	133					8																	38913107		2203	4300	6503	SO:0001819	synonymous_variant	8754	exon14			TCCAGGAGGTACT	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"ADAM metallopeptidase domain containing"	216	protein-coding gene	gene with protein product	"meltrin gamma"	602713	"a disintegrin and metalloproteinase domain 9 (meltrin gamma)", "cone rod dystrophy 9"	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.1407A>T	chr8.hg19:g.38913107A>T		113.0	0.0		183.0	98.0	NM_003816	B7ZLN7|Q10718|Q8NFM6	Silent	SNP	ENST00000487273.2	hg19	CCDS6112.1																																																																																			.	.		0.358	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			T	38913107	A	T	38913107	2	4	171	1	0	0	0	0	0	0	0	1	253	291	11	4		4	ADAM9	8	38913107	Silent	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	934623	38913107	107450915	49	25950										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77766536	77766536	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aaaacaaccccaacttatcgGaagacctccctcggcctctc	5	17	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr8:77766536G>T	ENST00000521891.2	+	10	7827	c.7379G>T	c.(7378-7380)gGa>gTa	p.G2460V	ZFHX4_ENST00000518282.1_Missense_Mutation_p.G2434V|ZFHX4_ENST00000050961.6_Missense_Mutation_p.G2415V|ZFHX4_ENST00000455469.2_Missense_Mutation_p.G2415V	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2415					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CAACTTATCGGAAGACCTCCC	0.557										HNSCC(33;0.089)																											p.G2460V		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G7379T						.						94	146	129					8																	77766536		2082	4222	6304	SO:0001583	missense	79776	exon10			TTATCGGAAGACC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.7379G>T	chr8.hg19:g.77766536G>T	ENSP00000430497:p.Gly2460Val	105.0	0.0		110.0	7.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	15.21	2.765045	0.49574	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.48522	0.81;0.86;0.83;0.82	5.23	5.23	0.72850	.	0.000000	0.43579	U	0.000552	T	0.50667	0.1629	L	0.44542	1.39	0.80722	D	1	P;D;D	0.53462	0.933;0.96;0.96	P;P;P	0.51229	0.462;0.663;0.663	T	0.30995	-0.9959	10	0.14656	T	0.56	.	18.9988	0.92824	0.0:0.0:1.0:0.0	.	2415;2415;2460	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	V	2460;2444;2415;2415;2434	ENSP00000430497:G2460V;ENSP00000399605:G2415V;ENSP00000050961:G2415V;ENSP00000430848:G2434V	ENSP00000050961:G2415V	G	+	2	0	ZFHX4	77929091	1.000000	0.71417	0.997000	0.53966	0.260000	0.26232	3.124000	0.50461	2.721000	0.93114	0.650000	0.86243	GGA	.	.		0.557	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77766536	G	T	77766536	3	4	171	1	0	0	0	0	1	0	0	0	17650	1174	41	3	7413	3	ZFHX4	8	77766536	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	38853429	77766536	68597486	50	25951										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113812467	113812467	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	agccacatttggctactcatGctcactatcaagtctggtac	7	12	4	0	rs201411480		TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr8:113812467G>T	ENST00000297405.5	-	13	2140	c.1896C>A	c.(1894-1896)agC>agA	p.S632R	CSMD3_ENST00000455883.2_Missense_Mutation_p.S528R|CSMD3_ENST00000352409.3_Missense_Mutation_p.S632R|CSMD3_ENST00000343508.3_Missense_Mutation_p.S592R	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	632	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GGCTACTCATGCTCACTATCA	0.393										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S632R		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C1896A						.						145	127	133					8																	113812467		2203	4300	6503	SO:0001583	missense	114788	exon13			ACTCATGCTCACT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1896C>A	chr8.hg19:g.113812467G>T	ENSP00000297405:p.Ser632Arg	89.0	0.0		121.0	48.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.930112	0.73327	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.83	3.06	0.35304	CUB (5);	0.000000	0.85682	D	0.000000	T	0.76335	0.3973	H	0.98980	4.39	0.33767	D	0.622589	D;D;D	0.76494	0.999;0.999;0.963	D;D;P	0.91635	0.998;0.999;0.775	D	0.86510	0.1809	10	0.59425	D	0.04	.	11.6159	0.51090	0.1957:0.0:0.8043:0.0	.	528;632;592	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	R	592;632;528;632	ENSP00000345799:S592R;ENSP00000297405:S632R;ENSP00000412263:S528R;ENSP00000343124:S632R	ENSP00000297405:S632R	S	-	3	2	CSMD3	113881643	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.400000	0.52594	0.828000	0.34709	-0.145000	0.13849	AGC	.	G|1.000;A|0.000		0.393	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113812467	G	T	113812467	3	4	171	1	0	0	0	0	1	0	0	0	3948	1310	46	3	9463	3	CSMD3	8	113812467	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	36045931	113812467	32551555	51	25952										
PTPN3	5774	hgsc.bcm.edu	37	chr9	112190926	112190926	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tctgtcgctgatgtatgaagAactttttccttttgaaagaa	8	6	1	5			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr9:112190926A>C	ENST00000374541.2	-	11	907	c.803T>G	c.(802-804)tTc>tGc	p.F268C	PTPN3_ENST00000262539.3_Missense_Mutation_p.F159C|PTPN3_ENST00000446349.1_Missense_Mutation_p.F137C|PTPN3_ENST00000412145.1_Missense_Mutation_p.F137C	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	268	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						ATGTATGAAGAACTTTTTCCT	0.388																																					p.F268C		Atlas-SNP	.											.	PTPN3	106	.	0			c.T803G						.						150	135	140					9																	112190926		2203	4299	6502	SO:0001583	missense	5774	exon11			ATGAAGAACTTTT		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.803T>G	chr9.hg19:g.112190926A>C	ENSP00000363667:p.Phe268Cys	79.0	0.0		44.0	32.0	NM_001145368	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	hg19	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.279192	0.80692	.	.	ENSG00000070159	ENST00000394831;ENST00000412145;ENST00000446349;ENST00000374541;ENST00000262539	D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49	5.43	4.29	0.51040	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.94618	0.8265	M	0.89214	3.015	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.94584	0.7782	10	0.87932	D	0	.	11.1579	0.48499	0.9266:0.0:0.0733:0.0	.	159;268;268	B7Z3H5;B7Z9V1;P26045	.;.;PTN3_HUMAN	C	268;137;137;268;159	ENSP00000416654:F137C;ENSP00000395384:F137C;ENSP00000363667:F268C;ENSP00000262539:F159C	ENSP00000262539:F159C	F	-	2	0	PTPN3	111230747	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.605000	0.82844	0.997000	0.38969	0.533000	0.62120	TTC	.	.		0.388	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			C	112190926	A	C	112190926	3	2	171	1	0	0	0	0	1	0	0	0	12804	246	9	5	2002	5	PTPN3	9	112190926	Missense_Mutation	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10		112190926	29022505	52	25953										
OR1J2	26740	hgsc.bcm.edu	37	chr9	125273731	125273731	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ttcatgtgtatcctggtatcAtatggctacattggggccac	10	9	2	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr9:125273731A>T	ENST00000335302.5	+	1	651	c.651A>T	c.(649-651)tcA>tcT	p.S217S		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						TCCTGGTATCATATGGCTACA	0.507																																					p.S217S		Atlas-SNP	.											.	OR1J2	64	.	0			c.A651T						.						138	111	120					9																	125273731		2203	4300	6503	SO:0001819	synonymous_variant	26740	exon1			GGTATCATATGGC		CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"GPCR / Class A : Olfactory receptors"	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.651A>T	chr9.hg19:g.125273731A>T		138.0	0.0		99.0	69.0	NM_054107	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Silent	SNP	ENST00000335302.5	hg19	CCDS35121.1																																																																																			.	.		0.507	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1			T	125273731	A	T	125273731	2	4	171	1	0	0	0	0	0	0	0	1	10969	204	8	4		4	OR1J2	9	125273731	Silent	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	13082805	125273731	15939700	53	25954										
ANK3	288	hgsc.bcm.edu	37	chr10	61833947	61833947	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tgcctttgcttaaaacccgaTtgtggtcatcttcttcacta	6	11	4	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr10:61833947T>A	ENST00000280772.2	-	37	6883	c.6692A>T	c.(6691-6693)aAt>aTt	p.N2231I	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2231					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.N2231S(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TAAAACCCGATTGTGGTCATC	0.418																																					p.N2231I		Atlas-SNP	.											ANK3,NS,carcinoma,-1,1	ANK3	703	.	1	Substitution - Missense(1)	lung(1)	c.A6692T						.						218	202	207					10																	61833947		2203	4300	6503	SO:0001583	missense	288	exon37			ACCCGATTGTGGT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.6692A>T	chr10.hg19:g.61833947T>A	ENSP00000280772:p.Asn2231Ile	107.0	0.0		96.0	19.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	T	7.328	0.618382	0.14129	.	.	ENSG00000151150	ENST00000280772	T	0.63913	-0.07	6.05	-6.05	0.02172	.	0.483365	0.17261	N	0.180784	T	0.39937	0.1097	N	0.08118	0	0.47214	D	0.999357	B	0.23540	0.087	B	0.28553	0.091	T	0.06826	-1.0805	10	0.87932	D	0	.	16.1838	0.81934	0.0:0.186:0.0:0.814	.	2231	Q12955	ANK3_HUMAN	I	2231	ENSP00000280772:N2231I	ENSP00000280772:N2231I	N	-	2	0	ANK3	61503953	0.031000	0.19500	0.011000	0.14972	0.785000	0.44390	0.111000	0.15458	-1.027000	0.03325	-0.255000	0.11280	AAT	.	.		0.418	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61833947	T	A	61833947	3	1	171	1	0	0	0	0	1	0	0	0	622	1493	52	4	6782	4	ANK3	10	61833947	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10		61833947	73700800	54	25955										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64968996	64968996	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	agccaaggactgggagaattCtattaacaaaacaaaacaaa	7	7	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr10:64968996C>A	ENST00000399262.2	-	9	2913		c.e9-1		JMJD1C_ENST00000399251.1_Splice_Site|JMJD1C_ENST00000402544.1_Splice_Site|JMJD1C_ENST00000542921.1_Splice_Site	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C						blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					TGGGAGAATTCTATTAACAAA	0.418																																					.		Atlas-SNP	.											.	JMJD1C	347	.	0			c.2695-1G>T						.						51	46	48					10																	64968996		1861	4095	5956	SO:0001630	splice_region_variant	221037	exon10			AGAATTCTATTAA	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.2695-1G>T	chr10.hg19:g.64968996C>A		108.0	0.0		102.0	49.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Splice_Site	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.635404	0.87760	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	JMJD1C	64639002	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.326000	0.65875	2.854000	0.98071	0.655000	0.94253	.	.	.		0.418	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	Intron	A	64968996	C	A	64968996	5	1	171	1	0	0	0	0	0	0	1	0	7959	927	32	3	5000	3	JMJD1C	10	64968996	Splice_Site	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	3135049	64968996	70565751	55	25956										
LIPF	8513	hgsc.bcm.edu	37	chr10	90431671	90431671	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cctgttgccactgtgaagtaTacaaaaagccttataaacaa	6	9	0	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr10:90431671T>C	ENST00000238983.4	+	6	664	c.618T>C	c.(616-618)taT>taC	p.Y206Y	LIPF_ENST00000394375.3_Silent_p.Y216Y|LIPF_ENST00000608620.1_Silent_p.Y173Y|LIPF_ENST00000355843.2_Silent_p.Y183Y	NM_004190.3	NP_004181.1	P07098	LIPG_HUMAN	lipase, gastric	206					lipid catabolic process (GO:0016042)|malate metabolic process (GO:0006108)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)	lipid binding (GO:0008289)|malate dehydrogenase activity (GO:0016615)|triglyceride lipase activity (GO:0004806)			NS(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(6)	13		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)	Orlistat(DB01083)	CTGTGAAGTATACAAAAAGCC	0.378																																					p.Y216Y		Atlas-SNP	.											.	LIPF	62	.	0			c.T648C						.						184	187	186					10																	90431671		2203	4300	6503	SO:0001819	synonymous_variant	8513	exon7			GAAGTATACAAAA	X05997	CCDS7389.1, CCDS55718.1, CCDS55719.1, CCDS65896.1	10q23	2005-10-30			ENSG00000182333	ENSG00000182333	3.1.1.3		6622	protein-coding gene	gene with protein product		601980				3304425, 9186906	Standard	NM_004190		Approved	HGL, HLAL	uc010qmt.2	P07098	OTTHUMG00000018695	ENST00000238983.4:c.618T>C	chr10.hg19:g.90431671T>C		136.0	0.0		122.0	65.0	NM_001198829	B7Z723|F5H1P4|Q2M1P6|Q5VXI7|Q5VXI8|Q658L8	Silent	SNP	ENST00000238983.4	hg19	CCDS7389.1																																																																																			.	.		0.378	LIPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049256.1			C	90431671	T	C	90431671	2	2	171	1	0	0	0	0	0	0	0	1	8831	1413	49	2		2	LIPF	10	90431671	Silent	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	25462675	90431671	45103076	56	25957										
ENTPD7	57089	hgsc.bcm.edu	37	chr10	101455831	101455831	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tttcggaggcaactttgcccGgcagcgctacgaagaccttg	12	12	0	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr10:101455831G>C	ENST00000370489.4	+	9	1140	c.962G>C	c.(961-963)cGg>cCg	p.R321P		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	321						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		AACTTTGCCCGGCAGCGCTAC	0.453																																					p.R321P		Atlas-SNP	.											.	ENTPD7	44	.	0			c.G962C						.						109	102	105					10																	101455831		2203	4300	6503	SO:0001583	missense	57089	exon9			TTGCCCGGCAGCG	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.962G>C	chr10.hg19:g.101455831G>C	ENSP00000359520:p.Arg321Pro	166.0	0.0		124.0	61.0	NM_020354	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	hg19	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.575504	0.86645	.	.	ENSG00000198018	ENST00000370489	T	0.12465	2.68	4.85	4.85	0.62838	.	0.066539	0.64402	D	0.000010	T	0.50939	0.1645	H	0.94658	3.565	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.65421	-0.6172	10	0.66056	D	0.02	-12.0459	18.5057	0.90896	0.0:0.0:1.0:0.0	.	321	Q9NQZ7	ENTP7_HUMAN	P	321	ENSP00000359520:R321P	ENSP00000359520:R321P	R	+	2	0	ENTPD7	101445821	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	9.601000	0.98297	2.675000	0.91044	0.655000	0.94253	CGG	.	.		0.453	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354		C	101455831	G	C	101455831	3	2	171	1	0	0	0	0	1	0	0	0	5146	1116	39	4	992	4	ENTPD7	10	101455831	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	11024160	101455831	34078916	57	25958										
CYP17A1	1586	hgsc.bcm.edu	37	chr10	104597106	104597106	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ggtaagcagcaagagagccaCgagctcccacatggtggctg	14	11	0	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr10:104597106C>G	ENST00000369887.3	-	1	184	c.13G>C	c.(13-15)Gtg>Ctg	p.V5L	CYP17A1_ENST00000489268.1_5'UTR|CYP17A1-AS1_ENST00000369884.4_RNA	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	5					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	AAGAGAGCCACGAGCTCCCAC	0.582																																					p.V5L		Atlas-SNP	.											.	CYP17A1	48	.	0			c.G13C						.						39	41	40					10																	104597106		2203	4300	6503	SO:0001583	missense	1586	exon1			GAGCCACGAGCTC	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"Cytochrome P450s"	2593	protein-coding gene	gene with protein product	"Steroid 17-alpha-monooxygenase"	609300	"cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.13G>C	chr10.hg19:g.104597106C>G	ENSP00000358903:p.Val5Leu	56.0	0.0		49.0	14.0	NM_000102	Q5TZV7	Missense_Mutation	SNP	ENST00000369887.3	hg19	CCDS7541.1	.	.	.	.	.	.	.	.	.	.	C	3.576	-0.086682	0.07097	.	.	ENSG00000148795	ENST00000369887	T	0.69175	-0.38	5.27	-2.77	0.05877	.	0.725648	0.13150	N	0.409983	T	0.36690	0.0976	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.32375	-0.9909	10	0.08381	T	0.77	.	9.4631	0.38796	0.2276:0.3558:0.4166:0.0	.	5	P05093	CP17A_HUMAN	L	5	ENSP00000358903:V5L	ENSP00000358903:V5L	V	-	1	0	CYP17A1	104587096	0.000000	0.05858	0.005000	0.12908	0.187000	0.23431	-2.011000	0.01452	-0.115000	0.11915	0.462000	0.41574	GTG	.	.		0.582	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102		G	104597106	C	G	104597106	3	3	171	1	0	0	0	0	1	0	0	0	4149	536	19	4	1545	4	CYP17A1	10	104597106	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	3141275	104597106	30937641	58	25959										
CHST15	51363	hgsc.bcm.edu	37	chr10	125798100	125798100	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aggcgtggatgaagtcctgcGtcagaaacggtggctcgcca	15	10	1	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr10:125798100G>A	ENST00000346248.5	-	5	1763	c.1121C>T	c.(1120-1122)aCg>aTg	p.T374M	CHST15_ENST00000435907.1_Missense_Mutation_p.T374M|CHST15_ENST00000421115.1_Missense_Mutation_p.T374M	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	374					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						GAAGTCCTGCGTCAGAAACGG	0.532																																					p.T374M		Atlas-SNP	.											.	CHST15	134	.	0			c.C1121T						.						127	99	109					10																	125798100		2203	4300	6503	SO:0001583	missense	51363	exon5			TCCTGCGTCAGAA	AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"Sulfotransferases, membrane-bound"	18137	protein-coding gene	gene with protein product	"B cell RAG associated protein", "N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1121C>T	chr10.hg19:g.125798100G>A	ENSP00000333947:p.Thr374Met	187.0	0.0		109.0	33.0	NM_014863	O60338|O60474|Q86VM4	Missense_Mutation	SNP	ENST00000346248.5	hg19	CCDS7638.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.491531	0.26774	.	.	ENSG00000182022	ENST00000346248;ENST00000435907;ENST00000546346;ENST00000421115	T;T;T	0.55413	0.52;0.52;0.52	5.12	2.7	0.31948	Sulfotransferase domain (1);	0.158508	0.56097	D	0.000027	T	0.32376	0.0827	N	0.08118	0	0.28764	N	0.900739	D;B	0.59357	0.985;0.375	P;B	0.46076	0.503;0.114	T	0.17379	-1.0371	10	0.49607	T	0.09	-24.7579	7.4829	0.27415	0.3052:0.0:0.6948:0.0	.	374;374	Q7LFX5-2;Q7LFX5	.;CHSTF_HUMAN	M	374	ENSP00000333947:T374M;ENSP00000402394:T374M;ENSP00000412477:T374M	ENSP00000333947:T374M	T	-	2	0	CHST15	125788090	1.000000	0.71417	0.997000	0.53966	0.043000	0.13939	3.006000	0.49529	0.764000	0.33197	0.561000	0.74099	ACG	.	.		0.532	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892		A	125798100	G	A	125798100	3	1	171	1	0	0	0	0	1	0	0	0	3405	1145	40	1	580	1	CHST15	10	125798100	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	21200994	125798100	9736647	59	25960										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135012081	135012082	+	Splice_Site	DNP	GG	GG	AT													0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tgagctctgctcctcccgtaGggaccagcctgccttggccc							TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr10:135012081_135012082GG>AT	ENST00000304613.3	+	14	2090_2091	c.2069_2070GG>AT	c.(2068-2070)aGG>aAT	p.R690N	KNDC1_ENST00000368572.2_Splice_Site_p.R690N|KNDC1_ENST00000368571.2_Splice_Site_p.R625N			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	690					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TCCTCCCGTAGGGACCAGCCTG	0.703																																					.|p.R690S		Atlas-SNP	.											.	KNDC1	155	.	0			c.2070-1G>A|c.G2070T						.																																			SO:0001630	splice_region_variant	85442	exon14			CCCGTAGGGACCA|CCGTAGGGACCAG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	Exception_encountered	chr10.hg19:g.135012081_135012082delinsAT		231.0	0.0		187.0|186.0	107.0|102.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Splice_Site|Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1																																																																																			.	.		0.703	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	Missense_Mutation	AT	135012082	GG	AT	135012081	5	1	171	1	0	0	0	0	0	0	1	0	8435	1014	35	3	2123	3	KNDC1	10	135012081	Splice_Site	DNP	GG	TCGA-DD-AACU-01A-11D-A40R-10	9213981	135012081	522666	60	25961										
RBMXL2	27288	hgsc.bcm.edu	37	chr11	7110726	7110726	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cggcgttccccatcccggggCgggcccgatgatgacggcgg	17	15	0	2	rs369241566	byFrequency	TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:7110726C>T	ENST00000306904.5	+	1	562	c.375C>T	c.(373-375)ggC>ggT	p.G125G		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	125	Arg/Gly/Pro-rich.					nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CATCCCGGGGCGGGCCCGATG	0.806													C|||	22	0.00439297	0	0	5008	,	,		3255	0.0208		0	False		,,,				2504	0.001				p.G125G		Atlas-SNP	.											.	RBMXL2	47	.	0			c.C375T						.						1	1	1					11																	7110726		516	1275	1791	SO:0001819	synonymous_variant	27288	exon1			CCGGGGCGGGCCC	AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"RNA binding motif (RRM) containing"	17886	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein G T"	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.375C>T	chr11.hg19:g.7110726C>T		4.0	0.0		22.0	14.0	NM_014469	Q6PEZ2|Q9NQU0	Silent	SNP	ENST00000306904.5	hg19	CCDS7777.1																																																																																			.	.		0.806	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469		T	7110726	C	T	7110726	2	4	171	1	0	0	0	0	0	0	0	1	13169	755	27	1		1	RBMXL2	11	7110726	Silent	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10		7110726	127895790	61	25962										
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7618805	7618805	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gaacaggtgagtgtcctcacAgaccaagtagaagcccaggg	13	10	1	3			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:7618805A>G	ENST00000299492.4	+	5	775	c.387A>G	c.(385-387)acA>acG	p.T129T	PPFIBP2_ENST00000533792.1_5'UTR|PPFIBP2_ENST00000528883.1_Silent_p.T17T	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	129					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		GTGTCCTCACAGACCAAGTAG	0.512																																					p.T129T		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.A387G						.						64	59	61					11																	7618805		2201	4296	6497	SO:0001819	synonymous_variant	8495	exon5			CCTCACAGACCAA	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"Sterile alpha motif (SAM) domain containing"	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.387A>G	chr11.hg19:g.7618805A>G		92.0	0.0		87.0	37.0	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Silent	SNP	ENST00000299492.4	hg19	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	A	10.64	1.406954	0.25378	.	.	ENSG00000166387	ENST00000524548	.	.	.	5.5	4.33	0.51752	.	.	.	.	.	T	0.57213	0.2038	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55256	-0.8169	4	.	.	.	-12.8079	7.5715	0.27911	0.6792:0.0:0.0:0.3208	.	.	.	.	R	84	.	.	Q	+	2	0	PPFIBP2	7575381	0.578000	0.26717	1.000000	0.80357	0.997000	0.91878	-0.108000	0.10857	2.102000	0.63906	0.533000	0.62120	CAG	.	.		0.512	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		G	7618805	A	G	7618805	2	3	171	1	0	0	0	0	0	0	0	1	12323	175	7	2		2	PPFIBP2	11	7618805	Silent	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	508079	7618805	127387711	62	25963										
PATL1	219988	hgsc.bcm.edu	37	chr11	59423093	59423093	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gaaggcacggaagcctggtgCtgggggaagcatctgcccaa	16	10	1	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:59423093C>T	ENST00000300146.9	-	8	1018	c.934G>A	c.(934-936)Gca>Aca	p.A312T		NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	312	Involved in RNA-binding.|Involved in nuclear foci localization.|Pro-rich.|Region N; interaction with decapping machinery.				cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						AAGCCTGGTGCTGGGGGAAGC	0.587																																					p.A312T		Atlas-SNP	.											.	PATL1	92	.	0			c.G934A						.						57	60	59					11																	59423093		1982	4160	6142	SO:0001583	missense	219988	exon8			CTGGTGCTGGGGG	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.934G>A	chr11.hg19:g.59423093C>T	ENSP00000300146:p.Ala312Thr	88.0	0.0		81.0	30.0	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Missense_Mutation	SNP	ENST00000300146.9	hg19	CCDS44613.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.900898	0.52227	.	.	ENSG00000166889	ENST00000300146;ENST00000428532	T	0.44482	0.92	4.86	3.93	0.45458	.	0.066293	0.56097	D	0.000025	T	0.21674	0.0522	N	0.08118	0	0.32355	N	0.557926	B;B	0.06786	0.001;0.001	B;B	0.12156	0.004;0.007	T	0.14282	-1.0478	10	0.15499	T	0.54	-12.3094	12.5459	0.56199	0.0:0.917:0.0:0.083	.	282;312	Q86TB9-4;Q86TB9	.;PATL1_HUMAN	T	312;282	ENSP00000300146:A312T	ENSP00000300146:A312T	A	-	1	0	PATL1	59179669	0.988000	0.35896	1.000000	0.80357	0.997000	0.91878	1.890000	0.39728	2.398000	0.81561	0.563000	0.77884	GCA	.	.		0.587	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716		T	59423093	C	T	59423093	3	4	171	1	0	0	0	0	1	0	0	0	11484	797	28	3	1426	3	PATL1	11	59423093	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	51804288	59423093	75583423	63	25964										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62288775	62288782	+	Frame_Shift_Del	DEL	TTGGACCC	TTGGACCC	-													0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	catctctggcatcttgaactTtggacccttgagttttgcat							TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	TTGGACCC	TTGGACCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:62288775_62288782delTTGGACCC	ENST00000378024.4	-	5	13381_13388	c.13107_13114delGGGTCCAA	c.(13105-13116)aagggtccaaagfs	p.KGPK4369fs	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4369					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				ATCTTGAACTTTGGACCCTTGAGTTTTG	0.466																																					p.4370_4372del		Atlas-INDEL	.											.	AHNAK	532	.	0			c.13108_13115del						.																																			SO:0001589	frameshift_variant	79026	exon5			.	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.13107_13114delGGGTCCAA	chr11.hg19:g.62288775_62288782delTTGGACCC	ENSP00000367263:p.Lys4369fs	131.0	0.0		150.0	13.0	NM_001620	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.466	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		-	62288782	TTGGACCC	-	62288775	7	5	171	1	0	1	0	1	0	0	0	0	414	1850	64	0	4678	0	AHNAK	11	62288775	Frame_Shift_Del	DEL	TTGGACCC	TCGA-DD-AACU-01A-11D-A40R-10	2865682	62288775	72717741	64	25965										
SLC22A10	387775	hgsc.bcm.edu	37	chr11	63071682	63071682	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cattgaactcatccccactgTtctcaggtataagagataca	6	11	2	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:63071682T>C	ENST00000332793.6	+	8	1390	c.1388T>C	c.(1387-1389)gTt>gCt	p.V463A	SLC22A10_ENST00000544661.1_Missense_Mutation_p.F262L|SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000526800.1_Intron	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	463						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	ATCCCCACTGTTCTCAGGTAT	0.443																																					p.V463A		Atlas-SNP	.											.	SLC22A10	79	.	0			c.T1388C						.						170	168	169					11																	63071682		1952	4182	6134	SO:0001583	missense	387775	exon8			CCACTGTTCTCAG	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.1388T>C	chr11.hg19:g.63071682T>C	ENSP00000327569:p.Val463Ala	45.0	0.0		64.0	18.0	NM_001039752	Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	hg19	CCDS41661.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.53|10.53	1.377226|1.377226	0.24944|0.24944	.|.	.|.	ENSG00000184999|ENSG00000184999	ENST00000544661|ENST00000332793	T|T	0.67865|0.56941	-0.29|0.43	3.05|3.05	-0.605|-0.605	0.11623|0.11623	.|Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.|0.277066	.|0.29558	.|N	.|0.011811	T|T	0.49253|0.49253	0.1546|0.1546	M|M	0.83692|0.83692	2.655|2.655	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.24092	0.0|0.097	B|B	0.01281|0.24974	0.0|0.057	T|T	0.50276|0.50276	-0.8847|-0.8847	9|10	0.46703|0.62326	T|D	0.11|0.03	.|.	5.5731|5.5731	0.17208|0.17208	0.0:0.4515:0.0:0.5485|0.0:0.4515:0.0:0.5485	.|.	257|463	E9PJB1|Q63ZE4	.|S22AA_HUMAN	L|A	262|463	ENSP00000445667:F262L|ENSP00000327569:V463A	ENSP00000433817:F257L|ENSP00000327569:V463A	F|V	+|+	1|2	0|0	SLC22A10|SLC22A10	62828258|62828258	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.006000|0.006000	0.05464|0.05464	0.285000|0.285000	0.18883|0.18883	0.024000|0.024000	0.15214|0.15214	0.472000|0.472000	0.43445|0.43445	TTC|GTT	.	.		0.443	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		C	63071682	T	C	63071682	3	2	171	1	0	0	0	0	1	0	0	0	14456	1725	60	2	1418	2	SLC22A10	11	63071682	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	782907	63071682	71934834	65	25966										
CATSPER1	117144	hgsc.bcm.edu	37	chr11	65784577	65784577	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cgatgacggctgcctgggagCggaacttctgctgctcctgc	14	13	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:65784577C>T	ENST00000312106.5	-	11	2407	c.2270G>A	c.(2269-2271)cGc>cAc	p.R757H		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	757					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						TGCCTGGGAGCGGAACTTCTG	0.647																																					p.R757H		Atlas-SNP	.											.	CATSPER1	101	.	0			c.G2270A						.						51	44	46					11																	65784577		2201	4296	6497	SO:0001583	missense	117144	exon11			TGGGAGCGGAACT	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"Voltage-gated ion channels / Cation channels, sperm associated"	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.2270G>A	chr11.hg19:g.65784577C>T	ENSP00000309052:p.Arg757His	44.0	0.0		56.0	20.0	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	hg19	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.981445	0.34942	.	.	ENSG00000175294	ENST00000312106	D	0.97480	-4.4	5.39	3.48	0.39840	.	0.000000	0.32769	U	0.005673	D	0.95076	0.8405	L	0.32530	0.975	0.27891	N	0.939311	D	0.67145	0.996	P	0.53689	0.732	D	0.90115	0.4195	10	0.48119	T	0.1	-21.4499	7.1435	0.25570	0.0:0.7343:0.1735:0.0922	.	757	Q8NEC5	CTSR1_HUMAN	H	757	ENSP00000309052:R757H	ENSP00000309052:R757H	R	-	2	0	CATSPER1	65541153	0.998000	0.40836	0.709000	0.30452	0.268000	0.26511	2.080000	0.41586	0.629000	0.30376	0.644000	0.83932	CGC	.	.		0.647	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		T	65784577	C	T	65784577	3	4	171	1	0	0	0	0	1	0	0	0	2689	768	27	1	80	1	CATSPER1	11	65784577	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	2712895	65784577	69221939	66	25967										
FAT3	120114	hgsc.bcm.edu	37	chr11	92616054	92616054	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gtggtggtacccaatatccaGgctggccactcctacgtggg	13	12	0	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:92616054G>T	ENST00000298047.6	+	23	12449	c.12432G>T	c.(12430-12432)caG>caT	p.Q4144H	FAT3_ENST00000533797.1_Missense_Mutation_p.Q479H|FAT3_ENST00000409404.2_Missense_Mutation_p.Q4144H|FAT3_ENST00000525166.1_Missense_Mutation_p.Q3994H			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4144					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CCAATATCCAGGCTGGCCACT	0.612										TCGA Ovarian(4;0.039)																											p.Q4144H		Atlas-SNP	.											.	FAT3	1822	.	0			c.G12432T						.						62	81	75					11																	92616054		2056	4196	6252	SO:0001583	missense	120114	exon23			TATCCAGGCTGGC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12432G>T	chr11.hg19:g.92616054G>T	ENSP00000298047:p.Gln4144His	110.0	0.0		95.0	25.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	17.57	3.422376	0.62622	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;D	0.86230	-0.91;-0.91;-0.91;-2.09	5.85	2.4	0.29515	.	.	.	.	.	D	0.87637	0.6227	L	0.53249	1.67	0.80722	D	1	D;D	0.65815	0.995;0.957	P;P	0.58172	0.834;0.719	D	0.84095	0.0392	9	0.38643	T	0.18	.	7.0344	0.24985	0.225:0.1497:0.6253:0.0	.	4144;4144	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	H	4144;4144;3994;479	ENSP00000298047:Q4144H;ENSP00000387040:Q4144H;ENSP00000432586:Q3994H;ENSP00000436399:Q479H	ENSP00000298047:Q4144H	Q	+	3	2	FAT3	92255702	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.357000	0.44125	0.757000	0.33036	0.655000	0.94253	CAG	.	.		0.612	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92616054	G	T	92616054	3	4	171	1	0	0	0	0	1	0	0	0	5699	991	35	3	12522	3	FAT3	11	92616054	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	26831477	92616054	42390462	67	25968										
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93796813	93796813	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gccaactgcctgacctgggtGtaccattcgcacatcgacgc	10	15	0	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:93796813G>A	ENST00000315765.9	+	3	563	c.555G>A	c.(553-555)gtG>gtA	p.V185V		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	185	Plastocyanin-like 1.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TGACCTGGGTGTACCATTCGC	0.532																																					p.V185V		Atlas-SNP	.											HEPHL1,right_upper_lobe,carcinoma,0,1	HEPHL1	144	.	0			c.G555A						.						104	104	104					11																	93796813		1974	4167	6141	SO:0001819	synonymous_variant	341208	exon3			CTGGGTGTACCAT	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.555G>A	chr11.hg19:g.93796813G>A		154.0	0.0		170.0	10.0	NM_001098672	Q3C1W7	Silent	SNP	ENST00000315765.9	hg19	CCDS44710.1																																																																																			.	.		0.532	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		A	93796813	G	A	93796813	2	1	171	1	0	0	0	0	0	0	0	1	7064	1364	48	3		3	HEPHL1	11	93796813	Silent	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	1180759	93796813	41209703	68	25969										
MMP20	9313	hgsc.bcm.edu	37	chr11	102487623	102487623	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	acatcaggaactccacagcgAggcttcttgatcacgttcat	8	12	4	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:102487623A>T	ENST00000260228.2	-	2	306	c.294T>A	c.(292-294)ccT>ccA	p.P98P	RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	88					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	CTCCACAGCGAGGCTTCTTGA	0.448																																					p.P98P		Atlas-SNP	.											.	MMP20	52	.	0			c.T294A						.						160	137	145					11																	102487623		2203	4299	6502	SO:0001819	synonymous_variant	9313	exon2			ACAGCGAGGCTTC	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"enamelysin"	604629	"matrix metalloproteinase 20 (enamelysin)"			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.294T>A	chr11.hg19:g.102487623A>T		170.0	0.0		198.0	78.0	NM_004771	D3DUA8|Q9H3Q0	Silent	SNP	ENST00000260228.2	hg19	CCDS8318.1																																																																																			.	.		0.448	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1			T	102487623	A	T	102487623	2	4	171	1	0	0	0	0	0	0	0	1	9668	291	11	4		4	MMP20	11	102487623	Silent	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	8690810	102487623	32518893	69	25970										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103091404	103091404	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aaacattaagcccgaatcacTttcagaaattcgctcactac	4	12	3	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:103091404T>C	ENST00000375735.2	+	57	9143	c.8999T>C	c.(8998-9000)cTt>cCt	p.L3000P	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.L3000P	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3000	Stalk. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CCCGAATCACTTTCAGAAATT	0.353																																					p.L3000P		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T8999C						.						104	103	103					11																	103091404		1866	4112	5978	SO:0001583	missense	79659	exon57			AATCACTTTCAGA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.8999T>C	chr11.hg19:g.103091404T>C	ENSP00000364887:p.Leu3000Pro	118.0	0.0		143.0	6.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.491429	0.84962	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	D;D	0.81908	-1.55;-1.55	5.99	5.99	0.97316	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.49916	U	0.000136	D	0.93032	0.7782	M	0.90922	3.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94346	0.7575	10	0.87932	D	0	.	16.4943	0.84223	0.0:0.0:0.0:1.0	.	3000;3000	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	P	3000	ENSP00000364887:L3000P;ENSP00000381167:L3000P	ENSP00000364887:L3000P	L	+	2	0	DYNC2H1	102596614	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	8.040000	0.89188	2.291000	0.77112	0.533000	0.62120	CTT	.	.		0.353	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103091404	T	C	103091404	3	2	171	1	0	0	0	0	1	0	0	0	4848	1609	56	2	9225	2	DYNC2H1	11	103091404	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	603781	103091404	31915112	70	25971										
KIAA1826	84437	hgsc.bcm.edu	37	chr11	105881275	105881275	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	atctgccacattttgccagtCaaaatttgcatcatttcgga	6	10	3	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:105881275C>T	ENST00000301919.4	-	2	1785	c.370G>A	c.(370-372)Gac>Aac	p.D124N	MSANTD4_ENST00000529805.1_5'Flank	NM_032424.1	NP_115800.1	Q8NCY6	MSD4_HUMAN	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	124						nucleus (GO:0005634)											TTTTGCCAGTCAAAATTTGCA	0.453																																					p.D124N		Atlas-SNP	.											.	.	.	.	0			c.G370A						.						138	141	140					11																	105881275		2201	4299	6500	SO:0001583	missense	84437	exon2			GCCAGTCAAAATT	AB058729	CCDS31663.1	11q22	2012-03-13	2012-03-13	2012-03-13	ENSG00000170903	ENSG00000170903			29383	protein-coding gene	gene with protein product			"KIAA1826"	KIAA1826			Standard	XM_005271697		Approved		uc001piz.3	Q8NCY6	OTTHUMG00000166240	ENST00000301919.4:c.370G>A	chr11.hg19:g.105881275C>T	ENSP00000304713:p.Asp124Asn	104.0	0.0		147.0	10.0	NM_032424	Q96JK1|Q96JZ3|Q9H2N4	Missense_Mutation	SNP	ENST00000301919.4	hg19	CCDS31663.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.790278	0.70337	.	.	ENSG00000170903	ENST00000301919;ENST00000530788	.	.	.	5.88	5.88	0.94601	.	0.157513	0.53938	D	0.000050	T	0.51449	0.1675	L	0.36672	1.1	0.39787	D	0.972385	B	0.31893	0.345	B	0.27170	0.077	T	0.53056	-0.8492	9	0.56958	D	0.05	-20.2628	20.2139	0.98290	0.0:1.0:0.0:0.0	.	124	Q8NCY6	K1826_HUMAN	N	124	.	ENSP00000304713:D124N	D	-	1	0	KIAA1826	105386485	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.697000	0.61782	2.782000	0.95742	0.561000	0.74099	GAC	.	.		0.453	MSANTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388619.1	NM_032424		T	105881275	C	T	105881275	3	4	171	1	0	0	0	0	1	0	0	0	8269	826	29	3	675	3	KIAA1826	11	105881275	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	2789871	105881275	29125241	71	25972										
TMEM45B	120224	hgsc.bcm.edu	37	chr11	129722516	129722516	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	attactatcagcgtctcgagAtcgtcgaagccgcaattagg	10	10	2	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr11:129722516A>G	ENST00000524567.1	+	2	420	c.139A>G	c.(139-141)Atc>Gtc	p.I47V	TMEM45B_ENST00000281441.3_Missense_Mutation_p.I47V			Q96B21	TM45B_HUMAN	transmembrane protein 45B	47						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)		GCGTCTCGAGATCGTCGAAGC	0.483																																					p.I47V		Atlas-SNP	.											.	TMEM45B	25	.	0			c.A139G						.						142	131	135					11																	129722516		2201	4297	6498	SO:0001583	missense	120224	exon2			CTCGAGATCGTCG	AK098106	CCDS8482.1	11q24.3	2008-02-05				ENSG00000151715			25194	protein-coding gene	gene with protein product						12477932	Standard	NM_138788		Approved	BC016153, FLJ40787	uc001qfe.1	Q96B21		ENST00000524567.1:c.139A>G	chr11.hg19:g.129722516A>G	ENSP00000436293:p.Ile47Val	170.0	0.0		157.0	63.0	NM_138788	A8K2L8	Missense_Mutation	SNP	ENST00000524567.1	hg19	CCDS8482.1	.	.	.	.	.	.	.	.	.	.	A	7.217	0.596632	0.13875	.	.	ENSG00000151715	ENST00000281441;ENST00000524567	T;T	0.29397	1.57;1.57	5.64	1.76	0.24704	.	0.466508	0.25388	N	0.031025	T	0.22742	0.0549	L	0.52905	1.665	0.27196	N	0.960285	B	0.09022	0.002	B	0.11329	0.006	T	0.21895	-1.0232	10	0.16896	T	0.51	0.1149	5.7621	0.18207	0.4164:0.4253:0.1583:0.0	.	47	Q96B21	TM45B_HUMAN	V	47	ENSP00000281441:I47V;ENSP00000436293:I47V	ENSP00000281441:I47V	I	+	1	0	TMEM45B	129227726	0.792000	0.28813	0.892000	0.35008	0.034000	0.12701	-0.134000	0.10436	0.389000	0.25086	0.533000	0.62120	ATC	.	.		0.483	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1	NM_138788		G	129722516	A	G	129722516	3	3	171	1	0	0	0	0	1	0	0	0	16185	333	12	2	141	2	TMEM45B	11	129722516	Missense_Mutation	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	23841241	129722516	5284000	72	25973										
C1RL	51279	hgsc.bcm.edu	37	chr12	7261740	7261740	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gcctttggagtgagggcttcTccagagatatttcccccaca	10	12	1	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr12:7261740T>A	ENST00000266542.4	-	1	129	c.37A>T	c.(37-39)Aga>Tga	p.R13*	C1RL-AS1_ENST00000435921.2_RNA|C1RL_ENST00000545280.1_Nonsense_Mutation_p.R13*|C1RL_ENST00000545337.1_Nonsense_Mutation_p.R13*|C1RL-AS1_ENST00000541775.1_RNA|C1RL-AS1_ENST00000536679.1_RNA|C1RL-AS1_ENST00000382215.3_RNA|C1RL_ENST00000544702.1_Nonsense_Mutation_p.R13*	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	13					complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TGAGGGCTTCTCCAGAGATAT	0.602											OREG0021648	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R13X		Atlas-SNP	.											.	C1RL	39	.	0			c.A37T						.						46	37	40					12																	7261740		2203	4300	6503	SO:0001587	stop_gained	51279	exon1			GGCTTCTCCAGAG	AF178985	CCDS8573.1, CCDS73431.1	12p13.31	2008-02-05				ENSG00000139178			21265	protein-coding gene	gene with protein product		608974				12838346	Standard	XM_005253385		Approved	C1r-LP, C1RL1	uc001qsn.3	Q9NZP8		ENST00000266542.4:c.37A>T	chr12.hg19:g.7261740T>A	ENSP00000266542:p.Arg13*	88.0	0.0	640	73.0	25.0	NM_016546	Q53GX9	Nonsense_Mutation	SNP	ENST00000266542.4	hg19	CCDS8573.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.152291	0.57259	.	.	ENSG00000139178	ENST00000545280;ENST00000266542;ENST00000396661;ENST00000544702;ENST00000543933;ENST00000545337	.	.	.	3.67	-0.00687	0.14011	.	0.776606	0.11337	N	0.574428	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.9941	0.19483	0.0:0.3373:0.0:0.6627	.	.	.	.	X	13	.	ENSP00000266542:R13X	R	-	1	2	C1RL	7153016	0.356000	0.24930	0.867000	0.34043	0.049000	0.14656	-0.024000	0.12435	0.004000	0.14682	0.317000	0.21355	AGA	.	.		0.602	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	NM_016546		A	7261740	T	A	7261740	4	1	171	1	0	0	0	0	0	1	0	0	1975	1559	54	4	1450	4	C1RL	12	7261740	Nonsense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10		7261740	126590155	73	25974										
ACSM4	341392	hgsc.bcm.edu	37	chr12	7479610	7479610	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gtcttagctgcaccctttaaGtcctacaacccagagaaatt	6	12	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr12:7479610G>T	ENST00000399422.4	+	12	1623	c.1575G>T	c.(1573-1575)aaG>aaT	p.K525N		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	525					acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty-acyl-CoA synthase activity (GO:0004321)|metal ion binding (GO:0046872)			endometrium(6)|kidney(1)|lung(14)	21						CACCCTTTAAGTCCTACAACC	0.373																																					p.K525N		Atlas-SNP	.											.	ACSM4	98	.	0			c.G1575T						.						72	65	67					12																	7479610		1839	4099	5938	SO:0001583	missense	341392	exon12			CTTTAAGTCCTAC		CCDS44825.1	12p13.31	2008-06-12			ENSG00000215009	ENSG00000215009		"Acyl-CoA synthetase family"	32016	protein-coding gene	gene with protein product	"similar to olfactory specific medium-chain acyl CoA synthetase"	614360				17762044	Standard	NM_001080454		Approved		uc001qsx.1	P0C7M7	OTTHUMG00000154975	ENST00000399422.4:c.1575G>T	chr12.hg19:g.7479610G>T	ENSP00000382349:p.Lys525Asn	90.0	0.0		87.0	24.0	NM_001080454	A8MTI6	Missense_Mutation	SNP	ENST00000399422.4	hg19	CCDS44825.1	.	.	.	.	.	.	.	.	.	.	G	2.590	-0.295463	0.05532	.	.	ENSG00000215009	ENST00000399422	T	0.10763	2.84	2.55	-1.63	0.08345	.	0.390868	0.18012	U	0.154528	T	0.07413	0.0187	L	0.46670	1.46	0.33804	D	0.627097	B	0.24533	0.105	B	0.21917	0.037	T	0.24119	-1.0169	10	0.25751	T	0.34	-11.0269	4.101	0.10014	0.3618:0.2102:0.428:0.0	.	525	P0C7M7	ACSM4_HUMAN	N	525	ENSP00000382349:K525N	ENSP00000382349:K525N	K	+	3	2	ACSM4	7370877	0.001000	0.12720	0.924000	0.36721	0.878000	0.50629	-0.018000	0.12568	-0.287000	0.09064	-1.012000	0.02466	AAG	.	.		0.373	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454		T	7479610	G	T	7479610	3	4	171	1	0	0	0	0	1	0	0	0	186	1020	36	3	1621	3	ACSM4	12	7479610	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	217870	7479610	126372285	74	25975										
WIF1	11197	hgsc.bcm.edu	37	chr12	65471574	65471574	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cagagggacattgacggttgGatctgccatgatgcctttat	12	8	1	3			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr12:65471574G>T	ENST00000286574.4	-	3	723	c.349C>A	c.(349-351)Cca>Aca	p.P117T		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	117	WIF. {ECO:0000255|PROSITE- ProRule:PRU00222}.				multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		TTGACGGTTGGATCTGCCATG	0.458			T	HMGA2	pleomorphic salivary gland adenoma																																p.P117T	Esophageal Squamous(148;1595 1816 48559 49439 49664)	Atlas-SNP	.		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	WIF1	96	.	0			c.C349A						.						126	106	113					12																	65471574		2203	4300	6503	SO:0001583	missense	11197	exon3			CGGTTGGATCTGC	AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.349C>A	chr12.hg19:g.65471574G>T	ENSP00000286574:p.Pro117Thr	115.0	0.0		130.0	47.0	NM_007191	Q6UXI1|Q8WVG4	Missense_Mutation	SNP	ENST00000286574.4	hg19	CCDS8971.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.403689	0.83230	.	.	ENSG00000156076	ENST00000286574;ENST00000546001	T;T	0.58940	0.3;0.3	5.35	5.35	0.76521	WIF domain (4);	0.000000	0.85682	D	0.000000	T	0.73837	0.3638	L	0.58810	1.83	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71431	-0.4595	9	.	.	.	.	19.4405	0.94817	0.0:0.0:1.0:0.0	.	117	Q9Y5W5	WIF1_HUMAN	T	117;55	ENSP00000286574:P117T;ENSP00000442063:P55T	.	P	-	1	0	WIF1	63757841	1.000000	0.71417	0.999000	0.59377	0.882000	0.50991	7.700000	0.84556	2.689000	0.91719	0.650000	0.86243	CCA	.	.		0.458	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2			T	65471574	G	T	65471574	3	4	171	1	0	0	0	0	1	0	0	0	17381	1174	41	3	822	3	WIF1	12	65471574	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	57991964	65471574	68380321	75	25976										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70986218	70986218	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gatggtccctttgtgagacaGggtgatattgtaagaatcca	12	6	0	3			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr12:70986218G>T	ENST00000261266.5	-	5	999	c.970C>A	c.(970-972)Ctg>Atg	p.L324M	PTPRB_ENST00000538708.1_Missense_Mutation_p.L324M|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000451516.2_Missense_Mutation_p.L324M|PTPRB_ENST00000334414.6_Missense_Mutation_p.L542M|PTPRB_ENST00000550857.1_Missense_Mutation_p.L324M|PTPRB_ENST00000551525.1_Missense_Mutation_p.L541M|PTPRB_ENST00000550358.1_Missense_Mutation_p.L542M	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	324	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TTGTGAGACAGGGTGATATTG	0.418																																					p.L542M		Atlas-SNP	.											.	PTPRB	676	.	0			c.C1624A						.						71	65	67					12																	70986218		1853	4094	5947	SO:0001583	missense	5787	exon7			GAGACAGGGTGAT	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.970C>A	chr12.hg19:g.70986218G>T	ENSP00000261266:p.Leu324Met	165.0	0.0		140.0	49.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.806807	0.31961	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.58652	0.32;0.32;0.32;0.32;0.32;0.32;0.32;0.32	5.96	1.58	0.23477	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.142736	0.47455	D	0.000231	T	0.73567	0.3603	M	0.87269	2.87	0.30963	N	0.723477	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;0.999;0.998;0.999;0.995	T	0.71381	-0.4610	10	0.52906	T	0.07	.	6.9284	0.24428	0.325:0.1225:0.5525:0.0	.	324;324;421;542;541;542;324;542	P23467-2;F5H3G6;Q6ZR19;Q6ZTX7;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;.;PTPRB_HUMAN;.	M	542;324;542;542;324;324;324;541;421	ENSP00000334928:L542M;ENSP00000393028:L324M;ENSP00000448058:L542M;ENSP00000438927:L324M;ENSP00000447302:L324M;ENSP00000261266:L324M;ENSP00000448349:L541M;ENSP00000446982:L421M	ENSP00000261266:L324M	L	-	1	2	PTPRB	69272485	0.996000	0.38824	0.874000	0.34290	0.084000	0.17831	0.989000	0.29629	0.422000	0.26005	0.655000	0.94253	CTG	.	.		0.418	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70986218	G	T	70986218	3	4	171	1	0	0	0	0	1	0	0	0	12811	991	35	3	5135	3	PTPRB	12	70986218	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	5514644	70986218	62865677	76	25977										
SLC41A2	84102	hgsc.bcm.edu	37	chr12	105289099	105289099	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	taggttccacttttcaatggGtgaatccatcttcccaatat	6	10	2	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr12:105289099G>C	ENST00000258538.3	-	3	815	c.688C>G	c.(688-690)Ccc>Gcc	p.P230A		NM_032148.3	NP_115524.3	Q96JW4	S41A2_HUMAN	solute carrier family 41 (magnesium transporter), member 2	230					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	22						TTTTCAATGGGTGAATCCATC	0.353																																					p.P230A	Esophageal Squamous(195;176 2919 4272 35572)	Atlas-SNP	.											.	SLC41A2	66	.	0			c.C688G						.						143	129	134					12																	105289099		2203	4300	6503	SO:0001583	missense	84102	exon3			CAATGGGTGAATC	BC036734	CCDS9100.2	12q24.11	2013-07-17	2013-07-17		ENSG00000136052	ENSG00000136052		"Solute carriers"	31045	protein-coding gene	gene with protein product		610802	"solute carrier family 41, member 2"				Standard	NM_032148		Approved	DKFZP434K0427	uc001tla.3	Q96JW4	OTTHUMG00000156965	ENST00000258538.3:c.688C>G	chr12.hg19:g.105289099G>C	ENSP00000258538:p.Pro230Ala	89.0	0.0		85.0	5.0	NM_032148	Q3KP68|Q9H0E5	Missense_Mutation	SNP	ENST00000258538.3	hg19	CCDS9100.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.78|14.78	2.637265|2.637265	0.47049|0.47049	.|.	.|.	ENSG00000136052|ENSG00000136052	ENST00000437220|ENST00000258538	.|T	.|0.21932	.|1.98	5.65|5.65	4.77|4.77	0.60923|0.60923	.|MgtE magnesium transporter, integral membrane (1);	.|0.182059	.|0.49305	.|D	.|0.000155	T|T	0.13586|0.13586	0.0329|0.0329	N|N	0.20685|0.20685	0.6|0.6	0.80722|0.80722	D|D	1|1	.|P	.|0.40000	.|0.698	.|B	.|0.37550	.|0.253	T|T	0.08126|0.08126	-1.0737|-1.0737	5|10	.|0.14656	.|T	.|0.56	-11.0024|-11.0024	14.5831|14.5831	0.68305|0.68305	0.0705:0.0:0.9295:0.0|0.0705:0.0:0.9295:0.0	.|.	.|230	.|Q96JW4	.|S41A2_HUMAN	Q|A	85|230	.|ENSP00000258538:P230A	.|ENSP00000258538:P230A	H|P	-|-	3|1	2|0	SLC41A2|SLC41A2	103813229|103813229	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	8.886000|8.886000	0.92447|0.92447	1.391000|1.391000	0.46566|0.46566	0.591000|0.591000	0.81541|0.81541	CAC|CCC	.	.		0.353	SLC41A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346850.3	NM_032148		C	105289099	G	C	105289099	3	2	171	1	0	0	0	0	1	0	0	0	14645	1261	44	4	1065	4	SLC41A2	12	105289099	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	34302881	105289099	28562796	77	25978										
PIWIL1	9271	hgsc.bcm.edu	37	chr12	130847644	130847644	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aacactggtgaactacgaagTgccacagtttttggattgtc	10	8	0	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr12:130847644T>C	ENST00000245255.3	+	18	2422	c.2150T>C	c.(2149-2151)gTg>gCg	p.V717A		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	717	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		AACTACGAAGTGCCACAGTTT	0.438																																					p.V717A		Atlas-SNP	.											.	PIWIL1	157	.	0			c.T2150C						.						111	110	111					12																	130847644		2203	4300	6503	SO:0001583	missense	9271	exon18			ACGAAGTGCCACA	AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.2150T>C	chr12.hg19:g.130847644T>C	ENSP00000245255:p.Val717Ala	142.0	0.0		151.0	7.0	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	hg19	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.150177	0.57151	.	.	ENSG00000125207	ENST00000245255	T	0.37235	1.21	5.71	5.71	0.89125	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.112361	0.64402	D	0.000011	T	0.62097	0.2400	M	0.82517	2.595	0.58432	D	0.999998	P;D	0.64830	0.68;0.994	P;D	0.66847	0.562;0.947	T	0.65569	-0.6136	10	0.48119	T	0.1	-12.0576	15.1655	0.72821	0.0:0.0:0.0:1.0	.	717;717	Q96J94;Q96J94-2	PIWL1_HUMAN;.	A	717	ENSP00000245255:V717A	ENSP00000245255:V717A	V	+	2	0	PIWIL1	129413597	1.000000	0.71417	0.909000	0.35828	0.014000	0.08584	7.670000	0.83925	2.176000	0.68965	0.383000	0.25322	GTG	.	.		0.438	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			C	130847644	T	C	130847644	3	2	171	1	0	0	0	0	1	0	0	0	11966	1696	59	2	2216	2	PIWIL1	12	130847644	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	25558545	130847644	3004251	78	25979										
SACS	26278	hgsc.bcm.edu	37	chr13	23909599	23909599	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ttcagagtcctcagtatccaTagtataggttatttgttgaa	8	6	2	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr13:23909599T>C	ENST00000382292.3	-	9	8689	c.8416A>G	c.(8416-8418)Atg>Gtg	p.M2806V	SACS_ENST00000402364.1_Missense_Mutation_p.M2056V|SACS_ENST00000382298.3_Missense_Mutation_p.M2806V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2806					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TCAGTATCCATAGTATAGGTT	0.348																																					p.M2806V		Atlas-SNP	.											.	SACS	871	.	0			c.A8416G						.						105	100	102					13																	23909599		2203	4299	6502	SO:0001583	missense	26278	exon10			TATCCATAGTATA	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.8416A>G	chr13.hg19:g.23909599T>C	ENSP00000371729:p.Met2806Val	44.0	0.0		44.0	24.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	18.27	3.587158	0.66105	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.86627	-1.95;-2.15;-1.95	5.65	3.15	0.36227	.	0.040409	0.85682	D	0.000000	T	0.74520	0.3727	N	0.15975	0.35	0.30551	N	0.76544	P	0.38565	0.637	B	0.37047	0.24	T	0.71623	-0.4537	10	0.48119	T	0.1	.	8.4391	0.32805	0.0:0.0683:0.132:0.7997	.	2806	Q9NZJ4	SACS_HUMAN	V	2806;2056;2806	ENSP00000371729:M2806V;ENSP00000385844:M2056V;ENSP00000371735:M2806V	ENSP00000371729:M2806V	M	-	1	0	SACS	22807599	1.000000	0.71417	0.961000	0.40146	0.983000	0.72400	4.849000	0.62882	0.403000	0.25479	0.454000	0.30748	ATG	.	.		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23909599	T	C	23909599	3	2	171	1	0	0	0	0	1	0	0	0	13819	1406	49	2	5327	2	SACS	13	23909599	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10		23909599	91260279	79	25980										
OR4K1	79544	hgsc.bcm.edu	37	chr14	20404228	20404228	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	agcctctgcactacagtacaAttatgaaccggaggctctgt	9	11	2	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr14:20404228A>T	ENST00000285600.4	+	1	462	c.403A>T	c.(403-405)Att>Ttt	p.I135F		NM_001004063.2	NP_001004063.2	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K, member 1	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(24)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		CTACAGTACAATTATGAACCG	0.438																																					p.I135F		Atlas-SNP	.											.	OR4K1	108	.	0			c.A403T						.						134	128	130					14																	20404228		2203	4300	6503	SO:0001583	missense	79544	exon1			AGTACAATTATGA		CCDS32025.1	14q11.2	2013-09-23			ENSG00000155249	ENSG00000155249		"GPCR / Class A : Olfactory receptors"	14726	protein-coding gene	gene with protein product							Standard	NM_001004063		Approved		uc001vwj.2	Q8NGD4	OTTHUMG00000170633	ENST00000285600.4:c.403A>T	chr14.hg19:g.20404228A>T	ENSP00000285600:p.Ile135Phe	131.0	0.0		102.0	42.0	NM_001004063	B9EKV9|Q8NGD6|Q96R73	Missense_Mutation	SNP	ENST00000285600.4	hg19	CCDS32025.1	.	.	.	.	.	.	.	.	.	.	.	15.38	2.816750	0.50633	.	.	ENSG00000155249	ENST00000285600	T	0.00912	5.55	4.94	4.94	0.65067	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000023	T	0.03564	0.0102	H	0.94264	3.515	0.42393	D	0.992539	P	0.36616	0.561	B	0.37422	0.249	T	0.00953	-1.1502	10	0.87932	D	0	.	12.5899	0.56437	1.0:0.0:0.0:0.0	.	135	Q8NGD4	OR4K1_HUMAN	F	135	ENSP00000285600:I135F	ENSP00000285600:I135F	I	+	1	0	OR4K1	19474068	0.008000	0.16893	0.918000	0.36340	0.902000	0.53008	1.011000	0.29911	2.066000	0.61787	0.533000	0.62120	ATT	.	.		0.438	OR4K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409881.1			T	20404228	A	T	20404228	3	4	171	1	0	0	0	0	1	0	0	0	11076	101	4	4	405	4	OR4K1	14	20404228	Missense_Mutation	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10		20404228	86945312	80	25981										
FANCM	57697	hgsc.bcm.edu	37	chr14	45650891	45650891	+	Frame_Shift_Del	DEL	A	A	-													0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ttcatgctgtcaaaaagcgcAgatttcctataaacagagta							TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr14:45650891delA	ENST00000267430.5	+	16	4454	c.4369delA	c.(4369-4371)agafs	p.R1457fs	FANCM_ENST00000542564.2_Frame_Shift_Del_p.R1431fs|FANCM_ENST00000555013.1_3'UTR	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1457					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						CAAAAAGCGCAGATTTCCTAT	0.308								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R1456fs		Atlas-INDEL	.											.	FANCM	225	.	0			c.4368delC						.						54	54	54					14																	45650891		2203	4295	6498	SO:0001589	frameshift_variant	57697	exon16	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.4369delA	chr14.hg19:g.45650891delA	ENSP00000267430:p.Arg1457fs	152.0	0.0		151.0	31.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Frame_Shift_Del	DEL	ENST00000267430.5	hg19	CCDS32070.1																																																																																			.	.		0.308	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		-	45650891	A	-	45650891	7	5	171	1	0	1	0	1	0	0	0	0	5679	180	7	0	4431	0	FANCM	14	45650891	Frame_Shift_Del	DEL	A	TCGA-DD-AACU-01A-11D-A40R-10	25246663	45650891	61698649	81	25982										
MAPK1IP1L	93487	hgsc.bcm.edu	37	chr14	55529487	55529487	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	atctggactcccaccaagtgCaacaccctccactgtgcctt	6	17	1	0	rs568012336		TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr14:55529487C>A	ENST00000395468.4	+	3	347	c.170C>A	c.(169-171)gCa>gAa	p.A57E	MAPK1IP1L_ENST00000554364.1_3'UTR	NM_144578.3	NP_653179.1	Q8NDC0	MISSL_HUMAN	mitogen-activated protein kinase 1 interacting protein 1-like	57	Pro-rich.									endometrium(2)|large_intestine(1)|lung(3)	6						CCACCAAGTGCAACACCCTCC	0.577																																					p.A57E		Atlas-SNP	.											.	MAPK1IP1L	14	.	0			c.C170A						.						87	74	79					14																	55529487		2203	4300	6503	SO:0001583	missense	93487	exon3			CAAGTGCAACACC	AK025580	CCDS32085.1	14q22.1	2008-01-30	2008-01-30	2008-01-16		ENSG00000168175			19840	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 32", "mitogen activated protein kinase 1 interacting protein 1-like"	C14orf32		12011110	Standard	NM_144578		Approved		uc001xbq.1	Q8NDC0		ENST00000395468.4:c.170C>A	chr14.hg19:g.55529487C>A	ENSP00000378851:p.Ala57Glu	136.0	0.0		108.0	5.0	NM_144578	B2RDD8|Q96BG5	Missense_Mutation	SNP	ENST00000395468.4	hg19	CCDS32085.1	.	.	.	.	.	.	.	.	.	.	.	19.32	3.804441	0.70682	.	.	ENSG00000168175	ENST00000395468	.	.	.	5.31	5.31	0.75309	.	0.099642	0.44688	D	0.000439	T	0.52693	0.1750	N	0.19112	0.55	0.39301	D	0.964902	P	0.40731	0.728	P	0.46076	0.503	T	0.60535	-0.7244	9	0.72032	D	0.01	-11.1092	17.3476	0.87314	0.0:1.0:0.0:0.0	.	57	Q8NDC0	MISSL_HUMAN	E	57	.	ENSP00000378851:A57E	A	+	2	0	MAPK1IP1L	54599240	0.998000	0.40836	0.995000	0.50966	0.407000	0.30961	4.330000	0.59266	2.768000	0.95171	0.650000	0.86243	GCA	.	.		0.577	MAPK1IP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411302.2	NM_144578		A	55529487	C	A	55529487	3	1	171	1	0	0	0	0	1	0	0	0	9287	710	25	3	176	3	MAPK1IP1L	14	55529487	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	9878596	55529487	51820053	82	25983										
DACT1	51339	hgsc.bcm.edu	37	chr14	59112146	59112146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	acgggaatgatgtatatcgcTatcccagtccacttcatgct	8	11	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr14:59112146T>C	ENST00000335867.4	+	4	829	c.805T>C	c.(805-807)Tat>Cat	p.Y269H	DACT1_ENST00000395153.3_Missense_Mutation_p.Y232H|DACT1_ENST00000556859.1_5'UTR|DACT1_ENST00000541264.2_5'UTR|DACT1_ENST00000555845.1_3'UTR			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	269					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						TGTATATCGCTATCCCAGTCC	0.488																																					p.Y269H		Atlas-SNP	.											.	DACT1	119	.	0			c.T805C						.						169	155	160					14																	59112146		2203	4300	6503	SO:0001583	missense	51339	exon4			TATCGCTATCCCA	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"dapper homolog 1, antagonist of beta-catenin (xenopus)", "dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.805T>C	chr14.hg19:g.59112146T>C	ENSP00000337439:p.Tyr269His	130.0	0.0		104.0	17.0	NM_016651	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	hg19	CCDS9736.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.062036	0.76187	.	.	ENSG00000165617	ENST00000395153;ENST00000335867	T;T	0.71579	-0.58;-0.58	5.71	5.71	0.89125	.	0.128441	0.53938	D	0.000047	D	0.84875	0.5569	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87035	0.2137	10	0.87932	D	0	-14.657	15.979	0.80091	0.0:0.0:0.0:1.0	.	232;269	A8MYJ2;Q9NYF0	.;DACT1_HUMAN	H	232;269	ENSP00000378582:Y232H;ENSP00000337439:Y269H	ENSP00000337439:Y269H	Y	+	1	0	DACT1	58181899	1.000000	0.71417	0.987000	0.45799	0.843000	0.47879	7.665000	0.83852	2.182000	0.69389	0.460000	0.39030	TAT	.	.		0.488	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651		C	59112146	T	C	59112146	3	2	171	1	0	0	0	0	1	0	0	0	4224	1522	53	2	819	2	DACT1	14	59112146	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	3582659	59112146	48237394	83	25984										
BTBD7	55727	hgsc.bcm.edu	37	chr14	93712481	93712481	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	agggaggtggtggagggggcAagggtggatggaaggccaca	23	4	0	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr14:93712481A>C	ENST00000334746.5	-	10	2580	c.2273T>G	c.(2272-2274)tTg>tGg	p.L758W	BTBD7_ENST00000393170.2_Missense_Mutation_p.L332W|BTBD7_ENST00000554565.1_Missense_Mutation_p.L407W	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	758	Pro-rich.				multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		TGGAGGGGGCAAGGGTGGATG	0.542																																					p.L758W		Atlas-SNP	.											.	BTBD7	112	.	0			c.T2273G						.						130	133	132					14																	93712481		2203	4300	6503	SO:0001583	missense	55727	exon10			GGGGGCAAGGGTG	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"BTB/POZ domain containing"	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.2273T>G	chr14.hg19:g.93712481A>C	ENSP00000335615:p.Leu758Trp	134.0	0.0		135.0	10.0	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.617463	0.87359	.	.	ENSG00000011114	ENST00000334746;ENST00000554565;ENST00000553975;ENST00000393170	T;T	0.62639	0.38;0.01	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.69735	0.3144	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.995	T	0.73658	-0.3913	10	0.72032	D	0.01	.	16.0605	0.80836	1.0:0.0:0.0:0.0	.	332;407;758	E7ERI4;Q9P203-5;Q9P203	.;.;BTBD7_HUMAN	W	758;407;373;332	ENSP00000335615:L758W;ENSP00000451010:L407W	ENSP00000335615:L758W	L	-	2	0	BTBD7	92782234	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.690000	0.91272	2.193000	0.70182	0.528000	0.53228	TTG	.	.		0.542	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		C	93712481	A	C	93712481	3	2	171	1	0	0	0	0	1	0	0	0	1548	131	5	5	1133	5	BTBD7	14	93712481	Missense_Mutation	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	34600335	93712481	13637059	84	25985										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25959142	25959142	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aagctccgaggcccagttgtCcgcctggctgctgtagccgt	13	14	0	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr15:25959142C>G	ENST00000356865.6	-	10	2134	c.2023G>C	c.(2023-2025)Gac>Cac	p.D675H		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	675					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GCCCAGTTGTCCGCCTGGCTG	0.692																																					p.D675H		Atlas-SNP	.											.	ATP10A	270	.	0			c.G2023C						.						24	26	25					15																	25959142		2199	4296	6495	SO:0001583	missense	57194	exon10			AGTTGTCCGCCTG	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2023G>C	chr15.hg19:g.25959142C>G	ENSP00000349325:p.Asp675His	51.0	0.0		50.0	16.0	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	7.682	0.689238	0.14973	.	.	ENSG00000206190	ENST00000356865	T	0.10763	2.84	3.77	2.83	0.33086	HAD-like domain (1);	1.723910	0.02350	N	0.075817	T	0.19248	0.0462	L	0.29908	0.895	0.09310	N	1	P	0.42248	0.774	P	0.53450	0.726	T	0.28004	-1.0057	10	0.48119	T	0.1	-3.2906	8.5411	0.33393	0.1612:0.525:0.3138:0.0	.	675	O60312	AT10A_HUMAN	H	675	ENSP00000349325:D675H	ENSP00000349325:D675H	D	-	1	0	ATP10A	23510235	0.002000	0.14202	0.003000	0.11579	0.038000	0.13279	1.500000	0.35682	0.911000	0.36747	0.561000	0.74099	GAC	.	.		0.692	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		G	25959142	C	G	25959142	3	3	171	1	0	0	0	0	1	0	0	0	1116	855	30	4	2524	4	ATP10A	15	25959142	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10		25959142	76572250	85	25986										
CTDSPL2	51496	hgsc.bcm.edu	37	chr15	44783063	44783063	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tgatatggaacaggtggatgAgatcactaccagtactacta	10	7	1	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr15:44783063A>T	ENST00000260327.4	+	5	1120	c.557A>T	c.(556-558)gAg>gTg	p.E186V	CTDSPL2_ENST00000396780.1_Intron|CTDSPL2_ENST00000558373.1_Intron|CTDSPL2_ENST00000558966.1_Missense_Mutation_p.E186V	NM_016396.2	NP_057480.2	Q05D32	CTSL2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	186							phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	13		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)		CAGGTGGATGAGATCACTACC	0.408																																					p.E186V		Atlas-SNP	.											.	CTDSPL2	31	.	0			c.A557T						.						159	147	151					15																	44783063		2198	4298	6496	SO:0001583	missense	51496	exon5			TGGATGAGATCAC	AF161478	CCDS10110.1	15q15.3-q21.1	2010-06-21			ENSG00000137770	ENSG00000137770		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	26936	protein-coding gene	gene with protein product							Standard	NM_016396		Approved	HSPC129, FLJ10523	uc001ztr.3	Q05D32	OTTHUMG00000131159	ENST00000260327.4:c.557A>T	chr15.hg19:g.44783063A>T	ENSP00000260327:p.Glu186Val	387.0	1.0		429.0	158.0	NM_016396	Q3ZTU1|Q6AI06|Q8IYI9|Q9NVT2|Q9NZX8|Q9P030	Missense_Mutation	SNP	ENST00000260327.4	hg19	CCDS10110.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.671372	0.88348	.	.	ENSG00000137770	ENST00000260327	T	0.79454	-1.27	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.77935	0.4205	L	0.34521	1.04	0.80722	D	1	D	0.60575	0.988	P	0.55577	0.779	T	0.77640	-0.2512	10	0.37606	T	0.19	-8.4198	14.8259	0.70113	1.0:0.0:0.0:0.0	.	186	Q05D32	CTSL2_HUMAN	V	186	ENSP00000260327:E186V	ENSP00000260327:E186V	E	+	2	0	CTDSPL2	42570355	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.007000	0.76335	1.962000	0.57031	0.459000	0.35465	GAG	.	.		0.408	CTDSPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253851.1	NM_016396		T	44783063	A	T	44783063	3	4	171	1	0	0	0	0	1	0	0	0	4008	304	11	4	571	4	CTDSPL2	15	44783063	Missense_Mutation	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	18823921	44783063	57748329	86	25987										
CYP11A1	1583	hgsc.bcm.edu	37	chr15	74637456	74637456	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cggagcccgccttcttgatgCgcctgtgcaggacactgacg	13	14	1	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr15:74637456C>T	ENST00000268053.6	-	3	708	c.554G>A	c.(553-555)cGc>cAc	p.R185H	CYP11A1_ENST00000541301.1_Intron|CYP11A1_ENST00000358632.4_Missense_Mutation_p.R27H|CYP11A1_ENST00000419019.2_Missense_Mutation_p.R27H	NM_000781.2	NP_000772.2	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A, polypeptide 1	185					biphenyl metabolic process (GO:0018879)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cerebellum development (GO:0021549)|cholesterol metabolic process (GO:0008203)|dibenzo-p-dioxin metabolic process (GO:0018894)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|granulosa cell differentiation (GO:0060014)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|maternal process involved in female pregnancy (GO:0060135)|mating behavior (GO:0007617)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|progesterone biosynthetic process (GO:0006701)|response to alkaloid (GO:0043279)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to gamma radiation (GO:0010332)|response to genistein (GO:0033595)|response to hydrogen peroxide (GO:0042542)|response to insecticide (GO:0017085)|response to L-ascorbic acid (GO:0033591)|response to salt stress (GO:0009651)|response to vitamin E (GO:0033197)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|testosterone biosynthetic process (GO:0061370)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	mitochondrial crista (GO:0030061)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|perikaryon (GO:0043204)	cholesterol binding (GO:0015485)|cholesterol monooxygenase (side-chain-cleaving) activity (GO:0008386)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.R185H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Clomifene(DB00882)|Clotrimazole(DB00257)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Glutethimide(DB01437)|Ketoconazole(DB01026)|Omeprazole(DB00338)|Saquinavir(DB01232)|Terbinafine(DB00857)|Testosterone(DB00624)	CTTCTTGATGCGCCTGTGCAG	0.582																																					p.R185H	Esophageal Squamous(87;818 1337 4093 9268 37314)	Atlas-SNP	.											CYP11A1,bladder,carcinoma,-1,2	CYP11A1	54	.	1	Substitution - Missense(1)	lung(1)	c.G554A						.						88	84	85					15																	74637456		2197	4296	6493	SO:0001583	missense	1583	exon3			TTGATGCGCCTGT	AK056794	CCDS32291.1, CCDS45303.1	15q23-q24	2010-05-04	2003-01-14	2003-01-17	ENSG00000140459	ENSG00000140459	1.14.15.6	"Cytochrome P450s"	2590	protein-coding gene	gene with protein product	"cholesterol monooxygenase (side-chain-cleaving)"	118485	"cytochrome P450, subfamily XIA (cholesterol side chain cleavage)"	CYP11A			Standard	NM_000781		Approved	P450SCC	uc002axt.2	P05108	OTTHUMG00000150716	ENST00000268053.6:c.554G>A	chr15.hg19:g.74637456C>T	ENSP00000268053:p.Arg185His	116.0	0.0		126.0	27.0	NM_000781	A8K8D5|B3KPU8|G3XAD7|Q15081|Q16805|Q8N1A7	Missense_Mutation	SNP	ENST00000268053.6	hg19	CCDS32291.1	.	.	.	.	.	.	.	.	.	.	C	14.88	2.668563	0.47677	.	.	ENSG00000140459	ENST00000268053;ENST00000358632;ENST00000419019;ENST00000450547	T;T;T	0.68903	-0.36;-0.36;-0.36	4.37	4.37	0.52481	.	0.165365	0.53938	D	0.000057	T	0.60521	0.2275	M	0.78344	2.41	0.80722	D	1	P;P;P	0.41910	0.764;0.583;0.616	B;B;B	0.34991	0.193;0.11;0.065	T	0.64795	-0.6323	10	0.46703	T	0.11	-17.2513	7.0912	0.25285	0.0:0.8342:0.0:0.1658	.	185;155;185	E7EPP8;B4DTE5;P05108	.;.;CP11A_HUMAN	H	185;27;27;97	ENSP00000268053:R185H;ENSP00000351455:R27H;ENSP00000405488:R27H	ENSP00000268053:R185H	R	-	2	0	CYP11A1	72424509	1.000000	0.71417	0.998000	0.56505	0.495000	0.33615	1.438000	0.35002	1.977000	0.57605	0.549000	0.68633	CGC	.	.		0.582	CYP11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319737.1			T	74637456	C	T	74637456	3	4	171	1	0	0	0	0	1	0	0	0	4146	768	27	1	1039	1	CYP11A1	15	74637456	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	29854393	74637456	27893936	87	25988										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	90977012	90977012	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	catgccaagatgtatctactGtatccatgcactcaggtagt	8	10	2	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr15:90977012G>C	ENST00000268182.5	+	5	576	c.452G>C	c.(451-453)tGt>tCt	p.C151S	IQGAP1_ENST00000560738.1_Intron	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	151	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)	p.C151F(1)		breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TGTATCTACTGTATCCATGCA	0.328																																					p.C151S		Atlas-SNP	.											IQGAP1,NS,carcinoma,0,1	IQGAP1	140	.	1	Substitution - Missense(1)	lung(1)	c.G452C						.						113	111	112					15																	90977012		2198	4297	6495	SO:0001583	missense	8826	exon5			TCTACTGTATCCA	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.452G>C	chr15.hg19:g.90977012G>C	ENSP00000268182:p.Cys151Ser	114.0	0.0		150.0	48.0	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	hg19	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.464398	0.84425	.	.	ENSG00000140575	ENST00000268182	D	0.95205	-3.64	5.28	5.28	0.74379	Calponin homology domain (5);	0.114370	0.64402	D	0.000012	D	0.97362	0.9137	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97411	1.0002	10	0.56958	D	0.05	-12.3997	18.0822	0.89444	0.0:0.0:1.0:0.0	.	151	P46940	IQGA1_HUMAN	S	151	ENSP00000268182:C151S	ENSP00000268182:C151S	C	+	2	0	IQGAP1	88778016	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.491000	0.97954	2.744000	0.94065	0.655000	0.94253	TGT	.	.		0.328	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		C	90977012	G	C	90977012	3	2	171	1	0	0	0	0	1	0	0	0	7823	1377	48	4	470	4	IQGAP1	15	90977012	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	16339556	90977012	11554380	88	25989										
MCTP2	55784	hgsc.bcm.edu	37	chr15	95001427	95001427	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	acaggatattgtttcaactgTtcaaaacgtcttggaggaaa	9	6	3	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr15:95001427T>C	ENST00000357742.4	+	19	2312	c.2312T>C	c.(2311-2313)gTt>gCt	p.V771A	MCTP2_ENST00000451018.3_Missense_Mutation_p.V716A	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	771					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			GTTTCAACTGTTCAAAACGTC	0.348																																					p.V771A		Atlas-SNP	.											.	MCTP2	122	.	0			c.T2312C						.						127	132	130					15																	95001427		2197	4298	6495	SO:0001583	missense	55784	exon19			CAACTGTTCAAAA	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.2312T>C	chr15.hg19:g.95001427T>C	ENSP00000350377:p.Val771Ala	144.0	0.0		170.0	41.0	NM_018349	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	hg19	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.466273	0.84425	.	.	ENSG00000140563	ENST00000451018;ENST00000357742	T;T	0.75704	-0.96;-0.56	4.94	4.94	0.65067	Phosphoribosyltransferase C-terminal (1);	0.063559	0.64402	D	0.000008	D	0.84629	0.5514	M	0.76433	2.335	0.80722	D	1	D;D	0.76494	0.997;0.999	P;D	0.66196	0.904;0.942	D	0.86947	0.2083	10	0.87932	D	0	.	14.931	0.70914	0.0:0.0:0.0:1.0	.	716;771	Q6DN12-2;Q6DN12	.;MCTP2_HUMAN	A	716;771	ENSP00000395109:V716A;ENSP00000350377:V771A	ENSP00000350377:V771A	V	+	2	0	MCTP2	92802431	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.630000	0.83225	1.976000	0.57569	0.454000	0.30748	GTT	.	.		0.348	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		C	95001427	T	C	95001427	3	2	171	1	0	0	0	0	1	0	0	0	9410	1725	60	2	2462	2	MCTP2	15	95001427	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	4024415	95001427	7529965	89	25990										
PPL	5493	hgsc.bcm.edu	37	chr16	4937194	4937194	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gcctctgtctgttgatggcaTaaacttcagtgaacttggcg	11	9	3	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr16:4937194T>A	ENST00000345988.2	-	21	2638	c.2549A>T	c.(2548-2550)tAt>tTt	p.Y850F	PPL_ENST00000590782.2_Missense_Mutation_p.Y848F	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	850					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						GTTGATGGCATAAACTTCAGT	0.463																																					p.Y850F		Atlas-SNP	.											.	PPL	168	.	0			c.A2549T						.						164	166	165					16																	4937194		2197	4300	6497	SO:0001583	missense	5493	exon21			ATGGCATAAACTT	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.2549A>T	chr16.hg19:g.4937194T>A	ENSP00000340510:p.Tyr850Phe	79.0	0.0		59.0	32.0	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	hg19	CCDS10526.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.226678	0.39300	.	.	ENSG00000118898	ENST00000345988	T	0.48201	0.82	5.41	3.16	0.36331	.	0.170917	0.49916	D	0.000128	T	0.22936	0.0554	N	0.08118	0	0.20074	N	0.999931	B	0.20550	0.046	B	0.19666	0.026	T	0.19192	-1.0313	10	0.12103	T	0.63	.	8.6546	0.34055	0.0:0.1603:0.0:0.8397	.	850	O60437	PEPL_HUMAN	F	850	ENSP00000340510:Y850F	ENSP00000340510:Y850F	Y	-	2	0	PPL	4877195	0.977000	0.34250	0.005000	0.12908	0.893000	0.52053	2.102000	0.41796	0.887000	0.36136	0.533000	0.62120	TAT	.	.		0.463	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705		A	4937194	T	A	4937194	3	1	171	1	0	0	0	0	1	0	0	0	12346	1406	49	4	2729	4	PPL	16	4937194	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10		4937194	85417559	90	25991										
ACSM2A	123876	hgsc.bcm.edu	37	chr16	20497911	20497911	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aacagatagagtttgtcttgAacctgcccaagactgtcaca	8	10	2	4			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr16:20497911A>C	ENST00000573854.1	+	14	1759	c.1645A>C	c.(1645-1647)Aac>Cac	p.N549H	ACSM2A_ENST00000219054.6_Missense_Mutation_p.N549H|ACSM2A_ENST00000575690.1_Missense_Mutation_p.N549H|ACSM2A_ENST00000396104.2_Missense_Mutation_p.N549H|ACSM2A_ENST00000417235.2_Missense_Mutation_p.N470H|AC137056.1_ENST00000593357.1_5'Flank|ACSM2A_ENST00000536134.1_Missense_Mutation_p.N321H	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	549					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						GTTTGTCTTGAACCTGCCCAA	0.488																																					p.N549H		Atlas-SNP	.											.	ACSM2A	120	.	0			c.A1645C						.						150	148	148					16																	20497911		2203	4300	6503	SO:0001583	missense	123876	exon15			GTCTTGAACCTGC	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"Acyl-CoA synthetase family"	32017	protein-coding gene	gene with protein product		614358	"acyl-CoA synthetase medium-chain family member 2"	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.1645A>C	chr16.hg19:g.20497911A>C	ENSP00000459451:p.Asn549His	183.0	0.0		110.0	71.0	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	hg19	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	A	6.415	0.444769	0.12164	.	.	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000536134;ENST00000396104	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	3.74	0.46	0.16684	.	1.079770	0.07321	N	0.877544	T	0.33498	0.0865	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.14578	0.011	T	0.31052	-0.9957	10	0.66056	D	0.02	-5.3894	5.0797	0.14649	0.2048:0.3202:0.475:0.0	.	549	Q08AH3	ACS2A_HUMAN	H	470;549;321;549	ENSP00000392169:N470H;ENSP00000219054:N549H;ENSP00000445082:N321H;ENSP00000379411:N549H	ENSP00000219054:N549H	N	+	1	0	ACSM2A	20405412	0.000000	0.05858	0.555000	0.28281	0.379000	0.30106	-0.009000	0.12765	0.243000	0.21327	0.254000	0.18369	AAC	.	.		0.488	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		C	20497911	A	C	20497911	3	2	171	1	0	0	0	0	1	0	0	0	183	246	9	5	1695	5	ACSM2A	16	20497911	Missense_Mutation	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	15560717	20497911	69856842	91	25992										
ZNF423	23090	hgsc.bcm.edu	37	chr16	49660081	49660081	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gggaggaaatgctctcttacCaatcatgtggttggcaacgt	12	8	2	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr16:49660081C>A	ENST00000561648.1	-	5	3630	c.3577G>T	c.(3577-3579)Gag>Tag	p.E1193*	ZNF423_ENST00000535559.1_Splice_Site_p.E1076*|ZNF423_ENST00000562520.1_Splice_Site_p.E1133*|ZNF423_ENST00000567169.1_Splice_Site_p.E1076*|ZNF423_ENST00000562871.1_Splice_Site_p.E1133*|ZNF423_ENST00000262383.2_Splice_Site_p.E1193*|ZNF423_ENST00000563137.2_Splice_Site_p.E1133*	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	1193					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GCTCTCTTACCAATCATGTGG	0.448																																					p.E1193X		Atlas-SNP	.											.	ZNF423	463	.	0			c.G3577T						.						268	239	248					16																	49660081		2199	4300	6499	SO:0001630	splice_region_variant	23090	exon5			TCTTACCAATCAT	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.3577+1G>T	chr16.hg19:g.49660081C>A		124.0	0.0		62.0	43.0	NM_015069	O94860|Q76N04|Q9NZ13	Nonsense_Mutation	SNP	ENST00000561648.1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	46	12.538145	0.99676	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	.	.	.	4.81	4.81	0.61882	.	0.221814	0.38058	N	0.001822	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-20.8225	18.2985	0.90155	0.0:1.0:0.0:0.0	.	.	.	.	X	1193;1076	.	.	E	-	1	0	ZNF423	48217582	1.000000	0.71417	0.989000	0.46669	0.960000	0.62799	7.439000	0.80444	2.399000	0.81585	0.306000	0.20318	GAG	.	.		0.448	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	Nonsense_Mutation	A	49660081	C	A	49660081	5	1	171	1	0	0	0	0	0	0	1	0	17913	608	21	3	293	3	ZNF423	16	49660081	Splice_Site	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	29162170	49660081	40694672	92	25993										
TP53	7157	hgsc.bcm.edu	37	chr17	7577545	7577545	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gaggatgggcctccggttcaTgccgcccatgcaggaactgt	14	12	1	0	rs483352695|rs397516437		TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr17:7577545T>C	ENST00000269305.4	-	7	925	c.736A>G	c.(736-738)Atg>Gtg	p.M246V	TP53_ENST00000455263.2_Missense_Mutation_p.M246V|TP53_ENST00000420246.2_Missense_Mutation_p.M246V|TP53_ENST00000445888.2_Missense_Mutation_p.M246V|TP53_ENST00000359597.4_Missense_Mutation_p.M246V|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.M246V	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	246	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		M -> I (in sporadic cancers; somatic mutation).|M -> K (in sporadic cancers; somatic mutation).|M -> L (in sporadic cancers; somatic mutation).|M -> R (in sporadic cancers; somatic mutation).|M -> T (in sporadic cancers; somatic mutation).|M -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.M246V(34)|p.0?(8)|p.?(5)|p.M246L(3)|p.G244_M246>V(3)|p.M246fs*1(2)|p.M153V(2)|p.M246_P250delMNRRP(2)|p.G151_M153>V(1)|p.G244fs*17(1)|p.C242fs*98(1)|p.G245fs*17(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*14(1)|p.G245fs*16(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTCCGGTTCATGCCGCCCATG	0.577		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.M246V	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,rectum,carcinoma,0,6	TP53	33396	.	67	Substitution - Missense(39)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - deletion inframe(5)|Unknown(5)|Deletion - In frame(3)	liver(8)|haematopoietic_and_lymphoid_tissue(7)|large_intestine(6)|biliary_tract(6)|lung(6)|ovary(6)|breast(5)|stomach(4)|bone(4)|upper_aerodigestive_tract(3)|urinary_tract(3)|oesophagus(3)|soft_tissue(2)|central_nervous_system(2)|pancreas(2)	c.A736G	GRCh37	CM942294	TP53	M		.						152	113	126					17																	7577545		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGTTCATGCCGCC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.736A>G	chr17.hg19:g.7577545T>C	ENSP00000269305:p.Met246Val	123.0	0.0		68.0	39.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.945888	0.73672	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99784	-6.74;-6.74;-6.74;-6.74;-6.74;-6.74;-6.74;-6.74	4.62	3.54	0.40534	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99684	0.9881	M	0.87971	2.92	0.53005	D	0.999962	D;P;P;D;P;D	0.76494	0.993;0.889;0.832;0.994;0.931;0.999	D;P;B;D;D;D	0.80764	0.972;0.545;0.403;0.984;0.947;0.994	D	0.98572	1.0646	10	0.87932	D	0	-28.5667	8.419	0.32690	0.0:0.0941:0.0:0.9059	.	246;246;153;246;246;246	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	V	246;246;246;246;246;246;235;153;114;153	ENSP00000410739:M246V;ENSP00000352610:M246V;ENSP00000269305:M246V;ENSP00000398846:M246V;ENSP00000391127:M246V;ENSP00000391478:M246V;ENSP00000425104:M114V;ENSP00000423862:M153V	ENSP00000269305:M246V	M	-	1	0	TP53	7518270	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.824000	0.86668	0.914000	0.36822	0.379000	0.24179	ATG	.	.		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577545	T	C	7577545	3	2	171	1	0	0	0	0	1	0	0	0	16396	1464	51	2	554	2	TP53	17	7577545	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10		7577545	73617665	93	25994										
GJD3	125111	hgsc.bcm.edu	37	chr17	38519621	38519621	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	agcgcctggccgcccaggaaGgtcagctcggccagcaggcg	16	15	1	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr17:38519621G>A	ENST00000578689.1	-	1	446	c.447C>T	c.(445-447)acC>acT	p.T149T	GJD3_ENST00000337376.4_Silent_p.T149T|CTD-2267D19.3_ENST00000578774.1_Missense_Mutation_p.G145S	NM_152219.3	NP_689343.3	Q8N144	CXD3_HUMAN	gap junction protein, delta 3, 31.9kDa	149					cell communication (GO:0007154)|gap junction assembly (GO:0016264)	cell surface (GO:0009986)|connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)						Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)			CGCCCAGGAAGGTCAGCTCGG	0.771																																					p.T149T		Atlas-SNP	.											.	GJD3	2	.	0			c.C447T						.						1	1	1					17																	38519621		905	1932	2837	SO:0001819	synonymous_variant	125111	exon1			CAGGAAGGTCAGC	AF514298	CCDS58547.1	17q21.1	2012-04-19	2007-11-06	2007-11-06	ENSG00000183153	ENSG00000183153		"Ion channels / Gap junction proteins (connexins)"	19147	protein-coding gene	gene with protein product	"connexin 31.9"	607425	"gap junction protein, chi 1, 31.9kDa"	GJC1		12176752	Standard	NM_152219		Approved	CX31.9, GJA11, Cx30.2	uc010cwz.3	Q8N144		ENST00000578689.1:c.447C>T	chr17.hg19:g.38519621G>A		20.0	0.0		32.0	12.0	NM_152219	Q6ZUW6	Silent	SNP	ENST00000578689.1	hg19	CCDS58547.1																																																																																			.	.		0.771	GJD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447449.1	NM_152219		A	38519621	G	A	38519621	2	1	171	1	0	0	0	0	0	0	0	1	6426	987	35	3		3	GJD3	17	38519621	Silent	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	30942076	38519621	42675589	94	25995										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2762109	2762109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ttttgttttgtaaggttataGttgaagtcctgcctaatcaa	8	5	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr18:2762109G>A	ENST00000320876.6	+	36	4779	c.4441G>A	c.(4441-4443)Gtt>Att	p.V1481I	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.V1481I	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1481					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TAAGGTTATAGTTGAAGTCCT	0.363																																					p.V1481I		Atlas-SNP	.											.	SMCHD1	88	.	0			c.G4441A						.						171	158	162					18																	2762109		1851	4106	5957	SO:0001583	missense	23347	exon36			GTTATAGTTGAAG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.4441G>A	chr18.hg19:g.2762109G>A	ENSP00000326603:p.Val1481Ile	157.0	0.0		139.0	59.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	G	2.651	-0.282036	0.05642	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.21932	1.98;1.99	5.34	1.49	0.22878	.	0.343185	0.30999	N	0.008447	T	0.08714	0.0216	N	0.11724	0.165	0.27226	N	0.959537	B	0.02656	0.0	B	0.04013	0.001	T	0.34428	-0.9829	10	0.12103	T	0.63	-15.5249	6.4522	0.21910	0.2793:0.0:0.5896:0.1311	.	1481	A6NHR9	SMHD1_HUMAN	I	1481	ENSP00000326603:V1481I;ENSP00000261598:V1481I	ENSP00000261598:V1481I	V	+	1	0	SMCHD1	2752109	0.485000	0.25972	0.998000	0.56505	0.885000	0.51271	-0.294000	0.08309	0.621000	0.30232	0.650000	0.86243	GTT	.	.		0.363	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			A	2762109	G	A	2762109	3	1	171	1	0	0	0	0	1	0	0	0	14803	1029	36	3	4583	3	SMCHD1	18	2762109	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10		2762109	75315139	95	25996										
RFX2	5990	hgsc.bcm.edu	37	chr19	6013025	6013025	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ctggtgcatgggctgctgccGcatggccatgtactgcgtgt	15	11	0	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr19:6013025G>T	ENST00000303657.5	-	8	1020	c.871C>A	c.(871-873)Cgg>Agg	p.R291R	RFX2_ENST00000592546.1_Silent_p.R266R|RFX2_ENST00000359161.3_Silent_p.R291R|CTC-232P5.1_ENST00000587836.1_RNA	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						GGCTGCTGCCGCATGGCCATG	0.622																																					p.R291R	Colon(38;171 817 19800 47433 48051)	Atlas-SNP	.											.	RFX2	60	.	0			c.C871A						.						103	103	103					19																	6013025		2203	4300	6503	SO:0001819	synonymous_variant	5990	exon8			GCTGCCGCATGGC		CCDS12157.1, CCDS12158.1	19p13.3	2011-11-23			ENSG00000087903	ENSG00000087903			9983	protein-coding gene	gene with protein product	"trans-acting regulatory factor 2", "DNA binding protein RFX2", "HLA class II regulatory factor RFX2"	142765				1505960	Standard	NM_000635		Approved	FLJ14226	uc002meb.3	P48378		ENST00000303657.5:c.871C>A	chr19.hg19:g.6013025G>T		39.0	0.0		28.0	21.0	NM_000635	A8K581|B3KNC4|Q6IQ44|Q8SNA2	Silent	SNP	ENST00000303657.5	hg19	CCDS12157.1																																																																																			.	.		0.622	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	NM_000635		T	6013025	G	T	6013025	2	4	171	1	0	0	0	0	0	0	0	1	13278	1086	38	1		1	RFX2	19	6013025	Silent	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10		6013025	53115958	96	25997										
CLEC4G	339390	hgsc.bcm.edu	37	chr19	7795018	7795018	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	aaagtagcaggagccctcgaAggacagccacgacgtggggc	15	11	0	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr19:7795018A>T	ENST00000328853.5	-	7	582	c.514T>A	c.(514-516)Ttc>Atc	p.F172I	CLEC4G_ENST00000598081.1_5'Flank	NM_001244856.1|NM_198492.3	NP_001231785.1|NP_940894.1	Q6UXB4	CLC4G_HUMAN	C-type lectin domain family 4, member G	172	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(1)|large_intestine(1)|lung(1)	6						GAGCCCTCGAAGGACAGCCAC	0.662																																					p.F172I	Esophageal Squamous(146;540 1807 3349 19438 30853)	Atlas-SNP	.											.	CLEC4G	18	.	0			c.T514A						.						17	21	19					19																	7795018		2165	4236	6401	SO:0001583	missense	339390	exon7			CCTCGAAGGACAG	AY358431	CCDS12185.1	19p13.2	2010-04-27	2008-11-04			ENSG00000182566		"C-type lectin domain containing"	24591	protein-coding gene	gene with protein product			"C-type lectin superfamily 4, member G"			12975309	Standard	NM_198492		Approved	UNQ431, LSECtin	uc002mhp.4	Q6UXB4		ENST00000328853.5:c.514T>A	chr19.hg19:g.7795018A>T	ENSP00000327599:p.Phe172Ile	134.0	0.0		89.0	5.0	NM_198492		Missense_Mutation	SNP	ENST00000328853.5	hg19	CCDS12185.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.141441	0.77775	.	.	ENSG00000182566	ENST00000328853;ENST00000381308	T	0.19394	2.15	5.52	5.52	0.82312	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.000000	0.38005	N	0.001853	T	0.55481	0.1923	M	0.93375	3.41	0.40952	D	0.984555	D	0.89917	1.0	D	0.80764	0.994	T	0.67749	-0.5590	10	0.72032	D	0.01	.	12.3072	0.54908	1.0:0.0:0.0:0.0	.	172	Q6UXB4	CLC4G_HUMAN	I	172;56	ENSP00000327599:F172I	ENSP00000327599:F172I	F	-	1	0	CLEC4G	7701018	1.000000	0.71417	0.867000	0.34043	0.331000	0.28603	3.707000	0.54838	2.224000	0.72417	0.533000	0.62120	TTC	.	.		0.662	CLEC4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461989.1	NM_198492		T	7795018	A	T	7795018	3	4	171	1	0	0	0	0	1	0	0	0	3519	72	3	4	379	4	CLEC4G	19	7795018	Missense_Mutation	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	1781993	7795018	51333965	97	25998										
ZNF844	284391	hgsc.bcm.edu	37	chr19	12186502	12186502	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	agcattcaaagacacatgatAatgcacaatggagatggaac	9	7	1	3			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr19:12186502A>T	ENST00000439326.3	+	4	742	c.567A>T	c.(565-567)atA>atT	p.I189I	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	189					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						GACACATGATAATGCACAATG	0.373																																					p.I189I		Atlas-SNP	.											.	ZNF844	69	.	0			c.A567T						.						43	36	38					19																	12186502		692	1591	2283	SO:0001819	synonymous_variant	284391	exon4			CATGATAATGCAC	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"Zinc fingers, C2H2-type", "-"	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.567A>T	chr19.hg19:g.12186502A>T		182.0	0.0		104.0	11.0	NM_001136501	Q5JPI8	Silent	SNP	ENST00000439326.3	hg19	CCDS45985.1																																																																																			.	.		0.373	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			T	12186502	A	T	12186502	2	4	171	1	0	0	0	0	0	0	0	1	18205	352	13	4		4	ZNF844	19	12186502	Silent	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	4391484	12186502	46942481	98	25999										
RYR1	6261	hgsc.bcm.edu	37	chr19	38979817	38979817	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	accgagactttgtcctgtagGtgatgggcatctttggcgat	13	8	1	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr19:38979817G>T	ENST00000359596.3	+	35	5548	c.5548G>T	c.(5548-5550)Gtg>Ttg	p.V1850L	RYR1_ENST00000355481.4_Splice_Site_p.V1850L|RYR1_ENST00000360985.3_Splice_Site_p.V1850L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1850	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGTCCTGTAGGTGATGGGCAT	0.532																																					p.V1850L		Atlas-SNP	.											.	RYR1	708	.	0			c.G5548T						.						126	107	113					19																	38979817		2203	4300	6503	SO:0001630	splice_region_variant	6261	exon35			CTGTAGGTGATGG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5548-1G>T	chr19.hg19:g.38979817G>T		60.0	0.0		38.0	23.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	g	11.59	1.682637	0.29872	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.74106	-0.81;-0.81;-0.81	4.06	4.06	0.47325	.	0.088140	0.42964	U	0.000637	T	0.54919	0.1888	N	0.16201	0.385	0.50813	D	0.999898	B;B	0.33637	0.42;0.063	B;B	0.32928	0.155;0.074	T	0.54186	-0.8331	9	.	.	.	.	11.6139	0.51078	0.0:0.0:1.0:0.0	.	1850;1850	P21817-2;P21817	.;RYR1_HUMAN	L	1850	ENSP00000352608:V1850L;ENSP00000347667:V1850L;ENSP00000354254:V1850L	.	V	+	1	0	RYR1	43671657	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.040000	0.57333	2.073000	0.62155	0.552000	0.68991	GTG	.	.		0.532	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		Missense_Mutation	T	38979817	G	T	38979817	5	4	171	1	0	0	0	0	0	0	1	0	13783	1275	44	3	5686	3	RYR1	19	38979817	Splice_Site	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	26793315	38979817	20149166	99	26000										
RYR1	6261	hgsc.bcm.edu	37	chr19	38995537	38995537	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ggcaactttgatccccggccTgtggagaccctcaagtgagg	13	12	1	3			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr19:38995537T>A	ENST00000359596.3	+	51	8217	c.8217T>A	c.(8215-8217)ccT>ccA	p.P2739P	RYR1_ENST00000355481.4_Silent_p.P2739P|RYR1_ENST00000360985.3_Silent_p.P2739P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2739	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ATCCCCGGCCTGTGGAGACCC	0.597																																					p.P2739P		Atlas-SNP	.											.	RYR1	708	.	0			c.T8217A						.						50	50	50					19																	38995537		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon51			CCGGCCTGTGGAG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.8217T>A	chr19.hg19:g.38995537T>A		104.0	0.0		81.0	57.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.597	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38995537	T	A	38995537	2	1	171	1	0	0	0	0	0	0	0	1	13783	1567	55	4		4	RYR1	19	38995537	Silent	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	15720	38995537	20133446	100	26001										
RYR1	6261	hgsc.bcm.edu	37	chr19	39009927	39009927	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ttcatcccaactatcgggcgGctgcgcaagagggcagggaa	14	11	1	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr19:39009927G>A	ENST00000359596.3	+	67	10092	c.10092G>A	c.(10090-10092)cgG>cgA	p.R3364R	RYR1_ENST00000355481.4_Silent_p.R3364R|RYR1_ENST00000360985.3_Silent_p.R3364R			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3364					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTATCGGGCGGCTGCGCAAGA	0.677																																					p.R3364R		Atlas-SNP	.											.	RYR1	708	.	0			c.G10092A						.						45	43	43					19																	39009927		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon67			CGGGCGGCTGCGC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.10092G>A	chr19.hg19:g.39009927G>A		144.0	0.0		103.0	75.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.677	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	39009927	G	A	39009927	2	1	171	1	0	0	0	0	0	0	0	1	13783	1190	42	3		3	RYR1	19	39009927	Silent	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	14390	39009927	20119056	101	26002										
MKKS	8195	hgsc.bcm.edu	37	chr20	10393861	10393861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tctgaacattttcaatcaggTtgcagcaaagaatagctgtg	9	7	3	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr20:10393861T>C	ENST00000347364.3	-	3	1064	c.302A>G	c.(301-303)aAc>aGc	p.N101S	MKKS_ENST00000399054.2_Missense_Mutation_p.N101S	NM_170784.2	NP_740754.1	Q9NPJ1	MKKS_HUMAN	McKusick-Kaufman syndrome	101					artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|chaperone-mediated protein complex assembly (GO:0051131)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|determination of left/right symmetry (GO:0007368)|fat cell differentiation (GO:0045444)|gonad development (GO:0008406)|heart development (GO:0007507)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of multicellular organism growth (GO:0040018)|protein folding (GO:0006457)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sensory perception of smell (GO:0007608)|social behavior (GO:0035176)|spermatid development (GO:0007286)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|stomach(2)	16						TTCAATCAGGTTGCAGCAAAG	0.393																																					p.N101S	Melanoma(79;1979 2212 6640)	Atlas-SNP	.											.	MKKS	35	.	0			c.A302G						.						120	110	113					20																	10393861		2203	4300	6503	SO:0001583	missense	8195	exon3			ATCAGGTTGCAGC	AF221993	CCDS13111.1	20p12	2013-01-08			ENSG00000125863	ENSG00000125863		"Heat Shock Proteins / Chaperonins"	7108	protein-coding gene	gene with protein product		604896		BBS6		9467007	Standard	NR_072977		Approved		uc002wnu.2	Q9NPJ1	OTTHUMG00000031868	ENST00000347364.3:c.302A>G	chr20.hg19:g.10393861T>C	ENSP00000246062:p.Asn101Ser	114.0	0.0		125.0	50.0	NM_170784	A8K7B0|D3DW18	Missense_Mutation	SNP	ENST00000347364.3	hg19	CCDS13111.1	.	.	.	.	.	.	.	.	.	.	T	7.328	0.618388	0.14129	.	.	ENSG00000125863	ENST00000347364;ENST00000399054	T;T	0.78481	-1.18;-1.18	6.07	3.75	0.43078	.	0.317552	0.36972	N	0.002313	T	0.66567	0.2802	L	0.42245	1.32	0.24460	N	0.994445	B	0.14012	0.009	B	0.18263	0.021	T	0.56456	-0.7976	10	0.42905	T	0.14	-31.6163	5.3612	0.16089	0.0:0.1845:0.1484:0.6671	.	101	Q9NPJ1	MKKS_HUMAN	S	101	ENSP00000246062:N101S;ENSP00000382008:N101S	ENSP00000246062:N101S	N	-	2	0	MKKS	10341861	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	2.005000	0.40864	0.499000	0.27970	0.477000	0.44152	AAC	.	.		0.393	MKKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077991.3			C	10393861	T	C	10393861	3	2	171	1	0	0	0	0	1	0	0	0	9609	1725	60	2	1426	2	MKKS	20	10393861	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10		10393861	52631659	102	26003										
MYH7B	57644	hgsc.bcm.edu	37	chr20	33578100	33578100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	agcatcgttccagacggtgtCccagctgcacaaggtaaggc	12	12	0	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr20:33578100C>T	ENST00000262873.7	+	20	2182	c.2090C>T	c.(2089-2091)tCc>tTc	p.S697F	MIR499A_ENST00000384903.1_RNA	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	655	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CAGACGGTGTCCCAGCTGCAC	0.617																																					p.S697F		Atlas-SNP	.											.	MYH7B	145	.	0			c.C2090T						.						98	101	100					20																	33578100		2203	4300	6503	SO:0001583	missense	57644	exon22			CGGTGTCCCAGCT	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.2090C>T	chr20.hg19:g.33578100C>T	ENSP00000262873:p.Ser697Phe	136.0	0.0		136.0	26.0	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	hg19	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.360033	0.82353	.	.	ENSG00000078814	ENST00000262873	D	0.88509	-2.39	4.39	4.39	0.52855	Myosin head, motor domain (2);	0.000000	0.37437	N	0.002091	D	0.97096	0.9051	H	0.99312	4.51	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99047	1.0826	10	0.87932	D	0	.	17.5203	0.87784	0.0:1.0:0.0:0.0	.	655	A7E2Y1	MYH7B_HUMAN	F	697	ENSP00000262873:S697F	ENSP00000262873:S697F	S	+	2	0	MYH7B	33041761	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.651000	0.83577	2.445000	0.82738	0.511000	0.50034	TCC	.	.		0.617	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33578100	C	T	33578100	3	4	171	1	0	0	0	0	1	0	0	0	10049	855	30	3	2168	3	MYH7B	20	33578100	Missense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	23184239	33578100	29447420	103	26004										
SALL4	57167	hgsc.bcm.edu	37	chr20	50406736	50406736	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	tctcccatcagcgaggatgaGtcgttggtcaagccatcgct	11	12	3	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr20:50406736G>C	ENST00000217086.4	-	2	2397	c.2286C>G	c.(2284-2286)gaC>gaG	p.D762E	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	762					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GCGAGGATGAGTCGTTGGTCA	0.582																																					p.D762E		Atlas-SNP	.											.	SALL4	168	.	0			c.C2286G						.						83	66	72					20																	50406736		2203	4300	6503	SO:0001583	missense	57167	exon2			GGATGAGTCGTTG	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2286C>G	chr20.hg19:g.50406736G>C	ENSP00000217086:p.Asp762Glu	111.0	0.0		140.0	38.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	hg19	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592760	0.28357	.	.	ENSG00000101115	ENST00000217086	T	0.10192	2.9	5.67	3.7	0.42460	.	0.000000	0.46442	D	0.000291	T	0.14442	0.0349	M	0.71036	2.16	0.80722	D	1	P	0.46706	0.883	B	0.43301	0.415	T	0.04454	-1.0950	10	0.30854	T	0.27	-43.5142	9.9426	0.41589	0.2691:0.0:0.7309:0.0	.	762	Q9UJQ4	SALL4_HUMAN	E	762	ENSP00000217086:D762E	ENSP00000217086:D762E	D	-	3	2	SALL4	49840143	0.999000	0.42202	0.981000	0.43875	0.799000	0.45148	0.530000	0.23036	1.375000	0.46248	0.655000	0.94253	GAC	.	.		0.582	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			C	50406736	G	C	50406736	3	2	171	1	0	0	0	0	1	0	0	0	13828	1020	36	4	887	4	SALL4	20	50406736	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	16828636	50406736	12618784	104	26005										
SLC5A1	6523	hgsc.bcm.edu	37	chr22	32464553	32464553	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ccaggtctacctttcccttcTgtccctgctgctctacattt	5	16	3	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chr22:32464553T>A	ENST00000266088.4	+	5	693	c.443T>A	c.(442-444)cTg>cAg	p.L148Q	SLC5A1_ENST00000543737.1_Missense_Mutation_p.L21Q	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	148					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	CTTTCCCTTCTGTCCCTGCTG	0.577																																					p.L148Q		Atlas-SNP	.											.	SLC5A1	80	.	0			c.T443A						.						154	120	131					22																	32464553		2203	4300	6503	SO:0001583	missense	6523	exon5			CCCTTCTGTCCCT		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"Solute carriers"	11036	protein-coding gene	gene with protein product	"sodium/glucose cotransporter 1"	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.443T>A	chr22.hg19:g.32464553T>A	ENSP00000266088:p.Leu148Gln	89.0	0.0		87.0	32.0	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Missense_Mutation	SNP	ENST00000266088.4	hg19	CCDS13902.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.591634	0.86953	.	.	ENSG00000100170	ENST00000266088;ENST00000543737	D;D	0.91686	-2.89;-2.89	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.97151	0.9069	H	0.95611	3.695	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.98227	1.0481	10	0.87932	D	0	.	14.2177	0.65805	0.0:0.0:0.0:1.0	.	148	P13866	SC5A1_HUMAN	Q	148;21	ENSP00000266088:L148Q;ENSP00000444898:L21Q	ENSP00000266088:L148Q	L	+	2	0	SLC5A1	30794553	1.000000	0.71417	0.995000	0.50966	0.936000	0.57629	7.574000	0.82434	2.042000	0.60477	0.455000	0.32223	CTG	.	.		0.577	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343		A	32464553	T	A	32464553	3	1	171	1	0	0	0	0	1	0	0	0	14676	1580	55	4	461	4	SLC5A1	22	32464553	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10		32464553	18840013	105	26006										
CXorf36	79742	hgsc.bcm.edu	37	chrX	45051186	45051186	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ggcgccagattttggaatcaTctgagtaatttgcaggataa	11	6	2	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chrX:45051186T>A	ENST00000398000.2	-	2	382	c.308A>T	c.(307-309)gAt>gTt	p.D103V	CXorf36_ENST00000477281.1_5'Flank|RP11-342D14.1_ENST00000438181.1_RNA|CXorf36_ENST00000377934.4_Missense_Mutation_p.D103V|RP11-342D14.1_ENST00000450527.1_RNA	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	103						extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						TTTGGAATCATCTGAGTAATT	0.483																																					p.D103V		Atlas-SNP	.											.	CXorf36	53	.	0			c.A308T						.						71	69	70					X																	45051186		2203	4300	6503	SO:0001583	missense	79742	exon2			GAATCATCTGAGT	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.308A>T	chrX.hg19:g.45051186T>A	ENSP00000381086:p.Asp103Val	47.0	0.0		62.0	51.0	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Missense_Mutation	SNP	ENST00000398000.2	hg19	CCDS48096.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.219113	0.79464	.	.	ENSG00000147113	ENST00000398000;ENST00000377934	T;T	0.40225	1.29;1.04	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.64382	0.2593	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.68712	-0.5336	10	0.87932	D	0	.	13.4411	0.61114	0.0:0.0:0.0:1.0	.	103;103	Q9H7Y0-2;Q9H7Y0	.;CX036_HUMAN	V	103	ENSP00000381086:D103V;ENSP00000367168:D103V	ENSP00000367168:D103V	D	-	2	0	CXorf36	44936130	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.176000	0.58269	1.891000	0.54761	0.486000	0.48141	GAT	.	.		0.483	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689		A	45051186	T	A	45051186	3	1	171	1	0	0	0	0	1	0	0	0	4108	1435	50	4	1064	4	CXorf36	23	45051186	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10		45051186	110219374	106	26007										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73962219	73962219	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	cttagattttaacctagcttCacttttaaatttgattttat	3	6	1	2			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chrX:73962219C>A	ENST00000055682.6	-	3	2784	c.2173G>T	c.(2173-2175)Gaa>Taa	p.E725*		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	725					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						AACCTAGCTTCACTTTTAAAT	0.413																																					p.E725X		Atlas-SNP	.											.	KIAA2022	262	.	0			c.G2173T						.						77	75	75					X																	73962219		2202	4300	6502	SO:0001587	stop_gained	340533	exon3			TAGCTTCACTTTT		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.2173G>T	chrX.hg19:g.73962219C>A	ENSP00000055682:p.Glu725*	51.0	0.0		65.0	6.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Nonsense_Mutation	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	C	44	10.846814	0.99477	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	.	.	.	5.73	5.73	0.89815	.	0.046391	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-18.9809	18.9182	0.92515	0.0:1.0:0.0:0.0	.	.	.	.	X	725	.	ENSP00000055682:E725X	E	-	1	0	KIAA2022	73878944	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.415000	0.81967	0.600000	0.82982	GAA	.	.		0.413	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		A	73962219	C	A	73962219	4	1	171	1	0	0	0	0	0	1	0	0	8278	835	29	3	2385	3	KIAA2022	23	73962219	Nonsense_Mutation	SNP	C	TCGA-DD-AACU-01A-11D-A40R-10	28911033	73962219	81308341	107	26008										
MAGEE2	139599	hgsc.bcm.edu	37	chrX	75004522	75004522	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	ggatctcagggaactgatctGagtactctctgagaaactcc	10	10	3	3			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chrX:75004522G>A	ENST00000373359.2	-	1	557	c.365C>T	c.(364-366)tCa>tTa	p.S122L		NM_138703.4	NP_619648.1	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	122	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.									autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GAACTGATCTGAGTACTCTCT	0.498																																					p.S122L		Atlas-SNP	.											.	MAGEE2	94	.	0			c.C365T						.						35	31	32					X																	75004522		2203	4300	6503	SO:0001583	missense	139599	exon1			TGATCTGAGTACT	AF490509	CCDS14431.1	Xq13	2008-02-05			ENSG00000186675	ENSG00000186675			24935	protein-coding gene	gene with protein product		300760				11454705	Standard	NM_138703		Approved	HCA3	uc004ecj.2	Q8TD90	OTTHUMG00000021870	ENST00000373359.2:c.365C>T	chrX.hg19:g.75004522G>A	ENSP00000362457:p.Ser122Leu	60.0	0.0		100.0	10.0	NM_138703	Q5JSI5	Missense_Mutation	SNP	ENST00000373359.2	hg19	CCDS14431.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.626081	0.46840	.	.	ENSG00000186675	ENST00000373359	T	0.05025	3.51	3.02	1.1	0.20463	.	.	.	.	.	T	0.10465	0.0256	L	0.29908	0.895	0.24936	N	0.991887	D	0.63046	0.992	P	0.60068	0.868	T	0.23726	-1.0180	9	0.62326	D	0.03	.	6.855	0.24036	0.0:0.0:0.5005:0.4995	.	122	Q8TD90	MAGE2_HUMAN	L	122	ENSP00000362457:S122L	ENSP00000362457:S122L	S	-	2	0	MAGEE2	74921247	1.000000	0.71417	0.908000	0.35775	0.708000	0.40852	1.576000	0.36504	0.148000	0.19059	0.370000	0.22315	TCA	.	.		0.498	MAGEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057288.1	NM_138703		A	75004522	G	A	75004522	3	1	171	1	0	0	0	0	1	0	0	0	9195	1294	45	3	1210	3	MAGEE2	23	75004522	Missense_Mutation	SNP	G	TCGA-DD-AACU-01A-11D-A40R-10	1042303	75004522	80266038	108	26009										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118222963	118222963	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	acttgtcatacccaaaacacTtgctgtaaaggtctggtgaa	8	9	2	1			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chrX:118222963T>A	ENST00000402510.2	-	11	2229	c.2230A>T	c.(2230-2232)Agt>Tgt	p.S744C		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	744										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						CCCAAAACACTTGCTGTAAAG	0.443																																					p.S744C		Atlas-SNP	.											.	KIAA1210	171	.	0			c.A2230T						.						37	36	36					X																	118222963		1905	4117	6022	SO:0001583	missense	57481	exon11			AAACACTTGCTGT	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.2230A>T	chrX.hg19:g.118222963T>A	ENSP00000384670:p.Ser744Cys	96.0	0.0		93.0	12.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.57|13.57	2.277806|2.277806	0.40294|0.40294	.|.	.|.	ENSG00000248857|ENSG00000250423	ENST00000440399|ENST00000402510	.|T	.|0.18810	.|2.19	4.18|4.18	0.506|0.506	0.16961|0.16961	.|.	.|.	.|.	.|.	.|.	T|T	0.28300|0.28300	0.0699|0.0699	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	.|D	.|0.71674	.|0.998	.|D	.|0.64776	.|0.929	T|T	0.11470|0.11470	-1.0586|-1.0586	5|9	.|0.56958	.|D	.|0.05	.|.	5.7972|5.7972	0.18394|0.18394	0.0:0.3605:0.0:0.6395|0.0:0.3605:0.0:0.6395	.|.	.|744	.|Q9ULL0	.|K1210_HUMAN	M|C	150|744	.|ENSP00000384670:S744C	.|ENSP00000384670:S744C	K|S	-|-	2|1	0|0	KIAA1210|RP13-347D8.6	118106991|118106991	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	0.180000|0.180000	0.16860|0.16860	-0.013000|-0.013000	0.14199|0.14199	-0.472000|-0.472000	0.04984|0.04984	AAG|AGT	.	.		0.443	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		A	118222963	T	A	118222963	3	1	171	1	0	0	0	0	1	0	0	0	8223	1609	56	4	2915	4	KIAA1210	23	118222963	Missense_Mutation	SNP	T	TCGA-DD-AACU-01A-11D-A40R-10	43218441	118222963	37047597	109	26010										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144904522	144904522	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.59822910902048	1.55827338129496	1.6120069461672	0.18266253869969	0.751940625889747	0	gacctcagggggaataggctAaaagtaatgccttttgctgg	13	7	1	0			TCGA-DD-AACU-01A-11D-A40R-10	TCGA-DD-AACU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d326320-5639-47af-8d15-1638282ab9d8	7534c02c-55eb-4c65-97dd-31520dc6d63a	g.chrX:144904522A>G	ENST00000370490.1	+	1	4834	c.579A>G	c.(577-579)ctA>ctG	p.L193L	SLITRK2_ENST00000428560.2_Silent_p.L193L|SLITRK2_ENST00000413937.2_Silent_p.L193L|SLITRK2_ENST00000434188.2_Silent_p.L193L|SLITRK2_ENST00000447897.2_Silent_p.L193L			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	193					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					GGAATAGGCTAAAAGTAATGC	0.473																																					p.L193L		Atlas-SNP	.											.	SLITRK2	221	.	0			c.A579G						.						142	124	130					X																	144904522		2203	4300	6503	SO:0001819	synonymous_variant	84631	exon5			TAGGCTAAAAGTA	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.579A>G	chrX.hg19:g.144904522A>G		104.0	0.0		100.0	24.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	hg19	CCDS14680.1																																																																																			.	.		0.473	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		G	144904522	A	G	144904522	2	3	171	1	0	0	0	0	0	0	0	1	14758	349	13	2		2	SLITRK2	23	144904522	Silent	SNP	A	TCGA-DD-AACU-01A-11D-A40R-10	26681559	144904522	10366038	110	26011										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12368658	12368658	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gaggaagcctcttaaccgagCcttgtaggctgaaattgcag	12	9	1	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr1:12368658C>T	ENST00000358136.3	+	27	6740	c.6610C>T	c.(6610-6612)Cct>Tct	p.P2204S	VPS13D_ENST00000356315.4_Missense_Mutation_p.P2204S	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CTTAACCGAGCCTTGTAGGCT	0.468																																					p.P2204S		Atlas-SNP	.											.	VPS13D	316	.	0			c.C6610T						.						143	140	141					1																	12368658		2203	4300	6503	SO:0001583	missense	55187	exon27			ACCGAGCCTTGTA	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.6610C>T	chr1.hg19:g.12368658C>T	ENSP00000350854:p.Pro2204Ser	134.0	0.0		218.0	107.0	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	hg19	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.958659	0.53400	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.38887	1.11;1.11	5.61	5.61	0.85477	.	0.114530	0.56097	D	0.000040	T	0.28034	0.0691	N	0.16368	0.405	0.80722	D	1	B;B	0.15719	0.014;0.008	B;B	0.17433	0.018;0.008	T	0.08391	-1.0724	9	.	.	.	.	14.4763	0.67548	0.147:0.853:0.0:0.0	.	2204;2204	Q5THJ4-2;Q5THJ4	.;VP13D_HUMAN	S	2204	ENSP00000348666:P2204S;ENSP00000350854:P2204S	.	P	+	1	0	VPS13D	12291245	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.298000	0.51818	2.636000	0.89361	0.650000	0.86243	CCT	.	.		0.468	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		T	12368658	C	T	12368658	3	4	172	1	0	0	0	0	1	0	0	0	17207	739	26	3	6712	3	VPS13D	1	12368658	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10		12368658	236881963	1	26012										
SLC9A1	6548	hgsc.bcm.edu	37	chr1	27434282	27434282	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tccacatcttcaggaagtatTtgatggtggtgtgggacttg	13	6	2	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr1:27434282T>C	ENST00000263980.3	-	4	1714	c.1139A>G	c.(1138-1140)aAa>aGa	p.K380R	SLC9A1_ENST00000374086.3_Missense_Mutation_p.K380R|SLC9A1_ENST00000545949.1_Missense_Mutation_p.K41R	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	380					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	CAGGAAGTATTTGATGGTGGT	0.592																																					p.K380R		Atlas-SNP	.											.	SLC9A1	68	.	0			c.A1139G						.						94	74	81					1																	27434282		2202	4294	6496	SO:0001583	missense	6548	exon4			AAGTATTTGATGG	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.1139A>G	chr1.hg19:g.27434282T>C	ENSP00000263980:p.Lys380Arg	78.0	0.0		103.0	53.0	NM_003047	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	ENST00000263980.3	hg19	CCDS295.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.045429	0.75846	.	.	ENSG00000090020	ENST00000263980;ENST00000545949;ENST00000374086	T;T;T	0.16196	2.36;2.36;2.36	5.6	5.6	0.85130	Cation/H+ exchanger (1);	0.042369	0.85682	D	0.000000	T	0.19327	0.0464	L	0.42245	1.32	0.80722	D	1	P;B	0.48089	0.905;0.136	B;B	0.43728	0.429;0.214	T	0.01432	-1.1356	10	0.31617	T	0.26	.	15.773	0.78187	0.0:0.0:0.0:1.0	.	380;380	P19634-2;P19634	.;SL9A1_HUMAN	R	380;41;380	ENSP00000263980:K380R;ENSP00000445520:K41R;ENSP00000363199:K380R	ENSP00000263980:K380R	K	-	2	0	SLC9A1	27306869	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	8.040000	0.89188	2.131000	0.65755	0.374000	0.22700	AAA	.	.		0.592	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		C	27434282	T	C	27434282	3	2	172	1	0	0	0	0	1	0	0	0	14724	1841	64	2	1344	2	SLC9A1	1	27434282	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	15065624	27434282	221816339	2	26013										
NTNG1	22854	hgsc.bcm.edu	37	chr1	107937924	107937924	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gtccaggctcctatctccccAtccccaaaggcactgcaaat	6	17	1	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr1:107937924A>G	ENST00000370068.1	+	4	1882	c.1036A>G	c.(1036-1038)Atc>Gtc	p.I346V	NTNG1_ENST00000542803.1_Missense_Mutation_p.I346V|NTNG1_ENST00000370074.4_Missense_Mutation_p.I346V|NTNG1_ENST00000370067.1_Missense_Mutation_p.I346V|NTNG1_ENST00000370073.2_Missense_Mutation_p.I346V|NTNG1_ENST00000370070.2_Missense_Mutation_p.I346V|NTNG1_ENST00000370066.1_Missense_Mutation_p.I346V|NTNG1_ENST00000370071.2_Missense_Mutation_p.I346V|NTNG1_ENST00000370061.3_Missense_Mutation_p.I346V|NTNG1_ENST00000370072.3_Missense_Mutation_p.I346V|NTNG1_ENST00000370065.1_Missense_Mutation_p.I346V			Q9Y2I2	NTNG1_HUMAN	netrin G1	346	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		CTATCTCCCCATCCCCAAAGG	0.463																																					p.I346V		Atlas-SNP	.											.	NTNG1	274	.	0			c.A1036G						.						154	153	154					1																	107937924		2203	4300	6503	SO:0001583	missense	22854	exon4			CTCCCCATCCCCA	AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"Netrins"	23319	protein-coding gene	gene with protein product	"netrin G1f", "Netrin-G1"	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.1036A>G	chr1.hg19:g.107937924A>G	ENSP00000359085:p.Ile346Val	101.0	0.0		156.0	68.0	NM_014917	Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Missense_Mutation	SNP	ENST00000370068.1	hg19	CCDS44180.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.598787	0.46318	.	.	ENSG00000162631	ENST00000370076;ENST00000370073;ENST00000370071;ENST00000542803;ENST00000370061;ENST00000370072;ENST00000370070;ENST00000535584;ENST00000370064;ENST00000370062;ENST00000370074;ENST00000370068;ENST00000294649;ENST00000370067;ENST00000370066;ENST00000370065	T;T;T;T;T;T;T;T;T;T;T	0.73047	0.88;-0.32;0.81;0.21;0.16;-0.45;-0.71;0.88;-0.47;-0.32;0.26	5.8	4.67	0.58626	EGF-like, laminin (2);	0.000000	0.64402	D	0.000008	T	0.49457	0.1558	M	0.63428	1.95	0.58432	D	0.999991	B;B;B;B;B	0.32031	0.352;0.212;0.04;0.039;0.044	B;B;B;B;B	0.32090	0.14;0.125;0.124;0.031;0.029	T	0.50931	-0.8769	10	0.13108	T	0.6	.	13.1587	0.59533	0.8665:0.1335:0.0:0.0	.	346;346;346;346;346	B4DKF0;Q9Y2I2;Q9Y2I2-4;Q9Y2I2-2;Q9Y2I2-1	.;NTNG1_HUMAN;.;.;.	V	346;346;346;346;346;346;346;346;107;107;346;346;346;346;346;346	ENSP00000359090:I346V;ENSP00000359088:I346V;ENSP00000440561:I346V;ENSP00000359078:I346V;ENSP00000359089:I346V;ENSP00000359087:I346V;ENSP00000359091:I346V;ENSP00000359085:I346V;ENSP00000359084:I346V;ENSP00000359083:I346V;ENSP00000359082:I346V	ENSP00000294649:I346V	I	+	1	0	NTNG1	107739447	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.070000	0.64376	1.014000	0.39417	0.528000	0.53228	ATC	.	.		0.463	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917		G	107937924	A	G	107937924	3	3	172	1	0	0	0	0	1	0	0	0	10713	217	8	2	1046	2	NTNG1	1	107937924	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	80503642	107937924	141312697	3	26014										
TARS2	80222	hgsc.bcm.edu	37	chr1	150471453	150471453	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ttctccttccgcctggcactGtccacccggccatctggctt	8	18	2	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr1:150471453G>A	ENST00000369064.3	+	12	1516	c.1482G>A	c.(1480-1482)ctG>ctA	p.L494L	TARS2_ENST00000369054.2_Silent_p.L364L|TARS2_ENST00000438568.2_3'UTR|TARS2_ENST00000606933.1_Silent_p.L412L|TARS2_ENST00000463555.1_3'UTR	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	494					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	GCCTGGCACTGTCCACCCGGC	0.557																																					p.L494L		Atlas-SNP	.											.	TARS2	91	.	0			c.G1482A						.						116	102	106					1																	150471453		2203	4300	6503	SO:0001819	synonymous_variant	80222	exon12			GGCACTGTCCACC	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	30740	protein-coding gene	gene with protein product	"threonine tRNA ligase 2, mitochondrial"	612805	"threonyl-tRNA synthetase-like 1"	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.1482G>A	chr1.hg19:g.150471453G>A		66.0	0.0		108.0	49.0	NM_025150	Q53GW7|Q96I50|Q9H9V2	Silent	SNP	ENST00000369064.3	hg19	CCDS952.1																																																																																			.	.		0.557	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150		A	150471453	G	A	150471453	2	1	172	1	0	0	0	0	0	0	0	1	15575	1364	48	3		3	TARS2	1	150471453	Silent	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	42533529	150471453	98779168	4	26015										
IL6R	3570	hgsc.bcm.edu	37	chr1	154422417	154422417	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ctaataaagacgatgataatAttctcttcagagattctgca	6	7	3	3			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr1:154422417A>G	ENST00000368485.3	+	8	1464	c.1027A>G	c.(1027-1029)Att>Gtt	p.I343V	IL6R_ENST00000344086.4_Missense_Mutation_p.I343V|IL6R_ENST00000507256.1_3'UTR	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	343					acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)		IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	CGATGATAATATTCTCTTCAG	0.443																																					p.I343V		Atlas-SNP	.											.	IL6R	47	.	0			c.A1027G						.						128	128	128					1																	154422417		2203	4300	6503	SO:0001583	missense	3570	exon8			GATAATATTCTCT	X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.1027A>G	chr1.hg19:g.154422417A>G	ENSP00000357470:p.Ile343Val	63.0	0.0		147.0	72.0	NM_000565	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Missense_Mutation	SNP	ENST00000368485.3	hg19	CCDS1067.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.722|6.722	0.501848|0.501848	0.12822|0.12822	.|.	.|.	ENSG00000160712|ENSG00000160712	ENST00000476006;ENST00000515190|ENST00000368485;ENST00000344086	.|T;T	.|0.18174	.|2.24;2.23	4.09|4.09	-0.854|-0.854	0.10705|0.10705	.|.	3.454680|3.454680	0.00817|0.00817	N|N	0.001545|0.001545	T|T	0.03959|0.03959	0.0111|0.0111	L|L	0.28274|0.28274	0.84|0.84	0.09310|0.09310	N|N	1|1	.|B;B	.|0.16166	.|0.016;0.013	.|B;B	.|0.16722	.|0.016;0.01	T|T	0.35500|0.35500	-0.9786|-0.9786	6|10	.|0.29301	.|T	.|0.29	3.4193|3.4193	7.3906|7.3906	0.26907|0.26907	0.4673:0.0:0.5327:0.0|0.4673:0.0:0.5327:0.0	.|.	.|343;343	.|P08887-2;P08887	.|.;IL6RA_HUMAN	M|V	281;145|343	.|ENSP00000357470:I343V;ENSP00000340589:I343V	.|ENSP00000340589:I343V	I|I	+|+	3|1	3|0	IL6R|IL6R	152689041|152689041	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-0.568000|-0.568000	0.05909|0.05909	-0.150000|-0.150000	0.11195|0.11195	-0.371000|-0.371000	0.07208|0.07208	ATA|ATT	.	.		0.443	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565		G	154422417	A	G	154422417	3	3	172	1	0	0	0	0	1	0	0	0	7711	449	16	2	1057	2	IL6R	1	154422417	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	3950964	154422417	94828204	5	26016										
OR10Z1	128368	hgsc.bcm.edu	37	chr1	158576368	158576368	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cagcaatgtcttcattatcaTagccatcaggctggatagcc	8	11	4	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr1:158576368T>C	ENST00000361284.1	+	1	140	c.140T>C	c.(139-141)aTa>aCa	p.I47T		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					TTCATTATCATAGCCATCAGG	0.498																																					p.I47T		Atlas-SNP	.											.	OR10Z1	99	.	0			c.T140C						.						244	232	236					1																	158576368		2203	4300	6503	SO:0001583	missense	128368	exon1			TTATCATAGCCAT	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.140T>C	chr1.hg19:g.158576368T>C	ENSP00000354707:p.Ile47Thr	97.0	0.0		163.0	66.0	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	hg19	CCDS30901.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.139622	0.00030	.	.	ENSG00000198967	ENST00000361284	T	0.01139	5.28	5.36	3.05	0.35203	GPCR, rhodopsin-like superfamily (1);	0.662303	0.12484	N	0.464829	T	0.00144	0.0004	N	0.00808	-1.17	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.19516	-1.0303	10	0.07030	T	0.85	.	7.9631	0.30083	0.0:0.2381:0.0:0.7619	.	47	Q8NGY1	O10Z1_HUMAN	T	47	ENSP00000354707:I47T	ENSP00000354707:I47T	I	+	2	0	OR10Z1	156842992	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	0.153000	0.16323	0.485000	0.27652	0.533000	0.62120	ATA	.	.		0.498	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		C	158576368	T	C	158576368	3	2	172	1	0	0	0	0	1	0	0	0	10932	1406	49	2	142	2	OR10Z1	1	158576368	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	4153951	158576368	90674253	6	26017										
RGS4	5999	hgsc.bcm.edu	37	chr1	163044190	163044190	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aacctgctttgatgaggcccAgaagaagattttcaacctga	9	9	1	6			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr1:163044190A>G	ENST00000367909.6	+	5	798	c.458A>G	c.(457-459)cAg>cGg	p.Q153R	RGS4_ENST00000367906.3_Missense_Mutation_p.Q135R|RGS4_ENST00000527809.1_Missense_Mutation_p.Q135R|RGS4_ENST00000367908.4_3'UTR|RGS4_ENST00000491263.1_3'UTR|RGS4_ENST00000421743.2_Missense_Mutation_p.Q250R|RGS4_ENST00000531057.1_Intron	NM_001113380.1|NM_005613.5	NP_001106851.1|NP_005604.1	P49798	RGS4_HUMAN	regulator of G-protein signaling 4	153	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				inactivation of MAPK activity (GO:0000188)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)	21						GATGAGGCCCAGAAGAAGATT	0.517																																					p.Q250R	Ovarian(76;1257 1738 3039 6086)	Atlas-SNP	.											.	RGS4	97	.	0			c.A749G						.						254	264	261					1																	163044190		2203	4300	6503	SO:0001583	missense	5999	exon6			AGGCCCAGAAGAA	BC051869	CCDS1243.1, CCDS44270.1, CCDS44271.1, CCDS44272.1	1q23.3	2008-05-14	2007-08-14		ENSG00000117152	ENSG00000117152		"Regulators of G-protein signaling"	10000	protein-coding gene	gene with protein product		602516	"regulator of G-protein signalling 4", "schizophrenia disorder 9"	SCZD9		8602223, 8756726	Standard	NM_001102445		Approved		uc001gcl.4	P49798	OTTHUMG00000034417	ENST00000367909.6:c.458A>G	chr1.hg19:g.163044190A>G	ENSP00000356885:p.Gln153Arg	101.0	0.0		183.0	95.0	NM_001102445	A7XA56|A7XA58|A7XA59|A7YVV7|B1APZ3	Missense_Mutation	SNP	ENST00000367909.6	hg19	CCDS1243.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.472758	0.84640	.	.	ENSG00000117152	ENST00000421743;ENST00000367909;ENST00000527809;ENST00000367906;ENST00000528938	T;T;T;T;T	0.02863	4.13;4.13;4.13;4.13;4.13	4.93	4.93	0.64822	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.15132	0.0365	H	0.95745	3.715	0.43421	D	0.995572	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.11690	-1.0577	9	0.87932	D	0	.	12.5856	0.56416	1.0:0.0:0.0:0.0	.	153;250	P49798;A7XA59	RGS4_HUMAN;.	R	250;153;135;135;135	ENSP00000397181:Q250R;ENSP00000356885:Q153R;ENSP00000433261:Q135R;ENSP00000356882:Q135R;ENSP00000432194:Q135R	ENSP00000356882:Q135R	Q	+	2	0	RGS4	161310814	1.000000	0.71417	0.997000	0.53966	0.872000	0.50106	8.930000	0.92872	2.062000	0.61559	0.533000	0.62120	CAG	.	.		0.517	RGS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083197.2	NM_005613		G	163044190	A	G	163044190	3	3	172	1	0	0	0	0	1	0	0	0	13322	188	7	2	771	2	RGS4	1	163044190	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	4467822	163044190	86206431	7	26018										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167064149	167064149	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	agcgaggaggacgaagccaaCgtgagggcggtgcaggccca	18	10	0	1	rs372564326		TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr1:167064149C>A	ENST00000361200.2	+	2	229	c.63C>A	c.(61-63)aaC>aaA	p.N21K	DUSP27_ENST00000271385.5_Missense_Mutation_p.N21K|DUSP27_ENST00000443333.1_Missense_Mutation_p.N21K			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	21					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						ACGAAGCCAACGTGAGGGCGG	0.602																																					p.N21K		Atlas-SNP	.											.	DUSP27	235	.	0			c.C63A						.	C	LYS/ASN	1,4405	2.1+/-5.4	0,1,2202	71	57	62		63	-3.7	0	1		62	0,8598		0,0,4299	no	missense	DUSP27	NM_001080426.1	94	0,1,6501	AA,AC,CC		0.0,0.0227,0.0077	benign	21/1159	167064149	1,13003	2203	4299	6502	SO:0001583	missense	92235	exon1			AGCCAACGTGAGG	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.63C>A	chr1.hg19:g.167064149C>A	ENSP00000354483:p.Asn21Lys	230.0	0.0		361.0	169.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	C	8.912	0.958968	0.18507	2.27E-4	0.0	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03035	4.07;4.07;4.07	5.27	-3.69	0.04450	.	0.797469	0.11523	N	0.555457	T	0.00637	0.0021	N	0.08118	0	0.09310	N	1	B	0.28350	0.208	B	0.20384	0.029	T	0.47071	-0.9145	10	0.87932	D	0	-5.4915	8.1317	0.31031	0.0:0.4512:0.1059:0.4429	.	21	Q5VZP5	DUS27_HUMAN	K	21	ENSP00000354483:N21K;ENSP00000271385:N21K;ENSP00000404874:N21K	ENSP00000271385:N21K	N	+	3	2	DUSP27	165330773	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-2.459000	0.01000	-0.594000	0.05836	0.655000	0.94253	AAC	.	.		0.602	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		A	167064149	C	A	167064149	3	1	172	1	0	0	0	0	1	0	0	0	4826	535	19	1	65	1	DUSP27	1	167064149	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	4019959	167064149	82186472	8	26019										
MIA3	375056	hgsc.bcm.edu	37	chr1	222801064	222801064	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ctttacaggatatggaaaaaAaccctgaattatctaaggaa	7	6	1	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr1:222801064A>T	ENST00000344922.5	+	4	527	c.502A>T	c.(502-504)Aac>Tac	p.N168Y	MIA3_ENST00000344441.6_Missense_Mutation_p.N168Y|MIA3_ENST00000344507.1_Missense_Mutation_p.N168Y|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	168					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		TATGGAAAAAAACCCTGAATT	0.368																																					p.N168Y		Atlas-SNP	.											.	MIA3	167	.	0			c.A502T						.						55	53	53					1																	222801064		1816	4073	5889	SO:0001583	missense	375056	exon4			GAAAAAAACCCTG		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.502A>T	chr1.hg19:g.222801064A>T	ENSP00000340900:p.Asn168Tyr	216.0	0.0		363.0	173.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	hg19	CCDS41470.1	.	.	.	.	.	.	.	.	.	.	A	9.707	1.156019	0.21454	.	.	ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000344507	T;T;T	0.47528	0.84;0.84;0.84	5.05	0.372	0.16173	.	.	.	.	.	T	0.22513	0.0543	N	0.14661	0.345	0.09310	N	1	B;B	0.33883	0.031;0.43	B;B	0.25759	0.037;0.063	T	0.13683	-1.0500	9	0.56958	D	0.05	.	2.1012	0.03680	0.1404:0.4683:0.1467:0.2447	.	168;168	Q5JRA6-2;Q5JRA6	.;MIA3_HUMAN	Y	168	ENSP00000340900:N168Y;ENSP00000340587:N168Y;ENSP00000341348:N168Y	ENSP00000325973:N168Y	N	+	1	0	MIA3	220867687	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.530000	0.06179	-0.146000	0.11274	-0.672000	0.03802	AAC	.	.		0.368	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		T	222801064	A	T	222801064	3	4	172	1	0	0	0	0	1	0	0	0	9574	14	1	4	516	4	MIA3	1	222801064	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	55736915	222801064	26449557	9	26020										
COLEC11	78989	hgsc.bcm.edu	37	chr2	3691387	3691387	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gaggagaagcgctacgcggaCgcccagctgtcctgccaggg	16	13	0	1	rs545129835		TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr2:3691387C>T	ENST00000349077.4	+	7	598	c.495C>T	c.(493-495)gaC>gaT	p.D165D	COLEC11_ENST00000418971.2_Silent_p.D179D|COLEC11_ENST00000236693.7_Silent_p.D162D|COLEC11_ENST00000402794.1_Silent_p.D115D|COLEC11_ENST00000404205.1_Silent_p.D91D|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000403096.3_Silent_p.D139D|COLEC11_ENST00000382062.2_Silent_p.D141D|COLEC11_ENST00000402922.1_Silent_p.D115D	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	165	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		GCTACGCGGACGCCCAGCTGT	0.662																																					p.D179D		Atlas-SNP	.											.	COLEC11	93	.	0			c.C537T						.						38	40	39					2																	3691387		2203	4298	6501	SO:0001819	synonymous_variant	78989	exon8			CGCGGACGCCCAG	BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"Collectins"	17213	protein-coding gene	gene with protein product	"Collectin K1"	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.495C>T	chr2.hg19:g.3691387C>T		129.0	0.0		162.0	76.0	NM_001255985	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Silent	SNP	ENST00000349077.4	hg19	CCDS1649.1																																																																																			.	.		0.662	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027		T	3691387	C	T	3691387	2	4	172	1	0	0	0	0	0	0	0	1	3713	535	19	1		1	COLEC11	2	3691387	Silent	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10		3691387	239507986	10	26021										
WDR92	116143	hgsc.bcm.edu	37	chr2	68384452	68384452	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cagctgaatgacgccggtgcCccgtgcgaagttgcccatgg	14	13	0	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr2:68384452C>T	ENST00000295121.6	-	1	240	c.124G>A	c.(124-126)Ggc>Agc	p.G42S	WDR92_ENST00000409164.1_Missense_Mutation_p.G42S|RP11-474G23.1_ENST00000406334.3_3'UTR|PNO1_ENST00000263657.2_5'Flank|WDR92_ENST00000406245.2_Intron|WDR92_ENST00000492039.2_Intron	NM_138458.3	NP_612467.1	Q96MX6	WDR92_HUMAN	WD repeat domain 92	42					apoptotic process (GO:0006915)|histone lysine methylation (GO:0034968)		methylated histone binding (GO:0035064)			endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|stomach(1)	12						ACGCCGGTGCCCCGTGCGAAG	0.607																																					p.G42S		Atlas-SNP	.											.	WDR92	21	.	0			c.G124A						.						73	70	71					2																	68384452		2203	4300	6503	SO:0001583	missense	116143	exon1			CGGTGCCCCGTGC	AK056303	CCDS1884.1, CCDS58712.1	2p14	2013-01-09			ENSG00000243667	ENSG00000243667		"WD repeat domain containing"	25176	protein-coding gene	gene with protein product		610729				16487927	Standard	NM_138458		Approved	FLJ31741, Monad	uc002see.2	Q96MX6	OTTHUMG00000152561	ENST00000295121.6:c.124G>A	chr2.hg19:g.68384452C>T	ENSP00000295121:p.Gly42Ser	87.0	0.0		99.0	48.0	NM_001256476	Q96CR6	Missense_Mutation	SNP	ENST00000295121.6	hg19	CCDS1884.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.372769	0.82573	.	.	ENSG00000243667	ENST00000295121;ENST00000409164	T;T	0.74209	1.72;-0.82	5.66	5.66	0.87406	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000002	T	0.70718	0.3256	L	0.60845	1.875	0.80722	D	1	P	0.43431	0.807	B	0.35510	0.204	T	0.72114	-0.4388	10	0.36615	T	0.2	.	19.76	0.96311	0.0:1.0:0.0:0.0	.	42	Q96MX6	WDR92_HUMAN	S	42	ENSP00000295121:G42S;ENSP00000386746:G42S	ENSP00000295121:G42S	G	-	1	0	WDR92	68237956	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	6.944000	0.75940	2.666000	0.90696	0.655000	0.94253	GGC	.	.		0.607	WDR92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251754.2	NM_138458		T	68384452	C	T	68384452	3	4	172	1	0	0	0	0	1	0	0	0	17354	623	22	3	981	3	WDR92	2	68384452	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	64693065	68384452	174814921	11	26022										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613037	+	Missense_Mutation	DNP	GA	GA	CT													0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	catggccgggcgagctggagGaggaggaggaggaggaggag					rs61156725|rs72319667|rs3074417	byFrequency	TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr2:73613036_73613037GA>CT	ENST00000264448.6	+	1	151_152	c.40_41GA>CT	c.(40-42)GAg>CTg	p.E14L	ALMS1_ENST00000377715.1_Missense_Mutation_p.E14L|ALMS1_ENST00000409009.1_Missense_Mutation_p.E14L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggaggag	0.693																																					p.E14Q|p.E14V		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C|c.A41T						.																																			SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG|TGGAGGAGGAGGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	Exception_encountered	chr2.hg19:g.73613036_73613037delinsCT	ENSP00000264448:p.Glu14Leu	129.0|130.0	0.0		266.0|268.0	20.0|23.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.693	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		CT	73613037	GA	CT	73613036	3	2	172	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	DNP	GA	TCGA-DD-AACV-01A-11D-A40R-10	5228584	73613036	169586337	12	26023										
SPEG	10290	hgsc.bcm.edu	37	chr2	220326770	220326770	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	actggctccaaggcacccccCaccttcaaggtcagacccct	7	19	2	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr2:220326770C>A	ENST00000312358.7	+	7	2739	c.2607C>A	c.(2605-2607)ccC>ccA	p.P869P	SPEG_ENST00000396689.2_Silent_p.P20P|SPEG_ENST00000396698.1_Silent_p.P765P|SPEG_ENST00000396695.2_Silent_p.P77P|SPEG_ENST00000485813.1_3'UTR|SPEG_ENST00000396688.1_Silent_p.P20P|SPEG_ENST00000396686.1_Silent_p.P20P	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	869	Ig-like 3.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		AGGCACCCCCCACCTTCAAGG	0.642																																					p.P869P		Atlas-SNP	.											.	SPEG	272	.	0			c.C2607A						.						31	35	33					2																	220326770		1892	4111	6003	SO:0001819	synonymous_variant	10290	exon7			ACCCCCCACCTTC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2607C>A	chr2.hg19:g.220326770C>A		85.0	0.0		97.0	51.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.642	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220326770	C	A	220326770	2	1	172	1	0	0	0	0	0	0	0	1	15051	581	21	3		3	SPEG	2	220326770	Silent	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	146713734	220326770	22872603	13	26024										
VPRBP	9730	hgsc.bcm.edu	37	chr3	51505011	51505011	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ttcagtttctttttcaatcaAttgagacatcctagcacaaa	4	9	4	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:51505011A>T	ENST00000335891.5	-	2	130	c.121T>A	c.(121-123)Ttg>Atg	p.L41M				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	41					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		TTTTCAATCAATTGAGACATC	0.403																																					p.L41M		Atlas-SNP	.											.	VPRBP	107	.	0			c.T121A						.						98	88	91					3																	51505011		1857	4106	5963	SO:0001583	missense	9730	exon4			CAATCAATTGAGA	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.121T>A	chr3.hg19:g.51505011A>T	ENSP00000338857:p.Leu41Met	64.0	0.0		112.0	54.0	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	hg19		.	.	.	.	.	.	.	.	.	.	A	16.50	3.140130	0.56936	.	.	ENSG00000145041	ENST00000335891;ENST00000504652	T;T	0.60797	0.16;0.55	4.93	2.47	0.30058	.	0.156624	0.42420	D	0.000718	T	0.68997	0.3062	M	0.65975	2.015	0.21386	N	0.999708	D	0.62365	0.991	D	0.75484	0.986	T	0.57723	-0.7762	10	0.66056	D	0.02	-0.471	7.8207	0.29286	0.7509:0.0:0.249:0.0	.	41	Q9Y4B6	VPRBP_HUMAN	M	41	ENSP00000338857:L41M;ENSP00000421724:L41M	ENSP00000338857:L41M	L	-	1	2	VPRBP	51480051	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	1.243000	0.32767	0.726000	0.32339	-0.587000	0.04127	TTG	.	.		0.403	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		T	51505011	A	T	51505011	3	4	172	1	0	0	0	0	1	0	0	0	17200	98	4	4	4327	4	VPRBP	3	51505011	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10		51505011	146517419	14	26025										
CADPS	8618	hgsc.bcm.edu	37	chr3	62467427	62467427	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tatatagcagccatccatgaCggtgccgaaaaagtaggcat	10	9	0	1	rs368961255		TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:62467427C>T	ENST00000383710.4	-	22	3493	c.3144G>A	c.(3142-3144)ccG>ccA	p.P1048P	CADPS_ENST00000283269.9_Intron|CADPS_ENST00000357948.3_Intron	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1048	Interaction with DRD2.|MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		CCATCCATGACGGTGCCGAAA	0.398																																					p.P1048P		Atlas-SNP	.											.	CADPS	387	.	0			c.G3144A						.	C	,,	1,3805		0,1,1902	202	188	193		3144,,	4.7	1	3		193	0,8254		0,0,4127	no	coding-synonymous,intron,intron	CADPS	NM_003716.3,NM_183393.2,NM_183394.2	,,	0,1,6029	TT,TC,CC		0.0,0.0263,0.0083	,,	1048/1354,,	62467427	1,12059	1903	4127	6030	SO:0001819	synonymous_variant	8618	exon22			CCATGACGGTGCC	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3144G>A	chr3.hg19:g.62467427C>T		161.0	0.0		186.0	72.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	C	7.200	0.593233	0.13875	2.63E-4	0.0	ENSG00000163618	ENST00000473635	.	.	.	5.52	4.65	0.58169	.	.	.	.	.	T	0.72732	0.3497	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72896	-0.4153	4	.	.	.	.	16.8253	0.85929	0.0:0.8714:0.1285:0.0	.	.	.	.	H	35	.	.	R	-	2	0	CADPS	62442467	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.995000	0.49441	1.460000	0.47911	0.563000	0.77884	CGT	.	.		0.398	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		T	62467427	C	T	62467427	2	4	172	1	0	0	0	0	0	0	0	1	2572	523	19	1		1	CADPS	3	62467427	Silent	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	10962416	62467427	135555003	15	26026										
OR5H2	79310	hgsc.bcm.edu	37	chr3	98001914	98001945	+	Frame_Shift_Del	DEL	CATCCCCATGTACTTTTTTCTTGGGAGTTTAG	CATCCCCATGTACTTTTTTCTTGGGAGTTTAG	-													0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tggaatgacccacaacttcaCatccccatgtacttttttct					rs143349446|rs547108121	byFrequency	TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	CATCCCCATGTACTTTTTTCTTGGGAGTTTAG	CATCCCCATGTACTTTTTTCTTGGGAGTTTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:98001914_98001945delCATCCCCATGTACTTTTTTCTTGGGAGTTTAG	ENST00000355273.2	+	1	183_214	c.183_214delCATCCCCATGTACTTTTTTCTTGGGAGTTTAG	c.(181-216)cacatccccatgtacttttttcttgggagtttagccfs	p.IPMYFFLGSLA62fs	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S70I(1)|p.G69W(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						CACAACTTCACATCCCCATGTACTTTTTTCTTGGGAGTTTAGCCTTTGTTGA	0.409																																					p.61_71del		Atlas-INDEL	.											.	OR5H2	63	.	2	Substitution - Missense(2)	ovary(1)|lung(1)	c.182_213del						.																																			SO:0001589	frameshift_variant	79310	exon1			.		CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"GPCR / Class A : Olfactory receptors"	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.183_214delCATCCCCATGTACTTTTTTCTTGGGAGTTTAG	chr3.hg19:g.98001914_98001945delCATCCCCATGTACTTTTTTCTTGGGAGTTTAG	ENSP00000347418:p.Ile62fs	113.0	0.0		136.0	26.0	NM_001005482	Q6IF87	Frame_Shift_Del	DEL	ENST00000355273.2	hg19	CCDS33801.1																																																																																			.	.		0.409	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2			-	98001945	CATCCCCATGTACTTTTTTCTTGGGAGTTTAG	-	98001914	7	5	172	1	0	1	0	1	0	0	0	0	11171	477	17	0	185	0	OR5H2	3	98001914	Frame_Shift_Del	DEL	CATCCCCATGTACTTTTTTCTTGGGAGTTTAG	TCGA-DD-AACV-01A-11D-A40R-10	35534487	98001914	100020516	16	26027										
MORC1	27136	hgsc.bcm.edu	37	chr3	108698449	108698449	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aagcaactttacaactgccaCtcacagaaactctggctatg	6	12	2	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:108698449C>T	ENST00000483760.1	-	23	2370	c.2327G>A	c.(2326-2328)aGt>aAt	p.S776N	MORC1_ENST00000232603.5_Missense_Mutation_p.S797N					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						ACAACTGCCACTCACAGAAAC	0.403																																					p.S797N		Atlas-SNP	.											.	MORC1	211	.	0			c.G2390A						.						118	112	114					3																	108698449		2203	4300	6503	SO:0001583	missense	27136	exon24			CTGCCACTCACAG	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2327G>A	chr3.hg19:g.108698449C>T	ENSP00000417282:p.Ser776Asn	98.0	0.0		134.0	57.0	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.49	1.363480	0.24684	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.06528	3.32;3.29	5.25	-3.69	0.04450	.	1.666880	0.03032	N	0.152287	T	0.03827	0.0108	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.38735	-0.9647	10	0.23891	T	0.37	-0.0757	2.2679	0.04083	0.1345:0.225:0.1329:0.5077	.	776;797	E7ERX1;Q86VD1	.;MORC1_HUMAN	N	797;776	ENSP00000232603:S797N;ENSP00000417282:S776N	ENSP00000232603:S797N	S	-	2	0	MORC1	110181139	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.337000	0.02657	-0.864000	0.04078	-0.165000	0.13383	AGT	.	.		0.403	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			T	108698449	C	T	108698449	3	4	172	1	0	0	0	0	1	0	0	0	9710	565	20	3	584	3	MORC1	3	108698449	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	10696535	108698449	89323981	17	26028										
CD200R1	131450	hgsc.bcm.edu	37	chr3	112647737	112647737	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aggtcacggtagacacattgTggacctcccagtggcatgta	12	10	1	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:112647737T>A	ENST00000471858.1	-	4	858	c.626A>T	c.(625-627)cAc>cTc	p.H209L	CD200R1_ENST00000308611.3_Missense_Mutation_p.H232L|CD200R1_ENST00000295863.4_Missense_Mutation_p.H187L	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	209	Ig-like C2-type.				regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						AGACACATTGTGGACCTCCCA	0.473																																					p.H232L		Atlas-SNP	.											.	CD200R1	91	.	0			c.A695T						.						115	95	102					3																	112647737		2203	4300	6503	SO:0001583	missense	131450	exon5			ACATTGTGGACCT	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"Immunoglobulin superfamily / C2-set domain containing"	24235	protein-coding gene	gene with protein product		607546	"MOX2 receptor"	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.626A>T	chr3.hg19:g.112647737T>A	ENSP00000418928:p.His209Leu	104.0	0.0		149.0	82.0	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	hg19	CCDS2970.1	.	.	.	.	.	.	.	.	.	.	T	10.82	1.458517	0.26248	.	.	ENSG00000163606	ENST00000471858;ENST00000308611;ENST00000295863	T;T;T	0.76186	-1.0;-1.0;-1.0	5.24	-10.5	0.00291	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);	2.147030	0.01987	N	0.045222	T	0.60235	0.2253	L	0.57536	1.79	0.09310	N	1	B;B;B	0.18166	0.026;0.001;0.001	B;B;B	0.20184	0.028;0.009;0.005	T	0.42882	-0.9425	10	0.11182	T	0.66	.	4.175	0.10348	0.1555:0.5168:0.2084:0.1193	.	187;209;232	B4E2U2;Q8TD46;Q8TD46-4	.;MO2R1_HUMAN;.	L	209;232;187	ENSP00000418928:H209L;ENSP00000311035:H232L;ENSP00000295863:H187L	ENSP00000295863:H187L	H	-	2	0	CD200R1	114130427	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-4.038000	0.00308	-1.592000	0.01619	-1.137000	0.01932	CAC	.	.		0.473	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806		A	112647737	T	A	112647737	3	1	172	1	0	0	0	0	1	0	0	0	2983	1696	59	4	367	4	CD200R1	3	112647737	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	3949288	112647737	85374693	18	26029										
TMEM39A	55254	hgsc.bcm.edu	37	chr3	119176876	119176878	+	In_Frame_Del	DEL	AAG	AAG	-													0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aagacttaccagtgatgtacAagaagcaggatgattgtaag							TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:119176876_119176878delAAG	ENST00000319172.5	-	3	743_745	c.323_325delCTT	c.(322-327)tcttgt>tgt	p.S108del	TMEM39A_ENST00000486159.1_5'UTR	NM_018266.1	NP_060736.1	Q9NV64	TM39A_HUMAN	transmembrane protein 39A	108						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	13				GBM - Glioblastoma multiforme(114;0.244)		AGTGATGTACAAGAAGCAGGATG	0.34																																					p.108_109del		Atlas-INDEL	.											.	TMEM39A	36	.	0			c.324_326del						.																																			SO:0001651	inframe_deletion	55254	exon3			.	BC021277	CCDS2987.1	3q13.33	2005-01-10			ENSG00000176142	ENSG00000176142			25600	protein-coding gene	gene with protein product						12477932	Standard	NM_018266		Approved	FLJ10902	uc003eck.2	Q9NV64	OTTHUMG00000159361	ENST00000319172.5:c.323_325delCTT	chr3.hg19:g.119176879_119176881delAAG	ENSP00000326063:p.Ser108del	105.0	0.0		144.0	59.0	NM_018266	D3DN80|Q53FN4|Q53GI1|Q6PKB5	In_Frame_Del	DEL	ENST00000319172.5	hg19	CCDS2987.1																																																																																			.	.		0.34	TMEM39A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354941.3	NM_018266		-	119176878	AAG	-	119176876	7	5	172	1	0	1	0	1	0	0	0	0	16176	130	5	0	1169	0	TMEM39A	3	119176876	In_Frame_Del	DEL	AAG	TCGA-DD-AACV-01A-11D-A40R-10	6529139	119176876	78845554	19	26030										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	120998775	120998775	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	taccagcgacaaccacggtcTcctcgaaaaaacaaacagtt	6	13	1	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:120998775T>A	ENST00000273666.6	+	19	2353	c.2082T>A	c.(2080-2082)tcT>tcA	p.S694S	STXBP5L_ENST00000492541.1_Silent_p.S694S|STXBP5L_ENST00000497029.1_Silent_p.S694S|STXBP5L_ENST00000472879.1_Silent_p.S694S|STXBP5L_ENST00000471454.1_Silent_p.S694S	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	694					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		AACCACGGTCTCCTCGAAAAA	0.388																																					p.S694S		Atlas-SNP	.											.	STXBP5L	159	.	0			c.T2082A						.						105	97	100					3																	120998775		1883	4115	5998	SO:0001819	synonymous_variant	9515	exon19			ACGGTCTCCTCGA	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.2082T>A	chr3.hg19:g.120998775T>A		115.0	0.0		151.0	77.0	NM_014980	Q4G1B4|Q6PIC3	Silent	SNP	ENST00000273666.6	hg19	CCDS43137.1																																																																																			.	.		0.388	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			A	120998775	T	A	120998775	2	1	172	1	0	0	0	0	0	0	0	1	15372	1538	54	4		4	STXBP5L	3	120998775	Silent	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	1821899	120998775	77023655	20	26031										
STAG1	10274	hgsc.bcm.edu	37	chr3	136060292	136060292	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gtaacacttacacagcatgcCtcactccagttctcactttc	4	15	2	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:136060292C>G	ENST00000383202.2	-	31	3804	c.3548G>C	c.(3547-3549)aGg>aCg	p.R1183T	STAG1_ENST00000434713.2_Missense_Mutation_p.R923T|STAG1_ENST00000236698.5_Intron|STAG1_ENST00000536929.1_Missense_Mutation_p.R767T	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1183					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						CACAGCATGCCTCACTCCAGT	0.418																																					p.R1183T		Atlas-SNP	.											.	STAG1	135	.	0			c.G3548C						.						270	202	225					3																	136060292		2203	4300	6503	SO:0001583	missense	10274	exon31			GCATGCCTCACTC	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.3548G>C	chr3.hg19:g.136060292C>G	ENSP00000372689:p.Arg1183Thr	47.0	0.0		74.0	36.0	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	hg19	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.198309	0.58126	.	.	ENSG00000118007	ENST00000383202;ENST00000434713;ENST00000536929	T;T;T	0.33438	1.8;1.78;1.41	5.72	5.72	0.89469	.	0.136113	0.52532	D	0.000071	T	0.31199	0.0789	L	0.41236	1.265	0.58432	D	0.999992	P	0.36683	0.565	B	0.35312	0.2	T	0.08848	-1.0702	10	0.72032	D	0.01	.	19.8868	0.96915	0.0:1.0:0.0:0.0	.	1183	Q8WVM7	STAG1_HUMAN	T	1183;923;767	ENSP00000372689:R1183T;ENSP00000404396:R923T;ENSP00000445787:R767T	ENSP00000372689:R1183T	R	-	2	0	STAG1	137542982	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	4.581000	0.60949	2.689000	0.91719	0.650000	0.86243	AGG	.	.		0.418	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		G	136060292	C	G	136060292	3	3	172	1	0	0	0	0	1	0	0	0	15257	681	24	4	244	4	STAG1	3	136060292	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	15061517	136060292	61962138	21	26032										
ZBTB38	253461	hgsc.bcm.edu	37	chr3	141161744	141161744	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	caaatgcattttccatcatcGaaacagaaaatagtaataac	4	8	1	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:141161744G>A	ENST00000514251.1	+	4	793	c.514G>A	c.(514-516)Gaa>Aaa	p.E172K	ZBTB38_ENST00000321464.5_Missense_Mutation_p.E173K|ZBTB38_ENST00000441582.2_Missense_Mutation_p.E172K					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						TTCCATCATCGAAACAGAAAA	0.418																																					p.E172K		Atlas-SNP	.											.	ZBTB38	92	.	0			c.G514A						.						92	86	88					3																	141161744		1918	4135	6053	SO:0001583	missense	253461	exon8			ATCATCGAAACAG	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	26636	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 171"	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.514G>A	chr3.hg19:g.141161744G>A	ENSP00000426387:p.Glu172Lys	103.0	0.0		144.0	74.0	NM_001080412		Missense_Mutation	SNP	ENST00000514251.1	hg19	CCDS43157.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.942240	0.92526	.	.	ENSG00000177311	ENST00000509883;ENST00000514251;ENST00000441582;ENST00000321464;ENST00000510726	T;T;T;T;D	0.83914	3.17;2.64;2.64;2.64;-1.78	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.87168	0.6110	L	0.34521	1.04	0.53688	D	0.999979	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.85338	0.1094	9	.	.	.	-10.0734	19.5786	0.95455	0.0:0.0:1.0:0.0	.	173;172	B4DYR8;Q8NAP3	.;ZBT38_HUMAN	K	172;172;172;173;172	ENSP00000424254:E172K;ENSP00000426387:E172K;ENSP00000406955:E172K;ENSP00000372635:E173K;ENSP00000422081:E172K	.	E	+	1	0	ZBTB38	142644434	1.000000	0.71417	0.905000	0.35620	0.993000	0.82548	9.041000	0.93788	2.699000	0.92147	0.591000	0.81541	GAA	.	.		0.418	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2			A	141161744	G	A	141161744	3	1	172	1	0	0	0	0	1	0	0	0	17554	1059	37	1	516	1	ZBTB38	3	141161744	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	5101452	141161744	56860686	22	26033										
AGTR1	185	hgsc.bcm.edu	37	chr3	148459155	148459155	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tcagccagcgtcagtttcaaCctgtacgctagtgtgtttct	9	11	4	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:148459155C>G	ENST00000497524.1	+	2	724	c.333C>G	c.(331-333)aaC>aaG	p.N111K	AGTR1_ENST00000418473.2_Missense_Mutation_p.N111K|AGTR1_ENST00000475347.1_Missense_Mutation_p.N111K|AGTR1_ENST00000402260.1_Missense_Mutation_p.N111K|AGTR1_ENST00000404754.2_Missense_Mutation_p.N111K|AGTR1_ENST00000542281.1_Missense_Mutation_p.N111K|AGTR1_ENST00000474935.1_Missense_Mutation_p.N111K|AGTR1_ENST00000349243.3_Missense_Mutation_p.N111K|AGTR1_ENST00000461609.1_Missense_Mutation_p.N111K	NM_009585.3	NP_033611.1	P30556	AGTR1_HUMAN	angiotensin II receptor, type 1	111					angiotensin-activated signaling pathway (GO:0038166)|calcium-mediated signaling (GO:0019722)|cell chemotaxis (GO:0060326)|G-protein coupled receptor signaling pathway (GO:0007186)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|phospholipase C-activating angiotensin-activated signaling pathway (GO:0086097)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of phospholipase A2 activity (GO:0032430)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|renin-angiotensin regulation of aldosterone production (GO:0002018)|Rho protein signal transduction (GO:0007266)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin type I receptor activity (GO:0001596)|angiotensin type II receptor activity (GO:0004945)|bradykinin receptor binding (GO:0031711)|protein heterodimerization activity (GO:0046982)			breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30			LUSC - Lung squamous cell carcinoma(72;0.127)|Lung(72;0.152)		Azilsartan medoxomil(DB08822)|Candesartan(DB00796)|Eprosartan(DB00876)|Forasartan(DB01342)|Irbesartan(DB01029)|Losartan(DB00678)|Olmesartan(DB00275)|Saprisartan(DB01347)|Tasosartan(DB01349)|Telmisartan(DB00966)|Valsartan(DB00177)	TCAGTTTCAACCTGTACGCTA	0.483																																					p.N146K		Atlas-SNP	.											.	AGTR1	63	.	0			c.C438G						.						104	101	102					3																	148459155		2203	4300	6503	SO:0001583	missense	185	exon4			TTTCAACCTGTAC	M87290	CCDS3137.1	3q24	2012-08-08	2002-02-20		ENSG00000144891	ENSG00000144891		"GPCR / Class A : Angiotensin receptors"	336	protein-coding gene	gene with protein product		106165	"angiotensin receptor 1B"	AGTR1B		1550596	Standard	NM_009585		Approved	AT1, AT2R1, AGTR1A, AT2R1A, HAT1R, AG2S, AT2R1B, AT1B	uc003ewh.4	P30556	OTTHUMG00000159503	ENST00000497524.1:c.333C>G	chr3.hg19:g.148459155C>G	ENSP00000419422:p.Asn111Lys	52.0	0.0		64.0	28.0	NM_031850	Q13725|Q8TBK4	Missense_Mutation	SNP	ENST00000497524.1	hg19	CCDS3137.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.922193	0.52653	.	.	ENSG00000144891	ENST00000497524;ENST00000349243;ENST00000542281;ENST00000418473;ENST00000404754;ENST00000475347;ENST00000474935;ENST00000461609;ENST00000402260	T;T;T;T;T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12;1.12;1.12;1.12;1.12	5.48	3.64	0.41730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.75635	0.3876	H	0.98818	4.34	0.58432	D	0.999993	D	0.89917	1.0	D	0.87578	0.998	T	0.81232	-0.1026	10	0.56958	D	0.05	-20.8487	9.673	0.40023	0.0:0.6769:0.0:0.3231	.	111	P30556	AGTR1_HUMAN	K	111	ENSP00000419422:N111K;ENSP00000273430:N111K;ENSP00000443186:N111K;ENSP00000398832:N111K;ENSP00000385612:N111K;ENSP00000419783:N111K;ENSP00000418084:N111K;ENSP00000418851:N111K;ENSP00000385641:N111K	ENSP00000273430:N111K	N	+	3	2	AGTR1	149941845	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	1.169000	0.31871	1.275000	0.44379	0.655000	0.94253	AAC	.	.		0.483	AGTR1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355807.1			G	148459155	C	G	148459155	3	3	172	1	0	0	0	0	1	0	0	0	401	506	18	4	335	4	AGTR1	3	148459155	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	7297411	148459155	49563275	23	26034										
CP	1356	hgsc.bcm.edu	37	chr3	148905856	148905856	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tacagtgcattttattagatTcctgaaagtcttcatcttcc	5	9	3	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:148905856T>C	ENST00000264613.6	-	10	2109	c.1847A>G	c.(1846-1848)gAa>gGa	p.E616G	CP_ENST00000462336.1_5'UTR	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	616	F5/8 type A 2.|Plastocyanin-like 4.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	TTTATTAGATTCCTGAAAGTC	0.338																																					p.E616G		Atlas-SNP	.											.	CP	112	.	0			c.A1847G						.						138	137	138					3																	148905856		2203	4297	6500	SO:0001583	missense	1356	exon10			TTAGATTCCTGAA	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1847A>G	chr3.hg19:g.148905856T>C	ENSP00000264613:p.Glu616Gly	73.0	0.0		80.0	36.0	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	hg19	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.840754	0.91197	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98792	-5.14;-5.14	6.16	6.16	0.99307	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.98748	0.9579	H	0.94423	3.535	0.80722	D	1	D;P;D;P	0.54047	0.964;0.927;0.964;0.927	B;B;B;B	0.43867	0.434;0.434;0.434;0.284	D	0.99533	1.0961	10	0.62326	D	0.03	-41.9819	16.8061	0.85666	0.0:0.0:0.0:1.0	.	616;616;616;616	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	G	616;399	ENSP00000264613:E616G;ENSP00000420545:E399G	ENSP00000264613:E616G	E	-	2	0	CP	150388546	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.459000	0.66685	2.367000	0.80283	0.528000	0.53228	GAA	.	.		0.338	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		C	148905856	T	C	148905856	3	2	172	1	0	0	0	0	1	0	0	0	3789	1783	62	2	1390	2	CP	3	148905856	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	446701	148905856	49116574	24	26035										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151171320	151171320	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aagttatcagacaagtatagGaacttaatgaaagagatttt	8	3	1	3			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:151171320G>A	ENST00000282466.3	-	3	566	c.567C>T	c.(565-567)ttC>ttT	p.F189F		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	189					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACAAGTATAGGAACTTAATGA	0.453																																					p.F189F		Atlas-SNP	.											.	IGSF10	279	.	0			c.C567T						.						116	122	120					3																	151171320		2203	4300	6503	SO:0001819	synonymous_variant	285313	exon3			GTATAGGAACTTA	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.567C>T	chr3.hg19:g.151171320G>A		163.0	0.0		225.0	90.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	hg19	CCDS3160.1																																																																																			.	.		0.453	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151171320	G	A	151171320	2	1	172	1	0	0	0	0	0	0	0	1	7606	1165	41	3		3	IGSF10	3	151171320	Silent	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	2265464	151171320	46851110	25	26036										
ABCF3	55324	hgsc.bcm.edu	37	chr3	183907511	183907511	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gctcaaccagcagcgtgaatAtgaggcgcagcagcagtatc	12	11	1	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr3:183907511A>G	ENST00000429586.2	+	13	1465	c.1280A>G	c.(1279-1281)tAt>tGt	p.Y427C	ABCF3_ENST00000292808.5_Missense_Mutation_p.Y421C|EIF2B5_ENST00000444495.1_Intron	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 3	427					defense response to virus (GO:0051607)	membrane (GO:0016020)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CAGCGTGAATATGAGGCGCAG	0.602																																					p.Y427C		Atlas-SNP	.											.	ABCF3	72	.	0			c.A1280G						.						35	33	33					3																	183907511		2203	4300	6503	SO:0001583	missense	55324	exon13			GTGAATATGAGGC	U66685	CCDS3254.1	3q27.1	2012-05-16			ENSG00000161204	ENSG00000161204		"ATP binding cassette transporters / subfamily F"	72	protein-coding gene	gene with protein product						8894702	Standard	NM_018358		Approved	EST201864	uc003fmz.2	Q9NUQ8	OTTHUMG00000156824	ENST00000429586.2:c.1280A>G	chr3.hg19:g.183907511A>G	ENSP00000411471:p.Tyr427Cys	44.0	0.0		91.0	61.0	NM_018358	A8K241|Q86UA2|Q8NAN1|Q96GS8|Q9H7A8	Missense_Mutation	SNP	ENST00000429586.2	hg19	CCDS3254.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.035655	0.35893	.	.	ENSG00000161204	ENST00000429586;ENST00000292808	D;D	0.92911	-3.13;-3.13	4.05	4.05	0.47172	.	0.000000	0.85682	D	0.000000	D	0.97031	0.9030	H	0.95982	3.75	0.80722	D	1	D;P	0.89917	1.0;0.585	D;B	0.79108	0.992;0.277	D	0.97737	1.0206	10	0.87932	D	0	-8.1136	12.3482	0.55132	1.0:0.0:0.0:0.0	.	421;427	Q9NUQ8-2;Q9NUQ8	.;ABCF3_HUMAN	C	427;421	ENSP00000411471:Y427C;ENSP00000292808:Y421C	ENSP00000292808:Y421C	Y	+	2	0	ABCF3	185390205	1.000000	0.71417	0.975000	0.42487	0.417000	0.31264	8.477000	0.90424	1.710000	0.51325	0.460000	0.39030	TAT	.	.		0.602	ABCF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346047.1	NM_018358		G	183907511	A	G	183907511	3	3	172	1	0	0	0	0	1	0	0	0	67	449	16	2	1330	2	ABCF3	3	183907511	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	32736191	183907511	14114919	26	26037										
PDLIM5	10611	hgsc.bcm.edu	37	chr4	95539284	95539284	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	acagctgcagctgccttcaaGcctgtaggatccactggcgt	11	13	1	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr4:95539284G>A	ENST00000317968.4	+	8	1186	c.1050G>A	c.(1048-1050)aaG>aaA	p.K350K	PDLIM5_ENST00000437932.1_Silent_p.K241K|PDLIM5_ENST00000542407.1_Silent_p.K228K|PDLIM5_ENST00000514743.1_Silent_p.K379K|PDLIM5_ENST00000380176.3_3'UTR	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	350					regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		CTGCCTTCAAGCCTGTAGGAT	0.572																																					p.K379K		Atlas-SNP	.											.	PDLIM5	76	.	0			c.G1137A						.						53	46	48					4																	95539284		2203	4300	6503	SO:0001819	synonymous_variant	10611	exon12			CTTCAAGCCTGTA	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.1050G>A	chr4.hg19:g.95539284G>A		180.0	0.0		118.0	110.0	NM_001256426	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Silent	SNP	ENST00000317968.4	hg19	CCDS3641.1																																																																																			.	.		0.572	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1			A	95539284	G	A	95539284	2	1	172	1	0	0	0	0	0	0	0	1	11692	962	34	3		3	PDLIM5	4	95539284	Silent	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10		95539284	95614992	27	26038										
CDH9	1007	hgsc.bcm.edu	37	chr5	26988368	26988368	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ataactgttaggtttttcttGtaataggatggtgtcaactg	10	4	2	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr5:26988368G>A	ENST00000231021.4	-	2	245	c.73C>T	c.(73-75)Caa>Taa	p.Q25*		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	25					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						GGTTTTTCTTGTAATAGGATG	0.393																																					p.Q25X	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.C73T						.						143	144	144					5																	26988368		2203	4300	6503	SO:0001587	stop_gained	1007	exon2			TTTCTTGTAATAG	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.73C>T	chr5.hg19:g.26988368G>A	ENSP00000231021:p.Gln25*	113.0	0.0		230.0	50.0	NM_016279	Q3B7I5	Nonsense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.034492	0.75617	.	.	ENSG00000113100	ENST00000231021;ENST00000513289;ENST00000511822	.	.	.	5.64	4.75	0.60458	.	1.038480	0.07520	N	0.910439	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6722	0.62432	0.0:0.2959:0.7041:0.0	.	.	.	.	X	25	.	.	Q	-	1	0	CDH9	27024125	0.994000	0.37717	0.265000	0.24526	0.114000	0.19823	2.481000	0.45215	1.338000	0.45544	0.591000	0.81541	CAA	.	.		0.393	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26988368	G	A	26988368	4	1	172	1	0	0	0	0	0	1	0	0	3119	1386	48	3	2340	3	CDH9	5	26988368	Nonsense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10		26988368	153926892	28	26039										
HMGCS1	3157	hgsc.bcm.edu	37	chr5	43298839	43298839	+	Frame_Shift_Del	DEL	T	T	-													0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ggaaaggttatttctctccaTaagattctgaaccacagtca							TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr5:43298839delT	ENST00000325110.6	-	3	435	c.229delA	c.(229-231)atgfs	p.M77fs	HMGCS1_ENST00000433297.2_Frame_Shift_Del_p.M77fs	NM_001098272.2	NP_001091742.1	Q01581	HMCS1_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)	77					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|lipid metabolic process (GO:0006629)|liver development (GO:0001889)|male gonad development (GO:0008584)|response to acid chemical (GO:0001101)|response to drug (GO:0042493)|response to lipoprotein particle (GO:0055094)|response to low light intensity stimulus (GO:0009645)|response to purine-containing compound (GO:0014074)|response to tellurium ion (GO:0046690)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hydroxymethylglutaryl-CoA synthase activity (GO:0004421)|isomerase activity (GO:0016853)|organic acid binding (GO:0043177)			NS(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|stomach(1)|urinary_tract(1)	15						TTTCTCTCCATAAGATTCTGA	0.428																																					p.M77fs		Atlas-INDEL	.											.	HMGCS1	33	.	0			c.230delT						.						128	125	126					5																	43298839		2203	4300	6503	SO:0001589	frameshift_variant	3157	exon2			.		CCDS34154.1	5p14-p13	2012-10-02	2010-04-30			ENSG00000112972	2.3.3.10		5007	protein-coding gene	gene with protein product	"3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase"	142940	"3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)"	HMGCS			Standard	NM_001098272		Approved		uc003jnq.5	Q01581		ENST00000325110.6:c.229delA	chr5.hg19:g.43298839delT	ENSP00000322706:p.Met77fs	145.0	0.0		297.0	216.0	NM_002130	B2RDL8	Frame_Shift_Del	DEL	ENST00000325110.6	hg19	CCDS34154.1																																																																																			.	.		0.428	HMGCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368022.1			-	43298839	T	-	43298839	7	5	172	1	0	1	0	1	0	0	0	0	7241	1406	49	0	1369	0	HMGCS1	5	43298839	Frame_Shift_Del	DEL	T	TCGA-DD-AACV-01A-11D-A40R-10	16310471	43298839	137616421	29	26040										
OR2J3	442186	hgsc.bcm.edu	37	chr6	29079833	29079833	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tcatcctgtcatacctggacTcccatctgcacacaccaatg	5	16	3	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr6:29079833T>G	ENST00000377169.1	+	1	166	c.166T>G	c.(166-168)Tcc>Gcc	p.S56A		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	56						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						ATACCTGGACTCCCATCTGCA	0.448																																					p.S56A		Atlas-SNP	.											.	OR2J3	53	.	0			c.T166G						.						289	303	299					6																	29079833		1360	2644	4004	SO:0001583	missense	442186	exon1			CTGGACTCCCATC		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"GPCR / Class A : Olfactory receptors"	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.166T>G	chr6.hg19:g.29079833T>G	ENSP00000366374:p.Ser56Ala	122.0	0.0		158.0	85.0	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	hg19	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	T	0.341	-0.950452	0.02285	.	.	ENSG00000204701	ENST00000377169	T	0.00424	7.45	2.78	0.256	0.15567	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	L	0.28740	0.885	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.18745	-1.0327	9	0.39692	T	0.17	.	4.4705	0.11710	0.0:0.184:0.1869:0.6291	.	56	O76001	OR2J3_HUMAN	A	56	ENSP00000366374:S56A	ENSP00000366374:S56A	S	+	1	0	OR2J3	29187812	0.000000	0.05858	0.930000	0.37139	0.050000	0.14768	-0.715000	0.04997	0.264000	0.21851	0.358000	0.22013	TCC	.	.		0.448	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			G	29079833	T	G	29079833	3	3	172	1	0	0	0	0	1	0	0	0	11013	1551	54	5	168	5	OR2J3	6	29079833	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10		29079833	142035234	30	26041										
TFEB	7942	hgsc.bcm.edu	37	chr6	41652806	41652806	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ggccgtgcactcgagcctgcAtctccagctcctgcagggga	13	15	1	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr6:41652806A>G	ENST00000230323.4	-	10	1263	c.962T>C	c.(961-963)aTg>aCg	p.M321T	TFEB_ENST00000403298.4_Missense_Mutation_p.M321T|TFEB_ENST00000373033.1_Missense_Mutation_p.M321T|TFEB_ENST00000420312.1_Missense_Mutation_p.M236T|TFEB_ENST00000358871.2_Missense_Mutation_p.M335T|AL035588.1_ENST00000597468.1_5'Flank	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	321					autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			TCGAGCCTGCATCTCCAGCTC	0.647			T	ALPHA	renal (childhood epithelioid)																																p.M335T		Atlas-SNP	.		Dom	yes		6	6p21	7942	transcription factor EB		"E,M"	.	TFEB	37	.	0			c.T1004C						.						13	13	13					6																	41652806		2174	4267	6441	SO:0001583	missense	7942	exon9			GCCTGCATCTCCA	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"Basic helix-loop-helix proteins"	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.962T>C	chr6.hg19:g.41652806A>G	ENSP00000230323:p.Met321Thr	120.0	0.0		149.0	77.0	NM_001167827	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Missense_Mutation	SNP	ENST00000230323.4	hg19	CCDS4858.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.389569	0.61956	.	.	ENSG00000112561	ENST00000406563;ENST00000343317;ENST00000230323;ENST00000358871;ENST00000403298;ENST00000420312;ENST00000373033	T;T;T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24;-0.24;-0.24	4.99	4.99	0.66335	.	0.079783	0.85682	D	0.000000	T	0.69557	0.3124	M	0.81802	2.56	0.54753	D	0.999982	D;D;D	0.59357	0.985;0.985;0.981	P;P;P	0.54499	0.754;0.754;0.64	T	0.76307	-0.3007	10	0.87932	D	0	-23.8157	10.5225	0.44927	0.8376:0.1624:0.0:0.0	.	335;321;236	B0QYS6;P19484;P19484-2	.;TFEB_HUMAN;.	T	179;407;321;335;321;236;321	ENSP00000383998:M179T;ENSP00000343948:M407T;ENSP00000230323:M321T;ENSP00000351742:M335T;ENSP00000384203:M321T;ENSP00000412551:M236T;ENSP00000362124:M321T	ENSP00000230323:M321T	M	-	2	0	TFEB	41760784	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.989000	0.63870	1.880000	0.54463	0.459000	0.35465	ATG	.	.		0.647	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3			G	41652806	A	G	41652806	3	3	172	1	0	0	0	0	1	0	0	0	15816	217	8	2	472	2	TFEB	6	41652806	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	12572973	41652806	129462261	31	26042										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102503262	102503262	+	Missense_Mutation	SNP	A	A	C													0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tcagctgcaagaggaaggcaAactgcatatgatgaaggaga							TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr6:102503262A>C	ENST00000421544.1	+	15	2859	c.2369A>C	c.(2368-2370)aAa>aCa	p.K790T	GRIK2_ENST00000369138.1_Missense_Mutation_p.K790T|GRIK2_ENST00000369134.4_Missense_Mutation_p.K741T|GRIK2_ENST00000369137.3_Missense_Mutation_p.K714T|GRIK2_ENST00000318991.6_Missense_Mutation_p.K790T|GRIK2_ENST00000413795.1_Missense_Mutation_p.K790T	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	790					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GAGGAAGGCAAACTGCATATG	0.458																																					p.K790T		Atlas-SNP	.											.	GRIK2	487	.	0			c.A2369C						.						91	92	91					6																	102503262		2203	4300	6503	SO:0001583	missense	2898	exon15			AAGGCAAACTGCA		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2369A>C	chr6.hg19:g.102503262A>C	ENSP00000397026:p.Lys790Thr	97.0	0.0		149.0	62.0	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	hg19	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.020954	0.54576	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000369134;ENST00000540076	T;T;T;T;T;T	0.09817	2.94;2.94;2.94;2.94;2.94;2.94	5.68	5.68	0.88126	Ionotropic glutamate receptor (2);	0.099481	0.64402	D	0.000002	T	0.04815	0.0130	N	0.12182	0.205	0.45066	D	0.998089	B;P;B	0.42757	0.262;0.789;0.262	B;P;B	0.47430	0.223;0.547;0.146	T	0.38607	-0.9653	10	0.51188	T	0.08	.	11.1174	0.48268	0.8622:0.0:0.0:0.1378	.	790;790;790	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	T	790;790;790;714;790;741;565	ENSP00000397026:K790T;ENSP00000405596:K790T;ENSP00000358134:K790T;ENSP00000358133:K714T;ENSP00000313276:K790T;ENSP00000358130:K741T	ENSP00000313276:K790T	K	+	2	0	GRIK2	102609955	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.338000	0.79269	2.176000	0.68965	0.477000	0.44152	AAA	.	.		0.458	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			C	102503262	A	C	102503262	3	2	172	1	0	0	0	0	1	0	0	0	6783	14	1	5	2427	5	GRIK2	6	102503262	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	60850456	102503262	68611805	32	26043	125	2								
GRIK2	2898	hgsc.bcm.edu	37	chr6	102503268	102503268	+	Missense_Mutation	SNP	A	A	G													0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gcaagaggaaggcaaactgcAtatgatgaaggagaaatggt							TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr6:102503268A>G	ENST00000421544.1	+	15	2865	c.2375A>G	c.(2374-2376)cAt>cGt	p.H792R	GRIK2_ENST00000369138.1_Missense_Mutation_p.H792R|GRIK2_ENST00000369134.4_Missense_Mutation_p.H743R|GRIK2_ENST00000369137.3_Missense_Mutation_p.H716R|GRIK2_ENST00000318991.6_Missense_Mutation_p.H792R|GRIK2_ENST00000413795.1_Missense_Mutation_p.H792R	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	792					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GGCAAACTGCATATGATGAAG	0.448																																					p.H792R		Atlas-SNP	.											.	GRIK2	487	.	0			c.A2375G						.						93	94	94					6																	102503268		2203	4300	6503	SO:0001583	missense	2898	exon15			AACTGCATATGAT		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2375A>G	chr6.hg19:g.102503268A>G	ENSP00000397026:p.His792Arg	95.0	0.0		151.0	62.0	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	hg19	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.634718	0.87660	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000369134;ENST00000540076	T;T;T;T;T;T	0.10573	2.86;2.86;2.86;2.86;2.86;2.86	5.68	5.68	0.88126	Ionotropic glutamate receptor (2);	0.046749	0.85682	D	0.000000	T	0.15003	0.0362	L	0.38838	1.175	0.58432	D	0.999993	D;D;D	0.56287	0.968;0.975;0.968	P;D;P	0.64321	0.875;0.924;0.832	T	0.01195	-1.1422	10	0.72032	D	0.01	.	15.9826	0.80125	1.0:0.0:0.0:0.0	.	792;792;792	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	R	792;792;792;716;792;743;567	ENSP00000397026:H792R;ENSP00000405596:H792R;ENSP00000358134:H792R;ENSP00000358133:H716R;ENSP00000313276:H792R;ENSP00000358130:H743R	ENSP00000313276:H792R	H	+	2	0	GRIK2	102609961	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.339000	0.96797	2.176000	0.68965	0.477000	0.44152	CAT	.	.		0.448	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			G	102503268	A	G	102503268	3	3	172	1	0	0	0	0	1	0	0	0	6783	217	8	2	2433	2	GRIK2	6	102503268	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	6	102503268	68611799	33	26044	125	2								
ADAT2	134637	hgsc.bcm.edu	37	chr6	143759816	143759816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aacaggaacttcagtattttCgagggcttctttggcctgaa	10	8	2	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr6:143759816C>T	ENST00000237283.8	-	2	126	c.112G>A	c.(112-114)Gaa>Aaa	p.E38K	ADAT2_ENST00000606514.1_5'UTR|AL031320.1_ENST00000595616.1_Intron	NM_182503.2	NP_872309.2	Q7Z6V5	ADAT2_HUMAN	adenosine deaminase, tRNA-specific 2	38					tRNA wobble adenosine to inosine editing (GO:0002100)		tRNA-specific adenosine deaminase activity (GO:0008251)|zinc ion binding (GO:0008270)	p.E38K(1)		endometrium(2)|large_intestine(3)|lung(3)	8				OV - Ovarian serous cystadenocarcinoma(155;5.61e-06)|GBM - Glioblastoma multiforme(68;0.0115)		TCAGTATTTTCGAGGGCTTCT	0.393																																					p.E38K		Atlas-SNP	.											ADAT2,rectum,carcinoma,0,1	ADAT2	18	.	1	Substitution - Missense(1)	large_intestine(1)	c.G112A						.						153	136	141					6																	143759816		1864	4095	5959	SO:0001583	missense	134637	exon2			TATTTTCGAGGGC	BC037955	CCDS43511.1, CCDS69219.1	6q24.2	2014-01-28	2011-05-19	2007-08-16	ENSG00000189007	ENSG00000189007			21172	protein-coding gene	gene with protein product	tRNA-specific adenosine deaminase 2 homolog (S. cerevisiae)	615388	"deaminase domain containing 1", "adenosine deaminase, tRNA-specific 2, TAD2 homolog (S. cerevisiae)"	DEADC1		12457566	Standard	NM_182503		Approved	dJ20N2.1, TAD2	uc003qjj.3	Q7Z6V5	OTTHUMG00000015725	ENST00000237283.8:c.112G>A	chr6.hg19:g.143759816C>T	ENSP00000237283:p.Glu38Lys	58.0	0.0		94.0	36.0	NM_182503	A6NL12|B3KWY3|Q7Z327|Q8IY39	Missense_Mutation	SNP	ENST00000237283.8	hg19	CCDS43511.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.577853	0.28180	.	.	ENSG00000189007	ENST00000237283	T	0.39592	1.07	5.89	5.03	0.67393	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.269079	0.42682	N	0.000677	T	0.07324	0.0185	N	0.04245	-0.25	0.80722	D	1	B	0.18166	0.026	B	0.14578	0.011	T	0.19289	-1.0310	10	0.07644	T	0.81	-10.9942	10.9233	0.47178	0.0:0.8581:0.0:0.1419	.	38	Q7Z6V5	ADAT2_HUMAN	K	38	ENSP00000237283:E38K	ENSP00000237283:E38K	E	-	1	0	ADAT2	143801509	0.996000	0.38824	0.517000	0.27799	0.677000	0.39632	2.248000	0.43160	1.507000	0.48752	0.563000	0.77884	GAA	.	.		0.393	ADAT2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042517.1	XM_059727		T	143759816	C	T	143759816	3	4	172	1	0	0	0	0	1	0	0	0	285	893	31	1	483	1	ADAT2	6	143759816	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	41256548	143759816	27355251	34	26045										
STXBP5	134957	hgsc.bcm.edu	37	chr6	147694876	147694876	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tgattttaaaggaaatgttgGgtgaactcttcactcctgta	9	6	2	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr6:147694876G>A	ENST00000321680.6	+	26	3091	c.3091G>A	c.(3091-3093)Ggt>Agt	p.G1031S	STXBP5_ENST00000367480.3_Missense_Mutation_p.G978S|STXBP5_ENST00000367481.3_Missense_Mutation_p.G995S|STXBP5_ENST00000179882.6_Missense_Mutation_p.G686S	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	1031					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		GGAAATGTTGGGTGAACTCTT	0.363																																					p.G1031S		Atlas-SNP	.											STXBP5_ENST00000321680,NS,carcinoma,0,2	STXBP5	163	.	0			c.G3091A						.						116	114	115					6																	147694876		2203	4300	6503	SO:0001583	missense	134957	exon26			ATGTTGGGTGAAC	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.3091G>A	chr6.hg19:g.147694876G>A	ENSP00000321826:p.Gly1031Ser	104.0	0.0		119.0	45.0	NM_001127715	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	hg19	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.779105	0.90195	.	.	ENSG00000164506	ENST00000367481;ENST00000321680;ENST00000367480;ENST00000179882	T;T;T;T	0.26518	1.87;1.73;2.01;2.51	5.71	5.71	0.89125	.	0.099686	0.64402	D	0.000002	T	0.23727	0.0574	L	0.58302	1.8	0.80722	D	1	B;P;P	0.38300	0.312;0.626;0.626	B;B;B	0.41619	0.103;0.361;0.361	T	0.01393	-1.1366	10	0.40728	T	0.16	.	19.8494	0.96733	0.0:0.0:1.0:0.0	.	995;1031;686	Q5T5C0-2;Q5T5C0;B3KXX0	.;STXB5_HUMAN;.	S	995;1031;978;686	ENSP00000356451:G995S;ENSP00000321826:G1031S;ENSP00000356450:G978S;ENSP00000179882:G686S	ENSP00000179882:G686S	G	+	1	0	STXBP5	147736569	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.312000	0.59154	2.705000	0.92388	0.585000	0.79938	GGT	.	.		0.363	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			A	147694876	G	A	147694876	3	1	172	1	0	0	0	0	1	0	0	0	15371	1232	43	3	3193	3	STXBP5	6	147694876	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	3935060	147694876	23420191	35	26046										
DGKB	1607	hgsc.bcm.edu	37	chr7	14733789	14733789	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cacggttccatcatgatcatAgtcaatttcttccatcattt	4	11	5	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr7:14733789A>G	ENST00000403951.2	-	9	1041	c.622T>C	c.(622-624)Tat>Cat	p.Y208H	DGKB_ENST00000406247.3_Missense_Mutation_p.Y208H|DGKB_ENST00000402815.1_Missense_Mutation_p.Y208H|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000407950.1_Missense_Mutation_p.Y201H|DGKB_ENST00000399322.3_Missense_Mutation_p.Y208H|DGKB_ENST00000444700.2_Missense_Mutation_p.Y201H|DGKB_ENST00000258767.5_Missense_Mutation_p.Y208H			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	208	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						TCATGATCATAGTCAATTTCT	0.398																																					p.Y208H		Atlas-SNP	.											.	DGKB	166	.	0			c.T622C						.						69	65	66					7																	14733789		1900	4136	6036	SO:0001583	missense	1607	exon8			GATCATAGTCAAT	AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"EF-hand domain containing"	2850	protein-coding gene	gene with protein product		604070	"diacylglycerol kinase, beta (90kD)"	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.622T>C	chr7.hg19:g.14733789A>G	ENSP00000385780:p.Tyr208His	68.0	0.0		108.0	53.0	NM_145695	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Missense_Mutation	SNP	ENST00000403951.2	hg19	CCDS47547.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.763706	0.89932	.	.	ENSG00000136267	ENST00000403951;ENST00000399322;ENST00000258767;ENST00000402815;ENST00000407950;ENST00000444700;ENST00000406247	T;T;T;T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5	5.72	5.72	0.89469	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79505	0.4457	L	0.43923	1.385	0.80722	D	1	D;D;D;D	0.89917	1.0;0.98;0.98;1.0	D;D;D;D	0.80764	0.994;0.929;0.929;0.987	T	0.80587	-0.1316	10	0.56958	D	0.05	.	15.9926	0.80217	1.0:0.0:0.0:0.0	.	208;201;208;208	B7ZL83;C9JTC0;Q9Y6T7-2;Q9Y6T7	.;.;.;DGKB_HUMAN	H	208;208;208;208;201;201;208	ENSP00000385780:Y208H;ENSP00000382260:Y208H;ENSP00000258767:Y208H;ENSP00000384909:Y208H;ENSP00000385031:Y201H;ENSP00000388451:Y201H;ENSP00000386066:Y208H	ENSP00000258767:Y208H	Y	-	1	0	DGKB	14700314	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	9.339000	0.96797	2.179000	0.69175	0.482000	0.46254	TAT	.	.		0.398	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080		G	14733789	A	G	14733789	3	3	172	1	0	0	0	0	1	0	0	0	4468	420	15	2	1879	2	DGKB	7	14733789	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10		14733789	144404874	36	26047										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	71130456	71130456	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cacgggtggcccacattgagCggaagaagaagccatataat	12	9	0	3			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr7:71130456C>T	ENST00000333538.5	+	7	1775	c.1141C>T	c.(1141-1143)Cgg>Tgg	p.R381W	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	381	Catalytic subdomain B.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CCACATTGAGCGGAAGAAGAA	0.488																																					p.R381W		Atlas-SNP	.											.	WBSCR17	208	.	0			c.C1141T						.						106	100	102					7																	71130456		2203	4300	6503	SO:0001583	missense	64409	exon7			ATTGAGCGGAAGA	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1141C>T	chr7.hg19:g.71130456C>T	ENSP00000329654:p.Arg381Trp	88.0	0.0		121.0	52.0	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	hg19	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.033947	0.75504	.	.	ENSG00000185274	ENST00000333538	T	0.69175	-0.38	5.85	1.83	0.25207	.	0.000000	0.85682	D	0.000000	D	0.88526	0.6460	H	0.98936	4.375	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.92381	0.5913	10	0.87932	D	0	.	15.3575	0.74440	0.6063:0.3937:0.0:0.0	.	381	Q6IS24	GLTL3_HUMAN	W	381	ENSP00000329654:R381W	ENSP00000329654:R381W	R	+	1	2	WBSCR17	70768392	0.877000	0.30153	1.000000	0.80357	0.987000	0.75469	1.218000	0.32467	0.362000	0.24319	-0.261000	0.10672	CGG	.	.		0.488	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		T	71130456	C	T	71130456	3	4	172	1	0	0	0	0	1	0	0	0	17279	759	27	1	1167	1	WBSCR17	7	71130456	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	56396667	71130456	88008207	37	26048										
PCLO	27445	hgsc.bcm.edu	37	chr7	82584355	82584355	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ttcttgccttgttagcagacTgccatctaccgatccattgt	7	12	2	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr7:82584355T>C	ENST00000333891.9	-	5	6251	c.5914A>G	c.(5914-5916)Agt>Ggt	p.S1972G	PCLO_ENST00000423517.2_Missense_Mutation_p.S1972G	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GTTAGCAGACTGCCATCTACC	0.368																																					p.S1972G		Atlas-SNP	.											.	PCLO	1506	.	0			c.A5914G						.						111	113	112					7																	82584355		1874	4099	5973	SO:0001583	missense	27445	exon5			GCAGACTGCCATC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5914A>G	chr7.hg19:g.82584355T>C	ENSP00000334319:p.Ser1972Gly	82.0	0.0		109.0	51.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	0.423	-0.907069	0.02434	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16897	2.31;2.31	5.57	1.97	0.26223	.	.	.	.	.	T	0.08133	0.0203	N	0.03115	-0.41	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.11329	0.006;0.006	T	0.32214	-0.9915	9	0.87932	D	0	.	8.8639	0.35274	0.0:0.2137:0.0:0.7863	.	1972;1972	Q9Y6V0-5;Q9Y6V0-6	.;.	G	1903;1972;1972	ENSP00000334319:S1972G;ENSP00000388393:S1972G	ENSP00000334319:S1972G	S	-	1	0	PCLO	82422291	0.094000	0.21725	0.039000	0.18376	0.313000	0.28021	0.211000	0.17474	0.408000	0.25621	0.533000	0.62120	AGT	.	.		0.368	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82584355	T	C	82584355	3	2	172	1	0	0	0	0	1	0	0	0	11592	1580	55	2	9615	2	PCLO	7	82584355	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	11453899	82584355	76554308	38	26049										
MLL5	55904	hgsc.bcm.edu	37	chr7	104749510	104749510	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aagcttgagcaacaatggtgAtggctgtgccagcagtaatg	13	7	0	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr7:104749510A>C	ENST00000311117.3	+	23	4135	c.3590A>C	c.(3589-3591)gAt>gCt	p.D1197A	KMT2E_ENST00000334877.4_Missense_Mutation_p.D1197A|KMT2E_ENST00000334914.7_Missense_Mutation_p.D252A|KMT2E_ENST00000257745.4_Missense_Mutation_p.D1197A|SRPK2_ENST00000493638.1_5'Flank	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1197					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										AACAATGGTGATGGCTGTGCC	0.468																																					p.D1197A		Atlas-SNP	.											.	MLL5	173	.	0			c.A3590C						.						109	94	99					7																	104749510		2203	4300	6503	SO:0001583	missense	55904	exon22			ATGGTGATGGCTG	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3590A>C	chr7.hg19:g.104749510A>C	ENSP00000312379:p.Asp1197Ala	126.0	0.0		148.0	69.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.03|10.03	1.238644|1.238644	0.22711|0.22711	.|.	.|.	ENSG00000005483|ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914|ENST00000473063	D;D;D;T|.	0.91686|.	-2.89;-2.53;-2.89;0.83|.	5.65|5.65	4.51|4.51	0.55191|0.55191	.|.	0.189244|.	0.37053|.	N|.	0.002273|.	T|.	0.44393|.	0.1291|.	L|L	0.27053|0.27053	0.805|0.805	0.39578|0.39578	D|D	0.969391|0.969391	B|.	0.34103|.	0.437|.	B|.	0.27608|.	0.081|.	T|.	0.36383|.	-0.9750|.	10|.	0.44086|.	T|.	0.13|.	.|.	9.7341|9.7341	0.40377|0.40377	0.9225:0.0:0.0775:0.0|0.9225:0.0:0.0775:0.0	.|.	1197|.	Q8IZD2|.	MLL5_HUMAN|.	A|C	1197;1197;1197;1117;1197;252|8	ENSP00000312379:D1197A;ENSP00000335599:D1197A;ENSP00000257745:D1197A;ENSP00000333986:D252A|.	ENSP00000257745:D1197A|.	D|X	+|+	2|3	0|0	MLL5|MLL5	104536746|104536746	0.997000|0.997000	0.39634|0.39634	0.114000|0.114000	0.21550|0.21550	0.478000|0.478000	0.33099|0.33099	2.948000|2.948000	0.49066|0.49066	2.150000|2.150000	0.67090|0.67090	0.383000|0.383000	0.25322|0.25322	GAT|TGA	.	.		0.468	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			C	104749510	A	C	104749510	3	2	172	1	0	0	0	0	1	0	0	0	9633	333	12	5	3672	5	MLL5	7	104749510	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	22165155	104749510	54389153	39	26050										
MLL5	55904	hgsc.bcm.edu	37	chr7	104751284	104751284	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	atccccagatacttctcaaaAtacttgtaaaagtcctccaa	3	12	1	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr7:104751284A>G	ENST00000311117.3	+	26	4582	c.4037A>G	c.(4036-4038)aAt>aGt	p.N1346S	KMT2E_ENST00000334877.4_Missense_Mutation_p.N1304S|KMT2E_ENST00000334914.7_Missense_Mutation_p.N401S|KMT2E_ENST00000257745.4_Missense_Mutation_p.N1346S|SRPK2_ENST00000493638.1_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1346					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										ACTTCTCAAAATACTTGTAAA	0.378																																					p.N1346S		Atlas-SNP	.											.	MLL5	173	.	0			c.A4037G						.						99	102	101					7																	104751284		2203	4300	6503	SO:0001583	missense	55904	exon25			CTCAAAATACTTG	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.4037A>G	chr7.hg19:g.104751284A>G	ENSP00000312379:p.Asn1346Ser	169.0	0.0		202.0	90.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	A	11.08	1.534681	0.27475	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914	D;D;D;T	0.91180	-2.8;-2.49;-2.8;0.96	4.48	-1.54	0.08584	.	0.703396	0.12818	N	0.436654	T	0.73087	0.3542	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.56673	-0.7940	10	0.09084	T	0.74	.	4.3451	0.11129	0.5002:0.0:0.1448:0.355	.	1266;1346	F8W6H1;Q8IZD2	.;MLL5_HUMAN	S	1346;1346;1304;1266;1346;401	ENSP00000312379:N1346S;ENSP00000335599:N1304S;ENSP00000257745:N1346S;ENSP00000333986:N401S	ENSP00000257745:N1346S	N	+	2	0	MLL5	104538520	1.000000	0.71417	0.483000	0.27378	0.888000	0.51559	1.336000	0.33850	-0.483000	0.06772	-0.669000	0.03829	AAT	.	.		0.378	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			G	104751284	A	G	104751284	3	3	172	1	0	0	0	0	1	0	0	0	9633	101	4	2	4131	2	MLL5	7	104751284	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	1774	104751284	54387379	40	26051										
PODXL	5420	hgsc.bcm.edu	37	chr7	131241029	131241029	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ggccactcaccattctgggaGggcgacggcgacggcgacgg	17	13	2	0	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000322985.9_Silent_p.P30P|PODXL_ENST00000541194.1_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		Atlas-SNP	.											.	PODXL	53	.	0			c.C90G						.						5	7	6					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	chr7.hg19:g.131241029G>C		89.0	0.0		88.0	8.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		C	131241029	G	C	131241029	2	2	172	1	0	0	0	0	0	0	0	1	12189	987	35	4		4	PODXL	7	131241029	Silent	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	26489745	131241029	27897634	41	26052			1	29		2	2	27	N	G_A	8.734393e-05
PODXL	5420	hgsc.bcm.edu	37	chr7	131241055	131241055	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cggcgacggcgacggcgacgAcggcagcagcggcggcgttg	20	13	0	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr7:131241055A>G	ENST00000378555.3	-	1	311	c.64T>C	c.(64-66)Tcg>Ccg	p.S22P	PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Missense_Mutation_p.S22P|PODXL_ENST00000322985.9_Missense_Mutation_p.S22P|PODXL_ENST00000541194.1_Missense_Mutation_p.S22P			O00592	PODXL_HUMAN	podocalyxin-like	22					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					gacggcgacgacggcagcagc	0.741																																					p.S22P		Atlas-SNP	.											.	PODXL	53	.	0			c.T64C						.						5	8	7					7																	131241055		1914	3836	5750	SO:0001583	missense	5420	exon1			GCGACGACGGCAG		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.64T>C	chr7.hg19:g.131241055A>G	ENSP00000367817:p.Ser22Pro	94.0	0.0		98.0	7.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	hg19	CCDS34755.1	.	.	.	.	.	.	.	.	.	.	A	10.93	1.488975	0.26686	.	.	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000378555;ENST00000322985	T;T;T;T	0.12774	2.82;2.65;2.82;2.85	.	.	.	.	7739.210000	0.00166	U	0.000000	T	0.08670	0.0215	N	0.14661	0.345	0.09310	N	0.999994	.	.	.	.	.	.	T	0.24728	-1.0152	6	0.29301	T	0.29	.	.	.	.	.	22;22	O00592-2;O00592	.;PODXL_HUMAN	P	22	ENSP00000440518:S22P;ENSP00000442655:S22P;ENSP00000367817:S22P;ENSP00000319782:S22P	ENSP00000319782:S22P	S	-	1	0	PODXL	130891595	0.001000	0.12720	0.027000	0.17364	0.027000	0.11550	0.743000	0.26231	0.056000	0.16144	0.055000	0.15244	TCG	.	.		0.741	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		G	131241055	A	G	131241055	3	3	172	1	0	0	0	0	1	0	0	0	12189	275	10	2	1648	2	PODXL	7	131241055	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	26	131241055	27897608	42	26053			1	29		2	2	27	N	G_A	8.734393e-05
PRKAG2	51422	hgsc.bcm.edu	37	chr7	151573596	151573596	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gagtgctgggactcaccggaAtgtgcacgcgcagcgaacgc	15	12	1	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr7:151573596A>C	ENST00000287878.4	-	1	614	c.110T>G	c.(109-111)aTt>aGt	p.I37S	PRKAG2-AS1_ENST00000464464.1_RNA|PRKAG2-AS1_ENST00000467458.1_RNA	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	37					ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	ACTCACCGGAATGTGCACGCG	0.662																																					p.I37S		Atlas-SNP	.											.	PRKAG2	86	.	0			c.T110G						.						86	86	86					7																	151573596		2203	4300	6503	SO:0001583	missense	51422	exon1			ACCGGAATGTGCA	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"AMPK gamma2"	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.110T>G	chr7.hg19:g.151573596A>C	ENSP00000287878:p.Ile37Ser	51.0	0.0		61.0	20.0	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Missense_Mutation	SNP	ENST00000287878.4	hg19	CCDS5928.1	.	.	.	.	.	.	.	.	.	.	A	16.88	3.244216	0.59103	.	.	ENSG00000106617	ENST00000287878	D	0.86097	-2.07	4.01	4.01	0.46588	.	0.062584	0.64402	D	0.000006	D	0.82788	0.5113	N	0.24115	0.695	0.80722	D	1	D;P	0.69078	0.997;0.808	P;B	0.62184	0.899;0.161	T	0.78952	-0.2001	10	0.22706	T	0.39	.	9.3009	0.37845	1.0:0.0:0.0:0.0	.	37;37	Q8NCK6;Q9UGJ0	.;AAKG2_HUMAN	S	37	ENSP00000287878:I37S	ENSP00000287878:I37S	I	-	2	0	PRKAG2	151204529	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.271000	0.58902	1.692000	0.51112	0.369000	0.22263	ATT	.	.		0.662	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		C	151573596	A	C	151573596	3	2	172	1	0	0	0	0	1	0	0	0	12513	101	4	5	1663	5	PRKAG2	7	151573596	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	20332541	151573596	7565067	43	26054										
ADAM7	8756	hgsc.bcm.edu	37	chr8	24346811	24346811	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tttgtggaaacaagaagttgGatgagggtgaagagtgtgac	16	2	0	5			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr8:24346811G>T	ENST00000175238.6	+	12	1314	c.1231G>T	c.(1231-1233)Gat>Tat	p.D411Y	RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000520720.1_Missense_Mutation_p.D183Y|RP11-561E1.1_ENST00000519364.1_RNA|ADAM7_ENST00000380789.1_Missense_Mutation_p.D411Y|RP11-624C23.1_ENST00000523578.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	411	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		CAAGAAGTTGGATGAGGGTGA	0.388																																					p.D411Y		Atlas-SNP	.											.	ADAM7	165	.	0			c.G1231T						.						100	87	92					8																	24346811		2203	4300	6503	SO:0001583	missense	8756	exon12			AAGTTGGATGAGG	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"ADAM metallopeptidase domain containing"	214	protein-coding gene	gene with protein product		607310	"a disintegrin and metalloproteinase domain 7"				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.1231G>T	chr8.hg19:g.24346811G>T	ENSP00000175238:p.Asp411Tyr	106.0	0.0		109.0	55.0	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	hg19	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.790132	0.70337	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.13307	2.6;2.6;2.6	5.74	5.74	0.90152	Blood coagulation inhibitor, Disintegrin (4);Metallopeptidase, catalytic domain (1);	0.220934	0.31709	N	0.007181	T	0.44644	0.1303	M	0.87097	2.86	0.46521	D	0.999081	D;D	0.89917	0.999;1.0	D;D	0.72338	0.964;0.977	T	0.48151	-0.9060	10	0.87932	D	0	.	17.4289	0.87534	0.0:0.0:1.0:0.0	.	183;411	E5RK87;Q9H2U9	.;ADAM7_HUMAN	Y	411;411;183;226	ENSP00000175238:D411Y;ENSP00000370166:D411Y;ENSP00000430400:D183Y	ENSP00000175238:D411Y	D	+	1	0	ADAM7	24402701	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	6.778000	0.75043	2.703000	0.92315	0.655000	0.94253	GAT	.	.		0.388	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		T	24346811	G	T	24346811	3	4	172	1	0	0	0	0	1	0	0	0	251	1174	41	3	1277	3	ADAM7	8	24346811	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10		24346811	122017211	44	26055										
C8orf41	80185	hgsc.bcm.edu	37	chr8	33360999	33360999	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ggtttccaatatcttcagtcTagcttcctcctcaggtccat	6	13	4	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr8:33360999T>C	ENST00000431156.2	-	6	1825	c.1207A>G	c.(1207-1209)Aga>Gga	p.R403G	TTI2_ENST00000360742.5_Missense_Mutation_p.R403G|TTI2_ENST00000520636.1_Missense_Mutation_p.R372G|TTI2_ENST00000519356.1_5'UTR	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	403																	ATCTTCAGTCTAGCTTCCTCC	0.448																																					p.R403G		Atlas-SNP	.											.	.	.	.	0			c.A1207G						.						169	169	169					8																	33360999		2203	4300	6503	SO:0001583	missense	80185	exon6			TCAGTCTAGCTTC	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1207A>G	chr8.hg19:g.33360999T>C	ENSP00000411169:p.Arg403Gly	85.0	0.0		112.0	44.0	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.510758	0.64522	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636	T;T;T	0.72505	-0.66;-0.66;-0.65	6.17	3.62	0.41486	.	0.000000	0.85682	D	0.000000	T	0.81777	0.4894	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.83330	-0.0013	10	0.72032	D	0.01	-20.8393	12.5136	0.56019	0.0:0.0:0.2627:0.7373	.	403;372	Q6NXR4;E5RIH5	TTI2_HUMAN;.	G	403;403;392;372	ENSP00000353971:R403G;ENSP00000411169:R403G;ENSP00000428401:R372G	ENSP00000353971:R403G	R	-	1	2	C8orf41	33480541	0.695000	0.27747	0.145000	0.22337	0.807000	0.45602	0.981000	0.29526	1.104000	0.41587	0.533000	0.62120	AGA	.	.		0.448	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		C	33360999	T	C	33360999	3	2	172	1	0	0	0	0	1	0	0	0	2429	1530	53	2	331	2	C8orf41	8	33360999	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	9014188	33360999	113003023	45	26056										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95531278	95531278	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tggagatttttctccagactAaaaacatggccaacagctga	8	9	1	3			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr8:95531278A>G	ENST00000297591.5	-	9	2523	c.2448T>C	c.(2446-2448)ttT>ttC	p.F816F	KIAA1429_ENST00000421249.2_Silent_p.F816F|KIAA1429_ENST00000437199.1_Silent_p.F816F	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	816					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TCTCCAGACTAAAAACATGGC	0.373																																					p.F816F		Atlas-SNP	.											.	KIAA1429	176	.	0			c.T2448C						.						57	62	60					8																	95531278		2203	4300	6503	SO:0001819	synonymous_variant	25962	exon9			CAGACTAAAAACA	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.2448T>C	chr8.hg19:g.95531278A>G		62.0	0.0		77.0	36.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	hg19	CCDS34923.1																																																																																			.	.		0.373	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		G	95531278	A	G	95531278	2	3	172	1	0	0	0	0	0	0	0	1	8240	359	13	2		2	KIAA1429	8	95531278	Silent	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	62170279	95531278	50832744	46	26057										
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104500017	104500017	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gggaccgcctagtccctggcTccggctcatccctctgggct	12	17	2	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr9:104500017T>C	ENST00000361820.3	-	1	845	c.245A>G	c.(244-246)gAg>gGg	p.E82G		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	82					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	AGTCCCTGGCTCCGGCTCATC	0.781																																					p.E82G		Atlas-SNP	.											.	GRIN3A	186	.	0			c.A245G						.						2	2	2					9																	104500017		1438	3039	4477	SO:0001583	missense	116443	exon1			CCTGGCTCCGGCT		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.245A>G	chr9.hg19:g.104500017T>C	ENSP00000355155:p.Glu82Gly	10.0	0.0		27.0	12.0	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	T	7.830	0.719635	0.15372	.	.	ENSG00000198785	ENST00000361820	T	0.10382	2.88	5.31	0.763	0.18459	.	1.535890	0.03332	N	0.193615	T	0.06005	0.0156	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34004	-0.9846	10	0.30854	T	0.27	.	4.7153	0.12893	0.0:0.2541:0.1614:0.5845	.	82	Q8TCU5	NMD3A_HUMAN	G	82	ENSP00000355155:E82G	ENSP00000355155:E82G	E	-	2	0	GRIN3A	103539838	0.023000	0.18921	0.129000	0.21949	0.850000	0.48378	0.664000	0.25068	0.291000	0.22468	0.533000	0.62120	GAG	.	.		0.781	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			C	104500017	T	C	104500017	3	2	172	1	0	0	0	0	1	0	0	0	6792	1551	54	2	3138	2	GRIN3A	9	104500017	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10		104500017	36713414	47	26058										
C5	727	hgsc.bcm.edu	37	chr9	123716025	123716025	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tacctgaaactgaaattgtaTtttatctggagggcttcttt	8	6	2	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr9:123716025T>C	ENST00000223642.1	-	40	4913	c.4884A>G	c.(4882-4884)aaA>aaG	p.K1628K		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1628	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	TGAAATTGTATTTTATCTGGA	0.343																																					p.K1628K		Atlas-SNP	.											.	C5	124	.	0			c.A4884G						.						112	112	112					9																	123716025		2203	4300	6503	SO:0001819	synonymous_variant	727	exon40			ATTGTATTTTATC	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.4884A>G	chr9.hg19:g.123716025T>C		104.0	0.0		159.0	72.0	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	hg19	CCDS6826.1																																																																																			.	.		0.343	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		C	123716025	T	C	123716025	2	2	172	1	0	0	0	0	0	0	0	1	2282	1490	52	2		2	C5	9	123716025	Silent	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	19216008	123716025	17497406	48	26059										
ASS1	445	hgsc.bcm.edu	37	chr9	133355124	133355124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ggtccctgtgaaggtgaccaAcgtcaaggatggcaccaccc	12	13	1	2	rs565520844		TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr9:133355124A>G	ENST00000372394.1	+	11	1191	c.710A>G	c.(709-711)aAc>aGc	p.N237S	ASS1_ENST00000372393.3_Missense_Mutation_p.N237S|ASS1_ENST00000493984.2_Intron|ASS1_ENST00000352480.5_Missense_Mutation_p.N237S			P00966	ASSY_HUMAN	argininosuccinate synthase 1	237					acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	AAGGTGACCAACGTCAAGGAT	0.647													A|||	1	0.000199681	0	0.0014	5008	,	,		15958	0		0	False		,,,				2504	0				p.N237S		Atlas-SNP	.											.	ASS1	37	.	0			c.A710G						.						75	69	71					9																	133355124		2203	4300	6503	SO:0001583	missense	445	exon10			TGACCAACGTCAA	X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"argininosuccinate synthetase"	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.710A>G	chr9.hg19:g.133355124A>G	ENSP00000361471:p.Asn237Ser	62.0	0.0		69.0	40.0	NM_054012	Q6LDL2|Q86UZ0|Q96GT4	Missense_Mutation	SNP	ENST00000372394.1	hg19	CCDS6933.1	.	.	.	.	.	.	.	.	.	.	A	10.37	1.331893	0.24167	.	.	ENSG00000130707	ENST00000334909;ENST00000352480;ENST00000372394;ENST00000372393	D;D;D	0.99070	-5.39;-5.39;-5.39	4.91	3.77	0.43336	Argininosuccinate synthetase, catalytic/multimerisation domain body (1);	0.108900	0.64402	U	0.000014	D	0.97099	0.9052	L	0.54965	1.715	0.42711	D	0.993645	B;B;B;B;B	0.27559	0.003;0.181;0.181;0.003;0.003	B;B;B;B;B	0.19148	0.01;0.024;0.024;0.01;0.01	D	0.95080	0.8212	10	0.72032	D	0.01	.	9.5703	0.39425	0.9164:0.0:0.0836:0.0	.	237;120;120;237;237	A8KAP9;B4E395;E9PDT0;Q5T6L4;P00966	.;.;.;.;ASSY_HUMAN	S	237	ENSP00000253004:N237S;ENSP00000361471:N237S;ENSP00000361469:N237S	ENSP00000361470:N237S	N	+	2	0	ASS1	132344945	1.000000	0.71417	0.997000	0.53966	0.947000	0.59692	6.347000	0.73004	0.729000	0.32403	0.383000	0.25322	AAC	.	.		0.647	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050		G	133355124	A	G	133355124	3	3	172	1	0	0	0	0	1	0	0	0	1061	43	2	2	744	2	ASS1	9	133355124	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	9639099	133355124	7858307	49	26060										
ANAPC2	29882	hgsc.bcm.edu	37	chr9	140077677	140077677	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	agagatatagagggtgatgaTgtcacacgtgttgacgccta	13	6	1	5			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr9:140077677T>A	ENST00000323927.2	-	6	1190	c.1186A>T	c.(1186-1188)Atc>Ttc	p.I396F		NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	396					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		AGGGTGATGATGTCACACGTG	0.622																																					p.I396F		Atlas-SNP	.											.	ANAPC2	57	.	0			c.A1186T						.						141	137	138					9																	140077677		2203	4300	6503	SO:0001583	missense	29882	exon6			TGATGATGTCACA	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"Anaphase promoting complex subunits"	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.1186A>T	chr9.hg19:g.140077677T>A	ENSP00000314004:p.Ile396Phe	84.0	0.0		115.0	51.0	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Missense_Mutation	SNP	ENST00000323927.2	hg19	CCDS7033.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.590530	0.86851	.	.	ENSG00000176248	ENST00000323927	T	0.03524	3.9	4.83	4.83	0.62350	.	0.071723	0.64402	D	0.000001	T	0.22627	0.0546	M	0.91920	3.255	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.78314	0.991;0.984	T	0.02844	-1.1103	10	0.87932	D	0	-30.9235	12.3771	0.55285	0.0:0.0:0.0:1.0	.	396;393	Q9UJX6;Q9UJX6-2	ANC2_HUMAN;.	F	396	ENSP00000314004:I396F	ENSP00000314004:I396F	I	-	1	0	ANAPC2	139197498	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.346000	0.79347	2.034000	0.60081	0.459000	0.35465	ATC	.	.		0.622	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366		A	140077677	T	A	140077677	3	1	172	1	0	0	0	0	1	0	0	0	603	1464	51	4	1314	4	ANAPC2	9	140077677	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	6722553	140077677	1135754	50	26061										
CACNA1B	774	hgsc.bcm.edu	37	chr9	141014753	141014753	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gcaccaccaccaccaccgctGccaccgccgcagggacagga	10	20	0	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr9:141014753G>A	ENST00000371372.1	+	45	6312	c.6167G>A	c.(6166-6168)tGc>tAc	p.C2056Y	CACNA1B_ENST00000371357.1_Missense_Mutation_p.C2055Y|CACNA1B_ENST00000371363.1_Missense_Mutation_p.C2054Y|CACNA1B_ENST00000277551.2_Missense_Mutation_p.C2056Y|CACNA1B_ENST00000371355.4_Missense_Mutation_p.C2057Y|CACNA1B_ENST00000277549.5_Missense_Mutation_p.C1250Y	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	2056					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CACCACCGCTGCCACCGCCGC	0.711																																					p.C2056Y		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G6167A						.						8	12	11					9																	141014753		2085	4168	6253	SO:0001583	missense	774	exon44			ACCGCTGCCACCG	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.6167G>A	chr9.hg19:g.141014753G>A	ENSP00000360423:p.Cys2056Tyr	58.0	0.0		37.0	21.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.843331	0.32606	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D;D	0.96967	-3.94;-3.99;-4.19;-3.94;-3.93;-3.93	4.44	4.44	0.53790	.	2.332040	0.01458	N	0.015755	D	0.96883	0.8982	L	0.36672	1.1	0.80722	D	1	D;D	0.76494	0.992;0.999	P;D	0.68621	0.901;0.959	D	0.86923	0.2068	10	0.02654	T	1	.	17.0694	0.86569	0.0:0.0:1.0:0.0	.	2055;2054	B1AQK7;B1AQK6	.;.	Y	2056;2056;1250;2054;2055;2057	ENSP00000360423:C2056Y;ENSP00000277551:C2056Y;ENSP00000277549:C1250Y;ENSP00000360414:C2054Y;ENSP00000360408:C2055Y;ENSP00000360406:C2057Y	ENSP00000277549:C1250Y	C	+	2	0	CACNA1B	140134574	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	8.703000	0.91344	2.027000	0.59764	0.313000	0.20887	TGC	.	.		0.711	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		A	141014753	G	A	141014753	3	1	172	1	0	0	0	0	1	0	0	0	2541	1319	46	3	6341	3	CACNA1B	9	141014753	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	937076	141014753	198678	51	26062										
SLC39A12	221074	hgsc.bcm.edu	37	chr10	18242319	18242319	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	caggatagcagaagccgtggGagttcaggccaaccggcaga	15	10	1	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr10:18242319G>C	ENST00000377369.2	+	2	387	c.114G>C	c.(112-114)ggG>ggC	p.G38G	SLC39A12_ENST00000377374.4_Silent_p.G38G|SLC39A12_ENST00000377371.3_Silent_p.G38G|SLC39A12_ENST00000539911.1_Intron	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	38					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						GAAGCCGTGGGAGTTCAGGCC	0.512																																					p.G38G		Atlas-SNP	.											.	SLC39A12	181	.	0			c.G114C						.						94	91	92					10																	18242319		2203	4300	6503	SO:0001819	synonymous_variant	221074	exon2			CCGTGGGAGTTCA		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"Solute carriers"	20860	protein-coding gene	gene with protein product		608734	"solute carrier family 39 (metal ion transporter), member 12"			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.114G>C	chr10.hg19:g.18242319G>C		143.0	0.0		205.0	101.0	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Silent	SNP	ENST00000377369.2	hg19	CCDS44362.1																																																																																			.	.		0.512	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725		C	18242319	G	C	18242319	2	2	172	1	0	0	0	0	0	0	0	1	14630	1161	41	4		4	SLC39A12	10	18242319	Silent	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10		18242319	117292428	52	26063										
DCLRE1A	9937	hgsc.bcm.edu	37	chr10	115612648	115612648	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tgagttctacagagttttccTggagtagtttccttgtcttg	10	7	2	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr10:115612648T>C	ENST00000361384.2	-	1	1211	c.294A>G	c.(292-294)ccA>ccG	p.P98P	DCLRE1A_ENST00000476112.1_5'Flank|NHLRC2_ENST00000369301.3_5'Flank|DCLRE1A_ENST00000369305.1_Silent_p.P98P	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	98	Nuclear localization region.				mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		AGAGTTTTCCTGGAGTAGTTT	0.438								Other identified genes with known or suspected DNA repair function																													p.P98P		Atlas-SNP	.											.	DCLRE1A	80	.	0			c.A294G						.						273	262	266					10																	115612648		2203	4300	6503	SO:0001819	synonymous_variant	9937	exon1			TTTTCCTGGAGTA		CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	609682	"DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.294A>G	chr10.hg19:g.115612648T>C		124.0	0.0		72.0	67.0	NM_014881	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Silent	SNP	ENST00000361384.2	hg19	CCDS7584.1																																																																																			.	.		0.438	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881		C	115612648	T	C	115612648	2	2	172	1	0	0	0	0	0	0	0	1	4296	1567	55	2		2	DCLRE1A	10	115612648	Silent	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	97370329	115612648	19922099	53	26064										
GPR123	84435	hgsc.bcm.edu	37	chr10	134942314	134942314	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gcccgccccgcaaggacgccCaccccgcacttgacgccaac	9	22	0	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr10:134942314C>T	ENST00000392607.3	+	7	1418	c.982C>T	c.(982-984)Cac>Tac	p.H328Y	GPR123_ENST00000392606.2_Missense_Mutation_p.H231Y|GPR123_ENST00000607359.1_Missense_Mutation_p.H1047Y	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	328					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CAAGGACGCCCACCCCGCACT	0.741																																					p.H328Y		Atlas-SNP	.											.	GPR123	118	.	0			c.C982T						.						19	18	18					10																	134942314		2154	4229	6383	SO:0001583	missense	84435	exon7			GACGCCCACCCCG	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"-", "GPCR / Class B : Orphans"	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.982C>T	chr10.hg19:g.134942314C>T	ENSP00000376384:p.His328Tyr	74.0	0.0		62.0	58.0	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Missense_Mutation	SNP	ENST00000392607.3	hg19	CCDS41580.1	.	.	.	.	.	.	.	.	.	.	.	0.007	-1.971817	0.00457	.	.	ENSG00000197177	ENST00000368577;ENST00000392607;ENST00000392606	T	0.03982	3.74	4.14	1.1	0.20463	.	0.933617	0.08910	N	0.875932	T	0.05181	0.0138	L	0.36672	1.1	0.09310	N	1	B;B	0.25351	0.0;0.124	B;B	0.26517	0.0;0.07	T	0.42531	-0.9446	10	0.49607	T	0.09	.	7.5999	0.28069	0.0:0.5681:0.3374:0.0945	.	328;1047	Q86SQ6;Q86SQ6-1	GP123_HUMAN;.	Y	1047;328;232	ENSP00000376384:H328Y	ENSP00000357566:H1047Y	H	+	1	0	GPR123	134792304	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-1.616000	0.02053	0.129000	0.18514	0.561000	0.74099	CAC	.	.		0.741	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2			T	134942314	C	T	134942314	3	4	172	1	0	0	0	0	1	0	0	0	6645	594	21	3	1004	3	GPR123	10	134942314	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	19329666	134942314	592433	54	26065										
INS	3630	hgsc.bcm.edu	37	chr11	2181222	2181222	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gcccccgcccagctccacctGccccactgccaggacgtgcc	9	23	0	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr11:2181222G>T	ENST00000397262.1	-	2	425	c.193C>A	c.(193-195)Cag>Aag	p.Q65K	INS-IGF2_ENST00000481781.1_5'Flank|INS_ENST00000250971.3_Missense_Mutation_p.Q65K|INS-IGF2_ENST00000397270.1_Intron|INS_ENST00000381330.4_Missense_Mutation_p.Q65K|INS_ENST00000512523.1_Intron	NM_001185098.1	NP_001172027.1	P01308	INS_HUMAN	insulin	65					activation of protein kinase B activity (GO:0032148)|acute-phase response (GO:0006953)|alpha-beta T cell activation (GO:0046631)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of fatty acid metabolic process (GO:0045922)|negative regulation of feeding behavior (GO:2000252)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of glycogen catabolic process (GO:0045818)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of protein secretion (GO:0050709)|negative regulation of proteolysis (GO:0045861)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|negative regulation of vasodilation (GO:0045908)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of respiratory burst (GO:0060267)|positive regulation of vasodilation (GO:0045909)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of insulin secretion (GO:0050796)|regulation of protein localization (GO:0032880)|regulation of protein secretion (GO:0050708)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transmembrane transporter activity (GO:0022898)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	endoplasmic reticulum lumen (GO:0005788)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|secretory granule lumen (GO:0034774)	hormone activity (GO:0005179)|identical protein binding (GO:0042802)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|protease binding (GO:0002020)			haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	5		Lung NSC(207;8.94e-06)|all_epithelial(84;3.17e-05)|all_lung(207;3.67e-05)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.14)		AGCTCCACCTGCCCCACTGCC	0.682																																					p.Q65K		Atlas-SNP	.											.	INS	10	.	0			c.C193A						.						19	19	19					11																	2181222		2170	4273	6443	SO:0001583	missense	3630	exon3			CCACCTGCCCCAC	X70508	CCDS7729.1	11p15.5	2014-02-03			ENSG00000254647	ENSG00000254647			6081	protein-coding gene	gene with protein product		176730	"insulin-dependent diabetes mellitus 2"	IDDM2, IDDM1		6243748, 7773291	Standard	NM_000207		Approved			P01308	OTTHUMG00000009558	ENST00000397262.1:c.193C>A	chr11.hg19:g.2181222G>T	ENSP00000380432:p.Gln65Lys	42.0	0.0		39.0	22.0	NM_001185097	Q5EEX2	Missense_Mutation	SNP	ENST00000397262.1	hg19	CCDS7729.1	.	.	.	.	.	.	.	.	.	.	G	2.388	-0.340403	0.05243	.	.	ENSG00000254647	ENST00000397262;ENST00000250971;ENST00000381330	D;D;D	0.88509	-2.39;-2.39;-2.39	3.5	1.44	0.22558	Insulin-like (4);	.	.	.	.	D	0.87633	0.6226	M	0.80028	2.48	0.09310	N	0.999998	B	0.31351	0.32	B	0.34991	0.193	T	0.72500	-0.4274	9	0.10111	T	0.7	.	11.4432	0.50109	0.0:0.3187:0.6813:0.0	.	65	P01308	INS_HUMAN	K	65	ENSP00000380432:Q65K;ENSP00000250971:Q65K;ENSP00000370731:Q65K	ENSP00000250971:Q65K	Q	-	1	0	INS	2137798	0.000000	0.05858	0.004000	0.12327	0.194000	0.23727	0.033000	0.13754	0.256000	0.21614	0.462000	0.41574	CAG	.	.		0.682	INS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026395.3	NM_000207		T	2181222	G	T	2181222	3	4	172	1	0	0	0	0	1	0	0	0	7771	1328	46	3	143	3	INS	11	2181222	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10		2181222	132825294	55	26066										
KIF18A	81930	hgsc.bcm.edu	37	chr11	28090820	28090820	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ttgtacctttggaatatgacCgttttgacttaagagtccca	8	8	0	3			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr11:28090820C>T	ENST00000263181.6	-	11	1866	c.1576G>A	c.(1576-1578)Ggt>Agt	p.G526S		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	526					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						GGAATATGACCGTTTTGACTT	0.358																																					p.G526S		Atlas-SNP	.											.	KIF18A	92	.	0			c.G1576A						.						97	95	95					11																	28090820		2202	4299	6501	SO:0001583	missense	81930	exon11			TATGACCGTTTTG	AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"Kinesins"	29441	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 99"	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.1576G>A	chr11.hg19:g.28090820C>T	ENSP00000263181:p.Gly526Ser	70.0	0.0		127.0	9.0	NM_031217	Q4VPE3|Q86VS5|Q9H0F3	Missense_Mutation	SNP	ENST00000263181.6	hg19	CCDS7867.1	.	.	.	.	.	.	.	.	.	.	C	18.80	3.701040	0.68501	.	.	ENSG00000121621	ENST00000263181	T	0.72282	-0.64	5.39	5.39	0.77823	.	0.100798	0.64402	D	0.000002	T	0.80341	0.4605	M	0.66939	2.045	0.53005	D	0.999967	D	0.89917	1.0	D	0.65140	0.932	T	0.74945	-0.3491	10	0.09338	T	0.73	.	18.7497	0.91809	0.0:1.0:0.0:0.0	.	526	Q8NI77	KI18A_HUMAN	S	526	ENSP00000263181:G526S	ENSP00000263181:G526S	G	-	1	0	KIF18A	28047396	1.000000	0.71417	1.000000	0.80357	0.562000	0.35680	5.407000	0.66363	2.537000	0.85549	0.655000	0.94253	GGT	.	.		0.358	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217		T	28090820	C	T	28090820	3	4	172	1	0	0	0	0	1	0	0	0	8289	652	23	1	1148	1	KIF18A	11	28090820	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	25909598	28090820	106915696	56	26067										
OR5M9	390162	hgsc.bcm.edu	37	chr11	56230823	56230823	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aaagagaacctgtagctcctGacgacaggtcagccccagga	11	12	1	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr11:56230823G>A	ENST00000279791.1	-	1	54	c.55C>T	c.(55-57)Cag>Tag	p.Q19*		NM_001004743.1	NP_001004743.1	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M, member 9	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	36	Esophageal squamous(21;0.00448)					TGTAGCTCCTGACGACAGGTC	0.428																																					p.Q19X		Atlas-SNP	.											.	OR5M9	75	.	0			c.C55T						.						36	36	36					11																	56230823		2201	4296	6497	SO:0001587	stop_gained	390162	exon1			GCTCCTGACGACA	AB065747	CCDS31531.1	11q11	2012-08-09			ENSG00000150269	ENSG00000150269		"GPCR / Class A : Olfactory receptors"	15294	protein-coding gene	gene with protein product							Standard	NM_001004743		Approved		uc010rjj.2	Q8NGP3	OTTHUMG00000166874	ENST00000279791.1:c.55C>T	chr11.hg19:g.56230823G>A	ENSP00000279791:p.Gln19*	200.0	1.0		122.0	107.0	NM_001004743	Q6IEW5|Q96RB9	Nonsense_Mutation	SNP	ENST00000279791.1	hg19	CCDS31531.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.802983	0.31869	.	.	ENSG00000150269	ENST00000279791	.	.	.	4.79	3.81	0.43845	.	0.000000	0.41396	D	0.000894	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-9.9619	9.7681	0.40574	0.0:0.0:0.7943:0.2057	.	.	.	.	X	19	.	ENSP00000279791:Q19X	Q	-	1	0	OR5M9	55987399	0.000000	0.05858	0.110000	0.21437	0.424000	0.31475	0.325000	0.19628	2.349000	0.79799	0.549000	0.68633	CAG	.	.		0.428	OR5M9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391638.1	NM_001004743		A	56230823	G	A	56230823	4	1	172	1	0	0	0	0	0	1	0	0	11186	1299	45	3	879	3	OR5M9	11	56230823	Nonsense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	28140003	56230823	78775693	57	26068										
ROBO4	54538	hgsc.bcm.edu	37	chr11	124756386	124756386	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	agacgcagtctgcctccctgGgctctagaccgaaaccaaag	10	14	2	2	rs377645881	byFrequency	TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr11:124756386G>A	ENST00000306534.3	-	16	3253	c.2768C>T	c.(2767-2769)cCc>cTc	p.P923L	RP11-664I21.5_ENST00000524453.1_RNA|ROBO4_ENST00000533054.1_Missense_Mutation_p.P778L	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	923					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		TGCCTCCCTGGGCTCTAGACC	0.547													G|||	2	0.000399361	0	0	5008	,	,		17877	0		0	False		,,,				2504	0.002				p.P923L		Atlas-SNP	.											.	ROBO4	130	.	0			c.C2768T						.						53	57	56					11																	124756386		2201	4299	6500	SO:0001583	missense	54538	exon16			TCCCTGGGCTCTA	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.2768C>T	chr11.hg19:g.124756386G>A	ENSP00000304945:p.Pro923Leu	132.0	0.0		75.0	67.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	hg19	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.941748	0.73557	.	.	ENSG00000154133	ENST00000306534;ENST00000533054	T;T	0.63417	-0.04;0.33	4.7	4.7	0.59300	.	0.000000	0.36034	N	0.002840	T	0.54919	0.1888	M	0.65975	2.015	0.35346	D	0.786902	B;B	0.30584	0.112;0.286	B;B	0.25140	0.049;0.058	T	0.66838	-0.5822	10	0.66056	D	0.02	.	6.7067	0.23254	0.0908:0.0:0.6805:0.2287	.	923;923	Q8WZ75-2;Q8WZ75	.;ROBO4_HUMAN	L	923;778	ENSP00000304945:P923L;ENSP00000437129:P778L	ENSP00000304945:P923L	P	-	2	0	ROBO4	124261596	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.284000	0.43478	2.319000	0.78375	0.655000	0.94253	CCC	.	.		0.547	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		A	124756386	G	A	124756386	3	1	172	1	0	0	0	0	1	0	0	0	13531	1232	43	3	267	3	ROBO4	11	124756386	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	68525563	124756386	10250130	58	26069										
GYS2	2998	hgsc.bcm.edu	37	chr12	21757510	21757510	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ccagggatgttacagagaggGatcggcctcgaagcattctt	13	9	1	1	rs141614479		TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr12:21757510G>C	ENST00000261195.2	-	1	271	c.17C>G	c.(16-18)tCc>tGc	p.S6C		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	6					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TACAGAGAGGGATCGGCCTCG	0.478																																					p.S6C	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											.	GYS2	110	.	0			c.C17G						.	G	CYS/SER	0,4406		0,0,2203	89	86	87		17	5.3	0.4	12	dbSNP_134	87	1,8597	1.2+/-3.3	0,1,4298	no	missense	GYS2	NM_021957.3	112	0,1,6501	CC,CG,GG		0.0116,0.0,0.0077	probably-damaging	6/704	21757510	1,13003	2203	4299	6502	SO:0001583	missense	2998	exon1			GAGAGGGATCGGC		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.17C>G	chr12.hg19:g.21757510G>C	ENSP00000261195:p.Ser6Cys	156.0	0.0		201.0	86.0	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	hg19	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.781198	0.70222	0.0	1.16E-4	ENSG00000111713	ENST00000261195	T	0.67345	-0.26	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.68393	0.2996	N	0.19112	0.55	0.54753	D	0.999985	D	0.71674	0.998	P	0.61201	0.885	T	0.71873	-0.4461	10	0.62326	D	0.03	-25.3852	15.9549	0.79880	0.0:0.0:1.0:0.0	.	6	P54840	GYS2_HUMAN	C	6	ENSP00000261195:S6C	ENSP00000261195:S6C	S	-	2	0	GYS2	21648777	1.000000	0.71417	0.396000	0.26296	0.761000	0.43186	7.158000	0.77470	2.756000	0.94617	0.655000	0.94253	TCC	.	G|1.000;C|0.000		0.478	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		C	21757510	G	C	21757510	3	2	172	1	0	0	0	0	1	0	0	0	6922	1174	41	4	2158	4	GYS2	12	21757510	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10		21757510	112094385	59	26070										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40689286	40689286	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cagcatttcttctctggcttCtgagagagaatatattacat	7	8	3	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr12:40689286C>T	ENST00000298910.7	+	23	2994	c.2936C>T	c.(2935-2937)tCt>tTt	p.S979F	LRRK2_ENST00000343742.2_Missense_Mutation_p.S979F	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	979					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TCTCTGGCTTCTGAGAGAGAA	0.353																																					p.S979F		Atlas-SNP	.											.	LRRK2	763	.	0			c.C2936T						.						71	72	72					12																	40689286		2203	4300	6503	SO:0001583	missense	120892	exon23			TGGCTTCTGAGAG	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.2936C>T	chr12.hg19:g.40689286C>T	ENSP00000298910:p.Ser979Phe	56.0	0.0		87.0	44.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.557009	0.65425	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	T;T	0.25085	2.18;1.82	5.71	1.58	0.23477	.	0.599767	0.17694	N	0.165143	T	0.15089	0.0364	L	0.27053	0.805	0.35598	D	0.807625	P;P	0.46706	0.883;0.788	B;B	0.39876	0.312;0.126	T	0.23261	-1.0193	10	0.19147	T	0.46	.	9.8616	0.41118	0.0:0.5249:0.4029:0.0722	.	979;979	E9PC85;Q5S007	.;LRRK2_HUMAN	F	979	ENSP00000341930:S979F;ENSP00000298910:S979F	ENSP00000298910:S979F	S	+	2	0	LRRK2	38975553	0.024000	0.19004	0.973000	0.42090	0.994000	0.84299	0.329000	0.19698	0.271000	0.22005	0.591000	0.81541	TCT	.	.		0.353	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40689286	C	T	40689286	3	4	172	1	0	0	0	0	1	0	0	0	9042	913	32	3	3026	3	LRRK2	12	40689286	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	18931776	40689286	93162609	60	26071										
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56811967	56811967	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ttgtgggctagcaagagggcCctcagggcttgtgctcggtg	17	9	1	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr12:56811967C>A	ENST00000553532.1	-	27	3555	c.3405G>T	c.(3403-3405)agG>agT	p.R1135S	TIMELESS_ENST00000554616.1_Missense_Mutation_p.R632S|TIMELESS_ENST00000229201.4_Missense_Mutation_p.R1134S					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						GCAAGAGGGCCCTCAGGGCTT	0.557																																					p.R1135S		Atlas-SNP	.											.	TIMELESS	107	.	0			c.G3405T						.						169	178	175					12																	56811967		2203	4300	6503	SO:0001583	missense	8914	exon27			GAGGGCCCTCAGG	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1"	603887	"timeless (Drosophila) homolog", "timeless homolog (Drosophila)"			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.3405G>T	chr12.hg19:g.56811967C>A	ENSP00000450607:p.Arg1135Ser	62.0	0.0		87.0	42.0	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	hg19	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.845766	0.32606	.	.	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.12255	2.7;2.7;2.7	5.27	0.953	0.19590	Timeless C-terminal (1);	0.727010	0.13293	N	0.398821	T	0.13372	0.0324	M	0.66939	2.045	0.09310	N	1	B	0.27910	0.193	B	0.28385	0.089	T	0.28964	-1.0027	10	0.49607	T	0.09	-1.4219	2.794	0.05396	0.3315:0.3384:0.0:0.3301	.	1135	Q9UNS1	TIM_HUMAN	S	1134;1135;632	ENSP00000229201:R1134S;ENSP00000450607:R1135S;ENSP00000450848:R632S	ENSP00000229201:R1135S	R	-	3	2	TIMELESS	55098234	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.663000	0.05299	-0.035000	0.13691	-0.137000	0.14449	AGG	.	.		0.557	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		A	56811967	C	A	56811967	3	1	172	1	0	0	0	0	1	0	0	0	15919	622	22	3	233	3	TIMELESS	12	56811967	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	16122681	56811967	77039928	61	26072										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80712338	80712338	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ttaactaggacttggagaagGaccatatatgctggcaagct	11	7	0	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr12:80712338G>T	ENST00000547103.1	+	32	3626	c.3620G>T	c.(3619-3621)gGa>gTa	p.G1207V	OTOGL_ENST00000458043.2_Missense_Mutation_p.G1207V			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1207					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						CTTGGAGAAGGACCATATATG	0.363																																					p.G1207V		Atlas-SNP	.											.	OTOGL	235	.	0			c.G3620T						.						43	40	41					12																	80712338		1545	3453	4998	SO:0001583	missense	283310	exon32			GAGAAGGACCATA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.3620G>T	chr12.hg19:g.80712338G>T	ENSP00000447211:p.Gly1207Val	67.0	0.0		77.0	39.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.	.	.	.	.	.	.	.	.	.	G	23.5	4.429089	0.83667	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.19806	2.12;2.13	5.43	5.43	0.79202	.	.	.	.	.	T	0.44685	0.1305	M	0.73962	2.25	0.80722	D	1	.	.	.	.	.	.	T	0.20773	-1.0265	7	0.39692	T	0.17	.	19.2361	0.93861	0.0:0.0:1.0:0.0	.	.	.	.	V	1207	ENSP00000447211:G1207V;ENSP00000400895:G1207V	ENSP00000400895:G1207V	G	+	2	0	OTOGL	79236469	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.939000	0.92951	2.528000	0.85240	0.655000	0.94253	GGA	.	.		0.363	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		T	80712338	G	T	80712338	3	4	172	1	0	0	0	0	1	0	0	0	1709	1174	41	3	3746	3	C12orf64	12	80712338	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	23900371	80712338	53139557	62	26073										
MIPEP	4285	hgsc.bcm.edu	37	chr13	24411689	24411689	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aaaagccctcctcatggctcAccagtgacgtgttggtaacg	10	12	2	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr13:24411689A>T	ENST00000382172.3	-	13	1642		c.e13+1			NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase						protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		CTCATGGCTCACCAGTGACGT	0.388																																					.		Atlas-SNP	.											.	MIPEP	53	.	0			c.1543+2T>A						.						132	127	129					13																	24411689		2203	4300	6503	SO:0001630	splice_region_variant	4285	exon14			TGGCTCACCAGTG		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1543+1T>A	chr13.hg19:g.24411689A>T		98.0	0.0		140.0	69.0	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Splice_Site	SNP	ENST00000382172.3	hg19	CCDS9303.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.681955	0.88542	.	.	ENSG00000027001	ENST00000382172	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1864	0.81955	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MIPEP	23309689	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	8.973000	0.93428	2.227000	0.72691	0.454000	0.30748	.	.	.		0.388	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		Intron	T	24411689	A	T	24411689	5	4	172	1	0	0	0	0	0	0	1	0	9601	173	6	4	624	4	MIPEP	13	24411689	Splice_Site	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10		24411689	90758189	63	26074										
FAM123A	219287	hgsc.bcm.edu	37	chr13	25744258	25744258	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ttgggctcctccttaggatgGggctcgatgggaatccggtt	15	9	0	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr13:25744258G>T	ENST00000515384.1	-	1	2167	c.1500C>A	c.(1498-1500)ccC>ccA	p.P500P	AMER2_ENST00000357816.2_Silent_p.P381P|AMER2_ENST00000381853.3_Silent_p.P381P|AMER2-AS1_ENST00000413501.1_lincRNA			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	500					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)										CCTTAGGATGGGGCTCGATGG	0.657																																					p.P500P		Atlas-SNP	.											.	.	.	.	0			c.C1500A						.						51	49	50					13																	25744258		2203	4300	6503	SO:0001819	synonymous_variant	219287	exon1			AGGATGGGGCTCG	AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"-"	26360	protein-coding gene	gene with protein product		614659	"family with sequence similarity 123A"	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1500C>A	chr13.hg19:g.25744258G>T		60.0	0.0		70.0	32.0	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Silent	SNP	ENST00000515384.1	hg19	CCDS53859.1																																																																																			.	.		0.657	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704		T	25744258	G	T	25744258	2	4	172	1	0	0	0	0	0	0	0	1	5427	1219	43	3		3	FAM123A	13	25744258	Silent	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	1332569	25744258	89425620	64	26075										
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42390845	42390846	+	Frame_Shift_Ins	INS	-	-	T													0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	agacttaccgttggatcctgINStgtttctctgagtttgtgtg							TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr13:42390845_42390846insT	ENST00000379310.3	-	16	2003_2004	c.1935_1936insA	c.(1933-1938)acacagfs	p.Q646fs	VWA8_ENST00000281496.6_Frame_Shift_Ins_p.Q646fs	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	646						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										GTTGGATCCTGTGTTTCTCTGA	0.356																																					p.Q646fs		Atlas-INDEL	.											.	.	.	.	0			c.1936_1937insA						.																																			SO:0001589	frameshift_variant	23078	exon16			.	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.1936dupA	chr13.hg19:g.42390846_42390846dupT	ENSP00000368612:p.Gln646fs	133.0	0.0		151.0	72.0	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Frame_Shift_Ins	INS	ENST00000379310.3	hg19	CCDS41881.1																																																																																			.	.		0.356	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		T	42390846	-	T	42390845	7	5	172	1	0	1	1	0	0	0	0	0	8194	1386	48	0	3905	0	KIAA0564	13	42390845	Frame_Shift_Ins	INS	-	TCGA-DD-AACV-01A-11D-A40R-10	16646587	42390845	72779033	65	26076										
PCDH20	64881	hgsc.bcm.edu	37	chr13	61985638	61985638	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tttgtggttctttctcctctAtattaatctctggttctttt	5	8	5	0	rs375289034		TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr13:61985638A>G	ENST00000409186.1	-	5	4699	c.2594T>C	c.(2593-2595)aTa>aCa	p.I865T	PCDH20_ENST00000409204.4_Missense_Mutation_p.I865T			Q8N6Y1	PCD20_HUMAN	protocadherin 20	865					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		TTTCTCCTCTATATTAATCTC	0.398																																					p.I865T		Atlas-SNP	.											.	PCDH20	265	.	0			c.T2594C						.	A	THR/ILE	2,4404	4.2+/-10.8	0,2,2201	73	69	70		2594	6.1	1	13		70	0,8600		0,0,4300	no	missense	PCDH20	NM_022843.3	89	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	benign	865/952	61985638	2,13004	2203	4300	6503	SO:0001583	missense	64881	exon2			TCCTCTATATTAA	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.2594T>C	chr13.hg19:g.61985638A>G	ENSP00000386653:p.Ile865Thr	103.0	0.0		68.0	62.0	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	hg19	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	A	11.33	1.608035	0.28623	4.54E-4	0.0	ENSG00000197991	ENST00000409204;ENST00000409186;ENST00000358674	T;T	0.55234	0.53;0.53	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.40595	0.1123	L	0.29908	0.895	0.51012	D	0.999902	P	0.43094	0.799	B	0.33339	0.162	T	0.46219	-0.9207	10	0.72032	D	0.01	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	865	A8K1K9	.	T	865;865;611	ENSP00000387250:I865T;ENSP00000386653:I865T	ENSP00000351500:I611T	I	-	2	0	PCDH20	60883639	1.000000	0.71417	0.996000	0.52242	0.787000	0.44495	8.610000	0.90902	2.326000	0.78906	0.533000	0.62120	ATA	.	.		0.398	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		G	61985638	A	G	61985638	3	3	172	1	0	0	0	0	1	0	0	0	11524	449	16	2	265	2	PCDH20	13	61985638	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	19594793	61985638	53184240	66	26077										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77661633	77661633	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	atttacttgttctgaattttCtttgcttgttttattttctt	4	5	3	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr13:77661633C>T	ENST00000544440.2	-	62	10764	c.10747G>A	c.(10747-10749)Gaa>Aaa	p.E3583K	MYCBP2-AS1_ENST00000422231.2_RNA|MYCBP2-AS1_ENST00000448470.2_RNA|MYCBP2-AS1_ENST00000593933.1_RNA|MYCBP2_ENST00000357337.6_Missense_Mutation_p.E3583K|MYCBP2_ENST00000407578.2_Missense_Mutation_p.E3621K|MYCBP2-AS1_ENST00000450627.2_RNA					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TCTGAATTTTCTTTGCTTGTT	0.343																																					p.E3621K		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.G10861A						.						99	81	87					13																	77661633		2202	4300	6502	SO:0001583	missense	23077	exon62			AATTTTCTTTGCT	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.10747G>A	chr13.hg19:g.77661633C>T	ENSP00000444596:p.Glu3583Lys	167.0	0.0		107.0	14.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.71|15.71	2.913267|2.913267	0.52439|0.52439	.|.	.|.	ENSG00000005810|ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440|ENST00000429715	T;T;T|.	0.27402|.	1.67;1.67;1.67|.	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.33059|0.33059	0.0850|0.0850	N|N	0.02011|0.02011	-0.69|-0.69	0.80722|0.80722	D|D	1|1	P|.	0.37781|.	0.608|.	B|.	0.32211|.	0.142|.	T|T	0.33137|0.33137	-0.9880|-0.9880	10|5	0.32370|.	T|.	0.25|.	.|.	18.6231|18.6231	0.91328|0.91328	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	3583|.	O75592|.	MYCB2_HUMAN|.	K|K	3583;3621;3583|6	ENSP00000349892:E3583K;ENSP00000384288:E3621K;ENSP00000444596:E3583K|.	ENSP00000349892:E3583K|.	E|R	-|-	1|2	0|0	MYCBP2|MYCBP2	76559634|76559634	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.104000|0.104000	0.19210|0.19210	7.809000|7.809000	0.86057|0.86057	2.379000|2.379000	0.81126|0.81126	0.563000|0.563000	0.77884|0.77884	GAA|AGA	.	.		0.343	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		T	77661633	C	T	77661633	3	4	172	1	0	0	0	0	1	0	0	0	10027	922	32	3	3263	3	MYCBP2	13	77661633	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	15675995	77661633	37508245	67	26078										
POTEM	641455	hgsc.bcm.edu	37	chr14	20019996	20019996	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gtgcccacgttgctcttgccGctccccctgcaccaggggaa	11	17	1	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr14:20019996G>A	ENST00000551509.1	-	1	276	c.225C>T	c.(223-225)agC>agT	p.S75S		NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN	POTE ankyrin domain family, member M	75								p.S75S(2)		endometrium(4)|kidney(1)|lung(4)	9						TGCTCTTGCCGCTCCCCCTGC	0.587																																					p.S75S		Atlas-SNP	.											POTEM_ENST00000551509,NS,carcinoma,-2,3	POTEM	51	.	2	Substitution - coding silent(2)	endometrium(2)	c.C225T						.						12	21	19					14																	20019996		316	1139	1455	SO:0001819	synonymous_variant	641455	exon1			CTTGCCGCTCCCC		CCDS73609.1	14q11.2	2013-01-10			ENSG00000187537	ENSG00000187537		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	37096	protein-coding gene	gene with protein product	"prostate-specific P704P"					16364570	Standard	NM_001145442		Approved	POTE14beta, P704P, ACT	uc001vwc.3	A6NI47		ENST00000551509.1:c.225C>T	chr14.hg19:g.20019996G>A		519.0	1.0		964.0	62.0	NM_001145442		Silent	SNP	ENST00000551509.1	hg19	CCDS45076.1																																																																																			.	.		0.587	POTEM-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409490.3	NM_001145442		A	20019996	G	A	20019996	2	1	172	1	0	0	0	0	0	0	0	1	12277	1078	38	1		1	POTEM	14	20019996	Silent	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10		20019996	87329544	68	26079										
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36155747	36155747	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aatatataaaataaaacttaCcgaggcattaccacttcgaa	4	8	0	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr14:36155747C>A	ENST00000389698.3	-	18	2950		c.e18+1		RALGAPA1_ENST00000382366.3_Splice_Site|RALGAPA1_ENST00000307138.6_Splice_Site|RALGAPA1_ENST00000258840.6_Splice_Site	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)						activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						ATAAAACTTACCGAGGCATTA	0.343																																					.		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.2559+1G>T						.						27	27	27					14																	36155747		2203	4300	6503	SO:0001630	splice_region_variant	253959	exon19			AACTTACCGAGGC	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.2559+1G>T	chr14.hg19:g.36155747C>A		335.0	0.0		167.0	153.0	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Splice_Site	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.543222	0.45280	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	.	.	.	5.98	5.98	0.97165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.452	0.99131	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RALGAPA1	35225498	1.000000	0.71417	1.000000	0.80357	0.384000	0.30261	6.829000	0.75314	2.838000	0.97847	0.591000	0.81541	.	.	.		0.343	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	Intron	A	36155747	C	A	36155747	5	1	172	1	0	0	0	0	0	0	1	0	13028	521	18	3	3795	3	RALGAPA1	14	36155747	Splice_Site	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	16135751	36155747	71193793	69	26080			2	30		2	2	22	N	G_C	7.054762e-05
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36155768	36155768	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cgaggcattaccacttcgaaGtcgttctgctataaactcat	7	11	2	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr14:36155768G>C	ENST00000389698.3	-	18	2929	c.2539C>G	c.(2539-2541)Ctt>Gtt	p.L847V	RALGAPA1_ENST00000382366.3_Missense_Mutation_p.L860V|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.L847V|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.L894V	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	847					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CCACTTCGAAGTCGTTCTGCT	0.368																																					p.L847V		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.C2539G						.						47	43	44					14																	36155768		2203	4300	6503	SO:0001583	missense	253959	exon18			TTCGAAGTCGTTC	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.2539C>G	chr14.hg19:g.36155768G>C	ENSP00000374348:p.Leu847Val	355.0	0.0		175.0	163.0	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.490314	0.44249	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	D;D;D;D;D	0.94966	-3.45;-3.46;-3.54;-3.57;-3.54	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.94548	0.8244	L	0.32530	0.975	0.45035	D	0.998052	D;D;P;D;P	0.71674	0.991;0.959;0.916;0.998;0.74	P;P;P;D;B	0.77557	0.861;0.556;0.527;0.99;0.313	D	0.91338	0.5095	10	0.13108	T	0.6	-19.1447	14.5704	0.68208	0.0695:0.0:0.9305:0.0	.	894;860;894;847;847	Q6GYQ0-6;B9EK38;Q6GYQ0-3;Q6GYQ0-2;Q6GYQ0	.;.;.;.;RGPA1_HUMAN	V	847;847;847;894;860;894	ENSP00000374348:L847V;ENSP00000302647:L847V;ENSP00000258840:L894V;ENSP00000371803:L860V;ENSP00000451877:L894V	ENSP00000258840:L894V	L	-	1	0	RALGAPA1	35225519	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	7.618000	0.83043	2.833000	0.97629	0.585000	0.79938	CTT	.	.		0.368	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		C	36155768	G	C	36155768	3	2	172	1	0	0	0	0	1	0	0	0	13028	1029	36	4	3816	4	RALGAPA1	14	36155768	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	21	36155768	71193772	70	26081			2	30		2	2	22	N	G_C	7.054762e-05
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493105	77493105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cgttgcgctgcttctccttcAactcgcgctcctggtctgtg	10	15	3	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr14:77493105A>G	ENST00000238647.3	-	1	1929	c.1031T>C	c.(1030-1032)tTg>tCg	p.L344S		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	344					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						CTTCTCCTTCAACTCGCGCTC	0.682																																					p.L344S		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.T1031C						.						29	30	30					14																	77493105		2203	4300	6503	SO:0001583	missense	64207	exon1			TCCTTCAACTCGC	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.1031T>C	chr14.hg19:g.77493105A>G	ENSP00000238647:p.Leu344Ser	83.0	0.0		115.0	42.0	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Missense_Mutation	SNP	ENST00000238647.3	hg19	CCDS9854.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.122702	0.77436	.	.	ENSG00000119669	ENST00000238647	T	0.65549	-0.16	3.73	3.73	0.42828	.	0.000000	0.49916	U	0.000129	T	0.52500	0.1738	L	0.29908	0.895	0.39300	D	0.964899	D	0.54601	0.967	P	0.50314	0.637	T	0.50808	-0.8784	10	0.07644	T	0.81	26.8	11.6991	0.51560	1.0:0.0:0.0:0.0	.	344	Q9H1B7	I2BPL_HUMAN	S	344	ENSP00000238647:L344S	ENSP00000238647:L344S	L	-	2	0	IRF2BPL	76562858	0.999000	0.42202	1.000000	0.80357	0.952000	0.60782	4.284000	0.58983	1.696000	0.51158	0.379000	0.24179	TTG	.	.		0.682	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		G	77493105	A	G	77493105	3	3	172	1	0	0	0	0	1	0	0	0	1775	131	5	2	1363	2	C14orf4	14	77493105	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	41337337	77493105	29856435	71	26082										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94004493	94004493	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gagactcacctctatcagacCtctcctccgcccatcaacac	4	19	5	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr14:94004493C>T	ENST00000393151.2	+	12	1281	c.1281C>T	c.(1279-1281)acC>acT	p.T427T	UNC79_ENST00000256339.4_Silent_p.T250T|UNC79_ENST00000553484.1_Silent_p.T427T|UNC79_ENST00000555664.1_Silent_p.T427T			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	427					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TCTATCAGACCTCTCCTCCGC	0.582																																					p.T250T		Atlas-SNP	.											.	UNC79	366	.	0			c.C750T						.						47	46	46					14																	94004493		2203	4300	6503	SO:0001819	synonymous_variant	57578	exon12			TCAGACCTCTCCT	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.1281C>T	chr14.hg19:g.94004493C>T		115.0	0.0		153.0	75.0	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	hg19																																																																																				.	.		0.582	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94004493	C	T	94004493	2	4	172	1	0	0	0	0	0	0	0	1	8239	668	24	3		3	KIAA1409	14	94004493	Silent	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	16511388	94004493	13345047	72	26083										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96775858	96775858	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cctccatagcatcactcatcAgatctcgtaacatttgttga	5	12	4	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr14:96775858A>G	ENST00000359933.4	-	29	5128	c.4235T>C	c.(4234-4236)cTg>cCg	p.L1412P	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1412					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		ATCACTCATCAGATCTCGTAA	0.448																																					p.L1412P		Atlas-SNP	.											.	ATG2B	169	.	0			c.T4235C						.						203	158	173					14																	96775858		2203	4300	6503	SO:0001583	missense	55102	exon29			CTCATCAGATCTC	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.4235T>C	chr14.hg19:g.96775858A>G	ENSP00000353010:p.Leu1412Pro	101.0	0.0		154.0	65.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	24.6	4.548517	0.86127	.	.	ENSG00000066739	ENST00000359933	T	0.64438	-0.1	5.58	5.58	0.84498	.	0.245457	0.35235	N	0.003356	T	0.79787	0.4506	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82184	-0.0583	10	0.66056	D	0.02	.	16.0556	0.80801	1.0:0.0:0.0:0.0	.	1412	Q96BY7	ATG2B_HUMAN	P	1412	ENSP00000353010:L1412P	ENSP00000261834:L56P	L	-	2	0	ATG2B	95845611	1.000000	0.71417	0.946000	0.38457	0.934000	0.57294	8.517000	0.90555	2.239000	0.73571	0.533000	0.62120	CTG	.	.		0.448	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96775858	A	G	96775858	3	3	172	1	0	0	0	0	1	0	0	0	1094	188	7	2	2057	2	ATG2B	14	96775858	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10	2771365	96775858	10573682	73	26084										
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102548068	102548068	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	attagtctacttcttccatgCgtgatgtgtcgtcatctcct	7	11	4	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr14:102548068C>T	ENST00000216281.8	-	11	2385	c.2180G>A	c.(2179-2181)cGc>cAc	p.R727H	HSP90AA1_ENST00000334701.7_Missense_Mutation_p.R849H	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	727	Required for homodimerization.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	TTCTTCCATGCGTGATGTGTC	0.408																																					p.R849H		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.G2546A						.						167	140	149					14																	102548068		2203	4300	6503	SO:0001583	missense	3320	exon12			TCCATGCGTGATG	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.2180G>A	chr14.hg19:g.102548068C>T	ENSP00000216281:p.Arg727His	66.0	0.0		85.0	38.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Missense_Mutation	SNP	ENST00000216281.8	hg19	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	c	17.11	3.305699	0.60305	.	.	ENSG00000080824	ENST00000216281;ENST00000334701	T;T	0.09723	2.95;2.95	4.21	4.21	0.49690	.	0.000000	0.85682	U	0.000000	T	0.14485	0.0350	L	0.60957	1.885	0.80722	D	1	P;P	0.44478	0.836;0.581	B;B	0.39971	0.211;0.315	T	0.06058	-1.0848	10	0.44086	T	0.13	-15.4851	16.9302	0.86188	0.0:1.0:0.0:0.0	.	849;727	P07900-2;P07900	.;HS90A_HUMAN	H	727;849	ENSP00000216281:R727H;ENSP00000335153:R849H	ENSP00000216281:R727H	R	-	2	0	HSP90AA1	101617821	1.000000	0.71417	0.998000	0.56505	0.707000	0.40811	5.810000	0.69179	2.070000	0.61991	0.305000	0.20034	CGC	.	.		0.408	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		T	102548068	C	T	102548068	3	4	172	1	0	0	0	0	1	0	0	0	7410	768	27	1	22	1	HSP90AA1	14	102548068	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	5772210	102548068	4801472	74	26085										
CHRNA7	1139	hgsc.bcm.edu	37	chr15	32455506	32455506	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gtgctgcagtaccaccaccaCgaccccgacgggggcaagat	12	15	0	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr15:32455506C>T	ENST00000306901.3	+	9	1057	c.960C>T	c.(958-960)caC>caT	p.H320H	CHRNA7_ENST00000454250.3_Silent_p.H349H|CHRNA7_ENST00000455693.2_Silent_p.H139H	NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)	320					activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)	p.H230H(1)|p.H320H(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	ACCACCACCACGACCCCGACG	0.597																																					p.H349H	Esophageal Squamous(193;529 2900 40232 43193)	Atlas-SNP	.											CHRNA7,NS,carcinoma,0,1	CHRNA7	57	.	2	Substitution - coding silent(2)	endometrium(2)	c.C1047T						.						25	24	24					15																	32455506		1245	2201	3446	SO:0001819	synonymous_variant	1139	exon9			CCACCACGACCCC	Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1960	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 7 (neuronal)"	118511	"cholinergic receptor, nicotinic, alpha polypeptide 7"			8188270	Standard	NM_001190455		Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.960C>T	chr15.hg19:g.32455506C>T		355.0	0.0		524.0	255.0	NM_001190455	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	Silent	SNP	ENST00000306901.3	hg19	CCDS10027.1																																																																																			.	.		0.597	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251410.2			T	32455506	C	T	32455506	2	4	172	1	0	0	0	0	0	0	0	1	3390	535	19	1		1	CHRNA7	15	32455506	Silent	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10		32455506	70075886	75	26086										
SPATA5L1	79029	hgsc.bcm.edu	37	chr15	45707864	45707864	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aatcttgggagctcgctcagCcagcaagacaggatgtgatg	13	9	2	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr15:45707864C>G	ENST00000305560.6	+	5	1823	c.1724C>G	c.(1723-1725)gCc>gGc	p.A575G	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.A575G	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	575						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		GCTCGCTCAGCCAGCAAGACA	0.378																																					p.A575G		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.C1724G						.						70	66	68					15																	45707864		2198	4298	6496	SO:0001583	missense	79029	exon5			GCTCAGCCAGCAA	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"ATPases / AAA-type"	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.1724C>G	chr15.hg19:g.45707864C>G	ENSP00000305494:p.Ala575Gly	63.0	0.0		112.0	53.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	hg19	CCDS10123.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.669|7.669	0.686509|0.686509	0.14973|0.14973	.|.	.|.	ENSG00000171763|ENSG00000171763	ENST00000305560|ENST00000531624	D|.	0.94723|.	-3.5|.	5.54|5.54	1.82|1.82	0.25136|0.25136	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);|.	1.437660|.	0.04074|.	N|.	0.308552|.	T|T	0.09379|0.09379	0.0231|0.0231	N|N	0.03016|0.03016	-0.435|-0.435	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.27020|0.27020	-1.0086|-1.0086	10|5	0.21014|.	T|.	0.42|.	-33.411|-33.411	1.2862|1.2862	0.02051|0.02051	0.1432:0.1723:0.1485:0.5361|0.1432:0.1723:0.1485:0.5361	.|.	575|.	Q9BVQ7|.	SPA5L_HUMAN|.	G|A	575|80	ENSP00000305494:A575G|.	ENSP00000305494:A575G|.	A|P	+|+	2|1	0|0	SPATA5L1|SPATA5L1	43495156|43495156	0.001000|0.001000	0.12720|0.12720	0.011000|0.011000	0.14972|0.14972	0.855000|0.855000	0.48748|0.48748	0.031000|0.031000	0.13710|0.13710	0.104000|0.104000	0.17725|0.17725	-0.302000|-0.302000	0.09304|0.09304	GCC|CCA	.	.		0.378	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		G	45707864	C	G	45707864	3	3	172	1	0	0	0	0	1	0	0	0	15027	739	26	4	1742	4	SPATA5L1	15	45707864	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	13252358	45707864	56823528	76	26087										
PYGO1	26108	hgsc.bcm.edu	37	chr15	55838901	55838901	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	caaatcggggttagaaacttGgctagcattctgtggaggaa	13	6	1	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr15:55838901G>T	ENST00000302000.6	-	3	674	c.580C>A	c.(580-582)Caa>Aaa	p.Q194K	PYGO1_ENST00000563719.1_Missense_Mutation_p.Q194K	NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	194	Asn-rich.				hematopoietic progenitor cell differentiation (GO:0002244)|kidney development (GO:0001822)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|spermatid nucleus differentiation (GO:0007289)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(6)|lung(6)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	27				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		TTAGAAACTTGGCTAGCATTC	0.338																																					p.Q194K		Atlas-SNP	.											.	PYGO1	56	.	0			c.C580A						.						74	78	77					15																	55838901		2193	4292	6485	SO:0001583	missense	26108	exon3			AAACTTGGCTAGC	AF457207	CCDS10155.1	15q21.1	2013-10-09	2013-10-09		ENSG00000171016	ENSG00000171016		"Zinc fingers, PHD-type"	30256	protein-coding gene	gene with protein product		606902	"pygopus homolog 1 (Drosophila)"			11988739	Standard	NM_015617		Approved		uc002adf.1	Q9Y3Y4	OTTHUMG00000132009	ENST00000302000.6:c.580C>A	chr15.hg19:g.55838901G>T	ENSP00000302327:p.Gln194Lys	148.0	0.0		237.0	107.0	NM_015617	A7Y2D6	Missense_Mutation	SNP	ENST00000302000.6	hg19	CCDS10155.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.660473	0.67586	.	.	ENSG00000171016	ENST00000302000;ENST00000401688	T	0.47869	0.83	4.99	4.99	0.66335	.	0.163511	0.42053	D	0.000779	T	0.56615	0.1997	L	0.32530	0.975	0.50632	D	0.99988	D;D	0.57899	0.981;0.981	D;P	0.65010	0.931;0.899	T	0.52223	-0.8604	10	0.32370	T	0.25	-10.5213	17.6483	0.88154	0.0:0.0:1.0:0.0	.	194;194	A7Y2D6;Q9Y3Y4	.;PYGO1_HUMAN	K	194	ENSP00000302327:Q194K	ENSP00000302327:Q194K	Q	-	1	0	PYGO1	53626193	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	7.287000	0.78681	2.484000	0.83849	0.585000	0.79938	CAA	.	.		0.338	PYGO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254977.2	NM_015617		T	55838901	G	T	55838901	3	4	172	1	0	0	0	0	1	0	0	0	12878	1357	47	3	683	3	PYGO1	15	55838901	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	10131037	55838901	46692491	77	26088										
DNAJA4	55466	hgsc.bcm.edu	37	chr15	78566662	78566662	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ccagaccgtgtgcatcgagtGcaagggccagggtgagcgca	16	11	0	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr15:78566662G>T	ENST00000394852.3	+	4	732	c.542G>T	c.(541-543)tGc>tTc	p.C181F	DNAJA4_ENST00000343789.3_Missense_Mutation_p.C181F|DNAJA4_ENST00000394855.3_Missense_Mutation_p.C210F|DNAJA4_ENST00000446172.2_Missense_Mutation_p.C154F	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	181					negative regulation of inclusion body assembly (GO:0090084)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	8						TGCATCGAGTGCAAGGGCCAG	0.607																																					p.C210F		Atlas-SNP	.											.	DNAJA4	63	.	0			c.G629T						.						78	65	70					15																	78566662		2196	4293	6489	SO:0001583	missense	55466	exon5			TCGAGTGCAAGGG	AF116663	CCDS10299.2, CCDS45316.1, CCDS45317.1	15q24.1	2011-09-02			ENSG00000140403	ENSG00000140403		"Heat shock proteins / DNAJ (HSP40)"	14885	protein-coding gene	gene with protein product						11147971	Standard	NM_018602		Approved	PRO1472	uc002bdi.3	Q8WW22	OTTHUMG00000143733	ENST00000394852.3:c.542G>T	chr15.hg19:g.78566662G>T	ENSP00000378321:p.Cys181Phe	144.0	0.0		139.0	42.0	NM_018602	E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Missense_Mutation	SNP	ENST00000394852.3	hg19	CCDS45316.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.475998	0.84640	.	.	ENSG00000140403	ENST00000394855;ENST00000343789;ENST00000394852;ENST00000446172	T;T;T;D	0.81659	-1.06;-0.87;-0.87;-1.52	5.63	4.72	0.59763	HSP40/DnaJ peptide-binding (1);Heat shock protein DnaJ, cysteine-rich domain (4);	0.000000	0.85682	D	0.000000	D	0.93654	0.7973	H	0.99650	4.68	0.80722	D	1	P;P;P;P	0.51933	0.83;0.949;0.866;0.749	P;P;P;P	0.60415	0.546;0.874;0.798;0.627	D	0.95595	0.8658	10	0.66056	D	0.02	-7.5969	13.7548	0.62930	0.0733:0.0:0.9267:0.0	.	96;154;181;210	Q9P1H1;E9PDM9;Q8WW22;Q8WW22-2	.;.;DNJA4_HUMAN;.	F	210;181;181;154	ENSP00000378324:C210F;ENSP00000339581:C181F;ENSP00000378321:C181F;ENSP00000413499:C154F	ENSP00000339581:C181F	C	+	2	0	DNAJA4	76353717	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.658000	0.98594	1.384000	0.46424	0.655000	0.94253	TGC	.	.		0.607	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	NM_018602		T	78566662	G	T	78566662	3	4	172	1	0	0	0	0	1	0	0	0	4616	1319	46	3	702	3	DNAJA4	15	78566662	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	22727761	78566662	23964730	78	26089										
SOLH	6650	hgsc.bcm.edu	37	chr16	597393	597394	+	Nonsense_Mutation	DNP	GG	GG	AT													0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cctgaggccctggtggtcccGgaagtggtggccccggccgg							TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr16:597393_597394GG>AT	ENST00000219611.2	+	4	918_919	c.555_556GG>AT	c.(553-558)ccGGaa>ccATaa	p.E186*	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	186					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TGGTGGTCCCGGAAGTGGTGGC	0.748																																					p.P185P|p.E186X		Atlas-SNP	.											.	SOLH	47	.	0			c.G555A|c.G556T						.																																			SO:0001587	stop_gained	6650	exon4			GGTCCCGGAAGTG|GTCCCGGAAGTGG	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"small optic lobes (Drosophila) homolog", "small optic lobes homolog (Drosophila)"	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	Exception_encountered	chr16.hg19:g.597393_597394delinsAT	ENSP00000219611:p.Glu186*	64.0|65.0	0.0		71.0	34.0	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Silent|Nonsense_Mutation	SNP	ENST00000219611.2	hg19	CCDS10410.1																																																																																			.	.		0.748	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		AT	597394	GG	AT	597393	4	1	172	1	0	0	0	0	0	1	0	0	14940	1103	39	1	557	1	SOLH	16	597393	Nonsense_Mutation	DNP	GG	TCGA-DD-AACV-01A-11D-A40R-10		597393	89757360	79	26090										
ACSM5	54988	hgsc.bcm.edu	37	chr16	20451162	20451162	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ccttactccagcctactcctCtcatgacccagaggcactaa	5	17	1	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr16:20451162C>G	ENST00000331849.4	+	13	1724	c.1577C>G	c.(1576-1578)tCt>tGt	p.S526C	CTD-2194A8.2_ENST00000574654.1_RNA|CTD-2194A8.2_ENST00000575772.1_RNA	NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	526					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						GCCTACTCCTCTCATGACCCA	0.468																																					p.S526C		Atlas-SNP	.											.	ACSM5	101	.	0			c.C1577G						.						112	104	106					16																	20451162		2203	4299	6502	SO:0001583	missense	54988	exon13			ACTCCTCTCATGA		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"Acyl-CoA synthetase family"	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1577C>G	chr16.hg19:g.20451162C>G	ENSP00000327916:p.Ser526Cys	140.0	0.0		169.0	47.0	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	hg19	CCDS10585.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.130367	0.37630	.	.	ENSG00000183549	ENST00000331849	T	0.50277	0.75	5.01	4.0	0.46444	.	0.241704	0.29307	N	0.012540	T	0.40932	0.1137	L	0.55481	1.735	0.09310	N	1	B	0.28208	0.203	B	0.23419	0.046	T	0.42224	-0.9464	10	0.62326	D	0.03	-10.8708	10.2397	0.43305	0.148:0.7079:0.1441:0.0	.	526	Q6NUN0	ACSM5_HUMAN	C	526	ENSP00000327916:S526C	ENSP00000327916:S526C	S	+	2	0	ACSM5	20358663	0.801000	0.28930	0.017000	0.16124	0.365000	0.29674	2.703000	0.47110	2.487000	0.83934	0.655000	0.94253	TCT	.	.		0.468	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888		G	20451162	C	G	20451162	3	3	172	1	0	0	0	0	1	0	0	0	187	913	32	4	1623	4	ACSM5	16	20451162	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	19853769	20451162	69903591	80	26091										
SLC12A4	6560	hgsc.bcm.edu	37	chr16	67995510	67995510	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ccggcgggtgccctccccacTctcggcctcctcatgctctt	9	20	3	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr16:67995510T>C	ENST00000316341.3	-	3	450	c.310A>G	c.(310-312)Agt>Ggt	p.S104G	SLC12A4_ENST00000572037.1_Missense_Mutation_p.S56G|SLC12A4_ENST00000576616.1_Missense_Mutation_p.S104G|SLC12A4_ENST00000541864.2_Missense_Mutation_p.S73G|SLC12A4_ENST00000572010.1_5'UTR|SLC12A4_ENST00000338335.3_Missense_Mutation_p.S104G|SLC12A4_ENST00000422611.2_Missense_Mutation_p.S106G|SLC12A4_ENST00000537830.2_Missense_Mutation_p.S98G	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	104					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCCTCCCCACTCTCGGCCTCC	0.627																																					p.S106G		Atlas-SNP	.											.	SLC12A4	81	.	0			c.A316G						.						68	67	68					16																	67995510		2198	4300	6498	SO:0001583	missense	6560	exon2			CCCCACTCTCGGC		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.310A>G	chr16.hg19:g.67995510T>C	ENSP00000318557:p.Ser104Gly	75.0	0.0		59.0	57.0	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	hg19	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	T	18.73	3.685424	0.68157	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	D;D;D;D;D	0.88741	-1.92;-1.91;-1.91;-2.42;-1.91	5.81	4.7	0.59300	.	0.137331	0.64402	D	0.000001	T	0.81856	0.4911	N	0.19112	0.55	0.58432	D	0.999993	B;B;B;B;B;B	0.25390	0.035;0.038;0.125;0.017;0.039;0.001	B;B;B;B;B;B	0.31946	0.062;0.044;0.138;0.039;0.039;0.002	T	0.75966	-0.3131	10	0.37606	T	0.19	.	10.9902	0.47545	0.1392:0.0:0.0:0.8608	.	106;104;73;98;104;104	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	G	106;73;98;104;104	ENSP00000395983:S106G;ENSP00000438334:S73G;ENSP00000445962:S98G;ENSP00000343374:S104G;ENSP00000318557:S104G	ENSP00000318557:S104G	S	-	1	0	SLC12A4	66553011	0.658000	0.27402	1.000000	0.80357	0.977000	0.68977	3.860000	0.55995	1.005000	0.39183	0.379000	0.24179	AGT	.	.		0.627	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		C	67995510	T	C	67995510	3	2	172	1	0	0	0	0	1	0	0	0	14400	1551	54	2	3035	2	SLC12A4	16	67995510	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	47544348	67995510	22359243	81	26092										
TP53	7157	hgsc.bcm.edu	37	chr17	7578500	7578500	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tgtggaatcaacccacagctGcacagggcaggtcttggcca	12	12	2	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr17:7578500G>A	ENST00000269305.4	-	5	619	c.430C>T	c.(430-432)Cag>Tag	p.Q144*	TP53_ENST00000359597.4_Nonsense_Mutation_p.Q144*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q144*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q144*|TP53_ENST00000445888.2_Nonsense_Mutation_p.Q144*|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q144*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	144	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Q -> H (in sporadic cancers; somatic mutation).|Q -> K (in sporadic cancers; somatic mutation).|Q -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q144*(36)|p.0?(8)|p.Q144fs*25(3)|p.Q144K(2)|p.Q12*(2)|p.Q144fs*26(2)|p.Q51*(2)|p.Q144_G154del11(1)|p.L137_W146del10(1)|p.Q51fs*25(1)|p.Q144del(1)|p.Q144fs*32(1)|p.Q144fs*16(1)|p.P142_Q144delPVQ(1)|p.Q144fs*4(1)|p.Q12fs*25(1)|p.V143_S149del(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACCCACAGCTGCACAGGGCAG	0.597		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Q144X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,bladder,carcinoma,0,3	TP53	33396	.	65	Substitution - Nonsense(40)|Deletion - Frameshift(10)|Whole gene deletion(8)|Deletion - In frame(5)|Substitution - Missense(2)	lung(11)|upper_aerodigestive_tract(10)|oesophagus(8)|breast(8)|endometrium(6)|ovary(5)|bone(4)|large_intestine(3)|stomach(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|soft_tissue(1)|liver(1)|skin(1)|prostate(1)	c.C430T						.						57	56	57					17																	7578500		2203	4300	6503	SO:0001587	stop_gained	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ACAGCTGCACAGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.430C>T	chr17.hg19:g.7578500G>A	ENSP00000269305:p.Gln144*	83.0	0.0		81.0	74.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.071217	0.55646	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	.	.	.	5.48	5.48	0.80851	.	0.121732	0.56097	D	0.000038	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-30.9139	17.2272	0.86973	0.0:0.0:1.0:0.0	.	.	.	.	X	144;144;144;144;144;144;133;51;12;51;12;144	.	ENSP00000269305:Q144X	Q	-	1	0	TP53	7519225	1.000000	0.71417	0.908000	0.35775	0.017000	0.09413	7.953000	0.87836	2.733000	0.93635	0.655000	0.94253	CAG	.	.		0.597	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578500	G	A	7578500	4	1	172	1	0	0	0	0	0	1	0	0	16396	1328	46	3	868	3	TP53	17	7578500	Nonsense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10		7578500	73616710	82	26093										
MYH1	4619	hgsc.bcm.edu	37	chr17	10408279	10408279	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	catctccttctctgtctctgCacttttgaggaggggtttga	10	10	3	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr17:10408279C>A	ENST00000226207.5	-	22	2633	c.2539G>T	c.(2539-2541)Gca>Tca	p.A847S	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	847					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TCTGTCTCTGCACTTTTGAGG	0.458																																					p.A847S		Atlas-SNP	.											.	MYH1	403	.	0			c.G2539T						.						136	127	130					17																	10408279		2203	4300	6503	SO:0001583	missense	4619	exon22			TCTCTGCACTTTT		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2539G>T	chr17.hg19:g.10408279C>A	ENSP00000226207:p.Ala847Ser	106.0	0.0		67.0	64.0	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.427227	0.83667	.	.	ENSG00000109061	ENST00000226207	D	0.82893	-1.66	5.48	5.48	0.80851	.	0.000000	0.42821	U	0.000642	D	0.86598	0.5971	M	0.75085	2.285	0.58432	D	0.999999	P	0.43973	0.823	P	0.46049	0.502	D	0.86322	0.1693	10	0.44086	T	0.13	.	19.7157	0.96119	0.0:1.0:0.0:0.0	.	847	P12882	MYH1_HUMAN	S	847	ENSP00000226207:A847S	ENSP00000226207:A847S	A	-	1	0	MYH1	10349004	1.000000	0.71417	1.000000	0.80357	0.698000	0.40448	7.692000	0.84203	2.749000	0.94314	0.655000	0.94253	GCA	.	.		0.458	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		A	10408279	C	A	10408279	3	1	172	1	0	0	0	0	1	0	0	0	10038	710	25	3	3356	3	MYH1	17	10408279	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	2829779	10408279	70786931	83	26094										
NOS2	4843	hgsc.bcm.edu	37	chr17	26089884	26089884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ctctgtgggcgtgtgatcccGggaggagctgatggagtaga	18	7	1	3			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr17:26089884G>A	ENST00000313735.6	-	22	2973	c.2740C>T	c.(2740-2742)Cgg>Tgg	p.R914W		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	914	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GTGTGATCCCGGGAGGAGCTG	0.642																																					p.R914W		Atlas-SNP	.											.	NOS2	113	.	0			c.C2740T						.						24	21	22					17																	26089884		2195	4294	6489	SO:0001583	missense	4843	exon22			GATCCCGGGAGGA	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"nitric oxide synthase 2A (inducible, hepatocytes)"	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2740C>T	chr17.hg19:g.26089884G>A	ENSP00000327251:p.Arg914Trp	67.0	0.0		90.0	7.0	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	hg19	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.449700	0.26074	.	.	ENSG00000007171	ENST00000313735;ENST00000379105	T	0.67171	-0.25	4.9	1.71	0.24356	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.860574	0.10294	N	0.691949	T	0.51075	0.1653	L	0.38838	1.175	0.25703	N	0.985562	B	0.11235	0.004	B	0.04013	0.001	T	0.46707	-0.9172	10	0.66056	D	0.02	.	1.8657	0.03198	0.1979:0.1233:0.4809:0.1978	.	914	P35228	NOS2_HUMAN	W	914;875	ENSP00000327251:R914W	ENSP00000327251:R914W	R	-	1	2	NOS2	23114011	0.985000	0.35326	0.367000	0.25926	0.287000	0.27160	2.186000	0.42593	0.072000	0.16694	-0.467000	0.05162	CGG	.	.		0.642	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		A	26089884	G	A	26089884	3	1	172	1	0	0	0	0	1	0	0	0	10552	1115	39	1	745	1	NOS2	17	26089884	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	15681605	26089884	55105326	84	26095										
MRM1	79154	hgsc.bcm.edu	37	chr17	34958498	34958498	+	IGR	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ggctgcaggggaagcgggccGagctgctccggatggccgag	20	11	0	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr17:34958498G>T	ENST00000251312.5	+	0	1598				MRM1_ENST00000585770.1_5'UTR|MRM1_ENST00000250156.7_Nonsense_Mutation_p.E87*	NM_024308.3	NP_077284.2	Q6UWP2	DHR11_HUMAN	dehydrogenase/reductase (SDR family) member 11							extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(4)	5						GAAGCGGGCCGAGCTGCTCCG	0.687																																					p.E87X		Atlas-SNP	.											.	MRM1	19	.	0			c.G259T						.						24	29	28					17																	34958498		2196	4284	6480	SO:0001628	intergenic_variant	79922	exon1			CGGGCCGAGCTGC		CCDS11315.2	17q12	2014-05-06			ENSG00000108272	ENSG00000278535		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	28639	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 24C, member 1"					12975309, 19027726	Standard	NM_024308		Approved	MGC4172, SDR24C1	uc002hnd.3	Q6UWP2	OTTHUMG00000188442		chr17.hg19:g.34958498G>T		52.0	0.0		66.0	38.0	NM_024864	B2RDZ3|Q9BUC7|Q9H674	Nonsense_Mutation	SNP	ENST00000251312.5	hg19	CCDS11315.2	.	.	.	.	.	.	.	.	.	.	G	36	5.676260	0.96764	.	.	ENSG00000129282	ENST00000250156	.	.	.	4.9	3.86	0.44501	.	0.248378	0.41194	D	0.000926	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-17.0011	12.0634	0.53574	0.0:0.1738:0.8262:0.0	.	.	.	.	X	87	.	ENSP00000250156:E87X	E	+	1	0	MRM1	32032611	0.999000	0.42202	1.000000	0.80357	0.314000	0.28054	3.234000	0.51320	2.423000	0.82170	0.555000	0.69702	GAG	.	.		0.687	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308		T	34958498	G	T	34958498	1	4	172	0	1	0	0	0	0	0	0	0	9780	1059	37	1		1	MRM1	17	34958498	IGR	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	8868614	34958498	46236712	85	26096										
MSI2	124540	hgsc.bcm.edu	37	chr17	55752442	55752442	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ggagtggggaattacataagTgcggccagcccacagccggg	16	10	0	0	rs376818853		TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr17:55752442T>C	ENST00000284073.2	+	12	1109	c.900T>C	c.(898-900)agT>agC	p.S300S	MSI2_ENST00000416426.2_Silent_p.S296S|MSI2_ENST00000442934.2_Silent_p.S239S	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	300						cytoplasm (GO:0005737)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	7	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		ATTACATAAGTGCGGCCAGCC	0.682			T	HOXA9	CML																																p.S300S		Atlas-SNP	.		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	.	MSI2	52	.	0			c.T900C						.	T		0,4406		0,0,2203	54	61	59		900	-6.2	1	17		59	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	MSI2	NM_138962.2		0,1,6501	CC,CT,TT		0.0116,0.0,0.0077		300/329	55752442	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	124540	exon12			CATAAGTGCGGCC	BC001526	CCDS11596.1, CCDS11597.1	17q23.2	2013-07-16	2012-12-13					"RNA binding motif (RRM) containing"	18585	protein-coding gene	gene with protein product		607897	"musashi homolog 2 (Drosophila)"			11588182	Standard	NM_138962		Approved		uc002iuz.1	Q96DH6		ENST00000284073.2:c.900T>C	chr17.hg19:g.55752442T>C		202.0	0.0		293.0	108.0	NM_138962	Q7Z6M7|Q8N9T4	Silent	SNP	ENST00000284073.2	hg19	CCDS11596.1																																																																																			.	.		0.682	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1			C	55752442	T	C	55752442	2	2	172	1	0	0	0	0	0	0	0	1	9885	1693	59	2		2	MSI2	17	55752442	Silent	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	20793944	55752442	25442768	86	26097										
C17orf71	55181	hgsc.bcm.edu	37	chr17	57290544	57290544	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tacaggtttggaccaacaggGctttattccaggaacaaatt	9	8	0	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr17:57290544G>A	ENST00000543872.2	+	4	2624	c.2360G>A	c.(2359-2361)gGc>gAc	p.G787D	SMG8_ENST00000300917.5_Missense_Mutation_p.G787D|CTD-2510F5.6_ENST00000577660.1_Intron			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	787					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						GACCAACAGGGCTTTATTCCA	0.438																																					p.G787D		Atlas-SNP	.											.	SMG8	79	.	0			c.G2360A						.						110	113	112					17																	57290544		2203	4300	6503	SO:0001583	missense	55181	exon3			AACAGGGCTTTAT	AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"chromosome 17 open reading frame 71", "smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.2360G>A	chr17.hg19:g.57290544G>A	ENSP00000438748:p.Gly787Asp	94.0	0.0		142.0	74.0	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	hg19	CCDS11615.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337042	0.81801	.	.	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.51574	0.7;0.7	6.07	6.07	0.98685	.	0.042937	0.85682	D	0.000000	T	0.69387	0.3105	M	0.75085	2.285	0.80722	D	1	D	0.64830	0.994	D	0.63703	0.917	T	0.70378	-0.4888	10	0.87932	D	0	-16.1888	19.6475	0.95784	0.0:0.0:1.0:0.0	.	787	Q8ND04	SMG8_HUMAN	D	787	ENSP00000300917:G787D;ENSP00000438748:G787D	ENSP00000300917:G787D	G	+	2	0	SMG8	54645326	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.885000	0.99019	0.655000	0.94253	GGC	.	.		0.438	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		A	57290544	G	A	57290544	3	1	172	1	0	0	0	0	1	0	0	0	1880	1203	42	3	2370	3	C17orf71	17	57290544	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	1538102	57290544	23904666	87	26098										
KIAA0195	9772	hgsc.bcm.edu	37	chr17	73487458	73487458	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gagactgtactgttcttcagCgggaaggtggagccccctca	13	11	3	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr17:73487458C>A	ENST00000314256.7	+	13	1702	c.1308C>A	c.(1306-1308)agC>agA	p.S436R	KIAA0195_ENST00000579208.1_Missense_Mutation_p.S87R|KIAA0195_ENST00000375248.5_Missense_Mutation_p.S446R	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	436						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGTTCTTCAGCGGGAAGGTGG	0.587																																					p.S436R		Atlas-SNP	.											.	KIAA0195	102	.	0			c.C1308A						.						103	90	94					17																	73487458		2203	4300	6503	SO:0001583	missense	9772	exon13			CTTCAGCGGGAAG		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.1308C>A	chr17.hg19:g.73487458C>A	ENSP00000313885:p.Ser436Arg	91.0	0.0		131.0	55.0	NM_014738	O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	hg19	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.966397	0.34659	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	T;T	0.42900	0.96;0.96	5.84	-9.99	0.00435	.	0.000000	0.85682	D	0.000000	T	0.44371	0.1290	N	0.25789	0.76	0.49299	D	0.99977	D;P;D	0.89917	0.999;0.882;1.0	D;P;D	0.85130	0.995;0.639;0.997	T	0.73411	-0.3991	10	0.31617	T	0.26	-12.4154	20.9608	0.99942	0.0:0.6813:0.0:0.3187	.	446;446;436	B4DGC6;C9JL75;Q12767	.;.;K0195_HUMAN	R	436;446	ENSP00000313885:S436R;ENSP00000364397:S446R	ENSP00000313885:S436R	S	+	3	2	KIAA0195	70999053	0.013000	0.17824	0.466000	0.27168	0.915000	0.54546	-0.941000	0.03925	-2.176000	0.00770	-0.948000	0.02665	AGC	.	.		0.587	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738		A	73487458	C	A	73487458	3	1	172	1	0	0	0	0	1	0	0	0	8169	767	27	1	1354	1	KIAA0195	17	73487458	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	16196914	73487458	7707752	88	26099										
KIAA0427	9811	hgsc.bcm.edu	37	chr18	46287893	46287893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ccttcatggaggaggcccagAactccaccaactccgaggag	11	14	1	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr18:46287893A>G	ENST00000256413.3	+	9	1499	c.1204A>G	c.(1204-1206)Aac>Gac	p.N402D	CTIF_ENST00000382998.4_Missense_Mutation_p.N404D	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	402	MIF4G.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						GGAGGCCCAGAACTCCACCAA	0.582																																					p.N404D		Atlas-SNP	.											.	CTIF	102	.	0			c.A1210G						.						165	97	120					18																	46287893		2203	4300	6503	SO:0001583	missense	9811	exon10			GCCCAGAACTCCA	AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"KIAA0427"	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.1204A>G	chr18.hg19:g.46287893A>G	ENSP00000256413:p.Asn402Asp	98.0	0.0		65.0	59.0	NM_001142397	B3KTR8|Q8IVD5	Missense_Mutation	SNP	ENST00000256413.3	hg19	CCDS11935.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.163539	0.78226	.	.	ENSG00000134030	ENST00000256413;ENST00000382998;ENST00000420275	T;T	0.21191	2.02;2.02	5.75	5.75	0.90469	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.138974	0.64402	D	0.000003	T	0.29288	0.0729	L	0.47716	1.5	0.47441	D	0.999426	P;P	0.50528	0.839;0.936	P;P	0.50082	0.497;0.63	T	0.01051	-1.1468	10	0.33141	T	0.24	-22.7557	15.7442	0.77926	1.0:0.0:0.0:0.0	.	404;402	O43310-2;O43310	.;CTIF_HUMAN	D	402;404;354	ENSP00000256413:N402D;ENSP00000372459:N404D	ENSP00000256413:N402D	N	+	1	0	CTIF	44541891	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.909000	0.56363	2.194000	0.70268	0.533000	0.62120	AAC	.	.		0.582	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772		G	46287893	A	G	46287893	3	3	172	1	0	0	0	0	1	0	0	0	8185	246	9	2	1240	2	KIAA0427	18	46287893	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10		46287893	31789355	89	26100										
SERPINB2	5055	hgsc.bcm.edu	37	chr18	61562581	61562581	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	agctgtgggttcatgcagcaGatccagaagggtagttatcc	13	8	1	2	rs149564761	byFrequency	TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr18:61562581G>A	ENST00000299502.4	+	3	332	c.252G>A	c.(250-252)caG>caA	p.Q84Q	SERPINB2_ENST00000457692.1_Silent_p.Q84Q|SERPINB2_ENST00000482254.1_3'UTR	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	84					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	TCATGCAGCAGATCCAGAAGG	0.428																																					p.Q84Q		Atlas-SNP	.											.	SERPINB2	63	.	0			c.G252A						.						191	186	188					18																	61562581		2203	4300	6503	SO:0001819	synonymous_variant	5055	exon3			GCAGCAGATCCAG	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"Serine (or cysteine) peptidase inhibitors"	8584	protein-coding gene	gene with protein product		173390	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.252G>A	chr18.hg19:g.61562581G>A		81.0	0.0		77.0	71.0	NM_002575	Q96E96	Silent	SNP	ENST00000299502.4	hg19	CCDS11989.1																																																																																			.	G|0.999;C|0.001		0.428	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575		A	61562581	G	A	61562581	2	1	172	1	0	0	0	0	0	0	0	1	14116	933	33	3		3	SERPINB2	18	61562581	Silent	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	15274688	61562581	16514667	90	26101										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23543926	23543926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	agtgtgtatcctcttatgtcTtcttagggttgaggaccata	10	7	3	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr19:23543926T>C	ENST00000300619.7	-	4	2060	c.1855A>G	c.(1855-1857)Aga>Gga	p.R619G	ZNF91_ENST00000397082.2_Missense_Mutation_p.R587G|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	619					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				CTCTTATGTCTTCTTAGGGTT	0.388																																					p.R619G		Atlas-SNP	.											.	ZNF91	349	.	0			c.A1855G						.						62	65	64					19																	23543926		2178	4284	6462	SO:0001583	missense	7644	exon4			TATGTCTTCTTAG	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1855A>G	chr19.hg19:g.23543926T>C	ENSP00000300619:p.Arg619Gly	104.0	0.0		128.0	59.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	T	2.108	-0.404500	0.04832	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.07216	3.21;3.21	1.78	-3.55	0.04639	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12944	0.0314	M	0.70903	2.155	0.09310	N	1	P;D	0.55172	0.721;0.97	B;P	0.56648	0.342;0.803	T	0.13150	-1.0520	9	0.22706	T	0.39	.	0.3269	0.00312	0.3421:0.1352:0.1724:0.3503	.	587;619	Q05481-2;Q05481	.;ZNF91_HUMAN	G	619;587	ENSP00000300619:R619G;ENSP00000380272:R587G	ENSP00000300619:R619G	R	-	1	2	ZNF91	23335766	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	-4.603000	0.00210	-0.769000	0.04620	0.260000	0.18958	AGA	.	.		0.388	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		C	23543926	T	C	23543926	3	2	172	1	0	0	0	0	1	0	0	0	18215	1617	56	2	1724	2	ZNF91	19	23543926	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10		23543926	35585057	91	26102										
ZNF569	148266	hgsc.bcm.edu	37	chr19	37904229	37904229	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	acatctgtataaaagctttcCcacattcattacactcataa	2	11	3	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr19:37904229C>T	ENST00000316950.6	-	6	1888	c.1331G>A	c.(1330-1332)gGg>gAg	p.G444E	ZNF569_ENST00000392150.2_Missense_Mutation_p.G285E|ZNF569_ENST00000392149.2_Missense_Mutation_p.G444E	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAAAGCTTTCCCACATTCATT	0.373																																					p.G444E		Atlas-SNP	.											.	ZNF569	101	.	0			c.G1331A						.						72	69	70					19																	37904229		2203	4300	6503	SO:0001583	missense	148266	exon6			GCTTTCCCACATT	AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.1331G>A	chr19.hg19:g.37904229C>T	ENSP00000325018:p.Gly444Glu	105.0	1.0		84.0	80.0	NM_152484	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	hg19	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	C	17.62	3.434040	0.62955	.	.	ENSG00000196437	ENST00000316950;ENST00000392149;ENST00000392150	T;T	0.01221	5.15;5.15	4.33	4.33	0.51752	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38492	N	0.001671	T	0.07098	0.0180	L	0.61387	1.9	0.50813	D	0.999896	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.17623	-1.0363	10	0.52906	T	0.07	.	16.0897	0.81084	0.0:1.0:0.0:0.0	.	285;444	Q17RR6;Q5MCW4	.;ZN569_HUMAN	E	444;100;285	ENSP00000325018:G444E;ENSP00000375993:G285E	ENSP00000325018:G444E	G	-	2	0	ZNF569	42596069	0.614000	0.27017	1.000000	0.80357	0.998000	0.95712	1.269000	0.33074	2.397000	0.81536	0.655000	0.94253	GGG	.	.		0.373	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		T	37904229	C	T	37904229	3	4	172	1	0	0	0	0	1	0	0	0	18015	623	22	3	733	3	ZNF569	19	37904229	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	14360303	37904229	21224754	92	26103										
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40580707	40580707	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ctttccagtatgaatacttcGatgttgattaagatttgaac	7	6	0	4	rs368327296		TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr19:40580707G>A	ENST00000595687.2	-	6	1851	c.1642C>T	c.(1642-1644)Cga>Tga	p.R548*	ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000455521.1_Nonsense_Mutation_p.R549*|ZNF780A_ENST00000450241.2_Nonsense_Mutation_p.R514*|ZNF780A_ENST00000594395.1_Nonsense_Mutation_p.R549*|ZNF780A_ENST00000340963.5_Nonsense_Mutation_p.R548*|AC005614.5_ENST00000595508.1_RNA	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	548					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TGAATACTTCGATGTTGATTA	0.378																																					p.R549X		Atlas-SNP	.											ZNF780A_ENST00000455521,colon,carcinoma,0,6	ZNF780A	156	.	0			c.C1645T						.	G	stop/ARG,stop/ARG,stop/ARG,	1,4405	2.1+/-5.4	0,1,2202	107	114	112		1642,1645,1642,	-1.3	0	19		112	0,8598		0,0,4299	no	stop-gained,stop-gained,stop-gained,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	,,,	548/642,549/643,548/642,	40580707	1,13003	2203	4299	6502	SO:0001587	stop_gained	284323	exon6			TACTTCGATGTTG	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"Zinc fingers, C2H2-type", "-"	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.1642C>T	chr19.hg19:g.40580707G>A	ENSP00000472189:p.Arg548*	117.0	0.0		601.0	489.0	NM_001142577	E9PB48|Q6ZN87	Nonsense_Mutation	SNP	ENST00000595687.2	hg19	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	g	38	6.890131	0.97912	2.27E-4	0.0	ENSG00000197782	ENST00000450241;ENST00000455521;ENST00000340963	.	.	.	1.93	-1.32	0.09201	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	.	6.9782	0.24688	0.0:0.0:0.5262:0.4738	.	.	.	.	X	548;549;548	.	ENSP00000341507:R548X	R	-	1	2	ZNF780A	45272547	0.000000	0.05858	0.010000	0.14722	0.974000	0.67602	-3.576000	0.00425	0.063000	0.16370	0.313000	0.20887	CGA	.	.		0.378	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		A	40580707	G	A	40580707	4	1	172	1	0	0	0	0	0	1	0	0	18167	1066	37	1	414	1	ZNF780A	19	40580707	Nonsense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	2676478	40580707	18548276	93	26104										
SIRPB1	10326	hgsc.bcm.edu	37	chr20	1551722	1551722	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	tagaaattgctcacctggcaGgtgacgtttgcctggttctc	11	10	2	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr20:1551722G>A	ENST00000381605.4	-	4	877	c.813C>T	c.(811-813)acC>acT	p.T271T	SIRPB1_ENST00000262929.5_Intron|SIRPB1_ENST00000381603.3_Intron|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	271	Ig-like C1-type 2.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						TCACCTGGCAGGTGACGTTTG	0.542																																					p.T271T		Atlas-SNP	.											.	SIRPB1	83	.	0			c.C813T						.						102	95	97					20																	1551722		2203	4300	6503	SO:0001819	synonymous_variant	10326	exon4			CTGGCAGGTGACG	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.813C>T	chr20.hg19:g.1551722G>A		120.0	0.0		263.0	83.0	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	hg19	CCDS13019.1																																																																																			.	.		0.542	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		A	1551722	G	A	1551722	2	1	172	1	0	0	0	0	0	0	0	1	14348	987	35	3		3	SIRPB1	20	1551722	Silent	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10		1551722	61473798	94	26105										
C20orf71	128861	hgsc.bcm.edu	37	chr20	31814800	31814800	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	actgttgaaaagcctcatagGtgagtgtctggtccatccag	11	9	2	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr20:31814800G>C	ENST00000375454.3	+	6	895		c.e6+1		BPIFA3_ENST00000490499.1_Splice_Site|BPIFA3_ENST00000375452.3_Splice_Site	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3							extracellular region (GO:0005576)	lipid binding (GO:0008289)										AGCCTCATAGGTGAGTGTCTG	0.577																																					.		Atlas-SNP	.											.	.	.	.	0			c.577+1G>C						.						112	109	110					20																	31814800		2203	4300	6503	SO:0001630	splice_region_variant	128861	exon5			TCATAGGTGAGTG		CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"BPI fold containing"	16204	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 71"	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.685+1G>C	chr20.hg19:g.31814800G>C		68.0	0.0		137.0	36.0	NM_001042439	Q5JWG8|Q6NZ38	Splice_Site	SNP	ENST00000375454.3	hg19	CCDS13216.2	.	.	.	.	.	.	.	.	.	.	G	13.49	2.251882	0.39797	.	.	ENSG00000131059	ENST00000375454;ENST00000375452	.	.	.	4.02	0.986	0.19784	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.5977	0.08012	0.2102:0.0:0.5941:0.1957	.	.	.	.	.	-1	.	.	.	+	.	.	BPIFA3	31278461	1.000000	0.71417	0.965000	0.40720	0.891000	0.51852	1.484000	0.35508	0.261000	0.21753	-0.448000	0.05591	.	.	.		0.577	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466	Intron	C	31814800	G	C	31814800	5	2	172	1	0	0	0	0	0	0	1	0	2119	1275	44	4	708	4	C20orf71	20	31814800	Splice_Site	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	30263078	31814800	31210720	95	26106										
PREX1	57580	hgsc.bcm.edu	37	chr20	47273593	47273593	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ctcactctttggccttcgtgGccaccaggaggcgcagaggg	14	13	2	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr20:47273593G>C	ENST00000371941.3	-	18	2130	c.2108C>G	c.(2107-2109)gCc>gGc	p.A703G	PREX1_ENST00000396220.1_Missense_Mutation_p.A703G	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	703	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GGCCTTCGTGGCCACCAGGAG	0.642																																					p.A703G		Atlas-SNP	.											.	PREX1	441	.	0			c.C2108G						.						54	43	47					20																	47273593		2203	4298	6501	SO:0001583	missense	57580	exon18			TTCGTGGCCACCA	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2108C>G	chr20.hg19:g.47273593G>C	ENSP00000361009:p.Ala703Gly	53.0	0.0		100.0	18.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.481397	0.63849	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.18016	2.24;2.24	5.12	5.12	0.69794	PDZ/DHR/GLGF (3);	0.000000	0.53938	U	0.000048	T	0.15349	0.0370	N	0.24115	0.695	0.58432	D	0.999999	B	0.12013	0.005	B	0.13407	0.009	T	0.04737	-1.0930	10	0.72032	D	0.01	.	18.5717	0.91137	0.0:0.0:1.0:0.0	.	703	Q8TCU6	PREX1_HUMAN	G	703	ENSP00000361009:A703G;ENSP00000379522:A703G	ENSP00000361009:A703G	A	-	2	0	PREX1	46707000	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.168000	0.71908	2.376000	0.81061	0.561000	0.74099	GCC	.	.		0.642	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		C	47273593	G	C	47273593	3	2	172	1	0	0	0	0	1	0	0	0	12488	1203	42	4	2963	4	PREX1	20	47273593	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	15458793	47273593	15751927	96	26107										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60907730	60907730	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cgtactccaccactagggcaTagcggcctggctgtggcact	12	14	0	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr20:60907730T>C	ENST00000252999.3	-	27	3392	c.3326A>G	c.(3325-3327)tAt>tGt	p.Y1109C	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1109	Domain IV 1 (domain IV B).				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CACTAGGGCATAGCGGCCTGG	0.701																																					p.Y1109C		Atlas-SNP	.											.	LAMA5	268	.	0			c.A3326G						.						25	28	27					20																	60907730		2197	4295	6492	SO:0001583	missense	3911	exon27			AGGGCATAGCGGC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.3326A>G	chr20.hg19:g.60907730T>C	ENSP00000252999:p.Tyr1109Cys	82.0	0.0		149.0	49.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.489108	0.44249	.	.	ENSG00000130702	ENST00000252999	T	0.35048	1.33	4.76	3.65	0.41850	.	0.000000	0.85682	U	0.000000	T	0.58366	0.2117	M	0.80332	2.49	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.63180	-0.6695	10	0.87932	D	0	.	9.701	0.40187	0.0:0.0836:0.0:0.9164	.	1109	O15230	LAMA5_HUMAN	C	1109	ENSP00000252999:Y1109C	ENSP00000252999:Y1109C	Y	-	2	0	LAMA5	60341125	1.000000	0.71417	0.251000	0.24312	0.038000	0.13279	4.900000	0.63252	1.765000	0.52091	0.240000	0.17902	TAT	.	.		0.701	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		C	60907730	T	C	60907730	3	2	172	1	0	0	0	0	1	0	0	0	8618	1406	49	2	7977	2	LAMA5	20	60907730	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	13634137	60907730	2117790	97	26108										
SIM2	6493	hgsc.bcm.edu	37	chr21	38098595	38098595	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gttcagggccagccttgaccTgaagctgatattcctggatt	11	10	1	3			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr21:38098595T>C	ENST00000290399.6	+	6	1332	c.719T>C	c.(718-720)cTg>cCg	p.L240P	SIM2_ENST00000430056.3_Missense_Mutation_p.L240P	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	240	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						AGCCTTGACCTGAAGCTGATA	0.577																																					p.L240P		Atlas-SNP	.											.	SIM2	55	.	0			c.T719C						.						74	53	60					21																	38098595		2203	4300	6503	SO:0001583	missense	6493	exon6			TTGACCTGAAGCT		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"Basic helix-loop-helix proteins"	10883	protein-coding gene	gene with protein product	"transcription factor SIM2"	600892	"single-minded (Drosophila) homolog 2", "single-minded homolog 2 (Drosophila)"	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.719T>C	chr21.hg19:g.38098595T>C	ENSP00000290399:p.Leu240Pro	46.0	0.0		62.0	24.0	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Missense_Mutation	SNP	ENST00000290399.6	hg19	CCDS13646.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.488329	0.84854	.	.	ENSG00000159263	ENST00000290399;ENST00000430056	T;T	0.17691	2.26;2.26	5.44	5.44	0.79542	PAS (2);	0.071377	0.56097	D	0.000037	T	0.39682	0.1087	M	0.90483	3.12	0.80722	D	1	P;P	0.49185	0.884;0.92	P;P	0.49561	0.465;0.615	T	0.52449	-0.8574	10	0.87932	D	0	.	15.804	0.78477	0.0:0.0:0.0:1.0	.	240;240	Q14190;Q14190-2	SIM2_HUMAN;.	P	240	ENSP00000290399:L240P;ENSP00000404176:L240P	ENSP00000290399:L240P	L	+	2	0	SIM2	37020465	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.505000	0.81655	2.193000	0.70182	0.533000	0.62120	CTG	.	.		0.577	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586		C	38098595	T	C	38098595	3	2	172	1	0	0	0	0	1	0	0	0	14339	1580	55	2	741	2	SIM2	21	38098595	Missense_Mutation	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10		38098595	10031300	98	26109										
PRDM15	63977	hgsc.bcm.edu	37	chr21	43299446	43299446	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cgatccgctccggaaactgcGcagcaccggaagccgggggg	16	14	0	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr21:43299446G>A	ENST00000269844.3	-	1	145	c.35C>T	c.(34-36)gCg>gTg	p.A12V	SNORA3_ENST00000515969.1_RNA|PRDM15_ENST00000398548.1_Missense_Mutation_p.A12V|PRDM15_ENST00000538201.1_5'UTR|AP001619.2_ENST00000432411.1_RNA|PRDM15_ENST00000422911.1_Missense_Mutation_p.A12V	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	12					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						CGGAAACTGCGCAGCACCGGA	0.761																																					p.A12V		Atlas-SNP	.											.	PRDM15	110	.	0			c.C35T						.						4	6	5					21																	43299446		1901	3904	5805	SO:0001583	missense	63977	exon1			AACTGCGCAGCAC	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.35C>T	chr21.hg19:g.43299446G>A	ENSP00000269844:p.Ala12Val	28.0	0.0		32.0	12.0	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	hg19	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	g	19.96	3.923243	0.73213	.	.	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000269844	T;T;T	0.10288	2.9;2.9;2.89	2.8	2.8	0.32819	.	.	.	.	.	T	0.14098	0.0341	N	0.08118	0	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.70716	0.97;0.97;0.97	T	0.28106	-1.0054	9	0.87932	D	0	.	12.5703	0.56332	0.0:0.0:1.0:0.0	.	12;12;12	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	V	12	ENSP00000408592:A12V;ENSP00000381556:A12V;ENSP00000269844:A12V	ENSP00000269844:A12V	A	-	2	0	PRDM15	42172515	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.651000	0.61447	1.582000	0.49881	0.446000	0.29264	GCG	.	.		0.761	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		A	43299446	G	A	43299446	3	1	172	1	0	0	0	0	1	0	0	0	12468	1087	38	1	4612	1	PRDM15	21	43299446	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	5200851	43299446	4830449	99	26110										
ATF4	468	hgsc.bcm.edu	37	chr22	39917506	39917506	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ggtgggggacttgatgtcccCcttcgaccagtcgggtttgg	16	10	0	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chr22:39917506C>T	ENST00000337304.2	+	1	938	c.56C>T	c.(55-57)cCc>cTc	p.P19L	ATF4_ENST00000404241.2_Missense_Mutation_p.P19L|ATF4_ENST00000396680.1_Missense_Mutation_p.P19L	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	19					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	TTGATGTCCCCCTTCGACCAG	0.537																																					p.P19L		Atlas-SNP	.											.	ATF4	27	.	0			c.C56T						.						66	65	66					22																	39917506		2203	4300	6503	SO:0001583	missense	468	exon1			TGTCCCCCTTCGA	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"basic leucine zipper proteins"	786	protein-coding gene	gene with protein product	"tax-responsive enhancer element B67"	604064	"activating transcription factor 4 (tax-responsive enhancer element B67)"	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.56C>T	chr22.hg19:g.39917506C>T	ENSP00000336790:p.Pro19Leu	157.0	0.0		158.0	84.0	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	hg19	CCDS13996.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201073	0.79015	.	.	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.59772	0.24;0.24;0.24	4.37	4.37	0.52481	.	0.000000	0.85682	D	0.000000	T	0.74816	0.3766	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.79460	-0.1794	10	0.87932	D	0	-10.014	16.9241	0.86170	0.0:1.0:0.0:0.0	.	19	P18848	ATF4_HUMAN	L	19	ENSP00000384587:P19L;ENSP00000336790:P19L;ENSP00000379912:P19L	ENSP00000336790:P19L	P	+	2	0	ATF4	38247452	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.037000	0.64170	1.983000	0.57843	0.561000	0.74099	CCC	.	.		0.537	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		T	39917506	C	T	39917506	3	4	172	1	0	0	0	0	1	0	0	0	1082	623	22	3	58	3	ATF4	22	39917506	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10		39917506	11387060	100	26111										
SLC25A6	293	hgsc.bcm.edu	37	chrX	1506264	1506264	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	cggccgtcacggtctgcgcgAtcatccagctcaccacgatg	11	16	4	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chrX:1506264A>G	ENST00000381401.5	-	3	1361	c.647T>C	c.(646-648)aTc>aCc	p.I216T	SLC25A6_ENST00000475167.1_5'UTR	NM_001636.3	NP_001627.2	P12236	ADT3_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6	216					active induction of host immune response by virus (GO:0046732)|ADP transport (GO:0015866)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|modulation by virus of host morphology or physiology (GO:0019048)|protein targeting to mitochondrion (GO:0006626)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP:ADP antiporter activity (GO:0005471)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(8)|upper_aerodigestive_tract(1)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Clodronate(DB00720)	GGTCTGCGCGATCATCCAGCT	0.682																																					p.I216T		Atlas-SNP	.											.	SLC25A6	27	.	0			c.T647C						.						115	99	104					X																	1506264		2203	4296	6499	SO:0001583	missense	293	exon3			TGCGCGATCATCC	AY007135	CCDS14114.1	Xp22.32 and Yp11.3	2013-05-22			ENSG00000169100	ENSG00000169100		"Pseudoautosomal regions / PAR1", "Solute carriers"	10992	protein-coding gene	gene with protein product		300151, 403000		ANT3			Standard	NM_001636		Approved	ANT3Y, MGC17525	uc004cpt.3	P12236	OTTHUMG00000021058	ENST00000381401.5:c.647T>C	chrX.hg19:g.1506264A>G	ENSP00000370808:p.Ile216Thr	105.0	0.0		167.0	8.0	NM_001636	Q96C49	Missense_Mutation	SNP	ENST00000381401.5	hg19	CCDS14114.1	.	.	.	.	.	.	.	.	.	.	.	16.39	3.109126	0.56398	.	.	ENSG00000169100	ENST00000381401	T	0.78595	-1.19	1.87	1.87	0.25490	Mitochondrial carrier domain (2);	0.000000	0.56097	U	0.000032	T	0.80544	0.4643	M	0.81614	2.55	0.09310	N	1	P	0.46912	0.886	P	0.48901	0.594	T	0.73170	-0.4067	10	0.87932	D	0	.	9.5023	0.39026	1.0:0.0:0.0:0.0	.	216	P12236	ADT3_HUMAN	T	216	ENSP00000370808:I216T	ENSP00000370808:I216T	I	-	2	0	SLC25A6	1466264	1.000000	0.71417	0.807000	0.32361	0.681000	0.39784	7.001000	0.76297	0.808000	0.34231	0.333000	0.21579	ATC	.	.		0.682	SLC25A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055596.1	NM_001636		G	1506264	A	G	1506264	3	3	172	1	0	0	0	0	1	0	0	0	14528	333	12	2	257	2	SLC25A6	23	1506264	Missense_Mutation	SNP	A	TCGA-DD-AACV-01A-11D-A40R-10		1506264	153764296	101	26112										
SHROOM2	357	hgsc.bcm.edu	37	chrX	9864618	9864618	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	aggaaacctctggaggccagGagctctgggcgctgccactc	14	13	2	0			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chrX:9864618G>T	ENST00000380913.3	+	4	2760	c.2670G>T	c.(2668-2670)agG>agT	p.R890S		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	890					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				TGGAGGCCAGGAGCTCTGGGC	0.627																																					p.R890S		Atlas-SNP	.											.	SHROOM2	139	.	0			c.G2670T						.						26	23	24					X																	9864618		2201	4300	6501	SO:0001583	missense	357	exon4			GGCCAGGAGCTCT	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"apical protein, Xenopus laevis-like", "apical protein-like (Xenopus laevis)"	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.2670G>T	chrX.hg19:g.9864618G>T	ENSP00000370299:p.Arg890Ser	119.0	1.0		136.0	125.0	NM_001649	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	hg19	CCDS14135.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.593372	0.46214	.	.	ENSG00000146950	ENST00000380913	T	0.18960	2.18	5.02	3.25	0.37280	.	0.223008	0.47093	D	0.000259	T	0.35885	0.0947	M	0.64404	1.975	0.18873	N	0.999988	D	0.89917	1.0	D	0.69307	0.963	T	0.14980	-1.0453	10	0.72032	D	0.01	-18.7123	5.1183	0.14847	0.251:0.1473:0.6018:0.0	.	890	Q13796	SHRM2_HUMAN	S	890	ENSP00000370299:R890S	ENSP00000370299:R890S	R	+	3	2	SHROOM2	9824618	0.991000	0.36638	0.005000	0.12908	0.486000	0.33341	2.222000	0.42926	0.377000	0.24735	0.600000	0.82982	AGG	.	.		0.627	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649		T	9864618	G	T	9864618	3	4	172	1	0	0	0	0	1	0	0	0	14309	1165	41	3	2684	3	SHROOM2	23	9864618	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	8358354	9864618	145405942	102	26113										
TLR8	51311	hgsc.bcm.edu	37	chrX	12938752	12938752	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	gaattttcagccattcctcaTgtcaaatatttggatttgac	6	8	3	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chrX:12938752T>C	ENST00000218032.6	+	2	1680	c.1593T>C	c.(1591-1593)caT>caC	p.H531H	TLR8_ENST00000311912.5_Silent_p.H549H	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	531					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CCATTCCTCATGTCAAATATT	0.353																																					p.H531H		Atlas-SNP	.											.	TLR8	134	.	0			c.T1593C						.						53	48	49					X																	12938752		2203	4300	6503	SO:0001819	synonymous_variant	51311	exon2			TCCTCATGTCAAA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1593T>C	chrX.hg19:g.12938752T>C		121.0	0.0		203.0	19.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	hg19	CCDS14152.1																																																																																			.	.		0.353	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		C	12938752	T	C	12938752	2	2	172	1	0	0	0	0	0	0	0	1	15972	1461	51	2		2	TLR8	23	12938752	Silent	SNP	T	TCGA-DD-AACV-01A-11D-A40R-10	3074134	12938752	142331808	103	26114										
CDKL5	6792	hgsc.bcm.edu	37	chrX	18602433	18602433	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	atgctaattacacagagtacGttgccaccagatggtatcgg	10	9	0	2			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chrX:18602433G>A	ENST00000379989.3	+	9	799	c.514G>A	c.(514-516)Gtt>Att	p.V172I	CDKL5_ENST00000379996.3_Missense_Mutation_p.V172I	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	172	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					CACAGAGTACGTTGCCACCAG	0.383																																					p.V172I		Atlas-SNP	.											.	CDKL5	124	.	0			c.G514A						.						162	137	145					X																	18602433		2203	4300	6503	SO:0001583	missense	6792	exon8			GAGTACGTTGCCA	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"Cyclin-dependent kinases"	11411	protein-coding gene	gene with protein product		300203	"serine/threonine kinase 9"	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.514G>A	chrX.hg19:g.18602433G>A	ENSP00000369325:p.Val172Ile	89.0	0.0		103.0	99.0	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	hg19	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	G	32	5.152620	0.94645	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.50548	0.74;0.74	5.74	5.74	0.90152	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.66376	0.2783	L	0.55990	1.75	0.58432	D	0.999999	D	0.76494	0.999	D	0.81914	0.995	T	0.67632	-0.5621	10	0.66056	D	0.02	-15.1468	18.8535	0.92241	0.0:0.0:1.0:0.0	.	172	O76039	CDKL5_HUMAN	I	172	ENSP00000369332:V172I;ENSP00000369325:V172I	ENSP00000369325:V172I	V	+	1	0	CDKL5	18512354	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	9.845000	0.99498	2.399000	0.81585	0.544000	0.68410	GTT	.	.		0.383	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159		A	18602433	G	A	18602433	3	1	172	1	0	0	0	0	1	0	0	0	3159	1145	40	1	540	1	CDKL5	23	18602433	Missense_Mutation	SNP	G	TCGA-DD-AACV-01A-11D-A40R-10	5663681	18602433	136668127	104	26115										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153135853	153135853	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0480769230769231	5	1	0.859758635039534	0.773782771535581	0.884323167469235	0.206349206349206	0.793487154311895	0	ccagactcacaagccctcggCgatgcactccaggaccaatg	9	16	1	1			TCGA-DD-AACV-01A-11D-A40R-10	TCGA-DD-AACV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcfe5003-d7c8-44d1-a477-87739185c5aa	6c521fa5-4471-4a49-9649-e0317e230699	g.chrX:153135853C>T	ENST00000370060.1	-	8	985	c.796G>A	c.(796-798)Gcc>Acc	p.A266T	L1CAM_ENST00000543994.1_Missense_Mutation_p.A268T|L1CAM_ENST00000361699.4_Missense_Mutation_p.A266T|L1CAM_ENST00000538883.1_Missense_Mutation_p.A268T|L1CAM_ENST00000361981.3_Missense_Mutation_p.A261T|L1CAM_ENST00000370057.3_Missense_Mutation_p.A266T|L1CAM_ENST00000370055.1_Missense_Mutation_p.A261T	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	266	Ig-like C2-type 3.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AAGCCCTCGGCGATGCACTCC	0.667																																					p.A266T		Atlas-SNP	.											.	L1CAM	189	.	0			c.G796A						.						51	49	50					X																	153135853		2203	4300	6503	SO:0001583	missense	3897	exon7			CCTCGGCGATGCA	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.796G>A	chrX.hg19:g.153135853C>T	ENSP00000359077:p.Ala266Thr	94.0	0.0		125.0	17.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	hg19	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.601892	0.87055	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699	T;T;T;T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32;-0.32;-0.32;-0.32	5.04	5.04	0.67666	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000047	D	0.83078	0.5176	M	0.84773	2.715	0.44330	D	0.997212	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.71870	0.957;0.971;0.975	D	0.86358	0.1715	10	0.72032	D	0.01	.	16.2554	0.82515	0.0:1.0:0.0:0.0	.	261;266;266	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	T	266;268;266;268;261;261;266	ENSP00000359077:A266T;ENSP00000438430:A268T;ENSP00000359074:A266T;ENSP00000439645:A268T;ENSP00000354712:A261T;ENSP00000359072:A261T;ENSP00000355380:A266T	ENSP00000355380:A266T	A	-	1	0	L1CAM	152789047	0.971000	0.33674	0.180000	0.23079	0.863000	0.49368	2.789000	0.47813	2.091000	0.63221	0.529000	0.55759	GCC	.	.		0.667	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		T	153135853	C	T	153135853	3	4	172	1	0	0	0	0	1	0	0	0	8597	768	27	1	3065	1	L1CAM	23	153135853	Missense_Mutation	SNP	C	TCGA-DD-AACV-01A-11D-A40R-10	134533420	153135853	2134707	105	26116										
TAS1R1	80835	hgsc.bcm.edu	37	chr1	6631122	6631122	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	tctgccaatgtgtatgccacGctgagagtgctctccctgcc	10	14	2	1	rs375985047		TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr1:6631122G>A	ENST00000333172.6	+	2	538	c.345G>A	c.(343-345)acG>acA	p.T115T	TAS1R1_ENST00000328191.4_Silent_p.T115T|TAS1R1_ENST00000351136.3_Silent_p.T115T	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	115					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		TGTATGCCACGCTGAGAGTGC	0.562																																					p.T115T		Atlas-SNP	.											.	TAS1R1	76	.	0			c.G345A						.	G	,	3,4403	6.2+/-15.9	0,3,2200	189	167	174		345,345	-10	0	1		174	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TAS1R1	NM_138697.3,NM_177540.2	,	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	,	115/842,115/588	6631122	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	80835	exon2			TGCCACGCTGAGA		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14448	protein-coding gene	gene with protein product		606225	"G protein-coupled receptor 70"	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.345G>A	chr1.hg19:g.6631122G>A		111.0	0.0		56.0	41.0	NM_177540	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Silent	SNP	ENST00000333172.6	hg19	CCDS81.1	.	.	.	.	.	.	.	.	.	.	G	4.906	0.168440	0.09339	6.81E-4	0.0	ENSG00000173662	ENST00000411823;ENST00000415267	.	.	.	5.08	-10.0	0.00425	.	.	.	.	.	T	0.21550	0.0519	.	.	.	0.31514	N	0.663209	.	.	.	.	.	.	T	0.14392	-1.0474	4	.	.	.	.	3.7175	0.08444	0.3702:0.3424:0.2037:0.0836	.	.	.	.	H	41	.	.	R	+	2	0	TAS1R1	6553709	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-5.044000	0.00157	-1.700000	0.01414	-0.827000	0.03088	CGC	.	.		0.562	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			A	6631122	G	A	6631122	2	1	173	1	0	0	0	0	0	0	0	1	15577	1074	38	1		1	TAS1R1	1	6631122	Silent	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10		6631122	242619499	1	26117										
NFYC	4802	hgsc.bcm.edu	37	chr1	41215315	41215315	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	tatcacagagttgactcttcGagcctggattcacacagaag	9	10	3	3			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr1:41215315G>C	ENST00000308733.5	+	3	254	c.248G>C	c.(247-249)cGa>cCa	p.R83P	NFYC_ENST00000440226.3_Missense_Mutation_p.R83P|NFYC_ENST00000372652.1_Missense_Mutation_p.R83P|NFYC_ENST00000447388.3_Missense_Mutation_p.R83P|NFYC_ENST00000456393.2_Missense_Mutation_p.R83P|NFYC_ENST00000372653.1_Missense_Mutation_p.R83P|NFYC_ENST00000427410.2_Intron|NFYC_ENST00000372651.1_Missense_Mutation_p.R83P|NFYC_ENST00000425457.2_Missense_Mutation_p.R83P|NFYC_ENST00000372654.1_Missense_Mutation_p.R83P			Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma	83					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription, DNA-templated (GO:0045893)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(1)|prostate(1)|skin(2)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)			TTGACTCTTCGAGCCTGGATT	0.478																																					p.R83P		Atlas-SNP	.											.	NFYC	39	.	0			c.G248C						.						92	92	92					1																	41215315		2203	4300	6503	SO:0001583	missense	4802	exon4			CTCTTCGAGCCTG	U78774	CCDS455.1, CCDS44120.1, CCDS44121.1, CCDS44122.1, CCDS44123.1	1p32	2008-11-11			ENSG00000066136	ENSG00000066136			7806	protein-coding gene	gene with protein product		605344				8921405, 9249075	Standard	NM_014223		Approved	CBF-C, NF-YC	uc009vwd.3	Q13952	OTTHUMG00000007729	ENST00000308733.5:c.248G>C	chr1.hg19:g.41215315G>C	ENSP00000312617:p.Arg83Pro	85.0	0.0		77.0	52.0	NM_001142587	B4DUS6|B4DW63|D3DPV9|F8VWM3|Q59GY4|Q5T6K8|Q5T6K9|Q5T6L1|Q5TZR6|Q92869|Q9HBX1|Q9NXB5|Q9UM67|Q9UML0|Q9UMT7	Missense_Mutation	SNP	ENST00000308733.5	hg19		.	.	.	.	.	.	.	.	.	.	G	18.40	3.616119	0.66672	.	.	ENSG00000066136	ENST00000447388;ENST00000425457;ENST00000453631;ENST00000456393;ENST00000372654;ENST00000372653;ENST00000372669;ENST00000372652;ENST00000372651;ENST00000440226;ENST00000525290;ENST00000530965;ENST00000416859;ENST00000308733	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9	5.85	4.93	0.64822	Histone-fold (2);Transcription factor CBF/NF-Y/archaeal histone (1);	0.000000	0.85682	D	0.000000	T	0.65059	0.2655	H	0.98238	4.18	0.80722	D	1	B;B;B;B;B;P	0.45634	0.064;0.005;0.021;0.004;0.004;0.863	B;B;B;B;B;B	0.43701	0.04;0.004;0.016;0.002;0.002;0.428	T	0.79412	-0.1814	10	0.87932	D	0	.	14.7411	0.69455	0.0:0.1457:0.8543:0.0	.	83;83;83;83;83;83	Q13952;Q5T6K9;Q13952-3;F8VWM3;Q13952-2;B4DUS6	NFYC_HUMAN;.;.;.;.;.	P	83;83;83;83;83;83;83;83;83;83;83;59;83;83	ENSP00000404427:R83P;ENSP00000396620:R83P;ENSP00000397647:R83P;ENSP00000408867:R83P;ENSP00000361738:R83P;ENSP00000361737:R83P;ENSP00000361754:R83P;ENSP00000361736:R83P;ENSP00000361734:R83P;ENSP00000414299:R83P;ENSP00000436710:R83P;ENSP00000433413:R59P;ENSP00000409219:R83P;ENSP00000312617:R83P	ENSP00000312617:R83P	R	+	2	0	NFYC	40987902	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.402000	0.97298	1.465000	0.48006	-0.175000	0.13238	CGA	.	.		0.478	NFYC-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000020802.1	NM_014223		C	41215315	G	C	41215315	3	2	173	1	0	0	0	0	1	0	0	0	10400	1058	37	4	258	4	NFYC	1	41215315	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	34584193	41215315	208035306	2	26118										
ZNF648	127665	hgsc.bcm.edu	37	chr1	182025619	182025619	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	gcaatgcggaaggccctgccGcactcggcacagaggaatcc	13	14	0	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr1:182025619G>A	ENST00000339948.3	-	2	1734	c.1527C>T	c.(1525-1527)tgC>tgT	p.C509C		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	509					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						AGGCCCTGCCGCACTCGGCAC	0.622																																					p.C509C	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											.	ZNF648	111	.	0			c.C1527T						.						96	80	85					1																	182025619		2203	4300	6503	SO:0001819	synonymous_variant	127665	exon2			CCTGCCGCACTCG	AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"Zinc fingers, C2H2-type"	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.1527C>T	chr1.hg19:g.182025619G>A		118.0	0.0		214.0	127.0	NM_001009992	B2RP16	Silent	SNP	ENST00000339948.3	hg19	CCDS30952.1																																																																																			.	.		0.622	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		A	182025619	G	A	182025619	2	1	173	1	0	0	0	0	0	0	0	1	18078	1079	38	1		1	ZNF648	1	182025619	Silent	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	140810304	182025619	67225002	3	26119										
UCHL5	51377	hgsc.bcm.edu	37	chr1	192992059	192992059	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	catttttaaaaacataccttGtatctttttaatttctgtac	2	7	2	0			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr1:192992059G>T	ENST00000367455.4	-	9	1078	c.843C>A	c.(841-843)taC>taA	p.Y281*	UCHL5_ENST00000367449.1_Nonsense_Mutation_p.Y280*|UCHL5_ENST00000367451.4_Nonsense_Mutation_p.Y307*|UCHL5_ENST00000367454.1_Nonsense_Mutation_p.Y280*|UCHL5_ENST00000367448.1_Nonsense_Mutation_p.Y280*|UCHL5_ENST00000367452.4_Nonsense_Mutation_p.Y156*|UCHL5_ENST00000530098.2_Nonsense_Mutation_p.Y157*	NM_001199261.1|NM_015984.3	NP_001186190.1|NP_057068.1	Q9Y5K5	UCHL5_HUMAN	ubiquitin carboxyl-terminal hydrolase L5	281					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|forebrain morphogenesis (GO:0048853)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein deubiquitination (GO:0016579)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	endopeptidase inhibitor activity (GO:0004866)|omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|proteasome binding (GO:0070628)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(1)|lung(9)|ovary(1)	19						AACATACCTTGTATCTTTTTA	0.308																																					p.Y281X		Atlas-SNP	.											.	UCHL5	41	.	0			c.C843A						.						96	102	100					1																	192992059		2203	4299	6502	SO:0001587	stop_gained	51377	exon9			TACCTTGTATCTT		CCDS1378.1, CCDS55668.1, CCDS55669.1, CCDS55670.1	1q32	2011-07-06			ENSG00000116750	ENSG00000116750		"INO80 complex subunits"	19678	protein-coding gene	gene with protein product	"INO80 complex subunit R"	610667				10810093, 16027725	Standard	NM_015984		Approved	UCH37, CGI-70, INO80R	uc001gsm.3	Q9Y5K5	OTTHUMG00000035561	ENST00000367455.4:c.843C>A	chr1.hg19:g.192992059G>T	ENSP00000356425:p.Tyr281*	84.0	0.0		141.0	8.0	NM_015984	Q5LJA6|Q5LJA7|Q8TBS4|Q96BJ9|Q9H1W5|Q9P0I3|Q9UQN2	Nonsense_Mutation	SNP	ENST00000367455.4	hg19	CCDS1378.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	19.84|19.84|19.84	3.901743|3.901743|3.901743	0.72754|0.72754|0.72754	.|.|.	.|.|.	ENSG00000116750|ENSG00000116750|ENSG00000116750	ENST00000449480;ENST00000443327;ENST00000416915|ENST00000420791|ENST00000367455;ENST00000367454;ENST00000367450;ENST00000367451;ENST00000367448;ENST00000367449;ENST00000367452;ENST00000530098;ENST00000391991	.|.|.	.|.|.	.|.|.	5.59|5.59|5.59	-1.04|-1.04|-1.04	0.10068|0.10068|0.10068	.|.|.	.|.|0.000000	.|.|0.85682	.|.|D	.|.|0.000000	T|T|.	0.35098|0.35098|.	0.0920|0.0920|.	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|.	0.41538|0.41538|.	-0.9503|-0.9503|.	3|3|.	.|.|0.07482	.|.|T	.|.|0.82	-26.5188|-26.5188|-26.5188	13.362|13.362|13.362	0.60661|0.60661|0.60661	0.343:0.0:0.657:0.0|0.343:0.0:0.657:0.0|0.343:0.0:0.657:0.0	.|.|.	.|.|.	.|.|.	.|.|.	K|K|X	69;137;63|172|281;280;320;307;280;280;156;157;271	.|.|.	.|.|ENSP00000356418:Y280X	Q|T|Y	-|-|-	1|2|3	0|0|2	UCHL5|UCHL5|UCHL5	191258682|191258682|191258682	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.884000|0.884000|0.884000	0.51177|0.51177|0.51177	0.588000|0.588000|0.588000	0.23924|0.23924|0.23924	-0.090000|-0.090000|-0.090000	0.12462|0.12462|0.12462	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	CAA|ACA|TAC	.	.		0.308	UCHL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086318.3	NM_015984		T	192992059	G	T	192992059	4	4	173	1	0	0	0	0	0	1	0	0	16937	1372	48	3	158	3	UCHL5	1	192992059	Nonsense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	10966440	192992059	56258562	4	26120										
PTCD3	55037	hgsc.bcm.edu	37	chr2	86362000	86362000	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	gactgtgctgctgatatcaaAtctgcgtatgaaagccaacc	9	10	2	2			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr2:86362000A>C	ENST00000254630.7	+	21	1734	c.1668A>C	c.(1666-1668)aaA>aaC	p.K556N	SNORD94_ENST00000386037.1_RNA	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	556					mitochondrial translation (GO:0032543)|regulation of translation (GO:0006417)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						CTGATATCAAATCTGCGTATG	0.468																																					p.K556N		Atlas-SNP	.											.	PTCD3	51	.	0			c.A1668C						.						137	144	142					2																	86362000		2203	4300	6503	SO:0001583	missense	55037	exon21			TATCAAATCTGCG		CCDS33235.1	2p11.2	2014-02-12	2012-02-24		ENSG00000132300	ENSG00000132300			24717	protein-coding gene	gene with protein product		614918				8889548	Standard	NM_017952		Approved	FLJ20758, DKFZp666K071	uc002sqw.2	Q96EY7	OTTHUMG00000153168	ENST00000254630.7:c.1668A>C	chr2.hg19:g.86362000A>C	ENSP00000254630:p.Lys556Asn	212.0	0.0		267.0	108.0	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Missense_Mutation	SNP	ENST00000254630.7	hg19	CCDS33235.1	.	.	.	.	.	.	.	.	.	.	A	14.10	2.435297	0.43224	.	.	ENSG00000132300	ENST00000254630	T	0.33865	1.39	5.71	-3.79	0.04320	.	0.088162	0.85682	D	0.000000	T	0.50480	0.1618	M	0.72576	2.205	0.34460	D	0.701648	D;D	0.76494	0.999;0.999	D;D	0.71656	0.973;0.974	T	0.58842	-0.7565	10	0.27785	T	0.31	-19.6377	14.1648	0.65469	0.4333:0.0:0.5667:0.0	.	147;556	Q96EY7-2;Q96EY7	.;PTCD3_HUMAN	N	556	ENSP00000254630:K556N	ENSP00000254630:K556N	K	+	3	2	PTCD3	86215511	0.986000	0.35501	0.383000	0.26132	0.202000	0.24057	0.600000	0.24104	-0.668000	0.05296	-0.250000	0.11733	AAA	.	.		0.468	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952		C	86362000	A	C	86362000	3	2	173	1	0	0	0	0	1	0	0	0	12741	98	4	5	1750	5	PTCD3	2	86362000	Missense_Mutation	SNP	A	TCGA-DD-AACW-01A-11D-A40R-10		86362000	156837373	5	26121										
TTN	7273	hgsc.bcm.edu	37	chr2	179647562	179647562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ccagatagcaggatgtgctgAcggttccagcctcatttaca	10	11	1	2			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr2:179647562A>G	ENST00000591111.1	-	18	3295	c.3071T>C	c.(3070-3072)gTc>gCc	p.V1024A	TTN_ENST00000359218.5_Missense_Mutation_p.V978A|TTN_ENST00000460472.2_Missense_Mutation_p.V978A|TTN_ENST00000342992.6_Missense_Mutation_p.V1024A|TTN_ENST00000342175.6_Missense_Mutation_p.V978A|TTN_ENST00000589042.1_Missense_Mutation_p.V1024A|TTN_ENST00000360870.5_Missense_Mutation_p.V1024A|RP11-88L24.4_ENST00000582038.2_RNA			Q8WZ42	TITIN_HUMAN	titin	32577	Ig-like 3.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGATGTGCTGACGGTTCCAGC	0.493																																					p.V1024A		Atlas-SNP	.											.	TTN	18412	.	0			c.T3071C						.						86	71	76					2																	179647562		2203	4300	6503	SO:0001583	missense	7273	exon18			GTGCTGACGGTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.3071T>C	chr2.hg19:g.179647562A>G	ENSP00000465570:p.Val1024Ala	105.0	0.0		150.0	58.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.58	2.875864	0.51695	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	6.17	6.17	0.99709	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60064	0.2240	N	0.03930	-0.32	0.34740	D	0.730685	D;D;D;D;D	0.69078	0.978;0.978;0.978;0.978;0.997	P;P;P;P;D	0.66084	0.829;0.829;0.829;0.829;0.941	T	0.75872	-0.3164	9	0.87932	D	0	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	978;978;978;1024;1024	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	A	1024;978;978;978;978;1024	ENSP00000343764:V1024A;ENSP00000434586:V978A;ENSP00000340554:V978A;ENSP00000352154:V978A;ENSP00000354117:V1024A	ENSP00000340554:V978A	V	-	2	0	TTN	179355807	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	9.307000	0.96226	2.371000	0.80710	0.533000	0.62120	GTC	.	.		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179647562	A	G	179647562	3	3	173	1	0	0	0	0	1	0	0	0	16750	275	10	2	108297	2	TTN	2	179647562	Missense_Mutation	SNP	A	TCGA-DD-AACW-01A-11D-A40R-10	93285562	179647562	63551811	6	26122										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230655847	230655847	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	tctaccatcttaccgtgccaTaactcatcatgcttttttgc	4	13	4	0			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr2:230655847T>C	ENST00000283943.5	-	29	4489	c.4311A>G	c.(4309-4311)ttA>ttG	p.L1437L	TRIP12_ENST00000389045.3_Silent_p.L1167L|TRIP12_ENST00000389044.4_Silent_p.L1485L	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1437					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TACCGTGCCATAACTCATCAT	0.378																																					p.L1437L		Atlas-SNP	.											.	TRIP12	207	.	0			c.A4311G						.						194	180	185					2																	230655847		2203	4300	6503	SO:0001819	synonymous_variant	9320	exon29			GTGCCATAACTCA	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.4311A>G	chr2.hg19:g.230655847T>C		97.0	0.0		132.0	57.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.		0.378	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		C	230655847	T	C	230655847	2	2	173	1	0	0	0	0	0	0	0	1	16571	1403	49	2		2	TRIP12	2	230655847	Silent	SNP	T	TCGA-DD-AACW-01A-11D-A40R-10	51008285	230655847	12543526	7	26123										
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022658	32022658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	cgccgccgtctgtgccctggActgccctctccatggtccgt	11	18	2	0			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr3:32022658A>G	ENST00000396556.2	-	1	136	c.14T>C	c.(13-15)gTc>gCc	p.V5A	OSBPL10_ENST00000438237.2_Missense_Mutation_p.V5A|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	5					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		TGTGCCCTGGACTGCCCTCTC	0.771																																					p.V5A		Atlas-SNP	.											.	OSBPL10	160	.	0			c.T14C						.						2	3	2					3																	32022658		967	1954	2921	SO:0001583	missense	114884	exon1			CCCTGGACTGCCC	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.14T>C	chr3.hg19:g.32022658A>G	ENSP00000379804:p.Val5Ala	30.0	0.0		44.0	13.0	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	hg19	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	G	8.089	0.774075	0.16051	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.22539	1.95;2.23	3.68	3.68	0.42216	.	0.394326	0.15996	N	0.234551	T	0.08758	0.0217	N	0.08118	0	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34825	-0.9813	10	0.02654	T	1	.	9.4284	0.38595	0.1093:0.0:0.8907:0.0	.	5;5	B4E212;Q9BXB5	.;OSB10_HUMAN	A	5	ENSP00000379804:V5A;ENSP00000406124:V5A	ENSP00000379804:V5A	V	-	2	0	OSBPL10	31997662	0.985000	0.35326	1.000000	0.80357	0.255000	0.26057	1.534000	0.36051	0.920000	0.36970	-0.711000	0.03637	GTC	.	.		0.771	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			G	32022658	A	G	32022658	3	3	173	1	0	0	0	0	1	0	0	0	11284	275	10	2	2328	2	OSBPL10	3	32022658	Missense_Mutation	SNP	A	TCGA-DD-AACW-01A-11D-A40R-10		32022658	165999772	8	26124										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48630101	48630101	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	gtggccggagaccccgcagcCgcacactggtctcaccagct	12	17	1	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr3:48630101C>A	ENST00000328333.8	-	7	985	c.878G>T	c.(877-879)cGg>cTg	p.R293L	COL7A1_ENST00000454817.1_Missense_Mutation_p.R293L	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	293	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region (NC1).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACCCCGCAGCCGCACACTGGT	0.617																																					p.R293L		Atlas-SNP	.											.	COL7A1	320	.	0			c.G878T						.						62	61	61					3																	48630101		2203	4300	6503	SO:0001583	missense	1294	exon7			CGCAGCCGCACAC	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.878G>T	chr3.hg19:g.48630101C>A	ENSP00000332371:p.Arg293Leu	45.0	0.0		42.0	24.0	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	hg19	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	6.375	0.437386	0.12104	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	T;T	0.56611	0.45;0.45	4.5	-0.437	0.12272	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.489800	0.04529	N	0.385986	T	0.27489	0.0675	N	0.03608	-0.345	0.09310	N	0.999999	B	0.18461	0.028	B	0.17433	0.018	T	0.16129	-1.0413	10	0.39692	T	0.17	.	3.8677	0.09024	0.2905:0.3712:0.0:0.3383	.	293	Q02388	CO7A1_HUMAN	L	293	ENSP00000332371:R293L;ENSP00000412569:R293L	ENSP00000332371:R293L	R	-	2	0	COL7A1	48605105	0.004000	0.15560	0.077000	0.20336	0.462000	0.32619	0.013000	0.13310	-0.007000	0.14345	0.462000	0.41574	CGG	.	.		0.617	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48630101	C	A	48630101	3	1	173	1	0	0	0	0	1	0	0	0	3706	652	23	1	8404	1	COL7A1	3	48630101	Missense_Mutation	SNP	C	TCGA-DD-AACW-01A-11D-A40R-10	16607443	48630101	149392329	9	26125										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130284086	130284086	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	agaacctttctccccgaactGggaaggcctatactggagct	10	12	1	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr3:130284086G>T	ENST00000358511.6	+	3	941	c.910G>T	c.(910-912)Ggg>Tgg	p.G304W	COL6A6_ENST00000453409.2_Missense_Mutation_p.G304W	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	304	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TCCCCGAACTGGGAAGGCCTA	0.478																																					p.G304W		Atlas-SNP	.											.	COL6A6	497	.	0			c.G910T						.						70	72	71					3																	130284086		1857	4099	5956	SO:0001583	missense	131873	exon3			CGAACTGGGAAGG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.910G>T	chr3.hg19:g.130284086G>T	ENSP00000351310:p.Gly304Trp	152.0	0.0		187.0	69.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.085166	0.36758	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.84944	-1.92;-1.92	5.01	4.14	0.48551	von Willebrand factor, type A (3);	0.195557	0.36374	N	0.002628	D	0.94258	0.8156	H	0.95712	3.71	0.49582	D	0.999808	D	0.89917	1.0	D	0.91635	0.999	D	0.95405	0.8493	10	0.87932	D	0	.	13.3765	0.60741	0.0775:0.0:0.9225:0.0	.	304	A6NMZ7	CO6A6_HUMAN	W	304	ENSP00000351310:G304W;ENSP00000399236:G304W	ENSP00000351310:G304W	G	+	1	0	COL6A6	131766776	1.000000	0.71417	0.189000	0.23252	0.005000	0.04900	7.150000	0.77403	1.250000	0.43966	-0.258000	0.10820	GGG	.	.		0.478	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130284086	G	T	130284086	3	4	173	1	0	0	0	0	1	0	0	0	3705	1348	47	3	920	3	COL6A6	3	130284086	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	81653985	130284086	67738344	10	26126										
FNDC3B	64778	hgsc.bcm.edu	37	chr3	172052790	172052790	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	agcgaagttcttgtttgtacGacgagtcctgacaggcctgg	13	9	1	1	rs139505585	byFrequency	TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr3:172052790G>T	ENST00000336824.4	+	15	1797	c.1698G>T	c.(1696-1698)acG>acT	p.T566T	FNDC3B_ENST00000415807.2_Silent_p.T566T|FNDC3B_ENST00000416957.1_Silent_p.T566T	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	566	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		TTGTTTGTACGACGAGTCCTG	0.463																																					p.T566T		Atlas-SNP	.											.	FNDC3B	118	.	0			c.G1698T						.						213	204	207					3																	172052790		2203	4300	6503	SO:0001819	synonymous_variant	64778	exon15			TTGTACGACGAGT	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.1698G>T	chr3.hg19:g.172052790G>T		136.0	0.0		238.0	66.0	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	hg19	CCDS3217.1																																																																																			.	G|0.998;A|0.002		0.463	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		T	172052790	G	T	172052790	2	4	173	1	0	0	0	0	0	0	0	1	5978	1045	37	1		1	FNDC3B	3	172052790	Silent	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	41768704	172052790	25969640	11	26127										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173996654	173996654	+	Frame_Shift_Del	DEL	T	T	-													0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	tgttgattttcccataggacTttttcaacgagcaatagctc							TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr3:173996654delT	ENST00000457714.1	+	6	1292	c.863delT	c.(862-864)cttfs	p.L288fs	NLGN1_ENST00000361589.4_Frame_Shift_Del_p.L288fs|NLGN1_ENST00000401917.3_Frame_Shift_Del_p.L328fs|NLGN1_ENST00000466350.1_3'UTR|NLGN1_ENST00000545397.1_Frame_Shift_Del_p.L288fs	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	305					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			CCCATAGGACTTTTTCAACGA	0.363																																					p.L288fs		Atlas-INDEL	.											.	NLGN1	209	.	0			c.862delC						.						43	45	44					3																	173996654		2200	4299	6499	SO:0001589	frameshift_variant	22871	exon6			.	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.863delT	chr3.hg19:g.173996654delT	ENSP00000392500:p.Leu288fs	40.0	0.0		54.0	17.0	NM_014932	Q9UPT2	Frame_Shift_Del	DEL	ENST00000457714.1	hg19	CCDS3222.1																																																																																			.	.		0.363	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		-	173996654	T	-	173996654	7	5	173	1	0	1	0	1	0	0	0	0	10470	1609	56	0	877	0	NLGN1	3	173996654	Frame_Shift_Del	DEL	T	TCGA-DD-AACW-01A-11D-A40R-10	1943864	173996654	24025776	12	26128										
ZNF639	51193	hgsc.bcm.edu	37	chr3	179047483	179047483	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	gttacagtgtctgttctatgAgacagccagatttaaaatat	8	6	2	2			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr3:179047483A>T	ENST00000326361.3	+	5	581	c.136A>T	c.(136-138)Aga>Tga	p.R46*	ZNF639_ENST00000484866.1_Nonsense_Mutation_p.R46*|ZNF639_ENST00000496856.1_Nonsense_Mutation_p.R46*|ZNF639_ENST00000466663.1_3'UTR	NM_016331.1	NP_057415.1	Q9UID6	ZN639_HUMAN	zinc finger protein 639	46					negative regulation by host of viral transcription (GO:0043922)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|transcription, DNA-templated (GO:0006351)|viral entry into host cell (GO:0046718)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein self-association (GO:0043621)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(10)|urinary_tract(1)	16	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			CTGTTCTATGAGACAGCCAGA	0.279																																					p.R46X		Atlas-SNP	.											.	ZNF639	45	.	0			c.A136T						.						100	106	104					3																	179047483		2203	4289	6492	SO:0001587	stop_gained	51193	exon5			TCTATGAGACAGC	BC020500	CCDS3227.1	3q27.1	2010-03-26			ENSG00000121864	ENSG00000121864		"Zinc fingers, C2H2-type"	30950	protein-coding gene	gene with protein product	"zinc finger amplified in esophageal squamous cell carcinomas 1"					14522885	Standard	NM_016331		Approved	ANC-2H01, ZASC1	uc003fjr.1	Q9UID6	OTTHUMG00000157439	ENST00000326361.3:c.136A>T	chr3.hg19:g.179047483A>T	ENSP00000325634:p.Arg46*	305.0	0.0		537.0	148.0	NM_016331	A9X3Z9|D3DNR3	Nonsense_Mutation	SNP	ENST00000326361.3	hg19	CCDS3227.1	.	.	.	.	.	.	.	.	.	.	A	41	8.666350	0.98908	.	.	ENSG00000121864	ENST00000496856;ENST00000491818;ENST00000481587;ENST00000326361;ENST00000466264;ENST00000484866;ENST00000494234	.	.	.	6.13	4.91	0.64330	.	0.171784	0.40728	N	0.001030	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.6953	0.28592	0.7896:0.1414:0.069:0.0	.	.	.	.	X	46	.	ENSP00000325634:R46X	R	+	1	2	ZNF639	180530177	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.222000	0.51223	2.364000	0.80123	0.524000	0.50904	AGA	.	.		0.279	ZNF639-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348855.1	NM_016331		T	179047483	A	T	179047483	4	4	173	1	0	0	0	0	0	1	0	0	18071	296	11	4	142	4	ZNF639	3	179047483	Nonsense_Mutation	SNP	A	TCGA-DD-AACW-01A-11D-A40R-10	5050829	179047483	18974947	13	26129										
ADIPOQ	9370	hgsc.bcm.edu	37	chr3	186570987	186570987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ggcgggcatcccagggcatcCgggccataatggggccccag	16	14	0	0	rs372597136		TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr3:186570987C>T	ENST00000412955.2	+	2	281	c.140C>T	c.(139-141)cCg>cTg	p.P47L	ADIPOQ_ENST00000320741.2_Missense_Mutation_p.P47L|ADIPOQ_ENST00000444204.2_Missense_Mutation_p.P47L|ADIPOQ-AS1_ENST00000422718.1_RNA			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	47	Collagen-like.				adiponectin-activated signaling pathway (GO:0033211)|brown fat cell differentiation (GO:0050873)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to insulin stimulus (GO:0032869)|circadian rhythm (GO:0007623)|detection of oxidative stress (GO:0070994)|fatty acid beta-oxidation (GO:0006635)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|low-density lipoprotein particle clearance (GO:0034383)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of hormone secretion (GO:0046888)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular protein transport (GO:0090317)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metanephric mesenchymal cell migration (GO:2000590)|negative regulation of phagocytosis (GO:0050765)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of receptor binding (GO:1900121)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of synaptic transmission (GO:0050805)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|positive regulation of blood pressure (GO:0045777)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of metanephric glomerular visceral epithelial cell development (GO:2000478)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myeloid cell apoptotic process (GO:0033034)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal albumin absorption (GO:2000534)|positive regulation of signal transduction (GO:0009967)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|regulation of glucose metabolic process (GO:0010906)|response to activity (GO:0014823)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to linoleic acid (GO:0070543)|response to nutrient (GO:0007584)|response to sucrose (GO:0009744)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|sialic acid binding (GO:0033691)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(2)	16	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)		CCAGGGCATCCGGGCCATAAT	0.617													C|||	1	0.000199681	0	0	5008	,	,		17067	0		0	False		,,,				2504	0.001				p.P47L		Atlas-SNP	.											.	ADIPOQ	35	.	0			c.C140T						.	C	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	38	41	40		140,140	5.2	1	3		40	0,8600		0,0,4300	no	missense,missense	ADIPOQ	NM_001177800.1,NM_004797.3	98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	47/245,47/245	186570987	1,13005	2203	4300	6503	SO:0001583	missense	9370	exon3			GGCATCCGGGCCA	D45371	CCDS3284.1	3q27	2013-02-26	2005-01-24	2005-01-27	ENSG00000181092	ENSG00000181092		"Endogenous ligands"	13633	protein-coding gene	gene with protein product	"adipose most abundant gene transcript 1", "adiponectin precursor"	605441	"adipocyte, C1Q and collagen domain containing"	ACDC		7592907, 8631877	Standard	NM_001177800		Approved	ACRP30, AdipoQ, apM1, GBP28, adiponectin	uc003fra.3	Q15848	OTTHUMG00000156521	ENST00000412955.2:c.140C>T	chr3.hg19:g.186570987C>T	ENSP00000405611:p.Pro47Leu	320.0	0.0		598.0	176.0	NM_001177800	Q58EX9	Missense_Mutation	SNP	ENST00000412955.2	hg19	CCDS3284.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.616746	0.87359	2.27E-4	0.0	ENSG00000181092	ENST00000412955;ENST00000320741;ENST00000444204	D;D;D	0.98684	-5.07;-5.07;-5.07	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.99227	0.9731	M	0.88310	2.945	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99250	1.0887	10	0.72032	D	0.01	.	16.6188	0.84924	0.0:1.0:0.0:0.0	.	47	Q15848	ADIPO_HUMAN	L	47	ENSP00000405611:P47L;ENSP00000320709:P47L;ENSP00000389814:P47L	ENSP00000320709:P47L	P	+	2	0	ADIPOQ	188053681	0.950000	0.32346	1.000000	0.80357	0.873000	0.50193	2.609000	0.46317	2.616000	0.88540	0.655000	0.94253	CCG	.	.		0.617	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344490.2	NM_004797		T	186570987	C	T	186570987	3	4	173	1	0	0	0	0	1	0	0	0	317	652	23	1	142	1	ADIPOQ	3	186570987	Missense_Mutation	SNP	C	TCGA-DD-AACW-01A-11D-A40R-10	7523504	186570987	11451443	14	26130										
FRYL	285527	hgsc.bcm.edu	37	chr4	48581248	48581248	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ctatcgagctagggcaatagAgcaaagtagtctatatggag	12	6	1	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr4:48581248A>T	ENST00000503238.1	-	20	2269	c.2270T>A	c.(2269-2271)cTc>cAc	p.L757H	FRYL_ENST00000537810.1_Missense_Mutation_p.L757H|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000507711.1_Missense_Mutation_p.L757H|FRYL_ENST00000358350.4_Missense_Mutation_p.L757H			O94915	FRYL_HUMAN	FRY-like	757					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						AGGGCAATAGAGCAAAGTAGT	0.318																																					p.L757H		Atlas-SNP	.											.	FRYL	242	.	0			c.T2270A						.						72	65	68					4																	48581248		1834	4078	5912	SO:0001583	missense	285527	exon23			CAATAGAGCAAAG	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.2270T>A	chr4.hg19:g.48581248A>T	ENSP00000426064:p.Leu757His	99.0	0.0		101.0	48.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.518817	0.64634	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711	T;T;T;T	0.06294	3.32;3.32;3.32;3.32	6.17	6.17	0.99709	.	0.000000	0.56097	U	0.000021	T	0.17831	0.0428	L	0.41492	1.28	0.80722	D	1	D;P	0.76494	0.999;0.836	D;B	0.77557	0.99;0.376	T	0.02059	-1.1221	10	0.30078	T	0.28	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	757;757	F2Z2S2;O94915	.;FRYL_HUMAN	H	757	ENSP00000426064:L757H;ENSP00000351113:L757H;ENSP00000441114:L757H;ENSP00000421584:L757H	ENSP00000351113:L757H	L	-	2	0	FRYL	48276005	1.000000	0.71417	0.999000	0.59377	0.449000	0.32228	8.962000	0.93254	2.371000	0.80710	0.533000	0.62120	CTC	.	.		0.318	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48581248	A	T	48581248	3	4	173	1	0	0	0	0	1	0	0	0	6072	304	11	4	6939	4	FRYL	4	48581248	Missense_Mutation	SNP	A	TCGA-DD-AACW-01A-11D-A40R-10		48581248	142573028	15	26131										
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67590433	67590433	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	aaatatttgaagaacagtgcCagacccaagagcggtacagc	10	9	0	4			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr5:67590433C>T	ENST00000521381.1	+	12	2111	c.1495C>T	c.(1495-1497)Cag>Tag	p.Q499*	PIK3R1_ENST00000274335.5_Nonsense_Mutation_p.Q499*|PIK3R1_ENST00000396611.1_Nonsense_Mutation_p.Q499*|PIK3R1_ENST00000521657.1_Nonsense_Mutation_p.Q499*|PIK3R1_ENST00000523872.1_Nonsense_Mutation_p.Q136*|PIK3R1_ENST00000336483.5_Nonsense_Mutation_p.Q229*|PIK3R1_ENST00000320694.8_Nonsense_Mutation_p.Q199*	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	499					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AGAACAGTGCCAGACCCAAGA	0.338			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.Q499X		Atlas-SNP	.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1	869	.	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	c.C1495T						.						72	72	72					5																	67590433		2203	4300	6503	SO:0001587	stop_gained	5295	exon12			CAGTGCCAGACCC	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1495C>T	chr5.hg19:g.67590433C>T	ENSP00000428056:p.Gln499*	126.0	0.0		143.0	57.0	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Nonsense_Mutation	SNP	ENST00000521381.1	hg19	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	C	37	6.058175	0.97246	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000521409;ENST00000336483;ENST00000519025;ENST00000523872	.	.	.	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-24.6309	19.2559	0.93945	0.0:1.0:0.0:0.0	.	.	.	.	X	499;499;499;499;199;136;229;172;136	.	ENSP00000274335:Q499X	Q	+	1	0	PIK3R1	67626189	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.609000	0.82925	2.861000	0.98227	0.650000	0.86243	CAG	.	.		0.338	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		T	67590433	C	T	67590433	4	4	173	1	0	0	0	0	0	1	0	0	11927	595	21	3	1667	3	PIK3R1	5	67590433	Nonsense_Mutation	SNP	C	TCGA-DD-AACW-01A-11D-A40R-10		67590433	113324827	16	26132										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130778197	130778197	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ctggagacatttcagatgatTtggctgatcttttctcactt	8	8	3	4			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr5:130778197T>G	ENST00000509018.1	-	23	3660	c.3455A>C	c.(3454-3456)aAa>aCa	p.K1152T	RAPGEF6_ENST00000296859.6_Missense_Mutation_p.K1160T|RAPGEF6_ENST00000512052.1_Missense_Mutation_p.K875T|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.K1165T|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.K1202T|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.K1152T|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.K1160T	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1152					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TTCAGATGATTTGGCTGATCT	0.443																																					p.K1165T	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.A3494C						.						167	155	159					5																	130778197		2203	4300	6503	SO:0001583	missense	51735	exon25			GATGATTTGGCTG	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3455A>C	chr5.hg19:g.130778197T>G	ENSP00000421684:p.Lys1152Thr	97.0	0.0		117.0	47.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.852456	0.71719	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000512052;ENST00000308008;ENST00000514667	T;T;T;T;T;T;T	0.30714	1.74;1.65;1.65;1.73;1.53;1.52;1.83	5.94	4.75	0.60458	Ras guanine nucleotide exchange factor, domain (1);	0.043748	0.85682	D	0.000000	T	0.48241	0.1489	M	0.66939	2.045	0.80722	D	1	P;B;D;B;D;P;B	0.60160	0.929;0.262;0.987;0.034;0.971;0.891;0.262	P;B;P;B;P;P;B	0.59825	0.645;0.11;0.864;0.038;0.752;0.812;0.158	T	0.47573	-0.9107	10	0.56958	D	0.05	.	12.2595	0.54642	0.0:0.0669:0.0:0.9331	.	1160;1160;1152;875;1202;1165;1152	A3KN82;B7ZML2;Q8TEU7-2;D6RE77;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;.;.;RPGF6_HUMAN	T	1152;1165;1160;1160;1165;875;1152;1202	ENSP00000421684:K1152T;ENSP00000309298:K1165T;ENSP00000426081:K1160T;ENSP00000296859:K1160T;ENSP00000426910:K875T;ENSP00000311419:K1152T;ENSP00000426948:K1202T	ENSP00000426948:K1202T	K	-	2	0	RAPGEF6;FNIP1	130806096	1.000000	0.71417	1.000000	0.80357	0.675000	0.39556	5.345000	0.65987	1.028000	0.39785	0.460000	0.39030	AAA	.	.		0.443	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		G	130778197	T	G	130778197	3	3	173	1	0	0	0	0	1	0	0	0	13063	1841	64	5	1809	5	RAPGEF6	5	130778197	Missense_Mutation	SNP	T	TCGA-DD-AACW-01A-11D-A40R-10	63187764	130778197	50137063	17	26133										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160047635	160047644	+	Frame_Shift_Del	DEL	CTGGCCAGGT	CTGGCCAGGT	-													0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	cctcgtaacagaactcaggcCtggccaggtctgtggctggg					rs535143119		TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	CTGGCCAGGT	CTGGCCAGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr5:160047635_160047644delCTGGCCAGGT	ENST00000327245.5	-	15	2972_2981	c.2126_2135delACCTGGCCAG	c.(2125-2136)gacctggccaggfs	p.DLAR709fs	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	709					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R712G(1)|p.A711A(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAACTCAGGCCTGGCCAGGTCTGTGGCTGG	0.629																																					p.709_712del		Atlas-INDEL	.											.	ATP10B	201	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|ovary(1)	c.2127_2136del						.																																			SO:0001589	frameshift_variant	23120	exon15			.	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.2126_2135delACCTGGCCAG	chr5.hg19:g.160047635_160047644delCTGGCCAGGT	ENSP00000313600:p.Asp709fs	63.0	0.0		97.0	39.0	NM_025153	Q9H725	Frame_Shift_Del	DEL	ENST00000327245.5	hg19	CCDS43394.1																																																																																			.	.		0.629	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		-	160047644	CTGGCCAGGT	-	160047635	7	5	173	1	0	1	0	1	0	0	0	0	1117	681	24	0	2298	0	ATP10B	5	160047635	Frame_Shift_Del	DEL	CTGGCCAGGT	TCGA-DD-AACW-01A-11D-A40R-10	29269438	160047635	20867625	18	26134										
PHACTR2	9749	hgsc.bcm.edu	37	chr6	144095324	144095324	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	aagaagagaggcaggaaatcCgacaacaaattggaaccaag	11	7	0	2			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr6:144095324C>T	ENST00000427704.2	+	8	1658	c.1528C>T	c.(1528-1530)Cga>Tga	p.R510*	PHACTR2_ENST00000440869.2_Nonsense_Mutation_p.R521*|PHACTR2_ENST00000367582.3_Nonsense_Mutation_p.R441*|PHACTR2_ENST00000367584.4_Nonsense_Mutation_p.R498*|PHACTR2_ENST00000305766.6_Nonsense_Mutation_p.R430*	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	510							protein phosphatase inhibitor activity (GO:0004864)			NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		GCAGGAAATCCGACAACAAAT	0.398																																					p.R521X	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)	Atlas-SNP	.											.	PHACTR2	99	.	0			c.C1561T						.						115	109	111					6																	144095324		1924	4136	6060	SO:0001587	stop_gained	9749	exon8			GAAATCCGACAAC	AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"Phosphatase and actin regulators"	20956	protein-coding gene	gene with protein product		608724	"chromosome 6 open reading frame 56"	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.1528C>T	chr6.hg19:g.144095324C>T	ENSP00000391763:p.Arg510*	149.0	0.0		103.0	84.0	NM_001100164	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Nonsense_Mutation	SNP	ENST00000427704.2	hg19	CCDS47492.1	.	.	.	.	.	.	.	.	.	.	C	42	9.255489	0.99115	.	.	ENSG00000112419	ENST00000367584;ENST00000427704;ENST00000305766;ENST00000440869;ENST00000367582	.	.	.	6.17	4.27	0.50696	.	0.112278	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.7605	0.28948	0.4225:0.5016:0.0:0.0759	.	.	.	.	X	498;510;430;521;441	.	ENSP00000305530:R430X	R	+	1	2	PHACTR2	144137017	0.908000	0.30866	1.000000	0.80357	0.992000	0.81027	1.032000	0.30178	1.575000	0.49775	0.655000	0.94253	CGA	.	.		0.398	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721		T	144095324	C	T	144095324	4	4	173	1	0	0	0	0	0	1	0	0	11819	644	23	1	1608	1	PHACTR2	6	144095324	Nonsense_Mutation	SNP	C	TCGA-DD-AACW-01A-11D-A40R-10		144095324	27019743	19	26135										
LPA	4018	hgsc.bcm.edu	37	chr6	160966486	160966486	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	acttaccacagagagggataTcacagtagtcaaaaagtttt	8	7	2	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr6:160966486T>C	ENST00000316300.5	-	33	5428	c.5384A>G	c.(5383-5385)gAt>gGt	p.D1795G	LPA_ENST00000447678.1_Missense_Mutation_p.D1795G			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4303	Kringle 16. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GAGAGGGATATCACAGTAGTC	0.388																																					p.D1795G		Atlas-SNP	.											LPA,NS,carcinoma,0,2	LPA	237	.	0			c.A5384G						.						102	110	107					6																	160966486		2203	4300	6503	SO:0001583	missense	4018	exon34			GGGATATCACAGT	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.5384A>G	chr6.hg19:g.160966486T>C	ENSP00000321334:p.Asp1795Gly	47.0	0.0		48.0	39.0	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	hg19	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	t	1.788	-0.480251	0.04383	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.65178	-0.14;-0.14	2.7	2.7	0.31948	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.52435	0.1734	L	0.52759	1.655	0.28141	N	0.929788	D	0.71674	0.998	D	0.71184	0.972	T	0.37934	-0.9684	9	0.11485	T	0.65	.	8.5172	0.33253	0.0:0.0:0.0:1.0	.	4303	P08519	APOA_HUMAN	G	1795	ENSP00000321334:D1795G;ENSP00000395608:D1795G	ENSP00000321334:D1795G	D	-	2	0	LPA	160886476	1.000000	0.71417	0.992000	0.48379	0.044000	0.14063	4.212000	0.58514	1.253000	0.44018	0.155000	0.16302	GAT	.	.		0.388	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		C	160966486	T	C	160966486	3	2	173	1	0	0	0	0	1	0	0	0	8912	1435	50	2	766	2	LPA	6	160966486	Missense_Mutation	SNP	T	TCGA-DD-AACW-01A-11D-A40R-10	16871162	160966486	10148581	20	26136										
HOXA11	3207	hgsc.bcm.edu	37	chr7	27224475	27224475	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	aggcacgccggccgcgctggGcgcctgcaggcagtctctgt	16	15	1	0	rs577175554	byFrequency	TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr7:27224475G>C	ENST00000006015.3	-	1	360	c.289C>G	c.(289-291)Ccc>Gcc	p.P97A	HOXA11-AS_ENST00000522863.1_RNA|HOXA11-AS_ENST00000520360.1_RNA|HOXA11-AS_ENST00000522674.1_RNA|RP1-170O19.14_ENST00000523331.1_lincRNA|HOXA11-AS_ENST00000520395.1_RNA|HOXA11-AS_ENST00000479766.1_RNA	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	97					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal joint morphogenesis (GO:0060272)|male gonad development (GO:0008584)|mesodermal cell fate specification (GO:0007501)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)	nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	16						GCCGCGCTGGGCGCCTGCAGG	0.662			T	NUP98	CML																																p.P97A		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.C289G						.						32	38	36					7																	27224475		2202	4299	6501	SO:0001583	missense	3207	exon1			CGCTGGGCGCCTG		CCDS5411.1	7p15.2	2014-09-17	2005-12-22		ENSG00000005073	ENSG00000005073		"Homeoboxes / ANTP class : HOXL subclass"	5101	protein-coding gene	gene with protein product		142958	"homeo box A11"	HOX1I, HOX1		1973146, 1358459	Standard	NM_005523		Approved		uc003syx.3	P31270	OTTHUMG00000023437	ENST00000006015.3:c.289C>G	chr7.hg19:g.27224475G>C	ENSP00000006015:p.Pro97Ala	41.0	0.0		56.0	8.0	NM_005523	A4D190	Missense_Mutation	SNP	ENST00000006015.3	hg19	CCDS5411.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.864827	0.32977	.	.	ENSG00000005073	ENST00000006015	T	0.39592	1.07	5.49	2.32	0.28847	Domain of unknown function DUF3528, homeobox protein, eukaryotic (1);	0.324752	0.32836	N	0.005595	T	0.21468	0.0517	N	0.17838	0.53	0.36129	D	0.845991	B	0.06786	0.001	B	0.08055	0.003	T	0.10543	-1.0625	10	0.32370	T	0.25	.	3.0466	0.06155	0.2858:0.0:0.4128:0.3014	.	97	P31270	HXA11_HUMAN	A	97	ENSP00000006015:P97A	ENSP00000006015:P97A	P	-	1	0	HOXA11	27191000	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.473000	0.35387	1.313000	0.45069	0.650000	0.86243	CCC	.	.		0.662	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1			C	27224475	G	C	27224475	3	2	173	1	0	0	0	0	1	0	0	0	7299	1203	42	4	660	4	HOXA11	7	27224475	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10		27224475	131914188	21	26137										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107706863	107706863	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	tccacaattgaagcatgaccCtgtctcaggatcacaaagtt	7	11	2	2			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr7:107706863C>A	ENST00000388781.3	-	20	2712	c.2629G>T	c.(2629-2631)Ggg>Tgg	p.G877W	LAMB4_ENST00000205386.4_Missense_Mutation_p.G877W|LAMB4_ENST00000388780.3_Missense_Mutation_p.G877W	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	877	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						AAGCATGACCCTGTCTCAGGA	0.463																																					p.G877W		Atlas-SNP	.											.	LAMB4	253	.	0			c.G2629T						.						69	64	66					7																	107706863		2203	4300	6503	SO:0001583	missense	22798	exon20			ATGACCCTGTCTC	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2629G>T	chr7.hg19:g.107706863C>A	ENSP00000373433:p.Gly877Trp	136.0	0.0		200.0	88.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	hg19	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	C	18.88	3.716510	0.68844	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780	T;T;T	0.67523	-0.27;-0.27;-0.27	4.92	4.92	0.64577	EGF-like, laminin (3);	0.000000	0.51477	D	0.000085	D	0.89001	0.6591	H	0.97874	4.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93114	0.6519	10	0.87932	D	0	.	18.299	0.90157	0.0:1.0:0.0:0.0	.	877	A4D0S4	LAMB4_HUMAN	W	877	ENSP00000205386:G877W;ENSP00000373433:G877W;ENSP00000373432:G877W	ENSP00000205386:G877W	G	-	1	0	LAMB4	107494099	1.000000	0.71417	0.992000	0.48379	0.581000	0.36288	7.092000	0.76930	2.556000	0.86216	0.563000	0.77884	GGG	.	.		0.463	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		A	107706863	C	A	107706863	3	1	173	1	0	0	0	0	1	0	0	0	8622	681	24	3	2716	3	LAMB4	7	107706863	Missense_Mutation	SNP	C	TCGA-DD-AACW-01A-11D-A40R-10	80482388	107706863	51431800	22	26138										
PDLIM2	64236	hgsc.bcm.edu	37	chr8	22451394	22451394	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	atgcccgccagcgctactccGcacctgccaccctcagctct	7	21	2	0	rs200868327	byFrequency	TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr8:22451394G>T	ENST00000397760.4	+	10	1430	c.1030G>T	c.(1030-1032)Gca>Tca	p.A344S	PDLIM2_ENST00000409417.1_Missense_Mutation_p.A344S|PDLIM2_ENST00000308354.7_Missense_Mutation_p.A594S|PDLIM2_ENST00000397761.2_Missense_Mutation_p.A344S|PDLIM2_ENST00000339162.7_3'UTR|PDLIM2_ENST00000265810.4_Intron|AC037459.4_ENST00000430850.2_Intron|PDLIM2_ENST00000409141.1_3'UTR|PDLIM2_ENST00000448520.1_3'UTR			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)	344	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		GCGCTACTCCGCACCTGCCAC	0.637																																					p.A594S		Atlas-SNP	.											PDLIM2_ENST00000308354,NS,carcinoma,0,1	PDLIM2	42	.	0			c.G1780T						.						28	20	23					8																	22451394		2153	4225	6378	SO:0001583	missense	64236	exon10			TACTCCGCACCTG	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270	ENST00000397760.4:c.1030G>T	chr8.hg19:g.22451394G>T	ENSP00000380867:p.Ala344Ser	40.0	1.0		60.0	27.0	NM_021630	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	hg19		.	.	.	.	.	.	.	.	.	.	G	8.015	0.758446	0.15846	.	.	ENSG00000120913	ENST00000308354;ENST00000397760;ENST00000397761;ENST00000409417	T;T;T;T	0.12984	3.51;2.63;2.63;2.63	4.71	-0.668	0.11392	Zinc finger, LIM-type (1);	0.985121	0.08185	N	0.984841	T	0.05914	0.0154	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.38908	-0.9639	10	0.66056	D	0.02	.	1.1387	0.01761	0.3392:0.1358:0.3724:0.1526	.	344	Q96JY6	PDLI2_HUMAN	S	594;344;344;344	ENSP00000312634:A594S;ENSP00000380867:A344S;ENSP00000380868:A344S;ENSP00000387084:A344S	ENSP00000312634:A594S	A	+	1	0	PDLIM2	22507339	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	0.242000	0.18087	-0.533000	0.06323	0.478000	0.44815	GCA	.	.		0.637	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1			T	22451394	G	T	22451394	3	4	173	1	0	0	0	0	1	0	0	0	11689	1087	38	1	1064	1	PDLIM2	8	22451394	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10		22451394	123912628	23	26139										
PTDSS1	9791	hgsc.bcm.edu	37	chr8	97332514	97332514	+	Frame_Shift_Del	DEL	G	G	-													0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ccattgtttgcataaaatttGgacaagatctcttctctaag							TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr8:97332514delG	ENST00000517309.1	+	10	1440	c.1114delG	c.(1114-1116)ggafs	p.G372fs	PTDSS1_ENST00000455950.2_Frame_Shift_Del_p.G226fs|PTDSS1_ENST00000522072.1_Frame_Shift_Del_p.G169fs	NM_014754.1	NP_055569.1	P48651	PTSS1_HUMAN	phosphatidylserine synthase 1	372					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|stomach(1)	29	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)	CATAAAATTTGGACAAGATCT	0.388																																					p.F371fs		Atlas-INDEL	.											.	PTDSS1	70	.	0			c.1113delT						.						260	243	249					8																	97332514		2203	4300	6503	SO:0001589	frameshift_variant	9791	exon10			.	D14694	CCDS6271.1	8q22	2008-05-02			ENSG00000156471	ENSG00000156471			9587	protein-coding gene	gene with protein product		612792					Standard	NM_014754		Approved	KIAA0024, PSSA, PSS1	uc003yht.1	P48651	OTTHUMG00000164687	ENST00000517309.1:c.1114delG	chr8.hg19:g.97332514delG	ENSP00000430548:p.Gly372fs	144.0	0.0		163.0	67.0	NM_014754	E5RFC5|Q9BUQ5	Frame_Shift_Del	DEL	ENST00000517309.1	hg19	CCDS6271.1																																																																																			.	.		0.388	PTDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379743.2			-	97332514	G	-	97332514	7	5	173	1	0	1	0	1	0	0	0	0	12748	1349	47	0	1152	0	PTDSS1	8	97332514	Frame_Shift_Del	DEL	G	TCGA-DD-AACW-01A-11D-A40R-10	74881120	97332514	49031508	24	26140										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2101571	2101571	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ctatctctctcttttaaaggAatcctttgctgaacacctag	5	11	2	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr9:2101571A>C	ENST00000382203.1	+	22	3289	c.3080A>C	c.(3079-3081)gAa>gCa	p.E1027A	SMARCA2_ENST00000357248.2_Splice_Site_p.E1027A|SMARCA2_ENST00000349721.2_Splice_Site_p.E1027A|SMARCA2_ENST00000382194.1_Splice_Site_p.E1027A			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	1027					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		CTTTTAAAGGAATCCTTTGCT	0.274																																					p.E1027A		Atlas-SNP	.											.	SMARCA2	313	.	0			c.A3080C						.						40	45	43					9																	2101571		2200	4294	6494	SO:0001630	splice_region_variant	6595	exon22			TAAAGGAATCCTT	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.3079-1A>C	chr9.hg19:g.2101571A>C		694.0	0.0		445.0	322.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.417151	0.83449	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000382203;ENST00000382194	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.71	5.71	0.89125	.	0.116735	0.56097	D	0.000022	D	0.86535	0.5956	M	0.69248	2.105	0.80722	D	1	B;D;P	0.56035	0.003;0.974;0.956	B;D;D	0.70487	0.02;0.969;0.931	D	0.86605	0.1869	10	0.48119	T	0.1	-23.5939	15.9892	0.80188	1.0:0.0:0.0:0.0	.	628;1027;1027	B4DK35;P51531-2;P51531	.;.;SMCA2_HUMAN	A	1027	ENSP00000265773:E1027A;ENSP00000349788:E1027A;ENSP00000371638:E1027A;ENSP00000371629:E1027A	ENSP00000265773:E1027A	E	+	2	0	SMARCA2	2091571	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.698000	0.91311	2.180000	0.69256	0.533000	0.62120	GAA	.	.		0.274	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	Missense_Mutation	C	2101571	A	C	2101571	5	2	173	1	0	0	0	0	0	0	1	0	14784	260	9	5	3162	5	SMARCA2	9	2101571	Splice_Site	SNP	A	TCGA-DD-AACW-01A-11D-A40R-10		2101571	139111860	25	26141										
ASPN	54829	hgsc.bcm.edu	37	chr9	95237030	95237030	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	aaaagagagttgtcctcatcAtcatcatcatcatcatcatc	4	11	8	1	rs143279922		TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr9:95237030A>C	ENST00000375544.3	-	2	393	c.150T>G	c.(148-150)gaT>gaG	p.D50E	ASPN_ENST00000395538.3_Missense_Mutation_p.D50E|ASPN_ENST00000450139.2_Missense_Mutation_p.D22E|CENPP_ENST00000375587.3_Intron|ASPN_ENST00000375543.1_Missense_Mutation_p.D50E	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	50	Poly-Asp.				bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						TGTCCtcatcatcatcatcat	0.398																																					p.D50E		Atlas-SNP	.											.	ASPN	52	.	0			c.T150G						.						112	102	105					9																	95237030		2203	4300	6503	SO:0001583	missense	54829	exon2			CTCATCATCATCA	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	14872	protein-coding gene	gene with protein product	"asporin proteoglycan"	608135	"asporin (LRR class 1)"				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.150T>G	chr9.hg19:g.95237030A>C	ENSP00000364694:p.Asp50Glu	65.0	0.0		112.0	7.0	NM_001193335	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	Missense_Mutation	SNP	ENST00000375544.3	hg19		.	.	.	.	.	.	.	.	.	.	A	2.759	-0.258312	0.05791	.	.	ENSG00000106819	ENST00000375544;ENST00000375543;ENST00000395538;ENST00000450139	T;T;T	0.52983	0.64;0.69;0.69	3.41	-5.95	0.02241	.	1.551710	0.03954	N	0.288946	T	0.32645	0.0836	L	0.40543	1.245	0.09310	N	1	B;B	0.32245	0.361;0.001	B;B	0.27380	0.079;0.001	T	0.11941	-1.0567	10	0.22109	T	0.4	.	7.6964	0.28598	0.4608:0.1193:0.4198:0.0	.	50;50	Q5TBF2;Q9BXN1	.;ASPN_HUMAN	E	50;50;50;22	ENSP00000364694:D50E;ENSP00000364693:D50E;ENSP00000378909:D50E	ENSP00000364693:D50E	D	-	3	2	ASPN	94276851	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.911000	0.01583	-2.152000	0.00794	-2.339000	0.00246	GAT	.	.		0.398	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680		C	95237030	A	C	95237030	3	2	173	1	0	0	0	0	1	0	0	0	1057	214	8	5	1020	5	ASPN	9	95237030	Missense_Mutation	SNP	A	TCGA-DD-AACW-01A-11D-A40R-10	93135459	95237030	45976401	26	26142										
UBAC1	10422	hgsc.bcm.edu	37	chr9	138838155	138838155	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	tccactgcatctgggttcagCgctaacagcttctgcgccac	9	15	3	0			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr9:138838155C>A	ENST00000371756.3	-	5	721	c.504G>T	c.(502-504)gcG>gcT	p.A168A	UBAC1_ENST00000465873.1_5'Flank	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	168					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		CTGGGTTCAGCGCTAACAGCT	0.512																																					p.A168A	NSCLC(78;973 1398 27381 29552 42415)	Atlas-SNP	.											.	UBAC1	40	.	0			c.G504T						.						111	101	104					9																	138838155		2203	4300	6503	SO:0001819	synonymous_variant	10422	exon5			GTTCAGCGCTAAC	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"ubiquitin associated domain containing 1"	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.504G>T	chr9.hg19:g.138838155C>A		83.0	0.0		129.0	53.0	NM_016172	O75500|Q9UMW7	Silent	SNP	ENST00000371756.3	hg19	CCDS35177.1																																																																																			.	.		0.512	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172		A	138838155	C	A	138838155	2	1	173	1	0	0	0	0	0	0	0	1	16849	755	27	1		1	UBAC1	9	138838155	Silent	SNP	C	TCGA-DD-AACW-01A-11D-A40R-10	43601125	138838155	2375276	27	26143										
C10orf137	26098	hgsc.bcm.edu	37	chr10	127451995	127451995	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	cgttatcgtccacctgctggGccagcttgccgccggcagtg	13	15	0	0			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr10:127451995G>T	ENST00000356792.4	+	25	3903	c.3671G>T	c.(3670-3672)gGc>gTc	p.G1224V	C10orf137_ENST00000337623.3_Missense_Mutation_p.G1190V	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		1224					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				CACCTGCTGGGCCAGCTTGCC	0.547																																					p.G1224V		Atlas-SNP	.											.	C10orf137	153	.	0			c.G3671T						.						69	55	60					10																	127451995		2203	4300	6503	SO:0001583	missense	26098	exon25			TGCTGGGCCAGCT																												ENST00000356792.4:c.3671G>T	chr10.hg19:g.127451995G>T	ENSP00000349244:p.Gly1224Val	26.0	0.0		46.0	21.0	NM_001202438	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	hg19	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.757724	0.31137	.	.	ENSG00000107938	ENST00000356792;ENST00000337623	.	.	.	5.13	-1.03	0.10102	.	0.607701	0.16352	N	0.218167	T	0.24736	0.0600	N	0.08118	0	0.33979	D	0.647688	B;B;B	0.30361	0.062;0.277;0.018	B;B;B	0.30943	0.069;0.122;0.043	T	0.23261	-1.0193	9	0.36615	T	0.2	.	10.7402	0.46149	0.6238:0.0:0.3762:0.0	.	1224;571;1190	Q3B7T1;Q5VZQ1;Q3B7T1-5	EDRF1_HUMAN;.;.	V	1224;1190	.	ENSP00000336727:G1190V	G	+	2	0	C10orf137	127441985	0.808000	0.29022	0.916000	0.36221	0.659000	0.38960	1.370000	0.34238	-0.088000	0.12506	-0.251000	0.11542	GGC	.	.		0.547	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			T	127451995	G	T	127451995	3	4	173	1	0	0	0	0	1	0	0	0	1596	1203	42	3	3663	3	C10orf137	10	127451995	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10		127451995	8082752	28	26144										
CRY2	1408	hgsc.bcm.edu	37	chr11	45882443	45882443	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	gccaccccttacatacaagcGctttcaggccatcatcagcc	6	17	3	0	rs369560580		TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr11:45882443G>T	ENST00000443527.2	+	4	597	c.575G>T	c.(574-576)cGc>cTc	p.R192L	CRY2_ENST00000473199.1_Intron|CRY2_ENST00000417225.2_Missense_Mutation_p.R110L	NM_021117.3	NP_066940.2	Q49AN0	CRY2_HUMAN	cryptochrome circadian clock 2	171					blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|glucose homeostasis (GO:0042593)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of phosphoprotein phosphatase activity (GO:0032515)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of sodium-dependent phosphate transport (GO:2000118)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|FAD binding (GO:0071949)|phosphatase binding (GO:0019902)|single-stranded DNA binding (GO:0003697)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(2)	15						ACATACAAGCGCTTTCAGGCC	0.582																																					p.R192L	Esophageal Squamous(106;91 1499 8126 12599 39610)	Atlas-SNP	.											.	CRY2	61	.	0			c.G575T						.						116	110	112					11																	45882443		2203	4299	6502	SO:0001583	missense	1408	exon4			ACAAGCGCTTTCA	AB014558	CCDS7915.2, CCDS44576.1	11p11.2	2014-01-17	2014-01-17		ENSG00000121671	ENSG00000121671			2385	protein-coding gene	gene with protein product		603732	"cryptochrome 2 (photolyase-like)"			8909283	Standard	NM_021117		Approved		uc010rgn.2	Q49AN0	OTTHUMG00000153225	ENST00000443527.2:c.575G>T	chr11.hg19:g.45882443G>T	ENSP00000406751:p.Arg192Leu	66.0	0.0		89.0	39.0	NM_021117	B4DH32|B4DZD6|O75148|Q8IV71	Missense_Mutation	SNP	ENST00000443527.2	hg19	CCDS7915.2	.	.	.	.	.	.	.	.	.	.	G	25.6	4.653622	0.88056	.	.	ENSG00000121671	ENST00000417225;ENST00000443527	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.62672	0.2447	L	0.52364	1.645	0.80722	D	1	B;B	0.30146	0.27;0.117	B;B	0.35899	0.106;0.213	T	0.55192	-0.8179	9	0.21014	T	0.42	-27.4279	20.5792	0.99380	0.0:0.0:1.0:0.0	.	192;110	B4DZD6;Q49AN0-2	.;.	L	110;192	.	ENSP00000397419:R110L	R	+	2	0	CRY2	45839019	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.873000	0.98535	0.561000	0.74099	CGC	.	.		0.582	CRY2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330235.2	NM_021117		T	45882443	G	T	45882443	3	4	173	1	0	0	0	0	1	0	0	0	3906	1087	38	1	625	1	CRY2	11	45882443	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10		45882443	89124073	29	26145										
C11orf80	79703	hgsc.bcm.edu	37	chr11	66563768	66563768	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	acaggttgatgaaaagcccaGaaccttgatgacagattgtc	10	8	0	6			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr11:66563768G>A	ENST00000360962.4	+	6	657	c.650G>A	c.(649-651)aGa>aAa	p.R217K	C11orf80_ENST00000346672.4_Missense_Mutation_p.R62K|C11orf80_ENST00000532565.2_5'UTR|C11orf80_ENST00000540737.1_Missense_Mutation_p.R51K|C11orf80_ENST00000527368.1_3'UTR|C11orf80_ENST00000525449.2_Missense_Mutation_p.R62K|C11orf80_ENST00000527634.1_5'UTR	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	217										autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						GAAAAGCCCAGAACCTTGATG	0.348																																					p.R217K		Atlas-SNP	.											.	C11orf80	31	.	0			c.G650A						.						120	112	115					11																	66563768		1847	4089	5936	SO:0001583	missense	79703	exon6			AGCCCAGAACCTT			11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.650G>A	chr11.hg19:g.66563768G>A	ENSP00000354227:p.Arg217Lys	137.0	0.0		195.0	82.0	NM_024650	Q9H677	Missense_Mutation	SNP	ENST00000360962.4	hg19	CCDS53664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.43|14.43	2.534340|2.534340	0.45073|0.45073	.|.	.|.	ENSG00000173715|ENSG00000173715	ENST00000532089|ENST00000525908;ENST00000360962;ENST00000346672;ENST00000528340;ENST00000540737;ENST00000525449	.|T;T	.|0.33865	.|1.39;1.39	5.48|5.48	2.17|2.17	0.27698|0.27698	.|.	.|0.338753	.|0.25566	.|N	.|0.029800	T|T	0.27629|0.27629	0.0679|0.0679	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	0.999991|0.999991	.|P	.|0.46912	.|0.886	.|B	.|0.44278	.|0.445	T|T	0.08889|0.08889	-1.0700|-1.0700	5|10	.|0.56958	.|D	.|0.05	-6.0338|-6.0338	8.8409|8.8409	0.35142|0.35142	0.088:0.3007:0.6113:0.0|0.088:0.3007:0.6113:0.0	.|.	.|51	.|E9PKZ8	.|.	K|K	43|168;217;62;51;51;62	.|ENSP00000432039:R168K;ENSP00000354227:R217K	.|ENSP00000317408:R62K	E|R	+|+	1|2	0|0	C11orf80|C11orf80	66320344|66320344	0.002000|0.002000	0.14202|0.14202	0.815000|0.815000	0.32552|0.32552	0.758000|0.758000	0.43043|0.43043	0.240000|0.240000	0.18042|0.18042	0.620000|0.620000	0.30215|0.30215	0.650000|0.650000	0.86243|0.86243	GAA|AGA	.	.		0.348	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024650		A	66563768	G	A	66563768	3	1	173	1	0	0	0	0	1	0	0	0	1666	942	33	3	672	3	C11orf80	11	66563768	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	20681325	66563768	68442748	30	26146										
ENDOD1	23052	hgsc.bcm.edu	37	chr11	94823356	94823356	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	gcgccccgcgccctgcgcccGgcggcgccgagcagcgatgg	17	19	0	0			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr11:94823356G>T	ENST00000278505.4	+	1	383	c.265G>T	c.(265-267)Ggc>Tgc	p.G89C		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	89						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				ccctgcgcccggcggcgccgA	0.746																																					p.G89C		Atlas-SNP	.											.	ENDOD1	26	.	0			c.G265T						.						2	3	3					11																	94823356		1503	3353	4856	SO:0001583	missense	23052	exon1			GCGCCCGGCGGCG	BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.265G>T	chr11.hg19:g.94823356G>T	ENSP00000278505:p.Gly89Cys	55.0	0.0		93.0	36.0	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	hg19	CCDS41699.1	.	.	.	.	.	.	.	.	.	.	G	8.532	0.871215	0.17322	.	.	ENSG00000149218	ENST00000278505	T	0.68025	-0.3	4.45	0.566	0.17317	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.758048	0.11438	N	0.564087	T	0.56187	0.1968	M	0.61703	1.905	0.09310	N	1	B	0.28760	0.221	B	0.24848	0.056	T	0.53486	-0.8432	10	0.66056	D	0.02	-11.7638	2.2712	0.04091	0.1901:0.5049:0.1498:0.1552	.	89	O94919	ENDD1_HUMAN	C	89	ENSP00000278505:G89C	ENSP00000278505:G89C	G	+	1	0	ENDOD1	94463004	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	0.483000	0.22292	0.212000	0.20703	0.650000	0.86243	GGC	.	.		0.746	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036		T	94823356	G	T	94823356	3	4	173	1	0	0	0	0	1	0	0	0	5116	1116	39	1	267	1	ENDOD1	11	94823356	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	28259588	94823356	40183160	31	26147										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31642418	31642418	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ctttacttcgaatacaatctAtaagctgccgatgtgagcgc	8	10	1	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr14:31642418A>G	ENST00000399332.1	-	6	1588	c.1100T>C	c.(1099-1101)aTa>aCa	p.I367T	HECTD1_ENST00000553700.1_Missense_Mutation_p.I367T	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	367					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		AATACAATCTATAAGCTGCCG	0.403																																					p.I367T		Atlas-SNP	.											.	HECTD1	159	.	0			c.T1100C						.						98	92	94					14																	31642418		1860	4109	5969	SO:0001583	missense	25831	exon6			CAATCTATAAGCT	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.1100T>C	chr14.hg19:g.31642418A>G	ENSP00000382269:p.Ile367Thr	169.0	0.0		207.0	76.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.527963	0.85706	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000556224	T;T;T	0.34472	1.36;1.36;1.36	6.07	6.07	0.98685	Ankyrin repeat-containing domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55800	0.1943	L	0.60455	1.87	0.80722	D	1	P	0.50156	0.932	P	0.61397	0.888	T	0.56780	-0.7922	10	0.87932	D	0	-22.5587	16.635	0.85050	1.0:0.0:0.0:0.0	.	367	Q9ULT8	HECD1_HUMAN	T	367	ENSP00000450697:I367T;ENSP00000382269:I367T;ENSP00000452015:I367T	ENSP00000261312:I367T	I	-	2	0	HECTD1	30712169	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.307000	0.96226	2.330000	0.79161	0.477000	0.44152	ATA	.	.		0.403	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			G	31642418	A	G	31642418	3	3	173	1	0	0	0	0	1	0	0	0	7048	449	16	2	6884	2	HECTD1	14	31642418	Missense_Mutation	SNP	A	TCGA-DD-AACW-01A-11D-A40R-10		31642418	75707122	32	26148										
ABHD12B	145447	hgsc.bcm.edu	37	chr14	51352570	51352570	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	agtggaccaaggcaagaagtGgcatcactcccgtgtgtctc	12	11	2	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr14:51352570G>A	ENST00000337334.2	+	7	634	c.619G>A	c.(619-621)Ggc>Agc	p.G207S	PYGL_ENST00000532462.1_Intron|ABHD12B_ENST00000395752.1_Missense_Mutation_p.G100S|ABHD12B_ENST00000353130.1_Missense_Mutation_p.G130S|ABHD12B_ENST00000554241.1_3'UTR	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	207							hydrolase activity (GO:0016787)	p.G207R(1)|p.G130R(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					GGCAAGAAGTGGCATCACTCC	0.522																																					p.G207S		Atlas-SNP	.											ABHD12B,NS,carcinoma,0,1	ABHD12B	53	.	2	Substitution - Missense(2)	lung(2)	c.G619A						.						196	178	184					14																	51352570		2203	4300	6503	SO:0001583	missense	145447	exon7			AGAAGTGGCATCA	BG698443	CCDS9702.1, CCDS55916.1	14q21.3	2009-10-09	2007-04-03	2007-04-03	ENSG00000131969	ENSG00000131969		"Abhydrolase domain containing"	19837	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 29"	C14orf29			Standard	NM_181814		Approved	BEM46L3	uc001wys.3	Q7Z5M8	OTTHUMG00000140286	ENST00000337334.2:c.619G>A	chr14.hg19:g.51352570G>A	ENSP00000336693:p.Gly207Ser	124.0	0.0		162.0	66.0	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Missense_Mutation	SNP	ENST00000337334.2	hg19	CCDS55916.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.278002	0.80692	.	.	ENSG00000131969	ENST00000353130;ENST00000337334;ENST00000395752	T;T;T	0.64260	-0.09;0.85;-0.09	5.76	5.76	0.90799	.	0.104019	0.64402	D	0.000002	T	0.63200	0.2491	M	0.66506	2.035	0.58432	D	0.999993	B;B	0.27068	0.149;0.167	B;B	0.35607	0.206;0.138	T	0.60393	-0.7272	10	0.39692	T	0.17	-17.8351	11.1522	0.48466	0.0837:0.0:0.9163:0.0	.	207;130	Q7Z5M8;Q7Z5M8-2	AB12B_HUMAN;.	S	130;207;100	ENSP00000343951:G130S;ENSP00000336693:G207S;ENSP00000379101:G100S	ENSP00000336693:G207S	G	+	1	0	ABHD12B	50422320	1.000000	0.71417	0.999000	0.59377	0.601000	0.36947	3.010000	0.49559	2.890000	0.99128	0.655000	0.94253	GGC	.	.		0.522	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1			A	51352570	G	A	51352570	3	1	173	1	0	0	0	0	1	0	0	0	77	1348	47	3	424	3	ABHD12B	14	51352570	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	19710152	51352570	55996970	33	26149										
WDR25	79446	hgsc.bcm.edu	37	chr14	100995511	100995511	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ctccactgtgtggccctaccGgatgagcagacggcggcgct	14	14	0	2			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr14:100995511G>A	ENST00000335290.6	+	6	1605	c.1379G>A	c.(1378-1380)cGg>cAg	p.R460Q	WDR25_ENST00000402312.3_Missense_Mutation_p.R460Q|WDR25_ENST00000554998.1_Missense_Mutation_p.R460Q|WDR25_ENST00000542471.2_Missense_Mutation_p.R203Q|WDR25_ENST00000557502.1_3'UTR	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	460										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				TGGCCCTACCGGATGAGCAGA	0.627																																					p.R460Q		Atlas-SNP	.											.	WDR25	37	.	0			c.G1379A						.						86	65	72					14																	100995511		2203	4300	6503	SO:0001583	missense	79446	exon6			CCTACCGGATGAG	BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"WD repeat domain containing"	21064	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 67"	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.1379G>A	chr14.hg19:g.100995511G>A	ENSP00000334148:p.Arg460Gln	90.0	0.0		89.0	36.0	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Missense_Mutation	SNP	ENST00000335290.6	hg19	CCDS32157.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.4|20.4	3.986745|3.986745	0.74589|0.74589	.|.	.|.	ENSG00000176473|ENSG00000176473	ENST00000555201|ENST00000554998;ENST00000402312;ENST00000335290;ENST00000542471	.|T;T;T;T	.|0.01287	.|5.05;5.05;5.05;5.05	3.64|3.64	2.73|2.73	0.32206|0.32206	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.245106	.|0.30630	.|U	.|0.009202	T|T	0.01320|0.01320	0.0043|0.0043	L|L	0.31065|0.31065	0.9|0.9	0.37246|0.37246	D|D	0.906361|0.906361	.|P;B	.|0.50272	.|0.933;0.27	.|B;B	.|0.42087	.|0.375;0.01	T|T	0.67941|0.67941	-0.5540|-0.5540	5|10	.|0.41790	.|T	.|0.15	.|.	7.1378|7.1378	0.25537|0.25537	0.217:0.0:0.783:0.0|0.217:0.0:0.783:0.0	.|.	.|203;460	.|Q64LD2-2;Q64LD2	.|.;WDR25_HUMAN	R|Q	68|460;460;460;203	.|ENSP00000450661:R460Q;ENSP00000385540:R460Q;ENSP00000334148:R460Q;ENSP00000441903:R203Q	.|ENSP00000334148:R460Q	G|R	+|+	1|2	0|0	WDR25|WDR25	100065264|100065264	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	4.116000|4.116000	0.57871|0.57871	2.033000|2.033000	0.60031|0.60031	0.563000|0.563000	0.77884|0.77884	GGA|CGG	.	.		0.627	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515		A	100995511	G	A	100995511	3	1	173	1	0	0	0	0	1	0	0	0	17297	1116	39	1	1397	1	WDR25	14	100995511	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	49642941	100995511	6354029	34	26150										
CYFIP1	23191	hgsc.bcm.edu	37	chr15	22960851	22960851	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	cccactacgcgctcaccaggTtcaacaagcagttcctgtac	7	16	2	0			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr15:22960851T>A	ENST00000313077.7	+	18	2169	c.2044T>A	c.(2044-2046)Ttc>Atc	p.F682I	CYFIP1_ENST00000435939.2_Missense_Mutation_p.F251I|CYFIP1_ENST00000560848.1_Missense_Mutation_p.F682I	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		GCTCACCAGGTTCAACAAGCA	0.527																																					p.F682I		Atlas-SNP	.											.	CYFIP1	159	.	0			c.T2044A						.						86	71	76					15																	22960851		2203	4300	6503	SO:0001583	missense	23191	exon18			ACCAGGTTCAACA	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"selective hybridizing clone", "cytoplasmic FMRP interacting protein 1"	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.2044T>A	chr15.hg19:g.22960851T>A	ENSP00000324549:p.Phe682Ile	67.0	0.0		87.0	32.0	NM_014608		Missense_Mutation	SNP	ENST00000313077.7	hg19	CCDS10009.1	.	.	.	.	.	.	.	.	.	.	T	36	5.703608	0.96812	.	.	ENSG00000068793	ENST00000313077;ENST00000412127;ENST00000435939	T;T	0.26957	1.7;1.7	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000001	T	0.56819	0.2011	M	0.87038	2.855	0.80722	D	1	D;D;P	0.76494	0.994;0.999;0.744	D;D;P	0.75020	0.985;0.962;0.482	T	0.64635	-0.6361	10	0.66056	D	0.02	-35.2083	15.887	0.79258	0.0:0.0:0.0:1.0	.	710;251;682	E7EQ04;Q7L576-2;Q7L576	.;.;CYFP1_HUMAN	I	682;710;251	ENSP00000324549:F682I;ENSP00000405956:F251I	ENSP00000324549:F682I	F	+	1	0	CYFIP1	20512292	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.862000	0.87013	2.208000	0.71279	0.533000	0.62120	TTC	.	.		0.527	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608		A	22960851	T	A	22960851	3	1	173	1	0	0	0	0	1	0	0	0	4139	1725	60	4	2491	4	CYFIP1	15	22960851	Missense_Mutation	SNP	T	TCGA-DD-AACW-01A-11D-A40R-10		22960851	79570541	35	26151										
ABCC6	368	hgsc.bcm.edu	37	chr16	16244619	16244619	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	tgccagacacaggagctgttTctggcccacgctgggaacga	13	12	1	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr16:16244619T>C	ENST00000205557.7	-	30	4248	c.4219A>G	c.(4219-4221)Aaa>Gaa	p.K1407E		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1407	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	AGGAGCTGTTTCTGGCCCACG	0.597																																					p.K1407E		Atlas-SNP	.											.	ABCC6	110	.	0			c.A4219G						.						36	32	33					16																	16244619		2197	4300	6497	SO:0001583	missense	368	exon30			GCTGTTTCTGGCC	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.4219A>G	chr16.hg19:g.16244619T>C	ENSP00000205557:p.Lys1407Glu	169.0	0.0		134.0	109.0	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	hg19	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	T	18.64	3.666544	0.67814	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.94723	-3.5	4.36	4.36	0.52297	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.45361	U	0.000364	D	0.96907	0.8990	M	0.86502	2.82	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.70487	0.969;0.969	D	0.97034	0.9752	10	0.87932	D	0	.	9.7455	0.40444	0.0:0.0:0.3183:0.6817	.	1407;1407	O95255;A8Y988	MRP6_HUMAN;.	E	1407;345	ENSP00000205557:K1407E	ENSP00000205557:K1407E	K	-	1	0	ABCC6	16152120	0.927000	0.31430	1.000000	0.80357	0.884000	0.51177	0.904000	0.28491	1.750000	0.51863	0.448000	0.29417	AAA	.	.		0.597	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			C	16244619	T	C	16244619	3	2	173	1	0	0	0	0	1	0	0	0	57	1792	62	2	300	2	ABCC6	16	16244619	Missense_Mutation	SNP	T	TCGA-DD-AACW-01A-11D-A40R-10		16244619	74110134	36	26152										
MED1	5469	hgsc.bcm.edu	37	chr17	37566444	37566444	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	tccccgagcatatttccatgCggggtgagccggaagaggag	15	10	0	2			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr17:37566444C>T	ENST00000300651.6	-	17	2253	c.2030G>A	c.(2029-2031)cGc>cAc	p.R677H	MED1_ENST00000394287.3_Intron	NM_004774.3	NP_004765.2	O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		TATTTCCATGCGGGGTGAGCC	0.463										HNSCC(31;0.082)																											p.R677H	Pancreas(21;279 768 2492 4877 24026)	Atlas-SNP	.											MED1,colon,carcinoma,0,2	MED1	123	.	0			c.G2030A						.						92	96	94					17																	37566444		2203	4300	6503	SO:0001583	missense	5469	exon17			TCCATGCGGGGTG	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"PPAR binding protein"	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000300651.6:c.2030G>A	chr17.hg19:g.37566444C>T	ENSP00000300651:p.Arg677His	75.0	0.0		132.0	62.0	NM_004774	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000300651.6	hg19	CCDS11336.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.311544	0.60414	.	.	ENSG00000125686	ENST00000300651	T	0.55930	0.49	5.59	5.59	0.84812	.	.	.	.	.	T	0.61590	0.2359	L	0.27053	0.805	0.54753	D	0.999985	D	0.76494	0.999	D	0.64506	0.926	T	0.63620	-0.6596	9	0.56958	D	0.05	-6.1628	19.593	0.95523	0.0:1.0:0.0:0.0	.	677	Q15648	MED1_HUMAN	H	677	ENSP00000300651:R677H	ENSP00000300651:R677H	R	-	2	0	MED1	34819970	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.956000	0.63645	2.629000	0.89072	0.561000	0.74099	CGC	.	.		0.463	MED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256943.3	NM_004774		T	37566444	C	T	37566444	3	4	173	1	0	0	0	0	1	0	0	0	9434	768	27	1	2719	1	MED1	17	37566444	Missense_Mutation	SNP	C	TCGA-DD-AACW-01A-11D-A40R-10		37566444	43628766	37	26153										
RNF213	57674	hgsc.bcm.edu	37	chr17	78327346	78327346	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	cgggcggaagacggccatgaGgaggcgatggagacggaggc	21	8	0	3			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr17:78327346G>A	ENST00000582970.1	+	34	10601	c.10458G>A	c.(10456-10458)gaG>gaA	p.E3486E	CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Silent_p.E1559E|RNF213_ENST00000508628.2_Silent_p.E3535E	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3486					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			ACGGCCATGAGGAGGCGATGG	0.597																																					p.E3486E		Atlas-SNP	.											.	RNF213	766	.	0			c.G10458A						.						78	65	70					17																	78327346		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon34			CCATGAGGAGGCG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.10458G>A	chr17.hg19:g.78327346G>A		159.0	0.0		165.0	67.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.		0.597	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		A	78327346	G	A	78327346	2	1	173	1	0	0	0	0	0	0	0	1	13492	991	35	3		3	RNF213	17	78327346	Silent	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	40760902	78327346	2867864	38	26154										
PAK4	10298	hgsc.bcm.edu	37	chr19	39668341	39668341	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	atctggtcgctggggataatGgtgattgagatggtggacgg	18	4	1	2			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr19:39668341G>T	ENST00000593690.1	+	10	1939	c.1512G>T	c.(1510-1512)atG>atT	p.M504I	PAK4_ENST00000599470.1_Missense_Mutation_p.M351I|PAK4_ENST00000360442.3_Missense_Mutation_p.M504I|PAK4_ENST00000358301.3_Missense_Mutation_p.M504I|PAK4_ENST00000321944.4_Missense_Mutation_p.M414I|PAK4_ENST00000599386.1_Missense_Mutation_p.M351I|PAK4_ENST00000435673.2_Missense_Mutation_p.M504I	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	504	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			TGGGGATAATGGTGATTGAGA	0.612																																					p.M504I		Atlas-SNP	.											.	PAK4	40	.	0			c.G1512T						.						145	117	127					19																	39668341		2203	4300	6503	SO:0001583	missense	10298	exon8			GATAATGGTGATT	AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"p21(CDKN1A)-activated kinase 4"			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.1512G>T	chr19.hg19:g.39668341G>T	ENSP00000469413:p.Met504Ile	156.0	0.0		215.0	72.0	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	hg19	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.812824	0.90707	.	.	ENSG00000130669	ENST00000358301;ENST00000321944;ENST00000358801;ENST00000542377;ENST00000435673;ENST00000360442	T;T;T	0.59906	0.23;0.23;0.23	5.07	5.07	0.68467	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.53417	0.1795	N	0.02708	-0.52	0.80722	D	1	P;D;D	0.60160	0.935;0.987;0.982	D;P;D	0.66979	0.926;0.891;0.948	T	0.67960	-0.5535	10	0.87932	D	0	.	15.9831	0.80127	0.0:0.0:1.0:0.0	.	414;351;504	O96013-4;O96013-3;O96013	.;.;PAK4_HUMAN	I	504;351;308;260;504;504	ENSP00000351049:M504I;ENSP00000392753:M504I;ENSP00000353625:M504I	ENSP00000326864:M351I	M	+	3	0	PAK4	44360181	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	9.578000	0.98200	2.629000	0.89072	0.555000	0.69702	ATG	.	.		0.612	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			T	39668341	G	T	39668341	3	4	173	1	0	0	0	0	1	0	0	0	11412	1348	47	3	1538	3	PAK4	19	39668341	Missense_Mutation	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10		39668341	19460642	39	26155										
ZNF222	7673	hgsc.bcm.edu	37	chr19	44535978	44535978	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	gtgtccttataggaggcaagAtccaaactgagatggagact	12	7	0	3			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr19:44535978A>T	ENST00000187879.8	+	4	313	c.151A>T	c.(151-153)Atc>Ttc	p.I51F	ZNF222_ENST00000391960.3_Missense_Mutation_p.I91F|ZNF223_ENST00000591793.1_Intron	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				AGGAGGCAAGATCCAAACTGA	0.488																																					p.I91F		Atlas-SNP	.											.	ZNF222	90	.	0			c.A271T						.						75	72	73					19																	44535978		2203	4300	6503	SO:0001583	missense	7673	exon4			GGCAAGATCCAAA	AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.151A>T	chr19.hg19:g.44535978A>T	ENSP00000187879:p.Ile51Phe	220.0	0.0		360.0	104.0	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Missense_Mutation	SNP	ENST00000187879.8	hg19	CCDS33045.1	.	.	.	.	.	.	.	.	.	.	A	9.200	1.028126	0.19512	.	.	ENSG00000159885	ENST00000391960;ENST00000187879	T;T	0.05925	3.37;5.64	2.14	-0.166	0.13351	Krueppel-associated box (3);	.	.	.	.	T	0.05044	0.0135	N	0.08118	0	0.09310	N	1	D;D	0.63880	0.987;0.993	P;P	0.59221	0.854;0.791	T	0.27502	-1.0072	9	0.11182	T	0.66	.	2.8703	0.05615	0.4398:0.2504:0.3098:0.0	.	91;51	G5E9B9;Q9UK12	.;ZN222_HUMAN	F	91;51	ENSP00000375822:I91F;ENSP00000187879:I51F	ENSP00000187879:I51F	I	+	1	0	ZNF222	49227818	0.000000	0.05858	0.000000	0.03702	0.740000	0.42216	0.738000	0.26158	-0.127000	0.11661	0.172000	0.16884	ATC	.	.		0.488	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			T	44535978	A	T	44535978	3	4	173	1	0	0	0	0	1	0	0	0	17791	333	12	4	304	4	ZNF222	19	44535978	Missense_Mutation	SNP	A	TCGA-DD-AACW-01A-11D-A40R-10	4867637	44535978	14593005	40	26156										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44739013	44739014	+	Frame_Shift_Ins	INS	-	-	T													0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	gttattacaaggtgactctaINSttcaggtttctgaaaatgag							TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr19:44739013_44739014insT	ENST00000313040.7	+	6	635_636	c.430_431insT	c.(430-432)attfs	p.I144fs	ZNF227_ENST00000589005.1_Frame_Shift_Ins_p.I93fs|ZNF227_ENST00000391961.2_Frame_Shift_Ins_p.I93fs	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	144					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				AGGTGACTCTATTCAGGTTTCT	0.386																																					p.I144fs		Atlas-INDEL	.											.	ZNF227	62	.	0			c.430_431insT						.																																			SO:0001589	frameshift_variant	7770	exon6			.	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.432dupT	chr19.hg19:g.44739015_44739015dupT	ENSP00000321049:p.Ile144fs	397.0	0.0		733.0	196.0	NM_182490	B3KRU7|B7Z5P9	Frame_Shift_Ins	INS	ENST00000313040.7	hg19	CCDS12636.1																																																																																			.	.		0.386	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		T	44739014	-	T	44739013	7	5	173	1	0	1	1	0	0	0	0	0	17796	449	16	0	444	0	ZNF227	19	44739013	Frame_Shift_Ins	INS	-	TCGA-DD-AACW-01A-11D-A40R-10	203035	44739013	14389970	41	26157										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20340921	20340921	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	tgaggaaatcaacccgactgAgaagcccaggcaatacctca	9	12	2	2			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr20:20340921A>G	ENST00000245957.5	+	27	3657	c.3581A>G	c.(3580-3582)gAg>gGg	p.E1194G	C20orf26_ENST00000377309.2_3'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		1194										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		AACCCGACTGAGAAGCCCAGG	0.448											OREG0025807	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E1194G		Atlas-SNP	.											.	C20orf26	188	.	0			c.A3581G						.						156	162	160					20																	20340921		2203	4300	6503	SO:0001583	missense	26074	exon27			CGACTGAGAAGCC																												ENST00000245957.5:c.3581A>G	chr20.hg19:g.20340921A>G	ENSP00000245957:p.Glu1194Gly	146.0	0.0	740	195.0	77.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	hg19	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	a	14.15	2.450779	0.43531	.	.	ENSG00000089101	ENST00000343997;ENST00000389655;ENST00000245957	T	0.12039	2.72	5.12	4.03	0.46877	.	0.138345	0.32868	N	0.005542	T	0.15046	0.0363	L	0.59436	1.845	0.80722	D	1	B	0.13594	0.008	B	0.14578	0.011	T	0.02646	-1.1129	10	0.51188	T	0.08	.	10.0311	0.42101	0.9184:0.0:0.0816:0.0	.	1194	Q8NHU2	CT026_HUMAN	G	1134;1160;1194	ENSP00000245957:E1194G	ENSP00000245957:E1194G	E	+	2	0	C20orf26	20288921	1.000000	0.71417	0.935000	0.37517	0.028000	0.11728	3.356000	0.52269	0.911000	0.36747	0.451000	0.29950	GAG	.	.		0.448	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			G	20340921	A	G	20340921	3	3	173	1	0	0	0	0	1	0	0	0	2108	304	11	2	3715	2	C20orf26	20	20340921	Missense_Mutation	SNP	A	TCGA-DD-AACW-01A-11D-A40R-10		20340921	42684599	42	26158										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35443555	35443555	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	gtctgagccaaggtcttttgCcagaagaatctccttagaga	10	9	3	4			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr20:35443555C>T	ENST00000357779.3	-	5	1902	c.1576G>A	c.(1576-1578)Gca>Aca	p.A526T	SOGA1_ENST00000456801.2_Missense_Mutation_p.A367T|SOGA1_ENST00000237536.4_Missense_Mutation_p.A764T|SOGA1_ENST00000279034.6_Missense_Mutation_p.A526T			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	526					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						AGGTCTTTTGCCAGAAGAATC	0.478																																					p.A764T		Atlas-SNP	.											.	SOGA1	136	.	0			c.G2290A						.						100	106	104					20																	35443555		1950	4147	6097	SO:0001583	missense	140710	exon5			CTTTTGCCAGAAG	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.1576G>A	chr20.hg19:g.35443555C>T	ENSP00000350424:p.Ala526Thr	94.0	0.0		146.0	68.0	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	hg19		.	.	.	.	.	.	.	.	.	.	C	13.16	2.155308	0.38021	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.07	3.07	0.35406	.	0.727131	0.13028	N	0.419568	T	0.26774	0.0655	N	0.22421	0.69	0.24024	N	0.996135	B	0.31949	0.348	B	0.32980	0.156	T	0.17561	-1.0365	10	0.21540	T	0.41	-15.2489	7.49	0.27456	0.1714:0.7398:0.0:0.0887	.	526	O94964-4	.	T	764;526;367;526	ENSP00000237536:A764T;ENSP00000279034:A526T;ENSP00000413886:A367T;ENSP00000350424:A526T	ENSP00000237536:A764T	A	-	1	0	KIAA0889	34876969	0.965000	0.33210	1.000000	0.80357	0.685000	0.39939	1.152000	0.31663	0.670000	0.31165	0.462000	0.41574	GCA	.	.		0.478	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		T	35443555	C	T	35443555	3	4	173	1	0	0	0	0	1	0	0	0	2085	739	26	3	2801	3	C20orf117	20	35443555	Missense_Mutation	SNP	C	TCGA-DD-AACW-01A-11D-A40R-10	15102634	35443555	27581965	43	26159										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32492952	32492952	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ctcatcatcgtcactgaggaTgtctgtctccttgatgtcat	8	11	6	2			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr21:32492952T>C	ENST00000286827.3	-	29	4981	c.4510A>G	c.(4510-4512)Atc>Gtc	p.I1504V	TIAM1_ENST00000541036.1_Missense_Mutation_p.I1444V	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1504					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						TCACTGAGGATGTCTGTCTCC	0.577																																					p.I1504V		Atlas-SNP	.											.	TIAM1	522	.	0			c.A4510G						.						128	104	112					21																	32492952		2203	4300	6503	SO:0001583	missense	7074	exon29			TGAGGATGTCTGT		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.4510A>G	chr21.hg19:g.32492952T>C	ENSP00000286827:p.Ile1504Val	57.0	0.0		78.0	34.0	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	hg19	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.400062	0.83120	.	.	ENSG00000156299	ENST00000286827;ENST00000541036	T;T	0.60548	0.18;0.27	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.72145	0.3424	L	0.58101	1.795	0.58432	D	0.999992	D;D	0.67145	0.996;0.994	D;D	0.77557	0.99;0.978	T	0.74630	-0.3601	10	0.59425	D	0.04	.	14.9878	0.71362	0.0:0.0:0.0:1.0	.	1444;1504	F5GZ53;Q13009	.;TIAM1_HUMAN	V	1504;1444	ENSP00000286827:I1504V;ENSP00000441570:I1444V	ENSP00000286827:I1504V	I	-	1	0	TIAM1	31414823	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.586000	0.82596	1.927000	0.55829	0.533000	0.62120	ATC	.	.		0.577	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		C	32492952	T	C	32492952	3	2	173	1	0	0	0	0	1	0	0	0	15905	1464	51	2	269	2	TIAM1	21	32492952	Missense_Mutation	SNP	T	TCGA-DD-AACW-01A-11D-A40R-10		32492952	15636943	44	26160										
MAPK1	5594	hgsc.bcm.edu	37	chr22	22160239	22160239	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ttaaccctctgaggatctggTagagaaaatagcagatatgg	11	6	2	3			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr22:22160239T>C	ENST00000215832.6	-	3	580	c.392A>G	c.(391-393)tAc>tGc	p.Y131C	MAPK1_ENST00000544786.1_Missense_Mutation_p.Y131C|MAPK1_ENST00000398822.3_Missense_Mutation_p.Y131C	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	131	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	GAGGATCTGGTAGAGAAAATA	0.438																																					p.Y131C		Atlas-SNP	.											.	MAPK1	38	.	0			c.A392G						.						207	193	198					22																	22160239		2203	4300	6503	SO:0001583	missense	5594	exon3			ATCTGGTAGAGAA	M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1			Standard	NM_138957		Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.392A>G	chr22.hg19:g.22160239T>C	ENSP00000215832:p.Tyr131Cys	124.0	0.0		174.0	69.0	NM_002745	A8CZ64	Missense_Mutation	SNP	ENST00000215832.6	hg19	CCDS13795.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.419991	0.83559	.	.	ENSG00000100030	ENST00000215832;ENST00000415911;ENST00000398822;ENST00000544786	T;T;T	0.47528	0.84;0.84;0.84	4.77	4.77	0.60923	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.62060	0.2397	L	0.48362	1.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.65656	-0.6115	10	0.87932	D	0	0.523	14.7475	0.69499	0.0:0.0:0.0:1.0	.	131;131	A8CZ64;P28482	.;MK01_HUMAN	C	131;119;131;131	ENSP00000215832:Y131C;ENSP00000381803:Y131C;ENSP00000440842:Y131C	ENSP00000215832:Y131C	Y	-	2	0	MAPK1	20490239	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.778000	0.85637	2.131000	0.65755	0.528000	0.53228	TAC	.	.		0.438	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075396.2			C	22160239	T	C	22160239	3	2	173	1	0	0	0	0	1	0	0	0	9280	1638	57	2	714	2	MAPK1	22	22160239	Missense_Mutation	SNP	T	TCGA-DD-AACW-01A-11D-A40R-10		22160239	29144327	45	26161										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885876	29885876	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	gaagctaagtccccagagaaGgccaagtccccagagaaggc	12	12	0	2	rs59890097|rs532587474	byFrequency	TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr22:29885876G>A	ENST00000310624.6	+	4	2280	c.2247G>A	c.(2245-2247)aaG>aaA	p.K749K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	755	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CCCCAGAGAAGGCCAAGTCCC	0.552																																					p.K749K		Atlas-SNP	.											.	NEFH	178	.	0			c.G2247A						.						99	98	99					22																	29885876		2203	4300	6503	SO:0001819	synonymous_variant	4744	exon4			AGAGAAGGCCAAG		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2247G>A	chr22.hg19:g.29885876G>A		6.0	0.0		141.0	18.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.552	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885876	G	A	29885876	2	1	173	1	0	0	0	0	0	0	0	1	10323	991	35	3		3	NEFH	22	29885876	Silent	SNP	G	TCGA-DD-AACW-01A-11D-A40R-10	7725637	29885876	21418690	46	26162										
TTLL1	25809	hgsc.bcm.edu	37	chr22	43464505	43464505	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	ccctgggccttgccacaaggCttcatgatccaggtgctgga	12	13	1	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chr22:43464505C>T	ENST00000266254.7	-	5	654	c.414G>A	c.(412-414)aaG>aaA	p.K138K	TTLL1_ENST00000331018.7_Silent_p.K138K	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	138	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		TGCCACAAGGCTTCATGATCC	0.527																																					p.K138K		Atlas-SNP	.											.	TTLL1	41	.	0			c.G414A						.						196	192	193					22																	43464505		2203	4300	6503	SO:0001819	synonymous_variant	25809	exon5			ACAAGGCTTCATG	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"Tubulin tyrosine ligase-like family"	1312	protein-coding gene	gene with protein product		608955	"tubulin tyrosine ligase-like 1"	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.414G>A	chr22.hg19:g.43464505C>T		118.0	0.0		117.0	35.0	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	hg19	CCDS14043.1	.	.	.	.	.	.	.	.	.	.	C	10.29	1.310605	0.23821	.	.	ENSG00000100271	ENST00000495814	.	.	.	5.54	0.973	0.19710	.	.	.	.	.	T	0.61464	0.2349	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58075	-0.7700	4	.	.	.	.	12.5566	0.56257	0.0:0.7525:0.0:0.2475	.	.	.	.	N	64	.	.	S	-	2	0	TTLL1	41794449	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	1.042000	0.30303	0.201000	0.20466	0.655000	0.94253	AGC	.	.		0.527	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263		T	43464505	C	T	43464505	2	4	173	1	0	0	0	0	0	0	0	1	16737	796	28	3		3	TTLL1	22	43464505	Silent	SNP	C	TCGA-DD-AACW-01A-11D-A40R-10	13578629	43464505	7840061	47	26163										
MAGEB4	4115	hgsc.bcm.edu	37	chrX	30261048	30261048	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0208333333333333	1	1	0.473039215686274	0	0.545814479638009	1	1	0	aggtgcccaacagtgatcccCcacgctatcaattcctgtgg	9	14	1	1			TCGA-DD-AACW-01A-11D-A40R-10	TCGA-DD-AACW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	990f7ea9-6799-410e-b224-27e27a625fb7	5dcdade5-76ff-4909-8133-c9f73a19baf7	g.chrX:30261048C>A	ENST00000378982.2	+	1	992	c.796C>A	c.(796-798)Cca>Aca	p.P266T	MAGEB1_ENST00000378981.3_5'Flank|MAGEB1_ENST00000397550.1_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	266	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						CAGTGATCCCCCACGCTATCA	0.493																																					p.P266T		Atlas-SNP	.											.	MAGEB4	75	.	0			c.C796A						.						69	66	67					X																	30261048		2202	4300	6502	SO:0001583	missense	4115	exon1			GATCCCCCACGCT		CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"melanoma-associated antigen B4", "cancer/testis antigen family 3, member 6"	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.796C>A	chrX.hg19:g.30261048C>A	ENSP00000368266:p.Pro266Thr	117.0	0.0		158.0	135.0	NM_002367	B2R9G0|Q6FHH4|Q8IZ00	Missense_Mutation	SNP	ENST00000378982.2	hg19	CCDS14221.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.742817	0.30865	.	.	ENSG00000120289	ENST00000378982	T	0.04706	3.57	3.22	1.38	0.22167	.	0.659026	0.12938	U	0.426810	T	0.19846	0.0477	M	0.88031	2.925	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.08911	-1.0699	10	0.72032	D	0.01	.	3.321	0.07050	0.2543:0.6002:0.0:0.1454	.	266	O15481	MAGB4_HUMAN	T	266	ENSP00000368266:P266T	ENSP00000368266:P266T	P	+	1	0	MAGEB4	30170969	0.008000	0.16893	0.002000	0.10522	0.009000	0.06853	0.225000	0.17757	0.234000	0.21139	-0.192000	0.12808	CCA	.	.		0.493	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367		A	30261048	C	A	30261048	3	1	173	1	0	0	0	0	1	0	0	0	9187	623	22	3	798	3	MAGEB4	23	30261048	Missense_Mutation	SNP	C	TCGA-DD-AACW-01A-11D-A40R-10		30261048	125009512	48	26164										
RPA2	6118	hgsc.bcm.edu	37	chr1	28224153	28224153	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tctgactttacctgaaaagaTctcaggtggcctgccacttt	8	11	2	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:28224153T>A	ENST00000373912.3	-	5	698	c.399A>T	c.(397-399)agA>agT	p.R133S	RPA2_ENST00000373909.3_Missense_Mutation_p.R141S|RPA2_ENST00000313433.7_Missense_Mutation_p.R221S	NM_002946.3	NP_002937.1	P15927	RFA2_HUMAN	replication protein A2, 32kDa	133	Arg/Lys-rich (basic).				base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of DNA damage checkpoint (GO:2000001)|regulation of double-strand break repair via homologous recombination (GO:0010569)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor A complex (GO:0005662)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|enzyme binding (GO:0019899)|protein phosphatase binding (GO:0019903)|single-stranded DNA binding (GO:0003697)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(3)|skin(1)	11		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.62e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00294)|STAD - Stomach adenocarcinoma(196;0.00308)|BRCA - Breast invasive adenocarcinoma(304;0.00613)|READ - Rectum adenocarcinoma(331;0.0649)		CCTGAAAAGATCTCAGGTGGC	0.343								Direct reversal of damage;Nucleotide excision repair (NER)																													p.R133S		Atlas-SNP	.											.	RPA2	34	.	0			c.A399T						.						69	73	72					1																	28224153		2203	4300	6503	SO:0001583	missense	6118	exon5			AAAAGATCTCAGG	BC021257	CCDS314.1, CCDS72740.1	1p35	2008-02-05	2002-08-29		ENSG00000117748	ENSG00000117748			10290	protein-coding gene	gene with protein product		179836	"replication protein A2 (32kD)"			8454588	Standard	XM_005245965		Approved		uc001bpe.1	P15927	OTTHUMG00000003915	ENST00000373912.3:c.399A>T	chr1.hg19:g.28224153T>A	ENSP00000363021:p.Arg133Ser	168.0	0.0		140.0	54.0	NM_002946	Q52II0|Q5TEI9|Q5TEJ5	Missense_Mutation	SNP	ENST00000373912.3	hg19	CCDS314.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.109663	0.77096	.	.	ENSG00000117748	ENST00000373912;ENST00000373909;ENST00000313433;ENST00000444045	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	5.0	-3.89	0.04193	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);Nucleic acid binding, OB-fold, tRNA/helicase-type (1);	0.000000	0.85682	D	0.000000	T	0.28962	0.0719	L	0.55017	1.72	0.48632	D	0.999684	D;D	0.71674	0.998;0.994	D;P	0.72625	0.978;0.842	T	0.22312	-1.0220	10	0.66056	D	0.02	-15.9008	4.367	0.11228	0.1132:0.4816:0.1148:0.2903	.	133;141	P15927;P15927-2	RFA2_HUMAN;.	S	133;141;221;137	ENSP00000363021:R133S;ENSP00000363017:R141S;ENSP00000363015:R221S;ENSP00000387649:R137S	ENSP00000363015:R221S	R	-	3	2	RPA2	28096740	0.347000	0.24853	0.992000	0.48379	0.997000	0.91878	-0.641000	0.05434	-0.281000	0.09141	0.454000	0.30748	AGA	.	.		0.343	RPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011179.1	NM_002946		A	28224153	T	A	28224153	3	1	174	1	0	0	0	0	1	0	0	0	13552	1432	50	4	433	4	RPA2	1	28224153	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10		28224153	221026468	1	26165										
PHC2	1912	hgsc.bcm.edu	37	chr1	33832762	33832762	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cacagcaggaaccgtccggcTgagcccagcccggccttcca	11	18	0	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:33832762T>G	ENST00000257118.5	-	6	984	c.931A>C	c.(931-933)Agc>Cgc	p.S311R	PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000431992.1_Missense_Mutation_p.S282R|PHC2_ENST00000419414.2_Missense_Mutation_p.S311R	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	311					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				ACCGTCCGGCTGAGCCCAGCC	0.592																																					p.S311R		Atlas-SNP	.											.	PHC2	78	.	0			c.A931C						.						80	80	80					1																	33832762		2203	4300	6503	SO:0001583	missense	1912	exon6			TCCGGCTGAGCCC	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"Sterile alpha motif (SAM) domain containing"	3183	protein-coding gene	gene with protein product		602979	"early development regulator 2 (homolog of polyhomeotic 2)", "polyhomeotic-like 2 (Drosophila)"	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.931A>C	chr1.hg19:g.33832762T>G	ENSP00000257118:p.Ser311Arg	99.0	0.0		92.0	31.0	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	hg19	CCDS378.1	.	.	.	.	.	.	.	.	.	.	T	12.56	1.973168	0.34848	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000419414	T;T;T	0.33216	1.79;1.42;1.83	5.88	-2.99	0.05497	.	0.525534	0.22971	N	0.053421	T	0.18341	0.0440	L	0.46157	1.445	0.52501	D	0.999954	P;B;B	0.37955	0.612;0.412;0.167	B;B;B	0.28553	0.091;0.091;0.057	T	0.17592	-1.0364	10	0.15499	T	0.54	0.0168	12.9202	0.58228	0.0:0.6588:0.0:0.3412	.	311;282;311	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	R	282;311;311	ENSP00000389436:S282R;ENSP00000257118:S311R;ENSP00000391440:S311R	ENSP00000257118:S311R	S	-	1	0	PHC2	33605349	0.987000	0.35691	0.561000	0.28357	0.916000	0.54674	0.454000	0.21827	-0.575000	0.05982	-0.256000	0.11100	AGC	.	.		0.592	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		G	33832762	T	G	33832762	3	3	174	1	0	0	0	0	1	0	0	0	11826	1580	55	5	1681	5	PHC2	1	33832762	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	5608609	33832762	215417859	2	26166										
NCDN	23154	hgsc.bcm.edu	37	chr1	36026670	36026670	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ggcagctccgggagcaagttCctggccctgctggtgaatct	14	12	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:36026670C>G	ENST00000373243.2	+	3	1301	c.918C>G	c.(916-918)ttC>ttG	p.F306L	NCDN_ENST00000356090.4_Missense_Mutation_p.F306L|NCDN_ENST00000373253.3_Missense_Mutation_p.F289L	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	306					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GGAGCAAGTTCCTGGCCCTGC	0.677																																					p.F306L		Atlas-SNP	.											.	NCDN	79	.	0			c.C918G						.						28	27	27					1																	36026670		2203	4294	6497	SO:0001583	missense	23154	exon3			CAAGTTCCTGGCC	AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.918C>G	chr1.hg19:g.36026670C>G	ENSP00000362340:p.Phe306Leu	71.0	0.0		76.0	24.0	NM_014284	D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Missense_Mutation	SNP	ENST00000373243.2	hg19	CCDS392.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.969056	0.74131	.	.	ENSG00000020129	ENST00000373253;ENST00000356090;ENST00000373243	T;T;T	0.68479	-0.33;-0.33;-0.33	4.76	3.72	0.42706	.	0.000000	0.85682	D	0.000000	T	0.75384	0.3842	L	0.61218	1.895	0.80722	D	1	D	0.71674	0.998	D	0.67103	0.949	T	0.74575	-0.3620	10	0.48119	T	0.1	.	9.6584	0.39941	0.0:0.8795:0.0:0.1205	.	306	Q9UBB6	NCDN_HUMAN	L	289;306;306	ENSP00000362350:F289L;ENSP00000348394:F306L;ENSP00000362340:F306L	ENSP00000348394:F306L	F	+	3	2	NCDN	35799257	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.349000	0.66010	1.025000	0.39708	0.561000	0.74099	TTC	.	.		0.677	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284		G	36026670	C	G	36026670	3	3	174	1	0	0	0	0	1	0	0	0	10223	854	30	4	928	4	NCDN	1	36026670	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	2193908	36026670	213223951	3	26167										
C8A	731	hgsc.bcm.edu	37	chr1	57340763	57340763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	aggatttccagtgtaaggagAcaggtgagtagcatttcagc	13	6	1	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:57340763A>G	ENST00000361249.3	+	3	409	c.313A>G	c.(313-315)Aca>Gca	p.T105A		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	105	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						GTGTAAGGAGACAGGTGAGTA	0.478																																					p.T105A		Atlas-SNP	.											.	C8A	103	.	0			c.A313G						.						77	69	72					1																	57340763		2203	4300	6503	SO:0001583	missense	731	exon3			AAGGAGACAGGTG	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"Complement system"	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.313A>G	chr1.hg19:g.57340763A>G	ENSP00000354458:p.Thr105Ala	68.0	0.0		73.0	36.0	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	hg19	CCDS606.1	.	.	.	.	.	.	.	.	.	.	A	16.30	3.085720	0.55861	.	.	ENSG00000157131	ENST00000361249	D	0.95377	-3.69	5.22	2.74	0.32292	.	0.266945	0.43747	D	0.000537	D	0.93141	0.7816	L	0.55213	1.73	0.35610	D	0.808619	P	0.41978	0.767	B	0.42245	0.381	D	0.93964	0.7243	10	0.66056	D	0.02	-12.4741	10.1722	0.42917	0.721:0.0:0.0:0.279	.	105	P07357	CO8A_HUMAN	A	105	ENSP00000354458:T105A	ENSP00000354458:T105A	T	+	1	0	C8A	57113351	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.798000	0.47884	0.986000	0.38683	0.528000	0.53228	ACA	.	.		0.478	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		G	57340763	A	G	57340763	3	3	174	1	0	0	0	0	1	0	0	0	2418	275	10	2	323	2	C8A	1	57340763	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	21314093	57340763	191909858	4	26168										
ZZZ3	26009	hgsc.bcm.edu	37	chr1	78098130	78098130	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	agatgactgagtttcagaaaAgggccctgtagctggctcag	13	8	2	4			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:78098130A>G	ENST00000370801.3	-	5	1385	c.910T>C	c.(910-912)Ttt>Ctt	p.F304L	ZZZ3_ENST00000370798.1_Intron|ZZZ3_ENST00000476275.1_5'UTR	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	304					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						GTTTCAGAAAAGGGCCCTGTA	0.453																																					p.F304L		Atlas-SNP	.											.	ZZZ3	80	.	0			c.T910C						.						109	106	107					1																	78098130		2203	4300	6503	SO:0001583	missense	26009	exon5			CAGAAAAGGGCCC	AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"Zinc fingers, ZZ-type"	24523	protein-coding gene	gene with protein product	"ATAC component 1 homolog (Drosophila)"					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.910T>C	chr1.hg19:g.78098130A>G	ENSP00000359837:p.Phe304Leu	86.0	0.0		64.0	26.0	NM_015534	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Missense_Mutation	SNP	ENST00000370801.3	hg19	CCDS677.1	.	.	.	.	.	.	.	.	.	.	A	0.116	-1.132011	0.01756	.	.	ENSG00000036549	ENST00000370801	.	.	.	5.49	-4.11	0.03928	.	0.812643	0.11566	N	0.551269	T	0.08447	0.0210	N	0.11427	0.14	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.28744	-1.0034	8	.	.	.	.	1.2163	0.01915	0.2412:0.1735:0.1321:0.4532	.	304;304;304	Q8IYH5-4;Q8IYH5;Q8IYH5-2	.;ZZZ3_HUMAN;.	L	304	.	.	F	-	1	0	ZZZ3	77870718	0.957000	0.32711	0.915000	0.36163	0.486000	0.33341	0.271000	0.18626	-0.711000	0.04995	-0.336000	0.08194	TTT	.	.		0.453	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1	NM_015534		G	78098130	A	G	78098130	3	3	174	1	0	0	0	0	1	0	0	0	18271	72	3	2	1845	2	ZZZ3	1	78098130	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	20757367	78098130	171152491	5	26169										
ABCA4	24	hgsc.bcm.edu	37	chr1	94466454	94466454	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ccctttaccatgatggccagCcgggtacacagtgcctcaca	9	15	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:94466454C>G	ENST00000370225.3	-	47	6503	c.6417G>C	c.(6415-6417)cgG>cgC	p.R2139R	ABCA4_ENST00000536513.1_Silent_p.R409R|ABCA4_ENST00000535881.1_Silent_p.R258R|ABCA4_ENST00000465352.1_5'Flank	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	2139	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> W (in STGD1). {ECO:0000269|PubMed:11527935}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TGATGGCCAGCCGGGTACACA	0.577																																					p.R2139R		Atlas-SNP	.											.	ABCA4	275	.	0			c.G6417C						.						147	114	125					1																	94466454		2203	4300	6503	SO:0001819	synonymous_variant	24	exon47			GGCCAGCCGGGTA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.6417G>C	chr1.hg19:g.94466454C>G		89.0	0.0		101.0	35.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	hg19	CCDS747.1																																																																																			.	.		0.577	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		G	94466454	C	G	94466454	2	3	174	1	0	0	0	0	0	0	0	1	34	726	26	4		4	ABCA4	1	94466454	Silent	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	16368324	94466454	154784167	6	26170										
TRIM46	80128	hgsc.bcm.edu	37	chr1	155147913	155147913	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tgtgcccagtgtgtcaagagAtgtacaagcagccactggtg	13	9	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:155147913A>C	ENST00000334634.4	+	2	115	c.115A>C	c.(115-117)Atg>Ctg	p.M39L	TRIM46_ENST00000368382.1_Missense_Mutation_p.M16L|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000368383.3_Missense_Mutation_p.M39L|KRTCAP2_ENST00000490672.1_5'Flank|TRIM46_ENST00000468878.1_3'UTR|KRTCAP2_ENST00000295682.4_5'Flank|TRIM46_ENST00000545012.1_Intron|TRIM46_ENST00000543729.1_Missense_Mutation_p.M46L|TRIM46_ENST00000392451.2_Missense_Mutation_p.M39L|TRIM46_ENST00000368385.4_Missense_Mutation_p.M39L	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	39						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GTGTCAAGAGATGTACAAGCA	0.582																																					p.M39L		Atlas-SNP	.											.	TRIM46	79	.	0			c.A115C						.						154	123	134					1																	155147913		2203	4300	6503	SO:0001583	missense	80128	exon2			CAAGAGATGTACA		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19019	protein-coding gene	gene with protein product		600986	"tripartite motif-containing 46"				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.115A>C	chr1.hg19:g.155147913A>C	ENSP00000334657:p.Met39Leu	116.0	0.0		214.0	61.0	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	hg19	CCDS1097.1	.	.	.	.	.	.	.	.	.	.	A	2.643	-0.283740	0.05642	.	.	ENSG00000163462	ENST00000543729;ENST00000430513;ENST00000368385;ENST00000392451;ENST00000368383;ENST00000368382;ENST00000334634	D;D;D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99;-1.99;-1.99	4.44	3.21	0.36854	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);Zinc finger, C3HC4 RING-type (1);	0.109105	0.64402	D	0.000008	T	0.32376	0.0827	N	0.00926	-1.1	0.80722	D	1	B;B;B;B;B;B	0.16396	0.009;0.008;0.017;0.011;0.008;0.009	B;B;B;B;B;B	0.17433	0.007;0.007;0.018;0.012;0.007;0.01	T	0.53027	-0.8496	10	0.02654	T	1	.	4.8439	0.13503	0.6232:0.1917:0.0:0.185	.	26;39;26;16;39;39	F5H5Z2;Q5VT61;B7Z3S2;B1AVQ4;Q7Z4K8;Q7Z4K8-2	.;.;.;.;TRI46_HUMAN;.	L	46;26;39;39;39;16;39	ENSP00000442719:M46L;ENSP00000357369:M39L;ENSP00000376245:M39L;ENSP00000357367:M39L;ENSP00000357366:M16L;ENSP00000334657:M39L	ENSP00000334657:M39L	M	+	1	0	TRIM46	153414537	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.265000	0.43311	1.766000	0.52107	0.477000	0.44152	ATG	.	.		0.582	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058		C	155147913	A	C	155147913	3	2	174	1	0	0	0	0	1	0	0	0	16536	333	12	5	121	5	TRIM46	1	155147913	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	60681459	155147913	94102708	7	26171										
CD1B	910	hgsc.bcm.edu	37	chr1	158301196	158301196	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	aagagaacagctaacagttgAaatggcagcagcagcatttc	10	8	0	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:158301196A>T	ENST00000368168.3	-	1	125	c.18T>A	c.(16-18)ttT>ttA	p.F6L		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	6					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					CTAACAGTTGAAATGGCAGCA	0.468																																					p.F6L		Atlas-SNP	.											.	CD1B	78	.	0			c.T18A						.						75	68	70					1																	158301196		2203	4300	6503	SO:0001583	missense	910	exon1			CAGTTGAAATGGC	M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1635	protein-coding gene	gene with protein product		188360	"CD1B antigen, b polypeptide", "CD1b antigen"	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.18T>A	chr1.hg19:g.158301196A>T	ENSP00000357150:p.Phe6Leu	195.0	0.0		280.0	80.0	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Missense_Mutation	SNP	ENST00000368168.3	hg19	CCDS1176.1	.	.	.	.	.	.	.	.	.	.	A	5.432	0.264859	0.10294	.	.	ENSG00000158485	ENST00000368168	T	0.01203	5.18	3.14	-2.21	0.06973	.	1.032930	0.07807	N	0.957420	T	0.00073	0.0002	N	0.00063	-2.32	0.09310	N	1	B;B	0.16802	0.019;0.0	B;B	0.19666	0.026;0.0	T	0.44143	-0.9347	10	0.02654	T	1	-3.9768	0.2938	0.00262	0.3607:0.2001:0.2445:0.1947	.	6;6	B4E0D2;P29016	.;CD1B_HUMAN	L	6	ENSP00000357150:F6L	ENSP00000357150:F6L	F	-	3	2	CD1B	156567820	0.000000	0.05858	0.001000	0.08648	0.714000	0.41099	-0.420000	0.07062	-0.486000	0.06744	0.528000	0.53228	TTT	.	.		0.468	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764		T	158301196	A	T	158301196	3	4	174	1	0	0	0	0	1	0	0	0	2977	243	9	4	1007	4	CD1B	1	158301196	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	3153283	158301196	90949425	8	26172										
APOBEC4	403314	hgsc.bcm.edu	37	chr1	183617328	183617328	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	acttataaagctgtggagaaCagaatgccagatcccaccac	8	11	0	3	rs576114883		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:183617328C>G	ENST00000308641.4	-	2	860	c.589G>C	c.(589-591)Gtt>Ctt	p.V197L	RGL1_ENST00000536277.1_Intron|APOBEC4_ENST00000481562.1_Intron|RGL1_ENST00000304685.4_Intron	NM_203454.2	NP_982279.1	Q8WW27	ABEC4_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	197					mRNA processing (GO:0006397)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)	p.V197F(1)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(6)|skin(1)	21						CTGTGGAGAACAGAATGCCAG	0.507																																					p.V197L		Atlas-SNP	.											APOBEC4,NS,carcinoma,0,1	APOBEC4	45	.	1	Substitution - Missense(1)	kidney(1)	c.G589C						.						63	65	64					1																	183617328		2203	4300	6503	SO:0001583	missense	403314	exon2			GGAGAACAGAATG	BC021711	CCDS1358.1	1q25.3	2008-02-05	2005-10-27	2005-10-27	ENSG00000173627	ENSG00000173627		"Apolipoprotein B mRNA editing enzymes"	32152	protein-coding gene	gene with protein product		609908	"chromosome 1 open reading frame 169"	C1orf169		16082223	Standard	NM_203454		Approved	MGC26594, FLJ25691, RP1-127C7.4	uc001gqn.3	Q8WW27	OTTHUMG00000035459	ENST00000308641.4:c.589G>C	chr1.hg19:g.183617328C>G	ENSP00000310622:p.Val197Leu	94.0	0.0		149.0	49.0	NM_203454	Q8N7F6	Missense_Mutation	SNP	ENST00000308641.4	hg19	CCDS1358.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.904261	0.00512	.	.	ENSG00000173627	ENST00000308641	T	0.61392	0.11	5.15	3.21	0.36854	.	0.242203	0.28225	N	0.016123	T	0.22742	0.0549	N	0.01352	-0.895	0.23120	N	0.998269	B	0.02656	0.0	B	0.04013	0.001	T	0.28713	-1.0035	10	0.02654	T	1	-11.8308	10.4785	0.44678	0.0:0.2662:0.5924:0.1413	.	197	Q8WW27	ABEC4_HUMAN	L	197	ENSP00000310622:V197L	ENSP00000310622:V197L	V	-	1	0	APOBEC4	181883951	1.000000	0.71417	0.995000	0.50966	0.182000	0.23217	1.341000	0.33907	0.518000	0.28383	-0.147000	0.13772	GTT	.	.		0.507	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454		G	183617328	C	G	183617328	3	3	174	1	0	0	0	0	1	0	0	0	796	478	17	4	518	4	APOBEC4	1	183617328	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	25316132	183617328	65633293	9	26173										
LGR6	59352	hgsc.bcm.edu	37	chr1	202163206	202163206	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cggcgccccccagcccggccCggggcccaccgcctgcccgg	14	24	0	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:202163206C>A	ENST00000367278.3	+	1	178	c.89C>A	c.(88-90)cCg>cAg	p.P30Q		NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	30	LRRNT.				G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						cagcccggcccggggcccacc	0.781																																					p.P30Q		Atlas-SNP	.											.	LGR6	102	.	0			c.C89A						.						4	4	4					1																	202163206		1461	3215	4676	SO:0001583	missense	59352	exon1			CCGGCCCGGGGCC	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"GPCR / Class A : Orphans"	19719	protein-coding gene	gene with protein product		606653	"leucine-rich repeat-containing G protein-coupled receptor 6"			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.89C>A	chr1.hg19:g.202163206C>A	ENSP00000356247:p.Pro30Gln	12.0	0.0		28.0	18.0	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Missense_Mutation	SNP	ENST00000367278.3	hg19	CCDS30971.1	.	.	.	.	.	.	.	.	.	.	C	2.278	-0.365291	0.05103	.	.	ENSG00000133067	ENST00000367278	T	0.60797	0.16	3.86	1.82	0.25136	.	0.414870	0.20151	U	0.098147	T	0.40909	0.1136	N	0.22421	0.69	0.09310	N	0.999996	B	0.06786	0.001	B	0.04013	0.001	T	0.28618	-1.0038	10	0.45353	T	0.12	.	10.7022	0.45934	0.3446:0.6554:0.0:0.0	.	30	Q9HBX8	LGR6_HUMAN	Q	30	ENSP00000356247:P30Q	ENSP00000356247:P30Q	P	+	2	0	LGR6	200429829	0.009000	0.17119	0.018000	0.16275	0.150000	0.21749	2.483000	0.45233	0.169000	0.19679	0.305000	0.20034	CCG	.	.		0.781	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636		A	202163206	C	A	202163206	3	1	174	1	0	0	0	0	1	0	0	0	8767	652	23	1	91	1	LGR6	1	202163206	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	18545878	202163206	47087415	10	26174										
NUP133	55746	hgsc.bcm.edu	37	chr1	229633911	229633912	+	Missense_Mutation	DNP	CC	CC	AA													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cactactaggagataaaattCcaaaaagagaagaaactttt							TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:229633911_229633912CC>AA	ENST00000261396.3	-	6	881_882	c.790_791GG>TT	c.(790-792)GGa>TTa	p.G264L	NUP133_ENST00000537506.1_Missense_Mutation_p.G248L	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	264					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.G264*(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				AGATAAAATTCCAAAAAGAGAA	0.356																																					p.G264V|p.G264X		Atlas-SNP	.											.|NUP133,colon,carcinoma,0,1	NUP133	111	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G791T|c.G790T						.																																			SO:0001583	missense	55746	exon6			AAAATTCCAAAAA|AAATTCCAAAAAG		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.790_791delinsAA	chr1.hg19:g.229633911_229633912delinsAA	ENSP00000261396:p.Gly264Leu	113.0	0.0		163.0|164.0	46.0|47.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000261396.3	hg19	CCDS1579.1																																																																																			.	.		0.356	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		AA	229633912	CC	AA	229633911	3	1	174	1	0	0	0	0	1	0	0	0	10763	855	30	3	2763	3	NUP133	1	229633911	Missense_Mutation	DNP	CC	TCGA-DD-AACX-01A-11D-A40R-10	27470705	229633911	19616710	11	26175										
CEP170	9859	hgsc.bcm.edu	37	chr1	243328222	243328222	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tactgagggctgtcttattcTcccactggactgaacaaatt	8	10	2	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:243328222T>A	ENST00000366542.1	-	13	3091	c.3040A>T	c.(3040-3042)Aga>Tga	p.R1014*	CEP170_ENST00000366544.1_Nonsense_Mutation_p.R916*|CEP170_ENST00000366543.1_Nonsense_Mutation_p.R916*|CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000422938.1_RNA|RP11-261C10.4_ENST00000437499.1_RNA	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	1014	Targeting to microtubules.					centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			TGTCTTATTCTCCCACTGGAC	0.403																																					p.R1014X		Atlas-SNP	.											.	CEP170	153	.	0			c.A3040T						.						154	137	142					1																	243328222		1903	4116	6019	SO:0001587	stop_gained	9859	exon13			TTATTCTCCCACT	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.3040A>T	chr1.hg19:g.243328222T>A	ENSP00000355500:p.Arg1014*	361.0	0.0		484.0	255.0	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Nonsense_Mutation	SNP	ENST00000366542.1	hg19	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	T	31	5.078262	0.94000	.	.	ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543	.	.	.	4.37	3.21	0.36854	.	0.108685	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.9387	10.3055	0.43678	0.0:0.0:0.166:0.834	.	.	.	.	X	1014;916;916	.	ENSP00000355500:R1014X	R	-	1	2	CEP170	241394845	1.000000	0.71417	0.977000	0.42913	0.597000	0.36814	2.064000	0.41432	0.680000	0.31366	0.454000	0.30748	AGA	.	.		0.403	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		A	243328222	T	A	243328222	4	1	174	1	0	0	0	0	0	1	0	0	3252	1559	54	4	1776	4	CEP170	1	243328222	Nonsense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	13694311	243328222	5922399	12	26176										
OR2W5	441932	hgsc.bcm.edu	37	chr1	247655265	247655265	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	agttcctgactctcttctacAccatcgtcattcccagcatc	4	16	3	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr1:247655265A>G	ENST00000522351.1	+	0	896							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			TCTCTTCTACACCATCGTCAT	0.522																																					p.H279R		Atlas-SNP	.											.	OR2W5	97	.	0			c.A836G						.						121	109	113					1																	247655265		2203	4300	6503			441932	exon1			TTCTACACCATCG			1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"GPCR / Class A : Olfactory receptors"	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		chr1.hg19:g.247655265A>G		168.0	0.0		241.0	70.0	NM_001004698	B9EH85	Missense_Mutation	SNP	ENST00000522351.1	hg19																																																																																				.	.		0.522	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698		G	247655265	A	G	247655265	1	3	174	0	1	0	0	0	0	0	0	0	11043	159	6	2		2	OR2W5	1	247655265	RNA	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	4327043	247655265	1595356	13	26177										
PUM2	23369	hgsc.bcm.edu	37	chr2	20507799	20507800	+	Frame_Shift_Ins	INS	-	-	TT													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tgttgagctgcagttaactgINSttgaactgttagtgcattag					rs149498911	byFrequency	TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr2:20507799_20507800insTT	ENST00000361078.2	-	6	844_845	c.822_823insAA	c.(820-825)caacagfs	p.Q275fs	PUM2_ENST00000338086.5_Frame_Shift_Ins_p.Q275fs|PUM2_ENST00000536417.1_Frame_Shift_Ins_p.Q219fs|PUM2_ENST00000420234.1_5'Flank|PUM2_ENST00000403432.1_Frame_Shift_Ins_p.Q275fs|PUM2_ENST00000319801.5_Frame_Shift_Ins_p.Q275fs			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	275					regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCAGTTAACTGTTGAACTGTTA	0.361																																					p.Q275fs		Atlas-INDEL	.											.	PUM2	91	.	0			c.823_824insAA						.																																			SO:0001589	frameshift_variant	23369	exon6			.	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"pumilio (Drosphila) homolog 2", "pumilio homolog 2 (Drosophila)"			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.821_822dupAA	chr2.hg19:g.20507800_20507801dupTT	ENSP00000354370:p.Gln275fs	57.0	0.0		55.0	23.0	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Frame_Shift_Ins	INS	ENST00000361078.2	hg19																																																																																				.	.		0.361	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		TT	20507800	-	TT	20507799	7	5	174	1	0	1	1	0	0	0	0	0	12841	1386	48	0	2431	0	PUM2	2	20507799	Frame_Shift_Ins	INS	-	TCGA-DD-AACX-01A-11D-A40R-10		20507799	222691574	14	26178										
EIF2AK2	5610	hgsc.bcm.edu	37	chr2	37349710	37349710	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ctcaagagaatcatcactggTctcaggatcataatcaaatc	6	10	6	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr2:37349710T>C	ENST00000233057.4	-	12	1328	c.1006A>G	c.(1006-1008)Acc>Gcc	p.T336A	EIF2AK2_ENST00000405334.1_Missense_Mutation_p.T295A|EIF2AK2_ENST00000395127.2_Missense_Mutation_p.T336A	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2	336	2 X 13 AA approximate repeats.|Interaction with TRAF5.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|evasion or tolerance by virus of host immune response (GO:0030683)|innate immune response (GO:0045087)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production (GO:0001819)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of hematopoietic progenitor cell differentiation (GO:1901532)|regulation of hematopoietic stem cell differentiation (GO:1902036)|regulation of hematopoietic stem cell proliferation (GO:1902033)|regulation of NLRP3 inflammasome complex assembly (GO:1900225)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)	22		all_hematologic(82;0.248)				TCATCACTGGTCTCAGGATCA	0.373																																					p.T336A		Atlas-SNP	.											.	EIF2AK2	54	.	0			c.A1006G						.						173	159	164					2																	37349710		2203	4300	6503	SO:0001583	missense	5610	exon12			CACTGGTCTCAGG	BC057805	CCDS1786.1, CCDS46259.1	2p22-p21	2014-06-12	2005-01-19	2005-01-19	ENSG00000055332	ENSG00000055332			9437	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 83"	176871	"protein kinase, interferon-inducible double stranded RNA dependent"	PRKR		1351683	Standard	NM_001135651		Approved	PKR, EIF2AK1, PPP1R83	uc010fac.3	P19525	OTTHUMG00000100962	ENST00000233057.4:c.1006A>G	chr2.hg19:g.37349710T>C	ENSP00000233057:p.Thr336Ala	74.0	0.0		111.0	49.0	NM_001135651	A8K3P0|D6W584|E9PC80|Q52M43|Q7Z6F6|Q9UIR4	Missense_Mutation	SNP	ENST00000233057.4	hg19	CCDS1786.1	.	.	.	.	.	.	.	.	.	.	T	0.839	-0.742478	0.03088	.	.	ENSG00000055332	ENST00000233057;ENST00000395127;ENST00000405334	T;T;T	0.76060	-0.95;-0.95;-0.99	2.53	-0.322	0.12713	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	3.067170	0.01163	N	0.006689	T	0.53965	0.1829	N	0.13299	0.325	0.09310	N	1	B;B;B	0.12013	0.004;0.0;0.005	B;B;B	0.08055	0.003;0.001;0.002	T	0.41910	-0.9482	10	0.08837	T	0.75	3.372	5.1114	0.14811	0.0:0.1223:0.1964:0.6813	.	336;336;295	Q8IW76;P19525;E9PC80	.;E2AK2_HUMAN;.	A	336;336;295	ENSP00000233057:T336A;ENSP00000378559:T336A;ENSP00000385014:T295A	ENSP00000233057:T336A	T	-	1	0	EIF2AK2	37203214	0.010000	0.17322	0.047000	0.18901	0.093000	0.18481	0.324000	0.19610	0.013000	0.14918	0.477000	0.44152	ACC	.	.		0.373	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	NM_002759		C	37349710	T	C	37349710	3	2	174	1	0	0	0	0	1	0	0	0	4999	1667	58	2	673	2	EIF2AK2	2	37349710	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	16841911	37349710	205849663	15	26179										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	catggccgggcgagctggagGaggaggaggaggaggaggag	24	5	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						.						3	4	4					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	159.0	0.0		205.0	13.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73613036	G	C	73613036	3	2	174	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	36263326	73613036	169586337	16	26180										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84960668	84960668	+	Frame_Shift_Del	DEL	A	A	-													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	agtttttcacggacttacccAaaatatattgtcacatccta							TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr2:84960668delA	ENST00000237449.6	+	61	10315	c.10307delA	c.(10306-10308)caafs	p.Q3436fs	DNAH6_ENST00000389394.3_Frame_Shift_Del_p.Q3436fs			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3436					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GGACTTACCCAAAATATATTG	0.433																																					p.Q3436fs		Atlas-INDEL	.											.	DNAH6	194	.	0			c.10306delC						.						151	123	131					2																	84960668		692	1591	2283	SO:0001589	frameshift_variant	1768	exon62			.	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.10307delA	chr2.hg19:g.84960668delA	ENSP00000237449:p.Gln3436fs	121.0	0.0		138.0	48.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Frame_Shift_Del	DEL	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.433	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		-	84960668	A	-	84960668	7	5	174	1	0	1	0	1	0	0	0	0	4607	130	5	0	10549	0	DNAH6	2	84960668	Frame_Shift_Del	DEL	A	TCGA-DD-AACX-01A-11D-A40R-10	11347632	84960668	158238705	17	26181										
RETSAT	54884	hgsc.bcm.edu	37	chr2	85571364	85571364	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cgggacgtgcagccccacctGggaatcggtcctcccaggtc	13	16	0	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr2:85571364G>A	ENST00000295802.4	-	8	1476	c.1364C>T	c.(1363-1365)cCa>cTa	p.P455L	RETSAT_ENST00000263854.6_Missense_Mutation_p.P455L|RETSAT_ENST00000475624.2_5'UTR|RETSAT_ENST00000457495.2_Missense_Mutation_p.P394L	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	455					oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	AGCCCCACCTGGGAATCGGTC	0.607																																					p.P455L		Atlas-SNP	.											.	RETSAT	56	.	0			c.C1364T						.						70	72	71					2																	85571364		2203	4300	6503	SO:0001583	missense	54884	exon8			CCACCTGGGAATC	AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	1.3.99.23		25991	protein-coding gene	gene with protein product						12975309, 15358783	Standard	NM_017750		Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.1364C>T	chr2.hg19:g.85571364G>A	ENSP00000295802:p.Pro455Leu	118.0	0.0		136.0	64.0	NM_017750	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Missense_Mutation	SNP	ENST00000295802.4	hg19	CCDS1972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.2|23.2	4.392273|4.392273	0.83011|0.83011	.|.	.|.	ENSG00000042445|ENSG00000042445	ENST00000295802;ENST00000263854;ENST00000457495|ENST00000449375	T;T|.	0.32988|.	1.43;1.43|.	4.58|4.58	4.58|4.58	0.56647|0.56647	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.82678|.	0.5089|.	M|M	0.89478|0.89478	3.035|3.035	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.83275|.	0.994;0.994;0.996|.	D|.	0.86103|.	0.1557|.	10|.	0.87932|.	D|.	0|.	-3.2977|-3.2977	15.2265|15.2265	0.73357|0.73357	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	394;394;455|.	G5E9N3;B4DKE1;Q6NUM9|.	.;.;RETST_HUMAN|.	L|X	455;455;394|244	ENSP00000295802:P455L;ENSP00000405040:P394L|.	ENSP00000263854:P455L|.	P|Q	-|-	2|1	0|0	RETSAT|RETSAT	85424875|85424875	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	5.498000|5.498000	0.66931|0.66931	2.252000|2.252000	0.74401|0.74401	0.561000|0.561000	0.74099|0.74099	CCA|CAG	.	.		0.607	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750		A	85571364	G	A	85571364	3	1	174	1	0	0	0	0	1	0	0	0	13253	1348	47	3	484	3	RETSAT	2	85571364	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	610696	85571364	157628009	18	26182										
CCDC138	165055	hgsc.bcm.edu	37	chr2	109411169	109411170	+	Frame_Shift_Ins	INS	-	-	AATTG													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	attatttcagatacatctgaINSaattgcaggtaagaactaaa							TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr2:109411169_109411170insAATTG	ENST00000295124.4	+	5	628_629	c.568_569insAATTG	c.(568-570)aaafs	p.-191fs	CCDC138_ENST00000412964.2_Frame_Shift_Ins_p.-191fs	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138											endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						GATACATCTGAAATTGCAGGTA	0.312																																					p.K190fs		Atlas-INDEL	.											.	CCDC138	49	.	0			c.568_569insAATTG						.																																			SO:0001589	frameshift_variant	165055	exon5			.	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.569_573dupAATTG	chr2.hg19:g.109411170_109411174dupAATTG	ENSP00000295124:p.Leu191fs	81.0	0.0		71.0	26.0	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Frame_Shift_Ins	INS	ENST00000295124.4	hg19	CCDS2080.1																																																																																			.	.		0.312	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978		AATTG	109411170	-	AATTG	109411169	7	5	174	1	0	1	1	0	0	0	0	0	2774	247	9	0	586	0	CCDC138	2	109411169	Frame_Shift_Ins	INS	-	TCGA-DD-AACX-01A-11D-A40R-10	23839805	109411169	133788204	19	26183										
KCNJ3	3760	hgsc.bcm.edu	37	chr2	155711241	155711241	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ttttctcttttcttgtagggAtgacttgtcaagctcgaaca	8	8	3	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr2:155711241A>G	ENST00000295101.2	+	3	1399	c.922A>G	c.(922-924)Atg>Gtg	p.M308V	KCNJ3_ENST00000493505.1_3'UTR|KCNJ3_ENST00000544049.1_Silent_p.G235G	NM_001260509.1|NM_002239.3	NP_001247438.1|NP_002230.1	P48549	KCNJ3_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 3	308					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to electrical stimulus (GO:0051602)|synaptic transmission (GO:0007268)	external side of plasma membrane (GO:0009897)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)			breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(30)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	54					Halothane(DB01159)	TCTTGTAGGGATGACTTGTCA	0.348																																					p.M308V		Atlas-SNP	.											.	KCNJ3	126	.	0			c.A922G						.						94	96	96					2																	155711241		2203	4300	6503	SO:0001583	missense	3760	exon3			GTAGGGATGACTT	U50964	CCDS2200.1, CCDS58733.1	2q24.1	2011-07-05			ENSG00000162989	ENSG00000162989		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6264	protein-coding gene	gene with protein product		601534				8088798, 16382105	Standard	NM_002239		Approved	Kir3.1, GIRK1, KGA	uc002tyv.2	P48549	OTTHUMG00000131937	ENST00000295101.2:c.922A>G	chr2.hg19:g.155711241A>G	ENSP00000295101:p.Met308Val	83.0	0.0		59.0	25.0	NM_002239	B4DEW7|Q8TBI0	Missense_Mutation	SNP	ENST00000295101.2	hg19	CCDS2200.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.119505	0.56505	.	.	ENSG00000162989	ENST00000295101	D	0.93763	-3.28	5.7	5.7	0.88788	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.035544	0.85682	D	0.000000	D	0.95175	0.8436	M	0.91972	3.26	0.80722	D	1	P	0.41265	0.744	B	0.42495	0.389	D	0.95750	0.8791	10	0.72032	D	0.01	.	15.1574	0.72755	1.0:0.0:0.0:0.0	.	308	P48549	IRK3_HUMAN	V	308	ENSP00000295101:M308V	ENSP00000295101:M308V	M	+	1	0	KCNJ3	155419487	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	9.339000	0.96797	2.184000	0.69523	0.528000	0.53228	ATG	.	.		0.348	KCNJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254890.2	NM_002239		G	155711241	A	G	155711241	3	3	174	1	0	0	0	0	1	0	0	0	8061	333	12	2	932	2	KCNJ3	2	155711241	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	46300072	155711241	87488132	20	26184										
SP100	6672	hgsc.bcm.edu	37	chr2	231368974	231368974	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gtgacctgtggtgaggtgaaGggcactctatataaggagcg	16	6	1	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr2:231368974G>A	ENST00000264052.5	+	21	2194	c.1839G>A	c.(1837-1839)aaG>aaA	p.K613K	RN7SL834P_ENST00000461450.2_RNA|SP100_ENST00000340126.4_Silent_p.K613K|SP100_ENST00000409112.1_Silent_p.K613K	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	613	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.				cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		GTGAGGTGAAGGGCACTCTAT	0.383																																					p.K613K		Atlas-SNP	.											.	SP100	167	.	0			c.G1839A						.						168	172	170					2																	231368974		2203	4300	6503	SO:0001819	synonymous_variant	6672	exon21			GGTGAAGGGCACT	AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"Zinc fingers, PHD-type"	11206	protein-coding gene	gene with protein product		604585	"nuclear antigen Sp100"			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.1839G>A	chr2.hg19:g.231368974G>A		123.0	0.0		113.0	35.0	NM_001080391	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Silent	SNP	ENST00000264052.5	hg19	CCDS2477.1																																																																																			.	.		0.383	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113		A	231368974	G	A	231368974	2	1	174	1	0	0	0	0	0	0	0	1	14975	991	35	3		3	SP100	2	231368974	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	75657733	231368974	11830399	21	26185										
CLASP2	23122	hgsc.bcm.edu	37	chr3	33759454	33759454	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ggccgccgacgtccttctgcTgcacctgggcgcagaagtac	13	15	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr3:33759454T>A	ENST00000468888.2	-	1	87	c.41A>T	c.(40-42)cAg>cTg	p.Q14L	CLASP2_ENST00000307312.7_5'UTR|CLASP2_ENST00000399362.4_Missense_Mutation_p.Q14L|CLASP2_ENST00000359576.5_Missense_Mutation_p.Q14L			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	0					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						GTCCTTCTGCTGCACCTGGGC	0.726																																					p.Q14L		Atlas-SNP	.											.	CLASP2	138	.	0			c.A41T						.						3	4	4					3																	33759454		1570	3576	5146	SO:0001583	missense	23122	exon1			TTCTGCTGCACCT	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.41A>T	chr3.hg19:g.33759454T>A	ENSP00000419974:p.Gln14Leu	98.0	0.0		90.0	37.0	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	hg19		.	.	.	.	.	.	.	.	.	.	T	15.95	2.982539	0.53827	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576	T;T;T	0.64085	-0.08;-0.08;-0.08	4.09	-0.376	0.12505	.	0.547964	0.15178	N	0.276247	T	0.29556	0.0737	N	0.01668	-0.77	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.03566	-1.1024	10	0.27082	T	0.32	1.3447	9.4237	0.38567	0.5562:0.0:0.0:0.4438	.	14	F5H604	.	L	14	ENSP00000419974:Q14L;ENSP00000382297:Q14L;ENSP00000352581:Q14L	ENSP00000352581:Q14L	Q	-	2	0	CLASP2	33734458	0.952000	0.32445	0.997000	0.53966	0.994000	0.84299	1.374000	0.34283	-0.170000	0.10816	0.459000	0.35465	CAG	.	.		0.726	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		A	33759454	T	A	33759454	3	1	174	1	0	0	0	0	1	0	0	0	3457	1580	55	4	4631	4	CLASP2	3	33759454	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10		33759454	164262976	22	26186										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266107	41266107	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gtcttacctggactctggaaTccattctggtgccactacca	8	13	3	0	rs121913416		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr3:41266107T>G	ENST00000349496.5	+	3	384	c.104T>G	c.(103-105)aTc>aGc	p.I35S	CTNNB1_ENST00000453024.1_Missense_Mutation_p.I28S|CTNNB1_ENST00000405570.1_Missense_Mutation_p.I35S|CTNNB1_ENST00000396183.3_Missense_Mutation_p.I35S|CTNNB1_ENST00000396185.3_Missense_Mutation_p.I35S	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	35			I -> S (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.I35S(20)|p.I35T(13)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.I35_S37>T(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.S29_H36del(1)|p.I35_T41del(1)|p.I35N(1)|p.I35_G38del(1)|p.I35K(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GACTCTGGAATCCATTCTGGT	0.493		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.I35S	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	169	Deletion - In frame(107)|Substitution - Missense(35)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(3)	liver(118)|large_intestine(19)|salivary_gland(12)|stomach(7)|soft_tissue(2)|small_intestine(2)|endometrium(2)|skin(2)|adrenal_gland(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|pituitary(1)|kidney(1)	c.T104G						.						95	80	85					3																	41266107		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTGGAATCCATTC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.104T>G	chr3.hg19:g.41266107T>G	ENSP00000344456:p.Ile35Ser	138.0	0.0		141.0	48.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.188620	0.78789	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	M	0.79614	2.46	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.73949	-0.3821	10	0.87932	D	0	-3.5499	16.0677	0.80897	0.0:0.0:0.0:1.0	.	35	P35222	CTNB1_HUMAN	S	28;35;35;35;35;28;35;35;35	ENSP00000400508:I28S;ENSP00000385604:I35S;ENSP00000412219:I35S;ENSP00000379486:I35S;ENSP00000344456:I35S;ENSP00000411226:I28S;ENSP00000379488:I35S;ENSP00000409302:I35S;ENSP00000401599:I35S	ENSP00000344456:I35S	I	+	2	0	CTNNB1	41241111	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	ATC	.	.		0.493	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266107	T	G	41266107	3	3	174	1	0	0	0	0	1	0	0	0	4018	1435	50	5	110	5	CTNNB1	3	41266107	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	7506653	41266107	156756323	23	26187										
MST1R	4486	hgsc.bcm.edu	37	chr3	49936356	49936356	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	acgactgacatcccgctgcaCgggctgcccactgtcaccca	9	18	1	1	rs148258933		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr3:49936356C>T	ENST00000296474.3	-	3	1519	c.1492G>A	c.(1492-1494)Gtg>Atg	p.V498M	MST1R_ENST00000344206.4_Missense_Mutation_p.V498M|CTD-2330K9.2_ENST00000435478.1_RNA	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	498	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		TCCCGCTGCACGGGCTGCCCA	0.592																																					p.V498M		Atlas-SNP	.											.	MST1R	205	.	0			c.G1492A						.	C	MET/VAL	0,4406		0,0,2203	94	95	94		1492	-2.1	0	3	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	missense	MST1R	NM_002447.2	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	498/1401	49936356	1,13005	2203	4300	6503	SO:0001583	missense	4486	exon3			GCTGCACGGGCTG	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.1492G>A	chr3.hg19:g.49936356C>T	ENSP00000296474:p.Val498Met	209.0	0.0		191.0	87.0	NM_001244937	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	hg19	CCDS2807.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.021501	0.54576	0.0	1.16E-4	ENSG00000164078	ENST00000296474;ENST00000344206	T;T	0.12569	2.67;2.67	5.93	-2.06	0.07298	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.582492	0.18236	N	0.147391	T	0.32102	0.0818	M	0.80183	2.485	0.09310	N	1	D;D;D	0.89917	1.0;0.991;0.994	D;D;P	0.73380	0.98;0.911;0.903	T	0.08186	-1.0734	10	0.87932	D	0	0.3246	9.2444	0.37515	0.1068:0.7876:0.0:0.1055	.	498;498;498	Q04912-6;Q04912-5;Q04912	.;.;RON_HUMAN	M	498	ENSP00000296474:V498M;ENSP00000341325:V498M	ENSP00000296474:V498M	V	-	1	0	MST1R	49911360	0.000000	0.05858	0.011000	0.14972	0.711000	0.40976	-0.324000	0.07986	-0.805000	0.04404	0.561000	0.74099	GTG	.	C|1.000;T|0.000		0.592	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			T	49936356	C	T	49936356	3	4	174	1	0	0	0	0	1	0	0	0	9900	536	19	1	2782	1	MST1R	3	49936356	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	8670249	49936356	148086074	24	26188										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52356615	52356615	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	actatgggttgggaaatcctCcagcccttgaccccaagctc	9	14	0	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr3:52356615C>A	ENST00000420323.2	+	2	418	c.157C>A	c.(157-159)Cca>Aca	p.P53T		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	53	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGGAAATCCTCCAGCCCTTGA	0.607																																					p.P53T		Atlas-SNP	.											.	DNAH1	534	.	0			c.C157A						.						56	60	59					3																	52356615		1872	4091	5963	SO:0001583	missense	25981	exon2			AATCCTCCAGCCC	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.157C>A	chr3.hg19:g.52356615C>A	ENSP00000401514:p.Pro53Thr	85.0	0.0		79.0	33.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	C	9.990	1.230557	0.22542	.	.	ENSG00000114841	ENST00000420323	T	0.26810	1.71	3.37	2.46	0.29980	.	2.465280	0.01785	N	0.031966	T	0.24314	0.0589	L	0.44542	1.39	0.09310	N	1	B;B	0.30281	0.079;0.275	B;B	0.33254	0.011;0.16	T	0.19614	-1.0300	10	0.23891	T	0.37	.	4.7207	0.12917	0.0:0.6502:0.2281:0.1217	.	53;53	C9JXH6;Q9P2D7-3	.;.	T	53	ENSP00000401514:P53T	ENSP00000401514:P53T	P	+	1	0	DNAH1	52331655	0.003000	0.15002	0.050000	0.19076	0.275000	0.26752	0.401000	0.20948	0.965000	0.38133	0.491000	0.48974	CCA	.	.		0.607	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52356615	C	A	52356615	3	1	174	1	0	0	0	0	1	0	0	0	4599	855	30	3	159	3	DNAH1	3	52356615	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	2420259	52356615	145665815	25	26189										
TKT	7086	hgsc.bcm.edu	37	chr3	53267208	53267208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cttgaaggtcttggcaatgaTggctgttggctggtgcttgg	16	6	1	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr3:53267208T>C	ENST00000462138.1	-	6	800	c.712A>G	c.(712-714)Atc>Gtc	p.I238V	TKT_ENST00000423525.2_Missense_Mutation_p.I238V|TKT_ENST00000423516.1_Missense_Mutation_p.I246V|TKT_ENST00000461139.1_5'Flank|TKT_ENST00000296289.6_Missense_Mutation_p.I191V			P29401	TKT_HUMAN	transketolase	238					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		TTGGCAATGATGGCTGTTGGC	0.617																																					p.I246V	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.A736G						.						107	93	98					3																	53267208		2203	4300	6503	SO:0001583	missense	7086	exon7			CAATGATGGCTGT		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"Wernicke-Korsakoff syndrome"	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.712A>G	chr3.hg19:g.53267208T>C	ENSP00000417773:p.Ile238Val	70.0	0.0		91.0	37.0	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Missense_Mutation	SNP	ENST00000462138.1	hg19	CCDS2871.1	.	.	.	.	.	.	.	.	.	.	T	13.53	2.264783	0.40095	.	.	ENSG00000163931	ENST00000462138;ENST00000423525;ENST00000423516;ENST00000296289;ENST00000414014	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	5.9	0.874	0.19124	Transketolase, N-terminal (1);	0.140001	0.64402	N	0.000005	T	0.33235	0.0856	M	0.62266	1.93	0.58432	D	0.999999	B;B;B	0.10296	0.002;0.003;0.003	B;B;B	0.20577	0.005;0.03;0.014	T	0.14671	-1.0464	10	0.41790	T	0.15	-26.8545	10.2209	0.43196	0.0:0.3227:0.0:0.6773	.	246;155;238	E7EPA7;B3KSI4;P29401	.;.;TKT_HUMAN	V	238;238;246;191;72	ENSP00000417773:I238V;ENSP00000405455:I238V;ENSP00000391481:I246V;ENSP00000296289:I191V	ENSP00000296289:I191V	I	-	1	0	TKT	53242248	1.000000	0.71417	0.970000	0.41538	0.987000	0.75469	3.518000	0.53451	0.156000	0.19299	0.528000	0.53228	ATC	.	.		0.617	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1			C	53267208	T	C	53267208	3	2	174	1	0	0	0	0	1	0	0	0	15949	1464	51	2	1195	2	TKT	3	53267208	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	910593	53267208	144755222	26	26190										
MRPS22	56945	hgsc.bcm.edu	37	chr3	139074588	139074588	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	atccagatggccagtcggctCaaggggccaaggatcaggct	14	11	2	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr3:139074588C>A	ENST00000495075.1	+	9	1375	c.943C>A	c.(943-945)Caa>Aaa	p.Q315K	MRPS22_ENST00000478464.1_Missense_Mutation_p.Q274K|MRPS22_ENST00000310776.4_Missense_Mutation_p.Q315K|MRPS22_ENST00000465056.1_Missense_Mutation_p.Q314K			P82650	RT22_HUMAN	mitochondrial ribosomal protein S22	315						mitochondrial ribosome (GO:0005761)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12						CCAGTCGGCTCAAGGGGCCAA	0.423																																					p.Q315K		Atlas-SNP	.											.	MRPS22	40	.	0			c.C943A						.						72	72	72					3																	139074588		2203	4300	6503	SO:0001583	missense	56945	exon7			TCGGCTCAAGGGG	AF226045	CCDS3107.1	3q23	2012-09-13			ENSG00000175110	ENSG00000175110		"Mitochondrial ribosomal proteins / small subunits"	14508	protein-coding gene	gene with protein product		605810				11175783	Standard	NM_020191		Approved	MRP-S22, GK002, C3orf5, GIBT	uc003etb.3	P82650	OTTHUMG00000159910	ENST00000495075.1:c.943C>A	chr3.hg19:g.139074588C>A	ENSP00000418008:p.Gln315Lys	196.0	0.0		178.0	83.0	NM_020191	Q9H3I1	Missense_Mutation	SNP	ENST00000495075.1	hg19	CCDS3107.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.31|18.31	3.596833|3.596833	0.66332|0.66332	.|.	.|.	ENSG00000175110|ENSG00000184432	ENST00000495075;ENST00000310776;ENST00000465056;ENST00000478464|ENST00000503326	D;D;D;D|.	0.82619|.	-1.63;-1.63;-1.62;-1.61|.	5.76|5.76	3.68|3.68	0.42216|0.42216	.|.	0.269566|.	0.41712|.	D|.	0.000834|.	T|.	0.35566|.	0.0936|.	N|N	0.12569|0.12569	0.235|0.235	0.80722|0.80722	D|D	1|1	B;B;B|.	0.10296|.	0.001;0.003;0.002|.	B;B;B|.	0.10450|.	0.002;0.005;0.002|.	T|.	0.06807|.	-1.0806|.	10|.	0.06099|.	T|.	0.92|.	-6.8611|-6.8611	8.1915|8.1915	0.31370|0.31370	0.3994:0.4882:0.1124:0.0|0.3994:0.4882:0.1124:0.0	.|.	274;314;315|.	G5E9W7;G5E9V5;P82650|.	.;.;RT22_HUMAN|.	K|L	315;315;314;274|96	ENSP00000418008:Q315K;ENSP00000310785:Q315K;ENSP00000418233:Q314K;ENSP00000419303:Q274K|.	ENSP00000310785:Q315K|.	Q|X	+|-	1|2	0|2	MRPS22|COPB2	140557278|140557278	0.990000|0.990000	0.36364|0.36364	0.985000|0.985000	0.45067|0.45067	0.980000|0.980000	0.70556|0.70556	1.570000|1.570000	0.36439|0.36439	2.723000|2.723000	0.93209|0.93209	0.655000|0.655000	0.94253|0.94253	CAA|TGA	.	.		0.423	MRPS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358120.1	NM_020191		A	139074588	C	A	139074588	3	1	174	1	0	0	0	0	1	0	0	0	9842	827	29	3	969	3	MRPS22	3	139074588	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	85807380	139074588	58947842	27	26191										
CCNL1	57018	hgsc.bcm.edu	37	chr3	156867722	156867722	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	aatttggcttcttgtaaggcTacttttcttttttctacttc	5	8	3	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr3:156867722T>C	ENST00000295926.3	-	8	1042	c.924A>G	c.(922-924)gtA>gtG	p.V308V	CCNL1_ENST00000479052.1_5'Flank|CCNL1_ENST00000461804.1_Silent_p.V308V	NM_020307.2	NP_064703.1	Q9UK58	CCNL1_HUMAN	cyclin L1	308					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|nucleus (GO:0005634)				NS(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308)			CTTGTAAGGCTACTTTTCTTT	0.403																																					p.V308V		Atlas-SNP	.											.	CCNL1	53	.	0			c.A924G						.						117	120	119					3																	156867722		2203	4300	6503	SO:0001819	synonymous_variant	57018	exon8			TAAGGCTACTTTT	AF180920	CCDS3178.1	3q25.31	2008-02-05			ENSG00000163660	ENSG00000163660			20569	protein-coding gene	gene with protein product		613384				11980906	Standard	NM_020307		Approved	ania-6a	uc003fbf.3	Q9UK58	OTTHUMG00000158713	ENST00000295926.3:c.924A>G	chr3.hg19:g.156867722T>C		149.0	0.0		140.0	50.0	NM_020307	B3KMY3|Q6NVY9|Q6UWS7|Q8NI48|Q96QT0|Q9NZF3	Silent	SNP	ENST00000295926.3	hg19	CCDS3178.1																																																																																			.	.		0.403	CCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351859.1	NM_020307		C	156867722	T	C	156867722	2	2	174	1	0	0	0	0	0	0	0	1	2933	1509	53	2		2	CCNL1	3	156867722	Silent	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	17793134	156867722	41154708	28	26192										
SERPINI1	5274	hgsc.bcm.edu	37	chr3	167542319	167542319	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	caagttattgtcgaccatccAtttttctttcttatcagaaa	4	9	3	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr3:167542319A>G	ENST00000295777.5	+	8	1556	c.1125A>G	c.(1123-1125)ccA>ccG	p.P375P	SERPINI1_ENST00000488374.1_3'UTR|SERPINI1_ENST00000446050.2_Silent_p.P375P	NM_005025.4	NP_005016.1	Q99574	NEUS_HUMAN	serpin peptidase inhibitor, clade I (neuroserpin), member 1	375					cell death (GO:0008219)|central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|peripheral nervous system development (GO:0007422)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(7)|skin(2)	20						TCGACCATCCATTTTTCTTTC	0.323																																					p.P375P		Atlas-SNP	.											.	SERPINI1	52	.	0			c.A1125G						.						121	116	118					3																	167542319		2203	4300	6503	SO:0001819	synonymous_variant	5274	exon8			CCATCCATTTTTC	Z81326	CCDS3203.1	3q26.1	2014-02-18	2005-08-18		ENSG00000163536	ENSG00000163536		"Serine (or cysteine) peptidase inhibitors"	8943	protein-coding gene	gene with protein product		602445	"serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1"	PI12		24172014	Standard	NM_005025		Approved	neuroserpin	uc003ffa.4	Q99574	OTTHUMG00000158450	ENST00000295777.5:c.1125A>G	chr3.hg19:g.167542319A>G		75.0	0.0		82.0	35.0	NM_005025	A8K217|D3DNP1|Q6AHZ4	Silent	SNP	ENST00000295777.5	hg19	CCDS3203.1	.	.	.	.	.	.	.	.	.	.	A	6.502	0.460851	0.12342	.	.	ENSG00000163536	ENST00000466865	.	.	.	5.57	3.05	0.35203	.	.	.	.	.	T	0.55721	0.1938	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46721	-0.9171	4	.	.	.	.	7.407	0.26995	0.7436:0.0:0.0738:0.1827	.	.	.	.	V	84	.	.	I	+	1	0	SERPINI1	169025013	0.977000	0.34250	1.000000	0.80357	0.697000	0.40408	0.140000	0.16056	0.392000	0.25172	-1.431000	0.01090	ATT	.	.		0.323	SERPINI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351056.1			G	167542319	A	G	167542319	2	3	174	1	0	0	0	0	0	0	0	1	14133	204	8	2		2	SERPINI1	3	167542319	Silent	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	10674597	167542319	30480111	29	26193										
FETUB	26998	hgsc.bcm.edu	37	chr3	186364073	186364073	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cttactttgtggaatacttaAttaaagaatcaccatgtact	5	7	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr3:186364073A>T	ENST00000265029.3	+	5	732	c.631A>T	c.(631-633)Att>Ttt	p.I211F	FETUB_ENST00000382136.3_Missense_Mutation_p.I174F|FETUB_ENST00000450521.1_Missense_Mutation_p.I211F|FETUB_ENST00000382134.3_Missense_Mutation_p.I146F|RP11-134F2.2_ENST00000455926.1_RNA|RP11-134F2.2_ENST00000428501.1_RNA|FETUB_ENST00000539949.1_Missense_Mutation_p.I63F	NM_014375.2	NP_055190.2	Q9UGM5	FETUB_HUMAN	fetuin B	211	Cystatin fetuin-B-type 2. {ECO:0000255|PROSITE-ProRule:PRU00862}.				binding of sperm to zona pellucida (GO:0007339)|negative regulation of endopeptidase activity (GO:0010951)|single fertilization (GO:0007338)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)	20	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		GGAATACTTAATTAAAGAATC	0.418																																					p.I211F		Atlas-SNP	.											.	FETUB	53	.	0			c.A631T						.						145	153	150					3																	186364073		2203	4300	6503	SO:0001583	missense	26998	exon5			TACTTAATTAAAG	AJ242928	CCDS3279.1	3q27.3	2008-05-15			ENSG00000090512	ENSG00000090512			3658	protein-coding gene	gene with protein product		605954				10947975	Standard	XM_005247350		Approved		uc003fqn.3	Q9UGM5	OTTHUMG00000156586	ENST00000265029.3:c.631A>T	chr3.hg19:g.186364073A>T	ENSP00000265029:p.Ile211Phe	115.0	0.0		134.0	59.0	NM_014375	B2RCW6|E9PG06|Q1RMZ0|Q5J876|Q6DK58|Q6GRB6|Q9Y6Z0	Missense_Mutation	SNP	ENST00000265029.3	hg19	CCDS3279.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.627381	0.46944	.	.	ENSG00000090512	ENST00000450521;ENST00000431018;ENST00000539949;ENST00000265029;ENST00000382134;ENST00000382136	T;T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42;1.42	4.97	2.55	0.30701	Proteinase inhibitor I25, cystatin (2);	0.218413	0.32624	N	0.005854	T	0.54351	0.1853	M	0.87180	2.865	0.49051	D	0.999742	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.77557	0.99;0.989;0.989	T	0.54186	-0.8331	10	0.87932	D	0	-21.1983	6.7585	0.23528	0.836:0.0:0.164:0.0	.	174;146;211	E9PG06;E9PG08;Q9UGM5	.;.;FETUB_HUMAN	F	211;63;63;211;146;174	ENSP00000404288:I211F;ENSP00000396581:I63F;ENSP00000443704:I63F;ENSP00000265029:I211F;ENSP00000371569:I146F;ENSP00000371571:I174F	ENSP00000265029:I211F	I	+	1	0	FETUB	187846767	0.991000	0.36638	0.524000	0.27887	0.471000	0.32888	0.637000	0.24659	0.455000	0.26910	-0.242000	0.12053	ATT	.	.		0.418	FETUB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344679.1	NM_014375		T	186364073	A	T	186364073	3	4	174	1	0	0	0	0	1	0	0	0	5829	101	4	4	649	4	FETUB	3	186364073	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	18821754	186364073	11658357	30	26194										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30732375	30732375	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ctttattttccttctttcagAtgcgtctacatccatacatt	3	11	3	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr4:30732375A>T	ENST00000361762.2	+	2	4183	c.3175A>T	c.(3175-3177)Atg>Ttg	p.M1059L	PCDH7_ENST00000543491.1_Intron	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	1059					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						CTTCTTTCAGATGCGTCTACA	0.363																																					p.M1059L		Atlas-SNP	.											.	PCDH7	215	.	0			c.A3175T						.						179	172	174					4																	30732375		2203	4300	6503	SO:0001630	splice_region_variant	5099	exon2			TTTCAGATGCGTC	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.3175-1A>T	chr4.hg19:g.30732375A>T		69.0	0.0		63.0	19.0	NM_002589	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.	.	.	.	.	.	.	.	.	.	A	9.082	0.999611	0.19121	.	.	ENSG00000169851	ENST00000361762	T	0.47528	0.84	5.5	5.5	0.81552	.	.	.	.	.	T	0.23688	0.0573	N	0.03608	-0.345	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.13872	-1.0493	8	.	.	.	.	12.0002	0.53226	1.0:0.0:0.0:0.0	.	1059	O60245	PCDH7_HUMAN	L	1059	ENSP00000355243:M1059L	.	M	+	1	0	PCDH7	30341473	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.842000	0.62831	2.099000	0.63709	0.533000	0.62120	ATG	.	.		0.363	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589	Missense_Mutation	T	30732375	A	T	30732375	5	4	174	1	0	0	0	0	0	0	1	0	11525	347	12	4	3226	4	PCDH7	4	30732375	Splice_Site	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10		30732375	160421901	31	26195										
ARAP2	116984	hgsc.bcm.edu	37	chr4	36230968	36230968	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gtaggtgatattccaattttCtgcagcaggctgtcatttat	9	7	2	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr4:36230968C>T	ENST00000303965.4	-	2	630	c.141G>A	c.(139-141)caG>caA	p.Q47Q		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	47	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TTCCAATTTTCTGCAGCAGGC	0.373																																					p.Q47Q		Atlas-SNP	.											.	ARAP2	210	.	0			c.G141A						.						66	68	68					4																	36230968		2203	4300	6503	SO:0001819	synonymous_variant	116984	exon2			AATTTTCTGCAGC	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.141G>A	chr4.hg19:g.36230968C>T		168.0	0.0		168.0	67.0	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Silent	SNP	ENST00000303965.4	hg19	CCDS3441.1																																																																																			.	.		0.373	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		T	36230968	C	T	36230968	2	4	174	1	0	0	0	0	0	0	0	1	839	912	32	3		3	ARAP2	4	36230968	Silent	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	5498593	36230968	154923308	32	26196										
FRYL	285527	hgsc.bcm.edu	37	chr4	48636346	48636346	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	aacttcaattttcttttcagCttgaacagcaaattctgcaa	4	9	4	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr4:48636346C>A	ENST00000503238.1	-	1	81	c.82G>T	c.(82-84)Gct>Tct	p.A28S	FRYL_ENST00000358350.4_Missense_Mutation_p.A28S|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.A28S|FRYL_ENST00000507711.1_Missense_Mutation_p.A28S|FRYL_ENST00000514783.1_5'Flank			O94915	FRYL_HUMAN	FRY-like	28					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						TTCTTTTCAGCTTGAACAGCA	0.353																																					p.A28S		Atlas-SNP	.											.	FRYL	242	.	0			c.G82T						.						114	106	109					4																	48636346		1856	4093	5949	SO:0001583	missense	285527	exon4			TTTCAGCTTGAAC	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.82G>T	chr4.hg19:g.48636346C>A	ENSP00000426064:p.Ala28Ser	240.0	0.0		229.0	91.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.361678	0.61403	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711;ENST00000505759	T;T;T;T	0.61274	1.08;1.08;1.08;0.12	5.0	5.0	0.66597	.	0.000000	0.64402	U	0.000003	T	0.52757	0.1754	L	0.40543	1.245	0.80722	D	1	B;B;B	0.33238	0.395;0.02;0.403	B;B;B	0.33890	0.172;0.006;0.145	T	0.55755	-0.8091	10	0.51188	T	0.08	.	18.659	0.91465	0.0:1.0:0.0:0.0	.	79;28;28	Q6ZNE6;F2Z2S2;O94915	.;.;FRYL_HUMAN	S	28;28;28;28;120	ENSP00000426064:A28S;ENSP00000351113:A28S;ENSP00000441114:A28S;ENSP00000421584:A28S	ENSP00000351113:A28S	A	-	1	0	FRYL	48331103	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.670000	0.68088	2.475000	0.83589	0.650000	0.86243	GCT	.	.		0.353	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			A	48636346	C	A	48636346	3	1	174	1	0	0	0	0	1	0	0	0	6072	797	28	3	9203	3	FRYL	4	48636346	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	12405378	48636346	142517930	33	26197			1	31		2	2	23	N	G_C	9.522523e-05
FRYL	285527	hgsc.bcm.edu	37	chr4	48636368	48636368	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tgaacagcaaattctgcaaaGaggctcttgatgacatattc	8	8	2	4			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr4:48636368G>T	ENST00000503238.1	-	1	59	c.60C>A	c.(58-60)ctC>ctA	p.L20L	FRYL_ENST00000358350.4_Silent_p.L20L|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Silent_p.L20L|FRYL_ENST00000507711.1_Silent_p.L20L|FRYL_ENST00000514783.1_5'Flank			O94915	FRYL_HUMAN	FRY-like	20					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						ATTCTGCAAAGAGGCTCTTGA	0.373																																					p.L20L		Atlas-SNP	.											.	FRYL	242	.	0			c.C60A						.						119	111	113					4																	48636368		1846	4090	5936	SO:0001819	synonymous_variant	285527	exon4			TGCAAAGAGGCTC	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.60C>A	chr4.hg19:g.48636368G>T		237.0	0.0		229.0	97.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	hg19	CCDS43227.1																																																																																			.	.		0.373	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48636368	G	T	48636368	2	4	174	1	0	0	0	0	0	0	0	1	6072	929	33	3		3	FRYL	4	48636368	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	22	48636368	142517908	34	26198			1	31		2	2	23	N	G_C	9.522523e-05
AFM	173	hgsc.bcm.edu	37	chr4	74364862	74364862	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ggctcacgaagatagctcccCaactctccactgaagaactg	8	14	2	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr4:74364862C>T	ENST00000226355.3	+	11	1414	c.1321C>T	c.(1321-1323)Caa>Taa	p.Q441*		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	441	Albumin 3. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GATAGCTCCCCAACTCTCCAC	0.428																																					p.Q441X		Atlas-SNP	.											.	AFM	101	.	0			c.C1321T						.						188	166	173					4																	74364862		2203	4300	6503	SO:0001587	stop_gained	173	exon11			GCTCCCCAACTCT	L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.1321C>T	chr4.hg19:g.74364862C>T	ENSP00000226355:p.Gln441*	97.0	0.0		75.0	23.0	NM_001133	A8K3E1|Q32MR3|Q4W5C5	Nonsense_Mutation	SNP	ENST00000226355.3	hg19	CCDS3557.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319814	0.60634	.	.	ENSG00000079557	ENST00000226355	.	.	.	5.55	4.65	0.58169	.	0.232350	0.35838	N	0.002956	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	11.5644	0.50796	0.0:0.8203:0.1797:0.0	.	.	.	.	X	441	.	ENSP00000226355:Q441X	Q	+	1	0	AFM	74583726	0.937000	0.31787	0.383000	0.26132	0.056000	0.15407	1.918000	0.40006	2.610000	0.88304	0.655000	0.94253	CAA	.	.		0.428	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			T	74364862	C	T	74364862	4	4	174	1	0	0	0	0	0	1	0	0	361	595	21	3	1363	3	AFM	4	74364862	Nonsense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	25728494	74364862	116789414	35	26199										
SLC7A11	23657	hgsc.bcm.edu	37	chr4	139153531	139153531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gggatatcacagcagtagctGcagggctaaaaaaaaatgta	11	6	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr4:139153531G>A	ENST00000280612.5	-	3	689	c.410C>T	c.(409-411)gCa>gTa	p.A137V		NM_014331.3	NP_055146.1	Q9UPY5	XCT_HUMAN	solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11	137					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|brain development (GO:0007420)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|lens fiber cell differentiation (GO:0070306)|leukocyte migration (GO:0050900)|platelet aggregation (GO:0070527)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	cystine:glutamate antiporter activity (GO:0015327)			breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)	18	all_hematologic(180;0.166)				Acetylcysteine(DB06151)|L-Cystine(DB00138)|Riluzole(DB00740)|Rosuvastatin(DB01098)|Sulfasalazine(DB00795)|Tauroursodeoxycholic acid(DB08834)	AGCAGTAGCTGCAGGGCTAAA	0.363																																					p.A137V		Atlas-SNP	.											.	SLC7A11	40	.	0			c.C410T						.						43	43	43					4																	139153531		2203	4300	6503	SO:0001583	missense	23657	exon3			GTAGCTGCAGGGC	AB026891	CCDS3742.1	4q28-q32	2013-05-22	2011-07-12		ENSG00000151012	ENSG00000151012		"Solute carriers"	11059	protein-coding gene	gene with protein product		607933				10206947, 12763038	Standard	XM_005262875		Approved	xCT	uc021xrw.1	Q9UPY5	OTTHUMG00000133396	ENST00000280612.5:c.410C>T	chr4.hg19:g.139153531G>A	ENSP00000280612:p.Ala137Val	206.0	0.0		224.0	110.0	NM_014331	A8K2U4	Missense_Mutation	SNP	ENST00000280612.5	hg19	CCDS3742.1	.	.	.	.	.	.	.	.	.	.	G	19.55	3.848782	0.71603	.	.	ENSG00000151012	ENST00000280612	D	0.88741	-2.42	5.64	3.86	0.44501	Amino acid permease domain (1);	0.095612	0.64402	D	0.000001	D	0.88440	0.6437	M	0.62723	1.935	0.58432	D	0.999997	B	0.28667	0.219	B	0.33121	0.158	D	0.85667	0.1292	10	0.59425	D	0.04	.	15.9042	0.79406	0.0:0.2646:0.7354:0.0	.	137	Q9UPY5	XCT_HUMAN	V	137	ENSP00000280612:A137V	ENSP00000280612:A137V	A	-	2	0	SLC7A11	139372981	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.640000	0.83355	0.700000	0.31782	0.655000	0.94253	GCA	.	.		0.363	SLC7A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257251.2			A	139153531	G	A	139153531	3	1	174	1	0	0	0	0	1	0	0	0	14709	1319	46	3	1135	3	SLC7A11	4	139153531	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	64788669	139153531	52000745	36	26200										
CCRN4L	25819	hgsc.bcm.edu	37	chr4	139966514	139966514	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gtaaggtcagctctcgatctGctcactgaagaacagattgg	11	9	4	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr4:139966514G>T	ENST00000280614.2	+	3	1375	c.1182G>T	c.(1180-1182)ctG>ctT	p.L394L	ELF2_ENST00000515489.1_Intron	NM_012118.2	NP_036250.2	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like (S. cerevisiae)	394					circadian regulation of gene expression (GO:0032922)|cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|regulation of circadian rhythm (GO:0042752)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|response to extracellular stimulus (GO:0009991)|response to lipopolysaccharide (GO:0032496)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A)-specific ribonuclease activity (GO:0004535)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(2)|large_intestine(3)|lung(3)|ovary(1)	9	all_hematologic(180;0.162)					CTCTCGATCTGCTCACTGAAG	0.473																																					p.L394L	Ovarian(144;566 1842 19130 21379 22209)	Atlas-SNP	.											.	CCRN4L	22	.	0			c.G1182T						.						106	103	104					4																	139966514		2203	4300	6503	SO:0001819	synonymous_variant	25819	exon3			CGATCTGCTCACT	AF183961	CCDS3743.1	4q31.1	2014-06-18	2001-11-28		ENSG00000151014	ENSG00000151014			14254	protein-coding gene	gene with protein product		608468	"CCR4-like (carbon catabolite repression 4, S.cerevisiae)"			10521507	Standard	NM_012118		Approved	CCR4L, Ccr4c	uc003ihl.3	Q9UK39	OTTHUMG00000161271	ENST00000280614.2:c.1182G>T	chr4.hg19:g.139966514G>T		112.0	0.0		92.0	4.0	NM_012118	D3DNY5|Q14D51|Q9HD93|Q9HD94|Q9HD95	Silent	SNP	ENST00000280614.2	hg19	CCDS3743.1																																																																																			.	.		0.473	CCRN4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257231.3	NM_012118		T	139966514	G	T	139966514	2	4	174	1	0	0	0	0	0	0	0	1	2953	1306	46	3		3	CCRN4L	4	139966514	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	812983	139966514	51187762	37	26201										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33616019	33616019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	atactgaaagacagtccctgCcagcttatagttcccgttcc	7	13	0	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:33616019C>T	ENST00000504830.1	-	15	2637	c.2302G>A	c.(2302-2304)Gca>Aca	p.A768T	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.A683T|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	768	Spacer 1.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						ACAGTCCCTGCCAGCTTATAG	0.483										HNSCC(64;0.19)																											p.A768T		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.G2302A						.						145	130	135					5																	33616019		2203	4300	6503	SO:0001583	missense	81792	exon15			TCCCTGCCAGCTT	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.2302G>A	chr5.hg19:g.33616019C>T	ENSP00000422554:p.Ala768Thr	75.0	0.0		99.0	36.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	33	5.288539	0.95517	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.54071	0.59;0.59	5.51	5.51	0.81932	ADAM-TS Spacer 1 (1);	0.157093	0.56097	D	0.000031	T	0.81375	0.4809	H	0.95365	3.66	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.76575	0.982;0.988	D	0.85328	0.1088	10	0.46703	T	0.11	.	19.015	0.92890	0.0:1.0:0.0:0.0	.	683;768	P58397-3;P58397	.;ATS12_HUMAN	T	768;683	ENSP00000422554:A768T;ENSP00000344847:A683T	ENSP00000344847:A683T	A	-	1	0	ADAMTS12	33651776	1.000000	0.71417	0.998000	0.56505	0.925000	0.55904	7.741000	0.84997	2.558000	0.86282	0.561000	0.74099	GCA	.	.		0.483	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		T	33616019	C	T	33616019	3	4	174	1	0	0	0	0	1	0	0	0	257	739	26	3	2522	3	ADAMTS12	5	33616019	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10		33616019	147299241	38	26202										
SPEF2	79925	hgsc.bcm.edu	37	chr5	35807283	35807283	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gccaagaacctggagccaatTgaagtcgctgttctcttgaa	10	10	1	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:35807283T>C	ENST00000356031.3	+	36	5461	c.5307T>C	c.(5305-5307)atT>atC	p.I1769I	SPEF2_ENST00000440995.2_Silent_p.I1764I|SPEF2_ENST00000303129.4_Silent_p.I566I|CTD-2113L7.1_ENST00000510433.1_RNA	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1769					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGGAGCCAATTGAAGTCGCTG	0.363																																					p.I1769I		Atlas-SNP	.											.	SPEF2	324	.	0			c.T5307C						.						144	140	141					5																	35807283		1812	4083	5895	SO:0001819	synonymous_variant	79925	exon36			GCCAATTGAAGTC	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.5307T>C	chr5.hg19:g.35807283T>C		91.0	0.0		85.0	34.0	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Silent	SNP	ENST00000356031.3	hg19	CCDS43309.1																																																																																			.	.		0.363	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		C	35807283	T	C	35807283	2	2	174	1	0	0	0	0	0	0	0	1	15050	1800	63	2		2	SPEF2	5	35807283	Silent	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	2191264	35807283	145107977	39	26203										
CARD6	84674	hgsc.bcm.edu	37	chr5	40843445	40843445	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	aaactagttatagggaaacaGctttgtctgccaggaagaat	10	6	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:40843445G>A	ENST00000254691.5	+	2	674	c.475G>A	c.(475-477)Gct>Act	p.A159T	CARD6_ENST00000381677.3_Missense_Mutation_p.A159T	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	159					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						TAGGGAAACAGCTTTGTCTGC	0.408																																					p.A159T		Atlas-SNP	.											.	CARD6	141	.	0			c.G475A						.						59	61	60					5																	40843445		2203	4300	6503	SO:0001583	missense	84674	exon2			GAAACAGCTTTGT	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.475G>A	chr5.hg19:g.40843445G>A	ENSP00000254691:p.Ala159Thr	157.0	0.0		168.0	59.0	NM_032587	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	hg19	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.257480	0.59321	.	.	ENSG00000132357	ENST00000254691;ENST00000381677;ENST00000444789;ENST00000509771	T;T	0.32272	2.68;1.46	5.12	2.22	0.28083	.	0.779066	0.11238	N	0.584886	T	0.21186	0.0510	L	0.32530	0.975	0.09310	N	1	B	0.26081	0.141	B	0.27170	0.077	T	0.17258	-1.0375	10	0.36615	T	0.2	-2.8775	5.3231	0.15891	0.0943:0.0:0.5411:0.3646	.	159	Q9BX69	CARD6_HUMAN	T	159	ENSP00000254691:A159T;ENSP00000371093:A159T	ENSP00000254691:A159T	A	+	1	0	CARD6	40879202	0.000000	0.05858	0.019000	0.16419	0.025000	0.11179	0.491000	0.22419	1.372000	0.46190	-0.182000	0.12963	GCT	.	.		0.408	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			A	40843445	G	A	40843445	3	1	174	1	0	0	0	0	1	0	0	0	2652	971	34	3	481	3	CARD6	5	40843445	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	5036162	40843445	140071815	40	26204										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101748694	101748694	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	taattataaaaaataattacCtttttttggttttgtgcttt	4	3	0	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:101748694C>G	ENST00000506729.1	-	9	1797	c.1626G>C	c.(1624-1626)aaG>aaC	p.K542N	SLCO6A1_ENST00000379810.1_Splice_Site_p.K289N|SLCO6A1_ENST00000379807.3_Splice_Site_p.K542N|SLCO6A1_ENST00000389019.3_Splice_Site_p.K480N|SLCO6A1_ENST00000513675.1_Splice_Site_p.K289N			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	542	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		aaataatTACCTTTTTTTGGT	0.234																																					p.K542N		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.G1626C						.						9	9	9					5																	101748694		2106	4220	6326	SO:0001630	splice_region_variant	133482	exon9			AATTACCTTTTTT	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1626+1G>C	chr5.hg19:g.101748694C>G		301.0	1.0		290.0	129.0	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	hg19	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.831131	0.32329	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.04758	3.56;3.56;3.56;3.56;3.56	5.17	3.27	0.37495	Major facilitator superfamily domain, general substrate transporter (1);Protease inhibitor, Kazal-type (1);	0.284988	0.28712	N	0.014390	T	0.19604	0.0471	M	0.85945	2.785	0.42524	D	0.993019	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.79108	0.982;0.992;0.99	T	0.00299	-1.1836	9	.	.	.	.	7.0636	0.25139	0.0:0.7265:0.1722:0.1013	.	480;289;542	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	N	542;542;480;289;289	ENSP00000421339:K542N;ENSP00000369135:K542N;ENSP00000373671:K480N;ENSP00000421990:K289N;ENSP00000369138:K289N	.	K	-	3	2	SLCO6A1	101776593	0.992000	0.36948	0.833000	0.33012	0.109000	0.19521	0.645000	0.24782	0.649000	0.30751	0.655000	0.94253	AAG	.	.		0.234	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	Missense_Mutation	G	101748694	C	G	101748694	5	3	174	1	0	0	0	0	0	0	1	0	14747	695	24	4	553	4	SLCO6A1	5	101748694	Splice_Site	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	60905249	101748694	79166566	41	26205										
FBN2	2201	hgsc.bcm.edu	37	chr5	127744443	127744443	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tagcttcccacggtgttggaAcattcaccagtttcacatat	7	11	2	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:127744443A>G	ENST00000508053.1	-	14	1976	c.1002T>C	c.(1000-1002)tgT>tgC	p.C334C	FBN2_ENST00000262464.4_Silent_p.C334C|FBN2_ENST00000508989.1_Silent_p.C301C			P35556	FBN2_HUMAN	fibrillin 2	334	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CGGTGTTGGAACATTCACCAG	0.438																																					p.C334C		Atlas-SNP	.											.	FBN2	858	.	0			c.T1002C						.						153	132	139					5																	127744443		2203	4300	6503	SO:0001819	synonymous_variant	2201	exon8			GTTGGAACATTCA	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.1002T>C	chr5.hg19:g.127744443A>G		266.0	0.0		258.0	109.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	.		0.438	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		G	127744443	A	G	127744443	2	3	174	1	0	0	0	0	0	0	0	1	5711	41	2	2		2	FBN2	5	127744443	Silent	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	25995749	127744443	53170817	42	26206										
PDLIM4	8572	hgsc.bcm.edu	37	chr5	131607555	131607555	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	agctgggcgctccgctgagcGgcctgcaggggctgcccgag	18	14	0	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:131607555G>A	ENST00000253754.3	+	6	806	c.742G>A	c.(742-744)Ggc>Agc	p.G248S	PDLIM4_ENST00000379018.3_Intron|P4HA2_ENST00000471826.1_Intron	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	248							zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|urinary_tract(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCCGCTGAGCGGCCTGCAGGG	0.726																																					p.G248S		Atlas-SNP	.											.	PDLIM4	22	.	0			c.G742A						.						11	14	13					5																	131607555		2177	4238	6415	SO:0001583	missense	8572	exon6			CTGAGCGGCCTGC	AF153882	CCDS4152.1, CCDS47261.1	5q31.1	2008-02-05			ENSG00000131435	ENSG00000131435			16501	protein-coding gene	gene with protein product		603422				9573374	Standard	NM_001131027		Approved	RIL	uc003kwn.3	P50479	OTTHUMG00000059645	ENST00000253754.3:c.742G>A	chr5.hg19:g.131607555G>A	ENSP00000253754:p.Gly248Ser	65.0	0.0		74.0	37.0	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Missense_Mutation	SNP	ENST00000253754.3	hg19	CCDS4152.1	.	.	.	.	.	.	.	.	.	.	G	15.30	2.791317	0.50102	.	.	ENSG00000131435	ENST00000253754	T	0.41065	1.01	5.09	4.01	0.46588	.	0.055489	0.64402	D	0.000001	T	0.23649	0.0572	N	0.25647	0.755	0.80722	D	1	P	0.40083	0.702	B	0.25987	0.065	T	0.08638	-1.0712	10	0.17369	T	0.5	-14.0795	14.4103	0.67111	0.0847:0.0:0.9153:0.0	.	248	P50479	PDLI4_HUMAN	S	248	ENSP00000253754:G248S	ENSP00000253754:G248S	G	+	1	0	PDLIM4	131635454	1.000000	0.71417	0.996000	0.52242	0.942000	0.58702	5.045000	0.64220	2.359000	0.80004	0.655000	0.94253	GGC	.	.		0.726	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687		A	131607555	G	A	131607555	3	1	174	1	0	0	0	0	1	0	0	0	11691	1116	39	1	764	1	PDLIM4	5	131607555	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	3863112	131607555	49307705	43	26207										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140562423	140562423	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tagatcgagaggagctatgcGgtcccactgagccttgcata	12	10	0	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:140562423G>C	ENST00000361016.2	+	1	1444	c.289G>C	c.(289-291)Ggt>Cgt	p.G97R		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	97	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGAGCTATGCGGTCCCACTGA	0.443																																					p.G97R		Atlas-SNP	.											.	PCDHB16	159	.	0			c.G289C						.						56	58	57					5																	140562423		2203	4300	6503	SO:0001583	missense	57717	exon1			CTATGCGGTCCCA	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.289G>C	chr5.hg19:g.140562423G>C	ENSP00000354293:p.Gly97Arg	132.0	0.0		127.0	62.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.574987	0.65878	.	.	ENSG00000196963	ENST00000361016	T	0.30981	1.51	4.84	3.96	0.45880	Cadherin, N-terminal (1);Cadherin (1);	0.000000	0.35040	N	0.003486	T	0.57504	0.2058	M	0.81682	2.555	0.27215	N	0.959804	D	0.76494	0.999	D	0.87578	0.998	T	0.57763	-0.7755	10	0.66056	D	0.02	.	14.9729	0.71249	0.0:0.1437:0.8563:0.0	.	97	Q9NRJ7	PCDBG_HUMAN	R	97	ENSP00000354293:G97R	ENSP00000354293:G97R	G	+	1	0	PCDHB16	140542607	0.005000	0.15991	0.009000	0.14445	0.672000	0.39443	1.172000	0.31908	0.991000	0.38814	0.655000	0.94253	GGT	.	.		0.443	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		C	140562423	G	C	140562423	3	2	174	1	0	0	0	0	1	0	0	0	11550	1116	39	4	291	4	PCDHB16	5	140562423	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	8954868	140562423	40352837	44	26208										
TCOF1	6949	hgsc.bcm.edu	37	chr5	149753925	149753925	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tctgacagtgaggaggagacGccagctgccaaggccctgct	14	12	1	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:149753925G>A	ENST00000504761.2	+	8	1059	c.1059G>A	c.(1057-1059)acG>acA	p.T353T	TCOF1_ENST00000323668.7_Silent_p.T276T|TCOF1_ENST00000377797.3_Silent_p.T353T|TCOF1_ENST00000513346.1_Silent_p.T353T|TCOF1_ENST00000445265.2_Silent_p.T276T|TCOF1_ENST00000439160.2_Silent_p.T353T|TCOF1_ENST00000394269.3_Silent_p.T353T|TCOF1_ENST00000451292.1_Silent_p.T353T			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	353					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGAGGAGACGCCAGCTGCCA	0.632																																					p.T353T		Atlas-SNP	.											.	TCOF1	154	.	0			c.G1059A						.						23	17	19					5																	149753925		2172	4256	6428	SO:0001819	synonymous_variant	6949	exon8			GGAGACGCCAGCT		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.1059G>A	chr5.hg19:g.149753925G>A		216.0	0.0		238.0	96.0	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Silent	SNP	ENST00000504761.2	hg19	CCDS54936.1																																																																																			.	.		0.632	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656		A	149753925	G	A	149753925	2	1	174	1	0	0	0	0	0	0	0	1	15723	1074	38	1		1	TCOF1	5	149753925	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	9191502	149753925	31161335	45	26209										
GALNT10	55568	hgsc.bcm.edu	37	chr5	153795396	153795396	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cctggagacccccagcacacCaagaagttctgctttgatgc	9	14	1	3	rs145718506		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:153795396C>T	ENST00000297107.6	+	11	1694	c.1557C>T	c.(1555-1557)acC>acT	p.T519T	GALNT10_ENST00000377657.3_Silent_p.T192T|SAP30L-AS1_ENST00000519727.1_RNA|GALNT10_ENST00000377661.2_Silent_p.T457T|SAP30L-AS1_ENST00000524264.1_RNA	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	519	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			CCCAGCACACCAAGAAGTTCT	0.527																																					p.T519T		Atlas-SNP	.											.	GALNT10	70	.	0			c.C1557T						.						125	118	120					5																	153795396		2203	4300	6503	SO:0001819	synonymous_variant	55568	exon11			GCACACCAAGAAG	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19873	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 10"	608043	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.1557C>T	chr5.hg19:g.153795396C>T		267.0	1.0		292.0	112.0	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Silent	SNP	ENST00000297107.6	hg19	CCDS4325.1																																																																																			.	C|0.999;G|0.001		0.527	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321		T	153795396	C	T	153795396	2	4	174	1	0	0	0	0	0	0	0	1	6216	581	21	3		3	GALNT10	5	153795396	Silent	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	4041471	153795396	27119864	46	26210										
KIF4B	285643	hgsc.bcm.edu	37	chr5	154396709	154396714	+	In_Frame_Del	DEL	AGCAGT	AGCAGT	-													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	caagggctggtgtgggaacaAgcagtgtgggtgcaggaagc					rs370374254		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	AGCAGT	AGCAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:154396709_154396714delAGCAGT	ENST00000435029.4	+	1	3450_3455	c.3290_3295delAGCAGT	c.(3289-3297)aagcagtgt>agt	p.1097_1099KQC>S		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	1097	Globular. {ECO:0000250}.|Interaction with PRC1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TGTGGGAACAAGCAGTGTGGGTGCAG	0.529																																					p.1097_1098del		Atlas-INDEL	.											.	KIF4B	307	.	0			c.3289_3294del						.																																			SO:0001651	inframe_deletion	285643	exon1			.	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"Kinesins"	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.3290_3295delAGCAGT	chr5.hg19:g.154396709_154396714delAGCAGT	ENSP00000387875:p.Lys1097_Cys1099delinsSer	233.0	0.0		228.0	88.0	NM_001099293		In_Frame_Del	DEL	ENST00000435029.4	hg19	CCDS47324.1																																																																																			.	.		0.529	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			-	154396714	AGCAGT	-	154396709	7	5	174	1	0	1	0	1	0	0	0	0	8313	72	3	0	3292	0	KIF4B	5	154396709	In_Frame_Del	DEL	AGCAGT	TCGA-DD-AACX-01A-11D-A40R-10	601313	154396709	26518551	47	26211										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160059155	160059155	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ctatggagctgctgaaggccAcaggaggctgtgagctttca	14	9	1	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:160059155A>G	ENST00000327245.5	-	13	2447	c.1601T>C	c.(1600-1602)gTg>gCg	p.V534A	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	534					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCTGAAGGCCACAGGAGGCTG	0.552																																					p.V534A		Atlas-SNP	.											.	ATP10B	201	.	0			c.T1601C						.						57	60	59					5																	160059155		1900	4128	6028	SO:0001583	missense	23120	exon13			AAGGCCACAGGAG	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.1601T>C	chr5.hg19:g.160059155A>G	ENSP00000313600:p.Val534Ala	55.0	0.0		60.0	28.0	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	hg19	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	A	10.71	1.427275	0.25726	.	.	ENSG00000118322	ENST00000327245;ENST00000520108	T;T	0.42513	0.97;2.07	5.3	5.3	0.74995	HAD-like domain (1);	0.153524	0.43110	D	0.000611	T	0.51227	0.1662	L	0.31207	0.915	0.41053	D	0.985313	D;P	0.76494	0.999;0.775	D;B	0.80764	0.994;0.426	T	0.48779	-0.9005	9	.	.	.	.	14.4591	0.67438	1.0:0.0:0.0:0.0	.	142;534	Q2YDW8;O94823	.;AT10B_HUMAN	A	534;142	ENSP00000313600:V534A;ENSP00000431081:V142A	.	V	-	2	0	ATP10B	159991733	1.000000	0.71417	0.997000	0.53966	0.877000	0.50540	4.844000	0.62846	2.000000	0.58554	0.533000	0.62120	GTG	.	.		0.552	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		G	160059155	A	G	160059155	3	3	174	1	0	0	0	0	1	0	0	0	1117	159	6	2	2840	2	ATP10B	5	160059155	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	5662446	160059155	20856105	48	26212										
FLT4	2324	hgsc.bcm.edu	37	chr5	180043367	180043367	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cctcaatggcctgcactcacActgcccttgcggacgtagtc	9	16	2	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr5:180043367A>T	ENST00000261937.6	-	23	3297	c.3219T>A	c.(3217-3219)agT>agA	p.S1073R	FLT4_ENST00000393347.3_Splice_Site_p.S1073R|FLT4_ENST00000502649.1_Splice_Site_p.S1073R	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1073	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGCACTCACACTGCCCTTGC	0.607																																					p.S1073R	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.T3219A						.						115	103	107					5																	180043367		2203	4300	6503	SO:0001630	splice_region_variant	2324	exon23			ACTCACACTGCCC	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3219+1T>A	chr5.hg19:g.180043367A>T		78.0	0.0		57.0	19.0	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	hg19	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.121663	0.37436	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649;ENST00000512795	D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67	3.19	-6.38	0.01957	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.73148	0.3550	L	0.28192	0.835	0.44168	D	0.996978	B;B	0.27229	0.172;0.172	B;B	0.38755	0.281;0.281	T	0.56001	-0.8051	8	.	.	.	.	13.0451	0.58922	0.4616:0.0:0.5384:0.0	.	1073;1073	E9PD35;P35916	.;VGFR3_HUMAN	R	1073;1073;1073;111	ENSP00000261937:S1073R;ENSP00000377016:S1073R;ENSP00000426057:S1073R;ENSP00000421535:S111R	.	S	-	3	2	FLT4	179975973	0.000000	0.05858	0.707000	0.30419	0.678000	0.39670	-1.980000	0.01492	-2.377000	0.00597	-1.369000	0.01192	AGT	.	.		0.607	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		Missense_Mutation	T	180043367	A	T	180043367	5	4	174	1	0	0	0	0	0	0	1	0	5952	173	6	4	912	4	FLT4	5	180043367	Splice_Site	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	19984212	180043367	871893	49	26213										
CD83	9308	hgsc.bcm.edu	37	chr6	14118190	14118190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ctttcttgtagcctacagccTggctcccgcgacgccggagg	12	15	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr6:14118190T>C	ENST00000379153.3	+	2	218	c.47T>C	c.(46-48)cTg>cCg	p.L16P		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	16					defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				GCCTACAGCCTGGCTCCCGCG	0.682																																					p.L16P		Atlas-SNP	.											.	CD83	23	.	0			c.T47C						.						22	23	23					6																	14118190		2203	4300	6503	SO:0001583	missense	9308	exon2			ACAGCCTGGCTCC	Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1703	protein-coding gene	gene with protein product		604534	"CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)", "CD83 molecule "			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.47T>C	chr6.hg19:g.14118190T>C	ENSP00000368450:p.Leu16Pro	41.0	0.0		54.0	27.0	NM_004233	Q5THX9	Missense_Mutation	SNP	ENST00000379153.3	hg19	CCDS4532.1	.	.	.	.	.	.	.	.	.	.	T	14.62	2.589937	0.46214	.	.	ENSG00000112149	ENST00000379153	T	0.53640	0.61	4.74	3.54	0.40534	.	0.831157	0.10016	N	0.726548	T	0.48943	0.1528	L	0.58101	1.795	0.51233	D	0.999917	D	0.63046	0.992	D	0.64144	0.922	T	0.43180	-0.9407	10	0.66056	D	0.02	-14.2866	8.3337	0.32202	0.0:0.0:0.2005:0.7995	.	16	Q01151	CD83_HUMAN	P	16	ENSP00000368450:L16P	ENSP00000368450:L16P	L	+	2	0	CD83	14226169	1.000000	0.71417	0.924000	0.36721	0.225000	0.24961	3.739000	0.55075	0.633000	0.30452	0.402000	0.26972	CTG	.	.		0.682	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1			C	14118190	T	C	14118190	3	2	174	1	0	0	0	0	1	0	0	0	3043	1580	55	2	53	2	CD83	6	14118190	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10		14118190	156996877	50	26214										
BRD2	6046	hgsc.bcm.edu	37	chr6	32947653	32947653	+	Frame_Shift_Del	DEL	T	T	-													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ccacctgccctgcctacaggTtatgattcagaggaggagga							TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr6:32947653delT	ENST00000374825.4	+	11	3591	c.1890delT	c.(1888-1890)ggtfs	p.G630fs	BRD2_ENST00000395289.2_Frame_Shift_Del_p.G665fs|BRD2_ENST00000443797.2_Frame_Shift_Del_p.G510fs|BRD2_ENST00000449085.2_Frame_Shift_Del_p.G583fs|BRD2_ENST00000395287.1_Frame_Shift_Del_p.G665fs|BRD2_ENST00000374831.4_Frame_Shift_Del_p.G630fs	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	630					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						TGCCTACAGGTTATGATTCAG	0.522																																					p.G665fs		Atlas-INDEL	.											.	BRD2	70	.	0			c.1994delG						.						45	47	46					6																	32947653		1509	2708	4217	SO:0001589	frameshift_variant	6046	exon11			.	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"bromodomain-containing 2"			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1890delT	chr6.hg19:g.32947653delT	ENSP00000363958:p.Gly630fs	122.0	0.0		108.0	50.0	NM_001199455	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Frame_Shift_Del	DEL	ENST00000374825.4	hg19	CCDS4762.1																																																																																			.	.		0.522	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			-	32947653	T	-	32947653	7	5	174	1	0	1	0	1	0	0	0	0	1504	1712	60	0	1928	0	BRD2	6	32947653	Frame_Shift_Del	DEL	T	TCGA-DD-AACX-01A-11D-A40R-10	18829463	32947653	138167414	51	26215										
SLC35B2	347734	hgsc.bcm.edu	37	chr6	44224447	44224447	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tccaggtagttcttccgcctGaagtactgcaccaggaggta	11	11	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr6:44224447G>T	ENST00000393812.3	-	2	323	c.180C>A	c.(178-180)ttC>ttA	p.F60L	SLC35B2_ENST00000495706.1_Intron|SLC35B2_ENST00000393810.1_Missense_Mutation_p.F60L|MIR4647_ENST00000583964.1_RNA|SLC35B2_ENST00000537814.1_Intron|SLC35B2_ENST00000538577.1_Nonsense_Mutation_p.S19*	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	60					3'-phospho-5'-adenylyl sulfate transmembrane transport (GO:1902559)|3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|3'-phosphoadenosine 5'-phosphosulfate transport (GO:0046963)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity (GO:0046964)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	15	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TCTTCCGCCTGAAGTACTGCA	0.547																																					p.F60L		Atlas-SNP	.											.	SLC35B2	40	.	0			c.C180A						.						121	129	127					6																	44224447		2203	4300	6503	SO:0001583	missense	347734	exon2			CCGCCTGAAGTAC	AK075456	CCDS34462.1, CCDS69127.1, CCDS75462.1, CCDS75463.1	6p12.1-p11.21	2013-07-17	2013-07-17		ENSG00000157593	ENSG00000157593		"Solute carriers"	16872	protein-coding gene	gene with protein product		610788	"solute carrier family 35, member B2"				Standard	NM_001286517		Approved	UGTrel4	uc003oxd.3	Q8TB61	OTTHUMG00000014760	ENST00000393812.3:c.180C>A	chr6.hg19:g.44224447G>T	ENSP00000377401:p.Phe60Leu	188.0	0.0		214.0	91.0	NM_178148	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Missense_Mutation	SNP	ENST00000393812.3	hg19	CCDS34462.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	37|37	6.227525|6.227525	0.97394|0.97394	.|.	.|.	ENSG00000157593|ENSG00000157593	ENST00000393810;ENST00000393812;ENST00000341553|ENST00000538577	T|.	0.26810|.	1.71|.	4.02|4.02	0.995|0.995	0.19838|0.19838	.|.	0.692137|.	0.14639|.	N|.	0.307359|.	T|.	0.18425|.	0.0442|.	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|.	0.06092|.	-1.0846|.	10|.	0.26408|0.26408	T|T	0.33|0.33	-16.7379|-16.7379	4.8954|4.8954	0.13748|0.13748	0.1671:0.0:0.5276:0.3053|0.1671:0.0:0.5276:0.3053	.|.	60|.	Q8TB61|.	S35B2_HUMAN|.	L|X	60|19	ENSP00000377401:F60L|.	ENSP00000342455:F60L|ENSP00000443845:S19X	F|S	-|-	3|2	2|0	SLC35B2|SLC35B2	44332425|44332425	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.920000|0.920000	0.55202|0.55202	1.086000|1.086000	0.30853|0.30853	-0.015000|-0.015000	0.14150|0.14150	-0.291000|-0.291000	0.09656|0.09656	TTC|TCA	.	.		0.547	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2			T	44224447	G	T	44224447	3	4	174	1	0	0	0	0	1	0	0	0	14591	1281	45	3	1130	3	SLC35B2	6	44224447	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	11276794	44224447	126890620	52	26216										
C6orf182	285753	hgsc.bcm.edu	37	chr6	109481821	109481821	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tgaaggaaactgaaagtcatTcagtctgtgacgacatagaa	10	6	3	4			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr6:109481821T>G	ENST00000517392.1	+	10	1489	c.1063T>G	c.(1063-1065)Tca>Gca	p.S355A	CEP57L1_ENST00000407272.1_Missense_Mutation_p.S355A|CEP57L1_ENST00000520883.1_Missense_Mutation_p.S255A|CEP57L1_ENST00000336977.4_Missense_Mutation_p.S255A|CEP57L1_ENST00000523787.1_Missense_Mutation_p.S358A|CEP57L1_ENST00000359793.3_Missense_Mutation_p.S355A|CEP57L1_ENST00000368968.2_Missense_Mutation_p.S355A|CEP57L1_ENST00000368970.2_Missense_Mutation_p.S372A|CEP57L1_ENST00000521522.1_Missense_Mutation_p.S302A	NM_001271852.1|NM_001271853.1	NP_001258781.1|NP_001258782.1	Q8IYX8	CE57L_HUMAN	centrosomal protein 57kDa-like 1	355					microtubule anchoring (GO:0034453)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)	11						TGAAAGTCATTCAGTCTGTGA	0.333																																					p.S355A		Atlas-SNP	.											.	CEP57L1	24	.	0			c.T1063G						.						86	84	84					6																	109481821		2203	4298	6501	SO:0001583	missense	285753	exon10			AGTCATTCAGTCT	AK092723	CCDS5071.1, CCDS64491.1	6q21	2014-01-28	2010-09-30	2010-09-30	ENSG00000183137	ENSG00000183137			21561	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 182"	C6orf182			Standard	NM_001083535		Approved	bA487F23.2, MGC21731	uc003psy.4	Q8IYX8	OTTHUMG00000015336	ENST00000517392.1:c.1063T>G	chr6.hg19:g.109481821T>G	ENSP00000427844:p.Ser355Ala	398.0	0.0		362.0	173.0	NM_001271853	G5E992	Missense_Mutation	SNP	ENST00000517392.1	hg19	CCDS5071.1	.	.	.	.	.	.	.	.	.	.	T	0.079	-1.187619	0.01620	.	.	ENSG00000183137	ENST00000517392;ENST00000407272;ENST00000336977;ENST00000521522;ENST00000368968;ENST00000368970;ENST00000520883;ENST00000523787;ENST00000359793;ENST00000523174	T;T;T;T;T;T;T;T;T	0.43294	0.99;0.99;0.96;0.95;0.99;0.95;0.96;0.99;0.99	5.19	2.82	0.32997	.	0.713091	0.13499	N	0.383388	T	0.14313	0.0346	L	0.50919	1.6	0.09310	N	1	B;B	0.13594	0.008;0.008	B;B	0.16289	0.015;0.009	T	0.14448	-1.0472	10	0.33940	T	0.23	-0.5491	3.2066	0.06667	0.1336:0.0802:0.4054:0.3809	.	355;355	Q8IYX8;G5E992	CE57L_HUMAN;.	A	355;355;255;302;355;372;255;358;355;136	ENSP00000427844:S355A;ENSP00000383936:S355A;ENSP00000337392:S255A;ENSP00000428344:S302A;ENSP00000357964:S355A;ENSP00000357966:S372A;ENSP00000430011:S255A;ENSP00000430529:S358A;ENSP00000352841:S355A	ENSP00000337392:S255A	S	+	1	0	CEP57L1	109588514	0.001000	0.12720	0.023000	0.16930	0.142000	0.21351	0.668000	0.25127	1.069000	0.40788	0.528000	0.53228	TCA	.	.		0.333	CEP57L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041734.4	NM_173830		G	109481821	T	G	109481821	3	3	174	1	0	0	0	0	1	0	0	0	2348	1783	62	5	1097	5	C6orf182	6	109481821	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	65257374	109481821	61633246	53	26217										
SLC22A16	85413	hgsc.bcm.edu	37	chr6	110763848	110763848	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	accaggtcctgaccaagtatCctgtcaaagccaccagcagg	9	14	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr6:110763848C>A	ENST00000368919.3	-	4	848	c.782G>T	c.(781-783)gGa>gTa	p.G261V	SLC22A16_ENST00000456137.2_3'UTR|SLC22A16_ENST00000439654.1_Missense_Mutation_p.G261V|RN7SL617P_ENST00000485298.2_RNA|SLC22A16_ENST00000330550.4_Missense_Mutation_p.G227V	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	261					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	GACCAAGTATCCTGTCAAAGC	0.502																																					p.G261V		Atlas-SNP	.											.	SLC22A16	81	.	0			c.G782T						.						98	96	96					6																	110763848		2203	4300	6503	SO:0001583	missense	85413	exon4			AAGTATCCTGTCA		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"Solute carriers"	20302	protein-coding gene	gene with protein product		608276	"solute carrier family 22 (organic cation transporter), member 16"			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.782G>T	chr6.hg19:g.110763848C>A	ENSP00000357915:p.Gly261Val	106.0	0.0		112.0	46.0	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	hg19	CCDS5084.1	.	.	.	.	.	.	.	.	.	.	C	19.37	3.813713	0.70912	.	.	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654;ENST00000434949;ENST00000437378	T;T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07;0.07	4.54	3.65	0.41850	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.104543	0.64402	D	0.000003	T	0.69886	0.3161	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.99	T	0.76708	-0.2860	10	0.87932	D	0	.	14.6209	0.68584	0.0:0.8528:0.1472:0.0	.	261;227	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	V	261;178;227;261;91;218	ENSP00000357915:G261V;ENSP00000395642:G178V;ENSP00000328583:G227V;ENSP00000408799:G261V;ENSP00000409306:G91V;ENSP00000416310:G218V	ENSP00000328583:G227V	G	-	2	0	SLC22A16	110870541	1.000000	0.71417	0.419000	0.26584	0.917000	0.54804	4.295000	0.59049	0.992000	0.38840	0.655000	0.94253	GGA	.	.		0.502	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125		A	110763848	C	A	110763848	3	1	174	1	0	0	0	0	1	0	0	0	14462	855	30	3	971	3	SLC22A16	6	110763848	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	1282027	110763848	60351219	54	26218										
NCOA7	135112	hgsc.bcm.edu	37	chr6	126199417	126199417	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tgattattctaggctggaaaCcaggacaccctaaactccat	7	11	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr6:126199417C>G	ENST00000368357.3	+	6	712	c.360C>G	c.(358-360)aaC>aaG	p.N120K	NCOA7_ENST00000229634.9_Missense_Mutation_p.N16K|RN7SKP56_ENST00000410513.1_RNA|NCOA7_ENST00000392477.2_Missense_Mutation_p.N120K	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	120					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		AGGCTGGAAACCAGGACACCC	0.318																																					p.N120K		Atlas-SNP	.											.	NCOA7	92	.	0			c.C360G						.						88	81	83					6																	126199417		2203	4300	6503	SO:0001583	missense	135112	exon6			TGGAAACCAGGAC	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 4"	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.360C>G	chr6.hg19:g.126199417C>G	ENSP00000357341:p.Asn120Lys	115.0	0.0		104.0	46.0	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	hg19	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.403278	0.42613	.	.	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000417494;ENST00000229634	T;T;T;T	0.36340	1.26;1.26;1.26;1.26	5.58	2.85	0.33270	Peptidoglycan-binding Lysin subgroup (1);Peptidoglycan-binding lysin domain (1);	0.372102	0.33792	N	0.004552	T	0.05593	0.0147	N	0.02225	-0.63	0.26556	N	0.973827	B;B;B;B	0.20164	0.042;0.034;0.01;0.007	B;B;B;B	0.22152	0.038;0.023;0.022;0.024	T	0.32981	-0.9886	10	0.45353	T	0.12	-19.4636	9.7919	0.40710	0.0:0.7009:0.0:0.2991	.	120;120;120;120	B3KXK4;Q8NI08-2;Q8NI08-4;Q8NI08	.;.;.;NCOA7_HUMAN	K	120;120;120;16	ENSP00000357341:N120K;ENSP00000376269:N120K;ENSP00000406363:N120K;ENSP00000229634:N16K	ENSP00000229634:N16K	N	+	3	2	NCOA7	126241110	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.905000	0.39878	0.403000	0.25479	0.655000	0.94253	AAC	.	.		0.318	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748		G	126199417	C	G	126199417	3	3	174	1	0	0	0	0	1	0	0	0	10243	506	18	4	374	4	NCOA7	6	126199417	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	15435569	126199417	44915650	55	26219										
IL20RA	53832	hgsc.bcm.edu	37	chr6	137330583	137330583	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gctgtcaggacaacagaaatGgacttctcatctgtagtcag	10	9	4	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr6:137330583G>T	ENST00000316649.5	-	4	685	c.450C>A	c.(448-450)tcC>tcA	p.S150S	IL20RA_ENST00000541547.1_Silent_p.S101S|IL20RA_ENST00000367748.1_Silent_p.S39S|IL20RA_ENST00000468393.1_5'UTR|IL20RA_ENST00000367746.3_Silent_p.S150S	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha	150	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		CAACAGAAATGGACTTCTCAT	0.428																																					p.S150S		Atlas-SNP	.											.	IL20RA	54	.	0			c.C450A						.						121	115	117					6																	137330583		2203	4300	6503	SO:0001819	synonymous_variant	53832	exon4			AGAAATGGACTTC	AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"Interleukins and interleukin receptors"	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.450C>A	chr6.hg19:g.137330583G>T		89.0	0.0		96.0	33.0	NM_014432	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Silent	SNP	ENST00000316649.5	hg19	CCDS5181.1																																																																																			.	.		0.428	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432		T	137330583	G	T	137330583	2	4	174	1	0	0	0	0	0	0	0	1	7677	1335	47	3		3	IL20RA	6	137330583	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	11131166	137330583	33784484	56	26220										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159672391	159672391	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cccgtgctctctgactgatgCactggatcacttccaagtgg	10	13	2	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr6:159672391C>A	ENST00000297267.9	+	17	5092	c.4892C>A	c.(4891-4893)gCa>gAa	p.A1631E	FNDC1_ENST00000340366.6_Missense_Mutation_p.A1568E	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1631					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CTGACTGATGCACTGGATCAC	0.512																																					p.A1631E		Atlas-SNP	.											.	FNDC1	250	.	0			c.C4892A						.						75	72	73					6																	159672391		2037	4188	6225	SO:0001583	missense	84624	exon17			CTGATGCACTGGA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.4892C>A	chr6.hg19:g.159672391C>A	ENSP00000297267:p.Ala1631Glu	74.0	0.0		107.0	36.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	hg19	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.8|29.8	5.038978|5.038978	0.93630|0.93630	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000297267;ENST00000340366|ENST00000329629	T;T|.	0.15952|.	2.38;3.2|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	0.180079|.	0.48767|.	D|.	0.000176|.	T|.	0.69851|.	0.3157|.	M|M	0.68952|0.68952	2.095|2.095	0.54753|0.54753	D|D	0.999987|0.999987	D|.	0.89917|.	1.0|.	D|.	0.74348|.	0.983|.	T|.	0.67515|.	-0.5651|.	9|.	.|.	.|.	.|.	-11.5313|-11.5313	19.4668|19.4668	0.94946|0.94946	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1631|.	Q4ZHG4|.	FNDC1_HUMAN|.	E|X	1631;1568|1526	ENSP00000297267:A1631E;ENSP00000342460:A1568E|.	.|.	A|C	+|+	2|3	0|2	FNDC1|FNDC1	159592381|159592381	1.000000|1.000000	0.71417|0.71417	0.885000|0.885000	0.34714|0.34714	0.989000|0.989000	0.77384|0.77384	5.858000|5.858000	0.69532|0.69532	2.613000|2.613000	0.88420|0.88420	0.585000|0.585000	0.79938|0.79938	GCA|TGC	.	.		0.512	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159672391	C	A	159672391	3	1	174	1	0	0	0	0	1	0	0	0	5976	710	25	3	4958	3	FNDC1	6	159672391	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	22341808	159672391	11442676	57	26221										
IKZF1	10320	hgsc.bcm.edu	37	chr7	50450271	50450271	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ccagtgcaatcagtgcggggCctcattcacccagaagggca	12	13	3	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr7:50450271C>T	ENST00000331340.3	+	5	610	c.455C>T	c.(454-456)gCc>gTc	p.A152V	IKZF1_ENST00000349824.4_Intron|IKZF1_ENST00000440768.2_Missense_Mutation_p.A152V|IKZF1_ENST00000438033.1_Missense_Mutation_p.A65V|IKZF1_ENST00000439701.1_Missense_Mutation_p.A152V|IKZF1_ENST00000343574.5_Missense_Mutation_p.A65V|IKZF1_ENST00000359197.5_Missense_Mutation_p.A152V|IKZF1_ENST00000346667.4_Intron|IKZF1_ENST00000357364.4_Missense_Mutation_p.A152V	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	152					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(131)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				CAGTGCGGGGCCTCATTCACC	0.602			"D,T"	BCL6	"ALL, DLBCL"																																p.A152V		Atlas-SNP	.		"Rec,Dom"	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	131	Unknown(131)	haematopoietic_and_lymphoid_tissue(131)	c.C455T						.						32	37	35					7																	50450271		2131	4255	6386	SO:0001583	missense	10320	exon5			GCGGGGCCTCATT	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13176	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 92"	603023	"zinc finger protein, subfamily 1A, 1 (Ikaros)"	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.455C>T	chr7.hg19:g.50450271C>T	ENSP00000331614:p.Ala152Val	53.0	0.0		64.0	24.0	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.330018	0.95733	.	.	ENSG00000185811	ENST00000343574;ENST00000359197;ENST00000440768;ENST00000357364;ENST00000331340;ENST00000438033;ENST00000439701	T;T;T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;2.2;1.21;1.21	6.08	6.08	0.98989	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.64886	0.2639	.	.	.	0.80722	D	1	D;D;P	0.76494	0.999;0.966;0.608	D;P;P	0.85130	0.997;0.801;0.722	T	0.62918	-0.6752	9	0.52906	T	0.07	-22.7845	20.6634	0.99662	0.0:1.0:0.0:0.0	.	65;152;152	Q13422-2;Q13422-7;Q13422	.;.;IKZF1_HUMAN	V	65;152;152;152;152;65;152	ENSP00000342750:A65V;ENSP00000352123:A152V;ENSP00000401507:A152V;ENSP00000349928:A152V;ENSP00000331614:A152V;ENSP00000396554:A65V;ENSP00000413025:A152V	ENSP00000331614:A152V	A	+	2	0	IKZF1	50417765	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.815000	0.86186	2.894000	0.99253	0.655000	0.94253	GCC	.	.		0.602	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060		T	50450271	C	T	50450271	3	4	174	1	0	0	0	0	1	0	0	0	7623	739	26	3	469	3	IKZF1	7	50450271	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10		50450271	108688392	58	26222										
RUNDC3B	154661	hgsc.bcm.edu	37	chr7	87369128	87369128	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	agattttatgaagatggagcAattgtcttgggtgaagaagc	13	3	1	5			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr7:87369128A>C	ENST00000338056.3	+	6	942	c.531A>C	c.(529-531)gcA>gcC	p.A177A	RUNDC3B_ENST00000493037.1_Silent_p.A160A|RUNDC3B_ENST00000394654.3_Silent_p.A160A|RUNDC3B_ENST00000496000.1_3'UTR	NM_001134405.1|NM_138290.2	NP_001127877.1|NP_612147.1	Q96NL0	RUN3B_HUMAN	RUN domain containing 3B	177	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.									breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(2)	26	Esophageal squamous(14;0.00164)					AAGATGGAGCAATTGTCTTGG	0.318																																					p.A177A		Atlas-SNP	.											.	RUNDC3B	63	.	0			c.A531C						.						66	65	66					7																	87369128		2203	4300	6503	SO:0001819	synonymous_variant	154661	exon6			TGGAGCAATTGTC		CCDS5609.1, CCDS47635.1, CCDS47636.1	7q21.12	2009-01-14			ENSG00000105784	ENSG00000105784			30286	protein-coding gene	gene with protein product						12645870	Standard	NM_138290		Approved	RPIP9, RPIB9	uc003ujb.3	Q96NL0	OTTHUMG00000131035	ENST00000338056.3:c.531A>C	chr7.hg19:g.87369128A>C		66.0	0.0		57.0	20.0	NM_138290	B4DFD0|E9PBR4|Q8IWW5|Q8NB55|Q8TBG7	Silent	SNP	ENST00000338056.3	hg19	CCDS5609.1																																																																																			.	.		0.318	RUNDC3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253679.1	NM_138290		C	87369128	A	C	87369128	2	2	174	1	0	0	0	0	0	0	0	1	13760	117	5	5		5	RUNDC3B	7	87369128	Silent	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	36918857	87369128	71769535	59	26223										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121652900	121652900	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gaccatttcctatgcaagtgAgaaatatgaaccagttttgt	8	7	0	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr7:121652900A>T	ENST00000393386.2	+	12	4211	c.3800A>T	c.(3799-3801)gAg>gTg	p.E1267V	PTPRZ1_ENST00000483028.1_3'UTR|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1267					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TATGCAAGTGAGAAATATGAA	0.398																																					p.E1267V		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.A3800T						.						92	93	93					7																	121652900		2203	4300	6503	SO:0001583	missense	5803	exon12			CAAGTGAGAAATA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.3800A>T	chr7.hg19:g.121652900A>T	ENSP00000377047:p.Glu1267Val	94.0	0.0		91.0	36.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	A	11.38	1.621581	0.28889	.	.	ENSG00000106278	ENST00000393386	T	0.52754	0.65	5.16	5.16	0.70880	.	0.208441	0.33401	N	0.004954	T	0.49372	0.1553	M	0.62723	1.935	0.80722	D	1	P	0.43477	0.808	B	0.41860	0.368	T	0.54807	-0.8238	10	0.52906	T	0.07	.	15.1545	0.72730	1.0:0.0:0.0:0.0	.	1267	P23471	PTPRZ_HUMAN	V	1267	ENSP00000377047:E1267V	ENSP00000377047:E1267V	E	+	2	0	PTPRZ1	121440136	1.000000	0.71417	0.993000	0.49108	0.458000	0.32498	6.533000	0.73829	2.160000	0.67779	0.454000	0.30748	GAG	.	.		0.398	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121652900	A	T	121652900	3	4	174	1	0	0	0	0	1	0	0	0	12829	304	11	4	3846	4	PTPRZ1	7	121652900	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	34283772	121652900	37485763	60	26224										
ZMAT4	79698	hgsc.bcm.edu	37	chr8	40532253	40532253	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ccccatatccagggttgtccCcagttgttctaacaaagcaa	7	13	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr8:40532253C>A	ENST00000297737.6	-	5	693	c.547G>T	c.(547-549)Ggg>Tgg	p.G183W	ZMAT4_ENST00000315769.7_Intron	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	183						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			AGGGTTGTCCCCAGTTGTTCT	0.473																																					p.G183W		Atlas-SNP	.											.	ZMAT4	47	.	0			c.G547T						.						148	137	141					8																	40532253		2203	4300	6503	SO:0001583	missense	79698	exon5			TTGTCCCCAGTTG	AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061		"Zinc fingers, matrin-type"	25844	protein-coding gene	gene with protein product						12477932	Standard	NM_024645		Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.547G>T	chr8.hg19:g.40532253C>A	ENSP00000297737:p.Gly183Trp	105.0	0.0		100.0	42.0	NM_024645	Q8WUT8	Missense_Mutation	SNP	ENST00000297737.6	hg19	CCDS34885.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951155	0.53186	.	.	ENSG00000165061	ENST00000297737;ENST00000519406	T;T	0.54479	0.7;0.57	5.85	4.98	0.66077	.	0.088880	0.85682	D	0.000000	T	0.77452	0.4132	M	0.91510	3.215	0.52501	D	0.999958	D	0.89917	1.0	D	0.79784	0.993	T	0.83041	-0.0157	10	0.87932	D	0	-19.7587	13.9182	0.63914	0.0:0.926:0.0:0.074	.	183	Q9H898	ZMAT4_HUMAN	W	183	ENSP00000297737:G183W;ENSP00000428423:G183W	ENSP00000297737:G183W	G	-	1	0	ZMAT4	40651410	1.000000	0.71417	0.866000	0.34008	0.261000	0.26267	7.404000	0.79996	1.485000	0.48380	-0.252000	0.11476	GGG	.	.		0.473	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376950.1	NM_024645		A	40532253	C	A	40532253	3	1	174	1	0	0	0	0	1	0	0	0	17709	623	22	3	154	3	ZMAT4	8	40532253	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10		40532253	105831769	61	26225										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95508121	95508121	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	catcatcttttgaatgttccTagatacaaataaaggcagaa	6	7	2	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr8:95508121T>C	ENST00000297591.5	-	19	4459		c.e19-2		KIAA1429_ENST00000437199.1_Splice_Site	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429						mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TGAATGTTCCTAGATACAAAT	0.373																																					.		Atlas-SNP	.											.	KIAA1429	176	.	0			c.4384-2A>G						.						72	65	68					8																	95508121		2203	4300	6503	SO:0001630	splice_region_variant	25962	exon20			TGTTCCTAGATAC	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.4384-2A>G	chr8.hg19:g.95508121T>C		59.0	0.0		61.0	23.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Splice_Site	SNP	ENST00000297591.5	hg19	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.141614	0.57044	.	.	ENSG00000164944	ENST00000297591	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.12	0.48284	0.1382:0.0:0.0:0.8618	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA1429	95577297	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	7.148000	0.77389	2.020000	0.59435	0.528000	0.53228	.	.	.		0.373	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	Intron	C	95508121	T	C	95508121	5	2	174	1	0	0	0	0	0	0	1	0	8240	1536	53	2	1080	2	KIAA1429	8	95508121	Splice_Site	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	54975868	95508121	50855901	62	26226										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121282378	121282378	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gctttctatacagcactgttGgagccctgaacaagattggc	10	10	1	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr8:121282378G>A	ENST00000297848.3	+	26	3448	c.3178G>A	c.(3178-3180)Gga>Aga	p.G1060R	COL14A1_ENST00000309791.4_Missense_Mutation_p.G1060R|COL14A1_ENST00000247781.3_Missense_Mutation_p.G965R|COL14A1_ENST00000432943.2_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			CAGCACTGTTGGAGCCCTGAA	0.383																																					p.G1060R		Atlas-SNP	.											.	COL14A1	292	.	0			c.G3178A						.						90	85	87					8																	121282378		2203	4299	6502	SO:0001583	missense	7373	exon26			ACTGTTGGAGCCC		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.3178G>A	chr8.hg19:g.121282378G>A	ENSP00000297848:p.Gly1060Arg	85.0	0.0		83.0	35.0	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	hg19	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.849903	0.91277	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781	T;T;T	0.77620	-1.11;-1.11;-1.11	5.21	5.21	0.72293	von Willebrand factor, type A (3);	0.051819	0.85682	D	0.000000	D	0.84561	0.5499	L	0.42529	1.33	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.85113	0.0964	10	0.59425	D	0.04	.	18.9528	0.92646	0.0:0.0:1.0:0.0	.	1060	Q05707	COEA1_HUMAN	R	1060;1060;965	ENSP00000311809:G1060R;ENSP00000297848:G1060R;ENSP00000247781:G965R	ENSP00000247781:G965R	G	+	1	0	COL14A1	121351559	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.657000	0.98554	2.716000	0.92895	0.561000	0.74099	GGA	.	.		0.383	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121282378	G	A	121282378	3	1	174	1	0	0	0	0	1	0	0	0	3673	1349	47	3	3276	3	COL14A1	8	121282378	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	25774257	121282378	25081644	63	26227										
KLHL38	340359	hgsc.bcm.edu	37	chr8	124664197	124664197	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	caaggtgatggcagaggcctTgtacagccgtgtcgggagtt	16	8	0	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr8:124664197T>C	ENST00000325995.7	-	1	993	c.970A>G	c.(970-972)Aag>Gag	p.K324E	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	324										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						GCAGAGGCCTTGTACAGCCGT	0.582																																					p.K324E		Atlas-SNP	.											.	KLHL38	81	.	0			c.A970G						.						67	70	69					8																	124664197		2017	4171	6188	SO:0001583	missense	340359	exon1			AGGCCTTGTACAG		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"Kelch-like", "BTB/POZ domain containing"	34435	protein-coding gene	gene with protein product			"kelch-like 38 (Drosophila)"				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.970A>G	chr8.hg19:g.124664197T>C	ENSP00000321475:p.Lys324Glu	80.0	0.0		109.0	50.0	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	hg19	CCDS43766.1	.	.	.	.	.	.	.	.	.	.	T	14.02	2.411100	0.42817	.	.	ENSG00000175946	ENST00000325995	T	0.65916	-0.18	5.18	5.18	0.71444	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.50956	0.1646	L	0.32530	0.975	0.52099	D	0.999942	P	0.37985	0.613	B	0.38264	0.269	T	0.46898	-0.9158	10	0.13108	T	0.6	.	15.3281	0.74182	0.0:0.0:0.0:1.0	.	324	Q2WGJ6	KLH38_HUMAN	E	324	ENSP00000321475:K324E	ENSP00000321475:K324E	K	-	1	0	KLHL38	124733378	1.000000	0.71417	1.000000	0.80357	0.363000	0.29612	6.092000	0.71414	2.079000	0.62486	0.459000	0.35465	AAG	.	.		0.582	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1			C	124664197	T	C	124664197	3	2	174	1	0	0	0	0	1	0	0	0	8399	1821	63	2	787	2	KLHL38	8	124664197	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	3381819	124664197	21699825	64	26228										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79318782	79318782	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	agttccctgcagccctgtttCtttggaacctacatacaatt	6	12	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr9:79318782C>T	ENST00000376718.3	-	9	7870	c.7747G>A	c.(7747-7749)Gaa>Aaa	p.E2583K	PRUNE2_ENST00000428286.1_Missense_Mutation_p.E2224K	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2583					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AGCCCTGTTTCTTTGGAACCT	0.418																																					p.E2583K		Atlas-SNP	.											.	PRUNE2	331	.	0			c.G7747A						.						145	134	137					9																	79318782		1568	3582	5150	SO:0001583	missense	158471	exon9			CTGTTTCTTTGGA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.7747G>A	chr9.hg19:g.79318782C>T	ENSP00000365908:p.Glu2583Lys	101.0	0.0		84.0	36.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.75|10.75	1.438340|1.438340	0.25900|0.25900	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.51071|.	0.72;0.73|.	5.63|5.63	3.73|3.73	0.42828|0.42828	.|.	0.319252|.	0.27354|.	N|.	0.019760|.	T|T	0.63768|0.63768	0.2539|0.2539	L|L	0.56769|0.56769	1.78|1.78	0.46954|0.46954	D|D	0.999264|0.999264	P;P|.	0.39282|.	0.617;0.666|.	B;B|.	0.35039|.	0.173;0.194|.	T|T	0.62817|0.62817	-0.6774|-0.6774	10|5	0.66056|.	D|.	0.02|.	-6.7965|-6.7965	13.4498|13.4498	0.61163|0.61163	0.0:0.4449:0.555:0.0|0.0:0.4449:0.555:0.0	.|.	2583;2583|.	Q8WUY3-3;Q8WUY3|.	.;PRUN2_HUMAN|.	K|K	2583;2224;2582|1904	ENSP00000365908:E2583K;ENSP00000397425:E2224K|.	ENSP00000365908:E2583K|.	E|R	-|-	1|2	0|0	PRUNE2|PRUNE2	78508602|78508602	0.891000|0.891000	0.30450|0.30450	0.035000|0.035000	0.18076|0.18076	0.006000|0.006000	0.05464|0.05464	1.099000|1.099000	0.31013|0.31013	1.356000|1.356000	0.45884|0.45884	0.591000|0.591000	0.81541|0.81541	GAA|AGA	.	.		0.418	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		T	79318782	C	T	79318782	3	4	174	1	0	0	0	0	1	0	0	0	12653	922	32	3	1563	3	PRUNE2	9	79318782	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10		79318782	61894649	65	26229										
GNAQ	2776	hgsc.bcm.edu	37	chr9	80537145	80537145	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gatcatggcctgcatggccgTgaagatgttctgatacacca	11	10	2	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr9:80537145T>G	ENST00000286548.4	-	2	475	c.253A>C	c.(253-255)Acg>Ccg	p.T85P		NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	85					action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)			NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						TGCATGGCCGTGAAGATGTTC	0.468			Mis		uveal melanoma																																p.T85P		Atlas-SNP	.		Dom	yes		9	9q21	2776	"guanine nucleotide binding protein (G protein), q polypeptide"		E	.	GNAQ	384	.	0			c.A253C						.						239	199	213					9																	80537145		2203	4300	6503	SO:0001583	missense	2776	exon2			TGGCCGTGAAGAT		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052			4390	protein-coding gene	gene with protein product		600998				8825633	Standard	NM_002072		Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.253A>C	chr9.hg19:g.80537145T>G	ENSP00000286548:p.Thr85Pro	67.0	0.0		57.0	20.0	NM_002072	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	Missense_Mutation	SNP	ENST00000286548.4	hg19	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.161484	0.78226	.	.	ENSG00000156052	ENST00000286548;ENST00000411677	D;D	0.88741	-2.42;-2.42	5.87	5.87	0.94306	G protein alpha subunit, helical insertion (2);	0.045905	0.85682	D	0.000000	D	0.93641	0.7969	M	0.83012	2.62	0.80722	D	1	B	0.22851	0.076	P	0.45119	0.47	D	0.92582	0.6075	10	0.72032	D	0.01	.	16.2813	0.82687	0.0:0.0:0.0:1.0	.	85	P50148	GNAQ_HUMAN	P	85;56	ENSP00000286548:T85P;ENSP00000391501:T56P	ENSP00000286548:T85P	T	-	1	0	GNAQ	79726965	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.040000	0.89188	2.244000	0.73946	0.533000	0.62120	ACG	.	.		0.468	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1	NM_002072		G	80537145	T	G	80537145	3	3	174	1	0	0	0	0	1	0	0	0	6517	1696	59	5	850	5	GNAQ	9	80537145	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	1218363	80537145	60676286	66	26230										
FBP2	8789	hgsc.bcm.edu	37	chr9	97325637	97325637	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gaattaccttgcccttagggCtcttctggttggctgggtac	12	10	2	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr9:97325637C>A	ENST00000375337.3	-	6	878	c.812G>T	c.(811-813)aGc>aTc	p.S271I	PCAT7_ENST00000452148.2_RNA	NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	271					carbohydrate metabolic process (GO:0005975)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(3)|lung(5)	9		Acute lymphoblastic leukemia(62;0.136)				GCCCTTAGGGCTCTTCTGGTT	0.602																																					p.S271I		Atlas-SNP	.											.	FBP2	26	.	0			c.G812T						.						124	110	115					9																	97325637		2203	4300	6503	SO:0001583	missense	8789	exon6			TTAGGGCTCTTCT	Y10812	CCDS6711.1	9q22.3	2012-08-13			ENSG00000130957	ENSG00000130957	3.1.3.11		3607	protein-coding gene	gene with protein product		603027				9678974	Standard	NM_003837		Approved		uc004auv.3	O00757	OTTHUMG00000020269	ENST00000375337.3:c.812G>T	chr9.hg19:g.97325637C>A	ENSP00000364486:p.Ser271Ile	91.0	0.0		64.0	27.0	NM_003837	Q17R39|Q6FI53	Missense_Mutation	SNP	ENST00000375337.3	hg19	CCDS6711.1	.	.	.	.	.	.	.	.	.	.	.	19.14	3.770242	0.69992	.	.	ENSG00000130957	ENST00000375337	T	0.72942	-0.7	4.82	2.98	0.34508	.	0.209991	0.64402	D	0.000020	D	0.82462	0.5042	M	0.83774	2.66	0.80722	D	1	D	0.64830	0.994	D	0.67548	0.952	D	0.83458	0.0052	10	0.87932	D	0	-7.7843	11.0091	0.47652	0.0:0.8485:0.0:0.1515	.	271	O00757	F16P2_HUMAN	I	271	ENSP00000364486:S271I	ENSP00000364486:S271I	S	-	2	0	FBP2	96365458	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	3.041000	0.49807	0.650000	0.30769	-0.384000	0.06662	AGC	.	.		0.602	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837		A	97325637	C	A	97325637	3	1	174	1	0	0	0	0	1	0	0	0	5714	797	28	3	215	3	FBP2	9	97325637	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	16788492	97325637	43887794	67	26231										
OR13C3	138803	hgsc.bcm.edu	37	chr9	107298521	107298521	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gaaaggcagtctcatggcaaGtaatgtttgcacagctgaat	11	7	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr9:107298521G>A	ENST00000374781.2	-	1	616	c.574C>T	c.(574-576)Ctt>Ttt	p.L192F		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						CTCATGGCAAGTAATGTTTGC	0.453																																					p.L192F	GBM(86;1248 1274 14222 15028 46219)	Atlas-SNP	.											.	OR13C3	45	.	0			c.C574T						.						137	137	137					9																	107298521		2203	4300	6503	SO:0001583	missense	138803	exon1			TGGCAAGTAATGT		CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"GPCR / Class A : Olfactory receptors"	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.574C>T	chr9.hg19:g.107298521G>A	ENSP00000363913:p.Leu192Phe	124.0	0.0		169.0	81.0	NM_001001961	Q5VVG1|Q6IF52	Missense_Mutation	SNP	ENST00000374781.2	hg19	CCDS35089.1	.	.	.	.	.	.	.	.	.	.	G	9.337	1.062024	0.19987	.	.	ENSG00000204246	ENST00000374781	T	0.00145	8.67	4.45	3.55	0.40652	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37219	N	0.002197	T	0.00144	0.0004	L	0.35288	1.05	0.20403	N	0.999907	P	0.37061	0.58	B	0.41036	0.346	T	0.38650	-0.9651	10	0.35671	T	0.21	.	10.1372	0.42715	0.0982:0.0:0.9018:0.0	.	192	Q8NGS6	O13C3_HUMAN	F	192	ENSP00000363913:L192F	ENSP00000363913:L192F	L	-	1	0	OR13C3	106338342	0.268000	0.24133	0.960000	0.40013	0.227000	0.25037	0.775000	0.26689	1.221000	0.43506	0.591000	0.81541	CTT	.	.		0.453	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2			A	107298521	G	A	107298521	3	1	174	1	0	0	0	0	1	0	0	0	10944	1029	36	3	473	3	OR13C3	9	107298521	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	9972884	107298521	33914910	68	26232										
OR1L3	26735	hgsc.bcm.edu	37	chr9	125437750	125437750	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ggaaacatagatagttatctCctggcggctatggccatcaa	10	9	2	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr9:125437750C>A	ENST00000304820.2	+	1	436	c.342C>A	c.(340-342)ctC>ctA	p.L114L		NM_001005234.1	NP_001005234.1	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L, member 3	114						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	16						ATAGTTATCTCCTGGCGGCTA	0.433																																					p.L114L		Atlas-SNP	.											.	OR1L3	51	.	0			c.C342A						.						153	154	154					9																	125437750		2203	4300	6503	SO:0001819	synonymous_variant	26735	exon1			TTATCTCCTGGCG		CCDS35128.1	9q33.2	2013-09-20			ENSG00000171481	ENSG00000171481		"GPCR / Class A : Olfactory receptors"	8215	protein-coding gene	gene with protein product							Standard	NM_001005234		Approved	OR9-D	uc011lzb.2	Q8NH93	OTTHUMG00000020619	ENST00000304820.2:c.342C>A	chr9.hg19:g.125437750C>A		62.0	0.0		76.0	25.0	NM_001005234	B2RNF4|Q6IFN1	Silent	SNP	ENST00000304820.2	hg19	CCDS35128.1																																																																																			.	.		0.433	OR1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053950.1			A	125437750	C	A	125437750	2	1	174	1	0	0	0	0	0	0	0	1	10973	842	30	3		3	OR1L3	9	125437750	Silent	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	18139229	125437750	15775681	69	26233										
NR5A1	2516	hgsc.bcm.edu	37	chr9	127253385	127253385	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ctgaagaggatgatgaacttGaggcagacaaactcctgccg	12	9	0	6			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr9:127253385G>A	ENST00000373588.4	-	6	1309	c.1113C>T	c.(1111-1113)ctC>ctT	p.L371L		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	371	Important for dimerization.				adrenal gland development (GO:0030325)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|hormone metabolic process (GO:0042445)|intracellular receptor signaling pathway (GO:0030522)|luteinization (GO:0001553)|maintenance of protein location in nucleus (GO:0051457)|male gonad development (GO:0008584)|multicellular organismal aging (GO:0010259)|negative regulation of female gonad development (GO:2000195)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|primary sex determination (GO:0007538)|regulation of steroid biosynthetic process (GO:0050810)|tissue development (GO:0009888)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)	2						TGATGAACTTGAGGCAGACAA	0.652																																					p.L371L		Atlas-SNP	.											.	NR5A1	32	.	0			c.C1113T						.						17	18	17					9																	127253385		2200	4298	6498	SO:0001819	synonymous_variant	2516	exon6			GAACTTGAGGCAG	D88155	CCDS6856.1	9q33	2013-01-16			ENSG00000136931	ENSG00000136931		"Nuclear hormone receptors"	7983	protein-coding gene	gene with protein product		184757		FTZF1		7789992	Standard	NM_004959		Approved	FTZ1, SF-1, ELP, AD4BP	uc004boo.1	Q13285	OTTHUMG00000020655	ENST00000373588.4:c.1113C>T	chr9.hg19:g.127253385G>A		131.0	0.0		131.0	53.0	NM_004959	O15196|Q5T6F5	Silent	SNP	ENST00000373588.4	hg19	CCDS6856.1																																																																																			.	.		0.652	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959		A	127253385	G	A	127253385	2	1	174	1	0	0	0	0	0	0	0	1	10644	1277	45	3		3	NR5A1	9	127253385	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	1815635	127253385	13960046	70	26234										
RALGDS	5900	hgsc.bcm.edu	37	chr9	135983386	135983386	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gctgctcaccgcatccatcaGtgtaaactgctctgccacca	7	16	3	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr9:135983386G>A	ENST00000372050.3	-	6	1207	c.1186C>T	c.(1186-1188)Ctg>Ttg	p.L396L	RALGDS_ENST00000542690.1_Silent_p.L467L|RALGDS_ENST00000372062.3_Silent_p.L367L|RALGDS_ENST00000469972.1_5'UTR|RALGDS_ENST00000372047.3_Silent_p.L384L|RALGDS_ENST00000393160.3_Silent_p.L341L|RALGDS_ENST00000393157.3_Silent_p.L395L	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	396	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		GCATCCATCAGTGTAAACTGC	0.592			T	CIITA	"PMBL, Hodgkin Lymphona, "																																p.L396L	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.C1186T						.						77	62	67					9																	135983386		2203	4299	6502	SO:0001819	synonymous_variant	5900	exon6			CCATCAGTGTAAA	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.1186C>T	chr9.hg19:g.135983386G>A		74.0	0.0		67.0	26.0	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	hg19	CCDS6959.1																																																																																			.	.		0.592	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266		A	135983386	G	A	135983386	2	1	174	1	0	0	0	0	0	0	0	1	13031	1020	36	3		3	RALGDS	9	135983386	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	8730001	135983386	5230045	71	26235										
TAF3	83860	hgsc.bcm.edu	37	chr10	8051233	8051233	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tccccgggtcccgccgcctcCggggccagtgccaaagcccc	12	21	0	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr10:8051233C>T	ENST00000344293.5	+	5	2714	c.2508C>T	c.(2506-2508)tcC>tcT	p.S836S		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	836					maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						ccgccgcctccGGGGCCAGTG	0.751																																					p.S836S		Atlas-SNP	.											.	TAF3	93	.	0			c.C2508T						.						7	7	7					10																	8051233		1524	3380	4904	SO:0001819	synonymous_variant	83860	exon5			CGCCTCCGGGGCC	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"Zinc fingers, PHD-type"	17303	protein-coding gene	gene with protein product		606576	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.2508C>T	chr10.hg19:g.8051233C>T		49.0	0.0		51.0	29.0	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Silent	SNP	ENST00000344293.5	hg19	CCDS41487.1																																																																																			.	.		0.751	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		T	8051233	C	T	8051233	2	4	174	1	0	0	0	0	0	0	0	1	15540	639	23	1		1	TAF3	10	8051233	Silent	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10		8051233	127483514	72	26236										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24832401	24832401	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tctttccagtggggaggtgcAtgatattgttagccaaaagg	13	6	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr10:24832401A>G	ENST00000376454.3	+	19	4232	c.4202A>G	c.(4201-4203)cAt>cGt	p.H1401R	KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376451.2_Missense_Mutation_p.H1084R|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000396446.1_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1401					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						GGGGAGGTGCATGATATTGTT	0.458																																					p.H1401R		Atlas-SNP	.											.	KIAA1217	235	.	0			c.A4202G						.						92	91	91					10																	24832401		2203	4300	6503	SO:0001583	missense	56243	exon19			AGGTGCATGATAT	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.4202A>G	chr10.hg19:g.24832401A>G	ENSP00000365637:p.His1401Arg	138.0	0.0		113.0	55.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	A	0.603	-0.828264	0.02734	.	.	ENSG00000120549	ENST00000442879;ENST00000376454;ENST00000450158;ENST00000376451	T;T	0.29655	1.98;1.56	5.66	-2.54	0.06307	.	0.558711	0.18634	N	0.135510	T	0.11324	0.0276	N	0.04880	-0.145	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.004;0.001	T	0.35943	-0.9768	10	0.07482	T	0.82	.	11.8256	0.52265	0.6774:0.0:0.3226:0.0	.	1084;1084;1401	C9JRK3;Q5T5P2-3;Q5T5P2	.;.;SKT_HUMAN	R	1084;1401;1084;1084	ENSP00000365637:H1401R;ENSP00000365634:H1084R	ENSP00000365634:H1084R	H	+	2	0	KIAA1217	24872407	0.660000	0.27420	0.014000	0.15608	0.014000	0.08584	1.429000	0.34903	-0.359000	0.08150	-0.366000	0.07423	CAT	.	.		0.458	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		G	24832401	A	G	24832401	3	3	174	1	0	0	0	0	1	0	0	0	8225	217	8	2	4276	2	KIAA1217	10	24832401	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	16781168	24832401	110702346	73	26237										
SVIL	6840	hgsc.bcm.edu	37	chr10	29818721	29818721	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gcctctgctccacagctgtgTttcttgagcgtcgctttgga	11	12	2	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr10:29818721T>G	ENST00000355867.4	-	12	2911	c.2159A>C	c.(2158-2160)aAc>aCc	p.N720T	SVIL_ENST00000375398.2_Missense_Mutation_p.N720T|SVIL_ENST00000375400.3_Missense_Mutation_p.N326T	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	720					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CACAGCTGTGTTTCTTGAGCG	0.483																																					p.N720T		Atlas-SNP	.											.	SVIL	226	.	0			c.A2159C						.						123	111	115					10																	29818721		2203	4300	6503	SO:0001583	missense	6840	exon12			GCTGTGTTTCTTG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.2159A>C	chr10.hg19:g.29818721T>G	ENSP00000348128:p.Asn720Thr	68.0	0.0		64.0	28.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	T	7.792	0.711711	0.15306	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.57107	0.42;0.42;0.42	5.14	1.41	0.22369	.	0.171432	0.64402	D	0.000009	T	0.51143	0.1657	M	0.75264	2.295	0.21445	N	0.999689	P;P	0.48089	0.905;0.749	P;B	0.45610	0.487;0.345	T	0.46541	-0.9184	9	.	.	.	-15.5244	5.7999	0.18408	0.0:0.2287:0.1314:0.64	.	326;720	O95425-2;O95425	.;SVIL_HUMAN	T	326;720;720	ENSP00000364549:N326T;ENSP00000364547:N720T;ENSP00000348128:N720T	.	N	-	2	0	SVIL	29858727	0.999000	0.42202	0.000000	0.03702	0.021000	0.10359	3.128000	0.50492	0.050000	0.15949	-0.347000	0.07816	AAC	.	.		0.483	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			G	29818721	T	G	29818721	3	3	174	1	0	0	0	0	1	0	0	0	15436	1725	60	5	4593	5	SVIL	10	29818721	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	4986320	29818721	105716026	74	26238										
GJD4	219770	hgsc.bcm.edu	37	chr10	35897329	35897329	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	attccggatgaggatgagagTgaggtgacatcctccgccag	14	9	0	4			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr10:35897329T>A	ENST00000321660.1	+	2	1046	c.888T>A	c.(886-888)agT>agA	p.S296R	RP11-425A6.5_ENST00000609313.1_RNA	NM_153368.2	NP_699199.2	Q96KN9	CXD4_HUMAN	gap junction protein, delta 4, 40.1kDa	296					cell communication (GO:0007154)|regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014717)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						AGGATGAGAGTGAGGTGACAT	0.711																																					p.S296R		Atlas-SNP	.											.	GJD4	38	.	0			c.T888A						.						16	17	17					10																	35897329		2069	4082	6151	SO:0001583	missense	219770	exon2			TGAGAGTGAGGTG	AJ414564	CCDS7191.1	10p11.22	2007-11-27			ENSG00000177291	ENSG00000177291		"Ion channels / Gap junction proteins (connexins)"	23296	protein-coding gene	gene with protein product	"connexin 40.1"	611922				12477932	Standard	NM_153368		Approved	CX40.1, FLJ90023	uc001iyy.1	Q96KN9	OTTHUMG00000017957	ENST00000321660.1:c.888T>A	chr10.hg19:g.35897329T>A	ENSP00000315070:p.Ser296Arg	68.0	0.0		65.0	26.0	NM_153368	Q8N2R7	Missense_Mutation	SNP	ENST00000321660.1	hg19	CCDS7191.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.173242	0.78452	.	.	ENSG00000177291	ENST00000321660	D	0.98135	-4.74	5.86	-5.48	0.02592	.	19.071300	0.00166	N	0.000000	D	0.93844	0.8031	L	0.32530	0.975	0.09310	N	1	B	0.34290	0.447	B	0.26094	0.066	D	0.89009	0.3427	10	0.40728	T	0.16	.	10.6215	0.45483	0.0:0.5915:0.1295:0.279	.	296	Q96KN9	CXD4_HUMAN	R	296	ENSP00000315070:S296R	ENSP00000315070:S296R	S	+	3	2	GJD4	35937335	0.001000	0.12720	0.117000	0.21633	0.282000	0.26991	-1.065000	0.03458	-0.794000	0.04468	-0.274000	0.10170	AGT	.	.		0.711	GJD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047576.1	NM_153368		A	35897329	T	A	35897329	3	1	174	1	0	0	0	0	1	0	0	0	6427	1693	59	4	894	4	GJD4	10	35897329	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	6078608	35897329	99637418	75	26239										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55780163	55780163	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	aagacacatttgctccaaggTcgacatctttggcctgtaat	8	10	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr10:55780163T>A	ENST00000320301.6	-	20	2934	c.2540A>T	c.(2539-2541)gAc>gTc	p.D847V	PCDH15_ENST00000437009.1_Missense_Mutation_p.D776V|PCDH15_ENST00000395445.1_Missense_Mutation_p.D854V|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000373955.1_Missense_Mutation_p.D847V|PCDH15_ENST00000395432.2_Missense_Mutation_p.D810V|PCDH15_ENST00000395430.1_Missense_Mutation_p.D847V|PCDH15_ENST00000395433.1_Missense_Mutation_p.D825V|PCDH15_ENST00000373965.2_Missense_Mutation_p.D854V|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.D847V|PCDH15_ENST00000395438.1_Missense_Mutation_p.D847V|PCDH15_ENST00000409834.1_Missense_Mutation_p.D458V|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000414778.1_Missense_Mutation_p.D852V	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	847	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TGCTCCAAGGTCGACATCTTT	0.398										HNSCC(58;0.16)																											p.D852V		Atlas-SNP	.											PCDH15_ENST00000417177,colon,carcinoma,-1,4	PCDH15	1715	.	0			c.A2555T						.						128	128	128					10																	55780163		2203	4298	6501	SO:0001583	missense	65217	exon21			CCAAGGTCGACAT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.2540A>T	chr10.hg19:g.55780163T>A	ENSP00000322604:p.Asp847Val	65.0	0.0		74.0	22.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.425635	0.83667	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87	5.92	5.92	0.95590	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.90403	0.6996	H	0.95816	3.725	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;0.999;0.999;0.999;0.999;0.999;1.0;0.995;0.998;0.999;0.999;0.998;0.992;0.999	D	0.93098	0.6506	9	0.87932	D	0	.	16.0292	0.80564	0.0:0.0:0.0:1.0	.	825;847;847;852;776;810;847;847;854;854;847;852;847;847	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	V	854;852;847;847;458;854;810;847;825;847;847;852;776;847	ENSP00000363076:D854V;ENSP00000410304:D852V;ENSP00000378826:D847V;ENSP00000386693:D458V;ENSP00000378832:D854V;ENSP00000378820:D810V;ENSP00000354950:D847V;ENSP00000378821:D825V;ENSP00000322604:D847V;ENSP00000378818:D847V;ENSP00000412628:D776V;ENSP00000363066:D847V	ENSP00000322604:D847V	D	-	2	0	PCDH15	55450169	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.274000	0.78538	2.254000	0.74563	0.528000	0.53228	GAC	.	.		0.398	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55780163	T	A	55780163	3	1	174	1	0	0	0	0	1	0	0	0	11520	1667	58	4	5002	4	PCDH15	10	55780163	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	19882834	55780163	79754584	76	26240										
LRRTM3	347731	hgsc.bcm.edu	37	chr10	68686716	68686716	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ctactgagcggatcagctgtAgcactggttatagcccccac	10	13	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr10:68686716A>G	ENST00000361320.4	+	2	620	c.42A>G	c.(40-42)gtA>gtG	p.V14V	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	14					positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						GATCAGCTGTAGCACTGGTTA	0.418																																					p.V14V		Atlas-SNP	.											.	LRRTM3	241	.	0			c.A42G						.						85	79	81					10																	68686716		2203	4300	6503	SO:0001819	synonymous_variant	347731	exon2			AGCTGTAGCACTG	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.42A>G	chr10.hg19:g.68686716A>G		98.0	0.0		85.0	36.0	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Silent	SNP	ENST00000361320.4	hg19	CCDS7270.1																																																																																			.	.		0.418	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011		G	68686716	A	G	68686716	2	3	174	1	0	0	0	0	0	0	0	1	9050	407	15	2		2	LRRTM3	10	68686716	Silent	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	12906553	68686716	66848031	77	26241										
TYSND1	219743	hgsc.bcm.edu	37	chr10	71905831	71905831	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gatccgcctcctcgtcctccGacacttcgtcatcccgcgcc	7	21	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr10:71905831G>C	ENST00000287078.6	-	1	511	c.512C>G	c.(511-513)tCg>tGg	p.S171W	TYSND1_ENST00000494143.1_5'Flank|TYSND1_ENST00000335494.5_Missense_Mutation_p.S171W	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	171					protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						CTCGTCCTCCGACACTTCGTC	0.706																																					p.S171W		Atlas-SNP	.											TYSND1,NS,carcinoma,0,1	TYSND1	20	.	0			c.C512G						.						21	22	21					10																	71905831		2198	4286	6484	SO:0001583	missense	219743	exon1			TCCTCCGACACTT	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.512C>G	chr10.hg19:g.71905831G>C	ENSP00000287078:p.Ser171Trp	101.0	1.0		132.0	55.0	NM_173555	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	Missense_Mutation	SNP	ENST00000287078.6	hg19	CCDS31213.1	.	.	.	.	.	.	.	.	.	.	G	11.11	1.542848	0.27563	.	.	ENSG00000156521	ENST00000287078;ENST00000335494	T;T	0.68181	-0.31;-0.31	3.93	3.02	0.34903	.	0.678025	0.14678	N	0.304895	T	0.71896	0.3394	L	0.57536	1.79	0.42249	D	0.991966	D;D	0.67145	0.996;0.979	P;P	0.58172	0.834;0.687	T	0.71573	-0.4552	10	0.72032	D	0.01	-22.5129	7.826	0.29315	0.1182:0.0:0.8818:0.0	.	171;171	Q2T9J0-2;Q2T9J0	.;TYSD1_HUMAN	W	171	ENSP00000287078:S171W;ENSP00000335673:S171W	ENSP00000287078:S171W	S	-	2	0	TYSND1	71575837	0.979000	0.34478	0.847000	0.33407	0.040000	0.13550	2.413000	0.44618	0.975000	0.38392	-0.657000	0.03884	TCG	.	.		0.706	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555		C	71905831	G	C	71905831	3	2	174	1	0	0	0	0	1	0	0	0	16832	1059	37	4	1204	4	TYSND1	10	71905831	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	3219115	71905831	63628916	78	26242										
C11orf17	56672	hgsc.bcm.edu	37	chr11	8940933	8940933	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	agaagtatatccagggacctAttctgtcactgtgggctcaa	10	9	3	1	rs148121612		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr11:8940933A>C	ENST00000309377.4	+	6	629	c.539A>C	c.(538-540)tAt>tCt	p.Y180S	AKIP1_ENST00000534147.1_Missense_Mutation_p.Y180S|AKIP1_ENST00000309357.4_Missense_Mutation_p.Y153S|AKIP1_ENST00000299576.5_Missense_Mutation_p.Y153S|AKIP1_ENST00000396648.2_Missense_Mutation_p.Y153S	NM_020642.3	NP_065693.2	Q9NQ31	AKIP1_HUMAN	A kinase (PRKA) interacting protein 1	180					substrate adhesion-dependent cell spreading (GO:0034446)	nucleus (GO:0005634)				kidney(1)|large_intestine(2)|lung(2)	5						CCAGGGACCTATTCTGTCACT	0.443																																					p.Y180S		Atlas-SNP	.											.	AKIP1	9	.	0			c.A539C						.						176	168	171					11																	8940933		2201	4296	6497	SO:0001583	missense	56672	exon6			GGACCTATTCTGT	AF512007	CCDS7793.1, CCDS55743.1, CCDS55744.1	11p15.3	2011-04-18	2011-04-18	2011-04-18	ENSG00000166452	ENSG00000166452			1170	protein-coding gene	gene with protein product		609191	"chromosome 11 open reading frame 17"	C11orf17		20562110, 18178962, 15630084	Standard	NM_020642		Approved	BCA3	uc001mgx.3	Q9NQ31	OTTHUMG00000165653	ENST00000309377.4:c.539A>C	chr11.hg19:g.8940933A>C	ENSP00000310459:p.Tyr180Ser	81.0	0.0		100.0	41.0	NM_020642	Q8NBS2|Q8TAC6|Q8TAD3|Q8TAE0	Missense_Mutation	SNP	ENST00000309377.4	hg19	CCDS7793.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.472495	0.84640	.	.	ENSG00000166452	ENST00000299576;ENST00000309377;ENST00000309357;ENST00000530281;ENST00000396648;ENST00000534147;ENST00000529942	T;T;T;T;T;T;T	0.62941	0.1;0.02;1.16;-0.01;0.1;0.02;0.19	6.07	6.07	0.98685	.	0.145914	0.47093	D	0.000242	T	0.79435	0.4445	M	0.78637	2.42	0.45452	D	0.998429	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.81920	-0.0712	10	0.87932	D	0	-13.4518	14.3816	0.66914	1.0:0.0:0.0:0.0	.	153;153;180	Q9NQ31-2;Q9NQ31-3;Q9NQ31	.;.;AKIP1_HUMAN	S	153;180;153;92;153;180;121	ENSP00000299576:Y153S;ENSP00000310459:Y180S;ENSP00000310644:Y153S;ENSP00000436989:Y92S;ENSP00000379885:Y153S;ENSP00000431331:Y180S;ENSP00000431602:Y121S	ENSP00000299576:Y153S	Y	+	2	0	AKIP1	8897509	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.888000	0.69758	2.326000	0.78906	0.533000	0.62120	TAT	.	A|1.000;G|0.000		0.443	AKIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385615.1	NM_020642		C	8940933	A	C	8940933	3	2	174	1	0	0	0	0	1	0	0	0	1634	449	16	5	557	5	C11orf17	11	8940933	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10		8940933	126065583	79	26243										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33628297	33628297	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tgcagctcattgccataaaaCccacagccctccccatggtg	7	16	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr11:33628297C>T	ENST00000321505.4	+	13	4279	c.4099C>T	c.(4099-4101)Ccc>Tcc	p.P1367S	KIAA1549L_ENST00000389726.3_Missense_Mutation_p.P1373S			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1367						integral component of membrane (GO:0016021)											TGCCATAAAACCCACAGCCCT	0.592																																					p.P1367S		Atlas-SNP	.											.	.	.	.	0			c.C4099T						.						42	47	45					11																	33628297		2045	4212	6257	SO:0001583	missense	25758	exon13			ATAAAACCCACAG	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.4099C>T	chr11.hg19:g.33628297C>T	ENSP00000315295:p.Pro1367Ser	135.0	0.0		111.0	43.0	NM_012194	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	hg19	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	C	29.1	4.974170	0.92919	.	.	ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000536568	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.83543	0.5277	M	0.80746	2.51	0.49130	D	0.999759	D	0.89917	1.0	D	0.97110	1.0	D	0.85544	0.1217	9	0.87932	D	0	-12.262	19.2455	0.93901	0.0:1.0:0.0:0.0	.	1373	E9PAT2	.	S	1367;1373;1206	.	ENSP00000315295:P1367S	P	+	1	0	C11orf41	33584873	1.000000	0.71417	0.995000	0.50966	0.911000	0.54048	7.001000	0.76297	2.553000	0.86117	0.561000	0.74099	CCC	.	.		0.592	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		T	33628297	C	T	33628297	3	4	174	1	0	0	0	0	1	0	0	0	1642	507	18	3	4167	3	C11orf41	11	33628297	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	24687364	33628297	101378219	80	26244										
FNBP4	23360	hgsc.bcm.edu	37	chr11	47765677	47765677	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gaacgtggactagaccctgaCacactaccatctccttcctc	6	16	1	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr11:47765677C>T	ENST00000263773.5	-	8	1296	c.1284G>A	c.(1282-1284)gtG>gtA	p.V428V	FNBP4_ENST00000534003.1_5'UTR	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	428						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						TAGACCCTGACACACTACCAT	0.413																																					p.V428V		Atlas-SNP	.											.	FNBP4	99	.	0			c.G1284A						.						116	106	109					11																	47765677		2060	4212	6272	SO:0001819	synonymous_variant	23360	exon8			CCCTGACACACTA	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.1284G>A	chr11.hg19:g.47765677C>T		81.0	0.0		89.0	50.0	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Silent	SNP	ENST00000263773.5	hg19	CCDS41644.1																																																																																			.	.		0.413	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			T	47765677	C	T	47765677	2	4	174	1	0	0	0	0	0	0	0	1	5975	465	17	3		3	FNBP4	11	47765677	Silent	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	14137380	47765677	87240839	81	26245										
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563337	55563337	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tactttagctgcatgatgcaGtacttcctgtcctgcactgc	8	12	0	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr11:55563337G>T	ENST00000335605.1	+	1	306	c.306G>T	c.(304-306)caG>caT	p.Q102H		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	102						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				GCATGATGCAGTACTTCCTGT	0.453																																					p.Q102H		Atlas-SNP	.											.	OR5D14	116	.	0			c.G306T						.						146	120	129					11																	55563337		2200	4296	6496	SO:0001583	missense	219436	exon1			GATGCAGTACTTC	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.306G>T	chr11.hg19:g.55563337G>T	ENSP00000334456:p.Gln102His	82.0	0.0		81.0	32.0	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	hg19	CCDS31508.1	.	.	.	.	.	.	.	.	.	.	g	10.81	1.455709	0.26161	.	.	ENSG00000186113	ENST00000335605	T	0.00472	7.19	5.08	-0.673	0.11373	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	D	0.000640	T	0.01905	0.0060	H	0.97564	4.03	0.25512	N	0.987452	D	0.89917	1.0	D	0.85130	0.997	T	0.23868	-1.0176	10	0.87932	D	0	-11.5909	6.5701	0.22533	0.3373:0.1282:0.5345:0.0	.	102	Q8NGL3	OR5DE_HUMAN	H	102	ENSP00000334456:Q102H	ENSP00000334456:Q102H	Q	+	3	2	OR5D14	55319913	0.000000	0.05858	0.113000	0.21522	0.018000	0.09664	-0.121000	0.10643	0.189000	0.20188	-0.149000	0.13747	CAG	.	.		0.453	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		T	55563337	G	T	55563337	3	4	174	1	0	0	0	0	1	0	0	0	11164	1020	36	3	308	3	OR5D14	11	55563337	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	7797660	55563337	79443179	82	26246										
SLC29A2	3177	hgsc.bcm.edu	37	chr11	66136932	66136932	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ttgaagttgaaggcatcctcGggacccgtgtggttggtgct	15	8	0	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr11:66136932G>A	ENST00000357440.2	-	3	411	c.183C>T	c.(181-183)ccC>ccT	p.P61P	SLC29A2_ENST00000546034.1_Silent_p.P61P|SLC29A2_ENST00000311161.7_Silent_p.P61P|SLC29A2_ENST00000544554.1_Silent_p.P61P	NM_001532.2	NP_001523.2	Q14542	S29A2_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 2	61					cell proliferation (GO:0008283)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			breast(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10					Didanosine(DB00900)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Zalcitabine(DB00943)|Zidovudine(DB00495)	AGGCATCCTCGGGACCCGTGT	0.627																																					p.P61P		Atlas-SNP	.											SLC29A2,NS,carcinoma,0,1	SLC29A2	24	.	0			c.C183T						.						204	194	198					11																	66136932		2200	4295	6495	SO:0001819	synonymous_variant	3177	exon3			ATCCTCGGGACCC	X86681	CCDS8137.1, CCDS73326.1	11q13	2013-07-17	2013-07-17		ENSG00000174669	ENSG00000174669		"Solute carriers"	11004	protein-coding gene	gene with protein product		602110	"solute carrier family 29 (nucleoside transporters), member 2"	ENT2, HNP36		9192854, 9478986	Standard	NM_001532		Approved	DER12	uc001oht.3	Q14542	OTTHUMG00000169056	ENST00000357440.2:c.183C>T	chr11.hg19:g.66136932G>A		107.0	0.0		124.0	63.0	NM_001532	B3KPY7|O43530|Q52M84|Q96R00|Q9UPE0	Silent	SNP	ENST00000357440.2	hg19	CCDS8137.1																																																																																			.	.		0.627	SLC29A2-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402093.1	NM_001532		A	66136932	G	A	66136932	2	1	174	1	0	0	0	0	0	0	0	1	14550	1103	39	1		1	SLC29A2	11	66136932	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	10573595	66136932	68869584	83	26247										
APOA1	335	hgsc.bcm.edu	37	chr11	116707867	116707867	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gctgccagaaatgccgagccTggctccctgagggtgggagg	17	11	0	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr11:116707867T>A	ENST00000236850.4	-	3	415	c.50A>T	c.(49-51)cAg>cTg	p.Q17L	APOA1_ENST00000359492.2_Missense_Mutation_p.Q17L|APOA1_ENST00000375329.2_Intron|APOA1_ENST00000375320.1_Missense_Mutation_p.Q17L|APOA1_ENST00000375323.1_Missense_Mutation_p.Q17L|AP006216.12_ENST00000444200.1_RNA	NM_000039.1	NP_000030.1	P02647	APOA1_HUMAN	apolipoprotein A-I	17					adrenal gland development (GO:0030325)|blood coagulation (GO:0007596)|blood vessel endothelial cell migration (GO:0043534)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endothelial cell proliferation (GO:0001935)|G-protein coupled receptor signaling pathway (GO:0007186)|glucocorticoid metabolic process (GO:0008211)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|integrin-mediated signaling pathway (GO:0007229)|lipid storage (GO:0019915)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|negative chemotaxis (GO:0050919)|negative regulation of cell adhesion molecule production (GO:0060354)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of lipase activity (GO:0060192)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of very-low-density lipoprotein particle remodeling (GO:0010903)|organ regeneration (GO:0031100)|peptidyl-methionine modification (GO:0018206)|peripheral nervous system axon regeneration (GO:0014012)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of hydrolase activity (GO:0051345)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transferase activity (GO:0051347)|protein oxidation (GO:0018158)|protein stabilization (GO:0050821)|regulation of Cdc42 protein signal transduction (GO:0032489)|regulation of intestinal cholesterol absorption (GO:0030300)|regulation of protein phosphorylation (GO:0001932)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to nutrient (GO:0007584)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule lumen (GO:0034774)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)|vesicle (GO:0031982)	apolipoprotein A-I receptor binding (GO:0034191)|apolipoprotein receptor binding (GO:0034190)|beta-amyloid binding (GO:0001540)|chemorepellent activity (GO:0045499)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|enzyme binding (GO:0019899)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor binding (GO:0070653)|identical protein binding (GO:0042802)|lipase inhibitor activity (GO:0055102)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)			cervix(1)|endometrium(1)|lung(4)|prostate(1)|skin(2)	9	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.59e-05)|all cancers(92;0.000162)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		ATGCCGAGCCTGGCTCCCTGA	0.637																																					p.Q17L		Atlas-SNP	.											.	APOA1	19	.	0			c.A50T	GRCh37	CI082223	APOA1	I		.						46	53	51					11																	116707867		2201	4293	6494	SO:0001583	missense	335	exon3			CGAGCCTGGCTCC	X02162	CCDS8378.1	11q23-q24	2014-09-17			ENSG00000118137	ENSG00000118137		"Apolipoproteins"	600	protein-coding gene	gene with protein product		107680					Standard	NM_000039		Approved		uc001ppv.1	P02647	OTTHUMG00000046112	ENST00000236850.4:c.50A>T	chr11.hg19:g.116707867T>A	ENSP00000236850:p.Gln17Leu	42.0	0.0		42.0	19.0	NM_000039	A8K866|Q6LDN9|Q6Q785|Q9UCS8|Q9UCT8	Missense_Mutation	SNP	ENST00000236850.4	hg19	CCDS8378.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.299122	0.81025	.	.	ENSG00000118137	ENST00000375320;ENST00000359492;ENST00000375323;ENST00000236850	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	4.76	4.76	0.60689	.	0.000000	0.45867	U	0.000325	D	0.86397	0.5923	M	0.91406	3.205	0.54753	D	0.999988	D	0.89917	1.0	D	0.71414	0.973	D	0.89682	0.3891	10	0.87932	D	0	-28.1483	14.2749	0.66173	0.0:0.0:0.0:1.0	.	17	P02647	APOA1_HUMAN	L	17	ENSP00000364469:Q17L;ENSP00000352471:Q17L;ENSP00000364472:Q17L;ENSP00000236850:Q17L	ENSP00000236850:Q17L	Q	-	2	0	APOA1	116213077	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.597000	0.54031	1.779000	0.52309	0.379000	0.24179	CAG	.	.		0.637	APOA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106281.2	NM_000039		A	116707867	T	A	116707867	3	1	174	1	0	0	0	0	1	0	0	0	780	1580	55	4	761	4	APOA1	11	116707867	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	50570935	116707867	18298649	84	26248										
ROBO3	64221	hgsc.bcm.edu	37	chr11	124740076	124740076	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	catagagcgtccctcattccTgcgcagaccagtgaatcagg	10	13	2	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr11:124740076T>A	ENST00000397801.1	+	5	974	c.782T>A	c.(781-783)cTg>cAg	p.L261Q	ROBO3_ENST00000538940.1_Missense_Mutation_p.L239Q	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	261	Ig-like C2-type 3.				axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		CCCTCATTCCTGCGCAGACCA	0.552																																					p.L261Q		Atlas-SNP	.											.	ROBO3	199	.	0			c.T782A						.						126	132	130					11																	124740076		2060	4202	6262	SO:0001583	missense	64221	exon5			CATTCCTGCGCAG	AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13433	protein-coding gene	gene with protein product		608630	"roundabout (axon guidance receptor, Drosophila) homolog 3", "horizontal gaze palsy with progressive scoliosis"	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.782T>A	chr11.hg19:g.124740076T>A	ENSP00000380903:p.Leu261Gln	107.0	0.0		117.0	54.0	NM_022370		Missense_Mutation	SNP	ENST00000397801.1	hg19	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	T	16.69	3.193156	0.58017	.	.	ENSG00000154134	ENST00000397801;ENST00000538940	T;T	0.41065	1.01;1.01	4.92	4.92	0.64577	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.29473	N	0.012046	T	0.55955	0.1953	L	0.52759	1.655	0.28212	N	0.926877	D	0.76494	0.999	D	0.75484	0.986	T	0.51521	-0.8695	10	0.49607	T	0.09	.	11.4352	0.50064	0.0:0.0:0.1505:0.8495	.	261	Q96MS0	ROBO3_HUMAN	Q	261;239	ENSP00000380903:L261Q;ENSP00000441797:L239Q	ENSP00000380903:L261Q	L	+	2	0	ROBO3	124245286	0.021000	0.18746	1.000000	0.80357	0.988000	0.76386	2.086000	0.41643	1.980000	0.57719	0.379000	0.24179	CTG	.	.		0.552	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		A	124740076	T	A	124740076	3	1	174	1	0	0	0	0	1	0	0	0	13530	1580	55	4	800	4	ROBO3	11	124740076	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	8032209	124740076	10266440	85	26249										
SLC37A2	219855	hgsc.bcm.edu	37	chr11	124949588	124949588	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ctctccctgcaggtctgtaaTggactcgtccagaccacagg	10	14	2	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr11:124949588T>C	ENST00000403796.2	+	6	760	c.459T>C	c.(457-459)aaT>aaC	p.N153N	SLC37A2_ENST00000308074.4_Silent_p.N153N|SLC37A2_ENST00000298280.5_Silent_p.N153N|SLC37A2_ENST00000407458.1_Silent_p.N153N	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	153					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		AGGTCTGTAATGGACTCGTCC	0.602																																					p.N153N	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.T459C						.						65	53	57					11																	124949588		2201	4299	6500	SO:0001819	synonymous_variant	219855	exon6			CTGTAATGGACTC	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"Solute carriers"	20644	protein-coding gene	gene with protein product			"solute carrier family 37 (glycerol-3-phosphate transporter), member 2"				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.459T>C	chr11.hg19:g.124949588T>C		111.0	0.0		112.0	43.0	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Silent	SNP	ENST00000403796.2	hg19	CCDS44757.1																																																																																			.	.		0.602	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184		C	124949588	T	C	124949588	2	2	174	1	0	0	0	0	0	0	0	1	14613	1461	51	2		2	SLC37A2	11	124949588	Silent	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	209512	124949588	10056928	86	26250										
CCND2	894	hgsc.bcm.edu	37	chr12	4387935	4387935	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ttcccctccaggagtgggaaCtggtggtgctggggaagttg	17	8	0	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr12:4387935C>G	ENST00000261254.3	+	3	690	c.421C>G	c.(421-423)Ctg>Gtg	p.L141V	RP11-264F23.3_ENST00000539135.1_RNA	NM_001759.3	NP_001750.1	P30279	CCND2_HUMAN	cyclin D2	141	Cyclin N-terminal.				cell cycle (GO:0007049)|cell division (GO:0051301)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of protein phosphorylation (GO:0001934)	chromatin (GO:0000785)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17			all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)			GGAGTGGGAACTGGTGGTGCT	0.572			T	IGL@	"NHL,CLL"																																p.L141V		Atlas-SNP	.		Dom	yes		12	12p13	894	cyclin D2		L	.	CCND2	50	.	0			c.C421G						.						88	93	91					12																	4387935		2203	4300	6503	SO:0001583	missense	894	exon3			TGGGAACTGGTGG	AF518005	CCDS8524.1	12p13	2008-08-04			ENSG00000118971	ENSG00000118971			1583	protein-coding gene	gene with protein product	"G1/S-specific cyclin D2"	123833				1386335	Standard	NM_001759		Approved		uc001qmo.3	P30279	OTTHUMG00000168123	ENST00000261254.3:c.421C>G	chr12.hg19:g.4387935C>G	ENSP00000261254:p.Leu141Val	63.0	0.0		62.0	23.0	NM_001759	A8K531|Q13955|Q5U035	Missense_Mutation	SNP	ENST00000261254.3	hg19	CCDS8524.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.71|12.71	2.019541|2.019541	0.35606|0.35606	.|.	.|.	ENSG00000118971|ENSG00000118971	ENST00000261254|ENST00000536537	T|.	0.12361|.	2.69|.	4.79|4.79	3.67|3.67	0.42095|0.42095	Cyclin, N-terminal (1);Cyclin-like (3);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.64204|0.64204	0.2577|0.2577	L|L	0.60845|0.60845	1.875|1.875	0.80722|0.80722	D|D	1|1	B|.	0.26876|.	0.162|.	B|.	0.39904|.	0.313|.	T|T	0.63346|0.63346	-0.6658|-0.6658	10|5	0.30078|.	T|.	0.28|.	.|.	12.9677|12.9677	0.58494|0.58494	0.0:0.9053:0.0:0.0947|0.0:0.9053:0.0:0.0947	.|.	141|.	P30279|.	CCND2_HUMAN|.	V|S	141|56	ENSP00000261254:L141V|.	ENSP00000261254:L141V|.	L|T	+|+	1|2	2|0	CCND2|CCND2	4258196|4258196	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.886000|0.886000	0.51366|0.51366	4.071000|4.071000	0.57556|0.57556	2.198000|2.198000	0.70561|0.70561	0.561000|0.561000	0.74099|0.74099	CTG|ACT	.	.		0.572	CCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398287.1	NM_001759		G	4387935	C	G	4387935	3	3	174	1	0	0	0	0	1	0	0	0	2919	564	20	4	431	4	CCND2	12	4387935	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10		4387935	129463960	87	26251										
KCNH3	23416	hgsc.bcm.edu	37	chr12	49943969	49943969	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ggccagccgcggctgcctgcGggcactgtctctggccctgc	15	17	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr12:49943969G>A	ENST00000257981.6	+	10	2035	c.1775G>A	c.(1774-1776)cGg>cAg	p.R592Q		NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	592					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						GGCTGCCTGCGGGCACTGTCT	0.677																																					p.R592Q		Atlas-SNP	.											.	KCNH3	88	.	0			c.G1775A						.						28	29	29					12																	49943969		2201	4298	6499	SO:0001583	missense	23416	exon10			GCCTGCGGGCACT	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.1775G>A	chr12.hg19:g.49943969G>A	ENSP00000257981:p.Arg592Gln	80.0	0.0		79.0	42.0	NM_012284	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	hg19	CCDS8786.1	.	.	.	.	.	.	.	.	.	.	G	36	5.915466	0.97099	.	.	ENSG00000135519	ENST00000257981	D	0.96685	-4.09	5.48	5.48	0.80851	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.000000	0.43919	D	0.000502	D	0.98369	0.9458	M	0.88570	2.965	0.54753	D	0.999986	D	0.89917	1.0	D	0.83275	0.996	D	0.99150	1.0858	10	0.87932	D	0	.	17.2178	0.86949	0.0:0.0:1.0:0.0	.	592	Q9ULD8	KCNH3_HUMAN	Q	592	ENSP00000257981:R592Q	ENSP00000257981:R592Q	R	+	2	0	KCNH3	48230236	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.869000	0.99810	2.755000	0.94549	0.655000	0.94253	CGG	.	.		0.677	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284		A	49943969	G	A	49943969	3	1	174	1	0	0	0	0	1	0	0	0	8042	1116	39	1	1813	1	KCNH3	12	49943969	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	45556034	49943969	83907926	88	26252										
STAB2	55576	hgsc.bcm.edu	37	chr12	104100584	104100584	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tttcagacgagagaatgctgTgccggcttctttggccccca	11	12	2	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr12:104100584T>C	ENST00000388887.2	+	38	4215	c.4011T>C	c.(4009-4011)tgT>tgC	p.C1337C		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GAGAATGCTGTGCCGGCTTCT	0.532																																					p.C1337C		Atlas-SNP	.											.	STAB2	370	.	0			c.T4011C						.						123	122	122					12																	104100584		2203	4300	6503	SO:0001819	synonymous_variant	55576	exon38			ATGCTGTGCCGGC	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.4011T>C	chr12.hg19:g.104100584T>C		107.0	0.0		97.0	34.0	NM_017564		Silent	SNP	ENST00000388887.2	hg19	CCDS31888.1																																																																																			.	.		0.532	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			C	104100584	T	C	104100584	2	2	174	1	0	0	0	0	0	0	0	1	15253	1702	59	2		2	STAB2	12	104100584	Silent	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	54156615	104100584	29751311	89	26253										
ZDHHC20	253832	hgsc.bcm.edu	37	chr13	22033279	22033279	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gcacccagcccacgacgcgcTggcagcagcgccacagcgtc	12	19	0	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr13:22033279T>C	ENST00000400590.3	-	1	230	c.32A>G	c.(31-33)cAg>cGg	p.Q11R	ZDHHC20_ENST00000415724.1_Missense_Mutation_p.Q11R|ZDHHC20_ENST00000542645.1_5'UTR|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.Q11R|ZDHHC20_ENST00000422251.1_Missense_Mutation_p.Q11R|ZDHHC20_ENST00000320220.9_Missense_Mutation_p.Q11R			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	11					protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		CACGACGCGCTGGCAGCAGCG	0.701																																					p.Q11R		Atlas-SNP	.											.	ZDHHC20	36	.	0			c.A32G						.						24	28	27					13																	22033279		2022	4191	6213	SO:0001583	missense	253832	exon1			ACGCGCTGGCAGC	AK090979	CCDS45017.1, CCDS73551.1	13q12.11	2008-10-21			ENSG00000180776	ENSG00000180776		"Zinc fingers, DHHC-type"	20749	protein-coding gene	gene with protein product							Standard	NM_153251		Approved	FLJ25952	uc001uoa.2	Q5W0Z9	OTTHUMG00000017410	ENST00000400590.3:c.32A>G	chr13.hg19:g.22033279T>C	ENSP00000383433:p.Gln11Arg	133.0	0.0		185.0	61.0	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	hg19		.	.	.	.	.	.	.	.	.	.	T	15.00	2.703080	0.48412	.	.	ENSG00000180776	ENST00000400590;ENST00000320220;ENST00000382466;ENST00000415724;ENST00000422251	T;T;T;T;T	0.77358	0.95;0.97;0.95;0.95;-1.09	3.88	1.24	0.21308	.	0.190986	0.47093	D	0.000258	T	0.63733	0.2536	L	0.52364	1.645	0.44570	D	0.997535	B	0.02656	0.0	B	0.08055	0.003	T	0.46005	-0.9222	10	0.11182	T	0.66	-7.3251	5.4619	0.16622	0.1532:0.0893:0.0:0.7575	.	11	Q5W0Z9-3	.	R	11	ENSP00000383433:Q11R;ENSP00000313583:Q11R;ENSP00000371905:Q11R;ENSP00000401232:Q11R;ENSP00000396819:Q11R	ENSP00000313583:Q11R	Q	-	2	0	ZDHHC20	20931279	1.000000	0.71417	0.831000	0.32960	0.915000	0.54546	2.911000	0.48774	0.035000	0.15519	0.260000	0.18958	CAG	.	.		0.701	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251		C	22033279	T	C	22033279	3	2	174	1	0	0	0	0	1	0	0	0	17626	1580	55	2	1080	2	ZDHHC20	13	22033279	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10		22033279	93136599	90	26254										
NAA16	79612	hgsc.bcm.edu	37	chr13	41910840	41910840	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gagggttaacttcagtaaagGctgcccacccttgtttacta	9	10	1	0	rs553717732		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr13:41910840G>T	ENST00000379406.3	+	9	1286	c.962G>T	c.(961-963)gGc>gTc	p.G321V	NAA16_ENST00000379367.3_Missense_Mutation_p.G321V|NAA16_ENST00000403412.3_Missense_Mutation_p.G321V	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	321					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						TTCAGTAAAGGCTGCCCACCC	0.318																																					p.G321V		Atlas-SNP	.											.	NAA16	74	.	0			c.G962T						.						115	123	120					13																	41910840		2203	4299	6502	SO:0001583	missense	79612	exon9			GTAAAGGCTGCCC	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.962G>T	chr13.hg19:g.41910840G>T	ENSP00000368716:p.Gly321Val	135.0	0.0		106.0	39.0	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.482745	0.84747	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.59906	0.23;0.23;0.23	5.39	5.39	0.77823	.	0.000000	0.64402	D	0.000001	D	0.82508	0.5052	M	0.92649	3.33	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.991	D	0.86491	0.1797	10	0.66056	D	0.02	-7.196	19.1432	0.93452	0.0:0.0:1.0:0.0	.	321;321	Q6N069;Q6N069-4	NAA16_HUMAN;.	V	321	ENSP00000368674:G321V;ENSP00000368716:G321V;ENSP00000386103:G321V	ENSP00000368674:G321V	G	+	2	0	NAA16	40808840	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	8.351000	0.90072	2.511000	0.84671	0.650000	0.86243	GGC	.	.		0.318	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		T	41910840	G	T	41910840	3	4	174	1	0	0	0	0	1	0	0	0	10128	1203	42	3	996	3	NAA16	13	41910840	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	19877561	41910840	73259038	91	26255										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77751932	77751932	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	catgaattccacctcctccaTagacagagaaaccaaccaca	4	15	0	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr13:77751932T>C	ENST00000544440.2	-	35	5194	c.5177A>G	c.(5176-5178)tAt>tGt	p.Y1726C	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000407578.2_Missense_Mutation_p.Y1764C|MYCBP2_ENST00000357337.6_Missense_Mutation_p.Y1726C					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		ACCTCCTCCATAGACAGAGAA	0.423																																					p.Y1764C		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A5291G						.						97	84	88					13																	77751932		2203	4300	6503	SO:0001583	missense	23077	exon35			CCTCCATAGACAG	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.5177A>G	chr13.hg19:g.77751932T>C	ENSP00000444596:p.Tyr1726Cys	108.0	0.0		113.0	40.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	T	23.7	4.446785	0.84101	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.56275	0.48;0.47;0.48	5.72	5.72	0.89469	PHR (1);	0.000000	0.64402	D	0.000001	T	0.76772	0.4034	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81300	-0.0995	10	0.87932	D	0	.	16.2962	0.82776	0.0:0.0:0.0:1.0	.	1726	O75592	MYCB2_HUMAN	C	1726;1764;1726	ENSP00000349892:Y1726C;ENSP00000384288:Y1764C;ENSP00000444596:Y1726C	ENSP00000349892:Y1726C	Y	-	2	0	MYCBP2	76649933	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.304000	0.77564	0.528000	0.53228	TAT	.	.		0.423	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77751932	T	C	77751932	3	2	174	1	0	0	0	0	1	0	0	0	10027	1406	49	2	8941	2	MYCBP2	13	77751932	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	35841092	77751932	37417946	92	26256										
FRMD6	122786	hgsc.bcm.edu	37	chr14	52188702	52188702	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ttgatgacccccgggatctgGagcagatgaatgaagagtct	13	8	2	6			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr14:52188702G>T	ENST00000344768.5	+	12	1592	c.1396G>T	c.(1396-1398)Gag>Tag	p.E466*	FRMD6_ENST00000554167.1_Nonsense_Mutation_p.E389*|FRMD6_ENST00000553556.1_Nonsense_Mutation_p.E108*|RNU6-301P_ENST00000384277.1_RNA|FRMD6_ENST00000395718.2_Nonsense_Mutation_p.E458*|FRMD6_ENST00000356218.4_Nonsense_Mutation_p.E458*			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	466					apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					CCGGGATCTGGAGCAGATGAA	0.453																																					p.E466X		Atlas-SNP	.											.	FRMD6	100	.	0			c.G1396T						.						124	119	121					14																	52188702		2203	4300	6503	SO:0001587	stop_gained	122786	exon12			GATCTGGAGCAGA	BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"expanded homolog"	614555	"chromosome 14 open reading frame 31"	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.1396G>T	chr14.hg19:g.52188702G>T	ENSP00000343899:p.Glu466*	81.0	0.0		93.0	40.0	NM_001267046	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Nonsense_Mutation	SNP	ENST00000344768.5	hg19	CCDS58318.1	.	.	.	.	.	.	.	.	.	.	G	39	7.527997	0.98339	.	.	ENSG00000139926	ENST00000356218;ENST00000395718;ENST00000344768;ENST00000554167;ENST00000555703;ENST00000553556	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	.	17.8984	0.88896	0.0:0.0:1.0:0.0	.	.	.	.	X	458;458;466;389;106;108	.	ENSP00000343899:E466X	E	+	1	0	FRMD6	51258452	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.140000	0.94607	2.835000	0.97688	0.650000	0.86243	GAG	.	.		0.453	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330		T	52188702	G	T	52188702	4	4	174	1	0	0	0	0	0	1	0	0	6062	1175	41	3	1414	3	FRMD6	14	52188702	Nonsense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10		52188702	55160838	93	26257										
DAAM1	23002	hgsc.bcm.edu	37	chr14	59834319	59834320	+	Splice_Site	INS	-	-	GA													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gctcgcatggaagctcaggtINSgagaggatgattaattgacc							TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr14:59834319_59834320insGA	ENST00000395125.1	+	24	3050		c.e24+2		DAAM1_ENST00000351081.1_Splice_Site|DAAM1_ENST00000360909.3_Splice_Site|DAAM1_ENST00000553966.1_Splice_Site	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1						actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		GAAGCTCAGGTGAGAGGATGAT	0.446																																					.		Atlas-INDEL	.											.	DAAM1	95	.	0			c.2997+2->GA						.																																			SO:0001630	splice_region_variant	23002	exon24			.	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.3027+2->GA	chr14.hg19:g.59834322_59834323dupGA		75.0	0.0		36.0	23.0	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Splice_Site	INS	ENST00000395125.1	hg19	CCDS9737.1																																																																																			.	.		0.446	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	Intron	GA	59834320	-	GA	59834319	8	5	174	1	0	1	1	0	0	0	1	0	4217	1710	59	0	3123	0	DAAM1	14	59834319	Splice_Site	INS	-	TCGA-DD-AACX-01A-11D-A40R-10	7645617	59834319	47515221	94	26258										
EDC3	80153	hgsc.bcm.edu	37	chr15	74967425	74967425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	agacacccaagctatctccaCaattgatggacacaatactt	5	12	1	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr15:74967425C>T	ENST00000315127.4	-	2	222	c.41G>A	c.(40-42)tGt>tAt	p.C14Y	EDC3_ENST00000426797.3_Missense_Mutation_p.C14Y|EDC3_ENST00000568176.1_Missense_Mutation_p.C14Y	NM_001142444.1|NM_025083.3	NP_001135916.1|NP_079359.2	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	14	Required for P-body targeting and interaction with DCP1A. {ECO:0000250}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|membrane (GO:0016020)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GCTATCTCCACAATTGATGGA	0.478																																					p.C14Y		Atlas-SNP	.											.	EDC3	32	.	0			c.G41A						.						287	264	272					15																	74967425		2197	4296	6493	SO:0001583	missense	80153	exon3			TCTCCACAATTGA	BC011534	CCDS10267.1	15q24.1	2013-05-02	2013-05-02	2006-07-07	ENSG00000179151	ENSG00000179151			26114	protein-coding gene	gene with protein product		609842	"yjeF domain containing (E.coli)", "LSM16 homolog (EDC3, S. cerevisiae)", "enhancer of mRNA decapping 3 homolog (S. cerevisiae)"	YJDC, LSM16		15225602, 17533573, 22483619	Standard	NM_025083		Approved	FLJ21128, hYjeF_N2-15q23, YJEFN2	uc002aym.3	Q96F86	OTTHUMG00000142815	ENST00000315127.4:c.41G>A	chr15.hg19:g.74967425C>T	ENSP00000320503:p.Cys14Tyr	50.0	0.0		70.0	28.0	NM_001142444	B3KPH0|D3DW61|Q9H797	Missense_Mutation	SNP	ENST00000315127.4	hg19	CCDS10267.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.048807	0.93740	.	.	ENSG00000179151	ENST00000315127;ENST00000426797	.	.	.	5.72	5.72	0.89469	Enhancer of mRNA-decapping protein 3, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80008	0.4545	M	0.74881	2.28	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.80953	-0.1152	9	0.66056	D	0.02	-2.1186	18.8652	0.92289	0.0:1.0:0.0:0.0	.	14	Q96F86	EDC3_HUMAN	Y	14	.	ENSP00000320503:C14Y	C	-	2	0	EDC3	72754478	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.361000	0.79497	2.709000	0.92574	0.561000	0.74099	TGT	.	.		0.478	EDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286399.1	NM_025083		T	74967425	C	T	74967425	3	4	174	1	0	0	0	0	1	0	0	0	4909	478	17	3	1509	3	EDC3	15	74967425	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10		74967425	27563967	95	26259										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9943750	9943750	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ttgtcatccggctcacagtcGgagaaggacttgtacctggg	13	10	2	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr16:9943750G>A	ENST00000396573.2	-	6	1500	c.1191C>T	c.(1189-1191)tcC>tcT	p.S397S	GRIN2A_ENST00000562109.1_Silent_p.S397S|GRIN2A_ENST00000396575.2_Silent_p.S397S|GRIN2A_ENST00000535259.1_Silent_p.S240S|GRIN2A_ENST00000404927.2_Silent_p.S397S|GRIN2A_ENST00000330684.3_Silent_p.S397S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	397					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTCACAGTCGGAGAAGGACT	0.582																																					p.S397S		Atlas-SNP	.											.	GRIN2A	366	.	0			c.C1191T						.						135	111	119					16																	9943750		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon6			ACAGTCGGAGAAG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.1191C>T	chr16.hg19:g.9943750G>A		88.0	0.0		90.0	38.0	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	hg19	CCDS10539.1																																																																																			.	.		0.582	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	9943750	G	A	9943750	2	1	174	1	0	0	0	0	0	0	0	1	6788	1103	39	1		1	GRIN2A	16	9943750	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10		9943750	80411003	96	26260										
CPPED1	55313	hgsc.bcm.edu	37	chr16	12897629	12897629	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	caccccccgcctctgcagccGacatggcgagcgagtttctg	11	17	2	0	rs577494472		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr16:12897629G>T	ENST00000381774.4	-	1	245	c.5C>A	c.(4-6)tCg>tAg	p.S2*	CPPED1_ENST00000261660.4_Nonsense_Mutation_p.S2*|CPPED1_ENST00000433677.2_Nonsense_Mutation_p.S2*	NM_018340.2	NP_060810.2	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain containing 1	2						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|urinary_tract(1)	18						CTCTGCAGCCGACATGGCGAG	0.662																																					p.S2X		Atlas-SNP	.											.	CPPED1	41	.	0			c.C5A						.						15	18	17					16																	12897629		1894	4096	5990	SO:0001587	stop_gained	55313	exon1			GCAGCCGACATGG	AK022710	CCDS42119.1, CCDS42120.1	16p13.12	2014-02-12	2009-03-13		ENSG00000103381	ENSG00000103381			25632	protein-coding gene	gene with protein product	"complete S transactivated protein 1"	615603				12477932	Standard	NM_018340		Approved	CSTP1, FLJ11151	uc002dca.4	Q9BRF8	OTTHUMG00000167711	ENST00000381774.4:c.5C>A	chr16.hg19:g.12897629G>T	ENSP00000371193:p.Ser2*	96.0	0.0		94.0	30.0	NM_001099455	B4DQ68|Q6MZY9|Q9H9M9|Q9NUT6	Nonsense_Mutation	SNP	ENST00000381774.4	hg19	CCDS42120.1	.	.	.	.	.	.	.	.	.	.	G	36	5.910995	0.97093	.	.	ENSG00000103381	ENST00000381774;ENST00000433677;ENST00000261660	.	.	.	4.51	3.55	0.40652	.	0.530450	0.16042	N	0.232366	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.592	7.7847	0.29085	0.1105:0.0:0.8895:0.0	.	.	.	.	X	2	.	ENSP00000261660:S2X	S	-	2	0	CPPED1	12805130	0.989000	0.36119	0.805000	0.32314	0.177000	0.22998	2.132000	0.42083	2.497000	0.84241	0.460000	0.39030	TCG	.	.		0.662	CPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395795.2	NM_018340		T	12897629	G	T	12897629	4	4	174	1	0	0	0	0	0	1	0	0	3824	1059	37	1	955	1	CPPED1	16	12897629	Nonsense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	2953879	12897629	77457124	97	26261										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21053420	21053420	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gatgaacacagcgcaggttgGgttcagagagagctcagtcc	14	9	2	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr16:21053420G>A	ENST00000261383.3	-	32	4566	c.4567C>T	c.(4567-4569)Cca>Tca	p.P1523S	DNAH3_ENST00000415178.1_Missense_Mutation_p.P1523S	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1523	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GCGCAGGTTGGGTTCAGAGAG	0.517																																					p.P1523S		Atlas-SNP	.											.	DNAH3	1142	.	0			c.C4567T						.						153	123	133					16																	21053420		2201	4300	6501	SO:0001583	missense	55567	exon32			AGGTTGGGTTCAG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.4567C>T	chr16.hg19:g.21053420G>A	ENSP00000261383:p.Pro1523Ser	84.0	0.0		98.0	49.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.289724	0.80914	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.15372	2.43;2.43	4.82	4.82	0.62117	ATPase, AAA+ type, core (1);	0.066892	0.64402	D	0.000013	T	0.40570	0.1122	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.71870	0.975	T	0.19811	-1.0294	10	0.66056	D	0.02	.	18.4632	0.90747	0.0:0.0:1.0:0.0	.	1523	Q8TD57	DYH3_HUMAN	S	1523	ENSP00000261383:P1523S;ENSP00000394245:P1523S	ENSP00000261383:P1523S	P	-	1	0	DNAH3	20960921	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.561000	0.82288	2.668000	0.90789	0.591000	0.81541	CCA	.	.		0.517	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21053420	G	A	21053420	3	1	174	1	0	0	0	0	1	0	0	0	4605	1232	43	3	7906	3	DNAH3	16	21053420	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	8155791	21053420	69301333	98	26262										
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29908302	29908302	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ggtcagcagttctggcgcagTggggcctgcccccctgaccc	14	16	2	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr16:29908302T>C	ENST00000308713.5	-	3	879	c.352A>G	c.(352-354)Act>Gct	p.T118A	SEZ6L2_ENST00000537485.1_Missense_Mutation_p.T74A|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.T118A|SEZ6L2_ENST00000350527.3_Intron|SEZ6L2_ENST00000562159.1_5'UTR	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	118	Pro-rich.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCTGGCGCAGTGGGGCCTGCC	0.721																																					p.T118A		Atlas-SNP	.											.	SEZ6L2	137	.	0			c.A352G						.						8	11	10					16																	29908302		2183	4251	6434	SO:0001583	missense	26470	exon3			GCGCAGTGGGGCC	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.352A>G	chr16.hg19:g.29908302T>C	ENSP00000312550:p.Thr118Ala	39.0	0.0		44.0	17.0	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	hg19	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.317735	0.60524	.	.	ENSG00000174938	ENST00000308713;ENST00000346932;ENST00000537485	T;T;T	0.42131	0.98;0.98;0.98	5.36	5.36	0.76844	.	0.000000	0.53938	D	0.000050	T	0.26484	0.0647	N	0.19112	0.55	0.26953	N	0.96599	P;P;P;P	0.41929	0.663;0.765;0.533;0.765	B;B;B;B	0.37731	0.257;0.131;0.131;0.209	T	0.13255	-1.0516	9	.	.	.	.	10.9136	0.47122	0.0:0.0:0.1571:0.8428	.	74;118;118;118	F5H293;B7Z5L4;Q9BW82;Q6UXD5	.;.;.;SE6L2_HUMAN	A	118;118;74	ENSP00000312550:T118A;ENSP00000319215:T118A;ENSP00000439412:T74A	.	T	-	1	0	SEZ6L2	29815803	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.536000	0.45693	2.041000	0.60428	0.459000	0.35465	ACT	.	.		0.721	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		C	29908302	T	C	29908302	3	2	174	1	0	0	0	0	1	0	0	0	14159	1696	59	2	2483	2	SEZ6L2	16	29908302	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	8854882	29908302	60446451	99	26263										
PRSS8	5652	hgsc.bcm.edu	37	chr16	31144008	31144008	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	agcgtcccacctcacctgagGgggccacatgaccccagcca	10	18	1	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr16:31144008G>C	ENST00000317508.6	-	4	796	c.533C>G	c.(532-534)cCc>cGc	p.P178R	PRSS8_ENST00000568261.1_Missense_Mutation_p.P124R|RP11-388M20.2_ENST00000563605.1_RNA	NM_002773.3	NP_002764.1	Q16651	PRSS8_HUMAN	protease, serine, 8	178	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				positive regulation of sodium ion transport (GO:0010765)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)	8						CTCACCTGAGGGGGCCACATG	0.657																																					p.P178R		Atlas-SNP	.											.	PRSS8	24	.	0			c.C533G						.						59	67	64					16																	31144008		2120	4230	6350	SO:0001583	missense	5652	exon4			CCTGAGGGGGCCA	U33446	CCDS45469.1	16p11.2	2010-05-07	2007-02-21			ENSG00000052344		"Serine peptidases / Serine peptidases"	9491	protein-coding gene	gene with protein product	"prostasin"	600823				8838796, 7768952	Standard	NM_002773		Approved		uc002ebc.4	Q16651		ENST00000317508.6:c.533C>G	chr16.hg19:g.31144008G>C	ENSP00000319730:p.Pro178Arg	53.0	0.0		77.0	33.0	NM_002773	B4DWP2|Q9UCA3	Missense_Mutation	SNP	ENST00000317508.6	hg19	CCDS45469.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.810248	0.50421	.	.	ENSG00000052344	ENST00000317508;ENST00000419768	D	0.88124	-2.34	5.45	3.26	0.37387	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.335769	0.25984	N	0.027050	D	0.84234	0.5427	N	0.21142	0.635	0.80722	D	1	P;D	0.56287	0.918;0.975	P;P	0.59012	0.693;0.85	T	0.80491	-0.1359	10	0.30854	T	0.27	.	8.9982	0.36066	0.0:0.1874:0.5741:0.2385	.	124;178	B4DWP2;Q16651	.;PRSS8_HUMAN	R	178;96	ENSP00000319730:P178R	ENSP00000319730:P178R	P	-	2	0	PRSS8	31051509	0.000000	0.05858	0.987000	0.45799	0.721000	0.41392	0.488000	0.22371	2.554000	0.86153	0.561000	0.74099	CCC	.	.		0.657	PRSS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433536.1	NM_002773		C	31144008	G	C	31144008	3	2	174	1	0	0	0	0	1	0	0	0	12647	1232	43	4	510	4	PRSS8	16	31144008	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	1235706	31144008	59210745	100	26264										
RBL2	5934	hgsc.bcm.edu	37	chr16	53498217	53498217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cactttttcttataagcctcCtgggaattttccatttatta	4	9	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr16:53498217C>T	ENST00000262133.6	+	12	1777	c.1640C>T	c.(1639-1641)cCt>cTt	p.P547L	RBL2_ENST00000544545.1_Missense_Mutation_p.P331L|RBL2_ENST00000379935.4_3'UTR	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	547	Domain A.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TATAAGCCTCCTGGGAATTTT	0.338																																					p.P547L		Atlas-SNP	.											RBL2,rectum,NS,0,1	RBL2	115	.	0			c.C1640T						.						90	93	92					16																	53498217		2198	4300	6498	SO:0001583	missense	5934	exon12			AGCCTCCTGGGAA	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.1640C>T	chr16.hg19:g.53498217C>T	ENSP00000262133:p.Pro547Leu	126.0	0.0		100.0	46.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	hg19	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156323	0.57259	.	.	ENSG00000103479	ENST00000262133;ENST00000544405;ENST00000379935;ENST00000544545	D;D;D	0.86956	-2.19;-2.19;-2.19	5.86	5.86	0.93980	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.050790	0.85682	D	0.000000	D	0.92828	0.7719	M	0.79475	2.455	0.58432	D	0.999997	D;D;P;D	0.63880	0.982;0.98;0.741;0.993	P;P;P;P	0.58620	0.767;0.833;0.589;0.842	D	0.92913	0.6349	10	0.72032	D	0.01	-15.6206	20.1996	0.98256	0.0:1.0:0.0:0.0	.	331;547;257;547	B7Z913;Q8NE70;E9PG04;Q08999	.;.;.;RBL2_HUMAN	L	547;473;257;331	ENSP00000262133:P547L;ENSP00000443744:P473L;ENSP00000444685:P331L	ENSP00000262133:P547L	P	+	2	0	RBL2	52055718	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	3.599000	0.54045	2.776000	0.95493	0.650000	0.86243	CCT	.	.		0.338	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		T	53498217	C	T	53498217	3	4	174	1	0	0	0	0	1	0	0	0	13125	681	24	3	1686	3	RBL2	16	53498217	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	22354209	53498217	36856536	101	26265										
FLCN	201163	hgsc.bcm.edu	37	chr17	17127383	17127385	+	In_Frame_Del	DEL	GAA	GAA	-													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ctggccaggctgtccttgatGaagaaggtgtggctgaacac							TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr17:17127383_17127385delGAA	ENST00000285071.4	-	6	923_925	c.469_471delTTC	c.(469-471)ttcdel	p.F157del	RP11-45M22.4_ENST00000427497.3_Intron|FLCN_ENST00000389169.5_In_Frame_Del_p.F157del	NM_144997.5	NP_659434.2	Q8NFG4	FLCN_HUMAN	folliculin	157			Missing (in PSP; impaired protein stability). {ECO:0000269|PubMed:18505456}.		cell-cell junction assembly (GO:0007043)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in kidney development (GO:1901723)|negative regulation of energy homeostasis (GO:2000506)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of gene expression (GO:0010629)|negative regulation of mitochondrion organization (GO:0010823)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of gene expression (GO:0010628)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cytokinesis (GO:0032465)|regulation of histone acetylation (GO:0035065)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|regulation of TOR signaling (GO:0032006)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|stomach(1)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TGTCCTTGATGAAGAAGGTGTGG	0.596									Familial Non-VHL Clear Cell Renal Cancer;Birt-Hogg-Dub syndrome																												p.157_158del		Atlas-INDEL	.											.	FLCN	87	.	0			c.470_472del	GRCh37	CD083304	FLCN	D		.																																			SO:0001651	inframe_deletion	201163	exon6	Familial Cancer Database	Familial Clear Cell Renal Cell Cancer, FcRCC, Familial Non-VHL Non-Papillary Clear Cell Renal Cancer;BHD, Fibrofolliculomas with Trichodiscomas and Acrochordons, incl.: Hornstein-Knickenberg syndrome, Perifollicular Fibromatosis	.	AF517523	CCDS32579.1, CCDS32580.1	17p11.2	2014-09-17			ENSG00000154803	ENSG00000154803			27310	protein-coding gene	gene with protein product		607273					Standard	NM_144997		Approved	BHD, MGC17998, MGC23445	uc002gra.4	Q8NFG4	OTTHUMG00000059275	ENST00000285071.4:c.469_471delTTC	chr17.hg19:g.17127386_17127388delGAA	ENSP00000285071:p.Phe157del	108.0	0.0		71.0	44.0	NM_144997	A6NJJ8|Q6ZRX1|Q96BD2|Q96BE4	In_Frame_Del	DEL	ENST00000285071.4	hg19	CCDS32579.1																																																																																			.	.		0.596	FLCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131577.1	NM_144606		-	17127385	GAA	-	17127383	7	5	174	1	0	1	0	1	0	0	0	0	5929	1281	45	0	1462	0	FLCN	17	17127383	In_Frame_Del	DEL	GAA	TCGA-DD-AACX-01A-11D-A40R-10		17127383	64067827	102	26266										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18023832	18023832	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tcgccctgccacctcgcttgCgcggttcctcaagaagacgc	10	17	1	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr17:18023832C>T	ENST00000205890.5	+	2	2056	c.1718C>T	c.(1717-1719)gCg>gTg	p.A573V		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	573					inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					ACCTCGCTTGCGCGGTTCCTC	0.741																																					p.A573V		Atlas-SNP	.											.	MYO15A	268	.	0			c.C1718T						.						5	6	6					17																	18023832		1766	3906	5672	SO:0001583	missense	51168	exon2			CGCTTGCGCGGTT	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.1718C>T	chr17.hg19:g.18023832C>T	ENSP00000205890:p.Ala573Val	330.0	0.0		250.0	179.0	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.662294	0.67700	.	.	ENSG00000091536	ENST00000205890	D	0.89343	-2.5	4.95	3.91	0.45181	.	.	.	.	.	D	0.84920	0.5579	L	0.27053	0.805	0.80722	D	1	D	0.64830	0.994	P	0.49999	0.628	D	0.84661	0.0706	9	0.49607	T	0.09	.	10.4251	0.44373	0.0:0.8017:0.1983:0.0	.	573	Q9UKN7	MYO15_HUMAN	V	573	ENSP00000205890:A573V	ENSP00000205890:A573V	A	+	2	0	MYO15A	17964557	0.793000	0.28825	0.949000	0.38748	0.897000	0.52465	1.203000	0.32284	2.295000	0.77249	0.448000	0.29417	GCG	.	.		0.741	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		T	18023832	C	T	18023832	3	4	174	1	0	0	0	0	1	0	0	0	10072	768	27	1	1720	1	MYO15A	17	18023832	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	896449	18023832	63171378	103	26267										
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19454772	19454772	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	atgttacaagttaaatatttGctcaaccaggtaatactgac	6	7	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr17:19454772G>T	ENST00000270570.4	+	6	620	c.534G>T	c.(532-534)ttG>ttT	p.L178F	SLC47A1_ENST00000542886.1_Missense_Mutation_p.L178F|SLC47A1_ENST00000575023.1_Intron|SLC47A1_ENST00000457293.1_Missense_Mutation_p.L178F|SLC47A1_ENST00000571335.1_Missense_Mutation_p.C30F|SLC47A1_ENST00000584348.1_3'UTR|SLC47A1_ENST00000436810.2_Missense_Mutation_p.L155F|SLC47A1_ENST00000395585.1_Missense_Mutation_p.L178F	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	178					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	TTAAATATTTGCTCAACCAGG	0.438																																					p.L178F		Atlas-SNP	.											.	SLC47A1	55	.	0			c.G534T						.						158	147	151					17																	19454772		2203	4300	6503	SO:0001583	missense	55244	exon6			ATATTTGCTCAAC		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"Solute carriers"	25588	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 1"	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.534G>T	chr17.hg19:g.19454772G>T	ENSP00000270570:p.Leu178Phe	73.0	0.0		35.0	27.0	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	hg19	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.059089	0.76074	.	.	ENSG00000142494	ENST00000436810;ENST00000270570;ENST00000457293;ENST00000542886;ENST00000395585	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.64450	0.2599	M	0.85299	2.745	0.49798	D	0.999827	D;D;D	0.64830	0.987;0.994;0.981	D;D;P	0.66196	0.942;0.942;0.86	T	0.69851	-0.5033	10	0.87932	D	0	-17.2865	10.7957	0.46459	0.088:0.0:0.912:0.0	.	155;178;178	E7EX57;Q96FL8;Q96FL8-3	.;S47A1_HUMAN;.	F	155;178;178;178;178	ENSP00000407155:L155F;ENSP00000270570:L178F;ENSP00000415586:L178F;ENSP00000378951:L178F	ENSP00000270570:L178F	L	+	3	2	SLC47A1	19395364	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.321000	0.43805	2.399000	0.81585	0.561000	0.74099	TTG	.	.		0.438	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		T	19454772	G	T	19454772	3	4	174	1	0	0	0	0	1	0	0	0	14662	1310	46	3	556	3	SLC47A1	17	19454772	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	1430940	19454772	61740438	104	26268										
TAOK1	57551	hgsc.bcm.edu	37	chr17	27835056	27835056	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tgagatggatgaacatcgccTcagattagacaaagatcttg	10	7	2	5			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr17:27835056T>G	ENST00000261716.3	+	14	2000	c.1481T>G	c.(1480-1482)cTc>cGc	p.L494R	TAOK1_ENST00000536202.1_Missense_Mutation_p.L494R	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	494					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|execution phase of apoptosis (GO:0097194)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of cytoskeleton organization (GO:0051493)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28			Colorectal(6;0.198)			GAACATCGCCTCAGATTAGAC	0.428																																					p.L494R		Atlas-SNP	.											.	TAOK1	151	.	0			c.T1481G						.						84	76	79					17																	27835056		2203	4300	6503	SO:0001583	missense	57551	exon14			ATCGCCTCAGATT	AB037782	CCDS32601.1, CCDS56024.1	17q11.2	2014-01-28				ENSG00000160551			29259	protein-coding gene	gene with protein product		610266				10718198, 14517247	Standard	NM_020791		Approved	KIAA1361, MARKK, PSK2, MAP3K16, FLJ14314, TAO1	uc002hdz.2	Q7L7X3		ENST00000261716.3:c.1481T>G	chr17.hg19:g.27835056T>G	ENSP00000261716:p.Leu494Arg	194.0	0.0		277.0	55.0	NM_025142	A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Missense_Mutation	SNP	ENST00000261716.3	hg19	CCDS32601.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.372845	0.61624	.	.	ENSG00000160551	ENST00000261716;ENST00000536202	T;T	0.46063	0.88;0.88	5.18	5.18	0.71444	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.51500	0.1678	L	0.55834	1.745	0.80722	D	1	D;P;P	0.58970	0.984;0.951;0.737	P;P;B	0.57101	0.661;0.813;0.374	T	0.43956	-0.9359	10	0.15952	T	0.53	.	15.0568	0.71921	0.0:0.0:0.0:1.0	.	494;320;494	B7ZLV6;Q7L7X3-2;Q7L7X3	.;.;TAOK1_HUMAN	R	494	ENSP00000261716:L494R;ENSP00000438819:L494R	ENSP00000261716:L494R	L	+	2	0	TAOK1	24859182	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.031000	0.88826	1.959000	0.56917	0.533000	0.62120	CTC	.	.		0.428	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791		G	27835056	T	G	27835056	3	3	174	1	0	0	0	0	1	0	0	0	15562	1551	54	5	1531	5	TAOK1	17	27835056	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	8380284	27835056	53360154	105	26269										
KRT28	162605	hgsc.bcm.edu	37	chr17	38955938	38955938	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tccagcaaagccaatacaagCagcatttccaagggcaccac	7	14	0	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr17:38955938C>T	ENST00000306658.7	-	1	273	c.208G>A	c.(208-210)Gct>Act	p.A70T		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				CCAATACAAGCAGCATTTCCA	0.532																																					p.A70T	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.G208A						.						77	76	76					17																	38955938		2203	4300	6503	SO:0001583	missense	162605	exon1			TACAAGCAGCATT	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"-", "Intermediate filaments type I, keratins (acidic)"	30842	protein-coding gene	gene with protein product			"keratin 25D"	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.208G>A	chr17.hg19:g.38955938C>T	ENSP00000305263:p.Ala70Thr	98.0	0.0		164.0	52.0	NM_181535		Missense_Mutation	SNP	ENST00000306658.7	hg19	CCDS11376.1	.	.	.	.	.	.	.	.	.	.	C	6.875	0.530807	0.13127	.	.	ENSG00000173908	ENST00000306658	T	0.75477	-0.94	5.02	-0.168	0.13343	.	0.980375	0.08334	N	0.961878	T	0.49150	0.1540	N	0.04959	-0.14	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.30765	-0.9967	10	0.22706	T	0.39	.	6.3853	0.21558	0.3023:0.5398:0.0:0.1578	.	70	Q7Z3Y7	K1C28_HUMAN	T	70	ENSP00000305263:A70T	ENSP00000305263:A70T	A	-	1	0	KRT28	36209464	0.000000	0.05858	0.001000	0.08648	0.701000	0.40568	-0.820000	0.04457	0.226000	0.20979	0.650000	0.86243	GCT	.	.		0.532	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535		T	38955938	C	T	38955938	3	4	174	1	0	0	0	0	1	0	0	0	8474	710	25	3	1218	3	KRT28	17	38955938	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	11120882	38955938	42239272	106	26270										
TMEM101	84336	hgsc.bcm.edu	37	chr17	42089361	42089361	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	actctctccaaggagcttcaTctggttccagaactcaacac	6	14	4	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr17:42089361T>C	ENST00000589334.1	-	5	1024	c.709A>G	c.(709-711)Atg>Gtg	p.M237V	TMEM101_ENST00000206380.3_Missense_Mutation_p.M237V|TMEM101_ENST00000542039.1_Missense_Mutation_p.M179V			Q96IK0	TM101_HUMAN	transmembrane protein 101	237					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Breast(137;0.0264)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.113)		AGGAGCTTCATCTGGTTCCAG	0.552																																					p.M237V		Atlas-SNP	.											.	TMEM101	18	.	0			c.A709G						.						103	88	93					17																	42089361		2203	4300	6503	SO:0001583	missense	84336	exon4			GCTTCATCTGGTT	AK172826	CCDS11474.1	17q21.31	2005-12-16							28653	protein-coding gene	gene with protein product						12761501	Standard	NM_032376		Approved	MGC4251, FLJ23987	uc002ieu.3	Q96IK0		ENST00000589334.1:c.709A>G	chr17.hg19:g.42089361T>C	ENSP00000468025:p.Met237Val	56.0	0.0		106.0	26.0	NM_032376	B2R9N6	Missense_Mutation	SNP	ENST00000589334.1	hg19	CCDS11474.1	.	.	.	.	.	.	.	.	.	.	T	9.660	1.143996	0.21205	.	.	ENSG00000091947	ENST00000206380;ENST00000542039	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.40932	0.1137	N	0.19112	0.55	0.52099	D	0.999944	B	0.17268	0.021	B	0.16722	0.016	T	0.29243	-1.0018	9	0.12103	T	0.63	-12.6751	13.6738	0.62440	0.0:0.0:0.0:1.0	.	237	Q96IK0	TM101_HUMAN	V	237;179	.	ENSP00000206380:M237V	M	-	1	0	TMEM101	39444887	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.078000	0.71282	2.113000	0.64589	0.397000	0.26171	ATG	.	.		0.552	TMEM101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457665.1	NM_032376		C	42089361	T	C	42089361	3	2	174	1	0	0	0	0	1	0	0	0	16031	1435	50	2	68	2	TMEM101	17	42089361	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	3133423	42089361	39105849	107	26271										
STRADA	92335	hgsc.bcm.edu	37	chr17	61781755	61781755	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	caaagtggtggaagtgggggGagaaggttcggtggtagggg	23	2	0	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr17:61781755G>A	ENST00000336174.6	-	11	1158	c.1046C>T	c.(1045-1047)tCc>tTc	p.S349F	STRADA_ENST00000582137.1_Intron|STRADA_ENST00000580039.1_5'UTR|STRADA_ENST00000579340.1_3'UTR|STRADA_ENST00000392950.4_Missense_Mutation_p.S312F|STRADA_ENST00000245865.5_3'UTR|STRADA_ENST00000375840.4_Missense_Mutation_p.S291F|STRADA_ENST00000447001.3_Intron|RP11-51F16.8_ENST00000580553.1_3'UTR	NM_001003787.2	NP_001003787.1	Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha	349	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|protein export from nucleus (GO:0006611)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|prostate(2)	13						GAAGTGGGGGGAGAAGGTTCG	0.667																																					p.S349F		Atlas-SNP	.											.	STRADA	27	.	0			c.C1046T						.						19	20	20					17																	61781755		2202	4299	6501	SO:0001583	missense	92335	exon11			TGGGGGGAGAAGG	AF308302	CCDS11642.1, CCDS32703.1, CCDS42367.1, CCDS54156.1, CCDS58585.1	17q23.3	2014-09-04			ENSG00000266173	ENSG00000266173			30172	protein-coding gene	gene with protein product	"STE20-like pseudokinase"	608626				12805220, 17921699	Standard	NM_153335		Approved	NY-BR-96, LYK5, Stlk, STRAD	uc002jbm.3	Q7RTN6	OTTHUMG00000178908	ENST00000336174.6:c.1046C>T	chr17.hg19:g.61781755G>A	ENSP00000336655:p.Ser349Phe	50.0	0.0		49.0	29.0	NM_001003787	B4DDE3|B4DW17|J3KTC9|Q5JPI2|Q7Z4K9|Q8NC31|Q8NCF1|Q9H272	Missense_Mutation	SNP	ENST00000336174.6	hg19	CCDS32703.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.222880	0.79464	.	.	ENSG00000125695	ENST00000336174;ENST00000375840;ENST00000392950;ENST00000245865	T;T;T	0.60299	0.2;0.22;1.43	4.91	4.91	0.64330	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.111386	0.64402	D	0.000006	D	0.84538	0.5494	H	0.96916	3.905	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.90005	0.4117	10	0.87932	D	0	.	18.2873	0.90118	0.0:0.0:1.0:0.0	.	291;312;312;349	Q5JPI2;Q7RTN6-2;Q7RTN6-3;Q7RTN6	.;.;.;STRAA_HUMAN	F	349;291;312;311	ENSP00000336655:S349F;ENSP00000365000:S291F;ENSP00000376677:S312F	ENSP00000245865:S311F	S	-	2	0	STRADA	59135487	1.000000	0.71417	0.956000	0.39512	0.929000	0.56500	5.565000	0.67365	2.549000	0.85964	0.491000	0.48974	TCC	.	.		0.667	STRADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443894.1			A	61781755	G	A	61781755	3	1	174	1	0	0	0	0	1	0	0	0	15339	1174	41	3	319	3	STRADA	17	61781755	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	19692394	61781755	19413455	108	26272										
CDK3	1018	hgsc.bcm.edu	37	chr17	73999349	73999349	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tatctttcgtatgctggggaCacccagcgaagacacatggc	11	11	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr17:73999349C>G	ENST00000425876.2	+	6	750	c.662C>G	c.(661-663)aCa>aGa	p.T221R	CDK3_ENST00000448471.1_Missense_Mutation_p.T221R|TEN1-CDK3_ENST00000567351.1_RNA			Q00526	CDK3_HUMAN	cyclin-dependent kinase 3	221	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|G0 to G1 transition (GO:0045023)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			central_nervous_system(1)	1						ATGCTGGGGACACCCAGCGAA	0.537																																					p.T221R		Atlas-SNP	.											.	CDK3	31	.	0			c.C662G						.						145	157	153					17																	73999349		2203	4300	6503	SO:0001583	missense	1018	exon7			TGGGGACACCCAG	X66357	CCDS11736.1	17q25.1	2012-09-20			ENSG00000250506	ENSG00000250506		"Cyclin-dependent kinases"	1772	protein-coding gene	gene with protein product		123828				1639063	Standard	NM_001258		Approved		uc010dgt.3	Q00526	OTTHUMG00000154861	ENST00000425876.2:c.662C>G	chr17.hg19:g.73999349C>G	ENSP00000410561:p.Thr221Arg	112.0	0.0		119.0	30.0	NM_001258		Missense_Mutation	SNP	ENST00000425876.2	hg19	CCDS11736.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.463762	0.84425	.	.	ENSG00000250506	ENST00000448471;ENST00000425876	T;T	0.65178	-0.14;-0.14	4.72	4.72	0.59763	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000027	T	0.70780	0.3263	L	0.28608	0.87	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.75113	-0.3432	10	0.87932	D	0	-15.8149	17.8863	0.88855	0.0:1.0:0.0:0.0	.	221	Q00526	CDK3_HUMAN	R	221	ENSP00000400088:T221R;ENSP00000410561:T221R	ENSP00000410561:T221R	T	+	2	0	CDK3	71510944	1.000000	0.71417	0.999000	0.59377	0.946000	0.59487	7.592000	0.82676	2.455000	0.83008	0.511000	0.50034	ACA	.	.		0.537	CDK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337389.2	NM_001258		G	73999349	C	G	73999349	3	3	174	1	0	0	0	0	1	0	0	0	3142	478	17	4	684	4	CDK3	17	73999349	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	12217594	73999349	7195861	109	26273										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6965285	6965307	+	Splice_Site	DEL	TACCTTGCTTCCGGTTTCGCTGG	TACCTTGCTTCCGGTTTCGCTGG	-													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gtgagtccatctgtgtccctAccttgcttccggtttcgctg					rs140792199|rs542213899|rs200776408		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	TACCTTGCTTCCGGTTTCGCTGG	TACCTTGCTTCCGGTTTCGCTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr18:6965285_6965307delTACCTTGCTTCCGGTTTCGCTGG	ENST00000389658.3	-	50	7268_7289	c.7175_7196delCCAGCGAAACCGGAAGCAAGGTA	c.(7174-7197)tccagcgaaaccggaagcaaggta>ta	p.SSETGSKV2392fs		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2392	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.R2396Q(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CTGTGTCCCTACCTTGCTTCCGGTTTCGCTGGAAGGCAATTTT	0.439																																					p.2393_2399del		Atlas-INDEL	.											.	LAMA1	458	.	1	Substitution - Missense(1)	ovary(1)	c.7177_7195del						.																																			SO:0001630	splice_region_variant	284217	exon50			.	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.7195+1CCAGCGAAACCGGAAGCAAGGTA>-	chr18.hg19:g.6965285_6965307delTACCTTGCTTCCGGTTTCGCTGG		93.0	0.0		74.0	18.0	NM_005559		Frame_Shift_Del	DEL	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.439	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	Frame_Shift_Del	-	6965307	TACCTTGCTTCCGGTTTCGCTGG	-	6965285	8	5	174	1	0	1	0	1	0	0	1	0	8614	405	14	0	2086	0	LAMA1	18	6965285	Splice_Site	DEL	TACCTTGCTTCCGGTTTCGCTGG	TCGA-DD-AACX-01A-11D-A40R-10		6965285	71111963	110	26274										
OR7A5	26659	hgsc.bcm.edu	37	chr19	14938490	14938490	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ttaagaaagctatcagaacaAgcaagttggatgacctgatt	9	6	1	4			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr19:14938490A>C	ENST00000322301.3	-	2	651	c.564T>G	c.(562-564)gcT>gcG	p.A188A	OR7A5_ENST00000601611.1_Intron|OR7A5_ENST00000594432.1_Silent_p.A188A			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	188					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						TATCAGAACAAGCAAGTTGGA	0.423																																					p.A188A		Atlas-SNP	.											.	OR7A5	43	.	0			c.T564G						.						73	70	71					19																	14938490		2203	4300	6503	SO:0001819	synonymous_variant	26659	exon1			AGAACAAGCAAGT	X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"GPCR / Class A : Olfactory receptors"	8368	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily A, member 5 pseudogene"				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.564T>G	chr19.hg19:g.14938490A>C		212.0	0.0		239.0	95.0	NM_017506	B2R682|Q6IFP1|Q96R96	Silent	SNP	ENST00000322301.3	hg19	CCDS12318.1																																																																																			.	.		0.423	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506		C	14938490	A	C	14938490	2	2	174	1	0	0	0	0	0	0	0	1	11225	59	3	5		5	OR7A5	19	14938490	Silent	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10		14938490	44190493	111	26275			2	32		2	2	23	A		9.522523e-05
OR7A5	26659	hgsc.bcm.edu	37	chr19	14938512	14938512	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	caagttggatgacctgattaAgttcacagaaaaagtggggg	13	5	1	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr19:14938512A>C	ENST00000322301.3	-	2	629	c.542T>G	c.(541-543)cTt>cGt	p.L181R	OR7A5_ENST00000601611.1_Intron|OR7A5_ENST00000594432.1_Missense_Mutation_p.L181R			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	181					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						GACCTGATTAAGTTCACAGAA	0.453																																					p.L181R		Atlas-SNP	.											.	OR7A5	43	.	0			c.T542G						.						73	71	72					19																	14938512		2203	4300	6503	SO:0001583	missense	26659	exon1			TGATTAAGTTCAC	X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"GPCR / Class A : Olfactory receptors"	8368	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily A, member 5 pseudogene"				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.542T>G	chr19.hg19:g.14938512A>C	ENSP00000316955:p.Leu181Arg	230.0	0.0		237.0	95.0	NM_017506	B2R682|Q6IFP1|Q96R96	Missense_Mutation	SNP	ENST00000322301.3	hg19	CCDS12318.1	.	.	.	.	.	.	.	.	.	.	a	10.95	1.494733	0.26774	.	.	ENSG00000188269	ENST00000322301	T	0.00084	8.75	3.13	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.344301	0.15974	U	0.235614	T	0.00524	0.0017	M	0.90759	3.145	0.09310	N	0.999998	D	0.64830	0.994	D	0.71414	0.973	T	0.29640	-1.0005	10	0.87932	D	0	.	9.762	0.40537	1.0:0.0:0.0:0.0	.	181	Q15622	OR7A5_HUMAN	R	181	ENSP00000316955:L181R	ENSP00000316955:L181R	L	-	2	0	OR7A5	14799512	0.000000	0.05858	0.763000	0.31416	0.494000	0.33585	0.992000	0.29667	1.474000	0.48178	0.113000	0.15668	CTT	.	.		0.453	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506		C	14938512	A	C	14938512	3	2	174	1	0	0	0	0	1	0	0	0	11225	72	3	5	421	5	OR7A5	19	14938512	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	22	14938512	44190471	112	26276			2	32		2	2	23	A		9.522523e-05
CEACAM1	634	hgsc.bcm.edu	37	chr19	43023248	43023249	+	In_Frame_Ins	INS	-	-	AGACTC													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tcatcctctccgaggacgggINSagactctggtttttgaagaa							TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr19:43023248_43023249insAGACTC	ENST00000161559.6	-	5	1231_1232	c.1097_1098insGAGTCT	c.(1096-1098)ctc>ctGAGTCTc	p.366_366L>LSL	LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000352591.5_Intron|CEACAM1_ENST00000599389.1_Intron|CEACAM1_ENST00000403444.3_In_Frame_Ins_p.366_366L>LSL|CEACAM1_ENST00000351134.3_Intron|CEACAM1_ENST00000403461.1_Intron|CEACAM1_ENST00000358394.3_Intron|CEACAM1_ENST00000308072.4_Intron	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	366	Ig-like C2-type 3.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	CCGAGGACGGGAGACTCTGGTT	0.525																																					p.L366delinsLSL		Atlas-INDEL	.											.	CEACAM1	43	.	0			c.1098_1099insGAGTCT						.																																			SO:0001652	inframe_insertion	634	exon5			.	M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.1092_1097dupGAGTCT	chr19.hg19:g.43023249_43023254dupAGACTC	ENSP00000161559:p.SerLeu366dup	185.0	0.0		146.0	49.0	NM_001205344	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	In_Frame_Ins	INS	ENST00000161559.6	hg19	CCDS12609.1																																																																																			.	.		0.525	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712		AGACTC	43023249	-	AGACTC	43023248	7	5	174	1	0	1	1	0	0	0	0	0	3189	1161	41	0	599	0	CEACAM1	19	43023248	In_Frame_Ins	INS	-	TCGA-DD-AACX-01A-11D-A40R-10	28084736	43023248	16105735	113	26277										
PVR	5817	hgsc.bcm.edu	37	chr19	45153129	45153129	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gaaggtccagctcactggagAgccagtgcccatggcccgct	13	14	1	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr19:45153129A>G	ENST00000425690.3	+	3	775	c.476A>G	c.(475-477)gAg>gGg	p.E159G	PVR_ENST00000406449.4_Missense_Mutation_p.E159G|CTB-171A8.1_ENST00000590796.1_RNA|PVR_ENST00000403059.4_Missense_Mutation_p.E159G|PVR_ENST00000344956.4_Missense_Mutation_p.E159G	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	159	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		CTCACTGGAGAGCCAGTGCCC	0.612																																					p.E159G		Atlas-SNP	.											.	PVR	23	.	0			c.A476G						.						101	108	106					19																	45153129		2203	4300	6503	SO:0001583	missense	5817	exon3			CTGGAGAGCCAGT	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9705	protein-coding gene	gene with protein product	"nectin-like 5"	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.476A>G	chr19.hg19:g.45153129A>G	ENSP00000402060:p.Glu159Gly	79.0	0.0		59.0	29.0	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	hg19	CCDS12640.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.119996	0.37436	.	.	ENSG00000073008	ENST00000344956;ENST00000425690;ENST00000406449;ENST00000403059	T;T;T;T	0.08984	3.03;3.03;3.03;3.03	4.54	-0.842	0.10748	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.486060	0.04131	N	0.317900	T	0.10766	0.0263	L	0.39245	1.2	0.09310	N	1	B;B;B;B	0.33883	0.43;0.361;0.201;0.239	B;B;B;P	0.44732	0.228;0.241;0.329;0.459	T	0.43294	-0.9400	10	0.13108	T	0.6	.	5.8806	0.18854	0.4342:0.461:0.1048:0.0	.	159;159;159;159	P15151-2;P15151-3;P15151-4;P15151	.;.;.;PVR_HUMAN	G	159	ENSP00000340870:E159G;ENSP00000402060:E159G;ENSP00000383907:E159G;ENSP00000385344:E159G	ENSP00000340870:E159G	E	+	2	0	PVR	49844969	0.000000	0.05858	0.004000	0.12327	0.005000	0.04900	-0.010000	0.12743	0.125000	0.18397	0.402000	0.26972	GAG	.	.		0.612	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505		G	45153129	A	G	45153129	3	3	174	1	0	0	0	0	1	0	0	0	12852	304	11	2	486	2	PVR	19	45153129	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	2129881	45153129	13975854	114	26278			3	33	30214617	2	2	12	A		4.761375e-05
PVR	5817	hgsc.bcm.edu	37	chr19	45153140	45153140	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tcactggagagccagtgcccAtggcccgctgcgtctccaca	11	16	2	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr19:45153140A>C	ENST00000425690.3	+	3	786	c.487A>C	c.(487-489)Atg>Ctg	p.M163L	PVR_ENST00000406449.4_Missense_Mutation_p.M163L|CTB-171A8.1_ENST00000590796.1_RNA|PVR_ENST00000403059.4_Missense_Mutation_p.M163L|PVR_ENST00000344956.4_Missense_Mutation_p.M163L	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	163	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		GCCAGTGCCCATGGCCCGCTG	0.607																																					p.M163L		Atlas-SNP	.											.	PVR	23	.	0			c.A487C						.						89	96	94					19																	45153140		2203	4300	6503	SO:0001583	missense	5817	exon3			GTGCCCATGGCCC	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9705	protein-coding gene	gene with protein product	"nectin-like 5"	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.487A>C	chr19.hg19:g.45153140A>C	ENSP00000402060:p.Met163Leu	76.0	0.0		62.0	28.0	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	hg19	CCDS12640.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.999321	0.35226	.	.	ENSG00000073008	ENST00000344956;ENST00000425690;ENST00000406449;ENST00000403059	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	4.54	0.465	0.16711	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.320727	0.22262	N	0.062392	T	0.05593	0.0147	N	0.11427	0.14	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.13407	0.0;0.005;0.009;0.006	T	0.35025	-0.9805	10	0.27785	T	0.31	.	4.5987	0.12343	0.3527:0.1699:0.4774:0.0	.	163;163;163;163	P15151-2;P15151-3;P15151-4;P15151	.;.;.;PVR_HUMAN	L	163	ENSP00000340870:M163L;ENSP00000402060:M163L;ENSP00000383907:M163L;ENSP00000385344:M163L	ENSP00000340870:M163L	M	+	1	0	PVR	49844980	0.019000	0.18553	0.021000	0.16686	0.057000	0.15508	-0.017000	0.12590	0.011000	0.14865	-0.320000	0.08662	ATG	.	.		0.607	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505		C	45153140	A	C	45153140	3	2	174	1	0	0	0	0	1	0	0	0	12852	217	8	5	497	5	PVR	19	45153140	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	11	45153140	13975843	115	26279			3	33	30214617	2	2	12	A		4.761375e-05
SIGLEC6	946	hgsc.bcm.edu	37	chr19	52031035	52031035	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ccatgacggggttcacatcaTccgtgttttgcactggctgg	12	11	2	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr19:52031035T>G	ENST00000425629.3	-	7	1308	c.1154A>C	c.(1153-1155)gAt>gCt	p.D385A	SIGLEC6_ENST00000359982.4_Intron|SIGLEC6_ENST00000343300.4_Intron|SIGLEC6_ENST00000436458.1_Missense_Mutation_p.D333A|SIGLEC6_ENST00000474054.1_5'UTR|SIGLEC6_ENST00000391797.3_Intron|SIGLEC6_ENST00000346477.3_Missense_Mutation_p.D369A	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	385					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GTTCACATCATCCGTGTTTTG	0.502																																					p.D385A		Atlas-SNP	.											.	SIGLEC6	142	.	0			c.A1154C						.						193	192	192					19																	52031035		1954	4153	6107	SO:0001583	missense	946	exon7			ACATCATCCGTGT	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.1154A>C	chr19.hg19:g.52031035T>G	ENSP00000401502:p.Asp385Ala	90.0	0.0		77.0	34.0	NM_001245	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	hg19	CCDS12834.3	.	.	.	.	.	.	.	.	.	.	.	4.770	0.143268	0.09083	.	.	ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000436458	T;T	0.52754	1.09;0.65	3.02	0.74	0.18330	.	.	.	.	.	T	0.33000	0.0848	L	0.61218	1.895	0.09310	N	1	P;B;P	0.39216	0.495;0.181;0.664	B;B;B	0.30401	0.077;0.054;0.115	T	0.15983	-1.0418	9	0.19590	T	0.45	.	3.2494	0.06808	0.0:0.1378:0.2426:0.6197	.	333;369;385	C9JBE5;O43699-3;O43699	.;.;SIGL6_HUMAN	A	358;369;385;333	ENSP00000401502:D385A;ENSP00000410679:D333A	ENSP00000344064:D358A	D	-	2	0	SIGLEC6	56722847	0.001000	0.12720	0.000000	0.03702	0.028000	0.11728	0.909000	0.28558	0.080000	0.16959	0.338000	0.21704	GAT	.	.		0.502	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245		G	52031035	T	G	52031035	3	3	174	1	0	0	0	0	1	0	0	0	14327	1435	50	5	215	5	SIGLEC6	19	52031035	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	6877895	52031035	7097948	116	26280										
FPR2	2358	hgsc.bcm.edu	37	chr19	52272248	52272248	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	acatcaacctctttggaagtGtcttcttgattggtttcatt	7	8	5	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr19:52272248G>A	ENST00000598776.1	+	2	1109	c.337G>A	c.(337-339)Gtc>Atc	p.V113I	FPR2_ENST00000340023.6_Missense_Mutation_p.V113I|FPR2_ENST00000598953.1_Missense_Mutation_p.V113I	NM_001462.3	NP_001453.1	P25090	FPR2_HUMAN	formyl peptide receptor 2	113					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|N-formyl peptide receptor activity (GO:0004982)			endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33						CTTTGGAAGTGTCTTCTTGAT	0.493																																					p.V113I		Atlas-SNP	.											.	FPR2	66	.	0			c.G337A						.						179	155	163					19																	52272248		2203	4300	6503	SO:0001583	missense	2358	exon2			GGAAGTGTCTTCT	M88107	CCDS12840.1	19q13.3-q13.4	2012-08-10	2008-04-17	2008-04-17		ENSG00000171049		"GPCR / Class A : Formyl peptide receptors", "GPCR / Class A : Leukotriene receptors"	3827	protein-coding gene	gene with protein product		136538	"formyl peptide receptor-like 1"	FPRL1		9054386	Standard	NM_001462		Approved	LXA4R, HM63, FPRH2, FMLPX, FPR2A, FMLP-R-II, ALXR	uc002pxr.3	P25090		ENST00000598776.1:c.337G>A	chr19.hg19:g.52272248G>A	ENSP00000468897:p.Val113Ile	91.0	0.0		92.0	38.0	NM_001005738	A8K3E2	Missense_Mutation	SNP	ENST00000598776.1	hg19	CCDS12840.1	.	.	.	.	.	.	.	.	.	.	.	12.64	1.998503	0.35226	.	.	ENSG00000171049	ENST00000340023	T	0.69561	-0.41	3.47	2.42	0.29668	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000005	T	0.51363	0.1670	N	0.21240	0.645	0.35791	D	0.822428	P	0.37083	0.581	B	0.39971	0.315	T	0.58498	-0.7626	10	0.45353	T	0.12	.	8.6931	0.34278	0.119:0.0:0.881:0.0	.	113	P25090	FPR2_HUMAN	I	113	ENSP00000340191:V113I	ENSP00000340191:V113I	V	+	1	0	FPR2	56964060	1.000000	0.71417	0.950000	0.38849	0.388000	0.30384	3.324000	0.52022	0.803000	0.34113	0.491000	0.48974	GTC	.	.		0.493	FPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466912.2	NM_001005738		A	52272248	G	A	52272248	3	1	174	1	0	0	0	0	1	0	0	0	6047	1377	48	3	339	3	FPR2	19	52272248	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	241213	52272248	6856735	117	26281										
ZNF665	79788	hgsc.bcm.edu	37	chr19	53667735	53667735	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	atgaattcttcgatgttttgCaaggtttgaattttgagtaa	9	3	1	3			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr19:53667735C>G	ENST00000600412.1	-	2	1928	c.1813G>C	c.(1813-1815)Gca>Cca	p.A605P	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Missense_Mutation_p.A670P			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	605					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		CGATGTTTTGCAAGGTTTGAA	0.478																																					p.A670P		Atlas-SNP	.											.	ZNF665	136	.	0			c.G2008C						.						44	46	46					19																	53667735		2178	4290	6468	SO:0001583	missense	79788	exon4			GTTTTGCAAGGTT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1813G>C	chr19.hg19:g.53667735C>G	ENSP00000469154:p.Ala605Pro	42.0	0.0		44.0	13.0	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.16	1.557920	0.27827	.	.	ENSG00000197497	ENST00000396424	T	0.36520	1.25	2.33	-0.0644	0.13772	.	.	.	.	.	T	0.37732	0.1014	L	0.45352	1.415	0.09310	N	1	D	0.55800	0.973	P	0.55871	0.786	T	0.19031	-1.0318	9	0.52906	T	0.07	.	3.3365	0.07103	0.2055:0.5358:0.0:0.2587	.	670	Q9H7R5-2	.	P	670	ENSP00000379702:A670P	ENSP00000379702:A670P	A	-	1	0	ZNF665	58359547	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-2.977000	0.00664	-0.076000	0.12775	-0.399000	0.06403	GCA	.	.		0.478	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		G	53667735	C	G	53667735	3	3	174	1	0	0	0	0	1	0	0	0	18088	710	25	4	32	4	ZNF665	19	53667735	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	1395487	53667735	5461248	118	26282										
ZNF132	7691	hgsc.bcm.edu	37	chr19	58945805	58945805	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tgagtgaattctctgatgatGaacaaatgtgagtttgtggt	12	3	1	6			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr19:58945805G>C	ENST00000254166.3	-	3	1406	c.1006C>G	c.(1006-1008)Cat>Gat	p.H336D		NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	336					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		CTCTGATGATGAACAAATGTG	0.403																																					p.H336D		Atlas-SNP	.											.	ZNF132	56	.	0			c.C1006G						.						74	70	72					19																	58945805		2203	4300	6503	SO:0001583	missense	7691	exon3			GATGATGAACAAA	U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"Zinc fingers, C2H2-type", "-"	12916	protein-coding gene	gene with protein product		604074	"zinc finger protein 132 (clone pHZ-12)"			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.1006C>G	chr19.hg19:g.58945805G>C	ENSP00000254166:p.His336Asp	91.0	0.0		94.0	4.0	NM_003433	Q32MI9	Missense_Mutation	SNP	ENST00000254166.3	hg19	CCDS12980.1	.	.	.	.	.	.	.	.	.	.	G	4.060	0.008878	0.07912	.	.	ENSG00000131849	ENST00000254166	T	0.14766	2.48	3.19	0.778	0.18543	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05364	0.0142	N	0.11756	0.17	0.09310	N	1	B	0.29716	0.255	B	0.30251	0.113	T	0.39623	-0.9605	9	0.12103	T	0.63	.	1.4943	0.02463	0.1216:0.1715:0.3803:0.3266	.	336	P52740	ZN132_HUMAN	D	336	ENSP00000254166:H336D	ENSP00000254166:H336D	H	-	1	0	ZNF132	63637617	0.000000	0.05858	0.816000	0.32577	0.962000	0.63368	-0.197000	0.09518	0.672000	0.31204	-0.140000	0.14226	CAT	.	.		0.403	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433		C	58945805	G	C	58945805	3	2	174	1	0	0	0	0	1	0	0	0	17737	1290	45	4	1118	4	ZNF132	19	58945805	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	5278070	58945805	183178	119	26283										
TMC2	117532	hgsc.bcm.edu	37	chr20	2591139	2591139	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	atcgctgccctggagaattaCcacccacgcactggactgaa	9	14	0	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr20:2591139C>T	ENST00000358864.1	+	12	1503	c.1488C>T	c.(1486-1488)taC>taT	p.Y496Y	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	496					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TGGAGAATTACCACCCACGCA	0.532																																					p.Y496Y		Atlas-SNP	.											.	TMC2	121	.	0			c.C1488T						.						256	212	227					20																	2591139		2203	4300	6503	SO:0001819	synonymous_variant	117532	exon12			GAATTACCACCCA	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1488C>T	chr20.hg19:g.2591139C>T		110.0	0.0		83.0	65.0	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Silent	SNP	ENST00000358864.1	hg19	CCDS13029.2																																																																																			.	.		0.532	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			T	2591139	C	T	2591139	2	4	174	1	0	0	0	0	0	0	0	1	16000	518	18	3		3	TMC2	20	2591139	Silent	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10		2591139	60434381	120	26284										
CRLS1	54675	hgsc.bcm.edu	37	chr20	6012689	6012689	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	caagtatttcaatccttgctAtgccactgctaggttaaaac	6	10	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr20:6012689A>G	ENST00000378863.4	+	5	849	c.692A>G	c.(691-693)tAt>tGt	p.Y231C	CRLS1_ENST00000452938.1_Silent_p.L202L|CRLS1_ENST00000464921.1_3'UTR|CRLS1_ENST00000378868.4_Missense_Mutation_p.Y132C	NM_019095.4	NP_061968.1	Q9UJA2	CRLS1_HUMAN	cardiolipin synthase 1	231					cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			lung(3)|ovary(1)	4						AATCCTTGCTATGCCACTGCT	0.294																																					p.Y231C		Atlas-SNP	.											.	CRLS1	14	.	0			c.A692G						.						111	109	110					20																	6012689		2203	4300	6503	SO:0001583	missense	54675	exon5			CTTGCTATGCCAC	AF241784	CCDS13096.1, CCDS46578.1	20p13-p12.3	2006-04-04	2006-04-04	2006-04-04	ENSG00000088766	ENSG00000088766			16148	protein-coding gene	gene with protein product	"GCD10 homolog (S. cerevisiae)"	608188	"chromosome 20 open reading frame 155"	C20orf155		16547353	Standard	NM_019095		Approved	dJ967N21.6, CLS1, GCD10	uc002wmn.4	Q9UJA2	OTTHUMG00000031823	ENST00000378863.4:c.692A>G	chr20.hg19:g.6012689A>G	ENSP00000368140:p.Tyr231Cys	496.0	0.0		220.0	174.0	NM_019095	D3DW09|E9PAT4|Q27RP0|Q69YQ5	Missense_Mutation	SNP	ENST00000378863.4	hg19	CCDS13096.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.966316	0.74131	.	.	ENSG00000088766	ENST00000378863;ENST00000378868	.	.	.	5.97	5.97	0.96955	.	0.055339	0.85682	D	0.000000	T	0.77738	0.4175	M	0.73962	2.25	0.58432	D	0.999996	D;D	0.76494	0.999;0.999	D;D	0.70487	0.947;0.969	T	0.78432	-0.2206	9	0.46703	T	0.11	-23.9434	14.4129	0.67128	1.0:0.0:0.0:0.0	.	132;231	Q9UJA2-2;Q9UJA2	.;CRLS1_HUMAN	C	231;132	.	ENSP00000368140:Y231C	Y	+	2	0	CRLS1	5960689	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.354000	0.79424	2.288000	0.76882	0.533000	0.62120	TAT	.	.		0.294	CRLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077902.2	NM_019095		G	6012689	A	G	6012689	3	3	174	1	0	0	0	0	1	0	0	0	3891	449	16	2	723	2	CRLS1	20	6012689	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	3421550	6012689	57012831	121	26285										
LRRN4	164312	hgsc.bcm.edu	37	chr20	6022515	6022515	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	caagctcgggggcatgttctCctcggtgctgggtcctggtg	16	11	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr20:6022515C>A	ENST00000378858.4	-	5	1600	c.1376G>T	c.(1375-1377)gGa>gTa	p.G459V		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	459					long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	27						GGCATGTTCTCCTCGGTGCTG	0.652																																					p.G459V		Atlas-SNP	.											.	LRRN4	54	.	0			c.G1376T						.						135	128	130					20																	6022515		2203	4300	6503	SO:0001583	missense	164312	exon5			TGTTCTCCTCGGT	AL118505	CCDS13097.1	20p12.3	2013-02-11	2008-05-20	2008-05-20	ENSG00000125872	ENSG00000125872		"Fibronectin type III domain containing"	16208	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 75"	C20orf75		15870286	Standard	NM_152611		Approved	dJ1056H1.1, NLRR4	uc002wmo.3	Q8WUT4	OTTHUMG00000031825	ENST00000378858.4:c.1376G>T	chr20.hg19:g.6022515C>A	ENSP00000368135:p.Gly459Val	74.0	0.0		60.0	45.0	NM_152611	A8K258|Q5JWV6|Q9H419	Missense_Mutation	SNP	ENST00000378858.4	hg19	CCDS13097.1	.	.	.	.	.	.	.	.	.	.	C	12.89	2.072530	0.36566	.	.	ENSG00000125872	ENST00000378858	T	0.57107	0.42	4.86	-6.66	0.01789	.	1.870380	0.03186	U	0.172668	T	0.26268	0.0641	N	0.14661	0.345	0.09310	N	0.999992	B	0.29432	0.244	B	0.22386	0.039	T	0.07501	-1.0769	10	0.27785	T	0.31	1.1873	2.4386	0.04489	0.1015:0.2082:0.2304:0.4599	.	459	Q8WUT4	LRRN4_HUMAN	V	459	ENSP00000368135:G459V	ENSP00000368135:G459V	G	-	2	0	LRRN4	5970515	0.000000	0.05858	0.000000	0.03702	0.353000	0.29299	-2.039000	0.01418	-0.776000	0.04578	0.561000	0.74099	GGA	.	.		0.652	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611		A	6022515	C	A	6022515	3	1	174	1	0	0	0	0	1	0	0	0	9046	855	30	3	850	3	LRRN4	20	6022515	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10	9826	6022515	57003005	122	26286										
ZNF337	26152	hgsc.bcm.edu	37	chr20	25655715	25655718	+	Frame_Shift_Del	DEL	GTAA	GTAA	-													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tgtacaaaaacgcttctcacGtaagtgtctctttaagtgct							TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr20:25655715_25655718delGTAA	ENST00000376436.1	-	4	2745_2748	c.2206_2209delTTAC	c.(2206-2211)ttacgtfs	p.LR736fs	ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000428254.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA|ZNF337_ENST00000538750.1_Frame_Shift_Del_p.LR704fs|RP4-694B14.5_ENST00000414393.1_RNA|RP4-694B14.5_ENST00000421829.1_RNA|ZNF337_ENST00000252979.5_Frame_Shift_Del_p.LR736fs|RP4-694B14.5_ENST00000439498.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	736					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CGCTTCTCACGTAAGTGTCTCTTT	0.426																																					p.736_737del		Atlas-INDEL	.											.	ZNF337	65	.	0			c.2207_2210del						.																																			SO:0001589	frameshift_variant	26152	exon5			.		CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"Zinc fingers, C2H2-type", "-"	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.2206_2209delTTAC	chr20.hg19:g.25655715_25655718delGTAA	ENSP00000365619:p.Leu736fs	81.0	0.0		83.0	38.0	NM_015655	B4DSM2|Q9Y3Y5	Frame_Shift_Del	DEL	ENST00000376436.1	hg19	CCDS13174.1																																																																																			.	.		0.426	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1			-	25655718	GTAA	-	25655715	7	5	174	1	0	1	0	1	0	0	0	0	17868	1145	40	0	50	0	ZNF337	20	25655715	Frame_Shift_Del	DEL	GTAA	TCGA-DD-AACX-01A-11D-A40R-10	19633200	25655715	37369805	123	26287										
SDC4	6385	hgsc.bcm.edu	37	chr20	43956037	43956037	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cggcaaagaggatgcccacgAtgccacccacaatcagagct	10	14	1	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr20:43956037A>G	ENST00000372733.3	-	5	503	c.464T>C	c.(463-465)aTc>aCc	p.I155T	SDC4_ENST00000537976.1_Missense_Mutation_p.I83T	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	155					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)		SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				GATGCCCACGATGCCACCCAC	0.542			T	ROS1	NSCLC																																p.I155T		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	.	SDC4	16	.	0			c.T464C						.						77	72	74					20																	43956037		2203	4300	6503	SO:0001583	missense	6385	exon5			CCCACGATGCCAC	X67016, D13292	CCDS13350.1	20q12	2010-03-25	2007-02-15		ENSG00000124145	ENSG00000124145		"Proteoglycans / Cell Surface : Syndecans"	10661	protein-coding gene	gene with protein product	"syndecan proteoglycan 4"	600017	"syndecan 4 (amphiglycan, ryudocan)"			7916598, 1500433	Standard	NM_002999		Approved	SYND4, amphiglycan, ryudocan	uc002xnu.3	P31431	OTTHUMG00000033083	ENST00000372733.3:c.464T>C	chr20.hg19:g.43956037A>G	ENSP00000361818:p.Ile155Thr	58.0	0.0		54.0	16.0	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	hg19	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	A	8.434	0.849361	0.17034	.	.	ENSG00000124145	ENST00000372733;ENST00000537976	T	0.31510	1.49	5.37	-0.0764	0.13723	.	0.586050	0.17268	N	0.180512	T	0.17109	0.0411	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16482	-1.0401	10	0.72032	D	0.01	-4.6192	5.5791	0.17241	0.5167:0.2839:0.1994:0.0	.	155	P31431	SDC4_HUMAN	T	155;83	ENSP00000361818:I155T	ENSP00000361818:I155T	I	-	2	0	SDC4	43389451	0.000000	0.05858	0.003000	0.11579	0.445000	0.32107	0.498000	0.22530	0.036000	0.15547	0.533000	0.62120	ATC	.	.		0.542	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999		G	43956037	A	G	43956037	3	3	174	1	0	0	0	0	1	0	0	0	13969	333	12	2	136	2	SDC4	20	43956037	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	18300322	43956037	19069483	124	26288										
PMEPA1	56937	hgsc.bcm.edu	37	chr20	56227494	56227494	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gggtgcaggggccctggtagGgtgggggctcctccccgtct	19	12	1	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr20:56227494G>T	ENST00000341744.3	-	4	798	c.479C>A	c.(478-480)cCc>cAc	p.P160H	PMEPA1_ENST00000395814.1_Missense_Mutation_p.P110H|PMEPA1_ENST00000395816.3_Missense_Mutation_p.P110H|PMEPA1_ENST00000265626.4_Missense_Mutation_p.P110H|PMEPA1_ENST00000347215.4_Missense_Mutation_p.P125H	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	160					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						GCCCTGGTAGGGTGGGGGCTC	0.667																																					p.P160H		Atlas-SNP	.											PMEPA1,NS,carcinoma,0,1	PMEPA1	29	.	0			c.C479A						.						31	35	33					20																	56227494		2203	4299	6502	SO:0001583	missense	56937	exon4			TGGTAGGGTGGGG	AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"solid tumor-associated 1"	606564	"transmembrane, prostate androgen induced RNA"	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.479C>A	chr20.hg19:g.56227494G>T	ENSP00000345826:p.Pro160His	61.0	0.0		89.0	31.0	NM_020182	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Missense_Mutation	SNP	ENST00000341744.3	hg19	CCDS13463.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.479742	0.84747	.	.	ENSG00000124225	ENST00000341744;ENST00000347215;ENST00000395816;ENST00000265626;ENST00000395814;ENST00000414037;ENST00000395819	T;T;T;T;T;T;T	0.69806	0.02;0.11;0.06;0.06;0.06;0.2;-0.43	5.42	4.48	0.54585	.	0.055200	0.64402	D	0.000001	T	0.81763	0.4891	M	0.80616	2.505	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.971	D	0.84419	0.0570	10	0.87932	D	0	-31.1453	13.7523	0.62915	0.0739:0.0:0.9261:0.0	.	125;160	Q5JY37;Q969W9	.;PMEPA_HUMAN	H	160;125;110;110;110;132;217	ENSP00000345826:P160H;ENSP00000344014:P125H;ENSP00000379161:P110H;ENSP00000265626:P110H;ENSP00000379159:P110H;ENSP00000401506:P132H;ENSP00000379164:P217H	ENSP00000265626:P110H	P	-	2	0	PMEPA1	55660900	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.622000	0.98378	1.280000	0.44463	0.650000	0.86243	CCC	.	.		0.667	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182		T	56227494	G	T	56227494	3	4	174	1	0	0	0	0	1	0	0	0	12141	1232	43	3	388	3	PMEPA1	20	56227494	Missense_Mutation	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	12271457	56227494	6798026	125	26289										
OPRL1	4987	hgsc.bcm.edu	37	chr20	62729870	62729870	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gtgttcgtgggctgctggacGcctgtccaggtcttcgtgct	15	11	1	0	rs144338110		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr20:62729870G>A	ENST00000349451.3	+	6	1243	c.831G>A	c.(829-831)acG>acA	p.T277T	OPRL1_ENST00000336866.2_Silent_p.T277T|OPRL1_ENST00000355631.4_Silent_p.T277T	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	277					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavior (GO:0007610)|opioid receptor signaling pathway (GO:0038003)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|nociceptin receptor activity (GO:0001626)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					GCTGCTGGACGCCTGTCCAGG	0.672																																					p.T277T		Atlas-SNP	.											.	OPRL1	47	.	0			c.G831A						.						62	55	57					20																	62729870		2200	4296	6496	SO:0001819	synonymous_variant	4987	exon4			CTGGACGCCTGTC		CCDS13556.1	20q13.33	2012-08-08			ENSG00000125510	ENSG00000125510		"GPCR / Class A : Opioid receptors"	8155	protein-coding gene	gene with protein product	"LC132 receptor-like", "orphanin FQ receptor", "kappa3-related opioid receptor"	602548				8137918	Standard	NM_000913		Approved	NOCIR, ORL1, OOR, KOR-3	uc021wgs.1	P41146	OTTHUMG00000033027	ENST00000349451.3:c.831G>A	chr20.hg19:g.62729870G>A		85.0	0.0		101.0	55.0	NM_000913	Q8TD34|Q8WYH9|Q9H4K4	Silent	SNP	ENST00000349451.3	hg19	CCDS13556.1																																																																																			.	G|1.000;T|0.000		0.672	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647		A	62729870	G	A	62729870	2	1	174	1	0	0	0	0	0	0	0	1	10895	1074	38	1		1	OPRL1	20	62729870	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	6502376	62729870	295650	126	26290										
POTEH	23784	hgsc.bcm.edu	37	chr22	16267071	16267071	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gaatcccatatgagtacttcCgtgcttcttcatttcttctt	5	11	4	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr22:16267071C>T	ENST00000343518.6	-	9	1429	c.1378G>A	c.(1378-1380)Gga>Aga	p.G460R		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	460										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						TGAGTACTTCCGTGCTTCTTC	0.363																																					p.G460R		Atlas-SNP	.											POTEH,NS,carcinoma,0,1	POTEH	114	.	0			c.G1378A						.						241	214	222					22																	16267071		692	1591	2283	SO:0001583	missense	23784	exon9			TACTTCCGTGCTT	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	133	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 7"	608913	"actin, beta-like 1", "ANKRD26-like family C, member 3"	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.1378G>A	chr22.hg19:g.16267071C>T	ENSP00000340610:p.Gly460Arg	918.0	0.0		971.0	133.0	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Missense_Mutation	SNP	ENST00000343518.6	hg19	CCDS46658.1	.	.	.	.	.	.	.	.	.	.	C	0.306	-0.970906	0.02232	.	.	ENSG00000198062	ENST00000359587;ENST00000343518	T	0.24151	1.87	1.4	-2.79	0.05841	.	.	.	.	.	T	0.10380	0.0254	N	0.12746	0.255	0.09310	N	1	B;B	0.27286	0.174;0.041	B;B	0.17979	0.02;0.005	T	0.16867	-1.0388	9	0.36615	T	0.2	.	3.3264	0.07068	0.0:0.2957:0.2166:0.4876	.	460;423	Q6S545;A6NKF6	POTEH_HUMAN;.	R	423;460	ENSP00000340610:G460R	ENSP00000340610:G460R	G	-	1	0	POTEH	14647071	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.911000	0.01583	-1.522000	0.01769	-1.206000	0.01644	GGA	.	.		0.363	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		T	16267071	C	T	16267071	3	4	174	1	0	0	0	0	1	0	0	0	12276	661	23	1	267	1	POTEH	22	16267071	Missense_Mutation	SNP	C	TCGA-DD-AACX-01A-11D-A40R-10		16267071	35037495	127	26291										
CABIN1	23523	hgsc.bcm.edu	37	chr22	24494016	24494016	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gacgaggactcccactcttcAgctgggacactgccgggccc	12	16	2	0			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr22:24494016A>G	ENST00000398319.2	+	26	4363	c.3978A>G	c.(3976-3978)tcA>tcG	p.S1326S	CABIN1_ENST00000405822.2_Silent_p.S1276S|CABIN1_ENST00000263119.5_Silent_p.S1326S	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1326					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						CCCACTCTTCAGCTGGGACAC	0.612																																					p.S1326S		Atlas-SNP	.											.	CABIN1	153	.	0			c.A3978G						.						103	91	95					22																	24494016		2203	4300	6503	SO:0001819	synonymous_variant	23523	exon26			CTCTTCAGCTGGG	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.3978A>G	chr22.hg19:g.24494016A>G		134.0	0.0		153.0	61.0	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Silent	SNP	ENST00000398319.2	hg19	CCDS13823.1																																																																																			.	.		0.612	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		G	24494016	A	G	24494016	2	3	174	1	0	0	0	0	0	0	0	1	2530	175	7	2		2	CABIN1	22	24494016	Silent	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	8226945	24494016	26810550	128	26292										
PLA2G6	8398	hgsc.bcm.edu	37	chr22	38524361	38524361	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	gcagagccctgctccgcgggGaccccgtggatgggtgggaa	18	12	0	1	rs375896475		TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr22:38524361G>A	ENST00000332509.3	-	9	1446	c.1263C>T	c.(1261-1263)gtC>gtT	p.V421V	PLA2G6_ENST00000490473.1_5'Flank|PLA2G6_ENST00000335539.3_Intron|PLA2G6_ENST00000402064.1_Intron	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	421					cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	GCTCCGCGGGGACCCCGTGGA	0.612																																					p.V421V		Atlas-SNP	.											.	PLA2G6	54	.	0			c.C1263T						.	G	,,	0,4406		0,0,2203	101	93	96		,,1263	-0.1	0	22		96	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,coding-synonymous	PLA2G6	NM_001004426.1,NM_001199562.1,NM_003560.2	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	,,421/807	38524361	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8398	exon9			CGCGGGGACCCCG	AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"Patatin-like phospholipase domain containing", "Parkinson disease", "Ankyrin repeat domain containing"	9039	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 2"	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.1263C>T	chr22.hg19:g.38524361G>A		79.0	0.0		94.0	44.0	NM_003560	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Silent	SNP	ENST00000332509.3	hg19	CCDS13967.1	.	.	.	.	.	.	.	.	.	.	G	0.221	-1.028616	0.02045	0.0	1.16E-4	ENSG00000184381	ENST00000452794;ENST00000427114	.	.	.	4.78	-0.0792	0.13711	.	.	.	.	.	T	0.24314	0.0589	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26780	-1.0093	4	.	.	.	-2.0931	5.0374	0.14441	0.1656:0.0:0.4424:0.392	.	.	.	.	F	78;226	.	.	S	-	2	0	PLA2G6	36854307	0.004000	0.15560	0.012000	0.15200	0.101000	0.19017	0.060000	0.14342	0.514000	0.28300	0.563000	0.77884	TCC	.	.		0.612	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426		A	38524361	G	A	38524361	2	1	174	1	0	0	0	0	0	0	0	1	12017	1161	41	3		3	PLA2G6	22	38524361	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	14030345	38524361	12780205	129	26293										
ADSL	158	hgsc.bcm.edu	37	chr22	40742624	40742624	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ctcacctcttgcctcccgctAtgccagcccggagatgtgct	9	17	2	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr22:40742624A>G	ENST00000216194.7	+	1	118	c.62A>G	c.(61-63)tAt>tGt	p.Y21C	ADSL_ENST00000342312.6_Missense_Mutation_p.Y21C|ADSL_ENST00000454266.2_Missense_Mutation_p.Y21C	NM_000026.2	NP_000017.1	P30566	PUR8_HUMAN	adenylosuccinate lyase	21	Substrate binding; shared with neighboring subunit.				'de novo' AMP biosynthetic process (GO:0044208)|'de novo' IMP biosynthetic process (GO:0006189)|aerobic respiration (GO:0009060)|AMP biosynthetic process (GO:0006167)|metabolic process (GO:0008152)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity (GO:0070626)|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity (GO:0004018)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(2)|ovary(1)|prostate(1)	19						GCCTCCCGCTATGCCAGCCCG	0.642																																					p.Y21C	Colon(4;65 130 1097 1516)	Atlas-SNP	.											.	ADSL	98	.	0			c.A62G						.						37	31	33					22																	40742624		2203	4300	6503	SO:0001583	missense	158	exon1			CCCGCTATGCCAG	X65867	CCDS14001.1, CCDS46714.1	22q13.1	2011-02-17			ENSG00000239900	ENSG00000239900	4.3.2.2		291	protein-coding gene	gene with protein product		608222				8404037	Standard	NM_000026		Approved		uc003ayp.4	P30566	OTTHUMG00000166425	ENST00000216194.7:c.62A>G	chr22.hg19:g.40742624A>G	ENSP00000216194:p.Tyr21Cys	46.0	0.0		41.0	17.0	NM_001123378	B0QY76|O75495|Q5TI34	Missense_Mutation	SNP	ENST00000216194.7	hg19	CCDS14001.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.462024	0.84425	.	.	ENSG00000239900	ENST00000216194;ENST00000544206;ENST00000425605;ENST00000454266;ENST00000342312	D;D;D	0.98617	-3.98;-3.98;-5.03	4.8	4.8	0.61643	L-Aspartase-like (1);L-Aspartase-like, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99260	0.9742	M	0.92317	3.295	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.72625	0.954;0.978;0.97;0.97	D	0.98985	1.0806	10	0.87932	D	0	-16.8225	14.5069	0.67758	1.0:0.0:0.0:0.0	.	21;21;21;21	E7ERF4;P30566-2;Q71UA4;P30566	.;.;.;PUR8_HUMAN	C	21	ENSP00000216194:Y21C;ENSP00000390107:Y21C;ENSP00000341429:Y21C	ENSP00000216194:Y21C	Y	+	2	0	ADSL	39072570	1.000000	0.71417	0.995000	0.50966	0.727000	0.41649	7.908000	0.87438	2.148000	0.66965	0.524000	0.50904	TAT	.	.		0.642	ADSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321386.1	NM_000026		G	40742624	A	G	40742624	3	3	174	1	0	0	0	0	1	0	0	0	346	449	16	2	64	2	ADSL	22	40742624	Missense_Mutation	SNP	A	TCGA-DD-AACX-01A-11D-A40R-10	2218263	40742624	10561942	130	26294										
EP300	2033	hgsc.bcm.edu	37	chr22	41574913	41574913	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tgggactcagcaccgataacTcagacttgaattcaaacctc	7	12	3	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr22:41574913T>A	ENST00000263253.7	+	31	8417	c.7198T>A	c.(7198-7200)Tca>Aca	p.S2400T	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2400					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CACCGATAACTCAGACTTGAA	0.453			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.S2400T		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.T7198A						.						51	52	52					22																	41574913		2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	GATAACTCAGACT	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.7198T>A	chr22.hg19:g.41574913T>A	ENSP00000263253:p.Ser2400Thr	65.0	0.0		84.0	29.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	T	10.50	1.367727	0.24771	.	.	ENSG00000100393	ENST00000263253	D	0.83075	-1.68	5.65	2.21	0.28008	.	0.190634	0.25517	N	0.030134	T	0.71039	0.3293	L	0.36672	1.1	0.22719	N	0.998815	B	0.12630	0.006	B	0.15870	0.014	T	0.49163	-0.8968	10	0.02654	T	1	-0.5412	13.2545	0.60070	0.0:0.0:0.3926:0.6074	.	2400	Q09472	EP300_HUMAN	T	2400	ENSP00000263253:S2400T	ENSP00000263253:S2400T	S	+	1	0	EP300	39904859	1.000000	0.71417	0.986000	0.45419	0.996000	0.88848	2.532000	0.45659	0.060000	0.16281	0.533000	0.62120	TCA	.	.		0.453	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		A	41574913	T	A	41574913	3	1	174	1	0	0	0	0	1	0	0	0	5150	1551	54	4	7320	4	EP300	22	41574913	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	832289	41574913	9729653	131	26295										
ZC3H7B	23264	hgsc.bcm.edu	37	chr22	41723227	41723227	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	cagggcctgtatgagaaggcGctggaggacagcgagaaggc	18	8	0	2			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chr22:41723227G>T	ENST00000352645.4	+	5	560	c.303G>T	c.(301-303)gcG>gcT	p.A101A	ZC3H7B_ENST00000351589.4_Silent_p.A101A	NM_017590.4	NP_060060.3	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	101					viral process (GO:0016032)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						ATGAGAAGGCGCTGGAGGACA	0.627																																					p.A101A		Atlas-SNP	.											.	ZC3H7B	82	.	0			c.G303T						.						104	83	90					22																	41723227		2203	4300	6503	SO:0001819	synonymous_variant	23264	exon5			GAAGGCGCTGGAG		CCDS14013.1	22q13.2	2013-01-10		2005-08-09	ENSG00000100403	ENSG00000100403		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30869	protein-coding gene	gene with protein product						10470851, 11230166	Standard	NM_017590		Approved	RoXaN, FLJ13787, DKFZp434K0920, KIAA1031	uc003azw.4	Q9UGR2	OTTHUMG00000150969	ENST00000352645.4:c.303G>T	chr22.hg19:g.41723227G>T		63.0	0.0		52.0	19.0	NM_017590	A7YY88|B2RCA4|Q5TFX9|Q8TBT9|Q9H8B6|Q9UGQ9|Q9UGR0|Q9UGR1|Q9UK03|Q9UPW9	Silent	SNP	ENST00000352645.4	hg19	CCDS14013.1																																																																																			.	.		0.627	ZC3H7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320696.1	NM_017590		T	41723227	G	T	41723227	2	4	174	1	0	0	0	0	0	0	0	1	17588	1074	38	1		1	ZC3H7B	22	41723227	Silent	SNP	G	TCGA-DD-AACX-01A-11D-A40R-10	148314	41723227	9581339	132	26296										
CFP	5199	hgsc.bcm.edu	37	chrX	47485892	47485892	+	Frame_Shift_Del	DEL	C	C	-													0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	tcggatacaggggctccactCcccccacgagtcccactccc							TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chrX:47485892delC	ENST00000396992.3	-	7	1087	c.967delG	c.(967-969)gagfs	p.E323fs	CFP_ENST00000480317.1_5'Flank|CFP_ENST00000247153.3_Frame_Shift_Del_p.E323fs|CFP_ENST00000377005.2_Frame_Shift_Del_p.E323fs	NM_001145252.1	NP_001138724.1	P27918	PROP_HUMAN	complement factor properdin	323	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	18						GGGCTCCACTCCCCCCACGAG	0.602																																					p.E323fs		Atlas-INDEL	.											.	CFP	43	.	0			c.968delA						.						43	35	38					X																	47485892		2203	4300	6503	SO:0001589	frameshift_variant	5199	exon7			.	M83652	CCDS14282.1	Xp11.4	2014-09-17	2006-03-02	2006-03-02	ENSG00000126759	ENSG00000126759		"Complement system"	8864	protein-coding gene	gene with protein product		300383	"properdin P factor, complement"	PFC		1783405	Standard	NM_001145252		Approved		uc004dih.3	P27918	OTTHUMG00000021451	ENST00000396992.3:c.967delG	chrX.hg19:g.47485892delC	ENSP00000380189:p.Glu323fs	67.0	0.0		57.0	47.0	NM_001145252	O15134|O15135|O15136|O75826	Frame_Shift_Del	DEL	ENST00000396992.3	hg19	CCDS14282.1																																																																																			.	.		0.602	CFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056435.2	NM_002621		-	47485892	C	-	47485892	7	5	174	1	0	1	0	1	0	0	0	0	3295	864	30	0	454	0	CFP	23	47485892	Frame_Shift_Del	DEL	C	TCGA-DD-AACX-01A-11D-A40R-10		47485892	107784668	133	26297										
TBC1D25	4943	hgsc.bcm.edu	37	chrX	48418426	48418426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0298507462686567	4	1	0.637330754352031	0.576048951048951	0.660762032085562	0.559440559440559	1	0	ccgcgccatggccaccaagtTtgcacacttgaagctgttgc	10	14	0	1			TCGA-DD-AACX-01A-11D-A40R-10	TCGA-DD-AACX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a122c38-1433-433c-855c-db0cc9656a78	7645f6cb-664b-4790-b507-7f04d533a3d2	g.chrX:48418426T>C	ENST00000376771.4	+	6	1471	c.1130T>C	c.(1129-1131)tTt>tCt	p.F377S	snoU13_ENST00000459609.1_RNA|TBC1D25_ENST00000537536.1_Missense_Mutation_p.F123S	NM_002536.2	NP_002527.1	Q3MII6	TBC25_HUMAN	TBC1 domain family, member 25	377	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of autophagic vacuole maturation (GO:1901096)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4						GCCACCAAGTTTGCACACTTG	0.557																																					p.F377S		Atlas-SNP	.											.	TBC1D25	70	.	0			c.T1130C						.						45	30	35					X																	48418426		2202	4300	6502	SO:0001583	missense	4943	exon6			CCAAGTTTGCACA	L08240	CCDS35242.1	Xp11.23	2014-01-28	2007-01-12	2007-01-12	ENSG00000068354	ENSG00000068354			8092	protein-coding gene	gene with protein product		311240	"ornithine aminotransferase-like 1"	OATL1		21383079	Standard	NM_002536		Approved		uc004dka.1	Q3MII6	OTTHUMG00000024123	ENST00000376771.4:c.1130T>C	chrX.hg19:g.48418426T>C	ENSP00000365962:p.Phe377Ser	47.0	0.0		50.0	41.0	NM_002536	Q08AN9|Q3MII4|Q8TAR9	Missense_Mutation	SNP	ENST00000376771.4	hg19	CCDS35242.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.858072	0.51376	.	.	ENSG00000068354	ENST00000376771;ENST00000537536	T;T	0.22945	1.93;1.93	5.65	5.65	0.86999	Rab-GAP/TBC domain (5);	0.000000	0.85682	D	0.000000	T	0.51736	0.1692	M	0.78285	2.405	0.54753	D	0.999986	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.998;0.99	T	0.56811	-0.7917	10	0.87932	D	0	-16.9959	12.708	0.57073	0.0:0.0:0.0:1.0	.	381;319;377	B4DF03;B4DGU3;Q3MII6	.;.;TBC25_HUMAN	S	377;123	ENSP00000365962:F377S;ENSP00000444091:F123S	ENSP00000365962:F377S	F	+	2	0	TBC1D25	48303370	1.000000	0.71417	0.998000	0.56505	0.301000	0.27625	7.396000	0.79891	1.908000	0.55244	0.352000	0.21897	TTT	.	.		0.557	TBC1D25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060764.2	NM_002536		C	48418426	T	C	48418426	3	2	174	1	0	0	0	0	1	0	0	0	15630	1841	64	2	1152	2	TBC1D25	23	48418426	Missense_Mutation	SNP	T	TCGA-DD-AACX-01A-11D-A40R-10	932534	48418426	106852134	134	26298										
MACF1	23499	hgsc.bcm.edu	37	chr1	39824861	39824862	+	Frame_Shift_Ins	INS	-	-	A													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	agtacctgtggaaaaactccINSaaaaagtagctcgtgacata							TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:39824861_39824862insA	ENST00000372915.3	+	46	12271_12272	c.12184_12185insA	c.(12184-12186)caafs	p.Q4062fs	MACF1_ENST00000317713.7_Frame_Shift_Ins_p.Q1995fs|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000545844.1_Frame_Shift_Ins_p.Q1995fs|MACF1_ENST00000539005.1_Frame_Shift_Ins_p.Q1995fs|MACF1_ENST00000567887.1_Frame_Shift_Ins_p.Q4094fs|MACF1_ENST00000361689.2_Frame_Shift_Ins_p.Q1995fs|MACF1_ENST00000289893.4_Frame_Shift_Ins_p.Q2497fs|MACF1_ENST00000564288.1_Frame_Shift_Ins_p.Q4057fs			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4062					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GGAAAAACTCCAAAAAGTAGCT	0.411																																					p.Q1995fs		Atlas-INDEL	.											.	MACF1	909	.	0			c.5983_5984insA						.																																			SO:0001589	frameshift_variant	23499	exon43			.	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.12189dupA	chr1.hg19:g.39824866_39824866dupA	ENSP00000362006:p.Gln4062fs	484.0	0.0		399.0	51.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Frame_Shift_Ins	INS	ENST00000372915.3	hg19																																																																																				.	.		0.411	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39824862	-	A	39824861	7	5	175	1	0	1	1	0	0	0	0	0	9153	595	21	0	12300	0	MACF1	1	39824861	Frame_Shift_Ins	INS	-	TCGA-DD-AACY-01A-11D-A40R-10		39824861	209425760	1	26299										
SCMH1	22955	hgsc.bcm.edu	37	chr1	41608748	41608748	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gtcctgtgcttccaatttcaTactgatcttgaactcgttgc	7	11	2	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:41608748T>A	ENST00000326197.7	-	5	483	c.184A>T	c.(184-186)Atg>Ttg	p.M62L	SCMH1_ENST00000361191.5_Start_Codon_SNP_p.M1L|SCMH1_ENST00000402904.2_Missense_Mutation_p.M62L|SCMH1_ENST00000372596.1_Start_Codon_SNP_p.M1L|SCMH1_ENST00000456518.2_Missense_Mutation_p.M15L|SCMH1_ENST00000337495.5_Missense_Mutation_p.M72L|SCMH1_ENST00000361705.3_Missense_Mutation_p.M15L|SCMH1_ENST00000372597.1_Missense_Mutation_p.M15L|SCMH1_ENST00000397171.2_Start_Codon_SNP_p.M1L|SCMH1_ENST00000372595.1_Start_Codon_SNP_p.M1L|SCMH1_ENST00000397174.2_Missense_Mutation_p.M42L					sex comb on midleg homolog 1 (Drosophila)											breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				TCCAATTTCATACTGATCTTG	0.488																																					p.M72L		Atlas-SNP	.											.	SCMH1	120	.	0			c.A214T						.						205	203	204					1																	41608748		2203	4300	6503	SO:0001583	missense	22955	exon6			ATTTCATACTGAT	AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"Sterile alpha motif (SAM) domain containing"	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.184A>T	chr1.hg19:g.41608748T>A	ENSP00000318094:p.Met62Leu	65.0	0.0		56.0	20.0	NM_001172219		Missense_Mutation	SNP	ENST00000326197.7	hg19	CCDS30688.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.790054	0.90367	.	.	ENSG00000010803	ENST00000361705;ENST00000456518;ENST00000402904;ENST00000397174;ENST00000397171;ENST00000361191;ENST00000372597;ENST00000372596;ENST00000337495;ENST00000372595;ENST00000326197	T;T;T;T;T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.68467	0.3004	M	0.87038	2.855	0.80722	D	1	P;D;P;D	0.58620	0.927;0.963;0.912;0.983	D;D;D;P	0.67725	0.945;0.953;0.949;0.891	T	0.73196	-0.4059	10	0.56958	D	0.05	.	15.4647	0.75390	0.0:0.0:0.0:1.0	.	15;72;15;62	B4DRQ8;Q96GD3-2;Q96GD3-4;Q96GD3	.;.;.;SCMH1_HUMAN	L	15;15;62;42;1;1;15;1;72;1;62	ENSP00000354996:M15L;ENSP00000403974:M15L;ENSP00000386079:M62L;ENSP00000380359:M42L;ENSP00000380356:M1L;ENSP00000354656:M1L;ENSP00000361678:M15L;ENSP00000361677:M1L;ENSP00000337352:M72L;ENSP00000361676:M1L;ENSP00000318094:M62L	ENSP00000318094:M62L	M	-	1	0	SCMH1	41381335	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.326000	0.78906	0.533000	0.62120	ATG	.	.		0.488	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1			A	41608748	T	A	41608748	3	1	175	1	0	0	0	0	1	0	0	0	13923	1406	49	4	1842	4	SCMH1	1	41608748	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	1783887	41608748	207641873	2	26300										
JAK1	3716	hgsc.bcm.edu	37	chr1	65311203	65311203	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	aggacattctcaccaagtagCtcagggcactggccagctgt	11	12	2	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:65311203C>A	ENST00000342505.4	-	15	2356	c.2108G>T	c.(2107-2109)aGc>aTc	p.S703I	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	703	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.S703T(2)|p.S703I(1)		breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CACCAAGTAGCTCAGGGCACT	0.542			Mis		ALL																																p.S703I		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	JAK1,colon,carcinoma,-1,6	JAK1	209	.	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.G2108T						.						170	175	174					1																	65311203		1982	4155	6137	SO:0001583	missense	3716	exon15			AAGTAGCTCAGGG	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2108G>T	chr1.hg19:g.65311203C>A	ENSP00000343204:p.Ser703Ile	84.0	0.0		62.0	29.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.010965	0.75046	.	.	ENSG00000162434	ENST00000342505	D	0.83335	-1.71	4.72	4.72	0.59763	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.89942	0.6861	M	0.86097	2.795	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.87323	0.2319	9	0.23302	T	0.38	-6.6389	18.2436	0.89977	0.0:1.0:0.0:0.0	.	703	P23458	JAK1_HUMAN	I	703	ENSP00000343204:S703I	ENSP00000343204:S703I	S	-	2	0	JAK1	65083791	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	7.206000	0.77891	2.594000	0.87642	0.655000	0.94253	AGC	.	.		0.542	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		A	65311203	C	A	65311203	3	1	175	1	0	0	0	0	1	0	0	0	7946	797	28	3	1400	3	JAK1	1	65311203	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	23702455	65311203	183939418	3	26301			1	34		2	2	17	N	G_C	5.168372e-05
JAK1	3716	hgsc.bcm.edu	37	chr1	65311219	65311219	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gtagctcagggcactggccaGctgtttggcaactttgaatt	12	9	1	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:65311219G>A	ENST00000342505.4	-	15	2340	c.2092C>T	c.(2092-2094)Ctg>Ttg	p.L698L	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	698	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GCACTGGCCAGCTGTTTGGCA	0.532			Mis		ALL																																p.L698L		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.C2092T						.						168	174	172					1																	65311219		1976	4159	6135	SO:0001819	synonymous_variant	3716	exon15			TGGCCAGCTGTTT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2092C>T	chr1.hg19:g.65311219G>A		92.0	0.0		67.0	31.0	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	hg19	CCDS41346.1																																																																																			.	.		0.532	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		A	65311219	G	A	65311219	2	1	175	1	0	0	0	0	0	0	0	1	7946	962	34	3		3	JAK1	1	65311219	Silent	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	16	65311219	183939402	4	26302			1	34		2	2	17	N	G_C	5.168372e-05
WDR63	126820	hgsc.bcm.edu	37	chr1	85537689	85537689	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	actaaaaccagtattagctgGtaggaatatttcttcattga	7	6	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:85537689G>A	ENST00000294664.6	+	2	244		c.e2+1		WDR63_ENST00000326813.8_Splice_Site|WDR63_ENST00000370596.1_Splice_Site	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63											NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		GTATTAGCTGGTAGGAATATT	0.308																																					.		Atlas-SNP	.											.	WDR63	91	.	0			c.64+1G>A						.						75	81	79					1																	85537689		2203	4300	6503	SO:0001630	splice_region_variant	126820	exon2			TAGCTGGTAGGAA		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"WD repeat domain containing"	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.64+1G>A	chr1.hg19:g.85537689G>A		285.0	1.0		210.0	80.0	NM_145172	A8K988|Q96L72|Q96NU4	Splice_Site	SNP	ENST00000294664.6	hg19	CCDS702.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.752739	0.31046	.	.	ENSG00000162643	ENST00000370596;ENST00000326813;ENST00000294664;ENST00000528899	.	.	.	4.21	3.29	0.37713	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.9752	0.30151	0.1097:0.0:0.8903:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WDR63	85310277	1.000000	0.71417	0.637000	0.29366	0.160000	0.22226	3.812000	0.55628	1.371000	0.46172	0.655000	0.94253	.	.	.		0.308	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172	Intron	A	85537689	G	A	85537689	5	1	175	1	0	0	0	0	0	0	1	0	17329	1275	44	3	67	3	WDR63	1	85537689	Splice_Site	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	20226470	85537689	163712932	5	26303										
RWDD3	25950	hgsc.bcm.edu	37	chr1	95710153	95710153	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	caaagactaaatatgtcaaaAttgtggagaagtgggcttca	10	5	2	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:95710153A>G	ENST00000370202.4	+	2	548	c.472A>G	c.(472-474)Att>Gtt	p.I158V	RWDD3_ENST00000263893.6_Missense_Mutation_p.I158V|RWDD3_ENST00000495272.1_3'UTR|RWDD3_ENST00000429514.2_Missense_Mutation_p.I143V|RP11-57H12.5_ENST00000444665.1_RNA|RP11-57H12.6_ENST00000604534.1_3'UTR	NM_001199682.1|NM_015485.4	NP_001186611.1|NP_056300	Q9Y3V2	RWDD3_HUMAN	RWD domain containing 3	158					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of hypoxia-inducible factor-1alpha signaling pathway (GO:1902073)|positive regulation of protein sumoylation (GO:0033235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(1)|large_intestine(2)|lung(6)|ovary(1)	10		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)		ATATGTCAAAATTGTGGAGAA	0.373																																					p.I158V		Atlas-SNP	.											.	RWDD3	24	.	0			c.A472G						.						119	111	113					1																	95710153		1893	4115	6008	SO:0001583	missense	25950	exon2			GTCAAAATTGTGG	BC010936	CCDS41357.1, CCDS44177.1	1p22.1	2012-12-07			ENSG00000122481	ENSG00000122481			21393	protein-coding gene	gene with protein product		615875				11230166	Standard	NM_015485		Approved	DKFZP566K023	uc009wdu.3	Q9Y3V2	OTTHUMG00000010910	ENST00000370202.4:c.472A>G	chr1.hg19:g.95710153A>G	ENSP00000359221:p.Ile158Val	149.0	0.0		137.0	57.0	NM_001128142	A6NP44|A8K9F0|C9J9L7|C9JI45|Q08AJ7|Q6FID3|Q9BX35	Missense_Mutation	SNP	ENST00000370202.4	hg19	CCDS41357.1	.	.	.	.	.	.	.	.	.	.	A	0.316	-0.965001	0.02249	.	.	ENSG00000122481	ENST00000370202;ENST00000429514;ENST00000263893	T;T;T	0.35605	1.3;1.36;1.31	5.38	4.26	0.50523	.	0.361794	0.32175	N	0.006468	T	0.05823	0.0152	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.32640	-0.9899	10	0.25751	T	0.34	-0.3507	10.6502	0.45645	0.9235:0.0:0.0765:0.0	.	143;158;158;143;158	E7ES73;Q9Y3V2;D3DT49;Q9Y3V2-3;Q9Y3V2-2	.;RWDD3_HUMAN;.;.;.	V	158;143;158	ENSP00000359221:I158V;ENSP00000397398:I143V;ENSP00000263893:I158V	ENSP00000263893:I158V	I	+	1	0	RWDD3	95482741	1.000000	0.71417	0.005000	0.12908	0.979000	0.70002	4.092000	0.57707	1.000000	0.39049	0.528000	0.53228	ATT	.	.		0.373	RWDD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030078.1	NM_015485		G	95710153	A	G	95710153	3	3	175	1	0	0	0	0	1	0	0	0	13772	101	4	2	478	2	RWDD3	1	95710153	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	10172464	95710153	153540468	6	26304										
PALMD	54873	hgsc.bcm.edu	37	chr1	100152744	100152744	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gatgatgaacaaaataggaaAggtatatgagaaatctgtgt	11	2	1	3			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:100152744A>G	ENST00000263174.4	+	6	888	c.513A>G	c.(511-513)aaA>aaG	p.K171K	PALMD_ENST00000605497.1_Splice_Site_p.K171K	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	171					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)		p.K171K(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		AAAATAGGAAAGGTATATGAG	0.333																																					p.K171K		Atlas-SNP	.											PALMD,NS,carcinoma,0,1	PALMD	64	.	1	Substitution - coding silent(1)	endometrium(1)	c.A513G						.						72	77	76					1																	100152744		2199	4298	6497	SO:0001630	splice_region_variant	54873	exon6			TAGGAAAGGTATA	AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.514+1A>G	chr1.hg19:g.100152744A>G		359.0	0.0		307.0	107.0	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Silent	SNP	ENST00000263174.4	hg19	CCDS758.1																																																																																			.	.		0.333	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734	Silent	G	100152744	A	G	100152744	5	3	175	1	0	0	0	0	0	0	1	0	11420	86	3	2	535	2	PALMD	1	100152744	Splice_Site	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	4442591	100152744	149097877	7	26305										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109814231	109814231	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ttgcctgccagggccccttcAtcttcctctcctatgtggtg	9	15	3	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:109814231A>T	ENST00000271332.3	+	28	7874	c.7813A>T	c.(7813-7815)Atc>Ttc	p.I2605F	CELSR2_ENST00000498157.1_3'UTR	NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2605					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GGGCCCCTTCATCTTCCTCTC	0.612																																					p.I2605F	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.A7813T						.						104	91	96					1																	109814231		2203	4300	6503	SO:0001583	missense	1952	exon28			CCCTTCATCTTCC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.7813A>T	chr1.hg19:g.109814231A>T	ENSP00000271332:p.Ile2605Phe	104.0	0.0		91.0	43.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	A	18.67	3.673902	0.67928	.	.	ENSG00000143126	ENST00000271332	T	0.55234	0.53	4.96	4.96	0.65561	GPCR, family 2-like (1);	.	.	.	.	T	0.65396	0.2687	M	0.88979	2.995	0.43814	D	0.996378	D	0.63880	0.993	D	0.68353	0.957	T	0.72669	-0.4223	9	0.72032	D	0.01	.	6.7614	0.23542	0.7684:0.1536:0.078:0.0	.	2605	Q9HCU4	CELR2_HUMAN	F	2605	ENSP00000271332:I2605F	ENSP00000271332:I2605F	I	+	1	0	CELSR2	109615754	0.986000	0.35501	1.000000	0.80357	0.977000	0.68977	1.657000	0.37366	2.089000	0.63090	0.459000	0.35465	ATC	.	.		0.612	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		T	109814231	A	T	109814231	3	4	175	1	0	0	0	0	1	0	0	0	3224	217	8	4	7923	4	CELSR2	1	109814231	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	9661487	109814231	139436390	8	26306										
ETV3	2117	hgsc.bcm.edu	37	chr1	157103988	157103988	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ggtaaatcttttcccttttgTtttatgaaggatcctcttgt	7	7	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:157103988T>G	ENST00000368192.4	-	4	380	c.316A>C	c.(316-318)Aca>Cca	p.T106P	ETV3_ENST00000460850.1_5'Flank|ETV3_ENST00000326786.4_Missense_Mutation_p.T106P	NM_001145312.1	NP_001138784.1	P41162	ETV3_HUMAN	ets variant 3	106					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	9	Hepatocellular(266;0.158)	Prostate(1639;0.174)				TTCCCTTTTGTTTTATGAAGG	0.368																																					p.T106P		Atlas-SNP	.											.	ETV3	50	.	0			c.A316C						.						153	132	139					1																	157103988		2203	4300	6503	SO:0001583	missense	2117	exon4			CTTTTGTTTTATG	BC022868	CCDS1164.1, CCDS44250.1	1q21-q23	2008-09-12	2008-09-12		ENSG00000117036	ENSG00000117036			3492	protein-coding gene	gene with protein product		164873	"ets variant gene 3, ETS family transcriptional repressor", "ets variant gene 3"			8020980	Standard	NM_005240		Approved	PE-1	uc001fqr.2	P41162	OTTHUMG00000034298	ENST00000368192.4:c.316A>C	chr1.hg19:g.157103988T>G	ENSP00000357175:p.Thr106Pro	85.0	0.0		111.0	45.0	NM_005240	B4E3M7|Q8TAC8|Q9BX30	Missense_Mutation	SNP	ENST00000368192.4	hg19	CCDS44250.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.843142	0.91197	.	.	ENSG00000117036	ENST00000368192;ENST00000326786	T;T	0.55588	0.51;0.51	6.06	6.06	0.98353	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.077028	0.53938	D	0.000055	T	0.56891	0.2016	L	0.37850	1.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.991;0.998	T	0.63005	-0.6733	10	0.87932	D	0	.	15.598	0.76602	0.0:0.0:0.0:1.0	.	106;106	P41162-2;P41162	.;ETV3_HUMAN	P	106	ENSP00000357175:T106P;ENSP00000327316:T106P	ENSP00000327316:T106P	T	-	1	0	ETV3	155370612	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.987000	0.88182	2.315000	0.78130	0.533000	0.62120	ACA	.	.		0.368	ETV3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082843.2	NM_005240		G	157103988	T	G	157103988	3	3	175	1	0	0	0	0	1	0	0	0	5281	1725	60	5	1262	5	ETV3	1	157103988	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	47289757	157103988	92146633	9	26307			2	35	91792769	2	2	18	T		5.491386e-05
ETV3	2117	hgsc.bcm.edu	37	chr1	157104005	157104005	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ttgttttatgaaggatcctcTtgttgtaatagtatctgtaa	8	4	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:157104005T>C	ENST00000368192.4	-	4	363	c.299A>G	c.(298-300)aAg>aGg	p.K100R	ETV3_ENST00000460850.1_5'Flank|ETV3_ENST00000326786.4_Missense_Mutation_p.K100R	NM_001145312.1	NP_001138784.1	P41162	ETV3_HUMAN	ets variant 3	100					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	9	Hepatocellular(266;0.158)	Prostate(1639;0.174)				AAGGATCCTCTTGTTGTAATA	0.373																																					p.K100R		Atlas-SNP	.											.	ETV3	50	.	0			c.A299G						.						157	131	140					1																	157104005		2203	4300	6503	SO:0001583	missense	2117	exon4			ATCCTCTTGTTGT	BC022868	CCDS1164.1, CCDS44250.1	1q21-q23	2008-09-12	2008-09-12		ENSG00000117036	ENSG00000117036			3492	protein-coding gene	gene with protein product		164873	"ets variant gene 3, ETS family transcriptional repressor", "ets variant gene 3"			8020980	Standard	NM_005240		Approved	PE-1	uc001fqr.2	P41162	OTTHUMG00000034298	ENST00000368192.4:c.299A>G	chr1.hg19:g.157104005T>C	ENSP00000357175:p.Lys100Arg	78.0	0.0		101.0	38.0	NM_005240	B4E3M7|Q8TAC8|Q9BX30	Missense_Mutation	SNP	ENST00000368192.4	hg19	CCDS44250.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.002970	0.93287	.	.	ENSG00000117036	ENST00000368192;ENST00000326786	T;T	0.57752	0.38;0.38	6.06	6.06	0.98353	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.64402	D	0.000001	T	0.55752	0.1940	L	0.35487	1.065	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.62492	-0.6843	10	0.87932	D	0	.	15.598	0.76602	0.0:0.0:0.0:1.0	.	100;100	P41162-2;P41162	.;ETV3_HUMAN	R	100	ENSP00000357175:K100R;ENSP00000327316:K100R	ENSP00000327316:K100R	K	-	2	0	ETV3	155370629	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.987000	0.88182	2.315000	0.78130	0.533000	0.62120	AAG	.	.		0.373	ETV3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082843.2	NM_005240		C	157104005	T	C	157104005	3	2	175	1	0	0	0	0	1	0	0	0	5281	1609	56	2	1279	2	ETV3	1	157104005	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	17	157104005	92146616	10	26308			2	35	91792769	2	2	18	T		5.491386e-05
C1orf112	55732	hgsc.bcm.edu	37	chr1	169819420	169819420	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	taatagggaacaaatcatgaAgagatagttccacagtgtct	9	6	2	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:169819420A>C	ENST00000286031.6	+	22	2878	c.2178A>C	c.(2176-2178)gaA>gaC	p.E726D	C1orf112_ENST00000498289.1_3'UTR|SCYL3_ENST00000367771.6_3'UTR|C1orf112_ENST00000359326.4_Missense_Mutation_p.E726D	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	726										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CAAATCATGAAGAGATAGTTC	0.323																																					p.E726D		Atlas-SNP	.											.	C1orf112	74	.	0			c.A2178C						.						68	68	68					1																	169819420		2203	4300	6503	SO:0001583	missense	55732	exon22			TCATGAAGAGATA	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.2178A>C	chr1.hg19:g.169819420A>C	ENSP00000286031:p.Glu726Asp	64.0	0.0		101.0	42.0	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	hg19	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133743	0.77662	.	.	ENSG00000000460	ENST00000359326;ENST00000286031	T;T	0.47528	0.84;0.84	5.66	3.26	0.37387	.	0.046551	0.85682	N	0.000000	T	0.52837	0.1759	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.56475	-0.7973	10	0.66056	D	0.02	-11.5746	5.7481	0.18132	0.7724:0.0:0.08:0.1476	.	668;726	B4DGF2;Q9NSG2	.;CA112_HUMAN	D	726	ENSP00000352276:E726D;ENSP00000286031:E726D	ENSP00000286031:E726D	E	+	3	2	C1orf112	168086044	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.052000	0.30429	0.378000	0.24764	0.496000	0.49642	GAA	.	.		0.323	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		C	169819420	A	C	169819420	3	2	175	1	0	0	0	0	1	0	0	0	1987	69	3	5	2256	5	C1orf112	1	169819420	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	12715415	169819420	79431201	11	26309										
TOR3A	64222	hgsc.bcm.edu	37	chr1	179063230	179063230	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	agctcttgtctctttcagtaAtctcaggggcgatataatca	8	9	5	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr1:179063230A>T	ENST00000367627.3	+	5	1573	c.821A>T	c.(820-822)aAt>aTt	p.N274I	TOR3A_ENST00000352445.6_Missense_Mutation_p.N274I	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	274					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						TCTTTCAGTAATCTCAGGGGC	0.443																																					p.N274I		Atlas-SNP	.											.	TOR3A	28	.	0			c.A821T						.						86	86	86					1																	179063230		2203	4300	6503	SO:0001583	missense	64222	exon5			TCAGTAATCTCAG	BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"ATP-dependant interferon responsive"	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.821A>T	chr1.hg19:g.179063230A>T	ENSP00000356599:p.Asn274Ile	104.0	0.0		133.0	48.0	NM_022371	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Missense_Mutation	SNP	ENST00000367627.3	hg19	CCDS1329.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.195323	0.78902	.	.	ENSG00000186283	ENST00000367627;ENST00000352445;ENST00000447595	T;T;T	0.47528	0.84;0.84;0.84	5.55	5.55	0.83447	.	0.043895	0.85682	D	0.000000	T	0.72969	0.3527	M	0.91818	3.245	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.79902	-0.1607	10	0.87932	D	0	-28.8565	13.437	0.61090	1.0:0.0:0.0:0.0	.	274	Q9H497	TOR3A_HUMAN	I	274;274;166	ENSP00000356599:N274I;ENSP00000335351:N274I;ENSP00000410195:N166I	ENSP00000335351:N274I	N	+	2	0	TOR3A	177329853	1.000000	0.71417	1.000000	0.80357	0.536000	0.34869	8.530000	0.90606	2.107000	0.64212	0.459000	0.35465	AAT	.	.		0.443	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371		T	179063230	A	T	179063230	3	4	175	1	0	0	0	0	1	0	0	0	16391	101	4	4	839	4	TOR3A	1	179063230	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	9243810	179063230	70187391	12	26310										
OSR1	130497	hgsc.bcm.edu	37	chr2	19553489	19553489	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	actgtgggcaggccgttcacTgcctgaaggaaggagtagtt	15	8	1	1	rs368651434		TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:19553489T>G	ENST00000272223.2	-	2	422	c.78A>C	c.(76-78)gcA>gcC	p.A26A	OSR1_ENST00000536433.1_Silent_p.A26A	NM_145260.2	NP_660303.1	Q8TAX0	OSR1_HUMAN	odd-skipped related transciption factor 1	26					cell differentiation (GO:0030154)|cell proliferation involved in kidney development (GO:0072111)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|gonad development (GO:0008406)|heart development (GO:0007507)|intermediate mesoderm development (GO:0048389)|mesangial cell development (GO:0072143)|mesonephric duct morphogenesis (GO:0072180)|mesonephros development (GO:0001823)|metanephric cap mesenchymal cell proliferation involved in metanephros development (GO:0090094)|metanephric epithelium development (GO:0072207)|metanephric glomerulus vasculature development (GO:0072239)|metanephric interstitial fibroblast development (GO:0072259)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephric nephron tubule development (GO:0072234)|metanephric smooth muscle tissue development (GO:0072208)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of nephron tubule epithelial cell differentiation (GO:0072183)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|palate development (GO:0060021)|pattern specification involved in metanephros development (GO:0072268)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posterior mesonephric tubule development (GO:0072166)|pronephros development (GO:0048793)|renal vesicle progenitor cell differentiation (GO:0072184)|specification of anterior mesonephric tubule identity (GO:0072168)|specification of posterior mesonephric tubule identity (GO:0072169)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)|ureter urothelium development (GO:0072190)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|large_intestine(2)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)				GGCCGTTCACTGCCTGAAGGA	0.602																																					p.A26A		Atlas-SNP	.											.	OSR1	29	.	0			c.A78C						.						53	50	51					2																	19553489		2203	4300	6503	SO:0001819	synonymous_variant	130497	exon2			GTTCACTGCCTGA	BC025712	CCDS1694.1	2p24.1	2013-10-17	2013-10-17	2004-11-26	ENSG00000143867	ENSG00000143867		"Zinc fingers, C2H2-type"	8111	protein-coding gene	gene with protein product		608891	"odd-skipped (Drosophila) homolog", "odd-skipped related 1 (Drosophila)"	ODD		2120051, 12119563	Standard	XM_006711942		Approved		uc002rdc.3	Q8TAX0	OTTHUMG00000088793	ENST00000272223.2:c.78A>C	chr2.hg19:g.19553489T>G		104.0	0.0		98.0	42.0	NM_145260	B3KV97|D6W521	Silent	SNP	ENST00000272223.2	hg19	CCDS1694.1																																																																																			.	.		0.602	OSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000201432.2	NM_145260		G	19553489	T	G	19553489	2	3	175	1	0	0	0	0	0	0	0	1	11302	1567	55	5		5	OSR1	2	19553489	Silent	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10		19553489	223645884	13	26311										
DHX57	90957	hgsc.bcm.edu	37	chr2	39033812	39033812	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gctccagtactggtcttctgAaattttccttctgggctttt	8	10	3	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:39033812A>C	ENST00000295373.6	-	22	3831	c.3705T>G	c.(3703-3705)ttT>ttG	p.F1235L		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1235							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TGGTCTTCTGAAATTTTCCTT	0.363																																					p.F1235L	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.T3705G						.						124	114	117					2																	39033812		2203	4300	6503	SO:0001583	missense	90957	exon22			CTTCTGAAATTTT	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3705T>G	chr2.hg19:g.39033812A>C	ENSP00000295373:p.Phe1235Leu	102.0	0.0		100.0	38.0	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	hg19	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.604269	0.46423	.	.	ENSG00000163214	ENST00000295373	T	0.02656	4.21	5.37	-0.156	0.13391	Domain of unknown function DUF1605 (1);	0.112412	0.40385	N	0.001113	T	0.03390	0.0098	L	0.49640	1.575	0.35861	D	0.827502	B	0.16166	0.016	B	0.16722	0.016	T	0.34428	-0.9829	10	0.42905	T	0.14	.	9.977	0.41791	0.5542:0.0:0.4458:0.0	.	1235	Q6P158	DHX57_HUMAN	L	1235	ENSP00000295373:F1235L	ENSP00000295373:F1235L	F	-	3	2	DHX57	38887316	1.000000	0.71417	0.988000	0.46212	0.992000	0.81027	0.801000	0.27055	-0.262000	0.09392	0.379000	0.24179	TTT	.	.		0.363	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		C	39033812	A	C	39033812	3	2	175	1	0	0	0	0	1	0	0	0	4515	243	9	5	467	5	DHX57	2	39033812	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	19480323	39033812	204165561	14	26312										
HAAO	23498	hgsc.bcm.edu	37	chr2	43019665	43019665	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	acccaggccctcactcccagGcggcgctccatgactgtccc	9	20	1	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:43019665G>A	ENST00000294973.6	-	1	67	c.12C>T	c.(10-12)cgC>cgT	p.R4R		NM_012205.2	NP_036337.2			3-hydroxyanthranilate 3,4-dioxygenase											breast(2)|cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(2)	11						TCACTCCCAGGCGGCGCTCCA	0.692																																					p.R4R		Atlas-SNP	.											.	HAAO	26	.	0			c.C12T						.						28	34	32					2																	43019665		2203	4300	6503	SO:0001819	synonymous_variant	23498	exon1			TCCCAGGCGGCGC	Z29481	CCDS33187.1	2p	2008-02-05			ENSG00000162882	ENSG00000162882	1.13.11.6		4796	protein-coding gene	gene with protein product		604521				7514594	Standard	NM_012205		Approved		uc002rst.4	P46952	OTTHUMG00000152348	ENST00000294973.6:c.12C>T	chr2.hg19:g.43019665G>A		91.0	0.0		69.0	27.0	NM_012205		Silent	SNP	ENST00000294973.6	hg19	CCDS33187.1																																																																																			.	.		0.692	HAAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325948.2			A	43019665	G	A	43019665	2	1	175	1	0	0	0	0	0	0	0	1	6946	1190	42	3		3	HAAO	2	43019665	Silent	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	3985853	43019665	200179708	15	26313										
EPAS1	2034	hgsc.bcm.edu	37	chr2	46609728	46609728	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	acagcctgtcgtcagcccacAaggtgtcaggtgggtgtgcc	14	12	2	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:46609728A>G	ENST00000263734.3	+	15	2962	c.2452A>G	c.(2452-2454)Aag>Gag	p.K818E		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	818					angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			GTCAGCCCACAAGGTGTCAGG	0.607																																					p.K818E		Atlas-SNP	.											.	EPAS1	83	.	0			c.A2452G						.						60	56	57					2																	46609728		2203	4300	6503	SO:0001583	missense	2034	exon15			GCCCACAAGGTGT	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"Basic helix-loop-helix proteins"	3374	protein-coding gene	gene with protein product	"HIF-1 alpha-like factor"	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.2452A>G	chr2.hg19:g.46609728A>G	ENSP00000263734:p.Lys818Glu	79.0	0.0		90.0	33.0	NM_001430	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	hg19	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	A	14.53	2.562019	0.45590	.	.	ENSG00000116016	ENST00000263734	T	0.56275	0.47	5.64	5.64	0.86602	.	0.755598	0.13214	N	0.404965	T	0.35998	0.0951	N	0.08118	0	0.40713	D	0.982596	P	0.38992	0.653	B	0.36666	0.23	T	0.43956	-0.9359	10	0.87932	D	0	.	14.0822	0.64932	1.0:0.0:0.0:0.0	.	818	Q99814	EPAS1_HUMAN	E	818	ENSP00000263734:K818E	ENSP00000263734:K818E	K	+	1	0	EPAS1	46463232	1.000000	0.71417	0.997000	0.53966	0.346000	0.29079	4.043000	0.57354	2.143000	0.66587	0.533000	0.62120	AAG	.	.		0.607	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430		G	46609728	A	G	46609728	3	3	175	1	0	0	0	0	1	0	0	0	5152	131	5	2	2510	2	EPAS1	2	46609728	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	3590063	46609728	196589645	16	26314										
FOXN2	3344	hgsc.bcm.edu	37	chr2	48602157	48602167	+	Frame_Shift_Del	DEL	TCTTTAGCCAC	TCTTTAGCCAC	-													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	tacgattacaagagagtgatTctttagccaccagcattgat					rs368599437		TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	TCTTTAGCCAC	TCTTTAGCCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:48602157_48602167delTCTTTAGCCAC	ENST00000340553.3	+	7	1132_1142	c.871_881delTCTTTAGCCAC	c.(871-882)tctttagccaccfs	p.SLAT291fs		NM_002158.3	NP_002149.2	P32314	FOXN2_HUMAN	forkhead box N2	291					transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)			AGAGAGTGATTCTTTAGCCACCAGCATTGAT	0.45																																					p.290_294del		Atlas-INDEL	.											.	FOXN2	39	.	0			c.870_880del						.																																			SO:0001589	frameshift_variant	3344	exon7			.		CCDS1838.1	2p22-p16	2008-02-05	2006-10-02	2006-10-02	ENSG00000170802	ENSG00000170802		"Forkhead boxes"	5281	protein-coding gene	gene with protein product		143089	"human T-cell leukemia virus enhancer factor"	HTLF		1639393	Standard	NM_002158		Approved		uc002rwh.1	P32314	OTTHUMG00000129168	ENST00000340553.3:c.871_881delTCTTTAGCCAC	chr2.hg19:g.48602157_48602167delTCTTTAGCCAC	ENSP00000343633:p.Ser291fs	154.0	0.0		116.0	39.0	NM_002158	Q15769|Q6P4Q2	Frame_Shift_Del	DEL	ENST00000340553.3	hg19	CCDS1838.1																																																																																			.	.		0.45	FOXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251240.3	NM_002158		-	48602167	TCTTTAGCCAC	-	48602157	7	5	175	1	0	1	0	1	0	0	0	0	6028	1783	62	0	889	0	FOXN2	2	48602157	Frame_Shift_Del	DEL	TCTTTAGCCAC	TCGA-DD-AACY-01A-11D-A40R-10	1992429	48602157	194597216	17	26315										
FOXN2	3344	hgsc.bcm.edu	37	chr2	48602189	48602189	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	agcattgatccaaaagaagaTcacaattacagtgcaagtag	8	7	1	3			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:48602189T>G	ENST00000340553.3	+	7	1164	c.903T>G	c.(901-903)gaT>gaG	p.D301E		NM_002158.3	NP_002149.2	P32314	FOXN2_HUMAN	forkhead box N2	301					transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)			CAAAAGAAGATCACAATTACA	0.438																																					p.D301E		Atlas-SNP	.											.	FOXN2	39	.	0			c.T903G						.						117	96	103					2																	48602189		2203	4300	6503	SO:0001583	missense	3344	exon7			AGAAGATCACAAT		CCDS1838.1	2p22-p16	2008-02-05	2006-10-02	2006-10-02	ENSG00000170802	ENSG00000170802		"Forkhead boxes"	5281	protein-coding gene	gene with protein product		143089	"human T-cell leukemia virus enhancer factor"	HTLF		1639393	Standard	NM_002158		Approved		uc002rwh.1	P32314	OTTHUMG00000129168	ENST00000340553.3:c.903T>G	chr2.hg19:g.48602189T>G	ENSP00000343633:p.Asp301Glu	146.0	0.0		104.0	36.0	NM_002158	Q15769|Q6P4Q2	Missense_Mutation	SNP	ENST00000340553.3	hg19	CCDS1838.1	.	.	.	.	.	.	.	.	.	.	T	19.90	3.912695	0.72983	.	.	ENSG00000170802	ENST00000304367;ENST00000340553	D	0.98012	-4.66	4.73	-0.115	0.13560	.	0.000000	0.85682	D	0.000000	D	0.97508	0.9184	L	0.58810	1.83	0.41689	D	0.989338	D	0.76494	0.999	D	0.78314	0.991	D	0.95687	0.8737	10	0.66056	D	0.02	.	8.1204	0.30967	0.0:0.3712:0.0:0.6288	.	301	P32314	FOXN2_HUMAN	E	210;301	ENSP00000343633:D301E	ENSP00000305685:D210E	D	+	3	2	FOXN2	48455693	0.998000	0.40836	0.998000	0.56505	0.999000	0.98932	0.372000	0.20467	-0.057000	0.13199	0.533000	0.62120	GAT	.	.		0.438	FOXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251240.3	NM_002158		G	48602189	T	G	48602189	3	3	175	1	0	0	0	0	1	0	0	0	6028	1432	50	5	921	5	FOXN2	2	48602189	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	32	48602189	194597184	18	26316										
KIF5C	3800	hgsc.bcm.edu	37	chr2	149868088	149868088	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	tgttggttggatacagccaaGcccatccgccccggacacta	10	14	0	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:149868088G>A	ENST00000435030.1	+	25	3140	c.2772G>A	c.(2770-2772)aaG>aaA	p.K924K	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000414838.2_Silent_p.K829K|KIF5C_ENST00000397413.1_Silent_p.K692K			O60282	KIF5C_HUMAN	kinesin family member 5C	924	Globular.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		ATACAGCCAAGCCCATCCGCC	0.502																																					p.K924K		Atlas-SNP	.											.	KIF5C	166	.	0			c.G2772A						.						51	52	52					2																	149868088		1874	4110	5984	SO:0001819	synonymous_variant	3800	exon25			AGCCAAGCCCATC	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.2772G>A	chr2.hg19:g.149868088G>A		66.0	0.0		68.0	23.0	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	hg19																																																																																				.	.		0.502	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		A	149868088	G	A	149868088	2	1	175	1	0	0	0	0	0	0	0	1	8316	962	34	3		3	KIF5C	2	149868088	Silent	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	101265899	149868088	93331285	19	26317										
ITGA6	3655	hgsc.bcm.edu	37	chr2	173338923	173338923	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cacatctcctccctgagcacAtattcgatggagaaggtctg	9	12	2	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:173338923A>G	ENST00000264106.6	+	7	1236	c.1033A>G	c.(1033-1035)Ata>Gta	p.I345V	ITGA6_ENST00000264107.7_Missense_Mutation_p.I306V|ITGA6_ENST00000409080.1_Missense_Mutation_p.I306V|ITGA6_ENST00000409532.1_Missense_Mutation_p.I187V|ITGA6_ENST00000375221.2_Missense_Mutation_p.I345V|ITGA6_ENST00000343713.4_Missense_Mutation_p.I301V			P23229	ITA6_HUMAN	integrin, alpha 6	345					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			CCCTGAGCACATATTCGATGG	0.498																																					p.I306V		Atlas-SNP	.											.	ITGA6	171	.	0			c.A916G						.						140	127	132					2																	173338923		2203	4300	6503	SO:0001583	missense	3655	exon6			GAGCACATATTCG		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"CD molecules", "Integrins"	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.1033A>G	chr2.hg19:g.173338923A>G	ENSP00000264106:p.Ile345Val	129.0	0.0		121.0	45.0	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	hg19		.	.	.	.	.	.	.	.	.	.	A	5.011	0.187758	0.09547	.	.	ENSG00000091409	ENST00000412899;ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358	T;T;T;T;T;T;T;T;T	0.71222	-0.55;0.07;-0.29;-0.27;-0.28;-0.3;-0.29;-0.27;-0.3	5.36	0.644	0.17776	.	0.372053	0.33691	N	0.004643	T	0.43433	0.1247	N	0.16602	0.42	0.44104	D	0.996871	B;B;B	0.10296	0.0;0.001;0.003	B;B;B	0.15052	0.001;0.012;0.007	T	0.25847	-1.0120	10	0.06099	T	0.92	.	6.0431	0.19746	0.5862:0.2093:0.2045:0.0	.	301;306;306	P23229-4;G5E9H1;P23229-2	.;.;.	V	192;187;306;345;345;301;306;345;301	ENSP00000413470:I192V;ENSP00000386614:I187V;ENSP00000264107:I306V;ENSP00000264106:I345V;ENSP00000364369:I345V;ENSP00000341078:I301V;ENSP00000386896:I306V;ENSP00000406694:I345V;ENSP00000394169:I301V	ENSP00000264106:I345V	I	+	1	0	ITGA6	173047169	0.939000	0.31865	1.000000	0.80357	0.950000	0.60333	1.251000	0.32862	0.871000	0.35750	-0.264000	0.10439	ATA	.	.		0.498	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				G	173338923	A	G	173338923	3	3	175	1	0	0	0	0	1	0	0	0	7889	217	8	2	938	2	ITGA6	2	173338923	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	23470835	173338923	69860450	20	26318										
PDK1	5163	hgsc.bcm.edu	37	chr2	173429803	173429803	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gtacttgaagttattaaaggTaaatactgacatttctcctt	6	6	1	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:173429803T>G	ENST00000282077.3	+	5	873		c.e5+2		PDK1_ENST00000392571.2_Splice_Site|PDK1_ENST00000543905.1_Splice_Site|PDK1_ENST00000544863.1_Splice_Site|PDK1_ENST00000410055.1_Splice_Site			Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase, isozyme 1						cell proliferation (GO:0008283)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.12)			TTATTAAAGGTAAATACTGAC	0.289									Autosomal Dominant Polycystic Kidney Disease																												.		Atlas-SNP	.											.	PDK1	39	.	0			c.691+2T>G						.						94	88	90					2																	173429803		2203	4299	6502	SO:0001630	splice_region_variant	5163	exon5	Familial Cancer Database	ADPKD	TAAAGGTAAATAC	L42450	CCDS2250.1, CCDS63059.1	2q31.1	2008-05-23	2005-11-16		ENSG00000152256	ENSG00000152256			8809	protein-coding gene	gene with protein product		602524	"pyruvate dehydrogenase kinase, isoenzyme 1"			7499431	Standard	NR_103731		Approved		uc002uhs.3	Q15118	OTTHUMG00000132285	ENST00000282077.3:c.691+2T>G	chr2.hg19:g.173429803T>G		74.0	0.0		80.0	27.0	NM_002610	B2R6T1|B7Z937|D3DPD8|E9PD65|Q308M4	Splice_Site	SNP	ENST00000282077.3	hg19	CCDS2250.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.428600	0.83667	.	.	ENSG00000152256	ENST00000543905;ENST00000544863;ENST00000282077;ENST00000392571;ENST00000410055;ENST00000416991	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3939	0.83550	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PDK1	173138049	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	7.798000	0.85924	2.276000	0.75962	0.455000	0.32223	.	.	.		0.289	PDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255380.3	NM_002610	Intron	G	173429803	T	G	173429803	5	3	175	1	0	0	0	0	0	0	1	0	11684	1652	57	5	711	5	PDK1	2	173429803	Splice_Site	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	90880	173429803	69769570	21	26319										
HECW2	57520	hgsc.bcm.edu	37	chr2	197092916	197092916	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	attcaaataagccataatatGggttaaagagttctctggat	8	5	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:197092916G>C	ENST00000260983.3	-	22	4009	c.3827C>G	c.(3826-3828)cCa>cGa	p.P1276R	HECW2_ENST00000409111.1_Missense_Mutation_p.P920R	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1276	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						GCCATAATATGGGTTAAAGAG	0.353																																					p.P1276R		Atlas-SNP	.											.	HECW2	239	.	0			c.C3827G						.						89	91	90					2																	197092916		2203	4300	6503	SO:0001583	missense	57520	exon22			TAATATGGGTTAA	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.3827C>G	chr2.hg19:g.197092916G>C	ENSP00000260983:p.Pro1276Arg	282.0	0.0		250.0	110.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.634422	0.87660	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	T;T	0.59083	0.29;0.29	5.44	5.44	0.79542	HECT (4);	0.000000	0.85682	D	0.000000	D	0.84074	0.5392	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88221	0.2897	10	0.87932	D	0	.	19.4586	0.94906	0.0:0.0:1.0:0.0	.	1276	Q9P2P5	HECW2_HUMAN	R	920;1276	ENSP00000386775:P920R;ENSP00000260983:P1276R	ENSP00000260983:P1276R	P	-	2	0	HECW2	196801161	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.657000	0.98554	2.828000	0.97474	0.655000	0.94253	CCA	.	.		0.353	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		C	197092916	G	C	197092916	3	2	175	1	0	0	0	0	1	0	0	0	7052	1348	47	4	923	4	HECW2	2	197092916	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	23663113	197092916	46106457	22	26320										
SMARCAL1	50485	hgsc.bcm.edu	37	chr2	217341834	217341834	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	caattcctggacacacaggtGctgatccaggctgaggaccg	12	12	0	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr2:217341834G>T	ENST00000357276.4	+	16	2760	c.2430G>T	c.(2428-2430)gtG>gtT	p.V810V	AC098820.3_ENST00000453157.1_RNA|SMARCAL1_ENST00000358207.5_Silent_p.V810V	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	810	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		ACACACAGGTGCTGATCCAGG	0.567									Schimke Immuno-Osseous Dysplasia																												p.V810V		Atlas-SNP	.											.	SMARCAL1	93	.	0			c.G2430T						.						70	57	62					2																	217341834		2201	4293	6494	SO:0001819	synonymous_variant	50485	exon16	Familial Cancer Database	SIOD	ACAGGTGCTGATC	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"HepA-related protein", "ATP-driven annealing helicase"	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.2430G>T	chr2.hg19:g.217341834G>T		46.0	0.0		37.0	15.0	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Silent	SNP	ENST00000357276.4	hg19	CCDS2403.1																																																																																			.	.		0.567	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			T	217341834	G	T	217341834	2	4	175	1	0	0	0	0	0	0	0	1	14788	1306	46	3		3	SMARCAL1	2	217341834	Silent	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	20248918	217341834	25857539	23	26321										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9102039	9102039	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	tgttctcagagtacttggccTgcctctggaagaagaaaaga	11	8	2	4			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr3:9102039T>G	ENST00000383836.3	-	6	1104	c.677A>C	c.(676-678)cAg>cCg	p.Q226P	SRGAP3_ENST00000433332.3_5'UTR|SRGAP3_ENST00000360413.3_Missense_Mutation_p.Q226P	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	226	F-BAR domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GTACTTGGCCTGCCTCTGGAA	0.428			T	RAF1	pilocytic astrocytoma																																p.Q226P		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.A677C						.						138	126	130					3																	9102039		2203	4300	6503	SO:0001583	missense	9901	exon6			TTGGCCTGCCTCT	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.677A>C	chr3.hg19:g.9102039T>G	ENSP00000373347:p.Gln226Pro	86.0	0.0		75.0	29.0	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.350524	0.82132	.	.	ENSG00000196220	ENST00000383836;ENST00000360413;ENST00000544908	T;T	0.15834	2.39;2.39	5.27	5.27	0.74061	.	0.217293	0.41938	D	0.000784	T	0.46308	0.1386	M	0.86028	2.79	0.80722	D	1	D;B;P;P	0.67145	0.996;0.0;0.952;0.92	D;B;P;B	0.72982	0.979;0.0;0.629;0.425	T	0.53725	-0.8398	10	0.72032	D	0.01	.	14.8468	0.70267	0.0:0.0:0.0:1.0	.	226;95;226;226	C7TPG7;Q9ULR4;O43295-2;O43295	.;.;.;SRGP2_HUMAN	P	226;226;106	ENSP00000373347:Q226P;ENSP00000353587:Q226P	ENSP00000353587:Q226P	Q	-	2	0	SRGAP3	9077039	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	7.873000	0.87193	1.992000	0.58205	0.377000	0.23210	CAG	.	.		0.428	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			G	9102039	T	G	9102039	3	3	175	1	0	0	0	0	1	0	0	0	15162	1580	55	5	2725	5	SRGAP3	3	9102039	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10		9102039	188920391	24	26322										
PPARG	5468	hgsc.bcm.edu	37	chr3	12458591	12458591	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	tgagtttgctgtgaagttcaAtgcactggaattagatgaca	11	5	1	4			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr3:12458591A>T	ENST00000287820.6	+	6	1329	c.1208A>T	c.(1207-1209)aAt>aTt	p.N403I	PPARG_ENST00000539812.1_Intron|PPARG_ENST00000397012.2_Missense_Mutation_p.N375I|PPARG_ENST00000397015.2_Missense_Mutation_p.N375I|PPARG_ENST00000397026.2_Missense_Mutation_p.N381I|PPARG_ENST00000309576.6_Missense_Mutation_p.N375I|PPARG_ENST00000397010.2_Missense_Mutation_p.N375I|PPARG_ENST00000397000.1_Intron	NM_015869.4	NP_056953.2	P37231	PPARG_HUMAN	peroxisome proliferator-activated receptor gamma	403	Ligand-binding.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|brown fat cell differentiation (GO:0050873)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|cellular response to lithium ion (GO:0071285)|epithelial cell differentiation (GO:0030855)|fatty acid oxidation (GO:0019395)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|innate immune response (GO:0045087)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|lipoprotein transport (GO:0042953)|long-chain fatty acid transport (GO:0015909)|low-density lipoprotein particle receptor biosynthetic process (GO:0045713)|monocyte differentiation (GO:0030224)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of cell growth (GO:0030308)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ regeneration (GO:0031100)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|placenta development (GO:0001890)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood pressure (GO:0008217)|regulation of cholesterol transporter activity (GO:0060694)|regulation of transcription involved in cell fate commitment (GO:0060850)|response to caffeine (GO:0031000)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to lipid (GO:0033993)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|arachidonic acid binding (GO:0050544)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|prostaglandin receptor activity (GO:0004955)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)		PAX8/PPARG(117)	breast(2)|endometrium(4)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20					Balsalazide(DB01014)|Bezafibrate(DB01393)|Glipizide(DB01067)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Mesalazine(DB00244)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Pioglitazone(DB01132)|Repaglinide(DB00912)|Rosiglitazone(DB00412)|Sulfasalazine(DB00795)|Telmisartan(DB00966)	GTGAAGTTCAATGCACTGGAA	0.433			T	PAX8	follicular thyroid		"Insulin resistance ; lipodystrophy, familial partial L;diabetes mellitus, insulin-resistantI, with acanthosis nigricans and hypertension"																														p.N403I		Atlas-SNP	.		Dom	yes		3	3p25	5468	"peroxisome proliferative activated receptor, gamma"	yes	E	.	PPARG	49	.	0			c.A1208T						.						44	43	43					3																	12458591		2203	4299	6502	SO:0001583	missense	5468	exon6			AGTTCAATGCACT	X90563	CCDS2609.1, CCDS2610.2	3p25	2013-01-16	2006-10-17		ENSG00000132170	ENSG00000132170		"Nuclear hormone receptors"	9236	protein-coding gene	gene with protein product		601487	"peroxisome proliferative activated receptor, gamma"			7862171, 9750197	Standard	NM_005037		Approved	PPARG1, PPARG2, NR1C3, PPARgamma	uc003bwx.3	P37231	OTTHUMG00000129764	ENST00000287820.6:c.1208A>T	chr3.hg19:g.12458591A>T	ENSP00000287820:p.Asn403Ile	110.0	0.0		70.0	20.0	NM_015869	A8K3G6|B5BUA1|O00684|O00710|O14515|Q0QJH8|Q15178|Q15179|Q15180|Q15832|Q86U60|Q96J12	Missense_Mutation	SNP	ENST00000287820.6	hg19	CCDS2609.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.260454	0.80246	.	.	ENSG00000132170	ENST00000397010;ENST00000309576;ENST00000397015;ENST00000397012;ENST00000397026;ENST00000287820	T;T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56;-0.56	5.99	4.83	0.62350	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.86347	0.5911	M	0.91459	3.21	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.88229	0.2902	10	0.72032	D	0.01	.	12.1936	0.54284	0.9336:0.0:0.0664:0.0	.	403	P37231	PPARG_HUMAN	I	375;375;375;375;381;403	ENSP00000380205:N375I;ENSP00000312472:N375I;ENSP00000380210:N375I;ENSP00000380207:N375I;ENSP00000380221:N381I;ENSP00000287820:N403I	ENSP00000287820:N403I	N	+	2	0	PPARG	12433591	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.302000	0.96175	1.079000	0.41038	0.533000	0.62120	AAT	.	.		0.433	PPARG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251979.2	NM_005037		T	12458591	A	T	12458591	3	4	175	1	0	0	0	0	1	0	0	0	12308	101	4	4	1230	4	PPARG	3	12458591	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	3356552	12458591	185563839	25	26323										
RFTN1	23180	hgsc.bcm.edu	37	chr3	16368341	16368341	+	Frame_Shift_Del	DEL	G	G	-													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ctgccagccataggccgccaGcgagttcagcaggggcacgt							TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr3:16368341delG	ENST00000334133.4	-	8	1461	c.1189delC	c.(1189-1191)ctgfs	p.L397fs	OXNAD1_ENST00000605932.1_Intron|OXNAD1_ENST00000544043.1_Intron|RFTN1_ENST00000483671.1_5'UTR|RFTN1_ENST00000432519.1_Frame_Shift_Del_p.L361fs|OXNAD1_ENST00000435829.2_Intron|OXNAD1_ENST00000606098.1_Intron	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	397					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						TAGGCCGCCAGCGAGTTCAGC	0.542																																					p.L397fs		Atlas-INDEL	.											.	RFTN1	79	.	0			c.1190delT						.						54	46	49					3																	16368341		2203	4300	6503	SO:0001589	frameshift_variant	23180	exon8			.	D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"raft-linking protein"					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.1189delC	chr3.hg19:g.16368341delG	ENSP00000334153:p.Leu397fs	47.0	0.0		28.0	17.0	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Frame_Shift_Del	DEL	ENST00000334133.4	hg19	CCDS33712.1																																																																																			.	.		0.542	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150		-	16368341	G	-	16368341	7	5	175	1	0	1	0	1	0	0	0	0	13273	962	34	0	559	0	RFTN1	3	16368341	Frame_Shift_Del	DEL	G	TCGA-DD-AACY-01A-11D-A40R-10	3909750	16368341	181654089	26	26324										
PXK	5162	hgsc.bcm.edu	37	chr3	58410540	58410540	+	IGR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ccagcagctcccttgcctccTgcgagcaccgaggcacctgc	10	19	0	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr3:58410540T>G	ENST00000302746.6	-	0	1527				PXK_ENST00000536660.1_Silent_p.P393P|PXK_ENST00000463280.1_3'UTR|PXK_ENST00000383716.3_Silent_p.P497P|PXK_ENST00000479241.1_Missense_Mutation_p.C524G|PXK_ENST00000356151.2_Silent_p.P530P|PXK_ENST00000302779.5_Silent_p.P513P	NM_000925.3|NM_001173468.1	NP_000916.2|NP_001166939.1	P11177	ODPB_HUMAN	pyruvate dehydrogenase (lipoamide) beta						acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	9				BRCA - Breast invasive adenocarcinoma(55;0.000179)|Kidney(10;0.00231)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.187)	Pyruvic acid(DB00119)	CCTTGCCTCCTGCGAGCACCG	0.572																																					p.P530P		Atlas-SNP	.											.	PXK	89	.	0			c.T1590G						.						63	45	51					3																	58410540		2203	4300	6503	SO:0001628	intergenic_variant	54899	exon18			GCCTCCTGCGAGC		CCDS2890.1, CCDS54602.1	3p21.1-p14.2	1995-12-20			ENSG00000168291	ENSG00000168291	1.2.4.1		8808	protein-coding gene	gene with protein product		179060					Standard	NR_033384		Approved		uc003dkf.4	P11177	OTTHUMG00000159157		chr3.hg19:g.58410540T>G		143.0	0.0		137.0	47.0	NM_017771	B2R7L0|B4DDD7|Q6FH45|Q9BQ27|Q9UFK3	Silent	SNP	ENST00000302746.6	hg19	CCDS2890.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.18|13.18	2.159306|2.159306	0.38119|0.38119	.|.	.|.	ENSG00000168297|ENSG00000168297	ENST00000479241|ENST00000479134	T|.	0.33438|.	1.41|.	6.03|6.03	-12.1|-12.1	0.00011|0.00011	.|.	.|.	.|.	.|.	.|.	T|T	0.30634|0.30634	0.0771|0.0771	.|.	.|.	.|.	0.42227|0.42227	D|D	0.991879|0.991879	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.38672|0.38672	-0.9650|-0.9650	6|4	0.10377|.	T|.	0.69|.	-1.5322|-1.5322	1.7683|1.7683	0.03007|0.03007	0.3742:0.3075:0.1516:0.1667|0.3742:0.3075:0.1516:0.1667	.|.	.|.	.|.	.|.	G|R	524|264	ENSP00000419049:C524G|.	ENSP00000419049:C524G|.	C|L	+|+	1|2	0|0	PXK|PXK	58385580|58385580	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.831000|0.831000	0.47069|0.47069	-1.242000|-1.242000	0.02908|0.02908	-2.146000|-2.146000	0.00800|0.00800	-1.140000|-1.140000	0.01884|0.01884	TGC|CTG	.	.		0.572	PDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353558.1			G	58410540	T	G	58410540	1	3	175	0	1	0	0	0	0	0	0	0	12864	1567	55	5		5	PXK	3	58410540	IGR	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	42042199	58410540	139611890	27	26325										
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122631890	122631890	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gggaggtgctcccgctgcgcAggaggacctccaccagggct	16	14	0	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr3:122631890A>G	ENST00000357599.3	-	18	2911	c.2525T>C	c.(2524-2526)cTg>cCg	p.L842P	SEMA5B_ENST00000195173.4_Missense_Mutation_p.L841P|SEMA5B_ENST00000451055.2_Missense_Mutation_p.L896P	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	842					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		CCCGCTGCGCAGGAGGACCTC	0.796																																					p.L896P		Atlas-SNP	.											.	SEMA5B	303	.	0			c.T2687C						.						4	6	5					3																	122631890		2050	3964	6014	SO:0001583	missense	54437	exon18			CTGCGCAGGAGGA	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.2525T>C	chr3.hg19:g.122631890A>G	ENSP00000350215:p.Leu842Pro	48.0	0.0		31.0	16.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	hg19	CCDS35491.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018592	0.75275	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.37915	1.18;1.17;1.24;1.3	5.01	5.01	0.66863	.	0.254680	0.32719	N	0.005723	T	0.54854	0.1884	L	0.56769	1.78	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.70716	0.97;0.934	T	0.57400	-0.7818	10	0.62326	D	0.03	.	14.0489	0.64722	1.0:0.0:0.0:0.0	.	784;842	D3YTI7;Q9P283	.;SEM5B_HUMAN	P	842;841;784;896;842	ENSP00000350215:L842P;ENSP00000195173:L841P;ENSP00000389588:L896P;ENSP00000377208:L842P	ENSP00000195173:L841P	L	-	2	0	SEMA5B	124114580	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.158000	0.58150	2.114000	0.64651	0.533000	0.62120	CTG	.	.		0.796	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		G	122631890	A	G	122631890	3	3	175	1	0	0	0	0	1	0	0	0	14053	188	7	2	954	2	SEMA5B	3	122631890	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	64221350	122631890	75390540	28	26326										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134873108	134873108	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cctggactatgagatccggtActatgagaaggtgagccagc	13	9	0	3			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr3:134873108A>G	ENST00000398015.3	+	6	1782	c.1412A>G	c.(1411-1413)tAc>tGc	p.Y471C	EPHB1_ENST00000493838.1_Missense_Mutation_p.Y32C	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	471	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						GAGATCCGGTACTATGAGAAG	0.547																																					p.Y471C		Atlas-SNP	.											EPHB1_ENST00000398015,colon,carcinoma,0,2	EPHB1	519	.	0			c.A1412G						.						96	99	98					3																	134873108		2185	4299	6484	SO:0001583	missense	2047	exon6			TCCGGTACTATGA	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.1412A>G	chr3.hg19:g.134873108A>G	ENSP00000381097:p.Tyr471Cys	89.0	0.0		70.0	27.0	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	hg19	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.504021	0.85176	.	.	ENSG00000154928	ENST00000398015;ENST00000493838	T;T	0.61274	0.12;0.12	5.21	5.21	0.72293	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.136209	0.51477	D	0.000099	T	0.78515	0.4295	M	0.88979	2.995	0.80722	D	1	D	0.71674	0.998	D	0.67382	0.951	T	0.82829	-0.0264	10	0.62326	D	0.03	.	14.9025	0.70689	1.0:0.0:0.0:0.0	.	471	P54762	EPHB1_HUMAN	C	471;32	ENSP00000381097:Y471C;ENSP00000419574:Y32C	ENSP00000381097:Y471C	Y	+	2	0	EPHB1	136355798	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.193000	0.77780	2.195000	0.70347	0.533000	0.62120	TAC	.	.		0.547	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		G	134873108	A	G	134873108	3	3	175	1	0	0	0	0	1	0	0	0	5176	391	14	2	1434	2	EPHB1	3	134873108	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	12241218	134873108	63149322	29	26327										
DHX36	170506	hgsc.bcm.edu	37	chr3	154032979	154032979	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ctgttcctgattctaaacatTtttttttcttgatttatcaa	3	7	3	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr3:154032979T>A	ENST00000496811.1	-	3	539	c.459A>T	c.(457-459)aaA>aaT	p.K153N	DHX36_ENST00000329463.5_Missense_Mutation_p.K153N|DHX36_ENST00000544526.1_Missense_Mutation_p.K153N|DHX36_ENST00000308361.6_Missense_Mutation_p.K153N	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	153					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTCTAAACATTTTTTTTTCTT	0.343																																					p.K153N		Atlas-SNP	.											.	DHX36	98	.	0			c.A459T						.						78	78	78					3																	154032979		2202	4299	6501	SO:0001583	missense	170506	exon3			AAACATTTTTTTT	AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.459A>T	chr3.hg19:g.154032979T>A	ENSP00000417078:p.Lys153Asn	175.0	0.0		154.0	7.0	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Missense_Mutation	SNP	ENST00000496811.1	hg19	CCDS3171.1	.	.	.	.	.	.	.	.	.	.	T	3.592	-0.083380	0.07141	.	.	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	T;T;T;T;T	0.09538	2.97;2.97;2.97;2.97;2.97	5.63	0.0334	0.14179	.	0.941655	0.08967	N	0.867787	T	0.05914	0.0154	L	0.27053	0.805	0.09310	N	1	B;B;B	0.32071	0.302;0.355;0.201	B;B;B	0.24541	0.054;0.047;0.036	T	0.42783	-0.9431	10	0.19590	T	0.45	.	5.1712	0.15110	0.0:0.3743:0.1502:0.4755	.	153;153;153	Q9H2U1-2;Q9H2U1-3;Q9H2U1	.;.;DHX36_HUMAN	N	153;153;153;153;67	ENSP00000417078:K153N;ENSP00000309296:K153N;ENSP00000444247:K153N;ENSP00000330113:K153N;ENSP00000419862:K67N	ENSP00000309296:K153N	K	-	3	2	DHX36	155515673	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.450000	0.06803	-0.014000	0.14175	-0.350000	0.07774	AAA	.	.		0.343	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		A	154032979	T	A	154032979	3	1	175	1	0	0	0	0	1	0	0	0	4511	1838	64	4	2659	4	DHX36	3	154032979	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	19159871	154032979	43989451	30	26328										
SI	6476	hgsc.bcm.edu	37	chr3	164776811	164776811	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cacacatgttgtgtgtttccCctctcataggttgcatatgt	8	10	1	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr3:164776811C>T	ENST00000264382.3	-	12	1400	c.1338G>A	c.(1336-1338)agG>agA	p.R446R		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	446	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	GTGTGTTTCCCCTCTCATAGG	0.353										HNSCC(35;0.089)																											p.R446R		Atlas-SNP	.											.	SI	500	.	0			c.G1338A						.						109	96	101					3																	164776811		2203	4300	6503	SO:0001819	synonymous_variant	6476	exon12			GTTTCCCCTCTCA	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.1338G>A	chr3.hg19:g.164776811C>T		123.0	0.0		124.0	8.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	hg19	CCDS3196.1																																																																																			.	.		0.353	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		T	164776811	C	T	164776811	2	4	175	1	0	0	0	0	0	0	0	1	14312	622	22	3		3	SI	3	164776811	Silent	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	10743832	164776811	33245619	31	26329										
RPL35A	6165	hgsc.bcm.edu	37	chr3	197678059	197678059	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	caaggccatttttgctggctAtaagcggggtctccggaacc	12	11	1	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr3:197678059A>G	ENST00000464167.1	+	3	308	c.41A>G	c.(40-42)tAt>tGt	p.Y14C	IQCG_ENST00000480302.1_Intron|IQCG_ENST00000455191.1_5'Flank|RPL35A_ENST00000448864.1_Missense_Mutation_p.Y14C|IQCG_ENST00000265239.6_Intron|IQCG_ENST00000453254.1_5'Flank|RPL35A_ENST00000329092.8_3'UTR	NM_000996.2	NP_000987.2	P18077	RL35A_HUMAN	ribosomal protein L35a	14					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|tRNA binding (GO:0000049)			lung(1)|prostate(1)|urinary_tract(1)	3	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;1.04e-23)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.182)		TTTGCTGGCTATAAGCGGGGT	0.443																																					p.Y14C		Atlas-SNP	.											.	RPL35A	9	.	0			c.A41G						.						73	73	73					3																	197678059		2202	4298	6500	SO:0001583	missense	6165	exon3			CTGGCTATAAGCG	X52966	CCDS33930.1	3q29	2011-04-06			ENSG00000182899	ENSG00000182899		"L ribosomal proteins"	10345	protein-coding gene	gene with protein product		180468				1577483, 8786106	Standard	NM_000996		Approved	L35A	uc003fyr.3	P18077	OTTHUMG00000155386	ENST00000464167.1:c.41A>G	chr3.hg19:g.197678059A>G	ENSP00000419117:p.Tyr14Cys	59.0	0.0		59.0	23.0	NM_000996	Q08ES9|Q9BVN7	Missense_Mutation	SNP	ENST00000464167.1	hg19	CCDS33930.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.837717	0.91117	.	.	ENSG00000182899	ENST00000464167;ENST00000448864;ENST00000442341	.	.	.	5.59	5.59	0.84812	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	D	0.87716	0.6247	H	0.96518	3.835	0.80722	D	1	P	0.34684	0.463	P	0.51193	0.662	D	0.89768	0.3952	9	0.72032	D	0.01	-18.4759	15.8211	0.78644	1.0:0.0:0.0:0.0	.	14	P18077	RL35A_HUMAN	C	14	.	ENSP00000398058:Y14C	Y	+	2	0	RPL35A	199162456	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.883000	0.92426	2.150000	0.67090	0.529000	0.55759	TAT	.	.		0.443	RPL35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339788.1	NM_000996		G	197678059	A	G	197678059	3	3	175	1	0	0	0	0	1	0	0	0	13600	449	16	2	47	2	RPL35A	3	197678059	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	32901248	197678059	344371	32	26330										
GRSF1	2926	hgsc.bcm.edu	37	chr4	71705447	71705447	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ggatagagccagcggcggagTagaagggcaggcaggcggcg	21	8	0	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr4:71705447T>G	ENST00000254799.6	-	1	215	c.98A>C	c.(97-99)tAc>tCc	p.Y33S	GRSF1_ENST00000439371.1_5'Flank|GRSF1_ENST00000508091.1_5'Flank|GRSF1_ENST00000545193.1_5'Flank|GRSF1_ENST00000502323.1_5'Flank	NM_002092.3	NP_002083	Q12849	GRSF1_HUMAN	G-rich RNA sequence binding factor 1	33					anterior/posterior pattern specification (GO:0009952)|morphogenesis of embryonic epithelium (GO:0016331)|mRNA polyadenylation (GO:0006378)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(2)	17		all_hematologic(202;0.21)	Lung(101;0.235)			AGCGGCGGAGTAGAAGGGCAG	0.771																																					p.Y33S		Atlas-SNP	.											.	GRSF1	35	.	0			c.A98C						.						1	2	2					4																	71705447		610	1532	2142	SO:0001583	missense	2926	exon1			GCGGAGTAGAAGG	BC040485	CCDS47069.1, CCDS47070.1	4q13	2013-07-16				ENSG00000132463		"RNA binding motif (RRM) containing"	4610	protein-coding gene	gene with protein product		604851				8036161	Standard	NM_001098477		Approved		uc010iia.1	Q12849		ENST00000254799.6:c.98A>C	chr4.hg19:g.71705447T>G	ENSP00000254799:p.Tyr33Ser	2.0	0.0		6.0	6.0	NM_002092	B3KPW0|Q4W5S5|Q6ZST3|Q8IWD6|Q8NBD2	Missense_Mutation	SNP	ENST00000254799.6	hg19	CCDS47069.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.119113	0.37436	.	.	ENSG00000132463	ENST00000254799;ENST00000540657	T	0.23754	1.89	3.41	2.15	0.27550	.	0.000000	0.30704	U	0.009058	T	0.13329	0.0323	N	0.14661	0.345	0.20703	N	0.999861	B	0.18310	0.027	B	0.17433	0.018	T	0.18871	-1.0323	10	0.41790	T	0.15	-0.5051	7.5729	0.27918	0.0:0.0:0.2184:0.7816	.	33	Q12849	GRSF1_HUMAN	S	33	ENSP00000254799:Y33S	ENSP00000254799:Y33S	Y	-	2	0	GRSF1	71924311	0.001000	0.12720	0.015000	0.15790	0.001000	0.01503	0.124000	0.15728	0.455000	0.26910	0.477000	0.44152	TAC	.	.		0.771	GRSF1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362642.1	NM_002092		G	71705447	T	G	71705447	3	3	175	1	0	0	0	0	1	0	0	0	6818	1638	57	5	1380	5	GRSF1	4	71705447	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10		71705447	119448829	33	26331										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123179993	123179993	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	atagtgactctgcattaaaaAtaaaggtatattattgctct	6	5	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr4:123179993A>G	ENST00000264501.4	+	42	7130	c.6757A>G	c.(6757-6759)Ata>Gta	p.I2253V	KIAA1109_ENST00000388738.3_Missense_Mutation_p.I2253V|KIAA1109_ENST00000455637.1_Missense_Mutation_p.I2253V			Q2LD37	K1109_HUMAN	KIAA1109	2253					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TGCATTAAAAATAAAGGTATA	0.368																																					p.I2253V		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A6757G						.						64	60	61					4																	123179993		1816	4078	5894	SO:0001583	missense	84162	exon40			TTAAAAATAAAGG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.6757A>G	chr4.hg19:g.123179993A>G	ENSP00000264501:p.Ile2253Val	80.0	0.0		70.0	28.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.17|19.17	3.776138|3.776138	0.70107|0.70107	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000419325	T;T;T|.	0.26067|.	2.39;2.39;1.76|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.000000|.	0.56097|.	U|.	0.000031|.	T|T	0.53948|0.53948	0.1828|0.1828	N|N	0.24115|0.24115	0.695|0.695	0.46725|0.46725	D|D	0.999173|0.999173	P;P;P|.	0.48640|.	0.65;0.876;0.913|.	P;D;P|.	0.64595|.	0.743;0.927;0.891|.	T|T	0.50668|0.50668	-0.8801|-0.8801	10|5	0.02654|.	T|.	1|.	.|.	16.4221|16.4221	0.83766|0.83766	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	2253;2252;2253|.	Q2LD37-6;Q2LD37-2;Q2LD37|.	.;.;K1109_HUMAN|.	V|S	2253|210	ENSP00000264501:I2253V;ENSP00000373390:I2253V;ENSP00000389925:I2253V|.	ENSP00000264501:I2253V|.	I|N	+|+	1|2	0|0	KIAA1109|KIAA1109	123399443|123399443	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	8.885000|8.885000	0.92439|0.92439	2.283000|2.283000	0.76528|0.76528	0.477000|0.477000	0.44152|0.44152	ATA|AAT	.	.		0.368	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123179993	A	G	123179993	3	3	175	1	0	0	0	0	1	0	0	0	8217	101	4	2	6915	2	KIAA1109	4	123179993	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	51474546	123179993	67974283	34	26332										
RASA1	5921	hgsc.bcm.edu	37	chr5	86633866	86633867	+	Missense_Mutation	DNP	AG	AG	GA													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	tgggttacaaatttaagaacAgatgaacaaggccttattgt							TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr5:86633866_86633867AG>GA	ENST00000274376.6	+	5	1539_1540	c.975_976AG>GA	c.(973-978)acAGat>acGAat	p.D326N	RASA1_ENST00000506290.1_Missense_Mutation_p.D160N|RASA1_ENST00000456692.2_Missense_Mutation_p.D149N|RASA1_ENST00000512763.1_Missense_Mutation_p.D159N	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	326	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		ATTTAAGAACAGATGAACAAGG	0.287																																					p.T325T|p.D326N		Atlas-SNP	.											.|RASA1_ENST00000456692,NS,carcinoma,0,2	RASA1	213	.	0			c.A975G|c.G976A						.																																			SO:0001583	missense	5921	exon5			AAGAACAGATGAA|AGAACAGATGAAC		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	Exception_encountered	chr5.hg19:g.86633866_86633867delinsGA	ENSP00000274376:p.Asp326Asn	394.0|391.0	0.0		314.0|316.0	108.0|107.0	NM_002890	B2R6W3|Q9UDI1	Silent|Missense_Mutation	SNP	ENST00000274376.6	hg19	CCDS34200.1																																																																																			.	.		0.287	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		GA	86633867	AG	GA	86633866	3	3	175	1	0	0	0	0	1	0	0	0	13075	175	7	2	1005	2	RASA1	5	86633866	Missense_Mutation	DNP	AG	TCGA-DD-AACY-01A-11D-A40R-10		86633866	94281394	35	26333										
CHD1	1105	hgsc.bcm.edu	37	chr5	98262046	98262046	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gtgcttacttaccttgattcTccactactgtttctaacact	4	12	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr5:98262046T>G	ENST00000284049.3	-	1	194	c.45A>C	c.(43-45)ggA>ggC	p.G15G	CTD-2007H13.3_ENST00000513175.1_lincRNA	NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	15	Ser-rich.				chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	ACCTTGATTCTCCACTACTGT	0.274																																					p.G15G		Atlas-SNP	.											.	CHD1	137	.	0			c.A45C						.						117	113	114					5																	98262046		2201	4294	6495	SO:0001819	synonymous_variant	1105	exon1			TGATTCTCCACTA	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.45A>C	chr5.hg19:g.98262046T>G		75.0	0.0		61.0	21.0	NM_001270	Q17RZ3	Silent	SNP	ENST00000284049.3	hg19	CCDS34204.1																																																																																			.	.		0.274	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		G	98262046	T	G	98262046	2	3	175	1	0	0	0	0	0	0	0	1	3325	1538	54	5		5	CHD1	5	98262046	Silent	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	11628180	98262046	82653214	36	26334										
SAR1B	51128	hgsc.bcm.edu	37	chr5	133942642	133942642	+	Stop_Codon_Del	DEL	A	A	-													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	aaccaatgtgagtttgtgttAatcaatgtactgtgccatcc							TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr5:133942642delA	ENST00000402673.2	-	0	873				SAR1B_ENST00000507419.1_Stop_Codon_Del|SAR1B_ENST00000509937.1_Stop_Codon_Del|SAR1B_ENST00000439578.1_Stop_Codon_Del|SAR1B_ENST00000502539.1_Stop_Codon_Del	NM_016103.3	NP_057187.1	Q9Y6B6	SAR1B_HUMAN	secretion associated, Ras related GTPase 1B						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|GTP catabolic process (GO:0006184)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			kidney(2)|lung(2)|urinary_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGTTTGTGTTAATCAATGTAC	0.423																																					p.X199Y		Atlas-INDEL	.											.	SAR1B	19	.	0			c.596delA						.						165	153	157					5																	133942642		2203	4300	6503	SO:0001567	stop_retained_variant	51128	exon8			.	AF092130	CCDS4177.1	5q31.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000152700	ENSG00000152700			10535	protein-coding gene	gene with protein product		607690	"SAR1a gene homolog (S. cerevisiae) 2", "SAR1a gene homolog 2 (S. cerevisiae)", "SAR1 homolog B (S. cerevisiae)"	SARA2			Standard	NM_001033503		Approved		uc003kzr.3	Q9Y6B6	OTTHUMG00000129114	Exception_encountered	chr5.hg19:g.133942642delA	Exception_encountered	114.0	0.0		96.0	45.0	NM_001033503	D3DQA4|Q567T4	Frame_Shift_Del	DEL	ENST00000402673.2	hg19	CCDS4177.1																																																																																			.	.		0.423	SAR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251158.2	NM_016103		-	133942642	A	-	133942642	7	5	175	1	0	1	0	1	0	0	0	0	13855	375	13	0	5	0	SAR1B	5	133942642	Stop_Codon_Del	DEL	A	TCGA-DD-AACY-01A-11D-A40R-10	35680596	133942642	46972618	37	26335										
CDC25C	995	hgsc.bcm.edu	37	chr5	137665271	137665271	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	caaggtctgcagaagtggtaAgctgagtggcagttatctcc	13	8	2	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr5:137665271A>T	ENST00000323760.6	-	3	538	c.260T>A	c.(259-261)cTt>cAt	p.L87H	CDC25C_ENST00000514555.1_Missense_Mutation_p.L87H|CDC25C_ENST00000415130.2_Intron|CDC25C_ENST00000356505.3_Missense_Mutation_p.L87H|CDC25C_ENST00000513970.1_Missense_Mutation_p.L87H|CDC25C_ENST00000357274.3_Intron|CDC25C_ENST00000348983.3_Intron	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	87					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)			endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			AGAAGTGGTAAGCTGAGTGGC	0.443																																					p.L87H		Atlas-SNP	.											.	CDC25C	37	.	0			c.T260A						.						170	167	168					5																	137665271		2203	4300	6503	SO:0001583	missense	995	exon3			GTGGTAAGCTGAG	M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"Protein tyrosine phosphatases / Class III Cys-based PTPs", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1727	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 60"	157680	"cell division cycle 25C", "cell division cycle 25 homolog C (S. cerevisiae)", "cell division cycle 25 homolog C (S. pombe)"	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.260T>A	chr5.hg19:g.137665271A>T	ENSP00000321656:p.Leu87His	70.0	0.0		89.0	23.0	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	hg19	CCDS4202.1	.	.	.	.	.	.	.	.	.	.	A	17.17	3.321697	0.60634	.	.	ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000513970;ENST00000534892;ENST00000514555;ENST00000503022;ENST00000510119	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	4.4	3.2	0.36748	.	0.764676	0.11327	N	0.575452	T	0.52240	0.1722	L	0.56769	1.78	0.09310	N	0.999997	D;D;D;D	0.71674	0.998;0.997;0.995;0.996	P;P;P;P	0.61592	0.891;0.781;0.847;0.754	T	0.32903	-0.9889	10	0.38643	T	0.18	-0.2367	6.6695	0.23060	0.8893:0.0:0.1107:0.0	.	104;104;87;87	G3V1P6;B4DX61;P30307-2;P30307	.;.;.;MPIP3_HUMAN	H	87;87;87;104;87;87;104	ENSP00000321656:L87H;ENSP00000348898:L87H;ENSP00000424795:L87H;ENSP00000425470:L87H;ENSP00000427251:L87H;ENSP00000427105:L104H	ENSP00000321656:L87H	L	-	2	0	CDC25C	137693170	0.157000	0.22836	0.115000	0.21578	0.950000	0.60333	2.386000	0.44380	1.855000	0.53841	0.460000	0.39030	CTT	.	.		0.443	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1			T	137665271	A	T	137665271	3	4	175	1	0	0	0	0	1	0	0	0	3066	72	3	4	1209	4	CDC25C	5	137665271	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	3722629	137665271	43249989	38	26336										
NMUR2	56923	hgsc.bcm.edu	37	chr5	151784554	151784554	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ggggaggaagaagtggctgcGccgaggtccgcagaggaagg	21	7	0	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr5:151784554G>A	ENST00000255262.3	-	1	286	c.121C>T	c.(121-123)Cgc>Tgc	p.R41C	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	41					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			AAGTGGCTGCGCCGAGGTCCG	0.537																																					p.R41C		Atlas-SNP	.											NMUR2,NS,haematopoietic_neoplasm,0,1	NMUR2	111	.	0			c.C121T						.						97	93	94					5																	151784554		2203	4300	6503	SO:0001583	missense	56923	exon1			GGCTGCGCCGAGG	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.121C>T	chr5.hg19:g.151784554G>A	ENSP00000255262:p.Arg41Cys	157.0	0.0		161.0	71.0	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	hg19	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.348860	0.61183	.	.	ENSG00000132911	ENST00000255262	T	0.38077	1.16	5.54	3.5	0.40072	.	0.000000	0.64402	D	0.000007	T	0.61311	0.2337	M	0.80746	2.51	0.54753	D	0.999988	D	0.89917	1.0	D	0.76575	0.988	T	0.69101	-0.5234	10	0.72032	D	0.01	-24.3232	14.9967	0.71436	0.0:0.0:0.7298:0.2702	.	41	Q9GZQ4	NMUR2_HUMAN	C	41	ENSP00000255262:R41C	ENSP00000255262:R41C	R	-	1	0	NMUR2	151764747	1.000000	0.71417	0.854000	0.33618	0.790000	0.44656	3.934000	0.56553	1.285000	0.44548	0.655000	0.94253	CGC	.	.		0.537	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		A	151784554	G	A	151784554	3	1	175	1	0	0	0	0	1	0	0	0	10516	1087	38	1	1142	1	NMUR2	5	151784554	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	14119283	151784554	29130706	39	26337										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327864	16327864	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	agccccggagccctgctgagGtgctgctgctgctgctgctg	15	14	0	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr6:16327864G>C	ENST00000244769.4	-	8	1614	c.678C>G	c.(676-678)caC>caG	p.H226Q	ATXN1_ENST00000436367.1_Missense_Mutation_p.H226Q	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	226					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CCCTGCTGAGGtgctgctgct	0.652																																					p.H226Q		Atlas-SNP	.											.,1	ATXN1	117	.	0			c.C678G						.						11	15	13					6																	16327864		2150	4194	6344	SO:0001583	missense	6310	exon7			GCTGAGGTGCTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.678C>G	chr6.hg19:g.16327864G>C	ENSP00000244769:p.His226Gln	63.0	0.0		48.0	4.0	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	G	1.926	-0.447046	0.04572	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.27256	1.68;1.68	4.74	0.503	0.16940	.	0.308295	0.34291	N	0.004091	T	0.05686	0.0149	L	0.39397	1.21	0.09310	N	0.999995	B	0.32245	0.361	B	0.28638	0.092	T	0.23976	-1.0173	10	0.48119	T	0.1	-16.8942	3.2876	0.06937	0.3032:0.0:0.385:0.3119	.	226	P54253	ATX1_HUMAN	Q	226	ENSP00000244769:H226Q;ENSP00000416360:H226Q	ENSP00000244769:H226Q	H	-	3	2	ATXN1	16435843	0.437000	0.25593	0.006000	0.13384	0.009000	0.06853	0.925000	0.28791	0.191000	0.20236	0.563000	0.77884	CAC	.	.		0.652	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		C	16327864	G	C	16327864	3	2	175	1	0	0	0	0	1	0	0	0	1209	1252	44	4	1777	4	ATXN1	6	16327864	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10		16327864	154787203	40	26338										
KIAA1949	170954	hgsc.bcm.edu	37	chr6	30652197	30652197	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ttccctacctgtttgtggtgTctttcgggggaccccttggc	12	12	1	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr6:30652197T>A	ENST00000274853.3	-	1	3475	c.1599A>T	c.(1597-1599)agA>agT	p.R533S	PPP1R18_ENST00000488324.1_5'UTR|PPP1R18_ENST00000399199.3_Missense_Mutation_p.R533S	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	533						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											GTTTGTGGTGTCTTTCGGGGG	0.542																																					p.R533S		Atlas-SNP	.											.	.	.	.	0			c.A1599T						.						56	60	58					6																	30652197		1206	2529	3735	SO:0001583	missense	170954	exon2			GTGGTGTCTTTCG	AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29413	protein-coding gene	gene with protein product	"protein phosphatase 1 F-actin cytoskeleton targeting subunit"	610990	"KIAA1949"	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.1599A>T	chr6.hg19:g.30652197T>A	ENSP00000274853:p.Arg533Ser	115.0	0.0		93.0	52.0	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	hg19	CCDS43444.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.371805	0.61624	.	.	ENSG00000146112	ENST00000274853;ENST00000399199	T;T	0.37235	1.21;1.21	4.52	1.53	0.23141	.	0.256528	0.29544	N	0.011848	T	0.23094	0.0558	N	0.16478	0.41	0.32141	N	0.585526	D	0.76494	0.999	D	0.85130	0.997	T	0.10683	-1.0619	10	0.62326	D	0.03	-13.0709	6.7082	0.23262	0.0:0.1857:0.0:0.8143	.	533	Q6NYC8	PPR18_HUMAN	S	533	ENSP00000274853:R533S;ENSP00000382150:R533S	ENSP00000274853:R533S	R	-	3	2	KIAA1949	30760176	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	0.744000	0.26245	0.366000	0.24427	0.533000	0.62120	AGA	.	.		0.542	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471		A	30652197	T	A	30652197	3	1	175	1	0	0	0	0	1	0	0	0	8272	1664	58	4	254	4	KIAA1949	6	30652197	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	14324333	30652197	140462870	41	26339										
VEGFA	7422	hgsc.bcm.edu	37	chr6	43746274	43746274	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cacaacaaatgtgaatgcagGtgaggatgtagtcacggatt	12	6	1	2	rs113966402		TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr6:43746274G>C	ENST00000523873.1	+	4	430		c.e4+1		VEGFA_ENST00000372055.4_Splice_Site|VEGFA_ENST00000372077.4_Splice_Site|VEGFA_ENST00000425836.2_Splice_Site|VEGFA_ENST00000482630.2_Splice_Site|VEGFA_ENST00000520948.1_Splice_Site|VEGFA_ENST00000417285.2_Splice_Site|VEGFA_ENST00000518824.1_Splice_Site|VEGFA_ENST00000523950.1_Splice_Site|VEGFA_ENST00000372064.4_Splice_Site|VEGFA_ENST00000413642.3_Splice_Site|VEGFA_ENST00000324450.6_Splice_Site|VEGFA_ENST00000518689.1_Splice_Site|VEGFA_ENST00000372067.3_Splice_Site|VEGFA_ENST00000457104.2_Splice_Site|VEGFA_ENST00000523125.1_Splice_Site|VEGFA_ENST00000230480.6_Splice_Site			P15692	VEGFA_HUMAN	vascular endothelial growth factor A						activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|artery morphogenesis (GO:0048844)|basophil chemotaxis (GO:0002575)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|camera-type eye morphogenesis (GO:0048593)|cardiac muscle fiber development (GO:0048739)|cardiac vascular smooth muscle cell development (GO:0060948)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to hypoxia (GO:0071456)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|dopaminergic neuron differentiation (GO:0071542)|endothelial cell chemotaxis (GO:0035767)|epithelial cell differentiation (GO:0030855)|eye photoreceptor cell development (GO:0042462)|growth (GO:0040007)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|induction of positive chemotaxis (GO:0050930)|kidney development (GO:0001822)|lactation (GO:0007595)|lung development (GO:0030324)|lymph vessel morphogenesis (GO:0036303)|macrophage differentiation (GO:0030225)|mammary gland alveolus development (GO:0060749)|mesoderm development (GO:0007498)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|outflow tract morphogenesis (GO:0003151)|ovarian follicle development (GO:0001541)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cellular component movement (GO:0051272)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine autophosphorylation (GO:1900086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein localization to early endosome (GO:1902966)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor internalization (GO:0002092)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular permeability (GO:0043117)|post-embryonic camera-type eye development (GO:0031077)|primitive erythrocyte differentiation (GO:0060319)|regulation of cell shape (GO:0008360)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)|surfactant homeostasis (GO:0043129)|tube formation (GO:0035148)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|VEGF-activated neuropilin signaling pathway (GO:0038190)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|neuropilin binding (GO:0038191)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor agonist activity (GO:0048018)|vascular endothelial growth factor receptor 1 binding (GO:0043183)|vascular endothelial growth factor receptor 2 binding (GO:0043184)|vascular endothelial growth factor receptor binding (GO:0005172)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9	all_cancers(18;5.46e-07)|all_epithelial(2;5.96e-08)|Lung NSC(15;0.000157)|all_lung(25;0.000486)|Hepatocellular(11;0.00309)		all cancers(41;0.000413)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0742)|OV - Ovarian serous cystadenocarcinoma(102;0.196)		Aflibercept(DB08885)|Bevacizumab(DB00112)|Carvedilol(DB01136)|Dalteparin(DB06779)|Gliclazide(DB01120)|Minocycline(DB01017)|Ranibizumab(DB01270)|Vandetanib(DB05294)	GTGAATGCAGGTGAGGATGTA	0.502																																					.		Atlas-SNP	.											.	VEGFA	21	.	0			c.392+1G>C						.						117	92	101					6																	43746274		2203	4300	6503	SO:0001630	splice_region_variant	7422	exon4			ATGCAGGTGAGGA	AB021221	CCDS34457.1, CCDS4907.2, CCDS34458.1, CCDS47432.1, CCDS47433.1, CCDS47434.1, CCDS47435.1, CCDS55007.1, CCDS55008.1, CCDS55009.1, CCDS55010.1, CCDS55011.1, CCDS55012.1, CCDS55013.1, CCDS55014.1, CCDS55015.1, CCDS69125.1	6p12	2008-02-05	2006-10-31	2006-10-31	ENSG00000112715	ENSG00000112715			12680	protein-coding gene	gene with protein product		192240	"vascular endothelial growth factor"	VEGF		8786112	Standard	NM_001025366		Approved	VEGF-A, VPF	uc003owh.3	P15692	OTTHUMG00000014745	ENST00000523873.1:c.392+1G>C	chr6.hg19:g.43746274G>C		99.0	0.0		77.0	5.0	NM_001171625	B5BU86|H0Y2S8|H0Y407|H0Y414|H0Y462|H0Y8N2|H3BLW7|O60720|O75875|Q074Z4|Q16889|Q5UB46|Q6P0P5|Q96KJ0|Q96L82|Q96NW5|Q9H1W8|Q9H1W9|Q9UH58|Q9UL23	Splice_Site	SNP	ENST00000523873.1	hg19	CCDS55010.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.282106	0.80692	.	.	ENSG00000112715	ENST00000372067;ENST00000324450;ENST00000417285;ENST00000413642;ENST00000372055;ENST00000482630;ENST00000425836;ENST00000372064;ENST00000372077;ENST00000519767;ENST00000520948;ENST00000523873;ENST00000523950;ENST00000457104;ENST00000518689;ENST00000523125;ENST00000518824;ENST00000230480	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8433	0.92194	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	VEGFA	43854252	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.125000	0.94402	2.707000	0.92482	0.561000	0.74099	.	.	.		0.502	VEGFA-021	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374460.1	NM_001025366	Intron	C	43746274	G	C	43746274	5	2	175	1	0	0	0	0	0	0	1	0	17165	1275	44	4	947	4	VEGFA	6	43746274	Splice_Site	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	13094077	43746274	127368793	42	26340										
MAP3K7	6885	hgsc.bcm.edu	37	chr6	91229026	91229026	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ccattgggatggagttatctGatccattggtatctggaatt	11	6	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr6:91229026G>A	ENST00000369329.3	-	15	1636	c.1475C>T	c.(1474-1476)tCa>tTa	p.S492L	MAP3K7_ENST00000369320.1_Missense_Mutation_p.S146L|MAP3K7_ENST00000479630.1_5'UTR|MAP3K7_ENST00000369332.3_Missense_Mutation_p.S465L|MAP3K7_ENST00000369327.3_Missense_Mutation_p.S465L|MAP3K7_ENST00000369325.3_Missense_Mutation_p.S492L	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	492					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		GGAGTTATCTGATCCATTGGT	0.328																																					p.S492L		Atlas-SNP	.											.	MAP3K7	100	.	0			c.C1475T						.						136	126	130					6																	91229026		2203	4299	6502	SO:0001583	missense	6885	exon15			TTATCTGATCCAT	AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.1475C>T	chr6.hg19:g.91229026G>A	ENSP00000358335:p.Ser492Leu	103.0	0.0		90.0	44.0	NM_145331	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Missense_Mutation	SNP	ENST00000369329.3	hg19	CCDS5028.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.469004	0.84533	.	.	ENSG00000135341	ENST00000369332;ENST00000369329;ENST00000369325;ENST00000369327;ENST00000369320;ENST00000450832	T;T;T;D	0.81579	-1.07;-1.06;-1.3;-1.51	6.06	6.06	0.98353	.	0.122293	0.64402	D	0.000019	D	0.85500	0.5711	L	0.46157	1.445	0.80722	D	1	P;B;D;P	0.76494	0.939;0.005;0.999;0.956	P;B;D;P	0.68192	0.703;0.011;0.956;0.549	D	0.85140	0.0980	10	0.66056	D	0.02	.	20.6314	0.99525	0.0:0.0:1.0:0.0	.	465;465;492;492	O43318-4;O43318-2;O43318-3;O43318	.;.;.;M3K7_HUMAN	L	465;492;492;465;146;392	ENSP00000358338:S465L;ENSP00000358335:S492L;ENSP00000358331:S492L;ENSP00000358333:S465L	ENSP00000358326:S146L	S	-	2	0	MAP3K7	91285747	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.650000	0.67944	2.885000	0.99019	0.579000	0.79373	TCA	.	.		0.328	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331		A	91229026	G	A	91229026	3	1	175	1	0	0	0	0	1	0	0	0	9264	1294	45	3	357	3	MAP3K7	6	91229026	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	47482752	91229026	79886041	43	26341										
EGFR	1956	hgsc.bcm.edu	37	chr7	55248998	55248999	+	In_Frame_Ins	INS	-	-	TGGCCAGCG													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cctccaggaagcctacgtgaINStggccagcgtggacaacccc							TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr7:55248998_55248999insTGGCCAGCG	ENST00000275493.2	+	20	2473_2474	c.2296_2297insTGGCCAGCG	c.(2296-2298)atg>aTGGCCAGCGtg	p.769_770insASV	EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_In_Frame_Ins_p.716_717insASV|EGFR_ENST00000455089.1_In_Frame_Ins_p.724_725insASV	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	769	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> M (found in a lung cancer sample; dbSNP:rs147149347). {ECO:0000269|PubMed:15623594}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.M766T(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	AGCCTACGTGATGGCCAGCGTG	0.644		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.M766delinsMASV		Atlas-INDEL	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	EGFR,caecum,carcinoma,0,1	EGFR	20426	.	1	Substitution - Missense(1)	lung(1)	c.2296_2297insTGGCCAGCG						.																																			SO:0001652	inframe_insertion	1956	exon20	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	.		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2297_2305dupTGGCCAGCG	chr7.hg19:g.55248999_55249007dupTGGCCAGCG	ENSP00000275493:p.Ala767_Val769dup	105.0	0.0		81.0	14.0	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	In_Frame_Ins	INS	ENST00000275493.2	hg19	CCDS5514.1																																																																																			.	.		0.644	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		TGGCCAGCG	55248999	-	TGGCCAGCG	55248998	7	5	175	1	0	1	1	0	0	0	0	0	4969	333	12	0	2638	0	EGFR	7	55248998	In_Frame_Ins	INS	-	TCGA-DD-AACY-01A-11D-A40R-10		55248998	103889665	44	26342										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98586442	98586442	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gtgcagatgcacgatgtgctGgtgaaagcctgggccatgtg	16	8	0	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr7:98586442G>T	ENST00000359863.4	+	62	9665	c.9456G>T	c.(9454-9456)ctG>ctT	p.L3152L	TRRAP_ENST00000446306.3_Silent_p.L3123L|TRRAP_ENST00000355540.3_Silent_p.L3123L	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	3152	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			ACGATGTGCTGGTGAAAGCCT	0.547																																					p.L3152L		Atlas-SNP	.											.	TRRAP	863	.	0			c.G9456T						.						98	97	97					7																	98586442		2203	4300	6503	SO:0001819	synonymous_variant	8295	exon62			TGTGCTGGTGAAA	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.9456G>T	chr7.hg19:g.98586442G>T		55.0	0.0		50.0	16.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	hg19	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	G	9.565	1.119624	0.20877	.	.	ENSG00000196367	ENST00000456197	.	.	.	5.53	4.65	0.58169	.	.	.	.	.	T	0.63885	0.2549	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62450	-0.6852	4	.	.	.	.	12.5982	0.56483	0.1394:0.0:0.8606:0.0	.	.	.	.	L	2863	.	.	W	+	2	0	TRRAP	98424378	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.313000	0.43735	1.326000	0.45319	0.655000	0.94253	TGG	.	.		0.547	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		T	98586442	G	T	98586442	2	4	175	1	0	0	0	0	0	0	0	1	16616	1335	47	3		3	TRRAP	7	98586442	Silent	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	43337444	98586442	60552221	45	26343										
ACHE	43	hgsc.bcm.edu	37	chr7	100491024	100491024	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gggccagctgcgtggccctgCgacgggcctctcccatgccc	14	18	1	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr7:100491024C>A	ENST00000412389.1	-	1	985	c.830G>T	c.(829-831)cGc>cTc	p.R277L	ACHE_ENST00000428317.1_Missense_Mutation_p.R277L|ACHE_ENST00000411582.1_Missense_Mutation_p.R277L|ACHE_ENST00000241069.5_Missense_Mutation_p.R277L|ACHE_ENST00000497647.1_5'Flank|ACHE_ENST00000302913.4_Missense_Mutation_p.R277L|ACHE_ENST00000419336.2_Missense_Mutation_p.R277L			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	277					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	CGTGGCCCTGCGACGGGCCTC	0.706																																					p.R277L		Atlas-SNP	.											.	ACHE	80	.	0			c.G830T						.						29	30	30					7																	100491024		2202	4299	6501	SO:0001583	missense	43	exon2			GCCCTGCGACGGG		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"Blood group antigens"	108	protein-coding gene	gene with protein product	"Yt blood group"	100740	"acetylcholinesterase (YT blood group)", "acetylcholinesterase (Yt blood group)", "acetylcholinesterase"	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.830G>T	chr7.hg19:g.100491024C>A	ENSP00000394976:p.Arg277Leu	45.0	0.0		41.0	17.0	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	hg19	CCDS5709.1	.	.	.	.	.	.	.	.	.	.	C	15.05	2.717703	0.48622	.	.	ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000302913;ENST00000412389;ENST00000426415;ENST00000430554;ENST00000411582;ENST00000422451	T;T;T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	4.95	4.95	0.65309	Carboxylesterase, type B (1);	0.000000	0.85682	D	0.000000	T	0.75384	0.3842	L	0.60845	1.875	0.80722	D	1	D;D;D;D	0.76494	0.997;0.998;0.999;0.997	D;P;P;D	0.63283	0.913;0.809;0.847;0.913	T	0.71547	-0.4560	10	0.20519	T	0.43	.	15.6562	0.77136	0.0:1.0:0.0:0.0	.	277;277;277;277	B7WPI6;P22303-3;P22303-2;P22303	.;.;.;ACES_HUMAN	L	277	ENSP00000403474:R277L;ENSP00000241069:R277L;ENSP00000414858:R277L;ENSP00000303211:R277L;ENSP00000394976:R277L;ENSP00000397143:R277L;ENSP00000399725:R277L;ENSP00000404865:R277L	ENSP00000241069:R277L	R	-	2	0	ACHE	100328960	0.068000	0.21057	1.000000	0.80357	0.833000	0.47200	1.142000	0.31540	2.281000	0.76405	0.484000	0.47621	CGC	.	.		0.706	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831		A	100491024	C	A	100491024	3	1	175	1	0	0	0	0	1	0	0	0	141	768	27	1	1165	1	ACHE	7	100491024	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	1904582	100491024	58647639	46	26344										
LHFPL3	375612	hgsc.bcm.edu	37	chr7	103969251	103969251	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cccggagccgccgccgctgcCgccgccgccgccgccgcgat	14	23	0	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr7:103969251C>T	ENST00000535008.1	+	1	148	c.24C>T	c.(22-24)gcC>gcT	p.A8A	LHFPL3_ENST00000401970.2_5'UTR|LHFPL3_ENST00000424859.1_5'UTR|LHFPL3_ENST00000543266.1_Silent_p.A8A			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	8						integral component of membrane (GO:0016021)		p.A8A(1)		kidney(1)|large_intestine(2)|lung(6)	9						ccgccgctgccgccgccgccg	0.721																																					p.A8A		Atlas-SNP	.											LHFPL3,NS,carcinoma,0,1	LHFPL3	24	.	1	Substitution - coding silent(1)	kidney(1)	c.C24T						.						11	14	13					7																	103969251		1949	4092	6041	SO:0001819	synonymous_variant	375612	exon1			CGCTGCCGCCGCC	AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416			6589	protein-coding gene	gene with protein product		609719	"lipoma HMGIC fusion partner-like 4"	LHFPL4		10329012	Standard	NM_199000		Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000535008.1:c.24C>T	chr7.hg19:g.103969251C>T		43.0	0.0		46.0	3.0	NM_199000	A1L383|A4D0Q5	Silent	SNP	ENST00000535008.1	hg19																																																																																				.	.		0.721	LHFPL3-201	KNOWN	basic	protein_coding	protein_coding		NM_199000		T	103969251	C	T	103969251	2	4	175	1	0	0	0	0	0	0	0	1	8775	639	23	1		1	LHFPL3	7	103969251	Silent	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	3478227	103969251	55169412	47	26345										
MLL3	58508	hgsc.bcm.edu	37	chr7	151874011	151874011	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	aacattatctttattctcatCatttttttcagtttcacatt	1	8	5	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr7:151874011C>T	ENST00000262189.6	-	38	8745	c.8527G>A	c.(8527-8529)Gat>Aat	p.D2843N	KMT2C_ENST00000355193.2_Missense_Mutation_p.D2843N	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2843					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTATTCTCATCATTTTTTTCA	0.383																																					p.D2843N		Atlas-SNP	.											.	MLL3	1564	.	0			c.G8527A						.						134	132	133					7																	151874011		2203	4300	6503	SO:0001583	missense	58508	exon38			TCTCATCATTTTT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8527G>A	chr7.hg19:g.151874011C>T	ENSP00000262189:p.Asp2843Asn	75.0	0.0		74.0	36.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	3.956	-0.011247	0.07727	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.85484	-1.97;-1.99	5.58	4.7	0.59300	.	0.608750	0.14192	N	0.335271	T	0.76300	0.3968	N	0.24115	0.695	0.80722	D	1	B;B;B	0.21520	0.057;0.0;0.0	B;B;B	0.15870	0.014;0.002;0.002	T	0.69068	-0.5243	10	0.33141	T	0.24	.	12.9312	0.58288	0.0:0.9248:0.0:0.0752	.	2843;1904;2843	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	MLL3_HUMAN;.;.	N	2843	ENSP00000262189:D2843N;ENSP00000347325:D2843N	ENSP00000262189:D2843N	D	-	1	0	MLL3	151504944	0.100000	0.21855	0.007000	0.13788	0.083000	0.17756	1.502000	0.35704	1.355000	0.45865	0.650000	0.86243	GAT	.	.		0.383	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151874011	C	T	151874011	3	4	175	1	0	0	0	0	1	0	0	0	9631	826	29	3	6296	3	MLL3	7	151874011	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	47904760	151874011	7264652	48	26346										
PABPC1	26986	hgsc.bcm.edu	37	chr8	101721828	101721828	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	tggcgctcttctttgcgctgAgctaaagctacatacaatgg	10	10	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr8:101721828A>C	ENST00000318607.5	-	8	2232	c.1104T>G	c.(1102-1104)gcT>gcG	p.A368A	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000522387.1_Silent_p.A336A|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000519004.1_Silent_p.A323A	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	368	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			CTTTGCGCTGAGCTAAAGCTA	0.473																																					p.A368A		Atlas-SNP	.											.	PABPC1	76	.	0			c.T1104G						.						127	110	116					8																	101721828		2203	4300	6503	SO:0001819	synonymous_variant	26986	exon8			GCGCTGAGCTAAA	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"RNA binding motif (RRM) containing"	8554	protein-coding gene	gene with protein product		604679	"poly(A)-binding protein, cytoplasmic 2"	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.1104T>G	chr8.hg19:g.101721828A>C		87.0	0.0		222.0	158.0	NM_002568	Q15097|Q93004	Silent	SNP	ENST00000318607.5	hg19	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.64|10.64	1.407262|1.407262	0.25378|0.25378	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519100|ENST00000519596	.|.	.|.	.|.	5.05|5.05	2.32|2.32	0.28847|0.28847	.|.	.|.	.|.	.|.	.|.	T|T	0.43831|0.43831	0.1265|0.1265	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.31308|0.31308	-0.9948|-0.9948	4|4	.|.	.|.	.|.	.|.	2.1503|2.1503	0.03798|0.03798	0.3536:0.0:0.1648:0.4816|0.3536:0.0:0.1648:0.4816	.|.	.|.	.|.	.|.	R|A	237|201	.|.	.|.	L|S	-|-	2|1	0|0	PABPC1|PABPC1	101791004|101791004	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	0.794000|0.794000	0.26958|0.26958	0.849000|0.849000	0.35215|0.35215	-0.496000|-0.496000	0.04628|0.04628	CTC|TCA	.	.		0.473	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568		C	101721828	A	C	101721828	2	2	175	1	0	0	0	0	0	0	0	1	11372	291	11	5		5	PABPC1	8	101721828	Silent	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10		101721828	44642194	49	26347										
KLF10	7071	hgsc.bcm.edu	37	chr8	103663642	103663642	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gggacttgtgtgcccatgaaCacaacaggggggcaaacggc	15	10	0	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr8:103663642C>A	ENST00000285407.6	-	3	1218	c.918G>T	c.(916-918)gtG>gtT	p.V306V	KLF10_ENST00000395884.3_Silent_p.V295V	NM_005655.2	NP_005646.1	Q13118	KLF10_HUMAN	Kruppel-like factor 10	306					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular response to peptide (GO:1901653)|cellular response to starvation (GO:0009267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of circadian rhythm (GO:0042752)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(3)	18	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			TGCCCATGAACACAACAGGGG	0.592																																					p.V306V	Esophageal Squamous(16;495 519 2144 16528 44005)	Atlas-SNP	.											.	KLF10	44	.	0			c.G918T						.						79	80	80					8																	103663642		2203	4300	6503	SO:0001819	synonymous_variant	7071	exon3			CATGAACACAACA	U21847	CCDS6294.1, CCDS47905.1	8q22.3	2014-09-17	2004-11-29	2004-12-01	ENSG00000155090	ENSG00000155090		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11810	protein-coding gene	gene with protein product		601878	"TGFB inducible early growth response"	TIEG		8584037, 9721211	Standard	NM_001032282		Approved	EGRA, TIEG1	uc011lhk.1	Q13118	OTTHUMG00000164735	ENST00000285407.6:c.918G>T	chr8.hg19:g.103663642C>A		123.0	0.0		284.0	86.0	NM_005655	A8MVH0|B2R794|L0R4P6|L0R679|O75411|Q503B2	Silent	SNP	ENST00000285407.6	hg19	CCDS6294.1																																																																																			.	.		0.592	KLF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379967.1			A	103663642	C	A	103663642	2	1	175	1	0	0	0	0	0	0	0	1	8347	465	17	3		3	KLF10	8	103663642	Silent	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	1941814	103663642	42700380	50	26348										
BNC2	54796	hgsc.bcm.edu	37	chr9	16436154	16436154	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	catgcctgggctcatctcctCttgggagtgacaatgattgt	11	10	3	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr9:16436154C>T	ENST00000380672.4	-	6	2095	c.2038G>A	c.(2038-2040)Gag>Aag	p.E680K	BNC2_ENST00000380666.2_Missense_Mutation_p.E680K|BNC2_ENST00000380667.2_Missense_Mutation_p.E613K|BNC2_ENST00000545497.1_Missense_Mutation_p.E585K	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		CTCATCTCCTCTTGGGAGTGA	0.478																																					p.E680K		Atlas-SNP	.											.	BNC2	166	.	0			c.G2038A						.						123	110	114					9																	16436154		2203	4300	6503	SO:0001583	missense	54796	exon6			TCTCCTCTTGGGA	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.2038G>A	chr9.hg19:g.16436154C>T	ENSP00000370047:p.Glu680Lys	103.0	0.0		51.0	21.0	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	hg19	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	C	15.51	2.854931	0.51376	.	.	ENSG00000173068	ENST00000380672;ENST00000411752;ENST00000418777;ENST00000380667;ENST00000545497;ENST00000544198;ENST00000380666;ENST00000540340	T;T;T;T;T;T	0.44482	1.49;0.92;1.51;1.5;1.5;1.5	5.79	5.79	0.91817	.	0.283148	0.40144	N	0.001164	T	0.32645	0.0836	N	0.24115	0.695	0.58432	D	0.999994	B;B;B;B;B;B;B;B;B	0.34290	0.081;0.048;0.447;0.447;0.039;0.048;0.155;0.155;0.023	B;B;B;B;B;B;B;B;B	0.30572	0.031;0.007;0.075;0.117;0.023;0.014;0.023;0.051;0.01	T	0.05533	-1.0879	10	0.33141	T	0.24	-11.814	20.0411	0.97590	0.0:1.0:0.0:0.0	.	585;613;680;506;680;637;680;585;445	F5H586;B1APH0;Q6ZN30-2;B4E3J2;F5H8G9;Q5H9S4;Q6ZN30;B4DR27;D3DRJ1	.;.;.;.;.;.;BNC2_HUMAN;.;.	K	680;73;637;613;585;506;680;680	ENSP00000370047:E680K;ENSP00000392212:E73K;ENSP00000408370:E637K;ENSP00000370042:E613K;ENSP00000444640:E585K;ENSP00000370041:E680K	ENSP00000370041:E680K	E	-	1	0	BNC2	16426154	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.759000	0.85235	2.739000	0.93911	0.655000	0.94253	GAG	.	.		0.478	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		T	16436154	C	T	16436154	3	4	175	1	0	0	0	0	1	0	0	0	1475	922	32	3	1269	3	BNC2	9	16436154	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10		16436154	124777277	51	26349										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79252403	79252403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	tcctccttcttggggttgcaCcattcaagtacacaatcata	6	12	3	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr9:79252403C>T	ENST00000376718.3	-	14	9017	c.8894G>A	c.(8893-8895)gGt>gAt	p.G2965D	PRUNE2_ENST00000466266.2_Intron|PRUNE2_ENST00000428286.1_Missense_Mutation_p.G2607D|PRUNE2_ENST00000443509.2_Missense_Mutation_p.G214D|PRUNE2_ENST00000223609.6_Missense_Mutation_p.G230D	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2965	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TGGGGTTGCACCATTCAAGTA	0.408																																					p.G2965D		Atlas-SNP	.											.	PRUNE2	331	.	0			c.G8894A						.						224	199	207					9																	79252403		1568	3582	5150	SO:0001583	missense	158471	exon14			GTTGCACCATTCA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.8894G>A	chr9.hg19:g.79252403C>T	ENSP00000365908:p.Gly2965Asp	69.0	0.0		70.0	20.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.6|25.6	4.659131|4.659131	0.88154|0.88154	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376717;ENST00000376718;ENST00000428286;ENST00000441554;ENST00000443509;ENST00000424866;ENST00000223609;ENST00000422033|ENST00000426088	T;T;T;T;T;T|.	0.36878|.	1.23;1.23;1.23;1.23;1.23;1.23|.	5.29|5.29	5.29|5.29	0.74685|0.74685	Cellular retinaldehyde-binding/triple function, C-terminal (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.86674|.	0.5989|.	M|M	0.92555|0.92555	3.32|3.32	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;0.999;1.0;1.0|.	D;D;D;D|.	0.97110|.	0.998;0.991;1.0;1.0|.	D|.	0.89579|.	0.3819|.	10|.	0.44086|.	T|.	0.13|.	-24.028|-24.028	19.2996|19.2996	0.94138|0.94138	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	230;229;214;2965|.	B4DSQ3;Q8WUY3-5;B4DJW7;Q8WUY3|.	.;.;.;PRUN2_HUMAN|.	D|X	230;2965;2607;186;214;138;230;2968|2289	ENSP00000365907:G230D;ENSP00000365908:G2965D;ENSP00000397425:G2607D;ENSP00000393843:G214D;ENSP00000393657:G138D;ENSP00000223609:G230D|.	ENSP00000223609:G230D|.	G|W	-|-	2|3	0|0	PRUNE2|PRUNE2	78442223|78442223	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.445000|7.445000	0.80570|0.80570	2.648000|2.648000	0.89879|0.89879	0.561000|0.561000	0.74099|0.74099	GGT|TGG	.	.		0.408	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		T	79252403	C	T	79252403	3	4	175	1	0	0	0	0	1	0	0	0	12653	507	18	3	396	3	PRUNE2	9	79252403	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	62816249	79252403	61961028	52	26350										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79322011	79322011	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cttaggatcagctgtgaccaAgaacttattagattcattca	7	8	3	3			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr9:79322011A>G	ENST00000376718.3	-	8	5302	c.5179T>C	c.(5179-5181)Ttg>Ctg	p.L1727L	PRUNE2_ENST00000428286.1_Silent_p.L1368L	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1727					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GCTGTGACCAAGAACTTATTA	0.428																																					p.L1727L		Atlas-SNP	.											.	PRUNE2	331	.	0			c.T5179C						.						140	116	123					9																	79322011		1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			TGACCAAGAACTT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.5179T>C	chr9.hg19:g.79322011A>G		75.0	0.0		111.0	7.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	A	2.831	-0.242542	0.05906	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.91	3.52	0.40303	.	0.168917	0.28414	N	0.015431	T	0.25195	0.0612	.	.	.	0.20196	N	0.999925	.	.	.	.	.	.	T	0.13845	-1.0494	5	.	.	.	-4.1287	3.5456	0.07827	0.6556:0.1387:0.0728:0.1329	.	.	.	.	P	1048	.	.	L	-	2	0	PRUNE2	78511831	0.265000	0.24102	0.667000	0.29798	0.682000	0.39822	1.173000	0.31920	0.463000	0.27118	0.533000	0.62120	CTT	.	.		0.428	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		G	79322011	A	G	79322011	2	3	175	1	0	0	0	0	0	0	0	1	12653	69	3	2		2	PRUNE2	9	79322011	Silent	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	69608	79322011	61891420	53	26351										
VIM	7431	hgsc.bcm.edu	37	chr10	17271486	17271486	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cggcggcccgggcaccgcgaGccggccgagctccagccgga	17	18	0	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr10:17271486G>T	ENST00000224237.5	+	1	210	c.65G>T	c.(64-66)aGc>aTc	p.S22I	VIM_ENST00000485947.1_3'UTR|VIM-AS1_ENST00000605833.1_RNA|VIM_ENST00000544301.1_Missense_Mutation_p.S22I|VIM-AS1_ENST00000437232.1_RNA			P08670	VIME_HUMAN	vimentin	22	Head.				apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GGCACCGCGAGCCGGCCGAGC	0.736																																					p.S22I		Atlas-SNP	.											.	VIM	71	.	0			c.G65T						.						10	10	10					10																	17271486		2112	4153	6265	SO:0001583	missense	7431	exon2			CCGCGAGCCGGCC	M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.65G>T	chr10.hg19:g.17271486G>T	ENSP00000224237:p.Ser22Ile	105.0	0.0		85.0	35.0	NM_003380	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Missense_Mutation	SNP	ENST00000224237.5	hg19	CCDS7120.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.209228	0.58343	.	.	ENSG00000026025	ENST00000544301;ENST00000224237;ENST00000545533	D;D	0.84800	-1.9;-1.9	4.49	3.58	0.41010	Intermediate filament head, DNA-binding domain (1);	0.132342	0.35124	N	0.003440	T	0.81216	0.4776	M	0.65498	2.005	0.46222	D	0.998931	B;B;P;B;B	0.40970	0.011;0.218;0.734;0.001;0.011	B;B;B;B;B	0.34536	0.009;0.116;0.185;0.003;0.009	T	0.81044	-0.1111	10	0.49607	T	0.09	.	12.2249	0.54455	0.0:0.0:0.8296:0.1704	.	22;9;9;22;22	Q53HU8;F5H288;B3KRK8;B0YJC4;P08670	.;.;.;.;VIME_HUMAN	I	22;22;9	ENSP00000446007:S22I;ENSP00000224237:S22I	ENSP00000224237:S22I	S	+	2	0	VIM	17311492	.	.	0.916000	0.36221	0.896000	0.52359	.	.	1.089000	0.41292	0.448000	0.29417	AGC	.	.		0.736	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		T	17271486	G	T	17271486	3	4	175	1	0	0	0	0	1	0	0	0	17181	971	34	3	67	3	VIM	10	17271486	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10		17271486	118263261	54	26352										
THNSL1	79896	hgsc.bcm.edu	37	chr10	25312254	25312254	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	catgcacagcgatttctttcAagaacctttgcacttgcgga	8	11	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr10:25312254A>C	ENST00000524413.1	+	3	449	c.102A>C	c.(100-102)tcA>tcC	p.S34S	THNSL1_ENST00000376356.4_Silent_p.S34S			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	34						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	GATTTCTTTCAAGAACCTTTG	0.398																																					p.S34S		Atlas-SNP	.											.	THNSL1	70	.	0			c.A102C						.						104	106	106					10																	25312254		2203	4300	6503	SO:0001819	synonymous_variant	79896	exon3			TCTTTCAAGAACC	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"threonine synthase-like 1 (bacterial)"			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.102A>C	chr10.hg19:g.25312254A>C		153.0	0.0		143.0	63.0	NM_024838	B3KWL1|D3DRV3|Q5VV21	Silent	SNP	ENST00000524413.1	hg19	CCDS7147.1																																																																																			.	.		0.398	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838		C	25312254	A	C	25312254	2	2	175	1	0	0	0	0	0	0	0	1	15877	117	5	5		5	THNSL1	10	25312254	Silent	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	8040768	25312254	110222493	55	26353										
TBC1D12	23232	hgsc.bcm.edu	37	chr10	96269915	96269915	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gacatatcccgtacatttccAtctctctacatctttcagaa	3	13	4	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr10:96269915A>T	ENST00000225235.4	+	8	1778	c.1668A>T	c.(1666-1668)ccA>ccT	p.P556P	TBC1D12_ENST00000485048.1_3'UTR	NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	556	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	20		Colorectal(252;0.0429)				GTACATTTCCATCTCTCTACA	0.353																																					p.P556P		Atlas-SNP	.											.	TBC1D12	51	.	0			c.A1668T						.						170	154	159					10																	96269915		1835	4097	5932	SO:0001819	synonymous_variant	23232	exon8			ATTTCCATCTCTC	AB011180	CCDS41553.1	10q23.33	2013-09-20			ENSG00000108239	ENSG00000108239			29082	protein-coding gene	gene with protein product						9628581	Standard	NM_015188		Approved	KIAA0608	uc001kjr.2	O60347	OTTHUMG00000018794	ENST00000225235.4:c.1668A>T	chr10.hg19:g.96269915A>T		105.0	0.0		98.0	47.0	NM_015188	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Silent	SNP	ENST00000225235.4	hg19	CCDS41553.1																																																																																			.	.		0.353	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2			T	96269915	A	T	96269915	2	4	175	1	0	0	0	0	0	0	0	1	15616	204	8	4		4	TBC1D12	10	96269915	Silent	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	70957661	96269915	39264832	56	26354										
BTRC	8945	hgsc.bcm.edu	37	chr10	103285923	103285923	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gagaatggtcaggacagattCtctgtggagaggcctggcag	16	7	2	3			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr10:103285923C>A	ENST00000370187.3	+	6	828	c.710C>A	c.(709-711)tCt>tAt	p.S237Y	BTRC_ENST00000393441.4_Missense_Mutation_p.S196Y|BTRC_ENST00000408038.2_Missense_Mutation_p.S201Y	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	237					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		AGGACAGATTCTCTGTGGAGA	0.483																																					p.S237Y		Atlas-SNP	.											BTRC,colon,carcinoma,0,2	BTRC	64	.	0			c.C710A						.						166	151	156					10																	103285923		2203	4300	6503	SO:0001583	missense	8945	exon6			CAGATTCTCTGTG	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.710C>A	chr10.hg19:g.103285923C>A	ENSP00000359206:p.Ser237Tyr	124.0	0.0		122.0	7.0	NM_033637	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	hg19	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278781	0.59758	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038	T;T;T	0.22134	1.97;1.97;1.97	5.54	5.54	0.83059	F-box domain, Skp2-like (1);	0.000000	0.64402	D	0.000001	T	0.35913	0.0948	M	0.80616	2.505	0.80722	D	1	B;B;B	0.25955	0.039;0.138;0.068	B;B;B	0.32724	0.031;0.151;0.009	T	0.21177	-1.0253	10	0.56958	D	0.05	-11.948	19.4875	0.95035	0.0:1.0:0.0:0.0	.	211;201;237	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	Y	237;196;201	ENSP00000359206:S237Y;ENSP00000377088:S196Y;ENSP00000385339:S201Y	ENSP00000359206:S237Y	S	+	2	0	BTRC	103275913	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.051000	0.71072	2.615000	0.88500	0.655000	0.94253	TCT	.	.		0.483	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		A	103285923	C	A	103285923	3	1	175	1	0	0	0	0	1	0	0	0	1571	913	32	3	732	3	BTRC	10	103285923	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	7016008	103285923	32248824	57	26355										
C10orf46	143384	hgsc.bcm.edu	37	chr10	120450798	120450798	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ttgtaaaaccattctgtataAgttctctttgaaatttctga	5	6	3	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr10:120450798A>C	ENST00000369151.3	-	7	1487	c.1004T>G	c.(1003-1005)cTt>cGt	p.L335R	CACUL1_ENST00000544392.1_5'UTR	NM_153810.4	NP_722517.3	Q86Y37	CACL1_HUMAN	CDK2-associated, cullin domain 1	335					G1/S transition of mitotic cell cycle (GO:0000082)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase activity (GO:0045860)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)	protein kinase binding (GO:0019901)										ATTCTGTATAAGTTCTCTTTG	0.383																																					p.L335R		Atlas-SNP	.											.	.	.	.	0			c.T1004G						.						134	138	137					10																	120450798		1818	4085	5903	SO:0001583	missense	143384	exon7			TGTATAAGTTCTC	AK097728	CCDS41570.1	10q26.13	2012-06-12	2012-06-12	2012-06-12	ENSG00000151893	ENSG00000151893			23727	protein-coding gene	gene with protein product	"Cdk-Associated Cullin1"		"chromosome 10 open reading frame 46"	C10orf46		19829063	Standard	NM_153810		Approved	FLJ40409, MGC33215, CAC1	uc001lds.1	Q86Y37	OTTHUMG00000019138	ENST00000369151.3:c.1004T>G	chr10.hg19:g.120450798A>C	ENSP00000358147:p.Leu335Arg	72.0	0.0		75.0	21.0	NM_153810	Q5XPL7|Q8IY11|Q8N7S4	Missense_Mutation	SNP	ENST00000369151.3	hg19	CCDS41570.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.701899	0.88924	.	.	ENSG00000151893	ENST00000544392;ENST00000369156;ENST00000369151	.	.	.	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.68007	0.2954	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.70586	-0.4831	9	0.66056	D	0.02	-4.4185	16.4696	0.84102	1.0:0.0:0.0:0.0	.	335	Q86Y37	CJ046_HUMAN	R	146;212;335	.	ENSP00000358147:L335R	L	-	2	0	C10orf46	120440788	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.064000	0.89483	2.289000	0.77006	0.482000	0.46254	CTT	.	.		0.383	CACUL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050612.2	NM_153810		C	120450798	A	C	120450798	3	2	175	1	0	0	0	0	1	0	0	0	1606	72	3	5	117	5	C10orf46	10	120450798	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	17164875	120450798	15083949	58	26356										
PLEKHA1	59338	hgsc.bcm.edu	37	chr10	124172538	124172538	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gaactgatattgttggtggcGtacccatcattactcccact	8	11	1	1	rs573666181		TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr10:124172538G>A	ENST00000368990.3	+	6	576	c.445G>A	c.(445-447)Gta>Ata	p.V149I	PLEKHA1_ENST00000433307.1_Missense_Mutation_p.V149I|PLEKHA1_ENST00000494222.1_3'UTR|PLEKHA1_ENST00000368988.1_Missense_Mutation_p.V149I|PLEKHA1_ENST00000538022.1_Missense_Mutation_p.V149I|PLEKHA1_ENST00000368989.2_Missense_Mutation_p.V149I	NM_001001974.2	NP_001001974.1	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	149					androgen metabolic process (GO:0008209)|B cell receptor signaling pathway (GO:0050853)|cellular response to hydrogen peroxide (GO:0070301)|establishment of protein localization (GO:0045184)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|multicellular organism growth (GO:0035264)|negative regulation of protein kinase B signaling (GO:0051898)|palate development (GO:0060021)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|ruffle organization (GO:0031529)|skeletal system morphogenesis (GO:0048705)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TGTTGGTGGCGTACCCATCAT	0.363													G|||	1	0.000199681	0	0	5008	,	,		13721	0		0	False		,,,				2504	0.001				p.V149I		Atlas-SNP	.											.	PLEKHA1	33	.	0			c.G445A						.						130	120	123					10																	124172538		2203	4300	6503	SO:0001583	missense	59338	exon6			GGTGGCGTACCCA	AF286160	CCDS7629.1, CCDS55730.1	10q26.3	2013-01-10	2002-01-14		ENSG00000107679	ENSG00000107679		"Pleckstrin homology (PH) domain containing"	14335	protein-coding gene	gene with protein product	"tandem PH domain containing protein-1"	607772	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 1"			11001876, 15485858	Standard	NM_001001974		Approved	TAPP1	uc001lge.2	Q9HB21	OTTHUMG00000019184	ENST00000368990.3:c.445G>A	chr10.hg19:g.124172538G>A	ENSP00000357986:p.Val149Ile	140.0	0.0		111.0	5.0	NM_021622	B3KQ55|D3DRE2|Q9BVK0	Missense_Mutation	SNP	ENST00000368990.3	hg19	CCDS7629.1	.	.	.	.	.	.	.	.	.	.	G	32	5.123233	0.94429	.	.	ENSG00000107679	ENST00000368990;ENST00000368989;ENST00000409427;ENST00000368988;ENST00000538022;ENST00000433307	T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.41003	0.1140	M	0.80982	2.52	0.80722	D	1	P;D	0.65815	0.68;0.995	B;D	0.64776	0.166;0.929	T	0.05500	-1.0881	10	0.39692	T	0.17	-16.352	20.2314	0.98350	0.0:0.0:1.0:0.0	.	149;149	B3KQ55;Q9HB21	.;PKHA1_HUMAN	I	149	ENSP00000357986:V149I;ENSP00000357985:V149I;ENSP00000357984:V149I;ENSP00000438608:V149I;ENSP00000394416:V149I	ENSP00000357984:V149I	V	+	1	0	PLEKHA1	124162528	1.000000	0.71417	0.870000	0.34147	0.946000	0.59487	9.011000	0.93618	2.789000	0.95967	0.591000	0.81541	GTA	.	.		0.363	PLEKHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050783.1	NM_001001974		A	124172538	G	A	124172538	3	1	175	1	0	0	0	0	1	0	0	0	12064	1145	40	1	463	1	PLEKHA1	10	124172538	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	3721740	124172538	11362209	59	26357										
DHX32	55760	hgsc.bcm.edu	37	chr10	127529548	127529549	+	Missense_Mutation	DNP	GT	GT	TG													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ttcagctccatgtggcacatGtgaaaagcaatttggagctt							TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr10:127529548_127529549GT>TG	ENST00000284690.3	-	8	2050_2051	c.1560_1561AC>CA	c.(1558-1563)tcACat>tcCAat	p.H521N	AL360176.1_ENST00000401153.1_RNA|BCCIP_ENST00000368759.5_Intron|DHX32_ENST00000368721.1_Missense_Mutation_p.H145N|BCCIP_ENST00000299130.3_Intron|BCCIP_ENST00000429863.2_Intron|DHX32_ENST00000284688.6_Missense_Mutation_p.H440N	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	521						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TGTGGCACATGTGAAAAGCAAT	0.426																																					p.H521N|p.S520S		Atlas-SNP	.											.	DHX32	67	.	0			c.C1561A|c.A1560C						.																																			SO:0001583	missense	55760	exon8			GCACATGTGAAAA|CACATGTGAAAAG		CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"DEAH-boxes"	16717	protein-coding gene	gene with protein product		607960	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.1560_1561delinsTG	chr10.hg19:g.127529548_127529549delinsTG	ENSP00000284690:p.His521Asn	86.0|87.0	0.0		73.0	27.0|28.0	NM_018180	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Missense_Mutation|Silent	SNP	ENST00000284690.3	hg19	CCDS7652.1																																																																																			.	.		0.426	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180		TG	127529549	GT	TG	127529548	3	4	175	1	0	0	0	0	1	0	0	0	4507	1377	48	3	686	3	DHX32	10	127529548	Missense_Mutation	DNP	GT	TCGA-DD-AACY-01A-11D-A40R-10	3357010	127529548	8005199	60	26358										
MUC2	4583	hgsc.bcm.edu	37	chr11	1094728	1094728	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cacccccagcactgtgcagaCgaccaccaccagtgcctgga	9	18	0	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr11:1094728C>T	ENST00000441003.2	+	31	5843	c.5816C>T	c.(5815-5817)aCg>aTg	p.T1939M	MUC2_ENST00000333592.6_Missense_Mutation_p.T227M|MUC2_ENST00000361558.6_Missense_Mutation_p.T77M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4301					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACTGTGCAGACGACCACCACC	0.637																																					p.T1935M		Atlas-SNP	.											.	MUC2	614	.	0			c.C5804T						.						110	131	124					11																	1094728		2100	4228	6328	SO:0001583	missense	4583	exon32			TGCAGACGACCAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5816C>T	chr11.hg19:g.1094728C>T	ENSP00000415183:p.Thr1939Met	91.0	0.0		78.0	30.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	c	11.73	1.727216	0.30593	.	.	ENSG00000198788	ENST00000441003;ENST00000361558;ENST00000333592	T;T;T	0.50548	2.62;0.74;2.98	1.74	1.74	0.24563	.	.	.	.	.	T	0.39759	0.1090	L	0.58101	1.795	0.09310	N	1	D	0.60575	0.988	B	0.39339	0.297	T	0.32348	-0.9910	9	0.59425	D	0.04	.	8.3718	0.32419	0.0:1.0:0.0:0.0	.	1939	E7EUV1	.	M	1939;77;227	ENSP00000415183:T1939M;ENSP00000354885:T77M;ENSP00000331373:T227M	ENSP00000331373:T227M	T	+	2	0	MUC2	1084728	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.326000	0.07965	0.965000	0.38133	0.479000	0.44913	ACG	.	.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1094728	C	T	1094728	3	4	175	1	0	0	0	0	1	0	0	0	9984	536	19	1	5930	1	MUC2	11	1094728	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10		1094728	133911788	61	26359										
OR52N5	390075	hgsc.bcm.edu	37	chr11	5799571	5799571	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gcattgaagttaatttctttGagactgaaccagaagatgca	9	6	1	5			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr11:5799571G>A	ENST00000317093.2	-	1	326	c.294C>T	c.(292-294)ctC>ctT	p.L98L	TRIM5_ENST00000380027.1_Intron	NM_001001922.2	NP_001001922.2	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N, member 5	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|liver(1)|lung(17)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		TAATTTCTTTGAGACTGAACC	0.478																																					p.L98L		Atlas-SNP	.											.	OR52N5	58	.	0			c.C294T						.						93	89	90					11																	5799571		2121	4087	6208	SO:0001819	synonymous_variant	390075	exon1			TTCTTTGAGACTG	AB065535	CCDS31397.1	11p15.4	2012-08-09			ENSG00000181009	ENSG00000181009		"GPCR / Class A : Olfactory receptors"	15231	protein-coding gene	gene with protein product							Standard	NM_001001922		Approved	OR52N5Q	uc010qzn.2	Q8NH56	OTTHUMG00000168799	ENST00000317093.2:c.294C>T	chr11.hg19:g.5799571G>A		189.0	0.0		183.0	14.0	NM_001001922	B9EH12|Q6IFG2	Silent	SNP	ENST00000317093.2	hg19	CCDS31397.1																																																																																			.	.		0.478	OR52N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401141.1	NM_001001922		A	5799571	G	A	5799571	2	1	175	1	0	0	0	0	0	0	0	1	11139	1277	45	3		3	OR52N5	11	5799571	Silent	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	4704843	5799571	129206945	62	26360										
C11orf66	220004	hgsc.bcm.edu	37	chr11	61252246	61252246	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gaagtgcctctgctccaccaGcagcagggccaggacccgct	12	16	1	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr11:61252246G>C	ENST00000338608.2	+	5	593	c.468G>C	c.(466-468)caG>caC	p.Q156H	RP11-286N22.8_ENST00000544880.1_3'UTR|PPP1R32_ENST00000432063.2_Missense_Mutation_p.Q156H	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	156							phosphatase binding (GO:0019902)										TGCTCCACCAGCAGCAGGGCC	0.672																																					p.Q156H		Atlas-SNP	.											.	.	.	.	0			c.G468C						.						23	24	24					11																	61252246		2202	4299	6501	SO:0001583	missense	220004	exon5			CCACCAGCAGCAG	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	28869	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 66"	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.468G>C	chr11.hg19:g.61252246G>C	ENSP00000344140:p.Gln156His	117.0	0.0		97.0	35.0	NM_001170753	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	hg19	CCDS8008.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.227940	0.58777	.	.	ENSG00000162148	ENST00000432063;ENST00000338608	T;T	0.46451	0.87;1.46	5.33	2.39	0.29439	.	0.221526	0.30565	N	0.009355	T	0.52980	0.1768	M	0.68317	2.08	0.80722	D	1	D;D	0.64830	0.987;0.994	P;P	0.62740	0.838;0.906	T	0.51795	-0.8660	9	.	.	.	-15.9934	6.9325	0.24449	0.3199:0.0:0.6801:0.0	.	156;156	Q7Z5V6-2;Q7Z5V6	.;PPR32_HUMAN	H	156	ENSP00000391560:Q156H;ENSP00000344140:Q156H	.	Q	+	3	2	C11orf66	61008822	0.985000	0.35326	1.000000	0.80357	0.680000	0.39746	1.482000	0.35486	1.249000	0.43950	0.462000	0.41574	CAG	.	.		0.672	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017		C	61252246	G	C	61252246	3	2	175	1	0	0	0	0	1	0	0	0	1658	962	34	4	482	4	C11orf66	11	61252246	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	55452675	61252246	73754270	63	26361										
CCND1	595	hgsc.bcm.edu	37	chr11	69466001	69466001	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ggaggaagaggaggaggaggAggtggacctggcttgcacac	20	6	0	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr11:69466001A>T	ENST00000227507.2	+	5	1066	c.839A>T	c.(838-840)gAg>gTg	p.E280V	ORAOV1_ENST00000542515.1_5'Flank	NM_053056.2	NP_444284.1	P24385	CCND1_HUMAN	cyclin D1	280	Poly-Glu.				canonical Wnt signaling pathway (GO:0060070)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|lactation (GO:0007595)|Leydig cell differentiation (GO:0033327)|liver development (GO:0001889)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ regeneration (GO:0031100)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|positive regulation of protein phosphorylation (GO:0001934)|re-entry into mitotic cell cycle (GO:0000320)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to organonitrogen compound (GO:0010243)|response to UV-A (GO:0070141)|response to vitamin E (GO:0033197)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)|transcriptional repressor complex (GO:0017053)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|proline-rich region binding (GO:0070064)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			NS(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|ovary(1)|urinary_tract(1)	23	all_cancers(3;2.01e-114)|all_epithelial(3;3.59e-122)|Breast(3;5.4e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;8.22e-16)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;7.2e-57)|all cancers(3;7.75e-51)|BRCA - Breast invasive adenocarcinoma(2;4.9e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)		Arsenic trioxide(DB01169)	gaggaggaggaggtggaCCTG	0.706			T	"IGH@, FSTL3"	"CLL, B-ALL, breast"					Multiple Myeloma(6;0.086)																											p.E280V	Pancreas(65;393 884 2788 21700 24360 27795 36895)	Atlas-SNP	.		Dom	yes		11	11q13	595	cyclin D1		"L, E"	.	CCND1	107	.	0			c.A839T						.						28	23	25					11																	69466001		2200	4294	6494	SO:0001583	missense	595	exon5			AGGAGGAGGTGGA	Z23022	CCDS8191.1	11q13	2008-07-18	2005-09-12		ENSG00000110092	ENSG00000110092			1582	protein-coding gene	gene with protein product	"parathyroid adenomatosis 1", "B-cell CLL/lymphoma 1", "G1/S-specific cyclin D1"	168461	"cyclin D1 (PRAD1: parathyroid adenomatosis 1)"	BCL1, D11S287E, PRAD1		1826542, 1833066	Standard	XM_006718653		Approved	U21B31	uc001opa.3	P24385	OTTHUMG00000167877	ENST00000227507.2:c.839A>T	chr11.hg19:g.69466001A>T	ENSP00000227507:p.Glu280Val	186.0	0.0		144.0	6.0	NM_053056	Q6LEF0	Missense_Mutation	SNP	ENST00000227507.2	hg19	CCDS8191.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.214161	0.79352	.	.	ENSG00000110092	ENST00000227507;ENST00000542897	T	0.10192	2.9	5.18	4.05	0.47172	.	0.220157	0.46442	D	0.000298	T	0.10637	0.0260	L	0.36672	1.1	0.80722	D	1	B	0.32382	0.368	B	0.35114	0.196	T	0.09207	-1.0685	10	0.54805	T	0.06	.	10.7647	0.46286	0.9251:0.0:0.0749:0.0	.	280	P24385	CCND1_HUMAN	V	280;146	ENSP00000227507:E280V	ENSP00000227507:E280V	E	+	2	0	CCND1	69175182	1.000000	0.71417	0.349000	0.25694	0.990000	0.78478	5.551000	0.67274	0.822000	0.34565	0.459000	0.35465	GAG	.	.		0.706	CCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396775.2	NM_053056		T	69466001	A	T	69466001	3	4	175	1	0	0	0	0	1	0	0	0	2918	304	11	4	857	4	CCND1	11	69466001	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	8213755	69466001	65540515	64	26362										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73817446	73817446	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ccaaatggagactgaccattTtcttgttgcactggaagctg	10	9	1	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr11:73817446T>G	ENST00000334126.7	-	13	2281	c.2055A>C	c.(2053-2055)gaA>gaC	p.E685D	C2CD3_ENST00000313663.7_Missense_Mutation_p.E685D			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	685					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					ACTGACCATTTTCTTGTTGCA	0.433																																					p.E685D		Atlas-SNP	.											.	C2CD3	288	.	0			c.A2055C						.						98	91	94					11																	73817446		2200	4293	6493	SO:0001583	missense	26005	exon13			ACCATTTTCTTGT	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.2055A>C	chr11.hg19:g.73817446T>G	ENSP00000334379:p.Glu685Asp	189.0	0.0		169.0	68.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	T	16.04	3.009282	0.54361	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.11169	2.8;2.81	5.47	3.16	0.36331	.	0.276343	0.39759	N	0.001265	T	0.21307	0.0513	M	0.68952	2.095	0.23113	N	0.998278	D	0.65815	0.995	P	0.57371	0.819	T	0.04579	-1.0941	10	0.54805	T	0.06	-9.629	7.1741	0.25734	0.0:0.3036:0.0:0.6964	.	685	Q4AC94-1	.	D	685	ENSP00000334379:E685D;ENSP00000323339:E685D	ENSP00000323339:E685D	E	-	3	2	C2CD3	73495094	0.995000	0.38212	0.900000	0.35374	0.310000	0.27922	1.054000	0.30455	0.467000	0.27218	0.482000	0.46254	GAA	.	.		0.433	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		G	73817446	T	G	73817446	3	3	175	1	0	0	0	0	1	0	0	0	2156	1838	64	5	3912	5	C2CD3	11	73817446	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	4351445	73817446	61189070	65	26363										
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14778727	14778727	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	agttaagtctgtcagccctgTccctctctgccttgtacagc	8	14	3	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr12:14778727T>G	ENST00000261170.3	-	21	2508	c.2372A>C	c.(2371-2373)gAc>gCc	p.D791A		NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	791					intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	GTCAGCCCTGTCCCTCTCTGC	0.453																																					p.D791A		Atlas-SNP	.											.	GUCY2C	126	.	0			c.A2372C						.						235	201	212					12																	14778727		2203	4300	6503	SO:0001583	missense	2984	exon21			GCCCTGTCCCTCT		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.2372A>C	chr12.hg19:g.14778727T>G	ENSP00000261170:p.Asp791Ala	119.0	0.0		85.0	4.0	NM_004963	B2RMY6	Missense_Mutation	SNP	ENST00000261170.3	hg19	CCDS8664.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.436009	0.83885	.	.	ENSG00000070019	ENST00000261170	T	0.80909	-1.43	5.35	5.35	0.76521	Adenylyl cyclase class-3/4/guanylyl cyclase (1);	0.000000	0.85682	D	0.000000	D	0.85164	0.5634	L	0.49256	1.55	0.80722	D	1	P	0.50443	0.935	P	0.59825	0.864	D	0.85178	0.1002	10	0.45353	T	0.12	.	15.633	0.76926	0.0:0.0:0.0:1.0	.	791	P25092	GUC2C_HUMAN	A	791	ENSP00000261170:D791A	ENSP00000261170:D791A	D	-	2	0	GUCY2C	14669994	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.943000	0.87716	2.155000	0.67459	0.482000	0.46254	GAC	.	.		0.453	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			G	14778727	T	G	14778727	3	3	175	1	0	0	0	0	1	0	0	0	6905	1667	58	5	877	5	GUCY2C	12	14778727	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10		14778727	119073168	66	26364										
ITGA7	3679	hgsc.bcm.edu	37	chr12	56081819	56081819	+	Missense_Mutation	SNP	A	A	G													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ccagtacagccaggaggatgAcccaccagggcactccttct							TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr12:56081819A>G	ENST00000555728.1	-	25	3279	c.3251T>C	c.(3250-3252)gTc>gCc	p.V1084A	ITGA7_ENST00000452168.2_Missense_Mutation_p.V947A|ITGA7_ENST00000394229.2_Missense_Mutation_p.V1040A|ITGA7_ENST00000394230.2_Missense_Mutation_p.V1044A|ITGA7_ENST00000257880.7_Missense_Mutation_p.V1084A|ITGA7_ENST00000257879.6_Missense_Mutation_p.V1040A|ITGA7_ENST00000553804.1_Missense_Mutation_p.V1044A|ITGA7_ENST00000347027.6_Missense_Mutation_p.V1034A			Q13683	ITA7_HUMAN	integrin, alpha 7	1084					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CAGGAGGATGACCCACCAGGG	0.602																																					p.V1044A		Atlas-SNP	.											.	ITGA7	194	.	0			c.T3131C						.						121	120	120					12																	56081819		2203	4300	6503	SO:0001583	missense	3679	exon24			AGGATGACCCACC		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.3251T>C	chr12.hg19:g.56081819A>G	ENSP00000452387:p.Val1084Ala	146.0	0.0		134.0	39.0	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Missense_Mutation	SNP	ENST00000555728.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.70	3.196816	0.58126	.	.	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000353687;ENST00000555728;ENST00000557555	T;T;T;T;T;T;T;T	0.56611	0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45	4.92	3.76	0.43208	.	0.147970	0.45361	D	0.000379	T	0.52964	0.1767	M	0.75264	2.295	0.31329	N	0.685098	B;B;B;P	0.37141	0.118;0.241;0.427;0.584	B;B;B;B	0.38985	0.139;0.103;0.287;0.207	T	0.62431	-0.6856	10	0.87932	D	0	.	8.9659	0.35877	0.9096:0.0:0.0903:0.0	.	947;1084;1044;1103	Q13683-13;Q13683;Q13683-3;Q4LE35	.;ITA7_HUMAN;.;.	A	1044;1040;1034;947;1084;1044;1040;913;1084;70	ENSP00000452120:V1044A;ENSP00000257879:V1040A;ENSP00000343009:V1034A;ENSP00000393844:V947A;ENSP00000257880:V1084A;ENSP00000377777:V1044A;ENSP00000377776:V1040A;ENSP00000452387:V1084A	ENSP00000257879:V1040A	V	-	2	0	ITGA7	54368086	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.712000	0.74681	0.726000	0.32339	0.386000	0.25728	GTC	.	.		0.602	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		G	56081819	A	G	56081819	3	3	175	1	0	0	0	0	1	0	0	0	7890	275	10	2	302	2	ITGA7	12	56081819	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	41303092	56081819	77770076	67	26365	126	2								
ITGA7	3679	hgsc.bcm.edu	37	chr12	56081826	56081826	+	Missense_Mutation	SNP	A	A	G													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	agccaggaggatgacccaccAgggcactccttctgccacca							TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr12:56081826A>G	ENST00000555728.1	-	25	3272	c.3244T>C	c.(3244-3246)Tgg>Cgg	p.W1082R	ITGA7_ENST00000452168.2_Missense_Mutation_p.W945R|ITGA7_ENST00000394229.2_Missense_Mutation_p.W1038R|ITGA7_ENST00000394230.2_Missense_Mutation_p.W1042R|ITGA7_ENST00000257880.7_Missense_Mutation_p.W1082R|ITGA7_ENST00000257879.6_Missense_Mutation_p.W1038R|ITGA7_ENST00000553804.1_Missense_Mutation_p.W1042R|ITGA7_ENST00000347027.6_Missense_Mutation_p.W1032R			Q13683	ITA7_HUMAN	integrin, alpha 7	1082					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						ATGACCCACCAGGGCACTCCT	0.597																																					p.W1042R		Atlas-SNP	.											.	ITGA7	194	.	0			c.T3124C						.						120	118	119					12																	56081826		2203	4300	6503	SO:0001583	missense	3679	exon24			CCCACCAGGGCAC		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.3244T>C	chr12.hg19:g.56081826A>G	ENSP00000452387:p.Trp1082Arg	143.0	0.0		142.0	43.0	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Missense_Mutation	SNP	ENST00000555728.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.0	4.083848	0.76642	.	.	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000353687;ENST00000555728;ENST00000557555	T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	4.92	4.92	0.64577	.	0.160277	0.45606	D	0.000354	T	0.68357	0.2992	M	0.81341	2.54	0.58432	D	0.999996	D;D;D;D	0.76494	0.995;0.995;0.999;0.998	D;D;D;D	0.74023	0.935;0.933;0.982;0.933	T	0.73257	-0.4040	10	0.72032	D	0.01	.	12.5563	0.56254	1.0:0.0:0.0:0.0	.	945;1082;1042;1101	Q13683-13;Q13683;Q13683-3;Q4LE35	.;ITA7_HUMAN;.;.	R	1042;1038;1032;945;1082;1042;1038;911;1082;68	ENSP00000452120:W1042R;ENSP00000257879:W1038R;ENSP00000343009:W1032R;ENSP00000393844:W945R;ENSP00000257880:W1082R;ENSP00000377777:W1042R;ENSP00000377776:W1038R;ENSP00000452387:W1082R	ENSP00000257879:W1038R	W	-	1	0	ITGA7	54368093	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.490000	0.90464	1.854000	0.53819	0.386000	0.25728	TGG	.	.		0.597	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		G	56081826	A	G	56081826	3	3	175	1	0	0	0	0	1	0	0	0	7890	188	7	2	309	2	ITGA7	12	56081826	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	7	56081826	77770069	68	26366	126	2								
CCT2	10576	hgsc.bcm.edu	37	chr12	69992133	69992133	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	catagctgacaatgcaggctAtgacagtgcagacctggtgg	13	9	0	3			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr12:69992133A>G	ENST00000299300.6	+	14	1555	c.1367A>G	c.(1366-1368)tAt>tGt	p.Y456C	CCT2_ENST00000544368.2_Missense_Mutation_p.Y456C|CCT2_ENST00000543146.2_Missense_Mutation_p.Y409C	NM_006431.2	NP_006422.1	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2 (beta)	456					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(1)	24	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			AATGCAGGCTATGACAGTGCA	0.468																																					p.Y456C		Atlas-SNP	.											.	CCT2	49	.	0			c.A1367G						.						97	91	93					12																	69992133		2203	4300	6503	SO:0001583	missense	10576	exon14			CAGGCTATGACAG	AF026293	CCDS8991.1, CCDS55843.1	12q14	2011-09-02						"Heat Shock Proteins / Chaperonins"	1615	protein-coding gene	gene with protein product		605139				9819444	Standard	NM_001198842		Approved	Cctb	uc001svb.1	P78371	OTTHUMG00000169383	ENST00000299300.6:c.1367A>G	chr12.hg19:g.69992133A>G	ENSP00000299300:p.Tyr456Cys	322.0	0.0		371.0	111.0	NM_006431	A8K402|B5BTY7|B7Z243|B7Z7K4|B7ZAT2|Q14D36|Q6IAT3	Missense_Mutation	SNP	ENST00000299300.6	hg19	CCDS8991.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.450764	0.84101	.	.	ENSG00000166226	ENST00000299300;ENST00000544368;ENST00000543146	T;T;T	0.78816	-1.21;-1.21;-1.21	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.88366	0.6417	M	0.80422	2.495	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72982	0.965;0.979	D	0.88780	0.3270	9	.	.	.	-8.0319	16.5582	0.84512	1.0:0.0:0.0:0.0	.	456;456	F5GWF6;P78371	.;TCPB_HUMAN	C	456;456;409	ENSP00000299300:Y456C;ENSP00000441847:Y456C;ENSP00000445471:Y409C	.	Y	+	2	0	CCT2	68278400	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	8.778000	0.91785	2.308000	0.77769	0.533000	0.62120	TAT	.	.		0.468	CCT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403818.1	NM_006431		G	69992133	A	G	69992133	3	3	175	1	0	0	0	0	1	0	0	0	2955	449	16	2	1421	2	CCT2	12	69992133	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	13910307	69992133	63859762	69	26367										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85441230	85441230	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	tttaaagttgaaaagaagaaAttagagaacattcagaaggt	9	2	1	5			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr12:85441230A>C	ENST00000393217.2	+	6	721	c.660A>C	c.(658-660)aaA>aaC	p.K220N		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	220	Glu-rich.									breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		AAAAGAAGAAATTAGAGAACA	0.308																																					p.K220N		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A660C						.						58	66	64					12																	85441230		2200	4297	6497	SO:0001583	missense	84125	exon6			GAAGAAATTAGAG	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.660A>C	chr12.hg19:g.85441230A>C	ENSP00000376910:p.Lys220Asn	486.0	1.0		633.0	159.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.28|16.28	3.077533|3.077533	0.55753|0.55753	.|.	.|.	ENSG00000133640|ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217|ENST00000533414	T|.	0.59224|.	0.28|.	5.23|5.23	-0.237|-0.237	0.13061|0.13061	.|.	0.839209|.	0.10519|.	N|.	0.665218|.	T|T	0.33904|0.33904	0.0879|0.0879	L|L	0.42245|0.42245	1.32|1.32	0.21604|0.21604	N|N	0.999627|0.999627	D;D;D|.	0.61697|.	0.989;0.965;0.99|.	P;P;P|.	0.57960|.	0.827;0.583;0.83|.	T|T	0.29731|0.29731	-1.0002|-1.0002	10|5	0.66056|.	D|.	0.02|.	.|.	5.4584|5.4584	0.16604|0.16604	0.4563:0.1542:0.3895:0.0|0.4563:0.1542:0.3895:0.0	.|.	220;220;220|.	Q96JM4-2;Q96JM4;C9JI57|.	.;LRIQ1_HUMAN;.|.	N|T	220|118	ENSP00000376910:K220N|.	ENSP00000256007:K220N|.	K|N	+|+	3|2	2|0	LRRIQ1|LRRIQ1	83965361|83965361	0.996000|0.996000	0.38824|0.38824	0.996000|0.996000	0.52242|0.52242	0.914000|0.914000	0.54420|0.54420	0.372000|0.372000	0.20467|0.20467	-0.052000|-0.052000	0.13311|0.13311	0.477000|0.477000	0.44152|0.44152	AAA|AAT	.	.		0.308	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		C	85441230	A	C	85441230	3	2	175	1	0	0	0	0	1	0	0	0	9038	98	4	5	678	5	LRRIQ1	12	85441230	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	15449097	85441230	48410665	70	26368										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24864943	24864943	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	acatcgccatcgacgggttcCtgctcacaccagtgcagaag	10	14	1	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr13:24864943C>G	ENST00000382095.4	+	8	1533	c.1126C>G	c.(1126-1128)Ctg>Gtg	p.L376V	SPATA13_ENST00000409126.1_Missense_Mutation_p.L236V|SPATA13_ENST00000424834.2_Missense_Mutation_p.L1001V|SPATA13_ENST00000382108.3_Missense_Mutation_p.L1001V|SPATA13_ENST00000343003.6_Missense_Mutation_p.L320V|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.L879V|SPATA13_ENST00000399949.2_Missense_Mutation_p.L298V	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	376	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		CGACGGGTTCCTGCTCACACC	0.572																																					p.L1001V		Atlas-SNP	.											.	SPATA13	92	.	0			c.C3001G						.						58	59	59					13																	24864943		2203	4300	6503	SO:0001583	missense	221178	exon9			GGGTTCCTGCTCA	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.1126C>G	chr13.hg19:g.24864943C>G	ENSP00000371527:p.Leu376Val	192.0	0.0		140.0	60.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	hg19	CCDS9305.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.49|18.49	3.635538|3.635538	0.67130|0.67130	.|.	.|.	ENSG00000182957|ENSG00000182957	ENST00000382108;ENST00000382095;ENST00000434675;ENST00000438694;ENST00000399949;ENST00000409126;ENST00000343003|ENST00000424834	D;D;D;D;D;D|.	0.83755|.	-1.76;-1.76;-1.76;-1.76;-1.76;-1.76|.	5.44|5.44	4.6|4.6	0.57074|0.57074	Dbl homology (DH) domain (5);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85261|0.85261	0.5656|0.5656	H|H	0.94582|0.94582	3.555|3.555	0.51012|0.51012	D|D	0.999902|0.999902	D;D;D;D;D;D|.	0.89917|.	0.999;1.0;0.998;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.97110|.	0.999;1.0;0.998;1.0;1.0;1.0|.	D|D	0.89017|0.89017	0.3432|0.3432	10|5	0.87932|.	D|.	0|.	.|.	13.3238|13.3238	0.60449|0.60449	0.0:0.9241:0.0:0.0759|0.0:0.9241:0.0:0.0759	.|.	236;320;260;322;298;376|.	E9PFR9;Q96N96-3;Q96N96-5;Q96N96-4;Q96N96-2;Q96N96|.	.;.;.;.;.;SPT13_HUMAN|.	V|R	1001;376;274;322;298;236;320|1038	ENSP00000371542:L1001V;ENSP00000371527:L376V;ENSP00000401605:L274V;ENSP00000382830:L298V;ENSP00000386471:L236V;ENSP00000343631:L320V|.	ENSP00000343631:L320V|.	L|P	+|+	1|2	2|0	SPATA13|SPATA13	23762943|23762943	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.977000|0.977000	0.68977|0.68977	3.671000|3.671000	0.54576|0.54576	1.314000|1.314000	0.45095|0.45095	-0.266000|-0.266000	0.10368|0.10368	CTG|CCT	.	.		0.572	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		G	24864943	C	G	24864943	3	3	175	1	0	0	0	0	1	0	0	0	15015	680	24	4	3031	4	SPATA13	13	24864943	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10		24864943	90304935	71	26369										
DHRS4L1	728635	hgsc.bcm.edu	37	chr14	24517969	24517969	+	RNA	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gagctggccccaaggaacatTagggtgaactgcctagcacc	12	12	0	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr14:24517969T>A	ENST00000558293.1	+	0	617					NR_102693.1																						CAAGGAACATTAGGGTGAACT	0.522																																					p.I208I		Atlas-SNP	.											.	.	.	.	0			c.T624A						.						154	152	153					14																	24517969		2203	4300	6503			728635	exon8			GAACATTAGGGTG																													chr14.hg19:g.24517969T>A		622.0	0.0		523.0	187.0	NM_001082488		Silent	SNP	ENST00000558293.1	hg19																																																																																				.	.		0.522	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1			A	24517969	T	A	24517969	1	1	175	0	1	0	0	0	0	0	0	0	4495	1742	61	4		4	DHRS4L1	14	24517969	RNA	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10		24517969	82831571	72	26370										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105407215	105407215	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	atttaggaaaagatacctgaCcaagagaaacaggaatcatg	9	6	1	3			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr14:105407215C>A	ENST00000333244.5	-	7	14692	c.14573G>T	c.(14572-14574)gGt>gTt	p.G4858V	AHNAK2_ENST00000557457.1_5'UTR	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4858						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			AGATACCTGACCAAGAGAAAC	0.493																																					p.G4858V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G14573T						.						28	30	30					14																	105407215		1920	4143	6063	SO:0001583	missense	113146	exon7			ACCTGACCAAGAG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.14573G>T	chr14.hg19:g.105407215C>A	ENSP00000353114:p.Gly4858Val	132.0	0.0		96.0	28.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	C	13.74	2.326148	0.41197	.	.	ENSG00000185567	ENST00000333244	T	0.05717	3.4	4.67	-1.39	0.08997	.	.	.	.	.	T	0.04227	0.0117	N	0.24115	0.695	0.09310	N	1	P	0.41673	0.759	B	0.41860	0.368	T	0.40683	-0.9550	9	0.27785	T	0.31	.	4.2791	0.10824	0.2811:0.3168:0.3289:0.0731	.	4858	Q8IVF2	AHNK2_HUMAN	V	4858	ENSP00000353114:G4858V	ENSP00000353114:G4858V	G	-	2	0	AHNAK2	104478260	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.215000	0.02985	-0.152000	0.11156	-0.311000	0.09066	GGT	.	.		0.493	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105407215	C	A	105407215	3	1	175	1	0	0	0	0	1	0	0	0	415	507	18	3	2818	3	AHNAK2	14	105407215	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	80889246	105407215	1942325	73	26371										
NOP10	55505	hgsc.bcm.edu	37	chr15	34634207	34634207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ttgctgggtcatgagcacctTgaagcgtttcttgatggtga	13	7	2	4			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr15:34634207T>C	ENST00000328848.4	-	2	260	c.157A>G	c.(157-159)Aag>Gag	p.K53E	NUTM1_ENST00000438749.3_5'Flank|NUTM1_ENST00000537011.1_5'Flank|NOP10_ENST00000557912.1_Silent_p.S33S	NM_018648.3	NP_061118.1	Q9NPE3	NOP10_HUMAN	NOP10 ribonucleoprotein	53					pseudouridine synthesis (GO:0001522)|rRNA processing (GO:0006364)	box H/ACA RNP complex (GO:0072588)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	snoRNA binding (GO:0030515)			lung(1)|ovary(1)	2						ATGAGCACCTTGAAGCGTTTC	0.537																																					p.K53E		Atlas-SNP	.											NOP10,colon,carcinoma,0,1	NOP10	8	.	0			c.A157G						.						167	126	140					15																	34634207		2201	4298	6499	SO:0001583	missense	55505	exon2			GCACCTTGAAGCG	AB043103	CCDS10037.1	15q14-q15	2014-09-17	2012-12-10	2008-10-13	ENSG00000182117	ENSG00000182117			14378	protein-coding gene	gene with protein product	"homolog of yeast Nop10p"	606471	"nucleolar protein family A, member 3 (H/ACA small nucleolar RNPs)", "NOP10 ribonucleoprotein homolog (yeast)"	NOLA3		11074001, 9843512	Standard	NM_018648		Approved	NOP10P, MGC70651	uc001zie.1	Q9NPE3	OTTHUMG00000129440	ENST00000328848.4:c.157A>G	chr15.hg19:g.34634207T>C	ENSP00000332198:p.Lys53Glu	113.0	0.0		91.0	40.0	NM_018648		Missense_Mutation	SNP	ENST00000328848.4	hg19	CCDS10037.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.991105	0.74703	.	.	ENSG00000182117	ENST00000328848	T	0.76448	-1.02	5.39	4.27	0.50696	.	0.178992	0.51477	D	0.000083	T	0.67655	0.2916	.	.	.	0.80722	D	1	B	0.23128	0.08	B	0.26202	0.067	T	0.67635	-0.5620	9	0.66056	D	0.02	.	5.3576	0.16069	0.0:0.245:0.0:0.755	.	53	Q9NPE3	NOP10_HUMAN	E	53	ENSP00000332198:K53E	ENSP00000332198:K53E	K	-	1	0	NOP10	32421499	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.774000	0.55341	2.043000	0.60533	0.533000	0.62120	AAG	.	.		0.537	NOP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251602.2	NM_018648		C	34634207	T	C	34634207	3	2	175	1	0	0	0	0	1	0	0	0	10544	1821	63	2	41	2	NOP10	15	34634207	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10		34634207	67897185	74	26372										
SH3GL3	6457	hgsc.bcm.edu	37	chr15	84237305	84237305	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cagagctaagctaggaatgcTgaacactgtgtcgaagatcc	11	9	0	3			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr15:84237305T>C	ENST00000427482.2	+	4	518	c.212T>C	c.(211-213)cTg>cCg	p.L71P	SH3GL3_ENST00000434347.1_Missense_Mutation_p.L79P|SH3GL3_ENST00000324537.5_Missense_Mutation_p.L79P|SH3GL3_ENST00000535412.1_Missense_Mutation_p.L71P	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	71	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.|Required for dimerization upon membrane association. {ECO:0000250}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						CTAGGAATGCTGAACACTGTG	0.453																																					p.L71P		Atlas-SNP	.											.	SH3GL3	91	.	0			c.T212C						.						81	79	79					15																	84237305		2203	4300	6503	SO:0001583	missense	6457	exon4			GAATGCTGAACAC	AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.212T>C	chr15.hg19:g.84237305T>C	ENSP00000391372:p.Leu71Pro	81.0	0.0		68.0	29.0	NM_003027	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	hg19	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	T	22.3	4.270980	0.80469	.	.	ENSG00000140600	ENST00000427482;ENST00000535412;ENST00000324537;ENST00000434347	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	4.86	4.86	0.63082	BAR (3);	0.076128	0.53938	D	0.000046	T	0.81833	0.4906	M	0.82323	2.585	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.991	D;D;D	0.72075	0.976;0.967;0.962	D	0.84011	0.0348	10	0.52906	T	0.07	-38.6117	13.9656	0.64207	0.0:0.0:0.0:1.0	.	71;71;79	Q8IVP1;Q99963;Q99963-3	.;SH3G3_HUMAN;.	P	71;71;79;79	ENSP00000391372:L71P;ENSP00000439239:L71P;ENSP00000320092:L79P;ENSP00000397871:L79P	ENSP00000320092:L79P	L	+	2	0	SH3GL3	82028309	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.781000	0.62389	1.947000	0.56498	0.445000	0.29226	CTG	.	.		0.453	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027		C	84237305	T	C	84237305	3	2	175	1	0	0	0	0	1	0	0	0	14267	1580	55	2	226	2	SH3GL3	15	84237305	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	49603098	84237305	18294087	75	26373										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86198736	86198736	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ggaccgacattcttctcatgGcagtgatgtgtctctctccc	9	13	4	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr15:86198736G>T	ENST00000394518.2	+	11	4558	c.4463G>T	c.(4462-4464)gGc>gTc	p.G1488V	RP11-815J21.4_ENST00000558980.1_RNA|AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000361243.2_Missense_Mutation_p.G1488V	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1488					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						TCTTCTCATGGCAGTGATGTG	0.507																																					p.G1488V	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G4463T						.						100	86	91					15																	86198736		2202	4299	6501	SO:0001583	missense	11214	exon11			CTCATGGCAGTGA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.4463G>T	chr15.hg19:g.86198736G>T	ENSP00000378026:p.Gly1488Val	84.0	0.0		93.0	4.0	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.187682	0.78789	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000452008	T;T	0.51071	0.72;0.72	5.37	5.37	0.77165	.	.	.	.	.	T	0.68531	0.3011	M	0.65975	2.015	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.70270	-0.4918	9	0.87932	D	0	.	18.2884	0.90121	0.0:0.0:1.0:0.0	.	1488;1488;1488	Q12802-4;Q12802;Q12802-2	.;AKP13_HUMAN;.	V	1488;1488;1487;1487;128	ENSP00000354718:G1488V;ENSP00000378026:G1488V	ENSP00000354718:G1488V	G	+	2	0	AKAP13	83999740	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	4.834000	0.62774	2.808000	0.96608	0.650000	0.86243	GGC	.	.		0.507	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		T	86198736	G	T	86198736	3	4	175	1	0	0	0	0	1	0	0	0	449	1203	42	3	4501	3	AKAP13	15	86198736	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	1961431	86198736	16332656	76	26374										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88670420	88670420	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gtgtcttcttctggtttgtgGgtcacagtgataggaggtgt	15	5	4	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr15:88670420G>C	ENST00000360948.2	-	11	1427	c.1266C>G	c.(1264-1266)acC>acG	p.T422T	NTRK3_ENST00000558676.1_Silent_p.T414T|NTRK3_ENST00000355254.2_Silent_p.T422T|NTRK3_ENST00000558306.1_5'UTR|NTRK3_ENST00000540489.2_Silent_p.T422T|NTRK3_ENST00000394480.2_Silent_p.T422T|NTRK3_ENST00000557856.1_Silent_p.T414T|NTRK3_ENST00000317501.3_Silent_p.T422T|NTRK3_ENST00000542733.2_Silent_p.T324T|NTRK3_ENST00000357724.2_Silent_p.T414T	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	422					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CTGGTTTGTGGGTCACAGTGA	0.483			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.T422T		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	NTRK3_ENST00000360948,NS,haematopoietic_neoplasm,0,3	NTRK3	587	.	0			c.C1266G						.						127	108	114					15																	88670420		2201	4299	6500	SO:0001819	synonymous_variant	4916	exon12			TTTGTGGGTCACA	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1266C>G	chr15.hg19:g.88670420G>C		225.0	0.0		171.0	79.0	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	ENST00000360948.2	hg19	CCDS32322.1																																																																																			.	.		0.483	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				C	88670420	G	C	88670420	2	2	175	1	0	0	0	0	0	0	0	1	10717	1219	43	4		4	NTRK3	15	88670420	Silent	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	2471684	88670420	13860972	77	26375										
CLDN9	9080	hgsc.bcm.edu	37	chr16	3063428	3063428	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gctgggctggctggggacccTggtgtcctgcgccctgcccc	16	16	0	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr16:3063428T>C	ENST00000445369.2	+	1	972	c.65T>C	c.(64-66)cTg>cCg	p.L22P		NM_020982.3	NP_066192.1	O95484	CLD9_HUMAN	claudin 9	22					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.L22P(1)		endometrium(2)|large_intestine(1)|lung(5)|prostate(2)	10						CTGGGGACCCTGGTGTCCTGC	0.667																																					p.L22P		Atlas-SNP	.											CLDN9,NS,carcinoma,0,1	CLDN9	33	.	1	Substitution - Missense(1)	lung(1)	c.T65C						.						95	80	85					16																	3063428		2198	4300	6498	SO:0001583	missense	9080	exon1			GGACCCTGGTGTC	AJ130941	CCDS10487.1	16p13.3	2008-08-01			ENSG00000213937	ENSG00000213937		"Claudins"	2051	protein-coding gene	gene with protein product		615799				9441748, 18234789	Standard	NM_020982		Approved		uc010uwo.1	O95484	OTTHUMG00000129000	ENST00000445369.2:c.65T>C	chr16.hg19:g.3063428T>C	ENSP00000398017:p.Leu22Pro	78.0	0.0		55.0	3.0	NM_020982		Missense_Mutation	SNP	ENST00000445369.2	hg19	CCDS10487.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.101022	0.76983	.	.	ENSG00000213937	ENST00000445369	D	0.93488	-3.23	4.79	4.79	0.61399	.	0.172969	0.38605	N	0.001639	D	0.96346	0.8808	M	0.86178	2.8	0.80722	D	1	D	0.64830	0.994	D	0.66196	0.942	D	0.96773	0.9570	10	0.87932	D	0	.	12.3183	0.54971	0.0:0.0:0.0:1.0	.	22	O95484	CLD9_HUMAN	P	22	ENSP00000398017:L22P	ENSP00000398017:L22P	L	+	2	0	CLDN9	3003429	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	7.833000	0.86765	2.011000	0.59026	0.482000	0.46254	CTG	.	.		0.667	CLDN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250989.1	NM_020982		C	3063428	T	C	3063428	3	2	175	1	0	0	0	0	1	0	0	0	3494	1580	55	2	67	2	CLDN9	16	3063428	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10		3063428	87291325	78	26376										
LOC81691	81691	hgsc.bcm.edu	37	chr16	20857589	20857589	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	agcagcctggcgctggagccGgaagattggaaagctctaca	14	10	1	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr16:20857589G>T	ENST00000261377.6	+	19	2380	c.2171G>T	c.(2170-2172)cGg>cTg	p.R724L	AC004381.6_ENST00000348433.6_Missense_Mutation_p.R693L|AC004381.6_ENST00000564274.1_Missense_Mutation_p.R724L|ERI2_ENST00000564349.1_Intron	NM_001199053.1|NM_030941.2	NP_001185982.1|NP_112203.2																					CGCTGGAGCCGGAAGATTGGA	0.537																																					p.R724L		Atlas-SNP	.											.	LOC81691	41	.	0			c.G2171T						.						154	153	153					16																	20857589		2201	4300	6501	SO:0001583	missense	0	exon19			GGAGCCGGAAGAT																												ENST00000261377.6:c.2171G>T	chr16.hg19:g.20857589G>T	ENSP00000261377:p.Arg724Leu	125.0	0.0		100.0	4.0	NM_030941		Missense_Mutation	SNP	ENST00000261377.6	hg19	CCDS10591.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.858002	0.51376	.	.	ENSG00000005189	ENST00000348433;ENST00000261377	T;T	0.34859	1.34;1.83	5.63	2.19	0.27852	.	0.514477	0.19584	N	0.110790	T	0.34048	0.0884	L	0.60455	1.87	0.28485	N	0.914781	B;B	0.30973	0.302;0.242	B;B	0.31946	0.138;0.089	T	0.34875	-0.9811	10	0.72032	D	0.01	-10.7206	10.123	0.42632	0.2606:0.0:0.7394:0.0	.	693;724	Q96IC2-2;Q96IC2	.;REXON_HUMAN	L	693;724	ENSP00000261378:R693L;ENSP00000261377:R724L	ENSP00000261377:R724L	R	+	2	0	AC004381.6	20765090	0.994000	0.37717	1.000000	0.80357	0.969000	0.65631	0.836000	0.27545	0.738000	0.32606	-0.254000	0.11334	CGG	.	.		0.537	AC004381.6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254418.2			T	20857589	G	T	20857589	3	4	175	1	0	0	0	0	1	0	0	0	8899	1116	39	1	2241	1	LOC81691	16	20857589	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	17794161	20857589	69497164	79	26377										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89337284	89337284	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ggagatgaactggcgggcgtTgaaacggtcgcgcactgact	16	9	0	4			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr16:89337284T>A	ENST00000301030.4	-	12	8207	c.7747A>T	c.(7747-7749)Aac>Tac	p.N2583Y	ANKRD11_ENST00000378330.2_Missense_Mutation_p.N2583Y|AC137932.1_ENST00000602042.1_3'UTR	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2583					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TGGCGGGCGTTGAAACGGTCG	0.602																																					p.N2583Y		Atlas-SNP	.											.	ANKRD11	195	.	0			c.A7747T						.						82	66	71					16																	89337284		2198	4300	6498	SO:0001583	missense	29123	exon12			GGGCGTTGAAACG	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.7747A>T	chr16.hg19:g.89337284T>A	ENSP00000301030:p.Asn2583Tyr	85.0	0.0		68.0	33.0	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.777247	0.90195	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.53857	0.6;0.6	4.53	4.53	0.55603	.	0.000000	0.64402	D	0.000002	T	0.73621	0.3610	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78775	-0.2072	10	0.87932	D	0	.	13.8323	0.63389	0.0:0.0:0.0:1.0	.	2583	Q6UB99	ANR11_HUMAN	Y	2583	ENSP00000301030:N2583Y;ENSP00000367581:N2583Y	ENSP00000301030:N2583Y	N	-	1	0	ANKRD11	87864785	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.858000	0.86971	1.806000	0.52798	0.397000	0.26171	AAC	.	.		0.602	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89337284	T	A	89337284	3	1	175	1	0	0	0	0	1	0	0	0	639	1812	63	4	252	4	ANKRD11	16	89337284	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	68479695	89337284	1017469	80	26378										
NCOR1	9611	hgsc.bcm.edu	37	chr17	15965046	15965046	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gacctgcttctcaaattttcTtctaacctggcagcttcatg	6	12	4	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr17:15965046T>A	ENST00000268712.3	-	37	5807	c.5550A>T	c.(5548-5550)gaA>gaT	p.E1850D	NCOR1_ENST00000395851.1_Intron|NCOR1_ENST00000395857.3_Missense_Mutation_p.E434D	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1850	Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TCAAATTTTCTTCTAACCTGG	0.488																																					p.E1850D		Atlas-SNP	.											.	NCOR1	240	.	0			c.A5550T						.						84	83	84					17																	15965046		2203	4300	6503	SO:0001583	missense	9611	exon37			ATTTTCTTCTAAC	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.5550A>T	chr17.hg19:g.15965046T>A	ENSP00000268712:p.Glu1850Asp	107.0	0.0		112.0	40.0	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	16.96	3.264824	0.59431	.	.	ENSG00000141027	ENST00000268712;ENST00000395849;ENST00000395857	T;T	0.46451	0.87;0.87	5.87	4.76	0.60689	.	0.092272	0.85682	D	0.000000	T	0.46908	0.1417	L	0.36672	1.1	0.39982	D	0.974938	D;D;B;B	0.69078	0.997;0.978;0.051;0.067	D;P;B;B	0.77557	0.99;0.76;0.015;0.084	T	0.38457	-0.9660	10	0.13108	T	0.6	-11.38	8.4628	0.32938	0.0:0.1486:0.0:0.8514	.	660;1754;1850;370	B4DZ48;E7EVK1;O75376;Q86YY1	.;.;NCOR1_HUMAN;.	D	1850;1754;434	ENSP00000268712:E1850D;ENSP00000379198:E434D	ENSP00000268712:E1850D	E	-	3	2	NCOR1	15905771	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.346000	0.19997	2.247000	0.74100	0.528000	0.53228	GAA	.	.		0.488	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		A	15965046	T	A	15965046	3	1	175	1	0	0	0	0	1	0	0	0	10244	1606	56	4	1812	4	NCOR1	17	15965046	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10		15965046	65230164	81	26379										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27027983	27027983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	tcccaacgccagcccagcagCcagtggccacaccactaatg	8	18	0	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr17:27027983C>T	ENST00000314616.6	+	36	5114	c.4831C>T	c.(4831-4833)Cca>Tca	p.P1611S	SUPT6H_ENST00000347486.4_Missense_Mutation_p.P1611S	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1611					chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					AGCCCAGCAGCCAGTGGCCAC	0.587																																					p.P1611S		Atlas-SNP	.											.	SUPT6H	165	.	0			c.C4831T						.						204	208	207					17																	27027983		2203	4300	6503	SO:0001583	missense	6830	exon36			CAGCAGCCAGTGG	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.4831C>T	chr17.hg19:g.27027983C>T	ENSP00000319104:p.Pro1611Ser	106.0	0.0		135.0	43.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	hg19	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.426930	0.62733	.	.	ENSG00000109111	ENST00000314616	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.35885	0.0947	N	0.05441	-0.05	0.80722	D	1	B	0.18741	0.03	B	0.11329	0.006	T	0.35549	-0.9784	9	0.02654	T	1	-7.0448	18.8074	0.92043	0.0:1.0:0.0:0.0	.	1611	Q7KZ85	SPT6H_HUMAN	S	1611	.	ENSP00000319104:P1611S	P	+	1	0	SUPT6H	24052110	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.973000	0.76116	2.465000	0.83290	0.650000	0.86243	CCA	.	.		0.587	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27027983	C	T	27027983	3	4	175	1	0	0	0	0	1	0	0	0	15415	739	26	3	4969	3	SUPT6H	17	27027983	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	11062937	27027983	54167227	82	26380										
COL1A1	1277	hgsc.bcm.edu	37	chr17	48266329	48266329	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	catgggaccagggggaccacGttcaccacttgctccagagg	13	13	1	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr17:48266329G>T	ENST00000225964.5	-	41	3098	c.2980C>A	c.(2980-2982)Cgt>Agt	p.R994S		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	994	Triple-helical region.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	GGGGGACCACGTTCACCACTT	0.617			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.R994S		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1	158	.	0			c.C2980A						.						72	71	71					17																	48266329		2203	4300	6503	SO:0001583	missense	1277	exon41			GACCACGTTCACC	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.2980C>A	chr17.hg19:g.48266329G>T	ENSP00000225964:p.Arg994Ser	155.0	0.0		112.0	38.0	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Missense_Mutation	SNP	ENST00000225964.5	hg19	CCDS11561.1	.	.	.	.	.	.	.	.	.	.	G	17.63	3.437806	0.62955	.	.	ENSG00000108821	ENST00000225964	D	0.92965	-3.14	3.83	3.83	0.44106	.	0.066944	0.64402	D	0.000018	D	0.94361	0.8187	L	0.54965	1.715	0.58432	D	0.999999	D	0.57571	0.98	D	0.72982	0.979	D	0.94590	0.7787	10	0.56958	D	0.05	.	14.7416	0.69461	0.0:0.0:1.0:0.0	.	994	P02452	CO1A1_HUMAN	S	994	ENSP00000225964:R994S	ENSP00000225964:R994S	R	-	1	0	COL1A1	45621328	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	7.705000	0.84606	1.998000	0.58463	0.298000	0.19748	CGT	.	.		0.617	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			T	48266329	G	T	48266329	3	4	175	1	0	0	0	0	1	0	0	0	3679	1145	40	1	1458	1	COL1A1	17	48266329	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	21238346	48266329	32928881	83	26381										
SOCS3	9021	hgsc.bcm.edu	37	chr17	76354878	76354878	+	Frame_Shift_Del	DEL	C	C	-													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cgctctgcagagagaagctgCccccctcacactggatgcgc							TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr17:76354878delC	ENST00000330871.2	-	2	714	c.299delG	c.(298-300)ggcfs	p.G100fs	RP11-806H10.4_ENST00000592569.1_lincRNA	NM_003955.3	NP_003946.3	O14543	SOCS3_HUMAN	suppressor of cytokine signaling 3	100	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase activity (GO:0006469)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|spongiotrophoblast differentiation (GO:0060708)|trophoblast giant cell differentiation (GO:0060707)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)	protein kinase inhibitor activity (GO:0004860)			kidney(1)|lung(2)|ovary(1)|pancreas(1)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(99;0.000688)|OV - Ovarian serous cystadenocarcinoma(97;0.0554)			AGAGAAGCTGCCCCCCTCACA	0.647																																					p.G100fs		Atlas-INDEL	.											.	SOCS3	16	.	0			c.300delC						.						37	36	36					17																	76354878		2202	4300	6502	SO:0001589	frameshift_variant	9021	exon2			.	AB004904	CCDS11756.1	17q25.3	2014-09-17						"Suppressors of cytokine signaling", "SH2 domain containing"	19391	protein-coding gene	gene with protein product		604176				9266833, 9344848	Standard	NM_003955		Approved	SSI-3, CIS3, SOCS-3, Cish3	uc002jvl.2	O14543		ENST00000330871.2:c.299delG	chr17.hg19:g.76354878delC	ENSP00000330341:p.Gly100fs	118.0	0.0		109.0	37.0	NM_003955	O14509	Frame_Shift_Del	DEL	ENST00000330871.2	hg19	CCDS11756.1																																																																																			.	.		0.647	SOCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437300.1			-	76354878	C	-	76354878	7	5	175	1	0	1	0	1	0	0	0	0	14930	739	26	0	382	0	SOCS3	17	76354878	Frame_Shift_Del	DEL	C	TCGA-DD-AACY-01A-11D-A40R-10	28088549	76354878	4840332	84	26382										
CARD14	79092	hgsc.bcm.edu	37	chr17	78164640	78164640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gatggcctgccaactctacaGggagaaggtgaatgcgctgc	14	10	1	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr17:78164640G>A	ENST00000573882.1	+	9	1567	c.1031G>A	c.(1030-1032)aGg>aAg	p.R344K	CARD14_ENST00000570421.1_Missense_Mutation_p.R344K|CARD14_ENST00000573754.1_3'UTR|CARD14_ENST00000344227.2_Missense_Mutation_p.R344K|CARD14_ENST00000392434.2_Missense_Mutation_p.R107K			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	344					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CAACTCTACAGGGAGAAGGTG	0.602																																					p.R344K		Atlas-SNP	.											.	CARD14	98	.	0			c.G1031A						.						84	80	81					17																	78164640		2203	4300	6503	SO:0001583	missense	79092	exon7			TCTACAGGGAGAA	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"psoriasis susceptibility 2"	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.1031G>A	chr17.hg19:g.78164640G>A	ENSP00000458715:p.Arg344Lys	87.0	0.0		66.0	17.0	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	hg19	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	g	4.604	0.112208	0.08831	.	.	ENSG00000141527	ENST00000344227;ENST00000392434;ENST00000309710	T;T	0.30714	1.52;1.52	4.26	-2.37	0.06643	.	0.243825	0.40640	N	0.001060	T	0.06962	0.0177	N	0.00793	-1.18	0.21020	N	0.999803	B;B;B	0.12630	0.001;0.006;0.0	B;B;B	0.10450	0.001;0.005;0.001	T	0.33059	-0.9883	10	0.02654	T	1	-15.8856	10.8681	0.46866	0.4696:0.0:0.5304:0.0	.	344;107;344	B8QQJ3;E7ETJ2;Q9BXL6	.;.;CAR14_HUMAN	K	344;107;107	ENSP00000344549:R344K;ENSP00000376229:R107K	ENSP00000308507:R107K	R	+	2	0	CARD14	75779235	1.000000	0.71417	0.668000	0.29813	0.296000	0.27459	0.804000	0.27098	-0.970000	0.03569	-0.310000	0.09108	AGG	.	.		0.602	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1			A	78164640	G	A	78164640	3	1	175	1	0	0	0	0	1	0	0	0	2648	1000	35	3	1053	3	CARD14	17	78164640	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	1809762	78164640	3030570	85	26383										
OSBPL1A	114876	hgsc.bcm.edu	37	chr18	21758132	21758132	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gggtgatggctgacctgttcGgagatgagtctaaatccaag	14	7	1	4	rs539256061	byFrequency	TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr18:21758132G>T	ENST00000319481.3	-	21	2144	c.1938C>A	c.(1936-1938)tcC>tcA	p.S646S	OSBPL1A_ENST00000357041.4_Silent_p.S264S|OSBPL1A_ENST00000399443.3_Silent_p.S133S	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	646					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					TGACCTGTTCGGAGATGAGTC	0.323																																					p.S646S		Atlas-SNP	.											.	OSBPL1A	94	.	0			c.C1938A						.						125	117	119					18																	21758132		2203	4300	6503	SO:0001819	synonymous_variant	114876	exon21			CTGTTCGGAGATG	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"Oxysterol binding proteins", "Ankyrin repeat domain containing"	16398	protein-coding gene	gene with protein product		606730	"oxysterol binding protein-like 1B"	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.1938C>A	chr18.hg19:g.21758132G>T		107.0	0.0		94.0	36.0	NM_080597	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	hg19	CCDS11884.1																																																																																			.	.		0.323	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		T	21758132	G	T	21758132	2	4	175	1	0	0	0	0	0	0	0	1	11286	1103	39	1		1	OSBPL1A	18	21758132	Silent	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10		21758132	56319116	86	26384										
CCDC102B	79839	hgsc.bcm.edu	37	chr18	66678323	66678323	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gaagaactaaagcagggactCaatcaaaaagaagatgaggt	11	5	2	4			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr18:66678323C>T	ENST00000360242.5	+	7	1533	c.1416C>T	c.(1414-1416)ctC>ctT	p.L472L	CCDC102B_ENST00000584156.1_Silent_p.L472L|CCDC102B_ENST00000319445.6_Silent_p.L472L	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	472										breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				AGCAGGGACTCAATCAAAAAG	0.363																																					p.L472L		Atlas-SNP	.											.	CCDC102B	92	.	0			c.C1416T						.						97	94	95					18																	66678323		2203	4300	6503	SO:0001819	synonymous_variant	79839	exon9			GGGACTCAATCAA	AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 14", "aminoacylase 1-like"	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.1416C>T	chr18.hg19:g.66678323C>T		263.0	0.0		329.0	22.0	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Silent	SNP	ENST00000360242.5	hg19	CCDS11996.2																																																																																			.	.		0.363	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781		T	66678323	C	T	66678323	2	4	175	1	0	0	0	0	0	0	0	1	2739	813	29	3		3	CCDC102B	18	66678323	Silent	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	44920191	66678323	11398925	87	26385										
MYO1F	4542	hgsc.bcm.edu	37	chr19	8587279	8587279	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	accttccatgaggatctcaaTgacctcgttcacgttgaagc	8	12	2	3			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr19:8587279T>C	ENST00000338257.8	-	27	3469	c.3202A>G	c.(3202-3204)Att>Gtt	p.I1068V		NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	1068	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						AGGATCTCAATGACCTCGTTC	0.612																																					p.I1068V		Atlas-SNP	.											.	MYO1F	128	.	0			c.A3202G						.						69	71	71					19																	8587279		2124	4232	6356	SO:0001583	missense	4542	exon27			TCTCAATGACCTC	X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"Myosins / Myosin superfamily : Class I"	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.3202A>G	chr19.hg19:g.8587279T>C	ENSP00000344871:p.Ile1068Val	45.0	0.0		43.0	23.0	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	hg19	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	T	12.20	1.866854	0.32977	.	.	ENSG00000142347	ENST00000338257	T	0.56444	0.46	5.5	5.5	0.81552	Src homology-3 domain (5);	.	.	.	.	T	0.40570	0.1122	L	0.27944	0.81	0.48040	D	0.999574	B	0.17268	0.021	B	0.24541	0.054	T	0.24048	-1.0171	9	0.15499	T	0.54	.	14.7786	0.69749	0.0:0.0:0.0:1.0	.	1068	O00160	MYO1F_HUMAN	V	1068	ENSP00000344871:I1068V	ENSP00000344871:I1068V	I	-	1	0	MYO1F	8493279	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	2.515000	0.45512	2.078000	0.62432	0.528000	0.53228	ATT	.	.		0.612	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			C	8587279	T	C	8587279	3	2	175	1	0	0	0	0	1	0	0	0	10082	1464	51	2	102	2	MYO1F	19	8587279	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10		8587279	50541704	88	26386										
PSMD8	5714	hgsc.bcm.edu	37	chr19	38867017	38867017	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	atactggagatcggggcccaAtggagcatcctacgcaagga	13	10	0	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr19:38867017A>T	ENST00000215071.4	+	3	525	c.459A>T	c.(457-459)caA>caT	p.Q153H	PSMD8_ENST00000592035.1_De_novo_Start_OutOfFrame|PSMD8_ENST00000602911.1_Missense_Mutation_p.Q90H	NM_002812.4	NP_002803.2	P48556	PSMD8_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	153					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(1)	6	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCGGGGCCCAATGGAGCATCC	0.557																																					p.Q153H		Atlas-SNP	.											.	PSMD8	31	.	0			c.A459T						.						55	46	49					19																	38867017		2162	4217	6379	SO:0001583	missense	5714	exon3			GGCCCAATGGAGC	D38047	CCDS12515.2	19q13.2	2009-05-07			ENSG00000099341	ENSG00000099341		"Proteasome (prosome, macropain) subunits"	9566	protein-coding gene	gene with protein product						7621825	Standard	NM_002812		Approved	S14, Nin1p, p31, HIP6, HYPF, Rpn12	uc002oii.4	P48556	OTTHUMG00000150691	ENST00000215071.4:c.459A>T	chr19.hg19:g.38867017A>T	ENSP00000215071:p.Gln153His	125.0	0.0		93.0	43.0	NM_002812	B4DX18|Q6P1L7	Missense_Mutation	SNP	ENST00000215071.4	hg19	CCDS12515.2	.	.	.	.	.	.	.	.	.	.	A	14.73	2.624068	0.46840	.	.	ENSG00000099341	ENST00000215071	.	.	.	4.44	-0.413	0.12363	.	0.200805	0.43260	D	0.000593	T	0.47248	0.1435	M	0.70595	2.14	0.80722	D	1	B	0.31318	0.319	B	0.27608	0.081	T	0.29305	-1.0016	9	0.21014	T	0.42	-22.6106	8.1873	0.31346	0.3854:0.0:0.6146:0.0	.	153	P48556	PSMD8_HUMAN	H	153	.	ENSP00000215071:Q153H	Q	+	3	2	PSMD8	43558857	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.346000	0.44027	0.180000	0.19960	-0.546000	0.04227	CAA	.	.		0.557	PSMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319627.1	NM_002812		T	38867017	A	T	38867017	3	4	175	1	0	0	0	0	1	0	0	0	12716	98	4	4	469	4	PSMD8	19	38867017	Missense_Mutation	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	30279738	38867017	20261966	89	26387										
PRKD2	25865	hgsc.bcm.edu	37	chr19	47200429	47200429	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cttaccttatagtatctgttGgtcgtgttgttctggaagag	11	6	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr19:47200429G>A	ENST00000291281.4	-	9	1527	c.1302C>T	c.(1300-1302)acC>acT	p.T434T	PRKD2_ENST00000601806.1_Silent_p.T277T|PRKD2_ENST00000600194.1_Silent_p.T277T|PRKD2_ENST00000433867.1_Silent_p.T434T|PRKD2_ENST00000595515.1_Silent_p.T434T			Q9BZL6	KPCD2_HUMAN	protein kinase D2	434	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		AGTATCTGTTGGTCGTGTTGT	0.542																																					p.T434T		Atlas-SNP	.											.	PRKD2	94	.	0			c.C1302T						.						147	119	129					19																	47200429		2203	4300	6503	SO:0001819	synonymous_variant	25865	exon9			TCTGTTGGTCGTG	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"Pleckstrin homology (PH) domain containing"	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.1302C>T	chr19.hg19:g.47200429G>A		83.0	0.0		60.0	29.0	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Silent	SNP	ENST00000291281.4	hg19	CCDS12689.1																																																																																			.	.		0.542	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		A	47200429	G	A	47200429	2	1	175	1	0	0	0	0	0	0	0	1	12531	1335	47	3		3	PRKD2	19	47200429	Silent	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	8333412	47200429	11928554	90	26388										
ZNF808	388558	hgsc.bcm.edu	37	chr19	53056997	53056997	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	cacaagcaataccttgcatgCcatcgtagatgtcacactgg	8	12	1	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr19:53056997C>G	ENST00000359798.4	+	5	1008	c.828C>G	c.(826-828)tgC>tgG	p.C276W		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	276					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		ACCTTGCATGCCATCGTAGAT	0.403																																					p.C276W		Atlas-SNP	.											.	ZNF808	81	.	0			c.C828G						.						173	170	171					19																	53056997		2203	4300	6503	SO:0001583	missense	388558	exon5			TGCATGCCATCGT	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.828C>G	chr19.hg19:g.53056997C>G	ENSP00000352846:p.Cys276Trp	149.0	0.0		121.0	40.0	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	hg19	CCDS46167.1	.	.	.	.	.	.	.	.	.	.	.	2.830	-0.242815	0.05906	.	.	ENSG00000198482	ENST00000359798	T	0.07444	3.19	1.53	-3.06	0.05379	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03263	0.0095	N	0.04880	-0.145	0.21473	N	0.999674	B	0.19200	0.034	B	0.21546	0.035	T	0.40515	-0.9559	9	0.62326	D	0.03	.	0.5512	0.00662	0.3021:0.3162:0.1406:0.2411	.	276	Q8N4W9	ZN808_HUMAN	W	276	ENSP00000352846:C276W	ENSP00000352846:C276W	C	+	3	2	ZNF808	57748809	0.848000	0.29623	0.000000	0.03702	0.005000	0.04900	0.516000	0.22817	-1.723000	0.01375	0.298000	0.19748	TGC	.	.		0.403	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		G	53056997	C	G	53056997	3	3	175	1	0	0	0	0	1	0	0	0	18188	747	26	4	838	4	ZNF808	19	53056997	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	5856568	53056997	6071986	91	26389										
ZNF83	55769	hgsc.bcm.edu	37	chr19	53117612	53117612	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	caaaattacattcatatgtaTgagaaatgtgggttttgaca	8	4	1	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr19:53117612T>G	ENST00000597597.1	-	2	2459	c.206A>C	c.(205-207)cAt>cCt	p.H69P	ZNF83_ENST00000301096.3_Missense_Mutation_p.H69P|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000536937.1_Missense_Mutation_p.H69P|ZNF83_ENST00000541777.2_Missense_Mutation_p.H69P|ZNF83_ENST00000545872.1_Missense_Mutation_p.H69P|ZNF83_ENST00000391789.4_Missense_Mutation_p.H69P|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000544146.1_Missense_Mutation_p.H69P			P51522	ZNF83_HUMAN	zinc finger protein 83	69					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		TTCATATGTATGAGAAATGTG	0.348																																					p.H69P		Atlas-SNP	.											.	ZNF83	73	.	0			c.A206C						.						74	76	76					19																	53117612		2203	4300	6503	SO:0001583	missense	55769	exon3			TATGTATGAGAAA	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"Zinc fingers, C2H2-type"	13158	protein-coding gene	gene with protein product		194558	"zinc finger protein 83 (HPF1)", "zinc finger protein 816B"	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.206A>C	chr19.hg19:g.53117612T>G	ENSP00000472619:p.His69Pro	137.0	0.0		137.0	54.0	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Missense_Mutation	SNP	ENST00000597597.1	hg19	CCDS12854.1	.	.	.	.	.	.	.	.	.	.	t	8.428	0.847877	0.17034	.	.	ENSG00000167766	ENST00000536937;ENST00000301096;ENST00000544146;ENST00000434535;ENST00000545872;ENST00000541777;ENST00000391789	T;T;T;T;T;T	0.08720	3.07;3.07;3.07;3.07;3.07;3.06	1.87	1.87	0.25490	.	.	.	.	.	T	0.07234	0.0183	L	0.41079	1.255	0.09310	N	1	P;D	0.54601	0.908;0.967	B;B	0.40329	0.211;0.326	T	0.31696	-0.9934	9	0.52906	T	0.07	.	7.4344	0.27148	0.0:0.0:0.0:1.0	.	69;69	P51522-2;P51522	.;ZNF83_HUMAN	P	69	ENSP00000445993:H69P;ENSP00000301096:H69P;ENSP00000445470:H69P;ENSP00000440713:H69P;ENSP00000439681:H69P;ENSP00000375666:H69P	ENSP00000301096:H69P	H	-	2	0	ZNF83	57809424	0.011000	0.17503	0.011000	0.14972	0.049000	0.14656	2.251000	0.43187	1.099000	0.41499	0.482000	0.46254	CAT	.	.		0.348	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300		G	53117612	T	G	53117612	3	3	175	1	0	0	0	0	1	0	0	0	18198	1464	51	5	1348	5	ZNF83	19	53117612	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	60615	53117612	6011371	92	26390										
CENPB	1059	hgsc.bcm.edu	37	chr20	3765921	3765921	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ctcctcctcttcctctccctCactcttgagggaagtggtga	8	15	4	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr20:3765921C>G	ENST00000379751.4	-	1	1416	c.1210G>C	c.(1210-1212)Gag>Cag	p.E404Q	CDC25B_ENST00000379598.5_5'Flank|CDC25B_ENST00000344256.6_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	404	Glu-rich (acidic).				regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)	centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|satellite DNA binding (GO:0003696)|sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(2)|lung(4)|skin(1)	8						tcctctccctcACTCTTGAGG	0.617																																					p.E404Q		Atlas-SNP	.											.	CENPB	24	.	0			c.G1210C						.						35	30	32					20																	3765921		2203	4299	6502	SO:0001583	missense	1059	exon1			CTCCCTCACTCTT	X05299	CCDS13064.1	20p13	2013-11-05	2002-08-29		ENSG00000125817	ENSG00000125817			1852	protein-coding gene	gene with protein product		117140	"centromere protein B (80kD)"			8406460, 11884609	Standard	NM_001810		Approved		uc002wjk.3	P07199	OTTHUMG00000031761	ENST00000379751.4:c.1210G>C	chr20.hg19:g.3765921C>G	ENSP00000369075:p.Glu404Gln	47.0	0.0		34.0	12.0	NM_001810	Q96EI4	Missense_Mutation	SNP	ENST00000379751.4	hg19	CCDS13064.1	.	.	.	.	.	.	.	.	.	.	c	12.59	1.983988	0.35036	.	.	ENSG00000125817	ENST00000379751	T	0.07444	3.19	4.47	4.47	0.54385	.	.	.	.	.	T	0.07234	0.0183	N	0.14661	0.345	0.27748	N	0.944252	P	0.51057	0.941	P	0.46389	0.515	T	0.27468	-1.0073	9	0.19590	T	0.45	-3.4795	12.6378	0.56692	0.0:1.0:0.0:0.0	.	404	P07199	CENPB_HUMAN	Q	404	ENSP00000369075:E404Q	ENSP00000369075:E404Q	E	-	1	0	CENPB	3713921	0.923000	0.31300	0.998000	0.56505	0.883000	0.51084	1.661000	0.37408	2.019000	0.59389	0.550000	0.68814	GAG	.	.		0.617	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810		G	3765921	C	G	3765921	3	3	175	1	0	0	0	0	1	0	0	0	3229	835	29	4	593	4	CENPB	20	3765921	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10		3765921	59259599	93	26391										
MKKS	8195	hgsc.bcm.edu	37	chr20	10393869	10393869	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	ttttcaatcaggttgcagcaAagaatagctgtgaataagcc	9	7	2	2			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr20:10393869A>C	ENST00000347364.3	-	3	1056	c.294T>G	c.(292-294)ctT>ctG	p.L98L	MKKS_ENST00000399054.2_Silent_p.L98L	NM_170784.2	NP_740754.1	Q9NPJ1	MKKS_HUMAN	McKusick-Kaufman syndrome	98					artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|chaperone-mediated protein complex assembly (GO:0051131)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|determination of left/right symmetry (GO:0007368)|fat cell differentiation (GO:0045444)|gonad development (GO:0008406)|heart development (GO:0007507)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of multicellular organism growth (GO:0040018)|protein folding (GO:0006457)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sensory perception of smell (GO:0007608)|social behavior (GO:0035176)|spermatid development (GO:0007286)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|stomach(2)	16						GGTTGCAGCAAAGAATAGCTG	0.393																																					p.L98L	Melanoma(79;1979 2212 6640)	Atlas-SNP	.											.	MKKS	35	.	0			c.T294G						.						123	113	116					20																	10393869		2203	4300	6503	SO:0001819	synonymous_variant	8195	exon3			GCAGCAAAGAATA	AF221993	CCDS13111.1	20p12	2013-01-08			ENSG00000125863	ENSG00000125863		"Heat Shock Proteins / Chaperonins"	7108	protein-coding gene	gene with protein product		604896		BBS6		9467007	Standard	NR_072977		Approved		uc002wnu.2	Q9NPJ1	OTTHUMG00000031868	ENST00000347364.3:c.294T>G	chr20.hg19:g.10393869A>C		113.0	0.0		84.0	30.0	NM_170784	A8K7B0|D3DW18	Silent	SNP	ENST00000347364.3	hg19	CCDS13111.1																																																																																			.	.		0.393	MKKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077991.3			C	10393869	A	C	10393869	2	2	175	1	0	0	0	0	0	0	0	1	9609	1	1	5		5	MKKS	20	10393869	Silent	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	6627948	10393869	52631651	94	26392										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33345769	33345769	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gttgttgttgctgctgctgcTgcagctggggaaaattagct	14	7	0	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr20:33345769T>A	ENST00000374796.2	-	8	3352	c.782A>T	c.(781-783)cAg>cTg	p.Q261L	NCOA6_ENST00000359003.2_Missense_Mutation_p.Q261L			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	261	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						ctgctgctgctgcagctgGGG	0.527																																					p.Q261L		Atlas-SNP	.											.	NCOA6	219	.	0			c.A782T						.						56	51	53					20																	33345769		2203	4300	6503	SO:0001583	missense	23054	exon7			TGCTGCTGCAGCT	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.782A>T	chr20.hg19:g.33345769T>A	ENSP00000363929:p.Gln261Leu	71.0	0.0		78.0	4.0	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	hg19	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	13.16	2.153279	0.38021	.	.	ENSG00000198646	ENST00000374796;ENST00000359003;ENST00000397675	T;T	0.33654	1.4;1.4	5.11	3.94	0.45596	.	.	.	.	.	T	0.26412	0.0645	L	0.27053	0.805	0.47659	D	0.999484	B;B	0.18741	0.003;0.03	B;B	0.17722	0.005;0.019	T	0.08207	-1.0733	9	0.49607	T	0.09	-2.628	11.6071	0.51039	0.0:0.0:0.1488:0.8512	.	261;261	F6M2K2;Q14686	.;NCOA6_HUMAN	L	261;261;218	ENSP00000363929:Q261L;ENSP00000351894:Q261L	ENSP00000351894:Q261L	Q	-	2	0	NCOA6	32809430	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	2.842000	0.48230	1.930000	0.55929	0.383000	0.25322	CAG	.	.		0.527	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		A	33345769	T	A	33345769	3	1	175	1	0	0	0	0	1	0	0	0	10242	1580	55	4	5445	4	NCOA6	20	33345769	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	22951900	33345769	29679751	95	26393										
CABIN1	23523	hgsc.bcm.edu	37	chr22	24515513	24515539	+	In_Frame_Del	DEL	CCCCAGGGGCTGCCGGCTGGTGCTGAG	CCCCAGGGGCTGCCGGCTGGTGCTGAG	-													0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	caggggagccagtggccttcCcccaggggctgccggctggt					rs200130091|rs200593206	byFrequency	TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	CCCCAGGGGCTGCCGGCTGGTGCTGAG	CCCCAGGGGCTGCCGGCTGGTGCTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr22:24515513_24515539delCCCCAGGGGCTGCCGGCTGGTGCTGAG	ENST00000398319.2	+	28	4865_4891	c.4480_4506delCCCCAGGGGCTGCCGGCTGGTGCTGAG	c.(4480-4506)ccccaggggctgccggctggtgctgagdel	p.PQGLPAGAE1494del	CABIN1_ENST00000405822.2_In_Frame_Del_p.PQGLPAGAE1415del|CABIN1_ENST00000263119.5_In_Frame_Del_p.PQGLPAGAE1494del	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1494					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.P1498Q(1)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AGTGGCCTTCCCCCAGGGGCTGCCGGCTGGTGCTGAGGAGCAGCGGC	0.648																																					p.1493_1502del		Atlas-INDEL	.											.	CABIN1	153	.	1	Substitution - Missense(1)	lung(1)	c.4479_4505del						.																																			SO:0001651	inframe_deletion	23523	exon28			.	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.4480_4506delCCCCAGGGGCTGCCGGCTGGTGCTGAG	chr22.hg19:g.24515513_24515539delCCCCAGGGGCTGCCGGCTGGTGCTGAG	ENSP00000381364:p.Pro1494_Glu1502del	91.0	0.0		62.0	12.0	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	In_Frame_Del	DEL	ENST00000398319.2	hg19	CCDS13823.1																																																																																			.	.		0.648	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		-	24515539	CCCCAGGGGCTGCCGGCTGGTGCTGAG	-	24515513	7	5	175	1	0	1	0	1	0	0	0	0	2530	623	22	0	4586	0	CABIN1	22	24515513	In_Frame_Del	DEL	CCCCAGGGGCTGCCGGCTGGTGCTGAG	TCGA-DD-AACY-01A-11D-A40R-10		24515513	26789053	96	26394										
TBC1D10A	83874	hgsc.bcm.edu	37	chr22	30690978	30690978	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gcggcaatgggcgcctgggcCtggcagtagccctcctcggg	17	14	0	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr22:30690978C>A	ENST00000215790.7	-	5	755	c.591G>T	c.(589-591)caG>caT	p.Q197H	TBC1D10A_ENST00000403477.3_Missense_Mutation_p.Q204H|RP1-130H16.18_ENST00000447976.1_Missense_Mutation_p.Q71H|TBC1D10A_ENST00000403362.1_Missense_Mutation_p.Q109H	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	197	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.	Glutamine finger. {ECO:0000250}.			activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)			cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						GCGCCTGGGCCTGGCAGTAGC	0.677																																					p.Q204H		Atlas-SNP	.											.	TBC1D10A	49	.	0			c.G612T						.						66	68	67					22																	30690978		2203	4300	6503	SO:0001583	missense	83874	exon5			CTGGGCCTGGCAG	AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"EBP50-PDZ interactor of 64 kD"	610020	"TBC1 domain family, member 10"	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.591G>T	chr22.hg19:g.30690978C>A	ENSP00000215790:p.Gln197His	102.0	0.0		103.0	24.0	NM_001204240	B3KXT8|O76053|Q20WK7|Q543A2	Missense_Mutation	SNP	ENST00000215790.7	hg19	CCDS13874.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.844758	0.71603	.	.	ENSG00000248751;ENSG00000099992;ENSG00000099992;ENSG00000099992;ENSG00000099992	ENST00000434291;ENST00000215790;ENST00000403477;ENST00000403362;ENST00000393906	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	4.33	2.25	0.28309	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.56804	0.2010	H	0.98256	4.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.998;0.999	T	0.61667	-0.7016	10	0.87932	D	0	.	7.2311	0.26043	0.0:0.7203:0.0:0.2797	.	197;204;197;197	Q20WK7;B3KXT8;Q9BXI6;A7E244	.;.;TB10A_HUMAN;.	H	71;197;204;109;109	ENSP00000401535:Q71H;ENSP00000215790:Q197H;ENSP00000384996:Q204H;ENSP00000385050:Q109H;ENSP00000377484:Q109H	ENSP00000331267:Q58H	Q	-	3	2	TBC1D10A;RP1-130H16.18	29020978	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.188000	0.50958	0.588000	0.29660	0.561000	0.74099	CAG	.	.		0.677	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937		A	30690978	C	A	30690978	3	1	175	1	0	0	0	0	1	0	0	0	15613	680	24	3	955	3	TBC1D10A	22	30690978	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10	6175465	30690978	20613588	97	26395										
HMOX1	3162	hgsc.bcm.edu	37	chr22	35782898	35782898	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	gaagcggctccacgaggtggGgcgcacagagcccgagctgc	17	13	0	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr22:35782898G>T	ENST00000216117.8	+	3	704	c.365G>T	c.(364-366)gGg>gTg	p.G122V		NM_002133.2	NP_002124.1	P09601	HMOX1_HUMAN	heme oxygenase (decycling) 1	122					angiogenesis (GO:0001525)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to cadmium ion (GO:0071276)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient (GO:0031670)|endothelial cell proliferation (GO:0001935)|erythrocyte homeostasis (GO:0034101)|excretion (GO:0007588)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|iron ion homeostasis (GO:0055072)|low-density lipoprotein particle clearance (GO:0034383)|negative regulation of DNA binding (GO:0043392)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smooth muscle cell proliferation (GO:0048662)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|protein homooligomerization (GO:0051260)|regulation of angiogenesis (GO:0045765)|regulation of blood pressure (GO:0008217)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to estrogen (GO:0043627)|response to hydrogen peroxide (GO:0042542)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|smooth muscle hyperplasia (GO:0014806)|transmembrane transport (GO:0055085)|wound healing involved in inflammatory response (GO:0002246)	caveola (GO:0005901)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)|phospholipase D activity (GO:0004630)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16					Vitamin E(DB00163)	CACGAGGTGGGGCGCACAGAG	0.657																																					p.G122V		Atlas-SNP	.											.	HMOX1	32	.	0			c.G365T						.						40	45	43					22																	35782898		2203	4300	6503	SO:0001583	missense	3162	exon3			AGGTGGGGCGCAC		CCDS13914.1	22q12	2003-10-13			ENSG00000100292	ENSG00000100292	1.14.99.3		5013	protein-coding gene	gene with protein product		141250				10591208	Standard	NM_002133		Approved	bK286B10, HO-1	uc003ant.2	P09601	OTTHUMG00000150960	ENST00000216117.8:c.365G>T	chr22.hg19:g.35782898G>T	ENSP00000216117:p.Gly122Val	95.0	0.0		77.0	7.0	NM_002133		Missense_Mutation	SNP	ENST00000216117.8	hg19	CCDS13914.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.368475	0.61513	.	.	ENSG00000100292	ENST00000412893;ENST00000216117	T;T	0.22134	1.97;1.97	5.8	4.78	0.61160	Haem oxygenase-like, multi-helical (2);	0.000000	0.85682	D	0.000000	T	0.47116	0.1428	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.52049	-0.8627	10	0.87932	D	0	-59.5041	16.231	0.82343	0.0:0.0:0.8659:0.1341	.	122	P09601	HMOX1_HUMAN	V	122	ENSP00000413316:G122V;ENSP00000216117:G122V	ENSP00000216117:G122V	G	+	2	0	HMOX1	34112898	1.000000	0.71417	0.991000	0.47740	0.138000	0.21146	9.746000	0.98859	1.448000	0.47680	-0.181000	0.13052	GGG	.	.		0.657	HMOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320657.1			T	35782898	G	T	35782898	3	4	175	1	0	0	0	0	1	0	0	0	7252	1232	43	3	375	3	HMOX1	22	35782898	Missense_Mutation	SNP	G	TCGA-DD-AACY-01A-11D-A40R-10	5091920	35782898	15521668	98	26396										
TOB2	10766	hgsc.bcm.edu	37	chr22	41833266	41833266	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	agccgctctagctcctccccAaacaggtctgcccggcgccg	10	19	2	0			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chr22:41833266A>G	ENST00000327492.3	-	2	790	c.84T>C	c.(82-84)ttT>ttC	p.F28F		NM_016272.3	NP_057356.1	Q14106	TOB2_HUMAN	transducer of ERBB2, 2	28					female gamete generation (GO:0007292)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ossification (GO:0045778)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10						GCTCCTCCCCAAACAGGTCTG	0.537																																					p.F28F		Atlas-SNP	.											.	TOB2	30	.	0			c.T84C						.						35	39	38					22																	41833266		2203	4300	6503	SO:0001819	synonymous_variant	10766	exon2			CTCCCCAAACAGG	D64109	CCDS14015.1	22q13.2	2010-02-26			ENSG00000183864	ENSG00000183864			11980	protein-coding gene	gene with protein product		607396		TROB2		10602502, 10591208	Standard	XM_005261315		Approved	TOBL, TOB4, bK223H9	uc003azz.1	Q14106	OTTHUMG00000150970	ENST00000327492.3:c.84T>C	chr22.hg19:g.41833266A>G		110.0	0.0		51.0	20.0	NM_016272	Q6FHR7|Q6PIT9|Q9BY97|Q9UBI0	Silent	SNP	ENST00000327492.3	hg19	CCDS14015.1																																																																																			.	.		0.537	TOB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320699.1	NM_016272		G	41833266	A	G	41833266	2	3	175	1	0	0	0	0	0	0	0	1	16363	127	5	2		2	TOB2	22	41833266	Silent	SNP	A	TCGA-DD-AACY-01A-11D-A40R-10	6050368	41833266	9471300	99	26397										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3240425	3240425	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	agacatactgctcattatacCcagtgtggagtcaggcaaag	10	9	2	1			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chrX:3240425C>T	ENST00000217939.6	-	5	3455	c.3301G>A	c.(3301-3303)Ggt>Agt	p.G1101S		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1101						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CTCATTATACCCAGTGTGGAG	0.498																																					p.G1101S		Atlas-SNP	.											.	MXRA5	815	.	0			c.G3301A						.						122	96	105					X																	3240425		2203	4300	6503	SO:0001583	missense	25878	exon5			TTATACCCAGTGT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.3301G>A	chrX.hg19:g.3240425C>T	ENSP00000217939:p.Gly1101Ser	82.0	0.0		60.0	4.0	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	c	1.681	-0.506384	0.04231	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.61627	0.09	2.85	0.366	0.16136	.	1.602580	0.04155	N	0.322097	T	0.37892	0.1020	N	0.19112	0.55	0.09310	N	1	B	0.28026	0.198	B	0.22386	0.039	T	0.14811	-1.0459	10	0.15499	T	0.54	.	5.5411	0.17038	0.0:0.4703:0.0:0.5297	.	1101	Q9NR99	MXRA5_HUMAN	S	1101	ENSP00000217939:G1101S	ENSP00000217939:G1101S	G	-	1	0	MXRA5	3250425	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.788000	0.04614	0.242000	0.21303	0.519000	0.50382	GGT	.	.		0.498	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3240425	C	T	3240425	3	4	175	1	0	0	0	0	1	0	0	0	10012	623	22	3	5197	3	MXRA5	23	3240425	Missense_Mutation	SNP	C	TCGA-DD-AACY-01A-11D-A40R-10		3240425	152030135	100	26398										
THOC2	57187	hgsc.bcm.edu	37	chrX	122772802	122772802	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.06	6	1	1.58681875792142	0.892585551330799	1.87912747648589	0.102564102564103	0.617038875103394	0	tacaggccaagacatcataaTtcagtgaagtgaggtatttc	9	7	2	3			TCGA-DD-AACY-01A-11D-A40R-10	TCGA-DD-AACY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b7cb238c-7b7f-41e9-acc4-2173a66c4f20	96563036-f486-49db-9442-d334ebc044a9	g.chrX:122772802T>G	ENST00000245838.8	-	17	1854	c.1823A>C	c.(1822-1824)aAt>aCt	p.N608T	THOC2_ENST00000355725.4_Missense_Mutation_p.N608T|THOC2_ENST00000491737.1_Missense_Mutation_p.N493T	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	608					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						GACATCATAATTCAGTGAAGT	0.299																																					p.N608T		Atlas-SNP	.											.	THOC2	310	.	0			c.A1823C						.						205	190	195					X																	122772802		1839	4079	5918	SO:0001583	missense	57187	exon17			TCATAATTCAGTG	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.1823A>C	chrX.hg19:g.122772802T>G	ENSP00000245838:p.Asn608Thr	192.0	0.0		147.0	113.0	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	hg19	CCDS43988.1	.	.	.	.	.	.	.	.	.	.	T	12.47	1.947656	0.34377	.	.	ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737;ENST00000408933	.	.	.	5.74	5.74	0.90152	THO complex, subunitTHOC2, N-terminal (1);	0.000000	0.64402	D	0.000001	T	0.26122	0.0637	N	0.01048	-1.04	0.54753	D	0.99998	B;B	0.21452	0.03;0.056	B;B	0.23275	0.045;0.038	T	0.16837	-1.0389	9	0.31617	T	0.26	-20.6516	15.049	0.71850	0.0:0.0:0.0:1.0	.	533;608	B4DKZ6;Q8NI27	.;THOC2_HUMAN	T	608;608;493;533	.	ENSP00000245838:N608T	N	-	2	0	THOC2	122600483	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	5.033000	0.64146	1.936000	0.56123	0.439000	0.28862	AAT	.	.		0.299	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			G	122772802	T	G	122772802	3	3	175	1	0	0	0	0	1	0	0	0	15880	1493	52	5	3046	5	THOC2	23	122772802	Missense_Mutation	SNP	T	TCGA-DD-AACY-01A-11D-A40R-10	119532377	122772802	32497758	101	26399										
MFAP2	4237	hgsc.bcm.edu	37	chr1	17303683	17303683	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aggtcatactggccctgagcCagcaagcctgctgtggggag	15	11	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:17303683C>A	ENST00000375535.3	-	3	337	c.48G>T	c.(46-48)ctG>ctT	p.L16L	MFAP2_ENST00000375534.3_Silent_p.L15L|MFAP2_ENST00000490075.1_5'UTR|RP1-37C10.3_ENST00000446261.1_RNA|MFAP2_ENST00000438542.1_Silent_p.L15L			P55001	MFAP2_HUMAN	microfibrillar-associated protein 2	16					extracellular matrix organization (GO:0030198)|platelet formation (GO:0030220)	extracellular region (GO:0005576)|microfibril (GO:0001527)				kidney(1)|lung(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000118)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000538)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|COAD - Colon adenocarcinoma(227;1.07e-05)|BRCA - Breast invasive adenocarcinoma(304;3.04e-05)|Kidney(64;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00544)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GGCCCTGAGCCAGCAAGCCTG	0.657																																					p.L16L		Atlas-SNP	.											.	MFAP2	8	.	0			c.G48T						.						29	26	27					1																	17303683		2202	4299	6501	SO:0001819	synonymous_variant	4237	exon3			CTGAGCCAGCAAG	BC015039	CCDS174.1, CCDS44071.1	1p36.1-p35	2008-02-05			ENSG00000117122	ENSG00000117122			7033	protein-coding gene	gene with protein product		156790				7759096	Standard	NM_017459		Approved	MAGP, MAGP-1	uc001azw.3	P55001	OTTHUMG00000002290	ENST00000375535.3:c.48G>T	chr1.hg19:g.17303683C>A		100.0	0.0		129.0	55.0	NM_017459	Q53X60|Q5JXY0	Silent	SNP	ENST00000375535.3	hg19	CCDS174.1																																																																																			.	.		0.657	MFAP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006609.1	NM_002403		A	17303683	C	A	17303683	2	1	176	1	0	0	0	0	0	0	0	1	9523	581	21	3		3	MFAP2	1	17303683	Silent	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10		17303683	231946938	1	26400										
C1orf151	440574	hgsc.bcm.edu	37	chr1	19950009	19950009	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tcggttctggcatgggattaGgaatggcttattccaactgt	12	7	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:19950009G>T	ENST00000322753.6	+	3	210	c.154G>T	c.(154-156)Gga>Tga	p.G52*	MINOS1-NBL1_ENST00000602662.1_Intron|MINOS1_ENST00000486890.1_3'UTR	NM_001032363.3|NM_001204082.1|NM_001204083.1	NP_001027535.1|NP_001191011.1|NP_001191012.1	Q5TGZ0	MIC10_HUMAN	mitochondrial inner membrane organizing system 1	52						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)											CATGGGATTAGGAATGGCTTA	0.388																																					p.G52X		Atlas-SNP	.											.	.	.	.	0			c.G154T						.						173	171	172					1																	19950009		2203	4300	6503	SO:0001587	stop_gained	440574	exon3			GGATTAGGAATGG	AK094318	CCDS30620.1, CCDS72719.1	1p36.13	2013-10-11	2011-10-04	2011-10-04	ENSG00000173436	ENSG00000173436			32068	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 151"	C1orf151		21944719	Standard	NM_001032363		Approved	RP5-1056L3.2, FLJ36999, MIO10	uc021ohu.1	Q5TGZ0	OTTHUMG00000002712	ENST00000322753.6:c.154G>T	chr1.hg19:g.19950009G>T	ENSP00000325562:p.Gly52*	52.0	0.0		46.0	11.0	NM_001032363	Q96G68	Nonsense_Mutation	SNP	ENST00000322753.6	hg19	CCDS30620.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.693479	0.68386	.	.	ENSG00000173436	ENST00000322753	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-7.6774	16.655	0.85226	0.0:0.0:1.0:0.0	.	.	.	.	X	52	.	ENSP00000325562:G52X	G	+	1	0	C1orf151	19822596	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	7.593000	0.82686	2.715000	0.92844	0.655000	0.94253	GGA	.	.		0.388	MINOS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007697.2	NM_001032363		T	19950009	G	T	19950009	4	4	176	1	0	0	0	0	0	1	0	0	2007	1001	35	3	164	3	C1orf151	1	19950009	Nonsense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	2646326	19950009	229300612	2	26401										
ZBTB40	9923	hgsc.bcm.edu	37	chr1	22837792	22837792	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	acctcctgtgcagtgtccacAaatcttttccaggcctgcag	8	14	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:22837792A>T	ENST00000375647.4	+	10	2161	c.1954A>T	c.(1954-1956)Aaa>Taa	p.K652*	ZBTB40_ENST00000404138.1_Nonsense_Mutation_p.K652*|ZBTB40_ENST00000374651.4_Nonsense_Mutation_p.K540*	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	652					bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		CAGTGTCCACAAATCTTTTCC	0.547																																					p.K652X		Atlas-SNP	.											.	ZBTB40	87	.	0			c.A1954T						.						62	64	63					1																	22837792		2203	4300	6503	SO:0001587	stop_gained	9923	exon11			GTCCACAAATCTT	AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.1954A>T	chr1.hg19:g.22837792A>T	ENSP00000364798:p.Lys652*	107.0	0.0		116.0	23.0	NM_001083621	O75066|Q5TFU5|Q8N1R1	Nonsense_Mutation	SNP	ENST00000375647.4	hg19	CCDS224.1	.	.	.	.	.	.	.	.	.	.	A	42	9.641536	0.99227	.	.	ENSG00000184677	ENST00000404138;ENST00000375647;ENST00000374651	.	.	.	5.97	-0.807	0.10872	.	1.064270	0.07352	N	0.882639	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.9724	4.5689	0.12200	0.3072:0.355:0.3378:0.0	.	.	.	.	X	652;652;540	.	ENSP00000363782:K540X	K	+	1	0	ZBTB40	22710379	0.000000	0.05858	0.031000	0.17742	0.930000	0.56654	0.330000	0.19715	-0.091000	0.12440	0.533000	0.62120	AAA	.	.		0.547	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870		T	22837792	A	T	22837792	4	4	176	1	0	0	0	0	0	1	0	0	17557	131	5	4	1988	4	ZBTB40	1	22837792	Nonsense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	2887783	22837792	226412829	3	26402										
RUNX3	864	hgsc.bcm.edu	37	chr1	25229122	25229123	+	Missense_Mutation	DNP	GG	GG	TT													0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggggaaggagcggtcaaactGgcgggggtcggagaatgggt							TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:25229122_25229123GG>TT	ENST00000308873.6	-	5	746_747	c.738_739CC>AA	c.(736-741)cgCCag>cgAAag	p.Q247K	RUNX3_ENST00000540420.1_Missense_Mutation_p.Q154K|RUNX3_ENST00000496967.1_5'UTR|RUNX3_ENST00000338888.3_Missense_Mutation_p.Q261K|RUNX3_ENST00000399916.1_Missense_Mutation_p.Q261K	NM_004350.2	NP_004341.1	Q13761	RUNX3_HUMAN	runt-related transcription factor 3	247	Pro/Ser/Thr-rich.				axon guidance (GO:0007411)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|hair follicle morphogenesis (GO:0031069)|interferon-gamma production (GO:0032609)|negative regulation of cell cycle (GO:0045786)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system neuron development (GO:0048935)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(3)	18		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		CGGTCAAACTGGCGGGGGTCGG	0.619																																					p.Q261K|p.R260R		Atlas-SNP	.											.	RUNX3	72	.	0			c.C781A|c.C780A						.																																			SO:0001583	missense	864	exon6			CAAACTGGCGGGG|AAACTGGCGGGGG	BC013362	CCDS257.1, CCDS30633.1	1p36	2008-02-05			ENSG00000020633	ENSG00000020633			10473	protein-coding gene	gene with protein product		600210		CBFA3		7835892	Standard	NM_001031680		Approved	AML2, PEBP2A3	uc001bjq.3	Q13761	OTTHUMG00000003316	ENST00000308873.6:c.738_739delinsTT	chr1.hg19:g.25229122_25229123delinsTT	ENSP00000308051:p.Gln247Lys	131.0	0.0		154.0|153.0	58.0	NM_001031680	B1AJV5|Q12969|Q13760	Missense_Mutation|Silent	SNP	ENST00000308873.6	hg19	CCDS257.1																																																																																			.	.		0.619	RUNX3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009284.1	NM_004350		TT	25229123	GG	TT	25229122	3	4	176	1	0	0	0	0	1	0	0	0	13764	1357	47	3	512	3	RUNX3	1	25229122	Missense_Mutation	DNP	GG	TCGA-DD-AACZ-01A-11D-A40R-10	2391330	25229122	224021499	4	26403										
USP24	23358	hgsc.bcm.edu	37	chr1	55609866	55609866	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttttcaaaaaaagttttaaaTaagttaaaacctgtaattat	3	3	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:55609866T>A	ENST00000294383.6	-	21	2372	c.2373A>T	c.(2371-2373)ttA>ttT	p.L791F	USP24_ENST00000407756.1_Missense_Mutation_p.L631F	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	791					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						AAGTTTTAAATAAGTTAAAAC	0.303																																					p.L791F		Atlas-SNP	.											.	USP24	323	.	0			c.A2373T						.						48	41	43					1																	55609866		1800	4061	5861	SO:0001583	missense	23358	exon21			TTTAAATAAGTTA	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.2373A>T	chr1.hg19:g.55609866T>A	ENSP00000294383:p.Leu791Phe	262.0	0.0		326.0	117.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	hg19	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	T	19.08	3.757440	0.69648	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.03524	3.9;3.9	5.25	4.12	0.48240	.	0.138749	0.48767	D	0.000169	T	0.06050	0.0157	L	0.29908	0.895	0.45354	D	0.998349	D	0.61080	0.989	P	0.53912	0.737	T	0.49031	-0.8981	10	0.38643	T	0.18	.	9.4055	0.38460	0.0:0.1443:0.0:0.8557	.	631	B7WPF4	.	F	791;631	ENSP00000294383:L791F;ENSP00000385700:L631F	ENSP00000294383:L791F	L	-	3	2	USP24	55382454	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.678000	0.25277	1.115000	0.41800	0.482000	0.46254	TTA	.	.		0.303	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			A	55609866	T	A	55609866	3	1	176	1	0	0	0	0	1	0	0	0	17070	1403	49	4	5681	4	USP24	1	55609866	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	30380744	55609866	193640755	5	26404										
KANK4	163782	hgsc.bcm.edu	37	chr1	62734068	62734068	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcaggtgagatgggcatcttTgacatgcttgtgatctgggc	15	7	2	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:62734068T>A	ENST00000371153.4	-	5	2500	c.2122A>T	c.(2122-2124)Aaa>Taa	p.K708*	KANK4_ENST00000354381.3_Nonsense_Mutation_p.K80*|KANK4_ENST00000371150.1_Nonsense_Mutation_p.K64*	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	708						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						TGGGCATCTTTGACATGCTTG	0.607																																					p.K708X		Atlas-SNP	.											.	KANK4	135	.	0			c.A2122T						.						98	78	85					1																	62734068		2203	4300	6503	SO:0001587	stop_gained	163782	exon5			CATCTTTGACATG	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	27263	protein-coding gene	gene with protein product		614612	"ankyrin repeat domain 38"	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.2122A>T	chr1.hg19:g.62734068T>A	ENSP00000360195:p.Lys708*	45.0	0.0		50.0	18.0	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Nonsense_Mutation	SNP	ENST00000371153.4	hg19	CCDS620.1	.	.	.	.	.	.	.	.	.	.	T	46	12.717165	0.99690	.	.	ENSG00000132854	ENST00000371153;ENST00000354381;ENST00000371150	.	.	.	6.17	3.77	0.43336	.	0.355289	0.20622	N	0.088754	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-9.5482	4.9508	0.14013	0.0:0.1572:0.2486:0.5942	.	.	.	.	X	708;80;64	.	ENSP00000346352:K80X	K	-	1	0	KANK4	62506656	0.002000	0.14202	0.018000	0.16275	0.004000	0.04260	0.484000	0.22308	1.166000	0.42689	0.533000	0.62120	AAA	.	.		0.607	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		A	62734068	T	A	62734068	4	1	176	1	0	0	0	0	0	1	0	0	7988	1821	63	4	889	4	KANK4	1	62734068	Nonsense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	7124202	62734068	186516553	6	26405										
HFM1	164045	hgsc.bcm.edu	37	chr1	91784922	91784922	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agcaaaatcttgtatgggaaTgcatcctagttgagcctgaa	10	7	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:91784922T>C	ENST00000370425.3	-	24	2706	c.2608A>G	c.(2608-2610)Att>Gtt	p.I870V	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Missense_Mutation_p.I549V|HFM1_ENST00000294696.5_Missense_Mutation_p.I102V	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	870	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TGTATGGGAATGCATCCTAGT	0.368																																					p.I870V		Atlas-SNP	.											.	HFM1	188	.	0			c.A2608G						.						103	99	100					1																	91784922		2203	4300	6503	SO:0001583	missense	164045	exon24			TGGGAATGCATCC	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2608A>G	chr1.hg19:g.91784922T>C	ENSP00000359454:p.Ile870Val	178.0	0.0		228.0	56.0	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	hg19	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	6.455	0.452153	0.12283	.	.	ENSG00000162669	ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	T;T;T	0.60672	0.17;0.17;0.17	5.0	3.79	0.43588	Sec63 domain (2);	0.112576	0.64402	D	0.000016	T	0.40448	0.1117	L	0.35854	1.095	0.34524	D	0.70844	B;P;B	0.46987	0.102;0.888;0.412	B;P;B	0.50934	0.03;0.654;0.179	T	0.39440	-0.9614	10	0.39692	T	0.17	.	8.2439	0.31675	0.13:0.0:0.1348:0.7352	.	549;125;870	A6NGI5;B1B0B5;A2PYH4	.;.;HFM1_HUMAN	V	870;102;549;554	ENSP00000359454:I870V;ENSP00000294696:I102V;ENSP00000359453:I549V	ENSP00000294696:I102V	I	-	1	0	HFM1	91557510	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.165000	0.42396	1.996000	0.58369	0.528000	0.53228	ATT	.	.		0.368	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		C	91784922	T	C	91784922	3	2	176	1	0	0	0	0	1	0	0	0	7092	1464	51	2	1763	2	HFM1	1	91784922	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	29050854	91784922	157465699	7	26406										
SYCP1	6847	hgsc.bcm.edu	37	chr1	115527442	115527442	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aaaaaaagagaaaaatggccTttgaatttgatattaattca	6	3	1	3	rs200809568		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:115527442T>A	ENST00000369522.3	+	30	2896	c.2656T>A	c.(2656-2658)Ttt>Att	p.F886I	SYCP1_ENST00000369518.1_Missense_Mutation_p.F886I|SYCP1_ENST00000477590.1_Intron	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	886					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAAAATGGCCTTTGAATTTGA	0.249																																					p.F886I		Atlas-SNP	.											.	SYCP1	149	.	0			c.T2656A						.						51	59	56					1																	115527442		2198	4274	6472	SO:0001583	missense	6847	exon30			ATGGCCTTTGAAT	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2656T>A	chr1.hg19:g.115527442T>A	ENSP00000358535:p.Phe886Ile	375.0	0.0		425.0	78.0	NM_003176	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	hg19	CCDS879.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.461868	0.43736	.	.	ENSG00000198765	ENST00000369522;ENST00000369518	T;T	0.29917	1.55;1.55	5.55	5.55	0.83447	.	0.246616	0.43110	D	0.000617	T	0.13200	0.0320	L	0.50333	1.59	0.26949	N	0.966068	P;P	0.37525	0.598;0.598	B;B	0.37346	0.247;0.247	T	0.08764	-1.0706	10	0.30854	T	0.27	-6.9628	8.6033	0.33758	0.0:0.0862:0.0:0.9138	.	886;886	B7ZLS9;Q15431	.;SYCP1_HUMAN	I	886	ENSP00000358535:F886I;ENSP00000358531:F886I	ENSP00000358531:F886I	F	+	1	0	SYCP1	115328965	1.000000	0.71417	0.999000	0.59377	0.917000	0.54804	2.585000	0.46111	2.238000	0.73509	0.533000	0.62120	TTT	.	T|1.000;G|0.000		0.249	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		A	115527442	T	A	115527442	3	1	176	1	0	0	0	0	1	0	0	0	15446	1609	56	4	2770	4	SYCP1	1	115527442	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	23742520	115527442	133723179	8	26407										
NHLH2	4808	hgsc.bcm.edu	37	chr1	116380919	116380919	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agcaccttggtgtccgtgccGcccagggactccggatccga	13	15	0	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:116380919G>A	ENST00000369506.1	-	1	5619	c.75C>T	c.(73-75)ggC>ggT	p.G25G	NHLH2_ENST00000320238.3_Silent_p.G25G			Q02577	HEN2_HUMAN	nescient helix loop helix 2	25					cell differentiation (GO:0030154)|central nervous system development (GO:0007417)|mating behavior (GO:0007617)|ovulation cycle (GO:0042698)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)			prostate(1)	1	Lung SC(450;0.184)	all_cancers(81;1.75e-06)|all_epithelial(167;1.16e-06)|all_lung(203;9.55e-06)|Lung NSC(69;5.83e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TGTCCGTGCCGCCCAGGGACT	0.687																																					p.G25G		Atlas-SNP	.											.	NHLH2	8	.	0			c.C75T						.						12	14	13					1																	116380919		2178	4269	6447	SO:0001819	synonymous_variant	4808	exon2			CGTGCCGCCCAGG		CCDS885.1	1p12-p11	2013-05-21			ENSG00000177551	ENSG00000177551		"Basic helix-loop-helix proteins"	7818	protein-coding gene	gene with protein product		162361		HEN2		1528853	Standard	NM_005599		Approved	NSCL2, bHLHa34	uc001efy.3	Q02577	OTTHUMG00000011969	ENST00000369506.1:c.75C>T	chr1.hg19:g.116380919G>A		78.0	0.0		121.0	39.0	NM_001111061	Q5T1P6	Silent	SNP	ENST00000369506.1	hg19	CCDS885.1																																																																																			.	.		0.687	NHLH2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033090.1	NM_005599		A	116380919	G	A	116380919	2	1	176	1	0	0	0	0	0	0	0	1	10413	1074	38	1		1	NHLH2	1	116380919	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	853477	116380919	132869702	9	26408										
OR10K1	391109	hgsc.bcm.edu	37	chr1	158435707	158435707	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cttcctgctggcagccatggGctatgatcgctatatggcca	11	12	0	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:158435707G>T	ENST00000289451.2	+	1	436	c.356G>T	c.(355-357)gGc>gTc	p.G119V		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, member 1	119						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					GCAGCCATGGGCTATGATCGC	0.537																																					p.G119V		Atlas-SNP	.											.	OR10K1	80	.	0			c.G356T						.						180	176	178					1																	158435707		2203	4300	6503	SO:0001583	missense	391109	exon1			CCATGGGCTATGA	AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"GPCR / Class A : Olfactory receptors"	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.356G>T	chr1.hg19:g.158435707G>T	ENSP00000289451:p.Gly119Val	112.0	0.0		149.0	27.0	NM_001004473	Q6IFS2	Missense_Mutation	SNP	ENST00000289451.2	hg19	CCDS30897.1	.	.	.	.	.	.	.	.	.	.	g	14.65	2.598649	0.46318	.	.	ENSG00000173285	ENST00000289451	T	0.37411	1.2	4.5	4.5	0.54988	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43919	D	0.000511	T	0.46367	0.1389	M	0.64404	1.975	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	T	0.48456	-0.9034	10	0.72032	D	0.01	.	11.1684	0.48556	0.0:0.3117:0.6883:0.0	.	119	Q8NGX5	O10K1_HUMAN	V	119	ENSP00000289451:G119V	ENSP00000289451:G119V	G	+	2	0	OR10K1	156702331	1.000000	0.71417	0.989000	0.46669	0.285000	0.27093	4.930000	0.63462	2.311000	0.77944	0.557000	0.71058	GGC	.	.		0.537	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1			T	158435707	G	T	158435707	3	4	176	1	0	0	0	0	1	0	0	0	10922	1203	42	3	358	3	OR10K1	1	158435707	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	42054788	158435707	90814914	10	26409										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214557127	214557127	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggtcttcttgtggtgatactGagggagctgggggacctcgt	17	7	2	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:214557127G>T	ENST00000366956.5	-	13	2265	c.2071C>A	c.(2071-2073)Cag>Aag	p.Q691K	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	691					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)	p.Q691E(1)		NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		TGGTGATACTGAGGGAGCTGG	0.632																																					p.Q691K	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											PTPN14,NS,carcinoma,0,1	PTPN14	168	.	1	Substitution - Missense(1)	lung(1)	c.C2071A						.						60	60	60					1																	214557127		2203	4300	6503	SO:0001583	missense	5784	exon13			GATACTGAGGGAG	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.2071C>A	chr1.hg19:g.214557127G>T	ENSP00000355923:p.Gln691Lys	51.0	1.0		80.0	18.0	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	G	3.999	-0.002920	0.07773	.	.	ENSG00000152104	ENST00000366956	T	0.66460	-0.21	5.0	2.98	0.34508	.	0.712333	0.13864	N	0.357462	T	0.42787	0.1218	N	0.08118	0	0.09310	N	0.999998	B	0.13145	0.007	B	0.06405	0.002	T	0.21861	-1.0233	10	0.22109	T	0.4	.	9.4153	0.38517	0.0:0.1386:0.5784:0.283	.	691	Q15678	PTN14_HUMAN	K	691	ENSP00000355923:Q691K	ENSP00000355923:Q691K	Q	-	1	0	PTPN14	212623750	0.153000	0.22777	0.406000	0.26421	0.387000	0.30353	1.742000	0.38248	1.104000	0.41587	0.563000	0.77884	CAG	.	.		0.632	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		T	214557127	G	T	214557127	3	4	176	1	0	0	0	0	1	0	0	0	12796	1299	45	3	1520	3	PTPN14	1	214557127	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	56121420	214557127	34693494	11	26410										
ESRRG	2104	hgsc.bcm.edu	37	chr1	216741353	216741353	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gctttttggctggctgaaccAgctgagggttcaggtatggg	16	7	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:216741353A>T	ENST00000408911.3	-	4	830	c.677T>A	c.(676-678)cTg>cAg	p.L226Q	ESRRG_ENST00000493603.1_Missense_Mutation_p.L203Q|ESRRG_ENST00000493748.1_Missense_Mutation_p.L203Q|ESRRG_ENST00000463665.1_Missense_Mutation_p.L164Q|ESRRG_ENST00000487276.1_Missense_Mutation_p.L203Q|ESRRG_ENST00000360012.3_Missense_Mutation_p.L203Q|ESRRG_ENST00000359162.2_Missense_Mutation_p.L203Q|ESRRG_ENST00000361395.2_Missense_Mutation_p.L203Q|ESRRG_ENST00000366937.1_Missense_Mutation_p.L231Q|ESRRG_ENST00000366940.2_Missense_Mutation_p.L203Q|ESRRG_ENST00000391890.3_Missense_Mutation_p.L203Q|ESRRG_ENST00000361525.3_Missense_Mutation_p.L203Q|ESRRG_ENST00000366938.2_Missense_Mutation_p.L203Q	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	226					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	TGGCTGAACCAGCTGAGGGTT	0.522																																					p.L231Q		Atlas-SNP	.											.	ESRRG	111	.	0			c.T692A						.						155	127	136					1																	216741353		2203	4300	6503	SO:0001583	missense	2104	exon5			TGAACCAGCTGAG	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"Nuclear hormone receptors"	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.677T>A	chr1.hg19:g.216741353A>T	ENSP00000386171:p.Leu226Gln	48.0	0.0		105.0	8.0	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	hg19	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	A	13.42	2.231887	0.39399	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748;ENST00000475275	D;D;D;D;D;D;D;D;D;D;T;D;D;D	0.94537	-3.44;-3.44;-3.31;-3.45;-3.44;-3.44;-3.44;-3.44;-3.44;-3.34;0.37;-3.44;-3.44;-3.27	5.76	5.76	0.90799	Nuclear hormone receptor, ligand-binding (1);	0.000000	0.85682	D	0.000000	D	0.92685	0.7675	L	0.51422	1.61	0.80722	D	1	B;P;P	0.47677	0.027;0.899;0.838	B;P;B	0.44990	0.007;0.466;0.154	D	0.91012	0.4850	10	0.14656	T	0.56	.	16.0728	0.80946	1.0:0.0:0.0:0.0	.	164;231;226	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	Q	203;203;231;226;203;203;203;203;203;203;164;203;203;203;203	ENSP00000355225:L203Q;ENSP00000355907:L203Q;ENSP00000355904:L231Q;ENSP00000386171:L226Q;ENSP00000352077:L203Q;ENSP00000354584:L203Q;ENSP00000355905:L203Q;ENSP00000353108:L203Q;ENSP00000419594:L203Q;ENSP00000375761:L203Q;ENSP00000418629:L164Q;ENSP00000419155:L203Q;ENSP00000417374:L203Q;ENSP00000419514:L203Q	ENSP00000346386:L203Q	L	-	2	0	ESRRG	214807976	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.201000	0.70794	0.528000	0.53228	CTG	.	.		0.522	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		T	216741353	A	T	216741353	3	4	176	1	0	0	0	0	1	0	0	0	5264	188	7	4	715	4	ESRRG	1	216741353	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	2184226	216741353	32509268	12	26411										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247016483	247016483	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tttagtacaccaacttctacTtcatgatcttcttttaagtt	3	9	4	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:247016483T>A	ENST00000391829.2	-	32	4596	c.4473A>T	c.(4471-4473)gaA>gaT	p.E1491D	AHCTF1_ENST00000326225.3_Missense_Mutation_p.E1500D|AHCTF1_ENST00000366508.1_Missense_Mutation_p.E1526D|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1491	Disordered. {ECO:0000250}.|Mediates transcriptional activity. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CAACTTCTACTTCATGATCTT	0.408																																					p.E1500D	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.A4500T						.						35	33	34					1																	247016483		2202	4280	6482	SO:0001583	missense	25909	exon32			TTCTACTTCATGA		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.4473A>T	chr1.hg19:g.247016483T>A	ENSP00000375705:p.Glu1491Asp	438.0	0.0		624.0	71.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	hg19		.	.	.	.	.	.	.	.	.	.	T	12.48	1.950028	0.34377	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.33216	1.42;1.43;1.43	5.76	4.64	0.57946	.	0.283135	0.30528	N	0.009439	T	0.28732	0.0712	L	0.40543	1.245	0.21445	N	0.999689	D;B;B	0.55385	0.971;0.241;0.156	P;B;B	0.49597	0.616;0.153;0.073	T	0.10019	-1.0648	10	0.28530	T	0.3	-15.661	6.0434	0.19746	0.0:0.0836:0.1644:0.752	.	352;1526;1491	B3KTD2;Q8WYP5-2;Q8WYP5	.;.;ELYS_HUMAN	D	1526;1500;1491	ENSP00000355464:E1526D;ENSP00000355465:E1500D;ENSP00000375705:E1491D	ENSP00000355465:E1500D	E	-	3	2	AHCTF1	245083106	0.153000	0.22777	0.614000	0.29051	0.556000	0.35491	1.088000	0.30877	1.017000	0.39495	0.528000	0.53228	GAA	.	.		0.408	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		A	247016483	T	A	247016483	3	1	176	1	0	0	0	0	1	0	0	0	408	1606	56	4	2347	4	AHCTF1	1	247016483	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	30275130	247016483	2234138	13	26412										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525837	248525837	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tcctcactccagtggtgaacCctttaatctatagtcttagg	7	11	3	1	rs375159583		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr1:248525837C>A	ENST00000366475.1	+	1	955	c.955C>A	c.(955-957)Cct>Act	p.P319T		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	319						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGTGGTGAACCCTTTAATCTA	0.458																																					p.P319T		Atlas-SNP	.											.	OR2T4	126	.	0			c.C955A						.						140	139	139					1																	248525837		2203	4300	6503	SO:0001583	missense	127074	exon1			GTGAACCCTTTAA	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.955C>A	chr1.hg19:g.248525837C>A	ENSP00000355431:p.Pro319Thr	480.0	0.0		639.0	57.0	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.675482	0.29783	.	.	ENSG00000196944	ENST00000366475	T	0.63913	-0.07	2.87	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000279	T	0.79131	0.4394	M	0.91038	3.17	0.36512	D	0.869679	D	0.60160	0.987	P	0.62813	0.907	D	0.83903	0.0291	10	0.87932	D	0	.	10.5129	0.44872	0.196:0.804:0.0:0.0	.	319	Q8NH00	OR2T4_HUMAN	T	319	ENSP00000355431:P319T	ENSP00000355431:P319T	P	+	1	0	OR2T4	246592460	0.916000	0.31088	0.875000	0.34327	0.057000	0.15508	3.115000	0.50391	0.381000	0.24851	0.485000	0.47835	CCT	.	.		0.458	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		A	248525837	C	A	248525837	3	1	176	1	0	0	0	0	1	0	0	0	11036	623	22	3	957	3	OR2T4	1	248525837	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	1509354	248525837	724784	14	26413										
ADCY3	109	hgsc.bcm.edu	37	chr2	25059804	25059804	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	acctgggcatcctgctcctcGggcttctccgacgtggaccc	11	17	1	0	rs372998415		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:25059804G>C	ENST00000260600.5	-	8	2495	c.1644C>G	c.(1642-1644)ccC>ccG	p.P548P	ADCY3_ENST00000405392.1_Silent_p.P181P	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	548					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					CCTGCTCCTCGGGCTTCTCCG	0.632																																					p.P548P		Atlas-SNP	.											.	ADCY3	114	.	0			c.C1644G						.						54	49	51					2																	25059804		2203	4300	6503	SO:0001819	synonymous_variant	109	exon8			CTCCTCGGGCTTC	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"Adenylate cyclases"	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.1644C>G	chr2.hg19:g.25059804G>C		53.0	0.0		99.0	7.0	NM_004036	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	hg19	CCDS1715.1																																																																																			.	.		0.632	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			C	25059804	G	C	25059804	2	2	176	1	0	0	0	0	0	0	0	1	295	1103	39	4		4	ADCY3	2	25059804	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10		25059804	218139569	15	26414										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25505281	25505281	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggtatgctggtgggcccagaAgaggctgcccctggtgctga	17	10	0	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:25505281A>G	ENST00000264709.3	-	4	786				DNMT3A_ENST00000321117.5_Intron|DNMT3A_ENST00000406659.3_Silent_p.S159S	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha						C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGGCCCAGAAGAGGCTGCCC	0.627			"Mis, F, N, S"		AML																																p.S159S		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.T477C						.						10	12	11					2																	25505281		2196	4282	6478	SO:0001627	intron_variant	1788	exon4			CCCAGAAGAGGCT		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.448+28T>C	chr2.hg19:g.25505281A>G		105.0	0.0		79.0	8.0	NM_175630	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Silent	SNP	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.		0.627	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		G	25505281	A	G	25505281	1	3	176	0	1	0	0	0	0	0	0	0	4678	59	3	2		2	DNMT3A	2	25505281	Intron	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	445477	25505281	217694092	16	26415										
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43924355	43924355	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tgtctctacactaaagctttCggaaggccagcgcctgagca	10	12	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:43924355C>T	ENST00000282406.4	+	7	658	c.548C>T	c.(547-549)tCg>tTg	p.S183L		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	183					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CTAAAGCTTTCGGAAGGCCAG	0.378																																					p.S183L		Atlas-SNP	.											PLEKHH2,colon,carcinoma,0,1	PLEKHH2	156	.	0			c.C548T						.						132	135	134					2																	43924355		2203	4300	6503	SO:0001583	missense	130271	exon7			AGCTTTCGGAAGG	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.548C>T	chr2.hg19:g.43924355C>T	ENSP00000282406:p.Ser183Leu	103.0	0.0		102.0	8.0	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.463759	0.26335	.	.	ENSG00000152527	ENST00000282406	T	0.50813	0.73	5.25	3.44	0.39384	.	0.690693	0.14177	N	0.336299	T	0.25382	0.0617	N	0.22421	0.69	0.09310	N	1	B;P	0.43287	0.019;0.802	B;B	0.31337	0.003;0.128	T	0.04454	-1.0950	10	0.21540	T	0.41	-0.3171	8.0407	0.30519	0.0:0.7042:0.1425:0.1533	.	183;183	Q8IVE3;Q8IVE3-3	PKHH2_HUMAN;.	L	183	ENSP00000282406:S183L	ENSP00000282406:S183L	S	+	2	0	PLEKHH2	43777859	0.000000	0.05858	0.006000	0.13384	0.797000	0.45037	-0.205000	0.09411	1.202000	0.43218	0.557000	0.71058	TCG	.	.		0.378	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		T	43924355	C	T	43924355	3	4	176	1	0	0	0	0	1	0	0	0	12086	893	31	1	570	1	PLEKHH2	2	43924355	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	18419074	43924355	199275018	17	26416										
ADD2	119	hgsc.bcm.edu	37	chr2	70910836	70910836	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggagcccacctcatggggccGgtgcttctcctgctccagga	13	15	2	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:70910836G>A	ENST00000264436.4	-	10	1456	c.1012C>T	c.(1012-1014)Cgg>Tgg	p.R338W	ADD2_ENST00000413157.2_Missense_Mutation_p.R338W|ADD2_ENST00000407644.2_Missense_Mutation_p.R338W|ADD2_ENST00000430656.1_Missense_Mutation_p.R354W|ADD2_ENST00000355733.3_Missense_Mutation_p.R338W	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	338					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						TCATGGGGCCGGTGCTTCTCC	0.627																																					p.R354W		Atlas-SNP	.											.	ADD2	261	.	0			c.C1060T						.						38	37	37					2																	70910836		2203	4300	6503	SO:0001583	missense	119	exon9			GGGGCCGGTGCTT	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.1012C>T	chr2.hg19:g.70910836G>A	ENSP00000264436:p.Arg338Trp	227.0	0.0		249.0	63.0	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	hg19	CCDS1906.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.548924	0.86127	.	.	ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000355733;ENST00000356565;ENST00000413157;ENST00000430656	T;T;T;T;T	0.09630	3.25;3.25;3.09;2.96;2.96	4.87	4.87	0.63330	Class II aldolase/adducin, N-terminal (2);	0.137242	0.47093	D	0.000250	T	0.26557	0.0649	L	0.48642	1.525	0.48571	D	0.999674	D;D;D;D	0.89917	0.986;1.0;1.0;1.0	P;D;D;D	0.74674	0.677;0.968;0.937;0.984	T	0.00523	-1.1690	10	0.87932	D	0	-14.5366	15.5561	0.76196	0.0:0.0:1.0:0.0	.	354;338;338;338	B4DM17;P35612-4;P35612;P35612-3	.;.;ADDB_HUMAN;.	W	338;338;338;338;338;354	ENSP00000264436:R338W;ENSP00000384677:R338W;ENSP00000347972:R338W;ENSP00000388072:R338W;ENSP00000398112:R354W	ENSP00000264436:R338W	R	-	1	2	ADD2	70764344	0.987000	0.35691	0.996000	0.52242	0.991000	0.79684	1.574000	0.36482	2.541000	0.85698	0.655000	0.94253	CGG	.	.		0.627	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		A	70910836	G	A	70910836	3	1	176	1	0	0	0	0	1	0	0	0	305	1115	39	1	1373	1	ADD2	2	70910836	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	26986481	70910836	172288537	18	26417										
DYSF	8291	hgsc.bcm.edu	37	chr2	71795093	71795093	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtacccagtatccgatggagAaggtgcctggcgcccggatg	15	11	0	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:71795093A>T	ENST00000258104.3	+	25	2801	c.2524A>T	c.(2524-2526)Aag>Tag	p.K842*	DYSF_ENST00000409762.1_Nonsense_Mutation_p.K859*|DYSF_ENST00000413539.2_Nonsense_Mutation_p.K873*|DYSF_ENST00000394120.2_Nonsense_Mutation_p.K843*|DYSF_ENST00000409744.1_Nonsense_Mutation_p.K829*|DYSF_ENST00000409651.1_Nonsense_Mutation_p.K874*|DYSF_ENST00000410020.3_Nonsense_Mutation_p.K860*|DYSF_ENST00000409582.3_Nonsense_Mutation_p.K859*|DYSF_ENST00000429174.2_Nonsense_Mutation_p.K842*|DYSF_ENST00000410041.1_Nonsense_Mutation_p.K860*|DYSF_ENST00000409366.1_Nonsense_Mutation_p.K843*	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	842					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TCCGATGGAGAAGGTGCCTGG	0.582																																					p.K874X		Atlas-SNP	.											.	DYSF	536	.	0			c.A2620T						.						120	116	117					2																	71795093		2203	4300	6503	SO:0001587	stop_gained	8291	exon26			ATGGAGAAGGTGC	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.2524A>T	chr2.hg19:g.71795093A>T	ENSP00000258104:p.Lys842*	125.0	0.0		167.0	35.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Nonsense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	A	43	10.297977	0.99378	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	.	.	.	4.81	0.892	0.19230	.	1.180440	0.05904	N	0.630456	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.0051	9.2953	0.37811	0.259:0.0:0.741:0.0	.	.	.	.	X	873;859;859;842;842;874;843;829;843;860;860	.	ENSP00000258104:K842X	K	+	1	0	DYSF	71648601	0.891000	0.30450	0.008000	0.14137	0.974000	0.67602	2.255000	0.43222	-0.146000	0.11274	0.448000	0.29417	AAG	.	.		0.582	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71795093	A	T	71795093	4	4	176	1	0	0	0	0	0	1	0	0	4861	247	9	4	2814	4	DYSF	2	71795093	Nonsense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	884257	71795093	171404280	19	26418										
CYP26B1	56603	hgsc.bcm.edu	37	chr2	72371128	72371128	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gagttcttaccttgcgcttgTtgcggtggatgtcgccaatg	13	9	1	0	rs200324765		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:72371128T>C	ENST00000001146.2	-	2	622	c.419A>G	c.(418-420)aAc>aGc	p.N140S	CYP26B1_ENST00000412253.1_5'Flank|CYP26B1_ENST00000546307.1_Intron	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily B, polypeptide 1	140					bone morphogenesis (GO:0060349)|cell fate determination (GO:0001709)|cellular response to retinoic acid (GO:0071300)|cornification (GO:0070268)|embryonic limb morphogenesis (GO:0030326)|establishment of skin barrier (GO:0061436)|male meiosis (GO:0007140)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of tongue muscle cell differentiation (GO:2001037)|proximal/distal pattern formation (GO:0009954)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|tongue morphogenesis (GO:0043587)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						CTTGCGCTTGTTGCGGTGGAT	0.622																																					p.N140S		Atlas-SNP	.											.	CYP26B1	73	.	0			c.A419G						.						53	53	53					2																	72371128		2203	4300	6503	SO:0001583	missense	56603	exon2			CGCTTGTTGCGGT		CCDS1919.1, CCDS62934.1	2p12	2006-11-24			ENSG00000003137	ENSG00000003137		"Cytochrome P450s"	20581	protein-coding gene	gene with protein product		605207				10545224	Standard	NM_019885		Approved	P450RAI-2	uc002sih.2	Q9NR63	OTTHUMG00000129756	ENST00000001146.2:c.419A>G	chr2.hg19:g.72371128T>C	ENSP00000001146:p.Asn140Ser	74.0	0.0		98.0	4.0	NM_019885	B2R8M7|B7Z2K6|B7Z2P4|B7Z3B8|E4W5W7|Q32MC0|Q53TW1|Q9NP41	Missense_Mutation	SNP	ENST00000001146.2	hg19	CCDS1919.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.112779	0.37242	.	.	ENSG00000003137	ENST00000001146;ENST00000461519	T;T	0.66638	-0.22;-0.22	4.78	4.78	0.61160	.	0.384245	0.30428	N	0.009642	T	0.42245	0.1194	N	0.03608	-0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.33803	-0.9854	10	0.29301	T	0.29	-44.6661	12.641	0.56709	0.0:0.0:0.0:1.0	.	123;140	B7Z2P4;Q9NR63	.;CP26B_HUMAN	S	140;123	ENSP00000001146:N140S;ENSP00000430871:N123S	ENSP00000001146:N140S	N	-	2	0	CYP26B1	72224636	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.646000	0.61411	2.166000	0.68216	0.454000	0.30748	AAC	.	T|1.000;A|0.000		0.622	CYP26B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251969.1	NM_019885		C	72371128	T	C	72371128	3	2	176	1	0	0	0	0	1	0	0	0	4158	1725	60	2	1139	2	CYP26B1	2	72371128	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	576035	72371128	170828245	20	26419										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613037	+	Missense_Mutation	DNP	GA	GA	CT													0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	catggccgggcgagctggagGaggaggaggaggaggaggag					rs61156725|rs72319667|rs3074417	byFrequency	TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:73613036_73613037GA>CT	ENST00000264448.6	+	1	151_152	c.40_41GA>CT	c.(40-42)GAg>CTg	p.E14L	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14L|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggaggag	0.693																																					p.E14Q|p.E14V		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C|c.A41T						.																																			SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG|TGGAGGAGGAGGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	Exception_encountered	chr2.hg19:g.73613036_73613037delinsCT	ENSP00000264448:p.Glu14Leu	150.0|149.0	0.0		289.0|292.0	27.0|30.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.693	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		CT	73613037	GA	CT	73613036	3	2	176	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	DNP	GA	TCGA-DD-AACZ-01A-11D-A40R-10	1241908	73613036	169586337	21	26420										
SNRNP200	23020	hgsc.bcm.edu	37	chr2	96949333	96949333	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	caatggcagtgaggcgggtcTgcttgcgagacggcacaaag	16	9	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:96949333T>G	ENST00000323853.5	-	33	4780	c.4703A>C	c.(4702-4704)cAg>cCg	p.Q1568P	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1568	Helicase C-terminal 2. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						GAGGCGGGTCTGCTTGCGAGA	0.582																																					p.Q1568P		Atlas-SNP	.											.	SNRNP200	195	.	0			c.A4703C						.						140	134	136					2																	96949333		2203	4300	6503	SO:0001583	missense	23020	exon33			CGGGTCTGCTTGC	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.4703A>C	chr2.hg19:g.96949333T>G	ENSP00000317123:p.Gln1568Pro	71.0	0.0		84.0	27.0	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	hg19	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.339422	0.81911	.	.	ENSG00000144028	ENST00000323853;ENST00000536601;ENST00000543553	D	0.85258	-1.96	5.0	5.0	0.66597	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93858	0.8035	H	0.97077	3.935	0.80722	D	1	D;D	0.59357	0.985;0.969	P;P	0.58780	0.845;0.845	D	0.95648	0.8704	10	0.87932	D	0	-21.5037	14.0005	0.64431	0.0:0.0:0.0:1.0	.	1319;1568	A4FU77;O75643	.;U520_HUMAN	P	1568;27;151	ENSP00000317123:Q1568P	ENSP00000317123:Q1568P	Q	-	2	0	SNRNP200	96313060	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.606000	0.82863	2.014000	0.59158	0.460000	0.39030	CAG	.	.		0.582	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		G	96949333	T	G	96949333	3	3	176	1	0	0	0	0	1	0	0	0	14867	1580	55	5	1759	5	SNRNP200	2	96949333	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	23336297	96949333	146250040	22	26421										
FER1L5	90342	hgsc.bcm.edu	37	chr2	97368053	97368053	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtggccacaggtatgagctgCgatgcatcatctggaagact	13	9	2	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:97368053C>T	ENST00000457909.1	+	0	4673							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						GTATGAGCTGCGATGCATCAT	0.552																																					p.R1760X		Atlas-SNP	.											.	FER1L5	113	.	0			c.C5278T						.						42	41	41					2																	97368053		2044	4196	6240			90342	exon46			GAGCTGCGATGCA	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		chr2.hg19:g.97368053C>T		199.0	0.0		335.0	84.0	NM_001113382	Q17RH2|Q6ZU24	Nonsense_Mutation	SNP	ENST00000457909.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.76	2.035740	0.35893	.	.	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	5.19	5.19	0.71726	.	0.000000	0.45867	U	0.000331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-29.9525	17.5041	0.87740	0.0:1.0:0.0:0.0	.	.	.	.	X	1760;1764;469	.	ENSP00000442027:R469X	R	+	1	2	FER1L5	96731780	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	4.762000	0.62250	2.431000	0.82371	0.655000	0.94253	CGA	.	.		0.552	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		T	97368053	C	T	97368053	1	4	176	0	1	0	0	0	0	0	0	0	5822	760	27	1		1	FER1L5	2	97368053	RNA	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	418720	97368053	145831320	23	26422										
MARCO	8685	hgsc.bcm.edu	37	chr2	119739022	119739022	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggcatgaaaggagatgcaggGgtcatggggcctcctggagc	18	8	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:119739022G>T	ENST00000327097.4	+	9	939	c.804G>T	c.(802-804)ggG>ggT	p.G268G	MARCO_ENST00000541757.1_Silent_p.G190G	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	268	Collagen-like.				apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						GAGATGCAGGGGTCATGGGGC	0.567																																					p.G268G	GBM(8;18 374 7467 11269 32796)	Atlas-SNP	.											.	MARCO	120	.	0			c.G804T						.						38	37	38					2																	119739022		2203	4300	6503	SO:0001819	synonymous_variant	8685	exon9			TGCAGGGGTCATG	AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"scavenger receptor class A, member 2"	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.804G>T	chr2.hg19:g.119739022G>T		133.0	0.0		184.0	38.0	NM_006770	B4DW79|Q9Y5S3	Silent	SNP	ENST00000327097.4	hg19	CCDS2124.1																																																																																			.	.		0.567	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770		T	119739022	G	T	119739022	2	4	176	1	0	0	0	0	0	0	0	1	9320	1219	43	3		3	MARCO	2	119739022	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	22370969	119739022	123460351	24	26423										
TTN	7273	hgsc.bcm.edu	37	chr2	179438250	179438250	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tccagtggctctcccactccAtatttatttacagccatgac	5	14	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:179438250A>T	ENST00000591111.1	-	276	67910	c.67686T>A	c.(67684-67686)taT>taA	p.Y22562*	TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.Y24203*|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.Y21635*|TTN_ENST00000359218.5_Nonsense_Mutation_p.Y15263*|TTN_ENST00000460472.2_Nonsense_Mutation_p.Y15138*|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.Y15330*|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	22562	Fibronectin type-III 63. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCCCACTCCATATTTATTTA	0.438																																					p.Y24203X		Atlas-SNP	.											.	TTN	18412	.	0			c.T72609A						.						152	154	153					2																	179438250		1928	4122	6050	SO:0001587	stop_gained	7273	exon326			CACTCCATATTTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.67686T>A	chr2.hg19:g.179438250A>T	ENSP00000465570:p.Tyr22562*	115.0	0.0		148.0	32.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	62	69.390303	0.99992	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	6.08	-3.37	0.04898	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	9.3725	0.38264	0.4875:0.1019:0.4106:0.0	.	.	.	.	X	21635;15138;15330;15263;15136	.	ENSP00000340554:Y15330X	Y	-	3	2	TTN	179146496	0.979000	0.34478	0.973000	0.42090	0.995000	0.86356	0.484000	0.22308	-0.577000	0.05967	-0.290000	0.09829	TAT	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179438250	A	T	179438250	4	4	176	1	0	0	0	0	0	1	0	0	16750	224	8	4	35518	4	TTN	2	179438250	Nonsense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	59699228	179438250	63761123	25	26424										
TTN	7273	hgsc.bcm.edu	37	chr2	179502130	179502130	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tttggcttggcagcctcttcCttaggtgctttggcttctga	11	10	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:179502130C>A	ENST00000591111.1	-	174	36194	c.35970G>T	c.(35968-35970)aaG>aaT	p.K11990N	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K13631N|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K11063N|TTN_ENST00000359218.5_Missense_Mutation_p.K4691N|TTN_ENST00000460472.2_Missense_Mutation_p.K4566N|TTN_ENST00000342175.6_Missense_Mutation_p.K4758N|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	11990	Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGCCTCTTCCTTAGGTGCTT	0.363																																					p.K13631N		Atlas-SNP	.											.	TTN	18412	.	0			c.G40893T						.						46	46	46					2																	179502130		1808	4075	5883	SO:0001583	missense	7273	exon224			CTCTTCCTTAGGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.35970G>T	chr2.hg19:g.179502130C>A	ENSP00000465570:p.Lys11990Asn	59.0	0.0		78.0	11.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.87	2.066744	0.36470	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68025	-0.3;0.03;0.01;-0.0	5.52	2.23	0.28157	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.74854	0.3771	L	0.58101	1.795	0.35438	D	0.794596	D;D;D;D	0.71674	0.998;0.998;0.998;0.998	D;D;D;D	0.76071	0.987;0.987;0.987;0.987	T	0.77210	-0.2671	9	0.87932	D	0	.	7.8107	0.29230	0.0:0.3389:0.0:0.6611	.	4566;4691;4758;11990	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	11063;4566;4758;4691;4566	ENSP00000343764:K11063N;ENSP00000434586:K4566N;ENSP00000340554:K4758N;ENSP00000352154:K4691N	ENSP00000340554:K4758N	K	-	3	2	TTN	179210375	0.998000	0.40836	0.999000	0.59377	0.971000	0.66376	0.208000	0.17415	0.172000	0.19760	0.491000	0.48974	AAG	.	.		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179502130	C	A	179502130	3	1	176	1	0	0	0	0	1	0	0	0	16750	680	24	3	67356	3	TTN	2	179502130	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	63880	179502130	63697243	26	26425										
NIF3L1	60491	hgsc.bcm.edu	37	chr2	201761875	201761875	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cctggcaaccatgattgatcGaataaaaagacacctaaaac	6	10	0	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:201761875G>C	ENST00000409020.1	+	5	1097	c.803G>C	c.(802-804)cGa>cCa	p.R268P	RNU6-762P_ENST00000517107.1_RNA|NIF3L1_ENST00000416651.1_Missense_Mutation_p.R268P|NIF3L1_ENST00000359683.4_Missense_Mutation_p.R241P|NIF3L1_ENST00000409357.1_Missense_Mutation_p.R268P|NIF3L1_ENST00000409588.1_Intron			Q9GZT8	GTPC1_HUMAN	NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae)	268					7,8-dihydroneopterin 3'-triphosphate biosynthetic process (GO:0035998)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTP cyclohydrolase I activity (GO:0003934)|metal ion binding (GO:0046872)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(2)	13						ATGATTGATCGAATAAAAAGA	0.433																																					p.R268P		Atlas-SNP	.											NIF3L1_ENST00000409020,colon,carcinoma,0,2	NIF3L1	51	.	0			c.G803C						.						131	121	124					2																	201761875		1922	4120	6042	SO:0001583	missense	60491	exon5			TTGATCGAATAAA	AB038949	CCDS42797.1, CCDS46485.1, CCDS46486.1	2q33	2011-11-10	2011-11-10		ENSG00000196290	ENSG00000196290			13390	protein-coding gene	gene with protein product		605778	"NIF3 (Ngg1 interacting factor 3, S.pombe homolog)-like 1", "NIF3 NGG1 interacting factor 3-like 1 (S. pombe)"	ALS2CR1		11124544, 11161814, 12522100	Standard	NM_001136039		Approved	CALS-7, MDS015	uc002uwm.2	Q9GZT8	OTTHUMG00000154588	ENST00000409020.1:c.803G>C	chr2.hg19:g.201761875G>C	ENSP00000386394:p.Arg268Pro	113.0	0.0		165.0	46.0	NM_001136039	Q53TX4|Q6X735|Q9H2D2|Q9HC18	Missense_Mutation	SNP	ENST00000409020.1	hg19	CCDS46485.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.6|21.6	4.179961|4.179961	0.78564|0.78564	.|.	.|.	ENSG00000196290|ENSG00000196290	ENST00000436412|ENST00000416651;ENST00000409020;ENST00000359683;ENST00000409357	.|T;T;T;T	.|0.46819	.|0.86;0.86;0.86;0.86	6.01|6.01	6.01|6.01	0.97437|0.97437	.|.	.|0.263821	.|0.38272	.|N	.|0.001752	T|T	0.75932|0.75932	0.3917|0.3917	M|M	0.90425|0.90425	3.115|3.115	0.49389|0.49389	D|D	0.999782|0.999782	.|D	.|0.76494	.|0.999	.|D	.|0.75484	.|0.986	T|T	0.75816|0.75816	-0.3184|-0.3184	5|10	.|0.39692	.|T	.|0.17	-10.4432|-10.4432	20.5141|20.5141	0.99211|0.99211	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|268	.|Q9GZT8	.|NIF3L_HUMAN	Q|P	27|268;268;241;268	.|ENSP00000400787:R268P;ENSP00000386394:R268P;ENSP00000352711:R241P;ENSP00000387315:R268P	.|ENSP00000352711:R241P	E|R	+|+	1|2	0|0	NIF3L1|NIF3L1	201470120|201470120	0.999000|0.999000	0.42202|0.42202	0.999000|0.999000	0.59377|0.59377	0.905000|0.905000	0.53344|0.53344	4.266000|4.266000	0.58871|0.58871	2.850000|2.850000	0.98022|0.98022	0.655000|0.655000	0.94253|0.94253	GAA|CGA	.	.		0.433	NIF3L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336201.1	NM_021824		C	201761875	G	C	201761875	3	2	176	1	0	0	0	0	1	0	0	0	10425	1058	37	4	817	4	NIF3L1	2	201761875	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	22259745	201761875	41437498	27	26426										
LANCL1	10314	hgsc.bcm.edu	37	chr2	211300146	211300146	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aaggggtgtctggtgttctgCatccatgttctccatactct	10	10	4	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr2:211300146C>T	ENST00000443314.1	-	8	1430	c.1088G>A	c.(1087-1089)tGc>tAc	p.C363Y	LANCL1_ENST00000441020.3_Missense_Mutation_p.C363Y|LANCL1_ENST00000431941.2_Missense_Mutation_p.C363Y|LANCL1_ENST00000450366.2_Missense_Mutation_p.C363Y|AC007970.1_ENST00000433296.1_RNA|LANCL1_ENST00000233714.4_Missense_Mutation_p.C363Y|AC007970.1_ENST00000420418.1_RNA			O43813	LANC1_HUMAN	LanC lantibiotic synthetase component C-like 1 (bacterial)	363					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|G-protein coupled receptor activity (GO:0004930)|glutathione binding (GO:0043295)|low-density lipoprotein particle receptor binding (GO:0050750)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|liver(1)|lung(4)|prostate(1)	12				Epithelial(149;0.00562)|Lung(261;0.0468)|LUSC - Lung squamous cell carcinoma(261;0.0495)|all cancers(144;0.0569)		TGGTGTTCTGCATCCATGTTC	0.363																																					p.C363Y		Atlas-SNP	.											.	LANCL1	23	.	0			c.G1088A						.						136	131	133					2																	211300146		2203	4300	6503	SO:0001583	missense	10314	exon9			GTTCTGCATCCAT	Y11395	CCDS2392.1	2q33-q35	2008-05-23	2001-12-04		ENSG00000115365	ENSG00000115365			6508	protein-coding gene	gene with protein product		604155	"LanC (bacterial lantibiotic synthetase component C)-like 1"	GPR69A		9512664	Standard	NM_001136574		Approved	p40	uc010zjh.2	O43813	OTTHUMG00000132991	ENST00000443314.1:c.1088G>A	chr2.hg19:g.211300146C>T	ENSP00000388713:p.Cys363Tyr	119.0	0.0		159.0	42.0	NM_001136574		Missense_Mutation	SNP	ENST00000443314.1	hg19	CCDS2392.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.066770|5.066770	0.93898|0.93898	.|.	.|.	ENSG00000115365|ENSG00000115365	ENST00000443314;ENST00000441020;ENST00000450366;ENST00000233714;ENST00000431941|ENST00000412863	T;T;T;T;T|.	0.40756|.	1.02;1.02;1.02;1.02;1.02|.	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75488|0.75488	0.3856|0.3856	M|M	0.64676|0.64676	1.99|1.99	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.70443|0.70443	-0.4870|-0.4870	10|5	0.30854|.	T|.	0.27|.	.|.	20.8598|20.8598	0.99761|0.99761	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	363|.	O43813|.	LANC1_HUMAN|.	Y|I	363|121	ENSP00000388713:C363Y;ENSP00000393323:C363Y;ENSP00000393597:C363Y;ENSP00000233714:C363Y;ENSP00000397646:C363Y|.	ENSP00000233714:C363Y|.	C|M	-|-	2|3	0|0	LANCL1|LANCL1	211008391|211008391	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	7.487000|7.487000	0.81328|0.81328	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	TGC|ATG	.	.		0.363	LANCL1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336817.1	NM_006055		T	211300146	C	T	211300146	3	4	176	1	0	0	0	0	1	0	0	0	8629	710	25	3	119	3	LANCL1	2	211300146	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	9538271	211300146	31899227	28	26427										
TRANK1	9881	hgsc.bcm.edu	37	chr3	36898772	36898772	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cctgcgtgctccagtcatccTgatcatcattgccctccttc	6	17	3	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr3:36898772T>A	ENST00000429976.2	-	12	2556	c.2309A>T	c.(2308-2310)cAg>cTg	p.Q770L	TRANK1_ENST00000428977.2_Missense_Mutation_p.Q220L|TRANK1_ENST00000301807.6_Missense_Mutation_p.Q220L	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	770							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						CCAGTCATCCTGATCATCATT	0.552																																					p.Q770L		Atlas-SNP	.											.	TRANK1	398	.	0			c.A2309T						.						214	208	210					3																	36898772		2051	4217	6268	SO:0001583	missense	9881	exon12			TCATCCTGATCAT	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.2309A>T	chr3.hg19:g.36898772T>A	ENSP00000416168:p.Gln770Leu	77.0	0.0		97.0	15.0	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	13.23	2.175994	0.38413	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.32515	1.45;1.82;1.45	5.75	-4.15	0.03881	.	0.650629	0.13438	N	0.387894	T	0.13713	0.0332	L	0.27053	0.805	0.09310	N	1	B	0.23937	0.094	B	0.18871	0.023	T	0.15350	-1.0440	10	0.44086	T	0.13	.	0.983	0.01440	0.4366:0.2137:0.1147:0.235	.	770	O15050	TRNK1_HUMAN	L	220;770;220	ENSP00000416826:Q220L;ENSP00000416168:Q770L;ENSP00000301807:Q220L	ENSP00000301807:Q220L	Q	-	2	0	TRANK1	36873776	0.407000	0.25352	0.002000	0.10522	0.178000	0.23041	0.476000	0.22180	-0.293000	0.08986	0.533000	0.62120	CAG	.	.		0.552	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36898772	T	A	36898772	3	1	176	1	0	0	0	0	1	0	0	0	16469	1580	55	4	6516	4	TRANK1	3	36898772	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10		36898772	161123658	29	26428										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111962868	111962868	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tagtaactgccactggcaaaAtaaatctattgacaacaagg	7	8	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr3:111962868A>C	ENST00000305815.5	-	11	1505	c.1253T>G	c.(1252-1254)aTt>aGt	p.I418S	SLC9C1_ENST00000487372.1_Missense_Mutation_p.I370S	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	418					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CACTGGCAAAATAAATCTATT	0.308																																					p.I418S		Atlas-SNP	.											.	.	.	.	0			c.T1253G						.						76	81	79					3																	111962868		2203	4300	6503	SO:0001583	missense	285335	exon11			GGCAAAATAAATC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.1253T>G	chr3.hg19:g.111962868A>C	ENSP00000306627:p.Ile418Ser	274.0	0.0		346.0	100.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	A	8.501	0.864294	0.17250	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.77229	-1.04;-1.08	5.11	3.79	0.43588	Cation/H+ exchanger (1);	0.216928	0.32258	N	0.006352	T	0.65770	0.2723	L	0.47716	1.5	0.27233	N	0.959345	B;B	0.32653	0.27;0.379	B;B	0.31390	0.096;0.129	T	0.57929	-0.7726	10	0.36615	T	0.2	-22.2886	5.2148	0.15336	0.838:0.0:0.162:0.0	.	370;418	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	S	418;370	ENSP00000306627:I418S;ENSP00000420688:I370S	ENSP00000306627:I418S	I	-	2	0	SLC9A10	113445558	0.996000	0.38824	0.985000	0.45067	0.034000	0.12701	2.849000	0.48286	2.044000	0.60594	0.352000	0.21897	ATT	.	.		0.308	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		C	111962868	A	C	111962868	3	2	176	1	0	0	0	0	1	0	0	0	14725	101	4	5	2356	5	SLC9A10	3	111962868	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	75064096	111962868	86059562	30	26429										
PIK3R4	30849	hgsc.bcm.edu	37	chr3	130424491	130424491	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tgcactgctcccgcttttgcTggatgagttgctgaagttca	11	10	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr3:130424491T>A	ENST00000356763.3	-	12	3403	c.2846A>T	c.(2845-2847)cAg>cTg	p.Q949L		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	949					innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						CCGCTTTTGCTGGATGAGTTG	0.403																																					p.Q949L		Atlas-SNP	.											.	PIK3R4	145	.	0			c.A2846T						.						193	180	184					3																	130424491		2203	4300	6503	SO:0001583	missense	30849	exon12			TTTTGCTGGATGA	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.2846A>T	chr3.hg19:g.130424491T>A	ENSP00000349205:p.Gln949Leu	140.0	0.0		171.0	67.0	NM_014602	Q2TBF4	Missense_Mutation	SNP	ENST00000356763.3	hg19	CCDS3067.1	.	.	.	.	.	.	.	.	.	.	T	12.22	1.873598	0.33069	.	.	ENSG00000196455	ENST00000356763	T	0.05786	3.39	5.72	5.72	0.89469	WD40 repeat-like-containing domain (1);	0.160586	0.56097	D	0.000026	T	0.06050	0.0157	L	0.27053	0.805	0.80722	D	1	B	0.20164	0.042	B	0.15484	0.013	T	0.42832	-0.9428	10	0.20046	T	0.44	-12.4214	15.9899	0.80197	0.0:0.0:0.0:1.0	.	949	Q99570	PI3R4_HUMAN	L	949	ENSP00000349205:Q949L	ENSP00000349205:Q949L	Q	-	2	0	PIK3R4	131907181	1.000000	0.71417	0.253000	0.24343	0.421000	0.31385	8.000000	0.88501	2.168000	0.68352	0.533000	0.62120	CAG	.	.		0.403	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		A	130424491	T	A	130424491	3	1	176	1	0	0	0	0	1	0	0	0	11930	1580	55	4	1266	4	PIK3R4	3	130424491	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	18461623	130424491	67597939	31	26430										
MBNL1	4154	hgsc.bcm.edu	37	chr3	152132806	152132806	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcagttggagataaatggacGcaataacttgattcagcaga	11	6	1	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr3:152132806G>A	ENST00000463374.1	+	2	762	c.251G>A	c.(250-252)cGc>cAc	p.R84H	MBNL1_ENST00000498502.1_Missense_Mutation_p.R84H|MBNL1_ENST00000357472.3_Missense_Mutation_p.R84H|MBNL1_ENST00000324196.5_Missense_Mutation_p.R84H|MBNL1_ENST00000485910.1_Missense_Mutation_p.R84H|MBNL1_ENST00000324210.5_Missense_Mutation_p.R84H|MBNL1_ENST00000485509.1_Missense_Mutation_p.R84H|MBNL1_ENST00000545754.1_Missense_Mutation_p.R84H|MBNL1_ENST00000493459.1_Missense_Mutation_p.R27H|MBNL1_ENST00000355460.2_Missense_Mutation_p.R84H|MBNL1_ENST00000282488.7_Missense_Mutation_p.R84H|MBNL1_ENST00000282486.6_Missense_Mutation_p.R84H|MBNL1_ENST00000492948.1_Missense_Mutation_p.R84H	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	84					alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R84H(2)		endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			ATAAATGGACGCAATAACTTG	0.478																																					p.R84H		Atlas-SNP	.											MBNL1_ENST00000282488,colon,carcinoma,0,2	MBNL1	100	.	2	Substitution - Missense(2)	large_intestine(2)	c.G251A						.						137	125	129					3																	152132806		2203	4300	6503	SO:0001583	missense	4154	exon3			ATGGACGCAATAA	Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"Zinc fingers, CCCH-type domain containing"	6923	protein-coding gene	gene with protein product		606516	"muscleblind (Drosophila)-like", "muscleblind-like (Drosophila)"	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.251G>A	chr3.hg19:g.152132806G>A	ENSP00000418108:p.Arg84His	142.0	0.0		195.0	70.0	NM_207292	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Missense_Mutation	SNP	ENST00000463374.1	hg19	CCDS3165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	5.989217|5.989217	0.97179|0.97179	.|.	.|.	ENSG00000152601|ENSG00000152601	ENST00000464596|ENST00000282486;ENST00000282488;ENST00000355460;ENST00000493459;ENST00000324210;ENST00000459747;ENST00000498502;ENST00000324196;ENST00000545754;ENST00000357472;ENST00000485910;ENST00000463374;ENST00000465907;ENST00000492948;ENST00000485509	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.51574	.|0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.70902|0.70902	0.3277|0.3277	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D;D	.|0.97110	.|0.993;0.999;0.999;0.998;0.993;0.993;0.997;1.0	T|T	0.71108|0.71108	-0.4688|-0.4688	5|10	.|0.87932	.|D	.|0	.|.	20.5948|20.5948	0.99439|0.99439	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|84;84;84;84;84;27;84;84	.|E9PBW7;Q9NR56-3;Q96RE3;Q9NR56;Q86UV8;Q86VM6;Q9NR56-2;Q96P92	.|.;.;.;MBNL1_HUMAN;.;.;.;.	T|H	83|84;84;84;27;84;28;84;84;84;84;84;84;84;84;84	.|ENSP00000282486:R84H;ENSP00000282488:R84H;ENSP00000347637:R84H;ENSP00000419347:R27H;ENSP00000319429:R84H;ENSP00000417169:R28H;ENSP00000420327:R84H;ENSP00000319374:R84H;ENSP00000437491:R84H;ENSP00000350064:R84H;ENSP00000418427:R84H;ENSP00000418108:R84H;ENSP00000417630:R84H;ENSP00000420103:R84H;ENSP00000418876:R84H	.|ENSP00000282486:R84H	A|R	+|+	1|2	0|0	MBNL1|MBNL1	153615496|153615496	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.731000|9.731000	0.98807|0.98807	2.873000|2.873000	0.98535|0.98535	0.563000|0.563000	0.77884|0.77884	GCA|CGC	.	.		0.478	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038		A	152132806	G	A	152132806	3	1	176	1	0	0	0	0	1	0	0	0	9362	1087	38	1	257	1	MBNL1	3	152132806	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	21708315	152132806	45889624	32	26431										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	193081052	193081052	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tctggctttattaaggcttgGtttatgacagagtggcggtc	13	6	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr3:193081052G>C	ENST00000342358.4	-	3	474	c.357C>G	c.(355-357)aaC>aaG	p.N119K		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	119						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TTAAGGCTTGGTTTATGACAG	0.383																																					p.N119K		Atlas-SNP	.											.	ATP13A5	171	.	0			c.C357G						.						98	97	97					3																	193081052		2203	4300	6503	SO:0001583	missense	344905	exon3			GGCTTGGTTTATG	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.357C>G	chr3.hg19:g.193081052G>C	ENSP00000341942:p.Asn119Lys	117.0	0.0		146.0	43.0	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	hg19	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	G	10.99	1.505942	0.26949	.	.	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.33865	1.39;1.39	5.12	3.31	0.37934	.	0.000000	0.85682	D	0.000000	T	0.31575	0.0801	L	0.54323	1.7	0.32700	N	0.513014	P	0.47106	0.89	P	0.45232	0.474	T	0.35699	-0.9778	10	0.12430	T	0.62	-18.9578	7.7121	0.28684	0.2653:0.0:0.7346:0.0	.	119	Q4VNC0	AT135_HUMAN	K	119;141	ENSP00000341942:N119K;ENSP00000389416:N141K	ENSP00000341942:N119K	N	-	3	2	ATP13A5	194563746	1.000000	0.71417	0.993000	0.49108	0.053000	0.15095	2.232000	0.43018	0.816000	0.34421	0.650000	0.86243	AAC	.	.		0.383	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		C	193081052	G	C	193081052	3	2	176	1	0	0	0	0	1	0	0	0	1127	1252	44	4	3409	4	ATP13A5	3	193081052	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	40948246	193081052	4941378	33	26432										
PROM1	8842	hgsc.bcm.edu	37	chr4	16025980	16025980	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gggccaatatatatttgattTgctgaaaaaagaacattctg	8	5	1	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr4:16025980T>A	ENST00000510224.1	-	7	880	c.632A>T	c.(631-633)cAa>cTa	p.Q211L	PROM1_ENST00000505450.1_Splice_Site_p.Q202L|PROM1_ENST00000447510.2_Splice_Site_p.Q211L|PROM1_ENST00000540805.1_Splice_Site_p.Q211L|PROM1_ENST00000539194.1_Splice_Site_p.Q211L|PROM1_ENST00000543373.1_Splice_Site_p.Q202L|PROM1_ENST00000502943.1_5'UTR|PROM1_ENST00000508167.1_Splice_Site_p.Q202L			O43490	PROM1_HUMAN	prominin 1	211					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						ATATTTGATTTGCTGAAAAAA	0.353																																					p.Q211L		Atlas-SNP	.											.	PROM1	91	.	0			c.A632T						.						112	104	107					4																	16025980		1833	4095	5928	SO:0001630	splice_region_variant	8842	exon6			TTGATTTGCTGAA	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.631-1A>T	chr4.hg19:g.16025980T>A		124.0	0.0		158.0	62.0	NM_006017	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	hg19	CCDS47029.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.496446	0.64186	.	.	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373	T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.56963	0.2021	M	0.80746	2.51	0.80722	D	1	P;P;P;P;B;P	0.41848	0.72;0.72;0.72;0.72;0.058;0.763	P;P;B;P;B;P	0.44921	0.447;0.447;0.333;0.447;0.046;0.464	T	0.65471	-0.6160	10	0.72032	D	0.01	-19.8061	13.9438	0.64071	0.0:0.0:0.0:1.0	.	202;211;202;211;202;211	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490	.;.;.;.;.;PROM1_HUMAN	L	211;211;211;202;202;211;202	ENSP00000415481:Q211L;ENSP00000438045:Q211L;ENSP00000443620:Q211L;ENSP00000426090:Q202L;ENSP00000427346:Q202L;ENSP00000426809:Q211L;ENSP00000445526:Q202L	ENSP00000415481:Q211L	Q	-	2	0	PROM1	15635078	1.000000	0.71417	0.997000	0.53966	0.511000	0.34104	6.143000	0.71756	1.833000	0.53350	0.459000	0.35465	CAA	.	.		0.353	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	Missense_Mutation	A	16025980	T	A	16025980	5	1	176	1	0	0	0	0	0	0	1	0	12567	1826	63	4	2049	4	PROM1	4	16025980	Splice_Site	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10		16025980	175128296	34	26433										
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25667799	25667799	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agctctattatgtccaacccTttgttggggctggtgatcgg	12	9	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr4:25667799T>A	ENST00000382051.3	+	5	479	c.429T>A	c.(427-429)ccT>ccA	p.P143P	SLC34A2_ENST00000510033.2_3'UTR|SLC34A2_ENST00000504570.1_Silent_p.P142P|SLC34A2_ENST00000503434.1_Silent_p.P142P	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	143					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				TGTCCAACCCTTTGTTGGGGC	0.498			T	ROS1	NSCLC																																p.P143P		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	.	SLC34A2	93	.	0			c.T429A						.						143	146	145					4																	25667799		2203	4300	6503	SO:0001819	synonymous_variant	10568	exon5			CAACCCTTTGTTG	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.429T>A	chr4.hg19:g.25667799T>A		51.0	0.0		73.0	14.0	NM_006424	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Silent	SNP	ENST00000382051.3	hg19	CCDS3435.1																																																																																			.	.		0.498	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		A	25667799	T	A	25667799	2	1	176	1	0	0	0	0	0	0	0	1	14583	1596	56	4		4	SLC34A2	4	25667799	Silent	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	9641819	25667799	165486477	35	26434										
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25819867	25819867	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tcgagggtctcccatacctgCgctggaggtccaggtaggag	15	11	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr4:25819867C>T	ENST00000399878.3	-	9	1579	c.1457G>A	c.(1456-1458)cGc>cAc	p.R486H	SEL1L3_ENST00000264868.5_Missense_Mutation_p.R451H|SEL1L3_ENST00000502949.1_Missense_Mutation_p.R333H	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	486						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						CCCATACCTGCGCTGGAGGTC	0.542																																					p.R486H		Atlas-SNP	.											.	SEL1L3	62	.	0			c.G1457A						.						53	55	55					4																	25819867		1958	4163	6121	SO:0001583	missense	23231	exon9			TACCTGCGCTGGA	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.1457G>A	chr4.hg19:g.25819867C>T	ENSP00000382767:p.Arg486His	128.0	0.0		154.0	37.0	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	C	4.392	0.072331	0.08436	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.14516	2.72;2.72;2.5	5.75	-1.97	0.07503	.	1.198870	0.05443	N	0.547975	T	0.07548	0.0190	N	0.24115	0.695	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.37337	-0.9710	10	0.33940	T	0.23	-2.4685	0.2933	0.00261	0.257:0.2612:0.1445:0.3372	.	486	Q68CR1	SE1L3_HUMAN	H	486;451;333	ENSP00000382767:R486H;ENSP00000264868:R451H;ENSP00000425438:R333H	ENSP00000264868:R451H	R	-	2	0	SEL1L3	25428965	0.000000	0.05858	0.039000	0.18376	0.001000	0.01503	-1.235000	0.02928	-0.399000	0.07668	-0.794000	0.03295	CGC	.	.		0.542	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		T	25819867	C	T	25819867	3	4	176	1	0	0	0	0	1	0	0	0	14027	768	27	1	2005	1	SEL1L3	4	25819867	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	152068	25819867	165334409	36	26435										
CWH43	80157	hgsc.bcm.edu	37	chr4	48996766	48996766	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ctcacccactgggtttttggAgaagtctctcttgtttccag	9	11	3	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr4:48996766A>G	ENST00000226432.4	+	5	825	c.642A>G	c.(640-642)ggA>ggG	p.G214G	CWH43_ENST00000513409.1_Silent_p.G187G	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	214					GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						GGGTTTTTGGAGAAGTCTCTC	0.542																																					p.G214G		Atlas-SNP	.											.	CWH43	101	.	0			c.A642G						.						115	109	111					4																	48996766		2203	4300	6503	SO:0001819	synonymous_variant	80157	exon5			TTTTGGAGAAGTC		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.642A>G	chr4.hg19:g.48996766A>G		150.0	0.0		222.0	50.0	NM_025087	B2RPD7	Silent	SNP	ENST00000226432.4	hg19	CCDS3486.1																																																																																			.	.		0.542	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		G	48996766	A	G	48996766	2	3	176	1	0	0	0	0	0	0	0	1	4075	291	11	2		2	CWH43	4	48996766	Silent	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	23176899	48996766	142157510	37	26436										
RUFY3	22902	hgsc.bcm.edu	37	chr4	71655272	71655272	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtcgcttggaagagaagactAatcagatggctgctaccatt	11	8	1	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr4:71655272A>T	ENST00000226328.4	+	12	1863	c.1300A>T	c.(1300-1302)Aat>Tat	p.N434Y	RUFY3_ENST00000502653.1_Missense_Mutation_p.N381Y|RUFY3_ENST00000536664.1_Missense_Mutation_p.N418Y|RUFY3_ENST00000381006.3_Missense_Mutation_p.N434Y|RUFY3_ENST00000417478.2_Missense_Mutation_p.N494Y	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	434					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			AGAGAAGACTAATCAGATGGC	0.348																																					p.N494Y		Atlas-SNP	.											.	RUFY3	61	.	0			c.A1480T						.						125	128	127					4																	71655272		2203	4300	6503	SO:0001583	missense	22902	exon12			AAGACTAATCAGA	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.1300A>T	chr4.hg19:g.71655272A>T	ENSP00000226328:p.Asn434Tyr	216.0	0.0		253.0	51.0	NM_001130709	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	hg19	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.427456	0.83667	.	.	ENSG00000018189	ENST00000417478;ENST00000381006;ENST00000226328;ENST00000536664;ENST00000502653	T;T;T;T;T	0.14022	2.54;2.54;2.54;2.54;2.54	5.47	5.47	0.80525	.	0.039429	0.85682	D	0.000000	T	0.37598	0.1009	M	0.73217	2.22	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.998;0.997	D;D;D;D	0.77557	0.984;0.983;0.99;0.964	T	0.17349	-1.0372	10	0.87932	D	0	-27.772	15.5336	0.75983	1.0:0.0:0.0:0.0	.	418;434;434;494	B4DKC2;Q7L099-3;Q7L099;Q7L099-2	.;.;RUFY3_HUMAN;.	Y	494;434;434;418;381	ENSP00000399771:N494Y;ENSP00000370394:N434Y;ENSP00000226328:N434Y;ENSP00000443652:N418Y;ENSP00000425400:N381Y	ENSP00000226328:N434Y	N	+	1	0	RUFY3	71874136	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.626000	0.90969	2.073000	0.62155	0.533000	0.62120	AAT	.	.		0.348	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		T	71655272	A	T	71655272	3	4	176	1	0	0	0	0	1	0	0	0	13755	362	13	4	1708	4	RUFY3	4	71655272	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	22658506	71655272	119499004	38	26437										
COL25A1	84570	hgsc.bcm.edu	37	chr4	109765684	109765684	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gggaaacttaccatggggccAggtgggccatggggacctgg	18	9	0	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr4:109765684A>T	ENST00000399132.1	-	30	2150	c.1620T>A	c.(1618-1620)ccT>ccA	p.P540P	COL25A1_ENST00000399126.1_Silent_p.P540P|COL25A1_ENST00000399127.1_Silent_p.P513P	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1											NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		CCATGgggccaggtgggccat	0.438																																					p.P540P		Atlas-SNP	.											.	COL25A1	178	.	0			c.T1620A						.						91	95	94					4																	109765684		1849	4096	5945	SO:0001819	synonymous_variant	84570	exon29			GGGGCCAGGTGGG	AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"Collagens"	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.1620T>A	chr4.hg19:g.109765684A>T		134.0	0.0		154.0	27.0	NM_198721		Silent	SNP	ENST00000399132.1	hg19	CCDS43258.1	.	.	.	.	.	.	.	.	.	.	A	14.09	2.431786	0.43122	.	.	ENSG00000188517	ENST00000443653	.	.	.	5.47	-2.13	0.07144	.	.	.	.	.	T	0.38453	0.1041	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30387	-0.9980	4	.	.	.	-4.3426	0.9855	0.01445	0.3115:0.094:0.1886:0.4059	.	.	.	.	R	456	.	.	W	-	1	0	COL25A1	109985133	0.977000	0.34250	0.997000	0.53966	0.985000	0.73830	-0.225000	0.09151	-0.252000	0.09528	-0.177000	0.13119	TGG	.	.		0.438	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518		T	109765684	A	T	109765684	2	4	176	1	0	0	0	0	0	0	0	1	3686	175	7	4		4	COL25A1	4	109765684	Silent	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	38110412	109765684	81388592	39	26438										
ANK2	287	hgsc.bcm.edu	37	chr4	114158756	114158756	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ccaaacaacactgcttcagaTgatggtgaataggacaactg	9	9	1	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr4:114158756T>C	ENST00000357077.4	+	7	724	c.671T>C	c.(670-672)aTg>aCg	p.M224T	ANK2_ENST00000394537.3_Splice_Site_p.M224T|ANK2_ENST00000264366.6_Splice_Site_p.M224T|ANK2_ENST00000506722.1_Splice_Site_p.M203T	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	224					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CTGCTTCAGATGATGGTGAAT	0.358																																					p.M224T		Atlas-SNP	.											.	ANK2	576	.	0			c.T671C						.						226	206	213					4																	114158756		2203	4300	6503	SO:0001630	splice_region_variant	287	exon7			TTCAGATGATGGT	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.670-1T>C	chr4.hg19:g.114158756T>C		99.0	0.0		98.0	22.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	T	16.72	3.201840	0.58234	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056	T;T;T;T;T;T;T	0.66280	-0.05;0.08;-0.16;-0.06;-0.13;-0.18;-0.2	5.65	5.65	0.86999	Ankyrin repeat-containing domain (3);	0.000000	0.64402	D	0.000002	T	0.68320	0.2988	N	0.25647	0.755	0.80722	D	1	D;D;D;D;P	0.65815	0.985;0.995;0.991;0.981;0.935	D;D;D;D;D	0.78314	0.979;0.991;0.991;0.98;0.914	T	0.66602	-0.5882	10	0.31617	T	0.26	.	16.1657	0.81754	0.0:0.0:0.0:1.0	.	224;224;224;203;203	Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	ANK2_HUMAN;.;.;.;.	T	203;203;203;239;224;224;224;203	ENSP00000423799:M203T;ENSP00000421011:M203T;ENSP00000421067:M203T;ENSP00000424722:M239T;ENSP00000378044:M224T;ENSP00000349588:M224T;ENSP00000264366:M224T	ENSP00000264366:M224T	M	+	2	0	ANK2	114378205	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.997000	0.88414	2.276000	0.75962	0.528000	0.53228	ATG	.	.		0.358	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	Missense_Mutation	C	114158756	T	C	114158756	5	2	176	1	0	0	0	0	0	0	1	0	621	1478	51	2	722	2	ANK2	4	114158756	Splice_Site	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	4393072	114158756	76995520	40	26439										
FSTL5	56884	hgsc.bcm.edu	37	chr4	162680644	162680644	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	caatagaacatacaaagtacAatcaaagagatccttgccaa	5	9	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr4:162680644A>G	ENST00000306100.5	-	6	1082	c.646T>C	c.(646-648)Tgt>Cgt	p.C216R	FSTL5_ENST00000536695.1_Missense_Mutation_p.C215R|FSTL5_ENST00000379164.4_Missense_Mutation_p.C215R|FSTL5_ENST00000427802.2_Missense_Mutation_p.C215R	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	216	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TACAAAGTACAATCAAAGAGA	0.303																																					p.C216R		Atlas-SNP	.											.	FSTL5	207	.	0			c.T646C						.						90	98	96					4																	162680644		2203	4300	6503	SO:0001583	missense	56884	exon6			AAGTACAATCAAA	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.646T>C	chr4.hg19:g.162680644A>G	ENSP00000305334:p.Cys216Arg	493.0	0.0		493.0	104.0	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	hg19	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	A	13.00	2.107376	0.37145	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.37	5.37	0.77165	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.40297	0.1111	L	0.47016	1.485	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.996;1.0;0.997	T	0.22730	-1.0208	10	0.87932	D	0	.	14.5345	0.67950	1.0:0.0:0.0:0.0	.	215;215;216	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	R	216;215;215;215	ENSP00000305334:C216R;ENSP00000368462:C215R;ENSP00000389270:C215R;ENSP00000440409:C215R	ENSP00000305334:C216R	C	-	1	0	FSTL5	162900094	1.000000	0.71417	0.908000	0.35775	0.028000	0.11728	6.778000	0.75043	2.030000	0.59900	0.472000	0.43445	TGT	.	.		0.303	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		G	162680644	A	G	162680644	3	3	176	1	0	0	0	0	1	0	0	0	6088	130	5	2	1941	2	FSTL5	4	162680644	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	48521888	162680644	28473632	41	26440										
CLCN3	1182	hgsc.bcm.edu	37	chr4	170613454	170613454	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttccaaagtatagcacaaacGaagctaaaaaaagggaggta	9	6	0	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr4:170613454G>A	ENST00000513761.1	+	7	1478	c.919G>A	c.(919-921)Gaa>Aaa	p.E307K	CLCN3_ENST00000347613.4_Missense_Mutation_p.E307K|CLCN3_ENST00000504131.2_Missense_Mutation_p.E290K|CLCN3_ENST00000360642.3_Missense_Mutation_p.E307K	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	307					chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)			breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		TAGCACAAACGAAGCTAAAAA	0.328																																					p.E307K		Atlas-SNP	.											.	CLCN3	85	.	0			c.G919A						.						108	109	109					4																	170613454		2203	4300	6503	SO:0001583	missense	1182	exon7			ACAAACGAAGCTA	X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.919G>A	chr4.hg19:g.170613454G>A	ENSP00000424603:p.Glu307Lys	236.0	0.0		188.0	46.0	NM_001243372	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	hg19	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	G	35	5.461222	0.96240	.	.	ENSG00000109572	ENST00000513761;ENST00000347613;ENST00000360642;ENST00000504131;ENST00000507875	D;D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45;-3.45	5.94	5.94	0.96194	Chloride channel, core (2);	0.044023	0.85682	D	0.000000	D	0.97185	0.9080	M	0.76433	2.335	0.80722	D	1	D;D;D;D;D	0.76494	0.995;0.999;0.999;0.995;0.994	D;D;D;D;P	0.71870	0.957;0.975;0.962;0.975;0.863	D	0.97134	0.9820	10	0.87932	D	0	-5.2076	20.419	0.99029	0.0:0.0:1.0:0.0	.	307;290;280;307;307	B7Z932;B9EGJ9;E9PE15;P51790;P51790-2	.;.;.;CLCN3_HUMAN;.	K	307;307;307;290;280	ENSP00000424603:E307K;ENSP00000261514:E307K;ENSP00000353857:E307K;ENSP00000424540:E290K;ENSP00000425323:E280K	ENSP00000261514:E307K	E	+	1	0	CLCN3	170850029	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.832000	0.97577	0.650000	0.86243	GAA	.	.		0.328	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			A	170613454	G	A	170613454	3	1	176	1	0	0	0	0	1	0	0	0	3466	1059	37	1	941	1	CLCN3	4	170613454	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	7932810	170613454	20540822	42	26441										
ADCY2	108	hgsc.bcm.edu	37	chr5	7520950	7520950	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tcctcacctcctcctcccacAccatcgtgcttagcgtctgc	5	20	2	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:7520950A>G	ENST00000338316.4	+	3	597	c.508A>G	c.(508-510)Acc>Gcc	p.T170A		NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	170					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CTCCTCCCACACCATCGTGCT	0.567																																					p.T170A		Atlas-SNP	.											.	ADCY2	337	.	0			c.A508G						.						199	129	152					5																	7520950		2203	4300	6503	SO:0001583	missense	108	exon3			TCCCACACCATCG	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.508A>G	chr5.hg19:g.7520950A>G	ENSP00000342952:p.Thr170Ala	75.0	0.0		113.0	11.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	A	17.30	3.353584	0.61293	.	.	ENSG00000078295	ENST00000338316;ENST00000541993	T	0.76578	-1.03	5.65	5.65	0.86999	.	0.054653	0.64402	D	0.000001	T	0.74604	0.3738	L	0.59436	1.845	0.80722	D	1	B	0.25312	0.123	B	0.22753	0.041	T	0.73610	-0.3928	10	0.66056	D	0.02	.	13.6275	0.62173	1.0:0.0:0.0:0.0	.	170	Q08462	ADCY2_HUMAN	A	170;21	ENSP00000342952:T170A	ENSP00000342952:T170A	T	+	1	0	ADCY2	7573950	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.506000	0.73712	2.143000	0.66587	0.528000	0.53228	ACC	.	.		0.567	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		G	7520950	A	G	7520950	3	3	176	1	0	0	0	0	1	0	0	0	294	159	6	2	518	2	ADCY2	5	7520950	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10		7520950	173394310	43	26442										
FAM134B	54463	hgsc.bcm.edu	37	chr5	16617067	16617067	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cctcggcgtgctccggaggcGccgggctcgccatcttcagc	14	17	2	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:16617067G>T	ENST00000306320.9	-	1	100	c.14C>A	c.(13-15)gCg>gAg	p.A5E	CTC-461F20.1_ENST00000504935.1_lincRNA|FAM134B_ENST00000509048.1_5'UTR|RP11-260E18.1_ENST00000499131.1_RNA	NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	5					sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						CTCCGGAGGCGCCGGGCTCGC	0.801																																					p.A5E		Atlas-SNP	.											.	FAM134B	72	.	0			c.C14A						.						1	1	1					5																	16617067		575	1410	1985	SO:0001583	missense	54463	exon1			GGAGGCGCCGGGC	BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153			25964	protein-coding gene	gene with protein product		613114				19838196, 24327336	Standard	NM_001034850		Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.14C>A	chr5.hg19:g.16617067G>T	ENSP00000304642:p.Ala5Glu	176.0	0.0		295.0	77.0	NM_001034850	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	Missense_Mutation	SNP	ENST00000306320.9	hg19	CCDS43304.1	.	.	.	.	.	.	.	.	.	.	G	9.810	1.183003	0.21870	.	.	ENSG00000154153	ENST00000306320	T	0.48836	0.8	2.96	-0.694	0.11294	.	.	.	.	.	T	0.29458	0.0734	N	0.19112	0.55	0.19775	N	0.99996	B	0.06786	0.001	B	0.04013	0.001	T	0.25152	-1.0140	9	0.72032	D	0.01	-20.5905	6.875	0.24141	0.0:0.3495:0.4723:0.1782	.	5	Q9H6L5	F134B_HUMAN	E	5	ENSP00000304642:A5E	ENSP00000304642:A5E	A	-	2	0	FAM134B	16670067	0.814000	0.29104	0.906000	0.35671	0.002000	0.02628	2.250000	0.43178	-0.049000	0.13379	-1.133000	0.01973	GCG	.	.		0.801	FAM134B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366090.1	NM_001034850		T	16617067	G	T	16617067	3	4	176	1	0	0	0	0	1	0	0	0	5451	1087	38	1	1554	1	FAM134B	5	16617067	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	9096117	16617067	164298193	44	26443										
ITGA2	3673	hgsc.bcm.edu	37	chr5	52371063	52371063	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttctatagtgaaagccaagaAgaaaacaaggctgataattt	8	5	1	4			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:52371063A>G	ENST00000296585.5	+	23	2897	c.2754A>G	c.(2752-2754)gaA>gaG	p.E918E		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	918					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				AAAGCCAAGAAGAAAACAAGG	0.348																																					p.E918E		Atlas-SNP	.											.	ITGA2	211	.	0			c.A2754G						.						69	71	71					5																	52371063		2203	4300	6503	SO:0001819	synonymous_variant	3673	exon23			CCAAGAAGAAAAC		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2754A>G	chr5.hg19:g.52371063A>G		150.0	0.0		204.0	43.0	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	hg19	CCDS3957.1																																																																																			.	.		0.348	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		G	52371063	A	G	52371063	2	3	176	1	0	0	0	0	0	0	0	1	7884	69	3	2		2	ITGA2	5	52371063	Silent	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	35753996	52371063	128544197	45	26444										
MAST4	375449	hgsc.bcm.edu	37	chr5	66391425	66391425	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	taaactcactttctcaatagGactgatggacgccgctggtc	9	11	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:66391425G>T	ENST00000404260.3	+	7	1151	c.843G>T	c.(841-843)agG>agT	p.R281S	MAST4_ENST00000261569.7_Splice_Site_p.R84S|MAST4_ENST00000490016.2_Splice_Site_p.R89S|MAST4_ENST00000405643.1_Splice_Site_p.R99S|MAST4_ENST00000403666.1_Splice_Site_p.R89S|MAST4_ENST00000403625.2_Splice_Site_p.R278S			O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	281						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TTCTCAATAGGACTGATGGAC	0.468																																					p.R278S		Atlas-SNP	.											.	MAST4	218	.	0			c.G834T						.						82	87	85					5																	66391425		1972	4164	6136	SO:0001583	missense	375449	exon7			CAATAGGACTGAT	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000404260.3:c.843G>T	chr5.hg19:g.66391425G>T	ENSP00000385048:p.Arg281Ser	93.0	0.0		124.0	37.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000404260.3	hg19		.	.	.	.	.	.	.	.	.	.	G	19.07	3.756108	0.69648	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000490016;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000436277;ENST00000432399	T;T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46;1.46;1.46	6.04	4.26	0.50523	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.349077	0.10870	U	0.624992	T	0.53498	0.1800	M	0.71920	2.185	0.32711	N	0.511522	P;D;D;P;P	0.67145	0.866;0.996;0.995;0.917;0.949	P;D;P;P;P	0.65773	0.61;0.938;0.844;0.637;0.733	T	0.59731	-0.7399	10	0.62326	D	0.03	.	12.1009	0.53783	0.1395:0.0:0.8605:0.0	.	99;281;84;89;89	E7EWQ5;O15021;O15021-2;O15021-3;D6RAK1	.;MAST4_HUMAN;.;.;.	S	281;278;89;89;99;99;84;84;84	ENSP00000385048:R281S;ENSP00000385727:R278S;ENSP00000421739:R89S;ENSP00000384313:R89S;ENSP00000384099:R99S;ENSP00000261569:R84S;ENSP00000392478:R84S	ENSP00000261569:R84S	R	+	3	2	MAST4	66427181	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	2.945000	0.49043	0.871000	0.35750	0.563000	0.77884	AGG	.	.		0.468	MAST4-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				T	66391425	G	T	66391425	3	4	176	1	0	0	0	0	1	0	0	0	9336	1188	41	3	990	3	MAST4	5	66391425	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	14020362	66391425	114523835	46	26445										
NAIP	4671	hgsc.bcm.edu	37	chr5	70308629	70308629	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tccttctgctcctcttcttcTagttcctttgccaactgaac	4	15	4	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:70308629T>A	ENST00000517649.1	-	4	404	c.114A>T	c.(112-114)ctA>ctT	p.L38L	NAIP_ENST00000194097.4_Silent_p.L38L|NAIP_ENST00000523981.1_Intron|NAIP_ENST00000503719.2_Intron|NAIP_ENST00000508426.2_Silent_p.L38L	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	38					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		CCTCTTCTTCTAGTTCCTTTG	0.463																																					p.L38L		Atlas-SNP	.											.	NAIP	38	.	0			c.A114T						.						150	136	141					5																	70308629		2202	4296	6498	SO:0001819	synonymous_variant	4671	exon4			TTCTTCTAGTTCC	U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"Baculoviral IAP repeat containing", "Nucleotide-binding domain and leucine rich repeat containing"	7634	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1", "NLR family, BIR domain containing 1"	600355	"baculoviral IAP repeat-containing 1"	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.114A>T	chr5.hg19:g.70308629T>A		148.0	0.0		173.0	29.0	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Silent	SNP	ENST00000517649.1	hg19	CCDS4009.1																																																																																			.	.		0.463	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536		A	70308629	T	A	70308629	2	1	176	1	0	0	0	0	0	0	0	1	10156	1509	53	4		4	NAIP	5	70308629	Silent	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	3917204	70308629	110606631	47	26446										
SPATA9	83890	hgsc.bcm.edu	37	chr5	94994511	94994511	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gctccgaaagcacaggctcaGaaaaggcttttctacaattt	8	10	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:94994511G>A	ENST00000274432.8	-	5	722	c.581C>T	c.(580-582)tCt>tTt	p.S194F	RFESD_ENST00000508206.1_Intron|SPATA9_ENST00000477047.2_5'UTR	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	194					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)	7		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)		CACAGGCTCAGAAAAGGCTTT	0.423																																					p.S194F		Atlas-SNP	.											.	SPATA9	17	.	0			c.C581T						.						119	110	113					5																	94994511		2203	4299	6502	SO:0001583	missense	83890	exon5			GGCTCAGAAAAGG	AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.581C>T	chr5.hg19:g.94994511G>A	ENSP00000274432:p.Ser194Phe	63.0	0.0		112.0	37.0	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Missense_Mutation	SNP	ENST00000274432.8	hg19	CCDS4076.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.598019	0.46318	.	.	ENSG00000145757	ENST00000274432	T	0.33438	1.41	5.35	5.35	0.76521	.	0.000000	0.56097	D	0.000031	T	0.42877	0.1222	L	0.27053	0.805	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.33059	-0.9883	10	0.87932	D	0	-21.0328	14.4496	0.67376	0.0:0.0:1.0:0.0	.	194	Q9BWV2	SPAT9_HUMAN	F	194	ENSP00000274432:S194F	ENSP00000274432:S194F	S	-	2	0	SPATA9	95020267	1.000000	0.71417	0.991000	0.47740	0.086000	0.17979	4.225000	0.58600	2.799000	0.96334	0.637000	0.83480	TCT	.	.		0.423	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952		A	94994511	G	A	94994511	3	1	176	1	0	0	0	0	1	0	0	0	15031	942	33	3	187	3	SPATA9	5	94994511	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	24685882	94994511	85920749	48	26447										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128887588	128887588	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtgtgcacaaagatgaaccaTgtgatactgttggtaagtgt	12	5	0	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:128887588T>C	ENST00000274487.4	+	7	1487	c.1342T>C	c.(1342-1344)Tgt>Cgt	p.C448R	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	448	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		AGATGAACCATGTGATACTGT	0.313																																					p.C448R		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.T1342C						.						59	60	60					5																	128887588		2202	4291	6493	SO:0001583	missense	171019	exon7			GAACCATGTGATA	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1342T>C	chr5.hg19:g.128887588T>C	ENSP00000274487:p.Cys448Arg	114.0	0.0		97.0	48.0	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.174304	0.57692	.	.	ENSG00000145808	ENST00000274487	D	0.86562	-2.14	3.83	3.83	0.44106	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.64402	D	0.000001	D	0.90940	0.7152	L	0.58583	1.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90283	0.4316	9	.	.	.	.	12.5284	0.56100	0.0:0.0:0.0:1.0	.	448	Q8TE59	ATS19_HUMAN	R	448	ENSP00000274487:C448R	.	C	+	1	0	ADAMTS19	128915487	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	5.127000	0.64727	1.968000	0.57251	0.482000	0.46254	TGT	.	.		0.313	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		C	128887588	T	C	128887588	3	2	176	1	0	0	0	0	1	0	0	0	264	1464	51	2	1368	2	ADAMTS19	5	128887588	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	33893077	128887588	52027672	49	26448										
CDC23	8697	hgsc.bcm.edu	37	chr5	137527198	137527198	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agagccattttctccacatcTcccacggcgtaagctctcca	6	16	3	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:137527198T>C	ENST00000394886.2	-	13	1419	c.1389A>G	c.(1387-1389)ggA>ggG	p.G463G		NM_004661.3	NP_004652.2	Q9UJX2	CDC23_HUMAN	cell division cycle 23	463					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of exit from mitosis (GO:0007096)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(6)|prostate(2)|skin(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCTCCACATCTCCCACGGCGT	0.428																																					p.G463G		Atlas-SNP	.											.	CDC23	46	.	0			c.A1389G						.						187	185	186					5																	137527198		2203	4300	6503	SO:0001819	synonymous_variant	8697	exon13			CACATCTCCCACG	AF053977	CCDS4200.2	5q31	2013-01-17	2013-01-17		ENSG00000094880	ENSG00000094880		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1724	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 8"	603462	"CDC23 (cell division cycle 23, yeast, homolog)", "cell division cycle 23 homolog (S. cerevisiae)"			9790767	Standard	NM_004661		Approved	APC8, ANAPC8, CUT23	uc003lcl.3	Q9UJX2	OTTHUMG00000129198	ENST00000394886.2:c.1389A>G	chr5.hg19:g.137527198T>C		116.0	0.0		137.0	67.0	NM_004661	A8K6E5|B4E3A2|B7WP05|D3DQB7|O75433|Q53FN2|Q9BS73	Silent	SNP	ENST00000394886.2	hg19	CCDS4200.2																																																																																			.	.		0.428	CDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251275.2			C	137527198	T	C	137527198	2	2	176	1	0	0	0	0	0	0	0	1	3063	1538	54	2		2	CDC23	5	137527198	Silent	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	8639610	137527198	43388062	50	26449										
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140559603	140559603	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cgccacgctgcacttgctccTggtggacggcttctcccagc	11	17	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:140559603T>A	ENST00000239444.2	+	1	2233	c.1988T>A	c.(1987-1989)cTg>cAg	p.L663Q	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	663	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CACTTGCTCCTGGTGGACGGC	0.697																																					p.L663Q		Atlas-SNP	.											.	PCDHB8	199	.	0			c.T1988A						.						33	35	35					5																	140559603		2157	4218	6375	SO:0001583	missense	56128	exon1			TGCTCCTGGTGGA	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.1988T>A	chr5.hg19:g.140559603T>A	ENSP00000239444:p.Leu663Gln	72.0	0.0		77.0	39.0	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	hg19	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	T	15.42	2.829244	0.50845	.	.	ENSG00000120322	ENST00000239444	T	0.70282	-0.47	4.22	4.22	0.49857	Cadherin (3);Cadherin-like (1);	.	.	.	.	D	0.88610	0.6483	H	0.96662	3.86	0.33998	D	0.649901	D	0.58268	0.982	D	0.73708	0.981	D	0.94239	0.7483	9	0.87932	D	0	.	13.0554	0.58977	0.0:0.0:0.0:1.0	.	663	Q9UN66	PCDB8_HUMAN	Q	663	ENSP00000239444:L663Q	ENSP00000239444:L663Q	L	+	2	0	PCDHB8	140539787	0.005000	0.15991	1.000000	0.80357	0.530000	0.34684	1.622000	0.36997	1.561000	0.49584	0.248000	0.18094	CTG	.	.		0.697	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		A	140559603	T	A	140559603	3	1	176	1	0	0	0	0	1	0	0	0	11557	1580	55	4	1990	4	PCDHB8	5	140559603	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	3032405	140559603	40355657	51	26450										
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140810730	140810730	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	caatgcgccttactttcgtgAaagtgaattagaaataaaaa	7	6	0	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:140810730A>T	ENST00000252085.3	+	1	546	c.404A>T	c.(403-405)gAa>gTa	p.E135V	PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB8P_ENST00000502926.1_RNA|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA8_ENST00000398604.2_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	135	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACTTTCGTGAAAGTGAATTA	0.413																																					p.E135V		Atlas-SNP	.											.	PCDHGA12	271	.	0			c.A404T						.						79	93	88					5																	140810730		2203	4300	6503	SO:0001583	missense	26025	exon1			TTCGTGAAAGTGA	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.404A>T	chr5.hg19:g.140810730A>T	ENSP00000252085:p.Glu135Val	148.0	0.0		220.0	121.0	NM_032094	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	hg19	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	a	5.240	0.229717	0.09916	.	.	ENSG00000253159	ENST00000252085	T	0.19938	2.11	5.79	5.79	0.91817	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.17066	0.0410	N	0.22421	0.69	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.002	T	0.15723	-1.0427	9	0.25751	T	0.34	.	15.8034	0.78473	1.0:0.0:0.0:0.0	.	135;135	O60330-2;O60330	.;PCDGC_HUMAN	V	135	ENSP00000252085:E135V	ENSP00000252085:E135V	E	+	2	0	PCDHGA12	140790914	0.000000	0.05858	0.236000	0.24074	0.721000	0.41392	0.592000	0.23984	2.215000	0.71742	0.528000	0.53228	GAA	.	.		0.413	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		T	140810730	A	T	140810730	3	4	176	1	0	0	0	0	1	0	0	0	11562	246	9	4	406	4	PCDHGA12	5	140810730	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	251127	140810730	40104530	52	26451										
SLC26A2	1836	hgsc.bcm.edu	37	chr5	149360924	149360924	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttgtagcccctctctactacAtaaacaaagaatgctttaaa	4	10	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:149360924A>T	ENST00000286298.4	+	3	2036	c.1768A>T	c.(1768-1770)Ata>Tta	p.I590L		NM_000112.3	NP_000103.2	P50443	S26A2_HUMAN	solute carrier family 26 (anion exchanger), member 2	590	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|ossification (GO:0001503)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(1)|prostate(2)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			TCTCTACTACATAAACAAAGA	0.398																																					p.I590L		Atlas-SNP	.											.	SLC26A2	48	.	0			c.A1768T						.						75	81	79					5																	149360924		2203	4300	6503	SO:0001583	missense	1836	exon3			TACTACATAAACA	U14528	CCDS4300.1	5q31-q34	2014-09-17	2013-07-18		ENSG00000155850	ENSG00000155850		"Solute carriers"	10994	protein-coding gene	gene with protein product		606718	"solute carrier family 26 (sulfate transporter), member 2"	DTD		7923357	Standard	NM_000112		Approved	DTDST	uc003lrh.3	P50443	OTTHUMG00000130054	ENST00000286298.4:c.1768A>T	chr5.hg19:g.149360924A>T	ENSP00000286298:p.Ile590Leu	64.0	0.0		91.0	48.0	NM_000112	A8K2U3|B2R6J1|Q6N051	Missense_Mutation	SNP	ENST00000286298.4	hg19	CCDS4300.1	.	.	.	.	.	.	.	.	.	.	A	14.07	2.425079	0.43020	.	.	ENSG00000155850	ENST00000286298	D	0.87729	-2.29	6.07	1.15	0.20763	Sulphate transporter/antisigma-factor antagonist STAS (4);	0.202691	0.53938	D	0.000051	T	0.81749	0.4888	L	0.44542	1.39	0.26728	N	0.970651	B	0.22414	0.069	B	0.29176	0.099	T	0.74124	-0.3766	10	0.87932	D	0	.	9.8135	0.40838	0.5896:0.0:0.4104:0.0	.	590	P50443	S26A2_HUMAN	L	590	ENSP00000286298:I590L	ENSP00000286298:I590L	I	+	1	0	SLC26A2	149341117	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	3.237000	0.51344	0.184000	0.20083	-0.250000	0.11733	ATA	.	.		0.398	SLC26A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252333.2	NM_000112		T	149360924	A	T	149360924	3	4	176	1	0	0	0	0	1	0	0	0	14532	217	8	4	1774	4	SLC26A2	5	149360924	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	8550194	149360924	31554336	53	26452										
CNOT8	9337	hgsc.bcm.edu	37	chr5	154242880	154242880	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aatagccaggttatctgtgaAgtgtgggccagtaatctaga	12	6	2	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:154242880A>C	ENST00000517876.1	+	3	518	c.42A>C	c.(40-42)gaA>gaC	p.E14D	CNOT8_ENST00000524105.1_Intron|CNOT8_ENST00000521402.1_3'UTR|CNOT8_ENST00000403027.2_Missense_Mutation_p.E14D|CNOT8_ENST00000521583.1_Intron|CNOT8_ENST00000521450.1_Intron|CNOT8_ENST00000519404.1_Missense_Mutation_p.E14D|CNOT8_ENST00000520671.1_Intron|CNOT8_ENST00000523698.1_Intron|CNOT8_ENST00000285896.6_Missense_Mutation_p.E14D			Q9UFF9	CNOT8_HUMAN	CCR4-NOT transcription complex, subunit 8	14					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|mRNA metabolic process (GO:0016071)|negative regulation of cell proliferation (GO:0008285)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TTATCTGTGAAGTGTGGGCCA	0.458																																					p.E14D	NSCLC(140;1804 1895 27149 29895 35312)	Atlas-SNP	.											.	CNOT8	20	.	0			c.A42C						.						206	191	196					5																	154242880		2203	4300	6503	SO:0001583	missense	9337	exon2			CTGTGAAGTGTGG	AF053318	CCDS4329.1, CCDS75361.1	5q31-q33	2008-07-18			ENSG00000155508	ENSG00000155508			9207	protein-coding gene	gene with protein product	"PGK promoter directed over production"	603731		POP2		10036195, 10637334	Standard	XM_005268527		Approved	CAF1, hCAF1, CALIF	uc003lvw.3	Q9UFF9	OTTHUMG00000130192	ENST00000517876.1:c.42A>C	chr5.hg19:g.154242880A>C	ENSP00000430493:p.Glu14Asp	137.0	0.0		189.0	10.0	NM_004779	B0AZS3|B2RAR8|B7Z8R1|D3DQI8|O95709|Q7Z521|Q9H6Y1	Missense_Mutation	SNP	ENST00000517876.1	hg19	CCDS4329.1	.	.	.	.	.	.	.	.	.	.	A	9.621	1.133845	0.21123	.	.	ENSG00000155508	ENST00000517876;ENST00000520472;ENST00000519211;ENST00000522458;ENST00000403027;ENST00000517568;ENST00000285896;ENST00000519430;ENST00000518028;ENST00000519404;ENST00000519394;ENST00000518775	T;T;T;T;T;T;T;T;T;T;T;T	0.42131	0.98;1.85;0.98;0.98;0.98;0.98;0.98;1.85;1.85;0.98;1.85;0.98	5.2	2.84	0.33178	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.18130	0.0435	N	0.04705	-0.18	0.52501	D	0.999956	B;B	0.14805	0.011;0.0	B;B	0.24155	0.051;0.003	T	0.09707	-1.0662	10	0.06757	T	0.87	-14.2761	8.241	0.31660	0.6843:0.0:0.3157:0.0	.	14;14	B7Z8R1;Q9UFF9	.;CNOT8_HUMAN	D	14	ENSP00000430493:E14D;ENSP00000430215:E14D;ENSP00000429108:E14D;ENSP00000428550:E14D;ENSP00000384747:E14D;ENSP00000428090:E14D;ENSP00000285896:E14D;ENSP00000429310:E14D;ENSP00000429810:E14D;ENSP00000430833:E14D;ENSP00000428842:E14D;ENSP00000429394:E14D	ENSP00000285896:E14D	E	+	3	2	CNOT8	154223073	1.000000	0.71417	0.998000	0.56505	0.867000	0.49689	1.580000	0.36547	0.326000	0.23384	-0.256000	0.11100	GAA	.	.		0.458	CNOT8-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377449.1	NM_004779		C	154242880	A	C	154242880	3	2	176	1	0	0	0	0	1	0	0	0	3627	69	3	5	44	5	CNOT8	5	154242880	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	4881956	154242880	26672380	54	26453										
SGCD	6444	hgsc.bcm.edu	37	chr5	156184773	156184773	+	Intron	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcttcaacaggccaacccttCccataactggttgacctcgg	8	15	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:156184773C>A	ENST00000435422.3	+	7	1183				SGCD_ENST00000517913.1_Missense_Mutation_p.P253T|SGCD_ENST00000447401.1_Missense_Mutation_p.P253T|SGCD_ENST00000337851.4_Intron	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)						muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GCCAACCCTTCCCATAACTGG	0.453																																					p.P253T		Atlas-SNP	.											.	SGCD	52	.	0			c.C757A						.						67	68	67					5																	156184773		1940	4152	6092	SO:0001627	intron_variant	6444	exon8			ACCCTTCCCATAA	BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29						10807	protein-coding gene	gene with protein product		601411	"sarcoglycan, delta (35kD dystrophin-associated glycoprotein)"			8776597, 8841194, 10974018	Standard	NM_000337		Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000435422.3:c.696+58C>A	chr5.hg19:g.156184773C>A		366.0	0.0		442.0	44.0	NM_172244	A8K9S9|Q53XA5|Q99644	Missense_Mutation	SNP	ENST00000435422.3	hg19	CCDS47327.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.512846	0.27123	.	.	ENSG00000170624	ENST00000517913;ENST00000447401	T;T	0.32515	1.45;1.45	3.97	2.13	0.27403	.	.	.	.	.	T	0.23492	0.0568	.	.	.	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.24512	-1.0158	8	0.87932	D	0	.	7.0782	0.25217	0.0:0.6924:0.1446:0.1629	.	253	Q92629-3	.	T	253	ENSP00000429378:P253T;ENSP00000408324:P253T	ENSP00000408324:P253T	P	+	1	0	SGCD	156117351	0.000000	0.05858	0.003000	0.11579	0.017000	0.09413	-0.320000	0.08028	0.615000	0.30124	0.655000	0.94253	CCC	.	.		0.453	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3			A	156184773	C	A	156184773	1	1	176	0	1	0	0	0	0	0	0	0	14216	855	30	3		3	SGCD	5	156184773	Intron	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	1941893	156184773	24730487	55	26454										
SOX30	11063	hgsc.bcm.edu	37	chr5	157065283	157065283	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtaggaagtaagggtgatgaAaagagaatcttggtggtgtc	16	2	1	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr5:157065283A>G	ENST00000265007.6	-	4	2176	c.1835T>C	c.(1834-1836)tTt>tCt	p.F612S	SOX30_ENST00000311371.5_Intron|SOX30_ENST00000519442.1_Missense_Mutation_p.F307S	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	612	Pro-rich.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AGGGTGATGAAAAGAGAATCT	0.478																																					p.F612S	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.T1835C						.						80	79	79					5																	157065283		2203	4300	6503	SO:0001583	missense	11063	exon4			TGATGAAAAGAGA	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"SRY (sex determining region Y)-boxes"	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.1835T>C	chr5.hg19:g.157065283A>G	ENSP00000265007:p.Phe612Ser	209.0	0.0		331.0	42.0	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	hg19	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	A	18.42	3.619753	0.66787	.	.	ENSG00000039600	ENST00000265007;ENST00000519442	D;D	0.98264	-4.7;-4.83	5.61	5.61	0.85477	.	0.000000	0.64402	D	0.000010	D	0.97430	0.9159	L	0.27053	0.805	0.38540	D	0.949194	D;D	0.89917	0.979;1.0	P;D	0.64144	0.702;0.922	D	0.98737	1.0715	10	0.87932	D	0	.	11.6296	0.51166	0.8523:0.1477:0.0:0.0	.	307;612	B4DXW7;O94993	.;SOX30_HUMAN	S	612;307	ENSP00000265007:F612S;ENSP00000427984:F307S	ENSP00000265007:F612S	F	-	2	0	SOX30	156997861	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.417000	0.59822	2.135000	0.66039	0.528000	0.53228	TTT	.	.		0.478	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		G	157065283	A	G	157065283	3	3	176	1	0	0	0	0	1	0	0	0	14967	14	1	2	434	2	SOX30	5	157065283	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	880510	157065283	23849977	56	26455										
ZNF391	346157	hgsc.bcm.edu	37	chr6	27368626	27368626	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	attgaacatcaaagaactcaCactggagagaaaccttatga	7	8	2	4			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr6:27368626C>T	ENST00000244576.4	+	3	1022	c.477C>T	c.(475-477)caC>caT	p.H159H		NM_001076781.1	NP_001070249.1	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	159					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(6)|lung(7)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	21						AAAGAACTCACACTGGAGAGA	0.393																																					p.H159H		Atlas-SNP	.											.	ZNF391	90	.	0			c.C477T						.						88	95	92					6																	27368626		2199	4298	6497	SO:0001819	synonymous_variant	346157	exon3			AACTCACACTGGA	BC132797	CCDS43429.1	6p21	2013-01-08			ENSG00000124613	ENSG00000124613		"Zinc fingers, C2H2-type"	18779	protein-coding gene	gene with protein product							Standard	NM_001076781		Approved	dJ153G14.3	uc003njf.1	Q9UJN7	OTTHUMG00000014477	ENST00000244576.4:c.477C>T	chr6.hg19:g.27368626C>T		164.0	0.0		206.0	82.0	NM_001076781	B4DH77	Silent	SNP	ENST00000244576.4	hg19	CCDS43429.1																																																																																			.	.		0.393	ZNF391-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040145.2	NM_001076781		T	27368626	C	T	27368626	2	4	176	1	0	0	0	0	0	0	0	1	17894	477	17	3		3	ZNF391	6	27368626	Silent	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10		27368626	143746441	57	26456										
RPP21	79897	hgsc.bcm.edu	37	chr6	30314488	30314488	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ctgattctgctcatttactcAgattccaaaccactacaacc	3	14	3	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr6:30314488A>T	ENST00000442966.2	+	5	380		c.e5-1		RPP21_ENST00000428040.2_Splice_Site|RPP21_ENST00000433076.2_Splice_Site|RPP21_ENST00000436442.2_Splice_Site|TRIM39-RPP21_ENST00000513556.1_Splice_Site			Q9H633	RPP21_HUMAN	ribonuclease P/MRP 21kDa subunit						response to drug (GO:0042493)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonuclease P activity (GO:0004526)			endometrium(2)|ovary(1)|prostate(1)	4						TCATTTACTCAGATTCCAAAC	0.463																																					.		Atlas-SNP	.											.	RPP21	11	.	0			c.375-2A>T						.						192	200	197					6																	30314488		1511	2709	4220	SO:0001630	splice_region_variant	79897	exon5			TTACTCAGATTCC	AK026291	CCDS4679.1, CCDS56409.1, CCDS56410.1	6p21.32	2012-05-21	2007-06-26	2004-03-19	ENSG00000241370	ENSG00000241370			21300	protein-coding gene	gene with protein product		612524	"chromosome 6 open reading frame 135", "ribonuclease P 21kDa subunit"	C6orf135			Standard	NM_001199120		Approved	FLJ22638, Em:AB014085.3		Q9H633	OTTHUMG00000031220	ENST00000442966.2:c.368-1A>T	chr6.hg19:g.30314488A>T		106.0	0.0		131.0	51.0	NM_001199121	A2AAZ8|B0S834|B0S835|Q5JPL9|Q5JPM1|Q5STF8|Q5STF9|Q5STG2|Q5SU41|Q5SU42|Q86Y49|Q86Y50|Q86Y51|Q96F16	Splice_Site	SNP	ENST00000442966.2	hg19	CCDS4679.1	.	.	.	.	.	.	.	.	.	.	A	11.12	1.545539	0.27652	.	.	ENSG00000204599;ENSG00000248167;ENSG00000241370;ENSG00000241370;ENSG00000241370;ENSG00000241370	ENST00000412529;ENST00000513556;ENST00000433076;ENST00000442966;ENST00000428040;ENST00000436442	.	.	.	4.94	3.76	0.43208	.	.	.	.	.	.	.	.	.	.	.	0.54753	D	0.999989	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.1552	0.31165	0.8221:0.0:0.0:0.1779	.	.	.	.	.	-1	.	.	.	+	.	.	RPP21;TRIM39-RPP21;TRIM39	30422467	0.962000	0.33011	0.137000	0.22149	0.096000	0.18686	2.370000	0.44240	0.994000	0.38892	0.533000	0.62120	.	.	.		0.463	RPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076451.2	NM_024839	Intron	T	30314488	A	T	30314488	5	4	176	1	0	0	0	0	0	0	1	0	13625	202	7	4	384	4	RPP21	6	30314488	Splice_Site	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	2945862	30314488	140800579	58	26457										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32180406	32180406	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cacataagtccatcagagtcTgaggggtgggagggagcgtg	17	7	2	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr6:32180406T>A	ENST00000375023.3	-	17	2665		c.e17-2		NOTCH4_ENST00000465528.1_Splice_Site	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4						cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CATCAGAGTCTGAGGGGTGGG	0.582																																					.		Atlas-SNP	.											.	NOTCH4	201	.	0			c.2527-2A>T						.						103	86	92					6																	32180406		1510	2707	4217	SO:0001630	splice_region_variant	4855	exon18			AGAGTCTGAGGGG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.2527-2A>T	chr6.hg19:g.32180406T>A		112.0	0.0		128.0	20.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Splice_Site	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.628123	0.46944	.	.	ENSG00000204301	ENST00000375023	.	.	.	4.35	4.35	0.52113	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.7824	0.52021	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NOTCH4	32288384	1.000000	0.71417	0.963000	0.40424	0.569000	0.35902	5.704000	0.68347	1.959000	0.56917	0.459000	0.35465	.	.	.		0.582	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		Intron	A	32180406	T	A	32180406	5	1	176	1	0	0	0	0	0	0	1	0	10560	1594	55	4	3542	4	NOTCH4	6	32180406	Splice_Site	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	1865918	32180406	138934661	59	26458										
HLA-DQB1	3119	hgsc.bcm.edu	37	chr6	32632742	32632742	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cccccacgtcgctgtcgaagCgcgcgtactcctctcggtta	10	17	1	0	rs281862072		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr6:32632742C>T	ENST00000399084.1	-	3	390	c.212G>A	c.(211-213)cGc>cAc	p.R71H	HLA-DQB1_ENST00000399082.3_Intron|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.R71H|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.R71H|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.R71H			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	71	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""Insulin(DB00071)"	GCTGTCGAAGCGCGCGTACTC	0.612									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.R71H	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G212A						.						38	38	38					6																	32632742		2138	4235	6373	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TCGAAGCGCGCGT		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.212G>A	chr6.hg19:g.32632742C>T	ENSP00000382034:p.Arg71His	61.0	0.0		69.0	30.0	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399084.1	hg19	CCDS43451.1	.	.	.	.	.	.	.	.	.	.	.	10.84	1.463525	0.26248	.	.	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.00367	7.78;7.78;7.78;7.78	4.06	3.19	0.36642	.	0.413935	0.22513	U	0.059068	T	0.00109	0.0003	M	0.73430	2.235	0.32384	N	0.554176	P;B;B;P;B	0.44429	0.835;0.251;0.407;0.55;0.136	B;B;B;B;B	0.33042	0.139;0.09;0.09;0.157;0.067	T	0.46610	-0.9179	10	0.72032	D	0.01	.	6.2113	0.20631	0.0:0.7732:0.0:0.2267	.	81;71;36;71;71	Q59F80;A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.;.	H	71	ENSP00000382029:R71H;ENSP00000364080:R71H;ENSP00000407332:R71H;ENSP00000382034:R71H	ENSP00000364080:R71H	R	-	2	0	HLA-DQB1	32740720	0.914000	0.31030	0.997000	0.53966	0.041000	0.13682	1.127000	0.31357	0.935000	0.37341	0.305000	0.20034	CGC	.	.		0.612	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123		T	32632742	C	T	32632742	3	4	176	1	0	0	0	0	1	0	0	0	7215	768	27	1	589	1	HLA-DQB1	6	32632742	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	452336	32632742	138482325	60	26459										
GJB7	375519	hgsc.bcm.edu	37	chr6	87994409	87994409	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agttgtaaggcccaaagtctGacttgggaaatggggaagaa	14	5	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr6:87994409G>A	ENST00000525899.1	-	3	567	c.222C>T	c.(220-222)gtC>gtT	p.V74V	GJB7_ENST00000296882.3_Silent_p.V74V	NM_198568.2	NP_940970.1	Q6PEY0	CXB7_HUMAN	gap junction protein, beta 7, 25kDa	74					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)	5		all_cancers(76;1.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;7.38e-10)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00323)		BRCA - Breast invasive adenocarcinoma(108;0.0167)		CCCAAAGTCTGACTTGGGAAA	0.448																																					p.V74V		Atlas-SNP	.											.	GJB7	28	.	0			c.C222T						.						118	111	114					6																	87994409		2203	4300	6503	SO:0001819	synonymous_variant	375519	exon3			AAGTCTGACTTGG	AJ414563	CCDS5008.1	6q15	2008-02-05	2007-11-06			ENSG00000164411		"Ion channels / Gap junction proteins (connexins)"	16690	protein-coding gene	gene with protein product	"connexin 25"	611921	"gap junction protein, beta 7"				Standard	NM_198568		Approved	CX25, bA136M9.1	uc003plo.2	Q6PEY0		ENST00000525899.1:c.222C>T	chr6.hg19:g.87994409G>A		144.0	0.0		204.0	56.0	NM_198568	B3KXL0|Q96KP0	Silent	SNP	ENST00000525899.1	hg19	CCDS5008.1																																																																																			.	.		0.448	GJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394780.1			A	87994409	G	A	87994409	2	1	176	1	0	0	0	0	0	0	0	1	6421	1277	45	3		3	GJB7	6	87994409	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	55361667	87994409	83120658	61	26460										
ROS1	6098	hgsc.bcm.edu	37	chr6	117609803	117609803	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cttctttcctcagaccacaaGattcagattcctgggagcct	7	13	3	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr6:117609803G>C	ENST00000368508.3	-	43	7094	c.6896C>G	c.(6895-6897)tCt>tGt	p.S2299C	ROS1_ENST00000368507.3_Missense_Mutation_p.S2293C	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2299					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CAGACCACAAGATTCAGATTC	0.473			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.S2299C		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.C6896G						.						104	105	105					6																	117609803		2203	4300	6503	SO:0001583	missense	6098	exon43			CCACAAGATTCAG	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.6896C>G	chr6.hg19:g.117609803G>C	ENSP00000357494:p.Ser2299Cys	110.0	0.0		174.0	70.0	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	hg19	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.426786	0.43020	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.72167	-0.62;-0.63	4.5	3.62	0.41486	.	0.129523	0.34986	N	0.003528	T	0.44767	0.1309	L	0.29908	0.895	0.09310	N	1	D	0.55172	0.97	P	0.47206	0.541	T	0.35943	-0.9768	10	0.54805	T	0.06	.	7.23	0.26036	0.0909:0.0:0.7427:0.1663	.	2299	P08922	ROS1_HUMAN	C	2299;2293	ENSP00000357494:S2299C;ENSP00000357493:S2293C	ENSP00000357493:S2293C	S	-	2	0	ROS1	117716496	0.269000	0.24143	0.248000	0.24265	0.979000	0.70002	1.170000	0.31883	1.082000	0.41137	0.563000	0.77884	TCT	.	.		0.473	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			C	117609803	G	C	117609803	3	2	176	1	0	0	0	0	1	0	0	0	13546	942	33	4	151	4	ROS1	6	117609803	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	29615394	117609803	53505264	62	26461										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157505501	157505501	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	caagatcgaacgtggggaggAgcccccgccggaagtcttca	14	12	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr6:157505501A>T	ENST00000350026.5	+	12	3444	c.3443A>T	c.(3442-3444)gAg>gTg	p.E1148V	ARID1B_ENST00000367148.1_Missense_Mutation_p.E1201V|ARID1B_ENST00000346085.5_Missense_Mutation_p.E1161V|ARID1B_ENST00000275248.4_Missense_Mutation_p.E1143V	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1148					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CGTGGGGAGGAGCCCCCGCCG	0.582																																					p.E1161V		Atlas-SNP	.											.	ARID1B	320	.	0			c.A3482T						.						58	59	58					6																	157505501		2203	4296	6499	SO:0001583	missense	57492	exon13			GGGAGGAGCCCCC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3443A>T	chr6.hg19:g.157505501A>T	ENSP00000055163:p.Glu1148Val	187.0	0.0		252.0	48.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	16.84	3.234045	0.58886	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000354354;ENST00000414678;ENST00000319584;ENST00000400790	T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.91	5.91	0.95273	ARID/BRIGHT DNA-binding domain (2);	0.000000	0.85682	D	0.000000	T	0.44767	0.1309	L	0.43152	1.355	0.80722	D	1	D;D;D;D	0.69078	0.997;0.988;0.993;0.993	P;P;P;P	0.59056	0.851;0.606;0.779;0.779	T	0.47086	-0.9144	10	0.72032	D	0.01	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	398;1148;1161;1143	Q8NFD5-4;Q8NFD5;Q8NFD5-2;G3XAA0	.;ARI1B_HUMAN;.;.	V	1161;1148;1201;1143;618;670;623;215	ENSP00000344546:E1161V;ENSP00000055163:E1148V;ENSP00000356116:E1201V;ENSP00000275248:E1143V;ENSP00000412835:E670V;ENSP00000313006:E623V;ENSP00000383596:E215V	ENSP00000275248:E1143V	E	+	2	0	ARID1B	157547193	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.329000	0.96413	2.254000	0.74563	0.533000	0.62120	GAG	.	.		0.582	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		T	157505501	A	T	157505501	3	4	176	1	0	0	0	0	1	0	0	0	914	304	11	4	3532	4	ARID1B	6	157505501	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	39895698	157505501	13609566	63	26462										
FRMD1	79981	hgsc.bcm.edu	37	chr6	168465694	168465694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcactgtgacctcagcacgcGctccttcaagtggcagtagt	11	13	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr6:168465694G>A	ENST00000283309.6	-	5	569	c.505C>T	c.(505-507)Cgc>Tgc	p.R169C	FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000537786.1_5'UTR|FRMD1_ENST00000440994.2_Missense_Mutation_p.R101C	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	169	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		CTCAGCACGCGCTCCTTCAAG	0.672																																					p.R169C	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.C505T						.						60	51	54					6																	168465694		2203	4300	6503	SO:0001583	missense	79981	exon5			GCACGCGCTCCTT		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.505C>T	chr6.hg19:g.168465694G>A	ENSP00000283309:p.Arg169Cys	30.0	0.0		54.0	7.0	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	hg19	CCDS5306.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.307886	0.40895	.	.	ENSG00000153303	ENST00000283309;ENST00000440994	T;T	0.78246	-1.16;-1.16	2.75	1.83	0.25207	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.374549	0.22213	U	0.063074	T	0.78304	0.4262	L	0.58101	1.795	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.75020	0.959;0.985;0.954	T	0.78473	-0.2190	10	0.62326	D	0.03	.	10.3608	0.43991	0.0:0.0:0.7875:0.2125	.	81;169;101	B7Z8G9;Q8N878;Q8N878-2	.;FRMD1_HUMAN;.	C	169;101	ENSP00000283309:R169C;ENSP00000414115:R101C	ENSP00000283309:R169C	R	-	1	0	FRMD1	168208543	1.000000	0.71417	0.530000	0.27963	0.051000	0.14879	6.047000	0.71038	0.307000	0.22880	0.313000	0.20887	CGC	.	.		0.672	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919		A	168465694	G	A	168465694	3	1	176	1	0	0	0	0	1	0	0	0	6057	1087	38	1	1172	1	FRMD1	6	168465694	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	10960193	168465694	2649373	64	26463										
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	10	12	0	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000230354.6_Silent_p.Q60Q|TBP_ENST00000540980.1_Silent_p.Q40Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		66.0	0.0		93.0	7.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	176	1	0	0	0	0	0	0	0	1	15659	962	34	3		3	TBP	6	170871004	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	2405310	170871004	244063	65	26464										
AMZ1	155185	hgsc.bcm.edu	37	chr7	2748314	2748314	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	acctgtacccccatgaggccTggagcttcaccttcagcaag	9	15	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:2748314T>A	ENST00000312371.4	+	4	933	c.565T>A	c.(565-567)Tgg>Agg	p.W189R	AMZ1_ENST00000407112.1_Missense_Mutation_p.W189R|AMZ1_ENST00000489665.1_3'UTR	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	189							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		CCATGAGGCCTGGAGCTTCAC	0.652																																					p.W189R		Atlas-SNP	.											.	AMZ1	41	.	0			c.T565A						.						95	80	85					7																	2748314		2203	4300	6503	SO:0001583	missense	155185	exon4			GAGGCCTGGAGCT	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"archaemetzincin-1"	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.565T>A	chr7.hg19:g.2748314T>A	ENSP00000308149:p.Trp189Arg	37.0	0.0		43.0	16.0	NM_133463	B3KRS0|Q8TF51	Missense_Mutation	SNP	ENST00000312371.4	hg19	CCDS34589.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.281509	0.59758	.	.	ENSG00000174945	ENST00000312371;ENST00000407112	T;T	0.77489	-1.1;-1.1	4.29	4.29	0.51040	.	0.000000	0.85682	D	0.000000	D	0.87696	0.6242	M	0.80183	2.485	0.49389	D	0.99978	D;P	0.89917	1.0;0.952	D;P	0.91635	0.999;0.694	D	0.89529	0.3784	10	0.87932	D	0	-24.9435	13.7325	0.62797	0.0:0.0:0.0:1.0	.	189;189	B3KRS0;Q400G9	.;AMZ1_HUMAN	R	189	ENSP00000308149:W189R;ENSP00000386020:W189R	ENSP00000308149:W189R	W	+	1	0	AMZ1	2714840	1.000000	0.71417	0.993000	0.49108	0.363000	0.29612	4.528000	0.60580	1.689000	0.51079	0.379000	0.24179	TGG	.	.		0.652	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463		A	2748314	T	A	2748314	3	1	176	1	0	0	0	0	1	0	0	0	596	1580	55	4	575	4	AMZ1	7	2748314	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10		2748314	156390349	66	26465										
GNA12	2768	hgsc.bcm.edu	37	chr7	2834735	2834735	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	attttcagaatactgccaagGaatgccaagcttatctcgtg	8	9	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:2834735G>C	ENST00000275364.3	-	2	514	c.352C>G	c.(352-354)Cct>Gct	p.P118A	GNA12_ENST00000407904.3_Missense_Mutation_p.P59A|GNA12_ENST00000544127.1_Missense_Mutation_p.P42A	NM_007353.2	NP_031379.2	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein) alpha 12	118					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic digit morphogenesis (GO:0042733)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|platelet activation (GO:0030168)|regulation of cell shape (GO:0008360)|regulation of fibroblast migration (GO:0010762)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)|response to drug (GO:0042493)|Rho protein signal transduction (GO:0007266)	brush border membrane (GO:0031526)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		TACTGCCAAGGAATGCCAAGC	0.478																																					p.P118A		Atlas-SNP	.											.	GNA12	35	.	0			c.C352G						.						157	152	154					7																	2834735		2203	4300	6503	SO:0001583	missense	2768	exon2			GCCAAGGAATGCC	L01694	CCDS5335.1, CCDS64584.1, CCDS64583.1	7p22.3	2006-07-08			ENSG00000146535	ENSG00000146535			4380	protein-coding gene	gene with protein product		604394				8423800, 16247467	Standard	NM_007353		Approved	gep	uc003smu.3	Q03113	OTTHUMG00000023064	ENST00000275364.3:c.352C>G	chr7.hg19:g.2834735G>C	ENSP00000275364:p.Pro118Ala	85.0	0.0		164.0	63.0	NM_007353	A4D204|B3KXS2|B7Z3F7|Q2T9L1|Q5PPR5|Q86UM8|Q8TD71|Q9UDU9	Missense_Mutation	SNP	ENST00000275364.3	hg19	CCDS5335.1	.	.	.	.	.	.	.	.	.	.	G	8.657	0.899656	0.17686	.	.	ENSG00000146535	ENST00000275364;ENST00000407904;ENST00000544127;ENST00000447791	D;D;D	0.88124	-2.34;-2.34;-2.34	5.58	5.58	0.84498	G protein alpha subunit, helical insertion (2);	0.300803	0.37393	N	0.002119	D	0.86306	0.5901	M	0.64404	1.975	0.54753	D	0.999987	B;B;B	0.18310	0.006;0.001;0.027	B;B;B	0.16289	0.006;0.006;0.015	T	0.82452	-0.0450	10	0.49607	T	0.09	.	17.7636	0.88470	0.0:0.0:1.0:0.0	.	118;118;59	Q5PPR5;Q03113;B3KXS2	.;GNA12_HUMAN;.	A	118;59;42;33	ENSP00000275364:P118A;ENSP00000385935:P59A;ENSP00000437469:P42A	ENSP00000275364:P118A	P	-	1	0	GNA12	2801261	1.000000	0.71417	0.173000	0.22940	0.700000	0.40528	2.881000	0.48538	2.641000	0.89580	0.563000	0.77884	CCT	.	.		0.478	GNA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241608.1	NM_007353		C	2834735	G	C	2834735	3	2	176	1	0	0	0	0	1	0	0	0	6508	1174	41	4	805	4	GNA12	7	2834735	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	86421	2834735	156303928	67	26466										
CARD11	84433	hgsc.bcm.edu	37	chr7	2946324	2946324	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tgcgctgctcctcgccgatcTtgtccttgacaacgcggagc	11	15	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:2946324T>A	ENST00000396946.4	-	25	3816	c.3413A>T	c.(3412-3414)aAg>aTg	p.K1138M		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	1138	Guanylate kinase-like.				Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CTCGCCGATCTTGTCCTTGAC	0.647			Mis		DLBCL																																p.K1138M		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.A3413T						.						93	76	82					7																	2946324		2203	4300	6503	SO:0001583	missense	84433	exon25			CCGATCTTGTCCT	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.3413A>T	chr7.hg19:g.2946324T>A	ENSP00000380150:p.Lys1138Met	98.0	0.0		188.0	63.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	14.92	2.680010	0.47886	.	.	ENSG00000198286	ENST00000396946	T	0.17054	2.3	3.68	2.52	0.30459	.	0.092076	0.44902	D	0.000419	T	0.12092	0.0294	L	0.44542	1.39	0.42253	D	0.99198	P	0.42078	0.77	B	0.35899	0.213	T	0.08827	-1.0703	10	0.39692	T	0.17	-25.6192	7.7319	0.28791	0.0:0.1867:0.0:0.8133	.	1138	Q9BXL7	CAR11_HUMAN	M	1138	ENSP00000380150:K1138M	ENSP00000380150:K1138M	K	-	2	0	CARD11	2912850	1.000000	0.71417	0.990000	0.47175	0.992000	0.81027	1.465000	0.35299	0.328000	0.23435	0.418000	0.28097	AAG	.	.		0.647	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2946324	T	A	2946324	3	1	176	1	0	0	0	0	1	0	0	0	2647	1609	56	4	55	4	CARD11	7	2946324	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	111589	2946324	156192339	68	26467										
TWIST1	7291	hgsc.bcm.edu	37	chr7	19156809	19156809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gggccccgcgccgccgcccgCgctgcgcctgctgctgcgcc	15	22	0	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:19156809C>T	ENST00000242261.5	-	1	486	c.136G>A	c.(136-138)Gcg>Acg	p.A46T	AC003986.7_ENST00000417460.1_RNA|AC003986.6_ENST00000419944.1_RNA	NM_000474.3	NP_000465.1	Q15672	TWST1_HUMAN	twist family bHLH transcription factor 1	46					aortic valve morphogenesis (GO:0003180)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in heart valve development (GO:2000793)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|cranial suture morphogenesis (GO:0060363)|embryonic camera-type eye formation (GO:0060900)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cushion morphogenesis (GO:0003203)|eyelid development in camera-type eye (GO:0061029)|in utero embryonic development (GO:0001701)|mitral valve morphogenesis (GO:0003183)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of oxidative phosphorylation uncoupler activity (GO:2000276)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|outer ear morphogenesis (GO:0042473)|palate development (GO:0060021)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell motility (GO:2000147)|positive regulation of endocardial cushion to mesenchymal transition involved in heart valve formation (GO:2000802)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of bone mineralization (GO:0030500)|rhythmic process (GO:0048511)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription factor binding (GO:0008134)			lung(2)|upper_aerodigestive_tract(1)	3						ccgccgcccgcgctgcgcctg	0.791																																					p.A46T		Atlas-SNP	.											.	TWIST1	18	.	0			c.G136A						.						1	1	1					7																	19156809		497	928	1425	SO:0001583	missense	7291	exon1			CGCCCGCGCTGCG	U80998	CCDS5367.1	7p21	2014-02-07	2013-10-17	2003-03-28	ENSG00000122691	ENSG00000122691		"Basic helix-loop-helix proteins"	12428	protein-coding gene	gene with protein product	"Saethre-Chotzen syndrome"	601622	"blepharophimosis, epicanthus inversus and ptosis 3", "acrocephalosyndactyly 3", "twist homolog 1 (Drosophila)", "twist basic helix-loop-helix transcription factor 1", "craniosynostosis"	ACS3, BPES3, TWIST, CRS		8995765, 11474656, 17343269	Standard	XR_428085		Approved	SCS, H-twist, BPES2, bHLHa38, CRS1	uc003sum.3	Q15672	OTTHUMG00000090821	ENST00000242261.5:c.136G>A	chr7.hg19:g.19156809C>T	ENSP00000242261:p.Ala46Thr	121.0	0.0		234.0	38.0	NM_000474	A4D128|Q92487|Q99804	Missense_Mutation	SNP	ENST00000242261.5	hg19	CCDS5367.1	.	.	.	.	.	.	.	.	.	.	N	11.31	1.599865	0.28534	.	.	ENSG00000122691	ENST00000242261	D	0.91686	-2.89	3.73	3.73	0.42828	.	0.459579	0.15411	U	0.263751	T	0.80989	0.4730	N	0.08118	0	0.25194	N	0.990101	B	0.27286	0.174	B	0.17722	0.019	T	0.68191	-0.5474	9	.	.	.	-1.7774	11.256	0.49054	0.0:0.6574:0.3426:0.0	.	46	Q15672	TWST1_HUMAN	T	46	ENSP00000242261:A46T	.	A	-	1	0	TWIST1	19123334	.	.	0.538000	0.28064	0.307000	0.27823	.	.	1.682000	0.51000	0.175000	0.17021	GCG	.	.		0.791	TWIST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207625.1	NM_000474		T	19156809	C	T	19156809	3	4	176	1	0	0	0	0	1	0	0	0	16798	768	27	1	476	1	TWIST1	7	19156809	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	16210485	19156809	139981854	69	26468										
BMPER	168667	hgsc.bcm.edu	37	chr7	34118743	34118743	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	atcgcgctcccctgccgcgcGccacacttccacatcgacct	7	21	0	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:34118743G>A	ENST00000297161.2	+	13	1727	c.1353G>A	c.(1351-1353)gcG>gcA	p.A451A	BMPER_ENST00000426693.1_Silent_p.A451A	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	451	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)		p.A451A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						CCTGCCGCGCGCCACACTTCC	0.657																																					p.A451A		Atlas-SNP	.											BMPER,NS,carcinoma,0,1	BMPER	131	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1353A						.						49	51	50					7																	34118743		2203	4300	6503	SO:0001819	synonymous_variant	168667	exon13			CCGCGCGCCACAC		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"crossveinless-2"	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.1353G>A	chr7.hg19:g.34118743G>A		139.0	1.0		221.0	87.0	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	hg19	CCDS5442.1																																																																																			.	.		0.657	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		A	34118743	G	A	34118743	2	1	176	1	0	0	0	0	0	0	0	1	1468	1074	38	1		1	BMPER	7	34118743	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	14961934	34118743	125019920	70	26469										
POU6F2	11281	hgsc.bcm.edu	37	chr7	39379608	39379608	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ccgctcacgccacccaatccTctacaggtatgctccccgtg	7	19	2	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:39379608T>A	ENST00000403058.1	+	6	1033	c.879T>A	c.(877-879)ccT>ccA	p.P293P	POU6F2_ENST00000559001.1_Silent_p.P285P|POU6F2_ENST00000518318.2_Silent_p.P293P|POU6F2_ENST00000517348.1_3'UTR	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	293	Gln-rich.|Pro-rich.				central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						CACCCAATCCTCTACAGGTAT	0.602																																					p.P293P		Atlas-SNP	.											.	POU6F2	117	.	0			c.T879A						.						93	105	101					7																	39379608		2203	4300	6503	SO:0001819	synonymous_variant	11281	exon6			CAATCCTCTACAG	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.879T>A	chr7.hg19:g.39379608T>A		35.0	0.0		61.0	25.0	NM_007252	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Silent	SNP	ENST00000403058.1	hg19	CCDS34620.2																																																																																			.	.		0.602	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252		A	39379608	T	A	39379608	2	1	176	1	0	0	0	0	0	0	0	1	12294	1538	54	4		4	POU6F2	7	39379608	Silent	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	5260865	39379608	119759055	71	26470										
ELN	2006	hgsc.bcm.edu	37	chr7	73442595	73442595	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	atcctccacccctctcggccTggaggtaaggacccctcgcc	9	19	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:73442595T>A	ENST00000252034.7	+	1	477	c.78T>A	c.(76-78)ccT>ccA	p.P26P	ELN_ENST00000445912.1_Silent_p.P26P|ELN_ENST00000380575.4_Silent_p.P26P|ELN_ENST00000320492.7_Silent_p.P26P|ELN_ENST00000380562.4_Silent_p.P26P|ELN_ENST00000380576.5_Silent_p.P26P|ELN_ENST00000358929.4_Silent_p.P26P|ELN_ENST00000429192.1_Silent_p.P26P|ELN_ENST00000414324.1_Silent_p.P26P|ELN_ENST00000458204.1_Silent_p.P26P|ELN_ENST00000320399.6_Silent_p.P26P|ELN_ENST00000357036.5_Silent_p.P26P|ELN_ENST00000380553.4_Silent_p.P26P|ELN_ENST00000380584.4_Silent_p.P26P	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	26					blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				CCTCTCGGCCTGGAGGTAAGG	0.711			T	PAX5	B-ALL		"Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"																														p.P26P		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN	81	.	0			c.T78A						.						19	20	20					7																	73442595		2197	4297	6494	SO:0001819	synonymous_variant	2006	exon1			TCGGCCTGGAGGT		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"tropoelastin", "supravalvular aortic stenosis", "Williams-Beuren syndrome"	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.78T>A	chr7.hg19:g.73442595T>A		34.0	0.0		25.0	8.0	NM_001081753	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Silent	SNP	ENST00000252034.7	hg19	CCDS5562.2																																																																																			.	.		0.711	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501		A	73442595	T	A	73442595	2	1	176	1	0	0	0	0	0	0	0	1	5073	1567	55	4		4	ELN	7	73442595	Silent	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	34062987	73442595	85696068	72	26471										
HGF	3082	hgsc.bcm.edu	37	chr7	81355282	81355282	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tttggatcagtggtaaaacaCcagggtgattcagacccatc	10	9	2	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:81355282C>G	ENST00000222390.5	-	9	1318	c.1092G>C	c.(1090-1092)tgG>tgC	p.W364C	HGF_ENST00000457544.2_Missense_Mutation_p.W359C	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	364	Kringle 3. {ECO:0000255|PROSITE- ProRule:PRU00121}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						TGGTAAAACACCAGGGTGATT	0.438																																					p.W364C		Atlas-SNP	.											.	HGF	171	.	0			c.G1092C						.						148	140	142					7																	81355282		2203	4300	6503	SO:0001583	missense	3082	exon9			AAAACACCAGGGT		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.1092G>C	chr7.hg19:g.81355282C>G	ENSP00000222390:p.Trp364Cys	163.0	0.0		167.0	16.0	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Missense_Mutation	SNP	ENST00000222390.5	hg19	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.100680	0.76983	.	.	ENSG00000019991	ENST00000222390;ENST00000457544	D;D	0.81579	-1.51;-1.51	5.51	5.51	0.81932	Kringle (4);Kringle-like fold (1);Kringle, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.94928	0.8360	H	0.99565	4.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97174	0.9846	10	0.87932	D	0	.	19.4111	0.94673	0.0:1.0:0.0:0.0	.	359;364	P14210-3;P14210	.;HGF_HUMAN	C	364;359	ENSP00000222390:W364C;ENSP00000391238:W359C	ENSP00000222390:W364C	W	-	3	0	HGF	81193218	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.935000	0.75886	2.580000	0.87095	0.591000	0.81541	TGG	.	.		0.438	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		G	81355282	C	G	81355282	3	3	176	1	0	0	0	0	1	0	0	0	7094	508	18	4	1134	4	HGF	7	81355282	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	7912687	81355282	77783381	73	26472										
PCLO	27445	hgsc.bcm.edu	37	chr7	82580060	82580060	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ctgagctaacgtctcctgccTcatcatgaactgggcttgcc	9	14	3	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:82580060T>A	ENST00000333891.9	-	6	10181	c.9844A>T	c.(9844-9846)Agg>Tgg	p.R3282W	PCLO_ENST00000423517.2_Missense_Mutation_p.R3282W|PCLO_ENST00000437081.1_Missense_Mutation_p.R2W	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GTCTCCTGCCTCATCATGAAC	0.483																																					p.R3282W		Atlas-SNP	.											.	PCLO	1506	.	0			c.A9844T						.						145	135	138					7																	82580060		1998	4192	6190	SO:0001583	missense	27445	exon6			CCTGCCTCATCAT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.9844A>T	chr7.hg19:g.82580060T>A	ENSP00000334319:p.Arg3282Trp	62.0	0.0		65.0	10.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	13.58	2.280802	0.40294	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.18810	2.19;2.19	5.29	5.29	0.74685	.	.	.	.	.	T	0.44030	0.1274	M	0.61703	1.905	0.42720	D	0.993671	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.74348	0.926;0.983;0.983	T	0.42189	-0.9466	9	0.87932	D	0	.	15.1715	0.72878	0.0:0.0:0.0:1.0	.	3213;3282;3282	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	W	3213;3282;3282;2	ENSP00000334319:R3282W;ENSP00000388393:R3282W	ENSP00000334319:R3282W	R	-	1	2	PCLO	82417996	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.560000	0.53763	2.128000	0.65567	0.460000	0.39030	AGG	.	.		0.483	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82580060	T	A	82580060	3	1	176	1	0	0	0	0	1	0	0	0	11592	1550	54	4	5681	4	PCLO	7	82580060	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	1224778	82580060	76558603	74	26473										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	82997259	82997259	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtatggacaaagctatgctcTactgtctggcaaaaataggt	10	7	2	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:82997259T>C	ENST00000307792.3	-	17	2438	c.1971A>G	c.(1969-1971)gtA>gtG	p.V657V	SEMA3E_ENST00000427262.1_Silent_p.V597V	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	657	Ig-like C2-type.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				AGCTATGCTCTACTGTCTGGC	0.458																																					p.V657V		Atlas-SNP	.											.	SEMA3E	125	.	0			c.A1971G						.						131	119	123					7																	82997259		2203	4300	6503	SO:0001819	synonymous_variant	9723	exon17			ATGCTCTACTGTC	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1971A>G	chr7.hg19:g.82997259T>C		101.0	0.0		94.0	20.0	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	hg19	CCDS34674.1																																																																																			.	.		0.458	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		C	82997259	T	C	82997259	2	2	176	1	0	0	0	0	0	0	0	1	14043	1509	53	2		2	SEMA3E	7	82997259	Silent	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	417199	82997259	76141404	75	26474										
ZNF394	84124	hgsc.bcm.edu	37	chr7	99096398	99096398	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ctctgcagaagtccctccgtGctgggtccaggcgctcccac	11	17	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:99096398G>A	ENST00000337673.6	-	2	727	c.524C>T	c.(523-525)gCa>gTa	p.A175V	ZNF394_ENST00000394177.3_5'UTR|ZNF789_ENST00000494186.1_Intron|ZNF394_ENST00000426306.2_Intron|ZNF789_ENST00000493485.1_Intron	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	175	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					GTCCCTCCGTGCTGGGTCCAG	0.582																																					p.A175V	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											.	ZNF394	48	.	0			c.C524T						.						116	89	98					7																	99096398		2203	4300	6503	SO:0001583	missense	84124	exon2			CTCCGTGCTGGGT	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"Zinc fingers, C2H2-type", "-", "-", "-"	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.524C>T	chr7.hg19:g.99096398G>A	ENSP00000337363:p.Ala175Val	66.0	0.0		63.0	16.0	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Missense_Mutation	SNP	ENST00000337673.6	hg19	CCDS5666.1	.	.	.	.	.	.	.	.	.	.	G	14.41	2.525650	0.44969	.	.	ENSG00000160908	ENST00000337673	T	0.02498	4.27	4.31	3.36	0.38483	Krueppel-associated box (4);	0.000000	0.43110	D	0.000615	T	0.02767	0.0083	L	0.49455	1.56	0.19300	N	0.999977	B	0.31910	0.346	B	0.30105	0.111	T	0.41963	-0.9479	10	0.19147	T	0.46	.	5.3024	0.15785	0.1218:0.2004:0.6778:0.0	.	175	Q53GI3	ZN394_HUMAN	V	175	ENSP00000337363:A175V	ENSP00000337363:A175V	A	-	2	0	ZNF394	98934334	0.009000	0.17119	0.028000	0.17463	0.115000	0.19883	0.508000	0.22692	1.286000	0.44565	0.563000	0.77884	GCA	.	.		0.582	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164		A	99096398	G	A	99096398	3	1	176	1	0	0	0	0	1	0	0	0	17895	1319	46	3	1169	3	ZNF394	7	99096398	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	16099139	99096398	60042265	76	26475										
PODXL	5420	hgsc.bcm.edu	37	chr7	131241035	131241035	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tcaccattctgggagggcgaCggcgacggcgacggcgacga	17	12	2	0	rs11277659|rs547816245|rs532078953	byFrequency	TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:131241035C>G	ENST00000378555.3	-	1	331	c.84G>C	c.(82-84)ccG>ccC	p.P28P	PODXL_ENST00000537928.1_Silent_p.P28P|PODXL_ENST00000541194.1_Silent_p.P28P|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000322985.9_Silent_p.P28P			O00592	PODXL_HUMAN	podocalyxin-like	28					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)		p.P30_S31delPS(2)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					GGGAGggcgacggcgacggcg	0.741																																					p.P28P		Atlas-SNP	.											.	PODXL	53	.	2	Deletion - In frame(2)	prostate(2)	c.G84C						.																																			SO:0001819	synonymous_variant	5420	exon1			GGGCGACGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.84G>C	chr7.hg19:g.131241035C>G		52.0	0.0		74.0	6.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.741	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		G	131241035	C	G	131241035	2	3	176	1	0	0	0	0	0	0	0	1	12189	523	19	4		4	PODXL	7	131241035	Silent	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	32144637	131241035	27897628	77	26476										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131872243	131872243	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gagttacctgtggaagagacAgggctgctttccaaacatca	11	9	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:131872243A>T	ENST00000359827.3	-	15	3942	c.2980T>A	c.(2980-2982)Tgt>Agt	p.C994S	PLXNA4_ENST00000321063.4_Missense_Mutation_p.C994S			Q9HCM2	PLXA4_HUMAN	plexin A4	994	IPT/TIG 2.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TGGAAGAGACAGGGCTGCTTT	0.552																																					p.C994S		Atlas-SNP	.											.	PLXNA4	873	.	0			c.T2980A						.						221	239	233					7																	131872243		2078	4221	6299	SO:0001583	missense	91584	exon15			AGAGACAGGGCTG	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2980T>A	chr7.hg19:g.131872243A>T	ENSP00000352882:p.Cys994Ser	63.0	0.0		69.0	14.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.653721	0.88056	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.62941	-0.01;-0.01	5.54	5.54	0.83059	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.83492	0.5266	M	0.92555	3.32	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.87696	0.2557	10	0.72032	D	0.01	.	15.6748	0.77307	1.0:0.0:0.0:0.0	.	994	Q9HCM2	PLXA4_HUMAN	S	994	ENSP00000323194:C994S;ENSP00000352882:C994S	ENSP00000323194:C994S	C	-	1	0	PLXNA4	131522783	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.930000	0.92872	2.114000	0.64651	0.454000	0.30748	TGT	.	.		0.552	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131872243	A	T	131872243	3	4	176	1	0	0	0	0	1	0	0	0	12131	188	7	4	2776	4	PLXNA4	7	131872243	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	631208	131872243	27266420	78	26477										
PDIA4	9601	hgsc.bcm.edu	37	chr7	148709035	148709035	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttcaggaactcctggacctgCttcagggtcagaatctcctt	9	12	4	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:148709035C>A	ENST00000286091.4	-	6	1114	c.882G>T	c.(880-882)aaG>aaT	p.K294N		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	294	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			CCTGGACCTGCTTCAGGGTCA	0.567																																					p.K294N		Atlas-SNP	.											.	PDIA4	57	.	0			c.G882T						.						94	86	89					7																	148709035		2203	4300	6503	SO:0001583	missense	9601	exon6			GACCTGCTTCAGG	BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"Protein disulfide isomerases"	30167	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 4"			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.882G>T	chr7.hg19:g.148709035C>A	ENSP00000286091:p.Lys294Asn	63.0	0.0		73.0	5.0	NM_004911	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	hg19	CCDS5893.1	.	.	.	.	.	.	.	.	.	.	c	17.89	3.498563	0.64298	.	.	ENSG00000155660	ENST00000286091	T	0.78003	-1.14	5.14	4.05	0.47172	Thioredoxin-like fold (3);	0.042698	0.85682	D	0.000000	T	0.81950	0.4931	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.80228	-0.1469	10	0.37606	T	0.19	.	12.4775	0.55823	0.0:0.858:0.0:0.142	.	294	P13667	PDIA4_HUMAN	N	294	ENSP00000286091:K294N	ENSP00000286091:K294N	K	-	3	2	PDIA4	148339968	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	0.808000	0.27154	2.423000	0.82170	0.639000	0.83563	AAG	.	.		0.567	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911		A	148709035	C	A	148709035	3	1	176	1	0	0	0	0	1	0	0	0	11679	796	28	3	1075	3	PDIA4	7	148709035	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	16836792	148709035	10429628	79	26478										
NOS3	4846	hgsc.bcm.edu	37	chr7	150698381	150698381	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tctttcatgaagcacctggaGaatgagcagaaggccagggg	14	8	2	4	rs145811781		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:150698381G>T	ENST00000484524.1	+	10	1296	c.1296G>T	c.(1294-1296)gaG>gaT	p.E432D	NOS3_ENST00000467517.1_Missense_Mutation_p.E432D|NOS3_ENST00000461406.1_Missense_Mutation_p.E226D|NOS3_ENST00000297494.3_Missense_Mutation_p.E432D	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGCACCTGGAGAATGAGCAGA	0.617																																					p.E432D		Atlas-SNP	.											.	NOS3	131	.	0			c.G1296T						.	G	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	0,4406		0,0,2203	66	69	68		1296,1296,1296,1296	1.2	1	7	dbSNP_134	68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	NOS3	NM_000603.4,NM_001160109.1,NM_001160110.1,NM_001160111.1	45,45,45,45	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	432/1204,432/597,432/615,432/630	150698381	1,13005	2203	4300	6503	SO:0001583	missense	4846	exon10			CCTGGAGAATGAG		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.1296G>T	chr7.hg19:g.150698381G>T	ENSP00000420215:p.Glu432Asp	46.0	0.0		49.0	12.0	NM_001160111	Q495E5	Missense_Mutation	SNP	ENST00000484524.1	hg19	CCDS55182.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.416681	0.42918	0.0	1.16E-4	ENSG00000164867	ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517	T;T;T;T	0.22539	1.95;1.95;1.95;1.95	5.13	1.22	0.21188	Nitric oxide synthase, oxygenase domain (2);	0.094778	0.42964	N	0.000631	T	0.25865	0.0630	L	0.48218	1.51	0.40758	D	0.982975	B;B;B;P;B	0.49862	0.001;0.001;0.03;0.929;0.377	B;B;B;P;B	0.56278	0.008;0.008;0.116;0.795;0.147	T	0.03795	-1.1003	10	0.42905	T	0.14	-13.1128	4.5865	0.12285	0.3514:0.1529:0.4957:0.0	.	432;432;432;226;432	A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474	.;.;.;.;NOS3_HUMAN	D	432;226;432;432	ENSP00000297494:E432D;ENSP00000417143:E226D;ENSP00000420215:E432D;ENSP00000420551:E432D	ENSP00000297494:E432D	E	+	3	2	NOS3	150329314	1.000000	0.71417	0.997000	0.53966	0.962000	0.63368	2.560000	0.45896	-0.056000	0.13221	-0.215000	0.12644	GAG	.	G|1.000;T|0.000		0.617	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		T	150698381	G	T	150698381	3	4	176	1	0	0	0	0	1	0	0	0	10553	933	33	3	1334	3	NOS3	7	150698381	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	1989346	150698381	8440282	80	26479										
INSIG1	3638	hgsc.bcm.edu	37	chr7	155094075	155094075	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttgggctggggatcaccataGcttttctagctacgctgatc	11	10	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr7:155094075G>A	ENST00000340368.4	+	4	863	c.652G>A	c.(652-654)Gct>Act	p.A218T	INSIG1_ENST00000342407.5_Intron|INSIG1_ENST00000344756.4_Missense_Mutation_p.A66T	NM_005542.4	NP_005533.2	O15503	INSI1_HUMAN	insulin induced gene 1	218					cell proliferation (GO:0008283)|cholesterol biosynthetic process (GO:0006695)|cranial suture morphogenesis (GO:0060363)|inner ear morphogenesis (GO:0042472)|metabolic process (GO:0008152)|middle ear morphogenesis (GO:0042474)|negative regulation of cargo loading into COPII-coated vesicle (GO:1901303)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of steroid biosynthetic process (GO:0010894)|palate development (GO:0060021)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|SREBP-SCAP-Insig complex (GO:0032937)				endometrium(2)|kidney(2)|large_intestine(1)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	19	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GATCACCATAGCTTTTCTAGC	0.438																																					p.A218T		Atlas-SNP	.											.	INSIG1	20	.	0			c.G652A						.						126	114	118					7																	155094075		2203	4300	6503	SO:0001583	missense	3638	exon4			ACCATAGCTTTTC		CCDS5938.1, CCDS5939.1	7q36	2008-07-18			ENSG00000186480	ENSG00000186480			6083	protein-coding gene	gene with protein product	"INSIG-1 membrane protein"	602055				9268630	Standard	NM_005542		Approved	CL-6, MGC1405	uc003wly.3	O15503	OTTHUMG00000151330	ENST00000340368.4:c.652G>A	chr7.hg19:g.155094075G>A	ENSP00000344741:p.Ala218Thr	106.0	0.0		104.0	37.0	NM_005542	A4D2N1|A8K6L0|Q53XW8|Q9BUV5	Missense_Mutation	SNP	ENST00000340368.4	hg19	CCDS5938.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.474863|5.474863	0.96291|0.96291	.|.	.|.	ENSG00000186480|ENSG00000186480	ENST00000340368;ENST00000344756|ENST00000476756	T;T|.	0.57107|.	0.42;0.43|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77818|0.77818	0.4187|0.4187	M|M	0.75447|0.75447	2.3|2.3	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.994;1.0|.	D;D|.	0.91635|.	0.946;0.999|.	T|T	0.76353|0.76353	-0.2990|-0.2990	10|5	0.54805|.	T|.	0.06|.	.|.	19.8944|19.8944	0.96949|0.96949	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	66;218|.	F5H6P3;O15503|.	.;INSI1_HUMAN|.	T|N	218;66|126	ENSP00000344741:A218T;ENSP00000340010:A66T|.	ENSP00000344741:A218T|.	A|S	+|+	1|2	0|0	INSIG1|INSIG1	154725010|154725010	1.000000|1.000000	0.71417|0.71417	0.884000|0.884000	0.34674|0.34674	0.844000|0.844000	0.47949|0.47949	9.113000|9.113000	0.94321|0.94321	2.695000|2.695000	0.91970|0.91970	0.650000|0.650000	0.86243|0.86243	GCT|AGC	.	.		0.438	INSIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322244.3	NM_198336		A	155094075	G	A	155094075	3	1	176	1	0	0	0	0	1	0	0	0	7774	971	34	3	662	3	INSIG1	7	155094075	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	4395694	155094075	4044588	81	26480										
PIWIL2	55124	hgsc.bcm.edu	37	chr8	22137035	22137035	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tgggcaggggagcacctgcaGgcagaggccatgtatttgga	17	8	0	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr8:22137035G>A	ENST00000454009.2	+	2	645	c.136G>A	c.(136-138)Ggc>Agc	p.G46S	PIWIL2_ENST00000521356.1_Missense_Mutation_p.G46S|PIWIL2_ENST00000356766.6_Missense_Mutation_p.G46S	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	46					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		AGCACCTGCAGGCAGAGGCCA	0.577																																					p.G46S		Atlas-SNP	.											.	PIWIL2	100	.	0			c.G136A						.						93	93	93					8																	22137035		2203	4300	6503	SO:0001583	missense	55124	exon2			CCTGCAGGCAGAG	AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"Argonaute/PIWI family"	17644	protein-coding gene	gene with protein product	"Hiwi-like", "cancer/testis antigen 80"	610312	"piwi-like 2 (Drosophila)"			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.136G>A	chr8.hg19:g.22137035G>A	ENSP00000406956:p.Gly46Ser	99.0	0.0		97.0	19.0	NM_001135721	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Missense_Mutation	SNP	ENST00000454009.2	hg19	CCDS6029.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.399050	0.42512	.	.	ENSG00000197181	ENST00000356766;ENST00000521356;ENST00000454009	T;T;T	0.05025	3.55;3.51;3.55	5.93	4.12	0.48240	.	0.072152	0.52532	D	0.000075	T	0.05044	0.0135	L	0.27053	0.805	0.29043	N	0.884999	B;B	0.18013	0.025;0.025	B;B	0.12837	0.008;0.008	T	0.09509	-1.0671	10	0.49607	T	0.09	-20.8528	9.0002	0.36077	0.1429:0.0:0.8571:0.0	.	46;46	E7ECA4;Q8TC59	.;PIWL2_HUMAN	S	46	ENSP00000349208:G46S;ENSP00000428267:G46S;ENSP00000406956:G46S	ENSP00000349208:G46S	G	+	1	0	PIWIL2	22192980	0.976000	0.34144	0.983000	0.44433	0.612000	0.37316	1.476000	0.35420	2.808000	0.96608	0.655000	0.94253	GGC	.	.		0.577	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1			A	22137035	G	A	22137035	3	1	176	1	0	0	0	0	1	0	0	0	11967	1000	35	3	138	3	PIWIL2	8	22137035	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10		22137035	124226987	82	26481										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73849796	73849796	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ccccgcccagcacagccaggCcactgccagtcaccacagct	8	21	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr8:73849796C>T	ENST00000523207.1	+	3	2794	c.2206C>T	c.(2206-2208)Cca>Tca	p.P736S		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	736					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	CACAGCCAGGCCACTGCCAGT	0.542																																					p.P736S		Atlas-SNP	.											.	KCNB2	228	.	0			c.C2206T						.						100	106	104					8																	73849796		2203	4300	6503	SO:0001583	missense	9312	exon3			GCCAGGCCACTGC	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.2206C>T	chr8.hg19:g.73849796C>T	ENSP00000430846:p.Pro736Ser	106.0	0.0		225.0	17.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	12.72	2.022416	0.35701	.	.	ENSG00000182674	ENST00000523207	T	0.23147	1.92	5.04	5.04	0.67666	.	0.960065	0.08478	N	0.939986	T	0.21145	0.0509	N	0.16368	0.405	0.42207	D	0.99179	B	0.12013	0.005	B	0.18263	0.021	T	0.04103	-1.0977	10	0.62326	D	0.03	.	14.2015	0.65707	0.0:0.8506:0.1494:0.0	.	736	Q92953	KCNB2_HUMAN	S	736	ENSP00000430846:P736S	ENSP00000430846:P736S	P	+	1	0	KCNB2	74012350	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	3.846000	0.55888	2.602000	0.87976	0.591000	0.81541	CCA	.	.		0.542	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		T	73849796	C	T	73849796	3	4	176	1	0	0	0	0	1	0	0	0	8022	739	26	3	2212	3	KCNB2	8	73849796	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	51712761	73849796	72514226	83	26482										
SLC10A5	347051	hgsc.bcm.edu	37	chr8	82606852	82606852	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcactttgactttcacattcTtgatttcttcaatgagtctt	5	9	5	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr8:82606852T>A	ENST00000518568.1	-	1	1557	c.356A>T	c.(355-357)aAg>aTg	p.K119M		NM_001010893.2	NP_001010893.1	Q5PT55	NTCP5_HUMAN	solute carrier family 10, member 5	119						integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)	15						TTTCACATTCTTGATTTCTTC	0.353																																					p.K119M		Atlas-SNP	.											.	SLC10A5	35	.	0			c.A356T						.						142	132	135					8																	82606852		2203	4300	6503	SO:0001583	missense	347051	exon1			ACATTCTTGATTT		CCDS34915.1	8q21.13	2013-07-18	2013-07-18		ENSG00000253598	ENSG00000253598		"Solute carriers"	22981	protein-coding gene	gene with protein product							Standard	NM_001010893		Approved		uc011lfs.2	Q5PT55	OTTHUMG00000164683	ENST00000518568.1:c.356A>T	chr8.hg19:g.82606852T>A	ENSP00000428612:p.Lys119Met	103.0	0.0		234.0	32.0	NM_001010893	B2RN26	Missense_Mutation	SNP	ENST00000518568.1	hg19	CCDS34915.1	.	.	.	.	.	.	.	.	.	.	T	16.38	3.105680	0.56291	.	.	ENSG00000253598	ENST00000518568	T	0.09445	2.98	5.7	3.29	0.37713	.	0.274240	0.26146	N	0.026076	T	0.11665	0.0284	L	0.27053	0.805	0.26302	N	0.97796	D	0.58620	0.983	P	0.52710	0.707	T	0.08493	-1.0719	10	0.56958	D	0.05	-2.3846	6.1091	0.20090	0.0:0.0838:0.1623:0.7539	.	119	Q5PT55	NTCP5_HUMAN	M	119	ENSP00000428612:K119M	ENSP00000428612:K119M	K	-	2	0	SLC10A5	82769407	0.956000	0.32656	1.000000	0.80357	0.957000	0.61999	0.545000	0.23268	0.412000	0.25729	0.533000	0.62120	AAG	.	.		0.353	SLC10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379736.1	XM_294493		A	82606852	T	A	82606852	3	1	176	1	0	0	0	0	1	0	0	0	14392	1609	56	4	962	4	SLC10A5	8	82606852	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	8757056	82606852	63757170	84	26483										
GRHL2	79977	hgsc.bcm.edu	37	chr8	102570707	102570707	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggaggagaaaaccgagtgcaAgtcctaaagactgttccagt	12	8	0	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr8:102570707A>T	ENST00000251808.3	+	4	683	c.345A>T	c.(343-345)caA>caT	p.Q115H	GRHL2_ENST00000395927.1_Missense_Mutation_p.Q99H	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	115					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			ACCGAGTGCAAGTCCTAAAGA	0.483																																					p.Q115H		Atlas-SNP	.											.	GRHL2	68	.	0			c.A345T						.						125	126	126					8																	102570707		2203	4300	6503	SO:0001583	missense	79977	exon4			AGTGCAAGTCCTA	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"deafness, autosomal dominant 28", "transcription factor CP2-like 3"	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.345A>T	chr8.hg19:g.102570707A>T	ENSP00000251808:p.Gln115His	146.0	0.0		352.0	41.0	NM_024915	A1L303|Q6NT03|Q9H8B8	Missense_Mutation	SNP	ENST00000251808.3	hg19	CCDS34931.1	.	.	.	.	.	.	.	.	.	.	A	9.039	0.989202	0.18966	.	.	ENSG00000083307	ENST00000251808;ENST00000395927;ENST00000395928	T;T	0.13196	2.61;2.62	5.26	3.33	0.38152	.	0.000000	0.85682	D	0.000000	T	0.22475	0.0542	L	0.44542	1.39	0.52501	D	0.999959	D;B	0.67145	0.996;0.054	D;B	0.75484	0.986;0.028	T	0.06006	-1.0851	10	0.20046	T	0.44	-23.8905	7.1112	0.25390	0.4104:0.0:0.5896:0.0	.	115;115	B4DL28;Q6ISB3	.;GRHL2_HUMAN	H	115;99;115	ENSP00000251808:Q115H;ENSP00000379260:Q99H	ENSP00000251808:Q115H	Q	+	3	2	GRHL2	102639883	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	2.227000	0.42972	0.493000	0.27837	-0.312000	0.09012	CAA	.	.		0.483	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915		T	102570707	A	T	102570707	3	4	176	1	0	0	0	0	1	0	0	0	6773	69	3	4	359	4	GRHL2	8	102570707	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	19963855	102570707	43793315	85	26484										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106331209	106331209	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcaaaccccggcagatcaaaCgtaagtttgcgcgcggggcc	13	13	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr8:106331209C>T	ENST00000407775.2	+	1	290	c.40C>T	c.(40-42)Cgg>Tgg	p.R14W	ZFPM2_ENST00000520492.1_5'Flank	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	14					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GCAGATCAAACGTAAGTTTGC	0.711																																					p.R14W		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C40T						.						5	7	6					8																	106331209		1557	3525	5082	SO:0001630	splice_region_variant	23414	exon1			ATCAAACGTAAGT	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.40+1C>T	chr8.hg19:g.106331209C>T		291.0	0.0		673.0	148.0	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	hg19	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	C	31	5.097507	0.94197	.	.	ENSG00000169946	ENST00000407775	T	0.22134	1.97	3.66	3.66	0.41972	.	.	.	.	.	T	0.30039	0.0752	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	P	0.57679	0.825	T	0.05370	-1.0889	9	0.54805	T	0.06	.	13.9515	0.64121	0.0:1.0:0.0:0.0	.	14	Q8WW38	FOG2_HUMAN	W	14	ENSP00000384179:R14W	ENSP00000384179:R14W	R	+	1	2	ZFPM2	106400385	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.319000	0.72871	1.582000	0.49881	0.585000	0.79938	CGG	.	.		0.711	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		Missense_Mutation	T	106331209	C	T	106331209	5	4	176	1	0	0	0	0	0	0	1	0	17673	550	19	1	42	1	ZFPM2	8	106331209	Splice_Site	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	3760502	106331209	40032813	86	26485										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116616720	116616720	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agatcattctgattaatgacAgagcccctggaaagcttatc	8	9	2	4			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr8:116616720A>G	ENST00000220888.5	-	3	1596	c.1437T>C	c.(1435-1437)tcT>tcC	p.S479S	TRPS1_ENST00000395715.3_Silent_p.S492S|TRPS1_ENST00000520276.1_Silent_p.S483S|TRPS1_ENST00000519674.1_Silent_p.S479S|TRPS1_ENST00000519076.1_Intron			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	479					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			GATTAATGACAGAGCCCCTGG	0.463									Langer-Giedion syndrome																												p.S492S		Atlas-SNP	.											.	TRPS1	516	.	0			c.T1476C						.						73	70	71					8																	116616720		1902	4116	6018	SO:0001819	synonymous_variant	7227	exon4	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AATGACAGAGCCC	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.1437T>C	chr8.hg19:g.116616720A>G		89.0	0.0		180.0	17.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	hg19																																																																																				.	.		0.463	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		G	116616720	A	G	116616720	2	3	176	1	0	0	0	0	0	0	0	1	16608	175	7	2		2	TRPS1	8	116616720	Silent	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	10285511	116616720	29747302	87	26486										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116631492	116631492	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcaccatgttatgaagggccAagattttgctgtccagctca	10	10	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr8:116631492A>T	ENST00000220888.5	-	2	953	c.794T>A	c.(793-795)tTg>tAg	p.L265*	TRPS1_ENST00000395715.3_Nonsense_Mutation_p.L278*|TRPS1_ENST00000520276.1_Nonsense_Mutation_p.L269*|TRPS1_ENST00000519674.1_Nonsense_Mutation_p.L265*|TRPS1_ENST00000519076.1_Nonsense_Mutation_p.L219*			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	265					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			ATGAAGGGCCAAGATTTTGCT	0.483									Langer-Giedion syndrome																												p.L278X		Atlas-SNP	.											.	TRPS1	516	.	0			c.T833A						.						101	98	99					8																	116631492		1937	4156	6093	SO:0001587	stop_gained	7227	exon3	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AGGGCCAAGATTT	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.794T>A	chr8.hg19:g.116631492A>T	ENSP00000220888:p.Leu265*	191.0	0.0		299.0	27.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Nonsense_Mutation	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	A	37	6.139141	0.97315	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276;ENST00000519674	.	.	.	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4401	0.75176	1.0:0.0:0.0:0.0	.	.	.	.	X	278;265;219;269;265	.	ENSP00000220888:L265X	L	-	2	0	TRPS1	116700667	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.339000	0.96797	2.056000	0.61249	0.377000	0.23210	TTG	.	.		0.483	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		T	116631492	A	T	116631492	4	4	176	1	0	0	0	0	0	1	0	0	16608	131	5	4	3071	4	TRPS1	8	116631492	Nonsense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	14772	116631492	29732530	88	26487										
KIFC2	90990	hgsc.bcm.edu	37	chr8	145698549	145698549	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggaggatctcggggagacagTctgctccctcaagttcgccg	14	12	3	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr8:145698549T>C	ENST00000301332.2	+	17	2610	c.2233T>C	c.(2233-2235)Tct>Cct	p.S745P	KIFC2_ENST00000301331.5_3'UTR|FOXH1_ENST00000525197.1_5'Flank	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	745	Pro-rich.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GGGGAGACAGTCTGCTCCCTC	0.741																																					p.S745P		Atlas-SNP	.											.	KIFC2	53	.	0			c.T2233C						.						8	10	9					8																	145698549		2148	4235	6383	SO:0001583	missense	90990	exon17			AGACAGTCTGCTC	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"Kinesins"	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.2233T>C	chr8.hg19:g.145698549T>C	ENSP00000301332:p.Ser745Pro	85.0	0.0		193.0	15.0	NM_145754	E9PHB2|Q96NN6	Missense_Mutation	SNP	ENST00000301332.2	hg19	CCDS6427.1	.	.	.	.	.	.	.	.	.	.	T	13.32	2.201064	0.38905	.	.	ENSG00000167702	ENST00000301332	T	0.71341	-0.56	4.45	4.45	0.53987	.	.	.	.	.	T	0.59224	0.2178	N	0.14661	0.345	0.80722	D	1	P;P	0.50943	0.94;0.79	P;B	0.48030	0.564;0.276	T	0.62435	-0.6855	9	0.45353	T	0.12	-1.3599	11.692	0.51521	0.0:0.0:0.0:1.0	.	133;745	Q96BU4;Q96AC6	.;KIFC2_HUMAN	P	745	ENSP00000301332:S745P	ENSP00000301332:S745P	S	+	1	0	KIFC2	145669357	0.994000	0.37717	0.986000	0.45419	0.377000	0.30045	5.212000	0.65225	1.882000	0.54519	0.397000	0.26171	TCT	.	.		0.741	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754		C	145698549	T	C	145698549	3	2	176	1	0	0	0	0	1	0	0	0	8322	1667	58	2	2299	2	KIFC2	8	145698549	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	29067057	145698549	665473	89	26488										
PSIP1	11168	hgsc.bcm.edu	37	chr9	15472658	15472658	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttccatttgttcctcttgctTgcgttttcgatctgctgctt	7	11	2	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr9:15472658T>G	ENST00000380733.4	-	10	1292	c.949A>C	c.(949-951)Aag>Cag	p.K317Q	PSIP1_ENST00000380738.4_Missense_Mutation_p.K317Q|PSIP1_ENST00000380715.1_Missense_Mutation_p.K317Q|PSIP1_ENST00000397519.2_Missense_Mutation_p.K317Q|PSIP1_ENST00000380716.4_Missense_Mutation_p.K317Q			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	317					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		TCCTCTTGCTTGCGTTTTCGA	0.363																																					p.K317Q		Atlas-SNP	.											.	PSIP1	93	.	0			c.A949C						.						192	168	176					9																	15472658		2202	4299	6501	SO:0001583	missense	11168	exon9			CTTGCTTGCGTTT	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"PC4 and SFRS1 interacting protein 2"	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.949A>C	chr9.hg19:g.15472658T>G	ENSP00000370109:p.Lys317Gln	87.0	0.0		84.0	46.0	NM_021144	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Missense_Mutation	SNP	ENST00000380733.4	hg19	CCDS6479.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.910404	0.72983	.	.	ENSG00000164985	ENST00000380733;ENST00000380738;ENST00000380715;ENST00000380716;ENST00000397519	T;T;T;T;T	0.54675	0.71;0.71;0.59;0.56;0.56	6.07	6.07	0.98685	.	0.260464	0.41194	D	0.000923	T	0.60869	0.2302	L	0.59436	1.845	0.36716	D	0.880892	P;P	0.51351	0.944;0.839	P;B	0.50617	0.646;0.276	T	0.70687	-0.4803	10	0.87932	D	0	.	15.2061	0.73180	0.0:0.0:0.0:1.0	.	317;317	O75475-2;O75475	.;PSIP1_HUMAN	Q	317	ENSP00000370109:K317Q;ENSP00000370114:K317Q;ENSP00000370091:K317Q;ENSP00000370092:K317Q;ENSP00000380653:K317Q	ENSP00000370091:K317Q	K	-	1	0	PSIP1	15462658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.157000	0.64911	2.330000	0.79161	0.477000	0.44152	AAG	.	.		0.363	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222		G	15472658	T	G	15472658	3	3	176	1	0	0	0	0	1	0	0	0	12675	1821	63	5	700	5	PSIP1	9	15472658	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10		15472658	125740773	90	26489										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79320430	79320430	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ctgactttcaggagaaaagcTgtctgatatccaagaaccgt	9	9	2	4			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr9:79320430T>A	ENST00000376718.3	-	8	6883	c.6760A>T	c.(6760-6762)Agc>Tgc	p.S2254C	PRUNE2_ENST00000428286.1_Missense_Mutation_p.S1895C	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2254					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GGAGAAAAGCTGTCTGATATC	0.448																																					p.S2254C		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A6760T						.						53	50	51					9																	79320430		1568	3582	5150	SO:0001583	missense	158471	exon8			AAAAGCTGTCTGA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.6760A>T	chr9.hg19:g.79320430T>A	ENSP00000365908:p.Ser2254Cys	152.0	0.0		141.0	35.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.83|15.83	2.948782|2.948782	0.53186|0.53186	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376718;ENST00000428286;ENST00000422033	.|T;T	.|0.47869	.|0.83;0.84	5.92|5.92	2.0|2.0	0.26442|0.26442	.|.	.|1.181910	.|0.06099	.|N	.|0.665088	T|T	0.38904|0.38904	0.1058|0.1058	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|P	.|0.48640	.|0.913	.|B	.|0.43103	.|0.408	T|T	0.37337|0.37337	-0.9710|-0.9710	5|10	.|0.87932	.|D	.|0	0.3904|0.3904	9.9257|9.9257	0.41492|0.41492	0.0:0.6552:0.0:0.3448|0.0:0.6552:0.0:0.3448	.|.	.|2254	.|Q8WUY3	.|PRUN2_HUMAN	L|C	1575|2254;1895;2253	.|ENSP00000365908:S2254C;ENSP00000397425:S1895C	.|ENSP00000365908:S2254C	Q|S	-|-	2|1	0|0	PRUNE2|PRUNE2	78510250|78510250	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.119000|0.119000	0.20118|0.20118	-0.423000|-0.423000	0.07034|0.07034	0.396000|0.396000	0.25283|0.25283	-0.242000|-0.242000	0.12053|0.12053	CAG|AGC	.	.		0.448	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79320430	T	A	79320430	3	1	176	1	0	0	0	0	1	0	0	0	12653	1580	55	4	2554	4	PRUNE2	9	79320430	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	63847772	79320430	61893001	91	26490										
TLE4	7091	hgsc.bcm.edu	37	chr9	82324551	82324551	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	attctaggtgggatttgatcCacaccatcacatgcgtgtgc	10	10	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr9:82324551C>G	ENST00000376552.2	+	14	2295	c.1277C>G	c.(1276-1278)cCa>cGa	p.P426R	TLE4_ENST00000376520.4_Missense_Mutation_p.P458R|TLE4_ENST00000376534.4_Missense_Mutation_p.P63R|TLE4_ENST00000376544.3_Missense_Mutation_p.P357R|TLE4_ENST00000265284.6_Missense_Mutation_p.P401R|TLE4_ENST00000376537.4_Missense_Mutation_p.P458R	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	426					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						GGATTTGATCCACACCATCAC	0.423																																					p.P426R		Atlas-SNP	.											.	TLE4	187	.	0			c.C1277G						.						97	98	97					9																	82324551		1914	4134	6048	SO:0001583	missense	7091	exon14			TTGATCCACACCA	M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"WD repeat domain containing"	11840	protein-coding gene	gene with protein product		605132	"transducin-like enhancer of split 4, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.1277C>G	chr9.hg19:g.82324551C>G	ENSP00000365735:p.Pro426Arg	75.0	0.0		78.0	21.0	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	hg19	CCDS43837.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.067392|5.067392	0.93898|0.93898	.|.	.|.	ENSG00000106829|ENSG00000106829	ENST00000417836|ENST00000376552;ENST00000376544;ENST00000376520;ENST00000376537;ENST00000376534;ENST00000265284;ENST00000467142	.|T;T;T;T;T;T;T	.|0.53857	.|0.63;0.79;0.83;0.84;0.6;0.73;0.92	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.78207|0.78207	0.4247|0.4247	M|M	0.87758|0.87758	2.905|2.905	0.80722|0.80722	D|D	1|1	.|P;D;P;P	.|0.76494	.|0.919;0.999;0.823;0.869	.|P;D;P;P	.|0.80764	.|0.807;0.994;0.751;0.646	T|T	0.80410|0.80410	-0.1394|-0.1394	5|10	.|0.72032	.|D	.|0.01	-11.3478|-11.3478	20.2963|20.2963	0.98556|0.98556	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|401;357;458;426	.|F8W6T6;Q04727-2;Q04727-3;Q04727	.|.;.;.;TLE4_HUMAN	D|R	191|426;357;458;458;63;401;154	.|ENSP00000365735:P426R;ENSP00000365727:P357R;ENSP00000365703:P458R;ENSP00000365720:P458R;ENSP00000365717:P63R;ENSP00000265284:P401R;ENSP00000418409:P154R	.|ENSP00000265284:P401R	H|P	+|+	1|2	0|0	TLE4|TLE4	81514371|81514371	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	7.559000|7.559000	0.82265|0.82265	2.813000|2.813000	0.96785|0.96785	0.655000|0.655000	0.94253|0.94253	CAC|CCA	.	.		0.423	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237		G	82324551	C	G	82324551	3	3	176	1	0	0	0	0	1	0	0	0	15956	594	21	4	1331	4	TLE4	9	82324551	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	3004121	82324551	58888880	92	26491										
FAM75C1	441452	hgsc.bcm.edu	37	chr9	90535925	90535925	+	RNA	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ccatcttcaatcctctttccCagtcctatctcctgcttttc	2	17	4	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr9:90535925C>G	ENST00000602681.1	+	0	1829							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TCCTCTTTCCCAGTCCTATCT	0.537																																					p.P368R		Atlas-SNP	.											.	.	.	.	0			c.C1103G						.						19	18	18					9																	90535925		691	1579	2270			441452	exon4			CTTTCCCAGTCCT	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"family with sequence similarity 75, member C1"	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		chr9.hg19:g.90535925C>G		126.0	0.0		143.0	41.0	NM_001145124		Missense_Mutation	SNP	ENST00000602681.1	hg19																																																																																				.	.		0.537	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124		G	90535925	C	G	90535925	1	3	176	0	1	0	0	0	0	0	0	0	5631	594	21	4		4	FAM75C1	9	90535925	RNA	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	8211374	90535925	50677506	93	26492										
SLC44A1	23446	hgsc.bcm.edu	37	chr9	108145486	108145486	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cacagtatgggtgctgcctcTgatcatcgtctgcctctttg	10	12	4	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr9:108145486T>A	ENST00000374720.3	+	14	1962	c.1715T>A	c.(1714-1716)cTg>cAg	p.L572Q	SLC44A1_ENST00000343170.7_Missense_Mutation_p.L364Q|SLC44A1_ENST00000374723.1_Missense_Mutation_p.L572Q|SLC44A1_ENST00000374724.1_Missense_Mutation_p.L572Q	NM_080546.3	NP_536856.2	Q8WWI5	CTL1_HUMAN	solute carrier family 44 (choline transporter), member 1	572					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	38					Choline(DB00122)	GTGCTGCCTCTGATCATCGTC	0.448																																					p.L572Q		Atlas-SNP	.											.	SLC44A1	61	.	0			c.T1715A						.						312	288	296					9																	108145486		2203	4300	6503	SO:0001583	missense	23446	exon14			TGCCTCTGATCAT	AJ420812	CCDS6763.1, CCDS75868.1	9q31.2	2014-01-28	2013-07-17	2005-09-06	ENSG00000070214	ENSG00000070214		"CD molecules", "Solute carriers"	18798	protein-coding gene	gene with protein product		606105	"CDW92 antigen"	CDW92		11698453, 10677542	Standard	NM_080546		Approved	CDw92, CTL1, CHTL1, CD92	uc004bcn.3	Q8WWI5	OTTHUMG00000020421	ENST00000374720.3:c.1715T>A	chr9.hg19:g.108145486T>A	ENSP00000363852:p.Leu572Gln	63.0	0.0		75.0	11.0	NM_080546	A6NLZ9|Q5VUB3|Q8WVB0|Q96KU3|Q9NY69	Missense_Mutation	SNP	ENST00000374720.3	hg19	CCDS6763.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.645622	0.87958	.	.	ENSG00000070214	ENST00000374723;ENST00000374720;ENST00000374724;ENST00000343170	T;T;T;T	0.25085	1.82;1.82;1.82;1.82	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.55033	0.1895	M	0.83483	2.645	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;0.996;1.0	T	0.62025	-0.6941	10	0.72032	D	0.01	-7.8064	15.465	0.75394	0.0:0.0:0.0:1.0	.	572;572;572	Q8WWI5-3;Q8WWI5-2;Q8WWI5	.;.;CTL1_HUMAN	Q	572;572;572;364	ENSP00000363855:L572Q;ENSP00000363852:L572Q;ENSP00000363856:L572Q;ENSP00000341856:L364Q	ENSP00000341856:L364Q	L	+	2	0	SLC44A1	107185307	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.538000	0.82048	2.115000	0.64714	0.528000	0.53228	CTG	.	.		0.448	SLC44A1-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053500.1	NM_080546		A	108145486	T	A	108145486	3	1	176	1	0	0	0	0	1	0	0	0	14650	1580	55	4	1769	4	SLC44A1	9	108145486	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	17609561	108145486	33067945	94	26493										
DAB2IP	153090	hgsc.bcm.edu	37	chr9	124535752	124535752	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gggggacagcccagaactgaAgccacgggcagtgcacaagc	15	12	0	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr9:124535752A>T	ENST00000408936.3	+	12	3127	c.2945A>T	c.(2944-2946)aAg>aTg	p.K982M	DAB2IP_ENST00000309989.1_Missense_Mutation_p.K858M|DAB2IP_ENST00000259371.2_Missense_Mutation_p.K954M			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	982					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						CCAGAACTGAAGCCACGGGCA	0.647																																					p.K954M		Atlas-SNP	.											.	DAB2IP	150	.	0			c.A2861T						.						12	14	13					9																	124535752		2185	4294	6479	SO:0001583	missense	153090	exon12			AACTGAAGCCACG	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.2945A>T	chr9.hg19:g.124535752A>T	ENSP00000386183:p.Lys982Met	135.0	0.0		123.0	26.0	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Missense_Mutation	SNP	ENST00000408936.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.46	3.628550	0.67015	.	.	ENSG00000136848	ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989	T;T;T;T	0.13538	2.58;2.58;2.58;2.58	4.97	4.97	0.65823	.	0.367322	0.32640	N	0.005831	T	0.34629	0.0904	M	0.70275	2.135	0.58432	D	0.999996	D;D	0.69078	0.997;0.965	D;P	0.66497	0.944;0.875	T	0.12319	-1.0552	10	0.87932	D	0	.	13.8386	0.63424	1.0:0.0:0.0:0.0	.	982;954	Q5VWQ8;G3XA90	DAB2P_HUMAN;.	M	954;982;891;858	ENSP00000259371:K954M;ENSP00000386183:K982M;ENSP00000362887:K891M;ENSP00000310827:K858M	ENSP00000259371:K954M	K	+	2	0	DAB2IP	123575573	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	5.501000	0.66950	1.874000	0.54306	0.260000	0.18958	AAG	.	.		0.647	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		T	124535752	A	T	124535752	3	4	176	1	0	0	0	0	1	0	0	0	4221	72	3	4	2907	4	DAB2IP	9	124535752	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	16390266	124535752	16677679	95	26494										
SSNA1	8636	hgsc.bcm.edu	37	chr9	140083520	140083520	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcccctcccggcccccaggcAtagaggagctgtgccagaag	13	16	0	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr9:140083520A>G	ENST00000322310.5	+	2	135	c.55A>G	c.(55-57)Ata>Gta	p.I19V	ANAPC2_ENST00000323927.2_5'Flank|SSNA1_ENST00000459860.1_3'UTR	NM_003731.2	NP_003722.2	O43805	SSNA1_HUMAN	Sjogren syndrome nuclear autoantigen 1	19					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport (GO:0042073)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(2)|kidney(1)|large_intestine(1)|lung(2)	6	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.43e-05)|Epithelial(140;0.00087)		GCCCCCAGGCATAGAGGAGCT	0.701																																					p.I19V		Atlas-SNP	.											.	SSNA1	11	.	0			c.A55G						.						8	8	8					9																	140083520		2165	4253	6418	SO:0001583	missense	8636	exon2			CCAGGCATAGAGG	Z96932	CCDS7034.1	9q34.3	2008-02-05	2007-10-04		ENSG00000176101	ENSG00000176101			11321	protein-coding gene	gene with protein product		610882	"Sjogren's syndrome nuclear autoantigen 1"			9430706	Standard	NM_003731		Approved	NA14, N14	uc004cls.2	O43805	OTTHUMG00000020982	ENST00000322310.5:c.55A>G	chr9.hg19:g.140083520A>G	ENSP00000313752:p.Ile19Val	89.0	0.0		100.0	15.0	NM_003731	Q5VSG0|Q6FG70|Q9BVW8	Missense_Mutation	SNP	ENST00000322310.5	hg19	CCDS7034.1	.	.	.	.	.	.	.	.	.	.	A	15.31	2.795245	0.50208	.	.	ENSG00000176101	ENST00000322310	D	0.82893	-1.66	4.31	4.31	0.51392	.	0.000000	0.85682	D	0.000000	D	0.86053	0.5841	M	0.92367	3.3	0.41029	D	0.985148	B	0.18863	0.031	B	0.23716	0.048	D	0.84586	0.0664	10	0.39692	T	0.17	-26.9482	11.7015	0.51573	1.0:0.0:0.0:0.0	.	19	O43805	SSNA1_HUMAN	V	19	ENSP00000313752:I19V	ENSP00000313752:I19V	I	+	1	0	SSNA1	139203341	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	4.437000	0.59955	1.699000	0.51192	0.459000	0.35465	ATA	.	.		0.701	SSNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055311.1	NM_003731		G	140083520	A	G	140083520	3	3	176	1	0	0	0	0	1	0	0	0	15202	217	8	2	61	2	SSNA1	9	140083520	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	15547768	140083520	1129911	96	26495										
GDI2	2665	hgsc.bcm.edu	37	chr10	5842576	5842576	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cttacatcttccaatggtgtTatagatgcactctctcctcc	5	13	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr10:5842576T>G	ENST00000380191.4	-	2	428	c.138A>C	c.(136-138)atA>atC	p.I46I	GDI2_ENST00000380132.4_Silent_p.I50I|GDI2_ENST00000380181.3_Silent_p.I46I	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2	46					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|Rab GDP-dissociation inhibitor activity (GO:0005093)|Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|large_intestine(1)|lung(6)|urinary_tract(1)	10						CCAATGGTGTTATAGATGCAC	0.388																																					p.I46I		Atlas-SNP	.											.	GDI2	26	.	0			c.A138C						.						200	174	183					10																	5842576		2203	4300	6503	SO:0001819	synonymous_variant	2665	exon2			TGGTGTTATAGAT	D13988	CCDS7071.1, CCDS44352.1	10p15	2010-03-16			ENSG00000057608	ENSG00000057608			4227	protein-coding gene	gene with protein product	"rab GDP-dissociation"	600767				9434952	Standard	NM_001494		Approved	RABGDIB	uc001iil.4	P50395	OTTHUMG00000017607	ENST00000380191.4:c.138A>C	chr10.hg19:g.5842576T>G		84.0	0.0		104.0	34.0	NM_001115156	O43928|Q5SX88|Q9UQM6	Silent	SNP	ENST00000380191.4	hg19	CCDS7071.1																																																																																			.	.		0.388	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	NM_001494		G	5842576	T	G	5842576	2	3	176	1	0	0	0	0	0	0	0	1	6329	1744	61	5		5	GDI2	10	5842576	Silent	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10		5842576	129692171	97	26496										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7618817	7618817	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tggcggtgacctccacgtgcAggtgatccagcttcctgtcc	12	14	0	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr10:7618817A>T	ENST00000256861.6	-	10	1655	c.1577T>A	c.(1576-1578)cTg>cAg	p.L526Q	ITIH5_ENST00000298441.6_Missense_Mutation_p.L312Q|ITIH5_ENST00000397145.2_Missense_Mutation_p.L526Q|ITIH5_ENST00000397146.2_Missense_Mutation_p.L526Q|ITIH5_ENST00000446830.2_Missense_Mutation_p.L308Q|ITIH5_ENST00000434980.1_5'UTR	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	526					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CTCCACGTGCAGGTGATCCAG	0.557																																					p.L526Q		Atlas-SNP	.											.	ITIH5	343	.	0			c.T1577A						.						90	82	85					10																	7618817		2203	4300	6503	SO:0001583	missense	80760	exon10			ACGTGCAGGTGAT			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.1577T>A	chr10.hg19:g.7618817A>T	ENSP00000256861:p.Leu526Gln	139.0	0.0		198.0	51.0	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	A	17.40	3.379338	0.61845	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21	5.68	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.40743	0.1129	.	.	.	0.30154	N	0.802797	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.99;0.974;0.988	T	0.46596	-0.9180	9	0.87932	D	0	-19.1765	12.1201	0.53887	0.8712:0.0:0.0:0.1288	.	526;526;312	G5E9D8;Q86UX2;Q86UX2-3	.;ITIH5_HUMAN;.	Q	526;526;312;308;526	ENSP00000256861:L526Q;ENSP00000380333:L526Q;ENSP00000298441:L312Q;ENSP00000387969:L308Q;ENSP00000380332:L526Q	ENSP00000256861:L526Q	L	-	2	0	ITIH5	7658823	1.000000	0.71417	0.016000	0.15963	0.777000	0.43975	8.832000	0.92079	0.953000	0.37825	0.379000	0.24179	CTG	.	.		0.557	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7618817	A	T	7618817	3	4	176	1	0	0	0	0	1	0	0	0	7916	188	7	4	1394	4	ITIH5	10	7618817	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	1776241	7618817	127915930	98	26497										
C10orf140	387640	hgsc.bcm.edu	37	chr10	21805483	21805483	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cccccctcctcctcctcttcCtcctcctcctcctctccctc	0	28	2	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr10:21805483C>T	ENST00000449193.2	-	4	3521	c.1269G>A	c.(1267-1269)gaG>gaA	p.E423E	SKIDA1_ENST00000487107.1_5'Flank|SKIDA1_ENST00000444772.3_Silent_p.E344E	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	342						nucleus (GO:0005634)											cctcctcttcctcctcctcct	0.627																																					p.E423E		Atlas-SNP	.											.	.	.	.	0			c.G1269A						.						5	6	6					10																	21805483		2007	4123	6130	SO:0001819	synonymous_variant	387640	exon4			CTCTTCCTCCTCC	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 140"	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.1269G>A	chr10.hg19:g.21805483C>T		59.0	0.0		89.0	5.0	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	ENST00000449193.2	hg19	CCDS44363.1																																																																																			.	.		0.627	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		T	21805483	C	T	21805483	2	4	176	1	0	0	0	0	0	0	0	1	1597	680	24	3		3	C10orf140	10	21805483	Silent	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	14186666	21805483	113729264	99	26498										
BMS1	9790	hgsc.bcm.edu	37	chr10	43312077	43312077	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cggtgactttgaagacttggAaacaggggacgtgcacaagg	15	7	0	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr10:43312077A>C	ENST00000374518.5	+	14	2423	c.2360A>C	c.(2359-2361)gAa>gCa	p.E787A		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	787					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GAAGACTTGGAAACAGGGGAC	0.527																																					p.E787A		Atlas-SNP	.											.	BMS1	132	.	0			c.A2360C						.						77	83	81					10																	43312077		2203	4300	6503	SO:0001583	missense	9790	exon14			ACTTGGAAACAGG	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2360A>C	chr10.hg19:g.43312077A>C	ENSP00000363642:p.Glu787Ala	16.0	0.0		16.0	5.0	NM_014753	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	hg19	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.155567	0.57259	.	.	ENSG00000165733	ENST00000374518	T	0.57752	0.38	4.51	4.51	0.55191	.	0.000000	0.85682	D	0.000000	T	0.53400	0.1794	M	0.81239	2.535	0.58432	D	0.999994	P	0.52316	0.952	B	0.38842	0.283	T	0.64588	-0.6372	10	0.56958	D	0.05	.	13.853	0.63508	1.0:0.0:0.0:0.0	.	787	Q14692	BMS1_HUMAN	A	787	ENSP00000363642:E787A	ENSP00000363642:E787A	E	+	2	0	BMS1	42632083	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	9.052000	0.93855	1.679000	0.50963	0.372000	0.22366	GAA	.	.		0.527	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		C	43312077	A	C	43312077	3	2	176	1	0	0	0	0	1	0	0	0	1472	246	9	5	2410	5	BMS1	10	43312077	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	21506594	43312077	92222670	100	26499										
ZWINT	11130	hgsc.bcm.edu	37	chr10	58119616	58119616	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gctgcaattgccttctgtccTgagatgagccaccaggaatg	11	11	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr10:58119616T>A	ENST00000373944.3	-	4	295		c.e4-2		ZWINT_ENST00000460654.1_5'Flank|ZWINT_ENST00000318387.2_5'Flank|ZWINT_ENST00000395405.1_Splice_Site|ZWINT_ENST00000361148.6_Splice_Site			O95229	ZWINT_HUMAN	ZW10 interacting kinetochore protein						establishment of localization in cell (GO:0051649)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|kinetochore (GO:0000776)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)	20						CCTTCTGTCCTGAGATGAGCC	0.552																																					.		Atlas-SNP	.											.	ZWINT	39	.	0			c.257-2A>T						.						77	71	73					10																	58119616		2203	4300	6503	SO:0001630	splice_region_variant	11130	exon5			CTGTCCTGAGATG	AF067656	CCDS7249.1, CCDS31205.1	10q21-q22	2013-05-01	2013-05-01		ENSG00000122952	ENSG00000122952			13195	protein-coding gene	gene with protein product		609177	"ZW10 interactor"				Standard	XM_005269463		Approved	KNTC2AP	uc001jka.1	O95229	OTTHUMG00000018261	ENST00000373944.3:c.257-2A>T	chr10.hg19:g.58119616T>A		53.0	0.0		85.0	23.0	NM_032997	A6NNV6|Q0D2I3|Q9BWD0	Splice_Site	SNP	ENST00000373944.3	hg19	CCDS7249.1	.	.	.	.	.	.	.	.	.	.	T	12.06	1.824330	0.32237	.	.	ENSG00000122952	ENST00000373944;ENST00000395405;ENST00000361148	.	.	.	4.21	2.97	0.34412	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3061	0.26449	0.0:0.0:0.2252:0.7748	.	.	.	.	.	-1	.	.	.	-	.	.	ZWINT	57789622	0.924000	0.31332	0.856000	0.33681	0.717000	0.41224	2.115000	0.41921	1.900000	0.55004	0.529000	0.55759	.	.	.		0.552	ZWINT-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048132.1		Intron	A	58119616	T	A	58119616	5	1	176	1	0	0	0	0	0	0	1	0	18264	1594	55	4	598	4	ZWINT	10	58119616	Splice_Site	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	14807539	58119616	77415131	101	26500										
IPMK	253430	hgsc.bcm.edu	37	chr10	59956280	59956280	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cttttctgccaaagttctgtCattcaattttgtagtggttg	8	7	4	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr10:59956280C>T	ENST00000373935.3	-	6	1130	c.808G>A	c.(808-810)Gac>Aac	p.D270N		NM_152230.4	NP_689416.1	Q8NFU5	IPMK_HUMAN	inositol polyphosphate multikinase	270					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|neural tube formation (GO:0001841)|small molecule metabolic process (GO:0044281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol tetrakisphosphate 3-kinase activity (GO:0000824)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)|inositol-1,4,5-trisphosphate 6-kinase activity (GO:0000823)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)	22						AAAGTTCTGTCATTCAATTTT	0.363																																					p.D270N		Atlas-SNP	.											.	IPMK	45	.	0			c.G808A						.						53	55	55					10																	59956280		2203	4300	6503	SO:0001583	missense	253430	exon6			TTCTGTCATTCAA	AF432853	CCDS7250.1	10q21.1	2010-11-29		2004-07-22	ENSG00000151151	ENSG00000151151			20739	protein-coding gene	gene with protein product		609851				12223481, 12027805	Standard	NM_152230		Approved		uc001jkb.3	Q8NFU5	OTTHUMG00000018268	ENST00000373935.3:c.808G>A	chr10.hg19:g.59956280C>T	ENSP00000363046:p.Asp270Asn	105.0	0.0		231.0	20.0	NM_152230		Missense_Mutation	SNP	ENST00000373935.3	hg19	CCDS7250.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.662168	0.47572	.	.	ENSG00000151151	ENST00000373935	T	0.19105	2.17	5.97	5.97	0.96955	.	0.209202	0.50627	D	0.000112	T	0.33118	0.0852	M	0.68952	2.095	0.44380	D	0.997283	P	0.43231	0.801	P	0.45829	0.494	T	0.01042	-1.1471	9	.	.	.	-6.3015	17.9263	0.88985	0.0:1.0:0.0:0.0	.	270	Q8NFU5	IPMK_HUMAN	N	270	ENSP00000363046:D270N	.	D	-	1	0	IPMK	59626286	1.000000	0.71417	0.999000	0.59377	0.659000	0.38960	6.346000	0.72999	2.833000	0.97629	0.585000	0.79938	GAC	.	.		0.363	IPMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048142.1	NM_152230		T	59956280	C	T	59956280	3	4	176	1	0	0	0	0	1	0	0	0	7801	826	29	3	446	3	IPMK	10	59956280	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	1836664	59956280	75578467	102	26501										
DDX21	9188	hgsc.bcm.edu	37	chr10	70719759	70719759	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tctcctaaaaccaaaagtttGagaaagaaaaaggagcccat	7	8	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr10:70719759G>A	ENST00000354185.4	+	2	383	c.285G>A	c.(283-285)ttG>ttA	p.L95L		NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	95					ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CCAAAAGTTTGAGAAAGAAAA	0.363																																					p.L95L		Atlas-SNP	.											DDX21,lower_third,carcinoma,0,1	DDX21	57	.	0			c.G285A						.						42	45	44					10																	70719759		2202	4298	6500	SO:0001819	synonymous_variant	9188	exon2			AAGTTTGAGAAAG	U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732		"DEAD-boxes"	2744	protein-coding gene	gene with protein product		606357	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 21"			8614622, 18180292	Standard	NM_004728		Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.285G>A	chr10.hg19:g.70719759G>A		505.0	1.0		540.0	229.0	NM_004728	B2RDL0|Q13436|Q5VX41|Q68D35	Silent	SNP	ENST00000354185.4	hg19	CCDS31211.1																																																																																			.	.		0.363	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048374.1	NM_004728		A	70719759	G	A	70719759	2	1	176	1	0	0	0	0	0	0	0	1	4351	1281	45	3		3	DDX21	10	70719759	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	10763479	70719759	64814988	103	26502										
NLRP6	171389	hgsc.bcm.edu	37	chr11	279503	279503	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggacctcgcggagcagctggCccagttctacggcccggagc	15	15	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:279503C>A	ENST00000312165.5	+	2	206	c.206C>A	c.(205-207)gCc>gAc	p.A69D	NLRP6_ENST00000534750.1_Missense_Mutation_p.A69D	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	69	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		GAGCAGCTGGCCCAGTTCTAC	0.761																																					p.A69D		Atlas-SNP	.											.	NLRP6	4	.	0			c.C206A						.						3	4	3					11																	279503		1806	3520	5326	SO:0001583	missense	171389	exon2			AGCTGGCCCAGTT	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"Nucleotide-binding domain and leucine rich repeat containing"	22944	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"	609650	"NACHT, leucine rich repeat and PYD containing 6"	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.206C>A	chr11.hg19:g.279503C>A	ENSP00000309767:p.Ala69Asp	104.0	0.0		91.0	32.0	NM_138329	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	hg19	CCDS7693.1	.	.	.	.	.	.	.	.	.	.	C	9.579	1.123103	0.20959	.	.	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.42900	0.96;0.96	3.71	-2.94	0.05581	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.18509	0.0444	N	0.08118	0	0.09310	N	1	P;B	0.38677	0.642;0.411	B;B	0.37015	0.223;0.239	T	0.19128	-1.0315	9	0.27785	T	0.31	.	6.8456	0.23987	0.0:0.1794:0.1483:0.6723	.	69;69	E9PJZ8;P59044	.;NALP6_HUMAN	D	69	ENSP00000433617:A69D;ENSP00000309767:A69D	ENSP00000309767:A69D	A	+	2	0	NLRP6	269503	0.000000	0.05858	0.000000	0.03702	0.201000	0.24016	-0.450000	0.06803	-0.492000	0.06687	0.491000	0.48974	GCC	.	.		0.761	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		A	279503	C	A	279503	3	1	176	1	0	0	0	0	1	0	0	0	10490	739	26	3	212	3	NLRP6	11	279503	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10		279503	134727013	104	26503										
KRTAP5-3	387266	hgsc.bcm.edu	37	chr11	1629046	1629046	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gactgggaacagcagggtttGcagcagctggactggcagca	16	9	0	0	rs12808755		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:1629046G>A	ENST00000399685.1	-	1	647	c.570C>T	c.(568-570)tgC>tgT	p.C190C		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	190	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		agcagggtttgcagcagctgg	0.622																																					p.C190C		Atlas-SNP	.											.	KRTAP5-3	33	.	0			c.C570T						.						161	162	162					11																	1629046		2202	4290	6492	SO:0001819	synonymous_variant	387266	exon1			GGGTTTGCAGCAG	AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"Keratin associated proteins"	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.570C>T	chr11.hg19:g.1629046G>A		47.0	0.0		57.0	6.0	NM_001012708	Q6PL44|Q701N3	Silent	SNP	ENST00000399685.1	hg19	CCDS41591.1																																																																																			.	.		0.622	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1			A	1629046	G	A	1629046	2	1	176	1	0	0	0	0	0	0	0	1	8571	1311	46	3		3	KRTAP5-3	11	1629046	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	1349543	1629046	133377470	105	26504										
OR51G1	79324	hgsc.bcm.edu	37	chr11	4945292	4945292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aacaggcagggatgccaatcTctctggtatcaaaccagaaa	9	10	3	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:4945292T>C	ENST00000321961.2	-	1	345	c.278A>G	c.(277-279)gAg>gGg	p.E93G	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGCCAATCTCTCTGGTATC	0.488																																					p.E93G		Atlas-SNP	.											.	OR51G1	74	.	0			c.A278G						.						86	81	83					11																	4945292		2201	4298	6499	SO:0001583	missense	79324	exon1			CCAATCTCTCTGG	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"GPCR / Class A : Olfactory receptors"	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.278A>G	chr11.hg19:g.4945292T>C	ENSP00000322546:p.Glu93Gly	133.0	0.0		168.0	30.0	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	hg19	CCDS31366.1	.	.	.	.	.	.	.	.	.	.	T	11.09	1.535375	0.27475	.	.	ENSG00000176879	ENST00000321961	T	0.00479	7.12	4.2	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39475	U	0.001354	T	0.00356	0.0011	L	0.41492	1.28	0.09310	N	0.999999	B	0.18166	0.026	B	0.18561	0.022	T	0.45775	-0.9238	10	0.52906	T	0.07	.	6.6867	0.23148	0.0:0.1952:0.0:0.8048	.	93	Q8NGK1	O51G1_HUMAN	G	93	ENSP00000322546:E93G	ENSP00000322546:E93G	E	-	2	0	OR51G1	4901868	0.000000	0.05858	0.999000	0.59377	0.916000	0.54674	-0.955000	0.03869	1.760000	0.52011	0.455000	0.32223	GAG	.	.		0.488	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237		C	4945292	T	C	4945292	3	2	176	1	0	0	0	0	1	0	0	0	11107	1551	54	2	689	2	OR51G1	11	4945292	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	3316246	4945292	130061224	106	26505										
OR8I2	120586	hgsc.bcm.edu	37	chr11	55861433	55861433	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ccttatcatcacagtcacttAtatcatcatcatctcagcca	2	14	7	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:55861433A>G	ENST00000302124.2	+	1	681	c.650A>G	c.(649-651)tAt>tGt	p.Y217C		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					ACAGTCACTTATATCATCATC	0.478																																					p.Y217C		Atlas-SNP	.											.	OR8I2	119	.	0			c.A650G						.						140	120	127					11																	55861433		2201	4296	6497	SO:0001583	missense	120586	exon1			TCACTTATATCAT	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.650A>G	chr11.hg19:g.55861433A>G	ENSP00000303864:p.Tyr217Cys	81.0	0.0		70.0	26.0	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	hg19	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	A	9.953	1.220788	0.22457	.	.	ENSG00000172154	ENST00000302124	T	0.00520	6.85	4.33	3.16	0.36331	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36740	U	0.002431	T	0.01695	0.0054	H	0.96398	3.815	0.35035	D	0.759193	P	0.41159	0.74	P	0.50352	0.638	T	0.02121	-1.1210	10	0.87932	D	0	-13.2475	6.7167	0.23308	0.7601:0.154:0.0859:0.0	.	217	Q8N0Y5	OR8I2_HUMAN	C	217	ENSP00000303864:Y217C	ENSP00000303864:Y217C	Y	+	2	0	OR8I2	55618009	1.000000	0.71417	0.018000	0.16275	0.013000	0.08279	8.312000	0.89976	0.603000	0.29913	-0.724000	0.03597	TAT	.	.		0.478	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		G	55861433	A	G	55861433	3	3	176	1	0	0	0	0	1	0	0	0	11249	449	16	2	652	2	OR8I2	11	55861433	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	50916141	55861433	79145083	107	26506										
ATG16L2	89849	hgsc.bcm.edu	37	chr11	72525573	72525573	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gctgcggcttcgggaccgtaCgcaaaaggcgcttttcctgg	14	12	0	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:72525573C>A	ENST00000321297.5	+	1	221	c.83C>A	c.(82-84)aCg>aAg	p.T28K	ATG16L2_ENST00000534905.1_Missense_Mutation_p.T28K	NM_033388.1	NP_203746.1	Q8NAA4	A16L2_HUMAN	autophagy related 16-like 2 (S. cerevisiae)	28					autophagy (GO:0006914)|negative stranded viral RNA replication (GO:0039689)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	14			BRCA - Breast invasive adenocarcinoma(5;2.73e-06)			CGGGACCGTACGCAAAAGGCG	0.741																																					p.T28K		Atlas-SNP	.											.	ATG16L2	26	.	0			c.C83A						.						26	28	27					11																	72525573		2177	4257	6434	SO:0001583	missense	89849	exon1			ACCGTACGCAAAA	AK024423	CCDS31634.1	11q13.4	2014-02-12	2012-06-06		ENSG00000168010	ENSG00000168010		"WD repeat domain containing"	25464	protein-coding gene	gene with protein product			"ATG16 autophagy related 16-like 2 (S. cerevisiae)"			11214971	Standard	XM_005274378		Approved	FLJ00012, WDR80, ATG16B	uc001otd.3	Q8NAA4	OTTHUMG00000167961	ENST00000321297.5:c.83C>A	chr11.hg19:g.72525573C>A	ENSP00000326340:p.Thr28Lys	131.0	0.0		141.0	25.0	NM_033388	A5PL30|B2RPK5|Q658V4|Q6PID3|Q8NBG0	Missense_Mutation	SNP	ENST00000321297.5	hg19	CCDS31634.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.81|16.81	3.224655|3.224655	0.58668|0.58668	.|.	.|.	ENSG00000168010|ENSG00000168010	ENST00000540567|ENST00000321297;ENST00000534905	.|T;T	.|0.42513	.|0.97;0.97	4.75|4.75	0.459|0.459	0.16678|0.16678	.|Autophagy-related protein 16 (1);	.|1.374300	.|0.04929	.|N	.|0.456436	T|T	0.22126|0.22126	0.0533|0.0533	N|N	0.12182|0.12182	0.205|0.205	0.27591|0.27591	N|N	0.949288|0.949288	.|B;B;B;P	.|0.49185	.|0.006;0.001;0.008;0.92	.|B;B;B;P	.|0.45829	.|0.01;0.01;0.03;0.494	T|T	0.17440|0.17440	-1.0369|-1.0369	5|10	.|0.05620	.|T	.|0.96	.|.	1.3522|1.3522	0.02175|0.02175	0.1665:0.4524:0.1829:0.1981|0.1665:0.4524:0.1829:0.1981	.|.	.|28;28;28;27	.|B4E090;F5GWZ9;Q8NAA4;Q2VPK0	.|.;.;A16L2_HUMAN;.	S|K	33|28	.|ENSP00000326340:T28K;ENSP00000441189:T28K	.|ENSP00000326340:T28K	R|T	+|+	1|2	0|0	ATG16L2|ATG16L2	72203221|72203221	0.987000|0.987000	0.35691|0.35691	0.997000|0.997000	0.53966|0.53966	0.438000|0.438000	0.31896|0.31896	0.203000|0.203000	0.17315|0.17315	0.229000|0.229000	0.21039|0.21039	-0.736000|-0.736000	0.03550|0.03550	CGC|ACG	.	.		0.741	ATG16L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397305.1	NM_033388		A	72525573	C	A	72525573	3	1	176	1	0	0	0	0	1	0	0	0	1092	536	19	1	85	1	ATG16L2	11	72525573	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	16664140	72525573	62480943	108	26507										
FAM168A	23201	hgsc.bcm.edu	37	chr11	73141779	73141779	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tggggtacaggctgggattgTaggcaggggcagctgctgga	20	6	0	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:73141779T>A	ENST00000064778.4	-	3	391	c.107A>T	c.(106-108)tAc>tTc	p.Y36F	FAM168A_ENST00000450446.2_Missense_Mutation_p.Y36F|FAM168A_ENST00000356467.4_Missense_Mutation_p.Y36F			Q92567	F168A_HUMAN	family with sequence similarity 168, member A	36										endometrium(3)|kidney(1)|lung(1)	5						GCTGGGATTGTAGGCAGGGGC	0.468																																					p.Y36F		Atlas-SNP	.											.	FAM168A	18	.	0			c.A107T						.						103	105	104					11																	73141779		1926	4124	6050	SO:0001583	missense	23201	exon3			GGATTGTAGGCAG	BC014932	CCDS41689.1, CCDS66165.1, CCDS73346.1	11q13.4	2008-06-11	2008-06-11	2008-06-11		ENSG00000054965			28999	protein-coding gene	gene with protein product	"tongue cancer chemotherapy resistance-associated protein 1"		"KIAA0280"	KIAA0280			Standard	XM_005273852		Approved	TCRP1	uc001oty.1	Q92567		ENST00000064778.4:c.107A>T	chr11.hg19:g.73141779T>A	ENSP00000064778:p.Tyr36Phe	78.0	0.0		114.0	19.0	NM_015159	A2ICY2|A2ID81|Q86UG2	Missense_Mutation	SNP	ENST00000064778.4	hg19		.	.	.	.	.	.	.	.	.	.	T	25.6	4.656184	0.88056	.	.	ENSG00000054965	ENST00000064778;ENST00000450446;ENST00000356467	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.75744	0.3891	M	0.62723	1.935	0.52099	D	0.999943	D;P;P	0.56035	0.974;0.927;0.927	D;D;D	0.70487	0.969;0.953;0.953	T	0.78178	-0.2305	9	0.87932	D	0	.	13.3716	0.60717	0.0:0.0:0.0:1.0	.	36;36;36	Q92567-3;Q92567;Q92567-2	.;F168A_HUMAN;.	F	36	.	ENSP00000064778:Y36F	Y	-	2	0	FAM168A	72819427	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.516000	0.60496	2.188000	0.69820	0.533000	0.62120	TAC	.	.		0.468	FAM168A-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000397424.1	NM_015159		A	73141779	T	A	73141779	3	1	176	1	0	0	0	0	1	0	0	0	5490	1638	57	4	620	4	FAM168A	11	73141779	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	616206	73141779	61864737	109	26508										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78369171	78369171	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gctgtctgacagttctgggtActgctcgacagagatcacga	12	10	3	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:78369171A>T	ENST00000278550.7	-	34	8704	c.8242T>A	c.(8242-8244)Tac>Aac	p.Y2748N		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2748					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										AGTTCTGGGTACTGCTCGACA	0.587																																					p.Y2748N		Atlas-SNP	.											.	.	.	.	0			c.T8242A						.						199	211	207					11																	78369171		2129	4221	6350	SO:0001583	missense	26011	exon34			CTGGGTACTGCTC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.8242T>A	chr11.hg19:g.78369171A>T	ENSP00000278550:p.Tyr2748Asn	92.0	0.0		90.0	35.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.515774	0.85495	.	.	ENSG00000149256	ENST00000278550	D	0.92299	-3.01	5.65	5.65	0.86999	.	0.065888	0.64402	D	0.000006	D	0.94591	0.8257	M	0.81239	2.535	0.58432	D	0.999999	D	0.61080	0.989	P	0.53450	0.726	D	0.94553	0.7755	9	.	.	.	.	16.0399	0.80667	1.0:0.0:0.0:0.0	.	2748	Q6N022	TEN4_HUMAN	N	2748	ENSP00000278550:Y2748N	.	Y	-	1	0	ODZ4	78046819	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.087000	0.94110	2.371000	0.80710	0.533000	0.62120	TAC	.	.		0.587	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78369171	A	T	78369171	3	4	176	1	0	0	0	0	1	0	0	0	10846	391	14	4	71	4	ODZ4	11	78369171	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	5227392	78369171	56637345	110	26509										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78387204	78387204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aggcctcgctcacccgcagcCggcgcccaaagacagtgacc	11	18	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:78387204C>T	ENST00000278550.7	-	30	5951	c.5489G>A	c.(5488-5490)cGg>cAg	p.R1830Q		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1830					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CACCCGCAGCCGGCGCCCAAA	0.637																																					p.R1830Q		Atlas-SNP	.											.	.	.	.	0			c.G5489A						.						7	9	9					11																	78387204		1946	4058	6004	SO:0001583	missense	26011	exon30			CGCAGCCGGCGCC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5489G>A	chr11.hg19:g.78387204C>T	ENSP00000278550:p.Arg1830Gln	47.0	0.0		54.0	9.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	32	5.177671	0.94846	.	.	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.89875	-2.58;0.86	4.47	4.47	0.54385	.	0.000000	0.85682	D	0.000000	D	0.91791	0.7403	L	0.43923	1.385	0.53688	D	0.999976	D	0.76494	0.999	D	0.72625	0.978	D	0.90877	0.4750	9	.	.	.	.	17.6814	0.88245	0.0:1.0:0.0:0.0	.	1830	Q6N022	TEN4_HUMAN	Q	1830;294	ENSP00000278550:R1830Q;ENSP00000431711:R294Q	.	R	-	2	0	ODZ4	78064852	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.904000	0.56325	2.468000	0.83385	0.650000	0.86243	CGG	.	.		0.637	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78387204	C	T	78387204	3	4	176	1	0	0	0	0	1	0	0	0	10846	652	23	1	2840	1	ODZ4	11	78387204	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	18033	78387204	56619312	111	26510										
TMEM135	65084	hgsc.bcm.edu	37	chr11	86802424	86802424	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gagagggctgctcacaatttAtatggccaacttggtaagta	11	7	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:86802424A>T	ENST00000305494.5	+	4	422	c.383A>T	c.(382-384)tAt>tTt	p.Y128F	TMEM135_ENST00000535167.1_Intron|TMEM135_ENST00000355734.4_Missense_Mutation_p.Y128F|TMEM135_ENST00000340353.7_Missense_Mutation_p.Y128F|TMEM135_ENST00000532959.1_Intron	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	128					peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CTCACAATTTATATGGCCAAC	0.269																																					p.Y128F		Atlas-SNP	.											.	TMEM135	40	.	0			c.A383T						.						112	114	113					11																	86802424		2201	4296	6497	SO:0001583	missense	65084	exon4			CAATTTATATGGC	BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.383A>T	chr11.hg19:g.86802424A>T	ENSP00000306344:p.Tyr128Phe	93.0	0.0		134.0	26.0	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Missense_Mutation	SNP	ENST00000305494.5	hg19	CCDS8280.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.959609	0.74016	.	.	ENSG00000166575	ENST00000340353;ENST00000526733;ENST00000525018;ENST00000355734;ENST00000305494	T;T;T;T	0.73469	0.41;0.18;2.61;-0.75	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.85075	0.5614	M	0.79614	2.46	0.80722	D	1	D;D;D	0.89917	0.999;0.997;1.0	D;D;D	0.87578	0.983;0.946;0.998	D	0.85886	0.1425	9	.	.	.	-12.9561	12.0643	0.53580	1.0:0.0:0.0:0.0	.	128;128;128	Q86UB9-2;Q86UB9;Q8N605	.;TM135_HUMAN;.	F	128;97;128;128;128	ENSP00000345513:Y128F;ENSP00000433927:Y128F;ENSP00000347973:Y128F;ENSP00000306344:Y128F	.	Y	+	2	0	TMEM135	86480072	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.824000	0.62701	2.103000	0.63969	0.383000	0.25322	TAT	.	.		0.269	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918		T	86802424	A	T	86802424	3	4	176	1	0	0	0	0	1	0	0	0	16066	449	16	4	397	4	TMEM135	11	86802424	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	8415220	86802424	48204092	112	26511										
TTC12	54970	hgsc.bcm.edu	37	chr11	113209515	113209515	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtctagagagtgttataagaAgatcttagaaataaacccca	8	6	2	4			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:113209515A>T	ENST00000529221.1	+	9	701	c.596A>T	c.(595-597)aAg>aTg	p.K199M	TTC12_ENST00000483239.2_Missense_Mutation_p.K205M|TTC12_ENST00000393020.1_Missense_Mutation_p.K199M|TTC12_ENST00000314756.3_Missense_Mutation_p.K199M	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	199										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		TGTTATAAGAAGATCTTAGAA	0.478																																					p.K199M		Atlas-SNP	.											.	TTC12	66	.	0			c.A596T						.						126	126	126					11																	113209515		2201	4296	6497	SO:0001583	missense	54970	exon9			ATAAGAAGATCTT	AK000542	CCDS8360.2	11q23.2	2013-01-10			ENSG00000149292	ENSG00000149292		"Tetratricopeptide (TTC) repeat domain containing"	23700	protein-coding gene	gene with protein product		610732				12964006	Standard	XM_005271607		Approved	FLJ13859, FLJ20535, TPARM	uc001pnu.3	Q9H892	OTTHUMG00000142832	ENST00000529221.1:c.596A>T	chr11.hg19:g.113209515A>T	ENSP00000433757:p.Lys199Met	122.0	0.0		139.0	62.0	NM_017868	Q8N5H9|Q9NWY3	Missense_Mutation	SNP	ENST00000529221.1	hg19	CCDS8360.2	.	.	.	.	.	.	.	.	.	.	A	20.3	3.971616	0.74246	.	.	ENSG00000149292	ENST00000529221;ENST00000442859;ENST00000529850;ENST00000314756;ENST00000525965;ENST00000393020;ENST00000483239;ENST00000524580	D;T;T;D;T;D;D	0.91011	-2.77;-0.64;-1.11;-2.77;-1.07;-2.77;-2.77	6.08	4.95	0.65309	Tetratricopeptide-like helical (1);Armadillo-type fold (1);Tetratricopeptide repeat-containing (1);	0.145302	0.64402	D	0.000010	D	0.95130	0.8422	M	0.87038	2.855	0.45403	D	0.99838	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	D	0.94866	0.8026	10	0.72032	D	0.01	-29.7996	10.2428	0.43324	0.9239:0.0:0.0761:0.0	.	199;199	A8K8G6;Q9H892	.;TTC12_HUMAN	M	199;199;179;199;155;199;205;25	ENSP00000433757:K199M;ENSP00000400039:K199M;ENSP00000431806:K179M;ENSP00000315160:K199M;ENSP00000435308:K155M;ENSP00000376743:K199M;ENSP00000419652:K205M	ENSP00000315160:K199M	K	+	2	0	TTC12	112714725	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.063000	0.57499	1.110000	0.41699	0.533000	0.62120	AAG	.	.		0.478	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2	NM_017868		T	113209515	A	T	113209515	3	4	176	1	0	0	0	0	1	0	0	0	16694	72	3	4	626	4	TTC12	11	113209515	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	26407091	113209515	21797001	113	26512										
VWA5A	4013	hgsc.bcm.edu	37	chr11	124013257	124013257	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aggtatgagtttggaagaaaTaatggctgcacagcctgccg	13	7	0	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr11:124013257T>C	ENST00000456829.2	+	17	2383	c.2132T>C	c.(2131-2133)aTa>aCa	p.I711T	VWA5A_ENST00000392748.1_Missense_Mutation_p.I711T|VWA5A_ENST00000360334.4_3'UTR	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	711										autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						TTGGAAGAAATAATGGCTGCA	0.423																																					p.I711T		Atlas-SNP	.											.	VWA5A	102	.	0			c.T2132C						.						111	104	107					11																	124013257		2201	4299	6500	SO:0001583	missense	4013	exon16			AAGAAATAATGGC	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"loss of heterozygosity, 11, chromosomal region 2, gene A"	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.2132T>C	chr11.hg19:g.124013257T>C	ENSP00000407726:p.Ile711Thr	93.0	0.0		101.0	35.0	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	hg19	CCDS8444.1	.	.	.	.	.	.	.	.	.	.	T	9.180	1.023365	0.19433	.	.	ENSG00000110002	ENST00000456829;ENST00000392748	T;T	0.04406	3.63;3.63	5.59	4.47	0.54385	.	1.550680	0.03130	N	0.165070	T	0.05547	0.0146	L	0.36672	1.1	0.18873	N	0.999988	B	0.14012	0.009	B	0.10450	0.005	T	0.41052	-0.9530	10	0.21014	T	0.42	-0.0235	5.118	0.14845	0.0:0.1538:0.0:0.8462	.	711	O00534	VMA5A_HUMAN	T	711	ENSP00000407726:I711T;ENSP00000376504:I711T	ENSP00000376504:I711T	I	+	2	0	VWA5A	123518467	0.013000	0.17824	0.004000	0.12327	0.022000	0.10575	1.629000	0.37071	2.131000	0.65755	0.459000	0.35465	ATA	.	.		0.423	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622		C	124013257	T	C	124013257	3	2	176	1	0	0	0	0	1	0	0	0	17257	1406	49	2	2194	2	VWA5A	11	124013257	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	10803742	124013257	10993259	114	26513										
ETV6	2120	hgsc.bcm.edu	37	chr12	12006418	12006418	+	Frame_Shift_Del	DEL	T	T	-													0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcagaggaaacctcggattcTtttttcaccattcttccacc							TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr12:12006418delT	ENST00000396373.4	+	4	660	c.386delT	c.(385-387)cttfs	p.L129fs		NM_001987.4	NP_001978.1	P41212	ETV6_HUMAN	ets variant 6	129					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		ETV6/JAK2(11)|ETV6/ITPR2(2)|ETV6/NTRK3(238)	breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(15)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				CCTCGGATTCTTTTTTCACCA	0.428			T	"NTRK3, RUNX1, PDGFRB, ABL1, MN1, ABL2, FACL6, CHIC2, ARNT, JAK2, EVI1, CDX2, STL, HLXB9, MDS2, PER1, SYK, TTL, FGFR3, PAX5"	"congenital fibrosarcoma, multiple leukemia and lymphoma,  secretory breast, MDS, ALL"																																p.L129fs		Atlas-INDEL	.		Dom	yes		12	12p13	2120	ets variant gene 6 (TEL oncogene)		"L, E, M"	.	ETV6	91	.	0			c.385delC						.						158	154	155					12																	12006418		2203	4300	6503	SO:0001589	frameshift_variant	2120	exon4			.	BC043399	CCDS8643.1	12p13	2014-09-17	2008-09-12		ENSG00000139083	ENSG00000139083			3495	protein-coding gene	gene with protein product	"TEL oncogene"	600618	"ets variant gene 6 (TEL oncogene)"			7731705	Standard	NM_001987		Approved	TEL	uc001qzz.3	P41212	OTTHUMG00000168538	ENST00000396373.4:c.386delT	chr12.hg19:g.12006418delT	ENSP00000379658:p.Leu129fs	92.0	0.0		129.0	31.0	NM_001987	A3QVP6|A8K076|Q9UMF6|Q9UMF7|Q9UMG0	Frame_Shift_Del	DEL	ENST00000396373.4	hg19	CCDS8643.1																																																																																			.	.		0.428	ETV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400130.2	NM_001987		-	12006418	T	-	12006418	7	5	176	1	0	1	0	1	0	0	0	0	5285	1609	56	0	400	0	ETV6	12	12006418	Frame_Shift_Del	DEL	T	TCGA-DD-AACZ-01A-11D-A40R-10		12006418	121845477	115	26514										
IPO8	10526	hgsc.bcm.edu	37	chr12	30837345	30837345	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcttctcctggtggaggttcTcgatctggccagtattgtgt	13	9	3	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr12:30837345T>A	ENST00000256079.4	-	3	551	c.213A>T	c.(211-213)cgA>cgT	p.R71R	IPO8_ENST00000538338.1_5'Flank	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	71	Importin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00115}.				intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					GTGGAGGTTCTCGATCTGGCC	0.413																																					p.R71R		Atlas-SNP	.											.	IPO8	105	.	0			c.A213T						.						265	227	240					12																	30837345		2203	4300	6503	SO:0001819	synonymous_variant	10526	exon3			AGGTTCTCGATCT	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.213A>T	chr12.hg19:g.30837345T>A		107.0	0.0		162.0	51.0	NM_006390	B7Z7M3	Silent	SNP	ENST00000256079.4	hg19	CCDS8719.1																																																																																			.	.		0.413	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		A	30837345	T	A	30837345	2	1	176	1	0	0	0	0	0	0	0	1	7807	1538	54	4		4	IPO8	12	30837345	Silent	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	18830927	30837345	103014550	116	26515										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41410583	41410583	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aaaaagtcacagttactaatCctgatactggccgatatgtc	7	9	1	1	rs566695601		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr12:41410583C>T	ENST00000551295.2	+	19	2401	c.2284C>T	c.(2284-2286)Cct>Tct	p.P762S	CNTN1_ENST00000348761.2_Missense_Mutation_p.P751S|CNTN1_ENST00000550305.1_3'UTR|CNTN1_ENST00000347616.1_Missense_Mutation_p.P762S	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	762	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.P762S(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				AGTTACTAATCCTGATACTGG	0.398													C|||	1	0.000199681	8e-04	0	5008	,	,		19518	0		0	False		,,,				2504	0				p.P762S		Atlas-SNP	.											CNTN1,colon,carcinoma,0,1	CNTN1	207	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2284T						.						128	111	117					12																	41410583		2203	4300	6503	SO:0001583	missense	1272	exon19			ACTAATCCTGATA	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.2284C>T	chr12.hg19:g.41410583C>T	ENSP00000447006:p.Pro762Ser	130.0	0.0		203.0	67.0	NM_001843	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.548129	0.65311	.	.	ENSG00000018236	ENST00000551295;ENST00000347616;ENST00000348761	T;T;T	0.55588	0.51;0.51;0.51	5.35	5.35	0.76521	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.053392	0.85682	D	0.000000	T	0.67711	0.2922	M	0.66506	2.035	0.80722	D	1	D;D	0.60575	0.984;0.988	P;P	0.60541	0.804;0.876	T	0.59710	-0.7403	10	0.17832	T	0.49	.	19.9544	0.97215	0.0:1.0:0.0:0.0	.	751;762	Q12860-2;Q12860	.;CNTN1_HUMAN	S	762;762;751	ENSP00000447006:P762S;ENSP00000325660:P762S;ENSP00000261160:P751S	ENSP00000325660:P762S	P	+	1	0	CNTN1	39696850	1.000000	0.71417	0.982000	0.44146	0.854000	0.48673	3.688000	0.54699	2.885000	0.99019	0.655000	0.94253	CCT	.	.		0.398	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		T	41410583	C	T	41410583	3	4	176	1	0	0	0	0	1	0	0	0	3642	855	30	3	2354	3	CNTN1	12	41410583	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	10573238	41410583	92441312	117	26516										
KRT74	121391	hgsc.bcm.edu	37	chr12	52962149	52962149	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tccccgctgctcagcgtcagCgatggccgtctccaggctgg	13	16	3	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr12:52962149C>T	ENST00000305620.2	-	7	1206	c.1159G>A	c.(1159-1161)Gct>Act	p.A387T	KRT74_ENST00000549343.1_Missense_Mutation_p.A401T	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	387	Coil 2.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	keratin filament binding (GO:1990254)|structural molecule activity (GO:0005198)			kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	28				BRCA - Breast invasive adenocarcinoma(357;0.191)		TCAGCGTCAGCGATGGCCGTC	0.577																																					p.A387T		Atlas-SNP	.											.	KRT74	67	.	0			c.G1159A						.						47	43	44					12																	52962149		2203	4300	6503	SO:0001583	missense	121391	exon7			CGTCAGCGATGGC	BK000977	CCDS8832.1	12q13.13	2013-06-25			ENSG00000170484	ENSG00000170484		"-", "Intermediate filaments type II, keratins (basic)"	28929	protein-coding gene	gene with protein product		608248				12648212, 16831889	Standard	NM_175053		Approved	K6IRS4, KRT5C, KRT6IRS4	uc001sap.1	Q7RTS7	OTTHUMG00000169658	ENST00000305620.2:c.1159G>A	chr12.hg19:g.52962149C>T	ENSP00000307240:p.Ala387Thr	84.0	0.0		113.0	11.0	NM_175053	B5MD61|Q86Y45	Missense_Mutation	SNP	ENST00000305620.2	hg19	CCDS8832.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.323785	0.41096	.	.	ENSG00000170484	ENST00000549343;ENST00000305620	D;T	0.89415	-2.51;-1.02	4.24	3.33	0.38152	Filament (1);	0.000000	0.33199	N	0.005166	D	0.87649	0.6230	L	0.60455	1.87	0.09310	N	1	P	0.36222	0.544	B	0.42112	0.376	T	0.79472	-0.1789	10	0.40728	T	0.16	.	11.4988	0.50424	0.4852:0.5148:0.0:0.0	.	387	Q7RTS7	K2C74_HUMAN	T	401;387	ENSP00000447447:A401T;ENSP00000307240:A387T	ENSP00000307240:A387T	A	-	1	0	KRT74	51248416	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-0.592000	0.05747	1.053000	0.40415	0.655000	0.94253	GCT	.	.		0.577	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053		T	52962149	C	T	52962149	3	4	176	1	0	0	0	0	1	0	0	0	8496	768	27	1	442	1	KRT74	12	52962149	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	11551566	52962149	80889746	118	26517										
KRT3	3850	hgsc.bcm.edu	37	chr12	53189455	53189455	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aagccaccagcccctccaaaGccaccagctccaccaaagcc	5	21	0	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr12:53189455G>A	ENST00000417996.2	-	1	446	c.372C>T	c.(370-372)ggC>ggT	p.G124G	KRT3_ENST00000309505.3_Silent_p.G124G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	124	Gly-rich.|Head.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						cccctccaaagccaccagctc	0.627																																					p.G124G		Atlas-SNP	.											.	KRT3	65	.	0			c.C372T						.						155	196	182					12																	53189455		2195	4290	6485	SO:0001819	synonymous_variant	3850	exon1			TCCAAAGCCACCA		CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"-", "Intermediate filaments type II, keratins (basic)"	6440	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 3", "cytokeratin 3"	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.372C>T	chr12.hg19:g.53189455G>A		113.0	0.0		151.0	45.0	NM_057088	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	hg19	CCDS44895.1																																																																																			.	.		0.627	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		A	53189455	G	A	53189455	2	1	176	1	0	0	0	0	0	0	0	1	8475	958	34	3		3	KRT3	12	53189455	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	227306	53189455	80662440	119	26518										
HOXC12	3228	hgsc.bcm.edu	37	chr12	54348808	54348808	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cttccccaacttccgcgcgtCcggggcgcagcttcccgggc	12	19	0	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr12:54348808C>A	ENST00000243103.3	+	1	191	c.95C>A	c.(94-96)tCc>tAc	p.S32Y	AC012531.23_ENST00000603432.1_lincRNA	NM_173860.1	NP_776272.1	P31275	HXC12_HUMAN	homeobox C12	32					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	12						TTCCGCGCGTCCGGGGCGCAG	0.652																																					p.S32Y		Atlas-SNP	.											.	HOXC12	19	.	0			c.C95A						.						31	37	35					12																	54348808		2203	4300	6503	SO:0001583	missense	3228	exon1			GCGCGTCCGGGGC	AF328962	CCDS8866.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123407	ENSG00000123407		"Homeoboxes / ANTP class : HOXL subclass"	5124	protein-coding gene	gene with protein product		142975	"homeo box C12"	HOX3, HOX3F, HOC3F		1973146, 1358459	Standard	NM_173860		Approved		uc010soq.2	P31275	OTTHUMG00000160010	ENST00000243103.3:c.95C>A	chr12.hg19:g.54348808C>A	ENSP00000243103:p.Ser32Tyr	188.0	0.0		299.0	87.0	NM_173860	Q9BXJ6	Missense_Mutation	SNP	ENST00000243103.3	hg19	CCDS8866.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.402220	0.62288	.	.	ENSG00000123407	ENST00000243103	D	0.93763	-3.28	2.85	1.9	0.25705	.	0.000000	0.64402	D	0.000002	D	0.94162	0.8127	M	0.78916	2.43	0.43453	D	0.995648	D	0.61080	0.989	P	0.53450	0.726	D	0.93084	0.6494	10	0.59425	D	0.04	.	10.2809	0.43539	0.2003:0.7997:0.0:0.0	.	32	P31275	HXC12_HUMAN	Y	32	ENSP00000243103:S32Y	ENSP00000243103:S32Y	S	+	2	0	HOXC12	52635075	0.971000	0.33674	0.977000	0.42913	0.950000	0.60333	3.466000	0.53071	0.708000	0.31955	0.455000	0.32223	TCC	.	.		0.652	HOXC12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358868.2	NM_173860		A	54348808	C	A	54348808	3	1	176	1	0	0	0	0	1	0	0	0	7320	855	30	3	97	3	HOXC12	12	54348808	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	1159353	54348808	79503087	120	26519										
ITGA5	3678	hgsc.bcm.edu	37	chr12	54797997	54797997	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aacatggcggggaagatggtGagggaggcactagcggacac	18	7	0	2	rs567536197	byFrequency	TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr12:54797997G>A	ENST00000293379.4	-	15	1758	c.1497C>T	c.(1495-1497)ctC>ctT	p.L499L	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	499					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						GGAAGATGGTGAGGGAGGCAC	0.577											OREG0021554	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L499L		Atlas-SNP	.											.	ITGA5	99	.	0			c.C1497T						.						61	69	67					12																	54797997		2203	4300	6503	SO:0001819	synonymous_variant	3678	exon15			GATGGTGAGGGAG		CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"CD molecules", "Integrins"	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.1497C>T	chr12.hg19:g.54797997G>A		106.0	0.0	1003	138.0	31.0	NM_002205	Q96HA5	Silent	SNP	ENST00000293379.4	hg19	CCDS8880.1																																																																																			.	.		0.577	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			A	54797997	G	A	54797997	2	1	176	1	0	0	0	0	0	0	0	1	7888	1277	45	3		3	ITGA5	12	54797997	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	449189	54797997	79053898	121	26520										
WIF1	11197	hgsc.bcm.edu	37	chr12	65460513	65460513	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tcatacatcgtggggtacaaAgggcttatagggagagagaa	14	5	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr12:65460513A>G	ENST00000286574.4	-	6	1012	c.638T>C	c.(637-639)cTt>cCt	p.L213P		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	213	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		TGGGGTACAAAGGGCTTATAG	0.433			T	HMGA2	pleomorphic salivary gland adenoma																																p.L213P	Esophageal Squamous(148;1595 1816 48559 49439 49664)	Atlas-SNP	.		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	WIF1	96	.	0			c.T638C						.						76	72	73					12																	65460513		2203	4300	6503	SO:0001583	missense	11197	exon6			GTACAAAGGGCTT	AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.638T>C	chr12.hg19:g.65460513A>G	ENSP00000286574:p.Leu213Pro	135.0	0.0		172.0	53.0	NM_007191	Q6UXI1|Q8WVG4	Missense_Mutation	SNP	ENST00000286574.4	hg19	CCDS8971.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.565601	0.45694	.	.	ENSG00000156076	ENST00000286574	T	0.05199	3.48	5.23	5.23	0.72850	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.068823	0.64402	D	0.000016	T	0.11750	0.0286	L	0.37561	1.115	0.80722	D	1	D	0.54772	0.968	P	0.53224	0.721	T	0.10474	-1.0628	9	.	.	.	.	15.8274	0.78725	1.0:0.0:0.0:0.0	.	213	Q9Y5W5	WIF1_HUMAN	P	213	ENSP00000286574:L213P	.	L	-	2	0	WIF1	63746780	1.000000	0.71417	0.982000	0.44146	0.098000	0.18820	7.369000	0.79578	2.279000	0.76181	0.533000	0.62120	CTT	.	.		0.433	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2			G	65460513	A	G	65460513	3	3	176	1	0	0	0	0	1	0	0	0	17381	72	3	2	521	2	WIF1	12	65460513	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	10662516	65460513	68391382	122	26521										
KCNC2	3747	hgsc.bcm.edu	37	chr12	75601469	75601469	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtcgaagaagaactcgcggcCgccaccgggatggtcgctgg	16	12	0	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr12:75601469C>A	ENST00000549446.1	-	2	975	c.295G>T	c.(295-297)Ggc>Tgc	p.G99C	KCNC2_ENST00000550433.1_Missense_Mutation_p.G99C|KCNC2_ENST00000548513.1_Missense_Mutation_p.G99C|KCNC2_ENST00000350228.2_Missense_Mutation_p.G99C|KCNC2_ENST00000540018.1_Missense_Mutation_p.G99C|KCNC2_ENST00000341669.3_Missense_Mutation_p.G99C|KCNC2_ENST00000393288.2_Missense_Mutation_p.G99C|KCNC2_ENST00000298972.1_Missense_Mutation_p.G99C	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	99	Gly/Pro-rich (insert).				action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	AACTCGCGGCCGCCACCGGGA	0.726																																					p.G99C		Atlas-SNP	.											.	KCNC2	239	.	0			c.G295T						.						8	11	10					12																	75601469		2184	4279	6463	SO:0001583	missense	3747	exon2			CGCGGCCGCCACC	AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.295G>T	chr12.hg19:g.75601469C>A	ENSP00000449253:p.Gly99Cys	224.0	0.0		304.0	81.0	NM_139137	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Missense_Mutation	SNP	ENST00000549446.1	hg19	CCDS9007.1	.	.	.	.	.	.	.	.	.	.	c	12.77	2.038852	0.35989	.	.	ENSG00000166006	ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000350228;ENST00000540018;ENST00000393288	T;T;T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	3.04	3.04	0.35103	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.38164	U	0.001790	T	0.72763	0.3501	N	0.25332	0.735	0.31854	N	0.621903	B;B;B;B;D	0.57257	0.024;0.024;0.014;0.024;0.979	B;B;B;B;P	0.51974	0.022;0.022;0.038;0.022;0.686	T	0.77466	-0.2577	10	0.56958	D	0.05	.	11.9715	0.53065	0.0:1.0:0.0:0.0	.	99;99;99;99;99	F5H030;Q96PR1-2;Q96PR1;Q96PR1-4;Q96PR1-3	.;.;KCNC2_HUMAN;.;.	C	99	ENSP00000448301:G99C;ENSP00000449941:G99C;ENSP00000449253:G99C;ENSP00000340121:G99C;ENSP00000298972:G99C;ENSP00000319877:G99C;ENSP00000438423:G99C;ENSP00000376966:G99C	ENSP00000298972:G99C	G	-	1	0	KCNC2	73887736	0.994000	0.37717	0.994000	0.49952	0.852000	0.48524	-0.266000	0.08631	2.004000	0.58718	0.457000	0.33378	GGC	.	.		0.726	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		A	75601469	C	A	75601469	3	1	176	1	0	0	0	0	1	0	0	0	8024	652	23	1	1703	1	KCNC2	12	75601469	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	10140956	75601469	58250426	123	26522										
ANO4	121601	hgsc.bcm.edu	37	chr12	101480526	101480526	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tgcctttaagtgggcgttaaTcaggaataactctcaggttg	11	7	2	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr12:101480526T>C	ENST00000392977.3	+	17	1835	c.1625T>C	c.(1624-1626)aTc>aCc	p.I542T	ANO4_ENST00000299222.9_Missense_Mutation_p.I62T|ANO4_ENST00000550015.1_Missense_Mutation_p.I62T|ANO4_ENST00000392979.3_Missense_Mutation_p.I507T			Q32M45	ANO4_HUMAN	anoctamin 4	542					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						TGGGCGTTAATCAGGAATAAC	0.507										HNSCC(74;0.22)																											p.I507T		Atlas-SNP	.											.	ANO4	183	.	0			c.T1520C						.						306	252	271					12																	101480526		2203	4300	6503	SO:0001583	missense	121601	exon16			CGTTAATCAGGAA	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.1625T>C	chr12.hg19:g.101480526T>C	ENSP00000376703:p.Ile542Thr	147.0	0.0		160.0	42.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	hg19		.	.	.	.	.	.	.	.	.	.	T	11.92	1.781366	0.31502	.	.	ENSG00000151572	ENST00000392979;ENST00000299222;ENST00000392977;ENST00000550015	T;T;T;T	0.68765	-0.34;-0.33;-0.35;-0.33	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.69663	0.3136	L	0.43646	1.37	0.58432	D	0.999998	P;P;P	0.52692	0.915;0.955;0.855	P;P;P	0.58660	0.574;0.843;0.64	T	0.64441	-0.6407	10	0.07175	T	0.84	.	15.924	0.79597	0.0:0.0:0.0:1.0	.	62;542;507	Q32M45-3;Q32M45;Q32M45-2	.;ANO4_HUMAN;.	T	507;62;542;62	ENSP00000376705:I507T;ENSP00000299222:I62T;ENSP00000376703:I542T;ENSP00000450192:I62T	ENSP00000299222:I62T	I	+	2	0	ANO4	100004657	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.997000	0.88414	2.217000	0.71921	0.533000	0.62120	ATC	.	.		0.507	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		C	101480526	T	C	101480526	3	2	176	1	0	0	0	0	1	0	0	0	699	1435	50	2	1578	2	ANO4	12	101480526	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	25879057	101480526	32371369	124	26523										
MTUS2	23281	hgsc.bcm.edu	37	chr13	30066851	30066851	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttgaaaaactgcggctgtcaTtgcaggttagtatttcttta	9	6	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr13:30066851T>A	ENST00000380808.2	+	5	727	c.511T>A	c.(511-513)Ttg>Atg	p.L171M	MTUS2-AS1_ENST00000323380.5_RNA|MTUS2_ENST00000431530.3_Missense_Mutation_p.L1202M|MTUS2_ENST00000542829.1_Missense_Mutation_p.L81M	NM_015233.5	NP_056048.1	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	1192						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						GCGGCTGTCATTGCAGGTTAG	0.363																																					p.L1202M		Atlas-SNP	.											.	MTUS2	279	.	0			c.T3604A						.						80	75	77					13																	30066851		1826	4083	5909	SO:0001583	missense	23281	exon10			CTGTCATTGCAGG	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000380808.2:c.511T>A	chr13.hg19:g.30066851T>A	ENSP00000370186:p.Leu171Met	89.0	0.0		116.0	19.0	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000380808.2	hg19	CCDS41874.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.042081	0.55003	.	.	ENSG00000132938	ENST00000431530;ENST00000380808;ENST00000542829;ENST00000417109	T;T;T	0.47177	1.74;0.95;0.85	5.15	-1.43	0.08884	.	0.000000	0.64402	D	0.000003	T	0.65709	0.2717	M	0.86178	2.8	0.48762	D	0.999703	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.66376	-0.5939	9	.	.	.	.	10.3517	0.43939	0.0:0.5778:0.0:0.4222	.	171;1192	Q5JR59-3;Q5JR59	.;MTUS2_HUMAN	M	1202;171;81;128	ENSP00000392057:L1202M;ENSP00000370186:L171M;ENSP00000445403:L81M	.	L	+	1	2	MTUS2	28964851	0.753000	0.28349	0.470000	0.27216	0.677000	0.39632	1.222000	0.32515	-0.194000	0.10399	-0.330000	0.08379	TTG	.	.		0.363	MTUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044335.2	XM_166270		A	30066851	T	A	30066851	3	1	176	1	0	0	0	0	1	0	0	0	9975	1490	52	4	3700	4	MTUS2	13	30066851	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10		30066851	85103027	125	26524										
USPL1	10208	hgsc.bcm.edu	37	chr13	31205172	31205172	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttgaacagcaaacataatggAgaagtatatgacgaaacctc	8	7	0	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr13:31205172A>G	ENST00000255304.4	+	4	771	c.429A>G	c.(427-429)ggA>ggG	p.G143G	USPL1_ENST00000465952.1_3'UTR	NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	143					Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		AACATAATGGAGAAGTATATG	0.368																																					p.G143G	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.A429G						.						69	70	70					13																	31205172		2203	4300	6503	SO:0001819	synonymous_variant	10208	exon4			TAATGGAGAAGTA	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 22"	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.429A>G	chr13.hg19:g.31205172A>G		117.0	0.0		148.0	14.0	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Silent	SNP	ENST00000255304.4	hg19	CCDS9336.1																																																																																			.	.		0.368	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		G	31205172	A	G	31205172	2	3	176	1	0	0	0	0	0	0	0	1	17107	291	11	2		2	USPL1	13	31205172	Silent	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	1138321	31205172	83964706	126	26525										
SCEL	8796	hgsc.bcm.edu	37	chr13	78163340	78163340	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ctcctgtttcttctcctaacCagctgagacaggataatagg	8	11	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr13:78163340C>A	ENST00000349847.3	+	10	691	c.607C>A	c.(607-609)Cag>Aag	p.Q203K	SCEL_ENST00000535157.1_Missense_Mutation_p.Q181K|SCEL_ENST00000377246.3_Missense_Mutation_p.Q203K	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	203					embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		TTCTCCTAACCAGCTGAGACA	0.433																																					p.Q203K		Atlas-SNP	.											.	SCEL	85	.	0			c.C607A						.						128	129	129					13																	78163340		2203	4300	6503	SO:0001583	missense	8796	exon10			CCTAACCAGCTGA	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.607C>A	chr13.hg19:g.78163340C>A	ENSP00000302579:p.Gln203Lys	85.0	0.0		110.0	25.0	NM_003843	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	hg19	CCDS9459.1	.	.	.	.	.	.	.	.	.	.	C	0.431	-0.903394	0.02453	.	.	ENSG00000136155	ENST00000348770;ENST00000535157;ENST00000377246;ENST00000349847	T;T;T	0.26518	1.73;1.73;1.73	5.56	4.69	0.59074	.	1.003600	0.08033	N	0.993797	T	0.29028	0.0721	M	0.65975	2.015	0.09310	N	1	B;B;P	0.34615	0.4;0.274;0.459	B;B;B	0.29353	0.075;0.101;0.101	T	0.19192	-1.0313	10	0.34782	T	0.22	2.3654	11.5458	0.50693	0.1787:0.8213:0.0:0.0	.	181;203;203	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	K	180;181;203;203	ENSP00000437895:Q181K;ENSP00000366454:Q203K;ENSP00000302579:Q203K	ENSP00000315127:Q180K	Q	+	1	0	SCEL	77061341	0.064000	0.20934	0.369000	0.25952	0.343000	0.28985	0.846000	0.27682	1.296000	0.44742	0.591000	0.81541	CAG	.	.		0.433	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777		A	78163340	C	A	78163340	3	1	176	1	0	0	0	0	1	0	0	0	13903	595	21	3	641	3	SCEL	13	78163340	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	46958168	78163340	37006538	127	26526										
EDNRB	1910	hgsc.bcm.edu	37	chr13	78472337	78472337	+	Nonstop_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cagtgaatagttcttctttcAagatgagctgtatttattac	7	6	3	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr13:78472337A>C	ENST00000334286.5	-	7	1563	c.1327T>G	c.(1327-1329)Tga>Gga	p.*443G	EDNRB_ENST00000377211.4_Nonstop_Mutation_p.*533G|EDNRB_ENST00000446573.1_Intron	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	0					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TTCTTCTTTCAAGATGAGCTG	0.323																																					p.X533G		Atlas-SNP	.											.	EDNRB	172	.	0			c.T1597G						.						96	88	91					13																	78472337		2202	4300	6502	SO:0001578	stop_lost	1910	exon8			TCTTTCAAGATGA	L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.1327T>G	chr13.hg19:g.78472337A>C	ENSP00000335311:p.*443Argext*18	42.0	0.0		80.0	14.0	NM_001201397	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Missense_Mutation	SNP	ENST00000334286.5	hg19	CCDS9461.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.118662	0.56505	.	.	ENSG00000136160	ENST00000377211;ENST00000334286	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4116	0.83717	1.0:0.0:0.0:0.0	.	.	.	.	G	533;443	.	.	X	-	1	0	EDNRB	77370338	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	6.316000	0.72857	2.276000	0.75962	0.528000	0.53228	TGA	.	.		0.323	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			C	78472337	A	C	78472337	4	2	176	1	0	0	0	0	0	0	0	0	4922	143	5	5	126	5	EDNRB	13	78472337	Nonstop_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	308997	78472337	36697541	128	26527										
C14orf119	55017	hgsc.bcm.edu	37	chr14	23567275	23567275	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	taccaagcagtggctgctacAgctggtaaggactgataggc	13	9	0	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr14:23567275A>G	ENST00000319074.4	+	2	1264	c.408A>G	c.(406-408)acA>acG	p.T136T	C14orf119_ENST00000554203.1_Silent_p.T136T|ACIN1_ENST00000457657.1_5'Flank|ACIN1_ENST00000605057.1_5'Flank|ACIN1_ENST00000262710.1_5'Flank|ACIN1_ENST00000555053.1_5'Flank	NM_017924.3	NP_060394.1	Q9NWQ9	CN119_HUMAN	chromosome 14 open reading frame 119	136						mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(1)|lung(1)	3	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00649)		TGGCTGCTACAGCTGGTAAGG	0.473																																					p.T136T		Atlas-SNP	.											.	C14orf119	7	.	0			c.A408G						.						58	61	60					14																	23567275		2203	4300	6503	SO:0001819	synonymous_variant	55017	exon2			TGCTACAGCTGGT		CCDS9588.1	14q11.2	2012-09-25			ENSG00000179933	ENSG00000179933			20270	protein-coding gene	gene with protein product							Standard	NM_017924		Approved	FLJ20671	uc001wiu.3	Q9NWQ9	OTTHUMG00000028717	ENST00000319074.4:c.408A>G	chr14.hg19:g.23567275A>G		73.0	0.0		70.0	17.0	NM_017924	Q6IAA7	Silent	SNP	ENST00000319074.4	hg19	CCDS9588.1																																																																																			.	.		0.473	C14orf119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071713.3	NM_017924		G	23567275	A	G	23567275	2	3	176	1	0	0	0	0	0	0	0	1	1744	175	7	2		2	C14orf119	14	23567275	Silent	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10		23567275	83782265	129	26528										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31604292	31604292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	atgacaatttaaagctgaatTatcacgacttagtatgtctt	6	6	2	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr14:31604292T>C	ENST00000399332.1	-	22	3852	c.3364A>G	c.(3364-3366)Aat>Gat	p.N1122D	HECTD1_ENST00000553700.1_Missense_Mutation_p.N1122D	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1122					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		AAAGCTGAATTATCACGACTT	0.413																																					p.N1122D		Atlas-SNP	.											.	HECTD1	159	.	0			c.A3364G						.						161	143	149					14																	31604292		1906	4130	6036	SO:0001583	missense	25831	exon22			CTGAATTATCACG	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.3364A>G	chr14.hg19:g.31604292T>C	ENSP00000382269:p.Asn1122Asp	124.0	0.0		96.0	16.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.263184	0.59431	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957	T;T;T	0.44083	0.93;0.93;0.93	6.03	4.87	0.63330	Galactose-binding domain-like (1);Sad1/UNC-like, C-terminal (1);	0.056301	0.64402	U	0.000002	T	0.28532	0.0706	N	0.14661	0.345	0.37834	D	0.928823	B;B	0.21309	0.054;0.005	B;B	0.19391	0.024;0.025	T	0.10268	-1.0637	10	0.49607	T	0.09	-18.083	13.5208	0.61566	0.0:0.0:0.1302:0.8698	.	1122;1122	D3DS86;Q9ULT8	.;HECD1_HUMAN	D	1122;1124;1122;596	ENSP00000450697:N1122D;ENSP00000382269:N1122D;ENSP00000451860:N596D	ENSP00000261312:N1124D	N	-	1	0	HECTD1	30674043	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.021000	0.88750	1.081000	0.41110	0.533000	0.62120	AAT	.	.		0.413	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			C	31604292	T	C	31604292	3	2	176	1	0	0	0	0	1	0	0	0	7048	1754	61	2	4556	2	HECTD1	14	31604292	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	8037017	31604292	75745248	130	26529										
FAM179B	23116	hgsc.bcm.edu	37	chr14	45465007	45465007	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gctttctcaaggaatgccagTcaatgatgatttatgtttta	8	6	2	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr14:45465007T>G	ENST00000361577.3	+	2	2319	c.2105T>G	c.(2104-2106)gTc>gGc	p.V702G	FAM179B_ENST00000361462.2_Missense_Mutation_p.V702G|FAM179B_ENST00000382233.2_Missense_Mutation_p.V702G|KLHL28_ENST00000553817.1_Intron	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	702										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						GGAATGCCAGTCAATGATGAT	0.318																																					p.V702G		Atlas-SNP	.											.	FAM179B	115	.	0			c.T2105G						.						92	89	90					14																	45465007		2203	4299	6502	SO:0001583	missense	23116	exon2			TGCCAGTCAATGA	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.2105T>G	chr14.hg19:g.45465007T>G	ENSP00000355045:p.Val702Gly	106.0	0.0		93.0	15.0	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.870680	0.51695	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233;ENST00000555874	T;T;T;T	0.03889	3.77;3.77;3.77;3.77	5.42	2.96	0.34315	Armadillo-type fold (1);	0.287440	0.24688	N	0.036414	T	0.02455	0.0075	N	0.12182	0.205	0.40305	D	0.978653	B;B;B;B	0.11235	0.004;0.001;0.003;0.002	B;B;B;B	0.12156	0.007;0.004;0.004;0.007	T	0.50583	-0.8811	10	0.36615	T	0.2	-0.562	1.619	0.02709	0.1359:0.1589:0.1408:0.5644	.	702;702;702;702	Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2	.;.;F179B_HUMAN;.	G	702;702;702;702;21	ENSP00000355045:V702G;ENSP00000354917:V702G;ENSP00000371668:V702G;ENSP00000451141:V21G	ENSP00000354917:V702G	V	+	2	0	FAM179B	44534757	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.373000	0.20484	0.334000	0.23590	0.477000	0.44152	GTC	.	.		0.318	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		G	45465007	T	G	45465007	3	3	176	1	0	0	0	0	1	0	0	0	5511	1667	58	5	2111	5	FAM179B	14	45465007	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	13860715	45465007	61884533	131	26530										
BMP4	652	hgsc.bcm.edu	37	chr14	54416923	54416923	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ctgcacaatggcatggttggTtgagttgaggtggtcagcca	15	7	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr14:54416923T>A	ENST00000245451.4	-	4	1447	c.1054A>T	c.(1054-1056)Acc>Tcc	p.T352S	BMP4_ENST00000417573.1_Missense_Mutation_p.T352S|BMP4_ENST00000558984.1_Missense_Mutation_p.T352S|MIR5580_ENST00000580850.1_RNA|BMP4_ENST00000559087.1_Missense_Mutation_p.T352S	NM_001202.3	NP_001193.2	P12644	BMP4_HUMAN	bone morphogenetic protein 4	352					activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification (GO:0009948)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|BMP signaling pathway involved in nephric duct formation (GO:0071893)|BMP signaling pathway involved in renal system segmentation (GO:0061151)|BMP signaling pathway involved in ureter morphogenesis (GO:0061149)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchus development (GO:0060433)|bud dilation involved in lung branching (GO:0060503)|bud elongation involved in lung branching (GO:0060449)|cardiac septum development (GO:0003279)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte differentiation (GO:0002062)|cloacal septation (GO:0060197)|common-partner SMAD protein phosphorylation (GO:0007182)|cranial suture morphogenesis (GO:0060363)|deltoid tuberosity development (GO:0035993)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint morphogenesis (GO:0060272)|endocardial cushion development (GO:0003197)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in lung morphogenesis (GO:0060502)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal cell signaling (GO:0060684)|erythrocyte differentiation (GO:0030218)|extracellular matrix organization (GO:0030198)|germ cell development (GO:0007281)|glomerular capillary formation (GO:0072104)|glomerular visceral epithelial cell development (GO:0072015)|hematopoietic progenitor cell differentiation (GO:0002244)|inner ear receptor cell differentiation (GO:0060113)|intermediate mesodermal cell differentiation (GO:0048392)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|mammary gland formation (GO:0060592)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal cell proliferation involved in ureter development (GO:0072198)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate determination (GO:0007500)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway (GO:0072097)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in heart morphogenesis (GO:2000137)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of glomerulus development (GO:0090194)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell proliferation involved in ureter development (GO:0072200)|negative regulation of metanephric comma-shaped body morphogenesis (GO:2000007)|negative regulation of metanephric S-shaped body morphogenesis (GO:2000005)|negative regulation of mitosis (GO:0045839)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of cardiac muscle fiber development (GO:0055020)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell death (GO:0010942)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of kidney development (GO:0090184)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|pulmonary artery endothelial tube morphogenesis (GO:0061155)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of smooth muscle cell differentiation (GO:0051150)|renal system development (GO:0072001)|renal system process (GO:0003014)|secondary heart field specification (GO:0003139)|SMAD protein signal transduction (GO:0060395)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|specification of organ position (GO:0010159)|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway (GO:0072101)|steroid hormone mediated signaling pathway (GO:0043401)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|tendon cell differentiation (GO:0035990)|trachea development (GO:0060438)|trachea formation (GO:0060440)|type B pancreatic cell development (GO:0003323)|ureter epithelial cell differentiation (GO:0072192)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	BMP receptor binding (GO:0070700)|chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|heparin binding (GO:0008201)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(3)|urinary_tract(1)	19						GCATGGTTGGTTGAGTTGAGG	0.552																																					p.T352S		Atlas-SNP	.											.	BMP4	45	.	0			c.A1054T						.						155	129	138					14																	54416923		2203	4300	6503	SO:0001583	missense	652	exon4			GGTTGGTTGAGTT	AF035427	CCDS9715.1	14q22-q23	2014-01-30			ENSG00000125378	ENSG00000125378		"Bone morphogenetic proteins", "Endogenous ligands"	1071	protein-coding gene	gene with protein product		112262		BMP2B		7558046, 7579580	Standard	NM_001202		Approved		uc010aoh.3	P12644	OTTHUMG00000140303	ENST00000245451.4:c.1054A>T	chr14.hg19:g.54416923T>A	ENSP00000245451:p.Thr352Ser	191.0	0.0		216.0	40.0	NM_130851	Q9UM80	Missense_Mutation	SNP	ENST00000245451.4	hg19	CCDS9715.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.090123	0.76756	.	.	ENSG00000125378	ENST00000245451;ENST00000417573	T;T	0.64438	-0.1;-0.1	5.53	5.53	0.82687	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.71970	0.3403	L	0.55017	1.72	0.80722	D	1	D	0.52996	0.957	P	0.58454	0.839	T	0.74957	-0.3487	10	0.87932	D	0	.	14.9972	0.71443	0.0:0.0:0.0:1.0	.	352	P12644	BMP4_HUMAN	S	352	ENSP00000245451:T352S;ENSP00000394165:T352S	ENSP00000245451:T352S	T	-	1	0	BMP4	53486673	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	7.861000	0.87004	2.324000	0.78689	0.533000	0.62120	ACC	.	.		0.552	BMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276894.2	NM_001202		A	54416923	T	A	54416923	3	1	176	1	0	0	0	0	1	0	0	0	1462	1725	60	4	176	4	BMP4	14	54416923	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	8951916	54416923	52932617	132	26531										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63246579	63246579	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agtacgtcagtgcccggacgTtcgcacatgcatgggcaagg	14	11	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr14:63246579T>C	ENST00000322893.7	-	10	2154	c.1886A>G	c.(1885-1887)aAc>aGc	p.N629S	KCNH5_ENST00000394968.1_Missense_Mutation_p.N571S|KCNH5_ENST00000420622.2_Intron	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	629					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TGCCCGGACGTTCGCACATGC	0.453																																					p.N629S		Atlas-SNP	.											.	KCNH5	320	.	0			c.A1886G						.						107	95	99					14																	63246579		2203	4300	6503	SO:0001583	missense	27133	exon10			CGGACGTTCGCAC	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.1886A>G	chr14.hg19:g.63246579T>C	ENSP00000321427:p.Asn629Ser	144.0	0.0		115.0	22.0	NM_139318	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	hg19	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	T	9.964	1.223736	0.22457	.	.	ENSG00000140015	ENST00000322893;ENST00000394968	D;D	0.91686	-2.89;-2.89	5.72	5.72	0.89469	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.88749	0.6521	N	0.10809	0.05	0.80722	D	1	P;P	0.46395	0.537;0.877	B;P	0.51016	0.155;0.656	D	0.89976	0.4097	10	0.44086	T	0.13	.	16.0003	0.80288	0.0:0.0:0.0:1.0	.	571;629	Q8NCM2-3;Q8NCM2	.;KCNH5_HUMAN	S	629;571	ENSP00000321427:N629S;ENSP00000378419:N571S	ENSP00000321427:N629S	N	-	2	0	KCNH5	62316332	1.000000	0.71417	0.992000	0.48379	0.023000	0.10783	8.036000	0.88901	2.183000	0.69458	0.477000	0.44152	AAC	.	.		0.453	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		C	63246579	T	C	63246579	3	2	176	1	0	0	0	0	1	0	0	0	8044	1725	60	2	1122	2	KCNH5	14	63246579	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	8829656	63246579	44102961	133	26532										
ZBTB1	22890	hgsc.bcm.edu	37	chr14	64998591	64998591	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tgtggcagtggtgaaataggGccttctaaacctgtggagaa	14	6	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr14:64998591G>A	ENST00000358738.3	+	3	2302	c.1911G>A	c.(1909-1911)ggG>ggA	p.G637G	RP11-973N13.4_ENST00000554918.1_RNA	NM_014950.2	NP_055765.2	Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	0					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		GTGAAATAGGGCCTTCTAAAC	0.363																																					p.G637G		Atlas-SNP	.											.	ZBTB1	93	.	0			c.G1911A						.						174	164	167					14																	64998591		2203	4300	6503	SO:0001819	synonymous_variant	22890	exon3			AATAGGGCCTTCT	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000358738.3:c.1911G>A	chr14.hg19:g.64998591G>A		91.0	0.0		106.0	19.0	NM_014950	A8K6S8|Q86SW8	Silent	SNP	ENST00000358738.3	hg19	CCDS32097.1																																																																																			.	.		0.363	ZBTB1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000411913.1			A	64998591	G	A	64998591	2	1	176	1	0	0	0	0	0	0	0	1	17537	1190	42	3		3	ZBTB1	14	64998591	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	1752012	64998591	42350949	134	26533										
EML5	161436	hgsc.bcm.edu	37	chr14	89258735	89258735	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cgccgacccccgccacgaagTatacgatctccttggccgca	9	18	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr14:89258735T>A	ENST00000380664.5	-	1	112	c.113A>T	c.(112-114)tAc>tTc	p.Y38F	EML5_ENST00000352093.5_Missense_Mutation_p.Y38F|EML5_ENST00000554922.1_Missense_Mutation_p.Y38F			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	38						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CGCCACGAAGTATACGATCTC	0.667																																					p.Y38F		Atlas-SNP	.											.	EML5	141	.	0			c.A113T						.						8	12	10					14																	89258735		1925	4073	5998	SO:0001583	missense	161436	exon1			ACGAAGTATACGA	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.113A>T	chr14.hg19:g.89258735T>A	ENSP00000370039:p.Tyr38Phe	95.0	0.0		64.0	14.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.513785	0.85389	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.43688	0.94;0.94;0.94	4.24	3.05	0.35203	HELP (1);	0.090074	0.46758	N	0.000266	T	0.60444	0.2269	M	0.82630	2.6	0.39162	D	0.962422	D	0.54207	0.965	P	0.60789	0.879	T	0.63739	-0.6569	10	0.56958	D	0.05	-4.9029	9.8227	0.40891	0.154:0.0:0.0:0.846	.	38	Q05BV3	EMAL5_HUMAN	F	38	ENSP00000451998:Y38F;ENSP00000298315:Y38F;ENSP00000370039:Y38F	ENSP00000298315:Y38F	Y	-	2	0	EML5	88328488	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.109000	0.77062	0.468000	0.27243	-0.669000	0.03829	TAC	.	.		0.667	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			A	89258735	T	A	89258735	3	1	176	1	0	0	0	0	1	0	0	0	5102	1638	57	4	5992	4	EML5	14	89258735	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	24260144	89258735	18090805	135	26534										
TDRD9	122402	hgsc.bcm.edu	37	chr14	104436890	104436890	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttttgtaggtacacgaacgaAcagaagaaatggatttcctg	10	6	0	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr14:104436890A>G	ENST00000409874.4	+	6	826	c.778A>G	c.(778-780)Aca>Gca	p.T260A	TDRD9_ENST00000339063.5_Missense_Mutation_p.T260A	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	260	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				ACACGAACGAACAGAAGAAAT	0.438																																					p.T260A		Atlas-SNP	.											.	TDRD9	175	.	0			c.A778G						.						216	180	191					14																	104436890		692	1591	2283	SO:0001583	missense	122402	exon6			GAACGAACAGAAG	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.778A>G	chr14.hg19:g.104436890A>G	ENSP00000387303:p.Thr260Ala	110.0	0.0		120.0	15.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Missense_Mutation	SNP	ENST00000409874.4	hg19	CCDS9987.2	.	.	.	.	.	.	.	.	.	.	A	17.76	3.467886	0.63625	.	.	ENSG00000156414	ENST00000409874;ENST00000339063	T;T	0.26810	1.71;1.71	5.87	5.87	0.94306	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	.	.	.	.	T	0.41488	0.1161	L	0.58510	1.815	0.58432	D	0.999995	B	0.29766	0.256	P	0.45276	0.475	T	0.33701	-0.9858	9	0.66056	D	0.02	.	16.2674	0.82597	1.0:0.0:0.0:0.0	.	260	Q8NDG6	TDRD9_HUMAN	A	260	ENSP00000387303:T260A;ENSP00000343545:T260A	ENSP00000343545:T260A	T	+	1	0	TDRD9	103506643	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	6.960000	0.76036	2.242000	0.73789	0.533000	0.62120	ACA	.	.		0.438	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		G	104436890	A	G	104436890	3	3	176	1	0	0	0	0	1	0	0	0	15751	43	2	2	800	2	TDRD9	14	104436890	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	15178155	104436890	2912650	136	26535										
DISP2	85455	hgsc.bcm.edu	37	chr15	40660665	40660665	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtcctgcctgtggacactggCgaccctctggaccctcgtag	12	15	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr15:40660665C>A	ENST00000267889.3	+	8	2439	c.2352C>A	c.(2350-2352)ggC>ggA	p.G784G	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	784					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)		p.G784G(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		TGGACACTGGCGACCCTCTGG	0.682																																					p.G784G		Atlas-SNP	.											DISP2,NS,carcinoma,0,1	DISP2	86	.	1	Substitution - coding silent(1)	lung(1)	c.C2352A						.						73	80	78					15																	40660665		2203	4299	6502	SO:0001819	synonymous_variant	85455	exon8			CACTGGCGACCCT	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2352C>A	chr15.hg19:g.40660665C>A		87.0	0.0		114.0	33.0	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	hg19	CCDS10056.1																																																																																			.	.		0.682	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		A	40660665	C	A	40660665	2	1	176	1	0	0	0	0	0	0	0	1	4542	755	27	1		1	DISP2	15	40660665	Silent	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10		40660665	61870727	137	26536										
MAP1A	4130	hgsc.bcm.edu	37	chr15	43819399	43819399	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cccccctggggaaggactacCgcaaggctgaaggggaaagg	16	11	0	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr15:43819399C>T	ENST00000300231.5	+	4	6178	c.5728C>T	c.(5728-5730)Cgc>Tgc	p.R1910C	MAP1A_ENST00000382031.1_Missense_Mutation_p.R2148C|MAP1A_ENST00000399453.1_Missense_Mutation_p.R1910C			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1910					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GAAGGACTACCGCAAGGCTGA	0.592																																					p.R1910C		Atlas-SNP	.											.	MAP1A	189	.	0			c.C5728T						.						68	83	78					15																	43819399		2088	4235	6323	SO:0001583	missense	4130	exon4			GACTACCGCAAGG	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.5728C>T	chr15.hg19:g.43819399C>T	ENSP00000300231:p.Arg1910Cys	176.0	0.0		218.0	39.0	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.241773	0.39598	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01947	4.54;4.54;4.54	4.88	3.97	0.46021	.	0.250675	0.21186	N	0.078733	T	0.02688	0.0081	L	0.36672	1.1	0.38562	D	0.949739	B	0.15930	0.015	B	0.12156	0.007	T	0.45026	-0.9289	10	0.72032	D	0.01	-2.3585	10.5645	0.45165	0.0:0.9088:0.0:0.0912	.	1910	P78559	MAP1A_HUMAN	C	2148;1910;1910	ENSP00000371462:R2148C;ENSP00000382380:R1910C;ENSP00000300231:R1910C	ENSP00000300231:R1910C	R	+	1	0	MAP1A	41606691	0.883000	0.30277	1.000000	0.80357	0.992000	0.81027	0.420000	0.21263	1.281000	0.44480	0.563000	0.77884	CGC	.	.		0.592	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		T	43819399	C	T	43819399	3	4	176	1	0	0	0	0	1	0	0	0	9236	652	23	1	5730	1	MAP1A	15	43819399	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	3158734	43819399	58711993	138	26537										
USP8	9101	hgsc.bcm.edu	37	chr15	50751310	50751310	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agaggatggtggcacattggCtaaaggctctttggagaatg	15	5	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr15:50751310C>T	ENST00000396444.3	+	5	787	c.449C>T	c.(448-450)gCt>gTt	p.A150V	USP8_ENST00000307179.4_Missense_Mutation_p.A150V|USP8_ENST00000433963.1_Missense_Mutation_p.A150V|USP8_ENST00000425032.3_Missense_Mutation_p.A73V	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	150					cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		GGCACATTGGCTAAAGGCTCT	0.413																																					p.A150V		Atlas-SNP	.											.	USP8	90	.	0			c.C449T						.						96	98	97					15																	50751310		2196	4294	6490	SO:0001583	missense	9101	exon5			CATTGGCTAAAGG	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"Ubiquitin-specific peptidases"	12631	protein-coding gene	gene with protein product		603158	"ubiquitin specific protease 8"			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.449C>T	chr15.hg19:g.50751310C>T	ENSP00000379721:p.Ala150Val	378.0	0.0		551.0	130.0	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	hg19	CCDS10137.1	.	.	.	.	.	.	.	.	.	.	C	10.62	1.402494	0.25291	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.19669	2.19;2.19;2.19;2.13	5.84	3.94	0.45596	.	0.525951	0.20912	N	0.083460	T	0.14399	0.0348	N	0.24115	0.695	0.19300	N	0.99998	B;B	0.24258	0.1;0.1	B;B	0.18561	0.022;0.022	T	0.16512	-1.0400	10	0.16896	T	0.51	-1.7553	15.019	0.71613	0.2602:0.7398:0.0:0.0	.	73;150	B4DKA8;P40818	.;UBP8_HUMAN	V	150;150;150;73	ENSP00000379721:A150V;ENSP00000405537:A150V;ENSP00000302239:A150V;ENSP00000412682:A73V	ENSP00000302239:A150V	A	+	2	0	USP8	48538602	0.009000	0.17119	0.100000	0.21137	0.183000	0.23260	1.515000	0.35845	0.779000	0.33543	0.650000	0.86243	GCT	.	.		0.413	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		T	50751310	C	T	50751310	3	4	176	1	0	0	0	0	1	0	0	0	17104	797	28	3	463	3	USP8	15	50751310	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	6931911	50751310	51780082	139	26538										
TRPM7	54822	hgsc.bcm.edu	37	chr15	50885907	50885907	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	caacacactgctcttcaaaaTcatgaagtttcttttgatct	4	10	5	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr15:50885907T>C	ENST00000313478.7	-	25	3796	c.3515A>G	c.(3514-3516)gAt>gGt	p.D1172G	TRPM7_ENST00000560955.1_Missense_Mutation_p.D1172G	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1172					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		CTCTTCAAAATCATGAAGTTT	0.343																																					p.D1172G		Atlas-SNP	.											.	TRPM7	145	.	0			c.A3515G						.						80	72	75					15																	50885907		1792	4058	5850	SO:0001583	missense	54822	exon25			TCAAAATCATGAA	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.3515A>G	chr15.hg19:g.50885907T>C	ENSP00000320239:p.Asp1172Gly	70.0	0.0		102.0	31.0	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	hg19	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.523899	0.85600	.	.	ENSG00000092439	ENST00000313478	T	0.47177	0.85	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.63295	0.2499	M	0.70595	2.14	0.80722	D	1	D	0.60575	0.988	P	0.57204	0.815	T	0.67753	-0.5589	10	0.66056	D	0.02	-23.1566	15.5611	0.76249	0.0:0.0:0.0:1.0	.	1172	Q96QT4	TRPM7_HUMAN	G	1172	ENSP00000320239:D1172G	ENSP00000320239:D1172G	D	-	2	0	TRPM7	48673199	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.661000	0.83786	2.087000	0.62958	0.454000	0.30748	GAT	.	.		0.343	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		C	50885907	T	C	50885907	3	2	176	1	0	0	0	0	1	0	0	0	16606	1435	50	2	2142	2	TRPM7	15	50885907	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	134597	50885907	51645485	140	26539										
BBS4	585	hgsc.bcm.edu	37	chr15	73020331	73020332	+	Frame_Shift_Ins	INS	-	-	A													0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	actttaggattactctacttINSacaggtaatgaaaactctgt					rs149663241		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr15:73020331_73020332insA	ENST00000268057.4	+	9	679_680	c.638_639insA	c.(637-642)ttacagfs	p.Q214fs	BBS4_ENST00000542334.1_Frame_Shift_Ins_p.Q42fs|BBS4_ENST00000395205.2_Frame_Shift_Ins_p.Q222fs|BBS4_ENST00000539603.1_Frame_Shift_Ins_p.Q202fs	NM_033028.4	NP_149017.2	Q96RK4	BBS4_HUMAN	Bardet-Biedl syndrome 4	214	Interaction with PCM1.				adult behavior (GO:0030534)|brain morphogenesis (GO:0048854)|centrosome organization (GO:0051297)|cerebral cortex development (GO:0021987)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|dendrite development (GO:0016358)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|maintenance of protein location in nucleus (GO:0051457)|melanosome transport (GO:0032402)|metabolic process (GO:0008152)|microtubule anchoring at centrosome (GO:0034454)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of systemic arterial blood pressure (GO:0003085)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of cilium assembly (GO:0045724)|positive regulation of multicellular organism growth (GO:0040018)|protein localization to centrosome (GO:0071539)|protein localization to organelle (GO:0033365)|protein transport (GO:0015031)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|regulation of cytokinesis (GO:0032465)|regulation of lipid metabolic process (GO:0019216)|retina homeostasis (GO:0001895)|retinal rod cell development (GO:0046548)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)|spermatid development (GO:0007286)|striatum development (GO:0021756)|visual perception (GO:0007601)	BBSome (GO:0034464)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary membrane (GO:0060170)|cilium (GO:0005929)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|pericentriolar material (GO:0000242)	alpha-tubulin binding (GO:0043014)|beta-tubulin binding (GO:0048487)|dynactin binding (GO:0034452)|microtubule motor activity (GO:0003777)|RNA polymerase II repressing transcription factor binding (GO:0001103)			autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(1)	19						TTACTCTACTTACAGGTAATGA	0.366									Bardet-Biedl syndrome																												p.L213fs		Atlas-INDEL	.											.	BBS4	34	.	0			c.638_639insA						.																																			SO:0001589	frameshift_variant	585	exon9	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	.	AF090947	CCDS10246.1, CCDS58377.1	15q22.3-q23	2013-01-10			ENSG00000140463	ENSG00000140463		"Tetratricopeptide (TTC) repeat domain containing"	969	protein-coding gene	gene with protein product		600374				7711739, 11381270	Standard	NM_033028		Approved		uc002avb.3	Q96RK4	OTTHUMG00000133510	ENST00000268057.4:c.639dupA	chr15.hg19:g.73020332_73020332dupA	ENSP00000268057:p.Gln214fs	72.0	0.0		81.0	22.0	NM_033028	B4E178|Q53DZ5|Q8NHU9|Q96H45	Frame_Shift_Ins	INS	ENST00000268057.4	hg19	CCDS10246.1																																																																																			.	.		0.366	BBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257473.2	NM_033028		A	73020332	-	A	73020331	7	5	176	1	0	1	1	0	0	0	0	0	1339	1764	61	0	672	0	BBS4	15	73020331	Frame_Shift_Ins	INS	-	TCGA-DD-AACZ-01A-11D-A40R-10	22134424	73020331	29511061	141	26540										
UBE2Q2	92912	hgsc.bcm.edu	37	chr15	76183289	76183289	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agtgcctactcaatagaatcGgtcatcatgcaaataaatgc	7	9	3	1	rs142780659		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr15:76183289G>C	ENST00000267938.4	+	11	1345	c.963G>C	c.(961-963)tcG>tcC	p.S321S	UBE2Q2_ENST00000561851.1_Silent_p.S305S|UBE2Q2_ENST00000569423.1_Silent_p.S286S|UBE2Q2_ENST00000338677.4_Intron	NM_173469.2	NP_775740.1	Q8WVN8	UB2Q2_HUMAN	ubiquitin-conjugating enzyme E2Q family member 2	321					protein K48-linked ubiquitination (GO:0070936)	cytoplasm (GO:0005737)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)	p.S321S(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	12						CAATAGAATCGGTCATCATGC	0.388																																					p.S321S		Atlas-SNP	.											UBE2Q2,NS,carcinoma,0,1	UBE2Q2	26	.	1	Substitution - coding silent(1)	endometrium(1)	c.G963C						.						116	118	118					15																	76183289		2197	4294	6491	SO:0001819	synonymous_variant	92912	exon11			AGAATCGGTCATC	BC017708	CCDS10286.1, CCDS45309.1, CCDS66839.1	15q24.2	2010-05-12	2008-05-02		ENSG00000140367	ENSG00000140367		"Ubiquitin-conjugating enzymes E2"	19248	protein-coding gene	gene with protein product		612501	"ubiquitin-conjugating enzyme E2Q (putative) 2"			16300736	Standard	NM_001145335		Approved	DKFZp762C143	uc002bbg.2	Q8WVN8	OTTHUMG00000142839	ENST00000267938.4:c.963G>C	chr15.hg19:g.76183289G>C		104.0	0.0		154.0	42.0	NM_173469	B7Z3Q2|H3BRG2|Q8N4G6|Q96J08	Silent	SNP	ENST00000267938.4	hg19	CCDS10286.1																																																																																			.	G|1.000;A|0.000		0.388	UBE2Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286475.1	NM_173469		C	76183289	G	C	76183289	2	2	176	1	0	0	0	0	0	0	0	1	16885	1103	39	4		4	UBE2Q2	15	76183289	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	3162958	76183289	26348103	142	26541										
WDR61	80349	hgsc.bcm.edu	37	chr15	78582307	78582307	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ccttacatatgcaatactaaGaatgaattttcctctcgtgt	5	9	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr15:78582307G>C	ENST00000267973.2	-	6	725	c.454C>G	c.(454-456)Ctt>Gtt	p.L152V	WDR61_ENST00000558311.1_Missense_Mutation_p.L152V|WDR61_ENST00000558459.1_Missense_Mutation_p.L59V			Q9GZS3	WDR61_HUMAN	WD repeat domain 61	152					histone H3-K4 trimethylation (GO:0080182)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9						GCAATACTAAGAATGAATTTT	0.423																																					p.L152V		Atlas-SNP	.											WDR61,NS,carcinoma,0,1	WDR61	26	.	0			c.C454G						.						88	85	86					15																	78582307		2196	4293	6489	SO:0001583	missense	80349	exon6			TACTAAGAATGAA		CCDS10300.1	15q25.1	2013-01-09			ENSG00000140395	ENSG00000140395		"WD repeat domain containing"	30300	protein-coding gene	gene with protein product		609540				12477932	Standard	NM_025234		Approved	REC14	uc002bdn.3	Q9GZS3	OTTHUMG00000143735	ENST00000267973.2:c.454C>G	chr15.hg19:g.78582307G>C	ENSP00000267973:p.Leu152Val	121.0	0.0		166.0	16.0	NM_025234	D3DW84|Q6IA22|Q7Z4X4	Missense_Mutation	SNP	ENST00000267973.2	hg19	CCDS10300.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.151101	0.78001	.	.	ENSG00000140395	ENST00000267973	T	0.60797	0.16	6.1	6.1	0.99115	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.52273	0.1724	L	0.41824	1.3	0.80722	D	1	P	0.44690	0.841	B	0.41723	0.365	T	0.41963	-0.9479	10	0.17369	T	0.5	-7.9757	19.7028	0.96062	0.0:0.0:1.0:0.0	.	152	Q9GZS3	WDR61_HUMAN	V	152	ENSP00000267973:L152V	ENSP00000267973:L152V	L	-	1	0	WDR61	76369362	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.554000	0.73923	2.902000	0.99343	0.650000	0.86243	CTT	.	.		0.423	WDR61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289803.3	NM_025234		C	78582307	G	C	78582307	3	2	176	1	0	0	0	0	1	0	0	0	17327	942	33	4	487	4	WDR61	15	78582307	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	2399018	78582307	23949085	143	26542										
NME3	4832	hgsc.bcm.edu	37	chr16	1821508	1821508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	acccgcggggaagaggttagCgaagatggtcagcaccaggc	16	10	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr16:1821508C>T	ENST00000219302.3	-	1	223	c.28G>A	c.(28-30)Gct>Act	p.A10T	NME3_ENST00000563498.1_5'UTR|EME2_ENST00000307394.7_5'Flank|EME2_ENST00000568449.1_5'Flank	NM_002513.2	NP_002504.2	Q13232	NDK3_HUMAN	NME/NM23 nucleoside diphosphate kinase 3	10					apoptotic process (GO:0006915)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|UTP biosynthetic process (GO:0006228)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			lung(1)	1						AAGAGGTTAGCGAAGATGGTC	0.781																																					p.A10T		Atlas-SNP	.											.	NME3	4	.	0			c.G28A						.						4	3	3					16																	1821508		1120	1911	3031	SO:0001583	missense	4832	exon1			GGTTAGCGAAGAT	U29656	CCDS10443.1	16q13.3	2013-04-29	2012-05-18		ENSG00000103024	ENSG00000103024			7851	protein-coding gene	gene with protein product		601817	"non-metastatic cells 3, protein expressed in"			9067290, 19852809	Standard	NM_002513		Approved	DR-nm23, NM23-H3, NDPKC	uc002cmm.3	Q13232	OTTHUMG00000128635	ENST00000219302.3:c.28G>A	chr16.hg19:g.1821508C>T	ENSP00000219302:p.Ala10Thr	55.0	0.0		87.0	18.0	NM_002513	Q9BWH4	Missense_Mutation	SNP	ENST00000219302.3	hg19	CCDS10443.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.099262	0.56183	.	.	ENSG00000103024	ENST00000219302	T	0.64085	-0.08	3.97	1.86	0.25419	.	0.222141	0.35466	N	0.003200	T	0.44644	0.1303	L	0.43152	1.355	0.41624	D	0.988989	P	0.46912	0.886	B	0.35607	0.206	T	0.33471	-0.9867	10	0.39692	T	0.17	0.0136	7.2678	0.26239	0.1643:0.7404:0.0:0.0952	.	10	Q13232	NDK3_HUMAN	T	10	ENSP00000219302:A10T	ENSP00000219302:A10T	A	-	1	0	NME3	1761509	0.001000	0.12720	0.465000	0.27155	0.923000	0.55619	0.324000	0.19610	0.614000	0.30107	0.456000	0.33151	GCT	.	.		0.781	NME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250505.2	NM_002513		T	1821508	C	T	1821508	3	4	176	1	0	0	0	0	1	0	0	0	10501	768	27	1	501	1	NME3	16	1821508	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10		1821508	88533245	144	26543										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24788429	24788429	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cagcagccacagcagcagccAcagccgcagccgcagcagca	11	18	0	0	rs10593507|rs60829899|rs71156436|rs71383714	byFrequency	TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr16:24788429A>G	ENST00000395799.3	+	5	468	c.339A>G	c.(337-339)ccA>ccG	p.P113P	TNRC6A_ENST00000315183.7_Silent_p.P113P	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	113	Gln-rich.|Interaction with argonaute family proteins.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		agcagcagccacagccgcagc	0.597																																					p.P113P		Atlas-SNP	.											.	TNRC6A	171	.	0			c.A339G						.						18	23	22					16																	24788429		2059	4012	6071	SO:0001819	synonymous_variant	27327	exon5			GCAGCCACAGCCG	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.339A>G	chr16.hg19:g.24788429A>G		77.0	0.0		88.0	6.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	hg19	CCDS10624.2																																																																																			.	.		0.597	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24788429	A	G	24788429	2	3	176	1	0	0	0	0	0	0	0	1	16355	146	6	2		2	TNRC6A	16	24788429	Silent	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	22966921	24788429	65566324	145	26544										
NUTF2	10204	hgsc.bcm.edu	37	chr16	67902495	67902495	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	catcagcatggttgtgggccAgcttaaggtaatggtactgc	13	8	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr16:67902495A>T	ENST00000219169.4	+	4	546	c.263A>T	c.(262-264)cAg>cTg	p.Q88L	NUTF2_ENST00000568396.2_Missense_Mutation_p.Q88L|NUTF2_ENST00000569436.2_Missense_Mutation_p.Q88L	NM_005796.1	NP_005787.1	P61970	NTF2_HUMAN	nuclear transport factor 2	88	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				protein export from nucleus (GO:0006611)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear pore (GO:0005643)	transporter activity (GO:0005215)			kidney(1)|lung(2)|upper_aerodigestive_tract(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00443)|Epithelial(162;0.0199)|all cancers(182;0.129)		GTTGTGGGCCAGCTTAAGGTA	0.547																																					p.Q88L		Atlas-SNP	.											.	NUTF2	11	.	0			c.A263T						.						113	106	109					16																	67902495		2198	4300	6498	SO:0001583	missense	10204	exon4			TGGGCCAGCTTAA	U43939	CCDS10848.1	16q22.1	2008-02-05			ENSG00000102898	ENSG00000102898			13722	protein-coding gene	gene with protein product		605813				7744965, 3380696	Standard	NM_005796		Approved	NTF2, PP15	uc002eup.3	P61970	OTTHUMG00000137540	ENST00000219169.4:c.263A>T	chr16.hg19:g.67902495A>T	ENSP00000219169:p.Gln88Leu	60.0	0.0		70.0	38.0	NM_005796	B2R4G7|P13662|Q6IB67	Missense_Mutation	SNP	ENST00000219169.4	hg19	CCDS10848.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.935562	0.92458	.	.	ENSG00000102898	ENST00000219169	.	.	.	5.7	5.7	0.88788	Nuclear transport factor 2, Eukaryote (1);Nuclear transport factor 2 (1);	0.054532	0.85682	N	0.000000	T	0.79251	0.4414	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.80527	-0.1343	9	0.49607	T	0.09	-6.5165	15.6194	0.76793	1.0:0.0:0.0:0.0	.	88	P61970	NTF2_HUMAN	L	88	.	ENSP00000219169:Q88L	Q	+	2	0	NUTF2	66459996	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.883000	0.92426	2.178000	0.69098	0.533000	0.62120	CAG	.	.		0.547	NUTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268871.1			T	67902495	A	T	67902495	3	4	176	1	0	0	0	0	1	0	0	0	10788	188	7	4	273	4	NUTF2	16	67902495	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	43114066	67902495	22452258	146	26545										
TP53	7157	hgsc.bcm.edu	37	chr17	7577148	7577148	+	Silent	SNP	G	G	A													0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aaagctgttccgtcccagtaGattaccactactcaggatag							TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:7577148G>A	ENST00000269305.4	-	8	979	c.790C>T	c.(790-792)Cta>Tta	p.L264L	TP53_ENST00000420246.2_Silent_p.L264L|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Silent_p.L264L|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Silent_p.L264L|TP53_ENST00000445888.2_Silent_p.L264L	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	264	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		L -> I (in sporadic cancers; somatic mutation).|L -> P (in a sporadic cancer; somatic mutation).|L -> Q (in a sporadic cancer; somatic mutation).|L -> R (in sporadic cancers; somatic mutation).|L -> V (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.L264L(5)|p.L264del(4)|p.L264I(3)|p.?(3)|p.L264fs*81(3)|p.G262_F270delGNLLGRNSF(2)|p.G262_S269delGNLLGRNS(2)|p.S261_L264>R(1)|p.N263fs*5(1)|p.E258fs*71(1)|p.L264V(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CGTCCCAGTAGATTACCACTA	0.517		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.L264L	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,+1,12	TP53	33396	.	35	Deletion - In frame(8)|Whole gene deletion(8)|Deletion - Frameshift(6)|Substitution - coding silent(5)|Substitution - Missense(4)|Unknown(3)|Complex - deletion inframe(1)	urinary_tract(6)|upper_aerodigestive_tract(5)|ovary(5)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|lung(3)|central_nervous_system(2)|breast(2)|large_intestine(1)|eye(1)|genital_tract(1)|stomach(1)	c.C790T						.						43	39	40					17																	7577148		2203	4299	6502	SO:0001819	synonymous_variant	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CCAGTAGATTACC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.790C>T	chr17.hg19:g.7577148G>A		85.0	0.0		71.0	33.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.517	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577148	G	A	7577148	2	1	176	1	0	0	0	0	0	0	0	1	16396	933	33	3		3	TP53	17	7577148	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10		7577148	73618062	147	26546	127	2								
TP53	7157	hgsc.bcm.edu	37	chr17	7577149	7577150	+	Frame_Shift_Ins	INS	-	-	C													0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agctgttccgtcccagtagaINSttaccactactcaggatagg							TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:7577149_7577150insC	ENST00000269305.4	-	8	977_978	c.788_789insG	c.(787-789)aatfs	p.N263fs	TP53_ENST00000420246.2_Frame_Shift_Ins_p.N263fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Ins_p.N263fs|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Frame_Shift_Ins_p.N263fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.N263fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	263	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		GN -> PD (in a sporadic cancer; somatic mutation).|N -> D (in sporadic cancers; somatic mutation).|N -> H (in sporadic cancers; somatic mutation).|N -> I (in sporadic cancers; somatic mutation).|N -> K (in a sporadic cancer; somatic mutation).|N -> S (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.N263I(2)|p.G262_S269delGNLLGRNS(2)|p.N263fs*5(1)|p.E258fs*71(1)|p.S261_L264>R(1)|p.N263K(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTCCCAGTAGATTACCACTACT	0.52		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.N263fs	Pancreas(47;798 1329 9957 10801)	Atlas-INDEL	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53,colon,carcinoma,-1,1	TP53	33396	.	22	Whole gene deletion(8)|Deletion - In frame(4)|Unknown(3)|Deletion - Frameshift(3)|Substitution - Missense(3)|Complex - deletion inframe(1)	large_intestine(4)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|lung(2)|ovary(2)|eye(1)|urinary_tract(1)|stomach(1)	c.789_790insG						.																																			SO:0001589	frameshift_variant	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.788_789insG	chr17.hg19:g.7577149_7577150insC	ENSP00000269305:p.Asn263fs	83.0	0.0		71.0	33.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.52	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577150	-	C	7577149	7	5	176	1	0	1	1	0	0	0	0	0	16396	330	12	0	497	0	TP53	17	7577149	Frame_Shift_Ins	INS	-	TCGA-DD-AACZ-01A-11D-A40R-10	1	7577149	73618061	148	26547	127	2								
GUCY2D	3000	hgsc.bcm.edu	37	chr17	7909980	7909980	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttcccgcgtgggggatcagcAcccggacctgacccctcgtg	13	16	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:7909980A>T	ENST00000254854.4	+	4	1476	c.1326A>T	c.(1324-1326)gcA>gcT	p.A442A		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	442					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				GGGGATCAGCACCCGGACCTG	0.642																																					p.A442A		Atlas-SNP	.											.	GUCY2D	82	.	0			c.A1326T						.						23	22	23					17																	7909980		2203	4300	6503	SO:0001819	synonymous_variant	3000	exon4			ATCAGCACCCGGA	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.1326A>T	chr17.hg19:g.7909980A>T		76.0	0.0		93.0	33.0	NM_000180	Q6LEA7	Silent	SNP	ENST00000254854.4	hg19	CCDS11127.1																																																																																			.	.		0.642	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			T	7909980	A	T	7909980	2	4	176	1	0	0	0	0	0	0	0	1	6906	146	6	4		4	GUCY2D	17	7909980	Silent	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	332831	7909980	73285230	149	26548										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11701056	11701056	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggaggccttggagaaccacaAtgaagtcaacacagtgatgg	13	8	1	3	rs145239685		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:11701056A>T	ENST00000262442.4	+	43	8434	c.8366A>T	c.(8365-8367)aAt>aTt	p.N2789I	DNAH9_ENST00000454412.2_Missense_Mutation_p.N2789I	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2789	AAA 4. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GAGAACCACAATGAAGTCAAC	0.478																																					p.N2789I		Atlas-SNP	.											.	DNAH9	695	.	0			c.A8366T						.						217	160	179					17																	11701056		2203	4300	6503	SO:0001583	missense	1770	exon43			ACCACAATGAAGT	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.8366A>T	chr17.hg19:g.11701056A>T	ENSP00000262442:p.Asn2789Ile	131.0	0.0		114.0	42.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.487301	0.84854	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.55052	0.54;0.54	5.68	5.68	0.88126	Dynein heavy chain, P-loop containing D4 domain (1);	0.162638	0.52532	D	0.000062	D	0.83487	0.5265	H	0.98664	4.295	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90128	0.4204	10	0.87932	D	0	.	15.9259	0.79615	1.0:0.0:0.0:0.0	.	2789	Q9NYC9	DYH9_HUMAN	I	2789;2789;1371	ENSP00000262442:N2789I;ENSP00000414874:N2789I	ENSP00000262442:N2789I	N	+	2	0	DNAH9	11641781	1.000000	0.71417	0.971000	0.41717	0.846000	0.48090	9.277000	0.95755	2.158000	0.67659	0.528000	0.53228	AAT	.	A|1.000;G|0.000		0.478	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11701056	A	T	11701056	3	4	176	1	0	0	0	0	1	0	0	0	4610	101	4	4	8536	4	DNAH9	17	11701056	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	3791076	11701056	69494154	150	26549										
GIT1	28964	hgsc.bcm.edu	37	chr17	27909015	27909015	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agccccatacactacaagcaGctcggcctgcagtgtctgtc	9	15	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:27909015G>T	ENST00000225394.3	-	5	801	c.553C>A	c.(553-555)Ctg>Atg	p.L185M	GIT1_ENST00000394869.3_Missense_Mutation_p.L185M|RP11-68I3.2_ENST00000581474.1_RNA|GIT1_ENST00000579937.1_Missense_Mutation_p.L185M|GIT1_ENST00000581348.1_Missense_Mutation_p.L185M	NM_014030.3	NP_054749.2	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 1	185					regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				READ - Rectum adenocarcinoma(3;0.0419)|Colorectal(3;0.069)		ACTACAAGCAGCTCGGCCTGC	0.622																																					p.L185M	Colon(81;41 1719 20078 35068)	Atlas-SNP	.											.	GIT1	84	.	0			c.C553A						.						76	63	67					17																	27909015		2203	4300	6503	SO:0001583	missense	28964	exon5			CAAGCAGCTCGGC	AF124490	CCDS11250.1, CCDS42290.1	17p11.2	2013-01-10	2008-09-05		ENSG00000108262	ENSG00000108262		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4272	protein-coding gene	gene with protein product		608434	"G protein-coupled receptor kinase interactor 1"			9826657, 10896954	Standard	NM_014030		Approved		uc002heg.2	Q9Y2X7	OTTHUMG00000132730	ENST00000225394.3:c.553C>A	chr17.hg19:g.27909015G>T	ENSP00000225394:p.Leu185Met	41.0	0.0		55.0	7.0	NM_014030	B4DGU9|B4DSV3|Q86SS0|Q9BRJ4	Missense_Mutation	SNP	ENST00000225394.3	hg19	CCDS11250.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.364256	0.61513	.	.	ENSG00000108262	ENST00000225394;ENST00000394869	T;T	0.71103	-0.54;-0.54	5.11	3.11	0.35812	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000005	T	0.76856	0.4046	L	0.48642	1.525	0.42278	D	0.992082	D;D;D;D	0.89917	1.0;0.998;0.999;1.0	D;D;D;D	0.87578	0.998;0.956;0.974;0.998	T	0.76236	-0.3033	10	0.54805	T	0.06	.	10.0098	0.41979	0.0723:0.0:0.7895:0.1382	.	189;185;185;185	Q59FC3;Q9Y2X7-3;B4DGU9;Q9Y2X7	.;.;.;GIT1_HUMAN	M	185	ENSP00000225394:L185M;ENSP00000378338:L185M	ENSP00000225394:L185M	L	-	1	2	GIT1	24933141	1.000000	0.71417	0.957000	0.39632	0.995000	0.86356	1.474000	0.35398	0.855000	0.35359	0.655000	0.94253	CTG	.	.		0.622	GIT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256073.1	NM_014030		T	27909015	G	T	27909015	3	4	176	1	0	0	0	0	1	0	0	0	6404	962	34	3	1827	3	GIT1	17	27909015	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	16207959	27909015	53286195	151	26550										
CPD	1362	hgsc.bcm.edu	37	chr17	28778776	28778776	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtcccttctctaaatccagaTgggcgagagagagctcaaga	11	10	2	4			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:28778776T>C	ENST00000225719.4	+	14	3193	c.3117T>C	c.(3115-3117)gaT>gaC	p.D1039D	CPD_ENST00000543464.2_Silent_p.D792D|CPD_ENST00000584051.1_3'UTR	NM_001304.4	NP_001295.2	O75976	CBPD_HUMAN	carboxypeptidase D	1039	Carboxypeptidase-like 3.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metallocarboxypeptidase activity (GO:0004181)|serine-type carboxypeptidase activity (GO:0004185)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						TAAATCCAGATGGGCGAGAGA	0.403																																					p.D1039D		Atlas-SNP	.											.	CPD	89	.	0			c.T3117C						.						161	150	154					17																	28778776		2203	4300	6503	SO:0001819	synonymous_variant	1362	exon14			TCCAGATGGGCGA	U65090	CCDS11257.1, CCDS56025.1	17q11.2	2012-02-10			ENSG00000108582	ENSG00000108582	3.4.17.22		2301	protein-coding gene	gene with protein product	"metallocarboxypeptidase D"	603102				9628828, 9355738	Standard	NM_001304		Approved	GP180	uc002hfb.2	O75976	OTTHUMG00000132797	ENST00000225719.4:c.3117T>C	chr17.hg19:g.28778776T>C		135.0	0.0		141.0	53.0	NM_001304	B7Z7T9|B7ZAU4|F5GZH6|O15377|Q86SH9|Q86XE6	Silent	SNP	ENST00000225719.4	hg19	CCDS11257.1																																																																																			.	.		0.403	CPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256214.3	NM_001304		C	28778776	T	C	28778776	2	2	176	1	0	0	0	0	0	0	0	1	3800	1461	51	2		2	CPD	17	28778776	Silent	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	869761	28778776	52416434	152	26551										
RHOT1	55288	hgsc.bcm.edu	37	chr17	30538176	30538176	+	Intron	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtgcacctgcaacaggtgtaCattttgcatctgtcagaact	9	10	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:30538176C>G	ENST00000333942.6	+	18	1978				RHOT1_ENST00000545287.2_Missense_Mutation_p.T594R|RHOT1_ENST00000358365.3_Missense_Mutation_p.T626R|RHOT1_ENST00000583994.1_Intron|RHOT1_ENST00000394692.2_Intron|RHOT1_ENST00000354266.3_Intron	NM_018307.3	NP_060777.3	Q8IXI2	MIRO1_HUMAN	ras homolog family member T1						cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				AACAGGTGTACATTTTGCATC	0.418																																					p.T626R		Atlas-SNP	.											.	RHOT1	69	.	0			c.C1877G						.						156	142	147					17																	30538176		2203	4300	6503	SO:0001627	intron_variant	55288	exon20			GGTGTACATTTTG	AJ517412	CCDS32610.1, CCDS32611.1, CCDS32612.1, CCDS74030.1, CCDS74031.1	17q11.2-q12	2013-01-10	2012-02-27	2004-03-24		ENSG00000126858		"EF-hand domain containing"	21168	protein-coding gene	gene with protein product	"mitochondrial Rho (MIRO) GTPase 1"	613888	"ras homolog gene family, member T1"	ARHT1		12482879	Standard	NM_001033567		Approved	MIRO-1, FLJ11040	uc002hgw.3	Q8IXI2		ENST00000333942.6:c.1739+2848C>G	chr17.hg19:g.30538176C>G		90.0	0.0		83.0	7.0	NM_001033568	A4FVB6|A6NFV0|B4DG48|J9JIH9|Q6NUR3|Q6P9F8|Q6PJG1|Q6YMW8|Q86UB0|Q8IW28|Q8IXJ7|Q9H067|Q9H9N8|Q9NUZ2	Missense_Mutation	SNP	ENST00000333942.6	hg19	CCDS32612.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.993448	0.35131	.	.	ENSG00000126858	ENST00000358365;ENST00000354266	T	0.76316	-1.01	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.80675	0.4668	N	0.22421	0.69	0.58432	D	0.999999	D;D	0.76494	0.997;0.999	D;D	0.83275	0.991;0.996	T	0.74147	-0.3759	10	0.12766	T	0.61	-12.982	19.9823	0.97331	0.0:1.0:0.0:0.0	.	594;626	Q8IXI2-5;Q8IXI2-3	.;.	R	626;594	ENSP00000351132:T626R	ENSP00000346215:T594R	T	+	2	0	RHOT1	27562289	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.419000	0.80179	2.788000	0.95919	0.650000	0.86243	ACA	.	.		0.418	RHOT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000447097.1	NM_018307		G	30538176	C	G	30538176	1	3	176	0	1	0	0	0	0	0	0	0	13358	478	17	4		4	RHOT1	17	30538176	Intron	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	1759400	30538176	50657034	153	26552										
KRTAP3-3	85293	hgsc.bcm.edu	37	chr17	39150197	39150197	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggaatgtggcagggtgggggAcagttgtcacagcaggtggg	21	5	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:39150197A>T	ENST00000391586.1	-	1	188	c.153T>A	c.(151-153)tgT>tgA	p.C51*		NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	51	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			lung(2)|prostate(2)	4		Breast(137;0.00043)				AGGGTGGGGGACAGTTGTCAC	0.617																																					p.C51X		Atlas-SNP	.											.	KRTAP3-3	11	.	0			c.T153A						.						125	87	100					17																	39150197		2203	4296	6499	SO:0001587	stop_gained	85293	exon1			TGGGGGACAGTTG	AJ406933	CCDS32643.1	17q21.2	2013-06-25			ENSG00000212899	ENSG00000212899		"Keratin associated proteins"	18890	protein-coding gene	gene with protein product						11279113	Standard	NM_033185		Approved	KAP3.3	uc002hvr.1	Q9BYR6	OTTHUMG00000133591	ENST00000391586.1:c.153T>A	chr17.hg19:g.39150197A>T	ENSP00000375428:p.Cys51*	242.0	0.0		250.0	15.0	NM_033185	Q52LP0|Q6NTD4	Nonsense_Mutation	SNP	ENST00000391586.1	hg19	CCDS32643.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.614439	0.87359	.	.	ENSG00000212899	ENST00000391586	.	.	.	5.89	0.489	0.16854	.	0.327533	0.27147	N	0.020712	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.2123	0.31490	0.4144:0.0:0.5856:0.0	.	.	.	.	X	51	.	ENSP00000375428:C51X	C	-	3	2	KRTAP3-3	36403723	0.025000	0.19082	0.996000	0.52242	0.994000	0.84299	-0.357000	0.07651	-0.086000	0.12550	-0.248000	0.11899	TGT	.	.		0.617	KRTAP3-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257695.1			T	39150197	A	T	39150197	4	4	176	1	0	0	0	0	0	1	0	0	8556	273	10	4	147	4	KRTAP3-3	17	39150197	Nonsense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	8612021	39150197	42045013	154	26553										
DHX8	1659	hgsc.bcm.edu	37	chr17	41590838	41590838	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tttacaattccaagacagggAttgaccagctcgtggtgacg	11	9	0	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:41590838A>T	ENST00000262415.3	+	17	2683	c.2611A>T	c.(2611-2613)Att>Ttt	p.I871F	DHX8_ENST00000540306.1_Missense_Mutation_p.I871F	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	871	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		CAAGACAGGGATTGACCAGCT	0.438																																					p.I871F	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.A2611T						.						178	141	153					17																	41590838		2203	4300	6503	SO:0001583	missense	1659	exon17			ACAGGGATTGACC	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"DEAH-boxes"	2749	protein-coding gene	gene with protein product		600396	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.2611A>T	chr17.hg19:g.41590838A>T	ENSP00000262415:p.Ile871Phe	151.0	0.0		161.0	72.0	NM_004941		Missense_Mutation	SNP	ENST00000262415.3	hg19	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	A	32	5.183427	0.94885	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.02737	4.18;4.18	5.87	5.87	0.94306	Helicase, C-terminal (3);	0.101679	0.64402	D	0.000004	T	0.06508	0.0167	L	0.45422	1.42	0.80722	D	1	P;P	0.45902	0.868;0.797	P;P	0.48334	0.494;0.574	T	0.12993	-1.0526	10	0.87932	D	0	.	15.5056	0.75739	1.0:0.0:0.0:0.0	.	871;871	F5H658;Q14562	.;DHX8_HUMAN	F	871	ENSP00000437886:I871F;ENSP00000262415:I871F	ENSP00000262415:I871F	I	+	1	0	DHX8	38946364	1.000000	0.71417	0.987000	0.45799	0.987000	0.75469	9.115000	0.94336	2.257000	0.74773	0.529000	0.55759	ATT	.	.		0.438	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			T	41590838	A	T	41590838	3	4	176	1	0	0	0	0	1	0	0	0	4517	333	12	4	2677	4	DHX8	17	41590838	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	2440641	41590838	39604372	155	26554										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48655580	48655580	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agctcttgcaagatctccagCccttgcttgaaagcagacag	9	12	2	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:48655580C>T	ENST00000359106.5	+	9	1956	c.1956C>T	c.(1954-1956)agC>agT	p.S652S	CACNA1G_ENST00000514079.1_Silent_p.S652S|CACNA1G_ENST00000360761.4_Silent_p.S652S|CACNA1G_ENST00000507510.2_Silent_p.S652S|CACNA1G_ENST00000507896.1_Silent_p.S652S|CACNA1G_ENST00000354983.4_Silent_p.S652S|CACNA1G_ENST00000515165.1_Silent_p.S652S|CACNA1G_ENST00000416767.4_Silent_p.S652S|CACNA1G_ENST00000352832.5_Silent_p.S652S|CACNA1G_ENST00000512389.1_Silent_p.S652S|CACNA1G_ENST00000507336.1_Silent_p.S652S|CACNA1G_ENST00000515411.1_Silent_p.S652S|CACNA1G_ENST00000442258.2_Silent_p.S652S|CACNA1G_ENST00000358244.5_Silent_p.S652S|CACNA1G_ENST00000502264.1_Silent_p.S652S|CACNA1G_ENST00000513964.1_Silent_p.S652S|CACNA1G_ENST00000510366.1_Silent_p.S652S|CACNA1G_ENST00000429973.2_Silent_p.S652S|CACNA1G_ENST00000514717.1_Silent_p.S652S|CACNA1G_ENST00000503485.1_Silent_p.S652S|CACNA1G_ENST00000514181.1_Silent_p.S652S|CACNA1G_ENST00000510115.1_Silent_p.S652S|CACNA1G_ENST00000507609.1_Silent_p.S652S|CACNA1G_ENST00000513689.2_Silent_p.S652S|CACNA1G_ENST00000505165.1_Silent_p.S652S|CACNA1G_ENST00000515765.1_Silent_p.S652S	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	652					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AGATCTCCAGCCCTTGCTTGA	0.617																																					p.S652S		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C1956T						.						43	48	46					17																	48655580		1985	4156	6141	SO:0001819	synonymous_variant	8913	exon9			CTCCAGCCCTTGC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.1956C>T	chr17.hg19:g.48655580C>T		127.0	0.0		121.0	10.0	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	hg19	CCDS45730.1																																																																																			.	.		0.617	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		T	48655580	C	T	48655580	2	4	176	1	0	0	0	0	0	0	0	1	2546	738	26	3		3	CACNA1G	17	48655580	Silent	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	7064742	48655580	32539630	156	26555										
KCNH6	81033	hgsc.bcm.edu	37	chr17	61623190	61623190	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ctccctccctgaacaccttgGctctgttcccaagcagctgg	8	17	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:61623190G>A	ENST00000583023.1	+	14	2923	c.2912G>A	c.(2911-2913)gGc>gAc	p.G971D	KCNH6_ENST00000456941.2_Missense_Mutation_p.G882D|KCNH6_ENST00000581784.1_Missense_Mutation_p.G882D|KCNH6_ENST00000314672.5_Missense_Mutation_p.G935D	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	971					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GAACACCTTGGCTCTGTTCCC	0.572																																					p.G971D		Atlas-SNP	.											.	KCNH6	122	.	0			c.G2912A						.						107	101	103					17																	61623190		2203	4300	6503	SO:0001583	missense	81033	exon14			ACCTTGGCTCTGT	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2912G>A	chr17.hg19:g.61623190G>A	ENSP00000463533:p.Gly971Asp	73.0	0.0		68.0	26.0	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	hg19	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	G	5.004	0.186415	0.09495	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D	0.99220	-5.58	4.57	1.3	0.21679	.	0.553031	0.14655	N	0.306375	D	0.96944	0.9002	L	0.46157	1.445	0.09310	N	1	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.06405	0.001;0.001;0.001;0.002	D	0.91443	0.5175	10	0.12430	T	0.62	.	8.1601	0.31194	0.4387:0.0:0.5613:0.0	.	812;935;882;971	B4DPJ3;B4DKC0;Q9H252-2;Q9H252	.;.;.;KCNH6_HUMAN	D	971;882	ENSP00000396900:G882D	ENSP00000318212:G971D	G	+	2	0	KCNH6	58976922	0.501000	0.26099	0.702000	0.30337	0.965000	0.64279	1.456000	0.35201	0.404000	0.25506	0.563000	0.77884	GGC	.	.		0.572	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		A	61623190	G	A	61623190	3	1	176	1	0	0	0	0	1	0	0	0	8045	1203	42	3	2966	3	KCNH6	17	61623190	Missense_Mutation	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	12967610	61623190	19572020	157	26556										
DDX42	11325	hgsc.bcm.edu	37	chr17	61895571	61895571	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gcatggggagaaccggggtgCaaatgatggtcggaatgggg	20	5	0	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:61895571C>T	ENST00000578681.1	+	19	3231	c.2630C>T	c.(2629-2631)gCa>gTa	p.A877V	DDX42_ENST00000457800.2_Missense_Mutation_p.A877V|DDX42_ENST00000582985.1_Intron|DDX42_ENST00000583590.1_Missense_Mutation_p.A877V|DDX42_ENST00000359353.5_Missense_Mutation_p.A758V|DDX42_ENST00000389924.2_Missense_Mutation_p.A877V	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	877	Gly-rich.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						AACCGGGGTGCAAATGATGGT	0.557																																					p.A877V		Atlas-SNP	.											.	DDX42	86	.	0			c.C2630T						.						97	93	94					17																	61895571		2203	4300	6503	SO:0001583	missense	11325	exon18			GGGGTGCAAATGA	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"DEAD-boxes"	18676	protein-coding gene	gene with protein product	"splicing factor 3b, subunit 8"	613369	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.2630C>T	chr17.hg19:g.61895571C>T	ENSP00000464050:p.Ala877Val	61.0	0.0		78.0	26.0	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	hg19	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	C	7.237	0.600555	0.13939	.	.	ENSG00000198231	ENST00000389924;ENST00000457800;ENST00000359353	T;T;T	0.19532	2.14;2.14;3.2	5.06	4.05	0.47172	.	2.449100	0.01420	N	0.014353	T	0.21387	0.0515	L	0.36672	1.1	0.09310	N	1	B;B	0.17038	0.02;0.02	B;B	0.15052	0.01;0.012	T	0.09975	-1.0650	10	0.36615	T	0.2	-1.1621	9.4757	0.38869	0.2282:0.6362:0.1356:0.0	.	423;877	B3KV84;Q86XP3	.;DDX42_HUMAN	V	877;877;594	ENSP00000374574:A877V;ENSP00000390121:A877V;ENSP00000352308:A594V	ENSP00000352308:A594V	A	+	2	0	DDX42	59249303	0.000000	0.05858	0.796000	0.32109	0.368000	0.29767	0.247000	0.18179	2.627000	0.88993	0.467000	0.42956	GCA	.	.		0.557	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372		T	61895571	C	T	61895571	3	4	176	1	0	0	0	0	1	0	0	0	4364	710	25	3	2696	3	DDX42	17	61895571	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	272381	61895571	19299639	158	26557										
CD79B	974	hgsc.bcm.edu	37	chr17	62007563	62007563	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gagggtggcgagagattcgtTctgggactcttccatgcggc	16	9	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:62007563T>A	ENST00000006750.3	-	3	393	c.301A>T	c.(301-303)Aac>Tac	p.N101Y	CD79B_ENST00000392795.3_Missense_Mutation_p.N102Y|CD79B_ENST00000349817.2_Intron	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	101	Ig-like V-type.				B cell receptor signaling pathway (GO:0050853)|immune response (GO:0006955)|signal transduction (GO:0007165)	B cell receptor complex (GO:0019815)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						AGAGATTCGTTCTGGGACTCT	0.562			"Mis, O"		DLBCL																																p.N102Y		Atlas-SNP	.		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	.	CD79B	38	.	0			c.A304T						.						157	132	141					17																	62007563		2203	4300	6503	SO:0001583	missense	974	exon3			ATTCGTTCTGGGA	L27587	CCDS11655.1, CCDS11656.1, CCDS42372.1	17q23	2014-09-17	2006-03-28			ENSG00000007312		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1699	protein-coding gene	gene with protein product		147245	"CD79B antigen (immunoglobulin-associated beta)"	IGB		9545642	Standard	XM_005257858		Approved	B29	uc002jdp.1	P40259		ENST00000006750.3:c.301A>T	chr17.hg19:g.62007563T>A	ENSP00000006750:p.Asn101Tyr	73.0	0.0		85.0	7.0	NM_001039933	Q53FS2|Q9BU06	Missense_Mutation	SNP	ENST00000006750.3	hg19	CCDS11655.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.252815	0.59212	.	.	ENSG00000007312	ENST00000392795;ENST00000006750	T;T	0.70869	-0.52;-0.52	5.49	4.42	0.53409	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.537006	0.20823	N	0.085021	T	0.78848	0.4348	M	0.65320	2	0.21499	N	0.999668	D	0.89917	1.0	D	0.71184	0.972	T	0.68296	-0.5446	10	0.51188	T	0.08	-29.8364	8.0253	0.30434	0.0:0.0923:0.0:0.9077	.	101	P40259	CD79B_HUMAN	Y	102;101	ENSP00000376544:N102Y;ENSP00000006750:N101Y	ENSP00000006750:N101Y	N	-	1	0	CD79B	59361295	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.338000	0.19858	0.936000	0.37367	0.459000	0.35465	AAC	.	.		0.562	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			A	62007563	T	A	62007563	3	1	176	1	0	0	0	0	1	0	0	0	3039	1783	62	4	404	4	CD79B	17	62007563	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	111992	62007563	19187647	159	26558										
SMURF2	64750	hgsc.bcm.edu	37	chr17	62553767	62553767	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	attgatctgcaatgtataaaTatcatctcttgaatactgga	6	6	3	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:62553767T>C	ENST00000262435.9	-	13	1577	c.1390A>G	c.(1390-1392)Att>Gtt	p.I464V		NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	464	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				BMP signaling pathway (GO:0030509)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|SMAD binding (GO:0046332)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(4)	22	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			AATGTATAAATATCATCTCTT	0.343																																					p.I464V		Atlas-SNP	.											.	SMURF2	63	.	0			c.A1390G						.						95	96	96					17																	62553767		2203	4298	6501	SO:0001583	missense	64750	exon13			TATAAATATCATC	AF301463	CCDS32707.1	17q22-q23	2012-10-05			ENSG00000108854	ENSG00000108854			16809	protein-coding gene	gene with protein product		605532				11016919	Standard	XM_005257585		Approved		uc002jep.1	Q9HAU4	OTTHUMG00000179189	ENST00000262435.9:c.1390A>G	chr17.hg19:g.62553767T>C	ENSP00000262435:p.Ile464Val	377.0	0.0		357.0	35.0	NM_022739	Q52LL1|Q9H260	Missense_Mutation	SNP	ENST00000262435.9	hg19	CCDS32707.1	.	.	.	.	.	.	.	.	.	.	T	15.04	2.715886	0.48622	.	.	ENSG00000108854	ENST00000262435	T	0.57273	0.41	5.81	5.81	0.92471	HECT (4);	0.000000	0.85682	D	0.000000	T	0.49915	0.1585	L	0.49350	1.555	0.80722	D	1	B	0.15141	0.012	B	0.18561	0.022	T	0.41645	-0.9497	10	0.39692	T	0.17	.	16.1607	0.81704	0.0:0.0:0.0:1.0	.	464	Q9HAU4	SMUF2_HUMAN	V	464	ENSP00000262435:I464V	ENSP00000262435:I464V	I	-	1	0	SMURF2	59984229	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.991000	0.88244	2.226000	0.72624	0.482000	0.46254	ATT	.	.		0.343	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739		C	62553767	T	C	62553767	3	2	176	1	0	0	0	0	1	0	0	0	14835	1406	49	2	884	2	SMURF2	17	62553767	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10	546204	62553767	18641443	160	26559										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76445590	76445590	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	agtaggtgatctcgtccgtcAggttgatcacccgctgcttc	11	12	3	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr17:76445590A>T	ENST00000585328.1	-	69	11226	c.11102T>A	c.(11101-11103)cTg>cAg	p.L3701Q	DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Missense_Mutation_p.L3692Q	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3692					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CTCGTCCGTCAGGTTGATCAC	0.562																																					p.L3706Q		Atlas-SNP	.											.	DNAH17	347	.	0			c.T11117A						.						122	92	103					17																	76445590		2203	4296	6499	SO:0001583	missense	8632	exon69			TCCGTCAGGTTGA	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.11102T>A	chr17.hg19:g.76445590A>T	ENSP00000465516:p.Leu3701Gln	114.0	0.0		131.0	54.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	A	22.2	4.252328	0.80135	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.68765	-0.35	4.85	4.85	0.62838	.	0.000000	0.43110	D	0.000602	D	0.87869	0.6286	H	0.97682	4.055	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	D	0.92084	0.5675	10	0.87932	D	0	.	14.456	0.67416	1.0:0.0:0.0:0.0	.	3701	E7EUM8	.	Q	3701;3692	ENSP00000374490:L3692Q	ENSP00000300671:L3701Q	L	-	2	0	DNAH17	73957185	1.000000	0.71417	0.997000	0.53966	0.708000	0.40852	9.153000	0.94687	1.821000	0.53095	0.459000	0.35465	CTG	.	.		0.562	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		T	76445590	A	T	76445590	3	4	176	1	0	0	0	0	1	0	0	0	4603	188	7	4	2323	4	DNAH17	17	76445590	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	13891823	76445590	4749620	161	26560										
SLC39A6	25800	hgsc.bcm.edu	37	chr18	33689641	33689641	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ccaaaagcatcccagcattcTgtaaaaagaaatacccccag	5	13	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr18:33689641T>A	ENST00000590986.1	-	10	2472	c.2183A>T	c.(2182-2184)cAg>cTg	p.Q728L	SLC39A6_ENST00000269187.5_Missense_Mutation_p.Q728L			Q13433	S39A6_HUMAN	solute carrier family 39 (zinc transporter), member 6	728					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|lamellipodium membrane (GO:0031258)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	41						CCCAGCATTCTGTAAAAAGAA	0.348																																					p.Q728L		Atlas-SNP	.											.	SLC39A6	81	.	0			c.A2183T						.						126	125	125					18																	33689641		1824	4080	5904	SO:0001583	missense	25800	exon10			GCATTCTGTAAAA	U41060	CCDS42428.1, CCDS45854.1	18q12.2	2013-05-22				ENSG00000141424		"Solute carriers"	18607	protein-coding gene	gene with protein product		608731	"solute carrier family 39 (metal ion transporter), member 6"			12659941, 12839489	Standard	NM_012319		Approved	LIV-1	uc010dmy.3	Q13433		ENST00000590986.1:c.2183A>T	chr18.hg19:g.33689641T>A	ENSP00000465915:p.Gln728Leu	339.0	0.0		378.0	196.0	NM_012319	B4DR49|B4E224|Q8IXR3|Q96HP5	Missense_Mutation	SNP	ENST00000590986.1	hg19	CCDS42428.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.683063	0.88542	.	.	ENSG00000141424	ENST00000269187;ENST00000543723	T	0.53640	0.61	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.63954	0.2555	L	0.53780	1.695	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.66705	-0.5856	10	0.87932	D	0	-14.6662	13.8924	0.63747	0.0:0.0:0.0:1.0	.	728	Q13433	S39A6_HUMAN	L	728;383	ENSP00000269187:Q728L	ENSP00000269187:Q728L	Q	-	2	0	SLC39A6	31943639	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.841000	0.86834	2.229000	0.72834	0.482000	0.46254	CAG	.	.		0.348	SLC39A6-004	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000444136.1			A	33689641	T	A	33689641	3	1	176	1	0	0	0	0	1	0	0	0	14637	1580	55	4	88	4	SLC39A6	18	33689641	Missense_Mutation	SNP	T	TCGA-DD-AACZ-01A-11D-A40R-10		33689641	44387607	162	26561										
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56056334	56056334	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tagttgctcatgtgcggcctCggtgatgtggatgtgaatga	15	6	1	3	rs375065890		TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr18:56056334C>T	ENST00000400345.3	+	28	2848	c.2565C>T	c.(2563-2565)ctC>ctT	p.L855L	NEDD4L_ENST00000431212.2_Silent_p.L734L|NEDD4L_ENST00000586263.1_Silent_p.L827L|NEDD4L_ENST00000456173.2_Silent_p.L714L|NEDD4L_ENST00000256832.7_Silent_p.L715L|NEDD4L_ENST00000435432.2_Silent_p.L714L|NEDD4L_ENST00000356462.6_Silent_p.L791L|NEDD4L_ENST00000456986.1_Silent_p.L734L|NEDD4L_ENST00000382850.4_Silent_p.L835L|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000256830.9_Silent_p.L751L|NEDD4L_ENST00000357895.5_Silent_p.L847L	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	855	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						TGTGCGGCCTCGGTGATGTGG	0.488																																					p.L855L		Atlas-SNP	.											.	NEDD4L	126	.	0			c.C2565T						.	C	,,,,,,,,	0,4076		0,0,2038	99	100	100		2202,2202,2202,2565,2541,2481,2142,2142,2505	-5.8	0.5	18		100	1,8373		0,1,4186	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEDD4L	NM_001144964.1,NM_001144965.1,NM_001144966.2,NM_001144967.2,NM_001144968.1,NM_001144969.1,NM_001144970.2,NM_001144971.1,NM_015277.5	,,,,,,,,	0,1,6224	TT,TC,CC		0.0119,0.0,0.0080	,,,,,,,,	734/855,734/855,734/855,855/976,847/968,827/948,714/835,714/835,835/956	56056334	1,12449	2038	4187	6225	SO:0001819	synonymous_variant	23327	exon28			CGGCCTCGGTGAT	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.2565C>T	chr18.hg19:g.56056334C>T		123.0	0.0		108.0	7.0	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	hg19	CCDS45872.1																																																																																			.	.		0.488	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			T	56056334	C	T	56056334	2	4	176	1	0	0	0	0	0	0	0	1	10320	871	31	1		1	NEDD4L	18	56056334	Silent	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	22366693	56056334	22020914	163	26562										
SERPINB4	6318	hgsc.bcm.edu	37	chr18	61310753	61310753	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tgttgttctcttttgattttCtgaactgttggaacagatcg	9	6	2	3			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr18:61310753C>G	ENST00000341074.5	-	2	174	c.59G>C	c.(58-60)aGa>aCa	p.R20T	SERPINB4_ENST00000356424.6_Missense_Mutation_p.R20T	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	20					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						TTTTGATTTTCTGAACTGTTG	0.423																																					p.R20T		Atlas-SNP	.											.	SERPINB4	89	.	0			c.G59C						.						291	262	272					18																	61310753		2203	4300	6503	SO:0001583	missense	6318	exon2			GATTTTCTGAACT	X89015	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073		"Serine (or cysteine) peptidase inhibitors"	10570	protein-coding gene	gene with protein product	"squamous cell carcinoma antigen 2"	600518	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"	SCCA2		7724531, 14630915, 24172014	Standard	NM_175041		Approved	PI11, LEUPIN, SCCA-2, SCCA1		P48594	OTTHUMG00000060405	ENST00000341074.5:c.59G>C	chr18.hg19:g.61310753C>G	ENSP00000343445:p.Arg20Thr	220.0	0.0		190.0	85.0	NM_002974	A8K847	Missense_Mutation	SNP	ENST00000341074.5	hg19	CCDS11986.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.82|10.82	1.457554|1.457554	0.26161|0.26161	.|.	.|.	ENSG00000206073|ENSG00000206073	ENST00000413673|ENST00000341074;ENST00000356424;ENST00000436264	.|D;D;D	.|0.84146	.|-1.81;-1.81;-1.81	3.77|3.77	0.424|0.424	0.16468|0.16468	.|Serpin domain (3);	.|0.717201	.|0.11987	.|N	.|0.510226	D|D	0.82291|0.82291	0.5005|0.5005	L|L	0.38733|0.38733	1.17|1.17	0.09310|0.09310	N|N	1|1	.|P;B	.|0.40398	.|0.716;0.277	.|P;B	.|0.54924	.|0.764;0.297	T|T	0.69109|0.69109	-0.5232|-0.5232	5|10	.|0.18276	.|T	.|0.48	.|.	4.1902|4.1902	0.10417|0.10417	0.1608:0.5313:0.0:0.3079|0.1608:0.5313:0.0:0.3079	.|.	.|20;20	.|P48594;Q9BYF7	.|SPB4_HUMAN;.	Q|T	22|20	.|ENSP00000343445:R20T;ENSP00000348795:R20T;ENSP00000399796:R20T	.|ENSP00000343445:R20T	E|R	-|-	1|2	0|0	SERPINB4|SERPINB4	59461733|59461733	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.028000|0.028000	0.11728|0.11728	-0.334000|-0.334000	0.07883|0.07883	0.213000|0.213000	0.20722|0.20722	0.603000|0.603000	0.83216|0.83216	GAA|AGA	.	.		0.423	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2	NM_175041		G	61310753	C	G	61310753	3	3	176	1	0	0	0	0	1	0	0	0	14118	913	32	4	1141	4	SERPINB4	18	61310753	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	5254419	61310753	16766495	164	26563										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11143993	11143993	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aagcgcaggaccgagcccacCgcatcgggcagcagaacgag	14	14	0	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr19:11143993C>T	ENST00000429416.3	+	27	3855	c.3574C>T	c.(3574-3576)Cgc>Tgc	p.R1192C	SMARCA4_ENST00000589677.1_Missense_Mutation_p.R1192C|SMARCA4_ENST00000444061.3_Missense_Mutation_p.R1192C|SMARCA4_ENST00000413806.3_Missense_Mutation_p.R1192C|SMARCA4_ENST00000450717.3_Missense_Mutation_p.R1192C|SMARCA4_ENST00000590574.1_Missense_Mutation_p.R1192C|SMARCA4_ENST00000358026.2_Missense_Mutation_p.R1192C|SMARCA4_ENST00000541122.2_Missense_Mutation_p.R1192C|SMARCA4_ENST00000344626.4_Missense_Mutation_p.R1192C	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1192	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.R1192C(1)|p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CCGAGCCCACCGCATCGGGCA	0.607			"F, N, Mis"		NSCLC																																p.R1192C		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	SMARCA4_ENST00000358026,NS,carcinoma,0,3	SMARCA4	502	.	2	Substitution - Missense(1)|Unknown(1)	lung(1)|central_nervous_system(1)	c.C3574T						.						61	61	61					19																	11143993		2203	4300	6503	SO:0001583	missense	6597	exon26			GCCCACCGCATCG	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3574C>T	chr19.hg19:g.11143993C>T	ENSP00000395654:p.Arg1192Cys	160.0	0.0		151.0	69.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507268	0.85282	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.97888	-4.59;-4.59;-4.59;-4.59;-4.59;-4.59;-4.59	4.74	4.74	0.60224	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99498	0.9821	H	0.99982	5.21	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97352	0.9964	10	0.87932	D	0	-34.1151	16.7067	0.85374	0.0:1.0:0.0:0.0	.	1192;1192;1192;1192;1192;412;1192	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	C	1192;1192;1256;1192;1192;1192;1192;1192	ENSP00000395654:R1192C;ENSP00000350720:R1192C;ENSP00000343896:R1192C;ENSP00000445036:R1192C;ENSP00000392837:R1192C;ENSP00000397783:R1192C;ENSP00000414727:R1192C	ENSP00000343896:R1192C	R	+	1	0	SMARCA4	11004993	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.675000	0.68123	2.488000	0.83962	0.558000	0.71614	CGC	.	.		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		T	11143993	C	T	11143993	3	4	176	1	0	0	0	0	1	0	0	0	14785	652	23	1	3672	1	SMARCA4	19	11143993	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10		11143993	47984990	165	26564										
CLIP3	25999	hgsc.bcm.edu	37	chr19	36510204	36510204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tcccacagaaccgcagtgtgCccgtctggggagagaaggga	15	11	1	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr19:36510204C>T	ENST00000360535.4	-	8	1150	c.923G>A	c.(922-924)gGc>gAc	p.G308D	AC002116.7_ENST00000586962.1_RNA|CLIP3_ENST00000593074.1_Missense_Mutation_p.G308D	NM_015526.2	NP_056341.1	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	308					chaperone-mediated protein transport (GO:0072321)|fat cell differentiation (GO:0045444)|membrane biogenesis (GO:0044091)|negative regulation of microtubule polymerization (GO:0031115)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein phosphorylation (GO:0001934)	early endosome membrane (GO:0031901)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)|trans-Golgi network membrane (GO:0032588)	ganglioside binding (GO:0035594)|microtubule binding (GO:0008017)			cervix(1)|endometrium(6)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	23	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CCGCAGTGTGCCCGTCTGGGG	0.652																																					p.G308D		Atlas-SNP	.											.	CLIP3	53	.	0			c.G923A						.						52	40	44					19																	36510204		2203	4299	6502	SO:0001583	missense	25999	exon7			AGTGTGCCCGTCT	AJ427922	CCDS12486.1	19q13.12	2014-08-12			ENSG00000105270	ENSG00000105270		"Ankyrin repeat domain containing"	24314	protein-coding gene	gene with protein product	"CLIP-170-related", "restin-like 1"	607382				11854307	Standard	NM_015526		Approved	CLIPR-59, RSNL1	uc002ocz.2	Q96DZ5	OTTHUMG00000181747	ENST00000360535.4:c.923G>A	chr19.hg19:g.36510204C>T	ENSP00000353732:p.Gly308Asp	38.0	0.0		40.0	25.0	NM_001199570	A8K0E4|Q8WWL1|Q96C99|Q9UFT7	Missense_Mutation	SNP	ENST00000360535.4	hg19	CCDS12486.1	.	.	.	.	.	.	.	.	.	.	c	31	5.060412	0.93846	.	.	ENSG00000105270	ENST00000360535;ENST00000544037;ENST00000534959	D	0.90844	-2.74	5.25	5.25	0.73442	Cytoskeleton-associated protein, Gly-rich domain (3);	0.000000	0.85682	D	0.000000	D	0.97455	0.9167	H	0.98738	4.315	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99050	1.0827	10	0.87932	D	0	-25.3401	16.3465	0.83134	0.0:1.0:0.0:0.0	.	308	Q96DZ5	CLIP3_HUMAN	D	308;190;284	ENSP00000353732:G308D	ENSP00000353732:G308D	G	-	2	0	CLIP3	41202044	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.608000	0.82898	2.478000	0.83669	0.580000	0.79431	GGC	.	.		0.652	CLIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457426.1	NM_015526		T	36510204	C	T	36510204	3	4	176	1	0	0	0	0	1	0	0	0	3536	739	26	3	748	3	CLIP3	19	36510204	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	25366211	36510204	22618779	166	26565										
WDR62	284403	hgsc.bcm.edu	37	chr19	36545927	36545927	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	aacgatgcaggggagaagctGccctctgtcatggcgggagt	16	9	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr19:36545927G>A	ENST00000270301.7	+	1	54	c.54G>A	c.(52-54)ctG>ctA	p.L18L	WDR62_ENST00000401500.2_Silent_p.L18L|WDR62_ENST00000378860.4_3'UTR|THAP8_ENST00000524106.1_5'Flank|WDR62_ENST00000388999.3_Silent_p.L18L|THAP8_ENST00000538849.1_5'Flank|THAP8_ENST00000292894.1_5'Flank			O43379	WDR62_HUMAN	WD repeat domain 62	18					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GGGAGAAGCTGCCCTCTGTCA	0.721																																					p.L18L		Atlas-SNP	.											.	WDR62	102	.	0			c.G54A						.						12	11	11					19																	36545927		2065	4121	6186	SO:0001819	synonymous_variant	284403	exon1			GAAGCTGCCCTCT	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"WD repeat domain containing"	24502	protein-coding gene	gene with protein product		613583	"chromosome 19 open reading frame 14", "microcephaly, primary autosomal recessive 2"	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.54G>A	chr19.hg19:g.36545927G>A		138.0	0.0		165.0	108.0	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	hg19	CCDS33001.1																																																																																			.	.		0.721	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671		A	36545927	G	A	36545927	2	1	176	1	0	0	0	0	0	0	0	1	17328	1306	46	3		3	WDR62	19	36545927	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	35723	36545927	22583056	167	26566										
LMTK3	114783	hgsc.bcm.edu	37	chr19	49001083	49001083	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gtcccgggttccagcgtcccGttcttgggggctgggccaag	16	13	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr19:49001083G>A	ENST00000600059.1	-	11	3470	c.3243C>T	c.(3241-3243)aaC>aaT	p.N1081N	LMTK3_ENST00000270238.3_Silent_p.N1110N			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	1081	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		CCAGCGTCCCGTTCTTGGGGG	0.736																																					p.N1110N		Atlas-SNP	.											.	LMTK3	125	.	0			c.C3330T						.						2	2	2					19																	49001083		1449	3344	4793	SO:0001819	synonymous_variant	114783	exon12			CGTCCCGTTCTTG	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 101"						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.3243C>T	chr19.hg19:g.49001083G>A		27.0	0.0		31.0	15.0	NM_001080434	Q4G0U1	Silent	SNP	ENST00000600059.1	hg19																																																																																				.	.		0.736	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895		A	49001083	G	A	49001083	2	1	176	1	0	0	0	0	0	0	0	1	8869	1136	40	1		1	LMTK3	19	49001083	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	12455156	49001083	10127900	168	26567										
ZNF628	89887	hgsc.bcm.edu	37	chr19	55995139	55995139	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggtccagctccagccagcacAggaggtgaccacggtccagc	13	15	0	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr19:55995139A>C	ENST00000598519.1	+	3	3132	c.2579A>C	c.(2578-2580)cAg>cCg	p.Q860P	ZNF628_ENST00000391718.2_Missense_Mutation_p.Q856P|NAT14_ENST00000205194.4_5'Flank|NAT14_ENST00000587400.1_5'Flank|NAT14_ENST00000591590.1_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	860	4 X approximate tandem repeats.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		CAGCCAGCACAGGAGGTGACC	0.637																																					p.Q860P		Atlas-SNP	.											.	ZNF628	75	.	0			c.A2579C						.						45	51	49					19																	55995139		2203	4300	6503	SO:0001583	missense	89887	exon3			CAGCACAGGAGGT	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"Zinc fingers, C2H2-type"	28054	protein-coding gene	gene with protein product	"Zinc finger expressed in Embryonal cells and Certain adult organs"	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.2579A>C	chr19.hg19:g.55995139A>C	ENSP00000469591:p.Gln860Pro	125.0	0.0		140.0	72.0	NM_033113	Q86X34	Missense_Mutation	SNP	ENST00000598519.1	hg19	CCDS33116.3	.	.	.	.	.	.	.	.	.	.	.	12.72	2.023561	0.35701	.	.	ENSG00000197483	ENST00000391718	T	0.06371	3.31	4.12	4.12	0.48240	.	0.174973	0.26035	U	0.026733	T	0.04724	0.0128	N	0.14661	0.345	0.23076	N	0.998334	B	0.22080	0.064	B	0.20184	0.028	T	0.33904	-0.9850	10	0.87932	D	0	.	11.3774	0.49737	1.0:0.0:0.0:0.0	.	856	Q5EBL2	ZN628_HUMAN	P	856	ENSP00000375598:Q856P	ENSP00000375598:Q856P	Q	+	2	0	ZNF628	60686951	0.000000	0.05858	0.892000	0.35008	0.666000	0.39218	0.988000	0.29616	1.632000	0.50472	0.370000	0.22315	CAG	.	.		0.637	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		C	55995139	A	C	55995139	3	2	176	1	0	0	0	0	1	0	0	0	18067	188	7	5	2569	5	ZNF628	19	55995139	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	6994056	55995139	3133844	169	26568										
TGM6	343641	hgsc.bcm.edu	37	chr20	2413197	2413197	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttgacatcaccccctccaaaAgtggcccaaggcagctgcag	9	15	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr20:2413197A>C	ENST00000202625.2	+	13	2090	c.2029A>C	c.(2029-2031)Agt>Cgt	p.S677R	TGM6_ENST00000381423.1_3'UTR	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	677					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	CCCCTCCAAAAGTGGCCCAAG	0.587																																					p.S677R		Atlas-SNP	.											.	TGM6	126	.	0			c.A2029C						.						129	106	114					20																	2413197		2203	4300	6503	SO:0001583	missense	343641	exon13			TCCAAAAGTGGCC	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"Transglutaminases"	16255	protein-coding gene	gene with protein product	"spinocerebellar ataxia 35"	613900	"transglutaminase 3-like"	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.2029A>C	chr20.hg19:g.2413197A>C	ENSP00000202625:p.Ser677Arg	100.0	0.0		151.0	34.0	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Missense_Mutation	SNP	ENST00000202625.2	hg19	CCDS13025.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.114366	0.77210	.	.	ENSG00000166948	ENST00000202625	T	0.69306	-0.39	4.97	4.97	0.65823	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.291279	0.39341	N	0.001387	T	0.80380	0.4612	M	0.81497	2.545	0.80722	D	1	D	0.69078	0.997	D	0.70016	0.967	T	0.82428	-0.0462	10	0.62326	D	0.03	-16.3713	11.2164	0.48830	1.0:0.0:0.0:0.0	.	677	O95932	TGM3L_HUMAN	R	677	ENSP00000202625:S677R	ENSP00000202625:S677R	S	+	1	0	TGM6	2361197	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.974000	0.63771	2.205000	0.71048	0.533000	0.62120	AGT	.	.		0.587	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		C	2413197	A	C	2413197	3	2	176	1	0	0	0	0	1	0	0	0	15849	72	3	5	2079	5	TGM6	20	2413197	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10		2413197	60612323	170	26569										
PLTP	5360	hgsc.bcm.edu	37	chr20	44533489	44533489	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cctcagcagcatgtccaggtCgtggggcacctgaacagggg	15	12	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr20:44533489C>T	ENST00000477313.1	-	9	1486	c.892G>A	c.(892-894)Gac>Aac	p.D298N	PLTP_ENST00000354050.4_Missense_Mutation_p.D246N|PLTP_ENST00000542937.1_Missense_Mutation_p.D318N|PLTP_ENST00000420868.2_Missense_Mutation_p.D203N|PLTP_ENST00000372420.1_Missense_Mutation_p.D210N|PLTP_ENST00000372431.3_Missense_Mutation_p.D298N			P55058	PLTP_HUMAN	phospholipid transfer protein	298					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)			endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				ATGTCCAGGTCGTGGGGCACC	0.602																																					p.D298N		Atlas-SNP	.											.	PLTP	49	.	0			c.G892A						.						110	104	106					20																	44533489		2203	4300	6503	SO:0001583	missense	5360	exon10			CCAGGTCGTGGGG	L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.892G>A	chr20.hg19:g.44533489C>T	ENSP00000417138:p.Asp298Asn	192.0	0.0		292.0	109.0	NM_006227	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Missense_Mutation	SNP	ENST00000477313.1	hg19	CCDS13386.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.922731	0.73213	.	.	ENSG00000100979	ENST00000372420;ENST00000372431;ENST00000354050;ENST00000477313;ENST00000542937;ENST00000420868	T;T;T;T;T;T	0.09817	2.94;2.94;2.94;2.94;2.94;2.94	5.0	5.0	0.66597	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.150336	0.64402	D	0.000014	T	0.27731	0.0682	M	0.67953	2.075	0.58432	D	0.999998	D;D;D;D;D;D;D	0.71674	0.997;0.997;0.997;0.997;0.996;0.997;0.998	P;P;P;P;P;P;P	0.61070	0.883;0.883;0.834;0.883;0.868;0.883;0.883	T	0.00503	-1.1701	10	0.33141	T	0.24	-14.5091	16.6413	0.85127	0.0:1.0:0.0:0.0	.	203;203;210;298;246;298;318	E7EV16;B4DRB4;B4DDD5;Q53H91;P55058-2;P55058;B3KUE5	.;.;.;.;.;PLTP_HUMAN;.	N	210;298;246;298;318;203	ENSP00000361497:D210N;ENSP00000361508:D298N;ENSP00000335290:D246N;ENSP00000417138:D298N;ENSP00000440296:D318N;ENSP00000411671:D203N	ENSP00000335290:D246N	D	-	1	0	PLTP	43966896	0.999000	0.42202	0.098000	0.21074	0.613000	0.37349	4.253000	0.58791	2.610000	0.88304	0.563000	0.77884	GAC	.	.		0.602	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		T	44533489	C	T	44533489	3	4	176	1	0	0	0	0	1	0	0	0	12123	884	31	1	617	1	PLTP	20	44533489	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	42120292	44533489	18492031	171	26570										
C20orf151	140893	hgsc.bcm.edu	37	chr20	60989520	60989520	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ggctctgaaggtgcagggacAgggggcggtttaggaggcag	21	6	1	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr20:60989520A>T	ENST00000252998.1	-	10	1043	c.887T>A	c.(886-888)cTg>cAg	p.L296Q		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	296						extracellular space (GO:0005615)											GTGCAGGGACAGGGGGCGGTT	0.711																																					p.L296Q		Atlas-SNP	.											.	.	.	.	0			c.T887A						.						3	5	4					20																	60989520		1759	3697	5456	SO:0001583	missense	140893	exon10			AGGGACAGGGGGC	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"hypothetical protein LOC140893"		"chromosome 20 open reading frame 151"	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.887T>A	chr20.hg19:g.60989520A>T	ENSP00000252998:p.Leu296Gln	88.0	0.0		128.0	43.0	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	hg19	CCDS13498.1	.	.	.	.	.	.	.	.	.	.	A	12.31	1.898564	0.33535	.	.	ENSG00000130701	ENST00000252998	T	0.38722	1.12	5.05	3.93	0.45458	.	0.111009	0.39407	N	0.001378	T	0.51363	0.1670	L	0.58810	1.83	0.09310	N	0.999997	D	0.60160	0.987	P	0.59703	0.862	T	0.41106	-0.9527	10	0.23891	T	0.37	-10.5506	10.3904	0.44164	0.8354:0.1646:0.0:0.0	.	296	Q8NC74	CT151_HUMAN	Q	296	ENSP00000252998:L296Q	ENSP00000252998:L296Q	L	-	2	0	C20orf151	60422915	0.137000	0.22531	0.006000	0.13384	0.007000	0.05969	2.874000	0.48483	0.738000	0.32606	0.402000	0.26972	CTG	.	.		0.711	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833		T	60989520	A	T	60989520	3	4	176	1	0	0	0	0	1	0	0	0	2093	188	7	4	1127	4	C20orf151	20	60989520	Missense_Mutation	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10	16456031	60989520	2036000	172	26571										
ITGB2	3689	hgsc.bcm.edu	37	chr21	46321441	46321441	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cctgcatcatggcgtccagcCcaccctcgggtgcatccagg	11	17	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr21:46321441C>A	ENST00000397850.2	-	7	1159	c.707G>T	c.(706-708)gGg>gTg	p.G236V	ITGB2_ENST00000397852.1_Missense_Mutation_p.G236V|ITGB2_ENST00000355153.4_Missense_Mutation_p.G236V|ITGB2_ENST00000397857.1_Missense_Mutation_p.G236V|ITGB2_ENST00000302347.5_Missense_Mutation_p.G236V|ITGB2_ENST00000397854.3_Missense_Mutation_p.G179V			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	236	VWFA.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	GGCGTCCAGCCCACCCTCGGG	0.652																																					p.G236V		Atlas-SNP	.											.	ITGB2	107	.	0			c.G707T						.						88	82	84					21																	46321441		2203	4300	6503	SO:0001583	missense	3689	exon6			TCCAGCCCACCCT	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.707G>T	chr21.hg19:g.46321441C>A	ENSP00000380948:p.Gly236Val	72.0	0.0		79.0	37.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	hg19	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.163397	0.78226	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347;ENST00000545414;ENST00000320216	D;D;D;D;D;D;D	0.95238	-3.65;-3.65;-3.65;-3.65;-3.65;-3.65;-3.65	4.2	4.2	0.49525	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	.	.	.	.	D	0.97321	0.9124	M	0.88031	2.925	0.80722	D	1	D;D	0.76494	0.985;0.999	D;D	0.74023	0.955;0.982	D	0.98021	1.0371	9	0.87932	D	0	.	14.0752	0.64887	0.0:1.0:0.0:0.0	.	179;236	A8MYE6;P05107	.;ITB2_HUMAN	V	236;236;179;236;236;236;179;227	ENSP00000380950:G236V;ENSP00000380955:G236V;ENSP00000380952:G179V;ENSP00000347279:G236V;ENSP00000380948:G236V;ENSP00000303242:G236V;ENSP00000317697:G227V	ENSP00000303242:G236V	G	-	2	0	ITGB2	45145869	1.000000	0.71417	0.998000	0.56505	0.682000	0.39822	7.201000	0.77847	2.175000	0.68902	0.555000	0.69702	GGG	.	.		0.652	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		A	46321441	C	A	46321441	3	1	176	1	0	0	0	0	1	0	0	0	7903	623	22	3	1646	3	ITGB2	21	46321441	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10		46321441	1808454	173	26572										
LSS	4047	hgsc.bcm.edu	37	chr21	47614405	47614405	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gacggtcccgtcgtccccacCgaacggccatcagccccatc	9	20	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr21:47614405C>T	ENST00000397728.3	-	20	2066	c.1988G>A	c.(1987-1989)cGg>cAg	p.R663Q	LSS_ENST00000356396.4_Splice_Site_p.R663Q|AP001468.1_ENST00000594486.1_5'Flank|LSS_ENST00000457828.2_Splice_Site_p.R583Q|LSS_ENST00000522411.1_Splice_Site_p.R652Q	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	663					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					TCGTCCCCACCGAACGGCCAT	0.617																																					p.R663Q	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.G1988A						.						81	66	71					21																	47614405		2203	4300	6503	SO:0001630	splice_region_variant	4047	exon20			CCCCACCGAACGG	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.1988+1G>A	chr21.hg19:g.47614405C>T		51.0	0.0		67.0	29.0	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	hg19	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.506819	0.44558	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.07	5.07	0.68467	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.043393	0.85682	D	0.000000	T	0.25195	0.0612	L	0.39020	1.185	0.80722	D	1	D;D	0.71674	0.997;0.998	P;B	0.48227	0.571;0.446	T	0.00958	-1.1500	9	.	.	.	.	18.4342	0.90638	0.0:1.0:0.0:0.0	.	652;663	E9PEI9;P48449	.;ERG7_HUMAN	Q	663;583;663;652	ENSP00000348762:R663Q;ENSP00000409191:R583Q;ENSP00000380837:R663Q;ENSP00000429133:R652Q	.	R	-	2	0	LSS	46438833	1.000000	0.71417	1.000000	0.80357	0.063000	0.16089	7.201000	0.77847	2.523000	0.85059	0.655000	0.94253	CGG	.	.		0.617	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		Missense_Mutation	T	47614405	C	T	47614405	5	4	176	1	0	0	0	0	0	0	1	0	9074	666	23	1	222	1	LSS	21	47614405	Splice_Site	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	1292964	47614405	515490	174	26573										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18347692	18347692	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tctctcagtggagctggccaCggcgttggcccgtccgtttg	14	13	2	0	rs199950640	byFrequency	TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr22:18347692C>T	ENST00000441493.2	-	19	2930	c.2578G>A	c.(2578-2580)Gtg>Atg	p.V860M	MICAL3_ENST00000585038.1_Missense_Mutation_p.V984M|MICAL3_ENST00000400561.2_Missense_Mutation_p.V860M|MICAL3_ENST00000383094.3_Missense_Mutation_p.V860M|MICAL3_ENST00000444520.1_Missense_Mutation_p.V860M|MICAL3_ENST00000207726.7_Missense_Mutation_p.V888M|MICAL3_ENST00000429452.1_Missense_Mutation_p.V984M|MICAL3_ENST00000414725.2_Missense_Mutation_p.V888M	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	860					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		GAGCTGGCCACGGCGTTGGCC	0.592													C|||	2	0.000399361	0	0	5008	,	,		11947	0		0.002	False		,,,				2504	0				p.V984M		Atlas-SNP	.											MICA3_HUMAN,NS,carcinoma,0,3	MICAL3	53	.	0			c.G2950A						.	C	MET/VAL,MET/VAL,MET/VAL	0,3136		0,0,1568	95	92	93		2578,2950,2578	-5.7	0	22		93	8,7156		0,8,3574	yes	missense,missense,missense	MICAL3	NM_001122731.1,NM_001136004.1,NM_015241.2	21,21,21	0,8,5142	TT,TC,CC		0.1117,0.0,0.0777	benign,benign,benign	860/967,984/1074,860/2003	18347692	8,10292	1568	3582	5150	SO:0001583	missense	57553	exon23			TGGCCACGGCGTT	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.2578G>A	chr22.hg19:g.18347692C>T	ENSP00000416015:p.Val860Met	97.0	0.0		97.0	14.0	NM_001136004	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	C	8.157	0.788774	0.16258	0.0	0.001117	ENSG00000093100;ENSG00000093100;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156	ENST00000441493;ENST00000429452;ENST00000400561;ENST00000444520;ENST00000414725;ENST00000383094;ENST00000207726	T;T;T;T;T;T;T	0.69435	-0.02;-0.4;-0.14;-0.14;-0.12;-0.13;-0.12	5.72	-5.71	0.02413	.	3.503140	0.00698	N	0.000764	T	0.62998	0.2474	N	0.19112	0.55	0.09310	N	1	D;P;P;P;B	0.71674	0.998;0.627;0.715;0.539;0.025	P;B;B;B;B	0.59171	0.853;0.172;0.073;0.107;0.005	T	0.60161	-0.7317	10	0.48119	T	0.1	.	7.7346	0.28806	0.0:0.3671:0.1925:0.4404	.	984;888;860;860;860	B2RXJ5;Q7RTP6-3;Q7RTP6-2;Q7RTP6-4;Q7RTP6	.;.;.;.;MICA3_HUMAN	M	860;984;860;860;888;860;888	ENSP00000416015:V860M;ENSP00000414846:V984M;ENSP00000383406:V860M;ENSP00000410315:V860M;ENSP00000391827:V888M;ENSP00000372574:V860M;ENSP00000207726:V888M	ENSP00000207726:V888M	V	-	1	0	XXbac-B461K10.4;MICAL3	16727692	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-2.043000	0.01413	-0.782000	0.04541	0.655000	0.94253	GTG	.	.		0.592	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18347692	C	T	18347692	3	4	176	1	0	0	0	0	1	0	0	0	9580	536	19	1	3835	1	MICAL3	22	18347692	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10		18347692	32956874	175	26574										
TXN2	25828	hgsc.bcm.edu	37	chr22	36863964	36863964	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	cacagtgggcaccgctgacaCctgggtggagaggacaaggg	17	10	0	2			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr22:36863964C>G	ENST00000216185.2	-	4	854	c.388G>C	c.(388-390)Gtg>Ctg	p.V130L	TXN2_ENST00000416967.1_Splice_Site_p.V28L|TXN2_ENST00000487725.1_5'UTR|TXN2_ENST00000403313.1_Splice_Site_p.V130L			Q99757	THIOM_HUMAN	thioredoxin 2	130	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|cellular response to nutrient levels (GO:0031669)|glycerol ether metabolic process (GO:0006662)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)	dendrite (GO:0030425)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)	protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|lung(1)|prostate(1)	3						ACCGCTGACACCTGGGTGGAG	0.557																																					p.V130L		Atlas-SNP	.											.	TXN2	15	.	0			c.G388C						.						82	67	72					22																	36863964		2203	4300	6503	SO:0001630	splice_region_variant	25828	exon4			CTGACACCTGGGT	U78678	CCDS13928.1	22q13.1	2008-06-11			ENSG00000100348	ENSG00000100348			17772	protein-coding gene	gene with protein product		609063				9006939, 17220299	Standard	NM_012473		Approved	MT-TRX	uc003apk.1	Q99757	OTTHUMG00000150596	ENST00000216185.2:c.388-1G>C	chr22.hg19:g.36863964C>G		65.0	0.0		77.0	54.0	NM_012473	Q5JZA0|Q6FH60|Q9UH29	Missense_Mutation	SNP	ENST00000216185.2	hg19	CCDS13928.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072645	0.76415	.	.	ENSG00000100348	ENST00000216185;ENST00000403313	T;T	0.07021	3.23;3.23	5.64	5.64	0.86602	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.130037	0.53938	D	0.000060	T	0.37100	0.0991	M	0.86953	2.85	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.26430	-1.0103	10	0.72032	D	0.01	-1.0201	19.7137	0.96107	0.0:1.0:0.0:0.0	.	130	Q99757	THIOM_HUMAN	L	130	ENSP00000216185:V130L;ENSP00000385393:V130L	ENSP00000216185:V130L	V	-	1	0	TXN2	35193910	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	7.352000	0.79404	2.655000	0.90218	0.462000	0.41574	GTG	.	.		0.557	TXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319016.1	NM_012473	Missense_Mutation	G	36863964	C	G	36863964	5	3	176	1	0	0	0	0	0	0	1	0	16806	521	18	4	116	4	TXN2	22	36863964	Splice_Site	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	18516272	36863964	14440602	176	26575										
MICALL1	85377	hgsc.bcm.edu	37	chr22	38328562	38328562	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ccaggcactgttgggcaggtCcaggctgaccagtacatccc	12	14	0	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chr22:38328562C>G	ENST00000215957.6	+	11	2145	c.2019C>G	c.(2017-2019)gtC>gtG	p.V673V	MICALL1_ENST00000402631.1_3'UTR	NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	673	RAB-binding domain (RBD); mediates the interaction with RAB13 and RAB35 and intramolecular interaction with the CH domain.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					TTGGGCAGGTCCAGGCTGACC	0.642																																					p.V673V		Atlas-SNP	.											.	MICALL1	53	.	0			c.C2019G						.						65	68	67					22																	38328562		2203	4300	6503	SO:0001819	synonymous_variant	85377	exon11			GCAGGTCCAGGCT	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"molecule interacting with Rab13"					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.2019C>G	chr22.hg19:g.38328562C>G		101.0	0.0		114.0	56.0	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Silent	SNP	ENST00000215957.6	hg19	CCDS13961.1	.	.	.	.	.	.	.	.	.	.	C	11.29	1.594261	0.28445	.	.	ENSG00000100139	ENST00000454685	.	.	.	5.48	2.15	0.27550	.	.	.	.	.	T	0.43100	0.1232	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24835	-1.0149	4	.	.	.	.	1.5047	0.02484	0.1226:0.3697:0.2385:0.2692	.	.	.	.	A	249	.	.	P	+	1	0	MICALL1	36658508	0.511000	0.26179	1.000000	0.80357	0.803000	0.45373	-0.280000	0.08468	0.262000	0.21774	0.491000	0.48974	CCA	.	.		0.642	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		G	38328562	C	G	38328562	2	3	176	1	0	0	0	0	0	0	0	1	9582	842	30	4		4	MICALL1	22	38328562	Silent	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	1464598	38328562	12976004	177	26576										
MOSPD2	158747	hgsc.bcm.edu	37	chrX	14915270	14915270	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	ttggacaaaaagaagctcatAgcattctggttggaacgtta	10	6	2	1			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chrX:14915270A>T	ENST00000380492.3	+	5	475	c.387A>T	c.(385-387)atA>atT	p.I129I	MOSPD2_ENST00000482354.1_Silent_p.I129I|MOSPD2_ENST00000495110.1_3'UTR	NM_001177475.1|NM_152581.3	NP_001170946.1|NP_689794.1	Q8NHP6	MSPD2_HUMAN	motile sperm domain containing 2	129	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	Hepatocellular(33;0.183)					AGAAGCTCATAGCATTCTGGT	0.358																																					p.I129I		Atlas-SNP	.											.	MOSPD2	46	.	0			c.A387T						.						148	138	142					X																	14915270		2203	4300	6503	SO:0001819	synonymous_variant	158747	exon5			GCTCATAGCATTC	AL834345	CCDS14162.1	Xp22.31	2006-03-16			ENSG00000130150	ENSG00000130150			28381	protein-coding gene	gene with protein product						15533722	Standard	NM_152581		Approved	MGC26706	uc004cwi.3	Q8NHP6	OTTHUMG00000021170	ENST00000380492.3:c.387A>T	chrX.hg19:g.14915270A>T		461.0	0.0		485.0	227.0	NM_152581	Q8N3H2|Q8NA83	Silent	SNP	ENST00000380492.3	hg19	CCDS14162.1																																																																																			.	.		0.358	MOSPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055837.1	NM_152581		T	14915270	A	T	14915270	2	4	176	1	0	0	0	0	0	0	0	1	9725	410	15	4		4	MOSPD2	23	14915270	Silent	SNP	A	TCGA-DD-AACZ-01A-11D-A40R-10		14915270	140355290	178	26577										
DMD	1756	hgsc.bcm.edu	37	chrX	32716095	32716095	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	gaagaagttctctcatatccCtgtgctagactgaccgtgat	9	10	2	4			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chrX:32716095C>A	ENST00000357033.4	-	9	1058	c.852G>T	c.(850-852)caG>caT	p.Q284H	DMD_ENST00000288447.4_Missense_Mutation_p.Q276H|DMD_ENST00000378677.2_Missense_Mutation_p.Q280H	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	284					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TCTCATATCCCTGTGCTAGAC	0.502																																					p.Q284H		Atlas-SNP	.											.	DMD	2127	.	0			c.G852T						.						130	90	104					X																	32716095		2202	4299	6501	SO:0001583	missense	1756	exon9			ATATCCCTGTGCT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.852G>T	chrX.hg19:g.32716095C>A	ENSP00000354923:p.Gln284His	173.0	0.0		171.0	46.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.598076	0.66332	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	T;T;T	0.74106	-0.02;-0.01;-0.81	5.63	3.86	0.44501	.	0.000000	0.35436	U	0.003207	T	0.77968	0.4210	L	0.59436	1.845	0.80722	D	1	P;P;P;P	0.52061	0.93;0.95;0.844;0.917	P;P;B;P	0.53809	0.564;0.735;0.428;0.548	T	0.77536	-0.2551	10	0.66056	D	0.02	.	11.2987	0.49292	0.0:0.8487:0.0:0.1513	.	276;276;284;280	Q4G0X0;P11532-4;P11532;E9PDN5	.;.;DMD_HUMAN;.	H	276;280;284;284;161;276	ENSP00000367948:Q280H;ENSP00000354923:Q284H;ENSP00000288447:Q276H	ENSP00000288447:Q276H	Q	-	3	2	DMD	32626016	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	3.506000	0.53364	0.541000	0.28827	0.538000	0.68166	CAG	.	.		0.502	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32716095	C	A	32716095	3	1	176	1	0	0	0	0	1	0	0	0	4582	680	24	3	10732	3	DMD	23	32716095	Missense_Mutation	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	17800825	32716095	122554465	179	26578										
DCAF12L1	139170	hgsc.bcm.edu	37	chrX	125686535	125686535	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	tgcgacggcgagctctcggcGtccgcctcgaccgcgggcgc	16	17	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chrX:125686535G>A	ENST00000371126.1	-	1	299	c.57C>T	c.(55-57)gaC>gaT	p.D19D		NM_178470.4	NP_848565.2	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	19			D -> G (in dbSNP:rs11095722). {ECO:0000269|PubMed:15489334}.					p.G19G(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(39)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68						AGCTCTCGGCGTCCGCCTCGA	0.726																																					p.D19D		Atlas-SNP	.											.	DCAF12L1	135	.	1	Substitution - coding silent(1)	prostate(1)	c.C57T						.						17	21	19					X																	125686535		2074	4074	6148	SO:0001819	synonymous_variant	139170	exon1			CTCGGCGTCCGCC	BC035674	CCDS14610.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198889	ENSG00000198889		"WD repeat domain containing"	29395	protein-coding gene	gene with protein product			"WD repeat domain 40B"	WDR40B		12477932	Standard	NM_178470		Approved	KIAA1892L	uc004eul.3	Q5VU92	OTTHUMG00000022353	ENST00000371126.1:c.57C>T	chrX.hg19:g.125686535G>A		139.0	0.0		113.0	46.0	NM_178470	Q8IYK3	Silent	SNP	ENST00000371126.1	hg19	CCDS14610.1																																																																																			.	.		0.726	DCAF12L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058186.1	NM_178470		A	125686535	G	A	125686535	2	1	176	1	0	0	0	0	0	0	0	1	4266	1136	40	1		1	DCAF12L1	23	125686535	Silent	SNP	G	TCGA-DD-AACZ-01A-11D-A40R-10	92970440	125686535	29584025	180	26579										
ELF4	2000	hgsc.bcm.edu	37	chrX	129205014	129205014	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	8	1	1.0231372812018	1.48674636174636	0.861881948838471	0.649916646820672	1	0	catcatcccaacagctcctaCcttagtgcccgccccattgt	5	18	1	0			TCGA-DD-AACZ-01A-11D-A40R-10	TCGA-DD-AACZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f597b1b-500d-482d-ade1-61d7dffef94e	437561b3-e574-4171-b2ca-dafac20f5230	g.chrX:129205014C>G	ENST00000308167.5	-	7	1189		c.e7+1		ELF4_ENST00000335997.7_Splice_Site	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)											breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						ACAGCTCCTACCTTAGTGCCC	0.522			T	ERG	AML																																.		Atlas-SNP	.		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	.	ELF4	67	.	0			c.809+1G>C						.						201	172	182					X																	129205014		2203	4300	6503	SO:0001630	splice_region_variant	2000	exon8			CTCCTACCTTAGT	U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.809+1G>C	chrX.hg19:g.129205014C>G		65.0	0.0		77.0	13.0	NM_001421		Splice_Site	SNP	ENST00000308167.5	hg19	CCDS14617.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.248415	0.59103	.	.	ENSG00000102034	ENST00000335997;ENST00000308167	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9152	0.70792	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ELF4	129032695	1.000000	0.71417	0.989000	0.46669	0.499000	0.33736	7.775000	0.85489	2.105000	0.64084	0.466000	0.42574	.	.	.		0.522	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421	Intron	G	129205014	C	G	129205014	5	3	176	1	0	0	0	0	0	0	1	0	5058	521	18	4	1193	4	ELF4	23	129205014	Splice_Site	SNP	C	TCGA-DD-AACZ-01A-11D-A40R-10	3518479	129205014	26065546	181	26580										
AGRN	375790	hgsc.bcm.edu	37	chr1	980903	980903	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	atggccggagtggctgtacaCgtgagtgacagggcccagga	17	9	0	2	rs138248828	byFrequency	TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:980903C>A	ENST00000379370.2	+	14	2586	c.2536C>A	c.(2536-2538)Ccc>Acc	p.P846T		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	846	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		TGGCTGTACACGTGAGTGACA	0.657																																					p.P846T		Atlas-SNP	.											.	AGRN	110	.	0			c.C2536A						.						39	36	37					1																	980903		2203	4300	6503	SO:0001630	splice_region_variant	375790	exon14			TGTACACGTGAGT	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"Proteoglycans / Extracellular Matrix : Other"	329	protein-coding gene	gene with protein product	"agrin proteoglycan"	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.2536+1C>A	chr1.hg19:g.980903C>A		48.0	0.0		27.0	26.0	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	hg19	CCDS30551.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.710250	0.68730	.	.	ENSG00000188157	ENST00000379370	T	0.80909	-1.43	5.36	5.36	0.76844	EGF-like, laminin (2);	0.000000	0.64402	D	0.000003	D	0.92224	0.7534	M	0.92784	3.345	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	D	0.92983	0.6408	10	0.49607	T	0.09	-26.0382	19.0743	0.93154	0.0:1.0:0.0:0.0	.	846	O00468	AGRIN_HUMAN	T	846	ENSP00000368678:P846T	ENSP00000368678:P846T	P	+	1	0	AGRN	970766	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	4.432000	0.59922	2.520000	0.84964	0.655000	0.94253	CCC	.	C|1.000;T|0.000		0.657	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	Missense_Mutation	A	980903	C	A	980903	5	1	177	1	0	0	0	0	0	0	1	0	397	550	19	1	2590	1	AGRN	1	980903	Splice_Site	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10		980903	248269718	1	26581										
ESPN	83715	hgsc.bcm.edu	37	chr1	6505818	6505819	+	Frame_Shift_Ins	INS	-	-	C													0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gcacgattgggaagcccacaINScccccaccacccccacccag							TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:6505818_6505819insC	ENST00000377828.1	+	7	1455_1456	c.1287_1288insC	c.(1288-1290)cccfs	p.P430fs	RP1-202O8.2_ENST00000419034.1_RNA|ESPN_ENST00000461727.1_5'Flank	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	430	Pro-rich.				locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GGAAGcccacacccccaccacc	0.688																																					p.T429fs		Atlas-INDEL	.											.	ESPN	32	.	0			c.1287_1288insC						.																																			SO:0001589	frameshift_variant	83715	exon7			.	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"Ankyrin repeat domain containing"	13281	protein-coding gene	gene with protein product		606351	"deafness, autosomal recessive 36"	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.1292dupC	chr1.hg19:g.6505823_6505823dupC	ENSP00000367059:p.Pro430fs	65.0	0.0		61.0	10.0	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Frame_Shift_Ins	INS	ENST00000377828.1	hg19	CCDS70.1																																																																																			.	.		0.688	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		C	6505819	-	C	6505818	7	5	177	1	0	1	1	0	0	0	0	0	5256	146	6	0	1313	0	ESPN	1	6505818	Frame_Shift_Ins	INS	-	TCGA-DD-AAD0-01A-11D-A40R-10	5524915	6505818	242744803	2	26582										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117122291	117122291	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tcgtcgtcgtcgtcgtcgtcCtcctcctcctcctcctccct	6	21	0	0	rs569343519	byFrequency	TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:117122291C>G	ENST00000369486.3	-	10	3822	c.3057G>C	c.(3055-3057)gaG>gaC	p.E1019D	IGSF3_ENST00000369483.1_Missense_Mutation_p.E1039D|IGSF3_ENST00000318837.6_Missense_Mutation_p.E1039D	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1019	Ig-like C2-type 8.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		cgtcgtcgtcctcctcctcct	0.637													C|||	12	0.00239617	0.0023	0	5008	,	,		18566	0.003		0	False		,,,				2504	0.0061				p.E1039D		Atlas-SNP	.											IGSF3_ENST00000369483,NS,carcinoma,0,4	IGSF3	294	.	0			c.G3117C						.						28	29	29					1																	117122291		2203	4300	6503	SO:0001583	missense	3321	exon11			GTCGTCCTCCTCC	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3057G>C	chr1.hg19:g.117122291C>G	ENSP00000358498:p.Glu1019Asp	68.0	0.0		70.0	4.0	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	0.860	-0.735766	0.03111	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.02863	4.15;4.13;4.13	2.7	-5.4	0.02656	Immunoglobulin subtype (1);Immunoglobulin-like (1);	1.696000	0.03619	N	0.236120	T	0.00384	0.0012	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48768	-0.9006	10	0.15952	T	0.53	-1.3732	1.6073	0.02687	0.152:0.1895:0.1511:0.5074	.	1019;1039	O75054;A6NJZ6	IGSF3_HUMAN;.	D	1019;1039;1039	ENSP00000358498:E1019D;ENSP00000358495:E1039D;ENSP00000321184:E1039D	ENSP00000321184:E1039D	E	-	3	2	IGSF3	116923814	0.018000	0.18449	0.000000	0.03702	0.117000	0.20001	-1.573000	0.02134	-1.538000	0.01734	0.462000	0.41574	GAG	.	.		0.637	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		G	117122291	C	G	117122291	3	3	177	1	0	0	0	0	1	0	0	0	7610	680	24	4	535	4	IGSF3	1	117122291	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	110616473	117122291	132128330	3	26583										
ATP8B2	57198	hgsc.bcm.edu	37	chr1	154318730	154318730	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gtccccgagcagcggagcatGgagtaccctaagctgtatga	13	11	0	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:154318730G>A	ENST00000368489.3	+	25	2901	c.2901G>A	c.(2899-2901)atG>atA	p.M967I		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	953					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AGCGGAGCATGGAGTACCCTA	0.582																																					p.M967I		Atlas-SNP	.											.	ATP8B2	158	.	0			c.G2901A						.						92	90	90					1																	154318730		2203	4300	6503	SO:0001583	missense	57198	exon25			GAGCATGGAGTAC	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.2901G>A	chr1.hg19:g.154318730G>A	ENSP00000357475:p.Met967Ile	115.0	0.0		151.0	38.0	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	hg19	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.489484	0.44249	.	.	ENSG00000143515	ENST00000368489	T	0.69306	-0.39	4.34	4.34	0.51931	.	0.292573	0.33217	N	0.005159	T	0.37919	0.1021	N	0.13327	0.33	0.80722	D	1	B	0.24186	0.099	B	0.28011	0.085	T	0.38650	-0.9651	10	0.40728	T	0.16	.	15.581	0.76439	0.0:0.0:1.0:0.0	.	967	P98198-3	.	I	967	ENSP00000357475:M967I	ENSP00000357475:M967I	M	+	3	0	ATP8B2	152585354	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.421000	0.59848	2.211000	0.71520	0.561000	0.74099	ATG	.	.		0.582	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		A	154318730	G	A	154318730	3	1	177	1	0	0	0	0	1	0	0	0	1195	1348	47	3	3129	3	ATP8B2	1	154318730	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	37196439	154318730	94931891	4	26584										
TMEM79	84283	hgsc.bcm.edu	37	chr1	156261286	156261286	+	Missense_Mutation	SNP	T	T	C													0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gtggaacctctactacatgtTcgtggtggagccggagcgca							TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:156261286T>C	ENST00000405535.2	+	4	1253	c.1082T>C	c.(1081-1083)tTc>tCc	p.F361S	C1orf85_ENST00000482579.1_5'Flank|TMEM79_ENST00000295694.5_Missense_Mutation_p.F361S|TMEM79_ENST00000357501.2_Silent_p.V122V|TMEM79_ENST00000495881.1_3'UTR	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	361					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					TACTACATGTTCGTGGTGGAG	0.667																																					p.F361S		Atlas-SNP	.											.	TMEM79	43	.	0			c.T1082C						.						127	121	123					1																	156261286		2203	4300	6503	SO:0001583	missense	84283	exon4			ACATGTTCGTGGT	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"mattrin"	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.1082T>C	chr1.hg19:g.156261286T>C	ENSP00000384748:p.Phe361Ser	58.0	0.0		87.0	25.0	NM_032323	B2RE22|D3DVB8	Missense_Mutation	SNP	ENST00000405535.2	hg19	CCDS1138.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.118018	0.77323	.	.	ENSG00000163472	ENST00000295694;ENST00000405535	T;T	0.65732	-0.17;-0.17	5.7	5.7	0.88788	.	0.112146	0.64402	D	0.000009	T	0.66655	0.2811	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.71892	-0.4455	10	0.87932	D	0	0.8416	14.8012	0.69916	0.0:0.0:0.0:1.0	.	361	Q9BSE2	TMM79_HUMAN	S	361	ENSP00000295694:F361S;ENSP00000384748:F361S	ENSP00000295694:F361S	F	+	2	0	TMEM79	154527910	1.000000	0.71417	0.994000	0.49952	0.537000	0.34900	4.651000	0.61447	2.170000	0.68504	0.533000	0.62120	TTC	.	.		0.667	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		C	156261286	T	C	156261286	3	2	177	1	0	0	0	0	1	0	0	0	16218	1783	62	2	1092	2	TMEM79	1	156261286	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	1942556	156261286	92989335	5	26585	128	2								
TMEM79	84283	hgsc.bcm.edu	37	chr1	156261289	156261289	+	Missense_Mutation	SNP	T	T	C													0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gaacctctactacatgttcgTggtggagccggagcgcatgc							TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:156261289T>C	ENST00000405535.2	+	4	1256	c.1085T>C	c.(1084-1086)gTg>gCg	p.V362A	C1orf85_ENST00000482579.1_5'Flank|TMEM79_ENST00000295694.5_Missense_Mutation_p.V362A|TMEM79_ENST00000357501.2_Silent_p.R123R|TMEM79_ENST00000495881.1_3'UTR	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	362					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					TACATGTTCGTGGTGGAGCCG	0.662																																					p.V362A		Atlas-SNP	.											.	TMEM79	43	.	0			c.T1085C						.						125	119	121					1																	156261289		2203	4300	6503	SO:0001583	missense	84283	exon4			TGTTCGTGGTGGA	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"mattrin"	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.1085T>C	chr1.hg19:g.156261289T>C	ENSP00000384748:p.Val362Ala	59.0	0.0		85.0	23.0	NM_032323	B2RE22|D3DVB8	Missense_Mutation	SNP	ENST00000405535.2	hg19	CCDS1138.1	.	.	.	.	.	.	.	.	.	.	T	8.842	0.942379	0.18281	.	.	ENSG00000163472	ENST00000295694;ENST00000405535	T;T	0.47528	0.84;0.84	5.7	2.15	0.27550	.	0.911947	0.09531	N	0.789595	T	0.10508	0.0257	N	0.08118	0	0.18873	N	0.999984	B	0.06786	0.001	B	0.04013	0.001	T	0.34825	-0.9813	10	0.35671	T	0.21	-4.44	8.6411	0.33978	0.0:0.2219:0.0:0.7781	.	362	Q9BSE2	TMM79_HUMAN	A	362	ENSP00000295694:V362A;ENSP00000384748:V362A	ENSP00000295694:V362A	V	+	2	0	TMEM79	154527913	0.145000	0.22656	0.892000	0.35008	0.021000	0.10359	2.703000	0.47110	0.119000	0.18210	-0.250000	0.11733	GTG	.	.		0.662	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		C	156261289	T	C	156261289	3	2	177	1	0	0	0	0	1	0	0	0	16218	1696	59	2	1095	2	TMEM79	1	156261289	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	3	156261289	92989332	6	26586	128	2								
COPA	1314	hgsc.bcm.edu	37	chr1	160309715	160309715	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gtaccttaatcttatagtcaTctcctccagagacgaacagt	6	11	3	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:160309715T>C	ENST00000241704.7	-	3	441	c.212A>G	c.(211-213)gAt>gGt	p.D71G	COPA_ENST00000368069.3_Missense_Mutation_p.D71G	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	71					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CTTATAGTCATCTCCTCCAGA	0.463																																					p.D71G		Atlas-SNP	.											.	COPA	181	.	0			c.A212G						.						123	126	125					1																	160309715		2203	4300	6503	SO:0001583	missense	1314	exon3			TAGTCATCTCCTC	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"WD repeat domain containing", "Endogenous ligands"	2230	protein-coding gene	gene with protein product	"proxenin", "xenin"	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.212A>G	chr1.hg19:g.160309715T>C	ENSP00000241704:p.Asp71Gly	71.0	0.0		105.0	61.0	NM_001098398	Q5T201|Q8IXZ9	Missense_Mutation	SNP	ENST00000241704.7	hg19	CCDS1202.1	.	.	.	.	.	.	.	.	.	.	T	31	5.063761	0.93898	.	.	ENSG00000122218	ENST00000368069;ENST00000241704	T;T	0.60672	0.17;0.17	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.70561	0.3238	M	0.74467	2.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.75605	-0.3260	10	0.87932	D	0	-19.2365	14.9083	0.70737	0.0:0.0:0.0:1.0	.	71;71	P53621;P53621-2	COPA_HUMAN;.	G	71	ENSP00000357048:D71G;ENSP00000241704:D71G	ENSP00000241704:D71G	D	-	2	0	COPA	158576339	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.191000	0.70037	0.533000	0.62120	GAT	.	.		0.463	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371		C	160309715	T	C	160309715	3	2	177	1	0	0	0	0	1	0	0	0	3729	1435	50	2	3613	2	COPA	1	160309715	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	4048426	160309715	88940906	7	26587										
USF1	7391	hgsc.bcm.edu	37	chr1	161011957	161011957	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ctgatggcgccagttccctcAgtttggccatccagctgccc	10	16	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:161011957A>C	ENST00000368021.3	-	5	429	c.225T>G	c.(223-225)acT>acG	p.T75T	USF1_ENST00000368020.1_Silent_p.T75T|USF1_ENST00000435396.1_Silent_p.T16T|USF1_ENST00000368019.1_Silent_p.T75T	NM_007122.3	NP_009053.1	P22415	USF1_HUMAN	upstream transcription factor 1	75					carbon catabolite regulation of transcription (GO:0045990)|cellular response to insulin stimulus (GO:0032869)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|late viral transcription (GO:0019086)|lipid homeostasis (GO:0055088)|negative regulation of fibrinolysis (GO:0051918)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter by glucose (GO:0000430)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CAGTTCCCTCAGTTTGGCCAT	0.527																																					p.T75T		Atlas-SNP	.											.	USF1	29	.	0			c.T225G						.						76	67	70					1																	161011957		2203	4300	6503	SO:0001819	synonymous_variant	7391	exon5			TCCCTCAGTTTGG	BC035505	CCDS1214.1	1q22-q23	2013-05-21			ENSG00000158773	ENSG00000158773		"Basic helix-loop-helix proteins"	12593	protein-coding gene	gene with protein product		191523				8486371	Standard	NM_007122		Approved	UEF, MLTFI, bHLHb11	uc031pqv.1	P22415	OTTHUMG00000031472	ENST00000368021.3:c.225T>G	chr1.hg19:g.161011957A>C		87.0	0.0		167.0	53.0	NM_001276373	B2RBZ4|Q5SY46|Q7Z5Y1	Silent	SNP	ENST00000368021.3	hg19	CCDS1214.1																																																																																			.	.		0.527	USF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077050.1	NM_007122		C	161011957	A	C	161011957	2	2	177	1	0	0	0	0	0	0	0	1	17047	175	7	5		5	USF1	1	161011957	Silent	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	702242	161011957	88238664	8	26588										
C1orf112	55732	hgsc.bcm.edu	37	chr1	169799444	169799444	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cttagtgctaatatgatcacCtctttgttagctatggatgc	8	8	2	1	rs532518246	byFrequency	TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:169799444C>A	ENST00000286031.6	+	14	2059	c.1359C>A	c.(1357-1359)acC>acA	p.T453T	C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Silent_p.T453T	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	453										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					ATATGATCACCTCTTTGTTAG	0.333																																					p.T453T		Atlas-SNP	.											.	C1orf112	74	.	0			c.C1359A						.						226	209	215					1																	169799444		2203	4300	6503	SO:0001819	synonymous_variant	55732	exon14			GATCACCTCTTTG	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.1359C>A	chr1.hg19:g.169799444C>A		49.0	0.0		84.0	34.0	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	hg19	CCDS1285.1																																																																																			.	.		0.333	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		A	169799444	C	A	169799444	2	1	177	1	0	0	0	0	0	0	0	1	1987	668	24	3		3	C1orf112	1	169799444	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	8787487	169799444	79451177	9	26589										
CR1	1378	hgsc.bcm.edu	37	chr1	207785177	207785177	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cgccccagggagactggagcCctgaagcccctagatgtaca	12	14	0	3			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:207785177C>T	ENST00000367049.4	+	38	6451	c.6451C>T	c.(6451-6453)Cct>Tct	p.P2151S	CR1_ENST00000400960.2_Missense_Mutation_p.P1701S|CR1_ENST00000367051.1_Missense_Mutation_p.P1701S|CR1_ENST00000367052.1_Missense_Mutation_p.P1701S|CR1_ENST00000367053.1_Missense_Mutation_p.P1701S	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1701					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						AGACTGGAGCCCTGAAGCCCC	0.532																																					p.P2151S		Atlas-SNP	.											.	CR1	354	.	0			c.C6451T						.						127	131	130					1																	207785177		1935	4127	6062	SO:0001583	missense	1378	exon38			TGGAGCCCTGAAG	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6451C>T	chr1.hg19:g.207785177C>T	ENSP00000356016:p.Pro2151Ser	125.0	0.0		189.0	124.0	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	hg19	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	C	9.275	1.046645	0.19748	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08	3.48	2.54	0.30619	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.66086	0.2754	L	0.42008	1.315	0.20196	N	0.999926	D;D	0.89917	0.99;1.0	P;D	0.87578	0.813;0.998	T	0.54268	-0.8319	9	0.10902	T	0.67	.	8.3958	0.32557	0.2316:0.7684:0.0:0.0	.	1701;2151	P17927;E9PDY4	CR1_HUMAN;.	S	1701;1701;1701;1701;2151	ENSP00000356019:P1701S;ENSP00000356018:P1701S;ENSP00000356020:P1701S;ENSP00000383744:P1701S;ENSP00000356016:P2151S	ENSP00000356016:P2151S	P	+	1	0	CR1	205851800	0.158000	0.22850	0.667000	0.29798	0.217000	0.24651	0.347000	0.20014	0.994000	0.38892	0.561000	0.74099	CCT	.	.		0.532	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		T	207785177	C	T	207785177	3	4	177	1	0	0	0	0	1	0	0	0	3842	623	22	3	6601	3	CR1	1	207785177	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	37985733	207785177	41465444	10	26590										
CAMK1G	57172	hgsc.bcm.edu	37	chr1	209785166	209785166	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aacgcagcagctgtggtgcaCcacatgaggaagctacacat	11	11	0	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:209785166C>A	ENST00000009105.1	+	11	1190	c.945C>A	c.(943-945)caC>caA	p.H315Q	CAMK1G_ENST00000494990.1_3'UTR|CAMK1G_ENST00000361322.2_Missense_Mutation_p.H315Q			Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	315	Autoinhibitory domain. {ECO:0000250}.|Calmodulin-binding. {ECO:0000250}.					calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|central_nervous_system(1)|large_intestine(8)|lung(8)|stomach(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		CTGTGGTGCACCACATGAGGA	0.567																																					p.H315Q	Ovarian(163;530 1939 9680 28669 48710)	Atlas-SNP	.											.	CAMK1G	49	.	0			c.C945A						.						95	99	97					1																	209785166		2203	4300	6503	SO:0001583	missense	57172	exon11			GGTGCACCACATG		CCDS1486.1	1q32.2	2012-09-20			ENSG00000008118	ENSG00000008118			14585	protein-coding gene	gene with protein product		614994				12637513	Standard	NM_020439		Approved	VWS1, CLICKIII, dJ272L16.1	uc001hhd.3	Q96NX5	OTTHUMG00000036361	ENST00000009105.1:c.945C>A	chr1.hg19:g.209785166C>A	ENSP00000009105:p.His315Gln	38.0	0.0		72.0	25.0	NM_020439	Q86UH5|Q9Y3J7	Missense_Mutation	SNP	ENST00000009105.1	hg19	CCDS1486.1	.	.	.	.	.	.	.	.	.	.	C	14.81	2.645393	0.47258	.	.	ENSG00000008118	ENST00000009105;ENST00000361322	T;T	0.66638	-0.22;-0.22	5.46	-0.322	0.12713	Protein kinase-like domain (1);	0.315637	0.27518	N	0.019016	T	0.40694	0.1127	N	0.11201	0.11	0.43771	D	0.996295	B;B	0.14438	0.01;0.002	B;B	0.12156	0.007;0.003	T	0.10177	-1.0641	10	0.48119	T	0.1	.	6.6192	0.22794	0.0:0.5171:0.1209:0.362	.	315;315	Q96NX5-2;Q96NX5	.;KCC1G_HUMAN	Q	315	ENSP00000009105:H315Q;ENSP00000354861:H315Q	ENSP00000009105:H315Q	H	+	3	2	CAMK1G	207851789	0.920000	0.31207	1.000000	0.80357	0.993000	0.82548	0.308000	0.19314	0.277000	0.22141	0.558000	0.71614	CAC	.	.		0.567	CAMK1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088526.1	NM_020439		A	209785166	C	A	209785166	3	1	177	1	0	0	0	0	1	0	0	0	2600	506	18	3	983	3	CAMK1G	1	209785166	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	1999989	209785166	39465455	11	26591										
RCOR3	55758	hgsc.bcm.edu	37	chr1	211486101	211486105	+	Frame_Shift_Del	DEL	ATGTA	ATGTA	-													0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	agattttcaagctattgcagAtgtaattggcaacaagactg							TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	ATGTA	ATGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:211486101_211486105delATGTA	ENST00000367005.4	+	10	1082_1086	c.941_945delATGTA	c.(940-945)gatgtafs	p.DV314fs	RCOR3_ENST00000526255.1_3'UTR|RCOR3_ENST00000419091.2_Frame_Shift_Del_p.DV372fs|RCOR3_ENST00000367006.4_Intron|RCOR3_ENST00000452621.2_Frame_Shift_Del_p.DV372fs	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	314	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		GCTATTGCAGATGTAATTGGCAACA	0.415																																					p.372_373del		Atlas-INDEL	.											.	RCOR3	51	.	0			c.1114_1118del						.																																			SO:0001589	frameshift_variant	55758	exon11			.	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.941_945delATGTA	chr1.hg19:g.211486101_211486105delATGTA	ENSP00000355972:p.Asp314fs	154.0	0.0		252.0	77.0	NM_001136225	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Frame_Shift_Del	DEL	ENST00000367005.4	hg19	CCDS31016.1																																																																																			.	.		0.415	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		-	211486105	ATGTA	-	211486101	7	5	177	1	0	1	0	1	0	0	0	0	13199	333	12	0	1157	0	RCOR3	1	211486101	Frame_Shift_Del	DEL	ATGTA	TCGA-DD-AAD0-01A-11D-A40R-10	1700935	211486101	37764520	12	26592										
FBXO28	23219	hgsc.bcm.edu	37	chr1	224340935	224340935	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	acttcaagaattaagggataTatcctctatggcaatggagt	9	6	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:224340935T>G	ENST00000366862.5	+	4	651	c.608T>G	c.(607-609)aTa>aGa	p.I203R	FBXO28_ENST00000424254.2_Intron	NM_015176.3	NP_055991.1	Q9NVF7	FBX28_HUMAN	F-box protein 28	203										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(2)|skin(1)	10	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		TTAAGGGATATATCCTCTATG	0.378																																					p.I203R		Atlas-SNP	.											.	FBXO28	34	.	0			c.T608G						.						132	144	140					1																	224340935		2203	4300	6503	SO:0001583	missense	23219	exon4			GGGATATATCCTC	AK001628	CCDS1539.1, CCDS44320.1	1q42.12	2011-08-12			ENSG00000143756	ENSG00000143756		"F-boxes /  "other""	29046	protein-coding gene	gene with protein product	"centromere protein 30"	609100				9455484	Standard	NM_015176		Approved	FLJ10766, KIAA0483, Fbx28, CENP-30	uc001hoh.3	Q9NVF7	OTTHUMG00000037495	ENST00000366862.5:c.608T>G	chr1.hg19:g.224340935T>G	ENSP00000355827:p.Ile203Arg	86.0	0.0		154.0	53.0	NM_015176	E9PEM8|O75070	Missense_Mutation	SNP	ENST00000366862.5	hg19	CCDS1539.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.741392	0.89573	.	.	ENSG00000143756	ENST00000366862	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.77785	0.4182	M	0.67700	2.07	0.80722	D	1	D	0.65815	0.995	D	0.75484	0.986	T	0.79978	-0.1575	9	0.87932	D	0	-14.1634	15.5489	0.76133	0.0:0.0:0.0:1.0	.	203	Q9NVF7	FBX28_HUMAN	R	203	.	ENSP00000355827:I203R	I	+	2	0	FBXO28	222407558	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	7.422000	0.80217	2.254000	0.74563	0.528000	0.53228	ATA	.	.		0.378	FBXO28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091283.2	NM_015176		G	224340935	T	G	224340935	3	3	177	1	0	0	0	0	1	0	0	0	5746	1406	49	5	622	5	FBXO28	1	224340935	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	12854834	224340935	24909686	13	26593										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228548151	228548151	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tgctgctcagcgtggggcatGcactgggtccccgaggccct	15	14	1	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:228548151G>T	ENST00000422127.1	+	80	18705				OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000284548.11_Missense_Mutation_p.A6520S|OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366709.4_Missense_Mutation_p.A3639S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CGTGGGGCATGCACTGGGTCC	0.697																																					p.A6520S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G19558T						.						19	23	21					1																	228548151		1979	4145	6124	SO:0001627	intron_variant	84033	exon81			GGGCATGCACTGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18662-2126G>T	chr1.hg19:g.228548151G>T		39.0	0.0		62.0	19.0	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.648454	0.67358	.	.	ENSG00000154358	ENST00000284548;ENST00000366709	T;T	0.55930	0.49;0.63	4.25	3.34	0.38264	.	.	.	.	.	T	0.34019	0.0883	N	0.08118	0	0.24853	N	0.992398	B	0.29301	0.241	B	0.27500	0.08	T	0.27400	-1.0075	9	0.52906	T	0.07	.	13.5187	0.61555	0.0:0.8198:0.1802:0.0	.	6520	Q5VST9-3	.	S	6520;3639	ENSP00000284548:A6520S;ENSP00000355670:A3639S	ENSP00000284548:A6520S	A	+	1	0	OBSCN	226614774	0.069000	0.21087	0.006000	0.13384	0.055000	0.15305	2.119000	0.41958	1.011000	0.39340	0.591000	0.81541	GCA	.	.		0.697	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228548151	G	T	228548151	1	4	177	0	1	0	0	0	0	0	0	0	10821	1319	46	3		3	OBSCN	1	228548151	Intron	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	4207216	228548151	20702470	14	26594										
RHOU	58480	hgsc.bcm.edu	37	chr1	228871685	228871685	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cggtgggcaagacgagcctgGtggtgagctacaccaccaac	14	12	0	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:228871685G>A	ENST00000366691.3	+	1	862	c.196G>A	c.(196-198)Gtg>Atg	p.V66M		NM_021205.5	NP_067028.1			ras homolog family member U											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	13	Breast(184;0.162)	Prostate(94;0.183)				GACGAGCCTGGTGGTGAGCTA	0.751																																					p.V66M		Atlas-SNP	.											.	RHOU	20	.	0			c.G196A						.						20	25	23					1																	228871685		2197	4293	6490	SO:0001583	missense	58480	exon1			AGCCTGGTGGTGA		CCDS1575.1	1q42.11-q42.3	2012-02-27	2012-02-27	2004-03-24	ENSG00000116574	ENSG00000116574			17794	protein-coding gene	gene with protein product	"Ryu GTPase", "Wnt-1 responsive Cdc42 homolog", "2310026M05Rik", "GTP-binding protein like 1", "CDC42-like GTPase", "GTP-binding protein SB128", "ras-like gene family member U"	606366	"ras homolog gene family, member U"	ARHU		11459829	Standard	NM_021205		Approved	WRCH-1, DJ646B12.2, FLJ10616, WRCH1, CDC42L1, hG28K, fJ646B12.2	uc001htf.3	Q7L0Q8	OTTHUMG00000037919	ENST00000366691.3:c.196G>A	chr1.hg19:g.228871685G>A	ENSP00000355652:p.Val66Met	32.0	0.0		76.0	25.0	NM_021205		Missense_Mutation	SNP	ENST00000366691.3	hg19	CCDS1575.1	.	.	.	.	.	.	.	.	.	.	.	13.33	2.204161	0.38905	.	.	ENSG00000116574	ENST00000366691	T	0.79141	-1.24	3.68	3.68	0.42216	Small GTP-binding protein domain (1);	0.257891	0.32918	N	0.005496	T	0.79106	0.4390	L	0.39326	1.205	0.41770	D	0.989767	D	0.56968	0.978	P	0.60789	0.879	T	0.80551	-0.1332	10	0.87932	D	0	.	9.0721	0.36500	0.0:0.2264:0.7736:0.0	.	66	Q7L0Q8	RHOU_HUMAN	M	66	ENSP00000355652:V66M	ENSP00000355652:V66M	V	+	1	0	RHOU	226938308	1.000000	0.71417	0.978000	0.43139	0.047000	0.14425	2.868000	0.48436	1.859000	0.53934	0.450000	0.29827	GTG	.	.		0.751	RHOU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092555.1	NM_021205		A	228871685	G	A	228871685	3	1	177	1	0	0	0	0	1	0	0	0	13360	1261	44	3	198	3	RHOU	1	228871685	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	323534	228871685	20378936	15	26595										
ZNF124	7678	hgsc.bcm.edu	37	chr1	247320147	247320147	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tgcttacatggatagggttcTtcaccagcatgagcctttat	9	9	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr1:247320147T>C	ENST00000543802.2	-	4	866	c.777A>G	c.(775-777)gaA>gaG	p.E259E	ZNF124_ENST00000491848.1_5'Flank|ZNF124_ENST00000340684.6_Silent_p.E197E|ZNF124_ENST00000491356.1_Intron|ZNF124_ENST00000472531.1_Intron			Q15973	ZN124_HUMAN	zinc finger protein 124	259					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(3)|urinary_tract(2)	14	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)			GATAGGGTTCTTCACCAGCAT	0.438																																					p.E197E		Atlas-SNP	.											.	ZNF124	39	.	0			c.A591G						.						132	127	128					1																	247320147		2203	4300	6503	SO:0001819	synonymous_variant	7678	exon4			GGGTTCTTCACCA	S54641	CCDS31089.1, CCDS58067.1, CCDS73057.1	1q44	2013-01-08	2006-06-13		ENSG00000196418	ENSG00000196418		"Zinc fingers, C2H2-type", "-"	12907	protein-coding gene	gene with protein product		194631	"zinc finger protein 124 (HZF-16)"			7916577	Standard	XM_005273256		Approved	HZF16, HZF-16	uc001icj.1	Q15973	OTTHUMG00000041112	ENST00000543802.2:c.777A>G	chr1.hg19:g.247320147T>C		95.0	0.0		141.0	39.0	NM_003431	B3KNP3|J3KSE1|Q15974|Q4VAJ7|Q5T2V4	Silent	SNP	ENST00000543802.2	hg19																																																																																				.	.		0.438	ZNF124-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000447393.1	NM_003431		C	247320147	T	C	247320147	2	2	177	1	0	0	0	0	0	0	0	1	17735	1606	56	2		2	ZNF124	1	247320147	Silent	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	18448462	247320147	1930474	16	26596										
MBOAT2	129642	hgsc.bcm.edu	37	chr2	9017206	9017206	+	Missense_Mutation	SNP	T	T	A													0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	actgtgtctcttcttttccaTtttcaccagattgtgtgata							TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:9017206T>A	ENST00000305997.3	-	7	842	c.644A>T	c.(643-645)aAt>aTt	p.N215I	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	215					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTCTTTTCCATTTTCACCAGA	0.398																																					p.N215I	Ovarian(194;1699 3813 22401)	Atlas-SNP	.											.	MBOAT2	36	.	0			c.A644T						.						218	193	202					2																	9017206		2203	4300	6503	SO:0001583	missense	129642	exon7			TTTCCATTTTCAC	BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"O-acyltransferase (membrane bound) domain containing 2"	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.644A>T	chr2.hg19:g.9017206T>A	ENSP00000302177:p.Asn215Ile	117.0	0.0		108.0	54.0	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Missense_Mutation	SNP	ENST00000305997.3	hg19	CCDS1660.1	.	.	.	.	.	.	.	.	.	.	T	19.32	3.805688	0.70682	.	.	ENSG00000143797	ENST00000305997	T	0.48836	0.8	5.56	3.18	0.36537	.	1.176190	0.06361	N	0.711654	T	0.61286	0.2335	M	0.70595	2.14	0.48040	D	0.999579	P;P	0.50272	0.933;0.933	P;P	0.53988	0.739;0.739	T	0.41805	-0.9488	10	0.39692	T	0.17	-2.266	9.7598	0.40526	0.0:0.1396:0.0:0.8604	.	215;215	B7Z3I3;Q6ZWT7	.;MBOA2_HUMAN	I	215	ENSP00000302177:N215I	ENSP00000302177:N215I	N	-	2	0	MBOAT2	8934657	0.691000	0.27709	0.000000	0.03702	0.156000	0.22039	1.577000	0.36515	0.410000	0.25675	0.528000	0.53228	AAT	.	.		0.398	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		A	9017206	T	A	9017206	3	1	177	1	0	0	0	0	1	0	0	0	9366	1493	52	4	946	4	MBOAT2	2	9017206	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10		9017206	234182167	17	26597	129	2								
MBOAT2	129642	hgsc.bcm.edu	37	chr2	9017208	9017208	+	Missense_Mutation	SNP	T	T	G													0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tgtgtctcttcttttccattTtcaccagattgtgtgatatg							TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:9017208T>G	ENST00000305997.3	-	7	840	c.642A>C	c.(640-642)gaA>gaC	p.E214D	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	214					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CTTTTCCATTTTCACCAGATT	0.403																																					p.E214D	Ovarian(194;1699 3813 22401)	Atlas-SNP	.											.	MBOAT2	36	.	0			c.A642C						.						216	192	200					2																	9017208		2203	4300	6503	SO:0001583	missense	129642	exon7			TCCATTTTCACCA	BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"O-acyltransferase (membrane bound) domain containing 2"	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.642A>C	chr2.hg19:g.9017208T>G	ENSP00000302177:p.Glu214Asp	121.0	0.0		108.0	55.0	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Missense_Mutation	SNP	ENST00000305997.3	hg19	CCDS1660.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.301998	0.23736	.	.	ENSG00000143797	ENST00000305997	T	0.42131	0.98	5.56	-1.7	0.08159	.	1.069410	0.07347	N	0.881810	T	0.20861	0.0502	N	0.22421	0.69	0.24276	N	0.995229	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.005	T	0.24119	-1.0169	10	0.07482	T	0.82	-0.4668	2.5261	0.04691	0.1178:0.1343:0.3653:0.3826	.	214;214	B7Z3I3;Q6ZWT7	.;MBOA2_HUMAN	D	214	ENSP00000302177:E214D	ENSP00000302177:E214D	E	-	3	2	MBOAT2	8934659	0.709000	0.27886	0.000000	0.03702	0.120000	0.20174	0.176000	0.16782	-0.173000	0.10761	0.528000	0.53228	GAA	.	.		0.403	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		G	9017208	T	G	9017208	3	3	177	1	0	0	0	0	1	0	0	0	9366	1838	64	5	948	5	MBOAT2	2	9017208	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	2	9017208	234182165	18	26598	129	2								
GREB1	9687	hgsc.bcm.edu	37	chr2	11751071	11751071	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ccacgtgcgggcccggctggCgctggaggagcactttgaga	17	12	0	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:11751071C>T	ENST00000381486.2	+	18	3224	c.2924C>T	c.(2923-2925)gCg>gTg	p.A975V	GREB1_ENST00000396123.1_5'Flank|GREB1_ENST00000234142.5_Missense_Mutation_p.A975V	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	975						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GCCCGGCTGGCGCTGGAGGAG	0.687																																					p.A975V	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.C2924T						.						13	16	15					2																	11751071		1997	4150	6147	SO:0001583	missense	9687	exon18			GGCTGGCGCTGGA		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.2924C>T	chr2.hg19:g.11751071C>T	ENSP00000370896:p.Ala975Val	184.0	0.0		177.0	71.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.618183	0.87359	.	.	ENSG00000196208	ENST00000381486;ENST00000234142	T;T	0.50548	0.74;0.74	5.17	5.17	0.71159	.	0.236828	0.35936	N	0.002900	T	0.42426	0.1202	L	0.47716	1.5	0.38494	D	0.948048	P	0.43909	0.821	B	0.38616	0.277	T	0.53961	-0.8364	10	0.87932	D	0	-46.7919	14.3023	0.66362	0.0:0.8514:0.1486:0.0	.	975	Q4ZG55	GREB1_HUMAN	V	975	ENSP00000370896:A975V;ENSP00000234142:A975V	ENSP00000234142:A975V	A	+	2	0	GREB1	11668522	1.000000	0.71417	0.998000	0.56505	0.952000	0.60782	3.980000	0.56895	2.410000	0.81850	0.563000	0.77884	GCG	.	.		0.687	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		T	11751071	C	T	11751071	3	4	177	1	0	0	0	0	1	0	0	0	6769	768	27	1	3098	1	GREB1	2	11751071	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	2733863	11751071	231448302	19	26599										
THADA	63892	hgsc.bcm.edu	37	chr2	43460007	43460007	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	agcgatggaggcatccacctGgcagaaggcaaactctgcaa	12	11	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:43460007G>T	ENST00000405006.4	-	37	5662	c.5311C>A	c.(5311-5313)Cag>Aag	p.Q1771K	THADA_ENST00000415080.2_Missense_Mutation_p.Q1452K|THADA_ENST00000330266.7_Intron|THADA_ENST00000405975.2_Missense_Mutation_p.Q1771K|AC010883.5_ENST00000423354.1_RNA	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1771										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				GCATCCACCTGGCAGAAGGCA	0.607																																					p.Q1771K		Atlas-SNP	.											.	THADA	131	.	0			c.C5311A						.						26	28	27					2																	43460007		2037	4198	6235	SO:0001583	missense	63892	exon37			CCACCTGGCAGAA	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.5311C>A	chr2.hg19:g.43460007G>T	ENSP00000385995:p.Gln1771Lys	180.0	0.0		189.0	85.0	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	hg19	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	G	15.96	2.986800	0.53934	.	.	ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006	T;T;T	0.65549	-0.16;-0.16;-0.16	5.39	4.32	0.51571	.	0.438767	0.21810	N	0.068796	T	0.47948	0.1473	M	0.63428	1.95	0.26586	N	0.973286	P;B	0.46395	0.877;0.41	B;B	0.40134	0.32;0.071	T	0.49579	-0.8925	10	0.06365	T	0.9	-27.1315	4.0593	0.09831	0.0873:0.1333:0.5222:0.2573	.	1698;1771	B6ZDQ0;Q6YHU6	.;THADA_HUMAN	K	1771;1698;1452;1771	ENSP00000386088:Q1771K;ENSP00000416048:Q1452K;ENSP00000385995:Q1771K	ENSP00000349464:Q1698K	Q	-	1	0	THADA	43313511	0.997000	0.39634	1.000000	0.80357	0.960000	0.62799	0.963000	0.29293	2.526000	0.85167	0.561000	0.74099	CAG	.	.		0.607	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		T	43460007	G	T	43460007	3	4	177	1	0	0	0	0	1	0	0	0	15855	1357	47	3	558	3	THADA	2	43460007	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	31708936	43460007	199739366	20	26600										
SFXN5	94097	hgsc.bcm.edu	37	chr2	73195626	73195626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tagcaccaggatgggcatggGcaggaccactcgcgtcagcg	15	12	1	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:73195626G>A	ENST00000272433.2	-	12	908	c.778C>T	c.(778-780)Ccc>Tcc	p.P260S	SFXN5_ENST00000410065.1_Intron|SFXN5_ENST00000474528.1_5'UTR	NM_144579.2	NP_653180.1	Q8TD22	SFXN5_HUMAN	sideroflexin 5	260					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)|citrate transmembrane transporter activity (GO:0015137)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9						ATGGGCATGGGCAGGACCACT	0.657																																					p.P260S		Atlas-SNP	.											.	SFXN5	31	.	0			c.C778T						.						55	47	50					2																	73195626		2203	4300	6503	SO:0001583	missense	94097	exon12			GCATGGGCAGGAC	AY044437	CCDS1922.1	2p13	2008-05-21			ENSG00000144040	ENSG00000144040		"Sideroflexins"	16073	protein-coding gene	gene with protein product		615572				12039050, 12150972	Standard	XM_005264648		Approved	BBG-TCC	uc002siq.3	Q8TD22	OTTHUMG00000129775	ENST00000272433.2:c.778C>T	chr2.hg19:g.73195626G>A	ENSP00000272433:p.Pro260Ser	209.0	0.0		211.0	95.0	NM_144579	A8K116|Q494Y3|Q53T29	Missense_Mutation	SNP	ENST00000272433.2	hg19	CCDS1922.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.139109	0.77775	.	.	ENSG00000144040	ENST00000272433	T	0.27557	1.66	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.46698	0.1406	L	0.48218	1.51	0.80722	D	1	D;B;D	0.89917	1.0;0.387;0.999	D;B;D	0.87578	0.998;0.349;0.974	T	0.17806	-1.0357	10	0.14656	T	0.56	-20.6576	16.3047	0.82843	0.0:0.0:1.0:0.0	.	109;156;260	B4DIJ8;B4DGS9;Q8TD22	.;.;SFXN5_HUMAN	S	260	ENSP00000272433:P260S	ENSP00000272433:P260S	P	-	1	0	SFXN5	73049134	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.250000	0.95477	2.456000	0.83038	0.655000	0.94253	CCC	.	.		0.657	SFXN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251991.1	NM_144579		A	73195626	G	A	73195626	3	1	177	1	0	0	0	0	1	0	0	0	14213	1203	42	3	256	3	SFXN5	2	73195626	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	29735619	73195626	170003747	21	26601										
CCT7	10574	hgsc.bcm.edu	37	chr2	73479792	73479792	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gtacatggtatggagtagacAtcaacaacgaggacattgct	11	7	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:73479792A>T	ENST00000258091.5	+	12	1576	c.1435A>T	c.(1435-1437)Atc>Ttc	p.I479F	CCT7_ENST00000398422.2_Missense_Mutation_p.I275F|CCT7_ENST00000538797.1_Missense_Mutation_p.I351F|CCT7_ENST00000539919.1_Missense_Mutation_p.I435F|CCT7_ENST00000537131.1_Missense_Mutation_p.I379F|CCT7_ENST00000540468.1_Missense_Mutation_p.I392F	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	479					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						TGGAGTAGACATCAACAACGA	0.473																																					p.I479F		Atlas-SNP	.											.	CCT7	60	.	0			c.A1435T						.						86	89	88					2																	73479792		2020	4194	6214	SO:0001583	missense	10574	exon12			GTAGACATCAACA	AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"Heat Shock Proteins / Chaperonins"	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	ENST00000258091.5:c.1435A>T	chr2.hg19:g.73479792A>T	ENSP00000258091:p.Ile479Phe	230.0	0.0		234.0	92.0	NM_006429	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Missense_Mutation	SNP	ENST00000258091.5	hg19	CCDS46336.1	.	.	.	.	.	.	.	.	.	.	A	15.11	2.737211	0.49045	.	.	ENSG00000135624	ENST00000540468;ENST00000539919;ENST00000258091;ENST00000398422;ENST00000537131;ENST00000538797;ENST00000409081	T;T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24;-1.24	5.0	-1.9	0.07665	.	0.275122	0.42420	D	0.000701	T	0.80412	0.4618	M	0.67625	2.065	0.53005	D	0.999965	P;P;P;P;B;D	0.53151	0.932;0.911;0.925;0.845;0.004;0.958	P;P;P;D;B;D	0.66602	0.645;0.871;0.861;0.918;0.024;0.945	T	0.74962	-0.3485	10	0.29301	T	0.29	-7.0484	6.5687	0.22527	0.3387:0.0:0.5088:0.1524	.	392;351;379;437;275;479	B7Z4Z7;B7Z1C9;F5GZK5;B8ZZC9;A8MWI8;Q99832	.;.;.;.;.;TCPH_HUMAN	F	392;435;479;275;379;351;437	ENSP00000442058:I392F;ENSP00000437824:I435F;ENSP00000258091:I479F;ENSP00000381456:I275F;ENSP00000444379:I379F;ENSP00000438462:I351F	ENSP00000258091:I479F	I	+	1	0	CCT7	73333300	1.000000	0.71417	0.997000	0.53966	0.719000	0.41307	1.143000	0.31553	-0.090000	0.12462	0.533000	0.62120	ATC	.	.		0.473	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2			T	73479792	A	T	73479792	3	4	177	1	0	0	0	0	1	0	0	0	2961	217	8	4	1481	4	CCT7	2	73479792	Missense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	284166	73479792	169719581	22	26602										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80816543	80816544	+	Missense_Mutation	DNP	GG	GG	TT													0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tggccaaatgggacgacagcGgcaatgatatcattgtactg					rs537442409		TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:80816543_80816544GG>TT	ENST00000402739.4	+	14	2127_2128	c.2122_2123GG>TT	c.(2122-2124)GGc>TTc	p.G708F	AC008067.2_ENST00000596887.1_RNA|CTNNA2_ENST00000540488.1_Missense_Mutation_p.G708F|AC008067.2_ENST00000595478.1_RNA|CTNNA2_ENST00000361291.4_Missense_Mutation_p.G742F|CTNNA2_ENST00000541047.1_Missense_Mutation_p.G708F|AC008067.2_ENST00000609950.1_RNA|CTNNA2_ENST00000343114.3_Missense_Mutation_p.G387F|CTNNA2_ENST00000466387.1_Missense_Mutation_p.G708F|CTNNA2_ENST00000496558.1_Missense_Mutation_p.G708F|AC008067.2_ENST00000430876.1_RNA	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	708					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GGACGACAGCGGCAATGATATC	0.475																																					p.G708C|p.G708V		Atlas-SNP	.											.	CTNNA2	462	.	0			c.G2122T|c.G2123T						.																																			SO:0001583	missense	1496	exon15			GACAGCGGCAATG|ACAGCGGCAATGA		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	Exception_encountered	chr2.hg19:g.80816543_80816544delinsTT	ENSP00000384638:p.Gly708Phe	230.0|234.0	0.0		215.0|211.0	94.0|91.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	hg19																																																																																				.	.		0.475	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		TT	80816544	GG	TT	80816543	3	4	177	1	0	0	0	0	1	0	0	0	4015	1116	39	1	1968	1	CTNNA2	2	80816543	Missense_Mutation	DNP	GG	TCGA-DD-AAD0-01A-11D-A40R-10	7336751	80816543	162382830	23	26603										
TMEM87B	84910	hgsc.bcm.edu	37	chr2	112839010	112839010	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	atattaagaatccagttctgGattgcagctgttattttttt	7	5	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:112839010G>A	ENST00000283206.4	+	8	1122	c.753G>A	c.(751-753)tgG>tgA	p.W251*		NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	251						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						TCCAGTTCTGGATTGCAGCTG	0.348																																					p.W251X		Atlas-SNP	.											.	TMEM87B	52	.	0			c.G753A						.						142	152	149					2																	112839010		2203	4300	6503	SO:0001587	stop_gained	84910	exon8			GTTCTGGATTGCA	AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.753G>A	chr2.hg19:g.112839010G>A	ENSP00000283206:p.Trp251*	74.0	0.0		96.0	47.0	NM_032824	A8K2M9|Q1RLN2|Q53R54	Nonsense_Mutation	SNP	ENST00000283206.4	hg19	CCDS33275.1	.	.	.	.	.	.	.	.	.	.	G	38	7.149870	0.98096	.	.	ENSG00000153214	ENST00000283206	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.606	17.1792	0.86850	0.0:0.0:1.0:0.0	.	.	.	.	X	251	.	ENSP00000283206:W251X	W	+	3	0	TMEM87B	112555481	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.864000	0.99589	2.650000	0.89964	0.585000	0.79938	TGG	.	.		0.348	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824		A	112839010	G	A	112839010	4	1	177	1	0	0	0	0	0	1	0	0	16226	1183	41	3	783	3	TMEM87B	2	112839010	Nonsense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	32022467	112839010	130360363	24	26604										
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113089743	113089743	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aagtggtggcttaaaaagtaGtgacaaaactgaaccttctc	9	7	1	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:113089743G>T	ENST00000409871.1	+	12	3649	c.3248G>T	c.(3247-3249)aGt>aTt	p.S1083I	AC115115.2_ENST00000607612.1_RNA|ZC3H6_ENST00000343936.4_Missense_Mutation_p.S1083I	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	1083							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						TTAAAAAGTAGTGACAAAACT	0.493																																					p.S1083I		Atlas-SNP	.											.	ZC3H6	93	.	0			c.G3248T						.						45	44	44					2																	113089743		1863	4114	5977	SO:0001583	missense	376940	exon12			AAAGTAGTGACAA	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.3248G>T	chr2.hg19:g.113089743G>T	ENSP00000386764:p.Ser1083Ile	310.0	0.0		302.0	148.0	NM_198581	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	hg19	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	G	9.375	1.071457	0.20147	.	.	ENSG00000188177	ENST00000409871;ENST00000343936	T;T	0.16897	2.31;2.31	5.43	2.04	0.26737	.	0.959069	0.08744	N	0.900058	T	0.19805	0.0476	L	0.56769	1.78	0.09310	N	0.999998	P	0.41041	0.736	B	0.41988	0.372	T	0.21655	-1.0239	10	0.72032	D	0.01	-2.1916	5.7125	0.17943	0.3664:0.181:0.4525:0.0	.	1083	P61129	ZC3H6_HUMAN	I	1083	ENSP00000386764:S1083I;ENSP00000340298:S1083I	ENSP00000340298:S1083I	S	+	2	0	ZC3H6	112806214	0.458000	0.25760	0.977000	0.42913	0.716000	0.41182	1.065000	0.30592	0.586000	0.29626	0.655000	0.94253	AGT	.	.		0.493	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		T	113089743	G	T	113089743	3	4	177	1	0	0	0	0	1	0	0	0	17586	1029	36	3	3294	3	ZC3H6	2	113089743	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	250733	113089743	130109630	25	26605										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160257109	160257109	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tattaaatttaagacttctaCctctagaatttgctgagctc	5	8	2	3			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:160257109C>A	ENST00000392783.2	-	17	3394		c.e17+1		AC008277.1_ENST00000608714.1_RNA|BAZ2B_ENST00000392782.1_Splice_Site|AC008277.1_ENST00000594921.1_RNA|BAZ2B_ENST00000355831.2_Splice_Site|BAZ2B_ENST00000343439.5_Splice_Site|AC008277.1_ENST00000420020.1_RNA	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						aaGACTTCTACCTCTAGAATT	0.269																																					.		Atlas-SNP	.											.	BAZ2B	196	.	0			c.2898+1G>T						.						42	37	39					2																	160257109		1775	4051	5826	SO:0001630	splice_region_variant	29994	exon18			CTTCTACCTCTAG	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.2898+1G>T	chr2.hg19:g.160257109C>A		249.0	1.0		277.0	134.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Splice_Site	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	20.8	4.046166	0.75846	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000294905	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9988	0.92824	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	BAZ2B	159965355	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.395000	0.79876	2.465000	0.83290	0.585000	0.79938	.	.	.		0.269	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		Intron	A	160257109	C	A	160257109	5	1	177	1	0	0	0	0	0	0	1	0	1332	521	18	3	3691	3	BAZ2B	2	160257109	Splice_Site	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	47167366	160257109	82942264	26	26606										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215876718	215876718	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tgttaatggaacacttctggGcagatgcatttgcttcaggg	12	7	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:215876718G>T	ENST00000272895.7	-	16	2317	c.2098C>A	c.(2098-2100)Ccc>Acc	p.P700T	ABCA12_ENST00000389661.4_Missense_Mutation_p.P382T	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	700					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ACACTTCTGGGCAGATGCATT	0.408																																					p.P700T	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C2098A						.						244	234	238					2																	215876718		2203	4300	6503	SO:0001583	missense	26154	exon16			TTCTGGGCAGATG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.2098C>A	chr2.hg19:g.215876718G>T	ENSP00000272895:p.Pro700Thr	92.0	0.0		95.0	49.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.365648	0.24684	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.87412	-2.25;-2.25	5.73	0.291	0.15732	.	0.239374	0.30011	N	0.010625	T	0.67059	0.2853	N	0.14661	0.345	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.001;0.002	T	0.53322	-0.8455	10	0.06494	T	0.89	.	4.0818	0.09929	0.3873:0.1705:0.4422:0.0	.	700;382	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	T	700;382	ENSP00000272895:P700T;ENSP00000374312:P382T	ENSP00000272895:P700T	P	-	1	0	ABCA12	215584963	0.998000	0.40836	0.974000	0.42286	0.978000	0.69477	0.408000	0.21065	0.372000	0.24591	0.655000	0.94253	CCC	.	.		0.408	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215876718	G	T	215876718	3	4	177	1	0	0	0	0	1	0	0	0	30	1203	42	3	5841	3	ABCA12	2	215876718	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	55619609	215876718	27322655	27	26607										
SCG2	7857	hgsc.bcm.edu	37	chr2	224462698	224462698	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ccctaaaagatttaaaatatCctcaacactgagcccgtctg	5	12	2	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:224462698C>A	ENST00000305409.2	-	2	1535	c.1303G>T	c.(1303-1305)Gat>Tat	p.D435Y		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		TTTAAAATATCCTCAACACTG	0.473																																					p.D435Y		Atlas-SNP	.											.	SCG2	99	.	0			c.G1303T						.						85	86	86					2																	224462698		2203	4300	6503	SO:0001583	missense	7857	exon2			AAATATCCTCAAC	M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"secretoneurin", "chromogranin C"	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.1303G>T	chr2.hg19:g.224462698C>A	ENSP00000304133:p.Asp435Tyr	61.0	0.0		83.0	41.0	NM_003469	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000305409.2	hg19	CCDS2457.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374561	0.61735	.	.	ENSG00000171951	ENST00000305409;ENST00000450330	T	0.02050	4.48	5.86	5.86	0.93980	.	0.120203	0.53938	D	0.000046	T	0.13756	0.0333	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00018	-1.2373	10	0.87932	D	0	.	20.1986	0.98248	0.0:1.0:0.0:0.0	.	435	P13521	SCG2_HUMAN	Y	435;295	ENSP00000304133:D435Y	ENSP00000304133:D435Y	D	-	1	0	SCG2	224170942	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.508000	0.53378	2.781000	0.95711	0.650000	0.86243	GAT	.	.		0.473	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		A	224462698	C	A	224462698	3	1	177	1	0	0	0	0	1	0	0	0	13906	855	30	3	554	3	SCG2	2	224462698	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	8585980	224462698	18736675	28	26608										
SP110	3431	hgsc.bcm.edu	37	chr2	231042313	231042313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	attccgtttccagttctttgCgttccttccttttccttcga	5	13	1	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr2:231042313C>T	ENST00000358662.4	-	14	1609	c.1531G>A	c.(1531-1533)Gca>Aca	p.A511T	SP110_ENST00000258382.5_Missense_Mutation_p.A511T|SP110_ENST00000392048.3_Missense_Mutation_p.A509T|SP110_ENST00000258381.6_Missense_Mutation_p.A511T|SP110_ENST00000540870.1_Missense_Mutation_p.A517T|SP110_ENST00000338556.3_Missense_Mutation_p.A213T	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	511	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		CAGTTCTTTGCGTTCCTTCCT	0.428																																					p.A517T		Atlas-SNP	.											SP110_ENST00000540870,right_upper_lobe,carcinoma,0,2	SP110	105	.	0			c.G1549A						.						334	312	319					2																	231042313		2203	4300	6503	SO:0001583	missense	3431	exon15			TCTTTGCGTTCCT	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"interferon-induced protein 41, 30kD"	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.1531G>A	chr2.hg19:g.231042313C>T	ENSP00000351488:p.Ala511Thr	93.0	0.0		102.0	39.0	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	hg19	CCDS2474.1	.	.	.	.	.	.	.	.	.	.	C	11.43	1.637080	0.29157	.	.	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000338556	T;T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04;-0.04	4.83	-0.844	0.10741	SAND domain-like (2);SAND domain (3);	1.300420	0.05910	N	0.631442	T	0.38374	0.1038	N	0.10874	0.06	0.09310	N	1	B;B;B;B;B	0.14012	0.0;0.009;0.0;0.002;0.002	B;B;B;B;B	0.12837	0.001;0.008;0.001;0.004;0.001	T	0.15925	-1.0420	10	0.24483	T	0.36	.	4.978	0.14151	0.3973:0.2829:0.0:0.3197	.	509;213;517;511;511	G5E9C0;E7ER70;F5H1M1;Q9HB58;Q9HB58-6	.;.;.;SP110_HUMAN;.	T	511;511;509;511;517;213	ENSP00000258381:A511T;ENSP00000351488:A511T;ENSP00000375902:A509T;ENSP00000258382:A511T;ENSP00000439558:A517T;ENSP00000344049:A213T	ENSP00000258381:A511T	A	-	1	0	SP110	230750557	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.427000	0.06999	-0.191000	0.10448	-0.339000	0.08088	GCA	.	.		0.428	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424		T	231042313	C	T	231042313	3	4	177	1	0	0	0	0	1	0	0	0	14976	768	27	1	698	1	SP110	2	231042313	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	6579615	231042313	12157060	29	26609										
BHLHE40	8553	hgsc.bcm.edu	37	chr3	5022091	5022091	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tacccgaacatctcaaacttAcagtaagtgagaagctggcc	8	11	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr3:5022091A>C	ENST00000256495.3	+	3	859	c.256A>C	c.(256-258)Aca>Cca	p.T86P	BHLHE40-AS1_ENST00000420832.1_RNA|BHLHE40-AS1_ENST00000441386.2_RNA|BHLHE40-AS1_ENST00000434530.1_RNA	NM_003670.2	NP_003661.1	O14503	BHE40_HUMAN	basic helix-loop-helix family, member e40	86	Essential for its interaction with ARNTL/BMAL1, E-box binding and repressor activity against the CLOCK-ARNTL/BMAL1 heterodimer.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|MRF binding (GO:0043426)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)	12						TCTCAAACTTACAGTAAGTGA	0.577											OREG0015367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T86P		Atlas-SNP	.											.	BHLHE40	35	.	0			c.A256C						.						52	54	54					3																	5022091		2203	4300	6503	SO:0001583	missense	8553	exon3			AAACTTACAGTAA	AB004066	CCDS2565.1	3p26	2009-01-12	2009-01-12	2009-01-12	ENSG00000134107	ENSG00000134107		"Basic helix-loop-helix proteins"	1046	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 1", " differentiated embryo chondrocyte expressed gene 1"	604256	"basic helix-loop-helix domain containing, class B, 2"	STRA13, BHLHB2		9240428, 10449910, 18557763	Standard	NM_003670		Approved	DEC1, bHLHe40	uc003bqf.3	O14503	OTTHUMG00000119035	ENST00000256495.3:c.256A>C	chr3.hg19:g.5022091A>C	ENSP00000256495:p.Thr86Pro	98.0	0.0	623	106.0	50.0	NM_003670	Q96TD3	Missense_Mutation	SNP	ENST00000256495.3	hg19	CCDS2565.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.042795	0.75732	.	.	ENSG00000134107	ENST00000256495	D	0.97976	-4.64	3.99	3.99	0.46301	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.95436	0.8518	N	0.14661	0.345	0.80722	D	1	P	0.50819	0.939	P	0.52031	0.688	D	0.95592	0.8655	10	0.54805	T	0.06	.	13.2035	0.59782	1.0:0.0:0.0:0.0	.	86	O14503	BHE40_HUMAN	P	86	ENSP00000256495:T86P	ENSP00000256495:T86P	T	+	1	0	BHLHE40	4997091	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.781000	0.91805	1.584000	0.49913	0.482000	0.46254	ACA	.	.		0.577	BHLHE40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239244.2	NM_003670		C	5022091	A	C	5022091	3	2	177	1	0	0	0	0	1	0	0	0	1423	391	14	5	266	5	BHLHE40	3	5022091	Missense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10		5022091	193000339	30	26610										
TATDN2	9797	hgsc.bcm.edu	37	chr3	10301858	10301858	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ttctcataactccacaaactCtgaatttgcagctgaagctg	6	11	2	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr3:10301858C>G	ENST00000287652.4	+	3	1503	c.452C>G	c.(451-453)tCt>tGt	p.S151C	RP11-438J1.1_ENST00000450534.1_Intron|TATDN2_ENST00000448281.2_Missense_Mutation_p.S151C	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	151					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						TCCACAAACTCTGAATTTGCA	0.433																																					p.S151C		Atlas-SNP	.											.	TATDN2	59	.	0			c.C452G						.						57	58	58					3																	10301858		2203	4300	6503	SO:0001583	missense	9797	exon3			CAAACTCTGAATT	D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.452C>G	chr3.hg19:g.10301858C>G	ENSP00000287652:p.Ser151Cys	192.0	0.0		198.0	94.0	NM_014760	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	hg19	CCDS33698.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.566441	0.45694	.	.	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.35605	1.3;1.3	4.41	3.53	0.40419	.	0.236309	0.22045	N	0.065391	T	0.51517	0.1679	M	0.62723	1.935	0.32603	N	0.525705	D	0.89917	1.0	D	0.68192	0.956	T	0.62661	-0.6807	10	0.87932	D	0	-12.039	8.4327	0.32769	0.0:0.896:0.0:0.104	.	151	Q93075	TATD2_HUMAN	C	151	ENSP00000287652:S151C;ENSP00000408736:S151C	ENSP00000287652:S151C	S	+	2	0	TATDN2	10276858	1.000000	0.71417	0.987000	0.45799	0.558000	0.35554	2.128000	0.42045	1.455000	0.47813	0.655000	0.94253	TCT	.	.		0.433	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		G	10301858	C	G	10301858	3	3	177	1	0	0	0	0	1	0	0	0	15607	913	32	4	458	4	TATDN2	3	10301858	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	5279767	10301858	187720572	31	26611										
TTC21A	199223	hgsc.bcm.edu	37	chr3	39159608	39159608	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gatgcctgccaaattctaacCgtgcatgagcttgcaagaga	10	10	1	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr3:39159608C>T	ENST00000431162.2	+	7	899	c.765C>T	c.(763-765)acC>acT	p.T255T	TTC21A_ENST00000301819.6_Silent_p.T255T|TTC21A_ENST00000440121.1_Silent_p.T214T			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	255								p.T255T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AAATTCTAACCGTGCATGAGC	0.423																																					p.T255T		Atlas-SNP	.											TTC21A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	TTC21A	96	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C765T						.						165	167	166					3																	39159608		2050	4195	6245	SO:0001819	synonymous_variant	199223	exon7			TCTAACCGTGCAT	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"Tetratricopeptide (TTC) repeat domain containing"	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.765C>T	chr3.hg19:g.39159608C>T		83.0	0.0		72.0	35.0	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Silent	SNP	ENST00000431162.2	hg19	CCDS46800.1																																																																																			.	.		0.423	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		T	39159608	C	T	39159608	2	4	177	1	0	0	0	0	0	0	0	1	16702	639	23	1		1	TTC21A	3	39159608	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	28857750	39159608	158862822	32	26612										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266113	41266113	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cctggactctggaatccattCtggtgccactaccacagctc	8	15	2	0	rs121913416|rs121913403		TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr3:41266113C>A	ENST00000349496.5	+	3	390	c.110C>A	c.(109-111)tCt>tAt	p.S37Y	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S37Y|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S30Y|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S37Y|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S37Y	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S37F(172)|p.S37C(141)|p.A5_A80del(53)|p.S37Y(31)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGAATCCATTCTGGTGCCACT	0.498	S37C(JHUEM2_ENDOMETRIUM)|S37C(SNU398_LIVER)|S37F(HUTU80_SMALL_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S37Y	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	474	Substitution - Missense(344)|Deletion - In frame(102)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(145)|endometrium(64)|stomach(38)|skin(34)|ovary(33)|central_nervous_system(28)|pancreas(28)|large_intestine(22)|pituitary(22)|lung(21)|biliary_tract(15)|thyroid(4)|soft_tissue(4)|urinary_tract(4)|small_intestine(3)|oesophagus(3)|adrenal_gland(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)|breast(1)	c.C110A						.						93	78	83					3																	41266113		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TCCATTCTGGTGC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.110C>A	chr3.hg19:g.41266113C>A	ENSP00000344456:p.Ser37Tyr	144.0	0.0		121.0	57.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475777	0.84640	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75297	-0.3367	10	0.87932	D	0	-15.9763	19.9596	0.97236	0.0:1.0:0.0:0.0	.	37	P35222	CTNB1_HUMAN	Y	30;37;37;37;37;30;37;37;37	ENSP00000400508:S30Y;ENSP00000385604:S37Y;ENSP00000412219:S37Y;ENSP00000379486:S37Y;ENSP00000344456:S37Y;ENSP00000411226:S30Y;ENSP00000379488:S37Y;ENSP00000409302:S37Y;ENSP00000401599:S37Y	ENSP00000344456:S37Y	S	+	2	0	CTNNB1	41241117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266113	C	A	41266113	3	1	177	1	0	0	0	0	1	0	0	0	4018	913	32	3	116	3	CTNNB1	3	41266113	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	2106505	41266113	156756317	33	26613										
PRSS42	339906	hgsc.bcm.edu	37	chr3	46871983	46871983	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	caagcggcccccagaatctcCctagagaaagagaaagaaac	9	12	1	4			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr3:46871983C>T	ENST00000429665.1	-	5	792	c.793G>A	c.(793-795)Gga>Aga	p.G265R	PRSS42_ENST00000447340.1_Splice_Site_p.G92E	NM_182702.1	NP_874361.1	Q7Z5A4	PRS42_HUMAN	protease, serine, 42	265	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				germ cell development (GO:0007281)|spermatogenesis (GO:0007283)	anchored component of plasma membrane (GO:0046658)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	8						CCAGAATCTCCCTAGAGAAAG	0.502																																					p.G265R		Atlas-SNP	.											.	PRSS42	17	.	0			c.G793A						.						32	32	32					3																	46871983		1849	4091	5940	SO:0001630	splice_region_variant	339906	exon5			AATCTCCCTAGAG		CCDS46816.1	3p21.31	2010-05-07			ENSG00000178055	ENSG00000178055		"Serine peptidases / Serine peptidases"	30716	protein-coding gene	gene with protein product	"testis serine protease 2"					12838346	Standard	NM_182702		Approved	TESSP2	uc011bap.2	Q7Z5A4	OTTHUMG00000156496	ENST00000429665.1:c.793-1G>A	chr3.hg19:g.46871983C>T		79.0	0.0		60.0	27.0	NM_182702		Missense_Mutation	SNP	ENST00000429665.1	hg19	CCDS46816.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.4|24.4	4.522414|4.522414	0.85600|0.85600	.|.	.|.	ENSG00000178055|ENSG00000178055	ENST00000447340|ENST00000429665	T|D	0.77877|0.98044	-1.13|-4.68	4.36|4.36	4.36|4.36	0.52297|0.52297	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000|0.000000	0.32093|0.32093	N|N	0.006582|0.006582	D|D	0.98966|0.98966	0.9648|0.9648	M|M	0.93854|0.93854	3.465|3.465	0.80722|0.80722	D|D	1|1	D|D	0.63046|0.89917	0.992|1.0	P|D	0.62740|0.97110	0.906|1.0	D|D	0.99174|0.99174	1.0865|1.0865	10|10	0.87932|0.87932	D|D	0|0	.|.	14.8301|14.8301	0.70142|0.70142	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	92|265	C9JX34|Q7Z5A4	.|PRS42_HUMAN	E|R	92|265	ENSP00000401581:G92E|ENSP00000401701:G265R	ENSP00000401581:G92E|ENSP00000401701:G265R	G|G	-|-	2|1	0|0	PRSS42|PRSS42	46846987|46846987	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.910000|0.910000	0.53928|0.53928	6.775000|6.775000	0.75018|0.75018	2.441000|2.441000	0.82636|0.82636	0.650000|0.650000	0.86243|0.86243	GGG|GGA	.	.		0.502	PRSS42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344347.1	NM_182702	Missense_Mutation	T	46871983	C	T	46871983	5	4	177	1	0	0	0	0	0	0	1	0	12640	637	22	3	91	3	PRSS42	3	46871983	Splice_Site	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	5605870	46871983	151150447	34	26614										
SETD2	29072	hgsc.bcm.edu	37	chr3	47161670	47161670	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aacaagtattaattagacttAcctttctgttaaataaacat	3	6	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr3:47161670A>C	ENST00000409792.3	-	3	4497		c.e3+1			NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2						angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AATTAGACTTACCTTTCTGTT	0.323			"N, F, S, Mis"		clear cell renal carcinoma																																.		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.4454+2T>G						.						51	52	52					3																	47161670		2203	4298	6501	SO:0001630	splice_region_variant	29072	exon4			AGACTTACCTTTC	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4454+1T>G	chr3.hg19:g.47161670A>C		34.0	0.0		42.0	24.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Splice_Site	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	A	22.3	4.277500	0.80580	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1821	0.72968	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SETD2	47136674	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.328000	0.79160	2.172000	0.68678	0.460000	0.39030	.	.	.		0.323	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	Intron	C	47161670	A	C	47161670	5	2	177	1	0	0	0	0	0	0	1	0	14146	405	14	5	3314	5	SETD2	3	47161670	Splice_Site	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	289687	47161670	150860760	35	26615										
AMIGO3	29925	hgsc.bcm.edu	37	chr3	49755432	49755432	+	3'UTR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	atggagctggcggactcagaGccagccttcagctgcaggcc	14	13	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr3:49755432G>T	ENST00000480687.1	-	0	4952				AMIGO3_ENST00000535833.1_Silent_p.G489G|RNF123_ENST00000327697.6_Intron|RNF123_ENST00000433785.1_Intron|AMIGO3_ENST00000320431.7_Silent_p.G489G			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CGGACTCAGAGCCAGCCTTCA	0.657																																					p.G489G		Atlas-SNP	.											.	AMIGO3	40	.	0			c.C1467A						.						38	42	40					3																	49755432		2203	4300	6503	SO:0001624	3_prime_UTR_variant	386724	exon1			CTCAGAGCCAGCC	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.*3753C>A	chr3.hg19:g.49755432G>T		44.0	0.0		58.0	8.0	NM_198722	A8K6N5|Q9H7U3	Silent	SNP	ENST00000480687.1	hg19	CCDS2803.1																																																																																			.	.		0.657	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334		T	49755432	G	T	49755432	1	4	177	0	1	0	0	0	0	0	0	0	577	958	34	3		3	AMIGO3	3	49755432	3'UTR	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	2593762	49755432	148266998	36	26616										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111901012	111901012	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tatataatctttgtttttatCtagccacggaatatgatata	5	5	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr3:111901012C>A	ENST00000305815.5	-	21	2869	c.2617G>T	c.(2617-2619)Gat>Tat	p.D873Y	SLC9C1_ENST00000487372.1_Missense_Mutation_p.D825Y	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	873					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TTGTTTTTATCTAGCCACGGA	0.264																																					p.D873Y		Atlas-SNP	.											.	.	.	.	0			c.G2617T						.						58	62	61					3																	111901012		2203	4299	6502	SO:0001583	missense	285335	exon21			TTTTATCTAGCCA	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2617G>T	chr3.hg19:g.111901012C>A	ENSP00000306627:p.Asp873Tyr	270.0	1.0		319.0	143.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.110871	0.37242	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.44881	0.91;0.91	5.45	3.29	0.37713	Cyclic nucleotide-binding-like (1);Cyclic nucleotide-binding domain (1);	0.516231	0.19154	N	0.121367	T	0.52565	0.1742	L	0.60455	1.87	0.25058	N	0.991087	D;D	0.64830	0.994;0.989	P;P	0.61592	0.891;0.817	T	0.38845	-0.9642	10	0.66056	D	0.02	.	7.8646	0.29530	0.0:0.7738:0.0:0.2262	.	825;873	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	Y	873;825	ENSP00000306627:D873Y;ENSP00000420688:D825Y	ENSP00000306627:D873Y	D	-	1	0	SLC9A10	113383702	0.949000	0.32298	0.990000	0.47175	0.401000	0.30781	0.572000	0.23684	1.262000	0.44165	0.536000	0.68110	GAT	.	.		0.264	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		A	111901012	C	A	111901012	3	1	177	1	0	0	0	0	1	0	0	0	14725	913	32	3	952	3	SLC9A10	3	111901012	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	62145580	111901012	86121418	37	26617										
TM4SF4	7104	hgsc.bcm.edu	37	chr3	149205519	149205519	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tgcctcatggccaatagtacAtggggctaccccttccacga	9	14	1	0	rs571739504	byFrequency	TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr3:149205519A>G	ENST00000305354.4	+	3	1282	c.378A>G	c.(376-378)acA>acG	p.T126T		NM_004617.3	NP_004608.1	P48230	T4S4_HUMAN	transmembrane 4 L six family member 4	126					tissue regeneration (GO:0042246)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)|ovary(1)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			CCAATAGTACATGGGGCTACC	0.522													A|||	3	0.000599042	0	0	5008	,	,		21028	0.003		0	False		,,,				2504	0				p.T126T		Atlas-SNP	.											.	TM4SF4	27	.	0			c.A378G						.						122	115	118					3																	149205519		1963	4164	6127	SO:0001819	synonymous_variant	7104	exon3			TAGTACATGGGGC		CCDS46932.1	3q25	2005-03-21	2005-03-21		ENSG00000169903	ENSG00000169903			11856	protein-coding gene	gene with protein product		606567	"transmembrane 4 superfamily member 4"			7665614	Standard	NM_004617		Approved	il-TMP	uc003exd.2	P48230	OTTHUMG00000159619	ENST00000305354.4:c.378A>G	chr3.hg19:g.149205519A>G		95.0	0.0		89.0	38.0	NM_004617	B2RDA4	Silent	SNP	ENST00000305354.4	hg19	CCDS46932.1																																																																																			.	.		0.522	TM4SF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356528.1			G	149205519	A	G	149205519	2	3	177	1	0	0	0	0	0	0	0	1	15985	204	8	2		2	TM4SF4	3	149205519	Silent	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	37304507	149205519	48816911	38	26618										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952085	178952085	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gaaacaaatgaatgatgcacAtcatggtggctggacaacaa	10	7	1	2	rs121913279		TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr3:178952085A>T	ENST00000263967.3	+	21	3297	c.3140A>T	c.(3139-3141)cAt>cTt	p.H1047L	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.H1047L	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,adenocarcinoma,0,2044	PIK3CA	8460	.	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)	c.A3140T						.						99	89	92					3																	178952085		1912	4130	6042	SO:0001583	missense	5290	exon21			ATGCACATCATGG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>T	chr3.hg19:g.178952085A>T	ENSP00000263967:p.His1047Leu	120.0	0.0		148.0	63.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	4.518	0.096038	0.08681	.	.	ENSG00000121879	ENST00000263967	T	0.78126	-1.15	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.47002	0.1422	N	0.00611	-1.325	0.80722	D	1	B	0.14438	0.01	B	0.12156	0.007	T	0.58053	-0.7704	10	0.02654	T	1	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	L	1047	ENSP00000263967:H1047L	ENSP00000263967:H1047L	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	.	.		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178952085	A	T	178952085	3	4	177	1	0	0	0	0	1	0	0	0	11922	217	8	4	3218	4	PIK3CA	3	178952085	Missense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	29746566	178952085	19070345	39	26619										
TADA2B	93624	hgsc.bcm.edu	37	chr4	7056326	7056326	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	accagttcatgtcatgcaagGagtttgatgacctttttgaa	9	7	2	3			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr4:7056326G>T	ENST00000310074.7	+	2	997	c.808G>T	c.(808-810)Gag>Tag	p.E270*	TADA2B_ENST00000512388.1_Nonsense_Mutation_p.E195*|TADA2B_ENST00000515646.1_Nonsense_Mutation_p.E178*	NM_152293.2	NP_689506.2	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2B	270					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	SAGA-type complex (GO:0070461)|STAGA complex (GO:0030914)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E270Q(1)		breast(3)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	18						GTCATGCAAGGAGTTTGATGA	0.517																																					p.E270X		Atlas-SNP	.											TADA2B,NS,carcinoma,0,1	TADA2B	29	.	1	Substitution - Missense(1)	lung(1)	c.G808T						.						40	46	44					4																	7056326		2056	4186	6242	SO:0001587	stop_gained	93624	exon2			TGCAAGGAGTTTG	AK026299	CCDS47007.1	4p16.1	2009-10-02			ENSG00000173011	ENSG00000173011			30781	protein-coding gene	gene with protein product		608790				12972612, 18936164	Standard	NM_152293		Approved	MGC21874	uc003gjw.4	Q86TJ2	OTTHUMG00000159983	ENST00000310074.7:c.808G>T	chr4.hg19:g.7056326G>T	ENSP00000308022:p.Glu270*	111.0	0.0		125.0	54.0	NM_152293	A0AUJ8|A4QMR7|B3KSN0|B3KU86|Q6MZG9	Nonsense_Mutation	SNP	ENST00000310074.7	hg19	CCDS47007.1	.	.	.	.	.	.	.	.	.	.	G	47	13.781184	0.99763	.	.	ENSG00000173011	ENST00000310074;ENST00000512388;ENST00000515646	.	.	.	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-46.6096	18.2471	0.89989	0.0:0.0:1.0:0.0	.	.	.	.	X	270;195;178	.	ENSP00000308022:E270X	E	+	1	0	TADA2B	7107227	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.135000	0.77276	2.307000	0.77673	0.561000	0.74099	GAG	.	.		0.517	TADA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358687.2	NM_152293		T	7056326	G	T	7056326	4	4	177	1	0	0	0	0	0	1	0	0	15526	1175	41	3	814	3	TADA2B	4	7056326	Nonsense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10		7056326	184097950	40	26620										
PCDH10	57575	hgsc.bcm.edu	37	chr4	134072506	134072506	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	actgggagacgtgcctttccGcctcaagtcttcctttaaga	9	12	2	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr4:134072506G>T	ENST00000264360.5	+	1	2037	c.1211G>T	c.(1210-1212)cGc>cTc	p.R404L	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	404	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		GTGCCTTTCCGCCTCAAGTCT	0.612																																					p.R404L		Atlas-SNP	.											.	PCDH10	290	.	0			c.G1211T						.						145	149	147					4																	134072506		2203	4300	6503	SO:0001583	missense	57575	exon1			CTTTCCGCCTCAA	AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.1211G>T	chr4.hg19:g.134072506G>T	ENSP00000264360:p.Arg404Leu	73.0	0.0		75.0	35.0	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	hg19	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.307806	0.40795	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.01767	4.65	4.68	3.82	0.43975	Cadherin (4);Cadherin-like (1);	0.000000	0.46145	D	0.000318	T	0.03136	0.0092	L	0.43598	1.365	0.46901	D	0.999243	P;B	0.49862	0.929;0.074	P;B	0.45639	0.488;0.069	T	0.55173	-0.8182	10	0.72032	D	0.01	.	13.7341	0.62807	0.0:0.0:0.8449:0.1551	.	404;404	Q9P2E7;Q96SF0	PCD10_HUMAN;.	L	404	ENSP00000264360:R404L	ENSP00000264360:R404L	R	+	2	0	PCDH10	134291956	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.953000	0.49105	1.146000	0.42352	0.561000	0.74099	CGC	.	.		0.612	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		T	134072506	G	T	134072506	3	4	177	1	0	0	0	0	1	0	0	0	11516	1087	38	1	1213	1	PCDH10	4	134072506	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	127016180	134072506	57081770	41	26621										
TTC29	83894	hgsc.bcm.edu	37	chr4	147724829	147724829	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aagcattcagaagctttgttGtagtatccctaaaaaggtaa	8	6	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr4:147724829G>A	ENST00000325106.4	-	11	1336	c.1110C>T	c.(1108-1110)taC>taT	p.Y370Y	TTC29_ENST00000398886.4_Silent_p.Y396Y|TTC29_ENST00000513335.1_Silent_p.Y396Y|TTC29_ENST00000506019.1_5'UTR	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	370										breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					AAGCTTTGTTGTAGTATCCCT	0.378																																					p.Y370Y		Atlas-SNP	.											.	TTC29	63	.	0			c.C1110T						.						41	39	39					4																	147724829		1860	4104	5964	SO:0001819	synonymous_variant	83894	exon11			TTTGTTGTAGTAT	AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"Tetratricopeptide (TTC) repeat domain containing"	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.1110C>T	chr4.hg19:g.147724829G>A		39.0	0.0		49.0	22.0	NM_031956	A4GU95|Q9BXB6	Silent	SNP	ENST00000325106.4	hg19	CCDS47141.1																																																																																			.	.		0.378	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956		A	147724829	G	A	147724829	2	1	177	1	0	0	0	0	0	0	0	1	16711	1372	48	3		3	TTC29	4	147724829	Silent	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	13652323	147724829	43429447	42	26622										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5461382	5461382	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ttgtctgttggcagtaatccCcagtcttcttctgggttaga	10	9	4	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr5:5461382C>T	ENST00000296564.7	+	13	2157	c.1935C>T	c.(1933-1935)ccC>ccT	p.P645P		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		645					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						GCAGTAATCCCCAGTCTTCTT	0.393																																					p.P645P		Atlas-SNP	.											.	KIAA0947	301	.	0			c.C1935T						.						89	89	89					5																	5461382		1889	4109	5998	SO:0001819	synonymous_variant	23379	exon13			TAATCCCCAGTCT																												ENST00000296564.7:c.1935C>T	chr5.hg19:g.5461382C>T		95.0	0.0		110.0	53.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	hg19	CCDS47187.1																																																																																			.	.		0.393	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			T	5461382	C	T	5461382	2	4	177	1	0	0	0	0	0	0	0	1	8211	610	22	3		3	KIAA0947	5	5461382	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10		5461382	175453878	43	26623										
NIPBL	25836	hgsc.bcm.edu	37	chr5	36971138	36971138	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gtgcacaggctaagtagtgaCgtatgtaatatattatcatt	9	5	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr5:36971138C>T	ENST00000282516.8	+	7	1270	c.771C>T	c.(769-771)gaC>gaT	p.D257D	NIPBL_ENST00000448238.2_Splice_Site_p.D257D|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	257					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TAAGTAGTGACGTATGTAATA	0.353																																					p.D257D		Atlas-SNP	.											.	NIPBL	513	.	0			c.C771T						.						81	74	76					5																	36971138		2203	4300	6503	SO:0001630	splice_region_variant	25836	exon7			TAGTGACGTATGT	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.771+1C>T	chr5.hg19:g.36971138C>T		190.0	0.0		201.0	84.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.		0.353	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	Silent	T	36971138	C	T	36971138	5	4	177	1	0	0	0	0	0	0	1	0	10437	550	19	1	793	1	NIPBL	5	36971138	Splice_Site	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	31509756	36971138	143944122	44	26624										
TRIM36	55521	hgsc.bcm.edu	37	chr5	114469810	114469810	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aaggcattgttataaactttGctctgttcctcattgatctc	6	9	3	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr5:114469810G>A	ENST00000282369.3	-	8	1402	c.1281C>T	c.(1279-1281)agC>agT	p.S427S	TRIM36_ENST00000513154.1_Silent_p.S415S|TRIM36_ENST00000514154.1_Silent_p.S272S	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	427	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		TATAAACTTTGCTCTGTTCCT	0.333																																					p.S427S		Atlas-SNP	.											.	TRIM36	126	.	0			c.C1281T						.						94	86	88					5																	114469810		2202	4300	6502	SO:0001819	synonymous_variant	55521	exon8			AACTTTGCTCTGT	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16280	protein-coding gene	gene with protein product	"zinc-binding protein Rbcc728", "tripartite motif protein 36", "RING finger protein 98"	609317	"tripartite motif-containing 36"			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.1281C>T	chr5.hg19:g.114469810G>A		65.0	0.0		63.0	25.0	NM_018700	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Silent	SNP	ENST00000282369.3	hg19	CCDS4115.1																																																																																			.	.		0.333	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		A	114469810	G	A	114469810	2	1	177	1	0	0	0	0	0	0	0	1	16525	1310	46	3		3	TRIM36	5	114469810	Silent	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	77498672	114469810	66445450	45	26625										
SLC23A1	9963	hgsc.bcm.edu	37	chr5	138713935	138713935	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gagagtgcagaacatgccccCcaggatggggtcagggagcg	17	10	1	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr5:138713935C>G	ENST00000348729.3	-	11	1331	c.1285G>C	c.(1285-1287)Ggg>Cgg	p.G429R	SLC23A1_ENST00000353963.3_Missense_Mutation_p.G433R|SLC23A1_ENST00000503919.1_5'Flank	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	429					brain development (GO:0007420)|dehydroascorbic acid transport (GO:0070837)|L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|lung development (GO:0030324)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|brush border (GO:0005903)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular organelle (GO:0043229)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dehydroascorbic acid transporter activity (GO:0033300)|L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium ion transmembrane transporter activity (GO:0015081)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(5)|ovary(1)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	AACATGCCCCCCAGGATGGGG	0.667																																					p.G433R		Atlas-SNP	.											.	SLC23A1	51	.	0			c.G1297C						.						48	47	48					5																	138713935		2202	4293	6495	SO:0001583	missense	9963	exon11			TGCCCCCCAGGAT	AF058317	CCDS4212.1, CCDS4213.1	5q31.2	2013-07-18	2013-07-18	2003-03-21	ENSG00000170482	ENSG00000170482		"Solute carriers"	10974	protein-coding gene	gene with protein product		603790	"solute carrier family 23 (nucleobase transporters), member 2"	SLC23A2		9804989, 10331392	Standard	NM_005847		Approved	YSPL3, SVCT1	uc003leg.3	Q9UHI7	OTTHUMG00000129228	ENST00000348729.3:c.1285G>C	chr5.hg19:g.138713935C>G	ENSP00000302701:p.Gly429Arg	249.0	0.0		281.0	116.0	NM_152685	O95191|Q8WWB6|Q9UGH4|Q9UI39	Missense_Mutation	SNP	ENST00000348729.3	hg19	CCDS4212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.240002|5.240002	0.95240|0.95240	.|.	.|.	ENSG00000170482|ENSG00000170482	ENST00000353963;ENST00000348729|ENST00000453898	T;T|.	0.33865|.	1.39;1.39|.	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	0.046521|.	0.85682|.	D|.	0.000000|.	D|D	0.87629|0.87629	0.6225|0.6225	H|H	0.96142|0.96142	3.775|3.775	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.999|.	D|D	0.89137|0.89137	0.3514|0.3514	10|6	0.87932|0.38643	D|T	0|0.18	-24.5758|-24.5758	18.5419|18.5419	0.91031|0.91031	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	429;433|.	Q9UHI7;Q9UHI7-2|.	S23A1_HUMAN;.|.	R|C	433;429|383	ENSP00000302851:G433R;ENSP00000302701:G429R|.	ENSP00000302701:G429R|ENSP00000406720:W383C	G|W	-|-	1|3	0|0	SLC23A1|SLC23A1	138741834|138741834	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.763000|0.763000	0.43281|0.43281	5.590000|5.590000	0.67530|0.67530	2.716000|2.716000	0.92895|0.92895	0.491000|0.491000	0.48974|0.48974	GGG|TGG	.	.		0.667	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374185.1	NM_152685		G	138713935	C	G	138713935	3	3	177	1	0	0	0	0	1	0	0	0	14477	623	22	4	527	4	SLC23A1	5	138713935	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	24244125	138713935	42201325	46	26626										
RARS	5917	hgsc.bcm.edu	37	chr5	167919732	167919732	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	attagccgcctacaagaggtCtttggtcatgcaattaaggc	10	9	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr5:167919732C>G	ENST00000231572.3	+	3	303	c.249C>G	c.(247-249)gtC>gtG	p.V83V	RARS_ENST00000538719.1_5'UTR	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	83					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		TACAAGAGGTCTTTGGTCATG	0.398																																					p.V83V		Atlas-SNP	.											.	RARS	58	.	0			c.C249G						.						123	123	123					5																	167919732		2203	4300	6503	SO:0001819	synonymous_variant	5917	exon3			AGAGGTCTTTGGT	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	9870	protein-coding gene	gene with protein product	"arginine tRNA ligase 1, cytoplasmic"	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.249C>G	chr5.hg19:g.167919732C>G		120.0	0.0		105.0	59.0	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	hg19	CCDS4367.1																																																																																			.	.		0.398	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887		G	167919732	C	G	167919732	2	3	177	1	0	0	0	0	0	0	0	1	13073	900	32	4		4	RARS	5	167919732	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	29205797	167919732	12995528	47	26627										
SCUBE3	222663	hgsc.bcm.edu	37	chr6	35207632	35207632	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aaaggctataagcttctcatCaatgagaggaactgccaggg	11	8	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr6:35207632C>G	ENST00000274938.7	+	8	933	c.933C>G	c.(931-933)atC>atG	p.I311M	SCUBE3_ENST00000394681.1_Missense_Mutation_p.I327M	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						AGCTTCTCATCAATGAGAGGA	0.512																																					p.I311M		Atlas-SNP	.											.	SCUBE3	99	.	0			c.C933G						.						68	61	63					6																	35207632		2203	4300	6503	SO:0001583	missense	222663	exon8			TCTCATCAATGAG	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"CUB domain and EGF-like repeat containing 3"	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.933C>G	chr6.hg19:g.35207632C>G	ENSP00000274938:p.Ile311Met	48.0	0.0		75.0	43.0	NM_152753		Missense_Mutation	SNP	ENST00000274938.7	hg19	CCDS4800.1	.	.	.	.	.	.	.	.	.	.	C	17.72	3.460031	0.63401	.	.	ENSG00000146197	ENST00000394681;ENST00000274938	D;D	0.96265	-3.96;-3.96	5.66	5.66	0.87406	EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.053027	0.85682	D	0.000000	D	0.93416	0.7900	N	0.10809	0.05	0.39049	D	0.960288	D;D	0.62365	0.989;0.991	P;P	0.60345	0.814;0.873	D	0.95164	0.8284	10	0.66056	D	0.02	.	13.8148	0.63285	0.2695:0.7305:0.0:0.0	.	327;311	Q8IX30-2;Q8IX30	.;SCUB3_HUMAN	M	327;311	ENSP00000378174:I327M;ENSP00000274938:I311M	ENSP00000274938:I311M	I	+	3	3	SCUBE3	35315610	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.167000	0.31847	2.648000	0.89879	0.655000	0.94253	ATC	.	.		0.512	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753		G	35207632	C	G	35207632	3	3	177	1	0	0	0	0	1	0	0	0	13961	816	29	4	963	4	SCUBE3	6	35207632	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10		35207632	135907435	48	26628										
GPR111	222611	hgsc.bcm.edu	37	chr6	47647896	47647896	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	accataacagatatgttgctAcaaaagtgtcccacagatct	6	10	1	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr6:47647896A>G	ENST00000296862.1	+	5	561	c.561A>G	c.(559-561)ctA>ctG	p.L187L	GPR111_ENST00000398742.2_Silent_p.L119L|GPR111_ENST00000507065.1_Silent_p.L119L			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	187					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						ATATGTTGCTACAAAAGTGTC	0.383																																					p.L119L		Atlas-SNP	.											.	GPR111	123	.	0			c.A357G						.						103	95	98					6																	47647896		1863	4105	5968	SO:0001819	synonymous_variant	222611	exon6			GTTGCTACAAAAG	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"-", "GPCR / Class B : Orphans"	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.561A>G	chr6.hg19:g.47647896A>G		207.0	0.0		213.0	93.0	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Silent	SNP	ENST00000296862.1	hg19																																																																																				.	.		0.383	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839		G	47647896	A	G	47647896	2	3	177	1	0	0	0	0	0	0	0	1	6636	378	14	2		2	GPR111	6	47647896	Silent	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	12440264	47647896	123467171	49	26629										
C6orf70	55780	hgsc.bcm.edu	37	chr6	170181592	170181592	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	atttagccaagaaatccacaAgtaaagtactcttatgaaaa	5	7	1	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr6:170181592A>G	ENST00000366773.3	+	18	2053	c.2020A>G	c.(2020-2022)Agt>Ggt	p.S674G	ERMARD_ENST00000588451.1_Missense_Mutation_p.S538G|ERMARD_ENST00000392095.4_Missense_Mutation_p.S548G|ERMARD_ENST00000418781.3_Missense_Mutation_p.S601G|ERMARD_ENST00000366772.2_Missense_Mutation_p.S627G	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	674					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											GAAATCCACAAGTAAAGTACT	0.323																																					p.S674G		Atlas-SNP	.											.	C6orf70	63	.	0			c.A2020G						.						56	57	57					6																	170181592		2203	4300	6503	SO:0001583	missense	55780	exon18			TCCACAAGTAAAG	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"chromosome 6 open reading frame 70"	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.2020A>G	chr6.hg19:g.170181592A>G	ENSP00000355735:p.Ser674Gly	185.0	0.0		90.0	85.0	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	hg19	CCDS34576.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.239575	0.39598	.	.	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095;ENST00000366771	T;T	0.46451	0.87;0.87	5.05	3.87	0.44632	.	2.408730	0.01876	N	0.037558	T	0.14960	0.0361	N	0.24115	0.695	0.09310	N	1	B;B;B	0.31817	0.008;0.341;0.131	B;B;B	0.28011	0.022;0.085;0.039	T	0.08932	-1.0698	10	0.41790	T	0.15	.	8.73	0.34494	0.9094:0.0:0.0906:0.0	.	627;601;674	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	G	674;627;601;548;322	ENSP00000355735:S674G;ENSP00000375945:S548G	ENSP00000355733:S322G	S	+	1	0	C6orf70	169923517	0.007000	0.16637	0.014000	0.15608	0.366000	0.29705	1.644000	0.37228	1.900000	0.55004	0.402000	0.26972	AGT	.	.		0.323	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341		G	170181592	A	G	170181592	3	3	177	1	0	0	0	0	1	0	0	0	2372	72	3	2	2090	2	C6orf70	6	170181592	Missense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	122533696	170181592	933475	50	26630										
DFNA5	1687	hgsc.bcm.edu	37	chr7	24784273	24784273	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ctctctacgcggctgctgccCcccaggttcagcttgacctt	9	17	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr7:24784273C>T	ENST00000342947.3	-	3	737	c.312G>A	c.(310-312)ggG>ggA	p.G104G	DFNA5_ENST00000419307.1_5'UTR|DFNA5_ENST00000545231.1_5'UTR|DFNA5_ENST00000409775.3_Silent_p.G104G|DFNA5_ENST00000409970.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	104					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						GGCTGCTGCCCCCCAGGTTCA	0.562																																					p.G104G	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.G312A						.						87	79	82					7																	24784273		2203	4300	6503	SO:0001819	synonymous_variant	1687	exon3			GCTGCCCCCCAGG	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.312G>A	chr7.hg19:g.24784273C>T		72.0	0.0		119.0	41.0	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Silent	SNP	ENST00000342947.3	hg19	CCDS5389.1																																																																																			.	.		0.562	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		T	24784273	C	T	24784273	2	4	177	1	0	0	0	0	0	0	0	1	4456	610	22	3		3	DFNA5	7	24784273	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10		24784273	134354390	51	26631										
SSPO	23145	hgsc.bcm.edu	37	chr7	149483308	149483308	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gcctcaccctgctctgggatGgagatcaggcccctgccctc	11	17	3	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr7:149483308G>A	ENST00000378016.2	+	0	3376							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GCTCTGGGATGGAGATCAGGC	0.642																																					p.G1126R		Atlas-SNP	.											.	.	.	.	0			c.G3376A						.						29	34	33					7																	149483308		2137	4223	6360			23145	exon23			TGGGATGGAGATC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149483308G>A		38.0	0.0		31.0	12.0	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.642	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149483308	G	A	149483308	1	1	177	0	1	0	0	0	0	0	0	0	15204	1349	47	3		3	SSPO	7	149483308	RNA	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	124699035	149483308	9655355	52	26632										
SHH	6469	hgsc.bcm.edu	37	chr7	155595681	155595681	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tggtagagcagctgcgagtaCcagtggatgcccgcggtggc	17	10	0	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr7:155595681C>T	ENST00000297261.2	-	3	1452	c.1302G>A	c.(1300-1302)tgG>tgA	p.W434*		NM_000193.2	NP_000184.1	Q15465	SHH_HUMAN	sonic hedgehog	434					androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|artery development (GO:0060840)|axon guidance (GO:0007411)|Bergmann glial cell differentiation (GO:0060020)|blood coagulation (GO:0007596)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bud outgrowth involved in lung branching (GO:0060447)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway (GO:0060070)|CD4-positive or CD8-positive, alpha-beta T cell lineage commitment (GO:0043369)|cell development (GO:0048468)|cell fate specification (GO:0001708)|cell-cell signaling (GO:0007267)|cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|cerebellar granule cell precursor proliferation (GO:0021930)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|dorsal/ventral neural tube patterning (GO:0021904)|dorsal/ventral pattern formation (GO:0009953)|ectoderm development (GO:0007398)|embryo development (GO:0009790)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal system development (GO:0048706)|endocytosis (GO:0006897)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|establishment of cell polarity (GO:0030010)|forebrain development (GO:0030900)|formation of anatomical boundary (GO:0048859)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|hindgut morphogenesis (GO:0007442)|inner ear development (GO:0048839)|intein-mediated protein splicing (GO:0016539)|intermediate filament organization (GO:0045109)|left lung development (GO:0060459)|limb bud formation (GO:0060174)|lung development (GO:0030324)|lung epithelium development (GO:0060428)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|lymphoid progenitor cell differentiation (GO:0002320)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal smoothened signaling pathway involved in prostate gland development (GO:0060783)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephros development (GO:0001656)|midbrain development (GO:0030901)|multicellular structure septum development (GO:0080125)|myoblast differentiation (GO:0045445)|myotube differentiation (GO:0014902)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell migration (GO:0030336)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of kidney smooth muscle cell differentiation (GO:2000357)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ureter smooth muscle cell differentiation (GO:2000062)|negative thymic T cell selection (GO:0045060)|neural crest cell migration (GO:0001755)|neuroblast proliferation (GO:0007405)|neuron fate commitment (GO:0048663)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|organ formation (GO:0048645)|osteoblast development (GO:0002076)|palate development (GO:0060021)|pancreas development (GO:0031016)|pattern specification process (GO:0007389)|patterning of blood vessels (GO:0001569)|polarity specification of anterior/posterior axis (GO:0009949)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of immature T cell proliferation in thymus (GO:0033092)|positive regulation of kidney smooth muscle cell differentiation (GO:2000358)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sclerotome development (GO:0061189)|positive regulation of skeletal muscle cell proliferation (GO:0014858)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of striated muscle cell differentiation (GO:0051155)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureter smooth muscle cell differentiation (GO:2000063)|positive regulation of Wnt signaling pathway (GO:0030177)|positive thymic T cell selection (GO:0045059)|primary prostatic bud elongation (GO:0060516)|prostate epithelial cord elongation (GO:0060523)|prostate gland development (GO:0030850)|protein localization to nucleus (GO:0034504)|regulation of cell proliferation (GO:0042127)|regulation of mesenchymal cell proliferation involved in prostate gland development (GO:0060782)|regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900175)|regulation of odontogenesis (GO:0042481)|regulation of prostatic bud formation (GO:0060685)|regulation of protein localization to nucleus (GO:1900180)|regulation of proteolysis (GO:0030162)|renal system development (GO:0072001)|right lung development (GO:0060458)|salivary gland cavitation (GO:0060662)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|somite development (GO:0061053)|spinal cord dorsal/ventral patterning (GO:0021513)|spinal cord motor neuron differentiation (GO:0021522)|stem cell development (GO:0048864)|striated muscle tissue development (GO:0014706)|T cell differentiation in thymus (GO:0033077)|telencephalon regionalization (GO:0021978)|thalamus development (GO:0021794)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|trachea morphogenesis (GO:0060439)|vasculogenesis (GO:0001570)|ventral midline development (GO:0007418)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|laminin-1 binding (GO:0043237)|morphogen activity (GO:0016015)|patched binding (GO:0005113)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			central_nervous_system(3)|kidney(1)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00882)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCTGCGAGTACCAGTGGATGC	0.736																																					p.W434X		Atlas-SNP	.											.	SHH	34	.	0			c.G1302A						.						11	12	12					7																	155595681		1610	3429	5039	SO:0001587	stop_gained	6469	exon3			CGAGTACCAGTGG		CCDS5942.1	7q36	2010-06-25	2010-06-25		ENSG00000164690	ENSG00000164690			10848	protein-coding gene	gene with protein product		600725	"sonic hedgehog (Drosophila) homolog", "sonic hedgehog homolog (Drosophila)"	HPE3, HLP3		7590746	Standard	NM_000193		Approved	HHG1, SMMCI, TPT, TPTPS, MCOPCB5	uc003wmk.1	Q15465	OTTHUMG00000151349	ENST00000297261.2:c.1302G>A	chr7.hg19:g.155595681C>T	ENSP00000297261:p.Trp434*	862.0	0.0		765.0	370.0	NM_000193	A4D247|Q75MC9	Nonsense_Mutation	SNP	ENST00000297261.2	hg19	CCDS5942.1	.	.	.	.	.	.	.	.	.	.	C	37	6.525458	0.97637	.	.	ENSG00000164690	ENST00000297261	.	.	.	3.8	3.8	0.43715	.	0.158188	0.45867	D	0.000324	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0393	0.64665	0.0:1.0:0.0:0.0	.	.	.	.	X	434	.	ENSP00000297261:W434X	W	-	3	0	SHH	155288442	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	6.990000	0.76225	1.954000	0.56735	0.561000	0.74099	TGG	.	.		0.736	SHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322327.1	NM_000193		T	155595681	C	T	155595681	4	4	177	1	0	0	0	0	0	1	0	0	14294	508	18	3	90	3	SHH	7	155595681	Nonsense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	6112373	155595681	3542982	53	26633										
RP1	6101	hgsc.bcm.edu	37	chr8	55539105	55539105	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tattttaagtaaacaacatgCtacaaccagggcaaattctt	5	8	1	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr8:55539105C>G	ENST00000220676.1	+	4	2811	c.2663C>G	c.(2662-2664)gCt>gGt	p.A888G		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	888					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AAACAACATGCTACAACCAGG	0.328																																					p.A888G	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.C2663G						.						33	36	35					8																	55539105		2199	4295	6494	SO:0001583	missense	6101	exon4			AACATGCTACAAC	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2663C>G	chr8.hg19:g.55539105C>G	ENSP00000220676:p.Ala888Gly	124.0	0.0		167.0	82.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	C	6.312	0.425664	0.11987	.	.	ENSG00000104237	ENST00000220676	T	0.46063	0.88	5.33	-1.29	0.09288	.	1.626540	0.03514	N	0.220068	T	0.27524	0.0676	N	0.22421	0.69	0.09310	N	1	P	0.34462	0.454	B	0.27380	0.079	T	0.30001	-0.9993	10	0.72032	D	0.01	.	7.0516	0.25075	0.1357:0.1966:0.0:0.6677	.	888	P56715	RP1_HUMAN	G	888	ENSP00000220676:A888G	ENSP00000220676:A888G	A	+	2	0	RP1	55701658	0.000000	0.05858	0.000000	0.03702	0.313000	0.28021	-0.131000	0.10482	-0.237000	0.09739	0.655000	0.94253	GCT	.	.		0.328	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55539105	C	G	55539105	3	3	177	1	0	0	0	0	1	0	0	0	13547	797	28	4	2673	4	RP1	8	55539105	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10		55539105	90824917	54	26634										
ARHGAP39	80728	hgsc.bcm.edu	37	chr8	145772918	145772918	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ctcggccaggggctgctccaCaagcaggtccccggggccct	14	17	0	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr8:145772918C>G	ENST00000276826.5	-	4	1753	c.1552G>C	c.(1552-1554)Gtg>Ctg	p.V518L	ARHGAP39_ENST00000377307.2_Missense_Mutation_p.V518L|ARHGAP39_ENST00000528810.1_5'Flank|ARHGAP39_ENST00000540274.1_Missense_Mutation_p.V518L			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	518					axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						GGCTGCTCCACAAGCAGGTCC	0.726																																					p.V518L		Atlas-SNP	.											.	ARHGAP39	80	.	0			c.G1552C						.						4	5	5					8																	145772918		2012	4028	6040	SO:0001583	missense	80728	exon6			GCTCCACAAGCAG		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"Rho GTPase activating proteins"	29351	protein-coding gene	gene with protein product	"RhoGAP93B homolog (Drosophila)", "crossGAP homolog (Drosophila)"	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.1552G>C	chr8.hg19:g.145772918C>G	ENSP00000276826:p.Val518Leu	26.0	0.0		56.0	18.0	NM_025251	B4E1I1	Missense_Mutation	SNP	ENST00000276826.5	hg19		.	.	.	.	.	.	.	.	.	.	C	1.742	-0.491430	0.04322	.	.	ENSG00000147799	ENST00000276826;ENST00000377307;ENST00000540274	T;T;T	0.67345	-0.26;-0.0;-0.26	5.0	-4.09	0.03951	.	1.450250	0.04111	N	0.314607	T	0.40694	0.1127	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.14282	-1.0478	10	0.41790	T	0.15	-12.8646	2.9044	0.05716	0.1112:0.2954:0.1211:0.4723	.	518;518	Q9C0H5;Q9C0H5-2	RHG39_HUMAN;.	L	518	ENSP00000276826:V518L;ENSP00000366522:V518L;ENSP00000445075:V518L	ENSP00000276826:V518L	V	-	1	0	ARHGAP39	145743726	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.959000	0.03853	-0.777000	0.04572	-0.910000	0.02820	GTG	.	.		0.726	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			G	145772918	C	G	145772918	3	3	177	1	0	0	0	0	1	0	0	0	884	478	17	4	1824	4	ARHGAP39	8	145772918	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	90233813	145772918	591104	55	26635										
APBA1	320	hgsc.bcm.edu	37	chr9	72131502	72131502	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gagccgcaggccgtcgcgtgCgtccagctcgggcgcgtccc	16	17	0	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr9:72131502C>T	ENST00000265381.4	-	2	847	c.625G>A	c.(625-627)Gca>Aca	p.A209T		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	209					axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						CCGTCGCGTGCGTCCAGCTCG	0.721																																					p.A209T		Atlas-SNP	.											.	APBA1	96	.	0			c.G625A						.						18	20	19					9																	72131502		2198	4296	6494	SO:0001583	missense	320	exon2			CGCGTGCGTCCAG	AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.625G>A	chr9.hg19:g.72131502C>T	ENSP00000265381:p.Ala209Thr	15.0	0.0		24.0	11.0	NM_001163	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	ENST00000265381.4	hg19	CCDS6630.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.405888	0.42715	.	.	ENSG00000107282	ENST00000265381	T	0.04015	3.73	5.26	4.37	0.52481	.	0.379769	0.28398	N	0.015499	T	0.02767	0.0083	N	0.14661	0.345	0.30068	N	0.810262	B	0.31519	0.327	B	0.17098	0.017	T	0.34104	-0.9842	10	0.22706	T	0.39	.	10.685	0.45837	0.0:0.8519:0.0:0.1481	.	209	Q02410	APBA1_HUMAN	T	209	ENSP00000265381:A209T	ENSP00000265381:A209T	A	-	1	0	APBA1	71321322	0.002000	0.14202	1.000000	0.80357	0.915000	0.54546	0.742000	0.26216	1.363000	0.46019	0.561000	0.74099	GCA	.	.		0.721	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		T	72131502	C	T	72131502	3	4	177	1	0	0	0	0	1	0	0	0	756	768	27	1	1936	1	APBA1	9	72131502	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10		72131502	69081929	56	26636										
FNBP1	23048	hgsc.bcm.edu	37	chr9	132662721	132662721	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gtacctctcacggtcctgggCgcagttgttgactgtgggtg	15	10	1	1	rs200153012	byFrequency	TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr9:132662721C>T	ENST00000446176.2	-	14	1720	c.1534G>A	c.(1534-1536)Gcc>Acc	p.A512T	FNBP1_ENST00000355681.3_Missense_Mutation_p.A483T|FNBP1_ENST00000420781.1_Missense_Mutation_p.A503T|FNBP1_ENST00000443566.2_Missense_Mutation_p.A140T|FNBP1_ENST00000478129.1_5'UTR	NM_015033.2	NP_055848.1	Q96RU3	FNBP1_HUMAN	formin binding protein 1	512	Interaction with PDE6G. {ECO:0000250}.|Interaction with RND2. {ECO:0000250}.|Required for self-association and induction of membrane tubulation.				endocytosis (GO:0006897)	coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)						Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		CGGTCCTGGGCGCAGTTGTTG	0.582			T	MLL	AML																																p.A512T		Atlas-SNP	.		Dom	yes		9	9q23	23048	formin binding protein 1 (FBP17)		L	.	FNBP1	51	.	0			c.G1534A						.						45	50	48					9																	132662721		2032	4177	6209	SO:0001583	missense	23048	exon14			CCTGGGCGCAGTT	AB011126	CCDS48040.1	9q34	2008-02-05			ENSG00000187239	ENSG00000187239			17069	protein-coding gene	gene with protein product		606191				9628581, 11438682	Standard	XM_005251815		Approved	FBP17, KIAA0554	uc004byw.1	Q96RU3	OTTHUMG00000020800	ENST00000446176.2:c.1534G>A	chr9.hg19:g.132662721C>T	ENSP00000413625:p.Ala512Thr	84.0	0.0		70.0	37.0	NM_015033	O60301|Q3MIN8|Q5TC87|Q5TC88|Q6P658|Q7LGG2|Q9H8H8|Q9NWD1	Missense_Mutation	SNP	ENST00000446176.2	hg19	CCDS48040.1	.	.	.	.	.	.	.	.	.	.	C	9.474	1.096361	0.20552	.	.	ENSG00000187239	ENST00000372416;ENST00000446176;ENST00000420781;ENST00000372415;ENST00000443566;ENST00000355681	T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76	4.24	4.24	0.50183	.	0.452086	0.23235	N	0.050411	T	0.67795	0.2931	L	0.46614	1.455	0.58432	D	0.999998	B;P;P;B;B;P;B;P	0.41232	0.033;0.5;0.743;0.003;0.024;0.5;0.024;0.5	B;B;B;B;B;B;B;B	0.38842	0.03;0.102;0.283;0.007;0.016;0.102;0.027;0.102	T	0.67288	-0.5708	10	0.25751	T	0.34	-18.395	16.1327	0.81454	0.0:1.0:0.0:0.0	.	507;502;140;446;483;463;507;512	B7ZL12;B7ZL13;E7EPB7;B7ZL14;Q96RU3-3;Q5QP69;Q96RU3-2;Q96RU3	.;.;.;.;.;.;.;FNBP1_HUMAN	T	512;512;503;512;140;483	ENSP00000413625:A512T;ENSP00000407548:A503T;ENSP00000389117:A140T;ENSP00000347907:A483T	ENSP00000347907:A483T	A	-	1	0	FNBP1	131702542	1.000000	0.71417	0.402000	0.26371	0.221000	0.24807	4.878000	0.63093	2.340000	0.79590	0.313000	0.20887	GCC	.	.		0.582	FNBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054630.2			T	132662721	C	T	132662721	3	4	177	1	0	0	0	0	1	0	0	0	5973	768	27	1	335	1	FNBP1	9	132662721	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	60531219	132662721	8550710	57	26637										
FCN1	2219	hgsc.bcm.edu	37	chr9	137804337	137804337	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cggcagtggccctaccctggGcagtcagggcgtggatgttg	17	11	1	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr9:137804337G>C	ENST00000371806.3	-	7	684	c.593C>G	c.(592-594)gCc>gGc	p.A198G		NM_002003.3	NP_001994.2	O00602	FCN1_HUMAN	ficolin (collagen/fibrinogen domain containing) 1	198	B domain; contributes to trimerization.|Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell surface pattern recognition receptor signaling pathway (GO:0002752)|complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of interleukin-8 secretion (GO:2000484)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extrinsic component of external side of plasma membrane (GO:0031232)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|G-protein coupled receptor binding (GO:0001664)|signaling pattern recognition receptor activity (GO:0008329)			endometrium(3)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	37		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		CCTACCCTGGGCAGTCAGGGC	0.637																																					p.A198G		Atlas-SNP	.											.	FCN1	62	.	0			c.C593G						.						43	41	41					9																	137804337		2203	4300	6503	SO:0001583	missense	2219	exon7			CCCTGGGCAGTCA	D83920	CCDS6985.1	9q34	2013-02-06	2002-01-14		ENSG00000085265	ENSG00000085265		"Fibrinogen C domain containing"	3623	protein-coding gene	gene with protein product		601252	"ficolin (collagen/fibrinogen domain-containing) 1"			8573080, 8884275	Standard	NM_002003		Approved	FCNM	uc004cfi.3	O00602	OTTHUMG00000020895	ENST00000371806.3:c.593C>G	chr9.hg19:g.137804337G>C	ENSP00000360871:p.Ala198Gly	24.0	0.0		40.0	25.0	NM_002003	Q5VYV5|Q92596	Missense_Mutation	SNP	ENST00000371806.3	hg19	CCDS6985.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.657097	0.29425	.	.	ENSG00000085265	ENST00000371806;ENST00000308299	T	0.20332	2.08	3.57	2.66	0.31614	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	.	.	.	.	T	0.22399	0.0540	L	0.61036	1.89	0.27524	N	0.951308	B	0.21071	0.051	B	0.21546	0.035	T	0.10823	-1.0613	9	0.52906	T	0.07	.	8.6147	0.33824	0.1212:0.0:0.8788:0.0	.	198	O00602	FCN1_HUMAN	G	198;186	ENSP00000360871:A198G	ENSP00000308877:A186G	A	-	2	0	FCN1	136944158	0.012000	0.17670	0.994000	0.49952	0.478000	0.33099	1.830000	0.39131	1.988000	0.58038	0.549000	0.68633	GCC	.	.		0.637	FCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054963.1	NM_002003		C	137804337	G	C	137804337	3	2	177	1	0	0	0	0	1	0	0	0	5799	1203	42	4	399	4	FCN1	9	137804337	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	5141616	137804337	3409094	58	26638										
KIAA1984	84960	hgsc.bcm.edu	37	chr9	139694929	139694929	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cctgctgtatttggacctgcTggattatctgaagacagtga	11	8	1	3			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr9:139694929T>A	ENST00000338005.6	+	5	562	c.527T>A	c.(526-528)cTg>cAg	p.L176Q	RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.L206Q|RP11-216L13.18_ENST00000471502.1_RNA|KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		176										biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		TTGGACCTGCTGGATTATCTG	0.632																																					p.L176Q		Atlas-SNP	.											.	KIAA1984	39	.	0			c.T527A						.						43	46	45					9																	139694929		1974	4151	6125	SO:0001583	missense	84960	exon5			ACCTGCTGGATTA																												ENST00000338005.6:c.527T>A	chr9.hg19:g.139694929T>A	ENSP00000338013:p.Leu176Gln	77.0	0.0		83.0	38.0	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	hg19	CCDS43906.1	.	.	.	.	.	.	.	.	.	.	T	13.90	2.374885	0.42105	.	.	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.13307	2.6	4.4	4.4	0.53042	.	0.275088	0.19040	U	0.124317	T	0.31199	0.0789	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.01416	-1.1360	10	0.44086	T	0.13	-13.1308	10.0186	0.42029	0.0:0.0:0.0:1.0	.	176	Q5T5S1	K1984_HUMAN	Q	176	ENSP00000338013:L176Q	ENSP00000338013:L176Q	L	+	2	0	KIAA1984	138814750	1.000000	0.71417	0.990000	0.47175	0.207000	0.24258	1.024000	0.30077	1.617000	0.50277	0.254000	0.18369	CTG	.	.		0.632	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1			A	139694929	T	A	139694929	3	1	177	1	0	0	0	0	1	0	0	0	8275	1580	55	4	545	4	KIAA1984	9	139694929	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	1890592	139694929	1518502	59	26639										
NSUN6	221078	hgsc.bcm.edu	37	chr10	18840757	18840757	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cagaccaccacatactgcagTgaagagttttcgctgtaatg	9	10	0	3			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr10:18840757T>A	ENST00000377304.4	-	9	1484	c.1066A>T	c.(1066-1068)Act>Tct	p.T356S	NSUN6_ENST00000493816.1_5'Flank	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	356							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						CATACTGCAGTGAAGAGTTTT	0.428																																					p.T356S		Atlas-SNP	.											.	NSUN6	46	.	0			c.A1066T						.						169	141	150					10																	18840757		2203	4300	6503	SO:0001583	missense	221078	exon9			CTGCAGTGAAGAG	BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"NOP2/Sun domain containing"	23529	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 6", "NOL1/NOP2/Sun domain family, member 6", "ARL5B antisense RNA 1"	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.1066A>T	chr10.hg19:g.18840757T>A	ENSP00000366519:p.Thr356Ser	117.0	0.0		127.0	57.0	NM_182543	B0YJ54	Missense_Mutation	SNP	ENST00000377304.4	hg19	CCDS7130.1	.	.	.	.	.	.	.	.	.	.	T	0.894	-0.724502	0.03158	.	.	ENSG00000241058	ENST00000377304	T	0.19938	2.11	5.8	-4.74	0.03249	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.697963	0.15563	N	0.255843	T	0.05318	0.0141	N	0.05280	-0.08	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.33445	-0.9868	10	0.09338	T	0.73	.	1.1283	0.01740	0.4004:0.1784:0.0978:0.3235	.	356	Q8TEA1	NSUN6_HUMAN	S	356	ENSP00000366519:T356S	ENSP00000366519:T356S	T	-	1	0	NSUN6	18880763	0.986000	0.35501	0.164000	0.22755	0.144000	0.21451	0.459000	0.21908	-0.872000	0.04037	0.459000	0.35465	ACT	.	.		0.428	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543		A	18840757	T	A	18840757	3	1	177	1	0	0	0	0	1	0	0	0	10691	1696	59	4	355	4	NSUN6	10	18840757	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10		18840757	116693990	60	26640										
PARG	8505	hgsc.bcm.edu	37	chr10	51028243	51028243	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tcctttcagtaaggaaaatgTgcatgctgtaaatgtctctc	8	8	2	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr10:51028243T>C	ENST00000402038.3	-	13	1288	c.1289A>G	c.(1288-1290)cAc>cGc	p.H430R		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	915	A-domain.				carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		AAGGAAAATGTGCATGCTGTA	0.428																																					p.H915R		Atlas-SNP	.											.	PARG	46	.	0			c.A2744G						.						141	117	124					10																	51028243		692	1591	2283	SO:0001583	missense	8505	exon17			AAAATGTGCATGC	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.1289A>G	chr10.hg19:g.51028243T>C	ENSP00000384408:p.His430Arg	108.0	0.0		102.0	50.0	NM_003631	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Missense_Mutation	SNP	ENST00000402038.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.8|20.8	4.051718|4.051718	0.75960|0.75960	.|.	.|.	ENSG00000227345|ENSG00000227345	ENST00000402038|ENST00000432127	.|.	.|.	.|.	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|.	.|.	.|.	.|.	T|T	0.71273|0.71273	0.3320|0.3320	L|L	0.58101|0.58101	1.795|1.795	.|.	.|.	.|.	D;D;D;D;D;D;D|.	0.76494|.	0.999;0.999;0.974;0.987;0.987;0.987;0.999|.	D;D;P;P;P;P;D|.	0.74023|.	0.982;0.959;0.719;0.794;0.794;0.794;0.949|.	T|T	0.70809|0.70809	-0.4771|-0.4771	7|4	0.38643|.	T|.	0.18|.	-12.5834|-12.5834	16.5582|16.5582	0.84512|0.84512	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	833;915;466;183;430;455;915|.	Q86W56-2;Q86W56;A5YBK3;B4DHS4;Q5SQP4;B4DX76;Q0MQR4|.	.;PARG_HUMAN;.;.;.;.;.|.	R|A	430|131	.|.	ENSP00000384408:H430R|.	H|T	-|-	2|1	0|0	PARG|PARG	50698249|50698249	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.199000|7.199000	0.77831|0.77831	2.308000|2.308000	0.77769|0.77769	0.533000|0.533000	0.62120|0.62120	CAC|ACA	.	.		0.428	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		C	51028243	T	C	51028243	3	2	177	1	0	0	0	0	1	0	0	0	11457	1696	59	2	194	2	PARG	10	51028243	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	32187486	51028243	84506504	61	26641										
PHYHIPL	84457	hgsc.bcm.edu	37	chr10	61005248	61005248	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ccctgtggatctttctgtggGcaccgtggcagaaatcactg	12	11	3	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr10:61005248G>C	ENST00000373880.4	+	5	1292	c.1028G>C	c.(1027-1029)gGc>gCc	p.G343A	PHYHIPL_ENST00000373878.3_Missense_Mutation_p.G317A	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	343						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(3)|skin(1)|urinary_tract(1)	18						CTTTCTGTGGGCACCGTGGCA	0.453																																					p.G343A		Atlas-SNP	.											.	PHYHIPL	44	.	0			c.G1028C						.						75	70	72					10																	61005248		2203	4300	6503	SO:0001583	missense	84457	exon5			CTGTGGGCACCGT	AL834339	CCDS7254.1, CCDS44405.1	10q21.1	2013-02-11	2006-01-09		ENSG00000165443	ENSG00000165443		"Fibronectin type III domain containing"	29378	protein-coding gene	gene with protein product			"phytanoyl-CoA hydroxylase interacting protein-like"			11347906	Standard	NM_032439		Approved	KIAA1796, Em:AC025038.1	uc001jkk.4	Q96FC7	OTTHUMG00000018276	ENST00000373880.4:c.1028G>C	chr10.hg19:g.61005248G>C	ENSP00000362987:p.Gly343Ala	98.0	0.0		47.0	45.0	NM_032439	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Missense_Mutation	SNP	ENST00000373880.4	hg19	CCDS7254.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.931341	0.73442	.	.	ENSG00000165443	ENST00000373880;ENST00000373878	D;D	0.90563	-2.69;-2.69	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000001	D	0.96005	0.8699	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.96243	0.9177	10	0.87932	D	0	-22.0001	19.5263	0.95208	0.0:0.0:1.0:0.0	.	317;343	Q96FC7-2;Q96FC7	.;PHIPL_HUMAN	A	343;317	ENSP00000362987:G343A;ENSP00000362985:G317A	ENSP00000362985:G317A	G	+	2	0	PHYHIPL	60675254	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.864000	0.99589	2.608000	0.88229	0.655000	0.94253	GGC	.	.		0.453	PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439		C	61005248	G	C	61005248	3	2	177	1	0	0	0	0	1	0	0	0	11876	1203	42	4	1078	4	PHYHIPL	10	61005248	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	9977005	61005248	74529499	62	26642										
EIF5AL1	143244	hgsc.bcm.edu	37	chr10	81272785	81272785	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	caaggagattgagcagaagtAcgactgtggagaagagatcc	14	6	0	5			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr10:81272785A>C	ENST00000520547.2	+	1	429	c.380A>C	c.(379-381)tAc>tCc	p.Y127S	AL133481.1_ENST00000538322.1_5'Flank	NM_001099692.1	NP_001093162.1	Q6IS14	IF5AL_HUMAN	eukaryotic translation initiation factor 5A-like 1	127					mRNA transport (GO:0051028)|peptidyl-lysine modification to peptidyl-hypusine (GO:0008612)|positive regulation of translational elongation (GO:0045901)|positive regulation of translational termination (GO:0045905)|protein transport (GO:0015031)|translational frameshifting (GO:0006452)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)	ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			endometrium(1)	1	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			GAGCAGAAGTACGACTGTGGA	0.552																																					p.Y127S		Atlas-SNP	.											EIF5AL1_ENST00000520547,NS,carcinoma,0,2	EIF5AL1	24	.	0			c.A380C						.						116	129	125					10																	81272785		2198	4298	6496	SO:0001583	missense	143244	exon1			AGAAGTACGACTG		CCDS53546.1	10q22.3	2012-04-19			ENSG00000253626	ENSG00000253626			17419	protein-coding gene	gene with protein product			"eukaryotic translation initiation factor 5A pseudogene 1"	EIF5AP1			Standard	NM_001099692		Approved	bA342M3.3	uc009xrx.3	Q6IS14	OTTHUMG00000018563	ENST00000520547.2:c.380A>C	chr10.hg19:g.81272785A>C	ENSP00000430706:p.Tyr127Ser	145.0	0.0		84.0	26.0	NM_001099692		Missense_Mutation	SNP	ENST00000520547.2	hg19	CCDS53546.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.537149	0.27475	.	.	ENSG00000253626	ENST00000520547	T	0.42131	0.98	0.843	0.843	0.18935	Nucleic acid-binding, OB-fold-like (1);Translation elongation factor, IF5A C-terminal (1);Nucleic acid-binding, OB-fold (1);	.	.	.	.	T	0.38081	0.1027	M	0.71036	2.16	0.24973	N	0.991655	P	0.41947	0.766	B	0.38428	0.273	T	0.32402	-0.9908	9	0.87932	D	0	.	5.6445	0.17582	1.0:0.0:0.0:0.0	.	127	Q6IS14	IF5AL_HUMAN	S	127	ENSP00000430706:Y127S	ENSP00000430706:Y127S	Y	+	2	0	EIF5AL1	80942791	0.994000	0.37717	0.368000	0.25939	0.447000	0.32167	0.621000	0.24418	0.311000	0.23014	0.305000	0.20034	TAC	.	.		0.552	EIF5AL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048954.4	NM_001099692		C	81272785	A	C	81272785	3	2	177	1	0	0	0	0	1	0	0	0	5045	391	14	5	382	5	EIF5AL1	10	81272785	Missense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	20267537	81272785	54261962	63	26643										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720875	89720875	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tacttttctccaaattttaaGgtcagttaaattaaacattt	3	6	2	0	rs398123313|rs398123314		TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr10:89720875G>T	ENST00000371953.3	+	8	2383	c.1026G>T	c.(1024-1026)aaG>aaT	p.K342N	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	342	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.		K -> N (in CWS1; reduced phosphatase activity towards Ins(1,3,4,5)P4 but PtdIns(3,4,5)P3 phosphatase activity is similar to wild-type).		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.K342N(2)|p.G165_*404del(1)|p.D326_K342del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		CAAATTTTAAGGTCAGTTAAA	0.328		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.K342N		Atlas-SNP	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,colon,carcinoma,+1,2	PTEN	3652	.	52	Whole gene deletion(37)|Deletion - Frameshift(9)|Substitution - Missense(2)|Deletion - In frame(2)|Unknown(2)	prostate(16)|central_nervous_system(11)|skin(6)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|breast(3)|ovary(3)|endometrium(2)|urinary_tract(2)|soft_tissue(1)	c.G1026T						.						45	48	47					10																	89720875		2203	4299	6502	SO:0001630	splice_region_variant	5728	exon8	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	TTTTAAGGTCAGT	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.1026+1G>T	chr10.hg19:g.89720875G>T		265.0	0.0		136.0	117.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.301086	0.81136	.	.	ENSG00000171862	ENST00000371953	D	0.86769	-2.17	5.37	5.37	0.77165	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.92747	0.7694	M	0.80616	2.505	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.92741	0.6208	9	.	.	.	-6.3339	12.4512	0.55679	0.0771:0.0:0.9229:0.0	.	342	P60484	PTEN_HUMAN	N	342	ENSP00000361021:K342N	.	K	+	3	2	PTEN	89710855	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.290000	0.65661	2.516000	0.84829	0.591000	0.81541	AAG	.	.		0.328	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	Missense_Mutation	T	89720875	G	T	89720875	5	4	177	1	0	0	0	0	0	0	1	0	12750	1014	35	3	1056	3	PTEN	10	89720875	Splice_Site	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	8448090	89720875	45813872	64	26644										
HMX3	340784	hgsc.bcm.edu	37	chr10	124895764	124895764	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tcggctgccgccgccgccgcCgctgccgctgccgcggcggc	16	21	0	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr10:124895764C>T	ENST00000357878.5	+	1	287	c.198C>T	c.(196-198)gcC>gcT	p.A66A		NM_001105574.1	NP_001099044.1	A6NHT5	HMX3_HUMAN	H6 family homeobox 3	66	Ala-rich.				brain development (GO:0007420)|cell differentiation (GO:0030154)|embryo implantation (GO:0007566)|inner ear morphogenesis (GO:0042472)|maternal process involved in female pregnancy (GO:0060135)|neuromuscular process controlling balance (GO:0050885)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(4)	4		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.122)|COAD - Colon adenocarcinoma(40;0.141)		ccgccgccgccgctgccgctg	0.751																																					p.A66A		Atlas-SNP	.											.	HMX3	24	.	0			c.C198T						.						2	2	2					10																	124895764		902	2340	3242	SO:0001819	synonymous_variant	340784	exon1			CGCCGCCGCTGCC		CCDS41575.1	10q26.13	2011-06-20	2007-07-09		ENSG00000188620	ENSG00000188620		"Homeoboxes / ANTP class : NKL subclass"	5019	protein-coding gene	gene with protein product		613380	"homeo box (H6 family) 3"				Standard	NM_001105574		Approved	NKX5-1	uc010quc.2	A6NHT5	OTTHUMG00000019199	ENST00000357878.5:c.198C>T	chr10.hg19:g.124895764C>T		127.0	0.0		122.0	5.0	NM_001105574	A8MU06	Silent	SNP	ENST00000357878.5	hg19	CCDS41575.1																																																																																			.	.		0.751	HMX3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050842.4	XM_291716		T	124895764	C	T	124895764	2	4	177	1	0	0	0	0	0	0	0	1	7257	639	23	1		1	HMX3	10	124895764	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	35174889	124895764	10638983	65	26645										
ANO9	338440	hgsc.bcm.edu	37	chr11	431763	431763	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	acgtcttcttcaggcgtcccTccccctggctcgggtgacag	11	16	3	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr11:431763T>C	ENST00000332826.6	-	7	554	c.470A>G	c.(469-471)gAg>gGg	p.E157G		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	157					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						CAGGCGTCCCTCCCCCTGGCT	0.647																																					p.E157G		Atlas-SNP	.											ANO9,bladder,carcinoma,0,1	ANO9	61	.	0			c.A470G						.						58	58	58					11																	431763		2203	4298	6501	SO:0001583	missense	338440	exon7			CGTCCCTCCCCCT	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	20679	protein-coding gene	gene with protein product			"tumor protein p53 inducible protein 5", "transmembrane protein 16J"	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.470A>G	chr11.hg19:g.431763T>C	ENSP00000332788:p.Glu157Gly	45.0	0.0		59.0	5.0	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	hg19	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.167925	0.57476	.	.	ENSG00000185101	ENST00000332826	T	0.69435	-0.4	4.25	4.25	0.50352	.	1.072170	0.07407	U	0.891802	T	0.56337	0.1978	L	0.29908	0.895	0.23889	N	0.996556	B	0.26577	0.153	B	0.19391	0.025	T	0.41016	-0.9532	10	0.28530	T	0.3	.	12.9873	0.58598	0.0:0.0:0.0:1.0	.	157	A1A5B4	ANO9_HUMAN	G	157	ENSP00000332788:E157G	ENSP00000332788:E157G	E	-	2	0	ANO9	421763	0.078000	0.21339	0.025000	0.17156	0.030000	0.12068	2.690000	0.47001	1.930000	0.55929	0.397000	0.26171	GAG	.	.		0.647	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302		C	431763	T	C	431763	3	2	177	1	0	0	0	0	1	0	0	0	704	1551	54	2	1946	2	ANO9	11	431763	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10		431763	134574753	66	26646										
FXC1	26515	hgsc.bcm.edu	37	chr11	6503054	6503054	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ccagcgctgtgtgcccagctTgcaccaccgagctctggacg	12	16	1	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr11:6503054T>C	ENST00000254616.6	+	2	177	c.107T>C	c.(106-108)tTg>tCg	p.L36S	ARFIP2_ENST00000254584.2_5'Flank|ARFIP2_ENST00000396777.3_5'Flank|ARFIP2_ENST00000445086.2_5'Flank|TIMM10B_ENST00000530751.1_Intron|TIMM10B_ENST00000472836.1_Missense_Mutation_p.L36S|ARFIP2_ENST00000525235.1_5'Flank|ARFIP2_ENST00000423813.2_5'Flank	NM_012192.3	NP_036324.1	Q9Y5J6	T10B_HUMAN	translocase of inner mitochondrial membrane 10 homolog B (yeast)	36					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial intermembrane space protein transporter complex (GO:0042719)	metal ion binding (GO:0046872)										GTGCCCAGCTTGCACCACCGA	0.562																																					p.L36S		Atlas-SNP	.											.	.	.	.	0			c.T107C						.						75	69	71					11																	6503054		2201	4296	6497	SO:0001583	missense	26515	exon2			CCAGCTTGCACCA	AF150105	CCDS7766.1	11p15.4	2012-12-07	2012-12-07	2012-12-07	ENSG00000132286	ENSG00000132286			4022	protein-coding gene	gene with protein product		607388	"fracture callus 1 (rat) homolog", "fracture callus 1 homolog (rat)"	FXC1		10552927	Standard	NM_012192		Approved	Tim9b, TIM10B	uc001mdn.4	Q9Y5J6	OTTHUMG00000133400	ENST00000254616.6:c.107T>C	chr11.hg19:g.6503054T>C	ENSP00000254616:p.Leu36Ser	40.0	0.0		45.0	22.0	NM_012192	Q96FF3	Missense_Mutation	SNP	ENST00000254616.6	hg19	CCDS7766.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.520846	0.85495	.	.	ENSG00000132286	ENST00000254616;ENST00000533379	T;T	0.65549	-0.16;-0.16	5.82	5.82	0.92795	.	0.200578	0.44483	D	0.000451	T	0.77170	0.4091	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.79629	-0.1724	10	0.87932	D	0	-8.9917	14.3986	0.67027	0.0:0.0:0.0:1.0	.	36	Q9Y5J6	TIM9B_HUMAN	S	36	ENSP00000254616:L36S;ENSP00000436948:L36S	ENSP00000254616:L36S	L	+	2	0	FXC1	6459630	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.170000	0.71920	2.214000	0.71695	0.460000	0.39030	TTG	.	.		0.562	TIMM10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257257.2	NM_012192		C	6503054	T	C	6503054	3	2	177	1	0	0	0	0	1	0	0	0	6121	1821	63	2	113	2	FXC1	11	6503054	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	6071291	6503054	128503462	67	26647										
TAF10	6881	hgsc.bcm.edu	37	chr11	6632187	6632187	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gcggcttcttcacattgatgCcatactcgctgagggcaggg	13	11	2	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr11:6632187C>A	ENST00000299424.4	-	5	1100	c.623G>T	c.(622-624)gGc>gTc	p.G208V	RP11-732A19.2_ENST00000527398.1_RNA|TAF10_ENST00000531760.1_5'Flank	NM_006284.3	NP_006275.1	Q12962	TAF10_HUMAN	TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa	208					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|perinuclear region of cytoplasm (GO:0048471)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|RNA polymerase binding (GO:0070063)|transcription coactivator activity (GO:0003713)						Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.0481)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CACATTGATGCCATACTCGCT	0.517																																					p.G208V		Atlas-SNP	.											.	TAF10	9	.	0			c.G623T						.						161	140	147					11																	6632187		2201	4296	6497	SO:0001583	missense	6881	exon5			TTGATGCCATACT	U13991, U25816	CCDS7769.1	11p15.5-p15.2	2006-11-14	2002-08-29	2001-12-07	ENSG00000166337	ENSG00000166337			11543	protein-coding gene	gene with protein product		600475	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, H, 30kD"	TAF2H, TAF2A		7923369	Standard	NM_006284		Approved	TAFII30	uc001mej.2	Q12962	OTTHUMG00000133402	ENST00000299424.4:c.623G>T	chr11.hg19:g.6632187C>A	ENSP00000299424:p.Gly208Val	154.0	0.0		172.0	84.0	NM_006284	O00703|Q13175|Q6FH13	Missense_Mutation	SNP	ENST00000299424.4	hg19	CCDS7769.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.419623	0.62622	.	.	ENSG00000166337	ENST00000299424	T	0.79749	-1.3	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.91486	0.7312	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93089	0.6498	10	0.87932	D	0	-15.8773	17.0075	0.86397	0.0:1.0:0.0:0.0	.	208	Q12962	TAF10_HUMAN	V	208	ENSP00000299424:G208V	ENSP00000299424:G208V	G	-	2	0	TAF10	6588763	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.804000	0.69135	2.582000	0.87167	0.655000	0.94253	GGC	.	.		0.517	TAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257259.2	NM_006284		A	6632187	C	A	6632187	3	1	177	1	0	0	0	0	1	0	0	0	15529	739	26	3	37	3	TAF10	11	6632187	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	129133	6632187	128374329	68	26648										
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563231	55563231	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tatgtactttttccttagtcAcctctcttttgttgattttt	4	8	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr11:55563231A>C	ENST00000335605.1	+	1	200	c.200A>C	c.(199-201)cAc>cCc	p.H67P		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	67						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				TTCCTTAGTCACCTCTCTTTT	0.383																																					p.H67P		Atlas-SNP	.											.	OR5D14	116	.	0			c.A200C						.						220	198	206					11																	55563231		2200	4296	6496	SO:0001583	missense	219436	exon1			TTAGTCACCTCTC	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.200A>C	chr11.hg19:g.55563231A>C	ENSP00000334456:p.His67Pro	78.0	0.0		75.0	40.0	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	hg19	CCDS31508.1	.	.	.	.	.	.	.	.	.	.	a	9.284	1.048796	0.19827	.	.	ENSG00000186113	ENST00000335605	T	0.12569	2.67	5.08	2.62	0.31277	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47455	D	0.000233	T	0.31040	0.0784	H	0.94771	3.58	0.09310	N	1	P	0.52577	0.954	P	0.49708	0.62	T	0.31420	-0.9944	10	0.72032	D	0.01	-12.2834	5.8009	0.18414	0.7686:0.0:0.0831:0.1483	.	67	Q8NGL3	OR5DE_HUMAN	P	67	ENSP00000334456:H67P	ENSP00000334456:H67P	H	+	2	0	OR5D14	55319807	0.003000	0.15002	0.234000	0.24042	0.016000	0.09150	2.096000	0.41738	0.792000	0.33850	-0.263000	0.10527	CAC	.	.		0.383	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		C	55563231	A	C	55563231	3	2	177	1	0	0	0	0	1	0	0	0	11164	159	6	5	202	5	OR5D14	11	55563231	Missense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	48931044	55563231	79443285	69	26649										
MS4A6E	245802	hgsc.bcm.edu	37	chr11	60107402	60107402	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gcctagctgtgctcactgctGtgctgcagtggaaacagact	12	11	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr11:60107402G>C	ENST00000300182.4	+	3	483	c.418G>C	c.(418-420)Gtg>Ctg	p.V140L		NM_139249.2	NP_640342.1	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member 6E	140						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(9)|stomach(1)	13						GCTCACTGCTGTGCTGCAGTG	0.483																																					p.V140L		Atlas-SNP	.											.	MS4A6E	22	.	0			c.G418C						.						237	217	224					11																	60107402		2203	4300	6503	SO:0001583	missense	245802	exon3			ACTGCTGTGCTGC	AF354931	CCDS7984.1	11q12	2008-03-25				ENSG00000166926			14285	protein-coding gene	gene with protein product		608402				11486273	Standard	NM_139249		Approved		uc001npd.3	Q96DS6		ENST00000300182.4:c.418G>C	chr11.hg19:g.60107402G>C	ENSP00000300182:p.Val140Leu	44.0	0.0		42.0	18.0	NM_139249	Q3MIL2|Q8NE56|Q96PG4|Q96PG5	Missense_Mutation	SNP	ENST00000300182.4	hg19	CCDS7984.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.470450	0.26423	.	.	ENSG00000166926	ENST00000300182	T	0.02498	4.27	1.6	0.641	0.17759	.	2.663120	0.01548	N	0.019541	T	0.08088	0.0202	L	0.42686	1.345	0.09310	N	1	P	0.48230	0.907	P	0.58820	0.846	T	0.18493	-1.0335	10	0.52906	T	0.07	.	3.7255	0.08473	0.2524:0.0:0.7476:0.0	.	140	Q96DS6	M4A6E_HUMAN	L	140	ENSP00000300182:V140L	ENSP00000300182:V140L	V	+	1	0	MS4A6E	59863978	0.002000	0.14202	0.132000	0.22025	0.108000	0.19459	-0.792000	0.04594	0.219000	0.20840	0.195000	0.17529	GTG	.	.		0.483	MS4A6E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394296.1			C	60107402	G	C	60107402	3	2	177	1	0	0	0	0	1	0	0	0	9874	1377	48	4	428	4	MS4A6E	11	60107402	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	4544171	60107402	74899114	70	26650										
GAL3ST3	89792	hgsc.bcm.edu	37	chr11	65810480	65810480	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cggcgcgcgcgttgagcttgGcgtagagcacgtcgtccagg	17	12	0	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr11:65810480G>A	ENST00000312006.4	-	3	1075	c.794C>T	c.(793-795)gCc>gTc	p.A265V	GAL3ST3_ENST00000527878.1_Missense_Mutation_p.A265V	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	265					monosaccharide metabolic process (GO:0005996)|oligosaccharide metabolic process (GO:0009311)|poly-N-acetyllactosamine metabolic process (GO:0030309)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|carbohydrate binding (GO:0030246)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			kidney(1)|lung(9)|ovary(2)|skin(2)	14						GTTGAGCTTGGCGTAGAGCAC	0.711																																					p.A265V		Atlas-SNP	.											.	GAL3ST3	40	.	0			c.C794T						.						18	18	18					11																	65810480		2199	4291	6490	SO:0001583	missense	89792	exon3			AGCTTGGCGTAGA	AY026481	CCDS8128.1	11q13.1	2014-08-12			ENSG00000175229	ENSG00000175229		"Sulfotransferases, membrane-bound"	24144	protein-coding gene	gene with protein product		608234				11323440, 11356829	Standard	NM_033036		Approved	GAL3ST2	uc001ogw.3	Q96A11	OTTHUMG00000166667	ENST00000312006.4:c.794C>T	chr11.hg19:g.65810480G>A	ENSP00000308591:p.Ala265Val	35.0	0.0		51.0	25.0	NM_033036	Q14D05	Missense_Mutation	SNP	ENST00000312006.4	hg19	CCDS8128.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.958602	0.53400	.	.	ENSG00000175229	ENST00000312006;ENST00000527878	T;T	0.14516	2.5;2.5	4.41	4.41	0.53225	.	0.154383	0.42682	D	0.000668	T	0.07863	0.0197	N	0.16478	0.41	0.39558	D	0.969088	B	0.18013	0.025	B	0.11329	0.006	T	0.26950	-1.0088	10	0.25106	T	0.35	-19.3267	8.6749	0.34174	0.1056:0.0:0.8944:0.0	.	265	Q96A11	G3ST3_HUMAN	V	265	ENSP00000308591:A265V;ENSP00000434829:A265V	ENSP00000308591:A265V	A	-	2	0	GAL3ST3	65567056	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.054000	0.71096	2.157000	0.67596	0.561000	0.74099	GCC	.	.		0.711	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391052.1	NM_033036		A	65810480	G	A	65810480	3	1	177	1	0	0	0	0	1	0	0	0	6207	1203	42	3	505	3	GAL3ST3	11	65810480	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	5703078	65810480	69196036	71	26651										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66456306	66456306	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ccctgcatctcttccaaacaCaagcacctccaaaactggca	4	17	1	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr11:66456306C>A	ENST00000533211.1	-	31	6380	c.6049G>T	c.(6049-6051)Gtg>Ttg	p.V2017L	SPTBN2_ENST00000309996.2_Missense_Mutation_p.V2017L|SPTBN2_ENST00000529997.1_Missense_Mutation_p.V2017L			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	2017					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CTTCCAAACACAAGCACCTCC	0.612																																					p.V2017L		Atlas-SNP	.											.	SPTBN2	188	.	0			c.G6049T						.						37	40	39					11																	66456306		2200	4295	6495	SO:0001583	missense	6712	exon30			CAAACACAAGCAC	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.6049G>T	chr11.hg19:g.66456306C>A	ENSP00000432568:p.Val2017Leu	33.0	0.0		33.0	10.0	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.586045	0.46110	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.47528	0.84;0.84;0.84	4.77	1.8	0.24995	.	0.312185	0.31531	N	0.007494	T	0.16599	0.0399	N	0.01202	-0.96	0.29311	N	0.86799	B	0.06786	0.001	B	0.10450	0.005	T	0.15665	-1.0429	10	0.25751	T	0.34	.	6.8592	0.24058	0.0:0.4958:0.0:0.5042	.	2017	O15020	SPTN2_HUMAN	L	2017	ENSP00000432568:V2017L;ENSP00000311489:V2017L;ENSP00000433593:V2017L	ENSP00000311489:V2017L	V	-	1	0	SPTBN2	66212882	0.430000	0.25538	0.929000	0.37066	0.965000	0.64279	0.707000	0.25704	0.202000	0.20498	-0.229000	0.12294	GTG	.	.		0.612	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		A	66456306	C	A	66456306	3	1	177	1	0	0	0	0	1	0	0	0	15135	478	17	3	1155	3	SPTBN2	11	66456306	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	645826	66456306	68550210	72	26652										
DLG2	1740	hgsc.bcm.edu	37	chr11	84996347	84996347	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	taaaacttgattggcttcttCtatcttctgctcacaacttt	4	10	5	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr11:84996347C>G	ENST00000376104.2	-	4	414	c.103G>C	c.(103-105)Gaa>Caa	p.E35Q	DLG2_ENST00000543673.1_Missense_Mutation_p.E35Q	NM_001142699.1	NP_001136171.1	Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0	L27 1. {ECO:0000255|PROSITE- ProRule:PRU00365}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				TTGGCTTCTTCTATCTTCTGC	0.353																																					p.E35Q		Atlas-SNP	.											.	DLG2	448	.	0			c.G103C						.						200	180	186					11																	84996347		1568	3581	5149	SO:0001583	missense	1740	exon4			CTTCTTCTATCTT	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000376104.2:c.103G>C	chr11.hg19:g.84996347C>G	ENSP00000365272:p.Glu35Gln	64.0	0.0		82.0	36.0	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000376104.2	hg19	CCDS44690.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.897745	0.52227	.	.	ENSG00000150672	ENST00000376104;ENST00000543673;ENST00000546021	T;T	0.12879	2.64;2.64	5.88	4.92	0.64577	.	0.312743	0.25222	N	0.032224	T	0.12646	0.0307	L	0.34521	1.04	0.80722	D	1	B	0.14012	0.009	B	0.08055	0.003	T	0.11324	-1.0592	9	.	.	.	.	18.3479	0.90328	0.0:0.8717:0.1283:0.0	.	35	Q15700-2	.	Q	35	ENSP00000365272:E35Q;ENSP00000441994:E35Q	.	E	-	1	0	DLG2	84673995	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.693000	0.47027	2.779000	0.95612	0.650000	0.86243	GAA	.	.		0.353	DLG2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259245.3	NM_001364		G	84996347	C	G	84996347	3	3	177	1	0	0	0	0	1	0	0	0	4557	922	32	4	3129	4	DLG2	11	84996347	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	18540041	84996347	50010169	73	26653										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2613673	2613673	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gtcatctttggatcctttttCgttctaaatctggttctcgg	8	9	5	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr12:2613673C>T	ENST00000399617.1	+	8	1185	c.1185C>T	c.(1183-1185)ttC>ttT	p.F395F	CACNA1C_ENST00000399621.1_Intron|CACNA1C_ENST00000399597.1_Intron|CACNA1C_ENST00000335762.5_Intron|CACNA1C_ENST00000399629.1_Intron|CACNA1C_ENST00000399591.1_Intron|CACNA1C_ENST00000399638.1_Intron|CACNA1C_ENST00000399634.1_Silent_p.F395F|CACNA1C_ENST00000399606.1_Intron|CACNA1C_ENST00000399641.1_Silent_p.F395F|CACNA1C_ENST00000402845.3_Intron|CACNA1C_ENST00000399637.1_Intron|CACNA1C_ENST00000347598.4_Intron|CACNA1C_ENST00000399603.1_Silent_p.F395F|CACNA1C_ENST00000480911.1_Intron|CACNA1C_ENST00000327702.7_Intron|CACNA1C_ENST00000491104.1_3'UTR|CACNA1C_ENST00000406454.3_Silent_p.F395F|CACNA1C_ENST00000399655.1_Intron|CACNA1C_ENST00000344100.3_Intron|CACNA1C_ENST00000399644.1_Intron|CACNA1C_ENST00000399649.1_Intron|CACNA1C_ENST00000399601.1_Intron|CACNA1C_ENST00000399595.1_Intron	NM_001167624.1	NP_001161096.1	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	395					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GATCCTTTTTCGTTCTAAATC	0.488																																					p.F395F		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.C1185T						.						295	247	261					12																	2613673		1568	3582	5150	SO:0001819	synonymous_variant	775	exon8			CTTTTTCGTTCTA	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000399617.1:c.1185C>T	chr12.hg19:g.2613673C>T		119.0	0.0		139.0	56.0	NM_001167623	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000399617.1	hg19	CCDS53733.1																																																																																			.	.		0.488	CACNA1C-013	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317031.1	NM_000719		T	2613673	C	T	2613673	2	4	177	1	0	0	0	0	0	0	0	1	2542	883	31	1		1	CACNA1C	12	2613673	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10		2613673	131238222	74	26654										
KRT2	3849	hgsc.bcm.edu	37	chr12	53045637	53045638	+	In_Frame_Ins	INS	-	-	CAAAGCCGCTGCCGCCTC													0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tccaaagctgctgccgcctcINScaaaaccacctcctctgcca							TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr12:53045637_53045638insCAAAGCCGCTGCCGCCTC	ENST00000309680.3	-	1	310_311	c.289_290insGAGGCGGCAGCGGCTTTG	c.(289-291)gga>gGAGGCGGCAGCGGCTTTGga	p.97_97G>GGGSGFG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	97	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		gctgccgcctccaaaaccacct	0.619																																					p.G97delinsGGGSGFG		Atlas-INDEL	.											.,2	KRT2	94	.	0			c.290_291insGAGGCGGCAGCGGCTTTG						.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.289_290insGAGGCGGCAGCGGCTTTG	chr12.hg19:g.53045637_53045638insCAAAGCCGCTGCCGCCTC	Exception_encountered	153.0	0.0		156.0	71.0	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.619	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		CAAAGCCGCTGCCGCCTC	53045638	-	CAAAGCCGCTGCCGCCTC	53045637	7	5	177	1	0	1	1	0	0	0	0	0	8466	855	30	0	1665	0	KRT2	12	53045637	In_Frame_Ins	INS	-	TCGA-DD-AAD0-01A-11D-A40R-10	50431964	53045637	80806258	75	26655										
DCN	1634	hgsc.bcm.edu	37	chr12	91552214	91552214	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	attcttggacagataaagtcGttccaacttcaccaaaggtg	8	9	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr12:91552214G>A	ENST00000052754.5	-	4	898	c.397C>T	c.(397-399)Cga>Tga	p.R133*	DCN_ENST00000420120.2_Intron|DCN_ENST00000441303.2_Intron|DCN_ENST00000228329.5_Intron|DCN_ENST00000303320.3_Intron|DCN_ENST00000547568.2_Intron|DCN_ENST00000425043.1_Intron|DCN_ENST00000552962.1_Nonsense_Mutation_p.R133*|DCN_ENST00000393155.1_Nonsense_Mutation_p.R133*|DCN_ENST00000456569.2_Intron	NM_001920.3	NP_001911.1	P07585	PGS2_HUMAN	decorin	133					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|kidney development (GO:0001822)|organ morphogenesis (GO:0009887)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|placenta development (GO:0001890)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	collagen type VI trimer (GO:0005589)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)|poly(A) RNA binding (GO:0044822)	p.R133*(1)		central_nervous_system(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|skin(1)	20						AGATAAAGTCGTTCCAACTTC	0.408																																					p.R133X		Atlas-SNP	.											DCN,rectum,carcinoma,+2,1	DCN	61	.	1	Substitution - Nonsense(1)	central_nervous_system(1)	c.C397T						.						131	127	128					12																	91552214		2203	4300	6503	SO:0001587	stop_gained	1634	exon4			AAAGTCGTTCCAA	AF138300	CCDS9039.1, CCDS9040.1, CCDS9041.1, CCDS9042.1, CCDS44951.1	12q21.33	2014-04-16			ENSG00000011465	ENSG00000011465		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	2705	protein-coding gene	gene with protein product	"decorin proteoglycan"	125255				8432526	Standard	NM_133507		Approved	DSPG2, SLRR1B	uc001tbt.3	P07585	OTTHUMG00000169998	ENST00000052754.5:c.397C>T	chr12.hg19:g.91552214G>A	ENSP00000052754:p.Arg133*	114.0	0.0		116.0	42.0	NM_001920	Q9P0Z0|Q9P0Z1|Q9Y5N8|Q9Y5N9	Nonsense_Mutation	SNP	ENST00000052754.5	hg19	CCDS9039.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.860018	0.91433	.	.	ENSG00000011465	ENST00000052754;ENST00000393155;ENST00000552962;ENST00000547937;ENST00000552145;ENST00000550563	.	.	.	5.69	1.07	0.20283	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	15.2272	0.73359	0.0:0.0:0.2263:0.7737	.	.	.	.	X	133	.	ENSP00000052754:R133X	R	-	1	2	DCN	90076345	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.109000	0.31135	0.276000	0.22118	0.650000	0.86243	CGA	.	.		0.408	DCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406799.3	NM_133507		A	91552214	G	A	91552214	4	1	177	1	0	0	0	0	0	1	0	0	4299	1153	40	1	702	1	DCN	12	91552214	Nonsense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	38506577	91552214	42299681	76	26656										
FREM2	341640	hgsc.bcm.edu	37	chr13	39435611	39435611	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ggggttgttggagcagagccGttctcagctaaattgcgcta	14	8	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr13:39435611G>C	ENST00000280481.7	+	15	7779	c.7563G>C	c.(7561-7563)ccG>ccC	p.P2521P		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2521					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GAGCAGAGCCGTTCTCAGCTA	0.438																																					p.P2521P		Atlas-SNP	.											.	FREM2	385	.	0			c.G7563C						.						151	125	133					13																	39435611		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon15			AGAGCCGTTCTCA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.7563G>C	chr13.hg19:g.39435611G>C		43.0	0.0		57.0	30.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39435611	G	C	39435611	2	2	177	1	0	0	0	0	0	0	0	1	6053	1132	40	4		4	FREM2	13	39435611	Silent	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10		39435611	75734267	77	26657										
PHF11	51131	hgsc.bcm.edu	37	chr13	50092193	50092193	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aaagaggagccaccgtgggaTgtgatttaaaaaactgtaac	11	6	0	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr13:50092193T>A	ENST00000378319.3	+	4	405	c.364T>A	c.(364-366)Tgt>Agt	p.C122S	PHF11_ENST00000357596.3_Missense_Mutation_p.C83S|PHF11_ENST00000488958.1_Missense_Mutation_p.C83S	NM_001040443.1	NP_001035533.1	Q9UIL8	PHF11_HUMAN	PHD finger protein 11	122					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(3)|lung(1)	4		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		CACCGTGGGATGTGATTTAAA	0.343																																					p.C122S		Atlas-SNP	.											.	PHF11	20	.	0			c.T364A						.						73	76	75					13																	50092193		2203	4300	6503	SO:0001583	missense	51131	exon4			GTGGGATGTGATT	AB011031	CCDS31975.1, CCDS41887.1	13q14.11	2014-05-20			ENSG00000136147	ENSG00000136147		"Zinc fingers, PHD-type"	17024	protein-coding gene	gene with protein product	"IgE responsiveness (atopic)"	607796				10508479, 15057823	Standard	XM_005266417		Approved	NY-REN-34, BCAP, IGER	uc001vdb.3	Q9UIL8	OTTHUMG00000016916	ENST00000378319.3:c.364T>A	chr13.hg19:g.50092193T>A	ENSP00000367570:p.Cys122Ser	307.0	0.0		298.0	134.0	NM_001040443	Q5W0A4|Q5W0A6|Q9Y5A2	Missense_Mutation	SNP	ENST00000378319.3	hg19	CCDS31975.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.52|16.52	3.147599|3.147599	0.57151|0.57151	.|.	.|.	ENSG00000136147|ENSG00000136147	ENST00000378319;ENST00000496612;ENST00000357596;ENST00000485919;ENST00000442195;ENST00000488958|ENST00000426879	D;D;D;D;D;D|.	0.98249|.	-4.82;-4.82;-4.82;-4.82;-4.82;-4.82|.	4.2|4.2	4.2|4.2	0.49525|0.49525	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);|.	0.000000|.	0.64402|.	D|.	0.000001|.	D|D	0.86289|0.86289	0.5897|0.5897	H|H	0.96777|0.96777	3.88|3.88	0.42650|0.42650	D|D	0.993444|0.993444	D;D|.	0.89917|.	1.0;0.999|.	D;D|.	0.77557|.	0.99;0.977|.	D|D	0.89843|0.89843	0.4004|0.4004	10|5	0.87932|.	D|.	0|.	-0.7518|-0.7518	11.1707|11.1707	0.48569|0.48569	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	122;122|.	B4DTX8;Q9UIL8|.	.;PHF11_HUMAN|.	S|E	122;54;83;83;83;83|76	ENSP00000367570:C122S;ENSP00000419229:C54S;ENSP00000350209:C83S;ENSP00000420129:C83S;ENSP00000405227:C83S;ENSP00000417539:C83S|.	ENSP00000350209:C83S|.	C|D	+|+	1|3	0|2	PHF11|PHF11	48990194|48990194	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.381000|0.381000	0.30169|0.30169	4.032000|4.032000	0.57274|0.57274	1.878000|1.878000	0.54408|0.54408	0.533000|0.533000	0.62120|0.62120	TGT|GAT	.	.		0.343	PHF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044915.1	NM_016119		A	50092193	T	A	50092193	3	1	177	1	0	0	0	0	1	0	0	0	11831	1464	51	4	378	4	PHF11	13	50092193	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	10656582	50092193	65077685	78	26658										
PSMB11	122706	hgsc.bcm.edu	37	chr14	23512092	23512092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cccaccgtgatgcctattcaGggggctctgtagaccttttc	10	13	2	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr14:23512092G>A	ENST00000408907.2	+	1	717	c.658G>A	c.(658-660)Ggg>Agg	p.G220R		NM_001099780.1	NP_001093250.1	A5LHX3	PSB11_HUMAN	proteasome (prosome, macropain) subunit, beta type, 11	220					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|kidney(2)|lung(4)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00643)		TGCCTATTCAGGGGGCTCTGT	0.612																																					p.G220R		Atlas-SNP	.											.	PSMB11	40	.	0			c.G658A						.						39	41	40					14																	23512092		2115	4232	6347	SO:0001583	missense	122706	exon1			TATTCAGGGGGCT		CCDS41923.1	14q11.2	2008-01-31				ENSG00000222028			31963	protein-coding gene	gene with protein product		611137				17540904	Standard	NM_001099780		Approved	beta5t	uc010ake.1	A5LHX3		ENST00000408907.2:c.658G>A	chr14.hg19:g.23512092G>A	ENSP00000386212:p.Gly220Arg	70.0	0.0		42.0	20.0	NM_001099780		Missense_Mutation	SNP	ENST00000408907.2	hg19	CCDS41923.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.301046	0.60195	.	.	ENSG00000222028	ENST00000408907	T	0.43688	0.94	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.77315	0.4112	H	0.97265	3.97	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.86395	0.1738	10	0.87932	D	0	-30.1628	16.824	0.85926	0.0:0.0:1.0:0.0	.	220	A5LHX3	PSB11_HUMAN	R	220	ENSP00000386212:G220R	ENSP00000386212:G220R	G	+	1	0	PSMB11	22581932	1.000000	0.71417	0.961000	0.40146	0.023000	0.10783	9.131000	0.94446	2.260000	0.74910	0.655000	0.94253	GGG	.	.		0.612	PSMB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408294.1	NM_001099780		A	23512092	G	A	23512092	3	1	177	1	0	0	0	0	1	0	0	0	12688	1000	35	3	660	3	PSMB11	14	23512092	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10		23512092	83837448	79	26659										
MYH6	4624	hgsc.bcm.edu	37	chr14	23869968	23869968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gactcctatgaagtactggcGtggctgcttggtctccaggg	14	10	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr14:23869968G>A	ENST00000356287.3	-	12	1389	c.1360C>T	c.(1360-1362)Cgc>Tgc	p.R454C	MYH6_ENST00000405093.3_Missense_Mutation_p.R454C			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	454	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		AAGTACTGGCGTGGCTGCTTG	0.567																																					p.R454C		Atlas-SNP	.											MYH6,NS,malignant_melanoma,+1,1	MYH6	274	.	0			c.C1360T						.						120	97	104					14																	23869968		2203	4300	6503	SO:0001583	missense	4624	exon13			ACTGGCGTGGCTG	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.1360C>T	chr14.hg19:g.23869968G>A	ENSP00000348634:p.Arg454Cys	108.0	0.0		107.0	51.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	.	18.71	3.683022	0.68157	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.87887	-2.31;-2.31	4.03	4.03	0.46877	Myosin head, motor domain (2);	.	.	.	.	D	0.94538	0.8241	H	0.95470	3.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	D	0.94986	0.8130	9	0.87932	D	0	.	9.9841	0.41830	0.0:0.0:0.6697:0.3303	.	454;454	D9YZU2;P13533	.;MYH6_HUMAN	C	454	ENSP00000386041:R454C;ENSP00000348634:R454C	ENSP00000348634:R454C	R	-	1	0	MYH6	22939808	0.921000	0.31238	0.997000	0.53966	0.999000	0.98932	1.388000	0.34442	1.978000	0.57642	0.580000	0.79431	CGC	.	.		0.567	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23869968	G	A	23869968	3	1	177	1	0	0	0	0	1	0	0	0	10047	1145	40	1	4567	1	MYH6	14	23869968	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	357876	23869968	83479572	80	26660										
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24530143	24530143	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cttccttctccagctgtttcCcagcctctatgagctgggcc	8	16	2	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr14:24530143C>G	ENST00000342740.5	+	26	2352	c.2198C>G	c.(2197-2199)cCc>cGc	p.P733R	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	733						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		CAGCTGTTTCCCAGCCTCTAT	0.582																																					p.P733R		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C2198G						.						48	37	41					14																	24530143		2006	3853	5859	SO:0001583	missense	90668	exon26			TGTTTCCCAGCCT	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.2198C>G	chr14.hg19:g.24530143C>G	ENSP00000340467:p.Pro733Arg	51.0	0.0		48.0	27.0	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	hg19	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	C	18.83	3.708211	0.68615	.	.	ENSG00000186648	ENST00000342740	T	0.24350	1.86	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000001	T	0.48519	0.1504	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.41502	-0.9505	10	0.66056	D	0.02	-10.2806	16.5424	0.84405	0.0:1.0:0.0:0.0	.	733	Q8ND23	LR16B_HUMAN	R	733	ENSP00000340467:P733R	ENSP00000340467:P733R	P	+	2	0	LRRC16B	23599983	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.794000	0.75135	2.774000	0.95407	0.561000	0.74099	CCC	.	.		0.582	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		G	24530143	C	G	24530143	3	3	177	1	0	0	0	0	1	0	0	0	8981	623	22	4	2300	4	LRRC16B	14	24530143	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	660175	24530143	82819397	81	26661										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64653174	64653174	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tctttggctagctggactcaGaacttgaaagaacttcaaac	8	9	3	3			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr14:64653174G>A	ENST00000344113.4	+	97	17801	c.17589G>A	c.(17587-17589)caG>caA	p.Q5863Q	SYNE2_ENST00000357395.3_Silent_p.Q2248Q|SYNE2_ENST00000394768.2_Silent_p.Q2248Q|SYNE2_ENST00000554584.1_Intron|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.Q2497Q|SYNE2_ENST00000358025.3_Silent_p.Q5863Q	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5863					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GCTGGACTCAGAACTTGAAAG	0.448																																					p.Q5863Q		Atlas-SNP	.											.	SYNE2	577	.	0			c.G17589A						.						205	214	211					14																	64653174		2203	4300	6503	SO:0001819	synonymous_variant	23224	exon97			GACTCAGAACTTG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.17589G>A	chr14.hg19:g.64653174G>A		152.0	0.0		159.0	65.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.448	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64653174	G	A	64653174	2	1	177	1	0	0	0	0	0	0	0	1	15461	933	33	3		3	SYNE2	14	64653174	Silent	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	40123031	64653174	42696366	82	26662										
PLEKHH1	57475	hgsc.bcm.edu	37	chr14	68042127	68042127	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aggtaaagcatggccactccAaggtggtctggtgcgctctt	13	10	2	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr14:68042127A>C	ENST00000329153.5	+	15	2239	c.2107A>C	c.(2107-2109)Aag>Cag	p.K703Q		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	703	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		TGGCCACTCCAAGGTGGTCTG	0.473																																					p.K703Q		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.A2107C						.						69	66	67					14																	68042127		1950	4139	6089	SO:0001583	missense	57475	exon15			CACTCCAAGGTGG	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"Pleckstrin homology (PH) domain containing"	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.2107A>C	chr14.hg19:g.68042127A>C	ENSP00000330278:p.Lys703Gln	83.0	0.0		71.0	33.0	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	hg19	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	A	31	5.093100	0.94149	.	.	ENSG00000054690	ENST00000329153	T	0.31769	1.48	5.9	5.9	0.94986	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.60261	0.2255	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.75484	0.983;0.986	T	0.66052	-0.6019	10	0.87932	D	0	.	16.3245	0.82970	1.0:0.0:0.0:0.0	.	218;703	Q9ULM0-2;Q9ULM0	.;PKHH1_HUMAN	Q	703	ENSP00000330278:K703Q	ENSP00000330278:K703Q	K	+	1	0	PLEKHH1	67111880	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	2.254000	0.74563	0.460000	0.39030	AAG	.	.		0.473	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		C	68042127	A	C	68042127	3	2	177	1	0	0	0	0	1	0	0	0	12085	131	5	5	2161	5	PLEKHH1	14	68042127	Missense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	3388953	68042127	39307413	83	26663										
TMEM90A	646658	hgsc.bcm.edu	37	chr14	74876360	74876360	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ttcctggcaggaccagctggGtggggtctccgggtagggat	18	9	1	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr14:74876360G>C	ENST00000554823.1	-	1	149	c.88C>G	c.(88-90)Ccc>Gcc	p.P30A	SYNDIG1L_ENST00000331628.3_Missense_Mutation_p.P30A			A6NDD5	SYN1L_HUMAN	synapse differentiation inducing 1-like	30					response to biotic stimulus (GO:0009607)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(8)|pancreas(1)|prostate(1)|skin(1)	14						GACCAGCTGGGTGGGGTCTCC	0.657																																					p.P30A		Atlas-SNP	.											.	SYNDIG1L	24	.	0			c.C88G						.						36	41	40					14																	74876360		1937	4135	6072	SO:0001583	missense	646658	exon2			AGCTGGGTGGGGT		CCDS41970.1	14q24.3	2011-06-30	2011-06-30	2011-06-30		ENSG00000183379			32388	protein-coding gene	gene with protein product	"caudate-and putamen-enriched sequence", "interferon induced transmembrane protein domain containing 4"	609999	"transmembrane protein 90A"	TMEM90A		16359841	Standard	NM_001105579		Approved	capucin, IFITMD4	uc001xpx.2	A6NDD5		ENST00000554823.1:c.88C>G	chr14.hg19:g.74876360G>C	ENSP00000450439:p.Pro30Ala	115.0	0.0		119.0	60.0	NM_001105579		Missense_Mutation	SNP	ENST00000554823.1	hg19	CCDS41970.1	.	.	.	.	.	.	.	.	.	.	G	9.001	0.980158	0.18812	.	.	ENSG00000183379	ENST00000331628;ENST00000554823;ENST00000554953	D;D	0.95205	-3.64;-3.64	4.44	3.53	0.40419	.	0.142496	0.47852	D	0.000220	D	0.88537	0.6463	N	0.19112	0.55	0.42940	D	0.994345	B	0.17038	0.02	B	0.12156	0.007	D	0.84034	0.0361	10	0.44086	T	0.13	-1.9818	12.0086	0.53274	0.0:0.0:0.8271:0.1729	.	30	A6NDD5	SYN1L_HUMAN	A	30	ENSP00000331474:P30A;ENSP00000450439:P30A	ENSP00000331474:P30A	P	-	1	0	SYNDIG1L	73946113	1.000000	0.71417	0.788000	0.31933	0.190000	0.23558	3.521000	0.53472	1.042000	0.40150	0.467000	0.42956	CCC	.	.		0.657	SYNDIG1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412341.1	XM_938515		C	74876360	G	C	74876360	3	2	177	1	0	0	0	0	1	0	0	0	16233	1261	44	4	640	4	TMEM90A	14	74876360	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	6834233	74876360	32473180	84	26664										
NDN	4692	hgsc.bcm.edu	37	chr15	23932089	23932089	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	accagctgcgccggggctggCggtgccgggcccggctgggc	20	15	0	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr15:23932089C>A	ENST00000331837.4	-	1	361	c.276G>T	c.(274-276)ccG>ccT	p.P92P		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	92					axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		CCGGGGCTGGCGGTGCCGGGC	0.697									Prader-Willi syndrome																												p.P92P		Atlas-SNP	.											.	NDN	79	.	0			c.G276T						.						21	22	22					15																	23932089		2202	4293	6495	SO:0001819	synonymous_variant	4692	exon1	Familial Cancer Database	Prader-Labhart-Willi syndrome	GGCTGGCGGTGCC	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"Prader-Willi syndrome chromosome region"	602117	"necdin (mouse) homolog", "necdin homolog (mouse)"			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.276G>T	chr15.hg19:g.23932089C>A		36.0	0.0		35.0	20.0	NM_002487	B2R6Z5	Silent	SNP	ENST00000331837.4	hg19	CCDS10014.1																																																																																			.	.		0.697	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487		A	23932089	C	A	23932089	2	1	177	1	0	0	0	0	0	0	0	1	10256	755	27	1		1	NDN	15	23932089	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10		23932089	78599303	85	26665										
NUSAP1	51203	hgsc.bcm.edu	37	chr15	41657598	41657598	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aaatgatgcattttctcttcAgcagcagcccatcaataagg	7	10	3	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr15:41657598A>T	ENST00000559596.1	+	7	747		c.e7-1		NUSAP1_ENST00000450318.1_Splice_Site|NUSAP1_ENST00000558123.1_Splice_Site|NUSAP1_ENST00000560747.1_Intron|NUSAP1_ENST00000450592.2_Intron|NUSAP1_ENST00000560177.1_Splice_Site|NUSAP1_ENST00000260359.6_Splice_Site|NUSAP1_ENST00000414849.2_Intron			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1						establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		TTTTCTCTTCAGCAGCAGCCC	0.498																																					.		Atlas-SNP	.											.	NUSAP1	32	.	0			c.661-2A>T						.						38	37	37					15																	41657598		1904	4130	6034	SO:0001630	splice_region_variant	51203	exon7			CTCTTCAGCAGCA	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.661-1A>T	chr15.hg19:g.41657598A>T		41.0	0.0		68.0	31.0	NM_016359	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Splice_Site	SNP	ENST00000559596.1	hg19	CCDS45234.1	.	.	.	.	.	.	.	.	.	.	A	9.138	1.013026	0.19277	.	.	ENSG00000137804	ENST00000260359;ENST00000450318	.	.	.	4.53	2.08	0.27032	.	.	.	.	.	.	.	.	.	.	.	0.20563	N	0.999884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.9308	0.13916	0.6168:0.2034:0.0:0.1798	.	.	.	.	.	-1	.	.	.	+	.	.	NUSAP1	39444890	0.990000	0.36364	0.010000	0.14722	0.133000	0.20885	2.723000	0.47277	0.314000	0.23086	0.482000	0.46254	.	.	.		0.498	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359	Intron	T	41657598	A	T	41657598	5	4	177	1	0	0	0	0	0	0	1	0	10787	202	7	4	685	4	NUSAP1	15	41657598	Splice_Site	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	17725509	41657598	60873794	86	26666										
RCN2	5955	hgsc.bcm.edu	37	chr15	77236169	77236169	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tcccggtttgagtcttgaagAatttattgcttttgagcatc	9	7	1	4			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr15:77236169A>G	ENST00000394885.3	+	4	741	c.518A>G	c.(517-519)gAa>gGa	p.E173G	RCN2_ENST00000320963.5_Missense_Mutation_p.E191G|RCN2_ENST00000394883.3_Missense_Mutation_p.E72G	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	173	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						AGTCTTGAAGAATTTATTGCT	0.303																																					p.E191G		Atlas-SNP	.											.	RCN2	16	.	0			c.A572G						.						72	74	73					15																	77236169		2196	4294	6490	SO:0001583	missense	5955	exon5			TTGAAGAATTTAT	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"EF-hand domain containing"	9935	protein-coding gene	gene with protein product	"Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.518A>G	chr15.hg19:g.77236169A>G	ENSP00000378349:p.Glu173Gly	230.0	0.0		286.0	138.0	NM_001271837	A8MTG6|F8WCY5|Q53XN8	Missense_Mutation	SNP	ENST00000394885.3	hg19	CCDS10291.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.827514	0.90955	.	.	ENSG00000117906	ENST00000394885;ENST00000320963;ENST00000394883	T;T;T	0.70399	-0.48;-0.48;-0.22	6.17	6.17	0.99709	EF-hand-like domain (1);	0.042626	0.85682	N	0.000000	D	0.87958	0.6309	M	0.92604	3.325	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.997;0.998;0.994	D	0.90566	0.4519	10	0.87932	D	0	-29.6729	16.0034	0.80327	1.0:0.0:0.0:0.0	.	72;191;173	A8MXP8;F8WCY5;Q14257	.;.;RCN2_HUMAN	G	173;191;72	ENSP00000378349:E173G;ENSP00000319739:E191G;ENSP00000378347:E72G	ENSP00000319739:E191G	E	+	2	0	RCN2	75023224	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.409000	0.80053	2.371000	0.80710	0.533000	0.62120	GAA	.	.		0.303	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902		G	77236169	A	G	77236169	3	3	177	1	0	0	0	0	1	0	0	0	13195	246	9	2	532	2	RCN2	15	77236169	Missense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	35578571	77236169	25295223	87	26667										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88476268	88476268	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gaacttattcaggtctccatGcttcatgtattcaaagacca	6	10	4	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr15:88476268G>T	ENST00000360948.2	-	15	2025	c.1864C>A	c.(1864-1866)Cat>Aat	p.H622N	NTRK3_ENST00000355254.2_Missense_Mutation_p.H622N|NTRK3_ENST00000557856.1_Missense_Mutation_p.H614N|NTRK3_ENST00000357724.2_Missense_Mutation_p.H614N|NTRK3_ENST00000542733.2_Missense_Mutation_p.H524N|NTRK3_ENST00000558676.1_Missense_Mutation_p.H614N|NTRK3_ENST00000394480.2_Missense_Mutation_p.H622N	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	622	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			AGGTCTCCATGCTTCATGTAT	0.542			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.H622N		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.C1864A						.						80	69	73					15																	88476268		2201	4299	6500	SO:0001583	missense	4916	exon16			CTCCATGCTTCAT	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1864C>A	chr15.hg19:g.88476268G>T	ENSP00000354207:p.His622Asn	95.0	0.0		78.0	28.0	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110965	0.77210	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000343782	D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32	5.49	5.49	0.81192	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85570	0.5727	N	0.04203	-0.255	0.80722	D	1	B;D;D;D;D	0.63880	0.276;0.993;0.975;0.991;0.975	B;D;D;D;P	0.72982	0.219;0.979;0.934;0.964;0.893	D	0.86052	0.1526	10	0.27082	T	0.32	.	18.3583	0.90365	0.0:0.0:1.0:0.0	.	524;614;614;622;622	B7Z7U4;E9PG56;B7Z4C5;Q16288-3;Q16288	.;.;.;.;NTRK3_HUMAN	N	622;622;614;622;524;118	ENSP00000377990:H622N;ENSP00000354207:H622N;ENSP00000350356:H614N;ENSP00000347397:H622N;ENSP00000437773:H524N	ENSP00000342792:H118N	H	-	1	0	NTRK3	86277272	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.623000	0.83113	2.574000	0.86865	0.650000	0.86243	CAT	.	.		0.542	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				T	88476268	G	T	88476268	3	4	177	1	0	0	0	0	1	0	0	0	10717	1319	46	3	675	3	NTRK3	15	88476268	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	11240099	88476268	14055124	88	26668										
SOLH	6650	hgsc.bcm.edu	37	chr16	601629	601629	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	atgccgcacggcagcagtgaGggtgtcttctggatggagta	16	8	2	1	rs534348403	byFrequency	TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr16:601629G>C	ENST00000219611.2	+	9	2673	c.2310G>C	c.(2308-2310)gaG>gaC	p.E770D	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	770	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GCAGCAGTGAGGGTGTCTTCT	0.682																																					p.E770D		Atlas-SNP	.											.	SOLH	47	.	0			c.G2310C						.						43	51	48					16																	601629		2199	4297	6496	SO:0001583	missense	6650	exon9			CAGTGAGGGTGTC	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"small optic lobes (Drosophila) homolog", "small optic lobes homolog (Drosophila)"	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.2310G>C	chr16.hg19:g.601629G>C	ENSP00000219611:p.Glu770Asp	35.0	0.0		27.0	16.0	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	hg19	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	g	13.48	2.248500	0.39797	.	.	ENSG00000103326	ENST00000219611	T	0.33216	1.42	5.26	2.2	0.27929	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.85682	D	0.000000	T	0.08179	0.0204	N	0.00690	-1.25	0.53688	D	0.999974	P	0.43431	0.807	B	0.41946	0.371	T	0.30060	-0.9991	10	0.02654	T	1	.	10.0439	0.42175	0.2178:0.0:0.7822:0.0	.	770	O75808	CAN15_HUMAN	D	770	ENSP00000219611:E770D	ENSP00000219611:E770D	E	+	3	2	SOLH	541630	1.000000	0.71417	0.997000	0.53966	0.503000	0.33858	1.222000	0.32515	0.225000	0.20959	0.556000	0.70494	GAG	.	.		0.682	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		C	601629	G	C	601629	3	2	177	1	0	0	0	0	1	0	0	0	14940	991	35	4	2332	4	SOLH	16	601629	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10		601629	89753124	89	26669										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31422694	31422694	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cacccctggggccgctttggGgcagccctgacagtgttggg	16	13	0	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr16:31422694G>A	ENST00000389202.2	+	14	1612	c.1563G>A	c.(1561-1563)ggG>ggA	p.G521G		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	521					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GCCGCTTTGGGGCAGCCCTGA	0.622																																					p.G521G		Atlas-SNP	.											.	ITGAD	154	.	0			c.G1563A						.						110	112	111					16																	31422694		2197	4300	6497	SO:0001819	synonymous_variant	3681	exon14			CTTTGGGGCAGCC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.1563G>A	chr16.hg19:g.31422694G>A		100.0	0.0		112.0	56.0	NM_005353	Q15575|Q15576	Silent	SNP	ENST00000389202.2	hg19	CCDS32438.1																																																																																			.	.		0.622	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		A	31422694	G	A	31422694	2	1	177	1	0	0	0	0	0	0	0	1	7893	1219	43	3		3	ITGAD	16	31422694	Silent	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	30821065	31422694	58932059	90	26670										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58579334	58579334	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ttgatgtcgtggtagctgtaCtgtggctgtggtggaaccgt	16	6	0	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr16:58579334C>A	ENST00000317147.5	-	30	4400	c.4068G>T	c.(4066-4068)caG>caT	p.Q1356H	CNOT1_ENST00000245138.4_Missense_Mutation_p.Q207H|CNOT1_ENST00000569240.1_Missense_Mutation_p.Q1351H|CNOT1_ENST00000441024.2_Missense_Mutation_p.Q1356H	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1356	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GGTAGCTGTACTGTGGCTGTG	0.438																																					p.Q1356H		Atlas-SNP	.											.	CNOT1	359	.	0			c.G4068T						.						247	196	213					16																	58579334		2198	4300	6498	SO:0001583	missense	23019	exon30			GCTGTACTGTGGC	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4068G>T	chr16.hg19:g.58579334C>A	ENSP00000320949:p.Gln1356His	148.0	0.0		184.0	103.0	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.703545	0.48412	.	.	ENSG00000125107	ENST00000317147;ENST00000245138;ENST00000394200;ENST00000441024	T;T	0.48836	0.86;0.8	5.71	4.75	0.60458	.	0.051608	0.85682	D	0.000000	T	0.50326	0.1609	L	0.31420	0.93	0.80722	D	1	B;D;B;B	0.71674	0.027;0.998;0.098;0.157	B;P;B;B	0.62560	0.016;0.904;0.013;0.03	T	0.25572	-1.0128	10	0.12766	T	0.61	-8.87	14.9778	0.71289	0.0:0.9306:0.0:0.0694	.	207;1356;1356;1351	B5MDN3;A5YKK6-4;A5YKK6;A5YKK6-2	.;.;CNOT1_HUMAN;.	H	1356;207;1351;1356	ENSP00000320949:Q1356H;ENSP00000413113:Q1356H	ENSP00000245138:Q207H	Q	-	3	2	CNOT1	57136835	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.527000	0.45615	2.697000	0.92050	0.655000	0.94253	CAG	.	.		0.438	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		A	58579334	C	A	58579334	3	1	177	1	0	0	0	0	1	0	0	0	3619	564	20	3	3364	3	CNOT1	16	58579334	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	27156640	58579334	31775419	91	26671										
TAT	6898	hgsc.bcm.edu	37	chr16	71604715	71604715	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tgagggtggccagtggttcaTatttgcaatccgaaaacacc	11	9	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr16:71604715T>C	ENST00000355962.4	-	8	912	c.779A>G	c.(778-780)tAt>tGt	p.Y260C	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	260					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	CAGTGGTTCATATTTGCAATC	0.557																																					p.Y260C	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.A779G						.						124	103	110					16																	71604715		2198	4300	6498	SO:0001583	missense	6898	exon8			GGTTCATATTTGC		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.779A>G	chr16.hg19:g.71604715T>C	ENSP00000348234:p.Tyr260Cys	114.0	0.0		115.0	51.0	NM_000353	B2R8I1|D3DWS2	Missense_Mutation	SNP	ENST00000355962.4	hg19	CCDS10903.1	.	.	.	.	.	.	.	.	.	.	T	11.39	1.624474	0.28889	.	.	ENSG00000198650	ENST00000355962	D	0.90788	-2.73	5.2	4.1	0.47936	Tyrosine aminotransferase (1);Aminotransferase, class I/classII (1);Tyrosine/nicotianamine aminotransferase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.325296	0.36703	N	0.002458	D	0.84795	0.5551	L	0.43923	1.385	0.34583	D	0.714688	B	0.10296	0.003	B	0.12156	0.007	T	0.82112	-0.0618	10	0.66056	D	0.02	-7.2444	5.5068	0.16858	0.3891:0.0:0.1267:0.4842	.	260	P17735	ATTY_HUMAN	C	260	ENSP00000348234:Y260C	ENSP00000348234:Y260C	Y	-	2	0	TAT	70162216	0.955000	0.32602	0.975000	0.42487	0.945000	0.59286	0.777000	0.26718	0.809000	0.34255	0.460000	0.39030	TAT	.	.		0.557	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1			C	71604715	T	C	71604715	3	2	177	1	0	0	0	0	1	0	0	0	15605	1406	49	2	605	2	TAT	16	71604715	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	13025381	71604715	18750038	92	26672										
C17orf66	256957	hgsc.bcm.edu	37	chr17	34192249	34192249	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ctctcattttcctcaacatcTtctcagcctccctttcctct	1	18	5	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr17:34192249T>A	ENST00000311880.2	-	3	438	c.290A>T	c.(289-291)aAg>aTg	p.K97M	C17orf66_ENST00000587585.1_5'UTR|C17orf66_ENST00000592980.1_Missense_Mutation_p.K97M	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		97					hematopoietic progenitor cell differentiation (GO:0002244)					breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		CCTCAACATCTTCTCAGCCTC	0.488																																					p.K97M		Atlas-SNP	.											.	C17orf66	57	.	0			c.A290T						.						253	222	232					17																	34192249		2203	4300	6503	SO:0001583	missense	256957	exon3			AACATCTTCTCAG																												ENST00000311880.2:c.290A>T	chr17.hg19:g.34192249T>A	ENSP00000309560:p.Lys97Met	96.0	0.0		124.0	58.0	NM_152781	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Missense_Mutation	SNP	ENST00000311880.2	hg19	CCDS11299.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.065808	0.55539	.	.	ENSG00000172653	ENST00000311880	T	0.54866	0.55	4.82	1.07	0.20283	.	0.394856	0.21663	N	0.070983	T	0.49609	0.1567	L	0.34521	1.04	0.09310	N	1	D;D;D	0.69078	0.997;0.995;0.996	D;P;P	0.63192	0.912;0.847;0.819	T	0.39502	-0.9611	10	0.72032	D	0.01	.	1.3007	0.02078	0.1755:0.1079:0.1822:0.5344	.	63;97;97	A2RTY3-4;A2RTY3-3;A2RTY3	.;.;CQ066_HUMAN	M	97	ENSP00000309560:K97M	ENSP00000309560:K97M	K	-	2	0	C17orf66	31216362	0.042000	0.20092	0.001000	0.08648	0.115000	0.19883	1.193000	0.32162	0.047000	0.15862	0.533000	0.62120	AAG	.	.		0.488	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1			A	34192249	T	A	34192249	3	1	177	1	0	0	0	0	1	0	0	0	1876	1609	56	4	1474	4	C17orf66	17	34192249	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10		34192249	47002961	93	26673										
KRTAP1-3	81850	hgsc.bcm.edu	37	chr17	39191019	39191019	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gcagcagctggagccgcatgTcccactggtggagcagctgg	16	12	0	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr17:39191019T>C	ENST00000344363.5	-	1	88	c.55A>G	c.(55-57)Aca>Gca	p.T19A		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	19						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GAGCCGCATGTCCCACTGGTG	0.582																																					p.T19A		Atlas-SNP	.											.	KRTAP1-3	18	.	0			c.A55G						.						49	56	54					17																	39191019		1972	4169	6141	SO:0001583	missense	81850	exon1			CGCATGTCCCACT	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"Keratin associated proteins"	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.55A>G	chr17.hg19:g.39191019T>C	ENSP00000344420:p.Thr19Ala	99.0	0.0		138.0	99.0	NM_030966	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	hg19	CCDS42323.1	.	.	.	.	.	.	.	.	.	.	T	9.721	1.159792	0.21454	.	.	ENSG00000221880	ENST00000344363	T	0.36157	1.27	4.31	2.04	0.26737	.	.	.	.	.	T	0.25232	0.0613	.	.	.	0.23473	N	0.997605	B	0.20887	0.049	B	0.22152	0.038	T	0.27640	-1.0068	8	0.72032	D	0.01	.	4.1403	0.10189	0.0:0.1075:0.2107:0.6817	.	19	Q8IUG1	KRA13_HUMAN	A	19	ENSP00000344420:T19A	ENSP00000344420:T19A	T	-	1	0	KRTAP1-3	36444545	0.090000	0.21635	0.593000	0.28771	0.495000	0.33615	1.629000	0.37071	0.412000	0.25729	0.460000	0.39030	ACA	.	.		0.582	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			C	39191019	T	C	39191019	3	2	177	1	0	0	0	0	1	0	0	0	8512	1667	58	2	452	2	KRTAP1-3	17	39191019	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	4998770	39191019	42004191	94	26674										
MPP3	4356	hgsc.bcm.edu	37	chr17	41898313	41898313	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gcctgccaccacgtggggtcGtcctggctcaccacctccag	11	18	1	0	rs377033537		TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr17:41898313G>A	ENST00000398389.4	-	11	963	c.798C>T	c.(796-798)gaC>gaT	p.D266D	MPP3_ENST00000398393.1_Silent_p.D291D	NM_001932.4	NP_001923.2	Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	266	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	guanylate kinase activity (GO:0004385)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		ACGTGGGGTCGTCCTGGCTCA	0.677																																					p.D266D		Atlas-SNP	.											.	MPP3	42	.	0			c.C798T						.						29	33	31					17																	41898313		1985	4144	6129	SO:0001819	synonymous_variant	4356	exon11			GGGGTCGTCCTGG		CCDS42344.1	17q12-q21	2008-07-18			ENSG00000161647	ENSG00000161647			7221	protein-coding gene	gene with protein product	"MAGUK p55 subfamily member 3", "discs, large (Drosophila) homolog 3", "membrane protein palmitoylated 3"	601114		DLG3		8824795	Standard	NR_003562		Approved		uc002iei.4	Q13368	OTTHUMG00000133838	ENST00000398389.4:c.798C>T	chr17.hg19:g.41898313G>A		99.0	0.0		153.0	41.0	NM_001932	B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	Silent	SNP	ENST00000398389.4	hg19	CCDS42344.1																																																																																			.	.		0.677	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1	NM_001932		A	41898313	G	A	41898313	2	1	177	1	0	0	0	0	0	0	0	1	9744	1136	40	1		1	MPP3	17	41898313	Silent	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	2707294	41898313	39296897	95	26675										
TBC1D16	125058	hgsc.bcm.edu	37	chr17	77921567	77921567	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gccaagatgggcgccaccagGtccgacatcccttgggaata	12	13	0	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr17:77921567G>A	ENST00000310924.2	-	9	1720	c.1605C>T	c.(1603-1605)gaC>gaT	p.D535D	TBC1D16_ENST00000340848.7_Silent_p.D173D|TBC1D16_ENST00000572862.1_Silent_p.D173D|TBC1D16_ENST00000576768.1_Silent_p.D160D|TBC1D16_ENST00000570373.1_Silent_p.D174D	NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	535	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			GCGCCACCAGGTCCGACATCC	0.607																																					p.D535D	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.C1605T						.						109	82	91					17																	77921567		2203	4300	6503	SO:0001819	synonymous_variant	125058	exon9			CACCAGGTCCGAC	AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.1605C>T	chr17.hg19:g.77921567G>A		98.0	0.0		126.0	47.0	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Silent	SNP	ENST00000310924.2	hg19	CCDS11766.1																																																																																			.	.		0.607	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020		A	77921567	G	A	77921567	2	1	177	1	0	0	0	0	0	0	0	1	15620	1252	44	3		3	TBC1D16	17	77921567	Silent	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	36023254	77921567	3273643	96	26676										
ZNF516	9658	hgsc.bcm.edu	37	chr18	74153982	74153982	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aagctgtccaggtttgtaaaCaggttcccgcacttggcgca	11	11	0	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr18:74153982C>A	ENST00000443185.2	-	3	1346	c.1029G>T	c.(1027-1029)ctG>ctT	p.L343L	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		GGTTTGTAAACAGGTTCCCGC	0.667																																					p.L343L		Atlas-SNP	.											.	ZNF516	102	.	0			c.G1029T						.						40	47	45					18																	74153982		2153	4261	6414	SO:0001819	synonymous_variant	9658	exon3			TGTAAACAGGTTC	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"Zinc fingers, C2H2-type"	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.1029G>T	chr18.hg19:g.74153982C>A		42.0	0.0		48.0	17.0	NM_014643		Silent	SNP	ENST00000443185.2	hg19																																																																																				.	.		0.667	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		A	74153982	C	A	74153982	2	1	177	1	0	0	0	0	0	0	0	1	17975	465	17	3		3	ZNF516	18	74153982	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10		74153982	3923266	97	26677										
ARRDC5	645432	hgsc.bcm.edu	37	chr19	4896768	4896768	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ctaaaatgtgttccctgcccAtgcaggaagcttgtacgaaa	9	10	0	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:4896768A>G	ENST00000381781.2	-	2	415	c.416T>C	c.(415-417)aTg>aCg	p.M139T		NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	139										endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		TTCCCTGCCCATGCAGGAAGC	0.468																																					p.M139T		Atlas-SNP	.											.	ARRDC5	19	.	0			c.T416C						.						138	129	132					19																	4896768		1919	4141	6060	SO:0001583	missense	645432	exon2			CTGCCCATGCAGG		CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.416T>C	chr19.hg19:g.4896768A>G	ENSP00000371200:p.Met139Thr	167.0	0.0		158.0	77.0	NM_001080523		Missense_Mutation	SNP	ENST00000381781.2	hg19	CCDS45929.1	.	.	.	.	.	.	.	.	.	.	A	8.064	0.768665	0.15983	.	.	ENSG00000205784	ENST00000381781	T	0.16324	2.35	4.37	1.09	0.20402	Immunoglobulin E-set (1);Arrestin-like, N-terminal (1);	0.791479	0.11031	N	0.607239	T	0.10981	0.0268	L	0.40543	1.245	0.21105	N	0.99979	B	0.14012	0.009	B	0.12837	0.008	T	0.40289	-0.9571	10	0.15066	T	0.55	-13.1819	3.2263	0.06732	0.5017:0.2152:0.2831:0.0	.	139	A6NEK1	ARRD5_HUMAN	T	139	ENSP00000371200:M139T	ENSP00000371200:M139T	M	-	2	0	ARRDC5	4847768	0.816000	0.29132	0.994000	0.49952	0.846000	0.48090	1.345000	0.33953	0.307000	0.22880	0.472000	0.43445	ATG	.	.		0.468	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1	XM_292803		G	4896768	A	G	4896768	3	3	177	1	0	0	0	0	1	0	0	0	986	217	8	2	620	2	ARRDC5	19	4896768	Missense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10		4896768	54232215	98	26678										
ZNF177	7730	hgsc.bcm.edu	37	chr19	9488995	9488995	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tacaggaggaagaatggctgCagggtggctgacaacctggt	16	7	0	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:9488995C>A	ENST00000589262.1	+	2	74	c.8C>A	c.(7-9)gCa>gAa	p.A3E	ZNF177_ENST00000446085.4_Missense_Mutation_p.A3E|ZNF177_ENST00000434737.2_Missense_Mutation_p.A3E|ZNF177_ENST00000590616.1_Missense_Mutation_p.A3E|ZNF177_ENST00000605471.1_3'UTR|ZNF177_ENST00000541595.2_Missense_Mutation_p.A3E|ZNF177_ENST00000343499.4_Missense_Mutation_p.A3E|ZNF177_ENST00000602856.1_Missense_Mutation_p.A3E|ZNF177_ENST00000602738.1_Missense_Mutation_p.A3E	NM_001172651.1	NP_001166122.1	Q13360	ZN177_HUMAN	zinc finger protein 177	3					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|stomach(2)	13						AGAATGGCTGCAGGGTGGCTG	0.507																																					p.A3E		Atlas-SNP	.											.	ZNF177	57	.	0			c.C8A						.						64	60	62					19																	9488995		2203	4300	6503	SO:0001583	missense	7730	exon5			TGGCTGCAGGGTG	U37263, BC012012	CCDS12212.1, CCDS54214.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type", "-"	12966	protein-coding gene	gene with protein product		601276					Standard	NM_003451		Approved		uc021uon.1	Q13360		ENST00000589262.1:c.8C>A	chr19.hg19:g.9488995C>A	ENSP00000468531:p.Ala3Glu	289.0	0.0		296.0	135.0	NM_003451	B4DY57|E9PDG0|I3L0I4|Q96ER2	Missense_Mutation	SNP	ENST00000589262.1	hg19	CCDS54214.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.183903	0.38609	.	.	ENSG00000188629	ENST00000541595;ENST00000446085;ENST00000343499;ENST00000434737	T;T;T;T	0.06294	3.45;5.58;3.45;3.32	2.14	2.14	0.27477	.	.	.	.	.	T	0.04724	0.0128	N	0.21545	0.675	0.25721	N	0.985377	P	0.37594	0.601	B	0.39119	0.291	T	0.27157	-1.0082	8	0.22109	T	0.4	.	7.8522	0.29462	0.0:1.0:0.0:0.0	.	3	Q13360	ZN177_HUMAN	E	3	ENSP00000445323:A3E;ENSP00000413568:A3E;ENSP00000341497:A3E;ENSP00000415070:A3E	ENSP00000341497:A3E	A	+	2	0	ZNF177	9349995	0.012000	0.17670	0.618000	0.29105	0.788000	0.44548	0.866000	0.27954	1.518000	0.48934	0.467000	0.42956	GCA	.	.		0.507	ZNF177-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449028.1	NM_003451		A	9488995	C	A	9488995	3	1	177	1	0	0	0	0	1	0	0	0	17761	710	25	3	10	3	ZNF177	19	9488995	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	4592227	9488995	49639988	99	26679										
MYO9B	4650	hgsc.bcm.edu	37	chr19	17298768	17298768	+	Frame_Shift_Del	DEL	C	C	-													0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	agctgtgctttgacgacgagCtggtcctgcagcagctgcgc							TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:17298768delC	ENST00000594824.1	+	19	2749	c.2602delC	c.(2602-2604)ctgfs	p.L868fs	MYO9B_ENST00000397274.2_Frame_Shift_Del_p.L868fs|MYO9B_ENST00000595618.1_Frame_Shift_Del_p.L868fs			Q13459	MYO9B_HUMAN	myosin IXB	868	Myosin motor.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						TGACGACGAGCTGGTCCTGCA	0.597																																					p.E867fs		Atlas-INDEL	.											.	MYO9B	264	.	0			c.2601delG						.						40	39	39					19																	17298768		2199	4296	6495	SO:0001589	frameshift_variant	4650	exon19			.		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"Myosins / Myosin superfamily : Class IX"	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.2602delC	chr19.hg19:g.17298768delC	ENSP00000471367:p.Leu868fs	48.0	0.0		54.0	34.0	NM_004145	O75314|Q9NUJ2|Q9UHN0	Frame_Shift_Del	DEL	ENST00000594824.1	hg19																																																																																				.	.		0.597	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			-	17298768	C	-	17298768	7	5	177	1	0	1	0	1	0	0	0	0	10094	796	28	0	2672	0	MYO9B	19	17298768	Frame_Shift_Del	DEL	C	TCGA-DD-AAD0-01A-11D-A40R-10	7809773	17298768	41830215	100	26680										
ZNF506	440515	hgsc.bcm.edu	37	chr19	19905517	19905544	+	Frame_Shift_Del	DEL	TCCAGTATGAATTATCTTATGTTCAGTT	TCCAGTATGAATTATCTTATGTTCAGTT	-													0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tcacatttgtacggtttctcTccagtatgaattatcttatg					rs368740670		TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	TCCAGTATGAATTATCTTATGTTCAGTT	TCCAGTATGAATTATCTTATGTTCAGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:19905517_19905544delTCCAGTATGAATTATCTTATGTTCAGTT	ENST00000540806.2	-	4	1240_1267	c.1152_1179delAACTGAACATAAGATAATTCATACTGGA	c.(1150-1179)ctaactgaacataagataattcatactggafs	p.LTEHKIIHTG384fs	CTC-559E9.4_ENST00000590274.1_lincRNA|CTC-559E9.6_ENST00000591884.1_RNA|ZNF506_ENST00000443905.2_Frame_Shift_Del_p.LTEHKIIHTG384fs|ZNF506_ENST00000450683.2_Frame_Shift_Del_p.LTEHKIIHTG352fs|ZNF506_ENST00000587461.1_Intron|CTC-559E9.6_ENST00000589657.1_RNA			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	384					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						ACGGTTTCTCTCCAGTATGAATTATCTTATGTTCAGTTAGAGTTGAGA	0.39																																					p.385_394del		Atlas-INDEL	.											.	ZNF506	36	.	0			c.1153_1180del						.																																			SO:0001589	frameshift_variant	440515	exon4			.	AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"Zinc fingers, C2H2-type", "-"	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.1152_1179delAACTGAACATAAGATAATTCATACTGGA	chr19.hg19:g.19905517_19905544delTCCAGTATGAATTATCTTATGTTCAGTT	ENSP00000440625:p.Leu384fs	60.0	0.0		48.0	16.0	NM_001099269	B3KTH6	Frame_Shift_Del	DEL	ENST00000540806.2	hg19	CCDS42531.1																																																																																			.	.		0.39	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218		-	19905544	TCCAGTATGAATTATCTTATGTTCAGTT	-	19905517	7	5	177	1	0	1	0	1	0	0	0	0	17967	1538	54	0	159	0	ZNF506	19	19905517	Frame_Shift_Del	DEL	TCCAGTATGAATTATCTTATGTTCAGTT	TCGA-DD-AAD0-01A-11D-A40R-10	2606749	19905517	39223466	101	26681										
ZNF93	81931	hgsc.bcm.edu	37	chr19	20044590	20044590	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cctcgacacttactaaacatAagaaaattcatactggagag	6	9	1	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:20044590A>T	ENST00000343769.5	+	4	854	c.826A>T	c.(826-828)Aag>Tag	p.K276*	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	276					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						TACTAAACATAAGAAAATTCA	0.353																																					p.K276X		Atlas-SNP	.											.	ZNF93	81	.	0			c.A826T						.						39	41	41					19																	20044590		2203	4298	6501	SO:0001587	stop_gained	81931	exon4			AAACATAAGAAAA	M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"Zinc fingers, C2H2-type", "-"	13169	protein-coding gene	gene with protein product		603975	"zinc finger protein 505", "zinc finger protein 93 (HTF34)"	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.826A>T	chr19.hg19:g.20044590A>T	ENSP00000342002:p.Lys276*	66.0	0.0		76.0	41.0	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Nonsense_Mutation	SNP	ENST00000343769.5	hg19	CCDS32973.1	.	.	.	.	.	.	.	.	.	.	a	15.78	2.935689	0.52972	.	.	ENSG00000184635	ENST00000343769;ENST00000427325	.	.	.	0.85	-1.7	0.08159	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.4846	0.11783	0.3838:0.6161:0.0:0.0	.	.	.	.	X	276	.	ENSP00000342002:K276X	K	+	1	0	ZNF93	19905590	0.000000	0.05858	0.053000	0.19242	0.053000	0.15095	-1.142000	0.03203	0.166000	0.19597	0.164000	0.16699	AAG	.	.		0.353	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218		T	20044590	A	T	20044590	4	4	177	1	0	0	0	0	0	1	0	0	18217	363	13	4	840	4	ZNF93	19	20044590	Nonsense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	139073	20044590	39084393	102	26682										
ZBTB32	27033	hgsc.bcm.edu	37	chr19	36207625	36207625	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cgtctcggccctcgacctctCcctgttgtccttcttcctcc	6	20	3	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:36207625C>A	ENST00000392197.2	+	7	1753	c.1435C>A	c.(1435-1437)Ccc>Acc	p.P479T	KMT2B_ENST00000222270.7_5'Flank|ZBTB32_ENST00000262630.3_Missense_Mutation_p.P479T|KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000341701.1_5'Flank|KMT2B_ENST00000420124.1_5'Flank			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	479					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTCGACCTCTCCCTGTTGTCC	0.627											OREG0025433	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P479T		Atlas-SNP	.											.	ZBTB32	33	.	0			c.C1435A						.						97	88	91					19																	36207625		2203	4300	6503	SO:0001583	missense	27033	exon6			ACCTCTCCCTGTT	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16763	protein-coding gene	gene with protein product	"repressor of GATA"	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.1435C>A	chr19.hg19:g.36207625C>A	ENSP00000376035:p.Pro479Thr	38.0	0.0	861	33.0	13.0	NM_014383	Q8WVP2	Missense_Mutation	SNP	ENST00000392197.2	hg19	CCDS12471.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.364321	0.61513	.	.	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.09350	2.99;2.99	4.34	3.26	0.37387	.	0.827279	0.10455	N	0.672671	T	0.07279	0.0184	N	0.19112	0.55	0.09310	N	0.999999	B	0.15719	0.014	B	0.11329	0.006	T	0.39941	-0.9589	10	0.16896	T	0.51	-3.831	9.422	0.38557	0.2125:0.7875:0.0:0.0	.	479	Q9Y2Y4	ZBT32_HUMAN	T	479	ENSP00000262630:P479T;ENSP00000376035:P479T	ENSP00000262630:P479T	P	+	1	0	ZBTB32	40899465	0.008000	0.16893	0.028000	0.17463	0.709000	0.40893	0.578000	0.23773	1.112000	0.41740	0.462000	0.41574	CCC	.	.		0.627	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383		A	36207625	C	A	36207625	3	1	177	1	0	0	0	0	1	0	0	0	17550	855	30	3	1453	3	ZBTB32	19	36207625	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	16163035	36207625	22921358	103	26683										
MLL4	9757	hgsc.bcm.edu	37	chr19	36213570	36213570	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	catggtgcctgaagatgtccCtcgcctcagtgccctccctc	9	17	1	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:36213570C>G	ENST00000222270.7	+	5	2672	c.2672C>G	c.(2671-2673)cCt>cGt	p.P891R	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.P891R	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	891					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GAAGATGTCCCTCGCCTCAGT	0.652																																					p.P891R		Atlas-SNP	.											.	MLL4	229	.	0			c.C2672G						.						38	41	40					19																	36213570		2041	4182	6223	SO:0001583	missense	8085	exon5			ATGTCCCTCGCCT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.2672C>G	chr19.hg19:g.36213570C>G	ENSP00000222270:p.Pro891Arg	81.0	0.0		79.0	41.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.323512	0.60634	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.85556	-2.0;-2.0	5.39	5.39	0.77823	.	0.000000	0.40222	N	0.001151	D	0.90861	0.7129	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91262	0.5037	10	0.87932	D	0	.	18.0965	0.89492	0.0:1.0:0.0:0.0	.	891	Q9UMN6	MLL4_HUMAN	R	891	ENSP00000222270:P891R;ENSP00000398837:P891R	ENSP00000222270:P891R	P	+	2	0	AD000671.1	40905410	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.969000	0.76092	2.804000	0.96469	0.655000	0.94253	CCT	.	.		0.652	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		G	36213570	C	G	36213570	3	3	177	1	0	0	0	0	1	0	0	0	9632	681	24	4	2690	4	MLL4	19	36213570	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	5945	36213570	22915413	104	26684										
MLL4	9757	hgsc.bcm.edu	37	chr19	36219050	36219050	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cccacgaccccaagtactggCgacggagtacccggctgcca	11	17	0	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:36219050C>T	ENST00000222270.7	+	19	4549	c.4549C>T	c.(4549-4551)Cga>Tga	p.R1517*	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Nonsense_Mutation_p.R1517*	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1517					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CAAGTACTGGCGACGGAGTAC	0.637																																					p.R1517X		Atlas-SNP	.											.	MLL4	229	.	0			c.C4549T						.						14	15	15					19																	36219050		2006	4176	6182	SO:0001587	stop_gained	8085	exon19			TACTGGCGACGGA	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.4549C>T	chr19.hg19:g.36219050C>T	ENSP00000222270:p.Arg1517*	61.0	0.0		63.0	29.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Nonsense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	43	10.083437	0.99332	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	.	.	.	5.31	3.01	0.34805	.	0.000000	0.34750	N	0.003713	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	10.3294	0.43814	0.4541:0.5459:0.0:0.0	.	.	.	.	X	1517	.	ENSP00000222270:R1517X	R	+	1	2	AD000671.1	40910890	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.896000	0.39789	1.403000	0.46800	0.655000	0.94253	CGA	.	.		0.637	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		T	36219050	C	T	36219050	4	4	177	1	0	0	0	0	0	1	0	0	9632	760	27	1	4623	1	MLL4	19	36219050	Nonsense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	5480	36219050	22909933	105	26685										
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48204913	48204913	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gcccggagccgcatcgggctCaagctcaagatcaagcagga	13	13	3	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:48204913C>T	ENST00000396720.3	+	15	4118	c.3924C>T	c.(3922-3924)ctC>ctT	p.L1308L	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1308										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		GCATCGGGCTCAAGCTCAAGA	0.701																																					p.L1308L		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.C3924T						.						7	9	8					19																	48204913		1892	4035	5927	SO:0001819	synonymous_variant	29998	exon15			CGGGCTCAAGCTC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.3924C>T	chr19.hg19:g.48204913C>T		156.0	0.0		164.0	83.0	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	hg19	CCDS46134.1																																																																																			.	.		0.701	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		T	48204913	C	T	48204913	2	4	177	1	0	0	0	0	0	0	0	1	6482	813	29	3		3	GLTSCR1	19	48204913	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	11985863	48204913	10924070	106	26686										
ZNF321	399669	hgsc.bcm.edu	37	chr19	53432594	53432594	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ctttcatgtctttgcaatgtCcctgtgtggatcacttctgt	8	10	4	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:53432594C>T	ENST00000391777.3	-	4	385	c.264G>A	c.(262-264)ggG>ggA	p.G88G	ZNF816-ZNF321P_ENST00000313956.4_RNA|ZNF816_ENST00000549216.1_Silent_p.G19G|ZNF816_ENST00000434371.2_Silent_p.G88G			Q8N8H1	ZN321_HUMAN	zinc finger protein 321, pseudogene	19										endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						TTTGCAATGTCCCTGTGTGGA	0.373																																					p.G88G		Atlas-SNP	.											.	.	.	.	0			c.G264A						.						132	140	137					19																	53432594		2202	4300	6502	SO:0001819	synonymous_variant	100529240	exon4			CAATGTCCCTGTG	AK096828		19q13.4	2013-01-08	2011-04-19	2011-04-19	ENSG00000221874	ENSG00000221874			13827	pseudogene	pseudogene			"zinc finger protein 321"	ZNF321			Standard	NR_037805		Approved	MGC35402		Q8N8H1	OTTHUMG00000167760	ENST00000391777.3:c.264G>A	chr19.hg19:g.53432594C>T		64.0	0.0		64.0	21.0	NM_001202473	B7ZB38|Q68DZ0|Q86SS5	Silent	SNP	ENST00000391777.3	hg19	CCDS56101.1																																																																																			.	.		0.373	ZNF321P-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000396130.1	NR_037805		T	53432594	C	T	53432594	2	4	177	1	0	0	0	0	0	0	0	1	17855	842	30	3		3	ZNF321	19	53432594	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	5227681	53432594	5696389	107	26687										
ZNF835	90485	hgsc.bcm.edu	37	chr19	57175001	57175001	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ctgccagggcacccctgttgAcaggtttctcctccctgtga	10	15	1	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr19:57175001A>G	ENST00000537055.2	-	2	1797	c.1566T>C	c.(1564-1566)tgT>tgC	p.C522C		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	522					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						ACCCCTGTTGACAGGTTTCTC	0.582																																					p.C522C		Atlas-SNP	.											.	ZNF835	106	.	0			c.T1566C						.						62	68	66					19																	57175001		2126	4248	6374	SO:0001819	synonymous_variant	90485	exon2			CTGTTGACAGGTT	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.1566T>C	chr19.hg19:g.57175001A>G		109.0	0.0		107.0	40.0	NM_001005850	B7Z5Y0|G3V1S0	Silent	SNP	ENST00000537055.2	hg19	CCDS56105.1																																																																																			.	.		0.582	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		G	57175001	A	G	57175001	2	3	177	1	0	0	0	0	0	0	0	1	18201	273	10	2		2	ZNF835	19	57175001	Silent	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10	3742407	57175001	1953982	108	26688										
CLDN8	9073	hgsc.bcm.edu	37	chr21	31587841	31587841	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ggcaacccagctcacagggaTgagcaccaccatgcccgtga	11	15	1	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr21:31587841T>G	ENST00000399899.1	-	1	550	c.403A>C	c.(403-405)Atc>Ctc	p.I135L	CLDN8_ENST00000286809.1_Missense_Mutation_p.I135L	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	135					calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						CTCACAGGGATGAGCACCACC	0.493																																					p.I135L		Atlas-SNP	.											.	CLDN8	40	.	0			c.A403C						.						93	85	87					21																	31587841		2203	4300	6503	SO:0001583	missense	9073	exon1			CAGGGATGAGCAC	AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284		"Claudins"	2050	protein-coding gene	gene with protein product		611231				9892664	Standard	NM_199328		Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.403A>C	chr21.hg19:g.31587841T>G	ENSP00000382783:p.Ile135Leu	67.0	0.0		69.0	31.0	NM_199328	D3DSE3|Q53EX7	Missense_Mutation	SNP	ENST00000399899.1	hg19	CCDS13587.1	.	.	.	.	.	.	.	.	.	.	T	17.32	3.359075	0.61403	.	.	ENSG00000156284	ENST00000399899;ENST00000286809;ENST00000536721	D;D	0.89746	-2.56;-2.56	4.84	2.52	0.30459	.	0.000000	0.85682	D	0.000000	D	0.93151	0.7819	M	0.84082	2.675	0.50171	D	0.999857	D	0.57899	0.981	D	0.66716	0.946	D	0.92694	0.6169	10	0.72032	D	0.01	.	9.5194	0.39126	0.0:0.1557:0.0:0.8443	.	135	P56748	CLD8_HUMAN	L	135	ENSP00000382783:I135L;ENSP00000286809:I135L	ENSP00000286809:I135L	I	-	1	0	CLDN8	30509712	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	1.685000	0.37659	0.989000	0.38761	-0.263000	0.10527	ATC	.	.		0.493	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	NM_199328		G	31587841	T	G	31587841	3	3	177	1	0	0	0	0	1	0	0	0	3493	1464	51	5	278	5	CLDN8	21	31587841	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10		31587841	16542054	109	26689										
RUNX1	861	hgsc.bcm.edu	37	chr21	36193995	36193995	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cagggtgctgtgtcttcctcTgagggagccatgtgtgacca	14	10	2	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr21:36193995T>A	ENST00000344691.4	-	4	2302				RUNX1_ENST00000399240.1_Intron|RUNX1_ENST00000325074.5_Intron|RUNX1_ENST00000300305.3_Intron|RUNX1_ENST00000358356.5_Splice_Site|RUNX1_ENST00000437180.1_Intron	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1						behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						TGTCTTCCTCTGAGGGAGCCA	0.502			T	"RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"	"AML, preB- ALL, T-ALL"																																.		Atlas-SNP	.		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	.	RUNX1	687	.	0			c.725-2A>T						.						56	58	57					21																	36193995		1568	3578	5146	SO:0001627	intron_variant	861	exon6			TTCCTCTGAGGGA	X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"aml1 oncogene"	151385	"acute myeloid leukemia 1"	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.724+12711A>T	chr21.hg19:g.36193995T>A		128.0	0.0		122.0	55.0	NM_001122607	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Splice_Site	SNP	ENST00000344691.4	hg19	CCDS42922.1	.	.	.	.	.	.	.	.	.	.	T	3.417	-0.119055	0.06838	.	.	ENSG00000159216	ENST00000358356	.	.	.	2.82	-4.11	0.03928	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.3962	0.02261	0.1873:0.3988:0.1757:0.2382	.	.	.	.	.	-1	.	.	.	-	.	.	RUNX1	35115865	0.000000	0.05858	0.000000	0.03702	0.117000	0.20001	-1.373000	0.02568	-1.005000	0.03417	0.528000	0.53228	.	.	.		0.502	RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1			A	36193995	T	A	36193995	1	1	177	0	1	0	0	0	0	0	0	0	13761	1594	55	4		4	RUNX1	21	36193995	Intron	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	4606154	36193995	11935900	110	26690										
SGSM1	129049	hgsc.bcm.edu	37	chr22	25251281	25251281	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	gtgccctagagtacaccaagAtgaagactgcagatcacttc	9	11	1	5			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr22:25251281A>G	ENST00000400359.4	+	7	560	c.553A>G	c.(553-555)Atg>Gtg	p.M185V	SGSM1_ENST00000400358.4_Missense_Mutation_p.M185V	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	185	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						GTACACCAAGATGAAGACTGC	0.622																																					p.M185V		Atlas-SNP	.											.	SGSM1	150	.	0			c.A553G						.						29	31	31					22																	25251281		2064	4196	6260	SO:0001583	missense	129049	exon7			ACCAAGATGAAGA	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"Small G protein signaling modulators"	29410	protein-coding gene	gene with protein product		611417	"RUN and TBC1 domain containing 2"	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.553A>G	chr22.hg19:g.25251281A>G	ENSP00000383212:p.Met185Val	61.0	0.0		61.0	26.0	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	hg19	CCDS46674.1	.	.	.	.	.	.	.	.	.	.	A	13.24	2.177388	0.38413	.	.	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.28666	1.6;1.6	4.48	4.48	0.54585	RUN (3);	0.000000	0.85682	D	0.000000	T	0.44787	0.1310	L	0.39566	1.225	0.58432	D	0.999999	P;P;B;D;P	0.60575	0.954;0.843;0.082;0.988;0.508	D;D;B;D;P	0.74348	0.943;0.926;0.219;0.983;0.59	T	0.34700	-0.9818	10	0.48119	T	0.1	-7.259	13.2818	0.60219	1.0:0.0:0.0:0.0	.	185;160;318;185;160	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1;B9A6J4	.;.;.;SGSM1_HUMAN;.	V	160;185;185	ENSP00000383211:M185V;ENSP00000383212:M185V	ENSP00000383211:M185V	M	+	1	0	SGSM1	23581281	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.278000	0.58946	1.792000	0.52537	0.472000	0.43445	ATG	.	.		0.622	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318		G	25251281	A	G	25251281	3	3	177	1	0	0	0	0	1	0	0	0	14237	333	12	2	579	2	SGSM1	22	25251281	Missense_Mutation	SNP	A	TCGA-DD-AAD0-01A-11D-A40R-10		25251281	26053285	111	26691										
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50719562	50719562	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	cccgcacgctctcctccaggCcctccagctgggacttgatc	9	19	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chr22:50719562C>A	ENST00000449103.1	-	23	3859	c.3719G>T	c.(3718-3720)gGc>gTc	p.G1240V	PLXNB2_ENST00000359337.4_Missense_Mutation_p.G1240V|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	1240					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTCCTCCAGGCCCTCCAGCTG	0.662																																					p.G1240V		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G3719T						.						31	36	34					22																	50719562		2173	4281	6454	SO:0001583	missense	23654	exon23			TCCAGGCCCTCCA		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.3719G>T	chr22.hg19:g.50719562C>A	ENSP00000409171:p.Gly1240Val	56.0	0.0		54.0	26.0	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	hg19	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.206927	0.79127	.	.	ENSG00000196576	ENST00000449103;ENST00000359337	T;T	0.03272	3.99;3.99	4.74	4.74	0.60224	.	0.000000	0.64402	D	0.000010	T	0.14614	0.0353	M	0.61703	1.905	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	T	0.13335	-1.0513	10	0.22109	T	0.4	.	17.6935	0.88275	0.0:1.0:0.0:0.0	.	1240	O15031	PLXB2_HUMAN	V	1240	ENSP00000409171:G1240V;ENSP00000352288:G1240V	ENSP00000352288:G1240V	G	-	2	0	PLXNB2	49061689	1.000000	0.71417	0.994000	0.49952	0.968000	0.65278	3.423000	0.52756	2.184000	0.69523	0.462000	0.41574	GGC	.	.		0.662	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		A	50719562	C	A	50719562	3	1	177	1	0	0	0	0	1	0	0	0	12133	739	26	3	1857	3	PLXNB2	22	50719562	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	25468281	50719562	585004	112	26692										
SSX7	280658	hgsc.bcm.edu	37	chrX	52682011	52682011	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tcccactctttcttagagaaGtatttggcaatatcatcgaa	6	9	3	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chrX:52682011G>T	ENST00000298181.5	-	3	251	c.93C>A	c.(91-93)taC>taA	p.Y31*		NM_173358.2	NP_775494.1	Q7RTT5	SSX7_HUMAN	synovial sarcoma, X breakpoint 7	31	KRAB-related. {ECO:0000255|PROSITE- ProRule:PRU00120}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.Y31*(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|skin(1)	16	Ovarian(276;0.236)					TCTTAGAGAAGTATTTGGCAA	0.393																																					p.Y31X		Atlas-SNP	.											.	SSX7	34	.	1	Substitution - Nonsense(1)	endometrium(1)	c.C93A						.						140	116	124					X																	52682011		2203	4300	6503	SO:0001587	stop_gained	280658	exon3			AGAGAAGTATTTG	BK000687	CCDS14343.1	Xp11.23	2011-02-10			ENSG00000187754	ENSG00000187754			19653	protein-coding gene	gene with protein product		300542				12216073	Standard	NM_173358		Approved		uc004dqx.1	Q7RTT5	OTTHUMG00000021572	ENST00000298181.5:c.93C>A	chrX.hg19:g.52682011G>T	ENSP00000298181:p.Tyr31*	695.0	0.0		736.0	340.0	NM_173358		Nonsense_Mutation	SNP	ENST00000298181.5	hg19	CCDS14343.1	.	.	.	.	.	.	.	.	.	.	N	11.27	1.588339	0.28357	.	.	ENSG00000187754	ENST00000298181	.	.	.	0.56	-1.12	0.09808	.	0.000000	0.44285	D	0.000466	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	31	.	ENSP00000298181:Y31X	Y	-	3	2	SSX7	52698736	0.962000	0.33011	0.037000	0.18230	0.010000	0.07245	2.195000	0.42677	-0.516000	0.06470	-1.166000	0.01754	TAC	.	.		0.393	SSX7-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056671.1	NM_173358		T	52682011	G	T	52682011	4	4	177	1	0	0	0	0	0	1	0	0	15224	1024	36	3	493	3	SSX7	23	52682011	Nonsense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10		52682011	102588549	113	26693										
SMC1A	8243	hgsc.bcm.edu	37	chrX	53442011	53442011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aaaggcccggttggcagctgGcttgcccacaggagctccat	13	13	0	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chrX:53442011G>A	ENST00000322213.4	-	2	344	c.217C>T	c.(217-219)Cca>Tca	p.P73S	SMC1A_ENST00000375340.6_Missense_Mutation_p.P73S	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	73					DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						TTGGCAGCTGGCTTGCCCACA	0.567																																					p.P73S		Atlas-SNP	.											.	SMC1A	112	.	0			c.C217T						.						64	53	57					X																	53442011		2203	4300	6503	SO:0001583	missense	8243	exon2			CAGCTGGCTTGCC	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"Structural maintenance of chromosomes proteins"	11111	protein-coding gene	gene with protein product		300040	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.217C>T	chrX.hg19:g.53442011G>A	ENSP00000323421:p.Pro73Ser	104.0	0.0		117.0	46.0	NM_006306	O14995|Q16351|Q2M228	Missense_Mutation	SNP	ENST00000322213.4	hg19	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.175423	0.57692	.	.	ENSG00000072501	ENST00000322213;ENST00000375340;ENST00000340213	T;T	0.66280	-0.2;-0.2	4.67	4.67	0.58626	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.78272	0.4257	M	0.73598	2.24	0.37577	D	0.919666	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.78314	0.99;0.991;0.971	T	0.82851	-0.0253	10	0.52906	T	0.07	.	15.8202	0.78633	0.0:0.0:1.0:0.0	.	73;51;73	B7Z709;Q6MZR8;Q14683	.;.;SMC1A_HUMAN	S	73	ENSP00000323421:P73S;ENSP00000364489:P73S	ENSP00000323421:P73S	P	-	1	0	SMC1A	53458736	1.000000	0.71417	1.000000	0.80357	0.026000	0.11368	9.640000	0.98453	2.067000	0.61834	0.600000	0.82982	CCA	.	.		0.567	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		A	53442011	G	A	53442011	3	1	177	1	0	0	0	0	1	0	0	0	14796	1203	42	3	3580	3	SMC1A	23	53442011	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	760000	53442011	101828549	114	26694										
DGAT2L6	347516	hgsc.bcm.edu	37	chrX	69424178	69424178	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ataccttgtcccttcatattCctttggtgagaacgaagttt	7	9	1	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chrX:69424178C>A	ENST00000333026.3	+	6	771	c.671C>A	c.(670-672)tCc>tAc	p.S224Y		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	224					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(1)	12						CCTTCATATTCCTTTGGTGAG	0.483																																					p.S224Y		Atlas-SNP	.											.	DGAT2L6	40	.	0			c.C671A						.						51	42	45					X																	69424178		2203	4300	6503	SO:0001583	missense	347516	exon6			CATATTCCTTTGG	AK129500	CCDS14397.1	Xq13.1	2008-02-05			ENSG00000184210	ENSG00000184210			23250	protein-coding gene	gene with protein product		300926				15671038	Standard	NM_198512		Approved	DC3, FLJ25989	uc004dxx.1	Q6ZPD8	OTTHUMG00000021774	ENST00000333026.3:c.671C>A	chrX.hg19:g.69424178C>A	ENSP00000328036:p.Ser224Tyr	237.0	0.0		243.0	121.0	NM_198512	Q6IEE2	Missense_Mutation	SNP	ENST00000333026.3	hg19	CCDS14397.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.016304	0.75161	.	.	ENSG00000184210	ENST00000333026	D	0.93133	-3.17	4.43	4.43	0.53597	.	0.092869	0.46758	D	0.000265	D	0.96078	0.8722	M	0.89968	3.075	0.58432	D	0.999999	P	0.45827	0.867	P	0.53224	0.721	D	0.96852	0.9626	10	0.87932	D	0	-9.1114	13.4557	0.61197	0.0:1.0:0.0:0.0	.	224	Q6ZPD8	DG2L6_HUMAN	Y	224	ENSP00000328036:S224Y	ENSP00000328036:S224Y	S	+	2	0	DGAT2L6	69340903	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	6.908000	0.75730	2.035000	0.60131	0.600000	0.82982	TCC	.	.		0.483	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057067.1	NM_198512		A	69424178	C	A	69424178	3	1	177	1	0	0	0	0	1	0	0	0	4461	855	30	3	693	3	DGAT2L6	23	69424178	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	15982167	69424178	85846382	115	26695										
CHIC1	53344	hgsc.bcm.edu	37	chrX	72783364	72783364	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tagtgagcgaggagcatctgCggagatatgctcccgaccct	13	11	1	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chrX:72783364C>T	ENST00000373502.5	+	1	321	c.244C>T	c.(244-246)Cgg>Tgg	p.R82W	MAP2K4P1_ENST00000602584.1_RNA|CHIC1_ENST00000373504.6_Missense_Mutation_p.R82W	NM_001039840.2	NP_001034929.2	Q5VXU3	CHIC1_HUMAN	cysteine-rich hydrophobic domain 1	82						cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(2)	4	Renal(35;0.156)					GGAGCATCTGCGGAGATATGC	0.602																																					p.R82W		Atlas-SNP	.											.	CHIC1	13	.	0			c.C244T						.						25	20	21					X																	72783364		2200	4293	6493	SO:0001583	missense	53344	exon1			CATCTGCGGAGAT	Y11897	CCDS35335.2, CCDS75993.1	Xq13.2	2008-05-14			ENSG00000204116	ENSG00000204116			1934	protein-coding gene	gene with protein product		300922				9321471, 11257495	Standard	NM_001039840		Approved	BRX	uc004ebk.4	Q5VXU3	OTTHUMG00000021835	ENST00000373502.5:c.244C>T	chrX.hg19:g.72783364C>T	ENSP00000362601:p.Arg82Trp	198.0	0.0		210.0	90.0	NM_001039840	A0PJZ2|B0QZ87|B9EGS5|Q5CZ84	Missense_Mutation	SNP	ENST00000373502.5	hg19	CCDS35335.2	.	.	.	.	.	.	.	.	.	.	C	21.2	4.119836	0.77323	.	.	ENSG00000204116	ENST00000373502;ENST00000373504	.	.	.	4.71	2.86	0.33363	.	0.336090	0.27236	N	0.020288	T	0.42040	0.1185	N	0.08118	0	0.34486	D	0.704467	D;D;D	0.69078	0.997;0.997;0.994	P;P;P	0.59948	0.841;0.866;0.739	T	0.57370	-0.7823	9	0.66056	D	0.02	-8.04	10.8659	0.46856	0.3404:0.6596:0.0:0.0	.	82;82;82	B7Z3I1;Q5VXU3-2;Q5VXU3	.;.;CHIC1_HUMAN	W	82	.	ENSP00000362601:R82W	R	+	1	2	CHIC1	72700089	0.990000	0.36364	1.000000	0.80357	0.962000	0.63368	0.801000	0.27055	0.332000	0.23536	0.292000	0.19580	CGG	.	.		0.602	CHIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057233.3			T	72783364	C	T	72783364	3	4	177	1	0	0	0	0	1	0	0	0	3345	759	27	1	246	1	CHIC1	23	72783364	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	3359186	72783364	82487196	116	26696										
ARMCX6	54470	hgsc.bcm.edu	37	chrX	100871397	100871397	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	aggttcagtccaatccccatCctcagtccagggccgagcca	9	16	2	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chrX:100871397C>T	ENST00000361910.4	-	3	558	c.214G>A	c.(214-216)Gat>Aat	p.D72N	ARMCX6_ENST00000538627.1_Missense_Mutation_p.D72N|ARMCX6_ENST00000539247.1_Missense_Mutation_p.D72N|ARMCX6_ENST00000497931.1_Intron	NM_019007.3	NP_061880.2	Q7L4S7	ARMX6_HUMAN	armadillo repeat containing, X-linked 6	72						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|liver(2)|lung(3)	9						CAATCCCCATCCTCAGTCCAG	0.587																																					p.D72N		Atlas-SNP	.											.	ARMCX6	21	.	0			c.G214A						.						73	67	69					X																	100871397		2203	4300	6503	SO:0001583	missense	54470	exon4			CCCCATCCTCAGT	BC007677	CCDS14488.1	Xq21.33-q22.3	2014-03-21			ENSG00000198960	ENSG00000198960		"Armadillo repeat containing"	26094	protein-coding gene	gene with protein product						16221301, 22569362	Standard	NM_001184768		Approved	FLJ20811, GASP10	uc004ehy.3	Q7L4S7	OTTHUMG00000022034	ENST00000361910.4:c.214G>A	chrX.hg19:g.100871397C>T	ENSP00000354708:p.Asp72Asn	91.0	0.0		99.0	42.0	NM_001184768	Q9NWJ3	Missense_Mutation	SNP	ENST00000361910.4	hg19	CCDS14488.1	.	.	.	.	.	.	.	.	.	.	.	11.79	1.745007	0.30865	.	.	ENSG00000198960	ENST00000361910;ENST00000539247;ENST00000538627	T;T;T	0.46063	0.88;0.88;0.88	3.56	2.69	0.31865	.	0.156544	0.30260	N	0.010028	T	0.26774	0.0655	L	0.36672	1.1	0.28202	N	0.927317	B	0.17038	0.02	B	0.12837	0.008	T	0.13495	-1.0507	10	0.18276	T	0.48	-6.4337	6.0133	0.19588	0.0:0.8561:0.0:0.1439	.	72	Q7L4S7	ARMX6_HUMAN	N	72	ENSP00000354708:D72N;ENSP00000444537:D72N;ENSP00000440648:D72N	ENSP00000354708:D72N	D	-	1	0	ARMCX6	100758053	0.988000	0.35896	1.000000	0.80357	0.828000	0.46876	0.242000	0.18087	0.891000	0.36235	0.472000	0.43445	GAT	.	.		0.587	ARMCX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057562.1	NM_019007		T	100871397	C	T	100871397	3	4	177	1	0	0	0	0	1	0	0	0	963	855	30	3	692	3	ARMCX6	23	100871397	Missense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	28088033	100871397	54399163	117	26697										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107821329	107821329	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ggaatatgggcttaaatttcCagggacccaaaggtgaaaaa	11	6	0	1			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chrX:107821329C>T	ENST00000361603.2	+	12	911	c.667C>T	c.(667-669)Cag>Tag	p.Q223*	COL4A5_ENST00000328300.6_Nonsense_Mutation_p.Q223*	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	223	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						CTTAAATTTCCAGGGACCCAA	0.363									Alport syndrome with Diffuse Leiomyomatosis																												p.Q223X		Atlas-SNP	.											.	COL4A5	262	.	0			c.C667T						.						37	38	38					X																	107821329		2182	4288	6470	SO:0001587	stop_gained	1287	exon12	Familial Cancer Database		AATTTCCAGGGAC	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.667C>T	chrX.hg19:g.107821329C>T	ENSP00000354505:p.Gln223*	490.0	0.0		548.0	233.0	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Nonsense_Mutation	SNP	ENST00000361603.2	hg19	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	C	39	7.488624	0.98316	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	.	.	.	5.0	5.0	0.66597	.	0.074820	0.53938	D	0.000044	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	17.4744	0.87655	0.0:1.0:0.0:0.0	.	.	.	.	X	223	.	ENSP00000331902:Q223X	Q	+	1	0	COL4A5	107707985	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.394000	0.66285	2.051000	0.60960	0.600000	0.82982	CAG	.	.		0.363	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			T	107821329	C	T	107821329	4	4	177	1	0	0	0	0	0	1	0	0	3696	595	21	3	713	3	COL4A5	23	107821329	Nonsense_Mutation	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	6949932	107821329	47449231	118	26698										
GUCY2F	2986	hgsc.bcm.edu	37	chrX	108718938	108718938	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	attcgctcaatggctaatcgCgcagcaacctcaggcagggc	11	13	2	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chrX:108718938C>T	ENST00000218006.2	-	2	519	c.228G>A	c.(226-228)gcG>gcA	p.A76A		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	76					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						TGGCTAATCGCGCAGCAACCT	0.532											OREG0019905	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A76A		Atlas-SNP	.											.	GUCY2F	178	.	0			c.G228A						.						80	75	76					X																	108718938		2203	4300	6503	SO:0001819	synonymous_variant	2986	exon2			TAATCGCGCAGCA	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"guanylate cyclase 2D-like, membrane (retina-specific)"	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.228G>A	chrX.hg19:g.108718938C>T		420.0	0.0	1414	392.0	181.0	NM_001522	Q9UJF1	Silent	SNP	ENST00000218006.2	hg19	CCDS14545.1																																																																																			.	.		0.532	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		T	108718938	C	T	108718938	2	4	177	1	0	0	0	0	0	0	0	1	6907	755	27	1		1	GUCY2F	23	108718938	Silent	SNP	C	TCGA-DD-AAD0-01A-11D-A40R-10	897609	108718938	46551622	119	26699										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123870898	123870898	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	tgggggagctggagcagctgGgctgggctggctgcgggtag	23	7	0	0			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chrX:123870898G>T	ENST00000371130.3	-	4	748	c.685C>A	c.(685-687)Cca>Aca	p.P229T	TENM1_ENST00000422452.2_Missense_Mutation_p.P229T	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	229	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GGAGCAGCTGGGCTGGGCTGG	0.602																																					p.P229T		Atlas-SNP	.											.	.	.	.	0			c.C685A						.						126	119	121					X																	123870898		2203	4300	6503	SO:0001583	missense	10178	exon4			CAGCTGGGCTGGG	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.685C>A	chrX.hg19:g.123870898G>T	ENSP00000360171:p.Pro229Thr	79.0	0.0		89.0	45.0	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	hg19	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021729	0.75275	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.50548	0.74;0.74	5.13	5.13	0.70059	Teneurin intracellular, N-terminal (2);	0.191381	0.36268	N	0.002686	T	0.47116	0.1428	L	0.29908	0.895	0.53005	D	0.999969	P;P;B	0.47841	0.901;0.901;0.028	B;P;B	0.47864	0.419;0.559;0.038	T	0.52373	-0.8584	10	0.72032	D	0.01	.	17.6714	0.88218	0.0:0.0:1.0:0.0	.	229;229;229	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	T	229	ENSP00000360171:P229T;ENSP00000403954:P229T	ENSP00000360171:P229T	P	-	1	0	ODZ1	123698579	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.230000	0.95299	2.102000	0.63906	0.600000	0.82982	CCA	.	.		0.602	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123870898	G	T	123870898	3	4	177	1	0	0	0	0	1	0	0	0	10843	1232	43	3	7629	3	ODZ1	23	123870898	Missense_Mutation	SNP	G	TCGA-DD-AAD0-01A-11D-A40R-10	15151960	123870898	31399662	120	26700										
RAB39B	116442	hgsc.bcm.edu	37	chrX	154490389	154490389	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0504201680672269	6	1	0.98282967032967	2.12946428571429	0.473214285714286	0.608391608391609	1	0	ccagaacaaatacaatttggTagggctgaacgtgtactttg	10	7	0	2			TCGA-DD-AAD0-01A-11D-A40R-10	TCGA-DD-AAD0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4463ea73-26d1-4e24-a97d-0302bb2dd21b	15b4a966-4206-4903-8558-da5d6cb55540	g.chrX:154490389T>A	ENST00000369454.3	-	2	641	c.341A>T	c.(340-342)tAc>tTc	p.Y114F		NM_171998.2	NP_741995.1	Q96DA2	RB39B_HUMAN	RAB39B, member RAS oncogene family	114					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|synapse organization (GO:0050808)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)			breast(1)|central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(12)	19	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TACAATTTGGTAGGGCTGAAC	0.493																																					p.Y114F		Atlas-SNP	.											.	RAB39B	37	.	0			c.A341T						.						177	163	167					X																	154490389		2203	4300	6503	SO:0001583	missense	116442	exon2			ATTTGGTAGGGCT	AY052478	CCDS14766.1	Xq28	2014-01-31			ENSG00000155961	ENSG00000155961		"RAB, member RAS oncogene"	16499	protein-coding gene	gene with protein product		300774	"mental retardation, X-linked 72"	MRX72		12438742, 20159109	Standard	NM_171998		Approved		uc004fne.3	Q96DA2	OTTHUMG00000022659	ENST00000369454.3:c.341A>T	chrX.hg19:g.154490389T>A	ENSP00000358466:p.Tyr114Phe	64.0	0.0		68.0	36.0	NM_171998	Q5JT79|Q8NEX3	Missense_Mutation	SNP	ENST00000369454.3	hg19	CCDS14766.1	.	.	.	.	.	.	.	.	.	.	T	7.684	0.689541	0.14973	.	.	ENSG00000155961	ENST00000369454	T	0.76578	-1.03	4.77	4.77	0.60923	Small GTP-binding protein domain (1);	0.063404	0.64402	D	0.000005	T	0.62490	0.2432	N	0.20574	0.59	0.38924	D	0.957807	B	0.02656	0.0	B	0.04013	0.001	T	0.59337	-0.7473	10	0.24483	T	0.36	.	11.6344	0.51196	0.0:0.0:0.0:1.0	.	114	Q96DA2	RB39B_HUMAN	F	114	ENSP00000358466:Y114F	ENSP00000358466:Y114F	Y	-	2	0	RAB39B	154143583	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	3.992000	0.56980	1.824000	0.53156	0.417000	0.27973	TAC	.	.		0.493	RAB39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058792.1	NM_171998		A	154490389	T	A	154490389	3	1	177	1	0	0	0	0	1	0	0	0	12945	1638	57	4	304	4	RAB39B	23	154490389	Missense_Mutation	SNP	T	TCGA-DD-AAD0-01A-11D-A40R-10	30619491	154490389	780171	121	26701										
ERRFI1	54206	hgsc.bcm.edu	37	chr1	8073367	8073367	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tttctgtggctgaagatataCcgcagtcagcaggtaatggc	12	8	2	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:8073367C>T	ENST00000377482.5	-	4	1515	c.1292G>A	c.(1291-1293)gGt>gAt	p.G431D	ERRFI1_ENST00000474874.1_Intron	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	431					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		TGAAGATATACCGCAGTCAGC	0.443																																					p.G431D		Atlas-SNP	.											.	ERRFI1	42	.	0			c.G1292A						.						151	140	144					1																	8073367		2203	4300	6503	SO:0001583	missense	54206	exon4			GATATACCGCAGT	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.1292G>A	chr1.hg19:g.8073367C>T	ENSP00000366702:p.Gly431Asp	170.0	0.0		126.0	30.0	NM_018948	B2RDX9|Q9NTG9|Q9UD05	Missense_Mutation	SNP	ENST00000377482.5	hg19	CCDS94.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376769	0.24857	.	.	ENSG00000116285	ENST00000377482	T	0.14640	2.49	5.9	4.98	0.66077	.	0.981135	0.08373	N	0.955827	T	0.10637	0.0260	N	0.22421	0.69	0.09310	N	0.999996	B	0.23735	0.09	B	0.21708	0.036	T	0.34650	-0.9820	10	0.12103	T	0.63	-10.0656	11.6364	0.51207	0.128:0.6245:0.2475:0.0	.	431	Q9UJM3	ERRFI_HUMAN	D	431	ENSP00000366702:G431D	ENSP00000366702:G431D	G	-	2	0	ERRFI1	7995954	0.001000	0.12720	0.002000	0.10522	0.011000	0.07611	1.062000	0.30555	1.466000	0.48025	0.650000	0.86243	GGT	.	.		0.443	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948		T	8073367	C	T	8073367	3	4	178	1	0	0	0	0	1	0	0	0	5246	507	18	3	100	3	ERRFI1	1	8073367	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10		8073367	241177254	1	26702										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12336568	12336568	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ttgagagcaatggccggtacAtttctgtgctcaaggtgttt	12	7	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:12336568A>G	ENST00000358136.3	+	19	3053	c.2923A>G	c.(2923-2925)Att>Gtt	p.I975V	VPS13D_ENST00000356315.4_Missense_Mutation_p.I975V	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TGGCCGGTACATTTCTGTGCT	0.507											OREG0013110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I975V		Atlas-SNP	.											.	VPS13D	316	.	0			c.A2923G						.						115	109	111					1																	12336568		2203	4300	6503	SO:0001583	missense	55187	exon19			CGGTACATTTCTG	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.2923A>G	chr1.hg19:g.12336568A>G	ENSP00000350854:p.Ile975Val	82.0	0.0	679	74.0	20.0	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	hg19	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	A	8.295	0.818710	0.16607	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.54279	0.58;0.58	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.43853	0.1266	L	0.37630	1.12	0.80722	D	1	B;B	0.33022	0.394;0.274	B;B	0.32465	0.146;0.069	T	0.31223	-0.9951	10	0.15499	T	0.54	.	16.6154	0.84909	1.0:0.0:0.0:0.0	.	975;975	Q5THJ4-2;Q5THJ4	.;VP13D_HUMAN	V	975	ENSP00000348666:I975V;ENSP00000350854:I975V	ENSP00000348666:I975V	I	+	1	0	VPS13D	12259155	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.957000	0.93082	2.315000	0.78130	0.533000	0.62120	ATT	.	.		0.507	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		G	12336568	A	G	12336568	3	3	178	1	0	0	0	0	1	0	0	0	17207	217	8	2	2993	2	VPS13D	1	12336568	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	4263201	12336568	236914053	2	26703										
MACF1	23499	hgsc.bcm.edu	37	chr1	39750866	39750866	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tggaacgagagaaatcacttCggccggctgtggagaggtgg	17	7	1	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:39750866C>A	ENST00000372915.3	+	11	1345	c.1258C>A	c.(1258-1260)Cgg>Agg	p.R420R	MACF1_ENST00000317713.7_Silent_p.R420R|MACF1_ENST00000361689.2_Silent_p.R420R|MACF1_ENST00000567887.1_Silent_p.R452R|MACF1_ENST00000545844.1_Silent_p.R420R|MACF1_ENST00000539005.1_Silent_p.R420R|MACF1_ENST00000564288.1_Silent_p.R415R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	420					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GAAATCACTTCGGCCGGCTGT	0.453																																					p.R420R		Atlas-SNP	.											.	MACF1	909	.	0			c.C1258A						.						125	127	126					1																	39750866		2203	4300	6503	SO:0001819	synonymous_variant	23499	exon13			TCACTTCGGCCGG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.1258C>A	chr1.hg19:g.39750866C>A		173.0	0.0		184.0	38.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	hg19																																																																																				.	.		0.453	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39750866	C	A	39750866	2	1	178	1	0	0	0	0	0	0	0	1	9153	875	31	1		1	MACF1	1	39750866	Silent	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	27414298	39750866	209499755	3	26704										
USP24	23358	hgsc.bcm.edu	37	chr1	55619849	55619849	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctcttgattgcttctttcacTgcatatgcatcactaaggat	6	10	4	1	rs377666153		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:55619849T>G	ENST00000294383.6	-	15	1754	c.1755A>C	c.(1753-1755)gcA>gcC	p.A585A	USP24_ENST00000407756.1_Silent_p.A441A	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	585					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						CTTCTTTCACTGCATATGCAT	0.448																																					p.A585A		Atlas-SNP	.											.	USP24	323	.	0			c.A1755C						.						123	116	119					1																	55619849		1954	4165	6119	SO:0001819	synonymous_variant	23358	exon15			TTTCACTGCATAT	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.1755A>C	chr1.hg19:g.55619849T>G		136.0	0.0		93.0	22.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	hg19	CCDS44154.2																																																																																			.	.		0.448	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			G	55619849	T	G	55619849	2	3	178	1	0	0	0	0	0	0	0	1	17070	1567	55	5		5	USP24	1	55619849	Silent	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	15868983	55619849	193630772	4	26705										
PTGER3	5733	hgsc.bcm.edu	37	chr1	71512635	71512635	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cccctcgcccggtgctgatgAagcaccacgtcccgggccac	11	19	0	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:71512635A>T	ENST00000306666.5	-	1	836	c.626T>A	c.(625-627)tTc>tAc	p.F209Y	PTGER3_ENST00000351052.5_Missense_Mutation_p.F209Y|ZRANB2-AS1_ENST00000450461.1_RNA|PTGER3_ENST00000354608.5_Missense_Mutation_p.F209Y|PTGER3_ENST00000414819.1_Missense_Mutation_p.F209Y|PTGER3_ENST00000370924.4_Missense_Mutation_p.F209Y|PTGER3_ENST00000370932.2_Missense_Mutation_p.F209Y|PTGER3_ENST00000356595.4_Missense_Mutation_p.F209Y|PTGER3_ENST00000370931.3_Missense_Mutation_p.F209Y|PTGER3_ENST00000460330.1_Missense_Mutation_p.F209Y	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	209					cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	GGTGCTGATGAAGCACCACGT	0.672																																					p.F209Y		Atlas-SNP	.											.	PTGER3	246	.	0			c.T626A						.						54	56	56					1																	71512635		2203	4300	6503	SO:0001583	missense	5733	exon1			CTGATGAAGCACC	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.626T>A	chr1.hg19:g.71512635A>T	ENSP00000302313:p.Phe209Tyr	143.0	0.0		109.0	21.0	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Missense_Mutation	SNP	ENST00000306666.5	hg19	CCDS657.1	.	.	.	.	.	.	.	.	.	.	A	33	5.208574	0.95069	.	.	ENSG00000050628	ENST00000370931;ENST00000370932;ENST00000351052;ENST00000460330;ENST00000370934;ENST00000354608;ENST00000356595;ENST00000414819;ENST00000306666;ENST00000370924	T;T;T;T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18	5.1	5.1	0.69264	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.52386	0.1731	M	0.76727	2.345	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999;0.998;0.999;0.999	T	0.57619	-0.7780	10	0.59425	D	0.04	-35.4192	15.0441	0.71813	1.0:0.0:0.0:0.0	.	209;209;209;209;209;209;209;209	Q147U0;Q6TTN3;F5H821;B1AK19;Q147X8;P43115-3;P43115-4;P43115	.;.;.;.;.;.;.;PE2R3_HUMAN	Y	209	ENSP00000359969:F209Y;ENSP00000359970:F209Y;ENSP00000280208:F209Y;ENSP00000418073:F209Y;ENSP00000346624:F209Y;ENSP00000349003:F209Y;ENSP00000401423:F209Y;ENSP00000302313:F209Y;ENSP00000359962:F209Y	ENSP00000302313:F209Y	F	-	2	0	PTGER3	71285223	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.008000	0.76341	2.136000	0.66102	0.379000	0.24179	TTC	.	.		0.672	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957		T	71512635	A	T	71512635	3	4	178	1	0	0	0	0	1	0	0	0	12757	246	9	4	865	4	PTGER3	1	71512635	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	15892786	71512635	177737986	5	26706										
WARS2	10352	hgsc.bcm.edu	37	chr1	119683215	119683215	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctgcggatcccttatgaagtGcccggatgaagctccagcgc	12	13	0	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:119683215G>T	ENST00000235521.4	-	1	79	c.53C>A	c.(52-54)gCa>gAa	p.A18E	WARS2_ENST00000497761.1_5'UTR|WARS2_ENST00000369426.5_Missense_Mutation_p.A18E|RP11-418J17.1_ENST00000425884.1_RNA|RP11-418J17.1_ENST00000457043.1_RNA|RP11-418J17.1_ENST00000440150.1_RNA|RP11-418J17.1_ENST00000418015.1_RNA|WARS2_ENST00000537870.1_5'Flank|RP11-418J17.1_ENST00000413531.1_RNA	NM_015836.3|NM_201263.2	NP_056651.1|NP_957715.1	Q9UGM6	SYWM_HUMAN	tryptophanyl tRNA synthetase 2, mitochondrial	18					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)|vasculogenesis (GO:0001570)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(2)	15	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	CTTATGAAGTGCCCGGATGAA	0.597																																					p.A18E		Atlas-SNP	.											.	WARS2	69	.	0			c.C53A						.						46	47	47					1																	119683215		2203	4300	6503	SO:0001583	missense	10352	exon1			TGAAGTGCCCGGA	BC021722	CCDS900.1, CCDS30817.1	1p12	2011-07-01	2007-02-23		ENSG00000116874	ENSG00000116874	6.1.1.2	"Aminoacyl tRNA synthetases / Class I"	12730	protein-coding gene	gene with protein product	"tryptophan tRNA ligase 2, mitochondrial"	604733				10072595, 10828066	Standard	NM_201263		Approved	TrpRS	uc001ehn.3	Q9UGM6	OTTHUMG00000012335	ENST00000235521.4:c.53C>A	chr1.hg19:g.119683215G>T	ENSP00000235521:p.Ala18Glu	77.0	0.0		76.0	12.0	NM_015836	B1ALR1|B2R9D4|Q53FT4|Q5VUD2|Q86TQ0	Missense_Mutation	SNP	ENST00000235521.4	hg19	CCDS900.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015510	0.75161	.	.	ENSG00000116874	ENST00000369426;ENST00000235521	T;T	0.47528	0.84;1.85	6.04	6.04	0.98038	.	0.197788	0.44902	D	0.000409	T	0.50429	0.1615	L	0.46157	1.445	0.80722	D	1	D;D;B;D	0.89917	1.0;1.0;0.026;1.0	D;D;B;D	0.83275	0.996;0.996;0.015;0.996	T	0.31336	-0.9947	10	0.14656	T	0.56	-17.0199	16.0793	0.80989	0.0:0.0:1.0:0.0	.	18;18;18;18	B7Z448;B7Z6G7;Q9UGM6;B1ALR1	.;.;SYWM_HUMAN;.	E	18	ENSP00000358434:A18E;ENSP00000235521:A18E	ENSP00000235521:A18E	A	-	2	0	WARS2	119484738	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	4.489000	0.60309	2.873000	0.98535	0.561000	0.74099	GCA	.	.		0.597	WARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034362.1	NM_015836		T	119683215	G	T	119683215	3	4	178	1	0	0	0	0	1	0	0	0	17265	1319	46	3	1082	3	WARS2	1	119683215	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	48170580	119683215	129567406	6	26707										
NUF2	83540	hgsc.bcm.edu	37	chr1	163318764	163318764	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	taaagttcaagaaaaaagagGtgctgtctatgaacgagtaa	10	4	2	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:163318764G>A	ENST00000271452.3	+	13	1433	c.1154G>A	c.(1153-1155)gGt>gAt	p.G385D	NUF2_ENST00000367900.3_Missense_Mutation_p.G385D|NUF2_ENST00000524800.1_Missense_Mutation_p.G338D	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	385	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					GAAAAAAGAGGTGCTGTCTAT	0.333																																					p.G385D		Atlas-SNP	.											.	NUF2	138	.	0			c.G1154A						.						72	77	75					1																	163318764		2203	4300	6503	SO:0001583	missense	83540	exon13			AAAGAGGTGCTGT	BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"cancer/testis antigen 106"	611772	"cell division cycle associated 1", "NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.1154G>A	chr1.hg19:g.163318764G>A	ENSP00000271452:p.Gly385Asp	596.0	0.0		658.0	122.0	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	hg19	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	G	8.839	0.941818	0.18281	.	.	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.31769	1.48;1.51;1.51	5.5	3.63	0.41609	.	0.555420	0.20424	N	0.092605	T	0.04952	0.0133	N	0.08118	0	0.31999	N	0.603575	B;B	0.21225	0.009;0.053	B;B	0.17722	0.005;0.019	T	0.35251	-0.9796	9	0.16420	T	0.52	-5.5482	9.0298	0.36252	0.1739:0.0:0.8261:0.0	.	338;385	E9PQC4;Q9BZD4	.;NUF2_HUMAN	D	338;385;385	ENSP00000436888:G338D;ENSP00000356875:G385D;ENSP00000271452:G385D	ENSP00000271452:G385D	G	+	2	0	NUF2	161585388	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	3.640000	0.54350	0.859000	0.35456	-0.150000	0.13652	GGT	.	.		0.333	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697		A	163318764	G	A	163318764	3	1	178	1	0	0	0	0	1	0	0	0	10756	1261	44	3	1200	3	NUF2	1	163318764	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	43635549	163318764	85931857	7	26708										
TOR3A	64222	hgsc.bcm.edu	37	chr1	179054765	179054765	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cctctttcctgtccttaggcTtagagtgggacctgaatgtg	11	10	1	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:179054765T>G	ENST00000367627.3	+	3	1128	c.376T>G	c.(376-378)Tta>Gta	p.L126V	TOR3A_ENST00000352445.6_Missense_Mutation_p.L126V	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	126					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						GTCCTTAGGCTTAGAGTGGGA	0.532																																					p.L126V		Atlas-SNP	.											.	TOR3A	28	.	0			c.T376G						.						148	156	153					1																	179054765		2203	4300	6503	SO:0001583	missense	64222	exon3			TTAGGCTTAGAGT	BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"ATP-dependant interferon responsive"	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.376T>G	chr1.hg19:g.179054765T>G	ENSP00000356599:p.Leu126Val	133.0	0.0		133.0	44.0	NM_022371	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Missense_Mutation	SNP	ENST00000367627.3	hg19	CCDS1329.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.149966	0.57151	.	.	ENSG00000186283	ENST00000367627;ENST00000352445;ENST00000447595	T;T;T	0.61510	0.1;0.1;0.1	5.57	2.48	0.30137	.	0.000000	0.64402	D	0.000001	T	0.72692	0.3492	M	0.82433	2.59	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71507	-0.4572	10	0.66056	D	0.02	-5.5424	6.6825	0.23127	0.0:0.5621:0.0:0.4379	.	126	Q9H497	TOR3A_HUMAN	V	126;126;18	ENSP00000356599:L126V;ENSP00000335351:L126V;ENSP00000410195:L18V	ENSP00000335351:L126V	L	+	1	2	TOR3A	177321388	0.995000	0.38212	0.925000	0.36789	0.420000	0.31355	0.404000	0.20999	0.566000	0.29273	0.459000	0.35465	TTA	.	.		0.532	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371		G	179054765	T	G	179054765	3	3	178	1	0	0	0	0	1	0	0	0	16391	1606	56	5	386	5	TOR3A	1	179054765	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	15736001	179054765	70195856	8	26709										
USH2A	7399	hgsc.bcm.edu	37	chr1	216462647	216462647	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cacaaagaatgctaccatttCtagtgccaactgtatcacag	6	11	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:216462647C>T	ENST00000307340.3	-	11	2332	c.1946G>A	c.(1945-1947)aGa>aAa	p.R649K	USH2A_ENST00000366943.2_Missense_Mutation_p.R649K|USH2A_ENST00000366942.3_Missense_Mutation_p.R649K	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	649	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GCTACCATTTCTAGTGCCAAC	0.408										HNSCC(13;0.011)																											p.R649K		Atlas-SNP	.											.	USH2A	1168	.	0			c.G1946A						.						157	139	145					1																	216462647		2203	4300	6503	SO:0001583	missense	7399	exon11			CCATTTCTAGTGC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.1946G>A	chr1.hg19:g.216462647C>T	ENSP00000305941:p.Arg649Lys	125.0	0.0		144.0	22.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.667344	0.00765	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.54279	0.58;0.58;0.58	5.43	2.5	0.30297	EGF-like, laminin (3);	0.317558	0.22531	N	0.058851	T	0.26085	0.0636	N	0.16790	0.44	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.12156	0.007;0.007	T	0.21621	-1.0240	10	0.05833	T	0.94	.	4.067	0.09864	0.2611:0.4529:0.0:0.286	.	649;649	O75445-2;O75445	.;USH2A_HUMAN	K	649	ENSP00000305941:R649K;ENSP00000355910:R649K;ENSP00000355909:R649K	ENSP00000305941:R649K	R	-	2	0	USH2A	214529270	0.997000	0.39634	0.004000	0.12327	0.044000	0.14063	1.831000	0.39141	0.784000	0.33661	0.557000	0.71058	AGA	.	.		0.408	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216462647	C	T	216462647	3	4	178	1	0	0	0	0	1	0	0	0	17051	913	32	3	13924	3	USH2A	1	216462647	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	37407882	216462647	32787974	9	26710										
RYR2	6262	hgsc.bcm.edu	37	chr1	237754010	237754010	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tcagaagtcttttggttctcAgaacagcaacactgatatca	7	9	4	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:237754010A>C	ENST00000366574.2	+	31	4195	c.3878A>C	c.(3877-3879)cAg>cCg	p.Q1293P	RYR2_ENST00000542537.1_Missense_Mutation_p.Q1277P|RYR2_ENST00000360064.6_Missense_Mutation_p.Q1291P	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1293	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTTGGTTCTCAGAACAGCAAC	0.512																																					p.Q1293P		Atlas-SNP	.											.	RYR2	1273	.	0			c.A3878C						.						250	237	241					1																	237754010		1964	4159	6123	SO:0001583	missense	6262	exon31			GTTCTCAGAACAG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.3878A>C	chr1.hg19:g.237754010A>C	ENSP00000355533:p.Gln1293Pro	85.0	0.0		71.0	13.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	a	15.51	2.854109	0.51270	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96802	-4.13;-4.1;-4.12	5.03	5.03	0.67393	.	0.000000	0.56097	D	0.000027	D	0.94195	0.8137	L	0.49640	1.575	0.80722	D	1	B	0.31153	0.31	B	0.31016	0.123	D	0.93338	0.6707	10	0.45353	T	0.12	-18.9629	15.2157	0.73264	1.0:0.0:0.0:0.0	.	1293	Q92736	RYR2_HUMAN	P	1293;1291;1277	ENSP00000355533:Q1293P;ENSP00000353174:Q1291P;ENSP00000443798:Q1277P	ENSP00000353174:Q1291P	Q	+	2	0	RYR2	235820633	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.985000	0.93487	2.241000	0.73720	0.533000	0.62120	CAG	.	.		0.512	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237754010	A	C	237754010	3	2	178	1	0	0	0	0	1	0	0	0	13784	188	7	5	4000	5	RYR2	1	237754010	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	21291363	237754010	11496611	10	26711										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245849955	245849955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gctctgcacgggccctggccTcgggctcgcggcccgtcagc	15	18	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:245849955T>C	ENST00000407071.2	+	12	4110	c.3670T>C	c.(3670-3672)Tcg>Ccg	p.S1224P	KIF26B_ENST00000366518.4_Missense_Mutation_p.S843P	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1224					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GGCCCTGGCCTCGGGCTCGCG	0.657																																					p.S1224P		Atlas-SNP	.											.	KIF26B	343	.	0			c.T3670C						.						19	26	23					1																	245849955		2106	4212	6318	SO:0001583	missense	55083	exon12			CTGGCCTCGGGCT	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.3670T>C	chr1.hg19:g.245849955T>C	ENSP00000385545:p.Ser1224Pro	97.0	0.0		62.0	10.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	T	14.53	2.563980	0.45694	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	D;D	0.81739	-1.53;-1.53	5.77	5.77	0.91146	.	.	.	.	.	T	0.80919	0.4716	M	0.75447	2.3	0.53005	D	0.999962	B;B	0.34372	0.451;0.451	B;B	0.33339	0.162;0.086	T	0.81339	-0.0977	9	0.51188	T	0.08	.	16.0977	0.81139	0.0:0.0:0.0:1.0	.	843;1224	B7WPD9;Q2KJY2	.;KI26B_HUMAN	P	1224;843;840	ENSP00000385545:S1224P;ENSP00000355475:S843P	ENSP00000355475:S843P	S	+	1	0	KIF26B	243916578	1.000000	0.71417	0.985000	0.45067	0.703000	0.40648	3.494000	0.53273	2.215000	0.71742	0.459000	0.35465	TCG	.	.		0.657	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		C	245849955	T	C	245849955	3	2	178	1	0	0	0	0	1	0	0	0	8304	1551	54	2	3716	2	KIF26B	1	245849955	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	8095945	245849955	3400666	11	26712										
ZNF695	57116	hgsc.bcm.edu	37	chr1	247150827	247150827	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gacaacaatttaaagactttGccacattcttcacacttgta	4	10	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:247150827G>T	ENST00000339986.7	-	4	1137	c.990C>A	c.(988-990)ggC>ggA	p.G330G	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	330					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TAAAGACTTTGCCACATTCTT	0.368																																					p.G330G		Atlas-SNP	.											.	ZNF695	55	.	0			c.C990A						.						34	36	35					1																	247150827		2110	4267	6377	SO:0001819	synonymous_variant	57116	exon4			GACTTTGCCACAT		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"Zinc fingers, C2H2-type", "-"	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.990C>A	chr1.hg19:g.247150827G>T		113.0	0.0		114.0	12.0	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Silent	SNP	ENST00000339986.7	hg19	CCDS44344.1																																																																																			.	.		0.368	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394		T	247150827	G	T	247150827	2	4	178	1	0	0	0	0	0	0	0	1	18113	1306	46	3		3	ZNF695	1	247150827	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	1300872	247150827	2099794	12	26713										
OR2T2	401992	hgsc.bcm.edu	37	chr1	248616773	248616773	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tacacgcacatcctcctgacTgtccacaggatgaactctgc	7	15	1	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr1:248616773T>A	ENST00000342927.3	+	1	697	c.675T>A	c.(673-675)acT>acA	p.T225T		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCTCCTGACTGTCCACAGGA	0.537																																					p.T225T		Atlas-SNP	.											.	OR2T2	73	.	0			c.T675A						.						142	98	113					1																	248616773		2186	4262	6448	SO:0001819	synonymous_variant	401992	exon1			CCTGACTGTCCAC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"GPCR / Class A : Olfactory receptors"	14725	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily T, member 2 pseudogene"	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.675T>A	chr1.hg19:g.248616773T>A		357.0	0.0		431.0	53.0	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	hg19	CCDS31116.1																																																																																			.	.		0.537	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136		A	248616773	T	A	248616773	2	1	178	1	0	0	0	0	0	0	0	1	11029	1567	55	4		4	OR2T2	1	248616773	Silent	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	1465946	248616773	633848	13	26714										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29296299	29296299	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gccattgagcacctgcagctTgctgactgtgtactgtagca	11	11	0	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:29296299T>C	ENST00000331664.5	-	1	828	c.829A>G	c.(829-831)Aag>Gag	p.K277E		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	277					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						ACCTGCAGCTTGCTGACTGTG	0.567																																					p.K277E		Atlas-SNP	.											.	C2orf71	146	.	0			c.A829G						.						75	77	77					2																	29296299		2035	4191	6226	SO:0001583	missense	388939	exon1			GCAGCTTGCTGAC		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.829A>G	chr2.hg19:g.29296299T>C	ENSP00000332809:p.Lys277Glu	84.0	0.0		51.0	12.0	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	hg19	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	T	18.77	3.693795	0.68386	.	.	ENSG00000179270	ENST00000331664	T	0.27720	1.65	5.62	1.77	0.24775	.	0.315716	0.33419	N	0.004934	T	0.46560	0.1399	M	0.68952	2.095	0.27947	N	0.937286	D	0.64830	0.994	P	0.58721	0.844	T	0.48151	-0.9060	10	0.72032	D	0.01	-16.5961	13.2868	0.60247	0.0:0.0:0.4096:0.5904	.	277	A6NGG8	CB071_HUMAN	E	277	ENSP00000332809:K277E	ENSP00000332809:K277E	K	-	1	0	C2orf71	29149803	1.000000	0.71417	0.948000	0.38648	0.931000	0.56810	3.228000	0.51270	0.054000	0.16065	0.459000	0.35465	AAG	.	.		0.567	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		C	29296299	T	C	29296299	3	2	178	1	0	0	0	0	1	0	0	0	2193	1821	63	2	3045	2	C2orf71	2	29296299	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10		29296299	213903074	14	26715										
AFTPH	54812	hgsc.bcm.edu	37	chr2	64800193	64800193	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	atgaacacatgtacatctgaTcagttccaggtaaaaatatc	6	8	2	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:64800193T>A	ENST00000422803.1	+	6	2699	c.2385T>A	c.(2383-2385)gaT>gaA	p.D795E	AFTPH_ENST00000238855.7_Missense_Mutation_p.D795E|AFTPH_ENST00000409933.1_Missense_Mutation_p.D795E|AFTPH_ENST00000487769.1_3'UTR|AFTPH_ENST00000409183.1_Missense_Mutation_p.D426E|AFTPH_ENST00000238856.4_Missense_Mutation_p.D795E			Q6ULP2	AFTIN_HUMAN	aftiphilin	795					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						GTACATCTGATCAGTTCCAGG	0.378																																					p.D795E		Atlas-SNP	.											.	AFTPH	117	.	0			c.T2385A						.						139	139	139					2																	64800193		2203	4300	6503	SO:0001583	missense	54812	exon6			ATCTGATCAGTTC	AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.2385T>A	chr2.hg19:g.64800193T>A	ENSP00000397726:p.Asp795Glu	337.0	0.0		310.0	28.0	NM_017657	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Missense_Mutation	SNP	ENST00000422803.1	hg19		.	.	.	.	.	.	.	.	.	.	T	21.7	4.187770	0.78789	.	.	ENSG00000119844	ENST00000238856;ENST00000422803;ENST00000238855;ENST00000409933;ENST00000409183	T;T;T;T;T	0.52983	1.52;1.63;1.63;1.63;0.64	5.41	2.02	0.26589	.	0.056188	0.64402	D	0.000002	T	0.60379	0.2264	M	0.65975	2.015	0.37846	D	0.929211	P;D;P;D	0.71674	0.938;0.997;0.746;0.998	P;D;B;D	0.72982	0.8;0.921;0.385;0.979	T	0.61806	-0.6987	10	0.72032	D	0.01	-5.9953	7.1758	0.25744	0.0:0.2677:0.0:0.7323	.	795;795;795;795	Q6ULP2;Q6ULP2-2;Q6ULP2-5;Q6ULP2-4	AFTIN_HUMAN;.;.;.	E	795;795;795;795;426	ENSP00000238856:D795E;ENSP00000397726:D795E;ENSP00000238855:D795E;ENSP00000387071:D795E;ENSP00000386913:D426E	ENSP00000238855:D795E	D	+	3	2	AFTPH	64653697	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.745000	0.38278	0.210000	0.20664	0.454000	0.30748	GAT	.	.		0.378	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657		A	64800193	T	A	64800193	3	1	178	1	0	0	0	0	1	0	0	0	364	1432	50	4	2403	4	AFTPH	2	64800193	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	35503894	64800193	178399180	15	26716										
GLI2	2736	hgsc.bcm.edu	37	chr2	121736076	121736076	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gccgctggcaggcctgcacgCgggagcagaagcccttcaag	15	14	1	1	rs121917708		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:121736076C>T	ENST00000452319.1	+	10	1495	c.1435C>T	c.(1435-1437)Cgg>Tgg	p.R479W	GLI2_ENST00000361492.4_Missense_Mutation_p.R479W|GLI2_ENST00000314490.11_Missense_Mutation_p.R151W|GLI2_ENST00000435313.2_3'UTR					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GGCCTGCACGCGGGAGCAGAA	0.622																																					p.R479W		Atlas-SNP	.											.	GLI2	187	.	0			c.C1435T	GRCh37	CM066094	GLI2	M	rs121917708	.						119	110	113					2																	121736076		2203	4300	6503	SO:0001583	missense	2736	exon9			TGCACGCGGGAGC		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.1435C>T	chr2.hg19:g.121736076C>T	ENSP00000390436:p.Arg479Trp	383.0	0.0		374.0	76.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.189275	0.78789	.	.	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	D;D;D	0.91577	-2.87;-2.87;-2.87	4.03	1.91	0.25777	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.96503	0.8859	H	0.97131	3.945	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.938;0.998;0.962;0.999;0.981	D	0.96186	0.9134	10	0.87932	D	0	.	12.274	0.54724	0.384:0.616:0.0:0.0	.	479;462;134;134;151	P10070;Q0VGA0;P10070-2;P10070-4;P10070-3	GLI2_HUMAN;.;.;.;.	W	479;479;151	ENSP00000390436:R479W;ENSP00000354586:R479W;ENSP00000312694:R151W	ENSP00000312694:R151W	R	+	1	2	GLI2	121452546	0.992000	0.36948	0.988000	0.46212	0.974000	0.67602	3.028000	0.49705	0.288000	0.22398	0.491000	0.48974	CGG	.	.		0.622	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121736076	C	T	121736076	3	4	178	1	0	0	0	0	1	0	0	0	6446	759	27	1	1469	1	GLI2	2	121736076	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	56935883	121736076	121463297	16	26717										
ARHGAP15	55843	hgsc.bcm.edu	37	chr2	144193255	144193255	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gttccacgctatcaaaaatgCaattgacagattggtatgta	8	7	1	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:144193255C>A	ENST00000295095.6	+	7	727	c.560C>A	c.(559-561)gCa>gAa	p.A187E	AC096558.1_ENST00000549032.1_RNA|AC096558.1_ENST00000550516.1_RNA|RP11-570L15.2_ENST00000546678.1_RNA|AC096558.1_ENST00000442794.1_RNA	NM_018460.3	NP_060930.3	Q53QZ3	RHG15_HUMAN	Rho GTPase activating protein 15	187	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)			endometrium(1)|kidney(5)|large_intestine(8)|liver(2)|lung(15)|ovary(1)|skin(2)	34				BRCA - Breast invasive adenocarcinoma(221;0.151)		ATCAAAAATGCAATTGACAGA	0.318																																					p.A187E		Atlas-SNP	.											.	ARHGAP15	99	.	0			c.C560A						.						135	121	126					2																	144193255		2203	4299	6502	SO:0001583	missense	55843	exon7			AAAATGCAATTGA	AY219338	CCDS2184.1	2q22.2-q22.3	2013-01-10			ENSG00000075884	ENSG00000075884		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	21030	protein-coding gene	gene with protein product		610578				12650940, 11042152	Standard	NM_018460		Approved	BM046	uc002tvm.4	Q53QZ3	OTTHUMG00000131845	ENST00000295095.6:c.560C>A	chr2.hg19:g.144193255C>A	ENSP00000295095:p.Ala187Glu	84.0	0.0		54.0	6.0	NM_018460	Q53R36|Q53RD7|Q53RT6|Q53SX9|Q584N9|Q6PJE6|Q86WP1|Q8IXX1|Q9NRL8|Q9NZ77|Q9NZ91	Missense_Mutation	SNP	ENST00000295095.6	hg19	CCDS2184.1	.	.	.	.	.	.	.	.	.	.	C	17.14	3.314412	0.60524	.	.	ENSG00000075884	ENST00000295095	D	0.82255	-1.59	5.52	5.52	0.82312	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.246700	0.40469	N	0.001094	D	0.87676	0.6237	M	0.72353	2.195	0.54753	D	0.999986	B;B	0.33299	0.407;0.008	B;B	0.43950	0.437;0.189	D	0.87200	0.2240	10	0.66056	D	0.02	.	19.7962	0.96484	0.0:1.0:0.0:0.0	.	187;187	B4E0R3;Q53QZ3	.;RHG15_HUMAN	E	187	ENSP00000295095:A187E	ENSP00000295095:A187E	A	+	2	0	ARHGAP15	143909725	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.704000	0.68347	2.744000	0.94065	0.650000	0.86243	GCA	.	.		0.318	ARHGAP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254793.2	NM_018460		A	144193255	C	A	144193255	3	1	178	1	0	0	0	0	1	0	0	0	866	710	25	3	582	3	ARHGAP15	2	144193255	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	22457179	144193255	99006118	17	26718										
LY75	4065	hgsc.bcm.edu	37	chr2	160708804	160708804	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cgaagaaacattatatttttCacagatgaagggcaacttgg	9	6	1	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:160708804C>T	ENST00000263636.4	-	21	2818	c.2791G>A	c.(2791-2793)Gaa>Aaa	p.E931K	LY75_ENST00000553424.1_Missense_Mutation_p.E931K|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.E931K|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.E931K|LY75_ENST00000554112.1_Missense_Mutation_p.E931K	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	931	C-type lectin 5. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		TTATATTTTTCACAGATGAAG	0.368																																					p.E931K		Atlas-SNP	.											.	LY75	151	.	0			c.G2791A						.						82	84	84					2																	160708804		2203	4300	6503	SO:0001583	missense	4065	exon21			ATTTTTCACAGAT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.2791G>A	chr2.hg19:g.160708804C>T	ENSP00000263636:p.Glu931Lys	177.0	0.0		158.0	30.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696368	0.68386	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.08370	3.1;3.1;3.1;3.1;3.1	5.12	5.12	0.69794	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.000000	0.32952	U	0.005443	T	0.26195	0.0639	M	0.81497	2.545	0.53005	D	0.999965	D;D;D	0.67145	0.996;0.981;0.986	D;P;P	0.62955	0.909;0.718;0.795	T	0.01988	-1.1234	10	0.23302	T	0.38	-26.0091	14.3894	0.66968	0.0:1.0:0.0:0.0	.	931;931;931	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	K	931	ENSP00000451511:E931K;ENSP00000451446:E931K;ENSP00000263636:E931K;ENSP00000423463:E931K;ENSP00000421035:E931K	ENSP00000423463:E931K	E	-	1	0	LY75;LY75-CD302	160417050	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.258000	0.58822	2.543000	0.85770	0.585000	0.79938	GAA	.	.		0.368	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			T	160708804	C	T	160708804	3	4	178	1	0	0	0	0	1	0	0	0	9108	835	29	3	2437	3	LY75	2	160708804	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	16515549	160708804	82490569	18	26719										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168101315	168101315	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tgaaactcagccacttgataCcataaaagatgactctgaaa	6	9	2	5			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:168101315C>A	ENST00000409195.1	+	9	3502	c.3413C>A	c.(3412-3414)aCc>aAc	p.T1138N	XIRP2_ENST00000409273.1_Missense_Mutation_p.T916N|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.T1138N	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	963					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CCACTTGATACCATAAAAGAT	0.383																																					p.T1138N		Atlas-SNP	.											.	XIRP2	914	.	0			c.C3413A						.						71	65	67					2																	168101315		1848	4098	5946	SO:0001583	missense	129446	exon9			TTGATACCATAAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.3413C>A	chr2.hg19:g.168101315C>A	ENSP00000386840:p.Thr1138Asn	314.0	0.0		331.0	51.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	3.032	-0.199422	0.06219	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02323	4.34;4.34;4.34	5.84	3.96	0.45880	.	0.647313	0.16942	N	0.193235	T	0.03011	0.0089	L	0.29908	0.895	0.21553	N	0.999645	B;B;B	0.20368	0.026;0.044;0.044	B;B;B	0.22601	0.018;0.04;0.04	T	0.41324	-0.9515	10	0.30854	T	0.27	-0.0844	11.6959	0.51542	0.1324:0.7227:0.1449:0.0	.	963;963;916	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	N	1138;1138;916	ENSP00000386840:T1138N;ENSP00000295237:T1138N;ENSP00000387255:T916N	ENSP00000295237:T1138N	T	+	2	0	XIRP2	167809561	0.002000	0.14202	0.986000	0.45419	0.603000	0.37013	1.371000	0.34250	1.455000	0.47813	0.655000	0.94253	ACC	.	.		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168101315	C	A	168101315	3	1	178	1	0	0	0	0	1	0	0	0	17445	507	18	3	3443	3	XIRP2	2	168101315	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	7392511	168101315	75098058	19	26720										
ZNF385B	151126	hgsc.bcm.edu	37	chr2	180634264	180634264	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctgctggggctggcctgggcGggtggtgggggctgcccatc	21	11	0	0	rs370441083		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:180634264G>A	ENST00000410066.1	-	3	822	c.219C>T	c.(217-219)ccC>ccT	p.P73P		NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	73	Required for induction of apoptosis.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			TGGCCTGGGCGGGTGGTGGGG	0.622																																					p.P73P	Colon(155;204 2491 32774 51842)	Atlas-SNP	.											.	ZNF385B	68	.	0			c.C219T						.	G		0,4406		0,0,2203	45	44	45		219	-12.1	0	2		45	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF385B	NM_152520.4		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		73/472	180634264	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	151126	exon3			CTGGGCGGGTGGT	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.219C>T	chr2.hg19:g.180634264G>A		87.0	0.0		74.0	7.0	NM_152520	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Silent	SNP	ENST00000410066.1	hg19	CCDS33339.1																																																																																			.	.		0.622	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		A	180634264	G	A	180634264	2	1	178	1	0	0	0	0	0	0	0	1	17892	1103	39	1		1	ZNF385B	2	180634264	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	12532949	180634264	62565109	20	26721										
ORC2L	4999	hgsc.bcm.edu	37	chr2	201798638	201798638	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tttagcttctgcagtgttctAtcagaggttaaaacttttga	8	6	3	2	rs149149549		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:201798638A>G	ENST00000234296.2	-	10	1017	c.768T>C	c.(766-768)gaT>gaC	p.D256D		NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	256					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						GCAGTGTTCTATCAGAGGTTA	0.353																																					p.D256D		Atlas-SNP	.											.	ORC2	48	.	0			c.T768C						.	A		0,4406		0,0,2203	105	108	107		768	-1.2	0.7	2	dbSNP_134	107	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ORC2	NM_006190.4		0,1,6501	GG,GA,AA		0.0116,0.0,0.0077		256/578	201798638	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	4999	exon10			TGTTCTATCAGAG		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"origin recognition complex, subunit 2 (yeast homolog)-like", "origin recognition complex, subunit 2-like (yeast)", "origin recognition complex, subunit 2 homolog (yeast)"	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.768T>C	chr2.hg19:g.201798638A>G		128.0	0.0		123.0	8.0	NM_006190	Q13204|Q53TX5	Silent	SNP	ENST00000234296.2	hg19	CCDS2334.1																																																																																			.	A|1.000;G|0.000		0.353	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190		G	201798638	A	G	201798638	2	3	178	1	0	0	0	0	0	0	0	1	11271	446	16	2		2	ORC2L	2	201798638	Silent	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	21164374	201798638	41400735	21	26722										
C2orf80	389073	hgsc.bcm.edu	37	chr2	209045541	209045541	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tcctcaatcgggatactgttCtgttaaacaacaacagcaat	6	10	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:209045541C>A	ENST00000341287.4	-	6	490		c.e6-1		C2orf80_ENST00000453017.1_Splice_Site|C2orf80_ENST00000451346.1_Splice_Site	NM_001099334.2	NP_001092804	Q0P641	CB080_HUMAN	chromosome 2 open reading frame 80											endometrium(2)|large_intestine(3)|lung(6)|skin(2)	13						GGATACTGTTCTGTTAAACAA	0.368																																					.		Atlas-SNP	.											.	C2orf80	19	.	0			c.295-1G>T						.						94	87	89					2																	209045541		1815	4087	5902	SO:0001630	splice_region_variant	389073	exon7			ACTGTTCTGTTAA	AC016697, AW136505, BC035737	CCDS42809.1	2q33.3	2013-10-31			ENSG00000188674	ENSG00000188674			34352	protein-coding gene	gene with protein product	"gonad development associated 1"	615536				22080834, 24055526	Standard	NM_001099334		Approved	LOC389073, GONDA1	uc002vcr.3	Q0P641	OTTHUMG00000154751	ENST00000341287.4:c.295-1G>T	chr2.hg19:g.209045541C>A		267.0	0.0		270.0	56.0	NM_001099334	A6NKZ3	Splice_Site	SNP	ENST00000341287.4	hg19	CCDS42809.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.995358	0.54147	.	.	ENSG00000188674	ENST00000451342;ENST00000341287;ENST00000451346;ENST00000428015;ENST00000453017;ENST00000423952	.	.	.	4.67	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2331	0.59955	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C2orf80	208753786	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.902000	0.56310	2.579000	0.87056	0.557000	0.71058	.	.	.		0.368	C2orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336931.1	NM_001099334	Intron	A	209045541	C	A	209045541	5	1	178	1	0	0	0	0	0	0	1	0	2199	927	32	3	303	3	C2orf80	2	209045541	Splice_Site	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	7246903	209045541	34153832	22	26723										
ITM2C	81618	hgsc.bcm.edu	37	chr2	231742197	231742197	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cagtgacaaggaggccctggGgtccttcatctaccacctgt	11	13	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:231742197G>A	ENST00000326427.6	+	5	770	c.644G>A	c.(643-645)gGg>gAg	p.G215E	ITM2C_ENST00000409704.2_Missense_Mutation_p.G153E|ITM2C_ENST00000335005.6_Missense_Mutation_p.G168E|ITM2C_ENST00000326407.6_Missense_Mutation_p.G178E	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	215	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GAGGCCCTGGGGTCCTTCATC	0.627																																					p.G215E		Atlas-SNP	.											.	ITM2C	17	.	0			c.G644A						.						112	105	107					2																	231742197		2203	4300	6503	SO:0001583	missense	81618	exon5			CCCTGGGGTCCTT	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"BRICHOS domain containing"	6175	protein-coding gene	gene with protein product	"BRICHOS domain containing 2C"	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.644G>A	chr2.hg19:g.231742197G>A	ENSP00000322730:p.Gly215Glu	192.0	0.0		200.0	11.0	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Missense_Mutation	SNP	ENST00000326427.6	hg19	CCDS2479.1	.	.	.	.	.	.	.	.	.	.	G	31	5.090283	0.94149	.	.	ENSG00000135916	ENST00000326427;ENST00000335005;ENST00000326407;ENST00000409704	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	5.22	5.22	0.72569	BRICHOS (2);	0.000000	0.85682	D	0.000000	D	0.91205	0.7229	M	0.83483	2.645	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.987;0.997	D	0.92316	0.5862	10	0.87932	D	0	-20.3815	14.3008	0.66352	0.0:0.0:1.0:0.0	.	178;168;215	Q9NQX7-3;Q9NQX7-2;Q9NQX7	.;.;ITM2C_HUMAN	E	215;168;178;153	ENSP00000322730:G215E;ENSP00000335121:G168E;ENSP00000322100:G178E;ENSP00000387242:G153E	ENSP00000322100:G178E	G	+	2	0	ITM2C	231450441	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.304000	0.96190	2.437000	0.82529	0.655000	0.94253	GGG	.	.		0.627	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926		A	231742197	G	A	231742197	3	1	178	1	0	0	0	0	1	0	0	0	7923	1232	43	3	662	3	ITM2C	2	231742197	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	22696656	231742197	11457176	23	26724										
CHRND	1144	hgsc.bcm.edu	37	chr2	233392134	233392134	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gaagttgaggagaccctcacTaccaatgtgtggatagagca	12	8	1	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:233392134T>A	ENST00000258385.3	+	3	254	c.222T>A	c.(220-222)acT>acA	p.T74T	CHRND_ENST00000543200.1_Intron|CHRND_ENST00000536614.1_Silent_p.T74T|CHRND_ENST00000457943.2_5'UTR	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)	74					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	AGACCCTCACTACCAATGTGT	0.537																																					p.T74T		Atlas-SNP	.											.	CHRND	67	.	0			c.T222A						.						145	128	134					2																	233392134		2203	4300	6503	SO:0001819	synonymous_variant	1144	exon3			CCTCACTACCAAT	X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1965	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, delta (muscle)"	100720	"cholinergic receptor, nicotinic, delta"	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.222T>A	chr2.hg19:g.233392134T>A		107.0	0.0		118.0	50.0	NM_000751	A8K661|B4DT92|Q52LH4	Silent	SNP	ENST00000258385.3	hg19	CCDS2494.1																																																																																			.	.		0.537	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2			A	233392134	T	A	233392134	2	1	178	1	0	0	0	0	0	0	0	1	3396	1509	53	4		4	CHRND	2	233392134	Silent	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	1649937	233392134	9807239	24	26725										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238296564	238296564	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctccaccacgaaatcaagggCgaggccgatattggccaact	10	13	1	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr2:238296564C>T	ENST00000295550.4	-	4	1425	c.973G>A	c.(973-975)Gcc>Acc	p.A325T	COL6A3_ENST00000346358.4_Missense_Mutation_p.A325T|COL6A3_ENST00000347401.3_Intron|COL6A3_ENST00000353578.4_Missense_Mutation_p.A119T|COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000392004.3_Missense_Mutation_p.A119T|COL6A3_ENST00000392003.2_Intron|COL6A3_ENST00000409809.1_Missense_Mutation_p.A119T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	325	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A325T(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AAATCAAGGGCGAGGCCGATA	0.617																																					p.A325T		Atlas-SNP	.											COL6A3,colon,carcinoma,0,1	COL6A3	608	.	1	Substitution - Missense(1)	large_intestine(1)	c.G973A						.						39	39	39					2																	238296564		2203	4300	6503	SO:0001583	missense	1293	exon4			CAAGGGCGAGGCC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.973G>A	chr2.hg19:g.238296564C>T	ENSP00000295550:p.Ala325Thr	224.0	0.0		202.0	10.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.365615	0.61513	.	.	ENSG00000163359	ENST00000295550;ENST00000353578;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000433762	D;D;D;D;D;D	0.99483	-2.56;-2.56;-2.56;-2.56;-2.56;-5.99	5.17	5.17	0.71159	von Willebrand factor, type A (3);	0.000000	0.47093	U	0.000243	D	0.99701	0.9886	H	0.95470	3.675	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.85130	0.997;0.928;0.978;0.996	D	0.97467	1.0038	10	0.66056	D	0.02	.	18.7072	0.91643	0.0:1.0:0.0:0.0	.	325;119;119;325	E9PCV6;E9PGQ9;P12111-2;P12111	.;.;.;CO6A3_HUMAN	T	325;119;119;325;119;325	ENSP00000295550:A325T;ENSP00000315873:A119T;ENSP00000386844:A119T;ENSP00000295546:A325T;ENSP00000375861:A119T;ENSP00000389539:A325T	ENSP00000295550:A325T	A	-	1	0	COL6A3	237961303	1.000000	0.71417	0.939000	0.37840	0.495000	0.33615	7.724000	0.84798	2.405000	0.81733	0.650000	0.86243	GCC	.	.		0.617	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238296564	C	T	238296564	3	4	178	1	0	0	0	0	1	0	0	0	3703	768	27	1	8771	1	COL6A3	2	238296564	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	4904430	238296564	4902809	25	26726										
GLYCTK	132158	hgsc.bcm.edu	37	chr3	52324605	52324605	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	agctgaggcaaaacctctacCtggtgggctttggcaaggct	13	10	1	1	rs374934931		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr3:52324605C>T	ENST00000436784.2	+	2	307	c.247C>T	c.(247-249)Ctg>Ttg	p.L83L	GLYCTK_ENST00000461183.1_Intron|GLYCTK_ENST00000305690.8_Silent_p.L83L|GLYCTK_ENST00000471180.1_Intron|GLYCTK-AS1_ENST00000493616.1_RNA|GLYCTK_ENST00000477382.1_Silent_p.L83L|GLYCTK_ENST00000354773.4_Silent_p.L83L|GLYCTK_ENST00000473032.1_Silent_p.L83L			Q8IVS8	GLCTK_HUMAN	glycerate kinase	83					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glycerate kinase activity (GO:0008887)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(193;3.56e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)|OV - Ovarian serous cystadenocarcinoma(275;0.235)		AAACCTCTACCTGGTGGGCTT	0.617																																					p.L83L		Atlas-SNP	.											.	GLYCTK	30	.	0			c.C247T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	49	45	46		247,247	3.3	1	3		46	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GLYCTK	NM_001144951.1,NM_145262.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	83/235,83/524	52324605	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	132158	exon2			CTCTACCTGGTGG		CCDS2852.1, CCDS46841.1	3p21.1	2008-01-22			ENSG00000168237	ENSG00000168237	2.7.1.31		24247	protein-coding gene	gene with protein product		610516				16753811	Standard	NM_145262		Approved	HBEBP4, HBEBP2	uc003ddo.3	Q8IVS8	OTTHUMG00000158380	ENST00000436784.2:c.247C>T	chr3.hg19:g.52324605C>T		116.0	0.0		92.0	13.0	NM_001144951	Q0P630|Q2EZ43|Q6Y2K6|Q7Z6G5|Q86YR8|Q8TED2|Q8WTY2	Silent	SNP	ENST00000436784.2	hg19	CCDS2852.1																																																																																			.	.		0.617	GLYCTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350835.1	NM_145262		T	52324605	C	T	52324605	2	4	178	1	0	0	0	0	0	0	0	1	6490	680	24	3		3	GLYCTK	3	52324605	Silent	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10		52324605	145697825	26	26727										
SEMA3G	56920	hgsc.bcm.edu	37	chr3	52471666	52471666	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tagaccatggtggctgccacAagtcccactgcctcttctgg	10	14	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr3:52471666A>T	ENST00000231721.2	-	15	1754	c.1755T>A	c.(1753-1755)ctT>ctA	p.L585L		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	585	Ig-like C2-type.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		TGGCTGCCACAAGTCCCACTG	0.617																																					p.L585L		Atlas-SNP	.											.	SEMA3G	58	.	0			c.T1755A						.						29	25	27					3																	52471666		2202	4293	6495	SO:0001819	synonymous_variant	56920	exon15			TGCCACAAGTCCC		CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.1755T>A	chr3.hg19:g.52471666A>T		149.0	0.0		147.0	41.0	NM_020163	Q7L9D9|Q9H7Q3	Silent	SNP	ENST00000231721.2	hg19	CCDS2856.1																																																																																			.	.		0.617	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163		T	52471666	A	T	52471666	2	4	178	1	0	0	0	0	0	0	0	1	14045	117	5	4		4	SEMA3G	3	52471666	Silent	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	147061	52471666	145550764	27	26728										
GPR149	344758	hgsc.bcm.edu	37	chr3	154146848	154146848	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	atagtacgtaggagctggagCagtccaccaggcagccccag	13	12	0	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr3:154146848C>A	ENST00000389740.2	-	1	656	c.557G>T	c.(556-558)tGc>tTc	p.C186F		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	186					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			GGAGCTGGAGCAGTCCACCAG	0.647																																					p.C186F		Atlas-SNP	.											GPR149,NS,carcinoma,0,1	GPR149	134	.	0			c.G557T						.						33	39	37					3																	154146848		2052	4196	6248	SO:0001583	missense	344758	exon1			CTGGAGCAGTCCA	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.557G>T	chr3.hg19:g.154146848C>A	ENSP00000374390:p.Cys186Phe	187.0	0.0		140.0	12.0	NM_001038705		Missense_Mutation	SNP	ENST00000389740.2	hg19	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.836008	0.71373	.	.	ENSG00000174948	ENST00000389740	T	0.34859	1.34	5.41	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.248609	0.47093	D	0.000251	T	0.43831	0.1265	M	0.81112	2.525	0.38092	D	0.936994	P	0.42941	0.794	B	0.42163	0.378	T	0.54820	-0.8236	10	0.48119	T	0.1	-8.4775	12.8223	0.57700	0.0:0.8669:0.0:0.1331	.	186	Q86SP6	GP149_HUMAN	F	186	ENSP00000374390:C186F	ENSP00000374390:C186F	C	-	2	0	GPR149	155629542	1.000000	0.71417	0.999000	0.59377	0.894000	0.52154	3.338000	0.52128	2.541000	0.85698	0.655000	0.94253	TGC	.	.		0.647	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		A	154146848	C	A	154146848	3	1	178	1	0	0	0	0	1	0	0	0	6662	710	25	3	1654	3	GPR149	3	154146848	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	101675182	154146848	43875582	28	26729										
TTC14	151613	hgsc.bcm.edu	37	chr3	180320103	180320103	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tgccacgggtcgtctttgctCtctctacttcggagcgaaca	10	13	3	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr3:180320103C>T	ENST00000296015.4	+	1	186	c.54C>T	c.(52-54)ctC>ctT	p.L18L	RP11-496B10.3_ENST00000472596.1_lincRNA|TTC14_ENST00000382584.4_Silent_p.L18L|TTC14_ENST00000412756.2_Silent_p.L18L	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	18							RNA binding (GO:0003723)			endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CGTCTTTGCTCTCTCTACTTC	0.657																																					p.L18L		Atlas-SNP	.											.	TTC14	112	.	0			c.C54T						.						61	58	59					3																	180320103		2203	4300	6503	SO:0001819	synonymous_variant	151613	exon1			TTTGCTCTCTCTA	AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"Tetratricopeptide (TTC) repeat domain containing"	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.54C>T	chr3.hg19:g.180320103C>T		40.0	0.0		55.0	9.0	NM_001042601	G5E9X0|Q6UWJ7|Q8TF22	Silent	SNP	ENST00000296015.4	hg19	CCDS3237.1																																																																																			.	.		0.657	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462		T	180320103	C	T	180320103	2	4	178	1	0	0	0	0	0	0	0	1	16696	900	32	3		3	TTC14	3	180320103	Silent	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	26173255	180320103	17702327	29	26730										
OPA1	4976	hgsc.bcm.edu	37	chr3	193376712	193376712	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	atgctttggaagaccgatccAtatctgataaacagcaatgg	9	8	1	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr3:193376712A>T	ENST00000392438.3	+	22	2437	c.2203A>T	c.(2203-2205)Ata>Tta	p.I735L	OPA1_ENST00000361828.2_Missense_Mutation_p.I753L|OPA1_ENST00000361150.2_Missense_Mutation_p.I736L|OPA1_ENST00000361908.3_Missense_Mutation_p.I772L|OPA1_ENST00000361510.2_Missense_Mutation_p.I790L|OPA1_ENST00000361715.2_Missense_Mutation_p.I754L	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	735					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		AGACCGATCCATATCTGATAA	0.378																																					p.I790L		Atlas-SNP	.											.	OPA1	79	.	0			c.A2368T						.						130	127	128					3																	193376712		2203	4300	6503	SO:0001583	missense	4976	exon24			CGATCCATATCTG	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.2203A>T	chr3.hg19:g.193376712A>T	ENSP00000376233:p.Ile735Leu	97.0	0.0		110.0	33.0	NM_130837	D3DNW4	Missense_Mutation	SNP	ENST00000392438.3	hg19	CCDS43186.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.780620	0.90195	.	.	ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361715;ENST00000361828;ENST00000361150	D;D;D;D;D;D	0.96011	-3.46;-3.49;-3.44;-3.44;-3.47;-3.88	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.96383	0.8820	M	0.64997	1.995	0.80722	D	1	P;P;P;P;P;P;D;P	0.53745	0.879;0.787;0.879;0.879;0.825;0.879;0.962;0.931	P;B;P;P;B;P;P;P	0.55965	0.688;0.322;0.688;0.688;0.397;0.688;0.788;0.688	D	0.96547	0.9405	10	0.62326	D	0.03	-23.7307	15.4968	0.75658	1.0:0.0:0.0:0.0	.	699;735;717;736;753;772;754;790	E5KLK2;O60313;E5KLK0;E5KLK1;E5KLJ6;E5KLJ7;E5KLJ9;E5KLJ5	.;OPA1_HUMAN;.;.;.;.;.;.	L	772;735;790;754;753;736	ENSP00000354681:I772L;ENSP00000376233:I735L;ENSP00000355324:I790L;ENSP00000355311:I754L;ENSP00000354429:I753L;ENSP00000354781:I736L	ENSP00000354781:I736L	I	+	1	0	OPA1	194859406	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.245000	0.73994	0.455000	0.32223	ATA	.	.		0.378	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		T	193376712	A	T	193376712	3	4	178	1	0	0	0	0	1	0	0	0	10880	217	8	4	2462	4	OPA1	3	193376712	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	13056609	193376712	4645718	30	26731										
TNIP2	79155	hgsc.bcm.edu	37	chr4	2746185	2746185	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ttgaatcctactttgagcccGttcccgatcggccctttctg	8	14	1	2	rs145123249	byFrequency	TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr4:2746185G>A	ENST00000315423.7	-	5	1041	c.955C>T	c.(955-957)Cgg>Tgg	p.R319W	TNIP2_ENST00000510267.1_Missense_Mutation_p.R212W|TNIP2_ENST00000503235.1_Missense_Mutation_p.R236W|TNIP2_ENST00000505186.1_5'UTR	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTTTGAGCCCGTTCCCGATCG	0.522																																					p.R319W		Atlas-SNP	.											.	TNIP2	28	.	0			c.C955T						.						145	146	146					4																	2746185		2203	4300	6503	SO:0001583	missense	79155	exon5			GAGCCCGTTCCCG	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.955C>T	chr4.hg19:g.2746185G>A	ENSP00000321203:p.Arg319Trp	116.0	0.0		93.0	7.0	NM_024309		Missense_Mutation	SNP	ENST00000315423.7	hg19	CCDS3362.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.416137	0.83449	.	.	ENSG00000168884	ENST00000510267;ENST00000315423;ENST00000503235	T;T;T	0.45276	0.9;0.9;0.9	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.67933	0.2946	M	0.85777	2.775	0.38741	D	0.953885	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.74124	-0.3766	10	0.72032	D	0.01	-46.7578	14.0902	0.64984	0.0:0.0:0.8497:0.1503	.	236;319	D6RGJ2;Q8NFZ5	.;TNIP2_HUMAN	W	212;319;236	ENSP00000427613:R212W;ENSP00000321203:R319W;ENSP00000426314:R236W	ENSP00000321203:R319W	R	-	1	2	TNIP2	2715983	1.000000	0.71417	0.972000	0.41901	0.979000	0.70002	3.483000	0.53194	2.791000	0.96007	0.561000	0.74099	CGG	.	G|1.000;T|0.000		0.522	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309		A	2746185	G	A	2746185	3	1	178	1	0	0	0	0	1	0	0	0	16330	1144	40	1	342	1	TNIP2	4	2746185	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10		2746185	188408091	31	26732										
NPFFR2	10886	hgsc.bcm.edu	37	chr4	72897911	72897911	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tgccgccgacagggctcgccGggagaggtaacagcatgggc	17	12	0	1	rs200084669		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr4:72897911G>A	ENST00000308744.6	+	1	391	c.293G>A	c.(292-294)cGg>cAg	p.R98Q	NPFFR2_ENST00000344413.5_Missense_Mutation_p.R98Q	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	98					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)	p.R98L(2)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			AGGGCTCGCCGGGAGAGGTAA	0.622																																					p.R98Q		Atlas-SNP	.											NPFFR2,NS,carcinoma,0,1	NPFFR2	98	.	2	Substitution - Missense(2)	lung(2)	c.G293A						.						24	29	27					4																	72897911		2203	4300	6503	SO:0001583	missense	10886	exon1			CTCGCCGGGAGAG	AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"GPCR / Class A :  Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors"	4525	protein-coding gene	gene with protein product	"neuropeptide FF 2"	607449	"G protein-coupled receptor 74"	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.293G>A	chr4.hg19:g.72897911G>A	ENSP00000307822:p.Arg98Gln	331.0	2.0		236.0	19.0	NM_004885	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	hg19	CCDS3551.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.588512	0.28357	.	.	ENSG00000056291	ENST00000308744;ENST00000344413	T	0.76968	-1.06	2.81	-2.9	0.05648	.	.	.	.	.	T	0.47875	0.1469	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28106	-1.0054	9	0.18710	T	0.47	.	0.3949	0.00417	0.2974:0.1979:0.3078:0.1969	.	98	Q9Y5X5	NPFF2_HUMAN	Q	98	ENSP00000307822:R98Q	ENSP00000307822:R98Q	R	+	2	0	NPFFR2	73116775	0.000000	0.05858	0.000000	0.03702	0.301000	0.27625	-3.211000	0.00556	-0.602000	0.05775	-0.802000	0.03209	CGG	.	G|1.000;C|0.000		0.622	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		A	72897911	G	A	72897911	3	1	178	1	0	0	0	0	1	0	0	0	10587	1116	39	1	295	1	NPFFR2	4	72897911	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	70151726	72897911	118256365	32	26733										
PDLIM5	10611	hgsc.bcm.edu	37	chr4	95583576	95583576	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gccctcccttaatacagattAttatgccctctttggtacta	5	12	1	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr4:95583576A>G	ENST00000317968.4	+	12	1725	c.1589A>G	c.(1588-1590)tAt>tGt	p.Y530C	PDLIM5_ENST00000437932.1_Missense_Mutation_p.Y421C|PDLIM5_ENST00000380176.3_3'UTR|PDLIM5_ENST00000514743.1_Missense_Mutation_p.Y559C|PDLIM5_ENST00000542407.1_Missense_Mutation_p.Y408C	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	530	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		AATACAGATTATTATGCCCTC	0.418																																					p.Y559C		Atlas-SNP	.											.	PDLIM5	76	.	0			c.A1676G						.						128	119	122					4																	95583576		2203	4300	6503	SO:0001583	missense	10611	exon16			CAGATTATTATGC	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.1589A>G	chr4.hg19:g.95583576A>G	ENSP00000321746:p.Tyr530Cys	56.0	0.0		50.0	10.0	NM_001256426	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	hg19	CCDS3641.1	.	.	.	.	.	.	.	.	.	.	A	18.51	3.640359	0.67244	.	.	ENSG00000163110	ENST00000437932;ENST00000317968;ENST00000503974;ENST00000542407;ENST00000514743	D;D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28;-3.28	5.61	5.61	0.85477	Zinc finger, LIM-type (3);	0.131094	0.52532	D	0.000066	D	0.97247	0.9100	M	0.89601	3.045	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.998;0.999;0.996	D	0.98111	1.0420	10	0.87932	D	0	.	15.8142	0.78586	1.0:0.0:0.0:0.0	.	427;559;530;421	E9PBF5;D6RB78;Q96HC4;Q96HC4-4	.;.;PDLI5_HUMAN;.	C	421;530;427;408;559	ENSP00000398469:Y421C;ENSP00000321746:Y530C;ENSP00000424297:Y427C;ENSP00000442187:Y408C;ENSP00000424360:Y559C	ENSP00000321746:Y530C	Y	+	2	0	PDLIM5	95802599	0.995000	0.38212	1.000000	0.80357	0.967000	0.64934	3.187000	0.50950	2.143000	0.66587	0.533000	0.62120	TAT	.	.		0.418	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1			G	95583576	A	G	95583576	3	3	178	1	0	0	0	0	1	0	0	0	11692	449	16	2	1791	2	PDLIM5	4	95583576	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	22685665	95583576	95570700	33	26734										
EGF	1950	hgsc.bcm.edu	37	chr4	110865040	110865040	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gtggctggaagcctttatagAgcagatctcgatggtgtggg	16	6	1	2	rs369090159		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr4:110865040A>G	ENST00000265171.5	+	4	997	c.552A>G	c.(550-552)agA>agG	p.R184R	EGF_ENST00000502723.1_3'UTR|EGF_ENST00000503392.1_Silent_p.R184R|EGF_ENST00000509793.1_Silent_p.R184R	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	184					activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	GCCTTTATAGAGCAGATCTCG	0.433																																					p.R184R		Atlas-SNP	.											.	EGF	113	.	0			c.A552G						.	A	,,	0,4406		0,0,2203	158	151	153		552,552,552	0.6	1	4		153	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	EGF	NM_001178130.1,NM_001178131.1,NM_001963.4	,,	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,,	184/1167,184/1166,184/1208	110865040	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1950	exon4			TTATAGAGCAGAT	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.552A>G	chr4.hg19:g.110865040A>G		188.0	0.0		193.0	34.0	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Silent	SNP	ENST00000265171.5	hg19	CCDS3689.1																																																																																			.	.		0.433	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			G	110865040	A	G	110865040	2	3	178	1	0	0	0	0	0	0	0	1	4964	301	11	2		2	EGF	4	110865040	Silent	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	15281464	110865040	80289236	34	26735										
PLRG1	5356	hgsc.bcm.edu	37	chr4	155462030	155462030	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cttactatcacgccccgcacAgtactaatatgcccagtcaa	5	15	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr4:155462030A>G	ENST00000499023.2	-	9	870	c.744T>C	c.(742-744)acT>acC	p.T248T	PLRG1_ENST00000302078.5_Silent_p.T239T|PLRG1_ENST00000393905.2_Silent_p.T248T	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	248					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				CGCCCCGCACAGTACTAATAT	0.403																																					p.T248T		Atlas-SNP	.											.	PLRG1	43	.	0			c.T744C						.						100	101	100					4																	155462030		2203	4300	6503	SO:0001819	synonymous_variant	5356	exon9			CCGCACAGTACTA	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.744T>C	chr4.hg19:g.155462030A>G		178.0	0.0		152.0	26.0	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	hg19	CCDS34083.1																																																																																			.	.		0.403	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669		G	155462030	A	G	155462030	2	3	178	1	0	0	0	0	0	0	0	1	12115	175	7	2		2	PLRG1	4	155462030	Silent	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	44596990	155462030	35692246	35	26736										
CDH18	1016	hgsc.bcm.edu	37	chr5	19473363	19473363	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ttctttcagattctatttctCcatagagttcagctaacttt	4	9	5	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr5:19473363C>A	ENST00000507958.1	-	15	3335	c.2345G>T	c.(2344-2346)gGa>gTa	p.G782V	CDH18_ENST00000510297.1_5'UTR|CDH18_ENST00000274170.4_Missense_Mutation_p.G782V|CDH18_ENST00000382275.1_Missense_Mutation_p.G782V			Q13634	CAD18_HUMAN	cadherin 18, type 2	782					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TTCTATTTCTCCATAGAGTTC	0.438																																					p.G782V		Atlas-SNP	.											.	CDH18	561	.	0			c.G2345T						.						81	85	84					5																	19473363		2203	4300	6503	SO:0001583	missense	1016	exon13			ATTTCTCCATAGA	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.2345G>T	chr5.hg19:g.19473363C>A	ENSP00000425093:p.Gly782Val	177.0	0.0		165.0	22.0	NM_004934	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.817622	0.70912	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170	T;T;T	0.79033	-1.23;-1.23;-1.23	5.21	5.21	0.72293	Cadherin, cytoplasmic domain (1);	0.058874	0.64402	D	0.000002	D	0.89719	0.6796	M	0.89214	3.015	0.80722	D	1	D	0.63046	0.992	D	0.70487	0.969	D	0.91009	0.4848	9	.	.	.	.	17.6979	0.88286	0.0:1.0:0.0:0.0	.	782	Q13634	CAD18_HUMAN	V	782	ENSP00000371710:G782V;ENSP00000425093:G782V;ENSP00000274170:G782V	.	G	-	2	0	CDH18	19509120	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.566000	0.53805	2.600000	0.87896	0.655000	0.94253	GGA	.	.		0.438	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		A	19473363	C	A	19473363	3	1	178	1	0	0	0	0	1	0	0	0	3105	855	30	3	31	3	CDH18	5	19473363	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10		19473363	161441897	36	26737										
NIPBL	25836	hgsc.bcm.edu	37	chr5	37048674	37048674	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	aatctatataataatattttAtctgataagaactcctcagt	3	6	3	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr5:37048674A>G	ENST00000282516.8	+	39	7159	c.6660A>G	c.(6658-6660)ttA>ttG	p.L2220L	NIPBL_ENST00000448238.2_Silent_p.L2220L	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2220					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			ATAATATTTTATCTGATAAGA	0.353																																					p.L2220L		Atlas-SNP	.											.	NIPBL	513	.	0			c.A6660G						.						37	44	42					5																	37048674		2180	4279	6459	SO:0001819	synonymous_variant	25836	exon39			TATTTTATCTGAT	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.6660A>G	chr5.hg19:g.37048674A>G		551.0	0.0		535.0	118.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.		0.353	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		G	37048674	A	G	37048674	2	3	178	1	0	0	0	0	0	0	0	1	10437	446	16	2		2	NIPBL	5	37048674	Silent	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	17575311	37048674	143866586	37	26738										
BDP1	55814	hgsc.bcm.edu	37	chr5	70806321	70806321	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	agggagaagacaccagaggtGattgatgccactgaggaaat	14	6	0	6			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr5:70806321G>A	ENST00000358731.4	+	17	3665	c.3402G>A	c.(3400-3402)gtG>gtA	p.V1134V	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	1134	9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		CACCAGAGGTGATTGATGCCA	0.468																																					p.V1134V		Atlas-SNP	.											.	BDP1	204	.	0			c.G3402A						.						82	81	81					5																	70806321		1816	4084	5900	SO:0001819	synonymous_variant	55814	exon17			AGAGGTGATTGAT	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.3402G>A	chr5.hg19:g.70806321G>A		242.0	0.0		243.0	58.0	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Silent	SNP	ENST00000358731.4	hg19	CCDS43328.1																																																																																			.	.		0.468	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		A	70806321	G	A	70806321	2	1	178	1	0	0	0	0	0	0	0	1	1395	1277	45	3		3	BDP1	5	70806321	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	33757647	70806321	110108939	38	26739										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167689579	167689579	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	aagagaaggcccgcgtcctgGaccaggcgagacagagggcc	16	12	0	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr5:167689579G>A	ENST00000518659.1	+	29	8128	c.8089G>A	c.(8089-8091)Gac>Aac	p.D2697N	TENM2_ENST00000520394.1_Missense_Mutation_p.D2458N|TENM2_ENST00000545108.1_Missense_Mutation_p.D2696N|TENM2_ENST00000403607.2_Missense_Mutation_p.D2521N|TENM2_ENST00000519204.1_Missense_Mutation_p.D2576N	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2697					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										CCGCGTCCTGGACCAGGCGAG	0.647																																					p.D2688N		Atlas-SNP	.											.	.	.	.	0			c.G8062A						.						11	12	12					5																	167689579		1998	4159	6157	SO:0001583	missense	57451	exon29			GTCCTGGACCAGG	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.8089G>A	chr5.hg19:g.167689579G>A	ENSP00000429430:p.Asp2697Asn	156.0	0.0		134.0	14.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	G	24.5	4.536592	0.85812	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89050	-1.99;-1.98;-2.09;-2.45;-2.46	5.14	5.14	0.70334	.	0.131315	0.64402	D	0.000002	D	0.88713	0.6511	L	0.29908	0.895	0.80722	D	1	P;P;P	0.44521	0.837;0.749;0.557	P;B;B	0.50314	0.637;0.248;0.12	D	0.90075	0.4166	10	0.72032	D	0.01	.	18.9479	0.92628	0.0:0.0:1.0:0.0	.	2696;2697;2458	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	N	2697;2696;2576;2458;2521	ENSP00000429430:D2697N;ENSP00000438635:D2696N;ENSP00000428964:D2576N;ENSP00000427874:D2458N;ENSP00000384905:D2521N	ENSP00000384905:D2521N	D	+	1	0	ODZ2	167622157	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.809000	0.99208	2.549000	0.85964	0.561000	0.74099	GAC	.	.		0.647	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167689579	G	A	167689579	3	1	178	1	0	0	0	0	1	0	0	0	10844	1174	41	3	8176	3	ODZ2	5	167689579	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	96883258	167689579	13225681	39	26740										
SH3PXD2B	285590	hgsc.bcm.edu	37	chr5	171766062	171766062	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tactgcctgggggccctcccCatccaacaaggacttgtctt	9	15	1	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr5:171766062C>A	ENST00000311601.5	-	13	2217	c.2047G>T	c.(2047-2049)Ggg>Tgg	p.G683W	SH3PXD2B_ENST00000519643.1_Intron	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	683					adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GGGCCCTCCCCATCCAACAAG	0.637																																					p.G683W		Atlas-SNP	.											.	SH3PXD2B	91	.	0			c.G2047T						.						65	62	63					5																	171766062		2203	4300	6503	SO:0001583	missense	285590	exon13			CCTCCCCATCCAA	AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"KIAA1295"	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.2047G>T	chr5.hg19:g.171766062C>A	ENSP00000309714:p.Gly683Trp	97.0	0.0		90.0	13.0	NM_001017995	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	hg19	CCDS34291.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.930625	0.34096	.	.	ENSG00000174705	ENST00000311601	T	0.60920	0.15	5.47	4.61	0.57282	.	0.534146	0.20054	N	0.100234	T	0.54919	0.1888	N	0.24115	0.695	0.09310	N	1	D	0.63046	0.992	P	0.55713	0.782	T	0.47032	-0.9148	9	.	.	.	-17.9254	11.9575	0.52988	0.0:0.9155:0.0:0.0845	.	683	A1X283	SPD2B_HUMAN	W	683	ENSP00000309714:G683W	.	G	-	1	0	SH3PXD2B	171698667	0.366000	0.25014	0.112000	0.21494	0.397000	0.30659	2.591000	0.46163	1.311000	0.45024	0.561000	0.74099	GGG	.	.		0.637	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963		A	171766062	C	A	171766062	3	1	178	1	0	0	0	0	1	0	0	0	14272	594	21	3	692	3	SH3PXD2B	5	171766062	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	4076483	171766062	9149198	40	26741										
HK3	3101	hgsc.bcm.edu	37	chr5	176310869	176310869	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	caaccacattcagctccactGcctgcacacaaaaggatgct	6	15	1	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr5:176310869G>A	ENST00000292432.5	-	15	2046	c.1955C>T	c.(1954-1956)gCa>gTa	p.A652V		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	652	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGCTCCACTGCCTGCACACA	0.587																																					p.A652V		Atlas-SNP	.											.	HK3	210	.	0			c.C1955T						.						188	145	159					5																	176310869		2203	4300	6503	SO:0001630	splice_region_variant	3101	exon15			TCCACTGCCTGCA		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1954-1C>T	chr5.hg19:g.176310869G>A		85.0	0.0		103.0	20.0	NM_002115	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	hg19	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.728878	0.48833	.	.	ENSG00000160883	ENST00000292432;ENST00000514058	D;D	0.98207	-4.79;-4.79	5.13	-0.494	0.12034	Hexokinase, N-terminal (1);	0.605120	0.14798	N	0.297838	D	0.91418	0.7292	N	0.01874	-0.695	0.37154	D	0.902298	B	0.26041	0.14	B	0.25506	0.061	D	0.84835	0.0804	10	0.87932	D	0	-0.6024	9.652	0.39904	0.0:0.4675:0.2091:0.3235	.	652	P52790	HXK3_HUMAN	V	652;33	ENSP00000292432:A652V;ENSP00000424632:A33V	ENSP00000292432:A652V	A	-	2	0	HK3	176243475	1.000000	0.71417	0.869000	0.34112	0.873000	0.50193	2.578000	0.46051	0.009000	0.14813	0.462000	0.41574	GCA	.	.		0.587	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		Missense_Mutation	A	176310869	G	A	176310869	5	1	178	1	0	0	0	0	0	0	1	0	7201	1333	46	3	836	3	HK3	5	176310869	Splice_Site	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	4544807	176310869	4604391	41	26742										
KIAA0319	9856	hgsc.bcm.edu	37	chr6	24566957	24566957	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tgtctgccaccagcccgggcTctgggaggactattattttc	11	12	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr6:24566957T>A	ENST00000378214.3	-	14	2684	c.2160A>T	c.(2158-2160)agA>agT	p.R720S	KIAA0319_ENST00000430948.2_Missense_Mutation_p.R675S|KIAA0319_ENST00000543707.1_Missense_Mutation_p.R720S|KIAA0319_ENST00000537886.1_Missense_Mutation_p.R720S|KIAA0319_ENST00000535378.1_Missense_Mutation_p.R711S	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	720	PKD 5. {ECO:0000255|PROSITE- ProRule:PRU00151}.				negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						CAGCCCGGGCTCTGGGAGGAC	0.383																																					p.R720S		Atlas-SNP	.											.	KIAA0319	117	.	0			c.A2160T						.						73	79	77					6																	24566957		2203	4300	6503	SO:0001583	missense	9856	exon14			CCGGGCTCTGGGA	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"neuronal migration"	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.2160A>T	chr6.hg19:g.24566957T>A	ENSP00000367459:p.Arg720Ser	70.0	0.0		70.0	12.0	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	hg19	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.958214	0.53400	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.13307	2.6;2.6;2.6;2.6;2.6	4.01	4.01	0.46588	PKD/Chitinase domain (1);Fibronectin, type III (1);PKD domain (1);	0.231080	0.36628	N	0.002486	T	0.12050	0.0293	L	0.41573	1.285	0.42507	D	0.992951	D;D;D	0.71674	0.998;0.972;0.978	D;P;P	0.63381	0.914;0.742;0.832	T	0.02942	-1.1091	10	0.45353	T	0.12	-15.4993	6.2059	0.20602	0.0:0.1584:0.0:0.8416	.	720;711;720	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	S	720;711;675;720;720	ENSP00000439700:R720S;ENSP00000442403:R711S;ENSP00000401086:R675S;ENSP00000367459:R720S;ENSP00000437656:R720S	ENSP00000367459:R720S	R	-	3	2	KIAA0319	24674936	0.972000	0.33761	1.000000	0.80357	0.996000	0.88848	1.524000	0.35942	1.671000	0.50874	0.482000	0.46254	AGA	.	.		0.383	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		A	24566957	T	A	24566957	3	1	178	1	0	0	0	0	1	0	0	0	8177	1548	54	4	1090	4	KIAA0319	6	24566957	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10		24566957	146548110	42	26743										
BTN3A3	10384	hgsc.bcm.edu	37	chr6	26452498	26452498	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctggagacaccactgaccccGggcttagctaatgaaagtgg	12	11	0	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr6:26452498G>A	ENST00000244519.2	+	11	1857	c.1614G>A	c.(1612-1614)ccG>ccA	p.P538P	BTN3A3_ENST00000339789.4_Silent_p.P496P|BTN3A3_ENST00000361232.3_Silent_p.P489P	NM_006994.4	NP_008925.1	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3	538					T cell mediated immunity (GO:0002456)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30						CACTGACCCCGGGCTTAGCTA	0.552																																					p.P538P		Atlas-SNP	.											.	BTN3A3	56	.	0			c.G1614A						.						48	47	47					6																	26452498		2203	4300	6503	SO:0001819	synonymous_variant	10384	exon11			GACCCCGGGCTTA	U90548	CCDS4611.1, CCDS4612.1, CCDS4612.2	6p22.1	2014-01-14			ENSG00000111801	ENSG00000111801		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1140	protein-coding gene	gene with protein product		613595				10354554, 9149941	Standard	NM_006994		Approved	BTF3, BTN3.3	uc003nhz.3	O00478	OTTHUMG00000014451	ENST00000244519.2:c.1614G>A	chr6.hg19:g.26452498G>A		80.0	0.0		65.0	11.0	NM_006994	B4DWI7|E9PCP5	Silent	SNP	ENST00000244519.2	hg19	CCDS4611.1																																																																																			.	.		0.552	BTN3A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040116.2	NM_006994		A	26452498	G	A	26452498	2	1	178	1	0	0	0	0	0	0	0	1	1566	1103	39	1		1	BTN3A3	6	26452498	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	1885541	26452498	144662569	43	26744										
OR14J1	442191	hgsc.bcm.edu	37	chr6	29274701	29274701	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tctctgtcacagtcccccagTccattgcaaattcacttatg	5	14	3	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr6:29274701T>C	ENST00000377160.2	+	1	299	c.235T>C	c.(235-237)Tcc>Ccc	p.S79P		NM_030946.1	NP_112208.1	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 14, subfamily J, member 1	79						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(2)	17						AGTCCCCCAGTCCATTGCAAA	0.463																																					p.S79P		Atlas-SNP	.											.	OR14J1	43	.	0			c.T235C						.						268	302	290					6																	29274701		1510	2709	4219	SO:0001583	missense	442191	exon1			CCCCAGTCCATTG		CCDS34362.1	6p21.3	2012-08-09	2008-04-02	2008-04-02	ENSG00000204695	ENSG00000204695		"GPCR / Class A : Olfactory receptors"	13971	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily U, member 1"	OR5U1			Standard	NM_030946		Approved	hs6M1-28	uc011dln.2	Q9UGF5	OTTHUMG00000031184	ENST00000377160.2:c.235T>C	chr6.hg19:g.29274701T>C	ENSP00000366365:p.Ser79Pro	149.0	0.0		149.0	25.0	NM_030946	A2BEC2|B0V078|Q5ST27	Missense_Mutation	SNP	ENST00000377160.2	hg19	CCDS34362.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.599013	0.46318	.	.	ENSG00000204695	ENST00000377160	T	0.03035	4.07	4.86	-1.13	0.09775	GPCR, rhodopsin-like superfamily (1);	0.536779	0.15489	N	0.259698	T	0.03136	0.0092	L	0.59436	1.845	0.09310	N	1	D	0.64830	0.994	P	0.60682	0.878	T	0.35301	-0.9794	10	0.59425	D	0.04	.	2.1407	0.03774	0.3596:0.0774:0.3414:0.2216	.	79	Q9UGF5	O14J1_HUMAN	P	79	ENSP00000366365:S79P	ENSP00000366365:S79P	S	+	1	0	OR14J1	29382680	0.000000	0.05858	0.694000	0.30210	0.666000	0.39218	-1.371000	0.02573	0.041000	0.15688	0.528000	0.53228	TCC	.	.		0.463	OR14J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076362.2			C	29274701	T	C	29274701	3	2	178	1	0	0	0	0	1	0	0	0	10957	1667	58	2	237	2	OR14J1	6	29274701	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	2822203	29274701	141840366	44	26745										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32182001	32182001	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctctgcctcacactctggccCcgtccaacccacgtcacaca	5	21	4	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr6:32182001C>A	ENST00000375023.3	-	13	2191	c.2053G>T	c.(2053-2055)Ggg>Tgg	p.G685W	NOTCH4_ENST00000465528.1_5'UTR	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	685	EGF-like 17. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CACTCTGGCCCCGTCCAACCC	0.597																																					p.G685W		Atlas-SNP	.											.	NOTCH4	201	.	0			c.G2053T						.						111	112	112					6																	32182001		2203	4300	6503	SO:0001583	missense	4855	exon13			CTGGCCCCGTCCA		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.2053G>T	chr6.hg19:g.32182001C>A	ENSP00000364163:p.Gly685Trp	135.0	0.0		134.0	23.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	C	16.47	3.133188	0.56828	.	.	ENSG00000204301	ENST00000375023	T	0.76709	-1.04	4.18	4.18	0.49190	EGF-like region, conserved site (2);	0.000000	0.42548	D	0.000688	D	0.92417	0.7593	H	0.99454	4.575	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95057	0.8192	10	0.87932	D	0	.	14.0247	0.64580	0.0:1.0:0.0:0.0	.	685	Q99466	NOTC4_HUMAN	W	685	ENSP00000364163:G685W	ENSP00000364163:G685W	G	-	1	0	NOTCH4	32289979	1.000000	0.71417	0.995000	0.50966	0.346000	0.29079	6.145000	0.71769	2.169000	0.68431	0.561000	0.74099	GGG	.	.		0.597	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32182001	C	A	32182001	3	1	178	1	0	0	0	0	1	0	0	0	10560	623	22	3	4030	3	NOTCH4	6	32182001	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	2907300	32182001	138933066	45	26746										
C6orf138	442213	hgsc.bcm.edu	37	chr6	47846992	47846992	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	atcctggacgctgctgttccAgtactctaggggctcataga	11	11	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr6:47846992A>G	ENST00000339488.4	-	3	1621	c.1588T>C	c.(1588-1590)Tgg>Cgg	p.W530R		NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	530						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										CTGCTGTTCCAGTACTCTAGG	0.483																																					p.W530R		Atlas-SNP	.											.	.	.	.	0			c.T1588C						.						54	48	50					6																	47846992		2203	4300	6503	SO:0001583	missense	442213	exon3			TGTTCCAGTACTC		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 138"	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.1588T>C	chr6.hg19:g.47846992A>G	ENSP00000341914:p.Trp530Arg	63.0	0.0		57.0	7.0	NM_001013732	B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	hg19	CCDS34473.2	.	.	.	.	.	.	.	.	.	.	A	13.47	2.247675	0.39697	.	.	ENSG00000244694	ENST00000339488	D	0.84516	-1.86	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	D	0.88562	0.6470	M	0.71036	2.16	0.80722	D	1	D	0.64830	0.994	D	0.74674	0.984	D	0.86550	0.1834	10	0.21540	T	0.41	.	15.5578	0.76213	1.0:0.0:0.0:0.0	.	530	Q6ZW05	CF138_HUMAN	R	530	ENSP00000341914:W530R	ENSP00000341914:W530R	W	-	1	0	C6orf138	47954951	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.962000	0.93254	2.095000	0.63458	0.528000	0.53228	TGG	.	.		0.483	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		G	47846992	A	G	47846992	3	3	178	1	0	0	0	0	1	0	0	0	2334	188	7	2	956	2	C6orf138	6	47846992	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	15664991	47846992	123268075	46	26747										
SLC2A12	154091	hgsc.bcm.edu	37	chr6	134323190	134323190	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gcatccctttgtctcaggtaTaaacataacaacaaaaagca	5	10	1	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr6:134323190T>G	ENST00000275230.5	-	4	1800	c.1645A>C	c.(1645-1647)Ata>Cta	p.I549L		NM_145176.2	NP_660159.1	Q8TD20	GTR12_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 12	549					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	17	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)		GTCTCAGGTATAAACATAACA	0.358																																					p.I549L	Melanoma(122;1663 1672 14489 35294 41228)	Atlas-SNP	.											.	SLC2A12	43	.	0			c.A1645C						.						113	106	108					6																	134323190		2203	4300	6503	SO:0001583	missense	154091	exon4			CAGGTATAAACAT	AL035699	CCDS5169.1	6q23.2	2013-05-22			ENSG00000146411	ENSG00000146411		"Solute carriers"	18067	protein-coding gene	gene with protein product		610372				11780753, 11832379	Standard	XM_006715349		Approved	GLUT12, GLUT8	uc003qem.1	Q8TD20	OTTHUMG00000015611	ENST00000275230.5:c.1645A>C	chr6.hg19:g.134323190T>G	ENSP00000275230:p.Ile549Leu	81.0	0.0		83.0	14.0	NM_145176	B3KV17|Q7Z6U3|Q96MR8	Missense_Mutation	SNP	ENST00000275230.5	hg19	CCDS5169.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.628339	0.46944	.	.	ENSG00000146411	ENST00000275230	T	0.72505	-0.66	5.78	5.78	0.91487	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.173351	0.51477	D	0.000095	T	0.28034	0.0691	N	0.02697	-0.525	0.36594	D	0.874266	B	0.02656	0.0	B	0.04013	0.001	T	0.19910	-1.0291	10	0.30854	T	0.27	-9.9787	10.4905	0.44748	0.0:0.072:0.0:0.928	.	549	Q8TD20	GTR12_HUMAN	L	549	ENSP00000275230:I549L	ENSP00000275230:I549L	I	-	1	0	SLC2A12	134364883	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.460000	0.53028	2.209000	0.71365	0.524000	0.50904	ATA	.	.		0.358	SLC2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042302.1			G	134323190	T	G	134323190	3	3	178	1	0	0	0	0	1	0	0	0	14556	1406	49	5	216	5	SLC2A12	6	134323190	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	86476198	134323190	36791877	47	26748										
PLG	5340	hgsc.bcm.edu	37	chr6	161127481	161127481	+	Frame_Shift_Del	DEL	C	C	-													0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctatgtgaatacccagggggCttcactgttcagtgtcacta							TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr6:161127481delC	ENST00000308192.9	+	2	155	c.92delC	c.(91-93)gctfs	p.A31fs	PLG_ENST00000462918.1_3'UTR|PLG_ENST00000366924.2_Frame_Shift_Del_p.A31fs	NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	31	PAN. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	ACCCAGGGGGCTTCACTGTTC	0.453																																					p.A31fs		Atlas-INDEL	.											.	PLG	150	.	0			c.91delG						.						116	116	116					6																	161127481		2203	4300	6503	SO:0001589	frameshift_variant	5340	exon2			.	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.92delC	chr6.hg19:g.161127481delC	ENSP00000308938:p.Ala31fs	582.0	0.0		614.0	134.0	NM_000301	Q15146|Q5TEH4|Q6PA00	Frame_Shift_Del	DEL	ENST00000308192.9	hg19	CCDS5279.1																																																																																			.	.		0.453	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		-	161127481	C	-	161127481	7	5	178	1	0	1	0	1	0	0	0	0	12095	797	28	0	98	0	PLG	6	161127481	Frame_Shift_Del	DEL	C	TCGA-DD-AAD1-01A-11D-A40R-10	26804291	161127481	9987586	48	26749										
PACRG	135138	hgsc.bcm.edu	37	chr6	163735950	163735950	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctggaggccttcgagcgctaCggaggagaaaatgcctttat	13	9	0	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr6:163735950C>T	ENST00000337019.3	+	7	1046	c.822C>T	c.(820-822)taC>taT	p.Y274Y	PACRG_ENST00000366889.2_Silent_p.Y235Y|PACRG_ENST00000366888.2_Silent_p.Y235Y	NM_152410.2	NP_689623.2	Q96M98	PACRG_HUMAN	PARK2 co-regulated	274					spermatid development (GO:0007286)	cell body (GO:0044297)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm midpiece (GO:0097225)				endometrium(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		TCGAGCGCTACGGAGGAGAAA	0.522																																					p.Y274Y		Atlas-SNP	.											.	PACRG	48	.	0			c.C822T						.						155	138	144					6																	163735950		2203	4300	6503	SO:0001819	synonymous_variant	135138	exon7			GCGCTACGGAGGA	AK057286	CCDS5284.1, CCDS43524.1	6q26	2004-07-01			ENSG00000112530	ENSG00000112530			19152	protein-coding gene	gene with protein product		608427				12547187	Standard	NM_001080378		Approved	PARK2CRG, FLJ32724, Glup, HAK005771	uc003qua.3	Q96M98	OTTHUMG00000016116	ENST00000337019.3:c.822C>T	chr6.hg19:g.163735950C>T		256.0	0.0		278.0	62.0	NM_152410	E1P5B5|Q6IMB8|Q8IZM1|Q8NHP5|Q9H1V9	Silent	SNP	ENST00000337019.3	hg19	CCDS5284.1																																																																																			.	.		0.522	PACRG-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400424.1	NM_152410		T	163735950	C	T	163735950	2	4	178	1	0	0	0	0	0	0	0	1	11379	547	19	1		1	PACRG	6	163735950	Silent	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	2608469	163735950	7379117	49	26750										
HOXA6	3203	hgsc.bcm.edu	37	chr7	27187096	27187096	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cccctctgcttgccactgccCgagggcgaggcgccactgag	13	17	1	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr7:27187096C>A	ENST00000222728.3	-	1	297	c.273G>T	c.(271-273)tcG>tcT	p.S91S	RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000521197.1_RNA|RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000524304.1_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA6_ENST00000521478.1_5'UTR|HOXA-AS3_ENST00000521231.1_RNA	NM_024014.3	NP_076919.1	P31267	HXA6_HUMAN	homeobox A6	91					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(5)|lung(3)|ovary(1)	10						TGCCACTGCCCGAGGGCGAGG	0.627																																					p.S91S		Atlas-SNP	.											.	HOXA6	25	.	0			c.G273T						.						43	45	44					7																	27187096		2203	4300	6503	SO:0001819	synonymous_variant	3203	exon1			ACTGCCCGAGGGC		CCDS5407.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106006	ENSG00000106006		"Homeoboxes / ANTP class : HOXL subclass"	5107	protein-coding gene	gene with protein product		142951	"homeo box A6"	HOX1B, HOX1		1973146, 1358459	Standard	NM_024014		Approved		uc003syo.2	P31267	OTTHUMG00000023216	ENST00000222728.3:c.273G>T	chr7.hg19:g.27187096C>A		142.0	0.0		111.0	25.0	NM_024014	A4D192|Q2M3G3|Q9UPM0	Silent	SNP	ENST00000222728.3	hg19	CCDS5407.1																																																																																			.	.		0.627	HOXA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358697.1			A	27187096	C	A	27187096	2	1	178	1	0	0	0	0	0	0	0	1	7305	639	23	1		1	HOXA6	7	27187096	Silent	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10		27187096	131951567	50	26751										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87179184	87179184	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tacatgaggcagtttcatgaTaaagtcataggcattggctt	10	6	2	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr7:87179184T>A	ENST00000265724.3	-	14	1954	c.1537A>T	c.(1537-1539)Atc>Ttc	p.I513F	ABCB1_ENST00000543898.1_Missense_Mutation_p.I449F	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	513	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	AGTTTCATGATAAAGTCATAG	0.428																																					p.I513F		Atlas-SNP	.											.	ABCB1	263	.	0			c.A1537T						.						239	226	230					7																	87179184		2203	4300	6503	SO:0001583	missense	5243	exon14			TCATGATAAAGTC	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.1537A>T	chr7.hg19:g.87179184T>A	ENSP00000265724:p.Ile513Phe	111.0	0.0		81.0	16.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	hg19	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.555663	0.86231	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.85556	-2.0;-2.0	6.02	6.02	0.97574	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.91469	0.7307	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.72982	0.94;0.979	D	0.92195	0.5763	10	0.87932	D	0	-24.2602	16.5494	0.84464	0.0:0.0:0.0:1.0	.	449;513	B5AK60;P08183	.;MDR1_HUMAN	F	294;513;449	ENSP00000265724:I513F;ENSP00000444095:I449F	ENSP00000265724:I513F	I	-	1	0	ABCB1	87017120	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.278000	0.72614	2.299000	0.77371	0.528000	0.53228	ATC	.	.		0.428	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		A	87179184	T	A	87179184	3	1	178	1	0	0	0	0	1	0	0	0	40	1406	49	4	2369	4	ABCB1	7	87179184	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	59992088	87179184	71959479	51	26752										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	132192559	132192559	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	accccactgcgctcacagccAatgggcacctctacatagga	8	16	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr7:132192559A>T	ENST00000359827.3	-	2	1856	c.894T>A	c.(892-894)atT>atA	p.I298I	PLXNA4_ENST00000321063.4_Silent_p.I298I|PLXNA4_ENST00000378539.5_Silent_p.I298I|PLXNA4_ENST00000423507.2_Silent_p.I298I			Q9HCM2	PLXA4_HUMAN	plexin A4	298	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						GCTCACAGCCAATGGGCACCT	0.602																																					p.I298I		Atlas-SNP	.											.	PLXNA4	873	.	0			c.T894A						.						62	45	51					7																	132192559		2203	4300	6503	SO:0001819	synonymous_variant	91584	exon2			ACAGCCAATGGGC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.894T>A	chr7.hg19:g.132192559A>T		105.0	0.0		90.0	11.0	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	hg19	CCDS43646.1																																																																																			.	.		0.602	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	132192559	A	T	132192559	2	4	178	1	0	0	0	0	0	0	0	1	12131	126	5	4		4	PLXNA4	7	132192559	Silent	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	45013375	132192559	26946104	52	26753										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2800024	2800024	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	agaggtaaaatgcaaaccctGataaaattagagcaaagaaa	8	5	0	4			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr8:2800024G>T	ENST00000520002.1	-	70	11063	c.10508C>A	c.(10507-10509)tCa>tAa	p.S3503*	CSMD1_ENST00000602723.1_Nonsense_Mutation_p.S3326*|CSMD1_ENST00000542608.1_Nonsense_Mutation_p.S3325*|CSMD1_ENST00000537824.1_Nonsense_Mutation_p.S3502*|CSMD1_ENST00000400186.3_Nonsense_Mutation_p.S3326*|CSMD1_ENST00000602557.1_Nonsense_Mutation_p.S3503*			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3503						integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TGCAAACCCTGATAAAATTAG	0.443																																					p.S3502X		Atlas-SNP	.											CSMD1_ENST00000537824,NS,malignant_melanoma,0,4	CSMD1	1469	.	0			c.C10505A						.						52	51	52					8																	2800024		1873	4101	5974	SO:0001587	stop_gained	64478	exon69			AACCCTGATAAAA			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.10508C>A	chr8.hg19:g.2800024G>T	ENSP00000430733:p.Ser3503*	109.0	0.0		77.0	18.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Nonsense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	G	53	20.696699	0.99933	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	.	.	.	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	19.7559	0.96291	0.0:0.0:1.0:0.0	.	.	.	.	X	3326;3503;3364;3502;3325	.	ENSP00000320445:S3364X	S	-	2	0	CSMD1	2787431	1.000000	0.71417	0.918000	0.36340	0.982000	0.71751	9.532000	0.98057	2.661000	0.90470	0.643000	0.83706	TCA	.	.		0.443	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	2800024	G	T	2800024	4	4	178	1	0	0	0	0	0	1	0	0	3946	1294	45	3	197	3	CSMD1	8	2800024	Nonsense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10		2800024	143563998	53	26754										
DLC1	10395	hgsc.bcm.edu	37	chr8	12957624	12957624	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ccgactggctgctgctgctgCtggtctgcgtggagttggaa	16	10	1	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr8:12957624C>G	ENST00000276297.4	-	9	2631	c.2222G>C	c.(2221-2223)aGc>aCc	p.S741T	DLC1_ENST00000520226.1_Missense_Mutation_p.S230T|DLC1_ENST00000358919.2_Missense_Mutation_p.S304T|DLC1_ENST00000512044.2_Missense_Mutation_p.S338T	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	741	Focal adhesion-targeting (FAT).|Poly-Ser.				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GCTGCTGCTGCTGGTCTGCGT	0.627																																					p.S741T		Atlas-SNP	.											DLC1,bladder,carcinoma,0,3	DLC1	411	.	0			c.G2222C						.						56	47	50					8																	12957624		2203	4300	6503	SO:0001583	missense	10395	exon9			CTGCTGCTGGTCT	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.2222G>C	chr8.hg19:g.12957624C>G	ENSP00000276297:p.Ser741Thr	51.0	2.0		39.0	3.0	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	hg19	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.320479	0.81469	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000512044;ENST00000520226	T;T;T;T	0.07688	3.42;3.19;3.19;3.17	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.31979	0.0814	M	0.80422	2.495	0.80722	D	1	D;B;D	0.65815	0.995;0.103;0.99	P;B;D	0.72982	0.795;0.132;0.979	T	0.09975	-1.0650	10	0.66056	D	0.02	.	17.9274	0.88987	0.0:1.0:0.0:0.0	.	741;338;304	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	T	741;304;338;230	ENSP00000276297:S741T;ENSP00000351797:S304T;ENSP00000422595:S338T;ENSP00000428028:S230T	ENSP00000276297:S741T	S	-	2	0	DLC1	13001995	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.462000	0.80851	2.527000	0.85204	0.561000	0.74099	AGC	.	.		0.627	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		G	12957624	C	G	12957624	3	3	178	1	0	0	0	0	1	0	0	0	4552	797	28	4	2404	4	DLC1	8	12957624	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	10157600	12957624	133406398	54	26755										
MYST3	7994	hgsc.bcm.edu	37	chr8	41805294	41805294	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	aaaagtagccaacaaggtggCagcccttgacatcattctgt	9	10	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr8:41805294C>A	ENST00000396930.3	-	12	2420	c.1877G>T	c.(1876-1878)tGc>tTc	p.C626F	KAT6A_ENST00000406337.1_Missense_Mutation_p.C626F|KAT6A_ENST00000485568.1_Missense_Mutation_p.C626F|KAT6A_ENST00000265713.2_Missense_Mutation_p.C626F	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	626	Catalytic.|Interaction with PML.|Interaction with RUNX1-1.|MYST-type HAT.|Mediates interaction with BRPF1, required for histone H3 acetyltransferase activity.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										AACAAGGTGGCAGCCCTTGAC	0.393																																					p.C626F		Atlas-SNP	.											.	.	.	.	0			c.G1877T						.						72	68	70					8																	41805294		2203	4300	6503	SO:0001583	missense	7994	exon12			AGGTGGCAGCCCT	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.1877G>T	chr8.hg19:g.41805294C>A	ENSP00000380136:p.Cys626Phe	189.0	0.0		157.0	20.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	C	14.37	2.516568	0.44763	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000418721;ENST00000485568	T;T;T;D	0.84730	0.13;0.13;0.13;-1.89	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.90703	0.7083	L	0.49126	1.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.90836	0.4720	10	0.56958	D	0.05	-16.0217	19.1789	0.93614	0.0:1.0:0.0:0.0	.	626;626	A5PLL3;Q92794	.;KAT6A_HUMAN	F	626;626;626;206;626	ENSP00000265713:C626F;ENSP00000385888:C626F;ENSP00000380136:C626F;ENSP00000430606:C626F	ENSP00000265713:C626F	C	-	2	0	KAT6A	41924451	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.773000	0.85462	2.530000	0.85305	0.655000	0.94253	TGC	.	.		0.393	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		A	41805294	C	A	41805294	3	1	178	1	0	0	0	0	1	0	0	0	10113	710	25	3	4165	3	MYST3	8	41805294	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	28847670	41805294	104558728	55	26756										
LRRC67	286187	hgsc.bcm.edu	37	chr8	67929857	67929857	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	aatttcaaagttcttacaatTgcatctatatttttgtctga	4	6	4	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr8:67929857T>C	ENST00000324682.5	-	2	270	c.126A>G	c.(124-126)gcA>gcG	p.A42A	PPP1R42_ENST00000522909.1_Silent_p.A42A|PPP1R42_ENST00000517834.1_5'UTR	NM_001013626.2	NP_001013648.1	Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	42					regulation of phosphatase activity (GO:0010921)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|manchette (GO:0002177)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)	actin binding (GO:0003779)|dynein binding (GO:0045502)|tubulin binding (GO:0015631)										TTCTTACAATTGCATCTATAT	0.264																																					p.A42A		Atlas-SNP	.											.	PPP1R42	2	.	0			c.A126G						.						34	32	32					8																	67929857		2189	4274	6463	SO:0001819	synonymous_variant	286187	exon2			TACAATTGCATCT	BC055413	CCDS34902.1	8q13.1-q13.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000178125	ENSG00000178125		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	33732	protein-coding gene	gene with protein product	"testis leucine-rich repeat"		"leucine rich repeat containing 67"	LRRC67			Standard	NM_001013626		Approved	dtr, TLLR	uc003xxc.3	Q7Z4L9	OTTHUMG00000164745	ENST00000324682.5:c.126A>G	chr8.hg19:g.67929857T>C		79.0	0.0		122.0	6.0	NM_001013626		Silent	SNP	ENST00000324682.5	hg19	CCDS34902.1																																																																																			.	.		0.264	PPP1R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380034.2	NM_001013626		C	67929857	T	C	67929857	2	2	178	1	0	0	0	0	0	0	0	1	9028	1799	63	2		2	LRRC67	8	67929857	Silent	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	26124563	67929857	78434165	56	26757										
C8orf76	84933	hgsc.bcm.edu	37	chr8	124253528	124253528	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gtcctgaccgccgctccggcCtctcctcgaacaccgagtcc	9	20	1	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr8:124253528C>A	ENST00000276704.4	-	1	110	c.59G>T	c.(58-60)aGg>aTg	p.R20M	ZHX1-C8ORF76_ENST00000357082.4_Intron|C8orf76_ENST00000521310.1_5'UTR	NM_032847.2	NP_116236.1	Q96K31	CH076_HUMAN	chromosome 8 open reading frame 76	20										NS(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(4)	17	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			CCGCTCCGGCCTCTCCTCGAA	0.721																																					p.R20M		Atlas-SNP	.											.	C8orf76	26	.	0			c.G59T						.						10	12	11					8																	124253528		2150	4247	6397	SO:0001583	missense	84933	exon1			TCCGGCCTCTCCT	AK027731	CCDS6341.1	8q24.13	2012-06-27			ENSG00000189376	ENSG00000189376			25924	protein-coding gene	gene with protein product							Standard	NM_032847		Approved	FLJ14825	uc003yqc.2	Q96K31	OTTHUMG00000172562	ENST00000276704.4:c.59G>T	chr8.hg19:g.124253528C>A	ENSP00000276704:p.Arg20Met	201.0	0.0		353.0	137.0	NM_032847	Q53HC1	Missense_Mutation	SNP	ENST00000276704.4	hg19	CCDS6341.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.676108	0.29783	.	.	ENSG00000189376	ENST00000276704	T	0.25912	1.77	5.68	2.92	0.33932	.	0.873937	0.10119	N	0.713701	T	0.28797	0.0714	L	0.60455	1.87	0.19945	N	0.999943	P	0.37276	0.589	B	0.39379	0.298	T	0.14615	-1.0466	10	0.49607	T	0.09	-0.0046	9.056	0.36405	0.0:0.7666:0.0:0.2334	.	20	Q96K31	CH076_HUMAN	M	20	ENSP00000276704:R20M	ENSP00000276704:R20M	R	-	2	0	C8orf76	124322709	0.238000	0.23825	0.010000	0.14722	0.229000	0.25112	1.216000	0.32443	0.336000	0.23639	-0.254000	0.11334	AGG	.	.		0.721	C8orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381748.1	NM_032847		A	124253528	C	A	124253528	3	1	178	1	0	0	0	0	1	0	0	0	2439	681	24	3	1107	3	C8orf76	8	124253528	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	56323671	124253528	22110494	57	26758										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125076745	125076745	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	atcctggttgacgtccctgaCtcatccccgatgctggagcc	10	15	1	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr8:125076745C>G	ENST00000522917.1	+	26	3692	c.3486C>G	c.(3484-3486)gaC>gaG	p.D1162E	FER1L6_ENST00000399018.1_Missense_Mutation_p.D1162E|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1162						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			ACGTCCCTGACTCATCCCCGA	0.542																																					p.D1162E		Atlas-SNP	.											.	FER1L6	268	.	0			c.C3486G						.						68	73	71					8																	125076745		1996	4176	6172	SO:0001583	missense	654463	exon26			CCCTGACTCATCC	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.3486C>G	chr8.hg19:g.125076745C>G	ENSP00000428280:p.Asp1162Glu	193.0	0.0		317.0	28.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	C	0.370	-0.934324	0.02340	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.80994	-1.44;-1.44	4.99	0.928	0.19443	.	1.362050	0.05001	U	0.469070	T	0.70055	0.3180	L	0.47716	1.5	0.36268	D	0.854972	B	0.29716	0.255	B	0.26614	0.071	T	0.58142	-0.7688	10	0.15066	T	0.55	-2.9503	3.22	0.06712	0.1856:0.5125:0.0:0.3019	.	1162	Q2WGJ9	FR1L6_HUMAN	E	1162	ENSP00000428280:D1162E;ENSP00000381982:D1162E	ENSP00000381982:D1162E	D	+	3	2	FER1L6	125145926	0.788000	0.28762	0.980000	0.43619	0.377000	0.30045	-0.437000	0.06914	0.163000	0.19507	0.462000	0.41574	GAC	.	.		0.542	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		G	125076745	C	G	125076745	3	3	178	1	0	0	0	0	1	0	0	0	5823	564	20	4	3584	4	FER1L6	8	125076745	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	823217	125076745	21287277	58	26759										
ADCY8	114	hgsc.bcm.edu	37	chr8	132052123	132052123	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gttgcgcagggtggggaaaaTgacccctcggtagctatagc	15	9	0	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr8:132052123T>A	ENST00000286355.5	-	1	2549	c.457A>T	c.(457-459)Att>Ttt	p.I153F	ADCY8_ENST00000377928.3_Missense_Mutation_p.I153F	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	153					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GTGGGGAAAATGACCCCTCGG	0.567										HNSCC(32;0.087)																											p.I153F		Atlas-SNP	.											.	ADCY8	291	.	0			c.A457T						.						43	41	42					8																	132052123		2203	4300	6503	SO:0001583	missense	114	exon1			GGAAAATGACCCC	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.457A>T	chr8.hg19:g.132052123T>A	ENSP00000286355:p.Ile153Phe	140.0	0.0		195.0	19.0	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	T	10.37	1.330990	0.24167	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.64618	-0.11;-0.11	5.26	5.26	0.73747	.	0.137925	0.47852	D	0.000216	T	0.42877	0.1222	N	0.16790	0.44	0.41965	D	0.990723	B;B	0.25667	0.131;0.131	B;B	0.16722	0.016;0.016	T	0.37267	-0.9713	10	0.09843	T	0.71	.	14.3502	0.66697	0.0:0.0:0.0:1.0	.	153;153	E7EVL1;P40145	.;ADCY8_HUMAN	F	153	ENSP00000286355:I153F;ENSP00000367161:I153F	ENSP00000286355:I153F	I	-	1	0	ADCY8	132121305	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	3.776000	0.55356	2.002000	0.58637	0.379000	0.24179	ATT	.	.		0.567	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	132052123	T	A	132052123	3	1	178	1	0	0	0	0	1	0	0	0	300	1464	51	4	3370	4	ADCY8	8	132052123	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	6975378	132052123	14311899	59	26760										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133152405	133152405	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	atagcccctgtcttccgccaTggggtcacctgtcccggcat	10	16	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr8:133152405T>C	ENST00000388996.4	-	11	1906	c.1486A>G	c.(1486-1488)Atg>Gtg	p.M496V	KCNQ3_ENST00000519445.1_Missense_Mutation_p.M496V|KCNQ3_ENST00000521134.1_Missense_Mutation_p.M376V	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	496					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TCTTCCGCCATGGGGTCACCT	0.607																																					p.M496V		Atlas-SNP	.											.	KCNQ3	164	.	0			c.A1486G						.						52	53	52					8																	133152405		2203	4300	6503	SO:0001583	missense	3786	exon11			CCGCCATGGGGTC	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1486A>G	chr8.hg19:g.133152405T>C	ENSP00000373648:p.Met496Val	29.0	0.0		73.0	17.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	hg19	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	T	0.018	-1.472431	0.01044	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.99479	-5.98;-5.98;-5.98	5.92	2.03	0.26663	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.579301	0.19542	N	0.111765	D	0.93953	0.8064	N	0.01729	-0.75	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.11329	0.006;0.006	D	0.90007	0.4118	10	0.02654	T	1	-4.8328	5.4871	0.16755	0.0:0.2194:0.1356:0.645	.	496;496	E7ET42;O43525	.;KCNQ3_HUMAN	V	496;376;496;485;375	ENSP00000373648:M496V;ENSP00000429799:M376V;ENSP00000428790:M496V	ENSP00000373648:M496V	M	-	1	0	KCNQ3	133221587	0.593000	0.26840	0.972000	0.41901	0.189000	0.23516	0.524000	0.22940	0.482000	0.27582	0.533000	0.62120	ATG	.	.		0.607	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		C	133152405	T	C	133152405	3	2	178	1	0	0	0	0	1	0	0	0	8093	1464	51	2	1152	2	KCNQ3	8	133152405	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	1100282	133152405	13211617	60	26761										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13133827	13133827	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ttcaaagcagatttaccttgGgaagctccagatgttgcaca	9	9	1	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr9:13133827G>A	ENST00000319217.7	-	32	4707	c.4460C>T	c.(4459-4461)cCc>cTc	p.P1487L	MPDZ_ENST00000540202.1_5'Flank|MPDZ_ENST00000447879.1_Missense_Mutation_p.P1454L|MPDZ_ENST00000536827.1_Missense_Mutation_p.P1454L|MPDZ_ENST00000546205.1_Missense_Mutation_p.P1501L|MPDZ_ENST00000541093.1_5'UTR|MPDZ_ENST00000541718.1_Missense_Mutation_p.P1487L|MPDZ_ENST00000538841.1_Missense_Mutation_p.P346L|MPDZ_ENST00000381015.4_Missense_Mutation_p.P1487L|MPDZ_ENST00000381022.2_Missense_Mutation_p.P1487L	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1487	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		ATTTACCTTGGGAAGCTCCAG	0.403																																					p.P1487L		Atlas-SNP	.											.	MPDZ	324	.	0			c.C4460T						.						78	75	76					9																	13133827		1876	4114	5990	SO:0001583	missense	8777	exon32			ACCTTGGGAAGCT	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.4460C>T	chr9.hg19:g.13133827G>A	ENSP00000320006:p.Pro1487Leu	156.0	0.0		128.0	23.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	G	15.55	2.866916	0.51588	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000438511;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68	5.68	3.84	0.44239	PDZ/DHR/GLGF (3);	0.146943	0.31784	N	0.007067	T	0.18676	0.0448	L	0.35414	1.06	0.80722	D	1	B;B;B;B;P;B;B	0.34724	0.018;0.0;0.0;0.003;0.465;0.014;0.004	B;B;B;B;B;B;B	0.33568	0.033;0.001;0.002;0.011;0.166;0.02;0.016	T	0.03728	-1.1009	10	0.28530	T	0.3	.	11.1255	0.48315	0.0665:0.0:0.8045:0.129	.	1454;346;192;1454;1367;1487;1487	B7ZMI4;B7ZB24;B4DGX5;O75970-3;E7EPZ1;O75970-2;O75970	.;.;.;.;.;.;MPDZ_HUMAN	L	1487;1487;1487;56;423;346;1454;1454;1487;1367;1501	ENSP00000320006:P1487L;ENSP00000439807:P1487L;ENSP00000370410:P1487L;ENSP00000415964:P56L;ENSP00000444230:P423L;ENSP00000444717:P346L;ENSP00000444151:P1454L;ENSP00000415208:P1454L;ENSP00000370403:P1487L;ENSP00000446358:P1501L	ENSP00000320006:P1487L	P	-	2	0	MPDZ	13123827	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.374000	0.59543	0.866000	0.35629	0.655000	0.94253	CCC	.	.		0.403	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		A	13133827	G	A	13133827	3	1	178	1	0	0	0	0	1	0	0	0	9731	1232	43	3	1725	3	MPDZ	9	13133827	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10		13133827	128079604	61	26762										
GCNT1	2650	hgsc.bcm.edu	37	chr9	79117570	79117570	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cgccctcggtggacacctgaCgactatataaacatgaccag	9	13	0	2	rs139014455		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr9:79117570C>T	ENST00000376730.4	+	4	756	c.273C>T	c.(271-273)gaC>gaT	p.D91D	GCNT1_ENST00000444201.2_Silent_p.D91D|GCNT1_ENST00000442371.1_Silent_p.D91D|GCNT1_ENST00000536223.1_Silent_p.D91D	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	91	Stem region. {ECO:0000250}.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						GGACACCTGACGACTATATAA	0.393																																					p.D91D		Atlas-SNP	.											.	GCNT1	52	.	0			c.C273T						.	C	,,,,	0,4406		0,0,2203	106	110	109		273,273,273,273,273	-11.7	0	9	dbSNP_134	109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GCNT1	NM_001097633.1,NM_001097634.1,NM_001097635.1,NM_001097636.1,NM_001490.4	,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,	91/429,91/429,91/429,91/429,91/429	79117570	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2650	exon4			ACCTGACGACTAT	L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4203	protein-coding gene	gene with protein product	"core 2 beta1,6 N-acetylglucosaminyltransferase-I", "beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"	600391	"glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.273C>T	chr9.hg19:g.79117570C>T		167.0	0.0		161.0	33.0	NM_001490	Q6DJZ4	Silent	SNP	ENST00000376730.4	hg19	CCDS6653.1																																																																																			.	C|1.000;T|0.000		0.393	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634		T	79117570	C	T	79117570	2	4	178	1	0	0	0	0	0	0	0	1	6308	535	19	1		1	GCNT1	9	79117570	Silent	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	65983743	79117570	62095861	62	26763										
GABBR2	9568	hgsc.bcm.edu	37	chr9	101056112	101056112	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	taggatctttgcatgttcgaGagggctctgttgtgttccac	12	8	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr9:101056112G>T	ENST00000259455.2	-	18	3074	c.2615C>A	c.(2614-2616)tCt>tAt	p.S872Y		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	872					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	GCATGTTCGAGAGGGCTCTGT	0.398																																					p.S872Y		Atlas-SNP	.											.	GABBR2	126	.	0			c.C2615A						.						245	239	241					9																	101056112		2203	4300	6503	SO:0001583	missense	9568	exon18			GTTCGAGAGGGCT	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.2615C>A	chr9.hg19:g.101056112G>T	ENSP00000259455:p.Ser872Tyr	82.0	0.0		82.0	15.0	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	hg19	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848565	0.91277	.	.	ENSG00000136928	ENST00000259455	D	0.82984	-1.67	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.74809	0.3765	N	0.14661	0.345	0.58432	D	0.999999	P	0.44090	0.826	B	0.43575	0.424	T	0.80134	-0.1509	10	0.87932	D	0	.	16.0535	0.80777	0.0:0.0:1.0:0.0	.	872	O75899	GABR2_HUMAN	Y	872	ENSP00000259455:S872Y	ENSP00000259455:S872Y	S	-	2	0	GABBR2	100095933	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	9.048000	0.93830	2.641000	0.89580	0.650000	0.86243	TCT	.	.		0.398	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			T	101056112	G	T	101056112	3	4	178	1	0	0	0	0	1	0	0	0	6164	942	33	3	218	3	GABBR2	9	101056112	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	21938542	101056112	40157319	63	26764										
GABBR2	9568	hgsc.bcm.edu	37	chr9	101470749	101470749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gtaggggcgcaggagtgactCgttgcggatctgctcgatgg	18	8	1	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr9:101470749C>T	ENST00000259455.2	-	1	730	c.271G>A	c.(271-273)Gag>Aag	p.E91K		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	91					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	AGGAGTGACTCGTTGCGGATC	0.677																																					p.E91K		Atlas-SNP	.											.	GABBR2	126	.	0			c.G271A						.						46	43	44					9																	101470749		2203	4300	6503	SO:0001583	missense	9568	exon1			GTGACTCGTTGCG	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.271G>A	chr9.hg19:g.101470749C>T	ENSP00000259455:p.Glu91Lys	64.0	0.0		68.0	8.0	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	hg19	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.068103	0.36470	.	.	ENSG00000136928	ENST00000259455	D	0.82433	-1.61	3.14	3.14	0.36123	Extracellular ligand-binding receptor (1);	0.456021	0.15896	U	0.239283	T	0.61986	0.2391	L	0.27053	0.805	0.37013	D	0.895826	P	0.38078	0.617	B	0.20184	0.028	T	0.61662	-0.7017	10	0.12766	T	0.61	.	6.0632	0.19848	0.0:0.857:0.0:0.143	.	91	O75899	GABR2_HUMAN	K	91	ENSP00000259455:E91K	ENSP00000259455:E91K	E	-	1	0	GABBR2	100510570	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.543000	0.53633	1.605000	0.50152	0.456000	0.33151	GAG	.	.		0.677	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			T	101470749	C	T	101470749	3	4	178	1	0	0	0	0	1	0	0	0	6164	893	31	1	2630	1	GABBR2	9	101470749	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	414637	101470749	39742682	64	26765										
SUSD1	64420	hgsc.bcm.edu	37	chr9	114840897	114840897	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctgacattgtagttggtaccCggacgtaggtccaagcacac	11	11	0	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr9:114840897C>T	ENST00000374270.3	-	12	1846	c.1674G>A	c.(1672-1674)ccG>ccA	p.P558P	SUSD1_ENST00000374264.2_Silent_p.P558P|SUSD1_ENST00000374263.3_Silent_p.P558P	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	558						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AGTTGGTACCCGGACGTAGGT	0.493																																					p.P558P		Atlas-SNP	.											.	SUSD1	51	.	0			c.G1674A						.						149	143	145					9																	114840897		2203	4300	6503	SO:0001819	synonymous_variant	64420	exon12			GGTACCCGGACGT	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1674G>A	chr9.hg19:g.114840897C>T		185.0	0.0		167.0	42.0	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Silent	SNP	ENST00000374270.3	hg19	CCDS6783.1	.	.	.	.	.	.	.	.	.	.	c	0.249	-1.007695	0.02112	.	.	ENSG00000106868	ENST00000355396	.	.	.	4.96	-2.95	0.05564	.	.	.	.	.	T	0.28896	0.0717	.	.	.	0.30697	N	0.750688	.	.	.	.	.	.	T	0.40683	-0.9550	4	.	.	.	-2.7763	5.3316	0.15936	0.1519:0.2489:0.0:0.5992	.	.	.	.	R	542	.	.	G	-	1	0	SUSD1	113880718	0.392000	0.25229	0.010000	0.14722	0.093000	0.18481	-0.895000	0.04118	-0.407000	0.07576	0.645000	0.84053	GGG	.	.		0.493	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		T	114840897	C	T	114840897	2	4	178	1	0	0	0	0	0	0	0	1	15422	639	23	1		1	SUSD1	9	114840897	Silent	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	13370148	114840897	26372534	65	26766										
CUBN	8029	hgsc.bcm.edu	37	chr10	16982125	16982125	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ccaacgatggaagaataattGagagggaaggagtttccaca	12	6	0	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr10:16982125G>T	ENST00000377833.4	-	37	5519	c.5454C>A	c.(5452-5454)ctC>ctA	p.L1818L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1818	CUB 12. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AAGAATAATTGAGAGGGAAGG	0.498																																					p.L1818L		Atlas-SNP	.											.	CUBN	515	.	0			c.C5454A						.						183	189	187					10																	16982125		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon37			ATAATTGAGAGGG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.5454C>A	chr10.hg19:g.16982125G>T		157.0	0.0		162.0	21.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.		0.498	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	16982125	G	T	16982125	2	4	178	1	0	0	0	0	0	0	0	1	4053	1277	45	3		3	CUBN	10	16982125	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10		16982125	118552622	66	26767										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64974046	64974046	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tgagtatctactgaagtattAagtttagattttatagtctc	7	4	2	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr10:64974046A>C	ENST00000399262.2	-	8	2099	c.1881T>G	c.(1879-1881)ctT>ctG	p.L627L	JMJD1C_ENST00000402544.1_Silent_p.L408L|JMJD1C_ENST00000542921.1_Silent_p.L445L|JMJD1C_ENST00000489372.2_5'Flank|JMJD1C_ENST00000399251.1_Silent_p.L408L	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	627					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					CTGAAGTATTAAGTTTAGATT	0.373																																					p.L627L		Atlas-SNP	.											.	JMJD1C	347	.	0			c.T1881G						.						121	109	113					10																	64974046		1840	4092	5932	SO:0001819	synonymous_variant	221037	exon8			AGTATTAAGTTTA	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.1881T>G	chr10.hg19:g.64974046A>C		114.0	0.0		69.0	15.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Silent	SNP	ENST00000399262.2	hg19	CCDS41532.1																																																																																			.	.		0.373	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		C	64974046	A	C	64974046	2	2	178	1	0	0	0	0	0	0	0	1	7959	349	13	5		5	JMJD1C	10	64974046	Silent	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	47991921	64974046	70560701	67	26768										
NUDT13	25961	hgsc.bcm.edu	37	chr10	74874164	74874164	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	agcttgcaggagaaaattttTttggtgctataggctgctgt	12	5	0	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr10:74874164T>C	ENST00000357321.4	+	2	159	c.41T>C	c.(40-42)tTt>tCt	p.F14S	NUDT13_ENST00000372997.3_Missense_Mutation_p.F14S|NUDT13_ENST00000544879.1_5'UTR|NUDT13_ENST00000537969.1_5'UTR|NUDT13_ENST00000349051.5_Missense_Mutation_p.F14S|NUDT13_ENST00000488223.1_3'UTR	NM_001283016.1|NM_015901.4	NP_001269945.1|NP_056985.3			nudix (nucleoside diphosphate linked moiety X)-type motif 13											large_intestine(2)|lung(5)	7	Prostate(51;0.0119)					AGAAAATTTTTTTGGTGCTAT	0.338																																					p.F14S		Atlas-SNP	.											.	NUDT13	16	.	0			c.T41C						.						99	98	99					10																	74874164		2203	4300	6503	SO:0001583	missense	25961	exon2			AATTTTTTTGGTG	AL050114	CCDS31220.1, CCDS60551.1, CCDS60552.1, CCDS60553.1, CCDS73148.1	10q22.3	2014-04-24			ENSG00000166321	ENSG00000166321		"Nudix motif containing"	18827	protein-coding gene	gene with protein product		609233				15164054	Standard	NM_001283019		Approved	DKFZp586P2219	uc001jtj.3	Q86X67	OTTHUMG00000018453	ENST00000357321.4:c.41T>C	chr10.hg19:g.74874164T>C	ENSP00000349874:p.Phe14Ser	63.0	0.0		84.0	8.0	NM_015901		Missense_Mutation	SNP	ENST00000357321.4	hg19	CCDS31220.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.482330	0.26598	.	.	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000372997	T;T;T	0.30182	2.04;1.61;1.54	5.16	-0.359	0.12571	.	1.064120	0.07258	N	0.867050	T	0.15132	0.0365	N	0.14661	0.345	0.09310	N	0.999993	B;B;B	0.12013	0.005;0.001;0.001	B;B;B	0.12156	0.007;0.002;0.0	T	0.29119	-1.0022	10	0.37606	T	0.19	.	1.6738	0.02817	0.1685:0.0972:0.3483:0.386	.	14;14;14	Q86X67-2;Q5SQM6;Q86X67	.;.;NUD13_HUMAN	S	14	ENSP00000349874:F14S;ENSP00000335326:F14S;ENSP00000362088:F14S	ENSP00000335326:F14S	F	+	2	0	NUDT13	74544170	0.388000	0.25197	0.768000	0.31515	0.796000	0.44982	0.045000	0.14013	0.302000	0.22762	0.533000	0.62120	TTT	.	.		0.338	NUDT13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048614.1	NM_015901		C	74874164	T	C	74874164	3	2	178	1	0	0	0	0	1	0	0	0	10738	1841	64	2	43	2	NUDT13	10	74874164	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	9900118	74874164	60660583	68	26769										
CPEB3	22849	hgsc.bcm.edu	37	chr10	93999237	93999237	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ggagaagggctttttgagcgGcgagatggggttgagcgggg	22	4	0	4			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr10:93999237G>A	ENST00000265997.4	-	2	1043	c.871C>T	c.(871-873)Ccg>Tcg	p.P291S	CPEB3_ENST00000412050.4_Missense_Mutation_p.P291S	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	291					3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				TTTTTGAGCGGCGAGATGGGG	0.697																																					p.P291S		Atlas-SNP	.											.	CPEB3	43	.	0			c.C871T						.						36	36	36					10																	93999237		2201	4298	6499	SO:0001583	missense	22849	exon2			TGAGCGGCGAGAT	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.871C>T	chr10.hg19:g.93999237G>A	ENSP00000265997:p.Pro291Ser	270.0	0.0		196.0	40.0	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	hg19	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.123376	0.77436	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.59224	0.28;0.3	3.7	3.7	0.42460	.	0.000000	0.85682	D	0.000000	T	0.68128	0.2967	L	0.41492	1.28	0.58432	D	0.999994	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.992;0.996	T	0.73257	-0.4040	10	0.87932	D	0	-6.759	16.0095	0.80391	0.0:0.0:1.0:0.0	.	291;291;291	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	S	291	ENSP00000398310:P291S;ENSP00000265997:P291S	ENSP00000265997:P291S	P	-	1	0	CPEB3	93989217	1.000000	0.71417	0.997000	0.53966	0.748000	0.42578	9.593000	0.98250	2.059000	0.61396	0.462000	0.41574	CCG	.	.		0.697	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		A	93999237	G	A	93999237	3	1	178	1	0	0	0	0	1	0	0	0	3804	1203	42	3	1288	3	CPEB3	10	93999237	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	19125073	93999237	41535510	69	26770										
SFRP5	6425	hgsc.bcm.edu	37	chr10	99527515	99527515	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ccagccgcttggtgtccttgCgcttcagggggcccggcttg	15	14	1	0	rs144307831		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr10:99527515C>T	ENST00000266066.3	-	3	828	c.710G>A	c.(709-711)cGc>cAc	p.R237H		NM_003015.3	NP_003006.2	Q5T4F7	SFRP5_HUMAN	secreted frizzled-related protein 5	237	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cell differentiation (GO:0030154)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|establishment or maintenance of cell polarity (GO:0007163)|gonad development (GO:0008406)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of Wnt signaling pathway involved in digestive tract morphogenesis (GO:2000057)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|post-anal tail morphogenesis (GO:0036342)|signal transduction (GO:0007165)|vasculature development (GO:0001944)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			large_intestine(1)|lung(4)	5		Colorectal(252;0.234)		Epithelial(162;4.98e-10)|all cancers(201;3.58e-08)		GGTGTCCTTGCGCTTCAGGGG	0.607																																					p.R237H		Atlas-SNP	.											.	SFRP5	32	.	0			c.G710A						.	C	HIS/ARG	0,4406		0,0,2203	53	58	56		710	5.7	1	10	dbSNP_134	56	1,8599	1.2+/-3.3	0,1,4299	no	missense	SFRP5	NM_003015.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	237/318	99527515	1,13005	2203	4300	6503	SO:0001583	missense	6425	exon3			TCCTTGCGCTTCA	AF017988	CCDS7472.1	10q24	2008-07-10			ENSG00000120057	ENSG00000120057		"Secreted frizzled-related proteins"	10779	protein-coding gene	gene with protein product	"secreted apoptosis related protein 3"	604158				9391078	Standard	NM_003015		Approved	SARP3	uc001kor.4	Q5T4F7	OTTHUMG00000018866	ENST00000266066.3:c.710G>A	chr10.hg19:g.99527515C>T	ENSP00000266066:p.Arg237His	83.0	0.0		69.0	14.0	NM_003015	O14780|Q86TH7	Missense_Mutation	SNP	ENST00000266066.3	hg19	CCDS7472.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.495903	0.85069	0.0	1.16E-4	ENSG00000120057	ENST00000266066	T	0.29917	1.55	5.74	5.74	0.90152	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.107337	0.64402	D	0.000019	T	0.53642	0.1809	L	0.54323	1.7	0.47214	D	0.999356	D	0.89917	1.0	D	0.74023	0.982	T	0.50709	-0.8796	10	0.62326	D	0.03	.	19.9077	0.97014	0.0:1.0:0.0:0.0	.	237	Q5T4F7	SFRP5_HUMAN	H	237	ENSP00000266066:R237H	ENSP00000266066:R237H	R	-	2	0	SFRP5	99517505	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.033000	0.57282	2.712000	0.92718	0.561000	0.74099	CGC	.	C|1.000;T|0.000		0.607	SFRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049742.1	NM_003015		T	99527515	C	T	99527515	3	4	178	1	0	0	0	0	1	0	0	0	14179	768	27	1	247	1	SFRP5	10	99527515	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	5528278	99527515	36007232	70	26771										
LZTS2	84445	hgsc.bcm.edu	37	chr10	102766667	102766667	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ttgcgggtggagctgcagcgGgagcggcggcggggtgagga	24	7	0	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr10:102766667G>T	ENST00000370220.1	+	4	4815	c.1752G>T	c.(1750-1752)cgG>cgT	p.R584R	LZTS2_ENST00000370223.3_Silent_p.R584R					leucine zipper, putative tumor suppressor 2											breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		AGCTGCAGCGGGAGCGGCGGC	0.692																																					p.R584R	Esophageal Squamous(8;38 437 13604 19902 37640)	Atlas-SNP	.											.	LZTS2	57	.	0			c.G1752T						.						16	12	13					10																	102766667		2121	4171	6292	SO:0001819	synonymous_variant	84445	exon5			GCAGCGGGAGCGG	AB058716	CCDS7507.1	10q24	2004-03-18			ENSG00000107816	ENSG00000107816			29381	protein-coding gene	gene with protein product		610454				11347906, 11709705	Standard	NM_032429		Approved	KIAA1813, LAPSER1	uc001ksj.3	Q9BRK4	OTTHUMG00000018914	ENST00000370220.1:c.1752G>T	chr10.hg19:g.102766667G>T		185.0	0.0		138.0	9.0	NM_032429		Silent	SNP	ENST00000370220.1	hg19	CCDS7507.1																																																																																			.	.		0.692	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743		T	102766667	G	T	102766667	2	4	178	1	0	0	0	0	0	0	0	1	9148	1219	43	3		3	LZTS2	10	102766667	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	3239152	102766667	32768080	71	26772										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6578767	6578767	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tctcaaactccagagatccaAgtctaacaccatccatagga	5	13	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr11:6578767A>G	ENST00000527990.2	+	23	8242	c.8242A>G	c.(8242-8244)Agt>Ggt	p.S2748G	DNHD1_ENST00000254579.6_Missense_Mutation_p.S2748G			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2748					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CAGAGATCCAAGTCTAACACC	0.498																																					p.S2748G		Atlas-SNP	.											.	DNHD1	198	.	0			c.A8242G						.						69	69	69					11																	6578767		692	1591	2283	SO:0001583	missense	144132	exon25			GATCCAAGTCTAA	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.8242A>G	chr11.hg19:g.6578767A>G	ENSP00000436180:p.Ser2748Gly	136.0	0.0		108.0	11.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	A	0.017	-1.508617	0.00984	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210	T;T	0.26373	1.74;1.74	4.55	-5.93	0.02254	.	.	.	.	.	T	0.09291	0.0229	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.11329	0.001;0.006	T	0.39643	-0.9604	9	0.13108	T	0.6	.	6.8744	0.24139	0.4689:0.0:0.4111:0.1201	.	2748;495	Q96M86;E9PHZ7	DNHD1_HUMAN;.	G	2748;2748;495	ENSP00000254579:S2748G;ENSP00000436180:S2748G	ENSP00000254579:S2748G	S	+	1	0	DNHD1	6535343	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.076000	0.03420	-0.957000	0.03627	0.454000	0.30748	AGT	.	.		0.498	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		G	6578767	A	G	6578767	3	3	178	1	0	0	0	0	1	0	0	0	4670	72	3	2	8341	2	DNHD1	11	6578767	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10		6578767	128427749	72	26773										
MICAL2	9645	hgsc.bcm.edu	37	chr11	12237867	12237867	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	acaaaggtgtcatcattaacGtacgtacctcttggctgcga	9	10	3	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr11:12237867G>T	ENST00000256194.4	+	8	1236		c.e8+1		MICAL2_ENST00000537344.1_Splice_Site|MICAL2_ENST00000379612.3_Splice_Site|MICAL2_ENST00000527546.1_Splice_Site|MICAL2_ENST00000342902.5_Splice_Site	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2						actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)	p.?(1)		breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		CATCATTAACGTACGTACCTC	0.507																																					.		Atlas-SNP	.											MICAL2_ENST00000379612,NS,carcinoma,0,2	MICAL2	114	.	1	Unknown(1)	endometrium(1)	c.948+1G>T						.						149	109	122					11																	12237867		2201	4294	6495	SO:0001630	splice_region_variant	9645	exon8			ATTAACGTACGTA	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.948+1G>T	chr11.hg19:g.12237867G>T		50.0	0.0		73.0	12.0	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Splice_Site	SNP	ENST00000256194.4	hg19	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	G	32	5.183917	0.94885	.	.	ENSG00000133816	ENST00000537344;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.19	0.89804	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MICAL2	12194443	1.000000	0.71417	0.116000	0.21606	0.770000	0.43624	9.628000	0.98415	2.620000	0.88729	0.563000	0.77884	.	.	.		0.507	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	Intron	T	12237867	G	T	12237867	5	4	178	1	0	0	0	0	0	0	1	0	9579	1159	40	1	971	1	MICAL2	11	12237867	Splice_Site	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	5659100	12237867	122768649	73	26774										
TSG101	7251	hgsc.bcm.edu	37	chr11	18503415	18503415	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctatgtttttatcaacctcgGcctgaaaacagaacagtcca	6	11	1	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr11:18503415G>C	ENST00000251968.3	-	9	1260	c.845C>G	c.(844-846)gCc>gGc	p.A282G	TSG101_ENST00000357193.3_Splice_Site_p.A177G|TSG101_ENST00000536719.1_Splice_Site_p.A282G	NM_006292.3	NP_006283.1	Q99816	TS101_HUMAN	tumor susceptibility 101	282					cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cellular protein modification process (GO:0006464)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|keratinocyte differentiation (GO:0030216)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell growth (GO:0001558)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral budding (GO:0046755)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transcription corepressor activity (GO:0003714)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	22						ATCAACCTCGGCCTGAAAACA	0.363																																					p.A282G	GBM(99;1348 1396 8611 26475 50572)	Atlas-SNP	.											.	TSG101	43	.	0			c.C845G						.						75	75	75					11																	18503415		2199	4293	6492	SO:0001630	splice_region_variant	7251	exon9			ACCTCGGCCTGAA	U82130	CCDS7842.1	11p15	2013-08-22	2013-08-22		ENSG00000074319	ENSG00000074319			15971	protein-coding gene	gene with protein product		601387	"tumor susceptibility gene 10", "tumor susceptibility gene 101"	TSG10		9019400, 9241264	Standard	NM_006292		Approved	VPS23	uc001mor.3	Q99816	OTTHUMG00000167725	ENST00000251968.3:c.844-1C>G	chr11.hg19:g.18503415G>C		71.0	0.0		59.0	10.0	NM_006292	Q9BUM5	Missense_Mutation	SNP	ENST00000251968.3	hg19	CCDS7842.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.938616	0.52972	.	.	ENSG00000074319	ENST00000536719;ENST00000251968;ENST00000357193	T;T;T	0.22134	1.97;1.97;1.97	5.97	5.05	0.67936	.	0.051891	0.85682	D	0.000000	T	0.25082	0.0609	M	0.76002	2.32	0.51767	D	0.99993	B	0.18310	0.027	B	0.13407	0.009	T	0.02484	-1.1152	10	0.24483	T	0.36	-18.221	12.9128	0.58189	0.0743:0.0:0.9257:0.0	.	282	Q99816	TS101_HUMAN	G	282;282;177	ENSP00000438471:A282G;ENSP00000251968:A282G;ENSP00000349721:A177G	ENSP00000251968:A282G	A	-	2	0	TSG101	18459991	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.259000	0.65485	2.828000	0.97474	0.655000	0.94253	GCC	.	.		0.363	TSG101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395906.1	NM_006292	Missense_Mutation	C	18503415	G	C	18503415	5	2	178	1	0	0	0	0	0	0	1	0	16631	1217	42	4	335	4	TSG101	11	18503415	Splice_Site	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	6265548	18503415	116503101	74	26775										
SLC17A6	57084	hgsc.bcm.edu	37	chr11	22364853	22364853	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tccacggttccttcttttggGgctacatcatcactcagatt	7	12	4	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr11:22364853G>A	ENST00000263160.3	+	3	837	c.400G>A	c.(400-402)Ggc>Agc	p.G134S		NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	134					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						CTTCTTTTGGGGCTACATCAT	0.562																																					p.G134S		Atlas-SNP	.											.	SLC17A6	135	.	0			c.G400A						.						88	92	91					11																	22364853		2203	4300	6503	SO:0001583	missense	57084	exon3			TTTTGGGGCTACA	AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"Solute carriers"	16703	protein-coding gene	gene with protein product	"vesicular glutamate transporter 2", "differentiation-associated Na-dependent inorganic phosphate cotransporter"	607563	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.400G>A	chr11.hg19:g.22364853G>A	ENSP00000263160:p.Gly134Ser	92.0	0.0		87.0	29.0	NM_020346	A6NKS2	Missense_Mutation	SNP	ENST00000263160.3	hg19	CCDS7856.1	.	.	.	.	.	.	.	.	.	.	G	36	5.754943	0.96898	.	.	ENSG00000091664	ENST00000263160;ENST00000546171	T	0.61627	0.09	5.4	5.4	0.78164	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.84977	0.5592	H	0.96604	3.85	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	D	0.90068	0.4161	10	0.87932	D	0	.	19.1827	0.93629	0.0:0.0:1.0:0.0	.	134	Q9P2U8	VGLU2_HUMAN	S	134;22	ENSP00000263160:G134S	ENSP00000263160:G134S	G	+	1	0	SLC17A6	22321429	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.517000	0.84864	0.655000	0.94253	GGC	.	.		0.562	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		A	22364853	G	A	22364853	3	1	178	1	0	0	0	0	1	0	0	0	14436	1232	43	3	410	3	SLC17A6	11	22364853	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	3861438	22364853	112641663	75	26776										
OR5J2	282775	hgsc.bcm.edu	37	chr11	55944930	55944930	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gtggtttctatgttctatacGctagggattcccatgttaaa	9	7	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr11:55944930G>A	ENST00000312298.1	+	1	837	c.837G>A	c.(835-837)acG>acA	p.T279T		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	279						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	44	Esophageal squamous(21;0.00693)					TGTTCTATACGCTAGGGATTC	0.403																																					p.T279T		Atlas-SNP	.											OR5J2,NS,carcinoma,0,1	OR5J2	98	.	0			c.G837A						.						98	100	99					11																	55944930		2201	4296	6497	SO:0001819	synonymous_variant	282775	exon1			CTATACGCTAGGG	AB065595	CCDS31522.1	11q11	2012-08-09			ENSG00000174957	ENSG00000174957		"GPCR / Class A : Olfactory receptors"	19612	protein-coding gene	gene with protein product							Standard	NM_001005492		Approved		uc010rjb.2	Q8NH18	OTTHUMG00000166835	ENST00000312298.1:c.837G>A	chr11.hg19:g.55944930G>A		55.0	0.0		42.0	7.0	NM_001005492	Q6IEU5	Silent	SNP	ENST00000312298.1	hg19	CCDS31522.1																																																																																			.	.		0.403	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492		A	55944930	G	A	55944930	2	1	178	1	0	0	0	0	0	0	0	1	11174	1074	38	1		1	OR5J2	11	55944930	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	33580077	55944930	79061586	76	26777										
MRPL48	51642	hgsc.bcm.edu	37	chr11	73555916	73555916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ggggacagattatgaatatgGggttttaaatattcatctga	11	3	2	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr11:73555916G>A	ENST00000310614.7	+	5	922	c.266G>A	c.(265-267)gGg>gAg	p.G89E	MRPL48_ENST00000314282.7_5'UTR|MRPL48_ENST00000411840.2_5'UTR|MRPL48_ENST00000398483.3_5'UTR|MRPL48_ENST00000535529.1_Missense_Mutation_p.G71E|MRPL48_ENST00000542303.1_Intron	NM_016055.5	NP_057139.1	Q96GC5	RM48_HUMAN	mitochondrial ribosomal protein L48	89						mitochondrial ribosome (GO:0005761)				kidney(1)	1						TATGAATATGGGGTTTTAAAT	0.393																																					p.G89E		Atlas-SNP	.											.	MRPL48	16	.	0			c.G266A						.						86	81	83					11																	73555916		1833	4077	5910	SO:0001583	missense	51642	exon5			AATATGGGGTTTT	AF151876	CCDS44676.1	11q13.4	2012-09-13			ENSG00000175581	ENSG00000175581		"Mitochondrial ribosomal proteins / large subunits"	16653	protein-coding gene	gene with protein product		611853				10810093	Standard	NM_016055		Approved	CGI-118	uc001ouh.4	Q96GC5	OTTHUMG00000168048	ENST00000310614.7:c.266G>A	chr11.hg19:g.73555916G>A	ENSP00000308717:p.Gly89Glu	105.0	0.0		112.0	38.0	NM_016055	B4DN34|Q49AK7|Q4U2Q4|Q9P091|Q9Y5J0	Missense_Mutation	SNP	ENST00000310614.7	hg19	CCDS44676.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.352154	0.82132	.	.	ENSG00000175581	ENST00000310614;ENST00000535529	T	0.44881	0.91	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.66197	0.2765	M	0.80847	2.515	0.58432	D	0.999999	D;D	0.89917	0.973;1.0	P;D	0.97110	0.845;1.0	T	0.63752	-0.6566	10	0.29301	T	0.29	-17.9086	16.9469	0.86232	0.0:0.0:1.0:0.0	.	71;89	B4DN34;Q96GC5	.;RM48_HUMAN	E	89;71	ENSP00000308717:G89E	ENSP00000308717:G89E	G	+	2	0	MRPL48	73233564	1.000000	0.71417	0.978000	0.43139	0.994000	0.84299	7.888000	0.87302	2.600000	0.87896	0.591000	0.81541	GGG	.	.		0.393	MRPL48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397733.1	NM_016055		A	73555916	G	A	73555916	3	1	178	1	0	0	0	0	1	0	0	0	9821	1232	43	3	284	3	MRPL48	11	73555916	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	17610986	73555916	61450600	77	26778										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103191757	103191757	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	agtgtttttttaaaattataGgtgccaaagatgtacaatgg	9	3	0	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr11:103191757G>T	ENST00000375735.2	+	81	11869		c.e81-1		DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Splice_Site	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TAAAATTATAGGTGCCAAAGA	0.284																																					.		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.11747-1G>T						.						50	46	48					11																	103191757		1790	4063	5853	SO:0001630	splice_region_variant	79659	exon82			ATTATAGGTGCCA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.11726-1G>T	chr11.hg19:g.103191757G>T		185.0	0.0		179.0	32.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Splice_Site	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.843950	0.71488	.	.	ENSG00000187240	ENST00000375735;ENST00000398093;ENST00000540621	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6123	0.95613	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DYNC2H1	102696967	1.000000	0.71417	0.995000	0.50966	0.783000	0.44284	9.230000	0.95299	2.647000	0.89833	0.650000	0.86243	.	.	.		0.284	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	Intron	T	103191757	G	T	103191757	5	4	178	1	0	0	0	0	0	0	1	0	4848	1014	35	3	12072	3	DYNC2H1	11	103191757	Splice_Site	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	29635841	103191757	31814759	78	26779										
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118502074	118502074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cctcacgaggccttgcagggGcctctgggcggagcagcgag	17	13	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr11:118502074G>A	ENST00000361417.2	+	8	2389	c.1978G>A	c.(1978-1980)Gcc>Acc	p.A660T	PHLDB1_ENST00000356063.5_Missense_Mutation_p.A660T|PHLDB1_ENST00000534672.1_3'UTR	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	660										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CCTTGCAGGGGCCTCTGGGCG	0.657																																					p.A660T		Atlas-SNP	.											.	PHLDB1	103	.	0			c.G1978A						.						29	32	31					11																	118502074		2200	4295	6495	SO:0001583	missense	23187	exon7			GCAGGGGCCTCTG		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.1978G>A	chr11.hg19:g.118502074G>A	ENSP00000354498:p.Ala660Thr	91.0	0.0		86.0	18.0	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	hg19	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	G	11.32	1.602800	0.28534	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000356063	T;T	0.27720	1.65;1.65	4.41	2.47	0.30058	.	1.532650	0.03390	N	0.201655	T	0.18964	0.0455	N	0.14661	0.345	0.09310	N	0.999999	B;B;B;B	0.19200	0.0;0.0;0.034;0.023	B;B;B;B	0.19391	0.0;0.001;0.025;0.021	T	0.23547	-1.0185	10	0.13470	T	0.59	-1.0907	6.1347	0.20225	0.1053:0.1907:0.7041:0.0	.	404;660;660;660	Q5W9G0;Q86UU1-3;Q86UU1-2;Q86UU1	.;.;.;PHLB1_HUMAN	T	660;419;660	ENSP00000354498:A660T;ENSP00000348359:A660T	ENSP00000348359:A660T	A	+	1	0	PHLDB1	118007284	0.001000	0.12720	0.217000	0.23759	0.962000	0.63368	0.677000	0.25262	0.408000	0.25621	0.555000	0.69702	GCC	.	.		0.657	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		A	118502074	G	A	118502074	3	1	178	1	0	0	0	0	1	0	0	0	11860	1203	42	3	2000	3	PHLDB1	11	118502074	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	15310317	118502074	16504442	79	26780										
LAG3	3902	hgsc.bcm.edu	37	chr12	6887023	6887023	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cctcctgctgtttctcatccTtggtgtcctttctctgctcc	6	16	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr12:6887023T>G	ENST00000203629.2	+	7	1700	c.1367T>G	c.(1366-1368)cTt>cGt	p.L456R		NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	456					cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TTTCTCATCCTTGGTGTCCTT	0.587																																					p.L456R		Atlas-SNP	.											.	LAG3	35	.	0			c.T1367G						.						126	120	122					12																	6887023		2203	4300	6503	SO:0001583	missense	3902	exon7			TCATCCTTGGTGT		CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.1367T>G	chr12.hg19:g.6887023T>G	ENSP00000203629:p.Leu456Arg	42.0	0.0		26.0	7.0	NM_002286	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	hg19	CCDS8561.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.429950	0.62844	.	.	ENSG00000089692	ENST00000203629	T	0.22743	1.94	5.32	5.32	0.75619	.	0.112768	0.40469	N	0.001097	T	0.43787	0.1263	M	0.69823	2.125	0.40676	D	0.982269	D	0.89917	1.0	D	0.81914	0.995	T	0.41233	-0.9520	10	0.52906	T	0.07	-17.4235	11.6703	0.51396	0.0:0.0:0.0:1.0	.	456	P18627	LAG3_HUMAN	R	456	ENSP00000203629:L456R	ENSP00000203629:L456R	L	+	2	0	LAG3	6757284	0.749000	0.28305	0.679000	0.29978	0.011000	0.07611	2.254000	0.43214	2.023000	0.59567	0.374000	0.22700	CTT	.	.		0.587	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1			G	6887023	T	G	6887023	3	3	178	1	0	0	0	0	1	0	0	0	8609	1609	56	5	1393	5	LAG3	12	6887023	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10		6887023	126964872	80	26781										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26709308	26709308	+	Splice_Site	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctccaaggaggccactacatCctagggaatgaaacacaaga	9	11	0	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr12:26709308C>G	ENST00000381340.3	-	36	5238	c.4822G>C	c.(4822-4824)Gat>Cat	p.D1608H		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1608					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GCCACTACATCCTAGGGAATG	0.433																																					p.D1608H		Atlas-SNP	.											.	ITPR2	270	.	0			c.G4822C						.						86	81	82					12																	26709308		1946	4152	6098	SO:0001630	splice_region_variant	3709	exon36			CTACATCCTAGGG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4822-1G>C	chr12.hg19:g.26709308C>G		80.0	0.0		58.0	8.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518550	0.44763	.	.	ENSG00000123104	ENST00000381340	T	0.70749	-0.51	5.17	5.17	0.71159	.	0.048114	0.85682	D	0.000000	T	0.81894	0.4919	M	0.75884	2.315	0.80722	D	1	D	0.55385	0.971	P	0.58454	0.839	T	0.82121	-0.0614	10	0.42905	T	0.14	.	18.6621	0.91474	0.0:1.0:0.0:0.0	.	1608	Q14571	ITPR2_HUMAN	H	1608	ENSP00000370744:D1608H	ENSP00000370744:D1608H	D	-	1	0	ITPR2	26600575	1.000000	0.71417	0.998000	0.56505	0.287000	0.27160	5.654000	0.67974	2.404000	0.81709	0.491000	0.48974	GAT	.	.		0.433	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	Missense_Mutation	G	26709308	C	G	26709308	5	3	178	1	0	0	0	0	0	0	1	0	7930	869	30	4	3371	4	ITPR2	12	26709308	Splice_Site	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	19822285	26709308	107142587	81	26782										
SLC38A2	54407	hgsc.bcm.edu	37	chr12	46764378	46764378	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	atcgcattgctcagattaaaTactgacattccaaaggaagt	7	8	1	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr12:46764378T>C	ENST00000256689.5	-	4	675	c.231A>G	c.(229-231)gtA>gtG	p.V77V	SLC38A2_ENST00000547252.1_5'UTR|RP11-474P2.2_ENST00000550319.1_RNA	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	77	Regulates protein turnover upon amino acid deprivation. {ECO:0000250}.				amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		TCAGATTAAATACTGACATTC	0.378																																					p.V77V	Ovarian(9;448 492 8335 28722 40361)	Atlas-SNP	.											.	SLC38A2	36	.	0			c.A231G						.						124	117	119					12																	46764378		2203	4300	6503	SO:0001819	synonymous_variant	54407	exon4			ATTAAATACTGAC	AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"Solute carriers"	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.231A>G	chr12.hg19:g.46764378T>C		200.0	0.0		183.0	40.0	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Silent	SNP	ENST00000256689.5	hg19	CCDS8749.1																																																																																			.	.		0.378	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1			C	46764378	T	C	46764378	2	2	178	1	0	0	0	0	0	0	0	1	14619	1393	49	2		2	SLC38A2	12	46764378	Silent	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	20055070	46764378	87087517	82	26783										
LASS5	91012	hgsc.bcm.edu	37	chr12	50524462	50524462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gctgctctccacatcactgcGatcatccttcgatacctggg	8	15	3	0	rs373121500		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr12:50524462G>A	ENST00000317551.6	-	10	1169	c.1045C>T	c.(1045-1047)Cgc>Tgc	p.R349C	CERS5_ENST00000422340.2_Missense_Mutation_p.R291C	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	349					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										ACATCACTGCGATCATCCTTC	0.512																																					p.R349C		Atlas-SNP	.											LASS5,colon,carcinoma,0,1	.	.	.	0			c.C1045T						.	G	CYS/ARG	0,4406		0,0,2203	165	129	141		1045	5.1	1	12		141	1,8599	1.2+/-3.3	0,1,4299	no	missense	CERS5	NM_147190.2	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	349/393	50524462	1,13005	2203	4300	6503	SO:0001583	missense	91012	exon10			CACTGCGATCATC		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"Homeoboxes / CERS class"	23749	protein-coding gene	gene with protein product		615335	"LAG1 longevity assurance homolog 5 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 5"	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.1045C>T	chr12.hg19:g.50524462G>A	ENSP00000325485:p.Arg349Cys	51.0	0.0		58.0	14.0	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	hg19	CCDS8801.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.832123	0.91036	0.0	1.16E-4	ENSG00000139624	ENST00000317551;ENST00000550919;ENST00000422340	T;T	0.19938	2.28;2.11	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.65749	0.2721	H	0.98507	4.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.951	T	0.80165	-0.1496	10	0.87932	D	0	-6.0999	19.1018	0.93276	0.0:0.0:1.0:0.0	.	291;349	B4DV54;Q8N5B7	.;CERS5_HUMAN	C	349;66;291	ENSP00000325485:R349C;ENSP00000389050:R291C	ENSP00000325485:R349C	R	-	1	0	CERS5	48810729	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.493000	0.81493	2.828000	0.97474	0.650000	0.86243	CGC	.	.		0.512	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190		A	50524462	G	A	50524462	3	1	178	1	0	0	0	0	1	0	0	0	8651	1058	37	1	137	1	LASS5	12	50524462	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	3760084	50524462	83327433	83	26784										
ZDHHC17	23390	hgsc.bcm.edu	37	chr12	77208983	77208983	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	taatgtgggcagcatatagaAcacataggtatgtaatgact	10	5	0	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr12:77208983A>G	ENST00000426126.2	+	6	1250	c.601A>G	c.(601-603)Aca>Gca	p.T201A	ZDHHC17_ENST00000334822.5_Missense_Mutation_p.T201A|ZDHHC17_ENST00000359019.4_Missense_Mutation_p.T151A	NM_015336.2	NP_056151.2	Q8IUH5	ZDH17_HUMAN	zinc finger, DHHC-type containing 17	201					lipoprotein transport (GO:0042953)|magnesium ion transport (GO:0015693)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein palmitoylation (GO:0018345)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(3)|liver(2)|lung(14)	23						AGCATATAGAACACATAGGTA	0.308																																					p.T201A		Atlas-SNP	.											.	ZDHHC17	45	.	0			c.A601G						.						46	47	46					12																	77208983		1829	4068	5897	SO:0001583	missense	23390	exon6			TATAGAACACATA	AB023163	CCDS44946.1	12q21.2	2013-01-10				ENSG00000186908		"Zinc fingers, DHHC-type", "Ankyrin repeat domain containing"	18412	protein-coding gene	gene with protein product		607799				9700202, 18794299	Standard	NM_015336		Approved	HIP14, HYPH, KIAA0946	uc001syk.1	Q8IUH5	OTTHUMG00000169917	ENST00000426126.2:c.601A>G	chr12.hg19:g.77208983A>G	ENSP00000403397:p.Thr201Ala	94.0	0.0		93.0	22.0	NM_015336	B4DR39|O75407|Q7Z2I0|Q86W89|Q86YK0|Q9P088|Q9UPZ8	Missense_Mutation	SNP	ENST00000426126.2	hg19	CCDS44946.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.712767	0.68730	.	.	ENSG00000186908	ENST00000426126;ENST00000334822;ENST00000359019;ENST00000550876	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	5.49	5.49	0.81192	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.29850	0.0746	N	0.03930	-0.32	0.80722	D	1	B	0.20550	0.046	B	0.27715	0.082	T	0.16335	-1.0406	10	0.51188	T	0.08	-14.306	15.5869	0.76491	1.0:0.0:0.0:0.0	.	201	Q8IUH5	ZDH17_HUMAN	A	201;201;151;38	ENSP00000403397:T201A;ENSP00000334868:T201A;ENSP00000351913:T151A;ENSP00000449734:T38A	ENSP00000334868:T201A	T	+	1	0	ZDHHC17	75733114	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.065000	0.93941	2.084000	0.62774	0.455000	0.32223	ACA	.	.		0.308	ZDHHC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406555.1	NM_015336		G	77208983	A	G	77208983	3	3	178	1	0	0	0	0	1	0	0	0	17622	43	2	2	623	2	ZDHHC17	12	77208983	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	26684521	77208983	56642912	84	26785										
ANO4	121601	hgsc.bcm.edu	37	chr12	101381411	101381411	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cagacctggaggagaatgacTgctacactgcccctttcagc	10	13	1	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr12:101381411T>A	ENST00000392977.3	+	8	907	c.697T>A	c.(697-699)Tgc>Agc	p.C233S	ANO4_ENST00000392979.3_Missense_Mutation_p.C198S|ANO4_ENST00000299222.9_5'UTR|ANO4_ENST00000538618.1_3'UTR			Q32M45	ANO4_HUMAN	anoctamin 4	233					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						GGAGAATGACTGCTACACTGC	0.507										HNSCC(74;0.22)	OREG0022059	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C198S		Atlas-SNP	.											.	ANO4	183	.	0			c.T592A						.						223	188	200					12																	101381411		2203	4300	6503	SO:0001583	missense	121601	exon7			AATGACTGCTACA	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.697T>A	chr12.hg19:g.101381411T>A	ENSP00000376703:p.Cys233Ser	69.0	0.0	1358	67.0	17.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	hg19		.	.	.	.	.	.	.	.	.	.	T	12.29	1.892920	0.33442	.	.	ENSG00000151572	ENST00000392979;ENST00000392977	T;T	0.65549	-0.16;-0.16	5.33	5.33	0.75918	.	0.062825	0.64402	D	0.000004	T	0.51193	0.1660	L	0.28115	0.83	0.80722	D	1	B;B	0.19331	0.009;0.035	B;B	0.16289	0.007;0.015	T	0.50338	-0.8840	10	0.62326	D	0.03	.	15.3283	0.74186	0.0:0.0:0.0:1.0	.	233;198	Q32M45;Q32M45-2	ANO4_HUMAN;.	S	198;233	ENSP00000376705:C198S;ENSP00000376703:C233S	ENSP00000376703:C233S	C	+	1	0	ANO4	99905542	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.763000	0.47605	2.020000	0.59435	0.533000	0.62120	TGC	.	.		0.507	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		A	101381411	T	A	101381411	3	1	178	1	0	0	0	0	1	0	0	0	699	1580	55	4	614	4	ANO4	12	101381411	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	24172428	101381411	32470484	85	26786										
NOS1	4842	hgsc.bcm.edu	37	chr12	117681160	117681160	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cggaacttgtttctcttccaGctgcgatcattgctgatgag	10	10	2	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr12:117681160G>T	ENST00000338101.4	-	19	3010	c.3006C>A	c.(3004-3006)agC>agA	p.S1002R	NOS1_ENST00000317775.6_Missense_Mutation_p.S968R|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		TTCTCTTCCAGCTGCGATCAT	0.512																																					p.S1002R	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C3006A						.						266	252	256					12																	117681160		2038	4194	6232	SO:0001583	missense	4842	exon20			CTTCCAGCTGCGA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.3006C>A	chr12.hg19:g.117681160G>T	ENSP00000337459:p.Ser1002Arg	109.0	0.0		116.0	7.0	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.718460	0.48622	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.01455	4.87;4.9	3.59	2.68	0.31781	Riboflavin synthase-like beta-barrel (1);	0.000000	0.85682	D	0.000000	T	0.07954	0.0199	M	0.70595	2.14	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.04708	-1.0932	10	0.72032	D	0.01	-34.1931	11.6807	0.51455	0.0946:0.0:0.9054:0.0	.	968	P29475	NOS1_HUMAN	R	863;968;968;1002	ENSP00000320758:S968R;ENSP00000337459:S1002R	ENSP00000320758:S968R	S	-	3	2	NOS1	116165543	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.025000	0.64097	2.006000	0.58801	0.305000	0.20034	AGC	.	.		0.512	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			T	117681160	G	T	117681160	3	4	178	1	0	0	0	0	1	0	0	0	10550	962	34	3	1444	3	NOS1	12	117681160	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	16299749	117681160	16170735	86	26787										
WSB2	55884	hgsc.bcm.edu	37	chr12	118474281	118474281	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gatggccctctagcttccgaAttaacgtgtaggacctcatg	10	11	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr12:118474281A>C	ENST00000315436.3	-	6	836	c.695T>G	c.(694-696)aTt>aGt	p.I232S	WSB2_ENST00000536738.1_5'UTR|WSB2_ENST00000535496.1_Missense_Mutation_p.I234S|WSB2_ENST00000441406.2_Missense_Mutation_p.I249S|WSB2_ENST00000542304.1_Missense_Mutation_p.I7S|WSB2_ENST00000544233.1_Missense_Mutation_p.I22S	NM_001278557.1|NM_018639.3	NP_001265486.1|NP_061109.1	Q9NYS7	WSB2_HUMAN	WD repeat and SOCS box containing 2	232					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TAGCTTCCGAATTAACGTGTA	0.498																																					p.I232S		Atlas-SNP	.											.	WSB2	32	.	0			c.T695G						.						155	139	144					12																	118474281		2203	4300	6503	SO:0001583	missense	55884	exon6			TTCCGAATTAACG	AF038187	CCDS9186.1, CCDS61251.1, CCDS61252.1	12q24.23	2013-01-09	2011-01-25		ENSG00000176871	ENSG00000176871		"WD repeat domain containing"	19222	protein-coding gene	gene with protein product			"WD repeat and SOCS box-containing 2"			12076535	Standard	NM_018639		Approved	SBA2, MGC10210	uc001twr.2	Q9NYS7	OTTHUMG00000168885	ENST00000315436.3:c.695T>G	chr12.hg19:g.118474281A>C	ENSP00000319474:p.Ile232Ser	116.0	0.0		106.0	22.0	NM_018639	B4DIE6|B4DPV6|Q9NRX9	Missense_Mutation	SNP	ENST00000315436.3	hg19	CCDS9186.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.556333	0.86231	.	.	ENSG00000176871	ENST00000315436;ENST00000542304;ENST00000441406;ENST00000544233;ENST00000535496;ENST00000537945	T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;4.85	5.66	5.66	0.87406	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.153965	0.56097	D	0.000036	T	0.65903	0.2736	L	0.46614	1.455	0.80722	D	1	D	0.56746	0.977	P	0.56434	0.798	T	0.69007	-0.5259	10	0.72032	D	0.01	-31.1876	15.5638	0.76273	1.0:0.0:0.0:0.0	.	232	Q9NYS7	WSB2_HUMAN	S	232;7;249;22;234;234	ENSP00000319474:I232S;ENSP00000445941:I7S;ENSP00000409131:I249S;ENSP00000444431:I22S;ENSP00000439450:I234S;ENSP00000440386:I234S	ENSP00000319474:I232S	I	-	2	0	WSB2	116958664	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	9.292000	0.96076	2.153000	0.67306	0.533000	0.62120	ATT	.	.		0.498	WSB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401515.1	NM_018639		C	118474281	A	C	118474281	3	2	178	1	0	0	0	0	1	0	0	0	17420	101	4	5	535	5	WSB2	12	118474281	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	793121	118474281	15377614	87	26788										
CDH24	64403	hgsc.bcm.edu	37	chr14	23524786	23524786	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	accagcatattcctcaatgaCaaagaactggttccagaccc	6	13	1	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr14:23524786C>T	ENST00000267383.5	-	1	249	c.157G>A	c.(157-159)Gtc>Atc	p.V53I	CDH24_ENST00000554034.1_Missense_Mutation_p.V53I|CDH24_ENST00000487137.2_Missense_Mutation_p.V53I|CDH24_ENST00000397359.3_Missense_Mutation_p.V53I			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	53	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		TCCTCAATGACAAAGAACTGG	0.622											OREG0022594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V53I		Atlas-SNP	.											.	CDH24	129	.	0			c.G157A						.						78	70	73					14																	23524786		2203	4300	6503	SO:0001583	missense	64403	exon2			CAATGACAAAGAA	AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"Cadherins / Major cadherins"	14265	protein-coding gene	gene with protein product			"cadherin-like 24"			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.157G>A	chr14.hg19:g.23524786C>T	ENSP00000267383:p.Val53Ile	194.0	0.0	764	187.0	10.0	NM_022478	D3DS44|Q86UP1|Q9NT84	Missense_Mutation	SNP	ENST00000267383.5	hg19	CCDS9585.1	.	.	.	.	.	.	.	.	.	.	C	19.54	3.846227	0.71603	.	.	ENSG00000139880	ENST00000397359;ENST00000487137;ENST00000422751;ENST00000554034;ENST00000267383	T;T;T;T	0.00507	6.92;6.92;6.92;6.92	4.06	4.06	0.47325	Cadherin-like (1);	0.000000	0.51477	D	0.000092	T	0.01454	0.0047	M	0.63169	1.94	0.44880	D	0.997892	P;D;P	0.71674	0.945;0.998;0.956	D;D;D	0.91635	0.986;0.999;0.992	T	0.73726	-0.3892	10	0.46703	T	0.11	.	15.5231	0.75881	0.0:1.0:0.0:0.0	.	53;53;53	Q86UP0-2;Q96LQ7;Q86UP0	.;.;CAD24_HUMAN	I	53	ENSP00000380517:V53I;ENSP00000434821:V53I;ENSP00000452493:V53I;ENSP00000267383:V53I	ENSP00000267383:V53I	V	-	1	0	CDH24	22594626	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.533000	0.67160	2.287000	0.76781	0.455000	0.32223	GTC	.	.		0.622	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2	NM_022478		T	23524786	C	T	23524786	3	4	178	1	0	0	0	0	1	0	0	0	3111	478	17	3	2350	3	CDH24	14	23524786	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10		23524786	83824754	88	26789										
DCAF5	8816	hgsc.bcm.edu	37	chr14	69520912	69520912	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	taagcgtccattgttgtggtTggcacagatggtttcgaggc	14	7	0	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr14:69520912T>G	ENST00000341516.5	-	9	2638	c.2491A>C	c.(2491-2493)Aac>Cac	p.N831H	DCAF5_ENST00000554215.1_Missense_Mutation_p.N749H|DCAF5_ENST00000553293.1_5'Flank|DCAF5_ENST00000556847.1_Missense_Mutation_p.N749H|DCAF5_ENST00000557386.1_Missense_Mutation_p.N830H	NM_001284206.1|NM_001284207.1|NM_003861.2	NP_001271135.1|NP_001271136.1|NP_003852.1	Q96JK2	DCAF5_HUMAN	DDB1 and CUL4 associated factor 5	831					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|upper_aerodigestive_tract(2)	29						TTGTTGTGGTTGGCACAGATG	0.592																																					p.N831H		Atlas-SNP	.											.	DCAF5	67	.	0			c.A2491C						.						156	146	149					14																	69520912		2203	4300	6503	SO:0001583	missense	8816	exon9			TGTGGTTGGCACA	AB058727	CCDS32106.1, CCDS61480.1, CCDS61481.1, CCDS73646.1	14q23-q24.1	2013-01-09	2009-07-17	2009-07-17				"WD repeat domain containing", "DDB1 and CUL4 associated factors"	20224	protein-coding gene	gene with protein product		603812	"WD repeat domain 22"	WDR22		9740667, 9521877	Standard	NM_003861		Approved	BCRP2, D14S1461E, BCRG2, KIAA1824	uc001xkp.3	Q96JK2		ENST00000341516.5:c.2491A>C	chr14.hg19:g.69520912T>G	ENSP00000341351:p.Asn831His	67.0	0.0		63.0	11.0	NM_003861	B2RN31|G3V4J7|O60559|Q8N3V3|Q8N3V5	Missense_Mutation	SNP	ENST00000341516.5	hg19	CCDS32106.1	.	.	.	.	.	.	.	.	.	.	T	9.017	0.984025	0.18889	.	.	ENSG00000139990	ENST00000341516;ENST00000554215;ENST00000556847;ENST00000557386	T;T;T;T	0.72282	-0.64;-0.46;-0.46;-0.07	5.09	5.09	0.68999	.	0.138816	0.49305	D	0.000153	T	0.53738	0.1815	N	0.17082	0.46	0.80722	D	1	B;B	0.23735	0.09;0.054	B;B	0.23419	0.046;0.021	T	0.52139	-0.8615	10	0.34782	T	0.22	-23.9641	11.095	0.48139	0.0:0.0:0.1547:0.8453	.	830;831	G3V4J7;Q96JK2	.;DCAF5_HUMAN	H	831;749;749;830	ENSP00000341351:N831H;ENSP00000451551:N749H;ENSP00000452052:N749H;ENSP00000451845:N830H	ENSP00000341351:N831H	N	-	1	0	DCAF5	68590665	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.658000	0.54482	2.139000	0.66308	0.459000	0.35465	AAC	.	.		0.592	DCAF5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414806.2	NM_003861		G	69520912	T	G	69520912	3	3	178	1	0	0	0	0	1	0	0	0	4275	1812	63	5	341	5	DCAF5	14	69520912	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	45996126	69520912	37828628	89	26790										
HERC2	8924	hgsc.bcm.edu	37	chr15	28443868	28443868	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	atgactttgccaacatcaccTtcgcacacttcttcatacgc	4	15	3	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr15:28443868T>G	ENST00000261609.7	-	49	7872	c.7764A>C	c.(7762-7764)gaA>gaC	p.E2588D		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CAACATCACCTTCGCACACTT	0.468																																					p.E2588D		Atlas-SNP	.											.	HERC2	501	.	0			c.A7764C						.						174	150	158					15																	28443868		2203	4300	6503	SO:0001583	missense	8924	exon49			ATCACCTTCGCAC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.7764A>C	chr15.hg19:g.28443868T>G	ENSP00000261609:p.Glu2588Asp	170.0	0.0		187.0	32.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	T	8.908	0.958009	0.18507	.	.	ENSG00000128731	ENST00000261609	T	0.39997	1.05	5.46	-0.796	0.10912	CPH domain (1);	0.108892	0.64402	D	0.000010	T	0.34687	0.0906	L	0.60455	1.87	0.47905	D	0.999546	B;B	0.18013	0.025;0.002	B;B	0.20184	0.028;0.01	T	0.12192	-1.0557	10	0.36615	T	0.2	.	9.9196	0.41457	0.0:0.337:0.0:0.663	.	55;2588	A8KAQ8;O95714	.;HERC2_HUMAN	D	2588	ENSP00000261609:E2588D	ENSP00000261609:E2588D	E	-	3	2	HERC2	26117463	1.000000	0.71417	0.918000	0.36340	0.025000	0.11179	0.756000	0.26419	-0.163000	0.10946	0.397000	0.26171	GAA	.	.		0.468	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		G	28443868	T	G	28443868	3	3	178	1	0	0	0	0	1	0	0	0	7067	1606	56	5	6920	5	HERC2	15	28443868	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10		28443868	74087524	90	26791										
LTK	4058	hgsc.bcm.edu	37	chr15	41804103	41804103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cttcgctcccatccatcgccGcgtgctcttcaacggctcga	8	18	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr15:41804103G>A	ENST00000263800.6	-	5	665	c.569C>T	c.(568-570)gCg>gTg	p.A190V	LTK_ENST00000453182.2_Missense_Mutation_p.A190V|LTK_ENST00000561619.1_Intron|LTK_ENST00000355166.5_Missense_Mutation_p.A190V	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	190					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		ATCCATCGCCGCGTGCTCTTC	0.746										TSP Lung(18;0.14)																											p.A190V		Atlas-SNP	.											.	LTK	117	.	0			c.C569T						.						3	4	4					15																	41804103		1793	3750	5543	SO:0001583	missense	4058	exon5			ATCGCCGCGTGCT	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.569C>T	chr15.hg19:g.41804103G>A	ENSP00000263800:p.Ala190Val	83.0	0.0		83.0	6.0	NM_001135685	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.387523	0.42308	.	.	ENSG00000062524	ENST00000360087;ENST00000355166;ENST00000263800;ENST00000453182	T;T;T	0.40225	1.04;1.04;1.04	3.63	-7.26	0.01466	.	1.605850	0.04446	N	0.371694	T	0.19046	0.0457	N	0.16478	0.41	0.09310	N	1	B;B;B	0.11235	0.004;0.001;0.004	B;B;B	0.04013	0.001;0.001;0.001	T	0.14117	-1.0484	10	0.13108	T	0.6	.	3.3134	0.07025	0.1556:0.0912:0.2284:0.5248	.	190;190;190	E9PFX4;P29376-4;P29376	.;.;LTK_HUMAN	V	190	ENSP00000347293:A190V;ENSP00000263800:A190V;ENSP00000392196:A190V	ENSP00000263800:A190V	A	-	2	0	LTK	39591395	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.937000	0.03942	-1.593000	0.01617	-0.218000	0.12543	GCG	.	.		0.746	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			A	41804103	G	A	41804103	3	1	178	1	0	0	0	0	1	0	0	0	9089	1087	38	1	2089	1	LTK	15	41804103	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	13360235	41804103	60727289	91	26792										
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81221411	81221411	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	aagcaagagataaagaacagCttgtttgttggcgagagtgg	14	4	0	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr15:81221411C>A	ENST00000394685.3	+	21	2927	c.2508C>A	c.(2506-2508)agC>agA	p.S836R	KIAA1199_ENST00000220244.3_Missense_Mutation_p.S836R|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_Missense_Mutation_p.S836R			Q8WUJ3	CEMIP_HUMAN		836					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TAAAGAACAGCTTGTTTGTTG	0.532																																					p.S836R		Atlas-SNP	.											.	KIAA1199	118	.	0			c.C2508A						.						141	132	135					15																	81221411		2203	4300	6503	SO:0001583	missense	57214	exon20			GAACAGCTTGTTT																												ENST00000394685.3:c.2508C>A	chr15.hg19:g.81221411C>A	ENSP00000378177:p.Ser836Arg	314.0	0.0		314.0	37.0	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	hg19	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.290089	0.59976	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	T;T;T	0.81330	-1.48;-1.48;-1.48	4.87	2.85	0.33270	Pectin lyase fold/virulence factor (1);	0.114346	0.64402	D	0.000018	D	0.87815	0.6272	M	0.79805	2.47	0.32107	N	0.589852	D	0.76494	0.999	D	0.80764	0.994	D	0.88077	0.2804	10	0.66056	D	0.02	-49.7366	9.3503	0.38133	0.0:0.7556:0.0:0.2444	.	836	Q8WUJ3	K1199_HUMAN	R	836	ENSP00000220244:S836R;ENSP00000378177:S836R;ENSP00000348583:S836R	ENSP00000220244:S836R	S	+	3	2	KIAA1199	79008466	0.869000	0.29996	0.998000	0.56505	0.920000	0.55202	0.229000	0.17833	1.283000	0.44513	-0.122000	0.15005	AGC	.	.		0.532	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			A	81221411	C	A	81221411	3	1	178	1	0	0	0	0	1	0	0	0	8222	796	28	3	2582	3	KIAA1199	15	81221411	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	39417308	81221411	21309981	92	26793										
WDR24	84219	hgsc.bcm.edu	37	chr16	735410	735410	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ggcaggcggctgtcgtagagCgcgtgtgagacagacaggag	19	8	0	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr16:735410C>T	ENST00000248142.6	-	11	2255	c.2256G>A	c.(2254-2256)gcG>gcA	p.A752A	JMJD8_ENST00000562824.1_5'Flank|JMJD8_ENST00000454700.1_5'Flank|WDR24_ENST00000293883.4_Silent_p.A622A|JMJD8_ENST00000562111.1_5'Flank|JMJD8_ENST00000609261.1_5'Flank|JMJD8_ENST00000293882.4_5'Flank|JMJD8_ENST00000412368.2_5'Flank			Q96S15	WDR24_HUMAN	WD repeat domain 24	752										breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(3)	19		Hepatocellular(780;0.0218)				TGTCGTAGAGCGCGTGTGAGA	0.672																																					p.A622A		Atlas-SNP	.											.	WDR24	111	.	0			c.G1866A						.						37	46	43					16																	735410		2201	4298	6499	SO:0001819	synonymous_variant	84219	exon7			GTAGAGCGCGTGT	AL136863	CCDS10420.1	16p13.3	2013-01-09			ENSG00000127580	ENSG00000127580		"WD repeat domain containing"	20852	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 21"	C16orf21		11230166	Standard	NM_032259		Approved	DKFZp434F054, JFP7	uc002ciz.1	Q96S15	OTTHUMG00000090421	ENST00000248142.6:c.2256G>A	chr16.hg19:g.735410C>T		139.0	0.0		125.0	8.0	NM_032259	A2IDB8|D3DU59|Q96GC7|Q9H0B7	Silent	SNP	ENST00000248142.6	hg19																																																																																				.	.		0.672	WDR24-201	KNOWN	basic	protein_coding	protein_coding		NM_032259		T	735410	C	T	735410	2	4	178	1	0	0	0	0	0	0	0	1	17296	755	27	1		1	WDR24	16	735410	Silent	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10		735410	89619343	93	26794										
HIRIP3	8479	hgsc.bcm.edu	37	chr16	30005783	30005783	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tctgggctaggatctcctctTcactctcctgttcactttcc	6	15	6	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr16:30005783T>G	ENST00000279392.3	-	4	1513	c.683A>C	c.(682-684)gAa>gCa	p.E228A	INO80E_ENST00000567254.1_5'Flank|INO80E_ENST00000304516.7_5'Flank|INO80E_ENST00000567705.1_5'Flank|HIRIP3_ENST00000566471.1_5'Flank|HIRIP3_ENST00000564026.1_Intron|INO80E_ENST00000563197.1_5'Flank	NM_003609.4	NP_003600.2	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3	228	Glu-rich.				chromatin assembly or disassembly (GO:0006333)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(9)	17						GATCTCCTCTTCACTCTCCTG	0.498																																					p.E228A		Atlas-SNP	.											.	HIRIP3	45	.	0			c.A683C						.						207	195	199					16																	30005783		2197	4300	6497	SO:0001583	missense	8479	exon4			TCCTCTTCACTCT	AJ223351	CCDS10664.1, CCDS58449.1	16p12.1	2008-02-05	2001-11-29		ENSG00000149929	ENSG00000149929			4917	protein-coding gene	gene with protein product		603365	"HIRA-interacting protein 3"			9710638	Standard	NM_003609		Approved		uc002dve.3	Q9BW71	OTTHUMG00000132118	ENST00000279392.3:c.683A>C	chr16.hg19:g.30005783T>G	ENSP00000279392:p.Glu228Ala	69.0	0.0		82.0	11.0	NM_003609	H3BSR3|O75707|O75708	Missense_Mutation	SNP	ENST00000279392.3	hg19	CCDS10664.1	.	.	.	.	.	.	.	.	.	.	T	11.63	1.695774	0.30052	.	.	ENSG00000149929	ENST00000279392	T	0.32753	1.44	4.35	3.22	0.36961	.	0.508000	0.18420	N	0.141763	T	0.22820	0.0551	L	0.32530	0.975	0.46356	D	0.999	P	0.42908	0.793	B	0.41374	0.355	T	0.01739	-1.1284	10	0.36615	T	0.2	-5.0832	8.2498	0.31710	0.0:0.098:0.0:0.902	.	228	Q9BW71	HIRP3_HUMAN	A	228	ENSP00000279392:E228A	ENSP00000279392:E228A	E	-	2	0	HIRIP3	29913284	0.000000	0.05858	0.018000	0.16275	0.051000	0.14879	0.141000	0.16076	0.669000	0.31146	0.482000	0.46254	GAA	.	.		0.498	HIRIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255160.2	NM_003609		G	30005783	T	G	30005783	3	3	178	1	0	0	0	0	1	0	0	0	7130	1783	62	5	1003	5	HIRIP3	16	30005783	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	29270373	30005783	60348970	94	26795										
BRD7	29117	hgsc.bcm.edu	37	chr16	50357551	50357552	+	Frame_Shift_Del	DEL	GT	GT	-													0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tccttttgttaaaacatccaGtaaactatctgccatgacat							TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr16:50357551_50357552delGT	ENST00000394688.3	-	12	1548_1549	c.1389_1390delAC	c.(1387-1392)ttactgfs	p.LL463fs	BRD7_ENST00000394689.2_Frame_Shift_Del_p.LL463fs			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	463					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				AAAACATCCAGTAAACTATCTG	0.421																																					p.464_464del		Atlas-INDEL	.											.	BRD7	61	.	0			c.1390_1391del						.																																			SO:0001589	frameshift_variant	29117	exon12			.	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"bromodomain-containing 7"			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.1389_1390delAC	chr16.hg19:g.50357551_50357552delGT	ENSP00000378180:p.Leu463fs	88.0	0.0		75.0	11.0	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Frame_Shift_Del	DEL	ENST00000394688.3	hg19	CCDS10742.1																																																																																			.	.		0.421	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		-	50357552	GT	-	50357551	7	5	178	1	0	1	0	1	0	0	0	0	1507	1020	36	0	592	0	BRD7	16	50357551	Frame_Shift_Del	DEL	GT	TCGA-DD-AAD1-01A-11D-A40R-10	20351768	50357551	39997202	95	26796										
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85699912	85699912	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tgcacatcagttccacgagtCagtgctgcagtccacccaga	9	14	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr16:85699912C>G	ENST00000253458.7	+	13	3265	c.3089C>G	c.(3088-3090)tCa>tGa	p.S1030*	GSE1_ENST00000405402.2_Nonsense_Mutation_p.S926*|GSE1_ENST00000393243.1_Nonsense_Mutation_p.S957*	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	1030																	TTCCACGAGTCAGTGCTGCAG	0.572																																					p.S1030X		Atlas-SNP	.											.	.	.	.	0			c.C3089G						.						61	60	60					16																	85699912		2198	4300	6498	SO:0001587	stop_gained	23199	exon13			ACGAGTCAGTGCT	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.3089C>G	chr16.hg19:g.85699912C>G	ENSP00000253458:p.Ser1030*	189.0	0.0		136.0	45.0	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Nonsense_Mutation	SNP	ENST00000253458.7	hg19	CCDS10952.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	43|43	10.417472|10.417472	0.99401|0.99401	.|.	.|.	ENSG00000131149|ENSG00000131149	ENST00000412692;ENST00000438180|ENST00000405402;ENST00000253458;ENST00000393243	.|.	.|.	.|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.81781|.	0.4895|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	D|.	0.83764|.	0.0216|.	3|.	.|0.87932	.|D	.|0	-22.627|-22.627	19.4403|19.4403	0.94817|0.94817	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	E|X	799;232|926;1030;957	.|.	.|ENSP00000253458:S1030X	Q|S	+|+	1|2	0|0	KIAA0182|KIAA0182	84257413|84257413	1.000000|1.000000	0.71417|0.71417	0.973000|0.973000	0.42090|0.42090	0.989000|0.989000	0.77384|0.77384	7.711000|7.711000	0.84669|0.84669	2.586000|2.586000	0.87340|0.87340	0.561000|0.561000	0.74099|0.74099	CAG|TCA	.	.		0.572	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		G	85699912	C	G	85699912	4	3	178	1	0	0	0	0	0	1	0	0	8168	838	29	4	3139	4	KIAA0182	16	85699912	Nonsense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	35342361	85699912	4654841	96	26797										
ACAP1	9744	hgsc.bcm.edu	37	chr17	7247924	7247924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gtggcctggtgatggaaggaCatctcttcaaacgggccagc	14	10	2	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:7247924C>T	ENST00000158762.3	+	10	1017	c.811C>T	c.(811-813)Cat>Tat	p.H271Y		NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	271	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.|Required for formation of endosomal tubules when overexpressed with PIP5K1C.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						GATGGAAGGACATCTCTTCAA	0.572																																					p.H271Y		Atlas-SNP	.											.	ACAP1	66	.	0			c.C811T						.						58	48	52					17																	7247924		2022	3844	5866	SO:0001583	missense	9744	exon10			GAAGGACATCTCT	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.811C>T	chr17.hg19:g.7247924C>T	ENSP00000158762:p.His271Tyr	70.0	0.0		60.0	5.0	NM_014716	Q53XN9	Missense_Mutation	SNP	ENST00000158762.3	hg19	CCDS11101.1	.	.	.	.	.	.	.	.	.	.	C	6.208	0.406620	0.11754	.	.	ENSG00000072818	ENST00000158762	T	0.03065	4.06	5.39	3.39	0.38822	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.342120	0.31821	N	0.007015	T	0.00695	0.0023	N	0.00060	-2.34	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39761	-0.9598	10	0.02654	T	1	.	6.7694	0.23585	0.0:0.7325:0.0:0.2675	.	271	Q15027	ACAP1_HUMAN	Y	271	ENSP00000158762:H271Y	ENSP00000158762:H271Y	H	+	1	0	ACAP1	7188648	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	5.079000	0.64431	1.426000	0.47256	0.563000	0.77884	CAT	.	.		0.572	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		T	7247924	C	T	7247924	3	4	178	1	0	0	0	0	1	0	0	0	118	478	17	3	849	3	ACAP1	17	7247924	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10		7247924	73947286	97	26798										
MYH8	4626	hgsc.bcm.edu	37	chr17	10298727	10298727	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ttaactcaagctggatacgcAgaatctttccttcttcatgt	6	10	4	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:10298727A>T	ENST00000403437.2	-	34	4779	c.4685T>A	c.(4684-4686)cTg>cAg	p.L1562Q	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1562					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						CTGGATACGCAGAATCTTTCC	0.388									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.L1562Q		Atlas-SNP	.											.	MYH8	346	.	0			c.T4685A						.						87	77	80					17																	10298727		2203	4300	6503	SO:0001583	missense	4626	exon34	Familial Cancer Database	Carney Complex Variant	ATACGCAGAATCT		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.4685T>A	chr17.hg19:g.10298727A>T	ENSP00000384330:p.Leu1562Gln	122.0	0.0		82.0	23.0	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	hg19	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.295618	0.81025	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.79033	-1.23	4.85	4.85	0.62838	Myosin tail (1);	0.000000	0.32952	U	0.005442	T	0.79209	0.4407	M	0.74881	2.28	0.58432	D	0.999998	B	0.25772	0.134	B	0.31442	0.13	T	0.79446	-0.1800	10	0.62326	D	0.03	.	14.6106	0.68514	1.0:0.0:0.0:0.0	.	1562	P13535	MYH8_HUMAN	Q	1562	ENSP00000384330:L1562Q	ENSP00000252173:L1562Q	L	-	2	0	MYH8	10239452	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.984000	0.93482	2.039000	0.60335	0.528000	0.53228	CTG	.	.		0.388	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10298727	A	T	10298727	3	4	178	1	0	0	0	0	1	0	0	0	10050	188	7	4	1156	4	MYH8	17	10298727	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	3050803	10298727	70896483	98	26799										
MYH4	4622	hgsc.bcm.edu	37	chr17	10351286	10351286	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tgctcctgatctcagcatccAgtgtactctgcattgactcc	7	14	2	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:10351286A>T	ENST00000255381.2	-	34	4924	c.4814T>A	c.(4813-4815)cTg>cAg	p.L1605Q	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1605					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						CTCAGCATCCAGTGTACTCTG	0.438																																					p.L1605Q		Atlas-SNP	.											.	MYH4	349	.	0			c.T4814A						.						265	232	243					17																	10351286		2203	4300	6503	SO:0001583	missense	4622	exon34			GCATCCAGTGTAC		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.4814T>A	chr17.hg19:g.10351286A>T	ENSP00000255381:p.Leu1605Gln	130.0	0.0		86.0	25.0	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.844378	0.51164	.	.	ENSG00000141048	ENST00000255381	D	0.85955	-2.05	5.52	5.52	0.82312	Myosin tail (1);	0.000000	0.30085	U	0.010448	D	0.92384	0.7583	M	0.88979	2.995	0.52501	D	0.999959	D	0.55385	0.971	P	0.58577	0.841	D	0.93773	0.7077	10	0.87932	D	0	.	15.9309	0.79659	1.0:0.0:0.0:0.0	.	1605	Q9Y623	MYH4_HUMAN	Q	1605	ENSP00000255381:L1605Q	ENSP00000255381:L1605Q	L	-	2	0	MYH4	10292011	1.000000	0.71417	0.458000	0.27068	0.114000	0.19823	9.269000	0.95684	2.217000	0.71921	0.533000	0.62120	CTG	.	.		0.438	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10351286	A	T	10351286	3	4	178	1	0	0	0	0	1	0	0	0	10046	188	7	4	1033	4	MYH4	17	10351286	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	52559	10351286	70843924	99	26800										
PRPSAP2	5636	hgsc.bcm.edu	37	chr17	18827289	18827289	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	atgttggaggaaggattgccAtcatcgtggtatgtagacct	13	6	1	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:18827289A>G	ENST00000268835.2	+	10	1079	c.796A>G	c.(796-798)Atc>Gtc	p.I266V	PRPSAP2_ENST00000419071.2_Missense_Mutation_p.I226V|PRPSAP2_ENST00000542013.1_Missense_Mutation_p.I266V|PRPSAP2_ENST00000536323.1_Missense_Mutation_p.I180V	NM_002767.3	NP_002758.1	O60256	KPRB_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 2	266					bone development (GO:0060348)|negative regulation of catalytic activity (GO:0043086)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11						AAGGATTGCCATCATCGTGGT	0.358																																					p.I266V		Atlas-SNP	.											.	PRPSAP2	23	.	0			c.A796G						.						111	102	105					17																	18827289		2203	4300	6503	SO:0001583	missense	5636	exon9			ATTGCCATCATCG	AB007851	CCDS11200.1, CCDS58525.1, CCDS58526.1, CCDS58527.1	17p12-p11.2	2008-05-14			ENSG00000141127	ENSG00000141127			9467	protein-coding gene	gene with protein product		603762				9806849	Standard	NM_002767		Approved	PAP41	uc002gup.2	O60256	OTTHUMG00000059406	ENST00000268835.2:c.796A>G	chr17.hg19:g.18827289A>G	ENSP00000268835:p.Ile266Val	135.0	0.0		102.0	33.0	NM_001243940	B4E1M8|B4E329|B7ZKZ1|E7EMY2|Q6IAS2	Missense_Mutation	SNP	ENST00000268835.2	hg19	CCDS11200.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.389746	0.61956	.	.	ENSG00000141127	ENST00000395656;ENST00000419071;ENST00000432893;ENST00000455992;ENST00000412418;ENST00000268835;ENST00000536323;ENST00000542013	T;T;T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01;-1.01;-1.01	5.81	4.72	0.59763	.	0.149974	0.64402	D	0.000015	T	0.74711	0.3752	M	0.66439	2.03	0.58432	D	0.999998	B;B;B	0.29886	0.0;0.26;0.185	B;B;B	0.31191	0.001;0.117;0.125	T	0.69855	-0.5032	10	0.31617	T	0.26	-15.0278	12.1095	0.53831	0.9326:0.0:0.0674:0.0	.	266;226;266	B7ZKZ1;E7EMY2;O60256	.;.;KPRB_HUMAN	V	266;226;266;266;266;266;180;266	ENSP00000392536:I226V;ENSP00000399625:I266V;ENSP00000402612:I266V;ENSP00000268835:I266V;ENSP00000443967:I180V;ENSP00000439129:I266V	ENSP00000268835:I266V	I	+	1	0	PRPSAP2	18768014	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.365000	0.79537	1.014000	0.39417	0.529000	0.55759	ATC	.	.		0.358	PRPSAP2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132112.3	NM_002767		G	18827289	A	G	18827289	3	3	178	1	0	0	0	0	1	0	0	0	12594	217	8	2	826	2	PRPSAP2	17	18827289	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	8476003	18827289	62367921	100	26801										
USP22	23326	hgsc.bcm.edu	37	chr17	20924519	20924519	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gcacagaaaacagtagatgcCtccgtacatcagatcaatgg	9	10	2	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:20924519C>T	ENST00000261497.4	-	3	528	c.325G>A	c.(325-327)Ggc>Agc	p.G109S	USP22_ENST00000455117.2_5'UTR|USP22_ENST00000537526.2_Missense_Mutation_p.G97S	NM_015276.1	NP_056091.1	Q9UPT9	UBP22_HUMAN	ubiquitin specific peptidase 22	109					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|embryo development (GO:0009790)|histone deubiquitination (GO:0016578)|histone H4 acetylation (GO:0043967)|histone ubiquitination (GO:0016574)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deubiquitination (GO:0016579)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	SAGA complex (GO:0000124)	enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|transcription coactivator activity (GO:0003713)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	15						CAGTAGATGCCTCCGTACATC	0.453																																					p.G109S		Atlas-SNP	.											.	USP22	45	.	0			c.G325A						.						76	73	74					17																	20924519		1979	4167	6146	SO:0001583	missense	23326	exon3			AGATGCCTCCGTA	AB028986	CCDS42285.1	17p11.2	2006-11-24	2005-08-08		ENSG00000124422	ENSG00000124422		"Ubiquitin-specific peptidases"	12621	protein-coding gene	gene with protein product		612116	"ubiquitin specific protease 22", "ubiquitin specific peptidase 3-like"	USP3L		12838346	Standard	NM_015276		Approved	KIAA1063	uc002gym.4	Q9UPT9	OTTHUMG00000133621	ENST00000261497.4:c.325G>A	chr17.hg19:g.20924519C>T	ENSP00000261497:p.Gly109Ser	102.0	0.0		66.0	5.0	NM_015276	A0JNS3|Q2NLE2|Q6MZY4|Q8TBS8|Q96IW5	Missense_Mutation	SNP	ENST00000261497.4	hg19	CCDS42285.1	.	.	.	.	.	.	.	.	.	.	c	15.32	2.797839	0.50208	.	.	ENSG00000124422	ENST00000455117;ENST00000537526;ENST00000261497	T;T	0.37752	1.18;1.18	4.44	4.44	0.53790	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (2);	0.000000	0.64402	D	0.000001	T	0.26955	0.0660	N	0.16368	0.405	0.54753	D	0.999987	B;B	0.25667	0.108;0.131	B;B	0.32393	0.089;0.145	T	0.06552	-1.0820	10	0.19590	T	0.45	.	17.0541	0.86529	0.0:1.0:0.0:0.0	.	97;109	Q9UPT9-2;Q9UPT9	.;UBP22_HUMAN	S	177;97;109	ENSP00000440950:G97S;ENSP00000261497:G109S	ENSP00000261497:G109S	G	-	1	0	USP22	20865111	1.000000	0.71417	0.988000	0.46212	0.982000	0.71751	5.296000	0.65698	1.991000	0.58162	0.563000	0.77884	GGC	.	.		0.453	USP22-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444169.1			T	20924519	C	T	20924519	3	4	178	1	0	0	0	0	1	0	0	0	17069	681	24	3	1296	3	USP22	17	20924519	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	2097230	20924519	60270691	101	26802										
TMIGD1	388364	hgsc.bcm.edu	37	chr17	28656398	28656398	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ggaattgattttgtttccagAtttcaaatccactctcccct	5	11	2	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:28656398A>T	ENST00000328886.4	-	3	304	c.232T>A	c.(232-234)Tct>Act	p.S78T	TMIGD1_ENST00000538566.2_Missense_Mutation_p.S78T	NM_206832.1	NP_996663.1	Q6UXZ0	TMIG1_HUMAN	transmembrane and immunoglobulin domain containing 1	78	Ig-like C2-type 1.					integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	12						TTGTTTCCAGATTTCAAATCC	0.488																																					p.S78T		Atlas-SNP	.											.	TMIGD1	38	.	0			c.T232A						.						141	124	130					17																	28656398		2203	4300	6503	SO:0001583	missense	388364	exon3			TTCCAGATTTCAA	AY358153	CCDS32605.1	17q11.2	2013-01-29	2006-07-05	2006-07-05		ENSG00000182271		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	32431	protein-coding gene	gene with protein product				TMIGD		12975309	Standard	NM_206832		Approved	UNQ9372	uc002hfa.1	Q6UXZ0		ENST00000328886.4:c.232T>A	chr17.hg19:g.28656398A>T	ENSP00000332404:p.Ser78Thr	133.0	0.0		112.0	25.0	NM_206832	A8K2K1|Q6ZMC6	Missense_Mutation	SNP	ENST00000328886.4	hg19	CCDS32605.1	.	.	.	.	.	.	.	.	.	.	A	10.92	1.485664	0.26686	.	.	ENSG00000182271	ENST00000328886;ENST00000538566	T;T	0.16073	2.37;2.37	5.52	-4.08	0.03963	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.640253	0.16221	N	0.224035	T	0.10380	0.0254	L	0.51422	1.61	0.09310	N	1	B;B	0.17667	0.019;0.023	B;B	0.12837	0.007;0.008	T	0.23404	-1.0189	10	0.41790	T	0.15	0.0514	1.0095	0.01494	0.2091:0.2905:0.2903:0.21	.	78;78	Q6UXZ0-2;Q6UXZ0	.;TMIG1_HUMAN	T	78	ENSP00000332404:S78T;ENSP00000446118:S78T	ENSP00000332404:S78T	S	-	1	0	TMIGD1	25680524	0.956000	0.32656	0.295000	0.24960	0.991000	0.79684	0.096000	0.15147	-0.327000	0.08551	-0.371000	0.07208	TCT	.	.		0.488	TMIGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447955.1	NM_206832		T	28656398	A	T	28656398	3	4	178	1	0	0	0	0	1	0	0	0	16245	333	12	4	576	4	TMIGD1	17	28656398	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	7731879	28656398	52538812	102	26803										
RHOT1	55288	hgsc.bcm.edu	37	chr17	30528018	30528018	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	agcggtgcctggaatatttgGgctatctaggctattcaata	11	7	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:30528018G>A	ENST00000333942.6	+	14	1383	c.1144G>A	c.(1144-1146)Ggc>Agc	p.G382S	RHOT1_ENST00000545287.2_Missense_Mutation_p.G382S|RHOT1_ENST00000583994.1_Missense_Mutation_p.G255S|RHOT1_ENST00000354266.3_Missense_Mutation_p.G361S|RHOT1_ENST00000358365.3_Missense_Mutation_p.G382S|RHOT1_ENST00000394692.2_Missense_Mutation_p.G382S|RHOT1_ENST00000581094.1_Missense_Mutation_p.G382S	NM_018307.3	NP_060777.3	Q8IXI2	MIRO1_HUMAN	ras homolog family member T1	382					cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				GGAATATTTGGGCTATCTAGG	0.363																																					p.G382S		Atlas-SNP	.											.	RHOT1	69	.	0			c.G1144A						.						130	124	126					17																	30528018		2203	4300	6503	SO:0001583	missense	55288	exon14			TATTTGGGCTATC	AJ517412	CCDS32610.1, CCDS32611.1, CCDS32612.1, CCDS74030.1, CCDS74031.1	17q11.2-q12	2013-01-10	2012-02-27	2004-03-24		ENSG00000126858		"EF-hand domain containing"	21168	protein-coding gene	gene with protein product	"mitochondrial Rho (MIRO) GTPase 1"	613888	"ras homolog gene family, member T1"	ARHT1		12482879	Standard	NM_001033567		Approved	MIRO-1, FLJ11040	uc002hgw.3	Q8IXI2		ENST00000333942.6:c.1144G>A	chr17.hg19:g.30528018G>A	ENSP00000334724:p.Gly382Ser	70.0	0.0		87.0	20.0	NM_001033568	A4FVB6|A6NFV0|B4DG48|J9JIH9|Q6NUR3|Q6P9F8|Q6PJG1|Q6YMW8|Q86UB0|Q8IW28|Q8IXJ7|Q9H067|Q9H9N8|Q9NUZ2	Missense_Mutation	SNP	ENST00000333942.6	hg19	CCDS32612.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.784083	0.70222	.	.	ENSG00000126858	ENST00000358365;ENST00000354266;ENST00000394692;ENST00000333942	T;T;T	0.73363	-0.71;-0.74;-0.72	5.72	5.72	0.89469	EF hand associated, type-1 (1);	0.000000	0.85682	D	0.000000	D	0.86456	0.5937	M	0.72353	2.195	0.80722	D	1	D;P;D;P	0.89917	1.0;0.935;0.966;0.929	D;P;P;P	0.87578	0.998;0.824;0.852;0.771	D	0.86653	0.1899	10	0.66056	D	0.02	-8.8202	19.8965	0.96963	0.0:0.0:1.0:0.0	.	382;382;382;382	Q8IXI2-2;Q8IXI2;Q8IXI2-5;Q8IXI2-3	.;MIRO1_HUMAN;.;.	S	382	ENSP00000351132:G382S;ENSP00000378184:G382S;ENSP00000334724:G382S	ENSP00000334724:G382S	G	+	1	0	RHOT1	27552131	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.025000	0.88777	2.717000	0.92951	0.655000	0.94253	GGC	.	.		0.363	RHOT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000447097.1	NM_018307		A	30528018	G	A	30528018	3	1	178	1	0	0	0	0	1	0	0	0	13358	1232	43	3	1198	3	RHOT1	17	30528018	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	1871620	30528018	50667192	103	26804										
KRTAP9-3	83900	hgsc.bcm.edu	37	chr17	39388885	39388885	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tgtgtttccagctgctgccaGccttgctgccacccaacttg	9	15	0	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:39388885G>A	ENST00000411528.2	+	1	171	c.132G>A	c.(130-132)caG>caA	p.Q44Q		NM_031962.2	NP_114168.1	Q9BYQ3	KRA93_HUMAN	keratin associated protein 9-3	44	16 X 5 AA repeats of C-C-[RQVSHE]-[SPTN]- [TASPI].					keratin filament (GO:0045095)				breast(1)|endometrium(3)|lung(2)|ovary(1)|prostate(1)	8		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GCTGCTGCCAGCCTTGCTGCC	0.617																																					p.Q44Q		Atlas-SNP	.											.	KRTAP9-3	11	.	0			c.G132A						.						60	63	62					17																	39388885		2099	4296	6395	SO:0001819	synonymous_variant	83900	exon1			CTGCCAGCCTTGC	AJ406947	CCDS11385.1	17q21.2	2013-06-25			ENSG00000204873	ENSG00000204873		"Keratin associated proteins"	16927	protein-coding gene	gene with protein product						11279113	Standard	NM_031962		Approved	KAP9.3	uc021txg.1	Q9BYQ3	OTTHUMG00000133427	ENST00000411528.2:c.132G>A	chr17.hg19:g.39388885G>A		118.0	0.0		82.0	12.0	NM_031962		Silent	SNP	ENST00000411528.2	hg19	CCDS11385.1																																																																																			.	.		0.617	KRTAP9-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257290.1			A	39388885	G	A	39388885	2	1	178	1	0	0	0	0	0	0	0	1	8583	962	34	3		3	KRTAP9-3	17	39388885	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	8860867	39388885	41806325	104	26805										
BRCA1	672	hgsc.bcm.edu	37	chr17	41245524	41245524	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tactcttcttggctccagttGcaggttctttaccttccatg	7	12	3	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:41245524G>C	ENST00000357654.3	-	10	2142	c.2024C>G	c.(2023-2025)gCa>gGa	p.A675G	BRCA1_ENST00000354071.3_Missense_Mutation_p.A675G|BRCA1_ENST00000346315.3_Missense_Mutation_p.A675G|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.A379G|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.A675G|BRCA1_ENST00000493795.1_Missense_Mutation_p.A628G|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000351666.3_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	675					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GGCTCCAGTTGCAGGTTCTTT	0.413			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.A675G		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.C2024G						.						107	96	99					17																	41245524		2202	4300	6502	SO:0001583	missense	672	exon10	Familial Cancer Database		CCAGTTGCAGGTT	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.2024C>G	chr17.hg19:g.41245524G>C	ENSP00000350283:p.Ala675Gly	121.0	0.0		98.0	17.0	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	hg19	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.814259	0.32053	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	D;D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58;-1.58	5.3	5.3	0.74995	.	0.644274	0.14501	N	0.315759	D	0.86590	0.5969	M	0.72624	2.21	0.09310	N	1	B;B;B;P;B;B	0.35307	0.045;0.045;0.343;0.494;0.024;0.438	B;B;P;B;B;B	0.45167	0.091;0.056;0.472;0.297;0.417;0.197	T	0.81120	-0.1077	10	0.72032	D	0.01	.	13.8762	0.63653	0.0:0.1521:0.8479:0.0	.	675;634;675;675;675;675	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	G	675;675;675;675;379;675;628	ENSP00000350283:A675G;ENSP00000326002:A675G;ENSP00000246907:A675G;ENSP00000310938:A379G;ENSP00000418960:A675G;ENSP00000418775:A628G	ENSP00000310938:A379G	A	-	2	0	BRCA1	38499050	0.004000	0.15560	0.007000	0.13788	0.222000	0.24845	1.448000	0.35112	2.763000	0.94921	0.561000	0.74099	GCA	.	.		0.413	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		C	41245524	G	C	41245524	3	2	178	1	0	0	0	0	1	0	0	0	1500	1319	46	4	3693	4	BRCA1	17	41245524	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	1856639	41245524	39949686	105	26806										
UNC13D	201294	hgsc.bcm.edu	37	chr17	73830716	73830716	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	taccatgttggctgcctggcCttggtccttctggcctgaag	12	12	1	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:73830716C>A	ENST00000207549.4	-	22	2453	c.2074G>T	c.(2074-2076)Ggc>Tgc	p.G692C	UNC13D_ENST00000412096.2_Missense_Mutation_p.G692C	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	692					defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCTGCCTGGCCTTGGTCCTTC	0.632									Familial Hemophagocytic Lymphohistiocytosis																												p.G692C		Atlas-SNP	.											.	UNC13D	68	.	0			c.G2074T						.						40	40	40					17																	73830716		2203	4300	6503	SO:0001583	missense	201294	exon22	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CCTGGCCTTGGTC	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.2074G>T	chr17.hg19:g.73830716C>A	ENSP00000207549:p.Gly692Cys	627.0	1.0		445.0	107.0	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.500901	0.64298	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.80994	-1.44;-1.44	4.63	2.62	0.31277	.	0.196855	0.43416	D	0.000573	T	0.78786	0.4338	L	0.38175	1.15	0.34957	D	0.751811	P;D	0.61080	0.932;0.989	P;P	0.56278	0.795;0.681	T	0.81055	-0.1106	10	0.46703	T	0.11	-20.5578	8.4371	0.32793	0.0:0.8176:0.0:0.1824	.	692;692	Q70J99-3;Q70J99	.;UN13D_HUMAN	C	692	ENSP00000207549:G692C;ENSP00000388093:G692C	ENSP00000207549:G692C	G	-	1	0	UNC13D	71342311	0.999000	0.42202	1.000000	0.80357	0.969000	0.65631	1.533000	0.36040	0.651000	0.30788	0.563000	0.77884	GGC	.	.		0.632	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		A	73830716	C	A	73830716	3	1	178	1	0	0	0	0	1	0	0	0	17002	681	24	3	1242	3	UNC13D	17	73830716	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	32585192	73830716	7364494	106	26807										
EXOC7	23265	hgsc.bcm.edu	37	chr17	74085364	74085364	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	aaggcactgacgcagtggatGtaggcatcggtctccacgtc	13	11	1	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr17:74085364G>A	ENST00000335146.7	-	9	1145	c.1092C>T	c.(1090-1092)taC>taT	p.Y364Y	EXOC7_ENST00000467929.2_Silent_p.Y272Y|EXOC7_ENST00000405575.4_Silent_p.Y336Y|EXOC7_ENST00000607838.1_Silent_p.Y336Y|EXOC7_ENST00000411744.2_Silent_p.Y305Y|EXOC7_ENST00000589210.1_Silent_p.Y313Y|EXOC7_ENST00000332065.5_Silent_p.Y282Y			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	364					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CGCAGTGGATGTAGGCATCGG	0.627																																					p.Y364Y		Atlas-SNP	.											.	EXOC7	47	.	0			c.C1092T						.						114	97	103					17																	74085364		2203	4300	6503	SO:0001819	synonymous_variant	23265	exon9			GTGGATGTAGGCA	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1092C>T	chr17.hg19:g.74085364G>A		67.0	0.0		70.0	9.0	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Silent	SNP	ENST00000335146.7	hg19	CCDS45782.1																																																																																			.	.		0.627	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		A	74085364	G	A	74085364	2	1	178	1	0	0	0	0	0	0	0	1	5312	1372	48	3		3	EXOC7	17	74085364	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	254648	74085364	7109846	107	26808										
EMILIN2	84034	hgsc.bcm.edu	37	chr18	2885112	2885112	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cgccccacgccggctcggccTcgaaacagcttgaagaaagc	11	16	0	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr18:2885112T>A	ENST00000254528.3	+	3	567	c.408T>A	c.(406-408)ccT>ccA	p.P136P		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	136					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		CGGCTCGGCCTCGAAACAGCT	0.512																																					p.P136P		Atlas-SNP	.											.	EMILIN2	97	.	0			c.T408A						.						63	64	64					18																	2885112		2203	4300	6503	SO:0001819	synonymous_variant	84034	exon3			TCGGCCTCGAAAC	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.408T>A	chr18.hg19:g.2885112T>A		90.0	0.0		105.0	22.0	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Silent	SNP	ENST00000254528.3	hg19	CCDS11828.1																																																																																			.	.		0.512	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		A	2885112	T	A	2885112	2	1	178	1	0	0	0	0	0	0	0	1	5096	1538	54	4		4	EMILIN2	18	2885112	Silent	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10		2885112	75192136	108	26809										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9254666	9254666	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gtagtttcaggtgaacacaaAcagaaaggcaaagttaaaag	10	5	1	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr18:9254666A>C	ENST00000262126.4	+	9	1641	c.1401A>C	c.(1399-1401)aaA>aaC	p.K467N	ANKRD12_ENST00000400020.3_Missense_Mutation_p.K444N|ANKRD12_ENST00000383440.2_Missense_Mutation_p.K444N	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	467						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						GTGAACACAaacagaaaggca	0.299																																					p.K467N		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A1401C						.						33	37	35					18																	9254666		2197	4288	6485	SO:0001583	missense	23253	exon9			ACACAAACAGAAA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.1401A>C	chr18.hg19:g.9254666A>C	ENSP00000262126:p.Lys467Asn	378.0	0.0		332.0	55.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.697780	0.30142	.	.	ENSG00000101745	ENST00000383440;ENST00000262126;ENST00000359158	T;T	0.05580	3.47;3.42	5.95	2.2	0.27929	.	0.000000	0.85682	D	0.000000	T	0.20495	0.0493	M	0.74881	2.28	0.54753	D	0.999987	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.983;0.963	T	0.00256	-1.1873	10	0.72032	D	0.01	-4.5051	9.1632	0.37035	0.7115:0.0:0.2885:0.0	.	94;444;467	Q9NXU3;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	N	444;467;174	ENSP00000372932:K444N;ENSP00000262126:K467N	ENSP00000262126:K467N	K	+	3	2	ANKRD12	9244666	0.994000	0.37717	1.000000	0.80357	0.998000	0.95712	0.457000	0.21875	0.425000	0.26087	0.528000	0.53228	AAA	.	.		0.299	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		C	9254666	A	C	9254666	3	2	178	1	0	0	0	0	1	0	0	0	640	40	2	5	1431	5	ANKRD12	18	9254666	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	6369554	9254666	68822582	109	26810										
DSC2	1824	hgsc.bcm.edu	37	chr18	28662231	28662231	+	Frame_Shift_Del	DEL	G	G	-													0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	acacaaagaactccttcattGgttttggcatctgttacaat							TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr18:28662231delG	ENST00000280904.6	-	9	1679	c.1236delC	c.(1234-1236)accfs	p.T412fs	DSC2_ENST00000251081.6_Frame_Shift_Del_p.T412fs	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	412	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			CTCCTTCATTGGTTTTGGCAT	0.294																																					p.N413fs		Atlas-INDEL	.											.	DSC2	168	.	0			c.1237delA						.						82	86	85					18																	28662231		2202	4295	6497	SO:0001589	frameshift_variant	1824	exon9			.	X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"Cadherins / Major cadherins"	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.1236delC	chr18.hg19:g.28662231delG	ENSP00000280904:p.Thr412fs	107.0	0.0		129.0	17.0	NM_004949		Frame_Shift_Del	DEL	ENST00000280904.6	hg19	CCDS11892.1																																																																																			.	.		0.294	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		-	28662231	G	-	28662231	7	5	178	1	0	1	0	1	0	0	0	0	4768	1335	47	0	1541	0	DSC2	18	28662231	Frame_Shift_Del	DEL	G	TCGA-DD-AAD1-01A-11D-A40R-10	19407565	28662231	49415017	110	26811										
RIT2	6014	hgsc.bcm.edu	37	chr18	40323617	40323617	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tcatcaatacagaatctgagGgctgcagaggtctcaaaaaa	9	8	4	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr18:40323617G>A	ENST00000326695.5	-	5	666	c.495C>T	c.(493-495)gcC>gcT	p.A165A	RIT2_ENST00000589109.1_3'UTR|RIT2_ENST00000590910.1_3'UTR	NM_002930.2	NP_002921.1	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	165					neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGAATCTGAGGGCTGCAGAGG	0.378																																					p.A165A		Atlas-SNP	.											.	RIT2	56	.	0			c.C495T						.						88	88	88					18																	40323617		2203	4300	6503	SO:0001819	synonymous_variant	6014	exon5			TCTGAGGGCTGCA	BC018060	CCDS11921.1, CCDS62431.1	18q12.3	2014-05-09	2002-09-11	2002-09-13	ENSG00000152214	ENSG00000152214			10017	protein-coding gene	gene with protein product		609592	"Ric (Drosophila)-like, expressed in neurons"	RIN		8824319, 8918462	Standard	NM_002930		Approved	RIBA	uc002lav.4	Q99578	OTTHUMG00000132611	ENST00000326695.5:c.495C>T	chr18.hg19:g.40323617G>A		177.0	0.0		187.0	30.0	NM_002930	B2R9L1|O15295|Q8TD69|Q8WVF6|Q92964	Silent	SNP	ENST00000326695.5	hg19	CCDS11921.1																																																																																			.	.		0.378	RIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255852.1	NM_002930		A	40323617	G	A	40323617	2	1	178	1	0	0	0	0	0	0	0	1	13402	1219	43	3		3	RIT2	18	40323617	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	11661386	40323617	37753631	111	26812										
MUC16	94025	hgsc.bcm.edu	37	chr19	9063744	9063744	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gggtgttcatggttatttctGctgattctgtcatgacaggg	13	6	4	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr19:9063744G>T	ENST00000397910.4	-	3	23905	c.23702C>A	c.(23701-23703)gCa>gAa	p.A7901E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7903	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGTTATTTCTGCTGATTCTGT	0.493																																					p.A7901E		Atlas-SNP	.											.	MUC16	4315	.	0			c.C23702A						.						223	203	210					19																	9063744		2019	4182	6201	SO:0001583	missense	94025	exon3			ATTTCTGCTGATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.23702C>A	chr19.hg19:g.9063744G>T	ENSP00000381008:p.Ala7901Glu	161.0	0.0		121.0	7.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	4.077	0.012247	0.07912	.	.	ENSG00000181143	ENST00000397910	T	0.02787	4.16	2.05	-0.565	0.11771	.	.	.	.	.	T	0.03520	0.0101	L	0.55481	1.735	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.17440	-1.0369	8	0.87932	D	0	.	6.2421	0.20797	0.0:0.0:0.4681:0.5319	.	7901	B5ME49	.	E	7901	ENSP00000381008:A7901E	ENSP00000381008:A7901E	A	-	2	0	MUC16	8924744	0.000000	0.05858	0.000000	0.03702	0.109000	0.19521	-1.613000	0.02059	-0.021000	0.14009	-1.243000	0.01532	GCA	.	.		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9063744	G	T	9063744	3	4	178	1	0	0	0	0	1	0	0	0	9982	1319	46	3	20149	3	MUC16	19	9063744	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10		9063744	50065239	112	26813										
FCHO1	23149	hgsc.bcm.edu	37	chr19	17877522	17877522	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cttccgcgtctcctcggacaAgctggcgctgtgccacctgg	12	16	1	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr19:17877522A>C	ENST00000596536.1	+	7	522	c.239A>C	c.(238-240)aAg>aCg	p.K80T	FCHO1_ENST00000594202.1_Missense_Mutation_p.K80T|FCHO1_ENST00000595033.1_Missense_Mutation_p.K30T|FCHO1_ENST00000597512.1_Missense_Mutation_p.K87T|FCHO1_ENST00000600676.1_Missense_Mutation_p.K80T|FCHO1_ENST00000389133.4_Missense_Mutation_p.K80T|FCHO1_ENST00000252771.7_Missense_Mutation_p.K80T|FCHO1_ENST00000596951.1_Missense_Mutation_p.K80T|FCHO1_ENST00000539407.1_Missense_Mutation_p.K80T	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	80	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.|Mediates membrane-binding.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						TCCTCGGACAAGCTGGCGCTG	0.627																																					p.K80T		Atlas-SNP	.											.	FCHO1	69	.	0			c.A239C						.						55	45	49					19																	17877522		2203	4300	6503	SO:0001583	missense	23149	exon6			CGGACAAGCTGGC	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.239A>C	chr19.hg19:g.17877522A>C	ENSP00000470731:p.Lys80Thr	155.0	0.0		137.0	25.0	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	hg19	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.723799	0.89298	.	.	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.18810	2.19;2.19;2.19	5.05	5.05	0.67936	Fps/Fes/Fer/CIP4 homology (3);	0.155164	0.56097	D	0.000033	T	0.32406	0.0828	L	0.56396	1.775	0.43313	D	0.995326	P;P;P	0.51653	0.483;0.947;0.888	B;P;P	0.54140	0.328;0.743;0.626	T	0.02766	-1.1113	10	0.37606	T	0.19	-24.6756	11.2137	0.48815	1.0:0.0:0.0:0.0	.	30;80;80	B4E120;O14526;O14526-2	.;FCHO1_HUMAN;.	T	80	ENSP00000252771:K80T;ENSP00000373785:K80T;ENSP00000437978:K80T	ENSP00000252771:K80T	K	+	2	0	FCHO1	17738522	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.594000	0.90836	1.911000	0.55334	0.454000	0.30748	AAG	.	.		0.627	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122		C	17877522	A	C	17877522	3	2	178	1	0	0	0	0	1	0	0	0	5795	72	3	5	253	5	FCHO1	19	17877522	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	8813778	17877522	41251461	113	26814										
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39329111	39329111	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gttgctggggtgctggatgcGgttcttggctgcctgctctg	17	9	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr19:39329111G>T	ENST00000221419.5	-	10	1849	c.1483C>A	c.(1483-1485)Cgc>Agc	p.R495S	AC104534.3_ENST00000594769.1_Silent_p.T111T|HNRNPL_ENST00000600873.1_Missense_Mutation_p.R362S	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	495	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			TGCTGGATGCGGTTCTTGGCT	0.577																																					p.R495S		Atlas-SNP	.											.	HNRNPL	67	.	0			c.C1483A						.						76	64	68					19																	39329111		2203	4296	6499	SO:0001583	missense	3191	exon10			GGATGCGGTTCTT	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1483C>A	chr19.hg19:g.39329111G>T	ENSP00000221419:p.Arg495Ser	105.0	0.0		100.0	5.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	hg19	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	G	17.84	3.488847	0.64074	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750	.	.	.	5.87	4.78	0.61160	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.78457	0.4286	M	0.81802	2.56	0.80722	D	1	D;D;D	0.89917	0.997;0.971;1.0	D;P;D	0.83275	0.941;0.536;0.996	T	0.77887	-0.2420	9	0.45353	T	0.12	.	13.4567	0.61204	0.0:0.0:0.7485:0.2515	.	495;464;478	P14866;B2R959;Q6NTA2	HNRPL_HUMAN;.;.	S	495;362;362	.	ENSP00000221419:R495S	R	-	1	0	HNRNPL	44020951	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.499000	0.45372	2.941000	0.99782	0.655000	0.94253	CGC	.	.		0.577	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			T	39329111	G	T	39329111	3	4	178	1	0	0	0	0	1	0	0	0	7279	1116	39	1	302	1	HNRNPL	19	39329111	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	21451589	39329111	19799872	114	26815										
SFRS16	11129	hgsc.bcm.edu	37	chr19	45567337	45567337	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cgaccccgggccgcgaggagAagatcacgttcatcaccagt	12	14	3	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr19:45567337A>G	ENST00000221455.3	+	12	1071	c.973A>G	c.(973-975)Aag>Gag	p.K325E	CLASRP_ENST00000391953.4_Missense_Mutation_p.K263E|CLASRP_ENST00000544944.2_Missense_Mutation_p.K325E	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	325					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						CCGCGAGGAGAAGATCACGTT	0.682																																					p.K325E		Atlas-SNP	.											.	CLASRP	44	.	0			c.A973G						.						18	23	22					19																	45567337		2203	4297	6500	SO:0001583	missense	11129	exon12			GAGGAGAAGATCA	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"Clk4 associating SR-related protein"		"splicing factor, arginine/serine-rich 16"	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.973A>G	chr19.hg19:g.45567337A>G	ENSP00000221455:p.Lys325Glu	104.0	0.0		106.0	32.0	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Missense_Mutation	SNP	ENST00000221455.3	hg19	CCDS12652.2	.	.	.	.	.	.	.	.	.	.	A	14.97	2.695648	0.48202	.	.	ENSG00000104859	ENST00000221455;ENST00000391952;ENST00000391953;ENST00000544944	T;T;T;T	0.12039	2.72;2.8;2.72;2.72	4.83	3.74	0.42951	.	0.000000	0.37906	U	0.001890	T	0.09992	0.0245	L	0.39245	1.2	0.44454	D	0.997384	B;B;B	0.26483	0.05;0.05;0.15	B;B;B	0.26310	0.047;0.047;0.068	T	0.15065	-1.0450	10	0.45353	T	0.12	-22.9827	3.6412	0.08168	0.7057:0.0:0.1013:0.193	.	263;325;325	F8WAG9;F5H0Q6;Q8N2M8	.;.;CLASR_HUMAN	E	325;325;263;325	ENSP00000221455:K325E;ENSP00000375814:K325E;ENSP00000375815:K263E;ENSP00000438702:K325E	ENSP00000221455:K325E	K	+	1	0	CLASRP	50259177	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.271000	0.65553	1.817000	0.53016	0.460000	0.39030	AAG	.	.		0.682	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056		G	45567337	A	G	45567337	3	3	178	1	0	0	0	0	1	0	0	0	14187	247	9	2	1015	2	SFRS16	19	45567337	Missense_Mutation	SNP	A	TCGA-DD-AAD1-01A-11D-A40R-10	6238226	45567337	13561646	115	26816										
PTPRH	5794	hgsc.bcm.edu	37	chr19	55715190	55715190	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tccacagagctatttactccGtctttctccacccacacaga	4	16	2	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr19:55715190G>A	ENST00000376350.3	-	5	868	c.846C>T	c.(844-846)gaC>gaT	p.D282D	PTPRH_ENST00000263434.5_Intron|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	282	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		TATTTACTCCGTCTTTCTCCA	0.488																																					p.D282D		Atlas-SNP	.											.	PTPRH	139	.	0			c.C846T						.						200	189	192					19																	55715190		2203	4300	6503	SO:0001819	synonymous_variant	5794	exon5			TACTCCGTCTTTC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.846C>T	chr19.hg19:g.55715190G>A		127.0	0.0		147.0	9.0	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Silent	SNP	ENST00000376350.3	hg19	CCDS33110.1																																																																																			.	.		0.488	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			A	55715190	G	A	55715190	2	1	178	1	0	0	0	0	0	0	0	1	12818	1136	40	1		1	PTPRH	19	55715190	Silent	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	10147853	55715190	3413793	116	26817										
ZNF135	7694	hgsc.bcm.edu	37	chr19	58579350	58579350	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cctatgaatgcaatgactgcGgcaaggcattcagtcacagc	10	11	2	2	rs566725358		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr19:58579350G>A	ENST00000313434.5	+	5	1599	c.1498G>A	c.(1498-1500)Ggc>Agc	p.G500S	RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000511556.1_Missense_Mutation_p.G512S|ZNF135_ENST00000439855.2_Missense_Mutation_p.G500S|ZNF135_ENST00000506786.1_Missense_Mutation_p.G458S|ZNF135_ENST00000401053.4_Missense_Mutation_p.G524S|ZNF135_ENST00000359978.6_Intron	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	500					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		CAATGACTGCGGCAAGGCATT	0.567													G|||	1	0.000199681	0	0	5008	,	,		20246	0.001		0	False		,,,				2504	0				p.G524S		Atlas-SNP	.											.	ZNF135	159	.	0			c.G1570A						.						89	81	84					19																	58579350		2203	4300	6503	SO:0001583	missense	7694	exon4			GACTGCGGCAAGG	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"Zinc fingers, C2H2-type", "-"	12919	protein-coding gene	gene with protein product		604077	"zinc finger protein 61", "zinc finger protein 135 (clone pHZ-17)"	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.1498G>A	chr19.hg19:g.58579350G>A	ENSP00000321406:p.Gly500Ser	120.0	0.0		94.0	19.0	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	hg19		.	.	.	.	.	.	.	.	.	.	G	11.77	1.738730	0.30774	.	.	ENSG00000176293	ENST00000401053;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	T;T;T;T;T	0.01455	4.87;4.87;4.87;4.87;4.87	3.26	2.17	0.27698	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05547	0.0146	L	0.48260	1.515	0.22552	N	0.998991	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.991	T	0.35251	-0.9796	9	0.66056	D	0.02	.	6.5543	0.22452	0.11:0.1874:0.7025:0.0	.	512;500	E9PEV2;P52742	.;ZN135_HUMAN	S	524;500;500;512;458	ENSP00000441410:G524S;ENSP00000444828:G500S;ENSP00000321406:G500S;ENSP00000422074:G512S;ENSP00000427691:G458S	ENSP00000321406:G500S	G	+	1	0	ZNF135	63271162	0.949000	0.32298	0.680000	0.29994	0.011000	0.07611	2.098000	0.41757	0.677000	0.31305	0.557000	0.71058	GGC	.	.		0.567	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		A	58579350	G	A	58579350	3	1	178	1	0	0	0	0	1	0	0	0	17740	1116	39	1	1701	1	ZNF135	19	58579350	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	2864160	58579350	549633	117	26818										
TH1L	51497	hgsc.bcm.edu	37	chr20	57568786	57568786	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tgtctggagaagctggacacTgacatttcactcattcgcta	9	10	3	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr20:57568786T>A	ENST00000344018.3	+	13	1602	c.1575T>A	c.(1573-1575)acT>acA	p.T525T	NELFCD_ENST00000602795.1_Silent_p.T534T|NELFCD_ENST00000479207.1_Intron			Q8IXH7	NELFD_HUMAN	negative elongation factor complex member C/D	525					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	membrane (GO:0016020)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)											AGCTGGACACTGACATTTCAC	0.448																																					p.T534T		Atlas-SNP	.											.	.	.	.	0			c.T1602A						.						202	178	186					20																	57568786		2203	4300	6503	SO:0001819	synonymous_variant	51497	exon13			GGACACTGACATT	AF161479	CCDS13473.1, CCDS13473.2	20q13	2013-01-31	2013-01-31	2013-01-31	ENSG00000101158	ENSG00000101158			15934	protein-coding gene	gene with protein product	"trihydrophobin 1"	605297	"TH1-like (Drosophila homolog)", "TH1-like (Drosophila)"	TH1L		11030415, 11042152	Standard	NM_198976		Approved	HSPC130, TH1, NELF-C, NELF-D	uc002yag.4	Q8IXH7	OTTHUMG00000032861	ENST00000344018.3:c.1575T>A	chr20.hg19:g.57568786T>A		86.0	0.0		85.0	16.0	NM_198976	B4DE06|Q9BYL2|Q9H405|Q9H888|Q9H8T3|Q9NVX5|Q9P029|Q9UGN1|Q9UGN2|Q9UGN3	Silent	SNP	ENST00000344018.3	hg19																																																																																				.	.		0.448	NELFCD-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198976		A	57568786	T	A	57568786	2	1	178	1	0	0	0	0	0	0	0	1	15854	1567	55	4		4	TH1L	20	57568786	Silent	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10		57568786	5456734	118	26819										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61542449	61542449	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ctctcagtgggctcctgttcCcgcttcctgcgaaggcgatt	11	14	1	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr20:61542449C>A	ENST00000266070.4	-	3	841	c.516G>T	c.(514-516)cgG>cgT	p.R172R	DIDO1_ENST00000395340.1_Silent_p.R172R|DIDO1_ENST00000354665.4_Silent_p.R172R|DIDO1_ENST00000395343.1_Silent_p.R172R|DIDO1_ENST00000266071.5_Silent_p.R172R|DIDO1_ENST00000395335.2_Silent_p.R172R|DIDO1_ENST00000370366.1_Silent_p.R172R|DIDO1_ENST00000370368.1_Silent_p.R172R|DIDO1_ENST00000370371.4_Silent_p.R172R	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	172					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GCTCCTGTTCCCGCTTCCTGC	0.612																																					p.R172R	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.G516T						.						55	52	53					20																	61542449		2203	4300	6503	SO:0001819	synonymous_variant	11083	exon3			CTGTTCCCGCTTC	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.516G>T	chr20.hg19:g.61542449C>A		98.0	0.0		64.0	19.0	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	hg19	CCDS33506.1																																																																																			.	.		0.612	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		A	61542449	C	A	61542449	2	1	178	1	0	0	0	0	0	0	0	1	4524	610	22	3		3	DIDO1	20	61542449	Silent	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10	3973663	61542449	1483071	119	26820										
PCNT	5116	hgsc.bcm.edu	37	chr21	47831466	47831466	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tgcagcagcgcctccagggcGcagaggaggctgcggagcta	17	12	0	1	rs563470468		TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr21:47831466G>T	ENST00000359568.5	+	28	5586	c.5479G>T	c.(5479-5481)Gca>Tca	p.A1827S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1827					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CCTCCAGGGCGCAGAGGAGGC	0.687																																					p.A1827S		Atlas-SNP	.											.	PCNT	283	.	0			c.G5479T						.						12	15	14					21																	47831466		2192	4281	6473	SO:0001583	missense	5116	exon28			CAGGGCGCAGAGG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.5479G>T	chr21.hg19:g.47831466G>T	ENSP00000352572:p.Ala1827Ser	142.0	0.0		101.0	25.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.839871	0.32513	.	.	ENSG00000160299	ENST00000359568	T	0.01629	4.72	5.91	1.91	0.25777	.	0.000000	0.33813	N	0.004536	T	0.02230	0.0069	L	0.34521	1.04	0.09310	N	1	P;P	0.44044	0.825;0.732	P;B	0.45099	0.469;0.279	T	0.46176	-0.9210	10	0.46703	T	0.11	.	9.7352	0.40384	0.2554:0.0:0.7446:0.0	.	1709;1827	O95613-2;O95613	.;PCNT_HUMAN	S	1827	ENSP00000352572:A1827S	ENSP00000352572:A1827S	A	+	1	0	PCNT	46655894	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.528000	0.23002	0.393000	0.25203	-0.119000	0.15052	GCA	.	.		0.687	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47831466	G	T	47831466	3	4	178	1	0	0	0	0	1	0	0	0	11599	1087	38	1	5589	1	PCNT	21	47831466	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10		47831466	298429	120	26821										
CARD10	29775	hgsc.bcm.edu	37	chr22	37887846	37887846	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	gcaccagctcccgcacacccCgagcacccagctccagcagg	9	21	0	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chr22:37887846C>A	ENST00000403299.1	-	20	2996	c.2780G>T	c.(2779-2781)cGg>cTg	p.R927L	CARD10_ENST00000251973.5_Missense_Mutation_p.R927L|CARD10_ENST00000406271.3_Missense_Mutation_p.R641L			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	927					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					CCGCACACCCCGAGCACCCAG	0.612																																					p.R927L		Atlas-SNP	.											.	CARD10	55	.	0			c.G2780T						.						92	70	77					22																	37887846		2203	4299	6502	SO:0001583	missense	29775	exon19			ACACCCCGAGCAC	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.2780G>T	chr22.hg19:g.37887846C>A	ENSP00000384570:p.Arg927Leu	42.0	0.0		48.0	6.0	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	hg19	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	C	7.526	0.657615	0.14645	.	.	ENSG00000100065	ENST00000403299;ENST00000406271;ENST00000251973	T;T;T	0.40225	1.04;1.44;1.04	5.64	2.19	0.27852	.	0.621303	0.15740	N	0.246959	T	0.24812	0.0602	N	0.22421	0.69	0.25506	N	0.987504	B;B	0.30146	0.116;0.27	B;B	0.31547	0.048;0.132	T	0.13019	-1.0525	10	0.29301	T	0.29	-40.128	5.1446	0.14977	0.0:0.5296:0.0:0.4704	.	927;641	Q9BWT7;Q8NC81	CAR10_HUMAN;.	L	927;641;927	ENSP00000384570:R927L;ENSP00000385799:R641L;ENSP00000251973:R927L	ENSP00000251973:R927L	R	-	2	0	CARD10	36217792	0.726000	0.28059	0.597000	0.28824	0.001000	0.01503	1.729000	0.38115	0.755000	0.32990	-0.751000	0.03497	CGG	.	.		0.612	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		A	37887846	C	A	37887846	3	1	178	1	0	0	0	0	1	0	0	0	2646	652	23	1	326	1	CARD10	22	37887846	Missense_Mutation	SNP	C	TCGA-DD-AAD1-01A-11D-A40R-10		37887846	13416720	121	26822										
BMX	660	hgsc.bcm.edu	37	chrX	15560110	15560110	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	atctgttatttccaggaaacTcagccatcccaagctggtta	7	11	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chrX:15560110T>C	ENST00000357607.2	+	15	1588	c.1400T>C	c.(1399-1401)cTc>cCc	p.L467P	BMX_ENST00000342014.6_Missense_Mutation_p.L467P|BMX_ENST00000348343.6_Missense_Mutation_p.L467P			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	467	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					TCCAGGAAACTCAGCCATCCC	0.363																																					p.L467P		Atlas-SNP	.											.	BMX	73	.	0			c.T1400C						.						105	100	101					X																	15560110		2203	4299	6502	SO:0001583	missense	660	exon15			GGAAACTCAGCCA	AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1079	protein-coding gene	gene with protein product	"BTK-like on X chromosome"	300101				7970727	Standard	NM_203281		Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.1400T>C	chrX.hg19:g.15560110T>C	ENSP00000350224:p.Leu467Pro	263.0	0.0		256.0	46.0	NM_001721	A6NIH9|O60564|Q12871	Missense_Mutation	SNP	ENST00000357607.2	hg19	CCDS14168.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.550941	0.65311	.	.	ENSG00000102010	ENST00000357607;ENST00000348343;ENST00000342014	D;D;D	0.92149	-2.98;-2.98;-2.98	4.84	4.84	0.62591	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.51477	D	0.000092	D	0.97356	0.9135	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98081	1.0404	10	0.87932	D	0	.	12.3781	0.55291	0.0:0.0:0.0:1.0	.	467	P51813	BMX_HUMAN	P	467	ENSP00000350224:L467P;ENSP00000308774:L467P;ENSP00000340082:L467P	ENSP00000340082:L467P	L	+	2	0	BMX	15470031	1.000000	0.71417	0.995000	0.50966	0.824000	0.46624	7.837000	0.86796	1.593000	0.50029	0.481000	0.45027	CTC	.	.		0.363	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	NM_001721		C	15560110	T	C	15560110	3	2	178	1	0	0	0	0	1	0	0	0	1473	1551	54	2	1454	2	BMX	23	15560110	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10		15560110	139710450	122	26823										
NR0B1	190	hgsc.bcm.edu	37	chrX	30327407	30327407	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tctctggagcctcaggagccGcgcgcgtttgcttcgcgctc	13	15	2	0			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chrX:30327407G>A	ENST00000378970.4	-	1	308	c.74C>T	c.(73-75)gCg>gTg	p.A25V	NR0B1_ENST00000453287.1_Missense_Mutation_p.A25V|NR0B1_ENST00000378963.1_5'Flank	NM_000475.4	NP_000466.2	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1	25	4 X 67 AA tandem repeats.				adrenal gland development (GO:0030325)|gene expression (GO:0010467)|gonad development (GO:0008406)|hypothalamus development (GO:0021854)|intracellular receptor signaling pathway (GO:0030522)|Leydig cell differentiation (GO:0033327)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of cell differentiation (GO:0045596)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|protein localization (GO:0008104)|response to immobilization stress (GO:0035902)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)|steroid biosynthetic process (GO:0006694)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	AF-2 domain binding (GO:0050682)|DNA binding (GO:0003677)|DNA hairpin binding (GO:0032448)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|steroid hormone receptor binding (GO:0035258)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	24					Dexamethasone(DB01234)|Tretinoin(DB00755)	CTCAGGAGCCGCGCGCGTTTG	0.692																																					p.A25V		Atlas-SNP	.											.	NR0B1	61	.	0			c.C74T						.						9	10	9					X																	30327407		2079	4083	6162	SO:0001583	missense	190	exon1			GGAGCCGCGCGCG	S74720	CCDS14223.1	Xp21.3	2014-06-28			ENSG00000169297	ENSG00000169297		"Nuclear hormone receptors"	7960	protein-coding gene	gene with protein product		300473	"dosage-sensitive sex reversal"	AHC, DSS		1301166, 10412368	Standard	NM_000475		Approved	DAX1, AHCH	uc004dcf.4	P51843	OTTHUMG00000021323	ENST00000378970.4:c.74C>T	chrX.hg19:g.30327407G>A	ENSP00000368253:p.Ala25Val	113.0	0.0		105.0	24.0	NM_000475	Q96F69	Missense_Mutation	SNP	ENST00000378970.4	hg19	CCDS14223.1	.	.	.	.	.	.	.	.	.	.	G	6.749	0.506986	0.12883	.	.	ENSG00000169297	ENST00000378970;ENST00000453287	D;D	0.98090	-3.84;-4.71	4.42	2.58	0.30949	.	0.605757	0.15887	N	0.239740	D	0.93976	0.8071	L	0.36672	1.1	0.09310	N	1	P	0.48016	0.904	B	0.41374	0.355	D	0.87868	0.2669	10	0.36615	T	0.2	-5.0009	6.7124	0.23284	0.0:0.1917:0.6061:0.2022	.	25	P51843	NR0B1_HUMAN	V	25	ENSP00000368253:A25V;ENSP00000396403:A25V	ENSP00000368253:A25V	A	-	2	0	NR0B1	30237328	0.000000	0.05858	0.002000	0.10522	0.247000	0.25773	-0.372000	0.07504	0.396000	0.25283	0.513000	0.50165	GCG	.	.		0.692	NR0B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056161.1	NM_000475		A	30327407	G	A	30327407	3	1	178	1	0	0	0	0	1	0	0	0	10622	1087	38	1	1346	1	NR0B1	23	30327407	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	14767297	30327407	124943153	123	26824										
COL4A6	1288	hgsc.bcm.edu	37	chrX	107464546	107464546	+	Frame_Shift_Del	DEL	G	G	-													0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tcaatcccgataaaccagtaGagccagtgaatccttgagga							TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chrX:107464546delG	ENST00000372216.4	-	4	306	c.206delC	c.(205-207)tctfs	p.S69fs	COL4A6_ENST00000334504.7_Frame_Shift_Del_p.S68fs|COL4A6_ENST00000545689.1_Frame_Shift_Del_p.S68fs|COL4A6_ENST00000394872.2_Frame_Shift_Del_p.S68fs|COL4A6_ENST00000538570.1_Frame_Shift_Del_p.S68fs	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	69	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						TAAACCAGTAGAGCCAGTGAA	0.478									Alport syndrome with Diffuse Leiomyomatosis																												p.S69fs	Melanoma(87;1895 1945 2589 7165)	Atlas-INDEL	.											.	COL4A6	270	.	0			c.207delT						.						146	125	133					X																	107464546		2203	4300	6503	SO:0001589	frameshift_variant	1288	exon4	Familial Cancer Database		.	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.206delC	chrX.hg19:g.107464546delG	ENSP00000361290:p.Ser69fs	191.0	0.0		194.0	25.0	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Frame_Shift_Del	DEL	ENST00000372216.4	hg19	CCDS14541.1																																																																																			.	.		0.478	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			-	107464546	G	-	107464546	7	5	178	1	0	1	0	1	0	0	0	0	3697	942	33	0	5037	0	COL4A6	23	107464546	Frame_Shift_Del	DEL	G	TCGA-DD-AAD1-01A-11D-A40R-10	77137139	107464546	47806014	124	26825										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107824223	107824223	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	tatcctatagggtaaaccagGcaaagatggagaaaatggcc	11	7	0	2			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chrX:107824223G>T	ENST00000361603.2	+	16	1146	c.902G>T	c.(901-903)gGc>gTc	p.G301V	COL4A5_ENST00000328300.6_Missense_Mutation_p.G301V	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	301	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GGTAAACCAGGCAAAGATGGA	0.373									Alport syndrome with Diffuse Leiomyomatosis																												p.G301V		Atlas-SNP	.											.	COL4A5	262	.	0			c.G902T						.						120	106	111					X																	107824223		2203	4300	6503	SO:0001583	missense	1287	exon16	Familial Cancer Database		AACCAGGCAAAGA	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.902G>T	chrX.hg19:g.107824223G>T	ENSP00000354505:p.Gly301Val	421.0	0.0		360.0	76.0	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	hg19	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.091071	0.55968	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.99353	-5.77;-5.77	5.5	4.63	0.57726	.	0.000000	0.85682	D	0.000000	D	0.99600	0.9855	H	0.96142	3.775	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97772	1.0227	10	0.87932	D	0	.	14.8262	0.70113	0.0:0.0:0.855:0.145	.	301;301	E7EVY4;P29400	.;CO4A5_HUMAN	V	301	ENSP00000331902:G301V;ENSP00000354505:G301V	ENSP00000331902:G301V	G	+	2	0	COL4A5	107710879	1.000000	0.71417	0.975000	0.42487	0.941000	0.58515	6.531000	0.73820	1.062000	0.40625	0.600000	0.82982	GGC	.	.		0.373	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			T	107824223	G	T	107824223	3	4	178	1	0	0	0	0	1	0	0	0	3696	1203	42	3	964	3	COL4A5	23	107824223	Missense_Mutation	SNP	G	TCGA-DD-AAD1-01A-11D-A40R-10	359677	107824223	47446337	125	26826										
SLC25A43	203427	hgsc.bcm.edu	37	chrX	118540512	118540512	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	cgcaggcatggtttccaccaTtgtaacatatcctacagacc	7	13	0	1			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chrX:118540512T>C	ENST00000217909.7	+	2	709	c.365T>C	c.(364-366)aTt>aCt	p.I122T	SLC25A43_ENST00000336249.7_Missense_Mutation_p.I122T|SLC25A43_ENST00000488158.1_3'UTR	NM_145305.2	NP_660348.2	Q8WUT9	S2543_HUMAN	solute carrier family 25, member 43	122					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	9						GTTTCCACCATTGTAACATAT	0.483																																					p.I122T		Atlas-SNP	.											.	SLC25A43	29	.	0			c.T365C						.						105	93	97					X																	118540512		2203	4300	6503	SO:0001583	missense	203427	exon2			CCACCATTGTAAC	BC019584	CCDS14577.1	Xq24	2013-05-22			ENSG00000077713	ENSG00000077713		"Solute carriers"	30557	protein-coding gene	gene with protein product		300641				16949250	Standard	NM_145305		Approved		uc004erd.3	Q8WUT9	OTTHUMG00000022272	ENST00000217909.7:c.365T>C	chrX.hg19:g.118540512T>C	ENSP00000217909:p.Ile122Thr	198.0	0.0		210.0	46.0	NM_145305	O75854|Q8N9L5	Missense_Mutation	SNP	ENST00000217909.7	hg19	CCDS14577.1	.	.	.	.	.	.	.	.	.	.	T	12.25	1.881574	0.33255	.	.	ENSG00000077713	ENST00000217909;ENST00000336249;ENST00000326714	T;T	0.77877	-1.13;-1.13	4.9	3.74	0.42951	Mitochondrial carrier domain (2);	0.448815	0.24490	N	0.038075	T	0.59715	0.2214	N	0.05414	-0.055	0.20489	N	0.999891	P;B	0.36086	0.536;0.259	B;B	0.40256	0.324;0.122	T	0.51156	-0.8741	10	0.32370	T	0.25	.	8.7394	0.34547	0.0:0.0909:0.0:0.9091	.	122;122	B4E1P8;Q8WUT9	.;S2543_HUMAN	T	122;122;70	ENSP00000217909:I122T;ENSP00000338628:I122T	ENSP00000217909:I122T	I	+	2	0	SLC25A43	118424540	1.000000	0.71417	0.707000	0.30419	0.891000	0.51852	5.443000	0.66581	0.569000	0.29329	0.237000	0.17872	ATT	.	.		0.483	SLC25A43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058028.1	NM_145305		C	118540512	T	C	118540512	3	2	178	1	0	0	0	0	1	0	0	0	14523	1493	52	2	371	2	SLC25A43	23	118540512	Missense_Mutation	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	10716289	118540512	36730048	126	26827										
MCF2	4168	hgsc.bcm.edu	37	chrX	138686908	138686908	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0393700787401575	5	1	0.790875688916105	1.21267605633803	0.727605633802817	0.294117647058823	0.979516806722687	0	ttccaggctgctcaagaaaaTgctgtgaaaatttcagagaa	9	7	2	3			TCGA-DD-AAD1-01A-11D-A40R-10	TCGA-DD-AAD1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8179bebc-0b69-4345-9585-b23ec97837a0	2397526c-9196-4093-8c57-e47020e03b20	g.chrX:138686908T>C	ENST00000370576.4	-	15	1884	c.1675A>G	c.(1675-1677)Att>Gtt	p.I559V	MCF2_ENST00000370573.4_Splice_Site_p.I559V|MCF2_ENST00000370578.4_Splice_Site_p.I704V|MCF2_ENST00000338585.6_Splice_Site_p.I575V|MCF2_ENST00000483690.1_5'Flank|MCF2_ENST00000414978.1_Splice_Site_p.I619V|MCF2_ENST00000520602.1_Splice_Site_p.I619V|MCF2_ENST00000519895.1_Splice_Site_p.I635V|MCF2_ENST00000536274.1_Splice_Site_p.I520V	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	559	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					CTCAAGAAAATGCTGTGAAAA	0.274																																					p.I635V		Atlas-SNP	.											.	MCF2	432	.	0			c.A1903G						.						26	26	26					X																	138686908		2201	4294	6495	SO:0001630	splice_region_variant	4168	exon19			AGAAAATGCTGTG		CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"Rho guanine nucleotide exchange factors"	6940	protein-coding gene	gene with protein product	"Oncogene MCF2 (oncogene DBL)"	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.1674-1A>G	chrX.hg19:g.138686908T>C		930.0	1.0		832.0	169.0	NM_001171876	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000370576.4	hg19	CCDS14667.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	5.167|5.167	0.216411|0.216411	0.09810|0.09810	.|.	.|.	ENSG00000101977|ENSG00000101977	ENST00000437564|ENST00000520602;ENST00000370576;ENST00000536274;ENST00000370578;ENST00000414978;ENST00000446225;ENST00000519895;ENST00000370573;ENST00000338585	.|T;T;T;T;T;T;T;T;T	.|0.44881	.|0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.56|5.56	3.14|3.14	0.36123|0.36123	.|Dbl homology (DH) domain (5);	.|0.177615	.|0.49916	.|D	.|0.000128	T|T	0.22627|0.22627	0.0546|0.0546	N|N	0.16307|0.16307	0.4|0.4	0.29987|0.29987	N|N	0.817223|0.817223	.|B;B;B;B;B;B;B;B	.|0.06786	.|0.001;0.0;0.0;0.001;0.0;0.001;0.0;0.001	.|B;B;B;B;B;B;B;B	.|0.12837	.|0.008;0.008;0.005;0.008;0.003;0.008;0.007;0.008	T|T	0.11916|0.11916	-1.0568|-1.0568	5|10	.|0.33141	.|T	.|0.24	.|.	4.7507|4.7507	0.13059|0.13059	0.0:0.1637:0.159:0.6773|0.0:0.1637:0.159:0.6773	.|.	.|635;704;520;559;559;704;575;559	.|E9PH77;B7Z3Z2;F5H091;B2R9S6;P10911-2;Q5JYJ7;P10911-4;P10911	.|.;.;.;.;.;.;.;MCF2_HUMAN	R|V	62|619;559;520;704;619;162;635;559;575	.|ENSP00000427745:I619V;ENSP00000359608:I559V;ENSP00000438155:I520V;ENSP00000359610:I704V;ENSP00000397055:I619V;ENSP00000405848:I162V;ENSP00000430276:I635V;ENSP00000359605:I559V;ENSP00000342204:I575V	.|ENSP00000342204:I575V	H|I	-|-	2|1	0|0	MCF2|MCF2	138514574|138514574	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.184000|0.184000	0.23303|0.23303	1.377000|1.377000	0.34317|0.34317	0.251000|0.251000	0.21505|0.21505	0.441000|0.441000	0.28932|0.28932	CAT|ATT	.	.		0.274	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369	Missense_Mutation	C	138686908	T	C	138686908	5	2	178	1	0	0	0	0	0	0	1	0	9387	1478	51	2	1174	2	MCF2	23	138686908	Splice_Site	SNP	T	TCGA-DD-AAD1-01A-11D-A40R-10	20146396	138686908	16583652	127	26828										
DNAJC16	23341	hgsc.bcm.edu	37	chr1	15888777	15888777	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	tcggcagcaggagtttgccgAcaccttactaccagacagtg	11	12	0	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr1:15888777A>T	ENST00000375847.3	+	9	1459	c.1295A>T	c.(1294-1296)gAc>gTc	p.D432V	DNAJC16_ENST00000483270.1_3'UTR|DNAJC16_ENST00000375838.1_Missense_Mutation_p.D432V|DNAJC16_ENST00000375849.1_Missense_Mutation_p.D432V	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	432					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GAGTTTGCCGACACCTTACTA	0.502																																					p.D432V		Atlas-SNP	.											.	DNAJC16	59	.	0			c.A1295T						.						137	121	126					1																	15888777		2203	4300	6503	SO:0001583	missense	23341	exon9			TTGCCGACACCTT	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.1295A>T	chr1.hg19:g.15888777A>T	ENSP00000365007:p.Asp432Val	90.0	0.0		96.0	13.0	NM_015291	Q68D57|Q86X32|Q8N5P4	Missense_Mutation	SNP	ENST00000375847.3	hg19	CCDS30606.1	.	.	.	.	.	.	.	.	.	.	A	8.231	0.804689	0.16467	.	.	ENSG00000116138	ENST00000375847;ENST00000375838;ENST00000375849;ENST00000546230	T;T;T	0.11930	2.73;2.73;2.73	6.06	-4.85	0.03142	.	0.782547	0.12931	N	0.427343	T	0.08582	0.0213	L	0.29908	0.895	0.28278	N	0.924114	B;B	0.19200	0.026;0.034	B;B	0.22880	0.03;0.042	T	0.20371	-1.0277	10	0.48119	T	0.1	-0.975	8.3892	0.32518	0.3052:0.2033:0.4915:0.0	.	432;432	Q9Y2G8;Q5TDG9	DJC16_HUMAN;.	V	432	ENSP00000365007:D432V;ENSP00000364998:D432V;ENSP00000365009:D432V	ENSP00000364998:D432V	D	+	2	0	DNAJC16	15761364	0.239000	0.23836	0.029000	0.17559	0.059000	0.15707	0.476000	0.22180	-1.197000	0.02673	-1.844000	0.00574	GAC	.	.		0.502	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		T	15888777	A	T	15888777	3	4	179	1	0	0	0	0	1	0	0	0	4637	275	10	4	1325	4	DNAJC16	1	15888777	Missense_Mutation	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10		15888777	233361844	1	26829										
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19166377	19166377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cagctctttgcccatgtaggCgaagctgaaacccaccactg	9	14	1	1	rs368636486		TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr1:19166377C>T	ENST00000375371.3	-	6	2257	c.2236G>A	c.(2236-2238)Gcc>Acc	p.A746T		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	746					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	CCCATGTAGGCGAAGCTGAAA	0.542																																					p.A746T		Atlas-SNP	.											TAS1R2,NS,carcinoma,0,1	TAS1R2	134	.	0			c.G2236A						.	C	THR/ALA	0,4406		0,0,2203	134	117	123		2236	4.1	1	1		123	2,8598	2.2+/-6.3	0,2,4298	no	missense	TAS1R2	NM_152232.2	58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	746/840	19166377	2,13004	2203	4300	6503	SO:0001583	missense	80834	exon6			TGTAGGCGAAGCT		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14905	protein-coding gene	gene with protein product		606226	"G protein-coupled receptor 71"	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.2236G>A	chr1.hg19:g.19166377C>T	ENSP00000364520:p.Ala746Thr	133.0	0.0		153.0	30.0	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	hg19	CCDS187.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.580666	0.46006	0.0	2.33E-4	ENSG00000179002	ENST00000375371	D	0.93763	-3.28	5.07	4.12	0.48240	GPCR, family 3, C-terminal (2);	0.142464	0.31589	N	0.007393	D	0.96402	0.8826	M	0.85710	2.77	0.37005	D	0.895437	D	0.89917	1.0	D	0.73380	0.98	D	0.97750	1.0214	10	0.59425	D	0.04	.	12.6819	0.56926	0.165:0.835:0.0:0.0	.	746	Q8TE23	TS1R2_HUMAN	T	746	ENSP00000364520:A746T	ENSP00000364520:A746T	A	-	1	0	TAS1R2	19038964	0.048000	0.20356	0.995000	0.50966	0.262000	0.26303	0.418000	0.21230	2.363000	0.80096	0.655000	0.94253	GCC	.	.		0.542	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			T	19166377	C	T	19166377	3	4	179	1	0	0	0	0	1	0	0	0	15578	768	27	1	287	1	TAS1R2	1	19166377	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	3277600	19166377	230084244	2	26830										
EIF2B3	8891	hgsc.bcm.edu	37	chr1	45363027	45363027	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	tctaccaccctttttcttacCcattttccattaggaaatcc	2	14	2	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr1:45363027C>T	ENST00000360403.2	-	6	782	c.656G>A	c.(655-657)gGg>gAg	p.G219E	EIF2B3_ENST00000372183.3_Splice_Site_p.G219E	NM_001261418.1|NM_020365.4	NP_001248347.1|NP_065098.1	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa	219					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|positive regulation of GTPase activity (GO:0043547)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	guanyl-nucleotide exchange factor activity (GO:0005085)|nucleotidyltransferase activity (GO:0016779)|translation initiation factor activity (GO:0003743)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	17	Acute lymphoblastic leukemia(166;0.155)					TTTTTCTTACCCATTTTCCAT	0.363																																					p.G219E	Colon(26;357 658 2581 11857 12657)	Atlas-SNP	.											.	EIF2B3	43	.	0			c.G656A						.						81	78	79					1																	45363027		2203	4300	6503	SO:0001630	splice_region_variant	8891	exon6			TCTTACCCATTTT	AF257077	CCDS517.1, CCDS53313.1, CCDS72775.1	1p34.1	2008-02-05	2002-08-29		ENSG00000070785	ENSG00000070785			3259	protein-coding gene	gene with protein product		606273	"eukaryotic translation initiation factor 2B, subunit 3 (gamma, 58kD)"			10900014	Standard	NM_020365		Approved	EIF2Bgamma, EIF-2B	uc001cmt.3	Q9NR50	OTTHUMG00000008585	ENST00000360403.2:c.656+1G>A	chr1.hg19:g.45363027C>T		46.0	0.0		38.0	6.0	NM_020365	B2RBH8|D3DPZ2|Q5QP89|Q5QP90|Q8NDB5|Q8WV57|Q9H850	Missense_Mutation	SNP	ENST00000360403.2	hg19	CCDS517.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.81|10.81	1.455052|1.455052	0.26161|0.26161	.|.	.|.	ENSG00000070785|ENSG00000070785	ENST00000360403;ENST00000372183|ENST00000439363	D;D|D	0.82711|0.85339	-1.64;-1.64|-1.97	5.21|5.21	-3.53|-3.53	0.04667|0.04667	.|.	0.741113|0.741113	0.13833|0.13833	N|N	0.359577|0.359577	T|T	0.55481|0.55481	0.1923|0.1923	N|N	0.00841|0.00841	-1.15|-1.15	0.26623|0.26623	N|N	0.972624|0.972624	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.0;0.001;0.0|.	T|T	0.51521|0.51521	-0.8695|-0.8695	9|7	.|.	.|.	.|.	-16.9435|-16.9435	12.8498|12.8498	0.57850|0.57850	0.0:0.7666:0.0:0.2334|0.0:0.7666:0.0:0.2334	.|.	219;219;219|.	Q9NR50-2;Q9NR50-3;Q9NR50|.	.;.;EI2BG_HUMAN|.	E|S	219|40	ENSP00000353575:G219E;ENSP00000361257:G219E|ENSP00000396985:G40S	.|.	G|G	-|-	2|1	0|0	EIF2B3|EIF2B3	45135614|45135614	1.000000|1.000000	0.71417|0.71417	0.461000|0.461000	0.27105|0.27105	0.491000|0.491000	0.33493|0.33493	0.548000|0.548000	0.23314|0.23314	-0.873000|-0.873000	0.04032|0.04032	-0.373000|-0.373000	0.07131|0.07131	GGG|GGT	.	.		0.363	EIF2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023724.1	NM_020365	Missense_Mutation	T	45363027	C	T	45363027	5	4	179	1	0	0	0	0	0	0	1	0	5004	637	22	3	767	3	EIF2B3	1	45363027	Splice_Site	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	26196650	45363027	203887594	3	26831										
NHLH2	4808	hgsc.bcm.edu	37	chr1	116380822	116380822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gctcagctgctgcgggtgcgGgtagagcgcggctcggctgc	19	12	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr1:116380822G>A	ENST00000369506.1	-	1	5716	c.172C>T	c.(172-174)Ccg>Tcg	p.P58S	NHLH2_ENST00000320238.3_Missense_Mutation_p.P58S			Q02577	HEN2_HUMAN	nescient helix loop helix 2	58					cell differentiation (GO:0030154)|central nervous system development (GO:0007417)|mating behavior (GO:0007617)|ovulation cycle (GO:0042698)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)			prostate(1)	1	Lung SC(450;0.184)	all_cancers(81;1.75e-06)|all_epithelial(167;1.16e-06)|all_lung(203;9.55e-06)|Lung NSC(69;5.83e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TGCGGGTGCGGGTAGAGCGCG	0.766																																					p.P58S		Atlas-SNP	.											.	NHLH2	8	.	0			c.C172T						.						5	7	6					1																	116380822		1991	3932	5923	SO:0001583	missense	4808	exon2			GGTGCGGGTAGAG		CCDS885.1	1p12-p11	2013-05-21			ENSG00000177551	ENSG00000177551		"Basic helix-loop-helix proteins"	7818	protein-coding gene	gene with protein product		162361		HEN2		1528853	Standard	NM_005599		Approved	NSCL2, bHLHa34	uc001efy.3	Q02577	OTTHUMG00000011969	ENST00000369506.1:c.172C>T	chr1.hg19:g.116380822G>A	ENSP00000358519:p.Pro58Ser	55.0	0.0		38.0	7.0	NM_001111061	Q5T1P6	Missense_Mutation	SNP	ENST00000369506.1	hg19	CCDS885.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.058825	0.36277	.	.	ENSG00000177551	ENST00000320238;ENST00000369506;ENST00000429731	D;D	0.96459	-4.02;-4.02	4.49	3.58	0.41010	.	0.096213	0.42821	D	0.000656	T	0.80660	0.4665	N	0.08118	0	0.31518	N	0.662774	B	0.17465	0.022	B	0.10450	0.005	T	0.70371	-0.4890	10	0.30854	T	0.27	-31.3868	6.1241	0.20170	0.0958:0.0:0.5863:0.3179	.	58	Q02577	HEN2_HUMAN	S	58	ENSP00000322087:P58S;ENSP00000358519:P58S	ENSP00000322087:P58S	P	-	1	0	NHLH2	116182345	0.537000	0.26386	1.000000	0.80357	0.981000	0.71138	0.923000	0.28757	0.890000	0.36211	0.561000	0.74099	CCG	.	.		0.766	NHLH2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033090.1	NM_005599		A	116380822	G	A	116380822	3	1	179	1	0	0	0	0	1	0	0	0	10413	1232	43	3	239	3	NHLH2	1	116380822	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	71017795	116380822	132869799	4	26832										
TDRD10	126668	hgsc.bcm.edu	37	chr1	154519928	154519928	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gtccatcgaatcctcaaaggGaaaatcactggtgctttgaa	9	9	2	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr1:154519928G>T	ENST00000368480.3	+	12	1081	c.996G>T	c.(994-996)ggG>ggT	p.G332G	TDRD10_ENST00000479937.1_3'UTR|TDRD10_ENST00000368482.4_Silent_p.G332G			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	332							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TCCTCAAAGGGAAAATCACTG	0.527																																					p.G332G		Atlas-SNP	.											.	TDRD10	48	.	0			c.G996T						.						184	150	162					1																	154519928		2203	4300	6503	SO:0001819	synonymous_variant	126668	exon12			CAAAGGGAAAATC	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"Tudor domain containing", "RNA binding motif (RRM) containing"	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.996G>T	chr1.hg19:g.154519928G>T		115.0	0.0		128.0	27.0	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Silent	SNP	ENST00000368480.3	hg19	CCDS41406.1																																																																																			.	.		0.527	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499		T	154519928	G	T	154519928	2	4	179	1	0	0	0	0	0	0	0	1	15746	1161	41	3		3	TDRD10	1	154519928	Silent	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	38139106	154519928	94730693	5	26833										
F5	2153	hgsc.bcm.edu	37	chr1	169505910	169505910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	tatcatcagagtcttcaataTctgtttccctgaaataataa	4	8	5	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr1:169505910T>C	ENST00000367797.3	-	14	5006	c.4805A>G	c.(4804-4806)gAt>gGt	p.D1602G	F5_ENST00000367796.3_Missense_Mutation_p.D1607G	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1602	F5/8 type A 3.|Plastocyanin-like 5.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GTCTTCAATATCTGTTTCCCT	0.338																																					p.D1602G		Atlas-SNP	.											.	F5	301	.	0			c.A4805G						.						58	61	60					1																	169505910		2203	4299	6502	SO:0001583	missense	2153	exon14			TCAATATCTGTTT	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.4805A>G	chr1.hg19:g.169505910T>C	ENSP00000356771:p.Asp1602Gly	69.0	0.0		68.0	16.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	hg19	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.003831	0.35320	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.98926	-5.24;-5.24	4.45	3.29	0.37713	Cupredoxin (2);	0.588932	0.18543	N	0.138122	D	0.93772	0.8009	L	0.31926	0.97	0.33339	D	0.569544	B	0.28900	0.227	B	0.34301	0.179	D	0.89764	0.3949	9	0.41790	T	0.15	-9.4708	7.7168	0.28708	0.1874:0.0:0.0:0.8126	.	1602	P12259	FA5_HUMAN	G	1602;1607	ENSP00000356771:D1602G;ENSP00000356770:D1607G	ENSP00000356770:D1607G	D	-	2	0	F5	167772534	0.001000	0.12720	0.004000	0.12327	0.068000	0.16541	0.891000	0.28309	0.784000	0.33661	0.460000	0.39030	GAT	.	.		0.338	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		C	169505910	T	C	169505910	3	2	179	1	0	0	0	0	1	0	0	0	5350	1435	50	2	1917	2	F5	1	169505910	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	14985982	169505910	79744711	6	26834										
DHX9	1660	hgsc.bcm.edu	37	chr1	182823255	182823255	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ctcgtctaaaccaatattttCagaaagaaaagatccaagga	6	8	2	3			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr1:182823255C>G	ENST00000367549.3	+	6	678	c.568C>G	c.(568-570)Cag>Gag	p.Q190E		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	190	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.|Interaction with CREBBP.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						CCAATATTTTCAGAAAGAAAA	0.383																																					p.Q190E	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.C568G						.						84	84	84					1																	182823255		1819	4078	5897	SO:0001583	missense	1660	exon6			TATTTTCAGAAAG	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.568C>G	chr1.hg19:g.182823255C>G	ENSP00000356520:p.Gln190Glu	189.0	0.0		238.0	36.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.041604	0.93685	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	T	0.79554	-1.28	5.39	5.39	0.77823	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.066083	0.64402	D	0.000011	D	0.92811	0.7714	H	0.94306	3.52	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.94558	0.7760	10	0.87932	D	0	.	18.7614	0.91853	0.0:1.0:0.0:0.0	.	190	Q08211	DHX9_HUMAN	E	190	ENSP00000356520:Q190E	ENSP00000356520:Q190E	Q	+	1	0	DHX9	181089878	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.242000	0.78210	2.528000	0.85240	0.655000	0.94253	CAG	.	.		0.383	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		G	182823255	C	G	182823255	3	3	179	1	0	0	0	0	1	0	0	0	4518	827	29	4	586	4	DHX9	1	182823255	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	13317345	182823255	66427366	7	26835										
C1orf115	79762	hgsc.bcm.edu	37	chr1	220870013	220870013	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gtcatcggcctgcaaggcttCgctgcagcctactccgcccc	10	18	1	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr1:220870013C>T	ENST00000294889.5	+	2	927	c.369C>T	c.(367-369)ttC>ttT	p.F123F		NM_024709.4	NP_078985.3	Q9H7X2	CA115_HUMAN	chromosome 1 open reading frame 115	123						integral component of membrane (GO:0016021)		p.F123F(1)		large_intestine(1)|lung(1)	2				GBM - Glioblastoma multiforme(131;0.0273)		TGCAAGGCTTCGCTGCAGCCT	0.557																																					p.F123F		Atlas-SNP	.											C1orf115,NS,carcinoma,0,1	C1orf115	6	.	1	Substitution - coding silent(1)	lung(1)	c.C369T						.						99	97	98					1																	220870013		2203	4300	6503	SO:0001819	synonymous_variant	79762	exon2			AGGCTTCGCTGCA	AK024208	CCDS1524.1	1q41	2008-02-05			ENSG00000162817	ENSG00000162817			25873	protein-coding gene	gene with protein product						12477932	Standard	NM_024709		Approved	FLJ14146	uc001hmp.1	Q9H7X2	OTTHUMG00000037361	ENST00000294889.5:c.369C>T	chr1.hg19:g.220870013C>T		95.0	0.0		138.0	40.0	NM_024709	B3KRN3|D3DTB2	Silent	SNP	ENST00000294889.5	hg19	CCDS1524.1																																																																																			.	.		0.557	C1orf115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090922.3	NM_024709		T	220870013	C	T	220870013	2	4	179	1	0	0	0	0	0	0	0	1	1990	883	31	1		1	C1orf115	1	220870013	Silent	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	38046758	220870013	28380608	8	26836										
ADAM17	6868	hgsc.bcm.edu	37	chr2	9642319	9642319	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	aacctgtgcagtaggacacgCctttgcaagtagcattaatc	9	10	0	0	rs375981644		TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr2:9642319C>A	ENST00000310823.3	-	13	1813	c.1631G>T	c.(1630-1632)gGc>gTc	p.G544V		NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	544	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		GTAGGACACGCCTTTGCAAGT	0.453																																					p.G544V		Atlas-SNP	.											.	ADAM17	61	.	0			c.G1631T						.						269	248	255					2																	9642319		2203	4300	6503	SO:0001583	missense	6868	exon13			GACACGCCTTTGC	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.1631G>T	chr2.hg19:g.9642319C>A	ENSP00000309968:p.Gly544Val	68.0	0.0		74.0	12.0	NM_003183	O60226	Missense_Mutation	SNP	ENST00000310823.3	hg19	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.402862	0.83230	.	.	ENSG00000151694	ENST00000310823	T	0.10382	2.88	5.16	5.16	0.70880	Blood coagulation inhibitor, Disintegrin (5);	0.000000	0.85682	D	0.000000	T	0.16854	0.0405	N	0.12961	0.28	0.80722	D	1	P;P	0.51240	0.943;0.943	P;P	0.62382	0.901;0.901	T	0.24621	-1.0155	10	0.23302	T	0.38	.	18.6464	0.91411	0.0:1.0:0.0:0.0	.	544;544	B2RNB2;P78536	.;ADA17_HUMAN	V	544	ENSP00000309968:G544V	ENSP00000309968:G544V	G	-	2	0	ADAM17	9559770	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	5.690000	0.68241	2.382000	0.81193	0.462000	0.41574	GGC	.	.		0.453	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			A	9642319	C	A	9642319	3	1	179	1	0	0	0	0	1	0	0	0	238	739	26	3	871	3	ADAM17	2	9642319	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10		9642319	233557054	9	26837										
APOB	338	hgsc.bcm.edu	37	chr2	21229941	21229941	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cacatagccgaatgccgacaTctctatggtgaatggagaca	10	10	1	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr2:21229941T>G	ENST00000233242.1	-	26	9926	c.9799A>C	c.(9799-9801)Atg>Ctg	p.M3267L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3267					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AATGCCGACATCTCTATGGTG	0.473																																					p.M3267L		Atlas-SNP	.											.	APOB	761	.	0			c.A9799C						.						79	72	74					2																	21229941		2203	4300	6503	SO:0001583	missense	338	exon26			CCGACATCTCTAT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9799A>C	chr2.hg19:g.21229941T>G	ENSP00000233242:p.Met3267Leu	140.0	0.0		122.0	20.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	1.336	-0.595426	0.03771	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.36157	1.27	4.6	3.35	0.38373	.	0.267525	0.30791	N	0.008879	T	0.28167	0.0695	L	0.52126	1.63	0.80722	D	1	B	0.13145	0.007	B	0.17722	0.019	T	0.05920	-1.0856	10	0.08837	T	0.75	.	10.7634	0.46279	0.0:0.0:0.3908:0.6092	.	3267	P04114	APOB_HUMAN	L	3267	ENSP00000233242:M3267L	ENSP00000233242:M3267L	M	-	1	0	APOB	21083446	0.999000	0.42202	0.287000	0.24848	0.692000	0.40212	0.560000	0.23500	1.703000	0.51240	0.460000	0.39030	ATG	.	.		0.473	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21229941	T	G	21229941	3	3	179	1	0	0	0	0	1	0	0	0	785	1435	50	5	3908	5	APOB	2	21229941	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	11587622	21229941	221969432	10	26838										
STON1	11037	hgsc.bcm.edu	37	chr2	48809324	48809324	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ggtttgagctgatgcgtttcAagactttgtataatggggat	13	4	1	3			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr2:48809324A>T	ENST00000406226.1	+	3	1747	c.1552A>T	c.(1552-1554)Aag>Tag	p.K518*	STON1_ENST00000404752.1_Nonsense_Mutation_p.K518*|STON1-GTF2A1L_ENST00000394751.3_Nonsense_Mutation_p.K518*|STON1-GTF2A1L_ENST00000402114.2_Nonsense_Mutation_p.K518*|STON1-GTF2A1L_ENST00000309827.2_Nonsense_Mutation_p.K518*|STON1-GTF2A1L_ENST00000405008.1_Nonsense_Mutation_p.K518*|STON1-GTF2A1L_ENST00000394754.1_Nonsense_Mutation_p.K518*|STON1_ENST00000309835.3_Nonsense_Mutation_p.K518*	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	518	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GATGCGTTTCAAGACTTTGTA	0.423																																					p.K518X		Atlas-SNP	.											.	STON1	100	.	0			c.A1552T						.						169	163	165					2																	48809324		2203	4300	6503	SO:0001587	stop_gained	11037	exon3			CGTTTCAAGACTT	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1552A>T	chr2.hg19:g.48809324A>T	ENSP00000384615:p.Lys518*	146.0	0.0		108.0	17.0	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Nonsense_Mutation	SNP	ENST00000406226.1	hg19	CCDS1841.1	.	.	.	.	.	.	.	.	.	.	A	40	8.121667	0.98665	.	.	ENSG00000243244;ENSG00000243244;ENSG00000243244;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781	ENST00000404752;ENST00000406226;ENST00000309835;ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751	.	.	.	5.3	5.3	0.74995	.	0.273553	0.42172	D	0.000756	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.4186	0.74991	1.0:0.0:0.0:0.0	.	.	.	.	X	518	.	ENSP00000310969:K518X	K	+	1	0	STON1-GTF2A1L;STON1	48662828	1.000000	0.71417	0.981000	0.43875	0.965000	0.64279	5.755000	0.68750	2.235000	0.73313	0.533000	0.62120	AAG	.	.		0.423	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		T	48809324	A	T	48809324	4	4	179	1	0	0	0	0	0	1	0	0	15331	131	5	4	1554	4	STON1	2	48809324	Nonsense_Mutation	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10	27579383	48809324	194390049	11	26839										
ZAP70	7535	hgsc.bcm.edu	37	chr2	98340506	98340506	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gaggcccaggggcgatgccaGaccccgcggcgcacctgccc	15	18	0	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr2:98340506G>T	ENST00000264972.5	+	3	222	c.7G>T	c.(7-9)Gac>Tac	p.D3Y	ZAP70_ENST00000442208.1_5'Flank	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	3					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						GGCGATGCCAGACCCCGCGGC	0.692																																					p.D3Y		Atlas-SNP	.											.	ZAP70	77	.	0			c.G7T						.						7	9	8					2																	98340506		2157	4227	6384	SO:0001583	missense	7535	exon3			ATGCCAGACCCCG	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"SH2 domain containing"	12858	protein-coding gene	gene with protein product		176947	"zeta-chain (TCR) associated protein kinase (70 kD)"	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.7G>T	chr2.hg19:g.98340506G>T	ENSP00000264972:p.Asp3Tyr	66.0	0.0		54.0	10.0	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Missense_Mutation	SNP	ENST00000264972.5	hg19	CCDS33254.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.489903	0.84962	.	.	ENSG00000115085	ENST00000264972	T	0.75260	-0.92	4.99	4.99	0.66335	.	0.000000	0.51477	D	0.000098	D	0.88916	0.6567	M	0.92604	3.325	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.70487	0.969;0.928	D	0.91550	0.5256	10	0.87932	D	0	.	16.1427	0.81536	0.0:0.0:1.0:0.0	.	3;3	B4E0E2;P43403	.;ZAP70_HUMAN	Y	3	ENSP00000264972:D3Y	ENSP00000264972:D3Y	D	+	1	0	ZAP70	97706938	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.314000	0.78988	2.507000	0.84556	0.585000	0.79938	GAC	.	.		0.692	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1			T	98340506	G	T	98340506	3	4	179	1	0	0	0	0	1	0	0	0	17529	942	33	3	9	3	ZAP70	2	98340506	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	49531182	98340506	144858867	12	26840										
TTN	7273	hgsc.bcm.edu	37	chr2	179447173	179447173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cacagttgcagagacttgagCccagttgggcctgcttgttt	12	10	0	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr2:179447173C>T	ENST00000591111.1	-	264	61311	c.61087G>A	c.(61087-61089)Gct>Act	p.A20363T	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A13131T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A22004T|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A12939T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A19436T|TTN_ENST00000359218.5_Missense_Mutation_p.A13064T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590743.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20363	Fibronectin type-III 47. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAGACTTGAGCCCAGTTGGGC	0.463																																					p.A22004T		Atlas-SNP	.											.	TTN	18412	.	0			c.G66010A						.						76	70	72					2																	179447173		1906	4134	6040	SO:0001583	missense	7273	exon314			CTTGAGCCCAGTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.61087G>A	chr2.hg19:g.179447173C>T	ENSP00000465570:p.Ala20363Thr	150.0	0.0		174.0	41.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.41	3.382043	0.61845	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.86	4.97	0.65823	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.43590	0.1254	N	0.02658	-0.545	0.80722	D	1	P;P;P;P	0.52692	0.955;0.955;0.955;0.919	P;P;P;P	0.54889	0.763;0.763;0.763;0.686	T	0.62445	-0.6853	9	0.87932	D	0	.	16.5647	0.84576	0.1312:0.8688:0.0:0.0	.	12939;13064;13131;20363	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	19436;12939;13131;13064;12937	ENSP00000343764:A19436T;ENSP00000434586:A12939T;ENSP00000340554:A13131T;ENSP00000352154:A13064T	ENSP00000340554:A13131T	A	-	1	0	TTN	179155419	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.818000	0.86416	1.452000	0.47756	0.655000	0.94253	GCT	.	.		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179447173	C	T	179447173	3	4	179	1	0	0	0	0	1	0	0	0	16750	739	26	3	42165	3	TTN	2	179447173	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	81106667	179447173	63752200	13	26841										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185802852	185802852	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ttctggtgaattgtcagatgTttccaatgatcccaccacat	7	10	2	3			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr2:185802852T>G	ENST00000302277.6	+	4	3323	c.2729T>G	c.(2728-2730)gTt>gGt	p.V910G		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	910							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						TTGTCAGATGTTTCCAATGAT	0.408																																					p.V910G		Atlas-SNP	.											.	ZNF804A	322	.	0			c.T2729G						.						92	88	89					2																	185802852		2203	4300	6503	SO:0001583	missense	91752	exon4			CAGATGTTTCCAA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.2729T>G	chr2.hg19:g.185802852T>G	ENSP00000303252:p.Val910Gly	132.0	0.0		97.0	22.0	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	T	3.078	-0.189584	0.06299	.	.	ENSG00000170396	ENST00000302277	T	0.07114	3.22	5.57	1.09	0.20402	.	1.445440	0.04172	N	0.324931	T	0.05044	0.0135	N	0.08118	0	0.09310	N	1	B	0.24823	0.112	B	0.25140	0.058	T	0.37753	-0.9692	10	0.87932	D	0	-1.9062	3.3912	0.07290	0.2682:0.2907:0.0:0.441	.	910	Q7Z570	Z804A_HUMAN	G	910	ENSP00000303252:V910G	ENSP00000303252:V910G	V	+	2	0	ZNF804A	185511097	0.000000	0.05858	0.027000	0.17364	0.016000	0.09150	-0.510000	0.06328	0.721000	0.32231	0.482000	0.46254	GTT	.	.		0.408	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		G	185802852	T	G	185802852	3	3	179	1	0	0	0	0	1	0	0	0	18185	1725	60	5	2743	5	ZNF804A	2	185802852	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	6355679	185802852	57396521	14	26842										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198266709	198266709	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	aaggtaattggtggatttacCtttcctctgtgttggcggat	12	6	1	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr2:198266709C>A	ENST00000335508.6	-	15	2314	c.2223G>T	c.(2221-2223)aaG>aaT	p.K741N	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	741					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.K741N(2)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTGGATTTACCTTTCCTCTGT	0.343			Mis		myelodysplastic syndrome																																p.K741N		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	SF3B1,NS,carcinoma,0,3	SF3B1	1038	.	2	Substitution - Missense(2)	lung(2)	c.G2223T						.						88	84	85					2																	198266709		2203	4300	6503	SO:0001630	splice_region_variant	23451	exon15			ATTTACCTTTCCT	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2223+1G>T	chr2.hg19:g.198266709C>A		250.0	0.0		252.0	48.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.426756	0.83667	.	.	ENSG00000115524	ENST00000335508	T	0.66099	-0.19	5.71	4.83	0.62350	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85120	0.5624	H	0.96175	3.78	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.89843	0.4004	9	.	.	.	.	14.6098	0.68507	0.0:0.9299:0.0:0.0701	.	741	O75533	SF3B1_HUMAN	N	741	ENSP00000335321:K741N	.	K	-	3	2	SF3B1	197974954	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	4.541000	0.60670	1.404000	0.46819	0.655000	0.94253	AAG	.	.		0.343	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		Missense_Mutation	A	198266709	C	A	198266709	5	1	179	1	0	0	0	0	0	0	1	0	14164	695	24	3	1735	3	SF3B1	2	198266709	Splice_Site	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	12463857	198266709	44932664	15	26843										
AOX1	316	hgsc.bcm.edu	37	chr2	201457898	201457898	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	aaaaatgtcgatcctgaaacAatgctgttgccttatttgag	8	7	0	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr2:201457898A>G	ENST00000374700.2	+	2	316	c.75A>G	c.(73-75)acA>acG	p.T25T		NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	25	2Fe-2S ferredoxin-type. {ECO:0000255|PROSITE-ProRule:PRU00465}.				inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	ATCCTGAAACAATGCTGTTGC	0.338																																					p.T25T		Atlas-SNP	.											.	AOX1	152	.	0			c.A75G						.						277	238	251					2																	201457898		2203	4300	6503	SO:0001819	synonymous_variant	316	exon2			TGAAACAATGCTG	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.75A>G	chr2.hg19:g.201457898A>G		65.0	0.0		95.0	16.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Silent	SNP	ENST00000374700.2	hg19	CCDS33360.1																																																																																			.	.		0.338	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		G	201457898	A	G	201457898	2	3	179	1	0	0	0	0	0	0	0	1	729	117	5	2		2	AOX1	2	201457898	Silent	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10	3191189	201457898	41741475	16	26844										
ZNF502	91392	hgsc.bcm.edu	37	chr3	44762762	44762763	+	Frame_Shift_Ins	INS	-	-	A													0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gtccaactctctgcacacagINSaaaaaatcttggaaatgtaa							TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr3:44762762_44762763insA	ENST00000296091.4	+	4	709_710	c.453_454insA	c.(454-456)aaafs	p.K152fs	ZNF502_ENST00000449836.1_Frame_Shift_Ins_p.K152fs|ZNF502_ENST00000436624.2_Frame_Shift_Ins_p.K152fs	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	152					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		TCTGCACACAGAAAAAATCTTG	0.396																																					p.Q151fs		Atlas-INDEL	.											.	ZNF502	58	.	0			c.453_454insA						.																																			SO:0001589	frameshift_variant	91392	exon3			.	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"Zinc fingers, C2H2-type"	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.459dupA	chr3.hg19:g.44762768_44762768dupA	ENSP00000296091:p.Lys152fs	278.0	0.0		260.0	42.0	NM_001134442		Frame_Shift_Ins	INS	ENST00000296091.4	hg19	CCDS2719.1																																																																																			.	.		0.396	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		A	44762763	-	A	44762762	7	5	179	1	0	1	1	0	0	0	0	0	17965	933	33	0	459	0	ZNF502	3	44762762	Frame_Shift_Ins	INS	-	TCGA-DD-AAD2-01A-11D-A40R-10		44762762	153259668	17	26845										
CACNA1D	776	hgsc.bcm.edu	37	chr3	53845336	53845336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	acaccggcaggactatgagcTacaggactttggtcctggct	12	11	0	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr3:53845336T>C	ENST00000350061.5	+	48	6900	c.6389T>C	c.(6388-6390)cTa>cCa	p.L2130P	CACNA1D_ENST00000422281.2_Missense_Mutation_p.L2106P|CACNA1D_ENST00000288139.4_Missense_Mutation_p.L2150P	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	2130					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GACTATGAGCTACAGGACTTT	0.602																																					p.L2150P		Atlas-SNP	.											.	CACNA1D	324	.	0			c.T6449C						.						68	63	65					3																	53845336		2203	4300	6503	SO:0001583	missense	776	exon49			ATGAGCTACAGGA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.6389T>C	chr3.hg19:g.53845336T>C	ENSP00000288133:p.Leu2130Pro	104.0	0.0		103.0	15.0	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.384600	0.61845	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478	D;D;D;D	0.96265	-3.93;-3.96;-3.95;-3.95	5.56	4.37	0.52481	.	0.786356	0.11452	N	0.562709	D	0.97455	0.9167	M	0.73962	2.25	0.80722	D	1	P;D;D;D	0.65815	0.836;0.994;0.966;0.995	P;P;P;D	0.63957	0.572;0.878;0.642;0.92	D	0.94470	0.7684	10	0.33940	T	0.23	.	12.0173	0.53321	0.1296:0.0:0.0:0.8703	.	2106;1823;2130;2150	B0FYA3;Q59GD8;Q01668;Q01668-2	.;.;CAC1D_HUMAN;.	P	2130;2150;2106;1823	ENSP00000288133:L2130P;ENSP00000288139:L2150P;ENSP00000409174:L2106P;ENSP00000418014:L1823P	ENSP00000288139:L2150P	L	+	2	0	CACNA1D	53820376	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	7.466000	0.80914	1.010000	0.39314	0.533000	0.62120	CTA	.	.		0.602	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		C	53845336	T	C	53845336	3	2	179	1	0	0	0	0	1	0	0	0	2543	1522	53	2	6751	2	CACNA1D	3	53845336	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	9082574	53845336	144177094	18	26846										
FOXP1	27086	hgsc.bcm.edu	37	chr3	71021808	71021808	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	caaaacacttgtgaagactaAgattatgacgcactgcattc	7	9	0	4			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr3:71021808A>C	ENST00000318789.4	-	18	2075	c.1550T>G	c.(1549-1551)cTt>cGt	p.L517R	FOXP1_ENST00000498215.1_Missense_Mutation_p.L517R|FOXP1_ENST00000475937.1_Missense_Mutation_p.L517R|FOXP1_ENST00000484350.1_Missense_Mutation_p.L441R|FOXP1_ENST00000468577.1_Intron|FOXP1_ENST00000491238.1_Missense_Mutation_p.L519R|FOXP1_ENST00000493089.1_Missense_Mutation_p.L516R	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	517					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GTGAAGACTAAGATTATGACG	0.378			T	PAX5	ALL																																p.L519R		Atlas-SNP	.		Dom	yes		3	3p14.1	27086	forkhead box P1		L	.	FOXP1	104	.	0			c.T1556G						.						479	387	418					3																	71021808		2203	4300	6503	SO:0001583	missense	27086	exon13			AGACTAAGATTAT	AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"Forkhead boxes"	3823	protein-coding gene	gene with protein product	"fork head-related protein like B", "glutamine-rich factor 1", "PAX5/FOXP1 fusion protein"	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.1550T>G	chr3.hg19:g.71021808A>C	ENSP00000318902:p.Leu517Arg	110.0	0.0		70.0	9.0	NM_001244815	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Missense_Mutation	SNP	ENST00000318789.4	hg19	CCDS2914.1	.	.	.	.	.	.	.	.	.	.	A	18.24	3.579940	0.65992	.	.	ENSG00000114861	ENST00000318789;ENST00000358280;ENST00000475937;ENST00000497355;ENST00000491238;ENST00000493089;ENST00000498215;ENST00000484350	D;D;D;D;D;D;D	0.98792	-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14	5.81	5.81	0.92471	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	D	0.000000	D	0.99609	0.9858	H	0.99642	4.675	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.999;0.997;1.0;0.999	D	0.97377	0.9980	10	0.87932	D	0	.	16.4563	0.84015	1.0:0.0:0.0:0.0	.	516;516;441;517	B3KV70;G5E9V8;Q8NAN6;Q9H334	.;.;.;FOXP1_HUMAN	R	517;329;517;413;519;516;517;441	ENSP00000318902:L517R;ENSP00000419393:L517R;ENSP00000418225:L413R;ENSP00000420736:L519R;ENSP00000418524:L516R;ENSP00000418102:L517R;ENSP00000417857:L441R	ENSP00000318902:L517R	L	-	2	0	FOXP1	71104498	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.343000	0.79666	0.533000	0.62120	CTT	.	.		0.378	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682		C	71021808	A	C	71021808	3	2	179	1	0	0	0	0	1	0	0	0	6034	72	3	5	499	5	FOXP1	3	71021808	Missense_Mutation	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10	17176472	71021808	127000622	19	26847										
FSTL5	56884	hgsc.bcm.edu	37	chr4	162577513	162577513	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	aaatctaaattatttagaatAatattgttccttttccagat	3	5	1	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr4:162577513A>G	ENST00000306100.5	-	7	1297	c.861T>C	c.(859-861)atT>atC	p.I287I	FSTL5_ENST00000427802.2_Silent_p.I286I|FSTL5_ENST00000536695.1_Silent_p.I286I|FSTL5_ENST00000379164.4_Silent_p.I286I|FSTL5_ENST00000511170.1_5'UTR	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	287	Ig-like 1.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TATTTAGAATAATATTGTTCC	0.348																																					p.I287I		Atlas-SNP	.											.	FSTL5	207	.	0			c.T861C						.						51	52	52					4																	162577513		2203	4300	6503	SO:0001819	synonymous_variant	56884	exon7			TAGAATAATATTG	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.861T>C	chr4.hg19:g.162577513A>G		61.0	0.0		52.0	8.0	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	hg19	CCDS3802.1																																																																																			.	.		0.348	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		G	162577513	A	G	162577513	2	3	179	1	0	0	0	0	0	0	0	1	6088	358	13	2		2	FSTL5	4	162577513	Silent	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10		162577513	28576763	20	26848										
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5190154	5190154	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ccagtggcagtctggattgaTggggaaagatgggactcgtc	16	7	1	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr5:5190154T>C	ENST00000274181.7	+	7	1256	c.1118T>C	c.(1117-1119)aTg>aCg	p.M373T	ADAMTS16_ENST00000511368.1_Missense_Mutation_p.M373T	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	373	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						TCTGGATTGATGGGGAAAGAT	0.527																																					p.M373T		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.T1118C						.						144	142	142					5																	5190154		2057	4198	6255	SO:0001583	missense	170690	exon7			GATTGATGGGGAA	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.1118T>C	chr5.hg19:g.5190154T>C	ENSP00000274181:p.Met373Thr	93.0	0.0		93.0	22.0	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	T	8.970	0.972698	0.18736	.	.	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	T;T	0.63255	-0.03;-0.03	5.37	1.63	0.23807	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.438058	0.25146	N	0.032784	T	0.35595	0.0937	N	0.11560	0.145	0.29594	N	0.848203	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.11329	0.003;0.002;0.006	T	0.16837	-1.0389	10	0.22109	T	0.4	.	6.1054	0.20071	0.0:0.1493:0.1478:0.7029	.	373;373;373	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	T	373	ENSP00000274181:M373T;ENSP00000421631:M373T	ENSP00000274181:M373T	M	+	2	0	ADAMTS16	5243154	0.993000	0.37304	0.952000	0.39060	0.953000	0.61014	0.511000	0.22739	0.040000	0.15660	-0.340000	0.08031	ATG	.	.		0.527	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		C	5190154	T	C	5190154	3	2	179	1	0	0	0	0	1	0	0	0	261	1464	51	2	1144	2	ADAMTS16	5	5190154	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10		5190154	175725106	21	26849			1	36		2	2	17	T		4.134718e-05
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5190170	5190170	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ttgatggggaaagatgggacTcgtcatgaccacgccatctt	12	9	2	3			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr5:5190170T>A	ENST00000274181.7	+	7	1272	c.1134T>A	c.(1132-1134)acT>acA	p.T378T	ADAMTS16_ENST00000511368.1_Silent_p.T378T	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	378	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						AAGATGGGACTCGTCATGACC	0.517																																					p.T378T		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.T1134A						.						156	154	155					5																	5190170		2070	4209	6279	SO:0001819	synonymous_variant	170690	exon7			TGGGACTCGTCAT	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.1134T>A	chr5.hg19:g.5190170T>A		85.0	0.0		95.0	23.0	NM_139056	C6G490|Q8IVE2	Silent	SNP	ENST00000274181.7	hg19	CCDS43299.1																																																																																			.	.		0.517	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		A	5190170	T	A	5190170	2	1	179	1	0	0	0	0	0	0	0	1	261	1538	54	4		4	ADAMTS16	5	5190170	Silent	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	16	5190170	175725090	22	26850			1	36		2	2	17	T		4.134718e-05
KIF2A	3796	hgsc.bcm.edu	37	chr5	61681317	61681317	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	tttctttttccaagataaagTgaaatctttccgtgcagctc	6	9	2	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr5:61681317T>A	ENST00000401507.3	+	20	2353	c.2042T>A	c.(2041-2043)gTg>gAg	p.V681E	KIF2A_ENST00000509663.2_Intron|KIF2A_ENST00000407818.3_Missense_Mutation_p.V719E|KIF2A_ENST00000506857.1_Missense_Mutation_p.V635E|KIF2A_ENST00000381103.2_Missense_Mutation_p.V661E	NM_001243953.1|NM_004520.4	NP_001230882.1|NP_004511.2	O00139	KIF2A_HUMAN	kinesin heavy chain member 2A	681					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|nervous system development (GO:0007399)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	15		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		CAAGATAAAGTGAAATCTTTC	0.413																																					p.V719E		Atlas-SNP	.											.	KIF2A	69	.	0			c.T2156A						.						48	46	46					5																	61681317		2203	4299	6502	SO:0001583	missense	3796	exon21			ATAAAGTGAAATC	BC031828	CCDS3980.2, CCDS47216.1, CCDS58949.1	5q12-q13	2008-02-05	2006-09-26	2006-09-26	ENSG00000068796	ENSG00000068796		"Kinesins"	6318	protein-coding gene	gene with protein product		602591	"kinesin heavy chain member 2"	KIF2		9177777	Standard	NM_001098511		Approved	HK2	uc003jsz.4	O00139	OTTHUMG00000097755	ENST00000401507.3:c.2042T>A	chr5.hg19:g.61681317T>A	ENSP00000385622:p.Val681Glu	84.0	0.0		113.0	28.0	NM_001098511	A5YM42|A5YM54|B4DY54|D3DW97|E9PB70|Q7Z5I3|Q8N5Q7	Missense_Mutation	SNP	ENST00000401507.3	hg19	CCDS3980.2	.	.	.	.	.	.	.	.	.	.	T	19.94	3.919950	0.73098	.	.	ENSG00000068796	ENST00000401507;ENST00000381103;ENST00000407818;ENST00000506857	T;T;T;T	0.76578	-0.78;-0.78;-1.03;-0.78	5.88	5.88	0.94601	.	0.124926	0.52532	D	0.000075	D	0.84556	0.5498	L	0.48642	1.525	0.80722	D	1	P;D;D;D	0.76494	0.868;0.959;0.999;0.996	P;P;D;D	0.71184	0.677;0.828;0.972;0.943	D	0.86032	0.1514	10	0.87932	D	0	.	16.3015	0.82820	0.0:0.0:0.0:1.0	.	719;719;681;661	B4DM85;O00139-4;O00139;E9PB70	.;.;KIF2A_HUMAN;.	E	681;661;719;635	ENSP00000385622:V681E;ENSP00000370493:V661E;ENSP00000385000:V719E;ENSP00000423772:V635E	ENSP00000370493:V661E	V	+	2	0	KIF2A	61717074	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.606000	0.82863	2.239000	0.73571	0.533000	0.62120	GTG	.	.		0.413	KIF2A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317989.1	NM_004520		A	61681317	T	A	61681317	3	1	179	1	0	0	0	0	1	0	0	0	8306	1696	59	4	2238	4	KIF2A	5	61681317	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	56491147	61681317	119233943	23	26851										
SPZ1	84654	hgsc.bcm.edu	37	chr5	79617277	79617277	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cccagttcaatattcatgttGcaagaaaagctcttagggga	9	8	3	1	rs541182711		TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr5:79617277G>A	ENST00000296739.4	+	1	1488	c.1243G>A	c.(1243-1245)Gca>Aca	p.A415T		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	415					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		TATTCATGTTGCAAGAAAAGC	0.368																																					p.A415T		Atlas-SNP	.											.	SPZ1	60	.	0			c.G1243A						.						62	61	61					5																	79617277		1822	4078	5900	SO:0001583	missense	84654	exon1			CATGTTGCAAGAA		CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 148"					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.1243G>A	chr5.hg19:g.79617277G>A	ENSP00000369611:p.Ala415Thr	161.0	0.0		193.0	22.0	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	hg19	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.916270	0.52546	.	.	ENSG00000164299	ENST00000296739	T	0.52754	0.65	4.07	3.18	0.36537	.	0.150029	0.31358	N	0.007785	T	0.49081	0.1536	L	0.55213	1.73	0.19575	N	0.999964	D	0.54964	0.969	P	0.53450	0.726	T	0.40021	-0.9585	10	0.62326	D	0.03	-4.3425	4.9724	0.14123	0.1062:0.0:0.6656:0.2282	.	415	Q9BXG8	SPZ1_HUMAN	T	415	ENSP00000369611:A415T	ENSP00000369611:A415T	A	+	1	0	SPZ1	79653033	0.796000	0.28864	0.210000	0.23637	0.016000	0.09150	1.691000	0.37721	1.263000	0.44181	0.557000	0.71058	GCA	.	.		0.368	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567		A	79617277	G	A	79617277	3	1	179	1	0	0	0	0	1	0	0	0	15142	1319	46	3	1245	3	SPZ1	5	79617277	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	17935960	79617277	101297983	24	26852										
FAM174A	345757	hgsc.bcm.edu	37	chr5	99871445	99871445	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	agcagccgggccgtggtctgGctgaagctgcggggccgcgg	20	12	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr5:99871445G>A	ENST00000312637.4	+	1	437	c.211G>A	c.(211-213)Gct>Act	p.A71T	CTD-2001C12.1_ENST00000499025.1_lincRNA	NM_198507.1	NP_940909.1	Q8TBP5	F174A_HUMAN	family with sequence similarity 174, member A	71						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						CCGTGGTCTGGCTGAAGCTGC	0.721																																					p.A71T		Atlas-SNP	.											.	FAM174A	13	.	0			c.G211A						.						9	13	12					5																	99871445		2160	4237	6397	SO:0001583	missense	345757	exon1			GGTCTGGCTGAAG	AY359108	CCDS4090.1	5q21.1	2008-06-19	2008-06-19	2008-06-19	ENSG00000174132	ENSG00000174132			24943	protein-coding gene	gene with protein product			"transmembrane protein 157"	TMEM157		12975309	Standard	NM_198507		Approved	UNQ1912	uc003knj.1	Q8TBP5	OTTHUMG00000128726	ENST00000312637.4:c.211G>A	chr5.hg19:g.99871445G>A	ENSP00000307954:p.Ala71Thr	39.0	0.0		79.0	20.0	NM_198507	A8K0H4	Missense_Mutation	SNP	ENST00000312637.4	hg19	CCDS4090.1	.	.	.	.	.	.	.	.	.	.	G	10.64	1.406295	0.25378	.	.	ENSG00000174132	ENST00000312637	T	0.46819	0.86	4.7	-1.31	0.09230	.	0.253589	0.20785	N	0.085723	T	0.29158	0.0725	L	0.36672	1.1	0.09310	N	1	B	0.27882	0.192	B	0.32342	0.144	T	0.10636	-1.0621	9	.	.	.	0.1082	2.2351	0.04006	0.0962:0.2806:0.2845:0.3387	.	71	Q8TBP5	F174A_HUMAN	T	71	ENSP00000307954:A71T	.	A	+	1	0	FAM174A	99899344	0.004000	0.15560	0.000000	0.03702	0.228000	0.25075	-0.207000	0.09384	-0.076000	0.12775	0.557000	0.71058	GCT	.	.		0.721	FAM174A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250631.2	NM_198507		A	99871445	G	A	99871445	3	1	179	1	0	0	0	0	1	0	0	0	5500	1203	42	3	213	3	FAM174A	5	99871445	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	20254168	99871445	81043815	25	26853										
WDR36	134430	hgsc.bcm.edu	37	chr5	110445992	110445992	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	atacatcgaggaagttttggCaaggatcaaggtagagaatt	12	4	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr5:110445992C>T	ENST00000513710.2	+	13	1603	c.1599C>T	c.(1597-1599)ggC>ggT	p.G533G	WDR36_ENST00000505303.1_Silent_p.G477G|WDR36_ENST00000506538.2_Silent_p.G533G			Q8NI36	WDR36_HUMAN	WD repeat domain 36	533					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		GAAGTTTTGGCAAGGATCAAG	0.358																																					p.G533G		Atlas-SNP	.											.	WDR36	111	.	0			c.C1599T						.						173	167	169					5																	110445992		2202	4300	6502	SO:0001819	synonymous_variant	134430	exon13			TTTTGGCAAGGAT	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.1599C>T	chr5.hg19:g.110445992C>T		97.0	0.0		105.0	28.0	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Silent	SNP	ENST00000513710.2	hg19	CCDS4102.1																																																																																			.	.		0.358	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		T	110445992	C	T	110445992	2	4	179	1	0	0	0	0	0	0	0	1	17305	697	25	3		3	WDR36	5	110445992	Silent	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	10574547	110445992	70469268	26	26854										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112899767	112899767	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	aaaacgtgcagctatgctttGtaggaaacgttttactgcag	10	7	0	0	rs199656628		TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr5:112899767G>T	ENST00000161863.4	+	20	2867	c.2654G>T	c.(2653-2655)tGt>tTt	p.C885F		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	885					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GCTATGCTTTGTAGGAAACGT	0.438																																					p.C885F		Atlas-SNP	.											.	YTHDC2	118	.	0			c.G2654T						.						131	130	130					5																	112899767		2202	4300	6502	SO:0001583	missense	64848	exon20			TGCTTTGTAGGAA	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.2654G>T	chr5.hg19:g.112899767G>T	ENSP00000161863:p.Cys885Phe	86.0	0.0		81.0	4.0	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.865121	0.51482	.	.	ENSG00000047188	ENST00000161863;ENST00000511372	T	0.28895	1.59	5.08	4.15	0.48705	Helicase-associated domain (2);	0.106535	0.64402	D	0.000004	T	0.24509	0.0594	L	0.35341	1.055	0.80722	D	1	B	0.22211	0.066	B	0.21360	0.034	T	0.04065	-1.0980	10	0.29301	T	0.29	.	15.275	0.73734	0.0:0.1406:0.8594:0.0	.	885	Q9H6S0	YTDC2_HUMAN	F	885;795	ENSP00000161863:C885F	ENSP00000161863:C885F	C	+	2	0	YTHDC2	112927666	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	5.529000	0.67135	2.529000	0.85273	0.655000	0.94253	TGT	.	.		0.438	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		T	112899767	G	T	112899767	3	4	179	1	0	0	0	0	1	0	0	0	17512	1377	48	3	2732	3	YTHDC2	5	112899767	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	2453775	112899767	68015493	27	26855										
IK	3550	hgsc.bcm.edu	37	chr5	140027509	140027509	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	acaaaatgccggagcgagatAgtaaggctcaggccatccgt	12	10	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr5:140027509A>T	ENST00000417647.2	+	1	155	c.16A>T	c.(16-18)Agt>Tgt	p.S6C	NDUFA2_ENST00000512088.1_5'Flank|MIR3655_ENST00000581765.1_RNA|NDUFA2_ENST00000510680.1_5'Flank|NDUFA2_ENST00000252102.4_5'Flank	NM_006083.3	NP_006074.2	Q13123	RED_HUMAN	IK cytokine, down-regulator of HLA II	6					cell-cell signaling (GO:0007267)|immune response (GO:0006955)	extracellular space (GO:0005615)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGCGAGATAGTAAGGCTCA	0.522																																					p.S6C		Atlas-SNP	.											.	IK	46	.	0			c.A16T						.						157	169	165					5																	140027509		2129	4234	6363	SO:0001630	splice_region_variant	3550	exon1			CGAGATAGTAAGG	BC051295	CCDS47280.1	5q31.3	2008-08-07			ENSG00000113141	ENSG00000113141			5958	protein-coding gene	gene with protein product		600549				7970704	Standard	NM_006083		Approved		uc003lgq.3	Q13123	OTTHUMG00000163374	ENST00000417647.2:c.16+1A>T	chr5.hg19:g.140027509A>T		133.0	0.0		165.0	19.0	NM_006083	Q6IPD8	Missense_Mutation	SNP	ENST00000417647.2	hg19	CCDS47280.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.958774	0.92726	.	.	ENSG00000113141	ENST00000417647;ENST00000507593;ENST00000508301;ENST00000261812	.	.	.	6.04	6.04	0.98038	.	.	.	.	.	T	0.37376	0.1001	N	0.19112	0.55	0.53005	D	0.999962	B;P	0.39131	0.051;0.661	B;B	0.33042	0.037;0.157	T	0.40440	-0.9563	8	0.66056	D	0.02	.	14.0995	0.65046	1.0:0.0:0.0:0.0	.	6;6	Q9UK43;Q13123	.;RED_HUMAN	C	6	.	ENSP00000261812:S6C	S	+	1	0	IK	140007693	0.997000	0.39634	1.000000	0.80357	0.720000	0.41350	3.567000	0.53813	2.317000	0.78254	0.459000	0.35465	AGT	.	.		0.522	IK-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372897.1	NM_006083	Missense_Mutation	T	140027509	A	T	140027509	5	4	179	1	0	0	0	0	0	0	1	0	7617	434	15	4	18	4	IK	5	140027509	Splice_Site	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10	27127742	140027509	40887751	28	26856										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140181355	140181355	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	aatgatgaggaaattaaatcCcttggactcgtgttgaaaaa	9	5	0	3			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr5:140181355C>T	ENST00000522353.2	+	1	573	c.573C>T	c.(571-573)tcC>tcT	p.S191S	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Silent_p.S191S|PCDHA2_ENST00000520672.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	191	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAATTAAATCCCTTGGACTCG	0.368																																					p.S191S		Atlas-SNP	.											.	PCDHA3	396	.	0			c.C573T						.						60	63	62					5																	140181355		2203	4300	6503	SO:0001819	synonymous_variant	56145	exon1			TAAATCCCTTGGA	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.573C>T	chr5.hg19:g.140181355C>T		118.0	0.0		159.0	35.0	NM_031497	O75286	Silent	SNP	ENST00000522353.2	hg19	CCDS54915.1																																																																																			.	.		0.368	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		T	140181355	C	T	140181355	2	4	179	1	0	0	0	0	0	0	0	1	11534	610	22	3		3	PCDHA3	5	140181355	Silent	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	153846	140181355	40733905	29	26857										
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140255556	140255556	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cggatatcggcgtaaactctCttttgacctatgcgttaagt	9	9	1	1	rs17844352		TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr5:140255556C>A	ENST00000398631.2	+	1	499	c.499C>A	c.(499-501)Ctt>Att	p.L167I	PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	167	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTAAACTCTCTTTTGACCTA	0.378																																					p.L167I	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,right_upper_lobe,carcinoma,0,1	PCDHA12	196	.	0			c.C499A						.						50	58	55					5																	140255556		2138	4270	6408	SO:0001583	missense	56137	exon1			AACTCTCTTTTGA	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.499C>A	chr5.hg19:g.140255556C>A	ENSP00000381628:p.Leu167Ile	135.0	0.0		200.0	50.0	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	hg19	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	C	7.354	0.623559	0.14193	.	.	ENSG00000251664	ENST00000398631	T	0.52057	0.68	5.07	2.23	0.28157	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.37320	0.0999	L	0.37466	1.105	0.09310	N	1	B;B	0.22080	0.042;0.064	B;B	0.34991	0.193;0.033	T	0.42498	-0.9448	9	0.45353	T	0.12	.	2.0818	0.03636	0.2761:0.4386:0.1341:0.1511	.	167;167	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	I	167	ENSP00000381628:L167I	ENSP00000381628:L167I	L	+	1	0	PCDHA12	140235740	0.000000	0.05858	0.005000	0.12908	0.819000	0.46315	-1.784000	0.01769	0.142000	0.18901	0.591000	0.81541	CTT	.	.		0.378	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140255556	C	A	140255556	3	1	179	1	0	0	0	0	1	0	0	0	11531	913	32	3	501	3	PCDHA12	5	140255556	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	74201	140255556	40659704	30	26858										
DST	667	hgsc.bcm.edu	37	chr6	56480793	56480793	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	actttttgccagtaagaggaTcaattatgccccctgtactg	8	10	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr6:56480793T>G	ENST00000370765.6	-	24	7579	c.7472A>C	c.(7471-7473)gAt>gCt	p.D2491A	DST_ENST00000361203.3_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000370788.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1787					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AGTAAGAGGATCAATTATGCC	0.498																																					p.D2491A		Atlas-SNP	.											.	DST	1427	.	0			c.A7472C						.						71	77	75					6																	56480793		2203	4300	6503	SO:0001583	missense	667	exon24			AGAGGATCAATTA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.7472A>C	chr6.hg19:g.56480793T>G	ENSP00000359801:p.Asp2491Ala	118.0	0.0		80.0	22.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	hg19	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.870331	0.51588	.	.	ENSG00000151914	ENST00000370765	D	0.83591	-1.74	5.94	5.94	0.96194	.	.	.	.	.	D	0.90154	0.6923	.	.	.	0.19775	N	0.999953	D	0.89917	1.0	D	0.97110	1.0	D	0.91579	0.5277	7	0.87932	D	0	.	16.3939	0.83550	0.0:0.0:0.0:1.0	.	2491	Q03001-3	.	A	2491	ENSP00000359801:D2491A	ENSP00000359801:D2491A	D	-	2	0	DST	56588752	1.000000	0.71417	0.996000	0.52242	0.975000	0.68041	8.040000	0.89188	2.276000	0.75962	0.455000	0.32223	GAT	.	.		0.498	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		G	56480793	T	G	56480793	3	3	179	1	0	0	0	0	1	0	0	0	4785	1435	50	5	12927	5	DST	6	56480793	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10		56480793	114634274	31	26859										
EYS	346007	hgsc.bcm.edu	37	chr6	66200596	66200596	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ccaattatttctgagcaattCtttcctataacaatgaaaaa	3	8	2	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr6:66200596C>G	ENST00000370621.3	-	5	1279	c.753G>C	c.(751-753)aaG>aaC	p.K251N	EYS_ENST00000370616.2_Missense_Mutation_p.K251N|EYS_ENST00000342421.5_Missense_Mutation_p.K251N|EYS_ENST00000393380.2_Missense_Mutation_p.K251N|EYS_ENST00000370618.3_Missense_Mutation_p.K251N|EYS_ENST00000503581.1_Missense_Mutation_p.K251N			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	251	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CTGAGCAATTCTTTCCTATAA	0.299																																					p.K251N		Atlas-SNP	.											EYS_ENST00000370621,NS,carcinoma,0,4	EYS	527	.	0			c.G753C						.						58	55	56					6																	66200596		2203	4297	6500	SO:0001583	missense	346007	exon5			GCAATTCTTTCCT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.753G>C	chr6.hg19:g.66200596C>G	ENSP00000359655:p.Lys251Asn	436.0	0.0		415.0	80.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	C	1.220	-0.627119	0.03610	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	D;D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18;-2.18	4.22	1.83	0.25207	.	.	.	.	.	T	0.75657	0.3879	L	0.53249	1.67	0.20489	N	0.999897	P;P;P	0.48998	0.815;0.899;0.918	P;P;P	0.49853	0.49;0.49;0.624	T	0.65022	-0.6269	9	0.18710	T	0.47	.	6.95	0.24540	0.0:0.1602:0.0:0.8398	.	251;251;251	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	N	251	ENSP00000424243:K251N;ENSP00000359655:K251N;ENSP00000359650:K251N;ENSP00000377042:K251N;ENSP00000341818:K251N;ENSP00000359652:K251N	ENSP00000341818:K251N	K	-	3	2	EYS	66257317	0.952000	0.32445	0.146000	0.22360	0.047000	0.14425	0.600000	0.24104	0.166000	0.19597	-0.251000	0.11542	AAG	.	.		0.299	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	66200596	C	G	66200596	3	3	179	1	0	0	0	0	1	0	0	0	5334	912	32	4	8799	4	EYS	6	66200596	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	9719803	66200596	104914471	32	26860										
WISP3	8838	hgsc.bcm.edu	37	chr6	112390640	112390641	+	Frame_Shift_Del	DEL	TT	TT	-													0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	actcagagttacaaacccacTttttgtggaatatgcttgga							TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr6:112390640_112390641delTT	ENST00000368666.2	+	5	1168_1169	c.882_883delTT	c.(880-885)acttttfs	p.F295fs	TUBE1_ENST00000604814.1_5'Flank|WISP3_ENST00000230529.5_Frame_Shift_Del_p.F295fs|WISP3_ENST00000409166.1_Frame_Shift_Del_p.F71fs|WISP3_ENST00000604763.1_Frame_Shift_Del_p.F295fs|WISP3_ENST00000368663.3_Frame_Shift_Del_p.F272fs|WISP3_ENST00000361714.1_Frame_Shift_Del_p.F313fs	NM_198239.1	NP_937882.1	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	295	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	13		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		ACAAACCCACTTTTTGTGGAAT	0.361																																					p.312_312del		Atlas-INDEL	.											.	WISP3	33	.	0			c.935_936del						.																																			SO:0001589	frameshift_variant	8838	exon5			.	AF100781	CCDS5097.1, CCDS5098.1	6q21	2014-05-06			ENSG00000112761	ENSG00000112761			12771	protein-coding gene	gene with protein product		603400				9843955	Standard	NM_003880		Approved	CCN6	uc003pvo.3	O95389	OTTHUMG00000185101	ENST00000368666.2:c.882_883delTT	chr6.hg19:g.112390642_112390643delTT	ENSP00000357655:p.Phe295fs	103.0	0.0		98.0	15.0	NM_198239	Q3KR29|Q5H8W4|Q6UXH6	Frame_Shift_Del	DEL	ENST00000368666.2	hg19	CCDS5098.1																																																																																			.	.		0.361	WISP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041873.2	NM_003880		-	112390641	TT	-	112390640	7	5	179	1	0	1	0	1	0	0	0	0	17389	1596	56	0	954	0	WISP3	6	112390640	Frame_Shift_Del	DEL	TT	TCGA-DD-AAD2-01A-11D-A40R-10	46190044	112390640	58724427	33	26861										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146276072	146276072	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ctttcggaaaaattttcaatTaaactctgtgcaggaagaag	8	6	2	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr6:146276072T>G	ENST00000367505.2	-	2	651	c.387A>C	c.(385-387)ttA>ttC	p.L129F	SHPRH_ENST00000438092.2_Missense_Mutation_p.L129F|SHPRH_ENST00000275233.7_Missense_Mutation_p.L129F|SHPRH_ENST00000367503.3_Missense_Mutation_p.L129F			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	129					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		AATTTTCAATTAAACTCTGTG	0.333																																					p.L129F		Atlas-SNP	.											.	SHPRH	169	.	0			c.A387C						.						63	59	60					6																	146276072		1811	4067	5878	SO:0001583	missense	257218	exon2			TTCAATTAAACTC	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.387A>C	chr6.hg19:g.146276072T>G	ENSP00000356475:p.Leu129Phe	136.0	0.0		103.0	20.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	hg19	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	T	15.00	2.702115	0.48307	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.66	5.66	0.87406	.	0.264260	0.27782	N	0.017870	T	0.58206	0.2106	L	0.54323	1.7	0.27666	N	0.946916	P;P	0.50443	0.893;0.935	P;P	0.51266	0.463;0.664	T	0.59643	-0.7416	10	0.59425	D	0.04	-12.6637	11.0328	0.47783	0.1387:0.0:0.0:0.8612	.	129;129	Q149N8;Q149N8-4	SHPRH_HUMAN;.	F	129	ENSP00000356475:L129F;ENSP00000356473:L129F;ENSP00000412797:L129F;ENSP00000275233:L129F	ENSP00000275233:L129F	L	-	3	2	SHPRH	146317765	0.473000	0.25878	0.952000	0.39060	0.626000	0.37791	1.052000	0.30429	2.158000	0.67659	0.533000	0.62120	TTA	.	.		0.333	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		G	146276072	T	G	146276072	3	3	179	1	0	0	0	0	1	0	0	0	14306	1751	61	5	4824	5	SHPRH	6	146276072	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	33885432	146276072	24838995	34	26862										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152793449	152793449	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ctcttacctctcggccatgtCctctaattgatcaggtggca	8	13	4	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr6:152793449C>A	ENST00000367255.5	-	15	2051	c.1450G>T	c.(1450-1452)Gac>Tac	p.D484Y	SYNE1_ENST00000367248.3_Missense_Mutation_p.D474Y|SYNE1_ENST00000265368.4_Missense_Mutation_p.D484Y|SYNE1_ENST00000423061.1_Missense_Mutation_p.D491Y|SYNE1_ENST00000413186.2_Missense_Mutation_p.D484Y|SYNE1_ENST00000367253.4_Missense_Mutation_p.D484Y|SYNE1_ENST00000448038.1_Missense_Mutation_p.D491Y|SYNE1_ENST00000495090.2_Missense_Mutation_p.D51Y|SYNE1_ENST00000466159.2_Missense_Mutation_p.D484Y|SYNE1_ENST00000341594.5_Missense_Mutation_p.D491Y	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	484					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCGGCCATGTCCTCTAATTGA	0.398										HNSCC(10;0.0054)																											p.D491Y		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G1471T						.						125	117	120					6																	152793449		2203	4300	6503	SO:0001583	missense	23345	exon15			CCATGTCCTCTAA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.1450G>T	chr6.hg19:g.152793449C>A	ENSP00000356224:p.Asp484Tyr	105.0	0.0		105.0	20.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	22.4	4.289987	0.80914	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000495090;ENST00000466159;ENST00000537750	T;T;T;T;T;D;D;D;T;D;D	0.91792	0.5;0.49;0.41;0.49;0.64;-2.31;-2.48;-2.45;2.02;-2.69;-2.91	5.87	5.87	0.94306	.	0.000000	0.64402	D	0.000006	D	0.95398	0.8506	M	0.63428	1.95	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.998;1.0;1.0	D	0.94878	0.8036	10	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	467;484;484;51;484;491	B3W695;Q8NF91;F5H4Q0;F5H422;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.	Y	484;491;484;491;491;484;474;484;51;484;467	ENSP00000356224:D484Y;ENSP00000396024:D491Y;ENSP00000265368:D484Y;ENSP00000390975:D491Y;ENSP00000341887:D491Y;ENSP00000356222:D484Y;ENSP00000356217:D474Y;ENSP00000414510:D484Y;ENSP00000438508:D51Y;ENSP00000446021:D484Y;ENSP00000441264:D467Y	ENSP00000265368:D484Y	D	-	1	0	SYNE1	152835142	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.445000	0.80570	2.941000	0.99782	0.655000	0.94253	GAC	.	.		0.398	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152793449	C	A	152793449	3	1	179	1	0	0	0	0	1	0	0	0	15460	855	30	3	25544	3	SYNE1	6	152793449	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	6517377	152793449	18321618	35	26863										
C6orf118	168090	hgsc.bcm.edu	37	chr6	165715430	165715430	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gggttcaggtacctgaacagCggggtgtcctgggcctcact	15	11	2	1	rs202048007		TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr6:165715430C>A	ENST00000230301.8	-	2	401	c.381G>T	c.(379-381)ccG>ccT	p.P127P	C6orf118_ENST00000543069.1_Silent_p.P23P	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	127										breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		ACCTGAACAGCGGGGTGTCCT	0.617																																					p.P127P		Atlas-SNP	.											.	C6orf118	116	.	0			c.G381T						.						67	72	71					6																	165715430		2203	4300	6503	SO:0001819	synonymous_variant	168090	exon2			GAACAGCGGGGTG		CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.381G>T	chr6.hg19:g.165715430C>A		65.0	0.0		48.0	9.0	NM_144980	Q8TC11	Silent	SNP	ENST00000230301.8	hg19	CCDS5288.1																																																																																			.	C|0.973;T|0.027		0.617	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980		A	165715430	C	A	165715430	2	1	179	1	0	0	0	0	0	0	0	1	2325	755	27	1		1	C6orf118	6	165715430	Silent	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	12921981	165715430	5399637	36	26864										
EPDR1	54749	hgsc.bcm.edu	37	chr7	37960698	37960698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	agcagtgggaggggcgccagGttatgtaccagcaaagtagc	16	8	0	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr7:37960698G>A	ENST00000199448.4	+	1	536	c.157G>A	c.(157-159)Gtt>Att	p.V53I	EPDR1_ENST00000559325.1_Missense_Mutation_p.V173I|EPDR1_ENST00000476620.1_Intron|EPDR1_ENST00000425345.1_5'Flank|EPDR1_ENST00000423717.1_Missense_Mutation_p.V53I	NM_017549.4	NP_060019.2	Q9UM22	EPDR1_HUMAN	ependymin related 1	53					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	22						GGGGCGCCAGGTTATGTACCA	0.726																																					p.V53I		Atlas-SNP	.											.	EPDR1	48	.	0			c.G157A						.						7	8	8					7																	37960698		2092	4150	6242	SO:0001583	missense	54749	exon1			CGCCAGGTTATGT	BC018299	CCDS5454.1, CCDS5454.2, CCDS59051.1, CCDS59052.1	7p14.1	2013-07-31	2013-07-31		ENSG00000086289	ENSG00000086289			17572	protein-coding gene	gene with protein product			"ependymin related protein 1 (zebrafish)"			11749721, 11248421	Standard	NM_001242946		Approved	MERP-1, MERP1, UCC1, EPDR	uc003tfp.4	Q9UM22	OTTHUMG00000102187	ENST00000199448.4:c.157G>A	chr7.hg19:g.37960698G>A	ENSP00000199448:p.Val53Ile	52.0	0.0		42.0	9.0	NM_001242946	A8K4C0|C9JYS3|Q06BL0|Q99M77	Missense_Mutation	SNP	ENST00000199448.4	hg19	CCDS5454.2	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768394	0.90020	.	.	ENSG00000086289	ENST00000199448;ENST00000423717	.	.	.	4.04	4.04	0.47022	.	0.125588	0.53938	D	0.000060	T	0.61974	0.2390	L	0.61218	1.895	0.80722	D	1	P	0.52170	0.951	P	0.49799	0.622	T	0.65014	-0.6271	9	0.45353	T	0.12	-17.2681	13.5461	0.61705	0.0:0.0:1.0:0.0	.	173	A4D1W8	.	I	173;147	.	ENSP00000199448:V173I	V	+	1	0	EPDR1	37927223	1.000000	0.71417	0.992000	0.48379	0.939000	0.58152	7.900000	0.87376	2.227000	0.72691	0.313000	0.20887	GTT	.	.		0.726	EPDR1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220037.3	NM_017549		A	37960698	G	A	37960698	3	1	179	1	0	0	0	0	1	0	0	0	5165	1261	44	3	519	3	EPDR1	7	37960698	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10		37960698	121177965	37	26865										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113363436	113363436	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ggattggataattccatcttCttacaggtcctggcatacat	8	9	2	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr8:113363436C>A	ENST00000297405.5	-	40	6537	c.6293G>T	c.(6292-6294)aGa>aTa	p.R2098I	CSMD3_ENST00000455883.2_Missense_Mutation_p.R1994I|CSMD3_ENST00000352409.3_Missense_Mutation_p.R2028I|CSMD3_ENST00000343508.3_Missense_Mutation_p.R2058I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2098	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATTCCATCTTCTTACAGGTCC	0.294										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.R2098I		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G6293T						.						121	125	123					8																	113363436		2203	4289	6492	SO:0001583	missense	114788	exon40			CATCTTCTTACAG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6293G>T	chr8.hg19:g.113363436C>A	ENSP00000297405:p.Arg2098Ile	125.0	0.0		193.0	13.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888311	0.91814	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11	4.47	4.47	0.54385	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.81250	0.4783	M	0.88570	2.965	0.80722	D	1	D;D;D	0.89917	0.999;0.98;1.0	D;D;D	0.97110	0.999;0.992;1.0	T	0.80589	-0.1315	10	0.23302	T	0.38	.	17.2721	0.87105	0.0:1.0:0.0:0.0	.	1994;2098;2058	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	I	2058;2098;1368;1994;2028	ENSP00000345799:R2058I;ENSP00000297405:R2098I;ENSP00000341558:R1368I;ENSP00000412263:R1994I;ENSP00000343124:R2028I	ENSP00000297405:R2098I	R	-	2	0	CSMD3	113432612	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.909000	0.69923	2.457000	0.83068	0.650000	0.86243	AGA	.	.		0.294	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113363436	C	A	113363436	3	1	179	1	0	0	0	0	1	0	0	0	3948	913	32	3	4958	3	CSMD3	8	113363436	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10		113363436	33000586	38	26866										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113697827	113697827	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ggattccaggtcaaagtcatTgaaagaaagatgtatccggc	11	7	2	3			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr8:113697827T>C	ENST00000297405.5	-	15	2534	c.2290A>G	c.(2290-2292)Aat>Gat	p.N764D	CSMD3_ENST00000455883.2_Missense_Mutation_p.N660D|CSMD3_ENST00000352409.3_Missense_Mutation_p.N764D|CSMD3_ENST00000343508.3_Missense_Mutation_p.N724D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	764	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TCAAAGTCATTGAAAGAAAGA	0.433										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.N764D		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A2290G						.						101	107	105					8																	113697827		2203	4300	6503	SO:0001583	missense	114788	exon15			AGTCATTGAAAGA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2290A>G	chr8.hg19:g.113697827T>C	ENSP00000297405:p.Asn764Asp	101.0	0.0		154.0	23.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	14.86	2.662811	0.47572	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.17370	2.28;2.28;2.28;2.28;2.28	5.96	5.96	0.96718	CUB (5);	0.000000	0.85682	D	0.000000	T	0.30135	0.0755	L	0.33245	0.995	0.33222	D	0.554789	D;D;D	0.76494	0.973;0.999;0.997	D;D;D	0.87578	0.98;0.998;0.984	T	0.21381	-1.0247	10	0.16420	T	0.52	.	16.4277	0.83824	0.0:0.0:0.0:1.0	.	660;764;724	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	D	724;764;104;660;764	ENSP00000345799:N724D;ENSP00000297405:N764D;ENSP00000341558:N104D;ENSP00000412263:N660D;ENSP00000343124:N764D	ENSP00000297405:N764D	N	-	1	0	CSMD3	113767003	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.186000	0.72026	2.279000	0.76181	0.533000	0.62120	AAT	.	.		0.433	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113697827	T	C	113697827	3	2	179	1	0	0	0	0	1	0	0	0	3948	1812	63	2	9061	2	CSMD3	8	113697827	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	334391	113697827	32666195	39	26867										
TG	7038	hgsc.bcm.edu	37	chr8	133941375	133941375	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ggtgatcttcgacgccaatgCtcctgtggctgtcagatcca	11	12	2	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr8:133941375C>A	ENST00000220616.4	+	23	4794	c.4754C>A	c.(4753-4755)gCt>gAt	p.A1585D	TG_ENST00000377869.1_Missense_Mutation_p.A1528D|TG_ENST00000542445.1_Missense_Mutation_p.A19D	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1585					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GACGCCAATGCTCCTGTGGCT	0.463																																					p.A1585D		Atlas-SNP	.											.	TG	416	.	0			c.C4754A						.						142	121	128					8																	133941375		2203	4300	6503	SO:0001583	missense	7038	exon23			CCAATGCTCCTGT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4754C>A	chr8.hg19:g.133941375C>A	ENSP00000220616:p.Ala1585Asp	87.0	0.0		145.0	13.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.198|0.198	-1.046980|-1.046980	0.01997|0.01997	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445|ENST00000519178	T;T;T|.	0.65732|.	-0.17;-0.17;-0.17|.	5.5|5.5	-1.08|-1.08	0.09936|0.09936	.|.	1.845860|.	0.02581|.	N|.	0.098887|.	T|.	0.14313|.	0.0346|.	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.0|.	B;B|.	0.09377|.	0.004;0.001|.	T|.	0.26467|.	-1.0102|.	10|.	0.06757|.	T|.	0.87|.	.|.	3.7294|3.7294	0.08487|0.08487	0.2064:0.3661:0.0:0.4275|0.2064:0.3661:0.0:0.4275	.|.	19;1585|.	F5GWW5;P01266|.	.;THYG_HUMAN|.	D|X	1528;391;1585;19|104	ENSP00000367100:A1528D;ENSP00000220616:A1585D;ENSP00000441693:A19D|.	ENSP00000220616:A1585D|.	A|C	+|+	2|3	0|2	TG|TG	134010557|134010557	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.064000|0.064000	0.14437|0.14437	0.015000|0.015000	0.14971|0.14971	-0.150000|-0.150000	0.13652|0.13652	GCT|TGC	.	.		0.463	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133941375	C	A	133941375	3	1	179	1	0	0	0	0	1	0	0	0	15828	797	28	3	4844	3	TG	8	133941375	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	20243548	133941375	12422647	40	26868										
SCRIB	23513	hgsc.bcm.edu	37	chr8	144887556	144887556	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cagtgccggccccccggagcGcctccacggcctcgtggtgc	14	19	0	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr8:144887556G>A	ENST00000320476.3	-	19	2402	c.2396C>T	c.(2395-2397)gCg>gTg	p.A799V	SCRIB_ENST00000377533.3_Missense_Mutation_p.A718V|SCRIB_ENST00000356994.2_Missense_Mutation_p.A799V	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	799	Interaction with ARHGEF7.|PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.|Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CCCCCGGAGCGCCTCCACGGC	0.701																																					p.A799V	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C2396T						.						9	10	10					8																	144887556		2160	4236	6396	SO:0001583	missense	23513	exon19			CGGAGCGCCTCCA	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.2396C>T	chr8.hg19:g.144887556G>A	ENSP00000322938:p.Ala799Val	30.0	0.0		55.0	9.0	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.336986	0.60963	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539;ENST00000531942	T;T;T;T	0.37915	2.35;2.35;2.35;1.17	4.37	4.37	0.52481	PDZ/DHR/GLGF (4);	.	.	.	.	T	0.47021	0.1423	L	0.42008	1.315	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.976;0.999	T	0.35500	-0.9786	9	0.05620	T	0.96	.	15.9021	0.79387	0.0:0.0:1.0:0.0	.	799;799	Q14160;Q14160-3	SCRIB_HUMAN;.	V	799;799;718;168;96	ENSP00000349486:A799V;ENSP00000322938:A799V;ENSP00000366756:A718V;ENSP00000433546:A96V	ENSP00000322938:A799V	A	-	2	0	SCRIB	144959544	1.000000	0.71417	0.873000	0.34254	0.285000	0.27093	9.133000	0.94460	1.962000	0.57031	0.563000	0.77884	GCG	.	.		0.701	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		A	144887556	G	A	144887556	3	1	179	1	0	0	0	0	1	0	0	0	13952	1087	38	1	2647	1	SCRIB	8	144887556	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	10946181	144887556	1476466	41	26869										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20821034	20821034	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ccaatgggagaaactgattgCaaaagcagcatcaatcagag	10	8	2	3			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr9:20821034C>G	ENST00000380249.1	+	16	2121	c.1757C>G	c.(1756-1758)gCa>gGa	p.A586G	FOCAD_ENST00000605086.1_Missense_Mutation_p.A22G|FOCAD_ENST00000338382.6_Missense_Mutation_p.A586G	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	586						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											AAACTGATTGCAAAAGCAGCA	0.378																																					p.A586G		Atlas-SNP	.											.	.	.	.	0			c.C1757G						.						189	176	180					9																	20821034		2203	4300	6503	SO:0001583	missense	54914	exon16			TGATTGCAAAAGC	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.1757C>G	chr9.hg19:g.20821034C>G	ENSP00000369599:p.Ala586Gly	67.0	0.0		74.0	15.0	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	hg19	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.637272	0.87760	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.22539	1.95;1.95	5.46	5.46	0.80206	Domain of unknown function DUF3730 (1);	0.099908	0.64402	D	0.000002	T	0.45935	0.1367	M	0.74881	2.28	0.80722	D	1	D	0.61080	0.989	P	0.59357	0.856	T	0.44050	-0.9353	10	0.66056	D	0.02	-21.3824	19.3768	0.94514	0.0:1.0:0.0:0.0	.	586	Q5VW36	K1797_HUMAN	G	586	ENSP00000369599:A586G;ENSP00000344307:A586G	ENSP00000344307:A586G	A	+	2	0	KIAA1797	20811034	1.000000	0.71417	0.376000	0.26042	0.977000	0.68977	6.253000	0.72453	2.584000	0.87258	0.456000	0.33151	GCA	.	.		0.378	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		G	20821034	C	G	20821034	3	3	179	1	0	0	0	0	1	0	0	0	8267	710	25	4	1807	4	KIAA1797	9	20821034	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10		20821034	120392397	42	26870										
WNK2	65268	hgsc.bcm.edu	37	chr9	96061396	96061396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gccctcccgctaaggaccctGcccaagccagtgtggggctc	12	17	0	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr9:96061396G>A	ENST00000297954.4	+	25	6079	c.6079G>A	c.(6079-6081)Gcc>Acc	p.A2027T	WNK2_ENST00000427277.2_Missense_Mutation_p.A1602T|WNK2_ENST00000356055.3_Splice_Site|WNK2_ENST00000395477.2_Missense_Mutation_p.A1990T|WNK2_ENST00000349097.3_Missense_Mutation_p.A1639T|WNK2_ENST00000395475.2_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	2027					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TAAGGACCCTGCCCAAGCCAG	0.706																																					p.A1990T		Atlas-SNP	.											.	WNK2	277	.	0			c.G5968A						.						24	24	24					9																	96061396		2196	4292	6488	SO:0001583	missense	65268	exon24			GACCCTGCCCAAG	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.6079G>A	chr9.hg19:g.96061396G>A	ENSP00000297954:p.Ala2027Thr	88.0	0.0		69.0	14.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.62|16.62	3.175297|3.175297	0.57692|0.57692	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000356055|ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277	.|T;T;T;T	.|0.69175	.|-0.38;-0.38;0.22;0.21	5.54|5.54	1.63|1.63	0.23807|0.23807	.|.	.|0.353172	.|0.30142	.|N	.|0.010320	.|T	.|0.62732	.|0.2452	L|L	0.34521|0.34521	1.04|1.04	0.58432|0.58432	D|D	0.999999|0.999999	.|B;D;B;D	.|0.69078	.|0.335;0.997;0.084;0.996	.|B;P;B;P	.|0.62382	.|0.19;0.901;0.022;0.867	.|T	.|0.57165	.|-0.7858	.|10	.|0.13470	.|T	.|0.59	.|.	6.8504|6.8504	0.24012|0.24012	0.3324:0.1216:0.546:0.0|0.3324:0.1216:0.546:0.0	.|.	.|1990;1985;1990;2027	.|Q9Y3S1-2;A6PVR3;F8W9F9;Q9Y3S1	.|.;.;.;WNK2_HUMAN	.|T	-1|2027;1990;1639;1602	.|ENSP00000297954:A2027T;ENSP00000378860:A1990T;ENSP00000297876:A1639T;ENSP00000411181:A1602T	.|ENSP00000297954:A2027T	.|A	+|+	.|1	.|0	WNK2|WNK2	95101217|95101217	0.160000|0.160000	0.22878|0.22878	0.988000|0.988000	0.46212|0.46212	0.998000|0.998000	0.95712|0.95712	0.854000|0.854000	0.27791|0.27791	0.310000|0.310000	0.22990|0.22990	0.655000|0.655000	0.94253|0.94253	.|GCC	.	.		0.706	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		A	96061396	G	A	96061396	3	1	179	1	0	0	0	0	1	0	0	0	17393	1319	46	3	6062	3	WNK2	9	96061396	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	75240362	96061396	45152035	43	26871										
FBXW5	54461	hgsc.bcm.edu	37	chr9	139837919	139837919	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cctccacgcagggcaccgtgTcatacagccgctggaactcc	10	17	1	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr9:139837919T>C	ENST00000325285.3	-	3	312	c.233A>G	c.(232-234)gAc>gGc	p.D78G	FBXW5_ENST00000483559.1_5'UTR|C8G_ENST00000224181.3_5'Flank	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	78					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		GGGCACCGTGTCATACAGCCG	0.657																																					p.D78G		Atlas-SNP	.											.	FBXW5	36	.	0			c.A233G						.						63	45	52					9																	139837919		2199	4299	6498	SO:0001583	missense	54461	exon3			ACCGTGTCATACA	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"F-boxes / WD-40 domains", "WD repeat domain containing"	13613	protein-coding gene	gene with protein product		609072	"F-box and WD-40 domain protein 5"				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.233A>G	chr9.hg19:g.139837919T>C	ENSP00000313034:p.Asp78Gly	89.0	0.0		83.0	15.0	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	hg19	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	t	18.13	3.556330	0.65425	.	.	ENSG00000159069	ENST00000325285;ENST00000428398;ENST00000443788	T;T;D	0.84070	-0.63;0.99;-1.8	4.32	3.17	0.36434	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);F-box domain, Skp2-like (1);	0.049177	0.85682	D	0.000000	D	0.86322	0.5905	M	0.76574	2.34	0.53005	D	0.999961	D	0.65815	0.995	P	0.55455	0.776	D	0.84579	0.0660	10	0.44086	T	0.13	-19.8322	9.7758	0.40618	0.0:0.0825:0.0:0.9175	.	78	Q969U6	FBXW5_HUMAN	G	78	ENSP00000313034:D78G;ENSP00000404829:D78G;ENSP00000394011:D78G	ENSP00000313034:D78G	D	-	2	0	FBXW5	138957740	1.000000	0.71417	0.014000	0.15608	0.976000	0.68499	7.258000	0.78371	0.687000	0.31509	0.454000	0.30748	GAC	.	.		0.657	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		C	139837919	T	C	139837919	3	2	179	1	0	0	0	0	1	0	0	0	5776	1667	58	2	1495	2	FBXW5	9	139837919	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	43776523	139837919	1375512	44	26872										
RASGEF1A	221002	hgsc.bcm.edu	37	chr10	43694571	43694571	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	atcatggagttgaagttcccGatgttgaagcactcccgggc	12	10	1	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr10:43694571G>A	ENST00000395809.1	-	8	3427	c.921C>T	c.(919-921)atC>atT	p.I307I	RASGEF1A_ENST00000374459.1_Silent_p.I315I|RASGEF1A_ENST00000395810.1_Silent_p.I307I|RASGEF1A_ENST00000472864.1_5'Flank			Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A	307	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cell migration (GO:0016477)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)	11						TGAAGTTCCCGATGTTGAAGC	0.602																																					p.I307I		Atlas-SNP	.											.	RASGEF1A	66	.	0			c.C921T						.						75	62	66					10																	43694571		2203	4300	6503	SO:0001819	synonymous_variant	221002	exon8			GTTCCCGATGTTG	AK095136	CCDS7202.2, CCDS60517.1	10q11.21	2006-01-11			ENSG00000198915	ENSG00000198915			24246	protein-coding gene	gene with protein product		614531				12477932	Standard	XM_005271808		Approved	CG4853, FLJ37817	uc001jap.1	Q8N9B8	OTTHUMG00000018025	ENST00000395809.1:c.921C>T	chr10.hg19:g.43694571G>A		97.0	0.0		75.0	21.0	NM_145313	Q8TBF1	Silent	SNP	ENST00000395809.1	hg19	CCDS7202.2	.	.	.	.	.	.	.	.	.	.	G	5.560	0.288196	0.10513	.	.	ENSG00000198915	ENST00000374455	.	.	.	5.26	-9.08	0.00720	.	.	.	.	.	T	0.58293	0.2112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67879	-0.5556	4	.	.	.	.	13.8525	0.63506	0.5851:0.0707:0.3442:0.0	.	.	.	.	W	209	.	.	R	-	1	2	RASGEF1A	43014577	0.011000	0.17503	0.336000	0.25522	0.744000	0.42396	-0.757000	0.04772	-2.469000	0.00531	-2.970000	0.00081	CGG	.	.		0.602	RASGEF1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313989.1	NM_145313		A	43694571	G	A	43694571	2	1	179	1	0	0	0	0	0	0	0	1	13084	1048	37	1		1	RASGEF1A	10	43694571	Silent	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10		43694571	91840176	45	26873										
OLFML1	283298	hgsc.bcm.edu	37	chr11	7530670	7530670	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gcataaagtctttgaaaataGtgaagaagatgatggacaca	10	4	1	5			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr11:7530670G>T	ENST00000329293.3	+	3	854	c.460G>T	c.(460-462)Gtg>Ttg	p.V154L	OLFML1_ENST00000530135.1_Missense_Mutation_p.V154L|OLFML1_ENST00000528758.1_3'UTR|CTD-2516F10.2_ENST00000530201.1_RNA	NM_198474.3	NP_940876.2	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1	154	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.					extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(3)|prostate(2)	24				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		TTTGAAAATAGTGAAGAAGAT	0.398																																					p.V154L		Atlas-SNP	.											.	OLFML1	54	.	0			c.G460T						.						113	111	112					11																	7530670		2201	4296	6497	SO:0001583	missense	283298	exon3			AAAATAGTGAAGA	AY358591	CCDS7779.1	11p15	2008-02-05			ENSG00000183801	ENSG00000183801			24473	protein-coding gene	gene with protein product							Standard	NM_198474		Approved	UNQ564	uc001mfi.3	Q6UWY5	OTTHUMG00000165527	ENST00000329293.3:c.460G>T	chr11.hg19:g.7530670G>T	ENSP00000332511:p.Val154Leu	115.0	0.0		106.0	5.0	NM_198474	B4DP03|Q569G4	Missense_Mutation	SNP	ENST00000329293.3	hg19	CCDS7779.1	.	.	.	.	.	.	.	.	.	.	G	11.81	1.749572	0.30955	.	.	ENSG00000183801	ENST00000530135;ENST00000329293	D;D	0.88741	-2.42;-2.42	5.78	4.86	0.63082	Olfactomedin-like (3);	0.124396	0.52532	D	0.000069	D	0.88370	0.6418	L	0.31207	0.915	0.80722	D	1	D;D	0.63046	0.992;0.992	P;D	0.65010	0.847;0.931	T	0.83283	-0.0037	10	0.10636	T	0.68	.	12.9717	0.58515	0.0797:0.0:0.9203:0.0	.	18;154	B4DN61;Q6UWY5	.;OLFL1_HUMAN	L	154	ENSP00000433455:V154L;ENSP00000332511:V154L	ENSP00000332511:V154L	V	+	1	0	OLFML1	7487246	0.999000	0.42202	1.000000	0.80357	0.922000	0.55478	2.781000	0.47750	2.724000	0.93272	0.563000	0.77884	GTG	.	.		0.398	OLFML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384656.1	NM_198474		T	7530670	G	T	7530670	3	4	179	1	0	0	0	0	1	0	0	0	10865	1029	36	3	470	3	OLFML1	11	7530670	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10		7530670	127475846	46	26874										
RAG1	5896	hgsc.bcm.edu	37	chr11	36597181	36597181	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	tgagtctgtggaagaactgcGggatcgggtgaaaggggtct	18	5	2	3			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr11:36597181G>T	ENST00000299440.5	+	2	2439	c.2327G>T	c.(2326-2328)cGg>cTg	p.R776L		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	776					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				GAAGAACTGCGGGATCGGGTG	0.488									Familial Hemophagocytic Lymphohistiocytosis																												p.R776L	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											RAG1,NS,carcinoma,+1,1	RAG1	151	.	0			c.G2327T						.						81	78	79					11																	36597181		2202	4298	6500	SO:0001583	missense	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AACTGCGGGATCG	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.2327G>T	chr11.hg19:g.36597181G>T	ENSP00000299440:p.Arg776Leu	77.0	0.0		59.0	5.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	hg19	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.390696	0.82902	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	D;D	0.87650	-2.28;-2.28	6.13	6.13	0.99165	.	0.000000	0.85682	D	0.000000	D	0.96137	0.8741	H	0.96333	3.805	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	D	0.96387	0.9286	10	0.87932	D	0	.	20.8401	0.99726	0.0:0.0:1.0:0.0	.	776	P15918	RAG1_HUMAN	L	776	ENSP00000434610:R776L;ENSP00000299440:R776L	ENSP00000299440:R776L	R	+	2	0	RAG1	36553757	1.000000	0.71417	0.975000	0.42487	0.913000	0.54294	9.476000	0.97823	2.932000	0.99384	0.644000	0.83932	CGG	.	.		0.488	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		T	36597181	G	T	36597181	3	4	179	1	0	0	0	0	1	0	0	0	13018	1116	39	1	2329	1	RAG1	11	36597181	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	29066511	36597181	98409335	47	26875										
CD82	3732	hgsc.bcm.edu	37	chr11	44639862	44639862	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	agggcttctgcgaggcccccGgcaacaggacccagagtggc	15	14	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr11:44639862G>A	ENST00000227155.4	+	8	837	c.589G>A	c.(589-591)Ggc>Agc	p.G197S	CD82_ENST00000530931.1_3'UTR|CD82_ENST00000342935.3_Missense_Mutation_p.G172S	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	197						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						CGAGGCCCCCGGCAACAGGAC	0.657																																					p.G197S		Atlas-SNP	.											.	CD82	27	.	0			c.G589A						.						37	36	36					11																	44639862		2203	4299	6502	SO:0001583	missense	3732	exon8			GCCCCCGGCAACA	U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"CD molecules", "Tetraspanins"	6210	protein-coding gene	gene with protein product	"suppression of tumorigenicity 6", "R2 leukocyte antigen"	600623	"kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))", "CD82 antigen"	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.589G>A	chr11.hg19:g.44639862G>A	ENSP00000227155:p.Gly197Ser	104.0	0.0		117.0	18.0	NM_002231	D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Missense_Mutation	SNP	ENST00000227155.4	hg19	CCDS7909.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.316841	0.23908	.	.	ENSG00000085117	ENST00000227155;ENST00000342935;ENST00000524750	T;T	0.76186	-1.0;-1.0	4.13	-4.63	0.03359	Tetraspanin, EC2 domain (1);	35.015100	0.00481	N	0.000133	T	0.44371	0.1290	N	0.02721	-0.515	0.09310	N	1	B;B	0.20550	0.046;0.017	B;B	0.15052	0.012;0.002	T	0.46176	-0.9210	10	0.09338	T	0.73	.	5.4746	0.16688	0.5037:0.2847:0.2116:0.0	.	172;197	E9PC70;P27701	.;CD82_HUMAN	S	197;172;15	ENSP00000227155:G197S;ENSP00000339686:G172S	ENSP00000227155:G197S	G	+	1	0	CD82	44596438	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-1.867000	0.01646	-0.876000	0.04017	0.561000	0.74099	GGC	.	.		0.657	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1			A	44639862	G	A	44639862	3	1	179	1	0	0	0	0	1	0	0	0	3042	1116	39	1	611	1	CD82	11	44639862	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	8042681	44639862	90366654	48	26876										
TRIM29	23650	hgsc.bcm.edu	37	chr11	120008061	120008061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ctccatcgtcttgccatgcaCgggacacttgcgggcctcaa	10	15	2	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr11:120008061C>T	ENST00000341846.5	-	1	1100	c.679G>A	c.(679-681)Gtg>Atg	p.V227M		NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	227					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		TTGCCATGCACGGGACACTTG	0.602																																					p.V227M		Atlas-SNP	.											.	TRIM29	78	.	0			c.G679A						.						69	68	68					11																	120008061		2203	4300	6503	SO:0001583	missense	23650	exon1			CATGCACGGGACA	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"Tripartite motif containing / Tripartite motif containing"	17274	protein-coding gene	gene with protein product	"tripartite motif protein TRIM29", "ataxia-telangiectasia group D-associated protein"	610658	"tripartite motif-containing 29"			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.679G>A	chr11.hg19:g.120008061C>T	ENSP00000343129:p.Val227Met	34.0	0.0		60.0	15.0	NM_012101	Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	hg19	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.168370	0.38315	.	.	ENSG00000137699	ENST00000341846	T	0.43294	0.95	5.76	-2.64	0.06114	Zinc finger, B-box (3);	0.514935	0.17375	N	0.176526	T	0.24431	0.0592	L	0.39898	1.24	0.58432	D	0.999999	B	0.22909	0.077	B	0.18561	0.022	T	0.04976	-1.0914	9	.	.	.	.	4.6247	0.12472	0.1062:0.3842:0.3402:0.1694	.	227	Q14134	TRI29_HUMAN	M	227	ENSP00000343129:V227M	.	V	-	1	0	TRIM29	119513271	0.001000	0.12720	0.581000	0.28614	0.967000	0.64934	-0.139000	0.10358	-0.428000	0.07339	-0.823000	0.03104	GTG	.	.		0.602	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101		T	120008061	C	T	120008061	3	4	179	1	0	0	0	0	1	0	0	0	16518	536	19	1	1123	1	TRIM29	11	120008061	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	75368199	120008061	14998455	49	26877										
GRAMD1B	57476	hgsc.bcm.edu	37	chr11	123474148	123474148	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ctgaagcctctgtgtcccaaGgagctctggcactttgttca	10	12	3	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr11:123474148G>A	ENST00000529750.1	+	8	963	c.636G>A	c.(634-636)aaG>aaA	p.K212K	GRAMD1B_ENST00000456860.2_Silent_p.K219K|GRAMD1B_ENST00000322282.7_Silent_p.K212K	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	212						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		TGTGTCCCAAGGAGCTCTGGC	0.587																																					p.K212K		Atlas-SNP	.											.	GRAMD1B	122	.	0			c.G636A						.						70	69	69					11																	123474148		1986	4161	6147	SO:0001819	synonymous_variant	57476	exon8			TCCCAAGGAGCTC	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.636G>A	chr11.hg19:g.123474148G>A		105.0	0.0		107.0	22.0	NM_020716	Q6UW85|Q9ULL9	Silent	SNP	ENST00000529750.1	hg19	CCDS53720.1																																																																																			.	.		0.587	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		A	123474148	G	A	123474148	2	1	179	1	0	0	0	0	0	0	0	1	6757	991	35	3		3	GRAMD1B	11	123474148	Silent	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	3466087	123474148	11532368	50	26878										
ROBO3	64221	hgsc.bcm.edu	37	chr11	124747876	124747876	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gctcagacggccaggggcacGgccgcccctggcgagggtcc	17	16	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr11:124747876G>A	ENST00000397801.1	+	21	3222	c.3030G>A	c.(3028-3030)acG>acA	p.T1010T	ROBO3_ENST00000538940.1_Silent_p.T988T|ROBO3_ENST00000543966.1_5'UTR|ROBO3_ENST00000525482.1_3'UTR	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	1010					axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		CCAGGGGCACGGCCGCCCCTG	0.607																																					p.T1010T		Atlas-SNP	.											.	ROBO3	199	.	0			c.G3030A						.						12	14	13					11																	124747876		1843	4079	5922	SO:0001819	synonymous_variant	64221	exon21			GGGCACGGCCGCC	AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13433	protein-coding gene	gene with protein product		608630	"roundabout (axon guidance receptor, Drosophila) homolog 3", "horizontal gaze palsy with progressive scoliosis"	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.3030G>A	chr11.hg19:g.124747876G>A		855.0	1.0		793.0	167.0	NM_022370		Silent	SNP	ENST00000397801.1	hg19	CCDS44755.1																																																																																			.	.		0.607	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		A	124747876	G	A	124747876	2	1	179	1	0	0	0	0	0	0	0	1	13530	1103	39	1		1	ROBO3	11	124747876	Silent	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	1273728	124747876	10258640	51	26879										
YAF2	10138	hgsc.bcm.edu	37	chr12	42555530	42555530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	aggcacaaactgctgagtaaCctgctgtgcaaccaactggg	11	11	0	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr12:42555530C>T	ENST00000534854.2	-	3	257	c.190G>A	c.(190-192)Gtt>Att	p.V64I	YAF2_ENST00000380790.4_Missense_Mutation_p.V22I|YAF2_ENST00000380788.3_Missense_Mutation_p.V55I|YAF2_ENST00000327791.4_Intron|YAF2_ENST00000442791.3_Missense_Mutation_p.V88I	NM_005748.4	NP_005739.2	Q8IY57	YAF2_HUMAN	YY1 associated factor 2	64					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(1)	8	all_cancers(12;0.000425)	Lung NSC(34;0.0402)|all_lung(34;0.057)		GBM - Glioblastoma multiforme(48;0.0514)		TGCTGAGTAACCTGCTGTGCA	0.353																																					p.V88I		Atlas-SNP	.											.	YAF2	16	.	0			c.G262A						.						95	95	95					12																	42555530		2203	4300	6503	SO:0001583	missense	10138	exon4			GAGTAACCTGCTG	U72209	CCDS31775.1, CCDS53778.1, CCDS53779.1, CCDS53780.1	12q12	2014-09-04			ENSG00000015153	ENSG00000015153			17363	protein-coding gene	gene with protein product		607534				9016636	Standard	NM_001190977		Approved		uc001rmw.3	Q8IY57	OTTHUMG00000169380	ENST00000534854.2:c.190G>A	chr12.hg19:g.42555530C>T	ENSP00000439256:p.Val64Ile	93.0	0.0		98.0	14.0	NM_001190979	A8K5P0|B4DFU3|G3V465|Q99710	Missense_Mutation	SNP	ENST00000534854.2	hg19	CCDS31775.1	.	.	.	.	.	.	.	.	.	.	C	17.22	3.332953	0.60853	.	.	ENSG00000015153	ENST00000442791;ENST00000534854;ENST00000380790;ENST00000380788;ENST00000548917	.	.	.	5.43	4.54	0.55810	.	0.054093	0.64402	D	0.000001	T	0.57946	0.2088	L	0.54323	1.7	0.80722	D	1	B;B;B	0.17465	0.004;0.022;0.002	B;B;B	0.14578	0.011;0.011;0.005	T	0.56535	-0.7963	9	0.46703	T	0.11	.	14.2203	0.65823	0.0:0.928:0.0:0.072	.	22;55;64	B4DFU3;A6NL56;Q8IY57	.;.;YAF2_HUMAN	I	88;64;22;55;25	.	ENSP00000370165:V55I	V	-	1	0	YAF2	40841797	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.398000	0.79919	1.413000	0.46997	0.650000	0.86243	GTT	.	.		0.353	YAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403781.1			T	42555530	C	T	42555530	3	4	179	1	0	0	0	0	1	0	0	0	17480	507	18	3	360	3	YAF2	12	42555530	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10		42555530	91296365	52	26880										
RAPGEF3	10411	hgsc.bcm.edu	37	chr12	48137437	48137437	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	agggtcaacactgagtggtcTggccggcagatgtcataggg	16	8	3	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr12:48137437T>A	ENST00000449771.2	-	18	1789	c.1701A>T	c.(1699-1701)ccA>ccT	p.P567P	RAPGEF3_ENST00000405493.2_Silent_p.P525P|RAPGEF3_ENST00000548919.1_Intron|RAPGEF3_ENST00000389212.3_Silent_p.P567P|RAPGEF3_ENST00000549151.1_Silent_p.P525P|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000171000.4_Silent_p.P525P			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	567					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		CTGAGTGGTCTGGCCGGCAGA	0.627																																					p.P567P		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.A1701T						.						61	51	54					12																	48137437		2203	4300	6503	SO:0001819	synonymous_variant	10411	exon18			GTGGTCTGGCCGG	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"exchange protein directly activated by cAMP 1"	606057	"RAP guanine-nucleotide-exchange factor (GEF) 3"			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1701A>T	chr12.hg19:g.48137437T>A		97.0	0.0		82.0	12.0	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Silent	SNP	ENST00000449771.2	hg19	CCDS41775.1																																																																																			.	.		0.627	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		A	48137437	T	A	48137437	2	1	179	1	0	0	0	0	0	0	0	1	13060	1567	55	4		4	RAPGEF3	12	48137437	Silent	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	5581907	48137437	85714458	53	26881										
MMP19	4327	hgsc.bcm.edu	37	chr12	56234593	56234593	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	aaggcttgacgcagggctgcCcgggctgtgtggggtggaag	20	8	0	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr12:56234593C>T	ENST00000322569.4	-	4	469	c.378G>A	c.(376-378)cgG>cgA	p.R126R	MMP19_ENST00000548629.1_Silent_p.R103R|MMP19_ENST00000394182.1_5'Flank|MMP19_ENST00000547487.1_5'Flank|MMP19_ENST00000409200.3_Silent_p.R126R	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	126					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	GCAGGGCTGCCCGGGCTGTGT	0.582																																					p.R126R		Atlas-SNP	.											MMP19,colon,carcinoma,-2,1	MMP19	61	.	0			c.G378A						.						95	88	90					12																	56234593		2203	4300	6503	SO:0001819	synonymous_variant	4327	exon4			GGCTGCCCGGGCT	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"matrix metalloproteinase 19"	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.378G>A	chr12.hg19:g.56234593C>T		90.0	0.0		85.0	13.0	NM_001272101	B4E030|O15278|O95606|Q99580	Silent	SNP	ENST00000322569.4	hg19	CCDS8895.1																																																																																			.	.		0.582	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429		T	56234593	C	T	56234593	2	4	179	1	0	0	0	0	0	0	0	1	9666	610	22	3		3	MMP19	12	56234593	Silent	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	8097156	56234593	77617302	54	26882										
FGD6	55785	hgsc.bcm.edu	37	chr12	95478307	95478307	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gagcatcctctgctttgaatAcataaaataacatgtttttg	6	7	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr12:95478307A>C	ENST00000343958.4	-	20	4446	c.4223T>G	c.(4222-4224)gTa>gGa	p.V1408G		NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1408	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						TGCTTTGAATACATAAAATAA	0.323																																					p.V1408G		Atlas-SNP	.											.	FGD6	127	.	0			c.T4223G						.						114	122	119					12																	95478307		2203	4300	6503	SO:0001583	missense	55785	exon20			TTGAATACATAAA	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.4223T>G	chr12.hg19:g.95478307A>C	ENSP00000344446:p.Val1408Gly	75.0	0.0		73.0	15.0	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	hg19	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.521199	0.64747	.	.	ENSG00000180263	ENST00000343958	T	0.13196	2.61	5.24	5.24	0.73138	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.360238	0.20173	N	0.097684	T	0.28466	0.0704	L	0.48642	1.525	0.80722	D	1	D	0.62365	0.991	P	0.61658	0.892	T	0.00852	-1.1540	10	0.52906	T	0.07	-6.3639	15.1513	0.72700	1.0:0.0:0.0:0.0	.	1408	Q6ZV73	FGD6_HUMAN	G	1408	ENSP00000344446:V1408G	ENSP00000344446:V1408G	V	-	2	0	FGD6	94002438	1.000000	0.71417	0.864000	0.33941	0.815000	0.46073	5.726000	0.68515	1.979000	0.57680	0.402000	0.26972	GTA	.	.		0.323	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		C	95478307	A	C	95478307	3	2	179	1	0	0	0	0	1	0	0	0	5845	391	14	5	77	5	FGD6	12	95478307	Missense_Mutation	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10	39243714	95478307	38373588	55	26883										
FGD6	55785	hgsc.bcm.edu	37	chr12	95478356	95478356	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ctgaaatactttagactcggAattctcatctttaacttgaa	5	8	2	3			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr12:95478356A>C	ENST00000343958.4	-	20	4397	c.4174T>G	c.(4174-4176)Tcc>Gcc	p.S1392A		NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1392	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						TTAGACTCGGAATTCTCATCT	0.353																																					p.S1392A		Atlas-SNP	.											.	FGD6	127	.	0			c.T4174G						.						99	107	104					12																	95478356		2203	4299	6502	SO:0001583	missense	55785	exon20			ACTCGGAATTCTC	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.4174T>G	chr12.hg19:g.95478356A>C	ENSP00000344446:p.Ser1392Ala	77.0	0.0		85.0	16.0	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	hg19	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	A	12.36	1.913463	0.33815	.	.	ENSG00000180263	ENST00000343958	T	0.75821	-0.97	4.98	3.8	0.43715	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.37012	N	0.002291	T	0.62109	0.2401	L	0.28649	0.875	0.80722	D	1	B	0.15719	0.014	B	0.24269	0.052	T	0.52609	-0.8553	10	0.23891	T	0.37	-6.7278	11.694	0.51532	0.8515:0.1485:0.0:0.0	.	1392	Q6ZV73	FGD6_HUMAN	A	1392	ENSP00000344446:S1392A	ENSP00000344446:S1392A	S	-	1	0	FGD6	94002487	0.738000	0.28186	0.996000	0.52242	0.769000	0.43574	1.817000	0.39002	0.706000	0.31912	0.402000	0.26972	TCC	.	.		0.353	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		C	95478356	A	C	95478356	3	2	179	1	0	0	0	0	1	0	0	0	5845	246	9	5	126	5	FGD6	12	95478356	Missense_Mutation	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10	49	95478356	38373539	56	26884										
MTUS2	23281	hgsc.bcm.edu	37	chr13	29933428	29933428	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	agcagaggactgcggcagctCgaaatgggtttccgcccaag	14	11	0	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr13:29933428C>T	ENST00000431530.3	+	6	3023	c.2965C>T	c.(2965-2967)Cga>Tga	p.R989*		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	979	Localization to the growing distal tip of microtubules.					cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						TGCGGCAGCTCGAAATGGGTT	0.582																																					p.R989X		Atlas-SNP	.											MTUS2_ENST00000431530,NS,carcinoma,0,1	MTUS2	279	.	0			c.C2965T						.						14	15	14					13																	29933428		1922	4129	6051	SO:0001587	stop_gained	23281	exon6			GCAGCTCGAAATG	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.2965C>T	chr13.hg19:g.29933428C>T	ENSP00000392057:p.Arg989*	184.0	0.0		175.0	41.0	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Nonsense_Mutation	SNP	ENST00000431530.3	hg19	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	C	39	7.545065	0.98348	.	.	ENSG00000132938	ENST00000431530	.	.	.	4.91	3.99	0.46301	.	0.224065	0.29861	N	0.011013	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7856	0.40675	0.3027:0.6973:0.0:0.0	.	.	.	.	X	989	.	.	R	+	1	2	MTUS2	28831428	0.893000	0.30496	0.906000	0.35671	0.374000	0.29953	1.365000	0.34182	2.560000	0.86352	0.591000	0.81541	CGA	.	.		0.582	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		T	29933428	C	T	29933428	4	4	179	1	0	0	0	0	0	1	0	0	9975	876	31	1	2987	1	MTUS2	13	29933428	Nonsense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10		29933428	85236450	57	26885										
NBEA	26960	hgsc.bcm.edu	37	chr13	35883725	35883726	+	Missense_Mutation	DNP	GG	GG	TT													0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ttattgagctcatcaatgaaGgaaggtaattaattttacaa							TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr13:35883725_35883726GG>TT	ENST00000400445.3	+	36	6433_6434	c.5899_5900GG>TT	c.(5899-5901)GGa>TTa	p.G1967L	NBEA_ENST00000310336.4_Missense_Mutation_p.G1967L|NBEA_ENST00000540320.1_Missense_Mutation_p.G1967L|NBEA_ENST00000379939.2_Missense_Mutation_p.G1964L	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1967					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CATCAATGAAGGAAGGTAATTA	0.347																																					p.G1967X|p.G1967V		Atlas-SNP	.											.	NBEA	340	.	0			c.G5899T|c.G5900T						.																																			SO:0001583	missense	26960	exon36			AATGAAGGAAGGT|ATGAAGGAAGGTA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	Exception_encountered	chr13.hg19:g.35883725_35883726delinsTT	ENSP00000383295:p.Gly1967Leu	208.0|205.0	0.0		213.0|211.0	36.0|34.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.347	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		TT	35883726	GG	TT	35883725	3	4	179	1	0	0	0	0	1	0	0	0	10196	1001	35	3	6041	3	NBEA	13	35883725	Missense_Mutation	DNP	GG	TCGA-DD-AAD2-01A-11D-A40R-10	5950297	35883725	79286153	58	26886										
TPPP2	122664	hgsc.bcm.edu	37	chr14	21498863	21498863	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	aaagactgtggcatcatggaTggcaagacagtcacctccac	10	11	2	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr14:21498863T>A	ENST00000321760.6	+	2	271	c.123T>A	c.(121-123)gaT>gaA	p.D41E	TPPP2_ENST00000530140.2_Missense_Mutation_p.D41E|RP11-998D10.1_ENST00000531638.1_5'Flank|TPPP2_ENST00000460647.2_Missense_Mutation_p.D41E|AL161668.5_ENST00000533984.1_lincRNA|NDRG2_ENST00000403829.3_Intron	NM_173846.4	NP_776245.2	P59282	TPPP2_HUMAN	tubulin polymerization-promoting protein family member 2	41						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		GCATCATGGATGGCAAGACAG	0.498																																					p.D41E		Atlas-SNP	.											.	TPPP2	22	.	0			c.T123A						.						100	72	81					14																	21498863		2203	4300	6503	SO:0001583	missense	122664	exon2			CATGGATGGCAAG	AY072034	CCDS9566.1	14q11.2	2014-01-21	2007-05-02	2007-05-02	ENSG00000179636	ENSG00000179636			19293	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 8"	C14orf8		15590652, 17105200	Standard	NM_173846		Approved	p25beta, p18, CT152	uc001vzh.3	P59282	OTTHUMG00000029642	ENST00000321760.6:c.123T>A	chr14.hg19:g.21498863T>A	ENSP00000317595:p.Asp41Glu	94.0	0.0		99.0	11.0	NM_173846	Q2VYF3	Missense_Mutation	SNP	ENST00000321760.6	hg19	CCDS9566.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.418688	0.83559	.	.	ENSG00000179636	ENST00000321760;ENST00000460647;ENST00000530140;ENST00000472458;ENST00000481535	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	5.37	-6.66	0.01789	.	0.000000	0.85682	D	0.000000	T	0.60945	0.2308	M	0.89214	3.015	0.52099	D	0.99994	D	0.54397	0.966	P	0.61397	0.888	T	0.67979	-0.5530	10	0.72032	D	0.01	-16.1604	8.7954	0.34876	0.1102:0.4846:0.0:0.4052	.	41	P59282	TPPP2_HUMAN	E	41;41;41;41;36	ENSP00000317595:D41E;ENSP00000427504:D41E;ENSP00000435356:D41E;ENSP00000423171:D41E;ENSP00000421438:D36E	ENSP00000317595:D41E	D	+	3	2	TPPP2	20568703	0.008000	0.16893	0.596000	0.28811	0.977000	0.68977	-1.049000	0.03514	-1.583000	0.01638	0.533000	0.62120	GAT	.	.		0.498	TPPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073914.3	NM_173846		A	21498863	T	A	21498863	3	1	179	1	0	0	0	0	1	0	0	0	16429	1461	51	4	125	4	TPPP2	14	21498863	Missense_Mutation	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10		21498863	85850677	59	26887										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33290961	33290961	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	aatccaaaggtcactggcatGacacagcctaatgttttaac	7	10	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr14:33290961G>T	ENST00000280979.4	+	13	4112	c.3942G>T	c.(3940-3942)atG>atT	p.M1314I	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1314					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TCACTGGCATGACACAGCCTA	0.408																																					p.M1314I	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.G3942T						.						53	51	52					14																	33290961		2203	4300	6503	SO:0001583	missense	9472	exon13			TGGCATGACACAG	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.3942G>T	chr14.hg19:g.33290961G>T	ENSP00000280979:p.Met1314Ile	72.0	0.0		62.0	11.0	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	G	2.092	-0.408108	0.04832	.	.	ENSG00000151320	ENST00000280979	T	0.04502	3.61	5.92	2.65	0.31530	.	0.761307	0.13175	N	0.407992	T	0.02649	0.0080	N	0.16478	0.41	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44952	-0.9294	10	0.33141	T	0.24	0.181	0.2613	0.00219	0.2332:0.1703:0.2484:0.348	.	1314	Q13023	AKAP6_HUMAN	I	1314	ENSP00000280979:M1314I	ENSP00000280979:M1314I	M	+	3	0	AKAP6	32360712	0.116000	0.22171	0.033000	0.17914	0.978000	0.69477	0.995000	0.29706	0.785000	0.33685	0.655000	0.94253	ATG	.	.		0.408	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33290961	G	T	33290961	3	4	179	1	0	0	0	0	1	0	0	0	455	1290	45	3	3988	3	AKAP6	14	33290961	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	11792098	33290961	74058579	60	26888										
PDE8A	5151	hgsc.bcm.edu	37	chr15	85634389	85634389	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ctgacttgctcgatactataAattcatgcatcaggataggc	8	9	2	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr15:85634389A>T	ENST00000310298.4	+	9	1081	c.829A>T	c.(829-831)Aat>Tat	p.N277Y	PDE8A_ENST00000339708.5_Intron|PDE8A_ENST00000394553.1_Missense_Mutation_p.N277Y|PDE8A_ENST00000557819.2_Intron|PDE8A_ENST00000557957.1_Missense_Mutation_p.N205Y			O60658	PDE8A_HUMAN	phosphodiesterase 8A	277	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	CGATACTATAAATTCATGCAT	0.383																																					p.N277Y		Atlas-SNP	.											.	PDE8A	50	.	0			c.A829T						.						79	77	78					15																	85634389		2203	4299	6502	SO:0001583	missense	5151	exon8			ACTATAAATTCAT	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"Phosphodiesterases"	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.829A>T	chr15.hg19:g.85634389A>T	ENSP00000311453:p.Asn277Tyr	157.0	0.0		151.0	24.0	NM_002605	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Missense_Mutation	SNP	ENST00000310298.4	hg19	CCDS10336.1	.	.	.	.	.	.	.	.	.	.	A	16.45	3.127204	0.56721	.	.	ENSG00000073417	ENST00000310298;ENST00000394553	T;T	0.76186	-1.0;-1.0	4.73	4.73	0.59995	PAS (3);PAS fold (1);	0.222920	0.44902	N	0.000414	D	0.82884	0.5134	M	0.70903	2.155	0.58432	D	0.999998	D	0.76494	0.999	D	0.69479	0.964	T	0.81967	-0.0690	10	0.33940	T	0.23	.	12.2422	0.54549	1.0:0.0:0.0:0.0	.	277	O60658	PDE8A_HUMAN	Y	277	ENSP00000311453:N277Y;ENSP00000378056:N277Y	ENSP00000311453:N277Y	N	+	1	0	PDE8A	83435393	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	8.188000	0.89710	1.981000	0.57761	0.460000	0.39030	AAT	.	.		0.383	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		T	85634389	A	T	85634389	3	4	179	1	0	0	0	0	1	0	0	0	11662	14	1	4	859	4	PDE8A	15	85634389	Missense_Mutation	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10		85634389	16897003	61	26889										
SLCO3A1	28232	hgsc.bcm.edu	37	chr15	92459637	92459637	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cccctgtgcagcccctgggcGtctcctacatcgacgaccac	9	19	1	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr15:92459637G>A	ENST00000318445.6	+	2	809	c.595G>A	c.(595-597)Gtc>Atc	p.V199I	SLCO3A1_ENST00000424469.2_Missense_Mutation_p.V199I	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	199					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	GCCCCTGGGCGTCTCCTACAT	0.602																																					p.V199I		Atlas-SNP	.											.	SLCO3A1	84	.	0			c.G595A						.						23	24	24					15																	92459637		2198	4298	6496	SO:0001583	missense	28232	exon2			CTGGGCGTCTCCT	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"Solute carriers"	10952	protein-coding gene	gene with protein product		612435	"solute carrier family 21 (organic anion transporter), member 11"	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.595G>A	chr15.hg19:g.92459637G>A	ENSP00000320634:p.Val199Ile	89.0	0.0		77.0	18.0	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Missense_Mutation	SNP	ENST00000318445.6	hg19	CCDS10371.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.880178	0.72294	.	.	ENSG00000176463	ENST00000318445;ENST00000424469	T;T	0.38401	1.14;1.14	5.44	5.44	0.79542	Major facilitator superfamily domain, general substrate transporter (1);	0.064935	0.64402	D	0.000007	T	0.40546	0.1121	N	0.17474	0.49	0.80722	D	1	D;D;B	0.76494	0.996;0.999;0.337	P;D;B	0.76071	0.732;0.987;0.093	T	0.08597	-1.0714	10	0.02654	T	1	.	18.267	0.90055	0.0:0.0:1.0:0.0	.	141;199;199	Q9UIG8-3;Q9UIG8-2;Q9UIG8	.;.;SO3A1_HUMAN	I	199	ENSP00000320634:V199I;ENSP00000387846:V199I	ENSP00000320634:V199I	V	+	1	0	SLCO3A1	90260641	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.323000	0.72891	2.567000	0.86603	0.655000	0.94253	GTC	.	.		0.602	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272		A	92459637	G	A	92459637	3	1	179	1	0	0	0	0	1	0	0	0	14743	1145	40	1	601	1	SLCO3A1	15	92459637	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	6825248	92459637	10071755	62	26890										
HEATR3	55027	hgsc.bcm.edu	37	chr16	50117925	50117925	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ctggaaattattgtcaacatGtgctgcaatgaaggtttgtt	10	5	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr16:50117925G>A	ENST00000299192.7	+	8	1310	c.1119G>A	c.(1117-1119)atG>atA	p.M373I	HEATR3_ENST00000285767.4_Missense_Mutation_p.M287I|HEATR3_ENST00000564942.1_3'UTR	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	373										cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TTGTCAACATGTGCTGCAATG	0.398																																					p.M373I		Atlas-SNP	.											.	HEATR3	59	.	0			c.G1119A						.						129	119	122					16																	50117925		2198	4300	6498	SO:0001583	missense	55027	exon8			CAACATGTGCTGC	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.1119G>A	chr16.hg19:g.50117925G>A	ENSP00000299192:p.Met373Ile	79.0	0.0		67.0	5.0	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Missense_Mutation	SNP	ENST00000299192.7	hg19	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.220261	0.58560	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	T;T	0.30182	1.54;1.54	6.03	6.03	0.97812	Armadillo-type fold (1);	0.034798	0.85682	D	0.000000	T	0.30198	0.0757	L	0.56769	1.78	0.80722	D	1	B;B	0.34372	0.023;0.451	B;B	0.26517	0.019;0.07	T	0.12192	-1.0557	10	0.10902	T	0.67	.	20.5752	0.99366	0.0:0.0:1.0:0.0	.	287;373	B7WNW7;Q7Z4Q2	.;HEAT3_HUMAN	I	287;373	ENSP00000285767:M287I;ENSP00000299192:M373I	ENSP00000285767:M287I	M	+	3	0	HEATR3	48675426	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.649000	0.91067	2.868000	0.98415	0.557000	0.71058	ATG	.	.		0.398	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		A	50117925	G	A	50117925	3	1	179	1	0	0	0	0	1	0	0	0	7038	1377	48	3	1149	3	HEATR3	16	50117925	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10		50117925	40236828	63	26891										
DYNC1LI2	1783	hgsc.bcm.edu	37	chr16	66785466	66785466	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gcccgttgggacctagcagcAgcttcttctccacccccacc	8	19	2	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr16:66785466A>T	ENST00000258198.2	-	1	235	c.29T>A	c.(28-30)cTg>cAg	p.L10Q	DYNC1LI2_ENST00000440564.2_Missense_Mutation_p.L10Q|RP11-61A14.4_ENST00000501143.1_lincRNA|DYNC1LI2_ENST00000443351.2_Missense_Mutation_p.L10Q|DYNC1LI2_ENST00000379482.2_Missense_Mutation_p.L10Q	NM_006141.2	NP_006132.1	O43237	DC1L2_HUMAN	dynein, cytoplasmic 1, light intermediate chain 2	10					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|centrosome localization (GO:0051642)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based movement (GO:0007018)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			central_nervous_system(3)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(4)|stomach(1)	15		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0907)|Epithelial(162;0.212)		ACCTAGCAGCAGCTTCTTCTC	0.746																																					p.L10Q		Atlas-SNP	.											.	DYNC1LI2	37	.	0			c.T29A						.						18	22	21					16																	66785466		2077	4079	6156	SO:0001583	missense	1783	exon1			AGCAGCAGCTTCT	AF035812	CCDS10818.1, CCDS67049.1	16q22.1	2008-02-05	2005-11-25	2005-11-25	ENSG00000135720	ENSG00000135720		"Cytoplasmic dyneins"	2966	protein-coding gene	gene with protein product		611406	"dynein, cytoplasmic, light intermediate polypeptide 2"	DNCLI2		16260502	Standard	NM_006141		Approved		uc002eqb.1	O43237	OTTHUMG00000137523	ENST00000258198.2:c.29T>A	chr16.hg19:g.66785466A>T	ENSP00000258198:p.Leu10Gln	88.0	0.0		61.0	8.0	NM_006141	A8K6V1|B4DZP4|Q8TAT3	Missense_Mutation	SNP	ENST00000258198.2	hg19	CCDS10818.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.179213	0.78564	.	.	ENSG00000135720	ENST00000258198;ENST00000379482;ENST00000443351;ENST00000440564	T;T;T;T	0.51325	2.08;0.71;0.71;1.21	4.01	4.01	0.46588	.	0.087247	0.49305	D	0.000145	T	0.55577	0.1929	L	0.51422	1.61	0.41912	D	0.990472	P;D;B;D	0.55172	0.954;0.97;0.007;0.97	P;P;B;P	0.57057	0.812;0.601;0.013;0.725	T	0.60500	-0.7251	10	0.72032	D	0.01	2.5683	12.0326	0.53406	1.0:0.0:0.0:0.0	.	10;10;10;10	B4E2E0;B4DHD8;B4DZP4;O43237	.;.;.;DC1L2_HUMAN	Q	10	ENSP00000258198:L10Q;ENSP00000368795:L10Q;ENSP00000394289:L10Q;ENSP00000408566:L10Q	ENSP00000258198:L10Q	L	-	2	0	DYNC1LI2	65342967	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.165000	0.58196	1.662000	0.50781	0.455000	0.32223	CTG	.	.		0.746	DYNC1LI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268846.1	NM_006141		T	66785466	A	T	66785466	3	4	179	1	0	0	0	0	1	0	0	0	4847	188	7	4	1501	4	DYNC1LI2	16	66785466	Missense_Mutation	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10	16667541	66785466	23569287	64	26892										
RFWD3	55159	hgsc.bcm.edu	37	chr16	74678544	74678544	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cggtggtccccagcattggtCcactgttccagacatattgt	10	12	0	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr16:74678544C>T	ENST00000361070.4	-	5	979	c.882G>A	c.(880-882)tgG>tgA	p.W294*	RFWD3_ENST00000571750.1_Nonsense_Mutation_p.W294*	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	294					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						CAGCATTGGTCCACTGTTCCA	0.498																																					p.W294X		Atlas-SNP	.											.	RFWD3	49	.	0			c.G882A						.						104	95	98					16																	74678544		2198	4300	6498	SO:0001587	stop_gained	55159	exon5			ATTGGTCCACTGT	AK001382	CCDS32486.1	16q22.3	2013-01-09						"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.882G>A	chr16.hg19:g.74678544C>T	ENSP00000354361:p.Trp294*	114.0	0.0		100.0	17.0	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Nonsense_Mutation	SNP	ENST00000361070.4	hg19	CCDS32486.1	.	.	.	.	.	.	.	.	.	.	C	40	8.344797	0.98769	.	.	ENSG00000168411	ENST00000361070	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.3476	20.328	0.98708	0.0:1.0:0.0:0.0	.	.	.	.	X	294	.	ENSP00000354361:W294X	W	-	3	0	RFWD3	73236045	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	7.239000	0.78182	2.802000	0.96397	0.561000	0.74099	TGG	.	.		0.498	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124		T	74678544	C	T	74678544	4	4	179	1	0	0	0	0	0	1	0	0	13276	856	30	3	1478	3	RFWD3	16	74678544	Nonsense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	7893078	74678544	15676209	65	26893										
MVD	4597	hgsc.bcm.edu	37	chr16	88722115	88722115	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cgcatgcccacggtactgccTgtcagcttcttctcagcgct	9	16	3	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr16:88722115T>A	ENST00000301012.3	-	6	656	c.627A>T	c.(625-627)acA>acT	p.T209T	MVD_ENST00000568709.1_5'Flank	NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	209					cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		CGGTACTGCCTGTCAGCTTCT	0.682																																					p.T209T		Atlas-SNP	.											.	MVD	27	.	0			c.A627T						.						37	30	32					16																	88722115		2173	4252	6425	SO:0001819	synonymous_variant	4597	exon6			ACTGCCTGTCAGC	U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4.1.1.33		7529	protein-coding gene	gene with protein product	"mevalonate pyrophosphate decarboxylase"	603236				8626466	Standard	NM_002461		Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.627A>T	chr16.hg19:g.88722115T>A		52.0	0.0		53.0	15.0	NM_002461	Q53Y65	Silent	SNP	ENST00000301012.3	hg19	CCDS10968.1																																																																																			.	.		0.682	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269547.2	NM_002461		A	88722115	T	A	88722115	2	1	179	1	0	0	0	0	0	0	0	1	10003	1567	55	4		4	MVD	16	88722115	Silent	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	14043571	88722115	1632638	66	26894										
DLG4	1742	hgsc.bcm.edu	37	chr17	7106632	7106632	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	tggttccctacgccccctgcGatgctgaagccaagacctgg	11	15	0	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr17:7106632G>A	ENST00000399506.2	-	7	713	c.522C>T	c.(520-522)atC>atT	p.I174I	DLG4_ENST00000399510.2_Silent_p.I217I|DLG4_ENST00000485100.1_Silent_p.I171I|DLG4_ENST00000302955.6_Silent_p.I171I			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	174	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	CGCCCCCTGCGATGCTGAAGC	0.577																																					p.I217I		Atlas-SNP	.											.	DLG4	110	.	0			c.C651T						.						60	59	59					17																	7106632		2003	4184	6187	SO:0001819	synonymous_variant	1742	exon9			CCCTGCGATGCTG	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.522C>T	chr17.hg19:g.7106632G>A		45.0	0.0		56.0	10.0	NM_001365	B7Z1S1|G5E939|Q92941|Q9UKK8	Silent	SNP	ENST00000399506.2	hg19																																																																																				.	.		0.577	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365		A	7106632	G	A	7106632	2	1	179	1	0	0	0	0	0	0	0	1	4559	1048	37	1		1	DLG4	17	7106632	Silent	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10		7106632	74088578	67	26895										
CNP	1267	hgsc.bcm.edu	37	chr17	40120710	40120710	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gcaaagccggccaggtcttcCtggaagagctggggaaccac	14	12	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr17:40120710C>G	ENST00000393892.3	+	2	772	c.628C>G	c.(628-630)Ctg>Gtg	p.L210V	CNP_ENST00000591072.1_Intron|CNP_ENST00000472031.1_Intron|CNP_ENST00000393888.1_Missense_Mutation_p.L190V	NM_033133.4	NP_149124.3	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase	210					adult locomotory behavior (GO:0008344)|aging (GO:0007568)|axonogenesis (GO:0007409)|cyclic nucleotide catabolic process (GO:0009214)|microtubule cytoskeleton organization (GO:0000226)|oligodendrocyte differentiation (GO:0048709)|regulation of mitochondrial membrane permeability (GO:0046902)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule (GO:0005874)|microvillus (GO:0005902)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|myelin sheath abaxonal region (GO:0035748)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity (GO:0004113)|cyclic nucleotide binding (GO:0030551)|RNA binding (GO:0003723)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	9		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)		CCAGGTCTTCCTGGAAGAGCT	0.597																																					p.L210V		Atlas-SNP	.											.	CNP	58	.	0			c.C628G						.						18	19	19					17																	40120710		1940	4157	6097	SO:0001583	missense	1267	exon2			GTCTTCCTGGAAG		CCDS11414.2	17q21	2008-02-05			ENSG00000173786	ENSG00000173786	3.1.4.37		2158	protein-coding gene	gene with protein product		123830				1322358	Standard	XM_006721701		Approved		uc002hyl.1	P09543	OTTHUMG00000133502	ENST00000393892.3:c.628C>G	chr17.hg19:g.40120710C>G	ENSP00000377470:p.Leu210Val	139.0	0.0		115.0	27.0	NM_033133		Missense_Mutation	SNP	ENST00000393892.3	hg19	CCDS11414.2	.	.	.	.	.	.	.	.	.	.	C	14.70	2.614459	0.46631	.	.	ENSG00000173786	ENST00000393892;ENST00000393888	T;T	0.59638	0.25;0.25	4.46	4.46	0.54185	RNA ligase/cyclic nucleotide phosphodiesterase (1);	0.000000	0.64402	D	0.000003	T	0.58949	0.2158	M	0.66939	2.045	0.80722	D	1	P;P	0.36438	0.553;0.497	B;B	0.43386	0.418;0.367	T	0.61372	-0.7076	10	0.48119	T	0.1	-14.907	8.5752	0.33595	0.0:0.8566:0.0:0.1434	.	210;190	P09543;P09543-2	CN37_HUMAN;.	V	210;190	ENSP00000377470:L210V;ENSP00000377466:L190V	ENSP00000377466:L190V	L	+	1	2	CNP	37374236	0.995000	0.38212	1.000000	0.80357	0.800000	0.45204	0.738000	0.26158	2.301000	0.77427	0.455000	0.32223	CTG	.	.		0.597	CNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257443.2			G	40120710	C	G	40120710	3	3	179	1	0	0	0	0	1	0	0	0	3628	680	24	4	634	4	CNP	17	40120710	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	33014078	40120710	41074500	68	26896										
ALPK2	115701	hgsc.bcm.edu	37	chr18	56204804	56204804	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	tgcttttgcacgtagacactGaagtctcagacacttgtgtc	9	10	1	3			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr18:56204804G>T	ENST00000361673.3	-	5	2828	c.2615C>A	c.(2614-2616)tCa>tAa	p.S872*	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	872						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CGTAGACACTGAAGTCTCAGA	0.423																																					p.S872X		Atlas-SNP	.											.	ALPK2	487	.	0			c.C2615A						.						62	56	58					18																	56204804		2203	4300	6503	SO:0001587	stop_gained	115701	exon5			GACACTGAAGTCT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2615C>A	chr18.hg19:g.56204804G>T	ENSP00000354991:p.Ser872*	127.0	0.0		123.0	6.0	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Nonsense_Mutation	SNP	ENST00000361673.3	hg19	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	G	39	7.832221	0.98513	.	.	ENSG00000198796	ENST00000361673	.	.	.	5.47	4.56	0.56223	.	0.464462	0.20763	N	0.086134	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-0.5793	8.8755	0.35343	0.11:0.0:0.89:0.0	.	.	.	.	X	872	.	ENSP00000354991:S872X	S	-	2	0	ALPK2	54355784	0.045000	0.20229	0.005000	0.12908	0.003000	0.03518	2.570000	0.45981	1.230000	0.43646	0.591000	0.81541	TCA	.	.		0.423	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		T	56204804	G	T	56204804	4	4	179	1	0	0	0	0	0	1	0	0	545	1294	45	3	3933	3	ALPK2	18	56204804	Nonsense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10		56204804	21872444	69	26897										
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1432588	1432588	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	tcctcctccaccagccactcCcggggcagcacctctggctt	8	20	1	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr19:1432588C>T	ENST00000233078.4	+	11	1108	c.947C>T	c.(946-948)cCc>cTc	p.P316L	DAZAP1_ENST00000336761.6_Missense_Mutation_p.P316L	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	316	Pro-rich.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGCCACTCCCGGGGCAGCA	0.647																																					p.P316L		Atlas-SNP	.											.	DAZAP1	52	.	0			c.C947T						.						64	73	70					19																	1432588		2203	4300	6503	SO:0001583	missense	26528	exon11			CCACTCCCGGGGC		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"RNA binding motif (RRM) containing"	2683	protein-coding gene	gene with protein product	"deleted in azoospermia associated protein 1"	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.947C>T	chr19.hg19:g.1432588C>T	ENSP00000233078:p.Pro316Leu	178.0	0.0		164.0	31.0	NM_018959	Q96MJ3|Q9NRR9	Missense_Mutation	SNP	ENST00000233078.4	hg19	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.611931	0.46631	.	.	ENSG00000071626	ENST00000233078;ENST00000336761	T;T	0.34859	1.34;1.38	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.44435	0.1293	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.994;0.994;0.998;0.998	T	0.17745	-1.0359	10	0.10111	T	0.7	.	16.8248	0.85928	0.0:1.0:0.0:0.0	.	383;316;316;82	Q5IRN4;Q96EP5;Q96EP5-2;B3KS63	.;DAZP1_HUMAN;.;.	L	316	ENSP00000233078:P316L;ENSP00000337132:P316L	ENSP00000233078:P316L	P	+	2	0	DAZAP1	1383588	1.000000	0.71417	0.219000	0.23793	0.223000	0.24884	7.773000	0.85462	2.215000	0.71742	0.561000	0.74099	CCC	.	.		0.647	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		T	1432588	C	T	1432588	3	4	179	1	0	0	0	0	1	0	0	0	4246	623	22	3	989	3	DAZAP1	19	1432588	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10		1432588	57696395	70	26898										
KANK3	256949	hgsc.bcm.edu	37	chr19	8400165	8400165	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	tgctcgcgcaccagctgcagTtgggcagggccgggcgaagc	17	13	0	0	rs201041593	byFrequency	TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr19:8400165T>C	ENST00000593649.1	-	3	611	c.546A>G	c.(544-546)caA>caG	p.Q182Q	KANK3_ENST00000330915.3_Silent_p.Q182Q			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	182										breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						CCAGCTGCAGTTGGGCAGGGC	0.791													T|||	11	0.00219649	0	0	5008	,	,		5754	0.0089		0.001	False		,,,				2504	0.001				p.Q182Q		Atlas-SNP	.											.	KANK3	35	.	0			c.A546G						.						1	1	1					19																	8400165		656	1410	2066	SO:0001819	synonymous_variant	256949	exon3			CTGCAGTTGGGCA	AK128815	CCDS12199.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000186994		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	24796	protein-coding gene	gene with protein product		614611	"ankyrin repeat domain 47"	ANKRD47		17996375, 19554261	Standard	NM_198471		Approved	FLJ46061	uc010dwa.3	Q6NY19		ENST00000593649.1:c.546A>G	chr19.hg19:g.8400165T>C		1.0	0.0		7.0	7.0	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	Silent	SNP	ENST00000593649.1	hg19																																																																																				.	.		0.791	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471		C	8400165	T	C	8400165	2	2	179	1	0	0	0	0	0	0	0	1	7987	1722	60	2		2	KANK3	19	8400165	Silent	SNP	T	TCGA-DD-AAD2-01A-11D-A40R-10	6967577	8400165	50728818	71	26899										
ZNF560	147741	hgsc.bcm.edu	37	chr19	9578805	9578805	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	catttaaaatcaggcggaaaGattttccatgcttactgaac	7	8	1	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr19:9578805G>C	ENST00000301480.4	-	10	1031	c.818C>G	c.(817-819)tCt>tGt	p.S273C		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	273					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						CAGGCGGAAAGATTTTCCATG	0.373																																					p.S273C		Atlas-SNP	.											.	ZNF560	162	.	0			c.C818G						.						103	98	100					19																	9578805		2203	4300	6503	SO:0001583	missense	147741	exon10			CGGAAAGATTTTC	AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"Zinc fingers, C2H2-type", "-"	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.818C>G	chr19.hg19:g.9578805G>C	ENSP00000301480:p.Ser273Cys	161.0	0.0		159.0	14.0	NM_152476	Q495S9|Q495T1	Missense_Mutation	SNP	ENST00000301480.4	hg19	CCDS12214.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.269902	0.40095	.	.	ENSG00000198028	ENST00000301480	T	0.05855	3.38	1.68	-2.14	0.07123	.	.	.	.	.	T	0.07369	0.0186	L	0.33668	1.02	0.09310	N	1	D	0.61697	0.99	P	0.53593	0.73	T	0.22347	-1.0219	9	0.62326	D	0.03	.	2.0663	0.03603	0.2802:0.0:0.4502:0.2696	.	273	Q96MR9	ZN560_HUMAN	C	273	ENSP00000301480:S273C	ENSP00000301480:S273C	S	-	2	0	ZNF560	9439805	0.000000	0.05858	0.000000	0.03702	0.289000	0.27227	-0.373000	0.07494	-0.441000	0.07201	0.491000	0.48974	TCT	.	.		0.373	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476		C	9578805	G	C	9578805	3	2	179	1	0	0	0	0	1	0	0	0	18006	942	33	4	1558	4	ZNF560	19	9578805	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	1178640	9578805	49550178	72	26900										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14020667	14020667	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	ggttgacctctccccagatgGcctgatgatccctgaggacg	12	13	1	5			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr19:14020667G>C	ENST00000318003.7	+	2	333	c.92G>C	c.(91-93)gGc>gCc	p.G31A	CC2D1A_ENST00000589606.1_Missense_Mutation_p.G31A	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	31					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			TCCCCAGATGGCCTGATGATC	0.597																																					p.G31A		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G92C						.						112	113	113					19																	14020667		1973	4178	6151	SO:0001583	missense	54862	exon2			CAGATGGCCTGAT	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.92G>C	chr19.hg19:g.14020667G>C	ENSP00000313601:p.Gly31Ala	98.0	0.0		99.0	14.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	hg19	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411683	0.83340	.	.	ENSG00000132024	ENST00000318003;ENST00000389233	T	0.21543	2.0	5.43	5.43	0.79202	.	0.000000	0.64402	D	0.000008	T	0.38746	0.1052	M	0.61703	1.905	0.40896	D	0.984114	D;D	0.67145	0.978;0.996	P;P	0.58266	0.679;0.836	T	0.06356	-1.0831	10	0.33141	T	0.24	-21.8567	16.153	0.81636	0.0:0.0:1.0:0.0	.	31;31	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	A	31;6	ENSP00000313601:G31A	ENSP00000313601:G31A	G	+	2	0	CC2D1A	13881667	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	5.771000	0.68881	2.547000	0.85894	0.655000	0.94253	GGC	.	.		0.597	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		C	14020667	G	C	14020667	3	2	179	1	0	0	0	0	1	0	0	0	2728	1203	42	4	98	4	CC2D1A	19	14020667	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	4441862	14020667	45108316	73	26901										
SNRPA	6626	hgsc.bcm.edu	37	chr19	41263356	41263356	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	tcttcaaggaggtcagcagcGccaccaacgccctgcgctcc	10	17	3	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr19:41263356G>T	ENST00000243563.3	+	2	743	c.193G>T	c.(193-195)Gcc>Tcc	p.A65S	SNRPA_ENST00000599570.1_3'UTR	NM_004596.4	NP_004587.1	P09012	SNRPA_HUMAN	small nuclear ribonucleoprotein polypeptide A	65	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snRNA binding (GO:0017069)	p.A65T(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GGTCAGCAGCGCCACCAACGC	0.542																																					p.A65S		Atlas-SNP	.											SNRPA,rectum,carcinoma,0,1	SNRPA	20	.	1	Substitution - Missense(1)	large_intestine(1)	c.G193T						.						88	83	85					19																	41263356		2203	4300	6503	SO:0001583	missense	6626	exon2			AGCAGCGCCACCA	X06347	CCDS12565.1	19q13.1	2013-02-12				ENSG00000077312		"RNA binding motif (RRM) containing"	11151	protein-coding gene	gene with protein product		182285				1701111	Standard	NM_004596		Approved	U1A, U1-A, Mud1	uc002ooz.3	P09012		ENST00000243563.3:c.193G>T	chr19.hg19:g.41263356G>T	ENSP00000243563:p.Ala65Ser	90.0	0.0		68.0	3.0	NM_004596		Missense_Mutation	SNP	ENST00000243563.3	hg19	CCDS12565.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.788663	0.49997	.	.	ENSG00000077312	ENST00000243563	T	0.30714	1.52	5.97	4.94	0.65067	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.103999	0.64402	D	0.000003	T	0.42245	0.1194	M	0.83852	2.665	0.58432	D	0.999997	B	0.11235	0.004	B	0.36289	0.221	T	0.33828	-0.9853	10	0.30078	T	0.28	-35.8883	9.6557	0.39925	0.0739:0.0:0.7848:0.1412	.	65	P09012	SNRPA_HUMAN	S	65	ENSP00000243563:A65S	ENSP00000243563:A65S	A	+	1	0	SNRPA	45955196	1.000000	0.71417	0.973000	0.42090	0.714000	0.41099	6.474000	0.73578	1.546000	0.49388	-0.136000	0.14681	GCC	.	.		0.542	SNRPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463118.2	NM_004596		T	41263356	G	T	41263356	3	4	179	1	0	0	0	0	1	0	0	0	14874	1087	38	1	199	1	SNRPA	19	41263356	Missense_Mutation	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	27242689	41263356	17865627	74	26902										
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48918223	48918223	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	atcggcttcagctacgacctCtacctggtcaccaatggcaa	8	14	3	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr19:48918223C>G	ENST00000263269.3	+	6	1603	c.1515C>G	c.(1513-1515)ctC>ctG	p.L505L		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	505					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTACGACCTCTACCTGGTCA	0.622																																					p.L505L		Atlas-SNP	.											.	GRIN2D	76	.	0			c.C1515G						.						49	47	48					19																	48918223		2203	4300	6503	SO:0001819	synonymous_variant	2906	exon6			CGACCTCTACCTG	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.1515C>G	chr19.hg19:g.48918223C>G		127.0	0.0		123.0	28.0	NM_000836		Silent	SNP	ENST00000263269.3	hg19	CCDS12719.1																																																																																			.	.		0.622	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			G	48918223	C	G	48918223	2	3	179	1	0	0	0	0	0	0	0	1	6791	900	32	4		4	GRIN2D	19	48918223	Silent	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10	7654867	48918223	10210760	75	26903										
LILRA6	79168	hgsc.bcm.edu	37	chr19	54746592	54746592	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cagagcagggctgtgagggcGggcgtcatggcgtctccttc	17	11	2	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr19:54746592G>A	ENST00000396365.2	-	1	48	c.9C>T	c.(7-9)ccC>ccT	p.P3P	LILRA6_ENST00000419410.2_Silent_p.P3P|LILRB3_ENST00000407860.2_Silent_p.P3P|LILRA6_ENST00000391735.3_Silent_p.P3P|LILRA6_ENST00000245621.5_Silent_p.P3P|LILRA6_ENST00000440558.2_Silent_p.P3P|LILRA6_ENST00000270464.5_Silent_p.P3P	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	3					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CTGTGAGGGCGGGCGTCATGG	0.642																																					p.P3P		Atlas-SNP	.											.	LILRA6	75	.	0			c.C9T						.						69	62	64					19																	54746592		2141	4264	6405	SO:0001819	synonymous_variant	79168	exon1			GAGGGCGGGCGTC	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15495	protein-coding gene	gene with protein product			"leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.9C>T	chr19.hg19:g.54746592G>A		238.0	0.0		270.0	62.0	NM_024318		Silent	SNP	ENST00000396365.2	hg19	CCDS42610.1																																																																																			.	.		0.642	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		A	54746592	G	A	54746592	2	1	179	1	0	0	0	0	0	0	0	1	8798	1103	39	1		1	LILRA6	19	54746592	Silent	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	5828369	54746592	4382391	76	26904										
PEG3	5178	hgsc.bcm.edu	37	chr19	57325481	57325481	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	gcatccccatttggctgctcGgcctctccatttggctgtcc	9	16	1	0			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr19:57325481G>C	ENST00000326441.9	-	10	4692	c.4329C>G	c.(4327-4329)gcC>gcG	p.A1443A	ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Silent_p.A1443A|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000601070.1_Intron|PEG3_ENST00000593695.1_Silent_p.A1317A|PEG3_ENST00000598410.1_Silent_p.A1319A|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1443	4 X 5 AA repeat of P-X-G-E-A.|Glu-rich.				apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.A1443A(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TTGGCTGCTCGGCCTCTCCAT	0.572																																					p.A1443A		Atlas-SNP	.											ZIM2_ENST00000326441,NS,carcinoma,0,4	PEG3	414	.	2	Substitution - coding silent(2)	lung(2)	c.C4329G						.						65	61	62					19																	57325481		2203	4300	6503	SO:0001819	synonymous_variant	5178	exon9			CTGCTCGGCCTCT	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.4329C>G	chr19.hg19:g.57325481G>C		94.0	1.0		83.0	12.0	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	ENST00000326441.9	hg19	CCDS12948.1																																																																																			.	.		0.572	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			C	57325481	G	C	57325481	2	2	179	1	0	0	0	0	0	0	0	1	11729	1103	39	4		4	PEG3	19	57325481	Silent	SNP	G	TCGA-DD-AAD2-01A-11D-A40R-10	2578889	57325481	1803502	77	26905										
TNRC6B	23112	hgsc.bcm.edu	37	chr22	40661255	40661255	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cacaggttagcacagtaggtCagacatccagggaacagcag	12	10	1	1			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chr22:40661255C>G	ENST00000454349.2	+	5	1232	c.1021C>G	c.(1021-1023)Cag>Gag	p.Q341E	TNRC6B_ENST00000402203.1_Intron|TNRC6B_ENST00000335727.9_Missense_Mutation_p.Q341E|TNRC6B_ENST00000301923.9_Intron	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	341	Interaction with argonaute proteins.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						CACAGTAGGTCAGACATCCAG	0.463																																					p.Q341E		Atlas-SNP	.											.	TNRC6B	195	.	0			c.C1021G						.						58	56	57					22																	40661255		1910	4128	6038	SO:0001583	missense	23112	exon5			GTAGGTCAGACAT	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.1021C>G	chr22.hg19:g.40661255C>G	ENSP00000401946:p.Gln341Glu	180.0	0.0		140.0	19.0	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Missense_Mutation	SNP	ENST00000454349.2	hg19	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	C	8.890	0.953868	0.18431	.	.	ENSG00000100354	ENST00000454349;ENST00000400140;ENST00000335727	T;T	0.52754	0.65;0.65	5.07	5.07	0.68467	.	0.374289	0.27749	N	0.018007	T	0.37237	0.0996	L	0.52011	1.625	0.29708	N	0.839624	B;P;P	0.40083	0.252;0.702;0.587	B;B;B	0.32022	0.049;0.066;0.139	T	0.46470	-0.9189	10	0.39692	T	0.17	-2.8204	11.0146	0.47681	0.0:0.915:0.0:0.085	.	341;341;341	Q9UPQ9;A8MYY3;Q9UPQ9-1	TNR6B_HUMAN;.;.	E	341	ENSP00000401946:Q341E;ENSP00000338371:Q341E	ENSP00000338371:Q341E	Q	+	1	0	TNRC6B	38991201	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.805000	0.38883	2.369000	0.80426	0.650000	0.86243	CAG	.	.		0.463	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				G	40661255	C	G	40661255	3	3	179	1	0	0	0	0	1	0	0	0	16356	827	29	4	1160	4	TNRC6B	22	40661255	Missense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10		40661255	10643311	78	26906										
DMD	1756	hgsc.bcm.edu	37	chrX	32536160	32536160	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	taagtctgagaagttgccttCcttccgaaagattgcaaatt	8	8	1	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chrX:32536160C>A	ENST00000357033.4	-	18	2463	c.2257G>T	c.(2257-2259)Gaa>Taa	p.E753*	DMD_ENST00000288447.4_Nonsense_Mutation_p.E745*|DMD_ENST00000378677.2_Nonsense_Mutation_p.E749*	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	753					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.E749K(2)|p.E748K(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AAGTTGCCTTCCTTCCGAAAG	0.383																																					p.E753X		Atlas-SNP	.											.	DMD	2127	.	3	Substitution - Missense(3)	prostate(3)	c.G2257T						.						73	65	67					X																	32536160		2202	4300	6502	SO:0001587	stop_gained	1756	exon18			TGCCTTCCTTCCG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.2257G>T	chrX.hg19:g.32536160C>A	ENSP00000354923:p.Glu753*	268.0	0.0		317.0	123.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Nonsense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	40	8.214672	0.98709	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	.	.	.	5.07	4.21	0.49690	.	0.251712	0.19274	U	0.118325	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	12.4582	0.55716	0.0:0.9151:0.0:0.0849	.	.	.	.	X	745;749;753;753;630;745	.	ENSP00000288447:E745X	E	-	1	0	DMD	32446081	1.000000	0.71417	0.994000	0.49952	0.975000	0.68041	5.505000	0.66981	0.913000	0.36797	0.583000	0.79449	GAA	.	.		0.383	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32536160	C	A	32536160	4	1	179	1	0	0	0	0	0	1	0	0	4582	864	30	3	9291	3	DMD	23	32536160	Nonsense_Mutation	SNP	C	TCGA-DD-AAD2-01A-11D-A40R-10		32536160	122734400	79	26907										
PABPC5	140886	hgsc.bcm.edu	37	chrX	90690668	90690668	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.14355400696864	4.44715447154472	0	0.0325077399380805	0.322451055174167	0	cttggacccagatgtcaccgAggacatgctctataagaagt	10	10	2	2			TCGA-DD-AAD2-01A-11D-A40R-10	TCGA-DD-AAD2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8f5469f1-7000-4a1b-834a-30e00f219671	ea06211a-5794-45d9-88ea-02b46933a273	g.chrX:90690668A>G	ENST00000312600.3	+	2	306	c.92A>G	c.(91-93)gAg>gGg	p.E31G	PABPC5_ENST00000373105.1_Intron|PABPC5-AS1_ENST00000456187.1_RNA	NM_080832.2	NP_543022.1	Q96DU9	PABP5_HUMAN	poly(A) binding protein, cytoplasmic 5	31	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.					mitochondrion (GO:0005739)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(1)|pancreas(1)	42						GATGTCACCGAGGACATGCTC	0.572																																					p.E31G		Atlas-SNP	.											.	PABPC5	92	.	0			c.A92G						.						65	50	55					X																	90690668		2203	4300	6503	SO:0001583	missense	140886	exon2			TCACCGAGGACAT	AJ278963	CCDS14460.1	Xq21.3	2013-02-12	2001-11-28		ENSG00000174740	ENSG00000174740		"RNA binding motif (RRM) containing"	13629	protein-coding gene	gene with protein product		300407	"poly(A)-binding protein, cytoplasmic 5"			11374897	Standard	NM_080832		Approved	PABP5	uc004efg.3	Q96DU9	OTTHUMG00000021959	ENST00000312600.3:c.92A>G	chrX.hg19:g.90690668A>G	ENSP00000308012:p.Glu31Gly	76.0	0.0		66.0	7.0	NM_080832	A8K240|Q5JQF4|Q6P529|Q9UFE5	Missense_Mutation	SNP	ENST00000312600.3	hg19	CCDS14460.1	.	.	.	.	.	.	.	.	.	.	A	19.14	3.769271	0.69992	.	.	ENSG00000174740	ENST00000312600	T	0.23348	1.91	4.43	4.43	0.53597	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.57755	0.2075	M	0.92784	3.345	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.67321	-0.5700	10	0.87932	D	0	.	10.9829	0.47506	1.0:0.0:0.0:0.0	.	31	Q96DU9	PABP5_HUMAN	G	31	ENSP00000308012:E31G	ENSP00000308012:E31G	E	+	2	0	PABPC5	90577324	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	8.747000	0.91610	1.957000	0.56846	0.486000	0.48141	GAG	.	.		0.572	PABPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057429.1	NM_080832		G	90690668	A	G	90690668	3	3	179	1	0	0	0	0	1	0	0	0	11376	304	11	2	94	2	PABPC5	23	90690668	Missense_Mutation	SNP	A	TCGA-DD-AAD2-01A-11D-A40R-10	58154508	90690668	64579892	80	26908										
CASP9	842	hgsc.bcm.edu	37	chr1	15821795	15821795	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	agtagagtaggacacaaagaTgtcactgggtgtgggcaaac	14	6	1	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:15821795T>C	ENST00000333868.5	-	7	1115	c.1021A>G	c.(1021-1023)Atc>Gtc	p.I341V	CASP9_ENST00000348549.5_Missense_Mutation_p.I191V|CASP9_ENST00000546424.1_Missense_Mutation_p.I341V|CASP9_ENST00000375890.4_Missense_Mutation_p.I258V	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	341					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		GACACAAAGATGTCACTGGGT	0.587																																					p.I341V		Atlas-SNP	.											.	CASP9	40	.	0			c.A1021G						.						102	73	83					1																	15821795		2203	4300	6503	SO:0001583	missense	842	exon7			CAAAGATGTCACT	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"Caspases", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1511	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 56"	602234	"caspase 9, apoptosis-related cysteine protease"			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.1021A>G	chr1.hg19:g.15821795T>C	ENSP00000330237:p.Ile341Val	217.0	0.0		148.0	6.0	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Missense_Mutation	SNP	ENST00000333868.5	hg19	CCDS158.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.692149	0.88735	.	.	ENSG00000132906	ENST00000546424;ENST00000333868;ENST00000348549;ENST00000375890;ENST00000447522	T;T;T;T;T	0.03065	4.06;4.06;4.06;4.06;4.06	5.36	5.36	0.76844	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.000000	0.85682	D	0.000000	T	0.15652	0.0377	M	0.69358	2.11	0.54753	D	0.999985	P;D;D	0.71674	0.93;0.998;0.981	D;D;D	0.76575	0.915;0.988;0.953	T	0.00149	-1.1987	10	0.62326	D	0.03	.	13.3131	0.60390	0.0:0.0:0.0:1.0	.	191;341;341	P55211-2;P55211;F8VVS7	.;CASP9_HUMAN;.	V	341;341;191;258;258	ENSP00000449584:I341V;ENSP00000330237:I341V;ENSP00000255256:I191V;ENSP00000365051:I258V;ENSP00000396540:I258V	ENSP00000330237:I341V	I	-	1	0	CASP9	15694382	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.976000	0.76135	2.037000	0.60232	0.459000	0.35465	ATC	.	.		0.587	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996		C	15821795	T	C	15821795	3	2	180	1	0	0	0	0	1	0	0	0	2681	1464	51	2	241	2	CASP9	1	15821795	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10		15821795	233428826	1	26909										
TMEM54	113452	hgsc.bcm.edu	37	chr1	33361532	33361532	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	aggggggtgctagggaggtaGcgtgacaacacgatggctgc	19	7	0	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:33361532G>T	ENST00000373463.3	-	3	368	c.249C>A	c.(247-249)cgC>cgA	p.R83R	TMEM54_ENST00000475208.1_Intron|TMEM54_ENST00000329151.5_Intron	NM_033504.2	NP_277039.1	Q969K7	TMM54_HUMAN	transmembrane protein 54	83						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				TAGGGAGGTAGCGTGACAACA	0.642																																					p.R83R		Atlas-SNP	.											.	TMEM54	12	.	0			c.C249A						.						68	58	61					1																	33361532		2203	4300	6503	SO:0001819	synonymous_variant	113452	exon3			GAGGTAGCGTGAC		CCDS371.1	1p35-p34	2008-02-05			ENSG00000121900	ENSG00000121900			24143	protein-coding gene	gene with protein product						9500206	Standard	NM_033504		Approved	CAC-1	uc001bwi.1	Q969K7	OTTHUMG00000004016	ENST00000373463.3:c.249C>A	chr1.hg19:g.33361532G>T		86.0	0.0		85.0	6.0	NM_033504	Q6UV18|Q8IVD0|Q9UM12	Silent	SNP	ENST00000373463.3	hg19	CCDS371.1																																																																																			.	.		0.642	TMEM54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011474.1	NM_033504		T	33361532	G	T	33361532	2	4	180	1	0	0	0	0	0	0	0	1	16195	958	34	3		3	TMEM54	1	33361532	Silent	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	17539737	33361532	215889089	2	26910										
MAP7D1	55700	hgsc.bcm.edu	37	chr1	36643703	36643703	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	agcgcagggccagtaacgagAaggagtcagcagccccagcc	14	13	1	1	rs3045695|rs141305015|rs200892098	byFrequency	TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:36643703A>G	ENST00000373151.2	+	9	1825	c.1609A>G	c.(1609-1611)Aag>Gag	p.K537E	MAP7D1_ENST00000373150.4_Missense_Mutation_p.K505E|MAP7D1_ENST00000373148.4_Missense_Mutation_p.K83E|MAP7D1_ENST00000316156.4_Missense_Mutation_p.K500E	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	537	Pro-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CAGTAACGAGAAGGAGTCAGC	0.721																																					p.K537E		Atlas-SNP	.											.,2	MAP7D1	62	.	0			c.A1609G						.						29	29	29					1																	36643703		2192	4270	6462	SO:0001583	missense	55700	exon9			AACGAGAAGGAGT	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"proline arginine rich coiled coil 1", "arginine/proline rich coiled-coil 1"	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.1609A>G	chr1.hg19:g.36643703A>G	ENSP00000362244:p.Lys537Glu	2.0	0.0		26.0	25.0	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Missense_Mutation	SNP	ENST00000373151.2	hg19	CCDS30673.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.555|6.555	0.470598|0.470598	0.12461|0.12461	.|.	.|.	ENSG00000116871|ENSG00000116871	ENST00000530975|ENST00000316156;ENST00000373150;ENST00000373151;ENST00000373148	T|T;T;T;T	0.57752|0.49720	0.38|0.77;0.77;0.77;0.77	5.03|5.03	2.66|2.66	0.31614|0.31614	.|.	.|0.493263	.|0.17209	.|N	.|0.182837	T|T	0.36358|0.36358	0.0964|0.0964	L|L	0.50333|0.50333	1.59|1.59	0.31867|0.31867	N|N	0.620209|0.620209	.|B;B;B;B;B	.|0.12013	.|0.001;0.001;0.005;0.002;0.001	.|B;B;B;B;B	.|0.08055	.|0.003;0.001;0.003;0.003;0.001	T|T	0.34875|0.34875	-0.9811|-0.9811	7|10	0.62326|0.19147	D|T	0.03|0.46	-11.1212|-11.1212	7.538|7.538	0.27721|0.27721	0.8218:0.0:0.1782:0.0|0.8218:0.0:0.1782:0.0	.|.	.|83;537;500;505;537	.|Q3KQU3-3;D3DPS3;Q3KQU3-2;Q3KQU3-4;Q3KQU3	.|.;.;.;.;MA7D1_HUMAN	G|E	119|500;505;537;83	ENSP00000437046:E119G|ENSP00000320228:K500E;ENSP00000362243:K505E;ENSP00000362244:K537E;ENSP00000362241:K83E	ENSP00000437046:E119G|ENSP00000320228:K500E	E|K	+|+	2|1	0|0	MAP7D1|MAP7D1	36416290|36416290	0.997000|0.997000	0.39634|0.39634	0.990000|0.990000	0.47175|0.47175	0.119000|0.119000	0.20118|0.20118	1.102000|1.102000	0.31050|0.31050	0.951000|0.951000	0.37770|0.37770	0.528000|0.528000	0.53228|0.53228	GAA|AAG	.	.		0.721	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067		G	36643703	A	G	36643703	3	3	180	1	0	0	0	0	1	0	0	0	9276	247	9	2	1643	2	MAP7D1	1	36643703	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	3282171	36643703	212606918	3	26911										
B4GALT2	8704	hgsc.bcm.edu	37	chr1	44456052	44456052	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	accaggtcttggaggtgtctCggcaaccactcttcaccaat	9	13	4	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:44456052C>T	ENST00000356836.6	+	7	1841	c.1051C>T	c.(1051-1053)Cgg>Tgg	p.R351W	B4GALT2_ENST00000372324.1_Missense_Mutation_p.R351W|B4GALT2_ENST00000309519.7_Missense_Mutation_p.R380W|CCDC24_ENST00000372318.3_5'Flank|B4GALT2_ENST00000434555.2_Missense_Mutation_p.R285W	NM_001005417.2|NM_030587.2	NP_001005417.1|NP_085076.2	O60909	B4GT2_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2	351					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			N-Acetyl-D-glucosamine(DB00141)	GGAGGTGTCTCGGCAACCACT	0.557																																					p.R380W		Atlas-SNP	.											.	B4GALT2	35	.	0			c.C1138T						.						177	179	178					1																	44456052		2203	4300	6503	SO:0001583	missense	8704	exon7			GTGTCTCGGCAAC	AF038660	CCDS506.1, CCDS55596.1	1p34-p33	2013-02-19			ENSG00000117411	ENSG00000117411		"Beta 4-glycosyltransferases"	925	protein-coding gene	gene with protein product		604013				9405390, 9597550	Standard	NM_003780		Approved	beta4Gal-T2	uc010okl.2	O60909	OTTHUMG00000008296	ENST00000356836.6:c.1051C>T	chr1.hg19:g.44456052C>T	ENSP00000349293:p.Arg351Trp	150.0	0.0		133.0	20.0	NM_030587	B3KTP0|B4DE14|D3DPY6|D3DPY7|O60511|Q4V9L9|Q5T4X5|Q5T4Y5|Q9BUP6|Q9NSY7	Missense_Mutation	SNP	ENST00000356836.6	hg19	CCDS506.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.879174	0.72294	.	.	ENSG00000117411	ENST00000372324;ENST00000434555;ENST00000356836;ENST00000309519	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	5.3	2.21	0.28008	.	0.130705	0.48767	D	0.000176	T	0.49167	0.1541	L	0.58101	1.795	0.42593	D	0.993258	B;D;D	0.89917	0.042;1.0;0.999	B;D;P	0.71184	0.003;0.972;0.878	T	0.41305	-0.9516	10	0.40728	T	0.16	-7.7526	8.6777	0.34189	0.3718:0.5587:0.0:0.0695	.	380;285;351	B4DE14;O60909-2;O60909	.;.;B4GT2_HUMAN	W	351;285;351;380	ENSP00000361399:R351W;ENSP00000407468:R285W;ENSP00000349293:R351W;ENSP00000310696:R380W	ENSP00000310696:R380W	R	+	1	2	B4GALT2	44228639	0.984000	0.35163	1.000000	0.80357	0.960000	0.62799	1.569000	0.36428	0.720000	0.32209	0.543000	0.68304	CGG	.	.		0.557	B4GALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022840.1	NM_003780		T	44456052	C	T	44456052	3	4	180	1	0	0	0	0	1	0	0	0	1271	875	31	1	1073	1	B4GALT2	1	44456052	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	7812349	44456052	204794569	4	26912										
CYP4A22	284541	hgsc.bcm.edu	37	chr1	47611805	47611805	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	caacacagccacgctttcctGcccttctcaggaggatcaag	8	15	2	0	rs140647389		TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:47611805G>T	ENST00000371891.3	+	11	1375	c.1344G>T	c.(1342-1344)ctG>ctT	p.L448L	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000371890.3_Silent_p.L350L|CYP4A22_ENST00000294337.3_Silent_p.L448L|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	448						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACGCTTTCCTGCCCTTCTCAG	0.527																																					p.L448L	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.G1344T						.						270	262	265					1																	47611805		2203	4298	6501	SO:0001819	synonymous_variant	284541	exon11			TTTCCTGCCCTTC		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"Cytochrome P450s"	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.1344G>T	chr1.hg19:g.47611805G>T		292.0	0.0		198.0	53.0	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Silent	SNP	ENST00000371891.3	hg19	CCDS30707.1																																																																																			.	G|1.000;A|0.000		0.527	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213		T	47611805	G	T	47611805	2	4	180	1	0	0	0	0	0	0	0	1	4186	1306	46	3		3	CYP4A22	1	47611805	Silent	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	3155753	47611805	201638816	5	26913										
BARHL2	343472	hgsc.bcm.edu	37	chr1	91180225	91180225	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ttgagctggtggtcggaaaaAgctgtccttgcttttcgagg	14	7	0	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:91180225A>T	ENST00000370445.4	-	2	755	c.714T>A	c.(712-714)gcT>gcA	p.A238A		NM_020063.1	NP_064447.1	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2	238					cell fate determination (GO:0001709)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|positive regulation of translation (GO:0045727)|regulation of axon extension (GO:0030516)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			cervix(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)		GGTCGGAAAAAGCTGTCCTTG	0.552																																					p.A238A	GBM(199;3561 4100 22440)	Atlas-SNP	.											.	BARHL2	62	.	0			c.T714A						.						190	180	183					1																	91180225		2203	4300	6503	SO:0001819	synonymous_variant	343472	exon2			GGAAAAAGCTGTC	AJ251753	CCDS730.1	1p22.2	2011-07-08	2007-07-09		ENSG00000143032	ENSG00000143032		"Homeoboxes / ANTP class : NKL subclass"	954	protein-coding gene	gene with protein product		605212	"BarH (Drosophila)-like 2"				Standard	NM_020063		Approved		uc001dns.3	Q9NY43	OTTHUMG00000010020	ENST00000370445.4:c.714T>A	chr1.hg19:g.91180225A>T		135.0	0.0		141.0	9.0	NM_020063	A0AVP2|Q7Z4N7	Silent	SNP	ENST00000370445.4	hg19	CCDS730.1																																																																																			.	.		0.552	BARHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027728.2			T	91180225	A	T	91180225	2	4	180	1	0	0	0	0	0	0	0	1	1314	59	3	4		4	BARHL2	1	91180225	Silent	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	43568420	91180225	158070396	6	26914										
LCE5A	254910	hgsc.bcm.edu	37	chr1	152484138	152484138	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ccctccccagtgttcagcccCatgcccacctccagtctctt	5	21	2	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:152484138C>T	ENST00000334269.2	+	2	304	c.128C>T	c.(127-129)cCa>cTa	p.P43L	CRCT1_ENST00000368790.3_5'Flank	NM_178438.4	NP_848525.1	Q5TCM9	LCE5A_HUMAN	late cornified envelope 5A	43	Cys-rich.				keratinization (GO:0031424)					lung(3)|ovary(1)|prostate(3)	7	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTTCAGCCCCATGCCCACCT	0.622																																					p.P43L		Atlas-SNP	.											.	LCE5A	15	.	0			c.C128T						.						90	85	87					1																	152484138		2203	4300	6503	SO:0001583	missense	254910	exon2			CAGCCCCATGCCC	BI670518	CCDS1011.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000186207	ENSG00000186207		"Late cornified envelopes"	16614	protein-coding gene	gene with protein product		612619	"small proline rich-like (epidermal differentiation complex) 5A"	SPRL5A		11698679	Standard	NM_178438		Approved	LEP18	uc001ezy.3	Q5TCM9	OTTHUMG00000014401	ENST00000334269.2:c.128C>T	chr1.hg19:g.152484138C>T	ENSP00000333952:p.Pro43Leu	194.0	0.0		220.0	9.0	NM_178438		Missense_Mutation	SNP	ENST00000334269.2	hg19	CCDS1011.1	.	.	.	.	.	.	.	.	.	.	C	6.492	0.459010	0.12342	.	.	ENSG00000186207	ENST00000334269	T	0.03607	3.87	4.08	1.54	0.23209	.	.	.	.	.	T	0.01061	0.0035	L	0.43152	1.355	0.09310	N	1	B	0.21225	0.053	B	0.17098	0.017	T	0.47497	-0.9113	9	0.38643	T	0.18	.	3.6105	0.08058	0.0:0.5651:0.2316:0.2033	.	43	Q5TCM9	LCE5A_HUMAN	L	43	ENSP00000333952:P43L	ENSP00000333952:P43L	P	+	2	0	LCE5A	150750762	0.011000	0.17503	0.001000	0.08648	0.805000	0.45488	0.815000	0.27253	0.087000	0.17167	0.505000	0.49811	CCA	.	.		0.622	LCE5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040059.1	NM_178438		T	152484138	C	T	152484138	3	4	180	1	0	0	0	0	1	0	0	0	8684	594	21	3	130	3	LCE5A	1	152484138	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	61303913	152484138	96766483	7	26915										
GON4L	54856	hgsc.bcm.edu	37	chr1	155823539	155823539	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ttatgctgtagggactctgtCactgtagttcttctcttctt	8	9	5	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:155823539C>A	ENST00000368331.1	-	2	81	c.33G>T	c.(31-33)gtG>gtT	p.V11V	GON4L_ENST00000271883.5_Silent_p.V11V|GON4L_ENST00000437809.1_Silent_p.V11V|GON4L_ENST00000361040.5_Silent_p.V11V|GON4L_ENST00000471341.1_5'UTR	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	11					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					GGGACTCTGTCACTGTAGTTC	0.383																																					p.V11V		Atlas-SNP	.											.	GON4L	392	.	0			c.G33T						.						97	89	92					1																	155823539		2203	4300	6503	SO:0001819	synonymous_variant	54856	exon2			CTCTGTCACTGTA	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.33G>T	chr1.hg19:g.155823539C>A		132.0	0.0		120.0	55.0	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Silent	SNP	ENST00000368331.1	hg19																																																																																				.	.		0.383	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		A	155823539	C	A	155823539	2	1	180	1	0	0	0	0	0	0	0	1	6580	813	29	3		3	GON4L	1	155823539	Silent	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	3339401	155823539	93427082	8	26916										
FAM163A	148753	hgsc.bcm.edu	37	chr1	179783118	179783118	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gccactgcactacctgctccCcatacagctcccccttttac	4	20	0	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:179783118C>A	ENST00000341785.4	+	5	694	c.298C>A	c.(298-300)Cca>Aca	p.P100T	RP11-12M5.3_ENST00000453051.1_RNA|RP11-12M5.3_ENST00000415218.1_RNA	NM_173509.2	NP_775780.1	Q96GL9	F163A_HUMAN	family with sequence similarity 163, member A	100						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)	15						TACCTGCTCCCCATACAGCTC	0.652																																					p.P100T		Atlas-SNP	.											.	FAM163A	24	.	0			c.C298A						.						51	47	48					1																	179783118		2203	4300	6503	SO:0001583	missense	148753	exon5			TGCTCCCCATACA	BC009382	CCDS1333.1	1q25.2	2008-06-05	2008-06-05	2008-06-05	ENSG00000143340	ENSG00000143340			28274	protein-coding gene	gene with protein product		611727	"chromosome 1 open reading frame 76"	C1orf76		12477932	Standard	NM_173509		Approved	MGC16664	uc001gnj.3	Q96GL9	OTTHUMG00000035262	ENST00000341785.4:c.298C>A	chr1.hg19:g.179783118C>A	ENSP00000354891:p.Pro100Thr	249.0	0.0		245.0	55.0	NM_173509	A8K8R7	Missense_Mutation	SNP	ENST00000341785.4	hg19	CCDS1333.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.592372	0.66219	.	.	ENSG00000143340	ENST00000341785	.	.	.	4.44	3.44	0.39384	.	0.069861	0.64402	D	0.000018	T	0.55257	0.1909	L	0.50333	1.59	0.48762	D	0.9997	B	0.20550	0.046	B	0.23419	0.046	T	0.55761	-0.8090	9	0.35671	T	0.21	-0.1809	13.0098	0.58725	0.1621:0.8378:0.0:0.0	.	100	Q96GL9	F163A_HUMAN	T	100	.	ENSP00000354891:P100T	P	+	1	0	FAM163A	178049741	1.000000	0.71417	0.937000	0.37676	0.849000	0.48306	5.283000	0.65621	2.187000	0.69744	0.462000	0.41574	CCA	.	.		0.652	FAM163A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085300.1	NM_173509		A	179783118	C	A	179783118	3	1	180	1	0	0	0	0	1	0	0	0	5481	623	22	3	304	3	FAM163A	1	179783118	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	23959579	179783118	69467503	9	26917										
C1orf131	8443	hgsc.bcm.edu	37	chr1	231376848	231376848	+	5'Flank	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ggaggaccccggcccttgctCctgcgacattgtggggtcag	15	13	1	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:231376848C>A	ENST00000366647.4	+	0	0				C1orf131_ENST00000366649.2_Nonsense_Mutation_p.E14*|C1orf131_ENST00000471936.1_5'UTR|GNPAT_ENST00000366646.3_5'Flank|C1orf131_ENST00000366651.3_Nonsense_Mutation_p.E14*|C1orf131_ENST00000318906.2_Nonsense_Mutation_p.E14*	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase						cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				GGCCCTTGCTCCTGCGACATT	0.652																																					p.E14X		Atlas-SNP	.											.	C1orf131	30	.	0			c.G40T						.						96	99	98					1																	231376848		2203	4300	6503	SO:0001631	upstream_gene_variant	128061	exon1			CTTGCTCCTGCGA	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024		chr1.hg19:g.231376848C>A	Exception_encountered	235.0	0.0		261.0	16.0	NM_152379	B4DNM9|Q5TBH7|Q9BWC2	Nonsense_Mutation	SNP	ENST00000366647.4	hg19	CCDS1592.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.350688	0.82132	.	.	ENSG00000143633	ENST00000366649;ENST00000318906;ENST00000366651;ENST00000366648	.	.	.	5.06	2.14	0.27477	.	0.743246	0.12591	N	0.455591	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-23.9359	6.0374	0.19716	0.0:0.6723:0.1562:0.1714	.	.	.	.	X	14;14;14;4	.	ENSP00000321341:E14X	E	-	1	0	C1orf131	229443471	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.713000	0.25794	0.301000	0.22738	-0.142000	0.14014	GAG	.	.		0.652	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1			A	231376848	C	A	231376848	1	1	180	0	1	0	0	0	0	0	0	0	2000	864	30	3		3	C1orf131	1	231376848	5'Flank	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	51593730	231376848	17873773	10	26918										
RGS7	6000	hgsc.bcm.edu	37	chr1	240969620	240969620	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ttcaggtcctccactgccagCcagaatctatgcagaatgtg	9	12	2	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr1:240969620C>G	ENST00000407727.1	-	14	1088	c.1089G>C	c.(1087-1089)tgG>tgC	p.W363C	RGS7_ENST00000366565.1_Missense_Mutation_p.W363C|RGS7_ENST00000401882.1_Missense_Mutation_p.W310C|RGS7_ENST00000366564.1_Missense_Mutation_p.W363C|RGS7_ENST00000366562.4_Missense_Mutation_p.W363C|RGS7_ENST00000331110.7_Missense_Mutation_p.W337C|RGS7_ENST00000446183.2_Missense_Mutation_p.W279C|RGS7_ENST00000348120.2_Missense_Mutation_p.W310C|RGS7_ENST00000366563.1_Missense_Mutation_p.W363C			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	363	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			CCACTGCCAGCCAGAATCTAT	0.468																																					p.W363C		Atlas-SNP	.											.	RGS7	308	.	0			c.G1089C						.						91	88	89					1																	240969620		2203	4300	6503	SO:0001583	missense	6000	exon15			TGCCAGCCAGAAT	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"Regulators of G-protein signaling"	10003	protein-coding gene	gene with protein product		602517	"regulator of G-protein signalling 7"			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.1089G>C	chr1.hg19:g.240969620C>G	ENSP00000384428:p.Trp363Cys	86.0	0.0		114.0	63.0	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.7	4.326660	0.81690	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000440928;ENST00000348120;ENST00000446183;ENST00000366562;ENST00000407727;ENST00000401882	T;T;T;T;T;T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65	5.95	5.95	0.96441	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.81356	0.4805	H	0.97465	4.01	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.997;0.999;0.995;1.0;0.998	D	0.87158	0.2213	10	0.87932	D	0	.	19.3906	0.94581	0.0:1.0:0.0:0.0	.	279;337;310;363;363;363;363	B7Z223;B7Z257;P49802-4;P49802-2;P49802-5;P49802-3;P49802	.;.;.;.;.;.;RGS7_HUMAN	C	337;363;363;363;194;310;279;363;363;310	ENSP00000331485:W337C;ENSP00000355523:W363C;ENSP00000355522:W363C;ENSP00000355521:W363C;ENSP00000404399:W194C;ENSP00000341242:W310C;ENSP00000390138:W279C;ENSP00000355520:W363C;ENSP00000384428:W363C;ENSP00000385508:W310C	ENSP00000331485:W337C	W	-	3	0	RGS7	239036243	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.818000	0.86416	2.827000	0.97445	0.650000	0.86243	TGG	.	.		0.468	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		G	240969620	C	G	240969620	3	3	180	1	0	0	0	0	1	0	0	0	13325	740	26	4	390	4	RGS7	1	240969620	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	9592772	240969620	8281001	11	26919										
DCTN1	1639	hgsc.bcm.edu	37	chr2	74596526	74596526	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cgcttctgggcctcacgaacCcgcgcgcctgccatgtccag	11	18	2	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr2:74596526C>A	ENST00000361874.3	-	14	1802	c.1485G>T	c.(1483-1485)cgG>cgT	p.R495R	DCTN1_ENST00000407639.2_Silent_p.R361R|DCTN1_ENST00000409567.3_Silent_p.R475R|DCTN1_ENST00000409240.1_Silent_p.R458R|DCTN1_ENST00000409438.1_Silent_p.R361R|DCTN1_ENST00000409868.1_Silent_p.R478R|DCTN1_ENST00000394003.3_Silent_p.R488R|DCTN1_ENST00000495643.1_5'Flank	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	495			R -> Q (in dbSNP:rs17721059).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CCTCACGAACCCGCGCGCCTG	0.597																																					p.R495R		Atlas-SNP	.											.	DCTN1	110	.	0			c.G1485T						.						93	94	93					2																	74596526		2203	4300	6503	SO:0001819	synonymous_variant	1639	exon14			ACGAACCCGCGCG		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"p150 glued homolog (Drosophila)"	601143	"dynactin 1 (p150, Glued (Drosophila) homolog)"			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.1485G>T	chr2.hg19:g.74596526C>A		92.0	0.0		98.0	32.0	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	hg19	CCDS1939.1																																																																																			.	.		0.597	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		A	74596526	C	A	74596526	2	1	180	1	0	0	0	0	0	0	0	1	4308	610	22	3		3	DCTN1	2	74596526	Silent	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10		74596526	168602847	12	26920										
GGCX	2677	hgsc.bcm.edu	37	chr2	85788530	85788530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tgagctgggcgaggtccgcgCggacccggcagacaccgcca	16	15	0	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr2:85788530C>T	ENST00000233838.4	-	1	102	c.22G>A	c.(22-24)Gcg>Acg	p.A8T	VAMP8_ENST00000432071.1_5'Flank|GGCX_ENST00000430215.3_Missense_Mutation_p.A8T	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	8					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	GAGGTCCGCGCGGACCCGGCA	0.697																																					p.A8T		Atlas-SNP	.											.	GGCX	44	.	0			c.G22A						.						6	8	8					2																	85788530		2132	4207	6339	SO:0001583	missense	2677	exon1			TCCGCGCGGACCC		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"vitamin K-dependent gamma-carboxylase"	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.22G>A	chr2.hg19:g.85788530C>T	ENSP00000233838:p.Ala8Thr	220.0	0.0		173.0	60.0	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Missense_Mutation	SNP	ENST00000233838.4	hg19	CCDS1978.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.033844	0.54896	.	.	ENSG00000115486	ENST00000233838;ENST00000430215	D;D	0.94537	-3.45;-3.27	3.16	2.28	0.28536	.	0.963056	0.08539	N	0.930906	D	0.89815	0.6824	L	0.36672	1.1	0.09310	N	1	B;B	0.24426	0.001;0.103	B;B	0.17098	0.001;0.017	T	0.80986	-0.1137	10	0.48119	T	0.1	-2.1536	6.619	0.22792	0.0:0.866:0.0:0.134	.	8;8	E9PEE1;P38435	.;VKGC_HUMAN	T	8	ENSP00000233838:A8T;ENSP00000408045:A8T	ENSP00000233838:A8T	A	-	1	0	GGCX	85642041	0.074000	0.21230	0.115000	0.21578	0.260000	0.26232	0.093000	0.15086	0.887000	0.36136	0.555000	0.69702	GCG	.	.		0.697	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		T	85788530	C	T	85788530	3	4	180	1	0	0	0	0	1	0	0	0	6364	768	27	1	2314	1	GGCX	2	85788530	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	11192004	85788530	157410843	13	26921										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212543805	212543805	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gaggttacaagactctatgcAgatccttcctctactgaagc	8	11	2	3			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr2:212543805A>G	ENST00000342788.4	-	13	1904	c.1594T>C	c.(1594-1596)Tgc>Cgc	p.C532R	ERBB4_ENST00000402597.1_Missense_Mutation_p.C532R|ERBB4_ENST00000436443.1_Missense_Mutation_p.C532R	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	532	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GACTCTATGCAGATCCTTCCT	0.468										TSP Lung(8;0.080)																											p.C532R		Atlas-SNP	.											.	ERBB4	480	.	0			c.T1594C						.						72	63	66					2																	212543805		2203	4300	6503	SO:0001583	missense	2066	exon13			CTATGCAGATCCT	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1594T>C	chr2.hg19:g.212543805A>G	ENSP00000342235:p.Cys532Arg	351.0	0.0		339.0	33.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	A	19.63	3.863343	0.71949	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	D;D;D	0.98192	-4.78;-4.78;-4.78	5.33	5.33	0.75918	Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.99363	0.9776	H	0.97783	4.075	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.98452	1.0592	10	0.87932	D	0	.	14.2874	0.66254	1.0:0.0:0.0:0.0	.	532;532;391;532;532	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.;.;.;.;ERBB4_HUMAN	R	532	ENSP00000342235:C532R;ENSP00000403204:C532R;ENSP00000385565:C532R	ENSP00000342235:C532R	C	-	1	0	ERBB4	212252050	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	8.566000	0.90734	2.018000	0.59344	0.482000	0.46254	TGC	.	.		0.468	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		G	212543805	A	G	212543805	3	3	180	1	0	0	0	0	1	0	0	0	5211	188	7	2	2396	2	ERBB4	2	212543805	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	126755275	212543805	30655568	14	26922										
ZCWPW2	152098	hgsc.bcm.edu	37	chr3	28476749	28476749	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cattcgttggacattatagtAtcacattaaaggtaggtatc	8	6	1	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr3:28476749A>G	ENST00000383768.2	+	4	669	c.481A>G	c.(481-483)Atc>Gtc	p.I161V	ZCWPW2_ENST00000421010.1_Missense_Mutation_p.I161V			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	161	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.						zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						ACATTATAGTATCACATTAAA	0.318																																					p.I161V		Atlas-SNP	.											.	ZCWPW2	49	.	0			c.A481G						.						92	95	94					3																	28476749		2203	4300	6503	SO:0001583	missense	152098	exon3			TATAGTATCACAT	BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.481A>G	chr3.hg19:g.28476749A>G	ENSP00000373278:p.Ile161Val	355.0	0.0		381.0	123.0	NM_001040432		Missense_Mutation	SNP	ENST00000383768.2	hg19	CCDS33723.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.28|10.28	1.306992|1.306992	0.23821|0.23821	.|.	.|.	ENSG00000206559|ENSG00000206559	ENST00000383768;ENST00000421010|ENST00000428875;ENST00000419130	T;T|.	0.31247|.	1.5;1.5|.	6.06|6.06	-0.402|-0.402	0.12404|0.12404	PWWP (1);|.	0.696518|.	0.14211|.	N|.	0.334049|.	T|T	0.24236|0.24236	0.0587|0.0587	L|L	0.31294|0.31294	0.92|0.92	0.22827|0.22827	N|N	0.99869|0.99869	B|.	0.10296|.	0.003|.	B|.	0.12156|.	0.007|.	T|T	0.27739|0.27739	-1.0065|-1.0065	10|5	0.27785|.	T|.	0.31|.	-0.0519|-0.0519	5.1496|5.1496	0.15002|0.15002	0.5138:0.1588:0.3274:0.0|0.5138:0.1588:0.3274:0.0	.|.	161|.	Q504Y3|.	ZCPW2_HUMAN|.	V|C	161|144;12	ENSP00000373278:I161V;ENSP00000412386:I161V|.	ENSP00000373278:I161V|.	I|Y	+|+	1|2	0|0	ZCWPW2|ZCWPW2	28451753|28451753	0.820000|0.820000	0.29190|0.29190	0.987000|0.987000	0.45799|0.45799	0.972000|0.972000	0.66771|0.66771	0.518000|0.518000	0.22847|0.22847	-0.059000|-0.059000	0.13154|0.13154	-0.297000|-0.297000	0.09499|0.09499	ATC|TAT	.	.		0.318	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384		G	28476749	A	G	28476749	3	3	180	1	0	0	0	0	1	0	0	0	17613	449	16	2	487	2	ZCWPW2	3	28476749	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10		28476749	169545681	15	26923										
MST1	327	hgsc.bcm.edu	37	chr3	49723115	49723115	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ggctatccccatctgggttcCggcagaagttctcctccagt	10	14	2	1	rs397833185		TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr3:49723115C>T	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000449682.2_Missense_Mutation_p.R434Q	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		ATCTGGGTTCCGGCAGAAGTT	0.582																																					p.R434Q		Atlas-SNP	.											.	MST1	84	.	0			c.G1301A						.						44	43	43					3																	49723115		2203	4300	6503	SO:0001628	intergenic_variant	4485	exon11			GGGTTCCGGCAGA	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		chr3.hg19:g.49723115C>T		140.0	0.0		146.0	6.0	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	C	35	5.586034	0.96578	.	.	ENSG00000173531	ENST00000449682	D	0.96774	-4.12	5.22	5.22	0.72569	.	0.000000	0.39020	N	0.001499	D	0.98576	0.9524	H	0.99634	4.67	0.80722	D	1	P	0.42649	0.786	P	0.46796	0.527	D	0.99848	1.1068	10	0.72032	D	0.01	.	17.5442	0.87856	0.0:1.0:0.0:0.0	.	434	G3XAK1	.	Q	434	ENSP00000414287:R434Q	ENSP00000414287:R434Q	R	-	2	0	MST1	49698119	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.441000	0.80485	2.428000	0.82296	0.655000	0.94253	CGG	.	.		0.582	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			T	49723115	C	T	49723115	1	4	180	0	1	0	0	0	0	0	0	0	9899	652	23	1		1	MST1	3	49723115	IGR	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	21246366	49723115	148299315	16	26924										
VPRBP	9730	hgsc.bcm.edu	37	chr3	51475613	51475613	+	Intron	DEL	G	G	-													0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	aaagttctctctgtcaccctGttttgctgacttgtttttct							TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr3:51475613delG	ENST00000335891.5	-	6	682							Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein						B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		CTGTCACCCTGTTTTGCTGAC	0.428																																					p.Q272fs		Atlas-INDEL	.											.	VPRBP	107	.	0			c.815delA						.						275	260	265					3																	51475613		1906	4123	6029	SO:0001627	intron_variant	9730	exon8			.	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.672+141C>-	chr3.hg19:g.51475613delG		173.0	0.0		139.0	42.0	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Frame_Shift_Del	DEL	ENST00000335891.5	hg19																																																																																				.	.		0.428	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		-	51475613	G	-	51475613	6	5	180	0	1	1	0	1	0	0	0	0	17200	1386	48	0		0	VPRBP	3	51475613	Intron	DEL	G	TCGA-DD-AAD3-01A-11D-A40R-10	1752498	51475613	146546817	17	26925										
IMPG2	50939	hgsc.bcm.edu	37	chr3	100947684	100947684	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tgcaaactcaggatcattggCatacagttccaaaactctca	6	11	3	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr3:100947684C>A	ENST00000193391.7	-	18	3857	c.3670G>T	c.(3670-3672)Gcc>Tcc	p.A1224S		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	1224					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	GGATCATTGGCATACAGTTCC	0.393																																					p.A1224S		Atlas-SNP	.											.	IMPG2	164	.	0			c.G3670T						.						111	110	111					3																	100947684		2203	4300	6503	SO:0001583	missense	50939	exon18			CATTGGCATACAG	AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.3670G>T	chr3.hg19:g.100947684C>A	ENSP00000193391:p.Ala1224Ser	122.0	0.0		93.0	24.0	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	hg19	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.858571	0.91433	.	.	ENSG00000081148	ENST00000193391	T	0.32023	1.47	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000001	T	0.57198	0.2037	M	0.71581	2.175	0.53005	D	0.999967	D;D	0.76494	0.999;0.999	D;D	0.68943	0.961;0.961	T	0.58696	-0.7591	10	0.87932	D	0	-12.1046	19.819	0.96583	0.0:1.0:0.0:0.0	.	1224;1224	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	S	1224	ENSP00000193391:A1224S	ENSP00000193391:A1224S	A	-	1	0	IMPG2	102430374	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.695000	0.54749	2.691000	0.91804	0.655000	0.94253	GCC	.	.		0.393	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			A	100947684	C	A	100947684	3	1	180	1	0	0	0	0	1	0	0	0	7738	710	25	3	63	3	IMPG2	3	100947684	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	49472071	100947684	97074746	18	26926										
SI	6476	hgsc.bcm.edu	37	chr3	164773036	164773036	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	aaaatactgcattcatttgcCcaccaatcaatgcagtttgg	6	10	2	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr3:164773036C>G	ENST00000264382.3	-	13	1520	c.1458G>C	c.(1456-1458)tgG>tgC	p.W486C		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	486	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	ATTCATTTGCCCACCAATCAA	0.348										HNSCC(35;0.089)																											p.W486C		Atlas-SNP	.											.	SI	500	.	0			c.G1458C						.						125	120	121					3																	164773036		2203	4300	6503	SO:0001583	missense	6476	exon13			ATTTGCCCACCAA	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.1458G>C	chr3.hg19:g.164773036C>G	ENSP00000264382:p.Trp486Cys	111.0	0.0		102.0	29.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	hg19	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.980608	0.74474	.	.	ENSG00000090402	ENST00000264382	D	0.95342	-3.68	5.13	5.13	0.70059	Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.98707	0.9566	H	0.99697	4.71	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.99651	1.0991	10	0.87932	D	0	.	17.5495	0.87872	0.0:1.0:0.0:0.0	.	486	P14410	SUIS_HUMAN	C	486	ENSP00000264382:W486C	ENSP00000264382:W486C	W	-	3	0	SI	166255730	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.048000	0.76606	2.368000	0.80403	0.585000	0.79938	TGG	.	.		0.348	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		G	164773036	C	G	164773036	3	3	180	1	0	0	0	0	1	0	0	0	14312	624	22	4	4169	4	SI	3	164773036	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	63825352	164773036	33249394	19	26927										
GPR78	27201	hgsc.bcm.edu	37	chr4	8582915	8582915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cacgctgctcggtgtgatgcGcgggcggacaccgtcggcgc	17	14	0	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr4:8582915G>A	ENST00000382487.4	+	1	623	c.206G>A	c.(205-207)cGc>cAc	p.R69H	GPR78_ENST00000509216.1_Intron	NM_080819.4	NP_543009.2	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	69					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(4)|kidney(4)|large_intestine(1)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	26						GGTGTGATGCGCGGGCGGACA	0.692																																					p.R69H		Atlas-SNP	.											.	GPR78	58	.	0			c.G206A						.						22	25	24					4																	8582915		2203	4298	6501	SO:0001583	missense	27201	exon1			TGATGCGCGGGCG	AF411107	CCDS3403.1	4p16.1	2012-08-21			ENSG00000155269	ENSG00000155269		"GPCR / Class A : Orphans"	4528	protein-coding gene	gene with protein product		606921				11574155	Standard	NM_080819		Approved		uc003glk.4	Q96P69	OTTHUMG00000128483	ENST00000382487.4:c.206G>A	chr4.hg19:g.8582915G>A	ENSP00000371927:p.Arg69His	67.0	0.0		52.0	13.0	NM_080819	Q8NGV3	Missense_Mutation	SNP	ENST00000382487.4	hg19	CCDS3403.1	.	.	.	.	.	.	.	.	.	.	G	1.661	-0.511435	0.04231	.	.	ENSG00000155269	ENST00000382487	T	0.37058	1.22	2.59	-1.06	0.10002	GPCR, rhodopsin-like superfamily (1);	0.771052	0.09787	U	0.755863	T	0.11196	0.0273	N	0.02802	-0.49	0.09310	N	1	B	0.18461	0.028	B	0.14023	0.01	T	0.26189	-1.0110	10	0.15952	T	0.53	.	0.7649	0.01013	0.2375:0.1845:0.39:0.1879	.	69	Q96P69	GPR78_HUMAN	H	69	ENSP00000371927:R69H	ENSP00000371927:R69H	R	+	2	0	GPR78	8633815	0.003000	0.15002	0.003000	0.11579	0.295000	0.27426	1.149000	0.31626	-0.381000	0.07882	-0.657000	0.03884	CGC	.	.		0.692	GPR78-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359201.1			A	8582915	G	A	8582915	3	1	180	1	0	0	0	0	1	0	0	0	6718	1087	38	1	208	1	GPR78	4	8582915	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10		8582915	182571361	20	26928										
STBD1	100631383	hgsc.bcm.edu	37	chr4	77231063	77231063	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tttgtgttggtagagaatggGggagttacccgctgggaaga	17	4	0	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr4:77231063G>T	ENST00000237642.6	+	2	1731	c.987G>T	c.(985-987)ggG>ggT	p.G329G	FAM47E-STBD1_ENST00000539752.1_Silent_p.G180G|FAM47E_ENST00000515604.1_3'UTR	NM_003943.4	NP_003934.1			FAM47E-STBD1 readthrough																		TAGAGAATGGGGGAGTTACCC	0.483																																					p.G329G		Atlas-SNP	.											.	STBD1	22	.	0			c.G987T						.						162	159	160					4																	77231063		2203	4300	6503	SO:0001819	synonymous_variant	8987	exon2			GAATGGGGGAGTT		CCDS58908.1	4q21.1	2013-04-23			ENSG00000118804	ENSG00000118804			44667	other	readthrough							Standard	NM_001242939		Approved				OTTHUMG00000160966	ENST00000237642.6:c.987G>T	chr4.hg19:g.77231063G>T		116.0	0.0		113.0	53.0	NM_003943		Silent	SNP	ENST00000237642.6	hg19	CCDS3578.1																																																																																			.	.		0.483	FAM47E-STBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252415.2			T	77231063	G	T	77231063	2	4	180	1	0	0	0	0	0	0	0	1	15289	1219	43	3		3	STBD1	4	77231063	Silent	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	68648148	77231063	113923213	21	26929										
ADH5	128	hgsc.bcm.edu	37	chr4	100002517	100002517	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	aacataaaaagatactaaccTtatcttctggcaaaggttag	6	7	2	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr4:100002517T>A	ENST00000296412.8	-	4	393	c.343A>T	c.(343-345)Aga>Tga	p.R115*	ADH5_ENST00000512991.1_5'UTR	NM_000671.3	NP_000662.3			alcohol dehydrogenase 5 (class III), chi polypeptide											endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.5e-07)		GATACTAACCTTATCTTCTGG	0.373																																					p.R115X		Atlas-SNP	.											.	ADH5	23	.	0			c.A343T						.						57	52	54					4																	100002517		1837	4095	5932	SO:0001630	splice_region_variant	128	exon4			CTAACCTTATCTT	M29872	CCDS47111.1	4q23	2012-07-13	2003-06-19		ENSG00000197894	ENSG00000197894	1.1.1.284	"Alcohol dehydrogenases"	253	protein-coding gene	gene with protein product		103710	"formaldehyde dehydrogenase"	FDH		1446828, 6424546	Standard	NM_000671		Approved	ADH-3, ADHX	uc003hui.3	P11766	OTTHUMG00000161230	ENST00000296412.8:c.344+1A>T	chr4.hg19:g.100002517T>A		429.0	0.0		304.0	130.0	NM_000671		Nonsense_Mutation	SNP	ENST00000296412.8	hg19	CCDS47111.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.776759	0.90195	.	.	ENSG00000197894	ENST00000296412;ENST00000503130	.	.	.	4.88	3.66	0.41972	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.7857	0.52041	0.0:0.0:0.1471:0.8529	.	.	.	.	X	115;102	.	.	R	-	1	2	ADH5	100221540	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.622000	0.46427	0.865000	0.35603	0.524000	0.50904	AGA	.	.		0.373	ADH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364224.1	NM_000671	Nonsense_Mutation	A	100002517	T	A	100002517	5	1	180	1	0	0	0	0	0	0	1	0	311	1623	56	4	805	4	ADH5	4	100002517	Splice_Site	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10	22771454	100002517	91151759	22	26930										
FAT4	79633	hgsc.bcm.edu	37	chr4	126242565	126242565	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	aggccccagtggagtattatAttgtttcagttcgttgtgaa	11	6	1	1	rs369211657		TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr4:126242565A>G	ENST00000394329.3	+	1	5012	c.4999A>G	c.(4999-5001)Att>Gtt	p.I1667V		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1667	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GGAGTATTATATTGTTTCAGT	0.438																																					p.I1667V		Atlas-SNP	.											.	FAT4	1752	.	0			c.A4999G						.						92	91	91					4																	126242565		1847	4091	5938	SO:0001583	missense	79633	exon1			TATTATATTGTTT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.4999A>G	chr4.hg19:g.126242565A>G	ENSP00000377862:p.Ile1667Val	159.0	0.0		237.0	58.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	5.827	0.336809	0.11013	.	.	ENSG00000196159	ENST00000394329	T	0.45276	0.9	4.35	4.35	0.52113	Cadherin (3);Cadherin-like (1);	0.000000	0.34725	U	0.003733	T	0.39886	0.1095	L	0.53780	1.695	0.80722	D	1	P	0.47350	0.894	B	0.42995	0.404	T	0.23084	-1.0198	10	0.25106	T	0.35	.	13.7352	0.62813	1.0:0.0:0.0:0.0	.	1667	Q6V0I7	FAT4_HUMAN	V	1667	ENSP00000377862:I1667V	ENSP00000377862:I1667V	I	+	1	0	FAT4	126462015	1.000000	0.71417	0.955000	0.39395	0.457000	0.32468	7.148000	0.77389	1.840000	0.53500	0.533000	0.62120	ATT	.	.		0.438	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		G	126242565	A	G	126242565	3	3	180	1	0	0	0	0	1	0	0	0	5700	449	16	2	5001	2	FAT4	4	126242565	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	26240048	126242565	64911711	23	26931										
TIGD4	201798	hgsc.bcm.edu	37	chr4	153691328	153691328	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cactcttcgttgctgggcttGaaattcctcatcaagctttc	7	12	3	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr4:153691328G>C	ENST00000304337.2	-	2	1649	c.829C>G	c.(829-831)Caa>Gaa	p.Q277E		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	277	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					TGCTGGGCTTGAAATTCCTCA	0.403																																					p.Q277E		Atlas-SNP	.											.	TIGD4	53	.	0			c.C829G						.						129	135	133					4																	153691328		2203	4300	6503	SO:0001583	missense	201798	exon2			GGGCTTGAAATTC	AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.829C>G	chr4.hg19:g.153691328G>C	ENSP00000355162:p.Gln277Glu	124.0	0.0		131.0	16.0	NM_145720	Q96LP5	Missense_Mutation	SNP	ENST00000304337.2	hg19	CCDS34079.1	.	.	.	.	.	.	.	.	.	.	G	5.132	0.209948	0.09757	.	.	ENSG00000169989	ENST00000304337	T	0.40756	1.02	6.03	6.03	0.97812	.	0.000000	0.48286	D	0.000190	T	0.21022	0.0506	N	0.05230	-0.09	0.29721	N	0.838652	B	0.18968	0.032	B	0.21151	0.033	T	0.08576	-1.0715	10	0.06365	T	0.9	-19.7998	13.652	0.62316	0.0:0.0:0.7351:0.2649	.	277	Q8IY51	TIGD4_HUMAN	E	277	ENSP00000355162:Q277E	ENSP00000355162:Q277E	Q	-	1	0	TIGD4	153910778	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.960000	0.49161	2.861000	0.98227	0.655000	0.94253	CAA	.	.		0.403	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		C	153691328	G	C	153691328	3	2	180	1	0	0	0	0	1	0	0	0	15913	1299	45	4	713	4	TIGD4	4	153691328	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	27448763	153691328	37462948	24	26932										
LRAT	9227	hgsc.bcm.edu	37	chr4	155665788	155665788	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tcatcctgggcgttattgtcAaagtggccagcatccgcgtg	12	11	2	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr4:155665788A>C	ENST00000336356.3	+	2	563	c.310A>C	c.(310-312)Aaa>Caa	p.K104Q	LRAT_ENST00000507827.1_Missense_Mutation_p.K104Q	NM_004744.3	NP_004735.2	O95237	LRAT_HUMAN	lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)	104					phototransduction, visible light (GO:0007603)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|rough endoplasmic reticulum (GO:0005791)	phosphatidylcholine-retinol O-acyltransferase activity (GO:0047173)|retinoic acid binding (GO:0001972)|retinol binding (GO:0019841)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)	16	all_hematologic(180;0.215)	Renal(120;0.0458)			Vitamin A(DB00162)	CGTTATTGTCAAAGTGGCCAG	0.577																																					p.K104Q		Atlas-SNP	.											.	LRAT	29	.	0			c.A310C						.						66	68	67					4																	155665788		2203	4300	6503	SO:0001583	missense	9227	exon2			ATTGTCAAAGTGG	AF071510	CCDS3789.1	4q32.1	2014-01-28			ENSG00000121207	ENSG00000121207	2.3.1.135		6685	protein-coding gene	gene with protein product		604863				9920938	Standard	XM_006714412		Approved	LCA14	uc003ion.1	O95237	OTTHUMG00000161418	ENST00000336356.3:c.310A>C	chr4.hg19:g.155665788A>C	ENSP00000337224:p.Lys104Gln	120.0	0.0		118.0	40.0	NM_004744	A8K983|Q8N716	Missense_Mutation	SNP	ENST00000336356.3	hg19	CCDS3789.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.285046	0.59867	.	.	ENSG00000121207	ENST00000507827;ENST00000336356	T;T	0.23552	1.9;1.9	5.53	2.98	0.34508	.	0.321668	0.40728	N	0.001023	T	0.48447	0.1500	M	0.83603	2.65	0.36789	D	0.884721	D	0.63046	0.992	P	0.60541	0.876	T	0.60136	-0.7322	10	0.62326	D	0.03	-4.0879	12.3403	0.55091	0.7327:0.2672:0.0:0.0	.	104	O95237	LRAT_HUMAN	Q	104	ENSP00000426761:K104Q;ENSP00000337224:K104Q	ENSP00000337224:K104Q	K	+	1	0	LRAT	155885238	0.838000	0.29461	0.028000	0.17463	0.667000	0.39255	4.454000	0.60068	0.337000	0.23665	-0.321000	0.08615	AAA	.	.		0.577	LRAT-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365246.1	NM_004744		C	155665788	A	C	155665788	3	2	180	1	0	0	0	0	1	0	0	0	8939	131	5	5	312	5	LRAT	4	155665788	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	1974460	155665788	35488488	25	26933										
DDX4	54514	hgsc.bcm.edu	37	chr5	55081630	55081630	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tttgcacattatcagacaggCataaacttcgacaaatacga	6	9	1	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr5:55081630C>A	ENST00000505374.1	+	13	887	c.795C>A	c.(793-795)ggC>ggA	p.G265G	DDX4_ENST00000514278.2_Silent_p.G245G|DDX4_ENST00000354991.5_Silent_p.G231G|DDX4_ENST00000353507.5_Silent_p.G231G|DDX4_ENST00000511853.1_Silent_p.G116G	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	265					male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				ATCAGACAGGCATAAACTTCG	0.403																																					p.G265G		Atlas-SNP	.											.	DDX4	194	.	0			c.C795A						.						99	82	88					5																	55081630		2203	4300	6503	SO:0001819	synonymous_variant	54514	exon13			GACAGGCATAAAC	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.795C>A	chr5.hg19:g.55081630C>A		245.0	0.0		217.0	63.0	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Silent	SNP	ENST00000505374.1	hg19	CCDS3969.1																																																																																			.	.		0.403	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		A	55081630	C	A	55081630	2	1	180	1	0	0	0	0	0	0	0	1	4362	697	25	3		3	DDX4	5	55081630	Silent	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10		55081630	125833630	26	26934										
PLK2	10769	hgsc.bcm.edu	37	chr5	57750578	57750578	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tggctacagatgatgattttTgtatgatcatggtagaaatt	10	3	1	5			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr5:57750578T>C	ENST00000274289.3	-	14	2190	c.1890A>G	c.(1888-1890)acA>acG	p.T630T	PLK2_ENST00000502671.1_Intron	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	630	POLO box 2. {ECO:0000255|PROSITE- ProRule:PRU00154}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		TGATGATTTTTGTATGATCAT	0.338																																					p.T630T		Atlas-SNP	.											.	PLK2	71	.	0			c.A1890G						.						93	86	88					5																	57750578		2203	4300	6503	SO:0001819	synonymous_variant	10769	exon14			GATTTTTGTATGA		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"serum-inducible kinase"	607023	"polo-like kinase 2 (Drosophila)"				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.1890A>G	chr5.hg19:g.57750578T>C		181.0	0.0		167.0	46.0	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	hg19	CCDS3974.1																																																																																			.	.		0.338	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		C	57750578	T	C	57750578	2	2	180	1	0	0	0	0	0	0	0	1	12105	1799	63	2		2	PLK2	5	57750578	Silent	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10	2668948	57750578	123164682	27	26935										
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140516856	140516856	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	aggccacggagcccgggctgTtcagcatgtgggcgcacaat	15	12	1	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr5:140516856T>C	ENST00000231134.5	+	1	2057	c.1840T>C	c.(1840-1842)Ttc>Ctc	p.F614L		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	614	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCCCGGGCTGTTCAGCATGTG	0.687																																					p.F614L		Atlas-SNP	.											.	PCDHB5	184	.	0			c.T1840C						.						52	55	54					5																	140516856		2177	4256	6433	SO:0001583	missense	26167	exon1			GGGCTGTTCAGCA	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.1840T>C	chr5.hg19:g.140516856T>C	ENSP00000231134:p.Phe614Leu	74.0	0.0		47.0	15.0	NM_015669	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	hg19	CCDS4247.1	.	.	.	.	.	.	.	.	.	.	T	17.35	3.366750	0.61513	.	.	ENSG00000113209	ENST00000231134	T	0.70749	-0.51	4.65	4.65	0.58169	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.86510	0.5950	M	0.91510	3.215	0.46521	D	0.999083	D	0.76494	0.999	D	0.73380	0.98	D	0.89808	0.3980	9	0.87932	D	0	.	14.3871	0.66953	0.0:0.0:0.0:1.0	.	614	Q9Y5E4	PCDB5_HUMAN	L	614	ENSP00000231134:F614L	ENSP00000231134:F614L	F	+	1	0	PCDHB5	140497040	1.000000	0.71417	0.989000	0.46669	0.170000	0.22686	6.027000	0.70881	1.863000	0.54032	0.352000	0.21897	TTC	.	.		0.687	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		C	140516856	T	C	140516856	3	2	180	1	0	0	0	0	1	0	0	0	11554	1725	60	2	1842	2	PCDHB5	5	140516856	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10	82766278	140516856	40398404	28	26936										
FGFR4	2264	hgsc.bcm.edu	37	chr5	176520328	176520328	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ctcccgcttccctctggcccGacaggtactgggcgcatccc	10	19	1	0	rs200070761		TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr5:176520328G>T	ENST00000292408.4	+	9	1492	c.1247G>T	c.(1246-1248)cGa>cTa	p.R416L	FGFR4_ENST00000393637.1_Intron|FGFR4_ENST00000292410.3_Intron|FGFR4_ENST00000502906.1_Missense_Mutation_p.R416L|FGFR4_ENST00000393648.2_Intron	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	416					alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	CCTCTGGCCCGACAGGTACTG	0.667										TSP Lung(9;0.080)																											p.R416L		Atlas-SNP	.											.	FGFR4	174	.	0			c.G1247T						.						62	67	66					5																	176520328		2203	4300	6503	SO:0001583	missense	2264	exon9			TGGCCCGACAGGT	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1247G>T	chr5.hg19:g.176520328G>T	ENSP00000292408:p.Arg416Leu	179.0	0.0		131.0	6.0	NM_002011	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898874	0.91962	.	.	ENSG00000160867	ENST00000292408;ENST00000502906;ENST00000377207	D;D	0.90563	-2.69;-2.69	4.25	4.25	0.50352	.	0.166797	0.50627	D	0.000108	D	0.94902	0.8352	M	0.78916	2.43	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.95041	0.8178	10	0.51188	T	0.08	.	16.4541	0.84007	0.0:0.0:1.0:0.0	.	416	P22455	FGFR4_HUMAN	L	416;416;644	ENSP00000292408:R416L;ENSP00000424960:R416L	ENSP00000292408:R416L	R	+	2	0	FGFR4	176452934	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	9.254000	0.95512	2.210000	0.71456	0.561000	0.74099	CGA	.	G|1.000;A|0.000		0.667	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			T	176520328	G	T	176520328	3	4	180	1	0	0	0	0	1	0	0	0	5876	1058	37	1	1277	1	FGFR4	5	176520328	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	36003472	176520328	4394932	29	26937										
BMP6	654	hgsc.bcm.edu	37	chr6	7879308	7879308	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ttttgatctcctccaacagaTtacaacagcagtgaattgaa	6	9	1	4			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr6:7879308T>C	ENST00000283147.6	+	5	1365	c.1206T>C	c.(1204-1206)gaT>gaC	p.D402D		NM_001718.4	NP_001709.1	P22004	BMP6_HUMAN	bone morphogenetic protein 6	402					BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular response to mechanical stimulus (GO:0071260)|endochondral ossification (GO:0001958)|eye development (GO:0001654)|growth (GO:0040007)|immune response (GO:0006955)|inflammatory response (GO:0006954)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|osteoblast differentiation (GO:0001649)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of bone mineralization (GO:0030501)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to activity (GO:0014823)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to retinoic acid (GO:0032526)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|type B pancreatic cell development (GO:0003323)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)|protein heterodimerization activity (GO:0046982)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	23	Ovarian(93;0.0721)					CTCCAACAGATTACAACAGCA	0.468																																					p.D402D		Atlas-SNP	.											.	BMP6	67	.	0			c.T1206C						.						150	150	150					6																	7879308		2203	4300	6503	SO:0001630	splice_region_variant	654	exon5			AACAGATTACAAC	AF083030	CCDS4503.1	6p24-p23	2014-01-30	2003-10-06		ENSG00000153162	ENSG00000153162		"Bone morphogenetic proteins", "Endogenous ligands"	1073	protein-coding gene	gene with protein product		112266	"vegetal related growth factor (TGFB-related)"	VGR		1427904, 1453478	Standard	NM_001718		Approved	VGR1	uc003mxu.4	P22004	OTTHUMG00000014217	ENST00000283147.6:c.1205-1T>C	chr6.hg19:g.7879308T>C		142.0	0.0		173.0	50.0	NM_001718	Q5TCP3	Silent	SNP	ENST00000283147.6	hg19	CCDS4503.1																																																																																			.	.		0.468	BMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039794.1	NM_001718	Silent	C	7879308	T	C	7879308	5	2	180	1	0	0	0	0	0	0	1	0	1464	1507	52	2	1224	2	BMP6	6	7879308	Splice_Site	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10		7879308	163235759	30	26938										
RANBP9	10048	hgsc.bcm.edu	37	chr6	13622650	13622650	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ggatccaattcctgatcgagCcatcagtcctagacattgtg	9	11	1	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr6:13622650C>T	ENST00000011619.3	-	14	2192	c.2134G>A	c.(2134-2136)Gct>Act	p.A712T	RANBP9_ENST00000469916.1_5'UTR|NOL7_ENST00000474485.1_Intron|AL441883.1_ENST00000600057.1_5'Flank|RANBP9_ENST00000539980.1_Missense_Mutation_p.A483T	NM_005493.2	NP_005484.2	Q96S59	RANB9_HUMAN	RAN binding protein 9	712	Interaction with FMR1.				axon guidance (GO:0007411)|microtubule nucleation (GO:0007020)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	16	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			CCTGATCGAGCCATCAGTCCT	0.438																																					p.A712T		Atlas-SNP	.											.	RANBP9	42	.	0			c.G2134A						.						127	105	112					6																	13622650		2203	4300	6503	SO:0001583	missense	10048	exon14			ATCGAGCCATCAG	AB008515	CCDS4529.1	6p23	2010-05-25			ENSG00000010017	ENSG00000010017			13727	protein-coding gene	gene with protein product	"Ran Binding Protein in the Microtubule organizing center"	603854				9817760	Standard	NM_005493		Approved	RanBPM	uc003nbb.3	Q96S59	OTTHUMG00000015642	ENST00000011619.3:c.2134G>A	chr6.hg19:g.13622650C>T	ENSP00000011619:p.Ala712Thr	93.0	0.0		128.0	35.0	NM_005493	A0PJA2|B2R8E1|O94764|Q6P3T7|Q7LBR2|Q7Z7F9	Missense_Mutation	SNP	ENST00000011619.3	hg19	CCDS4529.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752121	0.89753	.	.	ENSG00000010017	ENST00000011619;ENST00000539980	T	0.78816	-1.21	6.17	6.17	0.99709	Ran binding protein-like, CRA domain (1);Ran binding protein, CRA domain (1);	0.000000	0.85682	D	0.000000	D	0.85579	0.5729	L	0.56769	1.78	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	D	0.84819	0.0795	10	0.72032	D	0.01	-15.8012	20.8794	0.99867	0.0:1.0:0.0:0.0	.	712	Q96S59	RANB9_HUMAN	T	712;483	ENSP00000011619:A712T	ENSP00000011619:A712T	A	-	1	0	RANBP9	13730629	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.456000	0.80751	2.941000	0.99782	0.655000	0.94253	GCT	.	.		0.438	RANBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042373.1			T	13622650	C	T	13622650	3	4	180	1	0	0	0	0	1	0	0	0	13047	739	26	3	59	3	RANBP9	6	13622650	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	5743342	13622650	157492417	31	26939										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32183114	32183114	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tctggtccttacatatctgcTtgggctggcacaggttggga	13	9	2	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr6:32183114T>G	ENST00000375023.3	-	12	2048	c.1910A>C	c.(1909-1911)aAg>aCg	p.K637T	NOTCH4_ENST00000465528.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	637	EGF-like 16. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						ACATATCTGCTTGGGCTGGCA	0.572																																					p.K637T		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A1910C						.						98	69	80					6																	32183114		1511	2709	4220	SO:0001583	missense	4855	exon12			ATCTGCTTGGGCT		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.1910A>C	chr6.hg19:g.32183114T>G	ENSP00000364163:p.Lys637Thr	66.0	0.0		111.0	22.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.707419	0.30322	.	.	ENSG00000204301	ENST00000375023	T	0.68025	-0.3	4.23	0.39	0.16275	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	1.119980	0.06883	N	0.802840	T	0.34221	0.0890	L	0.48642	1.525	0.09310	N	1	P	0.38922	0.651	B	0.35470	0.203	T	0.32134	-0.9918	10	0.59425	D	0.04	.	3.2286	0.06740	0.0:0.2406:0.2151:0.5443	.	637	Q99466	NOTC4_HUMAN	T	637	ENSP00000364163:K637T	ENSP00000364163:K637T	K	-	2	0	NOTCH4	32291092	0.000000	0.05858	0.048000	0.18961	0.955000	0.61496	-0.354000	0.07681	-0.008000	0.14320	0.459000	0.35465	AAG	.	.		0.572	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			G	32183114	T	G	32183114	3	3	180	1	0	0	0	0	1	0	0	0	10560	1609	56	5	4177	5	NOTCH4	6	32183114	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10	18560464	32183114	138931953	32	26940										
SLC39A7	7922	hgsc.bcm.edu	37	chr6	33170833	33170833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tgctacatgaagtgccccacGaggtcggagactttgccatc	11	12	0	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr6:33170833G>A	ENST00000374677.3	+	6	1460	c.1087G>A	c.(1087-1089)Gag>Aag	p.E363K	HSD17B8_ENST00000374662.3_5'Flank|SLC39A7_ENST00000374675.3_Missense_Mutation_p.E363K|RXRB_ENST00000374680.3_5'Flank|SLC39A7_ENST00000463972.1_3'UTR|RXRB_ENST00000413614.2_5'Flank|RXRB_ENST00000374685.4_5'Flank|RXRB_ENST00000544186.1_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	363					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						AGTGCCCCACGAGGTCGGAGA	0.552																																					p.E363K		Atlas-SNP	.											.	SLC39A7	32	.	0			c.G1087A						.						184	213	203					6																	33170833		1386	2616	4002	SO:0001583	missense	7922	exon6			CCCCACGAGGTCG	AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"Solute carriers"	4927	protein-coding gene	gene with protein product		601416	"HLA class II region expressed gene KE4"	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.1087G>A	chr6.hg19:g.33170833G>A	ENSP00000363809:p.Glu363Lys	114.0	0.0		121.0	33.0	NM_006979	B0UXF6|Q5STP8|Q9UIQ0	Missense_Mutation	SNP	ENST00000374677.3	hg19	CCDS43453.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.019190	0.93462	.	.	ENSG00000112473	ENST00000374675;ENST00000446283;ENST00000445037;ENST00000374677	T;T	0.54479	0.57;0.57	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.79992	0.4542	H	0.97365	3.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.86707	0.1933	10	0.87932	D	0	-13.1223	15.8729	0.79136	0.0:0.0:1.0:0.0	.	344;363	B4DVK8;Q92504	.;S39A7_HUMAN	K	363;344;268;363	ENSP00000363807:E363K;ENSP00000363809:E363K	ENSP00000363807:E363K	E	+	1	0	SLC39A7	33278811	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	7.915000	0.87484	2.603000	0.88011	0.448000	0.29417	GAG	.	.		0.552	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979		A	33170833	G	A	33170833	3	1	180	1	0	0	0	0	1	0	0	0	14638	1059	37	1	1109	1	SLC39A7	6	33170833	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	987719	33170833	137944234	33	26941										
KCNK17	89822	hgsc.bcm.edu	37	chr6	39271749	39271749	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tcaccaatcacgtagtcgccGaagcccacggtgctgagggt	12	13	2	1	rs533411945	byFrequency	TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr6:39271749G>A	ENST00000373231.4	-	4	904	c.672C>T	c.(670-672)ttC>ttT	p.F224F	KCNK17_ENST00000453413.2_Silent_p.F224F	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	224					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						CGTAGTCGCCGAAGCCCACGG	0.617													G|||	2	0.000399361	0	0	5008	,	,		19215	0		0	False		,,,				2504	0.002				p.F224F		Atlas-SNP	.											KCNK17_ENST00000453413,NS,carcinoma,0,4	KCNK17	61	.	0			c.C672T						.						98	93	94					6																	39271749		2203	4300	6503	SO:0001819	synonymous_variant	89822	exon4			GTCGCCGAAGCCC	AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.672C>T	chr6.hg19:g.39271749G>A		80.0	0.0		101.0	6.0	NM_001135111	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Silent	SNP	ENST00000373231.4	hg19	CCDS4842.1																																																																																			.	.		0.617	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460		A	39271749	G	A	39271749	2	1	180	1	0	0	0	0	0	0	0	1	8073	1049	37	1		1	KCNK17	6	39271749	Silent	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	6100916	39271749	131843318	34	26942										
TJAP1	93643	hgsc.bcm.edu	37	chr6	43470061	43470061	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cttcccagcggaccaaccagGagttggaggacaagctgcac	12	13	0	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr6:43470061G>A	ENST00000372445.5	+	7	707	c.331G>A	c.(331-333)Gag>Aag	p.E111K	TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000372449.1_Missense_Mutation_p.E111K|TJAP1_ENST00000259751.1_Missense_Mutation_p.E111K|TJAP1_ENST00000438588.2_Missense_Mutation_p.E111K|TJAP1_ENST00000372444.2_Missense_Mutation_p.E111K|TJAP1_ENST00000372452.1_Missense_Mutation_p.E111K|TJAP1_ENST00000436109.2_Missense_Mutation_p.E111K	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	111					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			GACCAACCAGGAGTTGGAGGA	0.557																																					p.E111K		Atlas-SNP	.											.	TJAP1	35	.	0			c.G331A						.						95	76	83					6																	43470061		2203	4300	6503	SO:0001583	missense	93643	exon7			AACCAGGAGTTGG	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.331G>A	chr6.hg19:g.43470061G>A	ENSP00000361522:p.Glu111Lys	65.0	0.0		107.0	22.0	NM_080604	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	ENST00000372445.5	hg19	CCDS55004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.617397|5.617397	0.96649|0.96649	.|.	.|.	ENSG00000137221|ENSG00000137221	ENST00000372444;ENST00000372445;ENST00000436109;ENST00000442878;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588|ENST00000454762	T;T;T;T;T;T;T;T|.	0.50001|.	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.128709|.	0.52532|.	D|.	0.000066|.	T|T	0.61426|0.61426	0.2346|0.2346	L|L	0.55481|0.55481	1.735|1.735	0.47094|0.47094	D|D	0.999319|0.999319	B;D;P|.	0.63880|.	0.338;0.993;0.873|.	B;P;P|.	0.58520|.	0.115;0.84;0.461|.	T|T	0.60747|0.60747	-0.7202|-0.7202	10|5	0.49607|.	T|.	0.09|.	-15.4577|-15.4577	16.4138|16.4138	0.83727|0.83727	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	111;111;111|.	E2QRK7;Q5JTD0;Q5JTD0-2|.	.;TJAP1_HUMAN;.|.	K|E	111|68	ENSP00000361521:E111K;ENSP00000361522:E111K;ENSP00000407080:E111K;ENSP00000390981:E111K;ENSP00000259751:E111K;ENSP00000361530:E111K;ENSP00000361527:E111K;ENSP00000408769:E111K|.	ENSP00000259751:E111K|.	E|G	+|+	1|2	0|0	TJAP1|TJAP1	43578039|43578039	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	8.702000|8.702000	0.91338|0.91338	2.298000|2.298000	0.77334|0.77334	0.563000|0.563000	0.77884|0.77884	GAG|GGA	.	.		0.557	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		A	43470061	G	A	43470061	3	1	180	1	0	0	0	0	1	0	0	0	15943	1175	41	3	345	3	TJAP1	6	43470061	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	4198312	43470061	127645006	35	26943										
TINAG	27283	hgsc.bcm.edu	37	chr6	54191649	54191649	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ggggaatgactttagaagatGgttttaaatttcgccttggc	12	5	0	3			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr6:54191649G>T	ENST00000259782.4	+	4	655	c.559G>T	c.(559-561)Ggt>Tgt	p.G187C	TINAG_ENST00000370864.3_Missense_Mutation_p.G169C|TINAG_ENST00000370869.3_Missense_Mutation_p.G183C	NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	187					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			TTTAGAAGATGGTTTTAAATT	0.378																																					p.G187C		Atlas-SNP	.											.	TINAG	102	.	0			c.G559T						.						143	132	135					6																	54191649		2203	4300	6503	SO:0001583	missense	27283	exon4			GAAGATGGTTTTA	AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.559G>T	chr6.hg19:g.54191649G>T	ENSP00000259782:p.Gly187Cys	178.0	0.0		216.0	9.0	NM_014464	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	hg19	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.118357	0.77323	.	.	ENSG00000137251	ENST00000370869;ENST00000339741;ENST00000259782;ENST00000370864	T;T;T	0.52983	0.64;0.64;0.64	5.82	5.82	0.92795	.	0.180155	0.40064	N	0.001181	T	0.68504	0.3008	M	0.87827	2.91	0.58432	D	0.99999	D	0.89917	1.0	D	0.97110	1.0	T	0.73597	-0.3932	10	0.87932	D	0	.	15.6145	0.76753	0.0:0.0:1.0:0.0	.	187	Q9UJW2	TINAG_HUMAN	C	183;137;187;169	ENSP00000359906:G183C;ENSP00000259782:G187C;ENSP00000359901:G169C	ENSP00000259782:G187C	G	+	1	0	TINAG	54299608	1.000000	0.71417	0.997000	0.53966	0.932000	0.56968	5.426000	0.66476	2.751000	0.94390	0.643000	0.83706	GGT	.	.		0.378	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		T	54191649	G	T	54191649	3	4	180	1	0	0	0	0	1	0	0	0	15936	1348	47	3	573	3	TINAG	6	54191649	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	10721588	54191649	116923418	36	26944										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18624963	18624963	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tctcacctttagacctaaggAcagacctcaggatgatgatg	9	10	2	4			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr7:18624963A>T	ENST00000432645.2	+	2	82	c.82A>T	c.(82-84)Aca>Tca	p.T28S	HDAC9_ENST00000406072.1_Missense_Mutation_p.T56S|HDAC9_ENST00000441542.2_Missense_Mutation_p.T28S|HDAC9_ENST00000456174.2_5'UTR|HDAC9_ENST00000417496.2_Missense_Mutation_p.T70S|HDAC9_ENST00000405010.3_Missense_Mutation_p.T28S|HDAC9_ENST00000401921.1_Missense_Mutation_p.T28S|HDAC9_ENST00000476135.1_3'UTR|HDAC9_ENST00000406451.4_Missense_Mutation_p.T28S|HDAC9_ENST00000524023.1_5'UTR|HDAC9_ENST00000428307.2_Missense_Mutation_p.T28S	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	28					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	AGACCTAAGGACAGACCTCAG	0.502																																					p.T70S		Atlas-SNP	.											.	HDAC9	560	.	0			c.A208T						.						129	130	130					7																	18624963		1960	4171	6131	SO:0001583	missense	9734	exon5			CTAAGGACAGACC	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.82A>T	chr7.hg19:g.18624963A>T	ENSP00000410337:p.Thr28Ser	167.0	0.0		186.0	30.0	NM_001204144	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	hg19	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.578970	0.86645	.	.	ENSG00000048052	ENST00000417496;ENST00000262069;ENST00000413509;ENST00000413380;ENST00000405010;ENST00000406451;ENST00000428307;ENST00000406072;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000341009	T;T;T;T;T;T;T;T;T;T	0.59906	0.79;0.83;0.82;0.8;0.26;0.79;0.84;0.23;0.26;0.26	5.93	5.93	0.95920	.	0.199853	0.35207	N	0.003369	T	0.72495	0.3467	L	0.60455	1.87	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.76494	0.999;0.983;0.999;0.99;0.999;0.999;0.996;0.999;0.998;0.999	D;P;D;P;D;D;P;D;D;D	0.80764	0.962;0.791;0.957;0.86;0.962;0.962;0.874;0.962;0.994;0.918	T	0.70842	-0.4762	10	0.37606	T	0.19	-10.608	16.3766	0.83401	1.0:0.0:0.0:0.0	.	28;56;70;28;28;28;28;28;28;47	Q9UKV0-4;B5MCF1;B7Z917;Q68D71;Q9UKV0-6;Q9UKV0-7;Q9UKV0;Q9UKV0-5;Q9UKV0-3;Q8N879	.;.;.;.;.;.;HDAC9_HUMAN;.;.;.	S	70;73;28;28;28;28;28;56;28;28;28;28	ENSP00000401669:T70S;ENSP00000412497:T28S;ENSP00000392564:T28S;ENSP00000384382:T28S;ENSP00000384657:T28S;ENSP00000395655:T28S;ENSP00000384017:T56S;ENSP00000383912:T28S;ENSP00000410337:T28S;ENSP00000408617:T28S	ENSP00000262069:T73S	T	+	1	0	HDAC9	18591488	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.576000	0.82467	2.263000	0.75096	0.533000	0.62120	ACA	.	.		0.502	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18624963	A	T	18624963	3	4	180	1	0	0	0	0	1	0	0	0	7023	275	10	4	88	4	HDAC9	7	18624963	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10		18624963	140513700	37	26945										
MAGI2	9863	hgsc.bcm.edu	37	chr7	77789511	77789511	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gcgtggttgctgttggtgtaGgttgcgtagtcactgcgtgg	18	6	1	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr7:77789511G>T	ENST00000354212.4	-	16	2929	c.2676C>A	c.(2674-2676)acC>acA	p.T892T	MAGI2_ENST00000419488.1_Silent_p.T878T|MAGI2_ENST00000522391.1_Silent_p.T892T	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	892					cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TGTTGGTGTAGGTTGCGTAGT	0.587																																					p.T892T		Atlas-SNP	.											.	MAGI2	246	.	0			c.C2676A						.						165	139	148					7																	77789511		2203	4300	6503	SO:0001819	synonymous_variant	9863	exon16			GGTGTAGGTTGCG	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.2676C>A	chr7.hg19:g.77789511G>T		171.0	0.0		152.0	16.0	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	hg19	CCDS5594.1																																																																																			.	.		0.587	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		T	77789511	G	T	77789511	2	4	180	1	0	0	0	0	0	0	0	1	9200	987	35	3		3	MAGI2	7	77789511	Silent	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	59164548	77789511	81349152	38	26946										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88964202	88964202	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cctacatctctaggtttaaaAagcataaattgattccctgc	5	10	1	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr7:88964202A>G	ENST00000333190.4	+	4	2515	c.1906A>G	c.(1906-1908)Aag>Gag	p.K636E		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	636							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TAGGTTTAAAAAGCATAAATT	0.423										HNSCC(36;0.09)																											p.K636E		Atlas-SNP	.											.	ZNF804B	322	.	0			c.A1906G						.						83	86	85					7																	88964202		2203	4300	6503	SO:0001583	missense	219578	exon4			TTTAAAAAGCATA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1906A>G	chr7.hg19:g.88964202A>G	ENSP00000329638:p.Lys636Glu	228.0	0.0		192.0	55.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	A	9.035	0.988194	0.18966	.	.	ENSG00000182348	ENST00000333190	T	0.06933	3.24	5.48	4.33	0.51752	.	0.244896	0.35870	N	0.002926	T	0.06600	0.0169	L	0.29908	0.895	0.21897	N	0.99948	B	0.27498	0.18	B	0.23150	0.044	T	0.33650	-0.9860	10	0.24483	T	0.36	-2.6507	11.5151	0.50515	0.9302:0.0:0.0698:0.0	.	636	A4D1E1	Z804B_HUMAN	E	636	ENSP00000329638:K636E	ENSP00000329638:K636E	K	+	1	0	ZNF804B	88802138	1.000000	0.71417	0.539000	0.28077	0.018000	0.09664	4.919000	0.63383	1.093000	0.41377	0.528000	0.53228	AAG	.	.		0.423	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		G	88964202	A	G	88964202	3	3	180	1	0	0	0	0	1	0	0	0	18186	15	1	2	1920	2	ZNF804B	7	88964202	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	11174691	88964202	70174461	39	26947										
MLL5	55904	hgsc.bcm.edu	37	chr7	104753037	104753037	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ctccagggcattttttgcccTctcagaaccctaccattcac	5	16	2	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr7:104753037T>G	ENST00000311117.3	+	27	5379	c.4834T>G	c.(4834-4836)Tct>Gct	p.S1612A	KMT2E_ENST00000334877.4_Missense_Mutation_p.S1570A|KMT2E_ENST00000257745.4_Missense_Mutation_p.S1612A|SRPK2_ENST00000493638.1_Intron	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1612	Pro-rich. {ECO:0000255}.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										TTTTTTGCCCTCTCAGAACCC	0.542																																					p.S1612A		Atlas-SNP	.											.	MLL5	173	.	0			c.T4834G						.						165	141	149					7																	104753037		2203	4300	6503	SO:0001583	missense	55904	exon26			TTGCCCTCTCAGA	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.4834T>G	chr7.hg19:g.104753037T>G	ENSP00000312379:p.Ser1612Ala	122.0	0.0		109.0	7.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	T	5.361	0.251912	0.10185	.	.	ENSG00000005483	ENST00000311117;ENST00000334877;ENST00000351043;ENST00000257745	D;D;D	0.92495	-3.05;-2.89;-3.05	3.63	2.33	0.28932	.	0.000000	0.37136	N	0.002238	T	0.81437	0.4822	N	0.19112	0.55	0.80722	D	1	P;B	0.41673	0.759;0.243	B;B	0.36335	0.222;0.066	T	0.77146	-0.2695	10	0.21540	T	0.41	.	8.5771	0.33605	0.1721:0.0:0.0:0.8279	.	1532;1612	F8W6H1;Q8IZD2	.;MLL5_HUMAN	A	1612;1570;1532;1612	ENSP00000312379:S1612A;ENSP00000335599:S1570A;ENSP00000257745:S1612A	ENSP00000257745:S1612A	S	+	1	0	MLL5	104540273	0.932000	0.31603	0.944000	0.38274	0.781000	0.44180	1.391000	0.34475	1.426000	0.47256	0.254000	0.18369	TCT	.	.		0.542	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			G	104753037	T	G	104753037	3	3	180	1	0	0	0	0	1	0	0	0	9633	1551	54	5	4932	5	MLL5	7	104753037	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10	15788835	104753037	54385626	40	26948										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113518594	113518594	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gctttttgatattctgtaatGacccatgaggattcttccac	7	9	2	3			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr7:113518594G>A	ENST00000284601.3	-	4	2621	c.2553C>T	c.(2551-2553)gtC>gtT	p.V851V		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	851					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						ATTCTGTAATGACCCATGAGG	0.383																																					p.V851V		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.C2553T						.						180	169	173					7																	113518594		2203	4300	6503	SO:0001819	synonymous_variant	5506	exon4			TGTAATGACCCAT	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.2553C>T	chr7.hg19:g.113518594G>A		145.0	0.0		136.0	15.0	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Silent	SNP	ENST00000284601.3	hg19	CCDS5759.1																																																																																			.	.		0.383	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		A	113518594	G	A	113518594	2	1	180	1	0	0	0	0	0	0	0	1	12383	1277	45	3		3	PPP1R3A	7	113518594	Silent	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	8765557	113518594	45620069	41	26949										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52287173	52287173	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tcacctatctccatctcttaGccgctgaaactgggtaacaa	6	13	3	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr8:52287173G>A	ENST00000356297.4	-	18	3776	c.3676C>T	c.(3676-3678)Cta>Tta	p.L1226L	PXDNL_ENST00000543296.1_Silent_p.L1226L	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1226					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CCATCTCTTAGCCGCTGAAAC	0.388																																					p.L1226L		Atlas-SNP	.											.	PXDNL	414	.	0			c.C3676T						.						79	79	79					8																	52287173		1900	4123	6023	SO:0001819	synonymous_variant	137902	exon18			CTCTTAGCCGCTG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.3676C>T	chr8.hg19:g.52287173G>A		141.0	0.0		100.0	31.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	hg19	CCDS47855.1																																																																																			.	.		0.388	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52287173	G	A	52287173	2	1	180	1	0	0	0	0	0	0	0	1	12863	962	34	3		3	PXDNL	8	52287173	Silent	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10		52287173	94076849	42	26950										
PTAR1	375743	hgsc.bcm.edu	37	chr9	72333569	72333569	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gctgtgaggaaacctaccatTtaagtgatgctgaaggtaga	12	6	0	4			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr9:72333569T>C	ENST00000340434.4	-	7	982	c.979A>G	c.(979-981)Aat>Gat	p.N327D	PTAR1_ENST00000377200.5_Missense_Mutation_p.N248D	NM_001099666.1	NP_001093136.1	Q7Z6K3	PTAR1_HUMAN	protein prenyltransferase alpha subunit repeat containing 1	327					protein prenylation (GO:0018342)		protein prenyltransferase activity (GO:0008318)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)	5						AACCTACCATTTAAGTGATGC	0.473																																					p.N327D		Atlas-SNP	.											.	PTAR1	46	.	0			c.A979G						.						58	56	56					9																	72333569		1898	4115	6013	SO:0001583	missense	375743	exon7			TACCATTTAAGTG	BC053622	CCDS47978.1	9q21.13	2008-10-01			ENSG00000188647	ENSG00000188647		"Prenyltransferase alpha subunit repeat containing"	30449	protein-coding gene	gene with protein product						12477932	Standard	NM_001099666		Approved		uc004ahj.4	Q7Z6K3	OTTHUMG00000019982	ENST00000340434.4:c.979A>G	chr9.hg19:g.72333569T>C	ENSP00000344299:p.Asn327Asp	93.0	0.0		53.0	23.0	NM_001099666	Q5T7V5|Q5T7V6	Missense_Mutation	SNP	ENST00000340434.4	hg19	CCDS47978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.774|8.774	0.926679|0.926679	0.18056|0.18056	.|.	.|.	ENSG00000188647|ENSG00000188647	ENST00000415701|ENST00000377200;ENST00000340434	.|T;T	.|0.42131	.|0.98;0.98	6.02|6.02	0.654|0.654	0.17833|0.17833	.|Protein prenyltransferase (1);	.|0.889113	.|0.10054	.|N	.|0.721815	T|T	0.25494|0.25494	0.0620|0.0620	N|N	0.08118|0.08118	0|0	0.26592|0.26592	N|N	0.973183|0.973183	.|B	.|0.10296	.|0.003	.|B	.|0.11329	.|0.006	T|T	0.19257|0.19257	-1.0311|-1.0311	5|10	.|0.31617	.|T	.|0.26	.|.	15.0691|15.0691	0.72021|0.72021	0.0:0.0:0.4969:0.5031|0.0:0.0:0.4969:0.5031	.|.	.|327	.|Q7Z6K3	.|PTAR1_HUMAN	R|D	93|248;327	.|ENSP00000366405:N248D;ENSP00000344299:N327D	.|ENSP00000344299:N327D	K|N	-|-	2|1	0|0	PTAR1|PTAR1	71523389|71523389	0.690000|0.690000	0.27699|0.27699	0.269000|0.269000	0.24586|0.24586	0.975000|0.975000	0.68041|0.68041	1.514000|1.514000	0.35834|0.35834	0.138000|0.138000	0.18790|0.18790	-0.331000|-0.331000	0.08364|0.08364	AAA|AAT	.	.		0.473	PTAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052582.4	NM_001099666		C	72333569	T	C	72333569	3	2	180	1	0	0	0	0	1	0	0	0	12736	1841	64	2	237	2	PTAR1	9	72333569	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10		72333569	68879862	43	26951										
MYST4	23522	hgsc.bcm.edu	37	chr10	76789169	76789169	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gtcgatacagagttcaaagaGggaaacccagcaaccatgga	11	9	1	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr10:76789169G>A	ENST00000287239.4	+	18	5076	c.4587G>A	c.(4585-4587)gaG>gaA	p.E1529E	KAT6B_ENST00000372711.1_Silent_p.E1346E|KAT6B_ENST00000372725.1_Silent_p.E1237E|KAT6B_ENST00000372724.1_Silent_p.E1237E|KAT6B_ENST00000372714.1_Silent_p.E1237E	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1529					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										AGTTCAAAGAGGGAAACCCAG	0.532																																					p.E1529E		Atlas-SNP	.											.	.	.	.	0			c.G4587A						.						115	114	114					10																	76789169		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon18			CAAAGAGGGAAAC	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.4587G>A	chr10.hg19:g.76789169G>A		161.0	0.0		140.0	50.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.532	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		A	76789169	G	A	76789169	2	1	180	1	0	0	0	0	0	0	0	1	10114	991	35	3		3	MYST4	10	76789169	Silent	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10		76789169	58745578	44	26952										
LRIT1	26103	hgsc.bcm.edu	37	chr10	85992484	85992484	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cttgcccatagtgctcctggGctcccactgtgttctgtgga	11	13	1	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr10:85992484G>C	ENST00000372105.3	-	4	1092	c.1071C>G	c.(1069-1071)agC>agG	p.S357R		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	357						integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						GTGCTCCTGGGCTCCCACTGT	0.562																																					p.S357R		Atlas-SNP	.											.	LRIT1	73	.	0			c.C1071G						.						58	47	51					10																	85992484		2203	4300	6503	SO:0001583	missense	26103	exon4			TCCTGGGCTCCCA	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	23404	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 9"		"leucine rich repeat containing 21"	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1071C>G	chr10.hg19:g.85992484G>C	ENSP00000361177:p.Ser357Arg	125.0	0.0		96.0	23.0	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	hg19	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	G	0.428	-0.904638	0.02453	.	.	ENSG00000148602	ENST00000372105	T	0.36157	1.27	5.8	0.683	0.17998	.	0.840007	0.11543	N	0.553565	T	0.20941	0.0504	N	0.24115	0.695	0.09310	N	1	B	0.27166	0.17	B	0.24269	0.052	T	0.26326	-1.0106	10	0.15499	T	0.54	.	9.1011	0.36669	0.4715:0.0:0.5285:0.0	.	357	Q9P2V4	LRIT1_HUMAN	R	357	ENSP00000361177:S357R	ENSP00000361177:S357R	S	-	3	2	LRIT1	85982464	0.000000	0.05858	0.055000	0.19348	0.185000	0.23345	0.549000	0.23329	0.094000	0.17404	0.655000	0.94253	AGC	.	.		0.562	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		C	85992484	G	C	85992484	3	2	180	1	0	0	0	0	1	0	0	0	8956	1194	42	4	804	4	LRIT1	10	85992484	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	9203315	85992484	49542263	45	26953										
IDE	3416	hgsc.bcm.edu	37	chr10	94250296	94250296	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cttgtttgtactgggttccaTaccactcttctgtgcgatca	8	11	3	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr10:94250296T>C	ENST00000265986.6	-	12	1543	c.1487A>G	c.(1486-1488)tAt>tGt	p.Y496C	IDE_ENST00000496903.1_5'UTR|IDE_ENST00000371581.5_5'UTR	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	496					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	CTGGGTTCCATACCACTCTTC	0.378																																					p.Y496C		Atlas-SNP	.											.	IDE	77	.	0			c.A1487G						.						298	288	291					10																	94250296		2203	4300	6503	SO:0001583	missense	3416	exon12			GTTCCATACCACT	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.1487A>G	chr10.hg19:g.94250296T>C	ENSP00000265986:p.Tyr496Cys	99.0	0.0		107.0	12.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.402858	0.83230	.	.	ENSG00000119912	ENST00000265986	T	0.57107	0.42	5.41	5.41	0.78517	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.80003	0.4544	H	0.94264	3.515	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85863	0.1411	10	0.87932	D	0	-12.534	14.9135	0.70776	0.0:0.0:0.0:1.0	.	496	P14735	IDE_HUMAN	C	496	ENSP00000265986:Y496C	ENSP00000265986:Y496C	Y	-	2	0	IDE	94240276	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.478000	0.81082	2.169000	0.68431	0.533000	0.62120	TAT	.	.		0.378	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		C	94250296	T	C	94250296	3	2	180	1	0	0	0	0	1	0	0	0	7502	1406	49	2	1628	2	IDE	10	94250296	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10	8257812	94250296	41284451	46	26954										
TLL2	7093	hgsc.bcm.edu	37	chr10	98133500	98133500	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gggggccaggctgtccggccCgtcatacatttccaggtggt	15	12	1	0	rs141213956		TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr10:98133500C>T	ENST00000357947.3	-	19	2740	c.2515G>A	c.(2515-2517)Ggg>Agg	p.G839R		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	839	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		CTGTCCGGCCCGTCATACATT	0.547																																					p.G839R		Atlas-SNP	.											.	TLL2	122	.	0			c.G2515A						.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	60	63	62		2515	4.8	0.2	10	dbSNP_134	62	0,8600		0,0,4300	no	missense	TLL2	NM_012465.3	125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	839/1016	98133500	1,13005	2203	4300	6503	SO:0001583	missense	7093	exon19			CCGGCCCGTCATA	AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.2515G>A	chr10.hg19:g.98133500C>T	ENSP00000350630:p.Gly839Arg	90.0	0.0		69.0	23.0	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	hg19	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.527215	0.85706	2.27E-4	0.0	ENSG00000095587	ENST00000357947	T	0.26957	1.7	4.85	4.85	0.62838	CUB (5);	0.000000	0.46442	D	0.000300	T	0.66713	0.2817	H	0.98218	4.175	0.80722	D	1	D	0.76494	0.999	D	0.68039	0.955	T	0.80663	-0.1282	10	0.87932	D	0	.	17.4922	0.87707	0.0:1.0:0.0:0.0	.	839	Q9Y6L7	TLL2_HUMAN	R	839	ENSP00000350630:G839R	ENSP00000350630:G839R	G	-	1	0	TLL2	98123490	1.000000	0.71417	0.152000	0.22495	0.638000	0.38207	7.609000	0.82925	2.677000	0.91161	0.561000	0.74099	GGG	.	C|1.000;T|0.000		0.547	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			T	98133500	C	T	98133500	3	4	180	1	0	0	0	0	1	0	0	0	15961	652	23	1	544	1	TLL2	10	98133500	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	3883204	98133500	37401247	47	26955										
RNH1	6050	hgsc.bcm.edu	37	chr11	499113	499113	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ttgctaaccgtgagctccttGaagtccggcttggccctgag	12	12	0	3			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr11:499113G>A	ENST00000534797.1	-	4	1923	c.516C>T	c.(514-516)ttC>ttT	p.F172F	RNH1_ENST00000356187.5_Silent_p.F172F|RNH1_ENST00000438658.2_Silent_p.F172F|RNH1_ENST00000533592.1_5'Flank|RNH1_ENST00000397615.2_Silent_p.F172F|RNH1_ENST00000397614.1_Silent_p.F172F|RNH1_ENST00000533410.1_Silent_p.F172F|RNH1_ENST00000397604.3_Silent_p.F172F|RNH1_ENST00000354420.2_Silent_p.F172F			O60930	RNH1_HUMAN	ribonuclease/angiogenin inhibitor 1	0	RNase H. {ECO:0000255|PROSITE- ProRule:PRU00408}.				mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGAGCTCCTTGAAGTCCGGCT	0.642																																					p.F172F		Atlas-SNP	.											.	RNH1	24	.	0			c.C516T						.						67	53	58					11																	499113		2203	4300	6503	SO:0001819	synonymous_variant	6050	exon5			CTCCTTGAAGTCC		CCDS7697.1	11p15.5	2008-02-05	2005-06-01	2005-06-01	ENSG00000023191	ENSG00000023191			10074	protein-coding gene	gene with protein product		173320	"ribonuclease/angiogenin inhibitor"	RNH			Standard	NM_203386		Approved	RAI	uc001lpo.1	P13489	OTTHUMG00000119086	ENST00000534797.1:c.516C>T	chr11.hg19:g.499113G>A		107.0	0.0		87.0	10.0	NM_203384	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Silent	SNP	ENST00000534797.1	hg19	CCDS7697.1																																																																																			.	.		0.642	RNH1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384301.1	NM_203389		A	499113	G	A	499113	2	1	180	1	0	0	0	0	0	0	0	1	13519	1281	45	3		3	RNH1	11	499113	Silent	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10		499113	134507403	48	26956										
TRIM34	53840	hgsc.bcm.edu	37	chr11	5653572	5653572	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	aagcagtgcaatggcttcaaAaatcttgcttaacgtacaag	8	8	2	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr11:5653572A>G	ENST00000514226.1	+	2	348	c.11A>G	c.(10-12)aAa>aGa	p.K4R	TRIM34_ENST00000429814.2_Missense_Mutation_p.K4R|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Missense_Mutation_p.K358R|TRIM6-TRIM34_ENST00000457787.2_Missense_Mutation_p.K4R	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	4					positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.K4T(1)|p.K358T(1)		NS(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	17		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;5.72e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGGCTTCAAAAATCTTGCTT	0.527											OREG0003725	type=REGULATORY REGION|Gene=TRIM34|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.K358R		Atlas-SNP	.											TRIM6-TRIM34,NS,carcinoma,0,2	TRIM6-TRIM34	68	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1073G						.						124	111	116					11																	5653572		2201	4297	6498	SO:0001583	missense	445372	exon8			CTTCAAAAATCTT	AB039902	CCDS31391.1	11p15	2013-01-09	2011-01-25	2001-11-23		ENSG00000258659		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10063	protein-coding gene	gene with protein product		605684	"tripartite motif-containing 34"	RNF21			Standard	NM_130390		Approved			Q9BYJ4	OTTHUMG00000066892	ENST00000514226.1:c.11A>G	chr11.hg19:g.5653572A>G	ENSP00000422947:p.Lys4Arg	135.0	0.0	628	128.0	16.0	NM_001003819	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Missense_Mutation	SNP	ENST00000514226.1	hg19	CCDS31391.1	.	.	.	.	.	.	.	.	.	.	A	8.281	0.815570	0.16607	.	.	ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258588	ENST00000337072;ENST00000514226;ENST00000429814;ENST00000457787;ENST00000354852	D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83	3.07	-2.94	0.05581	Zinc finger, RING/FYVE/PHD-type (1);	1.851040	0.03314	N	0.190948	T	0.73860	0.3641	L	0.27975	0.815	0.09310	N	1	B;B;B	0.17465	0.002;0.022;0.012	B;B;B	0.20184	0.012;0.028;0.011	T	0.56372	-0.7990	10	0.40728	T	0.16	.	2.9257	0.05784	0.2305:0.5056:0.1085:0.1554	.	4;4;358	Q9BYJ4-2;Q9BYJ4;B2RNG4	.;TRI34_HUMAN;.	R	358;4;4;4;358	ENSP00000422947:K4R;ENSP00000402595:K4R;ENSP00000395982:K4R;ENSP00000346916:K358R	ENSP00000402595:K4R	K	+	2	0	TRIM34;TRIM6-TRIM34	5610148	0.000000	0.05858	0.000000	0.03702	0.259000	0.26198	-1.430000	0.02434	-0.595000	0.05828	-0.501000	0.04562	AAA	.	.		0.527	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2	NM_001003827		G	5653572	A	G	5653572	3	3	180	1	0	0	0	0	1	0	0	0	16523	14	1	2	13	2	TRIM34	11	5653572	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	5154459	5653572	129352944	49	26957										
ELP4	26610	hgsc.bcm.edu	37	chr11	31669307	31669307	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	agaataaagccattattgccCgtgtcacaaccttgtcagat	7	10	2	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr11:31669307C>T	ENST00000350638.5	+	8	981	c.946C>T	c.(946-948)Cgt>Tgt	p.R316C	ELP4_ENST00000395934.2_Missense_Mutation_p.R316C|ELP4_ENST00000379163.5_Missense_Mutation_p.R317C|Z83001.1_ENST00000429821.1_RNA	NM_019040.3	NP_061913.3	Q96EB1	ELP4_HUMAN	elongator acetyltransferase complex subunit 4	316					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)			breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)	20	Lung SC(675;0.225)					CATTATTGCCCGTGTCACAAC	0.328																																					p.R316C		Atlas-SNP	.											.	ELP4	78	.	0			c.C946T						.						207	185	192					11																	31669307		1841	4084	5925	SO:0001583	missense	26610	exon8			ATTGCCCGTGTCA	AJ276005	CCDS7875.2, CCDS73271.1, CCDS73272.1	11p13	2012-08-14	2012-08-08	2002-05-24	ENSG00000109911	ENSG00000109911		"Elongator acetyltransferase complex subunits"	1171	protein-coding gene	gene with protein product		606985	"chromosome 11 open reading frame 19", "elongation protein 4 homolog (S. cerevisiae)"	C11orf19		11889558, 11435442	Standard	XM_005252865		Approved	PAXNEB	uc001mtb.3	Q96EB1	OTTHUMG00000142919	ENST00000350638.5:c.946C>T	chr11.hg19:g.31669307C>T	ENSP00000298937:p.Arg316Cys	182.0	0.0		143.0	40.0	NM_019040	B4E3W0|E7EPZ6|Q9H4E8|Q9NX11	Missense_Mutation	SNP	ENST00000350638.5	hg19	CCDS7875.2	.	.	.	.	.	.	.	.	.	.	C	22.7	4.325658	0.81580	.	.	ENSG00000109911	ENST00000350638;ENST00000379163;ENST00000395934	T;T;T	0.46451	0.87;0.87;0.87	5.92	5.92	0.95590	.	0.170242	0.56097	D	0.000032	T	0.70631	0.3246	M	0.87682	2.9	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.68943	0.937;0.961;0.913	T	0.72587	-0.4248	10	0.52906	T	0.07	-5.7156	20.3172	0.98658	0.0:1.0:0.0:0.0	.	317;316;316	B4E3W0;G5E9D4;Q96EB1	.;.;ELP4_HUMAN	C	316;317;316	ENSP00000298937:R316C;ENSP00000368461:R317C;ENSP00000379267:R316C	ENSP00000298937:R316C	R	+	1	0	ELP4	31625883	1.000000	0.71417	0.998000	0.56505	0.790000	0.44656	4.704000	0.61831	2.801000	0.96364	0.650000	0.86243	CGT	.	.		0.328	ELP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286640.1	NM_019040		T	31669307	C	T	31669307	3	4	180	1	0	0	0	0	1	0	0	0	5084	652	23	1	976	1	ELP4	11	31669307	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	26015735	31669307	103337209	50	26958										
OR4A5	81318	hgsc.bcm.edu	37	chr11	51411980	51411980	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ccaccaccaacagaaggaagCaaacctgtcgattcatgatg	8	12	1	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr11:51411980C>A	ENST00000319760.6	-	1	468	c.416G>T	c.(415-417)tGc>tTc	p.C139F		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	139						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				CAGAAGGAAGCAAACCTGTCG	0.483																																					p.C139F		Atlas-SNP	.											.	OR4A5	116	.	0			c.G416T						.						83	78	80					11																	51411980		2201	4296	6497	SO:0001583	missense	81318	exon1			AGGAAGCAAACCT	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"GPCR / Class A : Olfactory receptors"	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.416G>T	chr11.hg19:g.51411980C>A	ENSP00000367664:p.Cys139Phe	145.0	0.0		147.0	6.0	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	hg19	CCDS31497.1	.	.	.	.	.	.	.	.	.	.	.	7.792	0.711705	0.15306	.	.	ENSG00000221840	ENST00000319760	T	0.00220	8.52	1.93	1.93	0.25924	GPCR, rhodopsin-like superfamily (1);	0.124345	0.36854	N	0.002373	T	0.00580	0.0019	M	0.93016	3.37	0.09310	N	1	P	0.48911	0.917	P	0.61132	0.884	T	0.11792	-1.0573	10	0.87932	D	0	.	9.9079	0.41388	0.0:1.0:0.0:0.0	.	139	Q8NH83	OR4A5_HUMAN	F	139	ENSP00000367664:C139F	ENSP00000367664:C139F	C	-	2	0	OR4A5	51268556	0.850000	0.29656	0.030000	0.17652	0.132000	0.20833	1.712000	0.37940	1.394000	0.46624	0.162000	0.16502	TGC	.	.		0.483	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		A	51411980	C	A	51411980	3	1	180	1	0	0	0	0	1	0	0	0	11052	710	25	3	535	3	OR4A5	11	51411980	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	19742673	51411980	83594536	51	26959										
CCDC89	220388	hgsc.bcm.edu	37	chr11	85396947	85396947	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tccgcttcaggatgcagatgAgctgggactgctcttcaatg	12	10	3	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr11:85396947A>G	ENST00000316398.3	-	1	373	c.227T>C	c.(226-228)cTc>cCc	p.L76P	CREBZF_ENST00000534224.1_5'Flank	NM_152723.1	NP_689936.1	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89	76						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	15		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GATGCAGATGAGCTGGGACTG	0.592																																					p.L76P		Atlas-SNP	.											.	CCDC89	45	.	0			c.T227C						.						66	58	60					11																	85396947		2203	4299	6502	SO:0001583	missense	220388	exon1			CAGATGAGCTGGG	AK095478	CCDS8270.1	11q14.1	2006-03-16			ENSG00000179071	ENSG00000179071			26762	protein-coding gene	gene with protein product						12477932	Standard	NM_152723		Approved	FLJ38159	uc001pau.1	Q8N998	OTTHUMG00000166976	ENST00000316398.3:c.227T>C	chr11.hg19:g.85396947A>G	ENSP00000320649:p.Leu76Pro	57.0	0.0		62.0	19.0	NM_152723		Missense_Mutation	SNP	ENST00000316398.3	hg19	CCDS8270.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.352444	0.82132	.	.	ENSG00000179071	ENST00000316398	.	.	.	5.91	5.91	0.95273	.	0.000000	0.64402	U	0.000003	T	0.79782	0.4505	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80717	-0.1258	8	.	.	.	-5.6455	16.3436	0.83110	1.0:0.0:0.0:0.0	.	76	Q8N998	CCD89_HUMAN	P	76	.	.	L	-	2	0	CCDC89	85074595	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.345000	0.72995	2.269000	0.75478	0.533000	0.62120	CTC	.	.		0.592	CCDC89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392182.1	NM_152723		G	85396947	A	G	85396947	3	3	180	1	0	0	0	0	1	0	0	0	2868	304	11	2	901	2	CCDC89	11	85396947	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	33984967	85396947	49609569	52	26960										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105775994	105775994	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	agagtcaattacacaatggaTgtgtttgagctgaaaagcac	10	6	1	3			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr11:105775994T>G	ENST00000530497.1	+	8	1125	c.1125T>G	c.(1123-1125)gaT>gaG	p.D375E	GRIA4_ENST00000525187.1_Missense_Mutation_p.D375E|GRIA4_ENST00000428631.2_Missense_Mutation_p.D375E|GRIA4_ENST00000282499.5_Missense_Mutation_p.D375E|GRIA4_ENST00000393125.2_Missense_Mutation_p.D375E|GRIA4_ENST00000393127.2_Missense_Mutation_p.D375E			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	375					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		ACACAATGGATGTGTTTGAGC	0.393																																					p.D375E		Atlas-SNP	.											.	GRIA4	380	.	0			c.T1125G						.						134	124	127					11																	105775994		2202	4299	6501	SO:0001583	missense	2893	exon9			AATGGATGTGTTT	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1125T>G	chr11.hg19:g.105775994T>G	ENSP00000435775:p.Asp375Glu	96.0	0.0		90.0	32.0	NM_001077244	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	t	20.9	4.069272	0.76301	.	.	ENSG00000152578	ENST00000393125;ENST00000282499;ENST00000393127;ENST00000428631;ENST00000530497;ENST00000525187	D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	5.75	5.75	0.90469	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.84374	0.5458	L	0.46157	1.445	0.58432	D	0.999993	B;B;B	0.34147	0.024;0.438;0.058	B;P;B	0.49140	0.101;0.601;0.197	D	0.85118	0.0967	10	0.87932	D	0	.	16.3663	0.83325	0.0:0.0:0.0:1.0	.	375;375;375	P48058;G3V164;Q86XE8	GRIA4_HUMAN;.;.	E	375	ENSP00000376833:D375E;ENSP00000282499:D375E;ENSP00000376835:D375E;ENSP00000415551:D375E;ENSP00000435775:D375E;ENSP00000432180:D375E	ENSP00000282499:D375E	D	+	3	2	GRIA4	105281204	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.799000	0.27028	2.320000	0.78422	0.524000	0.50904	GAT	.	.		0.393	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			G	105775994	T	G	105775994	3	3	180	1	0	0	0	0	1	0	0	0	6779	1461	51	5	1155	5	GRIA4	11	105775994	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10	20379047	105775994	29230522	53	26961										
ATN1	1822	hgsc.bcm.edu	37	chr12	7045873	7045873	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ccagtctcaacacatcaccaTcaccaccagcaacagcaaca	3	18	3	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr12:7045873T>C	ENST00000356654.4	+	5	1680	c.1443T>C	c.(1441-1443)caT>caC	p.H481H	ATN1_ENST00000396684.2_Silent_p.H481H	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	481	Poly-His.				cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						CACATCACCATCACCACcagc	0.627																																					p.H481H		Atlas-SNP	.											.	ATN1	95	.	0			c.T1443C						.						97	109	104					12																	7045873		2203	4300	6503	SO:0001819	synonymous_variant	1822	exon5			TCACCATCACCAC	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"dentatorubral-pallidoluysian atrophy (atrophin-1)"	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.1443T>C	chr12.hg19:g.7045873T>C		99.0	0.0		100.0	7.0	NM_001007026	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	hg19	CCDS31734.1																																																																																			.	.		0.627	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		C	7045873	T	C	7045873	2	2	180	1	0	0	0	0	0	0	0	1	1111	1432	50	2		2	ATN1	12	7045873	Silent	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10		7045873	126806022	54	26962										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20799827	20799827	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tatgtggctgcagccatgcaCgattatgatcatccaggaag	11	9	1	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr12:20799827C>A	ENST00000359062.3	+	12	2548	c.2508C>A	c.(2506-2508)caC>caA	p.H836Q	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	836	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	CAGCCATGCACGATTATGATC	0.413																																					p.H836Q		Atlas-SNP	.											PDE3A,NS,lymphoid_neoplasm,0,1	PDE3A	184	.	0			c.C2508A						.						165	154	158					12																	20799827		2203	4300	6503	SO:0001583	missense	5139	exon12			CATGCACGATTAT		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.2508C>A	chr12.hg19:g.20799827C>A	ENSP00000351957:p.His836Gln	188.0	0.0		167.0	50.0	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.689716	0.68271	.	.	ENSG00000172572	ENST00000359062	D	0.90732	-2.72	5.85	-4.11	0.03928	Metal-dependent phosphohydrolase, HD domain (1);-cyclic nucleotide phosphodiesterase, conserved site (1);5&apos (3);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (3);	0.192308	0.56097	D	0.000033	D	0.96595	0.8889	H	0.99058	4.415	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.95902	0.8916	10	0.87932	D	0	.	14.0685	0.64847	0.0:0.5746:0.0:0.4254	.	836	Q14432	PDE3A_HUMAN	Q	836	ENSP00000351957:H836Q	ENSP00000351957:H836Q	H	+	3	2	PDE3A	20691094	0.365000	0.25006	0.972000	0.41901	0.971000	0.66376	-0.348000	0.07740	-0.414000	0.07495	-1.552000	0.00895	CAC	.	.		0.413	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			A	20799827	C	A	20799827	3	1	180	1	0	0	0	0	1	0	0	0	11646	535	19	1	2554	1	PDE3A	12	20799827	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	13753954	20799827	113052068	55	26963										
ALG10B	144245	hgsc.bcm.edu	37	chr12	38714365	38714365	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tctgtttgacttggccctacAtccttctgggatttctgttt	8	10	3	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr12:38714365A>G	ENST00000308742.4	+	3	1088	c.772A>G	c.(772-774)Atc>Gtc	p.I258V	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	258					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				TTGGCCCTACATCCTTCTGGG	0.378																																					p.I258V		Atlas-SNP	.											.	ALG10B	58	.	0			c.A772G						.						248	249	249					12																	38714365		2203	4300	6503	SO:0001583	missense	144245	exon3			CCCTACATCCTTC	AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"		"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.772A>G	chr12.hg19:g.38714365A>G	ENSP00000310120:p.Ile258Val	187.0	0.0		134.0	42.0	NM_001013620	B2RPF4	Missense_Mutation	SNP	ENST00000308742.4	hg19	CCDS31772.1	.	.	.	.	.	.	.	.	.	.	a	0.048	-1.259056	0.01445	.	.	ENSG00000175548	ENST00000308742	T	0.56103	0.48	3.23	-2.39	0.06602	.	0.522394	0.21702	N	0.070419	T	0.28995	0.0720	L	0.28556	0.865	0.34075	D	0.658954	B	0.02656	0.0	B	0.09377	0.004	T	0.17440	-1.0369	10	0.14656	T	0.56	.	4.6475	0.12579	0.4902:0.1661:0.3438:0.0	.	258	Q5I7T1	AG10B_HUMAN	V	258	ENSP00000310120:I258V	ENSP00000310120:I258V	I	+	1	0	ALG10B	37000632	0.236000	0.23804	0.061000	0.19648	0.232000	0.25224	1.497000	0.35649	-0.481000	0.06792	-0.263000	0.10527	ATC	.	.		0.378	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620		G	38714365	A	G	38714365	3	3	180	1	0	0	0	0	1	0	0	0	512	217	8	2	782	2	ALG10B	12	38714365	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	17914538	38714365	95137530	56	26964										
OR9K2	441639	hgsc.bcm.edu	37	chr12	55523606	55523606	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	attttgccctgtgcctctcaAcaggtttctaccatgggtga	9	11	2	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr12:55523606A>G	ENST00000305377.5	+	1	142	c.54A>G	c.(52-54)caA>caG	p.Q18Q		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q18Q(1)		NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						GTGCCTCTCAACAGGTTTCTA	0.413																																					p.Q18Q		Atlas-SNP	.											OR9K2,NS,carcinoma,0,1	OR9K2	63	.	1	Substitution - coding silent(1)	kidney(1)	c.A54G						.						144	144	144					12																	55523606		2203	4300	6503	SO:0001819	synonymous_variant	441639	exon1			CTCTCAACAGGTT	BK004326	CCDS31814.1	12q13.2	2012-08-09						"GPCR / Class A : Olfactory receptors"	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.54A>G	chr12.hg19:g.55523606A>G		105.0	0.0		98.0	12.0	NM_001005243	B9EH19|Q6IFD6	Silent	SNP	ENST00000305377.5	hg19	CCDS31814.1																																																																																			.	.		0.413	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1			G	55523606	A	G	55523606	2	3	180	1	0	0	0	0	0	0	0	1	11263	40	2	2		2	OR9K2	12	55523606	Silent	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	16809241	55523606	78328289	57	26965										
STAT6	6778	hgsc.bcm.edu	37	chr12	57499293	57499293	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cttcatccagccggccagtcAgcgatgcccgggtcttgggc	13	15	3	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr12:57499293A>T	ENST00000300134.3	-	8	1095	c.770T>A	c.(769-771)cTg>cAg	p.L257Q	STAT6_ENST00000538913.2_Missense_Mutation_p.L147Q|STAT6_ENST00000537215.2_Missense_Mutation_p.L147Q|STAT6_ENST00000454075.3_Missense_Mutation_p.L257Q|STAT6_ENST00000543873.2_Missense_Mutation_p.L257Q|STAT6_ENST00000556155.1_Missense_Mutation_p.L257Q	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	257					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						CCGGCCAGTCAGCGATGCCCG	0.617																																					p.L257Q		Atlas-SNP	.											.	STAT6	69	.	0			c.T770A						.						49	53	52					12																	57499293		2203	4300	6503	SO:0001583	missense	6778	exon8			CCAGTCAGCGATG	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"SH2 domain containing"	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.770T>A	chr12.hg19:g.57499293A>T	ENSP00000300134:p.Leu257Gln	111.0	0.0		90.0	28.0	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	hg19	CCDS8931.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.391459	0.42410	.	.	ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516	T;T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43;-0.43	5.19	5.19	0.71726	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.256439	0.31495	N	0.007560	T	0.75391	0.3843	L	0.56199	1.76	0.58432	D	0.999995	P;P	0.51537	0.933;0.946	P;D	0.64042	0.853;0.921	T	0.77643	-0.2511	10	0.87932	D	0	-4.7184	11.355	0.49611	1.0:0.0:0.0:0.0	.	257;257	A8K4S9;P42226	.;STAT6_HUMAN	Q	257;147;147;257;257;147;257;147;257	ENSP00000300134:L257Q;ENSP00000445409:L147Q;ENSP00000438451:L257Q;ENSP00000451742:L257Q;ENSP00000444530:L147Q;ENSP00000401486:L257Q	ENSP00000300134:L257Q	L	-	2	0	STAT6	55785560	0.683000	0.27633	0.133000	0.22050	0.028000	0.11728	4.007000	0.57093	2.188000	0.69820	0.533000	0.62120	CTG	.	.		0.617	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		T	57499293	A	T	57499293	3	4	180	1	0	0	0	0	1	0	0	0	15285	188	7	4	1833	4	STAT6	12	57499293	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	1975687	57499293	76352602	58	26966										
ANO4	121601	hgsc.bcm.edu	37	chr12	101381339	101381339	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	tcgataaacaaataagcaggTttcggagatggttacctaag	10	6	0	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr12:101381339T>C	ENST00000392977.3	+	8	835	c.625T>C	c.(625-627)Ttt>Ctt	p.F209L	ANO4_ENST00000538618.1_3'UTR|ANO4_ENST00000299222.9_5'UTR|ANO4_ENST00000392979.3_Missense_Mutation_p.F174L			Q32M45	ANO4_HUMAN	anoctamin 4	209				F -> L (in Ref. 1; BAC03704). {ECO:0000305}.	chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						AATAAGCAGGTTTCGGAGATG	0.512										HNSCC(74;0.22)	OREG0022059	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F174L		Atlas-SNP	.											.	ANO4	183	.	0			c.T520C						.						303	295	298					12																	101381339		2203	4300	6503	SO:0001583	missense	121601	exon7			AGCAGGTTTCGGA	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.625T>C	chr12.hg19:g.101381339T>C	ENSP00000376703:p.Phe209Leu	108.0	0.0	1358	83.0	22.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	hg19		.	.	.	.	.	.	.	.	.	.	T	12.16	1.856062	0.32791	.	.	ENSG00000151572	ENST00000392979;ENST00000392977	T;T	0.67865	-0.28;-0.29	5.2	5.2	0.72013	.	0.074651	0.56097	D	0.000036	T	0.36524	0.0970	N	0.01219	-0.95	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.37361	-0.9709	10	0.10111	T	0.7	.	15.0946	0.72223	0.0:0.0:0.0:1.0	.	209;174	Q32M45;Q32M45-2	ANO4_HUMAN;.	L	174;209	ENSP00000376705:F174L;ENSP00000376703:F209L	ENSP00000376703:F209L	F	+	1	0	ANO4	99905470	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.914000	0.48797	1.966000	0.57179	0.460000	0.39030	TTT	.	.		0.512	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		C	101381339	T	C	101381339	3	2	180	1	0	0	0	0	1	0	0	0	699	1725	60	2	542	2	ANO4	12	101381339	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10	43882046	101381339	32470556	59	26967										
C14orf50	145376	hgsc.bcm.edu	37	chr14	65053933	65053933	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ccttttatactttctgtacaTatgtggcttggattgtcttc	7	8	2	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr14:65053933T>G	ENST00000298705.1	+	10	829	c.733T>G	c.(733-735)Tat>Gat	p.Y245D	RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	245					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TTTCTGTACATATGTGGCTTG	0.393																																					p.Y245D		Atlas-SNP	.											.	.	.	.	0			c.T733G						.						136	129	131					14																	65053933		2203	4300	6503	SO:0001583	missense	145376	exon10			TGTACATATGTGG		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20097	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 50"	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.733T>G	chr14.hg19:g.65053933T>G	ENSP00000298705:p.Tyr245Asp	186.0	0.0		162.0	52.0	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	hg19	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	T	13.26	2.184110	0.38609	.	.	ENSG00000165807	ENST00000298705	T	0.29142	1.58	5.55	3.19	0.36642	.	0.309581	0.28301	N	0.015849	T	0.47691	0.1459	M	0.69823	2.125	0.09310	N	1	D	0.67145	0.996	D	0.65874	0.939	T	0.34576	-0.9823	10	0.66056	D	0.02	-3.5713	7.2838	0.26326	0.0:0.175:0.0:0.825	.	245	Q96LQ0	PPR36_HUMAN	D	245	ENSP00000298705:Y245D	ENSP00000298705:Y245D	Y	+	1	0	C14orf50	64123686	0.064000	0.20934	0.001000	0.08648	0.641000	0.38312	1.727000	0.38095	0.391000	0.25143	0.533000	0.62120	TAT	.	.		0.393	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		G	65053933	T	G	65053933	3	3	180	1	0	0	0	0	1	0	0	0	1779	1406	49	5	771	5	C14orf50	14	65053933	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10		65053933	42295607	60	26968										
SPTB	6710	hgsc.bcm.edu	37	chr14	65252487	65252487	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ctgtcctcaatcagctgcacCttctccttgatcttgtctga	6	14	5	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr14:65252487C>G	ENST00000389721.5	-	16	3776	c.3744G>C	c.(3742-3744)aaG>aaC	p.K1248N	SPTB_ENST00000556626.1_Missense_Mutation_p.K1248N|SPTB_ENST00000542895.1_Missense_Mutation_p.K1248N|SPTB_ENST00000389720.3_Missense_Mutation_p.K1248N|SPTB_ENST00000389722.3_Missense_Mutation_p.K1248N	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1248					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		TCAGCTGCACCTTCTCCTTGA	0.577																																					p.K1248N		Atlas-SNP	.											SPTB_ENST00000542895,caecum,carcinoma,0,2	SPTB	378	.	0			c.G3744C						.						170	172	171					14																	65252487		2203	4300	6503	SO:0001583	missense	6710	exon16			CTGCACCTTCTCC		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.3744G>C	chr14.hg19:g.65252487C>G	ENSP00000374371:p.Lys1248Asn	70.0	0.0		74.0	24.0	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.412933	0.62511	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52	4.94	2.07	0.26955	.	0.000000	0.85682	D	0.000000	T	0.69833	0.3155	M	0.82716	2.605	0.54753	D	0.999989	D;D	0.76494	0.999;0.999	D;D	0.79784	0.993;0.988	T	0.71013	-0.4715	10	0.87932	D	0	.	8.8825	0.35382	0.0:0.6701:0.0:0.3299	.	1248;1252	P11277;Q59FP5	SPTB1_HUMAN;.	N	1252;1248;32;1248;1248;1248;1248	ENSP00000374372:K1248N;ENSP00000451752:K1248N;ENSP00000374371:K1248N;ENSP00000443882:K1248N;ENSP00000374370:K1248N	ENSP00000334218:K32N	K	-	3	2	SPTB	64322240	0.014000	0.17966	1.000000	0.80357	0.990000	0.78478	-0.040000	0.12104	0.607000	0.29982	-0.284000	0.09977	AAG	.	.		0.577	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			G	65252487	C	G	65252487	3	3	180	1	0	0	0	0	1	0	0	0	15133	680	24	4	3391	4	SPTB	14	65252487	Missense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	198554	65252487	42097053	61	26969										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54307145	54307145	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ttttgattatgaaacaaacaGtctttttgaccaacagcttg	6	7	1	3			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr15:54307145G>C	ENST00000260323.11	+	1	2045	c.2045G>C	c.(2044-2046)aGt>aCt	p.S682T	UNC13C_ENST00000537900.1_Missense_Mutation_p.S682T|UNC13C_ENST00000545554.1_Missense_Mutation_p.S682T	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	682					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GAAACAAACAGTCTTTTTGAC	0.398																																					p.S682T		Atlas-SNP	.											.	UNC13C	674	.	0			c.G2045C						.						78	74	75					15																	54307145		1855	4109	5964	SO:0001583	missense	440279	exon1			CAAACAGTCTTTT	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.2045G>C	chr15.hg19:g.54307145G>C	ENSP00000260323:p.Ser682Thr	187.0	0.0		170.0	51.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	7.691	0.691012	0.15039	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;T;T	0.81499	-1.5;-1.49;-1.49	5.18	5.18	0.71444	.	.	.	.	.	T	0.69342	0.3100	N	0.19112	0.55	0.34691	D	0.725698	P	0.38922	0.651	B	0.32677	0.15	T	0.79640	-0.1719	9	0.66056	D	0.02	.	17.8526	0.88751	0.0:0.0:1.0:0.0	.	682	Q8NB66	UN13C_HUMAN	T	682	ENSP00000260323:S682T;ENSP00000438156:S682T;ENSP00000442569:S682T	ENSP00000260323:S682T	S	+	2	0	UNC13C	52094437	1.000000	0.71417	0.763000	0.31416	0.111000	0.19643	7.396000	0.79891	2.695000	0.91970	0.650000	0.86243	AGT	.	.		0.398	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		C	54307145	G	C	54307145	3	2	180	1	0	0	0	0	1	0	0	0	17001	1029	36	4	2047	4	UNC13C	15	54307145	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10		54307145	48224247	62	26970										
NARG2	79664	hgsc.bcm.edu	37	chr15	60715904	60715904	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	agcaggcaagcaactgctttTggtttccatggaaactggat	11	8	0	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr15:60715904T>C	ENST00000261520.4	-	16	3112	c.2878A>G	c.(2878-2880)Aaa>Gaa	p.K960E	NARG2_ENST00000439632.1_Missense_Mutation_p.K823E	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						CAACTGCTTTTGGTTTCCATG	0.408																																					p.K960E		Atlas-SNP	.											.	NARG2	82	.	0			c.A2878G						.						84	71	76					15																	60715904		2203	4300	6503	SO:0001583	missense	79664	exon16			TGCTTTTGGTTTC																												ENST00000261520.4:c.2878A>G	chr15.hg19:g.60715904T>C	ENSP00000261520:p.Lys960Glu	209.0	0.0		164.0	53.0	NM_024611		Missense_Mutation	SNP	ENST00000261520.4	hg19	CCDS10176.1	.	.	.	.	.	.	.	.	.	.	T	16.00	2.999380	0.54147	.	.	ENSG00000128915	ENST00000261520;ENST00000439632	.	.	.	5.44	3.09	0.35607	.	0.356614	0.27253	N	0.020217	T	0.26521	0.0648	L	0.27053	0.805	0.27860	N	0.940436	B	0.26635	0.155	B	0.24155	0.051	T	0.17837	-1.0356	9	0.62326	D	0.03	-11.1147	6.0424	0.19742	0.1456:0.0777:0.0:0.7767	.	960	Q659A1	NARG2_HUMAN	E	960;823	.	ENSP00000261520:K960E	K	-	1	0	NARG2	58503196	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.664000	0.25068	1.011000	0.39340	-0.355000	0.07637	AAA	.	.		0.408	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			C	60715904	T	C	60715904	3	2	180	1	0	0	0	0	1	0	0	0	10178	1821	63	2	74	2	NARG2	15	60715904	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10	6408759	60715904	41815488	63	26971										
IL16	3603	hgsc.bcm.edu	37	chr15	81517759	81517759	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ggatggagtcgcacagccgcGctggaaagagcagaaaatct	14	9	1	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr15:81517759G>T	ENST00000302987.4	+	1	19	c.19G>T	c.(19-21)Gct>Tct	p.A7S	IL16_ENST00000394660.2_Missense_Mutation_p.A7S			Q14005	IL16_HUMAN	interleukin 16	7					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GCACAGCCGCGCTGGAAAGAG	0.532																																					p.A7S		Atlas-SNP	.											.	IL16	254	.	0			c.G19T						.						52	55	54					15																	81517759		2046	4196	6242	SO:0001583	missense	3603	exon2			AGCCGCGCTGGAA	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.19G>T	chr15.hg19:g.81517759G>T	ENSP00000302935:p.Ala7Ser	47.0	0.0		57.0	4.0	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.362630	0.00016	.	.	ENSG00000172349	ENST00000394655;ENST00000360547;ENST00000394660;ENST00000302987	T;T	0.18174	2.24;2.23	4.18	-8.36	0.00980	.	1.169440	0.06778	N	0.784710	T	0.04543	0.0124	N	0.02539	-0.55	0.29514	N	0.853986	B;B	0.10296	0.002;0.003	B;B	0.09377	0.002;0.004	T	0.33343	-0.9872	10	0.15066	T	0.55	.	5.4671	0.16650	0.2005:0.1223:0.4968:0.1804	.	7;7	Q14005;Q14005-2	IL16_HUMAN;.	S	7;49;7;7	ENSP00000378155:A7S;ENSP00000302935:A7S	ENSP00000302935:A7S	A	+	1	0	IL16	79304814	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.107000	0.03316	-2.578000	0.00464	-2.737000	0.00128	GCT	.	.		0.532	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		T	81517759	G	T	81517759	3	4	180	1	0	0	0	0	1	0	0	0	7642	1087	38	1	21	1	IL16	15	81517759	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	20801855	81517759	21013633	64	26972										
HBA1	3039	hgsc.bcm.edu	37	chr16	227353	227353	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ttcacccctgcggtgcacgcCtccctggacaagttcctggc	10	17	1	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr16:227353C>T	ENST00000320868.5	+	3	409	c.372C>T	c.(370-372)gcC>gcT	p.A124A	Y_RNA_ENST00000384514.1_RNA|HBA1_ENST00000397797.1_Silent_p.A92A	NM_000558.3	NP_000549.1	P69905	HBA_HUMAN	hemoglobin, alpha 1	124					bicarbonate transport (GO:0015701)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|positive regulation of cell death (GO:0010942)|protein heterooligomerization (GO:0051291)|response to hydrogen peroxide (GO:0042542)|small molecule metabolic process (GO:0044281)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)|hemoglobin complex (GO:0005833)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			lung(1)	1		all_cancers(16;2.03e-06)|all_epithelial(16;5.16e-06)|Hepatocellular(16;0.000325)|Lung NSC(18;0.0138)|all_lung(18;0.0306)			Iron Dextran(DB00893)|Mefloquine(DB00358)	CGGTGCACGCCTCCCTGGACA	0.652											OREG0003687	type=REGULATORY REGION|Gene=SERPINB9|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.A124A		Atlas-SNP	.											.	HBA1	2	.	0			c.C372T						.						46	40	42					16																	227353		2202	4295	6497	SO:0001819	synonymous_variant	3039	exon3			GCACGCCTCCCTG	AF349571	CCDS10399.1	16p13.3	2014-05-19			ENSG00000206172	ENSG00000206172			4823	protein-coding gene	gene with protein product		141800				1975428, 2649166	Standard	NM_000558		Approved	HBA-T3	uc002cfx.1	P69905	OTTHUMG00000060138	ENST00000320868.5:c.372C>T	chr16.hg19:g.227353C>T		305.0	0.0	586	258.0	17.0	NM_000558	P01922|Q1HDT5|Q3MIF5|Q53F97|Q96KF1|Q9NYR7|Q9UCM0	Silent	SNP	ENST00000320868.5	hg19	CCDS10399.1																																																																																			.	.		0.652	HBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133459.1	NM_000558		T	227353	C	T	227353	2	4	180	1	0	0	0	0	0	0	0	1	6985	668	24	3		3	HBA1	16	227353	Silent	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10		227353	90127400	65	26973										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30720956	30720956	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cttctgtctcagagcctcaaCcagccattaacctccagcaa	5	16	3	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr16:30720956C>T	ENST00000262518.4	+	7	1141	c.756C>T	c.(754-756)aaC>aaT	p.N252N	SNORA30_ENST00000384028.1_RNA|SRCAP_ENST00000395059.2_Silent_p.N252N|SRCAP_ENST00000344771.4_Silent_p.N252N	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	252					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AGAGCCTCAACCAGCCATTAA	0.557																																					p.N252N		Atlas-SNP	.											.	SRCAP	298	.	0			c.C756T						.						105	96	99					16																	30720956		2197	4300	6497	SO:0001819	synonymous_variant	10847	exon7			CCTCAACCAGCCA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.756C>T	chr16.hg19:g.30720956C>T		147.0	0.0		152.0	45.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.		0.557	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30720956	C	T	30720956	2	4	180	1	0	0	0	0	0	0	0	1	15150	506	18	3		3	SRCAP	16	30720956	Silent	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	30493603	30720956	59633797	66	26974										
SNTB2	6645	hgsc.bcm.edu	37	chr16	69333647	69333647	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gatggcatccgaaatctataCttggattttggtggtcccga	11	8	1	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr16:69333647C>A	ENST00000336278.4	+	6	1538	c.1500C>A	c.(1498-1500)taC>taA	p.Y500*	RP11-343C2.11_ENST00000570054.2_Nonsense_Mutation_p.Y21*	NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)	500	SU.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|microtubule (GO:0005874)|protein complex (GO:0043234)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		GAAATCTATACTTGGATTTTG	0.438																																					p.Y500X	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-SNP	.											.	SNTB2	22	.	0			c.C1500A						.						88	82	84					16																	69333647		2198	4300	6498	SO:0001587	stop_gained	6645	exon6			TCTATACTTGGAT	U40572	CCDS10873.1	16q22.1	2008-05-14	2002-08-29		ENSG00000168807	ENSG00000168807			11169	protein-coding gene	gene with protein product		600027	"syntrophin, beta 2 (dystrophin-associated protein A1, 59kD, basic component 2)"	SNT2B2, SNTL, D16S2531E		8576247, 8183929	Standard	NM_006750		Approved	EST25263, SNT3	uc002ewu.3	Q13425	OTTHUMG00000137567	ENST00000336278.4:c.1500C>A	chr16.hg19:g.69333647C>A	ENSP00000338191:p.Tyr500*	190.0	0.0		128.0	56.0	NM_006750	Q9BY09	Nonsense_Mutation	SNP	ENST00000336278.4	hg19	CCDS10873.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.997319	0.93167	.	.	ENSG00000168807	ENST00000336278;ENST00000467311	.	.	.	5.5	-2.74	0.05932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.2163	13.2277	0.59924	0.0:0.5131:0.0:0.4869	.	.	.	.	X	500;151	.	ENSP00000338191:Y500X	Y	+	3	2	SNTB2	67891148	0.959000	0.32827	0.633000	0.29310	0.798000	0.45092	0.558000	0.23469	-0.344000	0.08338	-0.251000	0.11542	TAC	.	.		0.438	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1			A	69333647	C	A	69333647	4	1	180	1	0	0	0	0	0	1	0	0	14888	576	20	3	1522	3	SNTB2	16	69333647	Nonsense_Mutation	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	38612691	69333647	21021106	67	26975										
ADAD2	161931	hgsc.bcm.edu	37	chr16	84228974	84228974	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gggcaccggcagcagctgctGtgctggctggctggagttct	17	11	1	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr16:84228974G>A	ENST00000315906.5	+	5	858	c.806G>A	c.(805-807)tGt>tAt	p.C269Y	RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.C351Y|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	269	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						AGCAGCTGCTGTGCTGGCTGG	0.692																																					p.C351Y		Atlas-SNP	.											.	ADAD2	46	.	0			c.G1052A						.						11	13	13					16																	84228974		2113	4153	6266	SO:0001583	missense	161931	exon6			GCTGCTGTGCTGG	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.806G>A	chr16.hg19:g.84228974G>A	ENSP00000325153:p.Cys269Tyr	102.0	0.0		63.0	32.0	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	hg19	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	G	10.12	1.262808	0.23051	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	D;D	0.93189	-3.18;-3.18	5.05	3.85	0.44370	Adenosine deaminase/editase (2);	0.254378	0.39615	N	0.001317	D	0.86977	0.6063	L	0.29908	0.895	0.39603	D	0.969763	B;B	0.22851	0.076;0.043	B;B	0.25884	0.064;0.038	D	0.83693	0.0178	10	0.54805	T	0.06	-16.3644	6.3636	0.21443	0.1627:0.0:0.8373:0.0	.	269;351	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	Y	269;351	ENSP00000325153:C269Y;ENSP00000268624:C351Y	ENSP00000268624:C351Y	C	+	2	0	ADAD2	82786475	0.597000	0.26874	0.950000	0.38849	0.466000	0.32739	0.744000	0.26245	2.500000	0.84329	0.650000	0.86243	TGT	.	.		0.692	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		A	84228974	G	A	84228974	3	1	180	1	0	0	0	0	1	0	0	0	232	1377	48	3	1074	3	ADAD2	16	84228974	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10	14895327	84228974	6125779	68	26976										
TP53	7157	hgsc.bcm.edu	37	chr17	7577126	7577126	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gacaggcacaaacacgcaccTcaaagctgttccgtcccagt	8	15	1	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr17:7577126T>A	ENST00000269305.4	-	8	1001	c.812A>T	c.(811-813)gAg>gTg	p.E271V	TP53_ENST00000359597.4_Missense_Mutation_p.E271V|TP53_ENST00000455263.2_Missense_Mutation_p.E271V|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.E271V|TP53_ENST00000445888.2_Missense_Mutation_p.E271V	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	271	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|E -> P (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation).|E -> R (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> V (in an osteosarcoma with no family history; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.E271V(6)|p.E271G(3)|p.?(2)|p.E271fs*74(2)|p.G266_E271delGRNSFE(2)|p.F270fs*72(1)|p.E271fs*73(1)|p.L265_K305del41(1)|p.E271P(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.E271del(1)|p.E271*(1)|p.S269fs*34(1)|p.F270_D281del12(1)|p.E271fs*34(1)|p.E271_R273delEVR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AACACGCACCTCAAAGCTGTT	0.532		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E271V	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,-1,1	TP53	33396	.	35	Substitution - Missense(10)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(6)|Unknown(2)|Substitution - Nonsense(1)	breast(5)|central_nervous_system(4)|urinary_tract(4)|bone(4)|upper_aerodigestive_tract(3)|large_intestine(3)|stomach(3)|haematopoietic_and_lymphoid_tissue(3)|oesophagus(2)|liver(2)|salivary_gland(1)|skin(1)	c.A812T	GRCh37	CM942136	TP53	M		.						60	52	55					17																	7577126		2203	4300	6503	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CGCACCTCAAAGC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.812A>T	chr17.hg19:g.7577126T>A	ENSP00000269305:p.Glu271Val	114.0	0.0		78.0	23.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.727540	0.89390	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99861	-7.26;-7.26;-7.26;-7.26;-7.26;-7.26	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99857	0.9933	M	0.88979	2.995	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.97110	0.999;0.992;0.999;1.0	D	0.96447	0.9331	10	0.87932	D	0	-38.0695	12.9367	0.58319	0.0:0.0:0.0:1.0	.	271;271;271;271	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	V	271;271;271;271;271;260;139	ENSP00000352610:E271V;ENSP00000269305:E271V;ENSP00000398846:E271V;ENSP00000391127:E271V;ENSP00000391478:E271V;ENSP00000425104:E139V	ENSP00000269305:E271V	E	-	2	0	TP53	7517851	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	7.802000	0.85969	2.154000	0.67381	0.379000	0.24179	GAG	.	.		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577126	T	A	7577126	3	1	180	1	0	0	0	0	1	0	0	0	16396	1551	54	4	474	4	TP53	17	7577126	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10		7577126	73618084	69	26977										
BRIP1	83990	hgsc.bcm.edu	37	chr17	59857746	59857746	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	caatggtctgaactttgccaTtaatatctgaaaaggcctaa	7	8	2	2			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr17:59857746T>C	ENST00000259008.2	-	13	2078	c.1811A>G	c.(1810-1812)aAt>aGt	p.N604S	BRIP1_ENST00000583837.1_5'Flank|BRIP1_ENST00000577598.1_Missense_Mutation_p.N604S	NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	604					DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						AACTTTGCCATTAATATCTGA	0.373			"F, N, Mis"			"AML, leukemia, breast"		Involved in tolerance or repair of DNA crosslinks																													p.N604S		Atlas-SNP	.	yes	Rec		"Fanconi anaemia J, breast cancer susceptiblity"	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"L, E"	.	BRIP1	237	.	0			c.A1811G						.						73	75	74					17																	59857746		2203	4300	6503	SO:0001583	missense	83990	exon13			TTGCCATTAATAT	AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492		"Fanconi anemia, complementation groups"	20473	protein-coding gene	gene with protein product	"BRCA1/BRCA2-associated helicase 1"	605882				11595410, 11301010	Standard	NM_032043		Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.1811A>G	chr17.hg19:g.59857746T>C	ENSP00000259008:p.Asn604Ser	324.0	0.0		259.0	84.0	NM_032043	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000259008.2	hg19	CCDS11631.1	.	.	.	.	.	.	.	.	.	.	T	9.665	1.145222	0.21288	.	.	ENSG00000136492	ENST00000259008	T	0.21191	2.02	5.6	4.49	0.54785	.	0.282155	0.43110	D	0.000602	T	0.07458	0.0188	N	0.02830	-0.485	0.37215	D	0.904985	B	0.14438	0.01	B	0.13407	0.009	T	0.27872	-1.0061	9	.	.	.	-12.2823	6.602	0.22705	0.0:0.2019:0.0:0.7981	.	604	Q9BX63	FANCJ_HUMAN	S	604	ENSP00000259008:N604S	.	N	-	2	0	BRIP1	57212528	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	2.009000	0.40903	2.127000	0.65507	0.533000	0.62120	AAT	.	.		0.373	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043		C	59857746	T	C	59857746	3	2	180	1	0	0	0	0	1	0	0	0	1516	1493	52	2	1970	2	BRIP1	17	59857746	Missense_Mutation	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10	52280620	59857746	21337464	70	26978										
SALL3	27164	hgsc.bcm.edu	37	chr18	76753069	76753069	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gtgcggcgcccggcctgccaAgtccgcttctacctcagact	11	17	2	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr18:76753069A>G	ENST00000537592.2	+	2	1078	c.1078A>G	c.(1078-1080)Agt>Ggt	p.S360G	SALL3_ENST00000536229.3_Missense_Mutation_p.S227G|SALL3_ENST00000575389.2_Missense_Mutation_p.S360G	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	360					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CGGCCTGCCAAGTCCGCTTCT	0.736																																					p.S360G		Atlas-SNP	.											.	SALL3	162	.	0			c.A1078G						.						11	13	12					18																	76753069		2164	4253	6417	SO:0001583	missense	27164	exon2			CTGCCAAGTCCGC	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.1078A>G	chr18.hg19:g.76753069A>G	ENSP00000441823:p.Ser360Gly	91.0	0.0		60.0	22.0	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	hg19	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	A	9.948	1.219310	0.22373	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.11277	2.79	4.37	4.37	0.52481	.	0.399043	0.22848	N	0.054888	T	0.08802	0.0218	N	0.21373	0.66	0.29757	N	0.835837	B	0.20261	0.043	B	0.22601	0.04	T	0.08806	-1.0704	10	0.33141	T	0.24	-23.0361	13.755	0.62930	1.0:0.0:0.0:0.0	.	360	Q9BXA9	SALL3_HUMAN	G	360;360;92	ENSP00000441823:S360G	ENSP00000299466:S360G	S	+	1	0	SALL3	74854057	1.000000	0.71417	0.793000	0.32043	0.011000	0.07611	4.806000	0.62569	1.841000	0.53522	0.377000	0.23210	AGT	.	.		0.736	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		G	76753069	A	G	76753069	3	3	180	1	0	0	0	0	1	0	0	0	13827	72	3	2	1084	2	SALL3	18	76753069	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10		76753069	1324179	71	26979										
MYO9B	4650	hgsc.bcm.edu	37	chr19	17322910	17322911	+	Frame_Shift_Del	DEL	GA	GA	-													0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gctgggcaccgggtgcccggGaggcggctgccccagtgcgg							TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr19:17322910_17322911delGA	ENST00000594824.1	+	40	6412_6413	c.6265_6266delGA	c.(6265-6267)gagfs	p.E2089fs	MYO9B_ENST00000397274.2_3'UTR|MYO9B_ENST00000595618.1_3'UTR			Q13459	MYO9B_HUMAN	myosin IXB	2089	Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						GGGTGCCCGGGAGGCGGCTGCC	0.728																																					p.2088_2089del		Atlas-INDEL	.											.	MYO9B	264	.	0			c.6264_6265del						.																																			SO:0001589	frameshift_variant	4650	exon40			.		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"Myosins / Myosin superfamily : Class IX"	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.6265_6266delGA	chr19.hg19:g.17322910_17322911delGA	ENSP00000471367:p.Glu2089fs	162.0	0.0		170.0	50.0	NM_004145	O75314|Q9NUJ2|Q9UHN0	Frame_Shift_Del	DEL	ENST00000594824.1	hg19																																																																																				.	.		0.728	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			-	17322911	GA	-	17322910	7	5	180	1	0	1	0	1	0	0	0	0	10094	1175	41	0	6430	0	MYO9B	19	17322910	Frame_Shift_Del	DEL	GA	TCGA-DD-AAD3-01A-11D-A40R-10		17322910	41806073	72	26980										
ARHGEF1	9138	hgsc.bcm.edu	37	chr19	42409114	42409114	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	cctgcagatcacaaagccttCtacgtcctttttacctggga	7	13	2	1			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr19:42409114C>T	ENST00000354532.3	+	23	2323	c.2175C>T	c.(2173-2175)ttC>ttT	p.F725F	ARHGEF1_ENST00000337665.4_Silent_p.F740F|ARHGEF1_ENST00000347545.4_Silent_p.F692F|ARHGEF1_ENST00000378152.4_Silent_p.F707F|ARHGEF1_ENST00000599846.1_Silent_p.F781F	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1	725	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		ACAAAGCCTTCTACGTCCTTT	0.597																																					p.F740F		Atlas-SNP	.											.	ARHGEF1	95	.	0			c.C2220T						.						62	58	59					19																	42409114		2203	4300	6503	SO:0001819	synonymous_variant	9138	exon23			AGCCTTCTACGTC	U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"Rho guanine nucleotide exchange factors"	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.2175C>T	chr19.hg19:g.42409114C>T		62.0	0.0		62.0	18.0	NM_199002	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Silent	SNP	ENST00000354532.3	hg19	CCDS12591.1																																																																																			.	.		0.597	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002		T	42409114	C	T	42409114	2	4	180	1	0	0	0	0	0	0	0	1	893	912	32	3		3	ARHGEF1	19	42409114	Silent	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10	25086204	42409114	16719869	73	26981										
KCNN4	3783	hgsc.bcm.edu	37	chr19	44273601	44273601	+	Frame_Shift_Del	DEL	T	T	-													0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	aagcggccctcacgcgttgaTggcggccagcagcttgcgct							TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr19:44273601delT	ENST00000262888.3	-	6	1437	c.1042delA	c.(1042-1044)atcfs	p.I348fs		NM_002250.2	NP_002241.1	O15554	KCNN4_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	348					calcium ion transport (GO:0006816)|cell volume homeostasis (GO:0006884)|defense response (GO:0006952)|immune system process (GO:0002376)|phospholipid translocation (GO:0045332)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell receptor signaling pathway (GO:0050862)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|saliva secretion (GO:0046541)|stabilization of membrane potential (GO:0030322)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|Intermediate conductance calcium-activated potassium channel activity (GO:0022894)|protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0352)			Clotrimazole(DB00257)|Enflurane(DB00228)|Halothane(DB01159)|Miconazole(DB01110)|Procaine(DB00721)|Quinine(DB00468)	CACGCGTTGATGGCGGCCAGC	0.587																																					p.I348fs		Atlas-INDEL	.											.	KCNN4	37	.	0			c.1043delT						.						74	67	69					19																	44273601		2203	4300	6503	SO:0001589	frameshift_variant	3783	exon6			.	AF022797	CCDS12630.1	19q13.2	2012-07-05				ENSG00000104783		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6293	protein-coding gene	gene with protein product		602754				9380751, 9407042, 16382103	Standard	NM_002250		Approved	KCa3.1, hSK4, hKCa4, hIKCa1	uc002oxl.3	O15554		ENST00000262888.3:c.1042delA	chr19.hg19:g.44273601delT	ENSP00000262888:p.Ile348fs	70.0	0.0		38.0	11.0	NM_002250	Q53XR4	Frame_Shift_Del	DEL	ENST00000262888.3	hg19	CCDS12630.1																																																																																			.	.		0.587	KCNN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463598.1	NM_002250		-	44273601	T	-	44273601	7	5	180	1	0	1	0	1	0	0	0	0	8090	1464	51	0	253	0	KCNN4	19	44273601	Frame_Shift_Del	DEL	T	TCGA-DD-AAD3-01A-11D-A40R-10	1864487	44273601	14855382	74	26982										
ZSWIM1	90204	hgsc.bcm.edu	37	chr20	44511555	44511555	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gtgcagctggagggtcatctTgcccgagcagtctactttgc	13	11	3	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr20:44511555T>A	ENST00000372523.1	+	2	419	c.324T>A	c.(322-324)ctT>ctA	p.L108L	ZSWIM1_ENST00000372520.1_Silent_p.L108L	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	108						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13		Myeloproliferative disorder(115;0.028)				AGGGTCATCTTGCCCGAGCAG	0.517																																					p.L108L		Atlas-SNP	.											.	ZSWIM1	35	.	0			c.T324A						.						79	75	77					20																	44511555		2203	4300	6503	SO:0001819	synonymous_variant	90204	exon2			TCATCTTGCCCGA	AL008726	CCDS13382.2	20q13.12	2013-09-20	2003-12-17	2003-12-19	ENSG00000168612	ENSG00000168612		"Zinc fingers, SWIM-type"	16155	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 162"	C20orf162			Standard	NM_080603		Approved	dJ337O18.5	uc010ghi.3	Q9BR11	OTTHUMG00000074023	ENST00000372523.1:c.324T>A	chr20.hg19:g.44511555T>A		184.0	0.0		177.0	56.0	NM_080603	Q5JZH2|Q9BR12|Q9BV30	Silent	SNP	ENST00000372523.1	hg19	CCDS13382.2																																																																																			.	.		0.517	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603		A	44511555	T	A	44511555	2	1	180	1	0	0	0	0	0	0	0	1	18255	1799	63	4		4	ZSWIM1	20	44511555	Silent	SNP	T	TCGA-DD-AAD3-01A-11D-A40R-10		44511555	18513965	75	26983										
SLC7A4	6545	hgsc.bcm.edu	37	chr22	21384617	21384617	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	gcgtggcagggagaagaggaGgctgagcaggacggtgttca	20	6	1	3			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr22:21384617G>A	ENST00000382932.2	-	3	1073	c.1006C>T	c.(1006-1008)Ctc>Ttc	p.L336F	AC002472.11_ENST00000450652.1_RNA|SLC7A4_ENST00000403586.1_Missense_Mutation_p.L336F	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	336					basic amino acid transport (GO:0015802)|cellular amino acid metabolic process (GO:0006520)|transport (GO:0006810)	integral component of membrane (GO:0016021)	basic amino acid transmembrane transporter activity (GO:0015174)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GAGAAGAGGAGGCTGAGCAGG	0.642																																					p.L336F		Atlas-SNP	.											.	SLC7A4	50	.	0			c.C1006T						.						48	39	42					22																	21384617		2203	4300	6503	SO:0001583	missense	6545	exon3			AGAGGAGGCTGAG	AJ000730	CCDS33608.1	22q11.21	2013-07-19	2013-07-19		ENSG00000099960	ENSG00000099960		"Solute carriers"	11062	protein-coding gene	gene with protein product		603752	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 4", "solute carrier family 7 (orphan transporter), member 4"			9598310, 11665818	Standard	NM_004173		Approved	HCAT3, CAT-4, VH	uc002zud.3	O43246	OTTHUMG00000150896	ENST00000382932.2:c.1006C>T	chr22.hg19:g.21384617G>A	ENSP00000372390:p.Leu336Phe	215.0	0.0		175.0	23.0	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Missense_Mutation	SNP	ENST00000382932.2	hg19	CCDS33608.1	.	.	.	.	.	.	.	.	.	.	G	10.13	1.265229	0.23136	.	.	ENSG00000099960	ENST00000403586;ENST00000382932	D;D	0.90563	-2.69;-2.69	4.69	2.52	0.30459	Amino acid permease domain (1);	0.363759	0.32343	N	0.006224	T	0.78916	0.4359	N	0.12182	0.205	0.27664	N	0.946971	B	0.09022	0.002	B	0.12156	0.007	T	0.68368	-0.5427	10	0.52906	T	0.07	.	5.6062	0.17381	0.0:0.0985:0.1818:0.7197	.	336	O43246	CTR4_HUMAN	F	336	ENSP00000384278:L336F;ENSP00000372390:L336F	ENSP00000372390:L336F	L	-	1	0	SLC7A4	19714617	1.000000	0.71417	0.881000	0.34555	0.227000	0.25037	3.707000	0.54838	0.403000	0.25479	-0.410000	0.06199	CTC	.	.		0.642	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173		A	21384617	G	A	21384617	3	1	180	1	0	0	0	0	1	0	0	0	14714	1000	35	3	913	3	SLC7A4	22	21384617	Missense_Mutation	SNP	G	TCGA-DD-AAD3-01A-11D-A40R-10		21384617	29919949	76	26984										
EP300	2033	hgsc.bcm.edu	37	chr22	41545769	41545769	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	ttttttattttaacaggcacAaatgtctagttcttcctgcc	5	9	2	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chr22:41545769A>G	ENST00000263253.7	+	14	3603	c.2384A>G	c.(2383-2385)cAa>cGa	p.Q795R		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	795					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TAACAGGCACAAATGTCTAGT	0.408			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.Q795R		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.A2384G						.						41	40	41					22																	41545769		2203	4300	6503	SO:0001583	missense	2033	exon14	Familial Cancer Database	Broad Thumb-Hallux syndrome	AGGCACAAATGTC	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.2384A>G	chr22.hg19:g.41545769A>G	ENSP00000263253:p.Gln795Arg	78.0	0.0		73.0	27.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	17.66	3.444442	0.63178	.	.	ENSG00000100393	ENST00000263253	D	0.84223	-1.82	5.84	5.84	0.93424	.	0.000000	0.43919	D	0.000510	D	0.89608	0.6764	M	0.72118	2.19	0.38127	D	0.938043	D	0.58620	0.983	P	0.58130	0.833	D	0.91742	0.5405	10	0.87932	D	0	-8.2779	12.1193	0.53883	0.857:0.143:0.0:0.0	.	795	Q09472	EP300_HUMAN	R	795	ENSP00000263253:Q795R	ENSP00000263253:Q795R	Q	+	2	0	EP300	39875715	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.969000	0.63735	2.243000	0.73865	0.482000	0.46254	CAA	.	.		0.408	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41545769	A	G	41545769	3	3	180	1	0	0	0	0	1	0	0	0	5150	130	5	2	2438	2	EP300	22	41545769	Missense_Mutation	SNP	A	TCGA-DD-AAD3-01A-11D-A40R-10	20161152	41545769	9758797	77	26985										
MAOB	4129	hgsc.bcm.edu	37	chrX	43698252	43698252	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0512820512820513	4	1	1.21144182450715	1.31239530988275	1.18115577889447	0.545454545454546	1	0	acatatttaaccttttggttCtgttttcccataggaaaaaa	5	7	1	0			TCGA-DD-AAD3-01A-11D-A40R-10	TCGA-DD-AAD3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de0a6b4c-0602-40a8-baa1-05b412f17031	ade9b5f7-213a-40a5-9ccd-45c50c735824	g.chrX:43698252C>A	ENST00000378069.4	-	3	289		c.e3-1		MAOB_ENST00000487544.1_Splice_Site|MAOB_ENST00000536181.1_Splice_Site|MAOB_ENST00000538942.1_Splice_Site	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B						negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	CCTTTTGGTTCTGTTTTCCCA	0.343																																					.		Atlas-SNP	.											.	MAOB	52	.	0			c.142-1G>T						.						76	67	70					X																	43698252		2203	4300	6503	SO:0001630	splice_region_variant	4129	exon4			TTGGTTCTGTTTT		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.142-1G>T	chrX.hg19:g.43698252C>A		87.0	0.0		58.0	26.0	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Splice_Site	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	C	11.84	1.758819	0.31137	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2696	0.90064	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MAOB	43583196	1.000000	0.71417	0.998000	0.56505	0.080000	0.17528	6.996000	0.76263	2.339000	0.79563	0.513000	0.50165	.	.	.		0.343	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898	Intron	A	43698252	C	A	43698252	5	1	180	1	0	0	0	0	0	0	1	0	9235	927	32	3	1473	3	MAOB	23	43698252	Splice_Site	SNP	C	TCGA-DD-AAD3-01A-11D-A40R-10		43698252	111572308	78	26986										
TTLL10	254173	hgsc.bcm.edu	37	chr1	1119315	1119315	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cccaggtacatccagaacccGctgctggtggacgggagaaa	13	12	0	2	rs371622937		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:1119315G>A	ENST00000379290.1	+	12	1277	c.1104G>A	c.(1102-1104)ccG>ccA	p.P368P	TTLL10_ENST00000379289.1_Silent_p.P368P|TTLL10_ENST00000379288.3_Silent_p.P295P			Q6ZVT0	TTL10_HUMAN	tubulin tyrosine ligase-like family, member 10	368	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)					haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(2)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;4.75e-36)|OV - Ovarian serous cystadenocarcinoma(86;5.82e-22)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TCCAGAACCCGCTGCTGGTGG	0.642													G|||	1	0.000199681	0	0	5008	,	,		17086	0		0.001	False		,,,				2504	0				p.P368P		Atlas-SNP	.											.	TTLL10	66	.	0			c.G1104A						.	G	,	0,4406		0,0,2203	266	221	237		1104,885	-7.4	0.4	1		237	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TTLL10	NM_001130045.1,NM_153254.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	368/674,295/405	1119315	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	254173	exon12			GAACCCGCTGCTG	AK093438	CCDS8.1, CCDS44036.1	1p36.33	2014-01-28	2005-07-29	2005-07-29	ENSG00000162571	ENSG00000162571		"Tubulin tyrosine ligase-like family"	26693	protein-coding gene	gene with protein product			"tubulin tyrosine ligase-like family, member 5"	TTLL5		15890843	Standard	NM_153254		Approved	FLJ36119	uc001acy.2	Q6ZVT0	OTTHUMG00000000851	ENST00000379290.1:c.1104G>A	chr1.hg19:g.1119315G>A		82.0	0.0		60.0	20.0	NM_001130045	B1AMF6|Q5T2W4|Q5T2W5|Q8N9X2	Silent	SNP	ENST00000379290.1	hg19	CCDS44036.1																																																																																			.	.		0.642	TTLL10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002421.3	NM_153254		A	1119315	G	A	1119315	2	1	181	1	0	0	0	0	0	0	0	1	16738	1074	38	1		1	TTLL10	1	1119315	Silent	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10		1119315	248131306	1	26987										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27089690	27089690	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ccacctcaggttgggtcaggGatgtgtcccccaccaggggg	15	13	2	0	rs149901342		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:27089690G>C	ENST00000324856.7	+	8	3017	c.2646G>C	c.(2644-2646)ggG>ggC	p.G882G	ARID1A_ENST00000457599.2_Silent_p.G882G|RN7SL501P_ENST00000578818.1_RNA|ARID1A_ENST00000374152.2_Silent_p.G499G	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	882					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TTGGGTCAGGGATGTGTCCCC	0.567			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.G882G		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.G2646C						.	G	,	0,4406		0,0,2203	60	54	56		2646,2646	4.7	1	1	dbSNP_134	56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ARID1A	NM_006015.4,NM_139135.2	,	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	,	882/2286,882/2069	27089690	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8289	exon8			GTCAGGGATGTGT	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2646G>C	chr1.hg19:g.27089690G>C		201.0	0.0		146.0	52.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Silent	SNP	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	G|1.000;C|0.000		0.567	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		C	27089690	G	C	27089690	2	2	181	1	0	0	0	0	0	0	0	1	913	1161	41	4		4	ARID1A	1	27089690	Silent	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	25970375	27089690	222160931	2	26988										
RCC1	1104	hgsc.bcm.edu	37	chr1	28863259	28863259	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ctctctccctcctcccatagGaaaagcatacagcctgggcc	7	17	1	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:28863259G>A	ENST00000373833.6	+	12	1223	c.938G>A	c.(937-939)gGa>gAa	p.G313E	RCC1_ENST00000398958.2_Splice_Site_p.G313E|RCC1_ENST00000373831.3_Splice_Site_p.G344E|RCC1_ENST00000373832.1_Splice_Site_p.G313E			P18754	RCC1_HUMAN	regulator of chromosome condensation 1	313					chromosome segregation (GO:0007059)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of Ran GTPase activity (GO:0032853)|regulation of mitosis (GO:0007088)|spindle assembly (GO:0051225)|viral process (GO:0016032)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosomal DNA binding (GO:0031492)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		CCTCCCATAGGAAAAGCATAC	0.602																																					p.G344E		Atlas-SNP	.											.	RCC1	61	.	0			c.G1031A						.						86	87	87					1																	28863259		2203	4300	6503	SO:0001630	splice_region_variant	1104	exon10			CCATAGGAAAAGC	X12654	CCDS323.1, CCDS41295.1	1p35.3	2008-08-18	2005-05-09	2005-05-09	ENSG00000180198	ENSG00000180198			1913	protein-coding gene	gene with protein product		179710	"chromosome condensation 1"	CHC1		7851910	Standard	NM_001048199		Approved		uc001bqf.2	P18754	OTTHUMG00000003645	ENST00000373833.6:c.938-1G>A	chr1.hg19:g.28863259G>A		49.0	0.0		51.0	19.0	NM_001048194	Q16269|Q6NT97	Missense_Mutation	SNP	ENST00000373833.6	hg19	CCDS323.1	.	.	.	.	.	.	.	.	.	.	G	32	5.132352	0.94473	.	.	ENSG00000180198	ENST00000398958;ENST00000373833;ENST00000373832;ENST00000373831;ENST00000411533	D;D;D;D;D	0.98028	-4.67;-4.67;-4.67;-4.67;-4.67	5.8	5.8	0.92144	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.047701	0.85682	D	0.000000	D	0.99284	0.9750	H	0.97491	4.015	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98829	1.0750	9	.	.	.	.	18.6252	0.91334	0.0:0.0:1.0:0.0	.	344;330;313	P18754-2;E9PAT9;P18754	.;.;RCC1_HUMAN	E	313;313;313;344;330	ENSP00000381931:G313E;ENSP00000362939:G313E;ENSP00000362938:G313E;ENSP00000362937:G344E;ENSP00000413644:G330E	.	G	+	2	0	RCC1	28735846	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.824000	0.99380	2.741000	0.93983	0.655000	0.94253	GGA	.	.		0.602	RCC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010323.3	NM_001269	Missense_Mutation	A	28863259	G	A	28863259	5	1	181	1	0	0	0	0	0	0	1	0	13188	1188	41	3	1065	3	RCC1	1	28863259	Splice_Site	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	1773569	28863259	220387362	3	26989										
EPHA10	284656	hgsc.bcm.edu	37	chr1	38227675	38227675	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ccagtctgcagccagttgtcCtggttgggctccagcacatt	11	13	1	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:38227675C>T	ENST00000373048.4	-	3	251	c.252G>A	c.(250-252)caG>caA	p.Q84Q	EPHA10_ENST00000427468.2_Silent_p.Q84Q|EPHA10_ENST00000319637.6_Silent_p.Q84Q	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	84	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GCCAGTTGTCCTGGTTGGGCT	0.612																																					p.Q84Q		Atlas-SNP	.											.	EPHA10	120	.	0			c.G252A						.						92	81	85					1																	38227675		2203	4300	6503	SO:0001819	synonymous_variant	284656	exon3			GTTGTCCTGGTTG	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.252G>A	chr1.hg19:g.38227675C>T		89.0	0.0		72.0	32.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	hg19	CCDS41305.1																																																																																			.	.		0.612	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		T	38227675	C	T	38227675	2	4	181	1	0	0	0	0	0	0	0	1	5168	680	24	3		3	EPHA10	1	38227675	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	9364416	38227675	211022946	4	26990										
C8A	731	hgsc.bcm.edu	37	chr1	57320606	57320606	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgttttcttcatcttgtcttTgatgacttgtcagcctgggg	10	8	5	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:57320606T>A	ENST00000361249.3	+	1	128	c.32T>A	c.(31-33)tTg>tAg	p.L11*		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	11					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						ATCTTGTCTTTGATGACTTGT	0.448																																					p.L11X		Atlas-SNP	.											.	C8A	103	.	0			c.T32A						.						209	160	177					1																	57320606		2203	4300	6503	SO:0001587	stop_gained	731	exon1			TGTCTTTGATGAC	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"Complement system"	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.32T>A	chr1.hg19:g.57320606T>A	ENSP00000354458:p.Leu11*	145.0	0.0		115.0	36.0	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Nonsense_Mutation	SNP	ENST00000361249.3	hg19	CCDS606.1	.	.	.	.	.	.	.	.	.	.	T	37	6.419765	0.97550	.	.	ENSG00000157131	ENST00000361249	.	.	.	4.94	3.78	0.43462	.	0.363846	0.21860	N	0.068041	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.4758	7.4091	0.27007	0.0:0.0992:0.0:0.9008	.	.	.	.	X	11	.	ENSP00000354458:L11X	L	+	2	0	C8A	57093194	0.912000	0.30974	0.953000	0.39169	0.996000	0.88848	1.457000	0.35212	2.073000	0.62155	0.533000	0.62120	TTG	.	.		0.448	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		A	57320606	T	A	57320606	4	1	181	1	0	0	0	0	0	1	0	0	2418	1821	63	4	34	4	C8A	1	57320606	Nonsense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	19092931	57320606	191930015	5	26991										
JAK1	3716	hgsc.bcm.edu	37	chr1	65310503	65310503	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gatgaatgggccacactcacTgtcgatgccctcacgggcca	11	14	2	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:65310503T>A	ENST00000342505.4	-	16	2433	c.2185A>T	c.(2185-2187)Agt>Tgt	p.S729C	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	729	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CCACACTCACTGTCGATGCCC	0.547			Mis		ALL																																p.S729C		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	JAK1,NS,carcinoma,0,2	JAK1	209	.	0			c.A2185T						.						96	113	107					1																	65310503		2115	4222	6337	SO:0001583	missense	3716	exon16			ACTCACTGTCGAT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2185A>T	chr1.hg19:g.65310503T>A	ENSP00000343204:p.Ser729Cys	158.0	0.0		135.0	59.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.814614	0.50527	.	.	ENSG00000162434	ENST00000342505	T	0.76839	-1.05	5.0	2.65	0.31530	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.65312	0.2679	L	0.54965	1.715	0.22552	N	0.998997	P	0.46142	0.873	P	0.46850	0.529	T	0.57177	-0.7856	9	0.72032	D	0.01	-5.9131	9.7115	0.40247	0.0:0.1625:0.0:0.8375	.	729	P23458	JAK1_HUMAN	C	729	ENSP00000343204:S729C	ENSP00000343204:S729C	S	-	1	0	JAK1	65083091	0.100000	0.21855	0.477000	0.27303	0.441000	0.31987	2.149000	0.42244	0.940000	0.37473	0.460000	0.39030	AGT	.	.		0.547	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		A	65310503	T	A	65310503	3	1	181	1	0	0	0	0	1	0	0	0	7946	1580	55	4	1319	4	JAK1	1	65310503	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	7989897	65310503	183940118	6	26992										
CLCA1	1179	hgsc.bcm.edu	37	chr1	86948018	86948018	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gtgagtttgttctccaatccCgccagacggagaaggcttct	11	11	2	3	rs149585400		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:86948018C>A	ENST00000234701.3	+	6	1039	c.688C>A	c.(688-690)Cgc>Agc	p.R230S	CLCA1_ENST00000394711.1_Missense_Mutation_p.R230S			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	230					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		TCTCCAATCCCGCCAGACGGA	0.428																																					p.R230S		Atlas-SNP	.											.	CLCA1	109	.	0			c.C688A						.						133	129	130					1																	86948018		2203	4300	6503	SO:0001583	missense	1179	exon5			CAATCCCGCCAGA		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.688C>A	chr1.hg19:g.86948018C>A	ENSP00000234701:p.Arg230Ser	165.0	0.0		119.0	45.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	hg19	CCDS709.1	.	.	.	.	.	.	.	.	.	.	C	1.086	-0.665490	0.03428	.	.	ENSG00000016490	ENST00000234701;ENST00000394711	T;T	0.10668	2.85;2.85	5.49	-5.56	0.02529	Chloride channel calcium-activated (1);	3.186930	0.00678	N	0.000661	T	0.00784	0.0026	N	0.04260	-0.245	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35276	-0.9795	10	0.06757	T	0.87	18.9392	0.5096	0.00593	0.3297:0.271:0.1846:0.2146	.	230	A8K7I4	CLCA1_HUMAN	S	230	ENSP00000234701:R230S;ENSP00000378200:R230S	ENSP00000234701:R230S	R	+	1	0	CLCA1	86720606	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.815000	0.00359	-0.742000	0.04790	0.655000	0.94253	CGC	.	C|1.000;T|0.000		0.428	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		A	86948018	C	A	86948018	3	1	181	1	0	0	0	0	1	0	0	0	3459	652	23	1	706	1	CLCA1	1	86948018	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	21637515	86948018	162302603	7	26993										
ABCA4	24	hgsc.bcm.edu	37	chr1	94522310	94522310	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agaaagcacagcatgatggtGgcagtggagaaagccaacaa	13	7	0	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:94522310G>A	ENST00000370225.3	-	15	2315	c.2229C>T	c.(2227-2229)gcC>gcT	p.A743A	ABCA4_ENST00000535735.1_Intron	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	743					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GCATGATGGTGGCAGTGGAGA	0.512																																					p.A743A		Atlas-SNP	.											.	ABCA4	275	.	0			c.C2229T						.						109	96	101					1																	94522310		2203	4300	6503	SO:0001819	synonymous_variant	24	exon15			GATGGTGGCAGTG	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.2229C>T	chr1.hg19:g.94522310G>A		208.0	0.0		135.0	30.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	hg19	CCDS747.1																																																																																			.	.		0.512	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94522310	G	A	94522310	2	1	181	1	0	0	0	0	0	0	0	1	34	1335	47	3		3	ABCA4	1	94522310	Silent	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	7574292	94522310	154728311	8	26994										
STXBP3	6814	hgsc.bcm.edu	37	chr1	109351498	109351498	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ctccttaattaaagatgaatAgcatttctttttggagggtt	8	5	1	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:109351498A>G	ENST00000370008.3	+	19	1828	c.1778A>G	c.(1777-1779)tAg>tGg	p.*593W		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	0					blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		AAAGATGAATAGCATTTCTTT	0.294																																					p.X593W		Atlas-SNP	.											.	STXBP3	44	.	0			c.A1778G						.						92	101	98					1																	109351498		2203	4299	6502	SO:0001578	stop_lost	6814	exon19			ATGAATAGCATTT	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1778A>G	chr1.hg19:g.109351498A>G	ENSP00000359025:p.*593Trpext*16	103.0	0.0		88.0	37.0	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	hg19	CCDS790.1	.	.	.	.	.	.	.	.	.	.	A	4.174	0.030769	0.08101	.	.	ENSG00000116266	ENST00000370008	.	.	.	5.08	3.94	0.45596	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.4814	0.38902	0.9162:0.0:0.0838:0.0	.	.	.	.	W	593	.	.	X	+	2	0	STXBP3	109153021	0.998000	0.40836	0.964000	0.40570	0.045000	0.14185	2.905000	0.48727	1.913000	0.55393	0.482000	0.46254	TAG	.	.		0.294	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		G	109351498	A	G	109351498	4	3	181	1	0	0	0	0	0	0	0	0	15369	433	15	2	1852	2	STXBP3	1	109351498	Nonstop_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	14829188	109351498	139899123	9	26995										
KCNA10	3744	hgsc.bcm.edu	37	chr1	111059915	111059915	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ggaacagccaccattggtctTattaagagagtctgtgctgc	11	9	2	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:111059915T>C	ENST00000369771.2	-	1	1882	c.1495A>G	c.(1495-1497)Aag>Gag	p.K499E		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	499					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	CCATTGGTCTTATTAAGAGAG	0.473																																					p.K499E		Atlas-SNP	.											.	KCNA10	92	.	0			c.A1495G						.						167	161	163					1																	111059915		2203	4300	6503	SO:0001583	missense	3744	exon1			TGGTCTTATTAAG	U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.1495A>G	chr1.hg19:g.111059915T>C	ENSP00000358786:p.Lys499Glu	112.0	0.0		74.0	15.0	NM_005549		Missense_Mutation	SNP	ENST00000369771.2	hg19	CCDS826.1	.	.	.	.	.	.	.	.	.	.	T	12.47	1.948675	0.34377	.	.	ENSG00000143105	ENST00000369771	D	0.97016	-4.21	5.78	4.59	0.56863	.	0.307811	0.29002	N	0.013450	D	0.90954	0.7156	M	0.66939	2.045	0.31947	N	0.610119	P	0.35745	0.518	B	0.27380	0.079	D	0.89599	0.3833	10	0.41790	T	0.15	.	11.6274	0.51153	0.0:0.0:0.1485:0.8515	.	499	Q16322	KCA10_HUMAN	E	499	ENSP00000358786:K499E	ENSP00000358786:K499E	K	-	1	0	KCNA10	110861438	1.000000	0.71417	0.925000	0.36789	0.975000	0.68041	4.132000	0.57977	2.211000	0.71520	0.459000	0.35465	AAG	.	.		0.473	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		C	111059915	T	C	111059915	3	2	181	1	0	0	0	0	1	0	0	0	8011	1763	61	2	44	2	KCNA10	1	111059915	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	1708417	111059915	138190706	10	26996										
GJA8	2703	hgsc.bcm.edu	37	chr1	147380358	147380358	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tccaccccgtccctgatgtaCgtggggcacgcggtgcacta	12	15	0	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:147380358C>A	ENST00000369235.1	+	1	276	c.276C>A	c.(274-276)taC>taA	p.Y92*	GJA8_ENST00000240986.4_Nonsense_Mutation_p.Y92*			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	92					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					CCCTGATGTACGTGGGGCACG	0.657																																					p.Y92X	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											.	GJA8	108	.	0			c.C276A						.						116	92	100					1																	147380358		2203	4300	6503	SO:0001587	stop_gained	2703	exon2			GATGTACGTGGGG	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.276C>A	chr1.hg19:g.147380358C>A	ENSP00000358238:p.Tyr92*	70.0	0.0		79.0	56.0	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Nonsense_Mutation	SNP	ENST00000369235.1	hg19	CCDS30834.1	.	.	.	.	.	.	.	.	.	.	c	33	5.246641	0.95305	.	.	ENSG00000121634	ENST00000240986;ENST00000369235	.	.	.	5.2	2.15	0.27550	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.8237	0.29303	0.1299:0.7277:0.0:0.1424	.	.	.	.	X	92	.	ENSP00000240986:Y92X	Y	+	3	2	GJA8	145846982	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	2.125000	0.42016	0.517000	0.28361	0.491000	0.48974	TAC	.	.		0.657	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		A	147380358	C	A	147380358	4	1	181	1	0	0	0	0	0	1	0	0	6413	547	19	1	278	1	GJA8	1	147380358	Nonsense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	36320443	147380358	101870263	11	26997										
TCHH	7062	hgsc.bcm.edu	37	chr1	152080637	152080637	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ttttctgtcacgctcttggcGgcgcagctgctgttcctccc	10	15	3	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:152080637G>A	ENST00000368804.1	-	2	5055	c.5056C>T	c.(5056-5058)Cgc>Tgc	p.R1686C		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1686	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGCTCTTGGCGGCGCAGCTGC	0.607																																					p.R1686C		Atlas-SNP	.											.	TCHH	275	.	0			c.C5056T						.						93	92	93					1																	152080637		1901	4112	6013	SO:0001583	missense	7062	exon3			CTTGGCGGCGCAG	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.5056C>T	chr1.hg19:g.152080637G>A	ENSP00000357794:p.Arg1686Cys	118.0	0.0		144.0	105.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.931220	0.52866	.	.	ENSG00000159450	ENST00000368804	T	0.05649	3.41	4.25	4.25	0.50352	.	.	.	.	.	T	0.12220	0.0297	M	0.72118	2.19	0.36811	D	0.88586	D	0.89917	1.0	D	0.68621	0.959	T	0.00664	-1.1620	9	0.52906	T	0.07	.	9.4177	0.38532	0.0:0.0:0.7877:0.2123	.	1686	Q07283	TRHY_HUMAN	C	1686	ENSP00000357794:R1686C	ENSP00000357794:R1686C	R	-	1	0	TCHH	150347261	.	.	0.965000	0.40720	0.879000	0.50718	.	.	2.193000	0.70182	0.467000	0.42956	CGC	.	.		0.607	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		A	152080637	G	A	152080637	3	1	181	1	0	0	0	0	1	0	0	0	15715	1116	39	1	779	1	TCHH	1	152080637	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	4700279	152080637	97169984	12	26998										
CEP350	9857	hgsc.bcm.edu	37	chr1	179993651	179993651	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agcattcatcaggagcccagTctgctgcatcgtctcgttca	9	13	5	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:179993651T>A	ENST00000367607.3	+	14	3902	c.3484T>A	c.(3484-3486)Tct>Act	p.S1162T		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1162	Ser-rich.				microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						AGGAGCCCAGTCTGCTGCATC	0.433																																					p.S1162T		Atlas-SNP	.											.	CEP350	418	.	0			c.T3484A						.						97	82	87					1																	179993651		2203	4300	6503	SO:0001583	missense	9857	exon14			GCCCAGTCTGCTG	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.3484T>A	chr1.hg19:g.179993651T>A	ENSP00000356579:p.Ser1162Thr	85.0	0.0		105.0	13.0	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433363	0.83776	.	.	ENSG00000135837	ENST00000367607	T	0.58940	0.3	5.61	5.61	0.85477	.	0.000000	0.44285	D	0.000461	T	0.64549	0.2608	L	0.32530	0.975	0.36378	D	0.86171	D;D	0.69078	0.982;0.997	D;D	0.73380	0.952;0.98	T	0.68884	-0.5291	9	.	.	.	.	13.1881	0.59693	0.0:0.0:0.0:1.0	.	1162;1162	E7EU22;Q5VT06	.;CE350_HUMAN	T	1162	ENSP00000356579:S1162T	.	S	+	1	0	CEP350	178260274	1.000000	0.71417	0.977000	0.42913	0.941000	0.58515	4.961000	0.63681	2.129000	0.65627	0.460000	0.39030	TCT	.	.		0.433	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		A	179993651	T	A	179993651	3	1	181	1	0	0	0	0	1	0	0	0	3256	1667	58	4	3534	4	CEP350	1	179993651	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	27913014	179993651	69256970	13	26999										
PIGR	5284	hgsc.bcm.edu	37	chr1	207106368	207106368	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgctctgctcccatcggcttGatctcttgtatctgccaccg	8	15	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:207106368G>A	ENST00000356495.4	-	7	2032	c.1849C>T	c.(1849-1851)Caa>Taa	p.Q617*	PIGR_ENST00000487208.1_5'Flank	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	617					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CCATCGGCTTGATCTCTTGTA	0.547																																					p.Q617X		Atlas-SNP	.											.	PIGR	98	.	0			c.C1849T						.						112	109	110					1																	207106368		2203	4300	6503	SO:0001587	stop_gained	5284	exon7			CGGCTTGATCTCT		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1849C>T	chr1.hg19:g.207106368G>A	ENSP00000348888:p.Gln617*	56.0	0.0		76.0	6.0	NM_002644	Q68D81|Q8IZY7	Nonsense_Mutation	SNP	ENST00000356495.4	hg19	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.853304	0.91355	.	.	ENSG00000162896	ENST00000356495	.	.	.	4.29	-1.02	0.10135	.	1.531900	0.03497	N	0.217532	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-10.6851	6.1526	0.20320	0.181:0.4485:0.3705:0.0	.	.	.	.	X	617	.	ENSP00000348888:Q617X	Q	-	1	0	PIGR	205172991	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.038000	0.13862	-0.153000	0.11137	-0.305000	0.09177	CAA	.	.		0.547	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		A	207106368	G	A	207106368	4	1	181	1	0	0	0	0	0	1	0	0	11906	1299	45	3	465	3	PIGR	1	207106368	Nonsense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	27112717	207106368	42144253	14	27000										
C1orf65	164127	hgsc.bcm.edu	37	chr1	223568318	223568318	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agtcagaggaacagaggaagAtgcgcaaaagaattctggtg	14	5	2	4			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:223568318A>T	ENST00000366875.3	+	1	1604	c.1501A>T	c.(1501-1503)Atg>Ttg	p.M501L		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		501										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		ACAGAGGAAGATGCGCAAAAG	0.607																																					p.M501L		Atlas-SNP	.											.	C1orf65	71	.	0			c.A1501T						.						86	102	97					1																	223568318		2203	4300	6503	SO:0001583	missense	164127	exon1			AGGAAGATGCGCA																												ENST00000366875.3:c.1501A>T	chr1.hg19:g.223568318A>T	ENSP00000355840:p.Met501Leu	122.0	0.0		184.0	18.0	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	hg19	CCDS1537.1	.	.	.	.	.	.	.	.	.	.	A	2.602	-0.292790	0.05568	.	.	ENSG00000178395	ENST00000366875	T	0.21031	2.03	5.48	0.268	0.15626	.	.	.	.	.	T	0.07683	0.0193	N	0.11427	0.14	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.38457	-0.9660	9	0.13470	T	0.59	.	0.8626	0.01196	0.374:0.2223:0.2588:0.1449	.	501	Q8N715	CA065_HUMAN	L	501	ENSP00000355840:M501L	ENSP00000355840:M501L	M	+	1	0	C1orf65	221634941	0.000000	0.05858	0.001000	0.08648	0.084000	0.17831	-0.281000	0.08456	0.465000	0.27167	-0.408000	0.06270	ATG	.	.		0.607	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			T	223568318	A	T	223568318	3	4	181	1	0	0	0	0	1	0	0	0	2057	333	12	4	1503	4	C1orf65	1	223568318	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	16461950	223568318	25682303	15	27001										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228467638	228467638	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ctgtgcagtggtacaaggatGacacgcccctgtctccctct	10	14	2	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:228467638G>A	ENST00000422127.1	+	28	7557	c.7513G>A	c.(7513-7515)Gac>Aac	p.D2505N	OBSCN_ENST00000284548.11_Missense_Mutation_p.D2505N|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.D2934N|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000359599.6_Missense_Mutation_p.D1352N	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2505	Ig-like 24.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTACAAGGATGACACGCCCCT	0.612																																					p.D2934N		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G8800A						.						23	29	27					1																	228467638		2123	4220	6343	SO:0001583	missense	84033	exon33			AAGGATGACACGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.7513G>A	chr1.hg19:g.228467638G>A	ENSP00000409493:p.Asp2505Asn	148.0	0.0		150.0	10.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	g	15.20	2.763802	0.49574	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599;ENST00000366706	T;T;T	0.41065	1.01;1.01;1.01	5.01	4.09	0.47781	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.308279	0.30704	N	0.009060	T	0.43166	0.1235	L	0.33792	1.035	0.25845	N	0.984009	D;B;D	0.61697	0.99;0.019;0.981	D;B;P	0.64042	0.921;0.005;0.813	T	0.21655	-1.0239	10	0.19147	T	0.46	.	6.1594	0.20356	0.1757:0.2065:0.6178:0.0	.	2505;2505;2505	Q5VST9;Q5VST9-2;Q5VST9-3	OBSCN_HUMAN;.;.	N	2505;2505;1352;204	ENSP00000284548:D2505N;ENSP00000409493:D2505N;ENSP00000352613:D1352N	ENSP00000284548:D2505N	D	+	1	0	OBSCN	226534261	0.161000	0.22892	0.023000	0.16930	0.856000	0.48823	2.010000	0.40913	1.123000	0.41961	0.550000	0.68814	GAC	.	.		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228467638	G	A	228467638	3	1	181	1	0	0	0	0	1	0	0	0	10821	1290	45	3	7619	3	OBSCN	1	228467638	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	4899320	228467638	20782983	16	27002										
RYR2	6262	hgsc.bcm.edu	37	chr1	237608813	237608813	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cacagtcttccttttcaataGatttataaggtactttttct	4	8	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr1:237608813G>T	ENST00000366574.2	+	14	1600	c.1283G>T	c.(1282-1284)aGa>aTa	p.R428I	RYR2_ENST00000542537.1_Missense_Mutation_p.R412I|RYR2_ENST00000360064.6_Missense_Mutation_p.R426I	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	428					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CTTTTCAATAGATTTATAAGG	0.373																																					p.R428I		Atlas-SNP	.											.	RYR2	1273	.	0			c.G1283T						.						133	126	128					1																	237608813		1849	4095	5944	SO:0001583	missense	6262	exon14			TCAATAGATTTAT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.1283G>T	chr1.hg19:g.237608813G>T	ENSP00000355533:p.Arg428Ile	133.0	0.0		167.0	8.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.649181	0.29336	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96651	-4.08;-4.05;-4.08	5.6	5.6	0.85130	.	0.284406	0.29653	N	0.011552	D	0.92990	0.7769	L	0.31926	0.97	0.80722	D	1	B	0.23806	0.091	B	0.15870	0.014	D	0.90249	0.4292	10	0.62326	D	0.03	.	14.4541	0.67404	0.0:0.0:0.8528:0.1471	.	428	Q92736	RYR2_HUMAN	I	428;426;412	ENSP00000355533:R428I;ENSP00000353174:R426I;ENSP00000443798:R412I	ENSP00000353174:R426I	R	+	2	0	RYR2	235675436	0.993000	0.37304	1.000000	0.80357	0.364000	0.29643	1.981000	0.40628	2.636000	0.89361	0.591000	0.81541	AGA	.	.		0.373	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237608813	G	T	237608813	3	4	181	1	0	0	0	0	1	0	0	0	13784	942	33	3	1337	3	RYR2	1	237608813	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	9141175	237608813	11641808	17	27003										
APOB	338	hgsc.bcm.edu	37	chr2	21236085	21236085	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agtcagccttcatgtggtaaCgagcccgaaggctgaaatgg	13	9	2	1	rs13306187	byFrequency	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:21236085C>G	ENST00000233242.1	-	25	4290	c.4163G>C	c.(4162-4164)cGt>cCt	p.R1388P		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1388			R -> H (in dbSNP:rs13306187).		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.R1388H(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATGTGGTAACGAGCCCGAAG	0.532																																					p.R1388P		Atlas-SNP	.											APOB,NS,malignant_melanoma,-1,1	APOB	761	.	1	Substitution - Missense(1)	endometrium(1)	c.G4163C						.						164	153	156					2																	21236085		2203	4300	6503	SO:0001583	missense	338	exon25			TGGTAACGAGCCC	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.4163G>C	chr2.hg19:g.21236085C>G	ENSP00000233242:p.Arg1388Pro	128.0	0.0		121.0	44.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	8.202	0.798337	0.16397	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00730	5.77	5.31	-10.5	0.00291	.	1.591350	0.03452	N	0.210873	T	0.00695	0.0023	L	0.36672	1.1	0.09310	N	0.999999	B	0.31730	0.337	B	0.30105	0.111	T	0.34477	-0.9827	10	0.38643	T	0.18	.	6.8848	0.24193	0.081:0.4751:0.2625:0.1814	.	1388	P04114	APOB_HUMAN	P	1388	ENSP00000233242:R1388P	ENSP00000233242:R1388P	R	-	2	0	APOB	21089590	0.000000	0.05858	0.002000	0.10522	0.140000	0.21249	-0.446000	0.06837	-1.859000	0.01156	-1.368000	0.01194	CGT	.	C|0.997;T|0.003		0.532	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21236085	C	G	21236085	3	3	181	1	0	0	0	0	1	0	0	0	785	536	19	4	9548	4	APOB	2	21236085	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10		21236085	221963288	18	27004										
GPR113	165082	hgsc.bcm.edu	37	chr2	26536264	26536264	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ccttggttctagtgaacaagGccaggagcctcgcatctgtg	12	11	2	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:26536264G>T	ENST00000311519.1	-	9	1453	c.1454C>A	c.(1453-1455)gCc>gAc	p.A485D	GPR113_ENST00000421160.2_Missense_Mutation_p.A416D|GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000333478.6_Missense_Mutation_p.A286D|GPR113_ENST00000541401.1_Missense_Mutation_p.A88D	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	485					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGTGAACAAGGCCAGGAGCCT	0.627																																					p.A485D		Atlas-SNP	.											.	GPR113	134	.	0			c.C1454A						.						23	24	23					2																	26536264		2202	4300	6502	SO:0001583	missense	165082	exon9			AACAAGGCCAGGA	AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"-", "GPCR / Class B : Orphans"	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.1454C>A	chr2.hg19:g.26536264G>T	ENSP00000307831:p.Ala485Asp	142.0	0.0		98.0	37.0	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	SNP	ENST00000311519.1	hg19	CCDS46239.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927315	0.34002	.	.	ENSG00000173567	ENST00000541401;ENST00000333478;ENST00000421160;ENST00000311519	T;T;T;T	0.27557	1.66;3.13;3.13;3.13	5.84	-0.543	0.11851	.	.	.	.	.	T	0.21801	0.0525	L	0.50919	1.6	0.09310	N	0.999999	B;B;B;B	0.15141	0.001;0.012;0.0;0.002	B;B;B;B	0.15052	0.001;0.012;0.001;0.007	T	0.34179	-0.9839	9	0.15066	T	0.55	-1.5879	5.3695	0.16132	0.0685:0.1138:0.3509:0.4668	.	416;286;485;88	E9PEV1;Q8IZF5-2;Q8IZF5;F5H1E4	.;.;GP113_HUMAN;.	D	88;286;416;485	ENSP00000445729:A88D;ENSP00000327396:A286D;ENSP00000388537:A416D;ENSP00000307831:A485D	ENSP00000307831:A485D	A	-	2	0	GPR113	26389768	0.001000	0.12720	0.024000	0.17045	0.362000	0.29581	-0.074000	0.11450	-0.164000	0.10927	0.561000	0.74099	GCC	.	.		0.627	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		T	26536264	G	T	26536264	3	4	181	1	0	0	0	0	1	0	0	0	6638	1203	42	3	1894	3	GPR113	2	26536264	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	5300179	26536264	216663109	19	27005										
NRXN1	9378	hgsc.bcm.edu	37	chr2	51255333	51255333	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aaactccagcccgctgcccaGctccgcccagcagcccagga	9	20	0	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:51255333G>A	ENST00000406316.2	-	2	1555	c.79C>T	c.(79-81)Ctg>Ttg	p.L27L	NRXN1_ENST00000404971.1_Silent_p.L27L|NRXN1_ENST00000406859.3_Silent_p.L27L|NRXN1_ENST00000405581.1_Silent_p.L27L|NRXN1_ENST00000402717.3_Silent_p.L27L|NRXN1_ENST00000405472.3_Silent_p.L27L|NRXN1_ENST00000401669.2_Silent_p.L27L	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	27					adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CCGCTGCCCAGCTCCGCCCAG	0.697																																					p.L27L		Atlas-SNP	.											.	NRXN1	1118	.	0			c.C79T						.						4	6	5					2																	51255333		1880	4057	5937	SO:0001819	synonymous_variant	9378	exon2			TGCCCAGCTCCGC	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.79C>T	chr2.hg19:g.51255333G>A		40.0	0.0		54.0	21.0	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	hg19	CCDS54360.1																																																																																			.	.		0.697	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	51255333	G	A	51255333	2	1	181	1	0	0	0	0	0	0	0	1	10674	962	34	3		3	NRXN1	2	51255333	Silent	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	24719069	51255333	191944040	20	27006										
EHBP1	23301	hgsc.bcm.edu	37	chr2	63206420	63206420	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gatgtcagaacttcccagctAtggtgaaatggctgcagaaa	11	8	1	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:63206420A>G	ENST00000263991.5	+	16	3145	c.2663A>G	c.(2662-2664)tAt>tGt	p.Y888C	EHBP1_ENST00000405015.3_Missense_Mutation_p.Y853C|EHBP1_ENST00000405289.1_Missense_Mutation_p.Y853C|EHBP1_ENST00000431489.1_Missense_Mutation_p.Y853C|EHBP1_ENST00000496857.1_3'UTR|EHBP1_ENST00000354487.3_Missense_Mutation_p.Y853C	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	888						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			CTTCCCAGCTATGGTGAAATG	0.463																																					p.Y888C		Atlas-SNP	.											.	EHBP1	127	.	0			c.A2663G						.						82	86	84					2																	63206420		2203	4300	6503	SO:0001583	missense	23301	exon16			CCAGCTATGGTGA	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.2663A>G	chr2.hg19:g.63206420A>G	ENSP00000263991:p.Tyr888Cys	130.0	0.0		114.0	42.0	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	hg19	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.941118	0.73557	.	.	ENSG00000115504	ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T	0.75154	-0.85;-0.85;-0.91;-0.9;-0.9	5.69	5.69	0.88448	.	0.153463	0.45867	D	0.000332	D	0.83843	0.5342	L	0.56769	1.78	0.50171	D	0.999857	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.84087	0.0388	10	0.48119	T	0.1	.	15.9451	0.79787	1.0:0.0:0.0:0.0	.	853;853;888	Q8NDI1-2;Q8NDI1-3;Q8NDI1	.;.;EHBP1_HUMAN	C	853;853;888;853;853	ENSP00000384143:Y853C;ENSP00000403783:Y853C;ENSP00000263991:Y888C;ENSP00000346482:Y853C;ENSP00000385524:Y853C	ENSP00000263991:Y888C	Y	+	2	0	EHBP1	63059924	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.310000	0.59141	2.177000	0.69029	0.533000	0.62120	TAT	.	.		0.463	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		G	63206420	A	G	63206420	3	3	181	1	0	0	0	0	1	0	0	0	4977	449	16	2	2721	2	EHBP1	2	63206420	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	11951087	63206420	179992953	21	27007										
SNRNP27	11017	hgsc.bcm.edu	37	chr2	70123665	70123665	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	caaaagaaacaaagagcaaaGaacggcagattactggtaat	9	6	0	4			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:70123665G>C	ENST00000244227.3	+	3	678	c.253G>C	c.(253-255)Gaa>Caa	p.E85Q	SNRNP27_ENST00000488986.1_3'UTR|SNRNP27_ENST00000409116.1_Missense_Mutation_p.E85Q	NM_006857.2	NP_006848.1	Q8WVK2	SNR27_HUMAN	small nuclear ribonucleoprotein 27kDa (U4/U6.U5)	85					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	11						aaagaGCAAAGAACGGCAGAT	0.323																																					p.E85Q		Atlas-SNP	.											.	SNRNP27	18	.	0			c.G253C						.						44	46	45					2																	70123665		2199	4300	6499	SO:0001583	missense	11017	exon3			AGCAAAGAACGGC	X76302	CCDS33219.1	2p14	2011-10-11			ENSG00000124380	ENSG00000124380			30240	protein-coding gene	gene with protein product	"nucleic acid binding protein RY 1"					7931148	Standard	NM_006857		Approved	RY1	uc002sfw.3	Q8WVK2	OTTHUMG00000152689	ENST00000244227.3:c.253G>C	chr2.hg19:g.70123665G>C	ENSP00000244227:p.Glu85Gln	77.0	0.0		64.0	14.0	NM_006857	Q15410	Missense_Mutation	SNP	ENST00000244227.3	hg19	CCDS33219.1	.	.	.	.	.	.	.	.	.	.	g	14.22	2.471214	0.43942	.	.	ENSG00000124380	ENST00000244227;ENST00000409116	T;T	0.35605	1.3;1.3	5.28	5.28	0.74379	Domain of unknown function DUF1777 (1);	0.167950	0.52532	D	0.000061	T	0.53254	0.1785	L	0.56769	1.78	0.46416	D	0.999034	D;P	0.62365	0.991;0.807	D;P	0.74023	0.982;0.728	T	0.37267	-0.9713	10	0.23302	T	0.38	.	14.285	0.66240	0.0:0.0:1.0:0.0	.	85;85	B8ZZ98;Q8WVK2	.;SNR27_HUMAN	Q	85	ENSP00000244227:E85Q;ENSP00000386608:E85Q	ENSP00000244227:E85Q	E	+	1	0	SNRNP27	69977169	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.313000	0.65798	2.750000	0.94351	0.585000	0.79938	GAA	.	.		0.323	SNRNP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327369.1	NM_006857		C	70123665	G	C	70123665	3	2	181	1	0	0	0	0	1	0	0	0	14869	943	33	4	263	4	SNRNP27	2	70123665	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	6917245	70123665	173075708	22	27008										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71591128	71591128	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgaaactccacgaagacgttCtcattcccccagtcctaggc	7	15	1	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:71591128C>G	ENST00000409544.1	+	5	2093	c.1463C>G	c.(1462-1464)tCt>tGt	p.S488C	ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000377802.2_Missense_Mutation_p.S488C|ZNF638_ENST00000264447.4_Missense_Mutation_p.S488C|ZNF638_ENST00000355812.3_Missense_Mutation_p.S488C	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	488	Arg-rich.				regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						CGAAGACGTTCTCATTCCCCC	0.438																																					p.S488C		Atlas-SNP	.											.	ZNF638	179	.	0			c.C1463G						.						113	107	109					2																	71591128		2203	4300	6503	SO:0001583	missense	27332	exon5			GACGTTCTCATTC	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.1463C>G	chr2.hg19:g.71591128C>G	ENSP00000386433:p.Ser488Cys	141.0	0.0		132.0	51.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.194738	0.58017	.	.	ENSG00000075292	ENST00000410075;ENST00000544512;ENST00000394137;ENST00000355812;ENST00000377802;ENST00000264447;ENST00000409544	T;T;T;T;T;T	0.74632	-0.27;-0.86;0.3;-0.26;1.3;1.3	5.61	5.61	0.85477	.	0.168609	0.42053	D	0.000770	T	0.77691	0.4168	N	0.19112	0.55	0.39194	D	0.963026	D;D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;0.999;0.999	D;D;D;D;P;D	0.85130	0.993;0.994;0.994;0.997;0.887;0.994	T	0.81444	-0.0930	10	0.72032	D	0.01	-11.8497	15.1409	0.72609	0.0:1.0:0.0:0.0	.	488;594;488;488;488;488	A8K583;F5H330;Q14966-4;Q14966-3;Q14966;Q14966-2	.;.;.;.;ZN638_HUMAN;.	C	488;594;67;488;488;488;488	ENSP00000386669:S488C;ENSP00000438189:S594C;ENSP00000348066:S488C;ENSP00000367033:S488C;ENSP00000264447:S488C;ENSP00000386433:S488C	ENSP00000264447:S488C	S	+	2	0	ZNF638	71444636	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.949000	0.56668	2.658000	0.90341	0.585000	0.79938	TCT	.	.		0.438	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		G	71591128	C	G	71591128	3	3	181	1	0	0	0	0	1	0	0	0	18070	913	32	4	1477	4	ZNF638	2	71591128	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	1467463	71591128	171608245	23	27009										
KDM3A	55818	hgsc.bcm.edu	37	chr2	86718396	86718408	+	Splice_Site	DEL	CAGGTAAAAATAG	CAGGTAAAAATAG	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ccaatcacgaagataaattaCaggtaaaaatagcaccaatt					rs367630615		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	CAGGTAAAAATAG	CAGGTAAAAATAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:86718396_86718408delCAGGTAAAAATAG	ENST00000409556.1	+	26	4248_4250	c.3883_3885delCAGGTAAAAATAG	c.(3883-3885)cagdel	p.Q1295fs	KDM3A_ENST00000542128.1_Splice_Site_p.Q1243fs|KDM3A_ENST00000409064.1_Splice_Site_p.Q1295fs|KDM3A_ENST00000312912.5_Splice_Site_p.Q1295fs			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	1295					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						AGATAAATTACAGGTAAAAATAGCACCAATTCC	0.399																																					p.1294_1295del	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-INDEL	.											.	KDM3A	179	.	0			c.3882_3885del						.																																			SO:0001630	splice_region_variant	55818	exon25			.	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"Chromatin-modifying enzymes / K-demethylases"	20815	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 2A"	611512	"jumonji domain containing 1", "jumonji domain containing 1A"	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.3885+1CAGGTAAAAATAG>-	chr2.hg19:g.86718396_86718408delCAGGTAAAAATAG		90.0	0.0		96.0	16.0	NM_018433	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Frame_Shift_Del	DEL	ENST00000409556.1	hg19	CCDS1990.1																																																																																			.	.		0.399	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	Frame_Shift_Del	-	86718408	CAGGTAAAAATAG	-	86718396	8	5	181	1	0	1	0	1	0	0	1	0	8135	479	17	0	3977	0	KDM3A	2	86718396	Splice_Site	DEL	CAGGTAAAAATAG	TCGA-DD-AAD5-01A-11D-A40R-10	15127268	86718396	156480977	24	27010										
C2orf15	80705	hgsc.bcm.edu	37	chr2	99767195	99767195	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	acaaatcaagaaaactttacAaggattgaagggactggcac	9	7	1	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:99767195A>G	ENST00000393483.3	-	1	225				C2ORF15_ENST00000302513.2_Silent_p.T92T|C2ORF15_ENST00000409684.1_Silent_p.T92T	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10						cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						AAAACTTTACAAGGATTGAAG	0.393																																					p.T92T		Atlas-SNP	.											.	C2orf15	11	.	0			c.A276G						.						86	89	88					2																	99767195		2203	4300	6503	SO:0001627	intron_variant	150590	exon4			CTTTACAAGGATT	AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.619+3960T>C	chr2.hg19:g.99767195A>G		477.0	0.0		418.0	120.0	NM_144706	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Silent	SNP	ENST00000393483.3	hg19	CCDS2037.1																																																																																			.	.		0.393	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		G	99767195	A	G	99767195	1	3	181	0	1	0	0	0	0	0	0	0	2158	117	5	2		2	C2orf15	2	99767195	Intron	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	13048799	99767195	143432178	25	27011										
EIF5B	9669	hgsc.bcm.edu	37	chr2	99976706	99976706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gttttcatttaagcaccaagGatgacattgatcttgatgcc	8	8	2	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:99976706G>A	ENST00000289371.6	+	2	245	c.43G>A	c.(43-45)Gat>Aat	p.D15N		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	15					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AAGCACCAAGGATGACATTGA	0.333																																					p.D15N	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											.	EIF5B	95	.	0			c.G43A						.						77	70	72					2																	99976706		1839	4086	5925	SO:0001583	missense	9669	exon2			ACCAAGGATGACA	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"translation initiation factor IF2"	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.43G>A	chr2.hg19:g.99976706G>A	ENSP00000289371:p.Asp15Asn	506.0	0.0		462.0	146.0	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Missense_Mutation	SNP	ENST00000289371.6	hg19	CCDS42721.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.415768	0.83449	.	.	ENSG00000158417	ENST00000289371	T	0.47528	0.84	5.32	5.32	0.75619	.	.	.	.	.	T	0.52240	0.1722	M	0.77103	2.36	0.80722	D	1	B	0.31383	0.321	B	0.29663	0.105	T	0.52571	-0.8558	8	.	.	.	-22.6289	19.3507	0.94384	0.0:0.0:1.0:0.0	.	15	O60841	IF2P_HUMAN	N	15	ENSP00000289371:D15N	.	D	+	1	0	EIF5B	99343138	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.942000	0.92970	2.633000	0.89246	0.655000	0.94253	GAT	.	.		0.333	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904		A	99976706	G	A	99976706	3	1	181	1	0	0	0	0	1	0	0	0	5046	1174	41	3	49	3	EIF5B	2	99976706	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	209511	99976706	143222667	26	27012										
SEPT10	151011	hgsc.bcm.edu	37	chr2	110332246	110332246	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agtagagacacacatggatgCgagaatcatggtaggtaaag	13	5	1	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:110332246C>A	ENST00000397712.2	-	5	890	c.512G>T	c.(511-513)cGc>cTc	p.R171L	SEPT10_ENST00000397714.2_Missense_Mutation_p.R148L|SEPT10_ENST00000334001.6_Missense_Mutation_p.R38L|SEPT10_ENST00000415095.1_Missense_Mutation_p.R171L|SEPT10_ENST00000437928.1_Missense_Mutation_p.R156L|SEPT10_ENST00000356688.4_Missense_Mutation_p.R171L|SEPT10_ENST00000545389.1_Intron	NM_144710.3	NP_653311.1	Q9P0V9	SEP10_HUMAN	septin 10	171	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			breast(2)|endometrium(3)|large_intestine(4)|lung(8)|prostate(1)	18						CACATGGATGCGAGAATCATG	0.443																																					p.R171L		Atlas-SNP	.											SEPT10_ENST00000397712,NS,carcinoma,0,4	SEPT10	58	.	0			c.G512T						.						137	128	131					2																	110332246		1933	4142	6075	SO:0001583	missense	151011	exon5			TGGATGCGAGAAT	AF146760	CCDS42726.1, CCDS46383.1	2q13	2013-01-21			ENSG00000186522	ENSG00000186522		"Septins"	14349	protein-coding gene	gene with protein product	"sept1-like"	611737				12711328	Standard	NM_144710		Approved	FLJ11619	uc002tew.4	Q9P0V9	OTTHUMG00000154957	ENST00000397712.2:c.512G>T	chr2.hg19:g.110332246C>A	ENSP00000380824:p.Arg171Leu	109.0	1.0		95.0	31.0	NM_144710	B3KRQ9|Q86VP5|Q9HAH6	Missense_Mutation	SNP	ENST00000397712.2	hg19	CCDS46383.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.541402	0.65085	.	.	ENSG00000186522	ENST00000352314;ENST00000356688;ENST00000397712;ENST00000397714;ENST00000334001;ENST00000437928;ENST00000415095	T;T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41;-0.41;-0.41	4.78	4.78	0.61160	.	0.000000	0.64402	D	0.000004	D	0.88618	0.6485	H	0.97214	3.96	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.982	D;D;D;P	0.97110	1.0;1.0;0.999;0.78	D	0.92620	0.6107	10	0.87932	D	0	.	18.3425	0.90311	0.0:1.0:0.0:0.0	.	38;171;148;171	B7Z371;B5ME97;Q9P0V9-3;Q9P0V9	.;.;.;SEP10_HUMAN	L	129;171;171;148;38;156;171	ENSP00000349116:R171L;ENSP00000380824:R171L;ENSP00000380826:R148L;ENSP00000334234:R38L;ENSP00000407790:R156L;ENSP00000396728:R171L	ENSP00000334234:R38L	R	-	2	0	SEPT10	109689535	1.000000	0.71417	0.971000	0.41717	0.077000	0.17291	7.171000	0.77595	2.634000	0.89283	0.491000	0.48974	CGC	.	.		0.443	SEPT10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337804.1	NM_144710		A	110332246	C	A	110332246	3	1	181	1	0	0	0	0	1	0	0	0	14075	768	27	1	880	1	SEPT10	2	110332246	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	10355540	110332246	132867127	27	27013										
FZD5	7855	hgsc.bcm.edu	37	chr2	208633107	208633107	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gcgaagccgtactggcgcatCagcggcgagcagccggcctt	15	14	1	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:208633107C>T	ENST00000295417.3	-	2	910	c.357G>A	c.(355-357)ctG>ctA	p.L119L		NM_003468.3	NP_003459.2	Q13467	FZD5_HUMAN	frizzled class receptor 5	119	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				angiogenesis (GO:0001525)|anterior/posterior axis specification, embryo (GO:0008595)|apoptotic process (GO:0006915)|apoptotic process involved in morphogenesis (GO:0060561)|axonogenesis (GO:0007409)|brain development (GO:0007420)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)|cell maturation (GO:0048469)|cellular response to molecule of bacterial origin (GO:0071219)|chorionic trophoblast cell differentiation (GO:0060718)|embryonic axis specification (GO:0000578)|embryonic camera-type eye development (GO:0031076)|gonad development (GO:0008406)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|neuron differentiation (GO:0030182)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic camera-type eye development (GO:0031077)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of chorionic trophoblast cell proliferation (GO:1901382)|regulation of tight junction assembly (GO:2000810)|Spemann organizer formation (GO:0060061)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell differentiation in thymus (GO:0033077)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	cell projection (GO:0042995)|cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			NS(1)|kidney(1)|lung(1)|ovary(2)|prostate(1)|skin(1)	7				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.13)|Lung(261;0.134)		ACTGGCGCATCAGCGGCGAGC	0.687																																					p.L119L		Atlas-SNP	.											.	FZD5	22	.	0			c.G357A						.						12	13	13					2																	208633107		2190	4278	6468	SO:0001819	synonymous_variant	7855	exon2			GCGCATCAGCGGC	U43318	CCDS33366.1	2q33.3	2014-01-29	2014-01-29		ENSG00000163251	ENSG00000163251		"GPCR / Class F : Frizzled receptors"	4043	protein-coding gene	gene with protein product		601723	"frizzled (Drosophila) homolog 5", "chromosome 2 open reading frame 31", "frizzled homolog 5 (Drosophila)", "frizzled 5, seven transmembrane spanning receptor", "frizzled family receptor 5"	C2orf31		8626800, 11408929	Standard	NM_003468		Approved	HFZ5, DKFZP434E2135	uc002vcj.3	Q13467	OTTHUMG00000154790	ENST00000295417.3:c.357G>A	chr2.hg19:g.208633107C>T		27.0	0.0		24.0	12.0	NM_003468	A8K2X1|B2RCZ1|Q53R22	Silent	SNP	ENST00000295417.3	hg19	CCDS33366.1																																																																																			.	.		0.687	FZD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337060.1	NM_003468		T	208633107	C	T	208633107	2	4	181	1	0	0	0	0	0	0	0	1	6141	813	29	3		3	FZD5	2	208633107	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	98300861	208633107	34566266	28	27014										
AGFG1	3267	hgsc.bcm.edu	37	chr2	228401645	228401645	+	Silent	SNP	T	T	A													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tccacaaatccatttgttgcTgctgctggtccttctgtggc							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:228401645T>A	ENST00000310078.8	+	10	1574	c.1314T>A	c.(1312-1314)gcT>gcA	p.A438A	AGFG1_ENST00000409315.1_Silent_p.A417A|AGFG1_ENST00000409979.2_Silent_p.A462A|AGFG1_ENST00000373671.3_Silent_p.A398A|AGFG1_ENST00000409171.1_Silent_p.A438A	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	438					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						CATTTGTTGCTGCTGCTGGTC	0.348																																					p.A462A		Atlas-SNP	.											.	AGFG1	80	.	0			c.T1386A						.						88	89	89					2																	228401645		2203	4300	6503	SO:0001819	synonymous_variant	3267	exon11			TGTTGCTGCTGCT		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"ADP-ribosylation factor GTPase activating proteins"	5175	protein-coding gene	gene with protein product		600862	"HIV-1 Rev binding protein"	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.1314T>A	chr2.hg19:g.228401645T>A		205.0	0.0		92.0	23.0	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Silent	SNP	ENST00000310078.8	hg19	CCDS2467.1																																																																																			.	.		0.348	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		A	228401645	T	A	228401645	2	1	181	1	0	0	0	0	0	0	0	1	380	1567	55	4		4	AGFG1	2	228401645	Silent	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	19768538	228401645	14797728	29	27015	130	3								
AGFG1	3267	hgsc.bcm.edu	37	chr2	228401648	228401648	+	Silent	SNP	T	T	A													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	acaaatccatttgttgctgcTgctggtccttctgtggcatc							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:228401648T>A	ENST00000310078.8	+	10	1577	c.1317T>A	c.(1315-1317)gcT>gcA	p.A439A	AGFG1_ENST00000409315.1_Silent_p.A418A|AGFG1_ENST00000409979.2_Silent_p.A463A|AGFG1_ENST00000373671.3_Silent_p.A399A|AGFG1_ENST00000409171.1_Silent_p.A439A	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	439					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						TTGTTGCTGCTGCTGGTCCTT	0.353																																					p.A463A		Atlas-SNP	.											.	AGFG1	80	.	0			c.T1389A						.						91	92	92					2																	228401648		2203	4300	6503	SO:0001819	synonymous_variant	3267	exon11			TGCTGCTGCTGGT		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"ADP-ribosylation factor GTPase activating proteins"	5175	protein-coding gene	gene with protein product		600862	"HIV-1 Rev binding protein"	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.1317T>A	chr2.hg19:g.228401648T>A		208.0	0.0		94.0	24.0	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Silent	SNP	ENST00000310078.8	hg19	CCDS2467.1																																																																																			.	.		0.353	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		A	228401648	T	A	228401648	2	1	181	1	0	0	0	0	0	0	0	1	380	1567	55	4		4	AGFG1	2	228401648	Silent	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	3	228401648	14797725	30	27016	130	3								
AGFG1	3267	hgsc.bcm.edu	37	chr2	228401650	228401679	+	In_Frame_Del	DEL	CTGGTCCTTCTGTGGCATCTTCTACAAACC	CTGGTCCTTCTGTGGCATCTTCTACAAACC	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aaatccatttgttgctgctgCtggtccttctgtggcatctt					rs576713176|rs144069697	byFrequency	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	CTGGTCCTTCTGTGGCATCTTCTACAAACC	CTGGTCCTTCTGTGGCATCTTCTACAAACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr2:228401650_228401679delCTGGTCCTTCTGTGGCATCTTCTACAAACC	ENST00000310078.8	+	10	1579_1608	c.1319_1348delCTGGTCCTTCTGTGGCATCTTCTACAAACC	c.(1318-1350)gctggtccttctgtggcatcttctacaaaccca>gca	p.GPSVASSTNP441del	AGFG1_ENST00000409315.1_In_Frame_Del_p.GPSVASSTNP420del|AGFG1_ENST00000409979.2_In_Frame_Del_p.GPSVASSTNP465del|AGFG1_ENST00000373671.3_In_Frame_Del_p.GPSVASSTNP401del|AGFG1_ENST00000409171.1_In_Frame_Del_p.GPSVASSTNP441del	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	441					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						GTTGCTGCTGCTGGTCCTTCTGTGGCATCTTCTACAAACCCATTTCAGAC	0.352																																					p.464_473del		Atlas-INDEL	.											.	AGFG1	80	.	0			c.1390_1419del						.																																			SO:0001651	inframe_deletion	3267	exon11			.		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"ADP-ribosylation factor GTPase activating proteins"	5175	protein-coding gene	gene with protein product		600862	"HIV-1 Rev binding protein"	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.1319_1348delCTGGTCCTTCTGTGGCATCTTCTACAAACC	chr2.hg19:g.228401650_228401679delCTGGTCCTTCTGTGGCATCTTCTACAAACC	ENSP00000312059:p.Gly441_Pro450del	205.0	0.0		93.0	12.0	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	In_Frame_Del	DEL	ENST00000310078.8	hg19	CCDS2467.1																																																																																			.	.		0.352	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		-	228401679	CTGGTCCTTCTGTGGCATCTTCTACAAACC	-	228401650	7	5	181	1	0	1	0	1	0	0	0	0	380	797	28	0	1433	0	AGFG1	2	228401650	In_Frame_Del	DEL	CTGGTCCTTCTGTGGCATCTTCTACAAACC	TCGA-DD-AAD5-01A-11D-A40R-10	2	228401650	14797723	31	27017	130	3								
OXSM	54995	hgsc.bcm.edu	37	chr3	25835810	25835810	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agcttttaccacattagcttGttattatcaaaaactaccac	3	10	1	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:25835810G>C	ENST00000280701.3	+	3	1304	c.1205G>C	c.(1204-1206)tGt>tCt	p.C402S	OXSM_ENST00000420173.2_Missense_Mutation_p.C319S	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	402					acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						ACATTAGCTTGTTATTATCAA	0.453																																					p.C402S		Atlas-SNP	.											.	OXSM	54	.	0			c.G1205C						.						109	111	111					3																	25835810		2203	4300	6503	SO:0001583	missense	54995	exon3			TAGCTTGTTATTA	BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	ENST00000280701.3:c.1205G>C	chr3.hg19:g.25835810G>C	ENSP00000280701:p.Cys402Ser	176.0	0.0		172.0	62.0	NM_017897		Missense_Mutation	SNP	ENST00000280701.3	hg19	CCDS2643.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.909715	0.92107	.	.	ENSG00000151093	ENST00000280701;ENST00000420173	.	.	.	5.52	5.52	0.82312	Beta-ketoacyl synthase, C-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	T	0.63082	0.2481	N	0.12182	0.205	0.48975	D	0.999735	D;D	0.61697	0.99;0.969	D;D	0.76575	0.988;0.987	T	0.70601	-0.4827	9	0.87932	D	0	-16.0775	19.4602	0.94914	0.0:0.0:1.0:0.0	.	319;402	Q9NWU1-2;Q9NWU1	.;OXSM_HUMAN	S	402;319	.	ENSP00000280701:C402S	C	+	2	0	OXSM	25810814	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	9.803000	0.99136	2.590000	0.87494	0.655000	0.94253	TGT	.	.		0.453	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		C	25835810	G	C	25835810	3	2	181	1	0	0	0	0	1	0	0	0	11344	1377	48	4	1211	4	OXSM	3	25835810	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10		25835810	172186620	32	27018										
PLCD1	5333	hgsc.bcm.edu	37	chr3	38049272	38049272	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gcttcctccagcctagtcctGgagggagatcttcacaaaga	10	12	2	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:38049272G>A	ENST00000334661.4	-	15	2485	c.2263C>T	c.(2263-2265)Cag>Tag	p.Q755*	PLCD1_ENST00000463876.1_Nonsense_Mutation_p.Q776*	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	755					angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		GCCTAGTCCTGGAGGGAGATC	0.627																																					p.Q776X		Atlas-SNP	.											.	PLCD1	87	.	0			c.C2326T						.						76	69	71					3																	38049272		2203	4300	6503	SO:0001587	stop_gained	5333	exon15			AGTCCTGGAGGGA		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"EF-hand domain containing"	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.2263C>T	chr3.hg19:g.38049272G>A	ENSP00000335600:p.Gln755*	95.0	0.0		88.0	36.0	NM_001130964	B3KR14|Q86VN8	Nonsense_Mutation	SNP	ENST00000334661.4	hg19	CCDS2671.1	.	.	.	.	.	.	.	.	.	.	G	41	8.576384	0.98870	.	.	ENSG00000187091	ENST00000463876;ENST00000334661	.	.	.	4.9	2.9	0.33743	.	0.527083	0.20603	N	0.089116	.	.	.	.	.	.	0.34752	D	0.731866	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.0853	0.14678	0.0799:0.2572:0.5277:0.1352	.	.	.	.	X	776;755	.	ENSP00000335600:Q755X	Q	-	1	0	PLCD1	38024276	0.502000	0.26107	0.903000	0.35520	0.920000	0.55202	0.872000	0.28037	1.128000	0.42052	0.655000	0.94253	CAG	.	.		0.627	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2			A	38049272	G	A	38049272	4	1	181	1	0	0	0	0	0	1	0	0	12040	1357	47	3	11	3	PLCD1	3	38049272	Nonsense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	12213462	38049272	159973158	33	27019										
WDR5B	54554	hgsc.bcm.edu	37	chr3	122133743	122133743	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aattttacaaaagagacaggAgggttatcgtcatcaacgag	10	6	2	1	rs559697273		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:122133743A>G	ENST00000330689.4	-	1	1139	c.633T>C	c.(631-633)ccT>ccC	p.P211P	RP11-299J3.8_ENST00000608015.1_RNA|RP11-299J3.8_ENST00000608465.1_RNA|RP11-299J3.8_ENST00000608756.1_RNA|RP11-299J3.8_ENST00000609469.1_RNA|RP11-299J3.8_ENST00000608346.1_RNA	NM_019069.3	NP_061942.2	Q86VZ2	WDR5B_HUMAN	WD repeat domain 5B	211										kidney(2)|large_intestine(4)|lung(2)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.0704)		AAGAGACAGGAGGGTTATCGT	0.433																																					p.P211P		Atlas-SNP	.											.	WDR5B	36	.	0			c.T633C						.						103	108	107					3																	122133743		2203	4300	6503	SO:0001819	synonymous_variant	54554	exon1			GACAGGAGGGTTA	AK002149	CCDS3012.1	3q21.1	2013-01-09			ENSG00000196981	ENSG00000196981		"WD repeat domain containing"	17826	protein-coding gene	gene with protein product						10369878	Standard	NM_019069		Approved	FLJ11287	uc003efa.1	Q86VZ2	OTTHUMG00000159489	ENST00000330689.4:c.633T>C	chr3.hg19:g.122133743A>G		97.0	0.0		96.0	35.0	NM_019069	B2RCM9|Q9NUL4	Silent	SNP	ENST00000330689.4	hg19	CCDS3012.1																																																																																			.	.		0.433	WDR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355753.1	NM_019069		G	122133743	A	G	122133743	2	3	181	1	0	0	0	0	0	0	0	1	17324	291	11	2		2	WDR5B	3	122133743	Silent	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	84084471	122133743	75888687	34	27020										
SNX4	8723	hgsc.bcm.edu	37	chr3	125195601	125195601	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tagagtcgatctgctactctCtgaaataaatatttaataga	6	6	2	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:125195601C>A	ENST00000251775.4	-	8	751		c.e8-1		SNX4_ENST00000536067.1_Splice_Site|SNX4_ENST00000473417.1_Splice_Site	NM_003794.2	NP_003785.1	O95219	SNX4_HUMAN	sorting nexin 4						endocytic recycling (GO:0032456)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|early endosome membrane (GO:0031901)|membrane (GO:0016020)|protein complex (GO:0043234)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			breast(2)|central_nervous_system(1)|lung(6)|ovary(1)|skin(1)	11						CTGCTACTCTCTGAAATAAAT	0.279																																					.		Atlas-SNP	.											.	SNX4	29	.	0			c.727-1G>T						.						47	49	48					3																	125195601		2202	4292	6494	SO:0001630	splice_region_variant	8723	exon9			TACTCTCTGAAAT	AF065485	CCDS3032.1	3q21.2	2014-02-12			ENSG00000114520	ENSG00000114520		"Sorting nexins"	11175	protein-coding gene	gene with protein product		605931				9819414	Standard	NM_003794		Approved	ATG24B	uc003eib.4	O95219	OTTHUMG00000159575	ENST00000251775.4:c.727-1G>T	chr3.hg19:g.125195601C>A		483.0	0.0		445.0	136.0	NM_003794	B3KMH0|B4DQV4|D3DNA3	Splice_Site	SNP	ENST00000251775.4	hg19	CCDS3032.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.383632	0.61845	.	.	ENSG00000114520	ENST00000251775;ENST00000536067	.	.	.	4.08	4.08	0.47627	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6388	0.62237	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SNX4	126678291	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.749000	0.62155	2.262000	0.75019	0.557000	0.71058	.	.	.		0.279	SNX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356299.1	NM_003794	Intron	A	125195601	C	A	125195601	5	1	181	1	0	0	0	0	0	0	1	0	14919	927	32	3	654	3	SNX4	3	125195601	Splice_Site	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	3061858	125195601	72826829	35	27021										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126736619	126736619	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	acctcttgccacctgcacccGgcaactcccgactcaactac	5	20	2	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:126736619G>T	ENST00000393409.2	+	18	3544	c.3544G>T	c.(3544-3546)Ggc>Tgc	p.G1182C	PLXNA1_ENST00000251772.4_Missense_Mutation_p.G1159C	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1182	IPT/TIG 4.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		ACCTGCACCCGGCAACTCCCG	0.657																																					p.G1182C		Atlas-SNP	.											.	PLXNA1	185	.	0			c.G3544T						.						101	92	95					3																	126736619		2203	4300	6503	SO:0001583	missense	5361	exon18			GCACCCGGCAACT	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.3544G>T	chr3.hg19:g.126736619G>T	ENSP00000377061:p.Gly1182Cys	94.0	0.0		93.0	37.0	NM_032242		Missense_Mutation	SNP	ENST00000393409.2	hg19	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	G	17.84	3.488066	0.64074	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.79454	-1.27;-1.27	4.49	3.59	0.41128	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.393150	0.23904	N	0.043410	D	0.89396	0.6703	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91123	0.4931	10	0.87932	D	0	.	13.6307	0.62193	0.0:0.0:0.8438:0.1562	.	1182	Q9UIW2	PLXA1_HUMAN	C	1182;1159	ENSP00000377061:G1182C;ENSP00000251772:G1159C	ENSP00000251772:G1159C	G	+	1	0	PLXNA1	128219309	1.000000	0.71417	0.740000	0.30986	0.410000	0.31052	9.556000	0.98127	1.052000	0.40392	0.591000	0.81541	GGC	.	.		0.657	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		T	126736619	G	T	126736619	3	4	181	1	0	0	0	0	1	0	0	0	12128	1116	39	1	3614	1	PLXNA1	3	126736619	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	1541018	126736619	71285811	36	27022										
CEP63	80254	hgsc.bcm.edu	37	chr3	134278032	134278032	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gacatgatggaataaagactGagcactacaaaacagatctt	8	7	1	4			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:134278032G>A	ENST00000337090.3	+	14	1887	c.1714G>A	c.(1714-1716)Gag>Aag	p.E572K	CEP63_ENST00000606977.1_Missense_Mutation_p.E572K|CEP63_ENST00000513612.2_Missense_Mutation_p.E572K|CEP63_ENST00000332047.5_Intron|CEP63_ENST00000383229.3_Intron|CEP63_ENST00000354446.3_Intron			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	572					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						AATAAAGACTGAGCACTACAA	0.433																																					p.E572K		Atlas-SNP	.											CEP63,bladder,carcinoma,0,1	CEP63	56	.	0			c.G1714A						.						139	139	139					3																	134278032		2203	4300	6503	SO:0001583	missense	80254	exon15			AAGACTGAGCACT	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1714G>A	chr3.hg19:g.134278032G>A	ENSP00000336524:p.Glu572Lys	135.0	0.0		159.0	39.0	NM_025180	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	hg19	CCDS3086.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627300	0.28978	.	.	ENSG00000182923	ENST00000337090;ENST00000513612	T;T	0.17854	2.25;2.25	4.77	3.87	0.44632	.	0.502640	0.20145	N	0.098283	T	0.16214	0.0390	L	0.50333	1.59	0.30373	N	0.782667	B	0.30634	0.288	B	0.33690	0.168	T	0.10086	-1.0645	10	0.14252	T	0.57	-5.5258	10.9666	0.47416	0.0:0.189:0.811:0.0	.	572	Q96MT8	CEP63_HUMAN	K	572	ENSP00000336524:E572K;ENSP00000426129:E572K	ENSP00000336524:E572K	E	+	1	0	CEP63	135760722	1.000000	0.71417	0.584000	0.28653	0.821000	0.46438	4.444000	0.60001	1.305000	0.44909	0.650000	0.86243	GAG	.	.		0.433	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180		A	134278032	G	A	134278032	3	1	181	1	0	0	0	0	1	0	0	0	3259	1291	45	3	1764	3	CEP63	3	134278032	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	7541413	134278032	63744398	37	27023										
ESYT3	83850	hgsc.bcm.edu	37	chr3	138153695	138153695	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ccagcgccctgggagcccagCgcacgccgggccccgagctg	15	19	0	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:138153695C>G	ENST00000389567.4	+	1	241	c.55C>G	c.(55-57)Cgc>Ggc	p.R19G	ESYT3_ENST00000289135.4_Missense_Mutation_p.R19G	NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	19					lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|organelle membrane contact site (GO:0044232)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	25						GGGAGCCCAGCGCACGCCGGG	0.706																																					p.R19G		Atlas-SNP	.											.	ESYT3	64	.	0			c.C55G						.						13	15	14					3																	138153695		1984	3860	5844	SO:0001583	missense	83850	exon1			GCCCAGCGCACGC	AJ303366	CCDS3101.2	3q22.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000158220	ENSG00000158220		"Synaptotagmins"	24295	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member C"	FAM62C		11543631, 17672888	Standard	NM_031913		Approved	CHR3SYT	uc003esk.3	A0FGR9	OTTHUMG00000147354	ENST00000389567.4:c.55C>G	chr3.hg19:g.138153695C>G	ENSP00000374218:p.Arg19Gly	45.0	0.0		43.0	15.0	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Missense_Mutation	SNP	ENST00000389567.4	hg19	CCDS3101.2	.	.	.	.	.	.	.	.	.	.	C	9.358	1.067160	0.20067	.	.	ENSG00000158220	ENST00000389567;ENST00000289135	T;T	0.37752	1.18;1.46	3.92	1.98	0.26296	.	0.801478	0.11504	N	0.557351	T	0.21468	0.0517	N	0.22421	0.69	0.09310	N	0.999994	B	0.02656	0.0	B	0.04013	0.001	T	0.25467	-1.0131	10	0.22706	T	0.39	-9.8139	6.4832	0.22075	0.209:0.5885:0.2025:0.0	.	19	A0FGR9	ESYT3_HUMAN	G	19	ENSP00000374218:R19G;ENSP00000289135:R19G	ENSP00000289135:R19G	R	+	1	0	ESYT3	139636385	0.937000	0.31787	0.026000	0.17262	0.030000	0.12068	1.496000	0.35638	0.356000	0.24157	0.561000	0.74099	CGC	.	.		0.706	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913		G	138153695	C	G	138153695	3	3	181	1	0	0	0	0	1	0	0	0	5268	768	27	4	57	4	ESYT3	3	138153695	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	3875663	138153695	59868735	38	27024										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140409822	140409822	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ttccataggtttactggacaTgtccagcagaagacgtggac	11	9	0	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:140409822T>C	ENST00000286349.3	+	4	2064	c.1873T>C	c.(1873-1875)Tgt>Cgt	p.C625R		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	625	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TTACTGGACATGTCCAGCAGA	0.398																																					p.C625R		Atlas-SNP	.											.	TRIM42	143	.	0			c.T1873C						.						115	105	108					3																	140409822		2203	4300	6503	SO:0001583	missense	287015	exon4			TGGACATGTCCAG	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.1873T>C	chr3.hg19:g.140409822T>C	ENSP00000286349:p.Cys625Arg	112.0	0.0		109.0	30.0	NM_152616	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	hg19	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	T	18.30	3.593379	0.66219	.	.	ENSG00000155890	ENST00000286349	T	0.55588	0.51	5.82	5.82	0.92795	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.59059	0.2166	N	0.24115	0.695	0.58432	D	0.999999	D	0.76494	0.999	D	0.87578	0.998	T	0.63857	-0.6542	10	0.87932	D	0	-29.5266	12.5738	0.56352	0.0:0.0:0.0:1.0	.	625	Q8IWZ5	TRI42_HUMAN	R	625	ENSP00000286349:C625R	ENSP00000286349:C625R	C	+	1	0	TRIM42	141892512	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.279000	0.51670	2.222000	0.72286	0.528000	0.53228	TGT	.	.		0.398	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		C	140409822	T	C	140409822	3	2	181	1	0	0	0	0	1	0	0	0	16532	1464	51	2	1887	2	TRIM42	3	140409822	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	2256127	140409822	57612608	39	27025										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151160830	151160830	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ccacattatttggggtttggGctccccagtggctgagcagt	13	10	0	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:151160830G>A	ENST00000282466.3	-	5	5904	c.5905C>T	c.(5905-5907)Ccc>Tcc	p.P1969S	IGSF10_ENST00000495443.1_5'Flank	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1969	Ig-like C2-type 6.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGGGGTTTGGGCTCCCCAGTG	0.478																																					p.P1969S		Atlas-SNP	.											.	IGSF10	279	.	0			c.C5905T						.						112	109	110					3																	151160830		2203	4300	6503	SO:0001583	missense	285313	exon5			GTTTGGGCTCCCC	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5905C>T	chr3.hg19:g.151160830G>A	ENSP00000282466:p.Pro1969Ser	94.0	0.0		73.0	16.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.390620	0.82902	.	.	ENSG00000152580	ENST00000489791;ENST00000282466;ENST00000544042	T;T	0.73897	-0.79;-0.79	5.38	5.38	0.77491	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.47852	D	0.000217	D	0.90469	0.7015	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92570	0.6065	10	0.62326	D	0.03	.	19.1316	0.93410	0.0:0.0:1.0:0.0	.	1969	Q6WRI0	IGS10_HUMAN	S	37;1969;596	ENSP00000417627:P37S;ENSP00000282466:P1969S	ENSP00000282466:P1969S	P	-	1	0	IGSF10	152643520	1.000000	0.71417	0.373000	0.26003	0.996000	0.88848	9.793000	0.99091	2.545000	0.85829	0.591000	0.81541	CCC	.	.		0.478	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151160830	G	A	151160830	3	1	181	1	0	0	0	0	1	0	0	0	7606	1203	42	3	2022	3	IGSF10	3	151160830	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	10751008	151160830	46861600	40	27026										
GFM1	85476	hgsc.bcm.edu	37	chr3	158407956	158407956	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tttttttttaacccagccttGgcaaatgcaacattatgtat	5	8	0	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:158407956G>C	ENST00000486715.1	+	16	2271	c.1914G>C	c.(1912-1914)ttG>ttC	p.L638F	GFM1_ENST00000264263.5_Missense_Mutation_p.L657F|RP11-379F4.7_ENST00000607624.1_lincRNA	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			ACCCAGCCTTGGCAAATGCAA	0.358																																					p.L638F		Atlas-SNP	.											.	GFM1	83	.	0			c.G1914C						.						94	99	97					3																	158407956		2203	4300	6503	SO:0001583	missense	85476	exon16			AGCCTTGGCAAAT	AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"G translation elongation factor, mitochondrial"			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.1914G>C	chr3.hg19:g.158407956G>C	ENSP00000419038:p.Leu638Phe	91.0	0.0		63.0	18.0	NM_024996		Missense_Mutation	SNP	ENST00000486715.1	hg19	CCDS33885.1	.	.	.	.	.	.	.	.	.	.	G	6.970	0.548868	0.13312	.	.	ENSG00000168827	ENST00000486715;ENST00000264263	T;T	0.32753	1.44;1.44	5.9	5.03	0.67393	Ribosomal protein S5 domain 2-type fold (1);Translation elongation factor EFG/EF2, domain IV (2);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.123048	0.52532	D	0.000073	T	0.11750	0.0286	N	0.01515	-0.825	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.12156	0.005;0.007	T	0.13202	-1.0518	10	0.07325	T	0.83	-0.6617	15.0639	0.71977	0.0677:0.0:0.9323:0.0	.	657;638	Q96RP9-2;Q96RP9	.;EFGM_HUMAN	F	638;657	ENSP00000419038:L638F;ENSP00000264263:L657F	ENSP00000264263:L657F	L	+	3	2	GFM1	159890650	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	6.298000	0.72763	1.496000	0.48567	0.650000	0.86243	TTG	.	.		0.358	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996		C	158407956	G	C	158407956	3	2	181	1	0	0	0	0	1	0	0	0	6349	1339	47	4	1976	4	GFM1	3	158407956	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	7247126	158407956	39614474	41	27027										
ECT2	1894	hgsc.bcm.edu	37	chr3	172479465	172479468	+	Frame_Shift_Del	DEL	GAAT	GAAT	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tataaagcttgggaaaggcgGaatgaacagtaagtgtttag					rs531984277		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	GAAT	GAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr3:172479465_172479468delGAAT	ENST00000392692.3	+	8	926_929	c.750_753delGAAT	c.(748-753)cggaatfs	p.RN250fs	ECT2_ENST00000417960.1_Frame_Shift_Del_p.RN218fs|ECT2_ENST00000441497.2_Frame_Shift_Del_p.RN219fs|ECT2_ENST00000540509.1_Frame_Shift_Del_p.RN250fs|ECT2_ENST00000427830.1_Frame_Shift_Del_p.RN219fs|ECT2_ENST00000232458.5_Frame_Shift_Del_p.RN219fs	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2	250	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				activation of protein kinase activity (GO:0032147)|activation of Rac GTPase activity (GO:0032863)|activation of Rho GTPase activity (GO:0032862)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular response to calcium ion (GO:0071277)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of Rho GTPase activity (GO:0032321)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|centralspindlin complex (GO:0097149)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			GGGAAAGGCGGAATGAACAGTAAG	0.309																																					p.250_251del		Atlas-INDEL	.											.	ECT2	79	.	0			c.749_752del						.																																			SO:0001589	frameshift_variant	1894	exon8			.	AA206473	CCDS3220.1, CCDS58860.1	3q26.1-q26.2	2014-03-11	2014-03-11		ENSG00000114346	ENSG00000114346		"Rho guanine nucleotide exchange factors"	3155	protein-coding gene	gene with protein product		600586	"epithelial cell transforming sequence 2 oncogene"			8464478, 10579713	Standard	NM_018098		Approved	ARHGEF31	uc003fil.2	Q9H8V3	OTTHUMG00000156762	ENST00000392692.3:c.750_753delGAAT	chr3.hg19:g.172479465_172479468delGAAT	ENSP00000376457:p.Arg250fs	130.0	0.0		165.0	74.0	NM_001258315	Q0MT80|Q2M269|Q6U836|Q9NSV8|Q9NVW9	Frame_Shift_Del	DEL	ENST00000392692.3	hg19	CCDS58860.1																																																																																			.	.		0.309	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	NM_018098		-	172479468	GAAT	-	172479465	7	5	181	1	0	1	0	1	0	0	0	0	4903	1161	41	0	679	0	ECT2	3	172479465	Frame_Shift_Del	DEL	GAAT	TCGA-DD-AAD5-01A-11D-A40R-10	14071509	172479465	25542965	42	27028										
HS3ST1	9957	hgsc.bcm.edu	37	chr4	11401299	11401299	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cactgtgagctggtgtggccAggagaagggcatctggctga	17	8	1	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr4:11401299A>T	ENST00000002596.5	-	2	1505	c.331T>A	c.(331-333)Tgg>Agg	p.W111R		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	111					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						TGGTGTGGCCAGGAGAAGGGC	0.627																																					p.W111R		Atlas-SNP	.											.	HS3ST1	41	.	0			c.T331A						.						80	75	77					4																	11401299		2203	4300	6503	SO:0001583	missense	9957	exon2			GTGGCCAGGAGAA	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"Sulfotransferases, membrane-bound"	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.331T>A	chr4.hg19:g.11401299A>T	ENSP00000002596:p.Trp111Arg	110.0	0.0		48.0	25.0	NM_005114	B3KUA6|Q6PEY8	Missense_Mutation	SNP	ENST00000002596.5	hg19	CCDS3408.1	.	.	.	.	.	.	.	.	.	.	A	10.08	1.252423	0.22880	.	.	ENSG00000002587	ENST00000002596	T	0.81330	-1.48	5.61	-1.52	0.08637	Sulfotransferase domain (1);	0.882108	0.10028	N	0.725175	T	0.51856	0.1699	N	0.01352	-0.895	0.09310	N	1	B	0.20261	0.043	B	0.12156	0.007	T	0.39603	-0.9606	10	0.28530	T	0.3	.	9.9307	0.41521	0.4753:0.4606:0.0641:0.0	.	111	O14792	HS3S1_HUMAN	R	111	ENSP00000002596:W111R	ENSP00000002596:W111R	W	-	1	0	HS3ST1	11010397	0.000000	0.05858	0.005000	0.12908	0.952000	0.60782	0.048000	0.14078	-0.382000	0.07870	0.533000	0.62120	TGG	.	.		0.627	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114		T	11401299	A	T	11401299	3	4	181	1	0	0	0	0	1	0	0	0	7372	188	7	4	596	4	HS3ST1	4	11401299	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10		11401299	179752977	43	27029										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30723995	30723995	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agcgtgtacgaggccgacttGgctgagaacagcgccccggg	16	12	0	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr4:30723995G>T	ENST00000361762.2	+	1	1959	c.951G>T	c.(949-951)ttG>ttT	p.L317F	PCDH7_ENST00000543491.1_Missense_Mutation_p.L317F	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	317	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						AGGCCGACTTGGCTGAGAACA	0.667																																					p.L317F		Atlas-SNP	.											.	PCDH7	215	.	0			c.G951T						.						15	19	18					4																	30723995		2192	4285	6477	SO:0001583	missense	5099	exon1			CGACTTGGCTGAG	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.951G>T	chr4.hg19:g.30723995G>T	ENSP00000355243:p.Leu317Phe	197.0	0.0		123.0	52.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.15|14.15	2.449958|2.449958	0.43531|0.43531	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000511884|ENST00000361762;ENST00000543491;ENST00000333135	.|T;T	.|0.54071	.|0.59;0.59	5.29|5.29	4.44|4.44	0.53790|0.53790	.|Cadherin (3);Cadherin-like (1);	.|.	.|.	.|.	.|.	T|T	0.72740|0.72740	0.3498|0.3498	M|M	0.75085|0.75085	2.285|2.285	0.46774|0.46774	D|D	0.99919|0.99919	.|D;D;D	.|0.65815	.|0.994;0.994;0.995	.|D;D;D	.|0.74348	.|0.983;0.983;0.982	T|T	0.75777|0.75777	-0.3198|-0.3198	5|9	.|0.72032	.|D	.|0.01	.|.	17.0418|17.0418	0.86491|0.86491	0.0683:0.0:0.9317:0.0|0.0683:0.0:0.9317:0.0	.|.	.|317;270;317	.|F5GWJ1;O60245-3;O60245	.|.;.;PCDH7_HUMAN	C|F	7|317;317;270	.|ENSP00000355243:L317F;ENSP00000441802:L317F	.|ENSP00000330302:L270F	G|L	+|+	1|3	0|2	PCDH7|PCDH7	30333093|30333093	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.781000|0.781000	0.44180|0.44180	1.711000|1.711000	0.37930|0.37930	0.616000|0.616000	0.30141|0.30141	-1.134000|-1.134000	0.01955|0.01955	GGC|TTG	.	.		0.667	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		T	30723995	G	T	30723995	3	4	181	1	0	0	0	0	1	0	0	0	11525	1339	47	3	953	3	PCDH7	4	30723995	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	19322696	30723995	160430281	44	27030										
NUDT6	11162	hgsc.bcm.edu	37	chr4	123818824	123818824	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gcctcctggaaacttccacaTatttttcaactgcagtataa	5	11	1	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr4:123818824T>C	ENST00000304430.5	-	4	541	c.508A>G	c.(508-510)Atg>Gtg	p.M170V	FGF2_ENST00000264498.3_3'UTR|NUDT6_ENST00000502270.1_Start_Codon_SNP_p.M1V|NUDT6_ENST00000339154.2_Start_Codon_SNP_p.M1V	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	170	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)			endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						AACTTCCACATATTTTTCAAC	0.313																																					p.M170V		Atlas-SNP	.											.	NUDT6	50	.	0			c.A508G						.						52	57	55					4																	123818824		2203	4298	6501	SO:0001583	missense	11162	exon4			TCCACATATTTTT	AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"Nudix motif containing"	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.508A>G	chr4.hg19:g.123818824T>C	ENSP00000306070:p.Met170Val	652.0	1.0		542.0	215.0	NM_007083	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	hg19	CCDS43268.1	.	.	.	.	.	.	.	.	.	.	T	11.19	1.565738	0.27915	.	.	ENSG00000170917	ENST00000304430;ENST00000339154;ENST00000510735;ENST00000502270	T;T;T	0.07567	3.18;3.18;3.18	5.08	3.91	0.45181	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.152108	0.56097	D	0.000022	T	0.04227	0.0117	N	0.13352	0.335	0.80722	D	1	B	0.23540	0.087	B	0.26770	0.073	T	0.41980	-0.9478	10	0.13108	T	0.6	1.6589	5.636	0.17536	0.0:0.2587:0.0:0.7413	.	170	P53370	NUDT6_HUMAN	V	170;1;40;1	ENSP00000306070:M170V;ENSP00000344011:M1V;ENSP00000424117:M1V	ENSP00000306070:M170V	M	-	1	0	NUDT6	124038274	1.000000	0.71417	0.976000	0.42696	0.984000	0.73092	3.242000	0.51384	2.130000	0.65690	0.477000	0.44152	ATG	.	.		0.313	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083		C	123818824	T	C	123818824	3	2	181	1	0	0	0	0	1	0	0	0	10752	1406	49	2	450	2	NUDT6	4	123818824	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	93094829	123818824	67335452	45	27031										
FAT1	2195	hgsc.bcm.edu	37	chr4	187541512	187541512	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ttgacaaacaccggcgcattAtcattttggtcttctacaat	6	10	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr4:187541512A>G	ENST00000441802.2	-	10	6437	c.6228T>C	c.(6226-6228)gaT>gaC	p.D2076D		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2076	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CCGGCGCATTATCATTTTGGT	0.493										HNSCC(5;0.00058)																											p.D2076D	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T6228C						.						164	158	160					4																	187541512		1973	4147	6120	SO:0001819	synonymous_variant	2195	exon10			CGCATTATCATTT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.6228T>C	chr4.hg19:g.187541512A>G		131.0	0.0		90.0	45.0	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.493	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187541512	A	G	187541512	2	3	181	1	0	0	0	0	0	0	0	1	5697	446	16	2		2	FAT1	4	187541512	Silent	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	63722688	187541512	3612764	46	27032										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5462837	5462838	+	Frame_Shift_Ins	INS	-	-	A													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	atgctcctgatgactcacagINSaaaaatttaggagacacaga					rs202082834	byFrequency	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr5:5462837_5462838insA	ENST00000296564.7	+	13	3612_3613	c.3390_3391insA	c.(3391-3393)aaafs	p.K1131fs		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1131					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						ATGACTCACAGAAAAATTTAGG	0.48																																					p.Q1130fs		Atlas-INDEL	.											KIAA0947_ENST00000296564,NS,carcinoma,0,1	KIAA0947	301	.	0			c.3390_3391insA						.																																			SO:0001589	frameshift_variant	23379	exon13			.																												ENST00000296564.7:c.3395dupA	chr5.hg19:g.5462842_5462842dupA	ENSP00000296564:p.Lys1131fs	71.0	0.0		91.0	14.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Frame_Shift_Ins	INS	ENST00000296564.7	hg19	CCDS47187.1																																																																																			.	.		0.48	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			A	5462838	-	A	5462837	7	5	181	1	0	1	1	0	0	0	0	0	8211	933	33	0	3440	0	KIAA0947	5	5462837	Frame_Shift_Ins	INS	-	TCGA-DD-AAD5-01A-11D-A40R-10		5462837	175452423	47	27033										
HAPLN1	1404	hgsc.bcm.edu	37	chr5	82940201	82940201	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ccattgaaattggatgtaaaAcagaaaacatcatatctgct	6	7	2	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr5:82940201A>G	ENST00000274341.4	-	4	1606	c.756T>C	c.(754-756)tgT>tgC	p.C252C		NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	252	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	TGGATGTAAAACAGAAAACAT	0.403																																					p.C252C		Atlas-SNP	.											.	HAPLN1	79	.	0			c.T756C						.						58	62	61					5																	82940201		2203	4300	6503	SO:0001819	synonymous_variant	1404	exon4			TGTAAAACAGAAA		CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"Immunoglobulin superfamily / V-set domain containing"	2380	protein-coding gene	gene with protein product	"Cartilage link protein", "hyaluronan and proteoglycan link protein 1"	115435	"cartilage linking protein 1"	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.756T>C	chr5.hg19:g.82940201A>G		198.0	0.0		146.0	18.0	NM_001884	B2R9A9	Silent	SNP	ENST00000274341.4	hg19	CCDS4061.1																																																																																			.	.		0.403	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884		G	82940201	A	G	82940201	2	3	181	1	0	0	0	0	0	0	0	1	6963	41	2	2		2	HAPLN1	5	82940201	Silent	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	77477364	82940201	97975059	48	27034										
GPR98	84059	hgsc.bcm.edu	37	chr5	90002212	90002212	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tcaacattaccattcttgagGtaaaactctttttttttttt	3	7	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr5:90002212G>A	ENST00000405460.2	+	38	8826		c.e38+1			NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98						detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CATTCTTGAGGTAAAACTCTT	0.338																																					.		Atlas-SNP	.											.	GPR98	605	.	0			c.8730+1G>A						.						34	33	33					5																	90002212		1806	4078	5884	SO:0001630	splice_region_variant	84059	exon38			CTTGAGGTAAAAC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.8730+1G>A	chr5.hg19:g.90002212G>A		239.0	0.0		226.0	43.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Splice_Site	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.980612	0.53827	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000509621	.	.	.	5.16	5.16	0.70880	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6378	0.91384	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPR98	90037968	1.000000	0.71417	1.000000	0.80357	0.410000	0.31052	9.110000	0.94302	2.403000	0.81681	0.460000	0.39030	.	.	.		0.338	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	Intron	A	90002212	G	A	90002212	5	1	181	1	0	0	0	0	0	0	1	0	6730	1275	44	3	8881	3	GPR98	5	90002212	Splice_Site	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	7062011	90002212	90913048	49	27035										
EGR1	1958	hgsc.bcm.edu	37	chr5	137801456	137801456	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gcctgctcgtccaggatggcCgcggccaaggccgagatgca	15	14	0	1	rs200905400		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr5:137801456C>G	ENST00000239938.4	+	1	278	c.6C>G	c.(4-6)gcC>gcG	p.A2A		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	2					BMP signaling pathway (GO:0030509)|cellular response to antibiotic (GO:0071236)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to gamma radiation (GO:0071480)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hyperoxia (GO:0071455)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to isoquinoline alkaloid (GO:0071317)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mycophenolic acid (GO:0071506)|cellular response to steroid hormone stimulus (GO:0071383)|circadian rhythm (GO:0007623)|cytokine-mediated signaling pathway (GO:0019221)|glomerular mesangial cell proliferation (GO:0072110)|interleukin-1-mediated signaling pathway (GO:0070498)|learning or memory (GO:0007611)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|positive regulation of glomerular metanephric mesangial cell proliferation (GO:0072303)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein sumoylation (GO:0033233)|response to amphetamine (GO:0001975)|response to carbon monoxide (GO:0034465)|response to cocaine (GO:0042220)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to norepinephrine (GO:0071873)|response to nutrient levels (GO:0031667)|skeletal muscle cell differentiation (GO:0035914)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CCAGGATGGCCGCGGCCAAGG	0.682																																					p.A2A		Atlas-SNP	.											.	EGR1	52	.	0			c.C6G						.						40	37	38					5																	137801456		2203	4300	6503	SO:0001819	synonymous_variant	1958	exon1			GATGGCCGCGGCC	M62829	CCDS4206.1	5q23-q31	2013-01-08			ENSG00000120738	ENSG00000120738		"Zinc fingers, C2H2-type"	3238	protein-coding gene	gene with protein product	"nerve growth factor-induced protein A", "transcription factor ETR103", "zinc finger protein 225", "early growth response protein 1"	128990				3127059	Standard	NM_001964		Approved	TIS8, G0S30, NGFI-A, KROX-24, ZIF-268, AT225, ZNF225	uc003ldb.1	P18146	OTTHUMG00000129197	ENST00000239938.4:c.6C>G	chr5.hg19:g.137801456C>G		118.0	0.0		113.0	16.0	NM_001964		Silent	SNP	ENST00000239938.4	hg19	CCDS4206.1																																																																																			.	.		0.682	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964		G	137801456	C	G	137801456	2	3	181	1	0	0	0	0	0	0	0	1	4973	639	23	4		4	EGR1	5	137801456	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	47799244	137801456	43113804	50	27036										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140262072	140262072	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gcgtccaaaagacacggggaCcttctggaggtaaatctgca	12	10	2	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr5:140262072C>A	ENST00000289272.2	+	1	219	c.219C>A	c.(217-219)gaC>gaA	p.D73E	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.D73E	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	73	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACACGGGGACCTTCTGGAGG	0.627																																					p.D73E	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.C219A						.						67	78	74					5																	140262072		2202	4293	6495	SO:0001583	missense	56136	exon1			CGGGGACCTTCTG	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.219C>A	chr5.hg19:g.140262072C>A	ENSP00000289272:p.Asp73Glu	142.0	0.0		111.0	54.0	NM_031865	O75277	Missense_Mutation	SNP	ENST00000289272.2	hg19	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.269838	0.23221	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.25912	1.77;1.77	5.54	2.72	0.32119	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.15652	0.0377	N	0.26042	0.785	0.19945	N	0.999944	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.17722	0.009;0.019;0.005	T	0.26503	-1.0101	9	0.56958	D	0.05	.	2.0063	0.03478	0.1259:0.4186:0.2452:0.2103	.	73;73;73	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	E	73	ENSP00000386821:D73E;ENSP00000289272:D73E	ENSP00000289272:D73E	D	+	3	2	PCDHA13	140242256	0.000000	0.05858	0.998000	0.56505	0.708000	0.40852	-0.445000	0.06845	0.682000	0.31407	0.556000	0.70494	GAC	.	.		0.627	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140262072	C	A	140262072	3	1	181	1	0	0	0	0	1	0	0	0	11532	506	18	3	221	3	PCDHA13	5	140262072	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	2460616	140262072	40653188	51	27037										
STK10	6793	hgsc.bcm.edu	37	chr5	171533682	171533682	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ggcgatctttagcaggacccGcatggggttgagctcgtggt	16	9	1	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr5:171533682G>A	ENST00000176763.5	-	6	1073	c.730C>T	c.(730-732)Cgg>Tgg	p.R244W		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	244	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AGCAGGACCCGCATGGGGTTG	0.652											OREG0017039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R244W		Atlas-SNP	.											.	STK10	100	.	0			c.C730T						.						117	107	110					5																	171533682		2203	4300	6503	SO:0001583	missense	6793	exon6			GGACCCGCATGGG	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.730C>T	chr5.hg19:g.171533682G>A	ENSP00000176763:p.Arg244Trp	106.0	0.0	1893	109.0	20.0	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	hg19	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.133946	0.56828	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.26518	1.73	4.86	2.03	0.26663	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.39226	0.1070	L	0.39633	1.23	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.11470	-1.0586	10	0.87932	D	0	.	12.003	0.53241	0.0:0.0:0.5475:0.4525	.	244	O94804	STK10_HUMAN	W	244	ENSP00000176763:R244W	ENSP00000176763:R244W	R	-	1	2	STK10	171466287	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	0.946000	0.29069	0.238000	0.21222	-0.181000	0.13052	CGG	.	.		0.652	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		A	171533682	G	A	171533682	3	1	181	1	0	0	0	0	1	0	0	0	15301	1086	38	1	2232	1	STK10	5	171533682	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	31271610	171533682	9381578	52	27038										
RNF44	22838	hgsc.bcm.edu	37	chr5	175959156	175959156	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gggagggtaagcgctcatccCgggcaggcgggctggccagg	20	11	1	0	rs545172577		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr5:175959156C>A	ENST00000274811.4	-	3	670	c.146G>T	c.(145-147)cGg>cTg	p.R49L	RNF44_ENST00000537487.1_Intron|RNF44_ENST00000509404.1_5'Flank	NM_014901.4	NP_055716.1	Q7L0R7	RNF44_HUMAN	ring finger protein 44	49	Pro-rich.						zinc ion binding (GO:0008270)			endometrium(2)|lung(3)|prostate(1)|skin(1)|stomach(1)	8	all_cancers(89;0.0029)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCGCTCATCCCGGGCAGGCGG	0.731																																					p.R49L		Atlas-SNP	.											.	RNF44	33	.	0			c.G146T						.						9	12	11					5																	175959156		2168	4234	6402	SO:0001583	missense	22838	exon3			TCATCCCGGGCAG	AB029023	CCDS4404.1	5q35.3	2013-01-09			ENSG00000146083	ENSG00000146083		"RING-type (C3HC4) zinc fingers"	19180	protein-coding gene	gene with protein product						10470851	Standard	NM_014901		Approved	KIAA1100	uc003mek.1	Q7L0R7	OTTHUMG00000130664	ENST00000274811.4:c.146G>T	chr5.hg19:g.175959156C>A	ENSP00000274811:p.Arg49Leu	243.0	0.0		206.0	27.0	NM_014901	B4DYE0|Q8ND05|Q9UPQ2	Missense_Mutation	SNP	ENST00000274811.4	hg19	CCDS4404.1	.	.	.	.	.	.	.	.	.	.	C	9.569	1.120613	0.20877	.	.	ENSG00000146083	ENST00000274811	T	0.32515	1.45	4.23	1.63	0.23807	.	0.353014	0.25291	N	0.031739	T	0.11836	0.0288	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10474	-1.0628	10	0.20046	T	0.44	-9.9867	4.2749	0.10804	0.175:0.0992:0.0:0.7258	.	49	Q7L0R7	RNF44_HUMAN	L	49	ENSP00000274811:R49L	ENSP00000274811:R49L	R	-	2	0	RNF44	175891762	1.000000	0.71417	1.000000	0.80357	0.347000	0.29111	2.359000	0.44142	0.623000	0.30267	-0.367000	0.07326	CGG	.	.		0.731	RNF44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253156.2			A	175959156	C	A	175959156	3	1	181	1	0	0	0	0	1	0	0	0	13511	652	23	1	1188	1	RNF44	5	175959156	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	4425474	175959156	4956104	53	27039										
SQSTM1	8878	hgsc.bcm.edu	37	chr5	179260608	179260608	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aacagatggagtcggataacTgttcaggaggagatgatgac	14	5	1	4			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr5:179260608T>A	ENST00000389805.4	+	7	1169	c.991T>A	c.(991-993)Tgt>Agt	p.C331S	SQSTM1_ENST00000360718.5_Missense_Mutation_p.C247S|SQSTM1_ENST00000376929.3_Missense_Mutation_p.C247S|SQSTM1_ENST00000510187.1_Intron|SQSTM1_ENST00000402874.3_Missense_Mutation_p.C247S	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	331	Interaction with NTRK1. {ECO:0000250}.|MAP1LC3B-binding.				apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cell differentiation (GO:0030154)|endosomal transport (GO:0016197)|immune system process (GO:0002376)|intracellular signal transduction (GO:0035556)|macroautophagy (GO:0016236)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein heterooligomerization (GO:0051291)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of Ras protein signal transduction (GO:0046578)|response to stress (GO:0006950)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|lysosome (GO:0005764)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)		SQSTM1/ALK(2)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(5)|ovary(1)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTCGGATAACTGTTCAGGAGG	0.547																																					p.C331S		Atlas-SNP	.											.	SQSTM1	30	.	0			c.T991A						.						95	86	89					5																	179260608		2203	4300	6503	SO:0001583	missense	8878	exon7			GATAACTGTTCAG	U46751	CCDS34317.1, CCDS47355.1	5q35	2008-02-05	2004-04-15		ENSG00000161011	ENSG00000161011			11280	protein-coding gene	gene with protein product		601530	"Paget disease of bone 3", "oxidative stress induced like"	PDB3, OSIL		8650207, 8551575	Standard	NM_003900		Approved	p62, p60, p62B, A170	uc003mkw.4	Q13501	OTTHUMG00000150643	ENST00000389805.4:c.991T>A	chr5.hg19:g.179260608T>A	ENSP00000374455:p.Cys331Ser	131.0	0.0		104.0	12.0	NM_003900	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	Missense_Mutation	SNP	ENST00000389805.4	hg19	CCDS34317.1	.	.	.	.	.	.	.	.	.	.	T	5.646	0.303895	0.10678	.	.	ENSG00000161011	ENST00000376929;ENST00000389805;ENST00000454378;ENST00000402874;ENST00000360718	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.26	4.07	0.47477	.	0.298040	0.37095	N	0.002246	T	0.78773	0.4336	L	0.39633	1.23	0.36545	D	0.871496	B	0.10296	0.003	B	0.10450	0.005	T	0.69650	-0.5088	10	0.07644	T	0.81	-11.8632	10.4894	0.44741	0.0:0.0:0.3132:0.6868	.	331	Q13501	SQSTM_HUMAN	S	247;331;187;247;247	ENSP00000366128:C247S;ENSP00000374455:C331S;ENSP00000385553:C247S;ENSP00000353944:C247S	ENSP00000353944:C247S	C	+	1	0	SQSTM1	179193214	0.472000	0.25870	0.945000	0.38365	0.690000	0.40134	0.428000	0.21395	0.805000	0.34159	0.459000	0.35465	TGT	.	.		0.547	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1			A	179260608	T	A	179260608	3	1	181	1	0	0	0	0	1	0	0	0	15145	1580	55	4	1017	4	SQSTM1	5	179260608	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	3301452	179260608	1654652	54	27040										
MAPK9	5601	hgsc.bcm.edu	37	chr5	179696379	179696380	+	Frame_Shift_Del	DEL	AT	AT	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cttagtttcttgactgcaacAtttatcccaagaactgtatc					rs1043993		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr5:179696379_179696380delAT	ENST00000452135.2	-	3	450_451	c.152_153delAT	c.(151-153)aatfs	p.N51fs	MAPK9_ENST00000393360.3_Frame_Shift_Del_p.N51fs|MAPK9_ENST00000455781.1_Frame_Shift_Del_p.N51fs|MAPK9_ENST00000425491.2_Frame_Shift_Del_p.N51fs|MAPK9_ENST00000397072.3_3'UTR|MAPK9_ENST00000347470.4_Frame_Shift_Del_p.N51fs|MAPK9_ENST00000343111.6_Frame_Shift_Del_p.N51fs|MAPK9_ENST00000539014.1_Frame_Shift_Del_p.N51fs			P45984	MK09_HUMAN	mitogen-activated protein kinase 9	51	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			N -> S (in Ref. 1; AAA56831 and 3; AAC50606/AAC50608/AAC50609). {ECO:0000305}.	cellular response to growth factor stimulus (GO:0071363)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV (GO:0034644)|central nervous system development (GO:0007417)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neuron projection development (GO:0031175)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell morphogenesis involved in differentiation (GO:0010770)|positive regulation of chemokine production (GO:0032722)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|protein targeting to mitochondrion (GO:0006626)|regulation of JNK cascade (GO:0046328)|regulation of protein ubiquitination (GO:0031396)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to amine (GO:0014075)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|JUN kinase activity (GO:0004705)|transcription factor binding (GO:0008134)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGACTGCAACATTTATCCCAAG	0.356																																					p.51_52del		Atlas-INDEL	.											.	MAPK9	173	.	0			c.153_154del						.																																			SO:0001589	frameshift_variant	5601	exon3			.	U09759	CCDS4453.1, CCDS4454.1, CCDS43409.1, CCDS43410.1, CCDS47356.1	5q35	2011-06-09			ENSG00000050748	ENSG00000050748	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6886	protein-coding gene	gene with protein product	"Jun kinase"	602896		PRKM9		8001819	Standard	NM_002752		Approved	JNK2, p54a, SAPK	uc003mls.4	P45984	OTTHUMG00000130934	ENST00000452135.2:c.152_153delAT	chr5.hg19:g.179696379_179696380delAT	ENSP00000394560:p.Asn51fs	149.0	0.0		171.0	34.0	NM_139068	A8K0S3|B5BU66|B5M0B4|D3DWQ8|D3DWQ9|Q15708|Q15710|Q15711|Q8N5C5	Frame_Shift_Del	DEL	ENST00000452135.2	hg19	CCDS4453.1																																																																																			.	.		0.356	MAPK9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253530.3			-	179696380	AT	-	179696379	7	5	181	1	0	1	0	1	0	0	0	0	9296	214	8	0	1283	0	MAPK9	5	179696379	Frame_Shift_Del	DEL	AT	TCGA-DD-AAD5-01A-11D-A40R-10	435771	179696379	1218881	55	27041										
FOXC1	2296	hgsc.bcm.edu	37	chr6	1611582	1611582	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gcccgcgccctccgccccgcCgccgcaccatagccagggct	11	23	0	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr6:1611582C>G	ENST00000380874.2	+	1	902	c.902C>G	c.(901-903)cCg>cGg	p.P301R		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	301					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		tccgccccgccgccgcACCAT	0.776																																					p.P301R	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.C902G						.						2	2	2					6																	1611582		887	2012	2899	SO:0001583	missense	2296	exon1			CCCCGCCGCCGCA	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"Forkhead boxes"	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.902C>G	chr6.hg19:g.1611582C>G	ENSP00000370256:p.Pro301Arg	89.0	0.0		62.0	34.0	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Missense_Mutation	SNP	ENST00000380874.2	hg19	CCDS4473.1	.	.	.	.	.	.	.	.	.	.	C	2.840	-0.240608	0.05944	.	.	ENSG00000054598	ENST00000380874	D	0.92965	-3.14	2.82	-1.18	0.09617	.	0.278524	0.27362	N	0.019717	T	0.68054	0.2959	N	0.22421	0.69	0.25048	N	0.991153	B	0.06786	0.001	B	0.04013	0.001	T	0.61836	-0.6981	10	0.22706	T	0.39	.	6.8262	0.23885	0.3461:0.5029:0.1511:0.0	.	301	Q12948	FOXC1_HUMAN	R	301	ENSP00000370256:P301R	ENSP00000370256:P301R	P	+	2	0	FOXC1	1556581	0.000000	0.05858	0.672000	0.29872	0.084000	0.17831	0.685000	0.25378	-0.044000	0.13491	-0.802000	0.03209	CCG	.	.		0.776	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			G	1611582	C	G	1611582	3	3	181	1	0	0	0	0	1	0	0	0	6002	652	23	4	904	4	FOXC1	6	1611582	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10		1611582	169503485	56	27042										
SLC22A23	63027	hgsc.bcm.edu	37	chr6	3273355	3273355	+	Silent	SNP	G	G	A													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tcacccgcggctgcggcatcGtggaggcccgagtagtcctt							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr6:3273355G>A	ENST00000406686.3	-	10	1994	c.1995C>T	c.(1993-1995)caC>caT	p.H665H	PSMG4_ENST00000451246.2_Intron|SLC22A23_ENST00000490273.1_Silent_p.H384H|SLC22A23_ENST00000380302.4_Silent_p.H384H|SLC22A23_ENST00000436008.2_Silent_p.H673H	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	665					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				CTGCGGCATCGTGGAGGCCCG	0.697																																					p.H665H		Atlas-SNP	.											.	SLC22A23	89	.	0			c.C1995T						.						44	50	48					6																	3273355		2203	4300	6503	SO:0001819	synonymous_variant	63027	exon10			GGCATCGTGGAGG	AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"Solute carriers"	21106	protein-coding gene	gene with protein product		611697	"chromosome 6 open reading frame 85"	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.1995C>T	chr6.hg19:g.3273355G>A		34.0	0.0		27.0	8.0	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Silent	SNP	ENST00000406686.3	hg19	CCDS47363.1																																																																																			.	.		0.697	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945		A	3273355	G	A	3273355	2	1	181	1	0	0	0	0	0	0	0	1	14467	1136	40	1		1	SLC22A23	6	3273355	Silent	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	1661773	3273355	167841712	57	27043	131	2								
SLC22A23	63027	hgsc.bcm.edu	37	chr6	3273357	3273357	+	Missense_Mutation	SNP	G	G	T													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	acccgcggctgcggcatcgtGgaggcccgagtagtccttga							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr6:3273357G>T	ENST00000406686.3	-	10	1992	c.1993C>A	c.(1993-1995)Cac>Aac	p.H665N	PSMG4_ENST00000451246.2_Intron|SLC22A23_ENST00000490273.1_Missense_Mutation_p.H384N|SLC22A23_ENST00000380302.4_Missense_Mutation_p.H384N|SLC22A23_ENST00000436008.2_Missense_Mutation_p.H673N	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	665					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				GCGGCATCGTGGAGGCCCGAG	0.687																																					p.H665N		Atlas-SNP	.											.	SLC22A23	89	.	0			c.C1993A						.						45	50	48					6																	3273357		2203	4300	6503	SO:0001583	missense	63027	exon10			CATCGTGGAGGCC	AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"Solute carriers"	21106	protein-coding gene	gene with protein product		611697	"chromosome 6 open reading frame 85"	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.1993C>A	chr6.hg19:g.3273357G>T	ENSP00000385028:p.His665Asn	33.0	0.0		27.0	8.0	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Missense_Mutation	SNP	ENST00000406686.3	hg19	CCDS47363.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.629267	0.67015	.	.	ENSG00000137266	ENST00000436008;ENST00000406686;ENST00000380302;ENST00000490273	T;T;T;T	0.72167	-0.57;-0.63;-0.47;-0.47	5.91	5.91	0.95273	.	0.105137	0.64402	D	0.000004	T	0.61540	0.2355	N	0.24115	0.695	0.80722	D	1	D	0.54207	0.965	P	0.50049	0.629	T	0.67086	-0.5759	10	0.66056	D	0.02	-27.2157	19.2867	0.94077	0.0:0.0:1.0:0.0	.	665	A1A5C7	S22AN_HUMAN	N	673;665;384;384	ENSP00000410245:H673N;ENSP00000385028:H665N;ENSP00000369657:H384N;ENSP00000419463:H384N	ENSP00000369657:H384N	H	-	1	0	SLC22A23	3218356	1.000000	0.71417	0.972000	0.41901	0.105000	0.19272	8.770000	0.91746	2.793000	0.96121	0.655000	0.94253	CAC	.	.		0.687	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945		T	3273357	G	T	3273357	3	4	181	1	0	0	0	0	1	0	0	0	14467	1348	47	3	71	3	SLC22A23	6	3273357	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	2	3273357	167841710	58	27044	131	2								
F13A1	2162	hgsc.bcm.edu	37	chr6	6145859	6145859	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gcttcctgtgcattcacatgGaaggtcgtctttgaatctgc	10	10	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr6:6145859G>A	ENST00000264870.3	-	15	2457	c.2192C>T	c.(2191-2193)tCc>tTc	p.S731F		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	731					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	CATTCACATGGAAGGTCGTCT	0.498																																					p.S731F		Atlas-SNP	.											.	F13A1	135	.	0			c.C2192T						.						127	117	120					6																	6145859		2203	4300	6503	SO:0001583	missense	2162	exon15			CACATGGAAGGTC	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"Transglutaminases"	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.2192C>T	chr6.hg19:g.6145859G>A	ENSP00000264870:p.Ser731Phe	114.0	0.0		97.0	24.0	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	hg19	CCDS4496.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.251741	0.22880	.	.	ENSG00000124491	ENST00000264870;ENST00000441301	T	0.79845	-1.31	5.67	3.72	0.42706	.	0.802956	0.10904	N	0.621307	T	0.57784	0.2077	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.54159	-0.8335	10	0.87932	D	0	.	8.15	0.31134	0.0873:0.0:0.7442:0.1685	.	731	P00488	F13A_HUMAN	F	731;625	ENSP00000264870:S731F	ENSP00000264870:S731F	S	-	2	0	F13A1	6090858	0.017000	0.18338	0.294000	0.24946	0.371000	0.29859	1.510000	0.35790	2.677000	0.91161	0.655000	0.94253	TCC	.	.		0.498	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129		A	6145859	G	A	6145859	3	1	181	1	0	0	0	0	1	0	0	0	5342	1174	41	3	10	3	F13A1	6	6145859	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	2872502	6145859	164969208	59	27045										
ZNF318	24149	hgsc.bcm.edu	37	chr6	43307288	43307288	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agccagggctgagagtctgaGatacaactgggtttgatttt	13	6	1	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr6:43307288G>A	ENST00000361428.2	-	10	4525	c.4448C>T	c.(4447-4449)tCt>tTt	p.S1483F	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1483	Pro-rich.				meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			GAGAGTCTGAGATACAACTGG	0.537																																					p.S1483F		Atlas-SNP	.											.	ZNF318	175	.	0			c.C4448T						.						65	61	62					6																	43307288		2203	4300	6503	SO:0001583	missense	24149	exon10			GTCTGAGATACAA	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.4448C>T	chr6.hg19:g.43307288G>A	ENSP00000354964:p.Ser1483Phe	97.0	0.0		92.0	31.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	G	14.33	2.503126	0.44558	.	.	ENSG00000171467	ENST00000361428	T	0.18174	2.23	4.96	4.96	0.65561	.	0.181162	0.35870	N	0.002923	T	0.12433	0.0302	N	0.19112	0.55	0.80722	D	1	D	0.53885	0.963	P	0.53809	0.735	T	0.02983	-1.1086	10	0.49607	T	0.09	-8.2732	15.0645	0.71983	0.0:0.0:1.0:0.0	.	1483	Q5VUA4	ZN318_HUMAN	F	1483	ENSP00000354964:S1483F	ENSP00000354964:S1483F	S	-	2	0	ZNF318	43415266	1.000000	0.71417	0.994000	0.49952	0.832000	0.47134	6.308000	0.72820	2.585000	0.87301	0.655000	0.94253	TCT	.	.		0.537	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		A	43307288	G	A	43307288	3	1	181	1	0	0	0	0	1	0	0	0	17851	942	33	3	2395	3	ZNF318	6	43307288	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	37161429	43307288	127807779	60	27046										
POLR1C	9533	hgsc.bcm.edu	37	chr6	43487179	43487179	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gacgaattctgctagctgagGtattggcaggcatggtgaca	14	7	1	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr6:43487179G>T	ENST00000372389.3	+	3	337		c.e3+1		RP3-337H4.9_ENST00000607571.1_RNA|POLR1C_ENST00000304004.3_Splice_Site|YIPF3_ENST00000506469.1_5'Flank|POLR1C_ENST00000372344.2_Splice_Site|YIPF3_ENST00000372422.2_5'Flank	NM_203290.2	NP_976035.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide C, 30kDa						gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			kidney(1)|large_intestine(2)|lung(1)|prostate(1)	5	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|all cancers(41;0.00511)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			GCTAGCTGAGGTATTGGCAGG	0.473																																					.		Atlas-SNP	.											.	POLR1C	52	.	0			c.249+1G>T						.						116	92	100					6																	43487179		2203	4300	6503	SO:0001630	splice_region_variant	9533	exon3			GCTGAGGTATTGG	AF008442	CCDS4901.1	6p21.1	2013-01-21			ENSG00000171453	ENSG00000171453		"RNA polymerase subunits"	20194	protein-coding gene	gene with protein product		610060				11042152, 12446911	Standard	NM_203290		Approved	RPA40, RPA39, RPA5, RPAC1	uc003ovn.3	O15160	OTTHUMG00000014739	ENST00000372389.3:c.249+1G>T	chr6.hg19:g.43487179G>T		144.0	0.0		117.0	39.0	NM_203290	O75395|Q5JTE3	Splice_Site	SNP	ENST00000372389.3	hg19	CCDS4901.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.819480	0.71028	.	.	ENSG00000171453	ENST00000428025;ENST00000372389;ENST00000372344;ENST00000304004;ENST00000423780	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5629	0.91107	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	POLR1C	43595157	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	9.311000	0.96282	2.446000	0.82766	0.557000	0.71058	.	.	.		0.473	POLR1C-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040652.3	NM_004875	Intron	T	43487179	G	T	43487179	5	4	181	1	0	0	0	0	0	0	1	0	12220	1275	44	3	260	3	POLR1C	6	43487179	Splice_Site	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	179891	43487179	127627888	61	27047										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51524083	51524087	+	Frame_Shift_Del	DEL	CTGTC	CTGTC	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgcgctttctttttgctctaCtgtcagcaatggcctttaag							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	CTGTC	CTGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr6:51524083_51524087delCTGTC	ENST00000371117.3	-	61	11112_11116	c.10837_10841delGACAG	c.(10837-10842)gacagtfs	p.DS3613fs		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3613					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TTTTGCTCTACTGTCAGCAATGGCC	0.42																																					p.3613_3614del		Atlas-INDEL	.											.	PKHD1	927	.	0			c.10838_10842del						.																																			SO:0001589	frameshift_variant	5314	exon61			.	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10837_10841delGACAG	chr6.hg19:g.51524083_51524087delCTGTC	ENSP00000360158:p.Asp3613fs	92.0	0.0		87.0	26.0	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Frame_Shift_Del	DEL	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.		0.42	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		-	51524087	CTGTC	-	51524083	7	5	181	1	0	1	0	1	0	0	0	0	11980	565	20	0	1411	0	PKHD1	6	51524083	Frame_Shift_Del	DEL	CTGTC	TCGA-DD-AAD5-01A-11D-A40R-10	8036904	51524083	119590984	62	27048										
PTPN12	5782	hgsc.bcm.edu	37	chr7	77256222	77256222	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agcagacctcaacagaaactAtagtaaatcaacagaacttc	5	10	2	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr7:77256222A>G	ENST00000248594.6	+	13	1498	c.1226A>G	c.(1225-1227)tAt>tGt	p.Y409C	PTPN12_ENST00000435495.2_Missense_Mutation_p.Y279C|PTPN12_ENST00000415482.2_Missense_Mutation_p.Y290C	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	409	Interaction with TGFB1I1. {ECO:0000250}.				protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						AACAGAAACTATAGTAAATCA	0.363																																					p.Y409C		Atlas-SNP	.											.	PTPN12	83	.	0			c.A1226G						.						52	53	53					7																	77256222		2203	4300	6503	SO:0001583	missense	5782	exon13			GAAACTATAGTAA		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.1226A>G	chr7.hg19:g.77256222A>G	ENSP00000248594:p.Tyr409Cys	140.0	0.0		132.0	39.0	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	hg19	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.108653	0.56291	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.07908	3.73;3.15;3.15	6.17	6.17	0.99709	.	0.241477	0.42964	D	0.000634	T	0.30759	0.0775	M	0.81497	2.545	0.53005	D	0.999965	D	0.76494	0.999	D	0.68765	0.96	T	0.01508	-1.1337	10	0.35671	T	0.21	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	409	Q05209	PTN12_HUMAN	C	409;290;290;279	ENSP00000248594:Y409C;ENSP00000392429:Y290C;ENSP00000397991:Y279C	ENSP00000248594:Y409C	Y	+	2	0	PTPN12	77094158	0.999000	0.42202	0.966000	0.40874	0.958000	0.62258	3.891000	0.56227	2.371000	0.80710	0.533000	0.62120	TAT	.	.		0.363	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			G	77256222	A	G	77256222	3	3	181	1	0	0	0	0	1	0	0	0	12794	449	16	2	1276	2	PTPN12	7	77256222	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10		77256222	81882441	63	27049										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131849014	131849014	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	catctgctgcttgatggcacAgaacagggagaagaggggct	15	8	1	4			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr7:131849014A>C	ENST00000359827.3	-	24	5349	c.4387T>G	c.(4387-4389)Tgt>Ggt	p.C1463G	PLXNA4_ENST00000321063.4_Missense_Mutation_p.C1463G			Q9HCM2	PLXA4_HUMAN	plexin A4	1463					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TTGATGGCACAGAACAGGGAG	0.592																																					p.C1463G		Atlas-SNP	.											.	PLXNA4	873	.	0			c.T4387G						.						58	58	58					7																	131849014		2203	4300	6503	SO:0001583	missense	91584	exon24			TGGCACAGAACAG	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.4387T>G	chr7.hg19:g.131849014A>C	ENSP00000352882:p.Cys1463Gly	84.0	0.0		66.0	22.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	A	19.99	3.928349	0.73327	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.11495	2.77;2.77	5.45	5.45	0.79879	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.37839	0.1018	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.28170	-1.0052	10	0.48119	T	0.1	.	15.542	0.76057	1.0:0.0:0.0:0.0	.	1463	Q9HCM2	PLXA4_HUMAN	G	1463	ENSP00000323194:C1463G;ENSP00000352882:C1463G	ENSP00000323194:C1463G	C	-	1	0	PLXNA4	131499554	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.576000	0.82467	2.064000	0.61679	0.533000	0.62120	TGT	.	.		0.592	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		C	131849014	A	C	131849014	3	2	181	1	0	0	0	0	1	0	0	0	12131	188	7	5	1333	5	PLXNA4	7	131849014	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	54592792	131849014	27289649	64	27050										
ADAM9	8754	hgsc.bcm.edu	37	chr8	38947598	38947598	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cattgagggacggacttctgGtcttcttcttcctaattgtt	9	9	4	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr8:38947598G>A	ENST00000487273.2	+	19	2179	c.2101G>A	c.(2101-2103)Gtc>Atc	p.V701I		NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	701					activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			CGGACTTCTGGTCTTCTTCTT	0.373																																					p.V701I		Atlas-SNP	.											.	ADAM9	66	.	0			c.G2101A						.						261	236	245					8																	38947598		2203	4300	6503	SO:0001583	missense	8754	exon19			CTTCTGGTCTTCT	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"ADAM metallopeptidase domain containing"	216	protein-coding gene	gene with protein product	"meltrin gamma"	602713	"a disintegrin and metalloproteinase domain 9 (meltrin gamma)", "cone rod dystrophy 9"	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.2101G>A	chr8.hg19:g.38947598G>A	ENSP00000419446:p.Val701Ile	143.0	0.0		67.0	35.0	NM_003816	B7ZLN7|Q10718|Q8NFM6	Missense_Mutation	SNP	ENST00000487273.2	hg19	CCDS6112.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.893542	0.33442	.	.	ENSG00000168615	ENST00000487273	D	0.87412	-2.25	5.55	3.76	0.43208	.	0.250218	0.39834	N	0.001248	T	0.73969	0.3655	N	0.20766	0.605	0.38465	D	0.947313	P	0.38922	0.651	B	0.35039	0.194	T	0.69964	-0.5002	10	0.11794	T	0.64	.	11.2857	0.49220	0.151:0.0:0.849:0.0	.	701	Q13443	ADAM9_HUMAN	I	701	ENSP00000419446:V701I	ENSP00000419446:V701I	V	+	1	0	ADAM9	39066755	1.000000	0.71417	0.924000	0.36721	0.841000	0.47740	4.010000	0.57117	0.823000	0.34589	0.563000	0.77884	GTC	.	.		0.373	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			A	38947598	G	A	38947598	3	1	181	1	0	0	0	0	1	0	0	0	253	1261	44	3	2175	3	ADAM9	8	38947598	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10		38947598	107416424	65	27051										
VCPIP1	80124	hgsc.bcm.edu	37	chr8	67578049	67578049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgtactttttaataaggtccTgaggcacaccccatgcttta	7	10	0	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr8:67578049T>C	ENST00000310421.4	-	1	1403	c.1145A>G	c.(1144-1146)cAg>cGg	p.Q382R	C8orf44_ENST00000521889.1_5'Flank|C8orf44_ENST00000519561.1_5'Flank|C8orf44-SGK3_ENST00000519289.1_5'Flank	NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	382					endoplasmic reticulum membrane fusion (GO:0016320)|Golgi reassembly (GO:0090168)|mitotic nuclear division (GO:0007067)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	ubiquitin-specific protease activity (GO:0004843)			breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			AATAAGGTCCTGAGGCACACC	0.423																																					p.Q382R	NSCLC(179;265 2915 6144 43644)	Atlas-SNP	.											.	VCPIP1	110	.	0			c.A1145G						.						122	119	120					8																	67578049		2203	4300	6503	SO:0001583	missense	80124	exon1			AGGTCCTGAGGCA	AB058753	CCDS6192.1	8q13	2014-02-24			ENSG00000175073	ENSG00000175073		"OTU domain containing"	30897	protein-coding gene	gene with protein product		611745				11347906, 12509440	Standard	NM_025054		Approved	VCIP135, KIAA1850, FLJ23132, DUBA3	uc003xwn.3	Q96JH7	OTTHUMG00000164560	ENST00000310421.4:c.1145A>G	chr8.hg19:g.67578049T>C	ENSP00000309031:p.Gln382Arg	105.0	0.0		105.0	35.0	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Missense_Mutation	SNP	ENST00000310421.4	hg19	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.418125	0.42918	.	.	ENSG00000175073	ENST00000310421	T	0.36340	1.26	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.57007	0.2024	M	0.64997	1.995	0.80722	D	1	D	0.54601	0.967	D	0.65140	0.932	T	0.59862	-0.7374	10	0.87932	D	0	-9.1665	16.0623	0.80847	0.0:0.0:0.0:1.0	.	382	Q96JH7	VCIP1_HUMAN	R	382	ENSP00000309031:Q382R	ENSP00000309031:Q382R	Q	-	2	0	VCPIP1	67740603	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.195000	0.70347	0.533000	0.62120	CAG	.	.		0.423	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			C	67578049	T	C	67578049	3	2	181	1	0	0	0	0	1	0	0	0	17156	1580	55	2	2535	2	VCPIP1	8	67578049	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	28630451	67578049	78785973	66	27052										
C8orf34	116328	hgsc.bcm.edu	37	chr8	69552726	69552726	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	caggccaaggtcacactgaaCatctgttcaaggtgtgccag	11	11	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr8:69552726C>T	ENST00000539993.1	+	8	1512	c.963C>T	c.(961-963)aaC>aaT	p.N321N	C8orf34_ENST00000518698.1_Silent_p.N407N|C8orf34_ENST00000325233.3_Silent_p.N65N|C8orf34_ENST00000337103.4_Silent_p.N296N			Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	321										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(12)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	36			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			TCACACTGAACATCTGTTCAA	0.393																																					p.N407N		Atlas-SNP	.											.	C8orf34	170	.	0			c.C1221T						.						85	78	81					8																	69552726		2203	4300	6503	SO:0001819	synonymous_variant	116328	exon8			ACTGAACATCTGT	AB056652	CCDS6203.1, CCDS6203.2	8q13	2009-10-01			ENSG00000165084	ENSG00000165084			30905	protein-coding gene	gene with protein product	"vestibule 1"						Standard	NM_052958		Approved	vest-1, VEST1	uc010lyz.3	Q49A92	OTTHUMG00000164438	ENST00000539993.1:c.963C>T	chr8.hg19:g.69552726C>T		138.0	0.0		144.0	72.0	NM_052958	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	Silent	SNP	ENST00000539993.1	hg19																																																																																				.	.		0.393	C8orf34-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_052958		T	69552726	C	T	69552726	2	4	181	1	0	0	0	0	0	0	0	1	2424	477	17	3		3	C8orf34	8	69552726	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	1974677	69552726	76811296	67	27053										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77768445	77768445	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cacggcatcagcctgccaacAgcctaccccggactccccgg	9	20	1	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr8:77768445A>T	ENST00000521891.2	+	10	9736	c.9288A>T	c.(9286-9288)acA>acT	p.T3096T	ZFHX4_ENST00000455469.2_Silent_p.T3051T|ZFHX4_ENST00000050961.6_Silent_p.T3051T|ZFHX4_ENST00000518282.1_Silent_p.T3070T	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3051	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GCCTGCCAACAGCCTACCCCG	0.542										HNSCC(33;0.089)																											p.T3096T		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A9288T						.						62	65	64					8																	77768445		2039	4193	6232	SO:0001819	synonymous_variant	79776	exon10			GCCAACAGCCTAC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.9288A>T	chr8.hg19:g.77768445A>T		97.0	0.0		135.0	51.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.542	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77768445	A	T	77768445	2	4	181	1	0	0	0	0	0	0	0	1	17650	175	7	4		4	ZFHX4	8	77768445	Silent	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	8215719	77768445	68595577	68	27054										
POP1	10940	hgsc.bcm.edu	37	chr8	99142204	99142214	+	Splice_Site	DEL	TGAAACTATAG	TGAAACTATAG	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gtccctctacttgaaactatAggcggagaaagccgtacatc					rs148946525|rs371691417|rs143675510	byFrequency	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	TGAAACTATAG	TGAAACTATAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr8:99142204_99142214delTGAAACTATAG	ENST00000401707.2	+	5	567_576	c.486_495delTGAAACTATAG	c.(484-495)gatgaaactata>ga	p.DETI162fs	POP1_ENST00000349693.3_Splice_Site_p.DETI162fs	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	162					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			TTGAAACTATAGGCGGAGAAAGCCGTACATC	0.36																																					.		Atlas-INDEL	.											.	POP1	85	.	0			.						.																																			SO:0001630	splice_region_variant	10940	.			.	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"processing of precursors 1"	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.487-1TGAAACTATAG>-	chr8.hg19:g.99142204_99142214delTGAAACTATAG		132.0	0.0		219.0	20.0	.	A8K5W9|Q15037	Splice_Site	DEL	ENST00000401707.2	hg19	CCDS6277.1																																																																																			.	.		0.36	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029	Frame_Shift_Del	-	99142214	TGAAACTATAG	-	99142204	8	5	181	1	0	1	0	1	0	0	1	0	12260	434	15	0	499	0	POP1	8	99142204	Splice_Site	DEL	TGAAACTATAG	TCGA-DD-AAD5-01A-11D-A40R-10	21373759	99142204	47221818	69	27055										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100123343	100123343	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tagcaactgatttggtgctgAgaaaggttatcaatttttct	9	5	2	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr8:100123343A>T	ENST00000358544.2	+	6	709	c.598A>T	c.(598-600)Aga>Tga	p.R200*	VPS13B_ENST00000395996.1_Nonsense_Mutation_p.R200*|VPS13B_ENST00000355155.1_Nonsense_Mutation_p.R200*|VPS13B_ENST00000441350.2_Nonsense_Mutation_p.R200*|VPS13B_ENST00000357162.2_Nonsense_Mutation_p.R200*	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	200					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTTGGTGCTGAGAAAGGTTAT	0.289																																					p.R200X	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A598T						.						62	66	65					8																	100123343		2198	4299	6497	SO:0001587	stop_gained	157680	exon6			GTGCTGAGAAAGG	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.598A>T	chr8.hg19:g.100123343A>T	ENSP00000351346:p.Arg200*	176.0	0.0		399.0	98.0	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Nonsense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	32	5.163764	0.94727	.	.	ENSG00000132549	ENST00000355155;ENST00000357162;ENST00000358544;ENST00000395996;ENST00000441350	.	.	.	5.32	4.11	0.48088	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.5279	0.61605	0.8612:0.1388:0.0:0.0	.	.	.	.	X	200	.	ENSP00000347281:R200X	R	+	1	2	VPS13B	100192519	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.692000	0.61746	2.005000	0.58758	0.454000	0.30748	AGA	.	.		0.289	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100123343	A	T	100123343	4	4	181	1	0	0	0	0	0	1	0	0	17205	296	11	4	616	4	VPS13B	8	100123343	Nonsense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	981139	100123343	46240679	70	27056										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106811123	106811123	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gtgccccttcccacagtgcaCcaagagcttttcaaatgctc	7	15	1	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr8:106811123C>G	ENST00000407775.2	+	7	1161	c.911C>G	c.(910-912)aCc>aGc	p.T304S	ZFPM2_ENST00000517361.1_Missense_Mutation_p.T172S|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000522296.1_3'UTR|ZFPM2_ENST00000520492.1_Missense_Mutation_p.T172S|ZFPM2_ENST00000378472.4_Missense_Mutation_p.T35S|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000509144.2_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	304					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			CCACAGTGCACCAAGAGCTTT	0.483																																					p.T304S		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C911G						.						119	121	121					8																	106811123		1988	4182	6170	SO:0001583	missense	23414	exon7			AGTGCACCAAGAG	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.911C>G	chr8.hg19:g.106811123C>G	ENSP00000384179:p.Thr304Ser	74.0	0.0		193.0	8.0	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	hg19	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.799942	0.70567	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35	6.06	6.06	0.98353	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.091944	0.85682	D	0.000000	T	0.45518	0.1346	N	0.02665	-0.54	0.45567	D	0.998515	P	0.44090	0.826	B	0.42462	0.388	T	0.50617	-0.8807	10	0.09084	T	0.74	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	304	Q8WW38	FOG2_HUMAN	S	304;172;172;35	ENSP00000384179:T304S;ENSP00000430757:T172S;ENSP00000428720:T172S;ENSP00000367733:T35S	ENSP00000367733:T35S	T	+	2	0	ZFPM2	106880299	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.914000	0.63348	2.880000	0.98712	0.650000	0.86243	ACC	.	.		0.483	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			G	106811123	C	G	106811123	3	3	181	1	0	0	0	0	1	0	0	0	17673	507	18	4	937	4	ZFPM2	8	106811123	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	6687780	106811123	39552899	71	27057										
ZNF250	58500	hgsc.bcm.edu	37	chr8	146107094	146107094	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gcccgtgtgggtcctcaggtGcacaatcagagttgctttca	12	11	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr8:146107094G>T	ENST00000292579.7	-	6	1605	c.1489C>A	c.(1489-1491)Cac>Aac	p.H497N	ZNF250_ENST00000342660.6_Intron|ZNF250_ENST00000417550.2_Missense_Mutation_p.H492N|ZNF250_ENST00000543949.1_Intron	NM_001109689.3|NM_021061.4	NP_001103159.1|NP_066405.1	P15622	ZN250_HUMAN	zinc finger protein 250	497					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(2)|lung(8)|skin(1)	15	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)		GTCCTCAGGTGCACAATCAGA	0.552																																					p.H497N	NSCLC(16;520 556 24096 40084 43446)	Atlas-SNP	.											.	ZNF250	37	.	0			c.C1489A						.						82	69	73					8																	146107094		2203	4300	6503	SO:0001583	missense	58500	exon6			TCAGGTGCACAAT	AK095705	CCDS34972.1, CCDS55282.1	8q24.3	2013-01-08	2004-11-08			ENSG00000196150		"Zinc fingers, C2H2-type", "-"	13044	protein-coding gene	gene with protein product			"zinc finger protein 647"	ZNF647		12477932	Standard	NM_021061		Approved	MGC9718, ZFP647	uc003zer.4	P15622		ENST00000292579.7:c.1489C>A	chr8.hg19:g.146107094G>T	ENSP00000292579:p.His497Asn	85.0	0.0		61.0	36.0	NM_021061	D3DWP1|Q59HE9|Q8N942|Q96AH9	Missense_Mutation	SNP	ENST00000292579.7	hg19	CCDS34972.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.709271	0.68615	.	.	ENSG00000196150	ENST00000292579;ENST00000417550;ENST00000394912	D;D	0.86865	-2.18;-2.18	3.95	3.95	0.45737	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000127	D	0.94699	0.8290	H	0.95470	3.675	0.80722	D	1	P;P	0.51147	0.77;0.942	P;P	0.60236	0.65;0.871	D	0.96167	0.9120	10	0.87932	D	0	-31.1942	15.9595	0.79918	0.0:0.0:1.0:0.0	.	492;497	D3DWP1;P15622	.;ZN250_HUMAN	N	497;492;380	ENSP00000292579:H497N;ENSP00000393442:H492N	ENSP00000292579:H497N	H	-	1	0	ZNF250	146077898	1.000000	0.71417	1.000000	0.80357	0.562000	0.35680	6.442000	0.73443	2.512000	0.84698	0.484000	0.47621	CAC	.	.		0.552	ZNF250-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382968.1	NM_021061		T	146107094	G	T	146107094	3	4	181	1	0	0	0	0	1	0	0	0	17810	1319	46	3	197	3	ZNF250	8	146107094	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	39295971	146107094	256928	72	27058										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21994138	21994138	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ttttcgagggcctttcctacCtggtcttctaggaagcggct	11	11	2	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr9:21994138C>G	ENST00000579755.1	-	1	485	c.193G>C	c.(193-195)Ggt>Cgt	p.G65R	CDKN2A_ENST00000494262.1_Intron|CDKN2A_ENST00000361570.3_Splice_Site_p.G106R|CDKN2B-AS1_ENST00000580467.1_RNA|CDKN2B-AS1_ENST00000582072.1_RNA|CDKN2B-AS1_ENST00000583719.1_RNA|CDKN2B-AS1_ENST00000581051.1_RNA|CDKN2B-AS1_ENST00000455933.2_RNA|CDKN2B-AS1_ENST00000468603.2_RNA|CDKN2B-AS1_ENST00000584816.1_RNA|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2B-AS1_ENST00000584351.1_RNA|RP11-149I2.4_ENST00000578935.1_RNA|CDKN2B-AS1_ENST00000580576.1_RNA|CDKN2B-AS1_ENST00000585267.1_RNA|CDKN2B-AS1_ENST00000577551.1_RNA|CDKN2B-AS1_ENST00000584637.1_RNA|CDKN2A_ENST00000530628.2_Splice_Site_p.G65R|CDKN2B-AS1_ENST00000582301.1_RNA|CDKN2B-AS1_ENST00000428597.1_RNA|CDKN2B-AS1_ENST00000584020.1_RNA|CDKN2A_ENST00000498628.2_Intron|CDKN2A_ENST00000470819.2_Intron			P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	82					cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(198)|p.0(1)|p.G106C(1)|p.?(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CCTTTCCTACCTGGTCTTCTA	0.602		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.G65R		Atlas-SNP	.											CDKN2A_ENST00000361570,NS,carcinoma,0,1	CDKN2A	4810	.	201	Whole gene deletion(199)|Substitution - Missense(1)|Unknown(1)	haematopoietic_and_lymphoid_tissue(34)|lung(33)|central_nervous_system(31)|skin(16)|kidney(14)|oesophagus(11)|bone(10)|pancreas(10)|urinary_tract(7)|breast(6)|soft_tissue(5)|thyroid(4)|pleura(4)|large_intestine(3)|stomach(3)|liver(3)|ovary(3)|upper_aerodigestive_tract(1)|vulva(1)|biliary_tract(1)|autonomic_ganglia(1)	c.G193C						.						13	15	14					9																	21994138		2172	4254	6426	SO:0001630	splice_region_variant	1029	exon1			TCCTACCTGGTCT	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000579755.1:c.193+1G>C	chr9.hg19:g.21994138C>G		47.0	0.0		56.0	16.0	NM_058195	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000579755.1	hg19	CCDS6511.2	.	.	.	.	.	.	.	.	.	.	C	22.9	4.346476	0.82022	.	.	ENSG00000147889	ENST00000361570;ENST00000530628	D;D	0.88818	-2.43;-2.34	4.23	4.23	0.50019	.	0.000000	0.40302	N	0.001140	D	0.90380	0.6989	L	0.36672	1.1	0.34024	D	0.653063	D	0.89917	1.0	D	0.87578	0.998	D	0.91461	0.5189	9	.	.	.	.	12.2937	0.54833	0.0:1.0:0.0:0.0	.	106	Q8N726	CD2A2_HUMAN	R	106;65	ENSP00000355153:G106R;ENSP00000432664:G65R	.	G	-	1	0	CDKN2A	21984138	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.177000	0.50871	2.367000	0.80283	0.555000	0.69702	GGT	.	.		0.602	CDKN2A-004	KNOWN	NMD_exception|upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051918.5	NM_000077	Missense_Mutation	G	21994138	C	G	21994138	5	3	181	1	0	0	0	0	0	0	1	0	3163	695	24	4	687	4	CDKN2A	9	21994138	Splice_Site	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10		21994138	119219293	73	27059										
GBA2	57704	hgsc.bcm.edu	37	chr9	35738529	35738530	+	Frame_Shift_Ins	INS	-	-	G													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cctacccgctaacctggggcINSctgtggtcacccatccatca							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr9:35738529_35738530insG	ENST00000378103.3	-	13	2570_2571	c.2047_2048insC	c.(2047-2049)ggcfs	p.G683fs	GBA2_ENST00000378094.4_Frame_Shift_Ins_p.G683fs|GBA2_ENST00000467252.1_5'UTR|GBA2_ENST00000545786.1_Frame_Shift_Ins_p.G689fs|GBA2_ENST00000378088.1_5'UTR	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2	683					bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TAACCTGGGGCCTGTGGTCACC	0.49																																					p.G683fs		Atlas-INDEL	.											.	GBA2	77	.	0			c.2048_2049insC						.																																			SO:0001589	frameshift_variant	57704	exon13			.	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024	ENST00000378103.3:c.2047_2048insC	chr9.hg19:g.35738529_35738530insG	ENSP00000367343:p.Gly683fs	81.0	0.0		64.0	27.0	NM_020944	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Frame_Shift_Ins	INS	ENST00000378103.3	hg19	CCDS6589.1																																																																																			.	.		0.49	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		G	35738530	-	G	35738529	7	5	181	1	0	1	1	0	0	0	0	0	6275	739	26	0	755	0	GBA2	9	35738529	Frame_Shift_Ins	INS	-	TCGA-DD-AAD5-01A-11D-A40R-10	13744391	35738529	105474902	74	27060										
TMC1	117531	hgsc.bcm.edu	37	chr9	75406907	75406907	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tcgctttgaaatggctactgGgacgcatttttgctcttctt	9	9	2	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr9:75406907G>C	ENST00000297784.5	+	16	1870	c.1330G>C	c.(1330-1332)Gga>Cga	p.G444R	TMC1_ENST00000396237.3_Missense_Mutation_p.G444R|TMC1_ENST00000340019.3_Missense_Mutation_p.G444R	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	444					auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						ATGGCTACTGGGACGCATTTT	0.383																																					p.G444R	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.G1330C						.						253	235	241					9																	75406907		2203	4300	6503	SO:0001583	missense	117531	exon16			CTACTGGGACGCA	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"transmembrane, cochlear expressed, 1"	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.1330G>C	chr9.hg19:g.75406907G>C	ENSP00000297784:p.Gly444Arg	188.0	0.0		142.0	49.0	NM_138691	A8MVZ2|B1AM91	Missense_Mutation	SNP	ENST00000297784.5	hg19	CCDS6643.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.394911	0.83011	.	.	ENSG00000165091	ENST00000297784;ENST00000340019;ENST00000396235;ENST00000537917;ENST00000538054;ENST00000542143;ENST00000396237	T;T;T	0.49720	0.77;0.77;0.77	5.93	5.04	0.67666	.	0.165138	0.53938	D	0.000052	T	0.66208	0.2766	M	0.76838	2.35	0.58432	D	0.999999	P;P;D	0.64830	0.875;0.875;0.994	P;P;D	0.64410	0.786;0.786;0.925	T	0.65635	-0.6120	10	0.25106	T	0.35	-10.6796	15.1374	0.72579	0.0676:0.0:0.9324:0.0	.	411;411;444	A5D8Y1;A4FUA6;Q8TDI8	.;.;TMC1_HUMAN	R	444;444;411;411;411;438;444	ENSP00000297784:G444R;ENSP00000341433:G444R;ENSP00000379538:G444R	ENSP00000297784:G444R	G	+	1	0	TMC1	74596727	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.939000	0.87685	1.519000	0.48950	0.650000	0.86243	GGA	.	.		0.383	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1			C	75406907	G	C	75406907	3	2	181	1	0	0	0	0	1	0	0	0	15999	1233	43	4	1376	4	TMC1	9	75406907	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	39668378	75406907	65806524	75	27061										
RASEF	158158	hgsc.bcm.edu	37	chr9	85640772	85640772	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gttctttataacatgttcatAtggctgaattaatcttggct	7	6	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr9:85640772A>G	ENST00000376447.3	-	2	756	c.496T>C	c.(496-498)Tat>Cat	p.Y166H		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	166					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(4)|liver(1)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						ACATGTTCATATGGCTGAATT	0.353																																					p.Y166H		Atlas-SNP	.											.	RASEF	69	.	0			c.T496C						.						191	176	181					9																	85640772		2203	4300	6503	SO:0001583	missense	158158	exon2			GTTCATATGGCTG	AK056176	CCDS6662.1	9q21.33	2014-05-09	2004-06-11	2004-06-16	ENSG00000165105	ENSG00000165105		"EF-hand domain containing", "RAB, member RAS oncogene"	26464	protein-coding gene	gene with protein product		611344	"RAB45, member RAS oncogene family"	RAB45		17448446	Standard	NM_152573		Approved	FLJ31614	uc004amo.2	Q8IZ41	OTTHUMG00000020100	ENST00000376447.3:c.496T>C	chr9.hg19:g.85640772A>G	ENSP00000365630:p.Tyr166His	146.0	0.0		94.0	4.0	NM_152573	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	hg19	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.281683	0.80692	.	.	ENSG00000165105	ENST00000376447	T	0.66460	-0.21	5.99	5.99	0.97316	.	0.203730	0.43747	D	0.000533	T	0.78886	0.4354	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.80589	-0.1315	10	0.87932	D	0	.	16.4943	0.84223	1.0:0.0:0.0:0.0	.	166	Q8IZ41	RASEF_HUMAN	H	166	ENSP00000365630:Y166H	ENSP00000365630:Y166H	Y	-	1	0	RASEF	84830592	1.000000	0.71417	0.904000	0.35570	0.988000	0.76386	6.606000	0.74159	2.291000	0.77112	0.533000	0.62120	TAT	.	.		0.353	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		G	85640772	A	G	85640772	3	3	181	1	0	0	0	0	1	0	0	0	13083	449	16	2	1790	2	RASEF	9	85640772	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	10233865	85640772	55572659	76	27062										
DIRAS2	54769	hgsc.bcm.edu	37	chr9	93375592	93375592	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cgtcgatctggagactcacgGtcctgcgcttctccaggttg	12	13	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr9:93375592G>T	ENST00000375765.3	-	2	906	c.518C>A	c.(517-519)aCc>aAc	p.T173N		NM_017594.3	NP_060064.2	Q96HU8	DIRA2_HUMAN	DIRAS family, GTP-binding RAS-like 2	173					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			kidney(1)|large_intestine(6)|lung(3)|skin(2)	12						GAGACTCACGGTCCTGCGCTT	0.547																																					p.T173N		Atlas-SNP	.											.	DIRAS2	21	.	0			c.C518A						.						150	135	140					9																	93375592		2203	4300	6503	SO:0001583	missense	54769	exon2			CTCACGGTCCTGC	AB076889	CCDS6687.1	9q22.32	2014-05-09			ENSG00000165023	ENSG00000165023			19323	protein-coding gene	gene with protein product		607863				12194967	Standard	NM_017594		Approved	Di-Ras2, DKFZp761C07121	uc004aqx.1	Q96HU8	OTTHUMG00000020196	ENST00000375765.3:c.518C>A	chr9.hg19:g.93375592G>T	ENSP00000364919:p.Thr173Asn	102.0	0.0		89.0	4.0	NM_017594	B3KVM2	Missense_Mutation	SNP	ENST00000375765.3	hg19	CCDS6687.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.487689	0.26686	.	.	ENSG00000165023	ENST00000375765	T	0.68903	-0.36	5.21	5.21	0.72293	.	0.118100	0.56097	D	0.000035	T	0.38719	0.1051	N	0.01431	-0.87	0.54753	D	0.999984	B	0.02656	0.0	B	0.04013	0.001	T	0.42103	-0.9471	10	0.07990	T	0.79	.	18.3183	0.90229	0.0:0.0:1.0:0.0	.	173	Q96HU8	DIRA2_HUMAN	N	173	ENSP00000364919:T173N	ENSP00000364919:T173N	T	-	2	0	DIRAS2	92415412	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.998000	0.57024	2.884000	0.98904	0.655000	0.94253	ACC	.	.		0.547	DIRAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053012.1			T	93375592	G	T	93375592	3	4	181	1	0	0	0	0	1	0	0	0	4533	1261	44	3	85	3	DIRAS2	9	93375592	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	7734820	93375592	47837839	77	27063										
LHX6	26468	hgsc.bcm.edu	37	chr9	124989224	124989224	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cggcagagggcggtgagcagAcagatggcgtgctgggcgta	20	8	0	4			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr9:124989224A>G	ENST00000373755.2	-	2	263	c.155T>C	c.(154-156)gTc>gCc	p.V52A	LHX6_ENST00000340587.3_Missense_Mutation_p.V81A|LHX6_ENST00000394319.4_Missense_Mutation_p.V81A|LHX6_ENST00000373754.2_Missense_Mutation_p.V52A|LHX6_ENST00000541397.2_Missense_Mutation_p.V70A|LHX6_ENST00000559529.1_5'Flank	NM_001242334.1	NP_001229263.1	Q9UPM6	LHX6_HUMAN	LIM homeobox 6	52					cell maturation (GO:0048469)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|forebrain neuron fate commitment (GO:0021877)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)	8						CGGTGAGCAGACAGATGGCGT	0.662																																					p.V81A		Atlas-SNP	.											.	LHX6	73	.	0			c.T242C						.						72	53	60					9																	124989224		2189	4278	6467	SO:0001583	missense	26468	exon3			GAGCAGACAGATG	AB031041	CCDS6837.2, CCDS6838.2, CCDS56583.1, CCDS56584.1, CCDS59144.1	9q33.2	2011-06-20			ENSG00000106852	ENSG00000106852		"Homeoboxes / LIM class"	21735	protein-coding gene	gene with protein product		608215				10393337	Standard	NM_014368		Approved	LHX6.1	uc004blx.4	Q9UPM6	OTTHUMG00000020601	ENST00000373755.2:c.155T>C	chr9.hg19:g.124989224A>G	ENSP00000362860:p.Val52Ala	49.0	0.0		27.0	11.0	NM_014368	A6PVQ1|A6PVQ2|A8K1B2|B7Z4D0|H0YN76|Q5T7S7|Q5T7S8|Q9NTK3|Q9UPM5	Missense_Mutation	SNP	ENST00000373755.2	hg19	CCDS56583.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.952524	0.53293	.	.	ENSG00000106852	ENST00000373755;ENST00000373754;ENST00000394319;ENST00000340587;ENST00000541397	D;D;D;D;D	0.87103	-2.21;-2.17;-2.06;-2.01;-2.1	5.44	5.44	0.79542	.	0.192922	0.44097	D	0.000485	T	0.79076	0.4385	L	0.29908	0.895	0.80722	D	1	B;B;B	0.32918	0.39;0.005;0.004	B;B;B	0.29862	0.108;0.004;0.005	T	0.76121	-0.3075	10	0.16420	T	0.52	.	14.6748	0.68972	1.0:0.0:0.0:0.0	.	52;81;81	Q9UPM6;Q9UPM6-4;Q9UPM6-3	LHX6_HUMAN;.;.	A	52;52;81;81;70	ENSP00000362860:V52A;ENSP00000362859:V52A;ENSP00000377854:V81A;ENSP00000340137:V81A;ENSP00000441464:V70A	ENSP00000340137:V81A	V	-	2	0	LHX6	124029045	0.998000	0.40836	0.994000	0.49952	0.963000	0.63663	3.962000	0.56766	2.055000	0.61198	0.379000	0.24179	GTC	.	.		0.662	LHX6-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053924.2	NM_014368		G	124989224	A	G	124989224	3	3	181	1	0	0	0	0	1	0	0	0	8784	275	10	2	1027	2	LHX6	9	124989224	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	31613632	124989224	16224207	78	27064										
AKR1C4	1109	hgsc.bcm.edu	37	chr10	5238850	5238850	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aatggatcccaaatatcagcGtgtagagctaaatgatggtc	10	7	1	2	rs373855442		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr10:5238850G>A	ENST00000380448.1	+	3	273	c.20G>A	c.(19-21)cGt>cAt	p.R7H	AKR1CL1_ENST00000445191.1_Intron|AKR1C4_ENST00000263126.1_Missense_Mutation_p.R7H|U8_ENST00000516100.1_RNA			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	7					androgen metabolic process (GO:0008209)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|bile acid transmembrane transporter activity (GO:0015125)|chlordecone reductase activity (GO:0047743)|electron carrier activity (GO:0009055)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|retinal dehydrogenase activity (GO:0001758)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	18						AAATATCAGCGTGTAGAGCTA	0.408																																					p.R7H		Atlas-SNP	.											.	AKR1C4	57	.	0			c.G20A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	253	205	221		20	-3.6	0	10		221	0,8600		0,0,4300	no	missense	AKR1C4	NM_001818.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	7/324	5238850	1,13005	2203	4300	6503	SO:0001583	missense	1109	exon1			ATCAGCGTGTAGA	M33375	CCDS7064.1	10p15.1	2012-12-04	2012-12-04		ENSG00000198610	ENSG00000198610	1.1.1.225	"Aldo-keto reductases"	387	protein-coding gene	gene with protein product	"chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4"	600451	"aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)"	CHDR		7789999	Standard	NM_001818		Approved	DD4, HAKRA, C11, 3-alpha-HSD, CDR, MGC22581	uc001ihw.2	P17516	OTTHUMG00000017591	ENST00000380448.1:c.20G>A	chr10.hg19:g.5238850G>A	ENSP00000369814:p.Arg7His	129.0	0.0		190.0	116.0	NM_001818	Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	ENST00000380448.1	hg19	CCDS7064.1	.	.	.	.	.	.	.	.	.	.	G	5.139	0.211236	0.09757	2.27E-4	0.0	ENSG00000198610	ENST00000380448;ENST00000263126;ENST00000397357	T;T	0.55930	0.49;0.49	2.92	-3.61	0.04556	NADP-dependent oxidoreductase domain (2);	1.662580	0.03590	N	0.231684	T	0.31327	0.0793	N	0.25485	0.75	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.05784	-1.0864	10	0.14656	T	0.56	.	1.2306	0.01943	0.3178:0.15:0.3804:0.1518	.	7	P17516	AK1C4_HUMAN	H	7	ENSP00000369814:R7H;ENSP00000263126:R7H	ENSP00000263126:R7H	R	+	2	0	AKR1C4	5228850	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.805000	0.04530	-0.745000	0.04772	0.591000	0.81541	CGT	.	.		0.408	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818		A	5238850	G	A	5238850	3	1	181	1	0	0	0	0	1	0	0	0	472	1145	40	1	22	1	AKR1C4	10	5238850	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10		5238850	130295897	79	27065										
FAM171A1	221061	hgsc.bcm.edu	37	chr10	15256432	15256432	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tccttcgtgccgggggcctcGgggcggccgtggctggtgac	19	13	0	1	rs143895945		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr10:15256432G>C	ENST00000378116.4	-	8	1161	c.1155C>G	c.(1153-1155)ccC>ccG	p.P385P	FAM171A1_ENST00000477161.1_5'UTR	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	385						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						CGGGGGCCTCGGGGCGGCCGT	0.602																																					p.P385P		Atlas-SNP	.											.	FAM171A1	252	.	0			c.C1155G						.						37	44	42					10																	15256432		2203	4300	6503	SO:0001819	synonymous_variant	221061	exon8			GGCCTCGGGGCGG	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 38"	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.1155C>G	chr10.hg19:g.15256432G>C		94.0	0.0		151.0	31.0	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Silent	SNP	ENST00000378116.4	hg19	CCDS31154.1																																																																																			.	G|1.000;A|0.000		0.602	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		C	15256432	G	C	15256432	2	2	181	1	0	0	0	0	0	0	0	1	5495	1103	39	4		4	FAM171A1	10	15256432	Silent	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	10017582	15256432	120278315	80	27066										
ZNF485	220992	hgsc.bcm.edu	37	chr10	44111881	44111881	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agctccacagagaagaactaTaagtgcaaggaatgtgggaa	12	6	0	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr10:44111881T>C	ENST00000361807.3	+	5	584	c.390T>C	c.(388-390)taT>taC	p.Y130Y	ZNF485_ENST00000374435.3_Silent_p.Y130Y|ZNF485_ENST00000374437.2_Silent_p.Y39Y	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	130					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						AGAAGAACTATAAGTGCAAGG	0.433																																					p.Y130Y		Atlas-SNP	.											.	ZNF485	102	.	0			c.T390C						.						92	94	93					10																	44111881		2203	4300	6503	SO:0001819	synonymous_variant	220992	exon5			GAACTATAAGTGC	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"Zinc fingers, C2H2-type", "-"	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.390T>C	chr10.hg19:g.44111881T>C		243.0	0.0		203.0	101.0	NM_145312	B4DSE6|Q96CL0	Silent	SNP	ENST00000361807.3	hg19	CCDS7205.2																																																																																			.	.		0.433	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312		C	44111881	T	C	44111881	2	2	181	1	0	0	0	0	0	0	0	1	17953	1413	49	2		2	ZNF485	10	44111881	Silent	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	28855449	44111881	91422866	81	27067										
STOX1	219736	hgsc.bcm.edu	37	chr10	70646233	70646233	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tcctcagaatcaggaaatgaGaaaacatttcccacaaaagt	6	9	2	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr10:70646233G>C	ENST00000298596.6	+	3	2764	c.2681G>C	c.(2680-2682)aGa>aCa	p.R894T	STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399165.4_Intron|STOX1_ENST00000421961.2_Missense_Mutation_p.R784T|STOX1_ENST00000399169.4_Missense_Mutation_p.R894T	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	894						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						CAGGAAATGAGAAAACATTTC	0.428																																					p.R894T		Atlas-SNP	.											.	STOX1	75	.	0			c.G2681C						.						65	68	67					10																	70646233		2096	4255	6351	SO:0001583	missense	219736	exon3			AAATGAGAAAACA	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"chromosome 10 open reading frame 24"	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.2681G>C	chr10.hg19:g.70646233G>C	ENSP00000298596:p.Arg894Thr	115.0	0.0		103.0	21.0	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	hg19	CCDS41535.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.299947	0.40694	.	.	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000421961	T;T;T	0.75821	-0.97;-0.97;-0.65	6.17	3.01	0.34805	.	0.297785	0.35772	N	0.002998	T	0.67534	0.2903	M	0.62723	1.935	0.09310	N	1	B	0.34372	0.451	B	0.30179	0.112	T	0.60541	-0.7243	10	0.72032	D	0.01	.	9.7037	0.40203	0.2483:0.0:0.7517:0.0	.	894	Q6ZVD7	STOX1_HUMAN	T	894;894;784	ENSP00000382121:R894T;ENSP00000298596:R894T;ENSP00000394509:R784T	ENSP00000298596:R894T	R	+	2	0	STOX1	70316239	0.018000	0.18449	0.354000	0.25760	0.892000	0.51952	1.008000	0.29872	0.328000	0.23435	0.655000	0.94253	AGA	.	.		0.428	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		C	70646233	G	C	70646233	3	2	181	1	0	0	0	0	1	0	0	0	15334	942	33	4	2691	4	STOX1	10	70646233	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	26534352	70646233	64888514	82	27068										
TMEM20	159371	hgsc.bcm.edu	37	chr10	95660950	95660950	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cttggcctcgttgaaagtgtCatcatcctctctgtattagg	9	10	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr10:95660950C>T	ENST00000427197.1	+	3	862	c.801C>T	c.(799-801)gtC>gtT	p.V267V	SLC35G1_ENST00000371408.3_Silent_p.V266V	NM_001134658.1|NM_153226.2	NP_001128130.1|NP_694958.1	Q2M3R5	S35G1_HUMAN	solute carrier family 35, member G1	267	EamA 2.				calcium ion export from cell (GO:1990034)|cytosolic calcium ion homeostasis (GO:0051480)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											TTGAAAGTGTCATCATCCTCT	0.428																																					p.V267V		Atlas-SNP	.											.	.	.	.	0			c.C801T						.						121	121	121					10																	95660950		2203	4300	6503	SO:0001819	synonymous_variant	159371	exon3			AAGTGTCATCATC	AK091309	CCDS7432.1, CCDS44459.1	10q23.33	2013-05-22	2011-08-03	2011-08-03	ENSG00000176273	ENSG00000176273		"Solute carriers"	26607	protein-coding gene	gene with protein product			"transmembrane protein 20"	TMEM20		21569384	Standard	NM_153226		Approved	FLJ33990, C10orf60	uc001kjg.2	Q2M3R5	OTTHUMG00000018779	ENST00000427197.1:c.801C>T	chr10.hg19:g.95660950C>T		168.0	0.0		161.0	28.0	NM_001134658	Q86YG5|Q8NBA5	Silent	SNP	ENST00000427197.1	hg19	CCDS44459.1																																																																																			.	.		0.428	SLC35G1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_153226		T	95660950	C	T	95660950	2	4	181	1	0	0	0	0	0	0	0	1	16137	813	29	3		3	TMEM20	10	95660950	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	25014717	95660950	39873797	83	27069										
SEC23IP	11196	hgsc.bcm.edu	37	chr10	121678006	121678006	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	atggagttgtgaagcagctaCattttcaggaaaagcaggta	12	5	1	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr10:121678006C>G	ENST00000369075.3	+	10	1927	c.1855C>G	c.(1855-1857)Cat>Gat	p.H619D	SEC23IP_ENST00000543134.1_Missense_Mutation_p.H408D	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	619					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		GAAGCAGCTACATTTTCAGGA	0.368																																					p.H619D		Atlas-SNP	.											.	SEC23IP	100	.	0			c.C1855G						.						111	105	107					10																	121678006		2203	4300	6503	SO:0001583	missense	11196	exon10			CAGCTACATTTTC	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.1855C>G	chr10.hg19:g.121678006C>G	ENSP00000358071:p.His619Asp	122.0	0.0		66.0	26.0	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Missense_Mutation	SNP	ENST00000369075.3	hg19	CCDS7618.1	.	.	.	.	.	.	.	.	.	.	C	3.986	-0.005505	0.07773	.	.	ENSG00000107651	ENST00000369075;ENST00000543134	T;T	0.43688	0.94;0.94	5.72	-0.446	0.12238	.	1.579740	0.02992	N	0.146968	T	0.22742	0.0549	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07121	-1.0789	10	0.10377	T	0.69	0.7776	1.0414	0.01559	0.3149:0.3034:0.2178:0.1639	.	408;619	F5H0L8;Q9Y6Y8	.;S23IP_HUMAN	D	619;408	ENSP00000358071:H619D;ENSP00000438773:H408D	ENSP00000358071:H619D	H	+	1	0	SEC23IP	121667996	0.000000	0.05858	0.011000	0.14972	0.990000	0.78478	0.689000	0.25437	0.087000	0.17167	0.655000	0.94253	CAT	.	.		0.368	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			G	121678006	C	G	121678006	3	3	181	1	0	0	0	0	1	0	0	0	14008	478	17	4	1893	4	SEC23IP	10	121678006	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	26017056	121678006	13856741	84	27070										
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7647047	7647070	+	In_Frame_Del	DEL	GATGCAGAAATTGAGCGTCTGCAC	GATGCAGAAATTGAGCGTCTGCAC	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aagaacaggtggccctgaaaGatgcagaaattgagcgtctg					rs144468110|rs148281709|rs376707389		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	GATGCAGAAATTGAGCGTCTGCAC	GATGCAGAAATTGAGCGTCTGCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr11:7647047_7647070delGATGCAGAAATTGAGCGTCTGCAC	ENST00000299492.4	+	8	1139_1162	c.751_774delGATGCAGAAATTGAGCGTCTGCAC	c.(751-774)gatgcagaaattgagcgtctgcacdel	p.DAEIERLH251del	PPFIBP2_ENST00000528883.1_In_Frame_Del_p.DAEIERLH139del|PPFIBP2_ENST00000530181.1_In_Frame_Del_p.DAEIERLH108del|PPFIBP2_ENST00000533792.1_In_Frame_Del_p.DAEIERLH93del	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	251					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		GGCCCTGAAAGATGCAGAAATTGAGCGTCTGCACAGCCAGCTCT	0.545																																					p.250_258del		Atlas-INDEL	.											.	PPFIBP2	87	.	0			c.750_773del						.																																			SO:0001651	inframe_deletion	8495	exon8			.	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"Sterile alpha motif (SAM) domain containing"	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.751_774delGATGCAGAAATTGAGCGTCTGCAC	chr11.hg19:g.7647047_7647070delGATGCAGAAATTGAGCGTCTGCAC	ENSP00000299492:p.Asp251_His258del	200.0	0.0		115.0	23.0	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	In_Frame_Del	DEL	ENST00000299492.4	hg19	CCDS31419.1																																																																																			.	.		0.545	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		-	7647070	GATGCAGAAATTGAGCGTCTGCAC	-	7647047	7	5	181	1	0	1	0	1	0	0	0	0	12323	942	33	0	777	0	PPFIBP2	11	7647047	In_Frame_Del	DEL	GATGCAGAAATTGAGCGTCTGCAC	TCGA-DD-AAD5-01A-11D-A40R-10		7647047	127359469	85	27071										
PTPN5	84867	hgsc.bcm.edu	37	chr11	18787389	18787389	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgcagcacatgtccagggccCctccctcggagtcatcagca	10	16	2	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr11:18787389C>T	ENST00000358540.2	-	3	492	c.62G>A	c.(61-63)gGg>gAg	p.G21E	PTPN5_ENST00000396171.4_Missense_Mutation_p.G21E|PTPN5_ENST00000396170.1_Missense_Mutation_p.G21E|PTPN5_ENST00000396168.1_5'UTR|PTPN5_ENST00000396167.2_Missense_Mutation_p.G21E	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	21					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						GTCCAGGGCCCCTCCCTCGGA	0.562																																					p.G21E		Atlas-SNP	.											.	PTPN5	163	.	0			c.G62A						.						65	52	56					11																	18787389		2198	4293	6491	SO:0001583	missense	84867	exon3			AGGGCCCCTCCCT	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.62G>A	chr11.hg19:g.18787389C>T	ENSP00000351342:p.Gly21Glu	98.0	0.0		94.0	27.0	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Missense_Mutation	SNP	ENST00000358540.2	hg19	CCDS7845.1	.	.	.	.	.	.	.	.	.	.	C	16.43	3.120724	0.56613	.	.	ENSG00000110786	ENST00000358540;ENST00000396170;ENST00000396171;ENST00000396167	T;T;T;T	0.08634	3.57;3.07;3.57;3.07	5.41	5.41	0.78517	.	0.000000	0.49305	D	0.000149	T	0.13670	0.0331	N	0.19112	0.55	0.29891	N	0.82521	D;D	0.64830	0.994;0.987	P;P	0.58454	0.839;0.737	T	0.01290	-1.1394	10	0.87932	D	0	.	14.7073	0.69200	0.0:1.0:0.0:0.0	.	21;21	P54829;B3KXG7	PTN5_HUMAN;.	E	21	ENSP00000351342:G21E;ENSP00000379473:G21E;ENSP00000379474:G21E;ENSP00000379470:G21E	ENSP00000351342:G21E	G	-	2	0	PTPN5	18743965	0.988000	0.35896	0.991000	0.47740	0.191000	0.23601	3.549000	0.53681	2.520000	0.84964	0.563000	0.77884	GGG	.	.		0.562	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970		T	18787389	C	T	18787389	3	4	181	1	0	0	0	0	1	0	0	0	12806	623	22	3	1687	3	PTPN5	11	18787389	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	11140342	18787389	116219127	86	27072										
CKAP5	9793	hgsc.bcm.edu	37	chr11	46765632	46765633	+	In_Frame_Ins	INS	-	-	GGA													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aagtcgtctatgttagctgtINSggaggaggaggaggtcacag							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr11:46765632_46765633insGGA	ENST00000529230.1	-	44	6085_6086	c.6039_6040insTCC	c.(6037-6042)tccaca>tccTCCaca	p.2013_2014insS	CKAP5_ENST00000415402.1_In_Frame_Ins_p.2020_2021insS|CKAP5_ENST00000312055.5_In_Frame_Ins_p.1953_1954insS|CKAP5_ENST00000354558.3_In_Frame_Ins_p.1953_1954insS			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	2013					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						ATGTTAGCTGTGGAGGAGGAGG	0.52																																					p.T2014delinsST	Ovarian(4;85 273 2202 4844 13323)	Atlas-INDEL	.											.	CKAP5	134	.	0			c.6040_6041insTCC						.																																			SO:0001652	inframe_insertion	9793	exon44			.		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.6037_6039dupTCC	chr11.hg19:g.46765639_46765641dupGGA	ENSP00000432768:p.Ser2013_Ser2013dup	163.0	0.0		96.0	34.0	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	In_Frame_Ins	INS	ENST00000529230.1	hg19	CCDS31477.1																																																																																			.	.		0.52	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		GGA	46765633	-	GGA	46765632	7	5	181	1	0	1	1	0	0	0	0	0	3447	1696	59	0	62	0	CKAP5	11	46765632	In_Frame_Ins	INS	-	TCGA-DD-AAD5-01A-11D-A40R-10	27978243	46765632	88240884	87	27073										
CCDC88B	283234	hgsc.bcm.edu	37	chr11	64110657	64110657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgctctcccaccaggaggagCgggtgctctcgggggtgctg	17	12	2	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr11:64110657C>T	ENST00000356786.5	+	11	1113	c.1069C>T	c.(1069-1071)Cgg>Tgg	p.R357W	CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000301897.4_5'Flank	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	357						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CCAGGAGGAGCGGGTGCTCTC	0.692																																					p.R357W		Atlas-SNP	.											.	CCDC88B	89	.	0			c.C1069T						.						9	7	8					11																	64110657		2079	4072	6151	SO:0001583	missense	283234	exon11			GAGGAGCGGGTGC	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"brain leucine zipper protein", "GRP78-interacting protein induced by ER stress"	611205	"coiled-coil domain containing 88"	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.1069C>T	chr11.hg19:g.64110657C>T	ENSP00000349238:p.Arg357Trp	36.0	0.0		29.0	12.0	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Missense_Mutation	SNP	ENST00000356786.5	hg19	CCDS8072.2	.	.	.	.	.	.	.	.	.	.	.	20.4	3.986989	0.74589	.	.	ENSG00000168071	ENST00000377638;ENST00000356786	T	0.17854	2.25	4.33	4.33	0.51752	.	.	.	.	.	T	0.37073	0.0990	M	0.74467	2.265	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.60886	0.88;0.88	T	0.26849	-1.0091	9	0.87932	D	0	.	12.7787	0.57464	0.0:1.0:0.0:0.0	.	357;357	B2RTU8;A6NC98	.;CC88B_HUMAN	W	357	ENSP00000349238:R357W	ENSP00000349238:R357W	R	+	1	2	CCDC88B	63867233	0.906000	0.30813	0.908000	0.35775	0.533000	0.34776	1.641000	0.37197	2.143000	0.66587	0.456000	0.33151	CGG	.	.		0.692	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251		T	64110657	C	T	64110657	3	4	181	1	0	0	0	0	1	0	0	0	2866	759	27	1	1111	1	CCDC88B	11	64110657	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	17345025	64110657	70895859	88	27074										
B3GNT1	11041	hgsc.bcm.edu	37	chr11	66114190	66114190	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cgccaacctggtagagctgcAccagctcgtttttgttcatg	10	12	1	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr11:66114190A>T	ENST00000311181.4	-	1	973	c.827T>A	c.(826-828)gTg>gAg	p.V276E	BRMS1_ENST00000425825.2_5'Flank|BRMS1_ENST00000359957.3_5'Flank|RP11-867G23.8_ENST00000531602.1_5'Flank	NM_006876.2	NP_006867.1	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1	276					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			breast(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	12						GTAGAGCTGCACCAGCTCGTT	0.612																																					p.V276E		Atlas-SNP	.											.	B3GNT1	28	.	0			c.T827A						.						60	64	63					11																	66114190		2200	4295	6495	SO:0001583	missense	11041	exon1			AGCTGCACCAGCT	AF029893	CCDS8136.1	11q13.2	2014-07-08	2006-04-12	2006-04-12	ENSG00000174684	ENSG00000174684	2.4.1.149	"Beta 3-glycosyltransferases"	15685	protein-coding gene	gene with protein product	"N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase"	605517	"UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6"	B3GNT6		9405606	Standard	NM_006876		Approved	iGNT, iGAT, iGnT, BETA3GNTI, B3GN-T1	uc001ohr.3	O43505	OTTHUMG00000167082	ENST00000311181.4:c.827T>A	chr11.hg19:g.66114190A>T	ENSP00000309096:p.Val276Glu	74.0	0.0		45.0	15.0	NM_006876	Q4TTN0	Missense_Mutation	SNP	ENST00000311181.4	hg19	CCDS8136.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.263086	0.39995	.	.	ENSG00000174684	ENST00000311181;ENST00000538757	T	0.21932	1.98	5.59	4.47	0.54385	.	0.501380	0.19877	N	0.104075	T	0.13114	0.0318	N	0.19112	0.55	0.50813	D	0.999892	B	0.22146	0.065	B	0.23150	0.044	T	0.10497	-1.0627	10	0.22706	T	0.39	-5.0474	9.6143	0.39681	0.917:0.0:0.083:0.0	.	276	O43505	B3GN1_HUMAN	E	276;47	ENSP00000309096:V276E	ENSP00000309096:V276E	V	-	2	0	B3GNT1	65870766	1.000000	0.71417	0.990000	0.47175	0.869000	0.49853	5.734000	0.68580	0.967000	0.38186	0.460000	0.39030	GTG	.	.		0.612	B3GNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392959.1	NM_006876		T	66114190	A	T	66114190	3	4	181	1	0	0	0	0	1	0	0	0	1256	159	6	4	428	4	B3GNT1	11	66114190	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	2003533	66114190	68892326	89	27075										
NUMA1	4926	hgsc.bcm.edu	37	chr11	71725431	71725431	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agcgaactccacacgctgctCgttgagggcgttctgcagcc	12	14	1	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr11:71725431C>T	ENST00000393695.3	-	15	3449	c.3118G>A	c.(3118-3120)Gag>Aag	p.E1040K	RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Missense_Mutation_p.E1040K|NUMA1_ENST00000351960.6_Intron	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						ACACGCTGCTCGTTGAGGGCG	0.647			T	RARA	APL																																p.E1040K		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.G3118A						.						50	51	50					11																	71725431		2199	4293	6492	SO:0001583	missense	4926	exon15			GCTGCTCGTTGAG	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.3118G>A	chr11.hg19:g.71725431C>T	ENSP00000377298:p.Glu1040Lys	56.0	0.0		23.0	9.0	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	hg19	CCDS31633.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.010106	0.54361	.	.	ENSG00000137497	ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	T;T	0.15256	2.44;2.45	5.07	5.07	0.68467	.	0.000000	0.64402	D	0.000019	T	0.32763	0.0840	L	0.50333	1.59	0.31343	N	0.683423	D;D;D;D	0.89917	1.0;0.998;0.994;1.0	D;P;P;D	0.79108	0.992;0.805;0.777;0.992	T	0.14896	-1.0456	9	.	.	.	.	10.8901	0.46990	0.0:0.913:0.0:0.087	.	1046;524;1040;1040	Q4LE64;Q59HB8;Q14980-2;Q14980	.;.;.;NUMA1_HUMAN	K	1040;1040;603;9	ENSP00000351851:E1040K;ENSP00000377298:E1040K	.	E	-	1	0	NUMA1	71403079	0.983000	0.35010	0.999000	0.59377	0.922000	0.55478	2.749000	0.47492	2.644000	0.89710	0.655000	0.94253	GAG	.	.		0.647	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			T	71725431	C	T	71725431	3	4	181	1	0	0	0	0	1	0	0	0	10759	893	31	1	3281	1	NUMA1	11	71725431	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	5611241	71725431	63281085	90	27076										
PGM2L1	283209	hgsc.bcm.edu	37	chr11	74058249	74058249	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aacggtagaaaagtctggatCaggatctttttgttctggta	11	5	4	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr11:74058249C>T	ENST00000298198.4	-	7	1194	c.883G>A	c.(883-885)Gat>Aat	p.D295N		NM_173582.3	NP_775853.2	Q6PCE3	PGM2L_HUMAN	phosphoglucomutase 2-like 1	295					glucose metabolic process (GO:0006006)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	glucose-1,6-bisphosphate synthase activity (GO:0047933)|intramolecular transferase activity, phosphotransferases (GO:0016868)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(11;3.32e-06)					AAGTCTGGATCAGGATCTTTT	0.348																																					p.D295N		Atlas-SNP	.											.	PGM2L1	59	.	0			c.G883A						.						74	75	75					11																	74058249		2200	4293	6493	SO:0001583	missense	283209	exon7			CTGGATCAGGATC	AB019210	CCDS8231.1	11q13.3	2008-12-01			ENSG00000165434	ENSG00000165434			20898	protein-coding gene	gene with protein product	"glucose-1,6-bisphosphate synthase"	611610				17804405	Standard	NM_173582		Approved	FLJ32029, BM32A	uc001ovb.1	Q6PCE3	OTTHUMG00000168132	ENST00000298198.4:c.883G>A	chr11.hg19:g.74058249C>T	ENSP00000298198:p.Asp295Asn	148.0	0.0		97.0	23.0	NM_173582	Q96MQ7|Q9UIK3	Missense_Mutation	SNP	ENST00000298198.4	hg19	CCDS8231.1	.	.	.	.	.	.	.	.	.	.	C	32	5.143109	0.94560	.	.	ENSG00000165434	ENST00000298198	T	0.69926	-0.44	5.45	5.45	0.79879	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);Alpha-D-phosphohexomutase, alpha/beta/alpha domain II (1);	0.000000	0.85682	D	0.000000	T	0.81083	0.4749	M	0.78456	2.415	0.80722	D	1	D	0.54397	0.966	D	0.64237	0.923	T	0.82137	-0.0606	10	0.52906	T	0.07	-21.9469	16.7933	0.85595	0.0:1.0:0.0:0.0	.	295	Q6PCE3	PGM2L_HUMAN	N	295	ENSP00000298198:D295N	ENSP00000298198:D295N	D	-	1	0	PGM2L1	73735897	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.535000	0.85469	0.563000	0.77884	GAT	.	.		0.348	PGM2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398324.1	NM_173582		T	74058249	C	T	74058249	3	4	181	1	0	0	0	0	1	0	0	0	11808	826	29	3	1017	3	PGM2L1	11	74058249	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	2332818	74058249	60948267	91	27077										
KCNE3	10008	hgsc.bcm.edu	37	chr11	74168597	74168597	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	taccaggtctccgttccattGgtagtctccatagcaacagg	9	12	2	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr11:74168597G>A	ENST00000310128.4	-	3	431	c.12C>T	c.(10-12)acC>acT	p.T4T	RP11-702H23.4_ENST00000533008.1_RNA|RP11-702H23.6_ENST00000530510.1_RNA|KCNE3_ENST00000525550.1_Silent_p.T4T	NM_005472.4	NP_005463.1	Q9Y6H6	KCNE3_HUMAN	potassium voltage-gated channel, Isk-related family, member 3	4			T -> A (in dbSNP:rs200856070). {ECO:0000269|PubMed:19306396}.		regulation of potassium ion transport (GO:0043266)	integral component of membrane (GO:0016021)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			cervix(1)|large_intestine(1)|lung(1)|ovary(1)	4	Breast(11;2.86e-06)					CCGTTCCATTGGTAGTCTCCA	0.562																																					p.T4T		Atlas-SNP	.											.	KCNE3	7	.	0			c.C12T						.						67	65	65					11																	74168597		2200	4293	6493	SO:0001819	synonymous_variant	10008	exon3			TCCATTGGTAGTC	AF076531	CCDS8232.1	11q13.4	2014-09-17				ENSG00000175538		"Potassium channels"	6243	protein-coding gene	gene with protein product		604433				10219239	Standard	NM_005472		Approved	MiRP2, HOKPP	uc001ovc.3	Q9Y6H6		ENST00000310128.4:c.12C>T	chr11.hg19:g.74168597G>A		138.0	0.0		88.0	26.0	NM_005472		Silent	SNP	ENST00000310128.4	hg19	CCDS8232.1																																																																																			.	.		0.562	KCNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385531.1	NM_005472		A	74168597	G	A	74168597	2	1	181	1	0	0	0	0	0	0	0	1	8033	1335	47	3		3	KCNE3	11	74168597	Silent	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	110348	74168597	60837919	92	27078										
TRPC6	7225	hgsc.bcm.edu	37	chr11	101344488	101344488	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	attatttgaggatcagagggGtcccactttatcctggctag	11	8	1	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr11:101344488G>T	ENST00000344327.3	-	7	2185	c.1761C>A	c.(1759-1761)gaC>gaA	p.D587E	TRPC6_ENST00000532133.1_Missense_Mutation_p.D509E|TRPC6_ENST00000348423.4_Missense_Mutation_p.D471E|TRPC6_ENST00000360497.4_Missense_Mutation_p.D532E	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	587					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		GATCAGAGGGGTCCCACTTTA	0.338																																					p.D587E	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											.	TRPC6	132	.	0			c.C1761A						.						67	70	69					11																	101344488		2203	4294	6497	SO:0001583	missense	7225	exon7			AGAGGGGTCCCAC	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.1761C>A	chr11.hg19:g.101344488G>T	ENSP00000340913:p.Asp587Glu	137.0	0.0		66.0	23.0	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	hg19	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	G	3.969	-0.008849	0.07727	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;D;D;D	0.99270	-1.13;-4.93;-5.66;-5.66	5.91	4.99	0.66335	Ion transport (1);	0.167845	0.50627	D	0.000113	D	0.96620	0.8897	N	0.25485	0.75	0.37480	D	0.915969	P;P;P	0.40066	0.652;0.481;0.701	B;B;P	0.45276	0.344;0.146;0.475	D	0.94292	0.7529	10	0.06494	T	0.89	-4.5201	4.8129	0.13353	0.1547:0.2084:0.6369:0.0	.	532;471;587	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	E	587;509;471;532	ENSP00000340913:D587E;ENSP00000435574:D509E;ENSP00000343672:D471E;ENSP00000353687:D532E	ENSP00000340913:D587E	D	-	3	2	TRPC6	100849698	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.723000	0.38053	2.793000	0.96121	0.655000	0.94253	GAC	.	.		0.338	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		T	101344488	G	T	101344488	3	4	181	1	0	0	0	0	1	0	0	0	16598	1252	44	3	1062	3	TRPC6	11	101344488	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	27175891	101344488	33662028	93	27079										
NEUROD4	58158	hgsc.bcm.edu	37	chr12	55420588	55420588	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	atgctactctaaaacccaaaAactttccaagatagagactc	4	11	1	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr12:55420588A>G	ENST00000242994.3	+	2	743	c.365A>G	c.(364-366)aAa>aGa	p.K122R		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	122	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				amacrine cell differentiation (GO:0035881)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch signaling pathway (GO:0007219)|positive regulation of cell differentiation (GO:0045597)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	41						AAAACCCAAAAACTTTCCAAG	0.498																																					p.K122R		Atlas-SNP	.											.	NEUROD4	87	.	0			c.A365G						.						81	86	85					12																	55420588		2203	4300	6503	SO:0001583	missense	58158	exon2			CCCAAAAACTTTC	AF203901	CCDS8886.1	12q13.13	2013-05-21	2012-02-22			ENSG00000123307		"Basic helix-loop-helix proteins"	13802	protein-coding gene	gene with protein product		611635	"neurogenic differentiation 4"				Standard	NM_021191		Approved	Atoh3, ATH-3, MATH-3, bHLHa4	uc001sgp.4	Q9HD90		ENST00000242994.3:c.365A>G	chr12.hg19:g.55420588A>G	ENSP00000242994:p.Lys122Arg	119.0	0.0		129.0	34.0	NM_021191	B2RAC9	Missense_Mutation	SNP	ENST00000242994.3	hg19	CCDS8886.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.115044	0.77210	.	.	ENSG00000123307	ENST00000242994	D	0.99098	-5.42	5.49	5.49	0.81192	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.98548	0.9515	L	0.37800	1.135	0.58432	D	0.999999	P	0.52061	0.95	D	0.64687	0.928	D	0.99694	1.1002	10	0.66056	D	0.02	-27.3093	13.8561	0.63527	1.0:0.0:0.0:0.0	.	122	Q9HD90	NDF4_HUMAN	R	122	ENSP00000242994:K122R	ENSP00000242994:K122R	K	+	2	0	NEUROD4	53706855	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	9.339000	0.96797	2.222000	0.72286	0.533000	0.62120	AAA	.	.		0.498	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1			G	55420588	A	G	55420588	3	3	181	1	0	0	0	0	1	0	0	0	10359	14	1	2	367	2	NEUROD4	12	55420588	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10		55420588	78431307	94	27080										
PTPRB	5787	hgsc.bcm.edu	37	chr12	71016198	71016198	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tggtgctggagaagggctgaGtagtcgacaaaacccatgat	14	7	0	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr12:71016198G>C	ENST00000550358.1	-	3	705	c.680C>G	c.(679-681)aCt>aGt	p.T227S	PTPRB_ENST00000334414.6_Missense_Mutation_p.T227S|PTPRB_ENST00000551525.1_Missense_Mutation_p.T226S|PTPRB_ENST00000538174.2_5'UTR			P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	0	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			GAAGGGCTGAGTAGTCGACAA	0.498																																					p.T227S		Atlas-SNP	.											.	PTPRB	676	.	0			c.C680G						.						162	174	170					12																	71016198		2049	4198	6247	SO:0001583	missense	5787	exon3			GGCTGAGTAGTCG	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000550358.1:c.680C>G	chr12.hg19:g.71016198G>C	ENSP00000448058:p.Thr227Ser	88.0	0.0		78.0	19.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000550358.1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.90	3.912715	0.72983	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000551525;ENST00000548122	T;T;T;T	0.05081	4.12;4.02;3.58;3.5	5.71	4.82	0.62117	.	.	.	.	.	T	0.09818	0.0241	L	0.51422	1.61	0.43531	D	0.99581	P;P;B;P;D	0.56521	0.682;0.952;0.149;0.675;0.976	B;P;B;B;P	0.49085	0.156;0.536;0.051;0.347;0.6	T	0.14952	-1.0454	9	0.06891	T	0.86	.	14.7664	0.69642	0.0:0.1442:0.8558:0.0	.	106;227;226;227;227	Q6ZR19;Q6ZTX7;F8VSD5;P23467-3;F8VU56	.;.;.;.;.	S	227;227;227;226;106	ENSP00000334928:T227S;ENSP00000448058:T227S;ENSP00000448349:T226S;ENSP00000446982:T106S	ENSP00000334928:T227S	T	-	2	0	PTPRB	69302465	0.414000	0.25408	0.014000	0.15608	0.806000	0.45545	2.026000	0.41069	1.399000	0.46721	0.650000	0.86243	ACT	.	.		0.498	PTPRB-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404436.1			C	71016198	G	C	71016198	3	2	181	1	0	0	0	0	1	0	0	0	12811	1029	36	4	6153	4	PTPRB	12	71016198	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	15595610	71016198	62835697	95	27081										
HAL	3034	hgsc.bcm.edu	37	chr12	96384225	96384225	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cacatcttcccttctccaacTagcccaagagcaagatgaga	6	14	2	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr12:96384225T>C	ENST00000261208.3	-	10	1169	c.801A>G	c.(799-801)ctA>ctG	p.L267L	HAL_ENST00000551562.1_5'UTR|HAL_ENST00000541929.1_Silent_p.L59L|HAL_ENST00000538703.1_Silent_p.L267L	NM_002108.3	NP_002099.1	P42357	HUTH_HUMAN	histidine ammonia-lyase	267					biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	histidine ammonia-lyase activity (GO:0004397)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	34					L-Histidine(DB00117)	CTTCTCCAACTAGCCCAAGAG	0.547																																					p.L267L	NSCLC(169;943 2815 23563 30031)	Atlas-SNP	.											.	HAL	73	.	0			c.A801G						.						165	136	146					12																	96384225		2203	4300	6503	SO:0001819	synonymous_variant	3034	exon10			TCCAACTAGCCCA		CCDS9058.1, CCDS58264.1, CCDS58265.1	12q22-q24.1	1991-07-12				ENSG00000084110	4.3.1.3		4806	protein-coding gene	gene with protein product		609457		HIS			Standard	NM_002108		Approved		uc001tem.2	P42357	OTTHUMG00000170354	ENST00000261208.3:c.801A>G	chr12.hg19:g.96384225T>C		125.0	0.0		112.0	36.0	NM_001258334	B4DQC1|B4E0V8|F5GXF2|F5H1U5|Q4VB92|Q4VB93	Silent	SNP	ENST00000261208.3	hg19	CCDS9058.1																																																																																			.	.		0.547	HAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408644.1			C	96384225	T	C	96384225	2	2	181	1	0	0	0	0	0	0	0	1	6956	1509	53	2		2	HAL	12	96384225	Silent	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	25368027	96384225	37467670	96	27082										
HCFC2	29915	hgsc.bcm.edu	37	chr12	104474581	104474581	+	Frame_Shift_Del	DEL	T	T	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agtgccacttccacgaagccTtcatacagccagtgttatag							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr12:104474581delT	ENST00000229330.4	+	5	844	c.740delT	c.(739-741)cttfs	p.L247fs		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	247					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						CCACGAAGCCTTCATACAGCC	0.318																																					p.L247fs	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-INDEL	.											.	HCFC2	94	.	0			c.739delC						.						108	108	108					12																	104474581		2202	4300	6502	SO:0001589	frameshift_variant	29915	exon5			.	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.740delT	chr12.hg19:g.104474581delT	ENSP00000229330:p.Leu247fs	131.0	0.0		124.0	38.0	NM_013320	B2R8Q5|C0H5X3	Frame_Shift_Del	DEL	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.318	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		-	104474581	T	-	104474581	7	5	181	1	0	1	0	1	0	0	0	0	7002	1609	56	0	758	0	HCFC2	12	104474581	Frame_Shift_Del	DEL	T	TCGA-DD-AAD5-01A-11D-A40R-10	8090356	104474581	29377314	97	27083										
ANKRD13A	88455	hgsc.bcm.edu	37	chr12	110463610	110463611	+	Frame_Shift_Ins	INS	-	-	A													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agaacatctgaccgaggaggINSaaaaaaagagatataaaggt							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr12:110463610_110463611insA	ENST00000261739.4	+	8	1031_1032	c.865_866insA	c.(865-867)gaafs	p.E289fs		NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	289						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						GACCGAGGAGGAAAAAAAGAGA	0.411																																					p.E289fs		Atlas-INDEL	.											.	ANKRD13A	39	.	0			c.865_866insA						.																																			SO:0001589	frameshift_variant	88455	exon8			.	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"Ankyrin repeat domain containing"	21268	protein-coding gene	gene with protein product		615123	"ankyrin repeat domain 13"	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.872dupA	chr12.hg19:g.110463617_110463617dupA	ENSP00000261739:p.Glu289fs	193.0	0.0		194.0	64.0	NM_033121	O60736	Frame_Shift_Ins	INS	ENST00000261739.4	hg19	CCDS9140.1																																																																																			.	.		0.411	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		A	110463611	-	A	110463610	7	5	181	1	0	1	1	0	0	0	0	0	641	1175	41	0	895	0	ANKRD13A	12	110463610	Frame_Shift_Ins	INS	-	TCGA-DD-AAD5-01A-11D-A40R-10	5989029	110463610	23388285	98	27084										
KL	9365	hgsc.bcm.edu	37	chr13	33629230	33629230	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	atcgggtataccgcatggtcCctcatggatggtttcgagtg	13	9	1	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr13:33629230C>G	ENST00000380099.3	+	3	1385	c.1377C>G	c.(1375-1377)tcC>tcG	p.S459S	KL_ENST00000426690.2_Silent_p.S152S|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	459	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)	p.S459S(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		CCGCATGGTCCCTCATGGATG	0.517																																					p.S459S		Atlas-SNP	.											KL,trunk,malignant_melanoma,0,1	KL	106	.	1	Substitution - coding silent(1)	skin(1)	c.C1377G						.						178	142	154					13																	33629230		2203	4300	6503	SO:0001819	synonymous_variant	9365	exon3			ATGGTCCCTCATG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1377C>G	chr13.hg19:g.33629230C>G		162.0	0.0		147.0	31.0	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	hg19	CCDS9347.1																																																																																			.	.		0.517	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			G	33629230	C	G	33629230	2	3	181	1	0	0	0	0	0	0	0	1	8340	610	22	4		4	KL	13	33629230	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10		33629230	81540648	99	27085										
PCID2	55795	hgsc.bcm.edu	37	chr13	113835450	113835450	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	taataatcactcaccaatagCatttttactggaagcaaata	4	8	2	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr13:113835450C>T	ENST00000337344.4	-	10	856	c.780G>A	c.(778-780)atG>atA	p.M260I	PCID2_ENST00000375459.1_Missense_Mutation_p.M258I|PCID2_ENST00000375457.2_Missense_Mutation_p.M258I|PCID2_ENST00000493650.1_5'UTR|PCID2_ENST00000375479.2_Missense_Mutation_p.M260I|PCID2_ENST00000375477.1_Missense_Mutation_p.M260I|PCID2_ENST00000246505.5_Missense_Mutation_p.M314I	NM_001127202.2	NP_001120674.1	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	260					negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mRNA stability (GO:0043488)|spleen development (GO:0048536)					breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)	20	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)			TCACCAATAGCATTTTTACTG	0.388																																					p.M314I		Atlas-SNP	.											.	PCID2	30	.	0			c.G942A						.						139	122	128					13																	113835450		2203	4300	6503	SO:0001583	missense	55795	exon10			CAATAGCATTTTT	AK002167	CCDS9532.2, CCDS58301.1, CCDS58302.1	13q34	2006-03-31			ENSG00000126226	ENSG00000126226			25653	protein-coding gene	gene with protein product		613713				12477932	Standard	NM_001127203		Approved	FLJ11305	uc031qnm.1	Q5JVF3	OTTHUMG00000017385	ENST00000337344.4:c.780G>A	chr13.hg19:g.113835450C>T	ENSP00000337405:p.Met260Ile	116.0	0.0		122.0	47.0	NM_001258212	A6NK09|Q3ZCX1|Q5TC57|Q5TC58|Q9H7K1|Q9HBZ7|Q9NUK6|Q9NVY1|Q9NW44|Q9NWH3	Missense_Mutation	SNP	ENST00000337344.4	hg19	CCDS9532.2	.	.	.	.	.	.	.	.	.	.	C	17.24	3.338430	0.60963	.	.	ENSG00000126226	ENST00000337344;ENST00000375479;ENST00000375477;ENST00000246505;ENST00000375459;ENST00000375457;ENST00000375462;ENST00000246506;ENST00000351317	.	.	.	5.25	5.25	0.73442	PCI/PINT associated module (1);	0.000000	0.85682	D	0.000000	T	0.71178	0.3309	L	0.51853	1.615	0.80722	D	1	D;D	0.64830	0.963;0.994	P;P	0.60173	0.827;0.87	T	0.65602	-0.6128	9	0.19590	T	0.45	-45.057	18.867	0.92296	0.0:1.0:0.0:0.0	.	314;260	Q5JVF3-4;Q5JVF3	.;PCID2_HUMAN	I	260;260;260;314;258;258;237;260;237	.	ENSP00000246505:M314I	M	-	3	0	PCID2	112883451	1.000000	0.71417	1.000000	0.80357	0.023000	0.10783	7.662000	0.83803	2.445000	0.82738	0.563000	0.77884	ATG	.	.		0.388	PCID2-002	KNOWN	alternative_3_UTR|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045897.1	NM_018386		T	113835450	C	T	113835450	3	4	181	1	0	0	0	0	1	0	0	0	11588	710	25	3	439	3	PCID2	13	113835450	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	80206220	113835450	1334428	100	27086										
LAMP1	3916	hgsc.bcm.edu	37	chr13	113975881	113975881	+	Missense_Mutation	SNP	T	T	G													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gtgtgttgcagaccctgcctTtaaagctgccaacggctccc							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr13:113975881T>G	ENST00000332556.4	+	8	1147	c.953T>G	c.(952-954)tTt>tGt	p.F318C	LAMP1_ENST00000397181.3_Missense_Mutation_p.F265C	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	318	Second lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			GACCCTGCCTTTAAAGCTGCC	0.622																																					p.F318C		Atlas-SNP	.											.	LAMP1	41	.	0			c.T953G						.						75	83	81					13																	113975881		1979	4152	6131	SO:0001583	missense	3916	exon8			CTGCCTTTAAAGC	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.953T>G	chr13.hg19:g.113975881T>G	ENSP00000333298:p.Phe318Cys	127.0	0.0		161.0	16.0	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Missense_Mutation	SNP	ENST00000332556.4	hg19	CCDS41909.1	.	.	.	.	.	.	.	.	.	.	T	19.90	3.912682	0.72983	.	.	ENSG00000185896	ENST00000332556;ENST00000397181	T;T	0.39406	1.08;1.08	5.27	5.27	0.74061	.	0.052087	0.85682	D	0.000000	T	0.70133	0.3189	M	0.89601	3.045	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.77004	0.983;0.989	T	0.77403	-0.2601	10	0.72032	D	0.01	-36.6196	14.376	0.66879	0.0:0.0:0.0:1.0	.	265;318	B4DWL3;P11279	.;LAMP1_HUMAN	C	318;265	ENSP00000333298:F318C;ENSP00000415354:F265C	ENSP00000333298:F318C	F	+	2	0	LAMP1	113023882	0.995000	0.38212	0.025000	0.17156	0.003000	0.03518	2.875000	0.48491	2.000000	0.58554	0.448000	0.29417	TTT	.	.		0.622	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			G	113975881	T	G	113975881	3	3	181	1	0	0	0	0	1	0	0	0	8626	1841	64	5	983	5	LAMP1	13	113975881	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	140431	113975881	1193997	101	27087	132	2								
LAMP1	3916	hgsc.bcm.edu	37	chr13	113975888	113975888	+	Frame_Shift_Del	DEL	T	T	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gcagaccctgcctttaaagcTgccaacggctccctgcgagc							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr13:113975888delT	ENST00000332556.4	+	8	1154	c.960delT	c.(958-960)gctfs	p.A321fs	LAMP1_ENST00000397181.3_Frame_Shift_Del_p.A268fs	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	321	Second lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			CCTTTAAAGCTGCCAACGGCT	0.612																																					p.A320fs		Atlas-INDEL	.											.	LAMP1	41	.	0			c.959delC						.						73	82	79					13																	113975888		1981	4159	6140	SO:0001589	frameshift_variant	3916	exon8			.	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.960delT	chr13.hg19:g.113975888delT	ENSP00000333298:p.Ala321fs	120.0	0.0		158.0	15.0	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Frame_Shift_Del	DEL	ENST00000332556.4	hg19	CCDS41909.1																																																																																			.	.		0.612	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			-	113975888	T	-	113975888	7	5	181	1	0	1	0	1	0	0	0	0	8626	1567	55	0	990	0	LAMP1	13	113975888	Frame_Shift_Del	DEL	T	TCGA-DD-AAD5-01A-11D-A40R-10	7	113975888	1193990	102	27088	132	2								
MDGA2	161357	hgsc.bcm.edu	37	chr14	48143777	48143777	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgtcagcagccacacgagacCgtacagtaaatccatcttca	7	13	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr14:48143777C>A	ENST00000399232.2	-	1	380	c.16G>T	c.(16-18)Ggt>Tgt	p.G6C	MDGA2_ENST00000439988.3_Missense_Mutation_p.G75C	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	6					pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						CACACGAGACCGTACAGTAAA	0.587																																					p.G75C		Atlas-SNP	.											.	MDGA2	470	.	0			c.G223T						.						204	187	192					14																	48143777		692	1591	2283	SO:0001583	missense	161357	exon1			CGAGACCGTACAG	AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.16G>T	chr14.hg19:g.48143777C>A	ENSP00000382178:p.Gly6Cys	159.0	0.0		102.0	26.0	NM_001113498	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	hg19		.	.	.	.	.	.	.	.	.	.	C	13.67	2.305657	0.40795	.	.	ENSG00000139915	ENST00000439988;ENST00000399232	T;T	0.64438	0.13;-0.1	5.07	4.17	0.49024	.	.	.	.	.	T	0.39036	0.1063	N	0.08118	0	0.80722	D	1	B	0.18461	0.028	B	0.16289	0.015	T	0.22277	-1.0221	8	.	.	.	.	12.2041	0.54342	0.0:0.9109:0.0:0.0891	.	6	Q7Z553	MDGA2_HUMAN	C	6;75	ENSP00000400011:G6C;ENSP00000382178:G75C	.	G	-	1	0	MDGA2	47213527	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.834000	0.39171	2.530000	0.85305	0.650000	0.86243	GGT	.	.		0.587	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		A	48143777	C	A	48143777	3	1	181	1	0	0	0	0	1	0	0	0	9416	652	23	1	2922	1	MDGA2	14	48143777	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10		48143777	59205763	103	27089										
ATL1	51062	hgsc.bcm.edu	37	chr14	51079994	51079994	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tagagtctgatatttcttgtTcgagactggagtttcccata	9	7	2	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr14:51079994T>C	ENST00000358385.6	+	7	889	c.648T>C	c.(646-648)gtT>gtC	p.V216V	ATL1_ENST00000441560.2_Silent_p.V216V|ATL1_ENST00000354525.4_Silent_p.V216V|ATL1_ENST00000357032.3_Silent_p.V216V	NM_015915.4	NP_056999.2	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	216	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						TATTTCTTGTTCGAGACTGGA	0.368																																					p.V216V		Atlas-SNP	.											.	ATL1	46	.	0			c.T648C						.						101	102	102					14																	51079994		2203	4300	6503	SO:0001819	synonymous_variant	51062	exon7			TCTTGTTCGAGAC	AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513			11231	protein-coding gene	gene with protein product	"atlastin"	606439	"spastic paraplegia 3A (autosomal dominant)"	SPG3, SPG3A		8252041, 7825576	Standard	NM_015915		Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000358385.6:c.648T>C	chr14.hg19:g.51079994T>C		112.0	0.0		109.0	16.0	NM_015915	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Silent	SNP	ENST00000358385.6	hg19	CCDS9700.1																																																																																			.	.		0.368	ATL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276884.2			C	51079994	T	C	51079994	2	2	181	1	0	0	0	0	0	0	0	1	1106	1770	62	2		2	ATL1	14	51079994	Silent	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	2936217	51079994	56269546	104	27090										
PCNX	22990	hgsc.bcm.edu	37	chr14	71479802	71479802	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ccctgacttggcagctacttAcggcccaacagaagaagctg	10	13	0	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr14:71479802A>G	ENST00000304743.2	+	11	3325	c.2879A>G	c.(2878-2880)tAc>tGc	p.Y960C	PCNX_ENST00000439984.3_Missense_Mutation_p.Y849C|PCNX_ENST00000238570.5_Missense_Mutation_p.Y960C	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	960						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GCAGCTACTTACGGCCCAACA	0.443																																					p.Y960C		Atlas-SNP	.											.	PCNX	198	.	0			c.A2879G						.						136	132	133					14																	71479802		2203	4300	6503	SO:0001583	missense	22990	exon11			CTACTTACGGCCC	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.2879A>G	chr14.hg19:g.71479802A>G	ENSP00000304192:p.Tyr960Cys	108.0	0.0		70.0	29.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.70|14.70	2.614360|2.614360	0.46631|0.46631	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000554691|ENST00000304743;ENST00000238570;ENST00000439984	.|T;T;T	.|0.21734	.|1.99;1.99;1.99	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	.|0.632079	.|0.16087	.|N	.|0.230254	T|T	0.10551|0.10551	0.0258|0.0258	N|N	0.08118|0.08118	0|0	0.20403|0.20403	N|N	0.999901|0.999901	.|P;B	.|0.45078	.|0.85;0.001	.|B;B	.|0.37780	.|0.258;0.001	T|T	0.10660|0.10660	-1.0620|-1.0620	5|10	.|0.37606	.|T	.|0.19	.|.	10.2511|10.2511	0.43370|0.43370	0.9155:0.0:0.0844:0.0|0.9155:0.0:0.0844:0.0	.|.	.|849;960	.|B2RTR6;Q96RV3	.|.;PCX1_HUMAN	A|C	19|960;960;849	.|ENSP00000304192:Y960C;ENSP00000238570:Y960C;ENSP00000396617:Y849C	.|ENSP00000238570:Y960C	T|Y	+|+	1|2	0|0	PCNX|PCNX	70549555|70549555	0.999000|0.999000	0.42202|0.42202	0.993000|0.993000	0.49108|0.49108	0.738000|0.738000	0.42128|0.42128	4.640000|4.640000	0.61368|0.61368	2.122000|2.122000	0.65172|0.65172	0.455000|0.455000	0.32223|0.32223	ACG|TAC	.	.		0.443	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		G	71479802	A	G	71479802	3	3	181	1	0	0	0	0	1	0	0	0	11600	391	14	2	2921	2	PCNX	14	71479802	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	20399808	71479802	35869738	105	27091										
PCNX	22990	hgsc.bcm.edu	37	chr14	71479827	71479827	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ccaacagaagaagctgcccaAaaggttaaacactattatcg	7	10	0	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr14:71479827A>G	ENST00000304743.2	+	11	3350	c.2904A>G	c.(2902-2904)caA>caG	p.Q968Q	PCNX_ENST00000439984.3_Silent_p.Q857Q|PCNX_ENST00000238570.5_Silent_p.Q968Q	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	968						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		AAGCTGCCCAAAAGGTTAAAC	0.438																																					p.Q968Q		Atlas-SNP	.											.	PCNX	198	.	0			c.A2904G						.						143	140	141					14																	71479827		2203	4300	6503	SO:0001819	synonymous_variant	22990	exon11			TGCCCAAAAGGTT	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.2904A>G	chr14.hg19:g.71479827A>G		100.0	0.0		71.0	30.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	hg19	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	A	7.884	0.730929	0.15507	.	.	ENSG00000100731	ENST00000554691	.	.	.	5.35	1.64	0.23874	.	.	.	.	.	T	0.53449	0.1797	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42999	-0.9418	4	.	.	.	.	5.9775	0.19389	0.7097:0.1385:0.1518:0.0	.	.	.	.	R	27	.	.	K	+	2	0	PCNX	70549580	0.978000	0.34361	0.996000	0.52242	0.758000	0.43043	0.230000	0.17852	0.409000	0.25649	0.455000	0.32223	AAA	.	.		0.438	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		G	71479827	A	G	71479827	2	3	181	1	0	0	0	0	0	0	0	1	11600	11	1	2		2	PCNX	14	71479827	Silent	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	25	71479827	35869713	106	27092										
C14orf166B	145497	hgsc.bcm.edu	37	chr14	77297607	77297607	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ctggaggcctgcaagctgatGggtgtagtgcctgtctccta	14	10	1	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr14:77297607G>A	ENST00000393774.3	+	3	403	c.279G>A	c.(277-279)atG>atA	p.M93I	C14orf166B_ENST00000460005.1_3'UTR|C14orf166B_ENST00000450042.2_Missense_Mutation_p.M76I	NM_194287.2	NP_919263.2														breast(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(1)	18			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		GCAAGCTGATGGGTGTAGTGC	0.517																																					p.M93I	Ovarian(165;1056 1958 32571 36789 48728)	Atlas-SNP	.											.	C14orf166B	52	.	0			c.G279A						.						132	110	117					14																	77297607		2203	4300	6503	SO:0001583	missense	145497	exon3			GCTGATGGGTGTA																												ENST00000393774.3:c.279G>A	chr14.hg19:g.77297607G>A	ENSP00000377369:p.Met93Ile	144.0	0.0		99.0	47.0	NM_194287		Missense_Mutation	SNP	ENST00000393774.3	hg19	CCDS9853.2	.	.	.	.	.	.	.	.	.	.	G	10.92	1.487686	0.26686	.	.	ENSG00000100565	ENST00000393774;ENST00000450042	T;T	0.52295	0.67;2.65	5.66	3.45	0.39498	.	0.649523	0.16225	N	0.223879	T	0.18800	0.0451	N	0.01576	-0.805	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.06409	-1.0828	10	0.15499	T	0.54	.	9.7627	0.40541	0.0836:0.0:0.7741:0.1423	.	93	Q0VAA2	CN16B_HUMAN	I	93;76	ENSP00000377369:M93I;ENSP00000396260:M76I	ENSP00000216450:M93I	M	+	3	0	C14orf166B	76367360	1.000000	0.71417	0.848000	0.33437	0.421000	0.31385	1.796000	0.38794	1.361000	0.45981	0.555000	0.69702	ATG	.	.		0.517	C14orf166B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316592.1			A	77297607	G	A	77297607	3	1	181	1	0	0	0	0	1	0	0	0	1759	1348	47	3	289	3	C14orf166B	14	77297607	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	5817780	77297607	30051933	107	27093										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105417141	105417141	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tggccagcctggacctccagGtcagcagaagggggctgtat	15	11	1	1	rs372521162	byFrequency	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr14:105417141G>T	ENST00000333244.5	-	7	4766	c.4647C>A	c.(4645-4647)gaC>gaA	p.D1549E	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1549						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGACCTCCAGGTCAGCAGAAG	0.647																																					p.D1549E		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4647A						.						104	102	103					14																	105417141		1909	4082	5991	SO:0001583	missense	113146	exon7			CTCCAGGTCAGCA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4647C>A	chr14.hg19:g.105417141G>T	ENSP00000353114:p.Asp1549Glu	217.0	0.0		175.0	7.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	13.60	2.286532	0.40494	.	.	ENSG00000185567	ENST00000333244	T	0.00856	5.61	4.16	-4.72	0.03269	.	.	.	.	.	T	0.00754	0.0025	L	0.45137	1.4	0.09310	N	1	B	0.18166	0.026	B	0.18871	0.023	T	0.48670	-0.9015	9	0.14252	T	0.57	-16.612	0.8937	0.01259	0.282:0.2045:0.3261:0.1874	.	1549	Q8IVF2	AHNK2_HUMAN	E	1549	ENSP00000353114:D1549E	ENSP00000353114:D1549E	D	-	3	2	AHNAK2	104488186	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-2.723000	0.00810	-0.739000	0.04809	-0.333000	0.08304	GAC	.	.		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105417141	G	T	105417141	3	4	181	1	0	0	0	0	1	0	0	0	415	1252	44	3	12744	3	AHNAK2	14	105417141	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	28119534	105417141	1932399	108	27094										
NIPA1	123606	hgsc.bcm.edu	37	chr15	23086388	23086388	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gccgccgccgccgccgccgcCgctgccgcagctgcagtccc	13	23	0	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr15:23086388C>A	ENST00000337435.4	-	1	48	c.24G>T	c.(22-24)gcG>gcT	p.A8A	NIPA1_ENST00000561183.1_Intron|NIPA1_ENST00000437912.2_Intron|NIPA1_ENST00000538684.1_5'Flank	NM_001142275.1|NM_144599.4	NP_001135747.1|NP_653200.2	Q7RTP0	NIPA1_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 1	8					cell death (GO:0008219)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)		ccgccgccgccgctgccgcAG	0.836																																					p.A8A		Atlas-SNP	.											NIPA1,NS,carcinoma,0,1	NIPA1	26	.	0			c.G24T						.						1	1	1					15																	23086388		42	63	105	SO:0001819	synonymous_variant	123606	exon1			CGCCGCCGCTGCC	BK001020	CCDS73691.1, CCDS73692.1	15q11.2	2006-10-06			ENSG00000170113	ENSG00000170113			17043	protein-coding gene	gene with protein product		608145	"spastic paraplegia 6 (autosomal dominant)"	SPG6		14508710	Standard	NM_144599		Approved	MGC35570	uc001yvc.3	Q7RTP0	OTTHUMG00000129099	ENST00000337435.4:c.24G>T	chr15.hg19:g.23086388C>A		130.0	0.0		42.0	2.0	NM_144599	B2RA76|Q5HYA9|Q7KZB0|Q86XW4	Silent	SNP	ENST00000337435.4	hg19	CCDS10011.1																																																																																			.	.		0.836	NIPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251135.2	NM_144599		A	23086388	C	A	23086388	2	1	181	1	0	0	0	0	0	0	0	1	10431	639	23	1		1	NIPA1	15	23086388	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10		23086388	79445004	109	27095										
TMEM62	80021	hgsc.bcm.edu	37	chr15	43446911	43446911	+	Frame_Shift_Del	DEL	T	T	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ctccattacttctgtcacagTtaagattgatggagttcatt							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr15:43446911delT	ENST00000260403.2	+	9	1343	c.1064delT	c.(1063-1065)gttfs	p.V355fs		NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	355						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		TCTGTCACAGTTAAGATTGAT	0.398																																					p.V355fs		Atlas-INDEL	.											.	TMEM62	47	.	0			c.1063delG						.						174	149	158					15																	43446911		2203	4299	6502	SO:0001589	frameshift_variant	80021	exon9			.	BC009981	CCDS32210.1	15q15.2	2014-09-11			ENSG00000137842	ENSG00000137842			26269	protein-coding gene	gene with protein product							Standard	NM_024956		Approved	FLJ23375	uc001zqr.3	Q0P6H9	OTTHUMG00000176485	ENST00000260403.2:c.1064delT	chr15.hg19:g.43446911delT	ENSP00000260403:p.Val355fs	68.0	0.0		73.0	24.0	NM_024956	Q6I9Y5|Q9H5J6	Frame_Shift_Del	DEL	ENST00000260403.2	hg19	CCDS32210.1																																																																																			.	.		0.398	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956		-	43446911	T	-	43446911	7	5	181	1	0	1	0	1	0	0	0	0	16204	1725	60	0	1098	0	TMEM62	15	43446911	Frame_Shift_Del	DEL	T	TCGA-DD-AAD5-01A-11D-A40R-10	20360523	43446911	59084481	110	27096										
C2CD4A	145741	hgsc.bcm.edu	37	chr15	62360051	62360051	+	Frame_Shift_Del	DEL	G	G	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gatggacgagggcgccggccGcacagactgggacccgcgct					rs376974409		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr15:62360051delG	ENST00000355522.5	+	2	380	c.239delG	c.(238-240)cgcfs	p.R80fs		NM_207322.2	NP_997205.2	Q8NCU7	C2C4A_HUMAN	C2 calcium-dependent domain containing 4A	80						nucleus (GO:0005634)											GGCGCCGGCCGCACAGACTGG	0.711																																					p.R80fs		Atlas-INDEL	.											.	C2CD4A	3	.	0			c.238delC						.						10	12	12					15																	62360051		2179	4278	6457	SO:0001589	frameshift_variant	145741	exon2			.	AF504646	CCDS32258.1	15q22.2	2009-09-28	2009-09-28	2009-09-28		ENSG00000198535			33627	protein-coding gene	gene with protein product	"nuclear localized factor 1"	610343	"family with sequence similarity 148, member A"	FAM148A			Standard	NM_207322		Approved	NLF1	uc002ahf.4	Q8NCU7		ENST00000355522.5:c.239delG	chr15.hg19:g.62360051delG	ENSP00000347712:p.Arg80fs	69.0	0.0		54.0	34.0	NM_207322		Frame_Shift_Del	DEL	ENST00000355522.5	hg19	CCDS32258.1																																																																																			.	.		0.711	C2CD4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416008.2	NM_207322		-	62360051	G	-	62360051	7	5	181	1	0	1	0	1	0	0	0	0	2157	1087	38	0	241	0	C2CD4A	15	62360051	Frame_Shift_Del	DEL	G	TCGA-DD-AAD5-01A-11D-A40R-10	18913140	62360051	40171341	111	27097										
HS3ST6	64711	hgsc.bcm.edu	37	chr16	1961878	1961878	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gctgaccagacgctccccgcTgacgaacaggaagtgggaca	13	13	0	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr16:1961878T>C	ENST00000293937.3	-	2	741	c.742A>G	c.(742-744)Agc>Ggc	p.S248G	HS3ST6_ENST00000454677.2_Missense_Mutation_p.S265G|HS3ST6_ENST00000443547.1_Missense_Mutation_p.S217G			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	248					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			endometrium(2)|lung(2)	4						CGCTCCCCGCTGACGAACAGG	0.667																																					p.S217G		Atlas-SNP	.											.	HS3ST6	26	.	0			c.A649G						.						43	53	50					16																	1961878		2191	4295	6486	SO:0001583	missense	64711	exon2			CCCCGCTGACGAA			16p13.3	2008-10-30	2003-06-11	2003-06-13	ENSG00000162040	ENSG00000162040		"Sulfotransferases, membrane-bound"	14178	protein-coding gene	gene with protein product			"heparan sulfate (glucosamine) 3-O-sulfotransferase 5"	HS3ST5		11157797	Standard	NM_001009606		Approved		uc002cnf.3	Q96QI5	OTTHUMG00000047860	ENST00000293937.3:c.742A>G	chr16.hg19:g.1961878T>C	ENSP00000293937:p.Ser248Gly	115.0	0.0		105.0	44.0	NM_001009606	Q96RX7	Missense_Mutation	SNP	ENST00000293937.3	hg19		.	.	.	.	.	.	.	.	.	.	T	18.16	3.563213	0.65538	.	.	ENSG00000162040	ENST00000293937;ENST00000443547;ENST00000454677	D;D	0.83335	-1.71;-1.71	4.84	4.84	0.62591	Sulfotransferase domain (1);	0.039671	0.85682	D	0.000000	D	0.92606	0.7651	M	0.93375	3.41	0.80722	D	1	D	0.69078	0.997	D	0.69654	0.965	D	0.94242	0.7486	10	0.72032	D	0.01	.	13.641	0.62251	0.0:0.0:0.0:1.0	.	248	Q96QI5	HS3S6_HUMAN	G	248;217;287	ENSP00000293937:S248G;ENSP00000390354:S217G	ENSP00000293937:S248G	S	-	1	0	HS3ST6	1901879	1.000000	0.71417	0.990000	0.47175	0.325000	0.28411	7.831000	0.86748	1.826000	0.53198	0.414000	0.27820	AGC	.	.		0.667	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606		C	1961878	T	C	1961878	3	2	181	1	0	0	0	0	1	0	0	0	7378	1580	55	2	290	2	HS3ST6	16	1961878	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10		1961878	88392875	112	27098										
LAT	27040	hgsc.bcm.edu	37	chr16	29001280	29001280	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgagttcccaggaggcagagGaagtggaggaagagggggct	20	5	0	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr16:29001280G>T	ENST00000360872.5	+	10	814	c.736G>T	c.(736-738)Gaa>Taa	p.E246*	RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000354453.4_Nonsense_Mutation_p.E236*|LAT_ENST00000395461.3_Nonsense_Mutation_p.E253*|LAT_ENST00000566177.1_Nonsense_Mutation_p.E245*|LAT_ENST00000454369.2_Nonsense_Mutation_p.E216*|RP11-264B17.5_ENST00000561471.1_RNA|LAT_ENST00000395456.2_Nonsense_Mutation_p.E217*|LAT_ENST00000564277.1_Nonsense_Mutation_p.E216*			O43561	LAT_HUMAN	linker for activation of T cells	246					blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|gene expression (GO:0010467)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lymphocyte homeostasis (GO:0002260)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|regulation of T cell activation (GO:0050863)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(2)|lung(3)|urinary_tract(1)	6		Hepatocellular(780;0.244)				GGAGGCAGAGGAAGTGGAGGA	0.637																																					p.E253X		Atlas-SNP	.											.	LAT	22	.	0			c.G757T						.						79	74	76					16																	29001280		2197	4300	6497	SO:0001587	stop_gained	27040	exon12			GCAGAGGAAGTGG	AF036905	CCDS10647.1, CCDS32425.1, CCDS45455.1, CCDS53999.1	16q13	2011-11-01			ENSG00000213658	ENSG00000213658			18874	protein-coding gene	gene with protein product	"linker for activation of T cells, transmembrane adaptor"	602354				9489702	Standard	NM_014387		Approved	LAT1	uc010vdj.2	O43561	OTTHUMG00000131761	ENST00000360872.5:c.736G>T	chr16.hg19:g.29001280G>T	ENSP00000354119:p.Glu246*	78.0	0.0		65.0	14.0	NM_001014989	B7WPI0|C7C5T6|G5E9K3|O43919	Nonsense_Mutation	SNP	ENST00000360872.5	hg19	CCDS10647.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333166	0.81801	.	.	ENSG00000213658	ENST00000395461;ENST00000395456;ENST00000454369;ENST00000360872;ENST00000354453	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.51482	D	0.999926	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	0.5174	14.2681	0.66135	0.0:0.0:1.0:0.0	.	.	.	.	X	253;217;216;246;236	.	ENSP00000346441:E236X	E	+	1	0	LAT	28908781	0.961000	0.32948	0.335000	0.25508	0.402000	0.30811	1.889000	0.39718	2.515000	0.84797	0.462000	0.41574	GAA	.	.		0.637	LAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254688.2			T	29001280	G	T	29001280	4	4	181	1	0	0	0	0	0	1	0	0	8653	1175	41	3	886	3	LAT	16	29001280	Nonsense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	27039402	29001280	61353473	113	27099										
TAOK2	9344	hgsc.bcm.edu	37	chr16	29998697	29998697	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cgtcctgggcctgagctggcGccgaggcctcatgggtgttc	16	13	1	1	rs144609126		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr16:29998697G>T	ENST00000308893.4	+	16	4147	c.3104G>T	c.(3103-3105)cGc>cTc	p.R1035L	TAOK2_ENST00000543033.1_Missense_Mutation_p.R922L|TAOK2_ENST00000416441.2_Missense_Mutation_p.R862L|TAOK2_ENST00000279394.3_Intron	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	1035	Leu-rich.				actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						CTGAGCTGGCGCCGAGGCCTC	0.657																																					p.R1035L		Atlas-SNP	.											.	TAOK2	142	.	0			c.G3104T						.						20	21	20					16																	29998697		2190	4285	6475	SO:0001583	missense	9344	exon16			GCTGGCGCCGAGG	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.3104G>T	chr16.hg19:g.29998697G>T	ENSP00000310094:p.Arg1035Leu	75.0	0.0		71.0	24.0	NM_016151	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Missense_Mutation	SNP	ENST00000308893.4	hg19	CCDS10663.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.068437	0.36470	.	.	ENSG00000149930	ENST00000308893;ENST00000543033	T;T	0.72505	-0.62;-0.66	4.8	3.85	0.44370	.	0.284001	0.29956	N	0.010777	T	0.50120	0.1597	N	0.14661	0.345	0.30449	N	0.775408	B;B;B	0.23185	0.02;0.081;0.02	B;B;B	0.23275	0.008;0.045;0.008	T	0.46748	-0.9169	9	.	.	.	.	10.1636	0.42866	0.0943:0.0:0.9057:0.0	.	1226;862;1035	Q86V37;Q9UL54-3;Q9UL54	.;.;TAOK2_HUMAN	L	1035;922	ENSP00000310094:R1035L;ENSP00000440336:R922L	.	R	+	2	0	TAOK2	29906198	0.988000	0.35896	1.000000	0.80357	0.996000	0.88848	2.946000	0.49050	1.260000	0.44134	0.563000	0.77884	CGC	.	G|1.000;A|0.000		0.657	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151		T	29998697	G	T	29998697	3	4	181	1	0	0	0	0	1	0	0	0	15563	1087	38	1	3162	1	TAOK2	16	29998697	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	997417	29998697	60356056	114	27100										
BRD7	29117	hgsc.bcm.edu	37	chr16	50357578	50357578	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	atctgccatgacatacggatAatcttggcacgtggccaaaa	9	10	2	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr16:50357578A>T	ENST00000394688.3	-	12	1522	c.1363T>A	c.(1363-1365)Tat>Aat	p.Y455N	BRD7_ENST00000394689.2_Missense_Mutation_p.Y455N			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	455					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				ACATACGGATAATCTTGGCAC	0.443																																					p.Y455N		Atlas-SNP	.											.	BRD7	61	.	0			c.T1363A						.						106	90	95					16																	50357578		2198	4300	6498	SO:0001583	missense	29117	exon12			ACGGATAATCTTG	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"bromodomain-containing 7"			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.1363T>A	chr16.hg19:g.50357578A>T	ENSP00000378180:p.Tyr455Asn	92.0	0.0		80.0	25.0	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	hg19	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	A	19.46	3.831090	0.71258	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.51574	0.7;0.7	5.53	5.53	0.82687	.	0.187371	0.48767	D	0.000165	T	0.64843	0.2635	M	0.73217	2.22	0.58432	D	0.999995	D;D	0.65815	0.995;0.994	D;D	0.68621	0.959;0.931	T	0.68352	-0.5431	10	0.72032	D	0.01	-35.8448	10.828	0.46645	0.859:0.0:0.0:0.141	.	455;455	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	N	455	ENSP00000378180:Y455N;ENSP00000378181:Y455N	ENSP00000378180:Y455N	Y	-	1	0	BRD7	48915079	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.637000	0.61346	2.096000	0.63516	0.533000	0.62120	TAT	.	.		0.443	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		T	50357578	A	T	50357578	3	4	181	1	0	0	0	0	1	0	0	0	1507	362	13	4	619	4	BRD7	16	50357578	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	20358881	50357578	39997175	115	27101										
CHD9	80205	hgsc.bcm.edu	37	chr16	53307551	53307551	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ttaacaggcctatcagctccTgtacccaggggtcgaaaagg	11	11	1	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr16:53307551T>A	ENST00000398510.3	+	22	4818	c.4731T>A	c.(4729-4731)ccT>ccA	p.P1577P	CHD9_ENST00000447540.1_Silent_p.P1577P|CHD9_ENST00000564845.1_Silent_p.P1577P|CHD9_ENST00000566029.1_Silent_p.P1577P			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1577					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TATCAGCTCCTGTACCCAGGG	0.348																																					p.P1577P		Atlas-SNP	.											.	CHD9	203	.	0			c.T4731A						.						30	28	28					16																	53307551		1793	4061	5854	SO:0001819	synonymous_variant	80205	exon23			AGCTCCTGTACCC	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.4731T>A	chr16.hg19:g.53307551T>A		405.0	0.0		362.0	120.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	hg19																																																																																				.	.		0.348	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		A	53307551	T	A	53307551	2	1	181	1	0	0	0	0	0	0	0	1	3334	1567	55	4		4	CHD9	16	53307551	Silent	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	2949973	53307551	37047202	116	27102										
TCF25	22980	hgsc.bcm.edu	37	chr16	89977033	89977033	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gccatggaaacaccattgctCtcttcttccggtcactgttg	8	13	3	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr16:89977033C>T	ENST00000263346.8	+	17	1890	c.1834C>T	c.(1834-1836)Ctc>Ttc	p.L612F	TCF25_ENST00000263347.7_Missense_Mutation_p.S416F|MC1R_ENST00000555427.1_5'Flank|RP11-566K11.7_ENST00000570217.1_RNA	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	612					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		CACCATTGCTCTCTTCTTCCG	0.537											OREG0024057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L612F		Atlas-SNP	.											.	TCF25	61	.	0			c.C1834T						.						219	178	192					16																	89977033		2198	4300	6498	SO:0001583	missense	22980	exon17			ATTGCTCTCTTCT	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.1834C>T	chr16.hg19:g.89977033C>T	ENSP00000263346:p.Leu612Phe	64.0	0.0	1271	51.0	12.0	NM_014972	Q2MK75|Q9UPV3	Missense_Mutation	SNP	ENST00000263346.8	hg19	CCDS10987.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.186|9.186	1.024790|1.024790	0.19433|0.19433	.|.	.|.	ENSG00000141002|ENSG00000141002	ENST00000263346|ENST00000263347	.|.	.|.	.|.	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	0.203280|.	0.41396|.	D|.	0.000889|.	T|T	0.40694|0.40694	0.1127|0.1127	L|L	0.47016|0.47016	1.485|1.485	0.28276|0.28276	N|N	0.924218|0.924218	B|B	0.23937|0.06786	0.094|0.001	B|B	0.23716|0.04013	0.048|0.001	T|T	0.15636|0.15636	-1.0430|-1.0430	9|7	0.48119|.	T|.	0.1|.	.|.	11.3502|11.3502	0.49583|0.49583	0.0:0.9182:0.0:0.0818|0.0:0.9182:0.0:0.0818	.|.	612|416	Q9BQ70|Q9H384	TCF25_HUMAN|.	F|F	612|416	.|.	ENSP00000263346:L612F|.	L|S	+|+	1|2	0|0	TCF25|TCF25	88504534|88504534	1.000000|1.000000	0.71417|0.71417	0.944000|0.944000	0.38274|0.38274	0.026000|0.026000	0.11368|0.11368	4.768000|4.768000	0.62293|0.62293	2.706000|2.706000	0.92434|0.92434	0.655000|0.655000	0.94253|0.94253	CTC|TCT	.	.		0.537	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972		T	89977033	C	T	89977033	3	4	181	1	0	0	0	0	1	0	0	0	15708	913	32	3	1900	3	TCF25	16	89977033	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	36669482	89977033	377720	117	27103										
TP53	7157	hgsc.bcm.edu	37	chr17	7574006	7574006	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ggcctcattcagctctcggaAcatctcgaagcgctcacgcc	9	16	5	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr17:7574006A>C	ENST00000269305.4	-	10	1210	c.1021T>G	c.(1021-1023)Ttc>Gtc	p.F341V	TP53_ENST00000455263.2_3'UTR|TP53_ENST00000420246.2_3'UTR|TP53_ENST00000445888.2_Missense_Mutation_p.F341V|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	341	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		F -> C (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.I332fs*5(1)|p.?(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGCTCTCGGAACATCTCGAAG	0.547		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.F341V	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000269305,colon,carcinoma,0,2	TP53	33396	.	10	Whole gene deletion(8)|Unknown(1)|Deletion - Frameshift(1)	bone(4)|haematopoietic_and_lymphoid_tissue(2)|central_nervous_system(2)|large_intestine(1)|stomach(1)	c.T1021G						.						62	48	53					17																	7574006		2203	4300	6503	SO:0001583	missense	7157	exon10	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CTCGGAACATCTC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.1021T>G	chr17.hg19:g.7574006A>C	ENSP00000269305:p.Phe341Val	147.0	0.0		109.0	74.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	17.36	3.370394	0.61624	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	D;D	0.93811	-3.29;-3.29	5.43	1.57	0.23409	p53, tetramerisation domain (3);	0.151595	0.47455	D	0.000237	D	0.92100	0.7496	M	0.73598	2.24	0.41275	D	0.986879	B	0.24043	0.096	B	0.37833	0.259	D	0.87444	0.2397	10	0.72032	D	0.01	-19.1541	4.0815	0.09929	0.5724:0.0:0.2749:0.1527	.	341	P04637	P53_HUMAN	V	341;341;330	ENSP00000269305:F341V;ENSP00000391478:F341V	ENSP00000269305:F341V	F	-	1	0	TP53	7514731	0.997000	0.39634	0.991000	0.47740	0.799000	0.45148	0.604000	0.24164	0.381000	0.24851	0.459000	0.35465	TTC	.	.		0.547	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7574006	A	C	7574006	3	2	181	1	0	0	0	0	1	0	0	0	16396	43	2	5	168	5	TP53	17	7574006	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10		7574006	73621204	118	27104										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18022452	18022473	+	Frame_Shift_Del	DEL	GCCGCCGTGGCTACGGCCGCCT	GCCGCCGTGGCTACGGCCGCCT	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	catggtgatccgcttcccagGccgccgtggctacggccgcc					rs536413670		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	GCCGCCGTGGCTACGGCCGCCT	GCCGCCGTGGCTACGGCCGCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr17:18022452_18022473delGCCGCCGTGGCTACGGCCGCCT	ENST00000205890.5	+	2	676_697	c.338_359delGCCGCCGTGGCTACGGCCGCCT	c.(337-360)ggccgccgtggctacggccgcctgfs	p.GRRGYGRL113fs		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	113					inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CGCTTCCCAGGCCGCCGTGGCTACGGCCGCCTGCGGCCGCGC	0.622																																					p.113_120del		Atlas-INDEL	.											.	MYO15A	268	.	0			c.337_358del						.																																			SO:0001589	frameshift_variant	51168	exon2			.	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.338_359delGCCGCCGTGGCTACGGCCGCCT	chr17.hg19:g.18022452_18022473delGCCGCCGTGGCTACGGCCGCCT	ENSP00000205890:p.Gly113fs	198.0	0.0		112.0	55.0	NM_016239	B4DFC7	Frame_Shift_Del	DEL	ENST00000205890.5	hg19	CCDS42271.1																																																																																			.	.		0.622	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		-	18022473	GCCGCCGTGGCTACGGCCGCCT	-	18022452	7	5	181	1	0	1	0	1	0	0	0	0	10072	1203	42	0	340	0	MYO15A	17	18022452	Frame_Shift_Del	DEL	GCCGCCGTGGCTACGGCCGCCT	TCGA-DD-AAD5-01A-11D-A40R-10	10448446	18022452	63172758	119	27105										
SLFN11	91607	hgsc.bcm.edu	37	chr17	33679852	33679852	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cttctaattacttgcatttcTttttgtaagtacttggctat	5	7	2	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr17:33679852T>A	ENST00000394566.1	-	7	2501	c.2229A>T	c.(2227-2229)aaA>aaT	p.K743N	SLFN11_ENST00000308377.4_Missense_Mutation_p.K743N	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	743					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTTGCATTTCTTTTTGTAAGT	0.463																																					p.K743N		Atlas-SNP	.											.	SLFN11	112	.	0			c.A2229T						.						116	111	113					17																	33679852		2203	4300	6503	SO:0001583	missense	91607	exon5			CATTTCTTTTTGT	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.2229A>T	chr17.hg19:g.33679852T>A	ENSP00000378067:p.Lys743Asn	91.0	0.0		130.0	35.0	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	hg19	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	t	9.782	1.175594	0.21704	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	D;D	0.86562	-2.14;-2.14	4.0	-3.4	0.04853	.	2.687990	0.01357	N	0.012105	T	0.79446	0.4447	L	0.46157	1.445	0.09310	N	1	B	0.19935	0.04	B	0.15870	0.014	T	0.56492	-0.7970	10	0.33940	T	0.23	.	0.1963	0.00140	0.3548:0.1993:0.1465:0.2994	.	743	Q7Z7L1	SLN11_HUMAN	N	743	ENSP00000312402:K743N;ENSP00000378067:K743N	ENSP00000312402:K743N	K	-	3	2	SLFN11	30703965	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.372000	0.01073	-0.894000	0.03925	0.533000	0.62120	AAA	.	.		0.463	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		A	33679852	T	A	33679852	3	1	181	1	0	0	0	0	1	0	0	0	14748	1606	56	4	480	4	SLFN11	17	33679852	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	15657400	33679852	47515358	120	27106										
SPATA20	64847	hgsc.bcm.edu	37	chr17	48632950	48632950	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ggaagaccaggccactgcatAtgtgtgtgagaatcaagcct	12	9	1	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr17:48632950A>G	ENST00000356488.4	+	16	2371	c.2288A>G	c.(2287-2289)tAt>tGt	p.Y763C	SPATA20_ENST00000006658.6_Missense_Mutation_p.Y779C|CACNA1G-AS1_ENST00000508920.1_RNA|CACNA1G-AS1_ENST00000505495.1_RNA|SPATA20_ENST00000511937.1_3'UTR|CACNA1G-AS1_ENST00000505793.1_RNA|SPATA20_ENST00000393244.3_Missense_Mutation_p.Y719C	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	763					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			GCCACTGCATATGTGTGTGAG	0.572																																					p.Y779C		Atlas-SNP	.											.	SPATA20	59	.	0			c.A2336G						.						101	90	93					17																	48632950		2203	4300	6503	SO:0001583	missense	64847	exon17			CTGCATATGTGTG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.2288A>G	chr17.hg19:g.48632950A>G	ENSP00000348878:p.Tyr763Cys	79.0	0.0		77.0	15.0	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	hg19	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	a	15.49	2.849179	0.51270	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244;ENST00000544362	T;T;T	0.31247	1.5;1.5;1.53	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000001	T	0.58032	0.2094	M	0.84948	2.725	0.51233	D	0.999919	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	T	0.64483	-0.6397	10	0.87932	D	0	-19.2086	10.9401	0.47268	0.9245:0.0:0.0755:0.0	.	763;779	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	C	779;763;719;52	ENSP00000006658:Y779C;ENSP00000348878:Y763C;ENSP00000376935:Y719C	ENSP00000006658:Y779C	Y	+	2	0	SPATA20	45987949	1.000000	0.71417	0.098000	0.21074	0.669000	0.39330	5.097000	0.64542	2.118000	0.64928	0.459000	0.35465	TAT	.	.		0.572	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		G	48632950	A	G	48632950	3	3	181	1	0	0	0	0	1	0	0	0	15021	449	16	2	2402	2	SPATA20	17	48632950	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	14953098	48632950	32562260	121	27107										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48653617	48653617	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gccagctctgggcccccaacCctcaccagcctcaacatccc	6	22	3	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr17:48653617C>T	ENST00000359106.5	+	8	1854	c.1854C>T	c.(1852-1854)acC>acT	p.T618T	CACNA1G_ENST00000514717.1_Silent_p.T618T|CACNA1G_ENST00000514079.1_Silent_p.T618T|CACNA1G_ENST00000503485.1_Silent_p.T618T|CACNA1G_ENST00000513964.1_Silent_p.T618T|CACNA1G_ENST00000510115.1_Silent_p.T618T|CACNA1G_ENST00000507609.1_Silent_p.T618T|CACNA1G_ENST00000513689.2_Silent_p.T618T|CACNA1G_ENST00000507336.1_Silent_p.T618T|CACNA1G_ENST00000429973.2_Silent_p.T618T|CACNA1G_ENST00000502264.1_Silent_p.T618T|CACNA1G_ENST00000515165.1_Silent_p.T618T|CACNA1G_ENST00000360761.4_Silent_p.T618T|CACNA1G_ENST00000507896.1_Silent_p.T618T|CACNA1G_ENST00000358244.5_Silent_p.T618T|CACNA1G_ENST00000352832.5_Silent_p.T618T|CACNA1G_ENST00000510366.1_Silent_p.T618T|CACNA1G_ENST00000505165.1_Silent_p.T618T|CACNA1G_ENST00000416767.4_Silent_p.T618T|CACNA1G_ENST00000514181.1_Silent_p.T618T|CACNA1G_ENST00000512389.1_Silent_p.T618T|CACNA1G_ENST00000515765.1_Silent_p.T618T|CACNA1G_ENST00000515411.1_Silent_p.T618T|CACNA1G_ENST00000507510.2_Silent_p.T618T|CACNA1G_ENST00000354983.4_Silent_p.T618T|CACNA1G_ENST00000442258.2_Silent_p.T618T	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	618					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GGCCCCCAACCCTCACCAGCC	0.627																																					p.T618T		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C1854T						.						11	15	13					17																	48653617		2032	4174	6206	SO:0001819	synonymous_variant	8913	exon8			CCCAACCCTCACC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.1854C>T	chr17.hg19:g.48653617C>T		306.0	0.0		351.0	105.0	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	hg19	CCDS45730.1																																																																																			.	.		0.627	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		T	48653617	C	T	48653617	2	4	181	1	0	0	0	0	0	0	0	1	2546	610	22	3		3	CACNA1G	17	48653617	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	20667	48653617	32541593	122	27108										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48696133	48696133	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tagtcaacgtggtgatcgccGtgctgatgaagcacctggag	14	9	1	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr17:48696133G>A	ENST00000359106.5	+	33	5545	c.5545G>A	c.(5545-5547)Gtg>Atg	p.V1849M	CACNA1G_ENST00000514717.1_Missense_Mutation_p.V1792M|CACNA1G_ENST00000514079.1_Missense_Mutation_p.V1856M|CACNA1G_ENST00000503485.1_Missense_Mutation_p.V1815M|CACNA1G_ENST00000513964.1_Missense_Mutation_p.V1804M|CACNA1G_ENST00000510115.1_Missense_Mutation_p.V1815M|CACNA1G_ENST00000507609.1_Missense_Mutation_p.V1842M|CACNA1G_ENST00000513689.2_Missense_Mutation_p.V1804M|CACNA1G_ENST00000507336.1_Missense_Mutation_p.V1838M|CACNA1G_ENST00000429973.2_Missense_Mutation_p.V1831M|CACNA1G_ENST00000502264.1_Missense_Mutation_p.V1826M|CACNA1G_ENST00000515165.1_Missense_Mutation_p.V1849M|CACNA1G_ENST00000360761.4_Missense_Mutation_p.V1826M|CACNA1G_ENST00000507896.1_Missense_Mutation_p.V1838M|CACNA1G_ENST00000358244.5_Missense_Mutation_p.V1815M|CACNA1G_ENST00000352832.5_Missense_Mutation_p.V1815M|CACNA1G_ENST00000510366.1_Missense_Mutation_p.V1797M|CACNA1G_ENST00000505165.1_Missense_Mutation_p.V1849M|CACNA1G_ENST00000514181.1_Missense_Mutation_p.V1824M|CACNA1G_ENST00000512389.1_Missense_Mutation_p.V1838M|CACNA1G_ENST00000515765.1_Missense_Mutation_p.V1838M|CACNA1G_ENST00000515411.1_Missense_Mutation_p.V1831M|CACNA1G_ENST00000507510.2_Missense_Mutation_p.V1849M|CACNA1G_ENST00000354983.4_Missense_Mutation_p.V1815M|CACNA1G_ENST00000442258.2_Missense_Mutation_p.V1808M	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1849					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GGTGATCGCCGTGCTGATGAA	0.592																																					p.V1856M		Atlas-SNP	.											.	CACNA1G	659	.	0			c.G5566A						.						59	63	62					17																	48696133		2162	4253	6415	SO:0001583	missense	8913	exon33			ATCGCCGTGCTGA	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.5545G>A	chr17.hg19:g.48696133G>A	ENSP00000352011:p.Val1849Met	151.0	0.0		133.0	25.0	NM_001256325	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	g	23.8	4.454168	0.84209	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98987	-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3	4.9	4.9	0.64082	Ion transport (1);	0.142026	0.47093	D	0.000254	D	0.99507	0.9824	H	0.95004	3.61	0.80722	D	1	P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;P;D;D;D;D	0.89917	0.932;1.0;0.982;1.0;1.0;0.962;0.962;0.981;0.962;0.999;0.997;1.0;1.0;1.0;0.982;1.0;0.997;1.0;1.0;0.999;0.942;1.0;0.99;1.0;1.0	P;D;P;D;D;P;P;D;P;D;D;D;D;D;P;D;D;D;D;D;P;D;D;D;D	0.97110	0.787;0.987;0.881;0.999;1.0;0.81;0.81;0.952;0.81;0.977;0.937;0.948;0.987;1.0;0.881;1.0;0.952;0.999;1.0;0.977;0.664;1.0;0.937;0.998;0.999	D	0.98149	1.0440	10	0.87932	D	0	.	18.1463	0.89656	0.0:0.0:1.0:0.0	.	1792;1804;1797;1831;1804;1824;1856;1815;1842;1838;1849;1826;1838;1838;1831;1838;1849;1826;1849;1815;1808;1815;1826;1849;1815	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.	M	1826;1815;1815;1808;1826;1838;1804;1792;1797;1815;1849;1838;1804;1842;1815;1849;1824;1838;1856;1815;1849;1831;1831;1849;1838	ENSP00000353990:V1826M;ENSP00000339302:V1815M;ENSP00000347078:V1815M;ENSP00000409759:V1808M;ENSP00000425522:V1826M;ENSP00000426261:V1838M;ENSP00000425451:V1804M;ENSP00000422407:V1792M;ENSP00000426814:V1797M;ENSP00000427238:V1815M;ENSP00000423112:V1849M;ENSP00000420918:V1838M;ENSP00000426172:V1804M;ENSP00000423045:V1842M;ENSP00000427173:V1815M;ENSP00000426098:V1849M;ENSP00000425698:V1824M;ENSP00000426232:V1838M;ENSP00000423317:V1856M;ENSP00000350979:V1815M;ENSP00000352011:V1849M;ENSP00000414388:V1831M;ENSP00000423155:V1831M;ENSP00000422268:V1849M;ENSP00000421518:V1838M	ENSP00000339302:V1815M	V	+	1	0	CACNA1G	46051132	1.000000	0.71417	0.930000	0.37139	0.974000	0.67602	9.866000	0.99616	2.286000	0.76751	0.552000	0.68991	GTG	.	.		0.592	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		A	48696133	G	A	48696133	3	1	181	1	0	0	0	0	1	0	0	0	2546	1145	40	1	5942	1	CACNA1G	17	48696133	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	42516	48696133	32499077	123	27109										
PGS1	9489	hgsc.bcm.edu	37	chr17	76411090	76411090	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gtgacggagaaccaggccctGcagcagcagcttcaccaggt	13	13	1	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr17:76411090G>A	ENST00000262764.6	+	8	1559	c.1533G>A	c.(1531-1533)ctG>ctA	p.L511L	PGS1_ENST00000588281.1_3'UTR|PGS1_ENST00000329897.7_Silent_p.L376L	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1	511					cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			ACCAGGCCCTGCAGCAGCAGC	0.632																																					p.L511L	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	PGS1	30	.	0			c.G1533A						.						44	47	46					17																	76411090		2045	4198	6243	SO:0001819	synonymous_variant	9489	exon8			GGCCCTGCAGCAG		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8		ENST00000262764.6:c.1533G>A	chr17.hg19:g.76411090G>A		99.0	0.0		104.0	46.0	NM_024419	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Silent	SNP	ENST00000262764.6	hg19	CCDS42391.1																																																																																			.	.		0.632	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419		A	76411090	G	A	76411090	2	1	181	1	0	0	0	0	0	0	0	1	11817	1306	46	3		3	PGS1	17	76411090	Silent	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	27714957	76411090	4784120	124	27110										
CDH2	1000	hgsc.bcm.edu	37	chr18	25589824	25589824	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cagtgaaaggtttttatctcTatcagacctgatctgaggat	9	7	3	4			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr18:25589824T>G	ENST00000269141.3	-	5	982	c.559A>C	c.(559-561)Aga>Cga	p.R187R	CDH2_ENST00000399380.3_Silent_p.R156R	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	187	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TTTTTATCTCTATCAGACCTG	0.453																																					p.R187R		Atlas-SNP	.											.	CDH2	194	.	0			c.A559C						.						75	68	70					18																	25589824		2203	4300	6503	SO:0001819	synonymous_variant	1000	exon5			TATCTCTATCAGA	S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"CD molecules", "Cadherins / Major cadherins"	1759	protein-coding gene	gene with protein product	"N-cadherin"	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.559A>C	chr18.hg19:g.25589824T>G		47.0	0.0		62.0	19.0	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Silent	SNP	ENST00000269141.3	hg19	CCDS11891.1																																																																																			.	.		0.453	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		G	25589824	T	G	25589824	2	3	181	1	0	0	0	0	0	0	0	1	3107	1530	53	5		5	CDH2	18	25589824	Silent	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10		25589824	52487424	125	27111										
GCDH	2639	hgsc.bcm.edu	37	chr19	13006809	13006810	+	Frame_Shift_Ins	INS	-	-	G													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgtcttgtgcctgcagccaaINSgggggagctcctgggctgct					rs200785120		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr19:13006809_13006810insG	ENST00000222214.5	+	7	720_721	c.509_510insG	c.(508-513)aaggggfs	p.KG170fs	GCDH_ENST00000422947.2_Frame_Shift_Ins_p.KG126fs|GCDH_ENST00000457854.1_Frame_Shift_Ins_p.KG170fs|GCDH_ENST00000591470.1_Frame_Shift_Ins_p.KG170fs			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase	170					cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	CCTGCAGCCAAGGGGGAGCTCC	0.584																																					p.Q170fs	GBM(123;875 1636 7726 16444 26754)	Atlas-INDEL	.											.	GCDH	76	.	0			c.509_510insG						.																																			SO:0001589	frameshift_variant	2639	exon7			.	AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"glutaryl-Coenzyme A dehydrogenase"			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.514dupG	chr19.hg19:g.13006814_13006814dupG	ENSP00000222214:p.Lys170fs	72.0	0.0		73.0	20.0	NM_013976	A8K2Z2|O14719	Frame_Shift_Ins	INS	ENST00000222214.5	hg19	CCDS12286.1																																																																																			.	.		0.584	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1			G	13006810	-	G	13006809	7	5	181	1	0	1	1	0	0	0	0	0	6295	72	3	0	531	0	GCDH	19	13006809	Frame_Shift_Ins	INS	-	TCGA-DD-AAD5-01A-11D-A40R-10		13006809	46122174	126	27112										
ZNF430	80264	hgsc.bcm.edu	37	chr19	21216318	21216318	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tctctggaggagtggcaatgCctggacactgctcagcagga	14	10	2	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr19:21216318C>T	ENST00000261560.5	+	3	334	c.153C>T	c.(151-153)tgC>tgT	p.C51C	ZNF430_ENST00000599548.1_Silent_p.C51C|ZNF430_ENST00000595401.1_Silent_p.C51C	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						AGTGGCAATGCCTGGACACTG	0.418																																					p.C51C		Atlas-SNP	.											.	ZNF430	59	.	0			c.C153T						.						120	124	123					19																	21216318		2203	4300	6503	SO:0001819	synonymous_variant	80264	exon3			GCAATGCCTGGAC	AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"Zinc fingers, C2H2-type", "-"	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.153C>T	chr19.hg19:g.21216318C>T		166.0	0.0		126.0	48.0	NM_025189	Q86V70	Silent	SNP	ENST00000261560.5	hg19	CCDS32978.1																																																																																			.	.		0.418	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189		T	21216318	C	T	21216318	2	4	181	1	0	0	0	0	0	0	0	1	17919	747	26	3		3	ZNF430	19	21216318	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	8209509	21216318	37912665	127	27113										
ZNF568	374900	hgsc.bcm.edu	37	chr19	37440949	37440949	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aaccttattagacaccacagAattcatactggggagaaacc	7	10	1	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr19:37440949A>T	ENST00000333987.7	+	7	1400	c.894A>T	c.(892-894)agA>agT	p.R298S	ZNF568_ENST00000415168.1_Missense_Mutation_p.R234S|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	298					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GACACCACAGAATTCATACTG	0.368																																					p.R298S		Atlas-SNP	.											.	ZNF568	106	.	0			c.A894T						.						36	40	38					19																	37440949		2159	4272	6431	SO:0001583	missense	374900	exon7			CCACAGAATTCAT	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.894A>T	chr19.hg19:g.37440949A>T	ENSP00000334685:p.Arg298Ser	122.0	0.0		115.0	15.0	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	hg19	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.777907	0.49786	.	.	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.24151	1.87;1.87	3.95	2.93	0.34026	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40385	N	0.001115	T	0.40862	0.1134	L	0.55743	1.74	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.15954	-1.0419	10	0.66056	D	0.02	.	7.4256	0.27096	0.8924:0.0:0.1076:0.0	.	298	Q3ZCX4	ZN568_HUMAN	S	298;234	ENSP00000334685:R298S;ENSP00000394514:R234S	ENSP00000334685:R298S	R	+	3	2	ZNF568	42132789	0.000000	0.05858	0.633000	0.29310	0.838000	0.47535	-0.097000	0.11042	0.680000	0.31366	0.533000	0.62120	AGA	.	.		0.368	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		T	37440949	A	T	37440949	3	4	181	1	0	0	0	0	1	0	0	0	18014	243	9	4	912	4	ZNF568	19	37440949	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	16224631	37440949	21688034	128	27114										
CYP2A6	1548	hgsc.bcm.edu	37	chr19	41355743	41355743	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	catagcctttgaagacccagTcgaaggtggcttgctcgcct	11	12	0	2			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr19:41355743T>C	ENST00000301141.5	-	2	343	c.323A>G	c.(322-324)gAc>gGc	p.D108G	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	108					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GAAGACCCAGTCGAAGGTGGC	0.642																																					p.D108G		Atlas-SNP	.											.	CYP2A6	69	.	0			c.A323G						.						69	66	67					19																	41355743		2203	4297	6500	SO:0001583	missense	1548	exon2			ACCCAGTCGAAGG	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.323A>G	chr19.hg19:g.41355743T>C	ENSP00000301141:p.Asp108Gly	228.0	0.0		200.0	46.0	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	hg19	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	15.15	2.748722	0.49257	.	.	ENSG00000255974	ENST00000301141	T	0.69306	-0.39	2.72	1.66	0.24008	.	0.796800	0.11430	U	0.564895	T	0.65852	0.2731	L	0.41710	1.295	0.09310	N	1	P	0.39094	0.659	P	0.50270	0.636	T	0.57148	-0.7861	10	0.66056	D	0.02	.	6.6893	0.23161	0.2373:0.0:0.0:0.7627	.	108	P11509	CP2A6_HUMAN	G	108	ENSP00000301141:D108G	ENSP00000301141:D108G	D	-	2	0	CYP2A6	46047583	0.000000	0.05858	0.001000	0.08648	0.359000	0.29487	-0.036000	0.12185	0.153000	0.19213	0.155000	0.16302	GAC	.	.		0.642	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		C	41355743	T	C	41355743	3	2	181	1	0	0	0	0	1	0	0	0	4164	1667	58	2	1193	2	CYP2A6	19	41355743	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	3914794	41355743	17773240	129	27115										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53856625	53856625	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ggtaaggtttttaatcaacaAgcacaccttgcatgtcatca	7	9	3	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr19:53856625A>G	ENST00000595091.1	+	5	2916	c.2697A>G	c.(2695-2697)caA>caG	p.Q899Q	ZNF845_ENST00000458035.1_Silent_p.Q899Q			Q96IR2	ZN845_HUMAN	zinc finger protein 845	899					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TTAATCAACAAGCACACCTTG	0.363																																					p.Q899Q		Atlas-SNP	.											.	ZNF845	101	.	0			c.A2697G						.						38	34	35					19																	53856625		692	1591	2283	SO:0001819	synonymous_variant	91664	exon4			TCAACAAGCACAC	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2697A>G	chr19.hg19:g.53856625A>G		149.0	0.0		160.0	55.0	NM_138374		Silent	SNP	ENST00000595091.1	hg19	CCDS46170.1																																																																																			.	.		0.363	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		G	53856625	A	G	53856625	2	3	181	1	0	0	0	0	0	0	0	1	18206	69	3	2		2	ZNF845	19	53856625	Silent	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	12500882	53856625	5272358	130	27116										
CSRP2BP	57325	hgsc.bcm.edu	37	chr20	18143146	18143146	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aggtcagaggccctgaacagAtaaagcaggaggtagagagt	15	6	1	4			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr20:18143146A>T	ENST00000435364.3	+	6	1569	c.1228A>T	c.(1228-1230)Ata>Tta	p.I410L	CSRP2BP_ENST00000377681.3_Missense_Mutation_p.I409L|CSRP2BP_ENST00000489634.2_Missense_Mutation_p.I282L	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	410					chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						CCCTGAACAGATAAAGCAGGA	0.512																																					p.I410L		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.A1228T						.						69	72	71					20																	18143146		2203	4300	6503	SO:0001583	missense	57325	exon6			GAACAGATAAAGC	AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"cysteine rich protein 2 binding protein", "ATAC component 2 homolog (Drosophila)"					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.1228A>T	chr20.hg19:g.18143146A>T	ENSP00000392318:p.Ile410Leu	190.0	0.0		152.0	8.0	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	hg19	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.638887	0.87760	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.16743	2.32;2.32;2.32;2.35	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.28896	0.0717	N	0.24115	0.695	0.80722	D	1	P;P	0.51147	0.942;0.904	D;P	0.64595	0.927;0.847	T	0.03121	-1.1070	10	0.62326	D	0.03	-14.0864	16.5655	0.84588	1.0:0.0:0.0:0.0	.	282;410	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	L	410;409;410;282	ENSP00000278816:I410L;ENSP00000366909:I409L;ENSP00000392318:I410L;ENSP00000425909:I282L	ENSP00000278816:I410L	I	+	1	0	CSRP2BP	18091146	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.450000	0.73477	2.302000	0.77476	0.533000	0.62120	ATA	.	.		0.512	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		T	18143146	A	T	18143146	3	4	181	1	0	0	0	0	1	0	0	0	3970	333	12	4	1250	4	CSRP2BP	20	18143146	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10		18143146	44882374	131	27117										
CSE1L	1434	hgsc.bcm.edu	37	chr20	47682737	47682737	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	ctttgcttttaggttgaagaTgaaccaaacaaaatttgtga	8	5	0	4			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr20:47682737T>G	ENST00000262982.2	+	4	360	c.237T>G	c.(235-237)gaT>gaG	p.D79E	CSE1L_ENST00000396192.3_Missense_Mutation_p.D79E|CSE1L_ENST00000542325.1_Intron	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	79	Importin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00115}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			AGGTTGAAGATGAACCAAACA	0.373																																					p.D79E		Atlas-SNP	.											.	CSE1L	83	.	0			c.T237G						.						81	76	78					20																	47682737		2203	4300	6503	SO:0001583	missense	1434	exon4			TGAAGATGAACCA	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.237T>G	chr20.hg19:g.47682737T>G	ENSP00000262982:p.Asp79Glu	135.0	0.0		114.0	37.0	NM_001256135	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Missense_Mutation	SNP	ENST00000262982.2	hg19	CCDS13412.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.305859	0.60305	.	.	ENSG00000124207	ENST00000262982;ENST00000396192	T;T	0.68181	-0.31;-0.31	5.62	4.52	0.55395	Armadillo-like helical (1);Armadillo-type fold (1);Importin-beta, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.69851	0.3157	L	0.46670	1.46	0.80722	D	1	P;D	0.59767	0.864;0.986	B;D	0.65573	0.393;0.936	T	0.66642	-0.5872	10	0.06365	T	0.9	-22.4861	11.5842	0.50908	0.0:0.0701:0.0:0.9299	.	79;79	F8W904;P55060	.;XPO2_HUMAN	E	79	ENSP00000262982:D79E;ENSP00000379495:D79E	ENSP00000262982:D79E	D	+	3	2	CSE1L	47116144	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.304000	0.72800	0.947000	0.37659	0.533000	0.62120	GAT	.	.		0.373	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		G	47682737	T	G	47682737	3	3	181	1	0	0	0	0	1	0	0	0	3932	1461	51	5	247	5	CSE1L	20	47682737	Missense_Mutation	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	29539591	47682737	15342783	132	27118										
ZFP64	55734	hgsc.bcm.edu	37	chr20	50803417	50803417	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	atggttctggtggtggtctgAgtctgggtggcaggcactgt	18	6	3	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr20:50803417A>C	ENST00000216923.4	-	2	589	c.240T>G	c.(238-240)acT>acG	p.T80T	ZFP64_ENST00000371515.4_Silent_p.T78T|ZFP64_ENST00000346617.4_Silent_p.T80T|ZFP64_ENST00000361387.2_Silent_p.T80T|ZFP64_ENST00000371518.2_Silent_p.T80T	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	80					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						TGGTGGTCTGAGTCTGGGTGG	0.587																																					p.T80T		Atlas-SNP	.											.	ZFP64	240	.	0			c.T240G						.						150	133	139					20																	50803417		2203	4300	6503	SO:0001819	synonymous_variant	55734	exon2			GGTCTGAGTCTGG	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.240T>G	chr20.hg19:g.50803417A>C		150.0	0.0		119.0	39.0	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	hg19	CCDS13440.1																																																																																			.	.		0.587	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197		C	50803417	A	C	50803417	2	2	181	1	0	0	0	0	0	0	0	1	17667	291	11	5		5	ZFP64	20	50803417	Silent	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	3120680	50803417	12222103	133	27119										
PCK1	5105	hgsc.bcm.edu	37	chr20	56138179	56138179	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tctcctttggcagtgggtacGgcgggaactcgctgctcggg	16	11	1	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr20:56138179G>A	ENST00000319441.4	+	5	870	c.706G>A	c.(706-708)Ggc>Agc	p.G236S	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Missense_Mutation_p.G104S	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	236					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CAGTGGGTACGGCGGGAACTC	0.622																																					p.G236S		Atlas-SNP	.											.	PCK1	95	.	0			c.G706A						.						73	79	77					20																	56138179		2203	4300	6503	SO:0001583	missense	5105	exon5			GGGTACGGCGGGA		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.706G>A	chr20.hg19:g.56138179G>A	ENSP00000319814:p.Gly236Ser	92.0	0.0		85.0	33.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	hg19	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	G	35	5.540586	0.96474	.	.	ENSG00000124253	ENST00000319441;ENST00000535860	T;T	0.34859	1.34;1.34	5.06	5.06	0.68205	Phosphoenolpyruvate carboxykinase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.76241	0.3960	H	0.98426	4.23	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.86489	0.1796	10	0.87932	D	0	-34.8333	18.8029	0.92025	0.0:0.0:1.0:0.0	.	236	P35558	PCKGC_HUMAN	S	236;104	ENSP00000319814:G236S;ENSP00000444342:G104S	ENSP00000319814:G236S	G	+	1	0	PCK1	55571585	1.000000	0.71417	0.995000	0.50966	0.862000	0.49288	9.282000	0.95840	2.520000	0.84964	0.655000	0.94253	GGC	.	.		0.622	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			A	56138179	G	A	56138179	3	1	181	1	0	0	0	0	1	0	0	0	11590	1116	39	1	720	1	PCK1	20	56138179	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	5334762	56138179	6887341	134	27120										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57766466	57766466	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gtcgccgggcctgggccccaCgctgggcagcccaggcaagg	17	16	0	0	rs143620250		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr20:57766466C>A	ENST00000371030.2	+	1	392	c.392C>A	c.(391-393)aCg>aAg	p.T131K		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	131							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CTGGGCCCCACGCTGGGCAGC	0.682																																					p.T131K		Atlas-SNP	.											.	ZNF831	287	.	0			c.C392A						.						25	29	28					20																	57766466		2045	4156	6201	SO:0001583	missense	128611	exon1			GCCCCACGCTGGG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.392C>A	chr20.hg19:g.57766466C>A	ENSP00000360069:p.Thr131Lys	116.0	0.0		134.0	43.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	C	9.754	1.168210	0.21621	.	.	ENSG00000124203	ENST00000371030	T	0.04970	3.52	5.41	4.47	0.54385	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	0.09310	N	1	B	0.30914	0.3	B	0.25884	0.064	T	0.39313	-0.9620	9	0.66056	D	0.02	0.0013	9.9438	0.41596	0.1371:0.7891:0.0:0.0738	.	131	Q5JPB2	ZN831_HUMAN	K	131	ENSP00000360069:T131K	ENSP00000360069:T131K	T	+	2	0	ZNF831	57199861	0.000000	0.05858	0.014000	0.15608	0.386000	0.30323	0.285000	0.18883	1.287000	0.44583	0.561000	0.74099	ACG	.	C|0.999;T|0.001		0.682	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57766466	C	A	57766466	3	1	181	1	0	0	0	0	1	0	0	0	18200	536	19	1	394	1	ZNF831	20	57766466	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	1628287	57766466	5259054	135	27121										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34053835	34053837	+	In_Frame_Del	DEL	CTG	CTG	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cccttcaagagctccagttcCtgcatatatcttactgattg							TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr21:34053835_34053837delCTG	ENST00000322229.7	-	10	1321_1323	c.1322_1324delCAG	c.(1321-1326)gcagga>gga	p.A441del	SYNJ1_ENST00000357345.3_In_Frame_Del_p.A441del|SYNJ1_ENST00000382491.3_In_Frame_Del_p.A441del|SYNJ1_ENST00000382499.2_In_Frame_Del_p.A480del|SYNJ1_ENST00000433931.2_In_Frame_Del_p.A480del			O43426	SYNJ1_HUMAN	synaptojanin 1	441	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						GCTCCAGTTCCTGCATATATCTT	0.399																																					p.480_481del		Atlas-INDEL	.											.	SYNJ1	253	.	0			c.1440_1442del						.																																			SO:0001651	inframe_deletion	8867	exon11			.	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.1322_1324delCAG	chr21.hg19:g.34053835_34053837delCTG	ENSP00000322234:p.Ala441del	128.0	0.0		110.0	16.0	NM_203446	O43425|O94984|Q4KMR1	In_Frame_Del	DEL	ENST00000322229.7	hg19	CCDS54484.1																																																																																			.	.		0.399	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				-	34053837	CTG	-	34053835	7	5	181	1	0	1	0	1	0	0	0	0	15467	690	24	0	3519	0	SYNJ1	21	34053835	In_Frame_Del	DEL	CTG	TCGA-DD-AAD5-01A-11D-A40R-10		34053835	14076060	136	27122	133	2								
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34053840	34053864	+	Frame_Shift_Del	DEL	TATATCTTACTGATTGAATCACCAT	TATATCTTACTGATTGAATCACCAT	-													0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	caagagctccagttcctgcaTatatcttactgattgaatca					rs369372843|rs540825481		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	TATATCTTACTGATTGAATCACCAT	TATATCTTACTGATTGAATCACCAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr21:34053840_34053864delTATATCTTACTGATTGAATCACCAT	ENST00000322229.7	-	10	1294_1318	c.1295_1319delATGGTGATTCAATCAGTAAGATATA	c.(1294-1320)aatggtgattcaatcagtaagatatatfs	p.NGDSISKIY432fs	SYNJ1_ENST00000357345.3_Frame_Shift_Del_p.NGDSISKIY432fs|SYNJ1_ENST00000382491.3_Frame_Shift_Del_p.NGDSISKIY432fs|SYNJ1_ENST00000382499.2_Frame_Shift_Del_p.NGDSISKIY471fs|SYNJ1_ENST00000433931.2_Frame_Shift_Del_p.NGDSISKIY471fs			O43426	SYNJ1_HUMAN	synaptojanin 1	432	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						AGTTCCTGCATATATCTTACTGATTGAATCACCATTCACGGACCA	0.382																																					p.471_479del		Atlas-INDEL	.											.	SYNJ1	253	.	0			c.1413_1437del						.																																			SO:0001589	frameshift_variant	8867	exon11			.	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.1295_1319delATGGTGATTCAATCAGTAAGATATA	chr21.hg19:g.34053840_34053864delTATATCTTACTGATTGAATCACCAT	ENSP00000322234:p.Asn432fs	132.0	0.0		98.0	16.0	NM_203446	O43425|O94984|Q4KMR1	Frame_Shift_Del	DEL	ENST00000322229.7	hg19	CCDS54484.1																																																																																			.	.		0.382	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				-	34053864	TATATCTTACTGATTGAATCACCAT	-	34053840	7	5	181	1	0	1	0	1	0	0	0	0	15467	1406	49	0	3524	0	SYNJ1	21	34053840	Frame_Shift_Del	DEL	TATATCTTACTGATTGAATCACCAT	TCGA-DD-AAD5-01A-11D-A40R-10	5	34053840	14076055	137	27123	133	2								
IFNGR2	3460	hgsc.bcm.edu	37	chr21	34805131	34805131	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	tgaaatatagaggcctgattAaatactggtttcacactcca	7	8	1	3			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr21:34805131A>C	ENST00000290219.6	+	6	1480	c.832A>C	c.(832-834)Aaa>Caa	p.K278Q	IFNGR2_ENST00000381995.1_Missense_Mutation_p.K297Q|IFNGR2_ENST00000405436.1_Missense_Mutation_p.K199Q	NM_005534.3	NP_005525.2	P38484	INGR2_HUMAN	interferon gamma receptor 2 (interferon gamma transducer 1)	278					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	interferon-gamma receptor activity (GO:0004906)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	13					Interferon gamma-1b(DB00033)	AGGCCTGATTAAATACTGGTT	0.458																																					p.K278Q		Atlas-SNP	.											.	IFNGR2	30	.	0			c.A832C						.						97	95	96					21																	34805131		2203	4300	6503	SO:0001583	missense	3460	exon6			CTGATTAAATACT		CCDS33544.1	21q22.1	2014-09-17			ENSG00000159128	ENSG00000159128		"Interferons", "Fibronectin type III domain containing"	5440	protein-coding gene	gene with protein product		147569		IFNGT1		3136170	Standard	NM_005534		Approved	AF-1	uc002yrp.4	P38484	OTTHUMG00000065188	ENST00000290219.6:c.832A>C	chr21.hg19:g.34805131A>C	ENSP00000290219:p.Lys278Gln	102.0	0.0		106.0	19.0	NM_005534	Q9BTL5	Missense_Mutation	SNP	ENST00000290219.6	hg19	CCDS33544.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.53|18.53	3.644284|3.644284	0.67244|0.67244	.|.	.|.	ENSG00000159128|ENSG00000159128	ENST00000290219;ENST00000381995;ENST00000405436|ENST00000421802	T;T;T|.	0.75477|.	0.2;0.26;-0.94|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.71533|0.71533	0.3351|0.3351	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	T|T	0.71873|0.71873	-0.4461|-0.4461	10|5	0.54805|.	T|.	0.06|.	-15.5322|-15.5322	12.35|12.35	0.55143|0.55143	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	297;278|.	E7EUY1;P38484|.	.;INGR2_HUMAN|.	Q|F	278;297;199|43	ENSP00000290219:K278Q;ENSP00000371425:K297Q;ENSP00000385044:K199Q|.	ENSP00000290219:K278Q|.	K|L	+|+	1|3	0|2	IFNGR2|IFNGR2	33727001|33727001	0.869000|0.869000	0.29996|0.29996	0.094000|0.094000	0.20943|0.20943	0.670000|0.670000	0.39368|0.39368	4.108000|4.108000	0.57817|0.57817	2.231000|2.231000	0.72958|0.72958	0.460000|0.460000	0.39030|0.39030	AAA|TTA	.	.		0.458	IFNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139916.1			C	34805131	A	C	34805131	3	2	181	1	0	0	0	0	1	0	0	0	7559	363	13	5	854	5	IFNGR2	21	34805131	Missense_Mutation	SNP	A	TCGA-DD-AAD5-01A-11D-A40R-10	751291	34805131	13324764	138	27124										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37617605	37617605	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	gccccggacagcagcgagcaCaccgagtctgcagatacaag	12	14	1	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr21:37617605C>T	ENST00000399151.3	+	19	3412	c.3327C>T	c.(3325-3327)caC>caT	p.H1109H		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1109					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GCAGCGAGCACACCGAGTCTG	0.632																																					p.H1109H		Atlas-SNP	.											.	DOPEY2	184	.	0			c.C3327T						.						132	93	106					21																	37617605		2203	4300	6503	SO:0001819	synonymous_variant	9980	exon19			CGAGCACACCGAG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.3327C>T	chr21.hg19:g.37617605C>T		85.0	0.0		76.0	15.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	hg19	CCDS13643.1																																																																																			.	.		0.632	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		T	37617605	C	T	37617605	2	4	181	1	0	0	0	0	0	0	0	1	4710	477	17	3		3	DOPEY2	21	37617605	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10	2812474	37617605	10512290	139	27125										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18324653	18324653	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	aggttgtgctcggcctgagtCtcctccggtacctcctgcag	12	14	1	1			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr22:18324653C>T	ENST00000441493.2	-	20	3088	c.2736G>A	c.(2734-2736)gaG>gaA	p.E912E	MICAL3_ENST00000400561.2_Silent_p.E912E|MICAL3_ENST00000383094.3_Silent_p.E912E|MICAL3_ENST00000207726.7_Silent_p.E940E|MICAL3_ENST00000414725.2_Silent_p.E940E|MICAL3_ENST00000444520.1_Silent_p.E912E	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	912	Glu-rich.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		CGGCCTGAGTCTCCTCCGGTA	0.692																																					p.E912E		Atlas-SNP	.											.	MICAL3	53	.	0			c.G2736A						.						17	18	18					22																	18324653		1567	3577	5144	SO:0001819	synonymous_variant	57553	exon20			CTGAGTCTCCTCC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.2736G>A	chr22.hg19:g.18324653C>T		56.0	0.0		27.0	12.0	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.		0.692	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18324653	C	T	18324653	2	4	181	1	0	0	0	0	0	0	0	1	9580	912	32	3		3	MICAL3	22	18324653	Silent	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10		18324653	32979913	140	27126										
ATF4	468	hgsc.bcm.edu	37	chr22	39918368	39918368	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	agaagatggtagcagcaaaaGtaaagggtgagaaactggat	14	3	0	3	rs372679887		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr22:39918368G>A	ENST00000337304.2	+	2	1699	c.817G>A	c.(817-819)Gta>Ata	p.V273I	ATF4_ENST00000404241.2_Missense_Mutation_p.V273I|ATF4_ENST00000396680.1_Missense_Mutation_p.V273I	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	273					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	AGCAGCAAAAGTAAAGGGTGA	0.522																																					p.V273I		Atlas-SNP	.											.	ATF4	27	.	0			c.G817A						.						21	22	21					22																	39918368		2203	4296	6499	SO:0001583	missense	468	exon2			GCAAAAGTAAAGG	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"basic leucine zipper proteins"	786	protein-coding gene	gene with protein product	"tax-responsive enhancer element B67"	604064	"activating transcription factor 4 (tax-responsive enhancer element B67)"	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.817G>A	chr22.hg19:g.39918368G>A	ENSP00000336790:p.Val273Ile	388.0	0.0		359.0	104.0	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	hg19	CCDS13996.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.842304	0.32513	.	.	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.25579	1.79;1.79;1.79	4.51	3.49	0.39957	.	1.006730	0.07979	N	0.985289	T	0.29256	0.0728	M	0.68952	2.095	0.09310	N	1	B	0.34372	0.451	B	0.30179	0.112	T	0.25916	-1.0118	10	0.87932	D	0	-19.7905	10.4544	0.44542	0.1621:0.0:0.8379:0.0	.	273	P18848	ATF4_HUMAN	I	273	ENSP00000384587:V273I;ENSP00000336790:V273I;ENSP00000379912:V273I	ENSP00000336790:V273I	V	+	1	0	ATF4	38248314	0.876000	0.30132	0.006000	0.13384	0.909000	0.53808	1.646000	0.37249	1.197000	0.43143	0.462000	0.41574	GTA	.	.		0.522	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		A	39918368	G	A	39918368	3	1	181	1	0	0	0	0	1	0	0	0	1082	1029	36	3	823	3	ATF4	22	39918368	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	21593715	39918368	11386198	141	27127										
CENPM	79019	hgsc.bcm.edu	37	chr22	42341233	42341233	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cgaggaacgtacttaccaccTgtggcgaggaaacacacctt	10	12	0	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chr22:42341233T>C	ENST00000215980.5	-	4	393	c.306A>G	c.(304-306)acA>acG	p.T102T	CENPM_ENST00000404067.1_Silent_p.T68T|CENPM_ENST00000407253.3_Silent_p.T102T|CENPM_ENST00000402338.1_Silent_p.T68T|CENPM_ENST00000402420.1_Missense_Mutation_p.R97G	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M	102					mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						ACTTACCACCTGTGGCGAGGA	0.612																																					p.T102T		Atlas-SNP	.											.	CENPM	8	.	0			c.A306G						.						100	77	85					22																	42341233		2203	4300	6503	SO:0001819	synonymous_variant	79019	exon4			ACCACCTGTGGCG	BC000705	CCDS14025.1, CCDS46719.1, CCDS46720.1	22q13.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000100162	ENSG00000100162			18352	protein-coding gene	gene with protein product		610152	"chromosome 22 open reading frame 18"	C22orf18		16622420, 16622419	Standard	NM_001110215		Approved	Pane1, CENP-M, MGC861	uc003bbn.3	Q9NSP4	OTTHUMG00000151277	ENST00000215980.5:c.306A>G	chr22.hg19:g.42341233T>C		161.0	0.0		167.0	37.0	NM_024053	A7LM22|B1AHQ9|Q6I9W3	Silent	SNP	ENST00000215980.5	hg19	CCDS14025.1	.	.	.	.	.	.	.	.	.	.	T	10.70	1.425331	0.25639	.	.	ENSG00000100162	ENST00000402420	.	.	.	5.71	-11.4	0.00090	.	.	.	.	.	T	0.28366	0.0701	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.44483	-0.9325	5	0.87932	D	0	-12.0161	2.6801	0.05091	0.3111:0.3296:0.2685:0.0908	.	.	.	.	G	97	.	ENSP00000384132:R97G	R	-	1	2	CENPM	40671179	0.000000	0.05858	0.001000	0.08648	0.393000	0.30537	-5.462000	0.00120	-4.081000	0.00075	-0.263000	0.10527	AGG	.	.		0.612	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053		C	42341233	T	C	42341233	2	2	181	1	0	0	0	0	0	0	0	1	3239	1567	55	2		2	CENPM	22	42341233	Silent	SNP	T	TCGA-DD-AAD5-01A-11D-A40R-10	2422865	42341233	8963333	142	27128										
ZBED1	9189	hgsc.bcm.edu	37	chrX	2408700	2408700	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cttccacaccttgctcttggCgcgggggtgggccaccagct	13	15	1	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chrX:2408700C>A	ENST00000381223.4	-	2	264	c.61G>T	c.(61-63)Gcc>Tcc	p.A21S	DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381218.3_Missense_Mutation_p.A21S|ZBED1_ENST00000381222.2_Missense_Mutation_p.A21S|ZBED1_ENST00000515319.1_5'Flank	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	21					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)			endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TTGCTCTTGGCGCGGGGGTGG	0.582																																					p.A21S		Atlas-SNP	.											.	ZBED1	64	.	0			c.G61T						.						138	141	140					X																	2408700		2203	4296	6499	SO:0001583	missense	9189	exon2			TCTTGGCGCGGGG	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"Pseudoautosomal regions / PAR1", "Zinc fingers, BED-type"	447	protein-coding gene	gene with protein product		300178	"Ac-like transposable element"	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.61G>T	chrX.hg19:g.2408700C>A	ENSP00000370621:p.Ala21Ser	111.0	0.0		114.0	25.0	NM_001171135	Q96BY4	Missense_Mutation	SNP	ENST00000381223.4	hg19	CCDS14118.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.724762	0.30593	.	.	ENSG00000214717	ENST00000381223;ENST00000381222;ENST00000381218;ENST00000461691	.	.	.	2.46	2.46	0.29980	Zinc finger, BED-type predicted (2);	0.115187	0.31290	U	0.007920	T	0.49490	0.1560	.	.	.	0.09310	N	1	D	0.71674	0.998	D	0.77557	0.99	T	0.43360	-0.9396	8	0.10111	T	0.7	-18.4507	12.7367	0.57228	0.0:1.0:0.0:0.0	.	21	O96006	ZBED1_HUMAN	S	21	.	ENSP00000370616:A21S	A	-	1	0	ZBED1	2418700	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	5.061000	0.64319	0.995000	0.38917	0.425000	0.28330	GCC	.	.		0.582	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729		A	2408700	C	A	2408700	3	1	181	1	0	0	0	0	1	0	0	0	17532	768	27	1	2027	1	ZBED1	23	2408700	Missense_Mutation	SNP	C	TCGA-DD-AAD5-01A-11D-A40R-10		2408700	152861860	143	27129										
MED12	9968	hgsc.bcm.edu	37	chrX	70346907	70346907	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0863309352517986	12	1	1.66991552956465	1.32610939112487	1.82788051209104	0.0542378965316102	0.459789441052059	0	cactactagcctgtgcctgtGcatcgtggctgtcctgcggc	12	14	0	0			TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	g.chrX:70346907G>T	ENST00000374080.3	+	20	2806	c.2774G>T	c.(2773-2775)tGc>tTc	p.C925F	MED12_ENST00000462984.1_3'UTR|MED12_ENST00000333646.6_Missense_Mutation_p.C925F|MED12_ENST00000374102.1_Missense_Mutation_p.C925F			Q93074	MED12_HUMAN	mediator complex subunit 12	925					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					CTGTGCCTGTGCATCGTGGCT	0.532			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.C925F		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.G2774T						.						87	79	81					X																	70346907		2120	4218	6338	SO:0001583	missense	9968	exon20			GCCTGTGCATCGT	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.2774G>T	chrX.hg19:g.70346907G>T	ENSP00000363193:p.Cys925Phe	52.0	0.0		45.0	30.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	hg19	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	21.7	4.193658	0.78902	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	D	0.85283	0.5661	L	0.54323	1.7	0.80722	D	1	D;P;P;D	0.65815	0.99;0.645;0.93;0.995	D;B;P;D	0.71414	0.942;0.204;0.787;0.973	D	0.86194	0.1614	10	0.54805	T	0.06	-14.4721	17.2458	0.87027	0.0:0.0:1.0:0.0	.	925;772;925;925	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	F	925;925;925;925;893	ENSP00000333125:C925F;ENSP00000363215:C925F;ENSP00000363193:C925F;ENSP00000414203:C893F	ENSP00000333125:C925F	C	+	2	0	MED12	70263632	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.964000	0.93389	2.252000	0.74401	0.436000	0.28706	TGC	.	.		0.532	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		T	70346907	G	T	70346907	3	4	181	1	0	0	0	0	1	0	0	0	9437	1319	46	3	2852	3	MED12	23	70346907	Missense_Mutation	SNP	G	TCGA-DD-AAD5-01A-11D-A40R-10	67938207	70346907	84923653	144	27130										
MASP2	10747	hgsc.bcm.edu	37	chr1	11087077	11087077	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	acaaaccacctctctgtttcActatctagaaacaccagtgc	4	14	3	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr1:11087077A>C	ENST00000400897.3	-	11	1941	c.1926T>G	c.(1924-1926)agT>agG	p.S642R	RP4-635E18.8_ENST00000607145.1_RNA	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	642	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		TCTCTGTTTCACTATCTAGAA	0.488																																					p.S642R	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											.	MASP2	71	.	0			c.T1926G						.						194	188	190					1																	11087077		2203	4300	6503	SO:0001583	missense	10747	exon11			TGTTTCACTATCT	X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"mannan-binding lectin serine protease 2", "mannan-binding lectin serine peptidase 1 pseudogene 1", "mannan-binding lectin serine protease 1 pseudogene 1"	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.1926T>G	chr1.hg19:g.11087077A>C	ENSP00000383690:p.Ser642Arg	196.0	0.0		105.0	94.0	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	hg19	CCDS123.1	.	.	.	.	.	.	.	.	.	.	A	0.918	-0.716889	0.03206	.	.	ENSG00000009724	ENST00000400897	D	0.88277	-2.36	5.11	-3.3	0.05003	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.827292	0.10853	N	0.626999	T	0.70072	0.3182	N	0.12502	0.225	0.21933	N	0.999464	B	0.06786	0.001	B	0.11329	0.006	T	0.57791	-0.7750	10	0.12103	T	0.63	.	1.801	0.03071	0.309:0.1146:0.3538:0.2226	.	642	O00187	MASP2_HUMAN	R	642	ENSP00000383690:S642R	ENSP00000383690:S642R	S	-	3	2	MASP2	11009664	0.000000	0.05858	0.001000	0.08648	0.203000	0.24098	-1.615000	0.02055	-0.528000	0.06366	0.460000	0.39030	AGT	.	.		0.488	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610		C	11087077	A	C	11087077	3	2	182	1	0	0	0	0	1	0	0	0	9332	156	6	5	138	5	MASP2	1	11087077	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10		11087077	238163544	1	27131										
RAVER2	55225	hgsc.bcm.edu	37	chr1	65243500	65243500	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cttatggaaatattgagagaTgttttctggtctatagtgaa	10	3	2	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr1:65243500T>A	ENST00000294428.3	+	3	589	c.511T>A	c.(511-513)Tgt>Agt	p.C171S	RAVER2_ENST00000430964.2_5'Flank|RAVER2_ENST00000371072.4_Missense_Mutation_p.C171S			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	171	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						TATTGAGAGATGTTTTCTGGT	0.393																																					p.C171S		Atlas-SNP	.											.	RAVER2	56	.	0			c.T511A						.						234	212	219					1																	65243500		1877	4109	5986	SO:0001583	missense	55225	exon3			GAGAGATGTTTTC	AB046799	CCDS41345.1	1p31.3	2013-02-12			ENSG00000162437	ENSG00000162437		"RNA binding motif (RRM) containing"	25577	protein-coding gene	gene with protein product		609953				16051233	Standard	NM_018211		Approved	KIAA1579, FLJ10770	uc001dbs.2	Q9HCJ3	OTTHUMG00000009102	ENST00000294428.3:c.511T>A	chr1.hg19:g.65243500T>A	ENSP00000294428:p.Cys171Ser	109.0	0.0		116.0	40.0	NM_018211	Q6P141|Q9NPV7	Missense_Mutation	SNP	ENST00000294428.3	hg19		.	.	.	.	.	.	.	.	.	.	T	19.48	3.836107	0.71373	.	.	ENSG00000162437	ENST00000371072;ENST00000294428	T;T	0.15834	2.39;2.39	5.41	5.41	0.78517	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.055297	0.85682	D	0.000000	T	0.23094	0.0558	L	0.52266	1.64	0.80722	D	1	D;D	0.76494	0.999;0.996	D;D	0.81914	0.995;0.977	T	0.01557	-1.1325	10	0.49607	T	0.09	-37.1727	10.6242	0.45497	0.0:0.0751:0.0:0.9249	.	171;171	Q9HCJ3;Q9HCJ3-2	RAVR2_HUMAN;.	S	171	ENSP00000360112:C171S;ENSP00000294428:C171S	ENSP00000294428:C171S	C	+	1	0	RAVER2	65016088	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	5.947000	0.70242	2.036000	0.60181	0.533000	0.62120	TGT	.	.		0.393	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211		A	65243500	T	A	65243500	3	1	182	1	0	0	0	0	1	0	0	0	13110	1464	51	4	521	4	RAVER2	1	65243500	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	54156423	65243500	184007121	2	27132										
HMGCS2	3158	hgsc.bcm.edu	37	chr1	120293471	120293471	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ggcgatgctgctcgtccactCgctccaggtaccaagtacct	10	15	0	0	rs587593961		TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr1:120293471C>A	ENST00000369406.3	-	9	1530	c.1481G>T	c.(1480-1482)cGa>cTa	p.R494L	HMGCS2_ENST00000544913.2_Missense_Mutation_p.R452L	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	494					cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)	p.R494P(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		CTCGTCCACTCGCTCCAGGTA	0.512																																					p.R494L		Atlas-SNP	.											HMGCS2,NS,carcinoma,0,1	HMGCS2	58	.	1	Substitution - Missense(1)	lung(1)	c.G1481T						.						77	67	71					1																	120293471		2203	4300	6503	SO:0001583	missense	3158	exon9			TCCACTCGCTCCA	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.1481G>T	chr1.hg19:g.120293471C>A	ENSP00000358414:p.Arg494Leu	94.0	0.0		100.0	38.0	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Missense_Mutation	SNP	ENST00000369406.3	hg19	CCDS905.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.486286	0.63962	.	.	ENSG00000134240	ENST00000369406;ENST00000544913	T;T	0.77489	-1.1;-1.1	5.3	0.203	0.15195	Hydroxymethylglutaryl-coenzyme A synthase C-terminal (1);Thiolase-like (1);	0.630492	0.14933	N	0.289963	T	0.59756	0.2217	L	0.57536	1.79	0.36290	D	0.856322	P;P	0.42620	0.785;0.611	B;B	0.40741	0.339;0.116	T	0.57911	-0.7729	10	0.54805	T	0.06	-0.9426	9.2302	0.37432	0.0:0.6239:0.0:0.3761	.	452;494	B7Z8R3;P54868	.;HMCS2_HUMAN	L	494;452	ENSP00000358414:R494L;ENSP00000439495:R452L	ENSP00000358414:R494L	R	-	2	0	HMGCS2	120094994	0.833000	0.29383	0.988000	0.46212	0.601000	0.36947	0.944000	0.29043	0.062000	0.16340	-0.291000	0.09656	CGA	.	.		0.512	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518		A	120293471	C	A	120293471	3	1	182	1	0	0	0	0	1	0	0	0	7242	884	31	1	49	1	HMGCS2	1	120293471	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	55049971	120293471	128957150	3	27133										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176563805	176563805	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	aaagccaccatcttgattagCcacagtcgctaccaaccagg	7	14	1	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr1:176563805C>T	ENST00000367662.3	+	3	2229	c.1065C>T	c.(1063-1065)agC>agT	p.S355S	PAPPA2_ENST00000367661.3_Silent_p.S355S	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	355					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TCTTGATTAGCCACAGTCGCT	0.587																																					p.S355S		Atlas-SNP	.											.	PAPPA2	665	.	0			c.C1065T						.						60	63	62					1																	176563805		2120	4233	6353	SO:0001819	synonymous_variant	60676	exon3			GATTAGCCACAGT	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1065C>T	chr1.hg19:g.176563805C>T		98.0	0.0		114.0	55.0	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.		0.587	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176563805	C	T	176563805	2	4	182	1	0	0	0	0	0	0	0	1	11442	738	26	3		3	PAPPA2	1	176563805	Silent	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	56270334	176563805	72686816	4	27134										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181687238	181687238	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tcttcctcttggagatgtccCtgaagatgtatggcatgggg	13	8	2	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr1:181687238C>A	ENST00000367573.2	+	12	1573	c.1573C>A	c.(1573-1575)Ctg>Atg	p.L525M	CACNA1E_ENST00000357570.5_Missense_Mutation_p.L476M|CACNA1E_ENST00000526775.1_Missense_Mutation_p.L525M|CACNA1E_ENST00000367570.1_Missense_Mutation_p.L525M|CACNA1E_ENST00000360108.3_Missense_Mutation_p.L525M|CACNA1E_ENST00000358338.5_Missense_Mutation_p.L476M|CACNA1E_ENST00000367567.4_Missense_Mutation_p.L132M	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	525					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GGAGATGTCCCTGAAGATGTA	0.478																																					p.L525M		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C1573A						.						107	102	104					1																	181687238		1879	4105	5984	SO:0001583	missense	777	exon12			ATGTCCCTGAAGA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1573C>A	chr1.hg19:g.181687238C>A	ENSP00000356545:p.Leu525Met	33.0	0.0		35.0	17.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068543	0.76301	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.99051	-5.37;-5.37;-5.37;-5.37;-5.37;-5.37;-5.37	5.57	4.66	0.58398	.	0.227161	0.39475	N	0.001354	D	0.98664	0.9552	M	0.68317	2.08	0.47441	D	0.999429	D;D	0.61080	0.989;0.989	P;P	0.61201	0.885;0.885	D	0.98939	1.0790	10	0.87932	D	0	.	7.1635	0.25677	0.0:0.7135:0.0:0.2865	.	525;525	Q15878-2;Q15878-3	.;.	M	525;525;476;476;132;525;525	ENSP00000356542:L525M;ENSP00000434814:L525M;ENSP00000350183:L476M;ENSP00000351101:L476M;ENSP00000356539:L132M;ENSP00000353222:L525M;ENSP00000356545:L525M	ENSP00000350183:L476M	L	+	1	2	CACNA1E	179953861	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	2.401000	0.44513	1.357000	0.45904	0.655000	0.94253	CTG	.	.		0.478	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181687238	C	A	181687238	3	1	182	1	0	0	0	0	1	0	0	0	2544	680	24	3	1619	3	CACNA1E	1	181687238	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	5123433	181687238	67563383	5	27135										
C1orf25	81627	hgsc.bcm.edu	37	chr1	185113145	185113145	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tctttcaaaatttccttaggTggtttagcagtggaagctaa	9	6	2	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr1:185113145T>A	ENST00000367506.5	-	6	940	c.672A>T	c.(670-672)ccA>ccT	p.P224P	TRMT1L_ENST00000367504.3_Silent_p.P68P	NM_001202423.1|NM_030934.4	NP_001189352.1|NP_112196.3	Q7Z2T5	TRM1L_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)-like	224					adult locomotory behavior (GO:0008344)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	21						TTTCCTTAGGTGGTTTAGCAG	0.333																																					p.P224P		Atlas-SNP	.											.	TRMT1L	50	.	0			c.A672T						.						70	71	71					1																	185113145		2203	4299	6502	SO:0001819	synonymous_variant	81627	exon6			CTTAGGTGGTTTA	AF288399	CCDS1366.1	1q25.2	2012-06-29	2012-06-29	2011-01-24	ENSG00000121486	ENSG00000121486			16782	protein-coding gene	gene with protein product	"TRM1-like"	611673	"chromosome 1 open reading frame 25", "TRM1 tRNA methyltransferase 1-like"	C1orf25		11318611, 17198746	Standard	NM_030934		Approved		uc001grf.4	Q7Z2T5	OTTHUMG00000035389	ENST00000367506.5:c.672A>T	chr1.hg19:g.185113145T>A		121.0	0.0		127.0	54.0	NM_030934	Q5TEN0|Q6ZMX0|Q8IWH5|Q8NC68|Q9BZQ1	Silent	SNP	ENST00000367506.5	hg19	CCDS1366.1																																																																																			.	.		0.333	TRMT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085787.1	NM_030934		A	185113145	T	A	185113145	2	1	182	1	0	0	0	0	0	0	0	1	2036	1683	59	4		4	C1orf25	1	185113145	Silent	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	3425907	185113145	64137476	6	27136										
ZNF281	23528	hgsc.bcm.edu	37	chr1	200377908	200377908	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gcttctctctactatgaattTtctcatgtctctgtagtagg	7	9	4	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr1:200377908T>G	ENST00000294740.3	-	2	1050	c.926A>C	c.(925-927)aAa>aCa	p.K309T	ZNF281_ENST00000367353.1_Missense_Mutation_p.K309T|ZNF281_ENST00000367352.3_Missense_Mutation_p.K273T	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	309					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						ACTATGAATTTTCTCATGTCT	0.423																																					p.K309T		Atlas-SNP	.											.	ZNF281	74	.	0			c.A926C						.						153	157	155					1																	200377908		2203	4300	6503	SO:0001583	missense	23528	exon2			TGAATTTTCTCAT	AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"Zinc fingers, C2H2-type"	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.926A>C	chr1.hg19:g.200377908T>G	ENSP00000294740:p.Lys309Thr	60.0	0.0		68.0	35.0	NM_012482	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Missense_Mutation	SNP	ENST00000294740.3	hg19	CCDS1402.1	.	.	.	.	.	.	.	.	.	.	T	19.03	3.747800	0.69533	.	.	ENSG00000162702	ENST00000294740;ENST00000367353;ENST00000367352;ENST00000537759	T;T;T	0.12147	2.71;2.71;2.71	5.64	5.64	0.86602	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.32133	0.0819	L	0.48260	1.515	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.01998	-1.1232	10	0.72032	D	0.01	-13.719	15.8694	0.79101	0.0:0.0:0.0:1.0	.	273;309	A6NF48;Q9Y2X9	.;ZN281_HUMAN	T	309;309;273;14	ENSP00000294740:K309T;ENSP00000356322:K309T;ENSP00000356321:K273T	ENSP00000294740:K309T	K	-	2	0	ZNF281	198644531	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.896000	0.87350	2.137000	0.66172	0.533000	0.62120	AAA	.	.		0.423	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		G	200377908	T	G	200377908	3	3	182	1	0	0	0	0	1	0	0	0	17833	1841	64	5	1765	5	ZNF281	1	200377908	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	15264763	200377908	48872713	7	27137										
ITPKB	3707	hgsc.bcm.edu	37	chr1	226923497	226923497	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gcaggccttcctcaggaaagGcttgtccggatcttggggta	14	10	2	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr1:226923497G>T	ENST00000272117.3	-	1	1662	c.1663C>A	c.(1663-1665)Cct>Act	p.P555T	ITPKB_ENST00000429204.1_Missense_Mutation_p.P555T|ITPKB_ENST00000366784.1_Missense_Mutation_p.P555T			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	555					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				CTCAGGAAAGGCTTGTCCGGA	0.612																																					p.P555T	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.C1663A						.						49	45	46					1																	226923497		2203	4300	6503	SO:0001583	missense	3707	exon2			GGAAAGGCTTGTC	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"inositol 1,4,5-trisphosphate 3-kinase B"			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1663C>A	chr1.hg19:g.226923497G>T	ENSP00000272117:p.Pro555Thr	52.0	0.0		73.0	28.0	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	hg19	CCDS1555.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.068080	0.55539	.	.	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.26373	1.81;1.81;1.74	5.54	3.42	0.39159	.	0.275088	0.35291	N	0.003305	T	0.16085	0.0387	N	0.24115	0.695	0.09310	N	1	B	0.24721	0.11	B	0.19148	0.024	T	0.15607	-1.0431	10	0.33940	T	0.23	-0.7294	10.6339	0.45554	0.0:0.1325:0.6724:0.1951	.	555	P27987	IP3KB_HUMAN	T	555	ENSP00000272117:P555T;ENSP00000411152:P555T;ENSP00000355748:P555T	ENSP00000272117:P555T	P	-	1	0	ITPKB	224990120	0.794000	0.28838	0.024000	0.17045	0.874000	0.50279	1.132000	0.31418	0.591000	0.29711	0.491000	0.48974	CCT	.	.		0.612	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		T	226923497	G	T	226923497	3	4	182	1	0	0	0	0	1	0	0	0	7927	1203	42	3	1205	3	ITPKB	1	226923497	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	26545589	226923497	22327124	8	27138										
RGS7	6000	hgsc.bcm.edu	37	chr1	241262053	241262053	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	atcttgcatccgtgctatgaCgtcttccatctaaacaataa	5	11	3	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr1:241262053C>T	ENST00000407727.1	-	2	87	c.88G>A	c.(88-90)Gtc>Atc	p.V30I	RGS7_ENST00000366565.1_Missense_Mutation_p.V30I|RGS7_ENST00000366564.1_Missense_Mutation_p.V30I|RGS7_ENST00000331110.7_Missense_Mutation_p.V4I|RGS7_ENST00000366562.4_Missense_Mutation_p.V30I|RGS7_ENST00000446183.2_5'UTR|RGS7_ENST00000348120.2_Missense_Mutation_p.V30I|RGS7_ENST00000366563.1_Missense_Mutation_p.V30I|RGS7_ENST00000401882.1_Missense_Mutation_p.V30I			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	30					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			CGTGCTATGACGTCTTCCATC	0.328																																					p.V30I		Atlas-SNP	.											RGS7,NS,carcinoma,0,1	RGS7	308	.	0			c.G88A						.						144	128	134					1																	241262053		2203	4300	6503	SO:0001583	missense	6000	exon3			CTATGACGTCTTC	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"Regulators of G-protein signaling"	10003	protein-coding gene	gene with protein product		602517	"regulator of G-protein signalling 7"			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.88G>A	chr1.hg19:g.241262053C>T	ENSP00000384428:p.Val30Ile	53.0	0.0		41.0	16.0	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	hg19		.	.	.	.	.	.	.	.	.	.	C	8.300	0.819614	0.16607	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000348120;ENST00000366562;ENST00000407727;ENST00000401882	T;T;T;T;T;T;T;T	0.28255	1.63;1.74;1.73;1.72;1.62;1.73;1.73;1.62	5.18	5.18	0.71444	.	0.000000	0.64402	D	0.000002	T	0.08582	0.0213	N	0.00538	-1.39	0.80722	D	1	B;B;B;B;B	0.24483	0.015;0.104;0.006;0.026;0.012	B;B;B;B;B	0.20577	0.008;0.03;0.006;0.03;0.014	T	0.31530	-0.9940	10	0.02654	T	1	.	14.5808	0.68288	0.0:1.0:0.0:0.0	.	4;30;30;30;30	B7Z257;P49802-4;P49802-2;P49802-5;P49802-3	.;.;.;.;.	I	4;30;30;30;30;30;30;30	ENSP00000331485:V4I;ENSP00000355523:V30I;ENSP00000355522:V30I;ENSP00000355521:V30I;ENSP00000341242:V30I;ENSP00000355520:V30I;ENSP00000384428:V30I;ENSP00000385508:V30I	ENSP00000331485:V4I	V	-	1	0	RGS7	239328676	0.882000	0.30256	0.999000	0.59377	0.983000	0.72400	1.642000	0.37207	2.572000	0.86782	0.655000	0.94253	GTC	.	.		0.328	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		T	241262053	C	T	241262053	3	4	182	1	0	0	0	0	1	0	0	0	13325	536	19	1	1439	1	RGS7	1	241262053	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	14338556	241262053	7988568	9	27139										
ABCG5	64240	hgsc.bcm.edu	37	chr2	44041655	44041655	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gtagaactcattgactacaaGaatctcactgcaatattttt	5	8	2	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr2:44041655G>C	ENST00000260645.1	-	12	1862	c.1723C>G	c.(1723-1725)Ctt>Gtt	p.L575V	ABCG5_ENST00000543989.1_Missense_Mutation_p.L180V|ABCG5_ENST00000405322.1_Missense_Mutation_p.L404V	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	575	ABC transmembrane type-2.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	TTGACTACAAGAATCTCACTG	0.303																																					p.L575V		Atlas-SNP	.											.	ABCG5	72	.	0			c.C1723G						.						77	78	78					2																	44041655		2202	4295	6497	SO:0001583	missense	64240	exon12			CTACAAGAATCTC	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"ATP binding cassette transporters / subfamily G"	13886	protein-coding gene	gene with protein product	"sterolin 1"	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.1723C>G	chr2.hg19:g.44041655G>C	ENSP00000260645:p.Leu575Val	209.0	0.0		217.0	92.0	NM_022436	Q2T9G2|Q96QZ2|Q96QZ3	Missense_Mutation	SNP	ENST00000260645.1	hg19	CCDS1814.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.861447	0.71949	.	.	ENSG00000138075	ENST00000260645;ENST00000405322;ENST00000543989	T;T;T	0.73897	-0.79;-0.79;-0.79	5.22	4.35	0.52113	ABC-2 type transporter (1);	0.398249	0.25762	N	0.028476	D	0.82733	0.5101	L	0.59436	1.845	0.58432	D	0.999998	D;D	0.89917	0.996;1.0	D;D	0.87578	0.944;0.998	T	0.82841	-0.0258	10	0.46703	T	0.11	.	13.4448	0.61134	0.0756:0.0:0.9244:0.0	.	404;575	E7EX35;Q9H222	.;ABCG5_HUMAN	V	575;404;180	ENSP00000260645:L575V;ENSP00000384513:L404V;ENSP00000445107:L180V	ENSP00000260645:L575V	L	-	1	0	ABCG5	43895159	1.000000	0.71417	0.978000	0.43139	0.939000	0.58152	6.653000	0.74382	1.427000	0.47276	0.650000	0.86243	CTT	.	.		0.303	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436		C	44041655	G	C	44041655	3	2	182	1	0	0	0	0	1	0	0	0	71	942	33	4	240	4	ABCG5	2	44041655	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10		44041655	199157718	10	27140										
VRK2	7444	hgsc.bcm.edu	37	chr2	58386604	58386604	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cattttatgagcctcatcaaGattttaccagtccagatata	5	9	2	3	rs201610023		TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr2:58386604G>C	ENST00000435505.2	+	16	2048	c.1303G>C	c.(1303-1305)Gat>Cat	p.D435H	VRK2_ENST00000412104.2_3'UTR|VRK2_ENST00000440705.2_Missense_Mutation_p.D412H|FANCL_ENST00000403295.3_3'UTR|VRK2_ENST00000340157.4_Missense_Mutation_p.D435H|FANCL_ENST00000233741.4_3'UTR|FANCL_ENST00000402135.3_3'UTR|VRK2_ENST00000417641.2_3'UTR			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	435	Interaction with MAP3K7.				cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						GCCTCATCAAGATTTTACCAG	0.368																																					p.D435H		Atlas-SNP	.											.	VRK2	46	.	0			c.G1303C						.						65	67	66					2																	58386604		2203	4299	6502	SO:0001583	missense	7444	exon13			CATCAAGATTTTA	AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.1303G>C	chr2.hg19:g.58386604G>C	ENSP00000408002:p.Asp435His	174.0	0.0		178.0	71.0	NM_001130480	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Missense_Mutation	SNP	ENST00000435505.2	hg19	CCDS1859.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.246002	0.59103	.	.	ENSG00000028116	ENST00000435505;ENST00000340157;ENST00000440705	T;T;T	0.07444	3.19;3.19;3.19	6.02	4.21	0.49690	.	0.374960	0.27109	N	0.020889	T	0.13030	0.0316	M	0.61703	1.905	0.19945	N	0.999947	P	0.50272	0.933	P	0.47206	0.541	T	0.10753	-1.0616	10	0.66056	D	0.02	-4.9525	7.7025	0.28632	0.0818:0.0:0.7563:0.1619	.	435	Q86Y07	VRK2_HUMAN	H	435;435;412	ENSP00000408002:D435H;ENSP00000342381:D435H;ENSP00000398323:D412H	ENSP00000342381:D435H	D	+	1	0	VRK2	58240108	0.658000	0.27402	0.002000	0.10522	0.151000	0.21798	2.440000	0.44855	0.863000	0.35553	0.650000	0.86243	GAT	.	G|0.999;A|0.001		0.368	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296		C	58386604	G	C	58386604	3	2	182	1	0	0	0	0	1	0	0	0	17235	942	33	4	1362	4	VRK2	2	58386604	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	14344949	58386604	184812769	11	27141										
USP34	9736	hgsc.bcm.edu	37	chr2	61538926	61538926	+	Frame_Shift_Del	DEL	G	G	-													0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	actatgtaagtaccttgtcaGgaagtccagctggctggcat							TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr2:61538926delG	ENST00000398571.2	-	26	3738	c.3662delC	c.(3661-3663)cctfs	p.P1221fs		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1221					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TACCTTGTCAGGAAGTCCAGC	0.383																																					p.P1221fs		Atlas-INDEL	.											.	USP34	334	.	0			c.3663delT						.						84	79	81					2																	61538926		1891	4129	6020	SO:0001589	frameshift_variant	9736	exon26			.	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.3662delC	chr2.hg19:g.61538926delG	ENSP00000381577:p.Pro1221fs	57.0	0.0		56.0	25.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Frame_Shift_Del	DEL	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.		0.383	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			-	61538926	G	-	61538926	7	5	182	1	0	1	0	1	0	0	0	0	17080	1000	35	0	7198	0	USP34	2	61538926	Frame_Shift_Del	DEL	G	TCGA-DD-AAD6-01A-11D-A40R-10	3152322	61538926	181660447	12	27142										
C2orf29	55571	hgsc.bcm.edu	37	chr2	101883295	101883295	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tcactgagtatttctctgtcCtggtcaatatggacatgtct	8	9	4	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr2:101883295C>G	ENST00000289382.3	+	5	1355	c.1192C>G	c.(1192-1194)Ctg>Gtg	p.L398V		NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	398					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											TTTCTCTGTCCTGGTCAATAT	0.388																																					p.L398V		Atlas-SNP	.											.	.	.	.	0			c.C1192G						.						164	158	160					2																	101883295		2203	4300	6503	SO:0001583	missense	55571	exon5			TCTGTCCTGGTCA	AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 29"	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.1192C>G	chr2.hg19:g.101883295C>G	ENSP00000289382:p.Leu398Val	101.0	0.0		127.0	56.0	NM_017546	Q6P2M9|Q8N681	Missense_Mutation	SNP	ENST00000289382.3	hg19	CCDS2050.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.6|20.6	4.019308|4.019308	0.75275|0.75275	.|.	.|.	ENSG00000158435|ENSG00000158435	ENST00000289382|ENST00000420107	.|.	.|.	.|.	5.95|5.95	4.14|4.14	0.48551|0.48551	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79003|0.79003	0.4373|0.4373	M|M	0.93062|0.93062	3.375|3.375	0.58432|0.58432	D|D	0.999999|0.999999	D|.	0.76494|.	0.999|.	D|.	0.74348|.	0.983|.	T|T	0.81835|0.81835	-0.0750|-0.0750	9|5	0.87932|.	D|.	0|.	-19.833|-19.833	8.0245|8.0245	0.30430|0.30430	0.0:0.7141:0.1421:0.1437|0.0:0.7141:0.1421:0.1437	.|.	398|.	Q9UKZ1|.	CB029_HUMAN|.	V|R	398|77	.|.	ENSP00000289382:L398V|.	L|P	+|+	1|2	2|0	C2orf29|C2orf29	101249727|101249727	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.988000|0.988000	0.76386|0.76386	3.848000|3.848000	0.55903|0.55903	1.514000|1.514000	0.48869|0.48869	0.655000|0.655000	0.94253|0.94253	CTG|CCT	.	.		0.388	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546		G	101883295	C	G	101883295	3	3	182	1	0	0	0	0	1	0	0	0	2163	680	24	4	1210	4	C2orf29	2	101883295	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	40344369	101883295	141316078	13	27143										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189875435	189875435	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tgtgcatctggcattccttcGacttctctccagccgagctt	8	14	2	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr2:189875435G>A	ENST00000304636.3	+	50	4243	c.4073G>A	c.(4072-4074)cGa>cAa	p.R1358Q	COL3A1_ENST00000317840.5_Missense_Mutation_p.R1055Q	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	1358	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	GCATTCCTTCGACTTCTCTCC	0.433																																					p.R1358Q		Atlas-SNP	.											.	COL3A1	292	.	0			c.G4073A						.						97	95	96					2																	189875435		2203	4300	6503	SO:0001583	missense	1281	exon50			TCCTTCGACTTCT	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.4073G>A	chr2.hg19:g.189875435G>A	ENSP00000304408:p.Arg1358Gln	133.0	0.0		142.0	49.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	hg19	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	35	5.441598	0.96187	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	T;T	0.76968	-1.06;-1.06	5.29	5.29	0.74685	Fibrillar collagen, C-terminal (3);	0.000000	0.47455	D	0.000238	D	0.85204	0.5643	L	0.50847	1.595	0.33052	D	0.532905	D	0.89917	1.0	D	0.87578	0.998	D	0.85832	0.1392	10	0.31617	T	0.26	.	18.9332	0.92574	0.0:0.0:1.0:0.0	.	1358	P02461	CO3A1_HUMAN	Q	1358;1055	ENSP00000304408:R1358Q;ENSP00000315243:R1055Q	ENSP00000304408:R1358Q	R	+	2	0	COL3A1	189583680	1.000000	0.71417	0.986000	0.45419	0.877000	0.50540	9.869000	0.99810	2.481000	0.83766	0.655000	0.94253	CGA	.	.		0.433	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		A	189875435	G	A	189875435	3	1	182	1	0	0	0	0	1	0	0	0	3690	1058	37	1	4271	1	COL3A1	2	189875435	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	87992140	189875435	53323938	14	27144										
HSPD1	3329	hgsc.bcm.edu	37	chr2	198353917	198353917	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gacctctccaacttttcctaAgtcatgaggctgaacgtctt	7	12	3	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr2:198353917A>C	ENST00000388968.3	-	9	1291	c.1024T>G	c.(1024-1026)Tta>Gta	p.L342V	HSPD1_ENST00000345042.2_Missense_Mutation_p.L342V	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	342					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			ACTTTTCCTAAGTCATGAGGC	0.398																																					p.L342V		Atlas-SNP	.											.	HSPD1	68	.	0			c.T1024G						.						58	57	58					2																	198353917		2203	4300	6503	SO:0001583	missense	3329	exon9			TTCCTAAGTCATG	M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"Heat Shock Proteins / Chaperonins"	5261	protein-coding gene	gene with protein product		118190	"heat shock 60kD protein 1 (chaperonin)", "spastic paraplegia 13 (autosomal dominant)"	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.1024T>G	chr2.hg19:g.198353917A>C	ENSP00000373620:p.Leu342Val	327.0	0.0		424.0	176.0	NM_002156	B2R5M6|B7Z712|Q38L19|Q9UCR6	Missense_Mutation	SNP	ENST00000388968.3	hg19	CCDS33357.1	.	.	.	.	.	.	.	.	.	.	A	18.61	3.662082	0.67700	.	.	ENSG00000144381	ENST00000388968;ENST00000345042;ENST00000536745	D;D	0.84516	-1.86;-1.86	4.99	4.99	0.66335	.	0.108901	0.64402	D	0.000005	D	0.94245	0.8152	H	0.96996	3.92	0.80722	D	1	B;B;B	0.31910	0.016;0.346;0.001	B;P;B	0.50570	0.207;0.644;0.009	D	0.95072	0.8205	10	0.87932	D	0	-6.7849	14.971	0.71235	1.0:0.0:0.0:0.0	.	333;342;342	B7Z597;B3GQS7;P10809	.;.;CH60_HUMAN	V	342;342;198	ENSP00000373620:L342V;ENSP00000340019:L342V	ENSP00000340019:L342V	L	-	1	2	HSPD1	198062162	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.316000	0.79007	1.994000	0.58287	0.397000	0.26171	TTA	.	.		0.398	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156		C	198353917	A	C	198353917	3	2	182	1	0	0	0	0	1	0	0	0	7437	69	3	5	713	5	HSPD1	2	198353917	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	8478482	198353917	44845456	15	27145										
RNF123	63891	hgsc.bcm.edu	37	chr3	49737930	49737930	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cgaggtacaagattgcctcaAgcagttgatgatgtctctgc	11	9	2	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr3:49737930A>T	ENST00000327697.6	+	14	1280	c.1136A>T	c.(1135-1137)aAg>aTg	p.K379M	RNF123_ENST00000432042.1_Missense_Mutation_p.K233M	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	379					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GATTGCCTCAAGCAGTTGATG	0.587																																					p.K379M		Atlas-SNP	.											.	RNF123	100	.	0			c.A1136T						.						104	95	98					3																	49737930		2203	4300	6503	SO:0001583	missense	63891	exon14			GCCTCAAGCAGTT	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1136A>T	chr3.hg19:g.49737930A>T	ENSP00000328287:p.Lys379Met	107.0	0.0		189.0	46.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.780438	0.90195	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.77358	-0.8;-1.09	5.4	5.4	0.78164	.	0.235838	0.42682	N	0.000675	T	0.80177	0.4575	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;0.998	D;P	0.68192	0.956;0.888	T	0.82874	-0.0241	10	0.66056	D	0.02	-32.2121	14.5929	0.68383	1.0:0.0:0.0:0.0	.	233;379	C9J266;Q5XPI4	.;RN123_HUMAN	M	379;379;233	ENSP00000328287:K379M;ENSP00000392443:K233M	ENSP00000328287:K379M	K	+	2	0	RNF123	49712934	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.792000	0.75125	2.045000	0.60652	0.533000	0.62120	AAG	.	.		0.587	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		T	49737930	A	T	49737930	3	4	182	1	0	0	0	0	1	0	0	0	13448	72	3	4	1186	4	RNF123	3	49737930	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10		49737930	148284500	16	27146										
POLQ	10721	hgsc.bcm.edu	37	chr3	121206681	121206681	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tcaatcttgctttttacttcAttattagaagaaaatgaaat	4	5	3	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr3:121206681A>G	ENST00000264233.5	-	16	5225	c.5097T>C	c.(5095-5097)aaT>aaC	p.N1699N		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1699					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TTTTTACTTCATTATTAGAAG	0.313								DNA polymerases (catalytic subunits)																													p.N1699N	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.T5097C						.						72	77	75					3																	121206681		2203	4300	6503	SO:0001819	synonymous_variant	10721	exon16			TACTTCATTATTA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.5097T>C	chr3.hg19:g.121206681A>G		88.0	0.0		81.0	38.0	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.313	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		G	121206681	A	G	121206681	2	3	182	1	0	0	0	0	0	0	0	1	12217	214	8	2		2	POLQ	3	121206681	Silent	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	71468751	121206681	76815749	17	27147										
MYLK	4638	hgsc.bcm.edu	37	chr3	123444795	123444795	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ggcagggggaactcaccattCagcagccaagtgatccgggg	15	11	2	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr3:123444795C>A	ENST00000475616.1	-	9	1646	c.1647G>T	c.(1645-1647)ctG>ctT	p.L549L	MYLK_ENST00000360304.3_Silent_p.L549L|MYLK_ENST00000359169.1_Silent_p.L549L|MYLK_ENST00000346322.5_Silent_p.L480L|MYLK_ENST00000360772.3_Silent_p.L549L			Q15746	MYLK_HUMAN	myosin light chain kinase	549	Ig-like C2-type 4.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		ACTCACCATTCAGCAGCCAAG	0.592																																					p.L549L		Atlas-SNP	.											.	MYLK	224	.	0			c.G1647T						.						44	48	47					3																	123444795		2203	4300	6503	SO:0001819	synonymous_variant	4638	exon12			ACCATTCAGCAGC	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7590	protein-coding gene	gene with protein product	"smooth muscle myosin light chain kinase"	600922	"myosin, light polypeptide kinase"			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.1647G>T	chr3.hg19:g.123444795C>A		502.0	1.0		459.0	210.0	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Silent	SNP	ENST00000475616.1	hg19	CCDS46896.1																																																																																			.	.		0.592	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		A	123444795	C	A	123444795	2	1	182	1	0	0	0	0	0	0	0	1	10065	813	29	3		3	MYLK	3	123444795	Silent	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	2238114	123444795	74577635	18	27148										
PLSCR4	57088	hgsc.bcm.edu	37	chr3	145912237	145912237	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ggagatctttcaaaatacatGaagtcctgaaattggaaaaa	8	5	2	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr3:145912237G>A	ENST00000354952.2	-	9	1191	c.951C>T	c.(949-951)ttC>ttT	p.F317F	PLSCR4_ENST00000493382.1_Silent_p.F317F|PLSCR4_ENST00000446574.2_Silent_p.F317F|PLSCR4_ENST00000383083.2_Silent_p.F227F|PLSCR4_ENST00000433593.2_Silent_p.F212F	NM_020353.2	NP_065086.2	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4	317					cellular response to lipopolysaccharide (GO:0071222)|phospholipid scrambling (GO:0017121)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|enzyme binding (GO:0019899)|phospholipid scramblase activity (GO:0017128)			kidney(1)|large_intestine(6)|lung(9)|urinary_tract(1)	17						CAAAATACATGAAGTCCTGAA	0.338																																					p.F317F		Atlas-SNP	.											.	PLSCR4	44	.	0			c.C951T						.						111	112	111					3																	145912237		2203	4300	6503	SO:0001819	synonymous_variant	57088	exon9			ATACATGAAGTCC	AF199023	CCDS3133.1, CCDS54651.1	3q24	2008-07-18			ENSG00000114698	ENSG00000114698			16497	protein-coding gene	gene with protein product		607612				10930526	Standard	NM_020353		Approved		uc003evt.4	Q9NRQ2	OTTHUMG00000159415	ENST00000354952.2:c.951C>T	chr3.hg19:g.145912237G>A		73.0	0.0		74.0	34.0	NM_020353	A8K2E9|Q2TTR3|Q658L3|Q6ZR73|Q7Z505	Silent	SNP	ENST00000354952.2	hg19	CCDS3133.1																																																																																			.	.		0.338	PLSCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355172.1	NM_020353		A	145912237	G	A	145912237	2	1	182	1	0	0	0	0	0	0	0	1	12121	1281	45	3		3	PLSCR4	3	145912237	Silent	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	22467442	145912237	52110193	19	27149										
FXR1	8087	hgsc.bcm.edu	37	chr3	180666182	180666182	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gacgctacttacaatgaaatAgtcacatttgaacgacttcg	7	9	1	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr3:180666182A>T	ENST00000357559.4	+	5	702	c.318A>T	c.(316-318)atA>atT	p.I106I	FXR1_ENST00000445140.2_Silent_p.I106I|FXR1_ENST00000480918.1_Silent_p.I93I|FXR1_ENST00000491062.1_Silent_p.I57I|FXR1_ENST00000468861.1_Silent_p.I21I|FXR1_ENST00000305586.7_Silent_p.I21I	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	106	Agenet-like 2.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			ACAATGAAATAGTCACATTTG	0.328																																					p.I106I		Atlas-SNP	.											.	FXR1	75	.	0			c.A318T						.						51	52	52					3																	180666182		2203	4300	6503	SO:0001819	synonymous_variant	8087	exon5			TGAAATAGTCACA	M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.318A>T	chr3.hg19:g.180666182A>T		122.0	0.0		114.0	11.0	NM_001013438	A8K9B8|Q7Z450|Q8N6R8	Silent	SNP	ENST00000357559.4	hg19	CCDS3238.1																																																																																			.	.		0.328	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5			T	180666182	A	T	180666182	2	4	182	1	0	0	0	0	0	0	0	1	6123	410	15	4		4	FXR1	3	180666182	Silent	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	34753945	180666182	17356248	20	27150										
CRMP1	1400	hgsc.bcm.edu	37	chr4	5827327	5827327	+	Frame_Shift_Del	DEL	T	T	-													0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gttgcatatttgggtgtagcTggtacctcgtacacaggacc							TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr4:5827327delT	ENST00000397890.2	-	13	1735	c.1521delA	c.(1519-1521)ccafs	p.P507fs	EVC_ENST00000382674.2_Intron|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000324989.7_Frame_Shift_Del_p.P621fs|CRMP1_ENST00000512574.1_Frame_Shift_Del_p.P505fs	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	507					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		TGGGTGTAGCTGGTACCTCGT	0.517																																					p.A622fs		Atlas-INDEL	.											.	CRMP1	118	.	0			c.1864delG						.						219	201	207					4																	5827327		2203	4300	6503	SO:0001589	frameshift_variant	1400	exon13			.	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1521delA	chr4.hg19:g.5827327delT	ENSP00000380987:p.Pro507fs	175.0	0.0		170.0	67.0	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Frame_Shift_Del	DEL	ENST00000397890.2	hg19	CCDS43207.1																																																																																			.	.		0.517	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		-	5827327	T	-	5827327	7	5	182	1	0	1	0	1	0	0	0	0	3892	1567	55	0	205	0	CRMP1	4	5827327	Frame_Shift_Del	DEL	T	TCGA-DD-AAD6-01A-11D-A40R-10		5827327	185326949	21	27151										
CPZ	8532	hgsc.bcm.edu	37	chr4	8594614	8594614	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gtcctggtcgtcgccgctgcCcggccggggtgcgagtttga	17	13	0	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr4:8594614C>A	ENST00000360986.4	+	1	228	c.54C>A	c.(52-54)gcC>gcA	p.A18A	CPZ_ENST00000506287.1_3'UTR|CPZ_ENST00000382480.2_5'UTR|CPZ_ENST00000315782.6_Silent_p.A18A	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	18					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TCGCCGCTGCCCGGCCGGGGT	0.716																																					p.A18A		Atlas-SNP	.											.	CPZ	95	.	0			c.C54A						.						2	3	3					4																	8594614		1721	3580	5301	SO:0001819	synonymous_variant	8532	exon1			CGCTGCCCGGCCG	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.54C>A	chr4.hg19:g.8594614C>A		119.0	0.0		137.0	50.0	NM_003652	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	hg19	CCDS33953.1																																																																																			.	.		0.716	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		A	8594614	C	A	8594614	2	1	182	1	0	0	0	0	0	0	0	1	3841	610	22	3		3	CPZ	4	8594614	Silent	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	2767287	8594614	182559662	22	27152										
BEND4	389206	hgsc.bcm.edu	37	chr4	42122083	42122083	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tgcagtacctcggaggcatgTtactttaactggatccagag	11	9	0	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr4:42122083T>C	ENST00000502486.1	-	5	1954	c.1375A>G	c.(1375-1377)Aca>Gca	p.T459A	BEND4_ENST00000504360.1_Intron	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	459	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.									NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						CGGAGGCATGTTACTTTAACT	0.527																																					p.T459A		Atlas-SNP	.											.	BEND4	67	.	0			c.A1375G						.						91	94	93					4																	42122083		2034	4192	6226	SO:0001583	missense	389206	exon5			GGCATGTTACTTT	AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"BEN domain containing"	23815	protein-coding gene	gene with protein product			"coiled-coil domain containing 4"	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.1375A>G	chr4.hg19:g.42122083T>C	ENSP00000421169:p.Thr459Ala	98.0	0.0		121.0	46.0	NM_207406	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Missense_Mutation	SNP	ENST00000502486.1	hg19	CCDS47048.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.121107	0.77436	.	.	ENSG00000188848	ENST00000411720;ENST00000502486	T	0.39997	1.05	5.87	5.87	0.94306	BEN domain (2);	0.050017	0.85682	D	0.000000	T	0.37489	0.1005	N	0.08118	0	0.80722	D	1	P;P	0.48503	0.891;0.911	P;P	0.51516	0.543;0.672	T	0.45920	-0.9228	10	0.72032	D	0.01	-11.2362	16.5764	0.84681	0.0:0.0:0.0:1.0	.	381;459	Q6ZU67-3;Q6ZU67	.;BEND4_HUMAN	A	330;459	ENSP00000421169:T459A	ENSP00000412495:T330A	T	-	1	0	BEND4	41816840	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.655000	0.83696	2.371000	0.80710	0.533000	0.62120	ACA	.	.		0.527	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406		C	42122083	T	C	42122083	3	2	182	1	0	0	0	0	1	0	0	0	1400	1725	60	2	237	2	BEND4	4	42122083	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	33527469	42122083	149032193	23	27153										
FRYL	285527	hgsc.bcm.edu	37	chr4	48517192	48517192	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cagtttcttctaaatcaagaAttccttgacacacaagagat	5	9	3	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr4:48517192A>C	ENST00000503238.1	-	53	7789	c.7790T>G	c.(7789-7791)aTt>aGt	p.I2597S	FRYL_ENST00000358350.4_Missense_Mutation_p.I2597S|FRYL_ENST00000537810.1_Missense_Mutation_p.I2597S|FRYL_ENST00000507873.2_5'UTR|FRYL_ENST00000264319.7_5'UTR			O94915	FRYL_HUMAN	FRY-like	2597					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						TAAATCAAGAATTCCTTGACA	0.398																																					p.I2597S		Atlas-SNP	.											.	FRYL	242	.	0			c.T7790G						.						126	118	120					4																	48517192		1852	4087	5939	SO:0001583	missense	285527	exon56			TCAAGAATTCCTT	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.7790T>G	chr4.hg19:g.48517192A>C	ENSP00000426064:p.Ile2597Ser	91.0	0.0		94.0	37.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	A	5.870	0.344747	0.11126	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810	T;T;T	0.21031	2.03;2.03;2.04	5.96	4.75	0.60458	.	1.325240	0.05140	N	0.494071	T	0.13970	0.0338	L	0.31207	0.915	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.40098	-0.9581	10	0.05959	T	0.93	.	4.0903	0.09967	0.6404:0.1888:0.1708:0.0	.	2597;2597	O94915;F5GX82	FRYL_HUMAN;.	S	2597	ENSP00000426064:I2597S;ENSP00000351113:I2597S;ENSP00000441114:I2597S	ENSP00000351113:I2597S	I	-	2	0	FRYL	48211949	1.000000	0.71417	0.566000	0.28421	0.973000	0.67179	3.550000	0.53691	1.036000	0.39998	0.477000	0.44152	ATT	.	.		0.398	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			C	48517192	A	C	48517192	3	2	182	1	0	0	0	0	1	0	0	0	6072	101	4	5	1287	5	FRYL	4	48517192	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	6395109	48517192	142637084	24	27154										
ALB	213	hgsc.bcm.edu	37	chr4	74276072	74276073	+	Frame_Shift_Del	DEL	AG	AG	-													0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gaaggcttcgtctgccaaacAgagactcaagtgtgccagtc					rs3210163		TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr4:74276072_74276073delAG	ENST00000503124.1	+	4	416_417	c.209_210delAG	c.(208-210)cagfs	p.Q70fs	ALB_ENST00000509063.1_Frame_Shift_Del_p.Q220fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Frame_Shift_Del_p.Q105fs|ALB_ENST00000295897.4_Frame_Shift_Del_p.Q220fs|ALB_ENST00000415165.2_Intron			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCTGCCAAACAGAGACTCAAGT	0.366																																					p.220_220del		Atlas-INDEL	.											.	ALB	132	.	0			c.658_659del						.																																			SO:0001589	frameshift_variant	213	exon6			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.209_210delAG	chr4.hg19:g.74276074_74276075delAG	ENSP00000421027:p.Gln70fs	344.0	0.0		330.0	132.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.366	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74276073	AG	-	74276072	7	5	182	1	0	1	0	1	0	0	0	0	486	188	7	0	681	0	ALB	4	74276072	Frame_Shift_Del	DEL	AG	TCGA-DD-AAD6-01A-11D-A40R-10	25758880	74276072	116878204	25	27155										
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141555157	141555157	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gagtctccattttcatctaaTaactggaacaagcgggaggc	10	9	3	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr4:141555157T>C	ENST00000442267.2	-	16	2765	c.2691A>G	c.(2689-2691)ttA>ttG	p.L897L		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	897	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				TTTCATCTAATAACTGGAACA	0.473																																					p.L897L		Atlas-SNP	.											.	TBC1D9	198	.	0			c.A2691G						.						62	62	62					4																	141555157		1946	4151	6097	SO:0001819	synonymous_variant	23158	exon16			ATCTAATAACTGG	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.2691A>G	chr4.hg19:g.141555157T>C		99.0	0.0		104.0	45.0	NM_015130	A6H8U8|D3DNZ1|O94958	Silent	SNP	ENST00000442267.2	hg19	CCDS47136.1																																																																																			.	.		0.473	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		C	141555157	T	C	141555157	2	2	182	1	0	0	0	0	0	0	0	1	15642	1403	49	2		2	TBC1D9	4	141555157	Silent	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	67279085	141555157	49599119	26	27156										
GAB1	2549	hgsc.bcm.edu	37	chr4	144381524	144381524	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tttctgtaattagctcttccAggtttcccatgtccccccga	6	14	2	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr4:144381524A>T	ENST00000262994.4	+	8	1989	c.1687A>T	c.(1687-1689)Agg>Tgg	p.R563W	GAB1_ENST00000505913.1_Missense_Mutation_p.R460W|GAB1_ENST00000262995.4_Missense_Mutation_p.R593W	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	563					activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					TAGCTCTTCCAGGTTTCCCAT	0.393																																					p.R593W		Atlas-SNP	.											.	GAB1	80	.	0			c.A1777T						.						125	124	125					4																	144381524		2203	4300	6503	SO:0001583	missense	2549	exon9			TCTTCCAGGTTTC	U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"Pleckstrin homology (PH) domain containing"	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.1687A>T	chr4.hg19:g.144381524A>T	ENSP00000262994:p.Arg563Trp	75.0	0.0		78.0	32.0	NM_207123	A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	ENST00000262994.4	hg19	CCDS3759.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.162266	0.78226	.	.	ENSG00000109458	ENST00000262995;ENST00000262994;ENST00000505913	T;T;T	0.16457	2.34;2.34;2.34	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.45836	0.1362	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.49254	-0.8959	10	0.72032	D	0.01	-2.3457	15.9132	0.79488	1.0:0.0:0.0:0.0	.	563;593	Q13480;Q13480-2	GAB1_HUMAN;.	W	593;563;460	ENSP00000262995:R593W;ENSP00000262994:R563W;ENSP00000424554:R460W	ENSP00000262994:R563W	R	+	1	2	GAB1	144600974	1.000000	0.71417	0.945000	0.38365	0.516000	0.34256	8.962000	0.93254	2.154000	0.67381	0.482000	0.46254	AGG	.	.		0.393	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039		T	144381524	A	T	144381524	3	4	182	1	0	0	0	0	1	0	0	0	6156	179	7	4	1811	4	GAB1	4	144381524	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	2826367	144381524	46772752	27	27157										
FSTL5	56884	hgsc.bcm.edu	37	chr4	162307202	162307202	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tattggtgggcttcagtaaaGgatggttgaaatgccagatc	13	5	1	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr4:162307202G>C	ENST00000306100.5	-	16	2677	c.2241C>G	c.(2239-2241)tcC>tcG	p.S747S	FSTL5_ENST00000536695.1_Silent_p.S746S|FSTL5_ENST00000379164.4_Silent_p.S746S|FSTL5_ENST00000427802.2_Silent_p.S737S|RP11-234O6.2_ENST00000508189.1_RNA	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	747						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		CTTCAGTAAAGGATGGTTGAA	0.408																																					p.S747S		Atlas-SNP	.											.	FSTL5	207	.	0			c.C2241G						.						89	86	87					4																	162307202		2203	4300	6503	SO:0001819	synonymous_variant	56884	exon16			AGTAAAGGATGGT	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.2241C>G	chr4.hg19:g.162307202G>C		117.0	0.0		123.0	55.0	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	hg19	CCDS3802.1																																																																																			.	.		0.408	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		C	162307202	G	C	162307202	2	2	182	1	0	0	0	0	0	0	0	1	6088	987	35	4		4	FSTL5	4	162307202	Silent	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	17925678	162307202	28847074	28	27158										
KIAA1712	80817	hgsc.bcm.edu	37	chr4	175220276	175220276	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gaatctgatgttaagtaatgGcaacaggtgacttaaaaaga	10	4	1	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr4:175220276G>A	ENST00000503780.1	+	3	418	c.4G>A	c.(4-6)Gca>Aca	p.A2T	CEP44_ENST00000296519.4_Missense_Mutation_p.A2T|CEP44_ENST00000457424.2_Missense_Mutation_p.A2T|CEP44_ENST00000426172.1_Missense_Mutation_p.A2T	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	2						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)				endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						TTAAGTAATGGCAACAGGTGA	0.373																																					p.A2T		Atlas-SNP	.											.	CEP44	35	.	0			c.G4A						.						98	99	99					4																	175220276		2203	4300	6503	SO:0001583	missense	80817	exon3			GTAATGGCAACAG	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"KIAA1712"	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.4G>A	chr4.hg19:g.175220276G>A	ENSP00000423153:p.Ala2Thr	76.0	0.0		73.0	20.0	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Missense_Mutation	SNP	ENST00000503780.1	hg19	CCDS34106.1	.	.	.	.	.	.	.	.	.	.	G	18.98	3.737048	0.69304	.	.	ENSG00000164118	ENST00000503780;ENST00000505124;ENST00000457424;ENST00000514712;ENST00000515299;ENST00000503053;ENST00000426172;ENST00000296519	T;T;T;T;T	0.59224	0.33;0.28;0.35;0.28;0.33	4.89	4.89	0.63831	.	0.333285	0.27402	N	0.019536	T	0.72779	0.3503	M	0.66297	2.02	0.41418	D	0.987788	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.74372	-0.3687	10	0.49607	T	0.09	.	13.4893	0.61386	0.0785:0.0:0.9215:0.0	.	2;2	Q9C0F1-2;Q9C0F1	.;CEP44_HUMAN	T	2	ENSP00000423153:A2T;ENSP00000389427:A2T;ENSP00000421128:A2T;ENSP00000408221:A2T;ENSP00000296519:A2T	ENSP00000296519:A2T	A	+	1	0	CEP44	175456851	1.000000	0.71417	1.000000	0.80357	0.745000	0.42441	4.383000	0.59600	2.255000	0.74692	0.585000	0.79938	GCA	.	.		0.373	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633		A	175220276	G	A	175220276	3	1	182	1	0	0	0	0	1	0	0	0	8262	1203	42	3	6	3	KIAA1712	4	175220276	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	12913074	175220276	15934000	29	27159										
NDUFS6	4726	hgsc.bcm.edu	37	chr5	1802445	1802445	+	Frame_Shift_Del	DEL	A	A	-													0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ttttttccaggtttatgatgAtaaagactacaggagaattc					rs199652659		TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr5:1802445delA	ENST00000274137.5	+	2	161	c.143delA	c.(142-144)gatfs	p.D48fs	MRPL36_ENST00000505059.2_5'Flank|MRPL36_ENST00000505818.1_5'Flank|MRPL36_ENST00000508987.1_5'Flank|NDUFS6_ENST00000469176.1_Frame_Shift_Del_p.D48fs|MRPL36_ENST00000382647.7_5'Flank	NM_004553.4	NP_004544.1	O75380	NDUS6_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 6, 13kDa (NADH-coenzyme Q reductase)	48					cardiovascular system development (GO:0072358)|cellular metabolic process (GO:0044237)|fatty acid metabolic process (GO:0006631)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrion morphogenesis (GO:0070584)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|muscle contraction (GO:0006936)|reproductive system development (GO:0061458)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	7						GTTTATGATGATAAAGACTAC	0.338																																					p.D48fs		Atlas-INDEL	.											.	NDUFS6	11	.	0			c.142delG						.						100	103	102					5																	1802445		2203	4300	6503	SO:0001589	frameshift_variant	4726	exon2			.	BC038664	CCDS3866.1	5p15.33	2011-07-04	2002-08-29		ENSG00000145494	ENSG00000145494	1.6.99.3, 1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7713	protein-coding gene	gene with protein product	"complex I 13kDa subunit A", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial"	603848	"NADH dehydrogenase (ubiquinone) Fe-S protein 6 (13kD) (NADH-coenzyme Q reductase)"			9763677	Standard	NM_004553		Approved	CI-13kA	uc003jcy.3	O75380	OTTHUMG00000090372	ENST00000274137.5:c.143delA	chr5.hg19:g.1802445delA	ENSP00000274137:p.Asp48fs	111.0	0.0		132.0	56.0	NM_004553		Frame_Shift_Del	DEL	ENST00000274137.5	hg19	CCDS3866.1																																																																																			.	.		0.338	NDUFS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206744.2	NM_004553		-	1802445	A	-	1802445	7	5	182	1	0	1	0	1	0	0	0	0	10305	333	12	0	149	0	NDUFS6	5	1802445	Frame_Shift_Del	DEL	A	TCGA-DD-AAD6-01A-11D-A40R-10		1802445	179112815	30	27160										
BRIX1	55299	hgsc.bcm.edu	37	chr5	34922835	34922835	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	aactgaagatgactggaaacTgtttgaaaggttctcggccc	11	8	1	4			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr5:34922835T>C	ENST00000336767.5	+	6	835	c.472T>C	c.(472-474)Tgt>Cgt	p.C158R	BRIX1_ENST00000506023.1_3'UTR	NM_018321.3	NP_060791.3	Q8TDN6	BRX1_HUMAN	BRX1, biogenesis of ribosomes, homolog (S. cerevisiae)	158	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				ribosome biogenesis (GO:0042254)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|large_intestine(2)|lung(1)	4						GACTGGAAACTGTTTGAAAGG	0.348																																					p.C158R		Atlas-SNP	.											.	BRIX1	21	.	0			c.T472C						.						108	114	112					5																	34922835		2203	4300	6503	SO:0001583	missense	55299	exon6			GGAAACTGTTTGA		CCDS34143.1	5p13.2	2009-09-25	2009-09-25	2009-09-25	ENSG00000113460	ENSG00000113460			24170	protein-coding gene	gene with protein product			"brix domain containing 2"	BXDC2		12477932	Standard	NM_018321		Approved	BRIX, FLJ11100	uc003jja.3	Q8TDN6	OTTHUMG00000162021	ENST00000336767.5:c.472T>C	chr5.hg19:g.34922835T>C	ENSP00000338862:p.Cys158Arg	270.0	0.0		261.0	91.0	NM_018321	A8K0P5|Q3ZTT4|Q8N453|Q96DH1	Missense_Mutation	SNP	ENST00000336767.5	hg19	CCDS34143.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.469739	0.84533	.	.	ENSG00000113460	ENST00000336767	T	0.21734	1.99	6.16	6.16	0.99307	Brix domain (3);Anticodon-binding (1);	0.000000	0.85682	D	0.000000	T	0.54951	0.1890	M	0.88310	2.945	0.80722	D	1	D;D	0.89917	1.0;0.988	D;P	0.83275	0.996;0.899	T	0.62407	-0.6861	10	0.66056	D	0.02	-14.0109	16.8061	0.85666	0.0:0.0:0.0:1.0	.	158;158	B4E0B8;Q8TDN6	.;BRX1_HUMAN	R	158	ENSP00000338862:C158R	ENSP00000338862:C158R	C	+	1	0	BRIX1	34958592	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.552000	0.82192	2.367000	0.80283	0.528000	0.53228	TGT	.	.		0.348	BRIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366826.2	NM_018321		C	34922835	T	C	34922835	3	2	182	1	0	0	0	0	1	0	0	0	1517	1580	55	2	494	2	BRIX1	5	34922835	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	33120390	34922835	145992425	31	27161										
C5orf35	133383	hgsc.bcm.edu	37	chr5	56212656	56212656	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tttcagcccacttcgatgtgTtgttcttgtcgcacttaggg	10	10	2	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr5:56212656T>G	ENST00000285947.2	+	6	1213	c.827T>G	c.(826-828)gTt>gGt	p.V276G	SETD9_ENST00000475908.1_3'UTR|SETD9_ENST00000541720.1_Intron	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	276	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)										CTTCGATGTGTTGTTCTTGTC	0.333																																					p.V276G		Atlas-SNP	.											.	.	.	.	0			c.T827G						.						165	155	159					5																	56212656		2203	4300	6503	SO:0001583	missense	133383	exon6			GATGTGTTGTTCT	BC036528	CCDS3972.1	5q11.2	2012-02-23	2012-02-23	2012-02-23	ENSG00000155542	ENSG00000155542			28508	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 35"	C5orf35		20930037	Standard	NM_153706		Approved	MGC33648	uc003jqx.3	Q8NE22	OTTHUMG00000059485	ENST00000285947.2:c.827T>G	chr5.hg19:g.56212656T>G	ENSP00000285947:p.Val276Gly	68.0	0.0		77.0	35.0	NM_153706	F5H713	Missense_Mutation	SNP	ENST00000285947.2	hg19	CCDS3972.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.324164	0.81580	.	.	ENSG00000155542	ENST00000285947	T	0.47869	0.83	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.73291	-0.4029	10	0.87932	D	0	-13.6371	14.8803	0.70528	0.0:0.0:0.0:1.0	.	276	Q8NE22	CE035_HUMAN	G	276	ENSP00000285947:V276G	ENSP00000285947:V276G	V	+	2	0	C5orf35	56248413	1.000000	0.71417	0.954000	0.39281	0.980000	0.70556	7.204000	0.77872	1.927000	0.55829	0.477000	0.44152	GTT	.	.		0.333	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706		G	56212656	T	G	56212656	3	3	182	1	0	0	0	0	1	0	0	0	2296	1725	60	5	849	5	C5orf35	5	56212656	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	21289821	56212656	124702604	32	27162										
DIAPH1	1729	hgsc.bcm.edu	37	chr5	140958709	140958709	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tccagcagcggctggaaacgTtccacttcatccatctcagc	8	15	2	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr5:140958709T>C	ENST00000398557.4	-	9	1019	c.879A>G	c.(877-879)gaA>gaG	p.E293E	DIAPH1_ENST00000253811.6_Silent_p.E293E|DIAPH1_ENST00000398566.3_Silent_p.E284E|DIAPH1_ENST00000389057.5_Silent_p.E284E|DIAPH1_ENST00000520569.1_Silent_p.E239E|DIAPH1_ENST00000389054.3_Silent_p.E293E|DIAPH1_ENST00000398562.2_Silent_p.E284E|DIAPH1_ENST00000518047.1_Silent_p.E284E	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	293	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGGAAACGTTCCACTTCAT	0.463																																					p.E293E		Atlas-SNP	.											.	DIAPH1	64	.	0			c.A879G						.						261	270	267					5																	140958709		1905	4122	6027	SO:0001819	synonymous_variant	1729	exon9			GAAACGTTCCACT	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.879A>G	chr5.hg19:g.140958709T>C		160.0	0.0		169.0	76.0	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Silent	SNP	ENST00000398557.4	hg19	CCDS43374.1																																																																																			.	.		0.463	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		C	140958709	T	C	140958709	2	2	182	1	0	0	0	0	0	0	0	1	4520	1722	60	2		2	DIAPH1	5	140958709	Silent	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	84746053	140958709	39956551	33	27163										
FLT4	2324	hgsc.bcm.edu	37	chr5	180040034	180040034	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gcgggagtggccagctccggGgccctcatccttgtgccgtc	15	15	1	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr5:180040034G>A	ENST00000261937.6	-	25	3486	c.3408C>T	c.(3406-3408)gcC>gcT	p.A1136A	FLT4_ENST00000502649.1_Silent_p.A1136A|FLT4_ENST00000393347.3_Silent_p.A1136A	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1136	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCAGCTCCGGGGCCCTCATCC	0.657																																					p.A1136A	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C3408T						.						56	66	62					5																	180040034		2203	4300	6503	SO:0001819	synonymous_variant	2324	exon25			CTCCGGGGCCCTC	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3408C>T	chr5.hg19:g.180040034G>A		85.0	0.0		89.0	34.0	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	hg19	CCDS4457.1																																																																																			.	.		0.657	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			A	180040034	G	A	180040034	2	1	182	1	0	0	0	0	0	0	0	1	5952	1219	43	3		3	FLT4	5	180040034	Silent	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	39081325	180040034	875226	34	27164										
AARS2	57505	hgsc.bcm.edu	37	chr6	44275036	44275037	+	Missense_Mutation	DNP	TG	TG	AA													0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tcagagatgcagacactgagTgtgcggatgtggtcagccac							TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr6:44275036_44275037TG>AA	ENST00000244571.4	-	6	991_992	c.989_990CA>TT	c.(988-990)aCA>aTT	p.T330I	TMEM151B_ENST00000438774.2_3'UTR|RP11-444E17.6_ENST00000505802.1_3'UTR	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AGACACTGAGTGTGCGGATGTG	0.644																																					p.T330T|p.T330I		Atlas-SNP	.											.	AARS2	77	.	0			c.A990T|c.C989T						.																																			SO:0001583	missense	57505	exon6			ACTGAGTGTGCGG|CTGAGTGTGCGGA	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	21022	protein-coding gene	gene with protein product	"alanine tRNA ligase 2, mitochondrial"	612035	"alanyl-tRNA synthetase like", "alanyl-tRNA synthetase 2, mitochondrial (putative)"	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.989_990delinsAA	chr6.hg19:g.44275036_44275037delinsAA	ENSP00000244571:p.Thr330Ile	56.0|57.0	0.0		70.0	25.0|24.0	NM_020745		Silent|Missense_Mutation	SNP	ENST00000244571.4	hg19	CCDS34464.1																																																																																			.	.		0.644	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		AA	44275037	TG	AA	44275036	3	1	182	1	0	0	0	0	1	0	0	0	20	1683	59	4	2035	4	AARS2	6	44275036	Missense_Mutation	DNP	TG	TCGA-DD-AAD6-01A-11D-A40R-10		44275036	126840031	35	27165										
GPR110	266977	hgsc.bcm.edu	37	chr6	46975013	46975013	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	actgtccaagagtattccaaAgcataagataaaaaatccct	5	9	0	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr6:46975013A>G	ENST00000371253.2	-	12	2724	c.2509T>C	c.(2509-2511)Ttt>Ctt	p.F837L	GPR110_ENST00000283297.5_Missense_Mutation_p.F640L|GPR110_ENST00000449332.2_5'UTR	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	837					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						AGTATTCCAAAGCATAAGATA	0.328																																					p.F837L		Atlas-SNP	.											.	GPR110	102	.	0			c.T2509C						.						53	53	53					6																	46975013		2203	4300	6503	SO:0001583	missense	266977	exon12			TTCCAAAGCATAA	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.2509T>C	chr6.hg19:g.46975013A>G	ENSP00000360299:p.Phe837Leu	370.0	0.0		340.0	150.0	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	hg19	CCDS34471.1	.	.	.	.	.	.	.	.	.	.	A	19.65	3.866864	0.72065	.	.	ENSG00000153292	ENST00000371253;ENST00000283297	T;T	0.54866	0.55;0.55	5.61	5.61	0.85477	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000012	T	0.45216	0.1331	M	0.66939	2.045	0.40239	D	0.977934	P	0.48294	0.908	B	0.44224	0.444	T	0.56619	-0.7949	10	0.87932	D	0	-19.0121	13.8418	0.63444	1.0:0.0:0.0:0.0	.	837	Q5T601	GP110_HUMAN	L	837;640	ENSP00000360299:F837L;ENSP00000283297:F640L	ENSP00000283297:F640L	F	-	1	0	GPR110	47082972	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.047000	0.76599	2.254000	0.74563	0.533000	0.62120	TTT	.	.		0.328	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		G	46975013	A	G	46975013	3	3	182	1	0	0	0	0	1	0	0	0	6635	72	3	2	239	2	GPR110	6	46975013	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	2699977	46975013	124140054	36	27166										
DST	667	hgsc.bcm.edu	37	chr6	56494214	56494214	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	taaggcatggaatacctgtcTcttttcatctacttcagatc	6	10	4	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr6:56494214T>C	ENST00000361203.3	-	28	3683	c.3676A>G	c.(3676-3678)Aga>Gga	p.R1226G	DST_ENST00000446842.2_Missense_Mutation_p.R900G|DST_ENST00000518935.1_Missense_Mutation_p.R900G|DST_ENST00000370765.6_Missense_Mutation_p.R900G|DST_ENST00000312431.6_Missense_Mutation_p.R1226G|DST_ENST00000370754.5_Missense_Mutation_p.R1404G|DST_ENST00000370788.2_Missense_Mutation_p.R1226G|DST_ENST00000244364.6_Missense_Mutation_p.R900G|DST_ENST00000370769.4_Missense_Mutation_p.R1226G|DST_ENST00000421834.2_Missense_Mutation_p.R1226G			Q03001	DYST_HUMAN	dystonin	1226					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AATACCTGTCTCTTTTCATCT	0.328																																					p.R900G		Atlas-SNP	.											.	DST	1427	.	0			c.A2698G						.						121	112	115					6																	56494214		2203	4300	6503	SO:0001583	missense	667	exon18			CCTGTCTCTTTTC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.3676A>G	chr6.hg19:g.56494214T>C	ENSP00000354508:p.Arg1226Gly	84.0	0.0		78.0	32.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	T	18.23	3.578853	0.65878	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;D;T;T;T;D;T;T	0.84070	1.07;-0.06;-0.07;0.03;0.88;-1.56;0.01;-0.09;-0.34;-1.8;-0.82;-0.16	5.7	3.1	0.35709	.	0.000000	0.56097	D	0.000029	D	0.84593	0.5506	L	0.54323	1.7	0.29256	N	0.871649	P;D;P;P;P;D;P;P	0.63880	0.651;0.993;0.651;0.61;0.896;0.989;0.651;0.73	B;D;B;B;P;D;B;P	0.72338	0.104;0.977;0.104;0.191;0.653;0.946;0.104;0.467	D	0.86361	0.1717	9	0.62326	D	0.03	.	13.6407	0.62249	0.0:0.0:0.3557:0.6442	.	1226;1226;1404;900;900;900;1226;900	Q5TBT1;E7ERU2;E9PEB9;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;DYST_HUMAN;.	G	900;1404;1226;1226;900;1226;1226;1226;900;1266;900;900	ENSP00000244364:R900G;ENSP00000359790:R1404G;ENSP00000359805:R1226G;ENSP00000400883:R1226G;ENSP00000393645:R900G;ENSP00000307959:R1226G;ENSP00000359824:R1226G;ENSP00000354508:R1226G;ENSP00000404924:R900G;ENSP00000431030:R1266G;ENSP00000359801:R900G;ENSP00000431003:R900G	ENSP00000244364:R900G	R	-	1	2	DST	56602173	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.296000	0.51802	0.953000	0.37825	0.533000	0.62120	AGA	.	.		0.328	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56494214	T	C	56494214	3	2	182	1	0	0	0	0	1	0	0	0	4785	1559	54	2	17725	2	DST	6	56494214	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	9519201	56494214	114620853	37	27167										
UTRN	7402	hgsc.bcm.edu	37	chr6	144783861	144783861	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gaagaaacaaaggctctggaGaaaaatgttcatcctgatgt	10	6	2	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr6:144783861G>T	ENST00000367545.3	+	22	2925	c.2925G>T	c.(2923-2925)gaG>gaT	p.E975D		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	975					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		AGGCTCTGGAGAAAAATGTTC	0.333																																					p.E975D		Atlas-SNP	.											.	UTRN	327	.	0			c.G2925T						.						61	71	67					6																	144783861		2202	4300	6502	SO:0001583	missense	7402	exon22			TCTGGAGAAAAAT	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.2925G>T	chr6.hg19:g.144783861G>T	ENSP00000356515:p.Glu975Asp	222.0	0.0		189.0	79.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.811625	0.32053	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.34859	1.34	5.36	4.49	0.54785	.	0.123547	0.36066	N	0.002801	T	0.11922	0.0290	L	0.32530	0.975	0.80722	D	1	B	0.32031	0.352	B	0.25759	0.063	T	0.05037	-1.0910	10	0.17832	T	0.49	.	13.6806	0.62481	0.074:0.0:0.926:0.0	.	975	P46939	UTRO_HUMAN	D	975	ENSP00000356515:E975D	ENSP00000356499:E975D	E	+	3	2	UTRN	144825554	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.721000	0.54941	1.243000	0.43853	0.655000	0.94253	GAG	.	.		0.333	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144783861	G	T	144783861	3	4	182	1	0	0	0	0	1	0	0	0	17118	933	33	3	3011	3	UTRN	6	144783861	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	88289647	144783861	26331206	38	27168										
UTRN	7402	hgsc.bcm.edu	37	chr6	144808683	144808683	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tttttcccatctccattccaGtctctggaatctgttctgcg	6	13	4	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr6:144808683G>T	ENST00000367545.3	+	28	3822		c.e28-1			NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin						aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		CTCCATTCCAGTCTCTGGAAT	0.403																																					.		Atlas-SNP	.											.	UTRN	327	.	0			c.3823-1G>T						.						58	64	62					6																	144808683		2203	4300	6503	SO:0001630	splice_region_variant	7402	exon28			ATTCCAGTCTCTG	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.3823-1G>T	chr6.hg19:g.144808683G>T		59.0	0.0		74.0	34.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Splice_Site	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	G	17.98	3.521423	0.64747	.	.	ENSG00000152818	ENST00000367545	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4129	0.94683	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UTRN	144850376	1.000000	0.71417	0.996000	0.52242	0.459000	0.32528	9.813000	0.99286	2.652000	0.90054	0.655000	0.94253	.	.	.		0.403	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		Intron	T	144808683	G	T	144808683	5	4	182	1	0	0	0	0	0	0	1	0	17118	1043	36	3	3932	3	UTRN	6	144808683	Splice_Site	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	24822	144808683	26306384	39	27169										
SP8	221833	hgsc.bcm.edu	37	chr7	20823935	20823935	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	taggccgttgcggtgcccggGctcggggggctgcagcagct	19	12	0	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr7:20823935G>C	ENST00000361443.4	-	3	1684	c.1447C>G	c.(1447-1449)Ccc>Gcc	p.P483A	SP8_ENST00000418710.2_Missense_Mutation_p.P501A	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	483					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						CGGTGCCCGGGCTCGGGGGGC	0.736																																					p.P501A		Atlas-SNP	.											.	SP8	43	.	0			c.C1501G						.						2	2	2					7																	20823935		1465	3031	4496	SO:0001583	missense	221833	exon2			GCCCGGGCTCGGG		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.1447C>G	chr7.hg19:g.20823935G>C	ENSP00000354482:p.Pro483Ala	15.0	0.0		22.0	6.0	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Missense_Mutation	SNP	ENST00000361443.4	hg19	CCDS5372.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.553651	0.65425	.	.	ENSG00000164651	ENST00000297210;ENST00000418710;ENST00000361443	T;T	0.12147	2.71;2.73	4.55	4.55	0.56014	.	0.166648	0.41500	U	0.000870	T	0.14141	0.0342	L	0.46157	1.445	0.37703	D	0.92428	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.04796	-1.0926	10	0.66056	D	0.02	.	12.4376	0.55608	0.0:0.1686:0.8314:0.0	.	483;483	Q7Z615;Q8IXZ3	.;SP8_HUMAN	A	459;501;483	ENSP00000408792:P501A;ENSP00000354482:P483A	ENSP00000297210:P459A	P	-	1	0	SP8	20790460	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	1.513000	0.35823	2.361000	0.80049	0.655000	0.94253	CCC	.	.		0.736	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			C	20823935	G	C	20823935	3	2	182	1	0	0	0	0	1	0	0	0	14985	1203	42	4	29	4	SP8	7	20823935	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10		20823935	138314728	40	27170										
LIMK1	3984	hgsc.bcm.edu	37	chr7	73521439	73521439	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tctgagtccctccgcgtagtCtgccggccacaccgcatctt	9	17	3	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr7:73521439C>G	ENST00000336180.2	+	8	1032	c.981C>G	c.(979-981)gtC>gtG	p.V327V	LIMK1_ENST00000538333.3_Silent_p.V293V|LIMK1_ENST00000418310.1_Silent_p.V357V	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	327					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	TCCGCGTAGTCTGCCGGCCAC	0.682																																					p.V327V		Atlas-SNP	.											.	LIMK1	55	.	0			c.C981G						.						38	36	37					7																	73521439		2203	4299	6502	SO:0001819	synonymous_variant	3984	exon8			CGTAGTCTGCCGG	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.981C>G	chr7.hg19:g.73521439C>G		78.0	0.0		92.0	39.0	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Silent	SNP	ENST00000336180.2	hg19	CCDS5563.1																																																																																			.	.		0.682	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		G	73521439	C	G	73521439	2	3	182	1	0	0	0	0	0	0	0	1	8810	900	32	4		4	LIMK1	7	73521439	Silent	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	52697504	73521439	85617224	41	27171										
HIP1	3092	hgsc.bcm.edu	37	chr7	75174049	75174049	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	aatttcatgagaacacaccaTtagctcctcaaatttccctc	3	13	2	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr7:75174049T>A	ENST00000336926.6	-	27	2736	c.2710A>T	c.(2710-2712)Atg>Ttg	p.M904L	HIP1_ENST00000434438.2_Missense_Mutation_p.M853L	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	904	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.|Important for actin binding. {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GAACACACCATTAGCTCCTCA	0.527			T	PDGFRB	CMML																																p.M904L		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A2710T						.						127	115	119					7																	75174049		2203	4300	6503	SO:0001583	missense	3092	exon27			ACACCATTAGCTC	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.2710A>T	chr7.hg19:g.75174049T>A	ENSP00000336747:p.Met904Leu	87.0	0.0		101.0	34.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	hg19	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	T	15.87	2.960048	0.53400	.	.	ENSG00000127946	ENST00000336926;ENST00000434438	T;T	0.38887	1.11;1.11	5.6	4.42	0.53409	I/LWEQ (4);	0.036491	0.85682	D	0.000000	T	0.40473	0.1118	L	0.56769	1.78	0.45318	D	0.998316	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.005	T	0.28902	-1.0029	10	0.72032	D	0.01	-29.6369	11.6222	0.51124	0.0:0.0:0.1493:0.8507	.	853;904	E7ES17;O00291	.;HIP1_HUMAN	L	904;853	ENSP00000336747:M904L;ENSP00000410300:M853L	ENSP00000336747:M904L	M	-	1	0	HIP1	75011985	1.000000	0.71417	0.900000	0.35374	0.985000	0.73830	4.906000	0.63293	0.926000	0.37118	0.533000	0.62120	ATG	.	.		0.527	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		A	75174049	T	A	75174049	3	1	182	1	0	0	0	0	1	0	0	0	7123	1493	52	4	423	4	HIP1	7	75174049	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	1652610	75174049	83964614	42	27172										
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107350597	107350597	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	atgatgctatactctatctaCagaaccaagtgaaatctcaa	5	9	3	3	rs397516428		TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr7:107350597C>G	ENST00000265715.3	+	19	2412	c.2188C>G	c.(2188-2190)Cag>Gag	p.Q730E	SLC26A4_ENST00000543100.1_Missense_Mutation_p.Q299E|SLC26A4_ENST00000544569.1_Missense_Mutation_p.Q317E|SLC26A4_ENST00000541474.1_Missense_Mutation_p.Q291E	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	730					chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						ACTCTATCTACAGAACCAAGT	0.363									Pendred syndrome																												p.Q730E		Atlas-SNP	.											.	SLC26A4	117	.	0			c.C2188G						.						109	101	104					7																	107350597		2203	4300	6503	SO:0001583	missense	5172	exon19	Familial Cancer Database	Goiter-Deafness syndrome	TATCTACAGAACC	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.2188C>G	chr7.hg19:g.107350597C>G	ENSP00000265715:p.Gln730Glu	130.0	0.0		134.0	62.0	NM_000441	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	hg19	CCDS5746.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.858313	0.32791	.	.	ENSG00000091137	ENST00000265715;ENST00000541474;ENST00000544569;ENST00000543100	D;D;D;D	0.95001	-3.19;-3.5;-3.55;-3.58	5.51	5.51	0.81932	.	0.216865	0.39146	N	0.001458	D	0.87103	0.6094	N	0.08118	0	0.29625	N	0.845925	B;B;B	0.09022	0.002;0.002;0.0	B;B;B	0.09377	0.004;0.003;0.001	T	0.77027	-0.2740	10	0.23302	T	0.38	.	15.287	0.73835	0.0:0.8604:0.1396:0.0	.	291;317;730	F5H104;B7Z6M6;O43511	.;.;S26A4_HUMAN	E	730;291;317;299	ENSP00000265715:Q730E;ENSP00000439743:Q291E;ENSP00000437427:Q317E;ENSP00000441209:Q299E	ENSP00000265715:Q730E	Q	+	1	0	SLC26A4	107137833	0.741000	0.28217	1.000000	0.80357	0.988000	0.76386	0.614000	0.24314	2.747000	0.94245	0.650000	0.86243	CAG	.	.		0.363	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		G	107350597	C	G	107350597	3	3	182	1	0	0	0	0	1	0	0	0	14534	479	17	4	2258	4	SLC26A4	7	107350597	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	32176548	107350597	51788066	43	27173										
WDR91	29062	hgsc.bcm.edu	37	chr7	134874129	134874129	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gacgccatcagctgcccctgTgaccagcaggttcccgttgt	11	15	1	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr7:134874129T>C	ENST00000354475.4	-	12	1766	c.1735A>G	c.(1735-1737)Aca>Gca	p.T579A	WDR91_ENST00000344400.5_Missense_Mutation_p.T579A|WDR91_ENST00000423565.1_Missense_Mutation_p.T544A	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	579										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						GCTGCCCCTGTGACCAGCAGG	0.468																																					p.T579A		Atlas-SNP	.											.	WDR91	82	.	0			c.A1735G						.						124	105	111					7																	134874129		2203	4300	6503	SO:0001583	missense	29062	exon12			CCCCTGTGACCAG	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.1735A>G	chr7.hg19:g.134874129T>C	ENSP00000346466:p.Thr579Ala	127.0	0.0		140.0	53.0	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	hg19	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	T	19.02	3.746033	0.69418	.	.	ENSG00000105875	ENST00000344400;ENST00000354475;ENST00000423565	T;T;T	0.66815	-0.23;-0.23;-0.23	4.62	3.44	0.39384	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.138419	0.64402	D	0.000003	T	0.71804	0.3383	M	0.64630	1.985	0.54753	D	0.999984	D	0.58268	0.982	P	0.54544	0.755	T	0.72544	-0.4261	10	0.54805	T	0.06	-12.018	10.8422	0.46722	0.1414:0.0:0.0:0.8586	.	579	A4D1P6	WDR91_HUMAN	A	579;579;544	ENSP00000340877:T579A;ENSP00000346466:T579A;ENSP00000392555:T544A	ENSP00000340877:T579A	T	-	1	0	WDR91	134524669	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	5.936000	0.70153	0.875000	0.35847	0.533000	0.62120	ACA	.	.		0.468	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		C	134874129	T	C	134874129	3	2	182	1	0	0	0	0	1	0	0	0	17353	1696	59	2	524	2	WDR91	7	134874129	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	27523532	134874129	24264534	44	27174										
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150761611	150761633	+	Splice_Site	DEL	TCCTCCCTGCAGACCACCGCCAG	TCCTCCCTGCAGACCACCGCCAG	-													0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	caagtccccctcctccctgcAgaccaccgccagtcctccca					rs143210272|rs387907523|rs1131280		TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	TCCTCCCTGCAGACCACCGCCAG	TCCTCCCTGCAGACCACCGCCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr7:150761611_150761633delTCCTCCCTGCAGACCACCGCCAG	ENST00000485713.1	+	4	1257_1278	c.217_238delTCCTCCCTGCAGACCACCGCCAG	c.(217-240)tcctccctgcagaccaccgccaga>ga	p.SSLQTTAR73fs	SLC4A2_ENST00000310317.5_Intron|SLC4A2_ENST00000461735.1_Splice_Site_p.SSLQTTAR59fs|SLC4A2_ENST00000413384.2_Splice_Site_p.SSLQTTAR73fs|SLC4A2_ENST00000392826.2_Splice_Site_p.SSLQTTAR64fs	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	73	Pro-rich.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)	p.Y73*(1)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCCTCCCTGCAGACCACCGCCAGTCCTCCCACCACATCCATCA	0.686																																					p.73_76del		Atlas-INDEL	.											.	SLC4A2	98	.	1	Substitution - Nonsense(1)	lung(1)	c.218_227del						.																																			SO:0001630	splice_region_variant	6522	exon4			.		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"Solute carriers"	11028	protein-coding gene	gene with protein product	"anion exchanger 2 type a", "anion exchanger 2 type b1", "anion exchanger 2 type b2"	109280	"erythrocyte membrane protein band 3-like 1", "solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.218-1TCCTCCCTGCAGACCACCGCCAG>-	chr7.hg19:g.150761611_150761633delTCCTCCCTGCAGACCACCGCCAG		88.0	0.0		91.0	24.0	NM_001199692	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Frame_Shift_Del	DEL	ENST00000485713.1	hg19	CCDS5917.1																																																																																			.	.		0.686	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	Frame_Shift_Del	-	150761633	TCCTCCCTGCAGACCACCGCCAG	-	150761611	8	5	182	1	0	1	0	1	0	0	1	0	14669	202	7	0	226	0	SLC4A2	7	150761611	Splice_Site	DEL	TCCTCCCTGCAGACCACCGCCAG	TCGA-DD-AAD6-01A-11D-A40R-10	15887482	150761611	8377052	45	27175										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124335222	124335222	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gtccttgcgatgccgataaaTacattggctgattactgcat	9	9	0	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr8:124335222T>C	ENST00000287394.5	-	27	4194	c.4087A>G	c.(4087-4089)Att>Gtt	p.I1363V	ATAD2_ENST00000521903.1_Missense_Mutation_p.I681V	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	1363					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			TGCCGATAAATACATTGGCTG	0.308																																					p.I1363V		Atlas-SNP	.											.	ATAD2	160	.	0			c.A4087G						.						149	140	143					8																	124335222		2203	4300	6503	SO:0001583	missense	29028	exon27			GATAAATACATTG	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.4087A>G	chr8.hg19:g.124335222T>C	ENSP00000287394:p.Ile1363Val	86.0	0.0		338.0	273.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	T	19.96	3.923980	0.73213	.	.	ENSG00000156802	ENST00000287394;ENST00000521903	D;T	0.94330	-3.4;1.07	5.66	5.66	0.87406	.	0.251992	0.43919	N	0.000514	D	0.91901	0.7436	M	0.71206	2.165	0.45035	D	0.998055	P	0.49559	0.925	B	0.38683	0.279	D	0.92303	0.5851	10	0.51188	T	0.08	-20.9848	15.5544	0.76180	0.0:0.0:0.0:1.0	.	1363	Q6PL18	ATAD2_HUMAN	V	1363;681	ENSP00000287394:I1363V;ENSP00000429213:I681V	ENSP00000287394:I1363V	I	-	1	0	ATAD2	124404403	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.212000	0.58514	2.143000	0.66587	0.533000	0.62120	ATT	.	.		0.308	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		C	124335222	T	C	124335222	3	2	182	1	0	0	0	0	1	0	0	0	1071	1406	49	2	93	2	ATAD2	8	124335222	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10		124335222	22028800	46	27176										
FAM135B	51059	hgsc.bcm.edu	37	chr8	139263244	139263244	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gctgaccatcggtgccccagCcacatccctcaacctagaag	8	17	1	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr8:139263244C>A	ENST00000395297.1	-	6	552	c.382G>T	c.(382-384)Gct>Tct	p.A128S		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	128										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GGTGCCCCAGCCACATCCCTC	0.577										HNSCC(54;0.14)																											p.A128S		Atlas-SNP	.											.	FAM135B	423	.	0			c.G382T						.						86	98	94					8																	139263244		2152	4250	6402	SO:0001583	missense	51059	exon6			CCCCAGCCACATC	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.382G>T	chr8.hg19:g.139263244C>A	ENSP00000378710:p.Ala128Ser	84.0	0.0		310.0	45.0	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	hg19	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	5.616	0.298356	0.10622	.	.	ENSG00000147724	ENST00000395297;ENST00000160713	T	0.13538	2.58	5.61	1.61	0.23674	.	0.291323	0.31601	N	0.007368	T	0.03390	0.0098	N	0.02539	-0.55	0.09310	N	1	B	0.18461	0.028	B	0.21360	0.034	T	0.38993	-0.9635	10	0.07482	T	0.82	-12.3262	2.0699	0.03611	0.1163:0.4419:0.2154:0.2264	.	128	Q49AJ0	F135B_HUMAN	S	128	ENSP00000378710:A128S	ENSP00000160713:A128S	A	-	1	0	FAM135B	139332426	0.737000	0.28175	0.931000	0.37212	0.587000	0.36485	0.433000	0.21477	0.310000	0.22990	0.655000	0.94253	GCT	.	.		0.577	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		A	139263244	C	A	139263244	3	1	182	1	0	0	0	0	1	0	0	0	5454	739	26	3	3898	3	FAM135B	8	139263244	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	14928022	139263244	7100778	47	27177										
PTK2	5747	hgsc.bcm.edu	37	chr8	141745494	141745494	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	caattcgaccgattacatcaTtgttcttcactccttgaaaa	4	11	3	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr8:141745494T>C	ENST00000522684.1	-	22	2115	c.1886A>G	c.(1885-1887)aAt>aGt	p.N629S	PTK2_ENST00000517887.1_Missense_Mutation_p.N673S|PTK2_ENST00000519465.1_Missense_Mutation_p.N257S|PTK2_ENST00000521059.1_Missense_Mutation_p.N629S|PTK2_ENST00000535192.1_Missense_Mutation_p.N629S|PTK2_ENST00000519419.1_Missense_Mutation_p.N673S|PTK2_ENST00000395218.2_Missense_Mutation_p.N629S|PTK2_ENST00000538769.1_Missense_Mutation_p.N297S|MIR151A_ENST00000521276.1_RNA|PTK2_ENST00000340930.3_Missense_Mutation_p.N629S	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	629	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			GATTACATCATTGTTCTTCAC	0.443																																					p.N651S		Atlas-SNP	.											.	PTK2	311	.	0			c.A1952G						.						171	145	154					8																	141745494		2203	4300	6503	SO:0001583	missense	5747	exon22			ACATCATTGTTCT	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9611	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 71"	600758	"PTK2 protein tyrosine kinase 2"			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.1886A>G	chr8.hg19:g.141745494T>C	ENSP00000429911:p.Asn629Ser	106.0	0.0		218.0	153.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.238905	0.79800	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000521986;ENST00000342207	D;D;D;D;D;D;D;D;D;D;D	0.81908	-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55	5.51	5.51	0.81932	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.75287	0.3829	N	0.11651	0.15	0.58432	D	0.999999	P;P;B;P;B;P;B;B;B;B	0.48162	0.906;0.883;0.16;0.887;0.092;0.861;0.16;0.094;0.019;0.008	P;P;B;P;B;B;B;B;B;B	0.49953	0.627;0.49;0.096;0.52;0.151;0.438;0.09;0.171;0.029;0.011	T	0.73780	-0.3875	10	0.16896	T	0.51	.	15.6208	0.76805	0.0:0.0:0.0:1.0	.	629;324;549;629;651;629;581;477;297;257	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	S	629;629;257;673;629;581;629;550;324;301;629;297;673;327;475	ENSP00000429911:N629S;ENSP00000438009:N629S;ENSP00000429170:N257S;ENSP00000429082:N673S;ENSP00000429474:N629S;ENSP00000378644:N629S;ENSP00000428492:N301S;ENSP00000341189:N629S;ENSP00000445742:N297S;ENSP00000429129:N673S;ENSP00000430603:N327S	ENSP00000341189:N629S	N	-	2	0	PTK2	141814676	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.859000	0.86982	2.098000	0.63641	0.533000	0.62120	AAT	.	.		0.443	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		C	141745494	T	C	141745494	3	2	182	1	0	0	0	0	1	0	0	0	12775	1493	52	2	1316	2	PTK2	8	141745494	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	2482250	141745494	4618528	48	27178										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21971108	21971108	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gaagccctcccgggcagcgtCgtgcacgggtcgggtgagag	18	12	0	1	rs11552822		TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr9:21971108C>A	ENST00000304494.5	-	2	520	c.250G>T	c.(250-252)Gac>Tac	p.D84Y	CDKN2A_ENST00000494262.1_Missense_Mutation_p.D33Y|CDKN2A_ENST00000446177.1_Missense_Mutation_p.D84Y|CDKN2A_ENST00000479692.2_Missense_Mutation_p.D33Y|CDKN2A_ENST00000578845.2_Missense_Mutation_p.D33Y|CDKN2A_ENST00000579755.1_Missense_Mutation_p.R98L|CDKN2A_ENST00000530628.2_Missense_Mutation_p.R98L|CDKN2A_ENST00000497750.1_Missense_Mutation_p.D33Y|CDKN2A_ENST00000498124.1_Missense_Mutation_p.D84Y|CDKN2A_ENST00000498628.2_Missense_Mutation_p.D33Y|CDKN2A_ENST00000579122.1_Missense_Mutation_p.D84Y|CDKN2A_ENST00000361570.3_Missense_Mutation_p.R139L|RP11-145E5.5_ENST00000404796.2_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	84			D -> E (in a bladder tumor).|D -> H (in non-small cell lung carcinoma). {ECO:0000269|PubMed:8060323}.|D -> N (in an esophagus, a head and neck and a lung tumor).|D -> Y (in CMM2; also found in a lung and a prostate tumor; dbSNP:rs11552822). {ECO:0000269|PubMed:10874641}.		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(44)|p.D84Y(11)|p.D84N(7)|p.D84fs*63(2)|p.D84H(2)|p.H83fs*2(2)|p.R139Q(2)|p.D84fs*1(1)|p.D84_F90del(1)|p.R139L(1)|p.0(1)|p.V82_G89>G(1)|p.E61_L94del(1)|p.R137fs*48(1)|p.A68fs*3(1)|p.P81_A85del(1)|p.R80fs*34(1)|p.V82_E88del(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CGGGCAGCGTCGTGCACGGGT	0.741	D84Y(DU145_PROSTATE)|D84Y(LK2_LUNG)	17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.R98L		Atlas-SNP	.											CDKN2A_ENST00000498124,left_upper_lobe,carcinoma,0,3	CDKN2A	4810	.	1396	Whole gene deletion(1316)|Unknown(44)|Substitution - Missense(23)|Deletion - Frameshift(5)|Deletion - In frame(4)|Insertion - Frameshift(3)|Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(283)|skin(175)|central_nervous_system(170)|lung(154)|urinary_tract(91)|bone(74)|soft_tissue(57)|oesophagus(54)|upper_aerodigestive_tract(52)|pleura(51)|ovary(36)|kidney(32)|breast(32)|pancreas(30)|biliary_tract(15)|thyroid(13)|NS(12)|stomach(12)|prostate(11)|autonomic_ganglia(9)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(5)|thymus(4)|vulva(2)|endometrium(2)|genital_tract(1)	c.G293T	GRCh37	CM085316|CM990358	CDKN2A	M	rs11552822	.						13	16	15					9																	21971108		2178	4258	6436	SO:0001583	missense	1029	exon2			CAGCGTCGTGCAC	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.250G>T	chr9.hg19:g.21971108C>A	ENSP00000307101:p.Asp84Tyr	113.0	0.0		104.0	43.0	NM_058195	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	hg19	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.137500|5.137500	0.94517|0.94517	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000304494;ENST00000446177|ENST00000361570;ENST00000530628	D;D|D;D	0.94232|0.84070	-3.38;-3.38|-1.8;-1.73	5.93|5.93	5.93|5.93	0.95920|0.95920	Ankyrin repeat-containing domain (4);|.	.|0.000000	.|0.30428	.|N	.|0.009646	D|D	0.87744|0.87744	0.6254|0.6254	L|L	0.32530|0.32530	0.975|0.975	0.49213|0.49213	D|D	0.999766|0.999766	D|D	0.89917|0.89917	1.0|1.0	D|D	0.97110|0.91635	1.0|0.999	D|D	0.88398|0.88398	0.3013|0.3013	9|10	0.02654|0.87932	T|D	1|0	-18.6892|-18.6892	19.1221|19.1221	0.93367|0.93367	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs11552822|rs11552822	84|139	P42771|Q8N726	CD2A1_HUMAN|CD2A2_HUMAN	Y|L	84|139;98	ENSP00000307101:D84Y;ENSP00000394932:D84Y|ENSP00000355153:R139L;ENSP00000432664:R98L	ENSP00000307101:D84Y|ENSP00000355153:R139L	D|R	-|-	1|2	0|0	CDKN2A|CDKN2A	21961108|21961108	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	6.879000|6.879000	0.75572|0.75572	2.808000|2.808000	0.96608|0.96608	0.655000|0.655000	0.94253|0.94253	GAC|CGA	.	C|1.000;|0.000		0.741	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		A	21971108	C	A	21971108	3	1	182	1	0	0	0	0	1	0	0	0	3163	884	31	1	228	1	CDKN2A	9	21971108	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10		21971108	119242323	49	27179										
UBAP2	54926	hgsc.bcm.edu	37	chr9	33922747	33922747	+	IGR	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gggctgctggtgggctggcaAgatgtgtaggaatggtgggg	22	4	0	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr9:33922747A>T	ENST00000263228.3	+	0	4075				UBAP2_ENST00000379235.1_Missense_Mutation_p.L307M|UBAP2_ENST00000539807.1_Missense_Mutation_p.L823M|UBAP2_ENST00000379239.4_Missense_Mutation_p.L801M|UBAP2_ENST00000379238.1_Missense_Mutation_p.L1068M|UBAP2_ENST00000360802.1_Missense_Mutation_p.L1068M|UBAP2_ENST00000449054.1_Missense_Mutation_p.L1068M	NM_017811.3	NP_060281.2	Q712K3	UB2R2_HUMAN	ubiquitin-conjugating enzyme E2R 2						protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8			LUSC - Lung squamous cell carcinoma(29;0.0176)	GBM - Glioblastoma multiforme(74;0.188)		TGGGCTGGCAAGATGTGTAGG	0.657																																					p.L1068M		Atlas-SNP	.											.	UBAP2	82	.	0			c.T3202A						.						65	75	71					9																	33922747		2203	4300	6503	SO:0001628	intergenic_variant	55833	exon28			CTGGCAAGATGTG	AK000426	CCDS6546.1	9p11.2	2008-02-05			ENSG00000107341	ENSG00000107341		"Ubiquitin-conjugating enzymes E2"	19907	protein-coding gene	gene with protein product		612506				12037680	Standard	XM_005251496		Approved	UBC3B, CDC34B, FLJ20419, MGC10481	uc003ztm.3	Q712K3	OTTHUMG00000019797		chr9.hg19:g.33922747A>T		56.0	0.0		69.0	37.0	NM_018449	D3DRL5|Q9NX64	Missense_Mutation	SNP	ENST00000263228.3	hg19	CCDS6546.1	.	.	.	.	.	.	.	.	.	.	A	12.50	1.957106	0.34565	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379235;ENST00000379239;ENST00000539807;ENST00000351580	T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63	5.65	2.4	0.29515	.	0.065811	0.64402	N	0.000006	T	0.28699	0.0711	N	0.20357	0.565	0.80722	D	1	P;P;P;P	0.42785	0.565;0.79;0.79;0.686	B;B;B;B	0.40256	0.324;0.324;0.324;0.133	T	0.02345	-1.1173	10	0.28530	T	0.3	-5.8834	7.6108	0.28129	0.1029:0.0:0.7484:0.1487	.	823;801;977;1068	F5H2U4;A6NCA8;F5H2C8;Q5T6F2	.;.;.;UBAP2_HUMAN	M	1068;1068;1068;977;307;801;823;502	ENSP00000368540:L1068M;ENSP00000416932:L1068M;ENSP00000354039:L1068M;ENSP00000368537:L307M;ENSP00000368541:L801M;ENSP00000439329:L823M	ENSP00000259602:L502M	L	-	1	2	UBAP2	33912747	1.000000	0.71417	0.997000	0.53966	0.341000	0.28922	2.938000	0.48987	0.291000	0.22468	0.533000	0.62120	TTG	.	.		0.657	UBE2R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052118.1	NM_017811		T	33922747	A	T	33922747	1	4	182	0	1	0	0	0	0	0	0	0	16852	69	3	4		4	UBAP2	9	33922747	IGR	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	11951639	33922747	107290684	50	27180										
FOXE1	2304	hgsc.bcm.edu	37	chr9	100616728	100616728	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ccgccgccgccgccgccgccGccgccatcttcccaggcgcg	12	24	1	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr9:100616728G>A	ENST00000375123.3	+	1	1193	c.532G>A	c.(532-534)Gcc>Acc	p.A178T		NM_004473.3	NP_004464.2	O00358	FOXE1_HUMAN	forkhead box E1 (thyroid transcription factor 2)	178	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|cell migration (GO:0016477)|embryonic organ morphogenesis (GO:0048562)|hair follicle morphogenesis (GO:0031069)|hard palate development (GO:0060022)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pharynx development (GO:0060465)|positive regulation of transcription, DNA-templated (GO:0045893)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(62;0.158)				cgccgccgccgccgccATCTT	0.791																																					p.A178T		Atlas-SNP	.											.	FOXE1	19	.	0			c.G532A						.						2	2	2					9																	100616728		529	1359	1888	SO:0001583	missense	2304	exon1			GCCGCCGCCGCCA	U89995	CCDS35078.1	9q22	2008-09-05			ENSG00000178919	ENSG00000178919		"Forkhead boxes"	3806	protein-coding gene	gene with protein product		602617	"forkhead box E2"	FKHL15, TITF2, FOXE2		9169137, 9697705	Standard	NM_004473		Approved	TTF-2, HFKH4	uc004axu.3	O00358	OTTHUMG00000020333	ENST00000375123.3:c.532G>A	chr9.hg19:g.100616728G>A	ENSP00000364265:p.Ala178Thr	123.0	0.0		212.0	14.0	NM_004473	O75765|Q5T109|Q99526	Missense_Mutation	SNP	ENST00000375123.3	hg19	CCDS35078.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.930555	0.52866	.	.	ENSG00000178919	ENST00000375123	D	0.93953	-3.32	3.94	3.02	0.34903	.	0.612880	0.14474	U	0.317365	D	0.83087	0.5178	L	0.34521	1.04	0.22571	N	0.998979	P	0.47253	0.892	B	0.30251	0.113	T	0.72969	-0.4130	10	0.13108	T	0.6	.	6.9037	0.24297	0.0993:0.1791:0.7216:0.0	.	178	O00358	FOXE1_HUMAN	T	178	ENSP00000364265:A178T	ENSP00000364265:A178T	A	+	1	0	FOXE1	99656549	0.087000	0.21565	0.898000	0.35279	0.822000	0.46500	0.422000	0.21296	0.758000	0.33059	0.557000	0.71058	GCC	.	.		0.791	FOXE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053341.1			A	100616728	G	A	100616728	3	1	182	1	0	0	0	0	1	0	0	0	6011	1087	38	1	534	1	FOXE1	9	100616728	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	66693981	100616728	40596703	51	27181										
C9orf86	55684	hgsc.bcm.edu	37	chr9	139733868	139733868	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ccccgagggacccattgctgCacaaatgctgtccttcgtca	9	15	1	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr9:139733868C>A	ENST00000311502.7	+	12	1924	c.1688C>A	c.(1687-1689)gCa>gAa	p.A563E	RABL6_ENST00000371663.4_Missense_Mutation_p.A564E|RABL6_ENST00000371675.3_Missense_Mutation_p.A448E|RABL6_ENST00000357466.2_Intron|RABL6_ENST00000432842.2_3'UTR			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	563					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										CCCATTGCTGCACAAATGCTG	0.642																																					p.A564E		Atlas-SNP	.											.	.	.	.	0			c.C1691A						.						36	43	40					9																	139733868		2124	4246	6370	SO:0001583	missense	55684	exon12			TTGCTGCACAAAT	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"Rab-like protein 1", "partner of ARF"	610615	"chromosome 9 open reading frame 86"	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1688C>A	chr9.hg19:g.139733868C>A	ENSP00000311134:p.Ala563Glu	124.0	0.0		146.0	98.0	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Missense_Mutation	SNP	ENST00000311502.7	hg19	CCDS48058.1	.	.	.	.	.	.	.	.	.	.	.	14.65	2.598707	0.46318	.	.	ENSG00000196642	ENST00000371663;ENST00000311502;ENST00000371675;ENST00000435930	T;T;T;T	0.64618	-0.1;-0.11;-0.1;-0.1	4.46	4.46	0.54185	.	0.290065	0.34725	N	0.003737	T	0.73690	0.3619	L	0.57536	1.79	0.36204	D	0.850934	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76575	0.988;0.983;0.963	T	0.75156	-0.3417	10	0.21014	T	0.42	-27.9152	15.6762	0.77326	0.0:1.0:0.0:0.0	.	357;564;563	B1AMX5;Q3YEC7-2;Q3YEC7	.;.;PARF_HUMAN	E	564;563;448;357	ENSP00000360727:A564E;ENSP00000311134:A563E;ENSP00000360740:A448E;ENSP00000408442:A357E	ENSP00000311134:A563E	A	+	2	0	C9orf86	138853689	0.874000	0.30092	0.999000	0.59377	0.253000	0.25986	4.122000	0.57910	2.037000	0.60232	0.462000	0.41574	GCA	.	.		0.642	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718		A	139733868	C	A	139733868	3	1	182	1	0	0	0	0	1	0	0	0	2504	710	25	3	1981	3	C9orf86	9	139733868	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	39117140	139733868	1479563	52	27182			1	37		2	2	21	N	C_A	6.718832e-05
C9orf86	55684	hgsc.bcm.edu	37	chr9	139733888	139733888	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cacaaatgctgtccttcgtcAtggatgaccccgactttgag	9	12	1	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr9:139733888A>C	ENST00000311502.7	+	12	1944	c.1708A>C	c.(1708-1710)Atg>Ctg	p.M570L	RABL6_ENST00000371663.4_Missense_Mutation_p.M571L|RABL6_ENST00000371675.3_Missense_Mutation_p.M455L|RABL6_ENST00000357466.2_Intron|RABL6_ENST00000432842.2_3'UTR			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	570					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										GTCCTTCGTCATGGATGACCC	0.647																																					p.M571L		Atlas-SNP	.											.	.	.	.	0			c.A1711C						.						36	41	39					9																	139733888		2124	4243	6367	SO:0001583	missense	55684	exon12			TTCGTCATGGATG	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"Rab-like protein 1", "partner of ARF"	610615	"chromosome 9 open reading frame 86"	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1708A>C	chr9.hg19:g.139733888A>C	ENSP00000311134:p.Met570Leu	129.0	0.0		166.0	108.0	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Missense_Mutation	SNP	ENST00000311502.7	hg19	CCDS48058.1	.	.	.	.	.	.	.	.	.	.	.	18.14	3.558594	0.65538	.	.	ENSG00000196642	ENST00000371663;ENST00000311502;ENST00000371675;ENST00000435930	T;T;T;T	0.74632	-0.59;-0.62;-0.61;-0.86	4.46	3.29	0.37713	.	0.000000	0.85682	D	0.000000	D	0.82857	0.5128	M	0.78049	2.395	0.58432	D	0.999993	D;P;P	0.56746	0.977;0.91;0.855	D;D;P	0.69654	0.965;0.909;0.813	T	0.79533	-0.1764	10	0.29301	T	0.29	-35.0482	10.0402	0.42153	0.8298:0.1702:0.0:0.0	.	364;571;570	B1AMX5;Q3YEC7-2;Q3YEC7	.;.;PARF_HUMAN	L	571;570;455;364	ENSP00000360727:M571L;ENSP00000311134:M570L;ENSP00000360740:M455L;ENSP00000408442:M364L	ENSP00000311134:M570L	M	+	1	0	C9orf86	138853709	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	5.018000	0.64054	0.562000	0.29204	-0.648000	0.03929	ATG	.	.		0.647	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718		C	139733888	A	C	139733888	3	2	182	1	0	0	0	0	1	0	0	0	2504	217	8	5	2001	5	C9orf86	9	139733888	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	20	139733888	1479543	53	27183			1	37		2	2	21	N	C_A	6.718832e-05
ADARB2	105	hgsc.bcm.edu	37	chr10	1405703	1405703	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gggcccccgcccatggccagGtgcgcctggcaggcgttggg	18	15	0	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr10:1405703G>T	ENST00000381312.1	-	3	922	c.597C>A	c.(595-597)caC>caA	p.H199Q	RP11-398B16.2_ENST00000432987.1_RNA	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	199					mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		ccATGGCCAGGTGCGCCTGGC	0.711																																					p.H199Q		Atlas-SNP	.											.	ADARB2	95	.	0			c.C597A						.						18	18	18					10																	1405703		2199	4299	6498	SO:0001583	missense	105	exon3			GGCCAGGTGCGCC	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.597C>A	chr10.hg19:g.1405703G>T	ENSP00000370713:p.His199Gln	115.0	0.0		131.0	55.0	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	hg19	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627245	0.28978	.	.	ENSG00000185736	ENST00000381312	T	0.25085	1.82	5.15	1.07	0.20283	.	0.046737	0.85682	N	0.000000	T	0.27063	0.0663	M	0.70595	2.14	0.80722	D	1	B	0.13145	0.007	B	0.17722	0.019	T	0.06391	-1.0829	10	0.52906	T	0.07	-23.5633	10.1953	0.43051	0.1288:0.2205:0.6507:0.0	.	199	Q9NS39	RED2_HUMAN	Q	199	ENSP00000370713:H199Q	ENSP00000370713:H199Q	H	-	3	2	ADARB2	1395703	1.000000	0.71417	0.531000	0.27976	0.776000	0.43924	2.332000	0.43903	-0.302000	0.08869	-1.134000	0.01955	CAC	.	.		0.711	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		T	1405703	G	T	1405703	3	4	182	1	0	0	0	0	1	0	0	0	283	1252	44	3	1654	3	ADARB2	10	1405703	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10		1405703	134129044	54	27184										
CUBN	8029	hgsc.bcm.edu	37	chr10	17087153	17087153	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gggtagttgggagatatgaaCgtgccgcttgaagtggtgag	18	4	0	4			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr10:17087153C>A	ENST00000377833.4	-	25	3590	c.3525G>T	c.(3523-3525)acG>acT	p.T1175T		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1175	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAGATATGAACGTGCCGCTTG	0.478																																					p.T1175T		Atlas-SNP	.											.	CUBN	515	.	0			c.G3525T						.						158	147	151					10																	17087153		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon25			TATGAACGTGCCG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.3525G>T	chr10.hg19:g.17087153C>A		162.0	0.0		158.0	63.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.		0.478	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	17087153	C	A	17087153	2	1	182	1	0	0	0	0	0	0	0	1	4053	523	19	1		1	CUBN	10	17087153	Silent	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	15681450	17087153	118447594	55	27185										
CUBN	8029	hgsc.bcm.edu	37	chr10	17113590	17113590	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	atgaccccttctccagttaaTtcatccccgcaagctgtaag	6	14	2	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr10:17113590T>G	ENST00000377833.4	-	19	2525	c.2460A>C	c.(2458-2460)gaA>gaC	p.E820D		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	820	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CTCCAGTTAATTCATCCCCGC	0.408																																					p.E820D		Atlas-SNP	.											.	CUBN	515	.	0			c.A2460C						.						50	52	52					10																	17113590		2203	4300	6503	SO:0001583	missense	8029	exon19			AGTTAATTCATCC	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2460A>C	chr10.hg19:g.17113590T>G	ENSP00000367064:p.Glu820Asp	34.0	0.0		35.0	15.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	13.63	2.293445	0.40594	.	.	ENSG00000107611	ENST00000377833	T	0.18502	2.21	5.31	-3.33	0.04958	CUB (5);	0.629948	0.12957	N	0.425337	T	0.10035	0.0246	L	0.34521	1.04	0.09310	N	1	B	0.30439	0.279	B	0.31869	0.137	T	0.33599	-0.9862	10	0.23891	T	0.37	.	6.1085	0.20087	0.1057:0.5383:0.1506:0.2054	.	820	O60494	CUBN_HUMAN	D	820	ENSP00000367064:E820D	ENSP00000367064:E820D	E	-	3	2	CUBN	17153596	0.004000	0.15560	0.005000	0.12908	0.827000	0.46813	-0.095000	0.11077	-0.522000	0.06417	0.411000	0.27672	GAA	.	.		0.408	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17113590	T	G	17113590	3	3	182	1	0	0	0	0	1	0	0	0	4053	1490	52	5	8607	5	CUBN	10	17113590	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	26437	17113590	118421157	56	27186										
CTNNA3	29119	hgsc.bcm.edu	37	chr10	69407267	69407267	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	atgtgattggtgtttcagctGacatgctgcctgtgcacaaa	11	8	1	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr10:69407267G>A	ENST00000433211.2	-	2	179	c.5C>T	c.(4-6)tCa>tTa	p.S2L	CTNNA3_ENST00000545309.1_Missense_Mutation_p.S2L|CTNNA3_ENST00000373744.4_Missense_Mutation_p.S2L	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						TGTTTCAGCTGACATGCTGCC	0.388																																					p.S2L		Atlas-SNP	.											.	CTNNA3	401	.	0			c.C5T						.						138	130	133					10																	69407267		2203	4300	6503	SO:0001583	missense	29119	exon2			TCAGCTGACATGC	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.5C>T	chr10.hg19:g.69407267G>A	ENSP00000389714:p.Ser2Leu	54.0	0.0		55.0	26.0	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	hg19	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.680412	0.47886	.	.	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000545309;ENST00000330298;ENST00000540598	T;T;T;T	0.60171	1.37;1.37;0.49;0.21	5.71	5.71	0.89125	.	0.254034	0.23736	N	0.045067	T	0.52370	0.1730	L	0.43152	1.355	0.31834	N	0.624397	B;P;B	0.35575	0.437;0.51;0.041	B;B;B	0.33620	0.14;0.167;0.023	T	0.65393	-0.6179	10	0.87932	D	0	-4.4896	16.7673	0.85527	0.0:0.0:1.0:0.0	.	2;2;2	F2Z2R0;Q9UI47-2;Q9UI47	.;.;CTNA3_HUMAN	L	2	ENSP00000389714:S2L;ENSP00000362849:S2L;ENSP00000441444:S2L;ENSP00000330570:S2L	ENSP00000330570:S2L	S	-	2	0	CTNNA3	69077273	1.000000	0.71417	0.984000	0.44739	0.442000	0.32017	5.536000	0.67180	2.688000	0.91661	0.655000	0.94253	TCA	.	.		0.388	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		A	69407267	G	A	69407267	3	1	182	1	0	0	0	0	1	0	0	0	4016	1294	45	3	2750	3	CTNNA3	10	69407267	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	52293677	69407267	66127480	57	27187										
KIF11	3832	hgsc.bcm.edu	37	chr10	94373259	94373259	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	attactgcccttgtagaaagAacacctcatgttccttatcg	6	11	1	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr10:94373259A>T	ENST00000260731.3	+	8	1005	c.915A>T	c.(913-915)agA>agT	p.R305S		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	305	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)			breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TTGTAGAAAGAACACCTCATG	0.428																																					p.R305S	Colon(47;212 1003 2764 4062 8431)	Atlas-SNP	.											.	KIF11	58	.	0			c.A915T						.						98	99	99					10																	94373259		2203	4300	6503	SO:0001583	missense	3832	exon8			AGAAAGAACACCT	X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"Kinesins"	6388	protein-coding gene	gene with protein product		148760	"kinesin-like 1"	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.915A>T	chr10.hg19:g.94373259A>T	ENSP00000260731:p.Arg305Ser	107.0	0.0		96.0	43.0	NM_004523	A0AV49|B2RMV3|Q15716|Q5VWX0	Missense_Mutation	SNP	ENST00000260731.3	hg19	CCDS7422.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.993775	0.74703	.	.	ENSG00000138160	ENST00000260731	D	0.85258	-1.96	5.58	5.58	0.84498	Kinesin, motor domain (3);	0.107189	0.64402	D	0.000005	T	0.80854	0.4703	L	0.31065	0.9	0.58432	D	0.999991	P	0.38788	0.647	B	0.40534	0.332	T	0.83177	-0.0091	10	0.72032	D	0.01	.	15.7561	0.78025	1.0:0.0:0.0:0.0	.	305	P52732	KIF11_HUMAN	S	305	ENSP00000260731:R305S	ENSP00000260731:R305S	R	+	3	2	KIF11	94363239	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.298000	0.51818	2.115000	0.64714	0.482000	0.46254	AGA	.	.		0.428	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523		T	94373259	A	T	94373259	3	4	182	1	0	0	0	0	1	0	0	0	8281	243	9	4	945	4	KIF11	10	94373259	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	24965992	94373259	41161488	58	27188										
COX15	1355	hgsc.bcm.edu	37	chr10	101491746	101491746	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	aggcgctgccctaggagccaGgagcggcagatactgcctcc	14	14	0	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr10:101491746G>A	ENST00000016171.5	-	1	111	c.61C>T	c.(61-63)Ctg>Ttg	p.L21L	COX15_ENST00000370483.5_Silent_p.L21L|CUTC_ENST00000370476.5_5'Flank|CUTC_ENST00000493385.1_Intron			Q7KZN9	COX15_HUMAN	cytochrome c oxidase assembly homolog 15 (yeast)	21					cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		CTAGGAGCCAGGAGCGGCAGA	0.607																																					p.L21L		Atlas-SNP	.											.	COX15	25	.	0			c.C61T						.						35	28	30					10																	101491746		2203	4300	6503	SO:0001819	synonymous_variant	1355	exon1			GAGCCAGGAGCGG	AF044323	CCDS7481.1, CCDS7482.1	10q24	2014-09-17	2012-10-15		ENSG00000014919	ENSG00000014919		"Mitochondrial respiratory chain complex assembly factors"	2263	protein-coding gene	gene with protein product		603646	"COX15 (yeast) homolog, cytochrome c oxidase assembly protein", "COX15 homolog, cytochrome c oxidase assembly protein (yeast)"			9878253	Standard	NM_078470		Approved		uc001kqb.4	Q7KZN9	OTTHUMG00000018893	ENST00000016171.5:c.61C>T	chr10.hg19:g.101491746G>A		181.0	0.0		183.0	96.0	NM_078470	A8K6I9|O60556|O75878|Q5TD00|Q5TD01|Q7Z3Q3|Q9NTN0	Silent	SNP	ENST00000016171.5	hg19	CCDS7482.1																																																																																			.	.		0.607	COX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049818.1	NP_510870		A	101491746	G	A	101491746	2	1	182	1	0	0	0	0	0	0	0	1	3766	991	35	3		3	COX15	10	101491746	Silent	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	7118487	101491746	34043001	59	27189										
OTUB1	55611	hgsc.bcm.edu	37	chr11	63765004	63765004	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	accggcctggacactacgatAtcctctacaaatagggctgg	10	12	1	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr11:63765004A>G	ENST00000538426.1	+	7	846	c.802A>G	c.(802-804)Atc>Gtc	p.I268V	OTUB1_ENST00000428192.2_Missense_Mutation_p.I268V|OTUB1_ENST00000543004.1_Missense_Mutation_p.I277V|OTUB1_ENST00000541478.1_Missense_Mutation_p.I167V|OTUB1_ENST00000422031.2_Missense_Mutation_p.I305V|OTUB1_ENST00000543988.1_Missense_Mutation_p.I238V|OTUB1_ENST00000535715.1_Intron	NM_017670.2	NP_060140.2	Q96FW1	OTUB1_HUMAN	OTU deubiquitinase, ubiquitin aldehyde binding 1	268	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|immune system process (GO:0002376)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein K48-linked deubiquitination (GO:0071108)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	NEDD8-specific protease activity (GO:0019784)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	6						ACACTACGATATCCTCTACAA	0.597																																					p.I268V		Atlas-SNP	.											.	OTUB1	19	.	0			c.A802G						.						71	70	70					11																	63765004		2201	4297	6498	SO:0001583	missense	55611	exon7			TACGATATCCTCT	AY177200	CCDS8055.1	11q13.1	2014-02-24	2014-02-24			ENSG00000167770		"OTU domain containing"	23077	protein-coding gene	gene with protein product		608337	"OTU domain, ubiquitin aldehyde binding 1"			12704427, 19383985	Standard	NM_017670		Approved	FLJ20113, FLJ40710	uc001nyf.1	Q96FW1		ENST00000538426.1:c.802A>G	chr11.hg19:g.63765004A>G	ENSP00000444357:p.Ile268Val	60.0	0.0		25.0	18.0	NM_017670	Q32Q78|Q96II3|Q9NXQ4|Q9P0B8	Missense_Mutation	SNP	ENST00000538426.1	hg19	CCDS8055.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.773126	0.49680	.	.	ENSG00000167770	ENST00000541478;ENST00000428192;ENST00000422031;ENST00000538426;ENST00000543004;ENST00000543988	T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86	5.17	2.72	0.32119	Ovarian tumour, otubain (1);	0.000000	0.85682	D	0.000000	T	0.41419	0.1158	M	0.62723	1.935	0.47276	D	0.999378	B;B;P;B	0.40066	0.441;0.219;0.701;0.441	B;B;B;B	0.38056	0.198;0.131;0.264;0.198	T	0.19031	-1.0318	10	0.46703	T	0.11	.	7.8337	0.29358	0.7197:0.1433:0.0:0.137	.	305;167;312;268	B4DPD5;F5H3F0;Q96FW1-2;Q96FW1	.;.;.;OTUB1_HUMAN	V	167;268;305;268;277;238	ENSP00000439142:I167V;ENSP00000402551:I268V;ENSP00000416973:I305V;ENSP00000444357:I268V;ENSP00000437453:I277V;ENSP00000441328:I238V	ENSP00000416973:I305V	I	+	1	0	OTUB1	63521580	1.000000	0.71417	0.709000	0.30452	0.983000	0.72400	8.909000	0.92647	0.331000	0.23511	0.379000	0.24179	ATC	.	.		0.597	OTUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396277.1	NM_017670		G	63765004	A	G	63765004	3	3	182	1	0	0	0	0	1	0	0	0	11320	449	16	2	828	2	OTUB1	11	63765004	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10		63765004	71241512	60	27190										
TAS2R13	50838	hgsc.bcm.edu	37	chr12	11061798	11061798	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ctctcttttactgacccagtCaatgcagttgatcagtacta	6	11	3	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr12:11061798C>A	ENST00000390677.2	-	1	363	c.100G>T	c.(100-102)Gac>Tac	p.D34Y	PRR4_ENST00000536668.1_Intron	NM_023920.2	NP_076409.1	Q9NYV9	T2R13_HUMAN	taste receptor, type 2, member 13	34					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						CTGACCCAGTCAATGCAGTTG	0.398																																					p.D34Y		Atlas-SNP	.											.	TAS2R13	29	.	0			c.G100T						.						61	57	58					12																	11061798		2203	4300	6503	SO:0001583	missense	50838	exon1			CCCAGTCAATGCA	AF227137	CCDS8635.1	12p13	2012-08-22			ENSG00000212128	ENSG00000212128		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14919	protein-coding gene	gene with protein product		604792				10761934, 10766242	Standard	NM_023920		Approved	T2R13, TRB3	uc001qzg.1	Q9NYV9		ENST00000390677.2:c.100G>T	chr12.hg19:g.11061798C>A	ENSP00000375095:p.Asp34Tyr	70.0	0.0		72.0	29.0	NM_023920	Q4G0I5|Q502V8|Q645X2	Missense_Mutation	SNP	ENST00000390677.2	hg19	CCDS8635.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.062554	0.36373	.	.	ENSG00000212128	ENST00000390677	T	0.01059	5.39	3.3	1.35	0.21983	.	0.984368	0.08250	U	0.974697	T	0.07188	0.0182	M	0.89785	3.06	0.09310	N	1	D	0.76494	0.999	D	0.76575	0.988	T	0.22521	-1.0214	10	0.87932	D	0	.	3.9964	0.09559	0.0:0.6067:0.2516:0.1417	.	34	Q9NYV9	T2R13_HUMAN	Y	34	ENSP00000375095:D34Y	ENSP00000375095:D34Y	D	-	1	0	TAS2R13	10953065	0.000000	0.05858	0.001000	0.08648	0.925000	0.55904	0.170000	0.16663	0.653000	0.30826	0.655000	0.94253	GAC	.	.		0.398	TAS2R13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400229.1			A	11061798	C	A	11061798	3	1	182	1	0	0	0	0	1	0	0	0	15582	826	29	3	815	3	TAS2R13	12	11061798	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10		11061798	122790097	61	27191										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32134716	32134716	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tgccacgcaaactgacaaaaGacctcctcctcctccttaca	4	17	0	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr12:32134716G>A	ENST00000312561.4	+	4	1241	c.827G>A	c.(826-828)aGa>aAa	p.R276K	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	276																	ACTGACAAAAGACCTCCTCCT	0.418																																					p.R276K		Atlas-SNP	.											.	.	.	.	0			c.G827A						.						95	93	93					12																	32134716		2203	4300	6503	SO:0001583	missense	55196	exon4			ACAAAAGACCTCC	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.827G>A	chr12.hg19:g.32134716G>A	ENSP00000310338:p.Arg276Lys	64.0	0.0		79.0	24.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	G	20.1	3.936031	0.73442	.	.	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.09817	3.54;2.94	5.68	4.79	0.61399	.	0.254572	0.28198	N	0.016236	T	0.18841	0.0452	L	0.34521	1.04	0.09310	N	1	D	0.61697	0.99	D	0.70935	0.971	T	0.04509	-1.0946	9	.	.	.	.	9.5846	0.39508	0.0927:0.0:0.9073:0.0	.	276	Q9HCM1	CL035_HUMAN	K	276	ENSP00000310338:R276K;ENSP00000370442:R276K	.	R	+	2	0	C12orf35	32025983	0.922000	0.31269	0.489000	0.27452	0.019000	0.09904	1.773000	0.38563	2.672000	0.90937	0.650000	0.86243	AGA	.	.		0.418	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		A	32134716	G	A	32134716	3	1	182	1	0	0	0	0	1	0	0	0	1684	942	33	3	829	3	C12orf35	12	32134716	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	21072918	32134716	101717179	62	27192										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43884211	43884211	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	aacttacctaacatgttacaTttctctttagatgaacaaat	3	8	1	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr12:43884211T>G	ENST00000389420.3	-	7	1103	c.1104A>C	c.(1102-1104)aaA>aaC	p.K368N	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.K368N	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	368	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ACATGTTACATTTCTCTTTAG	0.219																																					p.K368N		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A1104C						.						18	20	19					12																	43884211		2138	4209	6347	SO:0001583	missense	80070	exon7			GTTACATTTCTCT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1104A>C	chr12.hg19:g.43884211T>G	ENSP00000374071:p.Lys368Asn	480.0	0.0		458.0	207.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	15.20	2.763144	0.49574	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.63417	-0.04;-0.04	5.18	2.86	0.33363	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.53938	D	0.000044	T	0.53690	0.1812	L	0.37897	1.145	0.80722	D	1	P	0.37663	0.604	P	0.46685	0.524	T	0.50775	-0.8788	10	0.41790	T	0.15	.	3.6962	0.08365	0.0:0.1495:0.2107:0.6398	.	368	P59510	ATS20_HUMAN	N	368	ENSP00000374071:K368N;ENSP00000448341:K368N	ENSP00000374068:K368N	K	-	3	2	ADAMTS20	42170478	0.991000	0.36638	1.000000	0.80357	0.531000	0.34715	0.161000	0.16481	1.047000	0.40274	-0.291000	0.09656	AAA	.	.		0.219	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43884211	T	G	43884211	3	3	182	1	0	0	0	0	1	0	0	0	266	1490	52	5	4759	5	ADAMTS20	12	43884211	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	11749495	43884211	89967684	63	27193										
MLL2	8085	hgsc.bcm.edu	37	chr12	49433090	49433090	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	agggaaggaccctggccccaGgatggggccactcagcttgc	15	13	1	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr12:49433090G>A	ENST00000301067.7	-	33	8280	c.8281C>T	c.(8281-8283)Ctg>Ttg	p.L2761L	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2761					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CCTGGCCCCAGGATGGGGCCA	0.602																																					p.L2761L		Atlas-SNP	.											.	MLL2	1173	.	0			c.C8281T						.						33	39	37					12																	49433090		1858	4095	5953	SO:0001819	synonymous_variant	8085	exon33			GCCCCAGGATGGG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.8281C>T	chr12.hg19:g.49433090G>A		73.0	0.0		102.0	52.0	NM_003482	O14687	Silent	SNP	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.602	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49433090	G	A	49433090	2	1	182	1	0	0	0	0	0	0	0	1	9630	991	35	3		3	MLL2	12	49433090	Silent	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	5548879	49433090	84418805	64	27194										
KRT72	140807	hgsc.bcm.edu	37	chr12	52979915	52979915	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ggcgccaaagcccatgctgaAgccagcccctcctgccccag	10	19	0	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr12:52979915A>G	ENST00000537672.2	-	9	1397	c.1387T>C	c.(1387-1389)Ttc>Ctc	p.F463L	KRT72_ENST00000354310.4_Missense_Mutation_p.F421L|KRT72_ENST00000293745.2_Missense_Mutation_p.F463L|KRT72_ENST00000398066.3_Missense_Mutation_p.F275L	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	463	Tail.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		CCCATGCTGAAGCCAGCCCCT	0.592																																					p.F463L		Atlas-SNP	.											.	KRT72	70	.	0			c.T1387C						.						55	51	53					12																	52979915		2203	4300	6503	SO:0001583	missense	140807	exon9			TGCTGAAGCCAGC	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"-", "Intermediate filaments type II, keratins (basic)"	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.1387T>C	chr12.hg19:g.52979915A>G	ENSP00000441160:p.Phe463Leu	58.0	0.0		58.0	19.0	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	hg19	CCDS8833.1	.	.	.	.	.	.	.	.	.	.	A	4.366	0.067376	0.08388	.	.	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	T;T;T;T	0.81330	-1.41;-1.41;-1.48;-1.14	4.18	4.18	0.49190	.	0.000000	0.36167	N	0.002760	T	0.65144	0.2663	L	0.27053	0.805	0.34788	D	0.735388	B;B	0.29037	0.231;0.131	B;B	0.27608	0.081;0.023	T	0.65455	-0.6164	10	0.11485	T	0.65	.	9.8521	0.41064	1.0:0.0:0.0:0.0	.	421;463	B4DEI8;Q14CN4	.;K2C72_HUMAN	L	463;463;421;275	ENSP00000441160:F463L;ENSP00000293745:F463L;ENSP00000346269:F421L;ENSP00000446151:F275L	ENSP00000293745:F463L	F	-	1	0	KRT72	51266182	1.000000	0.71417	0.978000	0.43139	0.146000	0.21551	2.882000	0.48546	1.902000	0.55061	0.445000	0.29226	TTC	.	.		0.592	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747		G	52979915	A	G	52979915	3	3	182	1	0	0	0	0	1	0	0	0	8494	72	3	2	152	2	KRT72	12	52979915	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	3546825	52979915	80871980	65	27195										
CNOT2	4848	hgsc.bcm.edu	37	chr12	70724084	70724084	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	caggggtattttgcctatgaAtcctaggaatatgatgaacc	10	7	0	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr12:70724084A>G	ENST00000418359.3	+	7	855	c.404A>G	c.(403-405)aAt>aGt	p.N135S	CNOT2_ENST00000229195.3_Missense_Mutation_p.N135S|CNOT2_ENST00000548230.1_3'UTR	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	135					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription corepressor binding (GO:0001226)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(2)|urinary_tract(1)	20	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			TTGCCTATGAATCCTAGGAAT	0.403																																					p.N135S		Atlas-SNP	.											.	CNOT2	53	.	0			c.A404G						.						88	84	86					12																	70724084		2203	4300	6503	SO:0001583	missense	4848	exon7			CTATGAATCCTAG	AF180473	CCDS31857.1	12q15	2008-05-14				ENSG00000111596			7878	protein-coding gene	gene with protein product		604909		NOT2		10637334	Standard	NM_014515		Approved	CDC36, NOT2H	uc001svv.3	Q9NZN8		ENST00000418359.3:c.404A>G	chr12.hg19:g.70724084A>G	ENSP00000412091:p.Asn135Ser	97.0	0.0		89.0	32.0	NM_001199302	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Missense_Mutation	SNP	ENST00000418359.3	hg19	CCDS31857.1	.	.	.	.	.	.	.	.	.	.	A	10.49	1.363862	0.24684	.	.	ENSG00000111596	ENST00000552231;ENST00000229195;ENST00000418359;ENST00000550641;ENST00000548159;ENST00000549750;ENST00000551043;ENST00000551873;ENST00000550194	T;T;T;T	0.44881	0.91;0.91;0.92;0.91	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.30885	0.0779	L	0.29908	0.895	0.58432	D	0.999994	B	0.11235	0.004	B	0.10450	0.005	T	0.12293	-1.0553	10	0.08381	T	0.77	-7.0579	15.9985	0.80270	1.0:0.0:0.0:0.0	.	135	Q9NZN8	CNOT2_HUMAN	S	135;135;135;115;126;135;135;50;135	ENSP00000229195:N135S;ENSP00000412091:N135S;ENSP00000449659:N126S;ENSP00000449260:N135S	ENSP00000229195:N135S	N	+	2	0	CNOT2	69010351	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.145000	0.64839	2.233000	0.73108	0.455000	0.32223	AAT	.	.		0.403	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404260.1			G	70724084	A	G	70724084	3	3	182	1	0	0	0	0	1	0	0	0	3621	101	4	2	422	2	CNOT2	12	70724084	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	17744169	70724084	63127811	66	27196										
CEP290	80184	hgsc.bcm.edu	37	chr12	88522769	88522769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cagctaccataattggatcaTcttcttcattttttgatttc	4	9	4	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr12:88522769T>C	ENST00000552810.1	-	11	1239	c.896A>G	c.(895-897)gAt>gGt	p.D299G	CEP290_ENST00000397838.3_5'UTR|CEP290_ENST00000309041.7_Missense_Mutation_p.D299G	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	299					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						AATTGGATCATCTTCTTCATT	0.284																																					p.D299G		Atlas-SNP	.											.	CEP290	195	.	0			c.A896G						.						73	66	68					12																	88522769		1817	4067	5884	SO:0001583	missense	80184	exon11			GGATCATCTTCTT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.896A>G	chr12.hg19:g.88522769T>C	ENSP00000448012:p.Asp299Gly	26.0	0.0		38.0	18.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	T	16.18	3.049036	0.55110	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	T;T	0.59083	0.29;0.29	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.68769	0.3037	M	0.64997	1.995	0.80722	D	1	D;D	0.76494	0.999;0.996	D;D	0.73380	0.98;0.943	T	0.65278	-0.6207	10	0.18276	T	0.48	.	11.8163	0.52214	0.0:0.0:0.1462:0.8538	.	299;299	Q05BJ6;O15078	.;CE290_HUMAN	G	299;299;299;201	ENSP00000448012:D299G;ENSP00000308021:D299G	ENSP00000308021:D299G	D	-	2	0	CEP290	87046900	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	3.715000	0.54897	1.912000	0.55364	0.397000	0.26171	GAT	.	.		0.284	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88522769	T	C	88522769	3	2	182	1	0	0	0	0	1	0	0	0	3255	1435	50	2	6719	2	CEP290	12	88522769	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	17798685	88522769	45329126	67	27197										
PEBP1	5037	hgsc.bcm.edu	37	chr12	118577335	118577335	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tcctctccgattatgtgggcTcggggcctcccaagggcaca	12	14	1	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr12:118577335T>A	ENST00000261313.2	+	3	677	c.325T>A	c.(325-327)Tcg>Acg	p.S109T	PEBP1_ENST00000542939.1_3'UTR	NM_002567.2	NP_002558.1	P30086	PEBP1_HUMAN	phosphatidylethanolamine binding protein 1	109	Interaction with RAF1.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TTATGTGGGCTCGGGGCCTCC	0.517																																					p.S109T	NSCLC(44;94 1357 12187 49467)	Atlas-SNP	.											.	PEBP1	13	.	0			c.T325A						.						119	107	111					12																	118577335		2203	4300	6503	SO:0001583	missense	5037	exon3			GTGGGCTCGGGGC	X85033	CCDS9187.1	12q24	2009-06-16	2006-02-16	2006-02-16	ENSG00000089220	ENSG00000089220			8630	protein-coding gene	gene with protein product	"Raf kinase inhibitory protein", "hippocampal cholinergic neurostimulating peptide"	604591	"prostatic binding protein"	PBP		15782137	Standard	NM_002567		Approved	RKIP, HCNP, PEBP	uc001twu.1	P30086	OTTHUMG00000168860	ENST00000261313.2:c.325T>A	chr12.hg19:g.118577335T>A	ENSP00000261313:p.Ser109Thr	82.0	0.0		69.0	29.0	NM_002567	B2R4S1	Missense_Mutation	SNP	ENST00000261313.2	hg19	CCDS9187.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.442332	0.83993	.	.	ENSG00000089220	ENST00000261313;ENST00000418769	T	0.42900	0.96	5.43	5.43	0.79202	.	0.053251	0.85682	D	0.000000	T	0.60209	0.2251	M	0.88377	2.95	0.58432	D	0.999992	P;P	0.37233	0.588;0.506	P;B	0.45167	0.472;0.338	T	0.67473	-0.5662	10	0.66056	D	0.02	.	15.4783	0.75504	0.0:0.0:0.0:1.0	.	109;109	B4DRT4;P30086	.;PEBP1_HUMAN	T	109	ENSP00000261313:S109T	ENSP00000261313:S109T	S	+	1	0	PEBP1	117061718	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.754000	0.68743	2.057000	0.61298	0.460000	0.39030	TCG	.	.		0.517	PEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401405.1	NM_002567		A	118577335	T	A	118577335	3	1	182	1	0	0	0	0	1	0	0	0	11722	1551	54	4	335	4	PEBP1	12	118577335	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	30054566	118577335	15274560	68	27198										
PSMC6	5706	hgsc.bcm.edu	37	chr14	53185036	53185036	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tatgctagagatcatcaaccAtgcatcatttttatggatga	7	7	3	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr14:53185036A>G	ENST00000606149.1	+	9	697	c.681A>G	c.(679-681)ccA>ccG	p.P227P	PSMC6_ENST00000445930.2_Silent_p.P241P	NM_002806.3	NP_002797.3	P62333	PRS10_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 6	227					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein binding, bridging (GO:0030674)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	19	Breast(41;0.176)					ATCATCAACCATGCATCATTT	0.318																																					p.P241P		Atlas-SNP	.											.	PSMC6	71	.	0			c.A723G						.						94	99	97					14																	53185036		2203	4300	6503	SO:0001819	synonymous_variant	5706	exon9			TCAACCATGCATC		CCDS9710.2	14q22.1	2010-04-21			ENSG00000100519	ENSG00000100519		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9553	protein-coding gene	gene with protein product		602708				8674546, 9473509	Standard	NM_002806		Approved	p42	uc010tqx.2	P62333	OTTHUMG00000152333	ENST00000606149.1:c.681A>G	chr14.hg19:g.53185036A>G		120.0	0.0		114.0	54.0	NM_002806	B2R975|P49719|Q6IBU3|Q92524	Silent	SNP	ENST00000606149.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.958	1.221936	0.22457	.	.	ENSG00000100519	ENST00000555339;ENST00000556813	.	.	.	5.03	2.66	0.31614	.	.	.	.	.	T	0.52306	0.1726	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44406	-0.9330	4	.	.	.	.	5.0424	0.14465	0.5389:0.2292:0.2319:0.0	.	.	.	.	V	188;227	.	.	M	+	1	0	PSMC6	52254786	0.464000	0.25807	1.000000	0.80357	0.990000	0.78478	-0.108000	0.10857	0.869000	0.35703	0.482000	0.46254	ATG	.	.		0.318	PSMC6-018	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470741.1	NM_002806		G	53185036	A	G	53185036	2	3	182	1	0	0	0	0	0	0	0	1	12703	204	8	2		2	PSMC6	14	53185036	Silent	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10		53185036	54164504	69	27199										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102453099	102453099	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tgtcttcaacttccaagaaaAggtatgctctcatgtaatcc	6	10	3	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr14:102453099A>G	ENST00000360184.4	+	8	2701	c.2537A>G	c.(2536-2538)aAg>aGg	p.K846R		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	846	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TTCCAAGAAAAGGTATGCTCT	0.478																																					p.K846R		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A2537G						.						86	82	84					14																	102453099		2203	4300	6503	SO:0001630	splice_region_variant	1778	exon8			AAGAAAAGGTATG	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.2538+1A>G	chr14.hg19:g.102453099A>G		48.0	0.0		39.0	30.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	A	14.21	2.467198	0.43839	.	.	ENSG00000197102	ENST00000360184	T	0.29655	1.56	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.24586	0.0596	L	0.33485	1.01	0.80722	D	1	B	0.23591	0.088	B	0.21708	0.036	T	0.05801	-1.0863	10	0.15066	T	0.55	.	15.9355	0.79704	1.0:0.0:0.0:0.0	.	846	Q14204	DYHC1_HUMAN	R	846	ENSP00000348965:K846R	ENSP00000348965:K846R	K	+	2	0	DYNC1H1	101522852	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	8.885000	0.92439	2.234000	0.73211	0.533000	0.62120	AAG	.	.		0.478	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	Missense_Mutation	G	102453099	A	G	102453099	5	3	182	1	0	0	0	0	0	0	1	0	4843	86	3	2	2567	2	DYNC1H1	14	102453099	Splice_Site	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	49268063	102453099	4896441	70	27200										
GRINL1A	81488	hgsc.bcm.edu	37	chr15	58000999	58000999	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gccattgcagaatgtgaagaAgttagaagaaaaagtgaact	11	4	0	6			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr15:58000999A>C	ENST00000299638.3	+	2	415	c.201A>C	c.(199-201)gaA>gaC	p.E67D	GCOM1_ENST00000380568.3_Intron|POLR2M_ENST00000464308.1_3'UTR|GCOM1_ENST00000380569.2_Intron|POLR2M_ENST00000380557.4_Intron|POLR2M_ENST00000380563.2_Missense_Mutation_p.E67D|GCOM1_ENST00000484300.1_Intron|GCOM1_ENST00000587652.1_Missense_Mutation_p.E464D	NM_015532.3	NP_056347.1	P0CAP2	GRL1A_HUMAN	polymerase (RNA) II (DNA directed) polypeptide M	67					maintenance of ER location (GO:0051685)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)	DNA-directed RNA polymerase activity (GO:0003899)										AATGTGAAGAAGTTAGAAGAA	0.378																																					p.E67D		Atlas-SNP	.											.	POLR2M	2	.	0			c.A201C						.						74	73	73					15																	58000999		2192	4292	6484	SO:0001583	missense	81488	exon2			TGAAGAAGTTAGA	AF326773	CCDS32252.1, CCDS42045.1	15q21.3	2013-01-21	2011-11-07	2011-11-07		ENSG00000255529		"RNA polymerase subunits"	14862	protein-coding gene	gene with protein product		606485	"glutamate receptor, ionotropic, N-methyl D-aspartate-like 1A"	GRINL1A		16769904, 22850672	Standard	NM_015532		Approved	Gdown, Gdown1, GCOM1	uc002aev.1	P0CAP2	OTTHUMG00000166486	ENST00000299638.3:c.201A>C	chr15.hg19:g.58000999A>C	ENSP00000299638:p.Glu67Asp	191.0	0.0		175.0	69.0	NM_015532	Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5|Q9Y3V6	Missense_Mutation	SNP	ENST00000299638.3	hg19	CCDS32252.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.752154	0.49362	.	.	ENSG00000255529	ENST00000380563;ENST00000299638	T;T	0.37411	1.2;1.2	5.13	-2.76	0.05896	.	.	.	.	.	T	0.26882	0.0658	.	.	.	0.09310	N	0.999998	B	0.13594	0.008	B	0.17433	0.018	T	0.38520	-0.9657	8	0.87932	D	0	.	9.8146	0.40844	0.1084:0.2387:0.653:0.0	.	67	P0CAP2	GRL1A_HUMAN	D	67	ENSP00000369937:E67D;ENSP00000299638:E67D	ENSP00000299638:E67D	E	+	3	2	GRINL1A	55788291	0.007000	0.16637	0.022000	0.16811	0.815000	0.46073	-0.214000	0.09292	-0.229000	0.09854	-0.334000	0.08254	GAA	.	.		0.378	POLR2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255719.2			C	58000999	A	C	58000999	3	2	182	1	0	0	0	0	1	0	0	0	6795	69	3	5	207	5	GRINL1A	15	58000999	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10		58000999	44530393	71	27201										
MYH11	4629	hgsc.bcm.edu	37	chr16	15797859	15797859	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gaaagttgcttattcactggCcttggttccattgaagtctg	10	8	2	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr16:15797859C>A	ENST00000300036.5	-	41	6017	c.5908G>T	c.(5908-5910)Gcc>Tcc	p.A1970S	NDE1_ENST00000396354.1_Intron|MYH11_ENST00000396324.3_Missense_Mutation_p.A1977S|MYH11_ENST00000573908.1_5'UTR|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396355.1_Intron|MYH11_ENST00000576790.2_3'UTR|MYH11_ENST00000452625.2_3'UTR	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1970	C-terminal.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TATTCACTGGCCTTGGTTCCA	0.433			T	CBFB	AML																																p.A1977S		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.G5929T						.						231	227	228					16																	15797859		2197	4300	6497	SO:0001583	missense	4629	exon42			CACTGGCCTTGGT	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5908G>T	chr16.hg19:g.15797859C>A	ENSP00000300036:p.Ala1970Ser	114.0	0.0		130.0	49.0	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	hg19	CCDS10565.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.012|7.012	0.557056|0.557056	0.13436|0.13436	.|.	.|.	ENSG00000133392|ENSG00000133392	ENST00000300036;ENST00000396324|ENST00000396320	D;D|.	0.85258|.	-1.96;-1.96|.	5.43|5.43	3.39|3.39	0.38822|0.38822	.|.	0.298040|.	0.32343|.	N|.	0.006223|.	T|T	0.39145|0.39145	0.1067|0.1067	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	D|D	1|1	B;B|.	0.09022|.	0.002;0.002|.	B;B|.	0.13407|.	0.009;0.009|.	T|T	0.09378|0.09378	-1.0677|-1.0677	10|5	0.25751|.	T|.	0.34|.	.|.	11.7039|11.7039	0.51587|0.51587	0.3188:0.6811:0.0:0.0|0.3188:0.6811:0.0:0.0	.|.	1970;1977|.	P35749;Q3MNF1|.	MYH11_HUMAN;.|.	S|S	1970;1977|1989	ENSP00000300036:A1970S;ENSP00000379616:A1977S|.	ENSP00000300036:A1970S|.	A|R	-|-	1|3	0|2	MYH11|MYH11	15705360|15705360	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.955000|0.955000	0.61496|0.61496	1.431000|1.431000	0.34925|0.34925	0.595000|0.595000	0.29777|0.29777	0.561000|0.561000	0.74099|0.74099	GCC|AGG	.	.		0.433	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		A	15797859	C	A	15797859	3	1	182	1	0	0	0	0	1	0	0	0	10040	739	26	3	14	3	MYH11	16	15797859	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10		15797859	74556894	72	27202										
ZNF785	146540	hgsc.bcm.edu	37	chr16	30594587	30594587	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cacagtctgggcaagagtggGgcagtcttcgggtcagagtg	17	8	3	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr16:30594587G>A	ENST00000395216.2	-	3	671	c.512C>T	c.(511-513)cCc>cTc	p.P171L	AC002310.7_ENST00000492040.1_RNA|ZNF785_ENST00000470110.1_Missense_Mutation_p.P156L|RP11-146F11.5_ENST00000563540.1_RNA|AC002310.7_ENST00000486926.1_RNA	NM_152458.6	NP_689671.2	A8K8V0	ZN785_HUMAN	zinc finger protein 785	171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	9						GCAAGAGTGGGGCAGTCTTCG	0.657																																					p.P171L		Atlas-SNP	.											.	ZNF785	30	.	0			c.C512T						.						75	65	68					16																	30594587		2197	4300	6497	SO:0001583	missense	146540	exon3			GAGTGGGGCAGTC	BC040642	CCDS10685.1	16p11.2	2013-01-08			ENSG00000197162	ENSG00000197162		"Zinc fingers, C2H2-type", "-"	26496	protein-coding gene	gene with protein product						10493829	Standard	NM_152458		Approved	FLJ32130	uc002dyu.3	A8K8V0	OTTHUMG00000132398	ENST00000395216.2:c.512C>T	chr16.hg19:g.30594587G>A	ENSP00000378642:p.Pro171Leu	84.0	0.0		76.0	32.0	NM_152458	O75701|Q8IW91|Q8WV14|Q96MN0	Missense_Mutation	SNP	ENST00000395216.2	hg19	CCDS10685.1	.	.	.	.	.	.	.	.	.	.	g	17.85	3.491175	0.64074	.	.	ENSG00000197162	ENST00000470110;ENST00000395222;ENST00000395216	T;T	0.32515	1.45;1.45	4.34	3.38	0.38709	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35941	0.0949	N	0.14661	0.345	0.09310	N	1	B;D;P	0.89917	0.446;1.0;0.581	B;D;B	0.80764	0.043;0.994;0.094	T	0.15665	-1.0429	9	0.56958	D	0.05	.	10.3082	0.43693	0.0975:0.0:0.9025:0.0	.	136;171;156	B4DQL1;A8K8V0;A8K8V0-2	.;ZN785_HUMAN;.	L	156;136;171	ENSP00000420340:P156L;ENSP00000378642:P171L	ENSP00000378642:P171L	P	-	2	0	ZNF785	30502088	0.819000	0.29175	0.009000	0.14445	0.257000	0.26127	1.291000	0.33330	1.072000	0.40860	0.644000	0.83932	CCC	.	.		0.657	ZNF785-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255529.2	NM_152458		A	30594587	G	A	30594587	3	1	182	1	0	0	0	0	1	0	0	0	18172	1232	43	3	709	3	ZNF785	16	30594587	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	14796728	30594587	59760166	73	27203										
COG8	84342	hgsc.bcm.edu	37	chr16	69364961	69364961	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gcgccgatgttcacatgcccTaggttaccgtacttggagag	12	11	1	1	rs189199610	byFrequency	TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr16:69364961T>C	ENST00000306875.4	-	5	1734	c.1620A>G	c.(1618-1620)ctA>ctG	p.L540L	PDF_ENST00000288022.1_5'Flank|RP11-343C2.12_ENST00000562949.1_Intron|COG8_ENST00000564419.1_5'Flank	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	540					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						TCACATGCCCTAGGTTACCGT	0.512																																					p.L540L		Atlas-SNP	.											.	COG8	32	.	0			c.A1620G						.						55	52	53					16																	69364961		2198	4300	6498	SO:0001819	synonymous_variant	84342	exon5			ATGCCCTAGGTTA	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"Components of oligomeric golgi complex"	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.1620A>G	chr16.hg19:g.69364961T>C		109.0	0.0		71.0	32.0	NM_032382	Q0VAK2|Q8WVV6|Q9H6F8	Silent	SNP	ENST00000306875.4	hg19	CCDS10876.1																																																																																			.	T|0.997;G|0.003		0.512	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382		C	69364961	T	C	69364961	2	2	182	1	0	0	0	0	0	0	0	1	3666	1509	53	2		2	COG8	16	69364961	Silent	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	38770374	69364961	20989792	74	27204										
ADAD2	161931	hgsc.bcm.edu	37	chr16	84227641	84227641	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tcaaatatagagcccctggaGgagaggaattgaaagcaatg	12	6	1	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr16:84227641G>A	ENST00000315906.5	+	2	470				RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.G150R|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2						RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						AGCCCCTGGAGGAGAGGAATT	0.463																																					p.G150R		Atlas-SNP	.											.	ADAD2	46	.	0			c.G448A						.						75	80	78					16																	84227641		2200	4300	6500	SO:0001627	intron_variant	161931	exon2			CCTGGAGGAGAGG	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.419-407G>A	chr16.hg19:g.84227641G>A		164.0	0.0		167.0	82.0	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	hg19	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	G	7.666	0.685905	0.14973	.	.	ENSG00000140955	ENST00000268624	T	0.21543	2.0	1.85	0.725	0.18242	.	1.517390	0.05097	N	0.486342	T	0.09335	0.0230	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32107	-0.9919	10	0.12430	T	0.62	.	3.3213	0.07052	0.3532:0.0:0.6468:0.0	.	150	Q8NCV1-2	.	R	150	ENSP00000268624:G150R	ENSP00000268624:G150R	G	+	1	0	ADAD2	82785142	0.009000	0.17119	0.000000	0.03702	0.036000	0.12997	2.685000	0.46959	0.230000	0.21059	0.313000	0.20887	GGA	.	.		0.463	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		A	84227641	G	A	84227641	1	1	182	0	1	0	0	0	0	0	0	0	232	1001	35	3		3	ADAD2	16	84227641	Intron	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	14862680	84227641	6127112	75	27205										
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84402321	84402321	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	aggacgaagaggaagccttgGtgagtccccgcgactccgcg	15	12	0	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr16:84402321G>A	ENST00000262429.4	+	1	188		c.e1+1		ATP2C2_ENST00000416219.2_Splice_Site	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2						ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						GGAAGCCTTGGTGAGTCCCCG	0.706																																					.		Atlas-SNP	.											.	ATP2C2	75	.	0			c.99+1G>A						.						11	16	15					16																	84402321		1906	4066	5972	SO:0001630	splice_region_variant	9914	exon1			GCCTTGGTGAGTC	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"ATPases / P-type"	29103	protein-coding gene	gene with protein product	"secretory pathway calcium ATPase 2"	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.99+1G>A	chr16.hg19:g.84402321G>A		260.0	0.0		256.0	115.0	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Splice_Site	SNP	ENST00000262429.4	hg19	CCDS42207.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.438501	0.25900	.	.	ENSG00000064270	ENST00000416219;ENST00000262429	.	.	.	4.38	3.43	0.39272	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.1587	0.31185	0.1097:0.0:0.8903:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP2C2	82959822	1.000000	0.71417	0.995000	0.50966	0.176000	0.22953	2.638000	0.46562	1.067000	0.40740	0.514000	0.50259	.	.	.		0.706	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	Intron	A	84402321	G	A	84402321	5	1	182	1	0	0	0	0	0	0	1	0	1144	1275	44	3	102	3	ATP2C2	16	84402321	Splice_Site	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	174680	84402321	5952432	76	27206										
CCDC144A	9720	hgsc.bcm.edu	37	chr17	16676815	16676815	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ttgctttttttttcagctgcTactaaatatgaacctggatc	6	8	1	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr17:16676815T>C	ENST00000360524.8	+	18	4332	c.4256T>C	c.(4255-4257)cTa>cCa	p.L1419P	CCDC144A_ENST00000443444.2_Missense_Mutation_p.L1419P|RP11-219A15.1_ENST00000448331.3_Silent_p.A1382A|CCDC144A_ENST00000399273.1_Silent_p.A1382A	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	1419																	TTTCAGCTGCTACTAAATATG	0.328																																					p.L1419P		Atlas-SNP	.											.	CCDC144A	53	.	0			c.T4256C						.						5	5	5					17																	16676815		1331	3138	4469	SO:0001583	missense	9720	exon18			AGCTGCTACTAAA	BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.4256T>C	chr17.hg19:g.16676815T>C	ENSP00000353717:p.Leu1419Pro	263.0	0.0		134.0	101.0	NM_014695	O60311|Q6ZU57	Missense_Mutation	SNP	ENST00000360524.8	hg19	CCDS45621.1	.	.	.	.	.	.	.	.	.	.	.	8.585	0.883176	0.17467	.	.	ENSG00000170160	ENST00000443444;ENST00000360524	T;T	0.03212	4.01;4.01	2.29	1.11	0.20524	.	.	.	.	.	T	0.04907	0.0132	N	0.08118	0	0.51767	D	0.999934	D	0.71674	0.998	D	0.72982	0.979	T	0.54207	-0.8328	9	0.87932	D	0	.	4.3407	0.11108	0.2995:0.0:0.0:0.7005	.	1419	A2RUR9	C144A_HUMAN	P	1419	ENSP00000439262:L1419P;ENSP00000353717:L1419P	ENSP00000353717:L1419P	L	+	2	0	CCDC144A	16617540	0.999000	0.42202	0.561000	0.28357	0.067000	0.16453	1.034000	0.30204	0.105000	0.17753	0.164000	0.16699	CTA	.	.		0.328	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1			C	16676815	T	C	16676815	3	2	182	1	0	0	0	0	1	0	0	0	2779	1522	53	2	4326	2	CCDC144A	17	16676815	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10		16676815	64518395	77	27207										
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319861	21319861	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	aggacggccgaagccgggacGgcctcagcccccaggccagg	16	16	1	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr17:21319861G>A	ENST00000583088.1	+	3	2102	c.1207G>A	c.(1207-1209)Ggc>Agc	p.G403S	KCNJ12_ENST00000331718.5_Missense_Mutation_p.G403S	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	403					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	AAGCCGGGACGGCCTCAGCCC	0.667										Prostate(3;0.18)																											p.G403S		Atlas-SNP	.											.	.	.	.	0			c.G1207A						.																																			SO:0001583	missense	100134444	exon3			CGGGACGGCCTCA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1207G>A	chr17.hg19:g.21319861G>A	ENSP00000463778:p.Gly403Ser	43.0	0.0		44.0	7.0	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	hg19	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	4.044	0.005744	0.07866	.	.	ENSG00000184185	ENST00000331718	D	0.86956	-2.19	5.46	-0.0112	0.13993	.	1.494790	0.03838	N	0.270119	T	0.70876	0.3274	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.61128	-0.7125	10	0.06365	T	0.9	.	6.155	0.20332	0.318:0.1188:0.5632:0.0	.	403	Q14500	IRK12_HUMAN	S	403	ENSP00000328150:G403S	ENSP00000328150:G403S	G	+	1	0	KCNJ12	21260454	0.955000	0.32602	0.000000	0.03702	0.444000	0.32077	2.092000	0.41700	-0.186000	0.10533	-0.165000	0.13383	GGC	.	.		0.667	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21319861	G	A	21319861	3	1	182	1	0	0	0	0	1	0	0	0	8055	1116	39	1	1209	1	KCNJ12	17	21319861	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	4643046	21319861	59875349	78	27208										
TMEM132E	124842	hgsc.bcm.edu	37	chr17	32955721	32955721	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gggctcagagcacacccctgCcccccaggtgagcccgaggt	13	17	1	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr17:32955721C>A	ENST00000321639.5	+	4	1196	c.868C>A	c.(868-870)Ccc>Acc	p.P290T		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	290						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		CACACCCCTGCCCCCCAGGTG	0.622																																					p.P290T		Atlas-SNP	.											.	TMEM132E	122	.	0			c.C868A						.						37	30	32					17																	32955721		2203	4300	6503	SO:0001583	missense	124842	exon4			CCCCTGCCCCCCA	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.868C>A	chr17.hg19:g.32955721C>A	ENSP00000316532:p.Pro290Thr	65.0	0.0		57.0	23.0	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	hg19	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	c	0.012	-1.685598	0.00745	.	.	ENSG00000181291	ENST00000321639	T	0.14640	2.49	4.46	2.43	0.29744	.	0.781520	0.12298	N	0.481373	T	0.05364	0.0142	N	0.04959	-0.14	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33033	-0.9884	10	0.15952	T	0.53	-25.6004	4.2395	0.10642	0.1503:0.5927:0.1663:0.0907	.	290	Q6IEE7	T132E_HUMAN	T	290	ENSP00000316532:P290T	ENSP00000316532:P290T	P	+	1	0	TMEM132E	29979834	0.000000	0.05858	0.972000	0.41901	0.032000	0.12392	0.864000	0.27926	0.577000	0.29470	-2.552000	0.00177	CCC	.	.		0.622	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		A	32955721	C	A	32955721	3	1	182	1	0	0	0	0	1	0	0	0	16063	739	26	3	882	3	TMEM132E	17	32955721	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	11635860	32955721	48239489	79	27209										
KRT9	3857	hgsc.bcm.edu	37	chr17	39727697	39727697	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cgtaccaatcctggatcttaTtctccaggtcgttgttggcc	9	12	2	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr17:39727697T>A	ENST00000246662.4	-	1	613	c.548A>T	c.(547-549)aAt>aTt	p.N183I	KRT9_ENST00000588431.1_5'UTR	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	183	Coil 1A.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				CTGGATCTTATTCTCCAGGTC	0.478																																					p.N183I		Atlas-SNP	.											.	KRT9	78	.	0			c.A548T						.						141	142	142					17																	39727697		2203	4300	6503	SO:0001583	missense	3857	exon1			ATCTTATTCTCCA		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"-", "Intermediate filaments type I, keratins (acidic)"	6447	protein-coding gene	gene with protein product	"cytokeratin 9", "type I cytoskeletal 9", "epidermolytic palmoplantar keratoderma"	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.548A>T	chr17.hg19:g.39727697T>A	ENSP00000246662:p.Asn183Ile	78.0	0.0		149.0	42.0	NM_000226	O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	hg19	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	T	10.15	1.271537	0.23221	.	.	ENSG00000171403	ENST00000246662	D	0.87887	-2.31	4.64	-8.63	0.00878	Filament (1);	.	.	.	.	T	0.67702	0.2921	N	0.11698	0.16	0.09310	N	0.999999	B	0.13594	0.008	B	0.14023	0.01	T	0.54084	-0.8346	9	0.33141	T	0.24	.	4.0704	0.09879	0.0926:0.2:0.1837:0.5237	.	183	P35527	K1C9_HUMAN	I	183	ENSP00000246662:N183I	ENSP00000246662:N183I	N	-	2	0	KRT9	36981223	0.000000	0.05858	0.069000	0.20011	0.175000	0.22909	-6.907000	0.00050	-1.579000	0.01646	-0.472000	0.04984	AAT	.	.		0.478	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		A	39727697	T	A	39727697	3	1	182	1	0	0	0	0	1	0	0	0	8510	1493	52	4	1351	4	KRT9	17	39727697	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	6771976	39727697	41467513	80	27210										
ABCA9	10350	hgsc.bcm.edu	37	chr17	67013796	67013796	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	agcaactggagtccagcataCcttttcatcacctgacacaa	6	13	2	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr17:67013796C>G	ENST00000340001.4	-	21	3113		c.e21+1		ABCA9_ENST00000370732.2_Splice_Site|ABCA9-AS1_ENST00000458677.1_RNA|ABCA9_ENST00000453985.2_Splice_Site	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9						transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					GTCCAGCATACCTTTTCATCA	0.418																																					.		Atlas-SNP	.											.	ABCA9	192	.	0			c.2901+1G>C						.						308	289	296					17																	67013796		2203	4300	6503	SO:0001630	splice_region_variant	10350	exon22			AGCATACCTTTTC	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.2901+1G>C	chr17.hg19:g.67013796C>G		107.0	0.0		128.0	17.0	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Splice_Site	SNP	ENST00000340001.4	hg19	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	C	9.937	1.216409	0.22373	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2392	0.73455	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCA9	64525391	0.998000	0.40836	0.901000	0.35422	0.167000	0.22549	4.106000	0.57804	2.372000	0.80975	0.591000	0.81541	.	.	.		0.418	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386	Intron	G	67013796	C	G	67013796	5	3	182	1	0	0	0	0	0	0	1	0	39	521	18	4	2048	4	ABCA9	17	67013796	Splice_Site	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	27286099	67013796	14181414	81	27211										
SDK2	54549	hgsc.bcm.edu	37	chr17	71412072	71412072	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cctccagcagcaggttgttcAcatcagcatccgtgatgttc	9	13	2	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr17:71412072A>G	ENST00000392650.3	-	17	2246	c.2246T>C	c.(2245-2247)gTg>gCg	p.V749A	SDK2_ENST00000388726.3_Missense_Mutation_p.V749A	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	749	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CAGGTTGTTCACATCAGCATC	0.567																																					p.V749A		Atlas-SNP	.											.	SDK2	219	.	0			c.T2246C						.						99	74	82					17																	71412072		2203	4300	6503	SO:0001583	missense	54549	exon17			TTGTTCACATCAG	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.2246T>C	chr17.hg19:g.71412072A>G	ENSP00000376421:p.Val749Ala	71.0	0.0		100.0	19.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.953382	0.53293	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000316893	T;T	0.55234	0.53;0.53	5.95	5.95	0.96441	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.125964	0.53938	D	0.000054	T	0.32852	0.0843	N	0.04880	-0.145	0.44142	D	0.996933	B;B	0.14805	0.011;0.007	B;B	0.25506	0.061;0.043	T	0.23476	-1.0187	10	0.09084	T	0.74	.	16.4159	0.83738	1.0:0.0:0.0:0.0	.	749;749	Q58EX2-2;Q58EX2	.;SDK2_HUMAN	A	373;749;749;749	ENSP00000376421:V749A;ENSP00000373378:V749A	ENSP00000324967:V749A	V	-	2	0	SDK2	68923667	1.000000	0.71417	0.970000	0.41538	0.882000	0.50991	4.931000	0.63469	2.279000	0.76181	0.533000	0.62120	GTG	.	.		0.567	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		G	71412072	A	G	71412072	3	3	182	1	0	0	0	0	1	0	0	0	13984	159	6	2	4388	2	SDK2	17	71412072	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	4398276	71412072	9783138	82	27212										
FASN	2194	hgsc.bcm.edu	37	chr17	80041199	80041199	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ccccatcccggatgccggccTgcacaagcgcccacacctcc	8	22	0	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr17:80041199T>G	ENST00000306749.2	-	32	5662	c.5444A>C	c.(5443-5445)cAg>cCg	p.Q1815P	FASN_ENST00000579758.1_5'Flank	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1815	Enoyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GATGCCGGCCTGCACAAGCGC	0.622																																					p.Q1815P	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.A5444C						.						69	67	68					17																	80041199		2198	4298	6496	SO:0001583	missense	2194	exon32			CCGGCCTGCACAA	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.5444A>C	chr17.hg19:g.80041199T>G	ENSP00000304592:p.Gln1815Pro	72.0	0.0		161.0	45.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	T	5.675	0.309160	0.10733	.	.	ENSG00000169710	ENST00000306749;ENST00000545909	T	0.26810	1.71	4.25	-3.67	0.04476	Polyketide synthase, enoylreductase (1);NAD(P)-binding domain (1);	0.649919	0.15441	N	0.262195	T	0.21962	0.0529	L	0.46157	1.445	0.20196	N	0.999926	P	0.35433	0.501	B	0.41764	0.366	T	0.19128	-1.0315	10	0.32370	T	0.25	-11.3827	8.3006	0.32012	0.0:0.4211:0.1605:0.4184	.	1815	P49327	FAS_HUMAN	P	1815;780	ENSP00000304592:Q1815P	ENSP00000304592:Q1815P	Q	-	2	0	FASN	77634488	0.042000	0.20092	0.004000	0.12327	0.007000	0.05969	-0.171000	0.09883	-1.157000	0.02815	-0.441000	0.05720	CAG	.	.		0.622	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		G	80041199	T	G	80041199	3	3	182	1	0	0	0	0	1	0	0	0	5691	1580	55	5	2139	5	FASN	17	80041199	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	8629127	80041199	1154011	83	27213										
THOC1	9984	hgsc.bcm.edu	37	chr18	224989	224989	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cagttttcttcagtgtttaaTatatgctgggaaaaacaaag	8	5	2	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr18:224989T>C	ENST00000261600.6	-	15	1150	c.1143A>G	c.(1141-1143)atA>atG	p.I381M		NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	381					apoptotic process (GO:0006915)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of isotype switching to IgA isotypes (GO:0048297)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|regulation of DNA-templated transcription, elongation (GO:0032784)|replication fork processing (GO:0031297)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	20		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				CAGTGTTTAATATATGCTGGG	0.343																																					p.I381M		Atlas-SNP	.											.	THOC1	43	.	0			c.A1143G						.						85	74	77					18																	224989		1814	4064	5878	SO:0001583	missense	9984	exon15			GTTTAATATATGC	AK055354	CCDS45820.1	18p11.32	2013-02-11			ENSG00000079134	ENSG00000079134		"THO complex subunits"	19070	protein-coding gene	gene with protein product		606930				11979277	Standard	NM_005131		Approved	P84, HPR1	uc002kkj.4	Q96FV9		ENST00000261600.6:c.1143A>G	chr18.hg19:g.224989T>C	ENSP00000261600:p.Ile381Met	129.0	0.0		63.0	50.0	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Missense_Mutation	SNP	ENST00000261600.6	hg19	CCDS45820.1	.	.	.	.	.	.	.	.	.	.	T	12.97	2.098265	0.37048	.	.	ENSG00000079134	ENST00000261600	.	.	.	6.16	3.63	0.41609	.	0.000000	0.85682	D	0.000000	T	0.51958	0.1705	L	0.42581	1.335	0.58432	D	0.999991	P	0.48589	0.912	P	0.50791	0.65	T	0.46871	-0.9160	9	0.33940	T	0.23	-20.4748	11.2776	0.49176	0.2435:0.0:0.0:0.7565	.	381	Q96FV9	THOC1_HUMAN	M	381	.	ENSP00000261600:I381M	I	-	3	3	THOC1	214989	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.195000	0.42677	1.124000	0.41980	0.528000	0.53228	ATA	.	.		0.343	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131		C	224989	T	C	224989	3	2	182	1	0	0	0	0	1	0	0	0	15879	1396	49	2	858	2	THOC1	18	224989	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10		224989	77852259	84	27214										
CELF5	60680	hgsc.bcm.edu	37	chr19	3281279	3281279	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	catgcagcagatggtgggccAgctgggcatcctgacgccgt	15	12	0	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:3281279A>G	ENST00000292672.2	+	6	723	c.686A>G	c.(685-687)cAg>cGg	p.Q229R	CELF5_ENST00000541430.2_Missense_Mutation_p.Q229R	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	229					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						ATGGTGGGCCAGCTGGGCATC	0.677																																					p.Q229R		Atlas-SNP	.											.	CELF5	32	.	0			c.A686G						.						100	87	91					19																	3281279		2203	4300	6503	SO:0001583	missense	60680	exon6			TGGGCCAGCTGGG	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"RNA binding motif (RRM) containing"	14058	protein-coding gene	gene with protein product		612680	"Bruno (Drosophila) -like 5, RNA binding protein", "bruno-like 5, RNA binding protein (Drosophila)"	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.686A>G	chr19.hg19:g.3281279A>G	ENSP00000292672:p.Gln229Arg	30.0	0.0		15.0	12.0	NM_021938	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Missense_Mutation	SNP	ENST00000292672.2	hg19	CCDS12106.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.952051	0.53293	.	.	ENSG00000161082	ENST00000292672;ENST00000541430;ENST00000334293	T;T;T	0.34072	2.14;1.57;1.38	3.73	3.73	0.42828	.	0.275088	0.36034	N	0.002838	T	0.45316	0.1336	L	0.42245	1.32	0.47994	D	0.999567	B;D;B	0.54772	0.229;0.968;0.029	B;P;B	0.59221	0.104;0.854;0.035	T	0.41610	-0.9499	10	0.56958	D	0.05	-3.898	11.5678	0.50815	1.0:0.0:0.0:0.0	.	115;229;229	B4DFI3;Q8N6W0-2;Q8N6W0	.;.;CELF5_HUMAN	R	229;229;115	ENSP00000292672:Q229R;ENSP00000443498:Q229R;ENSP00000335182:Q115R	ENSP00000292672:Q229R	Q	+	2	0	CELF5	3232279	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.202000	0.95026	1.479000	0.48272	0.379000	0.24179	CAG	.	.		0.677	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938		G	3281279	A	G	3281279	3	3	182	1	0	0	0	0	1	0	0	0	3221	188	7	2	708	2	CELF5	19	3281279	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10		3281279	55847704	85	27215										
C3	718	hgsc.bcm.edu	37	chr19	6677908	6677908	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tgtggtcagttggggcacccAaagacaaccatgctctcggt	12	11	2	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:6677908A>G	ENST00000245907.6	-	41	5069	c.4977T>C	c.(4975-4977)ttT>ttC	p.F1659F	C3_ENST00000599668.1_5'UTR	NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1659	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGGGGCACCCAAAGACAACCA	0.552																																					p.F1659F		Atlas-SNP	.											.	C3	192	.	0			c.T4977C						.						99	81	87					19																	6677908		2203	4300	6503	SO:0001819	synonymous_variant	718	exon41			GCACCCAAAGACA	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.4977T>C	chr19.hg19:g.6677908A>G		53.0	0.0		39.0	30.0	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	hg19	CCDS32883.1																																																																																			.	.		0.552	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		G	6677908	A	G	6677908	2	3	182	1	0	0	0	0	0	0	0	1	2206	127	5	2		2	C3	19	6677908	Silent	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	3396629	6677908	52451075	86	27216										
MUC16	94025	hgsc.bcm.edu	37	chr19	9091765	9091765	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	tgctcctgctccctgtcatcAaggagcgggtgggagaagat	14	10	2	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:9091765A>T	ENST00000397910.4	-	1	253	c.50T>A	c.(49-51)tTg>tAg	p.L17*		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	17	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCCTGTCATCAAGGAGCGGGT	0.532																																					p.L17X		Atlas-SNP	.											.	MUC16	4315	.	0			c.T50A						.						78	76	77					19																	9091765		2010	4165	6175	SO:0001587	stop_gained	94025	exon1			GTCATCAAGGAGC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.50T>A	chr19.hg19:g.9091765A>T	ENSP00000381008:p.Leu17*	133.0	0.0		89.0	69.0	NM_024690	Q6ZQW5|Q96RK2	Nonsense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	19.18	3.777936	0.70107	.	.	ENSG00000181143	ENST00000397910	.	.	.	1.35	-2.7	0.06004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	7.91	0.29785	0.2987:0.7013:0.0:0.0	.	.	.	.	X	17	.	ENSP00000381008:L17X	L	-	2	0	MUC16	8952765	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.053000	0.01400	-1.258000	0.02471	-0.940000	0.02684	TTG	.	.		0.532	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9091765	A	T	9091765	4	4	182	1	0	0	0	0	0	1	0	0	9982	131	5	4	43809	4	MUC16	19	9091765	Nonsense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	2413857	9091765	50037218	87	27217										
SLC35E1	79939	hgsc.bcm.edu	37	chr19	16683112	16683112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cgcgccctcgcgcgccccacCactgctgctcgctgcgcccg	11	23	0	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:16683112C>T	ENST00000595753.1	-	1	81	c.64G>A	c.(64-66)Ggt>Agt	p.G22S	SLC35E1_ENST00000431408.1_5'Flank|CTD-3222D19.2_ENST00000409035.1_Intron	NM_024881.4	NP_079157.3	Q96K37	S35E1_HUMAN	solute carrier family 35, member E1	22					transport (GO:0006810)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(2)|ovary(1)	15						CGCGCCCCACCACTGCTGCTC	0.786																																					p.G22S		Atlas-SNP	.											.	SLC35E1	48	.	0			c.G64A						.						4	7	6					19																	16683112		611	1438	2049	SO:0001583	missense	79939	exon1			CCCCACCACTGCT	AK024313	CCDS12346.2	19p13.11	2013-05-22			ENSG00000127526	ENSG00000127526		"Solute carriers"	20803	protein-coding gene	gene with protein product							Standard	NM_024881		Approved	FLJ14251	uc010xph.2	Q96K37	OTTHUMG00000152575	ENST00000595753.1:c.64G>A	chr19.hg19:g.16683112C>T	ENSP00000470652:p.Gly22Ser	34.0	0.0		43.0	24.0	NM_024881	Q8NBQ2|Q96JV7	Missense_Mutation	SNP	ENST00000595753.1	hg19	CCDS12346.2	.	.	.	.	.	.	.	.	.	.	c	17.96	3.516317	0.64634	.	.	ENSG00000127526	ENST00000409648;ENST00000436553	.	.	.	3.0	-0.904	0.10530	.	.	.	.	.	T	0.12944	0.0314	N	0.08118	0	0.09310	N	0.999994	B	0.22746	0.074	B	0.15870	0.014	T	0.30592	-0.9973	8	0.02654	T	1	.	5.78	0.18301	0.2689:0.6144:0.0:0.1167	.	22	Q96K37	S35E1_HUMAN	S	22;2	.	ENSP00000387152:G22S	G	-	1	0	SLC35E1	16544112	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.180000	0.09754	-0.766000	0.04639	-1.829000	0.00594	GGT	.	.		0.786	SLC35E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326809.2	NM_024881		T	16683112	C	T	16683112	3	4	182	1	0	0	0	0	1	0	0	0	14599	594	21	3	1192	3	SLC35E1	19	16683112	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	7591347	16683112	42445871	88	27218										
JAK3	3718	hgsc.bcm.edu	37	chr19	17945987	17945987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cccgagccaggagcaccttcCgggcagagacattgccatgg	13	14	0	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:17945987C>T	ENST00000527670.1	-	14	1981	c.1952G>A	c.(1951-1953)cGg>cAg	p.R651Q	JAK3_ENST00000458235.1_Missense_Mutation_p.R651Q|JAK3_ENST00000534444.1_Missense_Mutation_p.R651Q			P52333	JAK3_HUMAN	Janus kinase 3	651	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GAGCACCTTCCGGGCAGAGAC	0.602		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.R651Q		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	JAK3	341	.	0			c.G1952A						.						33	36	35					19																	17945987		2203	4300	6503	SO:0001583	missense	3718	exon15			ACCTTCCGGGCAG	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1952G>A	chr19.hg19:g.17945987C>T	ENSP00000432511:p.Arg651Gln	68.0	0.0		88.0	29.0	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	hg19	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.488093	0.64074	.	.	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	D;D;D	0.87334	-2.24;-2.24;-2.24	5.1	4.0	0.46444	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.064498	0.64402	D	0.000017	T	0.81297	0.4793	L	0.52266	1.64	0.36834	D	0.887027	P;P	0.49783	0.928;0.792	B;B	0.42462	0.388;0.182	D	0.83950	0.0316	10	0.87932	D	0	-35.1193	4.6177	0.12435	0.0:0.7275:0.0:0.2725	.	651;651	P52333-2;P52333	.;JAK3_HUMAN	Q	651	ENSP00000391676:R651Q;ENSP00000432511:R651Q;ENSP00000436421:R651Q	ENSP00000391676:R651Q	R	-	2	0	JAK3	17806987	1.000000	0.71417	0.998000	0.56505	0.259000	0.26198	5.758000	0.68776	2.366000	0.80165	0.555000	0.69702	CGG	.	.		0.602	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		T	17945987	C	T	17945987	3	4	182	1	0	0	0	0	1	0	0	0	7948	652	23	1	1462	1	JAK3	19	17945987	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	1262875	17945987	41182996	89	27219										
WDR88	126248	hgsc.bcm.edu	37	chr19	33655144	33655144	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gatgttgccattagcaacaaCaagaaatggatcctgtctgc	9	9	1	1	rs1981827	byFrequency	TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:33655144C>A	ENST00000355868.3	+	9	1198	c.1122C>A	c.(1120-1122)aaC>aaA	p.N374K	WDR88_ENST00000361680.2_Missense_Mutation_p.N374K	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	374										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					TTAGCAACAACAAGAAATGGA	0.383																																					p.N374K		Atlas-SNP	.											.	WDR88	50	.	0			c.C1122A						.						158	147	151					19																	33655144		2203	4300	6503	SO:0001583	missense	126248	exon9			CAACAACAAGAAA	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"WD repeat domain containing"	26999	protein-coding gene	gene with protein product			"PQQ repeat and WD repeat domain containing"	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.1122C>A	chr19.hg19:g.33655144C>A	ENSP00000348129:p.Asn374Lys	134.0	0.0		142.0	65.0	NM_173479	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	hg19	CCDS12429.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457137	0.63401	.	.	ENSG00000166359	ENST00000355868;ENST00000361680	T;T	0.42900	0.96;0.96	5.18	4.14	0.48551	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.290359	0.36002	N	0.002843	T	0.40862	0.1134	L	0.40543	1.245	0.36102	P	0.155821	P	0.47484	0.896	P	0.46419	0.516	T	0.58657	-0.7598	9	0.72032	D	0.01	.	12.6303	0.56653	0.0:0.9187:0.0:0.0813	.	374	Q6ZMY6	WDR88_HUMAN	K	374	ENSP00000348129:N374K;ENSP00000355148:N374K	ENSP00000348129:N374K	N	+	3	2	WDR88	38346984	1.000000	0.71417	0.892000	0.35008	0.626000	0.37791	2.959000	0.49153	1.179000	0.42884	0.561000	0.74099	AAC	.	C|0.874;T|0.126		0.383	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479		A	33655144	C	A	33655144	3	1	182	1	0	0	0	0	1	0	0	0	17350	477	17	3	1156	3	WDR88	19	33655144	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	15709157	33655144	25473839	90	27220										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42853808	42853808	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ggcaggccctgggcacagcgAgctaactctgctgtgggatc	15	12	1	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:42853808A>G	ENST00000251268.6	+	14	2456	c.2456A>G	c.(2455-2457)gAg>gGg	p.E819G	MEGF8_ENST00000334370.4_Missense_Mutation_p.E752G	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	819					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				GGGCACAGCGAGCTAACTCTG	0.642																																					p.E819G		Atlas-SNP	.											.	MEGF8	358	.	0			c.A2456G						.						67	67	67					19																	42853808		2203	4300	6503	SO:0001583	missense	1954	exon14			ACAGCGAGCTAAC	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.2456A>G	chr19.hg19:g.42853808A>G	ENSP00000251268:p.Glu819Gly	60.0	0.0		57.0	23.0	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	A	17.45	3.393795	0.62066	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.23348	1.91;1.94	3.97	3.97	0.46021	.	0.176592	0.34986	N	0.003539	T	0.32315	0.0825	N	0.19112	0.55	0.80722	D	1	B;D	0.76494	0.016;0.999	B;D	0.75484	0.009;0.986	T	0.07177	-1.0786	10	0.45353	T	0.12	.	10.8281	0.46645	1.0:0.0:0.0:0.0	.	819;752	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	G	752;819	ENSP00000334219:E752G;ENSP00000251268:E819G	ENSP00000251268:E819G	E	+	2	0	MEGF8	47545648	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.943000	0.75934	1.674000	0.50907	0.402000	0.26972	GAG	.	.		0.642	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		G	42853808	A	G	42853808	3	3	182	1	0	0	0	0	1	0	0	0	9472	304	11	2	2305	2	MEGF8	19	42853808	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	9198664	42853808	16275175	91	27221										
PRKD2	25865	hgsc.bcm.edu	37	chr19	47214210	47214210	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	aggccgaagagcatctccccGcagtgatcacagaaggcagg	13	12	2	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:47214210G>T	ENST00000291281.4	-	3	690	c.465C>A	c.(463-465)tgC>tgA	p.C155*	PRKD2_ENST00000433867.1_Nonsense_Mutation_p.C155*|MIR320E_ENST00000390179.3_RNA|PRKD2_ENST00000595515.1_Nonsense_Mutation_p.C155*|PRKD2_ENST00000601806.1_5'UTR|PRKD2_ENST00000600194.1_5'UTR			Q9BZL6	KPCD2_HUMAN	protein kinase D2	155					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		GCATCTCCCCGCAGTGATCAC	0.672																																					p.C155X		Atlas-SNP	.											PRKD2,NS,carcinoma,0,1	PRKD2	94	.	0			c.C465A						.						28	23	25					19																	47214210		2189	4288	6477	SO:0001587	stop_gained	25865	exon3			CTCCCCGCAGTGA	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"Pleckstrin homology (PH) domain containing"	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.465C>A	chr19.hg19:g.47214210G>T	ENSP00000291281:p.Cys155*	54.0	0.0		74.0	4.0	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Nonsense_Mutation	SNP	ENST00000291281.4	hg19	CCDS12689.1	.	.	.	.	.	.	.	.	.	.	G	42	9.304725	0.99130	.	.	ENSG00000105287	ENST00000291281;ENST00000433867	.	.	.	5.61	2.2	0.27929	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-32.6988	10.9093	0.47099	0.2174:0.0:0.7826:0.0	.	.	.	.	X	155	.	ENSP00000291281:C155X	C	-	3	2	PRKD2	51906050	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	0.259000	0.18405	0.707000	0.31934	0.591000	0.81541	TGC	.	.		0.672	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		T	47214210	G	T	47214210	4	4	182	1	0	0	0	0	0	1	0	0	12531	1079	38	1	2235	1	PRKD2	19	47214210	Nonsense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	4360402	47214210	11914773	92	27222										
NOSIP	51070	hgsc.bcm.edu	37	chr19	50060189	50060189	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	agcgacgggatccagaagctGggcagcactttgtccttgtc	13	11	0	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:50060189G>A	ENST00000596358.1	-	6	538	c.480C>T	c.(478-480)ccC>ccT	p.P160P	NOSIP_ENST00000391853.3_Silent_p.P160P|NOSIP_ENST00000339093.3_Silent_p.P163P	NM_001270960.1	NP_001257889.1	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein	160					negative regulation of catalytic activity (GO:0043086)|negative regulation of nitric-oxide synthase activity (GO:0051001)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|skin(2)|urinary_tract(1)	11		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)		TCCAGAAGCTGGGCAGCACTT	0.667																																					p.P160P		Atlas-SNP	.											.	NOSIP	28	.	0			c.C480T						.						40	38	39					19																	50060189		2203	4298	6501	SO:0001819	synonymous_variant	51070	exon7			GAAGCTGGGCAGC	AF132959	CCDS12772.1	19q13.3	2008-02-05				ENSG00000142546			17946	protein-coding gene	gene with protein product						11149895, 10810093	Standard	NM_015953		Approved	CGI-25	uc002pol.4	Q9Y314		ENST00000596358.1:c.480C>T	chr19.hg19:g.50060189G>A		92.0	0.0		105.0	39.0	NM_015953	Q96FD2	Silent	SNP	ENST00000596358.1	hg19	CCDS12772.1																																																																																			.	.		0.667	NOSIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465423.1			A	50060189	G	A	50060189	2	1	182	1	0	0	0	0	0	0	0	1	10554	1335	47	3		3	NOSIP	19	50060189	Silent	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	2845979	50060189	9068794	93	27223										
ZNF415	55786	hgsc.bcm.edu	37	chr19	53612357	53612357	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ttttctgatgtagtgcaaggCatgaatttcgactgaagacc	10	7	1	4			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:53612357C>A	ENST00000500065.4	-	4	1274	c.941G>T	c.(940-942)tGc>tTc	p.C314F	ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000243643.4_Missense_Mutation_p.C314F|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000601493.1_Missense_Mutation_p.C84F|ZNF415_ENST00000455735.2_Missense_Mutation_p.C362F|ZNF415_ENST00000421033.1_Missense_Mutation_p.C326F|ZNF415_ENST00000448501.1_Missense_Mutation_p.C362F|ZNF415_ENST00000440291.1_Missense_Mutation_p.C301F|ZNF415_ENST00000594011.1_3'UTR	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	362					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		TAGTGCAAGGCATGAATTTCG	0.428																																					p.C314F		Atlas-SNP	.											.	ZNF415	68	.	0			c.G941T						.						95	87	90					19																	53612357		2203	4300	6503	SO:0001583	missense	55786	exon4			GCAAGGCATGAAT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.941G>T	chr19.hg19:g.53612357C>A	ENSP00000439435:p.Cys314Phe	42.0	0.0		38.0	15.0	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	hg19	CCDS54313.1	.	.	.	.	.	.	.	.	.	.	C	4.771	0.143398	0.09134	.	.	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.14640	2.49;2.49;2.49;2.49;2.49;2.49	2.78	-5.55	0.02536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07007	0.0178	N	0.17345	0.48	0.09310	N	1	B;B;B;P;B;B	0.41910	0.073;0.083;0.084;0.764;0.073;0.246	B;B;B;B;B;B	0.38500	0.004;0.015;0.005;0.275;0.004;0.049	T	0.14448	-1.0472	9	0.51188	T	0.08	.	7.2988	0.26408	0.0:0.193:0.2283:0.5787	.	314;362;362;314;301;326	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	F	314;314;362;326;362;301	ENSP00000243643:C314F;ENSP00000439435:C314F;ENSP00000396492:C362F;ENSP00000395055:C326F;ENSP00000388787:C362F;ENSP00000414601:C301F	ENSP00000243643:C314F	C	-	2	0	ZNF415	58304169	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.477000	0.00985	-2.564000	0.00472	-0.479000	0.04858	TGC	.	.		0.428	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		A	53612357	C	A	53612357	3	1	182	1	0	0	0	0	1	0	0	0	17907	710	25	3	730	3	ZNF415	19	53612357	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	3552168	53612357	5516626	94	27224										
ZNF304	57343	hgsc.bcm.edu	37	chr19	57868571	57868571	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gagagtccacacaggagcaaGatcctacgtgtgcagcaaat	11	10	0	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr19:57868571G>T	ENST00000282286.5	+	3	1507	c.1334G>T	c.(1333-1335)aGa>aTa	p.R445I	ZNF304_ENST00000391705.3_Missense_Mutation_p.R445I|ZNF304_ENST00000443917.2_Missense_Mutation_p.R492I|ZNF304_ENST00000598744.1_Missense_Mutation_p.R403I			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	445				R -> S (in Ref. 1; CAC06610). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		ACAGGAGCAAGATCCTACGTG	0.468																																					p.R445I		Atlas-SNP	.											.	ZNF304	74	.	0			c.G1334T						.						69	68	68					19																	57868571		2203	4300	6503	SO:0001583	missense	57343	exon3			GAGCAAGATCCTA	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"Zinc fingers, C2H2-type", "-"	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.1334G>T	chr19.hg19:g.57868571G>T	ENSP00000282286:p.Arg445Ile	143.0	0.0		166.0	68.0	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	hg19	CCDS12950.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.529477	0.44969	.	.	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.20332	2.08;2.08;2.08	3.67	0.343	0.16001	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42245	0.1194	M	0.88775	2.98	0.35693	D	0.815048	D;P	0.53151	0.958;0.952	P;P	0.59546	0.859;0.606	T	0.53136	-0.8481	9	0.87932	D	0	.	6.6031	0.22710	0.5349:0.0:0.4651:0.0	.	445;492	Q9HCX3;E7EQD3	ZN304_HUMAN;.	I	445;445;492	ENSP00000282286:R445I;ENSP00000375586:R445I;ENSP00000401642:R492I	ENSP00000282286:R445I	R	+	2	0	ZNF304	62560383	0.289000	0.24334	0.020000	0.16555	0.747000	0.42532	0.038000	0.13862	0.170000	0.19704	0.650000	0.86243	AGA	.	.		0.468	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1			T	57868571	G	T	57868571	3	4	182	1	0	0	0	0	1	0	0	0	17848	942	33	3	1344	3	ZNF304	19	57868571	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	4256214	57868571	1260412	95	27225										
FOXA2	3170	hgsc.bcm.edu	37	chr20	22562785	22562785	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ggcttcaggtgggcctcaggCggcaggcccgggtggtgggg	22	10	2	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr20:22562785C>A	ENST00000377115.4	-	3	1258	c.1077G>T	c.(1075-1077)ccG>ccT	p.P359P	FOXA2_ENST00000419308.2_Silent_p.P365P	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	359					adult locomotory behavior (GO:0008344)|cell development (GO:0048468)|cell differentiation in hindbrain (GO:0021533)|cell fate specification (GO:0001708)|chromatin modification (GO:0016568)|connective tissue development (GO:0061448)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral neural tube patterning (GO:0021904)|ectoderm formation (GO:0001705)|endocrine pancreas development (GO:0031018)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|in utero embryonic development (GO:0001701)|lung epithelial cell differentiation (GO:0060487)|negative regulation of detection of glucose (GO:2000971)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter by glucose (GO:0000433)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|regulation of blood coagulation (GO:0030193)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in detection of glucose (GO:2000976)|response to interleukin-6 (GO:0070741)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|urinary_tract(1)	22	Lung NSC(19;0.188)					GGGCCTCAGGCGGCAGGCCCG	0.721																																					p.P365P		Atlas-SNP	.											.	FOXA2	48	.	0			c.G1095T						.						44	35	38					20																	22562785		2174	4264	6438	SO:0001819	synonymous_variant	3170	exon2			CTCAGGCGGCAGG	AF147787	CCDS13147.1, CCDS46585.1	20p11	2008-04-10		2002-09-20	ENSG00000125798	ENSG00000125798		"Forkhead boxes"	5022	protein-coding gene	gene with protein product		600288	"hepatocyte nuclear factor 3, beta"	HNF3B		9119385, 11875061	Standard	NM_153675		Approved		uc002wsm.3	Q9Y261	OTTHUMG00000032041	ENST00000377115.4:c.1077G>T	chr20.hg19:g.22562785C>A		71.0	0.0		72.0	25.0	NM_021784	Q8WUW4|Q96DF7	Silent	SNP	ENST00000377115.4	hg19	CCDS13147.1																																																																																			.	.		0.721	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1			A	22562785	C	A	22562785	2	1	182	1	0	0	0	0	0	0	0	1	5998	755	27	1		1	FOXA2	20	22562785	Silent	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10		22562785	40462735	96	27226										
MYH7B	57644	hgsc.bcm.edu	37	chr20	33585321	33585321	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	agcaggcggagggcgcggcgGagctgggggagcaggtggac	24	8	0	0			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr20:33585321G>T	ENST00000262873.7	+	30	3843	c.3751G>T	c.(3751-3753)Gag>Tag	p.E1251*		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1209						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GGGCGCGGCGGAGCTGGGGGA	0.726																																					p.E1251X		Atlas-SNP	.											.	MYH7B	145	.	0			c.G3751T						.						26	28	27					20																	33585321		2196	4295	6491	SO:0001587	stop_gained	57644	exon32			GCGGCGGAGCTGG	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.3751G>T	chr20.hg19:g.33585321G>T	ENSP00000262873:p.Glu1251*	45.0	0.0		40.0	17.0	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Nonsense_Mutation	SNP	ENST00000262873.7	hg19	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	G	42	9.366419	0.99150	.	.	ENSG00000078814	ENST00000262873	.	.	.	4.73	4.73	0.59995	.	0.000000	0.38381	N	0.001715	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.9076	0.88923	0.0:0.0:1.0:0.0	.	.	.	.	X	1251	.	ENSP00000262873:E1251X	E	+	1	0	MYH7B	33048982	1.000000	0.71417	0.953000	0.39169	0.684000	0.39900	7.826000	0.86716	2.456000	0.83038	0.563000	0.77884	GAG	.	.		0.726	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33585321	G	T	33585321	4	4	182	1	0	0	0	0	0	1	0	0	10049	1175	41	3	3869	3	MYH7B	20	33585321	Nonsense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	11022536	33585321	29440199	97	27227										
CTNNBL1	56259	hgsc.bcm.edu	37	chr20	36374896	36374896	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ggaatccgagctggacctaaAtgacatcattcaggagatgc	11	9	2	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr20:36374896A>G	ENST00000361383.6	+	4	470	c.353A>G	c.(352-354)aAt>aGt	p.N118S	CTNNBL1_ENST00000373473.1_5'UTR|CTNNBL1_ENST00000405275.2_Missense_Mutation_p.N91S	NM_030877.3	NP_110517.2	Q8WYA6	CTBL1_HUMAN	catenin, beta like 1	118					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|positive regulation of apoptotic process (GO:0043065)|RNA splicing (GO:0008380)|somatic diversification of immunoglobulins (GO:0016445)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(6)|lung(6)|ovary(3)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				CTGGACCTAAATGACATCATT	0.502																																					p.N118S	Ovarian(184;582 2038 3273 4106 42608)	Atlas-SNP	.											.	CTNNBL1	78	.	0			c.A353G						.						147	134	139					20																	36374896		2203	4300	6503	SO:0001583	missense	56259	exon4			ACCTAAATGACAT	AL023804	CCDS13298.1	20q11.23-q12	2011-06-03	2002-05-27	2002-05-31	ENSG00000132792	ENSG00000132792			15879	protein-coding gene	gene with protein product	"nuclear associated protein"	611537	"chromosome 20 open reading frame 33"	C20orf33		12659813, 21385873	Standard	NM_030877		Approved	FLJ21108, P14L, P14, NAP, NYD-SP19	uc021wdj.1	Q8WYA6	OTTHUMG00000032428	ENST00000361383.6:c.353A>G	chr20.hg19:g.36374896A>G	ENSP00000355050:p.Asn118Ser	49.0	0.0		49.0	23.0	NM_030877	B4DE16|Q0VAL9|Q0VAM0|Q53HI8|Q5JWZ2|Q5JWZ3|Q5JWZ7|Q5JWZ8|Q8N454|Q8NCL2|Q8TBD6|Q96KD2|Q9H7A5|Q9NQF9|Q9NTX0|Q9Y3M7	Missense_Mutation	SNP	ENST00000361383.6	hg19	CCDS13298.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.103912	0.76983	.	.	ENSG00000132792	ENST00000361383;ENST00000447935;ENST00000405275	T;T	0.44083	0.93;0.94	5.15	5.15	0.70609	Domain of unknown function DUF1716, eukaryotic (1);	0.000000	0.85682	D	0.000000	T	0.58595	0.2133	M	0.69823	2.125	0.80722	D	1	P;B	0.52316	0.952;0.256	P;B	0.58620	0.842;0.312	T	0.59451	-0.7452	10	0.42905	T	0.14	-20.9336	14.3052	0.66380	1.0:0.0:0.0:0.0	.	118;91	Q8WYA6;A2A2P1	CTBL1_HUMAN;.	S	118;91;91	ENSP00000355050:N118S;ENSP00000384355:N91S	ENSP00000355050:N118S	N	+	2	0	CTNNBL1	35808310	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.081000	0.94049	2.165000	0.68154	0.482000	0.46254	AAT	.	.		0.502	CTNNBL1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079125.1	NM_030877		G	36374896	A	G	36374896	3	3	182	1	0	0	0	0	1	0	0	0	4020	101	4	2	367	2	CTNNBL1	20	36374896	Missense_Mutation	SNP	A	TCGA-DD-AAD6-01A-11D-A40R-10	2789575	36374896	26650624	98	27228										
ZNF335	63925	hgsc.bcm.edu	37	chr20	44592541	44592541	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	cccatggccaccaggtgtccTgggcctgaggagctgggagc	16	13	0	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr20:44592541T>A	ENST00000322927.2	-	8	1291	c.1191A>T	c.(1189-1191)ccA>ccT	p.P397P	ZNF335_ENST00000494955.1_5'Flank|ZNF335_ENST00000426788.1_Silent_p.P242P	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	397					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				CCAGGTGTCCTGGGCCTGAGG	0.642																																					p.P397P		Atlas-SNP	.											.	ZNF335	115	.	0			c.A1191T						.						52	48	49					20																	44592541		2203	4300	6503	SO:0001819	synonymous_variant	63925	exon8			GTGTCCTGGGCCT	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.1191A>T	chr20.hg19:g.44592541T>A		67.0	0.0		100.0	56.0	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	hg19	CCDS13389.1																																																																																			.	.		0.642	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		A	44592541	T	A	44592541	2	1	182	1	0	0	0	0	0	0	0	1	17867	1567	55	4		4	ZNF335	20	44592541	Silent	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10	8217645	44592541	18432979	99	27229										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58489232	58489232	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	atccattgaaaaccactgatGtgccagttcttgtctttgtt	7	9	2	2			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr20:58489232G>A	ENST00000357552.3	-	11	934	c.709C>T	c.(709-711)Cat>Tat	p.H237Y	SYCP2_ENST00000371001.2_Missense_Mutation_p.H237Y			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	237					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			AACCACTGATGTGCCAGTTCT	0.308																																					p.H237Y		Atlas-SNP	.											.	SYCP2	204	.	0			c.C709T						.						89	86	87					20																	58489232		2202	4295	6497	SO:0001583	missense	10388	exon10			ACTGATGTGCCAG	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.709C>T	chr20.hg19:g.58489232G>A	ENSP00000350162:p.His237Tyr	145.0	0.0		185.0	55.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	G	0.039	-1.293461	0.01375	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.04551	3.6;3.6;3.6	5.1	1.26	0.21427	.	0.360095	0.27420	N	0.019455	T	0.02193	0.0068	N	0.17082	0.46	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.48031	-0.9070	10	0.02654	T	1	-0.019	5.5285	0.16970	0.4451:0.0:0.079:0.4759	.	237;237	A2A341;Q9BX26	.;SYCP2_HUMAN	Y	237	ENSP00000360040:H237Y;ENSP00000350162:H237Y;ENSP00000402456:H237Y	ENSP00000350162:H237Y	H	-	1	0	SYCP2	57922627	0.001000	0.12720	0.906000	0.35671	0.805000	0.45488	0.023000	0.13533	0.343000	0.23821	-0.302000	0.09304	CAT	.	.		0.308	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		A	58489232	G	A	58489232	3	1	182	1	0	0	0	0	1	0	0	0	15447	1377	48	3	4023	3	SYCP2	20	58489232	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10	13896691	58489232	4536288	100	27230										
IGSF5	150084	hgsc.bcm.edu	37	chr21	41163986	41163986	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	actgagacagaaagtggaaaTgaaaactccggctacaattc	9	8	0	3			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr21:41163986T>A	ENST00000380588.4	+	7	1111	c.1008T>A	c.(1006-1008)aaT>aaA	p.N336K		NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	336					single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				AAAGTGGAAATGAAAACTCCG	0.398																																					p.N336K		Atlas-SNP	.											.	IGSF5	62	.	0			c.T1008A						.						71	69	69					21																	41163986		2203	4300	6503	SO:0001583	missense	150084	exon7			TGGAAATGAAAAC		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5952	protein-coding gene	gene with protein product	"junctional adhesion molecule 4"	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.1008T>A	chr21.hg19:g.41163986T>A	ENSP00000369962:p.Asn336Lys	431.0	0.0		221.0	163.0	NM_001080444		Missense_Mutation	SNP	ENST00000380588.4	hg19	CCDS33562.1	.	.	.	.	.	.	.	.	.	.	T	9.811	1.183176	0.21870	.	.	ENSG00000183067	ENST00000380588	T	0.04275	3.66	4.8	-2.44	0.06502	.	0.673858	0.15515	N	0.258333	T	0.01800	0.0057	N	0.17082	0.46	0.09310	N	1	B	0.22080	0.064	B	0.20184	0.028	T	0.44590	-0.9318	10	0.02654	T	1	-3.6287	1.1814	0.01846	0.1423:0.1871:0.3434:0.3272	.	336	Q9NSI5	IGSF5_HUMAN	K	336	ENSP00000369962:N336K	ENSP00000369962:N336K	N	+	3	2	IGSF5	40085856	0.046000	0.20272	0.080000	0.20451	0.457000	0.32468	-0.713000	0.05007	-0.169000	0.10834	-0.290000	0.09829	AAT	.	.		0.398	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1			A	41163986	T	A	41163986	3	1	182	1	0	0	0	0	1	0	0	0	7611	1461	51	4	1034	4	IGSF5	21	41163986	Missense_Mutation	SNP	T	TCGA-DD-AAD6-01A-11D-A40R-10		41163986	6965909	101	27231										
LZTR1	8216	hgsc.bcm.edu	37	chr22	21348001	21348001	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gaggactacgggcggctgtgGgagagccgccagttctgcga	18	10	1	1			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chr22:21348001G>A	ENST00000215739.8	+	12	1670	c.1311G>A	c.(1309-1311)tgG>tgA	p.W437*	LZTR1_ENST00000389355.3_Nonsense_Mutation_p.W418*|LZTR1_ENST00000479606.1_3'UTR	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	437					anatomical structure morphogenesis (GO:0009653)|regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)	42	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			GGCGGCTGTGGGAGAGCCGCC	0.627																																					p.W437X		Atlas-SNP	.											.	LZTR1	99	.	0			c.G1311A						.						48	44	45					22																	21348001		2200	4300	6500	SO:0001587	stop_gained	8216	exon12			GCTGTGGGAGAGC	D38496	CCDS33606.1	22q11.21	2013-01-09	2004-12-10		ENSG00000099949	ENSG00000099949		"BTB/POZ domain containing"	6742	protein-coding gene	gene with protein product		600574	"leucine-zipper-like transcriptional regulator 1"			7633402, 16356934	Standard	NM_006767		Approved	LZTR-1, BTBD29	uc002zto.3	Q8N653	OTTHUMG00000150878	ENST00000215739.8:c.1311G>A	chr22.hg19:g.21348001G>A	ENSP00000215739:p.Trp437*	61.0	0.0		42.0	4.0	NM_006767	Q14776|Q20WK0	Nonsense_Mutation	SNP	ENST00000215739.8	hg19	CCDS33606.1	.	.	.	.	.	.	.	.	.	.	G	42	9.285862	0.99125	.	.	ENSG00000099949	ENST00000539817;ENST00000215739;ENST00000389355	.	.	.	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-25.1965	13.0129	0.58741	0.0:0.0:1.0:0.0	.	.	.	.	X	396;437;418	.	ENSP00000215739:W437X	W	+	3	0	LZTR1	19678001	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.330000	0.79181	2.432000	0.82394	0.563000	0.77884	TGG	.	.		0.627	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767		A	21348001	G	A	21348001	4	1	182	1	0	0	0	0	0	1	0	0	9146	1241	43	3	1357	3	LZTR1	22	21348001	Nonsense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10		21348001	29956565	102	27232										
ARMCX2	9823	hgsc.bcm.edu	37	chrX	100911129	100911129	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	ccaactacttgaactgctgaGttcaggttagaggccatgat	10	9	1	4			TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chrX:100911129G>T	ENST00000328766.5	-	5	1899	c.1446C>A	c.(1444-1446)aaC>aaA	p.N482K	ARMCX2_ENST00000467416.1_5'Flank|ARMCX2_ENST00000356824.4_Missense_Mutation_p.N482K|ARMCX2_ENST00000330154.2_Missense_Mutation_p.N482K	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	482						integral component of membrane (GO:0016021)				NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(6)|prostate(1)|skin(1)	29						GAACTGCTGAGTTCAGGTTAG	0.388																																					p.N482K		Atlas-SNP	.											.	ARMCX2	75	.	0			c.C1446A						.						127	126	126					X																	100911129		2203	4300	6503	SO:0001583	missense	9823	exon5			TGCTGAGTTCAGG	AB011084	CCDS14490.1	Xq21.33-q22.2	2014-03-21			ENSG00000184867	ENSG00000184867		"Armadillo repeat containing"	16869	protein-coding gene	gene with protein product		300363				9628581, 11162520, 16221301, 22569362	Standard	XM_005278109		Approved	ALEX2, KIAA0512, GASP9	uc004eif.3	Q7L311	OTTHUMG00000022038	ENST00000328766.5:c.1446C>A	chrX.hg19:g.100911129G>T	ENSP00000331662:p.Asn482Lys	50.0	0.0		61.0	53.0	NM_014782	O60267|Q5H9D9	Missense_Mutation	SNP	ENST00000328766.5	hg19	CCDS14490.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.303840	0.40795	.	.	ENSG00000184867	ENST00000328766;ENST00000330154;ENST00000356824	T;T;T	0.47177	0.85;0.85;0.85	4.09	3.23	0.37069	Armadillo-like helical (1);Armadillo-type fold (1);	0.092515	0.64402	D	0.000001	T	0.60805	0.2297	M	0.66297	2.02	0.42916	D	0.994272	D	0.89917	1.0	D	0.80764	0.994	T	0.61352	-0.7080	10	0.59425	D	0.04	-9.4184	6.7153	0.23300	0.1294:0.0:0.8706:0.0	.	482	Q7L311	ARMX2_HUMAN	K	482	ENSP00000331662:N482K;ENSP00000328631:N482K;ENSP00000349281:N482K	ENSP00000331662:N482K	N	-	3	2	ARMCX2	100797785	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.972000	0.49256	1.073000	0.40885	0.422000	0.28245	AAC	.	.		0.388	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057586.1	NM_014782		T	100911129	G	T	100911129	3	4	182	1	0	0	0	0	1	0	0	0	960	1020	36	3	456	3	ARMCX2	23	100911129	Missense_Mutation	SNP	G	TCGA-DD-AAD6-01A-11D-A40R-10		100911129	54359431	103	27233										
CXorf48	54967	hgsc.bcm.edu	37	chrX	134305029	134305029	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	6	1	1.59795918367347	2.79642857142857	1.11857142857143	1	1	0	gaggccctgctgctgtgggcCctgtcgctctgcagggtcgg	17	13	1	0	rs367724422		TCGA-DD-AAD6-01A-11D-A40R-10	TCGA-DD-AAD6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e38cc549-ebc1-45a9-82a3-3f17720f4c67	d61125a0-8951-47b0-a531-d4685f12039c	g.chrX:134305029C>A	ENST00000276241.6	-	1	293	c.67G>T	c.(67-69)Ggc>Tgc	p.G23C	CXorf48_ENST00000344129.2_Missense_Mutation_p.G23C	NM_001031705.2	NP_001026875.1	Q8WUE5	CT55_HUMAN		23										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)	5	Acute lymphoblastic leukemia(192;0.000127)					TGCTGTGGGCCCTGTCGCTCT	0.637																																					p.G23C		Atlas-SNP	.											.	CXorf48	17	.	0			c.G67T						.						108	92	97					X																	134305029		2203	4300	6503	SO:0001583	missense	54967	exon1			GTGGGCCCTGTCG																												ENST00000276241.6:c.67G>T	chrX.hg19:g.134305029C>A	ENSP00000276241:p.Gly23Cys	87.0	0.0		96.0	85.0	NM_017863	Q9NWY8	Missense_Mutation	SNP	ENST00000276241.6	hg19	CCDS35400.1	.	.	.	.	.	.	.	.	.	.	C	9.809	1.182544	0.21870	.	.	ENSG00000169551	ENST00000276241;ENST00000344129	T;T	0.31769	1.48;1.48	1.53	-3.05	0.05396	.	.	.	.	.	T	0.20700	0.0498	L	0.42245	1.32	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.25187	-1.0139	9	0.66056	D	0.02	8.8294	3.2749	0.06894	0.4058:0.259:0.3352:0.0	.	23	Q8WUE5	CX048_HUMAN	C	23	ENSP00000276241:G23C;ENSP00000343893:G23C	ENSP00000276241:G23C	G	-	1	0	CXorf48	134132695	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.227000	0.01210	-1.184000	0.02720	-0.456000	0.05471	GGC	.	.		0.637	CXorf48-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058404.1			A	134305029	C	A	134305029	3	1	182	1	0	0	0	0	1	0	0	0	4113	623	22	3	755	3	CXorf48	23	134305029	Missense_Mutation	SNP	C	TCGA-DD-AAD6-01A-11D-A40R-10	33393900	134305029	20965531	104	27234										
EPHA10	284656	hgsc.bcm.edu	37	chr1	38197219	38197219	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	acggtgactgtgggcgccccTgtcttcaccatggagtaagt	13	11	2	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:38197219T>C	ENST00000373048.4	-	7	1526	c.1527A>G	c.(1525-1527)acA>acG	p.T509T	EPHA10_ENST00000540011.1_Silent_p.T4T|EPHA10_ENST00000330210.7_Silent_p.T4T|EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000427468.2_Silent_p.T509T	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	509	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TGGGCGCCCCTGTCTTCACCA	0.597																																					p.T509T		Atlas-SNP	.											.	EPHA10	120	.	0			c.A1527G						.						106	106	106					1																	38197219		1961	4150	6111	SO:0001819	synonymous_variant	284656	exon7			CGCCCCTGTCTTC	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.1527A>G	chr1.hg19:g.38197219T>C		74.0	0.0		78.0	19.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	hg19	CCDS41305.1																																																																																			.	.		0.597	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		C	38197219	T	C	38197219	2	2	183	1	0	0	0	0	0	0	0	1	5168	1567	55	2		2	EPHA10	1	38197219	Silent	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10		38197219	211053402	1	27235										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70541979	70541979	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gtatggatggatatccagagCaggtgagaagtgtttcttta	13	4	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:70541979C>G	ENST00000035383.5	+	22	4366	c.4336C>G	c.(4336-4338)Cag>Gag	p.Q1446E	LRRC7_ENST00000310961.5_Missense_Mutation_p.Q1404E|LRRC7_ENST00000415775.2_Missense_Mutation_p.Q730E	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1446	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						ATATCCAGAGCAGGTGAGAAG	0.463																																					p.Q1446E		Atlas-SNP	.											.	LRRC7	400	.	0			c.C4336G						.						53	54	54					1																	70541979		2203	4300	6503	SO:0001583	missense	57554	exon22			CCAGAGCAGGTGA		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.4336C>G	chr1.hg19:g.70541979C>G	ENSP00000035383:p.Gln1446Glu	161.0	0.0		187.0	118.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	hg19	CCDS645.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.331052	0.41297	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.35421	1.31;1.38;2.48	6.16	6.16	0.99307	PDZ/DHR/GLGF (1);	0.061229	0.64402	D	0.000002	T	0.30916	0.0780	N	0.25890	0.77	0.48040	D	0.999574	D;P;P	0.57257	0.979;0.954;0.924	P;D;P	0.67900	0.801;0.954;0.9	T	0.02081	-1.1217	10	0.02654	T	1	.	19.848	0.96722	0.0:1.0:0.0:0.0	.	730;1399;1446	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	E	1404;1446;730;1222	ENSP00000309245:Q1404E;ENSP00000035383:Q1446E;ENSP00000394867:Q730E	ENSP00000035383:Q1446E	Q	+	1	0	LRRC7	70314567	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.176000	0.71955	2.937000	0.99478	0.650000	0.86243	CAG	.	.		0.463	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		G	70541979	C	G	70541979	3	3	183	1	0	0	0	0	1	0	0	0	9029	711	25	4	4422	4	LRRC7	1	70541979	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	32344760	70541979	178708642	2	27236										
FNBP1L	54874	hgsc.bcm.edu	37	chr1	94012443	94012443	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tgtatatgagaagaatccacAaatgggggatccagggagtt	13	5	0	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:94012443A>T	ENST00000271234.7	+	13	1470	c.1319A>T	c.(1318-1320)cAa>cTa	p.Q440L	FNBP1L_ENST00000370256.4_Missense_Mutation_p.Q435L|FNBP1L_ENST00000260506.8_Missense_Mutation_p.Q382L|FNBP1L_ENST00000604705.1_Missense_Mutation_p.Q440L|FNBP1L_ENST00000370253.2_Missense_Mutation_p.Q382L	NM_001164473.2	NP_001157945.1	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like	440	Interaction with CDC42.				autophagy (GO:0006914)|clathrin-mediated endocytosis (GO:0072583)|membrane budding (GO:0006900)|membrane invagination (GO:0010324)|membrane tubulation (GO:0097320)|positive regulation of filopodium assembly (GO:0051491)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|urinary_tract(1)	11		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		AAGAATCCACAAATGGGGGAT	0.368																																					p.Q440L		Atlas-SNP	.											.	FNBP1L	56	.	0			c.A1319T						.						52	51	51					1																	94012443		1832	4077	5909	SO:0001583	missense	54874	exon13			ATCCACAAATGGG		CCDS53343.1, CCDS53344.1, CCDS60192.1	1p22.1	2008-02-05	2004-11-16	2004-11-17	ENSG00000137942	ENSG00000137942			20851	protein-coding gene	gene with protein product		608848	"chromosome 1 open reading frame 39"	C1orf39		14654988	Standard	NM_017737		Approved	TOCA1, FLJ20275	uc010otk.2	Q5T0N5	OTTHUMG00000010863	ENST00000271234.7:c.1319A>T	chr1.hg19:g.94012443A>T	ENSP00000271234:p.Gln440Leu	252.0	1.0		272.0	177.0	NM_001164473	J3QSS4|Q5T0N6|Q6B097|Q6P653|Q6R4Q4|Q9NXG1	Missense_Mutation	SNP	ENST00000271234.7	hg19	CCDS53343.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.892818	0.91889	.	.	ENSG00000137942	ENST00000370256;ENST00000271234;ENST00000260506;ENST00000370253;ENST00000424449;ENST00000541733	T;T;T	0.76578	-1.03;-1.03;-1.03	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.81669	0.4871	L	0.52126	1.63	0.80722	D	1	D;B;B;B	0.63046	0.992;0.02;0.02;0.176	D;B;B;B	0.72982	0.979;0.01;0.034;0.185	T	0.83117	-0.0120	10	0.52906	T	0.07	-17.5721	15.9763	0.80066	1.0:0.0:0.0:0.0	.	10;260;382;382	B4DKY5;B4DSI7;Q5T0N5-4;Q5T0N5-3	.;.;.;.	L	435;440;382;435;249;132	ENSP00000359278:Q435L;ENSP00000271234:Q440L;ENSP00000260506:Q382L	ENSP00000260506:Q382L	Q	+	2	0	FNBP1L	93785031	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.950000	0.93019	2.151000	0.67156	0.533000	0.62120	CAA	.	.		0.368	FNBP1L-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_017737		T	94012443	A	T	94012443	3	4	183	1	0	0	0	0	1	0	0	0	5974	130	5	4	1369	4	FNBP1L	1	94012443	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	23470464	94012443	155238178	3	27237										
HIPK1	204851	hgsc.bcm.edu	37	chr1	114498222	114498222	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	actggagactggaataaaatCaaaagaagctcggaagtaca	10	6	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:114498222C>T	ENST00000369558.1	+	5	1590	c.1358C>T	c.(1357-1359)tCa>tTa	p.S453L	HIPK1_ENST00000369561.4_Missense_Mutation_p.S453L|HIPK1_ENST00000426820.2_Missense_Mutation_p.S453L|HIPK1_ENST00000369555.2_Missense_Mutation_p.S453L|HIPK1_ENST00000406344.1_Missense_Mutation_p.S59L|HIPK1_ENST00000369559.4_Missense_Mutation_p.S453L|HIPK1_ENST00000369554.2_Missense_Mutation_p.S453L|HIPK1_ENST00000369553.1_Missense_Mutation_p.S59L|HIPK1_ENST00000340480.4_Missense_Mutation_p.S79L			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	453	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGAATAAAATCAAAAGAAGCT	0.318																																					p.S453L		Atlas-SNP	.											.	HIPK1	195	.	0			c.C1358T						.						105	121	115					1																	114498222		2203	4300	6503	SO:0001583	missense	204851	exon5			TAAAATCAAAAGA	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.1358C>T	chr1.hg19:g.114498222C>T	ENSP00000358571:p.Ser453Leu	351.0	1.0		464.0	176.0	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Missense_Mutation	SNP	ENST00000369558.1	hg19	CCDS867.1	.	.	.	.	.	.	.	.	.	.	C	34	5.312162	0.95655	.	.	ENSG00000163349	ENST00000426820;ENST00000369559;ENST00000443627;ENST00000369554;ENST00000369555;ENST00000369558;ENST00000369561;ENST00000340480;ENST00000369553;ENST00000406344	T;T;T;T;T;T;T;T;T;T	0.56444	0.47;0.48;0.52;0.46;0.46;0.52;0.53;3.55;2.54;2.54	5.1	5.1	0.69264	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	D	0.000077	T	0.54319	0.1851	N	0.25094	0.71	0.80722	D	1	D;D;D	0.89917	1.0;0.991;0.981	D;D;D	0.91635	0.999;0.987;0.962	T	0.60464	-0.7258	10	0.62326	D	0.03	.	18.7116	0.91659	0.0:1.0:0.0:0.0	.	59;453;453	Q86Z02-4;Q86Z02;Q86Z02-2	.;HIPK1_HUMAN;.	L	524;453;453;453;453;453;453;79;59;59	ENSP00000407442:S524L;ENSP00000358572:S453L;ENSP00000409673:S453L;ENSP00000358567:S453L;ENSP00000358568:S453L;ENSP00000358571:S453L;ENSP00000358574:S453L;ENSP00000340956:S79L;ENSP00000358566:S59L;ENSP00000384960:S59L	ENSP00000340956:S79L	S	+	2	0	HIPK1	114299745	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.651000	0.83577	2.634000	0.89283	0.655000	0.94253	TCA	.	.		0.318	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		T	114498222	C	T	114498222	3	4	183	1	0	0	0	0	1	0	0	0	7125	838	29	3	1390	3	HIPK1	1	114498222	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	20485779	114498222	134752399	4	27238										
ENSA	2029	hgsc.bcm.edu	37	chr1	150598960	150598960	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ggatgtttcacccaccatttCatccgcacagagaagcacac	7	14	2	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:150598960C>A	ENST00000369014.5	-	3	309				ENSA_ENST00000503241.1_Nonsense_Mutation_p.E76*|ENSA_ENST00000513281.1_Intron|ENSA_ENST00000369009.3_Intron|ENSA_ENST00000271690.8_Intron|ENSA_ENST00000339643.5_Nonsense_Mutation_p.E76*|ENSA_ENST00000361532.5_Intron|ENSA_ENST00000354702.3_Intron|ENSA_ENST00000356527.5_Intron|ENSA_ENST00000361631.5_Nonsense_Mutation_p.E72*|ENSA_ENST00000503345.1_Intron|ENSA_ENST00000369016.4_Nonsense_Mutation_p.E76*			O43768	ENSA_HUMAN	endosulfine alpha						G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|regulation of catalytic activity (GO:0050790)|regulation of insulin secretion (GO:0050796)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|transport (GO:0006810)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ion channel inhibitor activity (GO:0008200)|phosphatase inhibitor activity (GO:0019212)|potassium channel inhibitor activity (GO:0019870)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)	4	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;9.85e-23)|all cancers(9;5.06e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.67e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000701)|LUSC - Lung squamous cell carcinoma(543;0.171)			CCCACCATTTCATCCGCACAG	0.398																																					p.E76X	Esophageal Squamous(188;763 2078 3002 3411 26027)	Atlas-SNP	.											.	ENSA	41	.	0			c.G226T						.						139	124	129					1																	150598960		2203	4300	6503	SO:0001627	intron_variant	2029	exon3			CCATTTCATCCGC	X99906	CCDS958.1, CCDS959.1, CCDS960.1, CCDS961.1, CCDS962.1, CCDS963.1, CCDS964.1, CCDS965.1	1q21.3	2010-03-11			ENSG00000143420	ENSG00000143420			3360	protein-coding gene	gene with protein product		603061				9653196	Standard	NM_004436		Approved	MGC4319, MGC8394, MGC78563, ARPP-19e	uc001eve.3	O43768	OTTHUMG00000035004	ENST00000369014.5:c.184-676G>T	chr1.hg19:g.150598960C>A		73.0	0.0		77.0	33.0	NM_207043	A8K1Z9|E9PB69|Q5T5H2|Q68D48|Q6FHW0|Q6IAM4|Q6NUL2|Q6VUC6|Q6VUC7|Q6VUC8|Q6VUC9|Q6VUD0|Q6VUD1|Q9NRZ0	Nonsense_Mutation	SNP	ENST00000369014.5	hg19	CCDS958.1	.	.	.	.	.	.	.	.	.	.	C	8.670	0.902535	0.17760	.	.	ENSG00000143420	ENST00000369016;ENST00000361631;ENST00000339643;ENST00000502246;ENST00000503241	.	.	.	3.15	2.22	0.28083	.	1.881870	0.03411	U	0.204734	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.291	0.37786	0.0:0.8807:0.0:0.1193	.	.	.	.	X	76;72;76;76;76	.	ENSP00000341743:E76X	E	-	1	0	ENSA	148865584	0.000000	0.05858	0.011000	0.14972	0.001000	0.01503	-0.028000	0.12350	0.361000	0.24292	-1.119000	0.02030	GAA	.	.		0.398	ENSA-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000084720.2	NM_207042		A	150598960	C	A	150598960	1	1	183	0	1	0	0	0	0	0	0	0	5138	835	29	3		3	ENSA	1	150598960	Intron	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	36100738	150598960	98651661	5	27239										
SMCP	4184	hgsc.bcm.edu	37	chr1	152856963	152856963	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	caatcaatgctgcccaccacAgcagaaccagtgctgccagt	8	15	1	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:152856963A>T	ENST00000368765.3	+	2	215	c.65A>T	c.(64-66)cAg>cTg	p.Q22L		NM_030663.2	NP_109588.2	P49901	MCSP_HUMAN	sperm mitochondria-associated cysteine-rich protein	22	7 X 7 (OR 8) AA approximate repeats.				penetration of zona pellucida (GO:0007341)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(1)|lung(4)|urinary_tract(1)	8	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGCCCACCACAGCAGAACCAG	0.478																																					p.Q22L		Atlas-SNP	.											.	SMCP	13	.	0			c.A65T						.						102	92	95					1																	152856963		2203	4300	6503	SO:0001583	missense	4184	exon2			CACCACAGCAGAA	BC014593	CCDS1029.1	1q21.3	2009-03-19	2005-10-06	2005-10-06	ENSG00000163206	ENSG00000163206			6962	protein-coding gene	gene with protein product		601148	"mitochondrial capsule selenoprotein"	MCSP		8833144	Standard	NM_030663		Approved		uc001fat.3	P49901	OTTHUMG00000012452	ENST00000368765.3:c.65A>T	chr1.hg19:g.152856963A>T	ENSP00000357754:p.Gln22Leu	219.0	0.0		292.0	116.0	NM_030663	Q96A42	Missense_Mutation	SNP	ENST00000368765.3	hg19	CCDS1029.1	.	.	.	.	.	.	.	.	.	.	A	5.185	0.219675	0.09863	.	.	ENSG00000163206	ENST00000368765	T	0.56941	0.43	3.44	1.09	0.20402	.	0.442567	0.16719	N	0.202329	T	0.11750	0.0286	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29150	-1.0021	10	0.38643	T	0.18	-2.2026	8.0194	0.30400	0.4495:0.5504:0.0:0.0	.	22	P49901	MCSP_HUMAN	L	22	ENSP00000357754:Q22L	ENSP00000357754:Q22L	Q	+	2	0	SMCP	151123587	0.000000	0.05858	0.003000	0.11579	0.010000	0.07245	0.482000	0.22276	0.224000	0.20940	0.533000	0.62120	CAG	.	.		0.478	SMCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034665.1	NM_030663		T	152856963	A	T	152856963	3	4	183	1	0	0	0	0	1	0	0	0	14804	188	7	4	67	4	SMCP	1	152856963	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	2258003	152856963	96393658	6	27240										
MEF2D	4209	hgsc.bcm.edu	37	chr1	156452269	156452269	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tgcggctctcgtgtggctcaTtgtactccgtgtacttgagc	12	11	2	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:156452269T>C	ENST00000348159.4	-	3	698	c.218A>G	c.(217-219)aAt>aGt	p.N73S	Y_RNA_ENST00000383924.1_RNA|MEF2D_ENST00000353795.3_Missense_Mutation_p.N73S|MEF2D_ENST00000360595.3_Missense_Mutation_p.N73S|MEF2D_ENST00000368240.2_Missense_Mutation_p.N73S|MEF2D_ENST00000340875.5_Missense_Mutation_p.N73S|MEF2D_ENST00000464356.2_Missense_Mutation_p.N73S	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	73					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GTGTGGCTCATTGTACTCCGT	0.572																																					p.N73S		Atlas-SNP	.											.	MEF2D	43	.	0			c.A218G						.						390	310	337					1																	156452269		2203	4300	6503	SO:0001583	missense	4209	exon3			GGCTCATTGTACT	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"Myocyte enhancer factors"	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.218A>G	chr1.hg19:g.156452269T>C	ENSP00000271555:p.Asn73Ser	81.0	0.0		106.0	59.0	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Missense_Mutation	SNP	ENST00000348159.4	hg19	CCDS1143.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.809937	0.90707	.	.	ENSG00000116604	ENST00000348159;ENST00000340875;ENST00000368240;ENST00000353795;ENST00000360595;ENST00000541336;ENST00000454816	T;T;T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44;-1.44;-1.44	5.05	5.05	0.67936	Transcription factor, MADS-box (1);	0.000000	0.85682	D	0.000000	T	0.68100	0.2964	L	0.41356	1.27	0.80722	D	1	P;P;B	0.47762	0.727;0.9;0.336	B;B;B	0.43950	0.37;0.417;0.437	T	0.74084	-0.3779	10	0.56958	D	0.05	-22.345	13.6292	0.62186	0.0:0.0:0.0:1.0	.	78;73;73	Q4LE66;Q14814;Q14814-4	.;MEF2D_HUMAN;.	S	73	ENSP00000271555:N73S;ENSP00000343159:N73S;ENSP00000357223:N73S;ENSP00000344705:N73S;ENSP00000353803:N73S;ENSP00000388505:N73S	ENSP00000343159:N73S	N	-	2	0	MEF2D	154718893	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.170000	0.64990	1.912000	0.55364	0.459000	0.35465	AAT	.	.		0.572	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920		C	156452269	T	C	156452269	3	2	183	1	0	0	0	0	1	0	0	0	9467	1493	52	2	1387	2	MEF2D	1	156452269	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	3595306	156452269	92798352	7	27241										
TTC24	164118	hgsc.bcm.edu	37	chr1	156555548	156555548	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	aatcattcgcaccatctagcTtctagttgccccacgtttac	5	14	3	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:156555548T>A	ENST00000368237.3	+	8	1500	c.1500T>A	c.(1498-1500)gcT>gcA	p.A500A	TTC24_ENST00000368236.3_Silent_p.A500A|AL365181.1_ENST00000581084.1_RNA|TTC24_ENST00000478081.1_3'UTR			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	500										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ACCATCTAGCTTCTAGTTGCC	0.522																																					p.A500A		Atlas-SNP	.											.	TTC24	46	.	0			c.T1500A						.						130	130	130					1																	156555548		2111	4230	6341	SO:0001819	synonymous_variant	164118	exon9			TCTAGCTTCTAGT		CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"Tetratricopeptide (TTC) repeat domain containing"	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.1500T>A	chr1.hg19:g.156555548T>A		75.0	0.0		103.0	52.0	NM_001105669	Q5T3H7	Silent	SNP	ENST00000368237.3	hg19	CCDS53379.1	.	.	.	.	.	.	.	.	.	.	T	9.494	1.101438	0.20632	.	.	ENSG00000187862	ENST00000340086	.	.	.	2.22	-0.411	0.12370	.	.	.	.	.	T	0.09686	0.0238	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35450	-0.9788	4	.	.	.	.	5.0069	0.14293	0.0:0.6453:0.0:0.3547	.	.	.	.	H	273	.	.	L	+	2	0	TTC24	154822172	0.000000	0.05858	0.000000	0.03702	0.518000	0.34316	-0.026000	0.12392	-0.082000	0.12640	0.379000	0.24179	CTT	.	.		0.522	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		A	156555548	T	A	156555548	2	1	183	1	0	0	0	0	0	0	0	1	16707	1596	56	4		4	TTC24	1	156555548	Silent	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	103279	156555548	92695073	8	27242										
FCRL1	115350	hgsc.bcm.edu	37	chr1	157765954	157765954	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	cagcctggaatagatgtctaAggaaacctggaagcaaagat	11	7	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:157765954A>T	ENST00000368176.3	-	11	1292	c.1225T>A	c.(1225-1227)Tta>Ata	p.L409I	FCRL1_ENST00000358292.3_Silent_p.P366P|FCRL1_ENST00000491942.1_Missense_Mutation_p.L408I|FCRL1_ENST00000489998.1_5'UTR	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	409						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TAGATGTCTAAGGAAACCTGG	0.443																																					p.L409I	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.T1225A						.						127	109	115					1																	157765954		2203	4300	6503	SO:0001583	missense	115350	exon11			TGTCTAAGGAAAC	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.1225T>A	chr1.hg19:g.157765954A>T	ENSP00000357158:p.Leu409Ile	71.0	0.0		122.0	56.0	NM_052938	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Missense_Mutation	SNP	ENST00000368176.3	hg19	CCDS1170.1	.	.	.	.	.	.	.	.	.	.	A	8.633	0.894208	0.17613	.	.	ENSG00000163534	ENST00000368176;ENST00000491942	T;T	0.37235	1.21;1.22	4.37	-1.1	0.09872	.	2.291920	0.01966	N	0.043668	T	0.11793	0.0287	.	.	.	0.09310	N	1	B;B	0.32160	0.358;0.244	B;B	0.35971	0.215;0.107	T	0.20174	-1.0283	9	0.39692	T	0.17	.	6.3206	0.21215	0.3954:0.5081:0.0965:0.0	.	408;409	Q96LA6-2;Q96LA6	.;FCRL1_HUMAN	I	409;408	ENSP00000357158:L409I;ENSP00000418130:L408I	ENSP00000357158:L409I	L	-	1	2	FCRL1	156032578	0.001000	0.12720	0.000000	0.03702	0.050000	0.14768	0.354000	0.20146	-0.286000	0.09076	0.454000	0.30748	TTA	.	.		0.443	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938		T	157765954	A	T	157765954	3	4	183	1	0	0	0	0	1	0	0	0	5802	69	3	4	68	4	FCRL1	1	157765954	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	1210406	157765954	91484667	9	27243										
IGSF8	93185	hgsc.bcm.edu	37	chr1	160063091	160063091	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctgggccgatccgacgttcaCcaggccccactgtcactgcc	10	18	2	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:160063091C>T	ENST00000368086.1	-	4	1151	c.935G>A	c.(934-936)gGt>gAt	p.G312D	IGSF8_ENST00000314485.7_Missense_Mutation_p.G312D|IGSF8_ENST00000460351.1_5'Flank			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	312	Ig-like C2-type 3.				cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|nervous system development (GO:0007399)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(19)|pancreas(1)|prostate(1)|skin(1)	33	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CCGACGTTCACCAGGCCCCAC	0.617																																					p.G312D		Atlas-SNP	.											.	IGSF8	59	.	0			c.G935A						.						41	40	40					1																	160063091		2202	4299	6501	SO:0001583	missense	93185	exon4			CGTTCACCAGGCC	AF407274	CCDS1195.1	1q23.1	2013-01-11			ENSG00000162729	ENSG00000162729		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	17813	protein-coding gene	gene with protein product		606644				11504738, 11673522	Standard	NM_001206665		Approved	CD81P3, EWI2, PGRL, CD316	uc009wtf.3	Q969P0	OTTHUMG00000024075	ENST00000368086.1:c.935G>A	chr1.hg19:g.160063091C>T	ENSP00000357065:p.Gly312Asp	120.0	0.0		150.0	33.0	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Missense_Mutation	SNP	ENST00000368086.1	hg19	CCDS1195.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.787841	0.49997	.	.	ENSG00000162729	ENST00000314485;ENST00000368086;ENST00000358475	T;T	0.27402	1.67;1.67	3.65	3.65	0.41850	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.161058	0.40728	N	0.001031	T	0.22166	0.0534	L	0.34521	1.04	0.41634	D	0.989038	D	0.76494	0.999	D	0.66716	0.946	T	0.03453	-1.1035	10	0.08599	T	0.76	-10.0174	10.9917	0.47553	0.0:0.8085:0.1915:0.0	.	312	Q969P0	IGSF8_HUMAN	D	312	ENSP00000316664:G312D;ENSP00000357065:G312D	ENSP00000316664:G312D	G	-	2	0	IGSF8	158329715	0.116000	0.22171	0.929000	0.37066	0.843000	0.47879	1.092000	0.30927	1.870000	0.54199	0.313000	0.20887	GGT	.	.		0.617	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868		T	160063091	C	T	160063091	3	4	183	1	0	0	0	0	1	0	0	0	7613	507	18	3	918	3	IGSF8	1	160063091	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	2297137	160063091	89187530	10	27244										
RASAL2	9462	hgsc.bcm.edu	37	chr1	178427017	178427017	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	atgctgctcaagtggagcatGcatctgtcatgcttgatgtg	12	8	3	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:178427017G>T	ENST00000462775.1	+	12	2292	c.2167G>T	c.(2167-2169)Gca>Tca	p.A723S	RASAL2_ENST00000448150.3_Missense_Mutation_p.A853S|RASAL2_ENST00000367649.3_Missense_Mutation_p.A864S	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	723					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						AGTGGAGCATGCATCTGTCAT	0.527																																					p.A864S		Atlas-SNP	.											.	RASAL2	334	.	0			c.G2590T						.						88	82	84					1																	178427017		2203	4300	6503	SO:0001583	missense	9462	exon14			GAGCATGCATCTG	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"Pleckstrin homology (PH) domain containing"	9874	protein-coding gene	gene with protein product	"Ras GTPase activating protein-like", "Ras protein activator like 1"	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.2167G>T	chr1.hg19:g.178427017G>T	ENSP00000420558:p.Ala723Ser	120.0	0.0		130.0	9.0	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000462775.1	hg19	CCDS1322.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.163|0.163	-1.079048|-1.079048	0.01903|0.01903	.|.	.|.	ENSG00000075391|ENSG00000075391	ENST00000448150;ENST00000367649;ENST00000462775|ENST00000433130	T;T;T|.	0.10668|.	2.85;2.85;2.85|.	5.42|5.42	1.16|1.16	0.20824|0.20824	.|.	0.590474|.	0.16941|.	N|.	0.193284|.	T|T	0.18215|0.18215	0.0437|0.0437	N|N	0.17379|0.17379	0.485|0.485	0.09310|0.09310	N|N	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.06405|.	0.001;0.002;0.001|.	T|T	0.21109|0.21109	-1.0255|-1.0255	10|5	0.02654|.	T|.	1|.	.|.	2.2437|2.2437	0.04026|0.04026	0.1345:0.239:0.3808:0.2457|0.1345:0.239:0.3808:0.2457	.|.	853;723;864|.	B1AKC7;Q9UJF2;F8W755|.	.;NGAP_HUMAN;.|.	S|F	853;864;723|273	ENSP00000407768:A853S;ENSP00000356621:A864S;ENSP00000420558:A723S|.	ENSP00000356621:A864S|.	A|C	+|+	1|2	0|0	RASAL2|RASAL2	176693640|176693640	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.908000|0.908000	0.53690|0.53690	0.169000|0.169000	0.16641|0.16641	0.244000|0.244000	0.21351|0.21351	0.655000|0.655000	0.94253|0.94253	GCA|TGC	.	.		0.527	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692		T	178427017	G	T	178427017	3	4	183	1	0	0	0	0	1	0	0	0	13079	1319	46	3	2682	3	RASAL2	1	178427017	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	18363926	178427017	70823604	11	27245										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179347779	179347779	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tcttactttttagggatattTcttttctgtacgatgtaaca	6	6	3	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:179347779T>C	ENST00000367618.3	+	5	769	c.382T>C	c.(382-384)Tct>Cct	p.S128P	AXDND1_ENST00000461179.2_3'UTR|AXDND1_ENST00000457238.2_Missense_Mutation_p.S128P	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	128										NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						TAGGGATATTTCTTTTCTGTA	0.383																																					p.S128P		Atlas-SNP	.											.	AXDND1	142	.	0			c.T382C						.						76	69	72					1																	179347779		2203	4300	6503	SO:0001583	missense	126859	exon5			GATATTTCTTTTC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.382T>C	chr1.hg19:g.179347779T>C	ENSP00000356590:p.Ser128Pro	68.0	0.0		79.0	45.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.098948	0.76870	.	.	ENSG00000162779	ENST00000509175;ENST00000367618;ENST00000360322;ENST00000457238;ENST00000511889;ENST00000434088	T;T;T	0.62941	1.09;-0.01;1.26	4.81	4.81	0.61882	.	0.150426	0.45606	D	0.000358	T	0.72574	0.3477	M	0.63843	1.955	0.36779	D	0.884213	D;D	0.71674	0.998;0.998	P;P	0.62649	0.905;0.905	T	0.79713	-0.1688	10	0.87932	D	0	0.1187	11.043	0.47842	0.0:0.0:0.0:1.0	.	86;128	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	P	86;128;86;128;86;62	ENSP00000356590:S128P;ENSP00000416712:S128P;ENSP00000391716:S62P	ENSP00000353471:S86P	S	+	1	0	AXDND1	177614402	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.617000	0.46385	1.916000	0.55485	0.482000	0.46254	TCT	.	.		0.383	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179347779	T	C	179347779	3	2	183	1	0	0	0	0	1	0	0	0	1995	1783	62	2	396	2	C1orf125	1	179347779	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	920762	179347779	69902842	12	27246										
XPR1	9213	hgsc.bcm.edu	37	chr1	180804015	180804015	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ttttttttctttcagtttcgAgtatttacagcccccttcca	4	11	2	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:180804015A>T	ENST00000367590.4	+	10	1338	c.1140A>T	c.(1138-1140)cgA>cgT	p.R380R	XPR1_ENST00000367589.3_Silent_p.R380R	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	380					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						TTCAGTTTCGAGTATTTACAG	0.393																																					p.R380R		Atlas-SNP	.											.	XPR1	76	.	0			c.A1140T						.						54	55	55					1																	180804015		2203	4300	6503	SO:0001819	synonymous_variant	9213	exon10			GTTTCGAGTATTT	AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"xenotropic and polytropic retrovirus receptor"			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.1140A>T	chr1.hg19:g.180804015A>T		57.0	0.0		69.0	38.0	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	hg19	CCDS1340.1																																																																																			.	.		0.393	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		T	180804015	A	T	180804015	2	4	183	1	0	0	0	0	0	0	0	1	17466	291	11	4		4	XPR1	1	180804015	Silent	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	1456236	180804015	68446606	13	27247										
CAPN9	10753	hgsc.bcm.edu	37	chr1	230883256	230883256	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	agcagccatgccttacctctAccgggccccagggcctcagg	11	17	2	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:230883256A>T	ENST00000271971.2	+	1	127	c.14A>T	c.(13-15)tAc>tTc	p.Y5F	CAPN9_ENST00000366666.2_Missense_Mutation_p.Y5F|RP11-99J16__A.2_ENST00000412344.1_RNA|CAPN9_ENST00000354537.1_Missense_Mutation_p.Y5F	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	5					digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				CCTTACCTCTACCGGGCCCCA	0.612																																					p.Y5F		Atlas-SNP	.											.	CAPN9	116	.	0			c.A14T						.						55	62	60					1																	230883256		2203	4300	6503	SO:0001583	missense	10753	exon1			ACCTCTACCGGGC	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"EF-hand domain containing"	1486	protein-coding gene	gene with protein product	"novel calpain large subunit-4"	606401	"calpain 9 (nCL-4)"			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.14A>T	chr1.hg19:g.230883256A>T	ENSP00000271971:p.Tyr5Phe	157.0	0.0		244.0	125.0	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	hg19	CCDS1586.1	.	.	.	.	.	.	.	.	.	.	A	7.553	0.663136	0.14710	.	.	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	T;T;T	0.46819	0.86;0.86;0.86	5.29	2.95	0.34219	.	1.271780	0.04835	N	0.439406	T	0.28566	0.0707	N	0.19112	0.55	0.09310	N	1	B;B;B	0.28552	0.09;0.178;0.215	B;B;B	0.24155	0.024;0.049;0.051	T	0.23547	-1.0185	10	0.09590	T	0.72	.	3.9452	0.09346	0.6662:0.1339:0.0716:0.1283	.	5;5;5	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	F	5	ENSP00000271971:Y5F;ENSP00000346538:Y5F;ENSP00000355626:Y5F	ENSP00000271971:Y5F	Y	+	2	0	CAPN9	228949879	0.178000	0.23122	0.019000	0.16419	0.104000	0.19210	2.439000	0.44846	0.814000	0.34374	0.533000	0.62120	TAC	.	.		0.612	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615		T	230883256	A	T	230883256	3	4	183	1	0	0	0	0	1	0	0	0	2634	391	14	4	16	4	CAPN9	1	230883256	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	50079241	230883256	18367365	14	27248										
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233297033	233297033	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	atactcgcaatgacaggaatAcagtgctggcgctgactgca	11	10	0	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:233297033A>T	ENST00000258229.9	-	18	3584	c.3350T>A	c.(3349-3351)gTa>gAa	p.V1117E	PCNXL2_ENST00000520463.1_5'Flank|PCNXL2_ENST00000488780.2_Missense_Mutation_p.V250E	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1117						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				TGACAGGAATACAGTGCTGGC	0.468																																					p.V1117E		Atlas-SNP	.											.	PCNXL2	204	.	0			c.T3350A						.						74	77	76					1																	233297033		2086	4210	6296	SO:0001583	missense	80003	exon18			AGGAATACAGTGC	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.3350T>A	chr1.hg19:g.233297033A>T	ENSP00000258229:p.Val1117Glu	218.0	0.0		278.0	99.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	A	18.58	3.654648	0.67472	.	.	ENSG00000135749	ENST00000258229;ENST00000488780	T	0.12672	2.66	5.02	5.02	0.67125	.	.	.	.	.	T	0.42017	0.1184	M	0.84585	2.705	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.48328	-0.9045	9	0.87932	D	0	.	14.9104	0.70752	1.0:0.0:0.0:0.0	.	1117	A6NKB5	PCX2_HUMAN	E	1117;250	ENSP00000258229:V1117E	ENSP00000258229:V1117E	V	-	2	0	PCNXL2	231363656	1.000000	0.71417	0.988000	0.46212	0.972000	0.66771	6.375000	0.73137	2.098000	0.63641	0.482000	0.46254	GTA	.	.		0.468	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		T	233297033	A	T	233297033	3	4	183	1	0	0	0	0	1	0	0	0	11601	391	14	4	3131	4	PCNXL2	1	233297033	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	2413777	233297033	15953588	15	27249										
GNG4	2786	hgsc.bcm.edu	37	chr1	235747052	235747052	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	atgcttaccttgaccctgtcCatacaggcttccatctttag	6	13	1	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr1:235747052C>T	ENST00000366598.4	-	2	302	c.87G>A	c.(85-87)atG>atA	p.M29I	GNG4_ENST00000484517.1_5'UTR|GNG4_ENST00000450593.1_Missense_Mutation_p.M29I|GNG4_ENST00000391854.2_Missense_Mutation_p.M29I|GNG4_ENST00000366597.1_Missense_Mutation_p.M29I			P50150	GBG4_HUMAN	guanine nucleotide binding protein (G protein), gamma 4	29					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of cell growth (GO:0030308)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00168)|Prostate(94;0.0776)|Acute lymphoblastic leukemia(190;0.23)	OV - Ovarian serous cystadenocarcinoma(106;0.000882)			TGACCCTGTCCATACAGGCTT	0.517																																					p.M29I		Atlas-SNP	.											.	GNG4	18	.	0			c.G87A						.						186	169	175					1																	235747052		2203	4300	6503	SO:0001583	missense	2786	exon2			CCTGTCCATACAG	BC022485	CCDS1607.1	1q42.3	2008-02-05			ENSG00000168243	ENSG00000168243			4407	protein-coding gene	gene with protein product		604388				7665596	Standard	NM_001098721		Approved		uc001hxh.4	P50150	OTTHUMG00000040740	ENST00000366598.4:c.87G>A	chr1.hg19:g.235747052C>T	ENSP00000355557:p.Met29Ile	71.0	0.0		80.0	35.0	NM_004485		Missense_Mutation	SNP	ENST00000366598.4	hg19	CCDS1607.1	.	.	.	.	.	.	.	.	.	.	C	6.739	0.505111	0.12822	.	.	ENSG00000168243	ENST00000450593;ENST00000391854;ENST00000366598;ENST00000366597	T;T;T;T	0.21191	2.02;2.02;2.02;2.02	5.52	4.61	0.57282	G-protein gamma domain (5);	0.000000	0.85682	D	0.000000	T	0.09598	0.0236	.	.	.	0.39713	D	0.971364	B	0.02656	0.0	B	0.04013	0.001	T	0.11348	-1.0591	9	0.02654	T	1	-13.032	11.514	0.50509	0.0:0.9154:0.0:0.0846	.	29	P50150	GBG4_HUMAN	I	29	ENSP00000398629:M29I;ENSP00000375727:M29I;ENSP00000355557:M29I;ENSP00000355556:M29I	ENSP00000355556:M29I	M	-	3	0	GNG4	233813675	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.922000	0.56462	1.325000	0.45301	0.655000	0.94253	ATG	.	.		0.517	GNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097906.1	NM_004485		T	235747052	C	T	235747052	3	4	183	1	0	0	0	0	1	0	0	0	6537	594	21	3	148	3	GNG4	1	235747052	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	2450019	235747052	13503569	16	27250										
RTN4	57142	hgsc.bcm.edu	37	chr2	55253108	55253108	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gagaaatccggagctggttcAgcagaaagctttgtttcttt	11	7	2	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr2:55253108A>T	ENST00000337526.6	-	3	2370	c.2127T>A	c.(2125-2127)gcT>gcA	p.A709A	RTN4_ENST00000357376.3_Silent_p.A503A|RTN4_ENST00000354474.6_Silent_p.A477A|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000405240.1_Silent_p.A503A|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000404909.1_Silent_p.A503A|RTN4_ENST00000394611.2_Silent_p.A503A	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	709					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						GAGCTGGTTCAGCAGAAAGCT	0.368																																					p.A709A		Atlas-SNP	.											.	RTN4	189	.	0			c.T2127A						.						57	63	61					2																	55253108		2201	4295	6496	SO:0001819	synonymous_variant	57142	exon3			TGGTTCAGCAGAA	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.2127T>A	chr2.hg19:g.55253108A>T		27.0	0.0		34.0	20.0	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Silent	SNP	ENST00000337526.6	hg19	CCDS42684.1																																																																																			.	.		0.368	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			T	55253108	A	T	55253108	2	4	183	1	0	0	0	0	0	0	0	1	13743	175	7	4		4	RTN4	2	55253108	Silent	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10		55253108	187946265	17	27251										
ERCC3	2071	hgsc.bcm.edu	37	chr2	128044277	128044277	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	agctcagctccagcctgcttAcctggtatggtgtgcacttc	10	13	1	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr2:128044277A>G	ENST00000285398.2	-	8	1437		c.e8+1		ERCC3_ENST00000493187.2_Splice_Site	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3						7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CAGCCTGCTTACCTGGTATGG	0.552			"Mis, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												.		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"		E	.	ERCC3	73	.	0			c.1342+2T>C						.						79	77	78					2																	128044277		2203	4300	6503	SO:0001630	splice_region_variant	2071	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CTGCTTACCTGGT	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"General transcription factors", "General transcription factor IIH complex subunits"	3435	protein-coding gene	gene with protein product	"xeroderma pigmentosum group B complementing"	133510	"excision repair cross-complementing rodent repair deficiency, complementation group 3"			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.1342+1T>C	chr2.hg19:g.128044277A>G		30.0	0.0		54.0	26.0	NM_000122	Q53QM0	Splice_Site	SNP	ENST00000285398.2	hg19	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.936950	0.73557	.	.	ENSG00000163161	ENST00000285398;ENST00000493187	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2146	0.73254	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ERCC3	127760747	1.000000	0.71417	0.987000	0.45799	0.813000	0.45954	9.287000	0.95975	2.050000	0.60909	0.459000	0.35465	.	.	.		0.552	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122	Intron	G	128044277	A	G	128044277	5	3	183	1	0	0	0	0	0	0	1	0	5216	405	14	2	1036	2	ERCC3	2	128044277	Splice_Site	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	72791169	128044277	115155096	18	27252										
AGPS	8540	hgsc.bcm.edu	37	chr2	178370292	178370292	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	atttgctgacctatgttattGcatacattcgagtaagttat	7	6	0	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr2:178370292G>A	ENST00000264167.4	+	15	1680	c.1534G>A	c.(1534-1536)Gca>Aca	p.A512T	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	512					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			CTATGTTATTGCATACATTCG	0.313																																					p.A512T		Atlas-SNP	.											.	AGPS	56	.	0			c.G1534A						.						152	147	148					2																	178370292		2203	4298	6501	SO:0001583	missense	8540	exon15			GTTATTGCATACA	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.1534G>A	chr2.hg19:g.178370292G>A	ENSP00000264167:p.Ala512Thr	43.0	0.0		64.0	23.0	NM_003659	A5D8U9|Q2TU35	Missense_Mutation	SNP	ENST00000264167.4	hg19	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	G	32	5.153665	0.94645	.	.	ENSG00000018510	ENST00000264167	D	0.84223	-1.82	5.11	5.11	0.69529	FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93693	0.7985	M	0.89287	3.02	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94626	0.7817	10	0.66056	D	0.02	.	18.5216	0.90954	0.0:0.0:1.0:0.0	.	512	O00116	ADAS_HUMAN	T	512	ENSP00000264167:A512T	ENSP00000264167:A512T	A	+	1	0	AGPS	178078538	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.784000	0.91818	2.378000	0.81104	0.555000	0.69702	GCA	.	.		0.313	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			A	178370292	G	A	178370292	3	1	183	1	0	0	0	0	1	0	0	0	394	1319	46	3	1592	3	AGPS	2	178370292	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	50326015	178370292	64829081	19	27253										
TTN	7273	hgsc.bcm.edu	37	chr2	179407205	179407205	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctcagtggagcaccaccgtcCaattcaggtggttcccagga	11	13	2	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr2:179407205C>T	ENST00000591111.1	-	299	92579	c.92355G>A	c.(92353-92355)ttG>ttA	p.L30785L	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Silent_p.L32426L|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Silent_p.L23361L|TTN_ENST00000342992.6_Silent_p.L29858L|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000342175.6_Silent_p.L23553L|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Silent_p.L23486L|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30785	Fibronectin type-III 124. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACCACCGTCCAATTCAGGTG	0.468																																					p.L32426L		Atlas-SNP	.											.	TTN	18412	.	0			c.G97278A						.						60	60	60					2																	179407205		1947	4143	6090	SO:0001819	synonymous_variant	7273	exon349			ACCGTCCAATTCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.92355G>A	chr2.hg19:g.179407205C>T		79.0	0.0		124.0	52.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179407205	C	T	179407205	2	4	183	1	0	0	0	0	0	0	0	1	16750	593	21	3		3	TTN	2	179407205	Silent	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	1036913	179407205	63792168	20	27254										
TTN	7273	hgsc.bcm.edu	37	chr2	179465992	179465992	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	atttagattttaaagcttacAtatcggatctctggcagtgg	9	6	1	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr2:179465992A>T	ENST00000591111.1	-	237	51033	c.50809T>A	c.(50809-50811)Tat>Aat	p.Y16937N	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Splice_Site_p.Y18578N|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Splice_Site_p.Y9513N|TTN_ENST00000342992.6_Splice_Site_p.Y16010N|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Splice_Site_p.Y9705N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Splice_Site_p.Y9638N|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16937					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAAAGCTTACATATCGGATCT	0.353																																					p.Y18578N		Atlas-SNP	.											.	TTN	18412	.	0			c.T55732A						.						57	53	54					2																	179465992		1819	4084	5903	SO:0001630	splice_region_variant	7273	exon287			GCTTACATATCGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.50809+1T>A	chr2.hg19:g.179465992A>T		133.0	0.0		206.0	106.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.818	1.184896	0.21870	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	5.28	5.28	0.74379	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.27419	0.0673	N	0.17564	0.495	0.40822	D	0.983512	B;B;B;B	0.21606	0.058;0.058;0.058;0.058	B;B;B;B	0.20577	0.03;0.03;0.03;0.03	T	0.16482	-1.0401	8	.	.	.	.	5.9236	0.19096	0.7916:0.0:0.2084:0.0	.	9513;9638;9705;16937	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	16010;9513;9705;9638;9513	ENSP00000343764:Y16010N;ENSP00000434586:Y9513N;ENSP00000340554:Y9705N;ENSP00000352154:Y9638N	.	Y	-	1	0	TTN	179174237	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.879000	0.48522	2.118000	0.64928	0.460000	0.39030	TAT	.	.		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	Missense_Mutation	T	179465992	A	T	179465992	5	4	183	1	0	0	0	0	0	0	1	0	16750	231	8	4	52265	4	TTN	2	179465992	Splice_Site	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	58787	179465992	63733381	21	27255										
DPPA4	55211	hgsc.bcm.edu	37	chr3	109050838	109050838	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ggtatcttcttctgaggtctGgggttgtcagtgtgctctgc	14	8	6	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr3:109050838G>A	ENST00000335658.6	-	3	273	c.219C>T	c.(217-219)ccC>ccT	p.P73P	DPPA4_ENST00000478791.1_5'UTR	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	73					lung-associated mesenchyme development (GO:0060484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(17)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						TCTGAGGTCTGGGGTTGTCAG	0.443																																					p.P73P		Atlas-SNP	.											.	DPPA4	56	.	0			c.C219T						.						179	176	177					3																	109050838		2203	4300	6503	SO:0001819	synonymous_variant	55211	exon3			AGGTCTGGGGTTG	AK001575	CCDS33814.1	3q13.13	2014-01-28			ENSG00000121570	ENSG00000121570			19200	protein-coding gene	gene with protein product		614125					Standard	NM_018189		Approved	FLJ10713	uc003dxq.4	Q7L190	OTTHUMG00000159222	ENST00000335658.6:c.219C>T	chr3.hg19:g.109050838G>A		85.0	0.0		76.0	28.0	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Silent	SNP	ENST00000335658.6	hg19	CCDS33814.1																																																																																			.	.		0.443	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189		A	109050838	G	A	109050838	2	1	183	1	0	0	0	0	0	0	0	1	4738	1335	47	3		3	DPPA4	3	109050838	Silent	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10		109050838	88971592	22	27256										
ITGB5	3693	hgsc.bcm.edu	37	chr3	124540273	124540273	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gatgtggggcacatcatctgTtgtgaacaccagcaaatgca	11	9	2	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr3:124540273T>C	ENST00000296181.4	-	6	1125	c.829A>G	c.(829-831)Aca>Gca	p.T277A		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	277	VWFA.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		ACATCATCTGTTGTGAACACC	0.557																																					p.T277A		Atlas-SNP	.											.	ITGB5	66	.	0			c.A829G						.						156	123	134					3																	124540273		2203	4300	6503	SO:0001583	missense	3693	exon6			CATCTGTTGTGAA	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.829A>G	chr3.hg19:g.124540273T>C	ENSP00000296181:p.Thr277Ala	75.0	0.0		71.0	42.0	NM_002213	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	hg19	CCDS3030.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.11|19.11	3.762991|3.762991	0.69763|0.69763	.|.	.|.	ENSG00000082781|ENSG00000082781	ENST00000496703|ENST00000296181	.|D	.|0.99369	.|-5.78	5.52|5.52	3.0|3.0	0.34707|0.34707	.|Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	.|0.111989	.|0.64402	.|D	.|0.000010	D|D	0.99074|0.99074	0.9682|0.9682	M|M	0.93594|0.93594	3.435|3.435	0.80722|0.80722	D|D	1|1	.|P	.|0.51653	.|0.947	.|P	.|0.49752	.|0.621	D|D	0.98971|0.98971	1.0801|1.0801	5|10	.|0.87932	.|D	.|0	.|.	8.5722|8.5722	0.33576|0.33576	0.1245:0.0695:0.0:0.806|0.1245:0.0695:0.0:0.806	.|.	.|277	.|P18084	.|ITB5_HUMAN	S|A	73|277	.|ENSP00000296181:T277A	.|ENSP00000296181:T277A	N|T	-|-	2|1	0|0	ITGB5|ITGB5	126022963|126022963	1.000000|1.000000	0.71417|0.71417	0.021000|0.021000	0.16686|0.16686	0.793000|0.793000	0.44817|0.44817	6.073000|6.073000	0.71245|0.71245	1.107000|1.107000	0.41642|0.41642	0.460000|0.460000	0.39030|0.39030	AAC|ACA	.	.		0.557	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		C	124540273	T	C	124540273	3	2	183	1	0	0	0	0	1	0	0	0	7907	1725	60	2	1610	2	ITGB5	3	124540273	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	15489435	124540273	73482157	23	27257										
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42576682	42576682	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	cttcttaaactgcattacatTgcatgtcagagtaccagttt	6	9	2	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr4:42576682T>A	ENST00000381668.5	-	14	1480	c.1249A>T	c.(1249-1251)Aat>Tat	p.N417Y	ATP8A1_ENST00000264449.10_Missense_Mutation_p.N417Y	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	417					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	TGCATTACATTGCATGTCAGA	0.308																																					p.N417Y		Atlas-SNP	.											.	ATP8A1	206	.	0			c.A1249T						.						60	61	61					4																	42576682		2203	4299	6502	SO:0001583	missense	10396	exon14			TTACATTGCATGT	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1249A>T	chr4.hg19:g.42576682T>A	ENSP00000371084:p.Asn417Tyr	212.0	0.0		161.0	102.0	NM_001105529	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	hg19	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.542847	0.86022	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	D;D	0.91631	-2.88;-2.88	5.53	5.53	0.82687	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.97776	0.9270	H	0.98682	4.3	0.80722	D	1	D;D;D	0.89917	0.995;1.0;1.0	D;D;D	0.97110	0.979;1.0;1.0	D	0.99453	1.0941	10	0.87932	D	0	.	15.6709	0.77274	0.0:0.0:0.0:1.0	.	417;417;417	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	Y	417	ENSP00000371084:N417Y;ENSP00000264449:N417Y	ENSP00000264449:N417Y	N	-	1	0	ATP8A1	42271439	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.972000	0.88022	2.099000	0.63709	0.482000	0.46254	AAT	.	.		0.308	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		A	42576682	T	A	42576682	3	1	183	1	0	0	0	0	1	0	0	0	1192	1812	63	4	2341	4	ATP8A1	4	42576682	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10		42576682	148577594	24	27258										
FGF5	2250	hgsc.bcm.edu	37	chr4	81188186	81188186	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ccgcagcttctctgggcagcCaaggaagtggcttggagcag	15	11	1	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr4:81188186C>A	ENST00000312465.7	+	1	434	c.208C>A	c.(208-210)Caa>Aaa	p.Q70K	FGF5_ENST00000456523.3_Missense_Mutation_p.Q70K	NM_004464.3	NP_004455.2	P12034	FGF5_HUMAN	fibroblast growth factor 5	70					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell differentiation (GO:0010001)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction involved in regulation of gene expression (GO:0023019)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	fibroblast growth factor receptor binding (GO:0005104)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22						TCTGGGCAGCCAAGGAAGTGG	0.612																																					p.Q70K		Atlas-SNP	.											.	FGF5	49	.	0			c.C208A						.						61	66	65					4																	81188186		2203	4300	6503	SO:0001583	missense	2250	exon1			GGCAGCCAAGGAA	M23534	CCDS3586.1, CCDS34021.1	4q21	2014-01-30			ENSG00000138675	ENSG00000138675		"Endogenous ligands"	3683	protein-coding gene	gene with protein product		165190				3211147, 2577873	Standard	NM_001291812		Approved		uc003hmd.3	P12034	OTTHUMG00000130288	ENST00000312465.7:c.208C>A	chr4.hg19:g.81188186C>A	ENSP00000311697:p.Gln70Lys	180.0	0.0		145.0	12.0	NM_004464	B2R554|O75846|Q3Y8M3|Q8NF90	Missense_Mutation	SNP	ENST00000312465.7	hg19	CCDS34021.1	.	.	.	.	.	.	.	.	.	.	C	4.126	0.021564	0.08006	.	.	ENSG00000138675	ENST00000312465;ENST00000456523	T;T	0.07114	3.22;3.22	5.41	4.51	0.55191	.	6.705490	0.00166	N	0.000003	T	0.06142	0.0159	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.46303	-0.9201	10	0.05959	T	0.93	.	8.2031	0.31436	0.1648:0.6244:0.2108:0.0	.	70;70	P12034-2;P12034	.;FGF5_HUMAN	K	70	ENSP00000311697:Q70K;ENSP00000398353:Q70K	ENSP00000311697:Q70K	Q	+	1	0	FGF5	81407210	0.000000	0.05858	0.117000	0.21633	0.757000	0.42996	0.237000	0.17985	2.816000	0.96949	0.561000	0.74099	CAA	.	.		0.612	FGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252627.2			A	81188186	C	A	81188186	3	1	183	1	0	0	0	0	1	0	0	0	5863	595	21	3	210	3	FGF5	4	81188186	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	38611504	81188186	109966090	25	27259										
THAP9	79725	hgsc.bcm.edu	37	chr4	83829016	83829016	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	acaatttgcatgtacactctActtgtgcagtagcaaagtct	7	9	2	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr4:83829016A>C	ENST00000302236.5	+	4	710	c.659A>C	c.(658-660)tAc>tCc	p.Y220S	LIN54_ENST00000505905.1_5'Flank	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	220					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				TGTACACTCTACTTGTGCAGT	0.299																																					p.Y220S		Atlas-SNP	.											.	THAP9	65	.	0			c.A659C						.						86	92	90					4																	83829016		2203	4298	6501	SO:0001583	missense	79725	exon4			CACTCTACTTGTG	AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"THAP (C2CH-type zinc finger) domain containing"	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.659A>C	chr4.hg19:g.83829016A>C	ENSP00000305533:p.Tyr220Ser	329.0	0.0		242.0	131.0	NM_024672	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	hg19	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	A	14.31	2.497672	0.44455	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	T	0.38077	1.16	3.71	3.71	0.42584	.	0.481828	0.15578	N	0.255065	T	0.43523	0.1251	L	0.43152	1.355	0.28441	N	0.916816	D	0.65815	0.995	P	0.57911	0.829	T	0.18461	-1.0336	10	0.30078	T	0.28	-12.0798	11.0757	0.48030	1.0:0.0:0.0:0.0	.	220	Q9H5L6	THAP9_HUMAN	S	220	ENSP00000305533:Y220S	ENSP00000305533:Y220S	Y	+	2	0	THAP9	84048040	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.164000	0.64954	1.915000	0.55452	0.533000	0.62120	TAC	.	.		0.299	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672		C	83829016	A	C	83829016	3	2	183	1	0	0	0	0	1	0	0	0	15866	391	14	5	673	5	THAP9	4	83829016	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	2640830	83829016	107325260	26	27260										
MRPS18C	51023	hgsc.bcm.edu	37	chr4	84382321	84382321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctgcatatctcaaggaccctAaagtttgtaacatcagatat	6	9	2	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr4:84382321A>G	ENST00000295491.4	+	6	513	c.400A>G	c.(400-402)Aaa>Gaa	p.K134E	FAM175A_ENST00000321945.7_3'UTR|MRPS18C_ENST00000507019.1_Missense_Mutation_p.K106E|MRPS18C_ENST00000507349.1_3'UTR	NM_016067.2	NP_057151.1	Q9Y3D5	RT18C_HUMAN	mitochondrial ribosomal protein S18C	134					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5		Hepatocellular(203;0.114)				CAAGGACCCTAAAGTTTGTAA	0.338																																					p.K134E		Atlas-SNP	.											.	MRPS18C	11	.	0			c.A400G						.						100	101	100					4																	84382321		2203	4299	6502	SO:0001583	missense	51023	exon6			GACCCTAAAGTTT		CCDS3604.1, CCDS75159.1	4q21.21-q21.23	2012-09-13			ENSG00000163319	ENSG00000163319		"Mitochondrial ribosomal proteins / small subunits"	16633	protein-coding gene	gene with protein product		611983				11279123, 10810093	Standard	XM_005263043		Approved	MRPS18-1, CGI-134, FLJ11146, FLJ22967	uc003hor.4	Q9Y3D5	OTTHUMG00000130430	ENST00000295491.4:c.400A>G	chr4.hg19:g.84382321A>G	ENSP00000295491:p.Lys134Glu	85.0	0.0		85.0	27.0	NM_016067		Missense_Mutation	SNP	ENST00000295491.4	hg19	CCDS3604.1	.	.	.	.	.	.	.	.	.	.	A	19.75	3.886374	0.72410	.	.	ENSG00000163319	ENST00000295491;ENST00000507019	.	.	.	5.03	5.03	0.67393	.	0.158699	0.56097	D	0.000039	T	0.55497	0.1924	M	0.71036	2.16	0.80722	D	1	P	0.42871	0.792	B	0.35182	0.197	T	0.65352	-0.6189	9	0.72032	D	0.01	-8.2836	14.9268	0.70884	1.0:0.0:0.0:0.0	.	134	Q9Y3D5	RT18C_HUMAN	E	134;106	.	ENSP00000295491:K134E	K	+	1	0	MRPS18C	84601345	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.648000	0.83479	2.108000	0.64289	0.482000	0.46254	AAA	.	.		0.338	MRPS18C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252820.2			G	84382321	A	G	84382321	3	3	183	1	0	0	0	0	1	0	0	0	9839	363	13	2	422	2	MRPS18C	4	84382321	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	553305	84382321	106771955	27	27261										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123184690	123184690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ttggatgtcaaatgctgtggGtaatcgaggaagtgtgttac	14	4	1	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr4:123184690G>A	ENST00000264501.4	+	44	7449	c.7076G>A	c.(7075-7077)gGt>gAt	p.G2359D	KIAA1109_ENST00000455637.1_Missense_Mutation_p.G2359D|KIAA1109_ENST00000388738.3_Missense_Mutation_p.G2359D			Q2LD37	K1109_HUMAN	KIAA1109	2359					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AATGCTGTGGGTAATCGAGGA	0.378																																					p.G2359D		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G7076A						.						145	132	136					4																	123184690		1898	4112	6010	SO:0001583	missense	84162	exon42			CTGTGGGTAATCG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.7076G>A	chr4.hg19:g.123184690G>A	ENSP00000264501:p.Gly2359Asp	135.0	0.0		113.0	36.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.111431|5.111431	0.94339|0.94339	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000446180	T;T;T|.	0.24151|.	2.47;2.47;1.87|.	5.59|5.59	5.59|5.59	0.84812|0.84812	.|.	0.000000|.	0.48767|.	U|.	0.000163|.	T|T	0.54775|0.54775	0.1879|0.1879	N|N	0.19112|0.19112	0.55|0.55	0.58432|0.58432	D|D	0.999995|0.999995	P;D;P|.	0.89917|.	0.846;1.0;0.761|.	P;D;B|.	0.91635|.	0.461;0.999;0.338|.	T|T	0.48692|0.48692	-0.9013|-0.9013	10|5	0.34782|.	T|.	0.22|.	.|.	19.59|19.59	0.95506|0.95506	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	2359;2358;2359|.	Q2LD37-6;Q2LD37-2;Q2LD37|.	.;.;K1109_HUMAN|.	D|I	2359|932	ENSP00000264501:G2359D;ENSP00000373390:G2359D;ENSP00000389925:G2359D|.	ENSP00000264501:G2359D|.	G|V	+|+	2|1	0|0	KIAA1109|KIAA1109	123404140|123404140	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.787000|9.787000	0.99055|0.99055	2.639000|2.639000	0.89480|0.89480	0.655000|0.655000	0.94253|0.94253	GGT|GTA	.	.		0.378	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123184690	G	A	123184690	3	1	183	1	0	0	0	0	1	0	0	0	8217	1261	44	3	7242	3	KIAA1109	4	123184690	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	38802369	123184690	67969586	28	27262										
UCP1	7350	hgsc.bcm.edu	37	chr4	141481162	141481162	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gtcgcaagaaggaaggtaccAacctagaaaagtgcatgtca	11	8	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr4:141481162A>T	ENST00000262999.3	-	6	887	c.812T>A	c.(811-813)tTg>tAg	p.L271*		NM_021833.4	NP_068605.1	P25874	UCP1_HUMAN	uncoupling protein 1 (mitochondrial, proton carrier)	271					brown fat cell differentiation (GO:0050873)|cellular metabolic process (GO:0044237)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|stomach(1)	16	all_hematologic(180;0.162)					GGAAGGTACCAACCTAGAAAA	0.413																																					p.L271X		Atlas-SNP	.											.	UCP1	33	.	0			c.T812A						.						150	118	129					4																	141481162		2203	4300	6503	SO:0001587	stop_gained	7350	exon6			GGTACCAACCTAG	X51955	CCDS3753.1	4q28-q31	2013-05-22			ENSG00000109424	ENSG00000109424		"Solute carriers"	12517	protein-coding gene	gene with protein product		113730		UCP		2380264	Standard	NM_021833		Approved	SLC25A7	uc011chj.2	P25874	OTTHUMG00000133415	ENST00000262999.3:c.812T>A	chr4.hg19:g.141481162A>T	ENSP00000262999:p.Leu271*	63.0	0.0		47.0	15.0	NM_021833	Q13218|Q4KMZ3|Q68G66	Nonsense_Mutation	SNP	ENST00000262999.3	hg19	CCDS3753.1	.	.	.	.	.	.	.	.	.	.	A	32	5.146499	0.94603	.	.	ENSG00000109424	ENST00000262999	.	.	.	5.06	3.79	0.43588	.	0.294817	0.37857	N	0.001916	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	9.9714	0.41757	0.83:0.17:0.0:0.0	.	.	.	.	X	271	.	ENSP00000262999:L271X	L	-	2	0	UCP1	141700612	1.000000	0.71417	0.049000	0.19019	0.514000	0.34195	6.823000	0.75282	2.032000	0.59987	0.482000	0.46254	TTG	.	.		0.413	UCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257273.1			T	141481162	A	T	141481162	4	4	183	1	0	0	0	0	0	1	0	0	16945	131	5	4	113	4	UCP1	4	141481162	Nonsense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	18296472	141481162	49673114	29	27263										
AGA	175	hgsc.bcm.edu	37	chr4	178358643	178358643	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	accaggtggtttgtagggtcCgcagtattttgagggatctg	15	6	1	1	rs373865451		TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr4:178358643C>T	ENST00000264595.2	-	5	665	c.538G>A	c.(538-540)Gga>Aga	p.G180R	AGA_ENST00000506853.1_5'UTR	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase	180					protein deglycosylation (GO:0006517)|protein maturation (GO:0051604)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity (GO:0003948)|peptidase activity (GO:0008233)			endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|skin(2)	16		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		TTGTAGGGTCCGCAGTATTTT	0.338																																					p.G180R		Atlas-SNP	.											.	AGA	39	.	0			c.G538A						.	C	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	129	128	128		538,538	5.5	1	4		128	0,8600		0,0,4300	no	missense,missense	AGA	NM_000027.3,NM_001171988.1	125,125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	180/347,180/337	178358643	1,13005	2203	4300	6503	SO:0001583	missense	175	exon5			AGGGTCCGCAGTA	X55330	CCDS3829.1	4q34.3	2014-06-23			ENSG00000038002	ENSG00000038002	3.5.1.26		318	protein-coding gene	gene with protein product	"glycosylasparaginase", "N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase"	613228					Standard	NM_000027		Approved	ASRG	uc003iuu.2	P20933	OTTHUMG00000160723	ENST00000264595.2:c.538G>A	chr4.hg19:g.178358643C>T	ENSP00000264595:p.Gly180Arg	153.0	0.0		122.0	33.0	NM_000027	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Missense_Mutation	SNP	ENST00000264595.2	hg19	CCDS3829.1	.	.	.	.	.	.	.	.	.	.	C	32	5.161932	0.94727	2.27E-4	0.0	ENSG00000038002	ENST00000264595;ENST00000502310	D;D	0.87103	-2.21;-2.21	5.53	5.53	0.82687	.	0.048090	0.85682	D	0.000000	D	0.94781	0.8315	M	0.88031	2.925	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94963	0.8110	10	0.66056	D	0.02	-25.1685	19.4321	0.94775	0.0:1.0:0.0:0.0	.	180	P20933	ASPG_HUMAN	R	180;65	ENSP00000264595:G180R;ENSP00000423798:G65R	ENSP00000264595:G180R	G	-	1	0	AGA	178595637	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.108000	0.77055	2.770000	0.95276	0.655000	0.94253	GGA	.	.		0.338	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027		T	178358643	C	T	178358643	3	4	183	1	0	0	0	0	1	0	0	0	365	661	23	1	522	1	AGA	4	178358643	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	36877481	178358643	12795633	30	27264										
RICTOR	253260	hgsc.bcm.edu	37	chr5	38978734	38978734	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	atgtctgtagtgaaaatcagTatagggtgctaaaattctct	9	5	3	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr5:38978734T>A	ENST00000357387.3	-	9	802	c.772A>T	c.(772-774)Act>Tct	p.T258S	RICTOR_ENST00000296782.5_Missense_Mutation_p.T258S	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					TGAAAATCAGTATAGGGTGCT	0.294																																					p.T258S		Atlas-SNP	.											.	RICTOR	182	.	0			c.A772T						.						53	57	55					5																	38978734		2203	4296	6499	SO:0001583	missense	253260	exon9			AATCAGTATAGGG		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.772A>T	chr5.hg19:g.38978734T>A	ENSP00000349959:p.Thr258Ser	27.0	0.0		46.0	19.0	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.854145	0.91355	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.54866	0.55;0.56	5.69	5.69	0.88448	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.70386	0.3218	M	0.63843	1.955	0.80722	D	1	D;P;D	0.76494	0.999;0.918;0.996	D;P;D	0.83275	0.996;0.65;0.98	T	0.73493	-0.3965	10	0.87932	D	0	-18.9658	15.6101	0.76710	0.0:0.0:0.0:1.0	.	258;258;258	E7ETT0;Q6R327;Q6R327-3	.;RICTR_HUMAN;.	S	258	ENSP00000349959:T258S;ENSP00000296782:T258S	ENSP00000296782:T258S	T	-	1	0	RICTOR	39014491	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.439000	0.80444	2.171000	0.68590	0.377000	0.23210	ACT	.	.		0.294	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		A	38978734	T	A	38978734	3	1	183	1	0	0	0	0	1	0	0	0	13373	1638	57	4	4474	4	RICTOR	5	38978734	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10		38978734	141936526	31	27265										
C6	729	hgsc.bcm.edu	37	chr5	41181567	41181567	+	Frame_Shift_Del	DEL	T	T	-													0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	cactgaaagagctcccccccTgacttgagaatgagccttgt					rs199795699|rs557023458	byFrequency	TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr5:41181567delT	ENST00000263413.3	-	7	1085	c.821delA	c.(820-822)cagfs	p.Q274fs	C6_ENST00000337836.5_Frame_Shift_Del_p.Q274fs|C6_ENST00000475349.1_5'UTR	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	274	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				GCTCCCCCCCTGACTTGAGAA	0.393													T|T|-|deletion	3	0.000599042	0.0023	0	5008	,	,		15554	0		0	False		,,,				2504	0				p.Q274fs		Atlas-INDEL	.											.	C6	197	.	0			c.822delG	GRCh37	CD002162	C6	D		.		,	25,4241		0,25,2108	83	83	83		,	-7.2	0	5		84	0,8252		0,0,4126	no	frameshift,frameshift	C6	NM_001115131.1,NM_000065.2	,	0,25,6234	A1A1,A1R,RR		0.0,0.586,0.1997	,	,	41181567	25,12493	2203	4299	6502	SO:0001589	frameshift_variant	729	exon7			.	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"Complement system"	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.821delA	chr5.hg19:g.41181567delT	ENSP00000263413:p.Gln274fs	114.0	0.0		173.0	90.0	NM_001115131		Frame_Shift_Del	DEL	ENST00000263413.3	hg19	CCDS3936.1																																																																																			.	.		0.393	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			-	41181567	T	-	41181567	7	5	183	1	0	1	0	1	0	0	0	0	2317	1580	55	0	2031	0	C6	5	41181567	Frame_Shift_Del	DEL	T	TCGA-DD-AAD8-01A-11D-A40R-10	2202833	41181567	139733693	32	27266										
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109181594	109181594	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tagaatgacactgagcaaatTgcctcttcaagcaaatgtct	7	9	3	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr5:109181594T>G	ENST00000261483.4	+	18	3781	c.2729T>G	c.(2728-2730)tTg>tGg	p.L910W		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	910					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		CTGAGCAAATTGCCTCTTCAA	0.388																																					p.L910W		Atlas-SNP	.											.	MAN2A1	136	.	0			c.T2729G						.						197	184	189					5																	109181594		2202	4300	6502	SO:0001583	missense	4124	exon18			GCAAATTGCCTCT		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.2729T>G	chr5.hg19:g.109181594T>G	ENSP00000261483:p.Leu910Trp	69.0	0.0		66.0	18.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.668825	0.88348	.	.	ENSG00000112893	ENST00000261483	T	0.79033	-1.23	5.33	5.33	0.75918	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.64402	D	0.000001	D	0.90335	0.6976	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92550	0.6049	10	0.87932	D	0	-16.048	15.5882	0.76502	0.0:0.0:0.0:1.0	.	910	Q16706	MA2A1_HUMAN	W	910	ENSP00000261483:L910W	ENSP00000261483:L910W	L	+	2	0	MAN2A1	109209493	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.301000	0.78850	2.144000	0.66660	0.533000	0.62120	TTG	.	.		0.388	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			G	109181594	T	G	109181594	3	3	183	1	0	0	0	0	1	0	0	0	9223	1821	63	5	2799	5	MAN2A1	5	109181594	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	68000027	109181594	71733666	33	27267										
WDR36	134430	hgsc.bcm.edu	37	chr5	110462533	110462533	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	acccatttgcaatcactcttCaatcaaagcatgtgtatttt	4	10	4	0	rs79307023		TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr5:110462533C>A	ENST00000513710.2	+	23	2812	c.2808C>A	c.(2806-2808)ttC>ttA	p.F936L	WDR36_ENST00000506538.2_Missense_Mutation_p.F936L			Q8NI36	WDR36_HUMAN	WD repeat domain 36	936					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		AATCACTCTTCAATCAAAGCA	0.323																																					p.F936L		Atlas-SNP	.											WDR36,bladder,carcinoma,0,1	WDR36	111	.	0			c.C2808A						.						59	62	61					5																	110462533		2202	4300	6502	SO:0001583	missense	134430	exon23			ACTCTTCAATCAA	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.2808C>A	chr5.hg19:g.110462533C>A	ENSP00000424628:p.Phe936Leu	457.0	0.0		398.0	107.0	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	SNP	ENST00000513710.2	hg19	CCDS4102.1	.	.	.	.	.	.	.	.	.	.	C	8.606	0.888102	0.17540	.	.	ENSG00000134987	ENST00000506538;ENST00000513710	T;T	0.74632	-0.86;-0.86	5.93	3.22	0.36961	Small-subunit processome, Utp21 (1);	0.043594	0.85682	D	0.000000	T	0.60117	0.2244	N	0.21282	0.65	0.80722	D	1	B	0.26445	0.149	B	0.28709	0.093	T	0.56306	-0.8001	10	0.87932	D	0	-14.6538	9.1618	0.37028	0.0:0.726:0.0:0.274	.	936	Q8NI36	WDR36_HUMAN	L	936	ENSP00000423067:F936L;ENSP00000424628:F936L	ENSP00000423067:F936L	F	+	3	2	WDR36	110490432	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.403000	0.34612	0.416000	0.25844	-0.225000	0.12378	TTC	.	C|1.000;T|0.000		0.323	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		A	110462533	C	A	110462533	3	1	183	1	0	0	0	0	1	0	0	0	17305	825	29	3	2898	3	WDR36	5	110462533	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	1280939	110462533	70452727	34	27268										
TMEM173	340061	hgsc.bcm.edu	37	chr5	138857039	138857039	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ggctaaagccagcttgactgTattgtgacatggcaaacaaa	10	8	0	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr5:138857039T>C	ENST00000330794.4	-	7	1154	c.821A>G	c.(820-822)tAc>tGc	p.Y274C	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	274	c-di-GMP-binding domain (CBD).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGCTTGACTGTATTGTGACAT	0.567																																					p.Y274C		Atlas-SNP	.											.	TMEM173	19	.	0			c.A821G						.						87	85	86					5																	138857039		2203	4300	6503	SO:0001583	missense	340061	exon7			TGACTGTATTGTG		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.821A>G	chr5.hg19:g.138857039T>C	ENSP00000331288:p.Tyr274Cys	90.0	0.0		71.0	18.0	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	hg19	CCDS4215.1	.	.	.	.	.	.	.	.	.	.	T	10.52	1.371832	0.24857	.	.	ENSG00000184584	ENST00000330794	T	0.22134	1.97	5.6	4.43	0.53597	.	0.319937	0.32987	N	0.005401	T	0.15305	0.0369	N	0.22421	0.69	0.20926	N	0.999824	P	0.47409	0.895	B	0.44163	0.443	T	0.07501	-1.0769	10	0.54805	T	0.06	-6.4461	7.4088	0.27006	0.0:0.0731:0.1431:0.7838	.	274	Q86WV6	TM173_HUMAN	C	274	ENSP00000331288:Y274C	ENSP00000331288:Y274C	Y	-	2	0	TMEM173	138837223	0.998000	0.40836	0.571000	0.28486	0.015000	0.08874	3.523000	0.53488	0.970000	0.38263	-0.361000	0.07541	TAC	.	.		0.567	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282		C	138857039	T	C	138857039	3	2	183	1	0	0	0	0	1	0	0	0	16104	1638	57	2	326	2	TMEM173	5	138857039	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	28394506	138857039	42058221	35	27269										
ARHGAP26	23092	hgsc.bcm.edu	37	chr5	142253059	142253059	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	acagatgatgagatgtgtatAggtaagtcataactgtgcag	12	4	1	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr5:142253059A>T	ENST00000274498.4	+	2	627	c.249A>T	c.(247-249)atA>atT	p.I83I	ARHGAP26_ENST00000378004.3_Splice_Site_p.I83I	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	83					actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGATGTGTATAGGTAAGTCAT	0.393																																					p.I83I		Atlas-SNP	.											.	ARHGAP26	57	.	0			c.A249T						.						63	63	63					5																	142253059		2203	4300	6503	SO:0001630	splice_region_variant	23092	exon2			GTGTATAGGTAAG	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.250+1A>T	chr5.hg19:g.142253059A>T		54.0	0.0		45.0	17.0	NM_015071	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Silent	SNP	ENST00000274498.4	hg19	CCDS4277.1																																																																																			.	.		0.393	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071	Silent	T	142253059	A	T	142253059	5	4	183	1	0	0	0	0	0	0	1	0	875	434	15	4	255	4	ARHGAP26	5	142253059	Splice_Site	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	3396020	142253059	38662201	36	27270										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169505977	169505977	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tgctgcccctctggcctttcAgctttgacctggaattagca	9	13	2	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr5:169505977A>G	ENST00000256935.8	+	49	5074		c.e49-1		DOCK2_ENST00000540750.1_Splice_Site|DOCK2_ENST00000520908.1_Splice_Site|DOCK2_ENST00000523351.1_Splice_Site	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTGGCCTTTCAGCTTTGACCT	0.582																																					.		Atlas-SNP	.											.	DOCK2	389	.	0			c.4995-2A>G						.						93	101	98					5																	169505977		2203	4300	6503	SO:0001630	splice_region_variant	1794	exon49			CCTTTCAGCTTTG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4995-1A>G	chr5.hg19:g.169505977A>G		73.0	0.0		60.0	11.0	NM_004946	Q2M3I0|Q96AK7	Splice_Site	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.104891	0.37145	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	.	.	.	4.92	3.74	0.42951	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2343	0.48931	0.8462:0.1538:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DOCK2	169438555	1.000000	0.71417	0.931000	0.37212	0.512000	0.34134	4.609000	0.61148	0.819000	0.34492	0.529000	0.55759	.	.	.		0.582	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	Intron	G	169505977	A	G	169505977	5	3	183	1	0	0	0	0	0	0	1	0	4689	202	7	2	5187	2	DOCK2	5	169505977	Splice_Site	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	27252918	169505977	11409283	37	27271										
RANBP17	64901	hgsc.bcm.edu	37	chr5	170720952	170720952	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	aaccagtggtcagtatccagGcctctcctggggctcatcct	10	14	3	0	rs374592064		TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr5:170720952G>A	ENST00000523189.1	+	26	3173	c.3009G>A	c.(3007-3009)agG>agA	p.R1003R	RANBP17_ENST00000521759.1_3'UTR	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	1003					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CAGTATCCAGGCCTCTCCTGG	0.493			T	TRD@	ALL																																p.R1003R		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.G3009A						.						190	184	186					5																	170720952		2203	4300	6503	SO:0001819	synonymous_variant	64901	exon26			ATCCAGGCCTCTC	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.3009G>A	chr5.hg19:g.170720952G>A		90.0	0.0		65.0	17.0	NM_022897	Q8IU74	Silent	SNP	ENST00000523189.1	hg19	CCDS34287.1																																																																																			.	.		0.493	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		A	170720952	G	A	170720952	2	1	183	1	0	0	0	0	0	0	0	1	13042	1194	42	3		3	RANBP17	5	170720952	Silent	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	1214975	170720952	10194308	38	27272										
ZNF192	7745	hgsc.bcm.edu	37	chr6	28117277	28117277	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ccaggtctcagctcgcgtacAtggacatagggtactctggg	13	11	2	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr6:28117277A>G	ENST00000330236.6	+	3	618	c.434A>G	c.(433-435)cAt>cGt	p.H145R	ZKSCAN8_ENST00000457389.2_Missense_Mutation_p.H145R	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	145					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCTCGCGTACATGGACATAGG	0.458																																					p.H145R		Atlas-SNP	.											.	.	.	.	0			c.A434G						.						162	147	152					6																	28117277		2203	4300	6503	SO:0001583	missense	7745	exon3			GCGTACATGGACA		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"Zinc fingers, C2H2-type", "-", "-", "-"	12983	protein-coding gene	gene with protein product		602240	"zinc finger protein 192"	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	ENST00000330236.6:c.434A>G	chr6.hg19:g.28117277A>G	ENSP00000332750:p.His145Arg	108.0	0.0		114.0	50.0	NM_006298	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	Missense_Mutation	SNP	ENST00000330236.6	hg19	CCDS4645.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.426|2.426	-0.331918|-0.331918	0.05314|0.05314	.|.	.|.	ENSG00000198315|ENSG00000198315	ENST00000330236;ENST00000457389|ENST00000536028	T;T|T	0.05925|0.03152	3.37;3.37|4.03	4.68|4.68	-0.504|-0.504	0.11997|0.11997	Transcription regulator SCAN (1);|.	0.000000|.	0.51477|.	D|.	0.000090|.	T|T	0.00784|0.00784	0.0026|0.0026	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.47315|0.47315	-0.9127|-0.9127	10|7	0.41790|0.41790	T|T	0.15|0.15	.|.	4.1552|4.1552	0.10258|0.10258	0.5935:0.0:0.2602:0.1463|0.5935:0.0:0.2602:0.1463	.|.	145|.	Q15776|.	ZN192_HUMAN|.	R|V	145|150	ENSP00000332750:H145R;ENSP00000402948:H145R|ENSP00000439117:M150V	ENSP00000332750:H145R|ENSP00000439117:M150V	H|M	+|+	2|1	0|0	ZNF192|ZNF192	28225256|28225256	0.184000|0.184000	0.23200|0.23200	0.194000|0.194000	0.23346|0.23346	0.340000|0.340000	0.28889|0.28889	-0.098000|-0.098000	0.11024|0.11024	0.026000|0.026000	0.15269|0.15269	-0.400000|-0.400000	0.06385|0.06385	CAT|ATG	.	.		0.458	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2			G	28117277	A	G	28117277	3	3	183	1	0	0	0	0	1	0	0	0	17771	217	8	2	440	2	ZNF192	6	28117277	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10		28117277	142997790	39	27273										
IP6K3	117283	hgsc.bcm.edu	37	chr6	33690512	33690512	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	aagtttcattctccctcttgGatatcctgcaggatcctgat	7	11	3	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr6:33690512G>A	ENST00000293756.4	-	6	1544	c.1218C>T	c.(1216-1218)atC>atT	p.I406I	IP6K3_ENST00000451316.1_Silent_p.I406I	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	406					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						CTCCCTCTTGGATATCCTGCA	0.488																																					p.I406I		Atlas-SNP	.											.	IP6K3	52	.	0			c.C1218T						.						95	103	100					6																	33690512		2203	4300	6503	SO:0001819	synonymous_variant	117283	exon7			CTCTTGGATATCC	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"inositol hexaphosphate kinase 3"	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.1218C>T	chr6.hg19:g.33690512G>A		115.0	0.0		130.0	26.0	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	hg19	CCDS34435.1																																																																																			.	.		0.488	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111		A	33690512	G	A	33690512	2	1	183	1	0	0	0	0	0	0	0	1	7799	1164	41	3		3	IP6K3	6	33690512	Silent	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	5573235	33690512	137424555	40	27274										
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74228551	74228551	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ccatccttacgggtgactttCcatcccttgaaccaaggcat	7	14	0	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr6:74228551C>G	ENST00000316292.9	-	4	1633	c.642G>C	c.(640-642)tgG>tgC	p.W214C	EEF1A1_ENST00000309268.6_Missense_Mutation_p.W214C|EEF1A1_ENST00000331523.2_Missense_Mutation_p.W214C|EEF1A1_ENST00000491404.1_Intron	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	214	tr-type G.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						GGGTGACTTTCCATCCCTTGA	0.502											OREG0003891|OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=EEF1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.W214C		Atlas-SNP	.											.	EEF1A1	56	.	0			c.G642C						.						91	84	86					6																	74228551		2203	4300	6503	SO:0001583	missense	1915	exon5			GACTTTCCATCCC	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.642G>C	chr6.hg19:g.74228551C>G	ENSP00000339063:p.Trp214Cys	86.0	0.0	1151	80.0	25.0	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.727703	0.69074	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.47177	0.85;0.85;0.85	4.31	4.31	0.51392	Protein synthesis factor, GTP-binding (2);	0.000000	0.85682	U	0.000000	T	0.61311	0.2337	M	0.67625	2.065	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.67715	-0.5599	10	0.87932	D	0	.	17.2248	0.86966	0.0:1.0:0.0:0.0	.	214;214;214;214	P68104;Q53HR5;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;.;EF1A3_HUMAN	C	214;214;214;214;193	ENSP00000339063:W214C;ENSP00000339053:W214C;ENSP00000330054:W214C	ENSP00000339053:W214C	W	-	3	0	EEF1A1	74285272	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.442000	0.80503	2.115000	0.64714	0.549000	0.68633	TGG	.	.		0.502	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		G	74228551	C	G	74228551	3	3	183	1	0	0	0	0	1	0	0	0	4925	856	30	4	762	4	EEF1A1	6	74228551	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	40538039	74228551	96886516	41	27275										
HBS1L	10767	hgsc.bcm.edu	37	chr6	135358397	135358397	+	Intron	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tgtgaaactggcagatgactGgttacaaaggtcagataaag	12	5	1	4			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr6:135358397G>C	ENST00000367837.5	-	4	637				HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.Q400E|HBS1L_ENST00000367826.2_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		GCAGATGACTGGTTACAAAGG	0.413																																					p.Q400E		Atlas-SNP	.											.	HBS1L	75	.	0			c.C1198G						.						137	113	120					6																	135358397		692	1591	2283	SO:0001627	intron_variant	10767	exon5			ATGACTGGTTACA	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"eRF3 family member"	612450	"HBS1 (S. cerevisiae)-like", "HBS1-like (S. cerevisiae)"			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2313C>G	chr6.hg19:g.135358397G>C		89.0	0.0		79.0	23.0	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	hg19	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.686466	0.47991	.	.	ENSG00000112339	ENST00000367822	.	.	.	5.53	4.65	0.58169	.	.	.	.	.	T	0.37999	0.1024	.	.	.	0.80722	D	1	B	0.18166	0.026	B	0.16289	0.015	T	0.46162	-0.9211	7	0.72032	D	0.01	.	10.0568	0.42250	0.0717:0.1388:0.7895:0.0	.	400	Q9Y450-2	.	E	400	.	ENSP00000356796:Q400E	Q	-	1	0	HBS1L	135400090	1.000000	0.71417	0.479000	0.27329	0.871000	0.50021	1.940000	0.40223	1.445000	0.47624	0.655000	0.94253	CAG	.	.		0.413	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			C	135358397	G	C	135358397	1	2	183	0	1	0	0	0	0	0	0	0	6996	1357	47	4		4	HBS1L	6	135358397	Intron	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	61129846	135358397	35756670	42	27276										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161470546	161470546	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	aggattatgggcactgttttGggcatcaagaatttatcaga	11	5	2	2	rs529204751		TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr6:161470546G>A	ENST00000392142.4	+	3	1390	c.1242G>A	c.(1240-1242)ttG>ttA	p.L414L	MAP3K4_ENST00000366919.2_Silent_p.L414L|MAP3K4_ENST00000348824.7_Silent_p.L414L|MAP3K4_ENST00000366920.2_Silent_p.L414L	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	414					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		GCACTGTTTTGGGCATCAAGA	0.448																																					p.L414L		Atlas-SNP	.											.	MAP3K4	364	.	0			c.G1242A						.						76	79	78					6																	161470546		2203	4300	6503	SO:0001819	synonymous_variant	4216	exon3			TGTTTTGGGCATC	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.1242G>A	chr6.hg19:g.161470546G>A		93.0	0.0		90.0	24.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	hg19	CCDS34565.1																																																																																			.	.		0.448	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			A	161470546	G	A	161470546	2	1	183	1	0	0	0	0	0	0	0	1	9261	1339	47	3		3	MAP3K4	6	161470546	Silent	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	26112149	161470546	9644521	43	27277										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161523752	161523752	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	accagcatatccaagaggagAttcaagtgggtccacaagaa	10	9	1	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr6:161523752A>T	ENST00000392142.4	+	19	3945	c.3797A>T	c.(3796-3798)gAt>gTt	p.D1266V	MAP3K4_ENST00000366919.2_Missense_Mutation_p.D1216V|MAP3K4_ENST00000348824.7_Missense_Mutation_p.D1212V|MAP3K4_ENST00000366920.2_Missense_Mutation_p.D1262V	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1266					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		CCAAGAGGAGATTCAAGTGGG	0.328																																					p.D1266V		Atlas-SNP	.											.	MAP3K4	364	.	0			c.A3797T						.						43	43	43					6																	161523752		2203	4300	6503	SO:0001583	missense	4216	exon19			GAGGAGATTCAAG	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.3797A>T	chr6.hg19:g.161523752A>T	ENSP00000375986:p.Asp1266Val	472.0	0.0		408.0	246.0	NM_005922	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.645768	0.87958	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.72051	-0.57;-0.62;-0.61;-0.59	5.31	5.31	0.75309	.	0.068133	0.56097	D	0.000029	T	0.58779	0.2146	N	0.24115	0.695	0.80722	D	1	P;D;P;P	0.63880	0.835;0.993;0.928;0.947	P;P;P;P	0.52758	0.549;0.708;0.626;0.599	T	0.64668	-0.6353	10	0.46703	T	0.11	-35.5538	15.2821	0.73794	1.0:0.0:0.0:0.0	.	1262;202;1216;1266	F5H538;Q9P1M2;Q9Y6R4-2;Q9Y6R4	.;.;.;M3K4_HUMAN	V	1216;1266;1216;1262;1212	ENSP00000355886:D1216V;ENSP00000375986:D1266V;ENSP00000355887:D1262V;ENSP00000297332:D1212V	ENSP00000297332:D1212V	D	+	2	0	MAP3K4	161443742	1.000000	0.71417	0.977000	0.42913	0.960000	0.62799	8.317000	0.89987	2.013000	0.59113	0.533000	0.62120	GAT	.	.		0.328	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			T	161523752	A	T	161523752	3	4	183	1	0	0	0	0	1	0	0	0	9261	333	12	4	3871	4	MAP3K4	6	161523752	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	53206	161523752	9591315	44	27278										
FKBP9	11328	hgsc.bcm.edu	37	chr7	33044951	33044977	+	Stop_Codon_Del	DEL	CGATGAACTCTAAACCTGGCATGAACC	CGATGAACTCTAAACCTGGCATGAACC	-													0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	aaagaccaggaagccaaacaCgatgaactctaaacctggca							TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	CGATGAACTCTAAACCTGGCATGAACC	CGATGAACTCTAAACCTGGCATGAACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr7:33044951_33044977delCGATGAACTCTAAACCTGGCATGAACC	ENST00000242209.4	+	0	1870_1896				FKBP9_ENST00000538443.1_Stop_Codon_Del|FKBP9_ENST00000490776.2_Stop_Codon_Del|FKBP9_ENST00000538336.1_Stop_Codon_Del|AVL9_ENST00000404479.1_Intron	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa						chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			AAGCCAAACACGATGAACTCTAAACCTGGCATGAACCAGATGGTGCC	0.502																																					p.567_571del		Atlas-INDEL	.											.	FKBP9	335	.	0			c.1700_1894del						.																																			SO:0001567	stop_retained_variant	11328	exon10			.	AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"EF-hand domain containing"	3725	protein-coding gene	gene with protein product			"FK506-binding protein 9 (63 kD)"			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	Exception_encountered	chr7.hg19:g.33044951_33044977delCGATGAACTCTAAACCTGGCATGAACC		360.0	0.0		267.0	71.0	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Frame_Shift_Del	DEL	ENST00000242209.4	hg19	CCDS5439.1																																																																																			.	.		0.502	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270		-	33044977	CGATGAACTCTAAACCTGGCATGAACC	-	33044951	7	5	183	1	0	1	0	1	0	0	0	0	5923	535	19	0	1739	0	FKBP9	7	33044951	Stop_Codon_Del	DEL	CGATGAACTCTAAACCTGGCATGAACC	TCGA-DD-AAD8-01A-11D-A40R-10		33044951	126093712	45	27279										
MAGI2	9863	hgsc.bcm.edu	37	chr7	77973184	77973184	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	caggctcgtctccaccaatgAtggtaaatccaaagcccatg	8	13	1	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr7:77973184A>C	ENST00000354212.4	-	9	1572	c.1319T>G	c.(1318-1320)aTc>aGc	p.I440S	MAGI2_ENST00000535697.1_Missense_Mutation_p.I277S|MAGI2_ENST00000419488.1_Missense_Mutation_p.I440S|MAGI2_ENST00000522391.1_Missense_Mutation_p.I440S|MAGI2_ENST00000536571.1_Missense_Mutation_p.I272S	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	440	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TCCACCAATGATGGTAAATCC	0.478																																					p.I440S		Atlas-SNP	.											.	MAGI2	246	.	0			c.T1319G						.						121	105	110					7																	77973184		2203	4300	6503	SO:0001583	missense	9863	exon9			CCAATGATGGTAA	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1319T>G	chr7.hg19:g.77973184A>C	ENSP00000346151:p.Ile440Ser	185.0	0.0		229.0	48.0	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	hg19	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.582002	0.86748	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43	5.81	5.81	0.92471	PDZ/DHR/GLGF (4);	0.000000	0.37095	U	0.002250	T	0.81898	0.4920	H	0.97051	3.93	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.998;1.0;1.0;1.0;0.999	D	0.88026	0.2772	10	0.87932	D	0	.	15.3584	0.74448	1.0:0.0:0.0:0.0	.	277;272;440;440;440;440	F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8	.;.;.;.;.;MAGI2_HUMAN	S	440;440;440;440;272;277	ENSP00000405766:I440S;ENSP00000346151:I440S;ENSP00000428389:I440S;ENSP00000441584:I272S;ENSP00000441603:I277S	ENSP00000346151:I440S	I	-	2	0	MAGI2	77811120	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.217000	0.71921	0.482000	0.46254	ATC	.	.		0.478	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		C	77973184	A	C	77973184	3	2	183	1	0	0	0	0	1	0	0	0	9200	333	12	5	3104	5	MAGI2	7	77973184	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	44928233	77973184	81165479	46	27280										
C7orf51	222950	hgsc.bcm.edu	37	chr7	100088252	100088252	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ccagtgagaagccagggggcAgagggactgctggccaggat	18	9	0	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr7:100088252A>G	ENST00000300179.2	+	5	2217	c.2058A>G	c.(2056-2058)gcA>gcG	p.A686A	NYAP1_ENST00000454988.1_Silent_p.A630A|NYAP1_ENST00000496985.1_3'UTR|NYAP1_ENST00000423930.1_Silent_p.A687A	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	686					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GCCAGGGGGCAGAGGGACTGC	0.692																																					p.A686A		Atlas-SNP	.											.	.	.	.	0			c.A2058G						.						35	27	30					7																	100088252		2179	4279	6458	SO:0001819	synonymous_variant	222950	exon5			GGGGGCAGAGGGA	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.2058A>G	chr7.hg19:g.100088252A>G		203.0	0.0		223.0	100.0	NM_173564	Q6U9Y3|Q8N1V0	Silent	SNP	ENST00000300179.2	hg19	CCDS5696.1																																																																																			.	.		0.692	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		G	100088252	A	G	100088252	2	3	183	1	0	0	0	0	0	0	0	1	2402	175	7	2		2	C7orf51	7	100088252	Silent	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	22115068	100088252	59050411	47	27281										
C7orf66	154907	hgsc.bcm.edu	37	chr7	108524539	108524539	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	agtctctgatgagtgagatgAggtacagagagttgagaaag	15	3	1	6			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr7:108524539A>C	ENST00000379007.2	-	1	105	c.51T>G	c.(49-51)ccT>ccG	p.P17P		NM_001024607.1	NP_001019778.1	A4D0T2	CG066_HUMAN	chromosome 7 open reading frame 66	17						integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	15						GAGTGAGATGAGGTACAGAGA	0.388																																					p.P17P		Atlas-SNP	.											.	C7orf66	29	.	0			c.T51G						.						153	127	136					7																	108524539		2203	4300	6503	SO:0001819	synonymous_variant	154907	exon1			GAGATGAGGTACA	AF103078	CCDS34735.1	7q31.1	2009-03-06			ENSG00000205174	ENSG00000205174			33712	protein-coding gene	gene with protein product							Standard	NM_001024607		Approved		uc003vfo.3	A4D0T2	OTTHUMG00000154867	ENST00000379007.2:c.51T>G	chr7.hg19:g.108524539A>C		123.0	0.0		133.0	49.0	NM_001024607		Silent	SNP	ENST00000379007.2	hg19	CCDS34735.1																																																																																			.	.		0.388	C7orf66-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337420.1	NM_001024607		C	108524539	A	C	108524539	2	2	183	1	0	0	0	0	0	0	0	1	2414	291	11	5		5	C7orf66	7	108524539	Silent	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	8436287	108524539	50614124	48	27282										
ADAM2	2515	hgsc.bcm.edu	37	chr8	39645736	39645736	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctatccaaagctccaatgaaGacagaataattgtaatatta	5	7	0	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr8:39645736G>A	ENST00000265708.4	-	9	780	c.677C>T	c.(676-678)tCt>tTt	p.S226F	ADAM2_ENST00000379853.2_Intron|ADAM2_ENST00000521880.1_Missense_Mutation_p.S226F|ADAM2_ENST00000347580.4_Missense_Mutation_p.S207F	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	226	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		CTCCAATGAAGACAGAATAAT	0.259																																					p.S226F		Atlas-SNP	.											.	ADAM2	124	.	0			c.C677T						.						60	63	62					8																	39645736		2201	4288	6489	SO:0001583	missense	2515	exon9			AATGAAGACAGAA	U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"ADAM metallopeptidase domain containing"	198	protein-coding gene	gene with protein product	"cancer/testis antigen 15"	601533	"fertilin beta"	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.677C>T	chr8.hg19:g.39645736G>A	ENSP00000265708:p.Ser226Phe	54.0	0.0		33.0	19.0	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	hg19	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	G	12.95	2.090825	0.36855	.	.	ENSG00000104755	ENST00000347580;ENST00000265708;ENST00000521880	T;T;T	0.09538	2.97;2.97;2.97	4.71	4.71	0.59529	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	T	0.37320	0.0999	M	0.87381	2.88	0.35830	D	0.825248	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.83275	0.994;0.99;0.996	T	0.53858	-0.8379	8	.	.	.	.	13.5268	0.61599	0.0:0.0:1.0:0.0	.	226;207;226	B4DWY7;Q99965-2;Q99965	.;.;ADAM2_HUMAN	F	207;226;226	ENSP00000343854:S207F;ENSP00000265708:S226F;ENSP00000429352:S226F	.	S	-	2	0	ADAM2	39764893	1.000000	0.71417	0.966000	0.40874	0.017000	0.09413	5.479000	0.66813	2.332000	0.79248	0.460000	0.39030	TCT	.	.		0.259	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		A	39645736	G	A	39645736	3	1	183	1	0	0	0	0	1	0	0	0	241	942	33	3	1578	3	ADAM2	8	39645736	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10		39645736	106718286	49	27283										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116616870	116616870	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	caccagtagtaactggtggcCtctgtaccattttgtctaga	9	10	2	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr8:116616870C>A	ENST00000220888.5	-	3	1446	c.1287G>T	c.(1285-1287)gaG>gaT	p.E429D	TRPS1_ENST00000395715.3_Missense_Mutation_p.E442D|TRPS1_ENST00000519674.1_Missense_Mutation_p.E429D|TRPS1_ENST00000520276.1_Missense_Mutation_p.E433D|TRPS1_ENST00000519076.1_Intron			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	429					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			AACTGGTGGCCTCTGTACCAT	0.463									Langer-Giedion syndrome																												p.E442D		Atlas-SNP	.											.	TRPS1	516	.	0			c.G1326T						.						69	68	68					8																	116616870		1897	4124	6021	SO:0001583	missense	7227	exon4	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	GGTGGCCTCTGTA	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.1287G>T	chr8.hg19:g.116616870C>A	ENSP00000220888:p.Glu429Asp	85.0	0.0		65.0	21.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	C	3.978	-0.007091	0.07773	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000520276;ENST00000519674	T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41	5.69	3.73	0.42828	.	0.248028	0.39544	N	0.001326	T	0.51193	0.1660	N	0.02539	-0.55	0.31363	N	0.681095	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.47598	-0.9105	10	0.08179	T	0.78	.	7.0789	0.25219	0.5079:0.3973:0.0:0.0948	.	433;429;442	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	D	442;429;433;429	ENSP00000379065:E442D;ENSP00000220888:E429D;ENSP00000428680:E433D;ENSP00000429174:E429D	ENSP00000220888:E429D	E	-	3	2	TRPS1	116686045	0.989000	0.36119	1.000000	0.80357	0.996000	0.88848	0.336000	0.19823	0.798000	0.33994	0.655000	0.94253	GAG	.	.		0.463	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		A	116616870	C	A	116616870	3	1	183	1	0	0	0	0	1	0	0	0	16608	680	24	3	2574	3	TRPS1	8	116616870	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	76971134	116616870	29747152	50	27284										
CER1	9350	hgsc.bcm.edu	37	chr9	14722569	14722569	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tctctttgattccttggcagGagtacgggggaaagagaact	13	7	1	2	rs376786967		TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr9:14722569G>C	ENST00000380911.3	-	1	146	c.102C>G	c.(100-102)ctC>ctG	p.L34L		NM_005454.2	NP_005445.1	O95813	CER1_HUMAN	cerberus 1, DAN family BMP antagonist	34					anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|bone mineralization (GO:0030282)|cell migration involved in gastrulation (GO:0042074)|cellular response to BMP stimulus (GO:0071773)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|growth plate cartilage chondrocyte proliferation (GO:0003419)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mesoderm development (GO:2000381)|nervous system development (GO:0007399)|sequestering of BMP in extracellular matrix (GO:0035582)|signal transduction involved in regulation of gene expression (GO:0023019)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(6)	11				GBM - Glioblastoma multiforme(50;3.16e-06)		TCCTTGGCAGGAGTACGGGGG	0.547																																					p.L34L		Atlas-SNP	.											.	CER1	41	.	0			c.C102G						.						111	111	111					9																	14722569		2203	4300	6503	SO:0001819	synonymous_variant	9350	exon1			TGGCAGGAGTACG	AF090189	CCDS6476.1	9p23-p22	2013-02-26	2013-02-26		ENSG00000147869	ENSG00000147869			1862	protein-coding gene	gene with protein product		603777	"cerberus 1 (Xenopus laevis) homolog (cysteine knot superfamily)", "cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis)"			10049596	Standard	NM_005454		Approved	DAND4	uc003zlj.3	O95813	OTTHUMG00000021022	ENST00000380911.3:c.102C>G	chr9.hg19:g.14722569G>C		48.0	0.0		45.0	18.0	NM_005454	Q6ISJ1|Q6ISJ6|Q6ISQ2|Q6ISS1	Silent	SNP	ENST00000380911.3	hg19	CCDS6476.1																																																																																			.	.		0.547	CER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055453.1	NM_005454		C	14722569	G	C	14722569	2	2	183	1	0	0	0	0	0	0	0	1	3267	1161	41	4		4	CER1	9	14722569	Silent	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10		14722569	126490862	51	27285										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21974776	21974777	+	Frame_Shift_Ins	INS	-	-	GCCA													0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gaccccgggccgcggccgtgINSgccagccagtcagccgaagg					rs587782206		TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr9:21974776_21974777insGCCA	ENST00000304494.5	-	1	320_321	c.50_51insTGGC	c.(49-51)gccfs	p.-17fs	RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000579755.1_Intron|CDKN2A_ENST00000498628.2_Intron|CDKN2A_ENST00000446177.1_Frame_Shift_Ins_p.-17fs|CDKN2A_ENST00000494262.1_Intron|CDKN2A_ENST00000498124.1_Frame_Shift_Ins_p.-17fs|CDKN2A_ENST00000579122.1_Frame_Shift_Ins_p.-17fs|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000361570.3_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A						cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(23)|p.L16fs*9(3)|p.S12fs*6(1)|p.0(1)|p.A17_T18insTA(1)|p.A17fs*5(1)|p.S7_A19del(1)|p.S12fs*20(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CCGCGGCCGTGGCCAGCCAGTC	0.752		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.A17fs		Atlas-INDEL	.											.	CDKN2A	4810	.	1347	Whole gene deletion(1316)|Unknown(23)|Deletion - Frameshift(6)|Insertion - In frame(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(279)|skin(169)|central_nervous_system(164)|lung(146)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(52)|oesophagus(51)|upper_aerodigestive_tract(48)|ovary(34)|kidney(31)|pancreas(31)|breast(30)|thyroid(14)|biliary_tract(13)|NS(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(5)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.51_52insTGGC						.																																			SO:0001589	frameshift_variant	1029	exon1			.	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.47_50dupTGGC	chr9.hg19:g.21974781_21974784dupGCCA	ENSP00000307101:p.Ala17fs	59.0	0.0		57.0	28.0	NM_058197	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Frame_Shift_Ins	INS	ENST00000304494.5	hg19	CCDS6510.1																																																																																			.	.		0.752	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		GCCA	21974777	-	GCCA	21974776	7	5	183	1	0	1	1	0	0	0	0	0	3163	1335	47	0	632	0	CDKN2A	9	21974776	Frame_Shift_Ins	INS	-	TCGA-DD-AAD8-01A-11D-A40R-10	7252207	21974776	119238655	52	27286										
VCP	7415	hgsc.bcm.edu	37	chr9	35063004	35063004	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	agaagaagaaggctccagtcTcatttgctacagctcgagca	10	10	1	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr9:35063004T>A	ENST00000358901.6	-	7	1677	c.782A>T	c.(781-783)gAg>gTg	p.E261V		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	261					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GGCTCCAGTCTCATTTGCTAC	0.463																																					p.E261V		Atlas-SNP	.											.	VCP	64	.	0			c.A782T						.						212	207	208					9																	35063004		2203	4300	6503	SO:0001583	missense	7415	exon7			CCAGTCTCATTTG	AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"ATPases / AAA-type"	12666	protein-coding gene	gene with protein product		601023	"valosin-containing protein"			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.782A>T	chr9.hg19:g.35063004T>A	ENSP00000351777:p.Glu261Val	107.0	0.0		127.0	54.0	NM_007126	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Missense_Mutation	SNP	ENST00000358901.6	hg19	CCDS6573.1	.	.	.	.	.	.	.	.	.	.	T	33	5.263091	0.95399	.	.	ENSG00000165280	ENST00000358901	D	0.94417	-3.42	5.9	5.9	0.94986	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.97451	0.9166	M	0.84773	2.715	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98150	1.0441	10	0.87932	D	0	-20.8164	16.3317	0.83023	0.0:0.0:0.0:1.0	.	261	P55072	TERA_HUMAN	V	261	ENSP00000351777:E261V	ENSP00000351777:E261V	E	-	2	0	VCP	35053004	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.296000	0.72751	2.264000	0.75181	0.533000	0.62120	GAG	.	.		0.463	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126		A	35063004	T	A	35063004	3	1	183	1	0	0	0	0	1	0	0	0	17155	1551	54	4	1682	4	VCP	9	35063004	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	13088228	35063004	106150427	53	27287										
PAPPA	5069	hgsc.bcm.edu	37	chr9	119116067	119116067	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	agtgtgaagacagtgatgccTcccaggtaagcctcctggaa	12	10	0	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr9:119116067T>A	ENST00000328252.3	+	17	4711	c.4342T>A	c.(4342-4344)Tcc>Acc	p.S1448T	PAPPA_ENST00000534838.1_Missense_Mutation_p.S486T	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1448	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						CAGTGATGCCTCCCAGGTAAG	0.473																																					p.S1448T		Atlas-SNP	.											.	PAPPA	243	.	0			c.T4342A						.						155	133	140					9																	119116067		2203	4300	6503	SO:0001583	missense	5069	exon17			GATGCCTCCCAGG		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.4342T>A	chr9.hg19:g.119116067T>A	ENSP00000330658:p.Ser1448Thr	82.0	0.0		77.0	18.0	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	hg19	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	T	8.954	0.968821	0.18659	.	.	ENSG00000182752	ENST00000328252;ENST00000534838	T;T	0.62498	0.02;0.02	5.8	0.393	0.16294	Complement control module (2);Sushi/SCR/CCP (3);	0.903421	0.09681	N	0.769787	T	0.41282	0.1152	L	0.36672	1.1	0.22226	N	0.999279	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.21381	-1.0247	10	0.12103	T	0.63	-8.1269	0.2218	0.00169	0.3898:0.1687:0.2023:0.2392	.	486;1448	F5GZ19;Q13219	.;PAPP1_HUMAN	T	1448;486	ENSP00000330658:S1448T;ENSP00000441461:S486T	ENSP00000330658:S1448T	S	+	1	0	PAPPA	118155888	0.000000	0.05858	0.907000	0.35723	0.389000	0.30415	0.218000	0.17622	0.035000	0.15519	0.533000	0.62120	TCC	.	.		0.473	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		A	119116067	T	A	119116067	3	1	183	1	0	0	0	0	1	0	0	0	11441	1551	54	4	4408	4	PAPPA	9	119116067	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	84053063	119116067	22097364	54	27288										
EXD3	54932	hgsc.bcm.edu	37	chr9	140247240	140247240	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ggctctgccccaccaggcccTgtgaggagggtggccgtgag	17	13	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr9:140247240T>A	ENST00000340951.4	-	11	1066		c.e11-2		EXD3_ENST00000342129.4_Splice_Site	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3											NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CACCAGGCCCTGTGAGGAGGG	0.662																																					.		Atlas-SNP	.											.	EXD3	86	.	0			c.871-2A>T						.						9	12	11					9																	140247240		2035	4157	6192	SO:0001630	splice_region_variant	54932	exon12			AGGCCCTGTGAGG		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.871-2A>T	chr9.hg19:g.140247240T>A		147.0	0.0		86.0	22.0	NM_017820	Q6P1M1|Q8IXT8	Splice_Site	SNP	ENST00000340951.4	hg19	CCDS48066.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.450679	0.26074	.	.	ENSG00000187609	ENST00000340951	.	.	.	3.3	2.12	0.27331	.	.	.	.	.	.	.	.	.	.	.	0.35974	D	0.835537	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7647	0.18219	0.0:0.1375:0.0:0.8625	.	.	.	.	.	-1	.	.	.	-	.	.	EXD3	139367061	0.876000	0.30132	0.040000	0.18447	0.296000	0.27459	1.908000	0.39907	0.420000	0.25954	0.402000	0.26972	.	.	.		0.662	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	Intron	A	140247240	T	A	140247240	5	1	183	1	0	0	0	0	0	0	1	0	5301	1594	55	4	1809	4	EXD3	9	140247240	Splice_Site	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	21131173	140247240	966191	55	27289										
CAMK2G	818	hgsc.bcm.edu	37	chr10	75620639	75620639	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ccgagcctcacgttctagttTctggtgatctaaaagcagaa	9	10	4	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr10:75620639T>C	ENST00000351293.3	-	3	226	c.169A>G	c.(169-171)Aaa>Gaa	p.K57E	CAMK2G_ENST00000322635.3_Missense_Mutation_p.K57E|CAMK2G_ENST00000394762.2_Missense_Mutation_p.K57E|CAMK2G_ENST00000423381.1_Missense_Mutation_p.K57E|CAMK2G_ENST00000444854.2_Missense_Mutation_p.K57E|CAMK2G_ENST00000305762.7_Missense_Mutation_p.K57E|CAMK2G_ENST00000472912.1_5'UTR|CAMK2G_ENST00000372765.1_Missense_Mutation_p.K57E|CAMK2G_ENST00000322680.3_Missense_Mutation_p.K57E	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	57	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|dephosphorylation (GO:0016311)|G1/S transition of mitotic cell cycle (GO:0000082)|insulin secretion (GO:0030073)|interferon-gamma-mediated signaling pathway (GO:0060333)|nervous system development (GO:0007399)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of calcium ion transport (GO:0051924)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of skeletal muscle adaptation (GO:0014733)|synaptic transmission (GO:0007268)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			kidney(2)|large_intestine(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	15	Prostate(51;0.0112)				Bosutinib(DB06616)	CGTTCTAGTTTCTGGTGATCT	0.433																																					p.K57E		Atlas-SNP	.											.	CAMK2G	79	.	0			c.A169G						.						138	132	134					10																	75620639		2203	4300	6503	SO:0001583	missense	818	exon3			CTAGTTTCTGGTG	U81554	CCDS7336.1, CCDS7337.1, CCDS7338.1, CCDS73153.1	10q22	2008-10-30	2008-10-30		ENSG00000148660	ENSG00000148660			1463	protein-coding gene	gene with protein product		602123	"calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma"	CAMKG		8287681	Standard	NM_001204492		Approved		uc001jvm.2	Q13555	OTTHUMG00000018492	ENST00000351293.3:c.169A>G	chr10.hg19:g.75620639T>C	ENSP00000277853:p.Lys57Glu	150.0	0.0		82.0	67.0	NM_172170	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Missense_Mutation	SNP	ENST00000351293.3	hg19	CCDS7336.1	.	.	.	.	.	.	.	.	.	.	T	31	5.077357	0.94000	.	.	ENSG00000148660	ENST00000351293;ENST00000322635;ENST00000423381;ENST00000394763;ENST00000322680;ENST00000394762;ENST00000305762;ENST00000372765;ENST00000444854	T;T;T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	6.08	6.08	0.98989	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.64940	0.2644	N	0.12887	0.27	0.80722	D	1	D;P;D;D;D;P;D;D	0.89917	0.998;0.837;0.993;0.98;0.997;0.753;0.994;1.0	D;P;D;P;D;P;D;D	0.77557	0.974;0.724;0.926;0.852;0.936;0.749;0.91;0.99	T	0.71738	-0.4502	10	0.87932	D	0	.	14.8736	0.70478	0.0:0.0:0.0:1.0	.	49;57;57;57;57;57;57;57	B3KY86;Q13555-4;Q13555-6;Q13555-10;A8K6N9;Q13555;Q13555-5;Q13555-8	.;.;.;.;.;KCC2G_HUMAN;.;.	E	57	ENSP00000277853:K57E;ENSP00000315599:K57E;ENSP00000410298:K57E;ENSP00000319060:K57E;ENSP00000378243:K57E;ENSP00000307082:K57E;ENSP00000361851:K57E;ENSP00000399680:K57E	ENSP00000307082:K57E	K	-	1	0	CAMK2G	75290645	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.593000	0.74100	2.333000	0.79357	0.533000	0.62120	AAA	.	.		0.433	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169		C	75620639	T	C	75620639	3	2	183	1	0	0	0	0	1	0	0	0	2604	1792	62	2	1677	2	CAMK2G	10	75620639	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10		75620639	59914108	56	27290										
OR8J1	219477	hgsc.bcm.edu	37	chr11	56128125	56128125	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	accctctgctgtacatggtgGtggtgtctcggcggctctgc	14	12	3	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr11:56128125G>T	ENST00000303039.3	+	1	435	c.403G>T	c.(403-405)Gtg>Ttg	p.V135L		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					GTACATGGTGGTGGTGTCTCG	0.478																																					p.V135L		Atlas-SNP	.											.	OR8J1	87	.	0			c.G403T						.						133	126	128					11																	56128125		2201	4296	6497	SO:0001583	missense	219477	exon1			ATGGTGGTGGTGT	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"GPCR / Class A : Olfactory receptors"	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.403G>T	chr11.hg19:g.56128125G>T	ENSP00000304060:p.Val135Leu	121.0	0.0		78.0	46.0	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	hg19	CCDS31529.1	.	.	.	.	.	.	.	.	.	.	G	9.926	1.213454	0.22289	.	.	ENSG00000172487	ENST00000303039	T	0.11712	2.75	4.05	4.05	0.47172	GPCR, rhodopsin-like superfamily (1);	0.119777	0.38663	N	0.001609	T	0.07279	0.0184	N	0.10782	0.045	0.24340	N	0.994966	D	0.53462	0.96	P	0.49140	0.601	T	0.29427	-1.0012	10	0.23302	T	0.38	.	7.3413	0.26637	0.0:0.1822:0.63:0.1878	.	135	Q8NGP2	OR8J1_HUMAN	L	135	ENSP00000304060:V135L	ENSP00000304060:V135L	V	+	1	0	OR8J1	55884701	0.010000	0.17322	1.000000	0.80357	0.093000	0.18481	0.521000	0.22893	2.255000	0.74692	0.643000	0.83706	GTG	.	.		0.478	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205		T	56128125	G	T	56128125	3	4	183	1	0	0	0	0	1	0	0	0	11250	1261	44	3	405	3	OR8J1	11	56128125	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10		56128125	78878391	57	27291										
YIF1A	10897	hgsc.bcm.edu	37	chr11	66053219	66053219	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gccaggagcacgtaagtaatGaaggccatcgctgccaagtg	13	10	0	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr11:66053219G>T	ENST00000376901.4	-	5	622	c.438C>A	c.(436-438)ttC>ttA	p.F146L	YIF1A_ENST00000526497.1_5'UTR|YIF1A_ENST00000496746.1_5'Flank|YIF1A_ENST00000359461.6_Missense_Mutation_p.F146L|YIF1A_ENST00000471387.2_Missense_Mutation_p.F3L	NM_020470.2	NP_065203.2	O95070	YIF1A_HUMAN	Yip1 interacting factor homolog A (S. cerevisiae)	146					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|microtubule organizing center (GO:0005815)				endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	9						CGTAAGTAATGAAGGCCATCG	0.562																																					p.F146L		Atlas-SNP	.											.	YIF1A	29	.	0			c.C438A						.						96	74	82					11																	66053219		2200	4295	6495	SO:0001583	missense	10897	exon5			AGTAATGAAGGCC	AF004876	CCDS8132.1, CCDS73325.1	11q13	2009-01-05	2005-06-07	2005-06-07	ENSG00000174851	ENSG00000174851			16688	protein-coding gene	gene with protein product		611484	"Yip1 interacting factor homolog (S. cerevisiae)"	YIF1		8824393, 10970842, 18718466	Standard	NM_020470		Approved	YIF1P, 54TM, FinGER7	uc001ohk.4	O95070	OTTHUMG00000102079	ENST00000376901.4:c.438C>A	chr11.hg19:g.66053219G>T	ENSP00000366098:p.Phe146Leu	62.0	0.0		52.0	16.0	NM_020470	A6NM00|Q96G83|Q9BVD0	Missense_Mutation	SNP	ENST00000376901.4	hg19	CCDS8132.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.841727	0.51057	.	.	ENSG00000174851	ENST00000471387;ENST00000359461;ENST00000376901;ENST00000376904;ENST00000431556	T;T;T	0.42513	0.97;1.05;0.98	4.1	3.18	0.36537	.	0.000000	0.85682	D	0.000000	T	0.33030	0.0849	L	0.54323	1.7	0.58432	D	0.999991	P	0.35700	0.516	B	0.38194	0.267	T	0.06463	-1.0825	10	0.22109	T	0.4	-3.5029	4.7289	0.12955	0.2894:0.0:0.7106:0.0	.	146	O95070	YIF1A_HUMAN	L	3;146;146;150;146	ENSP00000352437:F146L;ENSP00000366098:F146L;ENSP00000401953:F146L	ENSP00000352437:F146L	F	-	3	2	YIF1A	65809795	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.664000	0.37439	2.289000	0.77006	0.462000	0.41574	TTC	.	.		0.562	YIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219903.3	NM_020470		T	66053219	G	T	66053219	3	4	183	1	0	0	0	0	1	0	0	0	17490	1281	45	3	459	3	YIF1A	11	66053219	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	9925094	66053219	68953297	58	27292										
A2M	2	hgsc.bcm.edu	37	chr12	9230420	9230420	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	atgaagatgtaggctcgagcTtgggcaaaagtcttcagaac	12	7	2	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr12:9230420T>G	ENST00000318602.7	-	26	3460	c.3153A>C	c.(3151-3153)caA>caC	p.Q1051H	A2M_ENST00000542567.1_5'UTR	NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	1051					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)	p.Q1051H(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	AGGCTCGAGCTTGGGCAAAAG	0.473																																					p.Q1051H		Atlas-SNP	.											A2M,NS,carcinoma,0,1	A2M	180	.	1	Substitution - Missense(1)	ovary(1)	c.A3153C						.						110	115	113					12																	9230420		2202	4300	6502	SO:0001583	missense	2	exon26			TCGAGCTTGGGCA	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.3153A>C	chr12.hg19:g.9230420T>G	ENSP00000323929:p.Gln1051His	119.0	0.0		94.0	28.0	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	hg19	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	T	18.23	3.578091	0.65878	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.35605	1.3	5.54	3.71	0.42584	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.353602	0.28088	N	0.016653	T	0.65428	0.2690	M	0.94021	3.485	0.31240	N	0.695256	D	0.76494	0.999	D	0.76071	0.987	T	0.71537	-0.4563	10	0.87932	D	0	.	8.5507	0.33449	0.0:0.7015:0.0:0.2985	.	1051	P01023	A2MG_HUMAN	H	1051;1066	ENSP00000323929:Q1051H	ENSP00000323929:Q1051H	Q	-	3	2	A2M	9121687	0.980000	0.34600	1.000000	0.80357	0.983000	0.72400	0.213000	0.17521	0.692000	0.31613	-0.472000	0.04984	CAA	.	.		0.473	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		G	9230420	T	G	9230420	3	3	183	1	0	0	0	0	1	0	0	0	4	1606	56	5	1315	5	A2M	12	9230420	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10		9230420	124621475	59	27293										
OR10A7	121364	hgsc.bcm.edu	37	chr12	55615504	55615504	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctgaggatgtcctctgccacTggccgccagaaggcattttc	11	13	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr12:55615504T>A	ENST00000326258.1	+	1	696	c.696T>A	c.(694-696)acT>acA	p.T232T		NM_001005280.1	NP_001005280.1	Q8NGE5	O10A7_HUMAN	olfactory receptor, family 10, subfamily A, member 7	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|lung(11)|ovary(4)|prostate(2)|skin(3)	24						CCTCTGCCACTGGCCGCCAGA	0.488																																					p.T232T		Atlas-SNP	.											.	OR10A7	53	.	0			c.T696A						.						121	100	107					12																	55615504		2203	4300	6503	SO:0001819	synonymous_variant	121364	exon1			TGCCACTGGCCGC	BK004327	CCDS31815.1	12q13.13	2012-08-09				ENSG00000179919		"GPCR / Class A : Olfactory receptors"	15329	protein-coding gene	gene with protein product							Standard	NM_001005280		Approved		uc010spf.2	Q8NGE5	OTTHUMG00000169860	ENST00000326258.1:c.696T>A	chr12.hg19:g.55615504T>A		75.0	0.0		71.0	24.0	NM_001005280	Q6IFD5|Q96R19	Silent	SNP	ENST00000326258.1	hg19	CCDS31815.1																																																																																			.	.		0.488	OR10A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406308.1			A	55615504	T	A	55615504	2	1	183	1	0	0	0	0	0	0	0	1	10904	1567	55	4		4	OR10A7	12	55615504	Silent	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	46385084	55615504	78236391	60	27294										
RASSF9	9182	hgsc.bcm.edu	37	chr12	86199277	86199277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	agaaactgtgtcctgcttaaTtttagccagtttccggaaag	9	8	0	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr12:86199277T>C	ENST00000361228.3	-	2	879	c.511A>G	c.(511-513)Att>Gtt	p.I171V		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	171					endosomal transport (GO:0016197)|protein targeting (GO:0006605)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|trans-Golgi network transport vesicle membrane (GO:0012510)	transporter activity (GO:0005215)			endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCCTGCTTAATTTTAGCCAGT	0.383																																					p.I171V		Atlas-SNP	.											.	RASSF9	100	.	0			c.A511G						.						162	156	157					12																	86199277		1838	4090	5928	SO:0001583	missense	9182	exon2			GCTTAATTTTAGC		CCDS44950.1	12q21.31	2008-02-22	2008-02-22	2008-02-22		ENSG00000198774			15739	protein-coding gene	gene with protein product		610383	"peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor"	PAMCI		9837933, 18272789	Standard	NM_005447		Approved	P-CIP1	uc001taf.1	O75901	OTTHUMG00000169831	ENST00000361228.3:c.511A>G	chr12.hg19:g.86199277T>C	ENSP00000354884:p.Ile171Val	71.0	0.0		71.0	22.0	NM_005447	B3KMQ4|Q8N5U8	Missense_Mutation	SNP	ENST00000361228.3	hg19	CCDS44950.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.454438	0.26161	.	.	ENSG00000198774	ENST00000361228	T	0.46819	0.86	4.91	4.91	0.64330	.	0.072502	0.53938	D	0.000043	T	0.43567	0.1253	L	0.61218	1.895	0.34664	D	0.722959	P	0.37207	0.587	B	0.36464	0.225	T	0.57493	-0.7802	10	0.30078	T	0.28	-9.4901	10.6704	0.45755	0.0:0.0:0.2983:0.7017	.	171	O75901	RASF9_HUMAN	V	171	ENSP00000354884:I171V	ENSP00000354884:I171V	I	-	1	0	RASSF9	84723408	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	1.734000	0.38166	1.979000	0.57680	0.533000	0.62120	ATT	.	.		0.383	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406109.1			C	86199277	T	C	86199277	3	2	183	1	0	0	0	0	1	0	0	0	13108	1493	52	2	800	2	RASSF9	12	86199277	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	30583773	86199277	47652618	61	27295										
SELPLG	6404	hgsc.bcm.edu	37	chr12	109017058	109017058	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	cccttgcgggagaggcggacCgccagcaccacagtgcacac	13	16	0	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr12:109017058C>T	ENST00000550948.1	-	2	1250	c.1026G>A	c.(1024-1026)gcG>gcA	p.A342A	SELPLG_ENST00000388962.3_Silent_p.A332A|SELPLG_ENST00000228463.6_Silent_p.A358A			Q14242	SELPL_HUMAN	selectin P ligand	342					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						AGAGGCGGACCGCCAGCACCA	0.617																																					p.A358A		Atlas-SNP	.											.	SELPLG	138	.	0			c.G1074A						.						49	46	47					12																	109017058		2203	4300	6503	SO:0001819	synonymous_variant	6404	exon2			GCGGACCGCCAGC		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"CD molecules", "Endogenous ligands"	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.1026G>A	chr12.hg19:g.109017058C>T		170.0	0.0		160.0	69.0	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Silent	SNP	ENST00000550948.1	hg19	CCDS31895.2																																																																																			.	.		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1			T	109017058	C	T	109017058	2	4	183	1	0	0	0	0	0	0	0	1	14035	639	23	1		1	SELPLG	12	109017058	Silent	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	22817781	109017058	24834837	62	27296										
PDS5B	23047	hgsc.bcm.edu	37	chr13	33338652	33338652	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	atagttctgaaatggatcacAgtgaaaatgaagattacaca	8	5	2	4			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr13:33338652A>T	ENST00000315596.10	+	31	3730	c.3544A>T	c.(3544-3546)Agt>Tgt	p.S1182C	RNY1P4_ENST00000384595.1_RNA	NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	1182					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		AATGGATCACAGTGAAAATGA	0.348																																					p.S1182C		Atlas-SNP	.											.	PDS5B	141	.	0			c.A3544T						.						106	103	104					13																	33338652		1847	4089	5936	SO:0001583	missense	23047	exon31			GATCACAGTGAAA	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"androgen-induced proliferation inhibitor"	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.3544A>T	chr13.hg19:g.33338652A>T	ENSP00000313851:p.Ser1182Cys	253.0	1.0		214.0	115.0	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	hg19	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.322661	0.81580	.	.	ENSG00000083642	ENST00000315596;ENST00000421084;ENST00000447833	.	.	.	5.39	5.39	0.77823	.	0.074919	0.85682	D	0.000000	T	0.60650	0.2285	N	0.19112	0.55	0.80722	D	1	D	0.65815	0.995	P	0.61940	0.896	T	0.64175	-0.6469	9	0.49607	T	0.09	-17.2789	15.6785	0.77349	1.0:0.0:0.0:0.0	.	1182	Q9NTI5	PDS5B_HUMAN	C	1182;1182;136	.	ENSP00000313851:S1182C	S	+	1	0	PDS5B	32236652	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.942000	0.87708	2.149000	0.67028	0.528000	0.53228	AGT	.	.		0.348	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		T	33338652	A	T	33338652	3	4	183	1	0	0	0	0	1	0	0	0	11701	188	7	4	3662	4	PDS5B	13	33338652	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10		33338652	81831226	63	27297										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77671529	77671529	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gtgagcttgtctcatgtgatAggtcaccgggtatggatgtg	15	6	2	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr13:77671529A>C	ENST00000544440.2	-	56	9663	c.9646T>G	c.(9646-9648)Tat>Gat	p.Y3216D	MYCBP2_ENST00000357337.6_Missense_Mutation_p.Y3216D|MYCBP2_ENST00000482517.1_5'Flank|MYCBP2_ENST00000407578.2_Missense_Mutation_p.Y3254D|MYCBP2-AS1_ENST00000593933.1_RNA					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		CTCATGTGATAGGTCACCGGG	0.438																																					p.Y3254D		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.T9760G						.						113	103	107					13																	77671529		2203	4300	6503	SO:0001583	missense	23077	exon56			TGTGATAGGTCAC	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.9646T>G	chr13.hg19:g.77671529A>C	ENSP00000444596:p.Tyr3216Asp	67.0	0.0		67.0	20.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	A	17.68	3.448518	0.63178	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.32023	1.47;1.47;1.47	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.53174	0.1780	L	0.57536	1.79	0.80722	D	1	D;D	0.76494	0.999;0.995	D;D	0.83275	0.996;0.986	T	0.54840	-0.8233	10	0.72032	D	0.01	.	16.0539	0.80782	1.0:0.0:0.0:0.0	.	3216;3216	O75592-2;O75592	.;MYCB2_HUMAN	D	3216;3254;3216	ENSP00000349892:Y3216D;ENSP00000384288:Y3254D;ENSP00000444596:Y3216D	ENSP00000349892:Y3216D	Y	-	1	0	MYCBP2	76569530	1.000000	0.71417	0.983000	0.44433	0.973000	0.67179	9.339000	0.96797	2.193000	0.70182	0.533000	0.62120	TAT	.	.		0.438	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77671529	A	C	77671529	3	2	183	1	0	0	0	0	1	0	0	0	10027	420	15	5	4388	5	MYCBP2	13	77671529	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	44332877	77671529	37498349	64	27298										
SCEL	8796	hgsc.bcm.edu	37	chr13	78133957	78133957	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	agagatgaaaattacggtagGgtggtgctcaaccgacataa	12	6	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr13:78133957G>A	ENST00000349847.3	+	4	264	c.180G>A	c.(178-180)agG>agA	p.R60R	SCEL_ENST00000535157.1_Silent_p.R60R|SCEL_ENST00000377246.3_Silent_p.R60R	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	60					embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		ATTACGGTAGGGTGGTGCTCA	0.418																																					p.R60R		Atlas-SNP	.											.	SCEL	85	.	0			c.G180A						.						249	220	230					13																	78133957		2203	4300	6503	SO:0001819	synonymous_variant	8796	exon4			CGGTAGGGTGGTG	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.180G>A	chr13.hg19:g.78133957G>A		124.0	0.0		86.0	49.0	NM_003843	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Silent	SNP	ENST00000349847.3	hg19	CCDS9459.1																																																																																			.	.		0.418	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777		A	78133957	G	A	78133957	2	1	183	1	0	0	0	0	0	0	0	1	13903	1223	43	3		3	SCEL	13	78133957	Silent	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	462428	78133957	37035921	65	27299										
VIPAR	63894	hgsc.bcm.edu	37	chr14	77895375	77895375	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gacgacatcatggcacttgaActtagtggctaagttcaact	9	9	2	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr14:77895375A>C	ENST00000553888.1	-	18	1840	c.1330T>G	c.(1330-1332)Ttc>Gtc	p.F444V	VIPAS39_ENST00000557658.1_Missense_Mutation_p.F444V|VIPAS39_ENST00000327028.4_Missense_Mutation_p.F431V|VIPAS39_ENST00000343765.2_Missense_Mutation_p.F444V|VIPAS39_ENST00000448935.2_Missense_Mutation_p.F395V|VIPAS39_ENST00000556412.1_Missense_Mutation_p.F470V	NM_001193314.1|NM_001193317.1|NM_022067.3	NP_001180243.1|NP_001180246.1|NP_071350.2	Q9H9C1	SPE39_HUMAN	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	444					cell differentiation (GO:0030154)|endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|late endosome (GO:0005770)|recycling endosome (GO:0055037)											TGGCACTTGAACTTAGTGGCT	0.443																																					p.F444V		Atlas-SNP	.											.	.	.	.	0			c.T1330G						.						151	119	130					14																	77895375		2203	4300	6503	SO:0001583	missense	63894	exon18			ACTTGAACTTAGT	AK022925	CCDS9862.1, CCDS53905.1	14q24.3-q31	2013-08-14	2012-07-24	2012-07-24	ENSG00000151445	ENSG00000151445			20347	protein-coding gene	gene with protein product	"VPS33B interacting protein, apical-basolateral polarity regulator"	613401	"chromosome 14 open reading frame 133"	C14orf133		20190753, 19109425, 22753090, 23002115, 23918659	Standard	NM_022067		Approved	VIPAR, VPS16B, SPE-39, SPE39, hSPE-39	uc001xtu.2	Q9H9C1		ENST00000553888.1:c.1330T>G	chr14.hg19:g.77895375A>C	ENSP00000452181:p.Phe444Val	53.0	0.0		58.0	29.0	NM_001193314	B4DPI6|O95434|Q9H7E1|Q9H9I9	Missense_Mutation	SNP	ENST00000553888.1	hg19	CCDS9862.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.869021	0.51588	.	.	ENSG00000151445	ENST00000343765;ENST00000553888;ENST00000327028;ENST00000557658;ENST00000448935;ENST00000556412	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.54	5.54	0.83059	.	0.158102	0.64402	D	0.000017	T	0.28366	0.0701	N	0.16368	0.405	0.41505	D	0.988301	B;B	0.16802	0.011;0.019	B;B	0.19666	0.014;0.026	T	0.10154	-1.0642	10	0.18276	T	0.48	-16.723	14.6448	0.68754	1.0:0.0:0.0:0.0	.	395;444	B4DPI6;Q9H9C1	.;VIPAR_HUMAN	V	444;444;431;444;395;470	ENSP00000339122:F444V;ENSP00000452181:F444V;ENSP00000313098:F431V;ENSP00000452191:F444V;ENSP00000404815:F395V;ENSP00000451857:F470V	ENSP00000313098:F431V	F	-	1	0	VIPAR	76965128	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.723000	0.61965	2.094000	0.63399	0.533000	0.62120	TTC	.	.		0.443	VIPAS39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414008.1	NM_022067		C	77895375	A	C	77895375	3	2	183	1	0	0	0	0	1	0	0	0	17183	43	2	5	163	5	VIPAR	14	77895375	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10		77895375	29454165	66	27300										
CLMN	79789	hgsc.bcm.edu	37	chr14	95677210	95677210	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gcaaagtcctgcaccgccacGccatacctgaaggaaaaaca	8	14	0	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr14:95677210G>C	ENST00000298912.4	-	7	728	c.615C>G	c.(613-615)ggC>ggG	p.G205G		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	205	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		GCACCGCCACGCCATACCTGA	0.582																																					p.G205G		Atlas-SNP	.											.	CLMN	103	.	0			c.C615G						.						73	79	77					14																	95677210		2203	4300	6503	SO:0001819	synonymous_variant	79789	exon7			CGCCACGCCATAC	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.615C>G	chr14.hg19:g.95677210G>C		61.0	0.0		84.0	23.0	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Silent	SNP	ENST00000298912.4	hg19	CCDS9933.1																																																																																			.	.		0.582	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			C	95677210	G	C	95677210	2	2	183	1	0	0	0	0	0	0	0	1	3544	1074	38	4		4	CLMN	14	95677210	Silent	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	17781835	95677210	11672330	67	27301										
BAHD1	22893	hgsc.bcm.edu	37	chr15	40757560	40757560	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	cagaatgaagtgtttgcatcGcgacatcaggaccagaacag	11	9	1	3	rs151097414		TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr15:40757560G>A	ENST00000416165.1	+	6	2150	c.2079G>A	c.(2077-2079)tcG>tcA	p.S693S	BAHD1_ENST00000561234.1_Silent_p.S692S|RP11-64K12.8_ENST00000559730.1_RNA|BAHD1_ENST00000560846.1_Silent_p.S690S	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	693	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		TGTTTGCATCGCGACATCAGG	0.537																																					p.S693S		Atlas-SNP	.											.	BAHD1	68	.	0			c.G2079A						.	G		0,4406		0,0,2203	214	151	173		2079	-5.4	0.4	15	dbSNP_134	173	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BAHD1	NM_014952.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		693/781	40757560	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	22893	exon6			TGCATCGCGACAT	AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.2079G>A	chr15.hg19:g.40757560G>A		64.0	0.0		77.0	17.0	NM_014952	Q8NDF7|Q9Y2F4	Silent	SNP	ENST00000416165.1	hg19	CCDS10058.1																																																																																			.	G|1.000;A|0.000		0.537	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		A	40757560	G	A	40757560	2	1	183	1	0	0	0	0	0	0	0	1	1297	1074	38	1		1	BAHD1	15	40757560	Silent	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10		40757560	61773832	68	27302										
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43712632	43712634	+	In_Frame_Del	DEL	CAG	CAG	-													0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	aaagagcaatttatacttccCagctccgacatctcgtgtga							TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr15:43712632_43712634delCAG	ENST00000263801.3	-	21	4787_4789	c.4535_4537delCTG	c.(4534-4539)gctggg>ggg	p.A1512del	TP53BP1_ENST00000450115.2_In_Frame_Del_p.A1517del|TP53BP1_ENST00000382044.4_In_Frame_Del_p.A1517del|TP53BP1_ENST00000382039.3_In_Frame_Del_p.A1467del	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1512	Interaction with dimethylated histone H4.|Tudor-like.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		TTATACTTCCCAGCTCCGACATC	0.488								Other conserved DNA damage response genes																													p.1517_1518del		Atlas-INDEL	.											.	TP53BP1	157	.	0			c.4551_4553del						.																																			SO:0001651	inframe_deletion	7158	exon21			.	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.4535_4537delCTG	chr15.hg19:g.43712632_43712634delCAG	ENSP00000263801:p.Ala1512del	105.0	0.0		105.0	50.0	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	In_Frame_Del	DEL	ENST00000263801.3	hg19	CCDS10096.1																																																																																			.	.		0.488	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			-	43712634	CAG	-	43712632	7	5	183	1	0	1	0	1	0	0	0	0	16398	594	21	0	1413	0	TP53BP1	15	43712632	In_Frame_Del	DEL	CAG	TCGA-DD-AAD8-01A-11D-A40R-10	2955072	43712632	58818760	69	27303										
SPATA5L1	79029	hgsc.bcm.edu	37	chr15	45695491	45695491	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gtgcggcgggtcttccagcgCgcccgggaactggccagccg	17	15	1	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr15:45695491C>T	ENST00000305560.6	+	1	963	c.864C>T	c.(862-864)cgC>cgT	p.R288R	GATM_ENST00000458245.5_5'Flank|SPATA5L1_ENST00000559860.1_Silent_p.R288R	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	288						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		TCTTCCAGCGCGCCCGGGAAC	0.741																																					p.R288R		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.C864T						.						4	6	5					15																	45695491		1991	3974	5965	SO:0001819	synonymous_variant	79029	exon1			CCAGCGCGCCCGG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"ATPases / AAA-type"	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.864C>T	chr15.hg19:g.45695491C>T		118.0	0.0		122.0	61.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Silent	SNP	ENST00000305560.6	hg19	CCDS10123.1																																																																																			.	.		0.741	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		T	45695491	C	T	45695491	2	4	183	1	0	0	0	0	0	0	0	1	15027	755	27	1		1	SPATA5L1	15	45695491	Silent	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	1982859	45695491	56835901	70	27304										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62155676	62155676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gattgtcttcttgcttccagGaatagcacagtggtatcggt	11	8	2	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr15:62155676G>A	ENST00000261517.5	-	82	10988	c.10915C>T	c.(10915-10917)Cct>Tct	p.P3639S	VPS13C_ENST00000249837.3_Missense_Mutation_p.P3596S	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TTGCTTCCAGGAATAGCACAG	0.368																																					p.P3639S		Atlas-SNP	.											.	VPS13C	506	.	0			c.C10915T						.						168	146	153					15																	62155676		2203	4300	6503	SO:0001583	missense	54832	exon82			TTCCAGGAATAGC	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.10915C>T	chr15.hg19:g.62155676G>A	ENSP00000261517:p.Pro3639Ser	120.0	0.0		105.0	6.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	6.397	0.441296	0.12164	.	.	ENSG00000129003	ENST00000249837;ENST00000261517	T;T	0.47177	0.86;0.85	5.68	1.42	0.22433	.	0.546215	0.19185	N	0.120573	T	0.32496	0.0831	L	0.42245	1.32	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.19910	-1.0291	10	0.18710	T	0.47	.	5.8851	0.18876	0.2662:0.1263:0.6075:0.0	.	3596;3639	Q709C8-3;Q709C8	.;VP13C_HUMAN	S	3596;3639	ENSP00000249837:P3596S;ENSP00000261517:P3639S	ENSP00000249837:P3596S	P	-	1	0	VPS13C	59942968	1.000000	0.71417	0.005000	0.12908	0.815000	0.46073	1.361000	0.34136	0.061000	0.16311	0.591000	0.81541	CCT	.	.		0.368	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62155676	G	A	62155676	3	1	183	1	0	0	0	0	1	0	0	0	17206	1174	41	3	362	3	VPS13C	15	62155676	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	16460185	62155676	40375716	71	27305										
LARP6	55323	hgsc.bcm.edu	37	chr15	71124687	71124687	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctccgccagtggggactttcTggaaacgcctttgcgttggg	14	11	1	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr15:71124687T>A	ENST00000299213.8	-	3	1250	c.1180A>T	c.(1180-1182)Aga>Tga	p.R394*	RP11-138H8.7_ENST00000592096.1_lincRNA	NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	394					regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						GGGGACTTTCTGGAAACGCCT	0.572																																					p.R394X		Atlas-SNP	.											.	LARP6	43	.	0			c.A1180T						.						48	44	46					15																	71124687		2199	4297	6496	SO:0001587	stop_gained	55323	exon3			ACTTTCTGGAAAC	BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"La ribonucleoprotein domain containing"	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.1180A>T	chr15.hg19:g.71124687T>A	ENSP00000299213:p.Arg394*	84.0	0.0		87.0	51.0	NM_018357	Q5XKE4|Q8N3N2|Q9NUR0	Nonsense_Mutation	SNP	ENST00000299213.8	hg19	CCDS32281.1	.	.	.	.	.	.	.	.	.	.	T	32	5.177942	0.94846	.	.	ENSG00000166173	ENST00000299213	.	.	.	4.68	0.9	0.19278	.	0.319263	0.37623	N	0.002019	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-10.2496	6.0294	0.19671	0.0:0.0867:0.313:0.6004	.	.	.	.	X	394	.	ENSP00000299213:R394X	R	-	1	2	LARP6	68911741	1.000000	0.71417	0.994000	0.49952	0.985000	0.73830	1.971000	0.40530	0.042000	0.15717	0.454000	0.30748	AGA	.	.		0.572	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357		A	71124687	T	A	71124687	4	1	183	1	0	0	0	0	0	1	0	0	8641	1588	55	4	299	4	LARP6	15	71124687	Nonsense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	8969011	71124687	31406705	72	27306										
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81225586	81225586	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctttcctgggctctgtttagAttacttccagagtgttcttc	8	10	2	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr15:81225586A>G	ENST00000394685.3	+	23	3213	c.2794A>G	c.(2794-2796)Att>Gtt	p.I932V	KIAA1199_ENST00000220244.3_Splice_Site_p.I932V|KIAA1199_ENST00000356249.5_Splice_Site_p.I932V|RP11-351M8.2_ENST00000560873.1_RNA			Q8WUJ3	CEMIP_HUMAN		932					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CTCTGTTTAGATTACTTCCAG	0.542																																					p.I932V		Atlas-SNP	.											.	KIAA1199	118	.	0			c.A2794G						.						67	65	66					15																	81225586		2203	4300	6503	SO:0001630	splice_region_variant	57214	exon22			GTTTAGATTACTT																												ENST00000394685.3:c.2794-1A>G	chr15.hg19:g.81225586A>G		82.0	0.0		135.0	73.0	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	hg19	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	A	2.055	-0.416742	0.04766	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	T;T;T	0.54675	0.56;0.56;0.56	4.37	4.37	0.52481	Pectin lyase fold/virulence factor (1);	0.127324	0.50627	D	0.000105	T	0.34978	0.0916	N	0.16478	0.41	0.41303	D	0.987053	B	0.06786	0.001	B	0.06405	0.002	T	0.14392	-1.0474	9	.	.	.	-10.6591	13.7257	0.62756	1.0:0.0:0.0:0.0	.	932	Q8WUJ3	K1199_HUMAN	V	932	ENSP00000220244:I932V;ENSP00000378177:I932V;ENSP00000348583:I932V	.	I	+	1	0	KIAA1199	79012641	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	6.292000	0.72725	1.832000	0.53329	0.460000	0.39030	ATT	.	.		0.542	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		Missense_Mutation	G	81225586	A	G	81225586	5	3	183	1	0	0	0	0	0	0	1	0	8222	347	12	2	2876	2	KIAA1199	15	81225586	Splice_Site	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	10100899	81225586	21305806	73	27307										
CASKIN1	57524	hgsc.bcm.edu	37	chr16	2231253	2231253	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	atctcccagcagctcctgcgAgctgctcatgtgccgtgccc	10	17	2	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr16:2231253A>G	ENST00000343516.6	-	18	2208	c.2116T>C	c.(2116-2118)Tcg>Ccg	p.S706P	CASKIN1_ENST00000564289.1_5'Flank	NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	706					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|liver(1)|lung(7)|ovary(4)|prostate(5)|skin(3)	28						AGCTCCTGCGAGCTGCTCATG	0.726																																					p.S706P		Atlas-SNP	.											.	CASKIN1	130	.	0			c.T2116C						.						10	12	11					16																	2231253		1863	4071	5934	SO:0001583	missense	57524	exon18			CCTGCGAGCTGCT	AF451977	CCDS42103.1	16p13.3	2013-01-10				ENSG00000167971		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20879	protein-coding gene	gene with protein product		612184				12040031	Standard	NM_020764		Approved	KIAA1306, ANKS5A	uc010bsg.1	Q8WXD9		ENST00000343516.6:c.2116T>C	chr16.hg19:g.2231253A>G	ENSP00000345436:p.Ser706Pro	65.0	0.0		64.0	10.0	NM_020764	Q9P2P0	Missense_Mutation	SNP	ENST00000343516.6	hg19	CCDS42103.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.171977	0.38315	.	.	ENSG00000167971	ENST00000343516;ENST00000382453	T	0.74842	-0.88	4.36	4.36	0.52297	.	.	.	.	.	T	0.80138	0.4568	L	0.54323	1.7	0.36837	D	0.887177	D	0.71674	0.998	P	0.60682	0.878	D	0.83886	0.0282	9	0.52906	T	0.07	-17.1702	12.504	0.55972	1.0:0.0:0.0:0.0	.	706	Q8WXD9	CSKI1_HUMAN	P	706;535	ENSP00000345436:S706P	ENSP00000345436:S706P	S	-	1	0	CASKIN1	2171254	1.000000	0.71417	0.996000	0.52242	0.954000	0.61252	3.136000	0.50554	1.828000	0.53243	0.454000	0.30748	TCG	.	.		0.726	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764		G	2231253	A	G	2231253	3	3	183	1	0	0	0	0	1	0	0	0	2668	304	11	2	2191	2	CASKIN1	16	2231253	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10		2231253	88123500	74	27308										
ABCA3	21	hgsc.bcm.edu	37	chr16	2339511	2339511	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	cggaggggtccatggccccaCagaggttgctgtccacagcc	14	14	0	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr16:2339511C>A	ENST00000301732.5	-	20	3324	c.2624G>T	c.(2623-2625)tGt>tTt	p.C875F	ABCA3_ENST00000382381.3_Missense_Mutation_p.C817F	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	875					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	CATGGCCCCACAGAGGTTGCT	0.662																																					p.C875F		Atlas-SNP	.											.	ABCA3	176	.	0			c.G2624T						.						32	29	30					16																	2339511		2194	4293	6487	SO:0001583	missense	21	exon20			GCCCCACAGAGGT	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.2624G>T	chr16.hg19:g.2339511C>A	ENSP00000301732:p.Cys875Phe	62.0	0.0		56.0	28.0	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	hg19	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	C	1.499	-0.552440	0.03996	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.93076	-3.16	4.68	3.72	0.42706	.	0.097592	0.64402	D	0.000002	D	0.85792	0.5779	N	0.19112	0.55	0.80722	D	1	B;B;B	0.27732	0.0;0.003;0.187	B;B;B	0.26693	0.0;0.001;0.072	T	0.80353	-0.1418	10	0.10111	T	0.7	.	13.7678	0.63006	0.0:0.8453:0.1547:0.0	.	875;879;875	A7MBM9;Q4LE27;Q99758	.;.;ABCA3_HUMAN	F	875;879	ENSP00000301732:C875F	ENSP00000301732:C875F	C	-	2	0	ABCA3	2279512	1.000000	0.71417	0.280000	0.24747	0.137000	0.21094	5.333000	0.65917	1.180000	0.42898	0.561000	0.74099	TGT	.	.		0.662	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2339511	C	A	2339511	3	1	183	1	0	0	0	0	1	0	0	0	33	478	17	3	2546	3	ABCA3	16	2339511	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	108258	2339511	88015242	75	27309										
SLC5A11	115584	hgsc.bcm.edu	37	chr16	24922649	24922650	+	Splice_Site	DEL	GT	GT	-													0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctttgctgggttctttctagGtgacatgaccccaaagcagt							TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr16:24922649_24922650delGT	ENST00000347898.3	+	16	2445_2446	c.1823_1824delGT	c.(1822-1824)tgt>t	p.C608fs	SLC5A11_ENST00000539472.1_Splice_Site_p.C544fs|SLC5A11_ENST00000565769.1_Splice_Site_p.C544fs|SLC5A11_ENST00000449109.2_Splice_Site_p.C452fs|SLC5A11_ENST00000569071.1_Splice_Site_p.C452fs|SLC5A11_ENST00000567758.1_Splice_Site_p.C573fs|SLC5A11_ENST00000545376.1_Splice_Site_p.C538fs|SLC5A11_ENST00000424767.2_Splice_Site_p.C573fs|SLC5A11_ENST00000568579.1_Splice_Site_p.C538fs	NM_052944.3	NP_443176.2			solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		TTCTTTCTAGGTGACATGACCC	0.54																																					p.608_608del		Atlas-INDEL	.											.	SLC5A11	97	.	0			c.1823_1823del						.																																			SO:0001630	splice_region_variant	115584	exon16			.	AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"Solute carriers"	23091	protein-coding gene	gene with protein product		610238	"solute carrier family 5 (sodium/glucose cotransporter), member 11"			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000347898.3:c.1823-1GT>-	chr16.hg19:g.24922649_24922650delGT		92.0	0.0		88.0	43.0	NM_052944		Frame_Shift_Del	DEL	ENST00000347898.3	hg19	CCDS10625.1																																																																																			.	.		0.54	SLC5A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214091.3	NM_052944	Frame_Shift_Del	-	24922650	GT	-	24922649	8	5	183	1	0	1	0	1	0	0	1	0	14678	1275	44	0	1881	0	SLC5A11	16	24922649	Splice_Site	DEL	GT	TCGA-DD-AAD8-01A-11D-A40R-10	22583138	24922649	65432104	76	27310										
ABCC11	85320	hgsc.bcm.edu	37	chr16	48239436	48239436	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctgcacccccaccgagccctCgagcaagtgcatctgcggca	10	18	1	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr16:48239436C>G	ENST00000394747.1	-	12	2042	c.1693G>C	c.(1693-1695)Gag>Cag	p.E565Q	ABCC11_ENST00000394748.1_Missense_Mutation_p.E565Q|ABCC11_ENST00000356608.2_Missense_Mutation_p.E565Q|ABCC11_ENST00000353782.5_Missense_Mutation_p.E565Q|ABCC11_ENST00000537808.1_Missense_Mutation_p.E565Q	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	565	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	ACCGAGCCCTCGAGCAAGTGC	0.642																																					p.E565Q		Atlas-SNP	.											.	ABCC11	177	.	0			c.G1693C						.						88	77	81					16																	48239436		2201	4300	6501	SO:0001583	missense	85320	exon12			AGCCCTCGAGCAA	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.1693G>C	chr16.hg19:g.48239436C>G	ENSP00000378230:p.Glu565Gln	58.0	0.0		76.0	31.0	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	hg19	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.688199	0.29962	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	D;D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45;-3.45	5.6	-1.05	0.10036	ABC transporter, transmembrane domain, type 1 (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.625745	0.16821	N	0.198149	D	0.83732	0.5318	N	0.13043	0.29	0.09310	N	1	B;B	0.18310	0.013;0.027	B;B	0.20384	0.002;0.029	T	0.71484	-0.4579	10	0.30078	T	0.28	-8.7067	1.8037	0.03076	0.1365:0.3873:0.2643:0.2119	.	565;565	Q96J66-2;Q96J66	.;ABCCB_HUMAN	Q	565	ENSP00000311326:E565Q;ENSP00000349017:E565Q;ENSP00000378231:E565Q;ENSP00000378230:E565Q;ENSP00000438530:E565Q	ENSP00000311326:E565Q	E	-	1	0	ABCC11	46796937	0.000000	0.05858	0.011000	0.14972	0.026000	0.11368	0.046000	0.14035	0.123000	0.18342	0.563000	0.77884	GAG	.	.		0.642	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		G	48239436	C	G	48239436	3	3	183	1	0	0	0	0	1	0	0	0	51	893	31	4	2527	4	ABCC11	16	48239436	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	23316787	48239436	42115317	77	27311										
ZNF423	23090	hgsc.bcm.edu	37	chr16	49559304	49559304	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	cacggggcatttgaaggtgcCgcccatgccctcgaagctgt	13	13	0	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr16:49559304C>T	ENST00000561648.1	-	6	3732	c.3679G>A	c.(3679-3681)Ggc>Agc	p.G1227S	ZNF423_ENST00000262383.2_Missense_Mutation_p.G1227S|ZNF423_ENST00000562871.1_Missense_Mutation_p.G1167S|ZNF423_ENST00000563137.2_Missense_Mutation_p.G1167S|ZNF423_ENST00000562520.1_Missense_Mutation_p.G1167S|ZNF423_ENST00000535559.1_Missense_Mutation_p.G1110S|ZNF423_ENST00000567169.1_Missense_Mutation_p.G1110S	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	1227					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				TTGAAGGTGCCGCCCATGCCC	0.577																																					p.G1227S		Atlas-SNP	.											ZNF423_ENST00000262383,NS,carcinoma,0,2	ZNF423	463	.	0			c.G3679A						.						108	87	94					16																	49559304		2199	4300	6499	SO:0001583	missense	23090	exon6			AGGTGCCGCCCAT	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.3679G>A	chr16.hg19:g.49559304C>T	ENSP00000455426:p.Gly1227Ser	144.0	0.0		104.0	27.0	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.325683	0.81580	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.08896	3.04;3.1	5.38	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.13157	0.0319	N	0.10837	0.055	0.45946	D	0.998779	D	0.89917	1.0	D	0.91635	0.999	T	0.37663	-0.9696	9	.	.	.	-28.7483	15.5465	0.76104	0.139:0.861:0.0:0.0	.	1227	Q2M1K9	ZN423_HUMAN	S	1227;1110	ENSP00000262383:G1227S;ENSP00000442321:G1110S	.	G	-	1	0	ZNF423	48116805	1.000000	0.71417	0.928000	0.36995	0.987000	0.75469	5.766000	0.68843	1.248000	0.43934	0.462000	0.41574	GGC	.	.		0.577	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49559304	C	T	49559304	3	4	183	1	0	0	0	0	1	0	0	0	17913	652	23	1	187	1	ZNF423	16	49559304	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	1319868	49559304	40795449	78	27312										
RBL2	5934	hgsc.bcm.edu	37	chr16	53488597	53488597	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	caataaggcctatgaggagtAtgttttatctgttgggaatt	11	4	1	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr16:53488597A>T	ENST00000262133.6	+	8	1159	c.1022A>T	c.(1021-1023)tAt>tTt	p.Y341F	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Missense_Mutation_p.Y125F	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	341					chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TATGAGGAGTATGTTTTATCT	0.383																																					p.Y341F		Atlas-SNP	.											.	RBL2	115	.	0			c.A1022T						.						132	130	130					16																	53488597		2198	4300	6498	SO:0001583	missense	5934	exon8			AGGAGTATGTTTT	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.1022A>T	chr16.hg19:g.53488597A>T	ENSP00000262133:p.Tyr341Phe	119.0	0.0		117.0	52.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	hg19	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	A	16.49	3.137519	0.56936	.	.	ENSG00000103479	ENST00000262133;ENST00000544405;ENST00000379935;ENST00000544545	D;D;D	0.91068	-2.78;-2.32;-1.98	5.5	5.5	0.81552	.	0.117769	0.64402	D	0.000018	D	0.89853	0.6835	L	0.58583	1.82	0.39473	D	0.967755	B;P;P;D	0.53151	0.0;0.564;0.723;0.958	B;B;B;P	0.45276	0.002;0.168;0.321;0.475	D	0.90315	0.4340	10	0.41790	T	0.15	-9.5506	15.6062	0.76672	1.0:0.0:0.0:0.0	.	125;341;51;341	B7Z913;Q8NE70;E9PG04;Q08999	.;.;.;RBL2_HUMAN	F	341;267;51;125	ENSP00000262133:Y341F;ENSP00000443744:Y267F;ENSP00000444685:Y125F	ENSP00000262133:Y341F	Y	+	2	0	RBL2	52046098	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.144000	0.77357	2.090000	0.63153	0.454000	0.30748	TAT	.	.		0.383	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		T	53488597	A	T	53488597	3	4	183	1	0	0	0	0	1	0	0	0	13125	449	16	4	1052	4	RBL2	16	53488597	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	3929293	53488597	36866156	79	27313										
PLCG2	5336	hgsc.bcm.edu	37	chr16	81891876	81891876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tctccactccagctgactctAaagaggatgcagttaactgg	9	11	2	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr16:81891876A>G	ENST00000359376.3	+	4	560	c.346A>G	c.(346-348)Aaa>Gaa	p.K116E	PLCG2_ENST00000565400.1_3'UTR	NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	116	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						AGCTGACTCTAAAGAGGATGC	0.493																																					p.K116E		Atlas-SNP	.											.	PLCG2	276	.	0			c.A346G						.						147	148	148					16																	81891876		2034	4191	6225	SO:0001583	missense	5336	exon4			GACTCTAAAGAGG		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.346A>G	chr16.hg19:g.81891876A>G	ENSP00000352336:p.Lys116Glu	93.0	0.0		118.0	58.0	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	hg19	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	A	2.819	-0.245300	0.05906	.	.	ENSG00000197943	ENST00000359376	T	0.61510	0.1	5.57	5.57	0.84162	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.345864	0.30676	N	0.009103	T	0.27798	0.0684	N	0.03948	-0.315	0.09310	N	1	B	0.12630	0.006	B	0.14023	0.01	T	0.22487	-1.0215	10	0.02654	T	1	.	9.2745	0.37692	0.9188:0.0:0.0812:0.0	.	116	P16885	PLCG2_HUMAN	E	116	ENSP00000352336:K116E	ENSP00000352336:K116E	K	+	1	0	PLCG2	80449377	0.948000	0.32251	0.030000	0.17652	0.752000	0.42762	4.720000	0.61944	2.126000	0.65437	0.482000	0.46254	AAA	.	.		0.493	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			G	81891876	A	G	81891876	3	3	183	1	0	0	0	0	1	0	0	0	12045	363	13	2	356	2	PLCG2	16	81891876	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	28403279	81891876	8462877	80	27314										
NLGN2	57555	hgsc.bcm.edu	37	chr17	7318992	7318992	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tctgcagagagcgaggacggTgtgtctgccagcgcctttga	15	10	2	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:7318992T>G	ENST00000302926.2	+	6	1273	c.1200T>G	c.(1198-1200)ggT>ggG	p.G400G	NLGN2_ENST00000575301.1_Silent_p.G400G	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	400					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				GCGAGGACGGTGTGTCTGCCA	0.547																																					p.G400G		Atlas-SNP	.											.	NLGN2	61	.	0			c.T1200G						.						208	170	183					17																	7318992		2203	4300	6503	SO:0001819	synonymous_variant	57555	exon6			GGACGGTGTGTCT	AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.1200T>G	chr17.hg19:g.7318992T>G		101.0	0.0		79.0	65.0	NM_020795	Q9P2I1	Silent	SNP	ENST00000302926.2	hg19	CCDS11103.1																																																																																			.	.		0.547	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795		G	7318992	T	G	7318992	2	3	183	1	0	0	0	0	0	0	0	1	10471	1683	59	5		5	NLGN2	17	7318992	Silent	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10		7318992	73876218	81	27315										
TP53	7157	hgsc.bcm.edu	37	chr17	7577610	7577610	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tggtacagtcagagccaaccTaggagataacacaggcccaa	10	11	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:7577610T>A	ENST00000269305.4	-	7	862		c.e7-2		TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000574684.1_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(43)|p.0?(8)|p.V225fs*24(1)|p.E224_V225insXX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGAGCCAACCTAGGAGATAAC	0.522		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,63	TP53	33396	.	53	Unknown(43)|Whole gene deletion(8)|Insertion - In frame(1)|Insertion - Frameshift(1)	lung(16)|liver(7)|upper_aerodigestive_tract(5)|biliary_tract(5)|ovary(5)|breast(4)|bone(4)|central_nervous_system(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|urinary_tract(1)|oesophagus(1)	c.673-2A>T						.						88	74	79					17																	7577610		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CCAACCTAGGAGA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.673-2A>T	chr17.hg19:g.7577610T>A		57.0	0.0		48.0	44.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.583355	0.65992	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	.	.	.	3.35	3.35	0.38373	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.3302	0.43818	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7518335	1.000000	0.71417	0.324000	0.25361	0.557000	0.35523	7.634000	0.83273	1.750000	0.51863	0.379000	0.24179	.	.	.		0.522	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	A	7577610	T	A	7577610	5	1	183	1	0	0	0	0	0	0	1	0	16396	1536	53	4	619	4	TP53	17	7577610	Splice_Site	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	258618	7577610	73617600	82	27316										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11757663	11757663	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ggtgttctgtgatgtggaacCcaagcgccaggcactgaaca	13	10	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:11757663C>A	ENST00000262442.4	+	50	9919	c.9851C>A	c.(9850-9852)cCc>cAc	p.P3284H	DNAH9_ENST00000454412.2_Missense_Mutation_p.P3284H	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3284	Stalk. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GATGTGGAACCCAAGCGCCAG	0.552																																					p.P3284H		Atlas-SNP	.											.	DNAH9	695	.	0			c.C9851A						.						81	83	82					17																	11757663		2203	4300	6503	SO:0001583	missense	1770	exon50			TGGAACCCAAGCG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.9851C>A	chr17.hg19:g.11757663C>A	ENSP00000262442:p.Pro3284His	199.0	0.0		93.0	77.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.242406	0.58995	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	D;D	0.82255	-1.59;-1.59	5.44	4.47	0.54385	Dynein heavy chain, coiled coil stalk (1);	0.324267	0.33691	N	0.004659	D	0.95149	0.8428	H	0.99273	4.495	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97610	1.0129	10	0.87932	D	0	.	16.3754	0.83383	0.0:0.8681:0.1319:0.0	.	3284	Q9NYC9	DYH9_HUMAN	H	3284;3284;1866	ENSP00000262442:P3284H;ENSP00000414874:P3284H	ENSP00000262442:P3284H	P	+	2	0	DNAH9	11698388	1.000000	0.71417	1.000000	0.80357	0.549000	0.35272	4.470000	0.60175	1.510000	0.48803	-0.176000	0.13171	CCC	.	.		0.552	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11757663	C	A	11757663	3	1	183	1	0	0	0	0	1	0	0	0	4610	623	22	3	10049	3	DNAH9	17	11757663	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	4180053	11757663	69437547	83	27317										
SLC46A1	113235	hgsc.bcm.edu	37	chr17	26732441	26732441	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gagccccaccaggaagccgcCcacgttcatgtagagggtcc	12	15	1	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:26732441C>T	ENST00000440501.1	-	2	369	c.274G>A	c.(274-276)Ggc>Agc	p.G92S	CTD-2350C19.2_ENST00000580714.1_RNA|SLC46A1_ENST00000584729.1_5'UTR|SLC46A1_ENST00000321666.5_Missense_Mutation_p.G92S|CTD-2350C19.1_ENST00000583956.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	92					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	AGGAAGCCGCCCACGTTCATG	0.647																																					p.G92S		Atlas-SNP	.											.	SLC46A1	17	.	0			c.G274A						.						12	14	13					17																	26732441		1976	4161	6137	SO:0001583	missense	113235	exon2			AGCCGCCCACGTT	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"Solute carriers"	30521	protein-coding gene	gene with protein product	"heme carrier protein 1", "proton-coupled folate transporter"	611672	"solute carrier family 46, member 1"			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.274G>A	chr17.hg19:g.26732441C>T	ENSP00000395653:p.Gly92Ser	115.0	0.0		124.0	60.0	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Missense_Mutation	SNP	ENST00000440501.1	hg19		.	.	.	.	.	.	.	.	.	.	c	15.09	2.729042	0.48833	.	.	ENSG00000076351	ENST00000440501;ENST00000321666	T;T	0.58060	0.36;0.36	5.38	2.99	0.34606	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.185960	0.56097	D	0.000023	T	0.32315	0.0825	.	.	.	0.49915	D	0.999838	B;B;B	0.25809	0.008;0.019;0.135	B;B;B	0.31495	0.014;0.051;0.131	T	0.05289	-1.0894	9	0.10377	T	0.69	-8.7901	7.4857	0.27432	0.2796:0.6164:0.0:0.104	.	92;92;92	B4DJ17;Q96NT5-2;Q96NT5	.;.;PCFT_HUMAN	S	92	ENSP00000395653:G92S;ENSP00000318828:G92S	ENSP00000318828:G92S	G	-	1	0	SLC46A1	23756568	0.097000	0.21791	0.997000	0.53966	0.995000	0.86356	1.439000	0.35013	1.394000	0.46624	0.556000	0.70494	GGC	.	.		0.647	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		T	26732441	C	T	26732441	3	4	183	1	0	0	0	0	1	0	0	0	14659	623	22	3	1122	3	SLC46A1	17	26732441	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	14974778	26732441	54462769	84	27318										
NF1	4763	hgsc.bcm.edu	37	chr17	29560090	29560090	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctgacaaaaatccttcaacaAggcacagaatttgacacact	5	11	1	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:29560090A>T	ENST00000358273.4	+	27	3950	c.3567A>T	c.(3565-3567)caA>caT	p.Q1189H	NF1_ENST00000356175.3_Missense_Mutation_p.Q1189H	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1189			Q -> R (in NF1). {ECO:0000269|PubMed:23758643}.		actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TCCTTCAACAAGGCACAGAAT	0.418			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.Q1189H		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.A3567T						.						124	107	113					17																	29560090		2203	4300	6503	SO:0001583	missense	4763	exon27	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	TCAACAAGGCACA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.3567A>T	chr17.hg19:g.29560090A>T	ENSP00000351015:p.Gln1189His	134.0	0.0		148.0	68.0	NM_000267	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880710	0.72294	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.64803	-0.12;2.95;2.63	5.73	4.66	0.58398	Armadillo-type fold (1);Ras GTPase-activating protein (1);	0.000000	0.85682	D	0.000000	T	0.78381	0.4274	M	0.87180	2.865	0.80722	D	1	D;D;D;P	0.89917	1.0;1.0;0.988;0.629	D;D;D;P	0.91635	0.999;0.987;0.984;0.54	T	0.80703	-0.1264	10	0.87932	D	0	.	6.9699	0.24642	0.8329:0.0:0.1671:0.0	.	1189;239;1189;1189	E1P657;Q59FX3;P21359-2;P21359	.;.;.;NF1_HUMAN	H	1189;1189;855	ENSP00000351015:Q1189H;ENSP00000348498:Q1189H;ENSP00000389907:Q855H	ENSP00000348498:Q1189H	Q	+	3	2	NF1	26584216	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.478000	0.45189	2.185000	0.69588	0.454000	0.30748	CAA	.	.		0.418	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		T	29560090	A	T	29560090	3	4	183	1	0	0	0	0	1	0	0	0	10365	69	3	4	3734	4	NF1	17	29560090	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	2827649	29560090	51635120	85	27319										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33504057	33504057	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ccctgattcccctggctttgGagggcacagatgtgggcaag	14	11	0	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:33504057G>A	ENST00000268876.5	+	16	2150	c.2053G>A	c.(2053-2055)Gag>Aag	p.E685K	UNC45B_ENST00000433649.1_Missense_Mutation_p.E683K|UNC45B_ENST00000591048.1_Missense_Mutation_p.E604K|UNC45B_ENST00000378449.1_Missense_Mutation_p.E604K|UNC45B_ENST00000394570.2_Missense_Mutation_p.E683K	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	685					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				CCTGGCTTTGGAGGGCACAGA	0.577																																					p.E685K		Atlas-SNP	.											.	UNC45B	133	.	0			c.G2053A						.						137	110	119					17																	33504057		2203	4300	6503	SO:0001583	missense	146862	exon16			GCTTTGGAGGGCA	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.2053G>A	chr17.hg19:g.33504057G>A	ENSP00000268876:p.Glu685Lys	75.0	0.0		76.0	20.0	NM_173167	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	hg19	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	G	35	5.463154	0.96257	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T	0.51817	0.69;3.17;0.69	5.08	5.08	0.68730	Armadillo-like helical (1);Armadillo-type fold (1);	0.113820	0.64402	D	0.000009	T	0.65698	0.2716	L	0.59436	1.845	0.80722	D	1	D;P;D	0.67145	0.996;0.853;0.97	D;P;P	0.76071	0.987;0.628;0.662	T	0.63532	-0.6616	10	0.45353	T	0.12	-47.432	18.0106	0.89222	0.0:0.0:1.0:0.0	.	604;683;685	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	K	685;685;683;604	ENSP00000268876:E685K;ENSP00000412840:E683K;ENSP00000367710:E604K	ENSP00000268876:E685K	E	+	1	0	UNC45B	30528170	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.612000	0.98347	2.814000	0.96858	0.563000	0.77884	GAG	.	.		0.577	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		A	33504057	G	A	33504057	3	1	183	1	0	0	0	0	1	0	0	0	17004	1175	41	3	2111	3	UNC45B	17	33504057	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	3943967	33504057	47691153	86	27320										
SLFN13	146857	hgsc.bcm.edu	37	chr17	33768135	33768135	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	aactactctggtgagctcttCtcttggatactgtgctgaga	10	9	3	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:33768135C>T	ENST00000285013.6	-	6	2448	c.2173G>A	c.(2173-2175)Gaa>Aaa	p.E725K	SLFN13_ENST00000542635.1_Missense_Mutation_p.E725K|SLFN13_ENST00000526861.1_Missense_Mutation_p.E725K|SLFN13_ENST00000534689.1_Missense_Mutation_p.E407K|SLFN13_ENST00000360502.2_Missense_Mutation_p.E407K|SLFN13_ENST00000533791.1_Missense_Mutation_p.E725K	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	725						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GTGAGCTCTTCTCTTGGATAC	0.443																																					p.E725K		Atlas-SNP	.											.	SLFN13	79	.	0			c.G2173A						.						140	149	146					17																	33768135		2203	4300	6503	SO:0001583	missense	146857	exon6			GCTCTTCTCTTGG	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.2173G>A	chr17.hg19:g.33768135C>T	ENSP00000285013:p.Glu725Lys	58.0	0.0		77.0	34.0	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	hg19	CCDS32620.1	.	.	.	.	.	.	.	.	.	.	c	12.73	2.026272	0.35701	.	.	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	3.27	2.28	0.28536	.	0.129452	0.35096	N	0.003456	T	0.80454	0.4626	L	0.48642	1.525	0.20563	N	0.999882	D;D	0.71674	0.998;0.997	D;D	0.77004	0.957;0.989	T	0.67768	-0.5585	10	0.10902	T	0.67	.	5.6584	0.17654	0.0:0.8466:0.0:0.1534	.	407;725	Q68D06-2;Q68D06	.;SLN13_HUMAN	K	725;407;725;725;407	ENSP00000285013:E725K;ENSP00000353692:E407K;ENSP00000434439:E725K;ENSP00000444016:E725K;ENSP00000435442:E407K	ENSP00000285013:E725K	E	-	1	0	SLFN13	30792248	0.010000	0.17322	0.054000	0.19295	0.019000	0.09904	0.671000	0.25172	1.811000	0.52892	0.407000	0.27541	GAA	.	.		0.443	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		T	33768135	C	T	33768135	3	4	183	1	0	0	0	0	1	0	0	0	14751	922	32	3	524	3	SLFN13	17	33768135	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	264078	33768135	47427075	87	27321										
CNTNAP1	8506	hgsc.bcm.edu	37	chr17	40835882	40835882	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ggtcccctgtatgcacgctcCctgggcgcctcctcctacta	9	18	0	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:40835882C>A	ENST00000264638.4	+	2	328	c.111C>A	c.(109-111)tcC>tcA	p.S37S	CTD-3193K9.4_ENST00000593139.1_RNA|CCR10_ENST00000591765.1_5'Flank|CCR10_ENST00000332438.4_5'Flank|CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	37	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				axon cargo transport (GO:0008088)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|neuron projection morphogenesis (GO:0048812)|neuronal action potential propagation (GO:0019227)|paranodal junction assembly (GO:0030913)|positive regulation of signal transduction (GO:0009967)|protein localization to paranode region of axon (GO:0002175)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|voltage-gated potassium channel complex (GO:0008076)	receptor activity (GO:0004872)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		ATGCACGCTCCCTGGGCGCCT	0.642																																					p.S37S		Atlas-SNP	.											.	CNTNAP1	116	.	0			c.C111A						.						42	39	40					17																	40835882		2203	4300	6503	SO:0001819	synonymous_variant	8506	exon2			ACGCTCCCTGGGC	U87223	CCDS11436.1	17q21	2008-07-18				ENSG00000108797			8011	protein-coding gene	gene with protein product	"neurexin 4"	602346		NRXN4		9118959	Standard	NM_003632		Approved	p190, Caspr, CNTNAP	uc002iay.3	P78357		ENST00000264638.4:c.111C>A	chr17.hg19:g.40835882C>A		51.0	0.0		62.0	28.0	NM_003632		Silent	SNP	ENST00000264638.4	hg19	CCDS11436.1																																																																																			.	.		0.642	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632		A	40835882	C	A	40835882	2	1	183	1	0	0	0	0	0	0	0	1	3648	610	22	3		3	CNTNAP1	17	40835882	Silent	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	7067747	40835882	40359328	88	27322										
ACBD4	79777	hgsc.bcm.edu	37	chr17	43214134	43214134	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	atcactgaaatgaaactggtGgcacagaaggtaagggctgc	13	7	1	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:43214134G>A	ENST00000376955.4	+	4	582	c.285G>A	c.(283-285)gtG>gtA	p.V95V	ACBD4_ENST00000586346.1_Silent_p.V95V|ACBD4_ENST00000431281.1_Silent_p.V95V|ACBD4_ENST00000591136.1_3'UTR|ACBD4_ENST00000592162.1_Silent_p.V95V|ACBD4_ENST00000321854.8_Silent_p.V95V|ACBD4_ENST00000591859.1_Silent_p.V95V|ACBD4_ENST00000398322.3_Silent_p.V95V	NM_001135707.1	NP_001129179.1	Q8NC06	ACBD4_HUMAN	acyl-CoA binding domain containing 4	95	ACB. {ECO:0000255|PROSITE- ProRule:PRU00573}.						fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)			kidney(1)|lung(3)|ovary(1)	5						TGAAACTGGTGGCACAGAAGG	0.597																																					p.V95V		Atlas-SNP	.											.	ACBD4	51	.	0			c.G285A						.						86	98	94					17																	43214134		2076	4198	6274	SO:0001819	synonymous_variant	79777	exon4			ACTGGTGGCACAG	BC029164	CCDS42348.1, CCDS45710.1, CCDS45711.1	17q21.31	2012-10-02	2010-04-30		ENSG00000181513	ENSG00000181513			23337	protein-coding gene	gene with protein product			"acyl-Coenzyme A binding domain containing 4"				Standard	NM_001135704		Approved	FLJ13322	uc002iie.3	Q8NC06	OTTHUMG00000180111	ENST00000376955.4:c.285G>A	chr17.hg19:g.43214134G>A		66.0	0.0		56.0	23.0	NM_001135707	D3DX64|Q8IUT1|Q9H8Q4	Silent	SNP	ENST00000376955.4	hg19	CCDS45711.1																																																																																			.	.		0.597	ACBD4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000449816.1	NM_024722		A	43214134	G	A	43214134	2	1	183	1	0	0	0	0	0	0	0	1	124	1335	47	3		3	ACBD4	17	43214134	Silent	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	2378252	43214134	37981076	89	27323										
NGFR	4804	hgsc.bcm.edu	37	chr17	47590366	47590367	+	Frame_Shift_Del	DEL	GT	GT	-													0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	agtccactgccacatccccgGtgtgagcccaaccggggagc							TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:47590366_47590367delGT	ENST00000172229.3	+	6	1404_1405	c.1279_1280delGT	c.(1279-1281)gtgfs	p.V427fs	RP5-1029K10.2_ENST00000514506.1_RNA|NGFR_ENST00000504201.1_Frame_Shift_Del_p.V333fs	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	427					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					CACATCCCCGGTGTGAGCCCAA	0.718																																					p.426_427del		Atlas-INDEL	.											.	NGFR	46	.	0			c.1278_1279del						.																																			SO:0001589	frameshift_variant	4804	exon6			.	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"Tumor necrosis factor receptor superfamily", "CD molecules"	7809	protein-coding gene	gene with protein product	"low affinity nerve growth factor receptor", "TNFR superfamily, member 16"	162010	"nerve growth factor receptor (TNFR superfamily, member 16)"			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.1279_1280delGT	chr17.hg19:g.47590368_47590369delGT	ENSP00000172229:p.Val427fs	49.0	0.0		61.0	22.0	NM_002507	B2R961|B4E096	Frame_Shift_Del	DEL	ENST00000172229.3	hg19	CCDS11549.1																																																																																			.	.		0.718	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1			-	47590367	GT	-	47590366	7	5	183	1	0	1	0	1	0	0	0	0	10405	1261	44	0	1301	0	NGFR	17	47590366	Frame_Shift_Del	DEL	GT	TCGA-DD-AAD8-01A-11D-A40R-10	4376232	47590366	33604844	90	27324										
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56383220	56383220	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	agggctgggcagggccttccGactcagctgtggaaagaatg	16	9	1	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:56383220G>T	ENST00000343736.4	-	27	5394	c.5231C>A	c.(5230-5232)tCg>tAg	p.S1744*	BZRAP1_ENST00000268893.6_Nonsense_Mutation_p.S1684*|BZRAP1_ENST00000355701.3_Nonsense_Mutation_p.S1744*			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1744						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGGGCCTTCCGACTCAGCTGT	0.667																																					p.S1744X		Atlas-SNP	.											.	BZRAP1	287	.	0			c.C5231A						.						46	45	45					17																	56383220		2203	4300	6503	SO:0001587	stop_gained	9256	exon27			CCTTCCGACTCAG	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.5231C>A	chr17.hg19:g.56383220G>T	ENSP00000345824:p.Ser1744*	45.0	0.0		54.0	15.0	NM_004758	O75111|Q8N5W3	Nonsense_Mutation	SNP	ENST00000343736.4	hg19	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	G	8.239	0.806310	0.16467	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	.	.	.	5.02	-5.59	0.02505	.	3.477390	0.00447	N	0.000096	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	.	2.5045	0.04641	0.4619:0.1199:0.2963:0.1219	.	.	.	.	X	1744;1744;1684	.	ENSP00000268893:S1684X	S	-	2	0	BZRAP1	53738219	0.000000	0.05858	0.000000	0.03702	0.107000	0.19398	-0.456000	0.06754	-1.368000	0.02149	0.561000	0.74099	TCG	.	.		0.667	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		T	56383220	G	T	56383220	4	4	183	1	0	0	0	0	0	1	0	0	1579	1059	37	1	362	1	BZRAP1	17	56383220	Nonsense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	8792854	56383220	24811990	91	27325										
BPTF	2186	hgsc.bcm.edu	37	chr17	65870972	65870972	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	aagagccaaaaagggagacaTtgataatgttaaaagcccag	10	6	0	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr17:65870972T>C	ENST00000321892.4	+	4	1761	c.1700T>C	c.(1699-1701)aTt>aCt	p.I567T	BPTF_ENST00000306378.6_Missense_Mutation_p.I567T|BPTF_ENST00000424123.3_Missense_Mutation_p.I428T|BPTF_ENST00000335221.5_Missense_Mutation_p.I567T			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	567					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAGGGAGACATTGATAATGTT	0.313																																					p.I567T		Atlas-SNP	.											.	BPTF	415	.	0			c.T1700C						.						74	78	76					17																	65870972		2203	4300	6503	SO:0001583	missense	2186	exon4			GAGACATTGATAA	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.1700T>C	chr17.hg19:g.65870972T>C	ENSP00000315454:p.Ile567Thr	374.0	1.0		487.0	235.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	T	4.630	0.117102	0.08881	.	.	ENSG00000171634	ENST00000544491;ENST00000306378;ENST00000335221;ENST00000321892;ENST00000544778	T;T;T	0.61980	0.06;0.08;0.08	4.79	2.5	0.30297	.	.	.	.	.	T	0.48926	0.1527	L	0.51422	1.61	0.26731	N	0.970594	B;B;P	0.37276	0.002;0.043;0.589	B;B;B	0.36608	0.004;0.011;0.229	T	0.34204	-0.9838	9	0.07482	T	0.82	-1.5246	7.5904	0.28017	0.0:0.173:0.0:0.827	.	567;567;567	Q12830;Q12830-2;Q12830-4	BPTF_HUMAN;.;.	T	472;567;567;567;428	ENSP00000307208:I567T;ENSP00000334351:I567T;ENSP00000315454:I567T	ENSP00000307208:I567T	I	+	2	0	BPTF	63301434	1.000000	0.71417	0.510000	0.27712	0.581000	0.36288	3.122000	0.50446	0.248000	0.21435	0.482000	0.46254	ATT	.	.		0.313	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		C	65870972	T	C	65870972	3	2	183	1	0	0	0	0	1	0	0	0	1497	1493	52	2	1714	2	BPTF	17	65870972	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	9487752	65870972	15324238	92	27326										
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56033235	56033235	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tttgtcttttgtgtaggctgAtatccccaataggtttgaaa	9	6	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr18:56033235A>T	ENST00000400345.3	+	21	2121	c.1838A>T	c.(1837-1839)gAt>gTt	p.D613V	NEDD4L_ENST00000356462.6_Missense_Mutation_p.D549V|NEDD4L_ENST00000456986.1_Missense_Mutation_p.D492V|NEDD4L_ENST00000357895.5_Missense_Mutation_p.D605V|NEDD4L_ENST00000431212.2_Missense_Mutation_p.D492V|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000435432.2_Missense_Mutation_p.D472V|NEDD4L_ENST00000256830.9_Missense_Mutation_p.D509V|NEDD4L_ENST00000256832.7_Missense_Mutation_p.D473V|NEDD4L_ENST00000382850.4_Missense_Mutation_p.D593V|NEDD4L_ENST00000456173.2_Missense_Mutation_p.D472V|NEDD4L_ENST00000586263.1_Missense_Mutation_p.D585V	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	613					cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						GTGTAGGCTGATATCCCCAAT	0.338																																					p.D613V		Atlas-SNP	.											.	NEDD4L	126	.	0			c.A1838T						.						75	68	70					18																	56033235		1821	4081	5902	SO:0001583	missense	23327	exon21			AGGCTGATATCCC	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1838A>T	chr18.hg19:g.56033235A>T	ENSP00000383199:p.Asp613Val	72.0	0.0		70.0	34.0	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	hg19	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.039288	0.75617	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	T;T;T;T;T;T;T;T;T;T	0.76186	1.08;1.08;1.08;1.08;-1.0;-1.0;1.08;-1.0;-1.0;-1.0	5.54	5.54	0.83059	HECT (1);	0.000000	0.85682	D	0.000000	T	0.81498	0.4835	L	0.39397	1.21	0.80722	D	1	D;P;D;D;D;P	0.69078	0.967;0.933;0.992;0.997;0.968;0.933	P;P;P;D;P;P	0.76575	0.819;0.795;0.708;0.988;0.787;0.684	D	0.83526	0.0088	10	0.87932	D	0	.	15.9755	0.80060	1.0:0.0:0.0:0.0	.	585;605;472;549;613;593	Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;.;NED4L_HUMAN;.	V	613;593;549;509;473;492;605;472;472;492	ENSP00000383199:D613V;ENSP00000372301:D593V;ENSP00000348847:D549V;ENSP00000256830:D509V;ENSP00000256832:D473V;ENSP00000411947:D492V;ENSP00000350569:D605V;ENSP00000393395:D472V;ENSP00000405440:D472V;ENSP00000389406:D492V	ENSP00000256830:D509V	D	+	2	0	NEDD4L	54184215	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	9.287000	0.95975	2.219000	0.72066	0.528000	0.53228	GAT	.	.		0.338	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			T	56033235	A	T	56033235	3	4	183	1	0	0	0	0	1	0	0	0	10320	333	12	4	1948	4	NEDD4L	18	56033235	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10		56033235	22044013	93	27327										
POLRMT	5442	hgsc.bcm.edu	37	chr19	621737	621737	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	cagagtgcggcgatgtccagGgcagcggggggcaaagcatg	19	9	0	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr19:621737G>A	ENST00000588649.2	-	10	2045	c.1961C>T	c.(1960-1962)cCc>cTc	p.P654L	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	654					gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGATGTCCAGGGCAGCGGGGG	0.672																																					p.P654L		Atlas-SNP	.											.	POLRMT	91	.	0			c.C1961T						.						23	26	25					19																	621737		2200	4300	6500	SO:0001583	missense	5442	exon10			GTCCAGGGCAGCG		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.1961C>T	chr19.hg19:g.621737G>A	ENSP00000465759:p.Pro654Leu	37.0	0.0		53.0	20.0	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	hg19	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	17.85	3.490176	0.64074	.	.	ENSG00000099821	ENST00000215591	T	0.57273	0.41	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.74794	0.3763	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79761	-0.1667	10	0.87932	D	0	-37.2048	16.5929	0.84772	0.0:0.0:1.0:0.0	.	654	O00411	RPOM_HUMAN	L	654	ENSP00000215591:P654L	ENSP00000215591:P654L	P	-	2	0	POLRMT	572737	1.000000	0.71417	1.000000	0.80357	0.024000	0.10985	9.017000	0.93651	2.398000	0.81561	0.455000	0.32223	CCC	.	.		0.672	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		A	621737	G	A	621737	3	1	183	1	0	0	0	0	1	0	0	0	12247	1232	43	3	1779	3	POLRMT	19	621737	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10		621737	58507246	94	27328										
INSR	3643	hgsc.bcm.edu	37	chr19	7152760	7152760	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gggacgaaaaccacgttgtgCaggtaatcctcaaacgtctt	10	10	2	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr19:7152760C>T	ENST00000302850.5	-	10	2350	c.2208G>A	c.(2206-2208)ctG>ctA	p.L736L	INSR_ENST00000341500.5_Silent_p.L736L	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	736	Insulin-binding.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""Insulin(DB00071)|""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	CCACGTTGTGCAGGTAATCCT	0.547																																					p.L736L		Atlas-SNP	.											.	INSR	265	.	0			c.G2208A						.						195	173	181					19																	7152760		2203	4300	6503	SO:0001819	synonymous_variant	3643	exon10			GTTGTGCAGGTAA	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"CD molecules", "Fibronectin type III domain containing"	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.2208G>A	chr19.hg19:g.7152760C>T		61.0	0.0		53.0	21.0	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	hg19	CCDS12176.1																																																																																			.	.		0.547	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			T	7152760	C	T	7152760	2	4	183	1	0	0	0	0	0	0	0	1	7782	697	25	3		3	INSR	19	7152760	Silent	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	6531023	7152760	51976223	95	27329										
FCER2	2208	hgsc.bcm.edu	37	chr19	7762139	7762139	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	caccctgagatttcaatctcTgctgttcagctcgaagttcc	7	13	3	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr19:7762139T>A	ENST00000346664.5	-	6	511	c.299A>T	c.(298-300)cAg>cTg	p.Q100L	FCER2_ENST00000597921.1_Missense_Mutation_p.Q100L|FCER2_ENST00000360067.4_Missense_Mutation_p.Q99L	NM_001220500.1|NM_002002.4	NP_001207429.1|NP_001993.2	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor for (CD23)	100					Notch signaling pathway (GO:0007219)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	10						TTTCAATCTCTGCTGTTCAGC	0.562																																					p.Q100L		Atlas-SNP	.											.	FCER2	19	.	0			c.A299T						.						88	84	86					19																	7762139		2203	4300	6503	SO:0001583	missense	2208	exon6			AATCTCTGCTGTT	M15059	CCDS12184.1	19p13.3	2011-08-30	2006-03-09			ENSG00000104921		"C-type lectin domain containing", "CD molecules"	3612	protein-coding gene	gene with protein product		151445	"Fc fragment of IgE, low affinity II, receptor for (CD23A)"	CD23A, FCE2			Standard	NM_002002		Approved	CLEC4J, CD23	uc002mhm.2	P06734		ENST00000346664.5:c.299A>T	chr19.hg19:g.7762139T>A	ENSP00000264072:p.Gln100Leu	103.0	0.0		66.0	16.0	NM_002002		Missense_Mutation	SNP	ENST00000346664.5	hg19	CCDS12184.1	.	.	.	.	.	.	.	.	.	.	T	2.309	-0.358417	0.05138	.	.	ENSG00000104921	ENST00000346664;ENST00000360067	T;T	0.17691	2.26;2.26	4.56	2.27	0.28462	.	0.679188	0.12112	N	0.498394	T	0.07548	0.0190	N	0.08118	0	0.09310	N	1	B;B	0.20671	0.017;0.047	B;B	0.17098	0.016;0.017	T	0.36986	-0.9725	10	0.25751	T	0.34	.	5.051	0.14508	0.1816:0.0:0.1887:0.6298	.	99;100	P06734-2;P06734	.;FCER2_HUMAN	L	100;99	ENSP00000264072:Q100L;ENSP00000353178:Q99L	ENSP00000264072:Q100L	Q	-	2	0	FCER2	7668139	0.061000	0.20836	0.144000	0.22314	0.054000	0.15201	0.045000	0.14013	0.745000	0.32763	0.533000	0.62120	CAG	.	.		0.562	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002		A	7762139	T	A	7762139	3	1	183	1	0	0	0	0	1	0	0	0	5784	1580	55	4	690	4	FCER2	19	7762139	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	609379	7762139	51366844	96	27330										
DMKN	93099	hgsc.bcm.edu	37	chr19	36003550	36003550	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctccttgaccccagggagctCcctgaggattcattccaaag	9	14	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr19:36003550C>A	ENST00000339686.3	-	2	745	c.569G>T	c.(568-570)gGa>gTa	p.G190V	DMKN_ENST00000440396.1_Missense_Mutation_p.G190V|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.G190V|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.G190V|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000429837.1_Missense_Mutation_p.G190V|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000419602.1_Missense_Mutation_p.G190V|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.G190V|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.G190V	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	190	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CCAGGGAGCTCCCTGAGGATT	0.612																																					p.G190V		Atlas-SNP	.											.	DMKN	116	.	0			c.G569T						.						91	96	94					19																	36003550		2203	4300	6503	SO:0001583	missense	93099	exon2			GGAGCTCCCTGAG	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.569G>T	chr19.hg19:g.36003550C>A	ENSP00000342012:p.Gly190Val	81.0	0.0		101.0	37.0	NM_001190347	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	hg19	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	C	11.47	1.648211	0.29336	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000429837;ENST00000419602;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T;T;T	0.54866	1.25;1.09;1.04;0.55;0.62;0.66;0.67;0.73	4.91	3.88	0.44766	.	0.194407	0.25613	N	0.029471	T	0.66723	0.2818	M	0.68317	2.08	0.24535	N	0.994095	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999;0.999;0.999	D;D;D;D;D;D;D	0.81914	0.995;0.995;0.995;0.995;0.991;0.991;0.991	T	0.58047	-0.7705	10	0.87932	D	0	-8.4188	8.9618	0.35851	0.0:0.8999:0.0:0.1001	.	190;190;190;190;190;190;190	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;C9J4P6;Q6E0U4-4;Q6E0U4	.;.;.;.;.;.;DMKN_HUMAN	V	190	ENSP00000342012:G190V;ENSP00000405503:G190V;ENSP00000391036:G190V;ENSP00000394908:G190V;ENSP00000415277:G190V;ENSP00000414743:G190V;ENSP00000388404:G190V;ENSP00000409513:G190V	ENSP00000342012:G190V	G	-	2	0	DMKN	40695390	0.984000	0.35163	0.494000	0.27515	0.026000	0.11368	1.956000	0.40382	1.276000	0.44395	0.655000	0.94253	GGA	.	.		0.612	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		A	36003550	C	A	36003550	3	1	183	1	0	0	0	0	1	0	0	0	4584	855	30	3	1238	3	DMKN	19	36003550	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	28241411	36003550	23125433	97	27331										
SLC8A2	6543	hgsc.bcm.edu	37	chr19	47944676	47944676	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tcatattcctcgtcatcaacTatcttcacctgaagagtttt	4	11	5	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr19:47944676T>A	ENST00000236877.6	-	5	2180	c.1785A>T	c.(1783-1785)atA>atT	p.I595I	SLC8A2_ENST00000542837.1_Silent_p.I351I|SLC8A2_ENST00000539381.1_Silent_p.I58I|SLC8A2_ENST00000601757.1_5'UTR	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	595	Calx-beta 2.				blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		CGTCATCAACTATCTTCACCT	0.542																																					p.I595I		Atlas-SNP	.											.	SLC8A2	77	.	0			c.A1785T						.						63	64	64					19																	47944676		2203	4300	6503	SO:0001819	synonymous_variant	6543	exon5			ATCAACTATCTTC	AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"Solute carriers"	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.1785A>T	chr19.hg19:g.47944676T>A		41.0	0.0		62.0	29.0	NM_015063	B4DYQ9	Silent	SNP	ENST00000236877.6	hg19	CCDS33065.1																																																																																			.	.		0.542	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1			A	47944676	T	A	47944676	2	1	183	1	0	0	0	0	0	0	0	1	14722	1512	53	4		4	SLC8A2	19	47944676	Silent	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	11941126	47944676	11184307	98	27332										
TMEM143	55260	hgsc.bcm.edu	37	chr19	48848536	48848536	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ccgaagcacctcctgctcatTagacagacgctggggatccg	11	14	1	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr19:48848536T>A	ENST00000293261.3	-	4	761	c.445A>T	c.(445-447)Aat>Tat	p.N149Y	TMEM143_ENST00000436660.2_Intron|TMEM143_ENST00000541566.1_Missense_Mutation_p.N39Y|TMEM143_ENST00000435956.3_Missense_Mutation_p.N114Y|TMEM143_ENST00000377431.2_Intron	NM_018273.2	NP_060743.2	Q96AN5	TM143_HUMAN	transmembrane protein 143	149					hematopoietic progenitor cell differentiation (GO:0002244)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	14		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)		TCCTGCTCATTAGACAGACGC	0.592																																					p.N149Y		Atlas-SNP	.											.	TMEM143	29	.	0			c.A445T						.						125	123	124					19																	48848536		2203	4300	6503	SO:0001583	missense	55260	exon4			GCTCATTAGACAG	AK129801	CCDS12716.1	19q13.32	2008-02-05				ENSG00000161558			25603	protein-coding gene	gene with protein product						12975309	Standard	NM_018273		Approved	FLJ10922	uc002pix.1	Q96AN5		ENST00000293261.3:c.445A>T	chr19.hg19:g.48848536T>A	ENSP00000293261:p.Asn149Tyr	159.0	0.0		188.0	88.0	NM_018273	A8K656|Q6UXY4|Q9NV49	Missense_Mutation	SNP	ENST00000293261.3	hg19	CCDS12716.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.700786	0.48307	.	.	ENSG00000161558	ENST00000293261;ENST00000435956;ENST00000541566	T;T;T	0.49139	0.79;0.8;0.79	4.33	4.33	0.51752	.	0.189716	0.34110	N	0.004257	T	0.28599	0.0708	N	0.24115	0.695	0.80722	D	1	P;P	0.44877	0.845;0.761	B;B	0.34722	0.188;0.123	T	0.14952	-1.0454	10	0.66056	D	0.02	-1.7925	8.8581	0.35240	0.1677:0.0:0.0:0.8323	.	114;149	B4DMT0;Q96AN5	.;TM143_HUMAN	Y	149;114;39	ENSP00000293261:N149Y;ENSP00000397038:N114Y;ENSP00000444275:N39Y	ENSP00000293261:N149Y	N	-	1	0	TMEM143	53540348	0.997000	0.39634	0.970000	0.41538	0.354000	0.29330	3.249000	0.51437	1.734000	0.51633	0.254000	0.18369	AAT	.	.		0.592	TMEM143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465622.1	NM_018273		A	48848536	T	A	48848536	3	1	183	1	0	0	0	0	1	0	0	0	16072	1754	61	4	954	4	TMEM143	19	48848536	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10	903860	48848536	10280447	99	27333										
LRRC4B	94030	hgsc.bcm.edu	37	chr19	51022527	51022527	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	cgaaggcctgcgtgggcaccGtggtcagccggttgtcaaaa	15	11	2	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr19:51022527G>A	ENST00000599957.1	-	3	640	c.443C>T	c.(442-444)aCg>aTg	p.T148M	LRRC4B_ENST00000389201.3_Missense_Mutation_p.T148M			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	148					positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		CGTGGGCACCGTGGTCAGCCG	0.632																																					p.T148M		Atlas-SNP	.											.	LRRC4B	89	.	0			c.C443T						.						53	58	56					19																	51022527		2201	4300	6501	SO:0001583	missense	94030	exon3			GGCACCGTGGTCA	BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"Immunoglobulin superfamily / I-set domain containing", "Endogenous ligands"	25042	protein-coding gene	gene with protein product	"netrin-G3 ligand"		"leucine-rich repeats and immunoglobulin-like domains 4"	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.443C>T	chr19.hg19:g.51022527G>A	ENSP00000471502:p.Thr148Met	80.0	0.0		109.0	19.0	NM_001080457	Q3ZCQ4|Q58F20	Missense_Mutation	SNP	ENST00000599957.1	hg19	CCDS42595.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.172669	0.38413	.	.	ENSG00000131409	ENST00000389201;ENST00000535879	D	0.91996	-2.95	3.96	3.96	0.45880	.	0.505755	0.17542	U	0.170501	D	0.89594	0.6760	L	0.57536	1.79	0.32427	N	0.548533	D	0.56968	0.978	B	0.41813	0.367	D	0.90656	0.4586	10	0.35671	T	0.21	.	13.9104	0.63864	0.0:0.0:1.0:0.0	.	148	Q9NT99	LRC4B_HUMAN	M	148	ENSP00000373853:T148M	ENSP00000373853:T148M	T	-	2	0	LRRC4B	55714339	0.999000	0.42202	0.998000	0.56505	0.994000	0.84299	4.110000	0.57831	2.235000	0.73313	0.491000	0.48974	ACG	.	.		0.632	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457		A	51022527	G	A	51022527	3	1	183	1	0	0	0	0	1	0	0	0	9016	1145	40	1	1702	1	LRRC4B	19	51022527	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	2173991	51022527	8106456	100	27334										
SIRPG	55423	hgsc.bcm.edu	37	chr20	1616155	1616155	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ccgaccaggtcagctgtaggCtctgggggtagaacttcctc	13	12	2	1			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr20:1616155C>A	ENST00000303415.3	-	4	903	c.839G>T	c.(838-840)aGc>aTc	p.S280I	SIRPG_ENST00000216927.4_Intron|RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000381583.2_Intron|RP11-77C3.3_ENST00000437384.1_RNA|SIRPG_ENST00000344103.4_Intron|SIRPG_ENST00000381580.1_Missense_Mutation_p.S247I	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	280	Ig-like C1-type 2.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						CAGCTGTAGGCTCTGGGGGTA	0.547																																					p.S280I		Atlas-SNP	.											.	SIRPG	61	.	0			c.G839T						.						148	128	135					20																	1616155		2203	4300	6503	SO:0001583	missense	55423	exon4			TGTAGGCTCTGGG	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.839G>T	chr20.hg19:g.1616155C>A	ENSP00000305529:p.Ser280Ile	187.0	0.0		232.0	116.0	NM_018556	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	hg19	CCDS13020.2	.	.	.	.	.	.	.	.	.	.	.	1.096	-0.662636	0.03454	.	.	ENSG00000089012	ENST00000381580;ENST00000303415	T;T	0.00622	6.16;6.16	1.6	-3.2	0.05156	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	1.719800	0.02509	N	0.091352	T	0.00724	0.0024	L	0.38953	1.18	0.09310	N	1	B	0.16603	0.018	B	0.16722	0.016	T	0.47142	-0.9140	10	0.39692	T	0.17	.	3.7544	0.08579	0.0:0.4327:0.2184:0.349	.	280	Q9P1W8	SIRPG_HUMAN	I	247;280	ENSP00000370992:S247I;ENSP00000305529:S280I	ENSP00000305529:S280I	S	-	2	0	SIRPG	1564155	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-5.626000	0.00108	-1.511000	0.01794	-1.076000	0.02234	AGC	.	.		0.547	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		A	1616155	C	A	1616155	3	1	183	1	0	0	0	0	1	0	0	0	14351	797	28	3	332	3	SIRPG	20	1616155	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10		1616155	61409365	101	27335										
CHGB	1114	hgsc.bcm.edu	37	chr20	5903869	5903869	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ccctgaggacctggagtgggAgcgctataggggcagaggaa	18	8	0	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr20:5903869A>T	ENST00000378961.4	+	4	1283	c.1079A>T	c.(1078-1080)gAg>gTg	p.E360V		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	360						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						CTGGAGTGGGAGCGCTATAGG	0.527																																					p.E360V		Atlas-SNP	.											.	CHGB	112	.	0			c.A1079T						.						87	89	88					20																	5903869		2203	4300	6503	SO:0001583	missense	1114	exon4			AGTGGGAGCGCTA		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1079A>T	chr20.hg19:g.5903869A>T	ENSP00000368244:p.Glu360Val	61.0	0.0		78.0	33.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	hg19	CCDS13092.1	.	.	.	.	.	.	.	.	.	.	A	5.131	0.209807	0.09757	.	.	ENSG00000089199	ENST00000378961	T	0.01422	4.91	5.37	-10.7	0.00240	.	1.911260	0.02637	N	0.104888	T	0.01254	0.0041	L	0.34521	1.04	0.09310	N	1	B	0.14805	0.011	B	0.15052	0.012	T	0.30208	-0.9986	10	0.49607	T	0.09	2.8012	5.1021	0.14764	0.1434:0.5006:0.1919:0.1642	.	360	P05060	SCG1_HUMAN	V	360	ENSP00000368244:E360V	ENSP00000368244:E360V	E	+	2	0	CHGB	5851869	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-0.697000	0.05098	-4.337000	0.00055	-0.490000	0.04691	GAG	.	.		0.527	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		T	5903869	A	T	5903869	3	4	183	1	0	0	0	0	1	0	0	0	3341	304	11	4	1093	4	CHGB	20	5903869	Missense_Mutation	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10	4287714	5903869	57121651	102	27336										
EPB41L1	2036	hgsc.bcm.edu	37	chr20	34810266	34810266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	tgctggtaaccaaagctgtcGtatacagagaaacagaccca	9	10	0	2	rs371978327		TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr20:34810266G>A	ENST00000338074.2	+	21	2748	c.2587G>A	c.(2587-2589)Gta>Ata	p.V863I	EPB41L1_ENST00000373946.3_Missense_Mutation_p.V683I|EPB41L1_ENST00000373941.1_Missense_Mutation_p.V862I|EPB41L1_ENST00000441639.1_Missense_Mutation_p.V761I|EPB41L1_ENST00000373950.2_Missense_Mutation_p.V754I|EPB41L1_ENST00000202028.5_Missense_Mutation_p.V761I	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	863	C-terminal (CTD).				cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.V863I(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					CAAAGCTGTCGTATACAGAGA	0.542													G|||	1	0.000199681	0	0	5008	,	,		19242	0		0.001	False		,,,				2504	0				p.V863I		Atlas-SNP	.											EPB41L1,rectum,carcinoma,0,1	EPB41L1	111	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2587A						.	G	ILE/VAL,ILE/VAL	0,4406		0,0,2203	115	107	110		2587,2281	4.6	1	20		110	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EPB41L1	NM_012156.2,NM_177996.1	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	863/882,761/780	34810266	1,13005	2203	4300	6503	SO:0001583	missense	2036	exon21			GCTGTCGTATACA	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.2587G>A	chr20.hg19:g.34810266G>A	ENSP00000337168:p.Val863Ile	67.0	0.0		61.0	30.0	NM_012156	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Missense_Mutation	SNP	ENST00000338074.2	hg19	CCDS13271.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.416844	0.83449	0.0	1.16E-4	ENSG00000088367	ENST00000202028;ENST00000373950;ENST00000373951;ENST00000441639;ENST00000373946;ENST00000338074;ENST00000373941	D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	4.61	4.61	0.57282	Band 4.1, C-terminal (1);	.	.	.	.	D	0.87962	0.6310	L	0.42686	1.345	0.53688	D	0.999972	D;D;D;D;D	0.89917	1.0;0.998;0.999;0.994;0.999	D;D;D;D;D	0.85130	0.997;0.972;0.993;0.972;0.991	D	0.89351	0.3661	9	0.87932	D	0	.	16.6051	0.84826	0.0:0.0:1.0:0.0	.	863;683;754;754;761	Q9H4G0;Q9H4G0-4;Q9H4G0-3;B3KUB6;Q9H4G0-2	E41L1_HUMAN;.;.;.;.	I	761;754;754;761;683;863;862	ENSP00000202028:V761I;ENSP00000363061:V754I;ENSP00000399214:V761I;ENSP00000363057:V683I;ENSP00000337168:V863I;ENSP00000363052:V862I	ENSP00000202028:V761I	V	+	1	0	EPB41L1	34273680	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.263000	0.95617	2.401000	0.81631	0.462000	0.41574	GTA	.	.		0.542	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		A	34810266	G	A	34810266	3	1	183	1	0	0	0	0	1	0	0	0	5154	1145	40	1	2665	1	EPB41L1	20	34810266	Missense_Mutation	SNP	G	TCGA-DD-AAD8-01A-11D-A40R-10	28906397	34810266	28215254	103	27337										
ZBTB46	140685	hgsc.bcm.edu	37	chr20	62378586	62378586	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ctggagccatgcctgatgccCacgctggcggcggacatgaa	14	13	0	2			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr20:62378586C>A	ENST00000245663.4	-	5	1617	c.1467G>T	c.(1465-1467)gtG>gtT	p.V489V	ZBTB46_ENST00000395104.1_Silent_p.V489V|ZBTB46_ENST00000302995.2_Silent_p.V489V|RP4-583P15.10_ENST00000433905.2_RNA|RP4-583P15.10_ENST00000447343.2_RNA	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	489					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GCCTGATGCCCACGCTGGCGG	0.697																																					p.V489V		Atlas-SNP	.											.	ZBTB46	72	.	0			c.G1467T						.						9	8	9					20																	62378586		2163	4219	6382	SO:0001819	synonymous_variant	140685	exon5			GATGCCCACGCTG	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1467G>T	chr20.hg19:g.62378586C>A		103.0	0.0		90.0	17.0	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	hg19	CCDS13538.1																																																																																			.	.		0.697	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		A	62378586	C	A	62378586	2	1	183	1	0	0	0	0	0	0	0	1	17562	581	21	3		3	ZBTB46	20	62378586	Silent	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	27568320	62378586	646934	104	27338										
ATP6V1E1	529	hgsc.bcm.edu	37	chr22	18095625	18095625	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gactttgagtctcgcttgatTcatcaaattggacatctgac	8	9	4	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr22:18095625T>C	ENST00000253413.5	-	4	411	c.229A>G	c.(229-231)Aat>Gat	p.N77D	ATP6V1E1_ENST00000399796.2_Missense_Mutation_p.N77D|ATP6V1E1_ENST00000478963.1_5'UTR|ATP6V1E1_ENST00000399798.2_Missense_Mutation_p.N55D	NM_001696.3	NP_001687.1	P36543	VATE1_HUMAN	ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E1	77					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting two-sector ATPase complex, catalytic domain (GO:0033178)	ATPase binding (GO:0051117)|hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|urinary_tract(1)	10		all_epithelial(15;0.206)		Lung(27;0.19)		CTCGCTTGATTCATCAAATTG	0.353																																					p.N77D		Atlas-SNP	.											.	ATP6V1E1	28	.	0			c.A229G						.						86	85	85					22																	18095625		2203	4300	6503	SO:0001583	missense	529	exon4			CTTGATTCATCAA	X76228	CCDS13745.1, CCDS42977.1, CCDS42978.1	22q11.2	2010-04-21	2006-01-13	2002-06-21	ENSG00000131100	ENSG00000131100	3.6.3.14	"ATPases / V-type"	857	protein-coding gene	gene with protein product		108746	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) 31kD", "ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E isoform 1"	ATP6E, ATP6V1E		8004105, 8250920	Standard	NM_001696		Approved	P31, Vma4, ATP6E2	uc002zmr.1	P36543	OTTHUMG00000059320	ENST00000253413.5:c.229A>G	chr22.hg19:g.18095625T>C	ENSP00000253413:p.Asn77Asp	356.0	0.0		378.0	77.0	NM_001039367	A8MUE4|A8MUN4	Missense_Mutation	SNP	ENST00000253413.5	hg19	CCDS13745.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.669777	0.88348	.	.	ENSG00000131100	ENST00000253413;ENST00000399796;ENST00000399798;ENST00000413576	.	.	.	4.64	4.64	0.57946	.	0.091661	0.64402	D	0.000001	D	0.86657	0.5985	H	0.96142	3.775	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.996	D	0.90545	0.4505	9	0.87932	D	0	-21.4191	13.175	0.59621	0.0:0.0:0.0:1.0	.	55;77;77	A8MUE4;A8MUN4;P36543	.;.;VATE1_HUMAN	D	77;77;55;78	.	ENSP00000253413:N77D	N	-	1	0	ATP6V1E1	16475625	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.454000	0.80714	1.941000	0.56285	0.533000	0.62120	AAT	.	.		0.353	ATP6V1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131790.3	NM_001696		C	18095625	T	C	18095625	3	2	183	1	0	0	0	0	1	0	0	0	1183	1783	62	2	475	2	ATP6V1E1	22	18095625	Missense_Mutation	SNP	T	TCGA-DD-AAD8-01A-11D-A40R-10		18095625	33208941	105	27339										
SLC25A1	6576	hgsc.bcm.edu	37	chr22	19166135	19166135	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	gtgcgtcagcttggccttccCggacgcgggcgcggcggccg	18	15	1	0			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chr22:19166135C>T	ENST00000215882.5	-	1	208	c.52G>A	c.(52-54)Ggg>Agg	p.G18R	CLTCL1_ENST00000442042.2_5'Flank|SLC25A1_ENST00000451283.1_5'Flank|SLC25A1_ENST00000461267.1_5'Flank	NM_005984.3	NP_005975.1	P53007	TXTP_HUMAN	solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1	18					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|citrate transport (GO:0015746)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	citrate transmembrane transporter activity (GO:0015137)			cervix(1)|lung(1)	2	Colorectal(54;0.0993)	all_lung(157;9.94e-09)		Lung(27;0.124)		TTGGCCTTCCCGGAcgcgggc	0.811																																					p.G18R		Atlas-SNP	.											.	SLC25A1	14	.	0			c.G52A						.						2	3	2					22																	19166135		1113	2188	3301	SO:0001583	missense	6576	exon1			CCTTCCCGGACGC	U25147	CCDS13758.1, CCDS74817.1	22q11	2013-05-22			ENSG00000100075	ENSG00000100075		"Solute carriers"	10979	protein-coding gene	gene with protein product		190315	"solute carrier family 20 (mitochondrial citrate transporter), member 3"	SLC20A3		8666394, 9254007	Standard	NM_001256534		Approved	CTP	uc002zoz.4	P53007	OTTHUMG00000150123	ENST00000215882.5:c.52G>A	chr22.hg19:g.19166135C>T	ENSP00000215882:p.Gly18Arg	7.0	0.0		10.0	7.0	NM_005984	A8K8E8|Q9BSK6	Missense_Mutation	SNP	ENST00000215882.5	hg19	CCDS13758.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.950915	0.92660	.	.	ENSG00000100075	ENST00000215882	T	0.79554	-1.28	3.24	3.24	0.37175	.	0.301431	0.30142	U	0.010309	T	0.75576	0.3868	L	0.47716	1.5	0.80722	D	1	D	0.63880	0.993	P	0.45167	0.472	T	0.77227	-0.2665	10	0.46703	T	0.11	-12.6645	12.1036	0.53798	0.0:1.0:0.0:0.0	.	18	P53007	TXTP_HUMAN	R	18	ENSP00000215882:G18R	ENSP00000215882:G18R	G	-	1	0	SLC25A1	17546135	0.018000	0.18449	0.143000	0.22291	0.919000	0.55068	0.863000	0.27913	1.832000	0.53329	0.442000	0.29010	GGG	.	.		0.811	SLC25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316441.1	NM_005984		T	19166135	C	T	19166135	3	4	183	1	0	0	0	0	1	0	0	0	14486	652	23	1	919	1	SLC25A1	22	19166135	Missense_Mutation	SNP	C	TCGA-DD-AAD8-01A-11D-A40R-10	1070510	19166135	32138431	106	27340										
EFHC2	80258	hgsc.bcm.edu	37	chrX	44101519	44101519	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0280373831775701	3	1	0.655043586550436	0	0.800608828006088	0.181818181818182	0.751940625889747	0	ggagaaggaggcttgcatgaAactgaggtaaagttctctag	14	5	1	3			TCGA-DD-AAD8-01A-11D-A40R-10	TCGA-DD-AAD8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e9bd10d3-14cc-458b-ad39-9001c8870b4e	8f73a6a2-ac9e-4907-8a3a-8b8d79b2d7d2	g.chrX:44101519A>C	ENST00000420999.1	-	8	1211	c.1128T>G	c.(1126-1128)gtT>gtG	p.V376V		NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	376							calcium ion binding (GO:0005509)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						GCTTGCATGAAACTGAGGTAA	0.373																																					p.V376V		Atlas-SNP	.											.	EFHC2	81	.	0			c.T1128G						.						56	47	50					X																	44101519		1845	4088	5933	SO:0001819	synonymous_variant	80258	exon8			GCATGAAACTGAG	AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"EF-hand domain containing"	26233	protein-coding gene	gene with protein product		300817	"mental retardation, X-linked 74"	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.1128T>G	chrX.hg19:g.44101519A>C		128.0	0.0		75.0	63.0	NM_025184	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Silent	SNP	ENST00000420999.1	hg19	CCDS55405.1	.	.	.	.	.	.	.	.	.	.	A	3.590	-0.083758	0.07141	.	.	ENSG00000183690	ENST00000441230	.	.	.	5.9	4.75	0.60458	.	.	.	.	.	T	0.57548	0.2061	.	.	.	0.49582	D	0.999805	.	.	.	.	.	.	T	0.56232	-0.8013	4	.	.	.	-9.4716	7.9529	0.30025	0.8459:0.0:0.1541:0.0	.	.	.	.	V	357	.	.	F	-	1	0	EFHC2	43986463	0.884000	0.30299	0.024000	0.17045	0.789000	0.44602	1.902000	0.39848	1.991000	0.58162	0.486000	0.48141	TTC	.	.		0.373	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184		C	44101519	A	C	44101519	2	2	183	1	0	0	0	0	0	0	0	1	4949	1	1	5		5	EFHC2	23	44101519	Silent	SNP	A	TCGA-DD-AAD8-01A-11D-A40R-10		44101519	111169041	107	27341										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12336579	12336579	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggccggtacatttctgtgctCaaggtgtttggtaccaatgc	12	9	2	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr1:12336579C>T	ENST00000358136.3	+	19	3064	c.2934C>T	c.(2932-2934)ctC>ctT	p.L978L	VPS13D_ENST00000356315.4_Silent_p.L978L	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TTTCTGTGCTCAAGGTGTTTG	0.502											OREG0013110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L978L		Atlas-SNP	.											.	VPS13D	316	.	0			c.C2934T						.						124	116	119					1																	12336579		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon19			TGTGCTCAAGGTG	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.2934C>T	chr1.hg19:g.12336579C>T		92.0	0.0	679	38.0	19.0	NM_015378		Silent	SNP	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.502	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		T	12336579	C	T	12336579	2	4	184	1	0	0	0	0	0	0	0	1	17207	813	29	3		3	VPS13D	1	12336579	Silent	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10		12336579	236914042	1	27342										
TMCO4	255104	hgsc.bcm.edu	37	chr1	20009838	20009838	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggagggcaggcagcctggggCcagcaagagccccttctcgt	16	13	1	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr1:20009838C>T	ENST00000294543.6	-	16	1841	c.1600G>A	c.(1600-1602)Gcc>Acc	p.A534T	TMCO4_ENST00000375127.1_Missense_Mutation_p.A534T|TMCO4_ENST00000375122.2_Missense_Mutation_p.A494T|TMCO4_ENST00000489814.1_5'UTR	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	534						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		CAGCCTGGGGCCAGCAAGAGC	0.672																																					p.A534T		Atlas-SNP	.											.	TMCO4	46	.	0			c.G1600A						.						30	33	32					1																	20009838		2203	4300	6503	SO:0001583	missense	255104	exon16			CTGGGGCCAGCAA		CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.1600G>A	chr1.hg19:g.20009838C>T	ENSP00000294543:p.Ala534Thr	192.0	0.0		93.0	48.0	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Missense_Mutation	SNP	ENST00000294543.6	hg19	CCDS198.1	.	.	.	.	.	.	.	.	.	.	C	13.23	2.175506	0.38413	.	.	ENSG00000162542	ENST00000294543;ENST00000375127;ENST00000375122	T;T;T	0.33654	1.43;1.45;1.4	5.11	4.13	0.48395	.	0.134780	0.33959	N	0.004400	T	0.24005	0.0581	L	0.32530	0.975	0.30657	N	0.754778	P;P;B	0.39480	0.675;0.664;0.42	B;B;B	0.35353	0.145;0.201;0.099	T	0.11131	-1.0600	10	0.20046	T	0.44	-0.7187	11.776	0.51985	0.1755:0.8245:0.0:0.0	.	118;534;494	Q6ZSC6;Q5TGY1;Q5TGY1-2	.;TMCO4_HUMAN;.	T	534;534;494	ENSP00000294543:A534T;ENSP00000364269:A534T;ENSP00000364264:A494T	ENSP00000294543:A534T	A	-	1	0	TMCO4	19882425	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	2.562000	0.45914	2.532000	0.85374	0.563000	0.77884	GCC	.	.		0.672	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719		T	20009838	C	T	20009838	3	4	184	1	0	0	0	0	1	0	0	0	16013	739	26	3	308	3	TMCO4	1	20009838	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	7673259	20009838	229240783	2	27343										
ASB17	127247	hgsc.bcm.edu	37	chr1	76397825	76397825	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	catacctcagaatttttgccAgtgatctgtaaatccttggt	7	9	2	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr1:76397825A>T	ENST00000284142.6	-	1	291	c.152T>A	c.(151-153)cTg>cAg	p.L51Q		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	51					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	21						AATTTTTGCCAGTGATCTGTA	0.393																																					p.L51Q		Atlas-SNP	.											.	ASB17	53	.	0			c.T152A						.						148	138	142					1																	76397825		2203	4300	6503	SO:0001583	missense	127247	exon1			TTTGCCAGTGATC	AF403035	CCDS671.1	1p22.3	2013-01-11	2011-01-25		ENSG00000154007	ENSG00000154007		"Ankyrin repeat domain containing"	19769	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 17"			12076535	Standard	NM_080868		Approved		uc001dhe.2	Q8WXJ9	OTTHUMG00000009787	ENST00000284142.6:c.152T>A	chr1.hg19:g.76397825A>T	ENSP00000284142:p.Leu51Gln	170.0	0.0		110.0	43.0	NM_080868	B1APB8|Q8N0X5	Missense_Mutation	SNP	ENST00000284142.6	hg19	CCDS671.1	.	.	.	.	.	.	.	.	.	.	A	18.48	3.634132	0.67130	.	.	ENSG00000154007	ENST00000284142	T	0.47869	0.83	6.08	6.08	0.98989	.	0.000000	0.45606	D	0.000348	T	0.46852	0.1414	L	0.27053	0.805	0.42010	D	0.990938	D	0.76494	0.999	D	0.85130	0.997	T	0.55872	-0.8072	10	0.87932	D	0	.	13.0348	0.58864	1.0:0.0:0.0:0.0	.	51	Q8WXJ9	ASB17_HUMAN	Q	51	ENSP00000284142:L51Q	ENSP00000284142:L51Q	L	-	2	0	ASB17	76170413	1.000000	0.71417	1.000000	0.80357	0.614000	0.37383	4.816000	0.62642	2.330000	0.79161	0.533000	0.62120	CTG	.	.		0.393	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868		T	76397825	A	T	76397825	3	4	184	1	0	0	0	0	1	0	0	0	1021	188	7	4	747	4	ASB17	1	76397825	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	56387987	76397825	172852796	3	27344										
ABCA4	24	hgsc.bcm.edu	37	chr1	94548954	94548954	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ataatattcctccccaagatCtcagattgataccttgagaa	5	10	1	4			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr1:94548954C>A	ENST00000370225.3	-	7	898	c.812G>T	c.(811-813)aGa>aTa	p.R271I	ABCA4_ENST00000535735.1_Missense_Mutation_p.R271I	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	271					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TCCCCAAGATCTCAGATTGAT	0.343																																					p.R271I		Atlas-SNP	.											.	ABCA4	275	.	0			c.G812T						.						187	206	199					1																	94548954		2203	4300	6503	SO:0001583	missense	24	exon7			CAAGATCTCAGAT	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.812G>T	chr1.hg19:g.94548954C>A	ENSP00000359245:p.Arg271Ile	70.0	0.0		49.0	11.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.700008	0.48307	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.91351	-2.72;-2.83	5.59	3.71	0.42584	.	0.621054	0.16066	N	0.231250	D	0.86669	0.5988	M	0.72894	2.215	0.53688	D	0.999978	P;B	0.38745	0.645;0.237	B;B	0.44163	0.443;0.054	D	0.84529	0.0632	10	0.31617	T	0.26	.	10.2021	0.43089	0.0:0.7506:0.0:0.2494	.	271;271	F5H6E5;P78363	.;ABCA4_HUMAN	I	271	ENSP00000359245:R271I;ENSP00000437682:R271I	ENSP00000359245:R271I	R	-	2	0	ABCA4	94321542	0.981000	0.34729	1.000000	0.80357	0.967000	0.64934	0.860000	0.27871	1.499000	0.48617	0.655000	0.94253	AGA	.	.		0.343	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94548954	C	A	94548954	3	1	184	1	0	0	0	0	1	0	0	0	34	913	32	3	6185	3	ABCA4	1	94548954	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	18151129	94548954	154701667	4	27345										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176762782	176762782	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ctgctgacactctggagcacTggatggaacctgtcaaagtc	11	11	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr1:176762782T>C	ENST00000367662.3	+	20	6271	c.5107T>C	c.(5107-5109)Tgg>Cgg	p.W1703R		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1703	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TCTGGAGCACTGGATGGAACC	0.478																																					p.W1703R		Atlas-SNP	.											.	PAPPA2	665	.	0			c.T5107C						.						136	133	134					1																	176762782		2001	4161	6162	SO:0001583	missense	60676	exon20			GAGCACTGGATGG	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.5107T>C	chr1.hg19:g.176762782T>C	ENSP00000356634:p.Trp1703Arg	117.0	0.0		146.0	27.0	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	hg19	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	T	14.63	2.591357	0.46214	.	.	ENSG00000116183	ENST00000367662	T	0.01804	4.63	5.17	5.17	0.71159	.	0.072004	0.64402	D	0.000009	T	0.03305	0.0096	L	0.53561	1.675	0.80722	D	1	B	0.32653	0.379	B	0.40165	0.321	T	0.50233	-0.8852	10	0.46703	T	0.11	-10.78	8.4751	0.33007	0.1733:0.0:0.0:0.8267	.	1703	Q9BXP8	PAPP2_HUMAN	R	1703	ENSP00000356634:W1703R	ENSP00000356634:W1703R	W	+	1	0	PAPPA2	175029405	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.871000	0.48459	1.946000	0.56461	0.533000	0.62120	TGG	.	.		0.478	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			C	176762782	T	C	176762782	3	2	184	1	0	0	0	0	1	0	0	0	11442	1580	55	2	5234	2	PAPPA2	1	176762782	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	82213828	176762782	72487839	5	27346										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179599927	179599928	+	Frame_Shift_Ins	INS	-	-	A													0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tttaaagagcaactatcaccINSaaaaaaattaggcttcttaa							TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr1:179599927_179599928insA	ENST00000367614.1	+	7	1357_1358	c.998_999insA	c.(997-1002)ccaaaafs	p.PK333fs	TDRD5_ENST00000444136.1_Frame_Shift_Ins_p.PK333fs|TDRD5_ENST00000294848.8_Frame_Shift_Ins_p.PK333fs	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	333	HTH OST-type 3. {ECO:0000255|PROSITE- ProRule:PRU00975}.				DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						CAACTATCACCAAAAAAATTAG	0.337																																					p.P333fs		Atlas-INDEL	.											.	TDRD5	149	.	0			c.998_999insA						.																																			SO:0001589	frameshift_variant	163589	exon7			.	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1005dupA	chr1.hg19:g.179599934_179599934dupA	ENSP00000356586:p.Pro333fs	224.0	0.0		308.0	30.0	NM_001199091	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Frame_Shift_Ins	INS	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.		0.337	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		A	179599928	-	A	179599927	7	5	184	1	0	1	1	0	0	0	0	0	15748	594	21	0	1020	0	TDRD5	1	179599927	Frame_Shift_Ins	INS	-	TCGA-DD-AADA-01A-11D-A40R-10	2837145	179599927	69650694	6	27347										
GLT25D2	23127	hgsc.bcm.edu	37	chr1	183942764	183942764	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	acttgccttaggggtgattcCgcaccagaaattagaataca	9	9	0	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr1:183942764C>T	ENST00000361927.4	-	4	984	c.613G>A	c.(613-615)Gga>Aga	p.G205R	COLGALT2_ENST00000546159.1_Missense_Mutation_p.G205R	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	205					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)	p.G205*(1)									GGGGTGATTCCGCACCAGAAA	0.453																																					p.G205R		Atlas-SNP	.											.	.	.	.	1	Substitution - Nonsense(1)	lung(1)	c.G613A						.						123	140	134					1																	183942764		2203	4300	6503	SO:0001583	missense	23127	exon4			TGATTCCGCACCA	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.613G>A	chr1.hg19:g.183942764C>T	ENSP00000354960:p.Gly205Arg	81.0	0.0		112.0	7.0	NM_015101	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	hg19	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	C	32	5.118350	0.94385	.	.	ENSG00000198756	ENST00000546159;ENST00000361927	T;T	0.23348	1.91;1.91	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.62307	0.2417	M	0.91920	3.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.71593	-0.4546	10	0.87932	D	0	.	19.2163	0.93780	0.0:1.0:0.0:0.0	.	205;205	F5H3T5;Q8IYK4	.;GT252_HUMAN	R	205	ENSP00000439112:G205R;ENSP00000354960:G205R	ENSP00000354960:G205R	G	-	1	0	GLT25D2	182209387	1.000000	0.71417	0.992000	0.48379	0.987000	0.75469	7.556000	0.82233	2.535000	0.85469	0.585000	0.79938	GGA	.	.		0.453	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		T	183942764	C	T	183942764	3	4	184	1	0	0	0	0	1	0	0	0	6475	661	23	1	1303	1	GLT25D2	1	183942764	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	4342837	183942764	65307857	7	27348										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186076063	186076063	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ctggcatccagtcctgcaggAgatgatgataaggaatatct	11	8	1	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr1:186076063A>T	ENST00000271588.4	+	70	11047	c.10818A>T	c.(10816-10818)ggA>ggT	p.G3606G	HMCN1_ENST00000367492.2_Silent_p.G3606G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3606	Ig-like C2-type 34.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GTCCTGCAGGAGATGATGATA	0.363																																					p.G3606G		Atlas-SNP	.											.	HMCN1	797	.	0			c.A10818T						.						179	178	179					1																	186076063		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon70			TGCAGGAGATGAT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.10818A>T	chr1.hg19:g.186076063A>T		61.0	0.0		113.0	31.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.363	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186076063	A	T	186076063	2	4	184	1	0	0	0	0	0	0	0	1	7229	291	11	4		4	HMCN1	1	186076063	Silent	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	2133299	186076063	63174558	8	27349										
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186880396	186880396	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	acagctcatgcccagacctaCgatttagtatggctctgtgt	9	11	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr1:186880396C>T	ENST00000367466.3	+	7	585	c.433C>T	c.(433-435)Cga>Tga	p.R145*	PLA2G4A_ENST00000442353.2_Intron|PLA2G4A_ENST00000466600.1_3'UTR	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	145	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.|Phospholipid binding. {ECO:0000305}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	CCCAGACCTACGATTTAGTAT	0.458																																					p.R145X		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.C433T						.						165	170	169					1																	186880396		2203	4300	6503	SO:0001587	stop_gained	5321	exon7			GACCTACGATTTA	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.433C>T	chr1.hg19:g.186880396C>T	ENSP00000356436:p.Arg145*	112.0	0.0		177.0	61.0	NM_024420	B1AKG4|Q29R80	Nonsense_Mutation	SNP	ENST00000367466.3	hg19	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	C	37	6.620513	0.97709	.	.	ENSG00000116711	ENST00000367466	.	.	.	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.1102	11.4285	0.50025	0.1803:0.8196:0.0:0.0	.	.	.	.	X	145	.	ENSP00000356436:R145X	R	+	1	2	PLA2G4A	185147019	1.000000	0.71417	0.979000	0.43373	0.997000	0.91878	2.752000	0.47516	2.437000	0.82529	0.650000	0.86243	CGA	.	.		0.458	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		T	186880396	C	T	186880396	4	4	184	1	0	0	0	0	0	1	0	0	12010	528	19	1	455	1	PLA2G4A	1	186880396	Nonsense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	804333	186880396	62370225	9	27350										
EXO1	9156	hgsc.bcm.edu	37	chr1	242042426	242042426	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ccctctccaagcacagcattGcagcagttccgaagaaagag	9	13	1	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr1:242042426G>A	ENST00000366548.3	+	13	2483	c.1890G>A	c.(1888-1890)ttG>ttA	p.L630L	EXO1_ENST00000518483.1_Silent_p.L630L|EXO1_ENST00000348581.5_Silent_p.L630L	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	630	Interaction with MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			GCACAGCATTGCAGCAGTTCC	0.483								Editing and processing nucleases																													p.L630L		Atlas-SNP	.											.	EXO1	103	.	0			c.G1890A						.						89	84	85					1																	242042426		2203	4300	6503	SO:0001819	synonymous_variant	9156	exon13			AGCATTGCAGCAG	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1890G>A	chr1.hg19:g.242042426G>A		160.0	0.0		205.0	15.0	NM_130398	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Silent	SNP	ENST00000366548.3	hg19	CCDS1620.1	.	.	.	.	.	.	.	.	.	.	G	2.775	-0.254860	0.05829	.	.	ENSG00000174371	ENST00000521202	.	.	.	5.72	2.71	0.32032	.	.	.	.	.	T	0.47563	0.1452	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34129	-0.9841	4	.	.	.	-6.3969	4.5686	0.12198	0.2555:0.1618:0.5827:0.0	.	.	.	.	T	29	.	.	A	+	1	0	EXO1	240109049	0.986000	0.35501	0.912000	0.35992	0.227000	0.25037	1.359000	0.34113	0.793000	0.33875	-0.145000	0.13849	GCA	.	.		0.483	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027		A	242042426	G	A	242042426	2	1	184	1	0	0	0	0	0	0	0	1	5302	1310	46	3		3	EXO1	1	242042426	Silent	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	55162030	242042426	7208195	10	27351										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37280689	37280689	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	aaatatgttaagctgcacagCctgctggcggacacctttag	10	10	0	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr2:37280689C>A	ENST00000233099.5	-	17	2556	c.2461G>T	c.(2461-2463)Gct>Tct	p.A821S	HEATR5B_ENST00000354531.2_Missense_Mutation_p.A821S	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	821						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				AGCTGCACAGCCTGCTGGCGG	0.299																																					p.A821S		Atlas-SNP	.											.	HEATR5B	185	.	0			c.G2461T						.						57	59	58					2																	37280689		2203	4300	6503	SO:0001583	missense	54497	exon17			GCACAGCCTGCTG	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.2461G>T	chr2.hg19:g.37280689C>A	ENSP00000233099:p.Ala821Ser	523.0	0.0		376.0	155.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	C	33	5.199134	0.94997	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.09255	3.0;3.0	5.85	5.85	0.93711	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.24547	0.0595	M	0.68317	2.08	0.80722	D	1	P	0.49185	0.92	P	0.49561	0.615	T	0.00106	-1.2055	10	0.52906	T	0.07	-22.1987	20.1736	0.98170	0.0:1.0:0.0:0.0	.	821	Q9P2D3	HTR5B_HUMAN	S	821	ENSP00000233099:A821S;ENSP00000346531:A821S	ENSP00000233099:A821S	A	-	1	0	HEATR5B	37134193	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.771000	0.85420	2.767000	0.95098	0.557000	0.71058	GCT	.	.		0.299	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37280689	C	A	37280689	3	1	184	1	0	0	0	0	1	0	0	0	7041	739	26	3	3834	3	HEATR5B	2	37280689	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10		37280689	205918684	11	27352										
GYPC	2995	hgsc.bcm.edu	37	chr2	127453545	127453545	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tgattgctgctgtggccatcGtcctagtctccctcctcttc	8	15	2	1	rs200879714		TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr2:127453545G>A	ENST00000259254.4	+	4	545	c.214G>A	c.(214-216)Gtc>Atc	p.V72I	GYPC_ENST00000464053.1_3'UTR|GYPC_ENST00000356887.7_Missense_Mutation_p.V51I|GYPC_ENST00000409836.3_Missense_Mutation_p.V53I	NM_002101.4	NP_002092.1	P04921	GLPC_HUMAN	glycophorin C (Gerbich blood group)	72						cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|prostate(2)|urinary_tract(1)	13	Colorectal(110;0.0533)			BRCA - Breast invasive adenocarcinoma(221;0.075)		TGTGGCCATCGTCCTAGTCTC	0.607																																					p.V72I	Melanoma(110;806 1600 6704 9981 33404)	Atlas-SNP	.											GYPC,right_upper_lobe,carcinoma,0,1	GYPC	27	.	0			c.G214A						.	G	ILE/VAL,ILE/VAL	0,4406		0,0,2203	196	153	167		214,157	2.4	0.3	2		167	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	GYPC	NM_002101.3,NM_016815.2	29,29	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	possibly-damaging,possibly-damaging	72/129,53/110	127453545	3,13003	2203	4300	6503	SO:0001583	missense	2995	exon4			GCCATCGTCCTAG		CCDS2136.1, CCDS46402.1, CCDS58724.1	2q14-q21	2014-07-19			ENSG00000136732	ENSG00000136732		"CD molecules", "Blood group antigens"	4704	protein-coding gene	gene with protein product		110750					Standard	NM_016815		Approved	GPC, GYPD, Ge, CD236, CD236R	uc002tnq.4	P04921	OTTHUMG00000131464	ENST00000259254.4:c.214G>A	chr2.hg19:g.127453545G>A	ENSP00000259254:p.Val72Ile	85.0	0.0		68.0	7.0	NM_002101	B2R522|Q53SV9|Q92642	Missense_Mutation	SNP	ENST00000259254.4	hg19	CCDS2136.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.666058	0.29604	0.0	3.49E-4	ENSG00000136732	ENST00000259254;ENST00000356887;ENST00000409836	T;T;T	0.17854	2.7;2.25;2.74	5.22	2.41	0.29592	.	.	.	.	.	T	0.11067	0.0270	L	0.47190	1.495	0.31909	N	0.6149	P;P	0.47545	0.597;0.897	B;B	0.31290	0.041;0.127	T	0.18840	-1.0324	9	0.44086	T	0.13	-5.7083	6.9613	0.24599	0.1526:0.0:0.7071:0.1403	.	51;72	P04921-2;P04921	.;GLPC_HUMAN	I	72;51;53	ENSP00000259254:V72I;ENSP00000349354:V51I;ENSP00000386904:V53I	ENSP00000259254:V72I	V	+	1	0	GYPC	127170015	0.995000	0.38212	0.285000	0.24819	0.020000	0.10135	2.361000	0.44160	0.201000	0.20466	0.561000	0.74099	GTC	.	.		0.607	GYPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254297.1	NM_002101		A	127453545	G	A	127453545	3	1	184	1	0	0	0	0	1	0	0	0	6919	1145	40	1	228	1	GYPC	2	127453545	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	90172856	127453545	115745828	12	27353										
DNAJB2	3300	hgsc.bcm.edu	37	chr2	220147607	220147607	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gaaccggggttcccgacactCaggccccttctttaccttct	8	16	3	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr2:220147607C>T	ENST00000336576.5	+	6	689	c.401C>T	c.(400-402)tCa>tTa	p.S134L	DNAJB2_ENST00000392086.4_Missense_Mutation_p.S134L|DNAJB2_ENST00000463463.1_3'UTR	NM_006736.5	NP_006727.2	P25686	DNJB2_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 2	134					cell death (GO:0008219)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of inclusion body assembly (GO:0090084)|negative regulation of protein deubiquitination (GO:0090086)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|inclusion body (GO:0016234)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14		Renal(207;0.0474)		Epithelial(149;1.97e-06)|all cancers(144;0.00028)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCCCGACACTCAGGCCCCTTC	0.542																																					p.S134L		Atlas-SNP	.											.	DNAJB2	31	.	0			c.C401T						.						126	121	122					2																	220147607		2203	4300	6503	SO:0001583	missense	3300	exon6			GACACTCAGGCCC		CCDS2439.1, CCDS46519.1	2q32-q34	2011-09-02			ENSG00000135924	ENSG00000135924		"Heat shock proteins / DNAJ (HSP40)"	5228	protein-coding gene	gene with protein product		604139		HSJ1		1599432, 10516435	Standard	NM_006736		Approved	HSPF3	uc002vkx.1	P25686	OTTHUMG00000133134	ENST00000336576.5:c.401C>T	chr2.hg19:g.220147607C>T	ENSP00000338019:p.Ser134Leu	91.0	0.0		60.0	14.0	NM_006736	A8K9P6|Q8IUK1|Q8IUK2|Q96F52	Missense_Mutation	SNP	ENST00000336576.5	hg19	CCDS2439.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.505689	0.26949	.	.	ENSG00000135924	ENST00000336576;ENST00000425450;ENST00000392086;ENST00000439026	T;T;T;T	0.71461	0.93;0.93;0.93;-0.57	5.37	4.49	0.54785	.	4.344530	0.00735	N	0.000971	T	0.58963	0.2159	N	0.20574	0.59	0.09310	N	1	B;B	0.28713	0.22;0.013	B;B	0.21708	0.036;0.015	T	0.49021	-0.8982	10	0.42905	T	0.14	.	8.563	0.33523	0.1496:0.7692:0.0:0.0812	.	134;134	P25686;P25686-2	DNJB2_HUMAN;.	L	134	ENSP00000338019:S134L;ENSP00000414796:S134L;ENSP00000375936:S134L;ENSP00000387951:S134L	ENSP00000338019:S134L	S	+	2	0	DNAJB2	219855851	0.013000	0.17824	0.088000	0.20740	0.534000	0.34807	1.944000	0.40263	2.500000	0.84329	0.563000	0.77884	TCA	.	.		0.542	DNAJB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256823.2			T	220147607	C	T	220147607	3	4	184	1	0	0	0	0	1	0	0	0	4622	838	29	3	419	3	DNAJB2	2	220147607	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	92694062	220147607	23051766	13	27354										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220500183	220500183	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tgaacagaccaaagtcgagaTgaccacacggggtggctaca	12	10	0	4			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr2:220500183T>A	ENST00000358055.3	+	13	2449	c.1937T>A	c.(1936-1938)aTg>aAg	p.M646K	SLC4A3_ENST00000373762.3_Missense_Mutation_p.M673K|SLC4A3_ENST00000273063.6_Missense_Mutation_p.M673K|SLC4A3_ENST00000317151.3_Missense_Mutation_p.M646K|SLC4A3_ENST00000373760.2_Missense_Mutation_p.M646K			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	646					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AAAGTCGAGATGACCACACGG	0.642																																					p.M673K		Atlas-SNP	.											.	SLC4A3	144	.	0			c.T2018A						.						52	49	50					2																	220500183		2203	4300	6503	SO:0001583	missense	6508	exon13			TCGAGATGACCAC		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1937T>A	chr2.hg19:g.220500183T>A	ENSP00000350756:p.Met646Lys	365.0	0.0		288.0	74.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	hg19	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	T	7.739	0.700922	0.15172	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151	T;T;T;T;T	0.72282	-0.63;-0.63;-0.64;-0.64;-0.63	4.92	-0.481	0.12082	.	0.504928	0.21041	N	0.081162	T	0.29491	0.0735	N	0.01352	-0.895	0.22317	N	0.999205	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35500	-0.9786	10	0.05620	T	0.96	.	4.3829	0.11302	0.1417:0.2965:0.0:0.5617	.	350;646;673	P48751-2;P48751;P48751-3	.;B3A3_HUMAN;.	K	646;646;673;673;646	ENSP00000350756:M646K;ENSP00000362865:M646K;ENSP00000273063:M673K;ENSP00000362867:M673K;ENSP00000314006:M646K	ENSP00000273063:M673K	M	+	2	0	SLC4A3	220208427	0.859000	0.29813	0.943000	0.38184	0.693000	0.40251	0.215000	0.17562	-0.016000	0.14127	0.523000	0.50628	ATG	.	.		0.642	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		A	220500183	T	A	220500183	3	1	184	1	0	0	0	0	1	0	0	0	14670	1464	51	4	2064	4	SLC4A3	2	220500183	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	352576	220500183	22699190	14	27355										
RFTN1	23180	hgsc.bcm.edu	37	chr3	16411777	16411777	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gtttgttgaaaagggtgaagAtctccatttctgttgggatt	12	4	2	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr3:16411777A>G	ENST00000334133.4	-	6	1108	c.836T>C	c.(835-837)aTc>aCc	p.I279T	RFTN1_ENST00000483671.1_5'UTR|RFTN1_ENST00000432519.1_Missense_Mutation_p.I243T	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	279					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						AAGGGTGAAGATCTCCATTTC	0.468																																					p.I279T		Atlas-SNP	.											.	RFTN1	79	.	0			c.T836C						.						180	180	180					3																	16411777		2203	4300	6503	SO:0001583	missense	23180	exon6			GTGAAGATCTCCA	D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"raft-linking protein"					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.836T>C	chr3.hg19:g.16411777A>G	ENSP00000334153:p.Ile279Thr	158.0	0.0		100.0	14.0	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Missense_Mutation	SNP	ENST00000334133.4	hg19	CCDS33712.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.987470	0.74589	.	.	ENSG00000131378	ENST00000432519;ENST00000334133	T;T	0.35605	1.3;1.3	5.68	5.68	0.88126	.	0.191940	0.49916	D	0.000134	T	0.55609	0.1931	M	0.63428	1.95	0.46954	D	0.999261	D;D	0.67145	0.996;0.996	P;P	0.62298	0.9;0.9	T	0.59139	-0.7510	10	0.87932	D	0	-34.2325	15.9355	0.79704	1.0:0.0:0.0:0.0	.	243;279	G3XAJ6;Q14699	.;RFTN1_HUMAN	T	243;279	ENSP00000403926:I243T;ENSP00000334153:I279T	ENSP00000334153:I279T	I	-	2	0	RFTN1	16386781	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.315000	0.78998	2.179000	0.69175	0.459000	0.35465	ATC	.	.		0.468	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150		G	16411777	A	G	16411777	3	3	184	1	0	0	0	0	1	0	0	0	13273	333	12	2	920	2	RFTN1	3	16411777	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10		16411777	181610653	15	27356										
CCDC13	152206	hgsc.bcm.edu	37	chr3	42799704	42799704	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ccaagggctcctcttggtcgTcagctctgcttttgaggctc	11	13	3	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr3:42799704T>C	ENST00000310232.6	-	2	217	c.134A>G	c.(133-135)gAc>gGc	p.D45G	CCDC13_ENST00000435327.2_5'UTR	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	45										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						CTCTTGGTCGTCAGCTCTGCT	0.498																																					p.D45G		Atlas-SNP	.											.	CCDC13	71	.	0			c.A134G						.						243	199	214					3																	42799704		2203	4300	6503	SO:0001583	missense	152206	exon2			TGGTCGTCAGCTC	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.134A>G	chr3.hg19:g.42799704T>C	ENSP00000309836:p.Asp45Gly	125.0	0.0		104.0	24.0	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	T	7.593	0.671158	0.14776	.	.	ENSG00000244607	ENST00000310232	T	0.23950	1.88	4.59	3.44	0.39384	.	0.686270	0.14217	N	0.333638	T	0.17831	0.0428	L	0.29908	0.895	0.20074	N	0.999932	B;P;B	0.36909	0.206;0.573;0.073	B;B;B	0.36666	0.124;0.23;0.088	T	0.11567	-1.0582	10	0.30854	T	0.27	.	8.0515	0.30581	0.0:0.0972:0.0:0.9028	.	45;45;45	B4DZD2;Q96LI1;Q8IYE1	.;.;CCD13_HUMAN	G	45	ENSP00000309836:D45G	ENSP00000309836:D45G	D	-	2	0	CCDC13	42774708	0.000000	0.05858	0.005000	0.12908	0.006000	0.05464	0.118000	0.15605	0.793000	0.33875	0.533000	0.62120	GAC	.	.		0.498	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		C	42799704	T	C	42799704	3	2	184	1	0	0	0	0	1	0	0	0	2767	1667	58	2	2073	2	CCDC13	3	42799704	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	26387927	42799704	155222726	16	27357										
BAP1	8314	hgsc.bcm.edu	37	chr3	52437795	52437795	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	aggaattgagaggtccttctGggactctttgagcttctcag	12	8	3	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr3:52437795G>A	ENST00000460680.1	-	13	1837	c.1366C>T	c.(1366-1368)Cag>Tag	p.Q456*	BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q438*	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		AGGTCCTTCTGGGACTCTTTG	0.597			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.Q456X	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.C1366T						.						77	79	78					3																	52437795		2203	4300	6503	SO:0001587	stop_gained	8314	exon13			CCTTCTGGGACTC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1366C>T	chr3.hg19:g.52437795G>A	ENSP00000417132:p.Gln456*	42.0	0.0		41.0	19.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Nonsense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	36	5.670842	0.96754	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	.	.	.	6.05	6.05	0.98169	.	0.054436	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	20.6086	0.99469	0.0:0.0:1.0:0.0	.	.	.	.	X	456;438	.	ENSP00000296288:Q438X	Q	-	1	0	BAP1	52412835	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.862000	0.92283	2.880000	0.98712	0.655000	0.94253	CAG	.	.		0.597	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52437795	G	A	52437795	4	1	184	1	0	0	0	0	0	1	0	0	1311	1357	47	3	843	3	BAP1	3	52437795	Nonsense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	9638091	52437795	145584635	17	27358										
BAP1	8314	hgsc.bcm.edu	37	chr3	52441304	52441304	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cactgcactaaggccattctGcttctcagggaggtggcgtg	13	11	2	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr3:52441304G>A	ENST00000460680.1	-	7	937	c.466C>T	c.(466-468)Cag>Tag	p.Q156*	BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q156*	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0	Interaction with HIP2.				anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q156*(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		AGGCCATTCTGCTTCTCAGGG	0.577			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.Q156X	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	BAP1,NS,carcinoma,0,1	BAP1	371	.	1	Substitution - Nonsense(1)	kidney(1)	c.C466T						.						79	81	80					3																	52441304		2203	4300	6503	SO:0001587	stop_gained	8314	exon7			CATTCTGCTTCTC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.466C>T	chr3.hg19:g.52441304G>A	ENSP00000417132:p.Gln156*	182.0	0.0		134.0	50.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Nonsense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	40	8.080308	0.98643	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000470173	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-6.3818	20.3927	0.98949	0.0:0.0:1.0:0.0	.	.	.	.	X	156;156;77	.	ENSP00000296288:Q156X	Q	-	1	0	BAP1	52416344	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.824000	0.99380	2.833000	0.97629	0.655000	0.94253	CAG	.	.		0.577	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52441304	G	A	52441304	4	1	184	1	0	0	0	0	0	1	0	0	1311	1328	46	3	1767	3	BAP1	3	52441304	Nonsense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	3509	52441304	145581126	18	27359										
FEZF2	55079	hgsc.bcm.edu	37	chr3	62358208	62358209	+	In_Frame_Ins	INS	-	-	CCA													0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gggcccccccgccgccgccgINSccgccaccgccgccgccgcc							TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr3:62358208_62358209insCCA	ENST00000283268.3	-	2	629_630	c.335_336insTGG	c.(334-336)ggc>ggTGGc	p.112_112G>GG	FEZF2_ENST00000475839.1_In_Frame_Ins_p.112_112G>GG|FEZF2_ENST00000486811.1_In_Frame_Ins_p.112_112G>GG	NM_018008.3	NP_060478.3	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2	112	Gly-rich.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cerebral cortex GABAergic interneuron migration (GO:0021853)|dendrite development (GO:0016358)|dentate gyrus development (GO:0021542)|forebrain anterior/posterior pattern specification (GO:0021797)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|lung(8)|skin(1)	20		Lung SC(41;0.0262)		BRCA - Breast invasive adenocarcinoma(55;0.000221)|KIRC - Kidney renal clear cell carcinoma(15;0.00834)|Kidney(15;0.00957)		cgccgccgccgccgccaccgcc	0.733																																					p.G112delinsGG	NSCLC(170;1772 2053 12525 15604 23984)	Atlas-INDEL	.											.	FEZF2	46	.	0			c.336_337insTGG						.																																			SO:0001652	inframe_insertion	55079	exon2			.	AF064845	CCDS2897.1	3p21.1	2013-01-08	2006-08-15	2006-08-15	ENSG00000153266	ENSG00000153266		"Zinc fingers, C2H2-type"	13506	protein-coding gene	gene with protein product		607414	"zinc finger protein 312"	ZNF312			Standard	NM_018008		Approved	FLJ10142, FKSG36, TOF, FEZL, Zfp312	uc003dli.2	Q8TBJ5	OTTHUMG00000158705	ENST00000283268.3:c.335_336insTGG	chr3.hg19:g.62358208_62358209insCCA	ENSP00000283268:p.Gly117dup	58.0	0.0		40.0	12.0	NM_018008	A8K349|Q9BZ91|Q9NWB9	In_Frame_Ins	INS	ENST00000283268.3	hg19	CCDS2897.1																																																																																			.	.		0.733	FEZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351813.1	NM_018008		CCA	62358209	-	CCA	62358208	7	5	184	1	0	1	1	0	0	0	0	0	5834	1074	38	0	1059	0	FEZF2	3	62358208	In_Frame_Ins	INS	-	TCGA-DD-AADA-01A-11D-A40R-10	9916904	62358208	135664222	19	27360										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78701075	78701075	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggtgacacagggtttccatgGgcatctgaaaagtcatcttc	11	9	3	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr3:78701075G>A	ENST00000464233.1	-	19	2732	c.2619C>T	c.(2617-2619)gcC>gcT	p.A873A	ROBO1_ENST00000436010.2_Silent_p.A834A|ROBO1_ENST00000467549.1_Silent_p.A837A|ROBO1_ENST00000495273.1_Silent_p.A837A	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	873	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GGTTTCCATGGGCATCTGAAA	0.468																																					p.A873A		Atlas-SNP	.											.	ROBO1	833	.	0			c.C2619T						.						127	125	126					3																	78701075		2000	4170	6170	SO:0001819	synonymous_variant	6091	exon19			TCCATGGGCATCT	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2619C>T	chr3.hg19:g.78701075G>A		113.0	0.0		103.0	35.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.		0.468	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78701075	G	A	78701075	2	1	184	1	0	0	0	0	0	0	0	1	13528	1219	43	3		3	ROBO1	3	78701075	Silent	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	16342867	78701075	119321355	20	27361										
OR5K1	26339	hgsc.bcm.edu	37	chr3	98189208	98189208	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cttcatgtacgttagaccaaAtttgcttgaagaaggggata	10	6	1	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr3:98189208A>C	ENST00000332650.5	+	1	885	c.788A>C	c.(787-789)aAt>aCt	p.N263T		NM_001004736.2	NP_001004736.2	Q8NHB7	OR5K1_HUMAN	olfactory receptor, family 5, subfamily K, member 1	263						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(4)|lung(21)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTTAGACCAAATTTGCTTGAA	0.363																																					p.N263T		Atlas-SNP	.											.	OR5K1	51	.	0			c.A788C						.						86	90	89					3																	98189208		2163	4289	6452	SO:0001583	missense	26339	exon1			GACCAAATTTGCT	X64984	CCDS43115.1	3q11.2	2013-09-23			ENSG00000232382	ENSG00000232382		"GPCR / Class A : Olfactory receptors"	8349	protein-coding gene	gene with protein product						1370859	Standard	NM_001004736		Approved	HTPCRX10, HSHTPCRX10	uc003dsm.3	Q8NHB7	OTTHUMG00000160048	ENST00000332650.5:c.788A>C	chr3.hg19:g.98189208A>C	ENSP00000373193:p.Asn263Thr	204.0	0.0		121.0	36.0	NM_001004736	B9EGY5|Q6IF46	Missense_Mutation	SNP	ENST00000332650.5	hg19	CCDS43115.1	.	.	.	.	.	.	.	.	.	.	A	10.65	1.411050	0.25465	.	.	ENSG00000232382	ENST00000332650	T	0.00076	8.76	4.47	1.97	0.26223	GPCR, rhodopsin-like superfamily (1);	0.326457	0.22045	N	0.065386	T	0.00109	0.0003	N	0.12831	0.26	0.09310	N	1	P	0.41848	0.763	P	0.49421	0.61	T	0.40117	-0.9580	10	0.38643	T	0.18	-17.0415	5.2294	0.15414	0.6584:0.0:0.3416:0.0	.	263	Q8NHB7	OR5K1_HUMAN	T	263	ENSP00000373193:N263T	ENSP00000373193:N263T	N	+	2	0	OR5K1	99671898	0.000000	0.05858	0.998000	0.56505	0.977000	0.68977	-0.293000	0.08320	0.690000	0.31570	0.496000	0.49642	AAT	.	.		0.363	OR5K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359019.1			C	98189208	A	C	98189208	3	2	184	1	0	0	0	0	1	0	0	0	11175	101	4	5	790	5	OR5K1	3	98189208	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	19488133	98189208	99833222	21	27362										
POLQ	10721	hgsc.bcm.edu	37	chr3	121228964	121228964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cacacaggcctcaatcgctcCaagctgaacagactcttgat	7	14	2	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr3:121228964C>T	ENST00000264233.5	-	11	1866	c.1738G>A	c.(1738-1740)Gga>Aga	p.G580R		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	580					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TCAATCGCTCCAAGCTGAACA	0.433								DNA polymerases (catalytic subunits)																													p.G580R	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G1738A						.						207	177	187					3																	121228964		2203	4300	6503	SO:0001583	missense	10721	exon11			TCGCTCCAAGCTG	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.1738G>A	chr3.hg19:g.121228964C>T	ENSP00000264233:p.Gly580Arg	138.0	0.0		78.0	25.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.686392	0.88639	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.40756	1.02	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.44435	0.1293	L	0.57536	1.79	0.58432	D	0.999999	B	0.15719	0.014	B	0.17098	0.017	T	0.44190	-0.9344	10	0.66056	D	0.02	.	17.9923	0.89172	0.0:1.0:0.0:0.0	.	580	O75417	DPOLQ_HUMAN	R	203;580;716	ENSP00000264233:G580R	ENSP00000264233:G580R	G	-	1	0	POLQ	122711654	1.000000	0.71417	0.998000	0.56505	0.872000	0.50106	7.368000	0.79567	2.236000	0.73375	0.460000	0.39030	GGA	.	.		0.433	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121228964	C	T	121228964	3	4	184	1	0	0	0	0	1	0	0	0	12217	603	21	3	6114	3	POLQ	3	121228964	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	23039756	121228964	76793466	22	27363										
WDR49	151790	hgsc.bcm.edu	37	chr3	167293897	167293897	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggggaaagaacaagctatccTctggatggacagctggtgtt	14	7	1	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr3:167293897T>A	ENST00000308378.3	-	4	600	c.295A>T	c.(295-297)Agg>Tgg	p.R99W	WDR49_ENST00000453925.2_Missense_Mutation_p.R152W|WDR49_ENST00000479765.1_Missense_Mutation_p.R440W|WDR49_ENST00000476376.1_5'Flank	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	99										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						CAAGCTATCCTCTGGATGGAC	0.393																																					p.R99W		Atlas-SNP	.											.	WDR49	188	.	0			c.A295T						.						86	83	84					3																	167293897		2203	4300	6503	SO:0001583	missense	151790	exon4			CTATCCTCTGGAT	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.295A>T	chr3.hg19:g.167293897T>A	ENSP00000311343:p.Arg99Trp	152.0	0.0		95.0	14.0	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	hg19	CCDS3201.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.99|19.99	3.928693|3.928693	0.73327|0.73327	.|.	.|.	ENSG00000174776|ENSG00000174776	ENST00000472600|ENST00000308378;ENST00000479765;ENST00000453925	.|T;T;T	.|0.46819	.|1.52;1.79;0.86	5.76|5.76	5.76|5.76	0.90799|0.90799	.|WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.099203|0.099203	0.64402|0.64402	D|D	0.000002|0.000002	T|T	0.64316|0.64316	0.2587|0.2587	M|M	0.67953|0.67953	2.075|2.075	0.25331|0.25331	N|N	0.989037|0.989037	.|D;D;D	.|0.89917	.|1.0;1.0;0.999	.|D;D;D	.|0.85130	.|0.997;0.997;0.987	T|T	0.60712|0.60712	-0.7209|-0.7209	6|10	.|0.62326	.|D	.|0.03	.|.	9.852|9.852	0.41061|0.41061	0.0:0.0784:0.0:0.9216|0.0:0.0784:0.0:0.9216	.|.	.|152;440;99	.|E7EQK3;E9PDB0;Q8IV35	.|.;.;WDR49_HUMAN	S|W	163|99;440;152	.|ENSP00000311343:R99W;ENSP00000419749:R440W;ENSP00000410863:R152W	.|ENSP00000311343:R99W	R|R	-|-	3|1	2|2	WDR49|WDR49	168776591|168776591	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.448000|2.448000	0.44926|0.44926	2.219000|2.219000	0.72066|0.72066	0.529000|0.529000	0.55759|0.55759	AGA|AGG	.	.		0.393	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		A	167293897	T	A	167293897	3	1	184	1	0	0	0	0	1	0	0	0	17317	1550	54	4	1846	4	WDR49	3	167293897	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	46064933	167293897	30728533	23	27364										
TMEM41A	90407	hgsc.bcm.edu	37	chr3	185213096	185213096	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gcccaaacaaggcaccagctAaaacattctgcaaataaaac	5	12	1	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr3:185213096A>G	ENST00000421852.1	-	3	376	c.281T>C	c.(280-282)tTa>tCa	p.L94S	TMEM41A_ENST00000296254.3_Intron|TMEM41A_ENST00000475480.1_5'UTR	NM_080652.3	NP_542383.1	Q96HV5	TM41A_HUMAN	transmembrane protein 41A	94						integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)|skin(1)	4	all_cancers(143;7.78e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			GGCACCAGCTAAAACATTCTG	0.527																																					p.L94S		Atlas-SNP	.											.	TMEM41A	18	.	0			c.T281C						.						62	58	59					3																	185213096		2203	4300	6503	SO:0001583	missense	90407	exon3			CCAGCTAAAACAT	BC019884	CCDS3271.1	3q27.2	2006-04-12			ENSG00000163900	ENSG00000163900			30544	protein-coding gene	gene with protein product						12975309	Standard	NM_080652		Approved	MGC15397	uc003fpj.2	Q96HV5	OTTHUMG00000156660	ENST00000421852.1:c.281T>C	chr3.hg19:g.185213096A>G	ENSP00000406885:p.Leu94Ser	112.0	0.0		118.0	38.0	NM_080652	A8K4B3|D3DNU2|Q6ZMJ0	Missense_Mutation	SNP	ENST00000421852.1	hg19	CCDS3271.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.937362	0.92458	.	.	ENSG00000163900	ENST00000421852	.	.	.	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000001	D	0.84593	0.5506	M	0.88377	2.95	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86809	0.1997	9	0.54805	T	0.06	-1.0592	16.1973	0.82040	1.0:0.0:0.0:0.0	.	94	Q96HV5	TM41A_HUMAN	S	94	.	ENSP00000406885:L94S	L	-	2	0	TMEM41A	186695790	0.994000	0.37717	0.998000	0.56505	0.994000	0.84299	9.231000	0.95317	2.222000	0.72286	0.533000	0.62120	TTA	.	.		0.527	TMEM41A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345174.1	NM_080652		G	185213096	A	G	185213096	3	3	184	1	0	0	0	0	1	0	0	0	16179	372	13	2	525	2	TMEM41A	3	185213096	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	17919199	185213096	12809334	24	27365										
GNPDA2	132789	hgsc.bcm.edu	37	chr4	44713036	44713036	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gttggcacttttgataaatcTccatcaaaatatttggcatt	6	7	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr4:44713036T>A	ENST00000295448.3	-	5	684	c.528A>T	c.(526-528)ggA>ggT	p.G176G	GNPDA2_ENST00000511187.1_Intron|GNPDA2_ENST00000507534.1_Silent_p.G106G|GNPDA2_ENST00000509756.1_Silent_p.G176G|GNPDA2_ENST00000507917.1_Silent_p.G142G	NM_138335.2	NP_612208.1	Q8TDQ7	GNPI2_HUMAN	glucosamine-6-phosphate deaminase 2	176					carbohydrate metabolic process (GO:0005975)|N-acetylglucosamine metabolic process (GO:0006044)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	glucosamine-6-phosphate deaminase activity (GO:0004342)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(1)|lung(7)|ovary(1)	11						TTGATAAATCTCCATCAAAAT	0.383																																					p.G176G	Colon(54;743 1010 7604 16453 19544)	Atlas-SNP	.											.	GNPDA2	28	.	0			c.A528T						.						123	116	119					4																	44713036		2203	4300	6503	SO:0001819	synonymous_variant	132789	exon5			TAAATCTCCATCA	AF247786	CCDS3469.1, CCDS59472.1, CCDS59473.1	4p13	2006-04-12			ENSG00000163281	ENSG00000163281	3.5.99.6		21526	protein-coding gene	gene with protein product	"glucosamine-6-phosphate isomerase"	613222				12965206	Standard	NM_001270880		Approved	SB52	uc003gwy.4	Q8TDQ7	OTTHUMG00000099415	ENST00000295448.3:c.528A>T	chr4.hg19:g.44713036T>A		109.0	0.0		84.0	20.0	NM_138335	B4DJF3|Q2VYF1|Q59EA7|Q8NCZ8|Q96BJ4|Q96NC6	Silent	SNP	ENST00000295448.3	hg19	CCDS3469.1																																																																																			.	.		0.383	GNPDA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216874.3	NM_138335		A	44713036	T	A	44713036	2	1	184	1	0	0	0	0	0	0	0	1	6551	1538	54	4		4	GNPDA2	4	44713036	Silent	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10		44713036	146441240	25	27366										
ALB	213	hgsc.bcm.edu	37	chr4	74279249	74279251	+	In_Frame_Del	DEL	ATG	ATG	-													0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ctgcattgccgaagtggaaaAtgatgagatgcctgctgact							TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr4:74279249_74279251delATG	ENST00000503124.1	+	6	713_715	c.506_508delATG	c.(505-510)aatgat>aat	p.D170del	ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_In_Frame_Del_p.D205del|ALB_ENST00000415165.2_In_Frame_Del_p.D128del|ALB_ENST00000509063.1_In_Frame_Del_p.D320del|ALB_ENST00000295897.4_In_Frame_Del_p.D320del			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GAAGTGGAAAATGATGAGATGCC	0.409																																					p.319_319del		Atlas-INDEL	.											.	ALB	132	.	0			c.955_957del						.																																			SO:0001651	inframe_deletion	213	exon8			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.506_508delATG	chr4.hg19:g.74279252_74279254delATG	ENSP00000421027:p.Asp170del	180.0	0.0		128.0	37.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	In_Frame_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.409	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74279251	ATG	-	74279249	7	5	184	1	0	1	0	1	0	0	0	0	486	101	4	0	986	0	ALB	4	74279249	In_Frame_Del	DEL	ATG	TCGA-DD-AADA-01A-11D-A40R-10	29566213	74279249	116875027	26	27367										
QRFPR	84109	hgsc.bcm.edu	37	chr4	122251606	122251606	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tcaatcatcatatggacaacAtggaatggtgcccagcacac	8	11	3	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr4:122251606A>T	ENST00000394427.2	-	5	1281	c.870T>A	c.(868-870)caT>caA	p.H290Q	QRFPR_ENST00000334383.5_Missense_Mutation_p.C253S|Y_RNA_ENST00000384419.1_RNA	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	290					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						TATGGACAACATGGAATGGTG	0.393																																					p.H290Q		Atlas-SNP	.											.	QRFPR	65	.	0			c.T870A						.						144	134	138					4																	122251606		2203	4300	6503	SO:0001583	missense	84109	exon5			GACAACATGGAAT	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"GPCR / Class A : RF amide peptide receptors"	15565	protein-coding gene	gene with protein product		606925	"G protein-coupled receptor 103"	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.870T>A	chr4.hg19:g.122251606A>T	ENSP00000377948:p.His290Gln	71.0	0.0		48.0	10.0	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	hg19	CCDS3719.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.80|15.80	2.940031|2.940031	0.52972|0.52972	.|.	.|.	ENSG00000186867|ENSG00000186867	ENST00000334383|ENST00000394427	T|T	0.69806|0.39229	-0.43|1.09	5.81|5.81	-5.91|-5.91	0.02269|0.02269	.|GPCR, rhodopsin-like superfamily (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.55625|0.55625	0.1932|0.1932	M|M	0.69463|0.69463	2.115|2.115	0.09310|0.09310	N|N	0.999997|0.999997	.|D	.|0.89917	.|1.0	.|D	.|0.85130	.|0.997	T|T	0.56763|0.56763	-0.7925|-0.7925	7|10	0.87932|0.31617	D|T	0|0.26	.|.	17.1154|17.1154	0.86687|0.86687	0.4553:0.0:0.5447:0.0|0.4553:0.0:0.5447:0.0	.|.	.|290	.|Q96P65	.|QRFPR_HUMAN	S|Q	253|290	ENSP00000335610:C253S|ENSP00000377948:H290Q	ENSP00000335610:C253S|ENSP00000377948:H290Q	C|H	-|-	1|3	0|2	QRFPR|QRFPR	122471056|122471056	0.000000|0.000000	0.05858|0.05858	0.011000|0.011000	0.14972|0.14972	0.961000|0.961000	0.63080|0.63080	-0.361000|-0.361000	0.07612|0.07612	-1.457000|-1.457000	0.01919|0.01919	0.533000|0.533000	0.62120|0.62120	TGT|CAT	.	.		0.393	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		T	122251606	A	T	122251606	3	4	184	1	0	0	0	0	1	0	0	0	12893	214	8	4	433	4	QRFPR	4	122251606	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	47972357	122251606	68902670	27	27368										
FAT4	79633	hgsc.bcm.edu	37	chr4	126398471	126398471	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	acccagccaagctttggcagCacaaggcatcctagatcagt	9	13	1	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr4:126398471C>T	ENST00000394329.3	+	13	12468	c.12455C>T	c.(12454-12456)gCa>gTa	p.A4152V	FAT4_ENST00000335110.5_Missense_Mutation_p.A2415V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4152	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GCTTTGGCAGCACAAGGCATC	0.398																																					p.A4152V		Atlas-SNP	.											.	FAT4	1752	.	0			c.C12455T						.						133	131	132					4																	126398471		2203	4300	6503	SO:0001583	missense	79633	exon13			TGGCAGCACAAGG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.12455C>T	chr4.hg19:g.126398471C>T	ENSP00000377862:p.Ala4152Val	97.0	0.0		78.0	14.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	18.00	3.525397	0.64747	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.78364	-1.17;-1.17	5.54	4.69	0.59074	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.34110	U	0.004257	T	0.61009	0.2313	N	0.08118	0	0.45354	D	0.998349	B;B;B	0.14805	0.004;0.002;0.011	B;B;B	0.14023	0.01;0.003;0.01	T	0.57225	-0.7848	10	0.46703	T	0.11	.	14.2117	0.65769	0.0:0.9282:0.0:0.0718	.	2415;4152;4152	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	V	4152;2415	ENSP00000377862:A4152V;ENSP00000335169:A2415V	ENSP00000335169:A2415V	A	+	2	0	FAT4	126617921	1.000000	0.71417	0.865000	0.33974	0.790000	0.44656	5.943000	0.70211	1.328000	0.45358	0.650000	0.86243	GCA	.	.		0.398	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126398471	C	T	126398471	3	4	184	1	0	0	0	0	1	0	0	0	5700	710	25	3	12505	3	FAT4	4	126398471	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	4146865	126398471	64755805	28	27369										
PHF17	79960	hgsc.bcm.edu	37	chr4	129792936	129792936	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	atcttttaaacagagtcacaAgcctctcaggtccacagatg	7	11	3	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr4:129792936A>G	ENST00000226319.6	+	11	2328	c.2048A>G	c.(2047-2049)aAg>aGg	p.K683R	PHF17_ENST00000512960.1_Missense_Mutation_p.K683R|PHF17_ENST00000452328.2_Missense_Mutation_p.K671R	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CAGAGTCACAAGCCTCTCAGG	0.498																																					p.K683R		Atlas-SNP	.											.	PHF17	63	.	0			c.A2048G						.						52	52	52					4																	129792936		2203	4300	6503	SO:0001583	missense	79960	exon11			GTCACAAGCCTCT																												ENST00000226319.6:c.2048A>G	chr4.hg19:g.129792936A>G	ENSP00000226319:p.Lys683Arg	236.0	0.0		184.0	24.0	NM_199320		Missense_Mutation	SNP	ENST00000226319.6	hg19	CCDS34062.1	.	.	.	.	.	.	.	.	.	.	A	12.69	2.014073	0.35511	.	.	ENSG00000077684	ENST00000226319;ENST00000452328;ENST00000512960;ENST00000535321	T;T;T	0.44881	0.91;0.93;0.91	4.59	4.59	0.56863	.	0.341890	0.32578	N	0.005914	T	0.22166	0.0534	N	0.12746	0.255	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.06405	0.001;0.002	T	0.08764	-1.0706	9	.	.	.	.	9.0514	0.36378	0.9179:0.0:0.0821:0.0	.	671;683	Q6IE81-2;Q6IE81	.;JADE1_HUMAN	R	683;671;683;683	ENSP00000226319:K683R;ENSP00000388015:K671R;ENSP00000425730:K683R	.	K	+	2	0	PHF17	130012386	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.163000	0.58183	2.058000	0.61347	0.533000	0.62120	AAG	.	.		0.498	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1			G	129792936	A	G	129792936	3	3	184	1	0	0	0	0	1	0	0	0	11837	72	3	2	2113	2	PHF17	4	129792936	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	3394465	129792936	61361340	29	27370										
CLCN3	1182	hgsc.bcm.edu	37	chr4	170618374	170618374	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tcctctcaaaactttatggaGatcattttttgctgctttag	6	8	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr4:170618374G>T	ENST00000513761.1	+	9	1611	c.1052G>T	c.(1051-1053)aGa>aTa	p.R351I	CLCN3_ENST00000504131.2_Missense_Mutation_p.R334I|CLCN3_ENST00000347613.4_Missense_Mutation_p.R351I|CLCN3_ENST00000360642.3_Missense_Mutation_p.R324I	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	351					chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)			breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		ACTTTATGGAGATCATTTTTT	0.308																																					p.R351I		Atlas-SNP	.											.	CLCN3	85	.	0			c.G1052T						.						78	79	79					4																	170618374		2203	4300	6503	SO:0001583	missense	1182	exon9			TATGGAGATCATT	X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.1052G>T	chr4.hg19:g.170618374G>T	ENSP00000424603:p.Arg351Ile	206.0	0.0		139.0	35.0	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	hg19	CCDS34101.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.6|28.6	4.932780|4.932780	0.92458|0.92458	.|.	.|.	ENSG00000109572|ENSG00000109572	ENST00000515420|ENST00000513761;ENST00000347613;ENST00000360642;ENST00000504131;ENST00000507875	.|D;D;D;D;D	.|0.93076	.|-3.16;-3.16;-3.16;-3.16;-3.16	5.84|5.84	5.84|5.84	0.93424|0.93424	.|Chloride channel, core (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.98204|0.98204	0.9406|0.9406	H|H	0.97415|0.97415	4|4	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;0.994;1.0;1.0;0.999	.|D;D;D;D;D	.|0.91635	.|0.999;0.987;0.992;0.992;0.993	D|D	0.98883|0.98883	1.0770|1.0770	5|10	.|0.87932	.|D	.|0	-11.6385|-11.6385	20.1392|20.1392	0.98050|0.98050	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|324;334;324;351;351	.|B7Z932;B9EGJ9;E9PE15;P51790;P51790-2	.|.;.;.;CLCN3_HUMAN;.	Y|I	33|351;351;324;334;324	.|ENSP00000424603:R351I;ENSP00000261514:R351I;ENSP00000353857:R324I;ENSP00000424540:R334I;ENSP00000425323:R324I	.|ENSP00000261514:R351I	D|R	+|+	1|2	0|0	CLCN3|CLCN3	170854949|170854949	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.869000|9.869000	0.99810|0.99810	2.765000|2.765000	0.95021|0.95021	0.557000|0.557000	0.71058|0.71058	GAT|AGA	.	.		0.308	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			T	170618374	G	T	170618374	3	4	184	1	0	0	0	0	1	0	0	0	3466	942	33	3	1082	3	CLCN3	4	170618374	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	40825438	170618374	20535902	30	27371										
NNT	23530	hgsc.bcm.edu	37	chr5	43649288	43649288	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tttgggcattgcggctcccaAtctagccttttctcagatgg	10	11	2	1	rs199609080		TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr5:43649288A>G	ENST00000264663.5	+	11	1705	c.1484A>G	c.(1483-1485)aAt>aGt	p.N495S	NNT_ENST00000512996.2_Missense_Mutation_p.N364S|NNT_ENST00000344920.4_Missense_Mutation_p.N495S	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	495					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					GCGGCTCCCAATCTAGCCTTT	0.493																																					p.N495S		Atlas-SNP	.											.	NNT	92	.	0			c.A1484G						.						351	326	335					5																	43649288		2203	4300	6503	SO:0001583	missense	23530	exon11			CTCCCAATCTAGC	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.1484A>G	chr5.hg19:g.43649288A>G	ENSP00000264663:p.Asn495Ser	161.0	0.0		120.0	40.0	NM_182977	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	hg19	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	A	12.56	1.973580	0.34848	.	.	ENSG00000112992	ENST00000264663;ENST00000344920;ENST00000512996	D;D;D	0.95377	-3.69;-3.69;-3.56	5.24	4.0	0.46444	.	0.180348	0.64402	D	0.000018	D	0.85097	0.5619	N	0.01809	-0.71	0.43959	D	0.996634	B	0.29085	0.232	B	0.26614	0.071	D	0.83414	0.0029	10	0.27082	T	0.32	-8.9477	11.8269	0.52271	0.8536:0.1464:0.0:0.0	.	495	Q13423	NNTM_HUMAN	S	495;495;364	ENSP00000264663:N495S;ENSP00000343873:N495S;ENSP00000426343:N364S	ENSP00000264663:N495S	N	+	2	0	NNT	43685045	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.861000	0.62969	1.993000	0.58246	0.524000	0.50904	AAT	.	A|0.999;G|0.001		0.493	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		G	43649288	A	G	43649288	3	3	184	1	0	0	0	0	1	0	0	0	10519	101	4	2	1522	2	NNT	5	43649288	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10		43649288	137265972	31	27372										
RGNEF	64283	hgsc.bcm.edu	37	chr5	73048892	73048892	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ccaatcgcctcacagcctgcAgccaccagaccctgctgacc	7	20	1	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr5:73048892A>T	ENST00000426542.2	+	3	360	c.340A>T	c.(340-342)Agc>Tgc	p.S114C	ARHGEF28_ENST00000545377.1_Missense_Mutation_p.S114C|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.S114C|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.S114C|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.S114C|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.S114C			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	114					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										CACAGCCTGCAGCCACCAGAC	0.617																																					p.S114C		Atlas-SNP	.											.	.	.	.	0			c.A340T						.						37	40	39					5																	73048892		2150	4260	6410	SO:0001583	missense	64283	exon4			GCCTGCAGCCACC		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.340A>T	chr5.hg19:g.73048892A>T	ENSP00000412175:p.Ser114Cys	81.0	0.0		57.0	18.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990050	0.74589	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542	T;T;T;T;T;T	0.11385	3.02;3.02;3.02;2.78;3.02;3.02	5.82	5.82	0.92795	.	.	.	.	.	T	0.30448	0.0765	L	0.57536	1.79	0.34904	D	0.746801	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.987;0.987;0.999;0.991	T	0.36138	-0.9760	9	0.87932	D	0	.	15.1644	0.72811	1.0:0.0:0.0:0.0	.	114;114;114;114	Q8N1W1;E9PC75;Q8N1W1-2;Q8N1W1-4	RGNEF_HUMAN;.;.;.	C	114	ENSP00000296794:S114C;ENSP00000441913:S114C;ENSP00000441436:S114C;ENSP00000287898:S114C;ENSP00000411459:S114C;ENSP00000412175:S114C	ENSP00000287898:S114C	S	+	1	0	RP11-428C6.1	73084648	1.000000	0.71417	0.956000	0.39512	0.549000	0.35272	6.112000	0.71547	2.225000	0.72522	0.459000	0.35465	AGC	.	.		0.617	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			T	73048892	A	T	73048892	3	4	184	1	0	0	0	0	1	0	0	0	13298	188	7	4	350	4	RGNEF	5	73048892	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	29399604	73048892	107866368	32	27373										
AQPEP	206338	hgsc.bcm.edu	37	chr5	115298661	115298661	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggagctgtggccgcagctgaGgcccgacgagcttccggccg	17	14	0	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr5:115298661G>A	ENST00000357872.4	+	1	471	c.347G>A	c.(346-348)aGg>aAg	p.R116K	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		116						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CCGCAGCTGAGGCCCGACGAG	0.697																																					p.R116K		Atlas-SNP	.											.	.	.	.	0			c.G347A						.						41	47	45					5																	115298661		2202	4298	6500	SO:0001583	missense	0	exon1			AGCTGAGGCCCGA																												ENST00000357872.4:c.347G>A	chr5.hg19:g.115298661G>A	ENSP00000350541:p.Arg116Lys	133.0	0.0		77.0	15.0	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	hg19	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	G	0.066	-1.213682	0.01555	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.03982	3.74	4.71	-1.58	0.08479	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.399189	0.18435	N	0.141301	T	0.01940	0.0061	N	0.02865	-0.47	0.29511	N	0.854174	P	0.34462	0.454	B	0.38156	0.266	T	0.47289	-0.9129	10	0.09843	T	0.71	.	8.7081	0.34367	0.5983:0.0:0.4017:0.0	.	116	Q6Q4G3	AMPQ_HUMAN	K	116	ENSP00000350541:R116K	ENSP00000350541:R116K	R	+	2	0	AC010282.1	115326560	0.000000	0.05858	0.439000	0.26833	0.070000	0.16714	-0.523000	0.06230	-0.152000	0.11156	0.650000	0.86243	AGG	.	.		0.697	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			A	115298661	G	A	115298661	3	1	184	1	0	0	0	0	1	0	0	0	834	1000	35	3	349	3	AQPEP	5	115298661	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	42249769	115298661	65616599	33	27374										
SPOCK1	6695	hgsc.bcm.edu	37	chr5	136476319	136476319	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	agggcggtctggtagtcctgGgtcacacacactttgtgagg	15	9	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr5:136476319G>A	ENST00000394945.1	-	4	466	c.297C>T	c.(295-297)acC>acT	p.T99T	SPOCK1_ENST00000282223.7_Silent_p.T99T	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	99					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GGTAGTCCTGGGTCACACACA	0.612																																					p.T99T		Atlas-SNP	.											.	SPOCK1	58	.	0			c.C297T						.						75	61	66					5																	136476319		2203	4300	6503	SO:0001819	synonymous_variant	6695	exon4			GTCCTGGGTCACA	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.297C>T	chr5.hg19:g.136476319G>A		115.0	0.0		91.0	11.0	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Silent	SNP	ENST00000394945.1	hg19	CCDS4191.1																																																																																			.	.		0.612	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		A	136476319	G	A	136476319	2	1	184	1	0	0	0	0	0	0	0	1	15094	1219	43	3		3	SPOCK1	5	136476319	Silent	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	21177658	136476319	44438941	34	27375										
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140176112	140176112	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggcaaggtgtacgcgctgcaGccgctggaccacgaggaagt	16	11	0	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr5:140176112G>T	ENST00000526136.1	+	1	1563	c.1563G>T	c.(1561-1563)caG>caT	p.Q521H	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Missense_Mutation_p.Q521H|PCDHA2_ENST00000520672.2_Missense_Mutation_p.Q521H	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	521	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGCGCTGCAGCCGCTGGACC	0.692																																					p.Q521H		Atlas-SNP	.											.	PCDHA2	404	.	0			c.G1563T						.						58	63	62					5																	140176112		2203	4293	6496	SO:0001583	missense	56146	exon1			GCTGCAGCCGCTG	AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"Cadherins / Protocadherins : Clustered"	8668	other	complex locus constituent	"KIAA0345-like 12"	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.1563G>T	chr5.hg19:g.140176112G>T	ENSP00000431748:p.Gln521His	110.0	0.0		101.0	26.0	NM_031495	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	hg19	CCDS54914.1	.	.	.	.	.	.	.	.	.	.	g	15.35	2.808775	0.50421	.	.	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.52754	0.65;0.65;0.65	3.88	3.0	0.34707	Cadherin (5);Cadherin-like (1);	0.000000	0.37955	U	0.001876	T	0.50939	0.1645	L	0.35341	1.055	0.22620	N	0.998924	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.993;0.998;0.993	T	0.30446	-0.9978	10	0.56958	D	0.05	.	5.228	0.15406	0.0845:0.1409:0.6294:0.1451	.	521;521;521	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	H	521	ENSP00000430584:Q521H;ENSP00000367372:Q521H;ENSP00000431748:Q521H	ENSP00000367372:Q521H	Q	+	3	2	PCDHA2	140156296	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-0.411000	0.07142	0.767000	0.33267	0.644000	0.83932	CAG	.	.		0.692	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		T	140176112	G	T	140176112	3	4	184	1	0	0	0	0	1	0	0	0	11533	962	34	3	1565	3	PCDHA2	5	140176112	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	3699793	140176112	40739148	35	27376										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140432819	140432819	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gaggcaggctacctagtgacCaaagtggtggctgtggatgg	17	7	0	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr5:140432819C>A	ENST00000306549.3	+	1	1841	c.1764C>A	c.(1762-1764)acC>acA	p.T588T		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	588	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T588T(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACCTAGTGACCAAAGTGGTGG	0.483																																					p.T588T		Atlas-SNP	.											PCDHB1,NS,haematopoietic_neoplasm,0,1	PCDHB1	148	.	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1764A						.						85	76	79					5																	140432819		2203	4300	6503	SO:0001819	synonymous_variant	29930	exon1			AGTGACCAAAGTG	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1764C>A	chr5.hg19:g.140432819C>A		130.0	1.0		88.0	31.0	NM_013340	Q2M257	Silent	SNP	ENST00000306549.3	hg19	CCDS4243.1																																																																																			.	.		0.483	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		A	140432819	C	A	140432819	2	1	184	1	0	0	0	0	0	0	0	1	11543	581	21	3		3	PCDHB1	5	140432819	Silent	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	256707	140432819	40482441	36	27377										
PDE6A	5145	hgsc.bcm.edu	37	chr5	149323845	149323845	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tgtccaaagggaagacgatcTcttggtcgggcatcaccagg	13	10	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr5:149323845T>A	ENST00000255266.5	-	1	511	c.392A>T	c.(391-393)gAg>gTg	p.E131V		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	131	GAF 1.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	GAAGACGATCTCTTGGTCGGG	0.557																																					p.E131V		Atlas-SNP	.											.	PDE6A	98	.	0			c.A392T						.						139	121	127					5																	149323845		2203	4300	6503	SO:0001583	missense	5145	exon1			ACGATCTCTTGGT		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.392A>T	chr5.hg19:g.149323845T>A	ENSP00000255266:p.Glu131Val	102.0	0.0		84.0	31.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.618201	0.87359	.	.	ENSG00000132915	ENST00000255266	T	0.70045	-0.45	5.26	5.26	0.73747	GAF (2);	0.000000	0.85682	D	0.000000	T	0.82259	0.4998	M	0.83118	2.625	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	D	0.84959	0.0876	10	0.72032	D	0.01	.	13.4185	0.60982	0.0:0.0:0.0:1.0	.	131	P16499	PDE6A_HUMAN	V	131	ENSP00000255266:E131V	ENSP00000255266:E131V	E	-	2	0	PDE6A	149304038	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	7.993000	0.88291	2.114000	0.64651	0.459000	0.35465	GAG	.	.		0.557	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			A	149323845	T	A	149323845	3	1	184	1	0	0	0	0	1	0	0	0	11654	1551	54	4	2278	4	PDE6A	5	149323845	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	8891026	149323845	31591415	37	27378										
LRRC16A	55604	hgsc.bcm.edu	37	chr6	25594713	25594713	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggggagagtggatgaaggtgTagatgaattttttaccaaga	15	2	0	5			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr6:25594713T>C	ENST00000329474.6	+	32	3445	c.3077T>C	c.(3076-3078)gTa>gCa	p.V1026A		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1026	Inhibits capping activity of CAPZA2. {ECO:0000250}.				actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						GATGAAGGTGTAGATGAATTT	0.358																																					p.V1026A		Atlas-SNP	.											.	LRRC16A	168	.	0			c.T3077C						.						145	135	138					6																	25594713		1881	4121	6002	SO:0001583	missense	55604	exon32			AAGGTGTAGATGA	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"	609593	"leucine rich repeat containing 16"	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.3077T>C	chr6.hg19:g.25594713T>C	ENSP00000331983:p.Val1026Ala	172.0	0.0		172.0	74.0	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	hg19	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.689294	0.88735	.	.	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.58358	0.34	5.26	5.26	0.73747	.	0.060906	0.64402	D	0.000003	T	0.57740	0.2074	M	0.65975	2.015	0.80722	D	1	D;D;D	0.67145	0.992;0.996;0.989	P;P;P	0.58077	0.764;0.764;0.832	T	0.60475	-0.7256	10	0.45353	T	0.12	.	15.4642	0.75387	0.0:0.0:0.0:1.0	.	1026;1026;1026	Q5VZK9;B2RTQ5;Q5VZK9-2	LR16A_HUMAN;.;.	A	1026	ENSP00000331983:V1026A	ENSP00000331983:V1026A	V	+	2	0	LRRC16A	25702692	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.272000	0.78516	2.104000	0.64026	0.455000	0.32223	GTA	.	.		0.358	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640		C	25594713	T	C	25594713	3	2	184	1	0	0	0	0	1	0	0	0	8980	1638	57	2	3203	2	LRRC16A	6	25594713	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10		25594713	145520354	38	27379										
ZBTB12	221527	hgsc.bcm.edu	37	chr6	31868735	31868735	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	agggcattccggcatttctcCaccacgtgctccatctgcag	9	15	2	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr6:31868735C>T	ENST00000375527.2	-	2	523	c.348G>A	c.(346-348)gtG>gtA	p.V116V	C2_ENST00000469372.1_Intron|C2_ENST00000452323.2_5'Flank	NM_181842.2	NP_862825.1	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(5)|prostate(1)|skin(1)	10						GGCATTTCTCCACCACGTGCT	0.562																																					p.V116V		Atlas-SNP	.											.	ZBTB12	25	.	0			c.G348A						.						78	74	75					6																	31868735		2203	4300	6503	SO:0001819	synonymous_variant	221527	exon2			TTTCTCCACCACG	BC043609	CCDS4727.1	6p21.31	2013-01-08	2004-04-15	2004-04-16	ENSG00000204366	ENSG00000204366		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	19066	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 46"	C6orf46		9545376	Standard	NM_181842		Approved	G10, NG35, D6S59E	uc003nyd.1	Q9Y330	OTTHUMG00000031169	ENST00000375527.2:c.348G>A	chr6.hg19:g.31868735C>T		110.0	0.0		129.0	24.0	NM_181842	B0UY00|Q5JQ98	Silent	SNP	ENST00000375527.2	hg19	CCDS4727.1																																																																																			.	.		0.562	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842		T	31868735	C	T	31868735	2	4	184	1	0	0	0	0	0	0	0	1	17540	581	21	3		3	ZBTB12	6	31868735	Silent	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	6274022	31868735	139246332	39	27380										
LRFN2	57497	hgsc.bcm.edu	37	chr6	40399807	40399807	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	caccactgtcctgagatgtgGtgatgaagatgtccagggtg	14	8	0	4			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr6:40399807G>T	ENST00000338305.6	-	2	1588	c.1046C>A	c.(1045-1047)aCc>aAc	p.T349N		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	349	Ig-like.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					CTGAGATGTGGTGATGAAGAT	0.607																																					p.T349N		Atlas-SNP	.											.	LRFN2	133	.	0			c.C1046A						.						63	46	52					6																	40399807		2202	4299	6501	SO:0001583	missense	57497	exon2			GATGTGGTGATGA	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	21226	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 2"	612808	"KIAA1246"	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.1046C>A	chr6.hg19:g.40399807G>T	ENSP00000345985:p.Thr349Asn	79.0	0.0		89.0	38.0	NM_020737	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	hg19	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.946224	0.73672	.	.	ENSG00000156564	ENST00000338305	T	0.67345	-0.26	5.43	5.43	0.79202	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.090535	0.85682	D	0.000000	T	0.81711	0.4880	M	0.87381	2.88	0.80722	D	1	D	0.63880	0.993	D	0.68621	0.959	D	0.84802	0.0785	10	0.87932	D	0	.	17.8027	0.88592	0.0:0.0:1.0:0.0	.	349	Q9ULH4	LRFN2_HUMAN	N	349	ENSP00000345985:T349N	ENSP00000345985:T349N	T	-	2	0	LRFN2	40507785	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.853000	0.99521	2.555000	0.86185	0.655000	0.94253	ACC	.	.		0.607	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		T	40399807	G	T	40399807	3	4	184	1	0	0	0	0	1	0	0	0	8947	1261	44	3	1331	3	LRFN2	6	40399807	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	8531072	40399807	130715260	40	27381										
AIM1	202	hgsc.bcm.edu	37	chr6	106967348	106967348	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	atagaaaccaaagttaccgtCtcggaagaagagattctgcc	9	9	2	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr6:106967348C>A	ENST00000369066.3	+	2	1528	c.1041C>A	c.(1039-1041)gtC>gtA	p.V347V		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		AAGTTACCGTCTCGGAAGAAG	0.443																																					p.V347V		Atlas-SNP	.											.	AIM1	161	.	0			c.C1041A						.						82	89	86					6																	106967348		2203	4300	6503	SO:0001819	synonymous_variant	202	exon2			TACCGTCTCGGAA	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1041C>A	chr6.hg19:g.106967348C>A		232.0	0.0		172.0	51.0	NM_001624	Q6P2P0|Q9BTM3	Silent	SNP	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.		0.443	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			A	106967348	C	A	106967348	2	1	184	1	0	0	0	0	0	0	0	1	430	900	32	3		3	AIM1	6	106967348	Silent	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	66567541	106967348	64147719	41	27382										
FRK	2444	hgsc.bcm.edu	37	chr6	116263781	116263781	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	atctggattacctgggcaccTgtcataccttgaaaatacag	8	10	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr6:116263781T>C	ENST00000606080.1	-	8	1760	c.1314A>G	c.(1312-1314)acA>acG	p.T438T	FRK_ENST00000538210.1_Silent_p.T296T	NM_002031.2	NP_002022.1	P42685	FRK_HUMAN	fyn-related Src family tyrosine kinase	438	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|skin(1)|urinary_tract(1)	27		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	Regorafenib(DB08896)	CCTGGGCACCTGTCATACCTT	0.383																																					p.T438T		Atlas-SNP	.											.	FRK	78	.	0			c.A1314G						.						97	91	93					6																	116263781		2203	4300	6503	SO:0001819	synonymous_variant	2444	exon8			GGCACCTGTCATA	U00803	CCDS5103.1	6q21-q22.3	2014-06-25	2014-06-25		ENSG00000111816	ENSG00000111816	2.7.10.1	"SH2 domain containing"	3955	protein-coding gene	gene with protein product		606573	"PTK5 protein tyrosine kinase 5", "fyn-related kinase"	PTK5		7510261	Standard	NM_002031		Approved	RAK, GTK	uc003pwi.1	P42685	OTTHUMG00000015424	ENST00000606080.1:c.1314A>G	chr6.hg19:g.116263781T>C		166.0	0.0		106.0	14.0	NM_002031	B4DY49|Q13128|Q9NTR5	Silent	SNP	ENST00000606080.1	hg19	CCDS5103.1																																																																																			.	.		0.383	FRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041924.2	NM_002031		C	116263781	T	C	116263781	2	2	184	1	0	0	0	0	0	0	0	1	6056	1567	55	2		2	FRK	6	116263781	Silent	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	9296433	116263781	54851286	42	27383										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128388924	128388924	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tgggtgcagttcttccacaaCaatctgataagcactttggg	10	9	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr6:128388924C>A	ENST00000368215.3	-	12	1896	c.1897G>T	c.(1897-1899)Gtt>Ttt	p.V633F	PTPRK_ENST00000368213.5_Missense_Mutation_p.V633F|PTPRK_ENST00000368210.3_Missense_Mutation_p.V633F|RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368227.3_Missense_Mutation_p.V633F|PTPRK_ENST00000368207.3_Missense_Mutation_p.V633F|PTPRK_ENST00000532331.1_Missense_Mutation_p.V633F|PTPRK_ENST00000368226.4_Missense_Mutation_p.V633F			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	633	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		TCTTCCACAACAATCTGATAA	0.413																																					p.V633F		Atlas-SNP	.											.	PTPRK	330	.	0			c.G1897T						.						58	63	61					6																	128388924		2203	4300	6503	SO:0001583	missense	5796	exon12			CCACAACAATCTG	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.1897G>T	chr6.hg19:g.128388924C>A	ENSP00000357198:p.Val633Phe	73.0	0.0		61.0	15.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	hg19		.	.	.	.	.	.	.	.	.	.	C	24.4	4.526193	0.85600	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000427676	T;T;T;T;T;T;T	0.10099	2.92;2.91;2.93;2.92;2.91;2.92;2.91	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.31734	0.0806	M	0.80422	2.495	0.80722	D	1	D;D;D;P;D;D	0.71674	0.998;0.985;0.991;0.92;0.99;0.994	D;P;D;P;D;D	0.78314	0.991;0.89;0.949;0.761;0.969;0.986	T	0.04593	-1.0940	10	0.87932	D	0	.	20.3409	0.98764	0.0:1.0:0.0:0.0	.	633;633;633;490;633;633	B4DHC3;B7ZMG0;Q15262-3;F5GWP2;Q15262;Q15262-2	.;.;.;.;PTPRK_HUMAN;.	F	633;633;633;633;633;633;633;490	ENSP00000357209:V633F;ENSP00000357210:V633F;ENSP00000432973:V633F;ENSP00000357196:V633F;ENSP00000357193:V633F;ENSP00000357198:V633F;ENSP00000357190:V633F	ENSP00000357190:V633F	V	-	1	0	PTPRK	128430617	1.000000	0.71417	0.979000	0.43373	0.978000	0.69477	7.487000	0.81328	2.814000	0.96858	0.655000	0.94253	GTT	.	.		0.413	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			A	128388924	C	A	128388924	3	1	184	1	0	0	0	0	1	0	0	0	12820	478	17	3	2523	3	PTPRK	6	128388924	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	12125143	128388924	42726143	43	27384										
PRPS1L1	221823	hgsc.bcm.edu	37	chr7	18066745	18066745	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	aacacaagtgtctgccatgtCatctacaaggatagccacac	7	12	3	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr7:18066745C>A	ENST00000506618.2	-	1	741	c.661G>T	c.(661-663)Gac>Tac	p.D221Y		NM_175886.2	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like 1	221	Binding of phosphoribosylpyrophosphate. {ECO:0000255}.				5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|nucleotide biosynthetic process (GO:0009165)|ribonucleoside monophosphate biosynthetic process (GO:0009156)		ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)	18	Lung NSC(10;0.0385)|all_lung(11;0.0736)					TCTGCCATGTCATCTACAAGG	0.448																																					p.D221Y		Atlas-SNP	.											.	PRPS1L1	90	.	0			c.G661T						.						118	114	115					7																	18066745		2203	4300	6503	SO:0001583	missense	221823	exon1			CCATGTCATCTAC	M57423	CCDS47552.1	7p21.1	2010-12-10			ENSG00000229937	ENSG00000229937			9463	protein-coding gene	gene with protein product		611566		PRPSL		2168892	Standard	NM_175886		Approved	PRPS3	uc003stz.3	P21108	OTTHUMG00000152742	ENST00000506618.2:c.661G>T	chr7.hg19:g.18066745C>A	ENSP00000424595:p.Asp221Tyr	175.0	0.0		110.0	42.0	NM_175886	Q6P5P6	Missense_Mutation	SNP	ENST00000506618.2	hg19	CCDS47552.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.346231	0.61073	.	.	ENSG00000229937	ENST00000506618	D	0.95622	-3.76	4.4	3.51	0.40186	Phosphoribosyltransferase (1);	.	.	.	.	D	0.98469	0.9490	H	0.98295	4.195	.	.	.	D	0.89917	1.0	D	0.97110	1.0	D	0.99907	1.1183	8	0.87932	D	0	.	10.5365	0.45007	0.0:0.9039:0.0:0.0961	.	221	P21108	PRPS3_HUMAN	Y	221	ENSP00000424595:D221Y	ENSP00000424595:D221Y	D	-	1	0	PRPS1L1	18033270	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.124000	0.57924	1.210000	0.43336	0.650000	0.86243	GAC	.	.		0.448	PRPS1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327667.1	NM_175886		A	18066745	C	A	18066745	3	1	184	1	0	0	0	0	1	0	0	0	12591	826	29	3	299	3	PRPS1L1	7	18066745	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10		18066745	141071918	44	27385										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44555418	44555418	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tcacccacgtagctgaggatGacgggcaggaagaccaagcc	13	12	1	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr7:44555418G>A	ENST00000289547.4	-	19	3916	c.3861C>T	c.(3859-3861)gtC>gtT	p.V1287V	NPC1L1_ENST00000381160.3_Silent_p.V1260V|NPC1L1_ENST00000546276.1_Silent_p.V1214V	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1287					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	AGCTGAGGATGACGGGCAGGA	0.557																																					p.V1287V		Atlas-SNP	.											.	NPC1L1	141	.	0			c.C3861T						.						82	79	80					7																	44555418		2203	4300	6503	SO:0001819	synonymous_variant	29881	exon19			GAGGATGACGGGC		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3861C>T	chr7.hg19:g.44555418G>A		138.0	0.0		114.0	16.0	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	hg19	CCDS5491.1																																																																																			.	.		0.557	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		A	44555418	G	A	44555418	2	1	184	1	0	0	0	0	0	0	0	1	10580	1277	45	3		3	NPC1L1	7	44555418	Silent	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	26488673	44555418	114583245	45	27386										
MLXIPL	51085	hgsc.bcm.edu	37	chr7	73020079	73020096	+	In_Frame_Del	DEL	GTCAGCATTGCCGACGTA	GTCAGCATTGCCGACGTA	-													0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gtcaggtccggctggatcatGtcagcattgccgacgtaggc					rs548938711|rs150292665|rs140121265|rs368793037		TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	GTCAGCATTGCCGACGTA	GTCAGCATTGCCGACGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr7:73020079_73020096delGTCAGCATTGCCGACGTA	ENST00000313375.3	-	7	870_887	c.823_840delTACGTCGGCAATGCTGAC	c.(823-840)tacgtcggcaatgctgacdel	p.YVGNAD275del	MLXIPL_ENST00000434326.1_In_Frame_Del_p.YVGNAD182del|MLXIPL_ENST00000414749.2_In_Frame_Del_p.YVGNAD275del|MLXIPL_ENST00000354613.1_In_Frame_Del_p.YVGNAD275del|MLXIPL_ENST00000429400.2_In_Frame_Del_p.YVGNAD275del|MLXIPL_ENST00000395189.1_In_Frame_Del_p.YVGNAD182del	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	275					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.D280H(1)		cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				GCTGGATCATGTCAGCATTGCCGACGTAGGCTGGAGGC	0.661																																					p.275_281del		Atlas-INDEL	.											.	MLXIPL	54	.	1	Substitution - Missense(1)	cervix(1)	c.824_841del						.																																			SO:0001651	inframe_deletion	51085	exon7			.	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"carbohydrate response element binding protein"	605678	"Williams Beuren syndrome chromosome region 14"	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.823_840delTACGTCGGCAATGCTGAC	chr7.hg19:g.73020079_73020096delGTCAGCATTGCCGACGTA	ENSP00000320886:p.Tyr275_Asp280del	120.0	0.0		79.0	18.0	NM_032953	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	In_Frame_Del	DEL	ENST00000313375.3	hg19	CCDS5553.1																																																																																			.	.		0.661	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951		-	73020096	GTCAGCATTGCCGACGTA	-	73020079	7	5	184	1	0	1	0	1	0	0	0	0	9646	1368	48	0	1762	0	MLXIPL	7	73020079	In_Frame_Del	DEL	GTCAGCATTGCCGACGTA	TCGA-DD-AADA-01A-11D-A40R-10	28464661	73020079	86118584	46	27387										
MAGI2	9863	hgsc.bcm.edu	37	chr7	77797303	77797303	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gctgcgtggtgcatgaggtcGatgacatagcggtgggtttt	17	6	0	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr7:77797303G>A	ENST00000354212.4	-	15	2779	c.2526C>T	c.(2524-2526)atC>atT	p.I842I	MAGI2_ENST00000522391.1_Silent_p.I842I|MAGI2_ENST00000419488.1_Silent_p.I828I	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	842	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GCATGAGGTCGATGACATAGC	0.567																																					p.I842I		Atlas-SNP	.											.	MAGI2	246	.	0			c.C2526T						.						198	177	184					7																	77797303		2203	4300	6503	SO:0001819	synonymous_variant	9863	exon15			GAGGTCGATGACA	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.2526C>T	chr7.hg19:g.77797303G>A		196.0	0.0		123.0	23.0	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	hg19	CCDS5594.1																																																																																			.	.		0.567	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		A	77797303	G	A	77797303	2	1	184	1	0	0	0	0	0	0	0	1	9200	1048	37	1		1	MAGI2	7	77797303	Silent	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	4777224	77797303	81341360	47	27388										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142564355	142564355	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	actatcagctccgctactatGaccaggtgcgcaggaggagt	12	11	1	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr7:142564355G>A	ENST00000392957.2	+	10	2366	c.1579G>A	c.(1579-1581)Gac>Aac	p.D527N	EPHB6_ENST00000411471.2_Missense_Mutation_p.D250N|EPHB6_ENST00000442129.1_Missense_Mutation_p.D527N	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	527	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					CCGCTACTATGACCAGGTGCG	0.627																																					p.D527N		Atlas-SNP	.											.	EPHB6	168	.	0			c.G1579A						.						73	74	74					7																	142564355		2203	4300	6503	SO:0001583	missense	2051	exon10			TACTATGACCAGG	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1579G>A	chr7.hg19:g.142564355G>A	ENSP00000376684:p.Asp527Asn	80.0	0.0		56.0	21.0	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	hg19	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686363	0.88639	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.56941	0.43;0.43;0.43	4.8	4.8	0.61643	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.49916	D	0.000137	T	0.63343	0.2503	L	0.41356	1.27	0.46823	D	0.999219	D	0.89917	1.0	D	0.87578	0.998	T	0.66139	-0.5998	10	0.87932	D	0	.	13.0794	0.59104	0.0:0.1615:0.8385:0.0	.	527	O15197	EPHB6_HUMAN	N	527;527;250	ENSP00000376684:D527N;ENSP00000410789:D527N;ENSP00000409061:D250N	ENSP00000376684:D527N	D	+	1	0	EPHB6	142274477	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	6.475000	0.73582	2.370000	0.80446	0.556000	0.70494	GAC	.	.		0.627	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			A	142564355	G	A	142564355	3	1	184	1	0	0	0	0	1	0	0	0	5180	1290	45	3	1601	3	EPHB6	7	142564355	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	64767052	142564355	16574308	48	27389										
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154759569	154759569	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gcttatcagacatctgctctGgataatccgcaattgcaaac	7	11	3	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr7:154759569G>T	ENST00000404141.1	-	8	2004	c.1850C>A	c.(1849-1851)cCa>cAa	p.P617Q	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Missense_Mutation_p.P617Q			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	617	BRCT 3. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Gln-rich.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		CATCTGCTCTGGATAATCCGC	0.398																																					p.P617Q		Atlas-SNP	.											.	PAXIP1	150	.	0			c.C1850A						.						73	72	73					7																	154759569		1948	4133	6081	SO:0001583	missense	22976	exon8			TGCTCTGGATAAT	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1850C>A	chr7.hg19:g.154759569G>T	ENSP00000384048:p.Pro617Gln	95.0	0.0		101.0	5.0	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	hg19	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910448	0.52439	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.79141	-1.24;-1.24	5.17	5.17	0.71159	BRCT (4);	0.000000	0.56097	U	0.000037	T	0.82199	0.4985	L	0.36672	1.1	0.58432	D	0.999996	P;D;D;D	0.89917	0.677;1.0;1.0;1.0	B;D;D;D	0.97110	0.418;0.999;0.999;1.0	T	0.76838	-0.2811	10	0.12766	T	0.61	-21.4467	18.6938	0.91593	0.0:0.0:1.0:0.0	.	570;526;583;617	B4DEQ6;Q6ZW49-3;Q6ZW49-1;Q6ZW49	.;.;.;PAXI1_HUMAN	Q	617;617;441;570	ENSP00000384048:P617Q;ENSP00000380376:P617Q	ENSP00000319149:P570Q	P	-	2	0	PAXIP1	154390502	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.769000	0.91742	2.403000	0.81681	0.655000	0.94253	CCA	.	.		0.398	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		T	154759569	G	T	154759569	3	4	184	1	0	0	0	0	1	0	0	0	11496	1348	47	3	1415	3	PAXIP1	7	154759569	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	12195214	154759569	4379094	49	27390										
CYP11B1	1584	hgsc.bcm.edu	37	chr8	143957288	143957288	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gagcgtcatcagcaagggaaAcaccgtctgcaggagacaca	12	11	3	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr8:143957288A>T	ENST00000292427.4	-	6	993	c.961T>A	c.(961-963)Ttt>Att	p.F321I	CYP11B1_ENST00000517471.1_Missense_Mutation_p.F321I|CYP11B1_ENST00000377675.3_Missense_Mutation_p.F392I	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	321					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	AGCAAGGGAAACACCGTCTGC	0.647									Familial Hyperaldosteronism type I																												p.F321I		Atlas-SNP	.											.	CYP11B1	128	.	0			c.T961A	GRCh37	HM972175	CYP11B1	M		.						89	85	87					8																	143957288		2203	4300	6503	SO:0001583	missense	1584	exon6	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	AGGGAAACACCGT	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"Cytochrome P450s"	2591	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	610613	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.961T>A	chr8.hg19:g.143957288A>T	ENSP00000292427:p.Phe321Ile	277.0	0.0		255.0	64.0	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	ENST00000292427.4	hg19	CCDS6392.1	.	.	.	.	.	.	.	.	.	.	.	0.798	-0.756407	0.03019	.	.	ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675	T;T;T	0.67345	-0.26;-0.26;-0.26	4.31	0.207	0.15214	.	0.801024	0.10849	N	0.627347	T	0.42988	0.1227	N	0.13140	0.3	0.09310	N	1	B;B;B;P	0.45176	0.016;0.009;0.027;0.852	B;B;B;B	0.42462	0.021;0.021;0.007;0.388	T	0.25433	-1.0132	10	0.21540	T	0.41	.	2.6093	0.04886	0.4147:0.0:0.229:0.3562	.	392;321;321;37	Q4VAR0;Q4VAQ9;P15538;Q8N9P8	.;.;C11B1_HUMAN;.	I	321;321;392	ENSP00000292427:F321I;ENSP00000428043:F321I;ENSP00000366903:F392I	ENSP00000292427:F321I	F	-	1	0	CYP11B1	143954290	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.053000	0.14184	-0.149000	0.11215	0.454000	0.30748	TTT	.	.		0.647	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			T	143957288	A	T	143957288	3	4	184	1	0	0	0	0	1	0	0	0	4147	43	2	4	566	4	CYP11B1	8	143957288	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10		143957288	2406734	50	27391										
ARHGAP39	80728	hgsc.bcm.edu	37	chr8	145759534	145759534	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ttcttggccccggtcagggcTgccttctgtagcttgtggta	13	11	3	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr8:145759534T>A	ENST00000276826.5	-	6	2775	c.2574A>T	c.(2572-2574)gcA>gcT	p.A858A	ARHGAP39_ENST00000540274.1_Silent_p.A858A|ARHGAP39_ENST00000377307.2_Silent_p.A889A			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	858	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.				axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						CGGTCAGGGCTGCCTTCTGTA	0.647																																					p.A889A		Atlas-SNP	.											.	ARHGAP39	80	.	0			c.A2667T						.						100	95	97					8																	145759534		2202	4300	6502	SO:0001819	synonymous_variant	80728	exon9			CAGGGCTGCCTTC		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"Rho GTPase activating proteins"	29351	protein-coding gene	gene with protein product	"RhoGAP93B homolog (Drosophila)", "crossGAP homolog (Drosophila)"	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.2574A>T	chr8.hg19:g.145759534T>A		47.0	0.0		49.0	9.0	NM_025251	B4E1I1	Silent	SNP	ENST00000276826.5	hg19																																																																																				.	.		0.647	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			A	145759534	T	A	145759534	2	1	184	1	0	0	0	0	0	0	0	1	884	1567	55	4		4	ARHGAP39	8	145759534	Silent	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	1802246	145759534	604488	51	27392										
KCNV2	169522	hgsc.bcm.edu	37	chr9	2718411	2718411	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cacgagctgcgcgcgcaggcGcaggtcgaggaggcggagga	20	11	0	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr9:2718411G>A	ENST00000382082.3	+	1	910	c.672G>A	c.(670-672)gcG>gcA	p.A224A		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	224					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		GCGCGCAGGCGCAGGTCGAGG	0.672																																					p.A224A		Atlas-SNP	.											.	KCNV2	72	.	0			c.G672A						.						9	9	9					9																	2718411		2141	4185	6326	SO:0001819	synonymous_variant	169522	exon1			GCAGGCGCAGGTC	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.672G>A	chr9.hg19:g.2718411G>A		134.0	0.0		81.0	36.0	NM_133497	Q5T6X0	Silent	SNP	ENST00000382082.3	hg19	CCDS6447.1																																																																																			.	.		0.672	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		A	2718411	G	A	2718411	2	1	184	1	0	0	0	0	0	0	0	1	8104	1074	38	1		1	KCNV2	9	2718411	Silent	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10		2718411	138495020	52	27393										
KIAA1432	57589	hgsc.bcm.edu	37	chr9	5770152	5770152	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	accttgagatggatgctggcAtctccaacatccagcgaagt	10	11	1	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr9:5770152A>G	ENST00000414202.2	+	23	3681	c.3490A>G	c.(3490-3492)Atc>Gtc	p.I1164V	KIAA1432_ENST00000418622.3_Missense_Mutation_p.I1085V|KIAA1432_ENST00000449720.2_Missense_Mutation_p.I1048V	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		GGATGCTGGCATCTCCAACAT	0.493																																					p.I1164V		Atlas-SNP	.											.	KIAA1432	97	.	0			c.A3490G						.						112	92	99					9																	5770152		2203	4300	6503	SO:0001583	missense	57589	exon23			GCTGGCATCTCCA																												ENST00000414202.2:c.3490A>G	chr9.hg19:g.5770152A>G	ENSP00000416696:p.Ile1164Val	78.0	0.0		68.0	15.0	NM_020829		Missense_Mutation	SNP	ENST00000414202.2	hg19	CCDS34982.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.330|7.330	0.618774|0.618774	0.14129|0.14129	.|.	.|.	ENSG00000107036|ENSG00000107036	ENST00000545641|ENST00000414202;ENST00000418622;ENST00000449720	.|.	.|.	.|.	5.56|5.56	-7.87|-7.87	0.01183|0.01183	.|.	.|0.647764	.|0.17225	.|N	.|0.182178	T|T	0.18923|0.18923	0.0454|0.0454	N|N	0.02011|0.02011	-0.69|-0.69	0.37765|0.37765	D|D	0.926486|0.926486	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.18023|0.18023	-1.0350|-1.0350	5|9	.|0.16420	.|T	.|0.52	-0.6967|-0.6967	13.6987|13.6987	0.62595|0.62595	0.3506:0.0867:0.5627:0.0|0.3506:0.0867:0.5627:0.0	.|.	.|1048;1164	.|B7ZM67;Q4ADV7	.|.;RIC1_HUMAN	R|V	1055|1164;1085;1048	.|.	.|ENSP00000416696:I1164V	H|I	+|+	2|1	0|0	KIAA1432|KIAA1432	5760152|5760152	0.000000|0.000000	0.05858|0.05858	0.030000|0.030000	0.17652|0.17652	0.944000|0.944000	0.59088|0.59088	-0.162000|-0.162000	0.10012|0.10012	-1.439000|-1.439000	0.01962|0.01962	0.459000|0.459000	0.35465|0.35465	CAT|ATC	.	.		0.493	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3			G	5770152	A	G	5770152	3	3	184	1	0	0	0	0	1	0	0	0	8242	217	8	2	3413	2	KIAA1432	9	5770152	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	3051741	5770152	135443279	53	27394										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79319835	79319835	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gcagcacagccagctgggatCcaggcagtctgtttttggtc	13	11	1	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr9:79319835C>A	ENST00000376718.3	-	8	7478	c.7355G>T	c.(7354-7356)gGa>gTa	p.G2452V	PRUNE2_ENST00000428286.1_Missense_Mutation_p.G2093V	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2452					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CAGCTGGGATCCAGGCAGTCT	0.507											OREG0019258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G2452V		Atlas-SNP	.											.	PRUNE2	331	.	0			c.G7355T						.						61	53	55					9																	79319835		1568	3582	5150	SO:0001583	missense	158471	exon8			TGGGATCCAGGCA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.7355G>T	chr9.hg19:g.79319835C>A	ENSP00000365908:p.Gly2452Val	153.0	0.0	1190	114.0	21.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.591|9.591	1.126120|1.126120	0.20959|0.20959	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.46819|.	0.86;0.87|.	5.93|5.93	0.369|0.369	0.16151|0.16151	.|.	0.568251|.	0.17238|.	N|.	0.181650|.	T|T	0.37156|0.37156	0.0993|0.0993	L|L	0.56769|0.56769	1.78|1.78	0.09310|0.09310	N|N	0.999999|0.999999	P|.	0.35077|.	0.483|.	B|.	0.33392|.	0.163|.	T|T	0.33394|0.33394	-0.9870|-0.9870	10|5	0.66056|.	D|.	0.02|.	-8.9788|-8.9788	1.9445|1.9445	0.03354|0.03354	0.1238:0.2525:0.3626:0.2611|0.1238:0.2525:0.3626:0.2611	.|.	2452|.	Q8WUY3|.	PRUN2_HUMAN|.	V|C	2452;2093;2451|1773	ENSP00000365908:G2452V;ENSP00000397425:G2093V|.	ENSP00000365908:G2452V|.	G|W	-|-	2|3	0|0	PRUNE2|PRUNE2	78509655|78509655	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.156000|0.156000	0.22039|0.22039	-0.087000|-0.087000	0.11215|0.11215	0.065000|0.065000	0.16485|0.16485	-0.127000|-0.127000	0.14921|0.14921	GGA|TGG	.	.		0.507	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79319835	C	A	79319835	3	1	184	1	0	0	0	0	1	0	0	0	12653	855	30	3	1959	3	PRUNE2	9	79319835	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	73549683	79319835	61893596	54	27395										
TRAF1	7185	hgsc.bcm.edu	37	chr9	123675664	123675664	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggctctggtggatagaggtgGccagggccaggtgggaggcc	21	8	1	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr9:123675664G>A	ENST00000373887.3	-	5	3092	c.647C>T	c.(646-648)gCc>gTc	p.A216V	TRAF1_ENST00000546084.1_Missense_Mutation_p.A94V|TRAF1_ENST00000540010.1_Missense_Mutation_p.A216V	NM_005658.4	NP_005649.1	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	216					apoptotic process (GO:0006915)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein complex assembly (GO:0006461)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(4)|pancreas(1)|skin(2)	22						GATAGAGGTGGCCAGGGCCAG	0.607																																					p.A216V		Atlas-SNP	.											.	TRAF1	42	.	0			c.C647T						.						50	42	44					9																	123675664		2203	4300	6503	SO:0001583	missense	7185	exon5			GAGGTGGCCAGGG	AK090468	CCDS6825.1, CCDS55335.1	9q33-q34	2008-02-05			ENSG00000056558	ENSG00000056558			12031	protein-coding gene	gene with protein product		601711				8069916	Standard	NM_001190945		Approved	EBI6	uc010mvl.2	Q13077	OTTHUMG00000020578	ENST00000373887.3:c.647C>T	chr9.hg19:g.123675664G>A	ENSP00000362994:p.Ala216Val	214.0	0.0		163.0	19.0	NM_005658	B4DJ77|Q658U1|Q8NF13	Missense_Mutation	SNP	ENST00000373887.3	hg19	CCDS6825.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.850101	0.51270	.	.	ENSG00000056558	ENST00000373887;ENST00000540010;ENST00000546084	T;T;T	0.45276	1.44;1.44;0.9	4.99	4.99	0.66335	.	0.159146	0.41500	D	0.000866	T	0.30854	0.0778	L	0.31664	0.95	0.37459	D	0.915149	B	0.30146	0.27	B	0.27715	0.082	T	0.22800	-1.0206	10	0.27785	T	0.31	-23.5276	13.855	0.63522	0.0:0.0:0.8469:0.1531	.	216	Q13077	TRAF1_HUMAN	V	216;216;94	ENSP00000362994:A216V;ENSP00000443183:A216V;ENSP00000438583:A94V	ENSP00000362994:A216V	A	-	2	0	TRAF1	122715485	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.364000	0.59479	2.301000	0.77427	0.563000	0.77884	GCC	.	.		0.607	TRAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053843.1	NM_005658		A	123675664	G	A	123675664	3	1	184	1	0	0	0	0	1	0	0	0	16452	1203	42	3	619	3	TRAF1	9	123675664	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	44355829	123675664	17537767	55	27396										
GRIN1	2902	hgsc.bcm.edu	37	chr9	140040236	140040236	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ctcccaccagtccagcgtgtGgtttgagatgatgcgtgtct	12	11	1	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr9:140040236G>T	ENST00000371561.3	+	3	1549	c.452G>T	c.(451-453)tGg>tTg	p.W151L	GRIN1_ENST00000315048.3_Missense_Mutation_p.W151L|GRIN1_ENST00000371559.4_Missense_Mutation_p.W151L|GRIN1_ENST00000371553.3_Missense_Mutation_p.W151L|GRIN1_ENST00000371555.4_Missense_Mutation_p.W151L|GRIN1_ENST00000371550.4_Missense_Mutation_p.W151L|GRIN1_ENST00000371546.4_Missense_Mutation_p.W151L|GRIN1_ENST00000371560.3_Missense_Mutation_p.W151L|GRIN1_ENST00000350902.5_Missense_Mutation_p.W151L|GRIN1_ENST00000471122.1_3'UTR	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	151					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TCCAGCGTGTGGTTTGAGATG	0.672																																					p.W151L	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											.	GRIN1	51	.	0			c.G452T						.						79	51	61					9																	140040236		2203	4299	6502	SO:0001583	missense	2902	exon3			GCGTGTGGTTTGA		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4584	protein-coding gene	gene with protein product		138249	"N-methyl-D-aspartate receptor subunit NR1"	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.452G>T	chr9.hg19:g.140040236G>T	ENSP00000360616:p.Trp151Leu	117.0	0.0		82.0	20.0	NM_000832	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Missense_Mutation	SNP	ENST00000371561.3	hg19	CCDS7031.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.503568	0.85176	.	.	ENSG00000176884	ENST00000371561;ENST00000315048;ENST00000350902;ENST00000371550;ENST00000371546;ENST00000371555;ENST00000371553;ENST00000371559;ENST00000371560	T;T;T;T;T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37	4.0	4.0	0.46444	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.88202	0.6373	M	0.75777	2.31	0.80722	D	1	D;B;D;D;D;D	0.89917	0.96;0.099;0.999;0.999;0.999;1.0	P;B;D;D;D;D	0.77557	0.893;0.141;0.941;0.956;0.974;0.99	D	0.87847	0.2655	10	0.37606	T	0.19	.	14.6551	0.68828	0.0:0.0:1.0:0.0	.	151;151;151;151;151;151	Q5VSF4;Q5VSF5;Q05586-2;Q05586-3;Q05586;A2AVK2	.;.;.;.;NMDZ1_HUMAN;.	L	151	ENSP00000360616:W151L;ENSP00000316696:W151L;ENSP00000316915:W151L;ENSP00000360605:W151L;ENSP00000360601:W151L;ENSP00000360610:W151L;ENSP00000360608:W151L;ENSP00000360614:W151L;ENSP00000360615:W151L	ENSP00000316696:W151L	W	+	2	0	GRIN1	139160057	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.181000	0.94874	1.787000	0.52448	0.313000	0.20887	TGG	.	.		0.672	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327		T	140040236	G	T	140040236	3	4	184	1	0	0	0	0	1	0	0	0	6787	1357	47	3	462	3	GRIN1	9	140040236	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	16364572	140040236	1173195	56	27397										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140943745	140943745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	acttcattgtggtcagtggcGccctggtggcgtttgctttc	13	10	2	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr9:140943745G>A	ENST00000371372.1	+	24	3833	c.3688G>A	c.(3688-3690)Gcc>Acc	p.A1230T	CACNA1B_ENST00000371363.1_Missense_Mutation_p.A1230T|CACNA1B_ENST00000371355.4_Missense_Mutation_p.A1231T|CACNA1B_ENST00000371357.1_Missense_Mutation_p.A1231T|CACNA1B_ENST00000277549.5_Missense_Mutation_p.A422T|CACNA1B_ENST00000545473.1_3'UTR|CACNA1B_ENST00000277551.2_Missense_Mutation_p.A1230T	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1230					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GGTCAGTGGCGCCCTGGTGGC	0.547																																					p.A1230T		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G3688A						.						151	147	148					9																	140943745		2075	4211	6286	SO:0001583	missense	774	exon24			AGTGGCGCCCTGG	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.3688G>A	chr9.hg19:g.140943745G>A	ENSP00000360423:p.Ala1230Thr	104.0	0.0		76.0	28.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	37	6.483172	0.97603	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D;D	0.98567	-5.0;-5.0;-5.0;-5.0;-5.0;-5.0	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.99045	0.9673	M	0.86740	2.835	0.80722	D	1	D;D;D	0.89917	0.976;1.0;1.0	P;D;D	0.81914	0.693;0.995;0.995	D	0.99777	1.1026	10	0.87932	D	0	.	18.1658	0.89724	0.0:0.0:1.0:0.0	.	1230;1231;1230	B1AQK4;B1AQK7;B1AQK6	.;.;.	T	1230;1230;422;1230;1231;1231	ENSP00000360423:A1230T;ENSP00000277551:A1230T;ENSP00000277549:A422T;ENSP00000360414:A1230T;ENSP00000360408:A1231T;ENSP00000360406:A1231T	ENSP00000277549:A422T	A	+	1	0	CACNA1B	140063566	1.000000	0.71417	0.994000	0.49952	0.973000	0.67179	9.711000	0.98735	2.386000	0.81285	0.491000	0.48974	GCC	.	.		0.547	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		A	140943745	G	A	140943745	3	1	184	1	0	0	0	0	1	0	0	0	2541	1087	38	1	3782	1	CACNA1B	9	140943745	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	903509	140943745	269686	57	27398										
HELLS	3070	hgsc.bcm.edu	37	chr10	96350209	96350209	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gtcctactggtcgaccaaaaCgacgaactagaaaatcaata	7	10	1	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr10:96350209C>T	ENST00000348459.5	+	14	1633	c.1528C>T	c.(1528-1530)Cga>Tga	p.R510*	HELLS_ENST00000239026.6_3'UTR|HELLS_ENST00000394045.1_Nonsense_Mutation_p.R412*|HELLS_ENST00000371332.4_Nonsense_Mutation_p.R556*|HELLS_ENST00000394036.1_3'UTR|RP11-119K6.6_ENST00000432120.1_RNA	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		TCGACCAAAACGACGAACTAG	0.343																																					p.R510X		Atlas-SNP	.											.	HELLS	63	.	0			c.C1528T						.						60	61	61					10																	96350209		2203	4300	6503	SO:0001587	stop_gained	3070	exon14			CCAAAACGACGAA	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6", "proliferation-associated SNF2-like protein"	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.1528C>T	chr10.hg19:g.96350209C>T	ENSP00000239027:p.Arg510*	325.0	0.0		197.0	8.0	NM_018063		Nonsense_Mutation	SNP	ENST00000348459.5	hg19	CCDS7434.1	.	.	.	.	.	.	.	.	.	.	C	39	7.807766	0.98501	.	.	ENSG00000119969	ENST00000348459;ENST00000394045;ENST00000371332	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.4508	16.5016	0.84259	0.0:1.0:0.0:0.0	.	.	.	.	X	510;412;556	.	ENSP00000239027:R510X	R	+	1	2	HELLS	96340199	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.356000	0.73046	2.559000	0.86315	0.655000	0.94253	CGA	.	.		0.343	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		T	96350209	C	T	96350209	4	4	184	1	0	0	0	0	0	1	0	0	7055	528	19	1	1582	1	HELLS	10	96350209	Nonsense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10		96350209	39184538	58	27399										
C10orf26	54838	hgsc.bcm.edu	37	chr10	104572770	104572770	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggcgcacccgacagcaaagaGaagacgcctgggagacatcg	14	12	0	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr10:104572770G>C	ENST00000369889.4	+	4	853	c.711G>C	c.(709-711)gaG>gaC	p.E237D	WBP1L_ENST00000448841.1_Missense_Mutation_p.E258D	NM_017787.4	NP_060257.4	Q9NX94	WBP1L_HUMAN	WW domain binding protein 1-like	237						integral component of membrane (GO:0016021)											ACAGCAAAGAGAAGACGCCTG	0.577																																					p.E258D		Atlas-SNP	.											.	.	.	.	0			c.G774C						.						59	55	56					10																	104572770		2203	4300	6503	SO:0001583	missense	54838	exon4			CAAAGAGAAGACG	AK056285	CCDS7540.1, CCDS44473.1	10q24.33	2012-05-02	2012-05-02	2012-05-02	ENSG00000166272	ENSG00000166272			23510	protein-coding gene	gene with protein product	"outcome predictor in acute leukemia 1"	611129	"chromosome 10 open reading frame 26"	C10orf26			Standard	NM_017787		Approved	FLJ20154, OPAL1	uc001kwf.4	Q9NX94	OTTHUMG00000018968	ENST00000369889.4:c.711G>C	chr10.hg19:g.104572770G>C	ENSP00000358905:p.Glu237Asp	65.0	0.0		47.0	8.0	NM_001083913	B3KPF4|B7Z6S7|D3DR90|Q1EG70|Q2HIY7|Q5F2G6	Missense_Mutation	SNP	ENST00000369889.4	hg19	CCDS7540.1	.	.	.	.	.	.	.	.	.	.	g	0.140	-1.103097	0.01828	.	.	ENSG00000166272	ENST00000448841;ENST00000369889	T;T	0.27402	1.72;1.67	6.05	3.14	0.36123	.	0.252002	0.46145	N	0.000316	T	0.07279	0.0184	N	0.00419	-1.52	0.24192	N	0.995543	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39313	-0.9620	10	0.02654	T	1	-18.7717	11.4177	0.49962	0.0:0.6649:0.2702:0.0649	.	258;237	Q9NX94-2;Q9NX94	.;OPA1L_HUMAN	D	258;237	ENSP00000414721:E258D;ENSP00000358905:E237D	ENSP00000358905:E237D	E	+	3	2	C10orf26	104562760	1.000000	0.71417	1.000000	0.80357	0.418000	0.31294	1.184000	0.32053	0.406000	0.25560	-0.218000	0.12543	GAG	.	.		0.577	WBP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050100.1	NM_017787		C	104572770	G	C	104572770	3	2	184	1	0	0	0	0	1	0	0	0	1601	933	33	4	819	4	C10orf26	10	104572770	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	8222561	104572770	30961977	59	27400										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108337267	108337267	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ttgcaatcggagagatgagtCaccaggttgagtagaagggg	16	5	1	4			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr10:108337267C>T	ENST00000263054.6	-	26	3425	c.3418G>A	c.(3418-3420)Gac>Aac	p.D1140N	SORCS1_ENST00000369698.1_3'UTR|SORCS1_ENST00000344440.6_Intron	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1140					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		AGAGATGAGTCACCAGGTTGA	0.502																																					p.D1140N		Atlas-SNP	.											.	SORCS1	534	.	0			c.G3418A						.						97	96	96					10																	108337267		2203	4300	6503	SO:0001583	missense	114815	exon26			ATGAGTCACCAGG	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3418G>A	chr10.hg19:g.108337267C>T	ENSP00000263054:p.Asp1140Asn	76.0	0.0		55.0	14.0	NM_052918	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.765459	0.31228	.	.	ENSG00000108018	ENST00000263054	T	0.16457	2.34	5.52	5.52	0.82312	.	.	.	.	.	T	0.09158	0.0226	N	0.08118	0	0.80722	D	1	B	0.23058	0.079	B	0.24269	0.052	T	0.32955	-0.9887	8	.	.	.	.	12.3392	0.55085	0.0:0.9223:0.0:0.0777	.	1140	Q8WY21	SORC1_HUMAN	N	1140	ENSP00000263054:D1140N	.	D	-	1	0	SORCS1	108327257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.135000	0.50546	2.759000	0.94783	0.555000	0.69702	GAC	.	.		0.502	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		T	108337267	C	T	108337267	3	4	184	1	0	0	0	0	1	0	0	0	14945	826	29	3	161	3	SORCS1	10	108337267	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	3764497	108337267	27197480	60	27401										
APBB1	322	hgsc.bcm.edu	37	chr11	6424420	6424420	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gggggaagcttctcctcctcTtggggcaacggctctgggct	15	12	3	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr11:6424420T>A	ENST00000609360.1	-	6	1158	c.1059A>T	c.(1057-1059)caA>caT	p.Q353H	APBB1_ENST00000609331.1_Missense_Mutation_p.Q118H|APBB1_ENST00000530885.1_Missense_Mutation_p.Q133H|APBB1_ENST00000299402.6_Missense_Mutation_p.Q353H|APBB1_ENST00000529519.1_Intron|APBB1_ENST00000608655.1_Missense_Mutation_p.Q133H|APBB1_ENST00000608394.1_Missense_Mutation_p.Q94H|APBB1_ENST00000608704.1_Missense_Mutation_p.Q94H|APBB1_ENST00000608645.1_Missense_Mutation_p.Q94H|APBB1_ENST00000311051.3_Missense_Mutation_p.Q353H|APBB1_ENST00000389906.2_Missense_Mutation_p.Q353H	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	353					apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		TCTCCTCCTCTTGGGGCAACG	0.547																																					p.Q353H	GBM(147;1810 2556 5672 39622)	Atlas-SNP	.											.	APBB1	73	.	0			c.A1059T						.						113	107	109					11																	6424420		2201	4296	6497	SO:0001583	missense	322	exon6			CTCCTCTTGGGGC	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.1059A>T	chr11.hg19:g.6424420T>A	ENSP00000477213:p.Gln353His	185.0	0.0		151.0	24.0	NM_001164	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.79	3.220285	0.58560	.	.	ENSG00000166313	ENST00000299402;ENST00000311051;ENST00000389906;ENST00000539758;ENST00000536523;ENST00000544288;ENST00000530885;ENST00000533407	T;T;T;T;T	0.14022	2.54;2.54;2.54;2.54;2.54	4.71	-0.0552	0.13810	.	0.336327	0.27486	N	0.019145	T	0.14830	0.0358	N	0.24115	0.695	0.33336	D	0.56924	P;P;P;D	0.60160	0.952;0.919;0.952;0.987	P;P;B;P	0.60789	0.496;0.503;0.399;0.879	T	0.20338	-1.0278	10	0.36615	T	0.2	-8.2289	6.9674	0.24631	0.0:0.4631:0.0:0.5369	.	202;118;133;353	B7Z1H5;F5H1C5;B7Z2Y0;O00213-2	.;.;.;.	H	353;353;353;202;94;118;133;94	ENSP00000299402:Q353H;ENSP00000311912:Q353H;ENSP00000374556:Q353H;ENSP00000433338:Q133H;ENSP00000437114:Q94H	ENSP00000299402:Q353H	Q	-	3	2	APBB1	6380996	0.993000	0.37304	1.000000	0.80357	0.852000	0.48524	0.031000	0.13710	0.076000	0.16826	0.402000	0.26972	CAA	.	.		0.547	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164		A	6424420	T	A	6424420	3	1	184	1	0	0	0	0	1	0	0	0	759	1606	56	4	1109	4	APBB1	11	6424420	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10		6424420	128582096	61	27402										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587664	55587664	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gtgagttctcctcactactcTccctttcttgctctgatact	5	14	5	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr11:55587664T>A	ENST00000333976.4	+	1	579	c.559T>A	c.(559-561)Tcc>Acc	p.S187T		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	187						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				CTCACTACTCTCCCTTTCTTG	0.408																																					p.S187T		Atlas-SNP	.											.	OR5D18	121	.	0			c.T559A						.						211	190	197					11																	55587664		2200	4296	6496	SO:0001583	missense	219438	exon1			CTACTCTCCCTTT	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.559T>A	chr11.hg19:g.55587664T>A	ENSP00000335025:p.Ser187Thr	121.0	0.0		84.0	8.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	hg19	CCDS31510.1	.	.	.	.	.	.	.	.	.	.	.	4.086	0.014011	0.07959	.	.	ENSG00000186119	ENST00000333976	T	0.00084	8.75	4.85	0.241	0.15494	GPCR, rhodopsin-like superfamily (1);	0.203139	0.24965	N	0.034191	T	0.00109	0.0003	L	0.39467	1.215	0.09310	N	1	B	0.18166	0.026	B	0.31016	0.123	T	0.40459	-0.9562	10	0.46703	T	0.11	-21.2578	1.4149	0.02299	0.4535:0.0935:0.1412:0.3118	.	187	Q8NGL1	OR5DI_HUMAN	T	187	ENSP00000335025:S187T	ENSP00000335025:S187T	S	+	1	0	OR5D18	55344240	0.000000	0.05858	0.005000	0.12908	0.013000	0.08279	-3.137000	0.00588	0.293000	0.22520	0.462000	0.41574	TCC	.	.		0.408	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		A	55587664	T	A	55587664	3	1	184	1	0	0	0	0	1	0	0	0	11166	1551	54	4	561	4	OR5D18	11	55587664	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	49163244	55587664	79418852	62	27403										
OR1S1	219959	hgsc.bcm.edu	37	chr11	57983133	57983133	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ccccttcatctacagcttgaGgaataaggatatgaaaggtg	10	8	2	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr11:57983133G>A	ENST00000309433.6	+	1	917	c.917G>A	c.(916-918)aGg>aAg	p.R306K		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	306						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TACAGCTTGAGGAATAAGGAT	0.438																																					p.R306K		Atlas-SNP	.											.	OR1S1	139	.	0			c.G917A						.						140	138	138					11																	57983133		2201	4295	6496	SO:0001583	missense	219959	exon1			GCTTGAGGAATAA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"GPCR / Class A : Olfactory receptors"	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.917G>A	chr11.hg19:g.57983133G>A	ENSP00000311688:p.Arg306Lys	127.0	0.0		105.0	12.0	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	hg19	CCDS31546.1	.	.	.	.	.	.	.	.	.	.	G	18.41	3.617173	0.66672	.	.	ENSG00000172774	ENST00000309433	T	0.39997	1.05	3.23	3.23	0.37069	.	0.000000	0.49916	D	0.000129	T	0.66237	0.2769	M	0.86097	2.795	0.24505	N	0.994232	D	0.89917	1.0	D	0.83275	0.996	T	0.60915	-0.7168	10	0.66056	D	0.02	.	13.6137	0.62094	0.0:0.0:1.0:0.0	.	306	Q8NH92	OR1S1_HUMAN	K	306	ENSP00000311688:R306K	ENSP00000311688:R306K	R	+	2	0	OR1S1	57739709	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.832000	0.55783	1.647000	0.50633	0.479000	0.44913	AGG	.	.		0.438	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458		A	57983133	G	A	57983133	3	1	184	1	0	0	0	0	1	0	0	0	10981	1000	35	3	919	3	OR1S1	11	57983133	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	2395469	57983133	77023383	63	27404										
CPT1A	1374	hgsc.bcm.edu	37	chr11	68540890	68540890	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tcagggaggtctctataaccTcttgacacttgagagaaaga	10	8	3	4			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr11:68540890T>A	ENST00000265641.5	-	14	1737	c.1583A>T	c.(1582-1584)gAg>gTg	p.E528V	CPT1A_ENST00000540367.1_Missense_Mutation_p.E528V|CPT1A_ENST00000537756.2_5'UTR|CPT1A_ENST00000539743.1_Missense_Mutation_p.E528V|CPT1A_ENST00000376618.2_Missense_Mutation_p.E528V	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	528					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	CTCTATAACCTCTTGACACTT	0.448																																					p.E528V		Atlas-SNP	.											.	CPT1A	89	.	0			c.A1583T						.						90	76	81					11																	68540890		2200	4294	6494	SO:0001583	missense	1374	exon14			ATAACCTCTTGAC	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.1583A>T	chr11.hg19:g.68540890T>A	ENSP00000265641:p.Glu528Val	70.0	0.0		65.0	13.0	NM_001876	Q8TCU0|Q9BWK0	Missense_Mutation	SNP	ENST00000265641.5	hg19	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.057710	0.36277	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	D;D;D;D	0.89552	-2.53;-2.53;-2.53;-2.53	4.79	4.79	0.61399	.	0.482483	0.23160	N	0.051247	D	0.89952	0.6864	M	0.69358	2.11	0.33712	D	0.615911	B;B	0.26318	0.146;0.02	B;B	0.39339	0.297;0.049	D	0.91423	0.5160	10	0.33940	T	0.23	.	14.6125	0.68526	0.0:0.0:0.0:1.0	.	528;528	P50416;P50416-2	CPT1A_HUMAN;.	V	528	ENSP00000439084:E528V;ENSP00000365803:E528V;ENSP00000265641:E528V;ENSP00000446108:E528V	ENSP00000265641:E528V	E	-	2	0	CPT1A	68297466	1.000000	0.71417	0.994000	0.49952	0.830000	0.47004	3.676000	0.54612	1.916000	0.55485	0.247000	0.18012	GAG	.	.		0.448	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876		A	68540890	T	A	68540890	3	1	184	1	0	0	0	0	1	0	0	0	3833	1551	54	4	802	4	CPT1A	11	68540890	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	10557757	68540890	66465626	64	27405										
PDZD3	79849	hgsc.bcm.edu	37	chr11	119058343	119058343	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cgggcaggggtgccccccggGgcccggctgctggaagtgaa	19	13	0	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr11:119058343G>A	ENST00000531114.1	+	4	1338	c.789G>A	c.(787-789)ggG>ggA	p.G263G	PDZD3_ENST00000355547.5_Silent_p.G197G|PDZD3_ENST00000322712.4_Silent_p.G197G|PDZD3_ENST00000392817.2_Silent_p.G263G|PDZD3_ENST00000525131.1_Silent_p.G184G			Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	263	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cGMP-mediated signaling (GO:0019934)|ion transport (GO:0006811)|negative regulation of cGMP biosynthetic process (GO:0030827)|negative regulation of guanylate cyclase activity (GO:0031283)|receptor guanylyl cyclase signaling pathway (GO:0007168)|response to toxic substance (GO:0009636)|water transport (GO:0006833)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|subapical complex (GO:0035003)	guanylate cyclase inhibitor activity (GO:0030251)|ion channel inhibitor activity (GO:0008200)|protein C-terminus binding (GO:0008022)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	14	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)		TGCCCCCCGGGGCCCGGCTGC	0.562																																					p.G197G		Atlas-SNP	.											.	PDZD3	42	.	0			c.G591A						.						16	20	18					11																	119058343		2177	4251	6428	SO:0001819	synonymous_variant	79849	exon6			CCCCGGGGCCCGG	AK091966	CCDS8417.1, CCDS53719.1	11q23.3	2008-02-05	2006-01-24	2006-01-24	ENSG00000172367	ENSG00000172367			19891	protein-coding gene	gene with protein product		607146	"PDZ domain containing 2"	PDZK2		11950846	Standard	NM_024791		Approved	FLJ22756, IKEPP	uc001pvz.3	Q86UT5	OTTHUMG00000166224	ENST00000531114.1:c.789G>A	chr11.hg19:g.119058343G>A		102.0	0.0		88.0	4.0	NM_001168468	Q8N6R4|Q8NAW7|Q8NEX7|Q9H5Z3	Silent	SNP	ENST00000531114.1	hg19																																																																																				.	.		0.562	PDZD3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388471.1	NM_024791		A	119058343	G	A	119058343	2	1	184	1	0	0	0	0	0	0	0	1	11711	1219	43	3		3	PDZD3	11	119058343	Silent	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	50517453	119058343	15948173	65	27406										
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128838980	128838980	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggtgctgaggcagggagtggTaatcttccaggttatcatac	14	7	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr11:128838980T>C	ENST00000310343.9	-	22	6085	c.6086A>G	c.(6085-6087)tAc>tGc	p.Y2029C	ARHGAP32_ENST00000527272.1_Missense_Mutation_p.Y1680C|ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.Y1680C	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	2029	Interaction with FYN.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						CAGGGAGTGGTAATCTTCCAG	0.587																																					p.Y2029C		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.A6086G						.						85	70	75					11																	128838980		2201	4297	6498	SO:0001583	missense	9743	exon22			GAGTGGTAATCTT	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.6086A>G	chr11.hg19:g.128838980T>C	ENSP00000310561:p.Tyr2029Cys	166.0	0.0		97.0	5.0	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.803923	0.31869	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.18502	2.21;2.21;2.21	5.68	4.56	0.56223	.	0.138816	0.49916	D	0.000129	T	0.18087	0.0434	L	0.54323	1.7	0.46416	D	0.99903	B	0.24533	0.105	B	0.22880	0.042	T	0.03493	-1.1031	10	0.87932	D	0	.	11.1206	0.48287	0.0:0.0717:0.0:0.9283	.	2029	A7KAX9	RHG32_HUMAN	C	2029;1680;1680	ENSP00000310561:Y2029C;ENSP00000376425:Y1680C;ENSP00000432862:Y1680C	ENSP00000310561:Y2029C	Y	-	2	0	ARHGAP32	128344190	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.860000	0.55995	2.176000	0.68965	0.529000	0.55759	TAC	.	.		0.587	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		C	128838980	T	C	128838980	3	2	184	1	0	0	0	0	1	0	0	0	881	1638	57	2	181	2	ARHGAP32	11	128838980	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	9780637	128838980	6167536	66	27407										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	KRAS_ENST00000256078,NS,adenocarcinoma,0,66	KRAS	30930	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A						.						91	81	85					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ACGCCACCAGCTC	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	chr12.hg19:g.25398284C>T	ENSP00000256078:p.Gly12Asp	163.0	0.0		142.0	21.0	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.	.		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	184	1	0	0	0	0	1	0	0	0	8447	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10		25398284	108453611	67	27408										
DPY19L2	283417	hgsc.bcm.edu	37	chr12	63974527	63974527	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	attatgctccattgattacgGaggtttgcataaccttgtat	8	7	0	1	rs140003085		TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr12:63974527G>A	ENST00000324472.4	-	19	1998	c.1815C>T	c.(1813-1815)ctC>ctT	p.L605L	DPY19L2_ENST00000413230.2_Silent_p.L52L	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	605					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)	p.L605L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		ATTGATTACGGAGGTTTGCAT	0.378																																					p.L605L		Atlas-SNP	.											DPY19L2,colon,carcinoma,-2,1	DPY19L2	97	.	1	Substitution - coding silent(1)	skin(1)	c.C1815T						.						75	72	73					12																	63974527		2203	4300	6503	SO:0001819	synonymous_variant	283417	exon19			ATTACGGAGGTTT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"spermatogenesis associated 34"	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.1815C>T	chr12.hg19:g.63974527G>A		247.0	0.0		163.0	50.0	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Silent	SNP	ENST00000324472.4	hg19	CCDS31851.1																																																																																			.	.		0.378	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812		A	63974527	G	A	63974527	2	1	184	1	0	0	0	0	0	0	0	1	4743	1161	41	3		3	DPY19L2	12	63974527	Silent	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	38576243	63974527	69877368	68	27409										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85450161	85450161	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cagtttccattgcaagaattAaagtctgatgcacaaaaaga	7	7	1	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr12:85450161A>T	ENST00000393217.2	+	8	1651	c.1590A>T	c.(1588-1590)ttA>ttT	p.L530F		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	530										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		TGCAAGAATTAAAGTCTGATG	0.299																																					p.L530F		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A1590T						.						45	51	49					12																	85450161		2190	4270	6460	SO:0001583	missense	84125	exon8			AGAATTAAAGTCT	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.1590A>T	chr12.hg19:g.85450161A>T	ENSP00000376910:p.Leu530Phe	426.0	0.0		269.0	37.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	A	15.97	2.990935	0.54041	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.57107	0.42	4.74	2.33	0.28932	.	1.108610	0.06791	N	0.787046	T	0.44414	0.1292	L	0.48642	1.525	0.09310	N	1	B;B	0.25719	0.079;0.132	B;B	0.25405	0.027;0.06	T	0.38499	-0.9658	10	0.49607	T	0.09	.	3.8399	0.08909	0.6558:0.0:0.1855:0.1587	.	530;505	Q96JM4;C9JI57	LRIQ1_HUMAN;.	F	530;505;530	ENSP00000376910:L530F	ENSP00000256007:L530F	L	+	3	2	LRRIQ1	83974292	0.000000	0.05858	0.381000	0.26106	0.141000	0.21300	-0.178000	0.09782	0.260000	0.21731	0.482000	0.46254	TTA	.	.		0.299	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85450161	A	T	85450161	3	4	184	1	0	0	0	0	1	0	0	0	9038	359	13	4	1616	4	LRRIQ1	12	85450161	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	21475634	85450161	48401734	69	27410										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124882700	124882700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ccatttcttcttctgtccagCgagaactctcattcagctcc	5	15	5	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr12:124882700C>T	ENST00000405201.1	-	16	1841	c.1841G>A	c.(1840-1842)cGc>cAc	p.R614H	NCOR2_ENST00000429285.2_Missense_Mutation_p.R613H|NCOR2_ENST00000397355.1_Missense_Mutation_p.R614H|NCOR2_ENST00000356219.3_Missense_Mutation_p.R614H|NCOR2_ENST00000404121.2_Missense_Mutation_p.R184H|NCOR2_ENST00000404621.1_Missense_Mutation_p.R613H			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	614	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TTCTGTCCAGCGAGAACTCTC	0.537																																					p.R614H		Atlas-SNP	.											.	NCOR2	475	.	0			c.G1841A						.						156	178	171					12																	124882700		1982	4163	6145	SO:0001583	missense	9612	exon18			GTCCAGCGAGAAC	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1841G>A	chr12.hg19:g.124882700C>T	ENSP00000384018:p.Arg614His	106.0	0.0		80.0	8.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	C	15.66	2.899745	0.52227	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69	4.91	4.91	0.64330	.	0.123300	0.56097	D	0.000030	T	0.71350	0.3329	M	0.80746	2.51	0.52099	D	0.99994	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.997	T	0.76677	-0.2871	10	0.87932	D	0	-31.0072	17.7087	0.88316	0.0:1.0:0.0:0.0	.	613;614;614	C9J0Q5;C9J239;C9JFD3	.;.;.	H	614;613;614;614;614;184;613;614	ENSP00000384018:R614H;ENSP00000384202:R613H;ENSP00000348551:R614H;ENSP00000380513:R614H;ENSP00000385618:R184H;ENSP00000400281:R613H;ENSP00000402808:R614H	ENSP00000348551:R614H	R	-	2	0	NCOR2	123448653	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	6.657000	0.74402	2.282000	0.76494	0.591000	0.81541	CGC	.	.		0.537	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		T	124882700	C	T	124882700	3	4	184	1	0	0	0	0	1	0	0	0	10245	768	27	1	5855	1	NCOR2	12	124882700	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	39432539	124882700	8969195	70	27411										
FREM2	341640	hgsc.bcm.edu	37	chr13	39262692	39262692	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cccttctgaagactctgaccAggagcgcctctttgaactgg	10	13	3	4			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr13:39262692A>T	ENST00000280481.7	+	1	1427	c.1211A>T	c.(1210-1212)cAg>cTg	p.Q404L		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	404					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GACTCTGACCAGGAGCGCCTC	0.542																																					p.Q404L		Atlas-SNP	.											.	FREM2	385	.	0			c.A1211T						.						65	72	70					13																	39262692		2203	4300	6503	SO:0001583	missense	341640	exon1			CTGACCAGGAGCG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.1211A>T	chr13.hg19:g.39262692A>T	ENSP00000280481:p.Gln404Leu	99.0	0.0		92.0	14.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	A	0.017	-1.505143	0.00992	.	.	ENSG00000150893	ENST00000280481	T	0.19394	2.15	5.94	0.95	0.19572	.	0.637859	0.15905	N	0.238894	T	0.17195	0.0413	L	0.46157	1.445	0.09310	N	1	B	0.13594	0.008	B	0.14023	0.01	T	0.21827	-1.0234	10	0.30854	T	0.27	.	9.4617	0.38789	0.5591:0.0:0.4409:0.0	.	404	Q5SZK8	FREM2_HUMAN	L	404	ENSP00000280481:Q404L	ENSP00000280481:Q404L	Q	+	2	0	FREM2	38160692	0.000000	0.05858	0.242000	0.24170	0.455000	0.32408	0.003000	0.13083	0.166000	0.19597	0.459000	0.35465	CAG	.	.		0.542	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39262692	A	T	39262692	3	4	184	1	0	0	0	0	1	0	0	0	6053	188	7	4	1213	4	FREM2	13	39262692	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10		39262692	75907186	71	27412										
COG3	83548	hgsc.bcm.edu	37	chr13	46067592	46067592	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ttgtgggattcttaaaaatgAggtgcttgaagatcatgtgc	12	4	2	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr13:46067592A>T	ENST00000349995.5	+	12	1410	c.1298A>T	c.(1297-1299)gAg>gTg	p.E433V	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	433					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		CTTAAAAATGAGGTGCTTGAA	0.343																																					p.E433V	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.A1298T						.						152	142	145					13																	46067592		2203	4300	6503	SO:0001583	missense	83548	exon12			AAAATGAGGTGCT	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1298A>T	chr13.hg19:g.46067592A>T	ENSP00000258654:p.Glu433Val	102.0	0.0		58.0	20.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.721587	0.89298	.	.	ENSG00000136152	ENST00000349995	T	0.55052	0.54	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.77485	0.4137	M	0.89968	3.075	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.998	T	0.82214	-0.0568	10	0.62326	D	0.03	-17.5228	15.0147	0.71576	1.0:0.0:0.0:0.0	.	270;433;433	B4E2F3;Q96JB2;Q96JB2-2	.;COG3_HUMAN;.	V	433	ENSP00000258654:E433V	ENSP00000258654:E433V	E	+	2	0	COG3	44965593	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.331000	0.96430	2.138000	0.66242	0.377000	0.23210	GAG	.	.		0.343	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			T	46067592	A	T	46067592	3	4	184	1	0	0	0	0	1	0	0	0	3661	304	11	4	1344	4	COG3	13	46067592	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	6804900	46067592	69102286	72	27413										
TEP1	7011	hgsc.bcm.edu	37	chr14	20847004	20847004	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggtactggtgagccttagtcTgcagcaccctatcccaggaa	11	12	1	1	rs111632717		TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr14:20847004T>C	ENST00000262715.5	-	37	5301	c.5261A>G	c.(5260-5262)cAg>cGg	p.Q1754R	TEP1_ENST00000545983.1_Missense_Mutation_p.Q92R|TEP1_ENST00000556935.1_Missense_Mutation_p.Q1646R	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1754					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AGCCTTAGTCTGCAGCACCCT	0.562																																					p.Q1754R		Atlas-SNP	.											.	TEP1	224	.	0			c.A5261G						.						76	74	75					14																	20847004		2203	4300	6503	SO:0001583	missense	7011	exon37			TTAGTCTGCAGCA		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5261A>G	chr14.hg19:g.20847004T>C	ENSP00000262715:p.Gln1754Arg	119.0	0.0		93.0	20.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	T	10.09	1.255869	0.22965	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	T;T;T	0.59638	0.25;0.25;0.25	5.76	4.63	0.57726	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.256208	0.37012	N	0.002290	T	0.24314	0.0589	N	0.01297	-0.9	0.35578	D	0.806001	B;P;B;P	0.35714	0.116;0.461;0.347;0.517	B;B;B;B	0.35931	0.057;0.136;0.085;0.214	T	0.33214	-0.9877	10	0.15066	T	0.55	-22.2884	7.7179	0.28715	0.0:0.0915:0.0:0.9085	.	92;1646;1097;1754	B4E0B6;G3V5X7;G3V2A4;Q99973	.;.;.;TEP1_HUMAN	R	1754;1754;1646;92	ENSP00000262715:Q1754R;ENSP00000452574:Q1646R;ENSP00000438849:Q92R	ENSP00000262715:Q1754R	Q	-	2	0	TEP1	19916844	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	1.772000	0.38552	2.200000	0.70718	0.460000	0.39030	CAG	.	T|0.500;C|0.500		0.562	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		C	20847004	T	C	20847004	3	2	184	1	0	0	0	0	1	0	0	0	15774	1580	55	2	2698	2	TEP1	14	20847004	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10		20847004	86502536	73	27414										
KHNYN	23351	hgsc.bcm.edu	37	chr14	24905674	24905674	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	aaacggccccaccctggatgAatttctgaagaagccagcca	9	13	1	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr14:24905674A>T	ENST00000251343.5	+	7	1905	c.1766A>T	c.(1765-1767)gAa>gTa	p.E589V	KHNYN_ENST00000556842.1_Missense_Mutation_p.E589V|KHNYN_ENST00000554268.1_Missense_Mutation_p.E34V|KHNYN_ENST00000553935.1_Missense_Mutation_p.E589V			O15037	KHNYN_HUMAN	KH and NYN domain containing	589							RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						ACCCTGGATGAATTTCTGAAG	0.562											OREG0022628	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E589V		Atlas-SNP	.											.	KHNYN	46	.	0			c.A1766T						.						54	49	51					14																	24905674		2203	4300	6503	SO:0001583	missense	23351	exon7			TGGATGAATTTCT	AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"KIAA0323"	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.1766A>T	chr14.hg19:g.24905674A>T	ENSP00000251343:p.Glu589Val	92.0	0.0	775	60.0	15.0	NM_015299	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	hg19	CCDS32058.1	.	.	.	.	.	.	.	.	.	.	A	18.52	3.641929	0.67244	.	.	ENSG00000100441	ENST00000251343;ENST00000556842;ENST00000553935;ENST00000554268	T;T;T	0.25912	1.77;1.77;1.77	5.54	5.54	0.83059	.	0.352940	0.32231	N	0.006393	T	0.50394	0.1613	M	0.76574	2.34	0.42409	D	0.99259	P;D	0.76494	0.87;0.999	P;D	0.70487	0.475;0.969	T	0.55179	-0.8181	10	0.87932	D	0	.	13.9171	0.63905	1.0:0.0:0.0:0.0	.	630;589	D3DS77;O15037	.;KHNYN_HUMAN	V	589;589;589;34	ENSP00000251343:E589V;ENSP00000451106:E589V;ENSP00000450799:E589V	ENSP00000251343:E589V	E	+	2	0	KHNYN	23975514	0.998000	0.40836	0.999000	0.59377	0.796000	0.44982	3.775000	0.55349	2.234000	0.73211	0.460000	0.39030	GAA	.	.		0.562	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1			T	24905674	A	T	24905674	3	4	184	1	0	0	0	0	1	0	0	0	8159	246	9	4	1788	4	KHNYN	14	24905674	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	4058670	24905674	82443866	74	27415										
NID2	22795	hgsc.bcm.edu	37	chr14	52485915	52485915	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggcaggaagttgccctgctcGtcgcattgggggatgtggaa	17	8	0	0	rs142814187		TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr14:52485915G>A	ENST00000216286.5	-	14	2891	c.2892C>T	c.(2890-2892)gaC>gaT	p.D964D	NID2_ENST00000541773.1_Silent_p.D863D	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	964	Thyroglobulin type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					TGCCCTGCTCGTCGCATTGGG	0.602																																					p.D964D		Atlas-SNP	.											.	NID2	201	.	0			c.C2892T						.	G		1,4405	2.1+/-5.4	0,1,2202	64	53	57		2892	-10.6	0	14	dbSNP_134	57	0,8600		0,0,4300	no	coding-synonymous	NID2	NM_007361.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		964/1376	52485915	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	22795	exon14			CTGCTCGTCGCAT	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.2892C>T	chr14.hg19:g.52485915G>A		141.0	0.0		86.0	16.0	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	hg19	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	G	0.315	-0.965618	0.02249	2.27E-4	0.0	ENSG00000087303	ENST00000556572	.	.	.	5.32	-10.6	0.00265	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3635	0.98874	0.3054:0.0:0.6946:0.0	.	.	.	.	X	233	.	.	R	-	1	2	NID2	51555665	0.671000	0.27521	0.000000	0.03702	0.083000	0.17756	-0.198000	0.09505	-2.344000	0.00622	-2.070000	0.00385	CGA	.	G|1.000;A|0.000		0.602	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			A	52485915	G	A	52485915	2	1	184	1	0	0	0	0	0	0	0	1	10424	1136	40	1		1	NID2	14	52485915	Silent	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	27580241	52485915	54863625	75	27416										
SLC8A3	6547	hgsc.bcm.edu	37	chr14	70633575	70633575	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	catggtcatcatccaagatgGtaactgtggccacacaaggg	11	10	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr14:70633575G>A	ENST00000381269.2	-	2	2318	c.1565C>T	c.(1564-1566)aCc>aTc	p.T522I	SLC8A3_ENST00000528359.1_Missense_Mutation_p.T522I|SLC8A3_ENST00000357887.3_Missense_Mutation_p.T522I|SLC8A3_ENST00000534137.1_Missense_Mutation_p.T522I|SLC8A3_ENST00000356921.2_Missense_Mutation_p.T522I	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	522	Calx-beta 2.				blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		ATCCAAGATGGTAACTGTGGC	0.502																																					p.T522I		Atlas-SNP	.											.	SLC8A3	234	.	0			c.C1565T						.						62	60	61					14																	70633575		2203	4300	6503	SO:0001583	missense	6547	exon2			AAGATGGTAACTG	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"Solute carriers"	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.1565C>T	chr14.hg19:g.70633575G>A	ENSP00000370669:p.Thr522Ile	107.0	0.0		70.0	9.0	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	hg19	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.945779	0.53079	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000534137;ENST00000528359	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	5.69	5.69	0.88448	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.70298	0.3208	M	0.85945	2.785	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.998;0.999	T	0.71731	-0.4504	10	0.48119	T	0.1	.	19.8067	0.96534	0.0:0.0:1.0:0.0	.	522;522;522;522	P57103-2;P57103;Q96QG2;Q96QG1	.;NAC3_HUMAN;.;.	I	522	ENSP00000349392:T522I;ENSP00000370669:T522I;ENSP00000350560:T522I;ENSP00000436688:T522I;ENSP00000433531:T522I	ENSP00000349392:T522I	T	-	2	0	SLC8A3	69703328	1.000000	0.71417	0.967000	0.41034	0.989000	0.77384	9.869000	0.99810	2.672000	0.90937	0.650000	0.86243	ACC	.	.		0.502	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			A	70633575	G	A	70633575	3	1	184	1	0	0	0	0	1	0	0	0	14723	1261	44	3	1357	3	SLC8A3	14	70633575	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	18147660	70633575	36715965	76	27417										
EML5	161436	hgsc.bcm.edu	37	chr14	89094074	89094074	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gccagtagcactgaagctgaCtgaacatactccctttgaat	8	11	0	4			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr14:89094074C>A	ENST00000380664.5	-	32	4422	c.4423G>T	c.(4423-4425)Gtc>Ttc	p.V1475F	EML5_ENST00000352093.5_Missense_Mutation_p.V1437F|EML5_ENST00000554922.1_Missense_Mutation_p.V1483F|EML5_ENST00000553320.1_5'Flank			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1475						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CTGAAGCTGACTGAACATACT	0.418																																					p.V1483F		Atlas-SNP	.											.	EML5	141	.	0			c.G4447T						.						84	81	82					14																	89094074		1897	4124	6021	SO:0001583	missense	161436	exon33			AGCTGACTGAACA	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.4423G>T	chr14.hg19:g.89094074C>A	ENSP00000370039:p.Val1475Phe	47.0	0.0		69.0	28.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.963838	0.92791	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.38722	1.12;1.12;1.12	5.29	5.29	0.74685	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.066219	0.64402	D	0.000013	T	0.74520	0.3727	H	0.94306	3.52	0.58432	D	0.999999	D;D	0.61080	0.989;0.975	D;P	0.67103	0.949;0.835	T	0.82045	-0.0652	10	0.87932	D	0	-12.599	19.1314	0.93408	0.0:1.0:0.0:0.0	.	1483;1475	Q05BV3-5;Q05BV3	.;EMAL5_HUMAN	F	1483;1437;1475	ENSP00000451998:V1483F;ENSP00000298315:V1437F;ENSP00000370039:V1475F	ENSP00000298315:V1437F	V	-	1	0	EML5	88163827	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.393000	0.59665	2.751000	0.94390	0.650000	0.86243	GTC	.	.		0.418	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			A	89094074	C	A	89094074	3	1	184	1	0	0	0	0	1	0	0	0	5102	565	20	3	1530	3	EML5	14	89094074	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	18460499	89094074	18255466	77	27418										
PRIMA1	145270	hgsc.bcm.edu	37	chr14	94245574	94245575	+	Frame_Shift_Ins	INS	-	-	GGGG													0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gtgggggcggcgggggcagcINSgggggagggggccggcactg					rs550883370		TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr14:94245574_94245575insGGGG	ENST00000393140.1	-	3	278_279	c.176_177insCCCC	c.(175-177)ccgfs	p.P59fs	PRIMA1_ENST00000393143.1_Frame_Shift_Ins_p.P59fs|PRIMA1_ENST00000316227.3_Frame_Shift_Ins_p.P59fs	NM_178013.3	NP_821092.1	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1	59	PRAD.				establishment of localization in cell (GO:0051649)|neurotransmitter catabolic process (GO:0042135)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|synapse (GO:0045202)				endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		gcgggggcagcgggggaggggg	0.629																																					p.P59fs		Atlas-INDEL	.											.	PRIMA1	21	.	0			c.177_178insCCCC						.																																			SO:0001589	frameshift_variant	145270	exon3			.		CCDS9912.1	14q32.13	2008-08-29			ENSG00000175785	ENSG00000175785			18319	protein-coding gene	gene with protein product	"membrane anchor of acetylcholinesterase"	613851				11804574	Standard	NM_178013		Approved	PRIMA	uc001ybw.1	Q86XR5	OTTHUMG00000141313	ENST00000393140.1:c.173_176dupCCCC	chr14.hg19:g.94245575_94245578dupGGGG	ENSP00000376848:p.Pro59fs	105.0	0.0		73.0	24.0	NM_178013	Q86XR6	Frame_Shift_Ins	INS	ENST00000393140.1	hg19	CCDS9912.1																																																																																			.	.		0.629	PRIMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280658.1	NM_178013		GGGG	94245575	-	GGGG	94245574	7	5	184	1	0	1	1	0	0	0	0	0	12504	755	27	0	296	0	PRIMA1	14	94245574	Frame_Shift_Ins	INS	-	TCGA-DD-AADA-01A-11D-A40R-10	5151500	94245574	13103966	78	27419										
RFX7	64864	hgsc.bcm.edu	37	chr15	56386765	56386765	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tggttttgtcagggtgtgtgGccatgggtctttgcatcggt	16	6	2	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr15:56386765G>C	ENST00000559447.2	-	9	3141	c.2870C>G	c.(2869-2871)gCc>gGc	p.A957G	RFX7_ENST00000423270.1_Missense_Mutation_p.A1054G|RFX7_ENST00000422057.1_Missense_Mutation_p.A957G|RFX7_ENST00000317318.6_Missense_Mutation_p.A1054G			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	957					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						AGGGTGTGTGGCCATGGGTCT	0.458																																					p.A1054G		Atlas-SNP	.											.	RFX7	170	.	0			c.C3161G						.						137	126	129					15																	56386765		1974	4163	6137	SO:0001583	missense	64864	exon9			TGTGTGGCCATGG			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.2870C>G	chr15.hg19:g.56386765G>C	ENSP00000453281:p.Ala957Gly	102.0	0.0		62.0	21.0	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	hg19		.	.	.	.	.	.	.	.	.	.	G	18.78	3.697075	0.68386	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	T;T;T	0.66280	-0.18;-0.2;-0.18	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.72827	0.3509	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.73914	-0.3832	10	0.87932	D	0	-12.9301	19.583	0.95478	0.0:0.0:1.0:0.0	.	957;957	Q2KHR2;C9JU50	RFX7_HUMAN;.	G	957;1054;1054	ENSP00000387504:A957G;ENSP00000313299:A1054G;ENSP00000397644:A1054G	ENSP00000313299:A1054G	A	-	2	0	RFX7	54174057	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.873000	0.98535	0.563000	0.77884	GCC	.	.		0.458	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		C	56386765	G	C	56386765	3	2	184	1	0	0	0	0	1	0	0	0	13283	1203	42	4	1225	4	RFX7	15	56386765	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10		56386765	46144627	79	27420										
MEF2A	4205	hgsc.bcm.edu	37	chr15	100252723	100252723	+	Missense_Mutation	SNP	A	A	C													0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gggcttccagcagcagcagcAgcagcagcagcagcagcagc							TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr15:100252723A>C	ENST00000557785.1	+	11	1590	c.1241A>C	c.(1240-1242)cAg>cCg	p.Q414P	MEF2A_ENST00000557942.1_Missense_Mutation_p.Q422P|MEF2A_ENST00000558812.1_Missense_Mutation_p.Q354P|MEF2A_ENST00000453228.2_Missense_Mutation_p.Q414P|MEF2A_ENST00000338042.6_Missense_Mutation_p.Q423P|MEF2A_ENST00000354410.5_Missense_Mutation_p.Q416P|MEF2A_ENST00000449277.2_Missense_Mutation_p.Q346P	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	424					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			cagcagcagcagcagcagcag	0.607																																					p.Q416P		Atlas-SNP	.											.	MEF2A	138	.	0			c.A1247C						.																																			SO:0001583	missense	4205	exon11			AGCAGCAGCAGCA		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"Myocyte enhancer factors"	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.1241A>C	chr15.hg19:g.100252723A>C	ENSP00000453441:p.Gln414Pro	30.0	0.0		32.0	7.0	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Missense_Mutation	SNP	ENST00000557785.1	hg19	CCDS53978.1	.	.	.	.	.	.	.	.	.	.	A	0.066	-1.211925	0.01555	.	.	ENSG00000068305	ENST00000453228;ENST00000354410;ENST00000338042;ENST00000449277	T;T;T	0.08282	3.11;3.11;3.11	4.82	2.38	0.29361	.	.	.	.	.	T	0.03520	0.0101	N	0.02539	-0.55	0.24848	N	0.992424	B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001;0.0	B;B;B;B;B;B	0.06405	0.001;0.001;0.0;0.0;0.002;0.001	T	0.45542	-0.9254	9	0.14252	T	0.57	0.0679	12.4364	0.55602	0.5037:0.4963:0.0:0.0	.	424;354;335;414;416;422	Q02078;B4DFQ7;Q7Z6C9;Q02078-6;Q02078-5;Q02078-2	MEF2A_HUMAN;.;.;.;.;.	P	414;416;423;354	ENSP00000404110:Q414P;ENSP00000346389:Q416P;ENSP00000337202:Q423P	ENSP00000337202:Q423P	Q	+	2	0	MEF2A	98070246	0.868000	0.29978	0.992000	0.48379	0.952000	0.60782	0.779000	0.26746	0.171000	0.19730	0.528000	0.53228	CAG	.	.		0.607	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1			C	100252723	A	C	100252723	3	2	184	1	0	0	0	0	1	0	0	0	9464	188	7	5	1445	5	MEF2A	15	100252723	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	43865958	100252723	2278669	80	27421	134	2								
MEF2A	4205	hgsc.bcm.edu	37	chr15	100252726	100252726	+	Missense_Mutation	SNP	A	A	C													0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cttccagcagcagcagcagcAgcagcagcagcagcagccgc					rs200861006		TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr15:100252726A>C	ENST00000557785.1	+	11	1593	c.1244A>C	c.(1243-1245)cAg>cCg	p.Q415P	MEF2A_ENST00000557942.1_Missense_Mutation_p.Q423P|MEF2A_ENST00000558812.1_Missense_Mutation_p.Q355P|MEF2A_ENST00000453228.2_Missense_Mutation_p.Q415P|MEF2A_ENST00000338042.6_Missense_Mutation_p.Q424P|MEF2A_ENST00000354410.5_Missense_Mutation_p.Q417P|MEF2A_ENST00000449277.2_Missense_Mutation_p.Q347P	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	425					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			cagcagcagcagcagcagcag	0.617																																					p.Q417P		Atlas-SNP	.											.	MEF2A	138	.	0			c.A1250C						.						6	9	8					15																	100252726		1716	3457	5173	SO:0001583	missense	4205	exon11			AGCAGCAGCAGCA		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"Myocyte enhancer factors"	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.1244A>C	chr15.hg19:g.100252726A>C	ENSP00000453441:p.Gln415Pro	30.0	0.0		32.0	5.0	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Missense_Mutation	SNP	ENST00000557785.1	hg19	CCDS53978.1	.	.	.	.	.	.	.	.	.	.	a	5.679	0.309950	0.10733	.	.	ENSG00000068305	ENST00000453228;ENST00000354410;ENST00000338042;ENST00000449277	T;T;T	0.08458	3.09;3.09;3.09	4.82	0.944	0.19537	.	.	.	.	.	T	0.03651	0.0104	N	0.02011	-0.69	0.23162	N	0.998192	B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001;0.0	B;B;B;B;B;B	0.06405	0.001;0.001;0.0;0.0;0.002;0.0	T	0.43310	-0.9399	9	0.37606	T	0.19	-0.1462	12.5533	0.56240	0.604:0.396:0.0:0.0	.	425;355;336;415;417;423	Q02078;B4DFQ7;Q7Z6C9;Q02078-6;Q02078-5;Q02078-2	MEF2A_HUMAN;.;.;.;.;.	P	415;417;424;355	ENSP00000404110:Q415P;ENSP00000346389:Q417P;ENSP00000337202:Q424P	ENSP00000337202:Q424P	Q	+	2	0	MEF2A	98070249	1.000000	0.71417	0.556000	0.28293	0.920000	0.55202	2.975000	0.49281	-0.113000	0.11958	0.528000	0.53228	CAG	.	.		0.617	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1			C	100252726	A	C	100252726	3	2	184	1	0	0	0	0	1	0	0	0	9464	188	7	5	1448	5	MEF2A	15	100252726	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	3	100252726	2278666	81	27422	134	2								
MEFV	4210	hgsc.bcm.edu	37	chr16	3304621	3304621	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ttcctcgacagccccctcccGgcctcgggctggctgcaccg	11	20	0	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr16:3304621G>A	ENST00000219596.1	-	2	486	c.447C>T	c.(445-447)gcC>gcT	p.A149A	MEFV_ENST00000536379.1_Intron|MEFV_ENST00000541159.1_Intron|MEFV_ENST00000339854.4_Intron	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	149					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GCCCCCTCCCGGCCTCGGGCT	0.736																																					p.A149A		Atlas-SNP	.											.	MEFV	170	.	0			c.C447T						.						10	11	11					16																	3304621		2150	4209	6359	SO:0001819	synonymous_variant	4210	exon2			CCTCCCGGCCTCG	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.447C>T	chr16.hg19:g.3304621G>A		39.0	0.0		20.0	6.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	hg19	CCDS10498.1																																																																																			.	.		0.736	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		A	3304621	G	A	3304621	2	1	184	1	0	0	0	0	0	0	0	1	9468	1103	39	1		1	MEFV	16	3304621	Silent	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10		3304621	87050132	82	27423										
KCTD13	253980	hgsc.bcm.edu	37	chr16	29934567	29934567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	caccaggtagtagcgtgcttCgcccagcagctcccccagtt	10	16	0	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr16:29934567C>T	ENST00000568000.1	-	2	1359	c.358G>A	c.(358-360)Gaa>Aaa	p.E120K	KCTD13_ENST00000568721.1_5'UTR|KCTD13_ENST00000561540.1_Missense_Mutation_p.E120K|CTD-2574D22.4_ENST00000567795.1_RNA	NM_178863.3	NP_849194.1	Q8WZ19	BACD1_HUMAN	potassium channel tetramerization domain containing 13	120					cell migration (GO:0016477)|DNA replication (GO:0006260)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of DNA replication (GO:0045740)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)	GTP-Rho binding (GO:0017049)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	7						TAGCGTGCTTCGCCCAGCAGC	0.617																																					p.E120K		Atlas-SNP	.											.	KCTD13	19	.	0			c.G358A						.						51	44	47					16																	29934567		2197	4300	6497	SO:0001583	missense	253980	exon2			GTGCTTCGCCCAG	AF289573	CCDS10661.1	16p11.2	2013-06-20	2013-06-20		ENSG00000174943	ENSG00000174943			22234	protein-coding gene	gene with protein product	"polymerase delta-interacting protein 1", "TNFAIP1-like"	608947	"potassium channel tetramerisation domain containing 13"			11593007	Standard	NM_178863		Approved	PDIP1, FKSG86, POLDIP1	uc002duv.4	Q8WZ19	OTTHUMG00000132120	ENST00000568000.1:c.358G>A	chr16.hg19:g.29934567C>T	ENSP00000455785:p.Glu120Lys	123.0	0.0		85.0	33.0	NM_178863	A8K0R5|Q96P93|Q96SA1	Missense_Mutation	SNP	ENST00000568000.1	hg19	CCDS10661.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.811639	0.90707	.	.	ENSG00000174943	ENST00000308768	D	0.86956	-2.19	5.02	5.02	0.67125	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.64402	D	0.000008	D	0.96327	0.8802	H	0.98612	4.28	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97907	1.0306	10	0.87932	D	0	.	17.2768	0.87118	0.0:1.0:0.0:0.0	.	120	Q8WZ19	BACD1_HUMAN	K	120	ENSP00000311202:E120K	ENSP00000311202:E120K	E	-	1	0	KCTD13	29842068	1.000000	0.71417	0.993000	0.49108	0.867000	0.49689	7.379000	0.79691	2.596000	0.87737	0.563000	0.77884	GAA	.	.		0.617	KCTD13-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255162.2	NM_178863		T	29934567	C	T	29934567	3	4	184	1	0	0	0	0	1	0	0	0	8109	893	31	1	651	1	KCTD13	16	29934567	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	26629946	29934567	60420186	83	27424										
VPS35	55737	hgsc.bcm.edu	37	chr16	46708524	46708524	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	aatatatcaaaaagtttaatAtccgctgggattccaggtcc	7	8	1	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr16:46708524A>C	ENST00000299138.7	-	9	1021	c.963T>G	c.(961-963)gaT>gaG	p.D321E	VPS35_ENST00000568642.1_5'UTR	NM_018206.4	NP_060676.2	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35 homolog (S. cerevisiae)	321					cell death (GO:0008219)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|retromer complex (GO:0030904)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|pancreas(1)|prostate(1)|urinary_tract(1)	23		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				AAAGTTTAATATCCGCTGGGA	0.363																																					p.D321E		Atlas-SNP	.											.	VPS35	49	.	0			c.T963G						.						47	46	46					16																	46708524		2203	4300	6503	SO:0001583	missense	55737	exon9			TTTAATATCCGCT	AF175265	CCDS10721.1	16q12	2012-06-27	2006-12-19		ENSG00000069329	ENSG00000069329		"Parkinson disease"	13487	protein-coding gene	gene with protein product		601501	"vacuolar protein sorting 35 (yeast homolog)", "vacuolar protein sorting 35 (yeast)"			11112353, 21763482	Standard	NM_018206		Approved	FLJ10752, MEM3, PARK17	uc002eef.4	Q96QK1	OTTHUMG00000132542	ENST00000299138.7:c.963T>G	chr16.hg19:g.46708524A>C	ENSP00000299138:p.Asp321Glu	137.0	0.0		77.0	11.0	NM_018206	Q561W2|Q9H016|Q9H096|Q9H4P3|Q9H8J0|Q9NRS7|Q9NVG2|Q9NX80|Q9NZK2	Missense_Mutation	SNP	ENST00000299138.7	hg19	CCDS10721.1	.	.	.	.	.	.	.	.	.	.	.	10.64	1.407448	0.25378	.	.	ENSG00000069329	ENST00000299138;ENST00000541330	T	0.42900	0.96	5.84	1.12	0.20585	.	0.094662	0.64402	N	0.000001	T	0.20170	0.0485	N	0.20986	0.625	0.38156	D	0.938897	B;B	0.06786	0.0;0.001	B;B	0.13407	0.009;0.004	T	0.26883	-1.0090	10	0.02654	T	1	-20.4863	6.4417	0.21853	0.6121:0.124:0.2639:0.0	.	321;186	Q96QK1;F5GYF5	VPS35_HUMAN;.	E	321;186	ENSP00000299138:D321E	ENSP00000299138:D321E	D	-	3	2	VPS35	45266025	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.073000	0.30691	0.129000	0.18514	0.482000	0.46254	GAT	.	.		0.363	VPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255742.3			C	46708524	A	C	46708524	3	2	184	1	0	0	0	0	1	0	0	0	17218	446	16	5	1463	5	VPS35	16	46708524	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	16773957	46708524	43646229	84	27425										
CDH1	999	hgsc.bcm.edu	37	chr16	68849632	68849632	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cacatcctacactgcccaggAgccagacacatttatggaac	7	14	0	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr16:68849632A>T	ENST00000261769.5	+	10	1726	c.1535A>T	c.(1534-1536)gAg>gTg	p.E512V	CDH1_ENST00000422392.2_Missense_Mutation_p.E451V|RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	512	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		ACTGCCCAGGAGCCAGACACA	0.423			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												p.E512V		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	.	CDH1	535	.	1	Unknown(1)	breast(1)	c.A1535T						.						111	101	104					16																	68849632		2198	4300	6498	SO:0001583	missense	999	exon10	Familial Cancer Database	HDGC	CCCAGGAGCCAGA	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1535A>T	chr16.hg19:g.68849632A>T	ENSP00000261769:p.Glu512Val	170.0	0.0		104.0	27.0	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	hg19	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.943810	0.73672	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.62364	0.03;0.03	5.32	5.32	0.75619	Cadherin (4);Cadherin-like (1);	0.759830	0.11540	N	0.553869	T	0.69495	0.3117	L	0.39898	1.24	0.47994	D	0.999564	P;P	0.49862	0.929;0.878	P;P	0.56216	0.794;0.787	T	0.68372	-0.5426	10	0.87932	D	0	.	14.944	0.71016	1.0:0.0:0.0:0.0	.	451;512	Q9UII8;P12830	.;CADH1_HUMAN	V	512;530;512;451	ENSP00000261769:E512V;ENSP00000414946:E451V	ENSP00000261769:E512V	E	+	2	0	CDH1	67407133	1.000000	0.71417	0.305000	0.25099	0.523000	0.34469	8.904000	0.92590	2.012000	0.59069	0.459000	0.35465	GAG	.	.		0.423	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		T	68849632	A	T	68849632	3	4	184	1	0	0	0	0	1	0	0	0	3097	304	11	4	1573	4	CDH1	16	68849632	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	22141108	68849632	21505121	85	27426										
CCDC103	100528020	hgsc.bcm.edu	37	chr17	42979763	42979763	+	De_novo_Start_InFrame	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ccctccagcccgagacgtctGctgacttctatcgtgattgg	10	14	2	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr17:42979763G>A	ENST00000331733.4	+	0	402				CCDC103_ENST00000410027.1_3'UTR|EFTUD2_ENST00000592576.1_5'Flank|CCDC103_ENST00000410006.2_Missense_Mutation_p.A103T|EFTUD2_ENST00000402521.3_5'Flank|FAM187A_ENST00000412523.2_Intron|AC015936.3_ENST00000441312.1_RNA|EFTUD2_ENST00000426333.2_5'Flank|CCDC103_ENST00000417826.2_Missense_Mutation_p.A103T	NM_001258399.1|NM_213607.2	NP_001245328.1|NP_998772.1	A6NFU0	F187A_HUMAN	family with sequence similarity 187, member A							integral component of membrane (GO:0016021)											CGAGACGTCTGCTGACTTCTA	0.597																																					p.C104Y		Atlas-SNP	.											.	CCDC103	15	.	0			c.G311A						.						76	79	78					17																	42979763		2203	4300	6503			388389	exon4			ACGTCTGCTGACT			17q21.31	2013-01-11			ENSG00000214447	ENSG00000214447		"Immunoglobulin superfamily / V-set domain containing"	35153	protein-coding gene	gene with protein product							Standard			Approved		uc002ihp.1	A6NFU0	OTTHUMG00000154266		chr17.hg19:g.42979763G>A		109.0	0.0		104.0	38.0	NM_001258399		Missense_Mutation	SNP	ENST00000331733.4	hg19		.	.	.	.	.	.	.	.	.	.	G	6.138	0.393675	0.11638	.	.	ENSG00000167131	ENST00000357776;ENST00000417826;ENST00000410006	T;T;T	0.55413	0.52;0.52;0.52	6.16	5.13	0.70059	.	0.394056	0.19633	U	0.109627	T	0.63815	0.2543	L	0.56769	1.78	0.23198	N	0.998137	D	0.60160	0.987	P	0.58620	0.842	T	0.55490	-0.8133	10	0.22706	T	0.39	-7.9467	16.6975	0.85339	0.0:0.0:0.8626:0.1374	.	103	Q8IW40	CC103_HUMAN	T	103	ENSP00000350420:A103T;ENSP00000391692:A103T;ENSP00000387252:A103T	ENSP00000350420:A103T	A	+	1	0	CCDC103	40335289	0.905000	0.30787	0.960000	0.40013	0.110000	0.19582	2.041000	0.41213	2.937000	0.99478	0.650000	0.86243	GCT	.	.		0.597	FAM187A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334584.1			A	42979763	G	A	42979763	1	1	184	1	0	1	0	0	0	0	0	0	2740	1319	46	3		3	CCDC103	17	42979763	De_novo_Start_InFrame	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10		42979763	38215447	86	27427										
TLK2	11011	hgsc.bcm.edu	37	chr17	60599622	60599622	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	aaagaaaagctgaaccatatGaaactagccaaggtagtaat	8	6	0	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr17:60599622G>A	ENST00000326270.9	+	4	479	c.211G>A	c.(211-213)Gaa>Aaa	p.E71K	TLK2_ENST00000343388.7_Missense_Mutation_p.E71K|TLK2_ENST00000582809.1_5'UTR|TLK2_ENST00000542523.1_Missense_Mutation_p.E71K|TLK2_ENST00000346027.5_Missense_Mutation_p.E71K	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	71					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						TGAACCATATGAAACTAGCCA	0.313																																					p.E71K		Atlas-SNP	.											.	TLK2	223	.	0			c.G211A						.						48	45	46					17																	60599622		2203	4300	6503	SO:0001583	missense	11011	exon4			CCATATGAAACTA	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.211G>A	chr17.hg19:g.60599622G>A	ENSP00000316512:p.Glu71Lys	474.0	0.0		373.0	128.0	NM_001112707	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	hg19		.	.	.	.	.	.	.	.	.	.	G	16.43	3.122393	0.56613	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.39	5.39	0.77823	.	0.096119	0.64402	D	0.000001	T	0.79907	0.4527	L	0.54323	1.7	0.51482	D	0.999925	B;B;B	0.31730	0.037;0.214;0.337	B;B;B	0.29077	0.028;0.098;0.098	T	0.76971	-0.2761	10	0.28530	T	0.3	-7.7637	17.7354	0.88391	0.0:0.0:1.0:0.0	.	71;71;71	Q86UE8;Q86UE8-3;Q86UE8-2	TLK2_HUMAN;.;.	K	71	ENSP00000275780:E71K;ENSP00000340800:E71K;ENSP00000316512:E71K;ENSP00000442311:E71K	ENSP00000316512:E71K	E	+	1	0	TLK2	57953354	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.454000	0.80714	2.516000	0.84829	0.563000	0.77884	GAA	.	.		0.313	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852		A	60599622	G	A	60599622	3	1	184	1	0	0	0	0	1	0	0	0	15959	1291	45	3	221	3	TLK2	17	60599622	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	17619859	60599622	20595588	87	27428										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6985272	6985272	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ctagtctctggaactcagcgGcatggtcctcagctctgtag	11	12	4	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr18:6985272G>C	ENST00000389658.3	-	39	5717	c.5624C>G	c.(5623-5625)gCc>gGc	p.A1875G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1875	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GAACTCAGCGGCATGGTCCTC	0.493																																					p.A1875G		Atlas-SNP	.											.	LAMA1	458	.	0			c.C5624G						.						202	164	177					18																	6985272		2203	4300	6503	SO:0001583	missense	284217	exon39			TCAGCGGCATGGT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5624C>G	chr18.hg19:g.6985272G>C	ENSP00000374309:p.Ala1875Gly	76.0	0.0		85.0	13.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.969664	0.53614	.	.	ENSG00000101680	ENST00000389658	T	0.40225	1.04	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000001	T	0.62319	0.2418	M	0.73962	2.25	0.53688	D	0.999975	D	0.59767	0.986	P	0.59115	0.852	T	0.65384	-0.6181	10	0.66056	D	0.02	.	17.741	0.88407	0.0:0.0:1.0:0.0	.	1875	P25391	LAMA1_HUMAN	G	1875	ENSP00000374309:A1875G	ENSP00000374309:A1875G	A	-	2	0	LAMA1	6975272	1.000000	0.71417	0.377000	0.26055	0.015000	0.08874	7.745000	0.85046	2.631000	0.89168	0.655000	0.94253	GCC	.	.		0.493	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		C	6985272	G	C	6985272	3	2	184	1	0	0	0	0	1	0	0	0	8614	1203	42	4	3703	4	LAMA1	18	6985272	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10		6985272	71091976	88	27429										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31323438	31323438	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ttctgatgaaaacatacctgTgtcacatttatctgagaaaa	6	7	3	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr18:31323438T>A	ENST00000269197.5	+	12	3626	c.3626T>A	c.(3625-3627)gTg>gAg	p.V1209E		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1209	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AACATACCTGTGTCACATTTA	0.403																																					p.V1209E		Atlas-SNP	.											ASXL3_ENST00000269197,NS,carcinoma,0,2	ASXL3	405	.	0			c.T3626A						.						71	66	67					18																	31323438		1853	4106	5959	SO:0001583	missense	80816	exon12			TACCTGTGTCACA	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.3626T>A	chr18.hg19:g.31323438T>A	ENSP00000269197:p.Val1209Glu	91.0	0.0		68.0	24.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.414656	0.42817	.	.	ENSG00000141431	ENST00000269197	T	0.49139	0.79	5.68	3.33	0.38152	.	2.380980	0.01586	N	0.021317	T	0.44052	0.1275	L	0.27053	0.805	0.35528	D	0.801988	P	0.45902	0.868	P	0.44860	0.462	T	0.33471	-0.9867	10	0.38643	T	0.18	.	9.5432	0.39264	0.0:0.1413:0.0:0.8587	.	1209	Q9C0F0	ASXL3_HUMAN	E	1209	ENSP00000269197:V1209E	ENSP00000269197:V1209E	V	+	2	0	ASXL3	29577436	1.000000	0.71417	0.901000	0.35422	0.976000	0.68499	3.241000	0.51376	0.991000	0.38814	0.533000	0.62120	GTG	.	.		0.403	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			A	31323438	T	A	31323438	3	1	184	1	0	0	0	0	1	0	0	0	1068	1696	59	4	3672	4	ASXL3	18	31323438	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	24338166	31323438	46753810	89	27430										
KIAA1543	57662	hgsc.bcm.edu	37	chr19	7676885	7676885	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ctggcctccccctacctgccCgaggggacctccaaaccact	8	20	0	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr19:7676885C>T	ENST00000160298.4	+	11	1607	c.1506C>T	c.(1504-1506)ccC>ccT	p.P502P	CAMSAP3_ENST00000446248.2_Silent_p.P529P	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	502	Pro-rich.				epithelial cell-cell adhesion (GO:0090136)|microtubule anchoring (GO:0034453)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of organelle organization (GO:0033043)|zonula adherens maintenance (GO:0045218)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)|zonula adherens (GO:0005915)	microtubule minus-end binding (GO:0051011)			cervix(1)|endometrium(7)|kidney(3)|lung(6)|urinary_tract(2)	19						CCTACCTGCCCGAGGGGACCT	0.682																																					p.P529P		Atlas-SNP	.											.	CAMSAP3	131	.	0			c.C1587T						.						40	47	45					19																	7676885		1995	4155	6150	SO:0001819	synonymous_variant	57662	exon13			CCTGCCCGAGGGG	AB040976	CCDS42489.1, CCDS45947.1	19p13.3-p13.2	2014-06-12	2011-08-18	2011-08-18		ENSG00000076826			29307	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 80"	612685	"KIAA1543"	KIAA1543		11318610, 10819331, 19041755, 19508979	Standard	NM_001080429		Approved	Nezha, PPP1R80	uc002mgu.4	Q9P1Y5		ENST00000160298.4:c.1506C>T	chr19.hg19:g.7676885C>T		100.0	0.0		58.0	7.0	NM_001080429	Q8NDF1	Silent	SNP	ENST00000160298.4	hg19	CCDS42489.1																																																																																			.	.		0.682	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362		T	7676885	C	T	7676885	2	4	184	1	0	0	0	0	0	0	0	1	8252	639	23	1		1	KIAA1543	19	7676885	Silent	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10		7676885	51452098	90	27431										
ZNF791	163049	hgsc.bcm.edu	37	chr19	12739581	12739581	+	Frame_Shift_Del	DEL	A	A	-													0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cactggagaaaaaccctatgAgtgtaaggaatgtgcaaaaa							TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr19:12739581delA	ENST00000343325.4	+	4	1400	c.1238delA	c.(1237-1239)gagfs	p.E413fs	ZNF791_ENST00000446165.1_3'UTR|ZNF490_ENST00000465656.1_Intron|ZNF791_ENST00000540038.1_Frame_Shift_Del_p.E304fs|AC010422.1_ENST00000408416.1_RNA|ZNF791_ENST00000458122.3_Frame_Shift_Del_p.E381fs	NM_153358.2	NP_699189.2	Q3KP31	ZN791_HUMAN	zinc finger protein 791	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)	19						AAACCCTATGAGTGTAAGGAA	0.398																																					p.E413fs		Atlas-INDEL	.											.	ZNF791	53	.	0			c.1237delG						.						102	108	106					19																	12739581		2203	4300	6503	SO:0001589	frameshift_variant	163049	exon4			.	AK074877	CCDS12273.1	19p13.2-p13.13	2013-01-08			ENSG00000173875	ENSG00000173875		"Zinc fingers, C2H2-type", "-"	26895	protein-coding gene	gene with protein product							Standard	NM_153358		Approved	FLJ90396	uc002mua.2	Q3KP31	OTTHUMG00000156426	ENST00000343325.4:c.1238delA	chr19.hg19:g.12739581delA	ENSP00000342974:p.Glu413fs	147.0	0.0		103.0	12.0	NM_153358	B7Z586|Q8NC99	Frame_Shift_Del	DEL	ENST00000343325.4	hg19	CCDS12273.1																																																																																			.	.		0.398	ZNF791-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344140.1	NM_153358		-	12739581	A	-	12739581	7	5	184	1	0	1	0	1	0	0	0	0	18178	304	11	0	1252	0	ZNF791	19	12739581	Frame_Shift_Del	DEL	A	TCGA-DD-AADA-01A-11D-A40R-10	5062696	12739581	46389402	91	27432										
WIZ	58525	hgsc.bcm.edu	37	chr19	15547669	15547669	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	caggtgggtggaaagggcacCgtgagaggtaagcggggccg	21	7	0	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr19:15547669C>T	ENST00000389282.4	-	4	2757	c.2544G>A	c.(2542-2544)acG>acA	p.T848T	WIZ_ENST00000263381.7_Silent_p.T159T			O95785	WIZ_HUMAN	widely interspaced zinc finger motifs	848					positive regulation of nuclear cell cycle DNA replication (GO:0010571)|protein heterotrimerization (GO:0070208)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	24						GAAAGGGCACCGTGAGAGGTA	0.706																																					p.T159T		Atlas-SNP	.											.	WIZ	152	.	0			c.G477A						.						20	24	23					19																	15547669		1880	4104	5984	SO:0001819	synonymous_variant	58525	exon3			GGGCACCGTGAGA	AK091183	CCDS42516.1	19p13.12	2012-10-05	2007-01-18		ENSG00000011451	ENSG00000011451		"Zinc fingers, C2H2-type"	30917	protein-coding gene	gene with protein product			"WIZ zinc finger"			9795207, 12226707	Standard	NM_021241		Approved	ZNF803	uc002nbb.4	O95785		ENST00000389282.4:c.2544G>A	chr19.hg19:g.15547669C>T		190.0	0.0		165.0	21.0	NM_021241	B3KVH1|B7ZM82|M0QY21|Q4G0E0|Q6P6B0|Q6ZN24|Q7LDY6|Q7LDZ1|Q96IG5|Q96SQ6|Q9BUR8|Q9NPT1	Silent	SNP	ENST00000389282.4	hg19																																																																																				.	.		0.706	WIZ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021241		T	15547669	C	T	15547669	2	4	184	1	0	0	0	0	0	0	0	1	17390	639	23	1		1	WIZ	19	15547669	Silent	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	2808088	15547669	43581314	92	27433										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30936235	30936236	+	Missense_Mutation	DNP	GC	GC	AA													0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ggttcacagcactaaagtggGcagccagagagacctgccaa							TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr19:30936235_30936236GC>AA	ENST00000355537.3	+	2	1913_1914	c.1766_1767GC>AA	c.(1765-1767)gGC>gAA	p.G589E		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	589					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					ACTAAAGTGGGCAGCCAGAGAG	0.515																																					p.G589D|p.G589G		Atlas-SNP	.											.	ZNF536	424	.	0			c.G1766A|c.C1767A						.																																			SO:0001583	missense	9745	exon2			AAGTGGGCAGCCA|AGTGGGCAGCCAG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		Exception_encountered	chr19.hg19:g.30936235_30936236delinsAA	ENSP00000347730:p.Gly589Glu	129.0	0.0		98.0	35.0	NM_014717	A2RU18	Missense_Mutation|Silent	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.		0.515	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		AA	30936236	GC	AA	30936235	3	1	184	1	0	0	0	0	1	0	0	0	17989	1203	42	3	1768	3	ZNF536	19	30936235	Missense_Mutation	DNP	GC	TCGA-DD-AADA-01A-11D-A40R-10	15388566	30936235	28192748	93	27434										
RYR1	6261	hgsc.bcm.edu	37	chr19	39034257	39034257	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gaacttctccaaagccatgtCggtggctaagcaggtgttca	11	10	2	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr19:39034257C>T	ENST00000359596.3	+	86	11864	c.11864C>T	c.(11863-11865)tCg>tTg	p.S3955L	RYR1_ENST00000360985.3_Missense_Mutation_p.S3950L|RYR1_ENST00000355481.4_Missense_Mutation_p.S3950L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3955					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	AAAGCCATGTCGGTGGCTAAG	0.597																																					p.S3955L		Atlas-SNP	.											.	RYR1	708	.	0			c.C11864T						.						93	89	90					19																	39034257		2203	4300	6503	SO:0001583	missense	6261	exon86			CCATGTCGGTGGC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.11864C>T	chr19.hg19:g.39034257C>T	ENSP00000352608:p.Ser3955Leu	84.0	0.0		71.0	7.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.748407	0.49257	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.95377	-3.69;-3.69;-3.69	4.3	4.3	0.51218	RyR/IP3R Homology associated domain (1);	0.195140	0.32287	U	0.006309	D	0.92195	0.7525	L	0.48642	1.525	0.41841	D	0.990127	P;P;P	0.38280	0.625;0.473;0.529	B;B;B	0.32465	0.128;0.09;0.146	D	0.91994	0.5605	10	0.33141	T	0.24	.	16.5433	0.84407	0.0:1.0:0.0:0.0	.	3950;3950;3955	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	L	3955;3950;3950	ENSP00000352608:S3955L;ENSP00000347667:S3950L;ENSP00000354254:S3950L	ENSP00000347667:S3950L	S	+	2	0	RYR1	43726097	0.996000	0.38824	0.987000	0.45799	0.975000	0.68041	3.528000	0.53524	2.240000	0.73641	0.486000	0.48141	TCG	.	.		0.597	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	39034257	C	T	39034257	3	4	184	1	0	0	0	0	1	0	0	0	13783	893	31	1	12206	1	RYR1	19	39034257	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	8098022	39034257	20094726	94	27435										
PRX	57716	hgsc.bcm.edu	37	chr19	40901569	40901569	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	caatttcaacagagggcactCggaagcccacttccctgacc	8	15	1	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr19:40901569C>T	ENST00000324001.7	-	7	2960	c.2690G>A	c.(2689-2691)cGa>cAa	p.R897Q	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	897					axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AGAGGGCACTCGGAAGCCCAC	0.612																																					p.R897Q		Atlas-SNP	.											.	PRX	151	.	0			c.G2690A						.						47	56	53					19																	40901569		2203	4300	6503	SO:0001583	missense	57716	exon7			GGCACTCGGAAGC	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.2690G>A	chr19.hg19:g.40901569C>T	ENSP00000326018:p.Arg897Gln	95.0	0.0		96.0	17.0	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	hg19	CCDS33028.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.931525	0.34096	.	.	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.01099	5.34	5.3	4.21	0.49690	.	0.354983	0.20353	N	0.094003	T	0.00724	0.0024	N	0.17082	0.46	0.37414	D	0.913344	B	0.33494	0.414	B	0.21360	0.034	T	0.64554	-0.6380	10	0.29301	T	0.29	-8.6739	4.1775	0.10358	0.0:0.6832:0.0:0.3168	.	897	Q9BXM0	PRAX_HUMAN	Q	897	ENSP00000326018:R897Q	ENSP00000326018:R897Q	R	-	2	0	PRX	45593409	0.000000	0.05858	0.928000	0.36995	0.979000	0.70002	0.904000	0.28491	2.496000	0.84212	0.650000	0.86243	CGA	.	.		0.612	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956		T	40901569	C	T	40901569	3	4	184	1	0	0	0	0	1	0	0	0	12654	884	31	1	1699	1	PRX	19	40901569	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	1867312	40901569	18227414	95	27436										
ZNF610	162963	hgsc.bcm.edu	37	chr19	52869167	52869167	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	aacacacatttttaataaatAtagaaatgatcttattgatt	3	4	1	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr19:52869167A>G	ENST00000403906.3	+	6	992	c.536A>G	c.(535-537)tAt>tGt	p.Y179C	ZNF610_ENST00000327920.8_Missense_Mutation_p.Y179C|ZNF610_ENST00000601151.1_Missense_Mutation_p.Y136C|ZNF610_ENST00000321287.8_Missense_Mutation_p.Y179C	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	179					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		TTTAATAAATATAGAAATGAT	0.303																																					p.Y179C		Atlas-SNP	.											.	ZNF610	84	.	0			c.A536G						.						43	50	47					19																	52869167		2197	4297	6494	SO:0001583	missense	162963	exon6			ATAAATATAGAAA	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"Zinc fingers, C2H2-type", "-"	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.536A>G	chr19.hg19:g.52869167A>G	ENSP00000383922:p.Tyr179Cys	165.0	0.0		139.0	48.0	NM_001161426	A8K4C3|Q86YH8|Q8NDS9	Missense_Mutation	SNP	ENST00000403906.3	hg19	CCDS12851.1	.	.	.	.	.	.	.	.	.	.	A	0.440	-0.898946	0.02472	.	.	ENSG00000167554	ENST00000403906;ENST00000321287;ENST00000327920	T;T	0.05580	3.42;3.42	1.11	0.00455	0.14059	.	.	.	.	.	T	0.03651	0.0104	L	0.37850	1.14	0.09310	N	1	B;B	0.19583	0.037;0.022	B;B	0.12837	0.008;0.003	T	0.46871	-0.9160	9	0.02654	T	1	.	3.1202	0.06388	0.718:0.0:0.282:0.0	.	136;179	Q8N9Z0-2;Q8N9Z0	.;ZN610_HUMAN	C	179;136;179	ENSP00000383922:Y179C;ENSP00000327597:Y179C	ENSP00000324441:Y136C	Y	+	2	0	ZNF610	57560979	0.002000	0.14202	0.002000	0.10522	0.023000	0.10783	-0.085000	0.11250	-0.062000	0.13088	0.260000	0.18958	TAT	.	.		0.303	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530		G	52869167	A	G	52869167	3	3	184	1	0	0	0	0	1	0	0	0	18051	449	16	2	550	2	ZNF610	19	52869167	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	11967598	52869167	6259816	96	27437										
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55593208	55593208	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gctgcagaagtcggcggaggCggccagggtgctggagcacc	19	11	0	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr19:55593208C>T	ENST00000201647.6	+	9	898	c.842C>T	c.(841-843)gCg>gTg	p.A281V	EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000540810.1_Missense_Mutation_p.A217V|EPS8L1_ENST00000588359.1_Intron|EPS8L1_ENST00000245618.5_Missense_Mutation_p.A154V|EPS8L1_ENST00000586329.1_Missense_Mutation_p.A263V	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	281					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		TCGGCGGAGGCGGCCAGGGTG	0.687																																					p.A281V	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.C842T						.						25	28	27					19																	55593208		2203	4298	6501	SO:0001583	missense	54869	exon9			CGGAGGCGGCCAG	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.842C>T	chr19.hg19:g.55593208C>T	ENSP00000201647:p.Ala281Val	185.0	0.0		168.0	34.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	hg19	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.654459	0.88056	.	.	ENSG00000131037	ENST00000310075;ENST00000201647;ENST00000540810;ENST00000245618	T;T;T	0.55930	0.49;0.49;0.49	3.83	3.83	0.44106	.	0.000000	0.85682	D	0.000000	T	0.72285	0.3441	M	0.80847	2.515	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.992;0.996;1.0;0.985	T	0.77397	-0.2603	10	0.72032	D	0.01	-18.9484	13.6195	0.62128	0.0:1.0:0.0:0.0	.	217;263;154;281	B4DKV7;Q8TE68-3;Q8TE68-2;Q8TE68	.;.;.;ES8L1_HUMAN	V	263;281;217;154	ENSP00000201647:A281V;ENSP00000437541:A217V;ENSP00000245618:A154V	ENSP00000201647:A281V	A	+	2	0	EPS8L1	60285020	1.000000	0.71417	0.660000	0.29694	0.406000	0.30931	6.401000	0.73256	1.868000	0.54150	0.313000	0.20887	GCG	.	.		0.687	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		T	55593208	C	T	55593208	3	4	184	1	0	0	0	0	1	0	0	0	5197	768	27	1	924	1	EPS8L1	19	55593208	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	2724041	55593208	3535775	97	27438										
ZNF544	27300	hgsc.bcm.edu	37	chr19	58772416	58772416	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ttcatggtactcacctcagaGagactgtttgctcaaaggga	10	9	4	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr19:58772416G>C	ENST00000596652.1	+	6	678	c.444G>C	c.(442-444)gaG>gaC	p.E148D	ZNF544_ENST00000415203.2_Missense_Mutation_p.E120D|ZNF544_ENST00000596929.1_Intron|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000599953.1_Missense_Mutation_p.E6D|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000600044.1_Missense_Mutation_p.E120D|ZNF544_ENST00000600220.1_Missense_Mutation_p.E120D|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000269829.4_Missense_Mutation_p.E148D|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000596825.1_3'UTR			Q6NX49	ZN544_HUMAN	zinc finger protein 544	148					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		TCACCTCAGAGAGACTGTTTG	0.448																																					p.E148D		Atlas-SNP	.											.	ZNF544	57	.	0			c.G444C						.						100	89	93					19																	58772416		2203	4300	6503	SO:0001583	missense	27300	exon7			CTCAGAGAGACTG	AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.444G>C	chr19.hg19:g.58772416G>C	ENSP00000469635:p.Glu148Asp	142.0	0.0		128.0	19.0	NM_014480	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	hg19	CCDS12973.1	.	.	.	.	.	.	.	.	.	.	G	9.437	1.087036	0.20390	.	.	ENSG00000198131	ENST00000269829;ENST00000415203	T;T	0.08634	3.13;3.07	3.12	-0.442	0.12253	.	.	.	.	.	T	0.04724	0.0128	N	0.20986	0.625	0.20489	N	0.999897	B;B;B	0.33857	0.024;0.016;0.429	B;B;B	0.33799	0.008;0.003;0.17	T	0.40701	-0.9549	9	0.30078	T	0.28	.	2.8128	0.05446	0.2573:0.0:0.5232:0.2195	.	120;120;148	B7ZAY1;B4DL50;Q6NX49	.;.;ZN544_HUMAN	D	148;120	ENSP00000269829:E148D;ENSP00000394341:E120D	ENSP00000269829:E148D	E	+	3	2	ZNF544	63464228	0.000000	0.05858	0.002000	0.10522	0.019000	0.09904	0.029000	0.13666	-0.096000	0.12329	0.655000	0.94253	GAG	.	.		0.448	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		C	58772416	G	C	58772416	3	2	184	1	0	0	0	0	1	0	0	0	17992	933	33	4	458	4	ZNF544	19	58772416	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	3179208	58772416	356567	98	27439										
TRPC4AP	26133	hgsc.bcm.edu	37	chr20	33657145	33657145	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tgtaagtatttggataagtgGtttcttgggtaagtttcctc	11	4	1	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr20:33657145G>C	ENST00000252015.2	-	3	457	c.368C>G	c.(367-369)aCc>aGc	p.T123S	TRPC4AP_ENST00000451813.2_Missense_Mutation_p.T123S|TRPC4AP_ENST00000432634.2_Intron			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	123	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			TGGATAAGTGGTTTCTTGGGT	0.338																																					p.T123S		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.C368G						.						133	136	135					20																	33657145		2203	4300	6503	SO:0001583	missense	26133	exon3			TAAGTGGTTTCTT	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.368C>G	chr20.hg19:g.33657145G>C	ENSP00000252015:p.Thr123Ser	411.0	0.0		316.0	111.0	NM_199368	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	hg19	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	9.138	1.013121	0.19277	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000541994	T;T	0.26810	1.71;1.71	5.5	5.5	0.81552	.	0.257250	0.46442	D	0.000284	T	0.08714	0.0216	N	0.01576	-0.805	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28459	-1.0043	10	0.07990	T	0.79	.	11.6972	0.51551	0.0809:0.0:0.9191:0.0	.	123;123	E1P5Q0;Q8TEL6	.;TP4AP_HUMAN	S	123;123;108	ENSP00000252015:T123S;ENSP00000400614:T123S	ENSP00000252015:T123S	T	-	2	0	TRPC4AP	33120806	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.893000	0.75649	2.868000	0.98415	0.555000	0.69702	ACC	.	.		0.338	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		C	33657145	G	C	33657145	3	2	184	1	0	0	0	0	1	0	0	0	16596	1261	44	4	2093	4	TRPC4AP	20	33657145	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10		33657145	29368375	99	27440										
EMILIN3	90187	hgsc.bcm.edu	37	chr20	39993687	39993687	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	gcacttacgtgactgtcccgGggcacttgggcccccatcta	11	15	1	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr20:39993687G>T	ENST00000332312.3	-	2	470	c.278C>A	c.(277-279)cCc>cAc	p.P93H		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	93	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				GACTGTCCCGGGGCACTTGGG	0.582																																					p.P93H		Atlas-SNP	.											.	EMILIN3	63	.	0			c.C278A						.						195	151	166					20																	39993687		2203	4300	6503	SO:0001583	missense	90187	exon2			GTCCCGGGGCACT	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"EMI domain containing"	16123	protein-coding gene	gene with protein product	"chromosome 20 open reading frame 130"	608929	"elastin microfibril interfacer 5"	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.278C>A	chr20.hg19:g.39993687G>T	ENSP00000332806:p.Pro93His	82.0	0.0		51.0	19.0	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Missense_Mutation	SNP	ENST00000332312.3	hg19	CCDS13316.1	.	.	.	.	.	.	.	.	.	.	G	19.93	3.917384	0.73098	.	.	ENSG00000183798	ENST00000332312	T	0.48522	0.81	4.55	3.6	0.41247	EMI domain (2);	0.060359	0.64402	D	0.000002	T	0.67458	0.2895	M	0.84846	2.72	0.45390	D	0.998377	D	0.89917	1.0	D	0.79784	0.993	T	0.69285	-0.5185	9	.	.	.	-17.6768	8.6507	0.34033	0.0812:0.1513:0.7675:0.0	.	93	Q9NT22	EMIL3_HUMAN	H	93	ENSP00000332806:P93H	.	P	-	2	0	EMILIN3	39427101	1.000000	0.71417	0.794000	0.32065	0.950000	0.60333	6.587000	0.74071	1.122000	0.41944	0.655000	0.94253	CCC	.	.		0.582	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741		T	39993687	G	T	39993687	3	4	184	1	0	0	0	0	1	0	0	0	5097	1232	43	3	2034	3	EMILIN3	20	39993687	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	6336542	39993687	23031833	100	27441										
JPH2	57158	hgsc.bcm.edu	37	chr20	42788721	42788721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ctggctacccacggacgtgcGcgactctgcgcgccgcagct	13	17	1	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr20:42788721G>A	ENST00000372980.3	-	2	1578	c.706C>T	c.(706-708)Cgc>Tgc	p.R236C		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	236					calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			ACGGACGTGCGCGACTCTGCG	0.751																																					p.R236C		Atlas-SNP	.											.	JPH2	86	.	0			c.C706T						.						4	5	4					20																	42788721		1976	3837	5813	SO:0001583	missense	57158	exon2			ACGTGCGCGACTC	AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.706C>T	chr20.hg19:g.42788721G>A	ENSP00000362071:p.Arg236Cys	188.0	0.0		114.0	8.0	NM_020433	E1P5X1|O95913|Q5JY74|Q9UJN4	Missense_Mutation	SNP	ENST00000372980.3	hg19	CCDS13325.1	.	.	.	.	.	.	.	.	.	.	g	17.29	3.352142	0.61183	.	.	ENSG00000149596	ENST00000372980	T	0.62498	0.02	3.03	2.05	0.26809	.	0.216427	0.41097	U	0.000941	T	0.65873	0.2733	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	P	0.54706	0.759	T	0.66069	-0.6015	10	0.66056	D	0.02	.	9.3739	0.38270	0.0:0.0:0.3823:0.6177	.	236	Q9BR39	JPH2_HUMAN	C	236	ENSP00000362071:R236C	ENSP00000362071:R236C	R	-	1	0	JPH2	42222135	1.000000	0.71417	0.769000	0.31535	0.783000	0.44284	2.479000	0.45197	0.465000	0.27167	0.298000	0.19748	CGC	.	.		0.751	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1			A	42788721	G	A	42788721	3	1	184	1	0	0	0	0	1	0	0	0	7970	1087	38	1	1400	1	JPH2	20	42788721	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10	2795034	42788721	20236799	101	27442										
SS18L1	26039	hgsc.bcm.edu	37	chr20	60739279	60739279	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ccagggcgccgcggagcccaTgggccagcagtactaccccg	14	17	0	0			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr20:60739279T>G	ENST00000331758.3	+	7	826	c.800T>G	c.(799-801)aTg>aGg	p.M267R	SS18L1_ENST00000421564.1_Missense_Mutation_p.M267R|SS18L1_ENST00000370848.4_Missense_Mutation_p.M270R	NM_198935.1	NP_945173.1	O75177	CREST_HUMAN	synovial sarcoma translocation gene on chromosome 18-like 1	267	Gln-rich.|MFD domain. {ECO:0000250}.				chromatin modification (GO:0016568)|dendrite development (GO:0016358)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of dendrite development (GO:0050773)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)|kinetochore (GO:0000776)|nuclear body (GO:0016604)|nucleus (GO:0005634)			SS18L1/SSX1(2)	ovary(2)|skin(1)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			GCGGAGCCCATGGGCCAGCAG	0.682			T	SSX1	synovial sarcoma																																p.M267R		Atlas-SNP	.		Dom	yes		20	20q13.3	26039	synovial sarcoma translocation gene on chromosome 18-like 1		M	.	SS18L1	37	.	0			c.T800G						.						22	18	19					20																	60739279		1887	3651	5538	SO:0001583	missense	26039	exon7			AGCCCATGGGCCA	AB014593	CCDS13491.1	20q13.3	2008-07-28			ENSG00000184402	ENSG00000184402			15592	protein-coding gene	gene with protein product		606472					Standard	XM_005260389		Approved	KIAA0693	uc002ycb.3	O75177	OTTHUMG00000032902	ENST00000331758.3:c.800T>G	chr20.hg19:g.60739279T>G	ENSP00000333012:p.Met267Arg	158.0	0.0		151.0	11.0	NM_198935	A6NNE3|A8K620|B3KWR8|E1P5H7|Q5JXJ3|Q6MZV9|Q6NTH3|Q6XYD9|Q8NE69|Q9BR55|Q9H4K6	Missense_Mutation	SNP	ENST00000331758.3	hg19	CCDS13491.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.134852	0.37728	.	.	ENSG00000184402	ENST00000421564;ENST00000331758;ENST00000370848	T;T;T	0.31247	1.51;1.51;1.5	5.18	5.18	0.71444	.	0.251770	0.45126	D	0.000389	T	0.30572	0.0769	L	0.48362	1.52	0.35617	D	0.809121	P;P	0.50528	0.936;0.855	B;B	0.41571	0.149;0.36	T	0.49532	-0.8930	10	0.87932	D	0	-8.2397	15.0176	0.71597	0.0:0.0:0.0:1.0	.	267;267	B4DSR7;O75177	.;CREST_HUMAN	R	267;267;270	ENSP00000393999:M267R;ENSP00000333012:M267R;ENSP00000359885:M270R	ENSP00000333012:M267R	M	+	2	0	SS18L1	60172674	1.000000	0.71417	1.000000	0.80357	0.294000	0.27393	5.338000	0.65947	1.960000	0.56953	0.260000	0.18958	ATG	.	.		0.682	SS18L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080004.2			G	60739279	T	G	60739279	3	3	184	1	0	0	0	0	1	0	0	0	15191	1464	51	5	826	5	SS18L1	20	60739279	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	17950558	60739279	2286241	102	27443										
COL20A1	57642	hgsc.bcm.edu	37	chr20	61951458	61951458	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ccggaaggtggctgagcggcCccttggggagatgggcagcc	19	11	0	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr20:61951458C>T	ENST00000358894.6	+	24	3084	c.2984C>T	c.(2983-2985)cCc>cTc	p.P995L	COL20A1_ENST00000422202.1_Missense_Mutation_p.P1002L|COL20A1_ENST00000326996.6_Missense_Mutation_p.P995L|COL20A1_ENST00000435874.1_Missense_Mutation_p.P1002L	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	995	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)		p.P995L(1)		NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GCTGAGCGGCCCCTTGGGGAG	0.706																																					p.P995L		Atlas-SNP	.											COL20A1,NS,malignant_melanoma,0,1	COL20A1	137	.	1	Substitution - Missense(1)	NS(1)	c.C2984T						.						8	9	9					20																	61951458		1897	4013	5910	SO:0001583	missense	57642	exon24			AGCGGCCCCTTGG	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.2984C>T	chr20.hg19:g.61951458C>T	ENSP00000351767:p.Pro995Leu	110.0	0.0		108.0	39.0	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	hg19	CCDS46628.1	.	.	.	.	.	.	.	.	.	.	C	7.009	0.556369	0.13436	.	.	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202;ENST00000415763;ENST00000455906	T;T;T;T;T;D	0.90385	4.41;4.41;4.41;4.41;4.41;-2.66	4.07	1.94	0.25998	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.214865	0.39909	N	0.001222	D	0.83640	0.5298	L	0.45137	1.4	0.38549	D	0.949401	B;B	0.26577	0.153;0.095	B;B	0.24155	0.051;0.023	T	0.82568	-0.0392	10	0.66056	D	0.02	.	5.8401	0.18629	0.1949:0.6949:0.0:0.1102	.	1002;995	Q9P218-2;Q9P218	.;COKA1_HUMAN	L	995;995;1002;1002;98;3	ENSP00000351767:P995L;ENSP00000323077:P995L;ENSP00000408690:P1002L;ENSP00000414753:P1002L;ENSP00000410799:P98L;ENSP00000406345:P3L	ENSP00000323077:P995L	P	+	2	0	COL20A1	61421903	0.002000	0.14202	0.932000	0.37286	0.042000	0.13812	0.165000	0.16564	2.002000	0.58637	0.462000	0.41574	CCC	.	.		0.706	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		T	61951458	C	T	61951458	3	4	184	1	0	0	0	0	1	0	0	0	3681	623	22	3	3074	3	COL20A1	20	61951458	Missense_Mutation	SNP	C	TCGA-DD-AADA-01A-11D-A40R-10	1212179	61951458	1074062	103	27444										
RCAN1	1827	hgsc.bcm.edu	37	chr21	35893850	35893850	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	catagtttatgactggggtcGcatcttccacttgtttccat	8	10	1	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr21:35893850G>A	ENST00000313806.4	-	3	663	c.533C>T	c.(532-534)gCg>gTg	p.A178V	RCAN1_ENST00000381135.3_Missense_Mutation_p.A168V|RCAN1_ENST00000492600.1_Missense_Mutation_p.A123V|RCAN1_ENST00000381132.2_Missense_Mutation_p.A123V|RCAN1_ENST00000489903.1_5'UTR|RCAN1_ENST00000482533.1_Missense_Mutation_p.A43V|RCAN1_ENST00000443408.2_Missense_Mutation_p.A43V|RCAN1_ENST00000399272.1_Missense_Mutation_p.A97V|RCAN1_ENST00000481448.1_Missense_Mutation_p.A168V|RCAN1_ENST00000487990.1_Missense_Mutation_p.A43V	NM_004414.5	NP_004405.3	P53805	RCAN1_HUMAN	regulator of calcineurin 1	178					blood circulation (GO:0008015)|calcineurin-NFAT signaling cascade (GO:0033173)|central nervous system development (GO:0007417)|locomotion involved in locomotory behavior (GO:0031987)|negative regulation of smooth muscle cell differentiation (GO:0051151)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|response to ischemia (GO:0002931)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|short-term memory (GO:0007614)|signal transduction (GO:0007165)|skeletal muscle fiber development (GO:0048741)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(1)|lung(2)	5						GACTGGGGTCGCATCTTCCAC	0.582																																					p.A178V		Atlas-SNP	.											.	RCAN1	37	.	0			c.C533T						.						93	85	88					21																	35893850		2203	4300	6503	SO:0001583	missense	1827	exon3			GGGGTCGCATCTT		CCDS13637.1, CCDS33551.1, CCDS42921.1, CCDS74788.1, CCDS74790.1	21q22.1-q22.2	2010-08-11	2007-06-26	2007-06-26	ENSG00000159200	ENSG00000159200			3040	protein-coding gene	gene with protein product		602917	"Down syndrome critical region gene 1"	DSCR1		8595418	Standard	XM_005260929		Approved		uc002yue.3	P53805	OTTHUMG00000086235	ENST00000313806.4:c.533C>T	chr21.hg19:g.35893850G>A	ENSP00000320768:p.Ala178Val	119.0	0.0		113.0	16.0	NM_004414	D3DSF9|O00582|O00583|Q53XT0|Q6IBC6|Q7Z555|Q96R03|Q9BU69|Q9UF15|Q9UME4	Missense_Mutation	SNP	ENST00000313806.4	hg19	CCDS13637.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.513992	0.85389	.	.	ENSG00000159200	ENST00000487990;ENST00000313806;ENST00000381132;ENST00000399272;ENST00000481448;ENST00000482533;ENST00000381135;ENST00000443408	.	.	.	5.61	5.61	0.85477	.	0.048431	0.85682	D	0.000000	T	0.78767	0.4335	M	0.75615	2.305	0.80722	D	1	D;D;P;P	0.89917	1.0;0.998;0.802;0.835	D;D;B;B	0.66602	0.931;0.945;0.152;0.234	T	0.77920	-0.2407	9	0.44086	T	0.13	-8.5056	19.2323	0.93845	0.0:0.0:1.0:0.0	.	123;178;97;123	B7Z1F0;P53805;P53805-3;Q6FGP2	.;RCAN1_HUMAN;.;.	V	43;178;123;97;168;43;168;43	.	ENSP00000320768:A178V	A	-	2	0	RCAN1	34815720	1.000000	0.71417	0.246000	0.24233	0.985000	0.73830	9.435000	0.97529	2.636000	0.89361	0.655000	0.94253	GCG	.	.		0.582	RCAN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194142.1			A	35893850	G	A	35893850	3	1	184	1	0	0	0	0	1	0	0	0	13183	1087	38	1	233	1	RCAN1	21	35893850	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10		35893850	12236045	104	27445										
NCF4	4689	hgsc.bcm.edu	37	chr22	37273743	37273743	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	atctggttcggctgctgtcgGatgaggacgtagcgctcatg	15	9	2	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chr22:37273743G>T	ENST00000248899.6	+	10	1082	c.898G>T	c.(898-900)Gat>Tat	p.D300Y	NCF4_ENST00000397147.4_3'UTR	NM_000631.4	NP_000622.2	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4, 40kDa	300	OPR.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of catalytic activity (GO:0043085)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|membrane (GO:0016020)|NADPH oxidase complex (GO:0043020)|phagolysosome (GO:0032010)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein dimerization activity (GO:0046983)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16					Dextromethorphan(DB00514)	GCTGCTGTCGGATGAGGACGT	0.592																																					p.D300Y		Atlas-SNP	.											.	NCF4	66	.	0			c.G898T						.						59	53	55					22																	37273743		2203	4300	6503	SO:0001583	missense	4689	exon10			CTGTCGGATGAGG	X77094	CCDS13934.1, CCDS13935.1	22q13.1	2014-09-17	2002-08-29		ENSG00000100365	ENSG00000100365			7662	protein-coding gene	gene with protein product	"neutrophil NADPH oxidase factor 4"	601488	"neutrophil cytosolic factor 4 (40kD)"			8839867	Standard	NM_013416		Approved	p40phox, SH3PXD4	uc003apy.4	Q15080	OTTHUMG00000150548	ENST00000248899.6:c.898G>T	chr22.hg19:g.37273743G>T	ENSP00000248899:p.Asp300Tyr	86.0	0.0		62.0	20.0	NM_000631	A8K4F9|O60808|Q86U56|Q9BU98|Q9NP45	Missense_Mutation	SNP	ENST00000248899.6	hg19	CCDS13934.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.073046	0.55646	.	.	ENSG00000100365	ENST00000248899	T	0.61859	0.07	5.44	5.44	0.79542	Phox/Bem1p (2);	.	.	.	.	T	0.77377	0.4121	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80091	-0.1527	9	0.87932	D	0	.	17.44	0.87562	0.0:0.0:1.0:0.0	.	300	Q15080	NCF4_HUMAN	Y	300	ENSP00000248899:D300Y	ENSP00000248899:D300Y	D	+	1	0	NCF4	35603689	1.000000	0.71417	0.202000	0.23494	0.165000	0.22458	5.574000	0.67424	2.556000	0.86216	0.650000	0.86243	GAT	.	.		0.592	NCF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318863.1	NM_000631		T	37273743	G	T	37273743	3	4	184	1	0	0	0	0	1	0	0	0	10227	1174	41	3	1177	3	NCF4	22	37273743	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10		37273743	14030823	105	27446										
ARSH	347527	hgsc.bcm.edu	37	chrX	2951122	2951122	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ccctgaaggaacaggtgcctGctatgggagtggaatatgtt	14	7	0	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chrX:2951122G>T	ENST00000381130.2	+	9	1385	c.1385G>T	c.(1384-1386)tGc>tTc	p.C462F		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	462					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				ACAGGTGCCTGCTATGGGAGT	0.453																																					p.C462F		Atlas-SNP	.											.	ARSH	72	.	0			c.G1385T						.						104	88	93					X																	2951122		2203	4300	6503	SO:0001583	missense	347527	exon9			GTGCCTGCTATGG	AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"Arylsulfatase family"	32488	protein-coding gene	gene with protein product		300586	"arylsulfatase H"			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.1385G>T	chrX.hg19:g.2951122G>T	ENSP00000370522:p.Cys462Phe	123.0	0.0		92.0	11.0	NM_001011719		Missense_Mutation	SNP	ENST00000381130.2	hg19	CCDS35198.1	.	.	.	.	.	.	.	.	.	.	g	11.80	1.747305	0.30955	.	.	ENSG00000205667	ENST00000381130	D	0.91011	-2.77	3.06	3.06	0.35304	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	U	0.000000	D	0.95664	0.8590	M	0.90705	3.14	0.52099	D	0.99994	D	0.89917	1.0	D	0.91635	0.999	D	0.96076	0.9050	10	0.59425	D	0.04	.	13.8623	0.63569	0.0:0.0:1.0:0.0	.	462	Q5FYA8	ARSH_HUMAN	F	462	ENSP00000370522:C462F	ENSP00000370522:C462F	C	+	2	0	ARSH	2961122	1.000000	0.71417	0.166000	0.22797	0.007000	0.05969	6.259000	0.72494	1.307000	0.44944	0.513000	0.50165	TGC	.	.		0.453	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719		T	2951122	G	T	2951122	3	4	184	1	0	0	0	0	1	0	0	0	993	1319	46	3	1419	3	ARSH	23	2951122	Missense_Mutation	SNP	G	TCGA-DD-AADA-01A-11D-A40R-10		2951122	152319438	106	27447										
MID1	4281	hgsc.bcm.edu	37	chrX	10535300	10535300	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	tcccgacgggtctcgctgggAgagttgggcccgctcactga	15	13	2	2			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chrX:10535300A>T	ENST00000317552.4	-	2	688	c.288T>A	c.(286-288)tcT>tcA	p.S96S	MID1_ENST00000380782.2_Silent_p.S96S|MID1_ENST00000380785.1_Silent_p.S96S|MID1_ENST00000380787.1_Silent_p.S96S|MID1_ENST00000380779.1_Silent_p.S96S|MID1_ENST00000380780.1_Silent_p.S96S|MID1_ENST00000453318.2_Silent_p.S96S	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	96					microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						TCTCGCTGGGAGAGTTGGGCC	0.612																																					p.S96S		Atlas-SNP	.											.	MID1	72	.	0			c.T288A						.						118	95	103					X																	10535300		2203	4300	6503	SO:0001819	synonymous_variant	4281	exon2			GCTGGGAGAGTTG	Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7095	protein-coding gene	gene with protein product	"Opitz/BBB syndrome"	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.288T>A	chrX.hg19:g.10535300A>T		157.0	0.0		74.0	14.0	NM_001193277	B2RCG2|O75361|Q9BZX5	Silent	SNP	ENST00000317552.4	hg19	CCDS14138.1																																																																																			.	.		0.612	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1			T	10535300	A	T	10535300	2	4	184	1	0	0	0	0	0	0	0	1	9585	291	11	4		4	MID1	23	10535300	Silent	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	7584178	10535300	144735260	107	27448										
MAP3K15	389840	hgsc.bcm.edu	37	chrX	19413261	19413261	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ctgaaacagagcccaggtacTgaacgatattgcggtgctta	11	9	0	3			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chrX:19413261T>A	ENST00000338883.4	-	16	2131	c.2132A>T	c.(2131-2133)cAg>cTg	p.Q711L	MAP3K15_ENST00000469203.2_Missense_Mutation_p.Q543L|MAP3K15_ENST00000359173.3_Missense_Mutation_p.Q146L|MAP3K15_ENST00000518578.1_5'UTR	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	711	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					GCCCAGGTACTGAACGATATT	0.488																																					p.Q711L		Atlas-SNP	.											.	MAP3K15	108	.	0			c.A2132T						.						173	143	153					X																	19413261		2203	4300	6503	SO:0001583	missense	389840	exon16			AGGTACTGAACGA	AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.2132A>T	chrX.hg19:g.19413261T>A	ENSP00000345629:p.Gln711Leu	144.0	0.0		70.0	16.0	NM_001001671	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Missense_Mutation	SNP	ENST00000338883.4	hg19		.	.	.	.	.	.	.	.	.	.	T	22.9	4.350332	0.82132	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	T;T;T	0.25749	1.78;1.78;1.78	5.69	3.32	0.38043	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.051587	0.85682	D	0.000000	T	0.31071	0.0785	L	0.49350	1.555	0.53005	D	0.99996	D;P	0.59767	0.986;0.931	P;P	0.51582	0.674;0.523	T	0.04579	-1.0941	10	0.87932	D	0	.	8.8504	0.35196	0.0:0.1531:0.0:0.8469	.	186;711	Q6ZN16-3;Q6ZN16	.;M3K15_HUMAN	L	711;146;543	ENSP00000345629:Q711L;ENSP00000352093:Q146L;ENSP00000428356:Q543L	ENSP00000345629:Q711L	Q	-	2	0	MAP3K15	19323182	1.000000	0.71417	0.944000	0.38274	0.993000	0.82548	4.777000	0.62361	0.787000	0.33731	0.483000	0.47432	CAG	.	.		0.488	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671		A	19413261	T	A	19413261	3	1	184	1	0	0	0	0	1	0	0	0	9258	1580	55	4	1865	4	MAP3K15	23	19413261	Missense_Mutation	SNP	T	TCGA-DD-AADA-01A-11D-A40R-10	8877961	19413261	135857299	108	27449										
PAK3	5063	hgsc.bcm.edu	37	chrX	110459745	110459745	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	ttttaaatcgctgtcttgagAtggatgtggataggcgagga	14	4	1	1			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chrX:110459745A>T	ENST00000372010.1	+	18	1991	c.1549A>T	c.(1549-1551)Atg>Ttg	p.M517L	PAK3_ENST00000519681.1_Missense_Mutation_p.M523L|PAK3_ENST00000425146.1_Missense_Mutation_p.M502L|PAK3_ENST00000372007.5_Missense_Mutation_p.M502L|PAK3_ENST00000360648.4_Missense_Mutation_p.M538L|PAK3_ENST00000518291.1_Missense_Mutation_p.M538L|PAK3_ENST00000262836.4_Missense_Mutation_p.M517L|PAK3_ENST00000417227.1_Missense_Mutation_p.M523L|PAK3_ENST00000446737.1_Missense_Mutation_p.M502L			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	517	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						CTGTCTTGAGATGGATGTGGA	0.428										TSP Lung(19;0.15)																											p.M538L		Atlas-SNP	.											.	PAK3	179	.	0			c.A1612T						.						138	129	132					X																	110459745		2203	4300	6503	SO:0001583	missense	5063	exon15			CTTGAGATGGATG	AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.1549A>T	chrX.hg19:g.110459745A>T	ENSP00000361080:p.Met517Leu	119.0	0.0		90.0	8.0	NM_001128168	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Missense_Mutation	SNP	ENST00000372010.1	hg19	CCDS48153.1	.	.	.	.	.	.	.	.	.	.	A	17.99	3.522344	0.64747	.	.	ENSG00000077264	ENST00000446737;ENST00000425146;ENST00000372010;ENST00000519681;ENST00000372007;ENST00000518291;ENST00000360648;ENST00000417227;ENST00000262836	T;T;T;T;T;T;T;T;T	0.12361	2.69;2.69;2.69;2.69;2.69;2.69;2.69;2.69;2.69	5.54	5.54	0.83059	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.10208	0.0250	N	0.11131	0.1	0.58432	D	0.999999	B;B;B;B;B	0.14012	0.002;0.0;0.009;0.0;0.009	B;B;B;B;B	0.26094	0.024;0.001;0.066;0.004;0.066	T	0.14254	-1.0479	10	0.59425	D	0.04	.	14.8035	0.69935	1.0:0.0:0.0:0.0	.	523;538;517;502;517	O75914-4;O75914-3;O75914;O75914-2;B1GX77	.;.;PAK3_HUMAN;.;.	L	502;502;517;523;502;538;538;523;517	ENSP00000410853:M502L;ENSP00000401982:M502L;ENSP00000361080:M517L;ENSP00000429113:M523L;ENSP00000361077:M502L;ENSP00000428921:M538L;ENSP00000353864:M538L;ENSP00000389172:M523L;ENSP00000262836:M517L	ENSP00000262836:M517L	M	+	1	0	PAK3	110346401	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.874000	0.92363	1.877000	0.54381	0.427000	0.28365	ATG	.	.		0.428	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		T	110459745	A	T	110459745	3	4	184	1	0	0	0	0	1	0	0	0	11411	333	12	4	1670	4	PAK3	23	110459745	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	91046484	110459745	44810815	109	27450										
SAGE1	55511	hgsc.bcm.edu	37	chrX	134988200	134988200	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.073394495412844	8	1	1.25842048323116	2.95728813559322	1.05617433414044	0.193027325346615	0.751940625889747	0	cagattctaccgtcactcacAatatccgtgaagagagaatg	8	10	3	4			TCGA-DD-AADA-01A-11D-A40R-10	TCGA-DD-AADA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01012d58-9532-4536-8712-4829e4645133	d5357b31-faf2-4e43-b215-8370741d689f	g.chrX:134988200A>T	ENST00000370709.3	+	5	472	c.472A>T	c.(472-474)Aat>Tat	p.N158Y	SAGE1_ENST00000537770.1_Intron|SAGE1_ENST00000535938.1_Missense_Mutation_p.N158Y|SAGE1_ENST00000324447.3_Missense_Mutation_p.N158Y			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	158						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					CGTCACTCACAATATCCGTGA	0.458																																					p.N158Y		Atlas-SNP	.											.	SAGE1	160	.	0			c.A472T						.						94	82	86					X																	134988200		2203	4300	6503	SO:0001583	missense	55511	exon6			ACTCACAATATCC	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.472A>T	chrX.hg19:g.134988200A>T	ENSP00000359743:p.Asn158Tyr	127.0	0.0		62.0	11.0	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	hg19	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	A	10.55	1.382634	0.25031	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000370709	T;T;T	0.36520	1.25;1.25;1.25	1.38	0.437	0.16555	.	0.133595	0.51477	U	0.000093	T	0.37945	0.1022	L	0.29908	0.895	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.12528	-1.0544	10	0.51188	T	0.08	.	3.3183	0.07041	0.3107:0.0:0.6893:0.0	.	158	Q9NXZ1	SAGE1_HUMAN	Y	158	ENSP00000323191:N158Y;ENSP00000445959:N158Y;ENSP00000359743:N158Y	ENSP00000323191:N158Y	N	+	1	0	SAGE1	134815866	0.001000	0.12720	0.017000	0.16124	0.044000	0.14063	0.024000	0.13555	0.068000	0.16574	0.158000	0.16466	AAT	.	.		0.458	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		T	134988200	A	T	134988200	3	4	184	1	0	0	0	0	1	0	0	0	13824	130	5	4	490	4	SAGE1	23	134988200	Missense_Mutation	SNP	A	TCGA-DD-AADA-01A-11D-A40R-10	24528455	134988200	20282360	110	27451										
DFFA	1676	hgsc.bcm.edu	37	chr1	10523576	10523576	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gactgacgcacttcctctctTtggtcaagcacctgttggag	10	12	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:10523576T>C	ENST00000377038.3	-	4	610	c.543A>G	c.(541-543)caA>caG	p.Q181Q	DFFA_ENST00000377036.2_Silent_p.Q181Q	NM_004401.2	NP_004392.1	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha polypeptide	181					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|negative regulation of apoptotic DNA fragmentation (GO:1902511)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of apoptotic process (GO:0043065)|thymocyte apoptotic process (GO:0070242)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				large_intestine(3)|lung(2)	5	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		CTTCCTCTCTTTGGTCAAGCA	0.567																																					p.Q181Q		Atlas-SNP	.											.	DFFA	24	.	0			c.A543G						.						93	85	88					1																	10523576		2203	4300	6503	SO:0001819	synonymous_variant	1676	exon4			CTCTCTTTGGTCA	AF087573	CCDS118.1, CCDS119.1	1p36.3-p36.2	2008-07-18	2002-08-29		ENSG00000160049	ENSG00000160049			2772	protein-coding gene	gene with protein product	"DNA fragmentation factor, 45 kD, alpha subunit"	601882	"DNA fragmentation factor, 45 kD, alpha polypeptide"			9605855, 9108473	Standard	NM_004401		Approved	DFF-45, DFF45, ICAD, DFF1	uc001arj.3	O00273	OTTHUMG00000001909	ENST00000377038.3:c.543A>G	chr1.hg19:g.10523576T>C		29.0	0.0		25.0	13.0	NM_004401	Q5T6G5|Q5T6G6|Q96I97|Q9Y6C6	Silent	SNP	ENST00000377038.3	hg19	CCDS118.1																																																																																			.	.		0.567	DFFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005418.1	NM_004401		C	10523576	T	C	10523576	2	2	185	1	0	0	0	0	0	0	0	1	4454	1838	64	2		2	DFFA	1	10523576	Silent	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10		10523576	238727045	1	27452										
MYCL1	4610	hgsc.bcm.edu	37	chr1	40366890	40366890	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cgagtggccccgggattccgCttcgtctccggtgcaccctc	12	17	1	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:40366890C>A	ENST00000372816.2	-	1	664	c.217G>T	c.(217-219)Gcg>Tcg	p.A73S	MYCL_ENST00000397332.2_Missense_Mutation_p.A103S|MYCL_ENST00000372815.1_Missense_Mutation_p.A103S|MYCL_ENST00000429311.1_Missense_Mutation_p.A73S|RP1-118J21.5_ENST00000418255.1_RNA			P12524	MYCL_HUMAN	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog	73						nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CGGGATTCCGCTTCGTCTCCG	0.726																																					p.A103S		Atlas-SNP	.											.	MYCL1	36	.	0			c.G307T						.						22	21	22					1																	40366890		2196	4293	6489	SO:0001583	missense	4610	exon2			ATTCCGCTTCGTC		CCDS30682.1, CCDS44117.1, CCDS44117.2, CCDS53300.1	1p34.3	2013-07-09	2013-07-09	2013-07-09	ENSG00000116990	ENSG00000116990		"Basic helix-loop-helix proteins"	7555	protein-coding gene	gene with protein product	"l-myc protein", "myc-related gene from lung cancer", "oncogene lmyc"	164850	"v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"	MYCL1		8978772	Standard	NM_001033082		Approved	LMYC, bHLHe38	uc001cer.2	P12524	OTTHUMG00000009243	ENST00000372816.2:c.217G>T	chr1.hg19:g.40366890C>A	ENSP00000361903:p.Ala73Ser	157.0	0.0		82.0	21.0	NM_005376	A2A2C9|B4DJH2|Q14897|Q5QPL0|Q5QPL1|Q9NUE9	Missense_Mutation	SNP	ENST00000372816.2	hg19	CCDS30682.1	.	.	.	.	.	.	.	.	.	.	c	14.54	2.565427	0.45694	.	.	ENSG00000116990	ENST00000397332;ENST00000372816;ENST00000372815;ENST00000429311;ENST00000450953	T;T;T;T;T	0.17213	2.29;2.29;2.29;2.29;2.29	4.53	2.66	0.31614	Transcription regulator Myc, N-terminal (1);	2.903690	0.00864	N	0.001942	T	0.13756	0.0333	L	0.27053	0.805	0.27567	N	0.950001	B;B	0.31548	0.328;0.062	B;B	0.34242	0.178;0.055	T	0.31052	-0.9957	10	0.09084	T	0.74	-3.8721	7.1237	0.25458	0.0:0.6942:0.1423:0.1635	.	73;73	P12524-2;P12524	.;MYCL1_HUMAN	S	103;73;103;73;73	ENSP00000380494:A103S;ENSP00000361903:A73S;ENSP00000361902:A103S;ENSP00000389358:A73S;ENSP00000434375:A73S	ENSP00000361902:A103S	A	-	1	0	MYCL1	40139477	0.028000	0.19301	0.995000	0.50966	0.682000	0.39822	0.943000	0.29030	0.648000	0.30732	0.558000	0.71614	GCG	.	.		0.726	MYCL-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277004.1	NM_001033082		A	40366890	C	A	40366890	3	1	185	1	0	0	0	0	1	0	0	0	10029	797	28	3	1010	3	MYCL1	1	40366890	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	29843314	40366890	208883731	2	27453										
SLC1A7	6512	hgsc.bcm.edu	37	chr1	53553703	53553703	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	agacattggtctccagctcaCtgatctggatggtgcagtgg	13	9	3	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:53553703C>T	ENST00000371494.4	-	11	1788	c.1661G>A	c.(1660-1662)aGt>aAt	p.S554N	SLC1A7_ENST00000488036.1_5'UTR|RP11-334A14.5_ENST00000447867.1_RNA	NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7	554					dicarboxylic acid transport (GO:0006835)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Colorectal(1306;0.234)		CTCCAGCTCACTGATCTGGAT	0.657																																					p.S554N	NSCLC(128;80 1811 21245 38490 51715)	Atlas-SNP	.											.	SLC1A7	65	.	0			c.G1661A						.						43	42	42					1																	53553703		2203	4300	6503	SO:0001583	missense	6512	exon11			AGCTCACTGATCT	U76362	CCDS574.1, CCDS72796.1, CCDS72797.1, CCDS72798.1	1p32.3	2013-05-22			ENSG00000162383	ENSG00000162383		"Solute carriers"	10945	protein-coding gene	gene with protein product		604471				9108121	Standard	NM_001287597		Approved	EAAT5	uc001cuy.3	O00341	OTTHUMG00000008937	ENST00000371494.4:c.1661G>A	chr1.hg19:g.53553703C>T	ENSP00000360549:p.Ser554Asn	107.0	0.0		86.0	49.0	NM_006671	Q5VVZ0|Q969Z8|Q9BW45	Missense_Mutation	SNP	ENST00000371494.4	hg19	CCDS574.1	.	.	.	.	.	.	.	.	.	.	C	0.088	-1.171696	0.01646	.	.	ENSG00000162383	ENST00000371494	T	0.49432	0.78	5.76	2.41	0.29592	.	0.230381	0.43260	N	0.000582	T	0.18341	0.0440	N	0.03608	-0.345	0.80722	D	1	B;B	0.14438	0.0;0.01	B;B	0.09377	0.0;0.004	T	0.21211	-1.0252	10	0.02654	T	1	0.4463	9.3022	0.37853	0.0:0.6597:0.0:0.3403	.	554;207	O00341;B3KSM4	EAA5_HUMAN;.	N	554	ENSP00000360549:S554N	ENSP00000360549:S554N	S	-	2	0	SLC1A7	53326291	0.801000	0.28930	0.643000	0.29450	0.172000	0.22775	1.258000	0.32944	0.757000	0.33036	0.655000	0.94253	AGT	.	.		0.657	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1	NM_006671		T	53553703	C	T	53553703	3	4	185	1	0	0	0	0	1	0	0	0	14452	565	20	3	25	3	SLC1A7	1	53553703	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	13186813	53553703	195696918	3	27454										
IVL	3713	hgsc.bcm.edu	37	chr1	152883884	152883884	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aaggacctggagcagcagaaGgggcagctggagcagcctgt	17	9	0	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:152883884G>A	ENST00000368764.3	+	2	1675	c.1611G>A	c.(1609-1611)aaG>aaA	p.K537K	IVL_ENST00000392667.2_Silent_p.K391K			P07476	INVO_HUMAN	involucrin	537	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			agcagcagaaggggcagctgg	0.577																																					p.K537K		Atlas-SNP	.											.	IVL	100	.	0			c.G1611A						.						57	56	56					1																	152883884		2203	4300	6503	SO:0001819	synonymous_variant	3713	exon2			GCAGAAGGGGCAG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1611G>A	chr1.hg19:g.152883884G>A		88.0	0.0		76.0	19.0	NM_005547	Q5T7P4	Silent	SNP	ENST00000368764.3	hg19	CCDS1030.1																																																																																			.	.		0.577	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		A	152883884	G	A	152883884	2	1	185	1	0	0	0	0	0	0	0	1	7938	991	35	3		3	IVL	1	152883884	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	99330181	152883884	96366737	4	27455										
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156503902	156503902	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tgcaaaacgctcctctggctCtggcacctggcaggctctat	10	14	3	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:156503902C>G	ENST00000361170.2	-	30	3782	c.3772G>C	c.(3772-3774)Gag>Cag	p.E1258Q		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1258					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TCCTCTGGCTCTGGCACCTGG	0.597																																					p.E1258Q		Atlas-SNP	.											.	IQGAP3	146	.	0			c.G3772C						.						110	102	104					1																	156503902		2203	4300	6503	SO:0001583	missense	128239	exon30			CTGGCTCTGGCAC	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.3772G>C	chr1.hg19:g.156503902C>G	ENSP00000354451:p.Glu1258Gln	26.0	0.0		29.0	9.0	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	hg19	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.669470	0.88348	.	.	ENSG00000183856	ENST00000361170	T	0.53640	0.61	4.88	4.88	0.63580	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.000000	0.85682	D	0.000000	T	0.65698	0.2716	M	0.83384	2.64	0.46927	D	0.999259	D	0.63046	0.992	D	0.66716	0.946	T	0.70335	-0.4900	10	0.72032	D	0.01	-33.8292	17.1295	0.86723	0.0:1.0:0.0:0.0	.	1258	Q86VI3	IQGA3_HUMAN	Q	1258	ENSP00000354451:E1258Q	ENSP00000354451:E1258Q	E	-	1	0	IQGAP3	154770526	1.000000	0.71417	0.996000	0.52242	0.979000	0.70002	4.725000	0.61979	2.700000	0.92200	0.462000	0.41574	GAG	.	.		0.597	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		G	156503902	C	G	156503902	3	3	185	1	0	0	0	0	1	0	0	0	7825	922	32	4	1159	4	IQGAP3	1	156503902	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	3620018	156503902	92746719	5	27456										
INSRR	3645	hgsc.bcm.edu	37	chr1	156815496	156815496	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctccagcgggggcagaacctGaccaggaggtgggtgctggc	18	11	0	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:156815496G>T	ENST00000368195.3	-	10	2485	c.2089C>A	c.(2089-2091)Cag>Aag	p.Q697K	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	697	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GGCAGAACCTGACCAGGAGGT	0.617																																					p.Q697K		Atlas-SNP	.											.	INSRR	309	.	0			c.C2089A						.						46	45	45					1																	156815496		2203	4300	6503	SO:0001583	missense	3645	exon10			GAACCTGACCAGG	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2089C>A	chr1.hg19:g.156815496G>T	ENSP00000357178:p.Gln697Lys	58.0	0.0		74.0	19.0	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	G	9.275	1.046560	0.19748	.	.	ENSG00000027644	ENST00000368195	T	0.55413	0.52	4.58	4.58	0.56647	Fibronectin, type III (2);	0.000000	0.45867	D	0.000333	T	0.22003	0.0530	.	.	.	0.25684	N	0.985763	B	0.26809	0.16	B	0.26094	0.066	T	0.03287	-1.1052	9	0.35671	T	0.21	.	10.3197	0.43758	0.0:0.0:0.8035:0.1965	.	697	P14616	INSRR_HUMAN	K	697	ENSP00000357178:Q697K	ENSP00000357178:Q697K	Q	-	1	0	INSRR	155082120	1.000000	0.71417	1.000000	0.80357	0.607000	0.37147	4.757000	0.62213	2.535000	0.85469	0.561000	0.74099	CAG	.	.		0.617	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		T	156815496	G	T	156815496	3	4	185	1	0	0	0	0	1	0	0	0	7783	1299	45	3	1855	3	INSRR	1	156815496	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	311594	156815496	92435125	6	27457										
ATP1A2	477	hgsc.bcm.edu	37	chr1	160093074	160093074	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gccctcacaccacctcccacAacccctgagtgggtcaagtt	7	18	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:160093074A>G	ENST00000361216.3	+	4	338	c.249A>G	c.(247-249)acA>acG	p.T83T	ATP1A2_ENST00000392233.3_Silent_p.T83T	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	83					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CACCTCCCACAACCCCTGAGT	0.632																																					p.T83T		Atlas-SNP	.											.	ATP1A2	167	.	0			c.A249G						.						158	157	158					1																	160093074		2203	4300	6503	SO:0001819	synonymous_variant	477	exon4			TCCCACAACCCCT	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.249A>G	chr1.hg19:g.160093074A>G		62.0	0.0		88.0	26.0	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	hg19	CCDS1196.1																																																																																			.	.		0.632	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		G	160093074	A	G	160093074	2	3	185	1	0	0	0	0	0	0	0	1	1129	117	5	2		2	ATP1A2	1	160093074	Silent	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	3277578	160093074	89157547	7	27458										
TNN	63923	hgsc.bcm.edu	37	chr1	175048844	175048844	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aggcctggactgtgcccaggGtgagagcggagatgtgccct	17	10	0	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:175048844G>A	ENST00000239462.4	+	3	897		c.e3+1			NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N						axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		TGTGCCCAGGGTGAGAGCGGA	0.602																																					.		Atlas-SNP	.											.	TNN	297	.	0			c.784+1G>A						.						24	18	20					1																	175048844		2157	4229	6386	SO:0001630	splice_region_variant	63923	exon3			CCCAGGGTGAGAG	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.784+1G>A	chr1.hg19:g.175048844G>A		107.0	0.0		98.0	34.0	NM_022093	B9EGP3|Q5R360	Splice_Site	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.507294	0.85282	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	.	.	.	4.7	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5932	0.88003	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TNN	173315467	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	8.917000	0.92751	2.321000	0.78463	0.491000	0.48974	.	.	.		0.602	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	Intron	A	175048844	G	A	175048844	5	1	185	1	0	0	0	0	0	0	1	0	16338	1275	44	3	791	3	TNN	1	175048844	Splice_Site	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	14955770	175048844	74201777	8	27459										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200946389	200946389	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gcccgaggcggcgtacagcaTggtgcccgaagggctgaggg	19	11	0	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:200946389T>C	ENST00000422435.2	-	31	4592	c.4276A>G	c.(4276-4278)Atg>Gtg	p.M1426V	KIF21B_ENST00000461742.2_Missense_Mutation_p.M1426V|KIF21B_ENST00000360529.5_Missense_Mutation_p.M1413V|KIF21B_ENST00000332129.2_Missense_Mutation_p.M1413V	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1426					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						GCGTACAGCATGGTGCCCGAA	0.632																																					p.M1426V		Atlas-SNP	.											.	KIF21B	208	.	0			c.A4276G						.						141	127	132					1																	200946389		2203	4300	6503	SO:0001583	missense	23046	exon31			ACAGCATGGTGCC	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.4276A>G	chr1.hg19:g.200946389T>C	ENSP00000411831:p.Met1426Val	72.0	0.0		64.0	20.0	NM_001252102	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	hg19	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	T	0.014	-1.572007	0.00895	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.05855	3.38;3.38;3.38;3.38	4.88	3.74	0.42951	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.340989	0.31636	N	0.007319	T	0.01661	0.0053	N	0.00583	-1.355	0.24546	N	0.994043	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.45279	-0.9272	10	0.16896	T	0.51	.	6.9738	0.24664	0.1331:0.075:0.0:0.7918	.	1413;1426;1426;1413	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	V	1413;1413;1426;1426;1426	ENSP00000328494:M1413V;ENSP00000353724:M1413V;ENSP00000433808:M1426V;ENSP00000411831:M1426V	ENSP00000328494:M1413V	M	-	1	0	KIF21B	199213012	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	1.537000	0.36083	0.692000	0.31613	-0.516000	0.04426	ATG	.	.		0.632	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		C	200946389	T	C	200946389	3	2	185	1	0	0	0	0	1	0	0	0	8298	1464	51	2	657	2	KIF21B	1	200946389	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	25897545	200946389	48304232	9	27460										
LGR6	59352	hgsc.bcm.edu	37	chr1	202273760	202273760	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tgcccaggctccgagtcctgTgagtgctcacaagaattcta	10	12	2	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:202273760T>A	ENST00000367278.3	+	11	1159		c.e11+2		LGR6_ENST00000255432.7_Splice_Site|LGR6_ENST00000308543.3_Splice_Site|LGR6_ENST00000439764.2_Splice_Site	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6						G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						CCGAGTCCTGTGAGTGCTCAC	0.597																																					.		Atlas-SNP	.											.	LGR6	102	.	0			c.1070+2T>A						.						48	52	51					1																	202273760		2203	4300	6503	SO:0001630	splice_region_variant	59352	exon11			GTCCTGTGAGTGC	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"GPCR / Class A : Orphans"	19719	protein-coding gene	gene with protein product		606653	"leucine-rich repeat-containing G protein-coupled receptor 6"			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.1070+2T>A	chr1.hg19:g.202273760T>A		77.0	0.0		105.0	23.0	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Splice_Site	SNP	ENST00000367278.3	hg19	CCDS30971.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.416715	0.83449	.	.	ENSG00000133067	ENST00000367278;ENST00000255432;ENST00000367277;ENST00000423542;ENST00000439764	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6335	0.56671	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	LGR6	200540383	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.464000	0.73534	1.966000	0.57179	0.533000	0.62120	.	.	.		0.597	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	Intron	A	202273760	T	A	202273760	5	1	185	1	0	0	0	0	0	0	1	0	8767	1710	59	4	1261	4	LGR6	1	202273760	Splice_Site	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	1327371	202273760	46976861	10	27461										
MFSD4	148808	hgsc.bcm.edu	37	chr1	205568372	205568372	+	Frame_Shift_Del	DEL	C	C	-													0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cacaggatgcaccctggactCccatcaggtaaggaaagtat							TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:205568372delC	ENST00000367147.4	+	9	1575	c.1482delC	c.(1480-1482)ctcfs	p.L494fs	MFSD4_ENST00000478555.1_3'UTR|MFSD4_ENST00000539267.1_3'UTR|MFSD4_ENST00000536357.1_Frame_Shift_Del_p.L407fs	NM_181644.4	NP_857595.3	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing 4	494					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			ACCCTGGACTCCCATCAGGTA	0.512																																					p.L494fs		Atlas-INDEL	.											.	MFSD4	46	.	0			c.1481delT						.						235	195	209					1																	205568372		2203	4300	6503	SO:0001589	frameshift_variant	148808	exon9			.	BC036549	CCDS1455.1	1q32.1	2008-02-05			ENSG00000174514	ENSG00000174514			25433	protein-coding gene	gene with protein product							Standard	NM_181644		Approved	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004	uc001hcv.4	Q8N468	OTTHUMG00000037197	ENST00000367147.4:c.1482delC	chr1.hg19:g.205568372delC	ENSP00000356115:p.Leu494fs	55.0	0.0		37.0	11.0	NM_181644	B7Z8X3|Q6UY25|Q8NAY0|Q8TCP4	Frame_Shift_Del	DEL	ENST00000367147.4	hg19	CCDS1455.1																																																																																			.	.		0.512	MFSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090391.1	NM_181644		-	205568372	C	-	205568372	7	5	185	1	0	1	0	1	0	0	0	0	9542	842	30	0	1516	0	MFSD4	1	205568372	Frame_Shift_Del	DEL	C	TCGA-DD-AADB-01A-11D-A40R-10	3294612	205568372	43682249	11	27462										
IRF6	3664	hgsc.bcm.edu	37	chr1	209961787	209961787	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	actggggaggcagggcagggGgcagttgcatgctgggggtg	23	6	0	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:209961787G>A	ENST00000367021.3	-	9	1554	c.1382C>T	c.(1381-1383)cCc>cTc	p.P461L	IRF6_ENST00000542854.1_Missense_Mutation_p.P366L|RP3-434O14.8_ENST00000430751.1_RNA	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	461					cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		CAGGGCAGGGGGCAGTTGCAT	0.468										HNSCC(57;0.16)																											p.P461L		Atlas-SNP	.											.	IRF6	65	.	0			c.C1382T						.						58	62	60					1																	209961787		2203	4300	6503	SO:0001583	missense	3664	exon9			GCAGGGGGCAGTT	AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595			6121	protein-coding gene	gene with protein product		607199	"Van der Woude syndrome"	VWS, LPS		12219090	Standard	NM_006147		Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.1382C>T	chr1.hg19:g.209961787G>A	ENSP00000355988:p.Pro461Leu	48.0	0.0		55.0	19.0	NM_006147	B4DLE2|D3DT90|F5GWX8|G0ZTL0	Missense_Mutation	SNP	ENST00000367021.3	hg19	CCDS1492.1	.	.	.	.	.	.	.	.	.	.	G	9.897	1.205880	0.22205	.	.	ENSG00000117595	ENST00000367021;ENST00000542854	D;D	0.97430	-4.38;-3.96	5.67	5.67	0.87782	.	1.245660	0.04898	N	0.450813	D	0.94208	0.8141	N	0.08118	0	0.37386	D	0.912241	B	0.13594	0.008	B	0.09377	0.004	T	0.73691	-0.3903	10	0.72032	D	0.01	.	19.7847	0.96432	0.0:0.0:1.0:0.0	.	461	O14896	IRF6_HUMAN	L	461;366	ENSP00000355988:P461L;ENSP00000440532:P366L	ENSP00000355988:P461L	P	-	2	0	IRF6	208028410	0.972000	0.33761	0.343000	0.25615	0.226000	0.24999	4.067000	0.57527	2.679000	0.91253	0.650000	0.86243	CCC	.	.		0.468	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088827.1	NM_006147		A	209961787	G	A	209961787	3	1	185	1	0	0	0	0	1	0	0	0	7843	1232	43	3	25	3	IRF6	1	209961787	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	4393415	209961787	39288834	12	27463										
TATDN3	128387	hgsc.bcm.edu	37	chr1	212977961	212977961	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tgtgcactcacgctctgctgGaagacctaccatcaaccttt	7	14	3	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:212977961G>C	ENST00000366974.4	+	7	549	c.455G>C	c.(454-456)gGa>gCa	p.G152A	TATDN3_ENST00000366973.4_Missense_Mutation_p.G152A|TATDN3_ENST00000526997.1_Missense_Mutation_p.G152A|TATDN3_ENST00000525569.1_3'UTR|TATDN3_ENST00000526641.1_Missense_Mutation_p.G131A|TATDN3_ENST00000532324.1_Missense_Mutation_p.G152A|TATDN3_ENST00000531963.1_Missense_Mutation_p.G152A	NM_001042552.2|NM_001042553.2|NM_001146169.1|NM_001146171.1	NP_001036017.1|NP_001036018.1|NP_001139641.1|NP_001139643.1	Q17R31	TATD3_HUMAN	TatD DNase domain containing 3	152					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00699)|all cancers(67;0.0118)|GBM - Glioblastoma multiforme(131;0.0801)|Epithelial(68;0.104)		CGCTCTGCTGGAAGACCTACC	0.343																																					p.G152A		Atlas-SNP	.											.	TATDN3	23	.	0			c.G455C						.						96	83	87					1																	212977961		2203	4300	6503	SO:0001583	missense	128387	exon7			CTGCTGGAAGACC	AL832248	CCDS31019.1, CCDS41465.1, CCDS53475.1, CCDS53476.1, CCDS53477.1	1q32.3	2008-02-05			ENSG00000203705	ENSG00000203705			27010	protein-coding gene	gene with protein product							Standard	NM_001042552		Approved		uc001hjo.2	Q17R31	OTTHUMG00000036805	ENST00000366974.4:c.455G>C	chr1.hg19:g.212977961G>C	ENSP00000355941:p.Gly152Ala	230.0	0.0		211.0	68.0	NM_001146169	A6NGS3|B7Z1C1|B7Z978|B7ZLQ6|E9PJE5|E9PNH3|G3V151|Q4G0L1	Missense_Mutation	SNP	ENST00000366974.4	hg19	CCDS31019.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.5|24.5	4.541482|4.541482	0.85917|0.85917	.|.	.|.	ENSG00000203705|ENSG00000203705	ENST00000527693|ENST00000532324;ENST00000366974;ENST00000526641;ENST00000531963;ENST00000366973;ENST00000526997;ENST00000530399	.|.	.|.	.|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.56307|0.56307	0.1976|0.1976	L|L	0.28776|0.28776	0.89|0.89	0.80722|0.80722	D|D	1|1	.|B;P;P;P;P;P	.|0.50617	.|0.214;0.737;0.838;0.937;0.652;0.866	.|B;P;P;P;B;P	.|0.53035	.|0.153;0.601;0.525;0.716;0.226;0.527	T|T	0.47169|0.47169	-0.9138|-0.9138	5|9	.|0.06365	.|T	.|0.9	-5.013|-5.013	19.4401|19.4401	0.94815|0.94815	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|100;131;152;152;152;152	.|B7Z2Z9;E9PNH3;G3V151;E9PJE5;Q17R31-2;Q17R31	.|.;.;.;.;.;TATD3_HUMAN	Q|A	1|152;152;131;152;152;152;151	.|.	.|ENSP00000355940:G152A	E|G	+|+	1|2	0|0	TATDN3|TATDN3	211044584|211044584	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.918000|8.918000	0.92759|0.92759	2.697000|2.697000	0.92050|0.92050	0.557000|0.557000	0.71058|0.71058	GAA|GGA	.	.		0.343	TATDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089396.2	XM_375838		C	212977961	G	C	212977961	3	2	185	1	0	0	0	0	1	0	0	0	15608	1174	41	4	481	4	TATDN3	1	212977961	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	3016174	212977961	36272660	13	27464										
ANGEL2	90806	hgsc.bcm.edu	37	chr1	213181634	213181634	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctggccgccggcaatgtctaTaaaggtgagagttatcttcc	11	10	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:213181634T>C	ENST00000366962.3	-	3	714	c.560A>G	c.(559-561)tAt>tGt	p.Y187C	ANGEL2_ENST00000540642.1_Missense_Mutation_p.Y61C|ANGEL2_ENST00000360506.2_Missense_Mutation_p.Y18C|ANGEL2_ENST00000535388.1_Missense_Mutation_p.Y18C|ANGEL2_ENST00000544555.1_Missense_Mutation_p.Y18C	NM_144567.3	NP_653168.2	Q5VTE6	ANGE2_HUMAN	angel homolog 2 (Drosophila)	187										central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(1)	24				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		GCAATGTCTATAAAGGTGAGA	0.353																																					p.Y187C		Atlas-SNP	.											.	ANGEL2	45	.	0			c.A560G						.						95	95	95					1																	213181634		2203	4300	6503	SO:0001583	missense	90806	exon3			TGTCTATAAAGGT	AL079275	CCDS1512.1, CCDS73027.1	1q32.3	2014-06-17			ENSG00000174606	ENSG00000174606			30534	protein-coding gene	gene with protein product						11943475	Standard	XM_005273344		Approved	KIAA0759L, FLJ12793, Ccr4d	uc001hjz.3	Q5VTE6	OTTHUMG00000036927	ENST00000366962.3:c.560A>G	chr1.hg19:g.213181634T>C	ENSP00000355929:p.Tyr187Cys	178.0	0.0		150.0	38.0	NM_144567	B7Z2U4|D3DTA3|Q86X13|Q8NHH3	Missense_Mutation	SNP	ENST00000366962.3	hg19	CCDS1512.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.188229	0.78789	.	.	ENSG00000174606	ENST00000366962;ENST00000360506;ENST00000544555;ENST00000540642;ENST00000535388;ENST00000310246	T;T;T;T;T	0.58060	1.31;0.36;0.36;0.96;0.55	5.76	4.64	0.57946	Endonuclease/exonuclease/phosphatase (2);	0.000000	0.85682	D	0.000000	T	0.79299	0.4422	H	0.95043	3.615	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.83764	0.0216	10	0.87932	D	0	-17.5195	11.6532	0.51301	0.0:0.0689:0.0:0.9311	.	61;165;187	F5H476;Q96AL9;Q5VTE6	.;.;ANGE2_HUMAN	C	187;18;18;61;18;165	ENSP00000355929:Y187C;ENSP00000353696:Y18C;ENSP00000443193:Y18C;ENSP00000446124:Y61C;ENSP00000438141:Y18C	ENSP00000309755:Y165C	Y	-	2	0	ANGEL2	211248257	1.000000	0.71417	0.745000	0.31077	0.989000	0.77384	7.603000	0.82811	1.010000	0.39314	0.533000	0.62120	TAT	.	.		0.353	ANGEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089693.1	NM_144567		C	213181634	T	C	213181634	3	2	185	1	0	0	0	0	1	0	0	0	609	1406	49	2	1102	2	ANGEL2	1	213181634	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	203673	213181634	36068987	14	27465										
TLR5	7100	hgsc.bcm.edu	37	chr1	223284946	223284946	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ttttctccaaggaaaagctgTtctaagctgggattctctga	9	8	3	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:223284946T>C	ENST00000540964.1	-	4	1889	c.1428A>G	c.(1426-1428)gaA>gaG	p.E476E	TLR5_ENST00000342210.6_Silent_p.E476E			O60602	TLR5_HUMAN	toll-like receptor 5	476			Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1). {ECO:0000269|PubMed:14623910}.		cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		GGAAAAGCTGTTCTAAGCTGG	0.423																																					p.E476E		Atlas-SNP	.											.	TLR5	86	.	0			c.A1428G						.						75	77	76					1																	223284946		2203	4300	6503	SO:0001819	synonymous_variant	7100	exon6			AAGCTGTTCTAAG		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"Toll/interleukin-1 receptor-like protein 3"	603031	"systemic lupus erythematosus susceptibility 1"	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.1428A>G	chr1.hg19:g.223284946T>C		79.0	0.0		102.0	13.0	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Silent	SNP	ENST00000540964.1	hg19	CCDS31033.1																																																																																			.	.		0.423	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		C	223284946	T	C	223284946	2	2	185	1	0	0	0	0	0	0	0	1	15969	1722	60	2		2	TLR5	1	223284946	Silent	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	10103312	223284946	25965675	15	27466										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228399589	228399589	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctcagctgccagatcgtgggTaatcccacgccacaggtgag	12	13	1	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:228399589T>G	ENST00000422127.1	+	2	149	c.105T>G	c.(103-105)ggT>ggG	p.G35G	OBSCN_ENST00000570156.2_Silent_p.G35G|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.G35G|OBSCN_ENST00000366709.4_5'UTR|C1orf145_ENST00000295012.5_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	35	Ig-like 1.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGATCGTGGGTAATCCCACGC	0.687																																					p.G35G		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T105G						.						10	12	12					1																	228399589		2037	4169	6206	SO:0001819	synonymous_variant	84033	exon2			CGTGGGTAATCCC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.105T>G	chr1.hg19:g.228399589T>G		119.0	0.0		128.0	32.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.687	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228399589	T	G	228399589	2	3	185	1	0	0	0	0	0	0	0	1	10821	1625	57	5		5	OBSCN	1	228399589	Silent	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	5114643	228399589	20851032	16	27467										
TARBP1	6894	hgsc.bcm.edu	37	chr1	234565278	234565278	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tggcatctgaacggcaggtaGaaacggttccagaatttcac	11	9	2	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:234565278G>A	ENST00000040877.1	-	16	2754	c.2755C>T	c.(2755-2757)Cta>Tta	p.L919L		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	919					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			ACGGCAGGTAGAAACGGTTCC	0.423																																					p.L919L		Atlas-SNP	.											.	TARBP1	111	.	0			c.C2755T						.						96	98	97					1																	234565278		2203	4300	6503	SO:0001819	synonymous_variant	6894	exon16			CAGGTAGAAACGG		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"tRNA methyltransferase 3 homolog (S. cerevisiae)"	605052	"Tar (HIV-1) RNA binding protein 1"			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.2755C>T	chr1.hg19:g.234565278G>A		149.0	0.0		161.0	39.0	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	hg19	CCDS1601.1																																																																																			.	.		0.423	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646		A	234565278	G	A	234565278	2	1	185	1	0	0	0	0	0	0	0	1	15570	933	33	3		3	TARBP1	1	234565278	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	6165689	234565278	14685343	17	27468										
ZP4	57829	hgsc.bcm.edu	37	chr1	238045816	238045816	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ttaaggtcccagaaaggcctGccacccacagaactttcgag	9	13	0	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr1:238045816G>T	ENST00000366570.4	-	12	1687	c.1529C>A	c.(1528-1530)gCa>gAa	p.A510E	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	510					acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			AGAAAGGCCTGCCACCCACAG	0.453																																					p.A510E	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.C1529A						.						114	115	115					1																	238045816		2203	4300	6503	SO:0001583	missense	57829	exon12			AGGCCTGCCACCC	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"Zona pellucida glycoproteins"	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.1529C>A	chr1.hg19:g.238045816G>T	ENSP00000355529:p.Ala510Glu	57.0	0.0		57.0	23.0	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	hg19	CCDS1615.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.381892	0.61845	.	.	ENSG00000116996	ENST00000366570	T	0.75367	-0.93	3.3	1.38	0.22167	.	0.999559	0.08091	N	0.999251	T	0.71804	0.3383	L	0.43923	1.385	0.21762	N	0.999558	D	0.57571	0.98	P	0.51701	0.677	T	0.58498	-0.7626	10	0.46703	T	0.11	-1.5864	5.0904	0.14706	0.2839:0.0:0.7161:0.0	.	510	Q12836	ZP4_HUMAN	E	510	ENSP00000355529:A510E	ENSP00000355529:A510E	A	-	2	0	ZP4	236112439	0.952000	0.32445	0.724000	0.30704	0.470000	0.32858	1.876000	0.39588	0.391000	0.25143	-0.150000	0.13652	GCA	.	.		0.453	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			T	238045816	G	T	238045816	3	4	185	1	0	0	0	0	1	0	0	0	18233	1319	46	3	97	3	ZP4	1	238045816	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	3480538	238045816	11204805	18	27469										
GEN1	348654	hgsc.bcm.edu	37	chr2	17962727	17962727	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tgcttcaagaagactataaaGtcaatacttctgtcccttat	5	9	3	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr2:17962727G>T	ENST00000381254.2	+	14	2462	c.2248G>T	c.(2248-2250)Gtc>Ttc	p.V750F	GEN1_ENST00000317402.7_Missense_Mutation_p.V750F|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	750					DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AGACTATAAAGTCAATACTTC	0.368								Homologous recombination																													p.V750F		Atlas-SNP	.											GEN1_ENST00000381254,NS,carcinoma,0,1	GEN1	79	.	0			c.G2248T						.						78	82	81					2																	17962727		2203	4298	6501	SO:0001583	missense	348654	exon14			TATAAAGTCAATA	AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"Holliday junction resolvase"	612449	"Gen endonuclease homolog 1 (Drosophila)"			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.2248G>T	chr2.hg19:g.17962727G>T	ENSP00000370653:p.Val750Phe	96.0	0.0		90.0	33.0	NM_182625	Q17RS9|Q6ZN37	Missense_Mutation	SNP	ENST00000381254.2	hg19	CCDS1691.1	.	.	.	.	.	.	.	.	.	.	G	8.702	0.910041	0.17833	.	.	ENSG00000178295	ENST00000317402;ENST00000381254;ENST00000536097	T;T	0.31769	1.48;1.48	5.19	-4.34	0.03666	.	1.705140	0.03574	N	0.229152	T	0.19685	0.0473	L	0.40543	1.245	0.09310	N	1	P	0.35982	0.531	B	0.30782	0.12	T	0.14008	-1.0488	10	0.62326	D	0.03	-23.9512	1.9392	0.03343	0.4547:0.0924:0.1723:0.2807	.	750	Q17RS7	GEN_HUMAN	F	750;750;387	ENSP00000318977:V750F;ENSP00000370653:V750F	ENSP00000318977:V750F	V	+	1	0	GEN1	17826208	0.000000	0.05858	0.000000	0.03702	0.323000	0.28346	-0.382000	0.07408	-1.052000	0.03222	0.655000	0.94253	GTC	.	.		0.368	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625		T	17962727	G	T	17962727	3	4	185	1	0	0	0	0	1	0	0	0	6343	1029	36	3	2298	3	GEN1	2	17962727	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10		17962727	225236646	19	27470										
TMEM214	54867	hgsc.bcm.edu	37	chr2	27261574	27261574	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cctttcttgtccataggtacAgaagtctttgcaagaaacca	7	10	2	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr2:27261574A>G	ENST00000238788.9	+	12	1360	c.1298A>G	c.(1297-1299)cAg>cGg	p.Q433R	TMEM214_ENST00000404032.3_Missense_Mutation_p.Q388R	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	433					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CCATAGGTACAGAAGTCTTTG	0.512																																					p.Q433R		Atlas-SNP	.											.	TMEM214	41	.	0			c.A1298G						.						54	57	56					2																	27261574		2017	4177	6194	SO:0001583	missense	54867	exon12			AGGTACAGAAGTC		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.1298A>G	chr2.hg19:g.27261574A>G	ENSP00000238788:p.Gln433Arg	58.0	0.0		56.0	21.0	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	hg19	CCDS42664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.52|10.52	1.372934|1.372934	0.24857|0.24857	.|.	.|.	ENSG00000119777|ENSG00000119777	ENST00000238788;ENST00000404032;ENST00000537397;ENST00000444135|ENST00000425720	T;T;T|.	0.39056|.	1.1;1.1;1.1|.	5.39|5.39	-1.48|-1.48	0.08745|0.08745	.|.	0.499938|.	0.22690|.	N|.	0.056831|.	T|T	0.19248|0.19248	0.0462|0.0462	N|N	0.11560|0.11560	0.145|0.145	0.25854|0.25854	N|N	0.983905|0.983905	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.06405|.	0.001;0.002|.	T|T	0.31138|0.31138	-0.9954|-0.9954	10|5	0.02654|.	T|.	1|.	-0.6395|-0.6395	10.9816|10.9816	0.47497|0.47497	0.3754:0.0:0.6246:0.0|0.3754:0.0:0.6246:0.0	.|.	388;433|.	Q6NUQ4-2;Q6NUQ4|.	.;TM214_HUMAN|.	R|G	433;388;173;93|218	ENSP00000238788:Q433R;ENSP00000384417:Q388R;ENSP00000392442:Q93R|.	ENSP00000238788:Q433R|.	Q|R	+|+	2|1	0|2	TMEM214|TMEM214	27115078|27115078	0.292000|0.292000	0.24362|0.24362	0.405000|0.405000	0.26409|0.26409	0.941000|0.941000	0.58515|0.58515	0.469000|0.469000	0.22067|0.22067	-0.202000|-0.202000	0.10268|0.10268	0.459000|0.459000	0.35465|0.35465	CAG|AGA	.	.		0.512	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727		G	27261574	A	G	27261574	3	3	185	1	0	0	0	0	1	0	0	0	16152	188	7	2	1344	2	TMEM214	2	27261574	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	9298847	27261574	215937799	20	27471										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50573856	50573856	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gcctcgcaaggatgccggtgAcctgtagattgcaataggca	13	10	0	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr2:50573856A>G	ENST00000406316.2	-	18	4841				NRXN1_ENST00000404971.1_Intron|NRXN1_ENST00000406859.3_Intron|NRXN1_ENST00000401710.1_Intron|NRXN1_ENST00000331040.5_Intron|NRXN1_ENST00000402717.3_Intron|NRXN1_ENST00000401669.2_Intron|NRXN1_ENST00000405472.3_Intron|NRXN1_ENST00000342183.5_Missense_Mutation_p.S78P	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1						adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GATGCCGGTGACCTGTAGATT	0.602																																					p.S78P		Atlas-SNP	.											.	NRXN1	1118	.	0			c.T232C						.						96	75	82					2																	50573856		2203	4300	6503	SO:0001627	intron_variant	9378	exon1			CCGGTGACCTGTA	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3365-109748T>C	chr2.hg19:g.50573856A>G		49.0	0.0		46.0	17.0	NM_138735	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.941531	0.73557	.	.	ENSG00000179915	ENST00000342183;ENST00000536347	T	0.48201	0.82	4.52	4.52	0.55395	.	.	.	.	.	T	0.43634	0.1256	L	0.46157	1.445	0.80722	D	1	B	0.12630	0.006	B	0.17979	0.02	T	0.44406	-0.9330	9	0.87932	D	0	.	13.9972	0.64409	1.0:0.0:0.0:0.0	.	78	P58400	NRX1B_HUMAN	P	78;32	ENSP00000341184:S78P	ENSP00000341184:S78P	S	-	1	0	NRXN1	50427360	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.569000	0.82380	1.916000	0.55485	0.379000	0.24179	TCA	.	.		0.602	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			G	50573856	A	G	50573856	1	3	185	0	1	0	0	0	0	0	0	0	10674	275	10	2		2	NRXN1	2	50573856	Intron	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	23312282	50573856	192625517	21	27472										
MEIS1	4211	hgsc.bcm.edu	37	chr2	66664888	66664888	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gtacgacgatctaccccattAcgggggcatggatggagtag	14	9	1	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr2:66664888A>G	ENST00000272369.9	+	2	489	c.32A>G	c.(31-33)tAc>tGc	p.Y11C	MEIS1_ENST00000488550.1_Missense_Mutation_p.Y11C|MEIS1-AS1_ENST00000454595.1_RNA|MEIS1-AS2_ENST00000439433.1_RNA|MEIS1_ENST00000398506.2_Missense_Mutation_p.Y9C|MEIS1_ENST00000407092.2_Missense_Mutation_p.Y11C|MEIS1_ENST00000444274.2_5'Flank|MEIS1_ENST00000495021.2_5'Flank|MEIS1_ENST00000560281.2_Missense_Mutation_p.Y11C	NM_002398.2	NP_002389.1	O00470	MEIS1_HUMAN	Meis homeobox 1	11					angiogenesis (GO:0001525)|definitive hemopoiesis (GO:0060216)|lens morphogenesis in camera-type eye (GO:0002089)|megakaryocyte development (GO:0035855)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron differentiation (GO:0045665)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	24						CTACCCCATTACGGGGGCATG	0.587																																					p.Y11C		Atlas-SNP	.											.	MEIS1	52	.	0			c.A32G						.						46	45	46					2																	66664888		1999	4188	6187	SO:0001583	missense	4211	exon2			CCCATTACGGGGG		CCDS46309.1	2p14	2011-06-20	2007-02-15		ENSG00000143995	ENSG00000143995		"Homeoboxes / TALE class"	7000	protein-coding gene	gene with protein product		601739	"Meis1 (mouse) homolog", "Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)"			7565694	Standard	NM_002398		Approved		uc002sdu.3	O00470	OTTHUMG00000150714	ENST00000272369.9:c.32A>G	chr2.hg19:g.66664888A>G	ENSP00000272369:p.Tyr11Cys	56.0	0.0		72.0	23.0	NM_002398	A8MV50	Missense_Mutation	SNP	ENST00000272369.9	hg19	CCDS46309.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.293359	0.80914	.	.	ENSG00000143995	ENST00000272369;ENST00000407092;ENST00000398506	T;T;T	0.30448	1.53;1.53;1.53	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.53818	0.1820	M	0.69823	2.125	0.80722	D	1	D;D;D	0.67145	0.996;0.975;0.996	D;P;D	0.66497	0.944;0.832;0.944	T	0.57323	-0.7831	10	0.66056	D	0.02	.	15.5973	0.76595	1.0:0.0:0.0:0.0	.	9;11;11	O00470-2;O00470;F8W8U3	.;MEIS1_HUMAN;.	C	11;11;9	ENSP00000272369:Y11C;ENSP00000384461:Y11C;ENSP00000381518:Y9C	ENSP00000272369:Y11C	Y	+	2	0	MEIS1	66518392	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.656000	0.91102	2.217000	0.71921	0.533000	0.62120	TAC	.	.		0.587	MEIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319725.4	NM_002398		G	66664888	A	G	66664888	3	3	185	1	0	0	0	0	1	0	0	0	9476	391	14	2	38	2	MEIS1	2	66664888	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	16091032	66664888	176534485	22	27473										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73680731	73680731	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tttattagttcaactacagtTagaagtcctctacaggaagc	7	8	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr2:73680731T>A	ENST00000264448.6	+	8	7185	c.7074T>A	c.(7072-7074)gtT>gtA	p.V2358V	ALMS1_ENST00000377715.1_Silent_p.V2358V|ALMS1_ENST00000409009.1_Silent_p.V2316V	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2358					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CAACTACAGTTAGAAGTCCTC	0.433																																					p.V2358V		Atlas-SNP	.											.	ALMS1	384	.	0			c.T7074A						.						63	58	60					2																	73680731		1875	4119	5994	SO:0001819	synonymous_variant	7840	exon8			TACAGTTAGAAGT	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7074T>A	chr2.hg19:g.73680731T>A		87.0	0.0		86.0	14.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.433	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73680731	T	A	73680731	2	1	185	1	0	0	0	0	0	0	0	1	535	1741	61	4		4	ALMS1	2	73680731	Silent	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	7015843	73680731	169518642	23	27474										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160879323	160879323	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gcaattacgattgtagggatTccagccaggctcacagtggg	13	9	1	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr2:160879323T>C	ENST00000283243.7	-	7	1353	c.1147A>G	c.(1147-1149)Aat>Gat	p.N383D	PLA2R1_ENST00000392771.1_Missense_Mutation_p.N383D	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	383					cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						TTGTAGGGATTCCAGCCAGGC	0.373																																					p.N383D		Atlas-SNP	.											.	PLA2R1	153	.	0			c.A1147G						.						137	135	135					2																	160879323		2203	4300	6503	SO:0001583	missense	22925	exon7			AGGGATTCCAGCC	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.1147A>G	chr2.hg19:g.160879323T>C	ENSP00000283243:p.Asn383Asp	87.0	0.0		66.0	22.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	hg19	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	T	13.83	2.354739	0.41700	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.16597	2.33;2.33	5.49	1.46	0.22682	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (1);	0.663319	0.16750	N	0.201075	T	0.11707	0.0285	L	0.51422	1.61	0.25529	N	0.9873	B;B;B	0.28820	0.043;0.118;0.224	B;B;B	0.24701	0.045;0.055;0.035	T	0.22977	-1.0201	10	0.35671	T	0.21	.	0.9544	0.01382	0.2883:0.0948:0.2595:0.3574	.	383;383;383	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	D	383	ENSP00000283243:N383D;ENSP00000376524:N383D	ENSP00000283243:N383D	N	-	1	0	PLA2R1	160587569	0.996000	0.38824	0.984000	0.44739	0.991000	0.79684	0.192000	0.17096	0.352000	0.24053	0.533000	0.62120	AAT	.	.		0.373	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			C	160879323	T	C	160879323	3	2	185	1	0	0	0	0	1	0	0	0	12019	1783	62	2	3348	2	PLA2R1	2	160879323	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	87198592	160879323	82320050	24	27475										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160901376	160901376	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gaggccaccactgtgttgtcAtgcgccacctggacagagta	12	12	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr2:160901376A>C	ENST00000283243.7	-	2	608	c.402T>G	c.(400-402)caT>caG	p.H134Q	PLA2R1_ENST00000392771.1_Missense_Mutation_p.H134Q	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	134	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CTGTGTTGTCATGCGCCACCT	0.463																																					p.H134Q		Atlas-SNP	.											.	PLA2R1	153	.	0			c.T402G						.						82	83	83					2																	160901376		2203	4300	6503	SO:0001583	missense	22925	exon2			GTTGTCATGCGCC	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.402T>G	chr2.hg19:g.160901376A>C	ENSP00000283243:p.His134Gln	106.0	0.0		80.0	10.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	hg19	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	A	0.062	-1.221360	0.01530	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.40756	1.02;1.02	5.69	-11.4	0.00090	Ricin B-related lectin (1);Ricin B lectin (1);	1.391850	0.04601	N	0.398467	T	0.11067	0.0270	N	0.00926	-1.1	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.27739	-1.0065	10	0.23302	T	0.38	.	4.7628	0.13116	0.4352:0.3369:0.0989:0.1291	.	134;134;134	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	Q	134	ENSP00000283243:H134Q;ENSP00000376524:H134Q	ENSP00000283243:H134Q	H	-	3	2	PLA2R1	160609622	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.280000	0.01158	-4.392000	0.00052	-1.055000	0.02315	CAT	.	.		0.463	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			C	160901376	A	C	160901376	3	2	185	1	0	0	0	0	1	0	0	0	12019	214	8	5	4113	5	PLA2R1	2	160901376	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	22053	160901376	82297997	25	27476										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212495254	212495254	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tccttctaacataaacagcaAatgtcagacccacaatgacc	4	13	2	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr2:212495254A>G	ENST00000342788.4	-	17	2322	c.2012T>C	c.(2011-2013)tTt>tCt	p.F671S	ERBB4_ENST00000436443.1_Missense_Mutation_p.F671S|ERBB4_ENST00000402597.1_Missense_Mutation_p.F661S	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	671					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ATAAACAGCAAATGTCAGACC	0.393										TSP Lung(8;0.080)																											p.F671S		Atlas-SNP	.											.	ERBB4	480	.	0			c.T2012C						.						102	106	105					2																	212495254		2203	4300	6503	SO:0001583	missense	2066	exon17			ACAGCAAATGTCA	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2012T>C	chr2.hg19:g.212495254A>G	ENSP00000342235:p.Phe671Ser	74.0	0.0		64.0	23.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	A	18.31	3.596329	0.66332	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.76839	-1.05;-1.04;-1.04	5.62	5.62	0.85841	.	0.049344	0.85682	D	0.000000	T	0.72763	0.3501	L	0.38531	1.155	0.58432	D	0.999997	P;B;B;P;P	0.42692	0.787;0.01;0.001;0.787;0.682	B;B;B;B;B	0.42282	0.382;0.01;0.002;0.382;0.212	T	0.75252	-0.3383	10	0.51188	T	0.08	.	15.8218	0.78654	1.0:0.0:0.0:0.0	.	661;661;530;671;671	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.;.;.;.;ERBB4_HUMAN	S	671;671;661	ENSP00000342235:F671S;ENSP00000403204:F671S;ENSP00000385565:F661S	ENSP00000342235:F671S	F	-	2	0	ERBB4	212203499	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.957000	0.93082	2.146000	0.66826	0.477000	0.44152	TTT	.	.		0.393	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		G	212495254	A	G	212495254	3	3	185	1	0	0	0	0	1	0	0	0	5211	14	1	2	1962	2	ERBB4	2	212495254	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	51593878	212495254	30704119	26	27477										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215890440	215890440	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctggaggaaagtaatcttcaTaggaaccattgcgaagaaaa	10	6	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr2:215890440T>C	ENST00000272895.7	-	11	1463	c.1244A>G	c.(1243-1245)tAt>tGt	p.Y415C	AC072062.3_ENST00000595058.1_RNA|AC072062.3_ENST00000419251.1_RNA|AC072062.3_ENST00000602182.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.Y97C|AC072062.3_ENST00000437897.3_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	415					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GTAATCTTCATAGGAACCATT	0.303																																					p.Y415C	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.A1244G						.						77	81	79					2																	215890440		2203	4300	6503	SO:0001583	missense	26154	exon11			TCTTCATAGGAAC	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.1244A>G	chr2.hg19:g.215890440T>C	ENSP00000272895:p.Tyr415Cys	47.0	0.0		31.0	10.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.550258	0.45383	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	T;T	0.54675	0.56;0.56	5.96	0.436	0.16549	.	0.473178	0.19903	N	0.103480	T	0.35098	0.0920	N	0.19112	0.55	0.80722	D	1	P;P	0.34892	0.472;0.474	B;B	0.39904	0.302;0.313	T	0.05402	-1.0887	10	0.40728	T	0.16	.	5.8502	0.18689	0.2849:0.0:0.2703:0.4448	.	415;97	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	C	415;97	ENSP00000272895:Y415C;ENSP00000374312:Y97C	ENSP00000272895:Y415C	Y	-	2	0	ABCA12	215598685	1.000000	0.71417	0.996000	0.52242	0.908000	0.53690	0.276000	0.18716	-0.153000	0.11137	0.533000	0.62120	TAT	.	.		0.303	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		C	215890440	T	C	215890440	3	2	185	1	0	0	0	0	1	0	0	0	30	1406	49	2	6715	2	ABCA12	2	215890440	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	3395186	215890440	27308933	27	27478										
D2HGDH	728294	hgsc.bcm.edu	37	chr2	242684139	242684139	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ccaaggtgctggccgacggcActgtcctggactgcctgacc	13	15	0	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr2:242684139A>G	ENST00000321264.4	+	6	909	c.700A>G	c.(700-702)Act>Gct	p.T234A	D2HGDH_ENST00000342518.6_Missense_Mutation_p.T234A|D2HGDH_ENST00000403782.1_Missense_Mutation_p.T100A|D2HGDH_ENST00000537090.1_Missense_Mutation_p.T234A	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	234	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		GGCCGACGGCACTGTCCTGGA	0.622																																					p.T234A		Atlas-SNP	.											.	D2HGDH	39	.	0			c.A700G						.						160	133	142					2																	242684139		2203	4298	6501	SO:0001583	missense	728294	exon6			GACGGCACTGTCC	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.700A>G	chr2.hg19:g.242684139A>G	ENSP00000315351:p.Thr234Ala	105.0	0.0		84.0	7.0	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	hg19	CCDS33426.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.621|9.621	1.133767|1.133767	0.21123|0.21123	.|.	.|.	ENSG00000180902|ENSG00000180902	ENST00000417686|ENST00000537090;ENST00000321264;ENST00000403782;ENST00000342518	.|D;D;D;D	.|0.96587	.|-4.06;-4.06;-4.06;-4.06	5.1|5.1	2.43|2.43	0.29744|0.29744	.|FAD-linked oxidase, FAD-binding, subdomain 2 (1);FAD-binding, type 2 (2);FAD linked oxidase, N-terminal (1);	.|0.505399	.|0.20924	.|N	.|0.083233	D|D	0.95843|0.95843	0.8647|0.8647	M|M	0.81497|0.81497	2.545|2.545	0.09310|0.09310	N|N	1|1	.|P	.|0.34462	.|0.454	.|B	.|0.43155	.|0.41	D|D	0.91429|0.91429	0.5164|0.5164	5|10	.|0.52906	.|T	.|0.07	0.1971|0.1971	6.7859|6.7859	0.23673|0.23673	0.5517:0.1093:0.0:0.339|0.5517:0.1093:0.0:0.339	.|.	.|234	.|Q8N465	.|D2HDH_HUMAN	R|A	75|234;234;100;234	.|ENSP00000442796:T234A;ENSP00000315351:T234A;ENSP00000384723:T100A;ENSP00000339536:T234A	.|ENSP00000315351:T234A	H|T	+|+	2|1	0|0	D2HGDH|D2HGDH	242332812|242332812	0.104000|0.104000	0.21937|0.21937	0.241000|0.241000	0.24154|0.24154	0.014000|0.014000	0.08584|0.08584	1.608000|1.608000	0.36847|0.36847	0.748000|0.748000	0.32831|0.32831	0.459000|0.459000	0.35465|0.35465	CAC|ACT	.	.		0.622	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783		G	242684139	A	G	242684139	3	3	185	1	0	0	0	0	1	0	0	0	4215	159	6	2	718	2	D2HGDH	2	242684139	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	26793699	242684139	515234	28	27479										
ABHD5	51099	hgsc.bcm.edu	37	chr3	43743957	43743957	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	agtgatgcagaagaagtggaGaatcagtttgtggaatccat	13	4	1	4			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr3:43743957G>A	ENST00000458276.2	+	3	507	c.384G>A	c.(382-384)gaG>gaA	p.E128E		NM_016006.4	NP_057090.2	Q8WTS1	ABHD5_HUMAN	abhydrolase domain containing 5	128					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|negative regulation of sequestering of triglyceride (GO:0010891)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|lysophosphatidic acid acyltransferase activity (GO:0042171)			kidney(3)|large_intestine(2)|liver(2)|lung(5)|ovary(1)|skin(1)	14		Renal(3;0.0134)		KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0687)		AAGAAGTGGAGAATCAGTTTG	0.458																																					p.E128E		Atlas-SNP	.											ABHD5,colon,carcinoma,0,1	ABHD5	33	.	0			c.G384A						.						269	258	262					3																	43743957		2203	4300	6503	SO:0001819	synonymous_variant	51099	exon3			AGTGGAGAATCAG	AF007132	CCDS2711.1	3p21.33	2012-05-16			ENSG00000011198	ENSG00000011198		"Abhydrolase domain containing"	21396	protein-coding gene	gene with protein product		604780				11590543, 18606822	Standard	NM_016006		Approved	CGI-58, NCIE2	uc003cmx.3	Q8WTS1	OTTHUMG00000133039	ENST00000458276.2:c.384G>A	chr3.hg19:g.43743957G>A		95.0	0.0		109.0	39.0	NM_016006	B2R9K0|Q9Y369	Silent	SNP	ENST00000458276.2	hg19	CCDS2711.1																																																																																			.	.		0.458	ABHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256644.2	NM_016006		A	43743957	G	A	43743957	2	1	185	1	0	0	0	0	0	0	0	1	85	933	33	3		3	ABHD5	3	43743957	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10		43743957	154278473	29	27480										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48624721	48624721	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	caggctctagccctgtcaccCgctgggagcttgagatccct	11	15	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr3:48624721C>T	ENST00000328333.8	-	23	3148	c.3041G>A	c.(3040-3042)cGg>cAg	p.R1014Q	COL7A1_ENST00000454817.1_Missense_Mutation_p.R1014Q	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1014	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region (NC1).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCCTGTCACCCGCTGGGAGCT	0.587																																					p.R1014Q		Atlas-SNP	.											.	COL7A1	320	.	0			c.G3041A						.						48	46	46					3																	48624721		2201	4300	6501	SO:0001583	missense	1294	exon23			GTCACCCGCTGGG	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.3041G>A	chr3.hg19:g.48624721C>T	ENSP00000332371:p.Arg1014Gln	159.0	0.0		176.0	62.0	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	hg19	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	9.898	1.205961	0.22205	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	T;T	0.56444	0.46;0.46	5.91	-1.36	0.09085	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.388231	0.18643	N	0.135226	T	0.30135	0.0755	N	0.11560	0.145	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.22626	-1.0211	10	0.46703	T	0.11	.	12.1584	0.54091	0.0:0.412:0.0:0.588	.	1014	Q02388	CO7A1_HUMAN	Q	1014	ENSP00000332371:R1014Q;ENSP00000412569:R1014Q	ENSP00000332371:R1014Q	R	-	2	0	COL7A1	48599725	0.001000	0.12720	0.964000	0.40570	0.468000	0.32798	-1.170000	0.03118	-0.092000	0.12417	-0.137000	0.14449	CGG	.	.		0.587	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		T	48624721	C	T	48624721	3	4	185	1	0	0	0	0	1	0	0	0	3706	652	23	1	6177	1	COL7A1	3	48624721	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	4880764	48624721	149397709	30	27481										
OR5H1	26341	hgsc.bcm.edu	37	chr3	97852199	97852199	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctattcttgtatcttatacaTttgttctcttcgcaatctta	3	9	4	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr3:97852199T>A	ENST00000354565.2	+	1	658	c.658T>A	c.(658-660)Ttt>Att	p.F220I	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						ATCTTATACATTTGTTCTCTT	0.333																																					p.F220I		Atlas-SNP	.											.	OR5H1	71	.	0			c.T658A						.						70	76	74					3																	97852199		2201	4299	6500	SO:0001583	missense	26341	exon1			TATACATTTGTTC	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"GPCR / Class A : Olfactory receptors"	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.658T>A	chr3.hg19:g.97852199T>A	ENSP00000346575:p.Phe220Ile	129.0	0.0		96.0	27.0	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	hg19	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	T	3.163	-0.171690	0.06421	.	.	ENSG00000231192	ENST00000354565	T	0.00115	8.71	3.57	-3.25	0.05079	GPCR, rhodopsin-like superfamily (1);	0.693493	0.12553	N	0.458902	T	0.00178	0.0005	M	0.73430	2.235	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.26467	-1.0102	10	0.72032	D	0.01	.	9.398	0.38415	0.0:0.2468:0.0:0.7532	.	220	A6NKK0	OR5H1_HUMAN	I	220	ENSP00000346575:F220I	ENSP00000346575:F220I	F	+	1	0	OR5H1	99334889	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-0.601000	0.05687	-0.674000	0.05253	0.164000	0.16699	TTT	.	.		0.333	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338		A	97852199	T	A	97852199	3	1	185	1	0	0	0	0	1	0	0	0	11168	1493	52	4	660	4	OR5H1	3	97852199	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	49227478	97852199	100170231	31	27482										
CP	1356	hgsc.bcm.edu	37	chr3	148924011	148924011	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tctataccagagggagcataGttccagatgatttcctcagc	9	10	2	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr3:148924011G>C	ENST00000264613.6	-	6	1414	c.1152C>G	c.(1150-1152)aaC>aaG	p.N384K		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	384	F5/8 type A 2.|Plastocyanin-like 3.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	AGGGAGCATAGTTCCAGATGA	0.398																																					p.N384K		Atlas-SNP	.											.	CP	112	.	0			c.C1152G						.						138	137	137					3																	148924011		2203	4300	6503	SO:0001583	missense	1356	exon6			AGCATAGTTCCAG	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1152C>G	chr3.hg19:g.148924011G>C	ENSP00000264613:p.Asn384Lys	76.0	0.0		97.0	24.0	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	hg19	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.306531	0.60305	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98978	-5.29;-5.29	5.81	-2.42	0.06542	Cupredoxin (2);	0.334565	0.38959	N	0.001515	D	0.97607	0.9216	M	0.75884	2.315	0.44927	D	0.997943	D;D;D;D	0.54047	0.964;0.964;0.964;0.964	B;B;B;B	0.42361	0.385;0.385;0.385;0.385	D	0.94716	0.7896	10	0.87932	D	0	-13.1636	12.8609	0.57913	0.5672:0.0:0.4328:0.0	.	384;384;384;384	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	K	384;167	ENSP00000264613:N384K;ENSP00000420545:N167K	ENSP00000264613:N384K	N	-	3	2	CP	150406701	1.000000	0.71417	0.539000	0.28077	0.890000	0.51754	1.024000	0.30077	-0.323000	0.08602	-0.736000	0.03550	AAC	.	.		0.398	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		C	148924011	G	C	148924011	3	2	185	1	0	0	0	0	1	0	0	0	3789	1020	36	4	2101	4	CP	3	148924011	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	51071812	148924011	49098419	32	27483										
COMMD2	51122	hgsc.bcm.edu	37	chr3	149468548	149468548	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aatcgttctgatctcttttcTgttgtccagataaagctgaa	7	8	3	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr3:149468548T>C	ENST00000473414.1	-	4	373	c.319A>G	c.(319-321)Aga>Gga	p.R107G		NM_016094.3	NP_057178.2	Q86X83	COMD2_HUMAN	COMM domain containing 2	107										NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			ATCTCTTTTCTGTTGTCCAGA	0.368																																					p.R107G		Atlas-SNP	.											.	COMMD2	21	.	0			c.A319G						.						142	137	138					3																	149468548		2203	4300	6503	SO:0001583	missense	51122	exon4			CTTTTCTGTTGTC	AY542158	CCDS3145.1	3q25.1	2004-02-20			ENSG00000114744	ENSG00000114744			24993	protein-coding gene	gene with protein product						15799966	Standard	NM_016094		Approved	HSPC042	uc003exj.2	Q86X83	OTTHUMG00000159616	ENST00000473414.1:c.319A>G	chr3.hg19:g.149468548T>C	ENSP00000419475:p.Arg107Gly	148.0	0.0		142.0	38.0	NM_016094	Q561V4|Q9H3L5|Q9Y5V1	Missense_Mutation	SNP	ENST00000473414.1	hg19	CCDS3145.1	.	.	.	.	.	.	.	.	.	.	T	19.80	3.895605	0.72639	.	.	ENSG00000114744	ENST00000473414	T	0.10763	2.84	5.58	4.39	0.52855	.	0.134163	0.64402	D	0.000003	T	0.23572	0.0570	M	0.85945	2.785	0.58432	D	0.99999	P	0.44946	0.846	P	0.46685	0.524	T	0.03139	-1.1068	10	0.62326	D	0.03	-23.518	12.1821	0.54218	0.0:0.0:0.2695:0.7305	.	107	Q86X83	COMD2_HUMAN	G	107	ENSP00000419475:R107G	ENSP00000419475:R107G	R	-	1	2	COMMD2	150951238	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.011000	0.40922	1.015000	0.39444	0.528000	0.53228	AGA	.	.		0.368	COMMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356515.1	NM_016094		C	149468548	T	C	149468548	3	2	185	1	0	0	0	0	1	0	0	0	3718	1588	55	2	288	2	COMMD2	3	149468548	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	544537	149468548	48553882	33	27484										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	193029669	193029669	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	atttcccactcattgcaaaaTggtaacagcttcctccttcc	4	14	1	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr3:193029669T>A	ENST00000342358.4	-	20	2498	c.2381A>T	c.(2380-2382)cAt>cTt	p.H794L	ATP13A5-AS1_ENST00000414634.1_RNA|ATP13A5_ENST00000495496.1_5'UTR	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	794						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		CATTGCAAAATGGTAACAGCT	0.393																																					p.H794L		Atlas-SNP	.											.	ATP13A5	171	.	0			c.A2381T						.						142	130	134					3																	193029669		2203	4300	6503	SO:0001583	missense	344905	exon20			GCAAAATGGTAAC	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.2381A>T	chr3.hg19:g.193029669T>A	ENSP00000341942:p.His794Leu	52.0	0.0		86.0	28.0	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	hg19	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.213913	0.79352	.	.	ENSG00000187527	ENST00000342358	D	0.84660	-1.88	5.81	5.81	0.92471	HAD-like domain (1);	0.083216	0.52532	D	0.000075	D	0.92496	0.7617	M	0.89095	3.005	0.49483	D	0.999798	D	0.69078	0.997	D	0.69479	0.964	D	0.91779	0.5434	10	0.27785	T	0.31	-17.2742	14.1191	0.65175	0.0:0.0:0.0:1.0	.	794	Q4VNC0	AT135_HUMAN	L	794	ENSP00000341942:H794L	ENSP00000341942:H794L	H	-	2	0	ATP13A5	194512363	1.000000	0.71417	1.000000	0.80357	0.652000	0.38707	6.817000	0.75252	2.224000	0.72417	0.528000	0.53228	CAT	.	.		0.393	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		A	193029669	T	A	193029669	3	1	185	1	0	0	0	0	1	0	0	0	1127	1464	51	4	1317	4	ATP13A5	3	193029669	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	43561121	193029669	4992761	34	27485										
BANK1	55024	hgsc.bcm.edu	37	chr4	102951351	102951351	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tcggtctttcattataaataGacctcctgcccccacacccc	4	17	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr4:102951351G>C	ENST00000322953.4	+	10	2103	c.1829G>C	c.(1828-1830)aGa>aCa	p.R610T	BANK1_ENST00000508653.1_Missense_Mutation_p.R477T|BANK1_ENST00000444316.2_Missense_Mutation_p.R580T|BANK1_ENST00000504592.1_Missense_Mutation_p.R595T|RP11-498M5.2_ENST00000505091.1_RNA|BANK1_ENST00000428908.1_Missense_Mutation_p.R477T	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	610					B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		ATTATAAATAGACCTCCTGCC	0.388																																					p.R610T		Atlas-SNP	.											.	BANK1	95	.	0			c.G1829C						.						103	112	109					4																	102951351		2203	4300	6503	SO:0001583	missense	55024	exon10			TAAATAGACCTCC	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.1829G>C	chr4.hg19:g.102951351G>C	ENSP00000320509:p.Arg610Thr	225.0	0.0		171.0	8.0	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	hg19	CCDS34038.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260884	0.80246	.	.	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.69061	0.3069	M	0.62723	1.935	0.39151	D	0.962228	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.64330	-0.6433	10	0.22706	T	0.39	.	16.9051	0.86124	0.0:0.0:1.0:0.0	.	477;610;595	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	T	595;610;477;477;580	ENSP00000421443:R595T;ENSP00000320509:R610T;ENSP00000412748:R477T;ENSP00000422314:R477T;ENSP00000388817:R580T	ENSP00000320509:R610T	R	+	2	0	BANK1	103170374	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	5.719000	0.68462	2.777000	0.95525	0.591000	0.81541	AGA	.	.		0.388	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		C	102951351	G	C	102951351	3	2	185	1	0	0	0	0	1	0	0	0	1309	942	33	4	1867	4	BANK1	4	102951351	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10		102951351	88202925	35	27486										
NDST4	64579	hgsc.bcm.edu	37	chr4	115754812	115754812	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gtaactcccagaaacttctgGacttcatccatcacagtagc	6	13	3	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr4:115754812G>T	ENST00000264363.2	-	12	3024	c.2346C>A	c.(2344-2346)gtC>gtA	p.V782V		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	782	Heparan sulfate N-sulfotransferase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		GAAACTTCTGGACTTCATCCA	0.363																																					p.V782V		Atlas-SNP	.											.	NDST4	193	.	0			c.C2346A						.						81	79	79					4																	115754812		2203	4300	6503	SO:0001819	synonymous_variant	64579	exon12			CTTCTGGACTTCA	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.2346C>A	chr4.hg19:g.115754812G>T		157.0	0.0		84.0	7.0	NM_022569	Q2KHM8	Silent	SNP	ENST00000264363.2	hg19	CCDS3706.1																																																																																			.	.		0.363	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		T	115754812	G	T	115754812	2	4	185	1	0	0	0	0	0	0	0	1	10267	1161	41	3		3	NDST4	4	115754812	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	12803461	115754812	75399464	36	27487										
SPCS3	60559	hgsc.bcm.edu	37	chr4	177249473	177249473	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	atacatatgaaataacgaagAgttattaaattattctgaat	5	3	1	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr4:177249473A>G	ENST00000503362.1	+	5	648	c.535A>G	c.(535-537)Agt>Ggt	p.S179G	SPCS3_ENST00000507001.1_3'UTR	NM_021928.3	NP_068747.1	P61009	SPCS3_HUMAN	signal peptidase complex subunit 3 homolog (S. cerevisiae)	179					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)			ovary(2)	2		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.43e-19)|Epithelial(43;1.84e-16)|OV - Ovarian serous cystadenocarcinoma(60;4.51e-09)|GBM - Glioblastoma multiforme(59;0.000142)|STAD - Stomach adenocarcinoma(60;0.00279)|LUSC - Lung squamous cell carcinoma(193;0.0319)		AATAACGAAGAGTTATTAAAT	0.338																																					p.S179G		Atlas-SNP	.											.	SPCS3	15	.	0			c.A535G						.						52	48	49					4																	177249473		1818	4075	5893	SO:0001583	missense	60559	exon5			ACGAAGAGTTATT	AK092634	CCDS54823.1	4q34.2	2008-02-05				ENSG00000129128			26212	protein-coding gene	gene with protein product						12477932	Standard	NM_021928		Approved	FLJ22649, SPC22/23, SPC3, YLR066W, PRO3567	uc003iur.4	P61009		ENST00000503362.1:c.535A>G	chr4.hg19:g.177249473A>G	ENSP00000427463:p.Ser179Gly	59.0	0.0		37.0	6.0	NM_021928	P12280|Q9H0S7	Missense_Mutation	SNP	ENST00000503362.1	hg19	CCDS54823.1	.	.	.	.	.	.	.	.	.	.	A	16.84	3.232932	0.58777	.	.	ENSG00000129128	ENST00000503362	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.50786	0.1636	N	0.22421	0.69	0.58432	D	0.999999	B	0.20368	0.044	B	0.19148	0.024	T	0.49835	-0.8897	9	0.62326	D	0.03	-6.5363	15.7533	0.78005	1.0:0.0:0.0:0.0	.	179	P61009	SPCS3_HUMAN	G	179	.	ENSP00000427463:S179G	S	+	1	0	SPCS3	177486467	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.660000	0.91121	2.170000	0.68504	0.528000	0.53228	AGT	.	.		0.338	SPCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362329.1	NM_021928		G	177249473	A	G	177249473	3	3	185	1	0	0	0	0	1	0	0	0	15040	304	11	2	553	2	SPCS3	4	177249473	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	61494661	177249473	13904803	37	27488										
IRX4	50805	hgsc.bcm.edu	37	chr5	1882113	1882113	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cgaggcggcgggcccggagtCcgccagcgtgcggcctccgg	19	16	0	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr5:1882113C>G	ENST00000505790.1	-	3	562	c.106G>C	c.(106-108)Gac>Cac	p.D36H	IRX4_ENST00000513692.1_Missense_Mutation_p.D36H|CTD-2194D22.3_ENST00000506335.1_RNA|IRX4_ENST00000505938.1_5'Flank|IRX4_ENST00000231357.2_Missense_Mutation_p.D36H	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	36					establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		GGCCCGGAGTCCGCCAGCGTG	0.736																																					p.D36H		Atlas-SNP	.											.	IRX4	45	.	0			c.G106C						.						2	2	2					5																	1882113		1412	3187	4599	SO:0001583	missense	50805	exon2			CGGAGTCCGCCAG	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"Homeoboxes / TALE class"	6129	protein-coding gene	gene with protein product		606199	"iroquois homeobox protein 4"			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.106G>C	chr5.hg19:g.1882113C>G	ENSP00000423161:p.Asp36His	89.0	0.0		65.0	17.0	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Missense_Mutation	SNP	ENST00000505790.1	hg19	CCDS3867.1	.	.	.	.	.	.	.	.	.	.	c	15.09	2.731551	0.48939	.	.	ENSG00000113430	ENST00000231357;ENST00000505790;ENST00000513692;ENST00000511126	T;T;T;D	0.83837	-0.39;-0.39;-0.39;-1.77	3.99	3.11	0.35812	.	0.124888	0.51477	U	0.000085	D	0.85004	0.5598	M	0.83384	2.64	0.80722	D	1	P	0.42039	0.769	B	0.42882	0.401	D	0.86414	0.1750	10	0.87932	D	0	-12.1117	13.4828	0.61345	0.0:0.8413:0.1587:0.0	.	36	P78413	IRX4_HUMAN	H	36	ENSP00000231357:D36H;ENSP00000423161:D36H;ENSP00000424235:D36H;ENSP00000421772:D36H	ENSP00000231357:D36H	D	-	1	0	IRX4	1935113	1.000000	0.71417	0.620000	0.29132	0.009000	0.06853	6.622000	0.74233	0.788000	0.33755	0.461000	0.40582	GAC	.	.		0.736	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358		G	1882113	C	G	1882113	3	3	185	1	0	0	0	0	1	0	0	0	7855	855	30	4	1469	4	IRX4	5	1882113	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10		1882113	179033147	38	27489										
MGC42105	167359	hgsc.bcm.edu	37	chr5	43280745	43280745	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gtgtcccagtcatgatgctaCcagaccctaaagaaagagac	9	11	1	4			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr5:43280745C>A	ENST00000512796.1	+	4	2724	c.1225C>A	c.(1225-1227)Cca>Aca	p.P409T	NIM1_ENST00000326035.2_Missense_Mutation_p.P409T			Q8IY84	NIM1_HUMAN		409					protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)										CATGATGCTACCAGACCCTAA	0.428																																					p.P409T		Atlas-SNP	.											.	.	.	.	0			c.C1225A						.						47	48	48					5																	43280745		2203	4300	6503	SO:0001583	missense	0	exon4			ATGCTACCAGACC																												ENST00000512796.1:c.1225C>A	chr5.hg19:g.43280745C>A	ENSP00000420849:p.Pro409Thr	49.0	0.0		51.0	17.0	NM_153361	B3KVM1	Missense_Mutation	SNP	ENST00000512796.1	hg19	CCDS3943.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.085169	0.36758	.	.	ENSG00000177453	ENST00000326035;ENST00000512796	T;T	0.71103	-0.54;-0.54	5.56	5.56	0.83823	.	0.437993	0.25447	N	0.030604	T	0.70316	0.3210	L	0.56769	1.78	0.58432	D	0.999995	B	0.18610	0.029	B	0.16722	0.016	T	0.65549	-0.6141	10	0.45353	T	0.12	.	19.5373	0.95257	0.0:1.0:0.0:0.0	.	409	Q8IY84	NIM1_HUMAN	T	409	ENSP00000313572:P409T;ENSP00000420849:P409T	ENSP00000313572:P409T	P	+	1	0	AC114947.1	43316502	0.971000	0.33674	0.976000	0.42696	0.819000	0.46315	2.500000	0.45381	2.629000	0.89072	0.655000	0.94253	CCA	.	.		0.428	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1			A	43280745	C	A	43280745	3	1	185	1	0	0	0	0	1	0	0	0	9561	507	18	3	1235	3	MGC42105	5	43280745	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	41398632	43280745	137634515	39	27490										
MTX3	345778	hgsc.bcm.edu	37	chr5	79285983	79285983	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cttcaaagtgaaccacccacCtgttttcttaaaaagtttag	5	10	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr5:79285983C>T	ENST00000512528.1	-	3	248	c.228G>A	c.(226-228)caG>caA	p.Q76Q	MTX3_ENST00000509852.1_Splice_Site_p.Q76Q|MTX3_ENST00000512560.1_Splice_Site_p.Q15Q			Q5HYI7	MTX3_HUMAN	metaxin 3	76					protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)				endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(1)	7		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)		AACCACCCACCTGTTTTCTTA	0.333																																					p.Q76Q		Atlas-SNP	.											.	MTX3	29	.	0			c.G228A						.						75	71	72					5																	79285983		1814	4069	5883	SO:0001630	splice_region_variant	345778	exon3			ACCCACCTGTTTT	BX538064	CCDS47239.1, CCDS47239.2, CCDS54872.1	5q14.1	2004-08-18				ENSG00000177034			24812	protein-coding gene	gene with protein product						15087125	Standard	NM_001010891		Approved		uc010jah.3	Q5HYI7		ENST00000512528.1:c.228+1G>A	chr5.hg19:g.79285983C>T		377.0	0.0		291.0	65.0	NM_001010891	B4DL65|E9PB57|Q7Z380|Q8NB92	Silent	SNP	ENST00000512528.1	hg19																																																																																				.	.		0.333	MTX3-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372567.1	XM_293971	Silent	T	79285983	C	T	79285983	5	4	185	1	0	0	0	0	0	0	1	0	9978	695	24	3	738	3	MTX3	5	79285983	Splice_Site	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	36005238	79285983	101629277	40	27491										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118560447	118560447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tgttagaagaatgacttctcAtccaactcttccttactgta	5	10	2	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr5:118560447A>G	ENST00000311085.8	+	37	8338	c.8258A>G	c.(8257-8259)cAt>cGt	p.H2753R	DMXL1_ENST00000505312.1_3'UTR|DMXL1_ENST00000539542.1_Missense_Mutation_p.H2774R	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2753										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		ATGACTTCTCATCCAACTCTT	0.239																																					p.H2753R		Atlas-SNP	.											.	DMXL1	268	.	0			c.A8258G						.						60	64	63					5																	118560447		2179	4245	6424	SO:0001583	missense	1657	exon37			CTTCTCATCCAAC	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.8258A>G	chr5.hg19:g.118560447A>G	ENSP00000309690:p.His2753Arg	239.0	0.0		194.0	48.0	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.075900	0.76415	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.01388	4.95;4.95	5.22	5.22	0.72569	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.10078	0.0247	M	0.84585	2.705	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00461	-1.1725	10	0.87932	D	0	-16.8583	15.0902	0.72188	1.0:0.0:0.0:0.0	.	2774;2753	F5H269;Q9Y485	.;DMXL1_HUMAN	R	2753;2774	ENSP00000309690:H2753R;ENSP00000439479:H2774R	ENSP00000309690:H2753R	H	+	2	0	DMXL1	118588346	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.875000	0.92372	1.963000	0.57068	0.397000	0.26171	CAT	.	.		0.239	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		G	118560447	A	G	118560447	3	3	185	1	0	0	0	0	1	0	0	0	4596	217	8	2	8404	2	DMXL1	5	118560447	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	39274464	118560447	62354813	41	27492										
CDC25C	995	hgsc.bcm.edu	37	chr5	137625188	137625188	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ccatctccagaaatctgcttActgtttctgggttgacatac	7	11	3	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr5:137625188A>G	ENST00000323760.6	-	10	1206		c.e10+1		CDC25C_ENST00000348983.3_Splice_Site|CDC25C_ENST00000415130.2_Splice_Site|CDC25C_ENST00000513970.1_Splice_Site|CDC25C_ENST00000356505.3_Splice_Site|CDC25C_ENST00000514555.1_Splice_Site|CDC25C_ENST00000357274.3_Splice_Site	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C						cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)			endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			AAATCTGCTTACTGTTTCTGG	0.418																																					.		Atlas-SNP	.											.	CDC25C	37	.	0			c.708+2T>C						.						154	137	143					5																	137625188		2203	4300	6503	SO:0001630	splice_region_variant	995	exon8			CTGCTTACTGTTT	M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"Protein tyrosine phosphatases / Class III Cys-based PTPs", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1727	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 60"	157680	"cell division cycle 25C", "cell division cycle 25 homolog C (S. cerevisiae)", "cell division cycle 25 homolog C (S. pombe)"	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.927+1T>C	chr5.hg19:g.137625188A>G		75.0	0.0		67.0	12.0	NM_022809	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Splice_Site	SNP	ENST00000323760.6	hg19	CCDS4202.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.276556	0.80580	.	.	ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000357274;ENST00000348983;ENST00000415130;ENST00000513970;ENST00000534892;ENST00000514555	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5357	0.67958	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDC25C	137653087	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.847000	0.75404	2.263000	0.75096	0.533000	0.62120	.	.	.		0.418	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1		Intron	G	137625188	A	G	137625188	5	3	185	1	0	0	0	0	0	0	1	0	3066	405	14	2	512	2	CDC25C	5	137625188	Splice_Site	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	19064741	137625188	43290072	42	27493										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140236128	140236128	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gcggatgttggagagaacgcAttgcttacttacaaactcag	11	8	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr5:140236128A>G	ENST00000307360.5	+	1	495	c.495A>G	c.(493-495)gcA>gcG	p.A165A	PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000506939.2_Silent_p.A165A|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	165	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGAGAACGCATTGCTTACTT	0.413																																					p.A165A		Atlas-SNP	.											.	PCDHA10	358	.	0			c.A495G						.						114	120	118					5																	140236128		2198	4271	6469	SO:0001819	synonymous_variant	56139	exon1			GAACGCATTGCTT	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.495A>G	chr5.hg19:g.140236128A>G		245.0	0.0		196.0	38.0	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	hg19	CCDS54921.1																																																																																			.	.		0.413	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		G	140236128	A	G	140236128	2	3	185	1	0	0	0	0	0	0	0	1	11529	204	8	2		2	PCDHA10	5	140236128	Silent	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	2610940	140236128	40679132	43	27494										
NR3C1	2908	hgsc.bcm.edu	37	chr5	142680245	142680245	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cgttgcaggaactattgtttTgttaccaggattttcagagg	11	6	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr5:142680245T>A	ENST00000343796.2	-	5	2545	c.1552A>T	c.(1552-1554)Aaa>Taa	p.K518*	NR3C1_ENST00000415690.2_Nonsense_Mutation_p.K518*|NR3C1_ENST00000504572.1_Nonsense_Mutation_p.K519*|NR3C1_ENST00000416954.2_Nonsense_Mutation_p.K121*|NR3C1_ENST00000231509.3_Nonsense_Mutation_p.K519*|NR3C1_ENST00000504336.1_5'UTR|NR3C1_ENST00000394466.2_Nonsense_Mutation_p.K519*|NR3C1_ENST00000394464.2_Nonsense_Mutation_p.K518*|NR3C1_ENST00000424646.2_Nonsense_Mutation_p.K492*|NR3C1_ENST00000503201.1_Nonsense_Mutation_p.K518*	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	518	Hinge.|Interaction with CLOCK.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	ACTATTGTTTTGTTACCAGGA	0.408																																					p.K519X		Atlas-SNP	.											.	NR3C1	124	.	0			c.A1555T						.						173	158	163					5																	142680245		2203	4300	6503	SO:0001587	stop_gained	2908	exon5			TTGTTTTGTTACC	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.1552A>T	chr5.hg19:g.142680245T>A	ENSP00000343205:p.Lys518*	118.0	0.0		90.0	14.0	NM_001024094	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Nonsense_Mutation	SNP	ENST00000343796.2	hg19	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	T	42	9.207009	0.99099	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000416954;ENST00000503201	.	.	.	5.69	5.69	0.88448	.	0.235606	0.42420	D	0.000711	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	15.94	0.79747	0.0:0.0:0.0:1.0	.	.	.	.	X	518;518;518;492;519;519;519;121;518	.	ENSP00000231509:K519X	K	-	1	0	NR3C1	142660438	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	5.430000	0.66501	2.156000	0.67533	0.533000	0.62120	AAA	.	.		0.408	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			A	142680245	T	A	142680245	4	1	185	1	0	0	0	0	0	1	0	0	10639	1821	63	4	853	4	NR3C1	5	142680245	Nonsense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	2444117	142680245	38235015	44	27495										
HIST1H2BM	8342	hgsc.bcm.edu	37	chr6	27782903	27782903	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aggctcagaagaaggatggaAagaagcgcaaacgcagccgc	14	9	1	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr6:27782903A>T	ENST00000359465.4	+	1	82	c.82A>T	c.(82-84)Aag>Tag	p.K28*	HIST1H2AJ_ENST00000333151.3_5'Flank	NM_003521.2	NP_003512.1	Q99879	H2B1M_HUMAN	histone cluster 1, H2bm	28					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	12						GAAGGATGGAAAGAAGCGCAA	0.498																																					p.K28X		Atlas-SNP	.											.	HIST1H2BM	36	.	0			c.A82T						.						150	145	147					6																	27782903		2203	4300	6503	SO:0001587	stop_gained	8342	exon1			GATGGAAAGAAGC	Z83738	CCDS4629.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196374	ENSG00000273703		"Histones / Replication-dependent"	4750	protein-coding gene	gene with protein product		602802	"H2B histone family, member E", "histone 1, H2bm"	H2BFE		9439656, 12408966	Standard	NM_003521		Approved	H2B/e, dJ160A22.3	uc003njo.3	Q99879	OTTHUMG00000014489	ENST00000359465.4:c.82A>T	chr6.hg19:g.27782903A>T	ENSP00000352442:p.Lys28*	111.0	0.0		88.0	37.0	NM_003521	Q6NWQ3	Nonsense_Mutation	SNP	ENST00000359465.4	hg19	CCDS4629.1	.	.	.	.	.	.	.	.	.	.	.	12.21	1.870568	0.33069	.	.	ENSG00000196374	ENST00000359465	.	.	.	3.73	3.73	0.42828	.	0.000000	0.64402	U	0.000012	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.6095	0.56544	1.0:0.0:0.0:0.0	.	.	.	.	X	28	.	ENSP00000352442:K28X	K	+	1	0	HIST1H2BM	27890882	0.974000	0.33945	0.999000	0.59377	0.015000	0.08874	2.243000	0.43115	1.914000	0.55421	0.460000	0.39030	AAG	.	.		0.498	HIST1H2BM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040157.1	NM_003521		T	27782903	A	T	27782903	4	4	185	1	0	0	0	0	0	1	0	0	7161	15	1	4	84	4	HIST1H2BM	6	27782903	Nonsense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10		27782903	143332164	45	27496										
DAAM2	23500	hgsc.bcm.edu	37	chr6	39867896	39867896	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ggtacgggagcccagtgacaAgtttgtccctgtcatgagcg	14	10	1	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr6:39867896A>C	ENST00000398904.2	+	23	2905	c.2723A>C	c.(2722-2724)aAg>aCg	p.K908T	DAAM2_ENST00000538976.1_Missense_Mutation_p.K907T|RP11-61I13.3_ENST00000437947.1_RNA|RP11-61I13.3_ENST00000420293.1_RNA|DAAM2_ENST00000274867.4_Missense_Mutation_p.K908T|RP11-61I13.3_ENST00000606829.1_RNA|RP11-61I13.3_ENST00000430595.1_RNA			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	908	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					CCCAGTGACAAGTTTGTCCCT	0.582																																					p.K908T		Atlas-SNP	.											.	DAAM2	101	.	0			c.A2723C						.						41	44	43					6																	39867896		2030	4170	6200	SO:0001583	missense	23500	exon23			GTGACAAGTTTGT	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.2723A>C	chr6.hg19:g.39867896A>C	ENSP00000381876:p.Lys908Thr	55.0	0.0		48.0	11.0	NM_001201427	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	A	12.77	2.038921	0.35989	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.19532	2.14;2.14;2.14	5.13	1.37	0.22104	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.231645	0.43260	D	0.000590	T	0.17365	0.0417	M	0.82323	2.585	0.80722	D	1	B;B	0.33022	0.188;0.394	B;B	0.40101	0.165;0.319	T	0.02781	-1.1111	10	0.72032	D	0.01	.	8.6463	0.34007	0.6292:0.0:0.3708:0.0	.	907;908	G5EA45;Q86T65	.;DAAM2_HUMAN	T	908;908;907	ENSP00000274867:K908T;ENSP00000381876:K908T;ENSP00000437808:K907T	ENSP00000274867:K908T	K	+	2	0	DAAM2	39975874	1.000000	0.71417	0.999000	0.59377	0.418000	0.31294	1.965000	0.40471	0.092000	0.17331	0.459000	0.35465	AAG	.	.		0.582	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			C	39867896	A	C	39867896	3	2	185	1	0	0	0	0	1	0	0	0	4218	72	3	5	2806	5	DAAM2	6	39867896	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	12084993	39867896	131247171	46	27497										
GPR110	266977	hgsc.bcm.edu	37	chr6	46982578	46982578	+	Missense_Mutation	SNP	G	G	T													0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aaagacaatgtcattacactGggctggaaacaaaagaaaac							TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr6:46982578G>T	ENST00000371253.2	-	9	981	c.766C>A	c.(766-768)Cag>Aag	p.Q256K	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.Q59K	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	256	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						TCATTACACTGGGCTGGAAAC	0.403																																					p.Q256K		Atlas-SNP	.											.	GPR110	102	.	0			c.C766A						.						46	42	43					6																	46982578		2203	4300	6503	SO:0001583	missense	266977	exon9			TACACTGGGCTGG	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.766C>A	chr6.hg19:g.46982578G>T	ENSP00000360299:p.Gln256Lys	62.0	0.0		51.0	13.0	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	hg19	CCDS34471.1	.	.	.	.	.	.	.	.	.	.	G	8.932	0.963615	0.18583	.	.	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000283297	T;T	0.31510	1.49;1.5	6.16	3.29	0.37713	.	0.490231	0.18826	N	0.130111	T	0.09862	0.0242	M	0.65975	2.015	0.09310	N	1	B	0.26672	0.156	B	0.19666	0.026	T	0.35549	-0.9784	10	0.07175	T	0.84	0.4581	8.9053	0.35519	0.0:0.3827:0.4729:0.1443	.	256	Q5T601	GP110_HUMAN	K	256;256;59	ENSP00000360299:Q256K;ENSP00000283297:Q59K	ENSP00000283297:Q59K	Q	-	1	0	GPR110	47090537	0.769000	0.28531	0.664000	0.29753	0.086000	0.17979	0.749000	0.26320	0.886000	0.36113	0.650000	0.86243	CAG	.	.		0.403	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		T	46982578	G	T	46982578	3	4	185	1	0	0	0	0	1	0	0	0	6635	1357	47	3	1994	3	GPR110	6	46982578	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	7114682	46982578	124132489	47	27498	135	2								
GPR110	266977	hgsc.bcm.edu	37	chr6	46982580	46982580	+	Splice_Site	SNP	G	G	C													0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	agacaatgtcattacactggGctggaaacaaaagaaaacaa							TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr6:46982580G>C	ENST00000371253.2	-	9	979	c.764C>G	c.(763-765)gCc>gGc	p.A255G	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Splice_Site_p.A58G	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	255	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						ATTACACTGGGCTGGAAACAA	0.398																																					p.A255G		Atlas-SNP	.											.	GPR110	102	.	0			c.C764G						.						45	41	42					6																	46982580		2203	4300	6503	SO:0001630	splice_region_variant	266977	exon9			CACTGGGCTGGAA	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.764-1C>G	chr6.hg19:g.46982580G>C		63.0	0.0		49.0	14.0	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	hg19	CCDS34471.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.169183	0.38315	.	.	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000283297	T;T	0.35605	1.33;1.3	6.16	1.24	0.21308	.	0.322217	0.26753	N	0.022676	T	0.18841	0.0452	M	0.66939	2.045	0.24316	N	0.995066	P	0.50819	0.939	P	0.45998	0.5	T	0.19386	-1.0307	10	0.25106	T	0.35	.	8.606	0.33773	0.381:0.0:0.619:0.0	.	255	Q5T601	GP110_HUMAN	G	255;255;58	ENSP00000360299:A255G;ENSP00000283297:A58G	ENSP00000283297:A58G	A	-	2	0	GPR110	47090539	0.774000	0.28592	0.653000	0.29593	0.095000	0.18619	-0.021000	0.12504	-0.057000	0.13199	0.650000	0.86243	GCC	.	.		0.398	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	Missense_Mutation	C	46982580	G	C	46982580	5	2	185	1	0	0	0	0	0	0	1	0	6635	1217	42	4	1996	4	GPR110	6	46982580	Splice_Site	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	2	46982580	124132487	48	27499	135	2								
TMEM196	256130	hgsc.bcm.edu	37	chr7	19812310	19812310	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gctcccaataatctgaccgcTggtgcacatccttcctcggt	8	15	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:19812310T>C	ENST00000405764.3	-	1	706	c.10A>G	c.(10-12)Agc>Ggc	p.S4G	TMEM196_ENST00000433641.1_Intron|TMEM196_ENST00000405844.1_Missense_Mutation_p.S4G|TMEM196_ENST00000422233.1_Intron|TMEM196_ENST00000493519.1_Intron	NM_152774.3	NP_689987.3	Q5HYL7	TM196_HUMAN	transmembrane protein 196	4						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(4)	6						ATCTGACCGCTGGTGCACATC	0.577																																					p.S4G		Atlas-SNP	.											.	TMEM196	34	.	0			c.A10G						.						47	55	53					7																	19812310		692	1591	2283	SO:0001583	missense	256130	exon1			GACCGCTGGTGCA		CCDS34607.2	7p15.3	2007-11-21			ENSG00000173452	ENSG00000173452			22431	protein-coding gene	gene with protein product							Standard	NM_152774		Approved	MGC42090	uc011jyg.2	Q5HYL7	OTTHUMG00000152504	ENST00000405764.3:c.10A>G	chr7.hg19:g.19812310T>C	ENSP00000384234:p.Ser4Gly	69.0	0.0		61.0	22.0	NM_152774	Q8N6I6	Missense_Mutation	SNP	ENST00000405764.3	hg19	CCDS34607.2	.	.	.	.	.	.	.	.	.	.	T	28.2	4.897781	0.91962	.	.	ENSG00000173452	ENST00000405844;ENST00000405764	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	T	0.62889	0.2465	N	0.19112	0.55	0.80722	D	1	P	0.52577	0.954	D	0.63597	0.916	T	0.66701	-0.5857	8	0.59425	D	0.04	0.0072	16.5582	0.84512	0.0:0.0:0.0:1.0	.	4	Q5HYL7-4	.	G	4	.	ENSP00000384234:S4G	S	-	1	0	TMEM196	19778835	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.594000	0.82698	2.308000	0.77769	0.533000	0.62120	AGC	.	.		0.577	TMEM196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326499.1	NM_152774		C	19812310	T	C	19812310	3	2	185	1	0	0	0	0	1	0	0	0	16133	1580	55	2	524	2	TMEM196	7	19812310	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10		19812310	139326353	49	27500										
C7orf16	10842	hgsc.bcm.edu	37	chr7	31735086	31735086	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tatcctgtcaaaattagatgAtctttcagaccagttcatta	5	8	4	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:31735086A>G	ENST00000342032.3	+	3	714	c.86A>G	c.(85-87)gAt>gGt	p.D29G	PPP1R17_ENST00000409146.3_Intron	NM_006658.4	NP_006649.2	O96001	PPR17_HUMAN	protein phosphatase 1, regulatory subunit 17	29					central nervous system development (GO:0007417)|intracellular signal transduction (GO:0035556)|regulation of phosphatase activity (GO:0010921)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)										AAATTAGATGATCTTTCAGAC	0.363																																					p.D29G		Atlas-SNP	.											.	.	.	.	0			c.A86G						.						69	70	70					7																	31735086		2203	4300	6503	SO:0001583	missense	10842	exon3			TAGATGATCTTTC	AF071789	CCDS5436.1, CCDS47570.1	7p15	2012-04-17	2011-10-11	2011-10-11	ENSG00000106341	ENSG00000106341		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16973	protein-coding gene	gene with protein product	"G-substrate"	604088	"chromosome 7 open reading frame 16"	C7orf16		10051666, 9920894	Standard	NM_006658		Approved	GSBS	uc003tcl.3	O96001	OTTHUMG00000128629	ENST00000342032.3:c.86A>G	chr7.hg19:g.31735086A>G	ENSP00000340125:p.Asp29Gly	54.0	0.0		77.0	22.0	NM_006658	B4DE58|Q9UDQ0	Missense_Mutation	SNP	ENST00000342032.3	hg19	CCDS5436.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.300939	0.81136	.	.	ENSG00000106341	ENST00000342032	T	0.38240	1.15	5.45	5.45	0.79879	.	0.273612	0.36740	N	0.002432	T	0.46964	0.1420	L	0.60455	1.87	0.80722	D	1	P	0.37330	0.59	P	0.46172	0.506	T	0.47699	-0.9097	10	0.62326	D	0.03	-10.7605	15.4777	0.75497	1.0:0.0:0.0:0.0	.	29	O96001	PPR17_HUMAN	G	29	ENSP00000340125:D29G	ENSP00000340125:D29G	D	+	2	0	C7orf16	31701611	1.000000	0.71417	0.992000	0.48379	0.986000	0.74619	4.687000	0.61708	2.195000	0.70347	0.533000	0.62120	GAT	.	.		0.363	PPP1R17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250498.1	NM_006658		G	31735086	A	G	31735086	3	3	185	1	0	0	0	0	1	0	0	0	2380	333	12	2	92	2	C7orf16	7	31735086	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	11922776	31735086	127403577	50	27501										
CDK13	8621	hgsc.bcm.edu	37	chr7	40102432	40102432	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctgtgttttttagtcggccgTatactaacaaggtaattact	8	7	0	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:40102432T>A	ENST00000181839.4	+	8	3213	c.2608T>A	c.(2608-2610)Tat>Aat	p.Y870N	CDK13_ENST00000484589.1_3'UTR|CDK13_ENST00000340829.5_Missense_Mutation_p.Y870N	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	870	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						TAGTCGGCCGTATACTAACAA	0.388																																					p.Y870N		Atlas-SNP	.											.	CDK13	114	.	0			c.T2608A						.						291	309	303					7																	40102432		2203	4300	6503	SO:0001583	missense	8621	exon8			CGGCCGTATACTA	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.2608T>A	chr7.hg19:g.40102432T>A	ENSP00000181839:p.Tyr870Asn	95.0	0.0		48.0	6.0	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Missense_Mutation	SNP	ENST00000181839.4	hg19	CCDS5461.1	.	.	.	.	.	.	.	.	.	.	.	18.49	3.634836	0.67130	.	.	ENSG00000065883	ENST00000181839;ENST00000340829	T;T	0.45276	0.9;0.9	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.59783	0.2219	L	0.55017	1.72	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.989	T	0.58115	-0.7693	8	.	.	.	-8.5737	15.6901	0.77442	0.0:0.0:0.0:1.0	.	256;870;870	Q9BVE2;Q14004-2;Q14004	.;.;CDK13_HUMAN	N	870	ENSP00000181839:Y870N;ENSP00000340557:Y870N	.	Y	+	1	0	CDK13	40068957	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.252000	0.72447	2.172000	0.68678	0.460000	0.39030	TAT	.	.		0.388	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		A	40102432	T	A	40102432	3	1	185	1	0	0	0	0	1	0	0	0	3131	1638	57	4	2638	4	CDK13	7	40102432	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	8367346	40102432	119036231	51	27502										
C7orf44	55744	hgsc.bcm.edu	37	chr7	43684913	43684913	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ttgagataatggatgttgagAggagggcccagagcttcctg	15	6	0	3	rs564919110		TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:43684913A>G	ENST00000395879.1	-	3	1882	c.201T>C	c.(199-201)ccT>ccC	p.P67P	COA1_ENST00000223336.6_Silent_p.P67P|COA1_ENST00000395880.3_Silent_p.P67P|COA1_ENST00000310564.6_Silent_p.P67P			Q9GZY4	COA1_HUMAN	cytochrome c oxidase assembly factor 1 homolog (S. cerevisiae)	67					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex IV assembly (GO:0033617)	cytoplasm (GO:0005737)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrion (GO:0005739)											GGATGTTGAGAGGAGGGCCCA	0.517													A|||	1	0.000199681	0	0	5008	,	,		15099	0		0	False		,,,				2504	0.001				p.P67P		Atlas-SNP	.											.	.	.	.	0			c.T201C						.						98	77	84					7																	43684913		2203	4300	6503	SO:0001819	synonymous_variant	55744	exon4			GTTGAGAGGAGGG	AK001665	CCDS5471.1	7p13	2012-12-05	2012-10-15	2012-06-25	ENSG00000106603	ENSG00000106603		"Mitochondrial respiratory chain complex assembly factors"	21868	protein-coding gene	gene with protein product		614769	"chromosome 7 open reading frame 44"	C7orf44		22356826	Standard	NM_018224		Approved	FLJ10803, MITRAC15	uc003tin.2	Q9GZY4	OTTHUMG00000128949	ENST00000395879.1:c.201T>C	chr7.hg19:g.43684913A>G		78.0	0.0		76.0	26.0	NM_018224	A6NJU8|A8KAH8|Q9HAB7|Q9NVD2	Silent	SNP	ENST00000395879.1	hg19	CCDS5471.1																																																																																			.	.		0.517	COA1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313664.1	NM_018224		G	43684913	A	G	43684913	2	3	185	1	0	0	0	0	0	0	0	1	2396	291	11	2		2	C7orf44	7	43684913	Silent	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	3582481	43684913	115453750	52	27503										
TNS3	64759	hgsc.bcm.edu	37	chr7	47476876	47476876	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tgtacctttgggttaagcttCgtaaggtcatatctcttttc	8	8	2	0	rs376868413		TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:47476876C>T	ENST00000398879.1	-	7	552	c.186G>A	c.(184-186)acG>acA	p.T62T	TNS3_ENST00000355730.3_Silent_p.T62T|TNS3_ENST00000311160.9_Silent_p.T62T|TNS3_ENST00000442536.2_Silent_p.T62T|TNS3_ENST00000458317.2_Silent_p.T62T			Q68CZ2	TENS3_HUMAN	tensin 3	62	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						GGTTAAGCTTCGTAAGGTCAT	0.269																																					p.T62T		Atlas-SNP	.											.	TNS3	140	.	0			c.G186A						.	C		1,3603		0,1,1801	68	68	68		186	-8.9	0.1	7		68	0,8130		0,0,4065	no	coding-synonymous	TNS3	NM_022748.11		0,1,5866	TT,TC,CC		0.0,0.0277,0.0085		62/1446	47476876	1,11733	1802	4065	5867	SO:0001819	synonymous_variant	64759	exon7			AAGCTTCGTAAGG	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.186G>A	chr7.hg19:g.47476876C>T		229.0	0.0		203.0	68.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Silent	SNP	ENST00000398879.1	hg19	CCDS5506.2																																																																																			.	.		0.269	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		T	47476876	C	T	47476876	2	4	185	1	0	0	0	0	0	0	0	1	16359	871	31	1		1	TNS3	7	47476876	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	3791963	47476876	111661787	53	27504										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48327638	48327638	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aaggcatctcattttatctgCtatacaaggggtcactttgg	9	8	3	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:48327638C>T	ENST00000435803.1	+	20	8942	c.8918C>T	c.(8917-8919)gCt>gTt	p.A2973V		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2973					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATTTTATCTGCTATACAAGGG	0.443																																					p.A2973V		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C8918T						.						175	170	172					7																	48327638		1861	4109	5970	SO:0001583	missense	154664	exon20			TATCTGCTATACA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.8918C>T	chr7.hg19:g.48327638C>T	ENSP00000411096:p.Ala2973Val	62.0	0.0		67.0	12.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	9.528	1.110158	0.20714	.	.	ENSG00000179869	ENST00000435803	D	0.86164	-2.08	5.63	2.54	0.30619	.	0.351640	0.20494	N	0.091221	T	0.72053	0.3413	N	0.11201	0.11	0.09310	N	1	B;B	0.17852	0.004;0.024	B;B	0.15052	0.006;0.012	T	0.62613	-0.6817	10	0.87932	D	0	.	5.2919	0.15731	0.0:0.4:0.0:0.6	.	675;2973	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	V	2973	ENSP00000411096:A2973V	ENSP00000411096:A2973V	A	+	2	0	ABCA13	48298184	0.000000	0.05858	0.003000	0.11579	0.528000	0.34623	0.059000	0.14322	0.266000	0.21894	0.591000	0.81541	GCT	.	.		0.443	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48327638	C	T	48327638	3	4	185	1	0	0	0	0	1	0	0	0	31	797	28	3	8825	3	ABCA13	7	48327638	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	850762	48327638	110811025	54	27505										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81591327	81591327	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gggaggccgtgaagtcatcaTcctccatctcaacttgggtg	12	11	3	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:81591327T>C	ENST00000356253.5	-	36	3140	c.2885A>G	c.(2884-2886)gAt>gGt	p.D962G	CACNA2D1_ENST00000356860.3_Missense_Mutation_p.D950G|CACNA2D1_ENST00000535308.1_Missense_Mutation_p.D162G			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	962					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GAAGTCATCATCCTCCATCTC	0.483																																					p.D950G		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A2849G						.						114	107	109					7																	81591327		2203	4300	6503	SO:0001583	missense	781	exon36			TCATCATCCTCCA	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2885A>G	chr7.hg19:g.81591327T>C	ENSP00000348589:p.Asp962Gly	79.0	0.0		55.0	13.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	hg19		.	.	.	.	.	.	.	.	.	.	T	13.98	2.398645	0.42512	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000535308	T;T;T	0.69306	-0.39;-0.39;-0.39	5.19	5.19	0.71726	.	0.308729	0.38778	N	0.001563	T	0.77598	0.4154	M	0.73962	2.25	0.47511	D	0.999444	D;B	0.52996	0.957;0.001	P;B	0.58577	0.841;0.012	T	0.76061	-0.3097	10	0.27082	T	0.32	-9.0925	15.3769	0.74615	0.0:0.0:0.0:1.0	.	162;950	B7Z658;P54289-2	.;.	G	950;969;962;162	ENSP00000349320:D950G;ENSP00000348589:D962G;ENSP00000443124:D162G	ENSP00000284088:D969G	D	-	2	0	CACNA2D1	81429263	1.000000	0.71417	0.438000	0.26821	0.924000	0.55760	5.186000	0.65082	2.093000	0.63338	0.529000	0.55759	GAT	.	.		0.483	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				C	81591327	T	C	81591327	3	2	185	1	0	0	0	0	1	0	0	0	2550	1435	50	2	442	2	CACNA2D1	7	81591327	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	33263689	81591327	77547336	55	27506										
PCLO	27445	hgsc.bcm.edu	37	chr7	82585807	82585807	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tttatggtccttgctggaagGaatatcttgttggctatctt	10	6	2	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:82585807G>A	ENST00000333891.9	-	5	4799	c.4462C>T	c.(4462-4464)Cct>Tct	p.P1488S	PCLO_ENST00000423517.2_Missense_Mutation_p.P1488S	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTGCTGGAAGGAATATCTTGT	0.348																																					p.P1488S		Atlas-SNP	.											.	PCLO	1506	.	0			c.C4462T						.						112	103	106					7																	82585807		1845	4086	5931	SO:0001583	missense	27445	exon5			TGGAAGGAATATC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.4462C>T	chr7.hg19:g.82585807G>A	ENSP00000334319:p.Pro1488Ser	50.0	0.0		49.0	14.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	0.373	-0.933117	0.02359	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.14893	2.47;2.48	5.43	3.64	0.41730	.	.	.	.	.	T	0.15912	0.0383	L	0.42245	1.32	0.09310	N	0.999999	B;B	0.16802	0.008;0.019	B;B	0.10450	0.003;0.005	T	0.19582	-1.0301	9	0.87932	D	0	.	8.8127	0.34976	0.2549:0.0:0.7451:0.0	.	1488;1488	Q9Y6V0-5;Q9Y6V0-6	.;.	S	1419;1488;1488	ENSP00000334319:P1488S;ENSP00000388393:P1488S	ENSP00000334319:P1488S	P	-	1	0	PCLO	82423743	0.980000	0.34600	0.064000	0.19789	0.087000	0.18053	1.903000	0.39858	0.691000	0.31592	-0.141000	0.14075	CCT	.	.		0.348	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82585807	G	A	82585807	3	1	185	1	0	0	0	0	1	0	0	0	11592	1174	41	3	11067	3	PCLO	7	82585807	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	994480	82585807	76552856	56	27507										
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106509974	106509974	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	agcttggaggacgatgatgtTctgcattaccttctacaatt	9	8	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:106509974T>C	ENST00000359195.3	+	2	2278	c.1968T>C	c.(1966-1968)gtT>gtC	p.V656V	PIK3CG_ENST00000440650.2_Silent_p.V656V|PIK3CG_ENST00000496166.1_Silent_p.V656V	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	656	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						acgatgatgttctgcattacc	0.438																																					p.V656V		Atlas-SNP	.											.	PIK3CG	279	.	0			c.T1968C						.						23	21	22					7																	106509974		2202	4296	6498	SO:0001819	synonymous_variant	5294	exon2			TGATGTTCTGCAT		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.1968T>C	chr7.hg19:g.106509974T>C		86.0	0.0		77.0	19.0	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Silent	SNP	ENST00000359195.3	hg19	CCDS5739.1																																																																																			.	.		0.438	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			C	106509974	T	C	106509974	2	2	185	1	0	0	0	0	0	0	0	1	11925	1770	62	2		2	PIK3CG	7	106509974	Silent	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	23924167	106509974	52628689	57	27508										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121651010	121651010	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ttccgaagattcaacttcatCaggttcagaagaatcactaa	6	9	5	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:121651010C>A	ENST00000393386.2	+	12	2321	c.1910C>A	c.(1909-1911)tCa>tAa	p.S637*	PTPRZ1_ENST00000449182.1_Nonsense_Mutation_p.S637*	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	637					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TCAACTTCATCAGGTTCAGAA	0.423																																					p.S637X		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.C1910A						.						59	57	58					7																	121651010		2203	4300	6503	SO:0001587	stop_gained	5803	exon12			CTTCATCAGGTTC	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.1910C>A	chr7.hg19:g.121651010C>A	ENSP00000377047:p.Ser637*	129.0	0.0		102.0	34.0	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Nonsense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	38	6.968175	0.97971	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	.	.	.	5.87	5.87	0.94306	.	0.445946	0.21442	N	0.074476	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4091	0.60931	0.0:0.9283:0.0:0.0717	.	.	.	.	X	637	.	ENSP00000377047:S637X	S	+	2	0	PTPRZ1	121438246	0.897000	0.30589	0.925000	0.36789	0.816000	0.46133	3.118000	0.50414	2.778000	0.95560	0.655000	0.94253	TCA	.	.		0.423	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121651010	C	A	121651010	4	1	185	1	0	0	0	0	0	1	0	0	12829	838	29	3	1956	3	PTPRZ1	7	121651010	Nonsense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	15141036	121651010	37487653	58	27509										
MGAM	8972	hgsc.bcm.edu	37	chr7	141762461	141762461	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aagaactatacaacaatccaCagaatccagagaggagcttg	8	9	0	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr7:141762461C>T	ENST00000549489.2	+	35	4311	c.4216C>T	c.(4216-4218)Cag>Tag	p.Q1406*	MGAM_ENST00000475668.2_Nonsense_Mutation_p.Q1406*	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1406	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CAACAATCCACAGAATCCAGA	0.428																																					p.Q1406X		Atlas-SNP	.											.	MGAM	767	.	0			c.C4216T						.						73	66	68					7																	141762461		1852	4079	5931	SO:0001587	stop_gained	8972	exon35			AATCCACAGAATC	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4216C>T	chr7.hg19:g.141762461C>T	ENSP00000447378:p.Gln1406*	312.0	0.0		285.0	77.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Nonsense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	C	40	8.484316	0.98832	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	.	.	.	4.04	-0.7	0.11273	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	7.9582	0.30055	0.2777:0.3081:0.4142:0.0	.	.	.	.	X	1406;1406;1283	.	ENSP00000316431:Q1283X	Q	+	1	0	MGAM	141408930	0.000000	0.05858	0.005000	0.12908	0.746000	0.42486	-1.044000	0.03532	-0.143000	0.11334	0.306000	0.20318	CAG	.	.		0.428	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141762461	C	T	141762461	4	4	185	1	0	0	0	0	0	1	0	0	9550	479	17	3	4350	3	MGAM	7	141762461	Nonsense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	20111451	141762461	17376202	59	27510										
CALB1	793	hgsc.bcm.edu	37	chr8	91094273	91094273	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ccaatccagccttctttcgcGcctgctggagctcctggatc	9	16	1	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr8:91094273G>T	ENST00000265431.3	-	2	318	c.137C>A	c.(136-138)gCg>gAg	p.A46E	CALB1_ENST00000518457.1_5'Flank	NM_004929.2	NP_004920.1	P05937	CALB1_HUMAN	calbindin 1, 28kDa	46	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to organic substance (GO:0071310)|cytosolic calcium ion homeostasis (GO:0051480)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|metanephric collecting duct development (GO:0072205)|metanephric connecting tubule development (GO:0072286)|metanephric distal convoluted tubule development (GO:0072221)|metanephric part of ureteric bud development (GO:0035502)|regulation of synaptic plasticity (GO:0048167)|retina layer formation (GO:0010842)|short-term memory (GO:0007614)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|vitamin D binding (GO:0005499)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(8)|pancreas(1)	11			BRCA - Breast invasive adenocarcinoma(11;0.00953)			CTTCTTTCGCGCCTGCTGGAG	0.443																																					p.A46E	Melanoma(46;573 1182 27367 39727 48386)	Atlas-SNP	.											.	CALB1	25	.	0			c.C137A						.						114	121	118					8																	91094273		2203	4300	6503	SO:0001583	missense	793	exon2			TTTCGCGCCTGCT		CCDS6251.1	8q21.3	2013-01-10	2002-08-29		ENSG00000104327	ENSG00000104327		"EF-hand domain containing"	1434	protein-coding gene	gene with protein product		114050		CALB			Standard	NM_004929		Approved		uc003yel.1	P05937	OTTHUMG00000134314	ENST00000265431.3:c.137C>A	chr8.hg19:g.91094273G>T	ENSP00000265431:p.Ala46Glu	60.0	0.0		53.0	28.0	NM_004929	B2R696|B7Z9J4	Missense_Mutation	SNP	ENST00000265431.3	hg19	CCDS6251.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.916510	0.73098	.	.	ENSG00000104327	ENST00000265431	D	0.90261	-2.64	5.48	5.48	0.80851	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.91205	0.7229	M	0.62723	1.935	0.80722	D	1	P	0.38370	0.628	P	0.49085	0.6	D	0.87147	0.2206	10	0.06099	T	0.92	-11.4282	16.6292	0.85029	0.0:0.0:1.0:0.0	.	46	P05937	CALB1_HUMAN	E	46	ENSP00000265431:A46E	ENSP00000265431:A46E	A	-	2	0	CALB1	91163449	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.344000	0.72991	2.744000	0.94065	0.563000	0.77884	GCG	.	.		0.443	CALB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259338.2	NM_004929		T	91094273	G	T	91094273	3	4	185	1	0	0	0	0	1	0	0	0	2575	1087	38	1	688	1	CALB1	8	91094273	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10		91094273	55269749	60	27511										
TSNARE1	203062	hgsc.bcm.edu	37	chr8	143427217	143427217	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctggcgacgggcaggggaaaTggcggattccatactcggtc	16	10	0	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr8:143427217T>C	ENST00000307180.3	-	3	242	c.125A>G	c.(124-126)cAt>cGt	p.H42R	TSNARE1_ENST00000520166.1_Missense_Mutation_p.H42R|TSNARE1_ENST00000524325.1_Missense_Mutation_p.H42R|TSNARE1_ENST00000519651.1_Intron	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	42					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GCAGGGGAAATGGCGGATTCC	0.617																																					p.H42R		Atlas-SNP	.											.	TSNARE1	59	.	0			c.A125G						.						138	110	119					8																	143427217		2203	4300	6503	SO:0001583	missense	203062	exon3			GGGAAATGGCGGA			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.125A>G	chr8.hg19:g.143427217T>C	ENSP00000303437:p.His42Arg	42.0	0.0		46.0	27.0	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.977061	0.53720	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000520462;ENST00000518720	T;T;T;T;T	0.30981	2.45;2.44;2.45;1.58;1.51	2.62	1.42	0.22433	.	0.725519	0.10837	U	0.628625	T	0.27384	0.0672	L	0.29908	0.895	0.21473	N	0.999678	D;D;D	0.53885	0.963;0.963;0.963	P;P;P	0.49421	0.61;0.61;0.61	T	0.12967	-1.0527	10	0.87932	D	0	-2.6256	5.6733	0.17735	0.0:0.0:0.2832:0.7168	.	42;42;42	B7ZLB0;Q96NA8;A0AVG3	.;TSNA1_HUMAN;.	R	42;42;42;42;58	ENSP00000428763:H42R;ENSP00000303437:H42R;ENSP00000427770:H42R;ENSP00000429626:H42R;ENSP00000430789:H58R	ENSP00000303437:H42R	H	-	2	0	TSNARE1	143425124	0.967000	0.33354	0.897000	0.35233	0.995000	0.86356	0.452000	0.21795	0.401000	0.25424	0.528000	0.53228	CAT	.	.		0.617	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003		C	143427217	T	C	143427217	3	2	185	1	0	0	0	0	1	0	0	0	16645	1464	51	2	1460	2	TSNARE1	8	143427217	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	52332944	143427217	2936805	61	27512										
PLEC	5339	hgsc.bcm.edu	37	chr8	144993679	144993679	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tgctgcccgagtaggggtctCtgtagccggtgacggccttc	15	12	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr8:144993679C>T	ENST00000322810.4	-	32	10890	c.10721G>A	c.(10720-10722)aGa>aAa	p.R3574K	PLEC_ENST00000345136.3_Missense_Mutation_p.R3437K|PLEC_ENST00000356346.3_Missense_Mutation_p.R3423K|PLEC_ENST00000527096.1_Missense_Mutation_p.R3460K|PLEC_ENST00000398774.2_Missense_Mutation_p.R3405K|PLEC_ENST00000436759.2_Missense_Mutation_p.R3464K|PLEC_ENST00000354589.3_Missense_Mutation_p.R3437K|PLEC_ENST00000354958.2_Missense_Mutation_p.R3415K|PLEC_ENST00000357649.2_Missense_Mutation_p.R3441K	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3574	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GTAGGGGTCTCTGTAGCCGGT	0.672																																					p.R3574K		Atlas-SNP	.											.	PLEC	1144	.	0			c.G10721A						.						38	45	43					8																	144993679		1984	4156	6140	SO:0001583	missense	5339	exon32			GGGTCTCTGTAGC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.10721G>A	chr8.hg19:g.144993679C>T	ENSP00000323856:p.Arg3574Lys	41.0	0.0		63.0	11.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	5.519	0.280777	0.10458	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;-0.19;-0.19;-0.19;-0.19	5.03	-4.09	0.03951	.	0.171407	0.35495	N	0.003174	T	0.18467	0.0443	N	0.00633	-1.31	0.22240	N	0.999269	B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.39542	-0.9609	10	0.02654	T	1	.	7.8396	0.29391	0.0:0.1366:0.4754:0.388	.	3464;3423;3415;3574;3405;3437;3441;3437	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	K	3437;3441;3437;3405;3574;3415;3423;3464;3460	ENSP00000344848:R3437K;ENSP00000350277:R3441K;ENSP00000346602:R3437K;ENSP00000381756:R3405K;ENSP00000323856:R3574K;ENSP00000347044:R3415K;ENSP00000348702:R3423K;ENSP00000388180:R3464K;ENSP00000434583:R3460K	ENSP00000323856:R3574K	R	-	2	0	PLEC	145065667	0.310000	0.24527	0.141000	0.22245	0.016000	0.09150	0.493000	0.22451	-0.925000	0.03775	-0.404000	0.06349	AGA	.	.		0.672	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144993679	C	T	144993679	3	4	185	1	0	0	0	0	1	0	0	0	12061	913	32	3	3337	3	PLEC	8	144993679	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	1566462	144993679	1370343	62	27513										
CPSF1	29894	hgsc.bcm.edu	37	chr8	145619689	145619689	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	caggatgaagttcttgacgcTgatcatctggtgtatgtaga	12	6	3	4			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr8:145619689T>C	ENST00000349769.3	-	32	3743	c.3649A>G	c.(3649-3651)Agc>Ggc	p.S1217G	CPSF1_ENST00000531727.1_5'Flank|MIR939_ENST00000401314.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	1217					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			TTCTTGACGCTGATCATCTGG	0.602																																					p.S1217G	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.A3649G						.						31	26	28					8																	145619689		2199	4299	6498	SO:0001583	missense	29894	exon32			TGACGCTGATCAT	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.3649A>G	chr8.hg19:g.145619689T>C	ENSP00000339353:p.Ser1217Gly	93.0	0.0		139.0	70.0	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	hg19	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.381571	0.61845	.	.	ENSG00000071894	ENST00000349769	T	0.49139	0.79	4.57	4.57	0.56435	Cleavage/polyadenylation specificity factor, A subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.50820	0.1638	L	0.58969	1.84	0.80722	D	1	P	0.40660	0.726	P	0.46510	0.519	T	0.49688	-0.8913	9	.	.	.	-44.2082	12.1733	0.54172	0.0:0.0:0.0:1.0	.	1217	Q10570	CPSF1_HUMAN	G	1217	ENSP00000339353:S1217G	.	S	-	1	0	CPSF1	145590497	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.809000	0.62591	1.843000	0.53566	0.459000	0.35465	AGC	.	.		0.602	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		C	145619689	T	C	145619689	3	2	185	1	0	0	0	0	1	0	0	0	3826	1580	55	2	710	2	CPSF1	8	145619689	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	626010	145619689	744333	63	27514										
TEK	7010	hgsc.bcm.edu	37	chr9	27157869	27157869	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gacttgatcttgatcaattcCctacctcttgtatctgatgc	6	11	4	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr9:27157869C>T	ENST00000380036.4	+	2	535	c.93C>T	c.(91-93)tcC>tcT	p.S31S	TEK_ENST00000519097.1_Intron|TEK_ENST00000406359.4_Silent_p.S31S	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	31					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	TGATCAATTCCCTACCTCTTG	0.458																																					p.S31S		Atlas-SNP	.											.	TEK	250	.	0			c.C93T						.						208	176	187					9																	27157869		2203	4300	6503	SO:0001819	synonymous_variant	7010	exon2			CAATTCCCTACCT	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.93C>T	chr9.hg19:g.27157869C>T		96.0	0.0		92.0	30.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	hg19	CCDS6519.1																																																																																			.	.		0.458	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			T	27157869	C	T	27157869	2	4	185	1	0	0	0	0	0	0	0	1	15766	610	22	3		3	TEK	9	27157869	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10		27157869	114055562	64	27515										
C9orf131	138724	hgsc.bcm.edu	37	chr9	35045263	35045263	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cagccacaggagtctggcagGgcggaacaagggtctcagag	16	10	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr9:35045263G>A	ENST00000312292.5	+	2	2684	c.2637G>A	c.(2635-2637)agG>agA	p.R879R	FLJ00273_ENST00000595331.1_5'Flank|C9orf131_ENST00000421362.2_Silent_p.R831R|C9orf131_ENST00000354479.5_Silent_p.R806R	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	879										cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			AGTCTGGCAGGGCGGAACAAG	0.562																																					p.R879R		Atlas-SNP	.											.	C9orf131	71	.	0			c.G2637A						.						202	212	209					9																	35045263		2203	4300	6503	SO:0001819	synonymous_variant	138724	exon2			TGGCAGGGCGGAA	BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.2637G>A	chr9.hg19:g.35045263G>A		67.0	0.0		67.0	14.0	NM_203299	A6NLE6|E9PB26|Q86XC6|Q9UF74	Silent	SNP	ENST00000312292.5	hg19	CCDS6572.2																																																																																			.	.		0.562	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299		A	35045263	G	A	35045263	2	1	185	1	0	0	0	0	0	0	0	1	2459	1223	43	3		3	C9orf131	9	35045263	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	7887394	35045263	106168168	65	27516										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113192616	113192616	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aacatgtgattttggttactCccatcaactggtatccttcc	6	11	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr9:113192616C>T	ENST00000401783.2	-	33	5804	c.5468G>A	c.(5467-5469)gGa>gAa	p.G1823E	SVEP1_ENST00000297826.5_5'Flank|SVEP1_ENST00000374469.1_Missense_Mutation_p.G1800E	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1823	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TTTGGTTACTCCCATCAACTG	0.408																																					p.G1823E		Atlas-SNP	.											.	SVEP1	326	.	0			c.G5468A						.						91	82	84					9																	113192616		1880	4113	5993	SO:0001583	missense	79987	exon33			GTTACTCCCATCA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.5468G>A	chr9.hg19:g.113192616C>T	ENSP00000384917:p.Gly1823Glu	86.0	0.0		92.0	23.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	19.75	3.884774	0.72410	.	.	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.72167	-0.63;-0.63	5.27	5.27	0.74061	Complement control module (2);Sushi/SCR/CCP (3);	0.048538	0.85682	D	0.000000	D	0.84719	0.5534	H	0.98068	4.14	0.80722	D	1	P	0.42357	0.777	B	0.42738	0.396	D	0.90065	0.4159	10	0.72032	D	0.01	.	19.0978	0.93260	0.0:1.0:0.0:0.0	.	1823	Q4LDE5	SVEP1_HUMAN	E	1823;1800	ENSP00000384917:G1823E;ENSP00000363593:G1800E	ENSP00000363593:G1800E	G	-	2	0	SVEP1	112232437	1.000000	0.71417	0.974000	0.42286	0.573000	0.36030	6.337000	0.72958	2.735000	0.93741	0.655000	0.94253	GGA	.	.		0.408	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113192616	C	T	113192616	3	4	185	1	0	0	0	0	1	0	0	0	15435	855	30	3	5311	3	SVEP1	9	113192616	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	78147353	113192616	28020815	66	27517										
PTGR1	22949	hgsc.bcm.edu	37	chr9	114325430	114325430	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cactattgtcttccccaaatTatctcctttcagcattccca	2	15	3	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr9:114325430T>C	ENST00000407693.2	-	10	1223	c.961A>G	c.(961-963)Aat>Gat	p.N321D	PTGR1_ENST00000309195.5_Missense_Mutation_p.N321D|PTGR1_ENST00000538962.1_Intron|ZNF483_ENST00000358151.4_Intron	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	321					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						TTCCCCAAATTATCTCCTTTC	0.353																																					p.N321D	Ovarian(200;132 2151 7551 19220 46064)	Atlas-SNP	.											.	PTGR1	23	.	0			c.A961G						.						161	141	148					9																	114325430		2202	4300	6502	SO:0001583	missense	22949	exon10			CCAAATTATCTCC	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.961A>G	chr9.hg19:g.114325430T>C	ENSP00000385763:p.Asn321Asp	40.0	0.0		33.0	9.0	NM_001146108	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Missense_Mutation	SNP	ENST00000407693.2	hg19	CCDS6779.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.306420	0.81247	.	.	ENSG00000106853	ENST00000309195;ENST00000407693	T;T	0.78707	-1.2;-1.2	5.01	5.01	0.66863	GroES-like (1);	0.000000	0.85682	D	0.000000	D	0.92522	0.7625	H	0.98849	4.35	0.80722	D	1	D	0.67145	0.996	D	0.69824	0.966	D	0.95122	0.8247	10	0.72032	D	0.01	-18.399	14.0142	0.64515	0.0:0.0:0.0:1.0	.	321	Q14914	PTGR1_HUMAN	D	321	ENSP00000311572:N321D;ENSP00000385763:N321D	ENSP00000311572:N321D	N	-	1	0	PTGR1	113365251	1.000000	0.71417	0.330000	0.25442	0.997000	0.91878	6.863000	0.75489	2.016000	0.59253	0.455000	0.32223	AAT	.	.		0.353	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			C	114325430	T	C	114325430	3	2	185	1	0	0	0	0	1	0	0	0	12766	1754	61	2	63	2	PTGR1	9	114325430	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	1132814	114325430	26888001	67	27518										
USP20	10868	hgsc.bcm.edu	37	chr9	132630495	132630495	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gggtgacgggcaggggcgtgGcgggggcagctcgcaggccg	24	10	0	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr9:132630495G>T	ENST00000315480.4	+	11	1060	c.902G>T	c.(901-903)gGc>gTc	p.G301V	USP20_ENST00000372429.3_Missense_Mutation_p.G301V|USP20_ENST00000358355.1_Missense_Mutation_p.G301V			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	301	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				CAGGGGCGTGGCGGGGGCAGC	0.642																																					p.G301V		Atlas-SNP	.											.	USP20	186	.	0			c.G902T						.						50	62	58					9																	132630495		2083	4203	6286	SO:0001583	missense	10868	exon11			GGCGTGGCGGGGG	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.902G>T	chr9.hg19:g.132630495G>T	ENSP00000313811:p.Gly301Val	107.0	0.0		98.0	25.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.493841	0.26774	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.17370	2.28;2.28;2.28	5.18	5.18	0.71444	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.812097	0.11437	N	0.564185	T	0.22781	0.0550	L	0.52573	1.65	0.58432	D	0.999999	B	0.21147	0.052	B	0.32677	0.15	T	0.03051	-1.1078	10	0.33141	T	0.24	.	14.1272	0.65228	0.0:0.1623:0.8377:0.0	.	301	Q9Y2K6	UBP20_HUMAN	V	301	ENSP00000361506:G301V;ENSP00000313811:G301V;ENSP00000351122:G301V	ENSP00000313811:G301V	G	+	2	0	USP20	131670316	1.000000	0.71417	0.640000	0.29408	0.480000	0.33159	8.416000	0.90244	2.406000	0.81754	0.561000	0.74099	GGC	.	.		0.642	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			T	132630495	G	T	132630495	3	4	185	1	0	0	0	0	1	0	0	0	17067	1203	42	3	936	3	USP20	9	132630495	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	18305065	132630495	8582936	68	27519										
IL2RA	3559	hgsc.bcm.edu	37	chr10	6061403	6061403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ccactcacctgctacctggtActctgttgtaaatatggacg	8	12	2	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr10:6061403A>G	ENST00000379959.3	-	6	888	c.715T>C	c.(715-717)Tac>Cac	p.Y239H	IL2RA_ENST00000379954.1_Missense_Mutation_p.Y167H|SNORA14_ENST00000516113.1_RNA|IL2RA_ENST00000256876.6_Missense_Mutation_p.Y230H	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	239					activation-induced cell death of T cells (GO:0006924)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of defense response to virus (GO:0050687)|negative regulation of immune response (GO:0050777)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell proliferation (GO:0042130)|Notch signaling pathway (GO:0007219)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of T cell differentiation (GO:0045582)|regulation of T cell homeostatic proliferation (GO:0046013)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|interleukin-2 receptor activity (GO:0004911)			endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	GCTACCTGGTACTCTGTTGTA	0.453																																					p.Y239H		Atlas-SNP	.											.	IL2RA	37	.	0			c.T715C						.						221	187	199					10																	6061403		2203	4300	6503	SO:0001583	missense	3559	exon6			CCTGGTACTCTGT	X01057	CCDS7076.1	10p15-p14	2014-09-17			ENSG00000134460	ENSG00000134460		"Interleukins and interleukin receptors", "CD molecules"	6008	protein-coding gene	gene with protein product		147730	"insulin-dependent diabetes mellitus 10"	IL2R, IDDM10		3925551, 17676041	Standard	NM_000417		Approved	CD25	uc001iiz.2	P01589	OTTHUMG00000017616	ENST00000379959.3:c.715T>C	chr10.hg19:g.6061403A>G	ENSP00000369293:p.Tyr239His	56.0	0.0		51.0	14.0	NM_000417	Q5W007	Missense_Mutation	SNP	ENST00000379959.3	hg19	CCDS7076.1	.	.	.	.	.	.	.	.	.	.	A	10.98	1.505359	0.26949	.	.	ENSG00000134460	ENST00000379959;ENST00000397240;ENST00000379954;ENST00000256876	T;T;T	0.57107	1.13;0.42;1.23	4.02	2.9	0.33743	.	0.612731	0.14663	N	0.305848	T	0.55641	0.1933	M	0.70275	2.135	0.09310	N	0.999998	D;D;B	0.56968	0.959;0.978;0.266	B;P;B	0.51170	0.425;0.661;0.077	T	0.47535	-0.9110	10	0.41790	T	0.15	-26.2052	5.5242	0.16949	0.8765:0.0:0.1235:0.0	.	167;129;239	Q5W005;E9PF94;P01589	.;.;IL2RA_HUMAN	H	239;129;167;230	ENSP00000369293:Y239H;ENSP00000369287:Y167H;ENSP00000256876:Y230H	ENSP00000256876:Y230H	Y	-	1	0	IL2RA	6101409	0.213000	0.23551	0.190000	0.23270	0.167000	0.22549	0.919000	0.28692	1.803000	0.52742	0.379000	0.24179	TAC	.	.		0.453	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	NM_000417		G	6061403	A	G	6061403	3	3	185	1	0	0	0	0	1	0	0	0	7695	391	14	2	115	2	IL2RA	10	6061403	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10		6061403	129473344	69	27520										
TMEM72	643236	hgsc.bcm.edu	37	chr10	45429084	45429084	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	acctggactccctctccccaGgtgtcaaccagggtccctgg	10	17	2	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr10:45429084G>T	ENST00000544540.1	+	3	339		c.e3-1		TMEM72-AS1_ENST00000450287.2_RNA			A0PK05	TMM72_HUMAN	transmembrane protein 72							integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						CCTCTCCCCAGGTGTCAACCA	0.607																																					.		Atlas-SNP	.											.	TMEM72	25	.	0			c.210-1G>T						.						59	60	59					10																	45429084		1568	3582	5150	SO:0001630	splice_region_variant	643236	exon4			TCCCCAGGTGTCA	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 127"	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.-145-1G>T	chr10.hg19:g.45429084G>T		43.0	0.0		43.0	13.0	NM_001123376	A1L181|Q5T740	Splice_Site	SNP	ENST00000544540.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.78	1.447607	0.26074	.	.	ENSG00000187783	ENST00000389583	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4359	0.75146	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM72	44749090	1.000000	0.71417	0.999000	0.59377	0.127000	0.20565	6.353000	0.73032	2.788000	0.95919	0.650000	0.86243	.	.	.		0.607	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376	Intron	T	45429084	G	T	45429084	5	4	185	1	0	0	0	0	0	0	1	0	16216	1014	35	3	223	3	TMEM72	10	45429084	Splice_Site	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	39367681	45429084	90105663	70	27521										
PCDH15	65217	hgsc.bcm.edu	37	chr10	56077047	56077047	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ttaccggagttctcaactcaGgtatggcagcttgataagtg	11	8	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr10:56077047G>T	ENST00000320301.6	-	8	1254	c.860C>A	c.(859-861)cCt>cAt	p.P287H	PCDH15_ENST00000361849.3_Missense_Mutation_p.P287H|PCDH15_ENST00000414778.1_Missense_Mutation_p.P292H|PCDH15_ENST00000395433.1_Missense_Mutation_p.P265H|PCDH15_ENST00000395446.1_Missense_Mutation_p.P287H|PCDH15_ENST00000437009.1_Missense_Mutation_p.P287H|PCDH15_ENST00000373965.2_Missense_Mutation_p.P287H|PCDH15_ENST00000395432.2_Missense_Mutation_p.P250H|PCDH15_ENST00000395445.1_Missense_Mutation_p.P287H|PCDH15_ENST00000395438.1_Missense_Mutation_p.P287H|PCDH15_ENST00000395440.1_Missense_Mutation_p.P287H|PCDH15_ENST00000395442.1_Missense_Mutation_p.P287H|PCDH15_ENST00000395430.1_Missense_Mutation_p.P287H|PCDH15_ENST00000373955.1_Missense_Mutation_p.P287H|PCDH15_ENST00000373957.3_Missense_Mutation_p.P265H|PCDH15_ENST00000409834.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	287	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TCTCAACTCAGGTATGGCAGC	0.398										HNSCC(58;0.16)																											p.P292H		Atlas-SNP	.											.	PCDH15	1715	.	0			c.C875A						.						113	101	105					10																	56077047		2203	4300	6503	SO:0001583	missense	65217	exon9			AACTCAGGTATGG	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.860C>A	chr10.hg19:g.56077047G>T	ENSP00000322604:p.Pro287His	113.0	0.0		100.0	10.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.739327	0.49045	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.59364	0.4;0.43;0.35;0.37;0.42;0.66;0.51;0.39;0.27;0.32;0.27;0.27;0.27;0.29;0.44	4.77	4.77	0.60923	Cadherin (1);Cadherin-like (1);	.	.	.	.	T	0.75547	0.3864	M	0.73217	2.22	0.50039	D	0.99984	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.999;1.0;1.0;0.999;0.999;0.999;0.999;1.0;0.972;0.988;0.999	D;D;D;D;D;D;D;D;D;D;D;D;P;P;D	0.91635	0.999;0.976;0.971;0.96;0.971;0.976;0.999;0.957;0.971;0.94;0.947;0.971;0.89;0.823;0.96	T	0.78001	-0.2375	9	0.56958	D	0.05	.	17.7447	0.88416	0.0:0.0:1.0:0.0	.	265;287;287;292;287;250;287;287;287;287;287;292;287;265;287	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	H	287;292;287;287;287;287;287;287;250;287;265;265;287;287;292;287;287	ENSP00000363076:P287H;ENSP00000410304:P292H;ENSP00000378826:P287H;ENSP00000378832:P287H;ENSP00000378833:P287H;ENSP00000378829:P287H;ENSP00000378827:P287H;ENSP00000378820:P250H;ENSP00000354950:P287H;ENSP00000378821:P265H;ENSP00000363068:P265H;ENSP00000322604:P287H;ENSP00000378818:P287H;ENSP00000412628:P287H;ENSP00000363066:P287H	ENSP00000322604:P287H	P	-	2	0	PCDH15	55747053	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.798000	0.55522	2.346000	0.79739	0.557000	0.71058	CCT	.	.		0.398	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	56077047	G	T	56077047	3	4	185	1	0	0	0	0	1	0	0	0	11520	1000	35	3	6755	3	PCDH15	10	56077047	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	10647963	56077047	79457700	71	27522										
H2AFY2	55506	hgsc.bcm.edu	37	chr10	71855484	71855484	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	attgtccacccaaccacagcCgaaattgacctcaaagaaga	6	13	1	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr10:71855484C>T	ENST00000373255.4	+	6	927	c.663C>T	c.(661-663)gcC>gcT	p.A221A		NM_018649.2	NP_061119.1	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2	221	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				brain development (GO:0007420)|chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(4)|skin(1)	15						CAACCACAGCCGAAATTGACC	0.468																																					p.A221A		Atlas-SNP	.											.	H2AFY2	30	.	0			c.C663T						.						110	101	104					10																	71855484		2203	4300	6503	SO:0001819	synonymous_variant	55506	exon6			CACAGCCGAAATT	AF336304	CCDS7296.1	10q22.1	2011-01-27			ENSG00000099284	ENSG00000099284		"Histones / Replication-independent"	14453	protein-coding gene	gene with protein product						11331621, 11262398	Standard	NM_018649		Approved	macroH2A2	uc001jqm.3	Q9P0M6	OTTHUMG00000018396	ENST00000373255.4:c.663C>T	chr10.hg19:g.71855484C>T		87.0	0.0		103.0	20.0	NM_018649	Q5SQT2	Silent	SNP	ENST00000373255.4	hg19	CCDS7296.1																																																																																			.	.		0.468	H2AFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048480.2	NM_018649		T	71855484	C	T	71855484	2	4	185	1	0	0	0	0	0	0	0	1	6939	639	23	1		1	H2AFY2	10	71855484	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	15778437	71855484	63679263	72	27523										
COL17A1	1308	hgsc.bcm.edu	37	chr10	105792488	105792488	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	caggtggcccaggatgacctGgtggcccagcagggcccctg	16	14	0	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr10:105792488G>T	ENST00000353479.5	-	55	4672	c.4382C>A	c.(4381-4383)cCa>cAa	p.P1461Q	COL17A1_ENST00000369733.3_Missense_Mutation_p.P1379Q	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1461	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		AGGATGACCTGGTGGCCCAGC	0.572																																					p.P1461Q		Atlas-SNP	.											.	COL17A1	149	.	0			c.C4382A						.						68	60	63					10																	105792488		2203	4300	6503	SO:0001583	missense	1308	exon55			TGACCTGGTGGCC	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.4382C>A	chr10.hg19:g.105792488G>T	ENSP00000340937:p.Pro1461Gln	51.0	0.0		44.0	13.0	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	hg19	CCDS7554.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.02|16.02	3.003229|3.003229	0.54254|0.54254	.|.	.|.	ENSG00000065618|ENSG00000065618	ENST00000353479;ENST00000369733|ENST00000433822	D;D|.	0.93366|.	-3.21;-3.21|.	6.17|6.17	5.27|5.27	0.74061|0.74061	.|.	0.341445|.	0.20569|.	N|.	0.089762|.	T|T	0.61388|0.61388	0.2343|0.2343	L|L	0.45744|0.45744	1.44|1.44	0.80722|0.80722	D|D	1|1	P|.	0.47841|.	0.901|.	P|.	0.49047|.	0.599|.	T|T	0.58769|0.58769	-0.7578|-0.7578	10|5	0.20046|.	T|.	0.44|.	-1.9356|-1.9356	14.3798|14.3798	0.66905|0.66905	0.0:0.2035:0.7965:0.0|0.0:0.2035:0.7965:0.0	rs34425293|rs34425293	1461|.	Q9UMD9|.	COHA1_HUMAN|.	Q|K	1461;1379|30	ENSP00000340937:P1461Q;ENSP00000358748:P1379Q|.	ENSP00000340937:P1461Q|.	P|Q	-|-	2|1	0|0	COL17A1|COL17A1	105782478|105782478	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.836000|0.836000	0.47400|0.47400	4.696000|4.696000	0.61774|0.61774	1.625000|1.625000	0.50366|0.50366	0.655000|0.655000	0.94253|0.94253	CCA|CAG	.	.		0.572	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		T	105792488	G	T	105792488	3	4	185	1	0	0	0	0	1	0	0	0	3676	1348	47	3	119	3	COL17A1	10	105792488	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	33937004	105792488	29742259	73	27524										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106937875	106937875	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aagtatggtttcacttcggtTcctctctttgttgacggggc	11	9	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr10:106937875T>A	ENST00000369701.3	+	14	2180	c.1953T>A	c.(1951-1953)gtT>gtA	p.V651V	SORCS3_ENST00000369699.4_Intron	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	651					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TCACTTCGGTTCCTCTCTTTG	0.473																																					p.V651V	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.T1953A						.						232	199	210					10																	106937875		2203	4300	6503	SO:0001819	synonymous_variant	22986	exon14			TTCGGTTCCTCTC	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1953T>A	chr10.hg19:g.106937875T>A		104.0	0.0		92.0	7.0	NM_014978	Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	hg19	CCDS7558.1																																																																																			.	.		0.473	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		A	106937875	T	A	106937875	2	1	185	1	0	0	0	0	0	0	0	1	14947	1770	62	4		4	SORCS3	10	106937875	Silent	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	1145387	106937875	28596872	74	27525										
MKI67	4288	hgsc.bcm.edu	37	chr10	129900917	129900917	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gtcgttgctgttcagctcttCcgcaggttcaattctttttg	9	10	4	0	rs542413191		TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr10:129900917C>T	ENST00000368654.3	-	13	9562	c.9187G>A	c.(9187-9189)Gaa>Aaa	p.E3063K	MKI67_ENST00000368653.3_Missense_Mutation_p.E2703K	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3063					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTCAGCTCTTCCGCAGGTTCA	0.458																																					p.E3063K		Atlas-SNP	.											.	MKI67	363	.	0			c.G9187A						.						249	226	234					10																	129900917		2203	4300	6503	SO:0001583	missense	4288	exon13			GCTCTTCCGCAGG	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.9187G>A	chr10.hg19:g.129900917C>T	ENSP00000357643:p.Glu3063Lys	83.0	0.0		55.0	22.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530756	0.27387	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02323	4.38;4.34	3.55	3.55	0.40652	.	2.393500	0.01685	N	0.026352	T	0.04048	0.0113	L	0.29908	0.895	0.09310	N	1	P;P;D	0.54207	0.801;0.718;0.965	B;B;B	0.43018	0.405;0.277;0.337	T	0.40001	-0.9586	10	0.21014	T	0.42	.	10.8089	0.46535	0.0:1.0:0.0:0.0	.	3062;2703;3063	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	K	3063;2703;3062	ENSP00000357643:E3063K;ENSP00000357642:E2703K	ENSP00000357642:E2703K	E	-	1	0	MKI67	129790907	0.002000	0.14202	0.002000	0.10522	0.002000	0.02628	1.553000	0.36255	1.972000	0.57404	0.563000	0.77884	GAA	.	.		0.458	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129900917	C	T	129900917	3	4	185	1	0	0	0	0	1	0	0	0	9607	864	30	3	595	3	MKI67	10	129900917	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	22963042	129900917	5633830	75	27526										
MUC6	4588	hgsc.bcm.edu	37	chr11	1017614	1017614	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gattggctggtcccactggtGgtcactgtcattggtggggt	16	8	2	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:1017614G>A	ENST00000421673.2	-	31	5237	c.5187C>T	c.(5185-5187)acC>acT	p.T1729T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1729	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.T1729T(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCCCACTGGTGGTCACTGTCA	0.537																																					p.T1729T		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	.	2	Substitution - coding silent(2)	kidney(2)	c.C5187T						.						426	437	433					11																	1017614		2178	4264	6442	SO:0001819	synonymous_variant	4588	exon31			ACTGGTGGTCACT	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5187C>T	chr11.hg19:g.1017614G>A		143.0	0.0		139.0	19.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	hg19	CCDS44513.1																																																																																			.	.		0.537	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1017614	G	A	1017614	2	1	185	1	0	0	0	0	0	0	0	1	9989	1335	47	3		3	MUC6	11	1017614	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10		1017614	133988902	76	27527										
OR51G1	79324	hgsc.bcm.edu	37	chr11	4944735	4944735	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	taccagcagatacacataggAcatgaagaggtgtacaacgc	10	9	0	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:4944735A>G	ENST00000321961.2	-	1	902	c.835T>C	c.(835-837)Tcc>Ccc	p.S279P	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	279						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TACACATAGGACATGAAGAGG	0.463																																					p.S279P		Atlas-SNP	.											.	OR51G1	74	.	0			c.T835C						.						201	173	182					11																	4944735		2201	4298	6499	SO:0001583	missense	79324	exon1			CATAGGACATGAA	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"GPCR / Class A : Olfactory receptors"	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.835T>C	chr11.hg19:g.4944735A>G	ENSP00000322546:p.Ser279Pro	101.0	0.0		74.0	24.0	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	hg19	CCDS31366.1	.	.	.	.	.	.	.	.	.	.	A	14.49	2.550430	0.45383	.	.	ENSG00000176879	ENST00000321961	T	0.00274	8.35	4.53	1.95	0.26073	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37136	U	0.002221	T	0.00666	0.0022	M	0.87971	2.92	0.26289	N	0.978153	D	0.76494	0.999	D	0.77557	0.99	T	0.20371	-1.0277	10	0.87932	D	0	.	11.0382	0.47814	0.5855:0.4145:0.0:0.0	.	279	Q8NGK1	O51G1_HUMAN	P	279	ENSP00000322546:S279P	ENSP00000322546:S279P	S	-	1	0	OR51G1	4901311	0.000000	0.05858	1.000000	0.80357	0.662000	0.39071	-0.048000	0.11944	0.735000	0.32537	0.455000	0.32223	TCC	.	.		0.463	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237		G	4944735	A	G	4944735	3	3	185	1	0	0	0	0	1	0	0	0	11107	275	10	2	132	2	OR51G1	11	4944735	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	3927121	4944735	130061781	77	27528										
OR6A2	8590	hgsc.bcm.edu	37	chr11	6816411	6816411	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gaaaaagtggttgatgatgtTggggccacagtaagagaggc	16	4	0	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:6816411T>A	ENST00000332601.3	-	1	717	c.529A>T	c.(529-531)Aac>Tac	p.N177Y		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	177					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTGATGATGTTGGGGCCACAG	0.483																																					p.N177Y		Atlas-SNP	.											.	OR6A2	68	.	0			c.A529T						.						122	124	123					11																	6816411		2201	4296	6497	SO:0001583	missense	8590	exon1			TGATGTTGGGGCC	AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"GPCR / Class A : Olfactory receptors"	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.529A>T	chr11.hg19:g.6816411T>A	ENSP00000330384:p.Asn177Tyr	79.0	0.0		66.0	10.0	NM_003696	Q3MJC7|Q6IF35|Q9H206	Missense_Mutation	SNP	ENST00000332601.3	hg19	CCDS7772.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.986157	0.53934	.	.	ENSG00000184933	ENST00000332601	T	0.00262	8.4	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.094954	0.45606	D	0.000348	T	0.00580	0.0019	M	0.82923	2.615	0.29716	N	0.839044	D	0.89917	1.0	D	0.77557	0.99	T	0.29731	-1.0002	10	0.87932	D	0	.	12.9235	0.58245	0.0:0.0:0.0:1.0	.	177	O95222	OR6A2_HUMAN	Y	177	ENSP00000330384:N177Y	ENSP00000330384:N177Y	N	-	1	0	OR6A2	6772987	0.000000	0.05858	1.000000	0.80357	0.844000	0.47949	0.235000	0.17948	2.219000	0.72066	0.533000	0.62120	AAC	.	.		0.483	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696		A	6816411	T	A	6816411	3	1	185	1	0	0	0	0	1	0	0	0	11195	1812	63	4	458	4	OR6A2	11	6816411	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	1871676	6816411	128190105	78	27529										
PRDM11	56981	hgsc.bcm.edu	37	chr11	45203392	45203392	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	atggtgacggtggtgaagacGgaggtctgctcaccactccg	15	10	2	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:45203392G>T	ENST00000530656.1	+	2	177	c.177G>T	c.(175-177)acG>acT	p.T59T	PRDM11_ENST00000424263.2_Silent_p.T25T|PRDM11_ENST00000263765.4_Silent_p.T59T			Q9NQV5	PRD11_HUMAN	PR domain containing 11	59				KTEVCSPLRD -> NPS (in Ref. 1; AAF87244). {ECO:0000305}.			methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						TGGTGAAGACGGAGGTCTGCT	0.622																																					p.T25T	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											.	PRDM11	53	.	0			c.G75T						.						80	66	71					11																	45203392		2203	4299	6502	SO:0001819	synonymous_variant	56981	exon2			GAAGACGGAGGTC	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"PR-domain containing protein 11"						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.177G>T	chr11.hg19:g.45203392G>T		34.0	0.0		48.0	18.0	NM_001256695	Q8N9F1	Silent	SNP	ENST00000530656.1	hg19																																																																																				.	.		0.622	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229		T	45203392	G	T	45203392	2	4	185	1	0	0	0	0	0	0	0	1	12464	1103	39	1		1	PRDM11	11	45203392	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	38386981	45203392	89803124	79	27530										
MAPK8IP1	9479	hgsc.bcm.edu	37	chr11	45926375	45926375	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cgtcaaggccgatgactcccAggaggccaaggtgacttctt	12	12	2	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:45926375A>T	ENST00000241014.2	+	9	2053	c.1883A>T	c.(1882-1884)cAg>cTg	p.Q628L	MAPK8IP1_ENST00000395629.2_Missense_Mutation_p.Q618L|RP11-618K13.2_ENST00000533218.1_RNA	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	628	Interaction with VRK2.|PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		GATGACTCCCAGGAGGCCAAG	0.612																																					p.Q628L		Atlas-SNP	.											.	MAPK8IP1	51	.	0			c.A1883T						.						98	109	105					11																	45926375		2203	4299	6502	SO:0001583	missense	9479	exon9			ACTCCCAGGAGGC		CCDS7916.1	11p11.2	2009-07-24			ENSG00000121653	ENSG00000121653			6882	protein-coding gene	gene with protein product		604641		PRKM8IP		9235893, 9442013	Standard	NM_005456		Approved	IB1, JIP-1, JIP1	uc001nbr.3	Q9UQF2	OTTHUMG00000134324	ENST00000241014.2:c.1883A>T	chr11.hg19:g.45926375A>T	ENSP00000241014:p.Gln628Leu	54.0	0.0		51.0	17.0	NM_005456	D3DQP4|O43407	Missense_Mutation	SNP	ENST00000241014.2	hg19	CCDS7916.1	.	.	.	.	.	.	.	.	.	.	A	12.31	1.898349	0.33535	.	.	ENSG00000121653	ENST00000241014;ENST00000395629	T;T	0.36878	1.23;1.23	5.31	2.94	0.34122	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.634090	0.16941	N	0.193268	T	0.18045	0.0433	N	0.12182	0.205	0.33274	D	0.561386	B	0.02656	0.0	B	0.08055	0.003	T	0.18398	-1.0338	10	0.23891	T	0.37	-14.8606	6.6442	0.22927	0.5938:0.1517:0.0:0.2545	.	628	Q9UQF2	JIP1_HUMAN	L	628;618	ENSP00000241014:Q628L;ENSP00000378991:Q618L	ENSP00000241014:Q628L	Q	+	2	0	MAPK8IP1	45882951	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.016000	0.40971	0.440000	0.26502	0.459000	0.35465	CAG	.	.		0.612	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456		T	45926375	A	T	45926375	3	4	185	1	0	0	0	0	1	0	0	0	9293	188	7	4	1917	4	MAPK8IP1	11	45926375	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	722983	45926375	89080141	80	27531										
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468271	56468271	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctttatgcccaggccatgtcCataaagctgtgtgcattgct	9	11	0	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:56468271C>A	ENST00000312153.1	+	1	408	c.408C>A	c.(406-408)tcC>tcA	p.S136S		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						AGGCCATGTCCATAAAGCTGT	0.507																																					p.S136S		Atlas-SNP	.											.	.	.	.	0			c.C408A						.						198	183	188					11																	56468271		2201	4296	6497	SO:0001819	synonymous_variant	504191	exon1			CATGTCCATAAAG	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"GPCR / Class A : Olfactory receptors"	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.408C>A	chr11.hg19:g.56468271C>A		125.0	0.0		101.0	15.0	NM_001013358	Q6IEU9|Q8NGQ0	Silent	SNP	ENST00000312153.1	hg19	CCDS31536.1																																																																																			.	.		0.507	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		A	56468271	C	A	56468271	2	1	185	1	0	0	0	0	0	0	0	1	11259	581	21	3		3	OR9G1	11	56468271	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	10541896	56468271	78538245	81	27532										
EHD1	10938	hgsc.bcm.edu	37	chr11	64627602	64627602	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gatcttgcccagggaccacaTgagggccccgtacacccgca	11	16	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:64627602T>C	ENST00000320631.3	-	3	963	c.709A>G	c.(709-711)Atg>Gtg	p.M237V	EHD1_ENST00000359393.2_Missense_Mutation_p.M237V	NM_001282445.1|NM_006795.2	NP_001269374.1|NP_006786.2	Q9H4M9	EHD1_HUMAN	EH-domain containing 1	237	Dynamin-type G.				blood coagulation (GO:0007596)|cellular response to nerve growth factor stimulus (GO:1990090)|cholesterol homeostasis (GO:0042632)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|low-density lipoprotein particle clearance (GO:0034383)|neuron projection development (GO:0031175)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein homooligomerization (GO:0051260)	early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12						AGGGACCACATGAGGGCCCCG	0.602																																					p.M237V		Atlas-SNP	.											.	EHD1	31	.	0			c.A709G						.						100	98	99					11																	64627602		2201	4297	6498	SO:0001583	missense	10938	exon3			ACCACATGAGGGC	AF099011	CCDS8084.1, CCDS73315.1	11q13	2013-01-10			ENSG00000110047	ENSG00000110047		"EF-hand domain containing"	3242	protein-coding gene	gene with protein product	"testilin"	605888		PAST1		10395801, 10673336	Standard	NM_001282444		Approved	H-PAST, HPAST1, FLJ42622, FLJ44618	uc001obu.1	Q9H4M9	OTTHUMG00000066832	ENST00000320631.3:c.709A>G	chr11.hg19:g.64627602T>C	ENSP00000320516:p.Met237Val	151.0	0.0		130.0	43.0	NM_006795	O14611|Q2M3Q4|Q9UNR3	Missense_Mutation	SNP	ENST00000320631.3	hg19	CCDS8084.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.706035	0.89018	.	.	ENSG00000110047	ENST00000320631;ENST00000359393;ENST00000541001;ENST00000421303;ENST00000421510;ENST00000433803;ENST00000455148	D;D;D;D;D	0.95307	-3.67;-3.67;-3.67;-3.67;-3.67	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.96787	0.8951	H	0.94771	3.58	0.80722	D	1	P;P	0.51147	0.942;0.942	P;P	0.50537	0.643;0.643	D	0.97515	1.0069	10	0.87932	D	0	-63.5857	12.823	0.57704	0.0:0.0:0.0:1.0	.	237;237	B2R5U3;Q9H4M9	.;EHD1_HUMAN	V	237;237;213;251;101;251;101	ENSP00000320516:M237V;ENSP00000352354:M237V;ENSP00000391429:M101V;ENSP00000404944:M251V;ENSP00000396273:M101V	ENSP00000320516:M237V	M	-	1	0	EHD1	64384178	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.803000	0.85983	2.132000	0.65825	0.459000	0.35465	ATG	.	.		0.602	EHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143229.2	NM_006795		C	64627602	T	C	64627602	3	2	185	1	0	0	0	0	1	0	0	0	4979	1464	51	2	907	2	EHD1	11	64627602	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	8159331	64627602	70378914	82	27533										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65351982	65351982	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	atgcctcgctagacccactcAacatcaagcagaacaacaag	6	14	2	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:65351982A>T	ENST00000309295.4	+	11	3542	c.3277A>T	c.(3277-3279)Aac>Tac	p.N1093Y		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	1093	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.					membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						AGACCCACTCAACATCAAGCA	0.587																																					p.N1093Y		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.A3277T						.						31	34	33					11																	65351982		2137	4236	6373	SO:0001583	missense	254102	exon11			CCACTCAACATCA	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.3277A>T	chr11.hg19:g.65351982A>T	ENSP00000312671:p.Asn1093Tyr	79.0	0.0		75.0	32.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.30|19.30	3.800612|3.800612	0.70567|0.70567	.|.	.|.	ENSG00000173442|ENSG00000173442	ENST00000309295;ENST00000533237|ENST00000533465	D;D|.	0.95171|.	-3.63;-3.63|.	5.31|5.31	1.78|1.78	0.24846|0.24846	Calponin homology domain (5);|.	0.063230|.	0.64402|.	D|.	0.000015|.	T|T	0.73110|0.73110	0.3545|0.3545	M|M	0.87827|0.87827	2.91|2.91	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.98|.	D;P|.	0.72075|.	0.976;0.814|.	T|T	0.70890|0.70890	-0.4749|-0.4749	10|5	0.87932|.	D|.	0|.	.|.	6.9188|6.9188	0.24376|0.24376	0.6358:0.0:0.3642:0.0|0.6358:0.0:0.3642:0.0	.|.	510;1093|.	E9PIH6;Q8N3D4|.	.;EH1L1_HUMAN|.	Y|L	1093;510|142	ENSP00000312671:N1093Y;ENSP00000431996:N510Y|.	ENSP00000312671:N1093Y|.	N|Q	+|+	1|2	0|0	EHBP1L1|EHBP1L1	65108558|65108558	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.924000|0.924000	0.55760|0.55760	2.207000|2.207000	0.42788|0.42788	0.345000|0.345000	0.23873|0.23873	-0.411000|-0.411000	0.06167|0.06167	AAC|CAA	.	.		0.587	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		T	65351982	A	T	65351982	3	4	185	1	0	0	0	0	1	0	0	0	4978	130	5	4	3319	4	EHBP1L1	11	65351982	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	724380	65351982	69654534	83	27534										
FOLR1	2348	hgsc.bcm.edu	37	chr11	71906452	71906452	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tgcaaacggcatttcatccaGgacacctgcctctacgagtg	9	13	2	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:71906452G>A	ENST00000393679.1	+	3	742	c.306G>A	c.(304-306)caG>caA	p.Q102Q	FOLR1_ENST00000312293.4_Silent_p.Q102Q|FOLR1_ENST00000393676.3_Silent_p.Q102Q|RP11-807H22.7_ENST00000378140.3_RNA|FOLR1_ENST00000393681.2_Silent_p.Q102Q			P15328	FOLR1_HUMAN	folate receptor 1 (adult)	102					cell death (GO:0008219)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|receptor-mediated endocytosis (GO:0006898)	anchored component of external side of plasma membrane (GO:0031362)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|receptor activity (GO:0004872)			cervix(2)|endometrium(1)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	14					Methotrexate(DB00563)	ATTTCATCCAGGACACCTGCC	0.547																																					p.Q102Q		Atlas-SNP	.											.	FOLR1	22	.	0			c.G306A						.						152	149	150					11																	71906452		2200	4293	6493	SO:0001819	synonymous_variant	2348	exon2			CATCCAGGACACC	J05013	CCDS8211.1	11q13.3-q14.1	2010-04-09			ENSG00000110195	ENSG00000110195			3791	protein-coding gene	gene with protein product		136430		FOLR		1717147	Standard	NM_000802		Approved		uc001osa.2	P15328		ENST00000393679.1:c.306G>A	chr11.hg19:g.71906452G>A		68.0	0.0		51.0	20.0	NM_016729	Q53EW2|Q6FGT8|Q6LC90|Q9UCT2	Silent	SNP	ENST00000393679.1	hg19	CCDS8211.1																																																																																			.	.		0.547	FOLR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396773.1	NM_016725		A	71906452	G	A	71906452	2	1	185	1	0	0	0	0	0	0	0	1	5989	991	35	3		3	FOLR1	11	71906452	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	6554470	71906452	63100064	84	27535										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73811676	73811676	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ttcaattaccatcacattgtTcttaagcctttccaggtatt	4	10	3	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:73811676T>C	ENST00000334126.7	-	15	2852	c.2626A>G	c.(2626-2628)Aac>Gac	p.N876D	C2CD3_ENST00000313663.7_Missense_Mutation_p.N876D			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	876					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					ATCACATTGTTCTTAAGCCTT	0.438																																					p.N876D		Atlas-SNP	.											.	C2CD3	288	.	0			c.A2626G						.						92	86	88					11																	73811676		2200	4293	6493	SO:0001583	missense	26005	exon15			CATTGTTCTTAAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.2626A>G	chr11.hg19:g.73811676T>C	ENSP00000334379:p.Asn876Asp	93.0	0.0		79.0	25.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	T	28.4	4.916534	0.92249	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	D;D	0.95137	-3.62;-3.62	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.95900	0.8665	L	0.48362	1.52	0.47778	D	0.999517	D	0.71674	0.998	D	0.80764	0.994	D	0.95504	0.8580	10	0.41790	T	0.15	-16.3026	15.9122	0.79479	0.0:0.0:0.0:1.0	.	876	Q4AC94-1	.	D	876	ENSP00000334379:N876D;ENSP00000323339:N876D	ENSP00000323339:N876D	N	-	1	0	C2CD3	73489324	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.109000	0.64615	2.237000	0.73441	0.528000	0.53228	AAC	.	.		0.438	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		C	73811676	T	C	73811676	3	2	185	1	0	0	0	0	1	0	0	0	2156	1783	62	2	3333	2	C2CD3	11	73811676	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	1905224	73811676	61194840	85	27536										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117651413	117651413	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	taccatcgaagggccgcgctGggggagcccgcggccgggca	18	14	0	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:117651413G>T	ENST00000321322.6	-	2	340	c.339C>A	c.(337-339)ccC>ccA	p.P113P	DSCAML1_ENST00000527706.1_Intron	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	53	Ig-like C2-type 1.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GGGCCGCGCTGGGGGAGCCCG	0.652																																					p.P113P		Atlas-SNP	.											.	DSCAML1	286	.	0			c.C339A						.						39	45	43					11																	117651413		2200	4295	6495	SO:0001819	synonymous_variant	57453	exon2			CGCGCTGGGGGAG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.339C>A	chr11.hg19:g.117651413G>T		45.0	0.0		46.0	12.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	hg19	CCDS8384.1																																																																																			.	.		0.652	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117651413	G	T	117651413	2	4	185	1	0	0	0	0	0	0	0	1	4771	1335	47	3		3	DSCAML1	11	117651413	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	43839737	117651413	17355103	86	27537										
GRIK4	2900	hgsc.bcm.edu	37	chr11	120831719	120831719	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cattgagtcagtggatgaccTggctgaccagaccgccattg	12	11	1	4			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:120831719T>G	ENST00000527524.2	+	17	2263	c.1976T>G	c.(1975-1977)cTg>cGg	p.L659R	GRIK4_ENST00000438375.2_Missense_Mutation_p.L659R	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	659					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		GTGGATGACCTGGCTGACCAG	0.542																																					p.L659R		Atlas-SNP	.											.	GRIK4	149	.	0			c.T1976G						.						132	107	115					11																	120831719		2203	4299	6502	SO:0001583	missense	2900	exon15			ATGACCTGGCTGA	S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1976T>G	chr11.hg19:g.120831719T>G	ENSP00000435648:p.Leu659Arg	55.0	0.0		86.0	30.0	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	hg19	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.830954	0.91036	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.23754	1.89;1.89	5.51	5.51	0.81932	Ionotropic glutamate receptor (2);	0.000000	0.64402	D	0.000001	T	0.65790	0.2725	H	0.96916	3.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78748	-0.2083	10	0.87932	D	0	.	15.3185	0.74102	0.0:0.0:0.0:1.0	.	659;659	A6H8K8;Q16099	.;GRIK4_HUMAN	R	659	ENSP00000435648:L659R;ENSP00000404063:L659R	ENSP00000404063:L659R	L	+	2	0	GRIK4	120336929	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.097000	0.63578	0.533000	0.62120	CTG	.	.		0.542	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		G	120831719	T	G	120831719	3	3	185	1	0	0	0	0	1	0	0	0	6785	1580	55	5	2034	5	GRIK4	11	120831719	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	3180306	120831719	14174797	87	27538										
OPCML	4978	hgsc.bcm.edu	37	chr11	132812856	132812856	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tccccctgccggaccgtcacGttgtccatagctttggggaa	11	14	1	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr11:132812856G>T	ENST00000331898.7	-	1	710	c.132C>A	c.(130-132)aaC>aaA	p.N44K	OPCML_ENST00000541867.1_Missense_Mutation_p.N44K|OPCML_ENST00000524381.1_Missense_Mutation_p.N37K|OPCML_ENST00000529038.1_Intron|OPCML_ENST00000374778.4_Missense_Mutation_p.N3K	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	44	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GGACCGTCACGTTGTCCATAG	0.667																																					p.N44K		Atlas-SNP	.											.	OPCML	166	.	0			c.C132A						.						64	69	67					11																	132812856		2201	4295	6496	SO:0001583	missense	4978	exon1			CGTCACGTTGTCC	BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.132C>A	chr11.hg19:g.132812856G>T	ENSP00000330862:p.Asn44Lys	63.0	0.0		50.0	16.0	NM_002545	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	hg19	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.579032	0.86645	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.6	4.7	0.59300	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.134612	0.47852	D	0.000218	T	0.63721	0.2535	M	0.92317	3.295	0.51767	D	0.999939	D;P;D;D	0.63880	0.981;0.86;0.981;0.993	D;P;D;D	0.69824	0.946;0.832;0.946;0.966	T	0.74109	-0.3771	10	0.87932	D	0	-20.4728	14.2764	0.66181	0.0714:0.0:0.9286:0.0	.	44;37;44;44	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	K	44;37;3;37;44	ENSP00000330862:N44K;ENSP00000434750:N37K;ENSP00000363910:N3K;ENSP00000445496:N44K	ENSP00000330862:N44K	N	-	3	2	OPCML	132318066	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.324000	0.72896	1.381000	0.46364	0.655000	0.94253	AAC	.	.		0.667	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		T	132812856	G	T	132812856	3	4	185	1	0	0	0	0	1	0	0	0	10883	1136	40	1	933	1	OPCML	11	132812856	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	11981137	132812856	2193660	88	27539										
CASC1	55259	hgsc.bcm.edu	37	chr12	25272106	25272106	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	atcccaccttacaaccacagGatcctcaaaaaagattacat	3	13	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr12:25272106G>C	ENST00000320267.9	-	11	1432	c.1351C>G	c.(1351-1353)Cct>Gct	p.P451A	CASC1_ENST00000354189.5_Missense_Mutation_p.P515A|CASC1_ENST00000395990.2_Missense_Mutation_p.P411A|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000537577.1_Missense_Mutation_p.P339A|CASC1_ENST00000395987.3_Missense_Mutation_p.P457A|CASC1_ENST00000545133.1_Missense_Mutation_p.P392A	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	451										breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			ACAACCACAGGATCCTCAAAA	0.373																																					p.P515A		Atlas-SNP	.											.	CASC1	146	.	0			c.C1543G						.						101	92	95					12																	25272106		2203	4300	6503	SO:0001583	missense	55259	exon12			CCACAGGATCCTC	AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 54"					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.1351C>G	chr12.hg19:g.25272106G>C	ENSP00000313141:p.Pro451Ala	82.0	0.0		79.0	32.0	NM_001082972	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Missense_Mutation	SNP	ENST00000320267.9	hg19	CCDS41762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.02|17.02	3.282367|3.282367	0.59867|0.59867	.|.	.|.	ENSG00000118307|ENSG00000118307	ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395990;ENST00000537577;ENST00000395992;ENST00000545133;ENST00000389246|ENST00000556006	T;T;T;T;T|.	0.61742|.	0.08;0.74;0.74;0.16;0.16|.	5.34|5.34	5.34|5.34	0.76211|0.76211	Casc1 domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77922|0.77922	0.4203|0.4203	M|M	0.82323|0.82323	2.585|2.585	0.49389|0.49389	D|D	0.999786|0.999786	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0;1.0|.	T|T	0.79725|0.79725	-0.1683|-0.1683	10|5	0.51188|.	T|.	0.08|.	-18.5658|-18.5658	15.7854|15.7854	0.78297|0.78297	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	339;392;515;451;457|.	F5H555;F5H6T6;Q6TDU7-3;Q6TDU7;F8W8F9|.	.;.;.;CASC1_HUMAN;.|.	A|C	515;457;451;411;339;457;392;261|287	ENSP00000346126:P515A;ENSP00000379310:P457A;ENSP00000313141:P451A;ENSP00000379313:P411A;ENSP00000437373:P392A|.	ENSP00000313141:P451A|.	P|S	-|-	1|2	0|0	CASC1|CASC1	25163373|25163373	1.000000|1.000000	0.71417|0.71417	0.196000|0.196000	0.23383|0.23383	0.744000|0.744000	0.42396|0.42396	6.375000|6.375000	0.73137|0.73137	2.496000|2.496000	0.84212|0.84212	0.650000|0.650000	0.86243|0.86243	CCT|TCC	.	.		0.373	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272		C	25272106	G	C	25272106	3	2	185	1	0	0	0	0	1	0	0	0	2662	1174	41	4	819	4	CASC1	12	25272106	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10		25272106	108579789	89	27540										
CCNT1	904	hgsc.bcm.edu	37	chr12	49099564	49099564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctcctacctcacttctagtaTcaggaagggattcctgagga	9	11	3	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr12:49099564T>C	ENST00000261900.3	-	3	581	c.359A>G	c.(358-360)gAt>gGt	p.D120G		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	120					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						ACTTCTAGTATCAGGAAGGGA	0.398																																					p.D120G		Atlas-SNP	.											.	CCNT1	55	.	0			c.A359G						.						123	111	115					12																	49099564		2203	4300	6503	SO:0001583	missense	904	exon3			CTAGTATCAGGAA	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.359A>G	chr12.hg19:g.49099564T>C	ENSP00000261900:p.Asp120Gly	43.0	0.0		52.0	20.0	NM_001240	A9XU13|E7EX76|O60581	Missense_Mutation	SNP	ENST00000261900.3	hg19	CCDS8766.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.087153	0.76642	.	.	ENSG00000129315	ENST00000261900	T	0.45668	0.89	5.39	5.39	0.77823	Cyclin, N-terminal (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.61451	0.2348	M	0.64080	1.96	0.80722	D	1	D	0.69078	0.997	D	0.74674	0.984	T	0.64980	-0.6279	10	0.87932	D	0	-16.2775	14.6959	0.69121	0.0:0.0:0.0:1.0	.	120	O60563	CCNT1_HUMAN	G	120	ENSP00000261900:D120G	ENSP00000261900:D120G	D	-	2	0	CCNT1	47385831	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	8.040000	0.89188	2.180000	0.69256	0.533000	0.62120	GAT	.	.		0.398	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		C	49099564	T	C	49099564	3	2	185	1	0	0	0	0	1	0	0	0	2936	1435	50	2	1849	2	CCNT1	12	49099564	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	23827458	49099564	84752331	90	27541										
TMEM194A	23306	hgsc.bcm.edu	37	chr12	57472462	57472462	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ccgcactgtcccaccgccccCgactcccgagccccagggcc	9	24	0	0	rs368361522		TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr12:57472462C>T	ENST00000300128.4	-	1	90	c.67G>A	c.(67-69)Ggg>Agg	p.G23R	TMEM194A_ENST00000553654.1_Intron|TMEM194A_ENST00000379391.3_Missense_Mutation_p.G23R	NM_001130963.1	NP_001124435.1	O14524	T194A_HUMAN	transmembrane protein 194A	23						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(3)|lung(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						CCACCGCCCCCGACTCCCGAG	0.682																																					p.G23R		Atlas-SNP	.											.	TMEM194A	64	.	0			c.G67A						.						46	60	56					12																	57472462		2198	4296	6494	SO:0001583	missense	23306	exon1			CGCCCCCGACTCC	AB006624	CCDS31841.1, CCDS44927.1	12q13.3	2008-06-10	2008-06-10	2008-06-10		ENSG00000166881			29001	protein-coding gene	gene with protein product			"transmembrane protein 194"	TMEM194			Standard	NM_015257		Approved	KIAA0286	uc001smy.3	O14524		ENST00000300128.4:c.67G>A	chr12.hg19:g.57472462C>T	ENSP00000300128:p.Gly23Arg	57.0	0.0		63.0	16.0	NM_015257	Q17R72|Q68DH0|Q6IQ25	Missense_Mutation	SNP	ENST00000300128.4	hg19	CCDS44927.1	.	.	.	.	.	.	.	.	.	.	C	0.018	-1.475085	0.01035	.	.	ENSG00000166881	ENST00000379391;ENST00000300128	T;T	0.43294	0.95;0.99	3.93	-3.63	0.04529	.	0.853469	0.09815	N	0.752230	T	0.28499	0.0705	L	0.51422	1.61	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.04013	0.001;0.001	T	0.26916	-1.0089	10	0.36615	T	0.2	0.1528	2.2295	0.03993	0.1449:0.2177:0.429:0.2085	.	23;23	O14524;O14524-2	T194A_HUMAN;.	R	23	ENSP00000368701:G23R;ENSP00000300128:G23R	ENSP00000300128:G23R	G	-	1	0	TMEM194A	55758729	0.000000	0.05858	0.004000	0.12327	0.048000	0.14542	-2.471000	0.00990	-0.758000	0.04690	-0.140000	0.14226	GGG	.	.		0.682	TMEM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411272.1	NM_015257		T	57472462	C	T	57472462	3	4	185	1	0	0	0	0	1	0	0	0	16131	652	23	1	1303	1	TMEM194A	12	57472462	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	8372898	57472462	76379433	91	27542										
LUM	4060	hgsc.bcm.edu	37	chr12	91501990	91501990	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aggacagatccagctcaaccAgggatgacacattgaaagaa	10	9	1	4			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr12:91501990A>G	ENST00000266718.4	-	2	1221	c.767T>C	c.(766-768)cTg>cCg	p.L256P	LUM_ENST00000548071.1_5'UTR	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	256					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						CAGCTCAACCAGGGATGACAC	0.388																																					p.L256P		Atlas-SNP	.											.	LUM	65	.	0			c.T767C						.						151	145	147					12																	91501990		2203	4300	6503	SO:0001583	missense	4060	exon2			TCAACCAGGGATG	BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6724	protein-coding gene	gene with protein product	"lumican proteoglycan"	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.767T>C	chr12.hg19:g.91501990A>G	ENSP00000266718:p.Leu256Pro	64.0	0.0		60.0	16.0	NM_002345	B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	hg19	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	A	19.11	3.763765	0.69878	.	.	ENSG00000139329	ENST00000266718	D	0.82711	-1.64	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.94000	0.8078	H	0.96489	3.83	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95783	0.8818	10	0.87932	D	0	-10.6372	15.7532	0.78005	1.0:0.0:0.0:0.0	.	256	P51884	LUM_HUMAN	P	256	ENSP00000266718:L256P	ENSP00000266718:L256P	L	-	2	0	LUM	90026121	1.000000	0.71417	0.055000	0.19348	0.994000	0.84299	8.962000	0.93254	2.117000	0.64856	0.460000	0.39030	CTG	.	.		0.388	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345		G	91501990	A	G	91501990	3	3	185	1	0	0	0	0	1	0	0	0	9094	188	7	2	257	2	LUM	12	91501990	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	34029528	91501990	42349905	92	27543										
BTBD11	121551	hgsc.bcm.edu	37	chr12	107713276	107713276	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cggctgcgctggccgcactgTccctctacaacatgagcagc	11	16	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr12:107713276T>A	ENST00000280758.5	+	1	1087	c.559T>A	c.(559-561)Tcc>Acc	p.S187T	BTBD11_ENST00000420571.2_Missense_Mutation_p.S187T|BTBD11_ENST00000490090.2_Missense_Mutation_p.S187T	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	187						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						GGCCGCACTGTCCCTCTACAA	0.692																																					p.S187T		Atlas-SNP	.											.	BTBD11	122	.	0			c.T559A						.						8	7	7					12																	107713276		2085	4074	6159	SO:0001583	missense	121551	exon1			GCACTGTCCCTCT	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.559T>A	chr12.hg19:g.107713276T>A	ENSP00000280758:p.Ser187Thr	47.0	0.0		60.0	20.0	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	hg19	CCDS31893.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.385026	0.61956	.	.	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000490090	T;T;T	0.20200	2.09;2.09;2.09	4.74	4.74	0.60224	Histone-fold (2);	0.000000	0.85682	D	0.000000	T	0.46054	0.1373	M	0.76328	2.33	0.80722	D	1	D;P;D	0.56035	0.974;0.956;0.974	D;P;D	0.70487	0.969;0.899;0.953	T	0.49273	-0.8957	10	0.72032	D	0.01	.	14.1921	0.65644	0.0:0.0:0.0:1.0	.	187;187;187	A6QL63-2;A6QL63;A6QL63-3	.;BTBDB_HUMAN;.	T	187	ENSP00000280758:S187T;ENSP00000413889:S187T;ENSP00000447319:S187T	ENSP00000280758:S187T	S	+	1	0	BTBD11	106237406	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.602000	0.82796	1.883000	0.54544	0.374000	0.22700	TCC	.	.		0.692	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		A	107713276	T	A	107713276	3	1	185	1	0	0	0	0	1	0	0	0	1541	1667	58	4	561	4	BTBD11	12	107713276	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10	16211286	107713276	26138619	93	27544										
ACACB	32	hgsc.bcm.edu	37	chr12	109690864	109690864	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tccaacaaccagctgggtggCgttcagatcatgcattacaa	9	11	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr12:109690864C>T	ENST00000338432.7	+	43	6065	c.5946C>T	c.(5944-5946)ggC>ggT	p.G1982G	ACACB_ENST00000543201.1_Silent_p.G648G|ACACB_ENST00000377854.5_Silent_p.G1912G|ACACB_ENST00000377848.3_Silent_p.G1982G			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1982	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	AGCTGGGTGGCGTTCAGATCA	0.522																																					p.G1982G		Atlas-SNP	.											.	ACACB	330	.	0			c.C5946T						.						327	260	282					12																	109690864		2203	4300	6503	SO:0001819	synonymous_variant	32	exon42			GGGTGGCGTTCAG	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.5946C>T	chr12.hg19:g.109690864C>T		102.0	0.0		76.0	20.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	hg19	CCDS31898.1																																																																																			.	.		0.522	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109690864	C	T	109690864	2	4	185	1	0	0	0	0	0	0	0	1	107	755	27	1		1	ACACB	12	109690864	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	1977588	109690864	24161031	94	27545										
NBEA	26960	hgsc.bcm.edu	37	chr13	35632909	35632909	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tgctgatgcaaatagggtatTctgtggtcaacttggtgccg	13	7	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr13:35632909T>G	ENST00000400445.3	+	8	1682	c.1148T>G	c.(1147-1149)tTc>tGc	p.F383C	NBEA_ENST00000310336.4_Missense_Mutation_p.F383C|NBEA_ENST00000379939.2_Missense_Mutation_p.F383C|NBEA_ENST00000540320.1_Missense_Mutation_p.F383C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	383					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AATAGGGTATTCTGTGGTCAA	0.358																																					p.F383C		Atlas-SNP	.											.	NBEA	340	.	0			c.T1148G						.						33	30	31					13																	35632909		1801	4067	5868	SO:0001583	missense	26960	exon8			GGGTATTCTGTGG	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.1148T>G	chr13.hg19:g.35632909T>G	ENSP00000383295:p.Phe383Cys	234.0	0.0		204.0	12.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.330602	0.81690	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.90511	0.7027	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91972	0.5587	10	0.72032	D	0.01	.	15.7723	0.78180	0.0:0.0:0.0:1.0	.	383	Q5T321	.	C	383	ENSP00000440951:F383C;ENSP00000383295:F383C;ENSP00000369271:F383C;ENSP00000308534:F383C	ENSP00000308534:F383C	F	+	2	0	NBEA	34530909	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.997000	0.88414	2.195000	0.70347	0.528000	0.53228	TTC	.	.		0.358	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35632909	T	G	35632909	3	3	185	1	0	0	0	0	1	0	0	0	10196	1783	62	5	1178	5	NBEA	13	35632909	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10		35632909	79536969	95	27546										
NBEA	26960	hgsc.bcm.edu	37	chr13	35770382	35770382	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	acctatcccatacccagatcCagcattgaagagagaaacac	6	13	0	4			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr13:35770382C>A	ENST00000400445.3	+	31	5843	c.5309C>A	c.(5308-5310)cCa>cAa	p.P1770Q	NBEA_ENST00000310336.4_Missense_Mutation_p.P1770Q|NBEA_ENST00000379939.2_Missense_Mutation_p.P1767Q|NBEA_ENST00000540320.1_Missense_Mutation_p.P1770Q	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1770					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TACCCAGATCCAGCATTGAAG	0.408																																					p.P1770Q		Atlas-SNP	.											.	NBEA	340	.	0			c.C5309A						.						68	66	67					13																	35770382		1879	4111	5990	SO:0001583	missense	26960	exon31			CAGATCCAGCATT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5309C>A	chr13.hg19:g.35770382C>A	ENSP00000383295:p.Pro1770Gln	69.0	0.0		69.0	25.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	12.89	2.073364	0.36566	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.36936	0.0985	N	0.21448	0.665	0.80722	D	1	B;B	0.18741	0.03;0.009	B;B	0.10450	0.005;0.004	T	0.14811	-1.0459	10	0.15952	T	0.53	.	20.0979	0.97857	0.0:1.0:0.0:0.0	.	1770;1767	Q8NFP9;Q5T321	NBEA_HUMAN;.	Q	1770;1770;1767;1770;397	ENSP00000440951:P1770Q;ENSP00000383295:P1770Q;ENSP00000369271:P1767Q;ENSP00000308534:P1770Q	ENSP00000308534:P1770Q	P	+	2	0	NBEA	34668382	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	4.344000	0.59354	2.767000	0.95098	0.585000	0.79938	CCA	.	.		0.408	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35770382	C	A	35770382	3	1	185	1	0	0	0	0	1	0	0	0	10196	594	21	3	5431	3	NBEA	13	35770382	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	137473	35770382	79399496	96	27547										
MYH6	4624	hgsc.bcm.edu	37	chr14	23872640	23872640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tcagctggaagatcacccggGacttctccagcaggtctgag	12	12	4	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr14:23872640G>A	ENST00000356287.3	-	9	844	c.815C>T	c.(814-816)tCc>tTc	p.S272F	MYH6_ENST00000405093.3_Missense_Mutation_p.S272F			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	272	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		GATCACCCGGGACTTCTCCAG	0.567																																					p.S272F		Atlas-SNP	.											.	MYH6	274	.	0			c.C815T						.						96	103	100					14																	23872640		2203	4300	6503	SO:0001583	missense	4624	exon10			ACCCGGGACTTCT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.815C>T	chr14.hg19:g.23872640G>A	ENSP00000348634:p.Ser272Phe	60.0	0.0		36.0	13.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	.	14.69	2.611837	0.46631	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.92149	-2.98;-2.98	3.74	3.74	0.42951	Myosin head, motor domain (2);	.	.	.	.	D	0.98201	0.9405	H	0.99970	5.115	0.80722	D	1	P;P	0.51351	0.944;0.944	D;D	0.64506	0.926;0.926	D	0.99120	1.0849	9	0.87932	D	0	.	15.4979	0.75669	0.0:0.0:1.0:0.0	.	272;272	D9YZU2;P13533	.;MYH6_HUMAN	F	272	ENSP00000386041:S272F;ENSP00000348634:S272F	ENSP00000348634:S272F	S	-	2	0	MYH6	22942480	1.000000	0.71417	1.000000	0.80357	0.029000	0.11900	9.358000	0.97109	1.808000	0.52836	0.462000	0.41574	TCC	.	.		0.567	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23872640	G	A	23872640	3	1	185	1	0	0	0	0	1	0	0	0	10047	1174	41	3	5124	3	MYH6	14	23872640	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10		23872640	83476900	97	27548										
MIA2	117153	hgsc.bcm.edu	37	chr14	39716660	39716660	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ccaaagacacagtctgaactAgcatctgagtcagagcacat	8	11	3	4			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr14:39716660A>G	ENST00000280082.3	+	4	1081	c.882A>G	c.(880-882)ctA>ctG	p.L294L	MIA2_ENST00000556784.1_Silent_p.L293L|RP11-407N17.3_ENST00000553728.1_Silent_p.L294L	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	294					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		AGTCTGAACTAGCATCTGAGT	0.413																																					p.L294L		Atlas-SNP	.											.	MIA2	82	.	0			c.A882G						.						122	121	121					14																	39716660		2203	4300	6503	SO:0001819	synonymous_variant	117153	exon4			TGAACTAGCATCT	BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.882A>G	chr14.hg19:g.39716660A>G		67.0	0.0		55.0	25.0	NM_054024	A1L4H0|Q9H6C1	Silent	SNP	ENST00000280082.3	hg19	CCDS9672.1																																																																																			.	.		0.413	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024		G	39716660	A	G	39716660	2	3	185	1	0	0	0	0	0	0	0	1	9573	407	15	2		2	MIA2	14	39716660	Silent	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	15844020	39716660	67632880	98	27549										
ZNF592	9640	hgsc.bcm.edu	37	chr15	85341894	85341894	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cggacacatcctcaagccgcCctggctctcgagttcccact	8	18	2	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr15:85341894C>T	ENST00000560079.2	+	8	3100	c.2812C>T	c.(2812-2814)Cct>Tct	p.P938S	ZNF592_ENST00000299927.3_Missense_Mutation_p.P938S	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	938					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CTCAAGCCGCCCTGGCTCTCG	0.637																																					p.P938S		Atlas-SNP	.											.	ZNF592	95	.	0			c.C2812T						.						32	35	34					15																	85341894		2203	4299	6502	SO:0001583	missense	9640	exon8			AGCCGCCCTGGCT	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"Zinc fingers, C2H2-type"	28986	protein-coding gene	gene with protein product		613624	"spinocerebellar ataxia, autosomal recessive 5"	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.2812C>T	chr15.hg19:g.85341894C>T	ENSP00000452877:p.Pro938Ser	60.0	0.0		32.0	14.0	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	hg19	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	5.299	0.240524	0.10023	.	.	ENSG00000166716	ENST00000299927	T	0.00627	6.12	4.75	1.65	0.23941	.	0.481435	0.23090	N	0.052041	T	0.00412	0.0013	N	0.11560	0.145	0.37541	D	0.918303	B	0.02656	0.0	B	0.08055	0.003	T	0.56643	-0.7945	10	0.18276	T	0.48	-4.0437	4.7023	0.12832	0.0:0.4523:0.3401:0.2076	.	938	Q92610	ZN592_HUMAN	S	938	ENSP00000299927:P938S	ENSP00000299927:P938S	P	+	1	0	ZNF592	83142898	0.458000	0.25760	0.579000	0.28588	0.021000	0.10359	0.364000	0.20325	0.146000	0.19002	-0.137000	0.14449	CCT	.	.		0.637	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		T	85341894	C	T	85341894	3	4	185	1	0	0	0	0	1	0	0	0	18037	623	22	3	2830	3	ZNF592	15	85341894	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10		85341894	17189498	99	27550										
RCCD1	91433	hgsc.bcm.edu	37	chr15	91500107	91500107	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctgccgcgtgagcgcgagctGgagctacaccgctttcgtga	14	13	0	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr15:91500107G>A	ENST00000394258.2	+	2	345	c.143G>A	c.(142-144)tGg>tAg	p.W48*	AC068831.6_ENST00000553321.1_RNA|RCCD1_ENST00000556618.1_Nonsense_Mutation_p.W48*|RCCD1_ENST00000556774.1_Intron|RCCD1_ENST00000555155.1_Nonsense_Mutation_p.W48*	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	48						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			AGCGCGAGCTGGAGCTACACC	0.731																																					p.W48X		Atlas-SNP	.											.	RCCD1	9	.	0			c.G143A						.						9	11	11					15																	91500107		2182	4272	6454	SO:0001587	stop_gained	91433	exon2			CGAGCTGGAGCTA		CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.143G>A	chr15.hg19:g.91500107G>A	ENSP00000377801:p.Trp48*	41.0	0.0		27.0	13.0	NM_001017919	B2RTP9|Q29RX6	Nonsense_Mutation	SNP	ENST00000394258.2	hg19	CCDS32333.1	.	.	.	.	.	.	.	.	.	.	G	37	6.189925	0.97362	.	.	ENSG00000166965	ENST00000394258;ENST00000555155;ENST00000556618	.	.	.	4.07	4.07	0.47477	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	11.9876	0.53157	0.0:0.0:1.0:0.0	.	.	.	.	X	48	.	ENSP00000377801:W48X	W	+	2	0	RCCD1	89301111	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	4.933000	0.63484	2.278000	0.76064	0.555000	0.69702	TGG	.	.		0.731	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544		A	91500107	G	A	91500107	4	1	185	1	0	0	0	0	0	1	0	0	13190	1357	47	3	145	3	RCCD1	15	91500107	Nonsense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	6158213	91500107	11031285	100	27551										
MYLK3	91807	hgsc.bcm.edu	37	chr16	46761274	46761274	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tctgtgatccggtcgaagagCtcacccccgtccacgctgcc	10	17	2	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr16:46761274C>T	ENST00000394809.4	-	8	1903	c.1788G>A	c.(1786-1788)gaG>gaA	p.E596E	MYLK3_ENST00000536476.1_Silent_p.E255E	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	596	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GGTCGAAGAGCTCACCCCCGT	0.572																																					p.E596E		Atlas-SNP	.											.	MYLK3	82	.	0			c.G1788A						.						132	87	102					16																	46761274		2203	4300	6503	SO:0001819	synonymous_variant	91807	exon8			GAAGAGCTCACCC	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.1788G>A	chr16.hg19:g.46761274C>T		61.0	0.0		43.0	17.0	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Silent	SNP	ENST00000394809.4	hg19	CCDS10723.2																																																																																			.	.		0.572	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		T	46761274	C	T	46761274	2	4	185	1	0	0	0	0	0	0	0	1	10067	796	28	3		3	MYLK3	16	46761274	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10		46761274	43593479	101	27552										
CDH11	1009	hgsc.bcm.edu	37	chr16	65032623	65032623	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gagccatcaacgtgtactggGctctctcttctcgatccaac	8	14	4	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr16:65032623G>T	ENST00000268603.4	-	4	980	c.365C>A	c.(364-366)gCc>gAc	p.A122D	CDH11_ENST00000566827.1_5'UTR|CDH11_ENST00000394156.3_Missense_Mutation_p.A122D	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	122	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CGTGTACTGGGCTCTCTCTTC	0.498			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.A122D		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	.	CDH11	260	.	0			c.C365A						.						162	122	136					16																	65032623		2203	4300	6503	SO:0001583	missense	1009	exon4			TACTGGGCTCTCT	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.365C>A	chr16.hg19:g.65032623G>T	ENSP00000268603:p.Ala122Asp	102.0	0.0		77.0	39.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	hg19	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.187190	0.78789	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000538390;ENST00000536902	T;T	0.60040	0.22;0.22	5.87	5.87	0.94306	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.70202	0.3197	L	0.38692	1.165	0.80722	D	1	D;P	0.89917	1.0;0.577	D;B	0.83275	0.996;0.203	T	0.70809	-0.4771	10	0.87932	D	0	.	19.5705	0.95413	0.0:0.0:1.0:0.0	.	122;122	P55287-2;P55287	.;CAD11_HUMAN	D	122;122;105;122	ENSP00000268603:A122D;ENSP00000377711:A122D	ENSP00000268603:A122D	A	-	2	0	CDH11	63590124	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.420000	0.97426	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.498	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		T	65032623	G	T	65032623	3	4	185	1	0	0	0	0	1	0	0	0	3099	1203	42	3	2065	3	CDH11	16	65032623	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	18271349	65032623	25322130	102	27553										
TP53	7157	hgsc.bcm.edu	37	chr17	7577121	7577121	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cccaggacaggcacaaacacGcacctcaaagctgttccgtc	8	16	1	0	rs121913343		TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr17:7577121G>T	ENST00000269305.4	-	8	1006	c.817C>A	c.(817-819)Cgt>Agt	p.R273S	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R273S|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R273S|TP53_ENST00000420246.2_Missense_Mutation_p.R273S|TP53_ENST00000359597.4_Missense_Mutation_p.R273S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCACAAACACGCACCTCAAAG	0.542	R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R273S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,adenocarcinoma,+1,1	TP53	33396	.	533	Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2)	central_nervous_system(117)|large_intestine(108)|ovary(32)|haematopoietic_and_lymphoid_tissue(31)|upper_aerodigestive_tract(30)|stomach(25)|urinary_tract(23)|lung(21)|breast(21)|liver(20)|endometrium(17)|oesophagus(17)|bone(16)|pancreas(15)|prostate(8)|skin(7)|cervix(6)|biliary_tract(6)|kidney(3)|thyroid(3)|vulva(2)|genital_tract(1)|penis(1)|adrenal_gland(1)|salivary_gland(1)|small_intestine(1)	c.C817A	GRCh37	CM010471|CM010473|CM951233	TP53	M	rs121913343	.						65	56	59					17																	7577121		2203	4300	6503	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AAACACGCACCTC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.817C>A	chr17.hg19:g.7577121G>T	ENSP00000269305:p.Arg273Ser	74.0	0.0		49.0	19.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.492993	0.64186	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.92	3.95	0.45737	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.90759	3.145	0.54753	D	0.999989	D;D;D;D	0.89917	0.999;1.0;0.999;1.0	D;D;D;D	0.83275	0.993;0.994;0.996;0.991	D	0.96877	0.9643	10	0.87932	D	0	-11.9995	11.2235	0.48869	0.0895:0.0:0.9105:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	S	273;273;273;273;273;262;141	ENSP00000352610:R273S;ENSP00000269305:R273S;ENSP00000398846:R273S;ENSP00000391127:R273S;ENSP00000391478:R273S;ENSP00000425104:R141S	ENSP00000269305:R273S	R	-	1	0	TP53	7517846	1.000000	0.71417	0.066000	0.19879	0.723000	0.41478	4.540000	0.60664	1.299000	0.44798	0.462000	0.41574	CGT	.	.		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577121	G	T	7577121	3	4	185	1	0	0	0	0	1	0	0	0	16396	1087	38	1	469	1	TP53	17	7577121	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10		7577121	73618089	103	27554										
ACLY	47	hgsc.bcm.edu	37	chr17	40049360	40049360	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tcaaagtccagcatgccttgCacggcccgggtctgcatgcc	11	15	2	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr17:40049360C>A	ENST00000352035.2	-	15	1657	c.1527G>T	c.(1525-1527)gtG>gtT	p.V509V	ACLY_ENST00000353196.1_Silent_p.V499V|ACLY_ENST00000590151.1_Silent_p.V509V|ACLY_ENST00000537919.1_Silent_p.V238V|ACLY_ENST00000393896.2_Silent_p.V499V	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	509					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				GCATGCCTTGCACGGCCCGGG	0.587																																					p.V509V	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.G1527T						.						106	99	101					17																	40049360		2203	4300	6503	SO:0001819	synonymous_variant	47	exon15			GCCTTGCACGGCC	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.1527G>T	chr17.hg19:g.40049360C>A		62.0	0.0		57.0	15.0	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Silent	SNP	ENST00000352035.2	hg19	CCDS11412.1																																																																																			.	.		0.587	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		A	40049360	C	A	40049360	2	1	185	1	0	0	0	0	0	0	0	1	143	697	25	3		3	ACLY	17	40049360	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	32472239	40049360	41145850	104	27555										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48683348	48683348	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gccgaggccagttaccggtgGgtccggcacaagtacaactt	13	12	0	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr17:48683348G>A	ENST00000359106.5	+	23	4386	c.4386G>A	c.(4384-4386)tgG>tgA	p.W1462*	CACNA1G_ENST00000503485.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000515165.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000510366.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000352832.5_Nonsense_Mutation_p.W1439*|CACNA1G_ENST00000358244.5_Nonsense_Mutation_p.W1439*|CACNA1G_ENST00000507609.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000514079.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000507336.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000513689.2_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000515411.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000513964.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000507896.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000442258.2_Nonsense_Mutation_p.W1439*|CACNA1G_ENST00000360761.4_Nonsense_Mutation_p.W1439*|CACNA1G_ENST00000354983.4_Nonsense_Mutation_p.W1439*|CACNA1G_ENST00000514181.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000429973.2_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000514717.1_Nonsense_Mutation_p.W1439*|CACNA1G_ENST00000505165.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000507510.2_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000416767.4_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000515765.1_Nonsense_Mutation_p.W1462*|CACNA1G_ENST00000510115.1_Nonsense_Mutation_p.W1439*|CACNA1G_ENST00000502264.1_Nonsense_Mutation_p.W1439*|CACNA1G_ENST00000512389.1_Nonsense_Mutation_p.W1462*	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1462					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GTTACCGGTGGGTCCGGCACA	0.582																																					p.W1462X		Atlas-SNP	.											.	CACNA1G	659	.	0			c.G4386A						.						45	52	50					17																	48683348		2177	4277	6454	SO:0001587	stop_gained	8913	exon23			CCGGTGGGTCCGG	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.4386G>A	chr17.hg19:g.48683348G>A	ENSP00000352011:p.Trp1462*	85.0	0.0		79.0	22.0	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Nonsense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	g	44	10.904226	0.99486	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896;ENST00000506520	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.279	0.94044	0.0:0.0:1.0:0.0	.	.	.	.	X	1439;1439;1462;1439;1439;1439;1462;1462;1439;1462;1462;1462;1462;1462;1462;1439;1462;1462;1462;1462;1439;1462;1462;1462;1462;1462;277	.	ENSP00000339302:W1439X	W	+	3	0	CACNA1G	46038347	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	9.869000	0.99810	2.560000	0.86352	0.655000	0.94253	TGG	.	.		0.582	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		A	48683348	G	A	48683348	4	1	185	1	0	0	0	0	0	1	0	0	2546	1241	43	3	4476	3	CACNA1G	17	48683348	Nonsense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	8633988	48683348	32511862	105	27556										
SFRS1	6426	hgsc.bcm.edu	37	chr17	56082796	56082796	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	agagcgagatctgctatgacGgggagaatagcgtggtgatc	16	6	1	5			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr17:56082796G>T	ENST00000258962.4	-	4	926	c.718C>A	c.(718-720)Cgt>Agt	p.R240S	SRSF1_ENST00000582730.2_3'UTR|SRSF1_ENST00000581497.1_5'Flank|SRSF1_ENST00000584773.1_Missense_Mutation_p.R240S|RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000585096.1_Intron	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	240	Arg/Ser-rich (RS domain).|Interacts with SAFB1.				cardiac muscle contraction (GO:0060048)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA 3'-end processing (GO:0031124)|mRNA 5'-splice site recognition (GO:0000395)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CTGCTATGACGGGGAGAATAG	0.458																																					p.R240S		Atlas-SNP	.											.	SRSF1	41	.	0			c.C718A						.						207	183	191					17																	56082796		2203	4300	6503	SO:0001583	missense	6426	exon4			TATGACGGGGAGA		CCDS11600.1, CCDS58580.1	17q22	2013-02-12	2010-06-22	2010-06-22	ENSG00000136450	ENSG00000136450		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10780	protein-coding gene	gene with protein product	"splicing factor 2", "pre-mRNA-splicing factor SF2, P33 subunit", "alternate splicing factor", "SR splicing factor 1"	600812	"splicing factor, arginine/serine-rich 1"	SFRS1		8530103, 20516191	Standard	NM_006924		Approved	ASF, SF2, SRp30a, SF2p33, MGC5228	uc002ivi.3	Q07955		ENST00000258962.4:c.718C>A	chr17.hg19:g.56082796G>T	ENSP00000258962:p.Arg240Ser	51.0	0.0		68.0	18.0	NM_006924	B2R6Z7|D3DTZ3|Q13809	Missense_Mutation	SNP	ENST00000258962.4	hg19	CCDS11600.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627224	0.28978	.	.	ENSG00000136450	ENST00000258962	T	0.06371	3.31	5.52	5.52	0.82312	.	1.477640	0.03973	N	0.291997	T	0.12944	0.0314	N	0.17474	0.49	0.80722	D	1	D	0.53745	0.962	P	0.53450	0.726	T	0.48747	-0.9008	10	0.20046	T	0.44	.	19.8212	0.96595	0.0:0.0:1.0:0.0	.	240	Q07955	SRSF1_HUMAN	S	240	ENSP00000258962:R240S	ENSP00000258962:R240S	R	-	1	0	SRSF1	53437795	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.282000	0.95840	2.759000	0.94783	0.557000	0.71058	CGT	.	.		0.458	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924		T	56082796	G	T	56082796	3	4	185	1	0	0	0	0	1	0	0	0	14180	1116	39	1	32	1	SFRS1	17	56082796	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	7399448	56082796	25112414	106	27557										
MAP3K3	4215	hgsc.bcm.edu	37	chr17	61771085	61771085	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ttttgtggaggctcgccagaGaccttcagctgaggagctgc	14	10	1	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr17:61771085G>A	ENST00000361733.3	+	16	2149	c.1829G>A	c.(1828-1830)aGa>aAa	p.R610K	MAP3K3_ENST00000361357.3_Missense_Mutation_p.R641K|MAP3K3_ENST00000584573.1_Missense_Mutation_p.R637K|MAP3K3_ENST00000577395.1_Missense_Mutation_p.R606K|MAP3K3_ENST00000579585.1_Missense_Mutation_p.R641K	NM_002401.3	NP_002392.2	Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3	610	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)			breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	28						GCTCGCCAGAGACCTTCAGCT	0.592																																					p.R641K		Atlas-SNP	.											.	MAP3K3	56	.	0			c.G1922A						.						79	75	77					17																	61771085		2203	4300	6503	SO:0001583	missense	4215	exon17			GCCAGAGACCTTC	U78876	CCDS32701.1, CCDS32702.1	17q	2011-06-09				ENSG00000198909		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6855	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 3", "MAPK/ERK kinase kinase 3"	602539		MEKK3		9006902	Standard	NM_002401		Approved	MAPKKK3	uc002jbf.3	Q99759		ENST00000361733.3:c.1829G>A	chr17.hg19:g.61771085G>A	ENSP00000354485:p.Arg610Lys	42.0	0.0		36.0	10.0	NM_203351	B2RCW2|D3DU15|Q5BKZ6|Q8N3I9	Missense_Mutation	SNP	ENST00000361733.3	hg19	CCDS32702.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.882528	0.91740	.	.	ENSG00000198909	ENST00000361357;ENST00000361733	T;T	0.70869	-0.52;-0.52	4.69	4.69	0.59074	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.89976	0.6871	H	0.97390	3.995	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.93930	0.7213	10	0.87932	D	0	.	17.6147	0.88064	0.0:0.0:1.0:0.0	.	606;578;610;641	Q1PBM3;Q96HN9;Q99759;Q99759-2	.;.;M3K3_HUMAN;.	K	641;610	ENSP00000354927:R641K;ENSP00000354485:R610K	ENSP00000354927:R641K	R	+	2	0	MAP3K3	59124817	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.835000	0.99442	2.148000	0.66965	0.561000	0.74099	AGA	.	.		0.592	MAP3K3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443867.1	NM_002401		A	61771085	G	A	61771085	3	1	185	1	0	0	0	0	1	0	0	0	9260	942	33	3	1988	3	MAP3K3	17	61771085	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	5688289	61771085	19424125	107	27558										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62045561	62045561	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gtggtgttggtgtcgttgaaCggcgggggccagcgcacaca	18	9	0	1	rs560230431		TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr17:62045561C>T	ENST00000435607.1	-	6	934	c.858G>A	c.(856-858)ccG>ccA	p.P286P	SCN4A_ENST00000578147.1_Silent_p.P286P	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	286					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGTCGTTGAACGGCGGGGGCC	0.542													C|||	1	0.000199681	0	0	5008	,	,		20313	0		0.001	False		,,,				2504	0				p.P286P		Atlas-SNP	.											.	SCN4A	205	.	0			c.G858A						.						185	186	185					17																	62045561		2180	4275	6455	SO:0001819	synonymous_variant	6329	exon6			GTTGAACGGCGGG	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.858G>A	chr17.hg19:g.62045561C>T		132.0	0.0		97.0	20.0	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	hg19	CCDS45761.1																																																																																			.	.		0.542	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62045561	C	T	62045561	2	4	185	1	0	0	0	0	0	0	0	1	13935	523	19	1		1	SCN4A	17	62045561	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	274476	62045561	19149649	108	27559										
MAP2K6	5608	hgsc.bcm.edu	37	chr17	67521046	67521046	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tctgtcttctttccagcctgAaagaataaacccagagctca	6	12	4	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr17:67521046A>G	ENST00000590474.1	+	9	955	c.668A>G	c.(667-669)gAa>gGa	p.E223G	MAP2K6_ENST00000589647.1_Missense_Mutation_p.E167G	NM_002758.3	NP_002749.2	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6	223	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|cardiac muscle contraction (GO:0060048)|cell cycle arrest (GO:0007050)|cellular response to sorbitol (GO:0072709)|DNA damage induced protein phosphorylation (GO:0006975)|innate immune response (GO:0045087)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to ischemia (GO:0002931)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	20	Breast(10;6.05e-10)					TTCCAGCCTGAAAGAATAAAC	0.463																																					p.E223G		Atlas-SNP	.											.	MAP2K6	41	.	0			c.A668G						.						89	82	84					17																	67521046		2203	4300	6503	SO:0001583	missense	5608	exon9			AGCCTGAAAGAAT	U39064	CCDS11686.1	17q	2011-06-09						"Mitogen-activated protein kinase cascade / Kinase kinases"	6846	protein-coding gene	gene with protein product	"protein kinase, mitogen-activated, kinase 6 (MAP kinase kinase 6)"	601254		PRKMK6		8621675	Standard	XM_005257515		Approved	MEK6, MKK6, SAPKK3, MAPKK6	uc002jij.3	P52564		ENST00000590474.1:c.668A>G	chr17.hg19:g.67521046A>G	ENSP00000468348:p.Glu223Gly	50.0	0.0		47.0	22.0	NM_002758		Missense_Mutation	SNP	ENST00000590474.1	hg19	CCDS11686.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.675245	0.88445	.	.	ENSG00000108984	ENST00000359094	.	.	.	5.2	5.2	0.72013	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.053993	0.64402	D	0.000001	D	0.88164	0.6363	H	0.98407	4.225	0.80722	D	1	D	0.69078	0.997	D	0.68483	0.958	D	0.92435	0.5957	8	.	.	.	-28.0371	14.3319	0.66564	1.0:0.0:0.0:0.0	.	223	P52564	MP2K6_HUMAN	G	223	.	.	E	+	2	0	MAP2K6	65032641	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.021000	0.93673	2.302000	0.77476	0.533000	0.62120	GAA	.	.		0.463	MAP2K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450689.1	NM_002758		G	67521046	A	G	67521046	3	3	185	1	0	0	0	0	1	0	0	0	9250	246	9	2	702	2	MAP2K6	17	67521046	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	5475485	67521046	13674164	109	27560										
COLEC12	81035	hgsc.bcm.edu	37	chr18	346626	346626	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aagagctggaagcgttcctcCagttggttgaacttgatggc	13	8	0	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr18:346626C>T	ENST00000400256.3	-	5	1203	c.996G>A	c.(994-996)ctG>ctA	p.L332L		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	332					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				AGCGTTCCTCCAGTTGGTTGA	0.468																																					p.L332L		Atlas-SNP	.											.	COLEC12	121	.	0			c.G996A						.						159	128	139					18																	346626		2203	4300	6503	SO:0001819	synonymous_variant	81035	exon5			TTCCTCCAGTTGG	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"Collectins"	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.996G>A	chr18.hg19:g.346626C>T		59.0	0.0		60.0	10.0	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Silent	SNP	ENST00000400256.3	hg19	CCDS32782.1																																																																																			.	.		0.468	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			T	346626	C	T	346626	2	4	185	1	0	0	0	0	0	0	0	1	3714	581	21	3		3	COLEC12	18	346626	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10		346626	77730622	110	27561										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8718623	8718623	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aggtggatggtgagcttattCgaagcctggagcaggacttg	16	6	0	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr18:8718623C>T	ENST00000306329.11	+	2	1255	c.1255C>T	c.(1255-1257)Cga>Tga	p.R419*	SOGA2_ENST00000517570.1_Nonsense_Mutation_p.R59*|SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000359865.3_Nonsense_Mutation_p.R59*|Y_RNA_ENST00000516510.1_RNA|SOGA2_ENST00000400050.3_Nonsense_Mutation_p.R59*																							TGAGCTTATTCGAAGCCTGGA	0.572																																					p.R59X		Atlas-SNP	.											.	.	.	.	0			c.C175T						.						121	94	103					18																	8718623		2203	4300	6503	SO:0001587	stop_gained	23255	exon3			CTTATTCGAAGCC																												ENST00000306329.11:c.1255C>T	chr18.hg19:g.8718623C>T	ENSP00000305027:p.Arg419*	79.0	0.0		55.0	21.0	NM_015210		Nonsense_Mutation	SNP	ENST00000306329.11	hg19		.	.	.	.	.	.	.	.	.	.	C	21.2	4.110217	0.77210	.	.	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050	.	.	.	4.87	-2.59	0.06209	.	0.000000	0.41294	D	0.000909	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.7107	17.161	0.86803	0.8109:0.1891:0.0:0.0	.	.	.	.	X	80;59;59;59	.	ENSP00000305027:R80X	R	+	1	2	CCDC165	8708623	0.924000	0.31332	0.708000	0.30435	0.470000	0.32858	0.440000	0.21592	-0.241000	0.09681	0.462000	0.41574	CGA	.	.		0.572	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			T	8718623	C	T	8718623	4	4	185	1	0	0	0	0	0	1	0	0	8203	876	31	1	177	1	KIAA0802	18	8718623	Nonsense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	8371997	8718623	69358625	111	27562										
ANGPTL4	51129	hgsc.bcm.edu	37	chr19	8436287	8436287	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tagcctgcagctcactgcacCcgtggccggccagctgggcg	14	16	1	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr19:8436287C>A	ENST00000301455.2	+	6	1091	c.920C>A	c.(919-921)cCc>cAc	p.P307H	RAB11B-AS1_ENST00000597785.1_RNA|ANGPTL4_ENST00000541807.1_Missense_Mutation_p.P140H|ANGPTL4_ENST00000393962.2_Missense_Mutation_p.P269H|RAB11B-AS1_ENST00000593581.1_RNA	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	307	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		P -> S. {ECO:0000269|PubMed:17322881}.		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular lipid metabolic process (GO:0044255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of lipoprotein lipase activity (GO:0051005)|positive regulation of angiogenesis (GO:0045766)|protein homooligomerization (GO:0051260)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	enzyme inhibitor activity (GO:0004857)			large_intestine(1)|lung(1)|ovary(2)|skin(2)	6						CTCACTGCACCCGTGGCCGGC	0.677																																					p.P307H		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.C920A						.						45	40	41					19																	8436287		2203	4299	6502	SO:0001583	missense	51129	exon6			CTGCACCCGTGGC	AF202636	CCDS12200.1, CCDS42493.1	19p13.3	2013-10-07				ENSG00000167772		"Fibrinogen C domain containing"	16039	protein-coding gene	gene with protein product	"fasting-induced adipose factor", "hepatic angiopoietin-related protein", "PPARG angiopoietin related protein", "hepatic fibrinogen/angiopoietin-related protein", "peroxisome proliferator-activated receptor (PPAR) gamma induced angiopoietin-related protein", "angiopoietin-related protein 4"	605910				10698685, 10866690, 23960078	Standard	NM_139314		Approved	pp1158, PGAR, ARP4, HFARP, FIAF, NL2	uc002mjq.1	Q9BY76		ENST00000301455.2:c.920C>A	chr19.hg19:g.8436287C>A	ENSP00000301455:p.Pro307His	71.0	0.0		56.0	16.0	NM_139314	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	hg19	CCDS12200.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.134569	0.37630	.	.	ENSG00000167772	ENST00000301455;ENST00000393962;ENST00000541807	T;T;T	0.20332	2.08;2.08;2.08	5.09	4.05	0.47172	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	1.501490	0.03608	N	0.234343	T	0.31979	0.0814	L	0.28504	0.86	0.09310	N	0.999993	D;D	0.53151	0.958;0.958	P;P	0.60068	0.868;0.868	T	0.31280	-0.9949	10	0.13853	T	0.58	.	11.7429	0.51803	0.0:0.9133:0.0:0.0867	.	269;307	A8MY84;Q9BY76	.;ANGL4_HUMAN	H	307;269;140	ENSP00000301455:P307H;ENSP00000377534:P269H;ENSP00000439833:P140H	ENSP00000301455:P307H	P	+	2	0	ANGPTL4	8342287	0.000000	0.05858	0.326000	0.25389	0.003000	0.03518	0.588000	0.23924	2.363000	0.80096	0.555000	0.69702	CCC	.	.		0.677	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314		A	8436287	C	A	8436287	3	1	185	1	0	0	0	0	1	0	0	0	616	623	22	3	942	3	ANGPTL4	19	8436287	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10		8436287	50692696	112	27563										
LGALS4	3960	hgsc.bcm.edu	37	chr19	39299453	39299453	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tttttgaagggcatgctcctCttcctctcctcgctgcccca	7	16	2	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr19:39299453C>T	ENST00000307751.4	-	3	747	c.270G>A	c.(268-270)aaG>aaA	p.K90K	LGALS4_ENST00000597803.1_Intron	NM_006149.3	NP_006140.1	P56470	LEG4_HUMAN	lectin, galactoside-binding, soluble, 4	90	Galectin 1. {ECO:0000255|PROSITE- ProRule:PRU00639}.				cell adhesion (GO:0007155)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17	all_cancers(60;1.02e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GCATGCTCCTCTTCCTCTCCT	0.567																																					p.K90K		Atlas-SNP	.											.	LGALS4	39	.	0			c.G270A						.						197	154	168					19																	39299453		2203	4300	6503	SO:0001819	synonymous_variant	3960	exon3			GCTCCTCTTCCTC		CCDS12521.1	19q13.2	2014-03-19	2008-07-25		ENSG00000171747	ENSG00000171747		"Lectins, galactoside-binding"	6565	protein-coding gene	gene with protein product	"galectin 4"	602518				8063692	Standard	NM_006149		Approved	GAL4	uc002ojg.3	P56470	OTTHUMG00000182608	ENST00000307751.4:c.270G>A	chr19.hg19:g.39299453C>T		95.0	0.0		132.0	21.0	NM_006149		Silent	SNP	ENST00000307751.4	hg19	CCDS12521.1																																																																																			.	.		0.567	LGALS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462641.1	NM_006149		T	39299453	C	T	39299453	2	4	185	1	0	0	0	0	0	0	0	1	8754	912	32	3		3	LGALS4	19	39299453	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	30863166	39299453	19829530	113	27564										
ETHE1	23474	hgsc.bcm.edu	37	chr19	44015587	44015587	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gctggataaaggagctggtcAccttgctggaagtctgtccg	14	9	2	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr19:44015587A>T	ENST00000292147.2	-	4	572		c.e4+1		ETHE1_ENST00000600651.1_Splice_Site	NM_014297.3	NP_055112.2	O95571	ETHE1_HUMAN	ethylmalonic encephalopathy 1						cellular nitrogen compound metabolic process (GO:0034641)|glutathione metabolic process (GO:0006749)|hydrogen sulfide metabolic process (GO:0070813)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|sulfur dioxygenase activity (GO:0050313)			central_nervous_system(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	5		Prostate(69;0.0153)				GGAGCTGGTCACCTTGCTGGA	0.493																																					.		Atlas-SNP	.											.	ETHE1	7	.	0			c.505+2T>A						.						107	76	87					19																	44015587		2203	4300	6503	SO:0001630	splice_region_variant	23474	exon5			CTGGTCACCTTGC		CCDS12622.1	19q13.32	2014-06-20				ENSG00000105755	1.13.11.18		23287	protein-coding gene	gene with protein product		608451				19136963	Standard	NM_014297		Approved	YF13H12, HSCO	uc002owp.3	O95571		ENST00000292147.2:c.505+1T>A	chr19.hg19:g.44015587A>T		62.0	0.0		77.0	23.0	NM_014297	Q96HR0|Q9H001	Splice_Site	SNP	ENST00000292147.2	hg19	CCDS12622.1	.	.	.	.	.	.	.	.	.	.	A	17.01	3.278724	0.59758	.	.	ENSG00000105755	ENST00000292147	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1154	0.59297	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ETHE1	48707427	1.000000	0.71417	0.973000	0.42090	0.523000	0.34469	7.965000	0.87945	2.265000	0.75225	0.449000	0.29647	.	.	.		0.493	ETHE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463184.1	NM_014297	Intron	T	44015587	A	T	44015587	5	4	185	1	0	0	0	0	0	0	1	0	5274	173	6	4	273	4	ETHE1	19	44015587	Splice_Site	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10	4716134	44015587	15113396	114	27565										
LILRB5	10990	hgsc.bcm.edu	37	chr19	54759290	54759290	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	ctgggagagcccagcctgggGctgctggccagagccctgga	17	13	0	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr19:54759290G>T	ENST00000316219.5	-	5	918	c.811C>A	c.(811-813)Ccc>Acc	p.P271T	LILRB5_ENST00000345866.6_Missense_Mutation_p.P171T|LILRB5_ENST00000449561.2_Missense_Mutation_p.P271T|LILRB5_ENST00000450632.1_Missense_Mutation_p.P262T	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	271	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCAGCCTGGGGCTGCTGGCCA	0.627																																					p.P271T		Atlas-SNP	.											.	LILRB5	176	.	0			c.C811A						.						45	46	46					19																	54759290		2203	4300	6503	SO:0001583	missense	10990	exon5			CCTGGGGCTGCTG	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.811C>A	chr19.hg19:g.54759290G>T	ENSP00000320390:p.Pro271Thr	124.0	0.0		177.0	53.0	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	hg19	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	G	9.724	1.160340	0.21454	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00691	5.84;5.84;5.84;5.84	2.19	-4.38	0.03622	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.405960	0.04922	N	0.455206	T	0.01558	0.0050	L	0.46567	1.45	0.09310	N	1	P;P;B;P;D	0.57257	0.952;0.591;0.073;0.944;0.979	P;P;B;P;P	0.57720	0.826;0.51;0.268;0.696;0.817	T	0.37430	-0.9706	10	0.28530	T	0.3	.	4.0167	0.09647	0.1434:0.0:0.2763:0.5803	.	262;162;171;271;271	C9JMK7;Q8NF80;O75023-2;O75023-3;O75023	.;.;.;.;LIRB5_HUMAN	T	271;262;271;171	ENSP00000320390:P271T;ENSP00000414225:P262T;ENSP00000406478:P271T;ENSP00000263430:P171T	ENSP00000320390:P271T	P	-	1	0	LILRB5	59451102	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.421000	0.07053	-0.890000	0.03945	-0.493000	0.04662	CCC	.	.		0.627	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			T	54759290	G	T	54759290	3	4	185	1	0	0	0	0	1	0	0	0	8803	1203	42	3	1000	3	LILRB5	19	54759290	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	10743703	54759290	4369693	115	27566										
ZNF582	147948	hgsc.bcm.edu	37	chr19	56895232	56895232	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aagtcacagtcacaattagcCtaggctaatgggctttcccc	8	12	2	0			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr19:56895232C>T	ENST00000301310.4	-	5	1712	c.1554G>A	c.(1552-1554)taG>taA	p.*518*	ZNF582_ENST00000586929.1_Silent_p.*518*	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		CACAATTAGCCTAGGCTAATG	0.413																																					p.X518X	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.G1554A						.						128	123	125					19																	56895232		2203	4300	6503	SO:0001819	synonymous_variant	147948	exon5			ATTAGCCTAGGCT	AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"Zinc fingers, C2H2-type", "-"	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.1554G>A	chr19.hg19:g.56895232C>T		38.0	0.0		44.0	20.0	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Silent	SNP	ENST00000301310.4	hg19	CCDS33121.1																																																																																			.	.		0.413	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		T	56895232	C	T	56895232	2	4	185	1	0	0	0	0	0	0	0	1	18029	692	24	3		3	ZNF582	19	56895232	Silent	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	2135942	56895232	2233751	116	27567										
ZNF419	79744	hgsc.bcm.edu	37	chr19	58004589	58004589	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aatatttacttgttcagcacCagagactacatgctgggaaa	8	8	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr19:58004589C>G	ENST00000221735.7	+	5	850	c.664C>G	c.(664-666)Cag>Gag	p.Q222E	ZNF419_ENST00000354197.4_Missense_Mutation_p.Q210E|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000442920.2_Missense_Mutation_p.Q209E|ZNF419_ENST00000426954.2_Missense_Mutation_p.Q210E|ZNF419_ENST00000347466.6_Missense_Mutation_p.Q190E|ZNF419_ENST00000424930.2_Missense_Mutation_p.Q223E|ZNF419_ENST00000415379.2_Missense_Mutation_p.Q176E			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	222					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		TGTTCAGCACCAGAGACTACA	0.408																																					p.Q223E		Atlas-SNP	.											.	ZNF419	134	.	0			c.C667G						.						71	74	73					19																	58004589		2202	4300	6502	SO:0001583	missense	79744	exon5			CAGCACCAGAGAC	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"Zinc fingers, C2H2-type", "-"	20648	protein-coding gene	gene with protein product			"zinc finger protein 419A"	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.664C>G	chr19.hg19:g.58004589C>G	ENSP00000221735:p.Gln222Glu	113.0	0.0		147.0	33.0	NM_001098491	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	hg19	CCDS54326.1	.	.	.	.	.	.	.	.	.	.	C	8.650	0.898020	0.17686	.	.	ENSG00000105136	ENST00000284020;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000442920;ENST00000517598;ENST00000347466;ENST00000415379;ENST00000221735	T;T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6;0.6	2.36	1.26	0.21427	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.48642	0.1511	N	0.20610	0.595	0.22185	N	0.999301	P;P;D;P;B;P;B	0.53619	0.664;0.906;0.961;0.906;0.043;0.952;0.043	B;P;P;P;B;P;B	0.61070	0.444;0.836;0.883;0.836;0.004;0.813;0.004	T	0.30592	-0.9973	9	0.54805	T	0.06	.	4.72	0.12913	0.2504:0.5043:0.2453:0.0	.	176;176;209;210;223;190;222	E9PFX9;B4DXU7;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;.;ZN419_HUMAN	E	225;223;210;210;209;223;190;176;222	ENSP00000388864:Q223E;ENSP00000390916:Q210E;ENSP00000346136:Q210E;ENSP00000414709:Q209E;ENSP00000299860:Q190E;ENSP00000392129:Q176E;ENSP00000221735:Q222E	ENSP00000221735:Q222E	Q	+	1	0	ZNF419	62696401	0.000000	0.05858	0.947000	0.38551	0.116000	0.19942	-0.322000	0.08007	0.294000	0.22547	0.205000	0.17691	CAG	.	.		0.408	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691		G	58004589	C	G	58004589	3	3	185	1	0	0	0	0	1	0	0	0	17911	595	21	4	685	4	ZNF419	19	58004589	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10	1109357	58004589	1124394	117	27568										
SLC27A5	10998	hgsc.bcm.edu	37	chr19	59010879	59010879	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	cggaaggtgtccccgaggcgGtcgcggaagtagaggaagcc	18	10	0	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr19:59010879G>A	ENST00000263093.2	-	7	1756	c.1647C>T	c.(1645-1647)gaC>gaT	p.D549D	SLC27A5_ENST00000594786.1_5'Flank|SLC27A5_ENST00000601355.1_Silent_p.D465D|SLC27A5_ENST00000599700.1_5'Flank	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	549					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		CCCCGAGGCGGTCGCGGAAGT	0.652																																					p.D549D		Atlas-SNP	.											.	SLC27A5	58	.	0			c.C1647T						.						51	49	50					19																	59010879		2203	4300	6503	SO:0001819	synonymous_variant	10998	exon7			GAGGCGGTCGCGG	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"Acyl-CoA synthetase family", "Solute carriers"	10999	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 3"	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.1647C>T	chr19.hg19:g.59010879G>A		75.0	0.0		91.0	21.0	NM_012254	B3KVP6|B4DPQ1	Silent	SNP	ENST00000263093.2	hg19	CCDS12983.1																																																																																			.	.		0.652	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		A	59010879	G	A	59010879	2	1	185	1	0	0	0	0	0	0	0	1	14544	1252	44	3		3	SLC27A5	19	59010879	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	1006290	59010879	118104	118	27569										
MACROD2	140733	hgsc.bcm.edu	37	chr20	15967381	15967381	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gttttgaacaggacaagagaAtgattcaacgaagaatgaaa	10	4	1	5			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr20:15967381A>T	ENST00000310348.4	+	14	995	c.995A>T	c.(994-996)aAt>aTt	p.N332I	MACROD2_ENST00000378058.3_Missense_Mutation_p.N97I|MACROD2_ENST00000402914.1_Missense_Mutation_p.N97I|MACROD2_ENST00000407045.3_De_novo_Start_OutOfFrame|MACROD2_ENST00000217246.4_Missense_Mutation_p.N332I			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	332	Glu-rich.				brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				GGACAAGAGAATGATTCAACG	0.333																																					p.N332I		Atlas-SNP	.											.	MACROD2	34	.	0			c.A995T						.						59	56	57					20																	15967381		2203	4300	6503	SO:0001583	missense	140733	exon14			AAGAGAATGATTC	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"chromosome 20 open reading frame 133"	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.995A>T	chr20.hg19:g.15967381A>T	ENSP00000309809:p.Asn332Ile	232.0	0.0		173.0	61.0	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	hg19	CCDS13120.2	.	.	.	.	.	.	.	.	.	.	A	13.08	2.129594	0.37630	.	.	ENSG00000172264	ENST00000217246;ENST00000310348;ENST00000402914;ENST00000378058	T;T;T;T	0.51325	2.25;2.26;0.71;0.71	5.7	0.912	0.19349	.	0.499688	0.18664	N	0.134651	T	0.33702	0.0872	L	0.51422	1.61	0.24148	N	0.9957	B;B	0.32467	0.255;0.372	B;B	0.30179	0.052;0.112	T	0.13150	-1.0520	10	0.28530	T	0.3	-8.5223	5.0353	0.14430	0.6273:0.1449:0.2278:0.0	.	332;332	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	I	332;332;97;97	ENSP00000217246:N332I;ENSP00000309809:N332I;ENSP00000385290:N97I;ENSP00000367297:N97I	ENSP00000217246:N332I	N	+	2	0	MACROD2	15915381	1.000000	0.71417	0.954000	0.39281	0.726000	0.41606	2.032000	0.41127	0.097000	0.17492	0.477000	0.44152	AAT	.	.		0.333	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676		T	15967381	A	T	15967381	3	4	185	1	0	0	0	0	1	0	0	0	9155	101	4	4	1049	4	MACROD2	20	15967381	Missense_Mutation	SNP	A	TCGA-DD-AADB-01A-11D-A40R-10		15967381	47058139	119	27570										
PREX1	57580	hgsc.bcm.edu	37	chr20	47271890	47271890	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tctggaagcacagtgtgtccGgctggtcggggattttgatg	16	7	1	1			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr20:47271890G>T	ENST00000371941.3	-	19	2169	c.2147C>A	c.(2146-2148)cCg>cAg	p.P716Q	PREX1_ENST00000396220.1_Missense_Mutation_p.P716Q	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	716					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CAGTGTGTCCGGCTGGTCGGG	0.572																																					p.P716Q		Atlas-SNP	.											.	PREX1	441	.	0			c.C2147A						.						107	79	89					20																	47271890		2203	4300	6503	SO:0001583	missense	57580	exon19			GTGTCCGGCTGGT	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2147C>A	chr20.hg19:g.47271890G>T	ENSP00000361009:p.Pro716Gln	92.0	0.0		87.0	30.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	G	15.96	2.985507	0.53934	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.50277	0.75;0.75	4.72	4.72	0.59763	PDZ/DHR/GLGF (1);	0.000000	0.53938	U	0.000044	T	0.59280	0.2182	L	0.43923	1.385	0.45762	D	0.998652	P;D	0.69078	0.922;0.997	P;D	0.68353	0.491;0.957	T	0.61372	-0.7076	10	0.56958	D	0.05	.	14.2325	0.65903	0.0:0.15:0.85:0.0	.	716;13	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	Q	716	ENSP00000361009:P716Q;ENSP00000379522:P716Q	ENSP00000361009:P716Q	P	-	2	0	PREX1	46705297	1.000000	0.71417	1.000000	0.80357	0.282000	0.26991	4.046000	0.57376	2.158000	0.67659	0.563000	0.77884	CCG	.	.		0.572	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47271890	G	T	47271890	3	4	185	1	0	0	0	0	1	0	0	0	12488	1116	39	1	2920	1	PREX1	20	47271890	Missense_Mutation	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	31304509	47271890	15753630	120	27571										
B3GALT5	10317	hgsc.bcm.edu	37	chr21	41032560	41032560	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tctttgtttgtattttagcaTgtacagtctaaatcctttca	5	7	3	0	rs545552313		TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr21:41032560T>C	ENST00000380620.4	+	5	666	c.74T>C	c.(73-75)aTg>aCg	p.M25T	B3GALT5_ENST00000380618.1_Missense_Mutation_p.M25T|B3GALT5_ENST00000398714.2_Missense_Mutation_p.M25T|B3GALT5_ENST00000343118.4_Missense_Mutation_p.M25T|AF064860.5_ENST00000416555.1_RNA			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	25					protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				TATTTTAGCATGTACAGTCTA	0.418																																					p.M25T		Atlas-SNP	.											.	B3GALT5	40	.	0			c.T74C						.						152	149	150					21																	41032560		2203	4300	6503	SO:0001583	missense	10317	exon3			TTAGCATGTACAG	AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"Beta 3-glycosyltransferases"	920	protein-coding gene	gene with protein product	"homolog of C. elegans Bt toxin resistance gene bre-5", "GlcNAc-beta-1,3-galactosyltransferase 5"	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.74T>C	chr21.hg19:g.41032560T>C	ENSP00000369994:p.Met25Thr	65.0	0.0		63.0	18.0	NM_033170	A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Missense_Mutation	SNP	ENST00000380620.4	hg19	CCDS13667.1	.	.	.	.	.	.	.	.	.	.	T	10.78	1.447534	0.26074	.	.	ENSG00000183778	ENST00000380620;ENST00000380618;ENST00000343118;ENST00000398714	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.75	2.06	0.26882	.	1.353810	0.05838	U	0.618754	T	0.43366	0.1244	L	0.60455	1.87	0.09310	N	1	B	0.27068	0.167	B	0.21360	0.034	T	0.21759	-1.0236	10	0.11794	T	0.64	.	4.1467	0.10219	0.2318:0.1992:0.0:0.569	.	25	Q9Y2C3	B3GT5_HUMAN	T	25	ENSP00000369994:M25T;ENSP00000369992:M25T;ENSP00000343318:M25T;ENSP00000381699:M25T	ENSP00000343318:M25T	M	+	2	0	B3GALT5	39954430	0.003000	0.15002	0.002000	0.10522	0.130000	0.20726	0.617000	0.24359	0.107000	0.17824	0.533000	0.62120	ATG	.	.		0.418	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	NM_033170		C	41032560	T	C	41032560	3	2	185	1	0	0	0	0	1	0	0	0	1250	1464	51	2	76	2	B3GALT5	21	41032560	Missense_Mutation	SNP	T	TCGA-DD-AADB-01A-11D-A40R-10		41032560	7097335	121	27572										
SLC5A4	6527	hgsc.bcm.edu	37	chr22	32633303	32633303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	gtctgtgtaaatcaccgaggCcaagccccctagtgagagaa	11	11	2	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr22:32633303C>T	ENST00000266086.4	-	7	603	c.592G>A	c.(592-594)Gcc>Acc	p.A198T	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	198					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						ATCACCGAGGCCAAGCCCCCT	0.502																																					p.A198T		Atlas-SNP	.											SLC5A4,NS,carcinoma,0,1	SLC5A4	82	.	0			c.G592A						.						72	55	61					22																	32633303		2203	4300	6503	SO:0001583	missense	6527	exon7			CCGAGGCCAAGCC	U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"Solute carriers"	11039	protein-coding gene	gene with protein product			"solute carrier family 5 (low affinity glucose cotransporter), member 4"			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.592G>A	chr22.hg19:g.32633303C>T	ENSP00000266086:p.Ala198Thr	73.0	0.0		77.0	25.0	NM_014227	O15279	Missense_Mutation	SNP	ENST00000266086.4	hg19	CCDS13903.1	.	.	.	.	.	.	.	.	.	.	.	17.54	3.414007	0.62511	.	.	ENSG00000100191	ENST00000266086	D	0.88586	-2.4	4.39	4.39	0.52855	Sodium/solute symporter, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.88385	0.6422	M	0.72624	2.21	0.80722	D	1	B	0.11235	0.004	B	0.26310	0.068	D	0.85360	0.1107	10	0.35671	T	0.21	.	14.821	0.70074	0.0:1.0:0.0:0.0	.	198	Q9NY91	SC5A4_HUMAN	T	198	ENSP00000266086:A198T	ENSP00000266086:A198T	A	-	1	0	SLC5A4	30963303	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	4.714000	0.61902	2.438000	0.82558	0.655000	0.94253	GCC	.	.		0.502	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227		T	32633303	C	T	32633303	3	4	185	1	0	0	0	0	1	0	0	0	14682	739	26	3	1423	3	SLC5A4	22	32633303	Missense_Mutation	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10		32633303	18671263	122	27573										
PARVB	29780	hgsc.bcm.edu	37	chr22	44527389	44527389	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	aaactggcagggtgcaagctGaatgtggctgaggtgacaca	15	7	0	3			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chr22:44527389G>C	ENST00000338758.7	+	5	462	c.399G>C	c.(397-399)ctG>ctC	p.L133L	PARVB_ENST00000406477.3_Silent_p.L166L|PARVB_ENST00000404989.1_Silent_p.L96L	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	133	CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				GGTGCAAGCTGAATGTGGCTG	0.567																																					p.L166L		Atlas-SNP	.											.	PARVB	44	.	0			c.G498C						.						89	73	79					22																	44527389		2203	4300	6503	SO:0001819	synonymous_variant	29780	exon6			CAAGCTGAATGTG	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"Parvins"	14653	protein-coding gene	gene with protein product	"affixin"	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.399G>C	chr22.hg19:g.44527389G>C		157.0	0.0		151.0	22.0	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Silent	SNP	ENST00000338758.7	hg19	CCDS14056.1																																																																																			.	.		0.567	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828		C	44527389	G	C	44527389	2	2	185	1	0	0	0	0	0	0	0	1	11478	1277	45	4		4	PARVB	22	44527389	Silent	SNP	G	TCGA-DD-AADB-01A-11D-A40R-10	11894086	44527389	6777177	123	27574										
NHSL2	340527	hgsc.bcm.edu	37	chrX	71358362	71358362	+	5'UTR	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0650406504065041	8	1	1.34664691103524	2.7143351800554	1.03403244954491	0.649916646820672	1	0	tcaggcccagtcactcagttCcagaaggggttcatggaaga	12	10	4	2			TCGA-DD-AADB-01A-11D-A40R-10	TCGA-DD-AADB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c88c0e3-7a9c-4f59-be35-f12dbd3a0676	be9289f1-a414-4a4f-a72d-ddbf960a9fcc	g.chrX:71358362C>A	ENST00000373677.1	+	0	1128				NHSL2_ENST00000535692.1_5'UTR|NHSL2_ENST00000540800.1_Missense_Mutation_p.P322T|NHSL2_ENST00000510661.1_Missense_Mutation_p.P91T			Q5HYW2	NHSL2_HUMAN	NHS-like 2											NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					TCACTCAGTTCCAGAAGGGGT	0.562																																					p.P322T		Atlas-SNP	.											.	NHSL2	148	.	0			c.C964A						.						67	56	59					X																	71358362		692	1591	2283	SO:0001623	5_prime_UTR_variant	340527	exon6			TCAGTTCCAGAAG			Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.-135C>A	chrX.hg19:g.71358362C>A		73.0	0.0		68.0	32.0	NM_001013627	B2RN94	Missense_Mutation	SNP	ENST00000373677.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.41	1.342182	0.24339	.	.	ENSG00000204131	ENST00000540800;ENST00000510661	T;T	0.50548	1.19;0.74	5.84	4.02	0.46733	.	.	.	.	.	T	0.33731	0.0873	L	0.29908	0.895	0.22050	N	0.999394	B;B	0.16603	0.01;0.018	B;B	0.17433	0.018;0.018	T	0.23297	-1.0192	8	.	.	.	.	8.3736	0.32430	0.1624:0.7539:0.0:0.0838	.	322;91	F5H593;D6RBM4	.;.	T	322;91	ENSP00000444617:P322T;ENSP00000424079:P91T	.	P	+	1	0	NHSL2	71275087	0.036000	0.19791	0.001000	0.08648	0.014000	0.08584	1.661000	0.37408	0.556000	0.29098	-0.297000	0.09499	CCA	.	.		0.562	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		A	71358362	C	A	71358362	1	1	185	0	1	0	0	0	0	0	0	0	10421	855	30	3		3	NHSL2	23	71358362	5'UTR	SNP	C	TCGA-DD-AADB-01A-11D-A40R-10		71358362	83912198	124	27575										
CCDC17	149483	hgsc.bcm.edu	37	chr1	46088962	46088962	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ctcgcgcgagtcctgaacagCgcccgcagccgctcgctggg	14	17	0	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:46088962C>T	ENST00000528266.1	-	3	567	c.420G>A	c.(418-420)gcG>gcA	p.A140A	CCDC17_ENST00000464739.1_5'Flank|CCDC17_ENST00000421127.2_Silent_p.A131A|CCDC17_ENST00000343901.2_Silent_p.A108A|CCDC17_ENST00000445048.2_Intron			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	140										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					TCCTGAACAGCGCCCGCAGCC	0.721																																					p.A140A		Atlas-SNP	.											.	CCDC17	54	.	0			c.G420A						.						6	9	8					1																	46088962		689	1581	2270	SO:0001819	synonymous_variant	149483	exon3			GAACAGCGCCCGC		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.420G>A	chr1.hg19:g.46088962C>T		44.0	0.0		51.0	28.0	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Silent	SNP	ENST00000528266.1	hg19	CCDS44131.2																																																																																			.	.		0.721	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500		T	46088962	C	T	46088962	2	4	186	1	0	0	0	0	0	0	0	1	2795	755	27	1		1	CCDC17	1	46088962	Silent	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10		46088962	203161659	1	27576										
DDX20	11218	hgsc.bcm.edu	37	chr1	112309297	112309297	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tcagattgcagactgaagccCaggaagatgattggtatgac	12	7	1	6			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:112309297C>A	ENST00000369702.4	+	11	2871	c.2251C>A	c.(2251-2253)Cag>Aag	p.Q751K	DDX20_ENST00000475700.1_Missense_Mutation_p.Q359K	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	751					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GACTGAAGCCCAGGAAGATGA	0.483																																					p.Q751K		Atlas-SNP	.											.	DDX20	50	.	0			c.C2251A						.						91	90	90					1																	112309297		2203	4300	6503	SO:0001583	missense	11218	exon11			GAAGCCCAGGAAG	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"DEAD-boxes"	2743	protein-coding gene	gene with protein product		606168	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2251C>A	chr1.hg19:g.112309297C>A	ENSP00000358716:p.Gln751Lys	165.0	0.0		212.0	59.0	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	hg19	CCDS842.1	.	.	.	.	.	.	.	.	.	.	C	7.570	0.666613	0.14710	.	.	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.32023	1.47;1.99	5.82	3.96	0.45880	.	0.823783	0.11427	N	0.565143	T	0.13415	0.0325	L	0.60455	1.87	0.45307	D	0.9983	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.04946	-1.0916	9	.	.	.	-1.705	7.4811	0.27406	0.3537:0.5695:0.0:0.0769	.	359;751	E9PJ60;Q9UHI6	.;DDX20_HUMAN	K	751;359	ENSP00000358716:Q751K;ENSP00000435660:Q359K	.	Q	+	1	0	DDX20	112110820	0.011000	0.17503	0.950000	0.38849	0.160000	0.22226	0.599000	0.24089	0.815000	0.34398	-0.152000	0.13540	CAG	.	.		0.483	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		A	112309297	C	A	112309297	3	1	186	1	0	0	0	0	1	0	0	0	4350	595	21	3	2293	3	DDX20	1	112309297	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	66220335	112309297	136941324	2	27577										
GATAD2B	57459	hgsc.bcm.edu	37	chr1	153788806	153788806	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gcctaccatgtagatgaactCgctattggctgcactaggca	10	11	0	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:153788806C>A	ENST00000368655.4	-	7	1402	c.1159G>T	c.(1159-1161)Gag>Tag	p.E387*		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	387	CR2; histone tail-binding.				ATP-dependent chromatin remodeling (GO:0043044)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	38	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TAGATGAACTCGCTATTGGCT	0.463																																					p.E387X		Atlas-SNP	.											.	GATAD2B	62	.	0			c.G1159T						.						92	78	83					1																	153788806		2203	4300	6503	SO:0001587	stop_gained	57459	exon7			TGAACTCGCTATT	AF411836	CCDS1054.1	1q21.3	2013-01-25			ENSG00000143614	ENSG00000143614		"GATA zinc finger domain containing"	30778	protein-coding gene	gene with protein product	"transcription repressor p66 beta component of the MeCP1 complex"	614998				10574461, 11756549	Standard	NM_020699		Approved	P66beta	uc001fdb.4	Q8WXI9	OTTHUMG00000037162	ENST00000368655.4:c.1159G>T	chr1.hg19:g.153788806C>A	ENSP00000357644:p.Glu387*	127.0	0.0		165.0	83.0	NM_020699	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Nonsense_Mutation	SNP	ENST00000368655.4	hg19	CCDS1054.1	.	.	.	.	.	.	.	.	.	.	C	38	6.995398	0.97990	.	.	ENSG00000143614	ENST00000368655	.	.	.	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-0.0201	17.0353	0.86473	0.0:1.0:0.0:0.0	.	.	.	.	X	387	.	ENSP00000357644:E387X	E	-	1	0	GATAD2B	152055430	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	7.626000	0.83164	2.549000	0.85964	0.563000	0.77884	GAG	.	.		0.463	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699		A	153788806	C	A	153788806	4	1	186	1	0	0	0	0	0	1	0	0	6269	893	31	1	642	1	GATAD2B	1	153788806	Nonsense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	41479509	153788806	95461815	3	27578										
TNN	63923	hgsc.bcm.edu	37	chr1	175067569	175067569	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ccattgacaagtacgtggtgCgctacacctctgctggtgga	12	11	1	1	rs199634558		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:175067569C>T	ENST00000239462.4	+	9	2070	c.1957C>T	c.(1957-1959)Cgc>Tgc	p.R653C		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	653	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GTACGTGGTGCGCTACACCTC	0.597																																					p.R653C		Atlas-SNP	.											.	TNN	297	.	0			c.C1957T						.	C	CYS/ARG	0,4406		0,0,2203	92	89	90		1957	0.7	1	1		90	1,8599	1.2+/-3.3	0,1,4299	no	missense	TNN	NM_022093.1	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	653/1300	175067569	1,13005	2203	4300	6503	SO:0001583	missense	63923	exon9			GTGGTGCGCTACA	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1957C>T	chr1.hg19:g.175067569C>T	ENSP00000239462:p.Arg653Cys	383.0	0.0		598.0	292.0	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.489934	0.26686	0.0	1.16E-4	ENSG00000120332	ENST00000239462	T	0.58652	0.32	5.14	0.658	0.17855	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.336638	0.35555	N	0.003128	T	0.73001	0.3531	M	0.89478	3.035	0.31421	N	0.674312	D;D	0.71674	0.997;0.998	P;D	0.63381	0.86;0.914	T	0.74300	-0.3710	10	0.49607	T	0.09	.	9.5181	0.39117	0.6598:0.265:0.0:0.0752	.	653;653	B3KXB6;Q9UQP3	.;TENN_HUMAN	C	653	ENSP00000239462:R653C	ENSP00000239462:R653C	R	+	1	0	TNN	173334192	1.000000	0.71417	0.995000	0.50966	0.045000	0.14185	2.396000	0.44468	-0.085000	0.12573	-0.378000	0.06908	CGC	.	.		0.597	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		T	175067569	C	T	175067569	3	4	186	1	0	0	0	0	1	0	0	0	16338	768	27	1	1987	1	TNN	1	175067569	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	21278763	175067569	74183052	4	27579										
SDCCAG8	10806	hgsc.bcm.edu	37	chr1	243589739	243589739	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tcacctctagatctgaaataGctcaactcagtcaagaaaaa	5	10	6	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:243589739G>T	ENST00000366541.3	+	16	1982	c.1864G>T	c.(1864-1866)Gct>Tct	p.A622S	SDCCAG8_ENST00000343783.6_Missense_Mutation_p.A477S|SDCCAG8_ENST00000355875.4_Missense_Mutation_p.A579S	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	622	Gln-rich.|Mediates interaction with OFD1.|Sufficient for homodimerization. {ECO:0000250}.				establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		ATCTGAAATAGCTCAACTCAG	0.318																																					p.A622S		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.G1864T						.						66	64	65					1																	243589739		2203	4300	6503	SO:0001583	missense	10806	exon16			GAAATAGCTCAAC	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.1864G>T	chr1.hg19:g.243589739G>T	ENSP00000355499:p.Ala622Ser	377.0	0.0		379.0	132.0	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	hg19	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.488945	0.26686	.	.	ENSG00000054282	ENST00000355875;ENST00000366541;ENST00000343783;ENST00000435549	T;T;T;T	0.43294	0.95;1.02;0.97;0.99	6.17	0.559	0.17272	.	1.082370	0.06931	N	0.811054	T	0.21801	0.0525	N	0.14661	0.345	0.09310	N	1	B;B	0.17667	0.008;0.023	B;B	0.12156	0.007;0.007	T	0.25467	-1.0131	10	0.10902	T	0.67	-0.1395	5.3204	0.15878	0.0719:0.1051:0.3617:0.4613	.	579;622	E9PFS7;Q86SQ7	.;SDCG8_HUMAN	S	579;622;477;323	ENSP00000348137:A579S;ENSP00000355499:A622S;ENSP00000341260:A477S;ENSP00000410200:A323S	ENSP00000341260:A477S	A	+	1	0	SDCCAG8	241656362	0.941000	0.31946	0.981000	0.43875	0.918000	0.54935	0.960000	0.29253	0.418000	0.25898	-0.169000	0.13324	GCT	.	.		0.318	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		T	243589739	G	T	243589739	3	4	186	1	0	0	0	0	1	0	0	0	13974	971	34	3	1926	3	SDCCAG8	1	243589739	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	68522170	243589739	5660882	5	27580										
ZNF238	10472	hgsc.bcm.edu	37	chr1	244218178	244218178	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	agagcagtctgctcccctacGtctccaacatcctgagcccc	7	18	2	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:244218178G>T	ENST00000358704.4	+	2	1251	c.1102G>T	c.(1102-1104)Gtc>Ttc	p.V368F		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	359	Interaction with DNMT3A.				cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCTCCCCTACGTCTCCAACAT	0.617																																					p.V368F		Atlas-SNP	.											.	.	.	.	0			c.G1102T						.						69	60	63					1																	244218178		2203	4300	6503	SO:0001583	missense	10472	exon2			CCCTACGTCTCCA	U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13030	protein-coding gene	gene with protein product		608433	"zinc finger protein 238"	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.1102G>T	chr1.hg19:g.244218178G>T	ENSP00000351539:p.Val368Phe	85.0	0.0		94.0	44.0	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	hg19	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.862771	0.71949	.	.	ENSG00000179456	ENST00000366538;ENST00000358704	T	0.13089	2.62	5.83	5.83	0.93111	.	0.059626	0.64402	D	0.000003	T	0.28632	0.0709	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.85130	0.993;0.997	T	0.01371	-1.1372	10	0.56958	D	0.05	.	20.1184	0.97949	0.0:0.0:1.0:0.0	.	359;368	Q99592;Q99592-2	ZN238_HUMAN;.	F	368	ENSP00000351539:V368F	ENSP00000351539:V368F	V	+	1	0	ZNF238	242284801	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.824000	0.99380	2.775000	0.95449	0.650000	0.86243	GTC	.	.		0.617	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768		T	244218178	G	T	244218178	3	4	186	1	0	0	0	0	1	0	0	0	17805	1145	40	1	1108	1	ZNF238	1	244218178	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	628439	244218178	5032443	6	27581										
ZNF672	79894	hgsc.bcm.edu	37	chr1	249142142	249142142	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	cacctgcagacgcactcgggGgagaaacccttcaagtgccc	11	15	1	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:249142142G>C	ENST00000306562.3	+	4	1415	c.669G>C	c.(667-669)ggG>ggC	p.G223G		NM_024836.1	NP_079112.1	Q499Z4	ZN672_HUMAN	zinc finger protein 672	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G223G(1)		endometrium(2)|kidney(2)|large_intestine(1)	5	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			CGCACTCGGGGGAGAAACCCT	0.662																																					p.G223G		Atlas-SNP	.											ZNF672,caecum,carcinoma,0,1	ZNF672	32	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G669C						.						10	10	10					1																	249142142		2195	4289	6484	SO:0001819	synonymous_variant	79894	exon4			CTCGGGGGAGAAA	AK027476	CCDS1638.1	1q44	2013-01-08			ENSG00000171161	ENSG00000171161		"Zinc fingers, C2H2-type"	26179	protein-coding gene	gene with protein product	"hypothetical protein FLJ22301"					12477932	Standard	NM_024836		Approved	FLJ22301	uc001iex.3	Q499Z4	OTTHUMG00000040377	ENST00000306562.3:c.669G>C	chr1.hg19:g.249142142G>C		75.0	0.0		62.0	16.0	NM_024836	Q96H65|Q96IM3|Q9H6G5	Silent	SNP	ENST00000306562.3	hg19	CCDS1638.1																																																																																			.	.		0.662	ZNF672-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097125.2	NM_024836		C	249142142	G	C	249142142	2	2	186	1	0	0	0	0	0	0	0	1	18094	1219	43	4		4	ZNF672	1	249142142	Silent	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	4923964	249142142	108479	7	27582										
OTOF	9381	hgsc.bcm.edu	37	chr2	26693553	26693554	+	In_Frame_Ins	INS	-	-	CTT													0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tctggctcctccgcagtgccINScttcttcttcttcttcttct					rs368148603		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:26693553_26693554insCTT	ENST00000272371.2	-	32	4056_4057	c.3930_3931insAAG	c.(3928-3933)aagggc>aagAAGggc	p.1310_1311insK	OTOF_ENST00000339598.3_In_Frame_Ins_p.543_544insK|OTOF_ENST00000402415.3_In_Frame_Ins_p.620_621insK|OTOF_ENST00000338581.6_In_Frame_Ins_p.543_544insK|OTOF_ENST00000403946.3_In_Frame_Ins_p.1310_1311insK	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1310	Poly-Lys.				membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCGCAGTGCCcttcttcttct	0.579																																					p.G1311delinsKG	GBM(102;732 1451 20652 24062 31372)	Atlas-INDEL	.											.	OTOF	524	.	0			c.3931_3932insAAG						.																																			SO:0001652	inframe_insertion	9381	exon32			.	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.3928_3930dupAAG	chr2.hg19:g.26693560_26693562dupCTT	ENSP00000272371:p.Lys1310_Lys1310dup	50.0	0.0		47.0	14.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	In_Frame_Ins	INS	ENST00000272371.2	hg19	CCDS1725.1																																																																																			.	.		0.579	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			CTT	26693554	-	CTT	26693553	7	5	186	1	0	1	1	0	0	0	0	0	11312	623	22	0	2307	0	OTOF	2	26693553	In_Frame_Ins	INS	-	TCGA-DD-AADC-01A-11D-A40R-10		26693553	216505820	8	27583										
UGP2	7360	hgsc.bcm.edu	37	chr2	64114716	64114716	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ttaatgcaggatctctgacaAtgagtgaaaagcgggaattt	11	5	1	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:64114716A>C	ENST00000337130.5	+	8	1728	c.1252A>C	c.(1252-1254)Atg>Ctg	p.M418L	UGP2_ENST00000394417.2_Missense_Mutation_p.M407L|UGP2_ENST00000445915.2_Missense_Mutation_p.M427L|UGP2_ENST00000467648.2_Missense_Mutation_p.M407L	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	418					carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)			endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						ATCTCTGACAATGAGTGAAAA	0.393																																					p.M418L		Atlas-SNP	.											.	UGP2	38	.	0			c.A1252C						.						150	153	152					2																	64114716		2203	4300	6503	SO:0001583	missense	7360	exon8			CTGACAATGAGTG		CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"UDP-glucose pyrophosphorylase 1"	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.1252A>C	chr2.hg19:g.64114716A>C	ENSP00000338703:p.Met418Leu	181.0	0.0		197.0	67.0	NM_006759	Q07131|Q0P6K2|Q86Y81|Q9BU15	Missense_Mutation	SNP	ENST00000337130.5	hg19	CCDS1875.1	.	.	.	.	.	.	.	.	.	.	A	13.53	2.265630	0.40095	.	.	ENSG00000169764	ENST00000394417;ENST00000467648;ENST00000337130;ENST00000445915	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.81	5.81	0.92471	.	0.034479	0.85682	D	0.000000	T	0.09774	0.0240	N	0.11427	0.14	0.80722	D	1	B;B	0.20887	0.049;0.049	B;B	0.31016	0.123;0.123	T	0.33394	-0.9870	10	0.16420	T	0.52	2.8559	16.1536	0.81640	1.0:0.0:0.0:0.0	.	427;418	E7EUC7;Q16851	.;UGPA_HUMAN	L	407;407;418;427	ENSP00000377939:M407L;ENSP00000420793:M407L;ENSP00000338703:M418L;ENSP00000411803:M427L	ENSP00000338703:M418L	M	+	1	0	UGP2	63968220	1.000000	0.71417	0.957000	0.39632	0.971000	0.66376	7.302000	0.78861	2.203000	0.70933	0.528000	0.53228	ATG	.	.		0.393	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759		C	64114716	A	C	64114716	3	2	186	1	0	0	0	0	1	0	0	0	16958	101	4	5	1282	5	UGP2	2	64114716	Missense_Mutation	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10	37421163	64114716	179084657	9	27584										
VPS54	51542	hgsc.bcm.edu	37	chr2	64176272	64176272	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tttatctatcagtttttctaAttcacaaagctgtgatccca	4	9	4	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:64176272A>G	ENST00000272322.4	-	8	1190	c.1036T>C	c.(1036-1038)Tta>Cta	p.L346L	VPS54_ENST00000354504.3_Silent_p.L229L|VPS54_ENST00000409558.4_Silent_p.L334L			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	346					growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						AGTTTTTCTAATTCACAAAGC	0.318																																					p.L346L		Atlas-SNP	.											.	VPS54	57	.	0			c.T1036C						.						56	54	54					2																	64176272		2201	4299	6500	SO:0001819	synonymous_variant	51542	exon8			TTTCTAATTCACA	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 164"	614633	"vacuolar protein sorting 54 (yeast)"			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.1036T>C	chr2.hg19:g.64176272A>G		57.0	0.0		57.0	14.0	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Silent	SNP	ENST00000272322.4	hg19	CCDS33208.1																																																																																			.	.		0.318	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516		G	64176272	A	G	64176272	2	3	186	1	0	0	0	0	0	0	0	1	17231	98	4	2		2	VPS54	2	64176272	Silent	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10	61556	64176272	179023101	10	27585										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71576746	71576746	+	Frame_Shift_Del	DEL	A	A	-													0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	aagcaaatatggctacacagAagatccacttgaagtacgta							TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:71576746delA	ENST00000409544.1	+	2	1292	c.662delA	c.(661-663)gaafs	p.E221fs	ZNF638_ENST00000377802.2_Frame_Shift_Del_p.E221fs|ZNF638_ENST00000264447.4_Frame_Shift_Del_p.E221fs|ZNF638_ENST00000355812.3_Frame_Shift_Del_p.E221fs|ZNF638_ENST00000410075.1_3'UTR	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	221					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GGCTACACAGAAGATCCACTT	0.383																																					p.E221fs		Atlas-INDEL	.											.	ZNF638	179	.	0			c.661delG						.						99	96	97					2																	71576746		2203	4300	6503	SO:0001589	frameshift_variant	27332	exon2			.	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.662delA	chr2.hg19:g.71576746delA	ENSP00000386433:p.Glu221fs	116.0	0.0		138.0	37.0	NM_001252612	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Frame_Shift_Del	DEL	ENST00000409544.1	hg19	CCDS1917.1																																																																																			.	.		0.383	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		-	71576746	A	-	71576746	7	5	186	1	0	1	0	1	0	0	0	0	18070	246	9	0	664	0	ZNF638	2	71576746	Frame_Shift_Del	DEL	A	TCGA-DD-AADC-01A-11D-A40R-10	7400474	71576746	171622627	11	27586										
CD302	9936	hgsc.bcm.edu	37	chr2	160654643	160654643	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gggactacgtaagggcttacCcgcgacggcagcagcggcga	16	12	0	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:160654643C>A	ENST00000259053.4	-	1	110	c.67G>T	c.(67-69)Gac>Tac	p.D23Y	LY75_ENST00000554112.1_Intron|LY75_ENST00000553424.1_Intron|LY75-CD302_ENST00000504764.1_Intron|LY75-CD302_ENST00000505052.1_Intron|CD302_ENST00000480212.1_5'UTR|CD302_ENST00000429078.2_Splice_Site_p.D23Y	NM_001198764.1|NM_014880.4	NP_001185693.1|NP_055695.2	Q8IX05	CD302_HUMAN	CD302 molecule	23					phagocytosis (GO:0006909)	cell cortex (GO:0005938)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						AAGGGCTTACCCgcgacggca	0.771																																					p.G23X		Atlas-SNP	.											.	CD302	22	.	0			c.G67T						.						6	7	7					2																	160654643		1735	3220	4955	SO:0001630	splice_region_variant	9936	exon1			GCTTACCCGCGAC	AY314007	CCDS33308.1, CCDS56139.1, CCDS74595.1	2q24.2	2011-08-30	2006-03-28		ENSG00000241399	ENSG00000241399		"CD molecules", "C-type lectin domain containing"	30843	protein-coding gene	gene with protein product	"C-type lectin domain family 13, member A"	612246	"CD302 antigen"			7584026, 7584028	Standard	NM_014880		Approved	DCL-1, KIAA0022, BIMLEC, CLEC13A		Q8IX05	OTTHUMG00000154080	ENST00000259053.4:c.67+1G>T	chr2.hg19:g.160654643C>A		43.0	0.0		66.0	20.0	NM_001198764	A8K5G4|B4E2T9|Q15009	Nonsense_Mutation	SNP	ENST00000259053.4	hg19	CCDS33308.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392147	0.42410	.	.	ENSG00000241399	ENST00000259053;ENST00000429078	T;T	0.07908	3.15;3.15	3.34	1.46	0.22682	C-type lectin fold (1);C-type lectin-like (1);	0.225788	0.29172	U	0.012922	T	0.18923	0.0454	.	.	.	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.71184	0.922;0.972	T	0.01448	-1.1352	8	.	.	.	-24.5116	4.657	0.12622	0.0:0.6475:0.2253:0.1273	.	23;23	B4E2T9;Q8IX05	.;CD302_HUMAN	Y	23	ENSP00000259053:D23Y;ENSP00000394301:D23Y	.	D	-	1	0	CD302	160362889	0.981000	0.34729	0.965000	0.40720	0.144000	0.21451	1.642000	0.37207	0.389000	0.25086	0.462000	0.41574	GAC	.	.		0.771	CD302-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333760.1	NM_014880	Missense_Mutation	A	160654643	C	A	160654643	5	1	186	1	0	0	0	0	0	0	1	0	3005	637	22	3	655	3	CD302	2	160654643	Splice_Site	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	89077897	160654643	82544730	12	27587										
ITGA6	3655	hgsc.bcm.edu	37	chr2	173355794	173355794	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	aacgggaaattactgaaaaaCagatagatgataacagaaaa	8	4	0	5			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:173355794C>G	ENST00000264106.6	+	22	3042	c.2839C>G	c.(2839-2841)Cag>Gag	p.Q947E	ITGA6_ENST00000264107.7_Missense_Mutation_p.Q908E|ITGA6_ENST00000409080.1_Missense_Mutation_p.Q908E|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000409532.1_Missense_Mutation_p.Q789E|ITGA6_ENST00000343713.4_Missense_Mutation_p.Q903E|ITGA6_ENST00000375221.2_Missense_Mutation_p.Q947E			P23229	ITA6_HUMAN	integrin, alpha 6	947					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TACTGAAAAACAGATAGATGA	0.303																																					p.Q908E		Atlas-SNP	.											.	ITGA6	171	.	0			c.C2722G						.						113	139	130					2																	173355794		2202	4299	6501	SO:0001583	missense	3655	exon21			GAAAAACAGATAG		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"CD molecules", "Integrins"	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.2839C>G	chr2.hg19:g.173355794C>G	ENSP00000264106:p.Gln947Glu	349.0	0.0		383.0	127.0	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	hg19		.	.	.	.	.	.	.	.	.	.	C	5.608	0.296873	0.10622	.	.	ENSG00000091409	ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358;ENST00000416789	T;T;T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;1.96	5.4	5.4	0.78164	.	0.361759	0.32015	N	0.006702	T	0.36386	0.0965	L	0.41824	1.3	0.52099	D	0.999942	B;B;P;P	0.37352	0.02;0.003;0.591;0.591	B;B;B;B	0.39876	0.03;0.018;0.312;0.312	T	0.08249	-1.0731	10	0.09590	T	0.72	.	16.3226	0.82956	0.0:1.0:0.0:0.0	.	903;932;908;908	P23229-4;P23229-9;G5E9H1;P23229-2	.;.;.;.	E	789;908;947;947;903;908;947;903;75	ENSP00000386614:Q789E;ENSP00000264107:Q908E;ENSP00000264106:Q947E;ENSP00000364369:Q947E;ENSP00000341078:Q903E;ENSP00000386896:Q908E;ENSP00000406694:Q947E;ENSP00000394169:Q903E;ENSP00000388435:Q75E	ENSP00000264106:Q947E	Q	+	1	0	ITGA6	173064040	0.073000	0.21202	1.000000	0.80357	0.907000	0.53573	1.103000	0.31062	2.534000	0.85438	0.460000	0.39030	CAG	.	.		0.303	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				G	173355794	C	G	173355794	3	3	186	1	0	0	0	0	1	0	0	0	7889	479	17	4	2804	4	ITGA6	2	173355794	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	12701151	173355794	69843579	13	27588										
PGAP1	80055	hgsc.bcm.edu	37	chr2	197738476	197738476	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ttaacaccactttccttgaaGacaatcctgttgaattcaaa	4	10	1	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:197738476G>C	ENST00000354764.4	-	15	1547	c.1433C>G	c.(1432-1434)tCt>tGt	p.S478C	PGAP1_ENST00000409475.1_Missense_Mutation_p.S478C	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	478					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TTTCCTTGAAGACAATCCTGT	0.303																																					p.S478C		Atlas-SNP	.											.	PGAP1	84	.	0			c.C1433G						.						87	90	89					2																	197738476		2202	4288	6490	SO:0001583	missense	80055	exon15			CTTGAAGACAATC		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.1433C>G	chr2.hg19:g.197738476G>C	ENSP00000346809:p.Ser478Cys	182.0	0.0		165.0	53.0	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	hg19	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.053488	0.55218	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475	.	.	.	5.13	4.25	0.50352	.	0.171557	0.52532	D	0.000070	T	0.47358	0.1441	N	0.19112	0.55	0.80722	D	1	D;D	0.57257	0.973;0.979	P;P	0.53360	0.724;0.514	T	0.43877	-0.9364	9	0.38643	T	0.18	-12.5885	11.7902	0.52065	0.0821:0.0:0.9179:0.0	.	478;478	Q75T13-3;Q75T13	.;PGAP1_HUMAN	C	258;478;478	.	ENSP00000346809:S478C	S	-	2	0	PGAP1	197446721	1.000000	0.71417	0.997000	0.53966	0.822000	0.46500	4.128000	0.57951	1.522000	0.49001	0.655000	0.94253	TCT	.	.		0.303	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		C	197738476	G	C	197738476	3	2	186	1	0	0	0	0	1	0	0	0	11786	942	33	4	1387	4	PGAP1	2	197738476	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	24382682	197738476	45460897	14	27589										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48680218	48680218	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ctggtcctgggtccggccggAgcgggcactgctcacagagg	17	13	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:48680218A>G	ENST00000164024.4	-	30	8786	c.8506T>C	c.(8506-8508)Tcc>Ccc	p.S2836P	CELSR3_ENST00000544264.1_Missense_Mutation_p.S2841P|MIR4793_ENST00000577502.1_RNA	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	2836					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GTCCGGCCGGAGCGGGCACTG	0.647																																					p.S2836P		Atlas-SNP	.											.	CELSR3	237	.	0			c.T8506C						.						42	47	45					3																	48680218		2203	4299	6502	SO:0001583	missense	1951	exon30			GGCCGGAGCGGGC	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.8506T>C	chr3.hg19:g.48680218A>G	ENSP00000164024:p.Ser2836Pro	83.0	0.0		62.0	38.0	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.906139	0.92107	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.72942	-0.7;-0.7	5.52	5.52	0.82312	.	.	.	.	.	D	0.83367	0.5239	M	0.77820	2.39	0.47819	D	0.999526	D;D;D	0.76494	0.998;0.996;0.999	P;P;D	0.66196	0.862;0.731;0.942	D	0.85871	0.1416	9	0.87932	D	0	.	15.6403	0.76993	1.0:0.0:0.0:0.0	.	2841;2836;2934	Q9NYQ7-2;Q9NYQ7;Q5Y190	.;CELR3_HUMAN;.	P	2836;2841	ENSP00000164024:S2836P;ENSP00000445694:S2841P	ENSP00000164024:S2836P	S	-	1	0	CELSR3	48655222	1.000000	0.71417	0.995000	0.50966	0.703000	0.40648	7.529000	0.81952	2.106000	0.64143	0.459000	0.35465	TCC	.	.		0.647	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		G	48680218	A	G	48680218	3	3	186	1	0	0	0	0	1	0	0	0	3225	304	11	2	1456	2	CELSR3	3	48680218	Missense_Mutation	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10		48680218	149342212	15	27590										
PROK2	60675	hgsc.bcm.edu	37	chr3	71830662	71830662	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gtctcccagtttgcccatagGtgtgcaaatccttatgctct	8	12	2	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:71830662G>T	ENST00000295619.3	-	2	186	c.178C>A	c.(178-180)Cct>Act	p.P60T	PROK2_ENST00000353065.3_Missense_Mutation_p.P60T	NM_001126128.1	NP_001119600.1	Q9HC23	PROK2_HUMAN	prokineticin 2	60					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of apoptotic process (GO:0043066)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of smooth muscle contraction (GO:0045987)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	G-protein coupled receptor binding (GO:0001664)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6		Prostate(10;0.00899)		BRCA - Breast invasive adenocarcinoma(55;1.89e-05)|Epithelial(33;0.000173)|LUSC - Lung squamous cell carcinoma(21;0.00168)|Lung(16;0.00306)		TTGCCCATAGGTGTGCAAATC	0.443																																					p.P60T		Atlas-SNP	.											.	PROK2	13	.	0			c.C178A						.						123	111	115					3																	71830662		2203	4300	6503	SO:0001583	missense	60675	exon2			CCATAGGTGTGCA	AF333025	CCDS2916.1, CCDS46868.1	3p21.1	2013-02-28			ENSG00000163421	ENSG00000163421		"Endogenous ligands"	18455	protein-coding gene	gene with protein product	"protein Bv8 homolog"	607002				11054548, 11259612	Standard	NM_021935		Approved	PK2, BV8, MIT1, KAL4	uc003dpa.4	Q9HC23	OTTHUMG00000158809	ENST00000295619.3:c.178C>A	chr3.hg19:g.71830662G>T	ENSP00000295619:p.Pro60Thr	224.0	0.0		152.0	76.0	NM_001126128	Q53Z79|Q6ISR0	Missense_Mutation	SNP	ENST00000295619.3	hg19	CCDS46868.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.717488	0.89205	.	.	ENSG00000163421	ENST00000353065;ENST00000295619	D;D	0.90563	-2.69;-2.69	5.72	5.72	0.89469	Prokineticin domain (2);	0.000000	0.85682	D	0.000000	D	0.95287	0.8471	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.95382	0.8474	10	0.87932	D	0	-2.2696	18.6538	0.91441	0.0:0.0:1.0:0.0	.	60;60	Q9HC23;Q6ISR0	PROK2_HUMAN;.	T	60	ENSP00000295618:P60T;ENSP00000295619:P60T	ENSP00000295619:P60T	P	-	1	0	PROK2	71913352	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.921000	0.92784	2.692000	0.91855	0.650000	0.86243	CCT	.	.		0.443	PROK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352302.1	NM_001126128		T	71830662	G	T	71830662	3	4	186	1	0	0	0	0	1	0	0	0	12563	1261	44	3	223	3	PROK2	3	71830662	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	23150444	71830662	126191768	16	27591										
CNTN3	5067	hgsc.bcm.edu	37	chr3	74548904	74548904	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	aatgctgttgctgggttcttTgataaatacagggccttgta	11	6	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:74548904T>C	ENST00000263665.6	-	2	115	c.88A>G	c.(88-90)Aaa>Gaa	p.K30E		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	30	Ig-like C2-type 1.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CTGGGTTCTTTGATAAATACA	0.378																																					p.K30E		Atlas-SNP	.											.	CNTN3	174	.	0			c.A88G						.						91	97	95					3																	74548904		2203	4300	6503	SO:0001583	missense	5067	exon2			GTTCTTTGATAAA	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.88A>G	chr3.hg19:g.74548904T>C	ENSP00000263665:p.Lys30Glu	66.0	0.0		41.0	24.0	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	hg19	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	T	6.701	0.498019	0.12762	.	.	ENSG00000113805	ENST00000263665	T	0.42131	0.98	5.54	4.34	0.51931	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.413872	0.24031	N	0.042191	T	0.18759	0.0450	N	0.05574	-0.02	0.34971	D	0.753177	B	0.02656	0.0	B	0.12156	0.007	T	0.22417	-1.0217	10	0.02654	T	1	.	9.3228	0.37975	0.0:0.0:0.1812:0.8188	.	30	Q9P232	CNTN3_HUMAN	E	30	ENSP00000263665:K30E	ENSP00000263665:K30E	K	-	1	0	CNTN3	74631594	1.000000	0.71417	0.956000	0.39512	0.950000	0.60333	1.601000	0.36773	0.882000	0.36016	0.533000	0.62120	AAA	.	.		0.378	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		C	74548904	T	C	74548904	3	2	186	1	0	0	0	0	1	0	0	0	3644	1821	63	2	3082	2	CNTN3	3	74548904	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	2718242	74548904	123473526	17	27592										
ATR	545	hgsc.bcm.edu	37	chr3	142188996	142188997	+	Frame_Shift_Ins	INS	-	-	A													0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	cattcgtggcattgactgatINSatatgaactgatttccatat							TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:142188996_142188997insA	ENST00000350721.4	-	37	6371_6372	c.6250_6251insT	c.(6250-6252)tatfs	p.Y2084fs	ATR_ENST00000383101.3_Frame_Shift_Ins_p.Y2020fs|RP11-383G6.3_ENST00000460977.1_RNA	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2084	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CATTGACTGATATATGAACTGA	0.302								Other conserved DNA damage response genes																													p.Y2084fs		Atlas-INDEL	.											.	ATR	285	.	0			c.6251_6252insT						.																																			SO:0001589	frameshift_variant	545	exon37			.	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.6251dupT	chr3.hg19:g.142188997_142188997dupA	ENSP00000343741:p.Tyr2084fs	89.0	0.0		109.0	31.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Frame_Shift_Ins	INS	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.302	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142188997	-	A	142188996	7	5	186	1	0	1	1	0	0	0	0	0	1204	1406	49	0	1727	0	ATR	3	142188996	Frame_Shift_Ins	INS	-	TCGA-DD-AADC-01A-11D-A40R-10	67640092	142188996	55833434	18	27593										
GOLIM4	27333	hgsc.bcm.edu	37	chr3	167750442	167750442	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tgcttgcccgacctgctccaTttcttcctcctccagggcct	7	18	1	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:167750442T>C	ENST00000470487.1	-	9	1731	c.1042A>G	c.(1042-1044)Atg>Gtg	p.M348V	GOLIM4_ENST00000309027.4_Missense_Mutation_p.M320V	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	348	Glu-rich.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						ACCTGCTCCATTTCTTCCTCC	0.557																																					p.M348V		Atlas-SNP	.											.	GOLIM4	71	.	0			c.A1042G						.						207	183	191					3																	167750442		2203	4300	6503	SO:0001583	missense	27333	exon9			GCTCCATTTCTTC	U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"golgi phosphoprotein 4"	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.1042A>G	chr3.hg19:g.167750442T>C	ENSP00000417354:p.Met348Val	123.0	0.0		265.0	49.0	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	hg19	CCDS3204.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.454101	0.63290	.	.	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	5.36	5.36	0.76844	.	0.152354	0.64402	D	0.000001	T	0.65842	0.2730	M	0.72118	2.19	0.51482	D	0.999929	D;P	0.54772	0.968;0.907	P;P	0.51415	0.6;0.669	T	0.65311	-0.6199	9	0.28530	T	0.3	-14.8158	15.0611	0.71955	0.0:0.0:0.0:1.0	.	320;348	F8W785;O00461	.;GOLI4_HUMAN	V	348;320	.	ENSP00000309893:M320V	M	-	1	0	GOLIM4	169233136	1.000000	0.71417	0.919000	0.36401	0.593000	0.36681	5.365000	0.66116	2.044000	0.60594	0.454000	0.30748	ATG	.	.		0.557	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2			C	167750442	T	C	167750442	3	2	186	1	0	0	0	0	1	0	0	0	6574	1493	52	2	1080	2	GOLIM4	3	167750442	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	25561446	167750442	30271988	19	27594										
PCYT1A	5130	hgsc.bcm.edu	37	chr3	195997368	195997368	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gcgcctcttttctcctcttcCttgcattgaccttggctgaa	7	14	3	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:195997368C>T	ENST00000292823.2	-	3	207	c.35G>A	c.(34-36)aGg>aAg	p.R12K	PCYT1A_ENST00000431016.1_Missense_Mutation_p.R12K|RP11-447L10.1_ENST00000431391.1_3'UTR|PCYT1A_ENST00000419333.1_Missense_Mutation_p.R12K|PCYT1A_ENST00000491544.1_5'UTR	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	12					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	TCTCCTCTTCCTTGCATTGAC	0.468																																					p.R12K		Atlas-SNP	.											.	PCYT1A	34	.	0			c.G35A						.						217	216	217					3																	195997368		2203	4300	6503	SO:0001583	missense	5130	exon3			CTCTTCCTTGCAT	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"phosphate cytidylyltransferase 1, choline, alpha isoform"	123695	"phosphate cytidylyltransferase 1, choline, alpha isoform"	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.35G>A	chr3.hg19:g.195997368C>T	ENSP00000292823:p.Arg12Lys	136.0	0.0		188.0	34.0	NM_005017	A9LYK9|D3DXB1|Q86Y88	Missense_Mutation	SNP	ENST00000292823.2	hg19	CCDS3315.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.818075	0.71028	.	.	ENSG00000161217	ENST00000441879;ENST00000419333;ENST00000292823;ENST00000416798;ENST00000431016;ENST00000411591;ENST00000412869;ENST00000443555	.	.	.	5.82	5.82	0.92795	.	0.123828	0.56097	D	0.000021	T	0.52075	0.1712	L	0.55481	1.735	0.80722	D	1	P	0.42692	0.787	B	0.38056	0.264	T	0.50145	-0.8862	9	0.25751	T	0.34	-28.5008	15.5992	0.76611	0.0:1.0:0.0:0.0	.	12	P49585	PCY1A_HUMAN	K	12	.	ENSP00000292823:R12K	R	-	2	0	PCYT1A	197481765	1.000000	0.71417	0.993000	0.49108	0.991000	0.79684	4.022000	0.57203	2.752000	0.94435	0.655000	0.94253	AGG	.	.		0.468	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017		T	195997368	C	T	195997368	3	4	186	1	0	0	0	0	1	0	0	0	11619	681	24	3	1100	3	PCYT1A	3	195997368	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	28246926	195997368	2025062	20	27595										
NR3C2	4306	hgsc.bcm.edu	37	chr4	149115896	149115896	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	aactaaaaatacaaaacttaCctcctaaattcattccagct	1	11	1	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr4:149115896C>A	ENST00000503313.1	-	2	211		c.e2+1		NR3C2_ENST00000511528.1_Splice_Site|RP11-76G10.1_ENST00000514843.1_RNA|NR3C2_ENST00000355292.3_Splice_Site|NR3C2_ENST00000344721.4_Splice_Site|NR3C2_ENST00000512865.1_Splice_Site|NR3C2_ENST00000358102.3_Splice_Site			P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2						gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	ACAAAACTTACCTCCTAAATT	0.353																																					.	Melanoma(27;428 957 40335 51025 51111)	Atlas-SNP	.											.	NR3C2	94	.	0			c.2014+1G>T						.						58	60	59					4																	149115896		2203	4300	6503	SO:0001630	splice_region_variant	4306	exon5			AACTTACCTCCTA	M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000503313.1:c.666+1G>T	chr4.hg19:g.149115896C>A		35.0	0.0		17.0	6.0	NM_000901	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Splice_Site	SNP	ENST00000503313.1	hg19		.	.	.	.	.	.	.	.	.	.	C	25.7	4.662245	0.88251	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000342437;ENST00000511528	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1979	0.98245	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NR3C2	149335346	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.776000	0.85560	2.846000	0.97976	0.650000	0.86243	.	.	.		0.353	NR3C2-007	PUTATIVE	basic|exp_conf	processed_transcript	protein_coding	OTTHUMT00000364990.1		Intron	A	149115896	C	A	149115896	5	1	186	1	0	0	0	0	0	0	1	0	10640	521	18	3	963	3	NR3C2	4	149115896	Splice_Site	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10		149115896	42038380	21	27596										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32087361	32087361	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gagaatcccagccagcctgcAtcgcccagggtcaccaagtg	11	15	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr5:32087361A>G	ENST00000438447.1	+	20	4195	c.3807A>G	c.(3805-3807)gcA>gcG	p.A1269A	PDZD2_ENST00000282493.3_Silent_p.A1269A			O15018	PDZD2_HUMAN	PDZ domain containing 2	1269					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GCCAGCCTGCATCGCCCAGGG	0.647																																					p.A1269A		Atlas-SNP	.											.	PDZD2	306	.	0			c.A3807G						.						65	75	71					5																	32087361		2203	4300	6503	SO:0001819	synonymous_variant	23037	exon19			GCCTGCATCGCCC	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3807A>G	chr5.hg19:g.32087361A>G		182.0	0.0		342.0	50.0	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	hg19	CCDS34137.1																																																																																			.	.		0.647	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			G	32087361	A	G	32087361	2	3	186	1	0	0	0	0	0	0	0	1	11710	204	8	2		2	PDZD2	5	32087361	Silent	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10		32087361	148827899	22	27597										
CAST	831	hgsc.bcm.edu	37	chr5	96062545	96062546	+	Frame_Shift_Ins	INS	-	-	A													0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gaccacatcttcctaacaagINSaaaaaacacaaaaaacaggt							TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr5:96062545_96062546insA	ENST00000341926.3	+	3	231_232	c.69_70insA	c.(70-72)aaafs	p.K24fs	CAST_ENST00000511049.1_Frame_Shift_Ins_p.K10fs|CAST_ENST00000511782.1_Frame_Shift_Ins_p.K10fs|CAST_ENST00000504465.1_Intron|CAST_ENST00000508830.1_Frame_Shift_Ins_p.K107fs|CAST_ENST00000508608.1_Intron|CAST_ENST00000359176.4_Frame_Shift_Ins_p.K107fs|CAST_ENST00000509903.1_Intron|CAST_ENST00000395813.1_Frame_Shift_Ins_p.K107fs|CAST_ENST00000325674.7_Intron|CAST_ENST00000395812.2_Intron|CAST_ENST00000309190.5_Intron|CAST_ENST00000510756.1_Intron|CAST_ENST00000338252.3_Frame_Shift_Ins_p.K24fs			P20810	ICAL_HUMAN	calpastatin	24					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		TTCCTAACAAGAAAAAACACAA	0.396																																					p.K23fs		Atlas-INDEL	.											.	CAST	58	.	0			c.69_70insA						.																																			SO:0001589	frameshift_variant	831	exon5			.	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.75dupA	chr5.hg19:g.96062551_96062551dupA	ENSP00000339914:p.Lys24fs	157.0	0.0		75.0	40.0	NM_001190442	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Frame_Shift_Ins	INS	ENST00000341926.3	hg19																																																																																				.	.		0.396	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062		A	96062546	-	A	96062545	7	5	186	1	0	1	1	0	0	0	0	0	2686	933	33	0	336	0	CAST	5	96062545	Frame_Shift_Ins	INS	-	TCGA-DD-AADC-01A-11D-A40R-10	63975184	96062545	84852715	23	27598										
APC	324	hgsc.bcm.edu	37	chr5	112175951	112175952	+	Frame_Shift_Ins	INS	-	-	A													0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	aaaccaagagaaagaggcagINSaaaaaactattgattctgaa					rs587783031		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr5:112175951_112175952insA	ENST00000457016.1	+	16	5040_5041	c.4660_4661insA	c.(4660-4662)gaafs	p.E1554fs	APC_ENST00000257430.4_Frame_Shift_Ins_p.E1554fs|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Frame_Shift_Ins_p.E1554fs			P25054	APC_HUMAN	adenomatous polyposis coli	1554	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.T1556fs*3(42)|p.E1554fs*5(2)|p.E1554fs*3(1)|p.?(1)|p.T1556fs*9(1)|p.?fs(1)|p.K1192fs*3(1)|p.E1554*(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAAAGAGGCAGAAAAAACTATT	0.342		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.E1554fs	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-INDEL	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	APC,colon,carcinoma,-1,58	APC	4158	.	50	Insertion - Frameshift(45)|Deletion - Frameshift(3)|Substitution - Nonsense(1)|Unknown(1)	large_intestine(45)|stomach(3)|soft_tissue(1)|skin(1)	c.4660_4661insA						.																																			SO:0001589	frameshift_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	.	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4666dupA	chr5.hg19:g.112175957_112175957dupA	ENSP00000413133:p.Glu1554fs	269.0	0.0		155.0	62.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Ins	INS	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.342	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112175952	-	A	112175951	7	5	186	1	0	1	1	0	0	0	0	0	763	943	33	0	4718	0	APC	5	112175951	Frame_Shift_Ins	INS	-	TCGA-DD-AADC-01A-11D-A40R-10	16113406	112175951	68739309	24	27599										
RREB1	6239	hgsc.bcm.edu	37	chr6	7230408	7230408	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ctcatccgccacctgcgcacGcacagtggggagcggcccta	12	17	1	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:7230408G>T	ENST00000349384.6	+	10	2390	c.2076G>T	c.(2074-2076)acG>acT	p.T692T	RREB1_ENST00000379933.3_Silent_p.T692T|RREB1_ENST00000379938.2_Silent_p.T692T|RREB1_ENST00000334984.6_Silent_p.T692T	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	692					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				ACCTGCGCACGCACAGTGGGG	0.632																																					p.T692T		Atlas-SNP	.											.	RREB1	242	.	0			c.G2076T						.						65	59	61					6																	7230408		2203	4300	6503	SO:0001819	synonymous_variant	6239	exon10			GCGCACGCACAGT	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.2076G>T	chr6.hg19:g.7230408G>T		98.0	0.0		51.0	25.0	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	hg19	CCDS34336.1																																																																																			.	.		0.632	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			T	7230408	G	T	7230408	2	4	186	1	0	0	0	0	0	0	0	1	13694	1074	38	1		1	RREB1	6	7230408	Silent	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10		7230408	163884659	25	27600										
EDN1	1906	hgsc.bcm.edu	37	chr6	12294631	12294631	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ttcagaggaacacctaagacAaaccaggtaagagggaagga	12	7	1	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:12294631A>C	ENST00000379375.5	+	4	794	c.527A>C	c.(526-528)cAa>cCa	p.Q176P		NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	176					artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				CACCTAAGACAAACCAGGTAA	0.428																																					p.Q176P		Atlas-SNP	.											.	EDN1	23	.	0			c.A527C						.						72	74	73					6																	12294631		2203	4300	6503	SO:0001583	missense	1906	exon4			TAAGACAAACCAG	S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401		"Endogenous ligands"	3176	protein-coding gene	gene with protein product		131240					Standard	NM_001168319		Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.527A>C	chr6.hg19:g.12294631A>C	ENSP00000368683:p.Gln176Pro	481.0	1.0		335.0	151.0	NM_001955	Q96DA1	Missense_Mutation	SNP	ENST00000379375.5	hg19	CCDS4522.1	.	.	.	.	.	.	.	.	.	.	A	9.235	1.036829	0.19669	.	.	ENSG00000078401	ENST00000379375	D	0.84146	-1.81	1.03	1.03	0.20045	.	0.534882	0.11761	U	0.532088	T	0.50205	0.1602	N	0.19112	0.55	0.19775	N	0.999955	B;B	0.33266	0.404;0.404	B;B	0.20384	0.029;0.029	T	0.40813	-0.9543	10	0.59425	D	0.04	.	4.4221	0.11486	1.0:0.0:0.0:0.0	.	176;176	Q6FH53;P05305	.;EDN1_HUMAN	P	176	ENSP00000368683:Q176P	ENSP00000368683:Q176P	Q	+	2	0	EDN1	12402617	0.314000	0.24563	0.420000	0.26596	0.304000	0.27724	0.681000	0.25320	0.263000	0.21812	0.260000	0.18958	CAA	.	.		0.428	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039872.1	NM_001955		C	12294631	A	C	12294631	3	2	186	1	0	0	0	0	1	0	0	0	4918	130	5	5	541	5	EDN1	6	12294631	Missense_Mutation	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10	5064223	12294631	158820436	26	27601										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38885133	38885133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gaaaattgaccctgttactaTggatccagaaaaatcttgct	7	8	1	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:38885133T>C	ENST00000359357.3	+	67	9862	c.9608T>C	c.(9607-9609)aTg>aCg	p.M3203T	DNAH8_ENST00000441566.1_Missense_Mutation_p.M3167T|DNAH8_ENST00000449981.2_Missense_Mutation_p.M3420T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3203	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CCTGTTACTATGGATCCAGAA	0.388																																					p.M3420T		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T10259C						.						135	127	130					6																	38885133		2203	4300	6503	SO:0001583	missense	1769	exon69			TTACTATGGATCC	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.9608T>C	chr6.hg19:g.38885133T>C	ENSP00000352312:p.Met3203Thr	91.0	0.0		97.0	39.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	T	10.20	1.284702	0.23392	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.73681	-0.77;-0.77;-0.77	5.75	5.75	0.90469	Dynein heavy chain, coiled coil stalk (1);	0.082491	0.85682	D	0.000000	T	0.46580	0.1400	N	0.20685	0.6	0.46222	D	0.998937	B	0.06786	0.001	B	0.14023	0.01	T	0.45600	-0.9250	10	0.22706	T	0.39	.	16.0591	0.80826	0.0:0.0:0.0:1.0	.	3203	Q96JB1	DYH8_HUMAN	T	3408;3408;3203;3167	ENSP00000333363:M3408T;ENSP00000352312:M3203T;ENSP00000402294:M3167T	ENSP00000333363:M3408T	M	+	2	0	DNAH8	38993111	0.990000	0.36364	1.000000	0.80357	0.994000	0.84299	2.214000	0.42853	2.190000	0.69967	0.482000	0.46254	ATG	.	.		0.388	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		C	38885133	T	C	38885133	3	2	186	1	0	0	0	0	1	0	0	0	4609	1464	51	2	9866	2	DNAH8	6	38885133	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	26590502	38885133	132229934	27	27602										
SLC29A1	2030	hgsc.bcm.edu	37	chr6	44197363	44197363	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ggacatgtcccagaatgtgtCcttggtcactgctgaactga	11	10	1	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:44197363C>A	ENST00000393841.1	+	5	640	c.149C>A	c.(148-150)tCc>tAc	p.S50Y	SLC29A1_ENST00000371740.5_Missense_Mutation_p.S50Y|SLC29A1_ENST00000472176.1_3'UTR|SLC29A1_ENST00000313248.7_Missense_Mutation_p.S129Y|SLC29A1_ENST00000371755.3_Missense_Mutation_p.S50Y|SLC29A1_ENST00000371713.1_Missense_Mutation_p.S50Y|SLC29A1_ENST00000393844.1_Missense_Mutation_p.S50Y|SLC29A1_ENST00000371724.1_Missense_Mutation_p.S50Y|SLC29A1_ENST00000427851.2_Missense_Mutation_p.S50Y|SLC29A1_ENST00000371708.1_Missense_Mutation_p.S50Y|SLC29A1_ENST00000371731.1_Missense_Mutation_p.S50Y	NM_001078177.1	NP_001071645.1	Q99808	S29A1_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 1	50					cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|lactation (GO:0007595)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sleep (GO:0030431)|transmembrane transport (GO:0055085)|uridine transport (GO:0015862)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	17	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Cytarabine(DB00987)|Didanosine(DB00900)|Fludarabine(DB01073)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Pemetrexed(DB00642)|Ribavirin(DB00811)|Zalcitabine(DB00943)	CAGAATGTGTCCTTGGTCACT	0.557																																					p.S50Y		Atlas-SNP	.											.	SLC29A1	45	.	0			c.C149A						.						113	107	109					6																	44197363		2203	4300	6503	SO:0001583	missense	2030	exon4			ATGTGTCCTTGGT	U81375	CCDS4908.1	6p21.1	2013-07-17	2013-07-17		ENSG00000112759	ENSG00000112759		"Solute carriers"	11003	protein-coding gene	gene with protein product		602193	"solute carrier family 29 (nucleoside transporters), member 1"	ENT1		8986748, 9344680	Standard	NM_004955		Approved		uc003owy.2	Q99808	OTTHUMG00000014759	ENST00000393841.1:c.149C>A	chr6.hg19:g.44197363C>A	ENSP00000377424:p.Ser50Tyr	64.0	0.0		76.0	29.0	NM_004955	B3KQV7|B3KQY5|Q5T9W9|Q9UJY2	Missense_Mutation	SNP	ENST00000393841.1	hg19	CCDS4908.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.846488	0.91277	.	.	ENSG00000112759	ENST00000544345;ENST00000393844;ENST00000313248;ENST00000427851;ENST00000371755;ENST00000371740;ENST00000371731;ENST00000393841;ENST00000371724;ENST00000371713;ENST00000371708	T;T;T;T;T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01;2.01;2.01;2.01;2.01	5.48	5.48	0.80851	.	1.265590	0.04916	N	0.454125	T	0.21387	0.0515	L	0.50333	1.59	0.20403	N	0.999902	P;P;D;P	0.53885	0.539;0.7;0.963;0.929	B;B;P;B	0.50970	0.281;0.281;0.655;0.427	T	0.22521	-1.0214	10	0.72032	D	0.01	-26.0206	12.8287	0.57735	0.0:0.8231:0.1769:0.0	.	50;69;129;50	B7Z1J8;B7Z914;B3KQV7;Q99808	.;.;.;S29A1_HUMAN	Y	69;50;129;50;50;50;50;50;50;50;50	ENSP00000377427:S50Y;ENSP00000319152:S129Y;ENSP00000392668:S50Y;ENSP00000360820:S50Y;ENSP00000360805:S50Y;ENSP00000360796:S50Y;ENSP00000377424:S50Y;ENSP00000360789:S50Y;ENSP00000360778:S50Y;ENSP00000360773:S50Y	ENSP00000319152:S129Y	S	+	2	0	SLC29A1	44305341	0.009000	0.17119	0.534000	0.28014	0.944000	0.59088	0.855000	0.27805	2.581000	0.87130	0.563000	0.77884	TCC	.	.		0.557	SLC29A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040721.1			A	44197363	C	A	44197363	3	1	186	1	0	0	0	0	1	0	0	0	14549	855	30	3	159	3	SLC29A1	6	44197363	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	5312230	44197363	126917704	28	27603										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138611075	138611075	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	aggcctggagatgggaagccAcaacccggactgctggccac	14	13	0	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:138611075A>G	ENST00000251691.4	+	18	3183	c.3017A>G	c.(3016-3018)cAc>cGc	p.H1006R		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		ATGGGAAGCCACAACCCGGAC	0.622																																					p.H1006R		Atlas-SNP	.											.	KIAA1244	236	.	0			c.A3017G						.						88	78	82					6																	138611075		2203	4300	6503	SO:0001583	missense	57221	exon18			GAAGCCACAACCC	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.3017A>G	chr6.hg19:g.138611075A>G	ENSP00000251691:p.His1006Arg	192.0	0.0		206.0	59.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	A	27.4	4.829504	0.90955	.	.	ENSG00000112379	ENST00000251691	T	0.28454	1.61	5.44	5.44	0.79542	.	0.186808	0.56097	D	0.000022	T	0.47322	0.1439	M	0.72894	2.215	0.58432	D	0.999999	D	0.63880	0.993	D	0.72338	0.977	T	0.52411	-0.8579	10	0.87932	D	0	-31.8043	15.7983	0.78428	1.0:0.0:0.0:0.0	.	1006	Q5TH69	BIG3_HUMAN	R	1006	ENSP00000251691:H1006R	ENSP00000251691:H1006R	H	+	2	0	KIAA1244	138652768	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.229000	0.95273	2.177000	0.69029	0.533000	0.62120	CAC	.	.		0.622	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		G	138611075	A	G	138611075	3	3	186	1	0	0	0	0	1	0	0	0	8226	159	6	2	3087	2	KIAA1244	6	138611075	Missense_Mutation	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10	94413712	138611075	32503992	29	27604										
PHACTR2	9749	hgsc.bcm.edu	37	chr6	144086750	144086750	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gcaccttctcctctggccccCcctctccctcttgaggatca	6	20	5	1	rs200488499		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:144086750C>T	ENST00000427704.2	+	6	1144	c.1014C>T	c.(1012-1014)ccC>ccT	p.P338P	PHACTR2_ENST00000305766.6_Silent_p.P258P|PHACTR2_ENST00000440869.2_Silent_p.P349P|PHACTR2_ENST00000367584.4_Silent_p.P326P|PHACTR2_ENST00000367582.3_Silent_p.P269P	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	338							protein phosphatase inhibitor activity (GO:0004864)			NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		CTCTGGCCCCCCCTCTCCCTC	0.587																																					p.P349P	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)	Atlas-SNP	.											.	PHACTR2	99	.	0			c.C1047T						.						58	65	63					6																	144086750		2027	4161	6188	SO:0001819	synonymous_variant	9749	exon6			GGCCCCCCCTCTC	AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"Phosphatase and actin regulators"	20956	protein-coding gene	gene with protein product		608724	"chromosome 6 open reading frame 56"	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.1014C>T	chr6.hg19:g.144086750C>T		126.0	0.0		107.0	48.0	NM_001100164	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Silent	SNP	ENST00000427704.2	hg19	CCDS47492.1																																																																																			.	C|1.000;G|0.000		0.587	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721		T	144086750	C	T	144086750	2	4	186	1	0	0	0	0	0	0	0	1	11819	610	22	3		3	PHACTR2	6	144086750	Silent	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	5475675	144086750	27028317	30	27605										
AUTS2	26053	hgsc.bcm.edu	37	chr7	70255636	70255636	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ccctcggcgggagcacgagcGgggaggccacctggacgagc	18	14	0	0	rs371317370		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr7:70255636G>A	ENST00000342771.4	+	19	3755	c.3434G>A	c.(3433-3435)cGg>cAg	p.R1145Q	AUTS2_ENST00000406775.2_Missense_Mutation_p.R1121Q	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1145	His-rich.									breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GAGCACGAGCGGGGAGGCCAC	0.692																																					p.R1145Q		Atlas-SNP	.											.	AUTS2	173	.	0			c.G3434A						.	G	GLN/ARG,GLN/ARG	2,4400		0,2,2199	21	23	22		3362,3434	4.8	0.9	7		22	2,8580		0,2,4289	no	missense,missense	AUTS2	NM_001127231.1,NM_015570.2	43,43	0,4,6488	AA,AG,GG		0.0233,0.0454,0.0308	probably-damaging,probably-damaging	1121/1236,1145/1260	70255636	4,12980	2201	4291	6492	SO:0001583	missense	26053	exon19			ACGAGCGGGGAGG	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.3434G>A	chr7.hg19:g.70255636G>A	ENSP00000344087:p.Arg1145Gln	124.0	0.0		143.0	54.0	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	hg19	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.903198	0.92035	4.54E-4	2.33E-4	ENSG00000158321	ENST00000406775;ENST00000342771	T;T	0.38722	1.17;1.12	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.60340	0.2261	L	0.56199	1.76	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.77557	0.99;0.99;0.99	T	0.59526	-0.7438	9	.	.	.	-14.7232	17.8486	0.88738	0.0:0.0:1.0:0.0	.	597;1121;1145	B4DLG0;Q8WXX7-2;Q8WXX7	.;.;AUTS2_HUMAN	Q	1121;1145	ENSP00000385263:R1121Q;ENSP00000344087:R1145Q	.	R	+	2	0	AUTS2	69893572	1.000000	0.71417	0.926000	0.36857	0.994000	0.84299	9.047000	0.93823	2.217000	0.71921	0.655000	0.94253	CGG	.	.		0.692	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			A	70255636	G	A	70255636	3	1	186	1	0	0	0	0	1	0	0	0	1225	1116	39	1	3653	1	AUTS2	7	70255636	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10		70255636	88883027	31	27606										
PON3	5446	hgsc.bcm.edu	37	chr7	95019498	95019498	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	agccagcccactaggaagtaTatcaatatcttcagagccac	7	12	3	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr7:95019498T>C	ENST00000265627.5	-	3	179	c.169A>G	c.(169-171)Ata>Gta	p.I57V	PON1_ENST00000542556.1_Intron|PON3_ENST00000475439.1_5'UTR|PON3_ENST00000451904.1_Missense_Mutation_p.I57V|PON3_ENST00000427422.1_Missense_Mutation_p.I57V	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	57					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	CTAGGAAGTATATCAATATCT	0.383																																					p.I57V		Atlas-SNP	.											.	PON3	59	.	0			c.A169G						.						205	216	212					7																	95019498		2203	4300	6503	SO:0001583	missense	5446	exon3			GAAGTATATCAAT	L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"Paraoxonases"	9206	protein-coding gene	gene with protein product	"arylesterase 3"	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.169A>G	chr7.hg19:g.95019498T>C	ENSP00000265627:p.Ile57Val	109.0	0.0		112.0	40.0	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Missense_Mutation	SNP	ENST00000265627.5	hg19	CCDS5639.1	.	.	.	.	.	.	.	.	.	.	T	9.170	1.020830	0.19433	.	.	ENSG00000105852	ENST00000265627;ENST00000427422	T;T	0.31247	1.5;1.5	4.93	3.78	0.43462	Six-bladed beta-propeller, TolB-like (1);	0.046816	0.85682	N	0.000000	T	0.24431	0.0592	L	0.49640	1.575	0.45662	D	0.998584	B;B	0.24426	0.103;0.004	B;B	0.20767	0.031;0.007	T	0.05194	-1.0900	10	0.27082	T	0.32	-14.874	7.4731	0.27361	0.0:0.0967:0.0:0.9033	.	57;57	B4E2I0;Q15166	.;PON3_HUMAN	V	57	ENSP00000265627:I57V;ENSP00000413276:I57V	ENSP00000265627:I57V	I	-	1	0	PON3	94857434	1.000000	0.71417	0.998000	0.56505	0.327000	0.28475	2.194000	0.42668	1.032000	0.39892	0.460000	0.39030	ATA	.	.		0.383	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940		C	95019498	T	C	95019498	3	2	186	1	0	0	0	0	1	0	0	0	12259	1406	49	2	923	2	PON3	7	95019498	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	24763862	95019498	64119165	32	27607										
DLX6	1750	hgsc.bcm.edu	37	chr7	96635420	96635420	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gcagcagcagcaacagcaacAgccgccgccgccgccgccgc	12	20	0	0	rs570498188|rs559903070	byFrequency	TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr7:96635420A>C	ENST00000518156.2	+	1	561	c.131A>C	c.(130-132)cAg>cCg	p.Q44P	DLX6-AS1_ENST00000458352.2_RNA|DLX6-AS1_ENST00000452769.2_RNA|DLX6-AS1_ENST00000437541.1_RNA|DLX6-AS2_ENST00000606174.1_RNA|DLX6_ENST00000555308.1_5'Flank|DLX6-AS1_ENST00000430404.2_RNA|DLX6_ENST00000007660.5_Intron|DLX6-AS1_ENST00000605417.1_RNA|DLX6-AS1_ENST00000430027.3_RNA|DLX6-AS1_ENST00000437331.2_RNA|DLX6-AS1_ENST00000431497.2_RNA			P56179	DLX6_HUMAN	distal-less homeobox 6	0					anatomical structure formation involved in morphogenesis (GO:0048646)|embryonic limb morphogenesis (GO:0030326)|epithelial cell differentiation (GO:0030855)|head development (GO:0060322)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|palate development (GO:0060021)|positive regulation of epithelial cell proliferation (GO:0050679)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(2)|urinary_tract(1)	12	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					caacagcaacagccgccgccg	0.697																																					p.Q44P		Atlas-SNP	.											.,1	DLX6	37	.	0			c.A131C						.						2	3	3					7																	96635420		1105	2646	3751	SO:0001583	missense	1750	exon1			AGCAACAGCCGCC		CCDS47647.1, CCDS47647.2	7q21.3	2011-06-20	2005-12-22		ENSG00000006377	ENSG00000006377		"Homeoboxes / ANTP class : NKL subclass"	2919	protein-coding gene	gene with protein product		600030	"distal-less homeo box 6"			7907794	Standard	NM_005222		Approved		uc022ahu.1	P56179	OTTHUMG00000154201	ENST00000518156.2:c.131A>C	chr7.hg19:g.96635420A>C	ENSP00000428480:p.Gln44Pro	32.0	0.0		46.0	4.0	NM_005222	A4D1I2|B3KSQ0|J3KR92|Q3ZAR6|Q9UPL2	Missense_Mutation	SNP	ENST00000518156.2	hg19	CCDS47647.2	.	.	.	.	.	.	.	.	.	.	a	7.009	0.556463	0.13436	.	.	ENSG00000006377	ENST00000518156	D	0.92545	-3.06	2.89	-0.0314	0.13910	.	.	.	.	.	D	0.89653	0.6777	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.82739	-0.0308	6	0.32370	T	0.25	.	6.6539	0.22977	0.4411:0.5589:0.0:0.0	.	.	.	.	P	44	ENSP00000428480:Q44P	ENSP00000428480:Q44P	Q	+	2	0	DLX6	96473356	.	.	0.983000	0.44433	0.971000	0.66376	.	.	0.205000	0.20568	0.156000	0.16432	CAG	.	.		0.697	DLX6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334373.4	NM_005222		C	96635420	A	C	96635420	3	2	186	1	0	0	0	0	1	0	0	0	4577	188	7	5	133	5	DLX6	7	96635420	Missense_Mutation	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10	1615922	96635420	62503243	33	27608										
COG5	10466	hgsc.bcm.edu	37	chr7	106898762	106898762	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	atacaatgaattcactactgCcacatttcttctctgtcctt	3	12	3	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr7:106898762C>A	ENST00000347053.3	-	15	1785	c.1735G>T	c.(1735-1737)Gca>Tca	p.A579S	COG5_ENST00000393603.2_Missense_Mutation_p.A579S|COG5_ENST00000297135.3_Missense_Mutation_p.A579S	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	579					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						TTCACTACTGCCACATTTCTT	0.338																																					p.A579S		Atlas-SNP	.											.	COG5	78	.	0			c.G1735T						.						199	183	189					7																	106898762		2203	4300	6503	SO:0001583	missense	10466	exon15			CTACTGCCACATT	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"Components of oligomeric golgi complex"	14857	protein-coding gene	gene with protein product		606821	"golgi transport complex 1 (90 kDa subunit)"	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1735G>T	chr7.hg19:g.106898762C>A	ENSP00000334703:p.Ala579Ser	107.0	0.0		119.0	35.0	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	hg19	CCDS5743.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348169	0.41599	.	.	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.58358	0.34;0.34;0.34	6.03	4.21	0.49690	.	0.271361	0.41500	N	0.000878	T	0.45013	0.1321	L	0.56199	1.76	0.39971	D	0.97479	B;B	0.27910	0.056;0.193	B;B	0.29942	0.028;0.109	T	0.29027	-1.0025	10	0.14252	T	0.57	-4.1358	10.409	0.44280	0.1349:0.7949:0.0:0.0702	.	579;579	Q9UP83;Q9UP83-2	COG5_HUMAN;.	S	579	ENSP00000334703:A579S;ENSP00000297135:A579S;ENSP00000377228:A579S	ENSP00000297135:A579S	A	-	1	0	COG5	106685998	0.998000	0.40836	0.999000	0.59377	0.979000	0.70002	3.080000	0.50112	0.860000	0.35481	-0.140000	0.14226	GCA	.	.		0.338	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			A	106898762	C	A	106898762	3	1	186	1	0	0	0	0	1	0	0	0	3663	739	26	3	883	3	COG5	7	106898762	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	10263342	106898762	52239901	34	27609										
TMEM68	137695	hgsc.bcm.edu	37	chr8	56668880	56668880	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	taaatattttagccatgaaaTagtaaaaatctataggaata	5	3	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:56668880T>C	ENST00000434581.2	-	4	615	c.416A>G	c.(415-417)tAt>tGt	p.Y139C	TMEM68_ENST00000523073.1_Missense_Mutation_p.Y25C|TMEM68_ENST00000519784.1_Missense_Mutation_p.Y25C|TMEM68_ENST00000334667.2_Missense_Mutation_p.Y139C			Q96MH6	TMM68_HUMAN	transmembrane protein 68	139						integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			NS(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6			Epithelial(17;0.000361)|all cancers(17;0.00326)			AGCCATGAAATAGTAAAAATC	0.323																																					p.Y139C		Atlas-SNP	.											.	TMEM68	25	.	0			c.A416G						.						50	54	53					8																	56668880		2202	4296	6498	SO:0001583	missense	137695	exon4			ATGAAATAGTAAA	AK056932	CCDS6161.1, CCDS75740.1, CCDS75741.1, CCDS75742.1	8q12.1	2011-12-12			ENSG00000167904	ENSG00000167904			26510	protein-coding gene	gene with protein product						12477932	Standard	XM_005251150		Approved	FLJ32370	uc003xsh.1	Q96MH6	OTTHUMG00000164293	ENST00000434581.2:c.416A>G	chr8.hg19:g.56668880T>C	ENSP00000395204:p.Tyr139Cys	108.0	0.0		92.0	27.0	NM_152417	Q658X6|Q8WUD2	Missense_Mutation	SNP	ENST00000434581.2	hg19		.	.	.	.	.	.	.	.	.	.	T	19.63	3.864066	0.71949	.	.	ENSG00000167904	ENST00000434581;ENST00000334667;ENST00000519784;ENST00000523073;ENST00000519780;ENST00000522090;ENST00000523423	D;D;D;D;D;D	0.97303	-3.22;-3.22;-3.22;-3.22;-4.33;-3.22	5.57	4.4	0.53042	Phospholipid/glycerol acyltransferase (2);	0.124094	0.56097	N	0.000028	D	0.98213	0.9409	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.98223	1.0479	10	0.62326	D	0.03	-10.7085	11.8537	0.52425	0.1312:0.0:0.0:0.8688	.	139;139	Q96MH6-2;Q96MH6	.;TMM68_HUMAN	C	139;139;25;25;25;139;139	ENSP00000395204:Y139C;ENSP00000335416:Y139C;ENSP00000428688:Y25C;ENSP00000429026:Y25C;ENSP00000429667:Y25C;ENSP00000430542:Y139C	ENSP00000335416:Y139C	Y	-	2	0	TMEM68	56831434	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.015000	0.88690	0.919000	0.36945	0.482000	0.46254	TAT	.	.		0.323	TMEM68-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000378137.1	NM_152417		C	56668880	T	C	56668880	3	2	186	1	0	0	0	0	1	0	0	0	16212	1406	49	2	369	2	TMEM68	8	56668880	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10		56668880	89695142	35	27610										
CNBD1	168975	hgsc.bcm.edu	37	chr8	87951908	87951908	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gtccatgttcagagagcacaTggtggccatattttatatag	10	7	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:87951908T>C	ENST00000518476.1	+	4	408	c.357T>C	c.(355-357)caT>caC	p.H119H		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	119										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						AGAGAGCACATGGTGGCCATA	0.333																																					p.H119H		Atlas-SNP	.											.	CNBD1	206	.	0			c.T357C						.						78	75	76					8																	87951908		1818	4085	5903	SO:0001819	synonymous_variant	168975	exon4			AGCACATGGTGGC	AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.357T>C	chr8.hg19:g.87951908T>C		411.0	0.0		760.0	143.0	NM_173538		Silent	SNP	ENST00000518476.1	hg19	CCDS55259.1																																																																																			.	.		0.333	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		C	87951908	T	C	87951908	2	2	186	1	0	0	0	0	0	0	0	1	3593	1461	51	2		2	CNBD1	8	87951908	Silent	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	31283028	87951908	58412114	36	27611										
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885852	88885852	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gggacgtagagggttttgtgCgggtatacccggagctcagg	18	7	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:88885852C>A	ENST00000319675.3	-	1	444	c.348G>T	c.(346-348)ccG>ccT	p.P116P		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	116										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						GGGTTTTGTGCGGGTATACCC	0.552																																					p.P116P		Atlas-SNP	.											.	DCAF4L2	187	.	0			c.G348T						.						128	124	125					8																	88885852		2203	4300	6503	SO:0001819	synonymous_variant	138009	exon1			TTTGTGCGGGTAT	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.348G>T	chr8.hg19:g.88885852C>A		104.0	0.0		167.0	34.0	NM_152418		Silent	SNP	ENST00000319675.3	hg19	CCDS6245.1																																																																																			.	.		0.552	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		A	88885852	C	A	88885852	2	1	186	1	0	0	0	0	0	0	0	1	4274	755	27	1		1	DCAF4L2	8	88885852	Silent	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	933944	88885852	57478170	37	27612										
LRP12	29967	hgsc.bcm.edu	37	chr8	105503525	105503525	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ttttctgtgtctgtatcatcAgactccacggaaaacaaact	6	10	4	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:105503525A>G	ENST00000276654.5	-	7	2064	c.1956T>C	c.(1954-1956)tcT>tcC	p.S652S	LRP12_ENST00000424843.2_Silent_p.S633S|LRP12_ENST00000518375.1_5'UTR	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	652					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CTGTATCATCAGACTCCACGG	0.478																																					p.S652S		Atlas-SNP	.											.	LRP12	124	.	0			c.T1956C						.						91	87	88					8																	105503525		2203	4300	6503	SO:0001819	synonymous_variant	29967	exon7			ATCATCAGACTCC	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.1956T>C	chr8.hg19:g.105503525A>G		104.0	0.0		160.0	100.0	NM_013437	A8K137|B4DRQ2	Silent	SNP	ENST00000276654.5	hg19	CCDS6303.1																																																																																			.	.		0.478	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		G	105503525	A	G	105503525	2	3	186	1	0	0	0	0	0	0	0	1	8963	175	7	2		2	LRP12	8	105503525	Silent	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10	16617673	105503525	40860497	38	27613										
KLHL38	340359	hgsc.bcm.edu	37	chr8	124664210	124664210	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gaggccttgtacagccgtgtCgggagtttggcaaggctctg	16	9	1	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:124664210C>G	ENST00000325995.7	-	1	980	c.957G>C	c.(955-957)ccG>ccC	p.P319P	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	319										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						ACAGCCGTGTCGGGAGTTTGG	0.592																																					p.P319P		Atlas-SNP	.											.	KLHL38	81	.	0			c.G957C						.						70	74	72					8																	124664210		2016	4164	6180	SO:0001819	synonymous_variant	340359	exon1			CCGTGTCGGGAGT		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"Kelch-like", "BTB/POZ domain containing"	34435	protein-coding gene	gene with protein product			"kelch-like 38 (Drosophila)"				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.957G>C	chr8.hg19:g.124664210C>G		122.0	0.0		191.0	76.0	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	hg19	CCDS43766.1																																																																																			.	.		0.592	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1			G	124664210	C	G	124664210	2	3	186	1	0	0	0	0	0	0	0	1	8399	871	31	4		4	KLHL38	8	124664210	Silent	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	19160685	124664210	21699812	39	27614										
PHF20L1	51105	hgsc.bcm.edu	37	chr8	133806672	133806673	+	Frame_Shift_Ins	INS	-	-	A													0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gaggtatccatcacgaattgINSaaaaaattgactatgaggag							TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:133806672_133806673insA	ENST00000395386.2	+	3	399_400	c.100_101insA	c.(100-102)gaafs	p.E34fs	PHF20L1_ENST00000395379.1_Frame_Shift_Ins_p.E34fs|PHF20L1_ENST00000395390.2_Frame_Shift_Ins_p.E34fs|PHF20L1_ENST00000395376.1_Frame_Shift_Ins_p.E34fs|PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000337920.4_Frame_Shift_Ins_p.E34fs	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	34	Tudor 1.						zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			ATCACGAATTGAAAAAATTGAC	0.351																																					p.E34fs		Atlas-INDEL	.											.	PHF20L1	129	.	0			c.100_101insA						.																																			SO:0001589	frameshift_variant	51105	exon3			.	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.106dupA	chr8.hg19:g.133806678_133806678dupA	ENSP00000378784:p.Glu34fs	163.0	0.0		271.0	95.0	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Frame_Shift_Ins	INS	ENST00000395386.2	hg19	CCDS6367.2																																																																																			.	.		0.351	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		A	133806673	-	A	133806672	7	5	186	1	0	1	1	0	0	0	0	0	11841	1291	45	0	106	0	PHF20L1	8	133806672	Frame_Shift_Ins	INS	-	TCGA-DD-AADC-01A-11D-A40R-10	9142462	133806672	12557350	40	27615										
PUF60	22827	hgsc.bcm.edu	37	chr8	144900554	144900554	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	cctgctgaccttgtgcttcaTggtgacggagtcccaggaca	12	12	1	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:144900554T>C	ENST00000526683.1	-	6	1054	c.499A>G	c.(499-501)Atg>Gtg	p.M167V	PUF60_ENST00000527197.1_Missense_Mutation_p.M121V|PUF60_ENST00000349157.6_Missense_Mutation_p.M150V|PUF60_ENST00000524570.1_5'UTR|PUF60_ENST00000313352.7_Missense_Mutation_p.M107V|PUF60_ENST00000453551.2_Missense_Mutation_p.M124V|PUF60_ENST00000456095.2_Missense_Mutation_p.M138V	NM_001271098.1|NM_078480.2	NP_001258027.1|NP_510965.1	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa	167	Inhibits homodimerization.|Inhibits transcriptional repression, interaction with ERCC3 and apoptosis induction.|RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(3)|lung(7)|prostate(2)	14	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			TTGTGCTTCATGGTGACGGAG	0.647																																					p.M167V		Atlas-SNP	.											.	PUF60	26	.	0			c.A499G						.						46	51	49					8																	144900554		2097	4216	6313	SO:0001583	missense	22827	exon6			GCTTCATGGTGAC	AF114818	CCDS47933.1, CCDS47934.1, CCDS47935.1, CCDS59514.1, CCDS59515.1, CCDS59516.1	8q24.3	2013-02-12	2007-07-27		ENSG00000179950	ENSG00000179950		"RNA binding motif (RRM) containing"	17042	protein-coding gene	gene with protein product	"siah binding protein 1", "FBP interacting repressor", "pyrimidine tract binding splicing factor", "Ro ribonucleoprotein binding protein 1"	604819				10668799, 10882074, 17579712	Standard	NM_078480		Approved	FIR, SIAHBP1, RoBPI	uc003yzs.4	Q9UHX1	OTTHUMG00000165155	ENST00000526683.1:c.499A>G	chr8.hg19:g.144900554T>C	ENSP00000434359:p.Met167Val	108.0	0.0		195.0	117.0	NM_078480	A8K8K8|Q969E7|Q96D94|Q96H63|Q99628|Q9NZA0|Q9UJY7	Missense_Mutation	SNP	ENST00000526683.1	hg19	CCDS47934.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.154406	0.57259	.	.	ENSG00000179950	ENST00000526683;ENST00000453551;ENST00000313352;ENST00000456095;ENST00000349157;ENST00000527197;ENST00000526459;ENST00000529999;ENST00000531897;ENST00000533162	T;T;T;T;T;T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;3.39;-0.81;1.32	4.94	4.94	0.65067	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.043220	0.85682	D	0.000000	T	0.71333	0.3327	N	0.24115	0.695	0.80722	D	1	B;B;B	0.28233	0.047;0.17;0.204	B;B;B	0.43950	0.018;0.31;0.437	T	0.71220	-0.4657	10	0.44086	T	0.13	.	13.7722	0.63034	0.0:0.0:0.0:1.0	.	138;150;167	Q9UHX1-5;Q9UHX1-2;Q9UHX1	.;.;PUF60_HUMAN	V	167;124;107;138;150;121;149;187;187;204	ENSP00000434359:M167V;ENSP00000402953:M124V;ENSP00000322016:M107V;ENSP00000395417:M138V;ENSP00000322036:M150V;ENSP00000431960:M121V;ENSP00000432610:M149V;ENSP00000434863:M187V;ENSP00000437309:M187V;ENSP00000433403:M204V	ENSP00000322016:M107V	M	-	1	0	PUF60	144972542	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.939000	0.87685	1.860000	0.53959	0.482000	0.46254	ATG	.	.		0.647	PUF60-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382222.1	NM_014281		C	144900554	T	C	144900554	3	2	186	1	0	0	0	0	1	0	0	0	12839	1464	51	2	1208	2	PUF60	8	144900554	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	11093882	144900554	1463468	41	27616										
KANK1	23189	hgsc.bcm.edu	37	chr9	711598	711598	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tgaaacgcctgaaggagctgGaggagcaggtgcgaaccatc	15	9	0	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:711598G>C	ENST00000382303.1	+	7	1484	c.832G>C	c.(832-834)Gag>Cag	p.E278Q	KANK1_ENST00000382293.3_Missense_Mutation_p.E120Q|KANK1_ENST00000382297.2_Missense_Mutation_p.E278Q|KANK1_ENST00000489369.1_3'UTR	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	278					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GAAGGAGCTGGAGGAGCAGGT	0.562																																					p.E278Q		Atlas-SNP	.											.	KANK1	231	.	0			c.G832C						.						86	81	82					9																	711598		2203	4300	6503	SO:0001583	missense	23189	exon7			GAGCTGGAGGAGC	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.832G>C	chr9.hg19:g.711598G>C	ENSP00000371740:p.Glu278Gln	118.0	0.0		58.0	34.0	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	hg19	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.514496	0.85389	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.00940	5.52;5.52;5.52	5.82	5.82	0.92795	.	0.239747	0.29668	N	0.011505	T	0.07818	0.0196	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.00492	-1.1707	10	0.87932	D	0	-0.0596	20.0953	0.97838	0.0:0.0:1.0:0.0	.	278;278	Q5W0W1;Q14678	.;KANK1_HUMAN	Q	278;278;278;120	ENSP00000371740:E278Q;ENSP00000371734:E278Q;ENSP00000371730:E120Q	ENSP00000346479:E278Q	E	+	1	0	KANK1	701598	1.000000	0.71417	0.990000	0.47175	0.987000	0.75469	9.363000	0.97131	2.767000	0.95098	0.655000	0.94253	GAG	.	.		0.562	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		C	711598	G	C	711598	3	2	186	1	0	0	0	0	1	0	0	0	7985	1175	41	4	838	4	KANK1	9	711598	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10		711598	140501833	42	27617										
PSIP1	11168	hgsc.bcm.edu	37	chr9	15469957	15469957	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tcgcttcttctccactttctTaacttctggcttctttcctt	3	14	5	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:15469957T>A	ENST00000380733.4	-	11	1355	c.1012A>T	c.(1012-1014)Aag>Tag	p.K338*	PSIP1_ENST00000380738.4_Nonsense_Mutation_p.K338*			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	338					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		TCCACTTTCTTAACTTCTGGC	0.308																																					p.K338X		Atlas-SNP	.											.	PSIP1	93	.	0			c.A1012T						.						101	99	100					9																	15469957		2203	4299	6502	SO:0001587	stop_gained	11168	exon11			CTTTCTTAACTTC	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"PC4 and SFRS1 interacting protein 2"	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.1012A>T	chr9.hg19:g.15469957T>A	ENSP00000370109:p.Lys338*	40.0	0.0		13.0	5.0	NM_001128217	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Nonsense_Mutation	SNP	ENST00000380733.4	hg19	CCDS6479.1	.	.	.	.	.	.	.	.	.	.	T	39	7.782769	0.98486	.	.	ENSG00000164985	ENST00000380733;ENST00000380738	.	.	.	6.02	6.02	0.97574	.	0.042947	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.2108	0.82158	0.0:0.0:0.0:1.0	.	.	.	.	X	338	.	ENSP00000370109:K338X	K	-	1	0	PSIP1	15459957	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.429000	0.66495	2.299000	0.77371	0.528000	0.53228	AAG	.	.		0.308	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222		A	15469957	T	A	15469957	4	1	186	1	0	0	0	0	0	1	0	0	12675	1763	61	4	604	4	PSIP1	9	15469957	Nonsense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	14758359	15469957	125743474	43	27618										
DENND4C	55667	hgsc.bcm.edu	37	chr9	19316742	19316742	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ggcatttttgcgctttatggCgtctattttaaaaggatata	9	5	1	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:19316742C>T	ENST00000380432.2	+	8	1037	c.1004C>T	c.(1003-1005)gCg>gTg	p.A335V	DENND4C_ENST00000434457.2_Missense_Mutation_p.A571V|DENND4C_ENST00000602925.1_Missense_Mutation_p.A571V			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	335	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CGCTTTATGGCGTCTATTTTA	0.418																																					p.A571V		Atlas-SNP	.											DENND4C,NS,carcinoma,-1,1	DENND4C	120	.	0			c.C1712T						.						122	136	132					9																	19316742		2203	4300	6503	SO:0001583	missense	55667	exon12			TTATGGCGTCTAT	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.1004C>T	chr9.hg19:g.19316742C>T	ENSP00000369797:p.Ala335Val	118.0	0.0		69.0	32.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	C	27.0	4.786761	0.90367	.	.	ENSG00000137145	ENST00000380437	.	.	.	5.13	5.13	0.70059	dDENN (3);	0.048658	0.85682	D	0.000000	T	0.79958	0.4536	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82004	-0.0672	9	0.87932	D	0	-17.9767	18.7716	0.91894	0.0:1.0:0.0:0.0	.	335	Q5VZ89	DEN4C_HUMAN	V	335	.	ENSP00000369802:A335V	A	+	2	0	DENND4C	19306742	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	7.599000	0.82757	2.672000	0.90937	0.460000	0.39030	GCG	.	.		0.418	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		T	19316742	C	T	19316742	3	4	186	1	0	0	0	0	1	0	0	0	4437	768	27	1	1034	1	DENND4C	9	19316742	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	3846785	19316742	121896689	44	27619										
KIAA1958	158405	hgsc.bcm.edu	37	chr9	115337110	115337110	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ccctcctgtgtagggtctgcTaaactgattccccatgtcac	8	14	2	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:115337110T>G	ENST00000337530.6	+	2	1046	c.750T>G	c.(748-750)gcT>gcG	p.A250A	KIAA1958_ENST00000374244.3_Silent_p.A250A|KIAA1958_ENST00000536272.1_Silent_p.A250A	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	250										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						TAGGGTCTGCTAAACTGATTC	0.542																																					p.A250A		Atlas-SNP	.											.	KIAA1958	52	.	0			c.T750G						.						175	149	158					9																	115337110		2203	4300	6503	SO:0001819	synonymous_variant	158405	exon2			GTCTGCTAAACTG	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.750T>G	chr9.hg19:g.115337110T>G		93.0	0.0		102.0	6.0	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Silent	SNP	ENST00000337530.6	hg19	CCDS35108.1																																																																																			.	.		0.542	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465		G	115337110	T	G	115337110	2	3	186	1	0	0	0	0	0	0	0	1	8273	1509	53	5		5	KIAA1958	9	115337110	Silent	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	96020368	115337110	25876321	45	27620										
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134477527	134477527	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gggatgtccgtctttcccagCcggtggctcctggaaagagg	15	11	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:134477527C>G	ENST00000372189.3	-	12	1987	c.1864G>C	c.(1864-1866)Gct>Cct	p.A622P	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.A640P|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.A639P	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	622					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		TCTTTCCCAGCCGGTGGCTCC	0.632																																					p.A640P		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G1918C						.						27	31	30					9																	134477527		1948	4133	6081	SO:0001583	missense	2889	exon12			TCCCAGCCGGTGG	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1864G>C	chr9.hg19:g.134477527C>G	ENSP00000361263:p.Ala622Pro	53.0	0.0		62.0	18.0	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	hg19	CCDS48047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.571|5.571	0.290177|0.290177	0.10567|0.10567	.|.	.|.	ENSG00000107263|ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000398415;ENST00000437236;ENST00000372191;ENST00000357686;ENST00000431470;ENST00000545785|ENST00000414781	T;T;T|.	0.26518|.	1.73;1.74;1.74|.	5.11|5.11	1.02|1.02	0.19986|0.19986	.|.	0.819730|.	0.11592|.	N|.	0.548659|.	T|T	0.11750|0.11750	0.0286|0.0286	N|N	0.08118|0.08118	0|0	0.21064|0.21064	N|N	0.999793|0.999793	B;B;B;B;B;B;B;B|.	0.06786|.	0.001;0.001;0.001;0.0;0.0;0.0;0.0;0.001|.	B;B;B;B;B;B;B;B|.	0.09377|.	0.004;0.004;0.004;0.001;0.001;0.001;0.001;0.001|.	T|T	0.27706|0.27706	-1.0066|-1.0066	10|5	0.31617|.	T|.	0.26|.	.|.	2.0677|2.0677	0.03606|0.03606	0.2235:0.4494:0.1096:0.2174|0.2235:0.4494:0.1096:0.2174	.|.	122;456;219;602;583;639;622;640|.	E7ERR9;E9PDT1;Q5JUE7;C9JL20;Q13905-2;Q68DL3;Q13905;Q13905-3|.	.;.;.;.;.;.;RPGF1_HUMAN;.|.	P|A	622;639;568;622;640;602;600;67;206;456;639;122;36|49	ENSP00000361269:A639P;ENSP00000361263:A622P;ENSP00000361264:A640P|.	ENSP00000266110:A622P|.	A|G	-|-	1|2	0|0	RAPGEF1|RAPGEF1	133467348|133467348	0.054000|0.054000	0.20591|0.20591	0.829000|0.829000	0.32907|0.32907	0.041000|0.041000	0.13682|0.13682	0.204000|0.204000	0.17335|0.17335	-0.226000|-0.226000	0.09899|0.09899	-1.134000|-1.134000	0.01955|0.01955	GCT|GGC	.	.		0.632	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		G	134477527	C	G	134477527	3	3	186	1	0	0	0	0	1	0	0	0	13058	739	26	4	1421	4	RAPGEF1	9	134477527	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	19140417	134477527	6735904	46	27621										
SDCCAG3	10807	hgsc.bcm.edu	37	chr9	139301664	139301664	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	actctccatgaaccgcaaagTctgcgctaggactccctgcc	8	16	2	1	rs527894531		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:139301664T>C	ENST00000357365.3	-	5	881	c.752A>G	c.(751-753)gAc>gGc	p.D251G	SDCCAG3_ENST00000371725.3_Missense_Mutation_p.D178G|SDCCAG3_ENST00000298537.7_Missense_Mutation_p.D228G|SDCCAG3_ENST00000461693.1_5'Flank	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	251						cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		AACCGCAAAGTCTGCGCTAGG	0.632																																					p.D251G		Atlas-SNP	.											.	SDCCAG3	41	.	0			c.A752G						.						32	34	34					9																	139301664		2004	4183	6187	SO:0001583	missense	10807	exon5			GCAAAGTCTGCGC	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.752A>G	chr9.hg19:g.139301664T>C	ENSP00000349929:p.Asp251Gly	120.0	0.0		122.0	40.0	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Missense_Mutation	SNP	ENST00000357365.3	hg19	CCDS43904.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.690091	0.48097	.	.	ENSG00000165689	ENST00000357365;ENST00000298537;ENST00000371725;ENST00000371723	T;T;T;T	0.36157	2.31;2.34;2.33;1.27	5.4	4.19	0.49359	.	0.605936	0.17111	N	0.186623	T	0.33498	0.0865	L	0.57536	1.79	0.22142	N	0.999337	B;B;B	0.31077	0.089;0.307;0.307	B;B;B	0.30572	0.075;0.117;0.117	T	0.24404	-1.0161	10	0.46703	T	0.11	-3.4979	9.3005	0.37842	0.0:0.0:0.309:0.691	.	178;228;251	Q96C92-4;Q96C92-2;Q96C92	.;.;SDCG3_HUMAN	G	251;228;178;201	ENSP00000349929:D251G;ENSP00000298537:D228G;ENSP00000360790:D178G;ENSP00000360788:D201G	ENSP00000298537:D228G	D	-	2	0	SDCCAG3	138421485	0.717000	0.27966	0.282000	0.24776	0.881000	0.50899	1.050000	0.30404	2.039000	0.60335	0.533000	0.62120	GAC	.	.		0.632	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643		C	139301664	T	C	139301664	3	2	186	1	0	0	0	0	1	0	0	0	13973	1667	58	2	579	2	SDCCAG3	9	139301664	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	4824137	139301664	1911767	47	27622										
SYNPO2L	79933	hgsc.bcm.edu	37	chr10	75407832	75407832	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ccagagactggcgcgtggctGggaacccctgaagtgaagct	15	11	0	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr10:75407832G>T	ENST00000394810.2	-	4	1727	c.1578C>A	c.(1576-1578)ccC>ccA	p.P526P	SYNPO2L_ENST00000372873.4_Silent_p.P302P	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	526	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					GCGCGTGGCTGGGAACCCCTG	0.687																																					p.P526P		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.C1578A						.						8	10	10					10																	75407832		2185	4278	6463	SO:0001819	synonymous_variant	79933	exon4			GTGGCTGGGAACC	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.1578C>A	chr10.hg19:g.75407832G>T		121.0	0.0		74.0	4.0	NM_001114133	A5PKV9|Q68A20	Silent	SNP	ENST00000394810.2	hg19	CCDS44438.1																																																																																			.	.		0.687	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875		T	75407832	G	T	75407832	2	4	186	1	0	0	0	0	0	0	0	1	15473	1335	47	3		3	SYNPO2L	10	75407832	Silent	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10		75407832	60126915	48	27623										
NRG3	10718	hgsc.bcm.edu	37	chr10	84118543	84118543	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	cgagcacttcaaaccctgccGagacaaggaccttgcatact	8	14	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr10:84118543G>T	ENST00000404547.1	+	2	872	c.872G>T	c.(871-873)cGa>cTa	p.R291L	NRG3_ENST00000372142.2_Missense_Mutation_p.R70L|NRG3_ENST00000556918.1_Missense_Mutation_p.R121L|NRG3_ENST00000372141.2_Missense_Mutation_p.R291L|NRG3_ENST00000404576.2_Missense_Mutation_p.R95L			P56975	NRG3_HUMAN	neuregulin 3	291	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		AAACCCTGCCGAGACAAGGAC	0.522																																					p.R291L		Atlas-SNP	.											.	NRG3	301	.	0			c.G872T						.						189	144	159					10																	84118543		2203	4300	6503	SO:0001583	missense	10718	exon2			CCTGCCGAGACAA	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.872G>T	chr10.hg19:g.84118543G>T	ENSP00000384796:p.Arg291Leu	158.0	0.0		163.0	48.0	NM_001165972	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	hg19	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	G	35	5.448643	0.96205	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287;ENST00000372142;ENST00000404576;ENST00000556918	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	5.72	4.72	0.59763	.	0.174915	0.27522	N	0.018988	T	0.14227	0.0344	N	0.01874	-0.695	0.80722	D	1	B;P;B	0.47191	0.431;0.891;0.312	B;B;B	0.43754	0.222;0.43;0.09	T	0.01697	-1.1293	10	0.29301	T	0.29	-12.557	5.3371	0.15963	0.2311:0.0:0.7689:0.0	.	291;70;291	B9EGV5;P56975-3;P56975-4	.;.;.	L	291;291;291;70;95;121	ENSP00000361214:R291L;ENSP00000384796:R291L;ENSP00000361215:R70L;ENSP00000385804:R95L;ENSP00000451376:R121L	ENSP00000361214:R291L	R	+	2	0	NRG3	84108523	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.063000	0.64332	2.711000	0.92665	0.655000	0.94253	CGA	.	.		0.522	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		T	84118543	G	T	84118543	3	4	186	1	0	0	0	0	1	0	0	0	10658	1058	37	1	1046	1	NRG3	10	84118543	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	8710711	84118543	51416204	49	27624										
INPP5A	3632	hgsc.bcm.edu	37	chr10	134595384	134595384	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gcccgtgttcctggccttccGaatcatgcccggggcaggta	13	14	1	0	rs374027590		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr10:134595384G>A	ENST00000368594.3	+	15	1455	c.1178G>A	c.(1177-1179)cGa>cAa	p.R393Q	RP11-288G11.3_ENST00000441365.2_lincRNA	NM_005539.3	NP_005530.3	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase, 40kDa	393					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|PH domain binding (GO:0042731)			cervix(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		CTGGCCTTCCGAATCATGCCC	0.612																																					p.R393Q	Pancreas(63;823 1267 11107 20380 51626)	Atlas-SNP	.											INPP5A_ENST00000445580,NS,carcinoma,+1,1	INPP5A	77	.	0			c.G1178A						.	G	GLN/ARG	1,4399	2.1+/-5.4	0,1,2199	107	122	117		1178	4.2	1	10		117	0,8582		0,0,4291	no	missense	INPP5A	NM_005539.3	43	0,1,6490	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	393/413	134595384	1,12981	2200	4291	6491	SO:0001583	missense	3632	exon15			CCTTCCGAATCAT	X77567	CCDS7669.2	10q26.3	2008-08-07	2002-08-29		ENSG00000068383	ENSG00000068383	3.1.3.56		6076	protein-coding gene	gene with protein product	"CTCL tumor antigen HD-CL-02", "43 kDa inositol polyphosphate 5-phophatase", "inositol polyphosphate 5-phophatase, 40kDa", "InsP3 5-phosphatase", "type I inositol-1,4,5-trisphosphate 5-phosphatase"	600106	"inositol polyphosphate-5-phosphatase, 40kD"			8013665	Standard	NM_005539		Approved	5PTASE	uc001llp.3	Q14642	OTTHUMG00000019293	ENST00000368594.3:c.1178G>A	chr10.hg19:g.134595384G>A	ENSP00000357583:p.Arg393Gln	133.0	0.0		106.0	36.0	NM_005539	D3DXI3|Q14640|Q5JSF1	Missense_Mutation	SNP	ENST00000368594.3	hg19	CCDS7669.2	.	.	.	.	.	.	.	.	.	.	G	28.6	4.932221	0.92389	2.27E-4	0.0	ENSG00000068383	ENST00000368594;ENST00000416326;ENST00000432898;ENST00000445580	T;D	0.95342	0.95;-3.68	4.15	4.15	0.48705	Endonuclease/exonuclease/phosphatase (1);Inositol polyphosphate-related phosphatase (1);	0.098789	0.43579	D	0.000552	D	0.96497	0.8857	M	0.66939	2.045	0.80722	D	1	P;D	0.76494	0.868;0.999	B;D	0.72625	0.294;0.978	D	0.96365	0.9269	10	0.45353	T	0.12	-4.1261	16.8306	0.85943	0.0:0.0:1.0:0.0	.	336;393	F5GWM1;Q14642	.;I5P1_HUMAN	Q	393;336;310;75	ENSP00000357583:R393Q;ENSP00000390749:R75Q	ENSP00000357583:R393Q	R	+	2	0	INPP5A	134445374	1.000000	0.71417	0.967000	0.41034	0.939000	0.58152	8.586000	0.90806	2.044000	0.60594	0.455000	0.32223	CGA	.	.		0.612	INPP5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051085.1	NM_005539		A	134595384	G	A	134595384	3	1	186	1	0	0	0	0	1	0	0	0	7763	1058	37	1	1236	1	INPP5A	10	134595384	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	50476841	134595384	939363	50	27625										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1262639	1262639	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ccagccccggtgtcagtggaCagagtggtttgatgaggact	15	9	1	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr11:1262639C>A	ENST00000529681.1	+	31	4587	c.4529C>A	c.(4528-4530)aCa>aAa	p.T1510K	MUC5B_ENST00000447027.1_Missense_Mutation_p.T1513K|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1510	7 X Cys-rich subdomain repeats.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TGTCAGTGGACAGAGTGGTTT	0.632																																					p.T1510K		Atlas-SNP	.											.	MUC5B	473	.	0			c.C4529A						.						48	58	55					11																	1262639		2090	4213	6303	SO:0001583	missense	727897	exon31			AGTGGACAGAGTG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.4529C>A	chr11.hg19:g.1262639C>A	ENSP00000436812:p.Thr1510Lys	143.0	0.0		144.0	52.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	13.52	2.261126	0.39995	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.26660	1.72;1.72	5.01	5.01	0.66863	.	.	.	.	.	T	0.55016	0.1894	M	0.81341	2.54	0.38443	D	0.946766	D;D	0.76494	0.999;0.999	D;D	0.72982	0.979;0.979	T	0.64799	-0.6322	9	0.87932	D	0	.	18.3736	0.90428	0.0:1.0:0.0:0.0	.	2203;1513	A7Y9J9;E9PBJ0	.;.	K	1510;1513;1511;1580	ENSP00000436812:T1510K;ENSP00000415793:T1513K	ENSP00000343037:T1511K	T	+	2	0	MUC5B	1219215	0.915000	0.31059	0.882000	0.34594	0.337000	0.28794	3.324000	0.52022	2.341000	0.79615	0.299000	0.19835	ACA	.	.		0.632	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1262639	C	A	1262639	3	1	186	1	0	0	0	0	1	0	0	0	9988	478	17	3	4660	3	MUC5B	11	1262639	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10		1262639	133743877	51	27626										
NLRP14	338323	hgsc.bcm.edu	37	chr11	7064609	7064609	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	agaaaatctcagaaggcttgGgttaactcaatctgatgtct	9	7	4	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr11:7064609G>T	ENST00000299481.4	+	4	1698	c.1352G>T	c.(1351-1353)gGg>gTg	p.G451V		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	451	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		AGAAGGCTTGGGTTAACTCAA	0.433																																					p.G451V		Atlas-SNP	.											.	NLRP14	187	.	0			c.G1352T						.						125	129	128					11																	7064609		2201	4296	6497	SO:0001583	missense	338323	exon4			GGCTTGGGTTAAC	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.1352G>T	chr11.hg19:g.7064609G>T	ENSP00000299481:p.Gly451Val	135.0	0.0		133.0	54.0	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	hg19	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	G	12.36	1.913891	0.33815	.	.	ENSG00000158077	ENST00000299481	D	0.86769	-2.17	4.34	2.42	0.29668	.	0.132021	0.35096	N	0.003447	D	0.89897	0.6848	M	0.88105	2.93	0.41912	D	0.990478	D	0.58268	0.982	P	0.53450	0.726	D	0.88525	0.3099	10	0.72032	D	0.01	.	3.7282	0.08482	0.2303:0.2084:0.5613:0.0	.	451	Q86W24	NAL14_HUMAN	V	451	ENSP00000299481:G451V	ENSP00000299481:G451V	G	+	2	0	NLRP14	7021185	0.003000	0.15002	0.881000	0.34555	0.440000	0.31957	0.267000	0.18552	1.156000	0.42514	0.655000	0.94253	GGG	.	.		0.433	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		T	7064609	G	T	7064609	3	4	186	1	0	0	0	0	1	0	0	0	10485	1232	43	3	1362	3	NLRP14	11	7064609	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	5801970	7064609	127941907	52	27627										
VWCE	220001	hgsc.bcm.edu	37	chr11	61032665	61032665	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tgatggggcagtccacggggGaacaggccactgagcccagc	16	12	0	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr11:61032665G>A	ENST00000335613.5	-	17	2371	c.1985C>T	c.(1984-1986)tCc>tTc	p.S662F	VWCE_ENST00000535710.1_Missense_Mutation_p.S127F	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	662	VWFC 5. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GTCCACGGGGGAACAGGCCAC	0.627																																					p.S662F		Atlas-SNP	.											.	VWCE	84	.	0			c.C1985T						.						44	36	38					11																	61032665		2181	4275	6456	SO:0001583	missense	220001	exon17			ACGGGGGAACAGG	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.1985C>T	chr11.hg19:g.61032665G>A	ENSP00000334186:p.Ser662Phe	325.0	0.0		341.0	102.0	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Missense_Mutation	SNP	ENST00000335613.5	hg19	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.910841	0.72983	.	.	ENSG00000167992	ENST00000335613;ENST00000535710	T;T	0.72835	-0.69;-0.69	4.88	4.88	0.63580	von Willebrand factor, type C (4);	0.000000	0.34802	N	0.003677	T	0.80297	0.4597	L	0.49699	1.58	0.41527	D	0.988433	D	0.76494	0.999	D	0.91635	0.999	T	0.80569	-0.1324	10	0.46703	T	0.11	.	16.2196	0.82251	0.0:0.0:1.0:0.0	.	662	Q96DN2	VWCE_HUMAN	F	662;127	ENSP00000334186:S662F;ENSP00000442570:S127F	ENSP00000334186:S662F	S	-	2	0	VWCE	60789241	1.000000	0.71417	0.934000	0.37439	0.987000	0.75469	4.669000	0.61575	2.421000	0.82119	0.555000	0.69702	TCC	.	.		0.627	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		A	61032665	G	A	61032665	3	1	186	1	0	0	0	0	1	0	0	0	17260	1174	41	3	898	3	VWCE	11	61032665	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	53968056	61032665	73973851	53	27628										
DAGLA	747	hgsc.bcm.edu	37	chr11	61511843	61511843	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gggtgagctcatggacctgaCgcccacgggcctcagtagcc	14	14	2	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr11:61511843C>A	ENST00000257215.5	+	20	3127	c.3011C>A	c.(3010-3012)aCg>aAg	p.T1004K	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	1004					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		ATGGACCTGACGCCCACGGGC	0.667																																					p.T1004K		Atlas-SNP	.											.	DAGLA	109	.	0			c.C3011A						.						47	51	50					11																	61511843		2202	4298	6500	SO:0001583	missense	747	exon20			ACCTGACGCCCAC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"neural stem cell-derived dendrite regulator"	614015	"chromosome 11 open reading frame 11"	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.3011C>A	chr11.hg19:g.61511843C>A	ENSP00000257215:p.Thr1004Lys	156.0	0.0		138.0	51.0	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	hg19	CCDS31578.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393229	0.62066	.	.	ENSG00000134780	ENST00000257215	T	0.27402	1.67	4.03	3.03	0.35002	.	0.190106	0.45867	D	0.000339	T	0.21427	0.0516	N	0.24115	0.695	0.46185	D	0.998919	B	0.15141	0.012	B	0.13407	0.009	T	0.12604	-1.0541	10	0.72032	D	0.01	-11.1783	12.6053	0.56519	0.1665:0.8335:0.0:0.0	.	1004	Q9Y4D2	DGLA_HUMAN	K	1004	ENSP00000257215:T1004K	ENSP00000257215:T1004K	T	+	2	0	DAGLA	61268419	0.996000	0.38824	0.990000	0.47175	0.990000	0.78478	3.539000	0.53604	1.979000	0.57680	0.462000	0.41574	ACG	.	.		0.667	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		A	61511843	C	A	61511843	3	1	186	1	0	0	0	0	1	0	0	0	4228	536	19	1	3085	1	DAGLA	11	61511843	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	479178	61511843	73494673	54	27629										
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126316746	126316746	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	atcagagcccagatccacgaGcaaggattggggttctgtgg	14	9	2	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr11:126316746G>A	ENST00000525144.2	-	9	1282	c.1033C>T	c.(1033-1035)Ctc>Ttc	p.L345F	KIRREL3_ENST00000525704.2_Missense_Mutation_p.L345F|KIRREL3_ENST00000529097.2_Missense_Mutation_p.L345F	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	345	Ig-like C2-type 4.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AGATCCACGAGCAAGGATTGG	0.612																																					p.L345F		Atlas-SNP	.											.	KIRREL3	183	.	0			c.C1033T						.						41	44	43					11																	126316746		2069	4197	6266	SO:0001583	missense	84623	exon9			CCACGAGCAAGGA	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.1033C>T	chr11.hg19:g.126316746G>A	ENSP00000435466:p.Leu345Phe	58.0	0.0		95.0	29.0	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Missense_Mutation	SNP	ENST00000525144.2	hg19	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.408497	0.62399	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000525704	T;T;T	0.67171	-0.25;-0.25;-0.25	4.55	2.64	0.31445	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.086699	0.47852	D	0.000214	T	0.60792	0.2296	L	0.28014	0.82	0.80722	D	1	D;D;P	0.59767	0.986;0.971;0.953	P;P;P	0.55303	0.563;0.773;0.718	T	0.58578	-0.7612	10	0.54805	T	0.06	.	6.6942	0.23189	0.084:0.0:0.6016:0.3145	.	345;345;345	Q8IZU9-2;E9PRX9;Q8IZU9	.;.;KIRR3_HUMAN	F	345	ENSP00000435466:L345F;ENSP00000434081:L345F;ENSP00000435094:L345F	ENSP00000435466:L345F	L	-	1	0	KIRREL3	125821956	1.000000	0.71417	0.465000	0.27155	0.906000	0.53458	2.233000	0.43027	0.335000	0.23614	0.297000	0.19635	CTC	.	.		0.612	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		A	126316746	G	A	126316746	3	1	186	1	0	0	0	0	1	0	0	0	8335	971	34	3	1446	3	KIRREL3	11	126316746	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	64804903	126316746	8689770	55	27630										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48388212	48388212	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	aacggtggcgtttacctgagGaccaggcggacccctttcac	12	13	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr12:48388212G>T	ENST00000380518.3	-	12	975	c.811C>A	c.(811-813)Cct>Act	p.P271T	COL2A1_ENST00000337299.6_Missense_Mutation_p.P202T	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	271	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	TTTACCTGAGGACCAGGCGGA	0.542																																					p.P271T		Atlas-SNP	.											.	COL2A1	368	.	0			c.C811A						.						130	107	115					12																	48388212		2203	4300	6503	SO:0001583	missense	1280	exon12			CCTGAGGACCAGG	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.811C>A	chr12.hg19:g.48388212G>T	ENSP00000369889:p.Pro271Thr	110.0	0.0		163.0	47.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.262627	0.59431	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	D;D	0.96856	-4.15;-4.15	3.91	3.91	0.45181	.	0.000000	0.85682	D	0.000000	D	0.97501	0.9182	M	0.65975	2.015	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.83275	0.993;0.996	D	0.97305	0.9933	10	0.49607	T	0.09	.	15.8912	0.79299	0.0:0.0:1.0:0.0	.	202;271	P02458-1;P02458	.;CO2A1_HUMAN	T	271;202;202	ENSP00000369889:P271T;ENSP00000338213:P202T	ENSP00000338213:P202T	P	-	1	0	COL2A1	46674479	1.000000	0.71417	1.000000	0.80357	0.768000	0.43524	9.323000	0.96364	2.478000	0.83669	0.561000	0.74099	CCT	.	.		0.542	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		T	48388212	G	T	48388212	3	4	186	1	0	0	0	0	1	0	0	0	3689	1174	41	3	3824	3	COL2A1	12	48388212	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10		48388212	85463683	56	27631										
NAV3	89795	hgsc.bcm.edu	37	chr12	78515815	78515815	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gcccagccctagtaccacatTagcgcggcaaggcagtctgg	12	14	1	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr12:78515815T>C	ENST00000397909.2	+	16	4018	c.3845T>C	c.(3844-3846)tTa>tCa	p.L1282S	NAV3_ENST00000228327.6_Missense_Mutation_p.L1282S|NAV3_ENST00000266692.7_Intron|NAV3_ENST00000536525.2_Missense_Mutation_p.L1282S			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1282	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						AGTACCACATTAGCGCGGCAA	0.562										HNSCC(70;0.22)																											p.L1282S		Atlas-SNP	.											.	NAV3	506	.	0			c.T3845C						.						53	52	52					12																	78515815		2076	4224	6300	SO:0001583	missense	89795	exon16			CCACATTAGCGCG	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.3845T>C	chr12.hg19:g.78515815T>C	ENSP00000381007:p.Leu1282Ser	124.0	0.0		122.0	41.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.44	3.124623	0.56613	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327	T;T;T	0.30981	1.52;1.51;1.51	5.96	5.96	0.96718	.	0.000000	0.31859	U	0.006956	T	0.43010	0.1228	N	0.22421	0.69	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.997;0.998;0.999	T	0.33189	-0.9878	10	0.44086	T	0.13	-10.6382	16.4338	0.83864	0.0:0.0:0.0:1.0	.	1282;1282;1282	E7EUC6;Q8IVL0;Q8IVL0-2	.;NAV3_HUMAN;.	S	1282	ENSP00000446132:L1282S;ENSP00000381007:L1282S;ENSP00000228327:L1282S	ENSP00000228327:L1282S	L	+	2	0	NAV3	77039946	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.806000	0.86020	2.270000	0.75569	0.533000	0.62120	TTA	.	.		0.562	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		C	78515815	T	C	78515815	3	2	186	1	0	0	0	0	1	0	0	0	10194	1764	61	2	3907	2	NAV3	12	78515815	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	30127603	78515815	55336080	57	27632										
MED13L	23389	hgsc.bcm.edu	37	chr12	116413042	116413042	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tctccagggtagagatgtcaTttggacaatccctatgcacc	9	11	2	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr12:116413042T>C	ENST00000281928.3	-	25	5871	c.5665A>G	c.(5665-5667)Atg>Gtg	p.M1889V		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1889						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		AGAGATGTCATTTGGACAATC	0.443																																					p.M1889V		Atlas-SNP	.											.	MED13L	193	.	0			c.A5665G						.						90	84	86					12																	116413042		2203	4300	6503	SO:0001583	missense	23389	exon25			ATGTCATTTGGAC	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.5665A>G	chr12.hg19:g.116413042T>C	ENSP00000281928:p.Met1889Val	130.0	0.0		152.0	63.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.55|16.55	3.154616|3.154616	0.57259|0.57259	.|.	.|.	ENSG00000123066|ENSG00000123066	ENST00000281928|ENST00000552447	D|.	0.82803|.	-1.65|.	5.78|5.78	4.63|4.63	0.57726|0.57726	.|.	0.074656|.	0.85682|.	N|.	0.000000|.	T|T	0.57666|0.57666	0.2069|0.2069	L|L	0.44542|0.44542	1.39|1.39	0.48511|0.48511	D|D	0.999661|0.999661	B|.	0.12013|.	0.005|.	B|.	0.14578|.	0.011|.	T|T	0.53697|0.53697	-0.8402|-0.8402	10|5	0.36615|.	T|.	0.2|.	.|.	11.8979|11.8979	0.52665|0.52665	0.0:0.0682:0.0:0.9318|0.0:0.0682:0.0:0.9318	.|.	1889|.	Q71F56|.	MD13L_HUMAN|.	V|S	1889|93	ENSP00000281928:M1889V|.	ENSP00000281928:M1889V|.	M|N	-|-	1|2	0|0	MED13L|MED13L	114897425|114897425	1.000000|1.000000	0.71417|0.71417	0.961000|0.961000	0.40146|0.40146	0.998000|0.998000	0.95712|0.95712	4.801000|4.801000	0.62532|0.62532	1.120000|1.120000	0.41904|0.41904	0.482000|0.482000	0.46254|0.46254	ATG|AAT	.	.		0.443	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			C	116413042	T	C	116413042	3	2	186	1	0	0	0	0	1	0	0	0	9440	1493	52	2	995	2	MED13L	12	116413042	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	37897227	116413042	17438853	58	27633										
PPP2R5E	5529	hgsc.bcm.edu	37	chr14	63881864	63881864	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	aataatttgcttacctgtaaTacaaatttctgatctatata	3	6	2	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr14:63881864T>C	ENST00000337537.3	-	5	1145	c.543A>G	c.(541-543)gtA>gtG	p.V181V	PPP2R5E_ENST00000553266.1_5'UTR|PPP2R5E_ENST00000422769.2_Silent_p.V105V|PPP2R5E_ENST00000555899.1_Silent_p.V181V	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	181					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		TTACCTGTAATACAAATTTCT	0.308																																					p.V181V		Atlas-SNP	.											.	PPP2R5E	43	.	0			c.A543G						.						88	90	90					14																	63881864		2202	4297	6499	SO:0001819	synonymous_variant	5529	exon5			CTGTAATACAAAT	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9313	protein-coding gene	gene with protein product		601647	"protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.543A>G	chr14.hg19:g.63881864T>C		205.0	0.0		196.0	62.0	NM_006246	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Silent	SNP	ENST00000337537.3	hg19	CCDS9758.1																																																																																			.	.		0.308	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246		C	63881864	T	C	63881864	2	2	186	1	0	0	0	0	0	0	0	1	12408	1393	49	2		2	PPP2R5E	14	63881864	Silent	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10		63881864	43467676	59	27634										
STON2	85439	hgsc.bcm.edu	37	chr14	81743600	81743600	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gtcctgagtgtgaaaggcaaGgtcttctcagcaaacactgt	11	9	2	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr14:81743600G>A	ENST00000267540.2	-	4	2255	c.2055C>T	c.(2053-2055)acC>acT	p.T685T	STON2_ENST00000556280.1_5'Flank|STON2_ENST00000555447.1_Silent_p.T685T	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	685	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		TGAAAGGCAAGGTCTTCTCAG	0.537																																					p.T685T		Atlas-SNP	.											STON2,right_upper_lobe,carcinoma,0,1	STON2	94	.	0			c.C2055T						.						124	117	119					14																	81743600		2203	4300	6503	SO:0001819	synonymous_variant	85439	exon6			AGGCAAGGTCTTC	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"stoned B homolog 2 (Drosophila)"	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.2055C>T	chr14.hg19:g.81743600G>A		169.0	0.0		150.0	93.0	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Silent	SNP	ENST00000267540.2	hg19	CCDS9875.1																																																																																			.	.		0.537	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104		A	81743600	G	A	81743600	2	1	186	1	0	0	0	0	0	0	0	1	15333	987	35	3		3	STON2	14	81743600	Silent	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	17861736	81743600	25605940	60	27635										
EMP2	2013	hgsc.bcm.edu	37	chr16	10631932	10631932	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	cgcctgcagcgtggagtactCtgcgggaaaagggcaggggc	18	10	1	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr16:10631932C>A	ENST00000359543.3	-	4	379		c.e4-1		EMP2_ENST00000536829.1_Splice_Site	NM_001424.4	NP_001415.1	P54851	EMP2_HUMAN	epithelial membrane protein 2						cell proliferation (GO:0008283)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|regulation of glomerular filtration (GO:0003093)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	integrin binding (GO:0005178)			NS(1)|endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6						GTGGAGTACTCTGCGGGAAAA	0.622																																					.	GBM(158;2021 2691 14714 39478)	Atlas-SNP	.											.	EMP2	21	.	0			c.170-1G>T						.						107	98	101					16																	10631932		2197	4300	6497	SO:0001630	splice_region_variant	2013	exon5			AGTACTCTGCGGG	U52100	CCDS10541.1	16p13.2	2008-08-01			ENSG00000213853	ENSG00000213853			3334	protein-coding gene	gene with protein product		602334				8996089, 10331954, 16216233	Standard	NM_001424		Approved	XMP	uc002czx.3	P54851	OTTHUMG00000129752	ENST00000359543.3:c.170-1G>T	chr16.hg19:g.10631932C>A		106.0	0.0		108.0	42.0	NM_001424	B2R7V6|D3DUF8	Splice_Site	SNP	ENST00000359543.3	hg19	CCDS10541.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.839259	0.51057	.	.	ENSG00000213853	ENST00000359543;ENST00000536829	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6338	0.91370	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	EMP2	10539433	1.000000	0.71417	0.600000	0.28864	0.011000	0.07611	4.741000	0.62095	2.620000	0.88729	0.655000	0.94253	.	.	.		0.622	EMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251965.1	NM_001424	Intron	A	10631932	C	A	10631932	5	1	186	1	0	0	0	0	0	0	1	0	5104	927	32	3	342	3	EMP2	16	10631932	Splice_Site	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10		10631932	79722821	61	27636										
PLD2	5338	hgsc.bcm.edu	37	chr17	4719981	4719981	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	acaaccaattcttctggctgGgcaaggactacagcaatctt	8	11	3	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:4719981G>A	ENST00000263088.6	+	15	1653	c.1522G>A	c.(1522-1524)Ggc>Agc	p.G508S	PLD2_ENST00000572940.1_Missense_Mutation_p.G508S	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	508	Catalytic.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	CTTCTGGCTGGGCAAGGACTA	0.617																																					p.G508S		Atlas-SNP	.											.	PLD2	138	.	0			c.G1522A						.						146	139	142					17																	4719981		2203	4300	6503	SO:0001583	missense	5338	exon15			TGGCTGGGCAAGG	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"choline phosphatase 2"	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1522G>A	chr17.hg19:g.4719981G>A	ENSP00000263088:p.Gly508Ser	136.0	0.0		90.0	44.0	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	hg19	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.901737	0.92035	.	.	ENSG00000129219	ENST00000263088	T	0.13657	2.57	4.62	4.62	0.57501	.	0.050614	0.85682	N	0.000000	T	0.45756	0.1358	H	0.95079	3.62	0.80722	D	1	P;P;P	0.47106	0.489;0.87;0.89	B;P;P	0.57548	0.066;0.823;0.671	T	0.61535	-0.7043	10	0.87932	D	0	-19.7883	14.9669	0.71201	0.0:0.0:1.0:0.0	.	365;508;508	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	S	508	ENSP00000263088:G508S	ENSP00000263088:G508S	G	+	1	0	PLD2	4666947	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.084000	0.94076	2.392000	0.81423	0.561000	0.74099	GGC	.	.		0.617	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663		A	4719981	G	A	4719981	3	1	186	1	0	0	0	0	1	0	0	0	12055	1232	43	3	1576	3	PLD2	17	4719981	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10		4719981	76475229	62	27637										
TP53	7157	hgsc.bcm.edu	37	chr17	7578555	7578555	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ttgttgagggcaggggagtaCtgtaggaagaggaaggagac	19	3	0	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:7578555C>T	ENST00000269305.4	-	5	565		c.e5-1		TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(39)|p.0?(8)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGGGGAGTACTGTAGGAAGA	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,58	TP53	33396	.	51	Unknown(39)|Whole gene deletion(8)|Deletion - Frameshift(3)|Insertion - In frame(1)	ovary(9)|pancreas(6)|bone(5)|upper_aerodigestive_tract(4)|liver(4)|lung(4)|breast(4)|large_intestine(3)|central_nervous_system(3)|oesophagus(3)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|endometrium(1)|urinary_tract(1)|autonomic_ganglia(1)	c.376-1G>A						.						42	42	42					17																	7578555		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGAGTACTGTAGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.376-1G>A	chr17.hg19:g.7578555C>T		93.0	0.0		57.0	30.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.431133	0.62844	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	.	.	.	4.87	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4246	0.50003	0.0:0.9094:0.0:0.0906	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519280	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	7.639000	0.83342	1.359000	0.45940	0.655000	0.94253	.	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	T	7578555	C	T	7578555	5	4	186	1	0	0	0	0	0	0	1	0	16396	579	20	3	923	3	TP53	17	7578555	Splice_Site	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	2858574	7578555	73616655	63	27638										
MYH13	8735	hgsc.bcm.edu	37	chr17	10206563	10206563	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	cactttggcctgcagcttgtCcaccaggtcctggagcctaa	10	14	0	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:10206563C>T	ENST00000418404.3	-	38	5780	c.5617G>A	c.(5617-5619)Gac>Aac	p.D1873N	MYH13_ENST00000252172.4_Missense_Mutation_p.D1873N|RP11-401O9.4_ENST00000609088.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1873					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						TGCAGCTTGTCCACCAGGTCC	0.587																																					p.D1873N		Atlas-SNP	.											.	MYH13	533	.	0			c.G5617A						.						150	157	155					17																	10206563		2151	4268	6419	SO:0001583	missense	8735	exon39			GCTTGTCCACCAG	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.5617G>A	chr17.hg19:g.10206563C>T	ENSP00000404570:p.Asp1873Asn	104.0	0.0		80.0	30.0	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	hg19	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.284484	0.80803	.	.	ENSG00000006788	ENST00000252172	D	0.85013	-1.93	3.81	3.81	0.43845	Myosin tail (1);	.	.	.	.	D	0.92384	0.7583	H	0.97440	4.005	0.45852	D	0.998717	B	0.24823	0.112	B	0.37387	0.248	D	0.93707	0.7020	9	0.87932	D	0	.	16.2342	0.82361	0.0:1.0:0.0:0.0	.	1873	Q9UKX3	MYH13_HUMAN	N	1873	ENSP00000252172:D1873N	ENSP00000252172:D1873N	D	-	1	0	MYH13	10147288	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.855000	0.69510	2.107000	0.64212	0.561000	0.74099	GAC	.	.		0.587	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		T	10206563	C	T	10206563	3	4	186	1	0	0	0	0	1	0	0	0	10041	855	30	3	211	3	MYH13	17	10206563	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	2628008	10206563	70988647	64	27639										
CYTSB	92521	hgsc.bcm.edu	37	chr17	20135682	20135682	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ggagctgggggatgtgcaggGccacggcagggtggtcacca	20	9	1	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:20135682G>A	ENST00000261503.5	+	7	2366	c.2315G>A	c.(2314-2316)gGc>gAc	p.G772D	SPECC1_ENST00000395529.3_Missense_Mutation_p.G772D|SPECC1_ENST00000584527.1_Missense_Mutation_p.G190D|SPECC1_ENST00000395530.2_Missense_Mutation_p.G691D|SPECC1_ENST00000395525.3_Missense_Mutation_p.G691D|SPECC1_ENST00000395527.4_Missense_Mutation_p.G772D|SPECC1_ENST00000472876.1_3'UTR|SPECC1_ENST00000395522.2_Missense_Mutation_p.G691D|SPECC1_ENST00000536879.1_Missense_Mutation_p.G112D|AC004702.2_ENST00000580225.1_lincRNA	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	772					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		GATGTGCAGGGCCACGGCAGG	0.632																																					p.G772D		Atlas-SNP	.											.	SPECC1	100	.	0			c.G2315A						.						23	24	23					17																	20135682		2202	4300	6502	SO:0001583	missense	92521	exon7			TGCAGGGCCACGG	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"sperm antigen HCMOGT 1", "cytokinesis and spindle organization B", "cytospin B"	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.2315G>A	chr17.hg19:g.20135682G>A	ENSP00000261503:p.Gly772Asp	98.0	0.0		84.0	27.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	hg19	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.104481	0.56291	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000536879;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	4.22	3.23	0.37069	.	0.147651	0.64402	D	0.000008	T	0.60547	0.2277	L	0.60455	1.87	0.58432	D	0.999996	P;D;D;D;P	0.61697	0.658;0.99;0.99;0.99;0.923	B;P;P;P;P	0.57324	0.283;0.628;0.818;0.818;0.493	T	0.59994	-0.7349	10	0.35671	T	0.21	-13.791	12.2339	0.54503	0.0:0.1737:0.8263:0.0	.	772;691;691;772;772	A8MV89;Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;.;CYTSB_HUMAN	D	772;772;772;112;691;691;691	ENSP00000261503:G772D;ENSP00000378900:G772D;ENSP00000438294:G112D;ENSP00000378893:G691D;ENSP00000378896:G691D	ENSP00000261503:G772D	G	+	2	0	SPECC1	20076274	1.000000	0.71417	0.961000	0.40146	0.908000	0.53690	3.352000	0.52239	1.336000	0.45506	0.655000	0.94253	GGC	.	.		0.632	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904		A	20135682	G	A	20135682	3	1	186	1	0	0	0	0	1	0	0	0	4212	1203	42	3	2381	3	CYTSB	17	20135682	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	9929119	20135682	61059528	65	27640										
SLC46A1	113235	hgsc.bcm.edu	37	chr17	26731821	26731821	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ccgattagtttggagtcccaGcagaggggtgtgcttagttc	14	8	0	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:26731821G>T	ENST00000440501.1	-	2	989	c.894C>A	c.(892-894)tgC>tgA	p.C298*	SLC46A1_ENST00000321666.5_Nonsense_Mutation_p.C298*|SLC46A1_ENST00000584729.1_5'UTR|CTD-2350C19.1_ENST00000583956.1_RNA|CTD-2350C19.2_ENST00000580714.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	298					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	TGGAGTCCCAGCAGAGGGGTG	0.547																																					p.C298X		Atlas-SNP	.											.	SLC46A1	17	.	0			c.C894A						.						101	110	107					17																	26731821		2028	4184	6212	SO:0001587	stop_gained	113235	exon2			GTCCCAGCAGAGG	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"Solute carriers"	30521	protein-coding gene	gene with protein product	"heme carrier protein 1", "proton-coupled folate transporter"	611672	"solute carrier family 46, member 1"			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.894C>A	chr17.hg19:g.26731821G>T	ENSP00000395653:p.Cys298*	195.0	0.0		285.0	143.0	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Nonsense_Mutation	SNP	ENST00000440501.1	hg19		.	.	.	.	.	.	.	.	.	.	G	33	5.212205	0.95069	.	.	ENSG00000076351	ENST00000440501;ENST00000321666	.	.	.	5.15	4.19	0.49359	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-23.5089	10.8105	0.46545	0.1519:0.0:0.8481:0.0	.	.	.	.	X	298	.	ENSP00000318828:C298X	C	-	3	2	SLC46A1	23755948	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	6.417000	0.73337	1.177000	0.42855	-0.251000	0.11542	TGC	.	.		0.547	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		T	26731821	G	T	26731821	4	4	186	1	0	0	0	0	0	1	0	0	14659	963	34	3	502	3	SLC46A1	17	26731821	Nonsense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	6596139	26731821	54463389	66	27641										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26946763	26946763	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	cttctggttcaggtcaagcaGattctcattcttgctgtcat	8	10	6	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:26946763G>C	ENST00000528896.2	-	31	5625	c.5551C>G	c.(5551-5553)Ctg>Gtg	p.L1851V	KIAA0100_ENST00000389003.3_Missense_Mutation_p.L1708V|KIAA0100_ENST00000544884.1_Missense_Mutation_p.L1708V|KIAA0100_ENST00000579924.2_5'UTR|SPAG5-AS1_ENST00000414744.1_RNA|SPAG5-AS1_ENST00000424210.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	1851						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					AGGTCAAGCAGATTCTCATTC	0.488																																					p.L1851V		Atlas-SNP	.											.	KIAA0100	175	.	0			c.C5551G						.						114	89	97					17																	26946763		2203	4300	6503	SO:0001583	missense	9703	exon31			CAAGCAGATTCTC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.5551C>G	chr17.hg19:g.26946763G>C	ENSP00000436773:p.Leu1851Val	87.0	0.0		109.0	31.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.206762	0.58343	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T;T	0.50813	0.73;1.54;1.56	5.75	2.68	0.31781	FMP27,  C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.56426	0.1984	L	0.51422	1.61	0.58432	D	0.999993	D	0.69078	0.997	D	0.85130	0.997	T	0.49952	-0.8884	10	0.24483	T	0.36	.	9.1525	0.36971	0.2952:0.0:0.7048:0.0	.	1851	Q14667	K0100_HUMAN	V	1851;1821;1851;1708	ENSP00000467716:L1821V;ENSP00000436773:L1851V;ENSP00000446443:L1708V	ENSP00000005905:L1851V	L	-	1	2	KIAA0100	23970890	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.120000	0.41968	0.758000	0.33059	0.655000	0.94253	CTG	.	.		0.488	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		C	26946763	G	C	26946763	3	2	186	1	0	0	0	0	1	0	0	0	8163	933	33	4	1192	4	KIAA0100	17	26946763	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	214942	26946763	54248447	67	27642										
TEX14	56155	hgsc.bcm.edu	37	chr17	56707834	56707834	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	atccataatccaccagaacaTcaacgaatttcctaaggccc	4	14	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:56707834T>A	ENST00000240361.8	-	3	303	c.218A>T	c.(217-219)gAt>gTt	p.D73V	U3_ENST00000390893.1_RNA|TEX14_ENST00000389934.3_Missense_Mutation_p.D73V|TEX14_ENST00000349033.5_Missense_Mutation_p.D73V			Q8IWB6	TEX14_HUMAN	testis expressed 14	73					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.D73G(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CACCAGAACATCAACGAATTT	0.378																																					p.D73V		Atlas-SNP	.											TEX14,NS,NS,0,1	TEX14	343	.	1	Substitution - Missense(1)	pancreas(1)	c.A218T						.						96	80	85					17																	56707834		2203	4300	6503	SO:0001583	missense	56155	exon3			AGAACATCAACGA	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.218A>T	chr17.hg19:g.56707834T>A	ENSP00000240361:p.Asp73Val	138.0	2.0		329.0	68.0	NM_198393	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.246914	0.80024	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.65549	-0.16;-0.16;-0.16	5.7	5.7	0.88788	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000010	T	0.69700	0.3140	L	0.28504	0.86	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.79784	0.993;0.988;0.988	T	0.73442	-0.3981	10	0.87932	D	0	-8.114	14.844	0.70246	0.0:0.0:0.0:1.0	.	73;73;73	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	V	73	ENSP00000240361:D73V;ENSP00000374584:D73V;ENSP00000268910:D73V	ENSP00000240361:D73V	D	-	2	0	TEX14	54062833	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	3.667000	0.54547	2.190000	0.69967	0.456000	0.33151	GAT	.	.		0.378	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			A	56707834	T	A	56707834	3	1	186	1	0	0	0	0	1	0	0	0	15793	1435	50	4	4381	4	TEX14	17	56707834	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	29761071	56707834	24487376	68	27643										
NDUFV2	4729	hgsc.bcm.edu	37	chr18	9117876	9117876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gcataagacagttatgcaaaAtggagctggaggagctttat	12	5	0	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr18:9117876A>G	ENST00000318388.6	+	2	209	c.95A>G	c.(94-96)aAt>aGt	p.N32S	NDUFV2_ENST00000400033.1_Missense_Mutation_p.N35S|RP11-143J12.3_ENST00000579467.1_RNA|RP11-21J18.1_ENST00000579126.1_RNA	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	32					cardiac muscle tissue development (GO:0048738)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|nervous system development (GO:0007399)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|lung(4)|ovary(1)|stomach(1)	7						GTTATGCAAAATGGAGCTGGA	0.279																																					p.N32S		Atlas-SNP	.											.	NDUFV2	17	.	0			c.A95G						.						61	67	65					18																	9117876		2203	4296	6499	SO:0001583	missense	4729	exon2			TGCAAAATGGAGC	X84421	CCDS11842.1	18p11.22	2011-07-04	2002-08-29		ENSG00000178127	ENSG00000178127	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7717	protein-coding gene	gene with protein product	"complex I 24kDa subunit", "NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial"	600532	"NADH dehydrogenase (ubiquinone) flavoprotein 2 (24kD)"			9763677, 7607668	Standard	NM_021074		Approved	CI-24k	uc002knu.3	P19404	OTTHUMG00000131593	ENST00000318388.6:c.95A>G	chr18.hg19:g.9117876A>G	ENSP00000327268:p.Asn32Ser	356.0	0.0		366.0	101.0	NM_021074	Q9BV41	Missense_Mutation	SNP	ENST00000318388.6	hg19	CCDS11842.1	.	.	.	.	.	.	.	.	.	.	A	6.981	0.551073	0.13374	.	.	ENSG00000178127	ENST00000318388;ENST00000400033	T;T	0.40756	1.02;1.03	5.55	4.38	0.52667	.	0.281089	0.47093	D	0.000247	T	0.22044	0.0531	N	0.12961	0.28	0.31897	N	0.616514	B	0.09022	0.002	B	0.04013	0.001	T	0.16217	-1.0410	10	0.08381	T	0.77	-25.8517	10.4518	0.44526	0.8762:0.0:0.1238:0.0	.	32	P19404	NDUV2_HUMAN	S	32;35	ENSP00000327268:N32S;ENSP00000382908:N35S	ENSP00000327268:N32S	N	+	2	0	NDUFV2	9107876	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	1.699000	0.37804	2.238000	0.73509	0.477000	0.44152	AAT	.	.		0.279	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254475.2	NM_021074		G	9117876	A	G	9117876	3	3	186	1	0	0	0	0	1	0	0	0	10309	101	4	2	101	2	NDUFV2	18	9117876	Missense_Mutation	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10		9117876	68959372	69	27644										
DSC3	1825	hgsc.bcm.edu	37	chr18	28598662	28598662	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ctgaaagtgggtgcattatcAtttgaatctgttactgttat	9	5	2	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr18:28598662A>C	ENST00000360428.4	-	8	1127	c.1047T>G	c.(1045-1047)aaT>aaG	p.N349K	DSC3_ENST00000434452.1_Missense_Mutation_p.N349K	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	349	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			GTGCATTATCATTTGAATCTG	0.308																																					p.N349K		Atlas-SNP	.											.	DSC3	225	.	0			c.T1047G						.						177	169	172					18																	28598662		2203	4300	6503	SO:0001583	missense	1825	exon8			ATTATCATTTGAA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"Cadherins / Major cadherins"	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.1047T>G	chr18.hg19:g.28598662A>C	ENSP00000353608:p.Asn349Lys	53.0	0.0		51.0	15.0	NM_024423	A6NN35|Q14200|Q9HAZ9	Missense_Mutation	SNP	ENST00000360428.4	hg19	CCDS32810.1	.	.	.	.	.	.	.	.	.	.	A	18.63	3.666011	0.67700	.	.	ENSG00000134762	ENST00000360428;ENST00000434452	T;T	0.77750	-1.12;-1.12	5.25	1.53	0.23141	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.35407	N	0.003228	D	0.91442	0.7299	H	0.99042	4.41	0.58432	D	0.999998	D;D	0.89917	0.999;1.0	D;D	0.83275	0.991;0.996	D	0.90723	0.4636	10	0.87932	D	0	.	9.2457	0.37525	0.7853:0.0:0.2147:0.0	.	349;349	Q14574;Q14574-2	DSC3_HUMAN;.	K	349	ENSP00000353608:N349K;ENSP00000392068:N349K	ENSP00000353608:N349K	N	-	3	2	DSC3	26852660	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	1.791000	0.38744	0.475000	0.27415	-0.341000	0.08007	AAT	.	.		0.308	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		C	28598662	A	C	28598662	3	2	186	1	0	0	0	0	1	0	0	0	4769	214	8	5	1710	5	DSC3	18	28598662	Missense_Mutation	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10	19480786	28598662	49478586	70	27645										
ST8SIA5	29906	hgsc.bcm.edu	37	chr18	44268787	44268787	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tgatgtggtagatgccactgGtgtccacctcatacttgagc	11	10	1	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr18:44268787G>T	ENST00000315087.7	-	4	1067	c.407C>A	c.(406-408)aCc>aAc	p.T136N	ST8SIA5_ENST00000590497.1_5'UTR|ST8SIA5_ENST00000536490.1_Missense_Mutation_p.T105N|ST8SIA5_ENST00000538168.1_Missense_Mutation_p.T172N	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	136					carbohydrate metabolic process (GO:0005975)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)			kidney(1)|large_intestine(10)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	22						GATGCCACTGGTGTCCACCTC	0.597																																					p.T136N		Atlas-SNP	.											.	ST8SIA5	57	.	0			c.C407A						.						194	165	175					18																	44268787		2203	4300	6503	SO:0001583	missense	29906	exon4			CCACTGGTGTCCA	U91641	CCDS11930.1	18q12.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000101638	ENSG00000101638		"Sialyltransferases"	17827	protein-coding gene	gene with protein product	"ST8Sia V"	607162	"sialyltransferase 8E (alpha-2, 8-polysialytransferase)"	SIAT8E		9199191	Standard	XM_005258250		Approved		uc002lcj.1	O15466	OTTHUMG00000132643	ENST00000315087.7:c.407C>A	chr18.hg19:g.44268787G>T	ENSP00000321343:p.Thr136Asn	82.0	0.0		115.0	61.0	NM_013305	B7Z1K9|Q6IAW7	Missense_Mutation	SNP	ENST00000315087.7	hg19	CCDS11930.1	.	.	.	.	.	.	.	.	.	.	G	11.11	1.541740	0.27563	.	.	ENSG00000101638	ENST00000315087;ENST00000538168;ENST00000536490	T;T;T	0.29142	1.58;1.58;1.58	5.59	2.78	0.32641	.	0.156981	0.56097	N	0.000025	T	0.16514	0.0397	N	0.16368	0.405	0.52501	D	0.999951	B;B;B	0.20261	0.002;0.0;0.043	B;B;B	0.19666	0.006;0.003;0.026	T	0.08146	-1.0736	10	0.24483	T	0.36	.	7.643	0.28305	0.0656:0.1207:0.6884:0.1254	.	105;172;136	F5H8D1;B7Z1K9;O15466	.;.;SIA8E_HUMAN	N	136;172;105	ENSP00000321343:T136N;ENSP00000445492:T172N;ENSP00000443683:T105N	ENSP00000321343:T136N	T	-	2	0	ST8SIA5	42522785	1.000000	0.71417	0.990000	0.47175	0.964000	0.63967	5.323000	0.65858	0.293000	0.22520	-0.224000	0.12420	ACC	.	.		0.597	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255892.1	NM_013305		T	44268787	G	T	44268787	3	4	186	1	0	0	0	0	1	0	0	0	15250	1261	44	3	739	3	ST8SIA5	18	44268787	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	15670125	44268787	33808461	71	27646										
CRB3	92359	hgsc.bcm.edu	37	chr19	6464770	6464770	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gcctgccgttcctgctggccCgctggggccgagcctggggg	18	15	0	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:6464770C>G	ENST00000598494.1	+	2	589	c.58C>G	c.(58-60)Cgc>Ggc	p.R20G	CRB3_ENST00000356762.3_Missense_Mutation_p.R20G|CRB3_ENST00000308243.7_Missense_Mutation_p.R20G|CRB3_ENST00000600229.1_Missense_Mutation_p.R20G			Q9BUF7	CRUM3_HUMAN	crumbs family member 3	20					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein localization to plasma membrane (GO:0072659)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|SH3 domain binding (GO:0017124)			endometrium(1)|large_intestine(1)|lung(1)	3						CCTGCTGGCCCGCTGGGGCCG	0.701																																					p.R20G		Atlas-SNP	.											.	CRB3	8	.	0			c.C58G						.						4	5	4					19																	6464770		1714	3666	5380	SO:0001583	missense	92359	exon2			CTGGCCCGCTGGG	AF503290	CCDS12166.1, CCDS12167.1	19p13.3	2014-02-06	2014-02-06		ENSG00000130545	ENSG00000130545			20237	protein-coding gene	gene with protein product		609737	"crumbs homolog 3 (Drosophila)"				Standard	XM_005259680		Approved	MGC17303	uc002mez.3	Q9BUF7	OTTHUMG00000181828	ENST00000598494.1:c.58C>G	chr19.hg19:g.6464770C>G	ENSP00000469707:p.Arg20Gly	39.0	0.0		26.0	12.0	NM_174881	A8KA91|D6W643|Q8N0V8|Q8WVA0	Missense_Mutation	SNP	ENST00000598494.1	hg19	CCDS12167.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.508142	0.27036	.	.	ENSG00000130545	ENST00000356762;ENST00000308243	.	.	.	4.01	0.0923	0.14472	.	0.494583	0.19462	N	0.113675	T	0.27663	0.0680	L	0.57536	1.79	0.22266	N	0.999249	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.005	T	0.26815	-1.0092	9	0.06625	T	0.88	-1.0174	3.6067	0.08045	0.0:0.506:0.2192:0.2748	.	20;20	Q9BUF7-2;Q9BUF7	.;CRUM3_HUMAN	G	20	.	ENSP00000310123:R20G	R	+	1	0	CRB3	6415770	0.000000	0.05858	0.901000	0.35422	0.300000	0.27592	-0.827000	0.04424	0.275000	0.22094	0.462000	0.41574	CGC	.	.		0.701	CRB3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457837.1			G	6464770	C	G	6464770	3	3	186	1	0	0	0	0	1	0	0	0	3852	652	23	4	60	4	CRB3	19	6464770	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10		6464770	52664213	72	27647										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17017877	17017877	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	taagggtccatggccaggggCgcagcagactccaggaagtg	16	10	0	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:17017877C>T	ENST00000443236.1	-	30	4084	c.4053G>A	c.(4051-4053)gcG>gcA	p.A1351A	RN7SL835P_ENST00000579920.1_RNA	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1304						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						TGGCCAGGGGCGCAGCAGACT	0.657																																					p.A1351A		Atlas-SNP	.											.	CPAMD8	192	.	0			c.G4053A						.						34	42	39					19																	17017877		2154	4254	6408	SO:0001819	synonymous_variant	27151	exon30			CAGGGGCGCAGCA	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.4053G>A	chr19.hg19:g.17017877C>T		131.0	0.0		108.0	57.0	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	hg19	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	C	0.039	-1.291064	0.01375	.	.	ENSG00000160111	ENST00000443236	.	.	.	3.07	-6.14	0.02111	.	.	.	.	.	T	0.24392	0.0591	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26643	-1.0097	4	.	.	.	.	5.792	0.18365	0.0:0.3732:0.2202:0.4065	.	.	.	.	H	1362	.	.	R	-	2	0	CPAMD8	16878877	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.852000	0.01667	-1.644000	0.01517	-1.607000	0.00807	CGC	.	.		0.657	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17017877	C	T	17017877	2	4	186	1	0	0	0	0	0	0	0	1	3797	755	27	1		1	CPAMD8	19	17017877	Silent	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	10553107	17017877	42111106	73	27648										
RPL18A	6142	hgsc.bcm.edu	37	chr19	17972267	17972267	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	agaagtcttcaggggagattGtctactgtgggcaggtatgg	16	5	3	2			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:17972267G>T	ENST00000222247.5	+	2	265	c.184G>T	c.(184-186)Gtc>Ttc	p.V62F	RPL18A_ENST00000599870.1_Missense_Mutation_p.V33F|RPL18A_ENST00000600147.1_Missense_Mutation_p.V62F|SNORA68_ENST00000384437.1_RNA|RPL18A_ENST00000599898.1_Missense_Mutation_p.V23F	NM_000980.3	NP_000971.1	Q02543	RL18A_HUMAN	ribosomal protein L18a	62					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(1)	5						AGGGGAGATTGTCTACTGTGG	0.512																																					p.V62F		Atlas-SNP	.											.	RPL18A	15	.	0			c.G184T						.						32	33	32					19																	17972267		2203	4300	6503	SO:0001583	missense	6142	exon2			GAGATTGTCTACT	AB007175	CCDS12367.1	19p13.11	2011-04-06			ENSG00000105640	ENSG00000105640		"L ribosomal proteins"	10311	protein-coding gene	gene with protein product	"60S ribosomal protein L18a", "ribosomal protein L18a-like protein"	604178				9582194	Standard	NM_000980		Approved	L18A	uc002nhp.3	Q02543		ENST00000222247.5:c.184G>T	chr19.hg19:g.17972267G>T	ENSP00000222247:p.Val62Phe	60.0	0.0		32.0	12.0	NM_000980		Missense_Mutation	SNP	ENST00000222247.5	hg19	CCDS12367.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.203390	0.58234	.	.	ENSG00000105640	ENST00000420197;ENST00000222247	.	.	.	4.11	4.11	0.48088	Ribosomal protein L18a/LX (1);	0.138713	0.47852	U	0.000207	D	0.83760	0.5324	M	0.90082	3.085	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	D	0.87704	0.2562	9	0.87932	D	0	.	14.229	0.65879	0.0:0.0:1.0:0.0	.	62	Q02543	RL18A_HUMAN	F	62	.	ENSP00000222247:V62F	V	+	1	0	RPL18A	17833267	1.000000	0.71417	0.896000	0.35187	0.068000	0.16541	9.415000	0.97375	2.019000	0.59389	0.563000	0.77884	GTC	.	.		0.512	RPL18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466679.1	NM_000980		T	17972267	G	T	17972267	3	4	186	1	0	0	0	0	1	0	0	0	13580	1377	48	3	190	3	RPL18A	19	17972267	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	954390	17972267	41156716	74	27649										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22156515	22156515	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gtgaattttcttatgttccaTaaggtttgaggaccagttga	10	5	1	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:22156515T>C	ENST00000397126.4	-	4	1469	c.1321A>G	c.(1321-1323)Atg>Gtg	p.M441V	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	441					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTATGTTCCATAAGGTTTGAG	0.373																																					p.M441V		Atlas-SNP	.											.	ZNF208	817	.	0			c.A1321G						.						82	89	87					19																	22156515		2119	4251	6370	SO:0001583	missense	7757	exon4			GTTCCATAAGGTT	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1321A>G	chr19.hg19:g.22156515T>C	ENSP00000380315:p.Met441Val	122.0	0.0		149.0	29.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	0.029	-1.346276	0.01266	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.16897	2.31	2.83	-3.15	0.05233	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10809	0.0264	.	.	.	0.09310	N	1	B	0.22346	0.068	B	0.34346	0.18	T	0.46624	-0.9178	8	0.23302	T	0.38	.	5.9142	0.19045	0.1678:0.573:0.0:0.2592	.	441	O43345	ZN208_HUMAN	V	441	ENSP00000380315:M441V	ENSP00000380315:M441V	M	-	1	0	ZNF208	21948355	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.193000	0.01244	-0.302000	0.08869	0.254000	0.18369	ATG	.	.		0.373	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		C	22156515	T	C	22156515	3	2	186	1	0	0	0	0	1	0	0	0	17781	1406	49	2	2525	2	ZNF208	19	22156515	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10	4184248	22156515	36972468	75	27650										
RYR1	6261	hgsc.bcm.edu	37	chr19	39034235	39034235	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tcattgaagagcagggcaagAggaacttctccaaagccatg	11	9	2	3			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:39034235A>C	ENST00000359596.3	+	86	11842	c.11842A>C	c.(11842-11844)Agg>Cgg	p.R3948R	RYR1_ENST00000355481.4_Silent_p.R3943R|RYR1_ENST00000360985.3_Silent_p.R3943R			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3948					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GCAGGGCAAGAGGAACTTCTC	0.602																																					p.R3948R		Atlas-SNP	.											.	RYR1	708	.	0			c.A11842C						.						90	84	86					19																	39034235		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon86			GGCAAGAGGAACT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.11842A>C	chr19.hg19:g.39034235A>C		94.0	0.0		112.0	17.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.602	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			C	39034235	A	C	39034235	2	2	186	1	0	0	0	0	0	0	0	1	13783	295	11	5		5	RYR1	19	39034235	Silent	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10	16877720	39034235	20094748	76	27651										
PSG3	5671	hgsc.bcm.edu	37	chr19	43236995	43236995	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tcactgggttccgtatttcaCattcatagggtcctgcagtg	10	10	3	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:43236995C>T	ENST00000327495.5	-	3	834	c.650G>A	c.(649-651)tGt>tAt	p.C217Y	PSG3_ENST00000595140.1_Missense_Mutation_p.C217Y|PSG3_ENST00000490592.1_5'Flank	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	217	Ig-like C2-type 1.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				CCGTATTTCACATTCATAGGG	0.517																																					p.C217Y		Atlas-SNP	.											.	PSG3	82	.	0			c.G650A						.						230	236	234					19																	43236995		2203	4298	6501	SO:0001583	missense	5671	exon3			ATTTCACATTCAT		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.650G>A	chr19.hg19:g.43236995C>T	ENSP00000332215:p.Cys217Tyr	73.0	0.0		145.0	88.0	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	hg19	CCDS12611.1	.	.	.	.	.	.	.	.	.	.	-	12.33	1.904323	0.33628	.	.	ENSG00000221826	ENST00000327495	T	0.58940	0.3	1.59	1.59	0.23543	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.78304	0.4262	M	0.93507	3.425	0.28060	N	0.933025	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.979	T	0.66452	-0.5920	9	0.87932	D	0	.	6.5812	0.22596	0.0:1.0:0.0:0.0	.	195;217	Q08266;Q16557	.;PSG3_HUMAN	Y	217	ENSP00000332215:C217Y	ENSP00000332215:C217Y	C	-	2	0	PSG3	47928835	0.064000	0.20934	0.284000	0.24805	0.019000	0.09904	0.781000	0.26774	0.871000	0.35750	0.393000	0.25936	TGT	.	.		0.517	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016		T	43236995	C	T	43236995	3	4	186	1	0	0	0	0	1	0	0	0	12668	478	17	3	652	3	PSG3	19	43236995	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	4202760	43236995	15891988	77	27652										
NKPD1	284353	hgsc.bcm.edu	37	chr19	45656158	45656158	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gaggaagaggtagccgttatCggccgtgcccttcatgttgc	14	10	1	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:45656158C>A	ENST00000438936.2	-	3	1082	c.871G>T	c.(871-873)Gat>Tat	p.D291Y	AC005757.7_ENST00000589594.1_lincRNA|NKPD1_ENST00000429338.1_Missense_Mutation_p.D291Y|NKPD1_ENST00000317951.4_Missense_Mutation_p.D513Y|NKPD1_ENST00000589776.1_Missense_Mutation_p.D291Y			Q17RQ9	NKPD1_HUMAN	NTPase, KAP family P-loop domain containing 1	291	KAP NTPase.					integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|prostate(2)|urinary_tract(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		TAGCCGTTATCGGCCGTGCCC	0.637																																					p.D513Y		Atlas-SNP	.											.	NKPD1	46	.	0			c.G1537T						.						11	14	13					19																	45656158		2085	4208	6293	SO:0001583	missense	284353	exon4			CGTTATCGGCCGT	AK090919		19q13.32	2012-07-02		2012-07-02	ENSG00000179846	ENSG00000179846			24739	protein-coding gene	gene with protein product						14702039	Standard	NM_198478		Approved	FLJ33600	uc010xxi.2	Q17RQ9	OTTHUMG00000160521	ENST00000438936.2:c.871G>T	chr19.hg19:g.45656158C>A	ENSP00000401739:p.Asp291Tyr	129.0	0.0		152.0	80.0	NM_198478	B7ZLG6|D6RH15|Q8N2A2	Missense_Mutation	SNP	ENST00000438936.2	hg19		.	.	.	.	.	.	.	.	.	.	C	15.05	2.717980	0.48622	.	.	ENSG00000179846	ENST00000317951;ENST00000438936;ENST00000429338	T;T;T	0.32753	1.44;1.44;1.44	5.3	5.3	0.74995	KAP P-loop (1);	0.051073	0.85682	D	0.000000	T	0.52549	0.1741	L	0.56769	1.78	0.49130	D	0.999752	D	0.89917	1.0	D	0.91635	0.999	T	0.50432	-0.8829	10	0.51188	T	0.08	-43.981	16.4297	0.83837	0.0:1.0:0.0:0.0	.	291	Q17RQ9	NKPD1_HUMAN	Y	513;291;291	ENSP00000321976:D513Y;ENSP00000401739:D291Y;ENSP00000404706:D291Y	ENSP00000321976:D513Y	D	-	1	0	NKPD1	50347998	1.000000	0.71417	1.000000	0.80357	0.626000	0.37791	5.687000	0.68219	2.476000	0.83614	0.462000	0.41574	GAT	.	.		0.637	NKPD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000360950.2	NM_198478		A	45656158	C	A	45656158	3	1	186	1	0	0	0	0	1	0	0	0	10455	884	31	1	965	1	NKPD1	19	45656158	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	2419163	45656158	13472825	78	27653										
SULF2	55959	hgsc.bcm.edu	37	chr20	46365492	46365492	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gtacacggcaaaggtgcggcTctcgtgctgtgcctgccagg	15	12	1	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr20:46365492T>C	ENST00000359930.4	-	3	1221	c.370A>G	c.(370-372)Agc>Ggc	p.S124G	SULF2_ENST00000478766.1_5'UTR|SULF2_ENST00000467815.1_Missense_Mutation_p.S124G|SULF2_ENST00000361612.4_Missense_Mutation_p.S124G|SULF2_ENST00000484875.1_Missense_Mutation_p.S124G	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	124					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						AAGGTGCGGCTCTCGTGCTGT	0.622																																					p.S124G		Atlas-SNP	.											.	SULF2	131	.	0			c.A370G						.						181	130	147					20																	46365492		2203	4300	6503	SO:0001583	missense	55959	exon3			TGCGGCTCTCGTG	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.370A>G	chr20.hg19:g.46365492T>C	ENSP00000353007:p.Ser124Gly	88.0	0.0		91.0	36.0	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	hg19	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.813584	0.50527	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815;ENST00000437955	D;D;D;D;D	0.98602	-5.02;-5.02;-5.02;-5.02;-5.02	5.34	1.82	0.25136	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.247613	0.47852	N	0.000218	D	0.95354	0.8492	L	0.34521	1.04	0.28885	N	0.894179	B;B;B	0.27971	0.027;0.048;0.196	B;B;B	0.33521	0.041;0.041;0.165	D	0.91927	0.5552	10	0.66056	D	0.02	-15.8801	8.9188	0.35599	0.0:0.2169:0.0:0.7831	.	124;124;124	G3XAE6;Q8IWU5-2;Q8IWU5	.;.;SULF2_HUMAN	G	124	ENSP00000353007:S124G;ENSP00000418290:S124G;ENSP00000354662:S124G;ENSP00000418442:S124G;ENSP00000410026:S124G	ENSP00000353007:S124G	S	-	1	0	SULF2	45798899	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	2.543000	0.45752	0.326000	0.23384	0.459000	0.35465	AGC	.	.		0.622	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		C	46365492	T	C	46365492	3	2	186	1	0	0	0	0	1	0	0	0	15386	1551	54	2	2318	2	SULF2	20	46365492	Missense_Mutation	SNP	T	TCGA-DD-AADC-01A-11D-A40R-10		46365492	16660028	79	27654										
PCNT	5116	hgsc.bcm.edu	37	chr21	47851867	47851867	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ggctgaggctcagaagcactGtgaggcgctcaggagagaga	17	8	2	5			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr21:47851867G>T	ENST00000359568.5	+	38	8596	c.8489G>T	c.(8488-8490)tGt>tTt	p.C2830F	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2830					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CAGAAGCACTGTGAGGCGCTC	0.567																																					p.C2830F		Atlas-SNP	.											.	PCNT	283	.	0			c.G8489T						.						65	58	61					21																	47851867		2203	4300	6503	SO:0001583	missense	5116	exon38			AGCACTGTGAGGC	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.8489G>T	chr21.hg19:g.47851867G>T	ENSP00000352572:p.Cys2830Phe	104.0	0.0		53.0	26.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	G	10.17	1.275595	0.23307	.	.	ENSG00000160299	ENST00000359568	T	0.01548	4.78	5.21	4.31	0.51392	.	0.217433	0.23700	N	0.045428	T	0.03651	0.0104	L	0.32530	0.975	0.09310	N	1	D;D	0.65815	0.995;0.991	P;P	0.58172	0.834;0.687	T	0.52859	-0.8519	10	0.19590	T	0.45	.	12.5238	0.56075	0.1353:0.0:0.8647:0.0	.	2712;2830	O95613-2;O95613	.;PCNT_HUMAN	F	2830	ENSP00000352572:C2830F	ENSP00000352572:C2830F	C	+	2	0	PCNT	46676295	0.000000	0.05858	0.065000	0.19835	0.056000	0.15407	0.400000	0.20932	2.606000	0.88127	0.655000	0.94253	TGT	.	.		0.567	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47851867	G	T	47851867	3	4	186	1	0	0	0	0	1	0	0	0	11599	1377	48	3	8639	3	PCNT	21	47851867	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10		47851867	278028	80	27655										
C22orf29	79680	hgsc.bcm.edu	37	chr22	19839750	19839750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	cggctgcccagatgggaatgCgagggccctgctgacggcac	16	13	0	2	rs9618711		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr22:19839750C>T	ENST00000405640.1	-	2	703	c.35G>A	c.(34-36)cGc>cAc	p.R12H	GNB1L_ENST00000405009.1_Intron|GNB1L_ENST00000329517.6_Intron|GNB1L_ENST00000403325.1_Intron|C22orf29_ENST00000328554.4_Missense_Mutation_p.R12H|C22orf29_ENST00000484072.1_Intron|GNB1L_ENST00000460402.1_Intron|C22orf29_ENST00000407472.1_Missense_Mutation_p.R12H			Q7L3V2	BOP_HUMAN	chromosome 22 open reading frame 29	12					mitochondrial outer membrane permeabilization (GO:0097345)|regulation of mitochondrial membrane potential (GO:0051881)	mitochondrion (GO:0005739)		p.R12H(1)		NS(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	7	Colorectal(54;0.0993)					GATGGGAATGCGAGGGCCCTG	0.637																																					p.R12H		Atlas-SNP	.											C22orf29,NS,carcinoma,-1,1	C22orf29	23	.	1	Substitution - Missense(1)	large_intestine(1)	c.G35A						.	C	HIS/ARG,	0,4406		0,0,2203	56	56	56		35,	-2.1	0	22	dbSNP_119	56	1,8589		0,1,4294	no	missense,intron	GNB1L,C22orf29	NM_024627.5,NM_053004.2	29,	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,	12/365,	19839750	1,12995	2203	4295	6498	SO:0001583	missense	79680	exon3			GGAATGCGAGGGC	BX640998	CCDS13769.1	22q11.21	2006-07-05			ENSG00000215012	ENSG00000215012			26112	protein-coding gene	gene with protein product						12477932	Standard	NM_024627		Approved	FLJ21125	uc002zqh.3	Q7L3V2	OTTHUMG00000030314	ENST00000405640.1:c.35G>A	chr22.hg19:g.19839750C>T	ENSP00000384924:p.Arg12His	127.0	0.0		132.0	42.0	NM_024627	A8K5E7|D3DX21|Q6MZM8|Q6N000|Q9H7A0	Missense_Mutation	SNP	ENST00000405640.1	hg19	CCDS13769.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.920401	0.33908	0.0	1.16E-4	ENSG00000215012	ENST00000407472;ENST00000328554;ENST00000405640;ENST00000416337	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	3.69	-2.1	0.07210	.	.	.	.	.	T	0.12220	0.0297	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.23226	-1.0194	9	0.33940	T	0.23	-0.2253	3.3818	0.07257	0.1819:0.3924:0.0:0.4257	rs9618711	12	Q7L3V2	CV029_HUMAN	H	12	ENSP00000386111:R12H;ENSP00000330596:R12H;ENSP00000384924:R12H;ENSP00000392994:R12H	ENSP00000330596:R12H	R	-	2	0	C22orf29	18219750	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.577000	0.05847	-0.296000	0.08947	-0.136000	0.14681	CGC	.	.		0.637	C22orf29-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317290.2	NM_024627		T	19839750	C	T	19839750	3	4	186	1	0	0	0	0	1	0	0	0	2143	768	27	1	1063	1	C22orf29	22	19839750	Missense_Mutation	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10		19839750	31464816	81	27656										
AMELX	265	hgsc.bcm.edu	37	chrX	11316227	11316227	+	Intron	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	cttctttcttttgtagaactCacattctcaggctatcaatg	5	10	5	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chrX:11316227C>G	ENST00000380714.3	+	4	170				ARHGAP6_ENST00000337414.4_Intron|AMELX_ENST00000348912.4_Intron|AMELX_ENST00000380712.3_Nonsense_Mutation_p.S36*|ARHGAP6_ENST00000380718.1_Intron|ARHGAP6_ENST00000380732.3_Intron|ARHGAP6_ENST00000413512.3_Intron|ARHGAP6_ENST00000380736.1_Intron	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked						biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						TTGTAGAACTCACATTCTCAG	0.358																																					p.S36X		Atlas-SNP	.											.	AMELX	31	.	0			c.C107G						.						236	226	229					X																	11316227		2203	4300	6503	SO:0001627	intron_variant	265	exon4			AGAACTCACATTC		CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"amelogenesis imperfecta 1"	300391	"amelogenin (X chromosome, amelogenesis imperfecta 1)"	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.103-129C>G	chrX.hg19:g.11316227C>G		151.0	0.0		215.0	88.0	NM_182680	Q96NW6|Q9UCA7	Nonsense_Mutation	SNP	ENST00000380714.3	hg19	CCDS14144.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.394290	0.62066	.	.	ENSG00000125363	ENST00000380712	.	.	.	4.56	2.73	0.32206	.	0.000000	0.29198	N	0.012860	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	4.5126	4.7718	0.13160	0.2125:0.6733:0.0:0.1142	.	.	.	.	X	36	.	ENSP00000370088:S36X	S	+	2	0	AMELX	11226148	0.261000	0.24063	0.029000	0.17559	0.933000	0.57130	0.431000	0.21444	0.458000	0.26988	0.459000	0.35465	TCA	.	.		0.358	AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055746.1	NM_001142		G	11316227	C	G	11316227	1	3	186	0	1	0	0	0	0	0	0	0	569	838	29	4		4	AMELX	23	11316227	Intron	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10		11316227	143954333	82	27657										
TLR8	51311	hgsc.bcm.edu	37	chrX	12940017	12940017	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	aaccaaaaaatatgcaaaaaGctggaactttaaaacagctt	5	7	0	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chrX:12940017G>C	ENST00000218032.6	+	2	2945	c.2858G>C	c.(2857-2859)aGc>aCc	p.S953T	TLR8_ENST00000311912.5_Missense_Mutation_p.S971T	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	953	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TATGCAAAAAGCTGGAACTTT	0.403																																					p.S953T		Atlas-SNP	.											.	TLR8	134	.	0			c.G2858C						.						63	61	62					X																	12940017		2203	4299	6502	SO:0001583	missense	51311	exon2			CAAAAAGCTGGAA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2858G>C	chrX.hg19:g.12940017G>C	ENSP00000218032:p.Ser953Thr	223.0	0.0		398.0	318.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	G	5.474	0.272429	0.10349	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.05025	3.51;3.51	5.7	-1.87	0.07737	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.146640	0.31188	N	0.008086	T	0.09335	0.0230	L	0.58428	1.81	0.29378	N	0.863525	D;D	0.53462	0.96;0.96	P;P	0.49799	0.622;0.622	T	0.14643	-1.0465	10	0.06891	T	0.86	.	15.475	0.75471	0.2651:0.0:0.7349:0.0	.	953;971	Q9NR97;D1CS70	TLR8_HUMAN;.	T	953;971	ENSP00000218032:S953T;ENSP00000312082:S971T	ENSP00000218032:S953T	S	+	2	0	TLR8	12849938	0.727000	0.28069	0.041000	0.18516	0.902000	0.53008	0.278000	0.18753	-0.805000	0.04404	-0.191000	0.12829	AGC	.	.		0.403	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		C	12940017	G	C	12940017	3	2	186	1	0	0	0	0	1	0	0	0	15972	971	34	4	2864	4	TLR8	23	12940017	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	1623790	12940017	142330543	83	27658										
PRPS1	5631	hgsc.bcm.edu	37	chrX	106890949	106890949	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	tgaggcagtagtagtcaccaAtaccatacctcaggaggaca	10	10	2	1			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chrX:106890949A>G	ENST00000372435.4	+	6	940	c.818A>G	c.(817-819)aAt>aGt	p.N273S	PRPS1_ENST00000372418.1_Missense_Mutation_p.N173S|PRPS1_ENST00000372428.4_Missense_Mutation_p.N206S|PRPS1_ENST00000543248.1_Missense_Mutation_p.N273S	NM_002764.3	NP_002755.1	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	273					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|hypoxanthine biosynthetic process (GO:0046101)|nervous system development (GO:0007399)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|pyrimidine nucleotide biosynthetic process (GO:0006221)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|urate biosynthetic process (GO:0034418)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			breast(3)|endometrium(2)|kidney(3)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	23						GTAGTCACCAATACCATACCT	0.453																																					p.N273S		Atlas-SNP	.											.	PRPS1	33	.	0			c.A818G						.						139	113	122					X																	106890949		2203	4300	6503	SO:0001583	missense	5631	exon6			TCACCAATACCAT	X15331	CCDS14529.1, CCDS76007.1	Xq22.3	2014-09-17			ENSG00000147224	ENSG00000147224	2.7.6.1		9462	protein-coding gene	gene with protein product	"PRS I", "ribose-phosphate diphosphokinase 1"	311850	"deafness, X-linked 2, perceptive, congenital"	DFN2		1962753, 20021999	Standard	NM_002764		Approved	CMTX5, DFNX1	uc004ene.4	P60891	OTTHUMG00000022167	ENST00000372435.4:c.818A>G	chrX.hg19:g.106890949A>G	ENSP00000361512:p.Asn273Ser	106.0	0.0		101.0	5.0	NM_002764	B1ALA8|B2R6T7|B4DNL6|D3DUX6|P09329	Missense_Mutation	SNP	ENST00000372435.4	hg19	CCDS14529.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.159280	0.78226	.	.	ENSG00000147224	ENST00000372435;ENST00000372428;ENST00000543248;ENST00000372418	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	3.76	3.76	0.43208	.	0.000000	0.85682	D	0.000000	D	0.88976	0.6584	M	0.93420	3.415	0.54753	D	0.999987	D;D	0.76494	0.999;0.999	D;D	0.62955	0.909;0.909	D	0.91190	0.4983	10	0.87932	D	0	.	11.5863	0.50920	1.0:0.0:0.0:0.0	.	273;273	Q53FW2;P60891	.;PRPS1_HUMAN	S	273;206;273;173	ENSP00000361512:N273S;ENSP00000361505:N206S;ENSP00000443185:N273S;ENSP00000361495:N173S	ENSP00000361495:N173S	N	+	2	0	PRPS1	106777605	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.576000	0.90770	1.699000	0.51192	0.486000	0.48141	AAT	.	.		0.453	PRPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057840.1			G	106890949	A	G	106890949	3	3	186	1	0	0	0	0	1	0	0	0	12590	101	4	2	840	2	PRPS1	23	106890949	Missense_Mutation	SNP	A	TCGA-DD-AADC-01A-11D-A40R-10	93950932	106890949	48379611	84	27659										
GPR101	83550	hgsc.bcm.edu	37	chrX	136112559	136112559	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	ggtacctgggtttcgacatcCacccacacggccaggactgc	11	15	0	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chrX:136112559C>T	ENST00000298110.1	-	1	1274	c.1275G>A	c.(1273-1275)gtG>gtA	p.V425V		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	425						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					TTTCGACATCCACCCACACGG	0.507																																					p.V425V		Atlas-SNP	.											.	GPR101	96	.	0			c.G1275A						.						88	76	80					X																	136112559		2203	4300	6503	SO:0001819	synonymous_variant	83550	exon1			GACATCCACCCAC	AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.1275G>A	chrX.hg19:g.136112559C>T		82.0	0.0		63.0	48.0	NM_054021	Q5JSM8|Q8NG93	Silent	SNP	ENST00000298110.1	hg19	CCDS14662.1																																																																																			.	.		0.507	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			T	136112559	C	T	136112559	2	4	186	1	0	0	0	0	0	0	0	1	6630	581	21	3		3	GPR101	23	136112559	Silent	SNP	C	TCGA-DD-AADC-01A-11D-A40R-10	29221610	136112559	19158001	85	27660										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153033156	153033156	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.825379266750948	2.31106194690265	0	0.142857142857143	0.729941291585128	0	gccagggcctcatccaggccGccttccttgccccgggcacc	11	20	1	0			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chrX:153033156G>T	ENST00000361971.5	+	3	988	c.874G>T	c.(874-876)Gcc>Tcc	p.A292S	PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538776.1_Intron|PLXNB3_ENST00000538282.1_Intron|U52111.14_ENST00000416854.1_RNA|U52111.14_ENST00000434284.1_RNA|PLXNB3_ENST00000538966.1_Missense_Mutation_p.A315S	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	292	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CATCCAGGCCGCCTTCCTTGC	0.706																																					p.A315S		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G943T						.						12	11	12					X																	153033156		2172	4254	6426	SO:0001583	missense	5365	exon4			CAGGCCGCCTTCC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.874G>T	chrX.hg19:g.153033156G>T	ENSP00000355378:p.Ala292Ser	111.0	0.0		95.0	72.0	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.084675	0.36758	.	.	ENSG00000198753	ENST00000538966;ENST00000361971	T;T	0.14266	2.52;2.52	5.1	4.23	0.50019	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.236856	0.21888	N	0.067630	T	0.41096	0.1144	M	0.86502	2.82	0.24828	N	0.992549	D;D	0.89917	1.0;0.973	D;P	0.80764	0.994;0.796	T	0.36480	-0.9746	10	0.44086	T	0.13	.	13.1238	0.59342	0.0:0.0:0.8386:0.1614	.	315;292	F5H773;Q9ULL4	.;PLXB3_HUMAN	S	315;292	ENSP00000442736:A315S;ENSP00000355378:A292S	ENSP00000355378:A292S	A	+	1	0	PLXNB3	152686350	1.000000	0.71417	0.040000	0.18447	0.077000	0.17291	6.946000	0.75953	0.932000	0.37266	-0.351000	0.07748	GCC	.	.		0.706	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			T	153033156	G	T	153033156	3	4	186	1	0	0	0	0	1	0	0	0	12134	1087	38	1	998	1	PLXNB3	23	153033156	Missense_Mutation	SNP	G	TCGA-DD-AADC-01A-11D-A40R-10	16920597	153033156	2237404	86	27661										
EDN2	1907	hgsc.bcm.edu	37	chr1	41948170	41948170	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ggcagaaggtggcacaggcgGggtccctggcactggagcac	18	11	0	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr1:41948170G>T	ENST00000372587.4	-	3	380	c.311C>A	c.(310-312)cCc>cAc	p.P104H	EDN2_ENST00000490783.1_5'UTR	NM_001956.3	NP_001947.1	P20800	EDN2_HUMAN	endothelin 2	104	Endothelin-like.				artery smooth muscle contraction (GO:0014824)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|energy homeostasis (GO:0097009)|hormonal regulation of the force of heart contraction (GO:0003058)|inositol phosphate-mediated signaling (GO:0048016)|lung alveolus development (GO:0048286)|macrophage activation (GO:0042116)|macrophage chemotaxis (GO:0048246)|neutrophil chemotaxis (GO:0030593)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of heart rate (GO:0010460)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of the force of heart contraction by chemical signal (GO:0003099)|prostaglandin biosynthetic process (GO:0001516)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|temperature homeostasis (GO:0001659)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)			endometrium(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	8	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GGCACAGGCGGGGTCCCTGGC	0.697																																					p.P104H		Atlas-SNP	.											.	EDN2	12	.	0			c.C311A						.						27	34	31					1																	41948170		2203	4298	6501	SO:0001583	missense	1907	exon3			CAGGCGGGGTCCC	M65199	CCDS462.1	1p34	2013-02-26			ENSG00000127129	ENSG00000127129		"Endogenous ligands"	3177	protein-coding gene	gene with protein product		131241					Standard	NM_001956		Approved	ET2	uc009vwh.3	P20800	OTTHUMG00000006362	ENST00000372587.4:c.311C>A	chr1.hg19:g.41948170G>T	ENSP00000361668:p.Pro104His	74.0	0.0		88.0	22.0	NM_001956	Q5T1R3	Missense_Mutation	SNP	ENST00000372587.4	hg19	CCDS462.1	.	.	.	.	.	.	.	.	.	.	G	4.494	0.091574	0.08632	.	.	ENSG00000127129	ENST00000372587	D	0.83591	-1.74	5.29	3.25	0.37280	Endothelin-like toxin, conserved site (1);Endothelin-like toxin (1);	0.863580	0.10508	N	0.666512	T	0.76905	0.4053	L	0.48642	1.525	0.09310	N	1	B	0.17852	0.024	B	0.12837	0.008	T	0.66472	-0.5915	10	0.51188	T	0.08	-9.2284	7.9387	0.29946	0.0:0.3082:0.5118:0.18	.	104	P20800	EDN2_HUMAN	H	104	ENSP00000361668:P104H	ENSP00000361668:P104H	P	-	2	0	EDN2	41720757	0.996000	0.38824	0.520000	0.27837	0.049000	0.14656	1.301000	0.33447	1.423000	0.47198	0.655000	0.94253	CCC	.	.		0.697	EDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000016983.1	NM_001956		T	41948170	G	T	41948170	3	4	187	1	0	0	0	0	1	0	0	0	4919	1232	43	3	237	3	EDN2	1	41948170	Missense_Mutation	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10		41948170	207302451	1	27662										
FUBP1	8880	hgsc.bcm.edu	37	chr1	78444594	78444594	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gggctctctgcagtgcatctTtgaaagcgtcgttaactcct	10	11	2	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr1:78444594T>C	ENST00000370768.2	-	1	176	c.95A>G	c.(94-96)aAa>aGa	p.K32R	FUBP1_ENST00000436586.2_Missense_Mutation_p.K32R|FUBP1_ENST00000370767.1_Missense_Mutation_p.K32R	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	32					positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						CAGTGCATCTTTGAAAGCGTC	0.607			"F, N"		oligodendroglioma																																p.K32R		Atlas-SNP	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1	112	.	0			c.A95G						.						83	92	89					1																	78444594		2203	4300	6503	SO:0001583	missense	8880	exon1			GCATCTTTGAAAG	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.95A>G	chr1.hg19:g.78444594T>C	ENSP00000359804:p.Lys32Arg	53.0	0.0		63.0	34.0	NM_003902	Q12828	Missense_Mutation	SNP	ENST00000370768.2	hg19	CCDS683.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.256329	0.80246	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586;ENST00000421641	T;T;T;T	0.47177	1.51;1.51;1.49;0.85	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.32615	0.0835	L	0.36672	1.1	0.58432	D	0.999998	P;P	0.50156	0.932;0.92	B;P	0.45232	0.326;0.474	T	0.29701	-1.0003	10	0.72032	D	0.01	-15.4291	15.0493	0.71854	0.0:0.0:0.0:1.0	.	32;32	B4DT31;Q96AE4	.;FUBP1_HUMAN	R	32	ENSP00000359803:K32R;ENSP00000359804:K32R;ENSP00000389536:K32R;ENSP00000402630:K32R	ENSP00000294623:K32R	K	-	2	0	FUBP1	78217182	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.625000	0.67770	2.100000	0.63781	0.459000	0.35465	AAA	.	.		0.607	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		C	78444594	T	C	78444594	3	2	187	1	0	0	0	0	1	0	0	0	6100	1841	64	2	1919	2	FUBP1	1	78444594	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	36496424	78444594	170806027	2	27663										
SLC16A4	9122	hgsc.bcm.edu	37	chr1	110921555	110921555	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ctaccaggtgaaaggtagggAtgaagtatgctaactgactg	13	6	0	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr1:110921555A>C	ENST00000369779.4	-	6	1199	c.950T>G	c.(949-951)aTc>aGc	p.I317S	SLC16A4_ENST00000472422.2_Missense_Mutation_p.I269S|SLC16A4_ENST00000497687.1_5'Flank|SLC16A4_ENST00000541986.1_Missense_Mutation_p.I255S|SLC16A4_ENST00000369781.4_Intron|SLC16A4_ENST00000437429.2_Missense_Mutation_p.I207S	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	317					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	AAAGGTAGGGATGAAGTATGC	0.428																																					p.I317S		Atlas-SNP	.											.	SLC16A4	47	.	0			c.T950G						.						112	107	109					1																	110921555		2203	4300	6503	SO:0001583	missense	9122	exon6			GTAGGGATGAAGT	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"Solute carriers"	10925	protein-coding gene	gene with protein product		603878	"solute carrier family 16 (monocarboxylic acid transporters), member 4", "solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.950T>G	chr1.hg19:g.110921555A>C	ENSP00000358794:p.Ile317Ser	161.0	0.0		190.0	108.0	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Missense_Mutation	SNP	ENST00000369779.4	hg19	CCDS823.1	.	.	.	.	.	.	.	.	.	.	a	22.2	4.260273	0.80246	.	.	ENSG00000168679	ENST00000369779;ENST00000472422;ENST00000437429;ENST00000541986;ENST00000467986	T;T;T;T;T	0.80480	0.35;0.35;0.35;0.35;-1.38	5.99	4.86	0.63082	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.310233	0.36303	N	0.002677	T	0.81307	0.4795	M	0.81497	2.545	0.40776	D	0.983132	P;P;B;P	0.50369	0.927;0.934;0.386;0.87	P;P;B;P	0.55785	0.601;0.784;0.273;0.688	T	0.80647	-0.1289	10	0.31617	T	0.26	.	10.7058	0.45954	0.9277:0.0:0.0723:0.0	.	207;255;269;317	E7EPY8;B4DJ67;G3V175;O15374	.;.;.;MOT5_HUMAN	S	317;269;207;255;84	ENSP00000358794:I317S;ENSP00000432495:I269S;ENSP00000394790:I207S;ENSP00000446087:I255S;ENSP00000435768:I84S	ENSP00000358794:I317S	I	-	2	0	SLC16A4	110723078	1.000000	0.71417	0.968000	0.41197	0.918000	0.54935	6.976000	0.76135	1.084000	0.41184	0.529000	0.55759	ATC	.	.		0.428	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696		C	110921555	A	C	110921555	3	2	187	1	0	0	0	0	1	0	0	0	14425	333	12	5	529	5	SLC16A4	1	110921555	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	32476961	110921555	138329066	3	27664										
WDR77	79084	hgsc.bcm.edu	37	chr1	111986674	111986674	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ggaagaaggagctatctcttAcctcgctgcatgaaagaaac	10	9	1	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr1:111986674A>C	ENST00000235090.5	-	5	771		c.e5+1		RP11-552M11.4_ENST00000416099.1_RNA|WDR77_ENST00000411751.2_Splice_Site|Y_RNA_ENST00000363020.1_RNA|WDR77_ENST00000497278.1_Splice_Site	NM_024102.2	NP_077007.1	Q9BQA1	MEP50_HUMAN	WD repeat domain 77						gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA metabolic process (GO:0016070)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|methylosome (GO:0034709)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_cancers(81;0.000902)|all_epithelial(167;0.00056)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		GCTATCTCTTACCTCGCTGCA	0.478																																					.		Atlas-SNP	.											.	WDR77	21	.	0			c.564+2T>G						.						139	137	138					1																	111986674		2203	4300	6503	SO:0001630	splice_region_variant	79084	exon6			TCTCTTACCTCGC	BC016946	CCDS835.1	1p13.2	2013-01-09		2005-08-09	ENSG00000116455	ENSG00000116455		"WD repeat domain containing"	29652	protein-coding gene	gene with protein product		611734				11756452, 8619474	Standard	NM_024102		Approved	MEP50	uc001ebb.3	Q9BQA1	OTTHUMG00000011748	ENST00000235090.5:c.564+1T>G	chr1.hg19:g.111986674A>C		279.0	0.0		297.0	153.0	NM_024102	B3KMW6|B4DP38|Q3LID2|Q53FU2|Q6JZZ5|Q96GK4|Q9BWY3	Splice_Site	SNP	ENST00000235090.5	hg19	CCDS835.1	.	.	.	.	.	.	.	.	.	.	A	10.90	1.480911	0.26598	.	.	ENSG00000116455	ENST00000235090;ENST00000411751;ENST00000449340	.	.	.	6.06	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8868	0.52606	0.9317:0.0:0.0683:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR77	111788197	1.000000	0.71417	0.963000	0.40424	0.091000	0.18340	7.043000	0.76572	1.110000	0.41699	-0.256000	0.11100	.	.	.		0.478	WDR77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032465.1	NM_024102	Intron	C	111986674	A	C	111986674	5	2	187	1	0	0	0	0	0	0	1	0	17342	405	14	5	486	5	WDR77	1	111986674	Splice_Site	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	1065119	111986674	137263947	4	27665										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120480003	120480003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ctcctcacagtagctcccagTatagcccagggggcactgac	10	15	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr1:120480003T>C	ENST00000256646.2	-	21	3643	c.3424A>G	c.(3424-3426)Act>Gct	p.T1142A		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1142	EGF-like 29. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TAGCTCCCAGTATAGCCCAGG	0.552			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.T1142A		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.A3424G						.						102	86	92					1																	120480003		2203	4300	6503	SO:0001583	missense	4853	exon21	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	TCCCAGTATAGCC	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.3424A>G	chr1.hg19:g.120480003T>C	ENSP00000256646:p.Thr1142Ala	115.0	0.0		132.0	61.0	NM_001200001	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	hg19	CCDS908.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.236234	0.58886	.	.	ENSG00000134250	ENST00000256646	D	0.88277	-2.36	5.06	3.88	0.44766	EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.202191	0.24350	U	0.039295	D	0.88385	0.6422	M	0.88105	2.93	0.46011	D	0.998818	B;B	0.32245	0.361;0.076	B;B	0.41332	0.354;0.076	D	0.87407	0.2373	10	0.54805	T	0.06	.	10.4841	0.44711	0.1456:0.0:0.0:0.8544	.	1142;1142	Q6IQ50;Q04721	.;NOTC2_HUMAN	A	1142	ENSP00000256646:T1142A	ENSP00000256646:T1142A	T	-	1	0	NOTCH2	120281526	1.000000	0.71417	0.994000	0.49952	0.597000	0.36814	4.651000	0.61447	0.812000	0.34326	0.482000	0.46254	ACT	.	.		0.552	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		C	120480003	T	C	120480003	3	2	187	1	0	0	0	0	1	0	0	0	10557	1638	57	2	4047	2	NOTCH2	1	120480003	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	8493329	120480003	128770618	5	27666										
SHE	126669	hgsc.bcm.edu	37	chr1	154474168	154474206	+	In_Frame_Del	DEL	ATCAGACCCTGCAGGCTGTCGCGGGACAGCCGGCTGTCC	ATCAGACCCTGCAGGCTGTCGCGGGACAGCCGGCTGTCC	-													0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ccttgcccgcggcggcctgaAtcagaccctgcaggctgtcg					rs200876451		TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	ATCAGACCCTGCAGGCTGTCGCGGGACAGCCGGCTGTCC	ATCAGACCCTGCAGGCTGTCGCGGGACAGCCGGCTGTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr1:154474168_154474206delATCAGACCCTGCAGGCTGTCGCGGGACAGCCGGCTGTCC	ENST00000304760.2	-	1	383_421	c.297_335delGGACAGCCGGCTGTCCCGCGACAGCCTGCAGGGTCTGAT	c.(295-336)aaggacagccggctgtcccgcgacagcctgcagggtctgatt>aat	p.99_112KDSRLSRDSLQGLI>N	TDRD10_ENST00000368480.3_5'Flank|TDRD10_ENST00000368482.4_5'Flank	NM_001010846.2	NP_001010846.1	Q5VZ18	SHE_HUMAN	Src homology 2 domain containing E	99										breast(4)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	14	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			GGCGGCCTGAATCAGACCCTGCAGGCTGTCGCGGGACAGCCGGCTGTCCTTGGGGCCGA	0.724																																					p.100_112del		Atlas-INDEL	.											.	SHE	41	.	0			c.298_336del						.																																			SO:0001651	inframe_deletion	126669	exon1			.	AK074067	CCDS30877.1	1q21.3	2013-02-14			ENSG00000169291	ENSG00000169291		"SH2 domain containing"	27004	protein-coding gene	gene with protein product		610482				9315092	Standard	NM_001010846		Approved		uc001ffb.3	Q5VZ18	OTTHUMG00000036072	ENST00000304760.2:c.297_335delGGACAGCCGGCTGTCCCGCGACAGCCTGCAGGGTCTGAT	chr1.hg19:g.154474168_154474206delATCAGACCCTGCAGGCTGTCGCGGGACAGCCGGCTGTCC	ENSP00000307369:p.Lys99_Ile112delinsAsn	39.0	0.0		48.0	12.0	NM_001010846	Q8TEQ5	In_Frame_Del	DEL	ENST00000304760.2	hg19	CCDS30877.1																																																																																			.	.		0.724	SHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087910.2	NM_001010846		-	154474206	ATCAGACCCTGCAGGCTGTCGCGGGACAGCCGGCTGTCC	-	154474168	7	5	187	1	0	1	0	1	0	0	0	0	14291	101	4	0	1176	0	SHE	1	154474168	In_Frame_Del	DEL	ATCAGACCCTGCAGGCTGTCGCGGGACAGCCGGCTGTCC	TCGA-DD-AADD-01A-11D-A40R-10	33994165	154474168	94776453	6	27667										
CLK2	1196	hgsc.bcm.edu	37	chr1	155233082	155233082	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gaaggcgggcgaagaaaggaTgctgaagggcttcacccaag	16	8	1	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr1:155233082T>A	ENST00000368361.4	-	13	1742	c.1427A>T	c.(1426-1428)cAt>cTt	p.H476L	SCAMP3_ENST00000472397.1_5'Flank|CLK2_ENST00000536801.1_Missense_Mutation_p.H476L|SCAMP3_ENST00000302631.3_5'Flank|CLK2_ENST00000355560.4_Missense_Mutation_p.H474L|CLK2_ENST00000497188.1_5'UTR|CLK2_ENST00000361168.5_Missense_Mutation_p.H475L|SCAMP3_ENST00000355379.3_5'Flank			P49760	CLK2_HUMAN	CDC-like kinase 2	476	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GAAGAAAGGATGCTGAAGGGC	0.582								Other conserved DNA damage response genes																													p.H475L		Atlas-SNP	.											.	CLK2	55	.	0			c.A1424T						.						73	67	69					1																	155233082		2203	4300	6503	SO:0001583	missense	1196	exon13			AAAGGATGCTGAA	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"CDC-like kinases"	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.1427A>T	chr1.hg19:g.155233082T>A	ENSP00000357345:p.His476Leu	58.0	0.0		101.0	63.0	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Missense_Mutation	SNP	ENST00000368361.4	hg19		.	.	.	.	.	.	.	.	.	.	.	26.4	4.734389	0.89482	.	.	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000424156;ENST00000536801	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.11	5.11	0.69529	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.045516	0.85682	D	0.000000	T	0.56062	0.1960	M	0.93328	3.405	0.80722	D	1	D;D	0.62365	0.991;0.98	D;P	0.64321	0.924;0.775	T	0.68842	-0.5302	10	0.72032	D	0.01	.	14.1493	0.65373	0.0:0.0:0.0:1.0	.	476;475	P49760;P49760-3	CLK2_HUMAN;.	L	475;476;474;248;476	ENSP00000354856:H475L;ENSP00000357345:H476L;ENSP00000347759:H474L;ENSP00000441023:H476L	ENSP00000347759:H474L	H	-	2	0	CLK2	153499706	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	7.825000	0.86693	2.271000	0.75665	0.459000	0.35465	CAT	.	.		0.582	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993		A	155233082	T	A	155233082	3	1	187	1	0	0	0	0	1	0	0	0	3539	1464	51	4	76	4	CLK2	1	155233082	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	758914	155233082	94017539	7	27668										
SMG7	9887	hgsc.bcm.edu	37	chr1	183515342	183515342	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	caaggtcccagaattctactGggattcttcctacagcatgg	9	11	2	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr1:183515342G>A	ENST00000347615.2	+	17	2731	c.2612G>A	c.(2611-2613)tGg>tAg	p.W871*	SMG7_ENST00000508461.1_Nonsense_Mutation_p.W829*|SMG7_ENST00000367537.3_Nonsense_Mutation_p.W854*|SMG7_ENST00000507469.1_Nonsense_Mutation_p.W825*|SMG7_ENST00000515829.2_Nonsense_Mutation_p.W825*|SMG7_ENST00000456731.2_Nonsense_Mutation_p.W783*	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	871					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.W871L(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						GAATTCTACTGGGATTCTTCC	0.478																																					p.W871X		Atlas-SNP	.											.	SMG7	165	.	1	Substitution - Missense(1)	lung(1)	c.G2612A						.						77	78	78					1																	183515342		2203	4300	6503	SO:0001587	stop_gained	9887	exon17			TCTACTGGGATTC	D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.2612G>A	chr1.hg19:g.183515342G>A	ENSP00000340766:p.Trp871*	203.0	0.0		259.0	124.0	NM_173156	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Nonsense_Mutation	SNP	ENST00000347615.2	hg19	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	G	39	7.489930	0.98316	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000347615;ENST00000507469;ENST00000515829	.	.	.	5.62	5.62	0.85841	.	0.360996	0.31071	N	0.008304	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.0255	19.6614	0.95875	0.0:0.0:1.0:0.0	.	.	.	.	X	783;854;829;871;825;825	.	ENSP00000340766:W871X	W	+	2	0	SMG7	181781965	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.741000	0.91583	2.633000	0.89246	0.655000	0.94253	TGG	.	.		0.478	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		A	183515342	G	A	183515342	4	1	187	1	0	0	0	0	0	1	0	0	14813	1357	47	3	2678	3	SMG7	1	183515342	Nonsense_Mutation	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	28282260	183515342	65735279	8	27669										
C1orf101	257044	hgsc.bcm.edu	37	chr1	244735632	244735632	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	aacttttctcttttttccagAttattatggagatattttgg	6	5	1	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr1:244735632A>G	ENST00000366534.4	+	11	1562	c.1508A>G	c.(1507-1509)gAt>gGt	p.D503G	C1orf101_ENST00000366533.4_Splice_Site_p.D503G|C1orf101_ENST00000366531.3_Splice_Site_p.D352G|C1orf101_ENST00000473875.1_3'UTR	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	503						CatSper complex (GO:0036128)				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			TTTTTTCCAGATTATTATGGA	0.269																																					p.D503G		Atlas-SNP	.											.	C1orf101	158	.	0			c.A1508G						.						25	23	23					1																	244735632		2179	4252	6431	SO:0001630	splice_region_variant	257044	exon11			TTCCAGATTATTA	BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.1508-1A>G	chr1.hg19:g.244735632A>G		341.0	0.0		375.0	169.0	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Missense_Mutation	SNP	ENST00000366534.4	hg19	CCDS44340.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.675714	0.67928	.	.	ENSG00000179397	ENST00000391841;ENST00000366534;ENST00000366533;ENST00000428042;ENST00000366531	T;T;T;T	0.25250	1.81;1.81;1.81;1.81	5.19	5.19	0.71726	.	0.000000	0.56097	D	0.000023	T	0.46112	0.1376	L	0.61218	1.895	0.34120	D	0.663963	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.996;0.999;0.999	T	0.59484	-0.7446	9	.	.	.	.	11.71	0.51620	1.0:0.0:0.0:0.0	.	423;503;503;352	B1AQM6;Q5SY80;Q5SY80-2;B4DZR4	.;CA101_HUMAN;.;.	G	503;503;503;423;352	ENSP00000355492:D503G;ENSP00000355491:D503G;ENSP00000395796:D423G;ENSP00000355489:D352G	.	D	+	2	0	C1orf101	242802255	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.993000	0.63895	2.090000	0.63153	0.528000	0.53228	GAT	.	.		0.269	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807	Missense_Mutation	G	244735632	A	G	244735632	5	3	187	1	0	0	0	0	0	0	1	0	1978	347	12	2	1550	2	C1orf101	1	244735632	Splice_Site	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	61220290	244735632	4514989	9	27670										
MAPRE3	22924	hgsc.bcm.edu	37	chr2	27245167	27245167	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cttgcatgggtcaacgactcCctgcacctcaactataccaa	6	15	2	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr2:27245167C>T	ENST00000233121.2	+	2	279	c.81C>T	c.(79-81)tcC>tcT	p.S27S	MAPRE3_ENST00000405074.3_Silent_p.S27S|MAPRE3_ENST00000491354.1_3'UTR|MAPRE3_ENST00000402218.1_Silent_p.S27S			Q9UPY8	MARE3_HUMAN	microtubule-associated protein, RP/EB family, member 3	27	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				mitotic nuclear division (GO:0007067)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule plus-end binding (GO:1903033)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAACGACTCCCTGCACCTCA	0.498																																					p.S27S		Atlas-SNP	.											.	MAPRE3	40	.	0			c.C81T						.						147	136	140					2																	27245167		2203	4300	6503	SO:0001819	synonymous_variant	22924	exon2			CGACTCCCTGCAC	Y11174	CCDS1731.1	2p23.3-p23.1	2008-06-04			ENSG00000084764	ENSG00000084764			6892	protein-coding gene	gene with protein product		605788				9233623	Standard	NM_012326		Approved	RP3, EB3	uc002rhw.3	Q9UPY8	OTTHUMG00000097067	ENST00000233121.2:c.81C>T	chr2.hg19:g.27245167C>T		78.0	0.0		70.0	12.0	NM_012326	B7WPK5|O00265|Q6FHB0|Q6FI15|Q9BZP7|Q9BZP8	Silent	SNP	ENST00000233121.2	hg19	CCDS1731.1																																																																																			.	.		0.498	MAPRE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214183.1	NM_012326		T	27245167	C	T	27245167	2	4	187	1	0	0	0	0	0	0	0	1	9305	610	22	3		3	MAPRE3	2	27245167	Silent	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10		27245167	215954206	10	27671										
CCDC104	112942	hgsc.bcm.edu	37	chr2	55750945	55750945	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cacttctcctcttgcaaagaCccatacatcacaggtttttg	5	13	3	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr2:55750945C>G	ENST00000349456.4	+	3	417	c.269C>G	c.(268-270)aCc>aGc	p.T90S	CCDC104_ENST00000339012.3_Missense_Mutation_p.T115S|CCDC104_ENST00000406691.3_Missense_Mutation_p.T90S|CCDC104_ENST00000407816.3_Missense_Mutation_p.T90S|CCDC104_ENST00000403007.3_Missense_Mutation_p.T90S			Q96G28	CFA36_HUMAN		90										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(2)|lung(1)|ovary(2)	14			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CTTGCAAAGACCCATACATCA	0.338																																					p.T90S		Atlas-SNP	.											.	CCDC104	35	.	0			c.C269G						.						102	95	97					2																	55750945		2203	4299	6502	SO:0001583	missense	112942	exon3			CAAAGACCCATAC																												ENST00000349456.4:c.269C>G	chr2.hg19:g.55750945C>G	ENSP00000295117:p.Thr90Ser	300.0	0.0		259.0	81.0	NM_080667	Q53SF0|Q53ST9|Q6UY34	Missense_Mutation	SNP	ENST00000349456.4	hg19	CCDS1854.2	.	.	.	.	.	.	.	.	.	.	C	8.722	0.914563	0.17907	.	.	ENSG00000163001	ENST00000339012;ENST00000406691;ENST00000349456;ENST00000407816;ENST00000403007	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.7	4.82	0.62117	ADP-ribosylation factor-like 2-binding protein, domain (2);	0.318671	0.38217	N	0.001771	T	0.17534	0.0421	N	0.02011	-0.69	0.33014	D	0.52799	B;B	0.18166	0.0;0.026	B;B	0.12156	0.005;0.007	T	0.14699	-1.0463	10	0.08837	T	0.75	.	14.4807	0.67579	0.0:0.9297:0.0:0.0703	.	90;115	Q96G28;Q96G28-2	CC104_HUMAN;.	S	115;90;90;90;90	ENSP00000342699:T115S;ENSP00000385400:T90S;ENSP00000295117:T90S;ENSP00000385376:T90S;ENSP00000385972:T90S	ENSP00000342699:T115S	T	+	2	0	CCDC104	55604449	0.997000	0.39634	0.872000	0.34217	0.932000	0.56968	4.345000	0.59360	1.425000	0.47237	0.655000	0.94253	ACC	.	.		0.338	CCDC104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319610.2			G	55750945	C	G	55750945	3	3	187	1	0	0	0	0	1	0	0	0	2741	507	18	4	279	4	CCDC104	2	55750945	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	28505778	55750945	187448428	11	27672										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166245957	166245957	+	Frame_Shift_Del	DEL	G	G	-													0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cccttcgaatacagatggaaGagcgattcatggcatcaaac							TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr2:166245957delG	ENST00000375437.2	+	27	5931	c.5641delG	c.(5641-5643)gagfs	p.E1881fs	SCN2A_ENST00000375427.2_Frame_Shift_Del_p.E1881fs|SCN2A_ENST00000283256.6_Frame_Shift_Del_p.E1881fs|SCN2A_ENST00000357398.3_Frame_Shift_Del_p.E1881fs	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1881					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ACAGATGGAAGAGCGATTCAT	0.463																																					p.E1880fs		Atlas-INDEL	.											.	SCN2A	589	.	0			c.5640delA						.						109	95	100					2																	166245957		2203	4300	6503	SO:0001589	frameshift_variant	6326	exon27			.	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.5641delG	chr2.hg19:g.166245957delG	ENSP00000364586:p.Glu1881fs	242.0	0.0		169.0	97.0	NM_001040142	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Frame_Shift_Del	DEL	ENST00000375437.2	hg19	CCDS33314.1																																																																																			.	.		0.463	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		-	166245957	G	-	166245957	7	5	187	1	0	1	0	1	0	0	0	0	13931	943	33	0	5839	0	SCN2A	2	166245957	Frame_Shift_Del	DEL	G	TCGA-DD-AADD-01A-11D-A40R-10	110495012	166245957	76953416	12	27673										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10384604	10384604	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cagcgaggcaaacgtgtccaTgatgaggttcacccagagca	12	11	1	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr3:10384604T>A	ENST00000352432.4	-	18	2818	c.2749A>T	c.(2749-2751)Atg>Ttg	p.M917L	ATP2B2_ENST00000397077.1_Missense_Mutation_p.M872L|ATP2B2_ENST00000383800.4_Missense_Mutation_p.M872L|ATP2B2_ENST00000360273.2_Missense_Mutation_p.M917L|ATP2B2_ENST00000343816.4_Missense_Mutation_p.M903L			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	917					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						AACGTGTCCATGATGAGGTTC	0.647																																					p.M917L	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A2749T						.						102	88	93					3																	10384604		2203	4300	6503	SO:0001583	missense	491	exon19			TGTCCATGATGAG	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.2749A>T	chr3.hg19:g.10384604T>A	ENSP00000324172:p.Met917Leu	64.0	0.0		84.0	39.0	NM_001001331	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	t	16.68	3.191706	0.58017	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000429937;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.95918	-3.85;-3.85;-3.85;-3.85;-3.85;-3.85	3.55	3.55	0.40652	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.038560	0.85682	D	0.000000	D	0.97142	0.9066	H	0.95645	3.7	0.80722	D	1	B;B;P	0.38711	0.0;0.152;0.643	B;B;P	0.45310	0.001;0.314;0.476	D	0.98130	1.0430	10	0.72032	D	0.01	-40.4095	12.8286	0.57735	0.0:0.0:0.0:1.0	.	852;884;917	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	L	917;872;872;917;903;852;106;773;917	ENSP00000324172:M917L;ENSP00000373311:M872L;ENSP00000380267:M872L;ENSP00000353414:M917L;ENSP00000344677:M903L;ENSP00000414854:M773L	ENSP00000342954:M917L	M	-	1	0	ATP2B2	10359604	1.000000	0.71417	1.000000	0.80357	0.775000	0.43874	7.738000	0.84966	1.571000	0.49722	0.248000	0.18094	ATG	.	.		0.647	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10384604	T	A	10384604	3	1	187	1	0	0	0	0	1	0	0	0	1140	1464	51	4	1002	4	ATP2B2	3	10384604	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10		10384604	187637826	13	27674										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266101	41266101	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gcaacagtcttacctggactCtggaatccattctggtgcca	9	12	3	0	rs121913416|rs121913400		TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr3:41266101C>A	ENST00000349496.5	+	3	378	c.98C>A	c.(97-99)tCt>tAt	p.S33Y	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26Y|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33Y|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33Y|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33Y	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33Y	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,359	CTNNB1	4904	.	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98A						.						92	77	82					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>A	chr3.hg19:g.41266101C>A	ENSP00000344456:p.Ser33Tyr	186.0	0.0		142.0	54.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.449496	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	Y	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26Y;ENSP00000385604:S33Y;ENSP00000412219:S33Y;ENSP00000379486:S33Y;ENSP00000344456:S33Y;ENSP00000411226:S26Y;ENSP00000379488:S33Y;ENSP00000409302:S33Y;ENSP00000401599:S33Y	ENSP00000344456:S33Y	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266101	C	A	41266101	3	1	187	1	0	0	0	0	1	0	0	0	4018	913	32	3	104	3	CTNNB1	3	41266101	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	30881497	41266101	156756329	14	27675										
SETD2	29072	hgsc.bcm.edu	37	chr3	47161866	47161866	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	actttctttctgtcctgaagCtcaccatcactttcagaatc	4	13	5	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr3:47161866C>T	ENST00000409792.3	-	3	4302	c.4260G>A	c.(4258-4260)gaG>gaA	p.E1420E		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1420					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGTCCTGAAGCTCACCATCAC	0.433			"N, F, S, Mis"		clear cell renal carcinoma																																p.E1420E		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.G4260A						.						183	176	178					3																	47161866		2203	4300	6503	SO:0001819	synonymous_variant	29072	exon3			CTGAAGCTCACCA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4260G>A	chr3.hg19:g.47161866C>T		146.0	0.0		116.0	24.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.		0.433	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		T	47161866	C	T	47161866	2	4	187	1	0	0	0	0	0	0	0	1	14146	796	28	3		3	SETD2	3	47161866	Silent	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	5895765	47161866	150860564	15	27676										
NIT2	56954	hgsc.bcm.edu	37	chr3	100059950	100059950	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	agaggatgctgggaaattatAtaacacctgtgctgtgtttg	12	5	0	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr3:100059950A>G	ENST00000394140.4	+	4	372	c.281A>G	c.(280-282)tAt>tGt	p.Y94C		NM_020202.4	NP_064587.1	Q9NQR4	NIT2_HUMAN	nitrilase family, member 2	94	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				asparagine metabolic process (GO:0006528)|glutamine metabolic process (GO:0006541)|oxaloacetate metabolic process (GO:0006107)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	omega-amidase activity (GO:0050152)			breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)	17						GGGAAATTATATAACACCTGT	0.383																																					p.Y94C		Atlas-SNP	.											.	NIT2	35	.	0			c.A281G						.						130	122	125					3																	100059950		2203	4300	6503	SO:0001583	missense	56954	exon4			AATTATATAACAC	AF284574	CCDS33806.1	3q12.3	2004-07-12			ENSG00000114021	ENSG00000114021			29878	protein-coding gene	gene with protein product						10959838	Standard	NM_020202		Approved		uc003dtv.3	Q9NQR4	OTTHUMG00000159066	ENST00000394140.4:c.281A>G	chr3.hg19:g.100059950A>G	ENSP00000377696:p.Tyr94Cys	92.0	0.0		100.0	40.0	NM_020202	B2R9A3|D3DN47|Q8WUF0	Missense_Mutation	SNP	ENST00000394140.4	hg19	CCDS33806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.9|22.9	4.352401|4.352401	0.82132|0.82132	.|.	.|.	ENSG00000114021|ENSG00000114021	ENST00000497785|ENST00000394140	.|D	.|0.89485	.|-2.52	5.68|5.68	5.68|5.68	0.88126|0.88126	.|Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	.|0.109437	.|0.64402	.|D	.|0.000004	D|D	0.95937|0.95937	0.8677|0.8677	M|M	0.93678|0.93678	3.445|3.445	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	D|D	0.96983|0.96983	0.9716|0.9716	5|10	.|0.87932	.|D	.|0	-10.0363|-10.0363	15.934|15.934	0.79688|0.79688	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|94;94	.|B7Z3F9;Q9NQR4	.|.;NIT2_HUMAN	M|C	187|94	.|ENSP00000377696:Y94C	.|ENSP00000377696:Y94C	I|Y	+|+	3|2	3|0	NIT2|NIT2	101542640|101542640	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	6.498000|6.498000	0.73679|0.73679	2.174000|2.174000	0.68829|0.68829	0.523000|0.523000	0.50628|0.50628	ATA|TAT	.	.		0.383	NIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353142.2	NM_020202		G	100059950	A	G	100059950	3	3	187	1	0	0	0	0	1	0	0	0	10443	449	16	2	295	2	NIT2	3	100059950	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	52898084	100059950	97962480	16	27677										
WDR5B	54554	hgsc.bcm.edu	37	chr3	122133978	122133978	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	taaggttggatggcggattgAagttacaacaaaagacataa	11	4	0	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr3:122133978A>C	ENST00000330689.4	-	1	904	c.398T>G	c.(397-399)tTc>tGc	p.F133C	RP11-299J3.8_ENST00000608465.1_RNA|RP11-299J3.8_ENST00000608756.1_RNA|RP11-299J3.8_ENST00000608015.1_RNA|RP11-299J3.8_ENST00000608346.1_RNA|RP11-299J3.8_ENST00000609469.1_RNA	NM_019069.3	NP_061942.2	Q86VZ2	WDR5B_HUMAN	WD repeat domain 5B	133										kidney(2)|large_intestine(4)|lung(2)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.0704)		TGGCGGATTGAAGTTACAACA	0.378																																					p.F133C		Atlas-SNP	.											.	WDR5B	36	.	0			c.T398G						.						100	96	97					3																	122133978		2203	4300	6503	SO:0001583	missense	54554	exon1			GGATTGAAGTTAC	AK002149	CCDS3012.1	3q21.1	2013-01-09			ENSG00000196981	ENSG00000196981		"WD repeat domain containing"	17826	protein-coding gene	gene with protein product						10369878	Standard	NM_019069		Approved	FLJ11287	uc003efa.1	Q86VZ2	OTTHUMG00000159489	ENST00000330689.4:c.398T>G	chr3.hg19:g.122133978A>C	ENSP00000330381:p.Phe133Cys	160.0	0.0		97.0	45.0	NM_019069	B2RCM9|Q9NUL4	Missense_Mutation	SNP	ENST00000330689.4	hg19	CCDS3012.1	.	.	.	.	.	.	.	.	.	.	A	18.08	3.544027	0.65198	.	.	ENSG00000196981	ENST00000330689	T	0.67865	-0.29	4.58	4.58	0.56647	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84051	0.5387	M	0.91459	3.21	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87123	0.2192	10	0.66056	D	0.02	.	12.2375	0.54524	1.0:0.0:0.0:0.0	.	133	Q86VZ2	WDR5B_HUMAN	C	133	ENSP00000330381:F133C	ENSP00000330381:F133C	F	-	2	0	WDR5B	123616668	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	8.137000	0.89612	2.054000	0.61138	0.379000	0.24179	TTC	.	.		0.378	WDR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355753.1	NM_019069		C	122133978	A	C	122133978	3	2	187	1	0	0	0	0	1	0	0	0	17324	246	9	5	598	5	WDR5B	3	122133978	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	22074028	122133978	75888452	17	27678			1	38		2	2	14	A		3.779398e-05
WDR5B	54554	hgsc.bcm.edu	37	chr3	122133991	122133991	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cggattgaagttacaacaaaAgacataattactgtgcccct	7	9	0	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr3:122133991A>C	ENST00000330689.4	-	1	891	c.385T>G	c.(385-387)Ttt>Gtt	p.F129V	RP11-299J3.8_ENST00000608465.1_RNA|RP11-299J3.8_ENST00000608756.1_RNA|RP11-299J3.8_ENST00000608015.1_RNA|RP11-299J3.8_ENST00000608346.1_RNA|RP11-299J3.8_ENST00000609469.1_RNA	NM_019069.3	NP_061942.2	Q86VZ2	WDR5B_HUMAN	WD repeat domain 5B	129										kidney(2)|large_intestine(4)|lung(2)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.0704)		TTACAACAAAAGACATAATTA	0.383																																					p.F129V		Atlas-SNP	.											.	WDR5B	36	.	0			c.T385G						.						103	100	101					3																	122133991		2203	4300	6503	SO:0001583	missense	54554	exon1			AACAAAAGACATA	AK002149	CCDS3012.1	3q21.1	2013-01-09			ENSG00000196981	ENSG00000196981		"WD repeat domain containing"	17826	protein-coding gene	gene with protein product						10369878	Standard	NM_019069		Approved	FLJ11287	uc003efa.1	Q86VZ2	OTTHUMG00000159489	ENST00000330689.4:c.385T>G	chr3.hg19:g.122133991A>C	ENSP00000330381:p.Phe129Val	160.0	0.0		94.0	42.0	NM_019069	B2RCM9|Q9NUL4	Missense_Mutation	SNP	ENST00000330689.4	hg19	CCDS3012.1	.	.	.	.	.	.	.	.	.	.	A	19.95	3.922284	0.73213	.	.	ENSG00000196981	ENST00000330689	T	0.59906	0.23	4.64	4.64	0.57946	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63838	0.2545	L	0.38838	1.175	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.61884	-0.6971	10	0.35671	T	0.21	.	12.3576	0.55184	1.0:0.0:0.0:0.0	.	129	Q86VZ2	WDR5B_HUMAN	V	129	ENSP00000330381:F129V	ENSP00000330381:F129V	F	-	1	0	WDR5B	123616681	1.000000	0.71417	0.995000	0.50966	0.918000	0.54935	8.137000	0.89612	2.082000	0.62665	0.379000	0.24179	TTT	.	.		0.383	WDR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355753.1	NM_019069		C	122133991	A	C	122133991	3	2	187	1	0	0	0	0	1	0	0	0	17324	72	3	5	611	5	WDR5B	3	122133991	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	13	122133991	75888439	18	27679			1	38		2	2	14	A		3.779398e-05
MYLK	4638	hgsc.bcm.edu	37	chr3	123452969	123452969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ggagcagttcttgcttttggCtgcagcctccagactgtcca	11	12	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr3:123452969C>T	ENST00000475616.1	-	7	873	c.874G>A	c.(874-876)Gcc>Acc	p.A292T	MYLK_ENST00000360772.3_Missense_Mutation_p.A292T|MYLK_ENST00000360304.3_Missense_Mutation_p.A292T|MYLK_ENST00000346322.5_Missense_Mutation_p.A292T|MYLK_ENST00000359169.1_Missense_Mutation_p.A292T			Q15746	MYLK_HUMAN	myosin light chain kinase	292					actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TTGCTTTTGGCTGCAGCCTCC	0.547																																					p.A292T		Atlas-SNP	.											MYLK,colon,carcinoma,0,1	MYLK	224	.	0			c.G874A						.						63	61	62					3																	123452969		2203	4300	6503	SO:0001583	missense	4638	exon10			TTTTGGCTGCAGC	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7590	protein-coding gene	gene with protein product	"smooth muscle myosin light chain kinase"	600922	"myosin, light polypeptide kinase"			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.874G>A	chr3.hg19:g.123452969C>T	ENSP00000418335:p.Ala292Thr	934.0	0.0		823.0	376.0	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	hg19	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	C	11.94	1.788850	0.31685	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.67171	-0.25;-0.2;-0.25;-0.18;-0.2	5.43	3.6	0.41247	.	.	.	.	.	T	0.46444	0.1393	N	0.17082	0.46	0.23076	N	0.998336	B;B;B;B;B	0.16603	0.007;0.002;0.018;0.002;0.001	B;B;B;B;B	0.14578	0.011;0.01;0.011;0.01;0.002	T	0.22487	-1.0215	9	0.12766	T	0.61	.	9.7159	0.40274	0.0:0.8333:0.0:0.1667	.	292;292;292;292;292	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	T	292	ENSP00000354004:A292T;ENSP00000353452:A292T;ENSP00000352088:A292T;ENSP00000320622:A292T;ENSP00000418335:A292T	ENSP00000320622:A292T	A	-	1	0	MYLK	124935659	0.000000	0.05858	0.115000	0.21578	0.204000	0.24138	0.075000	0.14686	1.515000	0.48885	0.655000	0.94253	GCC	.	.		0.547	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		T	123452969	C	T	123452969	3	4	187	1	0	0	0	0	1	0	0	0	10065	797	28	3	4970	3	MYLK	3	123452969	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	1318978	123452969	74569461	19	27680										
EMCN	51705	hgsc.bcm.edu	37	chr4	101401107	101401107	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tccagttgttggtgtgacaaCatttttctgtaatgattctg	9	6	2	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr4:101401107C>T	ENST00000296420.4	-	2	332	c.154G>A	c.(154-156)Gtt>Att	p.V52I	EMCN_ENST00000305864.3_Missense_Mutation_p.V52I|EMCN_ENST00000511970.1_Missense_Mutation_p.V52I|EMCN_ENST00000502327.1_5'UTR	NM_001159694.1|NM_016242.3	NP_001153166.1|NP_057326.2	Q9ULC0	MUCEN_HUMAN	endomucin	52	Thr-rich.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)		GGTGTGACAACATTTTTCTGT	0.299																																					p.V52I		Atlas-SNP	.											.	EMCN	37	.	0			c.G154A						.						175	163	167					4																	101401107		2201	4294	6495	SO:0001583	missense	51705	exon2			TGACAACATTTTT	AF205940	CCDS3655.1, CCDS54782.1	4q22.1	2008-02-05			ENSG00000164035	ENSG00000164035		"Mucins"	16041	protein-coding gene	gene with protein product		608350				11418125, 11594763	Standard	NM_016242		Approved	MUC14	uc003hvr.3	Q9ULC0	OTTHUMG00000131051	ENST00000296420.4:c.154G>A	chr4.hg19:g.101401107C>T	ENSP00000296420:p.Val52Ile	109.0	0.0		82.0	41.0	NM_001159694	A8K716|B4E347|Q8NEY5|Q8WWE7|Q9NRM8	Missense_Mutation	SNP	ENST00000296420.4	hg19	CCDS3655.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.761439	0.31228	.	.	ENSG00000164035	ENST00000296420;ENST00000305864;ENST00000511970;ENST00000502569	.	.	.	4.1	-3.82	0.04281	.	2.935940	0.01707	N	0.027481	T	0.15739	0.0379	N	0.19112	0.55	0.09310	N	1	P;P;P	0.39862	0.642;0.692;0.692	B;B;B	0.36244	0.14;0.22;0.22	T	0.05886	-1.0858	9	0.40728	T	0.16	1.8157	0.2282	0.00177	0.2474:0.2176:0.2677:0.2673	.	52;52;52	Q9ULC0-2;B4E347;Q9ULC0	.;.;MUCEN_HUMAN	I	52	.	ENSP00000296420:V52I	V	-	1	0	EMCN	101620130	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.041000	0.12084	-0.957000	0.03627	-0.182000	0.12963	GTT	.	.		0.299	EMCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253699.2	NM_016242		T	101401107	C	T	101401107	3	4	187	1	0	0	0	0	1	0	0	0	5088	478	17	3	671	3	EMCN	4	101401107	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10		101401107	89753169	20	27681										
FAT4	79633	hgsc.bcm.edu	37	chr4	126371527	126371527	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tgcaagagatagagatgcagCgatgaatggcttgattaagt	13	4	0	4			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr4:126371527C>T	ENST00000394329.3	+	9	9369	c.9356C>T	c.(9355-9357)gCg>gTg	p.A3119V	FAT4_ENST00000335110.5_Missense_Mutation_p.A1417V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3119	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AGAGATGCAGCGATGAATGGC	0.413																																					p.A3119V		Atlas-SNP	.											.	FAT4	1752	.	0			c.C9356T						.						73	69	70					4																	126371527		2203	4300	6503	SO:0001583	missense	79633	exon9			ATGCAGCGATGAA	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9356C>T	chr4.hg19:g.126371527C>T	ENSP00000377862:p.Ala3119Val	118.0	0.0		64.0	15.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	13.66	2.303988	0.40795	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.53423	0.62;0.62	5.63	5.63	0.86233	Cadherin (4);Cadherin-like (1);	0.000000	0.34133	U	0.004240	T	0.60715	0.2290	L	0.56199	1.76	0.47065	D	0.999304	P;D;D	0.69078	0.948;0.992;0.997	B;P;P	0.55345	0.301;0.689;0.774	T	0.63065	-0.6720	10	0.87932	D	0	.	19.7096	0.96089	0.0:1.0:0.0:0.0	.	1417;3119;3119	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	V	3119;1417	ENSP00000377862:A3119V;ENSP00000335169:A1417V	ENSP00000335169:A1417V	A	+	2	0	FAT4	126590977	0.997000	0.39634	0.173000	0.22940	0.068000	0.16541	4.202000	0.58446	2.652000	0.90054	0.655000	0.94253	GCG	.	.		0.413	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126371527	C	T	126371527	3	4	187	1	0	0	0	0	1	0	0	0	5700	768	27	1	9390	1	FAT4	4	126371527	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	24970420	126371527	64782749	21	27682										
RICTOR	253260	hgsc.bcm.edu	37	chr5	38967502	38967502	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ccacaaagccatctgaaagcCtccaactgtcttggaacctc	6	15	2	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr5:38967502C>T	ENST00000357387.3	-	13	1118	c.1088G>A	c.(1087-1089)aGg>aAg	p.R363K	RICTOR_ENST00000296782.5_Missense_Mutation_p.R363K	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					ATCTGAAAGCCTCCAACTGTC	0.358																																					p.R363K		Atlas-SNP	.											.	RICTOR	182	.	0			c.G1088A						.						65	68	67					5																	38967502		2203	4300	6503	SO:0001583	missense	253260	exon13			GAAAGCCTCCAAC		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.1088G>A	chr5.hg19:g.38967502C>T	ENSP00000349959:p.Arg363Lys	154.0	0.0		100.0	90.0	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.468114	0.84533	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.44881	0.92;0.91	5.43	5.43	0.79202	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55433	0.1920	L	0.31664	0.95	0.80722	D	1	B;D	0.56035	0.066;0.974	B;D	0.70487	0.135;0.969	T	0.58070	-0.7701	10	0.87932	D	0	-12.4873	19.6092	0.95599	0.0:1.0:0.0:0.0	.	363;363	Q6R327;Q6R327-3	RICTR_HUMAN;.	K	363	ENSP00000349959:R363K;ENSP00000296782:R363K	ENSP00000296782:R363K	R	-	2	0	RICTOR	39003259	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.225000	0.78051	2.693000	0.91896	0.655000	0.94253	AGG	.	.		0.358	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		T	38967502	C	T	38967502	3	4	187	1	0	0	0	0	1	0	0	0	13373	681	24	3	4142	3	RICTOR	5	38967502	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10		38967502	141947758	22	27683										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140235813	140235813	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gagctggcggagctggtgcaGcgcctgttccgggtggcgtc	19	11	0	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr5:140235813G>A	ENST00000307360.5	+	1	180	c.180G>A	c.(178-180)caG>caA	p.Q60Q	PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Silent_p.Q60Q|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	60	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTGGTGCAGCGCCTGTTCC	0.617																																					p.Q60Q		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G180A						.						56	64	61					5																	140235813		2197	4267	6464	SO:0001819	synonymous_variant	56139	exon1			GGTGCAGCGCCTG	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.180G>A	chr5.hg19:g.140235813G>A		182.0	0.0		123.0	104.0	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	hg19	CCDS54921.1																																																																																			.	.		0.617	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		A	140235813	G	A	140235813	2	1	187	1	0	0	0	0	0	0	0	1	11529	962	34	3		3	PCDHA10	5	140235813	Silent	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	101268311	140235813	40679447	23	27684										
RNF145	153830	hgsc.bcm.edu	37	chr5	158603773	158603774	+	Frame_Shift_Ins	INS	-	-	CAAGG													0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	aacaattgtctccaaaggaaINScaaggcagagtcgtgctagc							TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr5:158603773_158603774insCAAGG	ENST00000424310.2	-	5	846_847	c.487_488insCCTTG	c.(487-489)gttfs	p.V163fs	RNF145_ENST00000521606.2_Frame_Shift_Ins_p.V180fs|RNF145_ENST00000519865.1_Frame_Shift_Ins_p.V163fs|RNF145_ENST00000274542.2_Frame_Shift_Ins_p.V191fs|RNF145_ENST00000520638.1_Frame_Shift_Ins_p.V177fs|RNF145_ENST00000518802.1_Frame_Shift_Ins_p.V193fs	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	163						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTCCAAAGGAACAAGGCAGAGT	0.386																																					p.V193fs		Atlas-INDEL	.											.	RNF145	110	.	0			c.578_579insCCTTG						.																																			SO:0001589	frameshift_variant	153830	exon5			.	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"RING-type (C3HC4) zinc fingers"	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.483_487dupCCTTG	chr5.hg19:g.158603774_158603778dupCAAGG	ENSP00000409064:p.Val163fs	485.0	0.0		294.0	160.0	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Frame_Shift_Ins	INS	ENST00000424310.2	hg19	CCDS56390.1																																																																																			.	.		0.386	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		CAAGG	158603774	-	CAAGG	158603773	7	5	187	1	0	1	1	0	0	0	0	0	13462	43	2	0	1531	0	RNF145	5	158603773	Frame_Shift_Ins	INS	-	TCGA-DD-AADD-01A-11D-A40R-10	18367960	158603773	22311487	24	27685										
CFB	629	hgsc.bcm.edu	37	chr6	31918947	31918947	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	agctgctccctgcacaggatAtcaaagctctgtttgtgtct	9	11	3	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr6:31918947A>G	ENST00000425368.2	+	15	2395	c.1882A>G	c.(1882-1884)Atc>Gtc	p.I628V	CFB_ENST00000456570.1_Missense_Mutation_p.I1130V|CFB_ENST00000477310.1_Missense_Mutation_p.I979V|CFB_ENST00000556679.1_Missense_Mutation_p.I1130V	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	628	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						TGCACAGGATATCAAAGCTCT	0.512																																					p.I628V		Atlas-SNP	.											.	CFB	33	.	0			c.A1882G						.						101	103	102					6																	31918947		1511	2708	4219	SO:0001583	missense	629	exon15			CAGGATATCAAAG	L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"Complement system"	1037	protein-coding gene	gene with protein product		138470	"B-factor, properdin"	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.1882A>G	chr6.hg19:g.31918947A>G	ENSP00000416561:p.Ile628Val	76.0	0.0		53.0	31.0	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	hg19	CCDS4729.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.440|0.440	-0.899173|-0.899173	0.02472|0.02472	.|.	.|.	ENSG00000243649|ENSG00000243649;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000483004|ENST00000556679;ENST00000425368;ENST00000456570;ENST00000477310	.|D;D;D;D	.|0.88586	.|-2.4;-2.4;-2.4;-2.4	5.41|5.41	-0.9|-0.9	0.10544|0.10544	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.734237|0.734237	0.11509|0.11509	N|N	0.556869|0.556869	T|T	0.46444|0.46444	0.1393|0.1393	N|N	0.02181|0.02181	-0.65|-0.65	0.18873|0.18873	N|N	0.999988|0.999988	.|B;B	.|0.06786	.|0.001;0.0	.|B;B	.|0.14023	.|0.01;0.002	T|T	0.52215|0.52215	-0.8605|-0.8605	6|10	.|0.02654	.|T	.|1	-8.7653|-8.7653	14.2047|14.2047	0.65728|0.65728	0.1148:0.0:0.8852:0.0|0.1148:0.0:0.8852:0.0	.|.	.|1130;628	.|B4E1Z4;P00751	.|.;CFAB_HUMAN	M|V	168|1130;628;1130;979	.|ENSP00000451848:I1130V;ENSP00000416561:I628V;ENSP00000410815:I1130V;ENSP00000418996:I979V	.|ENSP00000416561:I628V	I|I	+|+	3|1	3|0	CFB|CFB;XXbac-BPG116M5.17	32026926|32026926	0.037000|0.037000	0.19845|0.19845	0.039000|0.039000	0.18376|0.18376	0.853000|0.853000	0.48598|0.48598	-0.002000|-0.002000	0.12924|0.12924	-0.577000|-0.577000	0.05967|0.05967	-0.326000|-0.326000	0.08463|0.08463	ATA|ATC	.	.		0.512	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		G	31918947	A	G	31918947	3	3	187	1	0	0	0	0	1	0	0	0	3280	449	16	2	1940	2	CFB	6	31918947	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10		31918947	139196120	25	27686										
MDGA1	266727	hgsc.bcm.edu	37	chr6	37614143	37614143	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gccttgaccaccgcattgtgCtggttcaactgttaagtaca	9	11	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr6:37614143C>T	ENST00000434837.3	-	11	3233	c.2055G>A	c.(2053-2055)caG>caA	p.Q685Q	MDGA1_ENST00000510077.1_5'UTR|MDGA1_ENST00000297153.7_Silent_p.Q688Q|MDGA1_ENST00000505425.1_Silent_p.Q685Q	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	685	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						CCGCATTGTGCTGGTTCAACT	0.577																																					p.Q685Q		Atlas-SNP	.											.	MDGA1	104	.	0			c.G2055A						.						40	44	43					6																	37614143		2093	4196	6289	SO:0001819	synonymous_variant	266727	exon11			ATTGTGCTGGTTC	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.2055G>A	chr6.hg19:g.37614143C>T		57.0	0.0		43.0	29.0	NM_153487	A6NHG0|Q8NBE3	Silent	SNP	ENST00000434837.3	hg19	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	C	7.065	0.567126	0.13560	.	.	ENSG00000112139	ENST00000418178	.	.	.	4.85	2.94	0.34122	.	.	.	.	.	T	0.46833	0.1413	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44513	-0.9323	4	.	.	.	.	9.6802	0.40065	0.1393:0.7828:0.0:0.0779	.	.	.	.	N	3	.	.	S	-	2	0	MDGA1	37722121	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	0.678000	0.25277	1.401000	0.46761	0.563000	0.77884	AGC	.	.		0.577	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			T	37614143	C	T	37614143	2	4	187	1	0	0	0	0	0	0	0	1	9415	796	28	3		3	MDGA1	6	37614143	Silent	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	5695196	37614143	133500924	26	27687										
KIAA0240	23506	hgsc.bcm.edu	37	chr6	42797158	42797158	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gtccacacatgtctgtgaacAttgtaaaccaacagaacaca	6	11	1	2	rs367929984		TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr6:42797158A>T	ENST00000314073.5	+	6	1263	c.1087A>T	c.(1087-1089)Att>Ttt	p.I363F	GLTSCR1L_ENST00000394168.1_Missense_Mutation_p.I363F			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	363																	GTCTGTGAACATTGTAAACCA	0.507																																					p.I363F		Atlas-SNP	.											.	.	.	.	0			c.A1087T						.						153	146	148					6																	42797158		2203	4300	6503	SO:0001583	missense	23506	exon5			GTGAACATTGTAA	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"KIAA0240"	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.1087A>T	chr6.hg19:g.42797158A>T	ENSP00000313933:p.Ile363Phe	95.0	0.0		70.0	12.0	NM_015349	A1L3W2|Q5TFZ3|Q92514	Missense_Mutation	SNP	ENST00000314073.5	hg19	CCDS34451.1	.	.	.	.	.	.	.	.	.	.	A	16.57	3.160186	0.57368	.	.	ENSG00000112624	ENST00000394167;ENST00000536004;ENST00000314073;ENST00000394168	T;T	0.38077	1.16;1.16	5.51	5.51	0.81932	.	0.079666	0.53938	D	0.000054	T	0.41719	0.1171	L	0.44542	1.39	0.47584	D	0.999466	D;D;D	0.69078	0.997;0.958;0.995	D;P;P	0.75484	0.986;0.563;0.77	T	0.24333	-1.0163	10	0.40728	T	0.16	-19.1624	14.502	0.67729	1.0:0.0:0.0:0.0	.	363;363;363	F5H616;Q6AI39;B7Z2G7	.;K0240_HUMAN;.	F	363	ENSP00000313933:I363F;ENSP00000377723:I363F	ENSP00000313933:I363F	I	+	1	0	KIAA0240	42905136	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.718000	0.61930	2.217000	0.71921	0.482000	0.46254	ATT	.	.		0.507	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		T	42797158	A	T	42797158	3	4	187	1	0	0	0	0	1	0	0	0	8173	217	8	4	1101	4	KIAA0240	6	42797158	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	5183015	42797158	128317909	27	27688										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51609283	51609283	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ccatccagatccttgaagagAtattttcttggacttgcaca	7	10	1	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr6:51609283A>G	ENST00000371117.3	-	60	10331	c.10056T>C	c.(10054-10056)taT>taC	p.Y3352Y	PKHD1_ENST00000340994.4_Silent_p.Y3352Y	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3352					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CCTTGAAGAGATATTTTCTTG	0.428																																					p.Y3352Y		Atlas-SNP	.											.	PKHD1	927	.	0			c.T10056C						.						95	92	93					6																	51609283		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon60			GAAGAGATATTTT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10056T>C	chr6.hg19:g.51609283A>G		81.0	0.0		68.0	12.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.		0.428	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51609283	A	G	51609283	2	3	187	1	0	0	0	0	0	0	0	1	11980	340	12	2		2	PKHD1	6	51609283	Silent	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	8812125	51609283	119505784	28	27689										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102503227	102503227	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tctccatatcgagacaaaatTaccatagcaattcttcagct	4	11	3	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr6:102503227T>G	ENST00000421544.1	+	15	2824	c.2334T>G	c.(2332-2334)atT>atG	p.I778M	GRIK2_ENST00000318991.6_Missense_Mutation_p.I778M|GRIK2_ENST00000413795.1_Missense_Mutation_p.I778M|GRIK2_ENST00000369138.1_Missense_Mutation_p.I778M|GRIK2_ENST00000369137.3_Missense_Mutation_p.I702M|GRIK2_ENST00000369134.4_Missense_Mutation_p.I729M	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	778					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GAGACAAAATTACCATAGCAA	0.418																																					p.I778M		Atlas-SNP	.											.	GRIK2	487	.	0			c.T2334G						.						71	71	71					6																	102503227		2203	4300	6503	SO:0001583	missense	2898	exon15			CAAAATTACCATA		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2334T>G	chr6.hg19:g.102503227T>G	ENSP00000397026:p.Ile778Met	135.0	0.0		86.0	9.0	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	hg19	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.074598	0.55646	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000369134;ENST00000540076	T;T;T;T;T;T	0.14516	2.5;2.5;2.5;2.5;2.5;2.5	5.68	2.93	0.34026	Ionotropic glutamate receptor (2);	0.049050	0.85682	N	0.000000	T	0.18923	0.0454	M	0.69523	2.12	0.41946	D	0.990634	D;D;D	0.56287	0.969;0.975;0.969	D;D;D	0.69824	0.943;0.966;0.943	T	0.01596	-1.1316	10	0.87932	D	0	.	5.7468	0.18124	0.1374:0.6395:0.0:0.2231	.	778;778;778	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	M	778;778;778;702;778;729;553	ENSP00000397026:I778M;ENSP00000405596:I778M;ENSP00000358134:I778M;ENSP00000358133:I702M;ENSP00000313276:I778M;ENSP00000358130:I729M	ENSP00000313276:I778M	I	+	3	3	GRIK2	102609920	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	1.274000	0.33132	0.750000	0.32877	-0.473000	0.04963	ATT	.	.		0.418	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			G	102503227	T	G	102503227	3	3	187	1	0	0	0	0	1	0	0	0	6783	1742	61	5	2392	5	GRIK2	6	102503227	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	50893944	102503227	68611840	29	27690										
SYNJ2	8871	hgsc.bcm.edu	37	chr6	158510898	158510898	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ctcggactggaataagtaaaCcttataatgtcaagcagatc	8	8	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr6:158510898C>T	ENST00000355585.4	+	25	3559	c.3484C>T	c.(3484-3486)Cct>Tct	p.P1162S	SYNJ2_ENST00000367112.1_Missense_Mutation_p.P247S|SYNJ2_ENST00000367122.2_Missense_Mutation_p.P1117S|SYNJ2_ENST00000367121.3_Missense_Mutation_p.P1162S	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	1162					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		AATAAGTAAACCTTATAATGT	0.537																																					p.P1162S		Atlas-SNP	.											.	SYNJ2	111	.	0			c.C3484T						.						71	60	64					6																	158510898		2203	4300	6503	SO:0001583	missense	8871	exon25			AGTAAACCTTATA	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.3484C>T	chr6.hg19:g.158510898C>T	ENSP00000347792:p.Pro1162Ser	102.0	0.0		79.0	18.0	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	hg19	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.289875	0.80914	.	.	ENSG00000078269	ENST00000367122;ENST00000367121;ENST00000355585;ENST00000367112	D;D;D;T	0.96745	-4.11;-3.42;-3.36;-0.14	5.38	5.38	0.77491	.	0.000000	0.64402	D	0.000018	D	0.96700	0.8923	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.97540	1.0085	10	0.66056	D	0.02	.	19.1543	0.93504	0.0:1.0:0.0:0.0	.	557;1162;1162	B4DLC4;O15056;O15056-3	.;SYNJ2_HUMAN;.	S	1117;1162;1162;247	ENSP00000356089:P1117S;ENSP00000356088:P1162S;ENSP00000347792:P1162S;ENSP00000356079:P247S	ENSP00000347792:P1162S	P	+	1	0	SYNJ2	158430886	0.998000	0.40836	0.862000	0.33874	0.915000	0.54546	5.022000	0.64078	2.521000	0.84997	0.555000	0.69702	CCT	.	.		0.537	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			T	158510898	C	T	158510898	3	4	187	1	0	0	0	0	1	0	0	0	15468	507	18	3	3582	3	SYNJ2	6	158510898	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	56007671	158510898	12604169	30	27691										
MACC1	346389	hgsc.bcm.edu	37	chr7	20199561	20199561	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tctaaaatgtccagaagttcTgaaacacttttagatcttcc	5	9	3	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr7:20199561T>G	ENST00000400331.5	-	5	731	c.423A>C	c.(421-423)tcA>tcC	p.S141S	MACC1_ENST00000589011.1_Silent_p.S141S|MACC1_ENST00000332878.4_Silent_p.S141S	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	141					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						CCAGAAGTTCTGAAACACTTT	0.393																																					p.S141S		Atlas-SNP	.											.	MACC1	99	.	0			c.A423C						.						72	67	69					7																	20199561		2203	4300	6503	SO:0001819	synonymous_variant	346389	exon5			AAGTTCTGAAACA		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.423A>C	chr7.hg19:g.20199561T>G		88.0	0.0		81.0	33.0	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Silent	SNP	ENST00000400331.5	hg19	CCDS5369.1																																																																																			.	.		0.393	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		G	20199561	T	G	20199561	2	3	187	1	0	0	0	0	0	0	0	1	9152	1567	55	5		5	MACC1	7	20199561	Silent	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10		20199561	138939102	31	27692										
HOXA7	3204	hgsc.bcm.edu	37	chr7	27194719	27194719	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	aatctggcgctcggtgaggcAgagcgcgtgggcgatttcaa	16	9	2	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr7:27194719A>C	ENST00000242159.3	-	2	635	c.502T>G	c.(502-504)Tgc>Ggc	p.C168G	RP1-170O19.22_ENST00000467897.2_RNA|HOXA7_ENST00000523796.2_5'UTR|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000521197.1_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA-AS3_ENST00000521231.1_RNA|HOXA-AS3_ENST00000524304.1_RNA|RP1-170O19.23_ENST00000498652.1_RNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	168					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						TCGGTGAGGCAGAGCGCGTGG	0.612																																					p.C168G		Atlas-SNP	.											.	HOXA7	34	.	0			c.T502G						.						92	101	98					7																	27194719		2203	4300	6503	SO:0001583	missense	3204	exon2			TGAGGCAGAGCGC		CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"Homeoboxes / ANTP class : HOXL subclass"	5108	protein-coding gene	gene with protein product		142950	"homeo box A7"	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.502T>G	chr7.hg19:g.27194719A>C	ENSP00000242159:p.Cys168Gly	152.0	0.0		129.0	58.0	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	hg19	CCDS5408.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.240164	0.58995	.	.	ENSG00000122592	ENST00000242159	D	0.94232	-3.38	4.96	4.96	0.65561	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.77103	0.4081	N	0.00176	-1.92	0.80722	D	1	B	0.14012	0.009	B	0.22601	0.04	T	0.75181	-0.3408	10	0.41790	T	0.15	.	14.6809	0.69017	1.0:0.0:0.0:0.0	.	168	P31268	HXA7_HUMAN	G	168	ENSP00000242159:C168G	ENSP00000242159:C168G	C	-	1	0	HOXA7	27161244	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.782000	0.62396	1.883000	0.54544	0.374000	0.22700	TGC	.	.		0.612	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1			C	27194719	A	C	27194719	3	2	187	1	0	0	0	0	1	0	0	0	7306	188	7	5	194	5	HOXA7	7	27194719	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	6995158	27194719	131943944	32	27693										
TBX20	57057	hgsc.bcm.edu	37	chr7	35293157	35293157	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ttctccttagagccgccgctCgacatgagcgcggcaatgga	12	13	1	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr7:35293157C>G	ENST00000408931.3	-	1	601	c.75G>C	c.(73-75)tcG>tcC	p.S25S		NM_001077653.2|NM_001166220.1	NP_001071121.1|NP_001159692.1	Q9UMR3	TBX20_HUMAN	T-box 20	25					aortic valve morphogenesis (GO:0003180)|atrial septum morphogenesis (GO:0060413)|blood circulation (GO:0008015)|cardiac chamber formation (GO:0003207)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|dorsal/ventral pattern formation (GO:0009953)|embryonic heart tube elongation (GO:0036306)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion formation (GO:0003272)|endocardial cushion morphogenesis (GO:0003203)|endoderm formation (GO:0001706)|foramen ovale closure (GO:0035922)|heart looping (GO:0001947)|lateral mesoderm formation (GO:0048370)|muscle contraction (GO:0006936)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|outflow tract septum morphogenesis (GO:0003148)|patterning of blood vessels (GO:0001569)|pericardium morphogenesis (GO:0003344)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve formation (GO:0003193)|pulmonary vein morphogenesis (GO:0060577)|tricuspid valve development (GO:0003175)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(9)|prostate(1)|skin(1)|stomach(1)	18						AGCCGCCGCTCGACATGAGCG	0.652																																					p.S25S		Atlas-SNP	.											.	TBX20	96	.	0			c.G75C						.						44	43	43					7																	35293157		2203	4300	6503	SO:0001819	synonymous_variant	57057	exon1			GCCGCTCGACATG	AJ237589	CCDS43568.1	7p14.3	2014-09-17			ENSG00000164532	ENSG00000164532		"T-boxes"	11598	protein-coding gene	gene with protein product		606061				10936053	Standard	NM_001077653		Approved		uc011kas.2	Q9UMR3	OTTHUMG00000099411	ENST00000408931.3:c.75G>C	chr7.hg19:g.35293157C>G		44.0	0.0		52.0	27.0	NM_001077653	A4D1Y6|Q000T4|Q0IJ70|Q0VAS1|Q9Y2N5	Silent	SNP	ENST00000408931.3	hg19	CCDS43568.1																																																																																			.	.		0.652	TBX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216870.2	NM_020417		G	35293157	C	G	35293157	2	3	187	1	0	0	0	0	0	0	0	1	15671	871	31	4		4	TBX20	7	35293157	Silent	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	8098438	35293157	123845506	33	27694										
RALA	5898	hgsc.bcm.edu	37	chr7	39730078	39730078	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cgatatcttagatacagctgGgcaggaggactacgctgcaa	12	9	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr7:39730078G>A	ENST00000005257.2	+	3	592	c.212G>A	c.(211-213)gGg>gAg	p.G71E	RALA_ENST00000468201.1_Intron	NM_005402.3	NP_005393.2	P11233	RALA_HUMAN	v-ral simian leukemia viral oncogene homolog A (ras related)	71					actin cytoskeleton reorganization (GO:0031532)|chemotaxis (GO:0006935)|cytokinesis (GO:0000910)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|membrane raft localization (GO:0051665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of filopodium assembly (GO:0051491)|Ras protein signal transduction (GO:0007265)|regulation of exocytosis (GO:0017157)|signal transduction (GO:0007165)|viral process (GO:0016032)	cell surface (GO:0009986)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(9)|skin(3)	16						GATACAGCTGGGCAGGAGGAC	0.473																																					p.G71E		Atlas-SNP	.											.	RALA	39	.	0			c.G212A						.						98	100	100					7																	39730078		2203	4300	6503	SO:0001583	missense	5898	exon3			CAGCTGGGCAGGA		CCDS5460.1	7p22-p15	2014-05-09			ENSG00000006451	ENSG00000006451			9839	protein-coding gene	gene with protein product	"RAS-like protein A", "Ras-related protein Ral-A", "Ras family small GTP binding protein RALA", "ras related GTP binding protein A"	179550		RAL		3292391	Standard	NM_005402		Approved		uc003thd.3	P11233	OTTHUMG00000128775	ENST00000005257.2:c.212G>A	chr7.hg19:g.39730078G>A	ENSP00000005257:p.Gly71Glu	115.0	0.0		110.0	46.0	NM_005402	A4D1W3	Missense_Mutation	SNP	ENST00000005257.2	hg19	CCDS5460.1	.	.	.	.	.	.	.	.	.	.	G	31	5.101048	0.94245	.	.	ENSG00000006451	ENST00000005257;ENST00000436179	D;D	0.93659	-3.26;-3.26	4.91	4.91	0.64330	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.98292	0.9434	H	0.98918	4.37	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99764	1.1022	10	0.87932	D	0	.	18.287	0.90118	0.0:0.0:1.0:0.0	.	71	P11233	RALA_HUMAN	E	71	ENSP00000005257:G71E;ENSP00000388975:G71E	ENSP00000005257:G71E	G	+	2	0	RALA	39696603	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	9.601000	0.98297	2.551000	0.86045	0.467000	0.42956	GGG	.	.		0.473	RALA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250696.2	NM_005402		A	39730078	G	A	39730078	3	1	187	1	0	0	0	0	1	0	0	0	13025	1232	43	3	218	3	RALA	7	39730078	Missense_Mutation	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	4436921	39730078	119408585	34	27695										
CNPY4	245812	hgsc.bcm.edu	37	chr7	99720107	99720107	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ttcctctctttccacagagaGacaaggctggaagaggcctt	10	11	1	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr7:99720107G>A	ENST00000262932.3	+	3	381	c.249G>A	c.(247-249)gaG>gaA	p.E83E	TAF6_ENST00000437822.2_5'Flank|CNPY4_ENST00000480692.1_3'UTR|RP11-506M12.1_ENST00000494221.1_RNA	NM_152755.1	NP_689968.1	Q8N129	CNPY4_HUMAN	canopy FGF signaling regulator 4	83						extracellular region (GO:0005576)				breast(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TCCACAGAGAGACAAGGCTGG	0.532																																					p.E83E		Atlas-SNP	.											.	CNPY4	18	.	0			c.G249A						.						119	128	125					7																	99720107		2203	4300	6503	SO:0001819	synonymous_variant	245812	exon3			CAGAGAGACAAGG	AK075537	CCDS34701.1	7q22.1	2013-07-23	2013-07-23		ENSG00000166997	ENSG00000166997			28631	protein-coding gene	gene with protein product	"protein associated with TLR4"	610047	"canopy 4 homolog (zebrafish)"			12975309	Standard	NM_152755		Approved	MGC40499, PRAT4B	uc003uto.3	Q8N129	OTTHUMG00000154817	ENST00000262932.3:c.249G>A	chr7.hg19:g.99720107G>A		110.0	0.0		103.0	60.0	NM_152755	Q8WUN9	Silent	SNP	ENST00000262932.3	hg19	CCDS34701.1																																																																																			.	.		0.532	CNPY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337224.4	NM_152755		A	99720107	G	A	99720107	2	1	187	1	0	0	0	0	0	0	0	1	3632	933	33	3		3	CNPY4	7	99720107	Silent	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	59990029	99720107	59418556	35	27696										
FAM82B	51115	hgsc.bcm.edu	37	chr8	87519286	87519286	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ggtaagtttcaaaacccaaaTacgacaaagctgagagtaaa	8	7	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr8:87519286T>C	ENST00000406452.3	-	2	344	c.185A>G	c.(184-186)tAt>tGt	p.Y62C	RMDN1_ENST00000523911.1_Missense_Mutation_p.Y18C|RMDN1_ENST00000519966.1_Missense_Mutation_p.Y62C|CPNE3_ENST00000198765.4_Intron|RMDN1_ENST00000430676.2_Missense_Mutation_p.Y62C|RMDN1_ENST00000518772.1_5'UTR	NM_016033.2	NP_057117.2	Q96DB5	RMD1_HUMAN	regulator of microtubule dynamics 1	62						microtubule (GO:0005874)|mitochondrion (GO:0005739)											AAAACCCAAATACGACAAAGC	0.363																																					p.Y62C		Atlas-SNP	.											.	.	.	.	0			c.A185G						.						126	137	133					8																	87519286		2203	4300	6503	SO:0001583	missense	51115	exon2			CCCAAATACGACA	AK000672	CCDS34918.1, CCDS69509.1, CCDS69510.1	8q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000176623	ENSG00000176623			24285	protein-coding gene	gene with protein product		611871	"family with sequence similarity 82, member B"	FAM82B		10810093	Standard	NM_016033		Approved	CGI-90, FLJ20665, RMD1	uc003ydu.3	Q96DB5	OTTHUMG00000163692	ENST00000406452.3:c.185A>G	chr8.hg19:g.87519286T>C	ENSP00000385927:p.Tyr62Cys	224.0	0.0		303.0	172.0	NM_016033	A9UMZ8|B4DNF5|B4DZW6|B5MC61|C9JSC6|E7EVI2|Q9Y398	Missense_Mutation	SNP	ENST00000406452.3	hg19	CCDS34918.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.131869	0.56828	.	.	ENSG00000176623	ENST00000406452;ENST00000523911;ENST00000519966;ENST00000430676;ENST00000521045	T;T;T;T;T	0.51817	1.43;1.48;0.84;0.82;0.69	4.4	4.4	0.53042	.	0.483859	0.22233	N	0.062781	T	0.41373	0.1156	L	0.55481	1.735	0.80722	D	1	B;B;B	0.21821	0.061;0.061;0.012	B;B;B	0.18561	0.022;0.022;0.009	T	0.32693	-0.9897	10	0.38643	T	0.18	-8.922	9.9687	0.41741	0.0:0.0:0.0:1.0	.	62;62;62	B4DZW6;E7EVI2;Q96DB5	.;.;RMD1_HUMAN	C	62;18;62;62;18	ENSP00000385927:Y62C;ENSP00000429899:Y18C;ENSP00000428661:Y62C;ENSP00000409661:Y62C;ENSP00000428743:Y18C	ENSP00000385927:Y62C	Y	-	2	0	FAM82B	87588402	0.935000	0.31712	0.996000	0.52242	0.846000	0.48090	0.981000	0.29526	1.850000	0.53721	0.533000	0.62120	TAT	.	.		0.363	RMDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374770.2	NM_016033		C	87519286	T	C	87519286	3	2	187	1	0	0	0	0	1	0	0	0	5640	1406	49	2	795	2	FAM82B	8	87519286	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10		87519286	58844736	36	27697										
OXR1	55074	hgsc.bcm.edu	37	chr8	107531242	107531242	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tttggctggtgcaggaaagcAaacaccacaagccagtaagc	11	10	0	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr8:107531242A>T	ENST00000442977.2	+	2	197	c.98A>T	c.(97-99)cAa>cTa	p.Q33L	OXR1_ENST00000445937.1_Missense_Mutation_p.Q32L|OXR1_ENST00000531443.1_Missense_Mutation_p.Q32L|RP11-649G15.2_ENST00000518591.1_RNA|OXR1_ENST00000517566.2_Missense_Mutation_p.Q32L|OXR1_ENST00000452423.2_5'UTR	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	33					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			GCAGGAAAGCAAACACCACAA	0.488																																					p.Q33L		Atlas-SNP	.											.	OXR1	190	.	0			c.A98T						.						63	69	67					8																	107531242		692	1591	2283	SO:0001583	missense	55074	exon2			GAAAGCAAACACC	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 3"	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.98A>T	chr8.hg19:g.107531242A>T	ENSP00000405424:p.Gln33Leu	271.0	0.0		277.0	127.0	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Missense_Mutation	SNP	ENST00000442977.2	hg19	CCDS56548.1	.	.	.	.	.	.	.	.	.	.	A	10.74	1.434249	0.25813	.	.	ENSG00000164830	ENST00000445937;ENST00000531443;ENST00000517566;ENST00000442977	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	5.2	2.56	0.30785	.	.	.	.	.	T	0.05364	0.0142	N	0.03608	-0.345	0.40803	D	0.983352	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.29518	-1.0009	9	0.62326	D	0.03	.	11.6655	0.51370	0.599:0.401:0.0:0.0	.	33;32	Q8N573;Q8N573-5	OXR1_HUMAN;.	L	32;32;32;33	ENSP00000402918:Q32L;ENSP00000431966:Q32L;ENSP00000429205:Q32L;ENSP00000405424:Q33L	ENSP00000405424:Q33L	Q	+	2	0	OXR1	107600418	0.070000	0.21116	0.683000	0.30040	0.526000	0.34562	0.297000	0.19101	0.884000	0.36064	0.533000	0.62120	CAA	.	.		0.488	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		T	107531242	A	T	107531242	3	4	187	1	0	0	0	0	1	0	0	0	11343	130	5	4	101	4	OXR1	8	107531242	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	20011956	107531242	38832780	37	27698										
EIF3E	3646	hgsc.bcm.edu	37	chr8	109226891	109226891	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ctcaaatatgaagagacgggCattttcaatgaaatcctcaa	7	8	3	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr8:109226891C>T	ENST00000220849.5	-	10	1068	c.1006G>A	c.(1006-1008)Gcc>Acc	p.A336T	EIF3E_ENST00000519517.1_5'UTR|EIF3E_ENST00000519030.1_Missense_Mutation_p.A243T	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E										EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			AAGAGACGGGCATTTTCAATG	0.358																																					p.A336T	GBM(15;360 410 8460 34179 52246)	Atlas-SNP	.											.	EIF3E	73	.	0			c.G1006A						.						93	89	90					8																	109226891		2203	4300	6503	SO:0001583	missense	3646	exon10			GACGGGCATTTTC	U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"eukaryotic translation initiation factor 3, subunit 6 48kDa"	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.1006G>A	chr8.hg19:g.109226891C>T	ENSP00000220849:p.Ala336Thr	353.0	0.0		362.0	186.0	NM_001568		Missense_Mutation	SNP	ENST00000220849.5	hg19	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	C	36	5.671262	0.96754	.	.	ENSG00000104408	ENST00000220849;ENST00000519030;ENST00000519627	T;T;T	0.59364	1.59;1.59;0.27	5.52	5.52	0.82312	Proteasome component (PCI) domain (2);	0.000000	0.85682	D	0.000000	D	0.85017	0.5601	H	0.96633	3.855	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.89561	0.3806	10	0.87932	D	0	-4.5573	19.8061	0.96532	0.0:1.0:0.0:0.0	.	336	P60228	EIF3E_HUMAN	T	336;243;209	ENSP00000220849:A336T;ENSP00000428796:A243T;ENSP00000430839:A209T	ENSP00000220849:A336T	A	-	1	0	EIF3E	109296067	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.772000	0.85439	2.756000	0.94617	0.655000	0.94253	GCC	.	.		0.358	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		T	109226891	C	T	109226891	3	4	187	1	0	0	0	0	1	0	0	0	5017	710	25	3	347	3	EIF3E	8	109226891	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	1695649	109226891	37137131	38	27699										
KIAA0020	9933	hgsc.bcm.edu	37	chr9	2812219	2812219	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	agccattctacttggttttaCctgtgtgcatttccatctcc	6	12	2	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr9:2812219C>T	ENST00000397885.2	-	14	1619		c.e14+1			NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020							endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		CTTGGTTTTACCTGTGTGCAT	0.413																																					.		Atlas-SNP	.											.	KIAA0020	56	.	0			c.1412+1G>A						.						237	218	224					9																	2812219		2203	4300	6503	SO:0001630	splice_region_variant	9933	exon15			GTTTTACCTGTGT	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"penguin homolog (Drosophila)", "minor histocompatibility antigen HA-8"	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1412+1G>A	chr9.hg19:g.2812219C>T		103.0	0.0		60.0	51.0	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Splice_Site	SNP	ENST00000397885.2	hg19	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	C	23.8	4.462797	0.84425	.	.	ENSG00000080608	ENST00000397885	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7537	0.96281	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA0020	2802219	1.000000	0.71417	0.998000	0.56505	0.891000	0.51852	4.507000	0.60434	2.736000	0.93811	0.591000	0.81541	.	.	.		0.413	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	Intron	T	2812219	C	T	2812219	5	4	187	1	0	0	0	0	0	0	1	0	8161	521	18	3	553	3	KIAA0020	9	2812219	Splice_Site	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10		2812219	138401212	39	27700										
OR2K2	26248	hgsc.bcm.edu	37	chr9	114089907	114089907	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	agcaacgagatgattttgtcTattttttgtgcatttgatga	9	4	1	4			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr9:114089907T>C	ENST00000374428.1	-	1	893	c.894A>G	c.(892-894)atA>atG	p.I298M	OR2K2_ENST00000302681.1_Missense_Mutation_p.I269M			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						TGATTTTGTCTATTTTTTGTG	0.388																																					p.I269M		Atlas-SNP	.											.	OR2K2	77	.	0			c.A807G						.						132	128	129					9																	114089907		2203	4300	6503	SO:0001583	missense	26248	exon1			TTTGTCTATTTTT	X64977	CCDS6778.1	9q31.3	2012-08-09			ENSG00000171133	ENSG00000171133		"GPCR / Class A : Olfactory receptors"	8264	protein-coding gene	gene with protein product				OR2AR1P		1370859, 17010214	Standard	NM_205859		Approved	HTPCRH06, HSHTPCRH06	uc011lwp.2	Q8NGT1	OTTHUMG00000020488	ENST00000374428.1:c.894A>G	chr9.hg19:g.114089907T>C	ENSP00000363550:p.Ile298Met	167.0	0.0		169.0	148.0	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Missense_Mutation	SNP	ENST00000374428.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.91	1.779142	0.31502	.	.	ENSG00000171133	ENST00000302681;ENST00000374428	T;T	0.00137	8.68;8.68	4.55	2.16	0.27623	GPCR, rhodopsin-like superfamily (1);	0.629960	0.13303	U	0.398057	T	0.00178	0.0005	N	0.17594	0.5	0.09310	N	1	D	0.60575	0.988	P	0.58721	0.844	T	0.56056	-0.8042	10	0.66056	D	0.02	.	6.1858	0.20495	0.159:0.0:0.1658:0.6752	.	298	Q8NGT1	OR2K2_HUMAN	M	269;298	ENSP00000305055:I269M;ENSP00000363550:I298M	ENSP00000305055:I269M	I	-	3	3	OR2K2	113129728	0.000000	0.05858	0.789000	0.31954	0.944000	0.59088	-0.127000	0.10547	0.351000	0.24027	0.482000	0.46254	ATA	.	.		0.388	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859		C	114089907	T	C	114089907	3	2	187	1	0	0	0	0	1	0	0	0	11014	1512	53	2	146	2	OR2K2	9	114089907	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	111277688	114089907	27123524	40	27701										
ARPC5L	81873	hgsc.bcm.edu	37	chr9	127631658	127631658	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tgtggacgagcaggaggaggCggcggcggcggcggcggagc	24	9	0	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr9:127631658C>A	ENST00000353214.2	+	3	1341	c.89C>A	c.(88-90)gCg>gAg	p.A30E	ARPC5L_ENST00000259477.6_Missense_Mutation_p.A30E			Q9BPX5	ARP5L_HUMAN	actin related protein 2/3 complex, subunit 5-like	30				Missing (in Ref. 1; AAP97155). {ECO:0000305}.	regulation of actin filament polymerization (GO:0030833)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)				large_intestine(2)|lung(1)	3						CAGGAGGAggcggcggcggcg	0.711																																					p.A30E		Atlas-SNP	.											.	ARPC5L	8	.	0			c.C89A						.						6	7	7					9																	127631658		1664	3204	4868	SO:0001583	missense	81873	exon1			AGGAGGCGGCGGC	AF087842	CCDS6859.1	9q34.11	2011-07-06			ENSG00000136950	ENSG00000136950		"Actin related protein 2/3 complex subunits"	23366	protein-coding gene	gene with protein product							Standard	NM_030978		Approved	MGC3038, ARC16-2	uc004bpa.4	Q9BPX5	OTTHUMG00000020660	ENST00000353214.2:c.89C>A	chr9.hg19:g.127631658C>A	ENSP00000345361:p.Ala30Glu	117.0	0.0		125.0	5.0	NM_030978	Q7Z523	Missense_Mutation	SNP	ENST00000353214.2	hg19	CCDS6859.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.494499	0.26774	.	.	ENSG00000136950	ENST00000353214;ENST00000259477	.	.	.	5.0	5.0	0.66597	.	0.069901	0.56097	D	0.000037	T	0.39708	0.1088	N	0.10972	0.075	0.40179	D	0.977265	B	0.02656	0.0	B	0.09377	0.004	T	0.37079	-0.9721	9	0.87932	D	0	-0.4887	13.7282	0.62771	0.0:1.0:0.0:0.0	.	30	Q9BPX5	ARP5L_HUMAN	E	30	.	ENSP00000259477:A30E	A	+	2	0	ARPC5L	126671479	0.995000	0.38212	1.000000	0.80357	0.997000	0.91878	0.335000	0.19806	2.597000	0.87782	0.650000	0.86243	GCG	.	.		0.711	ARPC5L-002	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054041.1	NM_030978		A	127631658	C	A	127631658	3	1	187	1	0	0	0	0	1	0	0	0	975	768	27	1	91	1	ARPC5L	9	127631658	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	13541751	127631658	13581773	41	27702										
TDRD1	56165	hgsc.bcm.edu	37	chr10	115966040	115966040	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gtgcttatagaaatgggataTggcttgaaacccagtggaca	12	6	0	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr10:115966040T>A	ENST00000369280.1	+	11	1795	c.1335T>A	c.(1333-1335)taT>taA	p.Y445*	TDRD1_ENST00000369281.2_Nonsense_Mutation_p.Y445*|TDRD1_ENST00000251864.2_Nonsense_Mutation_p.Y445*|TDRD1_ENST00000422662.1_Nonsense_Mutation_p.Y106*|TDRD1_ENST00000369282.1_Nonsense_Mutation_p.Y445*			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	445					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		AAATGGGATATGGCTTGAAAC	0.348																																					p.Y445X		Atlas-SNP	.											.	TDRD1	126	.	0			c.T1335A						.						93	90	91					10																	115966040		2203	4300	6503	SO:0001587	stop_gained	56165	exon11			GGGATATGGCTTG	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.1335T>A	chr10.hg19:g.115966040T>A	ENSP00000358286:p.Tyr445*	127.0	0.0		102.0	75.0	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Nonsense_Mutation	SNP	ENST00000369280.1	hg19		.	.	.	.	.	.	.	.	.	.	T	39	7.327152	0.98214	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000422662;ENST00000369280	.	.	.	5.86	4.73	0.59995	.	0.451948	0.22869	N	0.054648	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.3227	8.561	0.33511	0.0:0.0865:0.0:0.9135	.	.	.	.	X	445;445;445;106;445	.	ENSP00000251864:Y445X	Y	+	3	2	TDRD1	115956030	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.614000	0.46359	1.052000	0.40392	0.482000	0.46254	TAT	.	.		0.348	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			A	115966040	T	A	115966040	4	1	187	1	0	0	0	0	0	1	0	0	15745	1471	51	4	1373	4	TDRD1	10	115966040	Nonsense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10		115966040	19568707	42	27703										
OR51A4	401666	hgsc.bcm.edu	37	chr11	4967515	4967515	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tttgccatgagaacattaatGaggggagagacatgccgggc	14	7	0	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr11:4967515G>C	ENST00000380373.2	-	1	841	c.816C>G	c.(814-816)ctC>ctG	p.L272L	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GAACATTAATGAGGGGAGAGA	0.443																																					p.L272L		Atlas-SNP	.											.	OR51A4	73	.	0			c.C816G						.						169	163	165					11																	4967515		2201	4298	6499	SO:0001819	synonymous_variant	401666	exon1			ATTAATGAGGGGA	AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497		"GPCR / Class A : Olfactory receptors"	14795	protein-coding gene	gene with protein product							Standard	NM_001005329		Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.816C>G	chr11.hg19:g.4967515G>C		571.0	0.0		347.0	26.0	NM_001005329		Silent	SNP	ENST00000380373.2	hg19	CCDS31367.1																																																																																			.	.		0.443	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329		C	4967515	G	C	4967515	2	2	187	1	0	0	0	0	0	0	0	1	11096	1277	45	4		4	OR51A4	11	4967515	Silent	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10		4967515	130039001	43	27704										
RRP8	23378	hgsc.bcm.edu	37	chr11	6622002	6622002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cacagactcatcctccagagGaacctgtggagagtgagagt	12	10	1	4			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr11:6622002G>A	ENST00000254605.6	-	5	1168	c.1051C>T	c.(1051-1053)Cct>Tct	p.P351S	ILK_ENST00000537806.1_5'Flank|ILK_ENST00000420936.2_5'Flank|RRP8_ENST00000534343.1_Missense_Mutation_p.P35S|RP11-732A19.8_ENST00000527191.1_RNA|ILK_ENST00000299421.4_5'Flank	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	351					cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						TCCTCCAGAGGAACCTGTGGA	0.498																																					p.P351S		Atlas-SNP	.											.	RRP8	40	.	0			c.C1051T						.						81	81	81					11																	6622002		2201	4296	6497	SO:0001583	missense	23378	exon5			CCAGAGGAACCTG	AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"KIAA0409"	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.1051C>T	chr11.hg19:g.6622002G>A	ENSP00000254605:p.Pro351Ser	115.0	0.0		80.0	48.0	NM_015324	Q7KZ78|Q9BVM6	Missense_Mutation	SNP	ENST00000254605.6	hg19	CCDS31411.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.355471	0.82243	.	.	ENSG00000132275	ENST00000254605;ENST00000534343	T;T	0.63913	-0.07;-0.07	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.75737	0.3890	L	0.49571	1.57	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76119	-0.3076	10	0.66056	D	0.02	-33.5919	18.1469	0.89661	0.0:0.0:1.0:0.0	.	351	O43159	RRP8_HUMAN	S	351;35	ENSP00000254605:P351S;ENSP00000436960:P35S	ENSP00000254605:P351S	P	-	1	0	RRP8	6578578	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.025000	0.76449	2.861000	0.98227	0.655000	0.94253	CCT	.	.		0.498	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		A	6622002	G	A	6622002	3	1	187	1	0	0	0	0	1	0	0	0	13705	1174	41	3	331	3	RRP8	11	6622002	Missense_Mutation	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	1654487	6622002	128384514	44	27705										
OR5I1	10798	hgsc.bcm.edu	37	chr11	55703134	55703134	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cttggtagatcgtcactgaaGtcaggtgagaggcgcatgta	14	7	2	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr11:55703134G>T	ENST00000301532.3	-	1	742	c.743C>A	c.(742-744)aCt>aAt	p.T248N		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	248					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						CGTCACTGAAGTCAGGTGAGA	0.433																																					p.T248N		Atlas-SNP	.											.	OR5I1	110	.	0			c.C743A						.						76	74	75					11																	55703134		2201	4295	6496	SO:0001583	missense	10798	exon1			ACTGAAGTCAGGT	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"GPCR / Class A : Olfactory receptors"	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.743C>A	chr11.hg19:g.55703134G>T	ENSP00000301532:p.Thr248Asn	142.0	0.0		95.0	26.0	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	hg19	CCDS7949.1	.	.	.	.	.	.	.	.	.	.	G	13.99	2.400979	0.42613	.	.	ENSG00000167825	ENST00000301532	T	0.39229	1.09	5.16	2.25	0.28309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000167	T	0.69342	0.3100	H	0.96662	3.86	0.27946	N	0.937343	D	0.69078	0.997	D	0.64776	0.929	T	0.64980	-0.6279	10	0.87932	D	0	.	7.213	0.25945	0.1581:0.14:0.7018:0.0	.	248	Q13606	OR5I1_HUMAN	N	248	ENSP00000301532:T248N	ENSP00000301532:T248N	T	-	2	0	OR5I1	55459710	0.000000	0.05858	0.230000	0.23976	0.506000	0.33950	0.143000	0.16115	0.274000	0.22072	0.643000	0.83706	ACT	.	.		0.433	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637		T	55703134	G	T	55703134	3	4	187	1	0	0	0	0	1	0	0	0	11173	1029	36	3	204	3	OR5I1	11	55703134	Missense_Mutation	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	49081132	55703134	79303382	45	27706										
DTX4	23220	hgsc.bcm.edu	37	chr11	58949569	58949569	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gccccccatgtccccctgctCctgtccccagtgtgtcttgg	9	19	1	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr11:58949569C>T	ENST00000227451.3	+	2	673	c.569C>T	c.(568-570)tCc>tTc	p.S190F	DTX4_ENST00000532982.1_Missense_Mutation_p.S84F	NM_015177.1	NP_055992.1	Q9Y2E6	DTX4_HUMAN	deltex 4, E3 ubiquitin ligase	190					innate immune response (GO:0045087)|Notch signaling pathway (GO:0007219)|positive regulation of type I interferon production (GO:0032481)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.S190F(1)|p.S84F(1)		central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	20		all_epithelial(135;0.125)				TCCCCCTGCTCCTGTCCCCAG	0.632																																					p.S190F		Atlas-SNP	.											DTX4_ENST00000227451,NS,carcinoma,0,2	DTX4	84	.	2	Substitution - Missense(2)	lung(2)	c.C569T						.						30	35	33					11																	58949569		2074	4187	6261	SO:0001583	missense	23220	exon2			CCTGCTCCTGTCC	AB023154	CCDS44612.1	11q12.2	2014-01-28	2014-01-28		ENSG00000110042	ENSG00000110042		"RING-type (C3HC4) zinc fingers"	29151	protein-coding gene	gene with protein product			"deltex 4 homolog (Drosophila)", "deltex homolog 4 (Drosophila)"			10231032, 22388039	Standard	NM_015177		Approved	KIAA0937, RNF155	uc001nns.2	Q9Y2E6	OTTHUMG00000167336	ENST00000227451.3:c.569C>T	chr11.hg19:g.58949569C>T	ENSP00000227451:p.Ser190Phe	72.0	0.0		37.0	18.0	NM_015177	Q0VF38	Missense_Mutation	SNP	ENST00000227451.3	hg19	CCDS44612.1	.	.	.	.	.	.	.	.	.	.	C	13.59	2.282873	0.40394	.	.	ENSG00000110042	ENST00000532982;ENST00000227451	T;T	0.16897	2.31;2.69	4.32	4.32	0.51571	.	0.416020	0.24454	N	0.038381	T	0.20170	0.0485	L	0.54323	1.7	0.39963	D	0.974698	B	0.25169	0.119	B	0.25759	0.063	T	0.06162	-1.0842	10	0.48119	T	0.1	.	16.0922	0.81098	0.0:1.0:0.0:0.0	.	190	Q9Y2E6	DTX4_HUMAN	F	84;190	ENSP00000434055:S84F;ENSP00000227451:S190F	ENSP00000227451:S190F	S	+	2	0	DTX4	58706145	0.912000	0.30974	1.000000	0.80357	0.770000	0.43624	2.484000	0.45242	2.410000	0.81850	0.655000	0.94253	TCC	.	.		0.632	DTX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394228.1	XM_166213		T	58949569	C	T	58949569	3	4	187	1	0	0	0	0	1	0	0	0	4799	855	30	3	575	3	DTX4	11	58949569	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	3246435	58949569	76056947	46	27707										
SCYL1	57410	hgsc.bcm.edu	37	chr11	65302729	65302729	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cctggccccaaagctgaacgAggccaacctcaatgtggagc	11	14	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr11:65302729A>C	ENST00000270176.5	+	10	1339	c.1262A>C	c.(1261-1263)gAg>gCg	p.E421A	SCYL1_ENST00000525364.1_Missense_Mutation_p.E421A|SCYL1_ENST00000420247.2_Missense_Mutation_p.E421A|SCYL1_ENST00000279270.6_Missense_Mutation_p.E421A|SCYL1_ENST00000527009.1_Missense_Mutation_p.E278A|SCYL1_ENST00000524944.1_Missense_Mutation_p.E421A|SCYL1_ENST00000533862.1_Missense_Mutation_p.E421A	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	421					peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						AAGCTGAACGAGGCCAACCTC	0.597																																					p.E421A		Atlas-SNP	.											.	SCYL1	76	.	0			c.A1262C						.						100	103	102					11																	65302729		2163	4257	6420	SO:0001583	missense	57410	exon10			TGAACGAGGCCAA	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"teratoma-associated tyrosine kinase", "telomerase transcriptional elements-interacting factor", "telomerase regulation-associated protein"	607982	"N-terminal kinase-like"	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.1262A>C	chr11.hg19:g.65302729A>C	ENSP00000270176:p.Glu421Ala	96.0	0.0		50.0	15.0	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Missense_Mutation	SNP	ENST00000270176.5	hg19	CCDS41672.1	.	.	.	.	.	.	.	.	.	.	A	12.26	1.884833	0.33255	.	.	ENSG00000142186	ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000527009	T;T;T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36	4.64	4.64	0.57946	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.48768	0.1518	M	0.75615	2.305	0.80722	D	1	P;P;P;P;P	0.45531	0.63;0.86;0.732;0.567;0.781	B;P;P;P;B	0.51170	0.358;0.661;0.561;0.458;0.254	T	0.48340	-0.9044	10	0.37606	T	0.19	-12.7312	12.0046	0.53251	1.0:0.0:0.0:0.0	.	421;421;421;421;421	E9PS17;Q96KG9-4;Q96KG9-6;Q96KG9-2;Q96KG9	.;.;.;.;NTKL_HUMAN	A	421;421;421;421;421;421;421;421;278	ENSP00000270176:E421A;ENSP00000431635:E421A;ENSP00000408192:E421A;ENSP00000437254:E421A;ENSP00000433450:E421A;ENSP00000279270:E421A;ENSP00000432175:E421A;ENSP00000436993:E278A	ENSP00000270176:E421A	E	+	2	0	SCYL1	65059305	1.000000	0.71417	0.827000	0.32855	0.078000	0.17371	6.397000	0.73239	1.736000	0.51660	0.260000	0.18958	GAG	.	.		0.597	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		C	65302729	A	C	65302729	3	2	187	1	0	0	0	0	1	0	0	0	13962	304	11	5	1300	5	SCYL1	11	65302729	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	6353160	65302729	69703787	47	27708										
SORL1	6653	hgsc.bcm.edu	37	chr11	121458790	121458790	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cgccagcagtgcctgttccaCtccatggtctgtgacggaat	11	13	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr11:121458790C>A	ENST00000260197.7	+	28	4005	c.3876C>A	c.(3874-3876)caC>caA	p.H1292Q	SORL1_ENST00000532694.1_Missense_Mutation_p.H138Q|SORL1_ENST00000527934.1_5'Flank|SORL1_ENST00000525532.1_Missense_Mutation_p.H236Q|SORL1_ENST00000534286.1_Missense_Mutation_p.H202Q	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1292	LDL-receptor class A 6. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		GCCTGTTCCACTCCATGGTCT	0.582																																					p.H1292Q		Atlas-SNP	.											.	SORL1	218	.	0			c.C3876A						.						131	106	114					11																	121458790		2203	4299	6502	SO:0001583	missense	6653	exon28			GTTCCACTCCATG	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.3876C>A	chr11.hg19:g.121458790C>A	ENSP00000260197:p.His1292Gln	52.0	0.0		57.0	29.0	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	hg19	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	C	11.91	1.778884	0.31502	.	.	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286	D;D;D;D	0.95447	-3.71;-3.71;-3.71;-3.71	5.52	2.6	0.31112	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.303615	0.37095	N	0.002255	D	0.85164	0.5634	N	0.04132	-0.27	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.75252	-0.3383	10	0.13108	T	0.6	.	8.4342	0.32778	0.0:0.6227:0.2433:0.134	.	1292	Q92673	SORL_HUMAN	Q	1292;236;138;202	ENSP00000260197:H1292Q;ENSP00000434634:H236Q;ENSP00000432131:H138Q;ENSP00000436447:H202Q	ENSP00000260197:H1292Q	H	+	3	2	SORL1	120964000	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.162000	0.31786	0.694000	0.31654	0.655000	0.94253	CAC	.	.		0.582	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		A	121458790	C	A	121458790	3	1	187	1	0	0	0	0	1	0	0	0	14949	564	20	3	3986	3	SORL1	11	121458790	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	56156061	121458790	13547726	48	27709										
NFRKB	4798	hgsc.bcm.edu	37	chr11	129754739	129754739	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gctcggaagccatgagctgaGatcttcaaaagaaaattgtt	10	7	2	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr11:129754739G>A	ENST00000446488.3	-	6	746	c.643C>T	c.(643-645)Ctc>Ttc	p.L215F	NFRKB_ENST00000304521.5_Missense_Mutation_p.L215F|NFRKB_ENST00000524746.1_Missense_Mutation_p.L215F|NFRKB_ENST00000524794.1_Missense_Mutation_p.L240F	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	215					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		CATGAGCTGAGATCTTCAAAA	0.512																																					p.L240F		Atlas-SNP	.											.	NFRKB	101	.	0			c.C718T						.						71	73	72					11																	129754739		2201	4297	6498	SO:0001583	missense	4798	exon5			AGCTGAGATCTTC		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"INO80 complex subunits"	7802	protein-coding gene	gene with protein product	"nuclear factor related to kappa B binding protein", "DNA-binding protein R kappa B", "INO80 complex subunit G"	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.643C>T	chr11.hg19:g.129754739G>A	ENSP00000400476:p.Leu215Phe	73.0	0.0		66.0	18.0	NM_006165	Q12869|Q15312|Q9H048	Missense_Mutation	SNP	ENST00000446488.3	hg19	CCDS44770.1	.	.	.	.	.	.	.	.	.	.	g	17.04	3.288381	0.59976	.	.	ENSG00000170322	ENST00000304521;ENST00000446488;ENST00000524794;ENST00000524746;ENST00000531755	.	.	.	5.45	5.45	0.79879	.	0.210927	0.40908	D	0.000982	T	0.54581	0.1867	N	0.24115	0.695	0.51482	D	0.999926	D;D;D;D	0.76494	0.998;0.998;0.999;0.999	D;D;D;D	0.83275	0.991;0.991;0.996;0.996	T	0.45220	-0.9276	9	0.10902	T	0.67	-16.4776	12.6158	0.56576	0.0756:0.0:0.9244:0.0	.	227;215;215;240	B4DSL1;Q6P4R8;Q6P4R8-3;Q6P4R8-2	.;NFRKB_HUMAN;.;.	F	215;215;240;215;227	.	ENSP00000303800:L215F	L	-	1	0	NFRKB	129259949	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.443000	0.44881	2.558000	0.86282	0.651000	0.88453	CTC	.	.		0.512	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		A	129754739	G	A	129754739	3	1	187	1	0	0	0	0	1	0	0	0	10393	942	33	3	3340	3	NFRKB	11	129754739	Missense_Mutation	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	8295949	129754739	5251777	49	27710										
ANO2	57101	hgsc.bcm.edu	37	chr12	5841762	5841762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tctcctttagcattttctctCgaactttggtttcatactca	4	11	4	0	rs375457985		TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:5841762C>T	ENST00000356134.5	-	16	1543	c.1472G>A	c.(1471-1473)cGa>cAa	p.R491Q	ANO2_ENST00000538154.1_5'UTR|ANO2_ENST00000546188.1_Missense_Mutation_p.R491Q|ANO2_ENST00000327087.8_Missense_Mutation_p.R490Q	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	495					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						CATTTTCTCTCGAACTTTGGT	0.448													C|||	1	0.000199681	8e-04	0	5008	,	,		23076	0		0	False		,,,				2504	0				p.R490Q		Atlas-SNP	.											.	ANO2	309	.	0			c.G1469A						.	C	GLN/ARG	0,3960		0,0,1980	108	103	105		1469	4.8	1	12		105	1,8325		0,1,4162	no	missense	ANO2	NM_020373.2	43	0,1,6142	TT,TC,CC		0.012,0.0,0.0081	benign	490/999	5841762	1,12285	1980	4163	6143	SO:0001583	missense	57101	exon15			TTCTCTCGAACTT	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	1183	protein-coding gene	gene with protein product	"transmembrane protein 16B (eight membrane-spanning domains)"	610109	"chromosome 12 open reading frame 3", "transmembrane protein 16B", "anoctamin 2"	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.1472G>A	chr12.hg19:g.5841762C>T	ENSP00000348453:p.Arg491Gln	90.0	0.0		63.0	44.0	NM_020373	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	hg19		.	.	.	.	.	.	.	.	.	.	C	12.57	1.976945	0.34848	0.0	1.2E-4	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277;ENST00000545860	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	4.84	4.84	0.62591	.	0.064980	0.64402	D	0.000006	T	0.47600	0.1454	L	0.34521	1.04	0.32319	N	0.562659	B	0.28900	0.227	B	0.19148	0.024	T	0.51988	-0.8635	10	0.13853	T	0.58	.	15.4822	0.75537	0.0:1.0:0.0:0.0	.	490	Q9NQ90-3	.	Q	490;491;491;495;50	ENSP00000314048:R490Q;ENSP00000348453:R491Q;ENSP00000440981:R491Q;ENSP00000443813:R50Q	ENSP00000314048:R490Q	R	-	2	0	ANO2	5712023	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.866000	0.56040	2.507000	0.84556	0.655000	0.94253	CGA	.	.		0.448	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		T	5841762	C	T	5841762	3	4	187	1	0	0	0	0	1	0	0	0	697	884	31	1	1575	1	ANO2	12	5841762	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10		5841762	128010133	50	27711										
USP5	8078	hgsc.bcm.edu	37	chr12	6961443	6961443	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	aagacgagtgcgccttctccTtcgacacgccggtaagccca	10	15	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:6961443T>G	ENST00000229268.8	+	1	152	c.100T>G	c.(100-102)Ttc>Gtc	p.F34V	USP5_ENST00000389231.5_Missense_Mutation_p.F34V|CDCA3_ENST00000540683.1_5'Flank|CDCA3_ENST00000538862.2_5'Flank|CDCA3_ENST00000229265.6_5'Flank|CDCA3_ENST00000535406.1_5'Flank|CDCA3_ENST00000422785.3_5'Flank	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	34					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						CGCCTTCTCCTTCGACACGCC	0.637																																					p.F34V		Atlas-SNP	.											.	USP5	124	.	0			c.T100G						.						100	80	87					12																	6961443		2202	4300	6502	SO:0001583	missense	8078	exon1			TTCTCCTTCGACA	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"Ubiquitin-specific peptidases"	12628	protein-coding gene	gene with protein product		601447	"ubiquitin specific protease 5 (isopeptidase T)"			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.100T>G	chr12.hg19:g.6961443T>G	ENSP00000229268:p.Phe34Val	34.0	0.0		32.0	16.0	NM_003481	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	hg19	CCDS41743.1	.	.	.	.	.	.	.	.	.	.	T	35	5.559727	0.96514	.	.	ENSG00000111667	ENST00000229268;ENST00000389231;ENST00000542087	T;T	0.29655	1.56;1.58	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.57725	0.2073	M	0.81942	2.565	0.80722	D	1	P;D	0.71674	0.893;0.998	P;D	0.70016	0.504;0.967	T	0.63457	-0.6633	10	0.72032	D	0.01	.	15.5613	0.76249	0.0:0.0:0.0:1.0	.	34;34	P45974;P45974-2	UBP5_HUMAN;.	V	34	ENSP00000229268:F34V;ENSP00000373883:F34V	ENSP00000229268:F34V	F	+	1	0	USP5	6831704	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.830000	0.69324	2.269000	0.75478	0.533000	0.62120	TTC	.	.		0.637	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1			G	6961443	T	G	6961443	3	3	187	1	0	0	0	0	1	0	0	0	17096	1609	56	5	102	5	USP5	12	6961443	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	1119681	6961443	126890452	51	27712										
RIMKLB	57494	hgsc.bcm.edu	37	chr12	8866531	8866531	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	atcagggaagactatcctcaAaaagagattttacgagcatt	8	7	2	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:8866531A>G	ENST00000538135.1	+	2	894	c.69A>G	c.(67-69)caA>caG	p.Q23Q	RIMKLB_ENST00000535829.1_Silent_p.Q23Q|RIMKLB_ENST00000357529.3_Silent_p.Q23Q|RIMKLB_ENST00000299673.5_3'UTR			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	23					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|citrate-L-glutamate ligase activity (GO:0072591)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ACTATCCTCAAAAAGAGATTT	0.468																																					p.Q23Q		Atlas-SNP	.											.	RIMKLB	47	.	0			c.A69G						.						135	137	136					12																	8866531		1977	4148	6125	SO:0001819	synonymous_variant	57494	exon3			TCCTCAAAAAGAG	AB033064	CCDS41748.1	12p13.31	2011-09-21	2008-10-13	2008-10-13	ENSG00000166532	ENSG00000166532	6.3.2.N6		29228	protein-coding gene	gene with protein product	"N-acetylaspartyl-glutamate synthetase"	614054	"family with sequence similarity 80, member B"	FAM80B		10574462, 20643647	Standard	XM_006719116		Approved	KIAA1238, NAAGS, NAAGS-I	uc001qux.2	Q9ULI2		ENST00000538135.1:c.69A>G	chr12.hg19:g.8866531A>G		108.0	0.0		63.0	5.0	NM_020734	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Silent	SNP	ENST00000538135.1	hg19	CCDS41748.1																																																																																			.	.		0.468	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1	NM_020734		G	8866531	A	G	8866531	2	3	187	1	0	0	0	0	0	0	0	1	13381	11	1	2		2	RIMKLB	12	8866531	Silent	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	1905088	8866531	124985364	52	27713										
KIF21A	55605	hgsc.bcm.edu	37	chr12	39735325	39735325	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	acctttttcatctgattcagAatctgattcatcagaacttt	4	9	6	4			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:39735325A>C	ENST00000361418.5	-	14	1918	c.1903T>G	c.(1903-1905)Tct>Gct	p.S635A	KIF21A_ENST00000541463.2_Missense_Mutation_p.S622A|KIF21A_ENST00000544797.2_Missense_Mutation_p.S622A|KIF21A_ENST00000395670.3_Missense_Mutation_p.S635A|KIF21A_ENST00000361961.3_Missense_Mutation_p.S622A			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	635					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				TCTGATTCAGAATCTGATTCA	0.393																																					p.S635A		Atlas-SNP	.											.	KIF21A	238	.	0			c.T1903G						.						120	117	118					12																	39735325		2203	4300	6503	SO:0001583	missense	55605	exon14			ATTCAGAATCTGA	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.1903T>G	chr12.hg19:g.39735325A>C	ENSP00000354878:p.Ser635Ala	66.0	0.0		44.0	14.0	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	hg19	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.420819	0.83559	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000544797;ENST00000361418;ENST00000541463	T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34	5.68	5.68	0.88126	.	0.000000	0.49305	D	0.000142	T	0.79604	0.4474	M	0.64404	1.975	0.45747	D	0.998649	D;D;D;P	0.61697	0.974;0.99;0.982;0.872	D;D;D;P	0.72982	0.969;0.979;0.952;0.529	T	0.80407	-0.1395	10	0.52906	T	0.07	.	15.9265	0.79621	1.0:0.0:0.0:0.0	.	622;622;635;622	F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2	.;.;KI21A_HUMAN;.	A	622;635;635;622;635;622	ENSP00000354851:S622A;ENSP00000379029:S635A;ENSP00000445606:S622A;ENSP00000354878:S635A;ENSP00000438075:S622A	ENSP00000344501:S635A	S	-	1	0	KIF21A	38021592	1.000000	0.71417	0.996000	0.52242	0.829000	0.46940	8.107000	0.89557	2.159000	0.67721	0.533000	0.62120	TCT	.	.		0.393	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		C	39735325	A	C	39735325	3	2	187	1	0	0	0	0	1	0	0	0	8297	246	9	5	3221	5	KIF21A	12	39735325	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	30868794	39735325	94116570	53	27714										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43826591	43826591	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gaccacattgggatgaacatTcacttttgccaataacatgc	7	10	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:43826591T>C	ENST00000389420.3	-	20	2743	c.2744A>G	c.(2743-2745)gAa>gGa	p.E915G	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.E915G|ADAMTS20_ENST00000395541.2_Missense_Mutation_p.E69G	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	915	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		GGATGAACATTCACTTTTGCC	0.363																																					p.E915G		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A2744G						.						165	150	155					12																	43826591		2203	4300	6503	SO:0001583	missense	80070	exon20			GAACATTCACTTT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2744A>G	chr12.hg19:g.43826591T>C	ENSP00000374071:p.Glu915Gly	127.0	0.0		108.0	30.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	18.69	3.678551	0.68042	.	.	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.64618	0.09;0.05;0.05;-0.11	4.43	4.43	0.53597	.	0.251496	0.27473	N	0.019201	T	0.71307	0.3324	M	0.66297	2.02	0.37318	D	0.909439	D;P	0.55385	0.971;0.736	P;B	0.54924	0.764;0.223	T	0.78484	-0.2186	10	0.56958	D	0.05	.	14.4249	0.67207	0.0:0.0:0.0:1.0	.	915;69	P59510;E9PBD5	ATS20_HUMAN;.	G	915;81;69;915;915	ENSP00000374071:E915G;ENSP00000447427:E81G;ENSP00000378911:E69G;ENSP00000448341:E915G	ENSP00000374068:E915G	E	-	2	0	ADAMTS20	42112858	1.000000	0.71417	0.753000	0.31225	0.759000	0.43091	7.558000	0.82253	1.931000	0.55961	0.533000	0.62120	GAA	.	.		0.363	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		C	43826591	T	C	43826591	3	2	187	1	0	0	0	0	1	0	0	0	266	1783	62	2	3067	2	ADAMTS20	12	43826591	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	4091266	43826591	90025304	54	27715										
AQP2	359	hgsc.bcm.edu	37	chr12	50344682	50344682	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ttcctggccacactcctcttCgtcttctttggcctcggctc	7	17	3	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:50344682C>A	ENST00000199280.3	+	1	154	c.69C>A	c.(67-69)ttC>ttA	p.F23L	RP11-469H8.6_ENST00000552379.1_RNA|RP11-469H8.6_ENST00000550530.1_RNA	NM_000486.5	NP_000477.1	P41181	AQP2_HUMAN	aquaporin 2 (collecting duct)	23					actin filament depolymerization (GO:0030042)|aging (GO:0007568)|apoptotic process (GO:0006915)|cell volume homeostasis (GO:0006884)|cellular response to copper ion (GO:0071280)|cellular response to mercury ion (GO:0071288)|cellular response to water deprivation (GO:0042631)|excretion (GO:0007588)|female pregnancy (GO:0007565)|glycerol transport (GO:0015793)|hyperosmotic response (GO:0006972)|metanephric collecting duct development (GO:0072205)|positive regulation of calcium ion transport (GO:0051928)|renal water transport (GO:0003097)|response to calcium ion (GO:0051592)|response to glucagon (GO:0033762)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to salt stress (GO:0009651)|response to starvation (GO:0042594)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|recycling endosome (GO:0055037)|rough endoplasmic reticulum (GO:0005791)|trans-Golgi network (GO:0005802)|transport vesicle membrane (GO:0030658)	glycerol transmembrane transporter activity (GO:0015168)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(4)|ovary(2)	10						CACTCCTCTTCGTCTTCTTTG	0.622																																					p.F23L		Atlas-SNP	.											.	AQP2	34	.	0			c.C69A						.						102	81	88					12																	50344682		2203	4300	6503	SO:0001583	missense	359	exon1			CCTCTTCGTCTTC		CCDS8792.1	12q12-q13	2014-09-17				ENSG00000167580		"Ion channels / Aquaporins"	634	protein-coding gene	gene with protein product		107777				7512890	Standard	NM_000486		Approved		uc001rvn.3	P41181		ENST00000199280.3:c.69C>A	chr12.hg19:g.50344682C>A	ENSP00000199280:p.Phe23Leu	56.0	0.0		36.0	6.0	NM_000486	Q9UD68	Missense_Mutation	SNP	ENST00000199280.3	hg19	CCDS8792.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.690040	0.29962	.	.	ENSG00000167580	ENST00000199280;ENST00000550862	D;T	0.90197	-2.63;1.51	4.89	-9.78	0.00496	Aquaporin-like (2);	0.000000	0.64402	D	0.000012	D	0.90978	0.7163	L	0.38733	1.17	0.25314	N	0.989177	D	0.89917	1.0	D	0.78314	0.991	D	0.90248	0.4291	10	0.56958	D	0.05	-15.3635	21.4074	0.99953	0.0:0.2015:0.0:0.7985	.	23	P41181	AQP2_HUMAN	L	23	ENSP00000199280:F23L;ENSP00000450022:F23L	ENSP00000199280:F23L	F	+	3	2	AQP2	48630949	0.000000	0.05858	0.074000	0.20217	0.920000	0.55202	-2.731000	0.00805	-3.379000	0.00175	-1.655000	0.00754	TTC	.	.		0.622	AQP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405540.1	NM_000486		A	50344682	C	A	50344682	3	1	187	1	0	0	0	0	1	0	0	0	826	883	31	1	71	1	AQP2	12	50344682	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	6518091	50344682	83507213	55	27716										
DIP2B	57609	hgsc.bcm.edu	37	chr12	51064971	51064971	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ttttctaattccacacagacAcatcttcggcctctgaggat	6	12	3	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:51064971A>G	ENST00000301180.5	+	5	464	c.430A>G	c.(430-432)Aca>Gca	p.T144A		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	144						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						CCACACAGACACATCTTCGGC	0.483																																					p.T144A		Atlas-SNP	.											.	DIP2B	167	.	0			c.A430G						.						89	78	82					12																	51064971		2203	4300	6503	SO:0001583	missense	57609	exon5			ACAGACACATCTT	AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.430A>G	chr12.hg19:g.51064971A>G	ENSP00000301180:p.Thr144Ala	50.0	0.0		34.0	10.0	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.021942	0.54576	.	.	ENSG00000066084	ENST00000455310;ENST00000301180	T	0.24723	1.84	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.27967	0.0689	M	0.61703	1.905	0.58432	D	0.999999	P;P	0.41450	0.701;0.75	B;B	0.39935	0.314;0.236	T	0.05582	-1.0876	10	0.15499	T	0.54	-11.9823	15.4023	0.74852	1.0:0.0:0.0:0.0	.	144;154	Q9P265;E9PHD6	DIP2B_HUMAN;.	A	154;144	ENSP00000301180:T144A	ENSP00000301180:T144A	T	+	1	0	DIP2B	49351238	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.961000	0.70356	2.229000	0.72834	0.533000	0.62120	ACA	.	.		0.483	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		G	51064971	A	G	51064971	3	3	187	1	0	0	0	0	1	0	0	0	4530	159	6	2	448	2	DIP2B	12	51064971	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	720289	51064971	82786924	56	27717										
KRT2	3849	hgsc.bcm.edu	37	chr12	53045638	53045639	+	In_Frame_Ins	INS	-	-	AAAGCCGCTGCCGCCTCC													0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ccaaagctgctgccgcctccINSaaaaccacctcctctgccac							TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:53045638_53045639insAAAGCCGCTGCCGCCTCC	ENST00000309680.3	-	1	309_310	c.288_289insGGAGGCGGCAGCGGCTTT	c.(286-291)tttgga>tttGGAGGCGGCAGCGGCTTTgga	p.96_97FG>FGGGSGFG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	96	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		ctgccgcctccaaaaccacctc	0.619																																					p.G97delinsGGGSGFG		Atlas-INDEL	.											.	KRT2	94	.	0			c.289_290insGGAGGCGGCAGCGGCTTT						.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.288_289insGGAGGCGGCAGCGGCTTT	chr12.hg19:g.53045638_53045639insAAAGCCGCTGCCGCCTCC	ENSP00000310861:p.Phe96_Gly97insGlyGlyGlySerGlyPhe	171.0	0.0		160.0	59.0	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.619	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		AAAGCCGCTGCCGCCTCC	53045639	-	AAAGCCGCTGCCGCCTCC	53045638	7	5	187	1	0	1	1	0	0	0	0	0	8466	603	21	0	1666	0	KRT2	12	53045638	In_Frame_Ins	INS	-	TCGA-DD-AADD-01A-11D-A40R-10	1980667	53045638	80806257	57	27718										
GRIP1	23426	hgsc.bcm.edu	37	chr12	66786264	66786264	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tagaaatagggaacttcttgGggctcgatgctgactgggct	14	7	1	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:66786264G>A	ENST00000398016.3	-	18	2200	c.2132C>T	c.(2131-2133)cCc>cTc	p.P711L	GRIP1_ENST00000542021.1_5'Flank|GRIP1_ENST00000359742.4_Missense_Mutation_p.P763L|GRIP1_ENST00000286445.7_Missense_Mutation_p.P763L	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GAACTTCTTGGGGCTCGATGC	0.463																																					p.P711L		Atlas-SNP	.											.	GRIP1	106	.	0			c.C2132T						.						111	108	109					12																	66786264		1915	4137	6052	SO:0001583	missense	23426	exon18			TTCTTGGGGCTCG	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.2132C>T	chr12.hg19:g.66786264G>A	ENSP00000381098:p.Pro711Leu	142.0	0.0		103.0	64.0	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	hg19	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.68|13.68	2.309870|2.309870	0.40895|0.40895	.|.	.|.	ENSG00000155974|ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215|ENST00000538164	T;T;T;T;T;T|T	0.24151|0.15139	1.87;1.88;1.89;1.89;1.97;1.98|2.45	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	0.188887|0.188887	0.45867|0.45867	D|D	0.000336|0.000336	T|T	0.37732|0.37732	0.1014|0.1014	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	B;P;B;P|.	0.40398|.	0.023;0.565;0.004;0.716|.	B;B;B;B|.	0.36134|.	0.028;0.218;0.007;0.21|.	T|T	0.05599|0.05599	-1.0875|-1.0875	9|7	.|.	.|.	.|.	-14.5159|-14.5159	18.2146|18.2146	0.89881|0.89881	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	711;763;711;763|.	F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2|.	.;GRIP1_HUMAN;.;.|.	L|S	711;763;763;711;655;603|578	ENSP00000381098:P711L;ENSP00000352780:P763L;ENSP00000286445:P763L;ENSP00000446047:P711L;ENSP00000446024:P655L;ENSP00000446011:P603L|ENSP00000439053:P578S	.|.	P|P	-|-	2|1	0|0	GRIP1|GRIP1	65072531|65072531	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	5.802000|5.802000	0.69122|0.69122	2.622000|2.622000	0.88805|0.88805	0.462000|0.462000	0.41574|0.41574	CCC|CCA	.	.		0.463	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			A	66786264	G	A	66786264	3	1	187	1	0	0	0	0	1	0	0	0	6796	1232	43	3	1126	3	GRIP1	12	66786264	Missense_Mutation	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	13740626	66786264	67065631	58	27719										
TRHDE	29953	hgsc.bcm.edu	37	chr12	73014936	73014936	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	catatatcaagcttgggtggCcgaaaaataattttaatgga	9	5	1	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:73014936C>A	ENST00000261180.4	+	14	2479	c.2383C>A	c.(2383-2385)Ccg>Acg	p.P795T		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	795					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						GCTTGGGTGGCCGAAAAATAA	0.313																																					p.P795T		Atlas-SNP	.											.	TRHDE	194	.	0			c.C2383A						.						107	101	103					12																	73014936		2203	4300	6503	SO:0001583	missense	29953	exon14			GGGTGGCCGAAAA	AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"pyroglutamyl-peptidase II", "pyroglutamyl aminopeptidase II", "TRH-specific aminopeptidase"	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.2383C>A	chr12.hg19:g.73014936C>A	ENSP00000261180:p.Pro795Thr	143.0	0.0		110.0	61.0	NM_013381	A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	hg19	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	C	9.033	0.987767	0.18966	.	.	ENSG00000072657	ENST00000261180	T	0.05855	3.38	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.03871	0.0109	N	0.02765	-0.5	0.80722	D	1	B	0.26258	0.145	B	0.30105	0.111	T	0.54549	-0.8277	10	0.13470	T	0.59	.	19.1084	0.93307	0.0:1.0:0.0:0.0	.	795	Q9UKU6	TRHDE_HUMAN	T	795	ENSP00000261180:P795T	ENSP00000261180:P795T	P	+	1	0	TRHDE	71301203	1.000000	0.71417	1.000000	0.80357	0.530000	0.34684	6.052000	0.71080	2.820000	0.97059	0.650000	0.86243	CCG	.	.		0.313	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		A	73014936	C	A	73014936	3	1	187	1	0	0	0	0	1	0	0	0	16494	739	26	3	2437	3	TRHDE	12	73014936	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	6228672	73014936	60836959	59	27720										
ZNF10	7556	hgsc.bcm.edu	37	chr12	133732822	133732822	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	aaagaatgtggaaaatccttCagctggttctctcaccttgt	8	9	3	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr12:133732822C>T	ENST00000248211.6	+	5	1212	c.990C>T	c.(988-990)ttC>ttT	p.F330F	ZNF268_ENST00000416488.1_Intron|ZNF10_ENST00000426665.2_Silent_p.F330F|CTD-2140B24.4_ENST00000540096.2_Intron|ZNF10_ENST00000402932.2_Silent_p.F196F	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	330					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		GAAAATCCTTCAGCTGGTTCT	0.423																																					p.F330F		Atlas-SNP	.											.	ZNF10	58	.	0			c.C990T						.						97	104	102					12																	133732822		2203	4300	6503	SO:0001819	synonymous_variant	7556	exon5			ATCCTTCAGCTGG	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"Zinc fingers, C2H2-type", "-"	12879	protein-coding gene	gene with protein product		194538	"zinc finger protein 10 (KOX 1)"			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.990C>T	chr12.hg19:g.133732822C>T		90.0	0.0		71.0	21.0	NM_015394	B2RBS1|Q8TC91	Silent	SNP	ENST00000248211.6	hg19	CCDS9283.1																																																																																			.	.		0.423	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394		T	133732822	C	T	133732822	2	4	187	1	0	0	0	0	0	0	0	1	17727	825	29	3		3	ZNF10	12	133732822	Silent	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	60717886	133732822	119073	60	27721										
C13orf23	80209	hgsc.bcm.edu	37	chr13	39587547	39587547	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cctttgaaggccgagggagtAggacttgtgggctcagtttt	15	7	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr13:39587547A>G	ENST00000352251.3	-	11	2675	c.1842T>C	c.(1840-1842)ccT>ccC	p.P614P	PROSER1_ENST00000484434.3_Intron|PROSER1_ENST00000350125.3_Silent_p.P592P	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	614	Ser-rich.							p.P614P(1)									CCGAGGGAGTAGGACTTGTGG	0.502																																					p.P614P		Atlas-SNP	.											C13orf23,rectum,carcinoma,0,1	.	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1842C						.						155	164	161					13																	39587547		2203	4300	6503	SO:0001819	synonymous_variant	80209	exon11			GGGAGTAGGACTT	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.1842T>C	chr13.hg19:g.39587547A>G		103.0	0.0		50.0	2.0	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	hg19	CCDS9368.2																																																																																			.	.		0.502	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		G	39587547	A	G	39587547	2	3	187	1	0	0	0	0	0	0	0	1	1723	407	15	2		2	C13orf23	13	39587547	Silent	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10		39587547	75582331	61	27722										
COCH	1690	hgsc.bcm.edu	37	chr14	31355229	31355229	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gtttccaacatagccaagacTtttgaaatctcggacattgg	8	9	1	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr14:31355229T>G	ENST00000396618.3	+	11	1244	c.1188T>G	c.(1186-1188)acT>acG	p.T396T	COCH_ENST00000216361.4_Silent_p.T396T|COCH_ENST00000460581.2_Silent_p.T284T|RP11-829H16.3_ENST00000556786.1_RNA|RP11-829H16.3_ENST00000468444.2_RNA|RP11-829H16.3_ENST00000555421.1_RNA|RP11-829H16.3_ENST00000555108.1_RNA|COCH_ENST00000382493.4_Silent_p.T247T|COCH_ENST00000475087.1_Silent_p.T396T	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	396	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)		TAGCCAAGACTTTTGAAATCT	0.423																																					p.T396T		Atlas-SNP	.											.	COCH	54	.	0			c.T1188G						.						112	99	103					14																	31355229		2203	4300	6503	SO:0001819	synonymous_variant	1690	exon11			CAAGACTTTTGAA		CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"coagulation factor C (Limulus polyphemus homolog); cochlin", "coagulation factor C homolog, cochlin (Limulus polyphemus)"	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.1188T>G	chr14.hg19:g.31355229T>G		117.0	0.0		65.0	56.0	NM_004086	A8K9K9|D3DS84|Q96IU6	Silent	SNP	ENST00000396618.3	hg19	CCDS9640.1	.	.	.	.	.	.	.	.	.	.	T	11.95	1.792419	0.31685	.	.	ENSG00000100473	ENST00000468826	.	.	.	6.02	-4.42	0.03579	.	.	.	.	.	T	0.35422	0.0931	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41787	-0.9489	4	.	.	.	-7.0074	0.2487	0.00202	0.2674:0.1948:0.2678:0.2701	.	.	.	.	R	280	.	.	L	+	2	0	COCH	30424980	0.146000	0.22672	0.989000	0.46669	0.986000	0.74619	-0.592000	0.05747	-0.345000	0.08325	-0.267000	0.10333	CTT	.	.		0.423	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086		G	31355229	T	G	31355229	2	3	187	1	0	0	0	0	0	0	0	1	3658	1596	56	5		5	COCH	14	31355229	Silent	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10		31355229	75994311	62	27723										
FANCM	57697	hgsc.bcm.edu	37	chr14	45618114	45618114	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gaagattctccagatattttGacatattctcatgaaagaaa	6	6	2	5			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr14:45618114G>T	ENST00000267430.5	+	4	919	c.834G>T	c.(832-834)ttG>ttT	p.L278F	FANCM_ENST00000542564.2_Missense_Mutation_p.L252F|FANCM_ENST00000556036.1_Missense_Mutation_p.L278F	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	278					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						CAGATATTTTGACATATTCTC	0.353								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.L278F		Atlas-SNP	.											.	FANCM	225	.	0			c.G834T						.						71	71	71					14																	45618114		2203	4299	6502	SO:0001583	missense	57697	exon4	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TATTTTGACATAT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.834G>T	chr14.hg19:g.45618114G>T	ENSP00000267430:p.Leu278Phe	106.0	0.0		43.0	37.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	G	13.80	2.346083	0.41599	.	.	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564	T;T;T	0.06068	3.35;3.35;3.35	5.55	-1.14	0.09741	DEAD-like helicase (1);	0.138112	0.45867	D	0.000324	T	0.10895	0.0266	L	0.57536	1.79	0.27474	N	0.952795	D;D;P	0.61697	0.99;0.99;0.642	P;P;B	0.57679	0.825;0.825;0.397	T	0.10109	-1.0644	10	0.36615	T	0.2	.	5.0477	0.14492	0.3834:0.2611:0.3555:0.0	.	252;278;278	B2RTQ9;Q8IYD8;Q8IYD8-2	.;FANCM_HUMAN;.	F	278;278;252	ENSP00000450596:L278F;ENSP00000267430:L278F;ENSP00000442493:L252F	ENSP00000267430:L278F	L	+	3	2	FANCM	44687864	1.000000	0.71417	0.925000	0.36789	0.556000	0.35491	1.200000	0.32247	-0.101000	0.12219	0.650000	0.86243	TTG	.	.		0.353	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45618114	G	T	45618114	3	4	187	1	0	0	0	0	1	0	0	0	5679	1281	45	3	848	3	FANCM	14	45618114	Missense_Mutation	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	14262885	45618114	61731426	63	27724										
SMEK1	55671	hgsc.bcm.edu	37	chr14	91943274	91943274	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	aattcctgtcttttttcctcAtctgttgcttcatctgttag	5	10	5	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr14:91943274A>T	ENST00000554943.1	-	5	1087	c.972T>A	c.(970-972)gaT>gaA	p.D324E	SMEK1_ENST00000337238.4_Missense_Mutation_p.D324E|SMEK1_ENST00000554684.1_Missense_Mutation_p.D324E|SMEK1_ENST00000428424.2_Missense_Mutation_p.D85E|SMEK1_ENST00000555462.1_Missense_Mutation_p.D85E			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	324					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		TTTTTTCCTCATCTGTTGCTT	0.373																																					p.D324E		Atlas-SNP	.											.	SMEK1	94	.	0			c.T972A						.						135	124	128					14																	91943274		2200	4297	6497	SO:0001583	missense	55671	exon6			TTCCTCATCTGTT	AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"KIAA2010"	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.972T>A	chr14.hg19:g.91943274A>T	ENSP00000450883:p.Asp324Glu	202.0	0.0		110.0	90.0	NM_032560	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Missense_Mutation	SNP	ENST00000554943.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.57|17.57	3.421696|3.421696	0.62622|0.62622	.|.	.|.	ENSG00000100796|ENSG00000100796	ENST00000554684;ENST00000337238;ENST00000428424;ENST00000554943;ENST00000555462;ENST00000554390;ENST00000555029;ENST00000417249|ENST00000555470	T;T;T;T;T;T;T|.	0.35048|.	1.58;1.58;1.33;1.58;1.33;1.58;1.33|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Armadillo-like helical (1);Domain of unknown function DUF625 (1);Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.49304|.	0.1549|.	N|N	0.15975|0.15975	0.35|0.35	0.80722|0.80722	D|D	1|1	D;B;B;B|.	0.61697|.	0.99;0.004;0.025;0.02|.	D;B;B;B|.	0.73380|.	0.98;0.004;0.093;0.02|.	T|.	0.46289|.	-0.9202|.	10|.	0.15952|.	T|.	0.53|.	-19.3695|-19.3695	16.3948|16.3948	0.83586|0.83586	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	85;324;324;324|.	Q6IN85-4;G3V5Z3;Q6IN85;Q6IN85-2|.	.;.;P4R3A_HUMAN;.|.	E|R	324;324;85;324;85;324;85;114|119	ENSP00000450864:D324E;ENSP00000337125:D324E;ENSP00000392704:D85E;ENSP00000450883:D324E;ENSP00000450891:D85E;ENSP00000452596:D324E;ENSP00000452257:D85E|.	ENSP00000337125:D324E|.	D|X	-|-	3|1	2|0	SMEK1|SMEK1	91013027|91013027	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.121000|4.121000	0.57904|0.57904	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	GAT|TGA	.	.		0.373	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560		T	91943274	A	T	91943274	3	4	187	1	0	0	0	0	1	0	0	0	14808	214	8	4	1534	4	SMEK1	14	91943274	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	46325160	91943274	15406266	64	27725										
PPP4R4	57718	hgsc.bcm.edu	37	chr14	94711989	94711989	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	atgtctactggtggagaaagCagtgttcaagaaaataaggt	12	4	2	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr14:94711989C>T	ENST00000304338.3	+	13	1564	c.1410C>T	c.(1408-1410)agC>agT	p.S470S		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	470					negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)			NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						GTGGAGAAAGCAGTGTTCAAG	0.338																																					p.S470S		Atlas-SNP	.											.	PPP4R4	107	.	0			c.C1410T						.						98	100	100					14																	94711989		2203	4298	6501	SO:0001819	synonymous_variant	57718	exon13			AGAAAGCAGTGTT	AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	23788	protein-coding gene	gene with protein product	"cilia and flagella associated protein 14"		"KIAA1622"	KIAA1622		18715871	Standard	NM_020958		Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.1410C>T	chr14.hg19:g.94711989C>T		276.0	0.0		151.0	7.0	NM_058237	Q9BUF8|Q9HCF0	Silent	SNP	ENST00000304338.3	hg19	CCDS9921.1																																																																																			.	.		0.338	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		T	94711989	C	T	94711989	2	4	187	1	0	0	0	0	0	0	0	1	12417	709	25	3		3	PPP4R4	14	94711989	Silent	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	2768715	94711989	12637551	65	27726										
APBA2	321	hgsc.bcm.edu	37	chr15	29406146	29406146	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tgtgggccaccgcatcatcgAgatcaacgggcagagcgtgg	15	11	2	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr15:29406146A>G	ENST00000558402.1	+	15	2704	c.2105A>G	c.(2104-2106)gAg>gGg	p.E702G	APBA2_ENST00000411764.1_Missense_Mutation_p.E690G|APBA2_ENST00000561069.1_Missense_Mutation_p.E702G|APBA2_ENST00000558330.1_Missense_Mutation_p.E690G|APBA2_ENST00000558259.1_Missense_Mutation_p.E702G			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	702	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CGCATCATCGAGATCAACGGG	0.597																																					p.E702G		Atlas-SNP	.											.	APBA2	132	.	0			c.A2105G						.						127	96	107					15																	29406146		2203	4300	6503	SO:0001583	missense	321	exon13			TCATCGAGATCAA	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.2105A>G	chr15.hg19:g.29406146A>G	ENSP00000453293:p.Glu702Gly	72.0	0.0		51.0	26.0	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	hg19	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.727396	0.89390	.	.	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.57752	0.38	4.36	4.36	0.52297	PDZ/DHR/GLGF (4);	0.174542	0.34484	N	0.003940	T	0.77274	0.4106	M	0.92219	3.285	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.981	T	0.83050	-0.0153	10	0.87932	D	0	.	12.7391	0.57241	1.0:0.0:0.0:0.0	.	690;702	E9PGI4;Q99767	.;APBA2_HUMAN	G	690;702	ENSP00000409312:E690G	ENSP00000219865:E702G	E	+	2	0	APBA2	27193438	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.105000	0.94246	1.595000	0.50050	0.379000	0.24179	GAG	.	.		0.597	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		G	29406146	A	G	29406146	3	3	187	1	0	0	0	0	1	0	0	0	757	304	11	2	2147	2	APBA2	15	29406146	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10		29406146	73125246	66	27727										
LPCAT4	254531	hgsc.bcm.edu	37	chr15	34651465	34651465	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gtaggtgctgaagagtttccCatagagtgggtcatggaggg	17	5	1	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr15:34651465C>T	ENST00000314891.6	-	14	1615	c.1438G>A	c.(1438-1440)Ggg>Agg	p.G480R		NM_153613.2	NP_705841.2	Q643R3	LPCT4_HUMAN	lysophosphatidylcholine acyltransferase 4	480					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphoethanolamine O-acyltransferase activity (GO:0047166)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|calcium ion binding (GO:0005509)|lysophospholipid acyltransferase activity (GO:0071617)			NS(1)|breast(1)|large_intestine(2)|lung(5)|prostate(1)	10						AAGAGTTTCCCATAGAGTGGG	0.537																																					p.G480R		Atlas-SNP	.											.	LPCAT4	36	.	0			c.G1438A						.						87	87	87					15																	34651465		2196	4287	6483	SO:0001583	missense	254531	exon14			GTTTCCCATAGAG	AF542964	CCDS32191.1	15q14	2008-07-02	2008-06-24	2008-06-24		ENSG00000176454			30059	protein-coding gene	gene with protein product	"lysophosphatidylethanolamine acyltransferase 2"	612039	"acyltransferase like 3", "1-acylglycerol-3-phosphate O-acyltransferase 7 (lysophosphatidic acid acyltransferase, eta)"	AYTL3, AGPAT7		8619474, 9110174, 16243729, 18458083	Standard	XR_243087		Approved	FLJ10257, LPAAT-eta, LPEAT2	uc001zig.3	Q643R3		ENST00000314891.6:c.1438G>A	chr15.hg19:g.34651465C>T	ENSP00000317300:p.Gly480Arg	102.0	0.0		105.0	44.0	NM_153613	A8K2K8|O43412|Q7Z4P4|Q8IUL7|Q8TB38	Missense_Mutation	SNP	ENST00000314891.6	hg19	CCDS32191.1	.	.	.	.	.	.	.	.	.	.	C	11.30	1.596583	0.28445	.	.	ENSG00000176454	ENST00000314891	T	0.79749	-1.3	5.3	3.4	0.38934	.	0.434655	0.24912	N	0.034617	T	0.68311	0.2987	L	0.35414	1.06	0.32038	N	0.598591	B	0.02656	0.0	B	0.04013	0.001	T	0.63251	-0.6679	10	0.24483	T	0.36	-8.8618	9.5273	0.39171	0.0:0.8305:0.0:0.1695	.	480	Q643R3	LPCT4_HUMAN	R	480	ENSP00000317300:G480R	ENSP00000317300:G480R	G	-	1	0	LPCAT4	32438757	0.993000	0.37304	0.991000	0.47740	0.994000	0.84299	0.747000	0.26290	0.592000	0.29728	0.491000	0.48974	GGG	.	.		0.537	LPCAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418028.2	NM_153613		T	34651465	C	T	34651465	3	4	187	1	0	0	0	0	1	0	0	0	8922	594	21	3	140	3	LPCAT4	15	34651465	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	5245319	34651465	67879927	67	27728										
TMEM87A	25963	hgsc.bcm.edu	37	chr15	42536362	42536362	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	agtttgcaatggttcatgcaTtgcctagaaagggaaaaggg	13	5	1	1	rs145141787		TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr15:42536362T>C	ENST00000389834.4	-	7	772	c.508A>G	c.(508-510)Atg>Gtg	p.M170V	TMEM87A_ENST00000448392.1_Missense_Mutation_p.M109V	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	170						integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		GGTTCATGCATTGCCTAGAAA	0.343																																					p.M170V		Atlas-SNP	.											.	TMEM87A	56	.	0			c.A508G						.	T	VAL/MET	0,4406		0,0,2203	78	77	77		508	4.9	1	15	dbSNP_134	77	3,8593	3.0+/-9.4	0,3,4295	yes	missense	TMEM87A	NM_015497.3	21	0,3,6498	CC,CT,TT		0.0349,0.0,0.0231	benign	170/556	42536362	3,12999	2203	4298	6501	SO:0001583	missense	25963	exon7			CATGCATTGCCTA	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.508A>G	chr15.hg19:g.42536362T>C	ENSP00000374484:p.Met170Val	170.0	0.0		154.0	66.0	NM_015497	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Missense_Mutation	SNP	ENST00000389834.4	hg19	CCDS32205.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.473839	0.43942	0.0	3.49E-4	ENSG00000103978	ENST00000389834;ENST00000448392;ENST00000535305	.	.	.	4.93	4.93	0.64822	.	0.144336	0.64402	D	0.000009	T	0.37019	0.0988	N	0.24115	0.695	0.33966	D	0.646276	B;B	0.13594	0.002;0.008	B;B	0.20577	0.002;0.03	T	0.42682	-0.9437	9	0.12430	T	0.62	-18.1446	13.2976	0.60307	0.0:0.0:0.0:1.0	.	170;109	Q8NBN3;Q8NBN3-3	TM87A_HUMAN;.	V	170;109;146	.	ENSP00000374484:M170V	M	-	1	0	TMEM87A	40323654	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.537000	0.36083	2.077000	0.62373	0.477000	0.44152	ATG	.	T|1.000;C|0.000		0.343	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497		C	42536362	T	C	42536362	3	2	187	1	0	0	0	0	1	0	0	0	16225	1493	52	2	1215	2	TMEM87A	15	42536362	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	7884897	42536362	59995030	68	27729										
DUOX1	53905	hgsc.bcm.edu	37	chr15	45437208	45437208	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gctgcgggagcaggagctgaTgagagcagctgtgacacggg	19	8	0	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr15:45437208T>A	ENST00000321429.4	+	19	2659	c.2252T>A	c.(2251-2253)aTg>aAg	p.M751K	DUOX1_ENST00000561166.1_Missense_Mutation_p.M397K|DUOX1_ENST00000389037.3_Missense_Mutation_p.M751K	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	751					cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CAGGAGCTGATGAGAGCAGCT	0.587																																					p.M751K		Atlas-SNP	.											.	DUOX1	125	.	0			c.T2252A						.						100	99	99					15																	45437208		2198	4298	6496	SO:0001583	missense	53905	exon19			AGCTGATGAGAGC	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.2252T>A	chr15.hg19:g.45437208T>A	ENSP00000317997:p.Met751Lys	110.0	0.0		106.0	52.0	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	hg19	CCDS32221.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.659459	0.47467	.	.	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	D;D	0.86030	-2.06;-2.06	4.7	4.7	0.59300	.	0.286130	0.40908	D	0.000981	T	0.79257	0.4415	L	0.40543	1.245	0.49213	D	0.99976	B	0.11235	0.004	B	0.09377	0.004	T	0.75972	-0.3129	10	0.49607	T	0.09	-16.6098	12.4113	0.55469	0.0:0.0:0.0:1.0	.	751	Q9NRD9	DUOX1_HUMAN	K	751	ENSP00000317997:M751K;ENSP00000373689:M751K	ENSP00000317997:M751K	M	+	2	0	DUOX1	43224500	1.000000	0.71417	0.974000	0.42286	0.738000	0.42128	7.282000	0.78630	2.096000	0.63516	0.528000	0.53228	ATG	.	.		0.587	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		A	45437208	T	A	45437208	3	1	187	1	0	0	0	0	1	0	0	0	4802	1464	51	4	2318	4	DUOX1	15	45437208	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	2900846	45437208	57094184	69	27730										
WDR72	256764	hgsc.bcm.edu	37	chr15	53992110	53992110	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	agagccacggaatggtcaccGcacacacagcaaattatctg	9	12	2	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr15:53992110G>A	ENST00000396328.1	-	13	1841	c.1602C>T	c.(1600-1602)tgC>tgT	p.C534C	WDR72_ENST00000557913.1_Silent_p.C531C|WDR72_ENST00000559418.1_Silent_p.C544C|WDR72_ENST00000360509.5_Silent_p.C534C	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	534								p.C534*(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		AATGGTCACCGCACACACAGC	0.448																																					p.C534C		Atlas-SNP	.											WDR72,NS,carcinoma,0,2	WDR72	177	.	1	Substitution - Nonsense(1)	endometrium(1)	c.C1602T						.						103	108	106					15																	53992110		2194	4293	6487	SO:0001819	synonymous_variant	256764	exon13			GTCACCGCACACA	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"WD repeat domain containing"	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.1602C>T	chr15.hg19:g.53992110G>A		163.0	0.0		149.0	58.0	NM_182758	Q7Z3I3|Q8N8X2	Silent	SNP	ENST00000396328.1	hg19	CCDS10151.1																																																																																			.	.		0.448	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		A	53992110	G	A	53992110	2	1	187	1	0	0	0	0	0	0	0	1	17337	1079	38	1		1	WDR72	15	53992110	Silent	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	8554902	53992110	48539282	70	27731										
SCAMP2	10066	hgsc.bcm.edu	37	chr15	75142867	75142867	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tcactcacctaaaggccttaTagatgggtcggtaccaacaa	8	11	2	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr15:75142867T>C	ENST00000268099.9	-	6	729	c.620A>G	c.(619-621)tAt>tGt	p.Y207C		NM_005697.3	NP_005688.2	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2	207	Interaction with SLC9A7.				post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)|trans-Golgi network membrane (GO:0032588)|transport vesicle (GO:0030133)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	9						AAAGGCCTTATAGATGGGTCG	0.562																																					p.Y207C		Atlas-SNP	.											.	SCAMP2	18	.	0			c.A620G						.						149	150	149					15																	75142867		2197	4295	6492	SO:0001583	missense	10066	exon6			GCCTTATAGATGG	AF005038	CCDS10271.1	15q23-q25	2013-02-21			ENSG00000140497	ENSG00000140497		"Secretory carrier membrane proteins"	10564	protein-coding gene	gene with protein product		606912				9378760	Standard	NM_005697		Approved		uc002azb.1	O15127	OTTHUMG00000142817	ENST00000268099.9:c.620A>G	chr15.hg19:g.75142867T>C	ENSP00000268099:p.Tyr207Cys	87.0	0.0		81.0	35.0	NM_005697	B2RDF0|Q9BQE8	Missense_Mutation	SNP	ENST00000268099.9	hg19	CCDS10271.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.189909	0.78789	.	.	ENSG00000140497	ENST00000268099;ENST00000543345	T	0.55413	0.52	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.78039	0.4221	M	0.92649	3.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83939	0.0310	10	0.87932	D	0	.	13.7663	0.62997	0.0:0.0:0.0:1.0	.	207;176	O15127;B3KU14	SCAM2_HUMAN;.	C	207;176	ENSP00000268099:Y207C	ENSP00000268099:Y207C	Y	-	2	0	SCAMP2	72929920	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	7.997000	0.88414	1.915000	0.55452	0.402000	0.26972	TAT	.	.		0.562	SCAMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286403.3	NM_005697		C	75142867	T	C	75142867	3	2	187	1	0	0	0	0	1	0	0	0	13886	1406	49	2	385	2	SCAMP2	15	75142867	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	21150757	75142867	27388525	71	27732										
TP53	7157	hgsc.bcm.edu	37	chr17	7578190	7578190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	accagacctcaggcggctcaTagggcaccaccacactatgt	9	15	2	1	rs121912666		TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr17:7578190T>C	ENST00000269305.4	-	6	848	c.659A>G	c.(658-660)tAt>tGt	p.Y220C	TP53_ENST00000455263.2_Missense_Mutation_p.Y220C|TP53_ENST00000420246.2_Missense_Mutation_p.Y220C|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.Y220C|TP53_ENST00000359597.4_Missense_Mutation_p.Y220C|TP53_ENST00000445888.2_Missense_Mutation_p.Y220C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	220	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:9450901}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGGCGGCTCATAGGGCACCAC	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y220C	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	343	Substitution - Missense(315)|Unknown(11)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)|Insertion - Frameshift(1)	ovary(55)|breast(54)|lung(37)|upper_aerodigestive_tract(35)|urinary_tract(19)|oesophagus(19)|large_intestine(17)|liver(17)|central_nervous_system(16)|stomach(15)|haematopoietic_and_lymphoid_tissue(15)|endometrium(14)|soft_tissue(8)|biliary_tract(6)|bone(5)|pancreas(4)|prostate(4)|peritoneum(2)|small_intestine(1)	c.A659G	GRCh37	CM015378|CM951227	TP53	M	rs121912666	.						102	94	97					17																	7578190		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGCTCATAGGGCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.659A>G	chr17.hg19:g.7578190T>C	ENSP00000269305:p.Tyr220Cys	124.0	0.0		54.0	48.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.248510	0.80024	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99840	-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.89287	3.02	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.996;1.0;0.999;0.998;1.0	D	0.96735	0.9542	10	0.87932	D	0	-1.87	13.4753	0.61306	0.0:0.0:0.0:1.0	.	181;220;220;127;220;220;220	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	220;220;220;220;220;220;209;127;88;127	ENSP00000410739:Y220C;ENSP00000352610:Y220C;ENSP00000269305:Y220C;ENSP00000398846:Y220C;ENSP00000391127:Y220C;ENSP00000391478:Y220C;ENSP00000425104:Y88C;ENSP00000423862:Y127C	ENSP00000269305:Y220C	Y	-	2	0	TP53	7518915	1.000000	0.71417	0.585000	0.28666	0.993000	0.82548	6.232000	0.72313	2.128000	0.65567	0.460000	0.39030	TAT	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578190	T	C	7578190	3	2	187	1	0	0	0	0	1	0	0	0	16396	1406	49	2	635	2	TP53	17	7578190	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10		7578190	73617020	72	27733										
UTP6	55813	hgsc.bcm.edu	37	chr17	30207638	30207638	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tcatacacagcacagcacctCtcctccttccggccgacctc	5	20	2	0	rs139786553		TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr17:30207638C>A	ENST00000261708.4	-	11	1058	c.921G>T	c.(919-921)gaG>gaT	p.E307D	CTC-542B22.2_ENST00000583236.1_lincRNA	NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	307					rRNA processing (GO:0006364)	nucleolus (GO:0005730)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)	21		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				CACAGCACCTCTCCTCCTTCC	0.493																																					p.E307D		Atlas-SNP	.											UTP6,NS,carcinoma,0,1	UTP6	46	.	0			c.G921T						.						213	184	194					17																	30207638		2203	4300	6503	SO:0001583	missense	55813	exon11			GCACCTCTCCTCC	AF116631	CCDS11269.1	17q11.2	2010-06-24	2006-05-16	2006-05-16	ENSG00000108651	ENSG00000108651			18279	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated antigen 66"		"chromosome 17 open reading frame 40"	C17orf40		10843809, 16138909	Standard	NM_018428		Approved	HCA66	uc002hgr.3	Q9NYH9	OTTHUMG00000132815	ENST00000261708.4:c.921G>T	chr17.hg19:g.30207638C>A	ENSP00000261708:p.Glu307Asp	83.0	0.0		72.0	32.0	NM_018428	Q8IX96|Q96BL2|Q9NQ91	Missense_Mutation	SNP	ENST00000261708.4	hg19	CCDS11269.1	.	.	.	.	.	.	.	.	.	.	C	9.512	1.105917	0.20632	.	.	ENSG00000108651	ENST00000261708	T	0.40476	1.03	5.16	1.94	0.25998	.	0.046236	0.85682	N	0.000000	T	0.34832	0.0911	M	0.71581	2.175	0.53005	D	0.999968	B;B;B	0.16603	0.018;0.01;0.01	B;B;B	0.16722	0.016;0.014;0.008	T	0.09122	-1.0689	10	0.20046	T	0.44	-15.0264	4.7898	0.13243	0.0:0.4677:0.1651:0.3672	.	307;307;307	B4DSL9;B3KQ21;Q9NYH9	.;.;UTP6_HUMAN	D	307	ENSP00000261708:E307D	ENSP00000261708:E307D	E	-	3	2	UTP6	27231751	0.984000	0.35163	0.998000	0.56505	0.299000	0.27559	0.097000	0.15168	0.239000	0.21243	0.563000	0.77884	GAG	.	C|1.000;G|0.000		0.493	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428		A	30207638	C	A	30207638	3	1	187	1	0	0	0	0	1	0	0	0	17117	912	32	3	908	3	UTP6	17	30207638	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	22629448	30207638	50987572	73	27734										
DHX8	1659	hgsc.bcm.edu	37	chr17	41599464	41599471	+	Frame_Shift_Del	DEL	AAGGCCAT	AAGGCCAT	-													0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	agtccacagtccgagtgcagAaggccatctgcagtgggttc							TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	AAGGCCAT	AAGGCCAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr17:41599464_41599471delAAGGCCAT	ENST00000262415.3	+	22	3385_3392	c.3313_3320delAAGGCCAT	c.(3313-3321)aaggccatcfs	p.KAI1105fs	DHX8_ENST00000540306.1_Frame_Shift_Del_p.KAI1105fs	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	1105					ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		CCGAGTGCAGAAGGCCATCTGCAGTGGG	0.514																																					p.1104_1107del	NSCLC(56;1548 1661 49258 49987)	Atlas-INDEL	.											.	DHX8	98	.	0			c.3312_3319del						.																																			SO:0001589	frameshift_variant	1659	exon22			.	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"DEAH-boxes"	2749	protein-coding gene	gene with protein product		600396	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.3313_3320delAAGGCCAT	chr17.hg19:g.41599464_41599471delAAGGCCAT	ENSP00000262415:p.Lys1105fs	147.0	0.0		104.0	28.0	NM_004941		Frame_Shift_Del	DEL	ENST00000262415.3	hg19	CCDS11464.1																																																																																			.	.		0.514	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			-	41599471	AAGGCCAT	-	41599464	7	5	187	1	0	1	0	1	0	0	0	0	4517	247	9	0	3399	0	DHX8	17	41599464	Frame_Shift_Del	DEL	AAGGCCAT	TCGA-DD-AADD-01A-11D-A40R-10	11391826	41599464	39595746	74	27735										
MOCOS	55034	hgsc.bcm.edu	37	chr18	33775294	33775294	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	aaagcttcactagtgatctcAtggaaaacacttatggtaaa	7	7	2	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr18:33775294A>T	ENST00000261326.5	+	2	238	c.217A>T	c.(217-219)Atg>Ttg	p.M73L		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						TAGTGATCTCATGGAAAACAC	0.408																																					p.M73L		Atlas-SNP	.											.	MOCOS	84	.	0			c.A217T						.						112	114	114					18																	33775294		2203	4300	6503	SO:0001583	missense	55034	exon2			GATCTCATGGAAA	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.217A>T	chr18.hg19:g.33775294A>T	ENSP00000261326:p.Met73Leu	114.0	0.0		86.0	44.0	NM_017947		Missense_Mutation	SNP	ENST00000261326.5	hg19	CCDS11919.1	.	.	.	.	.	.	.	.	.	.	A	0.441	-0.898654	0.02472	.	.	ENSG00000075643	ENST00000261326	D	0.84873	-1.91	5.41	-0.141	0.13452	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.365157	0.28847	N	0.013948	T	0.66237	0.2769	N	0.20574	0.59	0.20563	N	0.999884	B	0.02656	0.0	B	0.04013	0.001	T	0.46679	-0.9174	10	0.21540	T	0.41	-10.9763	2.2817	0.04116	0.4034:0.3615:0.0883:0.1468	.	73	Q96EN8	MOCOS_HUMAN	L	73	ENSP00000261326:M73L	ENSP00000261326:M73L	M	+	1	0	MOCOS	32029292	0.549000	0.26481	0.993000	0.49108	0.103000	0.19146	0.384000	0.20668	0.030000	0.15379	0.460000	0.39030	ATG	.	.		0.408	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			T	33775294	A	T	33775294	3	4	187	1	0	0	0	0	1	0	0	0	9698	217	8	4	223	4	MOCOS	18	33775294	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10		33775294	44301954	75	27736										
PIGN	23556	hgsc.bcm.edu	37	chr18	59757812	59757812	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gtggaaagagagcttcatacCtaacaggtggggaaaggtag	15	5	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr18:59757812C>T	ENST00000357637.5	-	24	2596		c.e24-1		PIGN_ENST00000400334.3_Splice_Site	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N						C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				AGCTTCATACCTAACAGGTGG	0.318																																					.		Atlas-SNP	.											.	PIGN	62	.	0			c.2181-1G>A						.						65	59	61					18																	59757812		1815	4075	5890	SO:0001630	splice_region_variant	23556	exon24			TCATACCTAACAG	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.2181-1G>A	chr18.hg19:g.59757812C>T		88.0	0.0		79.0	23.0	NM_012327	Q7L8F8|Q8TC01|Q9NT05	Splice_Site	SNP	ENST00000357637.5	hg19	CCDS45879.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.535035	0.45073	.	.	ENSG00000197563	ENST00000357637;ENST00000400334	.	.	.	5.56	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4482	0.61153	0.0:0.9231:0.0:0.0769	.	.	.	.	.	-1	.	.	.	-	.	.	PIGN	57908792	1.000000	0.71417	0.960000	0.40013	0.441000	0.31987	6.668000	0.74457	1.359000	0.45940	0.491000	0.48974	.	.	.		0.318	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	Intron	T	59757812	C	T	59757812	5	4	187	1	0	0	0	0	0	0	1	0	11902	695	24	3	647	3	PIGN	18	59757812	Splice_Site	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	25982518	59757812	18319436	76	27737										
MUC16	94025	hgsc.bcm.edu	37	chr19	9026242	9026242	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	aacttcctggagccagtgcgAcgcatgtcctcctcgtactg	10	14	0	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr19:9026242A>T	ENST00000397910.4	-	14	36947	c.36744T>A	c.(36742-36744)cgT>cgA	p.R12248R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12250	SEA 2. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGCCAGTGCGACGCATGTCCT	0.552																																					p.R12248R		Atlas-SNP	.											.	MUC16	4315	.	0			c.T36744A						.						244	223	230					19																	9026242		2078	4214	6292	SO:0001819	synonymous_variant	94025	exon14			AGTGCGACGCATG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.36744T>A	chr19.hg19:g.9026242A>T		119.0	0.0		73.0	30.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.552	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9026242	A	T	9026242	2	4	187	1	0	0	0	0	0	0	0	1	9982	262	10	4		4	MUC16	19	9026242	Silent	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10		9026242	50102741	77	27738										
C19orf44	84167	hgsc.bcm.edu	37	chr19	16612008	16612009	+	Frame_Shift_Ins	INS	-	-	T													0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	agagagctgacagaatcctcINStctgggggtgcactcgaact							TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr19:16612008_16612009insT	ENST00000221671.3	+	2	561_562	c.405_406insT	c.(406-408)tctfs	p.S136fs	CTD-3222D19.2_ENST00000409035.1_Intron|C19orf44_ENST00000594035.1_Frame_Shift_Ins_p.S136fs	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	136										endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						ACAGAATCCTCTCTGGGGGTGC	0.515																																					p.L135fs		Atlas-INDEL	.											.	C19orf44	47	.	0			c.405_406insT						.																																			SO:0001589	frameshift_variant	84167	exon2			.	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.406dupT	chr19.hg19:g.16612009_16612009dupT	ENSP00000221671:p.Ser136fs	139.0	0.0		69.0	39.0	NM_032207	Q8N6Y7	Frame_Shift_Ins	INS	ENST00000221671.3	hg19	CCDS12345.1																																																																																			.	.		0.515	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207		T	16612009	-	T	16612008	7	5	187	1	0	1	1	0	0	0	0	0	1929	900	32	0	407	0	C19orf44	19	16612008	Frame_Shift_Ins	INS	-	TCGA-DD-AADD-01A-11D-A40R-10	7585766	16612008	42516975	78	27739										
NXNL1	115861	hgsc.bcm.edu	37	chr19	17571605	17571605	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tctccagcctgcgactgaccTcagcctccgtatccagctcg	8	18	2	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr19:17571605T>G	ENST00000301944.2	-	1	158	c.74A>C	c.(73-75)gAg>gCg	p.E25A	CTD-2521M24.10_ENST00000594663.1_5'UTR	NM_138454.1	NP_612463.1	Q96CM4	NXNL1_HUMAN	nucleoredoxin-like 1	25	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				photoreceptor cell maintenance (GO:0045494)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	6						GCGACTGACCTCAGCCTCCGT	0.607																																					p.E25A		Atlas-SNP	.											.	NXNL1	13	.	0			c.A74C						.						79	83	82					19																	17571605		2203	4300	6503	SO:0001583	missense	115861	exon1			CTGACCTCAGCCT	BC014127	CCDS12360.1	19p13.11	2014-05-21	2007-08-16	2007-08-16	ENSG00000171773	ENSG00000171773			25179	protein-coding gene	gene with protein product		608791	"thioredoxin-like 6"	TXNL6		12477932	Standard	NM_138454		Approved	RDCVF	uc002ngs.3	Q96CM4	OTTHUMG00000182798	ENST00000301944.2:c.74A>C	chr19.hg19:g.17571605T>G	ENSP00000305631:p.Glu25Ala	54.0	0.0		25.0	8.0	NM_138454	Q0QD37	Missense_Mutation	SNP	ENST00000301944.2	hg19	CCDS12360.1	.	.	.	.	.	.	.	.	.	.	t	11.62	1.692862	0.30052	.	.	ENSG00000171773	ENST00000301944	D	0.87966	-2.32	3.92	3.92	0.45320	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	D	0.88485	0.6449	L	0.43923	1.385	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	D	0.84469	0.0598	10	0.13108	T	0.6	-35.3915	10.7434	0.46166	0.0:0.0:0.0:1.0	.	25	Q96CM4	NXNL1_HUMAN	A	25	ENSP00000305631:E25A	ENSP00000305631:E25A	E	-	2	0	NXNL1	17432605	1.000000	0.71417	0.853000	0.33588	0.012000	0.07955	7.548000	0.82154	1.640000	0.50565	0.383000	0.25322	GAG	.	.		0.607	NXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463803.1	NM_138454		G	17571605	T	G	17571605	3	3	187	1	0	0	0	0	1	0	0	0	10797	1551	54	5	572	5	NXNL1	19	17571605	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	959597	17571605	41557378	79	27740										
DBP	1628	hgsc.bcm.edu	37	chr19	49134159	49134159	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gtagtgggacagctcctggcGcacggccacaacttcctgcc	12	15	0	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr19:49134159G>T	ENST00000222122.5	-	4	1356	c.913C>A	c.(913-915)Cgc>Agc	p.R305S	DBP_ENST00000593500.1_Missense_Mutation_p.R103S|DBP_ENST00000599385.1_Missense_Mutation_p.R103S	NM_001352.3	NP_001343.2	Q10586	DBP_HUMAN	D site of albumin promoter (albumin D-box) binding protein	305	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				liver development (GO:0001889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|rhythmic process (GO:0048511)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000112)|GBM - Glioblastoma multiforme(486;0.00615)|Epithelial(262;0.0155)		AGCTCCTGGCGCACGGCCACA	0.692																																					p.R305S		Atlas-SNP	.											.	DBP	16	.	0			c.C913A						.						20	21	21					19																	49134159		2202	4299	6501	SO:0001583	missense	1628	exon4			CCTGGCGCACGGC	U06936	CCDS12728.1	19q13.33	2013-09-20			ENSG00000105516	ENSG00000105516			2697	protein-coding gene	gene with protein product		124097				1535333, 7835883	Standard	XR_243907		Approved	DABP	uc002pjx.4	Q10586	OTTHUMG00000183319	ENST00000222122.5:c.913C>A	chr19.hg19:g.49134159G>T	ENSP00000222122:p.Arg305Ser	121.0	0.0		63.0	31.0	NM_001352	A2I2P4	Missense_Mutation	SNP	ENST00000222122.5	hg19	CCDS12728.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.434308	0.83776	.	.	ENSG00000105516	ENST00000222122	T	0.41758	0.99	4.28	4.28	0.50868	Basic-leucine zipper (bZIP) transcription factor (2);Basic leucine zipper (1);	0.000000	0.64402	U	0.000001	T	0.63355	0.2504	M	0.74647	2.275	0.80722	D	1	D	0.67145	0.996	D	0.74023	0.982	T	0.68584	-0.5370	10	0.87932	D	0	-9.8868	14.6085	0.68498	0.0:0.0:1.0:0.0	.	305	Q10586	DBP_HUMAN	S	305	ENSP00000222122:R305S	ENSP00000222122:R305S	R	-	1	0	DBP	53825971	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.018000	0.76406	2.364000	0.80123	0.563000	0.77884	CGC	.	.		0.692	DBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466167.1	NM_001352		T	49134159	G	T	49134159	3	4	187	1	0	0	0	0	1	0	0	0	4258	1087	38	1	68	1	DBP	19	49134159	Missense_Mutation	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10	31562554	49134159	9994824	80	27741										
C20orf103	24141	hgsc.bcm.edu	37	chr20	9496958	9496958	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ttggaggctgagcaaagtgcAgtttgtctacgactcctcgg	13	9	1	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr20:9496958A>C	ENST00000246070.2	+	4	917	c.425A>C	c.(424-426)cAg>cCg	p.Q142P	RP5-1119D9.4_ENST00000443469.1_RNA|LAMP5_ENST00000427562.2_Missense_Mutation_p.Q98P	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5	142						cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)											AGCAAAGTGCAGTTTGTCTAC	0.592																																					p.Q142P		Atlas-SNP	.											.	.	.	.	0			c.A425C						.						96	87	90					20																	9496958		2203	4300	6503	SO:0001583	missense	24141	exon4			AAGTGCAGTTTGT	AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"brain and dendritic cell associated LAMP"	614641	"chromosome 20 open reading frame 103"	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.425A>C	chr20.hg19:g.9496958A>C	ENSP00000246070:p.Gln142Pro	103.0	0.0		111.0	42.0	NM_012261	B4DHZ7|B7Z9Z9	Missense_Mutation	SNP	ENST00000246070.2	hg19	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.086851	0.76642	.	.	ENSG00000125869	ENST00000246070;ENST00000427562	T;T	0.34859	1.34;1.34	5.98	5.98	0.97165	.	0.103761	0.64402	D	0.000002	T	0.45438	0.1342	L	0.29908	0.895	0.58432	D	0.999997	P;D	0.63046	0.731;0.992	B;D	0.64506	0.244;0.926	T	0.28202	-1.0051	9	.	.	.	-5.8979	14.2137	0.65779	1.0:0.0:0.0:0.0	.	98;142	Q9UJQ1-2;Q9UJQ1	.;CT103_HUMAN	P	142;98	ENSP00000246070:Q142P;ENSP00000406360:Q98P	.	Q	+	2	0	C20orf103	9444958	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.583000	0.74053	2.296000	0.77279	0.482000	0.46254	CAG	.	.		0.592	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261		C	9496958	A	C	9496958	3	2	187	1	0	0	0	0	1	0	0	0	2077	188	7	5	439	5	C20orf103	20	9496958	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10		9496958	53528562	81	27742										
BRWD1	54014	hgsc.bcm.edu	37	chr21	40570714	40570714	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ataaaattgtttggtttttcTattttgtcatcatctgaatc	5	5	4	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr21:40570714T>C	ENST00000333229.2	-	40	5955	c.5628A>G	c.(5626-5628)atA>atG	p.I1876M	BRWD1_ENST00000380800.3_Missense_Mutation_p.I1876M|BRWD1_ENST00000342449.3_Missense_Mutation_p.I1876M	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1876					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TTGGTTTTTCTATTTTGTCAT	0.348																																					p.I1876M	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A5628G						.						72	65	67					21																	40570714		2203	4300	6503	SO:0001583	missense	54014	exon40			TTTTTCTATTTTG	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.5628A>G	chr21.hg19:g.40570714T>C	ENSP00000330753:p.Ile1876Met	129.0	0.0		96.0	16.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	hg19	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	T	9.841	1.190939	0.21954	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.59083	0.29;0.29;0.29	5.41	1.51	0.23008	.	0.836393	0.10792	N	0.633643	T	0.33469	0.0864	N	0.08118	0	0.09310	N	1	B;B	0.27679	0.054;0.185	B;B	0.28232	0.004;0.087	T	0.24154	-1.0168	10	0.49607	T	0.09	-0.9373	4.5645	0.12177	0.166:0.2475:0.0:0.5865	.	1876;1876	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	M	1876	ENSP00000330753:I1876M;ENSP00000344333:I1876M;ENSP00000370178:I1876M	ENSP00000330753:I1876M	I	-	3	3	BRWD1	39492584	0.053000	0.20554	0.082000	0.20525	0.809000	0.45718	0.793000	0.26944	0.373000	0.24621	0.533000	0.62120	ATA	.	.		0.348	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		C	40570714	T	C	40570714	3	2	187	1	0	0	0	0	1	0	0	0	1527	1512	53	2	1585	2	BRWD1	21	40570714	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10		40570714	7559181	82	27743										
FTCD	10841	hgsc.bcm.edu	37	chr21	47557204	47557205	+	Frame_Shift_Ins	INS	-	-	A													0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tcaggttgatgagcacgttgINSaaatatgcgccaaacacgcc							TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr21:47557204_47557205insA	ENST00000291670.5	-	13	1530_1531	c.1487_1488insT	c.(1486-1488)ttcfs	p.F496fs	FTCD_ENST00000397743.1_Frame_Shift_Ins_p.Q482fs|FTCD_ENST00000359679.2_Frame_Shift_Ins_p.F496fs|FTCD_ENST00000397748.1_Frame_Shift_Ins_p.F496fs|FTCD_ENST00000498355.2_5'UTR|FTCD_ENST00000397746.3_Frame_Shift_Ins_p.F496fs|FTCD_ENST00000355384.2_Frame_Shift_Ins_p.Q482fs	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	496	Cyclodeaminase/cyclohydrolase. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	TGAGCACGTTGAAATATGCGCC	0.609																																					p.F496fs		Atlas-INDEL	.											.	FTCD	59	.	0			c.1488_1489insT						.																																			SO:0001589	frameshift_variant	10841	exon13			.	U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"formiminotransferase cyclodeaminase"			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.1488dupT	chr21.hg19:g.47557207_47557207dupA	ENSP00000291670:p.Phe496fs	44.0	0.0		42.0	32.0	NM_206965	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Frame_Shift_Ins	INS	ENST00000291670.5	hg19	CCDS13731.1																																																																																			.	.		0.609	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657		A	47557205	-	A	47557204	7	5	187	1	0	1	1	0	0	0	0	0	6089	1281	45	0	145	0	FTCD	21	47557204	Frame_Shift_Ins	INS	-	TCGA-DD-AADD-01A-11D-A40R-10	6986490	47557204	572691	83	27744										
SF3A1	10291	hgsc.bcm.edu	37	chr22	30731656	30731656	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	catacctggtccgtgagtggGagggtgaagaccagcacctg	15	10	0	3			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr22:30731656G>C	ENST00000215793.8	-	14	2347	c.2193C>G	c.(2191-2193)ctC>ctG	p.L731L	SF3A1_ENST00000439242.1_Silent_p.L666L	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	731	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						CCGTGAGTGGGAGGGTGAAGA	0.537																																					p.L731L		Atlas-SNP	.											.	SF3A1	61	.	0			c.C2193G						.						220	159	179					22																	30731656		2203	4300	6503	SO:0001819	synonymous_variant	10291	exon14			GAGTGGGAGGGTG	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"splicing factor 3a, subunit 1, 120kD"			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.2193C>G	chr22.hg19:g.30731656G>C		99.0	0.0		101.0	33.0	NM_005877	E9PAW1	Silent	SNP	ENST00000215793.8	hg19	CCDS13875.1																																																																																			.	.		0.537	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877		C	30731656	G	C	30731656	2	2	187	1	0	0	0	0	0	0	0	1	14161	1161	41	4		4	SF3A1	22	30731656	Silent	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10		30731656	20572910	84	27745										
HMGXB4	10042	hgsc.bcm.edu	37	chr22	35689064	35689064	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	tggccccttggcatgtctcaCcacacaactacctgaattga	7	14	1	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr22:35689064C>G	ENST00000216106.5	+	10	1846	c.1718C>G	c.(1717-1719)aCc>aGc	p.T573S	HMGXB4_ENST00000444518.2_Missense_Mutation_p.T464S	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	573					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GCATGTCTCACCACACAACTA	0.507																																					p.T573S		Atlas-SNP	.											.	HMGXB4	52	.	0			c.C1718G						.						218	179	192					22																	35689064		2203	4300	6503	SO:0001583	missense	10042	exon10			GTCTCACCACACA	AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"High mobility group / Non-canonical"	5003	protein-coding gene	gene with protein product		604702	"high-mobility group protein 2-like 1"	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.1718C>G	chr22.hg19:g.35689064C>G	ENSP00000216106:p.Thr573Ser	104.0	0.0		111.0	54.0	NM_001003681	O75672|O75673|Q9UMT5	Missense_Mutation	SNP	ENST00000216106.5	hg19	CCDS33641.1	.	.	.	.	.	.	.	.	.	.	C	34	5.302695	0.95601	.	.	ENSG00000100281	ENST00000444518;ENST00000216106	T;T	0.35421	1.31;1.37	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.63768	0.2539	M	0.76574	2.34	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.64732	-0.6338	10	0.87932	D	0	-18.3183	20.2562	0.98421	0.0:1.0:0.0:0.0	.	573	Q9UGU5	HMGX4_HUMAN	S	464;573	ENSP00000398302:T464S;ENSP00000216106:T573S	ENSP00000216106:T573S	T	+	2	0	HMGXB4	34019064	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.716000	0.84723	2.797000	0.96272	0.563000	0.77884	ACC	.	.		0.507	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487		G	35689064	C	G	35689064	3	3	187	1	0	0	0	0	1	0	0	0	7248	507	18	4	1752	4	HMGXB4	22	35689064	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	4957408	35689064	15615502	85	27746										
SH3BP1	23616	hgsc.bcm.edu	37	chr22	38049838	38049838	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cccccaaggtcaccaggagtCccccggagacagctgcccca	10	19	1	1	rs373477637		TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chr22:38049838C>T	ENST00000357436.4	+	17	1964	c.1651C>T	c.(1651-1653)Ccc>Tcc	p.P551S	Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000599616.1_Missense_Mutation_p.P487S	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	551					signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					CACCAGGAGTCCCCCGGAGAC	0.662																																					p.P551S		Atlas-SNP	.											.	SH3BP1	41	.	0			c.C1651T						.						43	41	41					22																	38049838		2200	4300	6500	SO:0001583	missense	23616	exon17			AGGAGTCCCCCGG		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"Rho GTPase activating proteins"	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.1651C>T	chr22.hg19:g.38049838C>T	ENSP00000350018:p.Pro551Ser	296.0	0.0		294.0	126.0	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Missense_Mutation	SNP	ENST00000357436.4	hg19	CCDS13952.2	.	.	.	.	.	.	.	.	.	.	C	11.02	1.514981	0.27123	.	.	ENSG00000100092	ENST00000357436;ENST00000397014	T	0.19250	2.16	5.45	-2.26	0.06867	.	0.571527	0.16968	N	0.192216	T	0.07638	0.0192	N	0.20986	0.625	0.09310	N	0.999999	P;B;B;P	0.39282	0.666;0.004;0.011;0.666	B;B;B;B	0.30401	0.115;0.002;0.005;0.115	T	0.24584	-1.0156	10	0.28530	T	0.3	.	1.7025	0.02875	0.4038:0.3084:0.1313:0.1564	.	465;487;551;465	E7EUD3;Q6ZT62;Q9Y3L3;Q6ZTJ5	.;.;3BP1_HUMAN;.	S	551;465	ENSP00000350018:P551S	ENSP00000350018:P551S	P	+	1	0	SH3BP1	36379784	0.000000	0.05858	0.000000	0.03702	0.875000	0.50365	-0.803000	0.04540	-0.389000	0.07786	-0.182000	0.12963	CCC	.	.		0.662	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957		T	38049838	C	T	38049838	3	4	187	1	0	0	0	0	1	0	0	0	14259	855	30	3	1717	3	SH3BP1	22	38049838	Missense_Mutation	SNP	C	TCGA-DD-AADD-01A-11D-A40R-10	2360774	38049838	13254728	86	27747										
RP2	6102	hgsc.bcm.edu	37	chrX	46713108	46713108	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ggacccgtgaaaggcagcgtGtttttccggaattgcagaga	14	8	0	2			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chrX:46713108G>T	ENST00000218340.3	+	2	461	c.300G>T	c.(298-300)gtG>gtT	p.V100V		NM_006915.2	NP_008846.2	O75695	XRP2_HUMAN	retinitis pigmentosa 2 (X-linked recessive)	100	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|CTP biosynthetic process (GO:0006241)|cytoskeleton organization (GO:0007010)|GTP biosynthetic process (GO:0006183)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein transport (GO:0015031)|UTP biosynthetic process (GO:0006228)|visual perception (GO:0007601)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|periciliary membrane compartment (GO:1990075)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|nucleoside diphosphate kinase activity (GO:0004550)|unfolded protein binding (GO:0051082)			NS(1)|large_intestine(4)|lung(5)|stomach(1)	11						AAGGCAGCGTGTTTTTCCGGA	0.423																																					p.V100V		Atlas-SNP	.											.	RP2	37	.	0			c.G300T						.						146	130	135					X																	46713108		2203	4300	6503	SO:0001819	synonymous_variant	6102	exon2			CAGCGTGTTTTTC	AJ007590	CCDS14270.1	Xp11.3	2013-01-08			ENSG00000102218	ENSG00000102218			10274	protein-coding gene	gene with protein product		300757				6325945, 9697692, 19852809	Standard	NM_006915		Approved	TBCCD2, NME10, NM23-H10	uc004dgw.4	O75695	OTTHUMG00000021430	ENST00000218340.3:c.300G>T	chrX.hg19:g.46713108G>T		75.0	0.0		40.0	5.0	NM_006915	Q86XJ7|Q9NU67	Silent	SNP	ENST00000218340.3	hg19	CCDS14270.1																																																																																			.	.		0.423	RP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056375.1	NM_006915		T	46713108	G	T	46713108	2	4	187	1	0	0	0	0	0	0	0	1	13549	1364	48	3		3	RP2	23	46713108	Silent	SNP	G	TCGA-DD-AADD-01A-11D-A40R-10		46713108	108557452	87	27748										
LAS1L	81887	hgsc.bcm.edu	37	chrX	64738079	64738079	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	cctggtctggcaagacctctTtctcctccttctcctcttcc	5	18	5	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chrX:64738079T>G	ENST00000374811.3	-	12	1755	c.1715A>C	c.(1714-1716)aAa>aCa	p.K572T	LAS1L_ENST00000374804.5_Missense_Mutation_p.K513T|LAS1L_ENST00000312391.8_3'UTR|LAS1L_ENST00000374807.5_Missense_Mutation_p.K555T	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	572					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						CAAGACCTCTTTCTCCTCCTT	0.512																																					p.K572T		Atlas-SNP	.											.	LAS1L	72	.	0			c.A1715C						.						147	122	130					X																	64738079		2203	4300	6503	SO:0001583	missense	81887	exon12			ACCTCTTTCTCCT	BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.1715A>C	chrX.hg19:g.64738079T>G	ENSP00000363944:p.Lys572Thr	57.0	0.0		38.0	33.0	NM_031206	A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Missense_Mutation	SNP	ENST00000374811.3	hg19	CCDS14381.1	.	.	.	.	.	.	.	.	.	.	T	0.082	-1.181615	0.01633	.	.	ENSG00000001497	ENST00000374807;ENST00000374811;ENST00000374804	T	0.66815	-0.23	4.68	2.08	0.27032	.	1.255560	0.05805	N	0.612964	T	0.59487	0.2197	L	0.47716	1.5	0.09310	N	1	B;B;B;B	0.29037	0.144;0.062;0.037;0.231	B;B;B;B	0.24848	0.017;0.017;0.007;0.056	T	0.46373	-0.9196	10	0.49607	T	0.09	.	7.7562	0.28925	0.243:0.0:0.0:0.757	.	513;555;572;85	Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2;B3KNR6	.;.;LAS1L_HUMAN;.	T	555;572;513	ENSP00000363937:K513T	ENSP00000363937:K513T	K	-	2	0	LAS1L	64654804	0.014000	0.17966	0.000000	0.03702	0.004000	0.04260	1.880000	0.39628	0.007000	0.14760	0.441000	0.28932	AAA	.	.		0.512	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206		G	64738079	T	G	64738079	3	3	187	1	0	0	0	0	1	0	0	0	8645	1841	64	5	501	5	LAS1L	23	64738079	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	18024971	64738079	90532481	88	27749										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128623009	128623009	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	ggtggctccatgccgtatcaTttgtaacatttcctcttttg	8	10	2	0			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chrX:128623009T>C	ENST00000371122.4	-	16	2131	c.2002A>G	c.(2002-2004)Atg>Gtg	p.M668V	SMARCA1_ENST00000371123.1_Missense_Mutation_p.M656V|SMARCA1_ENST00000371121.3_Missense_Mutation_p.M656V	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	668					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						TGCCGTATCATTTGTAACATT	0.363																																					p.M668V		Atlas-SNP	.											.	SMARCA1	126	.	0			c.A2002G						.						163	125	138					X																	128623009		2203	4300	6503	SO:0001583	missense	6594	exon16			GTATCATTTGTAA	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.2002A>G	chrX.hg19:g.128623009T>C	ENSP00000360163:p.Met668Val	57.0	0.0		47.0	40.0	NM_003069	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	hg19	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.173596	0.57584	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.79476	0.4452	M	0.83384	2.64	0.58432	D	0.999999	B;B;B;B	0.32731	0.175;0.175;0.268;0.382	B;B;B;B	0.37888	0.133;0.133;0.26;0.133	T	0.81258	-0.1014	10	0.87932	D	0	-9.3705	14.6824	0.69028	0.0:0.0:0.0:1.0	.	647;668;656;668	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	V	656;656;668;647	ENSP00000360162:M656V;ENSP00000360164:M656V;ENSP00000360163:M668V;ENSP00000404275:M647V	ENSP00000360162:M656V	M	-	1	0	SMARCA1	128450690	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.033000	0.88852	1.848000	0.53677	0.441000	0.28932	ATG	.	.		0.363	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		C	128623009	T	C	128623009	3	2	187	1	0	0	0	0	1	0	0	0	14783	1493	52	2	1198	2	SMARCA1	23	128623009	Missense_Mutation	SNP	T	TCGA-DD-AADD-01A-11D-A40R-10	63884930	128623009	26647551	89	27750										
MTM1	4534	hgsc.bcm.edu	37	chrX	149814284	149814284	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0444444444444444	4	1	0.861738002594034	1.29260700389105	0.77556420233463	0.559440559440559	1	0	gttatcagggagactaataaAcaaatttctaaactcaccat	5	8	3	1			TCGA-DD-AADD-01A-11D-A40R-10	TCGA-DD-AADD-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41b8300c-eab5-44a5-ab8f-03914a67343e	80263fcb-f4b4-4a2d-ac6c-cf1a471a48be	g.chrX:149814284A>T	ENST00000370396.2	+	9	861	c.807A>T	c.(805-807)aaA>aaT	p.K269N	MTM1_ENST00000542741.1_Missense_Mutation_p.K174N|MTM1_ENST00000413012.2_Missense_Mutation_p.K232N|MTM1_ENST00000306167.7_3'UTR|MTM1_ENST00000543350.1_Missense_Mutation_p.K154N	NM_000252.2	NP_000243.1	Q13496	MTM1_HUMAN	myotubularin 1	269	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				endosome to lysosome transport (GO:0008333)|intermediate filament organization (GO:0045109)|mitochondrion distribution (GO:0048311)|mitochondrion morphogenesis (GO:0070584)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|protein transport (GO:0015031)|regulation of vacuole organization (GO:0044088)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	intermediate filament binding (GO:0019215)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Acute lymphoblastic leukemia(192;6.56e-05)					AGACTAATAAACAAATTTCTA	0.418																																					p.K269N		Atlas-SNP	.											.	MTM1	89	.	0			c.A807T						.						138	117	124					X																	149814284		2203	4300	6503	SO:0001583	missense	4534	exon9			TAATAAACAAATT	U46024	CCDS14694.1	Xq27.3-q28	2014-09-17			ENSG00000171100	ENSG00000171100		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7448	protein-coding gene	gene with protein product		300415	"myotubular myopathy 1"				Standard	NM_000252		Approved		uc004fef.4	Q13496	OTTHUMG00000024158	ENST00000370396.2:c.807A>T	chrX.hg19:g.149814284A>T	ENSP00000359423:p.Lys269Asn	169.0	0.0		115.0	109.0	NM_000252	A6NDB1|B7Z491|F2Z330|Q8NEL1	Missense_Mutation	SNP	ENST00000370396.2	hg19	CCDS14694.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.670962	0.29693	.	.	ENSG00000171100	ENST00000370396;ENST00000542741;ENST00000543350;ENST00000413012	D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57	5.93	2.3	0.28687	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.346500	0.33272	N	0.005087	T	0.79569	0.4468	N	0.26130	0.795	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.16722	0.016;0.012	T	0.69375	-0.5162	10	0.87932	D	0	.	5.5134	0.16894	0.5014:0.1438:0.3548:0.0	.	232;269	B7Z491;Q13496	.;MTM1_HUMAN	N	269;174;154;232	ENSP00000359423:K269N;ENSP00000444015:K174N;ENSP00000439784:K154N;ENSP00000389157:K232N	ENSP00000359423:K269N	K	+	3	2	MTM1	149564942	0.994000	0.37717	0.045000	0.18777	0.676000	0.39594	0.605000	0.24179	0.340000	0.23745	0.481000	0.45027	AAA	.	.		0.418	MTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060847.3	NM_000252		T	149814284	A	T	149814284	3	4	187	1	0	0	0	0	1	0	0	0	9946	40	2	4	837	4	MTM1	23	149814284	Missense_Mutation	SNP	A	TCGA-DD-AADD-01A-11D-A40R-10	21191275	149814284	5456276	90	27751										
DVL1	1855	hgsc.bcm.edu	37	chr1	1274773	1274775	+	In_Frame_Del	DEL	CGT	CGT	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	agggctcctgtcagtgccgcCgtgtgggacagccaggcggc							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	CGT	CGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr1:1274773_1274775delCGT	ENST00000378888.5	-	11	1383_1385	c.1099_1101delACG	c.(1099-1101)acgdel	p.T367del	DVL1_ENST00000378891.5_In_Frame_Del_p.T367del			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	367					axon extension (GO:0048675)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|collateral sprouting (GO:0048668)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|cytoplasmic microtubule organization (GO:0031122)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|negative regulation of protein binding (GO:0032091)|negative regulation of protein kinase activity (GO:0006469)|neural tube development (GO:0021915)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prepulse inhibition (GO:0060134)|protein localization to microtubule (GO:0035372)|protein localization to nucleus (GO:0034504)|receptor clustering (GO:0043113)|regulation of neurotransmitter levels (GO:0001505)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|social behavior (GO:0035176)|synapse organization (GO:0050808)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	axon (GO:0030424)|cell cortex (GO:0005938)|clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|growth cone (GO:0030426)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	enzyme binding (GO:0019899)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|Rac GTPase binding (GO:0048365)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TCAGTGCCGCCGTGTGGGACAGC	0.709																																					p.367_368del		Atlas-INDEL	.											.	DVL1	36	.	0			c.1100_1102del						.																																			SO:0001651	inframe_deletion	1855	exon11			.	AF006011	CCDS22.1	1p36	2013-05-22	2013-05-22		ENSG00000107404	ENSG00000107404		"Dishevelled homologs"	3084	protein-coding gene	gene with protein product		601365	"dishevelled 1 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 1 (Drosophila)"			8817329	Standard	NM_004421		Approved		uc001aer.4	O14640	OTTHUMG00000003069	ENST00000378888.5:c.1099_1101delACG	chr1.hg19:g.1274773_1274775delCGT	ENSP00000368166:p.Thr367del	165.0	0.0		103.0	38.0	NM_004421	Q5TA33|Q5TA35	In_Frame_Del	DEL	ENST00000378888.5	hg19																																																																																				.	.		0.709	DVL1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008490.1	NM_004421		-	1274775	CGT	-	1274773	7	5	188	1	0	1	0	1	0	0	0	0	4837	639	23	0	931	0	DVL1	1	1274773	In_Frame_Del	DEL	CGT	TCGA-DD-AADE-01A-11D-A40R-10		1274773	247975848	1	27752										
NR0B2	8431	hgsc.bcm.edu	37	chr1	27238458	27238458	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gagggtggaggccgtgaggaGgacacgggtcaggcggcctt	21	8	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr1:27238458G>C	ENST00000254227.3	-	2	677	c.652C>G	c.(652-654)Ctc>Gtc	p.L218V		NM_021969.2	NP_068804.1	Q15466	NR0B2_HUMAN	nuclear receptor subfamily 0, group B, member 2	218	Ligand-binding. {ECO:0000250}.				cholesterol metabolic process (GO:0008203)|gene expression (GO:0010467)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of insulin secretion (GO:0032024)|response to glucose (GO:0009749)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(3)	5		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.01e-51)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		GCCGTGAGGAGGACACGGGTC	0.622																																					p.L218V		Atlas-SNP	.											.	NR0B2	14	.	0			c.C652G						.						132	132	132					1																	27238458		2203	4300	6503	SO:0001583	missense	8431	exon2			TGAGGAGGACACG	AF044316	CCDS291.1	1p36.1	2013-01-16			ENSG00000131910	ENSG00000131910		"Nuclear hormone receptors"	7961	protein-coding gene	gene with protein product		604630				9603951	Standard	NM_021969		Approved	SHP	uc001bnf.3	Q15466	OTTHUMG00000004231	ENST00000254227.3:c.652C>G	chr1.hg19:g.27238458G>C	ENSP00000254227:p.Leu218Val	227.0	0.0		194.0	66.0	NM_021969	F1D8P5|Q5QP36	Missense_Mutation	SNP	ENST00000254227.3	hg19	CCDS291.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454253	0.63290	.	.	ENSG00000131910	ENST00000254227	D	0.98090	-4.71	6.04	6.04	0.98038	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.98868	0.9617	M	0.92691	3.335	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.99010	1.0814	10	0.66056	D	0.02	-9.9219	11.5227	0.50560	0.1202:0.0:0.8798:0.0	.	218	Q15466	NR0B2_HUMAN	V	218	ENSP00000254227:L218V	ENSP00000254227:L218V	L	-	1	0	NR0B2	27111045	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	3.169000	0.50809	2.873000	0.98535	0.561000	0.74099	CTC	.	.		0.622	NR0B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012185.1			C	27238458	G	C	27238458	3	2	188	1	0	0	0	0	1	0	0	0	10623	1000	35	4	125	4	NR0B2	1	27238458	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	25963685	27238458	222012163	2	27753										
FLG	2312	hgsc.bcm.edu	37	chr1	152280880	152280880	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gatgagaccctgagtgtccaGacctatctaccgattgctct	9	12	2	3			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr1:152280880G>C	ENST00000368799.1	-	3	6517	c.6482C>G	c.(6481-6483)tCt>tGt	p.S2161C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2161	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGAGTGTCCAGACCTATCTAC	0.567									Ichthyosis																												p.S2161C		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	.	0			c.C6482G						.						379	329	346					1																	152280880		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGTCCAGACCTAT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6482C>G	chr1.hg19:g.152280880G>C	ENSP00000357789:p.Ser2161Cys	132.0	0.0		128.0	37.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	5.167	0.216393	0.09810	.	.	ENSG00000143631	ENST00000368799	T	0.02280	4.36	2.53	2.53	0.30540	.	.	.	.	.	T	0.04815	0.0130	M	0.78049	2.395	0.09310	N	1	D	0.89917	1.0	D	0.65987	0.94	T	0.21999	-1.0229	9	0.87932	D	0	.	8.7315	0.34503	0.0:0.0:1.0:0.0	.	2161	P20930	FILA_HUMAN	C	2161	ENSP00000357789:S2161C	ENSP00000357789:S2161C	S	-	2	0	FLG	150547504	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	0.646000	0.24797	1.740000	0.51718	0.485000	0.47835	TCT	.	.		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152280880	G	C	152280880	3	2	188	1	0	0	0	0	1	0	0	0	5930	942	33	4	5707	4	FLG	1	152280880	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	125042422	152280880	96969741	3	27754										
FLG2	388698	hgsc.bcm.edu	37	chr1	152326575	152326575	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tgtctcccatgaactgtggaTcctgactctacttgttgaga	9	10	2	3			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr1:152326575T>A	ENST00000388718.5	-	3	3759	c.3687A>T	c.(3685-3687)ggA>ggT	p.G1229G	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1229	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAACTGTGGATCCTGACTCTA	0.483																																					p.G1229G		Atlas-SNP	.											.	FLG2	431	.	0			c.A3687T						.						178	171	173					1																	152326575		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			TGTGGATCCTGAC	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.3687A>T	chr1.hg19:g.152326575T>A		80.0	0.0		80.0	32.0	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	hg19	CCDS30861.1																																																																																			.	.		0.483	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152326575	T	A	152326575	2	1	188	1	0	0	0	0	0	0	0	1	5931	1422	50	4		4	FLG2	1	152326575	Silent	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	45695	152326575	96924046	4	27755										
NTRK1	4914	hgsc.bcm.edu	37	chr1	156849081	156849081	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggccacacgcaactgtctagTgggccagggactggtggtca	15	11	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr1:156849081T>C	ENST00000524377.1	+	15	2014	c.1973T>C	c.(1972-1974)gTg>gCg	p.V658A	NTRK1_ENST00000368196.3_Missense_Mutation_p.V652A|NTRK1_ENST00000358660.3_Missense_Mutation_p.V655A|NTRK1_ENST00000392302.2_Missense_Mutation_p.V622A	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	658	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	AACTGTCTAGTGGGCCAGGGA	0.592			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.V658A		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1	287	.	0			c.T1973C						.						73	63	67					1																	156849081		2203	4300	6503	SO:0001583	missense	4914	exon15			GTCTAGTGGGCCA	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.1973T>C	chr1.hg19:g.156849081T>C	ENSP00000431418:p.Val658Ala	46.0	0.0		36.0	12.0	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	hg19	CCDS1161.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.390885	0.82902	.	.	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03	4.37	4.37	0.52481	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.162238	0.29212	N	0.012817	D	0.92031	0.7475	M	0.91612	3.225	0.80722	D	1	D;D;B;D	0.67145	0.994;0.996;0.448;0.99	D;D;B;D	0.70935	0.971;0.969;0.393;0.931	D	0.93563	0.6897	10	0.87932	D	0	.	12.8118	0.57643	0.0:0.0:0.0:1.0	.	655;652;658;622	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	A	622;652;658;655	ENSP00000376120:V622A;ENSP00000357179:V652A;ENSP00000431418:V658A;ENSP00000351486:V655A	ENSP00000351486:V655A	V	+	2	0	NTRK1	155115705	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.783000	0.85696	1.968000	0.57251	0.459000	0.35465	GTG	.	.		0.592	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		C	156849081	T	C	156849081	3	2	188	1	0	0	0	0	1	0	0	0	10715	1696	59	2	2161	2	NTRK1	1	156849081	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	4522506	156849081	92401540	5	27756										
PTGS2	5743	hgsc.bcm.edu	37	chr1	186648486	186648486	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tttctccatagaatcctgtcCgggtacaatcgcacttatac	6	12	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr1:186648486C>T	ENST00000367468.5	-	2	273	c.137G>A	c.(136-138)cGg>cAg	p.R46Q	RP5-973M2.2_ENST00000608917.1_lincRNA|PTGS2_ENST00000490885.2_5'UTR	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	46	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	GAATCCTGTCCGGGTACAATC	0.438																																					p.R46Q		Atlas-SNP	.											PTGS2_ENST00000367468,bladder,carcinoma,0,2	PTGS2	144	.	0			c.G137A						.						135	114	121					1																	186648486		2203	4300	6503	SO:0001583	missense	5743	exon2			CCTGTCCGGGTAC	D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.137G>A	chr1.hg19:g.186648486C>T	ENSP00000356438:p.Arg46Gln	134.0	1.0		140.0	47.0	NM_000963	A8K802|Q16876	Missense_Mutation	SNP	ENST00000367468.5	hg19	CCDS1371.1	.	.	.	.	.	.	.	.	.	.	C	35	5.542524	0.96474	.	.	ENSG00000073756	ENST00000367468	T	0.68624	-0.34	5.27	5.27	0.74061	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.050276	0.85682	D	0.000000	T	0.54615	0.1869	L	0.28556	0.865	0.58432	D	0.999997	P	0.44260	0.83	B	0.34385	0.181	T	0.63844	-0.6545	10	0.72032	D	0.01	-18.2304	18.5108	0.90916	0.0:1.0:0.0:0.0	.	46	P35354	PGH2_HUMAN	Q	46	ENSP00000356438:R46Q	ENSP00000356438:R46Q	R	-	2	0	PTGS2	184915109	0.959000	0.32827	0.967000	0.41034	0.992000	0.81027	4.712000	0.61888	2.444000	0.82710	0.655000	0.94253	CGG	.	.		0.438	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963		T	186648486	C	T	186648486	3	4	188	1	0	0	0	0	1	0	0	0	12769	652	23	1	1713	1	PTGS2	1	186648486	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	29799405	186648486	62602135	6	27757										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227381544	227381544	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ctatcaccatctcagccaagTaaaatctagccatatcttca	3	13	5	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr1:227381544T>C	ENST00000366769.3	-	5	1833	c.542A>G	c.(541-543)tAc>tGc	p.Y181C	CDC42BPA_ENST00000366766.2_Missense_Mutation_p.Y181C|CDC42BPA_ENST00000366767.3_Missense_Mutation_p.Y181C|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.Y181C|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.Y181C|CDC42BPA_ENST00000366765.3_Missense_Mutation_p.Y181C|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.Y181C	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				CTCAGCCAAGTAAAATCTAGC	0.393																																					p.Y181C		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.A542G						.						120	108	112					1																	227381544		2203	4300	6503	SO:0001583	missense	8476	exon5			GCCAAGTAAAATC	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.542A>G	chr1.hg19:g.227381544T>C	ENSP00000355731:p.Tyr181Cys	73.0	0.0		74.0	23.0	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	hg19	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.309914	0.81247	.	.	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.71091	0.3299	M	0.90922	3.16	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;1.0	T	0.79130	-0.1930	10	0.87932	D	0	.	14.4689	0.67501	0.0:0.0:0.0:1.0	.	181;181;181;181	F5H5N0;Q5VT25-4;Q5VT25-3;Q5VT25-5	.;.;.;.	C	181	ENSP00000355731:Y181C;ENSP00000355729:Y181C;ENSP00000335341:Y181C;ENSP00000355728:Y181C;ENSP00000355726:Y181C;ENSP00000443275:Y181C;ENSP00000355727:Y181C	ENSP00000335341:Y181C	Y	-	2	0	CDC42BPA	225448167	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.977000	0.88081	1.825000	0.53177	0.460000	0.39030	TAC	.	.		0.393	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		C	227381544	T	C	227381544	3	2	188	1	0	0	0	0	1	0	0	0	3074	1638	57	2	4745	2	CDC42BPA	1	227381544	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	40733058	227381544	21869077	7	27758										
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233518139	233518139	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	agtcatctgccaagggaggtCtcacccaagaagcacagcac	10	13	3	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr1:233518139C>T	ENST00000366624.3	+	10	3054	c.2793C>T	c.(2791-2793)gtC>gtT	p.V931V	MLK4_ENST00000366622.1_Silent_p.V377V	NM_032435.2	NP_115811.2																					CAAGGGAGGTCTCACCCAAGA	0.587																																					p.V931V		Atlas-SNP	.											.	KIAA1804	129	.	0			c.C2793T						.						104	92	96					1																	233518139		2203	4300	6503	SO:0001819	synonymous_variant	0	exon10			GGAGGTCTCACCC																												ENST00000366624.3:c.2793C>T	chr1.hg19:g.233518139C>T		102.0	0.0		113.0	32.0	NM_032435		Silent	SNP	ENST00000366624.3	hg19	CCDS1598.1																																																																																			.	.		0.587	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			T	233518139	C	T	233518139	2	4	188	1	0	0	0	0	0	0	0	1	8268	900	32	3		3	KIAA1804	1	233518139	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	6136595	233518139	15732482	8	27759										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37283648	37283648	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	acagaagcatcaatgactgaGactccgagagggaggggacc	14	9	1	4	rs200961568		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:37283648G>A	ENST00000233099.5	-	16	2429	c.2334C>T	c.(2332-2334)gtC>gtT	p.V778V	HEATR5B_ENST00000354531.2_Silent_p.V778V	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	778						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				CAATGACTGAGACTCCGAGAG	0.448																																					p.V778V		Atlas-SNP	.											.	HEATR5B	185	.	0			c.C2334T						.						94	101	99					2																	37283648		2203	4300	6503	SO:0001819	synonymous_variant	54497	exon16			GACTGAGACTCCG	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.2334C>T	chr2.hg19:g.37283648G>A		529.0	0.0		488.0	150.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	hg19	CCDS33181.1																																																																																			.	G|0.999;C|0.001		0.448	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37283648	G	A	37283648	2	1	188	1	0	0	0	0	0	0	0	1	7041	929	33	3		3	HEATR5B	2	37283648	Silent	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10		37283648	205915725	9	27760										
SMEK2	57223	hgsc.bcm.edu	37	chr2	55826140	55826140	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tcagattcatcaatgaggtcCtgtgtgacttccactgatgg	10	9	3	4			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:55826140C>T	ENST00000345102.5	-	4	634	c.333G>A	c.(331-333)caG>caA	p.Q111Q	SMEK2_ENST00000407823.3_Silent_p.Q111Q|SMEK2_ENST00000272313.5_Silent_p.Q111Q	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	111					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CAATGAGGTCCTGTGTGACTT	0.348																																					p.Q111Q		Atlas-SNP	.											.	SMEK2	86	.	0			c.G333A						.						116	125	122					2																	55826140		2203	4300	6503	SO:0001819	synonymous_variant	57223	exon4			GAGGTCCTGTGTG	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.333G>A	chr2.hg19:g.55826140C>T		44.0	0.0		43.0	11.0	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Silent	SNP	ENST00000345102.5	hg19	CCDS46289.1																																																																																			.	.		0.348	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		T	55826140	C	T	55826140	2	4	188	1	0	0	0	0	0	0	0	1	14809	680	24	3		3	SMEK2	2	55826140	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	18542492	55826140	187373233	10	27761										
PROKR1	10887	hgsc.bcm.edu	37	chr2	68882356	68882356	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gcagatccgcaagaggctgcGctgccgcaggaagacggtcc	15	13	0	3			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:68882356G>T	ENST00000303786.3	+	3	1250	c.830G>T	c.(829-831)cGc>cTc	p.R277L	PROKR1_ENST00000394342.2_Missense_Mutation_p.R277L			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	277					negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			endometrium(3)|kidney(2)|large_intestine(14)|lung(9)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						AAGAGGCTGCGCTGCCGCAGG	0.622																																					p.R277L		Atlas-SNP	.											.	PROKR1	69	.	0			c.G830T						.						73	63	67					2																	68882356		2203	4300	6503	SO:0001583	missense	10887	exon2			GGCTGCGCTGCCG	AF506287	CCDS1889.1	2p14	2012-08-08	2006-02-15	2006-02-15	ENSG00000169618	ENSG00000169618		"GPCR / Class A : Prokineticin receptors"	4524	protein-coding gene	gene with protein product		607122	"G protein-coupled receptor 73"	GPR73		10760605	Standard	NM_138964		Approved	PKR1, ZAQ, GPR73a	uc010yqj.2	Q8TCW9	OTTHUMG00000129567	ENST00000303786.3:c.830G>T	chr2.hg19:g.68882356G>T	ENSP00000303775:p.Arg277Leu	76.0	0.0		94.0	32.0	NM_138964	A5JUU2|Q53QT9|Q8NFJ7	Missense_Mutation	SNP	ENST00000303786.3	hg19	CCDS1889.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.528070	0.85706	.	.	ENSG00000169618	ENST00000303786;ENST00000394342	T;T	0.41758	0.99;0.99	4.55	4.55	0.56014	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.57755	0.2075	M	0.71036	2.16	0.80722	D	1	P	0.43701	0.815	P	0.53760	0.734	T	0.61083	-0.7134	10	0.72032	D	0.01	.	15.6333	0.76929	0.0:0.0:1.0:0.0	.	277	Q8TCW9	PKR1_HUMAN	L	277	ENSP00000303775:R277L;ENSP00000377874:R277L	ENSP00000303775:R277L	R	+	2	0	PROKR1	68735860	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.091000	0.71406	2.816000	0.96949	0.563000	0.77884	CGC	.	.		0.622	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2			T	68882356	G	T	68882356	3	4	188	1	0	0	0	0	1	0	0	0	12564	1087	38	1	836	1	PROKR1	2	68882356	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	13056216	68882356	174317017	11	27762										
C2orf15	80705	hgsc.bcm.edu	37	chr2	99767090	99767090	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	atggattcaaaagtggatgaTcacttaatacgagggactga	11	5	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:99767090T>C	ENST00000393483.3	-	1	225				C2ORF15_ENST00000409684.1_Silent_p.D57D|C2ORF15_ENST00000302513.2_Silent_p.D57D	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10						cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						AAGTGGATGATCACTTAATAC	0.348																																					p.D57D		Atlas-SNP	.											.	C2orf15	11	.	0			c.T171C						.						72	72	72					2																	99767090		2203	4300	6503	SO:0001627	intron_variant	150590	exon4			GGATGATCACTTA	AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.619+4065A>G	chr2.hg19:g.99767090T>C		269.0	0.0		238.0	84.0	NM_144706	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Silent	SNP	ENST00000393483.3	hg19	CCDS2037.1																																																																																			.	.		0.348	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		C	99767090	T	C	99767090	1	2	188	0	1	0	0	0	0	0	0	0	2158	1432	50	2		2	C2orf15	2	99767090	Intron	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	30884734	99767090	143432283	12	27763										
SLC9A2	6549	hgsc.bcm.edu	37	chr2	103300708	103300708	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gccatctgttttgcgttagtGtttctccttcctgctgctgt	9	11	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:103300708G>T	ENST00000233969.2	+	5	1480	c.1338G>T	c.(1336-1338)gtG>gtT	p.V446V		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	446					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						TTGCGTTAGTGTTTCTCCTTC	0.438																																					p.V446V		Atlas-SNP	.											.	SLC9A2	112	.	0			c.G1338T						.						292	266	275					2																	103300708		2203	4300	6503	SO:0001819	synonymous_variant	6549	exon5			GTTAGTGTTTCTC		CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"Solute carriers"	11072	protein-coding gene	gene with protein product		600530	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 2"	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.1338G>T	chr2.hg19:g.103300708G>T		114.0	0.0		120.0	43.0	NM_003048	B2RMS2	Silent	SNP	ENST00000233969.2	hg19	CCDS2062.1																																																																																			.	.		0.438	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2			T	103300708	G	T	103300708	2	4	188	1	0	0	0	0	0	0	0	1	14727	1364	48	3		3	SLC9A2	2	103300708	Silent	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	3533618	103300708	139898665	13	27764										
EPB41L5	57669	hgsc.bcm.edu	37	chr2	120836088	120836088	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggctagagatgggaatgactAtagtttgggactaacaccaa	12	6	0	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:120836088A>T	ENST00000263713.5	+	10	948	c.734A>T	c.(733-735)tAt>tTt	p.Y245F	EPB41L5_ENST00000452780.1_Missense_Mutation_p.Y245F|EPB41L5_ENST00000331393.4_Missense_Mutation_p.Y245F|EPB41L5_ENST00000443124.1_Missense_Mutation_p.Y245F|EPB41L5_ENST00000443902.2_Missense_Mutation_p.Y245F	NM_020909.3	NP_065960.2	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	245	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actomyosin structure organization (GO:0031032)|apical constriction (GO:0003383)|axial mesoderm morphogenesis (GO:0048319)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ectoderm development (GO:0007398)|embryonic foregut morphogenesis (GO:0048617)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|in utero embryonic development (GO:0001701)|left/right axis specification (GO:0070986)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of protein binding (GO:0032091)|neural plate morphogenesis (GO:0001839)|paraxial mesoderm development (GO:0048339)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein binding (GO:0032092)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of establishment of protein localization (GO:0070201)|somite rostral/caudal axis specification (GO:0032525)|substrate-dependent cell migration, cell attachment to substrate (GO:0006931)|unidimensional cell growth (GO:0009826)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(12)|ovary(1)	26						GGGAATGACTATAGTTTGGGA	0.323																																					p.Y245F		Atlas-SNP	.											.	EPB41L5	98	.	0			c.A734T						.						117	115	115					2																	120836088		2203	4299	6502	SO:0001583	missense	57669	exon10			ATGACTATAGTTT	AK023019	CCDS2130.1, CCDS54392.1, CCDS54393.1	2q14.2	2009-07-28			ENSG00000115109	ENSG00000115109			19819	protein-coding gene	gene with protein product		611730					Standard	NM_001184937		Approved	KIAA1548, FLJ12957, BE37, YMO1	uc002tmg.3	Q9HCM4	OTTHUMG00000131433	ENST00000263713.5:c.734A>T	chr2.hg19:g.120836088A>T	ENSP00000263713:p.Tyr245Phe	105.0	0.0		109.0	34.0	NM_020909	Q7Z5S1|Q8IZ12|Q9H975	Missense_Mutation	SNP	ENST00000263713.5	hg19	CCDS2130.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.361465	0.82353	.	.	ENSG00000115109	ENST00000263713;ENST00000443902;ENST00000331393;ENST00000443124;ENST00000452780	D;D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17;-2.17	4.83	4.83	0.62350	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.64402	D	0.000001	D	0.94486	0.8225	M	0.90922	3.16	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.991;0.999;0.994;0.999	D	0.95323	0.8422	10	0.59425	D	0.04	.	14.3669	0.66812	1.0:0.0:0.0:0.0	.	245;245;245;245	Q9HCM4-3;Q9HCM4-4;Q9HCM4-2;Q9HCM4	.;.;.;E41L5_HUMAN	F	245	ENSP00000263713:Y245F;ENSP00000393856:Y245F;ENSP00000329687:Y245F;ENSP00000393722:Y245F;ENSP00000390439:Y245F	ENSP00000263713:Y245F	Y	+	2	0	EPB41L5	120552558	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	8.619000	0.90938	1.946000	0.56461	0.459000	0.35465	TAT	.	.		0.323	EPB41L5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254230.2	NM_020909		T	120836088	A	T	120836088	3	4	188	1	0	0	0	0	1	0	0	0	5159	449	16	4	768	4	EPB41L5	2	120836088	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	17535380	120836088	122363285	14	27765										
ERMN	57471	hgsc.bcm.edu	37	chr2	158178164	158178164	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggttttcgaaatcccagccaTtcaatttcagctgcctggtg	9	11	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:158178164T>C	ENST00000410096.1	-	3	765	c.474A>G	c.(472-474)gaA>gaG	p.E158E	ERMN_ENST00000397283.2_Silent_p.E171E|ERMN_ENST00000535935.1_Silent_p.E52E|ERMN_ENST00000420719.2_Silent_p.E138E	NM_020711.1	NP_065762.1	Q8TAM6	ERMIN_HUMAN	ermin, ERM-like protein	158					actin filament organization (GO:0007015)|morphogenesis of a branching structure (GO:0001763)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|internode region of axon (GO:0033269)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|paranode region of axon (GO:0033270)				endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12						ATCCCAGCCATTCAATTTCAG	0.428																																					p.E171E		Atlas-SNP	.											.	ERMN	31	.	0			c.A513G						.						180	169	172					2																	158178164		1928	4130	6058	SO:0001819	synonymous_variant	57471	exon4			CAGCCATTCAATT	AB033015	CCDS42764.1, CCDS46431.1	2q24	2008-02-05	2008-01-15	2008-01-15	ENSG00000136541	ENSG00000136541			29208	protein-coding gene	gene with protein product	"juxtanodin", "ermin"	610072	"KIAA1189"	KIAA1189		16051705, 16421295	Standard	NM_020711		Approved	JN, ERMIN	uc002tzi.3	Q8TAM6	OTTHUMG00000153843	ENST00000410096.1:c.474A>G	chr2.hg19:g.158178164T>C		94.0	0.0		91.0	28.0	NM_001009959	B4DKA6|Q9ULN1	Silent	SNP	ENST00000410096.1	hg19	CCDS46431.1																																																																																			.	.		0.428	ERMN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332659.1	NM_001009959		C	158178164	T	C	158178164	2	2	188	1	0	0	0	0	0	0	0	1	5237	1490	52	2		2	ERMN	2	158178164	Silent	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	37342076	158178164	85021209	15	27766										
FAP	2191	hgsc.bcm.edu	37	chr2	163045653	163045655	+	In_Frame_Del	DEL	GAG	GAG	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	cttctttgatctgtcaaattGaggaggaagaatcatcttgt							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:163045653_163045655delGAG	ENST00000188790.4	-	19	1784_1786	c.1577_1579delCTC	c.(1576-1581)cctcaa>caa	p.P526del	FAP_ENST00000443424.1_In_Frame_Del_p.P501del	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						CTGTCAAATTGAGGAGGAAGAAT	0.296																																					p.526_527del		Atlas-INDEL	.											.	FAP	122	.	0			c.1578_1580del						.																																			SO:0001651	inframe_deletion	2191	exon19			.	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.1577_1579delCTC	chr2.hg19:g.163045656_163045658delGAG	ENSP00000188790:p.Pro526del	320.0	0.0		313.0	98.0	NM_004460		In_Frame_Del	DEL	ENST00000188790.4	hg19	CCDS33311.1																																																																																			.	.		0.296	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			-	163045655	GAG	-	163045653	7	5	188	1	0	1	0	1	0	0	0	0	5681	1299	45	0	735	0	FAP	2	163045653	In_Frame_Del	DEL	GAG	TCGA-DD-AADE-01A-11D-A40R-10	4867489	163045653	80153720	16	27767										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225679061	225679061	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tgcatgtaactcttgagtcgAttctgaaggtgtcaaaggat	11	6	3	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:225679061A>G	ENST00000258390.7	-	31	3452	c.3385T>C	c.(3385-3387)Tcg>Ccg	p.S1129P	DOCK10_ENST00000409592.3_Missense_Mutation_p.S1123P	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1129					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TCTTGAGTCGATTCTGAAGGT	0.294																																					p.S1129P		Atlas-SNP	.											.	DOCK10	308	.	0			c.T3385C						.						30	28	29					2																	225679061		1500	3326	4826	SO:0001583	missense	55619	exon31			GAGTCGATTCTGA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3385T>C	chr2.hg19:g.225679061A>G	ENSP00000258390:p.Ser1129Pro	33.0	0.0		33.0	11.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	A	11.37	1.618675	0.28801	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.23950	1.88;1.88	5.87	3.43	0.39272	.	0.294855	0.32819	N	0.005606	T	0.27866	0.0686	M	0.62723	1.935	0.32573	N	0.529494	B;B	0.31730	0.337;0.337	B;B	0.32289	0.143;0.1	T	0.33904	-0.9850	10	0.59425	D	0.04	.	12.3596	0.55194	0.7353:0.2647:0.0:0.0	.	1129;1123	Q96BY6;B3FL70	DOC10_HUMAN;.	P	1123;1129	ENSP00000386694:S1123P;ENSP00000258390:S1129P	ENSP00000258390:S1129P	S	-	1	0	DOCK10	225387305	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	6.129000	0.71657	0.444000	0.26612	-1.236000	0.01555	TCG	.	.		0.294	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			G	225679061	A	G	225679061	3	3	188	1	0	0	0	0	1	0	0	0	4687	333	12	2	3279	2	DOCK10	2	225679061	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	62633408	225679061	17520312	17	27768										
SLC19A3	80704	hgsc.bcm.edu	37	chr2	228552226	228552226	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggatttggttgagtaggtaaTatacatgcttctcattagga	11	4	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:228552226T>C	ENST00000258403.3	-	6	1449	c.1378A>G	c.(1378-1380)Att>Gtt	p.I460V	SLC19A3_ENST00000409287.1_Intron|SLC19A3_ENST00000541617.1_Missense_Mutation_p.I456V	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	460					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)			breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	GAGTAGGTAATATACATGCTT	0.373																																					p.I460V		Atlas-SNP	.											.	SLC19A3	62	.	0			c.A1378G						.						143	142	142					2																	228552226		2203	4300	6503	SO:0001583	missense	80704	exon6			AGGTAATATACAT	AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"Solute carriers"	16266	protein-coding gene	gene with protein product	"thiamine transporter 2"	606152	"solute carrier family 19, member 3"			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.1378A>G	chr2.hg19:g.228552226T>C	ENSP00000258403:p.Ile460Val	93.0	0.0		91.0	28.0	NM_025243		Missense_Mutation	SNP	ENST00000258403.3	hg19	CCDS2468.1	.	.	.	.	.	.	.	.	.	.	T	6.005	0.369356	0.11352	.	.	ENSG00000135917	ENST00000258403;ENST00000541617	D;D	0.85773	-2.0;-2.03	5.65	3.29	0.37713	Major facilitator superfamily domain, general substrate transporter (1);	0.340782	0.30602	N	0.009279	T	0.79058	0.4382	L	0.60957	1.885	0.19300	N	0.999976	P;B	0.34615	0.459;0.059	B;B	0.30943	0.122;0.028	T	0.64588	-0.6372	10	0.27082	T	0.32	-16.8892	9.6299	0.39774	0.0:0.1405:0.0:0.8595	.	456;460	F5H2M8;Q9BZV2	.;S19A3_HUMAN	V	460;456	ENSP00000258403:I460V;ENSP00000445519:I456V	ENSP00000258403:I460V	I	-	1	0	SLC19A3	228260470	0.280000	0.24249	0.291000	0.24904	0.094000	0.18550	1.439000	0.35013	0.443000	0.26582	0.459000	0.35465	ATT	.	.		0.373	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			C	228552226	T	C	228552226	3	2	188	1	0	0	0	0	1	0	0	0	14445	1406	49	2	116	2	SLC19A3	2	228552226	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	2873165	228552226	14647147	18	27769										
NMUR1	10316	hgsc.bcm.edu	37	chr2	232390063	232390063	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tgcaggccatctgtccactgTgacacgacgctccacatgac	9	15	1	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr2:232390063T>C	ENST00000305141.4	-	3	1105	c.972A>G	c.(970-972)tcA>tcG	p.S324S		NM_006056.4	NP_006047.3	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	324					activation of phospholipase C activity (GO:0007202)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|chloride transport (GO:0006821)|G-protein coupled receptor signaling pathway (GO:0007186)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|smooth muscle contraction (GO:0006939)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuromedin U receptor activity (GO:0001607)|neuropeptide receptor activity (GO:0008188)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(12)|pancreas(1)|skin(1)	24		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;8.37e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		CTGTCCACTGTGACACGACGC	0.637																																					p.S324S		Atlas-SNP	.											.	NMUR1	46	.	0			c.A972G						.						69	57	61					2																	232390063		2203	4300	6503	SO:0001819	synonymous_variant	10316	exon3			CCACTGTGACACG	AF044600	CCDS2486.1	2q37.1	2012-08-08	2004-05-27	2004-05-28	ENSG00000171596	ENSG00000171596		"GPCR / Class A : Neuromedin U receptors"	4518	protein-coding gene	gene with protein product		604153	"G protein-coupled receptor 66"	GPR66		9782091	Standard	NM_006056		Approved	GPC-R, FM-3, NMU1R	uc002vry.4	Q9HB89	OTTHUMG00000133225	ENST00000305141.4:c.972A>G	chr2.hg19:g.232390063T>C		198.0	0.0		202.0	70.0	NM_006056	O43664|Q7LDP6|Q8NE20	Silent	SNP	ENST00000305141.4	hg19	CCDS2486.1																																																																																			.	.		0.637	NMUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256961.1	NM_006056		C	232390063	T	C	232390063	2	2	188	1	0	0	0	0	0	0	0	1	10515	1683	59	2		2	NMUR1	2	232390063	Silent	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	3837837	232390063	10809310	19	27770										
SETMAR	6419	hgsc.bcm.edu	37	chr3	4358293	4358293	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aaatcaaaaaaatcgtcgttTtgaagtgtcatcttctctta	5	7	4	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr3:4358293T>G	ENST00000358065.4	+	3	1485	c.1418T>G	c.(1417-1419)tTt>tGt	p.F473C	SETMAR_ENST00000425863.1_Missense_Mutation_p.F334C|SUMF1_ENST00000534863.1_Intron	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	473	Mariner transposase Hsmar1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		aatcgtcgttttgaagtgtca	0.413								Chromatin Structure																													p.F473C		Atlas-SNP	.											.	SETMAR	30	.	0			c.T1418G						.						10	10	10					3																	4358293		2065	3990	6055	SO:0001583	missense	6419	exon3			GTCGTTTTGAAGT	U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.1418T>G	chr3.hg19:g.4358293T>G	ENSP00000373354:p.Phe473Cys	107.0	0.0		95.0	36.0	NM_006515	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	hg19	CCDS2563.2	.	.	.	.	.	.	.	.	.	.	T	12.64	1.998926	0.35226	.	.	ENSG00000170364	ENST00000358065;ENST00000425863	T;T	0.35421	1.31;1.31	0.235	0.235	0.15431	Transposase, Tc1-like (1);	1.472990	0.04916	U	0.454141	T	0.56470	0.1987	M	0.71036	2.16	0.22701	N	0.998836	D;D;P;D	0.89917	0.999;1.0;0.94;1.0	D;D;D;D	0.79108	0.96;0.992;0.926;0.979	T	0.38200	-0.9672	9	0.44086	T	0.13	.	.	.	.	.	217;334;460;218	B4DND2;E7EN68;Q53H47;Q96H41	.;.;SETMR_HUMAN;.	C	473;334	ENSP00000373354:F473C;ENSP00000403145:F334C	ENSP00000373354:F473C	F	+	2	0	SETMAR	4333293	0.945000	0.32115	0.951000	0.38953	0.951000	0.60555	0.310000	0.19356	0.263000	0.21812	0.260000	0.18958	TTT	.	.		0.413	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515		G	4358293	T	G	4358293	3	3	188	1	0	0	0	0	1	0	0	0	14155	1841	64	5	1428	5	SETMAR	3	4358293	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10		4358293	193664137	20	27771			1	39		2	2	15	T		5.652895e-05
SETMAR	6419	hgsc.bcm.edu	37	chr3	4358307	4358307	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gtcgttttgaagtgtcatctTctcttattctacgcaaccac	6	11	4	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr3:4358307T>G	ENST00000358065.4	+	3	1499	c.1432T>G	c.(1432-1434)Tct>Gct	p.S478A	SETMAR_ENST00000425863.1_Missense_Mutation_p.S339A|SUMF1_ENST00000534863.1_Intron	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	478	Mariner transposase Hsmar1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		agtgtcatcttctcttattct	0.418								Chromatin Structure																													p.S478A		Atlas-SNP	.											.	SETMAR	30	.	0			c.T1432G						.						11	11	11					3																	4358307		1999	3813	5812	SO:0001583	missense	6419	exon3			TCATCTTCTCTTA	U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.1432T>G	chr3.hg19:g.4358307T>G	ENSP00000373354:p.Ser478Ala	112.0	0.0		88.0	35.0	NM_006515	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	hg19	CCDS2563.2	.	.	.	.	.	.	.	.	.	.	T	12.40	1.927317	0.34002	.	.	ENSG00000170364	ENST00000358065;ENST00000425863	T;T	0.31247	1.5;1.5	0.235	0.235	0.15431	.	0.081888	0.49305	U	0.000146	T	0.30198	0.0757	L	0.48174	1.505	0.09310	N	0.999992	P;P;B;D	0.59357	0.656;0.793;0.259;0.985	B;P;B;P	0.55749	0.358;0.74;0.299;0.783	T	0.27088	-1.0084	9	0.07813	T	0.8	.	.	.	.	.	222;339;465;223	B4DND2;E7EN68;Q53H47;Q96H41	.;.;SETMR_HUMAN;.	A	478;339	ENSP00000373354:S478A;ENSP00000403145:S339A	ENSP00000373354:S478A	S	+	1	0	SETMAR	4333307	0.503000	0.26115	0.810000	0.32431	0.811000	0.45836	0.310000	0.19356	0.263000	0.21812	0.260000	0.18958	TCT	.	.		0.418	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515		G	4358307	T	G	4358307	3	3	188	1	0	0	0	0	1	0	0	0	14155	1783	62	5	1442	5	SETMAR	3	4358307	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	14	4358307	193664123	21	27772			1	39		2	2	15	T		5.652895e-05
METTL6	131965	hgsc.bcm.edu	37	chr3	15466502	15466502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ttggagaaaaatcacaggcaTaggcaaagatattcggatct	10	6	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr3:15466502T>C	ENST00000443029.1	-	3	560	c.320A>G	c.(319-321)tAt>tGt	p.Y107C	EAF1_ENST00000432764.2_5'Flank|METTL6_ENST00000383790.3_Missense_Mutation_p.Y107C|METTL6_ENST00000383789.5_Missense_Mutation_p.Y107C|EAF1_ENST00000396842.2_5'Flank|METTL6_ENST00000450816.2_Intron			Q8TCB7	METL6_HUMAN	methyltransferase like 6	107							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(9)|lung(3)|prostate(1)	15						ATCACAGGCATAGGCAAAGAT	0.403																																					p.Y107C		Atlas-SNP	.											.	METTL6	27	.	0			c.A320G						.						115	107	109					3																	15466502		1879	4105	5984	SO:0001583	missense	131965	exon3			CAGGCATAGGCAA	AK057791	CCDS43056.1	3p25.1	2005-11-02			ENSG00000206562	ENSG00000206562			28343	protein-coding gene	gene with protein product						12477932	Standard	NM_152396		Approved	MGC24132	uc003bzs.1	Q8TCB7	OTTHUMG00000156431	ENST00000443029.1:c.320A>G	chr3.hg19:g.15466502T>C	ENSP00000407613:p.Tyr107Cys	244.0	0.0		249.0	78.0	NM_152396	Q96LU4	Missense_Mutation	SNP	ENST00000443029.1	hg19	CCDS43056.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.347938	0.82022	.	.	ENSG00000206562	ENST00000383790;ENST00000453819;ENST00000383789	T;T;T	0.69561	-0.41;3.7;-0.41	5.74	5.74	0.90152	Methyltransferase type 12 (1);	0.000000	0.85682	D	0.000000	D	0.87079	0.6088	H	0.95574	3.69	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.75484	0.973;0.986	D	0.90913	0.4777	10	0.87932	D	0	-20.2951	15.6946	0.77484	0.0:0.0:0.0:1.0	.	107;107	Q8TCB7-2;Q8TCB7	.;METL6_HUMAN	C	107;14;107	ENSP00000373300:Y107C;ENSP00000412006:Y14C;ENSP00000373299:Y107C	ENSP00000373299:Y107C	Y	-	2	0	METTL6	15441506	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.942000	0.87708	2.186000	0.69663	0.460000	0.39030	TAT	.	.		0.403	METTL6-007	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346373.1	NM_152396		C	15466502	T	C	15466502	3	2	188	1	0	0	0	0	1	0	0	0	9513	1406	49	2	550	2	METTL6	3	15466502	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	11108195	15466502	182555928	22	27773										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266100	41266100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	agcaacagtcttacctggacTctggaatccattctggtgcc	9	12	3	0	rs121913416		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr3:41266100T>C	ENST00000349496.5	+	3	377	c.97T>C	c.(97-99)Tct>Cct	p.S33P	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.S33P(47)|p.S33A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.W25_D32del(4)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.D32_S33insS(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.S33T(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TTACCTGGACTCTGGAATCCA	0.488		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	212	Deletion - In frame(115)|Substitution - Missense(70)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Insertion - In frame(1)	liver(130)|large_intestine(20)|endometrium(14)|stomach(10)|pituitary(9)|pancreas(9)|central_nervous_system(8)|adrenal_gland(2)|small_intestine(2)|biliary_tract(2)|skin(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|breast(1)	c.T97C						.						93	77	82					3																	41266100		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTGGACTCTGGAA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.97T>C	chr3.hg19:g.41266100T>C	ENSP00000344456:p.Ser33Pro	118.0	0.0		130.0	39.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.395782	0.83011	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70281	0.3206	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74509	-0.3642	10	0.87932	D	0	-10.7796	16.0677	0.80897	0.0:0.0:0.0:1.0	.	33	P35222	CTNB1_HUMAN	P	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26P;ENSP00000385604:S33P;ENSP00000412219:S33P;ENSP00000379486:S33P;ENSP00000344456:S33P;ENSP00000411226:S26P;ENSP00000379488:S33P;ENSP00000409302:S33P;ENSP00000401599:S33P	ENSP00000344456:S33P	S	+	1	0	CTNNB1	41241104	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266100	T	C	41266100	3	2	188	1	0	0	0	0	1	0	0	0	4018	1551	54	2	103	2	CTNNB1	3	41266100	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	25799598	41266100	156756330	23	27774										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266137	41266137	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tgccactaccacagctccttCtctgagtggtaaaggcaatc	8	13	1	1	rs121913409		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr3:41266137C>A	ENST00000349496.5	+	3	414	c.134C>A	c.(133-135)tCt>tAt	p.S45Y	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45Y|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45Y|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45Y|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38Y	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45F(384)|p.S45del(53)|p.A5_A80del(53)|p.S45C(19)|p.S45Y(17)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.S45fs*2(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACAGCTCCTTCTCTGAGTGGT	0.498	S45F(HCC15_LUNG)|S45F(LS180_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45Y	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+1,2	CTNNB1	4904	.	601	Substitution - Missense(421)|Deletion - In frame(152)|Complex - deletion inframe(20)|Unknown(7)|Deletion - Frameshift(1)	soft_tissue(233)|liver(141)|large_intestine(85)|kidney(74)|endometrium(16)|skin(11)|adrenal_gland(9)|stomach(7)|biliary_tract(5)|ovary(4)|lung(3)|central_nervous_system(2)|cervix(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(1)|pituitary(1)|prostate(1)|bone(1)|pancreas(1)	c.C134A						.						84	74	77					3																	41266137		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTCCTTCTCTGAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.134C>A	chr3.hg19:g.41266137C>A	ENSP00000344456:p.Ser45Tyr	102.0	0.0		115.0	45.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519229	0.85495	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.68659	0.3025	M	0.65677	2.01	0.80722	D	1	D	0.76494	0.999	D	0.67231	0.95	T	0.69320	-0.5176	10	0.87932	D	0	-13.6823	20.2983	0.98569	0.0:1.0:0.0:0.0	.	45	P35222	CTNB1_HUMAN	Y	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38Y;ENSP00000385604:S45Y;ENSP00000412219:S45Y;ENSP00000379486:S45Y;ENSP00000344456:S45Y;ENSP00000411226:S38Y;ENSP00000379488:S45Y;ENSP00000409302:S45Y;ENSP00000401599:S45Y	ENSP00000344456:S45Y	S	+	2	0	CTNNB1	41241141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266137	C	A	41266137	3	1	188	1	0	0	0	0	1	0	0	0	4018	913	32	3	140	3	CTNNB1	3	41266137	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	37	41266137	156756293	24	27775										
FAM19A1	407738	hgsc.bcm.edu	37	chr3	68588000	68588000	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tgacaattctggatggatgtGcgcaacaggcaacaaaatta	10	7	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr3:68588000G>T	ENST00000478136.1	+	4	843	c.353G>T	c.(352-354)tGc>tTc	p.C118F	FAM19A1_ENST00000496687.1_Missense_Mutation_p.C118F	NM_213609.3	NP_998774.2	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A1	118						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	7		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)		GGATGGATGTGCGCAACAGGC	0.428																																					p.C118F		Atlas-SNP	.											.	FAM19A1	58	.	0			c.G353T						.						131	130	130					3																	68588000		1977	4168	6145	SO:0001583	missense	407738	exon4			GGATGTGCGCAAC	AY325114	CCDS54606.1	3p14.1	2005-01-20			ENSG00000183662	ENSG00000183662			21587	protein-coding gene	gene with protein product						15028294	Standard	NM_213609		Approved	TAFA-1	uc003dnd.3	Q7Z5A9	OTTHUMG00000158745	ENST00000478136.1:c.353G>T	chr3.hg19:g.68588000G>T	ENSP00000418575:p.Cys118Phe	169.0	0.0		167.0	57.0	NM_213609	A8K0V3|Q8TCL8	Missense_Mutation	SNP	ENST00000478136.1	hg19	CCDS54606.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.501011	0.85176	.	.	ENSG00000183662	ENST00000478136;ENST00000496687	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.83285	0.5221	M	0.80183	2.485	0.52099	D	0.999945	D	0.69078	0.997	D	0.81914	0.995	D	0.85460	0.1166	9	0.87932	D	0	.	19.1554	0.93507	0.0:0.0:1.0:0.0	.	118	Q7Z5A9	F19A1_HUMAN	F	118	.	ENSP00000418575:C118F	C	+	2	0	FAM19A1	68670690	1.000000	0.71417	0.971000	0.41717	0.889000	0.51656	9.690000	0.98676	2.591000	0.87537	0.650000	0.86243	TGC	.	.		0.428	FAM19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352004.1	NM_213609		T	68588000	G	T	68588000	3	4	188	1	0	0	0	0	1	0	0	0	5536	1319	46	3	363	3	FAM19A1	3	68588000	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	27321863	68588000	129434430	25	27776										
OR5K4	403278	hgsc.bcm.edu	37	chr3	98073346	98073350	+	Frame_Shift_Del	DEL	TCTTA	TCTTA	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ccattgctactgtcttgatcTcttatctctgcatccttttg							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	TCTTA	TCTTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr3:98073346_98073350delTCTTA	ENST00000354924.2	+	1	649_653	c.649_653delTCTTA	c.(649-654)tcttatfs	p.SY217fs	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005517.1	NP_001005517.1	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K, member 4	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	21						TGTCTTGATCTCTTATCTCTGCATC	0.346																																					p.216_218del		Atlas-INDEL	.											.	OR5K4	75	.	0			c.648_652del						.																																			SO:0001589	frameshift_variant	403278	exon1			.		CCDS33802.1	3q11.2	2013-09-23			ENSG00000196098	ENSG00000196098		"GPCR / Class A : Olfactory receptors"	31291	protein-coding gene	gene with protein product							Standard	NM_001005517		Approved		uc011bgv.2	A6NMS3	OTTHUMG00000160081	ENST00000354924.2:c.649_653delTCTTA	chr3.hg19:g.98073346_98073350delTCTTA	ENSP00000347003:p.Ser217fs	98.0	0.0		81.0	26.0	NM_001005517		Frame_Shift_Del	DEL	ENST00000354924.2	hg19	CCDS33802.1																																																																																			.	.		0.346	OR5K4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359114.1			-	98073350	TCTTA	-	98073346	7	5	188	1	0	1	0	1	0	0	0	0	11178	1551	54	0	651	0	OR5K4	3	98073346	Frame_Shift_Del	DEL	TCTTA	TCGA-DD-AADE-01A-11D-A40R-10	29485346	98073346	99949084	26	27777										
NPHP3	27031	hgsc.bcm.edu	37	chr3	132400798	132400798	+	Frame_Shift_Del	DEL	T	T	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aacattaggagaatgagctgTttttaagctaaacgtgtctc							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr3:132400798delT	ENST00000337331.5	-	27	4035	c.3949delA	c.(3949-3951)acafs	p.T1317fs	NPHP3_ENST00000326682.8_3'UTR	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	1317					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GAATGAGCTGTTTTTAAGCTA	0.363																																					p.T1317fs		Atlas-INDEL	.											.	NPHP3	110	.	0			c.3950delC						.						162	157	159					3																	132400798		2203	4300	6503	SO:0001589	frameshift_variant	27031	exon27			.	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"Tetratricopeptide (TTC) repeat domain containing"	7907	protein-coding gene	gene with protein product	"nephrocystin-3", "Meckel syndrome, type 7", "cilia and flagella associated protein 31"	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.3949delA	chr3.hg19:g.132400798delT	ENSP00000338766:p.Thr1317fs	122.0	0.0		143.0	32.0	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Frame_Shift_Del	DEL	ENST00000337331.5	hg19	CCDS3078.1																																																																																			.	.		0.363	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		-	132400798	T	-	132400798	7	5	188	1	0	1	0	1	0	0	0	0	10589	1725	60	0	47	0	NPHP3	3	132400798	Frame_Shift_Del	DEL	T	TCGA-DD-AADE-01A-11D-A40R-10	34327452	132400798	65621632	27	27778										
DLG1	1739	hgsc.bcm.edu	37	chr3	196921381	196921381	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tctctgagacatgaaccaatTctggacctatcacttcattt	5	11	4	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr3:196921381T>G	ENST00000419354.1	-	5	684	c.398A>C	c.(397-399)gAa>gCa	p.E133A	DLG1_ENST00000357674.4_Missense_Mutation_p.E133A|DLG1_ENST00000314062.3_Missense_Mutation_p.E133A|DLG1_ENST00000392382.2_Missense_Mutation_p.E133A|DLG1_ENST00000422288.1_Missense_Mutation_p.E133A|DLG1_ENST00000485409.1_5'UTR|DLG1_ENST00000450955.1_Missense_Mutation_p.E133A|DLG1_ENST00000448528.2_Missense_Mutation_p.E133A|DLG1_ENST00000346964.2_Missense_Mutation_p.E133A			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	133					actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		ATGAACCAATTCTGGACCTAT	0.353																																					p.E133A		Atlas-SNP	.											.	DLG1	120	.	0			c.A398C						.						147	142	144					3																	196921381		2203	4299	6502	SO:0001583	missense	1739	exon5			ACCAATTCTGGAC	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"discs large homolog 1", "presynaptic protein SAP97", "synapse-associated protein 97"	601014	"discs, large (Drosophila) homolog 1"			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.398A>C	chr3.hg19:g.196921381T>G	ENSP00000407531:p.Glu133Ala	82.0	0.0		78.0	32.0	NM_001204386	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	hg19	CCDS43194.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.826674	0.50739	.	.	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000422288;ENST00000448528;ENST00000392382;ENST00000450955;ENST00000453607;ENST00000456699;ENST00000392380;ENST00000419553	T;T;T;T;T;T;T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6	5.67	5.67	0.87782	Membrane-associated guanylate kinase (MAGUK), PEST domain, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70527	0.3234	M	0.72118	2.19	0.58432	D	0.999999	D;D;B;D	0.76494	0.98;0.999;0.277;0.999	P;D;B;D	0.87578	0.842;0.998;0.179;0.998	T	0.69091	-0.5237	10	0.32370	T	0.25	.	15.1003	0.72269	0.0:0.0:0.0:1.0	.	133;133;133;133	Q12959-4;Q12959-3;Q12959;Q12959-2	.;.;DLG1_HUMAN;.	A	133;133;133;133;133;133;133;133;133;133;37;133;133;133	ENSP00000345731:E133A;ENSP00000350303:E133A;ENSP00000321087:E133A;ENSP00000407531:E133A;ENSP00000413238:E133A;ENSP00000391732:E133A;ENSP00000376187:E133A;ENSP00000411278:E133A;ENSP00000412579:E37A;ENSP00000396474:E133A;ENSP00000376185:E133A;ENSP00000414189:E133A	ENSP00000321087:E133A	E	-	2	0	DLG1	198405778	1.000000	0.71417	0.127000	0.21898	0.009000	0.06853	7.679000	0.84048	2.164000	0.68074	0.533000	0.62120	GAA	.	.		0.353	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087		G	196921381	T	G	196921381	3	3	188	1	0	0	0	0	1	0	0	0	4556	1783	62	5	2508	5	DLG1	3	196921381	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	64520583	196921381	1101049	28	27779										
WHSC1	7468	hgsc.bcm.edu	37	chr4	1952825	1952825	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gacagcccgggagacgagccCtcggagtccccatacgaaag	13	14	0	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr4:1952825C>T	ENST00000382895.3	+	12	2339	c.1908C>T	c.(1906-1908)ccC>ccT	p.P636P	WHSC1_ENST00000382888.3_5'Flank|WHSC1_ENST00000382892.2_Silent_p.P636P|WHSC1_ENST00000382891.5_Silent_p.P636P|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000508803.1_Silent_p.P636P	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	636					anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		GAGACGAGCCCTCGGAGTCCC	0.547			T	IGH@	MM																																p.P636P		Atlas-SNP	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.C1908T						.						85	77	80					4																	1952825		2203	4300	6503	SO:0001819	synonymous_variant	7468	exon10			CGAGCCCTCGGAG	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"Zinc fingers, PHD-type"	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.1908C>T	chr4.hg19:g.1952825C>T		76.0	0.0		64.0	14.0	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Silent	SNP	ENST00000382895.3	hg19	CCDS33940.1	.	.	.	.	.	.	.	.	.	.	C	8.942	0.966064	0.18659	.	.	ENSG00000109685	ENST00000514329	.	.	.	5.77	0.0947	0.14482	.	.	.	.	.	T	0.42086	0.1187	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23904	-1.0175	4	.	.	.	.	1.7661	0.03002	0.2998:0.3827:0.0995:0.218	.	.	.	.	F	49	.	.	L	+	1	0	WHSC1	1922623	0.013000	0.17824	0.693000	0.30195	0.759000	0.43091	-0.601000	0.05687	0.032000	0.15435	-0.345000	0.07892	CTC	.	.		0.547	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		T	1952825	C	T	1952825	2	4	188	1	0	0	0	0	0	0	0	1	17377	668	24	3		3	WHSC1	4	1952825	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10		1952825	189201451	29	27780										
EVC	2121	hgsc.bcm.edu	37	chr4	5812081	5812081	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tacagagaagcccctaaggaCtaaaaggaagaagcccctgc	10	11	0	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr4:5812081C>T	ENST00000264956.6	+	20	2982	c.2798C>T	c.(2797-2799)aCt>aTt	p.T933I	EVC_ENST00000382674.2_Missense_Mutation_p.T933I	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	933					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				CCCCTAAGGACTAAAAGGAAG	0.562																																					p.T933I		Atlas-SNP	.											.	EVC	90	.	0			c.C2798T						.						41	46	45					4																	5812081		2203	4300	6503	SO:0001583	missense	2121	exon20			TAAGGACTAAAAG	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.2798C>T	chr4.hg19:g.5812081C>T	ENSP00000264956:p.Thr933Ile	210.0	0.0		173.0	60.0	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	hg19	CCDS3383.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.428920	0.43122	.	.	ENSG00000072840	ENST00000264956;ENST00000382674	T;T	0.56444	0.46;0.46	4.91	2.99	0.34606	.	0.372093	0.21696	N	0.070483	T	0.54208	0.1844	L	0.54323	1.7	0.80722	D	1	D	0.58268	0.982	P	0.54924	0.764	T	0.51702	-0.8672	10	0.38643	T	0.18	.	6.5505	0.22431	0.2178:0.5993:0.1829:0.0	.	933	P57679	EVC_HUMAN	I	933	ENSP00000264956:T933I;ENSP00000372120:T933I	ENSP00000264956:T933I	T	+	2	0	EVC	5862982	0.962000	0.33011	0.994000	0.49952	0.177000	0.22998	0.571000	0.23669	2.266000	0.75297	0.650000	0.86243	ACT	.	.		0.562	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			T	5812081	C	T	5812081	3	4	188	1	0	0	0	0	1	0	0	0	5287	565	20	3	2876	3	EVC	4	5812081	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	3859256	5812081	185342195	30	27781										
GABRA2	2555	hgsc.bcm.edu	37	chr4	46264068	46264068	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	agcaataaaccagtccatggCagttgcataagccactttgg	9	10	0	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr4:46264068C>T	ENST00000510861.1	-	9	1107	c.934G>A	c.(934-936)Gcc>Acc	p.A312T	GABRA2_ENST00000540012.1_Missense_Mutation_p.A257T|GABRA2_ENST00000507069.1_Missense_Mutation_p.A312T|GABRA2_ENST00000356504.1_Missense_Mutation_p.A312T|GABRA2_ENST00000514090.1_Missense_Mutation_p.A312T|GABRA2_ENST00000381620.4_Missense_Mutation_p.A312T|GABRA2_ENST00000515082.1_Missense_Mutation_p.A312T			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	312					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	CAGTCCATGGCAGTTGCATAA	0.413																																					p.A312T		Atlas-SNP	.											.	GABRA2	134	.	0			c.G934A						.						137	124	128					4																	46264068		2203	4300	6503	SO:0001583	missense	2555	exon9			CCATGGCAGTTGC		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.934G>A	chr4.hg19:g.46264068C>T	ENSP00000421828:p.Ala312Thr	125.0	0.0		138.0	50.0	NM_000807	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	hg19	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	C	34	5.404546	0.96051	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000540012;ENST00000507069;ENST00000515082	D;D;D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42	5.35	5.35	0.76521	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.95639	0.8582	M	0.90759	3.145	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.96175	0.9126	10	0.87932	D	0	.	18.4017	0.90519	0.0:1.0:0.0:0.0	.	257;312;312	B7Z1H8;G5E9Z6;P47869	.;.;GBRA2_HUMAN	T	312;312;312;312;257;312;312	ENSP00000421828:A312T;ENSP00000421300:A312T;ENSP00000371033:A312T;ENSP00000348897:A312T;ENSP00000444409:A257T;ENSP00000427603:A312T;ENSP00000423840:A312T	ENSP00000348897:A312T	A	-	1	0	GABRA2	45958825	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.765000	0.85310	2.676000	0.91093	0.591000	0.81541	GCC	.	.		0.413	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			T	46264068	C	T	46264068	3	4	188	1	0	0	0	0	1	0	0	0	6169	710	25	3	429	3	GABRA2	4	46264068	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	40451987	46264068	144890208	31	27782										
TMPRSS11F	389208	hgsc.bcm.edu	37	chr4	68938054	68938054	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gacttacgtgtgagtctaaaTgatggtttgtttatggtcaa	11	4	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr4:68938054T>C	ENST00000356291.2	-	5	560	c.501A>G	c.(499-501)tcA>tcG	p.S167S	UBA6-AS1_ENST00000499180.2_RNA|UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000500538.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	167	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						TGAGTCTAAATGATGGTTTGT	0.294																																					p.S167S		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.A501G						.						77	78	78					4																	68938054		2203	4298	6501	SO:0001819	synonymous_variant	389208	exon5			TCTAAATGATGGT	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"Serine peptidases / Transmembrane"	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.501A>G	chr4.hg19:g.68938054T>C		49.0	0.0		45.0	18.0	NM_207407	A8MXX2	Silent	SNP	ENST00000356291.2	hg19	CCDS3520.1																																																																																			.	.		0.294	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		C	68938054	T	C	68938054	2	2	188	1	0	0	0	0	0	0	0	1	16258	1451	51	2		2	TMPRSS11F	4	68938054	Silent	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	22673986	68938054	122216222	32	27783										
MAML3	55534	hgsc.bcm.edu	37	chr4	140811058	140811069	+	In_Frame_Del	DEL	TGCTGTTGCTGC	TGCTGTTGCTGC	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aatttgaagtctgatttgagTgctgttgctgctgctgctgc					rs58015886|rs370122702		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	TGCTGTTGCTGC	TGCTGTTGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr4:140811058_140811069delTGCTGTTGCTGC	ENST00000509479.2	-	2	2377_2388	c.1521_1532delGCAGCAACAGCA	c.(1519-1533)cagcagcaacagcac>cac	p.QQQQ507del	MAML3_ENST00000398940.1_Splice_Site_p.AAT37del|MAML3_ENST00000327122.5_In_Frame_Del_p.QQQQ351del	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					CTGATTTGAGtgctgttgctgctgctgctgct	0.519																																					p.505_507del		Atlas-INDEL	.											.	MAML3	192	.	0			c.1513_1521del						.																																			SO:0001651	inframe_deletion	55534	exon3			.	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1521_1532delGCAGCAACAGCA	chr4.hg19:g.140811058_140811069delTGCTGTTGCTGC	ENSP00000421180:p.Gln507_Gln510del	63.0	0.0		71.0	10.0	NM_018717		In_Frame_Del	DEL	ENST00000509479.2	hg19	CCDS54805.1																																																																																			.	.		0.519	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			-	140811069	TGCTGTTGCTGC	-	140811058	7	5	188	1	0	1	0	1	0	0	0	0	9216	1696	59	0	1900	0	MAML3	4	140811058	In_Frame_Del	DEL	TGCTGTTGCTGC	TCGA-DD-AADE-01A-11D-A40R-10	71873004	140811058	50343218	33	27784										
GLRB	2743	hgsc.bcm.edu	37	chr4	158091870	158091870	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	caatgttatatattggtctaTatatttatgataaatctttt	4	3	2	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr4:158091870T>C	ENST00000264428.4	+	10	1754	c.1484T>C	c.(1483-1485)aTa>aCa	p.I495T	GLRB_ENST00000541722.1_3'UTR|GLRB_ENST00000509282.1_Missense_Mutation_p.I495T|GLRB_ENST00000512619.1_3'UTR	NM_000824.4	NP_000815.1	P48167	GLRB_HUMAN	glycine receptor, beta	495					acrosome reaction (GO:0007340)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|extracellular-glycine-gated ion channel activity (GO:0016933)|glycine binding (GO:0016594)			central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(6)|skin(5)|upper_aerodigestive_tract(1)	27	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Enflurane(DB00228)|Glycine(DB00145)|Lindane(DB00431)	TATTGGTCTATATATTTATGA	0.313																																					p.I495T		Atlas-SNP	.											.	GLRB	74	.	0			c.T1484C						.						53	57	56					4																	158091870		2202	4299	6501	SO:0001583	missense	2743	exon10			GGTCTATATATTT	U33267	CCDS3796.1, CCDS54813.1	4q31.3	2008-02-05			ENSG00000109738	ENSG00000109738			4329	protein-coding gene	gene with protein product		138492				9676428, 8717357	Standard	NM_000824		Approved		uc003ipj.2	P48167	OTTHUMG00000161954	ENST00000264428.4:c.1484T>C	chr4.hg19:g.158091870T>C	ENSP00000264428:p.Ile495Thr	40.0	0.0		46.0	14.0	NM_000824	A8K3K2|D3DP23|F5GWE1	Missense_Mutation	SNP	ENST00000264428.4	hg19	CCDS3796.1	.	.	.	.	.	.	.	.	.	.	T	11.74	1.729604	0.30684	.	.	ENSG00000109738	ENST00000264428;ENST00000509282	D;D	0.83837	-1.77;-1.77	5.95	5.95	0.96441	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.199081	0.56097	D	0.000032	T	0.72819	0.3508	N	0.16708	0.43	0.80722	D	1	B	0.12013	0.005	B	0.14023	0.01	T	0.67007	-0.5779	10	0.30078	T	0.28	.	16.4159	0.83738	0.0:0.0:0.0:1.0	.	495	P48167	GLRB_HUMAN	T	495	ENSP00000264428:I495T;ENSP00000427186:I495T	ENSP00000264428:I495T	I	+	2	0	GLRB	158311320	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.279000	0.76181	0.533000	0.62120	ATA	.	.		0.313	GLRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366507.1	NM_000824		C	158091870	T	C	158091870	3	2	188	1	0	0	0	0	1	0	0	0	6466	1406	49	2	1518	2	GLRB	4	158091870	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	17280812	158091870	33062406	34	27785										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169348266	169348266	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tgctttaaagcaggcaattaAtcctaacatttcaactccaa	4	10	1	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr4:169348266A>G	ENST00000511577.1	-	14	2132	c.1885T>C	c.(1885-1887)Tta>Cta	p.L629L	DDX60L_ENST00000505890.1_Silent_p.L629L|DDX60L_ENST00000260184.7_Silent_p.L629L			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	629							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CAGGCAATTAATCCTAACATT	0.338																																					p.L629L		Atlas-SNP	.											.	DDX60L	116	.	0			c.T1885C						.						83	72	76					4																	169348266		1849	4104	5953	SO:0001819	synonymous_variant	91351	exon14			CAATTAATCCTAA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.1885T>C	chr4.hg19:g.169348266A>G		139.0	0.0		150.0	6.0	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	hg19																																																																																				.	.		0.338	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		G	169348266	A	G	169348266	2	3	188	1	0	0	0	0	0	0	0	1	4381	98	4	2		2	DDX60L	4	169348266	Silent	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	11256396	169348266	21806010	35	27786										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55259984	55259986	+	In_Frame_Del	DEL	AGG	AGG	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ttataactacctttatatacAggatcaaaattgatatgatc							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr5:55259984_55259986delAGG	ENST00000381298.2	-	6	958_960	c.646_648delCCT	c.(646-648)cctdel	p.P216del	IL6ST_ENST00000577363.1_5'Flank|IL6ST_ENST00000522633.2_In_Frame_Del_p.P216del|IL6ST_ENST00000336909.5_In_Frame_Del_p.P216del|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000381294.3_In_Frame_Del_p.P216del|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000502326.3_In_Frame_Del_p.P216del|IL6ST_ENST00000536319.1_In_Frame_Del_p.P216del|IL6ST_ENST00000381287.4_In_Frame_Del_p.P216del	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	216	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				CTTTATATACAGGATCAAAATTG	0.3			O		hepatocellular ca																																p.216_217del		Atlas-INDEL	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.647_649del						.																																			SO:0001651	inframe_deletion	3572	exon6			.	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.646_648delCCT	chr5.hg19:g.55259984_55259986delAGG	ENSP00000370698:p.Pro216del	157.0	0.0		135.0	35.0	NM_002184	A0N0L4|Q5FC04|Q9UQ41	In_Frame_Del	DEL	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.		0.3	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		-	55259986	AGG	-	55259984	7	5	188	1	0	1	0	1	0	0	0	0	7712	175	7	0	2156	0	IL6ST	5	55259984	In_Frame_Del	DEL	AGG	TCGA-DD-AADE-01A-11D-A40R-10		55259984	125655276	36	27787										
MARVELD2	153562	hgsc.bcm.edu	37	chr5	68715559	68715559	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ctccgatggagtggagtgttCaccaccagcctctccagcaa	10	14	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr5:68715559C>A	ENST00000325631.5	+	2	421	c.347C>A	c.(346-348)tCa>tAa	p.S116*	MARVELD2_ENST00000413223.2_Nonsense_Mutation_p.S116*	NM_001038603.2|NM_001244734.1	NP_001033692.2|NP_001231663.1	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	116					cell-cell junction organization (GO:0045216)|establishment of endothelial barrier (GO:0061028)|sensory perception of sound (GO:0007605)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(4)|skin(1)|urinary_tract(1)	15		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		GTGGAGTGTTCACCACCAGCC	0.527																																					p.S116X		Atlas-SNP	.											.	MARVELD2	49	.	0			c.C347A						.						48	50	49					5																	68715559		2203	4300	6503	SO:0001587	stop_gained	153562	exon2			AGTGTTCACCACC	AK055094	CCDS34175.1, CCDS58956.1	5q13.1	2007-05-01	2004-07-12	2004-07-14	ENSG00000152939	ENSG00000152939			26401	protein-coding gene	gene with protein product	"tricellulin"	610572	"MARVEL (membrane-associating) domain containing 2", "deafness, autosomal recessive 49"	MRVLDC2, DFNB49		17186462	Standard	NM_001038603		Approved	FLJ30532, TRIC	uc003jwq.3	Q8N4S9	OTTHUMG00000162512	ENST00000325631.5:c.347C>A	chr5.hg19:g.68715559C>A	ENSP00000323264:p.Ser116*	58.0	0.0		78.0	31.0	NM_001244734	A1BQX0|A1BQX1|A8KA97|Q96NM9	Nonsense_Mutation	SNP	ENST00000325631.5	hg19	CCDS34175.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.191271	0.78902	.	.	ENSG00000152939	ENST00000325631;ENST00000282886;ENST00000454295;ENST00000515844;ENST00000512803;ENST00000436532;ENST00000413223	.	.	.	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.3572	17.4129	0.87492	0.0:1.0:0.0:0.0	.	.	.	.	X	116	.	ENSP00000282886:S116X	S	+	2	0	MARVELD2	68751315	1.000000	0.71417	0.773000	0.31616	0.513000	0.34164	7.304000	0.78882	2.396000	0.81511	0.655000	0.94253	TCA	.	.		0.527	MARVELD2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369583.1	NM_144724		A	68715559	C	A	68715559	4	1	188	1	0	0	0	0	0	1	0	0	9327	838	29	3	349	3	MARVELD2	5	68715559	Nonsense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	13455575	68715559	112199701	37	27788										
FNIP1	96459	hgsc.bcm.edu	37	chr5	131014861	131014861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	catcgtgtaaagattacaaaTtgttgttctaaaaagaggaa	8	4	1	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr5:131014861T>C	ENST00000510461.1	-	12	1305	c.1210A>G	c.(1210-1212)Att>Gtt	p.I404V	FNIP1_ENST00000307954.8_Missense_Mutation_p.I359V|FNIP1_ENST00000511848.1_Missense_Mutation_p.I404V|FNIP1_ENST00000307968.7_Missense_Mutation_p.I376V|CTC-432M15.3_ENST00000514667.1_Intron	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	404					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		AGATTACAAATTGTTGTTCTA	0.358																																					p.I404V		Atlas-SNP	.											.	FNIP1	104	.	0			c.A1210G						.																																			SO:0001583	missense	96459	exon12			TACAAATTGTTGT	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.1210A>G	chr5.hg19:g.131014861T>C	ENSP00000421985:p.Ile404Val	385.0	0.0		316.0	14.0	NM_133372	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	hg19	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	T	16.90	3.251249	0.59212	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461;ENST00000511848	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.06	3.89	0.44902	.	.	.	.	.	T	0.35393	0.0930	N	0.19112	0.55	0.53688	D	0.999979	D;P;D;B	0.62365	0.991;0.948;0.991;0.328	D;D;D;B	0.72625	0.978;0.949;0.978;0.239	T	0.04708	-1.0932	9	0.24483	T	0.36	-5.1033	10.8866	0.46971	0.0:0.0748:0.0:0.9252	.	404;404;376;404	A8K8V8;Q8TF40-2;Q8TF40-3;Q8TF40	.;.;.;FNIP1_HUMAN	V	376;359;164;404;404	ENSP00000309266:I376V;ENSP00000310453:I359V;ENSP00000421985:I404V;ENSP00000425619:I404V	ENSP00000310453:I359V	I	-	1	0	FNIP1	131042760	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.742000	0.68646	0.876000	0.35872	0.533000	0.62120	ATT	.	.		0.358	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		C	131014861	T	C	131014861	3	2	188	1	0	0	0	0	1	0	0	0	5983	1493	52	2	2318	2	FNIP1	5	131014861	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	62299302	131014861	49900399	38	27789										
RBM27	54439	hgsc.bcm.edu	37	chr5	145610481	145610481	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gcgatgcagagattatgatgGtaaaaatcaccaccttttct	8	8	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr5:145610481G>A	ENST00000265271.5	+	6	1016		c.e6+1		RBM27_ENST00000506502.1_Splice_Site	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27						mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GATTATGATGGTAAAAATCAC	0.348																																					.		Atlas-SNP	.											.	RBM27	119	.	0			c.850+1G>A						.						99	84	89					5																	145610481		1568	3582	5150	SO:0001630	splice_region_variant	54439	exon6			ATGATGGTAAAAA	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.850+1G>A	chr5.hg19:g.145610481G>A		103.0	0.0		82.0	27.0	NM_018989	Q8IYW9	Splice_Site	SNP	ENST00000265271.5	hg19	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.523236	0.85600	.	.	ENSG00000091009	ENST00000265271	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5365	0.95255	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBM27	145590674	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.556000	0.90697	2.614000	0.88457	0.563000	0.77884	.	.	.		0.348	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	Intron	A	145610481	G	A	145610481	5	1	188	1	0	0	0	0	0	0	1	0	13142	1275	44	3	873	3	RBM27	5	145610481	Splice_Site	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	14595620	145610481	35304779	39	27790										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160049550	160049550	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	caaccacagggcagcatctcGaaccttggtcagtaggtttt	10	11	2	0	rs374261198		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr5:160049550G>A	ENST00000327245.5	-	14	2509	c.1663C>T	c.(1663-1665)Cga>Tga	p.R555*	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	555					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCAGCATCTCGAACCTTGGTC	0.498																																					p.R555X		Atlas-SNP	.											.	ATP10B	201	.	0			c.C1663T						.						102	104	103					5																	160049550		1952	4147	6099	SO:0001587	stop_gained	23120	exon14			CATCTCGAACCTT	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.1663C>T	chr5.hg19:g.160049550G>A	ENSP00000313600:p.Arg555*	68.0	0.0		72.0	29.0	NM_025153	Q9H725	Nonsense_Mutation	SNP	ENST00000327245.5	hg19	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	G	46	12.587222	0.99680	.	.	ENSG00000118322	ENST00000327245;ENST00000520108	.	.	.	5.53	3.55	0.40652	.	0.412527	0.25456	N	0.030549	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.337	0.60522	0.0:0.0:0.5723:0.4277	.	.	.	.	X	555;163	.	.	R	-	1	2	ATP10B	159982128	0.350000	0.24878	0.381000	0.26106	0.888000	0.51559	2.752000	0.47516	1.307000	0.44944	0.655000	0.94253	CGA	.	.		0.498	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		A	160049550	G	A	160049550	4	1	188	1	0	0	0	0	0	1	0	0	1117	1066	37	1	2774	1	ATP10B	5	160049550	Nonsense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	14439069	160049550	20865710	40	27791										
CFB	629	hgsc.bcm.edu	37	chr6	31918993	31918993	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggagaaaaagctgactcggaAggaggtctacatcaagaatg	13	6	2	3			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr6:31918993A>C	ENST00000425368.2	+	15	2441	c.1928A>C	c.(1927-1929)aAg>aCg	p.K643T	CFB_ENST00000456570.1_Missense_Mutation_p.K1145T|CFB_ENST00000556679.1_Missense_Mutation_p.K1145T|CFB_ENST00000477310.1_Missense_Mutation_p.K994T	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	643	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						CTGACTCGGAAGGAGGTCTAC	0.498																																					p.K643T		Atlas-SNP	.											.	CFB	33	.	0			c.A1928C						.						92	93	92					6																	31918993		1511	2709	4220	SO:0001583	missense	629	exon15			CTCGGAAGGAGGT	L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"Complement system"	1037	protein-coding gene	gene with protein product		138470	"B-factor, properdin"	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.1928A>C	chr6.hg19:g.31918993A>C	ENSP00000416561:p.Lys643Thr	70.0	0.0		65.0	19.0	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	hg19	CCDS4729.1	.	.	.	.	.	.	.	.	.	.	A	18.75	3.689632	0.68271	.	.	ENSG00000243649;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000556679;ENST00000425368;ENST00000456570;ENST00000477310	D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47	5.41	3.01	0.34805	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.130715	0.34725	N	0.003737	T	0.80534	0.4641	N	0.10760	0.04	0.46437	D	0.999043	D;D	0.71674	0.998;0.98	D;P	0.71184	0.972;0.852	T	0.82623	-0.0366	10	0.62326	D	0.03	-19.5614	7.7646	0.28972	0.8305:0.0:0.1695:0.0	.	1145;643	B4E1Z4;P00751	.;CFAB_HUMAN	T	1145;643;1145;994	ENSP00000451848:K1145T;ENSP00000416561:K643T;ENSP00000410815:K1145T;ENSP00000418996:K994T	ENSP00000416561:K643T	K	+	2	0	CFB;XXbac-BPG116M5.17	32026972	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.779000	0.47734	0.363000	0.24346	0.482000	0.46254	AAG	.	.		0.498	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		C	31918993	A	C	31918993	3	2	188	1	0	0	0	0	1	0	0	0	3280	72	3	5	1986	5	CFB	6	31918993	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10		31918993	139196074	41	27792			2	40		2	2	18	A		6.864189e-05
CFB	629	hgsc.bcm.edu	37	chr6	31919010	31919010	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggaaggaggtctacatcaagAatggggataaggtgagaaac	15	4	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr6:31919010A>T	ENST00000425368.2	+	15	2458	c.1945A>T	c.(1945-1947)Aat>Tat	p.N649Y	CFB_ENST00000456570.1_Missense_Mutation_p.N1151Y|CFB_ENST00000556679.1_Missense_Mutation_p.N1151Y|CFB_ENST00000477310.1_Missense_Mutation_p.N1000Y	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	649	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						CTACATCAAGAATGGGGATAA	0.502																																					p.N649Y		Atlas-SNP	.											.	CFB	33	.	0			c.A1945T						.						82	83	82					6																	31919010		1511	2709	4220	SO:0001583	missense	629	exon15			ATCAAGAATGGGG	L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"Complement system"	1037	protein-coding gene	gene with protein product		138470	"B-factor, properdin"	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.1945A>T	chr6.hg19:g.31919010A>T	ENSP00000416561:p.Asn649Tyr	72.0	0.0		55.0	17.0	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	hg19	CCDS4729.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.17|16.17	3.048359|3.048359	0.55110|0.55110	.|.	.|.	ENSG00000243649;ENSG00000243649;ENSG00000244255;ENSG00000244255|ENSG00000243649	ENST00000556679;ENST00000425368;ENST00000456570;ENST00000477310|ENST00000483004	T;T;T;T|.	0.32753|.	1.44;1.44;1.44;1.44|.	5.53|5.53	3.01|3.01	0.34805|0.34805	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);|.	0.129562|.	0.34700|.	N|.	0.003751|.	T|T	0.35998|0.35998	0.0951|0.0951	L|L	0.46819|0.46819	1.47|1.47	0.35349|0.35349	D|D	0.787216|0.787216	D;D|.	0.89917|.	1.0;0.999|.	D;D|.	0.97110|.	1.0;0.99|.	T|T	0.13845|0.13845	-1.0494|-1.0494	10|5	0.26408|.	T|.	0.33|.	-23.6078|-23.6078	10.426|10.426	0.44378|0.44378	0.6849:0.3151:0.0:0.0|0.6849:0.3151:0.0:0.0	.|.	1151;649|.	B4E1Z4;P00751|.	.;CFAB_HUMAN|.	Y|S	1151;649;1151;1000|189	ENSP00000451848:N1151Y;ENSP00000416561:N649Y;ENSP00000410815:N1151Y;ENSP00000418996:N1000Y|.	ENSP00000416561:N649Y|.	N|R	+|+	1|3	0|2	CFB;XXbac-BPG116M5.17|CFB	32026989|32026989	0.999000|0.999000	0.42202|0.42202	0.941000|0.941000	0.38009|0.38009	0.883000|0.883000	0.51084|0.51084	1.258000|1.258000	0.32944|0.32944	0.339000|0.339000	0.23719|0.23719	0.482000|0.482000	0.46254|0.46254	AAT|AGA	.	.		0.502	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		T	31919010	A	T	31919010	3	4	188	1	0	0	0	0	1	0	0	0	3280	246	9	4	2003	4	CFB	6	31919010	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	17	31919010	139196057	42	27793			2	40		2	2	18	A		6.864189e-05
TNXB	7148	hgsc.bcm.edu	37	chr6	32038115	32038115	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	accgtccaggagaggcgcagTgagtctggggtggggtctgt	19	8	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr6:32038115T>C	ENST00000375244.3	-	14	5268	c.5067A>G	c.(5065-5067)tcA>tcG	p.S1689S	TNXB_ENST00000375247.2_Silent_p.S1689S			P22105	TENX_HUMAN	tenascin XB	1771	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						AGAGGCGCAGTGAGTCTGGGG	0.642																																					p.S1689S		Atlas-SNP	.											.	TNXB	553	.	0			c.A5067G						.						18	20	19					6																	32038115		1920	4123	6043	SO:0001819	synonymous_variant	7148	exon14			GCGCAGTGAGTCT	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5067A>G	chr6.hg19:g.32038115T>C		112.0	0.0		103.0	35.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	hg19																																																																																				.	.		0.642	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		C	32038115	T	C	32038115	2	2	188	1	0	0	0	0	0	0	0	1	16361	1683	59	2		2	TNXB	6	32038115	Silent	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	119105	32038115	139076952	43	27794										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33154482	33154482	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gatctctgggctctgtgaggCtgttggttttggggtctttc	15	7	3	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr6:33154482C>T	ENST00000374708.4	-	5	978	c.720G>A	c.(718-720)caG>caA	p.Q240Q	COL11A2_ENST00000374714.1_Silent_p.Q240Q|COL11A2_ENST00000374712.1_Silent_p.Q240Q|COL11A2_ENST00000374713.1_Silent_p.Q240Q|COL11A2_ENST00000357486.1_Silent_p.Q240Q|COL11A2_ENST00000341947.2_Silent_p.Q240Q|COL11A2_ENST00000395197.1_Silent_p.Q240Q|COL11A2_ENST00000395194.1_Silent_p.Q240Q|COL11A2_ENST00000361917.1_Silent_p.Q240Q	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	240	Nonhelical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CTCTGTGAGGCTGTTGGTTTT	0.577																																					p.Q240Q	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.G720A						.						266	242	250					6																	33154482		2203	4300	6503	SO:0001819	synonymous_variant	1302	exon5			GTGAGGCTGTTGG	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.720G>A	chr6.hg19:g.33154482C>T		117.0	0.0		80.0	23.0	NM_080681	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.577	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			T	33154482	C	T	33154482	2	4	188	1	0	0	0	0	0	0	0	1	3670	796	28	3		3	COL11A2	6	33154482	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	1116367	33154482	137960585	44	27795										
DAAM2	23500	hgsc.bcm.edu	37	chr6	39832239	39832239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	accccaacaagctggcaaccAgctggcctgactattacatc	7	15	0	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr6:39832239A>G	ENST00000398904.2	+	4	471	c.289A>G	c.(289-291)Agc>Ggc	p.S97G	DAAM2_ENST00000494405.1_3'UTR|DAAM2_ENST00000274867.4_Missense_Mutation_p.S97G|DAAM2_ENST00000538976.1_Missense_Mutation_p.S97G			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	97	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					GCTGGCAACCAGCTGGCCTGA	0.592																																					p.S97G		Atlas-SNP	.											.	DAAM2	101	.	0			c.A289G						.						73	72	72					6																	39832239		1999	4186	6185	SO:0001583	missense	23500	exon4			GCAACCAGCTGGC	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.289A>G	chr6.hg19:g.39832239A>G	ENSP00000381876:p.Ser97Gly	56.0	0.0		37.0	11.0	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.806040	0.90623	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	D;D;D	0.89270	-2.49;-2.49;-2.49	5.89	5.89	0.94794	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.000000	0.85682	D	0.000000	D	0.91199	0.7227	L	0.59912	1.85	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.79108	0.987;0.992	D	0.90099	0.4183	10	0.33141	T	0.24	.	15.2948	0.73894	1.0:0.0:0.0:0.0	.	97;97	G5EA45;Q86T65	.;DAAM2_HUMAN	G	97	ENSP00000274867:S97G;ENSP00000381876:S97G;ENSP00000437808:S97G	ENSP00000274867:S97G	S	+	1	0	DAAM2	39940217	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.254000	0.74563	0.459000	0.35465	AGC	.	.		0.592	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			G	39832239	A	G	39832239	3	3	188	1	0	0	0	0	1	0	0	0	4218	188	7	2	299	2	DAAM2	6	39832239	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	6677757	39832239	131282828	45	27796										
HSP90AB1	3326	hgsc.bcm.edu	37	chr6	44216462	44216462	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tccctcatcatcaataccttCtattccaacaaggagatttt	3	12	4	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr6:44216462C>A	ENST00000371554.1	+	2	310	c.96C>A	c.(94-96)ttC>ttA	p.F32L	HSP90AB1_ENST00000353801.3_Missense_Mutation_p.F32L|HSP90AB1_ENST00000371646.5_Missense_Mutation_p.F32L			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	32					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TCAATACCTTCTATTCCAACA	0.438																																					p.F32L		Atlas-SNP	.											.	HSP90AB1	83	.	0			c.C96A						.						179	179	179					6																	44216462		2203	4300	6503	SO:0001583	missense	3326	exon2			TACCTTCTATTCC	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"Heat shock proteins / HSPC"	5258	protein-coding gene	gene with protein product		140572	"heat shock 90kD protein 1, beta", "heat shock 90kDa protein 1, beta"	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.96C>A	chr6.hg19:g.44216462C>A	ENSP00000360609:p.Phe32Leu	66.0	0.0		73.0	15.0	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Missense_Mutation	SNP	ENST00000371554.1	hg19	CCDS4909.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.030558	0.54790	.	.	ENSG00000096384	ENST00000441736;ENST00000371646;ENST00000353801;ENST00000371554	T;T;T	0.15017	2.46;2.46;2.46	4.26	-0.976	0.10286	Heat shock protein Hsp90, N-terminal (1);ATPase-like, ATP-binding domain (2);	0.000000	0.64402	U	0.000001	T	0.11537	0.0281	L	0.31752	0.955	0.80722	D	1	P;B	0.49447	0.924;0.142	P;B	0.57776	0.827;0.021	T	0.04242	-1.0966	10	0.87932	D	0	-14.0797	10.0808	0.42388	0.0:0.6275:0.0:0.3725	.	32;32	B4DGL0;P08238	.;HS90B_HUMAN	L	32	ENSP00000360709:F32L;ENSP00000325875:F32L;ENSP00000360609:F32L	ENSP00000325875:F32L	F	+	3	2	HSP90AB1	44324440	0.972000	0.33761	0.973000	0.42090	0.949000	0.60115	0.228000	0.17814	-0.177000	0.10690	0.505000	0.49811	TTC	.	.		0.438	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355		A	44216462	C	A	44216462	3	1	188	1	0	0	0	0	1	0	0	0	7411	912	32	3	98	3	HSP90AB1	6	44216462	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	4384223	44216462	126898605	46	27797										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84304147	84304147	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aggggttggggtagctggtgCggcggccccttcggatgctg	20	9	0	0	rs200249566		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr6:84304147C>T	ENST00000439399.2	-	17	1694	c.1378G>A	c.(1378-1380)Gca>Aca	p.A460T	SNAP91_ENST00000521743.1_Missense_Mutation_p.A460T|SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000428679.2_Missense_Mutation_p.A460T|SNAP91_ENST00000195649.6_Missense_Mutation_p.A460T|SNAP91_ENST00000520302.1_Missense_Mutation_p.A458T|SNAP91_ENST00000369694.2_Missense_Mutation_p.A460T|SNAP91_ENST00000521485.1_Missense_Mutation_p.A460T|SNAP91_ENST00000437520.1_Intron	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	460	Ala-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		GTAGCTGGTGCGGCGGCCCCT	0.493																																					p.A460T		Atlas-SNP	.											.	SNAP91	199	.	0			c.G1378A						.	C	THR/ALA,THR/ALA,,THR/ALA	1,3591		0,1,1795	24	24	24		1378,1372,,1378	5.8	1	6		24	7,8053		0,7,4023	yes	missense,missense,intron,missense	SNAP91	NM_001242792.1,NM_001242793.1,NM_001242794.1,NM_014841.2	58,58,,58	0,8,5818	TT,TC,CC		0.0868,0.0278,0.0687	possibly-damaging,possibly-damaging,,possibly-damaging	460/908,458/878,,460/908	84304147	8,11644	1796	4030	5826	SO:0001583	missense	9892	exon16			CTGGTGCGGCGGC	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1378G>A	chr6.hg19:g.84304147C>T	ENSP00000400459:p.Ala460Thr	82.0	0.0		73.0	4.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.850394	0.71719	2.78E-4	8.68E-4	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000520302;ENST00000521743	T;T;T;T;T;T;T	0.16743	2.34;2.34;2.34;2.34;2.36;2.32;2.34	5.75	5.75	0.90469	.	0.188671	0.43919	D	0.000510	T	0.09992	0.0245	L	0.60455	1.87	0.80722	D	1	P;P;P	0.50943	0.893;0.94;0.94	B;B;B	0.35607	0.15;0.15;0.206	T	0.17018	-1.0383	10	0.21540	T	0.41	-6.0451	19.9421	0.97168	0.0:1.0:0.0:0.0	.	458;460;458	E5RI02;O60641;E1P549	.;AP180_HUMAN;.	T	460;460;460;460;460;458;460	ENSP00000429776:A460T;ENSP00000358708:A460T;ENSP00000400459:A460T;ENSP00000195649:A460T;ENSP00000412492:A460T;ENSP00000428511:A458T;ENSP00000428215:A460T	ENSP00000195649:A460T	A	-	1	0	SNAP91	84360866	1.000000	0.71417	0.991000	0.47740	0.538000	0.34931	4.078000	0.57606	2.714000	0.92807	0.561000	0.74099	GCA	.	.		0.493	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			T	84304147	C	T	84304147	3	4	188	1	0	0	0	0	1	0	0	0	14848	768	27	1	1397	1	SNAP91	6	84304147	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	40087685	84304147	86810920	47	27798										
MDN1	23195	hgsc.bcm.edu	37	chr6	90411385	90411385	+	Frame_Shift_Del	DEL	T	T	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tgttctgagacagtctgaacTtctttgtaatatctttaaag							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr6:90411385delT	ENST00000369393.3	-	55	8434	c.8319delA	c.(8317-8319)gaafs	p.E2773fs	MDN1_ENST00000428876.1_Frame_Shift_Del_p.E2773fs			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2773					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CAGTCTGAACTTCTTTGTAAT	0.423																																					p.V2774fs		Atlas-INDEL	.											.	MDN1	478	.	0			c.8320delG						.						41	42	41					6																	90411385		2203	4300	6503	SO:0001589	frameshift_variant	23195	exon55			.	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.8319delA	chr6.hg19:g.90411385delT	ENSP00000358400:p.Glu2773fs	92.0	0.0		102.0	46.0	NM_014611	O15019|Q5T794	Frame_Shift_Del	DEL	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.423	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			-	90411385	T	-	90411385	7	5	188	1	0	1	0	1	0	0	0	0	9424	1606	56	0	8663	0	MDN1	6	90411385	Frame_Shift_Del	DEL	T	TCGA-DD-AADE-01A-11D-A40R-10	6107238	90411385	80703682	48	27799										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146256475	146256475	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tggcaataaagctgtagagaTgctgaggattcttcttgcag	12	6	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr6:146256475T>C	ENST00000367505.2	-	12	2936	c.2672A>G	c.(2671-2673)cAt>cGt	p.H891R	SHPRH_ENST00000438092.2_Missense_Mutation_p.H891R|SHPRH_ENST00000275233.7_Missense_Mutation_p.H891R|SHPRH_ENST00000367503.3_Missense_Mutation_p.H891R			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	891					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		GCTGTAGAGATGCTGAGGATT	0.398																																					p.H891R		Atlas-SNP	.											.	SHPRH	169	.	0			c.A2672G						.						90	84	86					6																	146256475		1891	4108	5999	SO:0001583	missense	257218	exon12			TAGAGATGCTGAG	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.2672A>G	chr6.hg19:g.146256475T>C	ENSP00000356475:p.His891Arg	113.0	0.0		94.0	32.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	hg19	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	T	11.69	1.715325	0.30413	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88	5.73	-6.52	0.01872	SNF2-related (1);	0.558649	0.18320	N	0.144821	T	0.56232	0.1971	N	0.04043	-0.29	0.21675	N	0.999596	B;B;B	0.29805	0.168;0.257;0.217	B;B;B	0.28465	0.086;0.09;0.054	T	0.63829	-0.6548	10	0.21540	T	0.41	3.3162	7.902	0.29740	0.1551:0.0:0.473:0.3719	.	780;891;891	Q149N8-2;Q149N8;Q149N8-4	.;SHPRH_HUMAN;.	R	891	ENSP00000356475:H891R;ENSP00000356473:H891R;ENSP00000412797:H891R;ENSP00000275233:H891R	ENSP00000275233:H891R	H	-	2	0	SHPRH	146298168	0.750000	0.28316	0.024000	0.17045	0.998000	0.95712	1.020000	0.30027	-1.883000	0.01120	0.533000	0.62120	CAT	.	.		0.398	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		C	146256475	T	C	146256475	3	2	188	1	0	0	0	0	1	0	0	0	14306	1464	51	2	2499	2	SHPRH	6	146256475	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	55845090	146256475	24858592	49	27800										
OPRM1	4988	hgsc.bcm.edu	37	chr6	154414485	154414485	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	cctggaccactgcaaggaccTcttgtcagatatgacctccc	8	15	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr6:154414485T>A	ENST00000330432.7	+	3	1401				OPRM1_ENST00000229768.5_Silent_p.P415P|OPRM1_ENST00000524163.1_Intron|OPRM1_ENST00000419506.2_Intron|OPRM1_ENST00000522236.1_Intron|OPRM1_ENST00000452687.2_Intron|OPRM1_ENST00000337049.4_Intron|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000435918.2_Intron|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000360422.4_Intron|OPRM1_ENST00000522555.1_Intron|OPRM1_ENST00000434900.2_Intron|OPRM1_ENST00000414028.2_Intron	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1						adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	TGCAAGGACCTCTTGTCAGAT	0.522																																					p.P415P		Atlas-SNP	.											.	OPRM1	241	.	0			c.T1245A						.						244	233	236					6																	154414485		1979	4166	6145	SO:0001627	intron_variant	4988	exon4			AGGACCTCTTGTC	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.1164+1878T>A	chr6.hg19:g.154414485T>A		65.0	0.0		62.0	25.0	NM_001008505	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Silent	SNP	ENST00000330432.7	hg19	CCDS55070.1																																																																																			.	.		0.522	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		A	154414485	T	A	154414485	1	1	188	0	1	0	0	0	0	0	0	0	10896	1538	54	4		4	OPRM1	6	154414485	Intron	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	8158010	154414485	16700582	50	27801										
DFNA5	1687	hgsc.bcm.edu	37	chr7	24738645	24738645	+	Nonstop_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	cttctagttcacatatgacaTcatgaatgttctctgcctaa	5	10	4	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr7:24738645T>A	ENST00000342947.3	-	10	1916	c.1491A>T	c.(1489-1491)tgA>tgT	p.*497C	DFNA5_ENST00000545231.1_Nonstop_Mutation_p.*333C|DFNA5_ENST00000409775.3_Nonstop_Mutation_p.*497C|DFNA5_ENST00000419307.1_Nonstop_Mutation_p.*333C|DFNA5_ENST00000409970.1_Nonstop_Mutation_p.*333C	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	0					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						ACATATGACATCATGAATGTT	0.388																																					p.X497C	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.A1491T						.						68	65	66					7																	24738645		2203	4300	6503	SO:0001578	stop_lost	1687	exon10			ATGACATCATGAA	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.1491A>T	chr7.hg19:g.24738645T>A		138.0	0.0		137.0	56.0	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	hg19	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	T	13.49	2.253495	0.39797	.	.	ENSG00000105928	ENST00000342947;ENST00000419307;ENST00000545231;ENST00000409970;ENST00000409775	.	.	.	4.89	0.879	0.19155	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.0522	0.06173	0.4114:0.1138:0.0:0.4748	.	.	.	.	C	497;333;333;333;497	.	.	X	-	3	0	DFNA5	24705170	0.000000	0.05858	0.000000	0.03702	0.237000	0.25408	-0.136000	0.10405	0.225000	0.20959	0.455000	0.32223	TGA	.	.		0.388	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		A	24738645	T	A	24738645	4	1	188	1	0	0	0	0	0	0	0	0	4456	1448	50	4	3	4	DFNA5	7	24738645	Nonstop_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10		24738645	134400018	51	27802										
POM121L12	285877	hgsc.bcm.edu	37	chr7	53103849	53103849	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	acagagagcccgccccgcagGccgccccgccgcccaggagc	13	21	0	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr7:53103849G>A	ENST00000408890.4	+	1	501	c.485G>A	c.(484-486)gGc>gAc	p.G162D		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	162										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						cgccccgcaggccgccccgcc	0.731																																					p.G162D		Atlas-SNP	.											.	POM121L12	146	.	0			c.G485A						.						12	16	15					7																	53103849		1836	4040	5876	SO:0001583	missense	285877	exon1			CCGCAGGCCGCCC		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.485G>A	chr7.hg19:g.53103849G>A	ENSP00000386133:p.Gly162Asp	59.0	0.0		50.0	19.0	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	hg19	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	G	5.425	0.263636	0.10294	.	.	ENSG00000221900	ENST00000408890	T	0.23754	1.89	2.28	-2.06	0.07298	.	.	.	.	.	T	0.12518	0.0304	L	0.43923	1.385	0.09310	N	1	P	0.40211	0.707	B	0.29267	0.1	T	0.25984	-1.0116	9	0.15952	T	0.53	.	3.5864	0.07973	0.4777:0.2328:0.2896:0.0	.	162	Q8N7R1	P1L12_HUMAN	D	162	ENSP00000386133:G162D	ENSP00000386133:G162D	G	+	2	0	POM121L12	53071343	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.588000	0.05774	-0.600000	0.05790	0.505000	0.49811	GGC	.	.		0.731	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		A	53103849	G	A	53103849	3	1	188	1	0	0	0	0	1	0	0	0	12250	1203	42	3	487	3	POM121L12	7	53103849	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	28365204	53103849	106034814	52	27803										
ASL	435	hgsc.bcm.edu	37	chr7	65553861	65553861	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	atggccgaggacctcatcctCtactgcaccaaggaattcag	9	13	3	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr7:65553861C>G	ENST00000304874.9	+	11	888	c.786C>G	c.(784-786)ctC>ctG	p.L262L	ASL_ENST00000380839.4_Silent_p.L236L|ASL_ENST00000395331.3_Silent_p.L262L|ASL_ENST00000395332.3_Silent_p.L262L|AC068533.7_ENST00000450043.1_Missense_Mutation_p.L31V	NM_000048.3	NP_000039.2	P04424	ARLY_HUMAN	argininosuccinate lyase	262					arginine biosynthetic process via ornithine (GO:0042450)|arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|internal protein amino acid acetylation (GO:0006475)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	argininosuccinate lyase activity (GO:0004056)			breast(3)|endometrium(3)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	18					L-Arginine(DB00125)	ACCTCATCCTCTACTGCACCA	0.592																																					p.L262L		Atlas-SNP	.											.	ASL	39	.	0			c.C786G						.						95	72	80					7																	65553861		2203	4300	6503	SO:0001819	synonymous_variant	435	exon11			CATCCTCTACTGC		CCDS5531.1, CCDS47597.1, CCDS47598.1	7q11.21	2012-10-02			ENSG00000126522	ENSG00000126522	4.3.2.1		746	protein-coding gene	gene with protein product		608310					Standard	NM_001024943		Approved		uc003tuo.3	P04424	OTTHUMG00000022876	ENST00000304874.9:c.786C>G	chr7.hg19:g.65553861C>G		70.0	0.0		72.0	28.0	NM_000048	E7EMI0|E9PE48|Q6LDS5|Q96HS2	Silent	SNP	ENST00000304874.9	hg19	CCDS5531.1	.	.	.	.	.	.	.	.	.	.	c	6.793	0.515327	0.12944	.	.	ENSG00000249319	ENST00000450043	D	0.99488	-6.0	5.82	2.64	0.31445	.	0.232964	0.37053	N	0.002271	D	0.99026	0.9667	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.98894	1.0774	7	0.72032	D	0.01	.	8.9405	0.35727	0.0:0.7156:0.1289:0.1554	.	.	.	.	V	31	ENSP00000396527:L31V	ENSP00000396527:L31V	L	+	1	2	AC068533.7	65191296	0.997000	0.39634	1.000000	0.80357	0.621000	0.37620	0.360000	0.20250	1.443000	0.47586	0.561000	0.74099	CTA	.	.		0.592	ASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251695.2	NM_000048		G	65553861	C	G	65553861	2	3	188	1	0	0	0	0	0	0	0	1	1044	900	32	4		4	ASL	7	65553861	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	12450012	65553861	93584802	53	27804										
CDK14	5218	hgsc.bcm.edu	37	chr7	90546967	90546967	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	cttacatccaccagcgttatAttttgcacagagacctgaaa	6	11	0	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr7:90546967A>G	ENST00000380050.3	+	8	885	c.754A>G	c.(754-756)Att>Gtt	p.I252V	CDK14_ENST00000436577.2_Missense_Mutation_p.I123V|CDK14_ENST00000406263.1_Missense_Mutation_p.I206V|CDK14_ENST00000265741.3_Missense_Mutation_p.I234V			O94921	CDK14_HUMAN	cyclin-dependent kinase 14	252	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						CCAGCGTTATATTTTGCACAG	0.408																																					p.I234V	GBM(83;1228 1256 8311 16577 31299)	Atlas-SNP	.											.	CDK14	153	.	0			c.A700G						.						150	141	144					7																	90546967		2203	4300	6503	SO:0001583	missense	5218	exon7			CGTTATATTTTGC		CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"Cyclin-dependent kinases"	8883	protein-coding gene	gene with protein product		610679	"PFTAIRE protein kinase 1"	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.754A>G	chr7.hg19:g.90546967A>G	ENSP00000369390:p.Ile252Val	123.0	0.0		110.0	34.0	NM_012395	A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Missense_Mutation	SNP	ENST00000380050.3	hg19		.	.	.	.	.	.	.	.	.	.	A	6.556	0.470892	0.12461	.	.	ENSG00000058091	ENST00000380050;ENST00000265741;ENST00000406263;ENST00000436577	T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38	5.34	5.34	0.76211	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.55242	0.1908	N	0.21508	0.67	0.50039	D	0.999845	B;B;B	0.32781	0.015;0.384;0.049	B;B;B	0.41374	0.019;0.355;0.049	T	0.51919	-0.8644	10	0.02654	T	1	-16.7703	15.3134	0.74053	1.0:0.0:0.0:0.0	.	123;234;252	E7EUK8;O94921-2;O94921	.;.;CDK14_HUMAN	V	252;234;206;123	ENSP00000369390:I252V;ENSP00000265741:I234V;ENSP00000385034:I206V;ENSP00000398936:I123V	ENSP00000265741:I234V	I	+	1	0	CDK14	90384903	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.295000	0.72744	2.027000	0.59764	0.383000	0.25322	ATT	.	.		0.408	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5	NM_012395		G	90546967	A	G	90546967	3	3	188	1	0	0	0	0	1	0	0	0	3132	449	16	2	726	2	CDK14	7	90546967	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	24993106	90546967	68591696	54	27805										
MEST	4232	hgsc.bcm.edu	37	chr7	130140357	130140357	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tcacacgactgatgaacttcTttgtattctctcgagggtaa	8	9	3	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr7:130140357T>G	ENST00000223215.4	+	8	852	c.631T>G	c.(631-633)Ttt>Gtt	p.F211V	MEST_ENST00000393187.1_Missense_Mutation_p.F202V|MEST_ENST00000341441.5_Missense_Mutation_p.F202V|MEST_ENST00000378576.4_Missense_Mutation_p.F202V|MEST_ENST00000437945.1_Missense_Mutation_p.F211V|MEST_ENST00000462132.1_3'UTR|MEST_ENST00000416162.2_Missense_Mutation_p.F202V|hsa-mir-335_ENST00000604666.1_RNA	NM_001253900.1|NM_002402.3	NP_001240829.1|NP_002393.2	Q5EB52	MEST_HUMAN	mesoderm specific transcript	211					mesoderm development (GO:0007498)|regulation of lipid storage (GO:0010883)|response to retinoic acid (GO:0032526)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(2)	12	Melanoma(18;0.0435)					GATGAACTTCTTTGTATTCTC	0.473																																					p.F211V	Colon(126;2182 2305 6517 35181)	Atlas-SNP	.											.	MEST	28	.	0			c.T631G						.						80	68	72					7																	130140357		2203	4300	6503	SO:0001583	missense	4232	exon8			AACTTCTTTGTAT		CCDS5822.1, CCDS5823.1, CCDS59081.1	7q32	2014-08-22	2012-12-07		ENSG00000106484	ENSG00000106484			7028	protein-coding gene	gene with protein product	"Paternally-expressed gene 1"	601029	"mesoderm specific transcript (mouse) homolog", "mesoderm specific transcript homolog (mouse)"			8884280	Standard	NM_002402		Approved	PEG1	uc003vqg.3	Q5EB52	OTTHUMG00000156661	ENST00000223215.4:c.631T>G	chr7.hg19:g.130140357T>G	ENSP00000223215:p.Phe211Val	96.0	0.0		90.0	37.0	NM_002402	B2R6S1|O14973|O15007|Q6AI49|Q92571	Missense_Mutation	SNP	ENST00000223215.4	hg19	CCDS5822.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.071325	0.36566	.	.	ENSG00000106484	ENST00000341441;ENST00000427521;ENST00000416162;ENST00000378576;ENST00000393187;ENST00000421001;ENST00000223215;ENST00000437945	T;T;T;T;T;T;T;T	0.67698	-0.22;-0.28;-0.28;-0.28;-0.22;0.95;-0.22;-0.22	6.07	6.07	0.98685	.	0.303326	0.42053	D	0.000774	T	0.55673	0.1935	L	0.33485	1.01	0.34750	D	0.731646	B;B;B;B	0.17667	0.004;0.023;0.023;0.004	B;B;B;B	0.15052	0.003;0.012;0.012;0.007	T	0.59679	-0.7409	10	0.17832	T	0.49	.	15.4508	0.75271	0.0:0.0:0.0:1.0	.	197;211;211;202	B4DQW6;C9JW74;Q5EB52;Q5EB52-3	.;.;MEST_HUMAN;.	V	202;202;202;202;202;202;211;211	ENSP00000342749:F202V;ENSP00000409505:F202V;ENSP00000408933:F202V;ENSP00000367839:F202V;ENSP00000376884:F202V;ENSP00000407222:F202V;ENSP00000223215:F211V;ENSP00000401657:F211V	ENSP00000223215:F211V	F	+	1	0	MEST	129927593	1.000000	0.71417	0.999000	0.59377	0.665000	0.39181	2.756000	0.47549	2.326000	0.78906	0.528000	0.53228	TTT	.	.		0.473	MEST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345183.2	NM_002402		G	130140357	T	G	130140357	3	3	188	1	0	0	0	0	1	0	0	0	9493	1609	56	5	661	5	MEST	7	130140357	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	39593390	130140357	28998306	55	27806										
LUC7L2	100996928	hgsc.bcm.edu	37	chr7	139097314	139097314	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	taggtcccgatcacacagcaAgaatccaaaaaggtaggtgt	10	9	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr7:139097314A>T	ENST00000354926.4	+	8	1151	c.797A>T	c.(796-798)aAg>aTg	p.K266M	C7orf55-LUC7L2_ENST00000541170.3_Missense_Mutation_p.K263M|C7orf55-LUC7L2_ENST00000263545.6_Missense_Mutation_p.K265M|LUC7L2_ENST00000541515.3_Missense_Mutation_p.K332M	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough																		TCACACAGCAAGAATCCAAAA	0.289																																					p.K332M		Atlas-SNP	.											.	.	.	.	0			c.A995T						.						126	124	124					7																	139097314		1811	4069	5880	SO:0001583	missense	100996928	exon9			ACAGCAAGAATCC		CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.797A>T	chr7.hg19:g.139097314A>T	ENSP00000347005:p.Lys266Met	75.0	0.0		97.0	4.0	NM_001244584		Missense_Mutation	SNP	ENST00000354926.4	hg19	CCDS43656.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.032403	0.75504	.	.	ENSG00000146963	ENST00000541170;ENST00000541515;ENST00000545899;ENST00000354926;ENST00000263545	T;T;T;T	0.31769	1.48;1.48;1.48;3.22	5.49	5.49	0.81192	.	0.223475	0.43747	D	0.000528	T	0.36193	0.0958	N	0.14661	0.345	0.34584	D	0.714818	D;D;D;D	0.69078	0.995;0.989;0.997;0.989	P;P;D;P	0.64237	0.839;0.737;0.923;0.737	T	0.51252	-0.8729	9	0.59425	D	0.04	-15.0866	14.1756	0.65539	1.0:0.0:0.0:0.0	.	332;263;265;266	B7Z4Q3;B7Z500;Q9Y383-2;Q9Y383	.;.;.;LC7L2_HUMAN	M	263;332;266;266;265	ENSP00000441604:K263M;ENSP00000440222:K332M;ENSP00000347005:K266M;ENSP00000263545:K265M	ENSP00000263545:K265M	K	+	2	0	LUC7L2	138747854	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.717000	0.54911	2.089000	0.63090	0.528000	0.53228	AAG	.	.		0.289	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2			T	139097314	A	T	139097314	3	4	188	1	0	0	0	0	1	0	0	0	9092	72	3	4	827	4	LUC7L2	7	139097314	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	8956957	139097314	20041349	56	27807										
MGAM	8972	hgsc.bcm.edu	37	chr7	141764321	141764321	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	cccagaccagacccacatacGagtgagtctccgtctccctt	7	17	2	3	rs374771873		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr7:141764321G>T	ENST00000549489.2	+	37	4578	c.4483G>T	c.(4483-4485)Gaa>Taa	p.E1495*	MGAM_ENST00000475668.2_Splice_Site_p.E1495*	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1495	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ACCCACATACGAGTGAGTCTC	0.517																																					p.E1495X		Atlas-SNP	.											.	MGAM	767	.	0			c.G4483T						.	G	stop/GLU	0,3978		0,0,1989	18	20	19		4483	4.2	1	7		19	1,8297		0,1,4148	no	stop-gained-near-splice	MGAM	NM_004668.2		0,1,6137	TT,TG,GG		0.0121,0.0,0.0081		1495/1858	141764321	1,12275	1989	4149	6138	SO:0001630	splice_region_variant	8972	exon37			ACATACGAGTGAG	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4484+1G>T	chr7.hg19:g.141764321G>T		87.0	0.0		61.0	4.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Nonsense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	G	42	9.455672	0.99175	0.0	1.21E-4	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	.	.	.	4.22	4.22	0.49857	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	15.4323	0.75112	0.0:0.0:1.0:0.0	.	.	.	.	X	1495;1495;1372	.	ENSP00000316431:E1372X	E	+	1	0	MGAM	141410790	1.000000	0.71417	0.999000	0.59377	0.199000	0.23934	5.512000	0.67030	1.888000	0.54679	0.306000	0.20318	GAA	.	.		0.517	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		Nonsense_Mutation	T	141764321	G	T	141764321	5	4	188	1	0	0	0	0	0	0	1	0	9550	1072	37	1	4625	1	MGAM	7	141764321	Splice_Site	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	2667007	141764321	17374342	57	27808										
MYBL1	4603	hgsc.bcm.edu	37	chr8	67505381	67505381	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aaaggcagaagtaggctgaaCatgttctatacaattgcctt	9	7	1	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr8:67505381C>A	ENST00000522677.3	-	7	1146	c.736G>T	c.(736-738)Gtt>Ttt	p.V246F	MYBL1_ENST00000524176.2_Missense_Mutation_p.V246F|MYBL1_ENST00000517885.1_Intron	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	246	Transcriptional activation domain. {ECO:0000250}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			GTAGGCTGAACATGTTCTATA	0.303																																					p.V246F		Atlas-SNP	.											.	MYBL1	73	.	0			c.G736T						.						62	57	59					8																	67505381		1822	4081	5903	SO:0001583	missense	4603	exon7			GCTGAACATGTTC	X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.736G>T	chr8.hg19:g.67505381C>A	ENSP00000429633:p.Val246Phe	439.0	0.0		615.0	97.0	NM_001080416	E7EW29|Q495F9	Missense_Mutation	SNP	ENST00000522677.3	hg19	CCDS47867.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.835418	0.32421	.	.	ENSG00000185697	ENST00000522677;ENST00000524176	T;T	0.18657	2.68;2.2	5.66	1.93	0.25924	Transcription regulator Wos2-domain (1);	0.549745	0.18931	N	0.127216	T	0.11793	0.0287	N	0.25647	0.755	0.30933	N	0.726648	B;B;B	0.16166	0.002;0.016;0.001	B;B;B	0.16289	0.007;0.015;0.009	T	0.35251	-0.9796	10	0.09843	T	0.71	-5.0933	8.6068	0.33778	0.0:0.4931:0.0:0.5069	.	246;246;246	Q495F9;Q495G0;P10243	.;.;MYBA_HUMAN	F	246	ENSP00000429633:V246F;ENSP00000428011:V246F	ENSP00000429633:V246F	V	-	1	0	MYBL1	67667935	0.917000	0.31117	0.994000	0.49952	0.926000	0.56050	-0.116000	0.10724	0.068000	0.16574	-0.214000	0.12660	GTT	.	.		0.303	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		A	67505381	C	A	67505381	3	1	188	1	0	0	0	0	1	0	0	0	10018	478	17	3	1562	3	MYBL1	8	67505381	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10		67505381	78858641	58	27809										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125103743	125103743	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gcaaagacaacaagctggatGgaccctactttcaccctggg	10	12	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr8:125103743G>T	ENST00000522917.1	+	34	4677	c.4471G>T	c.(4471-4473)Gga>Tga	p.G1491*	FER1L6_ENST00000399018.1_Nonsense_Mutation_p.G1491*|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1491						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CAAGCTGGATGGACCCTACTT	0.448																																					p.G1491X		Atlas-SNP	.											.	FER1L6	268	.	0			c.G4471T						.						125	117	119					8																	125103743		1901	4113	6014	SO:0001587	stop_gained	654463	exon34			CTGGATGGACCCT	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.4471G>T	chr8.hg19:g.125103743G>T	ENSP00000428280:p.Gly1491*	145.0	0.0		283.0	37.0	NM_001039112		Nonsense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	43	10.513761	0.99419	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	.	.	.	5.86	5.86	0.93980	.	0.278293	0.35466	U	0.003194	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-18.2966	20.2019	0.98263	0.0:0.0:1.0:0.0	.	.	.	.	X	1491	.	ENSP00000381982:G1491X	G	+	1	0	FER1L6	125172924	1.000000	0.71417	0.990000	0.47175	0.226000	0.24999	7.682000	0.84083	2.776000	0.95493	0.655000	0.94253	GGA	.	.		0.448	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		T	125103743	G	T	125103743	4	4	188	1	0	0	0	0	0	1	0	0	5823	1349	47	3	4601	3	FER1L6	8	125103743	Nonsense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	57598362	125103743	21260279	59	27810										
CEP110	11064	hgsc.bcm.edu	37	chr9	123921275	123921275	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	actgggagagactgaagtaaCtgagaagtgcaatcacatta	11	6	1	3	rs145607154		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr9:123921275C>T	ENST00000373855.1	+	31	5167	c.4907C>T	c.(4906-4908)aCt>aTt	p.T1636I	CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000373850.1_Missense_Mutation_p.T1084I|CNTRL_ENST00000373844.1_Missense_Mutation_p.T81I|CNTRL_ENST00000238341.5_Missense_Mutation_p.T1636I			Q7Z7A1	CNTRL_HUMAN	centriolin	1636					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						ACTGAAGTAACTGAGAAGTGC	0.433																																					p.T1636I		Atlas-SNP	.											.	CNTRL	161	.	0			c.C4907T						.						152	158	156					9																	123921275		2203	4300	6503	SO:0001583	missense	11064	exon29			AAGTAACTGAGAA	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.4907C>T	chr9.hg19:g.123921275C>T	ENSP00000362962:p.Thr1636Ile	120.0	0.0		143.0	42.0	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.476772	0.26511	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000373850;ENST00000431571;ENST00000373845;ENST00000373844	T;T;T	0.29917	1.55;1.55;1.55	5.64	4.75	0.60458	.	.	.	.	.	T	0.27384	0.0672	L	0.44542	1.39	0.09310	N	1	B	0.16603	0.018	B	0.14023	0.01	T	0.16660	-1.0395	9	0.54805	T	0.06	.	9.8339	0.40958	0.1457:0.7799:0.0:0.0744	.	1636	Q7Z7A1	CNTRL_HUMAN	I	1636;1636;1636;392;1084;305;318;81	ENSP00000362962:T1636I;ENSP00000238341:T1636I;ENSP00000362956:T1084I	ENSP00000238341:T1636I	T	+	2	0	CNTRL	122961096	0.043000	0.20138	0.466000	0.27168	0.592000	0.36648	1.016000	0.29976	1.522000	0.49001	0.650000	0.86243	ACT	.	C|1.000;A|0.000		0.433	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		T	123921275	C	T	123921275	3	4	188	1	0	0	0	0	1	0	0	0	3247	565	20	3	5021	3	CEP110	9	123921275	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10		123921275	17292156	60	27811										
GRIN1	2902	hgsc.bcm.edu	37	chr9	140056943	140056943	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	atgtggttctcctggggcgtCctgctcaactccggcatcgg	13	13	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr9:140056943C>A	ENST00000371561.3	+	13	2936	c.1839C>A	c.(1837-1839)gtC>gtA	p.V613V	GRIN1_ENST00000371555.4_Silent_p.V634V|GRIN1_ENST00000315048.3_Silent_p.V613V|GRIN1_ENST00000371560.3_Silent_p.V634V|GRIN1_ENST00000350902.5_Silent_p.V613V|GRIN1_ENST00000371550.4_Silent_p.V613V|GRIN1_ENST00000371553.3_Silent_p.V634V|GRIN1_ENST00000471122.1_3'UTR|GRIN1_ENST00000371546.4_Silent_p.V634V|GRIN1_ENST00000371559.4_Silent_p.V613V	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	613					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCTGGGGCGTCCTGCTCAACT	0.716																																					p.V634V	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											.	GRIN1	51	.	0			c.C1902A						.						23	27	26					9																	140056943		2199	4299	6498	SO:0001819	synonymous_variant	2902	exon14			GGGCGTCCTGCTC		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4584	protein-coding gene	gene with protein product		138249	"N-methyl-D-aspartate receptor subunit NR1"	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.1839C>A	chr9.hg19:g.140056943C>A		72.0	0.0		62.0	29.0	NM_001185091	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Silent	SNP	ENST00000371561.3	hg19	CCDS7031.1																																																																																			.	.		0.716	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327		A	140056943	C	A	140056943	2	1	188	1	0	0	0	0	0	0	0	1	6787	842	30	3		3	GRIN1	9	140056943	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	16135668	140056943	1156488	61	27812										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88197724	88197724	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tttgagcatctctgtcattaTtgaaaagtctccttctggca	7	9	4	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr10:88197724T>C	ENST00000298767.5	-	18	3932	c.3460A>G	c.(3460-3462)Ata>Gta	p.I1154V	WAPAL_ENST00000484070.1_5'UTR|WAPAL_ENST00000263070.7_Missense_Mutation_p.I366V|WAPAL_ENST00000372075.1_Missense_Mutation_p.I366V	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	1154	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						TCTGTCATTATTGAAAAGTCT	0.333																																					p.I1154V		Atlas-SNP	.											.	WAPAL	81	.	0			c.A3460G						.						64	70	68					10																	88197724		2203	4300	6503	SO:0001583	missense	23063	exon18			TCATTATTGAAAA	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.3460A>G	chr10.hg19:g.88197724T>C	ENSP00000298767:p.Ile1154Val	360.0	0.0		392.0	123.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.222198	0.39300	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076;ENST00000372075;ENST00000263070	T;T;T	0.36699	1.24;1.24;1.24	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.25382	0.0617	N	0.15975	0.35	0.58432	D	0.999991	B;B;B;B	0.30563	0.157;0.076;0.157;0.285	B;B;B;B	0.35470	0.033;0.028;0.033;0.203	T	0.09058	-1.0692	10	0.12103	T	0.63	.	16.0204	0.80478	0.0:0.0:0.0:1.0	.	1148;1192;1154;1191	B2RTX8;E9PH12;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	V	1239;1154;1239;366;366	ENSP00000298767:I1154V;ENSP00000361145:I366V;ENSP00000263070:I366V	ENSP00000263070:I366V	I	-	1	0	WAPAL	88187704	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.928000	0.70088	2.174000	0.68829	0.533000	0.62120	ATA	.	.		0.333	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		C	88197724	T	C	88197724	3	2	188	1	0	0	0	0	1	0	0	0	17263	1493	52	2	120	2	WAPAL	10	88197724	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10		88197724	47337023	62	27813										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106865229	106865229	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggccttttgcccgctccattGacatcagttccctggttgtc	9	14	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr10:106865229G>T	ENST00000369701.3	+	7	1395	c.1168G>T	c.(1168-1170)Gac>Tac	p.D390Y		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	390					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CCGCTCCATTGACATCAGTTC	0.502																																					p.D390Y	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.G1168T						.						180	151	161					10																	106865229		2203	4300	6503	SO:0001583	missense	22986	exon7			TCCATTGACATCA	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1168G>T	chr10.hg19:g.106865229G>T	ENSP00000358715:p.Asp390Tyr	73.0	0.0		56.0	25.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.647053	0.67358	.	.	ENSG00000156395	ENST00000369701	T	0.40476	1.03	5.43	5.43	0.79202	VPS10 (1);	0.050677	0.85682	D	0.000000	T	0.64811	0.2632	M	0.78637	2.42	0.42010	D	0.990931	D	0.89917	1.0	D	0.70935	0.971	T	0.69386	-0.5159	10	0.87932	D	0	.	14.727	0.69351	0.0:0.0:1.0:0.0	.	390	Q9UPU3	SORC3_HUMAN	Y	390	ENSP00000358715:D390Y	ENSP00000358715:D390Y	D	+	1	0	SORCS3	106855219	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.115000	0.71566	2.536000	0.85505	0.462000	0.41574	GAC	.	.		0.502	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		T	106865229	G	T	106865229	3	4	188	1	0	0	0	0	1	0	0	0	14947	1290	45	3	1194	3	SORCS3	10	106865229	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	18667505	106865229	28669518	63	27814										
HABP2	3026	hgsc.bcm.edu	37	chr10	115337800	115337801	+	Missense_Mutation	DNP	GG	GG	AT													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	cacagtggttcctgtatgcaGgccaaacccctgccagaatg							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr10:115337800_115337801GG>AT	ENST00000351270.3	+	6	560_561	c.464_465GG>AT	c.(463-465)aGG>aAT	p.R155N	HABP2_ENST00000542051.1_Missense_Mutation_p.R129N|HABP2_ENST00000541666.1_Missense_Mutation_p.R155N|HABP2_ENST00000537906.1_Missense_Mutation_p.G144I	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2	155	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	CCTGTATGCAGGCCAAACCCCT	0.545																																					p.R155K|p.R155S		Atlas-SNP	.											.	HABP2	52	.	0			c.G464A|c.G465T						.																																			SO:0001583	missense	3026	exon6			TATGCAGGCCAAA|ATGCAGGCCAAAC		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"plasma hyaluronan binding protein", "factor VII activating protein"	603924	"hyaluronan-binding protein 2"			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	Exception_encountered	chr10.hg19:g.115337800_115337801delinsAT	ENSP00000277903:p.Arg155Asn	53.0|54.0	0.0		54.0	28.0	NM_004132	A8K467|B7Z8U5|F5H5M6|O00663	Missense_Mutation	SNP	ENST00000351270.3	hg19	CCDS7577.1																																																																																			.	.		0.545	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132		AT	115337801	GG	AT	115337800	3	1	188	1	0	0	0	0	1	0	0	0	6947	1000	35	3	486	3	HABP2	10	115337800	Missense_Mutation	DNP	GG	TCGA-DD-AADE-01A-11D-A40R-10	8472571	115337800	20196947	64	27815										
EBF3	253738	hgsc.bcm.edu	37	chr10	131671777	131671777	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aggcggcgggcccgcctcccGtgtttggaattgttgtgcac	15	12	0	0	rs368078346		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr10:131671777G>A	ENST00000355311.5	-	8	792	c.720C>T	c.(718-720)caC>caT	p.H240H	EBF3_ENST00000368648.3_Silent_p.H240H			Q9H4W6	COE3_HUMAN	early B-cell factor 3	240					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		CCCGCCTCCCGTGTTTGGAAT	0.512																																					p.H240H		Atlas-SNP	.											EBF3_ENST00000355311,NS,carcinoma,0,2	EBF3	193	.	0			c.C720T						.	G		0,4406		0,0,2203	60	59	60		720	0.9	1	10		60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EBF3	NM_001005463.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		240/552	131671777	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	253738	exon8			CCTCCCGTGTTTG		CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.720C>T	chr10.hg19:g.131671777G>A		59.0	0.0		29.0	13.0	NM_001005463	A0AUY1|Q5T6H9|Q9H4W5	Silent	SNP	ENST00000355311.5	hg19																																																																																				.	.		0.512	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		A	131671777	G	A	131671777	2	1	188	1	0	0	0	0	0	0	0	1	4884	1136	40	1		1	EBF3	10	131671777	Silent	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	16333977	131671777	3862970	65	27816										
MUC2	4583	hgsc.bcm.edu	37	chr11	1087896	1087896	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	agccatattctgcgactactAcaaccctccgcatgagtgtg	8	13	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr11:1087896A>G	ENST00000441003.2	+	25	3398	c.3371A>G	c.(3370-3372)tAc>tGc	p.Y1124C	MUC2_ENST00000359061.5_Missense_Mutation_p.Y1124C	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1124					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TGCGACTACTACAACCCTCCG	0.627																																					p.Y1124C		Atlas-SNP	.											.	MUC2	614	.	0			c.A3371G						.						57	63	61					11																	1087896		2124	4232	6356	SO:0001583	missense	4583	exon25			ACTACTACAACCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3371A>G	chr11.hg19:g.1087896A>G	ENSP00000415183:p.Tyr1124Cys	53.0	0.0		53.0	11.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	a	12.88	2.070145	0.36566	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.14766	2.48;2.48	3.84	3.84	0.44239	.	0.221298	0.29335	N	0.012458	T	0.40040	0.1101	M	0.86028	2.79	0.40527	D	0.980891	D	0.76494	0.999	D	0.79108	0.992	T	0.49224	-0.8962	10	0.87932	D	0	.	12.8325	0.57754	1.0:0.0:0.0:0.0	.	1124	E7EUV1	.	C	1124	ENSP00000415183:Y1124C;ENSP00000351956:Y1124C	ENSP00000351956:Y1124C	Y	+	2	0	MUC2	1077896	1.000000	0.71417	1.000000	0.80357	0.529000	0.34654	7.107000	0.77047	1.617000	0.50277	0.450000	0.29827	TAC	.	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1087896	A	G	1087896	3	3	188	1	0	0	0	0	1	0	0	0	9984	391	14	2	3469	2	MUC2	11	1087896	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10		1087896	133918620	66	27817										
SPRYD5	84767	hgsc.bcm.edu	37	chr11	55653151	55653151	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ttgccagaaaagccagcctcCggcaattccttagctctgag	9	13	1	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr11:55653151C>T	ENST00000449290.2	+	2	339	c.247C>T	c.(247-249)Cgg>Tgg	p.R83W	TRIM51_ENST00000244891.3_5'Flank	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	83						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										AGCCAGCCTCCGGCAATTCCT	0.483																																					p.R83W		Atlas-SNP	.											SPRYD5_ENST00000327733,NS,carcinoma,0,2	.	.	.	0			c.C247T						.						17	15	16					11																	55653151		692	1590	2282	SO:0001583	missense	84767	exon2			AGCCTCCGGCAAT	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19023	protein-coding gene	gene with protein product			"SPRY domain containing 5"	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.247C>T	chr11.hg19:g.55653151C>T	ENSP00000395086:p.Arg83Trp	120.0	0.0		102.0	5.0	NM_032681	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	hg19		.	.	.	.	.	.	.	.	.	.	.	0.878	-0.729638	0.03135	.	.	ENSG00000124900	ENST00000449290	T	0.63096	-0.02	.	.	.	Zinc finger, RING/FYVE/PHD-type (1);	.	.	.	.	T	0.34861	0.0912	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.10520	-1.0626	8	0.52906	T	0.07	.	5.1874	0.15191	0.3697:0.6303:0.0:0.0	.	83	Q9BSJ1	SPRY5_HUMAN	W	83	ENSP00000395086:R83W	ENSP00000395086:R83W	R	+	1	2	SPRYD5	55409727	0.002000	0.14202	0.027000	0.17364	0.057000	0.15508	-1.326000	0.02685	-1.461000	0.01909	-1.906000	0.00525	CGG	.	.		0.483	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681		T	55653151	C	T	55653151	3	4	188	1	0	0	0	0	1	0	0	0	15126	643	23	1	249	1	SPRYD5	11	55653151	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	54565255	55653151	79353365	67	27818										
TUT1	64852	hgsc.bcm.edu	37	chr11	62343405	62343405	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggagctgggggagctgggctGcagaagagggagcagccccc	20	10	0	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr11:62343405G>A	ENST00000476907.1	-	9	2477	c.1786C>T	c.(1786-1788)Cag>Tag	p.Q596*	EEF1G_ENST00000378019.3_5'Flank|EEF1G_ENST00000532986.1_5'Flank|TUT1_ENST00000308436.7_Nonsense_Mutation_p.Q634*|MIR3654_ENST00000496634.2_Intron|EEF1G_ENST00000329251.4_5'Flank			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	596					mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GAGCTGGGCTGCAGAAGAGGG	0.642																																					p.Q634X		Atlas-SNP	.											.	TUT1	122	.	0			c.C1900T						.						40	44	43					11																	62343405		2202	4299	6501	SO:0001587	stop_gained	64852	exon9			TGGGCTGCAGAAG	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"RNA binding motif (RRM) containing"	26184	protein-coding gene	gene with protein product	"RNA uridylyltransferase", "U6 TUTase", "TUTase 6"	610641	"RNA binding motif protein 21"	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.1786C>T	chr11.hg19:g.62343405G>A	ENSP00000419607:p.Gln596*	91.0	0.0		86.0	23.0	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Nonsense_Mutation	SNP	ENST00000476907.1	hg19		.	.	.	.	.	.	.	.	.	.	G	44	10.816036	0.99472	.	.	ENSG00000149016	ENST00000308436;ENST00000476907	.	.	.	5.52	5.52	0.82312	.	0.338854	0.32002	N	0.006728	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-6.5008	16.9363	0.86203	0.0:0.0:1.0:0.0	.	.	.	.	X	634;596	.	ENSP00000308000:Q634X	Q	-	1	0	TUT1	62099981	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	5.604000	0.67626	2.594000	0.87642	0.655000	0.94253	CAG	.	.		0.642	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		A	62343405	G	A	62343405	4	1	188	1	0	0	0	0	0	1	0	0	16795	1328	46	3	842	3	TUT1	11	62343405	Nonsense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	6690254	62343405	72663111	68	27819										
B3GAT3	26229	hgsc.bcm.edu	37	chr11	62388013	62388013	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tagatagtaggcagggcctcGggttcagggggctgggcagg	20	7	1	1	rs143334227	byFrequency	TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr11:62388013G>A	ENST00000265471.5	-	2	440	c.213C>T	c.(211-213)ccC>ccT	p.P71P	B3GAT3_ENST00000531383.1_Silent_p.P71P|B3GAT3_ENST00000534026.1_Silent_p.P71P	NM_012200.3	NP_036332.2	O94766	B3GA3_HUMAN	beta-1,3-glucuronyltransferase 3	71					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|glucuronosyltransferase activity (GO:0015020)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)|urinary_tract(1)	12						GCAGGGCCTCGGGTTCAGGGG	0.607													G|||	3	0.000599042	0	0	5008	,	,		14644	0		0.003	False		,,,				2504	0				p.P71P		Atlas-SNP	.											.	B3GAT3	24	.	0			c.C213T						.	G		0,4396		0,0,2198	17	23	21		213	-6.1	0.9	11	dbSNP_134	21	1,8587		0,1,4293	no	coding-synonymous	B3GAT3	NM_012200.3		0,1,6491	AA,AG,GG		0.0116,0.0,0.0077		71/336	62388013	1,12983	2198	4294	6492	SO:0001819	synonymous_variant	26229	exon2			GGCCTCGGGTTCA	AB009598	CCDS8025.1	11q12	2014-07-08	2014-07-08		ENSG00000149541	ENSG00000149541	2.4.1.135	"Beta-1,3-glucuronyltransferases"	923	protein-coding gene	gene with protein product	"glucuronosyltransferase I", "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3"	606374	"beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)"			9506957	Standard	NM_012200		Approved	GlcAT-I	uc001ntw.3	O94766	OTTHUMG00000167685	ENST00000265471.5:c.213C>T	chr11.hg19:g.62388013G>A		64.0	0.0		69.0	4.0	NM_012200	B7ZAB3|Q96I06|Q9UEP0	Silent	SNP	ENST00000265471.5	hg19	CCDS8025.1																																																																																			.	G|1.000;A|0.000		0.607	B3GAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395588.1	NM_012200		A	62388013	G	A	62388013	2	1	188	1	0	0	0	0	0	0	0	1	1255	1103	39	1		1	B3GAT3	11	62388013	Silent	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	44608	62388013	72618503	69	27820										
DCUN1D5	84259	hgsc.bcm.edu	37	chr11	102937078	102937078	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	catagatttagcagtatcaaTatcaaggcttctctgatctt	6	8	4	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr11:102937078T>C	ENST00000260247.5	-	6	817	c.475A>G	c.(475-477)Att>Gtt	p.I159V	DCUN1D5_ENST00000531543.1_Missense_Mutation_p.I74V	NM_032299.3	NP_115675.1	Q9BTE7	DCNL5_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 5	159	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.									NS(1)|central_nervous_system(1)|endometrium(2)	4		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.00032)|Epithelial(105;0.0689)|all cancers(92;0.186)		GCAGTATCAATATCAAGGCTT	0.343																																					p.I159V		Atlas-SNP	.											.	DCUN1D5	11	.	0			c.A475G						.						71	70	71					11																	102937078		2202	4298	6500	SO:0001583	missense	84259	exon6			TATCAATATCAAG		CCDS8325.1	11q22.3	2013-06-10	2013-06-10		ENSG00000137692	ENSG00000137692			28409	protein-coding gene	gene with protein product			"DCN1, defective in cullin neddylation 1, domain containing 5 (S. cerevisiae)"			15988528	Standard	NM_032299		Approved	MGC2714, FLJ32431	uc001phm.3	Q9BTE7	OTTHUMG00000165822	ENST00000260247.5:c.475A>G	chr11.hg19:g.102937078T>C	ENSP00000260247:p.Ile159Val	176.0	0.0		162.0	53.0	NM_032299	Q3ZTT2	Missense_Mutation	SNP	ENST00000260247.5	hg19	CCDS8325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.31|15.31	2.796290|2.796290	0.50208|0.50208	.|.	.|.	ENSG00000137692|ENSG00000137692	ENST00000260247;ENST00000531543|ENST00000527260	T|.	0.21191|.	2.02|.	5.9|5.9	5.9|5.9	0.94986|0.94986	Domain of unknown function DUF298 (2);|.	0.097389|.	0.64402|.	D|.	0.000001|.	T|T	0.56601|0.56601	0.1996|0.1996	L|L	0.31371|0.31371	0.925|0.925	0.50171|0.50171	D|D	0.999855|0.999855	B|.	0.25169|.	0.119|.	B|.	0.25614|.	0.062|.	T|T	0.52726|0.52726	-0.8537|-0.8537	10|5	0.49607|.	T|.	0.09|.	-22.6649|-22.6649	16.3246|16.3246	0.82970|0.82970	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	159|.	Q9BTE7|.	DCNL5_HUMAN|.	V|C	159;74|130	ENSP00000260247:I159V|.	ENSP00000260247:I159V|.	I|Y	-|-	1|2	0|0	DCUN1D5|DCUN1D5	102442288|102442288	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.046000|4.046000	0.57376|0.57376	2.256000|2.256000	0.74724|0.74724	0.528000|0.528000	0.53228|0.53228	ATT|TAT	.	.		0.343	DCUN1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386382.2	NM_032299		C	102937078	T	C	102937078	3	2	188	1	0	0	0	0	1	0	0	0	4319	1406	49	2	250	2	DCUN1D5	11	102937078	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	40549065	102937078	32069438	70	27821										
NFRKB	4798	hgsc.bcm.edu	37	chr11	129745336	129745336	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	cgtgtgccttctccattaggCagtcgagccgcagcgtcccg	12	15	1	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr11:129745336C>T	ENST00000446488.3	-	17	1873	c.1770G>A	c.(1768-1770)ctG>ctA	p.L590L	NFRKB_ENST00000304521.5_Silent_p.L590L|NFRKB_ENST00000524746.1_Silent_p.L590L|NFRKB_ENST00000524794.1_Silent_p.L615L	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	590					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		CTCCATTAGGCAGTCGAGCCG	0.542																																					p.L615L		Atlas-SNP	.											.	NFRKB	101	.	0			c.G1845A						.						82	58	66					11																	129745336		2201	4297	6498	SO:0001819	synonymous_variant	4798	exon16			ATTAGGCAGTCGA		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"INO80 complex subunits"	7802	protein-coding gene	gene with protein product	"nuclear factor related to kappa B binding protein", "DNA-binding protein R kappa B", "INO80 complex subunit G"	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.1770G>A	chr11.hg19:g.129745336C>T		60.0	0.0		53.0	20.0	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	hg19	CCDS44770.1																																																																																			.	.		0.542	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		T	129745336	C	T	129745336	2	4	188	1	0	0	0	0	0	0	0	1	10393	697	25	3		3	NFRKB	11	129745336	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	26808258	129745336	5261180	71	27822										
CLEC12B	387837	hgsc.bcm.edu	37	chr12	10163364	10163364	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gcgttttcttctacaatgtcTgaagaagtgacctacgcgac	9	10	3	3			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr12:10163364T>C	ENST00000338896.5	+	1	134	c.6T>C	c.(4-6)tcT>tcC	p.S2S	CLEC12B_ENST00000396502.1_Silent_p.S2S|CLEC1B_ENST00000428126.2_Intron	NM_001129998.1	NP_001123470.1	Q2HXU8	CL12B_HUMAN	C-type lectin domain family 12, member B	2						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|large_intestine(2)|lung(5)	9						CTACAATGTCTGAAGAAGTGA	0.398																																					p.S2S		Atlas-SNP	.											.	CLEC12B	25	.	0			c.T6C						.						52	50	51					12																	10163364		2203	4300	6503	SO:0001819	synonymous_variant	387837	exon1			AATGTCTGAAGAA	AK128243	CCDS8610.1, CCDS44830.1	12p13.2	2010-08-17			ENSG00000256660	ENSG00000256660		"C-type lectin domain containing"	31966	protein-coding gene	gene with protein product						17562706	Standard	NM_205852		Approved		uc001qwz.2	Q2HXU8	OTTHUMG00000168397	ENST00000338896.5:c.6T>C	chr12.hg19:g.10163364T>C		59.0	0.0		65.0	31.0	NM_001129998	Q6UWF2|Q6ZRG0	Silent	SNP	ENST00000338896.5	hg19	CCDS44830.1																																																																																			.	.		0.398	CLEC12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399554.2	NM_205852		C	10163364	T	C	10163364	2	2	188	1	0	0	0	0	0	0	0	1	3500	1567	55	2		2	CLEC12B	12	10163364	Silent	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10		10163364	123688531	72	27823										
MAP3K12	7786	hgsc.bcm.edu	37	chr12	53879856	53879856	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tcacttgggtgacttgagatCcctgtggataatcttgtgca	11	8	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr12:53879856C>G	ENST00000267079.2	-	5	931	c.706G>C	c.(706-708)Gat>Cat	p.D236H	MAP3K12_ENST00000547035.1_Missense_Mutation_p.D269H|MAP3K12_ENST00000547151.1_5'Flank|MAP3K12_ENST00000547488.1_Missense_Mutation_p.D269H	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	236	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						GACTTGAGATCCCTGTGGATA	0.572																																					p.D269H		Atlas-SNP	.											.	MAP3K12	160	.	0			c.G805C						.						131	111	118					12																	53879856		2203	4300	6503	SO:0001583	missense	7786	exon4			TGAGATCCCTGTG	U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.706G>C	chr12.hg19:g.53879856C>G	ENSP00000267079:p.Asp236His	55.0	0.0		52.0	16.0	NM_001193511	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Missense_Mutation	SNP	ENST00000267079.2	hg19	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.225734	0.79576	.	.	ENSG00000139625	ENST00000267079;ENST00000547488;ENST00000547035	D;D;D	0.96491	-4.03;-4.03;-4.03	5.36	5.36	0.76844	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48286	D	0.000194	D	0.98912	0.9631	H	0.97682	4.055	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99429	1.0935	10	0.87932	D	0	.	18.2434	0.89977	0.0:1.0:0.0:0.0	.	269;236	G3V1Y2;Q12852	.;M3K12_HUMAN	H	236;269;269	ENSP00000267079:D236H;ENSP00000449038:D269H;ENSP00000448689:D269H	ENSP00000267079:D236H	D	-	1	0	MAP3K12	52166123	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.818000	0.86416	2.688000	0.91661	0.561000	0.74099	GAT	.	.		0.572	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		G	53879856	C	G	53879856	3	3	188	1	0	0	0	0	1	0	0	0	9255	855	30	4	1917	4	MAP3K12	12	53879856	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	43716492	53879856	79972039	73	27824										
HOXC8	3224	hgsc.bcm.edu	37	chr12	54405052	54405052	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	accgaaggatgaagtggaaaAaggagaacaacaaggataaa	12	4	0	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr12:54405052A>G	ENST00000040584.4	+	2	853	c.616A>G	c.(616-618)Aag>Gag	p.K206E	RP11-834C11.12_ENST00000513209.1_Intron	NM_022658.3	NP_073149.1	P31273	HXC8_HUMAN	homeobox C8	206					anterior/posterior pattern specification (GO:0009952)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	8						GAAGTGGAAAAAGGAGAACAA	0.478																																					p.K206E	GBM(197;701 2226 7002 18822 41696)	Atlas-SNP	.											.	HOXC8	15	.	0			c.A616G						.						89	92	91					12																	54405052		2203	4300	6503	SO:0001583	missense	3224	exon2			TGGAAAAAGGAGA	X99680	CCDS8870.1	12q13.13	2011-06-20	2005-12-22			ENSG00000037965		"Homeoboxes / ANTP class : HOXL subclass"	5129	protein-coding gene	gene with protein product		142970	"homeo box C8"	HOX3, HOX3A		1973146, 1358459	Standard	NM_022658		Approved		uc001ser.3	P31273		ENST00000040584.4:c.616A>G	chr12.hg19:g.54405052A>G	ENSP00000040584:p.Lys206Glu	69.0	0.0		50.0	16.0	NM_022658	A8K4J4|O15221|O15362	Missense_Mutation	SNP	ENST00000040584.4	hg19	CCDS8870.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.275785	0.80580	.	.	ENSG00000037965	ENST00000040584	D	0.96802	-4.13	5.31	5.31	0.75309	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98686	0.9559	H	0.96430	3.82	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.99701	1.1004	10	0.87932	D	0	.	14.5515	0.68070	1.0:0.0:0.0:0.0	.	206	P31273	HXC8_HUMAN	E	206	ENSP00000040584:K206E	ENSP00000040584:K206E	K	+	1	0	HOXC8	52691319	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.148000	0.66965	0.533000	0.62120	AAG	.	.		0.478	HOXC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358957.2			G	54405052	A	G	54405052	3	3	188	1	0	0	0	0	1	0	0	0	7325	15	1	2	622	2	HOXC8	12	54405052	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	525196	54405052	79446843	74	27825										
MARS	4141	hgsc.bcm.edu	37	chr12	57908591	57908591	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	agcgcctgctggcccatgtcAccctggagctccagcactat	10	16	1	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr12:57908591A>G	ENST00000262027.5	+	16	2190	c.2056A>G	c.(2056-2058)Acc>Gcc	p.T686A	RN7SL312P_ENST00000582079.1_RNA|MARS_ENST00000315473.5_Missense_Mutation_p.T452A	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	686					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	GGCCCATGTCACCCTGGAGCT	0.527																																					p.T686A		Atlas-SNP	.											.	MARS	84	.	0			c.A2056G						.						207	205	206					12																	57908591		2203	4300	6503	SO:0001583	missense	4141	exon16			CATGTCACCCTGG	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.2056A>G	chr12.hg19:g.57908591A>G	ENSP00000262027:p.Thr686Ala	56.0	0.0		47.0	16.0	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	hg19	CCDS8942.1	.	.	.	.	.	.	.	.	.	.	A	11.57	1.676943	0.29783	.	.	ENSG00000166986	ENST00000262027;ENST00000315473;ENST00000552914	T;T;T	0.40225	1.04;1.04;1.04	5.55	1.76	0.24704	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.482752	0.23069	N	0.052298	T	0.12263	0.0298	N	0.01446	-0.86	0.25157	N	0.990387	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.21586	-1.0241	10	0.14252	T	0.57	-11.7149	3.5131	0.07716	0.5466:0.0:0.1484:0.305	.	452;686	A6NC17;P56192	.;SYMC_HUMAN	A	686;452;42	ENSP00000262027:T686A;ENSP00000314653:T452A;ENSP00000449787:T42A	ENSP00000262027:T686A	T	+	1	0	MARS	56194858	0.974000	0.33945	0.840000	0.33206	0.998000	0.95712	0.786000	0.26844	0.413000	0.25759	0.482000	0.46254	ACC	.	.		0.527	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		G	57908591	A	G	57908591	3	3	188	1	0	0	0	0	1	0	0	0	9325	159	6	2	2118	2	MARS	12	57908591	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	3503539	57908591	75943304	75	27826										
TRHDE	29953	hgsc.bcm.edu	37	chr12	72936117	72936117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	taattttatgggccattcagTtttccagaggggtttgcaag	11	6	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr12:72936117T>C	ENST00000261180.4	+	7	1730	c.1634T>C	c.(1633-1635)gTt>gCt	p.V545A		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	545					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						GGCCATTCAGTTTTCCAGAGG	0.303																																					p.V545A		Atlas-SNP	.											.	TRHDE	194	.	0			c.T1634C						.						116	113	114					12																	72936117		2203	4299	6502	SO:0001583	missense	29953	exon7			ATTCAGTTTTCCA	AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"pyroglutamyl-peptidase II", "pyroglutamyl aminopeptidase II", "TRH-specific aminopeptidase"	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.1634T>C	chr12.hg19:g.72936117T>C	ENSP00000261180:p.Val545Ala	65.0	0.0		55.0	23.0	NM_013381	A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	hg19	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.882023	0.51908	.	.	ENSG00000072657	ENST00000261180	T	0.04551	3.6	5.25	5.25	0.73442	.	0.144848	0.47455	D	0.000222	T	0.04679	0.0127	N	0.25825	0.765	0.47511	D	0.999447	B	0.25609	0.13	B	0.15870	0.014	T	0.48917	-0.8992	10	0.30854	T	0.27	.	15.4347	0.75137	0.0:0.0:0.0:1.0	.	545	Q9UKU6	TRHDE_HUMAN	A	545	ENSP00000261180:V545A	ENSP00000261180:V545A	V	+	2	0	TRHDE	71222384	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.764000	0.68826	2.104000	0.64026	0.459000	0.35465	GTT	.	.		0.303	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		C	72936117	T	C	72936117	3	2	188	1	0	0	0	0	1	0	0	0	16494	1725	60	2	1660	2	TRHDE	12	72936117	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	15027526	72936117	60915778	76	27827										
NR2C1	7181	hgsc.bcm.edu	37	chr12	95456409	95456413	+	Frame_Shift_Del	DEL	GAGTA	GAGTA	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggccagaatgactttgcttgGagtagagccgtcgtgatttg					rs377594230		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	GAGTA	GAGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr12:95456409_95456413delGAGTA	ENST00000333003.5	-	3	486_490	c.156_160delTACTC	c.(154-162)tctactccafs	p.TP53fs	NR2C1_ENST00000330677.7_Frame_Shift_Del_p.TP53fs|NR2C1_ENST00000393101.3_Frame_Shift_Del_p.TP53fs|NR2C1_ENST00000545833.1_5'UTR	NM_003297.3	NP_003288.2	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	53	Required for interaction with KAT2B. {ECO:0000250}.				gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	DNA binding (GO:0003677)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13						ACTTTGCTTGGAGTAGAGCCGTCGT	0.454																																					p.53_54del		Atlas-INDEL	.											.	NR2C1	56	.	0			c.157_161del						.																																			SO:0001589	frameshift_variant	7181	exon3			.	M29960	CCDS9051.1, CCDS41821.1, CCDS44953.1	12q22	2013-01-16				ENSG00000120798		"Nuclear hormone receptors"	7971	protein-coding gene	gene with protein product		601529		TR2		2597158	Standard	NM_001032287		Approved	TR2-11	uc001tdm.5	P13056	OTTHUMG00000170131	ENST00000333003.5:c.156_160delTACTC	chr12.hg19:g.95456409_95456413delGAGTA	ENSP00000333275:p.Thr53fs	87.0	0.0		69.0	22.0	NM_001032287	A8K5K4|Q15625|Q15626	Frame_Shift_Del	DEL	ENST00000333003.5	hg19	CCDS9051.1																																																																																			.	.		0.454	NR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407565.2	NM_003297		-	95456413	GAGTA	-	95456409	7	5	188	1	0	1	0	1	0	0	0	0	10631	1174	41	0	1777	0	NR2C1	12	95456409	Frame_Shift_Del	DEL	GAGTA	TCGA-DD-AADE-01A-11D-A40R-10	22520292	95456409	38395486	77	27828										
NR1H4	9971	hgsc.bcm.edu	37	chr12	100934530	100934539	+	Frame_Shift_Del	DEL	GAGATTTTCA	GAGATTTTCA	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ctatgttccttcgttcagctGagattttcaataagaaactt							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	GAGATTTTCA	GAGATTTTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr12:100934530_100934539delGAGATTTTCA	ENST00000551379.1	+	7	1070_1079	c.1042_1051delGAGATTTTCA	c.(1042-1053)gagattttcaatfs	p.EIFN348fs	NR1H4_ENST00000188403.7_Frame_Shift_Del_p.EIFN344fs|NR1H4_ENST00000548884.1_Frame_Shift_Del_p.EIFN334fs|NR1H4_ENST00000392986.3_Frame_Shift_Del_p.EIFN338fs|NR1H4_ENST00000549996.1_Frame_Shift_Del_p.EIFN287fs			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	348	Agonist binding. {ECO:0000250}.|Ligand-binding.				bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	TCGTTCAGCTGAGATTTTCAATAAGAAACT	0.395																																					p.347_350del		Atlas-INDEL	.											.	NR1H4	145	.	0			c.1041_1050del						.																																			SO:0001589	frameshift_variant	9971	exon7			.	U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"Nuclear hormone receptors"	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.1042_1051delGAGATTTTCA	chr12.hg19:g.100934530_100934539delGAGATTTTCA	ENSP00000447149:p.Glu348fs	87.0	0.0		64.0	16.0	NM_001206993	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Frame_Shift_Del	DEL	ENST00000551379.1	hg19	CCDS55876.1																																																																																			.	.		0.395	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123		-	100934539	GAGATTTTCA	-	100934530	7	5	188	1	0	1	0	1	0	0	0	0	10628	1291	45	0	1026	0	NR1H4	12	100934530	Frame_Shift_Del	DEL	GAGATTTTCA	TCGA-DD-AADE-01A-11D-A40R-10	5478121	100934530	32917365	78	27829										
CCDC62	84660	hgsc.bcm.edu	37	chr12	123265875	123265875	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ctcttctctctgaagaccttGaggttgggattagtttttga	10	7	3	4			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr12:123265875G>A	ENST00000253079.6	+	3	738	c.394G>A	c.(394-396)Gag>Aag	p.E132K	CCDC62_ENST00000537566.1_Intron|CCDC62_ENST00000392441.4_Missense_Mutation_p.E132K|CCDC62_ENST00000392440.2_Intron	NM_201435.4	NP_958843.2	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62	132					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		TGAAGACCTTGAGGTTGGGAT	0.428																																					p.E132K		Atlas-SNP	.											.	CCDC62	119	.	0			c.G394A						.						105	97	99					12																	123265875		2203	4300	6503	SO:0001583	missense	84660	exon3			GACCTTGAGGTTG		CCDS9238.1	12q24.31	2009-08-18			ENSG00000130783	ENSG00000130783			30723	protein-coding gene	gene with protein product	"cancer/testis antigen 109"	613481				18563714, 19126643	Standard	NM_201435		Approved	TSP-NY, FLJ40344, CT109, ERAP75	uc001udc.3	Q6P9F0	OTTHUMG00000168764	ENST00000253079.6:c.394G>A	chr12.hg19:g.123265875G>A	ENSP00000253079:p.Glu132Lys	69.0	0.0		96.0	36.0	NM_201435	A8K8V1|B3KUP3|Q6ZVF2|Q86VJ0|Q9BYZ5	Missense_Mutation	SNP	ENST00000253079.6	hg19	CCDS9238.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.317295	0.60524	.	.	ENSG00000130783	ENST00000253079;ENST00000392441	T;T	0.38401	1.14;1.14	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000003	T	0.59459	0.2195	M	0.72894	2.215	0.80722	D	1	D;D	0.76494	0.996;0.999	D;D	0.83275	0.919;0.996	T	0.56390	-0.7987	10	0.35671	T	0.21	-21.8044	16.6212	0.84931	0.0:0.0:1.0:0.0	.	132;132	Q6P9F0-2;Q6P9F0	.;CCD62_HUMAN	K	132	ENSP00000253079:E132K;ENSP00000376236:E132K	ENSP00000253079:E132K	E	+	1	0	CCDC62	121831828	1.000000	0.71417	1.000000	0.80357	0.103000	0.19146	4.572000	0.60886	2.527000	0.85204	0.557000	0.71058	GAG	.	.		0.428	CCDC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400930.1	NM_032573		A	123265875	G	A	123265875	3	1	188	1	0	0	0	0	1	0	0	0	2835	1291	45	3	404	3	CCDC62	12	123265875	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	22331345	123265875	10586020	79	27830										
SBNO1	55206	hgsc.bcm.edu	37	chr12	123834937	123834937	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aaagaggtcattcggactaaTtccactctcactcaaagcag	7	11	3	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr12:123834937T>C	ENST00000602398.1	-	2	179	c.52A>G	c.(52-54)Att>Gtt	p.I18V	Y_RNA_ENST00000384460.1_RNA|SBNO1_ENST00000267176.4_Missense_Mutation_p.I18V|SBNO1_ENST00000420886.2_Missense_Mutation_p.I18V|SBNO1_ENST00000602750.1_Missense_Mutation_p.I18V			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	18					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TTCGGACTAATTCCACTCTCA	0.413																																					p.I18V		Atlas-SNP	.											.	SBNO1	138	.	0			c.A52G						.						222	222	222					12																	123834937		2203	4300	6503	SO:0001583	missense	55206	exon1			GACTAATTCCACT	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.52A>G	chr12.hg19:g.123834937T>C	ENSP00000473665:p.Ile18Val	100.0	0.0		101.0	39.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	hg19	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	T	17.32	3.360602	0.61403	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	T;T	0.34667	1.36;1.35	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.45558	0.1348	L	0.34521	1.04	0.49483	D	0.999793	P;P;P	0.43314	0.803;0.65;0.65	P;P;P	0.55824	0.785;0.658;0.658	T	0.23940	-1.0174	10	0.34782	T	0.22	-24.8406	16.1026	0.81194	0.0:0.0:0.0:1.0	.	18;18;18	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	V	18	ENSP00000387361:I18V;ENSP00000267176:I18V	ENSP00000267176:I18V	I	-	1	0	SBNO1	122400890	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.898000	0.75676	2.198000	0.70561	0.383000	0.25322	ATT	.	.		0.413	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		C	123834937	T	C	123834937	3	2	188	1	0	0	0	0	1	0	0	0	13877	1493	52	2	4253	2	SBNO1	12	123834937	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	569062	123834937	10016958	80	27831										
ZNF140	7699	hgsc.bcm.edu	37	chr12	133683150	133683150	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	agctggagctcaaaccttgcTaaacatcagaggacacacac	8	12	2	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr12:133683150T>C	ENST00000355557.2	+	5	2570	c.1287T>C	c.(1285-1287)gcT>gcC	p.A429A	ZNF140_ENST00000440550.2_3'UTR|ZNF140_ENST00000544426.1_Silent_p.A326A	NM_003440.2	NP_003431.2	P52738	ZN140_HUMAN	zinc finger protein 140	429					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.114)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CAAACCTTGCTAAACATCAGA	0.398																																					p.A429A		Atlas-SNP	.											.	ZNF140	18	.	0			c.T1287C						.						79	77	78					12																	133683150		2203	4297	6500	SO:0001819	synonymous_variant	7699	exon5			CCTTGCTAAACAT	U09368	CCDS9282.1, CCDS73550.1	12q24.33	2013-01-08	2006-06-13		ENSG00000196387	ENSG00000196387		"Zinc fingers, C2H2-type", "-"	12925	protein-coding gene	gene with protein product		604082	"zinc finger protein 140 (clone pHZ-39)"			7557990	Standard	XR_245353		Approved	pHZ-39	uc001ulo.3	P52738	OTTHUMG00000167942	ENST00000355557.2:c.1287T>C	chr12.hg19:g.133683150T>C		33.0	0.0		34.0	14.0	NM_003440	D3DXJ3|Q05CP6|Q8IV75	Silent	SNP	ENST00000355557.2	hg19	CCDS9282.1																																																																																			.	.		0.398	ZNF140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397169.1	NM_003440		C	133683150	T	C	133683150	2	2	188	1	0	0	0	0	0	0	0	1	17744	1509	53	2		2	ZNF140	12	133683150	Silent	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	9848213	133683150	168745	81	27832										
PCDH8	5100	hgsc.bcm.edu	37	chr13	53422358	53422358	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ttcgcgcacccggagcagagAgctgttgaattgcttcatca	11	11	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr13:53422358A>T	ENST00000377942.3	-	1	417	c.214T>A	c.(214-216)Tct>Act	p.S72T	PCDH8_ENST00000338862.4_Missense_Mutation_p.S72T	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	72	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		CGGAGCAGAGAGCTGTTGAAT	0.677																																					p.S72T	GBM(36;25 841 9273 49207)	Atlas-SNP	.											.	PCDH8	95	.	0			c.T214A						.						73	74	74					13																	53422358		2203	4300	6503	SO:0001583	missense	5100	exon1			GCAGAGAGCTGTT	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"Cadherins / Protocadherins : Non-clustered"	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.214T>A	chr13.hg19:g.53422358A>T	ENSP00000367177:p.Ser72Thr	48.0	0.0		39.0	16.0	NM_032949	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	hg19	CCDS9438.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.040389	0.75732	.	.	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.27557	1.66;1.66	4.99	4.99	0.66335	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.39083	N	0.001478	T	0.55986	0.1955	M	0.77486	2.375	0.52501	D	0.999957	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.57619	-0.7780	10	0.39692	T	0.17	.	14.7172	0.69277	1.0:0.0:0.0:0.0	.	72;72	O95206-2;O95206	.;PCDH8_HUMAN	T	72	ENSP00000367177:S72T;ENSP00000341350:S72T	ENSP00000341350:S72T	S	-	1	0	PCDH8	52320359	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.473000	0.81007	1.895000	0.54865	0.459000	0.35465	TCT	.	.		0.677	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590		T	53422358	A	T	53422358	3	4	188	1	0	0	0	0	1	0	0	0	11526	304	11	4	3010	4	PCDH8	13	53422358	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10		53422358	61747520	82	27833										
CUL4A	8451	hgsc.bcm.edu	37	chr13	113900301	113900301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tcagagtgactcaggccctaTagacctcacagtgaacatac	8	12	3	4			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr13:113900301T>C	ENST00000375440.4	+	15	1646	c.1562T>C	c.(1561-1563)aTa>aCa	p.I521T	CUL4A_ENST00000326335.4_Missense_Mutation_p.I421T|CUL4A_ENST00000375441.3_Missense_Mutation_p.I421T|CUL4A_ENST00000451881.1_Missense_Mutation_p.I421T	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	521					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			TCAGGCCCTATAGACCTCACA	0.398																																					p.I521T		Atlas-SNP	.											.	CUL4A	50	.	0			c.T1562C						.						96	79	84					13																	113900301		2203	4300	6503	SO:0001583	missense	8451	exon15			GCCCTATAGACCT	U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.1562T>C	chr13.hg19:g.113900301T>C	ENSP00000364589:p.Ile521Thr	96.0	0.0		103.0	41.0	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	hg19	CCDS41908.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.883415	0.51908	.	.	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86	4.97	4.97	0.65823	Cullin, N-terminal (1);Cullin homology (3);	0.045201	0.85682	D	0.000000	D	0.86826	0.6026	M	0.89095	3.005	0.80722	D	1	B;B	0.30542	0.284;0.284	P;P	0.50231	0.635;0.635	D	0.87681	0.2547	10	0.59425	D	0.04	-37.075	14.9369	0.70964	0.0:0.0:0.0:1.0	.	521;521	Q13619;A8MSH7	CUL4A_HUMAN;.	T	421;421;421;521	ENSP00000364590:I421T;ENSP00000389118:I421T;ENSP00000322132:I421T;ENSP00000364589:I521T	ENSP00000322132:I421T	I	+	2	0	CUL4A	112948302	1.000000	0.71417	0.049000	0.19019	0.322000	0.28314	7.837000	0.86796	1.978000	0.57642	0.455000	0.32223	ATA	.	.		0.398	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589		C	113900301	T	C	113900301	3	2	188	1	0	0	0	0	1	0	0	0	4059	1406	49	2	1620	2	CUL4A	13	113900301	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	60477943	113900301	1269577	83	27834										
RAB15	376267	hgsc.bcm.edu	37	chr14	65418368	65418368	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gatggtctggtatctctcctGccctgcagtgtccctgcagg	12	13	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr14:65418368G>T	ENST00000533601.2	-	3	536	c.199C>A	c.(199-201)Cag>Aag	p.Q67K	CHURC1-FNTB_ENST00000549987.1_Intron|FNTB_ENST00000542227.1_Intron|RAB15_ENST00000426039.3_Missense_Mutation_p.Q21K|FNTB_ENST00000447296.2_Intron|RAB15_ENST00000436278.2_Missense_Mutation_p.Q21K|RAB15_ENST00000267512.5_Missense_Mutation_p.Q67K			P59190	RAB15_HUMAN	RAB15, member RAS oncogene family	67					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	8				all cancers(60;0.00136)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.0102)		TATCTCTCCTGCCCTGCAGTG	0.587																																					p.Q67K		Atlas-SNP	.											.	RAB15	23	.	0			c.C199A						.						129	100	110					14																	65418368		2203	4300	6503	SO:0001583	missense	376267	exon3			TCTCCTGCCCTGC	BC014511	CCDS9768.1	14q23.2	2012-02-28	2012-02-28		ENSG00000139998	ENSG00000139998		"RAB, member RAS oncogene"	20150	protein-coding gene	gene with protein product						11697911	Standard	NM_198686		Approved		uc001xhz.2	P59190	OTTHUMG00000142810	ENST00000533601.2:c.199C>A	chr14.hg19:g.65418368G>T	ENSP00000434103:p.Gln67Lys	97.0	0.0		65.0	24.0	NM_198686	G5EMR7|Q86TX7|Q8IW89	Missense_Mutation	SNP	ENST00000533601.2	hg19		.	.	.	.	.	.	.	.	.	.	G	26.6	4.750467	0.89753	.	.	ENSG00000139998	ENST00000267512;ENST00000533601;ENST00000426039;ENST00000554593	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73	5.46	5.46	0.80206	.	0.000000	0.35677	N	0.003053	D	0.92854	0.7727	M	0.91612	3.225	0.42181	D	0.991686	D	0.76494	0.999	D	0.68765	0.96	D	0.94343	0.7572	10	0.87932	D	0	.	18.0769	0.89430	0.0:0.0:1.0:0.0	.	67	P59190-2	.	K	67;67;21;21	ENSP00000267512:Q67K;ENSP00000434103:Q67K;ENSP00000433485:Q21K;ENSP00000452195:Q21K	ENSP00000267512:Q67K	Q	-	1	0	RAB15	64488121	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	9.084000	0.94076	2.556000	0.86216	0.561000	0.74099	CAG	.	.		0.587	RAB15-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000390443.2	NM_198686		T	65418368	G	T	65418368	3	4	188	1	0	0	0	0	1	0	0	0	12916	1328	46	3	447	3	RAB15	14	65418368	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10		65418368	41931172	84	27835										
SETD3	84193	hgsc.bcm.edu	37	chr14	99865113	99865113	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gactttcattttcggacctgGtcccattagggatagagttt	10	8	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr14:99865113G>C	ENST00000331768.5	-	13	1847	c.1688C>G	c.(1687-1689)aCc>aGc	p.T563S		NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	563					histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				TTCGGACCTGGTCCCATTAGG	0.468																																					p.T563S		Atlas-SNP	.											.	SETD3	56	.	0			c.C1688G						.						239	212	221					14																	99865113		2203	4300	6503	SO:0001583	missense	84193	exon13			GACCTGGTCCCAT	AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"chromosome 14 open reading frame 154"	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.1688C>G	chr14.hg19:g.99865113G>C	ENSP00000327436:p.Thr563Ser	110.0	0.0		72.0	23.0	NM_032233	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Missense_Mutation	SNP	ENST00000331768.5	hg19	CCDS9951.1	.	.	.	.	.	.	.	.	.	.	G	8.566	0.878911	0.17395	.	.	ENSG00000183576	ENST00000331768	T	0.14516	2.5	5.19	4.28	0.50868	.	0.228496	0.43579	N	0.000547	T	0.19167	0.0460	M	0.65498	2.005	0.80722	D	1	B	0.17038	0.02	B	0.19148	0.024	T	0.02411	-1.1163	10	0.52906	T	0.07	-7.8795	15.6068	0.76679	0.0:0.138:0.862:0.0	.	563	Q86TU7	SETD3_HUMAN	S	563	ENSP00000327436:T563S	ENSP00000327436:T563S	T	-	2	0	SETD3	98934866	1.000000	0.71417	0.192000	0.23308	0.103000	0.19146	3.092000	0.50207	1.153000	0.42468	0.655000	0.94253	ACC	.	.		0.468	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233		C	99865113	G	C	99865113	3	2	188	1	0	0	0	0	1	0	0	0	14147	1261	44	4	100	4	SETD3	14	99865113	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	34446745	99865113	7484427	85	27836										
RCOR1	23186	hgsc.bcm.edu	37	chr14	103188603	103188603	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gtggtacaagtgaaaaacttTtttgtaaattatcgacgccg	9	6	0	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr14:103188603T>G	ENST00000570597.1	+	11	1260	c.1260T>G	c.(1258-1260)ttT>ttG	p.F420L	RCOR1_ENST00000262241.6_Missense_Mutation_p.F423L			Q9UKL0	RCOR1_HUMAN	REST corepressor 1	420	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				blood coagulation (GO:0007596)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	12						TGAAAAACTTTTTTGTAAATT	0.413																																					p.F423L		Atlas-SNP	.											.	RCOR1	39	.	0			c.T1269G						.						86	91	89					14																	103188603		2203	4300	6503	SO:0001583	missense	23186	exon11			AAACTTTTTTGTA	AF155595	CCDS9974.1, CCDS9974.2	14q32.33	2004-04-16	2004-04-16	2004-04-16		ENSG00000089902			17441	protein-coding gene	gene with protein product		607675	"REST corepressor"	RCOR		10449787	Standard	NM_015156		Approved	COREST, KIAA0071	uc001ymb.4	Q9UKL0		ENST00000570597.1:c.1260T>G	chr14.hg19:g.103188603T>G	ENSP00000459789:p.Phe420Leu	348.0	0.0		371.0	114.0	NM_015156	Q15044|Q6P2I9|Q86VG5	Missense_Mutation	SNP	ENST00000570597.1	hg19		.	.	.	.	.	.	.	.	.	.	T	25.2	4.616586	0.87359	.	.	ENSG00000089902	ENST00000262241	.	.	.	5.74	2.05	0.26809	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	T	0.76321	0.3971	M	0.80982	2.52	0.80722	D	1	D	0.67145	0.996	D	0.76071	0.987	T	0.75246	-0.3385	9	0.87932	D	0	-17.6519	9.4748	0.38864	0.0:0.2018:0.0:0.7982	.	420	Q9UKL0	RCOR1_HUMAN	L	420	.	ENSP00000262241:F420L	F	+	3	2	RCOR1	102258356	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.385000	0.34408	0.111000	0.17947	0.533000	0.62120	TTT	.	.		0.413	RCOR1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015156		G	103188603	T	G	103188603	3	3	188	1	0	0	0	0	1	0	0	0	13197	1838	64	5	1302	5	RCOR1	14	103188603	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	3323490	103188603	4160937	86	27837										
OCA2	4948	hgsc.bcm.edu	37	chr15	28326852	28326852	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aggagcccaagagctctgccCggcagcccccctggggcagg	15	16	1	1	rs372901106		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr15:28326852C>T	ENST00000354638.3	-	2	324	c.169G>A	c.(169-171)Ggg>Agg	p.G57R	OCA2_ENST00000382996.2_Missense_Mutation_p.G57R|OCA2_ENST00000353809.5_Missense_Mutation_p.G57R	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	57					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)	p.G57W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		GAGCTCTGCCCGGCAGCCCCC	0.607									Oculocutaneous Albinism																												p.G57R		Atlas-SNP	.											OCA2,NS,carcinoma,0,1	OCA2	173	.	1	Substitution - Missense(1)	lung(1)	c.G169A						.	C	ARG/GLY	2,4404	4.2+/-10.8	0,2,2201	36	35	35		169	-0.3	0	15		35	0,8600		0,0,4300	no	missense	OCA2	NM_000275.2	125	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	57/839	28326852	2,13004	2203	4300	6503	SO:0001583	missense	4948	exon2	Familial Cancer Database		TCTGCCCGGCAGC		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"melanocyte-specific transporter protein"	611409	"oculocutaneous albinism II (pink-eye dilution (murine) homolog)", "eye color 3 (brown)", "eye color 2 (central brown)", "oculocutaneous albinism II (pink-eye dilution homolog, mouse)"	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.169G>A	chr15.hg19:g.28326852C>T	ENSP00000346659:p.Gly57Arg	144.0	1.0		142.0	7.0	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	hg19	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	C	9.349	1.065049	0.20067	4.54E-4	0.0	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996;ENST00000445578;ENST00000431101	D;D;D;D;D	0.96619	-3.31;-3.63;-3.34;-4.07;-2.78	2.82	-0.268	0.12934	.	0.398052	0.21970	N	0.066479	D	0.90611	0.7056	L	0.54323	1.7	0.09310	N	1	B;B	0.28667	0.219;0.14	B;B	0.21360	0.034;0.015	T	0.78409	-0.2215	10	0.07813	T	0.8	-0.5995	4.9821	0.14170	0.0:0.4427:0.4272:0.1301	.	57;57	Q04671-2;Q04671	.;P_HUMAN	R	57	ENSP00000346659:G57R;ENSP00000261276:G57R;ENSP00000372457:G57R;ENSP00000414425:G57R;ENSP00000415431:G57R	ENSP00000261276:G57R	G	-	1	0	OCA2	26000447	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.018000	0.12568	-0.033000	0.13736	-0.386000	0.06593	GGG	.	.		0.607	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275		T	28326852	C	T	28326852	3	4	188	1	0	0	0	0	1	0	0	0	10824	652	23	1	2439	1	OCA2	15	28326852	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10		28326852	74204540	87	27838										
SECISBP2L	9728	hgsc.bcm.edu	37	chr15	49284718	49284719	+	Frame_Shift_Del	DEL	TC	TC	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ttctactattgagctgcactTctacagatatgggttcatga							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr15:49284718_49284719delTC	ENST00000559471.1	-	18	3291_3292	c.3028_3029delGA	c.(3028-3030)gaafs	p.E1010fs	SECISBP2L_ENST00000261847.3_Frame_Shift_Del_p.E965fs	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	1010							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						GAGCTGCACTTCTACAGATATG	0.455																																					p.1010_1010del		Atlas-INDEL	.											.	SECISBP2L	118	.	0			c.3029_3030del						.																																			SO:0001589	frameshift_variant	9728	exon18			.	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.3028_3029delGA	chr15.hg19:g.49284718_49284719delTC	ENSP00000453854:p.Glu1010fs	86.0	0.0		88.0	36.0	NM_001193489	Q8N767	Frame_Shift_Del	DEL	ENST00000559471.1	hg19	CCDS53942.1																																																																																			.	.		0.455	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		-	49284719	TC	-	49284718	7	5	188	1	0	1	0	1	0	0	0	0	14022	1783	62	0	280	0	SECISBP2L	15	49284718	Frame_Shift_Del	DEL	TC	TCGA-DD-AADE-01A-11D-A40R-10	20957866	49284718	53246674	88	27839										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75980591	75980591	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	caacctcccatggcggggccGctccatgacctcatagaggt	11	15	1	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr15:75980591G>T	ENST00000308508.5	-	3	2907	c.2815C>A	c.(2815-2817)Cgg>Agg	p.R939R		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	939	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.|Interaction with COL6A2. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						TGGCGGGGCCGCTCCATGACC	0.587																																					p.R939R		Atlas-SNP	.											.	CSPG4	175	.	0			c.C2815A						.						75	78	77					15																	75980591		2193	4282	6475	SO:0001819	synonymous_variant	1464	exon3			GGGGCCGCTCCAT	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.2815C>A	chr15.hg19:g.75980591G>T		59.0	0.0		45.0	14.0	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	hg19	CCDS10284.1																																																																																			.	.		0.587	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75980591	G	T	75980591	2	4	188	1	0	0	0	0	0	0	0	1	3962	1086	38	1		1	CSPG4	15	75980591	Silent	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	26695873	75980591	26550801	89	27840										
SCAPER	49855	hgsc.bcm.edu	37	chr15	77154760	77154760	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	attttttaaatacataccatCatcatctttgctttctagtg	3	8	4	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr15:77154760C>A	ENST00000563290.1	-	3	216	c.121G>T	c.(121-123)Gat>Tat	p.D41Y	SCAPER_ENST00000324767.7_Missense_Mutation_p.D41Y|SCAPER_ENST00000538941.2_5'Flank			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	41						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.D40Y(1)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						TACATACCATCATCATCTTTG	0.353																																					p.D41Y		Atlas-SNP	.											SCAPER,colon,carcinoma,0,1	SCAPER	160	.	1	Substitution - Missense(1)	large_intestine(1)	c.G121T						.						97	88	91					15																	77154760		1833	4087	5920	SO:0001583	missense	49855	exon2			TACCATCATCATC	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.121G>T	chr15.hg19:g.77154760C>A	ENSP00000454973:p.Asp41Tyr	57.0	0.0		58.0	17.0	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	hg19	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.661629	0.88154	.	.	ENSG00000140386	ENST00000324767	T	0.25414	1.8	6.08	6.08	0.98989	.	0.102270	0.64402	D	0.000003	T	0.41119	0.1145	L	0.38175	1.15	0.58432	D	0.999999	D;D	0.60575	0.988;0.983	P;P	0.58873	0.847;0.837	T	0.08249	-1.0731	10	0.87932	D	0	.	20.2672	0.98462	0.0:1.0:0.0:0.0	.	41;56	Q6NSF1;Q9BY12-2	.;.	Y	41	ENSP00000326924:D41Y	ENSP00000326924:D41Y	D	-	1	0	SCAPER	74941815	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.237000	0.78164	2.894000	0.99253	0.591000	0.81541	GAT	.	.		0.353	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		A	77154760	C	A	77154760	3	1	188	1	0	0	0	0	1	0	0	0	13893	826	29	3	4239	3	SCAPER	15	77154760	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	1174169	77154760	25376632	90	27841										
ANPEP	290	hgsc.bcm.edu	37	chr15	90344728	90344728	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aggaagtgctcctgggaaagGgtccccgtgctggtatccac	14	11	0	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr15:90344728G>C	ENST00000300060.6	-	11	1993	c.1680C>G	c.(1678-1680)acC>acG	p.T560T	ANPEP_ENST00000558177.1_5'UTR	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	560	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	CCTGGGAAAGGGTCCCCGTGC	0.602																																					p.T560T	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.C1680G						.						115	108	111					15																	90344728		2200	4299	6499	SO:0001819	synonymous_variant	290	exon11			GGAAAGGGTCCCC	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.1680C>G	chr15.hg19:g.90344728G>C		138.0	0.0		131.0	39.0	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	hg19	CCDS10356.1																																																																																			.	.		0.602	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			C	90344728	G	C	90344728	2	2	188	1	0	0	0	0	0	0	0	1	710	1219	43	4		4	ANPEP	15	90344728	Silent	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	13189968	90344728	12186664	91	27842										
MPG	4350	hgsc.bcm.edu	37	chr16	129606	129606	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ccgggcccataccgcagcatCtatttctcaagcccaaaggg	9	15	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr16:129606C>G	ENST00000219431.4	+	3	453	c.222C>G	c.(220-222)atC>atG	p.I74M	MPG_ENST00000475280.1_3'UTR|MPG_ENST00000397817.1_Missense_Mutation_p.I57M	NM_002434.3	NP_002425.2	P29372	3MG_HUMAN	N-methylpurine-DNA glycosylase	74					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)	alkylbase DNA N-glycosylase activity (GO:0003905)|damaged DNA binding (GO:0003684)|DNA-3-methyladenine glycosylase activity (GO:0008725)|DNA-3-methylguanine glycosylase activity (GO:0052822)|DNA-7-methyladenine glycosylase activity (GO:0052821)|DNA-7-methylguanine glycosylase activity (GO:0043916)			endometrium(4)|kidney(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)				ACCGCAGCATCTATTTCTCAA	0.642								Base excision repair (BER), DNA glycosylases																													p.I74M		Atlas-SNP	.											.	MPG	26	.	0			c.C222G						.						29	36	33					16																	129606		2190	4297	6487	SO:0001583	missense	4350	exon3			CAGCATCTATTTC		CCDS32345.1, CCDS32346.1, CCDS42087.1	16p13.3	2008-07-29			ENSG00000103152	ENSG00000103152	3.2.2.21		7211	protein-coding gene	gene with protein product	"alkyladenine DNA glycosylase"	156565				1874728	Standard	NM_002434		Approved	MDG	uc002cfo.4	P29372	OTTHUMG00000047887	ENST00000219431.4:c.222C>G	chr16.hg19:g.129606C>G	ENSP00000219431:p.Ile74Met	105.0	0.0		97.0	27.0	NM_002434	G5E9E2|Q13770|Q15275|Q15961|Q5J9I4|Q96BZ6|Q96S33|Q9NNX5	Missense_Mutation	SNP	ENST00000219431.4	hg19	CCDS32346.1	.	.	.	.	.	.	.	.	.	.	c	11.68	1.709645	0.30322	.	.	ENSG00000103152	ENST00000436333;ENST00000397817;ENST00000356432;ENST00000219431	T;T;T;T	0.10573	2.86;3.03;3.01;3.01	5.12	2.06	0.26882	.	0.729988	0.13434	N	0.388187	T	0.10337	0.0253	L	0.36672	1.1	0.24063	N	0.996005	P;P;P	0.51240	0.943;0.943;0.943	B;P;P	0.47430	0.428;0.466;0.547	T	0.19321	-1.0309	10	0.42905	T	0.14	-8.5521	4.0102	0.09619	0.3554:0.4666:0.0:0.178	.	57;69;74	A2IDA3;Q5J9I4;P29372	.;.;3MG_HUMAN	M	57;57;69;74	ENSP00000388097:I57M;ENSP00000380918:I57M;ENSP00000348809:I69M;ENSP00000219431:I74M	ENSP00000219431:I74M	I	+	3	3	MPG	69606	0.998000	0.40836	0.848000	0.33437	0.210000	0.24377	0.354000	0.20146	0.302000	0.22762	0.556000	0.70494	ATC	.	.		0.642	MPG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109121.4			G	129606	C	G	129606	3	3	188	1	0	0	0	0	1	0	0	0	9733	903	32	4	256	4	MPG	16	129606	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10		129606	90225147	92	27843										
CLN3	1201	hgsc.bcm.edu	37	chr16	28495439	28495439	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gatgtgagcaacaagaaataGctaggagtaggatgaaggca	14	4	0	3			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr16:28495439G>A	ENST00000569430.1	-	11	1497	c.678C>T	c.(676-678)agC>agT	p.S226S	CLN3_ENST00000354630.5_Splice_Site_p.S226S|CLN3_ENST00000568224.1_Splice_Site_p.S148S|CLN3_ENST00000567963.1_Splice_Site_p.S226S|CLN3_ENST00000355477.5_Splice_Site_p.S178S|CLN3_ENST00000395653.4_Splice_Site_p.S126S|CLN3_ENST00000357857.9_Splice_Site_p.S172S|CLN3_ENST00000333496.9_Splice_Site_p.S202S|CLN3_ENST00000357076.5_Intron|CLN3_ENST00000565316.1_Splice_Site_p.S226S|CLN3_ENST00000357806.7_Splice_Site_p.C127C|CLN3_ENST00000359984.7_Splice_Site_p.S226S|CLN3_ENST00000360019.2_Splice_Site_p.S226S|CLN3_ENST00000535392.1_Splice_Site_p.S148S			Q13286	CLN3_HUMAN	ceroid-lipofuscinosis, neuronal 3	226					action potential (GO:0001508)|amyloid precursor protein catabolic process (GO:0042987)|arginine transport (GO:0015809)|associative learning (GO:0008306)|autophagic vacuole fusion (GO:0000046)|cell death (GO:0008219)|cellular amino acid metabolic process (GO:0006520)|ceramide metabolic process (GO:0006672)|cytosolic calcium ion homeostasis (GO:0051480)|galactosylceramide metabolic process (GO:0006681)|globoside metabolic process (GO:0001575)|glucosylceramide metabolic process (GO:0006678)|ionotropic glutamate receptor signaling pathway (GO:0035235)|lysosomal lumen acidification (GO:0007042)|lysosomal lumen pH elevation (GO:0035752)|lysosome organization (GO:0007040)|macroautophagy (GO:0016236)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of macroautophagy (GO:0016242)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteolysis (GO:0045861)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter metabolic process (GO:0042133)|protein catabolic process (GO:0030163)|protein processing (GO:0016485)|receptor-mediated endocytosis (GO:0006898)|sphingomyelin metabolic process (GO:0006684)|vacuolar transport (GO:0007034)|vesicle transport along microtubule (GO:0047496)	autophagic vacuole (GO:0005776)|caveola (GO:0005901)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|trans-Golgi network (GO:0005802)	unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(11)|upper_aerodigestive_tract(1)	15						ACAAGAAATAGCTAGGAGTAG	0.582																																					p.S226S		Atlas-SNP	.											.	CLN3	33	.	0			c.C678T						.						36	36	36					16																	28495439		2197	4300	6497	SO:0001630	splice_region_variant	1201	exon10			GAAATAGCTAGGA	U32680	CCDS10632.1, CCDS73852.1, CCDS73853.1, CCDS73854.1, CCDS73855.1	16p12	2014-09-17	2008-07-29		ENSG00000188603	ENSG00000188603			2074	protein-coding gene	gene with protein product	"juvenile neuronal ceroid lipofuscinosis"	607042	"Batten, Spielmeyer-Vogt disease"	BTS		18317235	Standard	NM_001042432		Approved	JNCL	uc002dpp.3	Q13286	OTTHUMG00000097024	ENST00000569430.1:c.678-1C>T	chr16.hg19:g.28495439G>A		49.0	0.0		44.0	13.0	NM_001042432	B2R7J1|O00668|O95089|Q549S9|Q9UP09|Q9UP11|Q9UP12|Q9UP13|Q9UP14	Silent	SNP	ENST00000569430.1	hg19	CCDS10632.1																																																																																			.	.		0.582	CLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214115.2		Silent	A	28495439	G	A	28495439	5	1	188	1	0	0	0	0	0	0	1	0	3545	985	34	3	666	3	CLN3	16	28495439	Splice_Site	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	28365833	28495439	61859314	93	27844										
SLC7A6OS	84138	hgsc.bcm.edu	37	chr16	68335257	68335257	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggtacttgctccacatccgcTgtctgctgctgcctctttcc	8	16	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr16:68335257T>A	ENST00000263997.6	-	5	869	c.851A>T	c.(850-852)cAg>cTg	p.Q284L	SLC7A6_ENST00000219343.6_3'UTR|SLC7A6_ENST00000566454.1_3'UTR	NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	284					hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		CCACATCCGCTGTCTGCTGCT	0.522																																					p.Q284L		Atlas-SNP	.											.	SLC7A6OS	22	.	0			c.A851T						.						193	150	164					16																	68335257		2198	4300	6498	SO:0001583	missense	84138	exon5			ATCCGCTGTCTGC		CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061			25807	protein-coding gene	gene with protein product							Standard	NM_032178		Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558	ENST00000263997.6:c.851A>T	chr16.hg19:g.68335257T>A	ENSP00000263997:p.Gln284Leu	49.0	0.0		43.0	11.0	NM_032178	Q8TCZ3|Q9H8R8	Missense_Mutation	SNP	ENST00000263997.6	hg19	CCDS10865.1	.	.	.	.	.	.	.	.	.	.	T	7.281	0.609100	0.14066	.	.	ENSG00000103061	ENST00000263997	T	0.18657	2.2	5.72	-1.51	0.08664	.	1.047410	0.07417	N	0.893357	T	0.15609	0.0376	L	0.36672	1.1	0.09310	N	1	B	0.19817	0.039	B	0.19391	0.025	T	0.38585	-0.9654	10	0.20519	T	0.43	-29.9379	8.9266	0.35643	0.0:0.4654:0.2327:0.3019	.	284	Q96CW6	S7A6O_HUMAN	L	284	ENSP00000263997:Q284L	ENSP00000263997:Q284L	Q	-	2	0	SLC7A6OS	66892758	0.003000	0.15002	0.001000	0.08648	0.039000	0.13416	-0.078000	0.11375	-0.532000	0.06332	-0.256000	0.11100	CAG	.	.		0.522	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178		A	68335257	T	A	68335257	3	1	188	1	0	0	0	0	1	0	0	0	14717	1580	55	4	82	4	SLC7A6OS	16	68335257	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	39839818	68335257	22019496	94	27845										
MVD	4597	hgsc.bcm.edu	37	chr16	88721205	88721205	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	cattggggcccgcgtcaaagGtgtacgccacctggaaccca	12	14	1	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr16:88721205G>A	ENST00000301012.3	-	8	937	c.908C>T	c.(907-909)aCc>aTc	p.T303I	MVD_ENST00000568709.1_5'Flank	NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	303					cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		CGCGTCAAAGGTGTACGCCAC	0.622																																					p.T303I		Atlas-SNP	.											.	MVD	27	.	0			c.C908T						.						88	72	78					16																	88721205		2198	4300	6498	SO:0001583	missense	4597	exon8			TCAAAGGTGTACG	U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4.1.1.33		7529	protein-coding gene	gene with protein product	"mevalonate pyrophosphate decarboxylase"	603236				8626466	Standard	NM_002461		Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.908C>T	chr16.hg19:g.88721205G>A	ENSP00000301012:p.Thr303Ile	66.0	0.0		74.0	26.0	NM_002461	Q53Y65	Missense_Mutation	SNP	ENST00000301012.3	hg19	CCDS10968.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.96|14.96	2.690649|2.690649	0.48097|0.48097	.|.	.|.	ENSG00000167508|ENSG00000167508	ENST00000378400|ENST00000301012	.|T	.|0.62788	.|-0.0	4.38|4.38	4.38|4.38	0.52667|0.52667	.|.	.|0.108077	.|0.64402	.|D	.|0.000007	D|D	0.82563|0.82563	0.5064|0.5064	H|H	0.95645|0.95645	3.7|3.7	0.54753|0.54753	D|D	0.999983|0.999983	.|D	.|0.89917	.|1.0	.|D	.|0.81914	.|0.995	D|D	0.85628|0.85628	0.1268|0.1268	6|10	0.87932|0.87932	D|D	0|0	-3.199|-3.199	8.6575|8.6575	0.34073|0.34073	0.0845:0.1522:0.7634:0.0|0.0845:0.1522:0.7634:0.0	.|.	.|303	.|P53602	.|MVD1_HUMAN	S|I	131|303	.|ENSP00000301012:T303I	ENSP00000367653:P131S|ENSP00000301012:T303I	P|T	-|-	1|2	0|0	MVD|MVD	87248706|87248706	0.998000|0.998000	0.40836|0.40836	0.939000|0.939000	0.37840|0.37840	0.506000|0.506000	0.33950|0.33950	2.610000|2.610000	0.46325|0.46325	2.156000|2.156000	0.67533|0.67533	0.491000|0.491000	0.48974|0.48974	CCT|ACC	.	.		0.622	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269547.2	NM_002461		A	88721205	G	A	88721205	3	1	188	1	0	0	0	0	1	0	0	0	10003	1261	44	3	306	3	MVD	16	88721205	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	20385948	88721205	1633548	95	27846										
DVL2	1856	hgsc.bcm.edu	37	chr17	7137429	7137429	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ttgaaaaagtacttggcgccCgcgggccgctgcaggacgct	14	12	0	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr17:7137429C>A	ENST00000005340.5	-	1	435	c.153G>T	c.(151-153)gcG>gcT	p.A51A	PHF23_ENST00000570753.1_5'Flank|DVL2_ENST00000575458.1_Silent_p.A51A	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	51	DIX. {ECO:0000255|PROSITE- ProRule:PRU00069}.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						ACTTGGCGCCCGCGGGCCGCT	0.597																																					p.A51A		Atlas-SNP	.											.	DVL2	49	.	0			c.G153T						.						99	118	112					17																	7137429		2203	4300	6503	SO:0001819	synonymous_variant	1856	exon1			GGCGCCCGCGGGC	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"Dishevelled homologs"	3086	protein-coding gene	gene with protein product		602151	"dishevelled 2 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 2 (Drosophila)"			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.153G>T	chr17.hg19:g.7137429C>A		81.0	0.0		37.0	22.0	NM_004422	D3DTN3|Q53XM0	Silent	SNP	ENST00000005340.5	hg19	CCDS11091.1																																																																																			.	.		0.597	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422		A	7137429	C	A	7137429	2	1	188	1	0	0	0	0	0	0	0	1	4838	639	23	1		1	DVL2	17	7137429	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10		7137429	74057781	96	27847										
MRPL45	84311	hgsc.bcm.edu	37	chr17	36476595	36476595	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ttcaagttcgctgttcaagtAtgatgaaccagggcaacgtg	11	8	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr17:36476595A>T	ENST00000312513.5	+	6	765	c.604A>T	c.(604-606)Atg>Ttg	p.M202L		NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	202						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CTGTTCAAGTATGATGAACCA	0.512																																					p.M202L		Atlas-SNP	.											.	MRPL45	27	.	0			c.A604T						.						212	190	197					17																	36476595		2203	4300	6503	SO:0001583	missense	84311	exon6			TCAAGTATGATGA	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"Mitochondrial ribosomal proteins / large subunits"	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.604A>T	chr17.hg19:g.36476595A>T	ENSP00000308901:p.Met202Leu	58.0	0.0		69.0	16.0	NM_032351	A1L436|Q6ZMJ5	Missense_Mutation	SNP	ENST00000312513.5	hg19	CCDS11326.1	.	.	.	.	.	.	.	.	.	.	A	9.689	1.151436	0.21371	.	.	ENSG00000174100	ENST00000312513	T	0.75589	-0.95	5.53	-3.36	0.04913	.	0.314836	0.35615	N	0.003086	T	0.44603	0.1301	N	0.12961	0.28	0.22710	N	0.998822	B	0.02656	0.0	B	0.06405	0.002	T	0.44726	-0.9309	10	0.02654	T	1	-1.7728	7.9544	0.30033	0.711:0.1299:0.0819:0.0773	.	202	Q9BRJ2	RM45_HUMAN	L	202	ENSP00000308901:M202L	ENSP00000308901:M202L	M	+	1	0	MRPL45	33730122	0.000000	0.05858	0.004000	0.12327	0.350000	0.29205	-0.084000	0.11268	-0.345000	0.08325	-0.666000	0.03841	ATG	.	.		0.512	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351		T	36476595	A	T	36476595	3	4	188	1	0	0	0	0	1	0	0	0	9818	449	16	4	556	4	MRPL45	17	36476595	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	29339166	36476595	44718615	97	27848										
ACBD4	79777	hgsc.bcm.edu	37	chr17	43213538	43213538	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	accgagaaagaaagcccagaGcccgactgccagaaacagtt	10	12	0	4			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr17:43213538G>T	ENST00000376955.4	+	2	324	c.27G>T	c.(25-27)gaG>gaT	p.E9D	ACBD4_ENST00000586346.1_Missense_Mutation_p.E9D|ACBD4_ENST00000431281.1_Missense_Mutation_p.E9D|ACBD4_ENST00000591859.1_Missense_Mutation_p.E9D|ACBD4_ENST00000321854.8_Missense_Mutation_p.E9D|ACBD4_ENST00000592162.1_Missense_Mutation_p.E9D|ACBD4_ENST00000398322.3_Missense_Mutation_p.E9D	NM_001135707.1	NP_001129179.1	Q8NC06	ACBD4_HUMAN	acyl-CoA binding domain containing 4	9							fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)			kidney(1)|lung(3)|ovary(1)	5						AAAGCCCAGAGCCCGACTGCC	0.612																																					p.E9D		Atlas-SNP	.											.	ACBD4	51	.	0			c.G27T						.						34	41	39					17																	43213538		2016	4174	6190	SO:0001583	missense	79777	exon2			CCCAGAGCCCGAC	BC029164	CCDS42348.1, CCDS45710.1, CCDS45711.1	17q21.31	2012-10-02	2010-04-30		ENSG00000181513	ENSG00000181513			23337	protein-coding gene	gene with protein product			"acyl-Coenzyme A binding domain containing 4"				Standard	NM_001135704		Approved	FLJ13322	uc002iie.3	Q8NC06	OTTHUMG00000180111	ENST00000376955.4:c.27G>T	chr17.hg19:g.43213538G>T	ENSP00000366154:p.Glu9Asp	54.0	0.0		84.0	14.0	NM_001135707	D3DX64|Q8IUT1|Q9H8Q4	Missense_Mutation	SNP	ENST00000376955.4	hg19	CCDS45711.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.128433	0.77549	.	.	ENSG00000181513	ENST00000431281;ENST00000321854;ENST00000398322;ENST00000376955	T;T;T;T	0.16597	2.37;2.61;2.61;2.33	5.94	1.38	0.22167	.	0.321335	0.30593	N	0.009281	T	0.16557	0.0398	L	0.40543	1.245	0.09310	N	0.999998	D;P;P	0.54047	0.964;0.905;0.828	P;B;P	0.49708	0.62;0.253;0.474	T	0.07770	-1.0755	10	0.62326	D	0.03	.	4.9459	0.13989	0.3108:0.0:0.5392:0.15	.	9;9;9	Q8NC06-3;Q8NC06;Q8NC06-2	.;ACBD4_HUMAN;.	D	9	ENSP00000405969:E9D;ENSP00000314440:E9D;ENSP00000381367:E9D;ENSP00000366154:E9D	ENSP00000314440:E9D	E	+	3	2	ACBD4	40569064	0.997000	0.39634	0.105000	0.21289	0.935000	0.57460	0.682000	0.25335	0.273000	0.22049	0.561000	0.74099	GAG	.	.		0.612	ACBD4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000449816.1	NM_024722		T	43213538	G	T	43213538	3	4	188	1	0	0	0	0	1	0	0	0	124	962	34	3	29	3	ACBD4	17	43213538	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	6736943	43213538	37981672	98	27849										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48667952	48667952	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gctacatcaagaatccctacAacatcttcgatggtgtcatt	6	11	3	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr17:48667952A>T	ENST00000359106.5	+	10	2422	c.2422A>T	c.(2422-2424)Aac>Tac	p.N808Y	CACNA1G_ENST00000514079.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000513689.2_Missense_Mutation_p.N808Y|CACNA1G_ENST00000510366.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000507896.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000416767.4_Missense_Mutation_p.N808Y|CACNA1G_ENST00000442258.2_Missense_Mutation_p.N808Y|CACNA1G_ENST00000354983.4_Missense_Mutation_p.N808Y|CACNA1G_ENST00000514717.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000515411.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000507609.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000360761.4_Missense_Mutation_p.N808Y|CACNA1G_ENST00000507510.2_Missense_Mutation_p.N808Y|CACNA1G_ENST00000512389.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000510115.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000514181.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000505165.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000358244.5_Missense_Mutation_p.N808Y|CACNA1G_ENST00000429973.2_Missense_Mutation_p.N808Y|CACNA1G_ENST00000502264.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000515765.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000503485.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000515165.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000507336.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000513964.1_Missense_Mutation_p.N808Y|CACNA1G_ENST00000352832.5_Missense_Mutation_p.N808Y	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	808					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GAATCCCTACAACATCTTCGA	0.537																																					p.N808Y		Atlas-SNP	.											.	CACNA1G	659	.	0			c.A2422T						.						108	105	106					17																	48667952		2021	4172	6193	SO:0001583	missense	8913	exon10			CCCTACAACATCT	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.2422A>T	chr17.hg19:g.48667952A>T	ENSP00000352011:p.Asn808Tyr	45.0	0.0		65.0	36.0	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	a	25.1	4.604033	0.87157	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.99259	-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64;-5.64	5.63	5.63	0.86233	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99654	0.9872	H	0.97365	3.99	0.80722	D	1	P;D;P;P;D;P;P;P;P;D;D;D;D;D;P;D;D;D;D;D;D;D;P;P;D;D	0.89917	0.785;0.989;0.839;0.71;0.995;0.905;0.817;0.903;0.817;1.0;0.984;0.986;0.989;0.99;0.888;0.969;0.995;0.96;0.995;0.995;1.0;0.997;0.944;0.907;1.0;0.993	P;D;P;P;D;P;P;D;P;D;D;D;D;D;P;D;D;P;D;D;D;D;D;P;D;D	0.91635	0.721;0.976;0.903;0.841;0.967;0.903;0.8;0.949;0.8;0.992;0.959;0.945;0.967;0.967;0.724;0.949;0.967;0.89;0.967;0.949;0.999;0.967;0.933;0.908;0.999;0.945	D	0.97456	1.0031	10	0.87932	D	0	.	15.8337	0.78782	1.0:0.0:0.0:0.0	.	808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808;808	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	Y	808	ENSP00000353990:N808Y;ENSP00000339302:N808Y;ENSP00000392390:N808Y;ENSP00000347078:N808Y;ENSP00000409759:N808Y;ENSP00000425522:N808Y;ENSP00000426261:N808Y;ENSP00000425451:N808Y;ENSP00000422407:N808Y;ENSP00000426814:N808Y;ENSP00000427238:N808Y;ENSP00000423112:N808Y;ENSP00000420918:N808Y;ENSP00000426172:N808Y;ENSP00000423045:N808Y;ENSP00000427173:N808Y;ENSP00000426098:N808Y;ENSP00000425698:N808Y;ENSP00000426232:N808Y;ENSP00000423317:N808Y;ENSP00000350979:N808Y;ENSP00000352011:N808Y;ENSP00000414388:N808Y;ENSP00000423155:N808Y;ENSP00000422268:N808Y;ENSP00000421518:N808Y	ENSP00000339302:N808Y	N	+	1	0	CACNA1G	46022951	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	2.152000	0.67230	0.459000	0.35465	AAC	.	.		0.537	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		T	48667952	A	T	48667952	3	4	188	1	0	0	0	0	1	0	0	0	2546	130	5	4	2460	4	CACNA1G	17	48667952	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	5454414	48667952	32527258	99	27850										
INTS2	57508	hgsc.bcm.edu	37	chr17	59989028	59989028	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tccaatgtcaaagccacaccAaggcctggcaagtgacattc	8	13	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr17:59989028A>G	ENST00000444766.3	-	7	906	c.831T>C	c.(829-831)ctT>ctC	p.L277L	INTS2_ENST00000251334.6_Silent_p.L269L	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	277					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						AAGCCACACCAAGGCCTGGCA	0.398																																					p.L277L		Atlas-SNP	.											.	INTS2	89	.	0			c.T831C						.						66	64	65					17																	59989028		1920	4142	6062	SO:0001819	synonymous_variant	57508	exon7			CACACCAAGGCCT	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.831T>C	chr17.hg19:g.59989028A>G		221.0	0.0		302.0	156.0	NM_020748	Q9ULD3	Silent	SNP	ENST00000444766.3	hg19	CCDS45750.1																																																																																			.	.		0.398	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		G	59989028	A	G	59989028	2	3	188	1	0	0	0	0	0	0	0	1	7787	117	5	2		2	INTS2	17	59989028	Silent	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	11321076	59989028	21206182	100	27851										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62034767	62034767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	caccacggcgaagatgaacaCgatgatagccagcaccagcg	11	13	0	3			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr17:62034767C>T	ENST00000435607.1	-	13	2207	c.2131G>A	c.(2131-2133)Gtg>Atg	p.V711M	SCN4A_ENST00000578147.1_Missense_Mutation_p.V711M	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	711					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAGATGAACACGATGATAGCC	0.567																																					p.V711M		Atlas-SNP	.											SCN4A,colon,carcinoma,0,1	SCN4A	205	.	0			c.G2131A						.						111	120	117					17																	62034767		2202	4300	6502	SO:0001583	missense	6329	exon13			TGAACACGATGAT	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.2131G>A	chr17.hg19:g.62034767C>T	ENSP00000396320:p.Val711Met	71.0	0.0		117.0	31.0	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	19.02	3.746783	0.69418	.	.	ENSG00000007314	ENST00000435607	D	0.98567	-5.0	3.66	3.66	0.41972	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97867	0.9299	L	0.37750	1.13	0.51233	D	0.99991	D	0.69078	0.997	D	0.68943	0.961	D	0.98487	1.0608	10	0.66056	D	0.02	.	14.9158	0.70795	0.0:1.0:0.0:0.0	.	711	P35499	SCN4A_HUMAN	M	711	ENSP00000396320:V711M	ENSP00000396320:V711M	V	-	1	0	SCN4A	59388499	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.609000	0.82925	2.062000	0.61559	0.561000	0.74099	GTG	.	.		0.567	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62034767	C	T	62034767	3	4	188	1	0	0	0	0	1	0	0	0	13935	536	19	1	3427	1	SCN4A	17	62034767	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	2045739	62034767	19160443	101	27852										
RNF213	57674	hgsc.bcm.edu	37	chr17	78247203	78247203	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gcctcctggaccgtccaagaAgtgagtgcactgcctcggct	12	14	0	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr17:78247203A>C	ENST00000582970.1	+	3	404	c.261A>C	c.(259-261)gaA>gaC	p.E87D	RNF213_ENST00000508628.2_Splice_Site_p.E87D|RNF213_ENST00000456466.1_Splice_Site_p.E87D|RNF213_ENST00000319921.4_Splice_Site_p.E87D	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	87					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CCGTCCAAGAAGTGAGTGCAC	0.627																																					p.E87D		Atlas-SNP	.											.	RNF213	766	.	1	Unknown(1)	autonomic_ganglia(1)	c.A261C						.						58	54	56					17																	78247203		2203	4299	6502	SO:0001630	splice_region_variant	57674	exon3			CCAAGAAGTGAGT	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.261+1A>C	chr17.hg19:g.78247203A>C		62.0	0.0		52.0	15.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	A	8.743	0.919411	0.17982	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T	0.23348	1.91	3.31	-3.2	0.05156	.	.	.	.	.	T	0.10337	0.0253	N	0.08118	0	0.35902	D	0.83043	B	0.25169	0.119	B	0.23574	0.047	T	0.37731	-0.9693	9	0.15499	T	0.54	.	9.6741	0.40030	0.197:0.0:0.803:0.0	.	87	Q9HCF4-2	.	D	87	ENSP00000425956:E87D	ENSP00000324392:E87D	E	+	3	2	RNF213	75861798	0.038000	0.19896	0.037000	0.18230	0.008000	0.06430	-0.193000	0.09573	-0.515000	0.06479	-0.417000	0.06048	GAA	.	.		0.627	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	Missense_Mutation	C	78247203	A	C	78247203	5	2	188	1	0	0	0	0	0	0	1	0	13492	86	3	5	267	5	RNF213	17	78247203	Splice_Site	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	16212436	78247203	2948007	102	27853										
MOCOS	55034	hgsc.bcm.edu	37	chr18	33795576	33795576	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	catgtcgacgctggatgatgTccaggcctttcttaggttca	11	10	2	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr18:33795576T>C	ENST00000261326.5	+	8	1454	c.1433T>C	c.(1432-1434)gTc>gCc	p.V478A		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CTGGATGATGTCCAGGCCTTT	0.552																																					p.V478A		Atlas-SNP	.											.	MOCOS	84	.	0			c.T1433C						.						71	69	69					18																	33795576		2203	4300	6503	SO:0001583	missense	55034	exon8			ATGATGTCCAGGC	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.1433T>C	chr18.hg19:g.33795576T>C	ENSP00000261326:p.Val478Ala	56.0	0.0		56.0	28.0	NM_017947		Missense_Mutation	SNP	ENST00000261326.5	hg19	CCDS11919.1	.	.	.	.	.	.	.	.	.	.	t	0.022	-1.407162	0.01155	.	.	ENSG00000075643	ENST00000261326	D	0.91631	-2.88	5.59	3.73	0.42828	Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.277081	0.42053	N	0.000775	T	0.79890	0.4524	N	0.03000	-0.44	0.22803	N	0.998712	B	0.06786	0.001	B	0.10450	0.005	T	0.59590	-0.7426	10	0.10636	T	0.68	-11.1231	15.2153	0.73261	0.0:0.9229:0.0:0.0771	.	478	Q96EN8	MOCOS_HUMAN	A	478	ENSP00000261326:V478A	ENSP00000261326:V478A	V	+	2	0	MOCOS	32049574	1.000000	0.71417	0.998000	0.56505	0.155000	0.21991	2.218000	0.42889	0.734000	0.32515	-1.204000	0.01649	GTC	.	.		0.552	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			C	33795576	T	C	33795576	3	2	188	1	0	0	0	0	1	0	0	0	9698	1667	58	2	1463	2	MOCOS	18	33795576	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10		33795576	44281672	103	27854										
MOCOS	55034	hgsc.bcm.edu	37	chr18	33840138	33840138	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	attggctctttgcgtttccaGgtaagtttggggaagttcta	12	6	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr18:33840138G>A	ENST00000261326.5	+	13	2430	c.2409G>A	c.(2407-2409)caG>caA	p.Q803Q	MOCOS_ENST00000588132.1_3'UTR	NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						TGCGTTTCCAGGTAAGTTTGG	0.443																																					p.Q803Q		Atlas-SNP	.											.	MOCOS	84	.	0			c.G2409A						.						188	183	184					18																	33840138		2203	4300	6503	SO:0001630	splice_region_variant	55034	exon13			TTTCCAGGTAAGT	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.2409+1G>A	chr18.hg19:g.33840138G>A		119.0	0.0		106.0	42.0	NM_017947		Silent	SNP	ENST00000261326.5	hg19	CCDS11919.1																																																																																			.	.		0.443	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1		Silent	A	33840138	G	A	33840138	5	1	188	1	0	0	0	0	0	0	1	0	9698	1014	35	3	2459	3	MOCOS	18	33840138	Splice_Site	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	44562	33840138	44237110	104	27855										
PIGN	23556	hgsc.bcm.edu	37	chr18	59815546	59815546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ttttagaaaacaaagactggTtgtttctggcatgatgaaag	10	4	1	4			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr18:59815546T>C	ENST00000357637.5	-	8	990	c.575A>G	c.(574-576)aAc>aGc	p.N192S	PIGN_ENST00000400334.3_Missense_Mutation_p.N192S	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	192					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				CAAAGACTGGTTGTTTCTGGC	0.274																																					p.N192S		Atlas-SNP	.											.	PIGN	62	.	0			c.A575G						.						21	19	19					18																	59815546		1585	3625	5210	SO:0001583	missense	23556	exon8			GACTGGTTGTTTC	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.575A>G	chr18.hg19:g.59815546T>C	ENSP00000350263:p.Asn192Ser	518.0	0.0		473.0	141.0	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Missense_Mutation	SNP	ENST00000357637.5	hg19	CCDS45879.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.421779	0.83559	.	.	ENSG00000197563	ENST00000357637;ENST00000400334	T;T	0.71698	-0.59;-0.59	5.73	5.73	0.89815	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.83478	0.5263	M	0.74389	2.26	0.58432	D	0.999999	D;D	0.71674	0.998;0.998	D;D	0.76575	0.988;0.988	D	0.84033	0.0360	9	.	.	.	-18.6256	16.0325	0.80588	0.0:0.0:0.0:1.0	.	192;192	B2RCI8;O95427	.;PIGN_HUMAN	S	192	ENSP00000350263:N192S;ENSP00000383188:N192S	.	N	-	2	0	PIGN	57966526	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.086000	0.64474	2.180000	0.69256	0.528000	0.53228	AAC	.	.		0.274	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		C	59815546	T	C	59815546	3	2	188	1	0	0	0	0	1	0	0	0	11902	1725	60	2	2316	2	PIGN	18	59815546	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	25975408	59815546	18261702	105	27856										
KANK2	25959	hgsc.bcm.edu	37	chr19	11286587	11286587	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ccagatcgtaccagctcccgCtctgtgagggcgttgggatt	13	12	1	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr19:11286587C>T	ENST00000586659.1	-	8	2153	c.1839G>A	c.(1837-1839)gaG>gaA	p.E613E	KANK2_ENST00000589359.1_Silent_p.E621E|KANK2_ENST00000589894.1_Silent_p.E613E|KANK2_ENST00000355150.5_Silent_p.E613E|KANK2_ENST00000432929.2_Silent_p.E621E			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	613					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CCAGCTCCCGCTCTGTGAGGG	0.627																																					p.E621E		Atlas-SNP	.											.	KANK2	47	.	0			c.G1863A						.						122	108	113					19																	11286587		2203	4300	6503	SO:0001819	synonymous_variant	25959	exon6			CTCCCGCTCTGTG	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	29300	protein-coding gene	gene with protein product		614610	"matrix-remodelling associated 3", "ankyrin repeat domain 25"	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.1839G>A	chr19.hg19:g.11286587C>T		58.0	0.0		78.0	31.0	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Silent	SNP	ENST00000586659.1	hg19	CCDS12255.1																																																																																			.	.		0.627	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493		T	11286587	C	T	11286587	2	4	188	1	0	0	0	0	0	0	0	1	7986	796	28	3		3	KANK2	19	11286587	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10		11286587	47842396	106	27857										
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11560181	11560181	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gacgccagccgcctgcccggAgccaccgcctgaagcaccca	11	20	0	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr19:11560181A>C	ENST00000589838.1	+	16	1541	c.1541A>C	c.(1540-1542)gAg>gCg	p.E514A	PRKCSH_ENST00000412601.1_Missense_Mutation_p.E511A|PRKCSH_ENST00000592741.1_Missense_Mutation_p.E521A|PRKCSH_ENST00000587327.1_Missense_Mutation_p.E511A|PRKCSH_ENST00000591462.1_Missense_Mutation_p.E511A|PRKCSH_ENST00000252455.2_Missense_Mutation_p.E514A			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	514					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						GCCTGCCCGGAGCCACCGCCT	0.672																																					p.E514A		Atlas-SNP	.											.	PRKCSH	55	.	0			c.A1541C						.						54	58	57					19																	11560181		2202	4299	6501	SO:0001583	missense	5589	exon17			GCCCGGAGCCACC		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"EF-hand domain containing"	9411	protein-coding gene	gene with protein product		177060	"polycystic liver disease"	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.1541A>C	chr19.hg19:g.11560181A>C	ENSP00000465461:p.Glu514Ala	65.0	0.0		78.0	22.0	NM_002743	A8K318|Q96BU9|Q96D06|Q9P0W9	Missense_Mutation	SNP	ENST00000589838.1	hg19	CCDS32911.1	.	.	.	.	.	.	.	.	.	.	A	9.117	1.008015	0.19199	.	.	ENSG00000130175	ENST00000252455;ENST00000412601	T;T	0.74002	-0.79;-0.8	3.7	2.67	0.31697	.	0.287297	0.32081	N	0.006602	T	0.71134	0.3304	M	0.81682	2.555	0.47183	D	0.999347	B;B;B;B	0.28128	0.09;0.09;0.019;0.201	B;B;B;B	0.28385	0.089;0.089;0.056;0.089	T	0.63580	-0.6605	10	0.27785	T	0.31	-22.6865	8.4396	0.32808	0.8251:0.0:0.0:0.1749	.	521;521;511;514	E7EQZ9;B4DJQ5;A8K318;P14314	.;.;.;GLU2B_HUMAN	A	514;511	ENSP00000252455:E514A;ENSP00000395616:E511A	ENSP00000252455:E514A	E	+	2	0	PRKCSH	11421181	1.000000	0.71417	0.500000	0.27589	0.003000	0.03518	5.872000	0.69636	0.479000	0.27511	-0.301000	0.09380	GAG	.	.		0.672	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			C	11560181	A	C	11560181	3	2	188	1	0	0	0	0	1	0	0	0	12528	304	11	5	1624	5	PRKCSH	19	11560181	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	273594	11560181	47568802	107	27858										
RAB8A	4218	hgsc.bcm.edu	37	chr19	16236349	16236350	+	Frame_Shift_Ins	INS	-	-	T													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ccggaactggattcgcaacaINSttgaggaggtgaggccctcc							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr19:16236349_16236350insT	ENST00000300935.3	+	4	589_590	c.316_317insT	c.(316-318)attfs	p.I106fs	CTD-2231E14.8_ENST00000597983.1_RNA|RAB8A_ENST00000586682.1_Frame_Shift_Ins_p.I106fs	NM_005370.4	NP_005361.2	P61006	RAB8A_HUMAN	RAB8A, member RAS oncogene family	106					axonogenesis (GO:0007409)|cellular response to insulin stimulus (GO:0032869)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi vesicle fusion to target membrane (GO:0048210)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein transport (GO:0051223)|small GTPase mediated signal transduction (GO:0007264)|vesicle docking involved in exocytosis (GO:0006904)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|neuronal cell body (GO:0043025)|nonmotile primary cilium (GO:0031513)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)|recycling endosome membrane (GO:0055038)|trans-Golgi network transport vesicle (GO:0030140)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			endometrium(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	8						GATTCGCAACATTGAGGAGGTG	0.574																																					p.I106fs		Atlas-INDEL	.											.	RAB8A	19	.	0			c.316_317insT						.																																			SO:0001589	frameshift_variant	4218	exon4			.		CCDS12339.1	19p13.2-p13.1	2008-05-14	2004-01-30	2004-01-30		ENSG00000167461		"RAB, member RAS oncogene"	7007	protein-coding gene	gene with protein product		165040	"mel transforming oncogene (derived from cell line NK14)"	MEL		1886711, 8408203	Standard	NM_005370		Approved	RAB8	uc002ndn.4	P61006		ENST00000300935.3:c.318dupT	chr19.hg19:g.16236351_16236351dupT	ENSP00000300935:p.Ile106fs	74.0	0.0		59.0	18.0	NM_005370	B4DEK7|P24407|Q6FHV5	Frame_Shift_Ins	INS	ENST00000300935.3	hg19	CCDS12339.1																																																																																			.	.		0.574	RAB8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460186.1	NM_005370		T	16236350	-	T	16236349	7	5	188	1	0	1	1	0	0	0	0	0	12971	217	8	0	330	0	RAB8A	19	16236349	Frame_Shift_Ins	INS	-	TCGA-DD-AADE-01A-11D-A40R-10	4676168	16236349	42892634	108	27859										
GMIP	51291	hgsc.bcm.edu	37	chr19	19753423	19753423	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	cctgccctcaggacctggggGgagtcctaggggaggggagt	19	10	1	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr19:19753423G>A	ENST00000203556.4	-	2	162	c.25C>T	c.(25-27)Ccc>Tcc	p.P9S	GMIP_ENST00000445806.2_Missense_Mutation_p.P9S|GMIP_ENST00000587238.1_Missense_Mutation_p.P9S	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	9					intracellular signal transduction (GO:0035556)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						GGACCTGGGGGGAGTCCTAGG	0.582																																					p.P9S		Atlas-SNP	.											.	GMIP	55	.	0			c.C25T						.						109	100	103					19																	19753423		2203	4300	6503	SO:0001583	missense	51291	exon2			CTGGGGGGAGTCC	AF132541	CCDS12408.1, CCDS74318.1	19p13.11	2011-09-07				ENSG00000089639		"Rho GTPase activating proteins"	24852	protein-coding gene	gene with protein product		609694				12093360, 16086184	Standard	XM_005259927		Approved	ARHGAP46	uc002nnd.3	Q9P107		ENST00000203556.4:c.25C>T	chr19.hg19:g.19753423G>A	ENSP00000203556:p.Pro9Ser	69.0	0.0		79.0	29.0	NM_016573	A0AVN9|B7ZLZ0	Missense_Mutation	SNP	ENST00000203556.4	hg19	CCDS12408.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.662555	0.29515	.	.	ENSG00000089639	ENST00000203556;ENST00000445806	T;T	0.19250	2.17;2.16	4.32	-1.37	0.09056	.	0.593417	0.14095	N	0.341739	T	0.14270	0.0345	L	0.44542	1.39	0.09310	N	1	B;B;B	0.20052	0.041;0.041;0.041	B;B;B	0.14578	0.011;0.011;0.011	T	0.26503	-1.0101	10	0.26408	T	0.33	-2.2825	7.2941	0.26383	0.0:0.1451:0.3897:0.4652	.	9;9;9	E7ERB7;B7ZLZ0;Q9P107	.;.;GMIP_HUMAN	S	9	ENSP00000203556:P9S;ENSP00000397075:P9S	ENSP00000203556:P9S	P	-	1	0	GMIP	19614423	0.001000	0.12720	0.010000	0.14722	0.050000	0.14768	-0.820000	0.04457	0.002000	0.14630	0.561000	0.74099	CCC	.	.		0.582	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573		A	19753423	G	A	19753423	3	1	188	1	0	0	0	0	1	0	0	0	6499	1232	43	3	2967	3	GMIP	19	19753423	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	3517074	19753423	39375560	109	27860										
CEACAM20	125931	hgsc.bcm.edu	37	chr19	45026913	45026913	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ccactggcaacaccagactcCaatttgatttcaacaggatc	6	13	1	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr19:45026913C>T	ENST00000454753.1	-	0	779							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				CACCAGACTCCAATTTGATTT	0.493																																					p.L167L		Atlas-SNP	.											.	CEACAM20	31	.	0			c.G501A						.						59	64	62					19																	45026913		2084	4233	6317			125931	exon4			AGACTCCAATTTG	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Immunoglobulin superfamily / I-set domain containing"	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		chr19.hg19:g.45026913C>T		72.0	0.0		89.0	28.0	NM_001102600		Silent	SNP	ENST00000454753.1	hg19																																																																																				.	.		0.493	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444		T	45026913	C	T	45026913	1	4	188	0	1	0	0	0	0	0	0	0	3193	593	21	3		3	CEACAM20	19	45026913	RNA	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10	25273490	45026913	14102070	110	27861										
SFRS16	11129	hgsc.bcm.edu	37	chr19	45567295	45567300	+	In_Frame_Del	DEL	TCCCGC	TCCCGC	-													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	cctcggagtccagctcagagTcccgctcccgctcccgctcc					rs199673955|rs537392385		TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	TCCCGC	TCCCGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr19:45567295_45567300delTCCCGC	ENST00000221455.3	+	12	1029_1034	c.931_936delTCCCGC	c.(931-936)tcccgcdel	p.SR315del	CLASRP_ENST00000544944.2_In_Frame_Del_p.SR315del|CLASRP_ENST00000391953.4_In_Frame_Del_p.SR253del	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	315					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						CAGCTCAGAGTCCCGCTCCCGCTCCC	0.67																																					p.310_312del		Atlas-INDEL	.											.	CLASRP	44	.	0			c.930_935del						.																																			SO:0001651	inframe_deletion	11129	exon12			.	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"Clk4 associating SR-related protein"		"splicing factor, arginine/serine-rich 16"	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.931_936delTCCCGC	chr19.hg19:g.45567301_45567306delTCCCGC	ENSP00000221455:p.Ser315_Arg316del	83.0	0.0		77.0	12.0	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	In_Frame_Del	DEL	ENST00000221455.3	hg19	CCDS12652.2																																																																																			.	.		0.67	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056		-	45567300	TCCCGC	-	45567295	7	5	188	1	0	1	0	1	0	0	0	0	14187	1667	58	0	973	0	SFRS16	19	45567295	In_Frame_Del	DEL	TCCCGC	TCGA-DD-AADE-01A-11D-A40R-10	540382	45567295	13561688	111	27862										
NR1H2	7376	hgsc.bcm.edu	37	chr19	50885832	50885832	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aagaagctgccgcctctgctGtcggagatctgggacgtcca	13	12	2	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr19:50885832G>C	ENST00000253727.5	+	10	1591	c.1356G>C	c.(1354-1356)ctG>ctC	p.L452L	NR1H2_ENST00000598168.1_Silent_p.L422L|NR1H2_ENST00000411902.2_Silent_p.L355L|POLD1_ENST00000440232.2_5'Flank|NR1H2_ENST00000593926.1_Silent_p.L452L|NR1H2_ENST00000542413.1_Silent_p.L183L|POLD1_ENST00000599857.1_5'Flank|NR1H2_ENST00000599105.1_Silent_p.L408L	NM_007121.5	NP_009052	P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2	452	Ligand-binding. {ECO:0000255}.				cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pinocytosis (GO:0048550)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	apolipoprotein A-I receptor binding (GO:0034191)|ATPase binding (GO:0051117)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	8		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		CGCCTCTGCTGTCGGAGATCT	0.647																																					p.L452L		Atlas-SNP	.											.	NR1H2	47	.	0			c.G1356C						.						27	34	31					19																	50885832		2032	4204	6236	SO:0001819	synonymous_variant	7376	exon10			TCTGCTGTCGGAG	U14534	CCDS42593.1, CCDS58673.1	19q13.3	2013-01-16				ENSG00000131408		"Nuclear hormone receptors"	7965	protein-coding gene	gene with protein product	"liver X receptor-beta"	600380	"ubiquitously-expressed nuclear receptor"	UNR		7782080, 7971966	Standard	NM_007121		Approved	NER, NER-I, RIP15, LXR-b	uc010enw.4	P55055		ENST00000253727.5:c.1356G>C	chr19.hg19:g.50885832G>C		30.0	0.0		33.0	12.0	NM_007121	A8K490|B4DNM6|E7EWA6|Q12970|Q5I0Y1	Silent	SNP	ENST00000253727.5	hg19	CCDS42593.1																																																																																			.	.		0.647	NR1H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464724.2			C	50885832	G	C	50885832	2	2	188	1	0	0	0	0	0	0	0	1	10626	1364	48	4		4	NR1H2	19	50885832	Silent	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	5318537	50885832	8243151	112	27863										
NLRP4	147945	hgsc.bcm.edu	37	chr19	56379080	56379080	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ttccctttcctgcaggctggTaaattgtcacctctcaccca	6	15	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr19:56379080T>C	ENST00000301295.6	+	6	2614	c.2192T>C	c.(2191-2193)gTa>gCa	p.V731A	NLRP4_ENST00000346986.5_Intron|NLRP4_ENST00000587891.1_Missense_Mutation_p.V656A	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	731					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TGCAGGCTGGTAAATTGTCAC	0.468																																					p.V731A		Atlas-SNP	.											NLRP4_ENST00000301295,NS,neuroblastoma,0,1	NLRP4	331	.	0			c.T2192C						.						181	145	157					19																	56379080		2203	4300	6503	SO:0001583	missense	147945	exon6			GGCTGGTAAATTG	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.2192T>C	chr19.hg19:g.56379080T>C	ENSP00000301295:p.Val731Ala	50.0	0.0		55.0	19.0	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	hg19	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.134523	0.00338	.	.	ENSG00000160505	ENST00000301295	T	0.07688	3.17	2.95	-5.89	0.02282	.	.	.	.	.	T	0.02727	0.0082	N	0.11673	0.155	0.09310	N	1	B;B	0.15141	0.012;0.012	B;B	0.18561	0.022;0.005	T	0.41945	-0.9480	9	0.08599	T	0.76	.	2.202	0.03926	0.1221:0.1572:0.2425:0.4782	.	656;731	Q96MN2-3;Q96MN2	.;NALP4_HUMAN	A	731	ENSP00000301295:V731A	ENSP00000301295:V731A	V	+	2	0	NLRP4	61070892	0.000000	0.05858	0.000000	0.03702	0.097000	0.18754	-2.321000	0.01119	-2.406000	0.00574	-0.526000	0.04340	GTA	.	.		0.468	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		C	56379080	T	C	56379080	3	2	188	1	0	0	0	0	1	0	0	0	10488	1638	57	2	2210	2	NLRP4	19	56379080	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	5493248	56379080	2749903	113	27864										
VN1R1	57191	hgsc.bcm.edu	37	chr19	57967008	57967008	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	atggactgaatagaaaacaaAaaaggagctcaccaggacca	9	8	1	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr19:57967008A>C	ENST00000321039.3	-	1	846	c.847T>G	c.(847-849)Ttt>Gtt	p.F283V	AC004076.9_ENST00000596831.1_Intron|AC004076.9_ENST00000415705.3_5'UTR	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	283					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		TAGAAAACAAAAAAGGAGCTC	0.488																																					p.F283V		Atlas-SNP	.											.	VN1R1	48	.	0			c.T847G						.						101	86	91					19																	57967008		2203	4300	6503	SO:0001583	missense	57191	exon1			AAACAAAAAAGGA	AF255342	CCDS12951.1	19q13.4	2012-08-22	2003-01-15		ENSG00000178201	ENSG00000178201		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	13548	protein-coding gene	gene with protein product		605234	"vomeronasal olfactory receptor, (chromosome 19) subtype I, member 1"	VNR19I1		10973240	Standard	NM_020633		Approved	V1RL1, ZVNR1, ZVNH1	uc002qos.2	Q9GZP7		ENST00000321039.3:c.847T>G	chr19.hg19:g.57967008A>C	ENSP00000322339:p.Phe283Val	92.0	0.0		87.0	33.0	NM_020633	B3KSV5|Q7Z5H8|Q7Z5H9	Missense_Mutation	SNP	ENST00000321039.3	hg19	CCDS12951.1	.	.	.	.	.	.	.	.	.	.	A	0.015	-1.541236	0.00934	.	.	ENSG00000178201	ENST00000321039	T	0.04603	3.59	4.07	-8.15	0.01065	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01222	0.0040	N	0.01742	-0.745	0.09310	N	1	B	0.17667	0.023	B	0.14023	0.01	T	0.37596	-0.9699	9	0.02654	T	1	.	5.2675	0.15607	0.5738:0.1768:0.1787:0.0708	.	283	Q9GZP7	VN1R1_HUMAN	V	283	ENSP00000322339:F283V	ENSP00000322339:F283V	F	-	1	0	VN1R1	62658820	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.891000	0.04135	-2.442000	0.00549	-0.339000	0.08088	TTT	.	.		0.488	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466464.1	NM_020633		C	57967008	A	C	57967008	3	2	188	1	0	0	0	0	1	0	0	0	17193	14	1	5	218	5	VN1R1	19	57967008	Missense_Mutation	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10	1587928	57967008	1161975	114	27865										
FASTKD5	60493	hgsc.bcm.edu	37	chr20	3128547	3128547	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gtcaggtgcatgacaccttgAactcccagggaaggaattcg	12	10	1	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr20:3128547A>T	ENST00000380266.3	-	2	1491	c.1170T>A	c.(1168-1170)gtT>gtA	p.V390V	UBOX5_ENST00000217173.2_Intron|UBOX5_ENST00000348031.2_Intron|UBOX5-AS1_ENST00000446537.1_RNA	NM_021826.4	NP_068598.1	Q7L8L6	FAKD5_HUMAN	FAST kinase domains 5	390					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(2)|endometrium(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(2)	19						TGACACCTTGAACTCCCAGGG	0.468																																					p.V390V		Atlas-SNP	.											.	FASTKD5	63	.	0			c.T1170A						.						84	78	80					20																	3128547		2203	4300	6503	SO:0001819	synonymous_variant	60493	exon2			ACCTTGAACTCCC	BC007413	CCDS13048.1	20p13	2006-07-07			ENSG00000215251	ENSG00000215251			25790	protein-coding gene	gene with protein product		614272				11347906	Standard	NM_021826		Approved	FLJ13149	uc002whz.4	Q7L8L6	OTTHUMG00000031727	ENST00000380266.3:c.1170T>A	chr20.hg19:g.3128547A>T		194.0	0.0		194.0	57.0	NM_021826	Q96JN3|Q9H5D1|Q9H8Y3	Silent	SNP	ENST00000380266.3	hg19	CCDS13048.1																																																																																			.	.		0.468	FASTKD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077701.2	NM_021826		T	3128547	A	T	3128547	2	4	188	1	0	0	0	0	0	0	0	1	5696	233	9	4		4	FASTKD5	20	3128547	Silent	SNP	A	TCGA-DD-AADE-01A-11D-A40R-10		3128547	59896973	115	27866										
C20orf165	128497	hgsc.bcm.edu	37	chr20	44515576	44515576	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tgcgggaatttgtggcagttTcggctgtattccttccgtag	13	8	0	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr20:44515576T>G	ENST00000372519.3	-	2	308	c.264A>C	c.(262-264)cgA>cgC	p.R88R		NM_080608.3	NP_542175.1	Q9BR10	SPT25_HUMAN	spermatogenesis associated 25	88					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TGTGGCAGTTTCGGCTGTATT	0.647																																					p.R88R		Atlas-SNP	.											.	.	.	.	0			c.A264C						.						117	118	118					20																	44515576		2203	4300	6503	SO:0001819	synonymous_variant	128497	exon2			GCAGTTTCGGCTG	AL008726	CCDS13383.1	20q13.12	2011-11-24	2011-11-24	2011-11-24	ENSG00000149634	ENSG00000149634			16158	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 165"	C20orf165		19240080	Standard	NM_080608		Approved	dJ337O18.8, TSG23	uc002xqf.3	Q9BR10	OTTHUMG00000032628	ENST00000372519.3:c.264A>C	chr20.hg19:g.44515576T>G		34.0	0.0		43.0	15.0	NM_080608		Silent	SNP	ENST00000372519.3	hg19	CCDS13383.1																																																																																			.	.		0.647	SPATA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079541.1			G	44515576	T	G	44515576	2	3	188	1	0	0	0	0	0	0	0	1	2096	1770	62	5		5	C20orf165	20	44515576	Silent	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	41387029	44515576	18509944	116	27867										
MMP9	4318	hgsc.bcm.edu	37	chr20	44642394	44642394	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gccccgcaagctggactcggTctttgaggagcggctctcca	13	14	2	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr20:44642394T>C	ENST00000372330.3	+	10	1728	c.1709T>C	c.(1708-1710)gTc>gCc	p.V570A	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	570					collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	CTGGACTCGGTCTTTGAGGAG	0.607											OREG0025990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V570A		Atlas-SNP	.											.	MMP9	84	.	0			c.T1709C						.						41	44	43					20																	44642394		2203	4300	6503	SO:0001583	missense	4318	exon10			ACTCGGTCTTTGA		CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)", "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.1709T>C	chr20.hg19:g.44642394T>C	ENSP00000361405:p.Val570Ala	114.0	0.0	925	103.0	35.0	NM_004994	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	hg19	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.259124	0.23051	.	.	ENSG00000100985	ENST00000372330;ENST00000545925	T	0.01369	4.97	4.85	2.9	0.33743	Hemopexin/matrixin, conserved site (1);Hemopexin/matrixin (2);	0.106602	0.64402	N	0.000005	T	0.00412	0.0013	N	0.00191	-1.88	0.26531	N	0.974259	B	0.02656	0.0	B	0.01281	0.0	T	0.45279	-0.9272	10	0.02654	T	1	.	7.6049	0.28097	0.0:0.7063:0.1376:0.1561	.	570	P14780	MMP9_HUMAN	A	570;140	ENSP00000361405:V570A	ENSP00000361405:V570A	V	+	2	0	MMP9	44075801	0.974000	0.33945	0.930000	0.37139	0.359000	0.29487	2.270000	0.43355	0.626000	0.30322	-0.846000	0.03041	GTC	.	.		0.607	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1			C	44642394	T	C	44642394	3	2	188	1	0	0	0	0	1	0	0	0	9678	1667	58	2	1747	2	MMP9	20	44642394	Missense_Mutation	SNP	T	TCGA-DD-AADE-01A-11D-A40R-10	126818	44642394	18383126	117	27868										
TMPRSS3	64699	hgsc.bcm.edu	37	chr21	43805592	43805592	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tcgatggacacaaactcctcCcggaactgcccctccagcga	8	17	0	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr21:43805592C>T	ENST00000291532.3	-	6	1453	c.498G>A	c.(496-498)cgG>cgA	p.R166R	TMPRSS3_ENST00000433957.2_Silent_p.R166R|TMPRSS3_ENST00000398397.3_Silent_p.R166R|TMPRSS3_ENST00000398405.1_Silent_p.R164R|TMPRSS3_ENST00000380399.1_Silent_p.R250R|TMPRSS3_ENST00000474596.1_5'UTR	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	166	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						CAAACTCCTCCCGGAACTGCC	0.507																																					p.R166R		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.G498A						.						178	162	167					21																	43805592		2203	4300	6503	SO:0001819	synonymous_variant	64699	exon6			CTCCTCCCGGAAC	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"Serine peptidases / Transmembrane"	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.498G>A	chr21.hg19:g.43805592C>T		92.0	0.0		99.0	34.0	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Silent	SNP	ENST00000291532.3	hg19	CCDS13686.1																																																																																			.	.		0.507	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1			T	43805592	C	T	43805592	2	4	188	1	0	0	0	0	0	0	0	1	16263	610	22	3		3	TMPRSS3	21	43805592	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10		43805592	4324303	118	27869										
TBX1	6899	hgsc.bcm.edu	37	chr22	19748651	19748651	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	accagcgccgccgccgagccCgagggccccggggccagctg	16	19	0	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chr22:19748651C>A	ENST00000329705.7	+	3	387	c.258C>A	c.(256-258)ccC>ccA	p.P86P	TBX1_ENST00000332710.4_Silent_p.P86P|TBX1_ENST00000359500.3_Silent_p.P86P	NM_080646.1	NP_542377.1	O43435	TBX1_HUMAN	T-box 1	86					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|aorta morphogenesis (GO:0035909)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|blood vessel morphogenesis (GO:0048514)|blood vessel remodeling (GO:0001974)|cell fate specification (GO:0001708)|cell proliferation (GO:0008283)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|coronary artery morphogenesis (GO:0060982)|determination of left/right symmetry (GO:0007368)|ear morphogenesis (GO:0042471)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic viscerocranium morphogenesis (GO:0048703)|enamel mineralization (GO:0070166)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|lymph vessel development (GO:0001945)|mesenchymal cell apoptotic process (GO:0097152)|mesoderm development (GO:0007498)|middle ear morphogenesis (GO:0042474)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle organ morphogenesis (GO:0048644)|muscle tissue morphogenesis (GO:0060415)|negative regulation of cell differentiation (GO:0045596)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|parathyroid gland development (GO:0060017)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of tongue muscle cell differentiation (GO:2001037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of organ morphogenesis (GO:2000027)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retinoic acid receptor signaling pathway (GO:0048384)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|social behavior (GO:0035176)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tongue morphogenesis (GO:0043587)|transcription, DNA-templated (GO:0006351)|vagus nerve morphogenesis (GO:0021644)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|lung(3)|ovary(2)	8	Colorectal(54;0.0993)	all_lung(157;3.05e-06)				ccgccgAGCCCGAGGGCCCCG	0.806																																					p.P86P		Atlas-SNP	.											.	TBX1	62	.	0			c.C258A						.						4	4	4					22																	19748651		1976	3914	5890	SO:0001819	synonymous_variant	6899	exon3			CGAGCCCGAGGGC	AF012131	CCDS13765.1, CCDS13766.1, CCDS13767.1	22q11.21	2014-09-17			ENSG00000184058	ENSG00000184058		"T-boxes"	11592	protein-coding gene	gene with protein product		602054	"velocardiofacial syndrome"	VCF		9268629, 23000736	Standard	NM_080646		Approved	CATCH22	uc002zqa.1	O43435	OTTHUMG00000150421	ENST00000329705.7:c.258C>A	chr22.hg19:g.19748651C>A		231.0	0.0		172.0	63.0	NM_080647	C6G493|C6G494|O43436|Q96RJ2	Silent	SNP	ENST00000329705.7	hg19	CCDS13766.1																																																																																			.	.		0.806	TBX1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318033.1	NM_080647		A	19748651	C	A	19748651	2	1	188	1	0	0	0	0	0	0	0	1	15665	639	23	1		1	TBX1	22	19748651	Silent	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10		19748651	31555915	119	27870										
PPP2R3B	28227	hgsc.bcm.edu	37	chrX	301663	301663	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	tccaggtccatgcagcggaaCcagtactcgatgctgcggca	12	13	0	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chrX:301663C>A	ENST00000390665.3	-	10	1206	c.1188G>T	c.(1186-1188)tgG>tgT	p.W396C		NM_013239.4	NP_037371.2	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'', beta	396	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|phosphoprotein phosphatase activity (GO:0004721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(5)|lung(5)|skin(1)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGCAGCGGAACCAGTACTCGA	0.687																																					p.W396C		Atlas-SNP	.											.	PPP2R3B	43	.	0			c.G1188T						.						102	78	86					X																	301663		2196	4288	6484	SO:0001583	missense	28227	exon10			GCGGAACCAGTAC	AF215840	CCDS14104.1	Xp22.3 and Yp11.3	2013-01-10	2010-06-18		ENSG00000167393	ENSG00000167393		"Pseudoautosomal regions / PAR1", "Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	13417	protein-coding gene	gene with protein product		300339	"protein phosphatase 2 (formerly 2A), regulatory subunit B'', beta"	PPP2R3L		11173861	Standard	NM_013239		Approved	PPP2R3LY, PR48	uc004cpg.3	Q9Y5P8	OTTHUMG00000021052	ENST00000390665.3:c.1188G>T	chrX.hg19:g.301663C>A	ENSP00000375080:p.Trp396Cys	131.0	0.0		80.0	33.0	NM_013239	Q6P4G9|Q7RTT1|Q96H01	Missense_Mutation	SNP	ENST00000390665.3	hg19	CCDS14104.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.907035	0.33628	.	.	ENSG00000167393	ENST00000390665	T	0.48522	0.81	2.05	2.05	0.26809	EF-hand-like domain (1);	0.000000	0.85682	U	0.000000	T	0.75324	0.3834	H	0.96460	3.825	0.32841	D	0.505407	D	0.89917	1.0	D	0.97110	1.0	T	0.83353	-0.0002	10	0.87932	D	0	.	11.0142	0.47679	0.0:1.0:0.0:0.0	.	396	Q9Y5P8	P2R3B_HUMAN	C	396	ENSP00000375080:W396C	ENSP00000375080:W396C	W	-	3	0	PPP2R3B	221663	1.000000	0.71417	0.994000	0.49952	0.297000	0.27493	5.819000	0.69243	0.600000	0.29862	0.174000	0.16983	TGG	.	.		0.687	PPP2R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055577.2	NM_013239		A	301663	C	A	301663	3	1	188	1	0	0	0	0	1	0	0	0	12401	508	18	3	555	3	PPP2R3B	23	301663	Missense_Mutation	SNP	C	TCGA-DD-AADE-01A-11D-A40R-10		301663	154968897	120	27871										
USP9X	8239	hgsc.bcm.edu	37	chrX	41075386	41075386	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	agagtgagcagtctgaaagtGagacagcaggaagcacaaaa	13	6	1	4			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chrX:41075386G>T	ENST00000324545.8	+	35	6199	c.5566G>T	c.(5566-5568)Gag>Tag	p.E1856*	USP9X_ENST00000378308.2_Nonsense_Mutation_p.E1856*	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1856	USP.				axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						GTCTGAAAGTGAGACAGCAGG	0.473																																					p.E1856X	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.G5566T						.						108	115	113					X																	41075386		2196	4294	6490	SO:0001587	stop_gained	8239	exon35			GAAAGTGAGACAG	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.5566G>T	chrX.hg19:g.41075386G>T	ENSP00000316357:p.Glu1856*	197.0	0.0		174.0	130.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Nonsense_Mutation	SNP	ENST00000324545.8	hg19	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	G	50	16.667748	0.99869	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	.	.	.	5.89	5.89	0.94794	.	0.094058	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	.	19.178	0.93611	0.0:0.0:1.0:0.0	.	.	.	.	X	1856	.	ENSP00000316357:E1856X	E	+	1	0	USP9X	40960330	1.000000	0.71417	0.798000	0.32154	0.990000	0.78478	6.168000	0.71908	2.480000	0.83734	0.600000	0.82982	GAG	.	.		0.473	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		T	41075386	G	T	41075386	4	4	188	1	0	0	0	0	0	1	0	0	17105	1291	45	3	5700	3	USP9X	23	41075386	Nonsense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	40773723	41075386	114195174	121	27872										
CFP	5199	hgsc.bcm.edu	37	chrX	47486303	47486303	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ggcccaggccacaggtcacaGggcaggggctcacagggccc	16	15	2	0			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chrX:47486303G>C	ENST00000396992.3	-	6	929	c.809C>G	c.(808-810)cCt>cGt	p.P270R	CFP_ENST00000480317.1_5'Flank|CFP_ENST00000247153.3_Missense_Mutation_p.P270R|CFP_ENST00000377005.2_Missense_Mutation_p.P270R	NM_001145252.1	NP_001138724.1	P27918	PROP_HUMAN	complement factor properdin	270	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	18						ACAGGTCACAGGGCAGGGGCT	0.662																																					p.P270R		Atlas-SNP	.											.	CFP	43	.	0			c.C809G						.						19	19	19					X																	47486303		2191	4280	6471	SO:0001583	missense	5199	exon6			GTCACAGGGCAGG	M83652	CCDS14282.1	Xp11.4	2014-09-17	2006-03-02	2006-03-02	ENSG00000126759	ENSG00000126759		"Complement system"	8864	protein-coding gene	gene with protein product		300383	"properdin P factor, complement"	PFC		1783405	Standard	NM_001145252		Approved		uc004dih.3	P27918	OTTHUMG00000021451	ENST00000396992.3:c.809C>G	chrX.hg19:g.47486303G>C	ENSP00000380189:p.Pro270Arg	84.0	0.0		61.0	37.0	NM_001145252	O15134|O15135|O15136|O75826	Missense_Mutation	SNP	ENST00000396992.3	hg19	CCDS14282.1	.	.	.	.	.	.	.	.	.	.	G	17.45	3.391986	0.62066	.	.	ENSG00000126759	ENST00000396992;ENST00000247153;ENST00000377005;ENST00000469388	T;T;T;T	0.52983	0.64;0.64;0.64;0.64	5.33	5.33	0.75918	.	0.552403	0.20365	N	0.093763	T	0.58807	0.2148	L	0.42632	1.34	0.24132	N	0.995763	P;P	0.50272	0.933;0.916	P;P	0.62435	0.902;0.818	T	0.53711	-0.8400	10	0.72032	D	0.01	.	13.5925	0.61967	0.0:0.0:1.0:0.0	.	206;270	B3KVK6;P27918	.;PROP_HUMAN	R	270;270;270;135	ENSP00000380189:P270R;ENSP00000247153:P270R;ENSP00000366204:P270R;ENSP00000418258:P135R	ENSP00000247153:P270R	P	-	2	0	CFP	47371247	0.985000	0.35326	0.759000	0.31340	0.983000	0.72400	5.583000	0.67484	2.365000	0.80145	0.529000	0.55759	CCT	.	.		0.662	CFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056435.2	NM_002621		C	47486303	G	C	47486303	3	2	188	1	0	0	0	0	1	0	0	0	3295	1000	35	4	616	4	CFP	23	47486303	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	6410917	47486303	107784257	122	27873										
SLC6A14	11254	hgsc.bcm.edu	37	chrX	115590099	115590099	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	ccatgaaatacctactgttaGtggcagcagaaaaccggaat	9	9	0	2			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chrX:115590099G>A	ENST00000371900.4	+	14	1995	c.1907G>A	c.(1906-1908)aGt>aAt	p.S636N	SLC6A14_ENST00000463626.1_3'UTR	NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	636					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CCTACTGTTAGTGGCAGCAGA	0.363																																					p.S636N		Atlas-SNP	.											.	SLC6A14	56	.	0			c.G1907A						.						114	108	110					X																	115590099		2203	4300	6503	SO:0001583	missense	11254	exon14			CTGTTAGTGGCAG	AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"Solute carriers"	11047	protein-coding gene	gene with protein product		300444	"solute carrier family 6 (neurotransmitter transporter), member 14"			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.1907G>A	chrX.hg19:g.115590099G>A	ENSP00000360967:p.Ser636Asn	355.0	0.0		292.0	200.0	NM_007231	Q5H942	Missense_Mutation	SNP	ENST00000371900.4	hg19	CCDS14570.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.862334	0.32884	.	.	ENSG00000087916	ENST00000371900	T	0.73575	-0.76	5.68	3.91	0.45181	.	0.316888	0.34879	N	0.003614	T	0.52240	0.1722	N	0.08118	0	0.28179	N	0.928251	B	0.10296	0.003	B	0.08055	0.003	T	0.42068	-0.9473	10	0.33141	T	0.24	.	9.5558	0.39337	0.1756:0.0:0.8244:0.0	.	636	Q9UN76	S6A14_HUMAN	N	636	ENSP00000360967:S636N	ENSP00000360967:S636N	S	+	2	0	SLC6A14	115504127	.	.	0.993000	0.49108	0.463000	0.32649	.	.	0.654000	0.30846	0.538000	0.68166	AGT	.	.		0.363	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			A	115590099	G	A	115590099	3	1	188	1	0	0	0	0	1	0	0	0	14692	1029	36	3	1961	3	SLC6A14	23	115590099	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	68103796	115590099	39680461	123	27874										
ZCCHC12	170261	hgsc.bcm.edu	37	chrX	117959625	117959626	+	Missense_Mutation	DNP	GC	GC	TT													0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	aattttttaacaccctacaaGctcaaggggagaaagcctcc							TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chrX:117959625_117959626GC>TT	ENST00000310164.2	+	4	925_926	c.418_419GC>TT	c.(418-420)GCt>TTt	p.A140F		NM_173798.2	NP_776159.1	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	140					BMP signaling pathway (GO:0030509)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	22						caccctacaagctcaaggggag	0.465																																					p.A140S|p.A140V		Atlas-SNP	.											.	ZCCHC12	60	.	0			c.G418T|c.C419T						.																																			SO:0001583	missense	170261	exon4			CTACAAGCTCAAG|TACAAGCTCAAGG	AK122676	CCDS14574.1	Xq24	2013-10-11			ENSG00000174460	ENSG00000174460		"Zinc fingers, CCHC domain containing", "Paraneoplastic Ma antigens"	27273	protein-coding gene	gene with protein product	"paraneoplastic Ma antigen family member 7A"	300701				21739307, 19578717	Standard	NM_173798		Approved	FLJ16123, SIZN, SIZN1, PNMA7A	uc004equ.3	Q6PEW1	OTTHUMG00000022261	Exception_encountered	chrX.hg19:g.117959625_117959626delinsTT	ENSP00000308921:p.Ala140Phe	106.0	0.0		69.0	7.0	NM_173798	B3KV48|Q6PID5|Q8N1C1	Missense_Mutation	SNP	ENST00000310164.2	hg19	CCDS14574.1																																																																																			.	.		0.465	ZCCHC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058014.1	NM_173798		TT	117959626	GC	TT	117959625	3	4	188	1	0	0	0	0	1	0	0	0	17596	971	34	3	420	3	ZCCHC12	23	117959625	Missense_Mutation	DNP	GC	TCGA-DD-AADE-01A-11D-A40R-10	2369526	117959625	37310935	124	27875										
SOX3	6658	hgsc.bcm.edu	37	chrX	139586656	139586656	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.048	6	1	1.13587044534413	2.39794871794872	0.744190981432361	1	1	0	gcgcgaagtcgcttggcctcGtcgatgaatggtcgcttctc	13	12	1	1			TCGA-DD-AADE-01A-11D-A40R-10	TCGA-DD-AADE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0c6e46a4-0a92-4775-9edb-024c9b2fba8d	c6c3ad3c-f886-41dc-8a10-31c20b29d836	g.chrX:139586656G>T	ENST00000370536.2	-	1	569	c.570C>A	c.(568-570)gaC>gaA	p.D190E		NM_005634.2	NP_005625.2	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	190					central nervous system development (GO:0007417)|face development (GO:0060324)|hypothalamus development (GO:0021854)|negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|sensory organ development (GO:0007423)|Sertoli cell development (GO:0060009)|sex determination (GO:0007530)|spermatid differentiation (GO:0048515)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	10	Acute lymphoblastic leukemia(192;7.65e-05)					GCTTGGCCTCGTCGATGAATG	0.572																																					p.D190E		Atlas-SNP	.											.	SOX3	44	.	0			c.C570A						.						75	67	70					X																	139586656		2203	4300	6503	SO:0001583	missense	6658	exon1			GGCCTCGTCGATG		CCDS14669.1	Xq27.1	2013-10-17			ENSG00000134595	ENSG00000134595		"SRY (sex determining region Y)-boxes"	11199	protein-coding gene	gene with protein product		313430	"panhypopituitarism"	PHP		15800844	Standard	NM_005634		Approved		uc004fbd.1	P41225	OTTHUMG00000022544	ENST00000370536.2:c.570C>A	chrX.hg19:g.139586656G>T	ENSP00000359567:p.Asp190Glu	351.0	2.0		294.0	204.0	NM_005634	P35714|Q5JWI3|Q9NP49	Missense_Mutation	SNP	ENST00000370536.2	hg19	CCDS14669.1	.	.	.	.	.	.	.	.	.	.	g	17.33	3.362026	0.61403	.	.	ENSG00000134595	ENST00000370536	D	0.99113	-5.44	4.12	3.25	0.37280	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	U	0.000000	D	0.96855	0.8973	N	0.12663	0.25	0.80722	D	1	P	0.37636	0.603	P	0.48982	0.597	D	0.93965	0.7244	9	.	.	.	.	10.5182	0.44903	0.0989:0.0:0.9011:0.0	.	190	P41225	SOX3_HUMAN	E	190	ENSP00000359567:D190E	.	D	-	3	2	SOX3	139414322	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.039000	0.64185	0.561000	0.29186	-0.351000	0.07748	GAC	.	.		0.572	SOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058577.1			T	139586656	G	T	139586656	3	4	188	1	0	0	0	0	1	0	0	0	14966	1136	40	1	774	1	SOX3	23	139586656	Missense_Mutation	SNP	G	TCGA-DD-AADE-01A-11D-A40R-10	21627031	139586656	15683904	125	27876										
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1895247	1895247	+	IGR	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	accagcttgcagtagttgatCgtgtaggtggtgtttaccaa	12	7	0	1	rs368592608		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:1895247C>A								TMEM52 (44535 upstream) : C1orf222 (24315 downstream)																							AGTAGTTGATCGTGTAGGTGG	0.552																																					p.T545T		Atlas-SNP	.											.	KIAA1751	92	.	0			c.G1635T						.						102	108	106					1																	1895247		1985	4155	6140	SO:0001628	intergenic_variant	85452	exon14			GTTGATCGTGTAG																													chr1.hg19:g.1895247C>A		49.0	0.0		35.0	13.0	NM_001080484		Silent	SNP		hg19																																																																																				.	.	0	0.552									A	1895247	C	A	1895247	1	1	189	0	1	0	0	0	0	0	0	0	8265	871	31	1		1	KIAA1751	1	1895247	IGR	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10		1895247	247355374	1	27877										
CHD5	26038	hgsc.bcm.edu	37	chr1	6228214	6228214	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aggtgctgcccctcacctctTtcttcttccgcttcccttta	5	17	4	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:6228214T>A	ENST00000262450.3	-	2	302	c.203A>T	c.(202-204)aAa>aTa	p.K68I	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0	Interaction with ASNA1/TRC40.				tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		CCTCACCTCTTTCTTCTTCCG	0.602																																					p.K68I		Atlas-SNP	.											.	CHD5	267	.	0			c.A203T						.						140	137	138					1																	6228214		2203	4300	6503	SO:0001583	missense	26038	exon2			ACCTCTTTCTTCT	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.203A>T	chr1.hg19:g.6228214T>A	ENSP00000262450:p.Lys68Ile	48.0	0.0		42.0	14.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	hg19	CCDS57.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.642470	0.67244	.	.	ENSG00000116254	ENST00000262450	D	0.92752	-3.1	4.9	3.78	0.43462	.	0.000000	0.44097	U	0.000482	D	0.92485	0.7614	L	0.58810	1.83	0.80722	D	1	D	0.59357	0.985	P	0.56278	0.795	D	0.90831	0.4716	10	0.56958	D	0.05	-12.4043	7.9342	0.29920	0.0:0.096:0.0:0.904	.	68	Q8TDI0	CHD5_HUMAN	I	68	ENSP00000262450:K68I	ENSP00000262450:K68I	K	-	2	0	CHD5	6150801	1.000000	0.71417	0.998000	0.56505	0.869000	0.49853	2.818000	0.48041	0.717000	0.32145	0.260000	0.18958	AAA	.	.		0.602	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		A	6228214	T	A	6228214	3	1	189	1	0	0	0	0	1	0	0	0	3330	1841	64	4	5821	4	CHD5	1	6228214	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	4332967	6228214	243022407	2	27878										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7721921	7721921	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	caactgcctctgcaccggcaGcctgggtgagccggggctcc	14	16	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:7721921G>C	ENST00000303635.7	+	8	1007	c.800G>C	c.(799-801)aGc>aCc	p.S267T	CAMTA1_ENST00000439411.2_Missense_Mutation_p.S267T	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	267					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TGCACCGGCAGCCTGGGTGAG	0.692			T	WWTR1	epitheliod hemangioendothelioma																																p.S267T		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.G800C						.						22	22	22					1																	7721921		2199	4298	6497	SO:0001583	missense	23261	exon8			CCGGCAGCCTGGG	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.800G>C	chr1.hg19:g.7721921G>C	ENSP00000306522:p.Ser267Thr	118.0	0.0		82.0	61.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	hg19	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	g	11.48	1.652696	0.29336	.	.	ENSG00000171735	ENST00000303635;ENST00000439411	T;T	0.38401	1.14;1.14	4.77	3.61	0.41365	.	0.173756	0.50627	D	0.000107	T	0.11324	0.0276	N	0.03608	-0.345	0.24235	N	0.99538	B	0.02656	0.0	B	0.01281	0.0	T	0.34700	-0.9818	10	0.07030	T	0.85	-13.1324	3.1519	0.06490	0.2659:0.2813:0.4528:0.0	.	267	Q9Y6Y1	CMTA1_HUMAN	T	267	ENSP00000306522:S267T;ENSP00000402561:S267T	ENSP00000306522:S267T	S	+	2	0	CAMTA1	7644508	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.411000	0.44600	2.382000	0.81193	0.543000	0.68304	AGC	.	.		0.692	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		C	7721921	G	C	7721921	3	2	189	1	0	0	0	0	1	0	0	0	2615	971	34	4	830	4	CAMTA1	1	7721921	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	1493707	7721921	241528700	3	27879										
FAM131C	348487	hgsc.bcm.edu	37	chr1	16390079	16390092	+	Frame_Shift_Del	DEL	GGGGTCCGCACCCT	GGGGTCCGCACCCT	-													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gagggcagatctgggttcaaGgggtccgcaccctggggcat					rs35576581|rs549929286	byFrequency	TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	GGGGTCCGCACCCT	GGGGTCCGCACCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:16390079_16390092delGGGGTCCGCACCCT	ENST00000375662.4	-	2	245_258	c.62_75delAGGGTGCGGACCCC	c.(61-75)cagggtgcggaccccfs	p.QGADP21fs	FAM131C_ENST00000494078.1_Intron	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	21										large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGGTTCAAGGGGTCCGCACCCTGGGGCATGGG	0.589																																					p.21_26del		Atlas-INDEL	.											.	FAM131C	21	.	0			c.63_76del						.																																			SO:0001589	frameshift_variant	348487	exon2			.		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 117"	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.62_75delAGGGTGCGGACCCC	chr1.hg19:g.16390079_16390092delGGGGTCCGCACCCT	ENSP00000364814:p.Gln21fs	100.0	0.0		65.0	17.0	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Frame_Shift_Del	DEL	ENST00000375662.4	hg19	CCDS41270.1																																																																																			.	.		0.589	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623		-	16390092	GGGGTCCGCACCCT	-	16390079	7	5	189	1	0	1	0	1	0	0	0	0	5446	987	35	0	791	0	FAM131C	1	16390079	Frame_Shift_Del	DEL	GGGGTCCGCACCCT	TCGA-DD-AADF-01A-11D-A40R-10	8668158	16390079	232860542	4	27880										
EPHA2	1969	hgsc.bcm.edu	37	chr1	16461026	16461026	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggaccacaccgacagccacgCcgccaatcaccgccaagttg	9	18	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:16461026C>T	ENST00000358432.5	-	8	1773	c.1619G>A	c.(1618-1620)gGc>gAc	p.G540D		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	540					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	GACAGCCACGCCGCCAATCAC	0.592																																					p.G540D		Atlas-SNP	.											.	EPHA2	102	.	0			c.G1619A						.						66	58	61					1																	16461026		2202	4300	6502	SO:0001583	missense	1969	exon8			GCCACGCCGCCAA	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3386	protein-coding gene	gene with protein product		176946	"EphA2"	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.1619G>A	chr1.hg19:g.16461026C>T	ENSP00000351209:p.Gly540Asp	175.0	0.0		161.0	57.0	NM_004431	B5A968|Q8N3Z2	Missense_Mutation	SNP	ENST00000358432.5	hg19	CCDS169.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.431187	0.43122	.	.	ENSG00000142627	ENST00000358432	T	0.11930	2.73	5.52	5.52	0.82312	.	0.000000	0.56097	D	0.000035	T	0.20007	0.0481	M	0.67569	2.06	0.80722	D	1	P	0.41748	0.761	B	0.40702	0.338	T	0.00790	-1.1565	10	0.51188	T	0.08	.	15.0049	0.71504	0.0:1.0:0.0:0.0	.	540	P29317	EPHA2_HUMAN	D	540	ENSP00000351209:G540D	ENSP00000351209:G540D	G	-	2	0	EPHA2	16333613	0.704000	0.27836	0.205000	0.23548	0.042000	0.13812	3.187000	0.50950	2.604000	0.88044	0.650000	0.86243	GGC	.	.		0.592	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431		T	16461026	C	T	16461026	3	4	189	1	0	0	0	0	1	0	0	0	5169	739	26	3	1351	3	EPHA2	1	16461026	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	70947	16461026	232789595	5	27881										
ARHGEF19	128272	hgsc.bcm.edu	37	chr1	16533490	16533490	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cagcgtggccaggacgccgcTgccgcgtacgtcggggatat	16	13	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:16533490T>A	ENST00000270747.3	-	6	1226	c.1090A>T	c.(1090-1092)Agc>Tgc	p.S364C	ARHGEF19_ENST00000478117.1_5'UTR	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	364					regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		AGGACGCCGCTGCCGCGTACG	0.766																																					p.S364C		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.A1090T						.						3	3	3					1																	16533490		1541	2886	4427	SO:0001583	missense	128272	exon6			CGCCGCTGCCGCG	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"Rho guanine nucleotide exchange factors"	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.1090A>T	chr1.hg19:g.16533490T>A	ENSP00000270747:p.Ser364Cys	69.0	0.0		50.0	23.0	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	hg19	CCDS170.1	.	.	.	.	.	.	.	.	.	.	T	33	5.196757	0.94960	.	.	ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607	T;T	0.33865	1.39;1.39	4.5	4.5	0.54988	Dbl homology (DH) domain (1);	0.190224	0.43110	D	0.000610	T	0.59376	0.2189	M	0.78049	2.395	0.52501	D	0.999956	D	0.89917	1.0	D	0.91635	0.999	T	0.64571	-0.6376	10	0.87932	D	0	.	11.8056	0.52152	0.0:0.0:0.0:1.0	.	364	Q8IW93	ARHGJ_HUMAN	C	364	ENSP00000270747:S364C;ENSP00000396001:S364C	ENSP00000270747:S364C	S	-	1	0	ARHGEF19	16406077	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.301000	0.65727	1.684000	0.51022	0.392000	0.25879	AGC	.	.		0.766	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213		A	16533490	T	A	16533490	3	1	189	1	0	0	0	0	1	0	0	0	902	1580	55	4	1362	4	ARHGEF19	1	16533490	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	72464	16533490	232717131	6	27882										
GPR3	2827	hgsc.bcm.edu	37	chr1	27720946	27720946	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	catgctgcagctctacgcccAaatctgccgcatcgtctgcc	8	17	3	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:27720946A>T	ENST00000374024.3	+	2	743	c.644A>T	c.(643-645)cAa>cTa	p.Q215L		NM_005281.3	NP_005272.1	P46089	GPR3_HUMAN	G protein-coupled receptor 3	215					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|regulation of meiosis (GO:0040020)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(3)|ovary(1)|skin(1)	8		Breast(348;1.53e-05)|Ovarian(437;0.0606)|all_lung(284;0.157)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;2.81e-26)|Colorectal(126;1.24e-08)|KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;4.45e-06)|Lung(427;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|LUSC - Lung squamous cell carcinoma(448;0.008)|READ - Rectum adenocarcinoma(331;0.0419)		CTCTACGCCCAAATCTGCCGC	0.577																																					p.Q215L		Atlas-SNP	.											.	GPR3	23	.	0			c.A644T						.						155	136	143					1																	27720946		2203	4300	6503	SO:0001583	missense	2827	exon2			ACGCCCAAATCTG	BC032702	CCDS303.1	1p36.1-p35	2012-08-21			ENSG00000181773	ENSG00000181773		"GPCR / Class A : Orphans"	4484	protein-coding gene	gene with protein product		600241				7851889	Standard	NM_005281		Approved	ACCA	uc001bod.4	P46089	OTTHUMG00000003397	ENST00000374024.3:c.644A>T	chr1.hg19:g.27720946A>T	ENSP00000363136:p.Gln215Leu	34.0	0.0		35.0	10.0	NM_005281	A8K570	Missense_Mutation	SNP	ENST00000374024.3	hg19	CCDS303.1	.	.	.	.	.	.	.	.	.	.	A	15.89	2.967601	0.53507	.	.	ENSG00000181773	ENST00000374024	T	0.32753	1.44	5.64	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.163532	0.40222	N	0.001157	T	0.29190	0.0726	L	0.46819	1.47	0.40591	D	0.981484	P	0.35124	0.485	B	0.37550	0.253	T	0.16217	-1.0410	10	0.59425	D	0.04	.	10.773	0.46334	0.9254:0.0:0.0746:0.0	.	215	P46089	GPR3_HUMAN	L	215	ENSP00000363136:Q215L	ENSP00000363136:Q215L	Q	+	2	0	GPR3	27593533	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.343000	0.59348	2.146000	0.66826	0.379000	0.24179	CAA	.	.		0.577	GPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009522.1	NM_005281		T	27720946	A	T	27720946	3	4	189	1	0	0	0	0	1	0	0	0	6694	130	5	4	646	4	GPR3	1	27720946	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	11187456	27720946	221529675	7	27883										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43903332	43903332	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctgcccccttccctcgctctGtcccgaagccaagagcccat	7	20	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:43903332G>A	ENST00000562955.1	+	44	6186	c.6186G>A	c.(6184-6186)ctG>ctA	p.L2062L	SZT2_ENST00000372442.1_Silent_p.L1220L	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2119					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CCCTCGCTCTGTCCCGAAGCC	0.577																																					p.L2062L		Atlas-SNP	.											.	SZT2	383	.	0			c.G6186A						.						38	37	37					1																	43903332		2203	4300	6503	SO:0001819	synonymous_variant	23334	exon44			CGCTCTGTCCCGA	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.6186G>A	chr1.hg19:g.43903332G>A		40.0	0.0		39.0	13.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	hg19	CCDS30694.2																																																																																			.	.		0.577	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		A	43903332	G	A	43903332	2	1	189	1	0	0	0	0	0	0	0	1	8187	1364	48	3		3	KIAA0467	1	43903332	Silent	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	16182386	43903332	205347289	8	27884										
AGBL4	84871	hgsc.bcm.edu	37	chr1	50163062	50163062	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	acaggtgtccggcctaatgaAcagatcatactcaaactcag	8	11	3	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:50163062A>T	ENST00000371839.1	-	3	321	c.205T>A	c.(205-207)Ttc>Atc	p.F69I	AGBL4_ENST00000371836.1_Missense_Mutation_p.F69I|AGBL4_ENST00000497451.1_5'UTR|AGBL4_ENST00000371838.1_Missense_Mutation_p.F69I	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	69					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		GGCCTAATGAACAGATCATAC	0.423																																					p.F69I		Atlas-SNP	.											.	AGBL4	54	.	0			c.T205A						.						148	128	134					1																	50163062		692	1590	2282	SO:0001583	missense	84871	exon3			TAATGAACAGATC	AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 6"					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.205T>A	chr1.hg19:g.50163062A>T	ENSP00000360905:p.Phe69Ile	345.0	0.0		340.0	103.0	NM_032785	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	hg19	CCDS44137.1	.	.	.	.	.	.	.	.	.	.	A	33	5.259026	0.95368	.	.	ENSG00000186094	ENST00000371839;ENST00000411952;ENST00000371838;ENST00000371836	T;T;T	0.29142	1.58;1.58;1.58	5.84	5.84	0.93424	.	0.163209	0.46442	D	0.000300	T	0.46014	0.1371	L	0.38531	1.155	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.77557	0.99;0.917	T	0.26224	-1.0109	9	.	.	.	-12.3973	16.2231	0.82269	1.0:0.0:0.0:0.0	.	69;69	Q5VU57-2;Q5VU57	.;CBPC6_HUMAN	I	69;63;69;69	ENSP00000360905:F69I;ENSP00000360904:F69I;ENSP00000360902:F69I	.	F	-	1	0	AGBL4	49935649	1.000000	0.71417	0.988000	0.46212	0.949000	0.60115	8.619000	0.90938	2.235000	0.73313	0.377000	0.23210	TTC	.	.		0.423	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785		T	50163062	A	T	50163062	3	4	189	1	0	0	0	0	1	0	0	0	377	43	2	4	1354	4	AGBL4	1	50163062	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	6259730	50163062	199087559	9	27885										
TTC22	55001	hgsc.bcm.edu	37	chr1	55252674	55252674	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggtccctgagtacccgcagtCatggacgcccatgggggtgg	16	12	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:55252674C>A	ENST00000371276.4	-	4	917	c.814G>T	c.(814-816)Gac>Tac	p.D272Y	TTC22_ENST00000371274.4_Missense_Mutation_p.D272Y	NM_001114108.1	NP_001107580.1	Q5TAA0	TTC22_HUMAN	tetratricopeptide repeat domain 22	272										kidney(1)|large_intestine(1)|lung(7)|skin(1)	10						TACCCGCAGTCATGGACGCCC	0.647																																					p.D272Y		Atlas-SNP	.											.	TTC22	40	.	0			c.G814T						.						26	24	25					1																	55252674		2201	4299	6500	SO:0001583	missense	55001	exon4			CGCAGTCATGGAC	AK000626	CCDS598.1, CCDS44152.1	1p32.3	2013-01-11			ENSG00000006555	ENSG00000006555		"Tetratricopeptide (TTC) repeat domain containing"	26067	protein-coding gene	gene with protein product							Standard	NM_017904		Approved	FLJ20619	uc009vzt.1	Q5TAA0	OTTHUMG00000009916	ENST00000371276.4:c.814G>T	chr1.hg19:g.55252674C>A	ENSP00000360323:p.Asp272Tyr	22.0	0.0		29.0	10.0	NM_001114108	Q9NWT4	Missense_Mutation	SNP	ENST00000371276.4	hg19	CCDS44152.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.054370	0.75960	.	.	ENSG00000006555	ENST00000371276;ENST00000371274;ENST00000448308	T;T	0.52983	0.64;0.73	4.22	4.22	0.49857	Tetratricopeptide-like helical (1);	0.057261	0.64402	D	0.000002	T	0.56396	0.1982	L	0.34521	1.04	0.58432	D	0.999997	D;D	0.76494	0.995;0.999	D;D	0.66351	0.92;0.943	T	0.62034	-0.6939	10	0.87932	D	0	-24.7697	15.547	0.76112	0.0:1.0:0.0:0.0	.	272;272	Q5TAA0;Q5TAA0-2	TTC22_HUMAN;.	Y	272;272;53	ENSP00000360323:D272Y;ENSP00000360321:D272Y	ENSP00000360321:D272Y	D	-	1	0	TTC22	55025262	1.000000	0.71417	0.975000	0.42487	0.764000	0.43329	6.707000	0.74654	2.195000	0.70347	0.655000	0.94253	GAC	.	.		0.647	TTC22-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027438.1	NM_017904		A	55252674	C	A	55252674	3	1	189	1	0	0	0	0	1	0	0	0	16704	826	29	3	1014	3	TTC22	1	55252674	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	5089612	55252674	193997947	10	27886										
HFM1	164045	hgsc.bcm.edu	37	chr1	91843601	91843601	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	catcctcagcatttggaattGttgcagatacagctacaaat	7	9	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:91843601G>C	ENST00000370425.3	-	11	1474	c.1376C>G	c.(1375-1377)aCa>aGa	p.T459R	HFM1_ENST00000370424.3_Missense_Mutation_p.T138R|HFM1_ENST00000294696.5_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	459	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		ATTTGGAATTGTTGCAGATAC	0.343																																					p.T459R		Atlas-SNP	.											.	HFM1	188	.	0			c.C1376G						.						121	109	113					1																	91843601		1826	4096	5922	SO:0001583	missense	164045	exon11			GGAATTGTTGCAG	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.1376C>G	chr1.hg19:g.91843601G>C	ENSP00000359454:p.Thr459Arg	233.0	0.0		243.0	60.0	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	hg19	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	G	22.9	4.346212	0.82022	.	.	ENSG00000162669	ENST00000370425;ENST00000370424;ENST00000370421;ENST00000541820	D;T	0.91686	-2.89;-0.89	5.54	5.54	0.83059	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.47093	U	0.000246	D	0.97860	0.9297	H	0.98238	4.18	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	D	0.99129	1.0852	10	0.87932	D	0	.	19.4569	0.94897	0.0:0.0:1.0:0.0	.	138;459;459	A6NGI5;B7ZM16;A2PYH4	.;.;HFM1_HUMAN	R	459;138;143;492	ENSP00000359454:T459R;ENSP00000359453:T138R	ENSP00000359450:T143R	T	-	2	0	HFM1	91616189	1.000000	0.71417	0.998000	0.56505	0.872000	0.50106	9.430000	0.97488	2.588000	0.87417	0.563000	0.77884	ACA	.	.		0.343	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		C	91843601	G	C	91843601	3	2	189	1	0	0	0	0	1	0	0	0	7092	1377	48	4	3047	4	HFM1	1	91843601	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	36590927	91843601	157407020	11	27887										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103444281	103444281	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tactctttcacctggagggcCaggagggccatcgccacctg	12	14	2	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:103444281C>A	ENST00000370096.3	-	35	3049	c.2737G>T	c.(2737-2739)Ggc>Tgc	p.G913C	COL11A1_ENST00000358392.2_Missense_Mutation_p.G925C|COL11A1_ENST00000353414.4_Missense_Mutation_p.G874C|COL11A1_ENST00000512756.1_Missense_Mutation_p.G797C	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	913	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCTGGAGGGCCAGGAGGGCCA	0.378																																					p.G925C		Atlas-SNP	.											.	COL11A1	972	.	0			c.G2773T						.						98	114	109					1																	103444281		2200	4300	6500	SO:0001583	missense	1301	exon35			GAGGGCCAGGAGG	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2737G>T	chr1.hg19:g.103444281C>A	ENSP00000359114:p.Gly913Cys	191.0	0.0		194.0	109.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	18.50	3.636626	0.67130	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.99637	-6.29;-6.29;-6.29;-6.29	5.35	5.35	0.76521	.	0.119990	0.56097	D	0.000023	D	0.99837	0.9926	H	0.97564	4.03	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;1.0;1.0;1.0;0.999	D	0.96736	0.9543	10	0.87932	D	0	.	19.0619	0.93096	0.0:1.0:0.0:0.0	.	797;874;925;913;133	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	C	913;925;874;133;797	ENSP00000359114:G913C;ENSP00000351163:G925C;ENSP00000302551:G874C;ENSP00000426533:G797C	ENSP00000302551:G874C	G	-	1	0	COL11A1	103216869	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.343000	0.79319	2.506000	0.84524	0.655000	0.94253	GGC	.	.		0.378	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103444281	C	A	103444281	3	1	189	1	0	0	0	0	1	0	0	0	3669	594	21	3	2815	3	COL11A1	1	103444281	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	11600680	103444281	145806340	12	27888										
POGZ	23126	hgsc.bcm.edu	37	chr1	151378800	151378800	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gtgatgggagtgctggggctAagggagttagtagctcttca	17	5	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:151378800A>G	ENST00000271715.2	-	19	3025	c.2711T>C	c.(2710-2712)tTa>tCa	p.L904S	POGZ_ENST00000368863.2_Missense_Mutation_p.L809S|POGZ_ENST00000409503.1_Missense_Mutation_p.L895S|POGZ_ENST00000361398.3_Missense_Mutation_p.L851S|POGZ_ENST00000491586.1_Missense_Mutation_p.L860S|POGZ_ENST00000540984.1_Missense_Mutation_p.L266S|POGZ_ENST00000531094.1_Missense_Mutation_p.L842S|POGZ_ENST00000392723.1_Missense_Mutation_p.L851S	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	904	Pro-rich.				kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TGCTGGGGCTAAGGGAGTTAG	0.592																																					p.L904S		Atlas-SNP	.											.	POGZ	211	.	0			c.T2711C						.						95	93	94					1																	151378800		2203	4300	6503	SO:0001583	missense	23126	exon19			GGGGCTAAGGGAG	AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.2711T>C	chr1.hg19:g.151378800A>G	ENSP00000271715:p.Leu904Ser	98.0	0.0		229.0	35.0	NM_015100	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	hg19	CCDS997.1	.	.	.	.	.	.	.	.	.	.	A	2.317	-0.356614	0.05138	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000540984;ENST00000491586;ENST00000529669	T;T;T;T;T;T;T;T;T	0.28666	5.92;5.95;5.92;5.91;5.93;5.93;1.96;5.42;1.6	5.54	1.78	0.24846	.	1.458230	0.03655	N	0.241564	T	0.03477	0.0100	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B	0.14012	0.002;0.002;0.0;0.009;0.004;0.002	B;B;B;B;B;B	0.16289	0.003;0.003;0.004;0.015;0.015;0.003	T	0.21690	-1.0238	10	0.06494	T	0.89	2.546	3.2365	0.06766	0.6308:0.0:0.1857:0.1835	.	842;895;809;860;851;904	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;POGZ_HUMAN	S	851;904;851;809;895;842;266;860;304	ENSP00000376484:L851S;ENSP00000271715:L904S;ENSP00000354467:L851S;ENSP00000357856:L809S;ENSP00000386836:L895S;ENSP00000431259:L842S;ENSP00000443547:L266S;ENSP00000418408:L860S;ENSP00000432295:L304S	ENSP00000271715:L904S	L	-	2	0	POGZ	149645424	0.072000	0.21174	0.202000	0.23494	0.009000	0.06853	0.427000	0.21379	0.539000	0.28788	0.533000	0.62120	TTA	.	.		0.592	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		G	151378800	A	G	151378800	3	3	189	1	0	0	0	0	1	0	0	0	12195	372	13	2	1525	2	POGZ	1	151378800	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	47934519	151378800	97871821	13	27889										
LOR	4014	hgsc.bcm.edu	37	chr1	153234128	153234128	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggtcgtccggcggcggcggcAgcggcggaagcggctgcttc	20	13	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:153234128A>T	ENST00000368742.3	+	2	760	c.703A>T	c.(703-705)Agc>Tgc	p.S235C		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	235					keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			lung(2)	2	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			cggcggcggcagcggcggaag	0.756																																					p.S235C		Atlas-SNP	.											.	LOR	19	.	0			c.A703T						.						1	2	2					1																	153234128		689	1874	2563	SO:0001583	missense	4014	exon2			GGCGGCAGCGGCG	M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.703A>T	chr1.hg19:g.153234128A>T	ENSP00000357731:p.Ser235Cys	11.0	0.0		19.0	8.0	NM_000427	Q5T869|Q5XKF8	Missense_Mutation	SNP	ENST00000368742.3	hg19	CCDS30870.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.728|1.728	-0.494799|-0.494799	0.04322|0.04322	.|.	.|.	ENSG00000203782|ENSG00000203782	ENST00000392652|ENST00000368742	.|T	.|0.37584	.|1.19	3.75|3.75	-7.49|-7.49	0.01355|0.01355	.|.	.|2.145430	.|0.02612	.|N	.|0.102296	T|T	0.09862|0.09862	0.0242|0.0242	L|L	0.39898|0.39898	1.24|1.24	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.28554|0.28554	-1.0040|-1.0040	6|10	0.87932|0.87932	D|D	0|0	1.1511|1.1511	5.1322|5.1322	0.14917|0.14917	0.0923:0.1049:0.1496:0.6532|0.0923:0.1049:0.1496:0.6532	.|.	.|235	.|P23490	.|LORI_HUMAN	L|C	234|235	.|ENSP00000357731:S235C	ENSP00000376422:Q234L|ENSP00000357731:S235C	Q|S	+|+	2|1	0|0	LOR|LOR	151500752|151500752	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-1.370000|-1.370000	0.02575|0.02575	-1.669000|-1.669000	0.01470|0.01470	-1.782000|-1.782000	0.00648|0.00648	CAG|AGC	.	.		0.756	LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039107.1	NM_000427		T	153234128	A	T	153234128	3	4	189	1	0	0	0	0	1	0	0	0	8906	188	7	4	705	4	LOR	1	153234128	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	1855328	153234128	96016493	14	27890										
THBS3	7059	hgsc.bcm.edu	37	chr1	155176111	155176111	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gaaggtggataagaggtagaTgtccccagcagtgagcaagg	16	6	0	3	rs143240289		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:155176111T>A	ENST00000368378.3	-	2	186	c.166A>T	c.(166-168)Atc>Ttc	p.I56F	RP11-263K19.4_ENST00000422665.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000430312.1_RNA|MTX1_ENST00000316721.4_5'Flank|THBS3_ENST00000457183.2_Missense_Mutation_p.I56F|THBS3_ENST00000486260.1_5'UTR|THBS3_ENST00000541990.1_5'UTR|MTX1_ENST00000609421.1_5'Flank|MTX1_ENST00000368376.3_5'Flank	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	56	Laminin G-like.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			AAGAGGTAGATGTCCCCAGCA	0.587													T|||	1	0.000199681	0	0.0014	5008	,	,		15048	0		0	False		,,,				2504	0				p.I56F		Atlas-SNP	.											.	THBS3	70	.	0			c.A166T						.						123	116	118					1																	155176111		2203	4300	6503	SO:0001583	missense	7059	exon2			GGTAGATGTCCCC	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.166A>T	chr1.hg19:g.155176111T>A	ENSP00000357362:p.Ile56Phe	97.0	0.0		185.0	53.0	NM_007112	B1AVR8|B4DQ20|Q8WV34	Missense_Mutation	SNP	ENST00000368378.3	hg19	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.117594	0.56505	.	.	ENSG00000169231	ENST00000368378;ENST00000457183;ENST00000428962	T;D;T	0.83591	5.0;-1.74;-1.3	5.63	4.34	0.51931	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.129727	0.52532	D	0.000067	T	0.47746	0.1462	N	0.14661	0.345	0.26769	N	0.969837	B;B;B;B;B	0.33512	0.148;0.201;0.276;0.415;0.415	B;B;B;B;B	0.29598	0.018;0.075;0.081;0.104;0.081	T	0.36962	-0.9726	10	0.52906	T	0.07	-12.3276	3.9589	0.09403	0.0:0.1284:0.2105:0.6611	.	56;56;56;56;56	B4DQ20;B4DQH6;Q53FK6;Q2HIZ0;P49746	.;.;.;.;TSP3_HUMAN	F	56	ENSP00000357362:I56F;ENSP00000392207:I56F;ENSP00000404040:I56F	ENSP00000357362:I56F	I	-	1	0	THBS3	153442735	0.929000	0.31497	1.000000	0.80357	0.998000	0.95712	-0.263000	0.08670	2.271000	0.75665	0.459000	0.35465	ATC	.	T|1.000;C|0.000		0.587	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		A	155176111	T	A	155176111	3	1	189	1	0	0	0	0	1	0	0	0	15870	1464	51	4	2792	4	THBS3	1	155176111	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	1941983	155176111	94074510	15	27891										
PIGM	93183	hgsc.bcm.edu	37	chr1	160000962	160000962	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tggaagcaggtggagggttaTgggaaggatgtaagtcactg	18	3	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:160000962T>C	ENST00000368090.2	-	1	821	c.568A>G	c.(568-570)Ata>Gta	p.I190V		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	190					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGGAGGGTTATGGGAAGGATG	0.478																																					p.I190V		Atlas-SNP	.											.	PIGM	27	.	0			c.A568G						.						118	117	117					1																	160000962		2203	4300	6503	SO:0001583	missense	93183	exon1			GGGTTATGGGAAG	AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	18858	protein-coding gene	gene with protein product	"GPI mannosyltransferase 1", "DPM:GlcN-(acyl-)PI mannosyltransferase", "dol-P-Man dependent GPI mannosyltransferase"	610273	"phosphatidylinositol glycan, class M"			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.568A>G	chr1.hg19:g.160000962T>C	ENSP00000357069:p.Ile190Val	172.0	0.0		341.0	88.0	NM_145167		Missense_Mutation	SNP	ENST00000368090.2	hg19	CCDS1192.1	.	.	.	.	.	.	.	.	.	.	T	17.18	3.324466	0.60634	.	.	ENSG00000143315	ENST00000368090	T	0.42900	0.96	5.16	3.99	0.46301	.	0.000000	0.85682	D	0.000000	T	0.23611	0.0571	M	0.64997	1.995	0.58432	D	0.999993	B	0.26002	0.139	B	0.30316	0.114	T	0.05162	-1.0902	9	.	.	.	-7.7319	10.1089	0.42550	0.0:0.0:0.1688:0.8312	.	190	Q9H3S5	PIGM_HUMAN	V	190	ENSP00000357069:I190V	.	I	-	1	0	PIGM	158267586	1.000000	0.71417	0.976000	0.42696	0.523000	0.34469	2.932000	0.48940	0.937000	0.37394	0.379000	0.24179	ATA	.	.		0.478	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167		C	160000962	T	C	160000962	3	2	189	1	0	0	0	0	1	0	0	0	11901	1464	51	2	707	2	PIGM	1	160000962	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	4824851	160000962	89249659	16	27892										
COPA	1314	hgsc.bcm.edu	37	chr1	160303437	160303437	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ttccacactcggatggtctgAtcatcggaggcactcagaat	10	11	3	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:160303437A>G	ENST00000241704.7	-	5	571	c.342T>C	c.(340-342)gaT>gaC	p.D114D	COPA_ENST00000368069.3_Silent_p.D114D	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	114					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGATGGTCTGATCATCGGAGG	0.408																																					p.D114D		Atlas-SNP	.											.	COPA	181	.	0			c.T342C						.						71	71	71					1																	160303437		2203	4300	6503	SO:0001819	synonymous_variant	1314	exon5			GGTCTGATCATCG	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"WD repeat domain containing", "Endogenous ligands"	2230	protein-coding gene	gene with protein product	"proxenin", "xenin"	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.342T>C	chr1.hg19:g.160303437A>G		80.0	0.0		194.0	25.0	NM_001098398	Q5T201|Q8IXZ9	Silent	SNP	ENST00000241704.7	hg19	CCDS1202.1																																																																																			.	.		0.408	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371		G	160303437	A	G	160303437	2	3	189	1	0	0	0	0	0	0	0	1	3729	330	12	2		2	COPA	1	160303437	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	302475	160303437	88947184	17	27893										
ABL2	27	hgsc.bcm.edu	37	chr1	179100575	179100575	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cctgatagcctcatttagtgCctggggttcaacatcacaac	8	12	3	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:179100575C>A	ENST00000502732.1	-	3	465	c.262G>T	c.(262-264)Gca>Tca	p.A88S	ABL2_ENST00000392043.3_Missense_Mutation_p.A67S|ABL2_ENST00000367623.4_Missense_Mutation_p.A67S|ABL2_ENST00000344730.3_Missense_Mutation_p.A73S|ABL2_ENST00000504405.1_Missense_Mutation_p.A52S|ABL2_ENST00000408940.3_Missense_Mutation_p.A52S|ABL2_ENST00000511413.1_Missense_Mutation_p.A88S|ABL2_ENST00000507173.1_Missense_Mutation_p.A67S|ABL2_ENST00000512653.1_Missense_Mutation_p.A73S	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	88	CAP.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	TCATTTAGTGCCTGGGGTTCA	0.458			T	ETV6	AML																																p.A88S		Atlas-SNP	.		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	ABL2_ENST00000512653,NS,carcinoma,0,3	ABL2	307	.	0			c.G262T						.						97	93	94					1																	179100575		2203	4300	6503	SO:0001583	missense	27	exon3			TTAGTGCCTGGGG	M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.262G>T	chr1.hg19:g.179100575C>A	ENSP00000427562:p.Ala88Ser	97.0	1.0		206.0	126.0	NM_007314	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Missense_Mutation	SNP	ENST00000502732.1	hg19	CCDS30947.1	.	.	.	.	.	.	.	.	.	.	C	31	5.059023	0.93846	.	.	ENSG00000143322	ENST00000502732;ENST00000408940;ENST00000344730;ENST00000512653;ENST00000504405;ENST00000367623;ENST00000507173;ENST00000511413;ENST00000392043	T;T;T;T;T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74	5.58	5.58	0.84498	.	0.000000	0.49916	D	0.000122	T	0.44117	0.1278	L	0.48642	1.525	0.80722	D	1	D;B;B;B;B;B;B;B;D;B;B	0.71674	0.998;0.216;0.216;0.104;0.104;0.002;0.097;0.129;0.986;0.059;0.34	D;B;B;B;B;B;B;B;P;B;B	0.80764	0.994;0.171;0.171;0.171;0.113;0.015;0.087;0.068;0.689;0.04;0.171	T	0.06588	-1.0818	10	0.18710	T	0.47	.	18.552	0.91068	0.0:1.0:0.0:0.0	.	67;67;88;52;52;67;52;88;73;52;73	P42684-6;P42684-7;P42684-5;P42684-4;P42684-9;P42684-8;P42684-2;P42684;P42684-3;D1MPS6;P42684-10	.;.;.;.;.;.;.;ABL2_HUMAN;.;.;.	S	88;52;73;73;52;67;67;88;67	ENSP00000427562:A88S;ENSP00000386152:A52S;ENSP00000339209:A73S;ENSP00000423578:A73S;ENSP00000426831:A52S;ENSP00000356595:A67S;ENSP00000423413:A67S;ENSP00000424697:A88S;ENSP00000375897:A67S	ENSP00000339209:A73S	A	-	1	0	ABL2	177367198	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.772000	0.68889	2.607000	0.88179	0.591000	0.81541	GCA	.	.		0.458	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		A	179100575	C	A	179100575	3	1	189	1	0	0	0	0	1	0	0	0	93	739	26	3	3371	3	ABL2	1	179100575	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	18797138	179100575	70150046	18	27894										
C1orf26	54823	hgsc.bcm.edu	37	chr1	185173859	185173859	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	acccttgaaagagagctataAggaggaatctacaaattctg	9	7	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:185173859A>T	ENST00000367500.4	+	12	1862	c.1697A>T	c.(1696-1698)aAg>aTg	p.K566M	SWT1_ENST00000367501.3_Missense_Mutation_p.K566M	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	566										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						GAGAGCTATAAGGAGGAATCT	0.303																																					p.K566M		Atlas-SNP	.											.	SWT1	88	.	0			c.A1697T						.						72	74	74					1																	185173859		2203	4298	6501	SO:0001583	missense	54823	exon12			GCTATAAGGAGGA	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.1697A>T	chr1.hg19:g.185173859A>T	ENSP00000356470:p.Lys566Met	278.0	0.0		528.0	145.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	hg19	CCDS1367.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.520298	0.44866	.	.	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.20463	2.07;2.07	5.79	1.96	0.26148	.	0.984678	0.08320	N	0.964015	T	0.20047	0.0482	L	0.36672	1.1	0.09310	N	1	D	0.60575	0.988	P	0.46975	0.533	T	0.16867	-1.0388	10	0.62326	D	0.03	.	5.4036	0.16308	0.573:0.2795:0.1475:0.0	.	566	Q5T5J6	SWT1_HUMAN	M	566	ENSP00000356471:K566M;ENSP00000356470:K566M	ENSP00000356470:K566M	K	+	2	0	SWT1	183440482	0.007000	0.16637	0.000000	0.03702	0.000000	0.00434	1.112000	0.31172	0.431000	0.26258	-0.361000	0.07541	AAG	.	.		0.303	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		T	185173859	A	T	185173859	3	4	189	1	0	0	0	0	1	0	0	0	2037	72	3	4	1739	4	C1orf26	1	185173859	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	6073284	185173859	64076762	19	27895										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186014950	186014950	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aaagacggccaccccttgctGaagaaaccaggcctcagtat	9	13	1	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:186014950G>A	ENST00000271588.4	+	41	6664	c.6435G>A	c.(6433-6435)ctG>ctA	p.L2145L	HMCN1_ENST00000367492.2_Silent_p.L2145L	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2145	Ig-like C2-type 19.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ACCCCTTGCTGAAGAAACCAG	0.388																																					p.L2145L		Atlas-SNP	.											.	HMCN1	797	.	0			c.G6435A						.						112	108	109					1																	186014950		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon41			CTTGCTGAAGAAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.6435G>A	chr1.hg19:g.186014950G>A		101.0	0.0		157.0	20.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.388	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186014950	G	A	186014950	2	1	189	1	0	0	0	0	0	0	0	1	7229	1277	45	3		3	HMCN1	1	186014950	Silent	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	841091	186014950	63235671	20	27896										
ADORA1	134	hgsc.bcm.edu	37	chr1	203134431	203134431	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cggagggcggcggtggccatAgccggctgctggatcctctc	17	13	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:203134431A>T	ENST00000367236.4	+	3	1305	c.384A>T	c.(382-384)atA>atT	p.I128I	ADORA1_ENST00000472535.1_3'UTR|ADORA1_ENST00000367235.1_3'UTR|ADORA1_ENST00000337894.4_Silent_p.I128I|ADORA1_ENST00000309502.3_Silent_p.I128I	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	128					activation of MAPKK activity (GO:0000186)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cognition (GO:0050890)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood pressure (GO:0045776)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heart contraction (GO:0045822)|negative regulation of hormone secretion (GO:0046888)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of mucus secretion (GO:0070256)|negative regulation of neurotrophin production (GO:0032900)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of vasodilation (GO:0045908)|nervous system development (GO:0007399)|phagocytosis (GO:0006909)|positive regulation of blood pressure (GO:0045777)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of nucleoside transport (GO:0032244)|positive regulation of peptide secretion (GO:0002793)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of protein dephosphorylation (GO:0035307)|protein targeting to membrane (GO:0006612)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glomerular filtration (GO:0003093)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|relaxation of vascular smooth muscle (GO:0060087)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|temperature homeostasis (GO:0001659)	asymmetric synapse (GO:0032279)|axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled adenosine receptor activity (GO:0001609)|phospholipase C activity (GO:0004629)|purine nucleoside binding (GO:0001883)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(9)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25					Adenosine(DB00640)|Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Gabapentin(DB00996)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Theobromine(DB01412)|Theophylline(DB00277)	CGGTGGCCATAGCCGGCTGCT	0.657																																					p.I128I		Atlas-SNP	.											.	ADORA1	62	.	0			c.A384T						.						49	55	53					1																	203134431		2203	4300	6503	SO:0001819	synonymous_variant	134	exon3			GGCCATAGCCGGC	BC026340	CCDS1434.1	1q32.1	2012-08-08			ENSG00000163485	ENSG00000163485		"GPCR / Class A : Adenosine receptors"	262	protein-coding gene	gene with protein product		102775				1662665, 2541503	Standard	NM_001048230		Approved	RDC7	uc001gzf.1	P30542	OTTHUMG00000042125	ENST00000367236.4:c.384A>T	chr1.hg19:g.203134431A>T		58.0	0.0		98.0	44.0	NM_001048230	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Silent	SNP	ENST00000367236.4	hg19	CCDS1434.1																																																																																			.	.		0.657	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674		T	203134431	A	T	203134431	2	4	189	1	0	0	0	0	0	0	0	1	326	410	15	4		4	ADORA1	1	203134431	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	17119481	203134431	46116190	21	27897										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227204675	227204675	+	Frame_Shift_Del	DEL	C	C	-													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gggactctgaaggaataacgCcgcttattgttaatgtttct							TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:227204675delC	ENST00000366769.3	-	32	5878	c.4587delG	c.(4585-4587)cggfs	p.R1530fs	CDC42BPA_ENST00000366767.3_Frame_Shift_Del_p.R1449fs|CDC42BPA_ENST00000366764.2_Frame_Shift_Del_p.R1502fs|CDC42BPA_ENST00000366765.3_Frame_Shift_Del_p.R1543fs|CDC42BPA_ENST00000334218.5_Frame_Shift_Del_p.R1530fs|CDC42BPA_ENST00000366766.2_Frame_Shift_Del_p.R1565fs|CDC42BPA_ENST00000535525.1_Frame_Shift_Del_p.R1510fs	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				AGGAATAACGCCGCTTATTGT	0.398																																					p.R1530fs		Atlas-INDEL	.											CDC42BPA_ENST00000366769,colon,carcinoma,0,3	CDC42BPA	528	.	0			c.4588delC						.						213	201	205					1																	227204675		2203	4300	6503	SO:0001589	frameshift_variant	8476	exon32			.	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.4587delG	chr1.hg19:g.227204675delC	ENSP00000355731:p.Arg1530fs	103.0	0.0		106.0	31.0	NM_003607		Frame_Shift_Del	DEL	ENST00000366769.3	hg19	CCDS1558.1																																																																																			.	.		0.398	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		-	227204675	C	-	227204675	7	5	189	1	0	1	0	1	0	0	0	0	3074	726	26	0	592	0	CDC42BPA	1	227204675	Frame_Shift_Del	DEL	C	TCGA-DD-AADF-01A-11D-A40R-10	24070244	227204675	22045946	22	27898										
RYR2	6262	hgsc.bcm.edu	37	chr1	237905615	237905615	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gagttgtcatgatgaggaagAtgacgatggtgaagaggaag	17	2	1	6			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:237905615A>T	ENST00000366574.2	+	80	11428	c.11111A>T	c.(11110-11112)gAt>gTt	p.D3704V	RYR2_ENST00000360064.6_Missense_Mutation_p.D3702V|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Missense_Mutation_p.D3688V	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3704					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GATGAGGAAGATGACGATGGT	0.318																																					p.D3704V		Atlas-SNP	.											.	RYR2	1273	.	0			c.A11111T						.						201	204	203					1																	237905615		1868	4091	5959	SO:0001583	missense	6262	exon80			AGGAAGATGACGA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.11111A>T	chr1.hg19:g.237905615A>T	ENSP00000355533:p.Asp3704Val	49.0	0.0		78.0	26.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.071034	0.36566	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.96913	-4.17;-4.12;-4.16	5.89	4.76	0.60689	.	0.077328	0.49916	D	0.000133	D	0.93871	0.8039	L	0.32530	0.975	0.80722	D	1	D;B	0.53462	0.96;0.346	P;B	0.47744	0.556;0.047	D	0.93001	0.6423	10	0.72032	D	0.01	-14.9408	9.9481	0.41623	0.9235:0.0:0.0765:0.0	.	659;3704	B4DGV4;Q92736	.;RYR2_HUMAN	V	3704;3702;3688;659	ENSP00000355533:D3704V;ENSP00000353174:D3702V;ENSP00000443798:D3688V	ENSP00000353174:D3702V	D	+	2	0	RYR2	235972238	1.000000	0.71417	0.997000	0.53966	0.287000	0.27160	6.112000	0.71547	1.052000	0.40392	0.477000	0.44152	GAT	.	.		0.318	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237905615	A	T	237905615	3	4	189	1	0	0	0	0	1	0	0	0	13784	333	12	4	11429	4	RYR2	1	237905615	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	10700940	237905615	11345006	23	27899										
SCCPDH	51097	hgsc.bcm.edu	37	chr1	246923257	246923257	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctttgtcttctccatcatctAggttcagtatgctgcgtatg	8	10	5	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr1:246923257A>T	ENST00000366510.3	+	8	1189		c.e8-1			NM_016002.2	NP_057086.2	Q8NBX0	SCPDL_HUMAN	saccharopine dehydrogenase (putative)							lipid particle (GO:0005811)|membrane (GO:0016020)|midbody (GO:0030496)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(9)|ovary(1)	17	all_cancers(71;6.8e-05)|all_epithelial(71;7.93e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0545)|Lung NSC(105;0.0618)	all_cancers(173;0.0343)	OV - Ovarian serous cystadenocarcinoma(106;0.00323)	GBM - Glioblastoma multiforme(49;0.0896)		TCCATCATCTAGGTTCAGTAT	0.383																																					.		Atlas-SNP	.											.	SCCPDH	37	.	0			c.814-2A>T						.						281	252	262					1																	246923257		2203	4300	6503	SO:0001630	splice_region_variant	51097	exon8			TCATCTAGGTTCA		CCDS31084.1	1q44	2009-11-06			ENSG00000143653	ENSG00000143653			24275	protein-coding gene	gene with protein product						10810093	Standard	NM_016002		Approved	CGI-49, NET11	uc001ibr.3	Q8NBX0	OTTHUMG00000040221	ENST00000366510.3:c.814-1A>T	chr1.hg19:g.246923257A>T		101.0	0.0		92.0	59.0	NM_016002	Q8TAR0|Q9Y363	Splice_Site	SNP	ENST00000366510.3	hg19	CCDS31084.1	.	.	.	.	.	.	.	.	.	.	A	14.80	2.643612	0.47258	.	.	ENSG00000143653	ENST00000366510;ENST00000366509	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8548	0.78968	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SCCPDH	244989880	1.000000	0.71417	0.767000	0.31495	0.273000	0.26683	8.281000	0.89905	2.212000	0.71576	0.533000	0.62120	.	.	.		0.383	SCCPDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096902.2	NM_016002	Intron	T	246923257	A	T	246923257	5	4	189	1	0	0	0	0	0	0	1	0	13900	434	15	4	842	4	SCCPDH	1	246923257	Splice_Site	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	9017642	246923257	2327364	24	27900										
KCNK3	3777	hgsc.bcm.edu	37	chr2	26950553	26950553	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aggctacgggcacgcggcacCcagcacggatggcggcaagg	17	13	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:26950553C>A	ENST00000302909.3	+	2	427	c.302C>A	c.(301-303)cCc>cAc	p.P101H		NM_002246.2	NP_002237.1	O14649	KCNK3_HUMAN	potassium channel, subfamily K, member 3	101					brain development (GO:0007420)|cellular response to hypoxia (GO:0071456)|cellular response to zinc ion (GO:0071294)|cochlea development (GO:0090102)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)|open rectifier potassium channel activity (GO:0005252)|potassium channel activity (GO:0005267)|potassium ion leak channel activity (GO:0022841)|S100 protein binding (GO:0044548)			endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Doxapram(DB00561)|Halothane(DB01159)	CACGCGGCACCCAGCACGGAT	0.612																																					p.P101H	GBM(80;1457 1631 27100 45946)	Atlas-SNP	.											.	KCNK3	43	.	0			c.C302A						.						134	136	136					2																	26950553		2203	4300	6503	SO:0001583	missense	3777	exon2			CGGCACCCAGCAC	AF006823	CCDS1727.1	2p23	2012-03-07			ENSG00000171303	ENSG00000171303		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6278	protein-coding gene	gene with protein product		603220				9312005, 9721223, 16382106	Standard	NM_002246		Approved	K2p3.1, TASK, TASK-1	uc002rhn.2	O14649	OTTHUMG00000125530	ENST00000302909.3:c.302C>A	chr2.hg19:g.26950553C>A	ENSP00000306275:p.Pro101His	97.0	0.0		148.0	31.0	NM_002246	Q53SU2	Missense_Mutation	SNP	ENST00000302909.3	hg19	CCDS1727.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.832039	0.71258	.	.	ENSG00000171303	ENST00000302909	T	0.59638	0.25	5.14	5.14	0.70334	Ion transport 2 (1);	0.000000	0.85682	D	0.000000	D	0.85474	0.5705	H	0.98559	4.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91076	0.4896	10	0.87932	D	0	.	16.4547	0.84008	0.0:1.0:0.0:0.0	.	101	O14649	KCNK3_HUMAN	H	101	ENSP00000306275:P101H	ENSP00000306275:P101H	P	+	2	0	KCNK3	26804057	1.000000	0.71417	0.998000	0.56505	0.884000	0.51177	7.757000	0.85209	2.550000	0.86006	0.462000	0.41574	CCC	.	.		0.612	KCNK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246861.2	NM_002246		A	26950553	C	A	26950553	3	1	189	1	0	0	0	0	1	0	0	0	8076	623	22	3	308	3	KCNK3	2	26950553	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10		26950553	216248820	25	27901										
CLIP4	79745	hgsc.bcm.edu	37	chr2	29355071	29355071	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gatggattgacagatatgacTcttttacattatacctgcaa	7	7	1	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:29355071T>A	ENST00000320081.5	+	4	582	c.327T>A	c.(325-327)acT>acA	p.T109T	CLIP4_ENST00000404424.1_Silent_p.T109T|CLIP4_ENST00000401617.2_Silent_p.T2T|CLIP4_ENST00000401605.1_Silent_p.T109T	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	109										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					CAGATATGACTCTTTTACATT	0.373																																					p.T109T		Atlas-SNP	.											.	CLIP4	69	.	0			c.T327A						.						257	244	248					2																	29355071		2203	4300	6503	SO:0001819	synonymous_variant	79745	exon4			TATGACTCTTTTA	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"Ankyrin repeat domain containing"	26108	protein-coding gene	gene with protein product			"restin-like 2"	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.327T>A	chr2.hg19:g.29355071T>A		81.0	0.0		147.0	101.0	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Silent	SNP	ENST00000320081.5	hg19	CCDS1770.1																																																																																			.	.		0.373	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		A	29355071	T	A	29355071	2	1	189	1	0	0	0	0	0	0	0	1	3537	1538	54	4		4	CLIP4	2	29355071	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	2404518	29355071	213844302	26	27902										
EML4	27436	hgsc.bcm.edu	37	chr2	42556058	42556058	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aaggatctgatgggacagatAtcaatgcactggtgcgatcc	12	8	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:42556058A>T	ENST00000318522.5	+	22	2636	c.2374A>T	c.(2374-2376)Atc>Ttc	p.I792F	EML4_ENST00000401738.3_Missense_Mutation_p.I803F|EML4_ENST00000402711.2_Missense_Mutation_p.I734F|EML4_ENST00000453191.2_Missense_Mutation_p.I56F	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	792					microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						TGGGACAGATATCAATGCACT	0.418			T	ALK	NSCLC																																p.I792F		Atlas-SNP	.		Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	.	EML4	92	.	0			c.A2374T						.						139	128	132					2																	42556058		2203	4300	6503	SO:0001583	missense	27436	exon22			ACAGATATCAATG	AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924		"WD repeat domain containing"	1316	protein-coding gene	gene with protein product		607442		C2orf2			Standard	NM_019063		Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.2374A>T	chr2.hg19:g.42556058A>T	ENSP00000320663:p.Ile792Phe	92.0	0.0		81.0	14.0	NM_019063	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	Missense_Mutation	SNP	ENST00000318522.5	hg19	CCDS1807.1	.	.	.	.	.	.	.	.	.	.	A	35	5.415559	0.96092	.	.	ENSG00000143924	ENST00000318522;ENST00000402711;ENST00000401738;ENST00000453191	T;T;T;T	0.74421	1.9;1.21;1.9;-0.84	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.88317	0.6404	M	0.86953	2.85	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;0.999;1.0	D;D;D;D	0.83275	0.996;0.957;0.972;0.996	D	0.89999	0.4113	10	0.87932	D	0	-14.0392	16.8222	0.85835	1.0:0.0:0.0:0.0	.	734;734;803;792	A6H8Y6;B5MCW9;B5MBZ0;Q9HC35	.;.;.;EMAL4_HUMAN	F	792;734;803;56	ENSP00000320663:I792F;ENSP00000385059:I734F;ENSP00000384939:I803F;ENSP00000400590:I56F	ENSP00000320663:I792F	I	+	1	0	EML4	42409562	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.220000	0.95180	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.418	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250463.3	NM_019063		T	42556058	A	T	42556058	3	4	189	1	0	0	0	0	1	0	0	0	5101	449	16	4	2460	4	EML4	2	42556058	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	13200987	42556058	200643315	27	27903										
FSHR	2492	hgsc.bcm.edu	37	chr2	49190816	49190816	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	agttaggatcactagcactaTgatgttcccagtgatggcca	10	9	1	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:49190816T>A	ENST00000406846.2	-	10	1263	c.1144A>T	c.(1144-1146)Ata>Tta	p.I382L	FSHR_ENST00000304421.4_Missense_Mutation_p.I356L|FSHR_ENST00000541117.1_Missense_Mutation_p.I118L|FSHR_ENST00000346173.3_Missense_Mutation_p.I320L	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	382					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	ACTAGCACTATGATGTTCCCA	0.458									Gonadal Dysgenesis, 46 XX																												p.I382L		Atlas-SNP	.											.	FSHR	164	.	0			c.A1144T						.						167	153	158					2																	49190816		2203	4300	6503	SO:0001583	missense	2492	exon10	Familial Cancer Database		GCACTATGATGTT		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.1144A>T	chr2.hg19:g.49190816T>A	ENSP00000384708:p.Ile382Leu	109.0	0.0		155.0	11.0	NM_000145	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Missense_Mutation	SNP	ENST00000406846.2	hg19	CCDS1843.1	.	.	.	.	.	.	.	.	.	.	T	7.897	0.733509	0.15574	.	.	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000541117	D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97	5.38	-2.55	0.06288	GPCR, rhodopsin-like superfamily (1);	0.847556	0.11041	N	0.606135	T	0.60327	0.2260	N	0.02368	-0.58	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.002;0.003	T	0.50668	-0.8801	9	.	.	.	.	8.3611	0.32359	0.0:0.5045:0.1281:0.3674	.	356;320;382	Q05AH0;G5E967;P23945	.;.;FSHR_HUMAN	L	382;320;356;118	ENSP00000384708:I382L;ENSP00000333908:I320L;ENSP00000306780:I356L;ENSP00000444172:I118L	.	I	-	1	0	FSHR	49044320	0.000000	0.05858	0.018000	0.16275	0.969000	0.65631	-0.675000	0.05227	-0.315000	0.08703	0.533000	0.62120	ATA	.	.		0.458	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2			A	49190816	T	A	49190816	3	1	189	1	0	0	0	0	1	0	0	0	6081	1464	51	4	947	4	FSHR	2	49190816	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	6634758	49190816	194008557	28	27904										
KIAA1841	84542	hgsc.bcm.edu	37	chr2	61333732	61333732	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gcctctgtgatgaaaagggtAtagaatgtgatgttttactg	12	4	1	4			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:61333732A>T	ENST00000402291.1	+	14	1787	c.1546A>T	c.(1546-1548)Ata>Tta	p.I516L	KIAA1841_ENST00000295031.5_Missense_Mutation_p.I516L|KIAA1841_ENST00000356719.2_Missense_Mutation_p.I516L|KIAA1841_ENST00000453873.1_Missense_Mutation_p.I516L	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	516										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			TGAAAAGGGTATAGAATGTGA	0.353																																					p.I516L		Atlas-SNP	.											.	KIAA1841	95	.	0			c.A1546T						.						132	147	142					2																	61333732		2203	4300	6503	SO:0001583	missense	84542	exon14			AAGGGTATAGAAT	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.1546A>T	chr2.hg19:g.61333732A>T	ENSP00000385579:p.Ile516Leu	134.0	0.0		153.0	40.0	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Missense_Mutation	SNP	ENST00000402291.1	hg19	CCDS46296.1	.	.	.	.	.	.	.	.	.	.	A	3.463	-0.109561	0.06924	.	.	ENSG00000162929	ENST00000402291;ENST00000295031;ENST00000356719;ENST00000453873	.	.	.	5.63	-1.14	0.09741	.	0.504108	0.20822	N	0.085056	T	0.07413	0.0187	N	0.03177	-0.4	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.25398	-1.0133	9	0.02654	T	1	-5.1694	0.5911	0.00728	0.3248:0.2449:0.1083:0.322	.	516;516	Q6NSI8-2;Q6NSI8	.;K1841_HUMAN	L	516	.	ENSP00000295031:I516L	I	+	1	0	KIAA1841	61187236	0.063000	0.20901	0.822000	0.32727	0.953000	0.61014	-0.022000	0.12480	0.074000	0.16767	-0.468000	0.05107	ATA	.	.		0.353	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506		T	61333732	A	T	61333732	3	4	189	1	0	0	0	0	1	0	0	0	8270	449	16	4	1592	4	KIAA1841	2	61333732	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	12142916	61333732	181865641	29	27905										
NMS	129521	hgsc.bcm.edu	37	chr2	101096962	101096962	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cctcatttccttgcagggctCggggactgctgcagtggact	13	12	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:101096962C>A	ENST00000376865.1	+	7	348	c.341C>A	c.(340-342)tCg>tAg	p.S114*		NM_001011717.1	NP_001011717.1	Q5H8A3	NMS_HUMAN	neuromedin S	114					neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				breast(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)	14						TTGCAGGGCTCGGGGACTGCT	0.542																																					p.S114X		Atlas-SNP	.											.	NMS	26	.	0			c.C341A						.						119	112	114					2																	101096962		2203	4300	6503	SO:0001587	stop_gained	129521	exon7			AGGGCTCGGGGAC	AB164464	CCDS33259.1	2q11.2	2013-02-26			ENSG00000204640	ENSG00000204640		"Endogenous ligands"	32203	protein-coding gene	gene with protein product	"prepro-NMS"					15635449	Standard	NM_001011717		Approved		uc002tan.1	Q5H8A3	OTTHUMG00000153142	ENST00000376865.1:c.341C>A	chr2.hg19:g.101096962C>A	ENSP00000366061:p.Ser114*	71.0	0.0		80.0	21.0	NM_001011717		Nonsense_Mutation	SNP	ENST00000376865.1	hg19	CCDS33259.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.872746	0.33069	.	.	ENSG00000204640	ENST00000376865	.	.	.	3.65	2.77	0.32553	.	0.603497	0.14808	N	0.297227	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.1112	7.2282	0.26028	0.0:0.8796:0.0:0.1204	.	.	.	.	X	114	.	ENSP00000366061:S114X	S	+	2	0	NMS	100463394	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	-0.617000	0.05584	1.114000	0.41781	0.650000	0.86243	TCG	.	.		0.542	NMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329737.1	NM_001011717		A	101096962	C	A	101096962	4	1	189	1	0	0	0	0	0	1	0	0	10511	893	31	1	367	1	NMS	2	101096962	Nonsense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	39763230	101096962	142102411	30	27906										
SLC9A4	389015	hgsc.bcm.edu	37	chr2	103142769	103142769	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	acccctacgggaatcctcagTctgcaggaagagacacaagg	11	12	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:103142769T>A	ENST00000295269.4	+	11	2459	c.2002T>A	c.(2002-2004)Tct>Act	p.S668T		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	668					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GAATCCTCAGTCTGCAGGAAG	0.507																																					p.S668T		Atlas-SNP	.											.	SLC9A4	115	.	0			c.T2002A						.						123	114	117					2																	103142769		2203	4300	6503	SO:0001583	missense	389015	exon11			CCTCAGTCTGCAG		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"Solute carriers"	11077	protein-coding gene	gene with protein product		600531	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 4", "solute carrier family 9 (sodium/hydrogen exchanger), member 4"			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.2002T>A	chr2.hg19:g.103142769T>A	ENSP00000295269:p.Ser668Thr	64.0	0.0		67.0	37.0	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	hg19	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	T	12.78	2.041269	0.35989	.	.	ENSG00000180251	ENST00000295269	T	0.43688	0.94	5.8	-11.3	0.00108	.	3.354190	0.00531	N	0.000206	T	0.21962	0.0529	L	0.33485	1.01	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.10382	-1.0632	10	0.13853	T	0.58	.	3.0559	0.06184	0.0911:0.1684:0.2501:0.4904	.	668	Q6AI14	SL9A4_HUMAN	T	668	ENSP00000295269:S668T	ENSP00000295269:S668T	S	+	1	0	SLC9A4	102509201	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.636000	0.02016	-1.996000	0.00970	-0.250000	0.11733	TCT	.	.		0.507	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		A	103142769	T	A	103142769	3	1	189	1	0	0	0	0	1	0	0	0	14731	1667	58	4	2044	4	SLC9A4	2	103142769	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	2045807	103142769	140056604	31	27907										
TFCP2L1	29842	hgsc.bcm.edu	37	chr2	122005784	122005784	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cgcagggtcccacaaaaactCgactgcattcagctgggtcg	11	13	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:122005784C>T	ENST00000263707.5	-	5	557	c.460G>A	c.(460-462)Gag>Aag	p.E154K		NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1	154					cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					CACAAAAACTCGACTGCATTC	0.547																																					p.E154K		Atlas-SNP	.											.	TFCP2L1	54	.	0			c.G460A						.						66	62	63					2																	122005784		2203	4300	6503	SO:0001583	missense	29842	exon5			AAAACTCGACTGC	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.460G>A	chr2.hg19:g.122005784C>T	ENSP00000263707:p.Glu154Lys	58.0	0.0		42.0	12.0	NM_014553	Q4ZG43	Missense_Mutation	SNP	ENST00000263707.5	hg19	CCDS2134.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.743314	0.89663	.	.	ENSG00000115112	ENST00000263707	T	0.18502	2.21	4.96	4.96	0.65561	CP2 transcription factor (1);	0.116475	0.56097	N	0.000024	T	0.48132	0.1483	M	0.88377	2.95	0.80722	D	1	B;D	0.60160	0.035;0.987	B;D	0.65874	0.137;0.939	T	0.53542	-0.8424	10	0.39692	T	0.17	.	18.6315	0.91361	0.0:1.0:0.0:0.0	.	154;154	Q5JV87;Q9NZI6	.;TF2L1_HUMAN	K	154	ENSP00000263707:E154K	ENSP00000263707:E154K	E	-	1	0	TFCP2L1	121722254	1.000000	0.71417	0.914000	0.36105	0.473000	0.32948	7.748000	0.85085	2.459000	0.83118	0.650000	0.86243	GAG	.	.		0.547	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553		T	122005784	C	T	122005784	3	4	189	1	0	0	0	0	1	0	0	0	15811	893	31	1	1023	1	TFCP2L1	2	122005784	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	18863015	122005784	121193589	32	27908										
TANC1	85461	hgsc.bcm.edu	37	chr2	160086859	160086859	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctccgtggctgtggacgcagCccctccaaaccaaggtgggc	13	15	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:160086859C>T	ENST00000263635.6	+	27	5159	c.4922C>T	c.(4921-4923)gCc>gTc	p.A1641V	TANC1_ENST00000454300.1_Missense_Mutation_p.A1535V	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1641					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GTGGACGCAGCCCCTCCAAAC	0.587																																					p.A1641V		Atlas-SNP	.											.	TANC1	157	.	0			c.C4922T						.						44	47	46					2																	160086859		2022	4182	6204	SO:0001583	missense	85461	exon27			ACGCAGCCCCTCC	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4922C>T	chr2.hg19:g.160086859C>T	ENSP00000263635:p.Ala1641Val	74.0	0.0		109.0	65.0	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	hg19	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	C	5.249	0.231423	0.09969	.	.	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.69806	-0.43;-0.43	5.19	2.38	0.29361	.	0.764830	0.12837	N	0.435168	T	0.53158	0.1779	L	0.40543	1.245	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.36792	-0.9733	9	.	.	.	.	7.7149	0.28698	0.0:0.7151:0.1349:0.15	.	1641	Q9C0D5	TANC1_HUMAN	V	1535;1641	ENSP00000396339:A1535V;ENSP00000263635:A1641V	.	A	+	2	0	TANC1	159795105	0.651000	0.27340	0.001000	0.08648	0.050000	0.14768	2.807000	0.47955	0.197000	0.20387	0.655000	0.94253	GCC	.	.		0.587	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			T	160086859	C	T	160086859	3	4	189	1	0	0	0	0	1	0	0	0	15559	739	26	3	5025	3	TANC1	2	160086859	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	38081075	160086859	83112514	33	27909										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168100737	168100737	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gaagttgacagaggagatgtGaagaattacacacatatctt	10	5	1	5			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:168100737G>A	ENST00000409195.1	+	9	2924	c.2835G>A	c.(2833-2835)gtG>gtA	p.V945V	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Silent_p.V945V|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.V723V	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	770					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GAGGAGATGTGAAGAATTACA	0.333																																					p.V945V		Atlas-SNP	.											.	XIRP2	914	.	0			c.G2835A						.						54	51	52					2																	168100737		1843	4088	5931	SO:0001819	synonymous_variant	129446	exon9			AGATGTGAAGAAT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2835G>A	chr2.hg19:g.168100737G>A		258.0	0.0		277.0	166.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.333	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168100737	G	A	168100737	2	1	189	1	0	0	0	0	0	0	0	1	17445	1277	45	3		3	XIRP2	2	168100737	Silent	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	8013878	168100737	75098636	34	27910										
TTN	7273	hgsc.bcm.edu	37	chr2	179560620	179560620	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	acctccttttgaacttgaatTacttccctttcttggtaagc	5	11	1	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:179560620T>A	ENST00000591111.1	-	112	30452	c.30228A>T	c.(30226-30228)gtA>gtT	p.V10076V	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Silent_p.V10393V|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.V9149V|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAACTTGAATTACTTCCCTTT	0.383																																					p.V10393V		Atlas-SNP	.											.	TTN	18412	.	0			c.A31179T						.						139	137	138					2																	179560620		1378	2827	4205	SO:0001819	synonymous_variant	7273	exon114			TTGAATTACTTCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30228A>T	chr2.hg19:g.179560620T>A		106.0	0.0		144.0	52.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179560620	T	A	179560620	2	1	189	1	0	0	0	0	0	0	0	1	16750	1741	61	4		4	TTN	2	179560620	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	11459883	179560620	63638753	35	27911										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185803176	185803176	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgtcagtggtcatacttttgTaacagctgagcaaatcctgg	10	8	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:185803176T>A	ENST00000302277.6	+	4	3647	c.3053T>A	c.(3052-3054)gTa>gAa	p.V1018E		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	1018							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						CATACTTTTGTAACAGCTGAG	0.408																																					p.V1018E		Atlas-SNP	.											.	ZNF804A	322	.	0			c.T3053A						.						94	90	91					2																	185803176		2203	4300	6503	SO:0001583	missense	91752	exon4			CTTTTGTAACAGC	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.3053T>A	chr2.hg19:g.185803176T>A	ENSP00000303252:p.Val1018Glu	116.0	0.0		126.0	28.0	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.468700	0.43839	.	.	ENSG00000170396	ENST00000302277	T	0.07114	3.22	5.29	5.29	0.74685	.	0.341386	0.21113	N	0.079941	T	0.13286	0.0322	L	0.44542	1.39	0.28996	N	0.887765	D	0.55385	0.971	P	0.52159	0.691	T	0.04481	-1.0948	10	0.62326	D	0.03	-2.8241	8.9995	0.36072	0.0:0.0826:0.0:0.9174	.	1018	Q7Z570	Z804A_HUMAN	E	1018	ENSP00000303252:V1018E	ENSP00000303252:V1018E	V	+	2	0	ZNF804A	185511421	0.999000	0.42202	0.942000	0.38095	0.638000	0.38207	3.295000	0.51794	1.992000	0.58205	0.383000	0.25322	GTA	.	.		0.408	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		A	185803176	T	A	185803176	3	1	189	1	0	0	0	0	1	0	0	0	18185	1638	57	4	3067	4	ZNF804A	2	185803176	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	6242556	185803176	57396197	36	27912										
MDH1B	130752	hgsc.bcm.edu	37	chr2	207620148	207620148	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgcttgttgtcaaatagagtTatgctaatttctgtatgcat	8	5	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:207620148T>A	ENST00000374412.3	-	5	770	c.495A>T	c.(493-495)atA>atT	p.I165I	MDH1B_ENST00000454776.2_Silent_p.I165I|MDH1B_ENST00000392214.2_Intron|MDH1B_ENST00000449792.1_Silent_p.I67I	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	165					carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		CAAATAGAGTTATGCTAATTT	0.488																																					p.I165I	Pancreas(76;29 1355 28675 37177 51207)	Atlas-SNP	.											.	MDH1B	89	.	0			c.A495T						.						93	83	86					2																	207620148		2203	4300	6503	SO:0001819	synonymous_variant	130752	exon5			TAGAGTTATGCTA		CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.495A>T	chr2.hg19:g.207620148T>A		71.0	0.0		69.0	19.0	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Silent	SNP	ENST00000374412.3	hg19	CCDS33365.1																																																																																			.	.		0.488	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845		A	207620148	T	A	207620148	2	1	189	1	0	0	0	0	0	0	0	1	9418	1744	61	4		4	MDH1B	2	207620148	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	21816972	207620148	35579225	37	27913										
IQCA1	79781	hgsc.bcm.edu	37	chr2	237285770	237285770	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gtaatcagagaggttgacttTcagagcctggatcagtaatc	11	7	3	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr2:237285770T>A	ENST00000409907.3	-	13	1811	c.1537A>T	c.(1537-1539)Aaa>Taa	p.K513*	IQCA1_ENST00000309507.5_Nonsense_Mutation_p.K510*|IQCA1_ENST00000431676.2_Nonsense_Mutation_p.K472*	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	513							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						AGGTTGACTTTCAGAGCCTGG	0.458																																					p.K521X		Atlas-SNP	.											.	IQCA1	170	.	0			c.A1561T						.						118	114	115					2																	237285770		1889	4125	6014	SO:0001587	stop_gained	79781	exon13			TGACTTTCAGAGC	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"ATPases / AAA-type"	26195	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 11"		"IQ motif containing with AAA domain"	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.1537A>T	chr2.hg19:g.237285770T>A	ENSP00000387347:p.Lys513*	46.0	0.0		45.0	13.0	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Nonsense_Mutation	SNP	ENST00000409907.3	hg19	CCDS46549.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	38|38	6.961480|6.961480	0.97964|0.97964	.|.	.|.	ENSG00000132321|ENSG00000132321	ENST00000418802|ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437	.|.	.|.	.|.	5.63|5.63	4.45|4.45	0.53987|0.53987	.|.	.|0.415223	.|0.23060	.|N	.|0.052393	T|.	0.26521|.	0.0648|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.28427|.	-1.0044|.	3|.	.|0.02654	.|T	.|1	.|.	11.522|11.522	0.50558|0.50558	0.0:0.0:0.2832:0.7168|0.0:0.0:0.2832:0.7168	.|.	.|.	.|.	.|.	V|X	532|513;521;510;472;510	.|.	.|ENSP00000254653:K514X	E|K	-|-	2|1	0|0	IQCA1|IQCA1	236950509|236950509	0.997000|0.997000	0.39634|0.39634	0.899000|0.899000	0.35326|0.35326	0.972000|0.972000	0.66771|0.66771	2.916000|2.916000	0.48813|0.48813	0.931000|0.931000	0.37242|0.37242	0.533000|0.533000	0.62120|0.62120	GAA|AAA	.	.		0.458	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		A	237285770	T	A	237285770	4	1	189	1	0	0	0	0	0	1	0	0	7811	1792	62	4	959	4	IQCA1	2	237285770	Nonsense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	29665622	237285770	5913603	38	27914										
LHFPL4	375323	hgsc.bcm.edu	37	chr3	9594117	9594130	+	Frame_Shift_Del	DEL	CGGTGAAGGAGCCC	CGGTGAAGGAGCCC	-													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggacgggatggtgctgaagtCggtgaaggagccccggcagg					rs370762541		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	CGGTGAAGGAGCCC	CGGTGAAGGAGCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:9594117_9594130delCGGTGAAGGAGCCC	ENST00000287585.6	-	2	519_532	c.234_247delGGGCTCCTTCACCG	c.(232-249)cggggctccttcaccgacfs	p.GSFTD79fs	LHFPL4_ENST00000495730.1_5'Flank	NM_198560.2	NP_940962.1	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 4	92						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(3)|skin(1)	10	Medulloblastoma(99;0.227)					GTGCTGAAGTCGGTGAAGGAGCCCCGGCAGGTGA	0.654																																					p.79_83del		Atlas-INDEL	.											.	LHFPL4	34	.	0			c.235_248del						.																																			SO:0001589	frameshift_variant	375323	exon2			.	AY278320	CCDS33691.1	3p25.3	2006-06-13			ENSG00000156959	ENSG00000156959			29568	protein-coding gene	gene with protein product		610240				15905332	Standard	NM_198560		Approved		uc003bry.3	Q7Z7J7	OTTHUMG00000155066	ENST00000287585.6:c.234_247delGGGCTCCTTCACCG	chr3.hg19:g.9594117_9594130delCGGTGAAGGAGCCC	ENSP00000287585:p.Gly79fs	107.0	0.0		101.0	11.0	NM_198560	A1L383|A4D0Q5	Frame_Shift_Del	DEL	ENST00000287585.6	hg19	CCDS33691.1																																																																																			.	.		0.654	LHFPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338298.1	NM_198560		-	9594130	CGGTGAAGGAGCCC	-	9594117	7	5	189	1	0	1	0	1	0	0	0	0	8776	884	31	0	508	0	LHFPL4	3	9594117	Frame_Shift_Del	DEL	CGGTGAAGGAGCCC	TCGA-DD-AADF-01A-11D-A40R-10		9594117	188428313	39	27915										
IQSEC1	9922	hgsc.bcm.edu	37	chr3	12957128	12957128	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	caatgagcttctccaccttcTgcacctgggacacatggtcc	8	15	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:12957128T>A	ENST00000273221.4	-	7	2384	c.2168A>T	c.(2167-2169)cAg>cTg	p.Q723L		NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1	723					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CTCCACCTTCTGCACCTGGGA	0.597																																					p.Q723L		Atlas-SNP	.											.	IQSEC1	88	.	0			c.A2168T						.						205	155	172					3																	12957128		2203	4300	6503	SO:0001583	missense	9922	exon7			ACCTTCTGCACCT	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"brefeldin A-resistant ARF-GEF2"	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.2168A>T	chr3.hg19:g.12957128T>A	ENSP00000273221:p.Gln723Leu	57.0	0.0		64.0	19.0	NM_014869	O94863|Q96D85	Missense_Mutation	SNP	ENST00000273221.4	hg19	CCDS33703.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.127665	0.77549	.	.	ENSG00000144711	ENST00000273221;ENST00000435445;ENST00000429247	T;T	0.13778	2.61;2.56	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.26882	0.0658	.	.	.	0.80722	D	1	B;D;B	0.62365	0.034;0.991;0.012	B;P;B	0.58130	0.035;0.833;0.024	T	0.01767	-1.1278	9	0.27785	T	0.31	.	14.1699	0.65503	0.0:0.0:0.0:1.0	.	709;709;723	E9PG60;C9JMG9;Q6DN90	.;.;IQEC1_HUMAN	L	723;709;709	ENSP00000273221:Q723L;ENSP00000402299:Q709L	ENSP00000273221:Q723L	Q	-	2	0	IQSEC1	12932128	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.145000	0.71769	1.809000	0.52856	0.533000	0.62120	CAG	.	.		0.597	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869		A	12957128	T	A	12957128	3	1	189	1	0	0	0	0	1	0	0	0	7826	1580	55	4	1300	4	IQSEC1	3	12957128	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	3363011	12957128	185065302	40	27916										
ARPP21	10777	hgsc.bcm.edu	37	chr3	35771014	35771014	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cccgcctggaagcatccttcTtaatccacacacaggtgagt	8	14	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:35771014T>A	ENST00000187397.4	+	15	1901	c.1445T>A	c.(1444-1446)cTt>cAt	p.L482H	ARPP21_ENST00000417925.1_Missense_Mutation_p.L448H|ARPP21_ENST00000458225.1_Missense_Mutation_p.L448H|ARPP21_ENST00000444190.1_Missense_Mutation_p.L428H|ARPP21_ENST00000337271.5_Missense_Mutation_p.L428H	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	482					cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						AGCATCCTTCTTAATCCACAC	0.473																																					p.L482H		Atlas-SNP	.											.	ARPP21	153	.	0			c.T1445A						.						48	47	47					3																	35771014		2203	4300	6503	SO:0001583	missense	10777	exon15			TCCTTCTTAATCC	AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"R3H domain containing 3"	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.1445T>A	chr3.hg19:g.35771014T>A	ENSP00000187397:p.Leu482His	84.0	0.0		90.0	52.0	NM_016300	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	hg19	CCDS2661.1	.	.	.	.	.	.	.	.	.	.	T	32	5.161632	0.94727	.	.	ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925	T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85	6.06	6.06	0.98353	.	0.142472	0.48767	D	0.000161	T	0.52517	0.1739	L	0.51422	1.61	0.58432	D	0.999993	P;P;P	0.52316	0.816;0.952;0.816	P;P;P	0.51833	0.678;0.681;0.678	T	0.43750	-0.9372	10	0.13470	T	0.59	-14.4824	16.6245	0.84952	0.0:0.0:0.0:1.0	.	448;482;428	Q9UBL0-3;Q9UBL0;Q9UBL0-4	.;ARP21_HUMAN;.	H	448;428;428;482;448	ENSP00000414351:L448H;ENSP00000337792:L428H;ENSP00000405276:L428H;ENSP00000187397:L482H;ENSP00000412326:L448H	ENSP00000187397:L482H	L	+	2	0	ARPP21	35746018	1.000000	0.71417	0.983000	0.44433	0.996000	0.88848	7.946000	0.87746	2.323000	0.78572	0.528000	0.53228	CTT	.	.		0.473	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		A	35771014	T	A	35771014	3	1	189	1	0	0	0	0	1	0	0	0	978	1609	56	4	1508	4	ARPP21	3	35771014	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	22813886	35771014	162251416	41	27917										
TGM4	7047	hgsc.bcm.edu	37	chr3	44935105	44935105	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gcctgatgaggacgagcgcaAagagtacatcctcaatgaca	11	10	1	4	rs74776426	byFrequency	TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:44935105A>T	ENST00000296125.4	+	5	535	c.467A>T	c.(466-468)aAa>aTa	p.K156I		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	156					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	GACGAGCGCAAAGAGTACATC	0.502																																					p.K156I		Atlas-SNP	.											.	TGM4	82	.	0			c.A467T						.						130	116	121					3																	44935105		2203	4300	6503	SO:0001583	missense	7047	exon5			AGCGCAAAGAGTA	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"Transglutaminases"	11780	protein-coding gene	gene with protein product		600585	"transglutaminase 4 (prostate)"			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.467A>T	chr3.hg19:g.44935105A>T	ENSP00000296125:p.Lys156Ile	93.0	0.0		115.0	69.0	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	hg19	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508466	0.27036	.	.	ENSG00000163810	ENST00000296125	D	0.88741	-2.42	2.32	-4.63	0.03359	.	1.413030	0.06453	U	0.727998	D	0.88228	0.6380	M	0.72894	2.215	0.09310	N	1	P	0.50943	0.94	P	0.44597	0.454	T	0.82752	-0.0302	10	0.56958	D	0.05	.	12.792	0.57539	0.3306:0.6694:0.0:0.0	.	156	P49221	TGM4_HUMAN	I	156	ENSP00000296125:K156I	ENSP00000296125:K156I	K	+	2	0	TGM4	44910109	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.425000	0.07017	-0.931000	0.03746	-0.644000	0.03951	AAA	.	A|0.978;G|0.022		0.502	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		T	44935105	A	T	44935105	3	4	189	1	0	0	0	0	1	0	0	0	15847	14	1	4	485	4	TGM4	3	44935105	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	9164091	44935105	153087325	42	27918										
CDHR4	389118	hgsc.bcm.edu	37	chr3	49831234	49831234	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cccagccctggggtggatgtAccgctgagacggtccacagc	14	14	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:49831234A>T	ENST00000412678.2	-	11	1492		c.e11+1		CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						GGGTGGATGTACCGCTGAGAC	0.592																																					.		Atlas-SNP	.											.	CDHR4	37	.	0			c.1483+2T>A						.						93	85	87					3																	49831234		692	1591	2283	SO:0001630	splice_region_variant	389118	exon12			GGATGTACCGCTG		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"Cadherins / Cadherin-related"	34527	protein-coding gene	gene with protein product			"cadherin-like 29"	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.1483+1T>A	chr3.hg19:g.49831234A>T		158.0	0.0		164.0	99.0	NM_001007540	Q6UXT0	Splice_Site	SNP	ENST00000412678.2	hg19	CCDS46829.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.668966	0.47677	.	.	ENSG00000187492	ENST00000412678	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3513	0.60603	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDHR4	49806238	1.000000	0.71417	0.999000	0.59377	0.574000	0.36063	4.942000	0.63547	1.986000	0.57962	0.529000	0.55759	.	.	.		0.592	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	Intron	T	49831234	A	T	49831234	5	4	189	1	0	0	0	0	0	0	1	0	3123	405	14	4	917	4	CDHR4	3	49831234	Splice_Site	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	4896129	49831234	148191196	43	27919										
CDHR4	389118	hgsc.bcm.edu	37	chr3	49836807	49836807	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	agcagttgaaggataaaaacTgaaggactgtgccagggccc	13	8	0	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:49836807T>G	ENST00000412678.2	-	2	121	c.113A>C	c.(112-114)cAg>cCg	p.Q38P	CDHR4_ENST00000343366.4_Missense_Mutation_p.Q38P|CDHR4_ENST00000487256.1_Missense_Mutation_p.Q38P	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	38					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						GGATAAAAACTGAAGGACTGT	0.572																																					p.Q38P		Atlas-SNP	.											.	CDHR4	37	.	0			c.A113C						.						82	88	86					3																	49836807		1932	4131	6063	SO:0001583	missense	389118	exon2			AAAAACTGAAGGA		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"Cadherins / Cadherin-related"	34527	protein-coding gene	gene with protein product			"cadherin-like 29"	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.113A>C	chr3.hg19:g.49836807T>G	ENSP00000391409:p.Gln38Pro	94.0	0.0		95.0	42.0	NM_001007540	Q6UXT0	Missense_Mutation	SNP	ENST00000412678.2	hg19	CCDS46829.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.863211	0.51482	.	.	ENSG00000187492	ENST00000412678;ENST00000343366;ENST00000487256	T;T;T	0.56444	0.46;0.88;0.88	4.66	1.92	0.25849	.	1.152800	0.06475	N	0.731813	T	0.49729	0.1574	L	0.50333	1.59	0.09310	N	1	P;B;P	0.47302	0.893;0.396;0.893	P;B;P	0.45310	0.476;0.188;0.476	T	0.41034	-0.9531	10	0.56958	D	0.05	-0.4162	4.7659	0.13132	0.1649:0.0947:0.0:0.7404	.	38;38;38	E9PFE8;A6H8M9;A6H8M9-2	.;CDHR4_HUMAN;.	P	38	ENSP00000391409:Q38P;ENSP00000341302:Q38P;ENSP00000420677:Q38P	ENSP00000341302:Q38P	Q	-	2	0	CDHR4	49811811	0.000000	0.05858	0.001000	0.08648	0.573000	0.36030	0.104000	0.15313	0.688000	0.31529	0.533000	0.62120	CAG	.	.		0.572	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540		G	49836807	T	G	49836807	3	3	189	1	0	0	0	0	1	0	0	0	3123	1580	55	5	2325	5	CDHR4	3	49836807	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	5573	49836807	148185623	44	27920										
BAP1	8314	hgsc.bcm.edu	37	chr3	52439294	52439294	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gcttgtgcgcatgaaccagcCgcctcctctgcaccatctga	9	16	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:52439294C>T	ENST00000460680.1	-	11	1419	c.948G>A	c.(946-948)gcG>gcA	p.A316A	BAP1_ENST00000296288.5_Silent_p.A298A	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		ATGAACCAGCCGCCTCCTCTG	0.597			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.A316A	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.G948A						.						97	100	99					3																	52439294		2203	4300	6503	SO:0001819	synonymous_variant	8314	exon11			ACCAGCCGCCTCC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.948G>A	chr3.hg19:g.52439294C>T		44.0	0.0		46.0	19.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Silent	SNP	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.597	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			T	52439294	C	T	52439294	2	4	189	1	0	0	0	0	0	0	0	1	1311	639	23	1		1	BAP1	3	52439294	Silent	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	2602487	52439294	145583136	45	27921										
FLNB	2317	hgsc.bcm.edu	37	chr3	58095360	58095360	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aagtgtttgggccaggtgtgGagagaagtggtctgaaggca	18	4	1	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:58095360G>C	ENST00000295956.4	+	15	2422	c.2257G>C	c.(2257-2259)Gag>Cag	p.E753Q	FLNB_ENST00000348383.5_Missense_Mutation_p.E753Q|FLNB_ENST00000358537.3_Missense_Mutation_p.E753Q|FLNB_ENST00000357272.4_Missense_Mutation_p.E753Q|FLNB_ENST00000493452.1_Missense_Mutation_p.E584Q|FLNB_ENST00000490882.1_Missense_Mutation_p.E753Q|FLNB_ENST00000429972.2_Missense_Mutation_p.E753Q|FLNB_ENST00000419752.2_Missense_Mutation_p.E584Q	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	753					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GCCAGGTGTGGAGAGAAGTGG	0.502																																					p.E753Q		Atlas-SNP	.											.	FLNB	430	.	0			c.G2257C						.						143	142	143					3																	58095360		2203	4300	6503	SO:0001583	missense	2317	exon15			GGTGTGGAGAGAA	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.2257G>C	chr3.hg19:g.58095360G>C	ENSP00000295956:p.Glu753Gln	115.0	0.0		124.0	29.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831298	0.91036	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1;-2.1;-2.1;-2.1;-2.1	5.54	5.54	0.83059	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93112	0.7807	M	0.72118	2.19	0.80722	D	1	D;D;D;P;D;D	0.76494	0.999;0.994;0.999;0.659;0.999;0.999	D;D;D;P;D;D	0.91635	0.998;0.962;0.999;0.607;0.999;0.999	D	0.92002	0.5611	10	0.40728	T	0.16	.	19.4738	0.94976	0.0:0.0:1.0:0.0	.	753;753;584;584;753;753	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	Q	753;753;753;753;753;753;584;584	ENSP00000295956:E753Q;ENSP00000420213:E753Q;ENSP00000351339:E753Q;ENSP00000415599:E753Q;ENSP00000232447:E753Q;ENSP00000349819:E753Q;ENSP00000418510:E584Q;ENSP00000414532:E584Q	ENSP00000295956:E753Q	E	+	1	0	FLNB	58070400	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	9.869000	0.99810	2.622000	0.88805	0.655000	0.94253	GAG	.	.		0.502	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		C	58095360	G	C	58095360	3	2	189	1	0	0	0	0	1	0	0	0	5942	1175	41	4	2315	4	FLNB	3	58095360	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	5656066	58095360	139927070	46	27922										
TMF1	7110	hgsc.bcm.edu	37	chr3	69084229	69084229	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cctcctttctggcagccgctTgttctgtacgctgcaatgca	9	14	2	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:69084229T>A	ENST00000398559.2	-	9	2405	c.2189A>T	c.(2188-2190)cAa>cTa	p.Q730L	CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.Q733L|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000601511.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000599467.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	730					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		GGCAGCCGCTTGTTCTGTACG	0.438																																					p.Q730L		Atlas-SNP	.											.	TMF1	77	.	0			c.A2189T						.						206	207	207					3																	69084229		1953	4143	6096	SO:0001583	missense	7110	exon9			GCCGCTTGTTCTG		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.2189A>T	chr3.hg19:g.69084229T>A	ENSP00000381567:p.Gln730Leu	78.0	0.0		90.0	54.0	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	hg19	CCDS43105.1	.	.	.	.	.	.	.	.	.	.	T	16.72	3.200606	0.58126	.	.	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248	T;T	0.21191	2.02;2.02	5.03	5.03	0.67393	.	0.115517	0.64402	D	0.000009	T	0.43433	0.1247	M	0.63428	1.95	0.58432	D	0.999997	D;D	0.76494	0.999;0.999	D;D	0.75484	0.986;0.976	T	0.28776	-1.0033	10	0.46703	T	0.11	-17.6263	15.0578	0.71927	0.0:0.0:0.0:1.0	.	733;730	P82094-2;P82094	.;TMF1_HUMAN	L	730;733;646	ENSP00000381567:Q730L;ENSP00000438706:Q733L	ENSP00000348582:Q646L	Q	-	2	0	TMF1	69166919	1.000000	0.71417	0.993000	0.49108	0.614000	0.37383	6.176000	0.71955	2.012000	0.59069	0.533000	0.62120	CAA	.	.		0.438	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		A	69084229	T	A	69084229	3	1	189	1	0	0	0	0	1	0	0	0	16243	1812	63	4	1128	4	TMF1	3	69084229	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	10988869	69084229	128938201	47	27923										
CRYBG3	131544	hgsc.bcm.edu	37	chr3	97605567	97605567	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gcagtccccaatttggaagaActgaatatctccaaatctgt	7	10	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:97605567A>G	ENST00000182096.4	+	5	1465	c.1401A>G	c.(1399-1401)gaA>gaG	p.E467E		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2415							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						ATTTGGAAGAACTGAATATCT	0.413																																					p.E2415E		Atlas-SNP	.											.	CRYBG3	86	.	0			c.A7245G						.						151	143	145					3																	97605567		1866	4099	5965	SO:0001819	synonymous_variant	131544	exon8			GGAAGAACTGAAT			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.1401A>G	chr3.hg19:g.97605567A>G		297.0	0.0		298.0	159.0	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Silent	SNP	ENST00000182096.4	hg19																																																																																				.	.		0.413	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605		G	97605567	A	G	97605567	2	3	189	1	0	0	0	0	0	0	0	1	3915	40	2	2		2	CRYBG3	3	97605567	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	28521338	97605567	100416863	48	27924										
CD86	942	hgsc.bcm.edu	37	chr3	121810486	121810486	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cattctctttgtgatggcctTcctgctctctggtaagaacc	8	12	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:121810486T>A	ENST00000330540.2	+	2	169	c.53T>A	c.(52-54)tTc>tAc	p.F18Y	CD86_ENST00000483949.1_3'UTR|CD86_ENST00000493101.1_Missense_Mutation_p.F18Y|CD86_ENST00000393627.2_Missense_Mutation_p.F12Y|CD86_ENST00000469710.1_Intron|CD86_ENST00000264468.5_Missense_Mutation_p.F18Y	NM_175862.4	NP_787058	P42081	CD86_HUMAN	CD86 molecule	18					aging (GO:0007568)|B cell activation (GO:0042113)|cell-cell signaling (GO:0007267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to metal ion (GO:0071248)|defense response to virus (GO:0051607)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|immune response (GO:0006955)|innate immune response (GO:0045087)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of T cell anergy (GO:0002668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of lymphotoxin A biosynthetic process (GO:0043017)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|response to interferon-gamma (GO:0034341)|response to yeast (GO:0001878)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell proliferation involved in immune response (GO:0002309)|toll-like receptor signaling pathway (GO:0002224)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|kidney(1)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	23				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)|Antithymocyte globulin(DB00098)|Belatacept(DB06681)	GTGATGGCCTTCCTGCTCTCT	0.443																																					p.F18Y	GBM(67;1379 1389 36064 39806)	Atlas-SNP	.											.	CD86	43	.	0			c.T53A						.						318	301	307					3																	121810486		2203	4300	6503	SO:0001583	missense	942	exon2			TGGCCTTCCTGCT		CCDS3009.1, CCDS43138.1, CCDS56272.1, CCDS56273.1, CCDS74991.1	3q21	2013-01-29	2006-03-28		ENSG00000114013	ENSG00000114013		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1705	protein-coding gene	gene with protein product	"B-lymphocyte antigen B7-2"	601020	"CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)"	CD28LG2		7513726	Standard	NM_006889		Approved	B7.2, B7-2	uc003eet.3	P42081	OTTHUMG00000159482	ENST00000330540.2:c.53T>A	chr3.hg19:g.121810486T>A	ENSP00000332049:p.Phe18Tyr	39.0	0.0		48.0	34.0	NM_001206924	A0N0P0|B7Z2F3|B7Z702|E7ETN5|E9PC27|Q13655|Q6FHB1|Q6GTS4|Q7M4L5	Missense_Mutation	SNP	ENST00000330540.2	hg19	CCDS3009.1	.	.	.	.	.	.	.	.	.	.	T	3.809	-0.040144	0.07497	.	.	ENSG00000114013	ENST00000493101;ENST00000330540;ENST00000264468;ENST00000482356;ENST00000393627	T;T;T;T;T	0.38240	2.37;4.29;1.15;3.48;4.27	4.42	1.9	0.25705	.	1.104600	0.06973	N	0.818459	T	0.25382	0.0617	L	0.44542	1.39	0.09310	N	1	B;B	0.21606	0.058;0.036	B;B	0.22152	0.038;0.026	T	0.31420	-0.9944	10	0.05436	T	0.98	1.1314	5.1143	0.14825	0.1815:0.0:0.1893:0.6293	.	18;18	E9PC27;P42081	.;CD86_HUMAN	Y	18;18;18;12;12	ENSP00000420230:F18Y;ENSP00000332049:F18Y;ENSP00000264468:F18Y;ENSP00000419116:F12Y;ENSP00000377248:F12Y	ENSP00000264468:F18Y	F	+	2	0	CD86	123293176	0.627000	0.27129	0.227000	0.23927	0.007000	0.05969	1.019000	0.30014	0.409000	0.25649	0.533000	0.62120	TTC	.	.		0.443	CD86-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355671.1	NM_006889		A	121810486	T	A	121810486	3	1	189	1	0	0	0	0	1	0	0	0	3045	1783	62	4	59	4	CD86	3	121810486	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	24204919	121810486	76211944	49	27925										
CHST13	166012	hgsc.bcm.edu	37	chr3	126260677	126260677	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cagcgcctgctacagccggaGgacctgcggcacgtgctggt	15	14	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:126260677G>C	ENST00000319340.2	+	3	332	c.282G>C	c.(280-282)gaG>gaC	p.E94D		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	94					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			central_nervous_system(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(114;0.151)		TACAGCCGGAGGACCTGCGGC	0.701																																					p.E94D		Atlas-SNP	.											.	CHST13	21	.	0			c.G282C						.						19	13	15					3																	126260677		2179	4263	6442	SO:0001583	missense	166012	exon3			GCCGGAGGACCTG	AY120869	CCDS3039.1	3q21.3	2008-02-05			ENSG00000180767	ENSG00000180767	2.8.2.5	"Sulfotransferases, membrane-bound"	21755	protein-coding gene	gene with protein product		610124				12080076	Standard	NM_152889		Approved	C4ST3	uc003eja.3	Q8NET6	OTTHUMG00000162721	ENST00000319340.2:c.282G>C	chr3.hg19:g.126260677G>C	ENSP00000317404:p.Glu94Asp	58.0	0.0		76.0	24.0	NM_152889	Q3SYA3|Q3SYA5	Missense_Mutation	SNP	ENST00000319340.2	hg19	CCDS3039.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.346376	0.24426	.	.	ENSG00000180767	ENST00000319340;ENST00000383575	T	0.68479	-0.33	4.84	3.05	0.35203	.	0.115936	0.56097	D	0.000027	T	0.58764	0.2145	M	0.66939	2.045	0.80722	D	1	B	0.18461	0.028	B	0.19148	0.024	T	0.49184	-0.8966	10	0.23302	T	0.38	-20.1085	7.1048	0.25358	0.2842:0.0:0.7158:0.0	.	94	Q8NET6	CHSTD_HUMAN	D	94	ENSP00000317404:E94D	ENSP00000317404:E94D	E	+	3	2	CHST13	127743367	0.997000	0.39634	0.936000	0.37596	0.774000	0.43823	0.243000	0.18106	0.459000	0.27016	-0.424000	0.05967	GAG	.	.		0.701	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889		C	126260677	G	C	126260677	3	2	189	1	0	0	0	0	1	0	0	0	3403	991	35	4	292	4	CHST13	3	126260677	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	4450191	126260677	71761753	50	27926										
C3orf58	205428	hgsc.bcm.edu	37	chr3	143708415	143708416	+	Missense_Mutation	DNP	GC	GC	TG													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgactgtgataaggaggcttGcttatcattttcaaaagaaa							TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:143708415_143708416GC>TG	ENST00000315691.3	+	3	1560_1561	c.1025_1026GC>TG	c.(1024-1026)tGC>tTG	p.C342L	C3orf58_ENST00000441925.2_Missense_Mutation_p.C104L|C3orf58_ENST00000493396.1_Intron|C3orf58_ENST00000495414.1_Missense_Mutation_p.C133L	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	342					cardiac muscle cell proliferation (GO:0060038)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	COPI vesicle coat (GO:0030126)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AAGGAGGCTTGCTTATCATTTT	0.396																																					p.C342F|p.C342W		Atlas-SNP	.											.	C3orf58	36	.	0			c.G1025T|c.C1026G						.																																			SO:0001583	missense	205428	exon3			AGGCTTGCTTATC|GGCTTGCTTATCA	AK095161	CCDS3130.1, CCDS46929.1	3q24	2013-12-06			ENSG00000181744	ENSG00000181744			28490	protein-coding gene	gene with protein product	"deleted in autism 1", "hypoxia and Akt induced stem cell factor"	612200				21283809, 23784961, 24269490	Standard	NM_173552		Approved	MGC33365, DIA1, HASF	uc003evo.3	Q8NDZ4	OTTHUMG00000159380	Exception_encountered	chr3.hg19:g.143708415_143708416delinsTG	ENSP00000320081:p.Cys342Leu	77.0	0.0		95.0|97.0	28.0|29.0	NM_173552	B2RCF2|B7Z1W3	Missense_Mutation	SNP	ENST00000315691.3	hg19	CCDS3130.1																																																																																			.	.		0.396	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552		TG	143708416	GC	TG	143708415	3	4	189	1	0	0	0	0	1	0	0	0	2238	1319	46	3	1069	3	C3orf58	3	143708415	Missense_Mutation	DNP	GC	TCGA-DD-AADF-01A-11D-A40R-10	17447738	143708415	54314015	51	27927										
KCNMB2	10242	hgsc.bcm.edu	37	chr3	178543411	178543411	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aatcagggaccatgacctccTggacaaaaggaaaacagtca	9	10	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr3:178543411T>A	ENST00000432997.1	+	3	444	c.92T>A	c.(91-93)cTg>cAg	p.L31Q	RP11-385J1.2_ENST00000451742.1_RNA|RP11-385J1.2_ENST00000425330.1_RNA|KCNMB2_ENST00000420517.2_Missense_Mutation_p.L31Q|RP11-385J1.2_ENST00000432385.1_RNA|RP11-385J1.2_ENST00000437488.1_RNA|KCNMB2_ENST00000358316.3_Missense_Mutation_p.L31Q|KCNMB2_ENST00000452583.1_Missense_Mutation_p.L31Q	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	43					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	CATGACCTCCTGGACAAAAGG	0.438																																					p.L31Q		Atlas-SNP	.											.	KCNMB2	35	.	0			c.T92A						.						143	135	138					3																	178543411		2203	4300	6503	SO:0001583	missense	10242	exon4			ACCTCCTGGACAA	AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584		"Potassium channels"	6286	protein-coding gene	gene with protein product		605214				10097176	Standard	NM_181361		Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.92T>A	chr3.hg19:g.178543411T>A	ENSP00000407592:p.Leu31Gln	78.0	0.0		77.0	41.0	NM_005832	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000432997.1	hg19	CCDS3223.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.542965	0.65198	.	.	ENSG00000197584	ENST00000437510;ENST00000420517;ENST00000452583;ENST00000432997;ENST00000455865;ENST00000358316;ENST00000457763	T;T;T;T;T;T	0.26660	2.03;2.89;2.89;2.89;1.72;2.89	5.38	5.38	0.77491	KCNMB2, ball/chain domain (2);	0.000000	0.85682	D	0.000000	T	0.37293	0.0998	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.972	T	0.16958	-1.0385	10	0.42905	T	0.14	-12.043	15.3897	0.74731	0.0:0.0:0.0:1.0	.	31;31	B5BNW9;Q9Y691	.;KCMB2_HUMAN	Q	31	ENSP00000395807:L31Q;ENSP00000408252:L31Q;ENSP00000397483:L31Q;ENSP00000407592:L31Q;ENSP00000399100:L31Q;ENSP00000351068:L31Q	ENSP00000351068:L31Q	L	+	2	0	KCNMB2	180026105	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	2.049000	0.60858	0.528000	0.53228	CTG	.	.		0.438	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348251.1	NM_181361		A	178543411	T	A	178543411	3	1	189	1	0	0	0	0	1	0	0	0	8084	1580	55	4	98	4	KCNMB2	3	178543411	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	34834996	178543411	19479019	52	27928										
EVC2	132884	hgsc.bcm.edu	37	chr4	5564738	5564738	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tttctgcccctacaatgggtAcaggggccagttcgccaatg	11	12	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr4:5564738A>T	ENST00000344408.5	-	22	3817	c.3764T>A	c.(3763-3765)gTa>gAa	p.V1255E	EVC2_ENST00000310917.2_Missense_Mutation_p.V1175E|EVC2_ENST00000344938.1_Intron	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	1255					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TACAATGGGTACAGGGGCCAG	0.468																																					p.V1255E		Atlas-SNP	.											.	EVC2	202	.	0			c.T3764A						.						128	135	132					4																	5564738		2203	4300	6503	SO:0001583	missense	132884	exon22			ATGGGTACAGGGG	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.3764T>A	chr4.hg19:g.5564738A>T	ENSP00000342144:p.Val1255Glu	64.0	0.0		101.0	38.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506804	0.44558	.	.	ENSG00000173040	ENST00000310917;ENST00000344408	T;T	0.78481	-1.18;-1.18	5.15	5.15	0.70609	.	1.086050	0.06967	N	0.817483	T	0.77212	0.4097	L	0.27053	0.805	0.45554	D	0.998502	D	0.62365	0.991	P	0.52109	0.69	T	0.69101	-0.5234	10	0.72032	D	0.01	-21.6719	11.3634	0.49657	1.0:0.0:0.0:0.0	.	1255	Q86UK5	LBN_HUMAN	E	1175;1255	ENSP00000311683:V1175E;ENSP00000342144:V1255E	ENSP00000311683:V1175E	V	-	2	0	EVC2	5615639	0.008000	0.16893	0.016000	0.15963	0.232000	0.25224	2.476000	0.45171	1.960000	0.56953	0.533000	0.62120	GTA	.	.		0.468	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		T	5564738	A	T	5564738	3	4	189	1	0	0	0	0	1	0	0	0	5288	391	14	4	166	4	EVC2	4	5564738	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10		5564738	185589538	53	27929										
PTTG2	23216	hgsc.bcm.edu	37	chr4	37962314	37962314	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ccagaaaacaaaaacagccaAgcttttctgccaaaaagatg	6	10	1	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr4:37962314A>T	ENST00000261439.4	+	3	772				TBC1D1_ENST00000508802.1_Intron|PTTG2_ENST00000504686.1_Missense_Mutation_p.S87C	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1						membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						AAAACAGCCAAGCTTTTCTGC	0.413																																					p.S87C		Atlas-SNP	.											.	PTTG2	15	.	0			c.A259T						.						79	88	85					4																	37962314		2198	4300	6498	SO:0001627	intron_variant	10744	exon1			CAGCCAAGCTTTT	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.418-53816A>T	chr4.hg19:g.37962314A>T		120.0	0.0		140.0	86.0	NM_006607	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	hg19	CCDS33972.1	.	.	.	.	.	.	.	.	.	.	A	10.49	1.364297	0.24684	.	.	ENSG00000250254	ENST00000504686	T	0.48522	0.81	1.42	-0.0777	0.13717	.	.	.	.	.	T	0.46249	0.1383	L	0.44542	1.39	0.09310	N	1	D	0.53885	0.963	P	0.55999	0.789	T	0.30563	-0.9974	9	0.34782	T	0.22	.	3.7523	0.08572	0.7474:0.0:0.2526:0.0	.	87	Q9NZH5-2	.	C	87	ENSP00000424261:S87C	ENSP00000424261:S87C	S	+	1	0	PTTG2	37638709	0.000000	0.05858	0.005000	0.12908	0.015000	0.08874	0.190000	0.17057	-0.210000	0.10140	-0.385000	0.06624	AGC	.	.		0.413	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173		T	37962314	A	T	37962314	1	4	189	0	1	0	0	0	0	0	0	0	12836	72	3	4		4	PTTG2	4	37962314	Intron	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	32397576	37962314	153191962	54	27930										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79461941	79461941	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggtagctgcgtccctgtcacAgactggggcgtccattggca	14	12	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr4:79461941A>T	ENST00000264895.6	+	74	12142	c.11702A>T	c.(11701-11703)cAg>cTg	p.Q3901L		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3897					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TCCCTGTCACAGACTGGGGCG	0.493																																					p.Q3901L		Atlas-SNP	.											.	FRAS1	779	.	0			c.A11702T						.						51	57	55					4																	79461941		2003	4180	6183	SO:0001583	missense	80144	exon74			TGTCACAGACTGG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11702A>T	chr4.hg19:g.79461941A>T	ENSP00000264895:p.Gln3901Leu	145.0	0.0		141.0	82.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	A	14.31	2.497196	0.44352	.	.	ENSG00000138759	ENST00000264895	T	0.52295	0.67	6.17	5.01	0.66863	.	0.184361	0.48286	D	0.000194	T	0.50343	0.1610	L	0.51422	1.61	0.80722	D	1	D	0.54207	0.965	P	0.50049	0.629	T	0.52563	-0.8559	10	0.56958	D	0.05	.	11.8368	0.52330	0.9327:0.0:0.0673:0.0	.	3901	E9PHH6	.	L	3901	ENSP00000264895:Q3901L	ENSP00000264895:Q3901L	Q	+	2	0	FRAS1	79680965	1.000000	0.71417	0.956000	0.39512	0.012000	0.07955	4.869000	0.63028	2.371000	0.80710	0.533000	0.62120	CAG	.	.		0.493	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79461941	A	T	79461941	3	4	189	1	0	0	0	0	1	0	0	0	6050	188	7	4	12071	4	FRAS1	4	79461941	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	41499627	79461941	111692335	55	27931										
BMPR1B	658	hgsc.bcm.edu	37	chr4	96052479	96052479	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgaagtccaccaccctagacGctaaatcaatgctgaagtta	7	11	1	3	rs373000965		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr4:96052479G>A	ENST00000515059.1	+	10	1175	c.892G>A	c.(892-894)Gct>Act	p.A298T	BMPR1B_ENST00000264568.4_Missense_Mutation_p.A298T|BMPR1B_ENST00000394931.1_Missense_Mutation_p.A298T|BMPR1B_ENST00000440890.2_Missense_Mutation_p.A328T	NM_001203.2	NP_001194.1	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	298	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				BMP signaling pathway (GO:0030509)|cartilage condensation (GO:0001502)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|eye development (GO:0001654)|inflammatory response (GO:0006954)|limb morphogenesis (GO:0035108)|ovarian cumulus expansion (GO:0001550)|ovulation cycle (GO:0042698)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell differentiation (GO:0045597)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|skeletal system development (GO:0001501)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		CACCCTAGACGCTAAATCAAT	0.428																																					p.A328T		Atlas-SNP	.											.	BMPR1B	121	.	0			c.G982A						.	A	THR/ALA	0,4406		0,0,2203	125	106	113		892	3.7	0	4		113	1,8599	819.2+/-406.8	0,1,4299	no	missense	BMPR1B	NM_001203.2	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	298/503	96052479	1,13005	2203	4300	6503	SO:0001583	missense	658	exon8			CTAGACGCTAAAT	D89675	CCDS3642.1, CCDS58919.1	4q23-q24	2008-02-05			ENSG00000138696	ENSG00000138696		"CD molecules"	1077	protein-coding gene	gene with protein product		603248				8140412, 9730621	Standard	NM_001203		Approved	ALK6, CDw293	uc031sgn.1	O00238	OTTHUMG00000130991	ENST00000515059.1:c.892G>A	chr4.hg19:g.96052479G>A	ENSP00000426617:p.Ala298Thr	164.0	0.0		144.0	44.0	NM_001256793	B2R953|B4DSV1|P78366	Missense_Mutation	SNP	ENST00000515059.1	hg19	CCDS3642.1	.	.	.	.	.	.	.	.	.	.	A	1.486	-0.555873	0.03967	0.0	1.16E-4	ENSG00000138696	ENST00000515059;ENST00000512312;ENST00000509540;ENST00000440890;ENST00000264568;ENST00000394931	D;D;D;D;D;D	0.93247	-3.19;-3.19;-3.19;-3.19;-3.19;-3.19	6.06	3.67	0.42095	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.639008	0.17282	N	0.179951	T	0.80752	0.4683	N	0.04245	-0.25	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.63395	-0.6647	10	0.02654	T	1	.	9.4564	0.38758	0.7982:0.0:0.2018:0.0	.	298	O00238	BMR1B_HUMAN	T	298;298;298;328;298;298	ENSP00000426617:A298T;ENSP00000425444:A298T;ENSP00000421671:A298T;ENSP00000401907:A328T;ENSP00000264568:A298T;ENSP00000378389:A298T	ENSP00000264568:A298T	A	+	1	0	BMPR1B	96271502	0.005000	0.15991	0.003000	0.11579	0.961000	0.63080	1.465000	0.35299	0.193000	0.20303	-0.254000	0.11334	GCT	.	.		0.428	BMPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253609.3	NM_001203		A	96052479	G	A	96052479	3	1	189	1	0	0	0	0	1	0	0	0	1470	1087	38	1	918	1	BMPR1B	4	96052479	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	16590538	96052479	95101797	56	27932										
DDIT4L	115265	hgsc.bcm.edu	37	chr4	101109256	101109256	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cattttaaccaaattctggcAagttgattcctcaaatatta	4	8	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr4:101109256A>T	ENST00000273990.2	-	3	374	c.160T>A	c.(160-162)Tgc>Agc	p.C54S	RP11-588P8.1_ENST00000515782.1_RNA|RP11-15B17.1_ENST00000515026.1_RNA	NM_145244.3	NP_660287.1	Q96D03	DDT4L_HUMAN	DNA-damage-inducible transcript 4-like	54					negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(2)	12				OV - Ovarian serous cystadenocarcinoma(123;5.75e-09)		AAATTCTGGCAAGTTGATTCC	0.393																																					p.C54S		Atlas-SNP	.											.	DDIT4L	33	.	0			c.T160A						.						89	93	91					4																	101109256		2203	4300	6503	SO:0001583	missense	115265	exon3			TCTGGCAAGTTGA	BC013592	CCDS34036.1	4q23	2008-02-05				ENSG00000145358			30555	protein-coding gene	gene with protein product	"regulated in development and DNA damage response 2", " similar to Smhs1 protein"	607730				12477932	Standard	NM_145244		Approved	REDD2, Rtp801L	uc003hvq.3	Q96D03		ENST00000273990.2:c.160T>A	chr4.hg19:g.101109256A>T	ENSP00000354830:p.Cys54Ser	36.0	0.0		61.0	16.0	NM_145244	B2R7C3	Missense_Mutation	SNP	ENST00000273990.2	hg19	CCDS34036.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.164571	0.78339	.	.	ENSG00000145358	ENST00000273990;ENST00000502763;ENST00000513992	T;T	0.50277	0.76;0.75	5.63	4.47	0.54385	.	0.120522	0.56097	D	0.000027	T	0.39963	0.1098	L	0.27053	0.805	0.41958	D	0.990692	P	0.47409	0.895	P	0.47044	0.535	T	0.33854	-0.9852	10	0.54805	T	0.06	-18.7937	10.1541	0.42812	0.9213:0.0:0.0787:0.0	.	54	Q96D03	DDT4L_HUMAN	S	54	ENSP00000354830:C54S;ENSP00000427301:C54S	ENSP00000354830:C54S	C	-	1	0	DDIT4L	101328279	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.614000	0.67695	2.145000	0.66743	0.533000	0.62120	TGC	.	.		0.393	DDIT4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363423.1	NM_145244		T	101109256	A	T	101109256	3	4	189	1	0	0	0	0	1	0	0	0	4334	130	5	4	425	4	DDIT4L	4	101109256	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	5056777	101109256	90045020	57	27933										
NEUROG2	63973	hgsc.bcm.edu	37	chr4	113436007	113436007	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	actccacgtggaggcgggcgAggggctgtctccgctgctgc	17	13	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr4:113436007A>C	ENST00000313341.3	-	2	951	c.625T>G	c.(625-627)Tcg>Gcg	p.S209A	RP11-402J6.1_ENST00000504009.1_RNA|RP11-402J6.1_ENST00000506057.1_RNA	NM_024019.3	NP_076924.1	Q9H2A3	NGN2_HUMAN	neurogenin 2	209	Ser-rich.				axon guidance (GO:0007411)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	E-box binding (GO:0070888)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(3)|lung(6)|skin(2)	12		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.00168)		GAGGCGGGCGAGGGGCTGTCT	0.721																																					p.S209A		Atlas-SNP	.											.	NEUROG2	25	.	0			c.T625G						.						22	26	24					4																	113436007		2197	4292	6489	SO:0001583	missense	63973	exon2			CGGGCGAGGGGCT	AF303002	CCDS3698.1	4q25	2013-05-21			ENSG00000178403	ENSG00000178403		"Basic helix-loop-helix proteins"	13805	protein-coding gene	gene with protein product		606624					Standard	NM_024019		Approved	Atoh4, Math4A, ngn-2, bHLHa8, NGN2	uc003ias.3	Q9H2A3	OTTHUMG00000132907	ENST00000313341.3:c.625T>G	chr4.hg19:g.113436007A>C	ENSP00000317333:p.Ser209Ala	24.0	0.0		48.0	20.0	NM_024019	Q8N416	Missense_Mutation	SNP	ENST00000313341.3	hg19	CCDS3698.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.470834	0.43942	.	.	ENSG00000178403	ENST00000313341	D	0.91521	-2.86	4.07	4.07	0.47477	.	0.000000	0.41605	D	0.000841	D	0.86209	0.5878	L	0.34521	1.04	0.37427	D	0.913875	D	0.56035	0.974	P	0.52267	0.694	T	0.83275	-0.0041	10	0.09590	T	0.72	-10.3413	7.5672	0.27885	0.782:0.218:0.0:0.0	.	209	Q9H2A3	NGN2_HUMAN	A	209	ENSP00000317333:S209A	ENSP00000317333:S209A	S	-	1	0	NEUROG2	113655456	0.967000	0.33354	0.989000	0.46669	0.868000	0.49771	0.922000	0.28734	1.706000	0.51276	0.533000	0.62120	TCG	.	.		0.721	NEUROG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256414.1	NM_024019		C	113436007	A	C	113436007	3	2	189	1	0	0	0	0	1	0	0	0	10362	304	11	5	197	5	NEUROG2	4	113436007	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	12326751	113436007	77718269	58	27934										
NAA15	80155	hgsc.bcm.edu	37	chr4	140264113	140264113	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	agaatttaggaaaacacaacAggtaataactagaagccatt	7	6	0	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr4:140264113A>T	ENST00000296543.5	+	5	859	c.536A>T	c.(535-537)cAg>cTg	p.Q179L	NAA15_ENST00000398947.1_Splice_Site_p.Q179L|NAA15_ENST00000480277.2_3'UTR	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	179					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						AAAACACAACAGGTAATAACT	0.308																																					p.Q179L		Atlas-SNP	.											.	NAA15	88	.	0			c.A536T						.						72	67	69					4																	140264113		1811	4077	5888	SO:0001630	splice_region_variant	80155	exon5			CACAACAGGTAAT	AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"N(alpha)-acetyltransferase subunits"	30782	protein-coding gene	gene with protein product		608000	"NMDA receptor regulated 1"	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.537+1A>T	chr4.hg19:g.140264113A>T		291.0	0.0		225.0	99.0	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Missense_Mutation	SNP	ENST00000296543.5	hg19	CCDS43270.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.357409	0.61293	.	.	ENSG00000164134	ENST00000296543;ENST00000544077;ENST00000398947	T;T	0.51574	0.7;0.7	4.69	4.69	0.59074	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.151493	0.47093	D	0.000249	T	0.44180	0.1281	L	0.46157	1.445	0.80722	D	1	B	0.26845	0.161	B	0.29598	0.104	T	0.45011	-0.9290	10	0.54805	T	0.06	-9.2365	14.6005	0.68438	1.0:0.0:0.0:0.0	.	179	Q9BXJ9	NAA15_HUMAN	L	179;53;179	ENSP00000296543:Q179L;ENSP00000381920:Q179L	ENSP00000296543:Q179L	Q	+	2	0	NAA15	140483563	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.585000	0.90802	2.094000	0.63399	0.383000	0.25322	CAG	.	.		0.308	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175	Missense_Mutation	T	140264113	A	T	140264113	5	4	189	1	0	0	0	0	0	0	1	0	10127	202	7	4	554	4	NAA15	4	140264113	Splice_Site	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	26828106	140264113	50890163	59	27935										
TMEM144	55314	hgsc.bcm.edu	37	chr4	159161486	159161486	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ttgcgcacttcagtggcatcTttcttacaagtactgtctac	7	11	4	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr4:159161486T>A	ENST00000296529.6	+	10	1238	c.718T>A	c.(718-720)Ttt>Att	p.F240I	TMEM144_ENST00000503404.1_3'UTR	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	240						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		CAGTGGCATCTTTCTTACAAG	0.348																																					p.F240I		Atlas-SNP	.											.	TMEM144	34	.	0			c.T718A						.						129	115	120					4																	159161486		2203	4300	6503	SO:0001583	missense	55314	exon10			GGCATCTTTCTTA	AK002017	CCDS3799.1	4q32.1	2008-02-05			ENSG00000164124	ENSG00000164124			25633	protein-coding gene	gene with protein product						12477932	Standard	NM_018342		Approved	FLJ11155	uc003ipx.3	Q7Z5S9	OTTHUMG00000162013	ENST00000296529.6:c.718T>A	chr4.hg19:g.159161486T>A	ENSP00000296529:p.Phe240Ile	110.0	0.0		113.0	32.0	NM_018342	D3DP24|Q49A05|Q9NUT3	Missense_Mutation	SNP	ENST00000296529.6	hg19	CCDS3799.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.505152	0.85282	.	.	ENSG00000164124	ENST00000296529	T	0.53206	0.63	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.69708	0.3141	M	0.88906	2.99	0.80722	D	1	D	0.58620	0.983	P	0.59487	0.858	T	0.75769	-0.3201	10	0.54805	T	0.06	-45.8651	14.3292	0.66541	0.0:0.0:0.0:1.0	.	240	Q7Z5S9	TM144_HUMAN	I	240	ENSP00000296529:F240I	ENSP00000296529:F240I	F	+	1	0	TMEM144	159380936	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	6.281000	0.72632	2.027000	0.59764	0.383000	0.25322	TTT	.	.		0.348	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342		A	159161486	T	A	159161486	3	1	189	1	0	0	0	0	1	0	0	0	16073	1609	56	4	748	4	TMEM144	4	159161486	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	18897373	159161486	31992790	60	27936										
PALLD	23022	hgsc.bcm.edu	37	chr4	169432856	169432856	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gaaaaggagatctcgcagatTttcagtacttctcctgcaag	9	9	3	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr4:169432856T>A	ENST00000505667.1	+	2	374	c.201T>A	c.(199-201)atT>atA	p.I67I	PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000261509.6_Silent_p.I67I|PALLD_ENST00000333488.4_5'UTR			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	67					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		TCTCGCAGATTTTCAGTACTT	0.498									Pancreatic Cancer, Familial Clustering of																												p.I67I	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.T201A						.						39	41	40					4																	169432856		2203	4300	6503	SO:0001819	synonymous_variant	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GCAGATTTTCAGT	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"Immunoglobulin superfamily / I-set domain containing"	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.201T>A	chr4.hg19:g.169432856T>A		223.0	0.0		234.0	63.0	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	hg19	CCDS54818.1																																																																																			.	.		0.498	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		A	169432856	T	A	169432856	2	1	189	1	0	0	0	0	0	0	0	1	11416	1829	64	4		4	PALLD	4	169432856	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	10271370	169432856	21721420	61	27937										
LRRC14B	389257	hgsc.bcm.edu	37	chr5	192291	192291	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tctggctggcccgggtgcccTgcgcaagctggaggtggtgc	18	12	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:192291T>A	ENST00000328278.3	+	1	666	c.638T>A	c.(637-639)cTg>cAg	p.L213Q		NM_001080478.1	NP_001073947.1	A6NHZ5	LR14B_HUMAN	leucine rich repeat containing 14B	213										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	10						CCGGGTGCCCTGCGCAAGCTG	0.736																																					p.L213Q		Atlas-SNP	.											.	LRRC14B	30	.	0			c.T638A						.						8	10	10					5																	192291		2044	4161	6205	SO:0001583	missense	389257	exon1			GTGCCCTGCGCAA		CCDS47184.1	5p15.33	2010-02-17			ENSG00000185028	ENSG00000185028			37268	protein-coding gene	gene with protein product							Standard	NM_001080478		Approved		uc003jal.1	A6NHZ5	OTTHUMG00000161578	ENST00000328278.3:c.638T>A	chr5.hg19:g.192291T>A	ENSP00000327675:p.Leu213Gln	80.0	0.0		158.0	80.0	NM_001080478		Missense_Mutation	SNP	ENST00000328278.3	hg19	CCDS47184.1	.	.	.	.	.	.	.	.	.	.	T	13.33	2.205881	0.39003	.	.	ENSG00000185028	ENST00000328278	T	0.62364	0.03	5.23	5.23	0.72850	.	0.214867	0.41938	D	0.000788	T	0.77253	0.4103	M	0.82323	2.585	0.20196	N	0.99993	D	0.76494	0.999	D	0.73380	0.98	T	0.71027	-0.4711	10	0.87932	D	0	.	7.7805	0.29062	0.0:0.0937:0.0:0.9063	.	213	A6NHZ5	LR14B_HUMAN	Q	213	ENSP00000327675:L213Q	ENSP00000327675:L213Q	L	+	2	0	LRRC14B	245291	0.983000	0.35010	0.415000	0.26534	0.587000	0.36485	4.745000	0.62125	1.983000	0.57843	0.379000	0.24179	CTG	.	.		0.736	LRRC14B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000365393.2	NM_001080478		A	192291	T	A	192291	3	1	189	1	0	0	0	0	1	0	0	0	8978	1580	55	4	640	4	LRRC14B	5	192291	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10		192291	180722969	62	27938										
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1094313	1094313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ttcaaagaagctctcttgttCcacctcgacattgttgagga	8	10	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:1094313C>T	ENST00000264930.5	-	2	218	c.175G>A	c.(175-177)Gaa>Aaa	p.E59K		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	59					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CTCTCTTGTTCCACCTCGACA	0.423																																					p.E59K		Atlas-SNP	.											.	SLC12A7	97	.	0			c.G175A						.						134	124	128					5																	1094313		2203	4300	6503	SO:0001583	missense	10723	exon2			CTTGTTCCACCTC	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.175G>A	chr5.hg19:g.1094313C>T	ENSP00000264930:p.Glu59Lys	75.0	0.0		145.0	48.0	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	hg19	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.161301	0.57368	.	.	ENSG00000113504	ENST00000264930;ENST00000343658	D	0.84442	-1.85	3.59	3.59	0.41128	.	0.481200	0.20635	N	0.088502	T	0.80706	0.4674	L	0.59436	1.845	0.41340	D	0.987298	B	0.15141	0.012	B	0.14578	0.011	T	0.74873	-0.3516	10	0.11485	T	0.65	.	14.1132	0.65137	0.0:1.0:0.0:0.0	.	59	Q9Y666	S12A7_HUMAN	K	59	ENSP00000264930:E59K	ENSP00000264930:E59K	E	-	1	0	SLC12A7	1147313	0.984000	0.35163	0.022000	0.16811	0.002000	0.02628	4.982000	0.63825	1.713000	0.51359	0.491000	0.48974	GAA	.	.		0.423	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		T	1094313	C	T	1094313	3	4	189	1	0	0	0	0	1	0	0	0	14403	864	30	3	3168	3	SLC12A7	5	1094313	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	902022	1094313	179820947	63	27939										
MAST4	375449	hgsc.bcm.edu	37	chr5	66462123	66462123	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gacagaagggcggaagggaaGaaatgcactgaagcacttta	14	6	0	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:66462123G>T	ENST00000403625.2	+	29	7411	c.7116G>T	c.(7114-7116)aaG>aaT	p.K2372N	MAST4_ENST00000403666.1_Missense_Mutation_p.K2183N|MAST4_ENST00000404260.3_Missense_Mutation_p.K2375N|MAST4_ENST00000261569.7_Missense_Mutation_p.K2178N|MAST4_ENST00000405643.1_Missense_Mutation_p.K2193N	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2375						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CGGAAGGGAAGAAATGCACTG	0.577											OREG0016638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K2372N		Atlas-SNP	.											.	MAST4	218	.	0			c.G7116T						.						21	31	28					5																	66462123		2090	4219	6309	SO:0001583	missense	375449	exon29			AGGGAAGAAATGC	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.7116G>T	chr5.hg19:g.66462123G>T	ENSP00000385727:p.Lys2372Asn	81.0	0.0	1092	133.0	19.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.23|12.23	1.875359|1.875359	0.33162|0.33162	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000443808|ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569	.|T;T;T;T;T	.|0.73575	.|-0.74;-0.74;-0.76;-0.76;-0.73	4.69|4.69	1.53|1.53	0.23141|0.23141	.|.	.|0.118515	.|0.37577	.|N	.|0.002034	.|T	.|0.55257	.|0.1909	L|L	0.32530|0.32530	0.975|0.975	0.22989|0.22989	N|N	0.998461|0.998461	.|B;B	.|0.10296	.|0.003;0.002	.|B;B	.|0.10450	.|0.002;0.005	.|T	.|0.43523	.|-0.9386	.|10	.|0.45353	.|T	.|0.12	-9.2249|-9.2249	0.9102|0.9102	0.01293|0.01293	0.2202:0.2016:0.3763:0.2019|0.2202:0.2016:0.3763:0.2019	.|.	.|2375;2183	.|O15021;O15021-3	.|MAST4_HUMAN;.	X|N	1429|2375;2372;2183;2193;2193;2178	.|ENSP00000385048:K2375N;ENSP00000385727:K2372N;ENSP00000384313:K2183N;ENSP00000384099:K2193N;ENSP00000261569:K2178N	.|ENSP00000261569:K2178N	E|K	+|+	1|3	0|2	MAST4|MAST4	66497879|66497879	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.044000|0.044000	0.14063|0.14063	1.785000|1.785000	0.38684|0.38684	0.127000|0.127000	0.18452|0.18452	-0.218000|-0.218000	0.12543|0.12543	GAA|AAG	.	.		0.577	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			T	66462123	G	T	66462123	3	4	189	1	0	0	0	0	1	0	0	0	9336	933	33	3	7360	3	MAST4	5	66462123	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	65367810	66462123	114453137	64	27940										
MCTP1	79772	hgsc.bcm.edu	37	chr5	94275891	94275891	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctttcagagtaagggtcacaTctgtgggcctgtgatagaaa	12	7	3	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:94275891T>A	ENST00000515393.1	-	5	1069	c.1070A>T	c.(1069-1071)gAt>gTt	p.D357V	MCTP1_ENST00000429576.2_Missense_Mutation_p.D136V|MCTP1_ENST00000505208.1_Missense_Mutation_p.D136V|MCTP1_ENST00000312216.8_Missense_Mutation_p.D136V	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	357					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		AAGGGTCACATCTGTGGGCCT	0.333																																					p.D357V		Atlas-SNP	.											.	MCTP1	110	.	0			c.A1070T						.						122	123	123					5																	94275891		2203	4300	6503	SO:0001583	missense	79772	exon5			GTCACATCTGTGG		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.1070A>T	chr5.hg19:g.94275891T>A	ENSP00000424126:p.Asp357Val	76.0	0.0		78.0	43.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Missense_Mutation	SNP	ENST00000515393.1	hg19	CCDS34203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.40|16.40	3.112821|3.112821	0.56398|0.56398	.|.	.|.	ENSG00000175471|ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000312216;ENST00000508509;ENST00000512425;ENST00000505208;ENST00000415885;ENST00000507214;ENST00000514780|ENST00000503301	T;T;T;T;T;T;T;T|.	0.78924|.	-0.2;-0.2;-0.2;-0.2;-1.22;-0.2;-0.2;-0.2|.	5.63|5.63	5.63|5.63	0.86233|0.86233	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.56277|0.56277	0.1974|0.1974	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;D;P|.	0.76494|.	0.999;0.993;0.843|.	D;D;B|.	0.73380|.	0.98;0.917;0.429|.	T|T	0.52480|0.52480	-0.8570|-0.8570	10|5	0.87932|.	D|.	0|.	-15.8603|-15.8603	16.1297|16.1297	0.81418|0.81418	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	357;136;136|.	Q6DN14;Q6DN14-3;Q6DN14-2|.	MCTP1_HUMAN;.;.|.	V|S	357;136;136;136;18;136;98;118;117|165	ENSP00000424126:D357V;ENSP00000391639:D136V;ENSP00000308957:D136V;ENSP00000423410:D136V;ENSP00000431075:D18V;ENSP00000426438:D136V;ENSP00000424936:D118V;ENSP00000421543:D117V|.	ENSP00000308957:D136V|.	D|R	-|-	2|3	0|2	MCTP1|MCTP1	94301647|94301647	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	6.573000|6.573000	0.74009|0.74009	2.270000|2.270000	0.75569|0.75569	0.460000|0.460000	0.39030|0.39030	GAT|AGA	.	.		0.333	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		A	94275891	T	A	94275891	3	1	189	1	0	0	0	0	1	0	0	0	9409	1435	50	4	2005	4	MCTP1	5	94275891	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	27813768	94275891	86639369	65	27941										
SPATA9	83890	hgsc.bcm.edu	37	chr5	95018538	95018538	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aacacctgcccacatatccaCccaacaggtttgattggcat	6	14	0	1	rs373326650		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:95018538C>T	ENST00000274432.8	-	1	162	c.21G>A	c.(19-21)ggG>ggA	p.G7G	SPATA9_ENST00000477047.2_5'UTR|SPATA9_ENST00000395899.3_Silent_p.G7G|RFESD_ENST00000508206.1_Intron	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	7					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)	7		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)		CACATATCCACCCAACAGGTT	0.458																																					p.G7G		Atlas-SNP	.											.	SPATA9	17	.	0			c.G21A						.						149	142	144					5																	95018538		2203	4300	6503	SO:0001819	synonymous_variant	83890	exon1			TATCCACCCAACA	AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.21G>A	chr5.hg19:g.95018538C>T		107.0	0.0		161.0	7.0	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Silent	SNP	ENST00000274432.8	hg19	CCDS4076.1																																																																																			.	.		0.458	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952		T	95018538	C	T	95018538	2	4	189	1	0	0	0	0	0	0	0	1	15031	494	18	3		3	SPATA9	5	95018538	Silent	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	742647	95018538	85896722	66	27942										
FBXL17	64839	hgsc.bcm.edu	37	chr5	107356642	107356642	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctaccataatctgtgattttAcaggacaccaaatatagctc	5	10	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:107356642A>T	ENST00000542267.1	-	7	2212	c.1806T>A	c.(1804-1806)tgT>tgA	p.C602*	FBXL17_ENST00000359660.5_Nonsense_Mutation_p.C204*|FBXL17_ENST00000496714.1_Nonsense_Mutation_p.C204*	NM_001163315.2	NP_001156787.2	Q9UF56	FXL17_HUMAN	F-box and leucine-rich repeat protein 17	602										endometrium(1)|large_intestine(4)|lung(1)	6		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)		CTGTGATTTTACAGGACACCA	0.328																																					p.C602X		Atlas-SNP	.											.	FBXL17	60	.	0			c.T1806A						.						109	110	110					5																	107356642		2202	4300	6502	SO:0001587	stop_gained	64839	exon7			GATTTTACAGGAC	AL133602	CCDS54886.1	5q21.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000145743	ENSG00000145743		"F-boxes / Leucine-rich repeats"	13615	protein-coding gene	gene with protein product		609083	"F-box only protein 13"	FBXO13			Standard	NM_001163315		Approved	DKFZP434C1715, Fbx13, Fbl17	uc011cvc.2	Q9UF56	OTTHUMG00000159785	ENST00000542267.1:c.1806T>A	chr5.hg19:g.107356642A>T	ENSP00000437464:p.Cys602*	56.0	0.0		70.0	19.0	NM_001163315	A1A4E3	Nonsense_Mutation	SNP	ENST00000542267.1	hg19	CCDS54886.1	.	.	.	.	.	.	.	.	.	.	A	40	8.386735	0.98789	.	.	ENSG00000145743	ENST00000359660;ENST00000542267;ENST00000496714	.	.	.	5.5	4.34	0.51931	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.4727	0.32995	0.8506:0.0:0.1494:0.0	.	.	.	.	X	204;602;204	.	ENSP00000352683:C204X	C	-	3	2	FBXL17	107384541	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.897000	0.48664	0.929000	0.37192	0.528000	0.53228	TGT	.	.		0.328	FBXL17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	107356642	A	T	107356642	4	4	189	1	0	0	0	0	0	1	0	0	5721	389	14	4	311	4	FBXL17	5	107356642	Nonsense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	12338104	107356642	73558618	67	27943										
LOX	4015	hgsc.bcm.edu	37	chr5	121405851	121405851	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ttcaggaaccaggtagctggGgtttacactgacctgggcaa	13	9	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:121405851G>A	ENST00000231004.4	-	6	1443	c.1144C>T	c.(1144-1146)Ccc>Tcc	p.P382S	LOX_ENST00000513319.1_5'UTR|SRFBP1_ENST00000504881.1_Intron	NM_001178102.1|NM_002317.5	NP_001171573.1|NP_002308.2	P28300	LYOX_HUMAN	lysyl oxidase	382	Lysyl-oxidase like.				blood vessel development (GO:0001568)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|wound healing (GO:0042060)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)			endometrium(1)|lung(6)|prostate(1)	8		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)		AGGTAGCTGGGGTTTACACTG	0.438																																					p.P382S		Atlas-SNP	.											.	LOX	29	.	0			c.C1144T						.						121	112	115					5																	121405851		2203	4300	6503	SO:0001583	missense	4015	exon6			AGCTGGGGTTTAC		CCDS4129.1	5q23.3-q31.2	2008-02-05			ENSG00000113083	ENSG00000113083	1.4.3.13		6664	protein-coding gene	gene with protein product		153455				1685472	Standard	NM_002317		Approved		uc003ksu.3	P28300	OTTHUMG00000128914	ENST00000231004.4:c.1144C>T	chr5.hg19:g.121405851G>A	ENSP00000231004:p.Pro382Ser	115.0	0.0		180.0	27.0	NM_002317	B2R5Q3|Q5FWF0	Missense_Mutation	SNP	ENST00000231004.4	hg19	CCDS4129.1	.	.	.	.	.	.	.	.	.	.	G	33	5.200061	0.94997	.	.	ENSG00000113083	ENST00000231004;ENST00000543620	T	0.47869	0.83	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.75817	0.3901	M	0.89904	3.07	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.81120	-0.1077	10	0.87932	D	0	.	19.3672	0.94468	0.0:0.0:1.0:0.0	.	382	P28300	LYOX_HUMAN	S	382;342	ENSP00000231004:P382S	ENSP00000231004:P382S	P	-	1	0	LOX	121433750	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.703000	0.98714	2.637000	0.89404	0.558000	0.71614	CCC	.	.		0.438	LOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250887.2			A	121405851	G	A	121405851	3	1	189	1	0	0	0	0	1	0	0	0	8907	1232	43	3	117	3	LOX	5	121405851	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	14049209	121405851	59509409	68	27944										
LOC153328	153328	hgsc.bcm.edu	37	chr5	135188444	135188444	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tggccggcgtggtctctgtcGggctgggagggcccgtggac	20	11	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:135188444G>C	ENST00000420621.1	+	4	527	c.355G>C	c.(355-357)Ggg>Cgg	p.G119R	SLC25A48_ENST00000274513.5_Missense_Mutation_p.G119R|SLC25A48_ENST00000412661.2_Missense_Mutation_p.G119R|SLC25A48_ENST00000433282.2_Missense_Mutation_p.G65R|SLC25A48_ENST00000425402.1_Intron			Q6ZT89	S2548_HUMAN	solute carrier family 25, member 48	119					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						GGTCTCTGTCGGGCTGGGAGG	0.672																																					p.G119R		Atlas-SNP	.											.	SLC25A48	37	.	0			c.G355C						.						33	37	36					5																	135188444		1967	4133	6100	SO:0001583	missense	153328	exon4			TCTGTCGGGCTGG		CCDS43366.2	5q31.1	2013-05-22			ENSG00000145832	ENSG00000145832		"Solute carriers"	30451	protein-coding gene	gene with protein product	"HCC-down-regulated mitochondrial carrier protein"					15322095, 19303656	Standard	NM_145282		Approved	FLJ44862, HDMCP	uc003lba.3	Q6ZT89	OTTHUMG00000157007	ENST00000420621.1:c.355G>C	chr5.hg19:g.135188444G>C	ENSP00000407973:p.Gly119Arg	135.0	0.0		207.0	22.0	NM_145282	Q8TAV9	Missense_Mutation	SNP	ENST00000420621.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.72	2.618770	0.46736	.	.	ENSG00000145832	ENST00000274513;ENST00000420621;ENST00000433282;ENST00000412661	T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.14	5.08	5.08	0.68730	.	0.105021	0.64402	D	0.000004	D	0.86414	0.5927	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.85130	0.979;0.997	D	0.84792	0.0779	10	0.33141	T	0.24	-28.3799	18.4819	0.90815	0.0:0.0:1.0:0.0	.	119;119	Q6ZT89-3;Q6ZT89-2	.;.	R	119;119;65;119	ENSP00000274513:G119R;ENSP00000407973:G119R;ENSP00000399834:G65R;ENSP00000413049:G119R	ENSP00000274513:G119R	G	+	1	0	SLC25A48	135216343	1.000000	0.71417	0.370000	0.25965	0.268000	0.26511	5.794000	0.69067	2.359000	0.80004	0.462000	0.41574	GGG	.	.		0.672	SLC25A48-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_145282		C	135188444	G	C	135188444	3	2	189	1	0	0	0	0	1	0	0	0	8880	1116	39	4	369	4	LOC153328	5	135188444	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	13782593	135188444	45726816	69	27945										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135651437	135651437	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cacgcccactacaaaatcctTgcattgcatagataacttcc	4	14	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:135651437T>G	ENST00000513104.1	-	3	1093	c.811A>C	c.(811-813)Aag>Cag	p.K271Q	TRPC7_ENST00000426057.2_Intron|TRPC7-AS2_ENST00000513958.1_RNA|TRPC7_ENST00000355180.3_Intron	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	271					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACAAAATCCTTGCATTGCATA	0.488																																					p.K271Q		Atlas-SNP	.											.	TRPC7	126	.	0			c.A811C						.						71	74	73					5																	135651437		2073	4231	6304	SO:0001583	missense	57113	exon3			AATCCTTGCATTG	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.811A>C	chr5.hg19:g.135651437T>G	ENSP00000426070:p.Lys271Gln	67.0	0.0		130.0	66.0	NM_020389	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	hg19	CCDS47267.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.5|21.5	4.157050|4.157050	0.78114|0.78114	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000513104;ENST00000265193|ENST00000502753	T|.	0.68903|.	-0.36|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58935|0.58935	0.2157|0.2157	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	D;P|.	0.71674|.	0.998;0.762|.	D;B|.	0.73380|.	0.98;0.403|.	T|T	0.54840|0.54840	-0.8233|-0.8233	10|5	0.14656|.	T|.	0.56|.	-27.9049|-27.9049	16.0238|16.0238	0.80522|0.80522	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	271;271|.	Q70T25;Q9HCX4|.	.;TRPC7_HUMAN|.	Q|P	271|270	ENSP00000426070:K271Q|.	ENSP00000265193:K271Q|.	K|Q	-|-	1|2	0|0	TRPC7|TRPC7	135679336|135679336	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.868000|7.868000	0.87116|0.87116	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	AAG|CAA	.	.		0.488	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		G	135651437	T	G	135651437	3	3	189	1	0	0	0	0	1	0	0	0	16599	1821	63	5	1817	5	TRPC7	5	135651437	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	462993	135651437	45263823	70	27946										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140262151	140262151	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aggagctgtgtgggcggagcGcggagtgcagcatccacctg	18	10	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:140262151G>A	ENST00000289272.2	+	1	298	c.298G>A	c.(298-300)Gcg>Acg	p.A100T	PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.A100T|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	100	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGGCGGAGCGCGGAGTGCAG	0.557																																					p.A100T	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.G298A						.						128	139	135					5																	140262151		2203	4298	6501	SO:0001583	missense	56136	exon1			CGGAGCGCGGAGT	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.298G>A	chr5.hg19:g.140262151G>A	ENSP00000289272:p.Ala100Thr	112.0	0.0		186.0	31.0	NM_031865	O75277	Missense_Mutation	SNP	ENST00000289272.2	hg19	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	9.105	1.005045	0.19199	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.27104	1.69;1.69	5.58	-1.46	0.08800	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.17704	0.0425	L	0.33189	0.99	0.09310	N	1	B;B;B	0.30033	0.197;0.168;0.266	B;B;B	0.26770	0.022;0.073;0.005	T	0.17137	-1.0379	9	0.37606	T	0.19	.	11.3185	0.49407	0.0:0.5547:0.1696:0.2757	.	100;100;100	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	T	100	ENSP00000386821:A100T;ENSP00000289272:A100T	ENSP00000289272:A100T	A	+	1	0	PCDHA13	140242335	0.000000	0.05858	0.953000	0.39169	0.737000	0.42083	-1.380000	0.02551	-0.247000	0.09597	-0.311000	0.09066	GCG	.	.		0.557	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140262151	G	A	140262151	3	1	189	1	0	0	0	0	1	0	0	0	11532	1087	38	1	300	1	PCDHA13	5	140262151	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	4610714	140262151	40653109	71	27947										
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140744468	140744468	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gcggaactgatggacaaaagTatccggagctggtgttggaa	15	6	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:140744468T>A	ENST00000518069.1	+	1	571	c.571T>A	c.(571-573)Tat>Aat	p.Y191N	PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	191	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGACAAAAGTATCCGGAGCT	0.562																																					p.Y191N		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.T571A						.						61	63	62					5																	140744468		2011	4178	6189	SO:0001583	missense	56110	exon1			CAAAAGTATCCGG	AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.571T>A	chr5.hg19:g.140744468T>A	ENSP00000429834:p.Tyr191Asn	96.0	0.0		186.0	77.0	NM_032054	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	hg19	CCDS54925.1	.	.	.	.	.	.	.	.	.	.	.	8.086	0.773421	0.16051	.	.	ENSG00000253485	ENST00000518069	T	0.19669	2.13	5.52	2.99	0.34606	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.20210	0.0486	M	0.65677	2.01	0.09310	N	1	B;B	0.14805	0.005;0.011	B;B	0.20577	0.03;0.02	T	0.25984	-1.0116	9	0.36615	T	0.2	.	2.9328	0.05804	0.2937:0.1777:0.0:0.5286	.	191;191	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	N	191	ENSP00000429834:Y191N	ENSP00000429834:Y191N	Y	+	1	0	PCDHGA5	140724652	0.000000	0.05858	0.930000	0.37139	0.915000	0.54546	-1.238000	0.02919	1.047000	0.40274	0.460000	0.39030	TAT	.	.		0.562	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		A	140744468	T	A	140744468	3	1	189	1	0	0	0	0	1	0	0	0	11566	1638	57	4	573	4	PCDHGA5	5	140744468	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	482317	140744468	40170792	72	27948										
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140811636	140811636	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gcccctatccacggaaactcAtatctcgctgaacgtggcag	9	14	2	1	rs572724741	byFrequency	TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:140811636A>G	ENST00000252085.3	+	1	1452	c.1310A>G	c.(1309-1311)cAt>cGt	p.H437R	PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	437	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGAAACTCATATCTCGCTG	0.542													a|||	7	0.00139776	0	0	5008	,	,		16557	0		0	False		,,,				2504	0.0072				p.H437R		Atlas-SNP	.											.	PCDHGA12	271	.	0			c.A1310G						.						60	66	64					5																	140811636		2203	4300	6503	SO:0001583	missense	26025	exon1			AAACTCATATCTC	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1310A>G	chr5.hg19:g.140811636A>G	ENSP00000252085:p.His437Arg	96.0	0.0		153.0	18.0	NM_032094	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	hg19	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	a	0.019	-1.454401	0.01071	.	.	ENSG00000253159	ENST00000252085	T	0.01647	4.71	5.36	2.92	0.33932	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.02193	0.0068	M	0.63208	1.945	0.09310	N	1	B;B	0.14805	0.011;0.006	B;B	0.21151	0.031;0.033	T	0.49781	-0.8903	9	0.25751	T	0.34	.	0.5167	0.00604	0.4307:0.1413:0.1555:0.2725	.	437;437	O60330-2;O60330	.;PCDGC_HUMAN	R	437	ENSP00000252085:H437R	ENSP00000252085:H437R	H	+	2	0	PCDHGA12	140791820	0.000000	0.05858	0.057000	0.19452	0.014000	0.08584	-0.521000	0.06245	0.324000	0.23333	0.533000	0.62120	CAT	.	.		0.542	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		G	140811636	A	G	140811636	3	3	189	1	0	0	0	0	1	0	0	0	11562	217	8	2	1312	2	PCDHGA12	5	140811636	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	67168	140811636	40103624	73	27949										
PRELID2	153768	hgsc.bcm.edu	37	chr5	145197614	145197614	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	attaggtactttcaaaatgcTcacctgtccaacagaaagaa	6	9	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:145197614T>A	ENST00000334744.4	-	5	299	c.247A>T	c.(247-249)Agc>Tgc	p.S83C	PRELID2_ENST00000358004.2_Missense_Mutation_p.S71C|PRELID2_ENST00000394450.2_Missense_Mutation_p.S42C|PRELID2_ENST00000511435.1_Missense_Mutation_p.S71C|PRELID2_ENST00000505416.1_Missense_Mutation_p.S71C	NM_182960.2	NP_892005.1	Q8N945	PRLD2_HUMAN	PRELI domain containing 2	83	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)			endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCAAAATGCTCACCTGTCCA	0.433																																					p.S83C		Atlas-SNP	.											.	PRELID2	16	.	0			c.A247T						.						76	66	70					5																	145197614		2203	4300	6503	SO:0001583	missense	153768	exon5			AAATGCTCACCTG	AK095695	CCDS34261.1, CCDS34262.1, CCDS43377.1	5q32	2012-04-23			ENSG00000186314	ENSG00000186314			28306	protein-coding gene	gene with protein product						12477932	Standard	NM_182960		Approved	MGC21644, FLJ38376	uc003lnq.1	Q8N945	OTTHUMG00000163384	ENST00000334744.4:c.247A>T	chr5.hg19:g.145197614T>A	ENSP00000335675:p.Ser83Cys	65.0	0.0		111.0	20.0	NM_182960	G5EA01|Q96EQ3	Missense_Mutation	SNP	ENST00000334744.4	hg19	CCDS34262.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.547265	0.65311	.	.	ENSG00000186314	ENST00000358004;ENST00000334744;ENST00000394450;ENST00000505416;ENST00000511435	T;T;T;T;T	0.48201	2.17;2.08;0.82;2.17;2.18	5.84	5.84	0.93424	PRELI/MSF1 (2);	0.116572	0.64402	D	0.000015	T	0.59569	0.2203	L	0.51422	1.61	0.46631	D	0.99913	P;P;D	0.62365	0.946;0.896;0.991	P;P;P	0.59288	0.733;0.487;0.855	T	0.61297	-0.7091	10	0.59425	D	0.04	-21.1438	15.2019	0.73147	0.0:0.0:0.0:1.0	.	71;71;83	D6RAB6;G5EA01;Q8N945	.;.;PRLD2_HUMAN	C	71;83;42;71;71	ENSP00000350694:S71C;ENSP00000335675:S83C;ENSP00000377965:S42C;ENSP00000424730:S71C;ENSP00000422789:S71C	ENSP00000335675:S83C	S	-	1	0	PRELID2	145177807	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	2.361000	0.44160	2.234000	0.73211	0.528000	0.53228	AGC	.	.		0.433	PRELID2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000372970.1	NM_182960		A	145197614	T	A	145197614	3	1	189	1	0	0	0	0	1	0	0	0	12484	1551	54	4	334	4	PRELID2	5	145197614	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	4385978	145197614	35717646	74	27950										
GABRP	2568	hgsc.bcm.edu	37	chr5	170232776	170232776	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgagagggaacgactctgtgCgtggactggaacacctgcgg	16	9	1	1	rs79061387	byFrequency	TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:170232776C>A	ENST00000518525.1	+	8	1062	c.598C>A	c.(598-600)Cgt>Agt	p.R200S	GABRP_ENST00000519385.1_Missense_Mutation_p.R200S|GABRP_ENST00000265294.4_Missense_Mutation_p.R200S|GABRP_ENST00000519598.1_Missense_Mutation_p.R200S			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	200					signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CGACTCTGTGCGTGGACTGGA	0.522																																					p.R200S		Atlas-SNP	.											.	GABRP	65	.	0			c.C598A						.						91	80	83					5																	170232776		2203	4300	6503	SO:0001583	missense	2568	exon7			TCTGTGCGTGGAC	U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4089	protein-coding gene	gene with protein product	"GABA(A) receptor, pi"	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.598C>A	chr5.hg19:g.170232776C>A	ENSP00000430100:p.Arg200Ser	106.0	0.0		135.0	49.0	NM_014211	A8KA36|D3DQL2|Q32MJ1	Missense_Mutation	SNP	ENST00000518525.1	hg19	CCDS4375.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.757949	0.49468	.	.	ENSG00000094755	ENST00000518525;ENST00000539175;ENST00000265294;ENST00000519385;ENST00000519598	T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08	5.12	5.12	0.69794	Neurotransmitter-gated ion-channel ligand-binding (3);	0.164522	0.53938	D	0.000043	T	0.59183	0.2175	N	0.05487	-0.04	0.42174	D	0.991651	B;B	0.31290	0.121;0.318	B;B	0.25405	0.06;0.057	T	0.59306	-0.7479	9	.	.	.	.	18.1856	0.89791	0.0:1.0:0.0:0.0	.	200;200	E7EWG0;O00591	.;GBRP_HUMAN	S	200;98;200;200;200	ENSP00000430100:R200S;ENSP00000265294:R200S;ENSP00000430727:R200S;ENSP00000430772:R200S	.	R	+	1	0	GABRP	170165354	0.986000	0.35501	1.000000	0.80357	0.995000	0.86356	5.867000	0.69597	2.384000	0.81235	0.655000	0.94253	CGT	.	C|0.999;T|0.001		0.522	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211		A	170232776	C	A	170232776	3	1	189	1	0	0	0	0	1	0	0	0	6182	768	27	1	620	1	GABRP	5	170232776	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	25035162	170232776	10682484	75	27951										
GPRIN1	114787	hgsc.bcm.edu	37	chr5	176024938	176024938	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tttctgctttgccaccagacTgcggctgtgctttccccgag	10	14	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr5:176024938T>A	ENST00000303991.4	-	2	2075	c.1898A>T	c.(1897-1899)cAg>cTg	p.Q633L		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	633					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCACCAGACTGCGGCTGTGC	0.592																																					p.Q633L		Atlas-SNP	.											.	GPRIN1	77	.	0			c.A1898T						.						46	46	46					5																	176024938		2203	4300	6503	SO:0001583	missense	114787	exon2			CCAGACTGCGGCT	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.1898A>T	chr5.hg19:g.176024938T>A	ENSP00000305839:p.Gln633Leu	41.0	0.0		72.0	45.0	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	hg19	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	T	9.638	1.138281	0.21123	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.08193	3.12	4.1	-6.77	0.01727	.	1.999330	0.02839	N	0.127779	T	0.05364	0.0142	L	0.36672	1.1	0.09310	N	1	B	0.18610	0.029	B	0.15870	0.014	T	0.34800	-0.9814	10	0.26408	T	0.33	3.8714	0.9331	0.01339	0.3874:0.2198:0.1003:0.2924	.	633	Q7Z2K8	GRIN1_HUMAN	L	633	ENSP00000305839:Q633L	ENSP00000305839:Q633L	Q	-	2	0	GPRIN1	175957544	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.372000	0.07504	-0.985000	0.03503	-0.475000	0.04921	CAG	.	.		0.592	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899		A	176024938	T	A	176024938	3	1	189	1	0	0	0	0	1	0	0	0	6738	1580	55	4	1132	4	GPRIN1	5	176024938	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	5792162	176024938	4890322	76	27952										
FOXQ1	94234	hgsc.bcm.edu	37	chr6	1313560	1313560	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gagtacaccttcgccgacggGgtcttccgccgccgccgcaa	12	17	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr6:1313560G>T	ENST00000296839.2	+	1	886	c.621G>T	c.(619-621)ggG>ggT	p.G207G		NM_033260.3	NP_150285.3	Q9C009	FOXQ1_HUMAN	forkhead box Q1	207					hair follicle morphogenesis (GO:0031069)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|urinary_tract(1)	2	Ovarian(93;0.0733)	Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.0954)|BRCA - Breast invasive adenocarcinoma(62;0.18)		TCGCCGACGGGGTCTTCCGCC	0.756																																					p.G207G		Atlas-SNP	.											.	FOXQ1	8	.	0			c.G621T						.						16	20	19					6																	1313560		2160	4257	6417	SO:0001819	synonymous_variant	94234	exon1			CGACGGGGTCTTC	AF153341	CCDS4471.1	6p25	2008-02-05			ENSG00000164379	ENSG00000164379		"Forkhead boxes"	20951	protein-coding gene	gene with protein product		612788				11747606, 12011061	Standard	NM_033260		Approved	HFH1	uc003mtl.4	Q9C009	OTTHUMG00000016160	ENST00000296839.2:c.621G>T	chr6.hg19:g.1313560G>T		78.0	0.0		114.0	56.0	NM_033260	Q9NS06	Silent	SNP	ENST00000296839.2	hg19	CCDS4471.1																																																																																			.	.		0.756	FOXQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043410.1	NM_033260		T	1313560	G	T	1313560	2	4	189	1	0	0	0	0	0	0	0	1	6038	1219	43	3		3	FOXQ1	6	1313560	Silent	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10		1313560	169801507	77	27953										
MBOAT1	154141	hgsc.bcm.edu	37	chr6	20131376	20131376	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggagggctgctgttcttaccAtcatgaacctggaatgccaa	11	10	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr6:20131376A>G	ENST00000324607.7	-	5	638	c.474T>C	c.(472-474)gaT>gaC	p.D158D	MBOAT1_ENST00000541730.1_Intron|MBOAT1_ENST00000536798.1_Splice_Site_p.D158D	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	158					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			TGTTCTTACCATCATGAACCT	0.433																																					p.D158D		Atlas-SNP	.											.	MBOAT1	48	.	0			c.T474C						.						155	144	148					6																	20131376		2203	4300	6503	SO:0001630	splice_region_variant	154141	exon5			CTTACCATCATGA	AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197			21579	protein-coding gene	gene with protein product	"lysophosphatidylethanolamine acyltransferase 1"	611732	"O-acyltransferase (membrane bound) domain containing 1"	OACT1		18287005	Standard	NM_001080480		Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.475+1T>C	chr6.hg19:g.20131376A>G		73.0	0.0		70.0	18.0	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Silent	SNP	ENST00000324607.7	hg19	CCDS34346.1																																																																																			.	.		0.433	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1		Silent	G	20131376	A	G	20131376	5	3	189	1	0	0	0	0	0	0	1	0	9365	231	8	2	1049	2	MBOAT1	6	20131376	Splice_Site	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	18817816	20131376	150983691	78	27954										
ZSCAN12	9753	hgsc.bcm.edu	37	chr6	28359478	28359479	+	Nonsense_Mutation	DNP	GC	GC	AA													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	catttcttcagaaacttcttGctttaaattcccatactcat							TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr6:28359478_28359479GC>AA	ENST00000361028.1	-	4	733_734	c.588_589GC>TT	c.(586-591)aaGCaa>aaTTaa	p.196_197KQ>N*	ZSCAN12_ENST00000396827.3_Nonsense_Mutation_p.196_197KQ>N*			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12	196					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|urinary_tract(1)	6						GAAACTTCTTGCTTTAAATTCC	0.351																																					p.Q197X|p.K196N		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.C589T|c.G588T						.																																			SO:0001587	stop_gained	9753	exon4			CTTCTTGCTTTAA|TTCTTGCTTTAAA	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"-", "Zinc fingers, C2H2-type"	13172	protein-coding gene	gene with protein product		603978	"zinc finger protein 305", "zinc finger protein 96"	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.588_589delinsAA	chr6.hg19:g.28359478_28359479delinsAA	ENSP00000354305:p.K196_Q197delinsN*	22.0	0.0		37.0|36.0	27.0|28.0	NM_001163391	O43724	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000361028.1	hg19																																																																																				.	.		0.351	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724		AA	28359479	GC	AA	28359478	4	1	189	1	0	0	0	0	0	1	0	0	18243	1328	46	3	1250	3	ZSCAN12	6	28359478	Nonsense_Mutation	DNP	GC	TCGA-DD-AADF-01A-11D-A40R-10	8228102	28359478	142755589	79	27955										
PSORS1C1	170679	hgsc.bcm.edu	37	chr6	31106509	31106509	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gaggaaactcgtcccccccaCgttaatcctgaccgactttg	8	15	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr6:31106509C>T	ENST00000259881.9	+	5	409	c.120C>T	c.(118-120)caC>caT	p.H40H	PSORS1C2_ENST00000259845.4_Intron|PSORS1C1_ENST00000547221.1_5'UTR|PSORS1C1_ENST00000481450.2_Intron	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	40										kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GTCCCCCCCACGTTAATCCTG	0.562																																					p.H40H		Atlas-SNP	.											.	PSORS1C1	11	.	0			c.C120T						.						150	149	149					6																	31106509		1511	2709	4220	SO:0001819	synonymous_variant	170679	exon5			CCCCCACGTTAAT	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"chromosome 6 open reading frame 16"	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.120C>T	chr6.hg19:g.31106509C>T		73.0	0.0		82.0	17.0	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	hg19	CCDS34390.1																																																																																			.	.		0.562	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		T	31106509	C	T	31106509	2	4	189	1	0	0	0	0	0	0	0	1	12726	535	19	1		1	PSORS1C1	6	31106509	Silent	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	2747031	31106509	140008558	80	27956										
FOXP4	116113	hgsc.bcm.edu	37	chr6	41566593	41566593	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aggcagcccgggcctcccctGggcgcccctaaccccagcgc	12	21	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr6:41566593G>C	ENST00000307972.4	+	16	1974	c.1962G>C	c.(1960-1962)ctG>ctC	p.L654L	FOXP4_ENST00000373057.3_Silent_p.L652L|MIR4641_ENST00000578353.1_RNA|FOXP4_ENST00000409208.1_Silent_p.L642L|FOXP4_ENST00000373060.1_Silent_p.L654L|FOXP4_ENST00000373063.3_Silent_p.L641L			Q8IVH2	FOXP4_HUMAN	forkhead box P4	654					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GGCCTCCCCTGGGCGCCCCTA	0.672																																					p.L654L		Atlas-SNP	.											.	FOXP4	83	.	0			c.G1962C						.						15	18	17					6																	41566593		2190	4282	6472	SO:0001819	synonymous_variant	116113	exon17			TCCCCTGGGCGCC	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"Forkhead boxes"	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.1962G>C	chr6.hg19:g.41566593G>C		200.0	0.0		174.0	78.0	NM_001012426	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Silent	SNP	ENST00000307972.4	hg19	CCDS34447.1																																																																																			.	.		0.672	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		C	41566593	G	C	41566593	2	2	189	1	0	0	0	0	0	0	0	1	6037	1335	47	4		4	FOXP4	6	41566593	Silent	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	10460084	41566593	129548474	81	27957										
MEP1A	4224	hgsc.bcm.edu	37	chr6	46803136	46803136	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cctacctgtcagcctgagccAggggcagcccagccgacaga	12	16	1	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr6:46803136A>T	ENST00000230588.4	+	13	1943	c.1934A>T	c.(1933-1935)cAg>cTg	p.Q645L		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	645					digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			AGCCTGAGCCAGGGGCAGCCC	0.607																																					p.Q645L		Atlas-SNP	.											.	MEP1A	93	.	0			c.A1934T						.						22	21	21					6																	46803136		2203	4300	6503	SO:0001583	missense	4224	exon13			TGAGCCAGGGGCA		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.1934A>T	chr6.hg19:g.46803136A>T	ENSP00000230588:p.Gln645Leu	67.0	0.0		95.0	26.0	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	hg19	CCDS4918.1	.	.	.	.	.	.	.	.	.	.	A	7.561	0.664682	0.14710	.	.	ENSG00000112818	ENST00000230588	T	0.24908	1.83	5.35	2.88	0.33553	.	0.784026	0.12295	N	0.481627	T	0.08582	0.0213	L	0.56769	1.78	0.18873	N	0.999981	B;B	0.30482	0.118;0.281	B;B	0.22601	0.025;0.04	T	0.27191	-1.0081	10	0.33940	T	0.23	-3.3402	6.602	0.22705	0.7619:0.1552:0.0828:0.0	.	673;645	B7ZL91;Q16819	.;MEP1A_HUMAN	L	645	ENSP00000230588:Q645L	ENSP00000230588:Q645L	Q	+	2	0	MEP1A	46911095	0.973000	0.33851	0.102000	0.21198	0.027000	0.11550	1.558000	0.36309	0.330000	0.23485	0.528000	0.53228	CAG	.	.		0.607	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		T	46803136	A	T	46803136	3	4	189	1	0	0	0	0	1	0	0	0	9484	188	7	4	1984	4	MEP1A	6	46803136	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	5236543	46803136	124311931	82	27958										
IL17A	3605	hgsc.bcm.edu	37	chr6	52053894	52053894	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	atatccctctgtgatctgggAggcaaagtgccgccacttgg	12	11	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr6:52053894A>T	ENST00000340057.1	+	3	317	c.272A>T	c.(271-273)gAg>gTg	p.E91V		NM_002190.2	NP_002181.1	Q16552	IL17_HUMAN	interleukin 17A	91					apoptotic process (GO:0006915)|cell death (GO:0008219)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|fibroblast activation (GO:0072537)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein glycosylation (GO:0006486)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)			endometrium(3)|large_intestine(2)|lung(8)|prostate(3)|skin(1)	17	Lung NSC(77;0.116)					GTGATCTGGGAGGCAAAGTGC	0.532																																					p.E91V		Atlas-SNP	.											.	IL17A	28	.	0			c.A272T						.						65	57	60					6																	52053894		2203	4300	6503	SO:0001583	missense	3605	exon3			TCTGGGAGGCAAA	U32659	CCDS4937.1	6p12	2011-07-14	2006-04-26	2006-04-26	ENSG00000112115	ENSG00000112115		"Interleukins and interleukin receptors"	5981	protein-coding gene	gene with protein product	"cytotoxic T-lymphocyte-associated protein 8"	603149	"interleukin 17 (cytotoxic T-lymphocyte-associated serine esterase 8)"	CTLA8, IL17		8390535	Standard	NM_002190		Approved	IL-17A, IL-17	uc003pak.1	Q16552	OTTHUMG00000014840	ENST00000340057.1:c.272A>T	chr6.hg19:g.52053894A>T	ENSP00000344192:p.Glu91Val	69.0	0.0		110.0	37.0	NM_002190	Q5T2P0	Missense_Mutation	SNP	ENST00000340057.1	hg19	CCDS4937.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.080477	0.76528	.	.	ENSG00000112115	ENST00000340057	T	0.63255	-0.03	5.64	5.64	0.86602	.	0.112907	0.56097	D	0.000022	T	0.73931	0.3650	M	0.76838	2.35	0.50632	D	0.999885	D	0.69078	0.997	D	0.70016	0.967	T	0.76247	-0.3029	10	0.48119	T	0.1	-26.5823	15.8596	0.79012	1.0:0.0:0.0:0.0	.	91	Q16552	IL17_HUMAN	V	91	ENSP00000344192:E91V	ENSP00000344192:E91V	E	+	2	0	IL17A	52161853	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	6.365000	0.73090	2.158000	0.67659	0.496000	0.49642	GAG	.	.		0.532	IL17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040892.1	NM_002190		T	52053894	A	T	52053894	3	4	189	1	0	0	0	0	1	0	0	0	7643	304	11	4	282	4	IL17A	6	52053894	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	5250758	52053894	119061173	83	27959										
EYS	346007	hgsc.bcm.edu	37	chr6	66115107	66115107	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cagtaccattctgacatggtActaatgaaaactcactgaca	6	10	2	3	rs149421359		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr6:66115107A>G	ENST00000370621.3	-	6	1542	c.1016T>C	c.(1015-1017)gTa>gCa	p.V339A	EYS_ENST00000370618.3_Missense_Mutation_p.V339A|EYS_ENST00000342421.5_Missense_Mutation_p.V339A|EYS_ENST00000503581.1_Missense_Mutation_p.V339A|EYS_ENST00000393380.2_Missense_Mutation_p.V339A|EYS_ENST00000370616.2_Missense_Mutation_p.V339A			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	339	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CTGACATGGTACTAATGAAAA	0.343																																					p.V339A		Atlas-SNP	.											.	EYS	527	.	0			c.T1016C						.	A	ALA/VAL,ALA/VAL,ALA/VAL	0,4406		0,0,2203	113	112	112		1016,1016,1016	-8.8	0	6	dbSNP_134	112	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	EYS	NM_198283.1,NM_001142801.1,NM_001142800.1	64,64,64	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign,benign	339/595,339/620,339/3145	66115107	1,13005	2203	4300	6503	SO:0001583	missense	346007	exon6			CATGGTACTAATG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1016T>C	chr6.hg19:g.66115107A>G	ENSP00000359655:p.Val339Ala	172.0	0.0		243.0	123.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	A	7.298	0.612430	0.14066	0.0	1.16E-4	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	D;D;D;T;T;T	0.85411	-1.98;-1.98;-1.98;1.62;1.62;1.62	4.4	-8.8	0.00817	.	.	.	.	.	T	0.33876	0.0878	N	0.05259	-0.085	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.34625	-0.9821	9	0.19147	T	0.46	.	2.0294	0.03526	0.1626:0.2329:0.3785:0.2261	.	339;339;339	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	A	339	ENSP00000424243:V339A;ENSP00000359655:V339A;ENSP00000359650:V339A;ENSP00000377042:V339A;ENSP00000341818:V339A;ENSP00000359652:V339A	ENSP00000341818:V339A	V	-	2	0	EYS	66171828	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.781000	0.04648	-2.117000	0.00829	-0.644000	0.03951	GTA	.	A|1.000;G|0.000		0.343	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	66115107	A	G	66115107	3	3	189	1	0	0	0	0	1	0	0	0	5334	391	14	2	8532	2	EYS	6	66115107	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	14061213	66115107	104999960	84	27960										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75799957	75799957	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gcgggcctggctggttgcgaCtggactggtaatcatttgga	16	8	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr6:75799957C>A	ENST00000322507.8	-	63	9119	c.8810G>T	c.(8809-8811)aGt>aTt	p.S2937I	COL12A1_ENST00000483888.2_Missense_Mutation_p.S2933I|COL12A1_ENST00000345356.6_Missense_Mutation_p.S1773I|COL12A1_ENST00000416123.2_Missense_Mutation_p.S2861I|COL12A1_ENST00000511023.1_5'UTR	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2937	Nonhelical region (NC2).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CTGGTTGCGACTGGACTGGTA	0.557																																					p.S2937I		Atlas-SNP	.											.	COL12A1	385	.	0			c.G8810T						.						155	165	162					6																	75799957		1898	4134	6032	SO:0001583	missense	1303	exon63			TTGCGACTGGACT	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.8810G>T	chr6.hg19:g.75799957C>A	ENSP00000325146:p.Ser2937Ile	47.0	0.0		60.0	17.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.934790	0.52866	.	.	ENSG00000111799	ENST00000322507;ENST00000425443;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	D;D;D;D;D	0.89875	-2.21;-2.58;-2.28;-2.2;-2.17	5.32	-4.65	0.03339	.	0.319059	0.29246	N	0.012719	T	0.66733	0.2819	N	0.03608	-0.345	0.25162	N	0.990341	P;P	0.45011	0.817;0.848	P;P	0.55999	0.684;0.789	T	0.70978	-0.4725	10	0.40728	T	0.16	.	6.7934	0.23711	0.1081:0.366:0.0:0.5259	.	1773;2937	Q99715-2;Q99715	.;COCA1_HUMAN	I	2937;575;2861;1773;2861;2933	ENSP00000325146:S2937I;ENSP00000399812:S575I;ENSP00000305147:S1773I;ENSP00000412864:S2861I;ENSP00000421216:S2933I	ENSP00000325146:S2937I	S	-	2	0	COL12A1	75856677	0.838000	0.29461	0.833000	0.33012	0.557000	0.35523	-0.281000	0.08456	-1.227000	0.02571	-0.961000	0.02630	AGT	.	.		0.557	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75799957	C	A	75799957	3	1	189	1	0	0	0	0	1	0	0	0	3671	565	20	3	397	3	COL12A1	6	75799957	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	9684850	75799957	95315110	85	27961										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101054670	101054671	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tccatcatagtattctgttcCcttaataattactaaatgag							TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr6:101054670_101054671CC>AA	ENST00000369162.2	-	32	5333_5334	c.4989_4990GG>TT	c.(4987-4992)aaGGga>aaTTga	p.1663_1664KG>N*		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1663	Helicase C-terminal 2. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TATTCTGTTCCCTTAATAATTA	0.312																																					p.G1664X|p.K1663N		Atlas-SNP	.											.	ASCC3	205	.	0			c.G4990T|c.G4989T						.																																			SO:0001587	stop_gained	10973	exon32			CTGTTCCCTTAAT|TGTTCCCTTAATA	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.4989_4990delinsAA	chr6.hg19:g.101054670_101054671delinsAA	ENSP00000358159:p.K1663_G1664delinsN*	87.0|86.0	0.0		67.0	30.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1																																																																																			.	.		0.312	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		AA	101054671	CC	AA	101054670	4	1	189	1	0	0	0	0	0	1	0	0	1033	632	22	3	1662	3	ASCC3	6	101054670	Nonsense_Mutation	DNP	CC	TCGA-DD-AADF-01A-11D-A40R-10	25254713	101054670	70060397	86	27962										
IGF2BP3	10643	hgsc.bcm.edu	37	chr7	23391100	23391100	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgcccaagcccccggcgaccTcggggctgctgcaaggggtt	15	15	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr7:23391100T>C	ENST00000258729.3	-	6	863	c.507A>G	c.(505-507)cgA>cgG	p.R169R	IGF2BP3_ENST00000491719.1_5'UTR	NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	169					anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						CCCGGCGACCTCGGGGCTGCT	0.547																																					p.R169R		Atlas-SNP	.											.	IGF2BP3	71	.	0			c.A507G						.						36	40	38					7																	23391100		2203	4300	6503	SO:0001819	synonymous_variant	10643	exon6			GCGACCTCGGGGC	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"RNA binding motif (RRM) containing"	28868	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 3", "cancer/testis antigen 98"	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.507A>G	chr7.hg19:g.23391100T>C		39.0	0.0		53.0	9.0	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Silent	SNP	ENST00000258729.3	hg19	CCDS5382.1																																																																																			.	.		0.547	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547		C	23391100	T	C	23391100	2	2	189	1	0	0	0	0	0	0	0	1	7584	1538	54	2		2	IGF2BP3	7	23391100	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10		23391100	135747563	87	27963										
C7orf16	10842	hgsc.bcm.edu	37	chr7	31732136	31732136	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gaccctcgttgcagccacttAggtaaacaaatgatcgattg	9	10	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr7:31732136A>T	ENST00000342032.3	+	2	709	c.81A>T	c.(79-81)ttA>ttT	p.L27F	PPP1R17_ENST00000409146.3_Splice_Site_p.L27F	NM_006658.4	NP_006649.2	O96001	PPR17_HUMAN	protein phosphatase 1, regulatory subunit 17	27					central nervous system development (GO:0007417)|intracellular signal transduction (GO:0035556)|regulation of phosphatase activity (GO:0010921)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)										GCAGCCACTTAGGTAAACAAA	0.522																																					p.L27F		Atlas-SNP	.											.	.	.	.	0			c.A81T						.						100	86	91					7																	31732136		2203	4300	6503	SO:0001630	splice_region_variant	10842	exon2			CCACTTAGGTAAA	AF071789	CCDS5436.1, CCDS47570.1	7p15	2012-04-17	2011-10-11	2011-10-11	ENSG00000106341	ENSG00000106341		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16973	protein-coding gene	gene with protein product	"G-substrate"	604088	"chromosome 7 open reading frame 16"	C7orf16		10051666, 9920894	Standard	NM_006658		Approved	GSBS	uc003tcl.3	O96001	OTTHUMG00000128629	ENST00000342032.3:c.82+1A>T	chr7.hg19:g.31732136A>T		73.0	0.0		63.0	40.0	NM_006658	B4DE58|Q9UDQ0	Missense_Mutation	SNP	ENST00000342032.3	hg19	CCDS5436.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.584144	0.46110	.	.	ENSG00000106341	ENST00000342032;ENST00000409146	T;T	0.35973	1.28;1.37	6.17	-2.02	0.07388	.	0.577406	0.16632	N	0.206029	T	0.46678	0.1405	L	0.50333	1.59	0.33508	D	0.590766	D;D	0.67145	0.996;0.979	D;P	0.63877	0.919;0.839	T	0.59343	-0.7472	10	0.59425	D	0.04	.	12.5375	0.56150	0.6118:0.0:0.3882:0.0	.	27;27	B4DE58;O96001	.;PPR17_HUMAN	F	27	ENSP00000340125:L27F;ENSP00000386459:L27F	ENSP00000340125:L27F	L	+	3	2	C7orf16	31698661	1.000000	0.71417	0.934000	0.37439	0.262000	0.26303	1.756000	0.38390	-0.220000	0.09988	0.533000	0.62120	TTA	.	.		0.522	PPP1R17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250498.1	NM_006658	Missense_Mutation	T	31732136	A	T	31732136	5	4	189	1	0	0	0	0	0	0	1	0	2380	434	15	4	83	4	C7orf16	7	31732136	Splice_Site	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	8341036	31732136	127406527	88	27964										
DBNL	28988	hgsc.bcm.edu	37	chr7	44089828	44089828	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ttgtgtttcgtttcagggctCtctttacctatgaaggcaac	9	9	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr7:44089828C>T	ENST00000448521.1	+	2	186	c.88C>T	c.(88-90)Ctc>Ttc	p.L30F	DBNL_ENST00000452943.1_Missense_Mutation_p.L30F|DBNL_ENST00000494774.1_Missense_Mutation_p.L30F|DBNL_ENST00000468694.1_Missense_Mutation_p.L30F|DBNL_ENST00000440166.1_Intron|DBNL_ENST00000497184.1_3'UTR|DBNL_ENST00000456905.1_Missense_Mutation_p.L30F|DBNL_ENST00000490734.2_5'UTR	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	30	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)			breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						TTTCAGGGCTCTCTTTACCTA	0.532																																					p.L30F	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											.	DBNL	26	.	0			c.C88T						.						171	148	156					7																	44089828		2203	4300	6503	SO:0001583	missense	28988	exon2			AGGGCTCTCTTTA	AF151364	CCDS34622.1, CCDS34623.1, CCDS47579.1, CCDS64633.1, CCDS64634.1	7p13	2004-07-22			ENSG00000136279	ENSG00000136279			2696	protein-coding gene	gene with protein product		610106				10087302	Standard	NM_014063		Approved	SH3P7, HIP-55	uc003tjq.4	Q9UJU6	OTTHUMG00000155350	ENST00000448521.1:c.88C>T	chr7.hg19:g.44089828C>T	ENSP00000411701:p.Leu30Phe	82.0	0.0		99.0	24.0	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Missense_Mutation	SNP	ENST00000448521.1	hg19	CCDS34623.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.013445	0.75161	.	.	ENSG00000136279	ENST00000448521;ENST00000456905;ENST00000452943;ENST00000468694;ENST00000494774	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.41	3.28	0.37604	Actin-binding, cofilin/tropomyosin type (3);	0.000000	0.64402	D	0.000011	T	0.70133	0.3189	M	0.92412	3.305	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.999;1.0	T	0.78069	-0.2348	10	0.72032	D	0.01	-33.5727	12.7176	0.57123	0.0:0.8406:0.0:0.1594	.	30;30;30;30;30	B4DDP6;B4DDD6;Q9UJU6-3;Q9UJU6;Q9UJU6-2	.;.;.;DBNL_HUMAN;.	F	30	ENSP00000411701:L30F;ENSP00000416421:L30F;ENSP00000405343:L30F;ENSP00000417653:L30F;ENSP00000419992:L30F	ENSP00000390397:L30F	L	+	1	0	DBNL	44056353	0.946000	0.32159	0.997000	0.53966	0.997000	0.91878	1.634000	0.37123	1.305000	0.44909	0.650000	0.86243	CTC	.	.		0.532	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063		T	44089828	C	T	44089828	3	4	189	1	0	0	0	0	1	0	0	0	4257	913	32	3	94	3	DBNL	7	44089828	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	12357692	44089828	115048835	89	27965										
FBXL13	222235	hgsc.bcm.edu	37	chr7	102603993	102603993	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tacttactgacagatctgaaAgttttgggtcggagaagaca	11	6	1	5			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr7:102603993A>T	ENST00000313221.4	-	8	1137	c.711T>A	c.(709-711)acT>acA	p.T237T	FBXL13_ENST00000471074.1_5'UTR|FBXL13_ENST00000455112.2_Silent_p.T237T|FBXL13_ENST00000379308.3_Silent_p.T237T|FBXL13_ENST00000379305.3_Silent_p.T237T|FBXL13_ENST00000393772.2_Silent_p.T237T|FBXL13_ENST00000379306.3_Silent_p.T237T|FBXL13_ENST00000436908.1_Silent_p.T237T|FBXL13_ENST00000456695.1_Silent_p.T237T	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	237										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						CAGATCTGAAAGTTTTGGGTC	0.328																																					p.T237T		Atlas-SNP	.											.	FBXL13	65	.	0			c.T711A						.						80	82	81					7																	102603993		2203	4300	6503	SO:0001819	synonymous_variant	222235	exon8			TCTGAAAGTTTTG	BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"F-boxes / Leucine-rich repeats"	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.711T>A	chr7.hg19:g.102603993A>T		46.0	0.0		45.0	11.0	NM_001111038	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Silent	SNP	ENST00000313221.4	hg19	CCDS5726.1																																																																																			.	.		0.328	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032		T	102603993	A	T	102603993	2	4	189	1	0	0	0	0	0	0	0	1	5717	59	3	4		4	FBXL13	7	102603993	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	58514165	102603993	56534670	90	27966										
LAMB1	3912	hgsc.bcm.edu	37	chr7	107635345	107635345	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ttcttaccttgaaagtcattAtgagatgagtaaaatggaat	8	4	2	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr7:107635345A>C	ENST00000222399.6	-	5	640	c.410T>G	c.(409-411)aTa>aGa	p.I137R	LAMB1_ENST00000393561.1_Missense_Mutation_p.I161R|LAMB1_ENST00000393560.1_Missense_Mutation_p.I137R	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	137	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GAAAGTCATTATGAGATGAGT	0.343																																					p.I137R		Atlas-SNP	.											.	LAMB1	185	.	0			c.T410G						.						100	97	98					7																	107635345		2203	4300	6503	SO:0001583	missense	3912	exon5			GTCATTATGAGAT	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.410T>G	chr7.hg19:g.107635345A>C	ENSP00000222399:p.Ile137Arg	49.0	0.0		43.0	23.0	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	hg19	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.678252	0.88542	.	.	ENSG00000091136	ENST00000393561;ENST00000222399;ENST00000393560	T;T;T	0.76968	-1.06;-1.06;-1.06	5.95	5.95	0.96441	Laminin, N-terminal (3);	.	.	.	.	D	0.86986	0.6065	M	0.67625	2.065	0.80722	D	1	D;D;D	0.76494	0.994;0.999;0.999	D;D;D	0.76071	0.963;0.987;0.957	D	0.88158	0.2855	9	0.87932	D	0	.	16.0971	0.81132	1.0:0.0:0.0:0.0	.	137;137;161	E7EPA6;P07942;G3XAI2	.;LAMB1_HUMAN;.	R	161;137;137	ENSP00000377191:I161R;ENSP00000222399:I137R;ENSP00000377190:I137R	ENSP00000222399:I137R	I	-	2	0	LAMB1	107422581	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.279000	0.76181	0.533000	0.62120	ATA	.	.		0.343	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		C	107635345	A	C	107635345	3	2	189	1	0	0	0	0	1	0	0	0	8619	449	16	5	5070	5	LAMB1	7	107635345	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	5031352	107635345	51503318	91	27967										
LMOD2	442721	hgsc.bcm.edu	37	chr7	123303032	123303032	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aacattgcagaagtcatcaaAcaacaggagagtgcccaacg	9	10	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr7:123303032A>G	ENST00000458573.2	+	2	1549	c.1392A>G	c.(1390-1392)aaA>aaG	p.K464K	LMOD2_ENST00000456238.2_Intron	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	464						cytoskeleton (GO:0005856)											AAGTCATCAAACAACAGGAGA	0.448																																					p.K464K		Atlas-SNP	.											.	LMOD2	62	.	0			c.A1392G						.						36	33	34					7																	123303032		1802	4015	5817	SO:0001819	synonymous_variant	442721	exon2			CATCAAACAACAG	AC006333	CCDS47693.1	7q31.32	2008-08-08			ENSG00000170807	ENSG00000170807			6648	protein-coding gene	gene with protein product		608006					Standard	NM_207163		Approved		uc003vky.2	Q6P5Q4	OTTHUMG00000157149	ENST00000458573.2:c.1392A>G	chr7.hg19:g.123303032A>G		151.0	0.0		128.0	59.0	NM_207163	A4D0W9|A4D0Y2|Q8WVJ8	Silent	SNP	ENST00000458573.2	hg19	CCDS47693.1																																																																																			.	.		0.448	LMOD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348525.1			G	123303032	A	G	123303032	2	3	189	1	0	0	0	0	0	0	0	1	8866	40	2	2		2	LMOD2	7	123303032	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	15667687	123303032	35835631	92	27968										
CALU	813	hgsc.bcm.edu	37	chr7	128407568	128407568	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gaatgggtaaagacagagcgAgagcagtttgttgagtttcg	15	4	0	4			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr7:128407568A>T	ENST00000249364.4	+	6	804	c.702A>T	c.(700-702)cgA>cgT	p.R234R	CALU_ENST00000479257.1_Silent_p.R242R|CALU_ENST00000542996.2_Silent_p.R242R|CALU_ENST00000538546.1_Silent_p.R83R|CALU_ENST00000535011.2_Intron|CALU_ENST00000449187.2_Silent_p.R234R|CALU_ENST00000535623.1_3'UTR	NM_001219.4	NP_001210.1	O43852	CALU_HUMAN	calumenin	234	EF-hand 5. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)			kidney(2)|large_intestine(3)|lung(5)	10						AGACAGAGCGAGAGCAGTTTG	0.458																																					p.R242R		Atlas-SNP	.											.	CALU	42	.	0			c.A726T						.						192	181	185					7																	128407568		2203	4300	6503	SO:0001819	synonymous_variant	813	exon7			AGAGCGAGAGCAG	AF013759	CCDS5805.1, CCDS47703.1, CCDS56506.1, CCDS56507.1, CCDS56508.1	7q32	2013-01-10			ENSG00000128595	ENSG00000128595		"EF-hand domain containing"	1458	protein-coding gene	gene with protein product		603420				9598325	Standard	NM_001219		Approved		uc003vnq.3	O43852	OTTHUMG00000158274	ENST00000249364.4:c.702A>T	chr7.hg19:g.128407568A>T		179.0	0.0		115.0	52.0	NM_001199671	B3KPG9|D6QS48|D6QS49|D6QS50|D6QS51|D6QS52|D6QS53|D6QS54|D6QS55|D6QS56|D6QS57|D6QS58|D6QS59|F5H1Q9|F5H879|O60456|Q6FHB9|Q96RL3|Q9NR43	Silent	SNP	ENST00000249364.4	hg19	CCDS5805.1	.	.	.	.	.	.	.	.	.	.	A	11.43	1.635997	0.29068	.	.	ENSG00000128595	ENST00000537014;ENST00000493278	.	.	.	5.44	-1.8	0.07907	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.044	5.2574	0.15553	0.5276:0.0:0.3338:0.1386	.	.	.	.	X	167;66	.	ENSP00000417973:R66X	R	+	1	2	CALU	128194804	0.954000	0.32549	0.999000	0.59377	0.997000	0.91878	0.128000	0.15810	0.042000	0.15717	0.460000	0.39030	AGA	.	.		0.458	CALU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350533.1	NM_001219		T	128407568	A	T	128407568	2	4	189	1	0	0	0	0	0	0	0	1	2596	291	11	4		4	CALU	7	128407568	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	5104536	128407568	30731095	93	27969										
TNPO3	23534	hgsc.bcm.edu	37	chr7	128612495	128612495	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cttacatcattggctaccccTgtatgaatgaggtctcgtag	9	10	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr7:128612495T>A	ENST00000265388.5	-	19	2558	c.2415A>T	c.(2413-2415)acA>acT	p.T805T	RN7SL306P_ENST00000492941.2_RNA|TNPO3_ENST00000471234.1_Silent_p.T741T|TNPO3_ENST00000393245.1_Silent_p.T839T|TNPO3_ENST00000471166.1_Silent_p.T839T|TNPO3_ENST00000482320.1_Silent_p.T739T			Q9Y5L0	TNPO3_HUMAN	transportin 3	805					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						TGGCTACCCCTGTATGAATGA	0.433																																					p.T805T	Pancreas(147;583 2585 39696 52331)	Atlas-SNP	.											TNPO3_ENST00000393245,rectum,carcinoma,0,2	TNPO3	148	.	0			c.A2415T						.						97	91	93					7																	128612495		2203	4300	6503	SO:0001819	synonymous_variant	23534	exon19			TACCCCTGTATGA	AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"Importins"	17103	protein-coding gene	gene with protein product	"importin 12"	610032	"limb girdle muscular dystrophy 1F (autosomal dominant)"	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.2415A>T	chr7.hg19:g.128612495T>A		62.0	0.0		49.0	19.0	NM_012470	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Silent	SNP	ENST00000265388.5	hg19	CCDS5809.1																																																																																			.	.		0.433	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470		A	128612495	T	A	128612495	2	1	189	1	0	0	0	0	0	0	0	1	16352	1567	55	4		4	TNPO3	7	128612495	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	204927	128612495	30526168	94	27970										
ADCK2	90956	hgsc.bcm.edu	37	chr7	140373721	140373721	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggggatgactgggggagcatCctctcttttgagaaccggga	16	8	1	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr7:140373721C>T	ENST00000072869.4	+	1	769	c.591C>T	c.(589-591)atC>atT	p.I197I	ADCK2_ENST00000476491.1_Silent_p.I197I	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	197						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15	Melanoma(164;0.00956)					GGGGGAGCATCCTCTCTTTTG	0.592																																					p.I197I		Atlas-SNP	.											.	ADCK2	37	.	0			c.C591T						.						58	63	61					7																	140373721		2203	4300	6503	SO:0001819	synonymous_variant	90956	exon1			GAGCATCCTCTCT	AF131745	CCDS5861.1	7q34	2003-07-21			ENSG00000133597	ENSG00000133597			19039	protein-coding gene	gene with protein product							Standard	NM_052853		Approved	MGC20727	uc003vvy.1	Q7Z695	OTTHUMG00000157409	ENST00000072869.4:c.591C>T	chr7.hg19:g.140373721C>T		56.0	0.0		36.0	13.0	NM_052853	Q96CN6|Q9Y6T5	Silent	SNP	ENST00000072869.4	hg19	CCDS5861.1	.	.	.	.	.	.	.	.	.	.	C	5.504	0.278019	0.10403	.	.	ENSG00000133597	ENST00000483369	.	.	.	4.63	3.69	0.42338	.	.	.	.	.	T	0.57592	0.2064	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.52682	-0.8543	4	.	.	.	-15.8898	7.7262	0.28761	0.0:0.7473:0.1595:0.0932	.	.	.	.	S	35	.	.	P	+	1	0	ADCK2	140020190	0.998000	0.40836	0.180000	0.23079	0.363000	0.29612	0.920000	0.28705	0.859000	0.35456	-0.367000	0.07326	CCT	.	.		0.592	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853		T	140373721	C	T	140373721	2	4	189	1	0	0	0	0	0	0	0	1	289	845	30	3		3	ADCK2	7	140373721	Silent	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	11761226	140373721	18764942	95	27971										
KEL	3792	hgsc.bcm.edu	37	chr7	142639612	142639612	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gccgtaacagcctcttgctgTatgcctgggtaggggtgggt	16	9	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr7:142639612T>C	ENST00000355265.2	-	18	2420	c.1946A>G	c.(1945-1947)tAc>tGc	p.Y649C		NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	649					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					CCTCTTGCTGTATGCCTGGGT	0.587																																					p.Y649C		Atlas-SNP	.											.	KEL	128	.	0			c.A1946G						.						55	37	43					7																	142639612		2203	4298	6501	SO:0001583	missense	3792	exon18			TTGCTGTATGCCT	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"CD molecules", "Blood group antigens"	6308	protein-coding gene	gene with protein product		613883	"Kell blood group", "Kell blood group, metalloendopeptidase"			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1946A>G	chr7.hg19:g.142639612T>C	ENSP00000347409:p.Tyr649Cys	54.0	0.0		45.0	27.0	NM_000420	B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	hg19	CCDS34766.1	.	.	.	.	.	.	.	.	.	.	T	12.96	2.095114	0.36952	.	.	ENSG00000197993	ENST00000355265	D	0.88277	-2.36	4.34	4.34	0.51931	Peptidase M13, neprilysin, C-terminal (1);	0.000000	0.43579	D	0.000555	D	0.95513	0.8542	H	0.95745	3.715	0.49915	D	0.999836	D	0.89917	1.0	D	0.97110	1.0	D	0.95757	0.8797	10	0.87932	D	0	-6.3936	9.8525	0.41066	0.0:0.0:0.0:1.0	.	649	P23276	KELL_HUMAN	C	649	ENSP00000347409:Y649C	ENSP00000347409:Y649C	Y	-	2	0	KEL	142349734	0.992000	0.36948	0.879000	0.34478	0.170000	0.22686	3.764000	0.55264	1.819000	0.53055	0.533000	0.62120	TAC	.	.		0.587	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		C	142639612	T	C	142639612	3	2	189	1	0	0	0	0	1	0	0	0	8151	1638	57	2	260	2	KEL	7	142639612	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	2265891	142639612	16499051	96	27972										
NPM2	10361	hgsc.bcm.edu	37	chr8	21891622	21891622	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tttcccatgctattacagaaGcatcagacctaacctgggag	8	11	1	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr8:21891622G>T	ENST00000397940.1	+	6	1382	c.367G>T	c.(367-369)Gca>Tca	p.A123S	NPM2_ENST00000521157.1_Missense_Mutation_p.A123S|NPM2_ENST00000381530.5_Intron|NPM2_ENST00000518119.1_Missense_Mutation_p.A123S|NPM2_ENST00000520180.1_3'UTR|NPM2_ENST00000289820.6_Missense_Mutation_p.A123S|snoU13_ENST00000459495.1_RNA			Q86SE8	NPM2_HUMAN	nucleophosmin/nucleoplasmin 2	123					chromatin remodeling (GO:0006338)|embryo development (GO:0009790)|oocyte differentiation (GO:0009994)|positive regulation of catalytic activity (GO:0043085)|positive regulation of DNA replication (GO:0045740)|positive regulation of meiosis (GO:0045836)|protein homooligomerization (GO:0051260)|regulation of exit from mitosis (GO:0007096)|single fertilization (GO:0007338)	cytoplasmic chromatin (GO:0000789)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleic acid binding (GO:0003676)			large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	4				Colorectal(74;8.48e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0618)		TATTACAGAAGCATCAGACCT	0.517																																					p.A123S		Atlas-SNP	.											.	NPM2	12	.	0			c.G367T						.						80	81	80					8																	21891622		2203	4300	6503	SO:0001583	missense	10361	exon6			ACAGAAGCATCAG	AY262113	CCDS6018.1, CCDS75703.1	8p21.3	2009-08-27	2009-08-27		ENSG00000158806	ENSG00000158806			7930	protein-coding gene	gene with protein product		608073				12714744	Standard	NM_182795		Approved		uc003xae.3	Q86SE8	OTTHUMG00000131129	ENST00000397940.1:c.367G>T	chr8.hg19:g.21891622G>T	ENSP00000381032:p.Ala123Ser	38.0	0.0		62.0	27.0	NM_182795	B3KSU0|D3DSQ8|Q6NVH6	Missense_Mutation	SNP	ENST00000397940.1	hg19	CCDS6018.1	.	.	.	.	.	.	.	.	.	.	G	2.746	-0.261090	0.05791	.	.	ENSG00000158806	ENST00000521157;ENST00000397940;ENST00000522813;ENST00000518119;ENST00000289820	T;T;T;T;T	0.41758	1.64;1.64;0.99;1.64;1.64	4.76	-2.33	0.06724	Nucleoplasmin core (2);	1.123880	0.06755	N	0.780735	T	0.17831	0.0428	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.16482	-1.0401	10	0.33940	T	0.23	1.8013	0.8021	0.01077	0.3751:0.1707:0.2891:0.1652	.	123	Q86SE8	NPM2_HUMAN	S	123	ENSP00000429413:A123S;ENSP00000381032:A123S;ENSP00000428016:A123S;ENSP00000427741:A123S;ENSP00000289820:A123S	ENSP00000289820:A123S	A	+	1	0	NPM2	21947568	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.542000	0.06091	-0.199000	0.10317	-1.271000	0.01417	GCA	.	.		0.517	NPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253810.2	NM_182795		T	21891622	G	T	21891622	3	4	189	1	0	0	0	0	1	0	0	0	10597	971	34	3	385	3	NPM2	8	21891622	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10		21891622	124472400	97	27973										
KLHL38	340359	hgsc.bcm.edu	37	chr8	124658143	124658143	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gtccgtggtcagccgccgccCgcccgtcacgtagagtttgt	13	15	2	1	rs559948746		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr8:124658143C>T	ENST00000325995.7	-	3	1605	c.1582G>A	c.(1582-1584)Ggg>Agg	p.G528R	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	528										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						AGCCGCCGCCCGCCCGTCACG	0.582													C|||	1	0.000199681	0	0	5008	,	,		18570	0		0	False		,,,				2504	0.001				p.G528R		Atlas-SNP	.											.	KLHL38	81	.	0			c.G1582A						.						96	112	106					8																	124658143		2098	4222	6320	SO:0001583	missense	340359	exon3			GCCGCCCGCCCGT		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"Kelch-like", "BTB/POZ domain containing"	34435	protein-coding gene	gene with protein product			"kelch-like 38 (Drosophila)"				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1582G>A	chr8.hg19:g.124658143C>T	ENSP00000321475:p.Gly528Arg	103.0	0.0		108.0	59.0	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	hg19	CCDS43766.1	.	.	.	.	.	.	.	.	.	.	C	32	5.107670	0.94292	.	.	ENSG00000175946	ENST00000325995	D	0.99494	-6.01	5.0	5.0	0.66597	Kelch-type beta propeller (1);	0.049697	0.85682	D	0.000000	D	0.99743	0.9898	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97021	0.9743	10	0.87932	D	0	.	18.2916	0.90133	0.0:1.0:0.0:0.0	.	528	Q2WGJ6	KLH38_HUMAN	R	528	ENSP00000321475:G528R	ENSP00000321475:G528R	G	-	1	0	KLHL38	124727324	1.000000	0.71417	0.985000	0.45067	0.940000	0.58332	7.818000	0.86416	2.323000	0.78572	0.455000	0.32223	GGG	.	.		0.582	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1			T	124658143	C	T	124658143	3	4	189	1	0	0	0	0	1	0	0	0	8399	652	23	1	167	1	KLHL38	8	124658143	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	102766521	124658143	21705879	98	27974										
ANXA13	312	hgsc.bcm.edu	37	chr8	124693593	124693593	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctttgctttgatcccctgaaGgtccacctgtagaaaaaata	7	10	0	3	rs531775603		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr8:124693593G>T	ENST00000419625.1	-	11	910	c.838C>A	c.(838-840)Ctt>Att	p.L280I	ANXA13_ENST00000262219.6_Missense_Mutation_p.L321I	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	280					cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			ATCCCCTGAAGGTCCACCTGT	0.443													G|||	1	0.000199681	8e-04	0	5008	,	,		18868	0		0	False		,,,				2504	0				p.L321I		Atlas-SNP	.											.	ANXA13	38	.	0			c.C961A						.						144	153	150					8																	124693593		2203	4300	6503	SO:0001583	missense	312	exon12			CCTGAAGGTCCAC	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"Annexins"	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.838C>A	chr8.hg19:g.124693593G>T	ENSP00000390809:p.Leu280Ile	56.0	0.0		49.0	7.0	NM_001003954	Q9BQR5	Missense_Mutation	SNP	ENST00000419625.1	hg19	CCDS47917.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.374909	0.42105	.	.	ENSG00000104537	ENST00000262219;ENST00000419625	T;T	0.05025	3.51;3.51	5.57	4.69	0.59074	Annexin repeat, conserved site (1);	0.186113	0.48767	D	0.000170	T	0.09335	0.0230	L	0.45698	1.435	0.46609	D	0.999125	P;P	0.52842	0.737;0.956	B;B	0.44108	0.36;0.441	T	0.03706	-1.1011	10	0.87932	D	0	.	13.7173	0.62705	0.0:0.1547:0.8453:0.0	.	280;321	P27216;P27216-2	ANX13_HUMAN;.	I	321;280	ENSP00000262219:L321I;ENSP00000390809:L280I	ENSP00000262219:L321I	L	-	1	0	ANXA13	124762774	1.000000	0.71417	0.998000	0.56505	0.044000	0.14063	4.711000	0.61881	1.347000	0.45714	0.655000	0.94253	CTT	.	.		0.443	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306		T	124693593	G	T	124693593	3	4	189	1	0	0	0	0	1	0	0	0	717	1000	35	3	116	3	ANXA13	8	124693593	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	35450	124693593	21670429	99	27975										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125072802	125072802	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tcctcaggttctcttctgggGagttcgggaaatgaagaagg	14	7	3	2	rs373037712		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr8:125072802G>T	ENST00000522917.1	+	24	3205	c.2999G>T	c.(2998-3000)gGa>gTa	p.G1000V	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6-AS2_ENST00000601180.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.G1000V	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1000						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CTCTTCTGGGGAGTTCGGGAA	0.567																																					p.G1000V		Atlas-SNP	.											.	FER1L6	268	.	0			c.G2999T						.	G	VAL/GLY	0,4406		0,0,2203	149	122	131		2999	5.7	1	8		131	1,8599	1.2+/-3.3	0,1,4299	no	missense	FER1L6	NM_001039112.2	109	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging	1000/1858	125072802	1,13005	2203	4300	6503	SO:0001583	missense	654463	exon24			TCTGGGGAGTTCG	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.2999G>T	chr8.hg19:g.125072802G>T	ENSP00000428280:p.Gly1000Val	81.0	0.0		91.0	13.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.541327	0.85917	0.0	1.16E-4	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.85556	-2.0;-2.0	5.66	5.66	0.87406	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	U	0.000000	D	0.94328	0.8177	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95032	0.8170	10	0.87932	D	0	-5.0631	19.329	0.94278	0.0:0.0:1.0:0.0	.	1000	Q2WGJ9	FR1L6_HUMAN	V	1000	ENSP00000428280:G1000V;ENSP00000381982:G1000V	ENSP00000381982:G1000V	G	+	2	0	FER1L6	125141983	1.000000	0.71417	0.997000	0.53966	0.714000	0.41099	7.910000	0.87451	2.661000	0.90470	0.655000	0.94253	GGA	.	.		0.567	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		T	125072802	G	T	125072802	3	4	189	1	0	0	0	0	1	0	0	0	5823	1174	41	3	3089	3	FER1L6	8	125072802	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	379209	125072802	21291220	100	27976										
HSF1	3297	hgsc.bcm.edu	37	chr8	145533158	145533158	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cagatggcttccggaaagtgGtccacatcgagcagggcggc	15	11	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr8:145533158G>T	ENST00000528838.1	+	3	404	c.244G>T	c.(244-246)Gtc>Ttc	p.V82F	HSF1_ENST00000400780.4_Missense_Mutation_p.V17F	NM_005526.2	NP_005517.1	Q00613	HSF1_HUMAN	heat shock transcription factor 1	82					cellular response to heat (GO:0034605)|defense response (GO:0006952)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|female meiotic division (GO:0007143)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)|response to lipopolysaccharide (GO:0032496)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pronucleus (GO:0045120)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)|urinary_tract(2)	11	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)			CCGGAAAGTGGTCCACATCGA	0.627																																					p.V82F		Atlas-SNP	.											.	HSF1	29	.	0			c.G244T						.						99	102	101					8																	145533158		2203	4296	6499	SO:0001583	missense	3297	exon3			AAAGTGGTCCACA	M64673	CCDS6419.1	8q24.3	2014-04-10			ENSG00000185122	ENSG00000185122			5224	protein-coding gene	gene with protein product		140580				1871105	Standard	NM_005526		Approved	HSTF1	uc003zbt.4	Q00613	OTTHUMG00000174604	ENST00000528838.1:c.244G>T	chr8.hg19:g.145533158G>T	ENSP00000431512:p.Val82Phe	175.0	1.0		204.0	118.0	NM_005526	A8K4L0|A8MW26|Q53XT4	Missense_Mutation	SNP	ENST00000528838.1	hg19	CCDS6419.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.792432	0.90453	.	.	ENSG00000185122	ENST00000528838;ENST00000533240;ENST00000400780	D;D;D	0.90133	-2.62;-2.62;-2.62	5.48	4.61	0.57282	Winged helix-turn-helix transcription repressor DNA-binding (1);Heat shock factor (HSF)-type, DNA-binding (2);	0.000000	0.85682	D	0.000000	D	0.94703	0.8291	M	0.81497	2.545	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.94968	0.8114	10	0.87932	D	0	-15.9657	12.3809	0.55305	0.0817:0.0:0.9183:0.0	.	82	Q00613	HSF1_HUMAN	F	82;17;17	ENSP00000431512:V82F;ENSP00000436616:V17F;ENSP00000383590:V17F	ENSP00000383590:V17F	V	+	1	0	HSF1	145503966	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.886000	0.63149	1.338000	0.45544	-0.124000	0.14976	GTC	.	.		0.627	HSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382053.1	NM_005526		T	145533158	G	T	145533158	3	4	189	1	0	0	0	0	1	0	0	0	7404	1261	44	3	254	3	HSF1	8	145533158	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	20460356	145533158	830864	101	27977										
LRRC24	441381	hgsc.bcm.edu	37	chr8	145748008	145748008	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gaacatctcgtggccgcgctCgtcgcggagctcctctagct	12	15	2	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr8:145748008C>G	ENST00000529415.2	-	5	1510	c.1393G>C	c.(1393-1395)Gag>Cag	p.E465Q	LRRC14_ENST00000528528.1_3'UTR|LRRC14_ENST00000292524.1_3'UTR|LRRC24_ENST00000533758.1_Missense_Mutation_p.E462Q			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	465						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TGGCCGCGCTCGTCGCGGAGC	0.697																																					p.E465Q		Atlas-SNP	.											.	LRRC24	11	.	0			c.G1393C						.						15	16	15					8																	145748008		2176	4282	6458	SO:0001583	missense	441381	exon5			CGCGCTCGTCGCG	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"Immunoglobulin superfamily / I-set domain containing"	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.1393G>C	chr8.hg19:g.145748008C>G	ENSP00000434849:p.Glu465Gln	91.0	0.0		92.0	25.0	NM_001024678		Missense_Mutation	SNP	ENST00000529415.2	hg19	CCDS34969.1	.	.	.	.	.	.	.	.	.	.	C	35	5.446886	0.96205	.	.	ENSG00000254402	ENST00000529415;ENST00000533758	T;T	0.60548	0.3;0.18	4.92	4.92	0.64577	.	0.225721	0.44483	N	0.000460	T	0.62648	0.2445	L	0.29908	0.895	0.58432	D	0.999995	D;D	0.71674	0.998;0.997	P;P	0.61003	0.882;0.766	T	0.65747	-0.6093	10	0.62326	D	0.03	.	15.6382	0.76973	0.0:1.0:0.0:0.0	.	462;465	G3V1D8;Q50LG9	.;LRC24_HUMAN	Q	465;462	ENSP00000434849:E465Q;ENSP00000435653:E462Q	ENSP00000434849:E465Q	E	-	1	0	LRRC24	145718816	1.000000	0.71417	0.987000	0.45799	0.863000	0.49368	3.336000	0.52113	2.565000	0.86533	0.561000	0.74099	GAG	.	.		0.697	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678		G	145748008	C	G	145748008	3	3	189	1	0	0	0	0	1	0	0	0	8988	893	31	4	152	4	LRRC24	8	145748008	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	214850	145748008	616014	102	27978										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20944683	20944683	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctcatgagccacagcagccaAatgcagtcccgcgttcacgt	9	15	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr9:20944683A>T	ENST00000380249.1	+	31	3829	c.3465A>T	c.(3463-3465)caA>caT	p.Q1155H	FOCAD_ENST00000605086.1_Missense_Mutation_p.Q591H|FOCAD_ENST00000338382.6_Missense_Mutation_p.Q1155H	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1155						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											ACAGCAGCCAAATGCAGTCCC	0.507																																					p.Q1155H		Atlas-SNP	.											.	.	.	.	0			c.A3465T						.						132	113	119					9																	20944683		2203	4300	6503	SO:0001583	missense	54914	exon31			CAGCCAAATGCAG	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.3465A>T	chr9.hg19:g.20944683A>T	ENSP00000369599:p.Gln1155His	74.0	0.0		100.0	25.0	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	hg19	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.891690	0.33442	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.69435	-0.4;-0.4	5.87	-6.82	0.01698	Armadillo-type fold (1);	0.385440	0.32190	N	0.006445	T	0.40094	0.1103	L	0.40543	1.245	0.20196	N	0.999925	B	0.09022	0.002	B	0.06405	0.002	T	0.41787	-0.9489	10	0.11794	T	0.64	-21.7829	2.4296	0.04468	0.364:0.3053:0.2347:0.096	.	1155	Q5VW36	K1797_HUMAN	H	1155	ENSP00000369599:Q1155H;ENSP00000344307:Q1155H	ENSP00000344307:Q1155H	Q	+	3	2	KIAA1797	20934683	0.017000	0.18338	0.000000	0.03702	0.787000	0.44495	-0.243000	0.08915	-1.451000	0.01933	0.533000	0.62120	CAA	.	.		0.507	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		T	20944683	A	T	20944683	3	4	189	1	0	0	0	0	1	0	0	0	8267	11	1	4	3575	4	KIAA1797	9	20944683	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10		20944683	120268748	103	27979										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79324389	79324389	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aggaatcttcccaaggaactAggacatctgaccctcctttc	7	13	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr9:79324389A>T	ENST00000376718.3	-	8	2924	c.2801T>A	c.(2800-2802)cTa>cAa	p.L934Q	PRUNE2_ENST00000428286.1_Missense_Mutation_p.L575Q	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	934					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CCAAGGAACTAGGACATCTGA	0.408																																					p.L934Q		Atlas-SNP	.											.	PRUNE2	331	.	0			c.T2801A						.						237	221	226					9																	79324389		1568	3582	5150	SO:0001583	missense	158471	exon8			GGAACTAGGACAT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.2801T>A	chr9.hg19:g.79324389A>T	ENSP00000365908:p.Leu934Gln	94.0	0.0		98.0	63.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	A	14.29	2.490692	0.44249	.	.	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.59083	0.31;0.29	5.89	3.25	0.37280	.	0.449885	0.16510	N	0.211288	T	0.58581	0.2132	L	0.29908	0.895	0.23314	N	0.997924	D	0.57899	0.981	P	0.57371	0.819	T	0.51036	-0.8756	10	0.87932	D	0	-3.5622	11.076	0.48032	0.855:0.0:0.145:0.0	.	934	Q8WUY3	PRUN2_HUMAN	Q	934;575;933	ENSP00000365908:L934Q;ENSP00000397425:L575Q	ENSP00000365908:L934Q	L	-	2	0	PRUNE2	78514209	0.127000	0.22367	0.709000	0.30452	0.834000	0.47266	1.768000	0.38511	1.061000	0.40601	0.459000	0.35465	CTA	.	.		0.408	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		T	79324389	A	T	79324389	3	4	189	1	0	0	0	0	1	0	0	0	12653	420	15	4	6513	4	PRUNE2	9	79324389	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	58379706	79324389	61889042	104	27980										
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84606346	84606346	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctaaatcaagtctcaccatcTtgaagacttttccggaaatg	6	10	3	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr9:84606346T>A	ENST00000344803.2	+	4	1008	c.961T>A	c.(961-963)Ttg>Atg	p.L321M		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	321					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TCTCACCATCTTGAAGACTTT	0.478																																					p.L321M		Atlas-SNP	.											.	.	.	.	0			c.T961A						.						198	178	184					9																	84606346		1936	4124	6060	SO:0001583	missense	389763	exon4			ACCATCTTGAAGA		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.961T>A	chr9.hg19:g.84606346T>A	ENSP00000341988:p.Leu321Met	132.0	0.0		142.0	98.0	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	hg19	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.888117	0.33348	.	.	ENSG00000214929	ENST00000344803	T	0.09255	3.0	2.99	-2.87	0.05700	.	.	.	.	.	T	0.17704	0.0425	L	0.52573	1.65	0.09310	N	1	D	0.69078	0.997	D	0.64237	0.923	T	0.11036	-1.0604	9	0.49607	T	0.09	.	4.4836	0.11780	0.0:0.4578:0.2069:0.3353	.	321	Q6ZQQ2	F75D1_HUMAN	M	321	ENSP00000341988:L321M	ENSP00000341988:L321M	L	+	1	2	FAM75D1	83796166	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.729000	0.04920	-0.595000	0.05828	0.529000	0.55759	TTG	.	.		0.478	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84606346	T	A	84606346	3	1	189	1	0	0	0	0	1	0	0	0	5940	1606	56	4	975	4	FLJ46321	9	84606346	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	5281957	84606346	56607085	105	27981										
EPB41L4B	54566	hgsc.bcm.edu	37	chr9	111979288	111979288	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	agaggctgtagtttgagtggTgctggtgctgatgctgatgc	17	5	0	4			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr9:111979288T>C	ENST00000374566.3	-	16	2064	c.1547A>G	c.(1546-1548)cAc>cGc	p.H516R		NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	516	His-rich.				actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTTTGAgtggtgctggtgctg	0.572																																					p.H516R		Atlas-SNP	.											.	EPB41L4B	111	.	0			c.A1547G						.						120	122	121					9																	111979288		2182	4280	6462	SO:0001583	missense	54566	exon16			GAGTGGTGCTGGT	AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.1547A>G	chr9.hg19:g.111979288T>C	ENSP00000363694:p.His516Arg	86.0	0.0		105.0	27.0	NM_019114	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Missense_Mutation	SNP	ENST00000374566.3	hg19	CCDS43859.1	.	.	.	.	.	.	.	.	.	.	T	8.639	0.895563	0.17686	.	.	ENSG00000095203	ENST00000262536;ENST00000374566	D	0.83837	-1.77	4.12	2.95	0.34219	.	0.182117	0.26991	N	0.021466	T	0.64316	0.2587	N	0.14661	0.345	0.80722	D	1	B	0.13145	0.007	B	0.08055	0.003	T	0.49312	-0.8953	10	0.15499	T	0.54	.	6.8643	0.24084	0.206:0.0:0.0:0.794	.	516	Q9H329	E41LB_HUMAN	R	201;516	ENSP00000363694:H516R	ENSP00000262536:H201R	H	-	2	0	EPB41L4B	111019109	1.000000	0.71417	0.998000	0.56505	0.744000	0.42396	3.135000	0.50546	0.466000	0.27193	-0.417000	0.06048	CAC	.	.		0.572	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424		C	111979288	T	C	111979288	3	2	189	1	0	0	0	0	1	0	0	0	5158	1696	59	2	1199	2	EPB41L4B	9	111979288	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	27372942	111979288	29234143	106	27982										
MUSK	4593	hgsc.bcm.edu	37	chr9	113459680	113459681	+	Missense_Mutation	DNP	TA	TA	GT													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aaaaggaagatgcaggacagTatcgatgtgtggcaaaaaac							TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T|A	T|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr9:113459680_113459681TA>GT	ENST00000374448.4	+	5	696_697	c.562_563TA>GT	c.(562-564)TAt>GTt	p.Y188V	MUSK_ENST00000416899.2_Missense_Mutation_p.Y188V|MUSK_ENST00000189978.5_Missense_Mutation_p.Y188V|MUSK_ENST00000374439.1_Missense_Mutation_p.Y70V|MUSK_ENST00000374440.3_Missense_Mutation_p.Y70V	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	188	Ig-like 2.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						TGCAGGACAGTATCGATGTGTG	0.47																																					p.Y188D|p.Y188F		Atlas-SNP	.											.	MUSK	112	.	0			c.T562G|c.A563T						.																																			SO:0001583	missense	4593	exon5			GGACAGTATCGAT|GACAGTATCGATG	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	Exception_encountered	chr9.hg19:g.113459680_113459681delinsGT	ENSP00000363571:p.Tyr188Val	122.0|123.0	0.0		157.0|154.0	47.0|46.0	NM_001166281	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	hg19	CCDS48005.1																																																																																			.	.		0.47	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				GT	113459681	TA	GT	113459680	3	3	189	1	0	0	0	0	1	0	0	0	9998	1638	57	5	580	5	MUSK	9	113459680	Missense_Mutation	DNP	TA	TCGA-DD-AADF-01A-11D-A40R-10	1480392	113459680	27753751	107	27983										
LAMC3	10319	hgsc.bcm.edu	37	chr9	133936495	133936495	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ccaggtttctatggcaacccTttcgcgggccaagccgacga	11	14	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr9:133936495T>A	ENST00000361069.4	+	13	2365	c.2232T>A	c.(2230-2232)ccT>ccA	p.P744P	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	744	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		ATGGCAACCCTTTCGCGGGCC	0.632																																					p.P744P		Atlas-SNP	.											.	LAMC3	167	.	0			c.T2232A						.						79	70	73					9																	133936495		2203	4300	6503	SO:0001819	synonymous_variant	10319	exon13			CAACCCTTTCGCG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.2232T>A	chr9.hg19:g.133936495T>A		34.0	0.0		43.0	33.0	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	hg19	CCDS6938.1																																																																																			.	.		0.632	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059		A	133936495	T	A	133936495	2	1	189	1	0	0	0	0	0	0	0	1	8625	1596	56	4		4	LAMC3	9	133936495	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	20476815	133936495	7276936	108	27984										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138662770	138662770	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tcctgctgaacccggggcccCggcacatcctggccgcctct	11	19	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr9:138662770C>G	ENST00000263604.3	+	18	1780	c.1780C>G	c.(1780-1782)Cgg>Ggg	p.R594G	KCNT1_ENST00000487664.1_Missense_Mutation_p.R568G|KCNT1_ENST00000298480.5_Missense_Mutation_p.R613G|KCNT1_ENST00000488444.2_Missense_Mutation_p.R594G|KCNT1_ENST00000371757.2_Missense_Mutation_p.R613G|KCNT1_ENST00000486577.2_Missense_Mutation_p.R574G|KCNT1_ENST00000490355.2_Missense_Mutation_p.R594G|KCNT1_ENST00000491806.2_Missense_Mutation_p.R580G			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	594	RCK N-terminal.				potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		CCCGGGGCCCCGGCACATCCT	0.602																																					p.R613G		Atlas-SNP	.											.	KCNT1	139	.	0			c.C1837G						.						47	42	44					9																	138662770		2202	4300	6502	SO:0001583	missense	57582	exon18			GGGCCCCGGCACA	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.1780C>G	chr9.hg19:g.138662770C>G	ENSP00000263604:p.Arg594Gly	142.0	0.0		165.0	61.0	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	C	12.42	1.931698	0.34096	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T	0.24908	1.85;1.84;1.84;1.83	3.88	2.95	0.34219	.	0.000000	0.64402	U	0.000002	T	0.20414	0.0491	L	0.41236	1.265	0.58432	D	0.999997	B;B;B;B	0.21821	0.061;0.005;0.003;0.007	B;B;B;B	0.17979	0.02;0.018;0.019;0.008	T	0.04427	-1.0952	10	0.44086	T	0.13	-18.4168	10.7263	0.46070	0.3457:0.6543:0.0:0.0	.	580;613;568;594	C9JYL2;B9EGP2;G5E9V0;Q5JUK3	.;.;.;KCNT1_HUMAN	G	568;613;613;574;580;594;594;594	ENSP00000417851:R568G;ENSP00000298480:R613G;ENSP00000360822:R613G;ENSP00000263604:R594G	ENSP00000263604:R594G	R	+	1	2	KCNT1	137802591	0.371000	0.25056	0.695000	0.30226	0.966000	0.64601	0.987000	0.29603	0.794000	0.33899	0.467000	0.42956	CGG	.	.		0.602	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		G	138662770	C	G	138662770	3	3	189	1	0	0	0	0	1	0	0	0	8100	643	23	4	1907	4	KCNT1	9	138662770	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	4726275	138662770	2550661	109	27985										
CCDC3	83643	hgsc.bcm.edu	37	chr10	13040480	13040480	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tggcatcttggaaattgactCcgtgaggcaagaggttataa	12	6	1	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr10:13040480C>A	ENST00000378825.3	-	2	533	c.407G>T	c.(406-408)gGa>gTa	p.G136V	CCDC3_ENST00000378839.1_Missense_Mutation_p.G11V	NM_031455.3	NP_113643.1	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3	136						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	11		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			GAAATTGACTCCGTGAGGCAA	0.453																																					p.G136V		Atlas-SNP	.											.	CCDC3	27	.	0			c.G407T						.						119	108	111					10																	13040480		2203	4300	6503	SO:0001583	missense	83643	exon2			TTGACTCCGTGAG	BC051334	CCDS7093.1, CCDS60484.1	10p14	2004-02-13			ENSG00000151468	ENSG00000151468			23813	protein-coding gene	gene with protein product							Standard	NM_031455		Approved	DKFZp761F241	uc001ilq.1	Q9BQI4	OTTHUMG00000017689	ENST00000378825.3:c.407G>T	chr10.hg19:g.13040480C>A	ENSP00000368102:p.Gly136Val	70.0	0.0		96.0	23.0	NM_031455	Q5VYV8|Q5VYV9	Missense_Mutation	SNP	ENST00000378825.3	hg19	CCDS7093.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.407966	0.83340	.	.	ENSG00000151468	ENST00000378839;ENST00000378825	.	.	.	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.79656	0.4483	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82004	-0.0672	9	0.72032	D	0.01	-22.1565	17.7904	0.88551	0.0:1.0:0.0:0.0	.	136	Q9BQI4	CCDC3_HUMAN	V	11;136	.	ENSP00000368102:G136V	G	-	2	0	CCDC3	13080486	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.426000	0.80270	2.433000	0.82419	0.462000	0.41574	GGA	.	.		0.453	CCDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046829.1	NM_031455		A	13040480	C	A	13040480	3	1	189	1	0	0	0	0	1	0	0	0	2806	855	30	3	413	3	CCDC3	10	13040480	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10		13040480	122494267	110	27986										
FAM188A	80013	hgsc.bcm.edu	37	chr10	15863696	15863696	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cattagtgttaaaaatcctaCtgctgcttgttcatgtatac	6	8	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr10:15863696C>G	ENST00000277632.3	-	9	980	c.760G>C	c.(760-762)Gta>Cta	p.V254L	FAM188A_ENST00000477891.1_5'UTR	NM_024948.2	NP_079224.1	Q9H8M7	F188A_HUMAN	family with sequence similarity 188, member A	254					apoptotic process (GO:0006915)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	22						AAAAATCCTACTGCTGCTTGT	0.303																																					p.V254L	Pancreas(159;946 1953 2111 4475 22008)	Atlas-SNP	.											.	FAM188A	44	.	0			c.G760C						.						102	96	98					10																	15863696		2202	4300	6502	SO:0001583	missense	80013	exon9			ATCCTACTGCTGC	AK023459	CCDS7110.1	10p13	2009-07-14	2009-07-14	2009-07-14	ENSG00000148481	ENSG00000148481			23578	protein-coding gene	gene with protein product	"caspase recruitment domain containing pro-apoptotic protein", "CARD-containing protein"	611649	"chromosome 10 open reading frame 97"	C10orf97		12054670, 17652099	Standard	XM_005252600		Approved	FLJ13397, CARP, my042, DERP5	uc001iod.1	Q9H8M7	OTTHUMG00000017734	ENST00000277632.3:c.760G>C	chr10.hg19:g.15863696C>G	ENSP00000277632:p.Val254Leu	79.0	0.0		126.0	71.0	NM_024948	Q5SZ68|Q5SZ69|Q5SZ70|Q6IA40|Q6P7P0|Q7Z2S1|Q8WUF1|Q9H3I4	Missense_Mutation	SNP	ENST00000277632.3	hg19	CCDS7110.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.053020	0.55218	.	.	ENSG00000148481	ENST00000277632;ENST00000418767;ENST00000436829	T;T;T	0.34667	1.35;1.35;1.35	5.26	4.34	0.51931	.	0.115270	0.64402	D	0.000019	T	0.38268	0.1034	L	0.61218	1.895	0.80722	D	1	B	0.20780	0.048	B	0.27170	0.077	T	0.26258	-1.0108	10	0.42905	T	0.14	-16.4026	13.7485	0.62890	0.0:0.919:0.0:0.081	.	254	Q9H8M7	F188A_HUMAN	L	254;94;107	ENSP00000277632:V254L;ENSP00000388661:V94L;ENSP00000389883:V107L	ENSP00000277632:V254L	V	-	1	0	FAM188A	15903702	1.000000	0.71417	0.997000	0.53966	0.970000	0.65996	3.282000	0.51693	2.613000	0.88420	0.467000	0.42956	GTA	.	.		0.303	FAM188A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046990.2	NM_024948		G	15863696	C	G	15863696	3	3	189	1	0	0	0	0	1	0	0	0	5519	565	20	4	605	4	FAM188A	10	15863696	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	2823216	15863696	119671051	111	27987										
HNRNPF	3185	hgsc.bcm.edu	37	chr10	43883327	43883327	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tcacctccctcagggcccagCatcatggacacttgtcaggg	10	15	4	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr10:43883327C>A	ENST00000544000.1	-	4	413	c.6G>T	c.(4-6)atG>atT	p.M2I	HNRNPF_ENST00000443950.2_Missense_Mutation_p.M2I|HNRNPF_ENST00000357065.4_Missense_Mutation_p.M2I|HNRNPF_ENST00000356053.3_Missense_Mutation_p.M2I|HNRNPF_ENST00000498176.1_5'UTR|HNRNPF_ENST00000337970.3_Missense_Mutation_p.M2I	NM_001098207.1	NP_001091677.1	P52597	HNRPF_HUMAN	heterogeneous nuclear ribonucleoprotein F	2					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|urinary_tract(1)	19						CAGGGCCCAGCATCATGGACA	0.498																																					p.M2I		Atlas-SNP	.											.	HNRNPF	57	.	0			c.G6T						.						42	45	44					10																	43883327		2198	4300	6498	SO:0001583	missense	3185	exon4			GCCCAGCATCATG		CCDS7204.1	10q11.21	2013-02-12		2008-04-18	ENSG00000169813	ENSG00000169813		"RNA binding motif (RRM) containing"	5039	protein-coding gene	gene with protein product		601037		HNRPF		7499401	Standard	NM_001098208		Approved		uc001jas.2	P52597	OTTHUMG00000018029	ENST00000544000.1:c.6G>T	chr10.hg19:g.43883327C>A	ENSP00000438061:p.Met2Ile	85.0	0.0		75.0	43.0	NM_001098204	B3KM84|Q5T0N2|Q96AU2	Missense_Mutation	SNP	ENST00000544000.1	hg19	CCDS7204.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.017369	0.54576	.	.	ENSG00000169813	ENST00000544000;ENST00000443950;ENST00000356053;ENST00000357065;ENST00000337970	T;T;T;T;T	0.08896	3.04;3.04;3.04;3.04;3.04	4.17	4.17	0.49024	.	0.076578	0.56097	D	0.000033	T	0.20659	0.0497	L	0.34521	1.04	0.48762	D	0.999702	P	0.38800	0.648	D	0.66084	0.941	T	0.01405	-1.1363	10	0.87932	D	0	-29.7191	14.7967	0.69884	0.0:1.0:0.0:0.0	.	2	P52597	HNRPF_HUMAN	I	2	ENSP00000438061:M2I;ENSP00000400433:M2I;ENSP00000348345:M2I;ENSP00000349573:M2I;ENSP00000338477:M2I	ENSP00000338477:M2I	M	-	3	0	HNRNPF	43203333	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.661000	0.61518	2.615000	0.88500	0.650000	0.86243	ATG	.	.		0.498	HNRNPF-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047705.2			A	43883327	C	A	43883327	3	1	189	1	0	0	0	0	1	0	0	0	7274	710	25	3	1245	3	HNRNPF	10	43883327	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	28019631	43883327	91651420	112	27988										
DLG5	9231	hgsc.bcm.edu	37	chr10	79553847	79553847	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	atgcctctgagtcaccttgtCcctcaggtagatggggtctc	11	12	4	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr10:79553847C>T	ENST00000372391.2	-	31	5580	c.5575G>A	c.(5575-5577)Gac>Aac	p.D1859N	RP13-39P12.3_ENST00000434097.2_RNA|RP13-39P12.3_ENST00000601701.1_RNA|DLG5_ENST00000372388.2_Missense_Mutation_p.D1519N|DLG5_ENST00000459739.1_5'UTR	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1859	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			GTCACCTTGTCCCTCAGGTAG	0.597																																					p.D1859N		Atlas-SNP	.											.	DLG5	154	.	0			c.G5575A						.						237	193	208					10																	79553847		2203	4300	6503	SO:0001583	missense	9231	exon31			CCTTGTCCCTCAG	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"discs, large (Drosophila) homolog 5"			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.5575G>A	chr10.hg19:g.79553847C>T	ENSP00000361467:p.Asp1859Asn	45.0	0.0		70.0	47.0	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	hg19	CCDS7353.2	.	.	.	.	.	.	.	.	.	.	C	36	5.910178	0.97093	.	.	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.38887	1.11;1.11;1.11	5.86	5.86	0.93980	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.000000	0.41396	D	0.000889	T	0.61135	0.2323	M	0.68317	2.08	0.58432	D	0.999999	P;P	0.50443	0.935;0.916	P;P	0.56700	0.804;0.76	T	0.61148	-0.7121	10	0.66056	D	0.02	.	20.1865	0.98220	0.0:1.0:0.0:0.0	.	1859;1519	Q8TDM6;Q8TDM6-2	DLG5_HUMAN;.	N	1859;820;1519	ENSP00000361467:D1859N;ENSP00000394797:D820N;ENSP00000361464:D1519N	ENSP00000361464:D1519N	D	-	1	0	DLG5	79223853	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.261000	0.78400	2.775000	0.95449	0.655000	0.94253	GAC	.	.		0.597	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			T	79553847	C	T	79553847	3	4	189	1	0	0	0	0	1	0	0	0	4560	855	30	3	192	3	DLG5	10	79553847	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	35670520	79553847	55980900	113	27989										
C10orf99	387695	hgsc.bcm.edu	37	chr10	85933619	85933619	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cttctcaccatgaggcttctAgtcctttccagcctgctctg	7	15	3	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr10:85933619A>T	ENST00000372126.3	+	1	126	c.12A>T	c.(10-12)ctA>ctT	p.L4L		NM_207373.2	NP_997256.1	Q6UWK7	CJ099_HUMAN	chromosome 10 open reading frame 99	4						extracellular region (GO:0005576)				endometrium(1)|lung(1)|pancreas(1)|prostate(1)	4						TGAGGCTTCTAGTCCTTTCCA	0.537																																					p.L4L		Atlas-SNP	.											.	C10orf99	8	.	0			c.A12T						.						253	194	214					10																	85933619		2203	4300	6503	SO:0001819	synonymous_variant	387695	exon1			GCTTCTAGTCCTT	AY358751	CCDS7371.1	10q23.2	2014-04-16			ENSG00000188373	ENSG00000188373			31428	protein-coding gene	gene with protein product						12975309	Standard	NM_207373		Approved	UNQ1833, RLLV1833, FLJ21763	uc001kcu.3	Q6UWK7	OTTHUMG00000018635	ENST00000372126.3:c.12A>T	chr10.hg19:g.85933619A>T		56.0	0.0		76.0	18.0	NM_207373		Silent	SNP	ENST00000372126.3	hg19	CCDS7371.1																																																																																			.	.		0.537	C10orf99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049114.1	NM_207373		T	85933619	A	T	85933619	2	4	189	1	0	0	0	0	0	0	0	1	1630	407	15	4		4	C10orf99	10	85933619	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	6379772	85933619	49601128	114	27990										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135020434	135020434	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aatccagggtgcaattcctcAgcttggtcaagaagtatctg	10	9	3	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr10:135020434A>T	ENST00000304613.3	+	19	3577	c.3556A>T	c.(3556-3558)Agc>Tgc	p.S1186C	KNDC1_ENST00000368571.2_Missense_Mutation_p.S1121C|KNDC1_ENST00000368572.2_Missense_Mutation_p.S1188C			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1186					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GCAATTCCTCAGCTTGGTCAA	0.577																																					p.S1186C		Atlas-SNP	.											.	KNDC1	155	.	0			c.A3556T						.						90	94	93					10																	135020434		2203	4300	6503	SO:0001583	missense	85442	exon19			TTCCTCAGCTTGG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.3556A>T	chr10.hg19:g.135020434A>T	ENSP00000304437:p.Ser1186Cys	159.0	0.0		161.0	82.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	A	13.11	2.140609	0.37825	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.18960	2.68;2.68;2.18	4.45	-0.254	0.12992	.	0.673655	0.13573	U	0.377902	T	0.15869	0.0382	N	0.22421	0.69	0.24037	N	0.99609	D;D	0.59357	0.979;0.985	P;B	0.46452	0.517;0.408	T	0.16305	-1.0407	10	0.66056	D	0.02	-15.3245	8.6044	0.33764	0.3388:0.0:0.6612:0.0	.	1121;1186	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	C	1186;1188;1121	ENSP00000304437:S1186C;ENSP00000357561:S1188C;ENSP00000357560:S1121C	ENSP00000304437:S1186C	S	+	1	0	KNDC1	134870424	0.959000	0.32827	0.622000	0.29159	0.798000	0.45092	1.035000	0.30216	-0.294000	0.08973	-0.417000	0.06048	AGC	.	.		0.577	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		T	135020434	A	T	135020434	3	4	189	1	0	0	0	0	1	0	0	0	8435	188	7	4	3630	4	KNDC1	10	135020434	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	49086815	135020434	514313	115	27991										
OR51G2	81282	hgsc.bcm.edu	37	chr11	4936771	4936771	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cagttgcccgggatggaaacCagatacatgaagcacagtgg	13	9	0	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:4936771C>A	ENST00000322013.3	-	1	151	c.123G>T	c.(121-123)ctG>ctT	p.L41L	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGATGGAAACCAGATACATGA	0.502																																					p.L41L		Atlas-SNP	.											.	OR51G2	70	.	0			c.G123T						.						90	84	86					11																	4936771		2201	4298	6499	SO:0001819	synonymous_variant	81282	exon1			GGAAACCAGATAC	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"GPCR / Class A : Olfactory receptors"	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.123G>T	chr11.hg19:g.4936771C>A		106.0	0.0		109.0	68.0	NM_001005238	Q6IFH7	Silent	SNP	ENST00000322013.3	hg19	CCDS31365.1																																																																																			.	.		0.502	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		A	4936771	C	A	4936771	2	1	189	1	0	0	0	0	0	0	0	1	11108	581	21	3		3	OR51G2	11	4936771	Silent	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10		4936771	130069745	116	27992										
OR51A2	401667	hgsc.bcm.edu	37	chr11	4976935	4976935	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tcaacatatgatgtgttgatAatggacatgattcattcata	7	5	3	3	rs148063081	byFrequency	TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:4976935A>T	ENST00000380371.1	-	1	8	c.9T>A	c.(7-9)atT>atA	p.I3I	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	3						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATGTGTTGATAATGGACATGA	0.428																																					p.I3I		Atlas-SNP	.											.	OR51A2	40	.	0			c.T9A						.						48	48	48					11																	4976935		2161	4276	6437	SO:0001819	synonymous_variant	401667	exon1			GTTGATAATGGAC	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"GPCR / Class A : Olfactory receptors"	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.9T>A	chr11.hg19:g.4976935A>T		245.0	0.0		304.0	77.0	NM_001004748		Silent	SNP	ENST00000380371.1	hg19	CCDS31368.1																																																																																			.	.		0.428	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748		T	4976935	A	T	4976935	2	4	189	1	0	0	0	0	0	0	0	1	11095	358	13	4		4	OR51A2	11	4976935	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	40164	4976935	130029581	117	27993										
OR10A5	144124	hgsc.bcm.edu	37	chr11	6866988	6866988	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tccctacctactgaaatacaGtcattgctcttcctgacatt	4	13	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:6866988G>C	ENST00000299454.4	+	1	106	c.75G>C	c.(73-75)caG>caC	p.Q25H	OR10A5_ENST00000379831.2_Missense_Mutation_p.Q29H			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	25					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTGAAATACAGTCATTGCTCT	0.428																																					p.Q25H	Pancreas(44;21 1072 25662 28041 45559)	Atlas-SNP	.											.	OR10A5	48	.	0			c.G75C						.						202	206	205					11																	6866988		2201	4296	6497	SO:0001583	missense	144124	exon1			AATACAGTCATTG	AF324499	CCDS7773.1	11p15.4	2012-08-09			ENSG00000166363	ENSG00000166363		"GPCR / Class A : Olfactory receptors"	15131	protein-coding gene	gene with protein product		608493		OR10A1			Standard	NM_178168		Approved	OR11-403, JCG6	uc001met.1	Q9H207	OTTHUMG00000165738	ENST00000299454.4:c.75G>C	chr11.hg19:g.6866988G>C	ENSP00000299454:p.Gln25His	105.0	0.0		133.0	8.0	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Missense_Mutation	SNP	ENST00000299454.4	hg19	CCDS7773.1	.	.	.	.	.	.	.	.	.	.	.	14.89	2.671689	0.47781	.	.	ENSG00000166363	ENST00000299454;ENST00000379831	T;T	0.00601	6.29;6.29	3.46	2.55	0.30701	.	0.000000	0.48767	D	0.000173	T	0.01489	0.0048	M	0.77486	2.375	0.30078	N	0.809437	P	0.52463	0.953	P	0.55577	0.779	T	0.17501	-1.0367	10	0.59425	D	0.04	.	5.578	0.17235	0.2471:0.0:0.7529:0.0	.	25	Q9H207	O10A5_HUMAN	H	25;29	ENSP00000299454:Q25H;ENSP00000369159:Q29H	ENSP00000299454:Q25H	Q	+	3	2	OR10A5	6823564	0.095000	0.21747	0.709000	0.30452	0.920000	0.55202	0.783000	0.26802	1.028000	0.39785	0.591000	0.81541	CAG	.	.		0.428	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168		C	6866988	G	C	6866988	3	2	189	1	0	0	0	0	1	0	0	0	10902	1020	36	4	77	4	OR10A5	11	6866988	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	1890053	6866988	128139528	118	27994										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17464328	17464328	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	atctccttcctgcgggtcgtCtccacccgcgtgcggaagat	11	15	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:17464328C>T	ENST00000389817.3	-	10	1637	c.1569G>A	c.(1567-1569)gaG>gaA	p.E523E	ABCC8_ENST00000302539.4_Silent_p.E523E|ABCC8_ENST00000528202.1_5'UTR			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	523	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	TGCGGGTCGTCTCCACCCGCG	0.597																																					p.E523E		Atlas-SNP	.											.	ABCC8	170	.	0			c.G1569A						.						100	88	92					11																	17464328		2200	4293	6493	SO:0001819	synonymous_variant	6833	exon10			GGTCGTCTCCACC	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.1569G>A	chr11.hg19:g.17464328C>T		50.0	0.0		77.0	19.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Silent	SNP	ENST00000389817.3	hg19	CCDS31437.1																																																																																			.	.		0.597	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		T	17464328	C	T	17464328	2	4	189	1	0	0	0	0	0	0	0	1	58	912	32	3		3	ABCC8	11	17464328	Silent	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	10597340	17464328	117542188	119	27995										
OR5R1	219479	hgsc.bcm.edu	37	chr11	56184984	56184984	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgacagtcaccatatgggagCcacaggtggaaatggctttg	13	8	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:56184984C>G	ENST00000312253.1	-	1	724	c.725G>C	c.(724-726)gGc>gCc	p.G242A		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	242						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					CATATGGGAGCCACAGGTGGA	0.458																																					p.G242A		Atlas-SNP	.											OR5R1,colon,carcinoma,0,1	OR5R1	83	.	0			c.G725C						.						153	143	147					11																	56184984		2201	4296	6497	SO:0001583	missense	219479	exon1			TGGGAGCCACAGG	AB065504	CCDS31530.1	11q11	2012-08-09		2004-03-10	ENSG00000174942	ENSG00000174942		"GPCR / Class A : Olfactory receptors"	14841	protein-coding gene	gene with protein product				OR5R1P			Standard	NM_001004744		Approved		uc010rji.2	Q8NH85	OTTHUMG00000154219	ENST00000312253.1:c.725G>C	chr11.hg19:g.56184984C>G	ENSP00000308595:p.Gly242Ala	121.0	0.0		144.0	32.0	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	hg19	CCDS31530.1	.	.	.	.	.	.	.	.	.	.	C	0.611	-0.825245	0.02755	.	.	ENSG00000174942	ENST00000312253	T	0.33654	1.4	5.62	3.61	0.41365	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33419	U	0.004934	T	0.18383	0.0441	N	0.04994	-0.135	0.09310	N	1	B	0.28082	0.2	B	0.37144	0.242	T	0.32025	-0.9922	10	0.02654	T	1	-10.9135	11.2781	0.49178	0.1218:0.5384:0.3398:0.0	.	242	Q8NH85	OR5R1_HUMAN	A	242	ENSP00000308595:G242A	ENSP00000308595:G242A	G	-	2	0	OR5R1	55941560	0.000000	0.05858	0.449000	0.26957	0.032000	0.12392	0.489000	0.22387	1.342000	0.45619	0.643000	0.83706	GGC	.	.		0.458	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744		G	56184984	C	G	56184984	3	3	189	1	0	0	0	0	1	0	0	0	11189	739	26	4	251	4	OR5R1	11	56184984	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	38720656	56184984	78821532	120	27996										
TMEM132A	54972	hgsc.bcm.edu	37	chr11	60703650	60703650	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gctctcccatccagccctgcTtggagcccaccagccacaga	8	19	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:60703650T>A	ENST00000453848.2	+	11	2501	c.2343T>A	c.(2341-2343)gcT>gcA	p.A781A	TMEM132A_ENST00000005286.4_Silent_p.A782A			Q24JP5	T132A_HUMAN	transmembrane protein 132A	781	Binds to HSPA5/GRP78. {ECO:0000250}.|Confers cellular localization similar to full-length form. {ECO:0000250}.					endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						CCAGCCCTGCTTGGAGCCCAC	0.701																																					p.A782A		Atlas-SNP	.											.	TMEM132A	135	.	0			c.T2346A						.						23	27	25					11																	60703650		2203	4294	6497	SO:0001819	synonymous_variant	54972	exon11			CCCTGCTTGGAGC	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.2343T>A	chr11.hg19:g.60703650T>A		77.0	0.0		61.0	32.0	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Silent	SNP	ENST00000453848.2	hg19	CCDS44618.1																																																																																			.	.		0.701	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		A	60703650	T	A	60703650	2	1	189	1	0	0	0	0	0	0	0	1	16060	1596	56	4		4	TMEM132A	11	60703650	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	4518666	60703650	74302866	121	27997										
LGALS12	85329	hgsc.bcm.edu	37	chr11	63283717	63283717	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ccctcatgtcctcctttcccAggtgctgctcctgttccagg	8	17	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:63283717A>T	ENST00000394618.3	+	9	1155		c.e9-1		LGALS12_ENST00000425950.2_Splice_Site|LGALS12_ENST00000340246.5_Splice_Site|LGALS12_ENST00000415491.2_Splice_Site|LGALS12_ENST00000255684.5_Splice_Site	NM_001142535.1|NM_033101.3	NP_001136007.1|NP_149092.2	Q96DT0	LEG12_HUMAN	lectin, galactoside-binding, soluble, 12						intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	16						CTCCTTTCCCAGGTGCTGCTC	0.632																																					.		Atlas-SNP	.											.	LGALS12	35	.	0			c.838-2A>T						.						47	46	46					11																	63283717		2201	4298	6499	SO:0001630	splice_region_variant	85329	exon8			TTTCCCAGGTGCT	AF222695	CCDS8045.1, CCDS44633.1, CCDS44634.1, CCDS44635.1, CCDS53648.1	11q13	2011-08-04	2008-07-25		ENSG00000133317	ENSG00000133317		"Lectins, galactoside-binding"	15788	protein-coding gene	gene with protein product	"galectin 12"	606096				11283015, 11435439	Standard	NM_033101		Approved	GRIP1	uc001nxc.2	Q96DT0	OTTHUMG00000167807	ENST00000394618.3:c.865-1A>T	chr11.hg19:g.63283717A>T		27.0	0.0		26.0	7.0	NM_001142536	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Splice_Site	SNP	ENST00000394618.3	hg19	CCDS8045.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.988595	0.74589	.	.	ENSG00000133317	ENST00000255684;ENST00000394618;ENST00000340246;ENST00000415491;ENST00000425950	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5857	0.56416	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LGALS12	63040293	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.851000	0.62896	2.288000	0.76882	0.533000	0.62120	.	.	.		0.632	LGALS12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396378.1	NM_033101	Intron	T	63283717	A	T	63283717	5	4	189	1	0	0	0	0	0	0	1	0	8748	202	7	4	900	4	LGALS12	11	63283717	Splice_Site	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	2580067	63283717	71722799	122	27998										
TRPC6	7225	hgsc.bcm.edu	37	chr11	101375006	101375006	+	Frame_Shift_Del	DEL	A	A	-													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gagggtatgcacaatttcatAttcctggcagtgggcagcca					rs200066139		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:101375006delA	ENST00000344327.3	-	2	1118	c.694delT	c.(694-696)tatfs	p.Y232fs	TRPC6_ENST00000526713.1_5'Flank|TRPC6_ENST00000532133.1_Frame_Shift_Del_p.Y232fs|TRPC6_ENST00000360497.4_Frame_Shift_Del_p.Y232fs|TRPC6_ENST00000348423.4_Frame_Shift_Del_p.Y232fs	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	232					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		ACAATTTCATATTCCTGGCAG	0.468																																					p.Y232fs	Colon(166;1315 1927 11094 12848 34731)	Atlas-INDEL	.											.	TRPC6	132	.	0			c.695delA						.						122	111	115					11																	101375006		2203	4299	6502	SO:0001589	frameshift_variant	7225	exon2			.	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.694delT	chr11.hg19:g.101375006delA	ENSP00000340913:p.Tyr232fs	51.0	0.0		63.0	13.0	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Frame_Shift_Del	DEL	ENST00000344327.3	hg19	CCDS8311.1																																																																																			.	.		0.468	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		-	101375006	A	-	101375006	7	5	189	1	0	1	0	1	0	0	0	0	16598	449	16	0	2149	0	TRPC6	11	101375006	Frame_Shift_Del	DEL	A	TCGA-DD-AADF-01A-11D-A40R-10	38091289	101375006	33631510	123	27999										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103339360	103339360	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	atgtagttttgatggaaatcAactttctgaaaatcagcttg	8	5	3	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:103339360A>T	ENST00000375735.2	+	88	12836	c.12692A>T	c.(12691-12693)cAa>cTa	p.Q4231L	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.Q4238L|DYNC2H1_ENST00000334267.7_Missense_Mutation_p.Q844L	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4231					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GATGGAAATCAACTTTCTGAA	0.388																																					p.Q4238L		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A12713T						.						158	149	152					11																	103339360		1922	4144	6066	SO:0001583	missense	79659	exon89			GAAATCAACTTTC	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.12692A>T	chr11.hg19:g.103339360A>T	ENSP00000364887:p.Gln4231Leu	86.0	0.0		104.0	67.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	A	11.43	1.635361	0.29068	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093;ENST00000540621;ENST00000533197	T;T;T;T	0.08370	3.1;3.1;3.1;3.1	5.69	1.6	0.23607	Dynein heavy chain (1);	0.565185	0.18135	N	0.150609	T	0.05456	0.0144	N	0.11560	0.145	0.28065	N	0.932818	B;B;B	0.22683	0.073;0.0;0.0	B;B;B	0.30029	0.11;0.004;0.003	T	0.30794	-0.9966	10	0.72032	D	0.01	.	9.671	0.40013	0.2804:0.0:0.7196:0.0	.	844;4231;4238	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	L	4231;844;4238;477;148	ENSP00000364887:Q4231L;ENSP00000334021:Q844L;ENSP00000381167:Q4238L;ENSP00000436736:Q148L	ENSP00000334021:Q844L	Q	+	2	0	DYNC2H1	102844570	0.995000	0.38212	0.686000	0.30086	0.571000	0.35966	2.287000	0.43505	0.343000	0.23821	-0.345000	0.07892	CAA	.	.		0.388	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103339360	A	T	103339360	3	4	189	1	0	0	0	0	1	0	0	0	4848	130	5	4	13067	4	DYNC2H1	11	103339360	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	1964354	103339360	31667156	124	28000										
SORL1	6653	hgsc.bcm.edu	37	chr11	121475846	121475846	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gttgactgtgtacaaagtacAgaatcttcagtggacagctg	11	7	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:121475846A>T	ENST00000260197.7	+	34	4805	c.4676A>T	c.(4675-4677)cAg>cTg	p.Q1559L	SORL1_ENST00000525532.1_Missense_Mutation_p.Q503L|SORL1_ENST00000534286.1_Missense_Mutation_p.Q469L|SORL1_ENST00000532694.1_Missense_Mutation_p.Q405L|SORL1_ENST00000527934.1_Missense_Mutation_p.Q174L	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1559	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		TACAAAGTACAGAATCTTCAG	0.443																																					p.Q1559L		Atlas-SNP	.											.	SORL1	218	.	0			c.A4676T						.						149	148	149					11																	121475846		2203	4299	6502	SO:0001583	missense	6653	exon34			AAGTACAGAATCT	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.4676A>T	chr11.hg19:g.121475846A>T	ENSP00000260197:p.Gln1559Leu	42.0	0.0		70.0	47.0	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	hg19	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	A	18.84	3.708816	0.68615	.	.	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37	5.19	5.19	0.71726	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.59998	0.2235	L	0.29908	0.895	0.58432	D	0.999998	D;D	0.69078	0.997;0.997	D;D	0.83275	0.994;0.996	T	0.56679	-0.7939	10	0.26408	T	0.33	.	14.7146	0.69257	1.0:0.0:0.0:0.0	.	174;1559	E9PKB0;Q92673	.;SORL_HUMAN	L	1559;503;405;469;174	ENSP00000260197:Q1559L;ENSP00000434634:Q503L;ENSP00000432131:Q405L;ENSP00000436447:Q469L;ENSP00000435405:Q174L	ENSP00000260197:Q1559L	Q	+	2	0	SORL1	120981056	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.159000	0.77483	1.968000	0.57251	0.533000	0.62120	CAG	.	.		0.443	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		T	121475846	A	T	121475846	3	4	189	1	0	0	0	0	1	0	0	0	14949	188	7	4	4810	4	SORL1	11	121475846	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	18136486	121475846	13530670	125	28001										
OR6M1	390261	hgsc.bcm.edu	37	chr11	123676807	123676807	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	atatggttttctcttctcctAggaggcaggccaacaacttt	8	10	2	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr11:123676807A>T	ENST00000309154.2	-	1	288	c.251T>A	c.(250-252)cTa>cAa	p.L84Q		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	84						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		CTCTTCTCCTAGGAGGCAGGC	0.443																																					p.L84Q		Atlas-SNP	.											.	OR6M1	60	.	0			c.T251A						.						109	100	103					11																	123676807		2202	4299	6501	SO:0001583	missense	390261	exon1			TCTCCTAGGAGGC	AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"GPCR / Class A : Olfactory receptors"	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.251T>A	chr11.hg19:g.123676807A>T	ENSP00000311038:p.Leu84Gln	83.0	0.0		103.0	52.0	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	hg19	CCDS31696.1	.	.	.	.	.	.	.	.	.	.	A	3.661	-0.069536	0.07228	.	.	ENSG00000196099	ENST00000309154	T	0.01438	4.89	3.76	2.58	0.30949	GPCR, rhodopsin-like superfamily (1);	0.000000	0.27744	U	0.018024	T	0.02119	0.0066	L	0.61387	1.9	0.09310	N	1	B	0.31193	0.312	B	0.31245	0.126	T	0.38023	-0.9680	10	0.66056	D	0.02	.	7.3755	0.26825	0.8047:0.0:0.0:0.1953	.	84	Q8NGM8	OR6M1_HUMAN	Q	84	ENSP00000311038:L84Q	ENSP00000311038:L84Q	L	-	2	0	OR6M1	123182017	0.000000	0.05858	0.001000	0.08648	0.083000	0.17756	0.775000	0.26689	0.459000	0.27016	0.533000	0.62120	CTA	.	.		0.443	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325		T	123676807	A	T	123676807	3	4	189	1	0	0	0	0	1	0	0	0	11214	420	15	4	693	4	OR6M1	11	123676807	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	2200961	123676807	11329709	126	28002										
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	663011	663011	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggaccagaccttcagtgcccGgaatctcgacttccaagccc	9	16	2	1	rs138791810	byFrequency	TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:663011G>T	ENST00000266383.5	+	14	1935	c.1922G>T	c.(1921-1923)cGg>cTg	p.R641L		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	641					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			TTCAGTGCCCGGAATCTCGAC	0.547																																					p.R641L		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G1922T						.						134	108	117					12																	663011		2203	4300	6503	SO:0001583	missense	283358	exon14			GTGCCCGGAATCT	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1922G>T	chr12.hg19:g.663011G>T	ENSP00000266383:p.Arg641Leu	117.0	0.0		177.0	36.0	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	G	9.647	1.140527	0.21205	.	.	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.31247	3.48;1.5	5.76	-2.92	0.05615	.	0.780907	0.12732	N	0.443754	T	0.19208	0.0461	L	0.46157	1.445	0.09310	N	1	P;B	0.36010	0.532;0.428	B;B	0.27608	0.071;0.081	T	0.04307	-1.0961	10	0.44086	T	0.13	-4.0594	7.1744	0.25736	0.4495:0.1091:0.4414:0.0	.	544;641	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	L	641;544	ENSP00000266383:R641L;ENSP00000322953:R544L	ENSP00000266383:R641L	R	+	2	0	B4GALNT3	533272	0.000000	0.05858	0.000000	0.03702	0.314000	0.28054	0.057000	0.14279	-1.001000	0.03434	-0.140000	0.14226	CGG	.	G|0.998;A|0.002		0.547	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		T	663011	G	T	663011	3	4	189	1	0	0	0	0	1	0	0	0	1268	1116	39	1	1976	1	B4GALNT3	12	663011	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10		663011	133188884	127	28003										
ERC1	23085	hgsc.bcm.edu	37	chr12	1553897	1553897	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggcttgggagaatgagctgcAgaagatgacccgggggcagg	19	7	0	5			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:1553897A>T	ENST00000397203.2	+	18	3600	c.3194A>T	c.(3193-3195)cAg>cTg	p.Q1065L	ERC1_ENST00000355446.5_Missense_Mutation_p.Q1065L|ERC1_ENST00000360905.4_Missense_Mutation_p.Q1065L|ERC1_ENST00000589028.1_Missense_Mutation_p.Q1065L|ERC1_ENST00000546231.2_Missense_Mutation_p.Q1069L|ERC1_ENST00000543086.3_Missense_Mutation_p.Q1037L			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	1065	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.				I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			AATGAGCTGCAGAAGATGACC	0.557																																					p.Q1065L		Atlas-SNP	.											.	ERC1	95	.	0			c.A3194T						.						62	65	64					12																	1553897		2203	4300	6503	SO:0001583	missense	23085	exon18			AGCTGCAGAAGAT	AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"RAB6 interacting protein 2"	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.3194A>T	chr12.hg19:g.1553897A>T	ENSP00000380386:p.Gln1065Leu	87.0	0.0		135.0	59.0	NM_178040	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	hg19	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.793415	0.50102	.	.	ENSG00000082805	ENST00000397203;ENST00000543086;ENST00000546231;ENST00000355446;ENST00000360905	T;T;T;T	0.25414	1.87;1.86;1.8;1.87	5.53	4.37	0.52481	Rab-binding domain FIP-RBD (1);	0.633137	0.15222	N	0.273846	T	0.21921	0.0528	L	0.32530	0.975	0.51233	D	0.999917	B;B	0.27732	0.187;0.016	B;B	0.24701	0.055;0.015	T	0.02797	-1.1109	10	0.72032	D	0.01	-24.8152	12.7198	0.57136	0.8625:0.1375:0.0:0.0	.	1037;1065	Q8IUD2-3;Q8IUD2	.;RB6I2_HUMAN	L	1065;1037;1065;1065;1065	ENSP00000380386:Q1065L;ENSP00000438546:Q1037L;ENSP00000347621:Q1065L;ENSP00000354158:Q1065L	ENSP00000347621:Q1065L	Q	+	2	0	ERC1	1424158	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.882000	0.69714	0.917000	0.36895	0.529000	0.55759	CAG	.	.		0.557	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		T	1553897	A	T	1553897	3	4	189	1	0	0	0	0	1	0	0	0	5212	188	7	4	3260	4	ERC1	12	1553897	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	890886	1553897	132297998	128	28004										
PTPN6	5777	hgsc.bcm.edu	37	chr12	7064872	7064872	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gcaccagcgtctggaagggcAgcggccagagaacaagggca	16	11	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:7064872A>T	ENST00000318974.9	+	7	1041	c.797A>T	c.(796-798)cAg>cTg	p.Q266L	PTPN6_ENST00000447931.2_Missense_Mutation_p.Q227L|PTPN6_ENST00000399448.1_Missense_Mutation_p.Q268L|PTPN6_ENST00000456013.1_Missense_Mutation_p.Q266L	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	266	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|apoptotic process (GO:0006915)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|natural killer cell mediated cytotoxicity (GO:0042267)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell proliferation (GO:0008285)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein dephosphorylation (GO:0006470)|regulation of B cell differentiation (GO:0045577)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|type I interferon signaling pathway (GO:0060337)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|prostate(3)	18						CTGGAAGGGCAGCGGCCAGAG	0.587																																					p.Q268L		Atlas-SNP	.											.	PTPN6	42	.	0			c.A803T						.						88	105	100					12																	7064872		2119	4225	6344	SO:0001583	missense	5777	exon7			AAGGGCAGCGGCC		CCDS41744.1, CCDS44820.1, CCDS44821.1	12p13.31	2013-02-14			ENSG00000111679	ENSG00000111679		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9658	protein-coding gene	gene with protein product		176883				1639416	Standard	NM_080548		Approved	HCP, HCPH, PTP-1C, SHP-1, SHP1	uc001qsa.1	P29350	OTTHUMG00000168518	ENST00000318974.9:c.797A>T	chr12.hg19:g.7064872A>T	ENSP00000326010:p.Gln266Leu	115.0	0.0		167.0	71.0	NM_080548	A8K306|G3V0F8|Q969V8|Q9UK67	Missense_Mutation	SNP	ENST00000318974.9	hg19	CCDS44820.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.117177	0.56505	.	.	ENSG00000111679	ENST00000399448;ENST00000447931;ENST00000318974;ENST00000456013	T;T;T;T	0.13657	2.63;2.59;2.57;2.57	5.4	4.24	0.50183	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.210095	0.41823	D	0.000807	T	0.09905	0.0243	L	0.31476	0.935	0.58432	D	0.999999	P;B;B;B;B	0.43352	0.804;0.051;0.055;0.008;0.016	B;B;B;B;B	0.38225	0.268;0.045;0.045;0.02;0.02	T	0.20840	-1.0263	10	0.18710	T	0.47	.	12.5704	0.56334	0.861:0.139:0.0:0.0	.	254;227;266;266;268	B4DPS0;P29350-2;G3V0F8;P29350;Q53XS4	.;.;.;PTN6_HUMAN;.	L	268;227;266;266	ENSP00000382376:Q268L;ENSP00000415979:Q227L;ENSP00000326010:Q266L;ENSP00000391592:Q266L	ENSP00000326010:Q266L	Q	+	2	0	PTPN6	6935133	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.582000	0.60957	0.871000	0.35750	0.459000	0.35465	CAG	.	.		0.587	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831		T	7064872	A	T	7064872	3	4	189	1	0	0	0	0	1	0	0	0	12807	188	7	4	841	4	PTPN6	12	7064872	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	5510975	7064872	126787023	129	28005										
MLL2	8085	hgsc.bcm.edu	37	chr12	49416526	49416526	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gccaggtacacgttgttcttCcattcggtgcgcagccgccg	12	14	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:49416526C>A	ENST00000301067.7	-	51	16184	c.16185G>T	c.(16183-16185)tgG>tgT	p.W5395C		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5395					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CGTTGTTCTTCCATTCGGTGC	0.552																																					p.W5395C		Atlas-SNP	.											.	MLL2	1173	.	0			c.G16185T						.						105	118	114					12																	49416526		2070	4197	6267	SO:0001583	missense	8085	exon51			GTTCTTCCATTCG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.16185G>T	chr12.hg19:g.49416526C>A	ENSP00000301067:p.Trp5395Cys	114.0	0.0		168.0	77.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.169412	0.38315	.	.	ENSG00000167548	ENST00000301067;ENST00000526209	D;D	0.85702	-2.02;-2.02	5.09	5.09	0.68999	.	0.000000	0.33534	N	0.004814	D	0.92136	0.7507	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92937	0.6369	10	0.87932	D	0	.	17.6392	0.88130	0.0:1.0:0.0:0.0	.	5395	O14686	MLL2_HUMAN	C	5395;76	ENSP00000301067:W5395C;ENSP00000435714:W76C	ENSP00000301067:W5395C	W	-	3	0	MLL2	47702793	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.734000	0.84928	2.546000	0.85860	0.591000	0.81541	TGG	.	.		0.552	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49416526	C	A	49416526	3	1	189	1	0	0	0	0	1	0	0	0	9630	856	30	3	444	3	MLL2	12	49416526	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	42351654	49416526	84435369	130	28006										
ACVRL1	94	hgsc.bcm.edu	37	chr12	52309133	52309133	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	acgctggagccccatctggcTctgaggctagctgtgtccgc	13	14	2	1	rs370666061		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:52309133T>A	ENST00000388922.4	+	7	1180	c.897T>A	c.(895-897)gcT>gcA	p.A299A	ACVRL1_ENST00000550683.1_Silent_p.A313A|ACVRL1_ENST00000419526.2_Silent_p.A125A	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	299	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	CCCATCTGGCTCTGAGGCTAG	0.627																																					p.A299A		Atlas-SNP	.											.	ACVRL1	60	.	0			c.T897A						.						60	56	57					12																	52309133		2203	4300	6503	SO:0001819	synonymous_variant	94	exon7			TCTGGCTCTGAGG	L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567			175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2		8397373, 8640225	Standard	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	ENST00000388922.4:c.897T>A	chr12.hg19:g.52309133T>A		74.0	0.0		102.0	51.0	NM_000020	A6NGA8	Silent	SNP	ENST00000388922.4	hg19	CCDS31804.1																																																																																			.	.		0.627	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2			A	52309133	T	A	52309133	2	1	189	1	0	0	0	0	0	0	0	1	225	1538	54	4		4	ACVRL1	12	52309133	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	2892607	52309133	81542762	131	28007										
KRT1	3848	hgsc.bcm.edu	37	chr12	53069093	53069093	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tatggagcctccagagctccCgccgccagagccccggccgc	12	19	0	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:53069093C>G	ENST00000252244.3	-	9	1877	c.1819G>C	c.(1819-1821)Ggg>Cgg	p.G607R		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	607	Gly/Ser-rich.|Tail.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						CCAGAGCTCCCGCCGCCAGAG	0.667																																					p.G607R		Atlas-SNP	.											.	KRT1	110	.	0			c.G1819C						.						20	27	25					12																	53069093		2193	4277	6470	SO:0001583	missense	3848	exon9			AGCTCCCGCCGCC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1819G>C	chr12.hg19:g.53069093C>G	ENSP00000252244:p.Gly607Arg	80.0	0.0		96.0	32.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	hg19	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	C	9.964	1.223634	0.22457	.	.	ENSG00000167768	ENST00000252244	D	0.96041	-3.89	4.32	2.37	0.29283	.	.	.	.	.	D	0.86797	0.6019	N	0.08118	0	0.09310	N	1	B	0.26744	0.158	B	0.22753	0.041	T	0.78583	-0.2148	9	0.37606	T	0.19	.	5.6336	0.17524	0.3479:0.556:0.0:0.096	.	607	P04264	K2C1_HUMAN	R	607	ENSP00000252244:G607R	ENSP00000252244:G607R	G	-	1	0	KRT1	51355360	0.000000	0.05858	0.004000	0.12327	0.391000	0.30476	0.019000	0.13444	0.894000	0.36317	0.313000	0.20887	GGG	.	.		0.667	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		G	53069093	C	G	53069093	3	3	189	1	0	0	0	0	1	0	0	0	8456	652	23	4	119	4	KRT1	12	53069093	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	759960	53069093	80782802	132	28008										
OR6C65	403282	hgsc.bcm.edu	37	chr12	55795077	55795077	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tcttatgggagttgcattttTatgtgtgtaaaaacatctgc	9	5	2	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:55795077T>A	ENST00000379665.2	+	1	864	c.765T>A	c.(763-765)ttT>ttA	p.F255L		NM_001005518.1	NP_001005518.1	A6NJZ3	O6C65_HUMAN	olfactory receptor, family 6, subfamily C, member 65	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(3)|lung(9)	15						GTTGCATTTTTATGTGTGTAA	0.383																																					p.F255L		Atlas-SNP	.											.	OR6C65	44	.	0			c.T765A						.						102	95	97					12																	55795077		2203	4300	6503	SO:0001583	missense	403282	exon1			CATTTTTATGTGT		CCDS31821.1	12q13.2	2013-09-23			ENSG00000205328	ENSG00000205328		"GPCR / Class A : Olfactory receptors"	31295	protein-coding gene	gene with protein product							Standard	NM_001005518		Approved		uc010spl.2	A6NJZ3	OTTHUMG00000169955	ENST00000379665.2:c.765T>A	chr12.hg19:g.55795077T>A	ENSP00000368986:p.Phe255Leu	94.0	0.0		92.0	26.0	NM_001005518	B2RNH9	Missense_Mutation	SNP	ENST00000379665.2	hg19	CCDS31821.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.878610	0.51801	.	.	ENSG00000205328	ENST00000379665	T	0.00241	8.46	3.56	-1.56	0.08532	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41500	U	0.000867	T	0.00412	0.0013	M	0.78916	2.43	0.18873	N	0.999988	D	0.89917	1.0	D	0.97110	1.0	T	0.39860	-0.9593	10	0.87932	D	0	.	8.489	0.33089	0.0:0.6152:0.0:0.3848	.	255	A6NJZ3	O6C65_HUMAN	L	255	ENSP00000368986:F255L	ENSP00000368986:F255L	F	+	3	2	OR6C65	54081344	0.000000	0.05858	0.180000	0.23079	0.686000	0.39977	-0.563000	0.05943	-0.495000	0.06659	0.348000	0.21847	TTT	.	.		0.383	OR6C65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406674.1			A	55795077	T	A	55795077	3	1	189	1	0	0	0	0	1	0	0	0	11204	1751	61	4	767	4	OR6C65	12	55795077	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	2725984	55795077	78056818	133	28009			1	41		3	3	85	N	T_G_C	1.440023e-07
OR6C65	403282	hgsc.bcm.edu	37	chr12	55795097	55795097	+	Frame_Shift_Del	DEL	C	C	-													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tatgtgtgtaaaaacatctgCaaaagaaggtatggctttga							TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:55795097delC	ENST00000379665.2	+	1	884	c.785delC	c.(784-786)gcafs	p.A262fs		NM_001005518.1	NP_001005518.1	A6NJZ3	O6C65_HUMAN	olfactory receptor, family 6, subfamily C, member 65	262						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(3)|lung(9)	15						AAAACATCTGCAAAAGAAGGT	0.393																																					p.A262fs		Atlas-INDEL	.											OR6C65,NS,carcinoma,0,1	OR6C65	44	.	0			c.784delG						.						97	92	94					12																	55795097		2203	4300	6503	SO:0001589	frameshift_variant	403282	exon1			.		CCDS31821.1	12q13.2	2013-09-23			ENSG00000205328	ENSG00000205328		"GPCR / Class A : Olfactory receptors"	31295	protein-coding gene	gene with protein product							Standard	NM_001005518		Approved		uc010spl.2	A6NJZ3	OTTHUMG00000169955	ENST00000379665.2:c.785delC	chr12.hg19:g.55795097delC	ENSP00000368986:p.Ala262fs	84.0	0.0		83.0	26.0	NM_001005518	B2RNH9	Frame_Shift_Del	DEL	ENST00000379665.2	hg19	CCDS31821.1																																																																																			.	.		0.393	OR6C65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406674.1			-	55795097	C	-	55795097	7	5	189	1	0	1	0	1	0	0	0	0	11204	710	25	0	787	0	OR6C65	12	55795097	Frame_Shift_Del	DEL	C	TCGA-DD-AADF-01A-11D-A40R-10	20	55795097	78056798	134	28010			1	41		3	3	85	N	T_G_C	1.440023e-07
OR6C65	403282	hgsc.bcm.edu	37	chr12	55795161	55795161	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	acctctgttgctcctatgttGaatccctttatttatacctt	4	11	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:55795161G>T	ENST00000379665.2	+	1	948	c.849G>T	c.(847-849)ttG>ttT	p.L283F		NM_001005518.1	NP_001005518.1	A6NJZ3	O6C65_HUMAN	olfactory receptor, family 6, subfamily C, member 65	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(3)|lung(9)	15						CTCCTATGTTGAATCCCTTTA	0.358																																					p.L283F		Atlas-SNP	.											.	OR6C65	44	.	0			c.G849T						.						67	65	66					12																	55795161		2203	4300	6503	SO:0001583	missense	403282	exon1			TATGTTGAATCCC		CCDS31821.1	12q13.2	2013-09-23			ENSG00000205328	ENSG00000205328		"GPCR / Class A : Olfactory receptors"	31295	protein-coding gene	gene with protein product							Standard	NM_001005518		Approved		uc010spl.2	A6NJZ3	OTTHUMG00000169955	ENST00000379665.2:c.849G>T	chr12.hg19:g.55795161G>T	ENSP00000368986:p.Leu283Phe	42.0	0.0		44.0	17.0	NM_001005518	B2RNH9	Missense_Mutation	SNP	ENST00000379665.2	hg19	CCDS31821.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.628726	0.28978	.	.	ENSG00000205328	ENST00000379665	T	0.48522	0.81	4.24	-0.00449	0.14022	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31071	U	0.008318	T	0.53562	0.1804	M	0.82323	2.585	0.21499	N	0.999667	P	0.51449	0.945	P	0.51324	0.666	T	0.50083	-0.8869	10	0.62326	D	0.03	.	4.8583	0.13570	0.347:0.1457:0.5072:0.0	.	283	A6NJZ3	O6C65_HUMAN	F	283	ENSP00000368986:L283F	ENSP00000368986:L283F	L	+	3	2	OR6C65	54081428	0.000000	0.05858	0.015000	0.15790	0.395000	0.30598	-2.726000	0.00808	-0.236000	0.09753	0.424000	0.28305	TTG	.	.		0.358	OR6C65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406674.1			T	55795161	G	T	55795161	3	4	189	1	0	0	0	0	1	0	0	0	11204	1281	45	3	851	3	OR6C65	12	55795161	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	64	55795161	78056734	135	28011			1	41		3	3	85	N	T_G_C	1.440023e-07
SOCS2	8835	hgsc.bcm.edu	37	chr12	93968804	93968804	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cccccggaacggcactgttcAcctttatctgaccaaaccgc	7	17	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:93968804A>T	ENST00000340600.2	+	3	1044	c.446A>T	c.(445-447)cAc>cTc	p.H149L	SOCS2_ENST00000548537.1_3'UTR|SOCS2_ENST00000549206.1_Missense_Mutation_p.H149L|SOCS2_ENST00000536696.2_Missense_Mutation_p.H149L|SOCS2_ENST00000551556.1_Missense_Mutation_p.H149L|SOCS2_ENST00000549122.1_Missense_Mutation_p.H149L	NM_001270468.1|NM_001270469.1|NM_001270471.1|NM_003877.4	NP_001257397.1|NP_001257398.1|NP_001257400.1|NP_003868.1	O14508	SOCS2_HUMAN	suppressor of cytokine signaling 2	149	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular response to hormone stimulus (GO:0032870)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of signal transduction (GO:0009967)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of signal transduction (GO:0009966)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	growth hormone receptor binding (GO:0005131)|insulin-like growth factor receptor binding (GO:0005159)|JAK pathway signal transduction adaptor activity (GO:0008269)|SH3/SH2 adaptor activity (GO:0005070)			cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)	14						GGCACTGTTCACCTTTATCTG	0.502																																					p.H149L		Atlas-SNP	.											.	SOCS2	23	.	0			c.A446T						.						91	84	86					12																	93968804		2203	4300	6503	SO:0001583	missense	8835	exon3			CTGTTCACCTTTA	AF037989	CCDS9047.1	12q	2013-02-14			ENSG00000120833	ENSG00000120833		"Suppressors of cytokine signaling", "SH2 domain containing"	19382	protein-coding gene	gene with protein product	"STAT-induced STAT inhibitor-2"	605117				9344848, 9266833	Standard	NM_003877		Approved	STATI2, SSI2, SOCS-2, SSI-2, CIS2, Cish2	uc031qjc.1	O14508		ENST00000340600.2:c.446A>T	chr12.hg19:g.93968804A>T	ENSP00000339428:p.His149Leu	116.0	0.0		115.0	73.0	NM_001270470	A8K3D1|O14542|O95102|Q9UKS5	Missense_Mutation	SNP	ENST00000340600.2	hg19	CCDS9047.1	.	.	.	.	.	.	.	.	.	.	A	11.35	1.611657	0.28712	.	.	ENSG00000120833	ENST00000340600;ENST00000549206;ENST00000536696;ENST00000539385;ENST00000549122;ENST00000549887;ENST00000551556	T;T;T;T;T;T	0.31510	1.93;1.93;1.93;1.93;1.49;1.93	5.84	5.84	0.93424	SH2 motif (2);	0.046636	0.85682	D	0.000000	T	0.17959	0.0431	N	0.25144	0.715	0.58432	D	0.999999	P	0.38455	0.632	B	0.24394	0.053	T	0.07673	-1.0760	10	0.17832	T	0.49	-2.5936	16.2108	0.82158	1.0:0.0:0.0:0.0	.	149	O14508	SOCS2_HUMAN	L	149;149;149;97;149;149;149	ENSP00000339428:H149L;ENSP00000448815:H149L;ENSP00000442898:H149L;ENSP00000447161:H149L;ENSP00000448611:H149L;ENSP00000449227:H149L	ENSP00000339428:H149L	H	+	2	0	SOCS2	92492935	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	7.114000	0.77103	2.232000	0.73038	0.533000	0.62120	CAC	.	.		0.502	SOCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407731.2			T	93968804	A	T	93968804	3	4	189	1	0	0	0	0	1	0	0	0	14929	159	6	4	452	4	SOCS2	12	93968804	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	38173643	93968804	39883091	136	28012										
NTN4	59277	hgsc.bcm.edu	37	chr12	96104336	96104336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gtcatcacagacaccaccacTacgattccctgatgcctccc	5	18	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:96104336T>C	ENST00000343702.4	-	5	1511	c.1063A>G	c.(1063-1065)Agt>Ggt	p.S355G	NTN4_ENST00000344911.4_Missense_Mutation_p.S318G|NTN4_ENST00000553059.1_Missense_Mutation_p.S355G|NTN4_ENST00000538383.1_Missense_Mutation_p.S318G|NTN4_ENST00000552603.1_5'Flank	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	355	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|extracellular matrix organization (GO:0030198)|neuron remodeling (GO:0016322)|regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling (GO:0060668)	basement membrane (GO:0005604)|plasma membrane (GO:0005886)				NS(2)|breast(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						ACACCACCACTACGATTCCCT	0.517																																					p.S355G		Atlas-SNP	.											.	NTN4	67	.	0			c.A1063G						.						198	134	156					12																	96104336		2203	4300	6503	SO:0001583	missense	59277	exon5			CACCACTACGATT	AF119916	CCDS9054.1	12q22	2013-03-01			ENSG00000074527	ENSG00000074527		"Netrins"	13658	protein-coding gene	gene with protein product	"beta-netrin", "Netrin-4"	610401				11038171	Standard	NM_021229		Approved		uc001tei.3	Q9HB63	OTTHUMG00000170290	ENST00000343702.4:c.1063A>G	chr12.hg19:g.96104336T>C	ENSP00000340998:p.Ser355Gly	85.0	0.0		74.0	16.0	NM_021229	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Missense_Mutation	SNP	ENST00000343702.4	hg19	CCDS9054.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.321950	0.60634	.	.	ENSG00000074527	ENST00000343702;ENST00000344911;ENST00000538383;ENST00000553059	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.39	5.39	0.77823	EGF-like, laminin (3);	0.173356	0.64402	D	0.000008	T	0.56906	0.2017	L	0.33485	1.01	0.58432	D	0.999993	B;B	0.23540	0.072;0.087	B;B	0.34590	0.045;0.186	T	0.53358	-0.8450	10	0.30854	T	0.27	.	15.7214	0.77713	0.0:0.0:0.0:1.0	.	355;355	Q9HB63-2;Q9HB63	.;NET4_HUMAN	G	355;318;318;355	ENSP00000340998:S355G;ENSP00000339436:S318G;ENSP00000444432:S318G;ENSP00000447292:S355G	ENSP00000340998:S355G	S	-	1	0	NTN4	94628467	1.000000	0.71417	0.803000	0.32268	0.024000	0.10985	5.953000	0.70290	2.188000	0.69820	0.533000	0.62120	AGT	.	.		0.517	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229		C	96104336	T	C	96104336	3	2	189	1	0	0	0	0	1	0	0	0	10711	1522	53	2	847	2	NTN4	12	96104336	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	2135532	96104336	37747559	137	28013										
SELPLG	6404	hgsc.bcm.edu	37	chr12	109017504	109017504	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctccatggctgctggtgcagTggtctgtgcctccaggcctg	14	13	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:109017504T>A	ENST00000550948.1	-	2	804	c.580A>T	c.(580-582)Act>Tct	p.T194S	SELPLG_ENST00000388962.3_Missense_Mutation_p.T184S|SELPLG_ENST00000228463.6_Missense_Mutation_p.T210S			Q14242	SELPL_HUMAN	selectin P ligand	194	12 X 10 AA tandem repeats.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GCTGGTGCAGTGGTCTGTGCC	0.622																																					p.T210S		Atlas-SNP	.											.	SELPLG	138	.	0			c.A628T						.						181	145	157					12																	109017504		2203	4300	6503	SO:0001583	missense	6404	exon2			GTGCAGTGGTCTG		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"CD molecules", "Endogenous ligands"	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.580A>T	chr12.hg19:g.109017504T>A	ENSP00000447752:p.Thr194Ser	99.0	0.0		92.0	26.0	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	hg19	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	T	6.124	0.391166	0.11581	.	.	ENSG00000110876	ENST00000388962;ENST00000550948;ENST00000228463	T;T;T	0.14516	2.5;2.5;2.5	3.31	0.741	0.18336	.	1.049680	0.07607	N	0.924631	T	0.08492	0.0211	N	0.25380	0.74	0.09310	N	1	B;B;B	0.33044	0.395;0.395;0.395	B;B;B	0.32289	0.143;0.143;0.143	T	0.40365	-0.9567	10	0.20046	T	0.44	-6.481	4.6405	0.12546	0.2906:0.0:0.3974:0.312	.	210;194;154	B7Z5C7;Q14242;B4DHR9	.;SELPL_HUMAN;.	S	184;194;210	ENSP00000373614:T184S;ENSP00000447752:T194S;ENSP00000228463:T210S	ENSP00000228463:T210S	T	-	1	0	SELPLG	107541633	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	0.015000	0.13355	0.130000	0.18549	0.402000	0.26972	ACT	.	.		0.622	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1			A	109017504	T	A	109017504	3	1	189	1	0	0	0	0	1	0	0	0	14035	1696	59	4	662	4	SELPLG	12	109017504	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	12913168	109017504	24834391	138	28014										
DHX37	57647	hgsc.bcm.edu	37	chr12	125435079	125435079	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cagggccgggatccactggaCctccacgctagagacgcctg	13	15	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr12:125435079C>T	ENST00000308736.2	-	23	3099	c.3001G>A	c.(3001-3003)Gtc>Atc	p.V1001I	DHX37_ENST00000544745.1_Missense_Mutation_p.V788I	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	1001							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		ATCCACTGGACCTCCACGCTA	0.697																																					p.V1001I		Atlas-SNP	.											.	DHX37	114	.	0			c.G3001A						.						18	25	23					12																	125435079		2197	4294	6491	SO:0001583	missense	57647	exon23			ACTGGACCTCCAC	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.3001G>A	chr12.hg19:g.125435079C>T	ENSP00000311135:p.Val1001Ile	120.0	0.0		66.0	22.0	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	hg19	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	C	5.938	0.357142	0.11239	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.03004	4.17;4.08	5.07	-3.55	0.04639	Domain of unknown function DUF1605 (1);	0.741508	0.12791	N	0.438895	T	0.03011	0.0089	L	0.34521	1.04	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.14023	0.003;0.01	T	0.35301	-0.9794	10	0.37606	T	0.19	-16.5356	8.9162	0.35583	0.0:0.3147:0.1261:0.5592	.	788;1001	F5H3Y4;Q8IY37	.;DHX37_HUMAN	I	1001;788	ENSP00000311135:V1001I;ENSP00000439009:V788I	ENSP00000311135:V1001I	V	-	1	0	DHX37	124001032	0.261000	0.24063	0.003000	0.11579	0.156000	0.22039	0.504000	0.22626	-1.301000	0.02338	-0.300000	0.09419	GTC	.	.		0.697	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		T	125435079	C	T	125435079	3	4	189	1	0	0	0	0	1	0	0	0	4512	507	18	3	492	3	DHX37	12	125435079	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	16417575	125435079	8416816	139	28015										
SACS	26278	hgsc.bcm.edu	37	chr13	23909572	23909572	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	acaaattagccacgtagtaaGatttccttcagagtcctcag	7	10	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr13:23909572G>T	ENST00000382292.3	-	9	8716	c.8443C>A	c.(8443-8445)Ctt>Att	p.L2815I	SACS_ENST00000402364.1_Missense_Mutation_p.L2065I|SACS_ENST00000382298.3_Missense_Mutation_p.L2815I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2815					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CACGTAGTAAGATTTCCTTCA	0.348																																					p.L2815I		Atlas-SNP	.											.	SACS	871	.	0			c.C8443A						.						101	95	97					13																	23909572		2203	4299	6502	SO:0001583	missense	26278	exon10			TAGTAAGATTTCC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.8443C>A	chr13.hg19:g.23909572G>T	ENSP00000371729:p.Leu2815Ile	43.0	0.0		94.0	14.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	20.3	3.972140	0.74246	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87029	-2.05;-2.2;-2.05	5.65	5.65	0.86999	.	0.073809	0.52532	D	0.000079	T	0.73048	0.3537	N	0.08118	0	0.28514	N	0.913406	P	0.42827	0.791	B	0.31946	0.138	T	0.66101	-0.6007	10	0.18276	T	0.48	.	19.7855	0.96434	0.0:0.0:1.0:0.0	.	2815	Q9NZJ4	SACS_HUMAN	I	2815;2065;2815	ENSP00000371729:L2815I;ENSP00000385844:L2065I;ENSP00000371735:L2815I	ENSP00000371729:L2815I	L	-	1	0	SACS	22807572	1.000000	0.71417	0.957000	0.39632	0.992000	0.81027	3.644000	0.54381	2.684000	0.91462	0.555000	0.69702	CTT	.	.		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23909572	G	T	23909572	3	4	189	1	0	0	0	0	1	0	0	0	13819	942	33	3	5300	3	SACS	13	23909572	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10		23909572	91260306	140	28016										
FAM48A	55578	hgsc.bcm.edu	37	chr13	37621713	37621713	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	acattcttcaatatacaagtCataaagtttttgaaatacag	4	6	3	1	rs530162287	byFrequency	TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr13:37621713C>A	ENST00000350612.6	-	5	344	c.124G>T	c.(124-126)Gac>Tac	p.D42Y	SUPT20H_ENST00000475892.1_Missense_Mutation_p.D42Y|SUPT20H_ENST00000464744.1_Missense_Mutation_p.D42Y|SUPT20H_ENST00000360252.4_Missense_Mutation_p.D42Y|SUPT20H_ENST00000542180.1_Missense_Mutation_p.D30Y|SUPT20H_ENST00000470359.2_5'UTR|SUPT20H_ENST00000356185.3_Missense_Mutation_p.D42Y	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	42					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										ATATACAAGTCATAAAGTTTT	0.234													C|||	2	0.000399361	0	0.0029	5008	,	,		15950	0		0	False		,,,				2504	0				p.D42Y		Atlas-SNP	.											.	.	.	.	0			c.G124T						.						16	16	16					13																	37621713		2122	4163	6285	SO:0001583	missense	55578	exon5			ACAAGTCATAAAG	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.124G>T	chr13.hg19:g.37621713C>A	ENSP00000218894:p.Asp42Tyr	398.0	0.0		145.0	95.0	NM_001014286	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	hg19	CCDS31959.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.764630	0.89932	.	.	ENSG00000102710	ENST00000360252;ENST00000475892;ENST00000350612;ENST00000356185;ENST00000536874;ENST00000464744;ENST00000542180;ENST00000497318	T;T;T;T;T;T;T	0.56776	0.44;0.51;1.05;0.44;0.44;0.61;0.69	6.02	6.02	0.97574	.	0.045079	0.85682	D	0.000000	T	0.68869	0.3048	L	0.46157	1.445	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.79108	0.986;0.986;0.987;0.986;0.992;0.992	T	0.68678	-0.5345	10	0.87932	D	0	-17.3561	19.5289	0.95219	0.0:1.0:0.0:0.0	.	30;42;42;42;42;42	B4E2D5;B3KNI1;E7ER46;A8K8L1;Q8NEM7-2;Q8NEM7	.;.;.;.;.;FA48A_HUMAN	Y	42;42;42;42;42;42;30;42	ENSP00000353388:D42Y;ENSP00000417510:D42Y;ENSP00000218894:D42Y;ENSP00000348512:D42Y;ENSP00000419754:D42Y;ENSP00000439000:D30Y;ENSP00000420170:D42Y	ENSP00000218894:D42Y	D	-	1	0	FAM48A	36519713	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.138000	0.77305	2.865000	0.98341	0.655000	0.94253	GAC	.	.		0.234	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		A	37621713	C	A	37621713	3	1	189	1	0	0	0	0	1	0	0	0	5580	826	29	3	2306	3	FAM48A	13	37621713	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	13712141	37621713	77548165	141	28017										
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60544097	60544097	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cctttttgttggcaacaaaaTgtattctcaagtttacaaag	6	7	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr13:60544097T>A	ENST00000400324.4	-	17	2275	c.2055A>T	c.(2053-2055)acA>acT	p.T685T	DIAPH3_ENST00000400319.1_Silent_p.T615T|DIAPH3_ENST00000400330.1_Silent_p.T685T|DIAPH3_ENST00000267215.4_Silent_p.T685T|DIAPH3_ENST00000377908.2_Silent_p.T674T|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Silent_p.T639T	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	685	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		GGCAACAAAATGTATTCTCAA	0.254																																					p.T685T		Atlas-SNP	.											.	DIAPH3	139	.	0			c.A2055T						.						63	59	60					13																	60544097		1805	4061	5866	SO:0001819	synonymous_variant	81624	exon17			ACAAAATGTATTC	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.2055A>T	chr13.hg19:g.60544097T>A		142.0	0.0		236.0	184.0	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	hg19	CCDS41898.1																																																																																			.	.		0.254	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		A	60544097	T	A	60544097	2	1	189	1	0	0	0	0	0	0	0	1	4522	1451	51	4		4	DIAPH3	13	60544097	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	22922384	60544097	54625781	142	28018										
NIN	51199	hgsc.bcm.edu	37	chr14	51224347	51224347	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gcctggtcacaccttctactTgcttcgttcggttttgctgt	9	12	2	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr14:51224347T>A	ENST00000382041.3	-	18	3591	c.3401A>T	c.(3400-3402)cAa>cTa	p.Q1134L	NIN_ENST00000382043.4_Intron|NIN_ENST00000530997.2_Missense_Mutation_p.Q1134L|NIN_ENST00000245441.5_Missense_Mutation_p.Q1134L|NIN_ENST00000324330.9_Missense_Mutation_p.Q1134L|NIN_ENST00000453196.1_Missense_Mutation_p.Q1134L|NIN_ENST00000389868.3_Intron	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1134					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					ACCTTCTACTTGCTTCGTTCG	0.483			T	PDGFRB	MPD																																p.Q1134L		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.A3401T						.						156	147	150					14																	51224347		2203	4300	6503	SO:0001583	missense	51199	exon18			TCTACTTGCTTCG	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.3401A>T	chr14.hg19:g.51224347T>A	ENSP00000371472:p.Gln1134Leu	98.0	0.0		81.0	67.0	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	hg19	CCDS32079.1	.	.	.	.	.	.	.	.	.	.	T	6.198	0.404728	0.11754	.	.	ENSG00000100503	ENST00000245441;ENST00000311149;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196	T;T;T;T	0.07688	3.43;3.17;3.17;3.17	5.93	-1.04	0.10068	.	0.892392	0.09791	N	0.755371	T	0.07324	0.0185	L	0.47716	1.5	0.09310	N	0.999997	B;B;P;P	0.38504	0.241;0.302;0.634;0.634	B;B;B;B	0.36766	0.08;0.124;0.232;0.232	T	0.35025	-0.9805	10	0.32370	T	0.25	-0.6246	6.248	0.20830	0.0:0.2752:0.1219:0.6028	.	1140;1134;1134;1134	Q8N4C6-5;C9J066;Q8N4C6;Q8N4C6-7	.;.;NIN_HUMAN;.	L	1134;1117;1140;1134;1134;1134	ENSP00000245441:Q1134L;ENSP00000371472:Q1134L;ENSP00000324210:Q1134L;ENSP00000412391:Q1134L	ENSP00000245441:Q1134L	Q	-	2	0	NIN	50294097	0.000000	0.05858	0.067000	0.19924	0.006000	0.05464	-0.480000	0.06559	-0.093000	0.12396	0.460000	0.39030	CAA	.	.		0.483	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		A	51224347	T	A	51224347	3	1	189	1	0	0	0	0	1	0	0	0	10426	1812	63	4	3204	4	NIN	14	51224347	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10		51224347	56125193	143	28019										
KTN1	3895	hgsc.bcm.edu	37	chr14	56113703	56113703	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tattttagcctaataaggatGttgtggaacaaatggaaaaa	9	3	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr14:56113703G>A	ENST00000395314.3	+	19	2253	c.2185G>A	c.(2185-2187)Gtt>Att	p.V729I	KTN1_ENST00000416613.1_Missense_Mutation_p.V729I|KTN1_ENST00000413890.2_Missense_Mutation_p.V729I|KTN1_ENST00000438792.2_Missense_Mutation_p.V729I|KTN1_ENST00000395309.3_Missense_Mutation_p.V729I|KTN1_ENST00000395308.1_Missense_Mutation_p.V729I|KTN1_ENST00000395311.1_Missense_Mutation_p.V729I|KTN1_ENST00000554507.1_Missense_Mutation_p.V24I	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	729					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TAATAAGGATGTTGTGGAACA	0.244			T	RET	papillary thryoid																																p.V729I		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.G2185A						.						92	92	92					14																	56113703		2202	4294	6496	SO:0001583	missense	3895	exon19			AAGGATGTTGTGG		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.2185G>A	chr14.hg19:g.56113703G>A	ENSP00000378725:p.Val729Ile	57.0	0.0		43.0	34.0	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.133093	0.37630	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613;ENST00000554507;ENST00000554890	T;T;T;T;T;T;T;T	0.46451	1.47;1.47;1.46;1.47;1.47;1.47;1.47;0.87	4.48	3.59	0.41128	.	0.324151	0.22338	N	0.061361	T	0.27313	0.0670	N	0.25647	0.755	0.21762	N	0.999557	B;B;B;B;B	0.16603	0.002;0.002;0.018;0.001;0.005	B;B;B;B;B	0.15052	0.005;0.012;0.011;0.005;0.005	T	0.13361	-1.0512	10	0.36615	T	0.2	-3.9708	7.9107	0.29789	0.0886:0.0:0.7131:0.1983	.	729;24;729;729;729	B4DZ88;G3V4Y7;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;.;KTN1_HUMAN	I	729;729;729;729;729;729;729;24;24	ENSP00000394992:V729I;ENSP00000378720:V729I;ENSP00000391964:V729I;ENSP00000378725:V729I;ENSP00000378719:V729I;ENSP00000378722:V729I;ENSP00000388807:V729I;ENSP00000452073:V24I	ENSP00000378719:V729I	V	+	1	0	KTN1	55183456	0.936000	0.31750	1.000000	0.80357	0.997000	0.91878	0.170000	0.16663	1.232000	0.43678	0.585000	0.79938	GTT	.	.		0.244	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			A	56113703	G	A	56113703	3	1	189	1	0	0	0	0	1	0	0	0	8594	1377	48	3	2255	3	KTN1	14	56113703	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	4889356	56113703	51235837	144	28020										
MUDENG	55745	hgsc.bcm.edu	37	chr14	57741303	57741303	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgaatttctttttgggatacAggattttctttattcaggtc	8	5	3	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr14:57741303A>C	ENST00000261558.3	+	2	822	c.416A>C	c.(415-417)cAg>cCg	p.Q139P	AP5M1_ENST00000431972.2_Missense_Mutation_p.Q153P	NM_018229.3	NP_060699.3	Q9H0R1	AP5M1_HUMAN	adaptor-related protein complex 5, mu 1 subunit	139					endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytosol (GO:0005829)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)											TTTGGGATACAGGATTTTCTT	0.408																																					p.Q139P		Atlas-SNP	.											.	.	.	.	0			c.A416C						.						55	58	57					14																	57741303		2203	4300	6503	SO:0001583	missense	55745	exon2			GGATACAGGATTT	AF094583	CCDS9729.1	14q22.2	2012-03-20	2012-03-20	2012-03-20	ENSG00000053770	ENSG00000053770			20192	protein-coding gene	gene with protein product	"Mu-2 related death-inducing gene"	614368	"chromosome 14 open reading frame 108", "MU-2/AP1M2 domain containing, death-inducing"	C14orf108, MUDENG		18395520	Standard	NM_018229		Approved	FLJ10813, MuD, mu5	uc001xcv.3	Q9H0R1	OTTHUMG00000140318	ENST00000261558.3:c.416A>C	chr14.hg19:g.57741303A>C	ENSP00000261558:p.Gln139Pro	78.0	0.0		65.0	47.0	NM_018229	O95354|Q6ZMD7|Q96DX3|Q9NVC5	Missense_Mutation	SNP	ENST00000261558.3	hg19	CCDS9729.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.261487	0.39995	.	.	ENSG00000053770	ENST00000261558;ENST00000556995;ENST00000431972	T;T	0.31769	1.49;1.48	5.78	4.51	0.55191	.	0.298284	0.38663	N	0.001608	T	0.29652	0.0740	L	0.43152	1.355	0.46185	D	0.998911	P;D	0.54964	0.536;0.969	B;P	0.47827	0.133;0.558	T	0.01617	-1.1311	10	0.36615	T	0.2	.	8.8224	0.35034	0.6433:0.0:0.0:0.3567	.	139;139	Q9H0R1;Q9H0R1-2	MUDEN_HUMAN;.	P	139;36;153	ENSP00000261558:Q139P;ENSP00000390531:Q153P	ENSP00000261558:Q139P	Q	+	2	0	MUDENG	56811056	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.333000	0.65917	2.333000	0.79357	0.482000	0.46254	CAG	.	.		0.408	AP5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276922.1	NM_018229		C	57741303	A	C	57741303	3	2	189	1	0	0	0	0	1	0	0	0	9992	188	7	5	422	5	MUDENG	14	57741303	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	1627600	57741303	49608237	145	28021										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68219127	68219127	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gtgtccccgtcacttttggcTgccatgcctgactcactgac	9	15	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr14:68219127T>A	ENST00000347230.4	-	40	7443	c.7305A>T	c.(7303-7305)gcA>gcT	p.A2435A	RN7SL213P_ENST00000463482.2_RNA|ZFYVE26_ENST00000557306.1_Silent_p.A281A	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	2435					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CACTTTTGGCTGCCATGCCTG	0.557																																					p.A2435A		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A7305T						.						111	70	84					14																	68219127		2203	4300	6503	SO:0001819	synonymous_variant	23503	exon40			TTTGGCTGCCATG	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.7305A>T	chr14.hg19:g.68219127T>A		72.0	0.0		72.0	43.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	hg19	CCDS9788.1																																																																																			.	.		0.557	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68219127	T	A	68219127	2	1	189	1	0	0	0	0	0	0	0	1	17683	1567	55	4		4	ZFYVE26	14	68219127	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	10477824	68219127	39130413	146	28022										
JAG2	3714	hgsc.bcm.edu	37	chr14	105609336	105609336	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgtggccccccggccgctcaAtggggttgcggatggggttg	18	11	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr14:105609336A>G	ENST00000331782.3	-	26	3816	c.3413T>C	c.(3412-3414)aTt>aCt	p.I1138T	JAG2_ENST00000347004.2_Missense_Mutation_p.I1100T	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	1138					auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		CGGCCGCTCAATGGGGTTGCG	0.721																																					p.I1138T		Atlas-SNP	.											.	JAG2	69	.	0			c.T3413C						.						17	21	20					14																	105609336		2169	4227	6396	SO:0001583	missense	3714	exon26			CGCTCAATGGGGT	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.3413T>C	chr14.hg19:g.105609336A>G	ENSP00000328169:p.Ile1138Thr	22.0	0.0		10.0	9.0	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	hg19	CCDS9998.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.488000	0.44249	.	.	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.87412	-2.22;-2.25	4.09	4.09	0.47781	.	0.340396	0.27080	N	0.021036	D	0.91395	0.7285	L	0.61218	1.895	0.40805	D	0.983373	D;D	0.76494	0.981;0.999	P;D	0.78314	0.795;0.991	D	0.92029	0.5632	10	0.59425	D	0.04	.	12.37	0.55250	1.0:0.0:0.0:0.0	.	1100;1138	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	T	1138;1100	ENSP00000328169:I1138T;ENSP00000328566:I1100T	ENSP00000328169:I1138T	I	-	2	0	JAG2	104680381	0.729000	0.28090	0.995000	0.50966	0.290000	0.27261	1.478000	0.35442	1.713000	0.51359	0.402000	0.26972	ATT	.	.		0.721	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			G	105609336	A	G	105609336	3	3	189	1	0	0	0	0	1	0	0	0	7944	101	4	2	307	2	JAG2	14	105609336	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	37390209	105609336	1740204	147	28023										
PLA2G4F	255189	hgsc.bcm.edu	37	chr15	42442915	42442915	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctggctctgtgggaggctgcAggggcaagagctgtggcttc	18	9	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr15:42442915A>T	ENST00000382396.4	-	8	748	c.662T>A	c.(661-663)cTg>cAg	p.L221Q	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.L221Q			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	221					arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		GGGAGGCTGCAGGGGCAAGAG	0.652																																					p.L221Q		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.T662A						.						46	45	45					15																	42442915		2203	4299	6502	SO:0001583	missense	255189	exon8			GGCTGCAGGGGCA		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.662T>A	chr15.hg19:g.42442915A>T	ENSP00000371833:p.Leu221Gln	62.0	0.0		45.0	11.0	NM_213600	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	hg19	CCDS32204.1	.	.	.	.	.	.	.	.	.	.	A	10.95	1.494551	0.26774	.	.	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000357924;ENST00000443825	T;T	0.01599	4.74;4.79	5.44	4.2	0.49525	.	0.788558	0.10772	N	0.635860	T	0.02047	0.0064	L	0.39898	1.24	0.26592	N	0.973173	B	0.29805	0.257	B	0.23419	0.046	T	0.37888	-0.9686	10	0.51188	T	0.08	-2.1656	7.604	0.28091	0.7673:0.0:0.0:0.2327	.	221	Q68DD2	PA24F_HUMAN	Q	217;221;221;221;221	ENSP00000380442:L221Q;ENSP00000371833:L221Q	ENSP00000290497:L217Q	L	-	2	0	PLA2G4F	40230207	0.271000	0.24162	1.000000	0.80357	0.166000	0.22503	0.890000	0.28295	2.212000	0.71576	0.529000	0.55759	CTG	.	.		0.652	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		T	42442915	A	T	42442915	3	4	189	1	0	0	0	0	1	0	0	0	12015	188	7	4	1939	4	PLA2G4F	15	42442915	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10		42442915	60088477	148	28024										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54305537	54305537	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aaaccaggcacaatcaacacAcacaatgccagttagacgca	6	13	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr15:54305537A>T	ENST00000260323.11	+	1	437	c.437A>T	c.(436-438)cAc>cTc	p.H146L	UNC13C_ENST00000545554.1_Missense_Mutation_p.H146L|UNC13C_ENST00000537900.1_Missense_Mutation_p.H146L	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	146					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CAATCAACACACACAATGCCA	0.468																																					p.H146L		Atlas-SNP	.											.	UNC13C	674	.	0			c.A437T						.						82	81	81					15																	54305537		2030	4186	6216	SO:0001583	missense	440279	exon1			CAACACACACAAT	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.437A>T	chr15.hg19:g.54305537A>T	ENSP00000260323:p.His146Leu	117.0	0.0		126.0	36.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	A	8.792	0.930707	0.18131	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.79141	-1.24;-1.24;-1.24	5.16	-1.81	0.07882	.	.	.	.	.	T	0.56717	0.2004	N	0.24115	0.695	0.29353	N	0.865229	B	0.02656	0.0	B	0.01281	0.0	T	0.45308	-0.9270	9	0.48119	T	0.1	.	0.8256	0.01120	0.466:0.1322:0.1466:0.2551	.	146	Q8NB66	UN13C_HUMAN	L	146	ENSP00000260323:H146L;ENSP00000438156:H146L;ENSP00000442569:H146L	ENSP00000260323:H146L	H	+	2	0	UNC13C	52092829	0.480000	0.25933	0.186000	0.23195	0.346000	0.29079	0.895000	0.28363	-0.263000	0.09378	0.533000	0.62120	CAC	.	.		0.468	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54305537	A	T	54305537	3	4	189	1	0	0	0	0	1	0	0	0	17001	159	6	4	439	4	UNC13C	15	54305537	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	11862622	54305537	48225855	149	28025										
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79066995	79066995	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ccacgggcacccatgtgtgcAgctggcccttgtagagcata	12	13	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr15:79066995A>T	ENST00000388820.4	-	12	2057	c.1847T>A	c.(1846-1848)cTg>cAg	p.L616Q	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	616	Cys-rich.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CCATGTGTGCAGCTGGCCCTT	0.637																																					p.L616Q		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.T1847A						.						55	54	55					15																	79066995		2196	4291	6487	SO:0001583	missense	11173	exon12			GTGTGCAGCTGGC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.1847T>A	chr15.hg19:g.79066995A>T	ENSP00000373472:p.Leu616Gln	36.0	0.0		12.0	5.0	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	hg19	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	A	14.15	2.449230	0.43531	.	.	ENSG00000136378	ENST00000388820	T	0.03951	3.75	3.61	0.836	0.18891	.	0.252100	0.32970	N	0.005426	T	0.04861	0.0131	L	0.53729	1.69	0.37090	D	0.899389	P;P	0.41929	0.609;0.765	B;B	0.37198	0.168;0.243	T	0.46857	-0.9161	10	0.40728	T	0.16	.	7.8919	0.29682	0.6764:0.0:0.0:0.3236	.	616;616	A8MQ00;Q9UKP4	.;ATS7_HUMAN	Q	616	ENSP00000373472:L616Q	ENSP00000373472:L616Q	L	-	2	0	ADAMTS7	76854050	1.000000	0.71417	0.773000	0.31616	0.966000	0.64601	5.687000	0.68219	0.524000	0.28502	0.240000	0.17902	CTG	.	.		0.637	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		T	79066995	A	T	79066995	3	4	189	1	0	0	0	0	1	0	0	0	271	188	7	4	3265	4	ADAMTS7	15	79066995	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	24761458	79066995	23464397	150	28026										
RGMA	56963	hgsc.bcm.edu	37	chr15	93588391	93588391	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gcatcttgacatcctccaacGcgtagtaggcggccagtgtg	12	12	1	1	rs201783150		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr15:93588391G>A	ENST00000329082.7	-	4	1461	c.1190C>T	c.(1189-1191)gCg>gTg	p.A397V	RGMA_ENST00000557301.1_Missense_Mutation_p.A405V|RGMA_ENST00000425933.2_Missense_Mutation_p.A381V|RGMA_ENST00000556658.1_Missense_Mutation_p.A288V|RGMA_ENST00000542321.2_Missense_Mutation_p.A381V|RGMA_ENST00000543599.1_Missense_Mutation_p.A381V|RGMA_ENST00000557420.1_3'UTR|RGMA_ENST00000538818.1_Missense_Mutation_p.A288V	NM_020211.2	NP_064596	Q96B86	RGMA_HUMAN	repulsive guidance molecule family member a	397					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|neural tube closure (GO:0001843)|regulation of BMP signaling pathway (GO:0030510)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	9	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)			ATCCTCCAACGCGTAGTAGGC	0.612																																					p.A405V		Atlas-SNP	.											.	RGMA	49	.	0			c.C1214T						.						40	44	42					15																	93588391		2097	4240	6337	SO:0001583	missense	56963	exon4			TCCAACGCGTAGT	AL390083	CCDS45357.1, CCDS53973.1, CCDS53974.1	15q26.1	2013-11-06	2013-11-06			ENSG00000182175			30308	protein-coding gene	gene with protein product		607362	"RGM domain family, member A"			15975920	Standard	NM_020211		Approved	RGM, RGMa	uc010urc.2	Q96B86		ENST00000329082.7:c.1190C>T	chr15.hg19:g.93588391G>A	ENSP00000330005:p.Ala397Val	113.0	0.0		87.0	41.0	NM_001166283	B2RTW1|B7Z5S8|F5GXQ7|F5GZU6|G3V518|Q0JV97|Q8NC80|Q9H0E6|Q9NPM3	Missense_Mutation	SNP	ENST00000329082.7	hg19	CCDS45357.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.631302	0.67015	.	.	ENSG00000182175	ENST00000543599;ENST00000425933;ENST00000329082;ENST00000542321;ENST00000538818;ENST00000557301	D;D;D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68;-2.68;-2.68	4.87	4.87	0.63330	Repulsive guidance molecule, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95915	0.8670	M	0.86502	2.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96751	0.9554	10	0.87932	D	0	-11.6506	17.6076	0.88042	0.0:0.0:1.0:0.0	.	405;397	G3V518;Q96B86	.;RGMA_HUMAN	V	381;381;397;381;288;405	ENSP00000442498:A381V;ENSP00000404442:A381V;ENSP00000330005:A397V;ENSP00000440025:A381V;ENSP00000442546:A288V;ENSP00000452126:A405V	ENSP00000330005:A397V	A	-	2	0	RGMA	91389395	1.000000	0.71417	0.679000	0.29978	0.002000	0.02628	9.733000	0.98818	2.240000	0.73641	0.491000	0.48974	GCG	.	G|1.000;T|0.000		0.612	RGMA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415091.1	NM_020211		A	93588391	G	A	93588391	3	1	189	1	0	0	0	0	1	0	0	0	13295	1087	38	1	166	1	RGMA	15	93588391	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	14521396	93588391	8943001	151	28027										
DOC2A	8448	hgsc.bcm.edu	37	chr16	30018203	30018203	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tccccggcgccgcgagctgtAgctgagactcagcaggatgc	14	14	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr16:30018203A>T	ENST00000350119.4	-	8	971	c.781T>A	c.(781-783)Tac>Aac	p.Y261N	DOC2A_ENST00000564944.1_Missense_Mutation_p.Y261N|DOC2A_ENST00000564979.1_Missense_Mutation_p.Y261N	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	261	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Interaction with UNC13D.				nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						CGCGAGCTGTAGCTGAGACTC	0.677																																					p.Y261N		Atlas-SNP	.											.	DOC2A	40	.	0			c.T781A						.						27	30	29					16																	30018203		2197	4299	6496	SO:0001583	missense	8448	exon8			AGCTGTAGCTGAG	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"Synaptotagmins"	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.781T>A	chr16.hg19:g.30018203A>T	ENSP00000340017:p.Tyr261Asn	109.0	0.0		92.0	53.0	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Missense_Mutation	SNP	ENST00000350119.4	hg19	CCDS10666.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.459666	0.84317	.	.	ENSG00000149927	ENST00000350119	T	0.75367	-0.93	5.14	5.14	0.70334	C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	0.000000	0.49305	D	0.000148	D	0.90003	0.6879	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92744	0.6210	10	0.87932	D	0	.	13.1768	0.59633	1.0:0.0:0.0:0.0	.	261	Q14183	DOC2A_HUMAN	N	261	ENSP00000340017:Y261N	ENSP00000340017:Y261N	Y	-	1	0	DOC2A	29925704	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.831000	0.75324	2.063000	0.61619	0.402000	0.26972	TAC	.	.		0.677	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586		T	30018203	A	T	30018203	3	4	189	1	0	0	0	0	1	0	0	0	4685	420	15	4	437	4	DOC2A	16	30018203	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10		30018203	60336550	152	28028										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31429500	31429500	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gtcaaccaccccatcttccaTgagggctctaacgtcagtgc	8	15	4	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr16:31429500T>A	ENST00000389202.2	+	21	2653	c.2604T>A	c.(2602-2604)caT>caA	p.H868Q		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	868					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CCATCTTCCATGAGGGCTCTA	0.567																																					p.H868Q		Atlas-SNP	.											.	ITGAD	154	.	0			c.T2604A						.						147	137	140					16																	31429500		2197	4300	6497	SO:0001583	missense	3681	exon21			CTTCCATGAGGGC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.2604T>A	chr16.hg19:g.31429500T>A	ENSP00000373854:p.His868Gln	71.0	0.0		96.0	26.0	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	T	8.519	0.868266	0.17250	.	.	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.42131	0.98	5.06	-10.1	0.00402	Integrin alpha-2 (1);	.	.	.	.	T	0.15782	0.0380	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.11329	0.006;0.006	T	0.20107	-1.0285	9	0.34782	T	0.22	.	4.4444	0.11589	0.1102:0.0937:0.4046:0.3915	.	884;868	Q59H14;Q13349	.;ITAD_HUMAN	Q	884;868	ENSP00000373854:H868Q	ENSP00000373854:H868Q	H	+	3	2	ITGAD	31337001	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-2.169000	0.01269	-2.969000	0.00287	-1.392000	0.01152	CAT	.	.		0.567	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		A	31429500	T	A	31429500	3	1	189	1	0	0	0	0	1	0	0	0	7893	1461	51	4	2686	4	ITGAD	16	31429500	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	1411297	31429500	58925253	153	28029										
ADAT1	23536	hgsc.bcm.edu	37	chr16	75642206	75642206	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ccaaaggctgctcaggaactGcactccagctgatggctatg	11	12	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr16:75642206G>A	ENST00000307921.3	-	9	1350	c.1205C>T	c.(1204-1206)gCa>gTa	p.A402V	RP11-77K12.8_ENST00000564489.1_RNA	NM_012091.3	NP_036223.2	Q9BUB4	ADAT1_HUMAN	adenosine deaminase, tRNA-specific 1	402	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|RNA binding (GO:0003723)|tRNA-specific adenosine deaminase activity (GO:0008251)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)	19						CTCAGGAACTGCACTCCAGCT	0.398																																					p.A402V		Atlas-SNP	.											.	ADAT1	45	.	0			c.C1205T						.						153	140	144					16																	75642206		2198	4300	6498	SO:0001583	missense	23536	exon9			GGAACTGCACTCC	AF125188	CCDS10922.1	16q23	2008-02-05			ENSG00000065457	ENSG00000065457			228	protein-coding gene	gene with protein product		604230				10430867	Standard	NM_012091		Approved		uc002feo.2	Q9BUB4	OTTHUMG00000137611	ENST00000307921.3:c.1205C>T	chr16.hg19:g.75642206G>A	ENSP00000310015:p.Ala402Val	59.0	0.0		79.0	20.0	NM_012091	Q9NVB7|Q9UNG3	Missense_Mutation	SNP	ENST00000307921.3	hg19	CCDS10922.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171620	0.78452	.	.	ENSG00000065457	ENST00000307921;ENST00000542252	D	0.93189	-3.18	5.41	5.41	0.78517	Adenosine deaminase/editase (3);	0.300277	0.36234	N	0.002703	D	0.92260	0.7545	L	0.42245	1.32	0.47009	D	0.999283	D	0.57899	0.981	P	0.50570	0.644	D	0.89808	0.3980	10	0.13853	T	0.58	0.2695	17.7735	0.88500	0.0:0.0:1.0:0.0	.	402	Q9BUB4	ADAT1_HUMAN	V	402;373	ENSP00000310015:A402V	ENSP00000310015:A402V	A	-	2	0	ADAT1	74199707	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.825000	0.75293	2.537000	0.85549	0.563000	0.77884	GCA	.	.		0.398	ADAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269027.1	NM_012091		A	75642206	G	A	75642206	3	1	189	1	0	0	0	0	1	0	0	0	284	1319	46	3	315	3	ADAT1	16	75642206	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	44212706	75642206	14712547	154	28030										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7643760	7643760	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tccgtgccggaatcaaggacCtggaggtgatgacccagaac	13	11	1	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr17:7643760C>A	ENST00000572933.1	+	10	2859	c.1399C>A	c.(1399-1401)Ctg>Atg	p.L467M	DNAH2_ENST00000570791.1_Missense_Mutation_p.L549M|DNAH2_ENST00000082259.3_Missense_Mutation_p.L549M|DNAH2_ENST00000389173.2_Missense_Mutation_p.L467M			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	467	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				AATCAAGGACCTGGAGGTGAT	0.627																																					p.L467M		Atlas-SNP	.											.	DNAH2	498	.	0			c.C1399A						.						134	114	121					17																	7643760		2203	4300	6503	SO:0001583	missense	146754	exon9			AAGGACCTGGAGG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.1399C>A	chr17.hg19:g.7643760C>A	ENSP00000458355:p.Leu467Met	106.0	0.0		59.0	49.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.476102	0.63737	.	.	ENSG00000183914	ENST00000360606;ENST00000389173;ENST00000082259	T;T	0.65549	-0.16;-0.16	4.18	2.12	0.27331	Dynein heavy chain, domain-1 (1);	0.092996	0.44688	D	0.000436	T	0.77130	0.4085	M	0.87682	2.9	0.26338	N	0.977408	B;D	0.76494	0.373;0.999	P;D	0.72075	0.688;0.976	T	0.66027	-0.6025	10	0.52906	T	0.07	.	8.2135	0.31496	0.0:0.7285:0.0:0.2715	.	467;549	Q9P225;Q9P225-3	DYH2_HUMAN;.	M	467;467;549	ENSP00000373825:L467M;ENSP00000082259:L549M	ENSP00000082259:L549M	L	+	1	2	DNAH2	7584485	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.496000	0.45346	0.995000	0.38917	-0.476000	0.04901	CTG	.	.		0.627	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7643760	C	A	7643760	3	1	189	1	0	0	0	0	1	0	0	0	4604	680	24	3	1433	3	DNAH2	17	7643760	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10		7643760	73551450	155	28031										
MYH4	4622	hgsc.bcm.edu	37	chr17	10348322	10348322	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cagtttctggatctgcttctTcccacccttcagcgccagct	7	16	4	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr17:10348322T>G	ENST00000255381.2	-	37	5547	c.5437A>C	c.(5437-5439)Aag>Cag	p.K1813Q	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1813					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						ATCTGCTTCTTCCCACCCTTC	0.552																																					p.K1813Q		Atlas-SNP	.											.	MYH4	349	.	0			c.A5437C						.						161	155	157					17																	10348322		2203	4300	6503	SO:0001583	missense	4622	exon37			GCTTCTTCCCACC		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.5437A>C	chr17.hg19:g.10348322T>G	ENSP00000255381:p.Lys1813Gln	91.0	0.0		76.0	57.0	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.731834	0.89390	.	.	ENSG00000141048	ENST00000255381	D	0.82526	-1.62	5.5	5.5	0.81552	Myosin tail (1);	0.000000	0.39146	U	0.001450	D	0.92541	0.7631	M	0.90369	3.11	0.52501	D	0.999951	D	0.89917	1.0	D	0.80764	0.994	D	0.94011	0.7284	10	0.87932	D	0	.	15.8867	0.79255	0.0:0.0:0.0:1.0	.	1813	Q9Y623	MYH4_HUMAN	Q	1813	ENSP00000255381:K1813Q	ENSP00000255381:K1813Q	K	-	1	0	MYH4	10289047	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.994000	0.88315	2.214000	0.71695	0.482000	0.46254	AAG	.	.		0.552	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		G	10348322	T	G	10348322	3	3	189	1	0	0	0	0	1	0	0	0	10046	1792	62	5	398	5	MYH4	17	10348322	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	2704562	10348322	70846888	156	28032										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12569544	12569544	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gagcattccttgctgattagGagcaagttcagatcaggtag	12	7	2	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr17:12569544G>T	ENST00000343344.4	+	1	39	c.39G>T	c.(37-39)agG>agT	p.R13S	MYOCD_ENST00000425538.1_Missense_Mutation_p.R13S			Q8IZQ8	MYCD_HUMAN	myocardin	13					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		TGCTGATTAGGAGCAAGTTCA	0.488																																					p.R13S		Atlas-SNP	.											.	MYOCD	291	.	0			c.G39T						.						97	81	87					17																	12569544		2203	4300	6503	SO:0001583	missense	93649	exon1			GATTAGGAGCAAG	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.39G>T	chr17.hg19:g.12569544G>T	ENSP00000341835:p.Arg13Ser	77.0	0.0		46.0	39.0	NM_001146312	Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	hg19	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.278333	0.40294	.	.	ENSG00000141052	ENST00000425538;ENST00000343344	T	0.50277	0.75	4.84	1.56	0.23342	.	0.068719	0.64402	D	0.000019	T	0.43500	0.1250	L	0.52364	1.645	0.80722	D	1	P;P	0.45827	0.867;0.79	P;B	0.48030	0.564;0.36	T	0.19910	-1.0291	10	0.46703	T	0.11	-1.799	5.807	0.18446	0.4614:0.0:0.5386:0.0	.	13;13	Q8IZQ8-3;Q8IZQ8	.;MYCD_HUMAN	S	13	ENSP00000341835:R13S	ENSP00000341835:R13S	R	+	3	2	MYOCD	12510269	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.177000	0.31969	0.113000	0.18004	0.563000	0.77884	AGG	.	.		0.488	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		T	12569544	G	T	12569544	3	4	189	1	0	0	0	0	1	0	0	0	10096	1165	41	3	41	3	MYOCD	17	12569544	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	2221222	12569544	68625666	157	28033										
RAPGEFL1	51195	hgsc.bcm.edu	37	chr17	38348509	38348509	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ttgtttcgcaaatttgagaaCctgacggtgagtgggtttgg	14	5	0	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr17:38348509C>T	ENST00000456989.2	+	11	1243	c.1197C>T	c.(1195-1197)aaC>aaT	p.N399N	RAPGEFL1_ENST00000436615.3_Silent_p.N344N|RAPGEFL1_ENST00000544503.1_Silent_p.N393N|RAPGEFL1_ENST00000264644.6_Silent_p.N344N			Q9UHV5	RPGFL_HUMAN	Rap guanine nucleotide exchange factor (GEF)-like 1	550					G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						AATTTGAGAACCTGACGGTGA	0.483																																					p.N344N	Esophageal Squamous(28;274 750 6870 14218 42203)	Atlas-SNP	.											.	RAPGEFL1	31	.	0			c.C1032T						.						172	176	175					17																	38348509		2203	4300	6503	SO:0001819	synonymous_variant	51195	exon11			TGAGAACCTGACG	AF117946	CCDS11363.1	17q21.2	2006-08-01	2004-03-26		ENSG00000108352	ENSG00000108352			17428	protein-coding gene	gene with protein product	"Link guanine nucleotide exchange factor II"		"RAP guanine-nucleotide-exchange factor (GEF)-like 1"				Standard	NM_016339		Approved	Link-GEFII	uc010cwu.1	Q9UHV5	OTTHUMG00000133325	ENST00000456989.2:c.1197C>T	chr17.hg19:g.38348509C>T		70.0	0.0		42.0	5.0	NM_016339		Silent	SNP	ENST00000456989.2	hg19																																																																																				.	.		0.483	RAPGEFL1-005	PUTATIVE	non_canonical_conserved|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000397518.1	NM_016339		T	38348509	C	T	38348509	2	4	189	1	0	0	0	0	0	0	0	1	13064	506	18	3		3	RAPGEFL1	17	38348509	Silent	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	25778965	38348509	42846701	158	28034										
KRT12	3859	hgsc.bcm.edu	37	chr17	39022937	39022937	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gctctgtgaagcatctgcagTcccagttcctcgtgtttcat	9	12	3	1	rs377161982		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr17:39022937T>A	ENST00000251643.4	-	1	525	c.502A>T	c.(502-504)Act>Tct	p.T168S		NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN	keratin 12	168	Linker 1.|Rod.				visual perception (GO:0007601)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	15		Breast(137;0.000301)			Griseofulvin(DB00400)	GCATCTGCAGTCCCAGTTCCT	0.413																																					p.T168S		Atlas-SNP	.											.	KRT12	53	.	0			c.A502T						.						128	129	129					17																	39022937		2203	4300	6503	SO:0001583	missense	3859	exon1			CTGCAGTCCCAGT		CCDS11378.1	17q21.2	2013-06-20	2008-08-01		ENSG00000187242	ENSG00000187242		"-", "Intermediate filaments type I, keratins (acidic)"	6414	protein-coding gene	gene with protein product	"Meesmann corneal dystrophy"	601687				9171831, 16831889	Standard	NM_000223		Approved	K12	uc002hvk.2	Q99456	OTTHUMG00000133369	ENST00000251643.4:c.502A>T	chr17.hg19:g.39022937T>A	ENSP00000251643:p.Thr168Ser	104.0	0.0		98.0	47.0	NM_000223	B2R9E0	Missense_Mutation	SNP	ENST00000251643.4	hg19	CCDS11378.1	.	.	.	.	.	.	.	.	.	.	T	0.017	-1.491964	0.01009	.	.	ENSG00000187242	ENST00000251643	D	0.85773	-2.03	5.84	-4.44	0.03557	Filament (1);	0.389002	0.22096	N	0.064683	T	0.54743	0.1877	N	0.04203	-0.255	0.09310	N	1	B	0.10296	0.003	B	0.12837	0.008	T	0.57283	-0.7838	10	0.02654	T	1	.	3.9266	0.09267	0.0907:0.3747:0.2345:0.3002	.	168	Q99456	K1C12_HUMAN	S	168	ENSP00000251643:T168S	ENSP00000251643:T168S	T	-	1	0	KRT12	36276463	.	.	0.000000	0.03702	0.247000	0.25773	.	.	-1.026000	0.03330	-0.274000	0.10170	ACT	.	.		0.413	KRT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257214.2	NM_000223		A	39022937	T	A	39022937	3	1	189	1	0	0	0	0	1	0	0	0	8458	1667	58	4	1014	4	KRT12	17	39022937	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	674428	39022937	42172273	159	28035										
KCNH4	23415	hgsc.bcm.edu	37	chr17	40330402	40330402	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	caagtcctgggcttccactcTgagtgatatccttgaaggaa	10	10	1	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr17:40330402T>A	ENST00000264661.3	-	3	736	c.404A>T	c.(403-405)cAg>cTg	p.Q135L	KCNH4_ENST00000607371.1_Missense_Mutation_p.Q135L	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	135	PAC. {ECO:0000255|PROSITE- ProRule:PRU00141}.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|urinary_tract(1)	32		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GCTTCCACTCTGAGTGATATC	0.567																																					p.Q135L	NSCLC(117;707 1703 2300 21308 31858)	Atlas-SNP	.											.	KCNH4	105	.	0			c.A404T						.						50	44	46					17																	40330402		2203	4300	6503	SO:0001583	missense	23415	exon3			CCACTCTGAGTGA	AB022698	CCDS11420.1	17q21	2012-07-05				ENSG00000089558		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6253	protein-coding gene	gene with protein product		604528				10455180, 16382104	Standard	NM_012285		Approved	Kv12.3, elk1	uc002hzb.2	Q9UQ05		ENST00000264661.3:c.404A>T	chr17.hg19:g.40330402T>A	ENSP00000264661:p.Gln135Leu	117.0	0.0		91.0	37.0	NM_012285		Missense_Mutation	SNP	ENST00000264661.3	hg19	CCDS11420.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.585567	0.46110	.	.	ENSG00000089558	ENST00000264661	D	0.99563	-6.17	4.99	3.89	0.44902	PAS-associated, C-terminal (1);PAS (1);	0.000000	0.38720	N	0.001588	D	0.98074	0.9365	L	0.34521	1.04	0.37116	D	0.900564	B	0.17465	0.022	B	0.25759	0.063	D	0.99748	1.1017	10	0.28530	T	0.3	.	12.1128	0.53848	0.0:0.0:0.1433:0.8567	.	135	Q9UQ05	KCNH4_HUMAN	L	135	ENSP00000264661:Q135L	ENSP00000264661:Q135L	Q	-	2	0	KCNH4	37583928	0.008000	0.16893	1.000000	0.80357	0.693000	0.40251	1.141000	0.31528	0.886000	0.36113	0.460000	0.39030	CAG	.	.		0.567	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285		A	40330402	T	A	40330402	3	1	189	1	0	0	0	0	1	0	0	0	8043	1580	55	4	2705	4	KCNH4	17	40330402	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	1307465	40330402	40864808	160	28036										
TRIM47	91107	hgsc.bcm.edu	37	chr17	73871178	73871178	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	caggaacttgtctgctgtgtCgctgtccaaatccacaatat	8	11	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr17:73871178C>T	ENST00000254816.2	-	6	1329	c.1303G>A	c.(1303-1305)Gac>Aac	p.D435N	RP11-552F3.9_ENST00000586076.1_RNA|TRIM47_ENST00000587339.1_Missense_Mutation_p.D197N	NM_033452.2	NP_258411.2	Q96LD4	TRI47_HUMAN	tripartite motif containing 47	435	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22			Epithelial(20;4.23e-06)|all cancers(21;5.24e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCTGCTGTGTCGCTGTCCAAA	0.577																																					p.D435N		Atlas-SNP	.											.	TRIM47	40	.	0			c.G1303A						.						58	63	61					17																	73871178		2202	4298	6500	SO:0001583	missense	91107	exon6			CTGTGTCGCTGTC	AY026763	CCDS32737.1	17q25	2013-01-09	2011-01-25			ENSG00000132481		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19020	protein-coding gene	gene with protein product		611041	"tripartite motif-containing 47"				Standard	NM_033452		Approved	GOA, RNF100	uc002jpw.3	Q96LD4		ENST00000254816.2:c.1303G>A	chr17.hg19:g.73871178C>T	ENSP00000254816:p.Asp435Asn	42.0	0.0		146.0	12.0	NM_033452	Q96AD0|Q96GU5|Q9BRN7	Missense_Mutation	SNP	ENST00000254816.2	hg19	CCDS32737.1	.	.	.	.	.	.	.	.	.	.	C	8.746	0.920131	0.17982	.	.	ENSG00000132481	ENST00000254816	T	0.59502	0.26	5.18	5.18	0.71444	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	0.000000	0.64402	D	0.000004	T	0.24586	0.0596	N	0.04669	-0.19	0.41135	D	0.985919	P	0.39601	0.68	B	0.26094	0.066	T	0.44847	-0.9301	10	0.02654	T	1	.	12.0839	0.53686	0.0:0.9211:0.0:0.0789	.	435	Q96LD4	TRI47_HUMAN	N	435	ENSP00000254816:D435N	ENSP00000254816:D435N	D	-	1	0	TRIM47	71382773	1.000000	0.71417	0.940000	0.37924	0.365000	0.29674	4.371000	0.59523	2.426000	0.82243	0.561000	0.74099	GAC	.	.		0.577	TRIM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448934.1			T	73871178	C	T	73871178	3	4	189	1	0	0	0	0	1	0	0	0	16537	884	31	1	617	1	TRIM47	17	73871178	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	33540776	73871178	7324032	161	28037										
QRICH2	84074	hgsc.bcm.edu	37	chr17	74288478	74288478	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gttgtgccaaaccatgctgaTccactccaggttggaccaaa	9	12	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr17:74288478T>C	ENST00000262765.5	-	4	2011	c.1832A>G	c.(1831-1833)gAt>gGt	p.D611G		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	611	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						ACCATGCTGATCCACTCCAGG	0.542																																					p.D611G		Atlas-SNP	.											.	QRICH2	143	.	0			c.A1832G						.						154	127	136					17																	74288478		2203	4300	6503	SO:0001583	missense	84074	exon4			TGCTGATCCACTC	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.1832A>G	chr17.hg19:g.74288478T>C	ENSP00000262765:p.Asp611Gly	77.0	0.0		138.0	10.0	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	hg19	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	T	1.387	-0.581946	0.03827	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.19250	2.16	4.74	-9.49	0.00587	.	.	.	.	.	T	0.02767	0.0083	N	0.00170	-1.935	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.40979	-0.9534	9	0.23302	T	0.38	0.4676	2.1613	0.03826	0.4626:0.2469:0.1587:0.1318	.	611;611	B5MD94;Q9H0J4	.;QRIC2_HUMAN	G	611	ENSP00000262765:D611G	ENSP00000262765:D611G	D	-	2	0	QRICH2	71800073	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.117000	0.00149	-4.204000	0.00065	-2.487000	0.00196	GAT	.	.		0.542	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		C	74288478	T	C	74288478	3	2	189	1	0	0	0	0	1	0	0	0	12895	1435	50	2	3223	2	QRICH2	17	74288478	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	417300	74288478	6906732	162	28038										
RAC3	5881	hgsc.bcm.edu	37	chr17	79991460	79991460	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cctacccacagggcctggccAtggcccgggagattggtggg	16	13	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr17:79991460A>T	ENST00000306897.4	+	5	571	c.433A>T	c.(433-435)Atg>Ttg	p.M145L	DCXR_ENST00000584318.1_5'Flank	NM_005052.2	NP_005043.1	P60763	RAC3_HUMAN	ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3)	145					actin cytoskeleton organization (GO:0030036)|cell projection assembly (GO:0030031)|GTP catabolic process (GO:0006184)|intracellular signal transduction (GO:0035556)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|kidney(1)|skin(1)	3	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GGGCCTGGCCATGGCCCGGGA	0.682																																					p.M145L		Atlas-SNP	.											.	RAC3	8	.	0			c.A433T						.						38	41	40					17																	79991460		2200	4298	6498	SO:0001583	missense	5881	exon5			CTGGCCATGGCCC	AF008591	CCDS11798.1	17q25.3	2014-01-30				ENSG00000169750		"Endogenous ligands"	9803	protein-coding gene	gene with protein product		602050					Standard	NM_005052		Approved		uc002kdf.3	P60763		ENST00000306897.4:c.433A>T	chr17.hg19:g.79991460A>T	ENSP00000304283:p.Met145Leu	75.0	0.0		375.0	17.0	NM_005052	O14658|Q5U0M8	Missense_Mutation	SNP	ENST00000306897.4	hg19	CCDS11798.1	.	.	.	.	.	.	.	.	.	.	a	8.380	0.837225	0.16891	.	.	ENSG00000169750	ENST00000306897	T	0.65732	-0.17	3.64	3.64	0.41730	.	0.100706	0.64402	D	0.000003	T	0.35595	0.0937	N	0.03983	-0.305	0.58432	D	0.999999	B	0.02656	0.0	B	0.14578	0.011	T	0.14448	-1.0472	9	.	.	.	.	12.4244	0.55538	1.0:0.0:0.0:0.0	.	145	P60763	RAC3_HUMAN	L	145	ENSP00000304283:M145L	.	M	+	1	0	RAC3	77584749	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	7.105000	0.77031	1.504000	0.48704	0.478000	0.44815	ATG	.	.		0.682	RAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442064.1			T	79991460	A	T	79991460	3	4	189	1	0	0	0	0	1	0	0	0	12991	217	8	4	451	4	RAC3	17	79991460	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	5702982	79991460	1203750	163	28039										
TUBB6	84617	hgsc.bcm.edu	37	chr18	12310993	12310993	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggacttagagccaggcaccaTggacagcgtgcggtctgggc	16	11	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr18:12310993T>A	ENST00000317702.5	+	3	452	c.218T>A	c.(217-219)aTg>aAg	p.M73K	TUBB6_ENST00000590967.1_Missense_Mutation_p.M73K|TUBB6_ENST00000591208.1_Missense_Mutation_p.M73K|TUBB6_ENST00000586653.1_Missense_Mutation_p.M73K|TUBB6_ENST00000592683.1_Missense_Mutation_p.M73K|TUBB6_ENST00000591909.1_Missense_Mutation_p.M73K			Q9BUF5	TBB6_HUMAN	tubulin, beta 6 class V	73					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)	14				READ - Rectum adenocarcinoma(1;0.0649)		CCAGGCACCATGGACAGCGTG	0.493																																					p.M73K		Atlas-SNP	.											.	TUBB6	35	.	0			c.T218A						.						89	80	83					18																	12310993		2203	4300	6503	SO:0001583	missense	84617	exon3			GCACCATGGACAG	AK001295	CCDS11858.1	18p11.21	2011-10-10	2011-10-10		ENSG00000176014	ENSG00000176014		"Tubulins"	20776	protein-coding gene	gene with protein product	"tubulin beta MGC4083", "class V beta-tubulin"	615103	"tubulin, beta 6"			12477932	Standard	NM_032525		Approved	MGC4083, HsT1601	uc002kqw.3	Q9BUF5	OTTHUMG00000131692	ENST00000317702.5:c.218T>A	chr18.hg19:g.12310993T>A	ENSP00000318697:p.Met73Lys	78.0	0.0		96.0	44.0	NM_032525	B3KM76|Q9HA42	Missense_Mutation	SNP	ENST00000317702.5	hg19	CCDS11858.1	.	.	.	.	.	.	.	.	.	.	T	19.61	3.860743	0.71834	.	.	ENSG00000176014	ENST00000317702;ENST00000417736;ENST00000445717	T	0.70045	-0.45	4.82	4.82	0.62117	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.84705	0.5531	M	0.93939	3.475	0.80722	D	1	P	0.48162	0.906	P	0.61275	0.886	D	0.88744	0.3245	10	0.87932	D	0	.	14.5111	0.67787	0.0:0.0:0.0:1.0	.	73	Q9BUF5	TBB6_HUMAN	K	73;1;73	ENSP00000318697:M73K	ENSP00000318697:M73K	M	+	2	0	TUBB6	12300993	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.504000	0.81646	2.150000	0.67090	0.533000	0.62120	ATG	.	.		0.493	TUBB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254600.2	NM_032525		A	12310993	T	A	12310993	3	1	189	1	0	0	0	0	1	0	0	0	16775	1464	51	4	228	4	TUBB6	18	12310993	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10		12310993	65766255	164	28040										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21474874	21474874	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gattgtggcccctacagattGcgacagctgtgtgatgaccc	12	11	0	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr18:21474874G>A	ENST00000313654.9	+	44	5706	c.5465G>A	c.(5464-5466)tGc>tAc	p.C1822Y	LAMA3_ENST00000399516.3_Missense_Mutation_p.C1822Y|LAMA3_ENST00000269217.6_Missense_Mutation_p.C213Y|AC010754.1_ENST00000408462.1_RNA|LAMA3_ENST00000587184.1_Missense_Mutation_p.C213Y	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1822	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					CCTACAGATTGCGACAGCTGT	0.612																																					p.C1822Y		Atlas-SNP	.											.	LAMA3	397	.	0			c.G5465A						.						65	54	58					18																	21474874		2203	4300	6503	SO:0001583	missense	3909	exon44			CAGATTGCGACAG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.5465G>A	chr18.hg19:g.21474874G>A	ENSP00000324532:p.Cys1822Tyr	38.0	0.0		52.0	14.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.501709	0.85176	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.35421	1.31;1.49;2.68	5.91	5.91	0.95273	.	.	.	.	.	T	0.67655	0.2916	M	0.86651	2.83	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.91635	0.996;0.997;0.999;0.999	T	0.71613	-0.4540	9	0.72032	D	0.01	.	19.0696	0.93127	0.0:0.0:1.0:0.0	.	213;213;1822;1822	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	Y	1822;1822;213	ENSP00000324532:C1822Y;ENSP00000382432:C1822Y;ENSP00000269217:C213Y	ENSP00000269217:C213Y	C	+	2	0	LAMA3	19728872	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.310000	0.78947	2.803000	0.96430	0.655000	0.94253	TGC	.	.		0.612	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		A	21474874	G	A	21474874	3	1	189	1	0	0	0	0	1	0	0	0	8616	1319	46	3	5814	3	LAMA3	18	21474874	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	9163881	21474874	56602374	165	28041										
KIAA1328	57536	hgsc.bcm.edu	37	chr18	34752988	34752988	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	acatctcctatgccaacaggAagcctaaaggattttgtcac	7	11	2	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr18:34752988A>C	ENST00000280020.5	+	9	1489	c.1467A>C	c.(1465-1467)ggA>ggC	p.G489G	KIAA1328_ENST00000543923.1_Silent_p.G381G|KIAA1328_ENST00000586135.1_Silent_p.G241G|KIAA1328_ENST00000591619.1_Silent_p.G485G|KIAA1328_ENST00000435985.2_Silent_p.G241G	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	489										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		TGCCAACAGGAAGCCTAAAGG	0.388																																					p.G489G		Atlas-SNP	.											.	KIAA1328	39	.	0			c.A1467C						.						143	150	148					18																	34752988		2031	4196	6227	SO:0001819	synonymous_variant	57536	exon9			AACAGGAAGCCTA	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.1467A>C	chr18.hg19:g.34752988A>C		89.0	0.0		95.0	9.0	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Silent	SNP	ENST00000280020.5	hg19	CCDS45855.1																																																																																			.	.		0.388	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776		C	34752988	A	C	34752988	2	2	189	1	0	0	0	0	0	0	0	1	8234	233	9	5		5	KIAA1328	18	34752988	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	13278114	34752988	43324260	166	28042										
PHLPP1	23239	hgsc.bcm.edu	37	chr18	60642658	60642658	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gaactgctgggcagaagcttGgtggtgccgctgtcctttgt	15	9	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr18:60642658G>A	ENST00000262719.5	+	16	4018	c.3784G>A	c.(3784-3786)Ggt>Agt	p.G1262S	PHLPP1_ENST00000400316.4_Missense_Mutation_p.G750S			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	1262	PP2C-like.				apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						GCAGAAGCTTGGTGGTGCCGC	0.517																																					p.G1262S		Atlas-SNP	.											.	PHLPP1	164	.	0			c.G3784A						.						139	134	136					18																	60642658		2032	4181	6213	SO:0001583	missense	23239	exon16			AAGCTTGGTGGTG	AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.3784G>A	chr18.hg19:g.60642658G>A	ENSP00000262719:p.Gly1262Ser	56.0	0.0		83.0	25.0	NM_194449	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Missense_Mutation	SNP	ENST00000262719.5	hg19	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	G	36	5.621017	0.96660	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	T;T	0.68181	-0.31;-0.31	5.28	5.28	0.74379	Protein phosphatase 2C-like (4);	.	.	.	.	T	0.81351	0.4804	M	0.73372	2.23	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78996	-0.1983	9	0.36615	T	0.2	-13.4424	19.1036	0.93283	0.0:0.0:1.0:0.0	.	1262	O60346	PHLP1_HUMAN	S	750;1262	ENSP00000383170:G750S;ENSP00000262719:G1262S	ENSP00000262719:G1262S	G	+	1	0	PHLPP1	58793638	1.000000	0.71417	0.993000	0.49108	0.806000	0.45545	9.623000	0.98386	2.751000	0.94390	0.555000	0.69702	GGT	.	.		0.517	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		A	60642658	G	A	60642658	3	1	189	1	0	0	0	0	1	0	0	0	11863	1348	47	3	3846	3	PHLPP1	18	60642658	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	25889670	60642658	17434590	167	28043										
SERPINB13	5275	hgsc.bcm.edu	37	chr18	61256029	61256029	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgcaattggcatggtcctccTggggacccgaggagccaccg	14	13	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr18:61256029T>A	ENST00000344731.5	+	2	230	c.128T>A	c.(127-129)cTg>cAg	p.L43Q	SERPINB13_ENST00000269489.5_Missense_Mutation_p.L43Q	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	43					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						ATGGTCCTCCTGGGGACCCGA	0.527																																					p.L43Q		Atlas-SNP	.											.	SERPINB13	51	.	0			c.T128A						.						59	60	60					18																	61256029		2203	4300	6503	SO:0001583	missense	5275	exon2			TCCTCCTGGGGAC	AF169949, BC101821	CCDS11985.1	18q21.33	2014-02-18	2005-08-18		ENSG00000197641	ENSG00000197641		"Serine (or cysteine) peptidase inhibitors"	8944	protein-coding gene	gene with protein product		604445	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13"	PI13		9297979, 10512713, 24172014	Standard	NM_012397		Approved	HUR7, hurpin, headpin	uc002ljc.3	Q9UIV8	OTTHUMG00000060406	ENST00000344731.5:c.128T>A	chr18.hg19:g.61256029T>A	ENSP00000341584:p.Leu43Gln	41.0	0.0		48.0	27.0	NM_012397	A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Missense_Mutation	SNP	ENST00000344731.5	hg19	CCDS11985.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.711990	0.48517	.	.	ENSG00000197641	ENST00000431153;ENST00000269489;ENST00000539341;ENST00000344731;ENST00000415733	D;D;D;D	0.86865	-2.18;-2.18;-2.03;-2.03	4.89	-0.357	0.12579	Serpin domain (3);	1.234140	0.05976	N	0.643329	D	0.91744	0.7389	M	0.79123	2.44	0.09310	N	0.999998	D;P	0.65815	0.995;0.484	D;P	0.67725	0.953;0.557	T	0.78008	-0.2372	10	0.87932	D	0	.	5.5245	0.16951	0.0:0.2216:0.1346:0.6438	.	43;43	B7ZKV6;Q9UIV8	.;SPB13_HUMAN	Q	73;43;43;43;22	ENSP00000388300:L73Q;ENSP00000269489:L43Q;ENSP00000341584:L43Q;ENSP00000391156:L22Q	ENSP00000269489:L43Q	L	+	2	0	SERPINB13	59407009	0.029000	0.19370	0.000000	0.03702	0.002000	0.02628	2.016000	0.40971	-0.202000	0.10268	-0.411000	0.06167	CTG	.	.		0.527	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397		A	61256029	T	A	61256029	3	1	189	1	0	0	0	0	1	0	0	0	14115	1580	55	4	130	4	SERPINB13	18	61256029	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	613371	61256029	16821219	168	28044										
RTTN	25914	hgsc.bcm.edu	37	chr18	67671402	67671402	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggcactcaggaagaattaagGagctgcacgaggttttcaag	13	7	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr18:67671402G>T	ENST00000255674.6	-	49	6952	c.6666C>A	c.(6664-6666)ctC>ctA	p.L2222L	RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	2222					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				AAGAATTAAGGAGCTGCACGA	0.428																																					p.L2222L		Atlas-SNP	.											.	RTTN	184	.	0			c.C6666A						.						140	134	136					18																	67671402		1887	4118	6005	SO:0001819	synonymous_variant	25914	exon49			ATTAAGGAGCTGC	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.6666C>A	chr18.hg19:g.67671402G>T		67.0	0.0		66.0	12.0	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Silent	SNP	ENST00000255674.6	hg19	CCDS42443.1																																																																																			.	.		0.428	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		T	67671402	G	T	67671402	2	4	189	1	0	0	0	0	0	0	0	1	13752	1161	41	3		3	RTTN	18	67671402	Silent	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	6415373	67671402	10405846	169	28045										
C19orf26	255057	hgsc.bcm.edu	37	chr19	1233486	1233486	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ttccacttcttgaccttgaaAtaggggctggccccatccag	9	13	1	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr19:1233486A>G	ENST00000382477.2	-	8	1252	c.978T>C	c.(976-978)taT>taC	p.Y326Y	C19orf26_ENST00000590083.1_Silent_p.Y306Y|C19orf26_ENST00000215376.6_Silent_p.Y300Y			Q8N350	DOS_HUMAN	chromosome 19 open reading frame 26	326						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGACCTTGAAATAGGGGCTGG	0.682										HNSCC(14;0.022)																											p.Y306Y		Atlas-SNP	.											.	C19orf26	31	.	0			c.T918C						.						16	16	16					19																	1233486		2171	4288	6459	SO:0001819	synonymous_variant	255057	exon8			CTTGAAATAGGGG	BC028156	CCDS12057.1, CCDS12057.2	19p13.3	2012-10-24			ENSG00000099625	ENSG00000099625			28617	protein-coding gene	gene with protein product	"downstream of STK11"					12477932	Standard	NM_152769		Approved	MGC40084, DOS	uc002lrm.3	Q8N350	OTTHUMG00000180141	ENST00000382477.2:c.978T>C	chr19.hg19:g.1233486A>G		108.0	0.0		156.0	65.0	NM_152769	O43385	Silent	SNP	ENST00000382477.2	hg19																																																																																				.	.		0.682	C19orf26-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_152769		G	1233486	A	G	1233486	2	3	189	1	0	0	0	0	0	0	0	1	1918	108	4	2		2	C19orf26	19	1233486	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10		1233486	57895497	170	28046										
MUC16	94025	hgsc.bcm.edu	37	chr19	9087179	9087179	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgttgagtgttcaatcacacTggtccacgtggttgtcagtg	12	8	3	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr19:9087179T>A	ENST00000397910.4	-	1	4839	c.4636A>T	c.(4636-4638)Agt>Tgt	p.S1546C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1546	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCAATCACACTGGTCCACGTG	0.478																																					p.S1546C		Atlas-SNP	.											.	MUC16	4315	.	0			c.A4636T						.						383	360	367					19																	9087179		2071	4213	6284	SO:0001583	missense	94025	exon1			TCACACTGGTCCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4636A>T	chr19.hg19:g.9087179T>A	ENSP00000381008:p.Ser1546Cys	127.0	0.0		156.0	77.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	6.152	0.396214	0.11638	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	0.235	0.235	0.15431	.	.	.	.	.	T	0.04092	0.0114	N	0.08118	0	.	.	.	D	0.67145	0.996	D	0.65773	0.938	T	0.45338	-0.9268	7	0.87932	D	0	.	.	.	.	.	1546	B5ME49	.	C	1546	ENSP00000381008:S1546C	ENSP00000381008:S1546C	S	-	1	0	MUC16	8948179	0.000000	0.05858	0.424000	0.26647	0.431000	0.31685	-0.250000	0.08830	0.263000	0.21812	0.260000	0.18958	AGT	.	.		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9087179	T	A	9087179	3	1	189	1	0	0	0	0	1	0	0	0	9982	1580	55	4	39223	4	MUC16	19	9087179	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	7853693	9087179	50041804	171	28047										
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13936403	13936403	+	Missense_Mutation	SNP	A	A	C													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cacggtactgggctccatccAgcagaacatccactctccgg							TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr19:13936403A>C	ENST00000254323.2	+	11	2093	c.1904A>C	c.(1903-1905)cAg>cCg	p.Q635P	ZSWIM4_ENST00000440752.2_Missense_Mutation_p.Q469P	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	635							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			GGCTCCATCCAGCAGAACATC	0.647																																					p.Q635P		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.A1904C						.						87	89	88					19																	13936403		2203	4300	6503	SO:0001583	missense	65249	exon11			CCATCCAGCAGAA	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.1904A>C	chr19.hg19:g.13936403A>C	ENSP00000254323:p.Gln635Pro	52.0	0.0		66.0	15.0	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	hg19	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.422675	0.83559	.	.	ENSG00000132003	ENST00000254323;ENST00000440752	T;T	0.53640	0.61;0.62	4.23	4.23	0.50019	.	0.000000	0.48767	D	0.000161	T	0.48642	0.1511	M	0.66297	2.02	0.45822	D	0.998693	B;B	0.23990	0.009;0.095	B;B	0.31245	0.013;0.126	T	0.53809	-0.8386	10	0.66056	D	0.02	-32.3189	11.299	0.49294	1.0:0.0:0.0:0.0	.	469;635	E7ERX2;Q9H7M6	.;ZSWM4_HUMAN	P	635;469	ENSP00000254323:Q635P;ENSP00000405278:Q469P	ENSP00000254323:Q635P	Q	+	2	0	ZSWIM4	13797403	1.000000	0.71417	0.999000	0.59377	0.925000	0.55904	8.659000	0.91116	1.767000	0.52121	0.482000	0.46254	CAG	.	.		0.647	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		C	13936403	A	C	13936403	3	2	189	1	0	0	0	0	1	0	0	0	18258	188	7	5	1946	5	ZSWIM4	19	13936403	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	4849224	13936403	45192580	172	28048	136	2								
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13936406	13936406	+	Missense_Mutation	SNP	A	A	C													0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggtactgggctccatccagcAgaacatccactctccggccc							TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr19:13936406A>C	ENST00000254323.2	+	11	2096	c.1907A>C	c.(1906-1908)cAg>cCg	p.Q636P	ZSWIM4_ENST00000440752.2_Missense_Mutation_p.Q470P	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	636							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			TCCATCCAGCAGAACATCCAC	0.642																																					p.Q636P		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.A1907C						.						87	89	88					19																	13936406		2203	4300	6503	SO:0001583	missense	65249	exon11			TCCAGCAGAACAT	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.1907A>C	chr19.hg19:g.13936406A>C	ENSP00000254323:p.Gln636Pro	51.0	0.0		65.0	15.0	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	hg19	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.829862	0.71258	.	.	ENSG00000132003	ENST00000254323;ENST00000440752	T;T	0.46063	0.88;0.88	4.23	4.23	0.50019	.	0.298357	0.22940	N	0.053790	T	0.50394	0.1613	L	0.53249	1.67	0.39318	D	0.965202	P;D	0.53151	0.95;0.958	P;P	0.54706	0.698;0.759	T	0.55256	-0.8169	10	0.59425	D	0.04	-30.8687	11.299	0.49294	1.0:0.0:0.0:0.0	.	470;636	E7ERX2;Q9H7M6	.;ZSWM4_HUMAN	P	636;470	ENSP00000254323:Q636P;ENSP00000405278:Q470P	ENSP00000254323:Q636P	Q	+	2	0	ZSWIM4	13797406	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.523000	0.67099	1.767000	0.52121	0.482000	0.46254	CAG	.	.		0.642	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		C	13936406	A	C	13936406	3	2	189	1	0	0	0	0	1	0	0	0	18258	188	7	5	1949	5	ZSWIM4	19	13936406	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	3	13936406	45192577	173	28049	136	2								
NANOS3	342977	hgsc.bcm.edu	37	chr19	13988410	13988410	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tacgtgtgtccccagtgcggCgccacacgtgagcgcgccca	13	16	0	1	rs535775641	byFrequency	TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr19:13988410C>A	ENST00000397555.2	+	2	291	c.291C>A	c.(289-291)ggC>ggA	p.G97G	NANOS3_ENST00000339133.5_Silent_p.G116G|MIR181C_ENST00000384881.1_RNA|NANOS3_ENST00000591727.1_Intron|MIR181D_ENST00000384853.1_RNA	NM_001098622.2	NP_001092092.1	P60323	NANO3_HUMAN	nanos homolog 3 (Drosophila)	97					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	7			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			CCCAGTGCGGCGCCACACGTG	0.662																																					p.G116G		Atlas-SNP	.											.	NANOS3	19	.	0			c.C348A						.						29	34	32					19																	13988410		2157	4264	6421	SO:0001819	synonymous_variant	342977	exon1			GTGCGGCGCCACA	BM702754	CCDS42511.1	19p13.13	2003-12-01				ENSG00000187556			22048	protein-coding gene	gene with protein product		608229					Standard	NM_001098622		Approved	NANOS1L, NOS3	uc002mxj.4	P60323		ENST00000397555.2:c.291C>A	chr19.hg19:g.13988410C>A		30.0	0.0		46.0	17.0	NM_001098622	Q495E5	Silent	SNP	ENST00000397555.2	hg19																																																																																				.	.		0.662	NANOS3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_292819		A	13988410	C	A	13988410	2	1	189	1	0	0	0	0	0	0	0	1	10162	755	27	1		1	NANOS3	19	13988410	Silent	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	52004	13988410	45140573	174	28050										
ZNF383	163087	hgsc.bcm.edu	37	chr19	37733636	37733636	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	catcaaataattaataatgaAgacagaccctatgaatgtaa	5	6	1	4			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr19:37733636A>T	ENST00000589413.1	+	8	1081	c.498A>T	c.(496-498)gaA>gaT	p.E166D	ZNF383_ENST00000352998.3_Missense_Mutation_p.E166D|ZNF383_ENST00000590503.1_Missense_Mutation_p.E166D			Q8NA42	ZN383_HUMAN	zinc finger protein 383	166					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)	15			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTAATAATGAAGACAGACCCT	0.323																																					p.E166D		Atlas-SNP	.											.	ZNF383	42	.	0			c.A498T						.						51	54	53					19																	37733636		2203	4299	6502	SO:0001583	missense	163087	exon5			TAATGAAGACAGA	AY438646	CCDS12501.1	19q13.13	2013-01-08				ENSG00000188283		"Zinc fingers, C2H2-type", "-"	18609	protein-coding gene	gene with protein product							Standard	NM_152604		Approved	FLJ35863	uc002ofu.1	Q8NA42		ENST00000589413.1:c.498A>T	chr19.hg19:g.37733636A>T	ENSP00000464871:p.Glu166Asp	116.0	0.0		150.0	63.0	NM_152604	Q6X2C7	Missense_Mutation	SNP	ENST00000589413.1	hg19	CCDS12501.1	.	.	.	.	.	.	.	.	.	.	A	3.884	-0.025269	0.07589	.	.	ENSG00000188283	ENST00000352998	T	0.15256	2.44	3.78	0.355	0.16069	.	0.256785	0.20487	N	0.091375	T	0.08223	0.0205	N	0.17838	0.53	0.20074	N	0.999932	B	0.09022	0.002	B	0.12837	0.008	T	0.25502	-1.0130	10	0.59425	D	0.04	.	0.9524	0.01379	0.4971:0.198:0.1136:0.1913	.	166	Q8NA42	ZN383_HUMAN	D	166	ENSP00000340132:E166D	ENSP00000340132:E166D	E	+	3	2	ZNF383	42425476	0.087000	0.21565	0.977000	0.42913	0.095000	0.18619	-0.007000	0.12810	-0.115000	0.11915	-0.371000	0.07208	GAA	.	.		0.323	ZNF383-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458141.1	NM_152604		T	37733636	A	T	37733636	3	4	189	1	0	0	0	0	1	0	0	0	17889	69	3	4	512	4	ZNF383	19	37733636	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	23745226	37733636	21395347	175	28051										
CATSPERG	57828	hgsc.bcm.edu	37	chr19	38857882	38857882	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tacacgctggaatacagccgCctgaagaacaaacactactt	7	12	0	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr19:38857882C>G	ENST00000409235.3	+	23	2815	c.2700C>G	c.(2698-2700)cgC>cgG	p.R900R	CATSPERG_ENST00000215069.4_3'UTR|CATSPERG_ENST00000410018.1_Silent_p.R860R	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	900					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						AATACAGCCGCCTGAAGAACA	0.577																																					p.R900R		Atlas-SNP	.											.	CATSPERG	121	.	0			c.C2700G						.						133	102	113					19																	38857882		2203	4300	6503	SO:0001819	synonymous_variant	57828	exon23			CAGCCGCCTGAAG	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"chromosome 19 open reading frame 15", "cation channel, sperm-associated, gamma"	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.2700C>G	chr19.hg19:g.38857882C>G		22.0	0.0		49.0	17.0	NM_021185	A6NEG6|Q659E1	Silent	SNP	ENST00000409235.3	hg19	CCDS12514.2																																																																																			.	.		0.577	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185		G	38857882	C	G	38857882	2	3	189	1	0	0	0	0	0	0	0	1	2694	726	26	4		4	CATSPERG	19	38857882	Silent	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	1124246	38857882	20271101	176	28052										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40398324	40398324	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gtcgtctgcggggtcctggtTgtagttcccgcataagccac	13	12	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr19:40398324T>A	ENST00000221347.6	-	14	6650	c.6643A>T	c.(6643-6645)Aac>Tac	p.N2215Y		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2215	VWFD 5. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGGTCCTGGTTGTAGTTCCCG	0.692																																					p.N2215Y		Atlas-SNP	.											.	FCGBP	416	.	0			c.A6643T						.						11	14	13					19																	40398324		1837	3506	5343	SO:0001583	missense	8857	exon14			CCTGGTTGTAGTT	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.6643A>T	chr19.hg19:g.40398324T>A	ENSP00000221347:p.Asn2215Tyr	131.0	0.0		172.0	51.0	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	T	14.60	2.583624	0.46006	.	.	ENSG00000090920	ENST00000221347	T	0.67865	-0.29	2.17	2.17	0.27698	von Willebrand factor, type D domain (3);	.	.	.	.	D	0.85517	0.5715	H	0.96604	3.85	0.45366	D	0.998355	D	0.89917	1.0	D	0.91635	0.999	D	0.87347	0.2335	9	0.87932	D	0	.	9.5999	0.39598	0.0:0.0:0.0:1.0	.	2215	Q9Y6R7	FCGBP_HUMAN	Y	2215	ENSP00000221347:N2215Y	ENSP00000221347:N2215Y	N	-	1	0	FCGBP	45090164	1.000000	0.71417	0.985000	0.45067	0.650000	0.38633	4.286000	0.58995	1.253000	0.44018	0.392000	0.25879	AAC	.	.		0.692	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40398324	T	A	40398324	3	1	189	1	0	0	0	0	1	0	0	0	5786	1812	63	4	9666	4	FCGBP	19	40398324	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	1540442	40398324	18730659	177	28053										
ZNF880	400713	hgsc.bcm.edu	37	chr19	52877651	52877651	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aatagcaaacaatccaggtgGcagggagtgcatcaaaggtg	13	7	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr19:52877651G>T	ENST00000422689.2	+	3	254	c.239G>T	c.(238-240)gGc>gTc	p.G80V	ZNF880_ENST00000597976.1_Missense_Mutation_p.G80V|ZNF880_ENST00000424032.2_Missense_Mutation_p.G80V|ZNF880_ENST00000344085.5_Intron|ZNF880_ENST00000600321.1_Missense_Mutation_p.G80V	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	80					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						AATCCAGGTGGCAGGGAGTGC	0.468																																					p.G80V		Atlas-SNP	.											.	ZNF880	45	.	0			c.G239T						.						78	71	73					19																	52877651		692	1591	2283	SO:0001583	missense	400713	exon3			CAGGTGGCAGGGA	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"Zinc fingers, C2H2-type", "-"	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.239G>T	chr19.hg19:g.52877651G>T	ENSP00000406318:p.Gly80Val	169.0	0.0		211.0	10.0	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	hg19	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	G	6.228	0.410122	0.11812	.	.	ENSG00000221923	ENST00000424032;ENST00000422689	T;T	0.06449	5.37;3.3	1.03	-1.36	0.09085	.	.	.	.	.	T	0.02571	0.0078	L	0.29908	0.895	0.09310	N	1	P	0.42993	0.797	B	0.23150	0.044	T	0.46205	-0.9208	9	0.17369	T	0.5	.	3.9207	0.09242	0.5188:0.0:0.4812:0.0	.	80	Q6PDB4	ZN880_HUMAN	V	80	ENSP00000414470:G80V;ENSP00000406318:G80V	ENSP00000406318:G80V	G	+	2	0	ZNF880	57569463	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	0.408000	0.21065	-0.461000	0.06993	0.448000	0.29417	GGC	.	.		0.468	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434		T	52877651	G	T	52877651	3	4	189	1	0	0	0	0	1	0	0	0	18212	1203	42	3	249	3	ZNF880	19	52877651	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	12479327	52877651	6251332	178	28054										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55495067	55495067	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	aatctcccggagaatgtcacTgcgtctgaatcagacgccga	10	12	4	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr19:55495067T>A	ENST00000543010.1	+	6	2144	c.2001T>A	c.(1999-2001)acT>acA	p.T667T	NLRP2_ENST00000427260.2_Silent_p.T644T|NLRP2_ENST00000537859.1_Silent_p.T645T|NLRP2_ENST00000538819.1_Silent_p.T643T|NLRP2_ENST00000339757.7_Silent_p.T645T|NLRP2_ENST00000391721.4_Silent_p.T643T|NLRP2_ENST00000263437.6_Silent_p.T664T|NLRP2_ENST00000448584.2_Silent_p.T667T	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	667					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		AGAATGTCACTGCGTCTGAAT	0.507																																					p.T667T		Atlas-SNP	.											.	NLRP2	161	.	0			c.T2001A						.						56	54	54					19																	55495067		2203	4300	6503	SO:0001819	synonymous_variant	55655	exon6			TGTCACTGCGTCT	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.2001T>A	chr19.hg19:g.55495067T>A		31.0	0.0		21.0	10.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	hg19	CCDS12913.1																																																																																			.	.		0.507	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		A	55495067	T	A	55495067	2	1	189	1	0	0	0	0	0	0	0	1	10486	1567	55	4		4	NLRP2	19	55495067	Silent	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	2617416	55495067	3633916	179	28055										
SNTA1	6640	hgsc.bcm.edu	37	chr20	32026678	32026678	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	acctccttgcctgtcttcttGaggacctgcaccgcctcatc	7	17	3	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr20:32026678G>C	ENST00000217381.2	-	2	736	c.465C>G	c.(463-465)ctC>ctG	p.L155L		NM_003098.2	NP_003089.1	Q13424	SNTA1_HUMAN	syntrophin, alpha 1	155	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|neuromuscular junction development (GO:0007528)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of vasoconstriction by circulating norepinephrine (GO:0003117)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular (GO:0005622)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	ATPase binding (GO:0051117)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)			breast(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(1)	13						CTGTCTTCTTGAGGACCTGCA	0.582																																					p.L155L		Atlas-SNP	.											.	SNTA1	35	.	0			c.C465G						.						168	150	156					20																	32026678		2203	4300	6503	SO:0001819	synonymous_variant	6640	exon2			CTTCTTGAGGACC	U40571	CCDS13220.1	20q11.2	2014-09-17	2012-06-15		ENSG00000101400	ENSG00000101400			11167	protein-coding gene	gene with protein product	"pro-TGF-alpha cytoplasmic domain-interacting protein 1", "dystrophin-associated protein A1, 59kDa, acidic component"	601017	"syntrophin, alpha 1 (dystrophin-associated protein A1, 59kD, acidic component)"	SNT1		8576247, 8612778	Standard	NM_003098		Approved	TACIP1, LQT12	uc002wzd.1	Q13424	OTTHUMG00000032259	ENST00000217381.2:c.465C>G	chr20.hg19:g.32026678G>C		81.0	0.0		155.0	26.0	NM_003098	A8K7H9|B4DX40|E1P5N1|Q16438	Silent	SNP	ENST00000217381.2	hg19	CCDS13220.1																																																																																			.	.		0.582	SNTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078704.2	NM_003098		C	32026678	G	C	32026678	2	2	189	1	0	0	0	0	0	0	0	1	14886	1277	45	4		4	SNTA1	20	32026678	Silent	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10		32026678	30998842	180	28056										
PREX1	57580	hgsc.bcm.edu	37	chr20	47268095	47268095	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gtcctcacacaggctcagccGgggacccagggacagcagtg	14	14	2	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr20:47268095G>A	ENST00000371941.3	-	22	2516	c.2494C>T	c.(2494-2496)Cgg>Tgg	p.R832W	PREX1_ENST00000396220.1_Missense_Mutation_p.R832W	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	832					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			AGGCTCAGCCGGGGACCCAGG	0.607																																					p.R832W		Atlas-SNP	.											.	PREX1	441	.	0			c.C2494T						.						51	48	49					20																	47268095		2203	4300	6503	SO:0001583	missense	57580	exon22			TCAGCCGGGGACC	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2494C>T	chr20.hg19:g.47268095G>A	ENSP00000361009:p.Arg832Trp	50.0	0.0		45.0	13.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.162437	0.57368	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.61859	0.09;0.07	4.82	4.82	0.62117	.	0.513361	0.16178	U	0.225959	T	0.43875	0.1267	N	0.14661	0.345	0.29711	N	0.839429	B;B	0.14805	0.001;0.011	B;B	0.09377	0.001;0.004	T	0.48581	-0.9023	10	0.72032	D	0.01	.	16.1203	0.81346	0.0:0.0:1.0:0.0	.	832;129	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	W	832	ENSP00000361009:R832W;ENSP00000379522:R832W	ENSP00000361009:R832W	R	-	1	2	PREX1	46701502	1.000000	0.71417	0.985000	0.45067	0.870000	0.49936	4.339000	0.59322	2.225000	0.72522	0.563000	0.77884	CGG	.	.		0.607	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47268095	G	A	47268095	3	1	189	1	0	0	0	0	1	0	0	0	12488	1115	39	1	2561	1	PREX1	20	47268095	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	15241417	47268095	15757425	181	28057										
ARFGAP1	55738	hgsc.bcm.edu	37	chr20	61919056	61919056	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gagcagcgacagctggacgtGcgcggacacctccaccgaga	14	14	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr20:61919056G>A	ENST00000370283.4	+	13	1192	c.1052G>A	c.(1051-1053)tGc>tAc	p.C351Y	ARFGAP1_ENST00000370275.4_3'UTR|ARFGAP1_ENST00000519273.2_Missense_Mutation_p.C238Y|ARFGAP1_ENST00000353546.3_Missense_Mutation_p.C359Y|ARFGAP1_ENST00000518794.2_3'UTR|ARFGAP1_ENST00000519604.1_Missense_Mutation_p.C306Y|MIR4326_ENST00000582203.1_RNA|ARFGAP1_ENST00000547204.1_Missense_Mutation_p.C285Y	NM_018209.2	NP_060679.1	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating protein 1	351					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPI coating of Golgi vesicle (GO:0048205)|endoplasmic reticulum unfolded protein response (GO:0030968)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cytosol (GO:0005829)|Golgi-associated vesicle membrane (GO:0030660)|synapse (GO:0045202)	ARF GTPase activator activity (GO:0008060)|GTPase activator activity (GO:0005096)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)	13	all_cancers(38;1.59e-09)					AGCTGGACGTGCGCGGACACC	0.642																																					p.C359Y		Atlas-SNP	.											.	ARFGAP1	38	.	0			c.G1076A						.						33	33	33					20																	61919056		2196	4297	6493	SO:0001583	missense	55738	exon14			GGACGTGCGCGGA	AK001629	CCDS13515.1, CCDS13516.1, CCDS63326.1, CCDS63327.1, CCDS63328.1	20q13.33	2009-11-30	2002-08-20	2002-08-23	ENSG00000101199	ENSG00000101199		"ADP-ribosylation factor GTPase activating proteins"	15852	protein-coding gene	gene with protein product		608377	"ADP-ribosylation factor 1 GTPase activating protein"	ARF1GAP		11210549	Standard	NM_018209		Approved	FLJ10767, bA261N11.3	uc002yel.3	Q8N6T3	OTTHUMG00000032965	ENST00000370283.4:c.1052G>A	chr20.hg19:g.61919056G>A	ENSP00000359306:p.Cys351Tyr	102.0	0.0		116.0	30.0	NM_175609	B7Z3U0|B7Z8H8|B7ZBI3|E1P5I9|E7EV62|Q6PK71|Q96KC4|Q96T02|Q9NSU3|Q9NVF6|Q9UIL0	Missense_Mutation	SNP	ENST00000370283.4	hg19	CCDS13515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.786|4.786	0.146162|0.146162	0.09134|0.09134	.|.	.|.	ENSG00000101199|ENSG00000101199	ENST00000549076|ENST00000370283;ENST00000547204;ENST00000523460;ENST00000519604;ENST00000519273;ENST00000353546	.|T;T;T;T;T	.|0.41758	.|1.59;1.0;1.0;0.99;1.59	4.95|4.95	3.75|3.75	0.43078|0.43078	.|.	.|0.621705	.|0.17967	.|N	.|0.155965	T|T	0.17109|0.17109	0.0411|0.0411	N|N	0.13043|0.13043	0.29|0.29	0.32563|0.32563	N|N	0.530815|0.530815	.|B;B;B;B	.|0.09022	.|0.002;0.0;0.0;0.0	.|B;B;B;B	.|0.09377	.|0.004;0.001;0.0;0.002	T|T	0.33727|0.33727	-0.9857|-0.9857	5|10	.|0.02654	.|T	.|1	-7.1054|-7.1054	2.3333|2.3333	0.04241|0.04241	0.2043:0.0:0.4925:0.3032|0.2043:0.0:0.4925:0.3032	.|.	.|238;306;351;359	.|B7Z8H8;E7EV62;Q8N6T3;Q8N6T3-2	.|.;.;ARFG1_HUMAN;.	T|Y	17|351;285;107;306;238;359	.|ENSP00000359306:C351Y;ENSP00000449800:C285Y;ENSP00000430500:C306Y;ENSP00000443716:C238Y;ENSP00000314615:C359Y	.|ENSP00000314615:C359Y	A|C	+|+	1|2	0|0	ARFGAP1|ARFGAP1	61389501|61389501	0.990000|0.990000	0.36364|0.36364	0.479000|0.479000	0.27329|0.27329	0.420000|0.420000	0.31355|0.31355	3.016000|3.016000	0.49607|0.49607	2.449000|2.449000	0.82847|0.82847	0.462000|0.462000	0.41574|0.41574	GCG|TGC	.	.		0.642	ARFGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080134.3	NM_018209		A	61919056	G	A	61919056	3	1	189	1	0	0	0	0	1	0	0	0	849	1319	46	3	1132	3	ARFGAP1	20	61919056	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	14650961	61919056	1106464	182	28058										
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62038313	62038313	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgcagcccggggtgtcctccTgccgcaggaactccatgctg	13	15	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr20:62038313T>A	ENST00000359125.2	-	17	2477	c.2303A>T	c.(2302-2304)cAg>cTg	p.Q768L	KCNQ2_ENST00000354587.3_Missense_Mutation_p.Q776L|KCNQ2_ENST00000359689.1_Missense_Mutation_p.Q768L|KCNQ2_ENST00000344462.4_Missense_Mutation_p.Q737L|KCNQ2_ENST00000370224.1_Missense_Mutation_p.Q776L|KCNQ2_ENST00000357249.2_Missense_Mutation_p.Q750L|KCNQ2_ENST00000360480.3_Missense_Mutation_p.Q740L	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	768					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GGTGTCCTCCTGCCGCAGGAA	0.731																																					p.Q768L		Atlas-SNP	.											.	KCNQ2	201	.	0			c.A2303T						.						9	8	8					20																	62038313		2136	4220	6356	SO:0001583	missense	3785	exon17			TCCTCCTGCCGCA	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.2303A>T	chr20.hg19:g.62038313T>A	ENSP00000352035:p.Gln768Leu	180.0	0.0		224.0	124.0	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	hg19	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	T	0.715	-0.785662	0.02907	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224	T;T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	4.95	-4.91	0.03085	.	1.340020	0.05022	N	0.472991	T	0.16557	0.0398	N	0.08118	0	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.13124	-1.0521	10	0.11794	T	0.64	-3.1419	2.4451	0.04504	0.3695:0.0698:0.3293:0.2314	.	740;750;737;768	O43526-3;O43526-2;O43526-4;O43526	.;.;.;KCNQ2_HUMAN	L	750;768;738;776;768;737;740;764;776	ENSP00000349789:Q750L;ENSP00000352035:Q768L;ENSP00000359246:Q738L;ENSP00000346601:Q776L;ENSP00000352718:Q768L;ENSP00000399612:Q737L;ENSP00000353668:Q740L;ENSP00000339611:Q764L;ENSP00000359244:Q776L	ENSP00000339611:Q764L	Q	-	2	0	KCNQ2	61508757	0.000000	0.05858	0.005000	0.12908	0.030000	0.12068	-0.161000	0.10026	-1.454000	0.01926	0.402000	0.26972	CAG	.	.		0.731	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		A	62038313	T	A	62038313	3	1	189	1	0	0	0	0	1	0	0	0	8092	1580	55	4	319	4	KCNQ2	20	62038313	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	119257	62038313	987207	183	28059										
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28338522	28338522	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ctcctgcgccgctgcgccagGgggtgcgggtggccgggagg	21	13	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr21:28338522G>T	ENST00000284987.5	-	1	310	c.189C>A	c.(187-189)ccC>ccA	p.P63P		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	63					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						GCTGCGCCAGGGGGTGCGGGT	0.746																																					p.P63P	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.C189A						.						18	19	18					21																	28338522		2101	4140	6241	SO:0001819	synonymous_variant	11096	exon1			CGCCAGGGGGTGC	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"ADAM metallopeptidases with thrombospondin type 1 motif"	221	protein-coding gene	gene with protein product	"aggrecanase-2"	605007	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.189C>A	chr21.hg19:g.28338522G>T		63.0	0.0		97.0	60.0	NM_007038	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	hg19	CCDS13579.1																																																																																			.	.		0.746	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			T	28338522	G	T	28338522	2	4	189	1	0	0	0	0	0	0	0	1	269	1219	43	3		3	ADAMTS5	21	28338522	Silent	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10		28338522	19791373	184	28060										
TTC3	7267	hgsc.bcm.edu	37	chr21	38567975	38567975	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggtgtggtgtgttcctcacaGgttcatcccgagttactccc	11	12	2	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr21:38567975G>A	ENST00000399017.2	+	42	7964		c.e42-1		TTC3-AS1_ENST00000424733.1_RNA|TTC3_ENST00000354749.2_Splice_Site|TTC3_ENST00000479930.1_Splice_Site|TTC3_ENST00000355666.1_Splice_Site	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3						negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GTTCCTCACAGGTTCATCCCG	0.537																																					.	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.5218-1G>A						.						268	278	275					21																	38567975		2203	4300	6503	SO:0001630	splice_region_variant	7267	exon42			CTCACAGGTTCAT	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5218-1G>A	chr21.hg19:g.38567975G>A		144.0	0.0		176.0	48.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Splice_Site	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	G	9.382	1.073249	0.20147	.	.	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749;ENST00000428693	.	.	.	4.72	3.56	0.40772	.	.	.	.	.	.	.	.	.	.	.	0.21020	N	0.999802	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.861	0.18747	0.1781:0.0:0.8219:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TTC3	37489845	0.159000	0.22864	0.095000	0.20976	0.003000	0.03518	1.405000	0.34635	2.348000	0.79779	0.563000	0.77884	.	.	.		0.537	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		Intron	A	38567975	G	A	38567975	5	1	189	1	0	0	0	0	0	0	1	0	16712	1014	35	3	5379	3	TTC3	21	38567975	Splice_Site	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	10229453	38567975	9561920	185	28061										
TTC3	7267	hgsc.bcm.edu	37	chr21	38567997	38567997	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ttcatcccgagttactccctGagtcttcaggcgacgatggc	10	13	3	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr21:38567997G>T	ENST00000399017.2	+	42	7986	c.5239G>T	c.(5239-5241)Gag>Tag	p.E1747*	TTC3-AS1_ENST00000424733.1_RNA|TTC3_ENST00000354749.2_Nonsense_Mutation_p.E1747*|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Nonsense_Mutation_p.E1747*	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1747					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GTTACTCCCTGAGTCTTCAGG	0.542																																					p.E1747X	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.G5239T						.						238	247	244					21																	38567997		2203	4300	6503	SO:0001587	stop_gained	7267	exon42			CTCCCTGAGTCTT	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5239G>T	chr21.hg19:g.38567997G>T	ENSP00000381981:p.Glu1747*	151.0	0.0		168.0	44.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Nonsense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	53|53	20.113003|20.113003	0.99927|0.99927	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749|ENST00000428693	.|.	.|.	.|.	4.72|4.72	0.712|0.712	0.18167|0.18167	.|.	0.700044|.	0.12264|.	N|.	0.484431|.	.|.	.|.	.|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.59425|.	D|.	0.04|.	-4.7468|-4.7468	3.9876|3.9876	0.09522|0.09522	0.303:0.1782:0.5188:0.0|0.303:0.1782:0.5188:0.0	.|.	.|.	.|.	.|.	X|L	1747|38	.|.	ENSP00000346791:E1747X|.	E|X	+|+	1|2	0|2	TTC3|TTC3	37489867|37489867	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.008000|0.008000	0.06430|0.06430	0.022000|0.022000	0.13511|0.13511	0.158000|0.158000	0.19367|0.19367	0.563000|0.563000	0.77884|0.77884	GAG|TGA	.	.		0.542	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38567997	G	T	38567997	4	4	189	1	0	0	0	0	0	1	0	0	16712	1291	45	3	5401	3	TTC3	21	38567997	Nonsense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	22	38567997	9561898	186	28062										
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057580	46057580	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cagcagtctagctgccagccGgattgctgcacctcctcccc	9	18	1	0	rs150687639	byFrequency	TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr21:46057580G>T	ENST00000380095.1	+	1	308	c.246G>T	c.(244-246)ccG>ccT	p.P82P	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	82	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						GCTGCCAGCCGGATTGCTGCA	0.652																																					p.P82P		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G246T						.						112	108	109					21																	46057580		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CCAGCCGGATTGC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"Keratin associated proteins"	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.246G>T	chr21.hg19:g.46057580G>T		31.0	0.0		36.0	14.0	NM_181688		Silent	SNP	ENST00000380095.1	hg19	CCDS33585.1																																																																																			.	G|0.999;A|0.001		0.652	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		T	46057580	G	T	46057580	2	4	189	1	0	0	0	0	0	0	0	1	8515	1103	39	1		1	KRTAP10-10	21	46057580	Silent	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	7489583	46057580	2072315	187	28063										
SCARF2	91179	hgsc.bcm.edu	37	chr22	20784091	20784091	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cctgagcacagtccgcgccgTggagtccgggcgggcacgtc	16	15	0	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr22:20784091T>A	ENST00000266214.5	-	7	1336	c.1232A>T	c.(1231-1233)cAc>cTc	p.H411L	SCARF2_ENST00000405555.3_Missense_Mutation_p.H411L	NM_153334.4	NP_699165.2	Q96GP6	SREC2_HUMAN	scavenger receptor class F, member 2	411					cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	10	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GTCCGCGCCGTGGAGTCCGGG	0.677																																					p.H411L		Atlas-SNP	.											.	SCARF2	23	.	0			c.A1232T						.						43	41	42					22																	20784091		2203	4299	6502	SO:0001583	missense	91179	exon7			GCGCCGTGGAGTC	AF522196	CCDS13779.1, CCDS46666.1	22q11.21	2011-10-10			ENSG00000244486	ENSG00000244486			19869	protein-coding gene	gene with protein product		613619				12154095	Standard	XM_006724364		Approved	SREC-II, SREC2, HUMZD58C02	uc002zsk.2	Q96GP6	OTTHUMG00000150779	ENST00000266214.5:c.1232A>T	chr22.hg19:g.20784091T>A	ENSP00000266214:p.His411Leu	118.0	0.0		88.0	40.0	NM_182895	E5RFB8|Q58A83|Q8IXF3|Q9BW74	Missense_Mutation	SNP	ENST00000266214.5	hg19	CCDS13779.1	.	.	.	.	.	.	.	.	.	.	T	16.56	3.156590	0.57259	.	.	ENSG00000244486	ENST00000405555;ENST00000341328;ENST00000266214	T;T	0.32753	1.44;1.44	4.11	2.97	0.34412	.	0.331162	0.28057	N	0.016765	T	0.18087	0.0434	L	0.27053	0.805	0.80722	D	1	P;B	0.35383	0.498;0.329	B;B	0.33454	0.164;0.095	T	0.04579	-1.0941	10	0.48119	T	0.1	-24.2577	6.4427	0.21859	0.3545:0.0:0.0:0.6455	.	411;411	E5RFB8;Q96GP6	.;SREC2_HUMAN	L	411	ENSP00000385589:H411L;ENSP00000266214:H411L	ENSP00000266214:H411L	H	-	2	0	SCARF2	19114091	0.995000	0.38212	0.996000	0.52242	0.872000	0.50106	2.314000	0.43743	1.614000	0.50241	0.383000	0.25322	CAC	.	.		0.677	SCARF2-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320047.1			A	20784091	T	A	20784091	3	1	189	1	0	0	0	0	1	0	0	0	13899	1696	59	4	1400	4	SCARF2	22	20784091	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10		20784091	30520475	188	28064										
KLHL22	84861	hgsc.bcm.edu	37	chr22	20819206	20819206	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gtcccctccaatcaagtataCgaagttgttgagcaccgcga	9	12	1	1	rs372979261		TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr22:20819206C>T	ENST00000328879.4	-	4	1207	c.1051G>A	c.(1051-1053)Gta>Ata	p.V351I	KLHL22_ENST00000440659.2_Missense_Mutation_p.V208I	NM_032775.3	NP_116164.2	Q53GT1	KLH22_HUMAN	kelch-like family member 22	351					cell division (GO:0051301)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein monoubiquitination (GO:0006513)	centrosome (GO:0005813)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|polar microtubule (GO:0005827)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	20	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			ATCAAGTATACGAAGTTGTTG	0.557																																					p.V351I		Atlas-SNP	.											KLHL22,colon,carcinoma,0,1	KLHL22	52	.	0			c.G1051A						.	C	ILE/VAL	0,4406		0,0,2203	99	89	93		1051	5.4	1	22		93	2,8598	1.2+/-3.3	0,2,4298	no	missense	KLHL22	NM_032775.3	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	351/635	20819206	2,13004	2203	4300	6503	SO:0001583	missense	84861	exon4			AGTATACGAAGTT		CCDS13780.1	22q11.21	2013-01-30	2013-01-30		ENSG00000099910	ENSG00000099910		"Kelch-like", "BTB/POZ domain containing"	25888	protein-coding gene	gene with protein product			"kelch-like 22 (Drosophila)"			12477932	Standard	NM_032775		Approved	FLJ14360, KELCHL	uc002zsl.2	Q53GT1	OTTHUMG00000150778	ENST00000328879.4:c.1051G>A	chr22.hg19:g.20819206C>T	ENSP00000331682:p.Val351Ile	48.0	0.0		31.0	10.0	NM_032775	A8K3Q4|A8MTV3|B7Z2G1|D3DX30|Q96B68|Q96KC6	Missense_Mutation	SNP	ENST00000328879.4	hg19	CCDS13780.1	.	.	.	.	.	.	.	.	.	.	C	19.77	3.890168	0.72524	0.0	2.33E-4	ENSG00000099910	ENST00000328879;ENST00000440659	T;T	0.63744	-0.06;-0.06	5.42	5.42	0.78866	Kelch-type beta propeller (1);	0.119762	0.56097	D	0.000033	T	0.55289	0.1911	N	0.21282	0.65	0.50313	D	0.999869	D;D	0.56968	0.978;0.957	P;B	0.47206	0.541;0.387	T	0.56396	-0.7986	10	0.38643	T	0.18	.	16.693	0.85327	0.0:1.0:0.0:0.0	.	208;351	B7Z2G1;Q53GT1	.;KLH22_HUMAN	I	351;208	ENSP00000331682:V351I;ENSP00000405521:V208I	ENSP00000331682:V351I	V	-	1	0	KLHL22	19149206	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	4.578000	0.60929	2.531000	0.85337	0.655000	0.94253	GTA	.	.		0.557	KLHL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320045.2	NM_032775		T	20819206	C	T	20819206	3	4	189	1	0	0	0	0	1	0	0	0	8386	536	19	1	869	1	KLHL22	22	20819206	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	35115	20819206	30485360	189	28065										
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50722376	50722376	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tcggggttagcggcccggcaCaggctgcagtcgctgcggcc	17	14	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chr22:50722376C>G	ENST00000449103.1	-	14	2447	c.2307G>C	c.(2305-2307)ctG>ctC	p.L769L	PLXNB2_ENST00000359337.4_Silent_p.L769L|PLXNB2_ENST00000496720.1_5'UTR			O15031	PLXB2_HUMAN	plexin B2	769					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CGGCCCGGCACAGGCTGCAGT	0.697																																					p.L769L		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G2307C						.						12	18	16					22																	50722376		2009	4127	6136	SO:0001819	synonymous_variant	23654	exon14			CCGGCACAGGCTG		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.2307G>C	chr22.hg19:g.50722376C>G		40.0	0.0		32.0	10.0	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	hg19	CCDS43035.1																																																																																			.	.		0.697	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		G	50722376	C	G	50722376	2	3	189	1	0	0	0	0	0	0	0	1	12133	465	17	4		4	PLXNB2	22	50722376	Silent	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	29903170	50722376	582190	190	28066										
TBL1X	6907	hgsc.bcm.edu	37	chrX	9677307	9677307	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	gaacgaggtcaacgccatcaAatgggatccgtctggaatgt	12	9	3	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chrX:9677307A>G	ENST00000217964.7	+	14	1896	c.1256A>G	c.(1255-1257)aAa>aGa	p.K419R	TBL1X_ENST00000380961.1_Missense_Mutation_p.K368R|TBL1X_ENST00000407597.2_Missense_Mutation_p.K419R|TBL1X_ENST00000536365.1_Missense_Mutation_p.K368R|TBL1X_ENST00000424279.1_Missense_Mutation_p.K368R	NM_005647.3	NP_005638.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	419					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				AACGCCATCAAATGGGATCCG	0.527											OREG0019658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K419R		Atlas-SNP	.											.	TBL1X	103	.	0			c.A1256G						.						113	78	90					X																	9677307		2203	4300	6503	SO:0001583	missense	6907	exon14			CCATCAAATGGGA	Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849		"WD repeat domain containing"	11585	protein-coding gene	gene with protein product		300196	"transducin (beta)-like 1"	TBL1		10330347	Standard	NM_005647		Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000217964.7:c.1256A>G	chrX.hg19:g.9677307A>G	ENSP00000217964:p.Lys419Arg	169.0	0.0	658	135.0	50.0	NM_001139466	A8K044|A8K4J7|Q86UY2	Missense_Mutation	SNP	ENST00000217964.7	hg19	CCDS14133.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.120678	0.77323	.	.	ENSG00000101849	ENST00000407597;ENST00000424279;ENST00000536365;ENST00000380961;ENST00000217964	T;T;T;T;T	0.60424	0.19;0.19;0.19;0.19;0.19	4.03	4.03	0.46877	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.50292	0.1607	N	0.04355	-0.22	0.58432	D	0.999998	D;D	0.63880	0.993;0.965	D;D	0.63381	0.914;0.914	T	0.54262	-0.8320	10	0.30854	T	0.27	.	12.8926	0.58080	1.0:0.0:0.0:0.0	.	382;419	Q59F53;O60907	.;TBL1X_HUMAN	R	419;368;368;368;419	ENSP00000385988:K419R;ENSP00000394097:K368R;ENSP00000445317:K368R;ENSP00000370348:K368R;ENSP00000217964:K419R	ENSP00000217964:K419R	K	+	2	0	TBL1X	9637307	1.000000	0.71417	0.978000	0.43139	0.951000	0.60555	8.650000	0.91073	1.569000	0.49696	0.481000	0.45027	AAA	.	.		0.527	TBL1X-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055709.1	NM_005647		G	9677307	A	G	9677307	3	3	189	1	0	0	0	0	1	0	0	0	15654	14	1	2	1298	2	TBL1X	23	9677307	Missense_Mutation	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10		9677307	145593253	191	28067										
PHF16	9767	hgsc.bcm.edu	37	chrX	46893038	46893038	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tccaggcctgctatggcatcCtcaaggtcccagaaggcagc	11	14	1	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chrX:46893038C>T	ENST00000218343.4	+	7	1001	c.703C>T	c.(703-705)Ctc>Ttc	p.L235F	PHF16_ENST00000397189.1_Missense_Mutation_p.L235F	NM_014735.3	NP_055550.1														NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						CTATGGCATCCTCAAGGTCCC	0.532																																					p.L235F		Atlas-SNP	.											.	PHF16	72	.	0			c.C703T						.						123	77	93					X																	46893038		2203	4300	6503	SO:0001583	missense	9767	exon7			GGCATCCTCAAGG																												ENST00000218343.4:c.703C>T	chrX.hg19:g.46893038C>T	ENSP00000218343:p.Leu235Phe	118.0	0.0		186.0	9.0	NM_001077445		Missense_Mutation	SNP	ENST00000218343.4	hg19	CCDS14271.1	.	.	.	.	.	.	.	.	.	.	c	21.3	4.122821	0.77436	.	.	ENSG00000102221	ENST00000397189;ENST00000218343	D;D	0.87809	-2.3;-2.3	5.39	5.39	0.77823	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.063541	0.64402	D	0.000008	D	0.90133	0.6917	M	0.66439	2.03	0.45962	D	0.998785	P	0.46277	0.875	P	0.54590	0.756	D	0.90341	0.4359	10	0.54805	T	0.06	.	11.9528	0.52964	0.0:0.9071:0.0:0.0929	.	235	Q92613	JADE3_HUMAN	F	235	ENSP00000380373:L235F;ENSP00000218343:L235F	ENSP00000218343:L235F	L	+	1	0	PHF16	46777982	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.210000	0.42816	2.240000	0.73641	0.591000	0.81541	CTC	.	.		0.532	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			T	46893038	C	T	46893038	3	4	189	1	0	0	0	0	1	0	0	0	11836	681	24	3	725	3	PHF16	23	46893038	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	37215731	46893038	108377522	192	28068										
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53279807	53279807	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggctggggctgggccttcagGggctgggtagtggcggtgtg	23	7	1	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chrX:53279807G>T	ENST00000375368.5	-	4	2121	c.1921C>A	c.(1921-1923)Cct>Act	p.P641T	IQSEC2_ENST00000375365.2_Missense_Mutation_p.P446T|IQSEC2_ENST00000396435.3_Missense_Mutation_p.P651T			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	641	Pro-rich.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						gggccttcaggggctgggTAG	0.701																																					p.P651T		Atlas-SNP	.											.	IQSEC2	195	.	0			c.C1951A						.						13	16	15					X																	53279807		2165	4215	6380	SO:0001583	missense	23096	exon5			CTTCAGGGGCTGG	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.1921C>A	chrX.hg19:g.53279807G>T	ENSP00000364517:p.Pro641Thr	73.0	0.0		80.0	22.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	g	14.11	2.436633	0.43224	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	T;T;T	0.11821	2.74;2.74;2.74	5.37	5.37	0.77165	.	0.448137	0.23319	N	0.049468	T	0.15219	0.0367	N	0.08118	0	0.52099	D	0.999941	D;D	0.59767	0.986;0.981	P;P	0.56563	0.801;0.732	T	0.30446	-0.9978	10	0.28530	T	0.3	.	16.8728	0.86044	0.0:0.0:1.0:0.0	.	651;446	Q5JU85-2;Q5JU85-3	.;.	T	651;641;446	ENSP00000379712:P651T;ENSP00000364517:P641T;ENSP00000364514:P446T	ENSP00000364514:P446T	P	-	1	0	IQSEC2	53296532	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.076000	0.76806	2.246000	0.74042	0.597000	0.82753	CCT	.	.		0.701	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		T	53279807	G	T	53279807	3	4	189	1	0	0	0	0	1	0	0	0	7827	1232	43	3	2559	3	IQSEC2	23	53279807	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	6386769	53279807	101990753	193	28069										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53591649	53591649	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tctgtctgagtgacatcatgAtcctcctcctgcacttctgc	7	14	4	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chrX:53591649A>G	ENST00000342160.3	-	50	7372	c.6915T>C	c.(6913-6915)gaT>gaC	p.D2305D	HUWE1_ENST00000262854.6_Silent_p.D2305D			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2305	Glu-rich.				base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TGACATCATGATCCTCCTCCT	0.532																																					p.D2305D		Atlas-SNP	.											.	HUWE1	724	.	0			c.T6915C						.						186	124	145					X																	53591649		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon51			ATCATGATCCTCC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.6915T>C	chrX.hg19:g.53591649A>G		71.0	0.0		78.0	23.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	A	7.025	0.559405	0.13436	.	.	ENSG00000086758	ENST00000427052	.	.	.	5.44	4.26	0.50523	.	.	.	.	.	T	0.56277	0.1974	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54390	-0.8301	4	.	.	.	.	6.6606	0.23012	0.8091:0.0:0.1909:0.0	.	.	.	.	P	1339	.	.	S	-	1	0	HUWE1	53608374	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.539000	0.45718	1.813000	0.52934	0.417000	0.27973	TCA	.	.		0.532	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		G	53591649	A	G	53591649	2	3	189	1	0	0	0	0	0	0	0	1	7470	330	12	2		2	HUWE1	23	53591649	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	311842	53591649	101678911	194	28070										
APEX2	27301	hgsc.bcm.edu	37	chrX	55026952	55026952	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	actgtgccgccgtggccgtgGggcgcattttggacgagctg	17	11	0	0			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chrX:55026952G>A	ENST00000374987.3	+	1	163	c.97G>A	c.(97-99)Ggg>Agg	p.G33R	PFKFB1_ENST00000545676.1_5'Flank|APEX2_ENST00000471758.1_3'UTR	NM_014481.2	NP_055296.2	Q9UBZ4	APEX2_HUMAN	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	33					base-excision repair (GO:0006284)|cell cycle (GO:0007049)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1)	21						CGTGGCCGTGGGGCGCATTTT	0.552								Other BER factors																													p.G33R		Atlas-SNP	.											.	APEX2	50	.	0			c.G97A						.						83	55	64					X																	55026952		2203	4300	6503	SO:0001583	missense	27301	exon1			GCCGTGGGGCGCA	AB021260	CCDS14365.1	Xp11.23	2014-02-18			ENSG00000169188	ENSG00000169188	4.2.99.18		17889	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 2"	300773				11376153	Standard	NM_014481		Approved	APEXL2, APE2, XTH2, ZGRF2	uc004dtz.4	Q9UBZ4	OTTHUMG00000021642	ENST00000374987.3:c.97G>A	chrX.hg19:g.55026952G>A	ENSP00000364126:p.Gly33Arg	128.0	0.0		143.0	48.0	NM_014481	Q9Y5X7	Missense_Mutation	SNP	ENST00000374987.3	hg19	CCDS14365.1	.	.	.	.	.	.	.	.	.	.	G	1.756	-0.488033	0.04352	.	.	ENSG00000169188	ENST00000374987	T	0.79554	-1.28	4.28	-0.352	0.12598	Endonuclease/exonuclease/phosphatase (2);	0.854101	0.09910	N	0.739931	T	0.41971	0.1182	N	0.00450	-1.49	0.09310	N	1	B	0.09022	0.002	B	0.16289	0.015	T	0.42275	-0.9461	10	0.10377	T	0.69	-0.2934	3.5056	0.07689	0.4379:0.2004:0.3617:0.0	.	33	Q9UBZ4	APEX2_HUMAN	R	33	ENSP00000364126:G33R	ENSP00000364126:G33R	G	+	1	0	APEX2	55043677	0.472000	0.25870	0.064000	0.19789	0.736000	0.42039	0.035000	0.13797	-0.044000	0.13491	0.544000	0.68410	GGG	.	.		0.552	APEX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056845.1			A	55026952	G	A	55026952	3	1	189	1	0	0	0	0	1	0	0	0	770	1232	43	3	99	3	APEX2	23	55026952	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	1435303	55026952	100243608	195	28071										
MED12	9968	hgsc.bcm.edu	37	chrX	70354642	70354642	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cagacatgtctagcatctcgCaaggtagcatggaggaaaac	11	9	2	1			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chrX:70354642C>A	ENST00000374080.3	+	35	4839	c.4807C>A	c.(4807-4809)Caa>Aaa	p.Q1603K	MED12_ENST00000333646.6_Missense_Mutation_p.Q1603K|MED12_ENST00000374102.1_Missense_Mutation_p.Q1603K			Q93074	MED12_HUMAN	mediator complex subunit 12	1603					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					TAGCATCTCGCAAGGTAGCAT	0.517			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.Q1603K		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.C4807A						.						104	89	94					X																	70354642		2062	4192	6254	SO:0001583	missense	9968	exon35			ATCTCGCAAGGTA	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.4807C>A	chrX.hg19:g.70354642C>A	ENSP00000363193:p.Gln1603Lys	199.0	0.0		188.0	61.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	hg19	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	-	18.36	3.605928	0.66445	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072;ENST00000439750	T;T;T;T;T	0.61742	0.33;0.08;0.33;0.08;1.39	4.28	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.51466	0.1676	L	0.31752	0.955	0.58432	D	0.999999	P;P;P;P	0.42785	0.762;0.616;0.739;0.79	B;B;P;B	0.44811	0.352;0.221;0.461;0.379	T	0.52434	-0.8576	10	0.35671	T	0.21	-0.2101	16.4023	0.83644	0.0:1.0:0.0:0.0	.	1603;1450;1603;1603	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	K	1603;1603;1603;1603;1571;348	ENSP00000333125:Q1603K;ENSP00000363215:Q1603K;ENSP00000363193:Q1603K;ENSP00000414203:Q1571K;ENSP00000408388:Q348K	ENSP00000333125:Q1603K	Q	+	1	0	MED12	70271367	1.000000	0.71417	0.514000	0.27761	0.707000	0.40811	5.546000	0.67243	2.129000	0.65627	0.529000	0.55759	CAA	.	.		0.517	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		A	70354642	C	A	70354642	3	1	189	1	0	0	0	0	1	0	0	0	9437	711	25	3	4945	3	MED12	23	70354642	Missense_Mutation	SNP	C	TCGA-DD-AADF-01A-11D-A40R-10	15327690	70354642	84915918	196	28072										
LRCH2	57631	hgsc.bcm.edu	37	chrX	114404863	114404863	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	tgtaagaatgttacattaccTgtctgtgagaggctgtgagg	13	5	1	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chrX:114404863T>A	ENST00000317135.8	-	6	1027	c.997A>T	c.(997-999)Agt>Tgt	p.S333C	LRCH2_ENST00000538422.1_Splice_Site_p.S333C	NM_020871.3	NP_065922.3	Q5VUJ6	LRCH2_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 2	333										breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	19						TTACATTACCTGTCTGTGAGA	0.353																																					p.S333C		Atlas-SNP	.											.	LRCH2	138	.	0			c.A997T						.						109	95	99					X																	114404863		1892	4094	5986	SO:0001630	splice_region_variant	57631	exon6			ATTACCTGTCTGT	AB040928	CCDS48155.1, CCDS59175.1	Xq24	2008-02-05			ENSG00000130224	ENSG00000130224			29292	protein-coding gene	gene with protein product						10819331	Standard	NM_020871		Approved	KIAA1495	uc010nqe.3	Q5VUJ6	OTTHUMG00000022233	ENST00000317135.8:c.998+1A>T	chrX.hg19:g.114404863T>A		202.0	0.0		197.0	54.0	NM_001243963	F5H2T1|Q08AD5|Q9HA88|Q9P233	Missense_Mutation	SNP	ENST00000317135.8	hg19	CCDS48155.1	.	.	.	.	.	.	.	.	.	.	T	17.71	3.457707	0.63401	.	.	ENSG00000130224	ENST00000317135;ENST00000538422	T;T	0.01015	5.5;5.44	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.03651	0.0104	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79108	0.99;0.992	T	0.65878	-0.6061	10	0.23302	T	0.38	-12.5504	13.7074	0.62648	0.0:0.0:0.0:1.0	.	333;333	Q5VUJ6;F5H2T1	LRCH2_HUMAN;.	C	333	ENSP00000325091:S333C;ENSP00000439366:S333C	ENSP00000325091:S333C	S	-	1	0	LRCH2	114311119	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.662000	0.83803	1.917000	0.55516	0.481000	0.45027	AGT	.	.		0.353	LRCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057971.2	NM_020871	Missense_Mutation	A	114404863	T	A	114404863	5	1	189	1	0	0	0	0	0	0	1	0	8942	1594	55	4	1364	4	LRCH2	23	114404863	Splice_Site	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	44050221	114404863	40865697	197	28073										
ARHGAP36	158763	hgsc.bcm.edu	37	chrX	130215821	130215821	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	cctctctgagctggagcgtcTgaagctgcaagagactgctt	12	11	2	3			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chrX:130215821T>A	ENST00000276211.5	+	2	527	c.182T>A	c.(181-183)cTg>cAg	p.L61Q	ARHGAP36_ENST00000370922.1_Missense_Mutation_p.L49Q|ARHGAP36_ENST00000370921.1_5'Flank	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	61					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						CTGGAGCGTCTGAAGCTGCAA	0.527																																					p.L61Q		Atlas-SNP	.											.	ARHGAP36	171	.	0			c.T182A						.						124	107	113					X																	130215821		2203	4300	6503	SO:0001583	missense	158763	exon2			AGCGTCTGAAGCT		CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"Rho GTPase activating proteins"	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.182T>A	chrX.hg19:g.130215821T>A	ENSP00000276211:p.Leu61Gln	88.0	0.0		99.0	27.0	NM_144967	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Missense_Mutation	SNP	ENST00000276211.5	hg19	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.297589	0.60086	.	.	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000423277;ENST00000412432	T;T;T	0.12569	2.67;2.69;2.71	4.16	4.16	0.48862	.	0.000000	0.36374	N	0.002633	T	0.16471	0.0396	N	0.19112	0.55	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.995	D;D;D	0.68943	0.961;0.961;0.916	T	0.12041	-1.0563	10	0.13108	T	0.6	.	8.6068	0.33778	0.0:0.0:0.0:1.0	.	30;49;61	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	Q	61;49;13;30	ENSP00000276211:L61Q;ENSP00000359960:L49Q;ENSP00000408515:L30Q	ENSP00000276211:L61Q	L	+	2	0	ARHGAP36	130043502	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.868000	0.48436	1.852000	0.53769	0.441000	0.28932	CTG	.	.		0.527	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967		A	130215821	T	A	130215821	3	1	189	1	0	0	0	0	1	0	0	0	883	1580	55	4	184	4	ARHGAP36	23	130215821	Missense_Mutation	SNP	T	TCGA-DD-AADF-01A-11D-A40R-10	15810958	130215821	25054739	198	28074										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144906061	144906061	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	atctacatgcagaaggaaggAgacccagtagcctattaccg	10	10	1	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chrX:144906061A>T	ENST00000370490.1	+	1	6373	c.2118A>T	c.(2116-2118)ggA>ggT	p.G706G	SLITRK2_ENST00000434188.2_Silent_p.G706G|SLITRK2_ENST00000428560.2_Silent_p.G706G|TMEM257_ENST00000408967.2_5'Flank|SLITRK2_ENST00000447897.2_Silent_p.G706G|SLITRK2_ENST00000413937.2_Silent_p.G706G			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	706					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					AGAAGGAAGGAGACCCAGTAG	0.488																																					p.G706G		Atlas-SNP	.											.	SLITRK2	221	.	0			c.A2118T						.						75	75	75					X																	144906061		2203	4300	6503	SO:0001819	synonymous_variant	84631	exon5			GGAAGGAGACCCA	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.2118A>T	chrX.hg19:g.144906061A>T		149.0	0.0		171.0	53.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	hg19	CCDS14680.1																																																																																			.	.		0.488	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		T	144906061	A	T	144906061	2	4	189	1	0	0	0	0	0	0	0	1	14758	291	11	4		4	SLITRK2	23	144906061	Silent	SNP	A	TCGA-DD-AADF-01A-11D-A40R-10	14690240	144906061	10364499	199	28075										
PLXNA3	55558	hgsc.bcm.edu	37	chrX	153690520	153690520	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0251256281407035	5	1	0.864273927392739	0.518564356435644	1.03712871287129	0.31077694235589	1	0	ggtgttgaaccagcctctggGaggcctgcatgtgatcgagg	16	9	1	2			TCGA-DD-AADF-01A-11D-A40R-10	TCGA-DD-AADF-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a59f4ad7-f2cf-4109-b2e9-fa35260a2fe0	87a7ce38-2b8a-42a0-b22f-33534f342ff4	g.chrX:153690520G>C	ENST00000369682.3	+	4	1362	c.1187G>C	c.(1186-1188)gGa>gCa	p.G396A		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	396	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CAGCCTCTGGGAGGCCTGCAT	0.632																																					p.G396A		Atlas-SNP	.											.	PLXNA3	156	.	0			c.G1187C						.						44	43	43					X																	153690520		2202	4300	6502	SO:0001583	missense	55558	exon4			CTCTGGGAGGCCT	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"Plexins"	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.1187G>C	chrX.hg19:g.153690520G>C	ENSP00000358696:p.Gly396Ala	174.0	0.0		154.0	37.0	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	hg19	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.051905	0.75960	.	.	ENSG00000130827	ENST00000369682	T	0.10288	2.89	4.9	4.9	0.64082	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.26340	0.0643	L	0.55213	1.73	0.80722	D	1	D	0.62365	0.991	D	0.64321	0.924	T	0.00525	-1.1689	10	0.42905	T	0.14	.	15.8369	0.78805	0.0:0.0:1.0:0.0	.	396	P51805	PLXA3_HUMAN	A	396	ENSP00000358696:G396A	ENSP00000358696:G396A	G	+	2	0	PLXNA3	153343714	1.000000	0.71417	0.922000	0.36590	0.458000	0.32498	9.574000	0.98184	2.251000	0.74343	0.597000	0.82753	GGA	.	.		0.632	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		C	153690520	G	C	153690520	3	2	189	1	0	0	0	0	1	0	0	0	12130	1174	41	4	1197	4	PLXNA3	23	153690520	Missense_Mutation	SNP	G	TCGA-DD-AADF-01A-11D-A40R-10	8784459	153690520	1580040	200	28076										
NPHP4	261734	hgsc.bcm.edu	37	chr1	6029260	6029260	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tcccgtttcttgccctcagcGaccacttccaccacagccac	5	20	2	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:6029260G>A	ENST00000378156.4	-	4	604	c.339C>T	c.(337-339)gtC>gtT	p.V113V	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	113					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCCTCAGCGACCACTTCCA	0.527																																					p.V113V		Atlas-SNP	.											.	NPHP4	119	.	0			c.C339T						.						78	86	83					1																	6029260		2004	4151	6155	SO:0001819	synonymous_variant	261734	exon4			CTCAGCGACCACT	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.339C>T	chr1.hg19:g.6029260G>A		115.0	0.0		148.0	59.0	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	hg19	CCDS44052.1																																																																																			.	.		0.527	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			A	6029260	G	A	6029260	2	1	190	1	0	0	0	0	0	0	0	1	10590	1045	37	1		1	NPHP4	1	6029260	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10		6029260	243221361	1	28077										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7796520	7796520	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aagcacttgatccactcaaaGactttccgcggaatgaccct	7	13	1	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:7796520G>C	ENST00000303635.7	+	13	3390	c.3183G>C	c.(3181-3183)aaG>aaC	p.K1061N	CAMTA1_ENST00000439411.2_Missense_Mutation_p.K1061N	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1061					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TCCACTCAAAGACTTTCCGCG	0.592			T	WWTR1	epitheliod hemangioendothelioma																																p.K1061N		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.G3183C						.						138	124	129					1																	7796520		2203	4300	6503	SO:0001583	missense	23261	exon13			CTCAAAGACTTTC	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3183G>C	chr1.hg19:g.7796520G>C	ENSP00000306522:p.Lys1061Asn	160.0	0.0		163.0	7.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	hg19	CCDS30576.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.2|22.2	4.252809|4.252809	0.80135|0.80135	.|.	.|.	ENSG00000171735|ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646|ENST00000495233	T;T|.	0.45276|.	0.9;0.9|.	5.58|5.58	3.73|3.73	0.42828|0.42828	Ankyrin repeat-containing domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.60011|0.60011	0.2236|0.2236	L|L	0.51422|0.51422	1.61|1.61	0.54753|0.54753	D|D	0.999989|0.999989	D;D;D;D|.	0.76494|.	0.995;0.999;0.996;0.997|.	D;D;P;D|.	0.80764|.	0.969;0.994;0.873;0.931|.	T|T	0.55425|0.55425	-0.8143|-0.8143	10|5	0.17369|.	T|.	0.5|.	-25.379|-25.379	12.042|12.042	0.53458|0.53458	0.1384:0.0:0.8616:0.0|0.1384:0.0:0.8616:0.0	.|.	1061;148;17;1061|.	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1|.	.;.;.;CMTA1_HUMAN|.	N|T	1061;1061;148;17|18	ENSP00000306522:K1061N;ENSP00000402561:K1061N|.	ENSP00000306522:K1061N|.	K|R	+|+	3|2	2|0	CAMTA1|CAMTA1	7719107|7719107	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.832000|0.832000	0.47134|0.47134	4.090000|4.090000	0.57693|0.57693	0.736000|0.736000	0.32559|0.32559	-0.122000|-0.122000	0.15005|0.15005	AAG|AGA	.	.		0.592	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		C	7796520	G	C	7796520	3	2	190	1	0	0	0	0	1	0	0	0	2615	933	33	4	3233	4	CAMTA1	1	7796520	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	1767260	7796520	241454101	2	28078										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12359278	12359278	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ggtgagagatcaagcccagcGctgttcacgggttctcctgg	14	11	3	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:12359278G>T	ENST00000358136.3	+	25	6183	c.6053G>T	c.(6052-6054)cGc>cTc	p.R2018L	VPS13D_ENST00000356315.4_Missense_Mutation_p.R2018L	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CAAGCCCAGCGCTGTTCACGG	0.438																																					p.R2018L		Atlas-SNP	.											VPS13D,NS,carcinoma,0,1	VPS13D	316	.	0			c.G6053T						.						96	96	96					1																	12359278		2203	4300	6503	SO:0001583	missense	55187	exon25			CCCAGCGCTGTTC	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.6053G>T	chr1.hg19:g.12359278G>T	ENSP00000350854:p.Arg2018Leu	76.0	0.0		87.0	4.0	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	hg19	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.8|29.8	5.037451|5.037451	0.93630|0.93630	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000011700|ENST00000356315;ENST00000358136	.|T;T	.|0.56941	.|0.43;0.44	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.71904|0.71904	0.3395|0.3395	M|M	0.74647|0.74647	2.275|2.275	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.998;0.997	.|D;P	.|0.65684	.|0.937;0.866	T|T	0.66945|0.66945	-0.5795|-0.5795	5|10	.|0.27785	.|T	.|0.31	.|.	19.9983|19.9983	0.97395|0.97395	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2018;2018	.|Q5THJ4-2;Q5THJ4	.|.;VP13D_HUMAN	S|L	841|2018	.|ENSP00000348666:R2018L;ENSP00000350854:R2018L	.|ENSP00000348666:R2018L	A|R	+|+	1|2	0|0	VPS13D|VPS13D	12281865|12281865	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.906000|0.906000	0.53458|0.53458	9.402000|9.402000	0.97298|0.97298	2.724000|2.724000	0.93272|0.93272	0.561000|0.561000	0.74099|0.74099	GCT|CGC	.	.		0.438	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		T	12359278	G	T	12359278	3	4	190	1	0	0	0	0	1	0	0	0	17207	1087	38	1	6147	1	VPS13D	1	12359278	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	4562758	12359278	236891343	3	28079										
C1orf158	93190	hgsc.bcm.edu	37	chr1	12820859	12820859	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ggtcccggtccctccccatcGcctgcatcctttcccacact	6	21	0	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:12820859G>T	ENST00000288048.5	+	4	776	c.560G>T	c.(559-561)cGc>cTc	p.R187L	C1orf158_ENST00000376210.3_Missense_Mutation_p.R149L	NM_152290.2	NP_689503.2	Q8N1D5	CA158_HUMAN	chromosome 1 open reading frame 158	187								p.R187P(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|ovary(1)|skin(2)|urinary_tract(3)	10	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CCTCCCCATCGCCTGCATCCT	0.577																																					p.R187L		Atlas-SNP	.											C1orf158,NS,lymphoid_neoplasm,0,2	C1orf158	28	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G560T						.						89	78	82					1																	12820859		2203	4300	6503	SO:0001583	missense	93190	exon4			CCCATCGCCTGCA	BX647383	CCDS147.1	1p36.21	2008-02-05			ENSG00000157330	ENSG00000157330			28567	protein-coding gene	gene with protein product						12477932	Standard	NM_152290		Approved	MGC35194	uc001auh.3	Q8N1D5	OTTHUMG00000001888	ENST00000288048.5:c.560G>T	chr1.hg19:g.12820859G>T	ENSP00000288048:p.Arg187Leu	70.0	0.0		76.0	18.0	NM_152290	Q5VUY4	Missense_Mutation	SNP	ENST00000288048.5	hg19	CCDS147.1	.	.	.	.	.	.	.	.	.	.	.	12.10	1.835737	0.32421	.	.	ENSG00000157330	ENST00000288048;ENST00000376210	T;T	0.48522	0.82;0.81	4.55	1.53	0.23141	.	0.476202	0.23712	N	0.045317	T	0.39384	0.1076	M	0.68317	2.08	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.33420	-0.9869	10	0.46703	T	0.11	-6.9156	3.9984	0.09569	0.2048:0.0:0.6083:0.1869	.	187	Q8N1D5	CA158_HUMAN	L	187;149	ENSP00000288048:R187L;ENSP00000365383:R149L	ENSP00000288048:R187L	R	+	2	0	C1orf158	12743446	0.002000	0.14202	0.028000	0.17463	0.003000	0.03518	0.745000	0.26259	0.520000	0.28426	0.563000	0.77884	CGC	.	.		0.577	C1orf158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005325.1	NM_152290		T	12820859	G	T	12820859	3	4	190	1	0	0	0	0	1	0	0	0	2009	1087	38	1	574	1	C1orf158	1	12820859	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	461581	12820859	236429762	4	28080										
PRAMEF18	391003	hgsc.bcm.edu	37	chr1	13475241	13475241	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ccataagttaatgccaatgtCtccaacgggctcttgaggca	9	11	2	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:13475241C>T	ENST00000376126.2	-	3	887	c.888G>A	c.(886-888)gaG>gaA	p.E296E		NM_001099850.1	NP_001093320.1	Q5VWM3	PRA18_HUMAN	PRAME family member 18	296					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					lung(2)|ovary(1)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATGCCAATGTCTCCAACGGGC	0.498																																					p.E296E		Atlas-SNP	.											PRAMEF18,NS,carcinoma,0,1	PRAMEF19	6	.	0			c.G888A						.						3	3	3					1																	13475241		1541	3394	4935	SO:0001819	synonymous_variant	645414	exon3			CAATGTCTCCAAC			1p36.21	2013-01-17			ENSG00000204491			"-"	30693	protein-coding gene	gene with protein product							Standard			Approved	OTTHUMG00000002932		Q5VWM3	OTTHUMG00000002932	ENST00000376126.2:c.888G>A	chr1.hg19:g.13475241C>T		263.0	0.0		272.0	17.0	NM_001099790		Silent	SNP	ENST00000376126.2	hg19	CCDS41258.1																																																																																			.	.		0.498	PRAMEF18-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008177.2	NM_001099850		T	13475241	C	T	13475241	2	4	190	1	0	0	0	0	0	0	0	1	12445	912	32	3		3	PRAMEF18	1	13475241	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	654382	13475241	235775380	5	28081										
PHC2	1912	hgsc.bcm.edu	37	chr1	33832725	33832725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgaagaccttacctggtgcaAtgagggggtgggcagccaca	15	9	0	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:33832725A>G	ENST00000257118.5	-	6	1021	c.968T>C	c.(967-969)aTt>aCt	p.I323T	PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000419414.2_Missense_Mutation_p.I323T|PHC2_ENST00000431992.1_Missense_Mutation_p.I294T	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	323					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				ACCTGGTGCAATGAGGGGGTG	0.567																																					p.I323T		Atlas-SNP	.											.	PHC2	78	.	0			c.T968C						.						67	71	69					1																	33832725		2201	4300	6501	SO:0001583	missense	1912	exon6			GGTGCAATGAGGG	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"Sterile alpha motif (SAM) domain containing"	3183	protein-coding gene	gene with protein product		602979	"early development regulator 2 (homolog of polyhomeotic 2)", "polyhomeotic-like 2 (Drosophila)"	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.968T>C	chr1.hg19:g.33832725A>G	ENSP00000257118:p.Ile323Thr	62.0	0.0		74.0	5.0	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	hg19	CCDS378.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.605231	0.46423	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000419414	T;T;T	0.36340	1.53;1.26;1.65	5.88	4.73	0.59995	.	0.284540	0.38326	N	0.001721	T	0.30135	0.0755	L	0.51422	1.61	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.07404	-1.0774	10	0.24483	T	0.36	-0.2548	9.0205	0.36198	0.9158:0.0:0.0842:0.0	.	323;294;323	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	T	294;323;323	ENSP00000389436:I294T;ENSP00000257118:I323T;ENSP00000391440:I323T	ENSP00000257118:I323T	I	-	2	0	PHC2	33605312	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.526000	0.53509	1.008000	0.39264	0.533000	0.62120	ATT	.	.		0.567	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		G	33832725	A	G	33832725	3	3	190	1	0	0	0	0	1	0	0	0	11826	101	4	2	1644	2	PHC2	1	33832725	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	20357484	33832725	215417896	6	28082										
FOXE3	2301	hgsc.bcm.edu	37	chr1	47882609	47882609	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgccgccgccttctgccggaCcgggcccctcgccgcccgcg	13	22	1	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:47882609C>A	ENST00000335071.2	+	1	866	c.622C>A	c.(622-624)Ccg>Acg	p.P208T		NM_012186.2	NP_036318.1	Q13461	FOXE3_HUMAN	forkhead box E3	208					camera-type eye development (GO:0043010)|cell development (GO:0048468)|positive regulation of epithelial cell proliferation (GO:0050679)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(3)|prostate(1)|upper_aerodigestive_tract(1)	5				READ - Rectum adenocarcinoma(2;0.0908)		TTCTGCCGGACCGGGCCCCTC	0.811																																					p.P208T		Atlas-SNP	.											.	FOXE3	8	.	0			c.C622A						.						1	1	1					1																	47882609		364	692	1056	SO:0001583	missense	2301	exon1			GCCGGACCGGGCC	AF275722	CCDS550.1	1p32	2008-02-05			ENSG00000186790	ENSG00000186790		"Forkhead boxes"	3808	protein-coding gene	gene with protein product		601094		FKHL12		8825632	Standard	NM_012186		Approved	FREAC8	uc001crk.3	Q13461	OTTHUMG00000007954	ENST00000335071.2:c.622C>A	chr1.hg19:g.47882609C>A	ENSP00000334472:p.Pro208Thr	21.0	0.0		26.0	8.0	NM_012186	Q5SVY9|Q9NQV9	Missense_Mutation	SNP	ENST00000335071.2	hg19	CCDS550.1	.	.	.	.	.	.	.	.	.	.	c	11.95	1.791118	0.31685	.	.	ENSG00000186790	ENST00000335071	D	0.94897	-3.55	3.35	3.35	0.38373	.	0.831414	0.09635	U	0.775714	D	0.87865	0.6285	N	0.19112	0.55	0.27231	N	0.959403	B	0.19331	0.035	B	0.17098	0.017	T	0.74034	-0.3794	10	0.08381	T	0.77	.	11.0831	0.48072	0.0:0.8116:0.1884:0.0	.	208	Q13461	FOXE3_HUMAN	T	208	ENSP00000334472:P208T	ENSP00000334472:P208T	P	+	1	0	FOXE3	47655196	0.008000	0.16893	0.035000	0.18076	0.017000	0.09413	0.981000	0.29526	1.706000	0.51276	0.448000	0.29417	CCG	.	.		0.811	FOXE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021836.1	NM_012186		A	47882609	C	A	47882609	3	1	190	1	0	0	0	0	1	0	0	0	6012	507	18	3	624	3	FOXE3	1	47882609	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	14049884	47882609	201368012	7	28083										
USP24	23358	hgsc.bcm.edu	37	chr1	55624658	55624658	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	caccagatccggttggaagcGcatgcaaagtaacttaacgg	11	10	0	1	rs374277857		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:55624658G>A	ENST00000294383.6	-	10	1119	c.1120C>T	c.(1120-1122)Cgc>Tgc	p.R374C	USP24_ENST00000407756.1_Missense_Mutation_p.R262C	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	374					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						GGTTGGAAGCGCATGCAAAGT	0.378																																					p.R374C		Atlas-SNP	.											.	USP24	323	.	0			c.C1120T						.	G	CYS/ARG	0,3846		0,0,1923	62	59	60		1120	5.4	1	1		60	2,8296		0,2,4147	no	missense	USP24	NM_015306.2	180	0,2,6070	AA,AG,GG		0.0241,0.0,0.0165	probably-damaging	374/2621	55624658	2,12142	1923	4149	6072	SO:0001583	missense	23358	exon10			GGAAGCGCATGCA	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.1120C>T	chr1.hg19:g.55624658G>A	ENSP00000294383:p.Arg374Cys	242.0	0.0		253.0	88.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	hg19	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	G	15.74	2.923658	0.52653	0.0	2.41E-4	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.37915	1.17;1.17	5.44	5.44	0.79542	.	0.064020	0.64402	D	0.000013	T	0.33381	0.0861	N	0.25485	0.75	0.54753	D	0.99998	D	0.63880	0.993	B	0.44315	0.446	T	0.09751	-1.0660	10	0.51188	T	0.08	.	19.6122	0.95610	0.0:0.0:1.0:0.0	.	262	B7WPF4	.	C	374;262	ENSP00000294383:R374C;ENSP00000385700:R262C	ENSP00000294383:R374C	R	-	1	0	USP24	55397246	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.116000	0.57871	2.709000	0.92574	0.591000	0.81541	CGC	.	.		0.378	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			A	55624658	G	A	55624658	3	1	190	1	0	0	0	0	1	0	0	0	17070	1087	38	1	6978	1	USP24	1	55624658	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	7742049	55624658	193625963	8	28084										
INADL	10207	hgsc.bcm.edu	37	chr1	62550246	62550246	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gtcccattgtccctggacagGaaatgattatagaaatatcc	8	9	0	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:62550246G>A	ENST00000371158.2	+	33	4417	c.4303G>A	c.(4303-4305)Gaa>Aaa	p.E1435K	INADL_ENST00000316485.6_Missense_Mutation_p.E1435K|INADL_ENST00000545929.1_Missense_Mutation_p.E108K|INADL_ENST00000543708.1_Missense_Mutation_p.E219K	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1435					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						CCCTGGACAGGAAATGATTAT	0.468																																					p.E1435K		Atlas-SNP	.											.	INADL	179	.	0			c.G4303A						.						92	89	90					1																	62550246		2203	4300	6503	SO:0001583	missense	10207	exon33			GGACAGGAAATGA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4303G>A	chr1.hg19:g.62550246G>A	ENSP00000360200:p.Glu1435Lys	131.0	0.0		150.0	10.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	G	28.4	4.915842	0.92178	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000543708;ENST00000545929	T;T;T;T	0.24350	2.27;2.14;1.86;2.27	5.02	5.02	0.67125	PDZ/DHR/GLGF (1);	0.000000	0.64402	D	0.000003	T	0.57519	0.2059	M	0.85777	2.775	0.58432	D	0.999999	D;P;D;D;P;D	0.89917	1.0;0.87;0.997;1.0;0.574;1.0	D;D;D;D;P;D	0.91635	0.997;0.951;0.995;0.999;0.861;0.977	T	0.63594	-0.6602	10	0.56958	D	0.05	.	18.6965	0.91603	0.0:0.0:1.0:0.0	.	108;219;894;1435;1435;1435	F5GY89;B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;.;INADL_HUMAN;.	K	1435;1435;1435;1435;219;108	ENSP00000360200:E1435K;ENSP00000326199:E1435K;ENSP00000445790:E219K;ENSP00000440094:E108K	ENSP00000326199:E1435K	E	+	1	0	INADL	62322834	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	8.067000	0.89488	2.477000	0.83638	0.655000	0.94253	GAA	.	.		0.468	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		A	62550246	G	A	62550246	3	1	190	1	0	0	0	0	1	0	0	0	7740	1175	41	3	4429	3	INADL	1	62550246	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	6925588	62550246	186700375	9	28085										
EFCAB7	84455	hgsc.bcm.edu	37	chr1	64021164	64021165	+	Frame_Shift_Ins	INS	-	-	TA													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tagagatgaaacaggggaatINStattccttacaaaggaattt							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:64021164_64021165insTA	ENST00000371088.4	+	9	1438_1439	c.1192_1193insTA	c.(1192-1194)ttafs	p.L398fs	EFCAB7_ENST00000461039.1_3'UTR	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	398							calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						AACAGGGGAATTATTCCTTACA	0.342																																					p.L398fs		Atlas-INDEL	.											.	EFCAB7	45	.	0			c.1192_1193insTA						.																																			SO:0001589	frameshift_variant	84455	exon9			.	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"EF-hand domain containing"	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.1193_1194dupTA	chr1.hg19:g.64021165_64021166dupTA	ENSP00000360129:p.Leu398fs	213.0	0.0		231.0	93.0	NM_032437	Q658P0|Q96B95|Q96JM6	Frame_Shift_Ins	INS	ENST00000371088.4	hg19	CCDS30737.1																																																																																			.	.		0.342	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437		TA	64021165	-	TA	64021164	7	5	190	1	0	1	1	0	0	0	0	0	4942	1490	52	0	1222	0	EFCAB7	1	64021164	Frame_Shift_Ins	INS	-	TCGA-DD-AADG-01A-11D-A40R-10	1470918	64021164	185229457	10	28086										
MIER1	57708	hgsc.bcm.edu	37	chr1	67450362	67450363	+	Frame_Shift_Ins	INS	-	-	C													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	taagaaaccacttcatgcagINSatatggatactaatggttat							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:67450362_67450363insC	ENST00000355356.3	+	13	1467_1468	c.1318_1319insC	c.(1318-1320)gatfs	p.D440fs	MIER1_ENST00000401042.3_Intron|MIER1_ENST00000357692.2_Frame_Shift_Ins_p.D457fs|MIER1_ENST00000371016.1_Intron|MIER1_ENST00000371018.3_Intron|MIER1_ENST00000371014.1_Intron|MIER1_ENST00000355977.6_Intron|MIER1_ENST00000401041.1_Frame_Shift_Ins_p.D493fs	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	440					positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						ACTTCATGCAGATATGGATACT	0.351																																					p.D493fs		Atlas-INDEL	.											.	MIER1	86	.	0			c.1477_1478insC						.																																			SO:0001589	frameshift_variant	57708	exon14			.		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	Exception_encountered	chr1.hg19:g.67450362_67450363insC	ENSP00000347514:p.Asp440fs	195.0	0.0		186.0	65.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Frame_Shift_Ins	INS	ENST00000355356.3	hg19	CCDS41348.1																																																																																			.	.		0.351	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948		C	67450363	-	C	67450362	7	5	190	1	0	1	1	0	0	0	0	0	9589	942	33	0	1608	0	MIER1	1	67450362	Frame_Shift_Ins	INS	-	TCGA-DD-AADG-01A-11D-A40R-10	3429198	67450362	181800259	11	28087	137	2								
MIER1	57708	hgsc.bcm.edu	37	chr1	67450363	67450364	+	In_Frame_Ins	INS	-	-	GAT													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aagaaaccacttcatgcagaINStatggatactaatggttatg							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:67450363_67450364insGAT	ENST00000355356.3	+	13	1468_1469	c.1319_1320insGAT	c.(1318-1323)gatatg>gaGATtatg	p.440_440D>EI	MIER1_ENST00000401042.3_Intron|MIER1_ENST00000357692.2_In_Frame_Ins_p.457_457D>EI|MIER1_ENST00000371016.1_Intron|MIER1_ENST00000371018.3_Intron|MIER1_ENST00000371014.1_Intron|MIER1_ENST00000355977.6_Intron|MIER1_ENST00000401041.1_In_Frame_Ins_p.493_493D>EI	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	440					positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						CTTCATGCAGATATGGATACTA	0.351																																					p.D493delinsEI		Atlas-INDEL	.											.	MIER1	86	.	0			c.1478_1479insGAT						.																																			SO:0001652	inframe_insertion	57708	exon14			.		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	Exception_encountered	chr1.hg19:g.67450363_67450364insGAT	ENSP00000347514:p.Asp440delinsGluIle	193.0	0.0		184.0	64.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	In_Frame_Ins	INS	ENST00000355356.3	hg19	CCDS41348.1																																																																																			.	.		0.351	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948		GAT	67450364	-	GAT	67450363	7	5	190	1	0	1	1	0	0	0	0	0	9589	333	12	0	1609	0	MIER1	1	67450363	In_Frame_Ins	INS	-	TCGA-DD-AADG-01A-11D-A40R-10	1	67450363	181800258	12	28088	137	2								
CSDE1	7812	hgsc.bcm.edu	37	chr1	115267860	115267860	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	acctgagtgtgttttgttcaCtttttctgcactgactttgt	8	8	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:115267860C>T	ENST00000358528.4	-	15	2161	c.1735G>A	c.(1735-1737)Gtg>Atg	p.V579M	Y_RNA_ENST00000365030.1_RNA|CSDE1_ENST00000369530.1_Missense_Mutation_p.V594M|CSDE1_ENST00000438362.2_Missense_Mutation_p.V625M|CSDE1_ENST00000530886.1_Missense_Mutation_p.V449M|CSDE1_ENST00000339438.6_Missense_Mutation_p.V548M|CSDE1_ENST00000261443.5_Missense_Mutation_p.V548M|CSDE1_ENST00000534699.1_Missense_Mutation_p.V579M	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	579	CSD 7.				male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTTTGTTCACTTTTTCTGCA	0.438																																					p.V625M		Atlas-SNP	.											.	CSDE1	145	.	0			c.G1873A						.						260	220	233					1																	115267860		2203	4300	6503	SO:0001583	missense	7812	exon16			TGTTCACTTTTTC		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"upstream of NRAS"	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1735G>A	chr1.hg19:g.115267860C>T	ENSP00000351329:p.Val579Met	118.0	0.0		128.0	35.0	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	hg19	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.989671	0.93106	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699	.	.	.	6.16	6.16	0.99307	Cold shock protein (1);Nucleic acid-binding, OB-fold-like (1);Cold-shock protein, DNA-binding (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	D	0.89508	0.6735	H	0.96175	3.78	0.80722	D	1	D;D;B	0.76494	0.999;0.999;0.226	D;D;B	0.85130	0.983;0.997;0.244	D	0.91254	0.5031	9	0.87932	D	0	-4.3418	20.8598	0.99761	0.0:1.0:0.0:0.0	.	594;579;625	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	M	548;625;579;548;449;594;579	.	ENSP00000261443:V548M	V	-	1	0	CSDE1	115069383	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.107000	0.77047	2.937000	0.99478	0.650000	0.86243	GTG	.	.		0.438	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		T	115267860	C	T	115267860	3	4	190	1	0	0	0	0	1	0	0	0	3931	565	20	3	685	3	CSDE1	1	115267860	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	47817497	115267860	133982761	13	28089										
RPTN	126638	hgsc.bcm.edu	37	chr1	152128252	152128252	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttctggccttgtctgtctggCtgaccatagtgggaactctg	12	10	4	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:152128252C>A	ENST00000316073.3	-	3	1387	c.1323G>T	c.(1321-1323)caG>caT	p.Q441H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	441	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						GTCTGTCTGGCTGACCATAGT	0.542																																					p.Q441H		Atlas-SNP	.											.	RPTN	123	.	0			c.G1323T						.						794	699	728					1																	152128252		1568	3582	5150	SO:0001583	missense	126638	exon3			GTCTGGCTGACCA	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1323G>T	chr1.hg19:g.152128252C>A	ENSP00000317895:p.Gln441His	108.0	0.0		199.0	44.0	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	hg19	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.482137	0.44147	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.15256	2.44	5.32	2.42	0.29668	.	.	.	.	.	T	0.09949	0.0244	M	0.89478	3.035	0.09310	N	0.999999	B	0.17852	0.024	B	0.18263	0.021	T	0.29274	-1.0017	9	0.33940	T	0.23	-5.7869	6.3659	0.21455	0.148:0.691:0.0:0.161	.	441	Q6XPR3	RPTN_HUMAN	H	441;96	ENSP00000317895:Q441H	ENSP00000317895:Q441H	Q	-	3	2	RPTN	150394876	0.001000	0.12720	0.021000	0.16686	0.001000	0.01503	-0.349000	0.07731	0.242000	0.21303	-0.302000	0.09304	CAG	.	.		0.542	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		A	152128252	C	A	152128252	3	1	190	1	0	0	0	0	1	0	0	0	13679	796	28	3	1035	3	RPTN	1	152128252	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	36860392	152128252	97122369	14	28090										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186113435	186113435	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gggtcctactgtgatggagcAgaaacacagatgcaagtttg	13	7	0	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:186113435A>C	ENST00000271588.4	+	90	14284	c.14055A>C	c.(14053-14055)gcA>gcC	p.A4685A	HMCN1_ENST00000367492.2_Silent_p.A4685A	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4685	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GTGATGGAGCAGAAACACAGA	0.403																																					p.A4685A		Atlas-SNP	.											.	HMCN1	797	.	0			c.A14055C						.						142	144	143					1																	186113435		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon90			TGGAGCAGAAACA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.14055A>C	chr1.hg19:g.186113435A>C		123.0	0.0		165.0	9.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.403	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186113435	A	C	186113435	2	2	190	1	0	0	0	0	0	0	0	1	7229	175	7	5		5	HMCN1	1	186113435	Silent	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	33985183	186113435	63137186	15	28091										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247587388	247587388	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgtttgaccccgatgatgagCattctgagcctgtgcacacc	10	12	1	4			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:247587388C>A	ENST00000336119.3	+	3	1389	c.643C>A	c.(643-645)Cat>Aat	p.H215N	NLRP3_ENST00000391827.2_Missense_Mutation_p.H215N|NLRP3_ENST00000391828.3_Missense_Mutation_p.H215N|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000348069.2_Missense_Mutation_p.H215N|NLRP3_ENST00000366497.2_Missense_Mutation_p.H215N|NLRP3_ENST00000366496.2_Missense_Mutation_p.H215N	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	215					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CGATGATGAGCATTCTGAGCC	0.582																																					p.H215N		Atlas-SNP	.											.	NLRP3	286	.	0			c.C643A						.						88	79	82					1																	247587388		2203	4300	6503	SO:0001583	missense	114548	exon3			GATGAGCATTCTG	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.643C>A	chr1.hg19:g.247587388C>A	ENSP00000337383:p.His215Asn	172.0	0.0		223.0	37.0	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	C	0.749	-0.773546	0.02951	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	T;T;T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31;-1.31;-1.31	4.27	-3.14	0.05250	.	1.401910	0.04258	N	0.339853	T	0.70325	0.3211	L	0.55481	1.735	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.0;0.0	B;B;B;B;B	0.10450	0.001;0.0;0.005;0.001;0.002	T	0.43212	-0.9405	10	0.27785	T	0.31	.	0.3018	0.00274	0.3576:0.2142:0.1332:0.295	.	215;215;215;215;215	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	N	215	ENSP00000375704:H215N;ENSP00000355453:H215N;ENSP00000337383:H215N;ENSP00000294752:H215N;ENSP00000355452:H215N;ENSP00000375703:H215N	ENSP00000337383:H215N	H	+	1	0	NLRP3	245654011	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.534000	0.06150	-0.618000	0.05656	-0.895000	0.02911	CAT	.	.		0.582	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		A	247587388	C	A	247587388	3	1	190	1	0	0	0	0	1	0	0	0	10487	710	25	3	653	3	NLRP3	1	247587388	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	61473953	247587388	1663233	16	28092										
TPO	7173	hgsc.bcm.edu	37	chr2	1499810	1499810	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cggatgcacagaggcgtgagCtggagaagcactccctgtct	14	11	1	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:1499810C>A	ENST00000345913.4	+	12	2147	c.2056C>A	c.(2056-2058)Ctg>Atg	p.L686M	TPO_ENST00000346956.3_Missense_Mutation_p.L686M|TPO_ENST00000382198.1_Missense_Mutation_p.L513M|TPO_ENST00000329066.4_Missense_Mutation_p.L686M|TPO_ENST00000337415.3_Missense_Mutation_p.L686M|TPO_ENST00000349624.3_Missense_Mutation_p.L513M|TPO_ENST00000382201.3_Missense_Mutation_p.L629M|TPO_ENST00000497517.2_Intron	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	686					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GAGGCGTGAGCTGGAGAAGCA	0.562																																					p.L686M		Atlas-SNP	.											.	TPO	224	.	0			c.C2056A						.						80	65	70					2																	1499810		2203	4300	6503	SO:0001583	missense	7173	exon12			CGTGAGCTGGAGA		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2056C>A	chr2.hg19:g.1499810C>A	ENSP00000318820:p.Leu686Met	61.0	0.0		67.0	22.0	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.05|15.05	2.717134|2.717134	0.48622|0.48622	.|.	.|.	ENSG00000115705|ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607|ENST00000446278	T;T;T;T;T;T;T;T;T|.	0.71579|.	-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58|.	4.52|4.52	3.64|3.64	0.41730|0.41730	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79335|0.79335	0.4428|0.4428	M|M	0.90759|0.90759	3.145|3.145	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;0.999;1.0;1.0|.	T|T	0.82604|0.82604	-0.0375|-0.0375	10|5	0.72032|.	D|.	0.01|.	-23.3431|-23.3431	12.5955|12.5955	0.56468|0.56468	0.0:0.9181:0.0:0.0819|0.0:0.9181:0.0:0.0819	.|.	686;513;629;686|.	P07202-4;P07202-5;P07202-2;P07202|.	.;.;.;PERT_HUMAN|.	M|R	686;686;686;513;686;629;513;615;160|160	ENSP00000337263:L686M;ENSP00000318820:L686M;ENSP00000263886:L686M;ENSP00000332044:L513M;ENSP00000329869:L686M;ENSP00000371636:L629M;ENSP00000371633:L513M;ENSP00000405788:L615M;ENSP00000419461:L160M|.	ENSP00000329869:L686M|.	L|S	+|+	1|3	2|2	TPO|TPO	1478817|1478817	1.000000|1.000000	0.71417|0.71417	0.226000|0.226000	0.23910|0.23910	0.339000|0.339000	0.28857|0.28857	4.317000|4.317000	0.59184|0.59184	1.032000|1.032000	0.39892|0.39892	0.561000|0.561000	0.74099|0.74099	CTG|AGC	.	.		0.562	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		A	1499810	C	A	1499810	3	1	190	1	0	0	0	0	1	0	0	0	16425	796	28	3	2098	3	TPO	2	1499810	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10		1499810	241699563	17	28093										
APOB	338	hgsc.bcm.edu	37	chr2	21228569	21228569	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgaatttatcagccaaaactTttacagggatggagaatgaa	9	5	1	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:21228569T>C	ENST00000233242.1	-	26	11298	c.11171A>G	c.(11170-11172)aAa>aGa	p.K3724R		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3724					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCCAAAACTTTTACAGGGAT	0.408																																					p.K3724R		Atlas-SNP	.											.	APOB	761	.	0			c.A11171G						.						97	101	100					2																	21228569		2203	4300	6503	SO:0001583	missense	338	exon26			AAAACTTTTACAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.11171A>G	chr2.hg19:g.21228569T>C	ENSP00000233242:p.Lys3724Arg	90.0	0.0		83.0	31.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077494	0.36662	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.69175	-0.38	5.53	5.53	0.82687	.	0.582952	0.15920	N	0.238180	T	0.53367	0.1792	L	0.29908	0.895	0.80722	D	1	B	0.14805	0.011	B	0.17098	0.017	T	0.46569	-0.9182	10	0.16896	T	0.51	.	11.9727	0.53071	0.1296:0.0:0.0:0.8704	.	3724	P04114	APOB_HUMAN	R	3724	ENSP00000233242:K3724R	ENSP00000233242:K3724R	K	-	2	0	APOB	21082074	0.996000	0.38824	0.991000	0.47740	0.078000	0.17371	1.812000	0.38952	2.103000	0.63969	0.533000	0.62120	AAA	.	.		0.408	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21228569	T	C	21228569	3	2	190	1	0	0	0	0	1	0	0	0	785	1841	64	2	2536	2	APOB	2	21228569	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	19728759	21228569	221970804	18	28094										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37297440	37297440	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttaacatttctccaccgctcTttaagaaacctgaccctcca	3	15	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:37297440T>C	ENST00000233099.5	-	7	955	c.860A>G	c.(859-861)aAg>aGg	p.K287R	HEATR5B_ENST00000354531.2_Missense_Mutation_p.K287R	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	287						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TCCACCGCTCTTTAAGAAACC	0.433																																					p.K287R		Atlas-SNP	.											.	HEATR5B	185	.	0			c.A860G						.						153	145	148					2																	37297440		2203	4300	6503	SO:0001583	missense	54497	exon7			CCGCTCTTTAAGA	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.860A>G	chr2.hg19:g.37297440T>C	ENSP00000233099:p.Lys287Arg	135.0	0.0		136.0	9.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.102515	0.37145	.	.	ENSG00000008869	ENST00000233099;ENST00000354531;ENST00000424416	T;T	0.08458	3.09;3.09	4.95	4.95	0.65309	Armadillo-like helical (1);Armadillo-type fold (1);	0.147769	0.56097	D	0.000031	T	0.04815	0.0130	N	0.04320	-0.23	0.58432	D	0.999997	B	0.22414	0.069	B	0.29942	0.109	T	0.42361	-0.9456	10	0.10377	T	0.69	-10.7144	14.9046	0.70709	0.0:0.0:0.0:1.0	.	287	Q9P2D3	HTR5B_HUMAN	R	287	ENSP00000233099:K287R;ENSP00000346531:K287R	ENSP00000233099:K287R	K	-	2	0	HEATR5B	37150944	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.747000	0.47475	1.969000	0.57287	0.460000	0.39030	AAG	.	.		0.433	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		C	37297440	T	C	37297440	3	2	190	1	0	0	0	0	1	0	0	0	7041	1609	56	2	5475	2	HEATR5B	2	37297440	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	16068871	37297440	205901933	19	28095										
ZFP36L2	678	hgsc.bcm.edu	37	chr2	43452453	43452453	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gtacttgcacgtgccgctctCctcgaagggccggcacagct	12	15	1	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:43452453C>A	ENST00000282388.3	-	2	783	c.490G>T	c.(490-492)Gag>Tag	p.E164*	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	164					cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				GTGCCGCTCTCCTCGAAGGGC	0.647																																					p.E164X		Atlas-SNP	.											.	ZFP36L2	56	.	0			c.G490T						.						42	40	41					2																	43452453		2203	4300	6503	SO:0001587	stop_gained	678	exon2			CGCTCTCCTCGAA	X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"RING-type (C3HC4) zinc fingers"	1108	protein-coding gene	gene with protein product		612053	"zinc finger protein 36, C3H type-like 1", "zinc finger protein 36, C3H type-like 2"	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.490G>T	chr2.hg19:g.43452453C>A	ENSP00000282388:p.Glu164*	36.0	0.0		58.0	21.0	NM_006887	Q53TB4|Q9BSJ3	Nonsense_Mutation	SNP	ENST00000282388.3	hg19	CCDS1811.1	.	.	.	.	.	.	.	.	.	.	C	39	7.785279	0.98489	.	.	ENSG00000152518	ENST00000282388	.	.	.	4.65	4.65	0.58169	.	0.062027	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-24.0185	16.3858	0.83504	0.0:1.0:0.0:0.0	.	.	.	.	X	164	.	ENSP00000282388:E164X	E	-	1	0	ZFP36L2	43305957	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.321000	0.79088	2.144000	0.66660	0.555000	0.69702	GAG	.	.		0.647	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887		A	43452453	C	A	43452453	4	1	190	1	0	0	0	0	0	1	0	0	17662	864	30	3	998	3	ZFP36L2	2	43452453	Nonsense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	6155013	43452453	199746920	20	28096										
USP34	9736	hgsc.bcm.edu	37	chr2	61542016	61542016	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttcaaatcacttaccattaaTataataggagttaatatact	3	6	2	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:61542016T>C	ENST00000398571.2	-	24	3452	c.3376A>G	c.(3376-3378)Att>Gtt	p.I1126V		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1126					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TTACCATTAATATAATAGGAG	0.338																																					p.I1126V		Atlas-SNP	.											.	USP34	334	.	0			c.A3376G						.						86	81	82					2																	61542016		1830	4076	5906	SO:0001583	missense	9736	exon24			CATTAATATAATA	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.3376A>G	chr2.hg19:g.61542016T>C	ENSP00000381577:p.Ile1126Val	298.0	0.0		287.0	12.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.826192	0.71143	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	T	0.03524	3.9	5.41	5.41	0.78517	.	0.048630	0.85682	D	0.000000	T	0.06188	0.0160	L	0.50333	1.59	0.58432	D	0.999995	B	0.18461	0.028	B	0.19391	0.025	T	0.22661	-1.0210	10	0.46703	T	0.11	.	15.7339	0.77827	0.0:0.0:0.0:1.0	.	1126	Q70CQ2	UBP34_HUMAN	V	974;974;1126	ENSP00000381577:I1126V	ENSP00000263989:I974V	I	-	1	0	USP34	61395520	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.803000	0.85983	2.169000	0.68431	0.477000	0.44152	ATT	.	.		0.338	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			C	61542016	T	C	61542016	3	2	190	1	0	0	0	0	1	0	0	0	17080	1406	49	2	7492	2	USP34	2	61542016	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	18089563	61542016	181657357	21	28097										
TEKT4	150483	hgsc.bcm.edu	37	chr2	95542383	95542383	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cggagcagtccctgcgcaacCtcgaggacatccacatgagc	11	15	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:95542383C>A	ENST00000295201.4	+	6	1314	c.1177C>A	c.(1177-1179)Ctc>Atc	p.L393I	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	393					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						CCTGCGCAACCTCGAGGACAT	0.587																																					p.L393I		Atlas-SNP	.											.	TEKT4	72	.	0			c.C1177A						.						74	57	63					2																	95542383		2203	4300	6503	SO:0001583	missense	150483	exon6			CGCAACCTCGAGG	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.1177C>A	chr2.hg19:g.95542383C>A	ENSP00000295201:p.Leu393Ile	19.0	0.0		23.0	8.0	NM_144705		Missense_Mutation	SNP	ENST00000295201.4	hg19	CCDS2005.1	.	.	.	.	.	.	.	.	.	.	.	17.48	3.399242	0.62177	.	.	ENSG00000163060	ENST00000295201	T	0.10288	2.89	2.43	2.43	0.29744	.	0.000000	0.64402	D	0.000003	T	0.40398	0.1115	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51624	-0.8682	10	0.66056	D	0.02	-14.2001	10.5484	0.45072	0.0:1.0:0.0:0.0	.	393	Q8WW24	TEKT4_HUMAN	I	393	ENSP00000295201:L393I	ENSP00000295201:L393I	L	+	1	0	TEKT4	94906110	0.688000	0.27680	0.998000	0.56505	0.509000	0.34042	0.438000	0.21559	1.049000	0.40321	0.281000	0.19383	CTC	.	.		0.587	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705		A	95542383	C	A	95542383	3	1	190	1	0	0	0	0	1	0	0	0	15770	681	24	3	1199	3	TEKT4	2	95542383	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	34000367	95542383	147656990	22	28098										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99012463	99012463	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cccagaagtgaggttcaaccGcctactgaagttttcccggc	10	13	1	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:99012463G>T	ENST00000272602.2	+	7	869	c.830G>T	c.(829-831)cGc>cTc	p.R277L	CNGA3_ENST00000393504.1_Missense_Mutation_p.R277L|CNGA3_ENST00000409937.1_Missense_Mutation_p.R281L|CNGA3_ENST00000436404.2_Missense_Mutation_p.R259L			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	277			R -> C (in ACHM2; also found in patients with cone-rod dystrophy). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:15712225, ECO:0000269|PubMed:18521937, ECO:0000269|PubMed:24903488}.|R -> H (in ACHM2; also found in patients with cone-rod dystrophy; does not form functional homomeric or heteromeric channels). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:24903488}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AGGTTCAACCGCCTACTGAAG	0.498																																					p.R277L		Atlas-SNP	.											.	CNGA3	118	.	0			c.G830T	GRCh37	CM014539	CNGA3	M		.						89	81	84					2																	99012463		2203	4300	6503	SO:0001583	missense	1261	exon8			TCAACCGCCTACT	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.830G>T	chr2.hg19:g.99012463G>T	ENSP00000272602:p.Arg277Leu	192.0	0.0		200.0	48.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.538890	0.85917	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.99338	-5.76;-5.76;-5.76;-5.76	5.15	5.15	0.70609	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99645	0.9869	H	0.96777	3.88	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.997;1.0	D	0.97631	1.0142	10	0.87932	D	0	.	17.5731	0.87940	0.0:0.0:1.0:0.0	.	281;259;277	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	L	277;259;277;281	ENSP00000377140:R277L;ENSP00000410070:R259L;ENSP00000272602:R277L;ENSP00000386761:R281L	ENSP00000272602:R277L	R	+	2	0	CNGA3	98378895	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.487000	0.81328	2.677000	0.91161	0.563000	0.77884	CGC	.	.		0.498	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		T	99012463	G	T	99012463	3	4	190	1	0	0	0	0	1	0	0	0	3600	1087	38	1	856	1	CNGA3	2	99012463	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	3470080	99012463	144186910	23	28099										
ARHGEF4	50649	hgsc.bcm.edu	37	chr2	131801059	131801059	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ggtcaggagctcagaactcaTctactcgggggagctgactc	13	11	4	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:131801059T>A	ENST00000326016.5	+	11	2021	c.1502T>A	c.(1501-1503)aTc>aAc	p.I501N	ARHGEF4_ENST00000409303.1_Missense_Mutation_p.I441N|ARHGEF4_ENST00000392953.3_Missense_Mutation_p.I501N|ARHGEF4_ENST00000428230.2_Intron|ARHGEF4_ENST00000355771.3_Missense_Mutation_p.I430N|ARHGEF4_ENST00000525839.1_Missense_Mutation_p.I501N	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	501	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		TCAGAACTCATCTACTCGGGG	0.537																																					p.I501N		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.T1502A						.						99	91	94					2																	131801059		2203	4300	6503	SO:0001583	missense	50649	exon11			AACTCATCTACTC	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	684	protein-coding gene	gene with protein product	"APC-stimulated guanine nucleotide exchange factor"	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1502T>A	chr2.hg19:g.131801059T>A	ENSP00000316845:p.Ile501Asn	82.0	0.0		93.0	30.0	NM_032995	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	hg19	CCDS2165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.2|24.2	4.506640|4.506640	0.85282|0.85282	.|.	.|.	ENSG00000136002|ENSG00000136002	ENST00000532720|ENST00000326016;ENST00000392953;ENST00000525839;ENST00000409303;ENST00000355771	.|D;D;D;D;D	.|0.90261	.|-2.64;-2.64;-2.64;-2.64;-2.64	5.02|5.02	5.02|5.02	0.67125|0.67125	.|Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.95121|0.95121	0.8419|0.8419	M|M	0.84326|0.84326	2.69|2.69	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.87578	.|0.998;0.997;0.998	D|D	0.95598|0.95598	0.8660|0.8660	5|10	.|0.87932	.|D	.|0	.|.	12.6975|12.6975	0.57012|0.57012	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|441;501;501	.|E9PEM0;Q9NR80-4;Q9NR80	.|.;.;ARHG4_HUMAN	Q|N	117|501;501;501;441;430	.|ENSP00000316845:I501N;ENSP00000376680:I501N;ENSP00000432267:I501N;ENSP00000387285:I441N;ENSP00000348017:I430N	.|ENSP00000316845:I501N	H|I	+|+	3|2	2|0	ARHGEF4|ARHGEF4	131517529|131517529	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	5.768000|5.768000	0.68858|0.68858	1.891000|1.891000	0.54761|0.54761	0.459000|0.459000	0.35465|0.35465	CAT|ATC	.	.		0.537	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			A	131801059	T	A	131801059	3	1	190	1	0	0	0	0	1	0	0	0	908	1435	50	4	1536	4	ARHGEF4	2	131801059	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	32788596	131801059	111398314	24	28100										
HOXD4	3233	hgsc.bcm.edu	37	chr2	177016412	177016412	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aagtatgtggaccccaagttCcctccgtgcgaggagtattt	11	10	0	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:177016412C>G	ENST00000306324.3	+	1	463	c.51C>G	c.(49-51)ttC>ttG	p.F17L	MIR10B_ENST00000385011.1_RNA|HOXD3_ENST00000468418.3_5'UTR	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	17					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F17L(1)		kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		ACCCCAAGTTCCCTCCGTGCG	0.542																																					p.F17L		Atlas-SNP	.											HOXD4,NS,carcinoma,0,1	HOXD4	32	.	1	Substitution - Missense(1)	kidney(1)	c.C51G						.						48	52	50					2																	177016412		2187	4235	6422	SO:0001583	missense	3233	exon1			CAAGTTCCCTCCG		CCDS2269.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170166	ENSG00000170166		"Homeoboxes / ANTP class : HOXL subclass"	5138	protein-coding gene	gene with protein product		142981	"homeo box D4"	HOX4B, HOX4		1973146, 1358459	Standard	NM_014621		Approved		uc002uks.3	P09016	OTTHUMG00000132515	ENST00000306324.3:c.51C>G	chr2.hg19:g.177016412C>G	ENSP00000302548:p.Phe17Leu	177.0	0.0		178.0	72.0	NM_014621	B2R9R3|Q96AU0	Missense_Mutation	SNP	ENST00000306324.3	hg19	CCDS2269.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447955	0.63178	.	.	ENSG00000170166	ENST00000306324	T	0.59772	0.24	5.12	-1.86	0.07760	.	0.249724	0.40728	N	0.001026	T	0.76364	0.3977	M	0.91717	3.235	0.53005	D	0.999968	D	0.89917	1.0	D	0.83275	0.996	T	0.78540	-0.2165	10	0.87932	D	0	.	11.2747	0.49159	0.0:0.3812:0.0:0.6188	.	17	P09016	HXD4_HUMAN	L	17	ENSP00000302548:F17L	ENSP00000302548:F17L	F	+	3	2	HOXD4	176724658	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	2.070000	0.41491	-0.223000	0.09943	0.655000	0.94253	TTC	.	.		0.542	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2			G	177016412	C	G	177016412	3	3	190	1	0	0	0	0	1	0	0	0	7333	854	30	4	53	4	HOXD4	2	177016412	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	45215353	177016412	66182961	25	28101										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196765131	196765131	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aatttttacagacagtggtcGagcagtgacaaacccacagg	10	9	0	2	rs376085913		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:196765131G>T	ENST00000312428.6	-	28	4523	c.4423C>A	c.(4423-4425)Cga>Aga	p.R1475R		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1475	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GACAGTGGTCGAGCAGTGACA	0.463																																					p.R1475R		Atlas-SNP	.											.	DNAH7	512	.	0			c.C4423A						.						177	176	176					2																	196765131		1982	4180	6162	SO:0001819	synonymous_variant	56171	exon28			GTGGTCGAGCAGT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.4423C>A	chr2.hg19:g.196765131G>T		183.0	0.0		188.0	71.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.463	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196765131	G	T	196765131	2	4	190	1	0	0	0	0	0	0	0	1	4608	1066	37	1		1	DNAH7	2	196765131	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	19748719	196765131	46434242	26	28102										
KCTD18	130535	hgsc.bcm.edu	37	chr2	201357908	201357908	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agataacctctttcgaattgGagccatgtgacgcaggcttc	10	10	1	2	rs146790839		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:201357908G>T	ENST00000359878.3	-	6	1261	c.751C>A	c.(751-753)Cca>Aca	p.P251T	KCTD18_ENST00000468413.1_5'Flank|KCTD18_ENST00000409157.1_Missense_Mutation_p.P251T	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	251					protein homooligomerization (GO:0051260)					endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						TTTCGAATTGGAGCCATGTGA	0.408																																					p.P251T		Atlas-SNP	.											.	KCTD18	44	.	0			c.C751A						.						76	70	72					2																	201357908		2203	4300	6503	SO:0001583	missense	130535	exon6			GAATTGGAGCCAT	AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 18"				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.751C>A	chr2.hg19:g.201357908G>T	ENSP00000352941:p.Pro251Thr	80.0	0.0		78.0	28.0	NM_152387	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Missense_Mutation	SNP	ENST00000359878.3	hg19	CCDS2330.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.907482	0.52333	.	.	ENSG00000155729	ENST00000359878;ENST00000409157	T;T	0.43294	0.95;0.95	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000017	T	0.54303	0.1850	L	0.32530	0.975	0.43351	D	0.995412	D	0.76494	0.999	D	0.68353	0.957	T	0.52064	-0.8625	10	0.48119	T	0.1	-18.7757	18.7156	0.91673	0.0:0.0:1.0:0.0	.	251	Q6PI47	KCD18_HUMAN	T	251	ENSP00000352941:P251T;ENSP00000386751:P251T	ENSP00000352941:P251T	P	-	1	0	KCTD18	201066153	1.000000	0.71417	0.728000	0.30774	0.004000	0.04260	5.299000	0.65716	2.810000	0.96702	0.650000	0.86243	CCA	.	G|1.000;A|0.000		0.408	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387		T	201357908	G	T	201357908	3	4	190	1	0	0	0	0	1	0	0	0	8114	1174	41	3	537	3	KCTD18	2	201357908	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	4592777	201357908	41841465	27	28103										
BMPR2	659	hgsc.bcm.edu	37	chr2	203383670	203383670	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gaaaagaacatttacagagtGcctttgatggaacatgacaa	9	6	0	4			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:203383670G>A	ENST00000374580.4	+	6	1286	c.747G>A	c.(745-747)gtG>gtA	p.V249V	BMPR2_ENST00000374574.2_Silent_p.V249V	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						TTTACAGAGTGCCTTTGATGG	0.413																																					p.V249V		Atlas-SNP	.											.	BMPR2	142	.	0			c.G747A						.						169	155	160					2																	203383670		2203	4300	6503	SO:0001819	synonymous_variant	659	exon6			CAGAGTGCCTTTG	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.747G>A	chr2.hg19:g.203383670G>A		132.0	0.0		137.0	9.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Silent	SNP	ENST00000374580.4	hg19	CCDS33361.1																																																																																			.	.		0.413	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204		A	203383670	G	A	203383670	2	1	190	1	0	0	0	0	0	0	0	1	1471	1306	46	3		3	BMPR2	2	203383670	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	2025762	203383670	39815703	28	28104										
MDH1B	130752	hgsc.bcm.edu	37	chr2	207622077	207622077	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	actccacttattcttttcacAcacatcttttagccaatcct	1	14	3	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:207622077A>T	ENST00000374412.3	-	3	429	c.154T>A	c.(154-156)Tgt>Agt	p.C52S	MDH1B_ENST00000454776.2_Missense_Mutation_p.C52S|MDH1B_ENST00000392214.2_Missense_Mutation_p.C52S|MDH1B_ENST00000449792.1_5'UTR	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	52					carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		TTCTTTTCACACACATCTTTT	0.363																																					p.C52S	Pancreas(76;29 1355 28675 37177 51207)	Atlas-SNP	.											.	MDH1B	89	.	0			c.T154A						.						118	115	116					2																	207622077		2203	4300	6503	SO:0001583	missense	130752	exon3			TTTCACACACATC		CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.154T>A	chr2.hg19:g.207622077A>T	ENSP00000363533:p.Cys52Ser	55.0	0.0		41.0	19.0	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	hg19	CCDS33365.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.148788	0.57151	.	.	ENSG00000138400	ENST00000374412;ENST00000454776;ENST00000392214	T;T;T	0.57436	0.4;0.4;0.4	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.74397	0.3711	M	0.81497	2.545	0.53688	D	0.99997	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.987	T	0.78298	-0.2258	10	0.87932	D	0	-26.2499	16.2159	0.82217	1.0:0.0:0.0:0.0	.	52;52	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	S	52	ENSP00000363533:C52S;ENSP00000389916:C52S;ENSP00000376049:C52S	ENSP00000363533:C52S	C	-	1	0	MDH1B	207330322	1.000000	0.71417	0.847000	0.33407	0.018000	0.09664	8.383000	0.90157	2.243000	0.73865	0.533000	0.62120	TGT	.	.		0.363	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845		T	207622077	A	T	207622077	3	4	190	1	0	0	0	0	1	0	0	0	9418	159	6	4	1442	4	MDH1B	2	207622077	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	4238407	207622077	35577296	29	28105										
PRKAG3	53632	hgsc.bcm.edu	37	chr2	219689003	219689003	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tctcgtggggctggcaggaaAggactccctccagacatagt	13	11	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:219689003A>G	ENST00000529249.1	-	12	1610	c.1295T>C	c.(1294-1296)cTt>cCt	p.L432P	PRKAG3_ENST00000439262.2_Missense_Mutation_p.L407P|PRKAG3_ENST00000545803.1_Missense_Mutation_p.L248P			Q9UGI9	AAKG3_HUMAN	protein kinase, AMP-activated, gamma 3 non-catalytic subunit	432	CBS 4. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)	AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|protein kinase binding (GO:0019901)			large_intestine(7)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Acetylsalicylic acid(DB00945)	CTGGCAGGAAAGGACTCCCTC	0.597																																					p.L432P		Atlas-SNP	.											.	PRKAG3	47	.	0			c.T1295C						.						85	82	83					2																	219689003		2203	4300	6503	SO:0001583	missense	53632	exon12			CAGGAAAGGACTC	AF214519	CCDS2424.1	2q35	2012-09-20			ENSG00000115592	ENSG00000115592			9387	protein-coding gene	gene with protein product		604976				10818001	Standard	NM_017431		Approved		uc002vjb.1	Q9UGI9	OTTHUMG00000133078	ENST00000529249.1:c.1295T>C	chr2.hg19:g.219689003A>G	ENSP00000436068:p.Leu432Pro	137.0	0.0		133.0	7.0	NM_017431	Q4QQG8|Q4V779|Q9NRL1	Missense_Mutation	SNP	ENST00000529249.1	hg19	CCDS2424.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.185248	0.78677	.	.	ENSG00000115592	ENST00000439262;ENST00000545803;ENST00000529249	D;D;D	0.93426	-3.22;-3.22;-3.22	5.08	5.08	0.68730	Cystathionine beta-synthase, core (3);	0.063176	0.64402	D	0.000004	D	0.95230	0.8453	L	0.56280	1.765	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.94725	0.7904	10	0.41790	T	0.15	-6.502	14.0592	0.64788	1.0:0.0:0.0:0.0	.	432	Q9UGI9	AAKG3_HUMAN	P	407;248;432	ENSP00000397133:L407P;ENSP00000444536:L248P;ENSP00000436068:L432P	ENSP00000233944:L432P	L	-	2	0	PRKAG3	219397247	1.000000	0.71417	0.990000	0.47175	0.989000	0.77384	9.084000	0.94076	1.904000	0.55121	0.533000	0.62120	CTT	.	.		0.597	PRKAG3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385992.1			G	219689003	A	G	219689003	3	3	190	1	0	0	0	0	1	0	0	0	12514	72	3	2	182	2	PRKAG3	2	219689003	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	12066926	219689003	23510370	30	28106										
KCNJ13	3769	hgsc.bcm.edu	37	chr2	233633278	233633278	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cgttagtggaaagatgaagaAtggacattcgtcagaactga	12	5	1	5			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:233633278A>T	ENST00000233826.3	-	3	845	c.706T>A	c.(706-708)Ttc>Atc	p.F236I	GIGYF2_ENST00000409547.1_Intron|KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000409451.3_Intron|GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000452341.2_Intron|KCNJ13_ENST00000410029.1_Missense_Mutation_p.F236I|AC064852.4_ENST00000427571.1_RNA	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	236					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		AAGATGAAGAATGGACATTCG	0.443																																					p.F236I		Atlas-SNP	.											.	KCNJ13	18	.	0			c.T706A						.						173	141	151					2																	233633278		2203	4300	6503	SO:0001583	missense	3769	exon3			TGAAGAATGGACA	AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.706T>A	chr2.hg19:g.233633278A>T	ENSP00000233826:p.Phe236Ile	180.0	0.0		194.0	60.0	NM_002242	A0PGH1|O76023|Q53SA1|Q8N3Y4	Missense_Mutation	SNP	ENST00000233826.3	hg19	CCDS2498.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.600030	0.46318	.	.	ENSG00000115474	ENST00000233826;ENST00000410029;ENST00000438786	D;D;D	0.95238	-3.65;-3.65;-3.65	6.07	4.91	0.64330	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.088508	0.85682	D	0.000000	D	0.92835	0.7721	L	0.56199	1.76	0.44175	D	0.996982	P	0.38300	0.626	B	0.40782	0.34	D	0.93322	0.6693	10	0.87932	D	0	.	12.5221	0.56065	0.9341:0.0:0.0659:0.0	.	236	O60928	IRK13_HUMAN	I	236;236;156	ENSP00000233826:F236I;ENSP00000386251:F236I;ENSP00000407284:F156I	ENSP00000233826:F236I	F	-	1	0	KCNJ13	233341522	1.000000	0.71417	0.985000	0.45067	0.958000	0.62258	4.987000	0.63857	2.326000	0.78906	0.533000	0.62120	TTC	.	.		0.443	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257036.1	NM_002242		T	233633278	A	T	233633278	3	4	190	1	0	0	0	0	1	0	0	0	8056	101	4	4	380	4	KCNJ13	2	233633278	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	13944275	233633278	9566095	31	28107										
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233674449	233674449	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gggagagctggaccaggaacGactgaccaggcagcaagaac	15	10	0	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:233674449G>T	ENST00000409547.1	+	18	2137	c.1826G>T	c.(1825-1827)cGa>cTa	p.R609L	GIGYF2_ENST00000409196.3_Missense_Mutation_p.R603L|GIGYF2_ENST00000373563.4_Missense_Mutation_p.R609L|GIGYF2_ENST00000409451.3_Missense_Mutation_p.R630L|GIGYF2_ENST00000373566.3_Missense_Mutation_p.R631L|GIGYF2_ENST00000409480.1_Missense_Mutation_p.R631L|GIGYF2_ENST00000452341.2_Missense_Mutation_p.R440L	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	609	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		GACCAGGAACGACTGACCAGG	0.428																																					p.R630L		Atlas-SNP	.											.	GIGYF2	288	.	0			c.G1889T						.						115	106	109					2																	233674449		2203	4300	6503	SO:0001583	missense	26058	exon18			AGGAACGACTGAC	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.1826G>T	chr2.hg19:g.233674449G>T	ENSP00000386537:p.Arg609Leu	257.0	0.0		297.0	127.0	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.977409	0.92982	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	T;T;T;T;T;T;T;T;T	0.75704	-0.8;-0.81;-0.8;-0.81;-0.94;-0.81;-0.8;-0.96;-0.68	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.85974	0.5822	M	0.66939	2.045	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;0.967;0.995	D;D;B;D	0.87578	0.996;0.998;0.386;0.968	D	0.83454	0.0050	10	0.41790	T	0.15	-11.169	20.6208	0.99490	0.0:0.0:1.0:0.0	.	440;630;609;603	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	L	631;552;609;631;609;609;552;603;630;603;440	ENSP00000362667:R631L;ENSP00000362664:R609L;ENSP00000386765:R631L;ENSP00000386537:R609L;ENSP00000404195:R552L;ENSP00000387070:R603L;ENSP00000387170:R630L;ENSP00000410297:R603L;ENSP00000411505:R440L	ENSP00000362664:R609L	R	+	2	0	GIGYF2	233382693	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.199000	0.95003	2.882000	0.98803	0.655000	0.94253	CGA	.	.		0.428	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		T	233674449	G	T	233674449	3	4	190	1	0	0	0	0	1	0	0	0	6386	1058	37	1	1950	1	GIGYF2	2	233674449	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	41171	233674449	9524924	32	28108										
USP40	55230	hgsc.bcm.edu	37	chr2	234399852	234399852	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agcgtggcatcttctgagatCtctatgtctcccaagtagag	10	10	4	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:234399852C>A	ENST00000427112.2	-	25	3005	c.2970G>T	c.(2968-2970)gaG>gaT	p.E990D	USP40_ENST00000251722.6_Missense_Mutation_p.E990D|USP40_ENST00000450966.1_Missense_Mutation_p.E1002D|USP40_ENST00000496298.1_5'Flank			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	990					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CTTCTGAGATCTCTATGTCTC	0.478																																					p.E1002D		Atlas-SNP	.											.	USP40	174	.	0			c.G3006T						.						46	46	46					2																	234399852		1905	4127	6032	SO:0001583	missense	55230	exon25			TGAGATCTCTATG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.2970G>T	chr2.hg19:g.234399852C>A	ENSP00000387898:p.Glu990Asp	379.0	1.0		400.0	158.0	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	hg19	CCDS46547.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.710|8.710	0.911866|0.911866	0.17907|0.17907	.|.	.|.	ENSG00000085982|ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112|ENST00000430158	T;T;T|.	0.08458|.	3.09;3.09;3.09|.	5.28|5.28	-10.6|-10.6	0.00265|0.00265	.|.	2.570310|.	0.01121|.	N|.	0.005789|.	T|T	0.27594|0.27594	0.0678|0.0678	L|L	0.41961|0.41961	1.31|1.31	0.29144|0.29144	N|N	0.878836|0.878836	B;B|.	0.31383|.	0.321;0.046|.	B;B|.	0.37239|.	0.244;0.027|.	T|T	0.09707|0.09707	-1.0662|-1.0662	10|5	0.59425|.	D|.	0.04|.	.|.	4.4271|4.4271	0.11509|0.11509	0.0739:0.3001:0.3266:0.2994|0.0739:0.3001:0.3266:0.2994	.|.	1002;650|.	Q9NVE5-3;B4DN96|.	.;.|.	D|I	1002;990;990|166	ENSP00000415434:E1002D;ENSP00000251722:E990D;ENSP00000387898:E990D|.	ENSP00000251722:E990D|.	E|R	-|-	3|2	2|0	USP40|USP40	234064591|234064591	0.031000|0.031000	0.19500|0.19500	0.007000|0.007000	0.13788|0.13788	0.011000|0.011000	0.07611|0.07611	-1.403000|-1.403000	0.02497|0.02497	-2.892000|-2.892000	0.00315|0.00315	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.		0.478	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		A	234399852	C	A	234399852	3	1	190	1	0	0	0	0	1	0	0	0	17087	912	32	3	765	3	USP40	2	234399852	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	725403	234399852	8799521	33	28109										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4853115	4853115	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgactttatcttggaagtagAtaggctgcccaatgaaacag	10	7	1	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:4853115A>G	ENST00000443694.2	+	53	7394	c.7394A>G	c.(7393-7395)gAt>gGt	p.D2465G	ITPR1_ENST00000354582.6_Missense_Mutation_p.D2465G|ITPR1_ENST00000302640.8_Missense_Mutation_p.D2465G|ITPR1_ENST00000456211.2_Missense_Mutation_p.D2417G|ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000544951.1_Missense_Mutation_p.D443G|ITPR1_ENST00000357086.4_Missense_Mutation_p.D2432G|ITPR1_ENST00000423119.2_Missense_Mutation_p.D2432G|AC018816.3_ENST00000489771.1_5'Flank			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2480					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TTGGAAGTAGATAGGCTGCCC	0.403																																					p.D2465G		Atlas-SNP	.											.	ITPR1	659	.	0			c.A7394G						.						129	127	128					3																	4853115		1903	4118	6021	SO:0001583	missense	3708	exon55			AAGTAGATAGGCT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.7394A>G	chr3.hg19:g.4853115A>G	ENSP00000401671:p.Asp2465Gly	66.0	0.0		68.0	36.0	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.790428	0.90367	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	D;D;D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97	5.62	5.62	0.85841	Ion transport (1);	0.141833	0.64402	D	0.000007	D	0.99089	0.9687	M	0.90369	3.11	0.80722	D	1	D;P;P	0.71674	0.998;0.555;0.586	D;B;P	0.77557	0.99;0.257;0.46	D	0.99552	1.0966	10	0.87932	D	0	.	15.8153	0.78595	1.0:0.0:0.0:0.0	.	443;2480;2432	B7ZMI3;Q14643;G5E9P1	.;ITPR1_HUMAN;.	G	2480;2465;2465;2432;926;2432;2417;443;2465	ENSP00000306253:D2465G;ENSP00000346595:D2465G;ENSP00000405934:D2432G;ENSP00000349597:D2432G;ENSP00000397885:D2417G;ENSP00000440564:D443G;ENSP00000401671:D2465G	ENSP00000306253:D2465G	D	+	2	0	ITPR1	4828115	1.000000	0.71417	0.644000	0.29465	0.888000	0.51559	9.224000	0.95209	2.143000	0.66587	0.460000	0.39030	GAT	.	.		0.403	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		G	4853115	A	G	4853115	3	3	190	1	0	0	0	0	1	0	0	0	7929	333	12	2	7653	2	ITPR1	3	4853115	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10		4853115	193169315	34	28110										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266113	41266113	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cctggactctggaatccattCtggtgccactaccacagctc	8	15	2	0	rs121913416|rs121913403		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:41266113C>G	ENST00000349496.5	+	3	390	c.110C>G	c.(109-111)tCt>tGt	p.S37C	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S30C|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S37C|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S37C|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S37C	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S37F(172)|p.S37C(141)|p.A5_A80del(53)|p.S37Y(31)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGAATCCATTCTGGTGCCACT	0.498	S37C(JHUEM2_ENDOMETRIUM)|S37C(SNU398_LIVER)|S37F(HUTU80_SMALL_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S37C	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	474	Substitution - Missense(344)|Deletion - In frame(102)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(145)|endometrium(64)|stomach(38)|skin(34)|ovary(33)|central_nervous_system(28)|pancreas(28)|large_intestine(22)|pituitary(22)|lung(21)|biliary_tract(15)|thyroid(4)|soft_tissue(4)|urinary_tract(4)|small_intestine(3)|oesophagus(3)|adrenal_gland(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)|breast(1)	c.C110G						.						93	78	83					3																	41266113		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TCCATTCTGGTGC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.110C>G	chr3.hg19:g.41266113C>G	ENSP00000344456:p.Ser37Cys	140.0	0.0		142.0	44.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.407996	0.83340	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71;0.71;0.71;0.71;0.71	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75297	-0.3367	10	0.87932	D	0	-15.9763	19.9596	0.97236	0.0:1.0:0.0:0.0	.	37	P35222	CTNB1_HUMAN	C	30;37;37;37;37;30;37;37;37	ENSP00000400508:S30C;ENSP00000385604:S37C;ENSP00000412219:S37C;ENSP00000379486:S37C;ENSP00000344456:S37C;ENSP00000411226:S30C;ENSP00000379488:S37C;ENSP00000409302:S37C;ENSP00000401599:S37C	ENSP00000344456:S37C	S	+	2	0	CTNNB1	41241117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266113	C	G	41266113	3	3	190	1	0	0	0	0	1	0	0	0	4018	913	32	4	116	4	CTNNB1	3	41266113	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	36412998	41266113	156756317	35	28111										
CCR5	1234	hgsc.bcm.edu	37	chr3	46414720	46414720	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ctcttgacagggctctatttTataggcttcttctctggaat	8	9	4	1	rs558483026		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:46414720T>C	ENST00000292303.4	+	2	473	c.327T>C	c.(325-327)ttT>ttC	p.F109F	CCR5_ENST00000343801.4_Silent_p.F109F|RP11-24F11.2_ENST00000451485.1_RNA|CCR5_ENST00000445772.1_Silent_p.F109F	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	109					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	GGCTCTATTTTATAGGCTTCT	0.473																																					p.F109F		Atlas-SNP	.											.	CCR5	128	.	0			c.T327C						.						146	159	155					3																	46414720		2203	4296	6499	SO:0001819	synonymous_variant	1234	exon3			CTATTTTATAGGC		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1606	protein-coding gene	gene with protein product		601373	"chemokine (C-C motif) receptor 5"	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.327T>C	chr3.hg19:g.46414720T>C		113.0	0.0		127.0	51.0	NM_000579	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Silent	SNP	ENST00000292303.4	hg19	CCDS2739.1																																																																																			.	.		0.473	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579		C	46414720	T	C	46414720	2	2	190	1	0	0	0	0	0	0	0	1	2946	1751	61	2		2	CCR5	3	46414720	Silent	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	5148607	46414720	151607710	36	28112										
CADPS	8618	hgsc.bcm.edu	37	chr3	62459851	62459851	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tttttttttttttttacctcTtggcccatttccatgctgca	4	10	1	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:62459851T>A	ENST00000383710.4	-	24	3823	c.3474A>T	c.(3472-3474)caA>caT	p.Q1158H	CADPS_ENST00000357948.3_Missense_Mutation_p.Q1079H|CADPS_ENST00000283269.9_Missense_Mutation_p.Q1119H	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1158					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TTTTTACCTCTTGGCCCATTT	0.353																																					p.Q1158H		Atlas-SNP	.											.	CADPS	387	.	0			c.A3474T						.						85	87	86					3																	62459851		2203	4300	6503	SO:0001583	missense	8618	exon24			TACCTCTTGGCCC	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3474A>T	chr3.hg19:g.62459851T>A	ENSP00000373215:p.Gln1158His	44.0	0.0		60.0	17.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	16.02|16.02|16.02	3.003747|3.003747|3.003747	0.54254|0.54254|0.54254	.|.|.	.|.|.	ENSG00000163618|ENSG00000163618|ENSG00000163618	ENST00000473635|ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269|ENST00000466621	.|T;T;T|.	.|0.32272|.	.|1.46;1.46;1.46|.	5.97|5.97|5.97	3.54|3.54|3.54	0.40534|0.40534|0.40534	.|.|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|.	0.69860|0.69860|.	0.3158|0.3158|.	M|M|M	0.75447|0.75447|0.75447	2.3|2.3|2.3	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;D;D;D|.	.|0.69078|.	.|0.997;0.995;0.996;0.997|.	.|D;D;D;D|.	.|0.77004|.	.|0.951;0.989;0.986;0.935|.	T|T|.	0.66846|0.66846|.	-0.5820|-0.5820|.	5|10|.	.|0.72032|.	.|D|.	.|0.01|.	.|.|.	10.0951|10.0951|10.0951	0.42471|0.42471|0.42471	0.0:0.1963:0.0:0.8037|0.0:0.1963:0.0:0.8037|0.0:0.1963:0.0:0.8037	.|.|.	.|1079;1119;1158;1158|.	.|Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4|.	.|.;.;CAPS1_HUMAN;.|.	M|H|X	145|1158;1158;1079;1119|70	.|ENSP00000373215:Q1158H;ENSP00000350632:Q1079H;ENSP00000283269:Q1119H|.	.|ENSP00000283269:Q1119H|.	K|Q|R	-|-|-	2|3|1	0|2|2	CADPS|CADPS|CADPS	62434891|62434891|62434891	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	1.421000|1.421000|1.421000	0.34815|0.34815|0.34815	0.485000|0.485000|0.485000	0.27652|0.27652|0.27652	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	AAG|CAA|AGA	.	.		0.353	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		A	62459851	T	A	62459851	3	1	190	1	0	0	0	0	1	0	0	0	2572	1606	56	4	615	4	CADPS	3	62459851	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	16045131	62459851	135562579	37	28113										
CADPS	8618	hgsc.bcm.edu	37	chr3	62459893	62459893	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agttttgttgattgagctttGgcatcaaccataacattaaa	7	6	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:62459893G>A	ENST00000383710.4	-	24	3781	c.3432C>T	c.(3430-3432)gcC>gcT	p.A1144A	CADPS_ENST00000357948.3_Silent_p.A1065A|CADPS_ENST00000283269.9_Silent_p.A1105A	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1144					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		ATTGAGCTTTGGCATCAACCA	0.358																																					p.A1144A		Atlas-SNP	.											.	CADPS	387	.	0			c.C3432T						.						156	156	156					3																	62459893		2203	4300	6503	SO:0001819	synonymous_variant	8618	exon24			AGCTTTGGCATCA	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3432C>T	chr3.hg19:g.62459893G>A		66.0	0.0		97.0	5.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	hg19	CCDS46858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.310|7.310	0.614793|0.614793	0.14129|0.14129	.|.	.|.	ENSG00000163618|ENSG00000163618	ENST00000473635|ENST00000466621	.|.	.|.	.|.	5.97|5.97	4.19|4.19	0.49359|0.49359	.|.	.|.	.|.	.|.	.|.	T|.	0.63522|.	0.2518|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.60505|.	-0.7250|.	4|.	.|.	.|.	.|.	.|.	12.4934|12.4934	0.55914|0.55914	0.1344:0.0:0.8656:0.0|0.1344:0.0:0.8656:0.0	.|.	.|.	.|.	.|.	L|X	131|56	.|.	.|.	P|Q	-|-	2|1	0|0	CADPS|CADPS	62434933|62434933	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.634000|6.634000	0.74290|0.74290	0.867000|0.867000	0.35654|0.35654	0.655000|0.655000	0.94253|0.94253	CCA|CAA	.	.		0.358	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		A	62459893	G	A	62459893	2	1	190	1	0	0	0	0	0	0	0	1	2572	1335	47	3		3	CADPS	3	62459893	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	42	62459893	135562537	38	28114										
C3orf17	25871	hgsc.bcm.edu	37	chr3	112729968	112729968	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttgatcttcatttgtttagcTttttttgaaattccaagcaa	5	6	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:112729968T>C	ENST00000314400.5	-	6	1028	c.837A>G	c.(835-837)aaA>aaG	p.K279K	C3orf17_ENST00000393857.2_Silent_p.K143K|C3orf17_ENST00000472762.1_5'UTR|C3orf17_ENST00000383675.2_Silent_p.K209K	NM_015412.3	NP_056227.2	Q6NW34	CC017_HUMAN	chromosome 3 open reading frame 17	279					negative regulation of neuron differentiation (GO:0045665)|positive regulation of Notch signaling pathway (GO:0045747)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|lung(6)|prostate(2)|skin(1)	13						TTTGTTTAGCTTTTTTTGAAA	0.328																																					p.K279K		Atlas-SNP	.											.	C3orf17	37	.	0			c.A837G						.						80	83	82					3																	112729968		2200	4296	6496	SO:0001819	synonymous_variant	25871	exon6			TTTAGCTTTTTTT	AL117573	CCDS33824.1	3q13.2	2009-11-06			ENSG00000163608	ENSG00000163608			24496	protein-coding gene	gene with protein product						12477932	Standard	NR_027794		Approved	DKFZP434F2021, NET17	uc003dzr.3	Q6NW34	OTTHUMG00000159286	ENST00000314400.5:c.837A>G	chr3.hg19:g.112729968T>C		108.0	0.0		139.0	39.0	NM_015412	D3DN69|Q68DM6|Q9H7U0|Q9UFM4	Silent	SNP	ENST00000314400.5	hg19	CCDS33824.1																																																																																			.	.		0.328	C3orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354405.3	NM_015412		C	112729968	T	C	112729968	2	2	190	1	0	0	0	0	0	0	0	1	2212	1606	56	2		2	C3orf17	3	112729968	Silent	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	50270075	112729968	85292462	39	28115										
TRPC1	7220	hgsc.bcm.edu	37	chr3	142522995	142522995	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	caaactgctggtggcaatgcTtcataaaagctttcagttga	9	8	2	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:142522995T>A	ENST00000476941.1	+	11	2420	c.1934T>A	c.(1933-1935)cTt>cAt	p.L645H	TRPC1_ENST00000273482.6_Missense_Mutation_p.L611H|RNU7-47P_ENST00000515978.1_RNA	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	645					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						GTGGCAATGCTTCATAAAAGC	0.383																																					p.L645H		Atlas-SNP	.											.	TRPC1	82	.	0			c.T1934A						.						160	138	146					3																	142522995		2203	4300	6503	SO:0001583	missense	7220	exon11			CAATGCTTCATAA	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"Voltage-gated ion channels / Transient receptor potential cation channels"	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.1934T>A	chr3.hg19:g.142522995T>A	ENSP00000419313:p.Leu645His	121.0	0.0		152.0	55.0	NM_001251845	Q14CE4	Missense_Mutation	SNP	ENST00000476941.1	hg19	CCDS58856.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.646844	0.87958	.	.	ENSG00000144935	ENST00000476941;ENST00000273482	T;T	0.81330	-1.16;-1.48	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.86585	0.5968	L	0.47716	1.5	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.973	D	0.88011	0.2762	10	0.87932	D	0	-12.5585	15.6063	0.76676	0.0:0.0:0.0:1.0	.	611;645;611	A7VJS2;P48995;P48995-2	.;TRPC1_HUMAN;.	H	645;611	ENSP00000419313:L645H;ENSP00000273482:L611H	ENSP00000273482:L611H	L	+	2	0	TRPC1	144005685	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	7.710000	0.84655	2.144000	0.66660	0.528000	0.53228	CTT	.	.		0.383	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304		A	142522995	T	A	142522995	3	1	190	1	0	0	0	0	1	0	0	0	16593	1609	56	4	1870	4	TRPC1	3	142522995	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	29793027	142522995	55499435	40	28116										
IL12A	3592	hgsc.bcm.edu	37	chr3	159713248	159713248	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cctcccttgaagaaccggatTtttataaaactaaaatcaag	5	9	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:159713248T>A	ENST00000305579.2	+	7	971	c.664T>A	c.(664-666)Ttt>Att	p.F222I	IL12A-AS1_ENST00000462431.1_RNA|IL12A_ENST00000466512.1_Missense_Mutation_p.F208I|IL12A_ENST00000480787.1_Missense_Mutation_p.F184I|IL12A-AS1_ENST00000497452.1_RNA	NM_000882.3	NP_000873.2	P29459	IL12A_HUMAN	interleukin 12A	188					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cell adhesion (GO:0045785)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|response to lipopolysaccharide (GO:0032496)|response to UV-B (GO:0010224)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)	interleukin-12 beta subunit binding (GO:0042163)|interleukin-12 receptor binding (GO:0005143)|interleukin-27 binding (GO:0045513)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)	9			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AGAACCGGATTTTTATAAAAC	0.388																																					p.F222I		Atlas-SNP	.											.	IL12A	23	.	0			c.T664A						.						92	94	93					3																	159713248		2203	4300	6503	SO:0001583	missense	3592	exon7			CCGGATTTTTATA	M65271	CCDS3187.1	3q25.33	2014-04-04	2014-04-04		ENSG00000168811	ENSG00000168811		"Interleukins and interleukin receptors"	5969	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor 1, 35 kD subunit", "cytotoxic lymphocyte maturation factor 1, p35", "interleukin 12, p35", "IL-12, subunit p35", "NF cell stimulatory factor chain 1", "interleukin-12 alpha chain", "IL35 subunit"	161560	"interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35)"	NKSF1		1673147	Standard	NM_000882		Approved	CLMF, IL-12A, p35, NFSK	uc003fcx.3	P29459	OTTHUMG00000158942	ENST00000305579.2:c.664T>A	chr3.hg19:g.159713248T>A	ENSP00000303231:p.Phe222Ile	124.0	0.0		130.0	13.0	NM_000882	Q96QZ1	Missense_Mutation	SNP	ENST00000305579.2	hg19	CCDS3187.1	.	.	.	.	.	.	.	.	.	.	T	10.07	1.250340	0.22880	.	.	ENSG00000168811	ENST00000305579;ENST00000480787;ENST00000466512	.	.	.	5.48	-1.08	0.09936	.	0.608922	0.18471	N	0.140220	T	0.38719	0.1051	M	0.69823	2.125	0.21386	N	0.999708	P	0.41643	0.758	B	0.39971	0.315	T	0.30475	-0.9977	9	0.52906	T	0.07	-1.1898	8.9887	0.36010	0.0:0.4387:0.0:0.5613	.	222	O60595	.	I	222;184;208	.	ENSP00000303231:F222I	F	+	1	0	IL12A	161195942	0.947000	0.32204	0.021000	0.16686	0.641000	0.38312	0.860000	0.27871	-0.424000	0.07382	0.533000	0.62120	TTT	.	.		0.388	IL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352602.2	NM_000882		A	159713248	T	A	159713248	3	1	190	1	0	0	0	0	1	0	0	0	7633	1841	64	4	690	4	IL12A	3	159713248	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	17190253	159713248	38309182	41	28117										
FGF12	2257	hgsc.bcm.edu	37	chr3	192078328	192078328	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aatccctttgagctggggttCtgcaaaacaaaataattatt	7	7	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:192078328C>T	ENST00000454309.2	-	2	1025		c.e2-1		FGF12_ENST00000264730.3_Splice_Site|FGF12_ENST00000430714.1_Intron|FGF12_ENST00000445105.2_Splice_Site|FGF12_ENST00000450716.1_Splice_Site	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12						adult locomotory behavior (GO:0008344)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell-cell signaling (GO:0007267)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|JNK cascade (GO:0007254)|negative regulation of cation channel activity (GO:2001258)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|regulation of membrane depolarization (GO:0003254)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)			endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		AGCTGGGGTTCTGCAAAACAA	0.383																																					.		Atlas-SNP	.											.	FGF12	88	.	0			c.14-1G>A						.						89	87	88					3																	192078328		2203	4300	6503	SO:0001630	splice_region_variant	2257	exon4			GGGGTTCTGCAAA	U66197	CCDS3301.1, CCDS46983.1	3q28	2008-07-18			ENSG00000114279	ENSG00000114279			3668	protein-coding gene	gene with protein product	"fibroblast growth factor 12B", "fibroblast growth factor homologous factor 1", "myocyte-activating factor", "fibroblast growth factor FGF-12b"	601513		FGF12B		8790420, 9345906	Standard	NM_021032		Approved	FHF1	uc003fsx.3	P61328	OTTHUMG00000156132	ENST00000454309.2:c.200-1G>A	chr3.hg19:g.192078328C>T		120.0	0.0		124.0	49.0	NM_004113	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Splice_Site	SNP	ENST00000454309.2	hg19	CCDS3301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.3|24.3	4.515649|4.515649	0.85389|0.85389	.|.	.|.	ENSG00000114279|ENSG00000114279	ENST00000264730;ENST00000445105;ENST00000454309;ENST00000450716;ENST00000418610|ENST00000392454	.|.	.|.	.|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74619	.|0.3740	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72940	.|-0.4139	.|4	.|.	.|.	.|.	.|.	18.4573|18.4573	0.90725|0.90725	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|K	-1|5	.|.	.|.	.|E	-|-	.|1	.|0	FGF12|FGF12	193561022|193561022	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.398000|7.398000	0.79919|0.79919	2.613000|2.613000	0.88420|0.88420	0.591000|0.591000	0.81541|0.81541	.|GAA	.	.		0.383	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032	Intron	T	192078328	C	T	192078328	5	4	190	1	0	0	0	0	0	0	1	0	5849	927	32	3	548	3	FGF12	3	192078328	Splice_Site	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	32365080	192078328	5944102	42	28118										
HTT	3064	hgsc.bcm.edu	37	chr4	3129224	3129224	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ccgtcccatctgaccctgccAtggacctgaatgatgggacc	10	15	1	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:3129224A>G	ENST00000355072.5	+	12	1781	c.1636A>G	c.(1636-1638)Atg>Gtg	p.M546V		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	546					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TGACCCTGCCATGGACCTGAA	0.602																																					p.M546V		Atlas-SNP	.											.	HTT	221	.	0			c.A1636G						.						55	61	59					4																	3129224		2107	4217	6324	SO:0001583	missense	3064	exon12			CCTGCCATGGACC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1636A>G	chr4.hg19:g.3129224A>G	ENSP00000347184:p.Met546Val	221.0	1.0		174.0	80.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	A	8.567	0.879088	0.17395	.	.	ENSG00000197386	ENST00000355072	T	0.04706	3.57	4.71	0.76	0.18442	Armadillo-type fold (1);	0.456130	0.27349	N	0.019767	T	0.02970	0.0088	N	0.20986	0.625	0.19575	N	0.999963	B	0.02656	0.0	B	0.01281	0.0	T	0.42189	-0.9466	10	0.31617	T	0.26	.	5.5418	0.17041	0.6356:0.1378:0.2266:0.0	.	546	P42858	HD_HUMAN	V	546	ENSP00000347184:M546V	ENSP00000347184:M546V	M	+	1	0	HTT	3099022	0.983000	0.35010	0.991000	0.47740	0.983000	0.72400	1.554000	0.36266	0.306000	0.22856	0.460000	0.39030	ATG	.	.		0.602	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		G	3129224	A	G	3129224	3	3	190	1	0	0	0	0	1	0	0	0	7466	217	8	2	1682	2	HTT	4	3129224	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10		3129224	188025052	43	28119										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30921844	30921844	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	atcaggggtcactgcagagtTgctatgacagcgggctggag	16	8	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:30921844T>A	ENST00000543491.1	+	2	3244	c.3244T>A	c.(3244-3246)Tgc>Agc	p.C1082S	PCDH7_ENST00000509925.1_3'UTR			O60245	PCDH7_HUMAN	protocadherin 7	0					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						ACTGCAGAGTTGCTATGACAG	0.502																																					p.C1082S		Atlas-SNP	.											.	PCDH7	215	.	0			c.T3244A						.						92	99	97					4																	30921844		2105	4240	6345	SO:0001583	missense	5099	exon2			CAGAGTTGCTATG	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000543491.1:c.3244T>A	chr4.hg19:g.30921844T>A	ENSP00000441802:p.Cys1082Ser	141.0	0.0		123.0	49.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000543491.1	hg19	CCDS54753.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.56|14.56	2.571339|2.571339	0.45798|0.45798	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000543491;ENST00000333135|ENST00000511884	T|.	0.52754|.	0.65|.	5.9|5.9	5.9|5.9	0.94986|0.94986	.|.	.|.	.|.	.|.	.|.	T|.	0.56615|.	0.1997|.	L|L	0.29908|0.29908	0.895|0.895	0.54753|0.54753	D|D	0.999989|0.999989	D;D|.	0.64830|.	0.99;0.994|.	P;P|.	0.59221|.	0.854;0.854|.	T|.	0.52756|.	-0.8533|.	9|.	0.12766|.	T|.	0.61|.	.|.	16.3322|16.3322	0.83039|0.83039	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1082;1035|.	F5GWJ1;O60245-3|.	.;.|.	S|X	1082;1035|771	ENSP00000441802:C1082S|.	ENSP00000330302:C1035S|.	C|L	+|+	1|2	0|0	PCDH7|PCDH7	30530942|30530942	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.698000|7.698000	0.84413|0.84413	2.251000|2.251000	0.74343|0.74343	0.528000|0.528000	0.53228|0.53228	TGC|TTG	.	.		0.502	PCDH7-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032457, NM_002589		A	30921844	T	A	30921844	3	1	190	1	0	0	0	0	1	0	0	0	11525	1812	63	4	3335	4	PCDH7	4	30921844	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	27792620	30921844	160232432	44	28120										
GABRB1	2560	hgsc.bcm.edu	37	chr4	47163447	47163447	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cacagtgaaaaatcgaatgaTtcgactgcatcctgatggaa	9	8	0	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:47163447T>A	ENST00000295454.3	+	4	714	c.422T>A	c.(421-423)aTt>aAt	p.I141N	GABRB1_ENST00000538619.1_Missense_Mutation_p.I71N	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	141					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AATCGAATGATTCGACTGCAT	0.388																																					p.I141N		Atlas-SNP	.											.	GABRB1	107	.	0			c.T422A						.						156	144	148					4																	47163447		2203	4300	6503	SO:0001583	missense	2560	exon4			GAATGATTCGACT		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4081	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 1"	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.422T>A	chr4.hg19:g.47163447T>A	ENSP00000295454:p.Ile141Asn	72.0	0.0		72.0	5.0	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Missense_Mutation	SNP	ENST00000295454.3	hg19	CCDS3474.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384909	0.82792	.	.	ENSG00000163288	ENST00000513567;ENST00000295454;ENST00000538619	T;T;T	0.80304	-1.36;-1.36;-1.36	4.85	4.85	0.62838	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.64402	D	0.000002	D	0.90331	0.6975	M	0.86864	2.845	0.58432	D	0.999996	D;D	0.76494	0.999;0.997	D;D	0.83275	0.987;0.996	D	0.92021	0.5626	10	0.87932	D	0	-17.8598	13.7596	0.62956	0.0:0.0:0.0:1.0	.	71;141	F5GXV5;P18505	.;GBRB1_HUMAN	N	108;141;71	ENSP00000426753:I108N;ENSP00000295454:I141N;ENSP00000440330:I71N	ENSP00000295454:I141N	I	+	2	0	GABRB1	46858204	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	7.868000	0.87116	2.030000	0.59900	0.454000	0.30748	ATT	.	.		0.388	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1			A	47163447	T	A	47163447	3	1	190	1	0	0	0	0	1	0	0	0	6174	1493	52	4	436	4	GABRB1	4	47163447	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	16241603	47163447	143990829	45	28121										
FRYL	285527	hgsc.bcm.edu	37	chr4	48512966	48512966	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tcaccaagaaagctgactgcCtcattagttatttctccaaa	5	11	3	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:48512966C>T	ENST00000503238.1	-	55	8180	c.8181G>A	c.(8179-8181)gaG>gaA	p.E2727E	FRYL_ENST00000537810.1_Silent_p.E2727E|FRYL_ENST00000507873.2_Silent_p.E123E|FRYL_ENST00000358350.4_Silent_p.E2727E|FRYL_ENST00000264319.7_Silent_p.E123E			O94915	FRYL_HUMAN	FRY-like	2727					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						AGCTGACTGCCTCATTAGTTA	0.368																																					p.E2727E		Atlas-SNP	.											.	FRYL	242	.	0			c.G8181A						.						85	79	81					4																	48512966		1896	4104	6000	SO:0001819	synonymous_variant	285527	exon58			GACTGCCTCATTA	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.8181G>A	chr4.hg19:g.48512966C>T		295.0	0.0		295.0	103.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	hg19	CCDS43227.1																																																																																			.	.		0.368	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48512966	C	T	48512966	2	4	190	1	0	0	0	0	0	0	0	1	6072	680	24	3		3	FRYL	4	48512966	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	1349519	48512966	142641310	46	28122										
AMBN	258	hgsc.bcm.edu	37	chr4	71467187	71467187	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tctcccatcacagccatcctTgaagcctcaacagccaggac	6	17	3	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:71467187T>C	ENST00000322937.6	+	6	450	c.347T>C	c.(346-348)tTg>tCg	p.L116S	AMBN_ENST00000449493.2_Missense_Mutation_p.L101S	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	116					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|odontogenesis of dentin-containing tooth (GO:0042475)	proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|structural constituent of tooth enamel (GO:0030345)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29			Lung(101;0.235)			CAGCCATCCTTGAAGCCTCAA	0.488											OREG0016218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L116S		Atlas-SNP	.											.	AMBN	73	.	0			c.T347C						.						140	142	141					4																	71467187		2203	4300	6503	SO:0001583	missense	258	exon6			CATCCTTGAAGCC	AF209780	CCDS3543.1	4q21	2006-11-28	2006-04-27		ENSG00000178522	ENSG00000178522			452	protein-coding gene	gene with protein product		601259	"ameloblastin, enamel matrix protein"			9126491	Standard	NM_016519		Approved		uc003hfl.3	Q9NP70	OTTHUMG00000129913	ENST00000322937.6:c.347T>C	chr4.hg19:g.71467187T>C	ENSP00000313809:p.Leu116Ser	106.0	0.0	1130	111.0	38.0	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Missense_Mutation	SNP	ENST00000322937.6	hg19	CCDS3543.1	.	.	.	.	.	.	.	.	.	.	T	12.09	1.832518	0.32421	.	.	ENSG00000178522	ENST00000322937;ENST00000538728;ENST00000449493	T;T	0.36157	1.27;1.27	5.65	3.11	0.35812	.	0.228662	0.30658	N	0.009159	T	0.50292	0.1607	M	0.62723	1.935	0.29718	N	0.838909	D	0.71674	0.998	D	0.64877	0.93	T	0.50250	-0.8850	10	0.66056	D	0.02	-4.8433	8.4246	0.32720	0.3133:0.0:0.0:0.6867	.	116	Q9NP70	AMBN_HUMAN	S	116;116;101	ENSP00000313809:L116S;ENSP00000391234:L101S	ENSP00000313809:L116S	L	+	2	0	AMBN	71501776	1.000000	0.71417	1.000000	0.80357	0.069000	0.16628	1.602000	0.36783	0.458000	0.26988	-0.490000	0.04691	TTG	.	.		0.488	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519		C	71467187	T	C	71467187	3	2	190	1	0	0	0	0	1	0	0	0	563	1821	63	2	369	2	AMBN	4	71467187	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	22954221	71467187	119687089	47	28123										
ALB	213	hgsc.bcm.edu	37	chr4	74282058	74282071	+	Splice_Site	DEL	AATTCCAGAATGCG	AATTCCAGAATGCG	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgagcagcttggagagtacaAattccagaatgcgtaagtaa					rs370819889		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	AATTCCAGAATGCG	AATTCCAGAATGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:74282058_74282071delAATTCCAGAATGCG	ENST00000503124.1	+	8	1034_1046	c.827_839delAATTCCAGAATGCG	c.(826-840)aaattccagaatgcg>ag	p.KFQNA276fs	ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Splice_Site_p.KFQNA311fs|ALB_ENST00000415165.2_Splice_Site_p.KFQNA234fs|ALB_ENST00000509063.1_Splice_Site_p.KFQNA426fs|ALB_ENST00000295897.4_Splice_Site_p.KFQNA426fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.A430V(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GGAGAGTACAAATTCCAGAATGCGTAAGTAATTT	0.29																																					p.426_430del		Atlas-INDEL	.											.	ALB	132	.	1	Substitution - Missense(1)	stomach(1)	c.1276_1289del						.																																			SO:0001630	splice_region_variant	213	exon10			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.839+1AATTCCAGAATGCG>-	chr4.hg19:g.74282058_74282071delAATTCCAGAATGCG		231.0	0.0		178.0	56.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.29	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	Frame_Shift_Del	-	74282071	AATTCCAGAATGCG	-	74282058	8	5	190	1	0	1	0	1	0	0	1	0	486	14	1	0	1315	0	ALB	4	74282058	Splice_Site	DEL	AATTCCAGAATGCG	TCGA-DD-AADG-01A-11D-A40R-10	2814871	74282058	116872218	48	28124										
LIN54	132660	hgsc.bcm.edu	37	chr4	83891563	83891563	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agttgatccaataacaccacTttcagatattgttatggtct	6	8	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:83891563T>C	ENST00000340417.3	-	4	1245	c.868A>G	c.(868-870)Agt>Ggt	p.S290G	LIN54_ENST00000446851.2_Missense_Mutation_p.S69G|LIN54_ENST00000395283.2_Intron|LIN54_ENST00000506560.1_Intron|LIN54_ENST00000510557.1_Missense_Mutation_p.S69G|LIN54_ENST00000442461.2_Missense_Mutation_p.S69G|LIN54_ENST00000395282.2_3'UTR|LIN54_ENST00000505397.1_Missense_Mutation_p.S290G	NM_194282.2	NP_919258.2	Q6MZP7	LIN54_HUMAN	lin-54 DREAM MuvB core complex component	290					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)	14		Hepatocellular(203;0.114)				ATAACACCACTTTCAGATATT	0.358																																					p.S290G		Atlas-SNP	.											.	LIN54	50	.	0			c.A868G						.						175	169	171					4																	83891563		2203	4300	6503	SO:0001583	missense	132660	exon4			CACCACTTTCAGA	BX537919	CCDS3599.1, CCDS47089.1, CCDS75157.1	4q21.22	2014-07-17	2014-07-17		ENSG00000189308	ENSG00000189308			25397	protein-coding gene	gene with protein product	"CXC domain containing 1"	613367	"lin-54 homolog (C. elegans)"			21498570	Standard	XM_005262749		Approved	MIP120, DKFZp686L1814, JC8.6, CXCDC1	uc003hnx.3	Q6MZP7	OTTHUMG00000130287	ENST00000340417.3:c.868A>G	chr4.hg19:g.83891563T>C	ENSP00000341947:p.Ser290Gly	106.0	0.0		128.0	53.0	NM_194282	Q32M68|Q32M69|Q6N071|Q76B60	Missense_Mutation	SNP	ENST00000340417.3	hg19	CCDS3599.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.739611	0.49045	.	.	ENSG00000189308	ENST00000340417;ENST00000442461;ENST00000446851;ENST00000510557;ENST00000505397	.	.	.	5.81	5.81	0.92471	.	0.247257	0.47455	D	0.000230	T	0.33177	0.0854	N	0.14661	0.345	0.80722	D	1	B;P	0.38827	0.0;0.649	B;B	0.32090	0.0;0.14	T	0.18366	-1.0339	9	0.17832	T	0.49	-7.2614	16.1756	0.81847	0.0:0.0:0.0:1.0	.	162;290	Q7Z3G2;Q6MZP7	.;LIN54_HUMAN	G	290;69;69;69;290	.	ENSP00000341947:S290G	S	-	1	0	LIN54	84110587	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.505000	0.66981	2.213000	0.71641	0.528000	0.53228	AGT	.	.		0.358	LIN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252626.2	NM_194282		C	83891563	T	C	83891563	3	2	190	1	0	0	0	0	1	0	0	0	8818	1609	56	2	1421	2	LIN54	4	83891563	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	9609505	83891563	107262713	49	28125										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537080	88537088	+	In_Frame_Del	DEL	ACAGCAGCA	ACAGCAGCA	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgaaagcagtgatagcagtgAcagcagcaatagcagtgaca					rs367717407|rs201754564|rs370267258|rs553101049	byFrequency	TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	ACAGCAGCA	ACAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:88537080_88537088delACAGCAGCA	ENST00000282478.7	+	4	3299_3307	c.3266_3274delACAGCAGCA	c.(3265-3276)gacagcagcaat>gat	p.SSN1090del	DSPP_ENST00000399271.1_In_Frame_Del_p.SSN1090del|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1090	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gatagcagtgacagcagcaatagcagtga	0.536																																					p.1089_1091del		Atlas-INDEL	.											.	DSPP	174	.	0			c.3265_3273del						.			1444,630		641,162,234						0.5	0			23	2259,1617		893,473,572	no	coding	DSPP	NM_014208.3		1534,635,806	A1A1,A1R,RR		41.7183,30.3761,37.7647				3703,2247				SO:0001651	inframe_deletion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3266_3274delACAGCAGCA	chr4.hg19:g.88537080_88537088delACAGCAGCA	ENSP00000282478:p.Ser1090_Asn1092del	233.0	0.0		256.0	51.0	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.536	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		-	88537088	ACAGCAGCA	-	88537080	7	5	190	1	0	1	0	1	0	0	0	0	4784	275	10	0	3280	0	DSPP	4	88537080	In_Frame_Del	DEL	ACAGCAGCA	TCGA-DD-AADG-01A-11D-A40R-10	4645517	88537080	102617196	50	28126										
PITX2	5308	hgsc.bcm.edu	37	chr4	111539720	111539720	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agttgttgtaggaatagcctGggtacatgtcgtcgtagggc	15	6	0	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:111539720G>T	ENST00000354925.2	-	7	2220	c.515C>A	c.(514-516)cCa>cAa	p.P172Q	PITX2_ENST00000556049.1_5'UTR|PITX2_ENST00000306732.3_Missense_Mutation_p.P179Q|PITX2_ENST00000355080.5_Missense_Mutation_p.P126Q|PITX2_ENST00000394595.3_Silent_p.P103P|PITX2_ENST00000394598.2_Missense_Mutation_p.P172Q	NM_001204397.1	NP_001191326.1	Q99697	PITX2_HUMAN	paired-like homeodomain 2	172					atrial cardiac muscle tissue morphogenesis (GO:0055009)|atrioventricular valve development (GO:0003171)|camera-type eye development (GO:0043010)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|deltoid tuberosity development (GO:0035993)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic hindlimb morphogenesis (GO:0035116)|endodermal digestive tract morphogenesis (GO:0061031)|extraocular skeletal muscle development (GO:0002074)|female gonad development (GO:0008585)|hair cell differentiation (GO:0035315)|hypothalamus cell migration (GO:0021855)|in utero embryonic development (GO:0001701)|iris morphogenesis (GO:0061072)|left lung morphogenesis (GO:0060460)|left/right axis specification (GO:0070986)|male gonad development (GO:0008584)|myoblast fusion (GO:0007520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|patterning of blood vessels (GO:0001569)|positive regulation of DNA binding (GO:0043388)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin secreting cell differentiation (GO:0060127)|pulmonary myocardium development (GO:0003350)|pulmonary vein morphogenesis (GO:0060577)|regulation of cell migration (GO:0030334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|response to vitamin A (GO:0033189)|somatotropin secreting cell differentiation (GO:0060126)|spleen development (GO:0048536)|subthalamic nucleus development (GO:0021763)|superior vena cava morphogenesis (GO:0060578)|vascular smooth muscle cell differentiation (GO:0035886)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)|ribonucleoprotein complex binding (GO:0043021)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		GGAATAGCCTGGGTACATGTC	0.562																																					p.P179Q		Atlas-SNP	.											.	PITX2	73	.	0			c.C536A						.						83	73	76					4																	111539720		2203	4300	6503	SO:0001583	missense	5308	exon3			TAGCCTGGGTACA	U69961	CCDS3692.1, CCDS3693.1, CCDS3694.1	4q25	2011-06-20	2007-07-12		ENSG00000164093	ENSG00000164093		"Homeoboxes / PRD class"	9005	protein-coding gene	gene with protein product		601542	"paired-like homeodomain transcription factor 2"	IRID2, IHG2, RIEG, RIEG1, RGS		9539779, 7581385	Standard	NM_000325		Approved	IGDS, RS, Brx1, Otlx2, ARP1	uc021xqr.1	Q99697	OTTHUMG00000132837	ENST00000354925.2:c.515C>A	chr4.hg19:g.111539720G>T	ENSP00000347004:p.Pro172Gln	120.0	0.0		113.0	41.0	NM_000325	A8K6C6|B2RA02|B3KXS0|O60578|O60579|O60580|Q3KQX9|Q9BY17	Missense_Mutation	SNP	ENST00000354925.2	hg19	CCDS3692.1	.	.	.	.	.	.	.	.	.	.	G	17.40	3.380658	0.61845	.	.	ENSG00000164093	ENST00000306732;ENST00000394598;ENST00000355080;ENST00000354925;ENST00000511837;ENST00000556049	D;D;D;D;D;T	0.94000	-2.96;-3.09;-3.23;-3.09;-3.33;-0.74	4.89	4.89	0.63831	.	0.106120	0.64402	D	0.000003	D	0.95595	0.8568	L	0.59436	1.845	0.80722	D	1	P;D;D;D	0.69078	0.904;0.997;0.984;0.973	P;D;P;P	0.63793	0.536;0.918;0.616;0.786	D	0.95878	0.8896	10	0.87932	D	0	.	18.6339	0.91370	0.0:0.0:1.0:0.0	.	126;126;172;179	A8K6C6;Q99697-3;Q99697;Q99697-2	.;.;PITX2_HUMAN;.	Q	179;172;126;172;172;96	ENSP00000304169:P179Q;ENSP00000378097:P172Q;ENSP00000347192:P126Q;ENSP00000347004:P172Q;ENSP00000421454:P172Q;ENSP00000450938:P96Q	ENSP00000304169:P179Q	P	-	2	0	PITX2	111759169	1.000000	0.71417	0.996000	0.52242	0.911000	0.54048	9.263000	0.95617	2.712000	0.92718	0.563000	0.77884	CCA	.	.		0.562	PITX2-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256308.2			T	111539720	G	T	111539720	3	4	190	1	0	0	0	0	1	0	0	0	11964	1348	47	3	442	3	PITX2	4	111539720	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	23002640	111539720	79614556	51	28127										
CCRN4L	25819	hgsc.bcm.edu	37	chr4	139965969	139965969	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tcctcagtagactaggctatCaaggcacgtttttccccaaa	7	12	2	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:139965969C>A	ENST00000280614.2	+	3	830	c.637C>A	c.(637-639)Caa>Aaa	p.Q213K	ELF2_ENST00000515489.1_Intron	NM_012118.2	NP_036250.2	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like (S. cerevisiae)	213					circadian regulation of gene expression (GO:0032922)|cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|regulation of circadian rhythm (GO:0042752)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|response to extracellular stimulus (GO:0009991)|response to lipopolysaccharide (GO:0032496)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A)-specific ribonuclease activity (GO:0004535)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(2)|large_intestine(3)|lung(3)|ovary(1)	9	all_hematologic(180;0.162)					ACTAGGCTATCAAGGCACGTT	0.463																																					p.Q213K	Ovarian(144;566 1842 19130 21379 22209)	Atlas-SNP	.											.	CCRN4L	22	.	0			c.C637A						.						130	112	118					4																	139965969		2203	4300	6503	SO:0001583	missense	25819	exon3			GGCTATCAAGGCA	AF183961	CCDS3743.1	4q31.1	2014-06-18	2001-11-28		ENSG00000151014	ENSG00000151014			14254	protein-coding gene	gene with protein product		608468	"CCR4-like (carbon catabolite repression 4, S.cerevisiae)"			10521507	Standard	NM_012118		Approved	CCR4L, Ccr4c	uc003ihl.3	Q9UK39	OTTHUMG00000161271	ENST00000280614.2:c.637C>A	chr4.hg19:g.139965969C>A	ENSP00000280614:p.Gln213Lys	160.0	0.0		166.0	64.0	NM_012118	D3DNY5|Q14D51|Q9HD93|Q9HD94|Q9HD95	Missense_Mutation	SNP	ENST00000280614.2	hg19	CCDS3743.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.313869	0.23908	.	.	ENSG00000151014	ENST00000280614	T	0.27720	1.65	5.5	5.5	0.81552	Endonuclease/exonuclease/phosphatase (2);	0.168168	0.52532	D	0.000062	T	0.24624	0.0597	N	0.20986	0.625	0.80722	D	1	B	0.25563	0.129	B	0.26517	0.07	T	0.04693	-1.0933	9	.	.	.	-7.1442	19.3911	0.94583	0.0:1.0:0.0:0.0	.	213	Q9UK39	NOCT_HUMAN	K	213	ENSP00000280614:Q213K	.	Q	+	1	0	CCRN4L	140185419	1.000000	0.71417	0.975000	0.42487	0.947000	0.59692	2.591000	0.46163	2.600000	0.87896	0.555000	0.69702	CAA	.	.		0.463	CCRN4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257231.3	NM_012118		A	139965969	C	A	139965969	3	1	190	1	0	0	0	0	1	0	0	0	2953	827	29	3	647	3	CCRN4L	4	139965969	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	28426249	139965969	51188307	52	28128										
GALNTL6	442117	hgsc.bcm.edu	37	chr4	173730589	173730589	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttcgcaccaagaaaagagaaGgactcatccggacccgtctc	9	13	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:173730589G>A	ENST00000506823.1	+	6	1288	c.631G>A	c.(631-633)Gga>Aga	p.G211R	GALNTL6_ENST00000508122.1_Missense_Mutation_p.G194R	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	211	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						GAAAAGAGAAGGACTCATCCG	0.512																																					p.G211R		Atlas-SNP	.											.	GALNTL6	102	.	0			c.G631A						.						99	92	94					4																	173730589		2203	4300	6503	SO:0001583	missense	442117	exon6			AGAGAAGGACTCA		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.631G>A	chr4.hg19:g.173730589G>A	ENSP00000423313:p.Gly211Arg	140.0	0.0		142.0	9.0	NM_001034845	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	hg19	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.703718	0.88924	.	.	ENSG00000174473	ENST00000506823;ENST00000404275;ENST00000508122	T;T	0.80214	-1.35;-1.35	5.45	5.45	0.79879	Glycosyl transferase, family 2 (1);	0.000000	0.64402	D	0.000009	D	0.94745	0.8304	H	0.99117	4.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96726	0.9536	10	0.87932	D	0	.	19.6346	0.95724	0.0:0.0:1.0:0.0	.	211	Q49A17	GLTL6_HUMAN	R	211;211;194	ENSP00000423313:G211R;ENSP00000423827:G194R	ENSP00000385382:G211R	G	+	1	0	GALNTL6	173967164	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	9.813000	0.99286	2.720000	0.93068	0.491000	0.48974	GGA	.	.		0.512	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		A	173730589	G	A	173730589	3	1	190	1	0	0	0	0	1	0	0	0	6233	1001	35	3	649	3	GALNTL6	4	173730589	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	33764620	173730589	17423687	53	28129										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186544895	186544895	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gagcgggggggccgctttgaTtttcttcctccagcaaatac	12	11	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:186544895T>C	ENST00000284776.7	-	13	2185	c.1676A>G	c.(1675-1677)aAt>aGt	p.N559S	SORBS2_ENST00000355634.5_Missense_Mutation_p.N659S|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000431808.1_Missense_Mutation_p.N559S|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.N463S|SORBS2_ENST00000448662.2_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	559					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GCCGCTTTGATTTTCTTCCTC	0.577																																					p.N659S	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.A1976G						.						30	35	33					4																	186544895		2202	4299	6501	SO:0001583	missense	8470	exon16			CTTTGATTTTCTT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1676A>G	chr4.hg19:g.186544895T>C	ENSP00000284776:p.Asn559Ser	166.0	0.0		189.0	76.0	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	hg19	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	T	0.441	-0.898616	0.02472	.	.	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.35973	1.38;1.38;1.28;1.38	5.36	-2.46	0.06461	.	1.102740	0.06553	N	0.745425	T	0.18676	0.0448	N	0.12182	0.205	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.28038	-1.0056	10	0.18710	T	0.47	-5.2441	8.5184	0.33259	0.0:0.2149:0.5245:0.2606	.	463;659;559	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	S	559;559;463;659	ENSP00000284776:N559S;ENSP00000411764:N559S;ENSP00000397482:N463S;ENSP00000347852:N659S	ENSP00000284776:N559S	N	-	2	0	SORBS2	186781889	0.389000	0.25205	0.001000	0.08648	0.007000	0.05969	0.215000	0.17562	-0.525000	0.06391	-0.488000	0.04728	AAT	.	.		0.577	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		C	186544895	T	C	186544895	3	2	190	1	0	0	0	0	1	0	0	0	14943	1493	52	2	1662	2	SORBS2	4	186544895	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	12814306	186544895	4609381	54	28130										
PRDM9	56979	hgsc.bcm.edu	37	chr5	23527459	23527459	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tatgtctgcagggagtgtggGcggggctttcgcgataagtc	17	7	1	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:23527459G>A	ENST00000296682.3	+	11	2444	c.2262G>A	c.(2260-2262)ggG>ggA	p.G754G		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	754					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGAGTGTGGGCGGGGCTTTC	0.582										HNSCC(3;0.000094)																											p.G754G		Atlas-SNP	.											.	PRDM9	344	.	0			c.G2262A						.						52	73	66					5																	23527459		2112	4293	6405	SO:0001819	synonymous_variant	56979	exon11			GTGTGGGCGGGGC	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2262G>A	chr5.hg19:g.23527459G>A		273.0	0.0		185.0	19.0	NM_020227	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	hg19	CCDS43307.1																																																																																			.	.		0.582	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		A	23527459	G	A	23527459	2	1	190	1	0	0	0	0	0	0	0	1	12475	1190	42	3		3	PRDM9	5	23527459	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10		23527459	157387801	55	28131										
NUP155	9631	hgsc.bcm.edu	37	chr5	37302983	37302983	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	atggctcgagcaatgtactcTagtcgctgctgaagtgaaat	11	8	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:37302983T>C	ENST00000231498.3	-	29	3548	c.3345A>G	c.(3343-3345)ctA>ctG	p.L1115L	NUP155_ENST00000381843.2_Silent_p.L1056L|NUP155_ENST00000513532.1_Silent_p.L1051L|NUP155_ENST00000502533.1_5'UTR	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	1115					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CAATGTACTCTAGTCGCTGCT	0.363																																					p.L1115L		Atlas-SNP	.											.	NUP155	116	.	0			c.A3345G						.						120	118	119					5																	37302983		2203	4300	6503	SO:0001819	synonymous_variant	9631	exon29			GTACTCTAGTCGC	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.3345A>G	chr5.hg19:g.37302983T>C		53.0	0.0		59.0	26.0	NM_153485	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	hg19	CCDS3921.1																																																																																			.	.		0.363	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		C	37302983	T	C	37302983	2	2	190	1	0	0	0	0	0	0	0	1	10765	1509	53	2		2	NUP155	5	37302983	Silent	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	13775524	37302983	143612277	56	28132										
SLC30A5	64924	hgsc.bcm.edu	37	chr5	68411780	68411780	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tggagtcttggttttctctcAttatgccttttgcaacggtt	9	8	3	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:68411780A>G	ENST00000396591.3	+	9	1421	c.811A>G	c.(811-813)Att>Gtt	p.I271V	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	271					cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		GTTTTCTCTCATTATGCCTTT	0.328																																					p.I271V		Atlas-SNP	.											.	SLC30A5	54	.	0			c.A811G						.						158	149	152					5																	68411780		2203	4300	6503	SO:0001583	missense	64924	exon9			TCTCTCATTATGC	AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"Solute carriers"	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.811A>G	chr5.hg19:g.68411780A>G	ENSP00000379836:p.Ile271Val	120.0	0.0		109.0	34.0	NM_022902	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Missense_Mutation	SNP	ENST00000396591.3	hg19	CCDS3996.1	.	.	.	.	.	.	.	.	.	.	A	13.02	2.112247	0.37242	.	.	ENSG00000145740	ENST00000396591	T	0.62788	-0.0	5.47	5.47	0.80525	.	0.087522	0.85682	D	0.000000	T	0.53433	0.1796	L	0.43152	1.355	0.80722	D	1	B;B	0.18166	0.004;0.026	B;B	0.14578	0.011;0.008	T	0.49370	-0.8947	10	0.15952	T	0.53	.	15.4982	0.75673	1.0:0.0:0.0:0.0	.	100;271	Q8TAD4-2;Q8TAD4	.;ZNT5_HUMAN	V	271	ENSP00000379836:I271V	ENSP00000379836:I271V	I	+	1	0	SLC30A5	68447536	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.328000	0.43867	2.206000	0.71126	0.477000	0.44152	ATT	.	.		0.328	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2			G	68411780	A	G	68411780	3	3	190	1	0	0	0	0	1	0	0	0	14573	217	8	2	933	2	SLC30A5	5	68411780	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	31108797	68411780	112503480	57	28133										
NUDT12	83594	hgsc.bcm.edu	37	chr5	102887925	102887925	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aattgaactttacctgttctCtagtgaaccagcgggcatcc	8	11	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:102887925C>G	ENST00000230792.2	-	6	1367	c.1271G>C	c.(1270-1272)aGa>aCa	p.R424T	NUDT12_ENST00000515407.1_5'Flank|NUDT12_ENST00000507423.1_Missense_Mutation_p.R406T	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	424	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		TACCTGTTCTCTAGTGAACCA	0.393																																					p.R424T		Atlas-SNP	.											.	NUDT12	27	.	0			c.G1271C						.						136	133	134					5																	102887925		2202	4300	6502	SO:0001583	missense	83594	exon6			TGTTCTCTAGTGA	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"Nudix motif containing", "Ankyrin repeat domain containing"	18826	protein-coding gene	gene with protein product	"nucleoside diphosphate linked moiety X-type motif 12"	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.1271G>C	chr5.hg19:g.102887925C>G	ENSP00000230792:p.Arg424Thr	94.0	0.0		124.0	25.0	NM_031438	B3KUW2|Q8TAL7	Missense_Mutation	SNP	ENST00000230792.2	hg19	CCDS4096.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148630	0.78001	.	.	ENSG00000112874	ENST00000230792;ENST00000507423	T;T	0.08193	3.12;3.12	5.46	4.57	0.56435	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.042117	0.85682	D	0.000000	T	0.32823	0.0842	M	0.86651	2.83	0.58432	D	0.999994	D;D	0.67145	0.993;0.996	D;D	0.72625	0.911;0.978	T	0.09729	-1.0661	10	0.56958	D	0.05	-26.4578	15.1505	0.72692	0.0:0.9285:0.0:0.0715	.	406;424	E7EM93;Q9BQG2	.;NUD12_HUMAN	T	424;406	ENSP00000230792:R424T;ENSP00000424521:R406T	ENSP00000230792:R424T	R	-	2	0	NUDT12	102915824	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.624000	0.61254	2.724000	0.93272	0.650000	0.86243	AGA	.	.		0.393	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438		G	102887925	C	G	102887925	3	3	190	1	0	0	0	0	1	0	0	0	10737	913	32	4	125	4	NUDT12	5	102887925	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	34476145	102887925	78027335	58	28134										
KCNN2	3781	hgsc.bcm.edu	37	chr5	113698857	113698857	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gccaccggcgcgccctgttcGaaaagcgcaagcggctcagc	13	16	1	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:113698857G>T	ENST00000512097.3	+	2	1403	c.385G>T	c.(385-387)Gaa>Taa	p.E129*	KCNN2_ENST00000507750.1_3'UTR|KCNN2_ENST00000264773.3_Nonsense_Mutation_p.E129*			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	129					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	CGCCCTGTTCGAAAAGCGCAA	0.622																																					p.E129X		Atlas-SNP	.											.	KCNN2	144	.	0			c.G385T						.						38	39	38					5																	113698857		2202	4300	6502	SO:0001587	stop_gained	3781	exon1			CTGTTCGAAAAGC	AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.385G>T	chr5.hg19:g.113698857G>T	ENSP00000427120:p.Glu129*	76.0	0.0		115.0	29.0	NM_021614	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Nonsense_Mutation	SNP	ENST00000512097.3	hg19	CCDS4114.1	.	.	.	.	.	.	.	.	.	.	G	48	14.308480	0.99789	.	.	ENSG00000080709	ENST00000512097;ENST00000264773	.	.	.	5.44	4.57	0.56435	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	13.8883	0.63721	0.0741:0.0:0.9259:0.0	.	.	.	.	X	129	.	ENSP00000264773:E129X	E	+	1	0	KCNN2	113726756	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.695000	0.84257	1.293000	0.44690	0.655000	0.94253	GAA	.	.		0.622	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614		T	113698857	G	T	113698857	4	4	190	1	0	0	0	0	0	1	0	0	8088	1059	37	1	387	1	KCNN2	5	113698857	Nonsense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	10810932	113698857	67216403	59	28135										
FTMT	94033	hgsc.bcm.edu	37	chr5	121187759	121187759	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gctcccgctgcgttgggcccCggggcgccccttggacccca	14	19	0	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:121187759C>A	ENST00000321339.1	+	1	110	c.101C>A	c.(100-102)cCg>cAg	p.P34Q		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	34					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		CGTTGGGCCCCGGGGCGCCCC	0.766																																					p.P34Q		Atlas-SNP	.											.	FTMT	71	.	0			c.C101A						.						8	9	9					5																	121187759		2156	4207	6363	SO:0001583	missense	94033	exon1			GGGCCCCGGGGCG	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.101C>A	chr5.hg19:g.121187759C>A	ENSP00000313691:p.Pro34Gln	22.0	0.0		56.0	19.0	NM_177478		Missense_Mutation	SNP	ENST00000321339.1	hg19	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	C	10.33	1.320220	0.23994	.	.	ENSG00000181867	ENST00000321339	T	0.64438	-0.1	3.06	1.21	0.21127	.	.	.	.	.	T	0.38214	0.1032	N	0.24115	0.695	0.09310	N	1	P	0.42357	0.777	B	0.32864	0.154	T	0.20207	-1.0282	9	0.48119	T	0.1	.	4.4736	0.11724	0.0:0.6377:0.23:0.1323	.	34	Q8N4E7	FTMT_HUMAN	Q	34	ENSP00000313691:P34Q	ENSP00000313691:P34Q	P	+	2	0	FTMT	121215658	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.154000	0.16343	0.303000	0.22785	-0.182000	0.12963	CCG	.	.		0.766	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		A	121187759	C	A	121187759	3	1	190	1	0	0	0	0	1	0	0	0	6093	652	23	1	103	1	FTMT	5	121187759	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	7488902	121187759	59727501	60	28136										
TCF7	6500	hgsc.bcm.edu	37	chr5	133481891	133481891	+	IGR	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gaattcaccctctgtttacaGataactctcttcactattcc	3	13	4	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:133481891G>A	ENST00000353411.6	-	0	9467				TCF7_ENST00000321603.6_Splice_Site|TCF7_ENST00000342854.5_Intron|TCF7_ENST00000395023.1_Intron|TCF7_ENST00000432532.2_Intron|TCF7_ENST00000395029.1_Intron|TCF7_ENST00000378560.4_Splice_Site|TCF7_ENST00000520958.1_Intron	NM_170679.2	NP_733779.1	P63208	SKP1_HUMAN	S-phase kinase-associated protein 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H2A monoubiquitination (GO:0035518)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	Cul7-RING ubiquitin ligase complex (GO:0031467)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTGTTTACAGATAACTCTCT	0.502											OREG0016787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	TCF7	81	.	0			c.804-1G>A						.						114	123	120					5																	133481891		2203	4300	6503	SO:0001628	intergenic_variant	6932	exon10			TTTACAGATAACT	U33760	CCDS4171.1, CCDS4172.1	5q31	2011-11-18	2007-11-13	2007-11-13	ENSG00000113558	ENSG00000113558			10899	protein-coding gene	gene with protein product		601434	"S-phase kinase-associated protein 1A (p19A)"	SKP1A		7553852, 8646875	Standard	NM_006930		Approved	EMC19, OCP2, TCEB1L, MGC34403, OCP-II, p19A	uc003kzc.4	P63208	OTTHUMG00000129117		chr5.hg19:g.133481891G>A		93.0	0.0	1603	143.0	34.0	NM_201634	D3DQ97|D3DQ98|P34991|Q8TAY2	Splice_Site	SNP	ENST00000353411.6	hg19	CCDS4171.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.345643	0.82022	.	.	ENSG00000081059	ENST00000321603;ENST00000378560	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4191	0.94713	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TCF7	133509790	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.942000	0.70203	2.586000	0.87340	0.563000	0.77884	.	.	.		0.502	SKP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251162.2	NM_170679		A	133481891	G	A	133481891	1	1	190	0	1	0	0	0	0	0	0	0	15711	956	33	3		3	TCF7	5	133481891	IGR	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	12294132	133481891	47433369	61	28137										
RBM27	54439	hgsc.bcm.edu	37	chr5	145640456	145640456	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aatttggaactattgttaatAtccaggtaaatgtggctatg	9	4	0	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:145640456A>G	ENST00000265271.5	+	12	2054	c.1888A>G	c.(1888-1890)Atc>Gtc	p.I630V	RBM27_ENST00000506502.1_Missense_Mutation_p.I575V	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	630	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TATTGTTAATATCCAGGTAAA	0.363																																					p.I630V		Atlas-SNP	.											.	RBM27	119	.	0			c.A1888G						.						164	143	149					5																	145640456		1568	3582	5150	SO:0001583	missense	54439	exon12			GTTAATATCCAGG	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1888A>G	chr5.hg19:g.145640456A>G	ENSP00000265271:p.Ile630Val	292.0	0.0		432.0	23.0	NM_018989	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	hg19	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.726745	0.89298	.	.	ENSG00000091009	ENST00000265271	T	0.51817	0.69	6.17	6.17	0.99709	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.59865	0.2225	L	0.37466	1.105	0.80722	D	1	P;D	0.58620	0.898;0.983	D;D	0.73708	0.956;0.981	T	0.56232	-0.8013	10	0.36615	T	0.2	-11.4254	16.8222	0.85835	1.0:0.0:0.0:0.0	.	630;575	Q9P2N5;B3KY61	RBM27_HUMAN;.	V	630	ENSP00000265271:I630V	ENSP00000265271:I630V	I	+	1	0	RBM27	145620649	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.763000	0.91715	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.363	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		G	145640456	A	G	145640456	3	3	190	1	0	0	0	0	1	0	0	0	13142	449	16	2	1934	2	RBM27	5	145640456	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	12158565	145640456	35274804	62	28138										
GPRIN1	114787	hgsc.bcm.edu	37	chr5	176026192	176026192	+	Frame_Shift_Del	DEL	C	C	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agcacaaaggatctacttttCccagggatccaagatcttcc							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:176026192delC	ENST00000303991.4	-	2	821	c.644delG	c.(643-645)ggafs	p.G215fs		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	215					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATCTACTTTTCCCAGGGATCC	0.502																																					p.G215fs		Atlas-INDEL	.											.	GPRIN1	77	.	0			c.645delA						.						77	78	77					5																	176026192		2203	4299	6502	SO:0001589	frameshift_variant	114787	exon2			.	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.644delG	chr5.hg19:g.176026192delC	ENSP00000305839:p.Gly215fs	56.0	0.0		103.0	22.0	NM_052899	C9JM70|Q8ND74|Q96PZ4	Frame_Shift_Del	DEL	ENST00000303991.4	hg19	CCDS4405.1																																																																																			.	.		0.502	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899		-	176026192	C	-	176026192	7	5	190	1	0	1	0	1	0	0	0	0	6738	855	30	0	2386	0	GPRIN1	5	176026192	Frame_Shift_Del	DEL	C	TCGA-DD-AADG-01A-11D-A40R-10	30385736	176026192	4889068	63	28139										
GRM6	2916	hgsc.bcm.edu	37	chr5	178418902	178418902	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	atctgaacgaaggcctcaacCccactttcgccatagttgcc	7	15	2	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:178418902C>T	ENST00000517717.1	-	3	725	c.687G>A	c.(685-687)ggG>ggA	p.G229G	GRM6_ENST00000231188.5_Silent_p.G229G|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	229					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		AGGCCTCAACCCCACTTTCGC	0.637																																					p.G229G		Atlas-SNP	.											.	GRM6	149	.	0			c.G687A						.						72	61	64					5																	178418902		2203	4300	6503	SO:0001819	synonymous_variant	2916	exon2			CTCAACCCCACTT	U82083	CCDS4442.1	5q35	2014-01-28						"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.687G>A	chr5.hg19:g.178418902C>T		120.0	0.0		135.0	18.0	NM_000843		Silent	SNP	ENST00000517717.1	hg19	CCDS4442.1																																																																																			.	.		0.637	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2			T	178418902	C	T	178418902	2	4	190	1	0	0	0	0	0	0	0	1	6810	610	22	3		3	GRM6	5	178418902	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	2392710	178418902	2496358	64	28140										
PRPF4B	8899	hgsc.bcm.edu	37	chr6	4032939	4032939	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agaagagccaagagccgatcCttagaaagaaaacgacgaga	11	8	0	6			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:4032939C>T	ENST00000337659.6	+	2	1288	c.1188C>T	c.(1186-1188)tcC>tcT	p.S396S	PRPF4B_ENST00000538861.1_Silent_p.S382S	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	396	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				AGAGCCGATCCTTAGAAAGAA	0.443																																					p.S396S		Atlas-SNP	.											.	PRPF4B	140	.	0			c.C1188T						.						73	82	79					6																	4032939		2203	4300	6503	SO:0001819	synonymous_variant	8899	exon2			CCGATCCTTAGAA	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.1188C>T	chr6.hg19:g.4032939C>T		153.0	0.0		236.0	30.0	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Silent	SNP	ENST00000337659.6	hg19	CCDS4488.1																																																																																			.	.		0.443	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			T	4032939	C	T	4032939	2	4	190	1	0	0	0	0	0	0	0	1	12585	668	24	3		3	PRPF4B	6	4032939	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10		4032939	167082128	65	28141										
GFOD1	54438	hgsc.bcm.edu	37	chr6	13365293	13365293	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tccggaagcagggagttgctCaccggcgtggcgtcctgcac	15	13	1	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:13365293C>G	ENST00000379287.3	-	2	1519	c.855G>C	c.(853-855)gtG>gtC	p.V285V	GFOD1_ENST00000379284.1_Silent_p.V182V	NM_018988.3	NP_061861.1	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain containing 1	285						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)	18	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)			GGGAGTTGCTCACCGGCGTGG	0.701																																					p.V285V		Atlas-SNP	.											.	GFOD1	38	.	0			c.G855C						.						40	42	41					6																	13365293		2203	4300	6503	SO:0001819	synonymous_variant	54438	exon2			GTTGCTCACCGGC	AK000337	CCDS4524.1, CCDS56397.1, CCDS64351.1	6p24.1-p23	2013-09-19			ENSG00000145990	ENSG00000145990			21096	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 114"	C6orf114			Standard	NM_018988		Approved	FLJ20330, ADG-90	uc003nat.2	Q9NXC2	OTTHUMG00000014276	ENST00000379287.3:c.855G>C	chr6.hg19:g.13365293C>G		58.0	0.0		89.0	32.0	NM_018988	A8E4L6|Q5T058|Q96JD4|Q9H5K2	Silent	SNP	ENST00000379287.3	hg19	CCDS4524.1																																																																																			.	.		0.701	GFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039902.1	NM_018988		G	13365293	C	G	13365293	2	3	190	1	0	0	0	0	0	0	0	1	6351	813	29	4		4	GFOD1	6	13365293	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	9332354	13365293	157749774	66	28142										
FAM8A1	51439	hgsc.bcm.edu	37	chr6	17601130	17601130	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cagtcccccaggccgcggcgCcgccgcccccgcagctgggc	14	22	0	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:17601130C>G	ENST00000259963.3	+	1	545	c.490C>G	c.(490-492)Ccg>Gcg	p.P164A		NM_016255.2	NP_057339.1	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	164	Poly-Pro.					integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(3)	6	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			ggccgcggcgccgccgccccc	0.751																																					p.P164A		Atlas-SNP	.											.	FAM8A1	26	.	0			c.C490G						.						4	6	6					6																	17601130		1472	3232	4704	SO:0001583	missense	51439	exon1			GCGGCGCCGCCGC	AF097027	CCDS4540.1	6p23	2010-11-22			ENSG00000137414	ENSG00000137414			16372	protein-coding gene	gene with protein product						11707071	Standard	NM_016255		Approved	AHCP	uc003ncc.3	Q9UBU6	OTTHUMG00000014309	ENST00000259963.3:c.490C>G	chr6.hg19:g.17601130C>G	ENSP00000259963:p.Pro164Ala	83.0	0.0		123.0	9.0	NM_016255	B2R725	Missense_Mutation	SNP	ENST00000259963.3	hg19	CCDS4540.1	.	.	.	.	.	.	.	.	.	.	C	3.098	-0.185400	0.06340	.	.	ENSG00000137414	ENST00000259963	.	.	.	3.8	1.95	0.26073	.	0.921406	0.09105	N	0.847962	T	0.08758	0.0217	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.39313	-0.9620	9	0.15952	T	0.53	-0.1795	6.4769	0.22041	0.0:0.7112:0.1834:0.1054	.	164	Q9UBU6	FA8A1_HUMAN	A	164	.	ENSP00000259963:P164A	P	+	1	0	FAM8A1	17709109	0.001000	0.12720	0.173000	0.22940	0.158000	0.22134	1.059000	0.30517	0.208000	0.20626	0.484000	0.47621	CCG	.	.		0.751	FAM8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039950.1			G	17601130	C	G	17601130	3	3	190	1	0	0	0	0	1	0	0	0	5657	739	26	4	492	4	FAM8A1	6	17601130	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	4235837	17601130	153513937	67	28143										
CDC5L	988	hgsc.bcm.edu	37	chr6	44414400	44414400	+	Frame_Shift_Del	DEL	A	A	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gaaaaggaacttcaacatagAtatgctgatttgctgctgga							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:44414400delA	ENST00000371477.3	+	16	2660	c.2361delA	c.(2359-2361)agafs	p.R787fs		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	787	Interaction with PLRG1.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TTCAACATAGATATGCTGATT	0.308																																					p.R787fs		Atlas-INDEL	.											CDC5L,NS,carcinoma,0,1	CDC5L	86	.	0			c.2360delG						.						106	115	112					6																	44414400		2203	4300	6503	SO:0001589	frameshift_variant	988	exon16			.	D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"CDC5 (cell division cycle 5, S. pombe, homolog)-like", "CDC5 cell division cycle 5-like (S. pombe)"			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.2361delA	chr6.hg19:g.44414400delA	ENSP00000360532:p.Arg787fs	62.0	0.0		108.0	27.0	NM_001253	Q76N46|Q99974	Frame_Shift_Del	DEL	ENST00000371477.3	hg19	CCDS4912.1																																																																																			.	.		0.308	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			-	44414400	A	-	44414400	7	5	190	1	0	1	0	1	0	0	0	0	3084	330	12	0	2423	0	CDC5L	6	44414400	Frame_Shift_Del	DEL	A	TCGA-DD-AADG-01A-11D-A40R-10	26813270	44414400	126700667	68	28144										
GOPC	57120	hgsc.bcm.edu	37	chr6	117890868	117890868	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gccccggatggatctcagagAtgaggattggaacaccatgt	13	9	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:117890868A>C	ENST00000368498.2	-	7	1019	c.944T>G	c.(943-945)aTc>aGc	p.I315S	GOPC_ENST00000535237.1_Missense_Mutation_p.I315S|DCBLD1_ENST00000296955.8_3'UTR|GOPC_ENST00000052569.6_Missense_Mutation_p.I307S|GOPC_ENST00000467125.1_5'UTR	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	315	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)		GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		GATCTCAGAGATGAGGATTGG	0.458			O	ROS1	glioblastoma																																p.I315S		Atlas-SNP	.		Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	GOPC,NS,carcinoma,0,1	GOPC	29	.	0			c.T944G						.						153	150	151					6																	117890868		2203	4300	6503	SO:0001583	missense	57120	exon7			TCAGAGATGAGGA	AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.944T>G	chr6.hg19:g.117890868A>C	ENSP00000357484:p.Ile315Ser	141.0	0.0		154.0	12.0	NM_020399	A6NM30|Q59FS4|Q969U8	Missense_Mutation	SNP	ENST00000368498.2	hg19	CCDS5117.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.001761	0.93227	.	.	ENSG00000047932	ENST00000052569;ENST00000368498;ENST00000535237	T;T;T	0.62941	-0.01;-0.01;-0.01	5.44	5.44	0.79542	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	D	0.85080	0.5615	H	0.97874	4.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.992;0.996;0.992	D	0.90820	0.4708	10	0.87932	D	0	-20.112	15.7835	0.78281	1.0:0.0:0.0:0.0	.	307;315;315	Q9HD26-2;Q9HD26;F5H1Y4	.;GOPC_HUMAN;.	S	307;315;315	ENSP00000052569:I307S;ENSP00000357484:I315S;ENSP00000445690:I315S	ENSP00000052569:I307S	I	-	2	0	GOPC	117997561	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.257000	0.95545	2.185000	0.69588	0.455000	0.32223	ATC	.	.		0.458	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399		C	117890868	A	C	117890868	3	2	190	1	0	0	0	0	1	0	0	0	6581	333	12	5	456	5	GOPC	6	117890868	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	73476468	117890868	53224199	69	28145										
EPB41L2	2037	hgsc.bcm.edu	37	chr6	131216151	131216151	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gaagttactgcgtttataggAaatttttaagattttcggcc	9	5	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:131216151A>C	ENST00000337057.3	-	9	1526	c.1345T>G	c.(1345-1347)Tcc>Gcc	p.S449A	EPB41L2_ENST00000528282.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000445890.2_Missense_Mutation_p.S449A|EPB41L2_ENST00000527411.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000525193.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000529208.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000530481.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000392427.3_Missense_Mutation_p.S449A|EPB41L2_ENST00000525271.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000368128.2_Missense_Mutation_p.S449A|EPB41L2_ENST00000527659.1_Missense_Mutation_p.S449A	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	449	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cortical actin cytoskeleton organization (GO:0030866)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|spectrin (GO:0008091)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2)	44	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		CGTTTATAGGAAATTTTTAAG	0.418																																					p.S449A		Atlas-SNP	.											.	EPB41L2	96	.	0			c.T1345G						.						103	94	97					6																	131216151		2203	4300	6503	SO:0001583	missense	2037	exon9			TATAGGAAATTTT	AF027299	CCDS5141.1, CCDS47474.1, CCDS56450.1, CCDS59037.1	6q23	2008-08-29			ENSG00000079819	ENSG00000079819			3379	protein-coding gene	gene with protein product		603237				9598318, 9828140	Standard	NM_001431		Approved	4.1-G	uc003qch.2	O43491	OTTHUMG00000015560	ENST00000337057.3:c.1345T>G	chr6.hg19:g.131216151A>C	ENSP00000338481:p.Ser449Ala	116.0	0.0		106.0	21.0	NM_001135554	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Missense_Mutation	SNP	ENST00000337057.3	hg19	CCDS5141.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.894923	0.91962	.	.	ENSG00000079819	ENST00000528282;ENST00000530481;ENST00000445890;ENST00000337057;ENST00000392427;ENST00000425439;ENST00000368128;ENST00000527411;ENST00000525271;ENST00000525193;ENST00000527659;ENST00000529208	D;D;D;D;D;D;D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52	5.68	5.68	0.88126	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.95085	0.8408	M	0.91663	3.23	0.80722	D	1	D;D;D;D;D	0.57571	0.98;0.98;0.98;0.977;0.98	D;D;D;D;D	0.85130	0.995;0.993;0.995;0.997;0.993	D	0.95799	0.8831	10	0.62326	D	0.03	.	15.9369	0.79717	1.0:0.0:0.0:0.0	.	449;449;449;449;449	E9PHY5;B4DHI8;E9PPD9;O43491;Q68DV2	.;.;.;E41L2_HUMAN;.	A	449	ENSP00000434308:S449A;ENSP00000434576:S449A;ENSP00000402041:S449A;ENSP00000338481:S449A;ENSP00000376222:S449A;ENSP00000357110:S449A;ENSP00000436348:S449A;ENSP00000432803:S449A;ENSP00000431988:S449A;ENSP00000431647:S449A;ENSP00000436641:S449A	ENSP00000338481:S449A	S	-	1	0	EPB41L2	131257844	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.303000	0.96183	2.172000	0.68678	0.533000	0.62120	TCC	.	.		0.418	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3			C	131216151	A	C	131216151	3	2	190	1	0	0	0	0	1	0	0	0	5155	246	9	5	1716	5	EPB41L2	6	131216151	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	13325283	131216151	39898916	70	28146										
KDELR2	11014	hgsc.bcm.edu	37	chr7	6505873	6505873	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gtagtgggtggtgatggtctCggcctccccagtcttgctga	15	10	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:6505873C>A	ENST00000258739.4	-	4	617	c.433G>T	c.(433-435)Gag>Tag	p.E145*	DAGLB_ENST00000436575.1_Intron|KDELR2_ENST00000490996.1_Intron|KDELR2_ENST00000463747.1_Intron	NM_006854.3	NP_006845.1	P33947	ERD22_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	145					intracellular protein transport (GO:0006886)|protein retention in ER lumen (GO:0006621)|vesicle-mediated transport (GO:0016192)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	KDEL sequence binding (GO:0005046)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		GTGATGGTCTCGGCCTCCCCA	0.517																																					p.E145X		Atlas-SNP	.											.	KDELR2	31	.	0			c.G433T						.						123	107	113					7																	6505873		2203	4300	6503	SO:0001587	stop_gained	11014	exon4			TGGTCTCGGCCTC	X63745	CCDS5351.1, CCDS43550.1	7p	2008-05-02			ENSG00000136240	ENSG00000136240			6305	protein-coding gene	gene with protein product		609024				1316805, 1325562	Standard	NM_006854		Approved	ELP-1, ERD2.2	uc003sqe.4	P33947	OTTHUMG00000023103	ENST00000258739.4:c.433G>T	chr7.hg19:g.6505873C>A	ENSP00000258739:p.Glu145*	88.0	0.0		76.0	22.0	NM_006854	A4D2P4|Q6IPC5|Q96E30	Nonsense_Mutation	SNP	ENST00000258739.4	hg19	CCDS5351.1	.	.	.	.	.	.	.	.	.	.	C	38	6.918416	0.97936	.	.	ENSG00000136240	ENST00000258739	.	.	.	5.18	4.29	0.51040	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-13.6006	13.9242	0.63952	0.0:0.9261:0.0:0.0739	.	.	.	.	X	145	.	ENSP00000258739:E145X	E	-	1	0	KDELR2	6472398	1.000000	0.71417	0.981000	0.43875	0.986000	0.74619	7.692000	0.84203	1.311000	0.45024	0.460000	0.39030	GAG	.	.		0.517	KDELR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059424.2			A	6505873	C	A	6505873	4	1	190	1	0	0	0	0	0	1	0	0	8129	893	31	1	388	1	KDELR2	7	6505873	Nonsense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10		6505873	152632790	71	28147										
TWIST1	7291	hgsc.bcm.edu	37	chr7	19156374	19156374	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ggaccaggccccctccatccTccagaccgagaaggcgtagc	11	17	0	2	rs200369729		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:19156374T>C	ENST00000242261.5	-	1	921	c.571A>G	c.(571-573)Agg>Ggg	p.R191G	AC003986.6_ENST00000419944.1_RNA	NM_000474.3	NP_000465.1	Q15672	TWST1_HUMAN	twist family bHLH transcription factor 1	191	Sufficient for transactivation activity. {ECO:0000250}.				aortic valve morphogenesis (GO:0003180)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in heart valve development (GO:2000793)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|cranial suture morphogenesis (GO:0060363)|embryonic camera-type eye formation (GO:0060900)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cushion morphogenesis (GO:0003203)|eyelid development in camera-type eye (GO:0061029)|in utero embryonic development (GO:0001701)|mitral valve morphogenesis (GO:0003183)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of oxidative phosphorylation uncoupler activity (GO:2000276)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|outer ear morphogenesis (GO:0042473)|palate development (GO:0060021)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell motility (GO:2000147)|positive regulation of endocardial cushion to mesenchymal transition involved in heart valve formation (GO:2000802)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of bone mineralization (GO:0030500)|rhythmic process (GO:0048511)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription factor binding (GO:0008134)			lung(2)|upper_aerodigestive_tract(1)	3						CCCTCCATCCTCCAGACCGAG	0.662																																					p.R191G		Atlas-SNP	.											.	TWIST1	18	.	0			c.A571G						.						38	34	35					7																	19156374		2203	4300	6503	SO:0001583	missense	7291	exon1			CCATCCTCCAGAC	U80998	CCDS5367.1	7p21	2014-02-07	2013-10-17	2003-03-28	ENSG00000122691	ENSG00000122691		"Basic helix-loop-helix proteins"	12428	protein-coding gene	gene with protein product	"Saethre-Chotzen syndrome"	601622	"blepharophimosis, epicanthus inversus and ptosis 3", "acrocephalosyndactyly 3", "twist homolog 1 (Drosophila)", "twist basic helix-loop-helix transcription factor 1", "craniosynostosis"	ACS3, BPES3, TWIST, CRS		8995765, 11474656, 17343269	Standard	XR_428085		Approved	SCS, H-twist, BPES2, bHLHa38, CRS1	uc003sum.3	Q15672	OTTHUMG00000090821	ENST00000242261.5:c.571A>G	chr7.hg19:g.19156374T>C	ENSP00000242261:p.Arg191Gly	204.0	0.0		200.0	79.0	NM_000474	A4D128|Q92487|Q99804	Missense_Mutation	SNP	ENST00000242261.5	hg19	CCDS5367.1	.	.	.	.	.	.	.	.	.	.	t	15.48	2.846069	0.51164	.	.	ENSG00000122691	ENST00000242261	D	0.98178	-4.77	4.29	3.11	0.35812	Helix-loop-helix DNA-binding (1);	0.000000	0.41605	D	0.000844	D	0.98748	0.9579	M	0.85945	2.785	0.58432	D	0.999992	D	0.89917	1.0	D	0.91635	0.999	D	0.98925	1.0785	10	0.87932	D	0	-19.5452	11.3659	0.49671	0.0:0.0:0.2112:0.7888	.	191	Q15672	TWST1_HUMAN	G	191	ENSP00000242261:R191G	ENSP00000242261:R191G	R	-	1	2	TWIST1	19122899	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.627000	0.46469	1.798000	0.52647	0.369000	0.22263	AGG	.	T|0.998;G|0.002		0.662	TWIST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207625.1	NM_000474		C	19156374	T	C	19156374	3	2	190	1	0	0	0	0	1	0	0	0	16798	1550	54	2	41	2	TWIST1	7	19156374	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	12650501	19156374	139982289	72	28148										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48314641	48314641	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	caccaaggaagacttcgcaaTtgtgataaaaattcttttgg	8	7	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:48314641T>C	ENST00000435803.1	+	17	5402	c.5378T>C	c.(5377-5379)aTt>aCt	p.I1793T		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1793					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GACTTCGCAATTGTGATAAAA	0.378																																					p.I1793T		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T5378C						.						43	42	42					7																	48314641		1847	4106	5953	SO:0001583	missense	154664	exon17			TCGCAATTGTGAT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.5378T>C	chr7.hg19:g.48314641T>C	ENSP00000411096:p.Ile1793Thr	121.0	0.0		121.0	45.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.254972	0.00265	.	.	ENSG00000179869	ENST00000435803	T	0.14266	2.52	5.92	-11.8	0.00035	.	2.777580	0.01395	N	0.013385	T	0.07773	0.0195	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20605	-1.0270	9	.	.	.	.	2.2718	0.04093	0.3058:0.3327:0.2423:0.1192	.	1793	Q86UQ4	ABCAD_HUMAN	T	1793	ENSP00000411096:I1793T	.	I	+	2	0	ABCA13	48285187	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.859000	0.04277	-2.135000	0.00811	-0.374000	0.07098	ATT	.	.		0.378	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48314641	T	C	48314641	3	2	190	1	0	0	0	0	1	0	0	0	31	1493	52	2	5273	2	ABCA13	7	48314641	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	29158267	48314641	110824022	73	28149										
POM121	9883	hgsc.bcm.edu	37	chr7	72413572	72413572	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ccacacctgcacctccgtccAtgatcaaggtcgtgcctgcg	9	17	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:72413572A>G	ENST00000434423.2	+	11	3040	c.3040A>G	c.(3040-3042)Atg>Gtg	p.M1014V	POM121_ENST00000358357.3_Missense_Mutation_p.M749V|POM121_ENST00000257622.4_Missense_Mutation_p.M749V|POM121_ENST00000395270.1_Missense_Mutation_p.M749V|POM121_ENST00000446813.1_Missense_Mutation_p.M749V			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	1014	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				ACCTCCGTCCATGATCAAGGT	0.632																																					p.M749V		Atlas-SNP	.											.	POM121	131	.	0			c.A2245G						.						91	88	89					7																	72413572		2203	4300	6503	SO:0001583	missense	9883	exon11			CCGTCCATGATCA	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"-"	19702	protein-coding gene	gene with protein product		615753	"POM121 membrane glycoprotein (rat)", "POM121 membrane glycoprotein"			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.3040A>G	chr7.hg19:g.72413572A>G	ENSP00000405562:p.Met1014Val	217.0	0.0		333.0	55.0	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.009	-1.805423	0.00606	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.04970	3.52;3.54;3.52;3.54;3.77	0.1	0.1	0.14510	.	.	.	.	.	T	0.02929	0.0087	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.47018	-0.9149	8	0.24483	T	0.36	.	.	.	.	.	749;1014	A8MXF9;Q96HA1	.;P121A_HUMAN	V	749;749;749;749;1014	ENSP00000393020:M749V;ENSP00000257622:M749V;ENSP00000378687:M749V;ENSP00000351124:M749V;ENSP00000405562:M1014V	ENSP00000257622:M749V	M	+	1	0	POM121	72051508	0.001000	0.12720	0.010000	0.14722	0.008000	0.06430	-0.585000	0.05794	0.147000	0.19030	0.145000	0.16022	ATG	.	.		0.632	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1			G	72413572	A	G	72413572	3	3	190	1	0	0	0	0	1	0	0	0	12248	217	8	2	2283	2	POM121	7	72413572	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	24098931	72413572	86725091	74	28150										
PCLO	27445	hgsc.bcm.edu	37	chr7	82538312	82538312	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	atcaaaccaatctgtttcctCacgacgcagatgataggctt	7	11	3	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:82538312C>A	ENST00000333891.9	-	8	13655	c.13318G>T	c.(13318-13320)Gag>Tag	p.E4440*	PCLO_ENST00000423517.2_Nonsense_Mutation_p.E4440*	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCTGTTTCCTCACGACGCAGA	0.458																																					p.E4440X		Atlas-SNP	.											.	PCLO	1506	.	0			c.G13318T						.						93	84	87					7																	82538312		1934	4148	6082	SO:0001587	stop_gained	27445	exon8			TTTCCTCACGACG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.13318G>T	chr7.hg19:g.82538312C>A	ENSP00000334319:p.Glu4440*	75.0	0.0		94.0	29.0	NM_014510		Nonsense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	56	26.217464	0.99968	.	.	ENSG00000186472	ENST00000333891;ENST00000423517	.	.	.	5.39	4.51	0.55191	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.2833	0.66228	0.0:0.9281:0.0:0.0719	.	.	.	.	X	4440	.	ENSP00000334319:E4440X	E	-	1	0	PCLO	82376248	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.647000	0.83462	1.409000	0.46915	0.591000	0.81541	GAG	.	.		0.458	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82538312	C	A	82538312	4	1	190	1	0	0	0	0	0	1	0	0	11592	835	29	3	2199	3	PCLO	7	82538312	Nonsense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	10124740	82538312	76600351	75	28151										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94057146	94057146	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ctgaaggctctagaaagaacCcagctcgcacatgccgtgac	10	13	1	4			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:94057146C>G	ENST00000297268.6	+	49	3946	c.3475C>G	c.(3475-3477)Cca>Gca	p.P1159A		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1159	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TAGAAAGAACCCAGCTCGCAC	0.502										HNSCC(75;0.22)																											p.P1159A		Atlas-SNP	.											.	COL1A2	240	.	0			c.C3475G						.						66	62	63					7																	94057146		2203	4300	6503	SO:0001583	missense	1278	exon49			AAGAACCCAGCTC	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3475C>G	chr7.hg19:g.94057146C>G	ENSP00000297268:p.Pro1159Ala	58.0	0.0		83.0	20.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159600	0.78226	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	T	0.80653	-1.4	5.65	5.65	0.86999	Fibrillar collagen, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.91855	0.7422	M	0.88512	2.96	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92493	0.6002	10	0.87932	D	0	.	20.1065	0.97896	0.0:1.0:0.0:0.0	.	1159	P08123	CO1A2_HUMAN	A	1159;1160	ENSP00000297268:P1159A	ENSP00000297268:P1159A	P	+	1	0	COL1A2	93895082	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.818000	0.86416	2.836000	0.97738	0.655000	0.94253	CCA	.	.		0.502	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		G	94057146	C	G	94057146	3	3	190	1	0	0	0	0	1	0	0	0	3680	623	22	4	3669	4	COL1A2	7	94057146	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	11518834	94057146	65081517	76	28152										
NAA38	84316	hgsc.bcm.edu	37	chr7	117832038	117832043	+	In_Frame_Del	DEL	AAATTC	AAATTC	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aatattcgagcagaacctttAaattctgtagcacactgagg							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	AAATTC	AAATTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:117832038_117832043delAAATTC	ENST00000249299.2	+	4	465_470	c.273_278delAAATTC	c.(271-279)ttaaattct>ttt	p.91_93LNS>F	NAA38_ENST00000424702.1_3'UTR|NAA38_ENST00000422760.1_In_Frame_Del_p.70_72LNS>F	NM_016200.4	NP_057284.1	Q9BRA0	LSMD1_HUMAN	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	0					negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	8						CAGAACCTTTAAATTCTGTAGCACAC	0.354																																					p.91_93del		Atlas-INDEL	.											.	NAA38	16	.	0			c.272_277del						.																																			SO:0001651	inframe_deletion	51691	exon4			.		CCDS11122.1	17p13.1	2014-01-21	2014-01-21	2014-01-21		ENSG00000183011		"N(alpha)-acetyltransferase subunits"	28212	protein-coding gene	gene with protein product			"LSM domain containing 1"	LSMD1		16484612, 19398576	Standard	NM_032356		Approved	MGC14151, PFAAP2	uc002gja.3	Q9BRA0		ENST00000249299.2:c.273_278delAAATTC	chr7.hg19:g.117832038_117832043delAAATTC	ENSP00000249299:p.Leu91_Ser93delinsPhe	132.0	0.0		149.0	34.0	NM_016200	Q8N4M0	In_Frame_Del	DEL	ENST00000249299.2	hg19	CCDS5775.1																																																																																			.	.		0.354	NAA38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346774.2	NM_032356		-	117832043	AAATTC	-	117832038	7	5	190	1	0	1	0	1	0	0	0	0	10133	359	13	0	287	0	NAA38	7	117832038	In_Frame_Del	DEL	AAATTC	TCGA-DD-AADG-01A-11D-A40R-10	23774892	117832038	41306625	77	28153										
GRM8	2918	hgsc.bcm.edu	37	chr7	126173564	126173564	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agaaaaatccccgttaggagCacgtaactaagttcgcgtcc	9	11	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:126173564C>A	ENST00000339582.2	-	9	2680	c.1872G>T	c.(1870-1872)gtG>gtT	p.V624V	GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000444921.2_Silent_p.V624V|GRM8_ENST00000358373.3_Silent_p.V624V			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	624					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				CCGTTAGGAGCACGTAACTAA	0.458										HNSCC(24;0.065)																											p.V624V		Atlas-SNP	.											.	GRM8	377	.	0			c.G1872T						.						107	106	106					7																	126173564		2203	4300	6503	SO:0001819	synonymous_variant	2918	exon8			TAGGAGCACGTAA		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1872G>T	chr7.hg19:g.126173564C>A		143.0	0.0		184.0	59.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Silent	SNP	ENST00000339582.2	hg19	CCDS5794.1																																																																																			.	.		0.458	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			A	126173564	C	A	126173564	2	1	190	1	0	0	0	0	0	0	0	1	6812	697	25	3		3	GRM8	7	126173564	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	8341526	126173564	32965099	78	28154										
MGAM	8972	hgsc.bcm.edu	37	chr7	141735987	141735988	+	Missense_Mutation	DNP	GG	GG	TT													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aggtgggtcctgacatatgtGgctttgctttggacacccct							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:141735987_141735988GG>TT	ENST00000549489.2	+	17	2073_2074	c.1978_1979GG>TT	c.(1978-1980)GGc>TTc	p.G660F	MGAM_ENST00000475668.2_Missense_Mutation_p.G660F	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	660	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGACATATGTGGCTTTGCTTTG	0.51																																					p.G660C|p.G660V		Atlas-SNP	.											.	MGAM	767	.	0			c.G1978T|c.G1979T						.																																			SO:0001583	missense	8972	exon17			ATATGTGGCTTTG|TATGTGGCTTTGC	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	Exception_encountered	chr7.hg19:g.141735987_141735988delinsTT	ENSP00000447378:p.Gly660Phe	121.0	0.0		161.0|165.0	36.0|38.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1																																																																																			.	.		0.51	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			TT	141735988	GG	TT	141735987	3	4	190	1	0	0	0	0	1	0	0	0	9550	1348	47	3	2040	3	MGAM	7	141735987	Missense_Mutation	DNP	GG	TCGA-DD-AADG-01A-11D-A40R-10	15562423	141735987	17402676	79	28155										
RP1	6101	hgsc.bcm.edu	37	chr8	55539282	55539282	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgaaacgagtgtggtaaattGtagcaataatagtttttcag	10	3	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:55539282G>T	ENST00000220676.1	+	4	2988	c.2840G>T	c.(2839-2841)tGt>tTt	p.C947F		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	947					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			GTGGTAAATTGTAGCAATAAT	0.313																																					p.C947F	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G2840T						.						41	45	43					8																	55539282		2203	4300	6503	SO:0001583	missense	6101	exon4			TAAATTGTAGCAA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2840G>T	chr8.hg19:g.55539282G>T	ENSP00000220676:p.Cys947Phe	233.0	0.0		195.0	11.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	0.812	-0.751697	0.03041	.	.	ENSG00000104237	ENST00000220676	T	0.46063	0.88	5.58	-1.12	0.09808	.	0.838095	0.10610	N	0.654635	T	0.26159	0.0638	L	0.43152	1.355	0.09310	N	1	P	0.41947	0.766	B	0.37198	0.243	T	0.13980	-1.0489	10	0.27082	T	0.32	.	2.9909	0.05982	0.2755:0.124:0.4864:0.114	.	947	P56715	RP1_HUMAN	F	947	ENSP00000220676:C947F	ENSP00000220676:C947F	C	+	2	0	RP1	55701835	0.000000	0.05858	0.011000	0.14972	0.020000	0.10135	-0.076000	0.11412	-0.100000	0.12241	-0.211000	0.12701	TGT	.	.		0.313	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55539282	G	T	55539282	3	4	190	1	0	0	0	0	1	0	0	0	13547	1377	48	3	2850	3	RP1	8	55539282	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10		55539282	90824740	80	28156										
OXR1	55074	hgsc.bcm.edu	37	chr8	107705036	107705036	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gcacgagttgtatcttcaacTtctgaggaggaggaagcatt	12	7	3	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:107705036T>G	ENST00000442977.2	+	6	708	c.609T>G	c.(607-609)acT>acG	p.T203T	OXR1_ENST00000445937.1_Silent_p.T202T|OXR1_ENST00000497705.1_Silent_p.T135T|OXR1_ENST00000452423.2_5'UTR|OXR1_ENST00000531443.1_Silent_p.T202T|OXR1_ENST00000517566.2_Silent_p.T202T|OXR1_ENST00000312046.6_Silent_p.T195T	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	203					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TATCTTCAACTTCTGAGGAGG	0.358																																					p.T203T		Atlas-SNP	.											.	OXR1	190	.	0			c.T609G						.						77	78	77					8																	107705036		2203	4300	6503	SO:0001819	synonymous_variant	55074	exon6			TTCAACTTCTGAG	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 3"	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.609T>G	chr8.hg19:g.107705036T>G		91.0	0.0		105.0	42.0	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	hg19	CCDS56548.1	.	.	.	.	.	.	.	.	.	.	T	5.147	0.212736	0.09757	.	.	ENSG00000164830	ENST00000517455	.	.	.	5.06	1.06	0.20224	.	.	.	.	.	T	0.51092	0.1654	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33904	-0.9850	4	.	.	.	-18.6337	5.0572	0.14539	0.4086:0.0762:0.0:0.5152	.	.	.	.	R	119	.	.	L	+	2	0	OXR1	107774212	0.867000	0.29959	0.998000	0.56505	0.453000	0.32348	0.087000	0.14958	-0.065000	0.13021	0.383000	0.25322	CTT	.	.		0.358	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		G	107705036	T	G	107705036	2	3	190	1	0	0	0	0	0	0	0	1	11343	1596	56	5		5	OXR1	8	107705036	Silent	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	52165754	107705036	38658986	81	28157										
EIF3E	3646	hgsc.bcm.edu	37	chr8	109226846	109226846	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gtgttcttacttaatgctgaTacactggtggatgcgacaga	11	7	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:109226846T>C	ENST00000220849.5	-	10	1113	c.1051A>G	c.(1051-1053)Atc>Gtc	p.I351V	EIF3E_ENST00000519517.1_5'UTR|EIF3E_ENST00000519030.1_Missense_Mutation_p.I258V	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E										EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			TTAATGCTGATACACTGGTGG	0.363																																					p.I351V	GBM(15;360 410 8460 34179 52246)	Atlas-SNP	.											.	EIF3E	73	.	0			c.A1051G						.						75	72	73					8																	109226846		2203	4300	6503	SO:0001583	missense	3646	exon10			TGCTGATACACTG	U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"eukaryotic translation initiation factor 3, subunit 6 48kDa"	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.1051A>G	chr8.hg19:g.109226846T>C	ENSP00000220849:p.Ile351Val	250.0	0.0		244.0	13.0	NM_001568		Missense_Mutation	SNP	ENST00000220849.5	hg19	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.417337	0.83449	.	.	ENSG00000104408	ENST00000220849;ENST00000519030;ENST00000519627	T;T;T	0.54675	1.05;1.05;0.56	5.52	5.52	0.82312	Winged helix-turn-helix transcription repressor DNA-binding (1);Proteasome component (PCI) domain (2);	0.000000	0.85682	D	0.000000	T	0.70945	0.3282	M	0.67625	2.065	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72795	-0.4185	10	0.54805	T	0.06	-16.4334	15.9416	0.79758	0.0:0.0:0.0:1.0	.	351	P60228	EIF3E_HUMAN	V	351;258;224	ENSP00000220849:I351V;ENSP00000428796:I258V;ENSP00000430839:I224V	ENSP00000220849:I351V	I	-	1	0	EIF3E	109296022	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.993000	0.88291	2.225000	0.72522	0.533000	0.62120	ATC	.	.		0.363	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		C	109226846	T	C	109226846	3	2	190	1	0	0	0	0	1	0	0	0	5017	1406	49	2	302	2	EIF3E	8	109226846	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	1521810	109226846	37137176	82	28158										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121296007	121296007	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tctgacccattggttggggtTattttagacagtaagtatat	10	5	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:121296007T>A	ENST00000297848.3	+	32	4227	c.3957T>A	c.(3955-3957)gtT>gtA	p.V1319V	COL14A1_ENST00000247781.3_Silent_p.V1224V|COL14A1_ENST00000309791.4_Silent_p.V1319V	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			TGGTTGGGGTTATTTTAGACA	0.358																																					p.V1319V		Atlas-SNP	.											.	COL14A1	292	.	0			c.T3957A						.						65	64	64					8																	121296007		2203	4300	6503	SO:0001819	synonymous_variant	7373	exon32			TGGGGTTATTTTA		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.3957T>A	chr8.hg19:g.121296007T>A		91.0	0.0		101.0	45.0	NM_021110		Silent	SNP	ENST00000297848.3	hg19	CCDS34938.1																																																																																			.	.		0.358	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121296007	T	A	121296007	2	1	190	1	0	0	0	0	0	0	0	1	3673	1741	61	4		4	COL14A1	8	121296007	Silent	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	12069161	121296007	25068015	83	28159										
MTBP	27085	hgsc.bcm.edu	37	chr8	121468896	121468896	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tatggagggggaaaatacagAtatgggaaagaaaggtaaat	14	1	0	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:121468896A>T	ENST00000305949.1	+	7	778	c.733A>T	c.(733-735)Ata>Tta	p.I245L		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	245					cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			GAAAATACAGATATGGGAAAG	0.308																																					p.I245L		Atlas-SNP	.											.	MTBP	77	.	0			c.A733T						.						99	114	109					8																	121468896		2203	4291	6494	SO:0001583	missense	27085	exon7			ATACAGATATGGG		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"MDM2 (mouse double minute 2)-binding protein, 104kD", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.733A>T	chr8.hg19:g.121468896A>T	ENSP00000303398:p.Ile245Leu	54.0	0.0		56.0	17.0	NM_022045	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	hg19	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	A	17.28	3.349396	0.61183	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.56	5.56	0.83823	.	0.118223	0.53938	D	0.000049	T	0.52629	0.1746	M	0.68952	2.095	0.50467	D	0.999872	P	0.40211	0.707	B	0.28916	0.096	T	0.59166	-0.7505	9	0.46703	T	0.11	-13.7942	15.7142	0.77655	1.0:0.0:0.0:0.0	.	245	Q96DY7	MTBP_HUMAN	L	245	.	ENSP00000303398:I245L	I	+	1	0	MTBP	121538077	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.143000	0.77348	2.120000	0.65058	0.372000	0.22366	ATA	.	.		0.308	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		T	121468896	A	T	121468896	3	4	190	1	0	0	0	0	1	0	0	0	9921	333	12	4	759	4	MTBP	8	121468896	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	172889	121468896	24895126	84	28160										
ANXA13	312	hgsc.bcm.edu	37	chr8	124696885	124696886	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gactatgcgaatcaacgtctCctcatcggtccccgcaccct							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:124696885_124696886CC>AA	ENST00000419625.1	-	10	867_868	c.795_796GG>TT	c.(793-798)gaGGag>gaTTag	p.265_266EE>D*	ANXA13_ENST00000262219.6_Nonsense_Mutation_p.306_307EE>D*	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	265					cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			ATCAACGTCTCCTCATCGGTCC	0.52																																					p.E307X|p.E306D		Atlas-SNP	.											.	ANXA13	38	.	0			c.G919T|c.G918T						.																																			SO:0001587	stop_gained	312	exon11			ACGTCTCCTCATC|CGTCTCCTCATCG	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"Annexins"	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.795_796delinsAA	chr8.hg19:g.124696885_124696886delinsAA	ENSP00000390809:p.E265_E266delinsD*	116.0	0.0		124.0|126.0	41.0	NM_001003954	Q9BQR5	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000419625.1	hg19	CCDS47917.1																																																																																			.	.		0.52	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306		AA	124696886	CC	AA	124696885	4	1	190	1	0	0	0	0	0	1	0	0	717	864	30	3	162	3	ANXA13	8	124696885	Nonsense_Mutation	DNP	CC	TCGA-DD-AADG-01A-11D-A40R-10	3227989	124696885	21667137	85	28161										
LYNX1	66004	hgsc.bcm.edu	37	chr8	143857324	143857324	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ctgtcctttgtccatcttacCcagaggtaagcccatgagga	9	12	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:143857324C>T	ENST00000335822.5	-	2	679	c.52G>A	c.(52-54)Gcc>Acc	p.A18T	LYNX1_ENST00000345173.6_Splice_Site_p.A18T|LYNX1_ENST00000523332.1_Splice_Site_p.A18T|LYNX1_ENST00000522906.1_Intron|LYNX1_ENST00000398906.1_Splice_Site_p.A18T|LYNX1_ENST00000395192.2_Splice_Site_p.A18T	NM_023946.2	NP_076435.1	Q9BZG9	LYNX1_HUMAN	Ly6/neurotoxin 1	18						anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|lung(2)|skin(1)	4	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TCCATCTTACCCAGAGGTAAG	0.602																																					p.A18T		Atlas-SNP	.											.	LYNX1	40	.	0			c.G52A						.						93	72	80					8																	143857324		2203	4300	6503	SO:0001630	splice_region_variant	66004	exon2			TCTTACCCAGAGG	AF321824	CCDS6389.1, CCDS34951.1, CCDS34952.1	8q24.3	2008-03-12			ENSG00000180155	ENSG00000180155			29604	protein-coding gene	gene with protein product		606110				12573258, 10402197	Standard	NM_023946		Approved	SLURP2	uc003yxd.1	Q9BZG9	OTTHUMG00000164694	ENST00000335822.5:c.52+1G>A	chr8.hg19:g.143857324C>T		45.0	0.0		67.0	22.0	NM_177477	D3DWI7|G3XAC2|Q86SR0	Missense_Mutation	SNP	ENST00000335822.5	hg19	CCDS34951.1	.	.	.	.	.	.	.	.	.	.	c	16.93	3.258937	0.59321	.	.	ENSG00000180155	ENST00000523332;ENST00000335822;ENST00000395192;ENST00000398906;ENST00000345173;ENST00000522929;ENST00000520131	T;T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63;1.63	3.34	3.34	0.38264	.	0.211384	0.26387	N	0.024675	T	0.32194	0.0821	M	0.70595	2.14	0.24881	N	0.992224	B;B	0.22683	0.043;0.073	B;B	0.27887	0.02;0.084	T	0.16837	-1.0389	9	.	.	.	-18.4559	10.3623	0.44001	0.0:1.0:0.0:0.0	.	18;18	Q9BZG9;G3XAC2	LYNX1_HUMAN;.	T	18	ENSP00000428713:A18T;ENSP00000337950:A18T;ENSP00000378618:A18T;ENSP00000381878:A18T;ENSP00000332495:A18T;ENSP00000429261:A18T;ENSP00000428157:A18T	.	A	-	1	0	LYNX1	143854326	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	3.350000	0.52224	1.865000	0.54081	0.650000	0.86243	GCC	.	.		0.602	LYNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379786.3	NM_177476	Missense_Mutation	T	143857324	C	T	143857324	5	4	190	1	0	0	0	0	0	0	1	0	9117	637	22	3	616	3	LYNX1	8	143857324	Splice_Site	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	19160439	143857324	2506698	86	28162										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21974751	21974760	+	Frame_Shift_Del	DEL	CTACCCGACC	CTACCCGACC	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cagcagcgcccgcacctcctCtacccgaccccgggccgcgg					rs104894097		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	CTACCCGACC	CTACCCGACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:21974751_21974760delCTACCCGACC	ENST00000304494.5	-	1	337_346	c.67_76delGGTCGGGTAG	c.(67-78)ggtcgggtagagfs	p.GRVE23fs	RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000498124.1_Frame_Shift_Del_p.GRVE23fs|CDKN2A_ENST00000579122.1_Frame_Shift_Del_p.GRVE23fs|CDKN2A_ENST00000494262.1_Intron|CDKN2A_ENST00000361570.3_Intron|CDKN2A_ENST00000579755.1_Intron|CDKN2A_ENST00000498628.2_Intron|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000446177.1_Frame_Shift_Del_p.GRVE23fs	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	23			G -> D (in a pancreas tumor and a melanoma; loss of CDK4 binding).		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(23)|p.E26*(3)|p.R24P(2)|p.V25fs*1(2)|p.G23S(1)|p.0(1)|p.S12fs*20(1)|p.R24fs*20(1)|p.R22fs*14(1)|p.G23G(1)|p.G23D(1)|p.R24Q(1)|p.E26K(1)|p.G23fs*3(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CGCACCTCCTCTACCCGACCCCGGGCCGCG	0.743		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.23_26del		Atlas-INDEL	.											.	CDKN2A	4810	.	1355	Whole gene deletion(1316)|Unknown(23)|Substitution - Missense(6)|Deletion - Frameshift(5)|Substitution - Nonsense(3)|Insertion - Frameshift(1)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(281)|skin(169)|central_nervous_system(164)|lung(148)|urinary_tract(90)|bone(73)|soft_tissue(58)|pleura(52)|oesophagus(50)|upper_aerodigestive_tract(49)|ovary(36)|kidney(31)|pancreas(30)|breast(30)|thyroid(14)|biliary_tract(14)|NS(12)|stomach(12)|large_intestine(7)|autonomic_ganglia(7)|liver(7)|meninges(7)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.68_77del	GRCh37	CM024657|CM056560|CM056561|CM072932|CM950224|CM980322	CDKN2A	M	rs104894097	.																																			SO:0001589	frameshift_variant	1029	exon1			.	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.67_76delGGTCGGGTAG	chr9.hg19:g.21974751_21974760delCTACCCGACC	ENSP00000307101:p.Gly23fs	79.0	0.0		83.0	26.0	NM_058197	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Frame_Shift_Del	DEL	ENST00000304494.5	hg19	CCDS6510.1																																																																																			.	.		0.743	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		-	21974760	CTACCCGACC	-	21974751	7	5	190	1	0	1	0	1	0	0	0	0	3163	922	32	0	607	0	CDKN2A	9	21974751	Frame_Shift_Del	DEL	CTACCCGACC	TCGA-DD-AADG-01A-11D-A40R-10		21974751	119238680	87	28163										
ACO1	48	hgsc.bcm.edu	37	chr9	32424547	32424547	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cttttctttggggtcaacagGttgtggaattagatttgaaa	11	4	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:32424547G>A	ENST00000309951.6	+	10	1210	c.1072G>A	c.(1072-1074)Gtt>Att	p.V358I	ACO1_ENST00000379923.1_Splice_Site_p.V358I|ACO1_ENST00000541043.1_Splice_Site_p.V259I	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	358					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		GGGTCAACAGGTTGTGGAATT	0.383																																					p.V358I		Atlas-SNP	.											.	ACO1	149	.	0			c.G1072A						.						107	116	113					9																	32424547		2203	4300	6503	SO:0001630	splice_region_variant	48	exon10			CAACAGGTTGTGG	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1072-1G>A	chr9.hg19:g.32424547G>A		115.0	0.0		95.0	6.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	hg19	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.917520	0.33815	.	.	ENSG00000122729	ENST00000432017;ENST00000309951;ENST00000379923;ENST00000379921;ENST00000541043	T;T;T	0.19250	2.16;2.16;2.16	5.86	2.0	0.26442	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 2 (1);	0.270323	0.41500	N	0.000863	T	0.18509	0.0444	L	0.55103	1.725	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.12837	0.008;0.002	T	0.06023	-1.0850	9	.	.	.	-9.0754	9.9743	0.41774	0.3496:0.0:0.6504:0.0	.	394;358	Q59FI0;P21399	.;ACOC_HUMAN	I	394;358;358;358;259	ENSP00000309477:V358I;ENSP00000369255:V358I;ENSP00000438733:V259I	.	V	+	1	0	ACO1	32414547	1.000000	0.71417	0.998000	0.56505	0.682000	0.39822	3.758000	0.55220	0.501000	0.28013	-0.157000	0.13467	GTT	.	.		0.383	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	Missense_Mutation	A	32424547	G	A	32424547	5	1	190	1	0	0	0	0	0	0	1	0	146	1275	44	3	1106	3	ACO1	9	32424547	Splice_Site	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	10449796	32424547	108788884	88	28164										
DAPK1	1612	hgsc.bcm.edu	37	chr9	90219888	90219888	+	Frame_Shift_Del	DEL	A	A	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gtggacagtttgcggttgtgAagaaatgccgtgagaaaagc							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:90219888delA	ENST00000408954.3	+	3	417	c.82delA	c.(82-84)aagfs	p.K29fs	DAPK1_ENST00000469640.2_Frame_Shift_Del_p.K29fs|DAPK1_ENST00000358077.5_Frame_Shift_Del_p.K29fs|DAPK1_ENST00000472284.1_Frame_Shift_Del_p.K29fs|DAPK1_ENST00000491893.1_Frame_Shift_Del_p.K29fs	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	29	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						TGCGGTTGTGAAGAAATGCCG	0.498									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.V27fs		Atlas-INDEL	.											.	DAPK1	329	.	0			c.81delG						.						33	34	33					9																	90219888		1997	4184	6181	SO:0001589	frameshift_variant	1612	exon3	Familial Cancer Database	Familial CLL	.	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.82delA	chr9.hg19:g.90219888delA	ENSP00000386135:p.Lys29fs	120.0	0.0		89.0	36.0	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Frame_Shift_Del	DEL	ENST00000408954.3	hg19	CCDS43842.1																																																																																			.	.		0.498	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		-	90219888	A	-	90219888	7	5	190	1	0	1	0	1	0	0	0	0	4237	247	9	0	88	0	DAPK1	9	90219888	Frame_Shift_Del	DEL	A	TCGA-DD-AADG-01A-11D-A40R-10	57795341	90219888	50993543	89	28165										
MUSK	4593	hgsc.bcm.edu	37	chr9	113550073	113550073	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cggactttcagagggaggcaGccctcatggcagaatttgac	13	10	2	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:113550073G>A	ENST00000374448.4	+	14	2016	c.1882G>A	c.(1882-1884)Gcc>Acc	p.A628T	MUSK_ENST00000374438.1_Missense_Mutation_p.A144T|MUSK_ENST00000416899.2_Missense_Mutation_p.A620T|MUSK_ENST00000189978.5_Missense_Mutation_p.A628T	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	628	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						GAGGGAGGCAGCCCTCATGGC	0.438																																					p.A628T		Atlas-SNP	.											.	MUSK	112	.	0			c.G1882A						.						56	53	54					9																	113550073		1882	4115	5997	SO:0001583	missense	4593	exon13			GAGGCAGCCCTCA	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.1882G>A	chr9.hg19:g.113550073G>A	ENSP00000363571:p.Ala628Thr	90.0	0.0		80.0	26.0	NM_005592	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	hg19	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	G	32	5.140558	0.94560	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000374441;ENST00000416899;ENST00000374438	D;D	0.82893	-1.66;-1.66	5.93	5.93	0.95920	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.83797	0.5332	N	0.16037	0.36	0.80722	D	1	D	0.63046	0.992	D	0.70016	0.967	D	0.83678	0.0170	10	0.36615	T	0.2	.	17.4968	0.87719	0.0:0.0:1.0:0.0	.	628	O15146	MUSK_HUMAN	T	634;628;628;542;542;144;626;144	ENSP00000363571:A628T;ENSP00000363561:A144T	ENSP00000189978:A634T	A	+	1	0	MUSK	112589894	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.476000	0.97823	2.814000	0.96858	0.655000	0.94253	GCC	.	.		0.438	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	113550073	G	A	113550073	3	1	190	1	0	0	0	0	1	0	0	0	9998	971	34	3	1968	3	MUSK	9	113550073	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	23330185	113550073	27663358	90	28166										
RGS3	5998	hgsc.bcm.edu	37	chr9	116247941	116247941	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gatgatcagaagcgtctcttGgttactgtgtggaacagggc	14	7	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:116247941G>T	ENST00000374140.2	+	8	866	c.657G>T	c.(655-657)ttG>ttT	p.L219F	RGS3_ENST00000350696.5_Missense_Mutation_p.L219F|RGS3_ENST00000317613.6_Missense_Mutation_p.L107F	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	219	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						AGCGTCTCTTGGTTACTGTGT	0.577																																					p.L219F		Atlas-SNP	.											.	RGS3	251	.	0			c.G657T						.						92	78	82					9																	116247941		2201	4299	6500	SO:0001583	missense	5998	exon8			TCTCTTGGTTACT	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"Regulators of G-protein signaling"	9999	protein-coding gene	gene with protein product		602189	"regulator of G-protein signalling 3"			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.657G>T	chr9.hg19:g.116247941G>T	ENSP00000363255:p.Leu219Phe	89.0	0.0		81.0	30.0	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	hg19	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.451695	0.63290	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613	T;T;T	0.69175	-0.38;-0.38;-0.38	4.66	2.75	0.32379	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.282287	0.24067	N	0.041852	T	0.78534	0.4298	M	0.83384	2.64	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.77004	0.989;0.981;0.984	T	0.74777	-0.3550	10	0.28530	T	0.3	.	7.9414	0.29961	0.1948:0.0:0.8052:0.0	.	109;107;219	B3KWG8;P49796-5;P49796	.;.;RGS3_HUMAN	F	219;219;107	ENSP00000363255:L219F;ENSP00000259406:L219F;ENSP00000312844:L107F	ENSP00000312844:L107F	L	+	3	2	RGS3	115287762	1.000000	0.71417	0.555000	0.28281	0.989000	0.77384	1.926000	0.40084	0.642000	0.30620	0.561000	0.74099	TTG	.	.		0.577	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		T	116247941	G	T	116247941	3	4	190	1	0	0	0	0	1	0	0	0	13321	1339	47	3	766	3	RGS3	9	116247941	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	2697868	116247941	24965490	91	28167										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123298694	123298694	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gccatcgccaagtccccctcGtgcatcttcttcatctctga	6	17	4	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:123298694G>A	ENST00000349780.4	-	7	797	c.618C>T	c.(616-618)caC>caT	p.H206H	CDK5RAP2_ENST00000360822.3_Silent_p.H206H|CDK5RAP2_ENST00000359309.3_Silent_p.H206H|CDK5RAP2_ENST00000360190.4_Silent_p.H206H	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	206					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						AGTCCCCCTCGTGCATCTTCT	0.547																																					p.H206H		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.C618T						.						144	124	131					9																	123298694		2203	4300	6503	SO:0001819	synonymous_variant	55755	exon7			CCCCTCGTGCATC	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.618C>T	chr9.hg19:g.123298694G>A		58.0	0.0		60.0	24.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	hg19	CCDS6823.1																																																																																			.	.		0.547	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		A	123298694	G	A	123298694	2	1	190	1	0	0	0	0	0	0	0	1	3148	1136	40	1		1	CDK5RAP2	9	123298694	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	7050753	123298694	17914737	92	28168										
SLC29A3	55315	hgsc.bcm.edu	37	chr10	73111483	73111483	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cggtgcctccactgtcttcaGcagcagcatctacggcatga	10	14	3	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:73111483G>C	ENST00000373189.5	+	4	600	c.548G>C	c.(547-549)aGc>aCc	p.S183T	SLC29A3_ENST00000469204.1_3'UTR	NM_001174098.1|NM_018344.5	NP_001167569.1|NP_060814.4	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 3	183					transmembrane transport (GO:0055085)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	15						ACTGTCTTCAGCAGCAGCATC	0.577																																					p.S183T	Esophageal Squamous(200;1319 2142 18949 31248 39672)	Atlas-SNP	.											.	SLC29A3	51	.	0			c.G548C						.						115	89	97					10																	73111483		2203	4300	6503	SO:0001583	missense	55315	exon4			TCTTCAGCAGCAG	AF326987	CCDS7310.1	10q22.2	2013-07-17	2013-07-17		ENSG00000198246	ENSG00000198246		"Solute carriers"	23096	protein-coding gene	gene with protein product		612373	"solute carrier family 29 (nucleoside transporters), member 3"			11396612	Standard	NM_018344		Approved	ENT3, FLJ11160	uc001jrr.4	Q9BZD2	OTTHUMG00000018424	ENST00000373189.5:c.548G>C	chr10.hg19:g.73111483G>C	ENSP00000362285:p.Ser183Thr	67.0	0.0		59.0	18.0	NM_018344	B2RB50|B4E2Z9|B7ZA37|Q0VAM9|Q5T465|Q7RTT8|Q8IVZ0|Q9BWI2|Q9NUS9	Missense_Mutation	SNP	ENST00000373189.5	hg19	CCDS7310.1	.	.	.	.	.	.	.	.	.	.	G	11.70	1.717128	0.30413	.	.	ENSG00000198246	ENST00000373189	T	0.63096	-0.02	5.83	-8.01	0.01122	.	0.608811	0.19482	N	0.113198	T	0.41419	0.1158	N	0.25890	0.77	0.32100	N	0.590761	B	0.14805	0.011	B	0.19666	0.026	T	0.04029	-1.0983	9	0.41790	T	0.15	-7.3834	12.8029	0.57596	0.6701:0.0835:0.2464:0.0	.	183	Q9BZD2	S29A3_HUMAN	T	183	ENSP00000362285:S183T	ENSP00000362285:S183T	S	+	2	0	SLC29A3	72781489	0.000000	0.05858	0.274000	0.24659	0.728000	0.41692	-0.879000	0.04188	-1.468000	0.01892	-0.266000	0.10368	AGC	.	.		0.577	SLC29A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048544.1	NM_018344		C	73111483	G	C	73111483	3	2	190	1	0	0	0	0	1	0	0	0	14551	971	34	4	562	4	SLC29A3	10	73111483	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10		73111483	62423264	93	28169										
DNAJB12	54788	hgsc.bcm.edu	37	chr10	74114738	74114738	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gccggcgcgtcgcgggcagcCgggcgcggagtgatgacatc	19	13	0	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:74114738C>T	ENST00000338820.3	-	1	169	c.20G>A	c.(19-21)cGg>cAg	p.R7Q	DNAJB12_ENST00000461919.1_5'Flank|DNAJB12_ENST00000444643.2_5'UTR|DNAJB12_ENST00000394903.2_Missense_Mutation_p.R7Q	NM_001002762.2	NP_001002762.2	Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	0						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						CGCGGGCAGCCGGGCGCGGAG	0.657																																					p.R7Q		Atlas-SNP	.											.	DNAJB12	22	.	0			c.G20A						.						12	17	15					10																	74114738		687	1576	2263	SO:0001583	missense	54788	exon1			GGCAGCCGGGCGC	AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"Heat shock proteins / DNAJ (HSP40)"	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000338820.3:c.20G>A	chr10.hg19:g.74114738C>T	ENSP00000345575:p.Arg7Gln	44.0	0.0		55.0	33.0	NM_017626	B7Z7I3|Q9H6H0	Missense_Mutation	SNP	ENST00000338820.3	hg19	CCDS7316.2	.	.	.	.	.	.	.	.	.	.	C	20.8	4.045610	0.75846	.	.	ENSG00000148719	ENST00000338820;ENST00000394903	T;T	0.63580	-0.05;-0.05	5.68	5.68	0.88126	.	.	.	.	.	T	0.73651	0.3614	.	.	.	0.26250	N	0.978734	.	.	.	.	.	.	T	0.68603	-0.5365	6	0.87932	D	0	.	18.5439	0.91039	0.0:1.0:0.0:0.0	.	.	.	.	Q	7	ENSP00000345575:R7Q;ENSP00000378363:R7Q	ENSP00000345575:R7Q	R	-	2	0	DNAJB12	73784744	0.792000	0.28813	0.946000	0.38457	0.097000	0.18754	1.525000	0.35953	2.669000	0.90835	0.561000	0.74099	CGG	.	.		0.657	DNAJB12-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	74114738	C	T	74114738	3	4	190	1	0	0	0	0	1	0	0	0	4619	652	23	1	1241	1	DNAJB12	10	74114738	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	1003255	74114738	61420009	94	28170										
PPP3CB	5532	hgsc.bcm.edu	37	chr10	75238300	75238300	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ccacataatcgccaagaaaaAggtatcgtgtattagcaggt	9	8	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:75238300A>G	ENST00000360663.5	-	3	479	c.368T>C	c.(367-369)cTt>cCt	p.L123P	PPP3CB_ENST00000342558.3_Missense_Mutation_p.L123P|PPP3CB_ENST00000394822.2_Missense_Mutation_p.L123P|PPP3CB_ENST00000394829.2_Missense_Mutation_p.L123P|PPP3CB_ENST00000545874.1_Missense_Mutation_p.L37P|PPP3CB_ENST00000394828.2_Missense_Mutation_p.L123P			P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta isozyme	123	Catalytic.				axon extension (GO:0048675)|calcium ion-dependent exocytosis (GO:0017156)|cellular response to drug (GO:0035690)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|learning (GO:0007612)|locomotion involved in locomotory behavior (GO:0031987)|memory (GO:0007613)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of transcription, DNA-templated (GO:0045893)|protein dephosphorylation (GO:0006470)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)|social behavior (GO:0035176)|T cell activation (GO:0042110)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein phosphatase 2B binding (GO:0030346)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(7)|skin(1)|urinary_tract(1)	22	Prostate(51;0.0119)					GCCAAGAAAAAGGTATCGTGT	0.348																																					p.L123P		Atlas-SNP	.											.	PPP3CB	68	.	0			c.T368C						.						112	108	109					10																	75238300		2203	4300	6503	SO:0001583	missense	5532	exon3			AGAAAAAGGTATC	M29551	CCDS7328.1, CCDS44436.1, CCDS44437.1	10q22.2	2010-03-17	2010-03-05		ENSG00000107758	ENSG00000107758	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9315	protein-coding gene	gene with protein product	"calcineurin A beta", "protein phosphatase 2B, catalytic subunit, beta isoform"	114106	"protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform (calcineurin A beta)", "protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform"	CALNB		1659808, 2558868	Standard	XM_005269944		Approved	CALNA2, CNA2, PP2Bbeta	uc001juf.3	P16298	OTTHUMG00000018472	ENST00000360663.5:c.368T>C	chr10.hg19:g.75238300A>G	ENSP00000353881:p.Leu123Pro	60.0	0.0		82.0	4.0	NM_001142354	P16299|Q5F2F9|Q8N1F0|Q8N3W4	Missense_Mutation	SNP	ENST00000360663.5	hg19	CCDS7328.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.754681	0.89843	.	.	ENSG00000107758	ENST00000360663;ENST00000394829;ENST00000394828;ENST00000342558;ENST00000545874;ENST00000394822	D;D;D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35;-2.35;-2.35	5.83	5.83	0.93111	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.092215	0.47093	D	0.000260	D	0.97648	0.9229	H	0.99967	5.1	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.999;1.0;1.0	D	0.99640	1.0988	10	0.87932	D	0	.	16.1946	0.82018	1.0:0.0:0.0:0.0	.	123;37;123;123;123	P16298-2;F5H0F8;P16298-3;Q8N1F0;P16298	.;.;.;.;PP2BB_HUMAN	P	123;123;123;123;37;123	ENSP00000353881:L123P;ENSP00000378306:L123P;ENSP00000378305:L123P;ENSP00000343147:L123P;ENSP00000439876:L37P;ENSP00000378299:L123P	ENSP00000343147:L123P	L	-	2	0	PPP3CB	74908306	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.329000	0.96413	2.228000	0.72767	0.528000	0.53228	CTT	.	.		0.348	PPP3CB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048669.1	NM_021132		G	75238300	A	G	75238300	3	3	190	1	0	0	0	0	1	0	0	0	12410	72	3	2	1257	2	PPP3CB	10	75238300	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	1123562	75238300	60296447	95	28171										
CH25H	9023	hgsc.bcm.edu	37	chr10	90966684	90966684	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aggatgtggtgcagcagcagGagcagctcgggagcttcgtg	18	8	0	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:90966684G>T	ENST00000371852.2	-	1	387	c.366C>A	c.(364-366)ctC>ctA	p.L122L		NM_003956.3	NP_003947.1	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	122					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol 25-hydroxylase activity (GO:0001567)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			kidney(1)|large_intestine(2)|lung(3)|stomach(1)	7		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		GCAGCAGCAGGAGCAGCTCGG	0.627																																					p.L122L		Atlas-SNP	.											.	CH25H	19	.	0			c.C366A						.						45	48	47					10																	90966684		2203	4300	6503	SO:0001819	synonymous_variant	9023	exon1			CAGCAGGAGCAGC	AF059212	CCDS7400.1	10q23	2013-03-04			ENSG00000138135	ENSG00000138135	1.14.99.38	"Fatty acid hydroxylase domain containing"	1907	protein-coding gene	gene with protein product		604551				9852097	Standard	NM_003956		Approved		uc001kfz.3	O95992	OTTHUMG00000018705	ENST00000371852.2:c.366C>A	chr10.hg19:g.90966684G>T		109.0	0.0		123.0	36.0	NM_003956	B2RBY3	Silent	SNP	ENST00000371852.2	hg19	CCDS7400.1																																																																																			.	.		0.627	CH25H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049291.1	NM_003956		T	90966684	G	T	90966684	2	4	190	1	0	0	0	0	0	0	0	1	3309	1161	41	3		3	CH25H	10	90966684	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	15728384	90966684	44568063	96	28172										
IFIT5	24138	hgsc.bcm.edu	37	chr10	91177145	91177145	+	Frame_Shift_Del	DEL	A	A	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttggcctatgtgaaacacctAaaaggccaaaataaagacgc							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:91177145delA	ENST00000371795.4	+	2	402	c.189delA	c.(187-189)ctafs	p.L63fs	IFIT5_ENST00000416601.1_Frame_Shift_Del_p.L63fs|LIPA_ENST00000371837.1_5'Flank	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	63					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						TGAAACACCTAAAAGGCCAAA	0.398																																					p.L63fs		Atlas-INDEL	.											.	IFIT5	32	.	0			c.188delT						.						69	71	71					10																	91177145		2203	4300	6503	SO:0001589	frameshift_variant	24138	exon2			.	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.189delA	chr10.hg19:g.91177145delA	ENSP00000360860:p.Leu63fs	167.0	0.0		160.0	51.0	NM_012420	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Frame_Shift_Del	DEL	ENST00000371795.4	hg19	CCDS7403.1																																																																																			.	.		0.398	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		-	91177145	A	-	91177145	7	5	190	1	0	1	0	1	0	0	0	0	7534	349	13	0	195	0	IFIT5	10	91177145	Frame_Shift_Del	DEL	A	TCGA-DD-AADG-01A-11D-A40R-10	210461	91177145	44357602	97	28173										
DNMBP	23268	hgsc.bcm.edu	37	chr10	101715378	101715378	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aatggggagaagtggataccGgagtacagggacgaggtggc	19	5	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:101715378G>A	ENST00000324109.4	-	4	1944	c.1853C>T	c.(1852-1854)cCg>cTg	p.P618L	DNMBP-AS1_ENST00000434409.1_RNA|DNMBP_ENST00000342239.3_Missense_Mutation_p.P618L	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	618	Pro-rich.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		AGTGGATACCGGAGTACAGGG	0.582																																					p.P618L		Atlas-SNP	.											.	DNMBP	173	.	0			c.C1853T						.						56	52	53					10																	101715378		2203	4300	6503	SO:0001583	missense	23268	exon4			GATACCGGAGTAC	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"Rho guanine nucleotide exchange factors"	30373	protein-coding gene	gene with protein product	"scaffold protein TUBA"	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.1853C>T	chr10.hg19:g.101715378G>A	ENSP00000315659:p.Pro618Leu	65.0	0.0		73.0	5.0	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	hg19	CCDS7485.1	.	.	.	.	.	.	.	.	.	.	G	5.836	0.338469	0.11069	.	.	ENSG00000107554	ENST00000342239;ENST00000324109	T;T	0.12672	2.72;2.66	5.9	4.99	0.66335	.	0.295265	0.24497	N	0.038016	T	0.12008	0.0292	L	0.41356	1.27	0.33465	D	0.585458	B	0.17465	0.022	B	0.12156	0.007	T	0.12319	-1.0552	10	0.22706	T	0.39	-1.0546	11.6108	0.51057	0.1532:0.0:0.8468:0.0	.	618	Q6XZF7	DNMBP_HUMAN	L	618	ENSP00000344914:P618L;ENSP00000315659:P618L	ENSP00000315659:P618L	P	-	2	0	DNMBP	101705368	1.000000	0.71417	0.003000	0.11579	0.038000	0.13279	5.907000	0.69908	1.483000	0.48342	0.561000	0.74099	CCG	.	.		0.582	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221		A	101715378	G	A	101715378	3	1	190	1	0	0	0	0	1	0	0	0	4676	1116	39	1	2936	1	DNMBP	10	101715378	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	10538233	101715378	33819369	98	28174										
SFXN2	118980	hgsc.bcm.edu	37	chr10	104489078	104489078	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	atctctctcctcccccaggcAgatggccctttcctacttca	5	18	3	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:104489078A>G	ENST00000369893.5	+	5	601	c.434A>G	c.(433-435)cAg>cGg	p.Q145R		NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	145				QMALSYFTATTTAVATAVGMNMLTKKAPPLVGRWVPFAAVA AANCVNIPMMRQQELIKGI -> KRRPWWAAGCPLPLWLRL TVSISP (in Ref. 4). {ECO:0000305}.	iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		TCCCCCAGGCAGATGGCCCTT	0.627											OREG0020485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q145R		Atlas-SNP	.											.	SFXN2	40	.	0			c.A434G						.						47	40	42					10																	104489078		2203	4300	6503	SO:0001583	missense	118980	exon5			CCAGGCAGATGGC	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"Sideroflexins"	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.434A>G	chr10.hg19:g.104489078A>G	ENSP00000358909:p.Gln145Arg	45.0	0.0	1382	74.0	31.0	NM_178858	Q5JSM6	Missense_Mutation	SNP	ENST00000369893.5	hg19	CCDS7539.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.447746	0.84101	.	.	ENSG00000156398	ENST00000369893	T	0.32988	1.43	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.52741	0.1753	M	0.65498	2.005	0.80722	D	1	D	0.67145	0.996	D	0.74023	0.982	T	0.50558	-0.8814	10	0.40728	T	0.16	-20.7158	14.5699	0.68203	1.0:0.0:0.0:0.0	.	145	Q96NB2	SFXN2_HUMAN	R	145	ENSP00000358909:Q145R	ENSP00000358909:Q145R	Q	+	2	0	SFXN2	104479068	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	8.363000	0.90103	2.179000	0.69175	0.482000	0.46254	CAG	.	.		0.627	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359		G	104489078	A	G	104489078	3	3	190	1	0	0	0	0	1	0	0	0	14210	188	7	2	448	2	SFXN2	10	104489078	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	2773700	104489078	31045669	99	28175										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117061424	117061424	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gctctctgaggacatcatgtTccaactgtacaagcaatggc	9	11	2	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:117061424T>C	ENST00000355044.3	+	17	2815	c.2689T>C	c.(2689-2691)Tcc>Ccc	p.S897P	ATRNL1_ENST00000423111.2_5'UTR|ATRNL1_ENST00000303745.7_5'Flank	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	897	PSI 4.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		GACATCATGTTCCAACTGTAC	0.383																																					p.S897P		Atlas-SNP	.											.	ATRNL1	219	.	0			c.T2689C						.						240	171	194					10																	117061424		2203	4300	6503	SO:0001583	missense	26033	exon17			TCATGTTCCAACT	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2689T>C	chr10.hg19:g.117061424T>C	ENSP00000347152:p.Ser897Pro	85.0	0.0		95.0	40.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.41|15.41	2.825704|2.825704	0.50739|0.50739	.|.	.|.	ENSG00000107518|ENSG00000107518	ENST00000526373|ENST00000355044	.|T	.|0.20738	.|2.05	5.31|5.31	0.218|0.218	0.15270|0.15270	.|.	.|0.560072	.|0.20925	.|N	.|0.083203	T|T	0.17066|0.17066	0.0410|0.0410	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	.|P	.|0.42584	.|0.784	.|P	.|0.45753	.|0.492	T|T	0.06463|0.06463	-1.0825|-1.0825	5|10	.|0.30854	.|T	.|0.27	-0.3001|-0.3001	6.3877|6.3877	0.21569|0.21569	0.0:0.1208:0.2636:0.6155|0.0:0.1208:0.2636:0.6155	.|.	.|897	.|Q5VV63	.|ATRN1_HUMAN	S|P	26|897	.|ENSP00000347152:S897P	.|ENSP00000347152:S897P	F|S	+|+	2|1	0|0	ATRNL1|ATRNL1	117051414|117051414	0.981000|0.981000	0.34729|0.34729	0.518000|0.518000	0.27811|0.27811	0.946000|0.946000	0.59487|0.59487	1.500000|1.500000	0.35682|0.35682	-0.203000|-0.203000	0.10251|0.10251	-0.435000|-0.435000	0.05868|0.05868	TTC|TCC	.	.		0.383	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		C	117061424	T	C	117061424	3	2	190	1	0	0	0	0	1	0	0	0	1207	1783	62	2	2755	2	ATRNL1	10	117061424	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	12572346	117061424	18473323	100	28176										
OR52R1	119695	hgsc.bcm.edu	37	chr11	4824778	4824778	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gtagatagagattagcaaacAggatgtgtacaactcggggc	13	6	0	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:4824778A>T	ENST00000356069.2	-	1	832	c.833T>A	c.(832-834)cTg>cAg	p.L278Q	OR52R1_ENST00000380382.1_Missense_Mutation_p.L357Q|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATTAGCAAACAGGATGTGTAC	0.463																																					p.L278Q		Atlas-SNP	.											.	OR52R1	81	.	0			c.T833A						.						142	143	142					11																	4824778		2201	4298	6499	SO:0001583	missense	119695	exon1			GCAAACAGGATGT	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"GPCR / Class A : Olfactory receptors"	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.833T>A	chr11.hg19:g.4824778A>T	ENSP00000348368:p.Leu278Gln	165.0	0.0		145.0	51.0	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	hg19	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	A	12.79	2.042329	0.35989	.	.	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00188	8.59;8.59	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.259956	0.28057	N	0.016768	T	0.00666	0.0022	H	0.96430	3.82	0.09310	N	0.999999	P	0.50066	0.931	P	0.52554	0.702	T	0.17289	-1.0374	10	0.87932	D	0	.	14.7065	0.69194	1.0:0.0:0.0:0.0	.	278	Q8NGF1	O52R1_HUMAN	Q	278;357	ENSP00000348368:L278Q;ENSP00000369742:L357Q	ENSP00000348368:L278Q	L	-	2	0	OR52R1	4781354	0.024000	0.19004	0.111000	0.21465	0.027000	0.11550	3.058000	0.49939	2.340000	0.79590	0.528000	0.53228	CTG	.	.		0.463	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177		T	4824778	A	T	4824778	3	4	190	1	0	0	0	0	1	0	0	0	11140	188	7	4	117	4	OR52R1	11	4824778	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10		4824778	130181738	101	28177										
OR52N4	390072	hgsc.bcm.edu	37	chr11	5776539	5776540	+	Missense_Mutation	DNP	CC	CC	AT													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	catgtctgtagccaaattgtCctgtggtaatgtcaaggtca							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:5776539_5776540CC>AT	ENST00000317254.3	+	1	617_618	c.569_570CC>AT	c.(568-570)tCC>tAT	p.S190Y	TRIM5_ENST00000380027.1_Intron	NM_001005175.2	NP_001005175.3	Q8NGI2	O52N4_HUMAN	olfactory receptor, family 52, subfamily N, member 4 (gene/pseudogene)	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;1.87e-10)|LUSC - Lung squamous cell carcinoma(625;0.114)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.197)		GCCAAATTGTCCTGTGGTAATG	0.46																																					p.S190Y|p.S190S		Atlas-SNP	.											.	OR52N4	55	.	0			c.C569A|c.C570T						.																																			SO:0001583	missense	390072	exon1			AATTGTCCTGTGG|ATTGTCCTGTGGT	AB065813	CCDS44528.1	11p15.4	2013-10-10	2013-10-10		ENSG00000181074	ENSG00000181074		"GPCR / Class A : Olfactory receptors"	15230	protein-coding gene	gene with protein product			"olfactory receptor, family 52, subfamily N, member 4"				Standard	NM_001005175		Approved		uc001mbu.3	Q8NGI2	OTTHUMG00000066887	Exception_encountered	chr11.hg19:g.5776539_5776540delinsAT	ENSP00000323224:p.Ser190Tyr	69.0	0.0		74.0|73.0	5.0	NM_001005175	B2RNP8|Q6IF77	Missense_Mutation|Silent	SNP	ENST00000317254.3	hg19	CCDS44528.1																																																																																			.	.		0.46	OR52N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143350.1	NM_001005175		AT	5776540	CC	AT	5776539	3	1	190	1	0	0	0	0	1	0	0	0	11138	855	30	3	571	3	OR52N4	11	5776539	Missense_Mutation	DNP	CC	TCGA-DD-AADG-01A-11D-A40R-10	951761	5776539	129229977	102	28178										
PAMR1	25891	hgsc.bcm.edu	37	chr11	35454063	35454063	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cccgggaaggacacagccgcGatgcctcctgtctctgcagt	12	15	1	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:35454063G>T	ENST00000378880.2	-	11	2449	c.2004C>A	c.(2002-2004)atC>atA	p.I668I	PAMR1_ENST00000532848.1_Silent_p.I628I|PAMR1_ENST00000378878.3_Silent_p.I557I|PAMR1_ENST00000278360.3_Silent_p.I685I	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	668	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						ACACAGCCGCGATGCCTCCTG	0.567																																					p.I685I		Atlas-SNP	.											PAMR1,NS,carcinoma,0,1	PAMR1	85	.	0			c.C2055A						.						81	74	76					11																	35454063		2202	4298	6500	SO:0001819	synonymous_variant	25891	exon12			AGCCGCGATGCCT		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"regeneration-associated muscle protease"					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.2004C>A	chr11.hg19:g.35454063G>T		70.0	0.0		70.0	3.0	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Silent	SNP	ENST00000378880.2	hg19	CCDS31460.1																																																																																			.	.		0.567	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430		T	35454063	G	T	35454063	2	4	190	1	0	0	0	0	0	0	0	1	11422	1048	37	1		1	PAMR1	11	35454063	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	29677524	35454063	99552453	103	28179										
CKAP5	9793	hgsc.bcm.edu	37	chr11	46771955	46771955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgtcagcatctgagtatttcTtcttatattcatataactct	4	8	6	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:46771955T>C	ENST00000529230.1	-	42	5619	c.5573A>G	c.(5572-5574)aAg>aGg	p.K1858R	MIR5582_ENST00000579697.1_RNA|CKAP5_ENST00000354558.3_Missense_Mutation_p.K1798R|CKAP5_ENST00000312055.5_Missense_Mutation_p.K1798R|CKAP5_ENST00000415402.1_Missense_Mutation_p.K1865R			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	1858					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						TGAGTATTTCTTCTTATATTC	0.433																																					p.K1858R	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.A5573G						.						106	103	104					11																	46771955		2201	4299	6500	SO:0001583	missense	9793	exon42			TATTTCTTCTTAT		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.5573A>G	chr11.hg19:g.46771955T>C	ENSP00000432768:p.Lys1858Arg	106.0	0.0		92.0	6.0	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	hg19	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	T	16.18	3.049826	0.55218	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558	T;T;T;T	0.64803	-0.12;-0.12;0.77;0.77	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.140992	0.64402	D	0.000004	T	0.52092	0.1713	L	0.40543	1.245	0.49051	D	0.999744	P;B;B	0.42248	0.774;0.386;0.267	B;B;B	0.36608	0.229;0.085;0.039	T	0.51601	-0.8685	10	0.26408	T	0.33	-12.3852	15.8087	0.78538	0.0:0.0:0.0:1.0	.	1865;1798;1858	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	R	1858;1865;1798;1798	ENSP00000432768:K1858R;ENSP00000395302:K1865R;ENSP00000310227:K1798R;ENSP00000346566:K1798R	ENSP00000310227:K1798R	K	-	2	0	CKAP5	46728531	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.759000	0.62227	2.140000	0.66376	0.449000	0.29647	AAG	.	.		0.433	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		C	46771955	T	C	46771955	3	2	190	1	0	0	0	0	1	0	0	0	3447	1609	56	2	537	2	CKAP5	11	46771955	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	11317892	46771955	88234561	104	28180										
OR6Q1	219952	hgsc.bcm.edu	37	chr11	57798664	57798664	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tggtacacttctgttacagtGcccaagatgctggctggttt	11	9	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:57798664G>C	ENST00000302622.3	+	1	263	c.240G>C	c.(238-240)gtG>gtC	p.V80V	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				CTGTTACAGTGCCCAAGATGC	0.473																																					p.V80V		Atlas-SNP	.											.	OR6Q1	58	.	0			c.G240C						.						174	166	168					11																	57798664		2201	4296	6497	SO:0001819	synonymous_variant	219952	exon1			TACAGTGCCCAAG	AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381		"GPCR / Class A : Olfactory receptors"	15302	protein-coding gene	gene with protein product							Standard	NM_001005186		Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.240G>C	chr11.hg19:g.57798664G>C		172.0	0.0		181.0	18.0	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Silent	SNP	ENST00000302622.3	hg19	CCDS31541.1																																																																																			.	.		0.473	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186		C	57798664	G	C	57798664	2	2	190	1	0	0	0	0	0	0	0	1	11217	1306	46	4		4	OR6Q1	11	57798664	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	11026709	57798664	77207852	105	28181										
OR9I1	219954	hgsc.bcm.edu	37	chr11	57886498	57886498	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ctaccaccaggctccagcagAgcctgggattcatggccacg	11	15	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:57886498A>G	ENST00000302610.1	-	1	418	c.419T>C	c.(418-420)cTc>cCc	p.L140P	OR9Q1_ENST00000335397.3_Intron	NM_001005211.1	NP_001005211.1	Q8NGQ6	OR9I1_HUMAN	olfactory receptor, family 9, subfamily I, member 1	140						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|liver(1)|lung(15)|pancreas(1)|skin(1)|urinary_tract(1)	23		Breast(21;0.0589)				GCTCCAGCAGAGCCTGGGATT	0.557																																					p.L140P		Atlas-SNP	.											.	OR9I1	53	.	0			c.T419C						.						42	42	42					11																	57886498		2201	4296	6497	SO:0001583	missense	219954	exon1			CAGCAGAGCCTGG	AB065733	CCDS31542.1	11q12.1	2012-08-09			ENSG00000172377	ENSG00000172377		"GPCR / Class A : Olfactory receptors"	14718	protein-coding gene	gene with protein product							Standard	NM_001005211		Approved		uc021qjl.1	Q8NGQ6	OTTHUMG00000167404	ENST00000302610.1:c.419T>C	chr11.hg19:g.57886498A>G	ENSP00000302606:p.Leu140Pro	80.0	0.0		71.0	7.0	NM_001005211	Q6IFH0|Q96RA8	Missense_Mutation	SNP	ENST00000302610.1	hg19	CCDS31542.1	.	.	.	.	.	.	.	.	.	.	A	5.924	0.354601	0.11239	.	.	ENSG00000172377	ENST00000302610	T	0.00241	8.46	5.05	1.08	0.20341	GPCR, rhodopsin-like superfamily (1);	0.837659	0.10227	N	0.700170	T	0.00241	0.0007	M	0.76433	2.335	0.09310	N	0.999997	P	0.38642	0.641	B	0.41764	0.366	T	0.29761	-1.0001	10	0.87932	D	0	-5.7039	2.6704	0.05065	0.4103:0.0:0.2456:0.3441	.	140	Q8NGQ6	OR9I1_HUMAN	P	140	ENSP00000302606:L140P	ENSP00000302606:L140P	L	-	2	0	OR9I1	57643074	0.000000	0.05858	0.485000	0.27403	0.019000	0.09904	0.569000	0.23638	0.372000	0.24591	0.377000	0.23210	CTC	.	.		0.557	OR9I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394539.1	NM_001005211		G	57886498	A	G	57886498	3	3	190	1	0	0	0	0	1	0	0	0	11262	304	11	2	529	2	OR9I1	11	57886498	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	87834	57886498	77120018	106	28182										
ZFP91	80829	hgsc.bcm.edu	37	chr11	58381796	58381796	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gcttcagaagcaacttctgcGacatgccaaacatcatacag	7	12	3	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:58381796G>T	ENST00000316059.6	+	9	1253	c.1082G>T	c.(1081-1083)cGa>cTa	p.R361L	ZFP91-CNTF_ENST00000389919.4_Missense_Mutation_p.R361L	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	361	Interaction with MAP3K14/NIK.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				CAACTTCTGCGACATGCCAAA	0.383																																					p.R361L		Atlas-SNP	.											.	ZFP91	66	.	0			c.G1082T						.						90	82	84					11																	58381796		2201	4294	6495	SO:0001583	missense	80829	exon9			TTCTGCGACATGC	AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"Zinc fingers, C2H2-type"	14983	protein-coding gene	gene with protein product			"zinc finger protein homologous to Zfp91 in mouse", "zinc finger protein 91 homolog (mouse)"			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.1082G>T	chr11.hg19:g.58381796G>T	ENSP00000339030:p.Arg361Leu	51.0	0.0		57.0	21.0	NM_053023	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Missense_Mutation	SNP	ENST00000316059.6	hg19	CCDS31553.1	.	.	.	.	.	.	.	.	.	.	G	34	5.315890	0.95655	.	.	ENSG00000186660	ENST00000316059;ENST00000389918	T	0.15372	2.43	5.97	5.97	0.96955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000007	T	0.38453	0.1041	L	0.49513	1.565	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.85130	0.994;0.997	T	0.00533	-1.1685	10	0.34782	T	0.22	-7.0583	19.2039	0.93722	0.0:0.0:1.0:0.0	.	361;361	Q96JP5-2;Q96JP5	.;ZFP91_HUMAN	L	361	ENSP00000339030:R361L	ENSP00000374569:R361L	R	+	2	0	ZFP91	58138372	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	9.476000	0.97823	2.833000	0.97629	0.585000	0.79938	CGA	.	.		0.383	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023		T	58381796	G	T	58381796	3	4	190	1	0	0	0	0	1	0	0	0	17670	1058	37	1	1116	1	ZFP91	11	58381796	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	495298	58381796	76624720	107	28183										
STIP1	10963	hgsc.bcm.edu	37	chr11	63963275	63963275	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ggaagaagatcttccagagaAtaagaagcaggtcttgtttt	11	5	2	4			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:63963275A>G	ENST00000305218.4	+	5	809	c.662A>G	c.(661-663)aAt>aGt	p.N221S	STIP1_ENST00000538945.1_Missense_Mutation_p.N197S|STIP1_ENST00000358794.5_Missense_Mutation_p.N268S|STIP1_ENST00000540501.1_3'UTR|STIP1_ENST00000543847.1_Missense_Mutation_p.N221S	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	221					response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						CTTCCAGAGAATAAGAAGCAG	0.448																																					p.N221S		Atlas-SNP	.											.	STIP1	63	.	0			c.A662G						.						138	149	145					11																	63963275		2201	4297	6498	SO:0001583	missense	10963	exon5			CAGAGAATAAGAA	BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"Tetratricopeptide (TTC) repeat domain containing"	11387	protein-coding gene	gene with protein product	"Hsp70/Hsp90-organizing protein"	605063	"stress-induced-phosphoprotein 1"			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.662A>G	chr11.hg19:g.63963275A>G	ENSP00000305958:p.Asn221Ser	239.0	0.0		260.0	109.0	NM_006819	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Missense_Mutation	SNP	ENST00000305218.4	hg19	CCDS8058.1	.	.	.	.	.	.	.	.	.	.	A	8.371	0.835428	0.16820	.	.	ENSG00000168439	ENST00000358794;ENST00000305218;ENST00000538945;ENST00000543847	T;T;T;T	0.70986	2.54;2.77;2.55;-0.53	5.05	3.9	0.45041	.	0.000000	0.85682	D	0.000000	T	0.68650	0.3024	M	0.62723	1.935	0.53688	D	0.999971	B;B;P	0.36048	0.2;0.245;0.534	B;B;B	0.42282	0.069;0.032;0.382	T	0.62435	-0.6855	10	0.19147	T	0.46	-43.5292	10.9318	0.47222	0.8591:0.0:0.0:0.1409	.	197;221;221	F5H0T1;P31948;F5H783	.;STIP1_HUMAN;.	S	268;221;197;221	ENSP00000351646:N268S;ENSP00000305958:N221S;ENSP00000445957:N197S;ENSP00000442704:N221S	ENSP00000305958:N221S	N	+	2	0	STIP1	63719851	1.000000	0.71417	1.000000	0.80357	0.349000	0.29174	7.731000	0.84895	1.005000	0.39183	-0.516000	0.04426	AAT	.	.		0.448	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819		G	63963275	A	G	63963275	3	3	190	1	0	0	0	0	1	0	0	0	15300	101	4	2	680	2	STIP1	11	63963275	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	5581479	63963275	71043241	108	28184										
CBL	867	hgsc.bcm.edu	37	chr11	119170325	119170325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tcctgccgcctctgctgccaCcgcctcacctcagctctcca	6	22	4	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:119170325C>T	ENST00000264033.4	+	16	2931	c.2555C>T	c.(2554-2556)aCc>aTc	p.T852I		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	852	Interaction with CD2AP.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TCTGCTGCCACCGCCTCACCT	0.562			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																												p.T852I		Atlas-SNP	.		"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.C2555T						.						154	154	154					11																	119170325		2199	4295	6494	SO:0001583	missense	867	exon16	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	CTGCCACCGCCTC	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2555C>T	chr11.hg19:g.119170325C>T	ENSP00000264033:p.Thr852Ile	92.0	0.0		88.0	5.0	NM_005188	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	hg19	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	C	5.511	0.279276	0.10458	.	.	ENSG00000110395	ENST00000264033	T	0.77358	-1.09	5.59	5.59	0.84812	.	0.495098	0.21803	N	0.068896	T	0.62502	0.2433	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.11329	0.006	T	0.59172	-0.7504	10	0.72032	D	0.01	-2.9898	15.4319	0.75105	0.0:0.8218:0.1782:0.0	.	852	P22681	CBL_HUMAN	I	852	ENSP00000264033:T852I	ENSP00000264033:T852I	T	+	2	0	CBL	118675535	0.177000	0.23109	0.084000	0.20598	0.190000	0.23558	2.726000	0.47302	2.639000	0.89480	0.655000	0.94253	ACC	.	.		0.562	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		T	119170325	C	T	119170325	3	4	190	1	0	0	0	0	1	0	0	0	2702	507	18	3	2617	3	CBL	11	119170325	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	55207050	119170325	15836191	109	28185										
LAG3	3902	hgsc.bcm.edu	37	chr12	6887494	6887511	+	In_Frame_Del	DEL	CCGGAGCCGGAGCCGGAG	CCGGAGCCGGAGCCGGAG	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tagaggagctggagcaagaaCcggagccggagccggagccg					rs566439838|rs566081528|rs149606091	byFrequency	TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	CCGGAGCCGGAGCCGGAG	CCGGAGCCGGAGCCGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:6887494_6887511delCCGGAGCCGGAGCCGGAG	ENST00000203629.2	+	8	1849_1866	c.1516_1533delCCGGAGCCGGAGCCGGAG	c.(1516-1533)ccggagccggagccggagdel	p.PEPEPE518del		NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	518	12 X 2 AA tandem repeats of E-X.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GGAGCAAGAAccggagccggagccggagccggaaccgg	0.615																																					p.505_511del		Atlas-INDEL	.											.	LAG3	35	.	0			c.1515_1532del						.																																			SO:0001651	inframe_deletion	3902	exon8			.		CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.1516_1533delCCGGAGCCGGAGCCGGAG	chr12.hg19:g.6887494_6887511delCCGGAGCCGGAGCCGGAG	ENSP00000203629:p.Pro518_Glu523del	67.0	0.0		56.0	22.0	NM_002286	A8K7T9|Q7Z643	In_Frame_Del	DEL	ENST00000203629.2	hg19	CCDS8561.1																																																																																			.	.		0.615	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1			-	6887511	CCGGAGCCGGAGCCGGAG	-	6887494	7	5	190	1	0	1	0	1	0	0	0	0	8609	507	18	0	1546	0	LAG3	12	6887494	In_Frame_Del	DEL	CCGGAGCCGGAGCCGGAG	TCGA-DD-AADG-01A-11D-A40R-10		6887494	126964401	110	28186										
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14577886	14577886	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	taaagctgataataatattgAtgctaatgaagaaactctag	7	4	1	4			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:14577886A>C	ENST00000540793.1	+	1	1192	c.1037A>C	c.(1036-1038)gAt>gCt	p.D346A	ATF7IP_ENST00000543189.1_Missense_Mutation_p.D346A|ATF7IP_ENST00000261168.4_Missense_Mutation_p.D346A|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000544627.1_Missense_Mutation_p.D354A|ATF7IP_ENST00000536444.1_Missense_Mutation_p.D346A			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	346					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						AATAATATTGATGCTAATGAA	0.313																																					p.D346A		Atlas-SNP	.											.	ATF7IP	136	.	0			c.A1037C						.						56	63	60					12																	14577886		2202	4298	6500	SO:0001583	missense	55729	exon2			ATATTGATGCTAA	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.1037A>C	chr12.hg19:g.14577886A>C	ENSP00000444589:p.Asp346Ala	122.0	0.0		90.0	34.0	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	hg19	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	A	8.855	0.945614	0.18356	.	.	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000396279;ENST00000540793	T;T;T;T;T;T	0.23147	2.24;2.23;2.24;2.23;1.92;2.24	5.55	0.497	0.16902	.	0.456909	0.20727	N	0.086784	T	0.11153	0.0272	N	0.16478	0.41	0.09310	N	1	B;B;B;B;B	0.24721	0.11;0.11;0.01;0.01;0.01	B;B;B;B;B	0.23419	0.046;0.046;0.006;0.006;0.006	T	0.18903	-1.0322	10	0.25751	T	0.34	-7.0378	2.1934	0.03905	0.5645:0.1135:0.1035:0.2185	.	354;346;346;346;346	B4E2A2;B4DRL6;G3V1U0;Q6VMQ6;Q6VMQ6-2	.;.;.;MCAF1_HUMAN;.	A	346;346;346;354;346;346	ENSP00000261168:D346A;ENSP00000443179:D346A;ENSP00000445955:D346A;ENSP00000440440:D354A;ENSP00000379575:D346A;ENSP00000444589:D346A	ENSP00000261168:D346A	D	+	2	0	ATF7IP	14469153	0.182000	0.23173	0.005000	0.12908	0.962000	0.63368	0.852000	0.27764	-0.083000	0.12618	0.533000	0.62120	GAT	.	.		0.313	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		C	14577886	A	C	14577886	3	2	190	1	0	0	0	0	1	0	0	0	1087	333	12	5	1039	5	ATF7IP	12	14577886	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	7690392	14577886	119274009	111	28187										
SLCO1C1	53919	hgsc.bcm.edu	37	chr12	20852565	20852565	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tctgcaaaacttcagtgcaaCctgttggaaggccttctttt	8	10	3	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:20852565C>A	ENST00000266509.2	+	2	423	c.55C>A	c.(55-57)Cct>Act	p.P19T	SLCO1C1_ENST00000381552.1_Missense_Mutation_p.P19T|SLCO1C1_ENST00000545102.1_Intron|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.P19T|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.P19T	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	19					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	TTCAGTGCAACCTGTTGGAAG	0.373																																					p.P19T		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C55A						.						65	64	64					12																	20852565		2203	4299	6502	SO:0001583	missense	53919	exon2			GTGCAACCTGTTG	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"Solute carriers"	13819	protein-coding gene	gene with protein product		613389	"solute carrier family 21 (organic anion transporter), member 14"	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.55C>A	chr12.hg19:g.20852565C>A	ENSP00000266509:p.Pro19Thr	286.0	0.0		254.0	94.0	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	hg19	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.627460	0.46944	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552	T;T;T;T	0.38077	1.16;1.24;1.22;1.16	4.86	4.86	0.63082	Major facilitator superfamily domain, general substrate transporter (1);	1.596860	0.03301	N	0.189018	T	0.25938	0.0632	N	0.08118	0	0.36994	D	0.894924	B;B;B	0.28233	0.054;0.204;0.054	B;B;B	0.27500	0.034;0.08;0.05	T	0.08330	-1.0727	10	0.51188	T	0.08	.	10.8646	0.46847	0.0:0.9137:0.0:0.0863	.	19;19;19	B7Z3Q3;Q5JPA4;Q9NYB5	.;.;SO1C1_HUMAN	T	19	ENSP00000444149:P19T;ENSP00000438665:P19T;ENSP00000266509:P19T;ENSP00000370964:P19T	ENSP00000266509:P19T	P	+	1	0	SLCO1C1	20743832	0.290000	0.24343	0.996000	0.52242	0.967000	0.64934	1.561000	0.36342	2.532000	0.85374	0.655000	0.94253	CCT	.	.		0.373	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		A	20852565	C	A	20852565	3	1	190	1	0	0	0	0	1	0	0	0	14740	507	18	3	57	3	SLCO1C1	12	20852565	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	6274679	20852565	112999330	112	28188										
SLC38A2	54407	hgsc.bcm.edu	37	chr12	46758276	46758276	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ctgtgttaaggtggtgtttaTtgtttcgttaattatcaaag	10	3	1	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:46758276T>C	ENST00000256689.5	-	10	1213	c.769A>G	c.(769-771)Ata>Gta	p.I257V	SLC38A2_ENST00000551374.1_Missense_Mutation_p.I95V|SLC38A2_ENST00000547252.1_5'Flank	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	257					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		GTGGTGTTTATTGTTTCGTTA	0.363																																					p.I257V	Ovarian(9;448 492 8335 28722 40361)	Atlas-SNP	.											.	SLC38A2	36	.	0			c.A769G						.						252	252	252					12																	46758276		2203	4300	6503	SO:0001583	missense	54407	exon10			TGTTTATTGTTTC	AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"Solute carriers"	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.769A>G	chr12.hg19:g.46758276T>C	ENSP00000256689:p.Ile257Val	157.0	0.0		126.0	33.0	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Missense_Mutation	SNP	ENST00000256689.5	hg19	CCDS8749.1	.	.	.	.	.	.	.	.	.	.	T	8.536	0.872107	0.17322	.	.	ENSG00000134294	ENST00000256689;ENST00000551374	T;T	0.02421	4.3;4.3	5.43	-5.76	0.02376	.	2.500020	0.01439	N	0.015034	T	0.01387	0.0045	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.46091	-0.9216	10	0.09084	T	0.74	0.7757	6.9081	0.24321	0.1459:0.5961:0.0856:0.1724	.	95;157;257	F8VQW8;Q96QD8-2;Q96QD8	.;.;S38A2_HUMAN	V	257;95	ENSP00000256689:I257V;ENSP00000450406:I95V	ENSP00000256689:I257V	I	-	1	0	SLC38A2	45044543	0.000000	0.05858	0.000000	0.03702	0.926000	0.56050	-2.806000	0.00758	-0.967000	0.03582	0.377000	0.23210	ATA	.	.		0.363	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1			C	46758276	T	C	46758276	3	2	190	1	0	0	0	0	1	0	0	0	14619	1493	52	2	779	2	SLC38A2	12	46758276	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	25905711	46758276	87093619	113	28189										
TFCP2	7024	hgsc.bcm.edu	37	chr12	51510198	51510198	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tcatggaacaccacacggaaTatactctaaaaggatacaac	6	10	2	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:51510198T>C	ENST00000257915.5	-	4	815	c.357A>G	c.(355-357)atA>atG	p.I119M	TFCP2_ENST00000549867.1_Missense_Mutation_p.I119M|TFCP2_ENST00000307660.4_Missense_Mutation_p.I119M|TFCP2_ENST00000548115.1_Missense_Mutation_p.I119M	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	119					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						CCACACGGAATATACTCTAAA	0.433																																					p.I119M		Atlas-SNP	.											.	TFCP2	49	.	0			c.A357G						.						91	84	87					12																	51510198		2203	4300	6503	SO:0001583	missense	7024	exon4			ACGGAATATACTC	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.357A>G	chr12.hg19:g.51510198T>C	ENSP00000257915:p.Ile119Met	96.0	0.0		74.0	37.0	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	hg19	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	T	12.52	1.963013	0.34659	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000549867;ENST00000548115;ENST00000548108	T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24	4.86	3.69	0.42338	CP2 transcription factor (1);	0.000000	0.85682	D	0.000000	T	0.21550	0.0519	L	0.55743	1.74	0.49051	D	0.999746	B;P;B;B	0.36733	0.021;0.567;0.372;0.185	B;P;B;B	0.44696	0.009;0.458;0.209;0.132	T	0.02161	-1.1203	10	0.87932	D	0	-18.7396	6.809	0.23794	0.1502:0.0:0.1565:0.6933	.	119;119;119;119	Q12800-2;F8VX55;Q12800;Q12800-4	.;.;TFCP2_HUMAN;.	M	119;119;119;119;21	ENSP00000257915:I119M;ENSP00000304411:I119M;ENSP00000449742:I119M;ENSP00000447991:I119M;ENSP00000449280:I21M	ENSP00000257915:I119M	I	-	3	3	TFCP2	49796465	0.866000	0.29940	1.000000	0.80357	0.835000	0.47333	-0.078000	0.11375	0.968000	0.38212	0.533000	0.62120	ATA	.	.		0.433	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653		C	51510198	T	C	51510198	3	2	190	1	0	0	0	0	1	0	0	0	15810	1396	49	2	1199	2	TFCP2	12	51510198	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	4751922	51510198	82341697	114	28190										
SLC26A10	65012	hgsc.bcm.edu	37	chr12	58018905	58018905	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	actgcccttctttacttataGgagacttcaaagccagatgg	8	10	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:58018905G>A	ENST00000320442.4	+	11	1655		c.e11-1		SLC26A10_ENST00000379218.2_Splice_Site|SLC26A10_ENST00000490243.1_Splice_Site	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10							integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					TTTACTTATAGGAGACTTCAA	0.532																																					.		Atlas-SNP	.											.	SLC26A10	89	.	0			c.1345-1G>A						.						267	262	264					12																	58018905		2203	4300	6503	SO:0001630	splice_region_variant	65012	exon11			CTTATAGGAGACT		CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"Solute carriers"	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.1345-1G>A	chr12.hg19:g.58018905G>A		138.0	0.0		169.0	66.0	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Splice_Site	SNP	ENST00000320442.4	hg19	CCDS8949.2	.	.	.	.	.	.	.	.	.	.	G	8.345	0.829641	0.16749	.	.	ENSG00000135502	ENST00000320442	.	.	.	4.44	4.44	0.53790	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4261	0.55548	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC26A10	56305172	0.207000	0.23482	0.942000	0.38095	0.266000	0.26442	2.021000	0.41020	2.297000	0.77311	0.561000	0.74099	.	.	.		0.532	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2		Intron	A	58018905	G	A	58018905	5	1	190	1	0	0	0	0	0	0	1	0	14530	1014	35	3	1386	3	SLC26A10	12	58018905	Splice_Site	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	6508707	58018905	75832990	115	28191										
NAV3	89795	hgsc.bcm.edu	37	chr12	78522622	78522622	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ccatgtcatcttctgcagctGgaaaataccacttttctaac	5	12	4	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:78522622G>A	ENST00000397909.2	+	18	4590	c.4417G>A	c.(4417-4419)Gga>Aga	p.G1473R	NAV3_ENST00000228327.6_Missense_Mutation_p.G1473R|NAV3_ENST00000266692.7_Missense_Mutation_p.G1296R|NAV3_ENST00000536525.2_Missense_Mutation_p.G1473R			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1473	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TTCTGCAGCTGGAAAATACCA	0.443										HNSCC(70;0.22)																											p.G1473R		Atlas-SNP	.											.	NAV3	506	.	0			c.G4417A						.						93	88	89					12																	78522622		1859	4111	5970	SO:0001583	missense	89795	exon18			GCAGCTGGAAAAT	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.4417G>A	chr12.hg19:g.78522622G>A	ENSP00000381007:p.Gly1473Arg	93.0	0.0		87.0	35.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.1|23.1	4.374909|4.374909	0.82573|0.82573	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788|ENST00000552895	T;T;T;T;T|.	0.32515|.	1.48;1.51;1.5;1.45;2.24|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.000000|.	0.39146|.	U|.	0.001455|.	T|.	0.75583|.	0.3869|.	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.999;0.996;1.0;1.0|.	D;D;D;D|.	0.97110|.	0.98;0.953;1.0;0.982|.	T|.	0.72367|.	-0.4315|.	10|.	0.36615|.	T|.	0.2|.	-15.7635|-15.7635	20.0755|20.0755	0.97742|0.97742	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1473;1296;1473;1473|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	R|X	1473;1473;1473;1296;94;102|367	ENSP00000446132:G1473R;ENSP00000381007:G1473R;ENSP00000228327:G1473R;ENSP00000266692:G1296R;ENSP00000448303:G102R|.	ENSP00000228327:G1473R|.	G|W	+|+	1|2	0|0	NAV3|NAV3	77046753|77046753	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	6.435000|6.435000	0.73412|0.73412	2.749000|2.749000	0.94314|0.94314	0.460000|0.460000	0.39030|0.39030	GGA|TGG	.	.		0.443	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78522622	G	A	78522622	3	1	190	1	0	0	0	0	1	0	0	0	10194	1349	47	3	4487	3	NAV3	12	78522622	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	20503717	78522622	55329273	116	28192										
C12orf26	84190	hgsc.bcm.edu	37	chr12	82792710	82792710	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	aaacagaaaattgaagaaacAttggaaactctgtcatgctc	7	7	2	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:82792710A>G	ENST00000248306.3	+	4	737	c.668A>G	c.(667-669)cAt>cGt	p.H223R	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	223							methyltransferase activity (GO:0008168)										TTGAAGAAACATTGGAAACTC	0.323																																					p.H223R		Atlas-SNP	.											.	.	.	.	0			c.A668G						.						61	59	60					12																	82792710		2203	4299	6502	SO:0001583	missense	84190	exon4			AGAAACATTGGAA	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 26"	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.668A>G	chr12.hg19:g.82792710A>G	ENSP00000248306:p.His223Arg	102.0	0.0		97.0	44.0	NM_032230	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	hg19	CCDS9024.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.57|10.57	1.386405|1.386405	0.25031|0.25031	.|.	.|.	ENSG00000127720|ENSG00000127720	ENST00000248306;ENST00000548200|ENST00000550058	T;T|.	0.18960|.	2.18;2.18|.	5.43|5.43	4.29|4.29	0.51040|0.51040	.|.	0.199004|.	0.56097|.	D|.	0.000040|.	T|T	0.54464|0.54464	0.1860|0.1860	L|L	0.49640|0.49640	1.575|1.575	0.33617|0.33617	D|D	0.604316|0.604316	B|.	0.19331|.	0.035|.	B|.	0.19666|.	0.026|.	T|T	0.63761|0.63761	-0.6564|-0.6564	10|5	0.25106|.	T|.	0.35|.	-8.0965|-8.0965	11.2669|11.2669	0.49116|0.49116	0.9282:0.0:0.0717:0.0|0.9282:0.0:0.0717:0.0	.|.	223|.	Q8N6Q8|.	CL026_HUMAN|.	R|V	223|182	ENSP00000248306:H223R;ENSP00000446878:H223R|.	ENSP00000248306:H223R|.	H|I	+|+	2|1	0|0	C12orf26|C12orf26	81316841|81316841	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.454000|0.454000	0.32378|0.32378	4.731000|4.731000	0.62022|0.62022	1.009000|1.009000	0.39289|0.39289	0.477000|0.477000	0.44152|0.44152	CAT|ATT	.	.		0.323	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		G	82792710	A	G	82792710	3	3	190	1	0	0	0	0	1	0	0	0	1681	217	8	2	682	2	C12orf26	12	82792710	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	4270088	82792710	51059185	117	28193										
NAA25	80018	hgsc.bcm.edu	37	chr12	112516482	112516482	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ctctttcaccattttttcgaCcattctctcagcaaggggca	6	13	4	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:112516482C>T	ENST00000261745.4	-	6	789	c.541G>A	c.(541-543)Gtc>Atc	p.V181I		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	181						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						ATTTTTTCGACCATTCTCTCA	0.358																																					p.V181I		Atlas-SNP	.											.	NAA25	105	.	0			c.G541A						.						170	154	159					12																	112516482		2203	4300	6503	SO:0001583	missense	80018	exon6			TTTCGACCATTCT	AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"N(alpha)-acetyltransferase subunits"	25783	protein-coding gene	gene with protein product		612755	"chromosome 12 open reading frame 30"	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.541G>A	chr12.hg19:g.112516482C>T	ENSP00000261745:p.Val181Ile	129.0	0.0		128.0	28.0	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	hg19	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	C	36	5.760438	0.96906	.	.	ENSG00000111300	ENST00000261745	T	0.37235	1.21	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.48114	0.1482	L	0.31752	0.955	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	T	0.13335	-1.0513	10	0.10111	T	0.7	-14.0427	20.6013	0.99457	0.0:1.0:0.0:0.0	.	181;181	A8K8X0;Q14CX7	.;NAA25_HUMAN	I	181	ENSP00000261745:V181I	ENSP00000261745:V181I	V	-	1	0	NAA25	111000865	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.251000	0.78297	2.878000	0.98634	0.650000	0.86243	GTC	.	.		0.358	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		T	112516482	C	T	112516482	3	4	190	1	0	0	0	0	1	0	0	0	10130	507	18	3	2453	3	NAA25	12	112516482	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	29723772	112516482	21335413	118	28194										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120595713	120595713	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agctgggcttggacagtgagGatctgaagaatctgggccat	15	7	2	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:120595713G>T	ENST00000300648.6	-	26	3039	c.3027C>A	c.(3025-3027)atC>atA	p.I1009I	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1009					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGACAGTGAGGATCTGAAGAA	0.602																																					p.I1009I		Atlas-SNP	.											.	GCN1L1	207	.	0			c.C3027A						.						50	57	55					12																	120595713		1971	4152	6123	SO:0001819	synonymous_variant	10985	exon26			AGTGAGGATCTGA	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.3027C>A	chr12.hg19:g.120595713G>T		98.0	0.0		113.0	39.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	hg19	CCDS41847.1																																																																																			.	.		0.602	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			T	120595713	G	T	120595713	2	4	190	1	0	0	0	0	0	0	0	1	6307	1164	41	3		3	GCN1L1	12	120595713	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	8079231	120595713	13256182	119	28195										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42874405	42874405	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ctcagttcttcgtacccaccAtactaataccctatcaaata	2	14	3	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr13:42874405A>G	ENST00000025301.2	+	8	1698	c.1523A>G	c.(1522-1524)cAt>cGt	p.H508R		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	508					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		CGTACCCACCATACTAATACC	0.299																																					p.H508R		Atlas-SNP	.											.	AKAP11	146	.	0			c.A1523G						.						68	69	69					13																	42874405		2203	4299	6502	SO:0001583	missense	11215	exon8			CCCACCATACTAA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.1523A>G	chr13.hg19:g.42874405A>G	ENSP00000025301:p.His508Arg	220.0	0.0		219.0	13.0	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	0.948	-0.707207	0.03230	.	.	ENSG00000023516	ENST00000025301	T	0.48522	0.81	5.63	0.322	0.15888	.	0.610881	0.17589	N	0.168822	T	0.35537	0.0935	M	0.63428	1.95	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.17745	-1.0359	10	0.30854	T	0.27	.	1.9061	0.03278	0.4875:0.2515:0.1395:0.1215	.	508	Q9UKA4	AKA11_HUMAN	R	508	ENSP00000025301:H508R	ENSP00000025301:H508R	H	+	2	0	AKAP11	41772405	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	0.305000	0.19254	0.473000	0.27368	0.477000	0.44152	CAT	.	.		0.299	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		G	42874405	A	G	42874405	3	3	190	1	0	0	0	0	1	0	0	0	447	217	8	2	1545	2	AKAP11	13	42874405	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10		42874405	72295473	120	28196										
TRIM13	10206	hgsc.bcm.edu	37	chr13	50586458	50586458	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gggagcacaccaaacatgtcTtctgttctattgaagatgcc	9	10	3	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr13:50586458T>C	ENST00000378182.3	+	2	1120	c.382T>C	c.(382-384)Ttc>Ctc	p.F128L	TRIM13_ENST00000420995.2_Missense_Mutation_p.F128L|TRIM13_ENST00000457662.2_Missense_Mutation_p.F128L|KCNRG_ENST00000312942.1_5'Flank|TRIM13_ENST00000478111.1_Intron|TRIM13_ENST00000298772.5_Missense_Mutation_p.F131L|KCNRG_ENST00000360473.4_5'Flank|TRIM13_ENST00000356017.4_Missense_Mutation_p.F131L	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13	128					anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		CAAACATGTCTTCTGTTCTAT	0.507																																					p.F131L		Atlas-SNP	.											.	TRIM13	30	.	0			c.T391C						.						136	124	128					13																	50586458		2203	4300	6503	SO:0001583	missense	10206	exon4			CATGTCTTCTGTT	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9976	protein-coding gene	gene with protein product		605661	"ret finger protein 2", "tripartite motif-containing 13"	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.382T>C	chr13.hg19:g.50586458T>C	ENSP00000367424:p.Phe128Leu	126.0	0.0		174.0	10.0	NM_001007278	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	Missense_Mutation	SNP	ENST00000378182.3	hg19	CCDS9423.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.911178	0.72983	.	.	ENSG00000204977	ENST00000442421;ENST00000378183;ENST00000420995;ENST00000378182;ENST00000356017;ENST00000457662;ENST00000298772	T;T;T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11;1.11;1.11	5.4	5.4	0.78164	Zinc finger, B-box (3);	0.000000	0.85682	D	0.000000	T	0.33644	0.0870	L	0.37800	1.135	0.47994	D	0.999563	P;P	0.39094	0.659;0.607	B;B	0.34873	0.191;0.12	T	0.11470	-1.0586	10	0.36615	T	0.2	-6.2555	15.4114	0.74923	0.0:0.0:0.0:1.0	.	128;131	O60858;O60858-3	TRI13_HUMAN;.	L	128;128;128;128;131;128;131	ENSP00000404586:F128L;ENSP00000367425:F128L;ENSP00000412943:F128L;ENSP00000367424:F128L;ENSP00000348299:F131L;ENSP00000399206:F128L;ENSP00000298772:F131L	ENSP00000298772:F131L	F	+	1	0	TRIM13	49484459	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.323000	0.52014	2.041000	0.60428	0.533000	0.62120	TTC	.	.		0.507	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278		C	50586458	T	C	50586458	3	2	190	1	0	0	0	0	1	0	0	0	16503	1609	56	2	397	2	TRIM13	13	50586458	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	7712053	50586458	64583420	121	28197										
OR4N5	390437	hgsc.bcm.edu	37	chr14	20612471	20612471	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agctggcctgcaccaataccTttgtggtggagcttctgatg	12	10	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:20612471T>C	ENST00000333629.1	+	1	577	c.577T>C	c.(577-579)Ttt>Ctt	p.F193L	RNA5SP381_ENST00000516076.1_RNA	NM_001004724.1	NP_001004724.1	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N, member 5	193						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(23)|ovary(1)|skin(2)|urinary_tract(1)	29	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)		CACCAATACCTTTGTGGTGGA	0.532																																					p.F193L		Atlas-SNP	.											.	OR4N5	72	.	0			c.T577C						.						103	85	91					14																	20612471		2203	4300	6503	SO:0001583	missense	390437	exon1			AATACCTTTGTGG		CCDS32031.1	14q11.2	2013-09-23			ENSG00000184394	ENSG00000184394		"GPCR / Class A : Olfactory receptors"	15358	protein-coding gene	gene with protein product							Standard	NM_001004724		Approved		uc010tla.2	Q8IXE1	OTTHUMG00000170784	ENST00000333629.1:c.577T>C	chr14.hg19:g.20612471T>C	ENSP00000332110:p.Phe193Leu	67.0	0.0		72.0	20.0	NM_001004724	Q6IF11	Missense_Mutation	SNP	ENST00000333629.1	hg19	CCDS32031.1	.	.	.	.	.	.	.	.	.	.	T	4.266	0.048476	0.08243	.	.	ENSG00000184394	ENST00000333629	T	0.00137	8.68	3.74	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45126	D	0.000400	T	0.00144	0.0004	L	0.49778	1.585	0.09310	N	1	B	0.18741	0.03	B	0.31751	0.135	T	0.33189	-0.9878	10	0.62326	D	0.03	.	4.9155	0.13844	0.0:0.1081:0.1911:0.7008	.	193	Q8IXE1	OR4N5_HUMAN	L	193	ENSP00000332110:F193L	ENSP00000332110:F193L	F	+	1	0	OR4N5	19682311	0.000000	0.05858	0.577000	0.28562	0.009000	0.06853	-0.484000	0.06528	0.587000	0.29643	-0.291000	0.09656	TTT	.	.		0.532	OR4N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410347.1			C	20612471	T	C	20612471	3	2	190	1	0	0	0	0	1	0	0	0	11088	1609	56	2	579	2	OR4N5	14	20612471	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10		20612471	86737069	122	28198										
OR11H4	390442	hgsc.bcm.edu	37	chr14	20711205	20711205	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cttgagatctggtatgtgtcCtccactattcctaacatgct	7	11	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:20711205C>G	ENST00000315409.2	+	1	308	c.255C>G	c.(253-255)tcC>tcG	p.S85S		NM_001004479.1	NP_001004479.1	Q8NGC9	O11H4_HUMAN	olfactory receptor, family 11, subfamily H, member 4	85						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S85S(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	29	all_cancers(95;0.000888)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0146)		GGTATGTGTCCTCCACTATTC	0.453																																					p.S85S		Atlas-SNP	.											OR11H4,rectum,carcinoma,0,3	OR11H4	63	.	1	Substitution - coding silent(1)	ovary(1)	c.C255G						.						168	162	164					14																	20711205		2203	4300	6503	SO:0001819	synonymous_variant	390442	exon1			TGTGTCCTCCACT		CCDS32034.1	14q11.2	2013-09-24			ENSG00000176198	ENSG00000176198		"GPCR / Class A : Olfactory receptors"	15347	protein-coding gene	gene with protein product							Standard	NM_001004479		Approved		uc010tld.2	Q8NGC9	OTTHUMG00000170852	ENST00000315409.2:c.255C>G	chr14.hg19:g.20711205C>G		137.0	0.0		145.0	12.0	NM_001004479	B2RNQ4|Q6IF07	Silent	SNP	ENST00000315409.2	hg19	CCDS32034.1																																																																																			.	.		0.453	OR11H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410678.1			G	20711205	C	G	20711205	2	3	190	1	0	0	0	0	0	0	0	1	10937	668	24	4		4	OR11H4	14	20711205	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	98734	20711205	86638335	123	28199										
FANCM	57697	hgsc.bcm.edu	37	chr14	45658480	45658480	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ctcagacttcaaacctcagaAtcataatgaagtccagtcta	5	11	5	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:45658480A>G	ENST00000267430.5	+	20	5340	c.5255A>G	c.(5254-5256)aAt>aGt	p.N1752S	FANCM_ENST00000542564.2_Missense_Mutation_p.N1726S	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1752	Interaction with FAAP24 and EME1.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AAACCTCAGAATCATAATGAA	0.398								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.N1752S		Atlas-SNP	.											.	FANCM	225	.	0			c.A5255G						.						125	128	127					14																	45658480		2203	4300	6503	SO:0001583	missense	57697	exon20	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTCAGAATCATAA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.5255A>G	chr14.hg19:g.45658480A>G	ENSP00000267430:p.Asn1752Ser	350.0	0.0		300.0	107.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	1.172	-0.640659	0.03557	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.15952	2.96;2.96;2.38	5.32	0.883	0.19177	.	1.390360	0.04022	N	0.299994	T	0.04634	0.0126	N	0.00972	-1.085	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.35301	-0.9794	10	0.02654	T	1	.	3.8973	0.09144	0.3582:0.1772:0.4645:0.0	.	1726;1752	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	S	1752;1726;1268	ENSP00000267430:N1752S;ENSP00000442493:N1726S;ENSP00000452033:N1268S	ENSP00000267430:N1752S	N	+	2	0	FANCM	44728230	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.183000	0.16919	-0.049000	0.13379	0.477000	0.44152	AAT	.	.		0.398	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45658480	A	G	45658480	3	3	190	1	0	0	0	0	1	0	0	0	5679	101	4	2	5333	2	FANCM	14	45658480	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	24947275	45658480	61691060	124	28200										
SIX6	4990	hgsc.bcm.edu	37	chr14	60976599	60976599	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cccagcaaaaaacgtgagctCgcccaggcaaccggactgac	10	15	0	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:60976599C>A	ENST00000327720.5	+	1	931	c.483C>A	c.(481-483)ctC>ctA	p.L161L		NM_007374.2	NP_031400.2	O95475	SIX6_HUMAN	SIX homeobox 6	161					organ morphogenesis (GO:0009887)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)	p.L161L(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)	11				OV - Ovarian serous cystadenocarcinoma(108;0.088)		AACGTGAGCTCGCCCAGGCAA	0.597																																					p.L161L		Atlas-SNP	.											SIX6,NS,carcinoma,0,1	SIX6	27	.	1	Substitution - coding silent(1)	endometrium(1)	c.C483A						.						49	43	45					14																	60976599		2201	4300	6501	SO:0001819	synonymous_variant	4990	exon1			TGAGCTCGCCCAG	AF141651	CCDS9747.1	14q23.1	2011-06-20	2007-07-13		ENSG00000184302	ENSG00000184302		"Homeoboxes / SINE class"	10892	protein-coding gene	gene with protein product		606326	"sine oculis homeobox (Drosophila) homolog 6", "sine oculis homeobox homolog 6 (Drosophila)"	OPTX2		10512683	Standard	NM_007374		Approved	Six9	uc001xfa.4	O95475	OTTHUMG00000152339	ENST00000327720.5:c.483C>A	chr14.hg19:g.60976599C>A		235.0	0.0		270.0	96.0	NM_007374	Q6NT42|Q9P1X8	Silent	SNP	ENST00000327720.5	hg19	CCDS9747.1																																																																																			.	.		0.597	SIX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276952.2			A	60976599	C	A	60976599	2	1	190	1	0	0	0	0	0	0	0	1	14366	871	31	1		1	SIX6	14	60976599	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	15318119	60976599	46372941	125	28201										
MLH3	27030	hgsc.bcm.edu	37	chr14	75500136	75500136	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ccttaccaatgataagctgcTccagacgtatacgctcatgg	8	12	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:75500136T>A	ENST00000556740.1	-	6	3736	c.3701A>T	c.(3700-3702)gAg>gTg	p.E1234V	MLH3_ENST00000355774.2_Missense_Mutation_p.E1234V|MLH3_ENST00000238662.7_Intron|MLH3_ENST00000544985.1_3'UTR|MLH3_ENST00000556257.1_Intron|MLH3_ENST00000380968.2_Missense_Mutation_p.E180V			Q9UHC1	MLH3_HUMAN	mutL homolog 3	1234					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GATAAGCTGCTCCAGACGTAT	0.473								Mismatch excision repair (MMR)																													p.E1234V		Atlas-SNP	.											.	MLH3	200	.	0			c.A3701T						.						73	58	63					14																	75500136		2203	4300	6503	SO:0001583	missense	27030	exon7			AGCTGCTCCAGAC	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.3701A>T	chr14.hg19:g.75500136T>A	ENSP00000452316:p.Glu1234Val	59.0	0.0		60.0	14.0	NM_001040108	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	hg19	CCDS32123.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.89|16.89	3.246788|3.246788	0.59103|0.59103	.|.	.|.	ENSG00000119684|ENSG00000119684	ENST00000355774;ENST00000380968;ENST00000556740|ENST00000553713	T;T;T|.	0.80566|.	-1.39;-1.39;-1.39|.	5.68|5.68	5.68|5.68	0.88126|0.88126	MutL, C-terminal, dimerisation (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85457|0.85457	0.5701|0.5701	M|M	0.92649|0.92649	3.33|3.33	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.89152|0.89152	0.3524|0.3524	10|5	0.87932|.	D|.	0|.	-15.2893|-15.2893	15.9394|15.9394	0.79743|0.79743	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1234|.	Q9UHC1|.	MLH3_HUMAN|.	V|C	1234;180;1234|258	ENSP00000348020:E1234V;ENSP00000370355:E180V;ENSP00000452316:E1234V|.	ENSP00000348020:E1234V|.	E|S	-|-	2|1	0|0	MLH3|MLH3	74569889|74569889	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.038000|0.038000	0.13279|0.13279	7.458000|7.458000	0.80787|0.80787	2.169000|2.169000	0.68431|0.68431	0.519000|0.519000	0.50382|0.50382	GAG|AGC	.	.		0.473	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		A	75500136	T	A	75500136	3	1	190	1	0	0	0	0	1	0	0	0	9627	1551	54	4	688	4	MLH3	14	75500136	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	14523537	75500136	31849404	126	28202										
C14orf156	81892	hgsc.bcm.edu	37	chr14	78174474	78174474	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gatggcggcctcagcagcgaGaggtgctgcggcgctgcgta	18	11	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:78174474G>A	ENST00000557342.1	+	1	61	c.20G>A	c.(19-21)aGa>aAa	p.R7K	ALKBH1_ENST00000216489.3_5'Flank|SLIRP_ENST00000557623.1_Missense_Mutation_p.R7K|SLIRP_ENST00000238688.5_Missense_Mutation_p.R7K|SLIRP_ENST00000557431.1_Missense_Mutation_p.R7K	NM_001267864.1|NM_031210.5	NP_001254793.1|NP_112487.1	Q9GZT3	SLIRP_HUMAN	SRA stem-loop interacting RNA binding protein	7					mitochondrion morphogenesis (GO:0070584)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of transcription, DNA-templated (GO:0006355)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	acrosomal vesicle (GO:0001669)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|sperm flagellum (GO:0036126)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			kidney(1)|prostate(1)	2						TCAGCAGCGAGAGGTGCTGCG	0.557																																					p.R7K		Atlas-SNP	.											SLIRP,NS,carcinoma,0,1	SLIRP	6	.	0			c.G20A						.						64	65	65					14																	78174474		2203	4300	6503	SO:0001583	missense	81892	exon1			CAGCGAGAGGTGC	AF253980	CCDS9866.1, CCDS58331.1, CCDS73668.1	14q24.3	2013-02-12	2011-06-17	2011-06-17	ENSG00000119705	ENSG00000119705		"RNA binding motif (RRM) containing"	20495	protein-coding gene	gene with protein product		610211	"chromosome 14 open reading frame 156"	C14orf156		16762838	Standard	NM_031210		Approved	DC50	uc001xue.5	Q9GZT3		ENST00000557342.1:c.20G>A	chr14.hg19:g.78174474G>A	ENSP00000450909:p.Arg7Lys	89.0	0.0		93.0	43.0	NM_001267864	J3KMY7	Missense_Mutation	SNP	ENST00000557342.1	hg19	CCDS9866.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.43|10.43	1.347405|1.347405	0.24426|0.24426	.|.	.|.	ENSG00000119705|ENSG00000119705	ENST00000556831|ENST00000557342;ENST00000238688;ENST00000557623;ENST00000557431	.|T;T;T;T	.|0.53857	.|1.02;1.04;1.33;0.6	5.93|5.93	2.05|2.05	0.26809|0.26809	.|.	.|0.367509	.|0.26776	.|N	.|0.022550	T|T	0.27384|0.27384	0.0672|0.0672	N|N	0.16307|0.16307	0.4|0.4	0.09310|0.09310	N|N	1|1	.|B	.|0.09022	.|0.002	.|B	.|0.10450	.|0.005	T|T	0.22277|0.22277	-1.0221|-1.0221	5|10	.|0.07325	.|T	.|0.83	-6.9568|-6.9568	5.6755|5.6755	0.17745|0.17745	0.2371:0.1418:0.6211:0.0|0.2371:0.1418:0.6211:0.0	.|.	.|7	.|Q9GZT3	.|SLIRP_HUMAN	K|K	5|7	.|ENSP00000450909:R7K;ENSP00000238688:R7K;ENSP00000452057:R7K;ENSP00000450849:R7K	.|ENSP00000238688:R7K	E|R	+|+	1|2	0|0	SLIRP|SLIRP	77244227|77244227	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.177000|-0.177000	0.09796|0.09796	0.109000|0.109000	0.17891|0.17891	-0.155000|-0.155000	0.13514|0.13514	GAG|AGA	.	.		0.557	SLIRP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413901.1	NM_031210		A	78174474	G	A	78174474	3	1	190	1	0	0	0	0	1	0	0	0	1756	942	33	3	22	3	C14orf156	14	78174474	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	2674338	78174474	29175066	127	28203										
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105350819	105350819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cgacagcctcagtgacgcagGgacatacaccatcgagaccg	11	14	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:105350819G>A	ENST00000414716.3	+	9	1931	c.1703G>A	c.(1702-1704)gGg>gAg	p.G568E	CEP170B_ENST00000556508.1_Missense_Mutation_p.G498E|CEP170B_ENST00000418279.1_Missense_Mutation_p.G498E|CEP170B_ENST00000453495.1_Missense_Mutation_p.G569E	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	568						cytoplasm (GO:0005737)|microtubule (GO:0005874)											AGTGACGCAGGGACATACACC	0.697																																					p.G568E		Atlas-SNP	.											.	.	.	.	0			c.G1703A						.						6	5	6					14																	105350819		1924	3925	5849	SO:0001583	missense	283638	exon9			ACGCAGGGACATA	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.1703G>A	chr14.hg19:g.105350819G>A	ENSP00000404151:p.Gly568Glu	179.0	0.0		174.0	78.0	NM_001112726	Q2KHR7|Q86TI7	Missense_Mutation	SNP	ENST00000414716.3	hg19	CCDS45175.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799953	0.70567	.	.	ENSG00000099814	ENST00000556508;ENST00000414716;ENST00000453495;ENST00000418279	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	4.26	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.54127	0.1839	M	0.80422	2.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.63510	-0.6621	10	0.87932	D	0	-32.3908	16.6737	0.85273	0.0:0.0:1.0:0.0	.	568;568;498	Q9Y4F5-2;Q9Y4F5;E9PFC1	.;K0284_HUMAN;.	E	498;568;569;498	ENSP00000451249:G498E;ENSP00000404151:G568E;ENSP00000407238:G569E;ENSP00000415006:G498E	ENSP00000404151:G568E	G	+	2	0	KIAA0284	104421864	1.000000	0.71417	0.284000	0.24805	0.299000	0.27559	9.545000	0.98095	1.908000	0.55244	0.313000	0.20887	GGG	.	.		0.697	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		A	105350819	G	A	105350819	3	1	190	1	0	0	0	0	1	0	0	0	8175	1232	43	3	1733	3	KIAA0284	14	105350819	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	27176345	105350819	1998721	128	28204										
GPR176	11245	hgsc.bcm.edu	37	chr15	40093462	40093462	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cccaaggggggaagcagccgCttcttgctgtttcgggtctc	14	12	2	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr15:40093462C>T	ENST00000561100.1	-	3	2284	c.1419G>A	c.(1417-1419)aaG>aaA	p.K473K	RP11-37C7.1_ENST00000558616.1_RNA|GPR176_ENST00000560729.1_5'Flank|GPR176_ENST00000299092.3_Silent_p.K472K|GPR176_ENST00000543580.1_Silent_p.K428K	NM_007223.1	NP_009154.1	Q14439	GP176_HUMAN	G protein-coupled receptor 176	473					G-protein coupled receptor signaling pathway (GO:0007186)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(9)|ovary(2)|pancreas(1)|skin(2)	23		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)		GAAGCAGCCGCTTCTTGCTGT	0.532																																					p.K473K		Atlas-SNP	.											.	GPR176	41	.	0			c.G1419A						.						66	68	67					15																	40093462		2203	4300	6503	SO:0001819	synonymous_variant	11245	exon3			CAGCCGCTTCTTG	BC067106	CCDS10051.1, CCDS61588.1, CCDS61589.1	15q14-q15.1	2012-08-21			ENSG00000166073	ENSG00000166073		"GPCR / Class A : Orphans"	32370	protein-coding gene	gene with protein product		612183				7893747	Standard	NM_007223		Approved	Gm1012	uc010uck.2	Q14439	OTTHUMG00000129873	ENST00000561100.1:c.1419G>A	chr15.hg19:g.40093462C>T		82.0	0.0		116.0	8.0	NM_007223	Q6NXF6	Silent	SNP	ENST00000561100.1	hg19	CCDS10051.1																																																																																			.	.		0.532	GPR176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252117.2	NM_007223		T	40093462	C	T	40093462	2	4	190	1	0	0	0	0	0	0	0	1	6681	796	28	3		3	GPR176	15	40093462	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10		40093462	62437930	129	28205										
CHST14	113189	hgsc.bcm.edu	37	chr15	40763663	40763664	+	Missense_Mutation	DNP	GC	GC	AA													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ccgcgagggcacagcctggcGcgggaaagcccccaagcctg							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr15:40763663_40763664GC>AA	ENST00000306243.5	+	1	504_505	c.251_252GC>AA	c.(250-252)cGC>cAA	p.R84Q	CHST14_ENST00000559991.1_Missense_Mutation_p.R84Q	NM_130468.3	NP_569735.1	Q8NCH0	CHSTE_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 14	84					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|dermatan sulfate proteoglycan metabolic process (GO:0050655)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)|phosphate ion binding (GO:0042301)			cervix(1)|large_intestine(1)|prostate(2)	4		all_cancers(109;2.34e-14)|all_epithelial(112;1.08e-11)|Lung NSC(122;2.95e-09)|all_lung(180;6.03e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;3e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0781)		ACAGCCTGGCGCGGGAAAGCCC	0.733																																					p.R84H|p.R84R		Atlas-SNP	.											.	CHST14	19	.	0			c.G251A|c.C252A						.																																			SO:0001583	missense	113189	exon1			CCTGGCGCGGGAA|CTGGCGCGGGAAA	AF401222	CCDS10059.1	15q15.1	2014-09-17	2007-03-27	2007-03-27	ENSG00000169105	ENSG00000169105		"Sulfotransferases, membrane-bound"	24464	protein-coding gene	gene with protein product		608429	"dermatan 4 sulfotransferase 1"	D4ST1		11470797	Standard	NM_130468		Approved	HD4ST, D4ST-1	uc001zlw.3	Q8NCH0	OTTHUMG00000129985	Exception_encountered	chr15.hg19:g.40763663_40763664delinsAA	ENSP00000307297:p.Arg84Gln	563.0|561.0	0.0		773.0|760.0	258.0|254.0	NM_130468	Q6PJ31|Q6UXA0|Q96P94	Missense_Mutation|Silent	SNP	ENST00000306243.5	hg19	CCDS10059.1																																																																																			.	.		0.733	CHST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252251.1	NM_130468		AA	40763664	GC	AA	40763663	3	1	190	1	0	0	0	0	1	0	0	0	3404	1087	38	1	253	1	CHST14	15	40763663	Missense_Mutation	DNP	GC	TCGA-DD-AADG-01A-11D-A40R-10	670201	40763663	61767729	130	28206										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48063146	48063146	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agagccactcagaaaaggccCatggccatggagcttcaagg	12	11	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr15:48063146C>T	ENST00000316364.5	+	19	2825	c.2386C>T	c.(2386-2388)Cat>Tat	p.H796Y	SEMA6D_ENST00000389432.2_Missense_Mutation_p.H753Y|SEMA6D_ENST00000558014.1_Missense_Mutation_p.H734Y|SEMA6D_ENST00000536845.2_Missense_Mutation_p.H796Y|SEMA6D_ENST00000354744.4_Missense_Mutation_p.H740Y|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000389433.2_Missense_Mutation_p.H777Y|SEMA6D_ENST00000389428.3_Missense_Mutation_p.H721Y|SEMA6D_ENST00000358066.4_Missense_Mutation_p.H734Y|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000537942.1_Missense_Mutation_p.H734Y	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	796					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AGAAAAGGCCCATGGCCATGG	0.537																																					p.H796Y		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C2386T						.						61	65	63					15																	48063146		2198	4297	6495	SO:0001583	missense	80031	exon19			AAGGCCCATGGCC	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.2386C>T	chr15.hg19:g.48063146C>T	ENSP00000324857:p.His796Tyr	142.0	0.0		175.0	11.0	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.300879	0.60195	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428	T;T;T;T;T;T;T;T	0.18016	2.24;2.27;2.27;2.27;2.24;2.24;2.24;2.25	5.19	5.19	0.71726	.	0.655751	0.16337	N	0.218873	T	0.23926	0.0579	L	0.36672	1.1	0.80722	D	1	P;P;P;D	0.54964	0.933;0.883;0.814;0.969	P;P;P;P	0.50440	0.641;0.641;0.589;0.641	T	0.01309	-1.1389	10	0.26408	T	0.33	.	18.8873	0.92383	0.0:1.0:0.0:0.0	.	721;740;796;734	Q8NFY4-3;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;SEM6D_HUMAN;.	Y	734;796;796;777;753;740;734;721	ENSP00000442040:H734Y;ENSP00000446152:H796Y;ENSP00000324857:H796Y;ENSP00000374084:H777Y;ENSP00000374083:H753Y;ENSP00000346786:H740Y;ENSP00000350770:H734Y;ENSP00000374079:H721Y	ENSP00000324857:H796Y	H	+	1	0	SEMA6D	45850438	0.999000	0.42202	0.997000	0.53966	0.925000	0.55904	4.420000	0.59841	2.681000	0.91329	0.655000	0.94253	CAT	.	.		0.537	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		T	48063146	C	T	48063146	3	4	190	1	0	0	0	0	1	0	0	0	14057	594	21	3	2499	3	SEMA6D	15	48063146	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	7299483	48063146	54468246	131	28207										
C16orf11	146325	hgsc.bcm.edu	37	chr16	613776	613776	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cagtgggctcctgcctgagtCgtggaagccggggatgggag	19	9	0	1	rs368085414		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr16:613776C>A	ENST00000409413.3	+	2	761	c.482C>A	c.(481-483)tCg>tAg	p.S161*		NM_145270.2	NP_660313.1	P0CG20	PRR35_HUMAN		161	Pro-rich.									central_nervous_system(1)|endometrium(1)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10						CTGCCTGAGTCGTGGAAGCCG	0.741																																					p.S161X		Atlas-SNP	.											.	C16orf11	27	.	0			c.C482A						.						4	5	5					16																	613776		1783	3930	5713	SO:0001587	stop_gained	146325	exon2			CTGAGTCGTGGAA																												ENST00000409413.3:c.482C>A	chr16.hg19:g.613776C>A	ENSP00000386499:p.Ser161*	67.0	0.0		64.0	5.0	NM_145270	B8ZZ27|Q8N233|Q96AX3|Q96S23	Nonsense_Mutation	SNP	ENST00000409413.3	hg19	CCDS45365.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.930759	0.92389	.	.	ENSG00000161992	ENST00000409413	.	.	.	4.96	0.245	0.15512	.	1.194090	0.06296	N	0.700005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.1771	0.31289	0.3994:0.3924:0.2082:0.0	.	.	.	.	X	161	.	ENSP00000386499:S161X	S	+	2	0	C16orf11	553777	0.002000	0.14202	0.029000	0.17559	0.289000	0.27227	0.499000	0.22546	0.460000	0.27045	0.563000	0.77884	TCG	.	.		0.741	C16orf11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000333913.1			A	613776	C	A	613776	4	1	190	1	0	0	0	0	0	1	0	0	1812	893	31	1	484	1	C16orf11	16	613776	Nonsense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10		613776	89740977	132	28208										
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11217616	11217616	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	caggacatgcaggtgactggCgtggaggacgacagccgtgc	17	10	0	1	rs200993240		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr16:11217616C>T	ENST00000409790.1	+	21	2516	c.2286C>T	c.(2284-2286)ggC>ggT	p.G762G	CLEC16A_ENST00000465491.1_3'UTR|CLEC16A_ENST00000381822.2_5'Flank|CLEC16A_ENST00000409552.3_Silent_p.G744G	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						AGGTGACTGGCGTGGAGGACG	0.577																																					p.G762G		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2286T						.						79	86	84					16																	11217616		2141	4240	6381	SO:0001819	synonymous_variant	23274	exon20			GACTGGCGTGGAG	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2286C>T	chr16.hg19:g.11217616C>T		49.0	0.0		70.0	12.0	NM_015226		Silent	SNP	ENST00000409790.1	hg19	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	C	8.075	0.771132	0.16051	.	.	ENSG00000038532	ENST00000428742	.	.	.	5.55	-11.1	0.00147	.	.	.	.	.	T	0.40522	0.1120	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50583	-0.8811	4	.	.	.	-16.5506	4.4251	0.11498	0.2912:0.0882:0.0612:0.5594	.	.	.	.	V	6	.	.	A	+	2	0	CLEC16A	11125117	0.003000	0.15002	0.044000	0.18714	0.922000	0.55478	-1.222000	0.02965	-3.244000	0.00206	-1.251000	0.01509	GCG	.	.		0.577	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		T	11217616	C	T	11217616	2	4	190	1	0	0	0	0	0	0	0	1	3502	755	27	1		1	CLEC16A	16	11217616	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	10603840	11217616	79137137	133	28209										
TBX6	6911	hgsc.bcm.edu	37	chr16	30097548	30097548	+	Nonstop_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gaggggcccagcagtggttcAgtacatgggtttggagccca	16	9	1	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr16:30097548A>C	ENST00000395224.2	-	9	1368	c.1309T>G	c.(1309-1311)Tga>Gga	p.*437G	TBX6_ENST00000279386.2_Nonstop_Mutation_p.*437G	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	0					anatomical structure morphogenesis (GO:0009653)|cell fate specification (GO:0001708)|mesoderm development (GO:0007498)|mesoderm formation (GO:0001707)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	9						GCAGTGGTTCAGTACATGGGT	0.657																																					p.X437G		Atlas-SNP	.											.	TBX6	29	.	0			c.T1309G						.						45	51	49					16																	30097548		2197	4300	6497	SO:0001578	stop_lost	6911	exon9			TGGTTCAGTACAT	AJ007989	CCDS10670.1	16p11.2	2008-02-05			ENSG00000149922	ENSG00000149922		"T-boxes"	11605	protein-coding gene	gene with protein product		602427				9888994, 9933572	Standard	NM_004608		Approved		uc010veh.2	O95947	OTTHUMG00000132115	ENST00000395224.2:c.1309T>G	chr16.hg19:g.30097548A>C	ENSP00000378650:p.*437Argext*81	139.0	0.0		169.0	37.0	NM_004608	Q8TAS4|Q9HA44	Missense_Mutation	SNP	ENST00000395224.2	hg19	CCDS10670.1	.	.	.	.	.	.	.	.	.	.	A	6.243	0.412985	0.11812	.	.	ENSG00000149922	ENST00000395224;ENST00000279386	.	.	.	4.69	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.1969	0.54303	1.0:0.0:0.0:0.0	.	.	.	.	G	437	.	.	X	-	1	0	TBX6	30005049	1.000000	0.71417	0.997000	0.53966	0.020000	0.10135	3.003000	0.49505	1.989000	0.58080	0.449000	0.29647	TGA	.	.		0.657	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758		C	30097548	A	C	30097548	4	2	190	1	0	0	0	0	0	0	0	0	15677	201	7	5	5	5	TBX6	16	30097548	Nonstop_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	18879932	30097548	60257205	134	28210										
P2RX1	5023	hgsc.bcm.edu	37	chr17	3806860	3806860	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cgcacctgttgaccttgaagCgtggaaagctgatgctgttc	12	10	0	3	rs367615874		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:3806860C>A	ENST00000225538.3	-	6	864	c.590G>T	c.(589-591)cGc>cTc	p.R197L		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1	197					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ceramide biosynthetic process (GO:0046513)|insemination (GO:0007320)|ion transport (GO:0006811)|neuronal action potential (GO:0019228)|platelet activation (GO:0030168)|positive regulation of ion transport (GO:0043270)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of vascular smooth muscle contraction (GO:0003056)|response to ATP (GO:0033198)|serotonin secretion by platelet (GO:0002554)|signal transduction (GO:0007165)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|vasoconstriction (GO:0042310)	external side of cell outer membrane (GO:0031240)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	13				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		GACCTTGAAGCGTGGAAAGCT	0.607																																					p.R197L		Atlas-SNP	.											.	P2RX1	38	.	0			c.G590T						.						81	81	81					17																	3806860		2203	4300	6503	SO:0001583	missense	5023	exon6			TTGAAGCGTGGAA	X83688	CCDS11040.1	17p13.3	2012-01-17				ENSG00000108405		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8533	protein-coding gene	gene with protein product		600845				8834001	Standard	NM_002558		Approved	P2X1	uc002fww.3	P51575		ENST00000225538.3:c.590G>T	chr17.hg19:g.3806860C>A	ENSP00000225538:p.Arg197Leu	29.0	0.0		24.0	15.0	NM_002558	Q9UK84	Missense_Mutation	SNP	ENST00000225538.3	hg19	CCDS11040.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.270514	0.59540	.	.	ENSG00000108405	ENST00000225538	T	0.04119	3.7	5.56	5.56	0.83823	.	0.265230	0.37393	N	0.002101	T	0.03915	0.0110	N	0.16266	0.395	0.37740	D	0.92558	B	0.19817	0.039	B	0.18561	0.022	T	0.48670	-0.9015	10	0.36615	T	0.2	-2.7716	11.84	0.52348	0.0:0.9116:0.0:0.0884	.	197	P51575	P2RX1_HUMAN	L	197	ENSP00000225538:R197L	ENSP00000225538:R197L	R	-	2	0	P2RX1	3753609	0.920000	0.31207	1.000000	0.80357	0.994000	0.84299	0.035000	0.13797	2.608000	0.88229	0.655000	0.94253	CGC	.	.		0.607	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1	NM_002558		A	3806860	C	A	3806860	3	1	190	1	0	0	0	0	1	0	0	0	11348	768	27	1	637	1	P2RX1	17	3806860	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10		3806860	77388350	135	28211										
SMCR8	140775	hgsc.bcm.edu	37	chr17	18220404	18220404	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	caagatggagcaggaactggGagatgaggagtacaaggaag	17	4	0	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:18220404G>A	ENST00000406438.3	+	1	1781	c.1301G>A	c.(1300-1302)gGa>gAa	p.G434E	TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	434						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						CAGGAACTGGGAGATGAGGAG	0.448																																					p.G434E		Atlas-SNP	.											.	SMCR8	62	.	0			c.G1301A						.						115	108	110					17																	18220404		2203	4300	6503	SO:0001583	missense	140775	exon1			AACTGGGAGATGA	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.1301G>A	chr17.hg19:g.18220404G>A	ENSP00000385025:p.Gly434Glu	131.0	0.0		85.0	12.0	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	hg19	CCDS11195.2	.	.	.	.	.	.	.	.	.	.	g	1.215	-0.628558	0.03610	.	.	ENSG00000176994	ENST00000406438	T	0.21361	2.01	5.8	2.74	0.32292	.	0.123741	0.53938	N	0.000047	T	0.14743	0.0356	L	0.53249	1.67	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.24225	-1.0166	10	0.15952	T	0.53	-35.0175	2.8074	0.05431	0.3239:0.0:0.4621:0.214	.	434	Q8TEV9	SMCR8_HUMAN	E	434	ENSP00000385025:G434E	ENSP00000385025:G434E	G	+	2	0	SMCR8	18161129	0.998000	0.40836	0.006000	0.13384	0.920000	0.55202	1.494000	0.35616	0.785000	0.33685	-0.119000	0.15052	GGA	.	.		0.448	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		A	18220404	G	A	18220404	3	1	190	1	0	0	0	0	1	0	0	0	14807	1174	41	3	1303	3	SMCR8	17	18220404	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	14413544	18220404	62974806	136	28212										
SUZ12	23512	hgsc.bcm.edu	37	chr17	30320261	30320261	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ataaaagtgtatgttttcagCtgttaaagaatcattgacta	7	4	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:30320261C>T	ENST00000322652.5	+	11	1431	c.1202C>T	c.(1201-1203)gCt>gTt	p.A401V	SUZ12_ENST00000580398.1_Splice_Site_p.A378V	NM_015355.2	NP_056170.2	Q15022	SUZ12_HUMAN	SUZ12 polycomb repressive complex 2 subunit	401					histone ubiquitination (GO:0016574)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)		SSH2/SUZ12(2)|JAZF1/SUZ12(133)	breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(5)|skin(1)	21		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				ATGTTTTCAGCTGTTAAAGAA	0.254			T	JAZF1	endometrial stromal tumours																																p.A401V		Atlas-SNP	.		Dom	yes		17	17q11.2	23512	suppressor of zeste 12 homolog (Drosophila)		M	.	SUZ12	61	.	0			c.C1202T						.						33	34	34					17																	30320261		2189	4278	6467	SO:0001630	splice_region_variant	23512	exon11			TTTCAGCTGTTAA	D63881	CCDS11270.1	17q21	2013-06-05	2013-06-05		ENSG00000178691	ENSG00000178691		"Zinc fingers, C2H2-type"	17101	protein-coding gene	gene with protein product		606245	"suppressor of zeste 12 homolog (Drosophila)"			8590280, 11371647, 18784248	Standard	NM_015355		Approved	JJAZ1, KIAA0160, CHET9	uc002hgs.2	Q15022	OTTHUMG00000132813	ENST00000322652.5:c.1202-1C>T	chr17.hg19:g.30320261C>T		633.0	0.0		457.0	27.0	NM_015355	Q96BD9	Missense_Mutation	SNP	ENST00000322652.5	hg19	CCDS11270.1	.	.	.	.	.	.	.	.	.	.	c	16.14	3.038045	0.54896	.	.	ENSG00000178691	ENST00000322652	T	0.48201	0.82	5.18	5.18	0.71444	.	0.153345	0.56097	D	0.000023	T	0.56804	0.2010	L	0.29908	0.895	0.80722	D	1	B;D	0.63880	0.267;0.993	B;D	0.65443	0.058;0.935	T	0.52373	-0.8584	9	.	.	.	.	19.097	0.93257	0.0:1.0:0.0:0.0	.	401;401	A8K1U9;Q15022	.;SUZ12_HUMAN	V	401	ENSP00000316578:A401V	.	A	+	2	0	SUZ12	27344374	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	5.459000	0.66685	2.592000	0.87571	0.644000	0.83932	GCT	.	.		0.254	SUZ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256260.2	NM_015355	Missense_Mutation	T	30320261	C	T	30320261	5	4	190	1	0	0	0	0	0	0	1	0	15431	811	28	3	1244	3	SUZ12	17	30320261	Splice_Site	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	12099857	30320261	50874949	137	28213										
LUC7L3	51747	hgsc.bcm.edu	37	chr17	48817694	48817694	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgaaaaaattcatgatgaaaAtctacgaaaacagtaagtta	6	4	2	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:48817694A>T	ENST00000505658.1	+	3	383	c.194A>T	c.(193-195)aAt>aTt	p.N65I	LUC7L3_ENST00000240304.1_Missense_Mutation_p.N65I|LUC7L3_ENST00000544170.1_5'UTR|LUC7L3_ENST00000393227.2_Missense_Mutation_p.N65I			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	65					mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						CATGATGAAAATCTACGAAAA	0.328																																					p.N65I		Atlas-SNP	.											.	LUC7L3	32	.	0			c.A194T						.						103	104	104					17																	48817694		2203	4300	6503	SO:0001583	missense	51747	exon3			ATGAAAATCTACG		CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"cisplatin resistance associated overexpressed protein", "CRE-associated protein"	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.194A>T	chr17.hg19:g.48817694A>T	ENSP00000425092:p.Asn65Ile	94.0	0.0		119.0	65.0	NM_006107	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Missense_Mutation	SNP	ENST00000505658.1	hg19	CCDS11573.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.835289	0.71373	.	.	ENSG00000108848	ENST00000505658;ENST00000393227;ENST00000240304;ENST00000542316;ENST00000505619	T;T;T;T	0.44083	1.23;1.23;1.23;0.93	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.56761	0.2007	L	0.46741	1.465	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.81914	0.995;0.995	T	0.54146	-0.8337	10	0.38643	T	0.18	-21.411	14.7778	0.69743	1.0:0.0:0.0:0.0	.	65;65	O95232;A8K3C5	LC7L3_HUMAN;.	I	65;65;65;65;114	ENSP00000425092:N65I;ENSP00000376919:N65I;ENSP00000240304:N65I;ENSP00000420933:N114I	ENSP00000240304:N65I	N	+	2	0	LUC7L3	46172693	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	8.296000	0.89940	2.149000	0.67028	0.477000	0.44152	AAT	.	.		0.328	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424		T	48817694	A	T	48817694	3	4	190	1	0	0	0	0	1	0	0	0	9093	101	4	4	204	4	LUC7L3	17	48817694	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	18497433	48817694	32377516	138	28214										
VEZF1	7716	hgsc.bcm.edu	37	chr17	56060489	56060489	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tctttggccgggacaccaacTtgatccctgtgtggcaggat	12	11	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:56060489T>G	ENST00000581208.1	-	2	339	c.299A>C	c.(298-300)aAg>aCg	p.K100T	VEZF1_ENST00000584396.1_Missense_Mutation_p.K91T	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	100					angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						GGACACCAACTTGATCCCTGT	0.522																																					p.K100T		Atlas-SNP	.											.	VEZF1	50	.	0			c.A299C						.						100	100	100					17																	56060489		2203	4300	6503	SO:0001583	missense	7716	exon2			ACCAACTTGATCC	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"Zinc fingers, C2H2-type"	12949	protein-coding gene	gene with protein product		606747	"zinc finger protein 161"	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.299A>C	chr17.hg19:g.56060489T>G	ENSP00000462337:p.Lys100Thr	80.0	0.0		97.0	27.0	NM_007146		Missense_Mutation	SNP	ENST00000581208.1	hg19	CCDS32687.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.937276	0.73557	.	.	ENSG00000136451	ENST00000258963	.	.	.	5.48	5.48	0.80851	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.64605	0.2613	L	0.27053	0.805	0.80722	D	1	D	0.57899	0.981	D	0.67900	0.954	T	0.69135	-0.5225	9	0.87932	D	0	-8.5753	15.5805	0.76432	0.0:0.0:0.0:1.0	.	100	Q14119	VEZF1_HUMAN	T	100	.	ENSP00000258963:K100T	K	-	2	0	VEZF1	53415488	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.690000	0.84178	2.094000	0.63399	0.523000	0.50628	AAG	.	.		0.522	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1			G	56060489	T	G	56060489	3	3	190	1	0	0	0	0	1	0	0	0	17170	1609	56	5	1286	5	VEZF1	17	56060489	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	7242795	56060489	25134721	139	28215										
RPTOR	57521	hgsc.bcm.edu	37	chr17	78704430	78704430	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gggcagcccgtcgatcttcgTctacgactgctccaatgctg	11	14	2	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:78704430T>C	ENST00000306801.3	+	5	940	c.578T>C	c.(577-579)gTc>gCc	p.V193A	RPTOR_ENST00000570891.1_Missense_Mutation_p.V193A|RPTOR_ENST00000537330.1_Missense_Mutation_p.V8A|RPTOR_ENST00000544334.2_Missense_Mutation_p.V193A	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	193					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						TCGATCTTCGTCTACGACTGC	0.542																																					p.V193A		Atlas-SNP	.											RPTOR,caecum,carcinoma,0,1	RPTOR	122	.	0			c.T578C						.						138	100	113					17																	78704430		2203	4300	6503	SO:0001583	missense	57521	exon5			TCTTCGTCTACGA		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.578T>C	chr17.hg19:g.78704430T>C	ENSP00000307272:p.Val193Ala	66.0	0.0		83.0	27.0	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	hg19	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.255592	0.59321	.	.	ENSG00000141564	ENST00000537330;ENST00000306801;ENST00000544334	T;T	0.63913	-0.07;-0.02	4.77	4.77	0.60923	.	0.000000	0.64402	D	0.000001	D	0.82930	0.5144	M	0.93678	3.445	0.80722	D	1	P;P;D	0.76494	0.954;0.946;0.999	D;P;D	0.67900	0.954;0.592;0.925	D	0.87850	0.2657	10	0.87932	D	0	.	14.4433	0.67333	0.0:0.0:0.0:1.0	.	193;8;193	F5H7J5;F5GXV9;Q8N122	.;.;RPTOR_HUMAN	A	8;193;193	ENSP00000307272:V193A;ENSP00000442479:V193A	ENSP00000307272:V193A	V	+	2	0	RPTOR	76319025	1.000000	0.71417	0.988000	0.46212	0.341000	0.28922	7.772000	0.85439	1.980000	0.57719	0.533000	0.62120	GTC	.	.		0.542	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		C	78704430	T	C	78704430	3	2	190	1	0	0	0	0	1	0	0	0	13680	1667	58	2	596	2	RPTOR	17	78704430	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	22643941	78704430	2490780	140	28216										
FSCN2	25794	hgsc.bcm.edu	37	chr17	79495626	79495626	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gtcaacgacactgaccgctaCctgacagctgagagcttcgg	11	13	1	3			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:79495626C>T	ENST00000417245.2	+	1	205	c.69C>T	c.(67-69)taC>taT	p.Y23Y	FSCN2_ENST00000334850.7_Silent_p.Y23Y|RP13-766D20.2_ENST00000430912.1_RNA|RP13-766D20.2_ENST00000442532.1_RNA	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	23					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|anatomical structure morphogenesis (GO:0009653)|eye photoreceptor cell development (GO:0042462)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|stereocilium (GO:0032420)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			endometrium(1)|lung(1)|prostate(1)|urinary_tract(1)	4	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			CTGACCGCTACCTGACAGCTG	0.637																																					p.Y23Y		Atlas-SNP	.											.	FSCN2	35	.	0			c.C69T						.						27	29	28					17																	79495626		2083	4208	6291	SO:0001819	synonymous_variant	25794	exon1			CCGCTACCTGACA	AF030165	CCDS45810.1, CCDS45811.1	17q25	2014-02-03	2014-02-03		ENSG00000186765	ENSG00000186765		"Fascins"	3960	protein-coding gene	gene with protein product		607643	"fascin (Strongylocentrotus purpuratus) homolog 2 (actin-bundling protein, retinal)", "fascin homolog 2, actin-bundling protein, retinal (Strongylocentrotus purpuratus)"			10234509	Standard	NM_012418		Approved	RP30, RFSN	uc010wuo.2	O14926	OTTHUMG00000167477	ENST00000417245.2:c.69C>T	chr17.hg19:g.79495626C>T		143.0	0.0		211.0	59.0	NM_001077182	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	hg19	CCDS45811.1																																																																																			.	.		0.637	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418		T	79495626	C	T	79495626	2	4	190	1	0	0	0	0	0	0	0	1	6076	518	18	3		3	FSCN2	17	79495626	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	791196	79495626	1699584	141	28217										
FASN	2194	hgsc.bcm.edu	37	chr17	80038048	80038048	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	catgtccgtgaactgctgcaCgaagaagcatatggcctccg	11	12	0	2	rs147197890		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:80038048C>G	ENST00000306749.2	-	41	7332	c.7114G>C	c.(7114-7116)Gtg>Ctg	p.V2372L	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2372	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	AACTGCTGCACGAAGAAGCAT	0.612																																					p.V2372L	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G7114C						.						133	115	121					17																	80038048		2202	4300	6502	SO:0001583	missense	2194	exon41			GCTGCACGAAGAA	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.7114G>C	chr17.hg19:g.80038048C>G	ENSP00000304592:p.Val2372Leu	79.0	0.0		103.0	49.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	8.317	0.823405	0.16678	.	.	ENSG00000169710	ENST00000306749	T	0.25414	1.8	4.68	-0.893	0.10567	Fatty acid synthase, domain 2 (1);Thioesterase (1);	0.494333	0.19981	N	0.101766	T	0.11495	0.0280	N	0.17474	0.49	0.34609	D	0.71739	B	0.09022	0.002	B	0.10450	0.005	T	0.21075	-1.0256	10	0.22109	T	0.4	-5.6822	5.308	0.15815	0.0:0.4874:0.1343:0.3783	.	2372	P49327	FAS_HUMAN	L	2372	ENSP00000304592:V2372L	ENSP00000304592:V2372L	V	-	1	0	FASN	77631337	0.819000	0.29175	0.879000	0.34478	0.495000	0.33615	-0.030000	0.12308	-0.272000	0.09259	0.591000	0.81541	GTG	.	C|1.000;T|0.000		0.612	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		G	80038048	C	G	80038048	3	3	190	1	0	0	0	0	1	0	0	0	5691	536	19	4	433	4	FASN	17	80038048	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	542422	80038048	1157162	142	28218										
DSC1	1823	hgsc.bcm.edu	37	chr18	28719849	28719849	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	atcttcatcccctaacttctGatacctaatttttagaaatc	2	11	3	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr18:28719849G>A	ENST00000257198.5	-	11	1786	c.1525C>T	c.(1525-1527)Cag>Tag	p.Q509*	DSC1_ENST00000257197.3_Nonsense_Mutation_p.Q509*|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	509	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CCTAACTTCTGATACCTAATT	0.294																																					p.Q509X		Atlas-SNP	.											.	DSC1	240	.	0			c.C1525T						.						39	39	39					18																	28719849		2202	4296	6498	SO:0001587	stop_gained	1823	exon11			ACTTCTGATACCT	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"Cadherins / Major cadherins"	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1525C>T	chr18.hg19:g.28719849G>A	ENSP00000257198:p.Gln509*	119.0	0.0		110.0	44.0	NM_004948	Q9HB01	Nonsense_Mutation	SNP	ENST00000257198.5	hg19	CCDS11894.1	.	.	.	.	.	.	.	.	.	.	G	36	5.627017	0.96671	.	.	ENSG00000134765	ENST00000257197;ENST00000257198	.	.	.	5.59	-7.33	0.01431	.	1.130530	0.06668	N	0.765600	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	15.1612	0.72788	0.0:0.0603:0.6806:0.2591	.	.	.	.	X	509	.	ENSP00000257197:Q509X	Q	-	1	0	DSC1	26973847	0.010000	0.17322	0.039000	0.18376	0.703000	0.40648	-0.498000	0.06420	-1.044000	0.03254	-1.350000	0.01237	CAG	.	.		0.294	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421		A	28719849	G	A	28719849	4	1	190	1	0	0	0	0	0	1	0	0	4767	1299	45	3	1223	3	DSC1	18	28719849	Nonsense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10		28719849	49357399	143	28219										
DSG3	1830	hgsc.bcm.edu	37	chr18	29052251	29052251	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttttgtttttcactagtggcCccccttctgctgttgacctg	8	12	2	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr18:29052251C>T	ENST00000257189.4	+	13	1985	c.1902C>T	c.(1900-1902)gcC>gcT	p.A634A		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	634					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CACTAGTGGCCCCCCTTCTGC	0.403																																					p.A634A		Atlas-SNP	.											.	DSG3	172	.	0			c.C1902T						.						92	97	95					18																	29052251		2203	4300	6503	SO:0001819	synonymous_variant	1830	exon13			AGTGGCCCCCCTT	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.1902C>T	chr18.hg19:g.29052251C>T		104.0	0.0		96.0	27.0	NM_001944	A8K2V2	Silent	SNP	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.403	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		T	29052251	C	T	29052251	2	4	190	1	0	0	0	0	0	0	0	1	4780	610	22	3		3	DSG3	18	29052251	Silent	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	332402	29052251	49024997	144	28220										
NFATC1	4772	hgsc.bcm.edu	37	chr18	77208981	77208981	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gccggagaacagcatgcgagCcgtgtaagccgcgggggacc	17	12	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr18:77208981C>A	ENST00000427363.2	+	4	1586	c.1586C>A	c.(1585-1587)gCc>gAc	p.A529D	NFATC1_ENST00000253506.5_Missense_Mutation_p.A529D|NFATC1_ENST00000318065.5_Missense_Mutation_p.A516D|NFATC1_ENST00000592223.1_Missense_Mutation_p.A516D|NFATC1_ENST00000586434.1_Missense_Mutation_p.A516D|NFATC1_ENST00000397790.2_Missense_Mutation_p.A57D|NFATC1_ENST00000587635.1_Missense_Mutation_p.A529D|NFATC1_ENST00000542384.1_Missense_Mutation_p.A529D|NFATC1_ENST00000591814.1_Missense_Mutation_p.A529D|NFATC1_ENST00000329101.4_Missense_Mutation_p.A516D|NFATC1_ENST00000545796.1_Missense_Mutation_p.A57D			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	529	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	AGCATGCGAGCCGTGTAAGCC	0.692																																					p.A529D	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C1586A						.						37	32	33					18																	77208981		2200	4297	6497	SO:0001583	missense	4772	exon4			TGCGAGCCGTGTA	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"Nuclear factor of activated T-cells"	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.1586C>A	chr18.hg19:g.77208981C>A	ENSP00000389377:p.Ala529Asp	95.0	0.0		86.0	42.0	NM_006162	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	hg19		.	.	.	.	.	.	.	.	.	.	C	22.2	4.256904	0.80246	.	.	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000397790;ENST00000542384;ENST00000329101;ENST00000545796;ENST00000427363;ENST00000397794	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	4.97	4.97	0.65823	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.054535	0.64402	D	0.000001	T	0.70850	0.3271	M	0.79123	2.44	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D	0.87578	0.99;0.99;0.986;0.998;0.998;0.996;0.986	T	0.75766	-0.3202	10	0.87932	D	0	-29.192	18.2452	0.89982	0.0:1.0:0.0:0.0	.	516;516;529;529;529;516;529	B5B2M7;B5B2N1;B5B2M6;O95644;B5B2M4;B5B2M5;Q2M1S3	.;.;.;NFAC1_HUMAN;.;.;.	D	529;529;57;529;516;57;516;493	ENSP00000253506:A529D;ENSP00000380892:A57D;ENSP00000442435:A529D;ENSP00000327850:A516D;ENSP00000439992:A57D	ENSP00000253506:A529D	A	+	2	0	NFATC1	75309969	1.000000	0.71417	0.670000	0.29842	0.547000	0.35210	7.450000	0.80656	2.301000	0.77427	0.655000	0.94253	GCC	.	.		0.692	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390		A	77208981	C	A	77208981	3	1	190	1	0	0	0	0	1	0	0	0	10370	739	26	3	1692	3	NFATC1	18	77208981	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	48156730	77208981	868267	145	28221										
RANBP3	8498	hgsc.bcm.edu	37	chr19	5925741	5925741	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cggcttcgtccacgctctcaTttatcagctgggaatgagac	10	12	2	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:5925741T>A	ENST00000340578.6	-	10	878	c.821A>T	c.(820-822)aAt>aTt	p.N274I	RANBP3_ENST00000034275.8_Missense_Mutation_p.N206I|RANBP3_ENST00000439268.2_Missense_Mutation_p.N269I|RANBP3_ENST00000591092.1_Missense_Mutation_p.N201I|RANBP3_ENST00000541471.1_Missense_Mutation_p.N146I	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3	274					intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						CACGCTCTCATTTATCAGCTG	0.577																																					p.N274I		Atlas-SNP	.											.	RANBP3	36	.	0			c.A821T						.						64	69	67					19																	5925741		2066	4189	6255	SO:0001583	missense	8498	exon10			CTCTCATTTATCA	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4		ENST00000340578.6:c.821A>T	chr19.hg19:g.5925741T>A	ENSP00000341483:p.Asn274Ile	33.0	0.0		25.0	8.0	NM_007322	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	hg19	CCDS42478.1	.	.	.	.	.	.	.	.	.	.	T	12.67	2.008564	0.35415	.	.	ENSG00000031823	ENST00000340578;ENST00000439268;ENST00000034275;ENST00000324807;ENST00000541471	T;T;T;T	0.32272	1.46;1.46;2.21;1.48	5.19	3.09	0.35607	.	0.706833	0.13753	N	0.365158	T	0.21103	0.0508	L	0.40543	1.245	0.09310	N	1	B;B;B;B;B;P;B	0.34977	0.33;0.346;0.222;0.138;0.216;0.478;0.346	B;B;B;B;B;B;B	0.29716	0.045;0.08;0.049;0.049;0.106;0.106;0.08	T	0.12091	-1.0561	10	0.41790	T	0.15	-6.5517	6.3179	0.21200	0.0:0.1931:0.0:0.8069	.	146;269;146;201;206;269;274	F5H4C2;Q53GE1;B7Z5P4;B7Z7F3;Q9H6Z4-3;Q9H6Z4-2;Q9H6Z4	.;.;.;.;.;.;RANB3_HUMAN	I	274;269;206;205;146	ENSP00000341483:N274I;ENSP00000404837:N269I;ENSP00000034275:N206I;ENSP00000445071:N146I	ENSP00000034275:N206I	N	-	2	0	RANBP3	5876741	0.002000	0.14202	0.001000	0.08648	0.024000	0.10985	1.038000	0.30254	0.919000	0.36945	0.459000	0.35465	AAT	.	.		0.577	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322		A	5925741	T	A	5925741	3	1	190	1	0	0	0	0	1	0	0	0	13044	1493	52	4	914	4	RANBP3	19	5925741	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10		5925741	53203242	146	28222										
TRIP10	9322	hgsc.bcm.edu	37	chr19	6743800	6743800	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ctcaactgcagcgcttcaacCgagaccaagcccacttctat	6	16	3	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:6743800C>T	ENST00000313244.9	+	7	630	c.595C>T	c.(595-597)Cga>Tga	p.R199*	TRIP10_ENST00000313285.8_Nonsense_Mutation_p.R199*|TRIP10_ENST00000600428.1_Nonsense_Mutation_p.R91*|TRIP10_ENST00000596758.1_Nonsense_Mutation_p.R199*			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	199	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						GCGCTTCAACCGAGACCAAGC	0.517																																					p.R199X		Atlas-SNP	.											TRIP10_ENST00000313244,NS,carcinoma,0,2	TRIP10	104	.	0			c.C595T						.						187	171	176					19																	6743800		2203	4300	6503	SO:0001587	stop_gained	9322	exon7			TTCAACCGAGACC	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"Cdc42-interacting protein"	604504	"salt tolerator"	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.595C>T	chr19.hg19:g.6743800C>T	ENSP00000320117:p.Arg199*	130.0	1.0		118.0	35.0	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Nonsense_Mutation	SNP	ENST00000313244.9	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.286356	0.95517	.	.	ENSG00000125733	ENST00000313285;ENST00000313244;ENST00000420690	.	.	.	4.78	3.73	0.42828	.	0.069844	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-6.3457	10.5836	0.45269	0.193:0.807:0.0:0.0	.	.	.	.	X	199	.	ENSP00000320117:R199X	R	+	1	2	TRIP10	6694800	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	1.430000	0.34914	1.121000	0.41925	0.462000	0.41574	CGA	.	.		0.517	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2			T	6743800	C	T	6743800	4	4	190	1	0	0	0	0	0	1	0	0	16569	644	23	1	621	1	TRIP10	19	6743800	Nonsense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	818059	6743800	52385183	147	28223										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10092740	10092740	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttacccccggtcatgactcaCcgacttccctttctctccta	4	18	3	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:10092740C>T	ENST00000264828.3	-	32	2546		c.e32+1			NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3						axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TCATGACTCACCGACTTCCCT	0.532																																					.		Atlas-SNP	.											.	COL5A3	243	.	0			c.2460+1G>A						.						152	133	139					19																	10092740		2203	4300	6503	SO:0001630	splice_region_variant	50509	exon33			GACTCACCGACTT	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.2460+1G>A	chr19.hg19:g.10092740C>T		101.0	0.0		119.0	47.0	NM_015719	Q9NZQ6	Splice_Site	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.149855	0.57151	.	.	ENSG00000080573	ENST00000264828	.	.	.	4.48	4.48	0.54585	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6721	0.68951	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL5A3	9953740	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	4.128000	0.57951	2.027000	0.59764	0.313000	0.20887	.	.	.		0.532	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	Intron	T	10092740	C	T	10092740	5	4	190	1	0	0	0	0	0	0	1	0	3700	521	18	3	2920	3	COL5A3	19	10092740	Splice_Site	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	3348940	10092740	49036243	148	28224										
LOC55908	55908	hgsc.bcm.edu	37	chr19	11350417	11350428	+	In_Frame_Del	DEL	TGACCCTGCTCT	TGACCCTGCTCT	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	actggcacagcatgaggagcTgaccctgctcttccatggga							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	TGACCCTGCTCT	TGACCCTGCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:11350417_11350428delTGACCCTGCTCT	ENST00000252453.8	+	1	123_134	c.104_115delTGACCCTGCTCT	c.(103-117)ctgaccctgctcttc>ctc	p.TLLF36del	DOCK6_ENST00000319867.7_5'Flank|DOCK6_ENST00000294618.7_Intron|C19orf80_ENST00000591200.1_Intron	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	36					cellular lipid metabolic process (GO:0044255)|glucose metabolic process (GO:0006006)|positive regulation of protein processing (GO:0010954)|regulation of lipoprotein metabolic process (GO:0050746)|triglyceride homeostasis (GO:0070328)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|breast(1)|endometrium(2)	4						CATGAGGAGCTGACCCTGCTCTTCCATGGGAC	0.67																																					p.35_38del		Atlas-INDEL	.											.	C19orf80	8	.	0			c.103_114del						.																																			SO:0001651	inframe_deletion	55908	exon1			.		CCDS54220.1	19p13.2	2014-02-13			ENSG00000130173	ENSG00000130173			24933	protein-coding gene	gene with protein product	"lipasin", "betatrophin"					22809513, 23150577, 24262987	Standard	NM_018687		Approved	TD26, RIFL, ANGPTL8	uc021upg.1	Q6UXH0		ENST00000252453.8:c.104_115delTGACCCTGCTCT	chr19.hg19:g.11350417_11350428delTGACCCTGCTCT	ENSP00000252453:p.Thr36_Phe39del	103.0	0.0		115.0	32.0	NM_018687	Q9NQZ1	In_Frame_Del	DEL	ENST00000252453.8	hg19	CCDS54220.1																																																																																			.	.		0.67	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687		-	11350428	TGACCCTGCTCT	-	11350417	7	5	190	1	0	1	0	1	0	0	0	0	8890	1580	55	0	106	0	LOC55908	19	11350417	In_Frame_Del	DEL	TGACCCTGCTCT	TCGA-DD-AADG-01A-11D-A40R-10	1257677	11350417	47778566	149	28225										
CYP4F3	4051	hgsc.bcm.edu	37	chr19	15758109	15758109	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gaagccctatatgaagatttTcaatgagagtgtgaacatca	9	6	2	4			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:15758109T>C	ENST00000221307.8	+	5	547	c.500T>C	c.(499-501)tTc>tCc	p.F167S	CYP4F3_ENST00000591058.1_Missense_Mutation_p.F167S|CYP4F3_ENST00000586182.2_Missense_Mutation_p.F167S|CYP4F3_ENST00000585846.1_Missense_Mutation_p.F167S	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	167					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)			endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						ATGAAGATTTTCAATGAGAGT	0.507																																					p.F167S		Atlas-SNP	.											.	CYP4F3	69	.	0			c.T500C						.						113	119	117					19																	15758109		2203	4300	6503	SO:0001583	missense	4051	exon5			AGATTTTCAATGA	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"Cytochrome P450s"	2646	protein-coding gene	gene with protein product		601270	"cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.500T>C	chr19.hg19:g.15758109T>C	ENSP00000221307:p.Phe167Ser	111.0	0.0		118.0	8.0	NM_001199209	B7Z8Z3|O60634|Q5U740	Missense_Mutation	SNP	ENST00000221307.8	hg19	CCDS12332.1	.	.	.	.	.	.	.	.	.	.	.	18.52	3.642685	0.67244	.	.	ENSG00000186529	ENST00000538865;ENST00000221307	T	0.69685	-0.42	3.4	3.4	0.38934	.	0.000000	0.64402	U	0.000001	D	0.84969	0.5590	H	0.95574	3.69	0.52099	D	0.999948	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.87298	0.2303	10	0.87932	D	0	.	9.8126	0.40833	0.0:0.0:0.0:1.0	.	167;167	B7Z8Z3;Q08477	.;CP4F3_HUMAN	S	94;167	ENSP00000221307:F167S	ENSP00000221307:F167S	F	+	2	0	CYP4F3	15619109	1.000000	0.71417	0.014000	0.15608	0.969000	0.65631	6.724000	0.74747	1.400000	0.46741	0.358000	0.22013	TTC	.	.		0.507	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		C	15758109	T	C	15758109	3	2	190	1	0	0	0	0	1	0	0	0	4192	1783	62	2	514	2	CYP4F3	19	15758109	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	4407692	15758109	43370874	150	28226										
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19756765	19756765	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tgaccaggcttggctcaaacTccttgtacaagtccacgaac	8	13	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:19756765T>G	ENST00000357324.6	-	24	3304	c.3278A>C	c.(3277-3279)gAg>gCg	p.E1093A	GMIP_ENST00000587238.1_5'Flank|GMIP_ENST00000203556.4_5'Flank|ATP13A1_ENST00000291503.5_Missense_Mutation_p.E975A|GMIP_ENST00000445806.2_5'Flank	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	1093						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						TGGCTCAAACTCCTTGTACAA	0.582																																					p.E1093A	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.A3278C						.						254	220	231					19																	19756765		2203	4300	6503	SO:0001583	missense	57130	exon24			TCAAACTCCTTGT	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"ATPases / P-type"	24215	protein-coding gene	gene with protein product	"cation transporting ATPase"		"ATPase type 13A"	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.3278A>C	chr19.hg19:g.19756765T>G	ENSP00000349877:p.Glu1093Ala	28.0	0.0		28.0	7.0	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Missense_Mutation	SNP	ENST00000357324.6	hg19	CCDS32970.2	.	.	.	.	.	.	.	.	.	.	T	13.80	2.346574	0.41599	.	.	ENSG00000105726	ENST00000291503;ENST00000357324	T;T	0.71698	-0.59;-0.59	5.13	3.01	0.34805	.	0.205916	0.49916	D	0.000132	T	0.64114	0.2569	M	0.65975	2.015	0.46499	D	0.999075	B;B	0.19445	0.01;0.036	B;B	0.20384	0.013;0.029	T	0.56613	-0.7950	10	0.42905	T	0.14	-31.3201	6.2417	0.20795	0.0:0.0864:0.1616:0.752	.	1093;975	Q9HD20;Q9HD20-2	AT131_HUMAN;.	A	975;1093	ENSP00000291503:E975A;ENSP00000349877:E1093A	ENSP00000291503:E975A	E	-	2	0	ATP13A1	19617765	1.000000	0.71417	0.559000	0.28332	0.899000	0.52679	4.745000	0.62125	0.280000	0.22209	0.402000	0.26972	GAG	.	.		0.582	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		G	19756765	T	G	19756765	3	3	190	1	0	0	0	0	1	0	0	0	1123	1551	54	5	348	5	ATP13A1	19	19756765	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	3998656	19756765	39372218	151	28227										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31769256	31769256	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttttgcttaggtttctcgtcAgtgaccgctttctccttgtc	8	11	3	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:31769256A>G	ENST00000240587.4	-	2	1770	c.1443T>C	c.(1441-1443)acT>acC	p.T481T		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	481					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GTTTCTCGTCAGTGACCGCTT	0.478																																					p.T481T		Atlas-SNP	.											.	TSHZ3	549	.	0			c.T1443C						.						184	186	186					19																	31769256		2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CTCGTCAGTGACC	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1443T>C	chr19.hg19:g.31769256A>G		61.0	0.0		70.0	23.0	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	hg19	CCDS12421.2																																																																																			.	.		0.478	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		G	31769256	A	G	31769256	2	3	190	1	0	0	0	0	0	0	0	1	16640	175	7	2		2	TSHZ3	19	31769256	Silent	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	12012491	31769256	27359727	152	28228										
MLL4	9757	hgsc.bcm.edu	37	chr19	36216399	36216399	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gctggtgttctgtcaagtctGctgtgacccattccacccat	9	13	3	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:36216399G>T	ENST00000222270.7	+	12	3662	c.3662G>T	c.(3661-3663)tGc>tTc	p.C1221F	KMT2B_ENST00000420124.1_Missense_Mutation_p.C1221F|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1221					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TGTCAAGTCTGCTGTGACCCA	0.617																																					p.C1221F		Atlas-SNP	.											.	MLL4	229	.	0			c.G3662T						.						209	224	219					19																	36216399		2101	4229	6330	SO:0001583	missense	8085	exon12			AAGTCTGCTGTGA	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.3662G>T	chr19.hg19:g.36216399G>T	ENSP00000222270:p.Cys1221Phe	32.0	0.0		25.0	11.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.459881	0.43736	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.99983	-11.16;-11.16	5.54	5.54	0.83059	Zinc finger, PHD-finger (1);Zinc finger, PHD-type (1);	0.000000	0.49305	D	0.000155	D	0.99984	0.9995	M	0.77313	2.365	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.95146	0.8268	10	0.87932	D	0	.	18.4191	0.90582	0.0:0.0:1.0:0.0	.	1221	Q9UMN6	MLL4_HUMAN	F	1221	ENSP00000222270:C1221F;ENSP00000398837:C1221F	ENSP00000222270:C1221F	C	+	2	0	AD000671.1	40908239	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.077000	0.94016	2.884000	0.98904	0.655000	0.94253	TGC	.	.		0.617	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		T	36216399	G	T	36216399	3	4	190	1	0	0	0	0	1	0	0	0	9632	1319	46	3	3708	3	MLL4	19	36216399	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	4447143	36216399	22912584	153	28229										
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47587632	47587632	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cgcccttccacgaagtacttGcaaatgactttgcctttctt	6	13	1	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:47587632G>T	ENST00000253048.5	-	9	1225	c.1188C>A	c.(1186-1188)tgC>tgA	p.C396*	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	396							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		CGAAGTACTTGCAAATGACTT	0.587																																					p.C396X		Atlas-SNP	.											.	ZC3H4	96	.	0			c.C1188A						.						78	83	81					19																	47587632		2101	4231	6332	SO:0001587	stop_gained	23211	exon9			GTACTTGCAAATG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"Zinc fingers, CCCH-type domain containing"	17808	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 7"	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1188C>A	chr19.hg19:g.47587632G>T	ENSP00000253048:p.Cys396*	62.0	0.0		94.0	4.0	NM_015168	Q9Y420	Nonsense_Mutation	SNP	ENST00000253048.5	hg19	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	G	38	6.933444	0.97944	.	.	ENSG00000130749	ENST00000253048	.	.	.	5.67	4.64	0.57946	.	0.105254	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.923	0.63945	0.0747:0.0:0.9253:0.0	.	.	.	.	X	396	.	ENSP00000253048:C396X	C	-	3	2	ZC3H4	52279472	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.910000	0.69931	1.542000	0.49330	-0.140000	0.14226	TGC	.	.		0.587	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			T	47587632	G	T	47587632	4	4	190	1	0	0	0	0	0	1	0	0	17585	1311	46	3	2751	3	ZC3H4	19	47587632	Nonsense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	11371233	47587632	11541351	154	28230										
SIGLEC6	946	hgsc.bcm.edu	37	chr19	52031019	52031019	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	accctggagcctgagaccatGacggggttcacatcatccgt	11	13	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:52031019G>T	ENST00000425629.3	-	7	1324	c.1170C>A	c.(1168-1170)gtC>gtA	p.V390V	SIGLEC6_ENST00000343300.4_Intron|SIGLEC6_ENST00000474054.1_5'UTR|SIGLEC6_ENST00000391797.3_Intron|SIGLEC6_ENST00000359982.4_Intron|SIGLEC6_ENST00000436458.1_Silent_p.V338V|SIGLEC6_ENST00000346477.3_Silent_p.V374V	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	390					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		CTGAGACCATGACGGGGTTCA	0.493																																					p.V390V		Atlas-SNP	.											.	SIGLEC6	142	.	0			c.C1170A						.						196	196	196					19																	52031019		1959	4154	6113	SO:0001819	synonymous_variant	946	exon7			GACCATGACGGGG	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.1170C>A	chr19.hg19:g.52031019G>T		72.0	0.0		64.0	8.0	NM_001245	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Silent	SNP	ENST00000425629.3	hg19	CCDS12834.3																																																																																			.	.		0.493	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245		T	52031019	G	T	52031019	2	4	190	1	0	0	0	0	0	0	0	1	14327	1277	45	3		3	SIGLEC6	19	52031019	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	4443387	52031019	7097964	155	28231										
PRKCG	5582	hgsc.bcm.edu	37	chr19	54395040	54395040	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	acgaaacagaagacccgaacGgtgaaagccacgctaaaccc	9	13	0	3	rs77550964	byFrequency	TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:54395040G>T	ENST00000263431.3	+	6	924	c.642G>T	c.(640-642)acG>acT	p.T214T	PRKCG_ENST00000536044.1_Silent_p.T214T|PRKCG_ENST00000540413.1_Silent_p.T214T|PRKCG_ENST00000542049.1_Silent_p.T101T	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	214	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	AGACCCGAACGGTGAAAGCCA	0.512																																					p.T214T		Atlas-SNP	.											.	PRKCG	246	.	0			c.G642T						.						136	104	115					19																	54395040		2203	4300	6503	SO:0001819	synonymous_variant	5582	exon6			CCGAACGGTGAAA	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.642G>T	chr19.hg19:g.54395040G>T		131.0	0.0		179.0	70.0	NM_002739	B7Z8Q0	Silent	SNP	ENST00000263431.3	hg19	CCDS12867.1																																																																																			.	G|0.999;A|0.001		0.512	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		T	54395040	G	T	54395040	2	4	190	1	0	0	0	0	0	0	0	1	12524	1103	39	1		1	PRKCG	19	54395040	Silent	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	2364021	54395040	4733943	156	28232										
ZSCAN22	342945	hgsc.bcm.edu	37	chr19	58850111	58850111	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ggaagaccccatatgcctgcAgcgagtgtgggaaagccttc	13	11	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:58850111A>T	ENST00000329665.4	+	3	1042	c.895A>T	c.(895-897)Agc>Tgc	p.S299C		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	299					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|pancreas(1)|prostate(2)	16		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		ATATGCCTGCAGCGAGTGTGG	0.597																																					p.S299C		Atlas-SNP	.											.	ZSCAN22	47	.	0			c.A895T						.						128	134	132					19																	58850111		2203	4300	6503	SO:0001583	missense	342945	exon3			GCCTGCAGCGAGT	M20675	CCDS12975.1	19q13.43	2013-01-08	2006-09-20	2006-09-20				"-", "Zinc fingers, C2H2-type"	4929	protein-coding gene	gene with protein product	"oncogene HKR2"	165260	"zinc finger protein 50", "GLI-Kruppel family member HKR2"	ZNF50, HKR2		2850480, 1505991	Standard	NM_181846		Approved		uc002qsc.2	P10073		ENST00000329665.4:c.895A>T	chr19.hg19:g.58850111A>T	ENSP00000332433:p.Ser299Cys	94.0	0.0		94.0	37.0	NM_181846	Q15922|Q7Z3L8	Missense_Mutation	SNP	ENST00000329665.4	hg19	CCDS12975.1	.	.	.	.	.	.	.	.	.	.	A	7.262	0.605325	0.14002	.	.	ENSG00000182318	ENST00000329665	T	0.08008	3.14	3.8	2.78	0.32641	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11879	0.0289	M	0.75447	2.3	0.09310	N	1	P	0.46020	0.871	B	0.43536	0.423	T	0.25047	-1.0143	9	0.62326	D	0.03	.	3.2886	0.06940	0.6847:0.0:0.1127:0.2025	.	299	P10073	ZSC22_HUMAN	C	299	ENSP00000332433:S299C	ENSP00000332433:S299C	S	+	1	0	ZSCAN22	63541923	0.000000	0.05858	0.299000	0.25016	0.381000	0.30169	-4.570000	0.00214	0.626000	0.30322	0.379000	0.24179	AGC	.	.		0.597	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846		T	58850111	A	T	58850111	3	4	190	1	0	0	0	0	1	0	0	0	18249	188	7	4	901	4	ZSCAN22	19	58850111	Missense_Mutation	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	4455071	58850111	278872	157	28233										
CST9L	128821	hgsc.bcm.edu	37	chr20	23549024	23549024	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ggcatagatcagcaggatctGggagcctaagagaagcagca	14	8	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr20:23549024G>T	ENST00000376979.3	-	1	362	c.64C>A	c.(64-66)Cag>Aag	p.Q22K		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	22						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					AGCAGGATCTGGGAGCCTAAG	0.572																																					p.Q22K		Atlas-SNP	.											.	CST9L	25	.	0			c.C64A						.						106	94	98					20																	23549024		2203	4300	6503	SO:0001583	missense	128821	exon1			GGATCTGGGAGCC		CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"cystatin 9 (mouse)-like"			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.64C>A	chr20.hg19:g.23549024G>T	ENSP00000366178:p.Gln22Lys	83.0	0.0		101.0	40.0	NM_080610	B2R5A1	Missense_Mutation	SNP	ENST00000376979.3	hg19	CCDS13157.1	.	.	.	.	.	.	.	.	.	.	G	6.184	0.402212	0.11696	.	.	ENSG00000101435	ENST00000376979	T	0.13196	2.61	2.03	-1.67	0.08238	.	1.922710	0.03608	N	0.234429	T	0.05960	0.0155	N	0.08118	0	0.09310	N	1	B	0.25007	0.116	B	0.14578	0.011	T	0.26360	-1.0105	10	0.30078	T	0.28	.	1.9722	0.03409	0.3802:0.0:0.3577:0.2622	.	22	Q9H4G1	CST9L_HUMAN	K	22	ENSP00000366178:Q22K	ENSP00000366178:Q22K	Q	-	1	0	CST9L	23497024	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.197000	0.09518	-0.428000	0.07339	0.313000	0.20887	CAG	.	.		0.572	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610		T	23549024	G	T	23549024	3	4	190	1	0	0	0	0	1	0	0	0	3982	1357	47	3	391	3	CST9L	20	23549024	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10		23549024	39476496	158	28234										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57829044	57829044	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tctgcaatctgacacctgccTggcagtggttaatgacgtgc	11	11	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr20:57829044T>C	ENST00000371030.2	+	5	4280	c.4280T>C	c.(4279-4281)cTg>cCg	p.L1427P		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1427							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GACACCTGCCTGGCAGTGGTT	0.522																																					p.L1427P		Atlas-SNP	.											.	ZNF831	287	.	0			c.T4280C						.						81	84	83					20																	57829044		2032	4207	6239	SO:0001583	missense	128611	exon5			CCTGCCTGGCAGT	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.4280T>C	chr20.hg19:g.57829044T>C	ENSP00000360069:p.Leu1427Pro	111.0	0.0		78.0	24.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	T	10.56	1.384367	0.25031	.	.	ENSG00000124203	ENST00000371030	T	0.10860	2.83	5.34	2.99	0.34606	.	0.521716	0.15872	N	0.240474	T	0.12817	0.0311	L	0.38175	1.15	0.09310	N	0.99999	D	0.55385	0.971	P	0.50440	0.641	T	0.15435	-1.0437	10	0.28530	T	0.3	-0.0836	9.5268	0.39169	0.0:0.0:0.3457:0.6543	.	1427	Q5JPB2	ZN831_HUMAN	P	1427	ENSP00000360069:L1427P	ENSP00000360069:L1427P	L	+	2	0	ZNF831	57262439	0.018000	0.18449	0.004000	0.12327	0.003000	0.03518	1.210000	0.32370	0.311000	0.23014	-0.321000	0.08615	CTG	.	.		0.522	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		C	57829044	T	C	57829044	3	2	190	1	0	0	0	0	1	0	0	0	18200	1580	55	2	4298	2	ZNF831	20	57829044	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	34280020	57829044	5196476	159	28235										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19726182	19726182	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttagtttcccaaatagaagcTacaaaataaaataaacaact	3	7	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr21:19726182T>A	ENST00000284885.3	-	9	914		c.e9-2			NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15							brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						AAATAGAAGCTACAAAATAAA	0.333																																					.		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.881-2A>T						.						48	53	51					21																	19726182		2202	4284	6486	SO:0001630	splice_region_variant	5651	exon10			AGAAGCTACAAAA		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.881-2A>T	chr21.hg19:g.19726182T>A		311.0	0.0		304.0	22.0	NM_002772	Q2NKL7	Splice_Site	SNP	ENST00000284885.3	hg19	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	T	13.18	2.158960	0.38119	.	.	ENSG00000154646	ENST00000284885	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9538	0.58415	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMPRSS15	18648053	1.000000	0.71417	0.951000	0.38953	0.424000	0.31475	4.858000	0.62947	1.934000	0.56057	0.528000	0.53228	.	.	.		0.333	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	Intron	A	19726182	T	A	19726182	5	1	190	1	0	0	0	0	0	0	1	0	16261	1536	53	4	2248	4	TMPRSS15	21	19726182	Splice_Site	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10		19726182	28403713	160	28236										
TMPRSS3	64699	hgsc.bcm.edu	37	chr21	43802299	43802299	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gggctggattgtccaacaggGaaactagacccacctggatg	13	10	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr21:43802299G>A	ENST00000291532.3	-	9	1782	c.827C>T	c.(826-828)tCc>tTc	p.S276F	TMPRSS3_ENST00000433957.2_Missense_Mutation_p.S276F|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.S276F|TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.S360F|TMPRSS3_ENST00000398405.1_Missense_Mutation_p.S274F	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	276	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						GTCCAACAGGGAAACTAGACC	0.502																																					p.S276F		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.C827T						.						106	81	89					21																	43802299		2203	4300	6503	SO:0001583	missense	64699	exon9			AACAGGGAAACTA	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"Serine peptidases / Transmembrane"	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.827C>T	chr21.hg19:g.43802299G>A	ENSP00000291532:p.Ser276Phe	95.0	0.0		90.0	27.0	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	hg19	CCDS13686.1	.	.	.	.	.	.	.	.	.	.	G	8.537	0.872348	0.17322	.	.	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	T;D;D;T;D	0.81821	0.17;-1.54;-1.54;0.17;-1.54	4.8	2.98	0.34508	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.358897	0.25762	N	0.028471	T	0.66703	0.2816	L	0.28344	0.845	0.23010	N	0.998432	B;P;B;P	0.47034	0.21;0.646;0.075;0.889	B;B;B;B	0.43575	0.096;0.111;0.063;0.424	T	0.57516	-0.7798	9	.	.	.	.	5.2162	0.15344	0.2401:0.1533:0.6065:0.0	.	276;276;276;274	P57727-3;P57727-5;P57727;B7WPR2	.;.;TMPS3_HUMAN;.	F	276;276;274;360;276	ENSP00000291532:S276F;ENSP00000411013:S276F;ENSP00000381442:S274F;ENSP00000369762:S360F;ENSP00000381434:S276F	.	S	-	2	0	TMPRSS3	42675368	0.998000	0.40836	0.692000	0.30179	0.101000	0.19017	1.938000	0.40203	1.020000	0.39573	-0.137000	0.14449	TCC	.	.		0.502	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1			A	43802299	G	A	43802299	3	1	190	1	0	0	0	0	1	0	0	0	16263	1174	41	3	640	3	TMPRSS3	21	43802299	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	24076117	43802299	4327596	161	28237										
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17073436	17073439	+	Start_Codon_Del	DEL	TCCA	TCCA	-													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	gggctgaagggactgtgctgTccatggcccgcagagagagg							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	TCCA	TCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr22:17073436_17073439delTCCA	ENST00000359963.3	-	0	261_264					NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2						anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				GACTGTGCTGTCCATGGCCCGCAG	0.623																																					p.1_2del		Atlas-INDEL	.											.	CCT8L2	150	.	0			c.3_6del						.																																			SO:0001582	initiator_codon_variant	150160	exon1			.	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302		chr22.hg19:g.17073436_17073439delTCCA		74.0	0.0		65.0	27.0	NM_014406	A4QPH3|Q9UJS3	Frame_Shift_Del	DEL	ENST00000359963.3	hg19	CCDS13738.1																																																																																			.	.		0.623	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			-	17073439	TCCA	-	17073436	7	5	190	1	0	1	0	1	0	0	0	0	2963	1667	58	0	1672	0	CCT8L2	22	17073436	Start_Codon_Del	DEL	TCCA	TCGA-DD-AADG-01A-11D-A40R-10		17073436	34231130	162	28238										
C22orf42	150297	hgsc.bcm.edu	37	chr22	32546378	32546378	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cctgatgtcatgaagtcttcAagagagacagataggctttc	10	8	3	5			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr22:32546378A>G	ENST00000382097.3	-	7	654	c.582T>C	c.(580-582)ctT>ctC	p.L194L	C22orf42_ENST00000490640.1_5'Flank	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	194										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						TGAAGTCTTCAAGAGAGACAG	0.438																																					p.L194L		Atlas-SNP	.											.	C22orf42	37	.	0			c.T582C						.						145	132	136					22																	32546378		2203	4300	6503	SO:0001819	synonymous_variant	150297	exon7			GTCTTCAAGAGAG	BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.582T>C	chr22.hg19:g.32546378A>G		437.0	1.0		450.0	172.0	NM_001010859	A4QPH5	Silent	SNP	ENST00000382097.3	hg19	CCDS33639.1																																																																																			.	.		0.438	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859		G	32546378	A	G	32546378	2	3	190	1	0	0	0	0	0	0	0	1	2151	117	5	2		2	C22orf42	22	32546378	Silent	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	15472942	32546378	18758188	163	28239										
L3MBTL2	83746	hgsc.bcm.edu	37	chr22	41616753	41616753	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttcagggtatcgggtgctgcTtcggtatgaaggctttgaaa	14	6	1	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr22:41616753T>A	ENST00000216237.5	+	7	892	c.734T>A	c.(733-735)cTt>cAt	p.L245H		NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	245					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CGGGTGCTGCTTCGGTATGAA	0.502																																					p.L245H		Atlas-SNP	.											.	L3MBTL2	61	.	0			c.T734A						.						109	98	102					22																	41616753		2203	4300	6503	SO:0001583	missense	83746	exon7			TGCTGCTTCGGTA	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.734T>A	chr22.hg19:g.41616753T>A	ENSP00000216237:p.Leu245His	54.0	0.0		59.0	26.0	NM_031488	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Missense_Mutation	SNP	ENST00000216237.5	hg19	CCDS14011.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.156726	0.78114	.	.	ENSG00000100395	ENST00000216237	T	0.58940	0.3	5.37	5.37	0.77165	.	0.318671	0.32608	N	0.005861	T	0.80904	0.4713	M	0.91717	3.235	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.79108	0.939;0.992	D	0.85647	0.1280	10	0.87932	D	0	.	15.677	0.77336	0.0:0.0:0.0:1.0	.	245;245	Q969R5-3;Q969R5	.;LMBL2_HUMAN	H	245	ENSP00000216237:L245H	ENSP00000216237:L245H	L	+	2	0	L3MBTL2	39946699	1.000000	0.71417	0.977000	0.42913	0.834000	0.47266	7.990000	0.88215	2.169000	0.68431	0.374000	0.22700	CTT	.	.		0.502	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488		A	41616753	T	A	41616753	3	1	190	1	0	0	0	0	1	0	0	0	8601	1609	56	4	760	4	L3MBTL2	22	41616753	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	9070375	41616753	9687813	164	28240										
SULT4A1	25830	hgsc.bcm.edu	37	chr22	44237809	44237809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ccacctcctgcagcaagctgGtgcctggaggggagaagccc	14	14	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr22:44237809G>A	ENST00000330884.4	-	2	293	c.173C>T	c.(172-174)aCc>aTc	p.T58I	SULT4A1_ENST00000249130.5_Missense_Mutation_p.T58I|SULT4A1_ENST00000540422.1_Intron	NM_014351.3	NP_055166.1	Q9BR01	ST4A1_HUMAN	sulfotransferase family 4A, member 1	58					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			kidney(1)|large_intestine(3)|lung(4)|ovary(1)	9		Ovarian(80;0.024)|all_neural(38;0.0416)		Colorectal(1;0.00242)|READ - Rectum adenocarcinoma(1;0.0419)		CAGCAAGCTGGTGCCTGGAGG	0.662																																					p.T58I		Atlas-SNP	.											.	SULT4A1	26	.	0			c.C173T						.						33	33	33					22																	44237809		2203	4299	6502	SO:0001583	missense	25830	exon2			AAGCTGGTGCCTG	AF188698	CCDS14051.1	22q13.2	2012-11-05			ENSG00000130540	ENSG00000130540		"Sulfotransferases, cytosolic"	14903	protein-coding gene	gene with protein product		608359				10698717	Standard	NM_014351		Approved	SULTX3, hBR-STL-1	uc003bee.1	Q9BR01	OTTHUMG00000141314	ENST00000330884.4:c.173C>T	chr22.hg19:g.44237809G>A	ENSP00000332565:p.Thr58Ile	35.0	0.0		47.0	17.0	NM_014351	B2R7N3|O43728	Missense_Mutation	SNP	ENST00000330884.4	hg19	CCDS14051.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.625606	0.87560	.	.	ENSG00000130540	ENST00000330884;ENST00000249130	T;T	0.05199	3.48;3.48	4.4	4.4	0.53042	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.31638	0.0803	M	0.89840	3.065	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.40403	-0.9565	10	0.87932	D	0	.	15.943	0.79771	0.0:0.0:1.0:0.0	.	58	Q9BR01	ST4A1_HUMAN	I	58	ENSP00000332565:T58I;ENSP00000249130:T58I	ENSP00000249130:T58I	T	-	2	0	SULT4A1	42569142	1.000000	0.71417	0.945000	0.38365	0.953000	0.61014	9.066000	0.93949	1.999000	0.58509	0.650000	0.86243	ACC	.	.		0.662	SULT4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280660.2	NM_014351		A	44237809	G	A	44237809	3	1	190	1	0	0	0	0	1	0	0	0	15398	1261	44	3	705	3	SULT4A1	22	44237809	Missense_Mutation	SNP	G	TCGA-DD-AADG-01A-11D-A40R-10	2621056	44237809	7066757	165	28241										
DMD	1756	hgsc.bcm.edu	37	chrX	32827649	32827649	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ctctatgcctaattgatatcTggcgatgttgaatgcatgtt	9	7	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:32827649T>A	ENST00000357033.4	-	7	816	c.610A>T	c.(610-612)Aga>Tga	p.R204*	DMD_ENST00000378677.2_Nonsense_Mutation_p.R200*|DMD_ENST00000288447.4_Nonsense_Mutation_p.R196*	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	204	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AATTGATATCTGGCGATGTTG	0.413																																					p.R204X		Atlas-SNP	.											.	DMD	2127	.	0			c.A610T						.						186	138	154					X																	32827649		2202	4300	6502	SO:0001587	stop_gained	1756	exon7			GATATCTGGCGAT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.610A>T	chrX.hg19:g.32827649T>A	ENSP00000354923:p.Arg204*	56.0	0.0		63.0	38.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Nonsense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	T	40	7.989021	0.98596	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	.	.	.	5.17	4.02	0.46733	.	0.514114	0.13704	U	0.368623	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	5.8858	0.18880	0.0:0.087:0.1646:0.7484	.	.	.	.	X	196;200;204;204;81;196	.	ENSP00000288447:R196X	R	-	1	2	DMD	32737570	1.000000	0.71417	0.285000	0.24819	0.952000	0.60782	2.851000	0.48302	0.642000	0.30620	0.345000	0.21793	AGA	.	.		0.413	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32827649	T	A	32827649	4	1	190	1	0	0	0	0	0	1	0	0	4582	1588	55	4	10982	4	DMD	23	32827649	Nonsense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10		32827649	122442911	166	28242										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412647	63412647	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ccggtgacggcggatactgcTaaaaaagccttttaggcctt	11	10	0	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:63412647T>C	ENST00000330258.3	-	2	792	c.520A>G	c.(520-522)Agc>Ggc	p.S174G	AMER1_ENST00000374869.3_Missense_Mutation_p.S174G|AMER1_ENST00000403336.1_Missense_Mutation_p.S174G	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	174					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									CGGATACTGCTAAAAAAGCCT	0.557																																					p.S174G		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.A520G						.						53	50	51					X																	63412647		2203	4300	6503	SO:0001583	missense	139285	exon2			TACTGCTAAAAAA	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.520A>G	chrX.hg19:g.63412647T>C	ENSP00000329117:p.Ser174Gly	48.0	0.0		44.0	32.0	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	hg19	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	T	14.39	2.521541	0.44866	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.23147	1.92;1.92;1.92	4.74	4.74	0.60224	.	0.458634	0.25058	N	0.033470	T	0.32793	0.0841	M	0.65975	2.015	0.29060	N	0.883973	P	0.52692	0.955	P	0.45753	0.492	T	0.36187	-0.9758	10	0.62326	D	0.03	-2.908	12.3652	0.55224	0.0:0.0:0.0:1.0	.	174	Q5JTC6	F123B_HUMAN	G	174	ENSP00000364003:S174G;ENSP00000329117:S174G;ENSP00000384722:S174G	ENSP00000329117:S174G	S	-	1	0	FAM123B	63329372	1.000000	0.71417	0.992000	0.48379	0.978000	0.69477	4.440000	0.59975	1.867000	0.54127	0.486000	0.48141	AGC	.	.		0.557	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		C	63412647	T	C	63412647	3	2	190	1	0	0	0	0	1	0	0	0	5428	1522	53	2	2891	2	FAM123B	23	63412647	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	30584998	63412647	91857913	167	28243										
ATP7A	538	hgsc.bcm.edu	37	chrX	77258571	77258571	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	ttcttatcaatgctcttaggAatatattctatacttgtggc	6	7	4	0			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:77258571A>T	ENST00000341514.6	+	6	1700	c.1545A>T	c.(1543-1545)ggA>ggT	p.G515G	ATP7A_ENST00000343533.5_Splice_Site_p.G515G|ATP7A_ENST00000350425.4_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	515	HMA 5. {ECO:0000255|PROSITE- ProRule:PRU00280}.				blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGCTCTTAGGAATATATTCTA	0.338																																					p.G515G		Atlas-SNP	.											.	ATP7A	248	.	0			c.A1545T						.						105	98	100					X																	77258571		2203	4295	6498	SO:0001630	splice_region_variant	538	exon6			CTTAGGAATATAT	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.1544-1A>T	chrX.hg19:g.77258571A>T		82.0	0.0		82.0	70.0	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Silent	SNP	ENST00000341514.6	hg19	CCDS35339.1																																																																																			.	.		0.338	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052	Silent	T	77258571	A	T	77258571	5	4	190	1	0	0	0	0	0	0	1	0	1190	260	9	4	1563	4	ATP7A	23	77258571	Splice_Site	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	13845924	77258571	78011989	168	28244										
IGSF1	3547	hgsc.bcm.edu	37	chrX	130420012	130420012	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tctatccacaactctggttgAgggtccatcactgttattcc	7	12	3	1			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:130420012A>G	ENST00000361420.3	-	4	187	c.108T>C	c.(106-108)ccT>ccC	p.P36P	IGSF1_ENST00000370903.3_Silent_p.P36P|IGSF1_ENST00000370910.1_Silent_p.P27P|IGSF1_ENST00000370901.4_Silent_p.P36P|IGSF1_ENST00000370904.1_Silent_p.P27P|IGSF1_ENST00000370900.1_Silent_p.P36P			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	36					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						ACTCTGGTTGAGGGTCCATCA	0.507																																					p.P36P		Atlas-SNP	.											.	IGSF1	231	.	0			c.T108C						.						78	77	77					X																	130420012		2203	4300	6503	SO:0001819	synonymous_variant	3547	exon4			TGGTTGAGGGTCC	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.108T>C	chrX.hg19:g.130420012A>G		65.0	0.0		49.0	30.0	NM_001555	B5MEG2|H9KV64|O15070|Q9NTC8	Silent	SNP	ENST00000361420.3	hg19	CCDS14629.1																																																																																			.	.		0.507	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			G	130420012	A	G	130420012	2	3	190	1	0	0	0	0	0	0	0	1	7605	291	11	2		2	IGSF1	23	130420012	Silent	SNP	A	TCGA-DD-AADG-01A-11D-A40R-10	53161441	130420012	24850548	169	28245										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142716502	142716502	+	Missense_Mutation	SNP	T	T	A													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	tcagttcaaaatactcactcTtcctttgttccacaacaatt							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:142716502T>A	ENST00000381779.4	-	2	2648	c.2423A>T	c.(2422-2424)aAg>aTg	p.K808M	SLITRK4_ENST00000356928.1_Missense_Mutation_p.K808M|SLITRK4_ENST00000338017.4_Missense_Mutation_p.K808M	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	808						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					ATACTCACTCTTCCTTTGTTC	0.423																																					p.K808M		Atlas-SNP	.											.	SLITRK4	162	.	0			c.A2423T						.						148	126	133					X																	142716502		2203	4300	6503	SO:0001583	missense	139065	exon2			TCACTCTTCCTTT	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.2423A>T	chrX.hg19:g.142716502T>A	ENSP00000371198:p.Lys808Met	67.0	0.0		72.0	8.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	T	18.90	3.722420	0.68959	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.62105	0.05;0.05;0.05	5.39	5.39	0.77823	.	0.000000	0.85682	U	0.000000	T	0.74876	0.3774	M	0.62723	1.935	0.80722	D	1	D	0.76494	0.999	D	0.66979	0.948	T	0.77838	-0.2439	10	0.87932	D	0	-8.2631	13.1568	0.59522	0.0:0.0:0.0:1.0	.	808	Q8IW52	SLIK4_HUMAN	M	808	ENSP00000371198:K808M;ENSP00000349400:K808M;ENSP00000336627:K808M	ENSP00000336627:K808M	K	-	2	0	SLITRK4	142544168	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	1.789000	0.52484	0.486000	0.48141	AAG	.	.		0.423	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		A	142716502	T	A	142716502	3	1	190	1	0	0	0	0	1	0	0	0	14760	1609	56	4	94	4	SLITRK4	23	142716502	Missense_Mutation	SNP	T	TCGA-DD-AADG-01A-11D-A40R-10	12296490	142716502	12554058	170	28246	138	2								
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142716504	142716504	+	Missense_Mutation	SNP	C	C	G													0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	agttcaaaatactcactcttCctttgttccacaacaatttt							TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:142716504C>G	ENST00000381779.4	-	2	2646	c.2421G>C	c.(2419-2421)agG>agC	p.R807S	SLITRK4_ENST00000356928.1_Missense_Mutation_p.R807S|SLITRK4_ENST00000338017.4_Missense_Mutation_p.R807S	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	807						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					ACTCACTCTTCCTTTGTTCCA	0.428																																					p.R807S		Atlas-SNP	.											.	SLITRK4	162	.	0			c.G2421C						.						148	126	133					X																	142716504		2203	4300	6503	SO:0001583	missense	139065	exon2			ACTCTTCCTTTGT	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.2421G>C	chrX.hg19:g.142716504C>G	ENSP00000371198:p.Arg807Ser	64.0	0.0		71.0	8.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	C	4.735	0.136613	0.09032	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.50813	0.73;0.73;0.73	5.39	2.18	0.27775	.	0.000000	0.85682	U	0.000000	T	0.25419	0.0618	N	0.20530	0.585	0.53688	D	0.999977	B	0.15473	0.013	B	0.17433	0.018	T	0.04767	-1.0928	10	0.11794	T	0.64	-6.163	5.7057	0.17907	0.0:0.4243:0.0:0.5757	.	807	Q8IW52	SLIK4_HUMAN	S	807	ENSP00000371198:R807S;ENSP00000349400:R807S;ENSP00000336627:R807S	ENSP00000336627:R807S	R	-	3	2	SLITRK4	142544170	0.690000	0.27699	1.000000	0.80357	0.996000	0.88848	-0.143000	0.10296	0.450000	0.26774	0.600000	0.82982	AGG	.	.		0.428	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		G	142716504	C	G	142716504	3	3	190	1	0	0	0	0	1	0	0	0	14760	854	30	4	96	4	SLITRK4	23	142716504	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	2	142716504	12554056	171	28247	138	2								
MAGEA1	4100	hgsc.bcm.edu	37	chrX	152482572	152482572	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0529411764705882	9	1	1.23080974325214	2.43675464320626	0.881720430107527	1	1	0	cagctgcaaggactcagaggCtttgccgaagatctcaggaa	12	10	2	2			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:152482572C>A	ENST00000356661.5	-	3	657	c.439G>T	c.(439-441)Gcc>Tcc	p.A147S		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	147	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GACTCAGAGGCTTTGCCGAAG	0.512																																					p.A147S		Atlas-SNP	.											.	MAGEA1	57	.	0			c.G439T						.						135	130	132					X																	152482572		2203	4300	6503	SO:0001583	missense	4100	exon3			CAGAGGCTTTGCC		CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"melanoma-associated antigen 1", "melanoma-associated antigen MZ2-E", "melanoma antigen MAGE-1", "melanoma antigen family A 1", "cancer/testis antigen family 1, member 1"	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.439G>T	chrX.hg19:g.152482572C>A	ENSP00000349085:p.Ala147Ser	116.0	0.0		131.0	8.0	NM_004988	B2RC81|O00346	Missense_Mutation	SNP	ENST00000356661.5	hg19	CCDS14720.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.452124	0.26074	.	.	ENSG00000198681	ENST00000356661	T	0.11277	2.79	1.28	0.37	0.16160	.	0.336075	0.33959	N	0.004387	T	0.28699	0.0711	M	0.88906	2.99	0.09310	N	1	P	0.49358	0.923	D	0.64506	0.926	T	0.07195	-1.0785	10	0.66056	D	0.02	.	3.7344	0.08504	0.0:0.7313:0.0:0.2687	.	147	P43355	MAGA1_HUMAN	S	147	ENSP00000349085:A147S	ENSP00000349085:A147S	A	-	1	0	MAGEA1	152135766	0.001000	0.12720	0.003000	0.11579	0.008000	0.06430	0.196000	0.17176	0.053000	0.16036	-1.130000	0.01982	GCC	.	.		0.512	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988		A	152482572	C	A	152482572	3	1	190	1	0	0	0	0	1	0	0	0	9172	797	28	3	494	3	MAGEA1	23	152482572	Missense_Mutation	SNP	C	TCGA-DD-AADG-01A-11D-A40R-10	9766068	152482572	2787988	172	28248										
ADAM30	11085	hgsc.bcm.edu	37	chr1	120438417	120438417	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ttctcataaggggccatctgCcattctatttcatcatcact	5	12	6	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:120438417C>G	ENST00000369400.1	-	1	701	c.543G>C	c.(541-543)tgG>tgC	p.W181C		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	181					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		GGGCCATCTGCCATTCTATTT	0.438																																					p.W181C		Atlas-SNP	.											.	ADAM30	88	.	0			c.G543C						.						86	84	85					1																	120438417		2203	4300	6503	SO:0001583	missense	11085	exon1			CATCTGCCATTCT	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.543G>C	chr1.hg19:g.120438417C>G	ENSP00000358407:p.Trp181Cys	54.0	0.0		90.0	4.0	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	hg19	CCDS907.1	.	.	.	.	.	.	.	.	.	.	C	7.667	0.686131	0.14973	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.01197	5.19	4.67	-3.78	0.04333	.	2.199350	0.03384	N	0.200754	T	0.00241	0.0007	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.46076	-0.9217	10	0.37606	T	0.19	.	1.216	0.01914	0.1264:0.3082:0.2478:0.3176	.	181	Q9UKF2	ADA30_HUMAN	C	181	ENSP00000358407:W181C	ENSP00000358407:W181C	W	-	3	0	ADAM30	120239940	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.492000	0.02300	-0.655000	0.05387	0.563000	0.77884	TGG	.	.		0.438	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		G	120438417	C	G	120438417	3	3	191	1	0	0	0	0	1	0	0	0	248	740	26	4	1833	4	ADAM30	1	120438417	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10		120438417	128812204	1	28249										
FLG2	388698	hgsc.bcm.edu	37	chr1	152328831	152328831	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gacccatgttgtccaaagccAgatgtcttacctgagctaga	9	11	1	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:152328831A>G	ENST00000388718.5	-	3	1503	c.1431T>C	c.(1429-1431)tcT>tcC	p.S477S	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	477	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTCCAAAGCCAGATGTCTTAC	0.522																																					p.S477S		Atlas-SNP	.											.	FLG2	431	.	0			c.T1431C						.						206	202	204					1																	152328831		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			AAAGCCAGATGTC	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.1431T>C	chr1.hg19:g.152328831A>G		105.0	0.0		212.0	9.0	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	hg19	CCDS30861.1																																																																																			.	.		0.522	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		G	152328831	A	G	152328831	2	3	191	1	0	0	0	0	0	0	0	1	5931	175	7	2		2	FLG2	1	152328831	Silent	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	31890414	152328831	96921790	2	28250										
C1orf77	26097	hgsc.bcm.edu	37	chr1	153617713	153617713	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	atgctgagttggatgcctacAtggcgcagacagatcccgaa	12	10	0	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:153617713A>G	ENST00000368694.3	+	6	1027	c.715A>G	c.(715-717)Atg>Gtg	p.M239V	CHTOP_ENST00000368687.1_Missense_Mutation_p.M214V|CHTOP_ENST00000368690.3_Missense_Mutation_p.M193V|CHTOP_ENST00000403433.1_Missense_Mutation_p.M193V|CHTOP_ENST00000495554.1_3'UTR	NM_001206612.1|NM_015607.3	NP_001193541.1|NP_056422.2	Q9Y3Y2	CHTOP_HUMAN	chromatin target of PRMT1	239					mRNA export from nucleus (GO:0006406)|positive regulation of ATPase activity (GO:0032781)|positive regulation of helicase activity (GO:0051096)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|transcription export complex (GO:0000346)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(6)	13						GGATGCCTACATGGCGCAGAC	0.473																																					p.M240V		Atlas-SNP	.											.	CHTOP	34	.	0			c.A718G						.						122	109	114					1																	153617713		2203	4300	6503	SO:0001583	missense	26097	exon6			GCCTACATGGCGC		CCDS1048.1, CCDS72917.1, CCDS72918.1	1q21.3	2011-03-24	2011-03-24	2011-03-24	ENSG00000160679	ENSG00000160679			24511	protein-coding gene	gene with protein product	"small protein rich in arginine and glycine", "Friend of Prmt1"	614206	"chromosome 1 open reading frame 77"	C1orf77		19254951	Standard	NM_015607		Approved	DKFZP547E1010, SRAG, FOP	uc001fcn.2	Q9Y3Y2	OTTHUMG00000037052	ENST00000368694.3:c.715A>G	chr1.hg19:g.153617713A>G	ENSP00000357683:p.Met239Val	57.0	0.0		166.0	7.0	NM_001206612	D3DV55|Q0VAQ8|Q2VPI9|Q5T7Y8|Q5T7Y9|Q5T7Z0|Q6NSM4|Q6PB28|Q8WYT9|Q9BUC5|Q9H034|Q9H2L0	Missense_Mutation	SNP	ENST00000368694.3	hg19	CCDS1048.1	.	.	.	.	.	.	.	.	.	.	A	18.18	3.566204	0.65651	.	.	ENSG00000160679	ENST00000368694;ENST00000403433;ENST00000368690;ENST00000368687	.	.	.	6.15	6.15	0.99193	.	0.000000	0.85682	D	0.000000	T	0.72740	0.3498	M	0.75085	2.285	0.80722	D	1	P;P	0.44776	0.811;0.843	P;P	0.61722	0.828;0.893	T	0.76124	-0.3074	9	0.72032	D	0.01	-24.2997	14.7406	0.69451	1.0:0.0:0.0:0.0	.	240;239	Q9Y3Y2-3;Q9Y3Y2	.;CHTOP_HUMAN	V	239;193;193;214	.	ENSP00000357676:M214V	M	+	1	0	CHTOP	151884337	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.958000	0.93099	2.363000	0.80096	0.523000	0.50628	ATG	.	.		0.473	CHTOP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089967.1	NM_015607		G	153617713	A	G	153617713	3	3	191	1	0	0	0	0	1	0	0	0	2061	217	8	2	733	2	C1orf77	1	153617713	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	1288882	153617713	95632908	3	28251										
GBA	2629	hgsc.bcm.edu	37	chr1	155208419	155208419	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tcacagctggccatgggtacCcggatgatgttatatccgat	11	10	1	1	rs75249684		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:155208419C>T	ENST00000327247.5	-	6	709	c.477G>A	c.(475-477)cgG>cgA	p.R159R	GBA_ENST00000536770.1_Silent_p.R46R|GBA_ENST00000493842.1_5'UTR|AL713999.1_ENST00000401290.1_RNA|GBA_ENST00000427500.3_Silent_p.R110R|GBA_ENST00000428024.3_Silent_p.R72R|GBA_ENST00000368373.3_Silent_p.R159R	NM_001005741.2|NM_001005742.2	NP_001005741.1|NP_001005742.1	P04062	GLCM_HUMAN	glucosidase, beta, acid	159			R -> Q (in GD; type 2; 13% of normal activity). {ECO:0000269|PubMed:10796875}.|R -> W (in GD; severe). {ECO:0000269|PubMed:10796875, ECO:0000269|PubMed:15605411, ECO:0000269|PubMed:9217217}.		carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glucosylceramide catabolic process (GO:0006680)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of MAP kinase activity (GO:0043407)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of water loss via skin (GO:0033561)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to pH (GO:0009268)|response to testosterone (GO:0033574)|response to thyroid hormone (GO:0097066)|skin morphogenesis (GO:0043589)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)|termination of signal transduction (GO:0023021)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)	glucosylceramidase activity (GO:0004348)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	26	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		Velaglucerase alfa(DB06720)	CCATGGGTACCCGGATGATGT	0.488									Gaucher disease type I																												p.R159R		Atlas-SNP	.											.	GBA	46	.	0			c.G477A						.						122	114	117					1																	155208419		2202	4299	6501	SO:0001819	synonymous_variant	2629	exon6	Familial Cancer Database	glucocerebrosidase insufficiency	GGGTACCCGGATG	M19285	CCDS1102.1, CCDS53373.1, CCDS53374.1	1q22	2010-01-19	2010-01-19		ENSG00000177628	ENSG00000177628	3.2.1.21		4177	protein-coding gene	gene with protein product		606463	"glucosylceramidase", "glucosidase, beta; acid (includes glucosylceramidase)"	GLUC		3359914	Standard	NM_001005742		Approved	GBA1	uc001fjl.3	P04062	OTTHUMG00000035841	ENST00000327247.5:c.477G>A	chr1.hg19:g.155208419C>T		272.0	0.0		649.0	59.0	NM_001005742	A8K796|B7Z5G2|B7Z6S1|J3KQG4|J3KQK9|Q16545|Q4VX22|Q6I9R6|Q9UMJ8	Silent	SNP	ENST00000327247.5	hg19	CCDS1102.1																																																																																			.	.		0.488	GBA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087204.1	NM_000157		T	155208419	C	T	155208419	2	4	191	1	0	0	0	0	0	0	0	1	6274	610	22	3		3	GBA	1	155208419	Silent	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	1590706	155208419	94042202	4	28252										
PKLR	5313	hgsc.bcm.edu	37	chr1	155264423	155264423	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	catgctccaccccgaagcgcAggtctcggacgtcctgctcg	11	17	1	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:155264423A>G	ENST00000342741.4	-	6	853	c.815T>C	c.(814-816)cTg>cCg	p.L272P	PKLR_ENST00000392414.3_Missense_Mutation_p.L241P	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	272			L -> V (in PKRD). {ECO:0000269|PubMed:19085939}.		ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	CCCGAAGCGCAGGTCTCGGAC	0.672																																					p.L272P		Atlas-SNP	.											.	PKLR	70	.	0			c.T815C						.						54	52	53					1																	155264423		2203	4300	6503	SO:0001583	missense	5313	exon6			AAGCGCAGGTCTC	BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.815T>C	chr1.hg19:g.155264423A>G	ENSP00000339933:p.Leu272Pro	72.0	0.0		180.0	75.0	NM_000298	O75758|P11973	Missense_Mutation	SNP	ENST00000342741.4	hg19	CCDS1109.1	.	.	.	.	.	.	.	.	.	.	A	18.60	3.659502	0.67586	.	.	ENSG00000143627	ENST00000423816;ENST00000392414;ENST00000342741;ENST00000271946	D;D	0.99857	-7.22;-7.22	4.48	4.48	0.54585	Pyruvate/Phosphoenolpyruvate kinase (2);Pyruvate kinase, barrel (1);	0.000000	0.64402	D	0.000001	D	0.99889	0.9947	H	0.94925	3.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.96278	0.9204	10	0.87932	D	0	-20.4261	12.022	0.53348	1.0:0.0:0.0:0.0	.	272;263	P30613;B1AVT1	KPYR_HUMAN;.	P	297;241;272;186	ENSP00000376214:L241P;ENSP00000339933:L272P	ENSP00000271946:L186P	L	-	2	0	PKLR	153531047	1.000000	0.71417	1.000000	0.80357	0.540000	0.34992	7.002000	0.76304	2.010000	0.58986	0.383000	0.25322	CTG	.	.		0.672	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298		G	155264423	A	G	155264423	3	3	191	1	0	0	0	0	1	0	0	0	11985	188	7	2	933	2	PKLR	1	155264423	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	56004	155264423	93986198	5	28253										
CD1E	913	hgsc.bcm.edu	37	chr1	158325883	158325889	+	Frame_Shift_Del	DEL	ATCATCC	ATCATCC	-													0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gtctagggggccatgatctaAtcatccattggggtgagaaa							TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	ATCATCC	ATCATCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:158325883_158325889delATCATCC	ENST00000368167.3	+	4	1131_1137	c.892_898delATCATCC	c.(892-900)atcatccatfs	p.IIH298fs	CD1E_ENST00000368164.3_Intron|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000434258.1_Frame_Shift_Del_p.IIH296fs|CD1E_ENST00000444681.2_Frame_Shift_Del_p.IIH199fs|CD1E_ENST00000368161.3_Intron|CD1E_ENST00000368156.1_Frame_Shift_Del_p.IIH208fs|CD1E_ENST00000368165.3_Frame_Shift_Del_p.IIH208fs|CD1E_ENST00000452291.2_Frame_Shift_Del_p.IIH109fs|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368166.3_Frame_Shift_Del_p.IIH109fs|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368163.3_Intron|CD1E_ENST00000368160.3_Frame_Shift_Del_p.IIH298fs	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	298	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					CCATGATCTAATCATCCATTGGGGTGA	0.551																																					p.297_299del		Atlas-INDEL	.											.	CD1E	129	.	0			c.891_897del						.																																			SO:0001589	frameshift_variant	913	exon4			.	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1638	protein-coding gene	gene with protein product		188411	"CD1E antigen, e polypeptide", "CD1e antigen"			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.892_898delATCATCC	chr1.hg19:g.158325883_158325889delATCATCC	ENSP00000357149:p.Ile298fs	54.0	0.0		108.0	14.0	NM_030893	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Frame_Shift_Del	DEL	ENST00000368167.3	hg19	CCDS41417.1																																																																																			.	.		0.551	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		-	158325889	ATCATCC	-	158325883	7	5	191	1	0	1	0	1	0	0	0	0	2980	101	4	0	906	0	CD1E	1	158325883	Frame_Shift_Del	DEL	ATCATCC	TCGA-DD-AADI-01A-11D-A40R-10	3061460	158325883	90924738	6	28254			1	42		2	2	13	N	ATCATCC_-	4.767834e-05
CD1E	913	hgsc.bcm.edu	37	chr1	158325895	158325896	+	Splice_Site	INS	-	-	T													0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tgatctaatcatccattgggINSgtgagaaacagctgaggctc							TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:158325895_158325896insT	ENST00000368167.3	+	4	1143	c.904_904insT	c.(904-906)ggt>Tggt	p.G302fs	CD1E_ENST00000368164.3_Intron|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000434258.1_Frame_Shift_Ins_p.G300fs|CD1E_ENST00000444681.2_Splice_Site_p.G203fs|CD1E_ENST00000368161.3_Intron|CD1E_ENST00000368156.1_Splice_Site_p.G212fs|CD1E_ENST00000368165.3_Splice_Site_p.G212fs|CD1E_ENST00000452291.2_Splice_Site_p.G113fs|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368166.3_Splice_Site_p.G113fs|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368163.3_Intron|CD1E_ENST00000368160.3_Splice_Site_p.G302fs	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	302					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					CATCCATTGGGGTGAGAAACAG	0.55																																					p.G302fs		Atlas-INDEL	.											.	CD1E	129	.	0			c.904_905insT						.																																			SO:0001630	splice_region_variant	913	exon4			.	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1638	protein-coding gene	gene with protein product		188411	"CD1E antigen, e polypeptide", "CD1e antigen"			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.904+1->T	chr1.hg19:g.158325895_158325896insT		48.0	0.0		103.0	17.0	NM_030893	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Frame_Shift_Ins	INS	ENST00000368167.3	hg19	CCDS41417.1																																																																																			.	.		0.55	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893	Frame_Shift_Ins	T	158325896	-	T	158325895	8	5	191	1	0	1	1	0	0	0	1	0	2980	1246	43	0	918	0	CD1E	1	158325895	Splice_Site	INS	-	TCGA-DD-AADI-01A-11D-A40R-10	12	158325895	90924726	7	28255			1	42		2	2	13	N	ATCATCC_-	4.767834e-05
OR10X1	128367	hgsc.bcm.edu	37	chr1	158548821	158548821	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agggggtaatgacagtataaGggactgctatgagtgtgtca	15	4	1	2	rs150430213		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:158548821G>A	ENST00000368150.1	-	1	868	c.869C>T	c.(868-870)cCt>cTt	p.P290L		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					GACAGTATAAGGGACTGCTAT	0.443													G|||	1	0.000199681	0	0	5008	,	,		22074	0		0	False		,,,				2504	0.001				p.P290L		Atlas-SNP	.											.	OR10X1	96	.	0			c.C869T						.	G	LEU/PRO	0,4406		0,0,2203	107	112	110		869	4.5	0.6	1	dbSNP_134	110	1,8599	1.2+/-3.3	0,1,4299	no	missense	OR10X1	NM_001004477.1	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	290/327	158548821	1,13005	2203	4300	6503	SO:0001583	missense	128367	exon1			GTATAAGGGACTG	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"GPCR / Class A : Olfactory receptors"	14995	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily X, member 1"	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.869C>T	chr1.hg19:g.158548821G>A	ENSP00000357132:p.Pro290Leu	97.0	0.0		193.0	44.0	NM_001004477	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	hg19	CCDS30900.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.707340	0.48412	0.0	1.16E-4	ENSG00000186400	ENST00000368150	T	0.00016	9.13	4.5	4.5	0.54988	.	0.000000	0.48286	D	0.000184	T	0.00039	0.0001	N	0.00242	-1.785	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.48514	-0.9029	10	0.08381	T	0.77	.	6.9583	0.24583	0.1895:0.0:0.8105:0.0	.	290	Q8NGY0	O10X1_HUMAN	L	290	ENSP00000357132:P290L	ENSP00000357132:P290L	P	-	2	0	OR10X1	156815445	0.007000	0.16637	0.650000	0.29550	0.993000	0.82548	1.975000	0.40569	2.473000	0.83533	0.563000	0.77884	CCT	.	G|1.000;A|0.000		0.443	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477		A	158548821	G	A	158548821	3	1	191	1	0	0	0	0	1	0	0	0	10931	1000	35	3	106	3	OR10X1	1	158548821	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	222926	158548821	90701800	8	28256										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176563717	176563717	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aggctgggccctggggatccGctcagggaaggacaagggaa	18	9	1	0	rs372509506		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:176563717G>A	ENST00000367662.3	+	3	2141	c.977G>A	c.(976-978)cGc>cAc	p.R326H	PAPPA2_ENST00000367661.3_Missense_Mutation_p.R326H	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	326					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CTGGGGATCCGCTCAGGGAAG	0.542																																					p.R326H		Atlas-SNP	.											.	PAPPA2	665	.	0			c.G977A						.	G	HIS/ARG,HIS/ARG	0,3972		0,0,1986	51	51	51		977,977	3.6	1	1		51	1,8329		0,1,4164	no	missense,missense	PAPPA2	NM_020318.2,NM_021936.2	29,29	0,1,6150	AA,AG,GG		0.012,0.0,0.0081	possibly-damaging,possibly-damaging	326/1792,326/828	176563717	1,12301	1986	4165	6151	SO:0001583	missense	60676	exon3			GGATCCGCTCAGG	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.977G>A	chr1.hg19:g.176563717G>A	ENSP00000356634:p.Arg326His	78.0	0.0		152.0	39.0	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	hg19	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.192772	0.38707	0.0	1.2E-4	ENSG00000116183	ENST00000367662;ENST00000367661	T;T	0.73897	-0.79;-0.79	5.45	3.59	0.41128	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.111801	0.64402	N	0.000007	T	0.63757	0.2538	L	0.45051	1.395	0.39139	D	0.962005	B;B	0.31125	0.026;0.309	B;B	0.27170	0.014;0.077	T	0.59736	-0.7398	10	0.30854	T	0.27	-19.5477	11.4449	0.50116	0.1471:0.0:0.8528:0.0	.	326;326	Q9BXP8;A9Z1Y8	PAPP2_HUMAN;.	H	326	ENSP00000356634:R326H;ENSP00000356633:R326H	ENSP00000356633:R326H	R	+	2	0	PAPPA2	174830340	0.009000	0.17119	1.000000	0.80357	0.984000	0.73092	0.828000	0.27435	0.677000	0.31305	0.650000	0.86243	CGC	.	.		0.542	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176563717	G	A	176563717	3	1	191	1	0	0	0	0	1	0	0	0	11442	1087	38	1	983	1	PAPPA2	1	176563717	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	18014896	176563717	72686904	9	28257										
IPO9	55705	hgsc.bcm.edu	37	chr1	201839912	201839912	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ccaaggcagggcgggaactcGgggagaatctagaccagatt	15	9	1	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:201839912G>A	ENST00000361565.4	+	18	2404	c.2335G>A	c.(2335-2337)Ggg>Agg	p.G779R		NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	779					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						GCGGGAACTCGGGGAGAATCT	0.592																																					p.G779R		Atlas-SNP	.											.	IPO9	98	.	0			c.G2335A						.						52	53	52					1																	201839912		2203	4300	6503	SO:0001583	missense	55705	exon18			GAACTCGGGGAGA	AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"Importins"	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.2335G>A	chr1.hg19:g.201839912G>A	ENSP00000354742:p.Gly779Arg	37.0	0.0		108.0	6.0	NM_018085	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Missense_Mutation	SNP	ENST00000361565.4	hg19	CCDS1415.1	.	.	.	.	.	.	.	.	.	.	G	31	5.093265	0.94149	.	.	ENSG00000198700	ENST00000361565	T	0.66280	-0.2	5.59	5.59	0.84812	Armadillo-like helical (1);Armadillo-type fold (1);	0.047505	0.85682	D	0.000000	T	0.76976	0.4063	M	0.71206	2.165	0.80722	D	1	D	0.76494	0.999	D	0.65010	0.931	T	0.76429	-0.2962	10	0.44086	T	0.13	-8.8262	17.091	0.86622	0.0:0.0:1.0:0.0	.	779	Q96P70	IPO9_HUMAN	R	779	ENSP00000354742:G779R	ENSP00000354742:G779R	G	+	1	0	IPO9	200106535	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.363000	0.97131	2.629000	0.89072	0.591000	0.81541	GGG	.	.		0.592	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085		A	201839912	G	A	201839912	3	1	191	1	0	0	0	0	1	0	0	0	7808	1116	39	1	2405	1	IPO9	1	201839912	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	25276195	201839912	47410709	10	28258										
C1orf58	148362	hgsc.bcm.edu	37	chr1	222900566	222900566	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctggactaattgctgcactgGcgtatgaaacagccaatttc	9	10	0	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:222900566G>A	ENST00000340934.5	+	8	1043	c.637G>A	c.(637-639)Gcg>Acg	p.A213T	BROX_ENST00000539697.1_Missense_Mutation_p.A181T|BROX_ENST00000537020.1_Missense_Mutation_p.A213T	NM_144695.2	NP_653296.2	Q5VW32	BROX_HUMAN	BRO1 domain and CAAX motif containing	213	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|stomach(1)	14						TGCTGCACTGGCGTATGAAAC	0.333																																					p.A213T		Atlas-SNP	.											.	BROX	45	.	0			c.G637A						.						113	112	112					1																	222900566		2203	4300	6503	SO:0001583	missense	148362	exon8			GCACTGGCGTATG		CCDS1534.1, CCDS73036.1, CCDS73037.1	1q41	2010-11-30	2010-11-30	2010-11-30	ENSG00000162819	ENSG00000162819			26512	protein-coding gene	gene with protein product	"BRO1 domain containing protein"		"chromosome 1 open reading frame 58"	C1orf58		18190528	Standard	XM_005273065		Approved	FLJ32421	uc001hnq.1	Q5VW32	OTTHUMG00000037650	ENST00000340934.5:c.637G>A	chr1.hg19:g.222900566G>A	ENSP00000343742:p.Ala213Thr	148.0	0.0		344.0	15.0	NM_144695	B7Z9G5|Q96MG1	Missense_Mutation	SNP	ENST00000340934.5	hg19	CCDS1534.1	.	.	.	.	.	.	.	.	.	.	g	35	5.576968	0.96565	.	.	ENSG00000162819	ENST00000340934;ENST00000426638;ENST00000537020;ENST00000539697	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.96	5.96	0.96718	BRO1 domain (3);	0.000000	0.85682	D	0.000000	T	0.62295	0.2416	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.988;0.983;0.993	T	0.63391	-0.6648	10	0.59425	D	0.04	-17.355	20.422	0.99049	0.0:0.0:1.0:0.0	.	213;181;213	F5GXQ0;B7Z9G5;Q5VW32	.;.;BROX_HUMAN	T	213;213;213;181	ENSP00000343742:A213T;ENSP00000398862:A213T;ENSP00000440041:A213T;ENSP00000441080:A181T	ENSP00000343742:A213T	A	+	1	0	BROX	220967189	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	8.950000	0.93019	2.832000	0.97577	0.655000	0.94253	GCG	.	.		0.333	BROX-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091815.2	NM_144695		A	222900566	G	A	222900566	3	1	191	1	0	0	0	0	1	0	0	0	2052	1203	42	3	663	3	C1orf58	1	222900566	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	21060654	222900566	26350055	11	28259										
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233394789	233394789	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ttctcactcccccacggctgGaaagaaacgtctgtttctag	8	13	3	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:233394789G>C	ENST00000258229.9	-	5	1053	c.819C>G	c.(817-819)ttC>ttG	p.F273L	PCNXL2_ENST00000430153.1_5'UTR	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	273						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CCCACGGCTGGAAAGAAACGT	0.522																																					p.F273L		Atlas-SNP	.											.	PCNXL2	204	.	0			c.C819G						.						54	58	57					1																	233394789		1925	4124	6049	SO:0001583	missense	80003	exon5			CGGCTGGAAAGAA	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.819C>G	chr1.hg19:g.233394789G>C	ENSP00000258229:p.Phe273Leu	72.0	0.0		202.0	39.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.842492	0.32606	.	.	ENSG00000135749	ENST00000258229	T	0.61980	0.06	4.4	2.45	0.29901	.	.	.	.	.	T	0.41351	0.1155	L	0.27053	0.805	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.32534	-0.9903	9	0.46703	T	0.11	.	1.2293	0.01940	0.1725:0.1468:0.3785:0.3022	.	273	A6NKB5	PCX2_HUMAN	L	273	ENSP00000258229:F273L	ENSP00000258229:F273L	F	-	3	2	PCNXL2	231461412	1.000000	0.71417	0.977000	0.42913	0.947000	0.59692	0.888000	0.28268	0.546000	0.28920	-0.263000	0.10527	TTC	.	.		0.522	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		C	233394789	G	C	233394789	3	2	191	1	0	0	0	0	1	0	0	0	11601	1165	41	4	5714	4	PCNXL2	1	233394789	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	10494223	233394789	15855832	12	28260										
OR14A16	284532	hgsc.bcm.edu	37	chr1	247978806	247978806	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	attggcgatagatttgggagCcgtgactgaaataaggcaga	14	5	0	4			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr1:247978806C>T	ENST00000357627.1	-	1	225	c.226G>A	c.(226-228)Gct>Act	p.A76T		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	76						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(32)|skin(2)|stomach(1)	45						GATTTGGGAGCCGTGACTGAA	0.418																																					p.A76T	Ovarian(112;180 1586 15073 21914 33526)	Atlas-SNP	.											OR14A16,NS,carcinoma,0,1	OR14A16	90	.	0			c.G226A						.						81	83	82					1																	247978806		2203	4300	6503	SO:0001583	missense	284532	exon1			TGGGAGCCGTGAC	BK004366	CCDS31097.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000196772	ENSG00000196772		"GPCR / Class A : Olfactory receptors"	15022	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily AT, member 1"	OR5AT1			Standard	NM_001001966		Approved		uc001idm.1	Q8NHC5	OTTHUMG00000040199	ENST00000357627.1:c.226G>A	chr1.hg19:g.247978806C>T	ENSP00000350248:p.Ala76Thr	186.0	0.0		404.0	45.0	NM_001001966	Q6IF96	Missense_Mutation	SNP	ENST00000357627.1	hg19	CCDS31097.1	.	.	.	.	.	.	.	.	.	.	C	10.94	1.491701	0.26774	.	.	ENSG00000196772	ENST00000357627	T	0.01197	5.19	3.51	-0.103	0.13609	GPCR, rhodopsin-like superfamily (1);	0.874344	0.09353	U	0.813915	T	0.00695	0.0023	N	0.03930	-0.32	0.09310	N	1	B	0.13594	0.008	B	0.17098	0.017	T	0.47005	-0.9150	10	0.42905	T	0.14	.	5.4843	0.16741	0.0:0.5641:0.1447:0.2912	.	76	Q8NHC5	O14AG_HUMAN	T	76	ENSP00000350248:A76T	ENSP00000350248:A76T	A	-	1	0	OR14A16	246045429	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.856000	0.00349	0.029000	0.15352	0.590000	0.80494	GCT	.	.		0.418	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1	NM_001001966		T	247978806	C	T	247978806	3	4	191	1	0	0	0	0	1	0	0	0	10954	739	26	3	707	3	OR14A16	1	247978806	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	14584017	247978806	1271815	13	28261										
SPAST	6683	hgsc.bcm.edu	37	chr2	32289153	32289153	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tctgccagcgcttctcccgcGccctcatggcagccaagagg	11	17	3	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr2:32289153G>A	ENST00000315285.3	+	1	378	c.253G>A	c.(253-255)Gcc>Acc	p.A85T	SPAST_ENST00000345662.1_Missense_Mutation_p.A85T	NM_014946.3	NP_055761.2			spastin											breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					CTTCTCCCGCGCCCTCATGGC	0.711																																					p.A85T		Atlas-SNP	.											.	SPAST	61	.	0			c.G253A						.						26	25	26					2																	32289153		2203	4300	6503	SO:0001583	missense	6683	exon1			TCCCGCGCCCTCA	AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"ATPases / AAA-type"	11233	protein-coding gene	gene with protein product		604277	"spastic paraplegia 4 (autosomal dominant; spastin)"	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.253G>A	chr2.hg19:g.32289153G>A	ENSP00000320885:p.Ala85Thr	553.0	0.0		713.0	124.0	NM_199436		Missense_Mutation	SNP	ENST00000315285.3	hg19	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	g	13.32	2.202123	0.38905	.	.	ENSG00000021574	ENST00000345662;ENST00000315285	D;D	0.93811	-3.29;-3.2	4.29	2.25	0.28309	.	0.495427	0.17461	N	0.173455	T	0.80727	0.4678	N	0.08118	0	0.35049	D	0.760482	B;B	0.31837	0.168;0.342	B;B	0.20184	0.013;0.028	T	0.77998	-0.2376	10	0.23891	T	0.37	-1.8705	7.0207	0.24912	0.095:0.3399:0.565:0.0	.	85;85	E5KRP6;Q9UBP0	.;SPAST_HUMAN	T	85	ENSP00000340817:A85T;ENSP00000320885:A85T	ENSP00000320885:A85T	A	+	1	0	SPAST	32142657	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	3.012000	0.49575	0.884000	0.36064	0.637000	0.83480	GCC	.	.		0.711	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436		A	32289153	G	A	32289153	3	1	191	1	0	0	0	0	1	0	0	0	15012	1087	38	1	255	1	SPAST	2	32289153	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10		32289153	210910220	14	28262										
SOS1	6654	hgsc.bcm.edu	37	chr2	39250269	39250269	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	acactgtccaatgtcttttcCctcccaaccatcaatattct	2	15	3	0	rs397517148		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr2:39250269C>T	ENST00000426016.1	-	11	1386	c.1300G>A	c.(1300-1302)Gga>Aga	p.G434R	SOS1_ENST00000402219.2_Missense_Mutation_p.G434R|SOS1_ENST00000472480.1_5'UTR|SOS1_ENST00000395038.2_Missense_Mutation_p.G434R			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	434			G -> K (in NS4; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:21387466}.|G -> R (in NS4). {ECO:0000269|PubMed:17143285, ECO:0000269|PubMed:21387466}.		apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				ATGTCTTTTCCCTCCCAACCA	0.388									Noonan syndrome																												p.G434R		Atlas-SNP	.											SOS1,scalp,malignant_melanoma,+1,1	SOS1	134	.	0			c.G1300A	GRCh37	CM070282|CM074572	SOS1	M		.						116	103	107					2																	39250269		2203	4300	6503	SO:0001583	missense	6654	exon10	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CTTTTCCCTCCCA	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1300G>A	chr2.hg19:g.39250269C>T	ENSP00000387784:p.Gly434Arg	63.0	0.0		83.0	25.0	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	hg19	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.490590	0.84962	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	D;D;D	0.91577	-2.87;-2.87;-2.87	5.52	5.52	0.82312	Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.95014	0.8386	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94925	0.8077	10	0.72032	D	0.01	.	19.8	0.96502	0.0:1.0:0.0:0.0	.	166;434	F5GX06;Q07889	.;SOS1_HUMAN	R	434;434;166;434;434	ENSP00000387784:G434R;ENSP00000384675:G434R;ENSP00000378479:G434R	ENSP00000263879:G434R	G	-	1	0	SOS1	39103773	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.666000	0.83877	2.753000	0.94483	0.557000	0.71058	GGA	.	.		0.388	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		T	39250269	C	T	39250269	3	4	191	1	0	0	0	0	1	0	0	0	14951	632	22	3	2757	3	SOS1	2	39250269	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	6961116	39250269	203949104	15	28263										
DYSF	8291	hgsc.bcm.edu	37	chr2	71839841	71839841	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cgataaccgccagtttggccGccggcctgtggtgggccagt	15	13	0	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr2:71839841G>A	ENST00000258104.3	+	39	4515	c.4238G>A	c.(4237-4239)cGc>cAc	p.R1413H	DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409366.1_Missense_Mutation_p.R1414H|DYSF_ENST00000409744.1_Missense_Mutation_p.R1400H|DYSF_ENST00000394120.2_Missense_Mutation_p.R1414H|DYSF_ENST00000409582.3_Missense_Mutation_p.R1430H|DYSF_ENST00000429174.2_Missense_Mutation_p.R1413H|DYSF_ENST00000409651.1_Missense_Mutation_p.R1445H|DYSF_ENST00000410020.3_Missense_Mutation_p.R1431H|DYSF_ENST00000410041.1_Missense_Mutation_p.R1431H|DYSF_ENST00000413539.2_Missense_Mutation_p.R1444H|DYSF_ENST00000409762.1_Missense_Mutation_p.R1430H	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1413	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.R1413L(1)|p.R1431L(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CAGTTTGGCCGCCGGCCTGTG	0.647																																					p.R1445H		Atlas-SNP	.											DYSF_ENST00000410020,NS,carcinoma,0,2	DYSF	536	.	2	Substitution - Missense(2)	lung(2)	c.G4334A						.						56	52	53					2																	71839841		2203	4300	6503	SO:0001583	missense	8291	exon40			TTGGCCGCCGGCC	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4238G>A	chr2.hg19:g.71839841G>A	ENSP00000258104:p.Arg1413His	143.0	0.0		199.0	56.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	35	5.553529	0.96501	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47;-1.47;-1.47;-1.47;-1.47;-1.47;-1.47;-1.47	5.52	5.52	0.82312	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.92024	0.7473	M	0.92833	3.35	0.58432	D	0.999996	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.993;1.0;0.996;1.0;1.0;1.0;1.0	D	0.93056	0.6470	10	0.54805	T	0.06	-23.5585	16.9157	0.86150	0.0:0.0:1.0:0.0	.	156;1445;1431;1414;1400;1431;1400;1430;1399;1444;1430;1413;1399;1414;1413	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	H	1444;1430;1430;1413;1413;1445;1414;1400;1414;1431;1431	ENSP00000407046:R1444H;ENSP00000387137:R1430H;ENSP00000386547:R1430H;ENSP00000398305:R1413H;ENSP00000258104:R1413H;ENSP00000386683:R1445H;ENSP00000377678:R1414H;ENSP00000386285:R1400H;ENSP00000386512:R1414H;ENSP00000386881:R1431H;ENSP00000386617:R1431H	ENSP00000258104:R1413H	R	+	2	0	DYSF	71693349	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.835000	0.86780	2.610000	0.88304	0.561000	0.74099	CGC	.	.		0.647	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71839841	G	A	71839841	3	1	191	1	0	0	0	0	1	0	0	0	4861	1087	38	1	4584	1	DYSF	2	71839841	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	32589572	71839841	171359532	16	28264										
ST6GAL2	84620	hgsc.bcm.edu	37	chr2	107450508	107450508	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cactccatctgtcttacctgCgaattaatgatgcgtatggt	8	10	2	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr2:107450508C>T	ENST00000409382.3	-	3	1648	c.1038G>A	c.(1036-1038)tcG>tcA	p.S346S	ST6GAL2_ENST00000409087.3_Silent_p.S346S|ST6GAL2_ENST00000361686.4_Silent_p.S346S|AC016994.2_ENST00000425419.1_RNA	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	346					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						GTCTTACCTGCGAATTAATGA	0.388																																					p.S346S		Atlas-SNP	.											.	ST6GAL2	159	.	0			c.G1038A						.						213	201	205					2																	107450508		2203	4300	6503	SO:0001819	synonymous_variant	84620	exon3			TACCTGCGAATTA	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"sialyltransferase 2 (monosialoganglioside sialyltransferase)"	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.1038G>A	chr2.hg19:g.107450508C>T		68.0	0.0		99.0	30.0	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	hg19	CCDS2073.1																																																																																			.	.		0.388	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		T	107450508	C	T	107450508	2	4	191	1	0	0	0	0	0	0	0	1	15237	755	27	1		1	ST6GAL2	2	107450508	Silent	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	35610667	107450508	135748865	17	28265										
SH3RF3	344558	hgsc.bcm.edu	37	chr2	109964272	109964272	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ccacggcgagctgcacggcaCacagggcttcctcccagcca	11	18	0	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr2:109964272C>A	ENST00000309415.6	+	2	716	c.716C>A	c.(715-717)aCa>aAa	p.T239K		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	239	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.						zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						CTGCACGGCACACAGGGCTTC	0.577																																					p.T239K		Atlas-SNP	.											.	SH3RF3	62	.	0			c.C716A						.						55	63	60					2																	109964272		2158	4250	6408	SO:0001583	missense	344558	exon2			ACGGCACACAGGG	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.716C>A	chr2.hg19:g.109964272C>A	ENSP00000309186:p.Thr239Lys	124.0	0.0		164.0	13.0	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	hg19		.	.	.	.	.	.	.	.	.	.	C	0.006	-2.078175	0.00375	.	.	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.41065	1.01;1.01	4.82	1.61	0.23674	Src homology-3 domain (4);	.	.	.	.	T	0.15522	0.0374	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.17979	0.02	T	0.31280	-0.9949	8	0.05620	T	0.96	.	2.7912	0.05388	0.4913:0.3035:0.0988:0.1063	.	239	Q8TEJ3	SH3R3_HUMAN	K	239	ENSP00000414997:T239K;ENSP00000309186:T239K	ENSP00000309186:T239K	T	+	2	0	SH3RF3	109330704	0.000000	0.05858	0.000000	0.03702	0.192000	0.23643	0.036000	0.13819	0.059000	0.16252	0.484000	0.47621	ACA	.	.		0.577	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		A	109964272	C	A	109964272	3	1	191	1	0	0	0	0	1	0	0	0	14275	478	17	3	722	3	SH3RF3	2	109964272	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	2513764	109964272	133235101	18	28266										
MAP1D	254042	hgsc.bcm.edu	37	chr2	172930371	172930371	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agatagatgctcttgttcatCgggaaatcatcagtcataat	8	7	5	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr2:172930371C>T	ENST00000315796.4	+	4	775	c.388C>T	c.(388-390)Cgg>Tgg	p.R130W	METAP1D_ENST00000488581.1_Intron	NM_199227.1	NP_954697.1	Q6UB28	MAP12_HUMAN	methionyl aminopeptidase type 1D (mitochondrial)	130					N-terminal protein amino acid modification (GO:0031365)|peptidyl-methionine modification (GO:0018206)|protein initiator methionine removal (GO:0070084)	mitochondrion (GO:0005739)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metalloaminopeptidase activity (GO:0070006)|metalloexopeptidase activity (GO:0008235)			NS(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)	8						TCTTGTTCATCGGGAAATCAT	0.368																																					p.R130W		Atlas-SNP	.											.	METAP1D	32	.	0			c.C388T						.						210	172	185					2																	172930371		2203	4300	6503	SO:0001583	missense	254042	exon4			GTTCATCGGGAAA	AY374142, BC029123	CCDS2246.1	2q31.1	2010-09-21			ENSG00000172878	ENSG00000172878			32583	protein-coding gene	gene with protein product	"methionine aminopeptidase 1D"	610267				14532271, 16568094	Standard	NM_199227		Approved	MAP1D, Metap1l	uc002uhk.3	Q6UB28	OTTHUMG00000132283	ENST00000315796.4:c.388C>T	chr2.hg19:g.172930371C>T	ENSP00000315152:p.Arg130Trp	68.0	0.0		89.0	6.0	NM_199227	Q1WNX3	Missense_Mutation	SNP	ENST00000315796.4	hg19	CCDS2246.1	.	.	.	.	.	.	.	.	.	.	C	5.241	0.230000	0.09969	.	.	ENSG00000172878	ENST00000315796	T	0.76968	-1.06	5.68	3.87	0.44632	Peptidase M24, structural domain (3);	0.314175	0.39615	N	0.001313	T	0.71617	0.3361	L	0.58810	1.83	0.24283	N	0.995196	B	0.06786	0.001	B	0.01281	0.0	T	0.64931	-0.6291	10	0.72032	D	0.01	-8.3285	8.5518	0.33455	0.0:0.7392:0.1253:0.1355	.	130	Q6UB28	AMP1D_HUMAN	W	130	ENSP00000315152:R130W	ENSP00000315152:R130W	R	+	1	2	METAP1D	172638617	1.000000	0.71417	0.999000	0.59377	0.009000	0.06853	2.805000	0.47939	0.846000	0.35142	-0.145000	0.13849	CGG	.	.		0.368	METAP1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255378.2	NM_199227		T	172930371	C	T	172930371	3	4	191	1	0	0	0	0	1	0	0	0	9238	875	31	1	402	1	MAP1D	2	172930371	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	62966099	172930371	70269002	19	28267										
HECW2	57520	hgsc.bcm.edu	37	chr2	197066049	197066049	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tcaactgctgtcaacagtttTtcataaagcatggaaaagga	8	7	3	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr2:197066049T>A	ENST00000260983.3	-	29	4853	c.4671A>T	c.(4669-4671)gaA>gaT	p.E1557D	HECW2_ENST00000409111.1_Missense_Mutation_p.E1201D	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1557	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						TCAACAGTTTTTCATAAAGCA	0.453																																					p.E1557D		Atlas-SNP	.											.	HECW2	239	.	0			c.A4671T						.						140	126	131					2																	197066049		2203	4300	6503	SO:0001583	missense	57520	exon29			CAGTTTTTCATAA	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.4671A>T	chr2.hg19:g.197066049T>A	ENSP00000260983:p.Glu1557Asp	95.0	0.0		92.0	24.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	T	14.08	2.428499	0.43122	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	T;T	0.51574	0.7;0.7	4.98	-2.07	0.07276	HECT (4);	0.000000	0.85682	D	0.000000	T	0.57710	0.2072	L	0.56340	1.77	0.47994	D	0.999566	D	0.57571	0.98	D	0.70935	0.971	T	0.53373	-0.8448	10	0.52906	T	0.07	.	12.7739	0.57436	0.0:0.3837:0.0:0.6163	.	1557	Q9P2P5	HECW2_HUMAN	D	1201;1557	ENSP00000386775:E1201D;ENSP00000260983:E1557D	ENSP00000260983:E1557D	E	-	3	2	HECW2	196774294	1.000000	0.71417	0.948000	0.38648	0.845000	0.48019	1.078000	0.30754	-0.920000	0.03799	-1.937000	0.00501	GAA	.	.		0.453	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		A	197066049	T	A	197066049	3	1	191	1	0	0	0	0	1	0	0	0	7052	1838	64	4	51	4	HECW2	2	197066049	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	24135678	197066049	46133324	20	28268										
SLC16A14	151473	hgsc.bcm.edu	37	chr2	230914607	230914607	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ccacaggtgttaatgaacaaGccgatgaaagggcctgtcac	11	10	1	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr2:230914607G>A	ENST00000295190.4	-	3	731	c.273C>T	c.(271-273)ggC>ggT	p.G91G		NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		TAATGAACAAGCCGATGAAAG	0.468																																					p.G91G		Atlas-SNP	.											.	SLC16A14	75	.	0			c.C273T						.						51	52	52					2																	230914607		2203	4300	6503	SO:0001819	synonymous_variant	151473	exon3			GAACAAGCCGATG	BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053		"Solute carriers"	26417	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 14"		"solute carrier family 16 (monocarboxylic acid transporters), member 14"				Standard	NM_152527		Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.273C>T	chr2.hg19:g.230914607G>A		238.0	0.0		300.0	101.0	NM_152527	A8KA08|Q53R92|Q96NI7	Silent	SNP	ENST00000295190.4	hg19	CCDS2473.1																																																																																			.	.		0.468	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256918.2	NM_152527		A	230914607	G	A	230914607	2	1	191	1	0	0	0	0	0	0	0	1	14422	958	34	3		3	SLC16A14	2	230914607	Silent	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	33848558	230914607	12284766	21	28269										
COLQ	8292	hgsc.bcm.edu	37	chr3	15498035	15498035	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gtctctgcggaaggcaatggCgttttgggtgttcagcctct	14	9	3	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr3:15498035C>T	ENST00000383788.5	-	14	1131	c.1006G>A	c.(1006-1008)Gcc>Acc	p.A336T	COLQ_ENST00000383781.4_Missense_Mutation_p.A326T|COLQ_ENST00000383786.5_Missense_Mutation_p.A302T|COLQ_ENST00000435459.2_Missense_Mutation_p.A326T|COLQ_ENST00000383787.2_Missense_Mutation_p.A327T|COLQ_ENST00000383785.2_3'UTR|COLQ_ENST00000603808.1_Missense_Mutation_p.A336T	NM_005677.3	NP_005668.2	Q9Y215	COLQ_HUMAN	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	336					acetylcholine catabolic process in synaptic cleft (GO:0001507)|asymmetric protein localization (GO:0008105)	basal lamina (GO:0005605)|cell junction (GO:0030054)|collagen trimer (GO:0005581)|extracellular space (GO:0005615)|synapse (GO:0045202)				endometrium(2)|large_intestine(4)|lung(10)|skin(3)	19						AAGGCAATGGCGTTTTGGGTG	0.537																																					p.A336T		Atlas-SNP	.											.	COLQ	82	.	0			c.G1006A						.						163	152	156					3																	15498035		2203	4300	6503	SO:0001583	missense	8292	exon14			CAATGGCGTTTTG	AF057036	CCDS33709.1, CCDS43057.1, CCDS46768.1	3p	2008-07-18			ENSG00000206561	ENSG00000206561			2226	protein-coding gene	gene with protein product	"single strand of homotrimeric collagen-like tail subunit of asymmetric acetylcholinesterase", "collagenic tail of endplate acetylcholinesterase", "AChE Q subunit", "acetylcholinesterase-associated collagen"	603033				9689136	Standard	NM_005677		Approved	EAD	uc003bzx.3	Q9Y215	OTTHUMG00000156233	ENST00000383788.5:c.1006G>A	chr3.hg19:g.15498035C>T	ENSP00000373298:p.Ala336Thr	28.0	0.0		55.0	15.0	NM_005677	B3KY09|Q6DK18|Q6YH18|Q6YH19|Q6YH20|Q6YH21|Q9NP18|Q9NP19|Q9NP20|Q9NP21|Q9NP22|Q9NP23|Q9NP24|Q9UP88	Missense_Mutation	SNP	ENST00000383788.5	hg19	CCDS33709.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.909156	0.72868	.	.	ENSG00000206561	ENST00000383787;ENST00000383781;ENST00000435459;ENST00000383788;ENST00000420589;ENST00000454772;ENST00000383786	D;D;D;D;D	0.93133	-2.8;-2.92;-3.17;-2.89;-2.91	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.95802	0.8634	L	0.60455	1.87	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.997;0.993;0.999	D	0.93918	0.7203	10	0.24483	T	0.36	-14.5069	19.4381	0.94806	0.0:1.0:0.0:0.0	.	302;327;336;326	Q9Y215-3;Q9Y215-5;Q9Y215;Q9Y215-2	.;.;COLQ_HUMAN;.	T	327;326;326;336;326;336;302	ENSP00000373297:A327T;ENSP00000373291:A326T;ENSP00000402511:A326T;ENSP00000373298:A336T;ENSP00000373296:A302T	ENSP00000373291:A326T	A	-	1	0	COLQ	15473039	1.000000	0.71417	0.960000	0.40013	0.979000	0.70002	5.743000	0.68655	2.606000	0.88127	0.561000	0.74099	GCC	.	.		0.537	COLQ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343575.1	NM_005677		T	15498035	C	T	15498035	3	4	191	1	0	0	0	0	1	0	0	0	3715	768	27	1	377	1	COLQ	3	15498035	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10		15498035	182524395	22	28270										
GADL1	339896	hgsc.bcm.edu	37	chr3	30842571	30842571	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cttggcagagtagcatttttTaagaagatccttcgaaaaag	9	6	0	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr3:30842571T>A	ENST00000282538.5	-	12	1210	c.1060A>T	c.(1060-1062)Aaa>Taa	p.K354*	GADL1_ENST00000454381.3_Nonsense_Mutation_p.K354*	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	354					carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						TAGCATTTTTTAAGAAGATCC	0.353																																					p.K354X		Atlas-SNP	.											.	GADL1	91	.	0			c.A1060T						.						72	67	69					3																	30842571		2203	4300	6503	SO:0001587	stop_gained	339896	exon12			ATTTTTTAAGAAG	AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644			27949	protein-coding gene	gene with protein product		615601					Standard	NM_207359		Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.1060A>T	chr3.hg19:g.30842571T>A	ENSP00000282538:p.Lys354*	58.0	0.0		85.0	29.0	NM_207359		Nonsense_Mutation	SNP	ENST00000282538.5	hg19	CCDS2649.2	.	.	.	.	.	.	.	.	.	.	T	16.81	3.226614	0.58668	.	.	ENSG00000144644	ENST00000282538;ENST00000454381	.	.	.	5.47	4.3	0.51218	.	0.233059	0.42172	D	0.000760	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	12.5695	0.56328	0.0:0.0:0.1392:0.8608	.	.	.	.	X	354	.	ENSP00000282538:K354X	K	-	1	0	GADL1	30817575	1.000000	0.71417	1.000000	0.80357	0.122000	0.20287	3.188000	0.50958	0.892000	0.36259	-0.449000	0.05564	AAA	.	.		0.353	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359		A	30842571	T	A	30842571	4	1	191	1	0	0	0	0	0	1	0	0	6193	1763	61	4	521	4	GADL1	3	30842571	Nonsense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	15344536	30842571	167179859	23	28271										
RASSF1	11186	hgsc.bcm.edu	37	chr3	50374725	50374725	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tgctgctccaggtcatttcgAaagaaggcgcctccgcctcg	11	14	1	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr3:50374725A>C	ENST00000327761.3	-	1	170	c.26T>G	c.(25-27)tTc>tGc	p.F9C	RASSF1_ENST00000488024.1_5'UTR|RASSF1_ENST00000359365.4_Intron|RASSF1_ENST00000395126.3_Intron|RASSF1_ENST00000357043.2_Intron	NM_170713.2	NP_733831.1			Ras association (RalGDS/AF-6) domain family member 1											lung(2)|ovary(1)|skin(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000278)|OV - Ovarian serous cystadenocarcinoma(275;0.0015)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GGTCATTTCGAAAGAAGGCGC	0.667																																					p.F9C		Atlas-SNP	.											.	RASSF1	46	.	0			c.T26G						.						57	56	57					3																	50374725		2203	4300	6503	SO:0001583	missense	11186	exon1			ATTTCGAAAGAAG	AF132675	CCDS2820.1, CCDS2821.1, CCDS2822.1, CCDS43096.1	3p21.3	2008-02-22	2008-02-22		ENSG00000068028	ENSG00000068028			9882	protein-coding gene	gene with protein product		605082					Standard	NM_170713		Approved	NORE2A, REH3P21, RDA32, 123F2	uc003dad.1	Q9NS23	OTTHUMG00000149958	ENST00000327761.3:c.26T>G	chr3.hg19:g.50374725A>C	ENSP00000333327:p.Phe9Cys	53.0	0.0		56.0	20.0	NM_170713		Missense_Mutation	SNP	ENST00000327761.3	hg19	CCDS2821.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.518993	0.85495	.	.	ENSG00000068028	ENST00000327761	T	0.11930	2.73	4.62	4.62	0.57501	.	.	.	.	.	T	0.15565	0.0375	L	0.57536	1.79	0.80722	D	1	P	0.50710	0.938	B	0.42771	0.397	T	0.01349	-1.1378	9	0.87932	D	0	.	8.3873	0.32508	0.9067:0.0:0.0933:0.0	.	9	Q5TZT2	.	C	9	ENSP00000333327:F9C	ENSP00000333327:F9C	F	-	2	0	RASSF1	50349729	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	6.037000	0.70956	1.935000	0.56089	0.448000	0.29417	TTC	.	.		0.667	RASSF1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314309.1			C	50374725	A	C	50374725	3	2	191	1	0	0	0	0	1	0	0	0	13099	246	9	5	806	5	RASSF1	3	50374725	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	19532154	50374725	147647705	24	28272										
APPL1	26060	hgsc.bcm.edu	37	chr3	57282311	57282311	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gatcccttatatgtgcctgaCccagaccccaccaaatttcc	5	16	0	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr3:57282311C>T	ENST00000288266.3	+	10	942	c.795C>T	c.(793-795)gaC>gaT	p.D265D		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	265	Required for RAB5A binding.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)			breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		ATGTGCCTGACCCAGACCCCA	0.403																																					p.D265D		Atlas-SNP	.											.	APPL1	59	.	0			c.C795T						.						113	108	110					3																	57282311		2203	4300	6503	SO:0001819	synonymous_variant	26060	exon10			GCCTGACCCAGAC	AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"Pleckstrin homology (PH) domain containing"	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.795C>T	chr3.hg19:g.57282311C>T		151.0	0.0		181.0	33.0	NM_012096	Q9P2B9	Silent	SNP	ENST00000288266.3	hg19	CCDS2882.1																																																																																			.	.		0.403	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096		T	57282311	C	T	57282311	2	4	191	1	0	0	0	0	0	0	0	1	817	506	18	3		3	APPL1	3	57282311	Silent	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	6907586	57282311	140740119	25	28273										
CCNL1	57018	hgsc.bcm.edu	37	chr3	156876717	156876717	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	acatctcttattcttctaggTgcttcttcgatttttgatgc	6	9	4	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr3:156876717T>C	ENST00000295926.3	-	3	544	c.426A>G	c.(424-426)gcA>gcG	p.A142A	CCNL1_ENST00000461804.1_Silent_p.A142A|CCNL1_ENST00000295925.4_Silent_p.A142A	NM_020307.2	NP_064703.1	Q9UK58	CCNL1_HUMAN	cyclin L1	142	Cyclin-like 1.				regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|nucleus (GO:0005634)				NS(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308)			TTCTTCTAGGTGCTTCTTCGA	0.368																																					p.A142A		Atlas-SNP	.											.	CCNL1	53	.	0			c.A426G						.						195	181	186					3																	156876717		2203	4300	6503	SO:0001819	synonymous_variant	57018	exon3			TCTAGGTGCTTCT	AF180920	CCDS3178.1	3q25.31	2008-02-05			ENSG00000163660	ENSG00000163660			20569	protein-coding gene	gene with protein product		613384				11980906	Standard	NM_020307		Approved	ania-6a	uc003fbf.3	Q9UK58	OTTHUMG00000158713	ENST00000295926.3:c.426A>G	chr3.hg19:g.156876717T>C		45.0	0.0		72.0	7.0	NM_020307	B3KMY3|Q6NVY9|Q6UWS7|Q8NI48|Q96QT0|Q9NZF3	Silent	SNP	ENST00000295926.3	hg19	CCDS3178.1																																																																																			.	.		0.368	CCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351859.1	NM_020307		C	156876717	T	C	156876717	2	2	191	1	0	0	0	0	0	0	0	1	2933	1683	59	2		2	CCNL1	3	156876717	Silent	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	99594406	156876717	41145713	26	28274										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gaaacaaatgaatgatgcacAtcatggtggctggacaacaa	10	7	1	2	rs121913279		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.H1047R	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,adenocarcinoma,0,2044	PIK3CA	8460	.	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)	c.A3140G						.						99	89	92					3																	178952085		1912	4130	6042	SO:0001583	missense	5290	exon21			ATGCACATCATGG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	chr3.hg19:g.178952085A>G	ENSP00000263967:p.His1047Arg	128.0	0.0		128.0	10.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	.	.		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952085	A	G	178952085	3	3	191	1	0	0	0	0	1	0	0	0	11922	217	8	2	3218	2	PIK3CA	3	178952085	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	22075368	178952085	19070345	27	28275										
STK32B	55351	hgsc.bcm.edu	37	chr4	5333066	5333066	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ggggactgtgaaactctacaTctgtgagctggcactggccc	13	11	2	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr4:5333066T>G	ENST00000282908.5	+	4	802	c.380T>G	c.(379-381)aTc>aGc	p.I127S	STK32B_ENST00000512636.1_Missense_Mutation_p.I80S|STK32B_ENST00000510398.1_Missense_Mutation_p.I80S	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						AAACTCTACATCTGTGAGCTG	0.577																																					p.I127S		Atlas-SNP	.											.	STK32B	87	.	0			c.T380G						.						106	91	96					4																	5333066		2203	4300	6503	SO:0001583	missense	55351	exon4			TCTACATCTGTGA	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.380T>G	chr4.hg19:g.5333066T>G	ENSP00000282908:p.Ile127Ser	48.0	0.0		66.0	30.0	NM_018401		Missense_Mutation	SNP	ENST00000282908.5	hg19	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.282690	0.40394	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.66460	-0.21;-0.21;-0.21	5.19	5.19	0.71726	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.42053	U	0.000770	T	0.71970	0.3403	L	0.31420	0.93	0.54753	D	0.999987	P	0.48503	0.911	D	0.63793	0.918	T	0.75584	-0.3267	10	0.87932	D	0	.	14.5285	0.67905	0.0:0.0:0.0:1.0	.	127	Q9NY57	ST32B_HUMAN	S	127;80;80	ENSP00000282908:I127S;ENSP00000423209:I80S;ENSP00000420984:I80S	ENSP00000282908:I127S	I	+	2	0	STK32B	5383967	1.000000	0.71417	1.000000	0.80357	0.321000	0.28281	7.434000	0.80377	2.068000	0.61886	0.460000	0.39030	ATC	.	.		0.577	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		G	5333066	T	G	5333066	3	3	191	1	0	0	0	0	1	0	0	0	15313	1435	50	5	394	5	STK32B	4	5333066	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10		5333066	185821210	28	28276										
GRXCR1	389207	hgsc.bcm.edu	37	chr4	42895607	42895607	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aaaaatggcacagtcagaggCgtcaaatacaaagtgagtgc	11	7	2	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr4:42895607C>A	ENST00000399770.2	+	1	324	c.324C>A	c.(322-324)ggC>ggA	p.G108G	RN7SKP82_ENST00000516786.1_RNA	NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	108					auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						CAGTCAGAGGCGTCAAATACA	0.433																																					p.G108G		Atlas-SNP	.											.	GRXCR1	78	.	0			c.C324A						.						110	112	112					4																	42895607		1960	4152	6112	SO:0001819	synonymous_variant	389207	exon1			CAGAGGCGTCAAA		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 88"	613283	"deafness, autosomal recessive 25"	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.324C>A	chr4.hg19:g.42895607C>A		65.0	0.0		72.0	6.0	NM_001080476		Silent	SNP	ENST00000399770.2	hg19	CCDS43225.1																																																																																			.	.		0.433	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476		A	42895607	C	A	42895607	2	1	191	1	0	0	0	0	0	0	0	1	6821	755	27	1		1	GRXCR1	4	42895607	Silent	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	37562541	42895607	148258669	29	28277										
GRXCR1	389207	hgsc.bcm.edu	37	chr4	42964912	42964912	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	caatgttttcccttcagcaaCcatcaactgatctagaattt	4	11	3	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr4:42964912C>A	ENST00000399770.2	+	2	388	c.388C>A	c.(388-390)Cca>Aca	p.P130T		NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	130	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						CCTTCAGCAACCATCAACTGA	0.358																																					p.P130T		Atlas-SNP	.											.	GRXCR1	78	.	0			c.C388A						.						154	148	150					4																	42964912		1868	4103	5971	SO:0001583	missense	389207	exon2			CAGCAACCATCAA		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 88"	613283	"deafness, autosomal recessive 25"	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.388C>A	chr4.hg19:g.42964912C>A	ENSP00000382670:p.Pro130Thr	101.0	0.0		131.0	49.0	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	hg19	CCDS43225.1	.	.	.	.	.	.	.	.	.	.	C	10.40	1.340764	0.24339	.	.	ENSG00000215203	ENST00000399770	T	0.32753	1.44	5.78	5.78	0.91487	Glutaredoxin (1);Thioredoxin-like fold (1);	0.254842	0.33834	U	0.004518	T	0.23492	0.0568	L	0.34521	1.04	0.35793	D	0.822526	B	0.26400	0.148	B	0.19946	0.027	T	0.17684	-1.0361	10	0.16420	T	0.52	-21.6966	15.2736	0.73726	0.0:0.8498:0.1501:0.0	.	130	A8MXD5	GRCR1_HUMAN	T	130	ENSP00000382670:P130T	ENSP00000382670:P130T	P	+	1	0	GRXCR1	42659669	1.000000	0.71417	1.000000	0.80357	0.529000	0.34654	1.623000	0.37008	2.724000	0.93272	0.655000	0.94253	CCA	.	.		0.358	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476		A	42964912	C	A	42964912	3	1	191	1	0	0	0	0	1	0	0	0	6821	507	18	3	394	3	GRXCR1	4	42964912	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	69305	42964912	148189364	30	28278										
LRRC66	339977	hgsc.bcm.edu	37	chr4	52883570	52883570	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tgtaagagaactctaaagaaAttgaaacttacatccacagt	6	7	1	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr4:52883570A>G	ENST00000343457.3	-	1	216	c.210T>C	c.(208-210)aaT>aaC	p.N70N		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	70						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(8)|lung(34)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	58						CTCTAAAGAAATTGAAACTTA	0.353																																					p.N70N		Atlas-SNP	.											.	LRRC66	128	.	0			c.T210C						.						88	87	87					4																	52883570		1839	4093	5932	SO:0001819	synonymous_variant	339977	exon1			AAAGAAATTGAAA	BC040414	CCDS43229.1	4q12	2008-08-08			ENSG00000188993	ENSG00000188993			34299	protein-coding gene	gene with protein product							Standard	XM_005265739		Approved		uc003gzi.3	Q68CR7	OTTHUMG00000160623	ENST00000343457.3:c.210T>C	chr4.hg19:g.52883570A>G		92.0	0.0		144.0	59.0	NM_001024611		Silent	SNP	ENST00000343457.3	hg19	CCDS43229.1																																																																																			.	.		0.353	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		G	52883570	A	G	52883570	2	3	191	1	0	0	0	0	0	0	0	1	9027	98	4	2		2	LRRC66	4	52883570	Silent	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	9918658	52883570	138270706	31	28279										
MANBA	4126	hgsc.bcm.edu	37	chr4	103561007	103561007	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctgttttgacacactgggccTgcatcacctgattcaggaaa	9	11	2	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr4:103561007T>A	ENST00000226578.4	-	14	1976	c.1877A>T	c.(1876-1878)cAg>cTg	p.Q626L	MANBA_ENST00000505239.1_Missense_Mutation_p.Q569L	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	626					cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)			cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		ACACTGGGCCTGCATCACCTG	0.448																																					p.Q626L		Atlas-SNP	.											.	MANBA	78	.	0			c.A1877T						.						108	95	99					4																	103561007		2203	4300	6503	SO:0001583	missense	4126	exon14			TGGGCCTGCATCA		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.1877A>T	chr4.hg19:g.103561007T>A	ENSP00000226578:p.Gln626Leu	78.0	0.0		81.0	13.0	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	hg19	CCDS3658.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.969171	0.92855	.	.	ENSG00000109323	ENST00000226578;ENST00000505239	D;D	0.97752	-4.52;-4.52	5.74	5.74	0.90152	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.99118	0.9696	H	0.95470	3.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.985;0.988	D	0.99282	1.0896	10	0.87932	D	0	-18.2689	16.0292	0.80564	0.0:0.0:0.0:1.0	.	569;626	E9PFW2;O00462	.;MANBA_HUMAN	L	626;569	ENSP00000226578:Q626L;ENSP00000427322:Q569L	ENSP00000226578:Q626L	Q	-	2	0	MANBA	103780055	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.626000	0.83164	2.187000	0.69744	0.533000	0.62120	CAG	.	.		0.448	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2			A	103561007	T	A	103561007	3	1	191	1	0	0	0	0	1	0	0	0	9228	1580	55	4	778	4	MANBA	4	103561007	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	50677437	103561007	87593269	32	28280										
TRIM2	23321	hgsc.bcm.edu	37	chr4	154191666	154191666	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ccctgtctgcacactttctgCgagaggtaagcctcctttgt	9	13	2	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr4:154191666C>A	ENST00000437508.2	+	2	330	c.129C>A	c.(127-129)tgC>tgA	p.C43*	TRIM2_ENST00000494872.1_3'UTR|TRIM2_ENST00000338700.5_Nonsense_Mutation_p.C70*	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	43					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		ACACTTTCTGCGAGAGGTAAG	0.498																																					p.C70X		Atlas-SNP	.											.	TRIM2	105	.	0			c.C210A						.						129	113	118					4																	154191666		2203	4300	6503	SO:0001587	stop_gained	23321	exon2			TTTCTGCGAGAGG	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15974	protein-coding gene	gene with protein product		614141	"tripartite motif-containing 2"			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.129C>A	chr4.hg19:g.154191666C>A	ENSP00000415812:p.Cys43*	104.0	0.0		97.0	62.0	NM_015271	D3DP09|O60272|Q9BSI9|Q9UFZ1	Nonsense_Mutation	SNP	ENST00000437508.2	hg19	CCDS47147.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332918	0.81801	.	.	ENSG00000109654	ENST00000441616;ENST00000437508;ENST00000338700	.	.	.	5.68	2.6	0.31112	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.8624	7.0645	0.25143	0.0:0.5496:0.0:0.4504	.	.	.	.	X	43;43;70	.	ENSP00000339659:C70X	C	+	3	2	TRIM2	154411116	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.773000	0.38563	0.761000	0.33130	0.650000	0.86243	TGC	.	.		0.498	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1			A	154191666	C	A	154191666	4	1	191	1	0	0	0	0	0	1	0	0	16509	776	27	1	216	1	TRIM2	4	154191666	Nonsense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	50630659	154191666	36962610	33	28281										
IRF2	3660	hgsc.bcm.edu	37	chr4	185339806	185339806	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	caaggaattcatggcgcatcTgaaattcgccttccatgttt	8	10	2	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr4:185339806T>C	ENST00000393593.3	-	4	451	c.244A>G	c.(244-246)Aga>Gga	p.R82G	IRF2_ENST00000512020.1_5'UTR	NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	82					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		ATGGCGCATCTGAAATTCGCC	0.393																																					p.R82G		Atlas-SNP	.											.	IRF2	53	.	0			c.A244G						.						103	100	101					4																	185339806		2203	4300	6503	SO:0001583	missense	3660	exon4			CGCATCTGAAATT		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.244A>G	chr4.hg19:g.185339806T>C	ENSP00000377218:p.Arg82Gly	76.0	0.0		59.0	22.0	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Missense_Mutation	SNP	ENST00000393593.3	hg19	CCDS3835.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.238810	0.79800	.	.	ENSG00000168310	ENST00000393593;ENST00000507523;ENST00000510814;ENST00000506230;ENST00000505316	D;D;D;D	0.98567	-5.0;-5.0;-5.0;-5.0	4.82	3.96	0.45880	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.065540	0.64402	D	0.000005	D	0.99155	0.9708	M	0.93197	3.39	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99293	1.0899	10	0.87932	D	0	-18.4248	14.8733	0.70474	0.0:0.0:0.8533:0.1467	.	82	P14316	IRF2_HUMAN	G	82	ENSP00000377218:R82G;ENSP00000427204:R82G;ENSP00000424552:R82G;ENSP00000422860:R82G	ENSP00000377218:R82G	R	-	1	2	IRF2	185576800	1.000000	0.71417	0.986000	0.45419	0.905000	0.53344	5.518000	0.67068	1.368000	0.46115	-0.302000	0.09304	AGA	.	.		0.393	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1			C	185339806	T	C	185339806	3	2	191	1	0	0	0	0	1	0	0	0	7837	1588	55	2	829	2	IRF2	4	185339806	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	31148140	185339806	5814470	34	28282										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5463105	5463105	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gtgaaataggagaaaaatacAgaaagcaaccctgtgaggaa	11	5	0	4			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr5:5463105A>T	ENST00000296564.7	+	13	3880	c.3658A>T	c.(3658-3660)Aga>Tga	p.R1220*		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1220					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AGAAAAATACAGAAAGCAACC	0.363																																					p.R1220X		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A3658T						.						51	50	50					5																	5463105		1832	4082	5914	SO:0001587	stop_gained	23379	exon13			AAATACAGAAAGC																												ENST00000296564.7:c.3658A>T	chr5.hg19:g.5463105A>T	ENSP00000296564:p.Arg1220*	151.0	0.0		146.0	44.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Nonsense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	A	41	9.095237	0.99064	.	.	ENSG00000164151	ENST00000296564	.	.	.	4.45	-0.765	0.11023	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-0.7671	8.1922	0.31374	0.3896:0.0:0.6104:0.0	.	.	.	.	X	1220	.	ENSP00000296564:R1220X	R	+	1	2	KIAA0947	5516105	0.000000	0.05858	0.000000	0.03702	0.127000	0.20565	-1.099000	0.03343	-0.148000	0.11234	0.254000	0.18369	AGA	.	.		0.363	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			T	5463105	A	T	5463105	4	4	191	1	0	0	0	0	0	1	0	0	8211	180	7	4	3708	4	KIAA0947	5	5463105	Nonsense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10		5463105	175452155	35	28283										
ZNF131	7690	hgsc.bcm.edu	37	chr5	43139306	43139306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tcgccatttaattgagttcaCatatacagcaaaattaatga	5	7	1	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr5:43139306C>T	ENST00000399534.1	+	4	310	c.266C>T	c.(265-267)aCa>aTa	p.T89I	ZNF131_ENST00000505606.2_Missense_Mutation_p.T89I|ZNF131_ENST00000306938.4_Missense_Mutation_p.T89I|ZNF131_ENST00000509634.1_Missense_Mutation_p.T89I|ZNF131_ENST00000509156.1_Missense_Mutation_p.T89I|ZNF131_ENST00000509931.1_Intron			P52739	ZN131_HUMAN	zinc finger protein 131	89	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	17						ATTGAGTTCACATATACAGCA	0.343																																					p.T89I		Atlas-SNP	.											.	ZNF131	51	.	0			c.C266T						.						104	99	101					5																	43139306		1865	4097	5962	SO:0001583	missense	7690	exon4			AGTTCACATATAC	U09410	CCDS43313.1	5p12	2013-01-09	2006-06-13		ENSG00000172262	ENSG00000172262		"Zinc fingers, C2H2-type", "-", "BTB/POZ domain containing"	12915	protein-coding gene	gene with protein product	"zinc finger and BTB domain containing 35"	604073	"zinc finger protein 131 (clone pHZ-10)"				Standard	XM_005248359		Approved	ZBTB35, pHZ-10	uc003jnk.3	P52739	OTTHUMG00000162223	ENST00000399534.1:c.266C>T	chr5.hg19:g.43139306C>T	ENSP00000382450:p.Thr89Ile	142.0	0.0		122.0	5.0	NM_003432	B4DRL3|Q6PIF0	Missense_Mutation	SNP	ENST00000399534.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.02	3.003305	0.54254	.	.	ENSG00000172262	ENST00000515326;ENST00000509156;ENST00000508259;ENST00000306938;ENST00000399534;ENST00000505606;ENST00000509634;ENST00000509341	T;T;T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08;0.08;0.08	5.34	5.34	0.76211	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.48241	0.1489	N	0.00788	-1.185	0.58432	D	0.999992	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.997	T	0.63817	-0.6551	10	0.18276	T	0.48	-11.4399	19.0469	0.93025	0.0:1.0:0.0:0.0	.	89;89	P52739;P52739-2	ZN131_HUMAN;.	I	89	ENSP00000422079:T89I;ENSP00000426504:T89I;ENSP00000422659:T89I;ENSP00000305804:T89I;ENSP00000382450:T89I;ENSP00000423945:T89I;ENSP00000421246:T89I;ENSP00000424771:T89I	ENSP00000305804:T89I	T	+	2	0	ZNF131	43175063	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.179000	0.77665	2.474000	0.83562	0.655000	0.94253	ACA	.	.		0.343	ZNF131-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000367982.1	NM_003432		T	43139306	C	T	43139306	3	4	191	1	0	0	0	0	1	0	0	0	17736	478	17	3	276	3	ZNF131	5	43139306	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	37676201	43139306	137775954	36	28284										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54640445	54640445	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctgcatcttgtggttgatgaAaatgtaagagagtaattgtc	11	4	1	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr5:54640445A>G	ENST00000230640.5	+	9	1256	c.1002A>G	c.(1000-1002)gaA>gaG	p.E334E	SKIV2L2_ENST00000545714.1_Silent_p.E233E	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	334					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TGGTTGATGAAAATGTAAGAG	0.338																																					p.E334E	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.A1002G						.						60	56	57					5																	54640445		2203	4300	6503	SO:0001819	synonymous_variant	23517	exon9			TGATGAAAATGTA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.1002A>G	chr5.hg19:g.54640445A>G		203.0	0.0		258.0	15.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	hg19	CCDS3967.1																																																																																			.	.		0.338	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			G	54640445	A	G	54640445	2	3	191	1	0	0	0	0	0	0	0	1	14375	11	1	2		2	SKIV2L2	5	54640445	Silent	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	11501139	54640445	126274815	37	28285										
DDX4	54514	hgsc.bcm.edu	37	chr5	55082361	55082361	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ttcagacttttgaagaagctAatctctgtcagacactgaat	7	8	3	5			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr5:55082361A>G	ENST00000505374.1	+	14	972	c.880A>G	c.(880-882)Aat>Gat	p.N294D	DDX4_ENST00000354991.5_Missense_Mutation_p.N260D|DDX4_ENST00000353507.5_Missense_Mutation_p.N260D|DDX4_ENST00000511853.1_Missense_Mutation_p.N145D|DDX4_ENST00000514278.2_Missense_Mutation_p.N274D	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	294					male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				TGAAGAAGCTAATCTCTGTCA	0.328																																					p.N294D		Atlas-SNP	.											.	DDX4	194	.	0			c.A880G						.						71	70	71					5																	55082361		2203	4300	6503	SO:0001583	missense	54514	exon14			GAAGCTAATCTCT	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.880A>G	chr5.hg19:g.55082361A>G	ENSP00000424838:p.Asn294Asp	98.0	0.0		110.0	31.0	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Missense_Mutation	SNP	ENST00000505374.1	hg19	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.596876	0.28445	.	.	ENSG00000152670	ENST00000353507;ENST00000514278;ENST00000505374;ENST00000506511;ENST00000354991;ENST00000511853	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	4.56	0.845	0.18950	RNA helicase, DEAD-box type, Q motif (1);	0.448366	0.25720	N	0.028741	T	0.20740	0.0499	N	0.13168	0.305	0.32535	N	0.534478	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.10450	0.002;0.001;0.005;0.002	T	0.12863	-1.0531	10	0.25751	T	0.34	-10.9394	6.349	0.21365	0.7003:0.1384:0.1612:0.0	.	274;145;260;294	D6RDK4;E9PCD8;Q9NQI0-2;Q9NQI0	.;.;.;DDX4_HUMAN	D	260;274;294;274;260;145	ENSP00000334167:N260D;ENSP00000425359:N274D;ENSP00000424838:N294D;ENSP00000427167:N274D;ENSP00000347087:N260D;ENSP00000423123:N145D	ENSP00000334167:N260D	N	+	1	0	DDX4	55118118	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	2.377000	0.44300	0.281000	0.22233	0.482000	0.46254	AAT	.	.		0.328	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		G	55082361	A	G	55082361	3	3	191	1	0	0	0	0	1	0	0	0	4362	362	13	2	971	2	DDX4	5	55082361	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	441916	55082361	125832899	38	28286										
FBN2	2201	hgsc.bcm.edu	37	chr5	127668623	127668623	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ccaatacacttgatgccgttTccaatccagccttctctgca	5	15	1	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr5:127668623T>C	ENST00000508053.1	-	38	5177	c.4203A>G	c.(4201-4203)ggA>ggG	p.G1401G	FBN2_ENST00000262464.4_Silent_p.G1401G|FBN2_ENST00000508989.1_Silent_p.G1368G|FBN2_ENST00000507835.1_Silent_p.G251G			P35556	FBN2_HUMAN	fibrillin 2	1401	EGF-like 22; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TGATGCCGTTTCCAATCCAGC	0.418																																					p.G1401G		Atlas-SNP	.											.	FBN2	858	.	0			c.A4203G						.						220	206	211					5																	127668623		2203	4300	6503	SO:0001819	synonymous_variant	2201	exon32			GCCGTTTCCAATC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.4203A>G	chr5.hg19:g.127668623T>C		158.0	0.0		174.0	51.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	.		0.418	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		C	127668623	T	C	127668623	2	2	191	1	0	0	0	0	0	0	0	1	5711	1770	62	2		2	FBN2	5	127668623	Silent	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	72586262	127668623	53246637	39	28287										
SLC4A9	83697	hgsc.bcm.edu	37	chr5	139743132	139743132	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cacagcccggagttgcagcgGaccggcaggtgaggcgagct	17	12	0	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr5:139743132G>T	ENST00000230993.6	+	8	1178	c.1143G>T	c.(1141-1143)cgG>cgT	p.R381R	SLC4A9_ENST00000507527.1_Silent_p.R381R|SLC4A9_ENST00000506757.2_Silent_p.R357R|SLC4A9_ENST00000506545.1_Silent_p.R357R|SLC4A9_ENST00000432095.2_Silent_p.R357R	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	381					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTTGCAGCGGACCGGCAGGT	0.677											OREG0016461	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R381R		Atlas-SNP	.											.	SLC4A9	125	.	0			c.G1143T						.						7	11	10					5																	139743132		2145	4200	6345	SO:0001819	synonymous_variant	83697	exon8			GCAGCGGACCGGC	AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"Solute carriers"	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.1143G>T	chr5.hg19:g.139743132G>T		83.0	0.0	1651	122.0	14.0	NM_001258428	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Silent	SNP	ENST00000230993.6	hg19	CCDS58973.1																																																																																			.	.		0.677	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467		T	139743132	G	T	139743132	2	4	191	1	0	0	0	0	0	0	0	1	14675	1161	41	3		3	SLC4A9	5	139743132	Silent	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	12074509	139743132	41172128	40	28288										
PDGFRB	5159	hgsc.bcm.edu	37	chr5	149515368	149515368	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ttgaggacaagctctggcccCgggggtgtgacgaccaggcc	16	12	1	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr5:149515368C>T	ENST00000261799.4	-	3	583	c.114G>A	c.(112-114)ccG>ccA	p.P38P		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	38	Ig-like C2-type 1.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GCTCTGGCCCCGGGGGTGTGA	0.597			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"																																p.P38P		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	.	PDGFRB	142	.	0			c.G114A						.						36	34	35					5																	149515368		2203	4300	6503	SO:0001819	synonymous_variant	5159	exon3			TGGCCCCGGGGGT	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.114G>A	chr5.hg19:g.149515368C>T		100.0	0.0		184.0	37.0	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	hg19	CCDS4303.1																																																																																			.	.		0.597	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		T	149515368	C	T	149515368	2	4	191	1	0	0	0	0	0	0	0	1	11671	639	23	1		1	PDGFRB	5	149515368	Silent	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	9772236	149515368	31399892	41	28289										
C1QTNF2	114898	hgsc.bcm.edu	37	chr5	159776448	159776448	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gtgatgtcgtaggtgaagtaGtagatcccaggcacgccgca	14	9	0	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr5:159776448G>A	ENST00000393975.3	-	3	723	c.720C>T	c.(718-720)taC>taT	p.Y240Y		NM_031908.4	NP_114114.2	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	195	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				activation of MAPK activity (GO:0000187)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(2)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	13	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGGTGAAGTAGTAGATCCCAG	0.587																																					p.Y240Y		Atlas-SNP	.											.	C1QTNF2	33	.	0			c.C720T						.						89	92	91					5																	159776448		2203	4300	6503	SO:0001819	synonymous_variant	114898	exon3			GAAGTAGTAGATC	AF329836	CCDS4351.2	5q33.3	2008-05-15			ENSG00000145861	ENSG00000145861			14325	protein-coding gene	gene with protein product							Standard	XM_005265815		Approved	CTRP2	uc003lyd.3	Q9BXJ5	OTTHUMG00000130323	ENST00000393975.3:c.720C>T	chr5.hg19:g.159776448G>A		43.0	0.0		74.0	8.0	NM_031908		Silent	SNP	ENST00000393975.3	hg19	CCDS4351.2																																																																																			.	.		0.587	C1QTNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252672.2			A	159776448	G	A	159776448	2	1	191	1	0	0	0	0	0	0	0	1	1965	1024	36	3		3	C1QTNF2	5	159776448	Silent	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	10261080	159776448	21138812	42	28290										
COL23A1	91522	hgsc.bcm.edu	37	chr5	177695729	177695729	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cacagcctctggcatcacttAccttttcccctttcgggcct	6	17	2	0	rs200266099		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr5:177695729A>G	ENST00000390654.3	-	7	853		c.e7+1		COL23A1_ENST00000407622.1_Splice_Site	NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1						collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		ggcaTCACTTACCTTTTCCCC	0.567																																					.		Atlas-SNP	.											.	COL23A1	47	.	0			c.495+2T>C						.						66	70	69					5																	177695729		1993	4174	6167	SO:0001630	splice_region_variant	91522	exon8			TCACTTACCTTTT	AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767		"Collagens"	22990	protein-coding gene	gene with protein product		610043				12644459	Standard	NM_173465		Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.495+1T>C	chr5.hg19:g.177695729A>G		29.0	0.0		62.0	21.0	NM_173465	Q8IVR4|Q9NT93	Splice_Site	SNP	ENST00000390654.3	hg19	CCDS4436.1	.	.	.	.	.	.	.	.	.	.	A	17.08	3.297773	0.60086	.	.	ENSG00000050767	ENST00000390654;ENST00000407622	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2526	0.49034	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL23A1	177628335	1.000000	0.71417	0.998000	0.56505	0.714000	0.41099	5.371000	0.66150	1.978000	0.57642	0.454000	0.30748	.	.	A|0.999;G|0.001		0.567	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465	Intron	G	177695729	A	G	177695729	5	3	191	1	0	0	0	0	0	0	1	0	3684	405	14	2	1217	2	COL23A1	5	177695729	Splice_Site	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	17919281	177695729	3219531	43	28291										
SLC17A3	10786	hgsc.bcm.edu	37	chr6	25849672	25849672	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tcgaaaatcctcttgatgctCccatgagaaaactggaatac	7	10	1	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr6:25849672C>G	ENST00000360657.3	-	10	1343	c.1058G>C	c.(1057-1059)gGa>gCa	p.G353A	SLC17A3_ENST00000361703.6_Missense_Mutation_p.G353A|SLC17A3_ENST00000397060.4_Missense_Mutation_p.G431A			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	353					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						TCTTGATGCTCCCATGAGAAA	0.433																																					p.G431A		Atlas-SNP	.											.	SLC17A3	95	.	0			c.G1292C						.						97	85	89					6																	25849672		2203	4300	6503	SO:0001583	missense	10786	exon11			GATGCTCCCATGA	U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"Solute carriers"	10931	protein-coding gene	gene with protein product		611034	"solute carrier family 17 (sodium phosphate), member 3"			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.1058G>C	chr6.hg19:g.25849672C>G	ENSP00000353873:p.Gly353Ala	84.0	0.0		132.0	46.0	NM_001098486	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Missense_Mutation	SNP	ENST00000360657.3	hg19	CCDS4566.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.45|13.45	2.241383|2.241383	0.39598|0.39598	.|.	.|.	ENSG00000124564|ENSG00000124564	ENST00000481949|ENST00000397060;ENST00000360657;ENST00000361703	.|T;T;T	.|0.63417	.|-0.04;-0.04;-0.04	4.4|4.4	4.4|4.4	0.53042|0.53042	.|Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.|0.000000	.|0.42964	.|D	.|0.000625	T|T	0.66036|0.66036	0.2749|0.2749	M|M	0.63843|0.63843	1.955|1.955	0.43953|0.43953	D|D	0.996623|0.996623	.|D;D	.|0.64830	.|0.966;0.994	.|D;D	.|0.67382	.|0.951;0.923	T|T	0.64428|0.64428	-0.6410|-0.6410	5|10	.|0.31617	.|T	.|0.26	.|.	12.8418|12.8418	0.57806|0.57806	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|431;353	.|B7Z511;O00476	.|.;NPT4_HUMAN	Q|A	32|431;353;353	.|ENSP00000380250:G431A;ENSP00000353873:G353A;ENSP00000355307:G353A	.|ENSP00000353873:G353A	E|G	-|-	1|2	0|0	SLC17A3|SLC17A3	25957651|25957651	0.962000|0.962000	0.33011|0.33011	0.984000|0.984000	0.44739|0.44739	0.088000|0.088000	0.18126|0.18126	3.495000|3.495000	0.53280|0.53280	2.150000|2.150000	0.67090|0.67090	0.650000|0.650000	0.86243|0.86243	GAG|GGA	.	.		0.433	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2			G	25849672	C	G	25849672	3	3	191	1	0	0	0	0	1	0	0	0	14433	855	30	4	212	4	SLC17A3	6	25849672	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10		25849672	145265395	44	28292										
HIST1H3B	8358	hgsc.bcm.edu	37	chr6	26032006	26032006	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	caagtaggcctcacaagcctCctgcagcgccatcaccgcag	9	17	2	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr6:26032006C>T	ENST00000244661.2	-	1	282	c.283G>A	c.(283-285)Gag>Aag	p.E95K		NM_003537.3	NP_003528.1	P68431	H31_HUMAN	histone cluster 1, H3b	95					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(10)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	25						TCACAAGCCTCCTGCAGCGCC	0.562																																					p.E95K		Atlas-SNP	.											HIST1H3B,NS,carcinoma,0,1	HIST1H3B	59	.	0			c.G283A						.						72	73	73					6																	26032006		2203	4300	6503	SO:0001583	missense	8358	exon1			AAGCCTCCTGCAG	X00090	CCDS4573.1	6p22.1	2011-01-27	2006-10-11	2003-03-14	ENSG00000124693	ENSG00000274267		"Histones / Replication-dependent"	4776	protein-coding gene	gene with protein product		602819	"H3 histone family, member L", "histone 1, H3b"	H3FL		6647026, 9119399, 12408966	Standard	NM_003537		Approved	H3/l	uc003nfs.1	P68431	OTTHUMG00000014415	ENST00000244661.2:c.283G>A	chr6.hg19:g.26032006C>T	ENSP00000244661:p.Glu95Lys	82.0	0.0		89.0	31.0	NM_003537	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000244661.2	hg19	CCDS4573.1	.	.	.	.	.	.	.	.	.	.	c	16.97	3.267456	0.59540	.	.	ENSG00000124693	ENST00000244661	T	0.70749	-0.51	5.07	5.07	0.68467	.	.	.	.	.	T	0.80003	0.4544	.	.	.	0.47994	D	0.999564	.	.	.	.	.	.	T	0.82824	-0.0266	6	0.87932	D	0	.	17.7852	0.88535	0.0:1.0:0.0:0.0	.	.	.	.	K	95	ENSP00000244661:E95K	ENSP00000244661:E95K	E	-	1	0	HIST1H3B	26139985	1.000000	0.71417	1.000000	0.80357	0.101000	0.19017	7.492000	0.81482	2.487000	0.83934	0.561000	0.74099	GAG	.	.		0.562	HIST1H3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040077.1	NM_003537		T	26032006	C	T	26032006	3	4	191	1	0	0	0	0	1	0	0	0	7165	864	30	3	131	3	HIST1H3B	6	26032006	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	182334	26032006	145083061	45	28293										
LEMD2	221496	hgsc.bcm.edu	37	chr6	33748859	33748859	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctgaagcctacttacggctaTatattcttgggcttccataa	7	10	1	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr6:33748859T>C	ENST00000293760.5	-	4	944	c.925A>G	c.(925-927)Ata>Gta	p.I309V	LEMD2_ENST00000508327.1_Missense_Mutation_p.I7V|LEMD2_ENST00000502643.1_5'UTR	NM_181336.3	NP_851853.1	Q8NC56	LEMD2_HUMAN	LEM domain containing 2	309					negative regulation of MAPK cascade (GO:0043409)|skeletal muscle cell differentiation (GO:0035914)	integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear membrane (GO:0031965)				central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(2)|pancreas(1)	9						CTTACGGCTATATATTCTTGG	0.408																																					p.I309V		Atlas-SNP	.											.	LEMD2	20	.	0			c.A925G						.						85	79	81					6																	33748859		2203	4300	6503	SO:0001583	missense	221496	exon4			CGGCTATATATTC		CCDS4785.1, CCDS47411.1	6p21.31	2009-11-06			ENSG00000161904	ENSG00000161904			21244	protein-coding gene	gene with protein product						12477932	Standard	NM_001143944		Approved	dJ482C21.1, NET25	uc011drm.2	Q8NC56	OTTHUMG00000014535	ENST00000293760.5:c.925A>G	chr6.hg19:g.33748859T>C	ENSP00000293760:p.Ile309Val	30.0	0.0		68.0	26.0	NM_181336	B4DVH5|E7EVT2|Q5T972|Q5T974	Missense_Mutation	SNP	ENST00000293760.5	hg19	CCDS4785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.035|7.035	0.561403|0.561403	0.13498|0.13498	.|.	.|.	ENSG00000161904|ENSG00000161904	ENST00000442696|ENST00000293760;ENST00000508327;ENST00000513701	.|.	.|.	.|.	5.65|5.65	-3.04|-3.04	0.05412|0.05412	.|Inner nuclear membrane protein MAN1 (1);	0.632623|0.632623	0.15520|0.15520	N|N	0.258115|0.258115	T|T	0.06781|0.06781	0.0173|0.0173	N|N	0.16903|0.16903	0.455|0.455	0.09310|0.09310	N|N	1|1	.|B	.|0.10296	.|0.003	.|B	.|0.10450	.|0.005	T|T	0.40421|0.40421	-0.9564|-0.9564	6|9	.|0.13853	.|T	.|0.58	-0.8734|-0.8734	7.8602|7.8602	0.29506|0.29506	0.0:0.2134:0.4858:0.3008|0.0:0.2134:0.4858:0.3008	.|.	.|309	.|Q8NC56	.|LEMD2_HUMAN	M|V	174|309;7;7	.|.	.|ENSP00000293760:I309V	I|I	-|-	3|1	3|0	LEMD2|LEMD2	33856837|33856837	0.010000|0.010000	0.17322|0.17322	0.004000|0.004000	0.12327|0.12327	0.673000|0.673000	0.39480|0.39480	-0.160000|-0.160000	0.10041|0.10041	-0.814000|-0.814000	0.04352|0.04352	0.533000|0.533000	0.62120|0.62120	ATA|ATA	.	.		0.408	LEMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040209.3	XM_166338		C	33748859	T	C	33748859	3	2	191	1	0	0	0	0	1	0	0	0	8729	1406	49	2	610	2	LEMD2	6	33748859	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	7716853	33748859	137366208	46	28294										
SEC63	11231	hgsc.bcm.edu	37	chr6	108214765	108214765	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	caggtgtaggttttttttttAaaggtttctttttttttgat	8	2	1	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr6:108214765A>T	ENST00000369002.4	-	16	1774	c.1595T>A	c.(1594-1596)tTa>tAa	p.L532*		NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	532	SEC63 1.				liver development (GO:0001889)|multicellular organismal aging (GO:0010259)|nitrogen compound metabolic process (GO:0006807)|posttranslational protein targeting to membrane (GO:0006620)|posttranslational protein targeting to membrane, translocation (GO:0031204)|protein targeting to membrane (GO:0006612)|renal system development (GO:0072001)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.L532*(2)		endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		TTTTTTTTTTAAAGGTTTCTT	0.368																																					p.L532X		Atlas-SNP	.											SEC63,NS,carcinoma,0,2	SEC63	79	.	2	Substitution - Nonsense(2)	lung(1)|kidney(1)	c.T1595A						.						114	119	117					6																	108214765		2202	4300	6502	SO:0001587	stop_gained	11231	exon16			TTTTTTAAAGGTT	BC048287	CCDS5061.1	6q21	2011-09-05	2006-09-12		ENSG00000025796	ENSG00000025796		"Heat shock proteins / DNAJ (HSP40)"	21082	protein-coding gene	gene with protein product		608648	"SEC63-like (S. cerevisiae)"			10219736, 10543453	Standard	NM_007214		Approved	SEC63L, PRO2507, ERdj2, DNAJC23	uc003psc.4	Q9UGP8	OTTHUMG00000015316	ENST00000369002.4:c.1595T>A	chr6.hg19:g.108214765A>T	ENSP00000357998:p.Leu532*	61.0	0.0		92.0	8.0	NM_007214	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	Nonsense_Mutation	SNP	ENST00000369002.4	hg19	CCDS5061.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	37|37	6.342620|6.342620	0.97489|0.97489	.|.	.|.	ENSG00000025796|ENSG00000025796	ENST00000423697|ENST00000369002;ENST00000437345	.|.	.|.	.|.	5.38|5.38	3.01|3.01	0.34805|0.34805	.|.	.|0.323197	.|0.31989	.|N	.|0.006744	T|.	0.17450|.	0.0419|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.07673|.	-1.0760|.	4|.	0.10636|0.14656	T|T	0.68|0.56	-2.4355|-2.4355	7.8269|7.8269	0.29320|0.29320	0.7741:0.0:0.2259:0.0|0.7741:0.0:0.2259:0.0	.|.	.|.	.|.	.|.	L|X	391|532;183	.|.	ENSP00000394572:F391L|ENSP00000357998:L532X	F|L	-|-	3|2	2|0	SEC63|SEC63	108321458|108321458	0.977000|0.977000	0.34250|0.34250	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	2.787000|2.787000	0.47798|0.47798	0.991000|0.991000	0.38814|0.38814	0.460000|0.460000	0.39030|0.39030	TTT|TTA	.	.		0.368	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214		T	108214765	A	T	108214765	4	4	191	1	0	0	0	0	0	1	0	0	14020	372	13	4	711	4	SEC63	6	108214765	Nonsense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	74465906	108214765	62900302	47	28295										
FABP7	2173	hgsc.bcm.edu	37	chr6	123101529	123101529	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agtggtcatcaggactctcaGcacattcaagaacacggaga	10	10	4	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr6:123101529G>A	ENST00000368444.3	+	2	487	c.167G>A	c.(166-168)aGc>aAc	p.S56N	FABP7_ENST00000356535.4_Missense_Mutation_p.S56N	NM_001446.3	NP_001437.1	O15540	FABP7_HUMAN	fatty acid binding protein 7, brain	56					cell proliferation in forebrain (GO:0021846)|epithelial cell proliferation (GO:0050673)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|prepulse inhibition (GO:0060134)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			kidney(1)|large_intestine(1)|lung(2)|stomach(1)	5				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|Dihomo-gamma-linolenic acid(DB00154)|Icosapent(DB00159)	AGGACTCTCAGCACATTCAAG	0.448																																					p.S56N		Atlas-SNP	.											.	FABP7	10	.	0			c.G167A						.						96	91	93					6																	123101529		2203	4300	6503	SO:0001583	missense	2173	exon2			CTCTCAGCACATT	D88648	CCDS5127.1	6q22-q23	2013-03-01			ENSG00000164434	ENSG00000164434		"Fatty acid binding protein family"	3562	protein-coding gene	gene with protein product	"brain lipid binding protein"	602965				9375786	Standard	NM_001446		Approved	B-FABP, BLBP	uc003pzf.3	O15540	OTTHUMG00000015489	ENST00000368444.3:c.167G>A	chr6.hg19:g.123101529G>A	ENSP00000357429:p.Ser56Asn	185.0	0.0		272.0	89.0	NM_001446	B2R4L1|O14951|Q6IAU7|Q9H047	Missense_Mutation	SNP	ENST00000368444.3	hg19	CCDS5127.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.350179	0.82132	.	.	ENSG00000164434	ENST00000368444;ENST00000356535	T;T	0.10288	2.89;2.89	5.54	4.66	0.58398	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.074834	0.85682	D	0.000000	T	0.30634	0.0771	M	0.89095	3.005	0.54753	D	0.999988	P;D;D	0.76494	0.847;0.999;0.998	D;D;D	0.76575	0.931;0.988;0.982	T	0.08680	-1.0710	10	0.72032	D	0.01	.	14.1479	0.65362	0.0723:0.0:0.9277:0.0	.	56;62;56	O15540;Q59HE4;Q9H047	FABP7_HUMAN;.;.	N	56	ENSP00000357429:S56N;ENSP00000348931:S56N	ENSP00000348931:S56N	S	+	2	0	FABP7	123143228	1.000000	0.71417	0.986000	0.45419	0.617000	0.37484	6.745000	0.74860	2.751000	0.94390	0.563000	0.77884	AGC	.	.		0.448	FABP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042037.1	NM_001446		A	123101529	G	A	123101529	3	1	191	1	0	0	0	0	1	0	0	0	5367	971	34	3	173	3	FABP7	6	123101529	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	14886764	123101529	48013538	48	28296										
STXBP5	134957	hgsc.bcm.edu	37	chr6	147646126	147646126	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	caccacttaaacagtctccaGgttatcaaacagaactagtt	5	11	2	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr6:147646126G>A	ENST00000321680.6	+	17	1834	c.1834G>A	c.(1834-1836)Ggt>Agt	p.G612S	STXBP5_ENST00000179882.6_Missense_Mutation_p.G283S|STXBP5_ENST00000367480.3_Missense_Mutation_p.G612S|STXBP5_ENST00000367481.3_Missense_Mutation_p.G612S	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	612					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		ACAGTCTCCAGGTTATCAAAC	0.353																																					p.G612S		Atlas-SNP	.											.	STXBP5	163	.	0			c.G1834A						.						67	71	70					6																	147646126		2203	4300	6503	SO:0001583	missense	134957	exon17			TCTCCAGGTTATC	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.1834G>A	chr6.hg19:g.147646126G>A	ENSP00000321826:p.Gly612Ser	333.0	0.0		465.0	37.0	NM_139244	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	hg19	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	G	35	5.426832	0.96131	.	.	ENSG00000164506	ENST00000367481;ENST00000321680;ENST00000367480;ENST00000179882	T;T;T;T	0.72167	-0.63;-0.12;-0.16;0.2	4.85	4.85	0.62838	WD40 repeat-like-containing domain (1);	0.105185	0.64402	D	0.000003	T	0.73628	0.3611	M	0.84219	2.685	0.80722	D	1	B;D;B	0.53885	0.357;0.963;0.291	B;P;B	0.47206	0.385;0.541;0.275	T	0.80699	-0.1266	10	0.87932	D	0	.	18.3063	0.90182	0.0:0.0:1.0:0.0	.	612;612;283	Q5T5C0-2;Q5T5C0;B3KXX0	.;STXB5_HUMAN;.	S	612;612;612;283	ENSP00000356451:G612S;ENSP00000321826:G612S;ENSP00000356450:G612S;ENSP00000179882:G283S	ENSP00000179882:G283S	G	+	1	0	STXBP5	147687819	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.385000	0.81259	0.655000	0.94253	GGT	.	.		0.353	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			A	147646126	G	A	147646126	3	1	191	1	0	0	0	0	1	0	0	0	15371	1000	35	3	1900	3	STXBP5	6	147646126	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	24544597	147646126	23468941	49	28297										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161494612	161494612	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agcccgactgcaacattgacGcttttgaagaggatctacat	9	10	1	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr6:161494612G>A	ENST00000392142.4	+	5	2213	c.2065G>A	c.(2065-2067)Gct>Act	p.A689T	MAP3K4_ENST00000366919.2_Missense_Mutation_p.A689T|MAP3K4_ENST00000366920.2_Missense_Mutation_p.A689T|MAP3K4_ENST00000348824.7_Missense_Mutation_p.A689T	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	689					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		CAACATTGACGCTTTTGAAGA	0.438																																					p.A689T		Atlas-SNP	.											.	MAP3K4	364	.	0			c.G2065A						.						101	104	103					6																	161494612		2203	4300	6503	SO:0001583	missense	4216	exon5			ATTGACGCTTTTG	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.2065G>A	chr6.hg19:g.161494612G>A	ENSP00000375986:p.Ala689Thr	107.0	0.0		113.0	32.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.443084	0.25987	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.15603	2.41;2.41;2.41;2.41	5.13	3.15	0.36227	.	0.229422	0.37304	N	0.002141	T	0.03011	0.0089	L	0.36672	1.1	0.30640	N	0.756567	P;P;P	0.41673	0.759;0.59;0.646	B;B;B	0.30401	0.115;0.077;0.054	T	0.37686	-0.9695	10	0.14252	T	0.57	-19.2576	8.0142	0.30372	0.0911:0.0:0.6106:0.2983	.	689;689;689	F5H538;Q9Y6R4-2;Q9Y6R4	.;.;M3K4_HUMAN	T	689	ENSP00000355886:A689T;ENSP00000375986:A689T;ENSP00000355887:A689T;ENSP00000297332:A689T	ENSP00000297332:A689T	A	+	1	0	MAP3K4	161414602	1.000000	0.71417	0.411000	0.26484	0.901000	0.52897	3.673000	0.54591	1.159000	0.42565	0.585000	0.79938	GCT	.	.		0.438	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			A	161494612	G	A	161494612	3	1	191	1	0	0	0	0	1	0	0	0	9261	1087	38	1	2083	1	MAP3K4	6	161494612	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	13848486	161494612	9620455	50	28298										
ZNF716	441234	hgsc.bcm.edu	37	chr7	57529086	57529086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aatgtggcaaagcctttagcCgctcttcaacacttactaac	6	12	2	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr7:57529086C>T	ENST00000420713.1	+	4	1031	c.919C>T	c.(919-921)Cgc>Tgc	p.R307C		NM_001159279.1	NP_001152751.1	A6NP11	ZN716_HUMAN	zinc finger protein 716	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|lung(20)|ovary(2)	24						AGCCTTTAGCCGCTCTTCAAC	0.423																																					p.R307C		Atlas-SNP	.											.	ZNF716	207	.	0			c.C919T						.						35	35	35					7																	57529086		692	1591	2283	SO:0001583	missense	441234	exon4			TTTAGCCGCTCTT	AK131575	CCDS55112.1	7p11.1	2013-01-08			ENSG00000182111	ENSG00000182111		"Zinc fingers, C2H2-type", "-"	32458	protein-coding gene	gene with protein product							Standard	NM_001159279		Approved	FLJ46189	uc011kdi.1	A6NP11	OTTHUMG00000156689	ENST00000420713.1:c.919C>T	chr7.hg19:g.57529086C>T	ENSP00000394248:p.Arg307Cys	60.0	0.0		74.0	24.0	NM_001159279		Missense_Mutation	SNP	ENST00000420713.1	hg19	CCDS55112.1	.	.	.	.	.	.	.	.	.	.	C	0.232	-1.020547	0.02061	.	.	ENSG00000182111	ENST00000420713;ENST00000418732	T	0.07567	3.18	0.109	-0.218	0.13142	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08980	0.0222	M	0.66297	2.02	0.09310	N	1	B	0.17038	0.02	B	0.06405	0.002	T	0.36768	-0.9734	9	0.30078	T	0.28	.	5.4529	0.16574	0.0:0.6456:0.3543:0.0	.	295	A6NP11	ZN716_HUMAN	C	307;295	ENSP00000394248:R307C	ENSP00000387687:R295C	R	+	1	0	ZNF716	57533028	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-3.527000	0.00441	-1.131000	0.02910	-1.174000	0.01732	CGC	.	.		0.423	ZNF716-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345309.1	NM_001159279		T	57529086	C	T	57529086	3	4	191	1	0	0	0	0	1	0	0	0	18134	652	23	1	933	1	ZNF716	7	57529086	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10		57529086	101609577	51	28299										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77579094	77579094	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ttctcctaagatttgttaccCttggatcagaaacaagtaaa	6	8	2	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr7:77579094C>T	ENST00000248550.7	+	16	2135	c.2059C>T	c.(2059-2061)Ctt>Ttt	p.L687F	PHTF2_ENST00000307305.8_Missense_Mutation_p.L649F|PHTF2_ENST00000275575.7_Intron|PHTF2_ENST00000416283.2_Missense_Mutation_p.L653F|PHTF2_ENST00000422959.2_Missense_Mutation_p.L653F			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	687					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						ATTTGTTACCCTTGGATCAGA	0.343																																					p.L653F		Atlas-SNP	.											PHTF2_ENST00000416283,NS,carcinoma,0,2	PHTF2	104	.	0			c.C1957T						.						106	94	98					7																	77579094		1843	4080	5923	SO:0001583	missense	57157	exon15			GTTACCCTTGGAT	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.2059C>T	chr7.hg19:g.77579094C>T	ENSP00000248550:p.Leu687Phe	89.0	0.0		113.0	38.0	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	hg19		.	.	.	.	.	.	.	.	.	.	C	31	5.090030	0.94149	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000416283;ENST00000248550	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.80265	0.4591	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.995;0.989	T	0.82065	-0.0642	9	0.87932	D	0	-15.5885	19.3637	0.94453	0.0:1.0:0.0:0.0	.	653;687;649	Q8N3S3-2;Q8N3S3;Q8N3S3-3	.;PHTF2_HUMAN;.	F	653;653;649;653;687	.	ENSP00000248550:L687F	L	+	1	0	PHTF2	77417030	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	7.776000	0.85560	2.648000	0.89879	0.655000	0.94253	CTT	.	.		0.343	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		T	77579094	C	T	77579094	3	4	191	1	0	0	0	0	1	0	0	0	11872	681	24	3	2069	3	PHTF2	7	77579094	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	20050008	77579094	81559569	52	28300										
LAMB1	3912	hgsc.bcm.edu	37	chr7	107603404	107603404	+	Frame_Shift_Del	DEL	A	A	-													0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	atggaatatggtatgttgtcAatgaaaaactccaaataagc							TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr7:107603404delA	ENST00000222399.6	-	15	2033	c.1803delT	c.(1801-1803)attfs	p.I601fs	LAMB1_ENST00000393560.1_Frame_Shift_Del_p.I601fs|LAMB1_ENST00000393561.1_Frame_Shift_Del_p.I625fs	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	601	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GTATGTTGTCAATGAAAAACT	0.507																																					p.D602fs		Atlas-INDEL	.											.	LAMB1	185	.	0			c.1804delG						.						114	113	113					7																	107603404		2203	4300	6503	SO:0001589	frameshift_variant	3912	exon15			.	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.1803delT	chr7.hg19:g.107603404delA	ENSP00000222399:p.Ile601fs	63.0	0.0		76.0	21.0	NM_002291	Q14D91	Frame_Shift_Del	DEL	ENST00000222399.6	hg19	CCDS5750.1																																																																																			.	.		0.507	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		-	107603404	A	-	107603404	7	5	191	1	0	1	0	1	0	0	0	0	8619	126	5	0	3637	0	LAMB1	7	107603404	Frame_Shift_Del	DEL	A	TCGA-DD-AADI-01A-11D-A40R-10	30024310	107603404	51535259	53	28301										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107808806	107808806	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	attggcataggtctcagcagCtgcagcagtaagattgctga	12	8	1	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr7:107808806C>A	ENST00000425651.2	-	26	3228	c.3229G>T	c.(3229-3231)Gct>Tct	p.A1077S	NRCAM_ENST00000379028.3_Missense_Mutation_p.A1077S|NRCAM_ENST00000351718.4_Intron|NRCAM_ENST00000413765.2_Intron|NRCAM_ENST00000379024.4_Intron|NRCAM_ENST00000379022.4_Missense_Mutation_p.A1077S	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1077	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GTCTCAGCAGCTGCAGCAGTA	0.378																																					p.A1077S		Atlas-SNP	.											.	NRCAM	267	.	0			c.G3229T						.						76	74	75					7																	107808806		1898	4126	6024	SO:0001583	missense	4897	exon26			CAGCAGCTGCAGC		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3229G>T	chr7.hg19:g.107808806C>A	ENSP00000401244:p.Ala1077Ser	71.0	0.0		84.0	32.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.37|14.37	2.514197|2.514197	0.44763|0.44763	.|.	.|.	ENSG00000091129|ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000425651;ENST00000379022|ENST00000445634	T;T;T|.	0.56611|.	0.45;0.45;0.45|.	5.64|5.64	5.64|5.64	0.86602|0.86602	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.374815|.	0.30101|.	N|.	0.010410|.	T|T	0.63153|0.63153	0.2487|0.2487	L|L	0.56769|0.56769	1.78|1.78	0.29775|0.29775	N|N	0.834471|0.834471	B|.	0.11235|.	0.004|.	B|.	0.23275|.	0.045|.	T|T	0.60924|0.60924	-0.7166|-0.7166	10|5	0.48119|.	T|.	0.1|.	.|.	17.864|17.864	0.88791|0.88791	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1077|.	Q92823|.	NRCAM_HUMAN|.	S|H	1077|26	ENSP00000368314:A1077S;ENSP00000401244:A1077S;ENSP00000368308:A1077S|.	ENSP00000368308:A1077S|.	A|Q	-|-	1|3	0|2	NRCAM|NRCAM	107596042|107596042	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.961000|0.961000	0.63080|0.63080	2.885000|2.885000	0.48570|0.48570	2.643000|2.643000	0.89663|0.89663	0.650000|0.650000	0.86243|0.86243	GCT|CAG	.	.		0.378	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		A	107808806	C	A	107808806	3	1	191	1	0	0	0	0	1	0	0	0	10653	797	28	3	735	3	NRCAM	7	107808806	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	205402	107808806	51329857	54	28302										
OR2F1	26211	hgsc.bcm.edu	37	chr7	143657530	143657530	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ggtcagtggcttcatcagctCtcctgtgcagactgctatca	10	12	5	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr7:143657530C>G	ENST00000392899.1	+	1	504	c.467C>G	c.(466-468)tCt>tGt	p.S156C	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	156					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					TTCATCAGCTCTCCTGTGCAG	0.522																																					p.S156C		Atlas-SNP	.											OR2F1,right_upper_lobe,carcinoma,0,2	OR2F1	71	.	0			c.C467G						.						140	117	125					7																	143657530		2203	4300	6503	SO:0001583	missense	26211	exon1			TCAGCTCTCCTGT	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"GPCR / Class A : Olfactory receptors"	8246	protein-coding gene	gene with protein product		608497	"olfactory receptor, family 2, subfamily F, member 1"	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.467C>G	chr7.hg19:g.143657530C>G	ENSP00000376633:p.Ser156Cys	104.0	0.0		137.0	45.0	NM_012369	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	hg19	CCDS5887.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.287663	0.40494	.	.	ENSG00000213215	ENST00000392899	T	0.44482	0.92	5.53	5.53	0.82687	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000066	T	0.69115	0.3075	M	0.85099	2.735	0.42344	D	0.992342	D	0.89917	1.0	D	0.91635	0.999	T	0.72994	-0.4122	10	0.66056	D	0.02	-25.1823	17.0114	0.86407	0.0:1.0:0.0:0.0	.	156	Q13607	OR2F1_HUMAN	C	156	ENSP00000376633:S156C	ENSP00000376633:S156C	S	+	2	0	OR2F1	143288463	0.000000	0.05858	0.578000	0.28575	0.022000	0.10575	0.316000	0.19469	2.871000	0.98454	0.655000	0.94253	TCT	.	.		0.522	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1			G	143657530	C	G	143657530	3	3	191	1	0	0	0	0	1	0	0	0	11005	913	32	4	469	4	OR2F1	7	143657530	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	35848724	143657530	15481133	55	28303										
TMUB1	83590	hgsc.bcm.edu	37	chr7	150778970	150778970	+	Missense_Mutation	SNP	C	C	G													0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tgagtcgcacctgctgttccCggccgggaaactgggtcctg					rs568920028		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr7:150778970C>G	ENST00000392818.3	-	3	764	c.407G>C	c.(406-408)cGg>cCg	p.R136P	FASTK_ENST00000489884.1_5'Flank|TMUB1_ENST00000462940.1_Missense_Mutation_p.R136P|FASTK_ENST00000297532.6_5'Flank|FASTK_ENST00000482571.1_5'Flank|FASTK_ENST00000540185.1_5'Flank|TMUB1_ENST00000476627.1_Missense_Mutation_p.R136P|TMUB1_ENST00000297533.4_Missense_Mutation_p.R136P|FASTK_ENST00000353841.2_5'Flank|TMUB1_ENST00000482202.1_Missense_Mutation_p.R136P	NM_031434.3	NP_113622.1	Q9BVT8	TMUB1_HUMAN	transmembrane and ubiquitin-like domain containing 1	136	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTGCTGTTCCCGGCCGGGAAA	0.647																																					p.R136P		Atlas-SNP	.											.	TMUB1	7	.	0			c.G407C						.						19	15	16					7																	150778970		2192	4294	6486	SO:0001583	missense	83590	exon3			TGTTCCCGGCCGG	BC000936	CCDS5920.1	7q36.1	2006-06-27	2006-06-27	2006-06-27	ENSG00000164897	ENSG00000164897			21709	protein-coding gene	gene with protein product		614792	"chromosome 7 open reading frame 21"	C7orf21			Standard	NM_001136044		Approved	SB144	uc003wjd.3	Q9BVT8	OTTHUMG00000158621	ENST00000392818.3:c.407G>C	chr7.hg19:g.150778970C>G	ENSP00000376565:p.Arg136Pro	25.0	0.0		27.0	7.0	NM_031434	D3DX06|Q53AQ2	Missense_Mutation	SNP	ENST00000392818.3	hg19	CCDS5920.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.824695	0.50739	.	.	ENSG00000164897	ENST00000297533;ENST00000392818;ENST00000462940;ENST00000482202;ENST00000476627;ENST00000488752;ENST00000492838	T;T;T;T;T;T	0.44482	0.94;0.94;0.94;0.94;0.94;0.92	4.9	-0.0351	0.13894	Ubiquitin supergroup (1);Ubiquitin (1);	0.254864	0.33272	N	0.005088	T	0.37073	0.0990	L	0.38531	1.155	0.30262	N	0.793023	P	0.47484	0.896	P	0.52481	0.7	T	0.35251	-0.9796	10	0.72032	D	0.01	.	4.264	0.10754	0.1547:0.4001:0.0:0.4452	.	136	Q9BVT8	TMUB1_HUMAN	P	136	ENSP00000297533:R136P;ENSP00000376565:R136P;ENSP00000417519:R136P;ENSP00000418709:R136P;ENSP00000419214:R136P;ENSP00000420692:R136P	ENSP00000297533:R136P	R	-	2	0	TMUB1	150409903	0.994000	0.37717	0.995000	0.50966	0.927000	0.56198	0.413000	0.21148	0.050000	0.15949	0.313000	0.20887	CGG	.	.		0.647	TMUB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351485.1	NM_031434		G	150778970	C	G	150778970	3	3	191	1	0	0	0	0	1	0	0	0	16279	652	23	4	337	4	TMUB1	7	150778970	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	7121440	150778970	8359693	56	28304	139	2								
TMUB1	83590	hgsc.bcm.edu	37	chr7	150778972	150778972	+	Silent	SNP	G	G	T													0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agtcgcacctgctgttcccgGccgggaaactgggtcctgag							TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr7:150778972G>T	ENST00000392818.3	-	3	762	c.405C>A	c.(403-405)ggC>ggA	p.G135G	FASTK_ENST00000489884.1_5'Flank|TMUB1_ENST00000462940.1_Silent_p.G135G|FASTK_ENST00000297532.6_5'Flank|FASTK_ENST00000482571.1_5'Flank|FASTK_ENST00000540185.1_5'Flank|TMUB1_ENST00000476627.1_Silent_p.G135G|TMUB1_ENST00000297533.4_Silent_p.G135G|FASTK_ENST00000353841.2_5'Flank|TMUB1_ENST00000482202.1_Silent_p.G135G	NM_031434.3	NP_113622.1	Q9BVT8	TMUB1_HUMAN	transmembrane and ubiquitin-like domain containing 1	135	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCTGTTCCCGGCCGGGAAACT	0.642																																					p.G135G		Atlas-SNP	.											.	TMUB1	7	.	0			c.C405A						.						17	14	15					7																	150778972		2191	4292	6483	SO:0001819	synonymous_variant	83590	exon3			TTCCCGGCCGGGA	BC000936	CCDS5920.1	7q36.1	2006-06-27	2006-06-27	2006-06-27	ENSG00000164897	ENSG00000164897			21709	protein-coding gene	gene with protein product		614792	"chromosome 7 open reading frame 21"	C7orf21			Standard	NM_001136044		Approved	SB144	uc003wjd.3	Q9BVT8	OTTHUMG00000158621	ENST00000392818.3:c.405C>A	chr7.hg19:g.150778972G>T		26.0	0.0		27.0	7.0	NM_031434	D3DX06|Q53AQ2	Silent	SNP	ENST00000392818.3	hg19	CCDS5920.1																																																																																			.	.		0.642	TMUB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351485.1	NM_031434		T	150778972	G	T	150778972	2	4	191	1	0	0	0	0	0	0	0	1	16279	1190	42	3		3	TMUB1	7	150778972	Silent	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	2	150778972	8359691	57	28305	139	2								
ADAM2	2515	hgsc.bcm.edu	37	chr8	39607233	39607233	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	acaatcataacccaagtatgAagaactcacacatctttgat	4	10	3	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr8:39607233A>T	ENST00000265708.4	-	17	1931	c.1828T>A	c.(1828-1830)Tca>Aca	p.S610T	ADAM2_ENST00000521880.1_Missense_Mutation_p.S547T|ADAM2_ENST00000347580.4_Missense_Mutation_p.S591T|ADAM2_ENST00000379853.2_Missense_Mutation_p.S454T	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	610					adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		CCCAAGTATGAAGAACTCACA	0.343																																					p.S610T		Atlas-SNP	.											.	ADAM2	124	.	0			c.T1828A						.						135	126	129					8																	39607233		2203	4300	6503	SO:0001583	missense	2515	exon17			AGTATGAAGAACT	U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"ADAM metallopeptidase domain containing"	198	protein-coding gene	gene with protein product	"cancer/testis antigen 15"	601533	"fertilin beta"	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.1828T>A	chr8.hg19:g.39607233A>T	ENSP00000265708:p.Ser610Thr	170.0	0.0		182.0	31.0	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	hg19	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	A	8.875	0.950200	0.18431	.	.	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	D;D;D;T	0.85339	-1.97;-1.97;-1.97;5.14	4.21	-8.42	0.00957	.	.	.	.	.	T	0.68522	0.3010	L	0.35854	1.095	0.09310	N	1	B;B;B;B	0.15719	0.005;0.01;0.014;0.005	B;B;B;B	0.18263	0.021;0.005;0.02;0.005	T	0.54497	-0.8285	9	0.18710	T	0.47	.	1.5026	0.02480	0.2766:0.3052:0.0814:0.3369	.	547;454;591;610	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	T	591;454;610;547	ENSP00000343854:S591T;ENSP00000369182:S454T;ENSP00000265708:S610T;ENSP00000429352:S547T	ENSP00000265708:S610T	S	-	1	0	ADAM2	39726390	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.494000	0.00972	-1.963000	0.01013	-0.313000	0.08912	TCA	.	.		0.343	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		T	39607233	A	T	39607233	3	4	191	1	0	0	0	0	1	0	0	0	241	246	9	4	395	4	ADAM2	8	39607233	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10		39607233	106756789	58	28306										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113403006	113403006	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tttgcgcttagttaaaattcCaccacagggcactgaaaata	7	9	0	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr8:113403006C>A	ENST00000297405.5	-	36	6065	c.5821G>T	c.(5821-5823)Gga>Tga	p.G1941*	CSMD3_ENST00000455883.2_Nonsense_Mutation_p.G1837*|CSMD3_ENST00000352409.3_Nonsense_Mutation_p.G1871*|CSMD3_ENST00000343508.3_Nonsense_Mutation_p.G1901*	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1941	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GTTAAAATTCCACCACAGGGC	0.408										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G1941X		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G5821T						.						78	72	74					8																	113403006		2203	4300	6503	SO:0001587	stop_gained	114788	exon36			AAATTCCACCACA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.5821G>T	chr8.hg19:g.113403006C>A	ENSP00000297405:p.Gly1941*	69.0	0.0		149.0	38.0	NM_198123	Q96PZ3	Nonsense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	44	11.125595	0.99519	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	.	.	.	5.24	4.35	0.52113	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	15.295	0.73898	0.1411:0.8589:0.0:0.0	.	.	.	.	X	1901;1941;1211;1837;1871	.	ENSP00000297405:G1941X	G	-	1	0	CSMD3	113472182	1.000000	0.71417	0.999000	0.59377	0.006000	0.05464	7.640000	0.83355	1.428000	0.47296	-0.518000	0.04402	GGA	.	.		0.408	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113403006	C	A	113403006	4	1	191	1	0	0	0	0	0	1	0	0	3948	603	21	3	5446	3	CSMD3	8	113403006	Nonsense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	73795773	113403006	32961016	59	28307										
SLC30A8	169026	hgsc.bcm.edu	37	chr8	118174119	118174119	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	taattagtgcacttattatcTactttaaggtgagtttgagt	8	4	1	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr8:118174119T>A	ENST00000456015.2	+	5	715	c.715T>A	c.(715-717)Tac>Aac	p.Y239N	SLC30A8_ENST00000427715.2_Missense_Mutation_p.Y190N|RN7SL826P_ENST00000479724.2_RNA|SLC30A8_ENST00000521243.1_Missense_Mutation_p.Y190N|SLC30A8_ENST00000519688.1_Missense_Mutation_p.Y190N	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	239					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			ACTTATTATCTACTTTAAGGT	0.413																																					p.Y239N	Ovarian(162;1202 1922 6011 16223 52092)	Atlas-SNP	.											.	SLC30A8	102	.	0			c.T715A						.						171	145	154					8																	118174119		2203	4300	6503	SO:0001583	missense	169026	exon5			ATTATCTACTTTA		CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"Solute carriers"	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.715T>A	chr8.hg19:g.118174119T>A	ENSP00000415011:p.Tyr239Asn	76.0	0.0		163.0	20.0	NM_173851	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation	SNP	ENST00000456015.2	hg19	CCDS6322.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.421387	0.83559	.	.	ENSG00000164756	ENST00000521243;ENST00000427715;ENST00000519688;ENST00000456015	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.47	4.32	0.51571	.	0.229124	0.46145	D	0.000319	T	0.76870	0.4048	M	0.81682	2.555	0.53005	D	0.999963	D	0.63880	0.993	D	0.71184	0.972	T	0.78976	-0.1991	10	0.59425	D	0.04	-16.8794	10.3447	0.43899	0.0:0.0771:0.0:0.9229	.	239	Q8IWU4	ZNT8_HUMAN	N	190;190;190;239	ENSP00000428545:Y190N;ENSP00000407505:Y190N;ENSP00000431069:Y190N;ENSP00000415011:Y239N	ENSP00000407505:Y190N	Y	+	1	0	SLC30A8	118243300	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.985000	0.63845	2.214000	0.71695	0.533000	0.62120	TAC	.	.		0.413	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851		A	118174119	T	A	118174119	3	1	191	1	0	0	0	0	1	0	0	0	14576	1522	53	4	733	4	SLC30A8	8	118174119	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	4771113	118174119	28189903	60	28308										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139696713	139696713	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ccaggtgatccacggagtccCtggagaaataaataatacaa	9	9	0	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr8:139696713C>A	ENST00000303045.6	-	39	3414		c.e39-1		COL22A1_ENST00000341807.4_Splice_Site|COL22A1_ENST00000435777.1_Splice_Site	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CACGGAGTCCCTGGAGAAATA	0.532										HNSCC(7;0.00092)																											.		Atlas-SNP	.											.	COL22A1	390	.	0			c.2968-1G>T						.						92	96	95					8																	139696713		2203	4300	6503	SO:0001630	splice_region_variant	169044	exon40			GAGTCCCTGGAGA	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2968-1G>T	chr8.hg19:g.139696713C>A		91.0	0.0		141.0	34.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Splice_Site	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.163351	0.38217	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	.	.	.	4.16	4.16	0.48862	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8162	0.52211	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL22A1	139765895	1.000000	0.71417	0.997000	0.53966	0.532000	0.34746	1.943000	0.40253	2.122000	0.65172	0.448000	0.29417	.	.	.		0.532	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	Intron	A	139696713	C	A	139696713	5	1	191	1	0	0	0	0	0	0	1	0	3683	695	24	3	2021	3	COL22A1	8	139696713	Splice_Site	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	21522594	139696713	6667309	61	28309										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37745441	37745441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aggattcaggtgactccccgGgtgatgtgtcaaataatgtt	12	7	2	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr9:37745441G>A	ENST00000539465.1	+	16	4005	c.3412G>A	c.(3412-3414)Ggt>Agt	p.G1138S	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.G1138S			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1138						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		TGACTCCCCGGGTGATGTGTC	0.433																																					p.G1138S		Atlas-SNP	.											.	FRMPD1	237	.	0			c.G3412A						.						56	57	57					9																	37745441		2203	4300	6503	SO:0001583	missense	22844	exon16			TCCCCGGGTGATG	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.3412G>A	chr9.hg19:g.37745441G>A	ENSP00000444411:p.Gly1138Ser	86.0	0.0		110.0	36.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	hg19	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	9.617	1.132800	0.21041	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.07021	3.23;3.23	5.12	1.56	0.23342	.	0.890085	0.09915	N	0.739211	T	0.04588	0.0125	L	0.27053	0.805	0.09310	N	1	B	0.20052	0.041	B	0.14023	0.01	T	0.45833	-0.9234	10	0.09338	T	0.73	-4.1821	2.935	0.05811	0.2648:0.0:0.5264:0.2089	.	1138	Q5SYB0	FRPD1_HUMAN	S	1138	ENSP00000366995:G1138S;ENSP00000444411:G1138S	ENSP00000366995:G1138S	G	+	1	0	FRMPD1	37735441	0.000000	0.05858	0.014000	0.15608	0.025000	0.11179	0.108000	0.15396	1.150000	0.42419	0.462000	0.41574	GGT	.	.		0.433	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37745441	G	A	37745441	3	1	191	1	0	0	0	0	1	0	0	0	6065	1232	43	3	3470	3	FRMPD1	9	37745441	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10		37745441	103467990	62	28310										
PTPDC1	138639	hgsc.bcm.edu	37	chr9	96864001	96864001	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tgttggttgacaggcgagcaGatgccgcagaagcacttttt	13	8	0	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr9:96864001G>A	ENST00000375360.3	+	8	2345	c.2005G>A	c.(2005-2007)Gat>Aat	p.D669N	PTPDC1_ENST00000288976.3_Missense_Mutation_p.D721N|PTPDC1_ENST00000467049.1_3'UTR	NM_001253830.1|NM_177995.2	NP_001240759.1|NP_818931.1	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	669					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	32						CAGGCGAGCAGATGCCGCAGA	0.453																																					p.D723N		Atlas-SNP	.											PTPDC1_ENST00000375360,NS,carcinoma,0,2	PTPDC1	134	.	0			c.G2167A						.						133	126	129					9																	96864001		2203	4300	6503	SO:0001583	missense	138639	exon7			CGAGCAGATGCCG	BC051654	CCDS6707.1, CCDS6708.1, CCDS75860.1	9q22.32	2011-06-09			ENSG00000158079	ENSG00000158079		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	30184	protein-coding gene	gene with protein product	"protein tyrosine phosphatase PTP9Q22"					14702039	Standard	NM_152422		Approved	PTP9Q22, FLJ37312	uc010mrj.2	A2A3K4	OTTHUMG00000020258	ENST00000375360.3:c.2005G>A	chr9.hg19:g.96864001G>A	ENSP00000364509:p.Asp669Asn	121.0	1.0		173.0	27.0	NM_001253829	Q5T3M4|Q6NXE8|Q8IWM1|Q8N1X4|Q8N9F5	Missense_Mutation	SNP	ENST00000375360.3	hg19	CCDS6707.1	.	.	.	.	.	.	.	.	.	.	G	12.30	1.896202	0.33442	.	.	ENSG00000158079	ENST00000375360;ENST00000288976	T;T	0.16597	2.33;2.33	5.6	5.6	0.85130	.	0.188820	0.56097	D	0.000037	T	0.19805	0.0476	L	0.49126	1.545	0.40210	D	0.977618	B;B;B;B	0.27264	0.108;0.173;0.108;0.108	B;B;B;B	0.33620	0.08;0.167;0.08;0.045	T	0.03051	-1.1078	10	0.39692	T	0.17	-16.9498	11.9896	0.53168	0.0784:0.0:0.9216:0.0	.	723;721;723;669	E7EN59;A2A3K4-2;A8K0X7;A2A3K4	.;.;.;PTPC1_HUMAN	N	669;721	ENSP00000364509:D669N;ENSP00000288976:D721N	ENSP00000288976:D721N	D	+	1	0	PTPDC1	95903822	1.000000	0.71417	0.354000	0.25760	0.482000	0.33219	3.349000	0.52217	2.630000	0.89119	0.655000	0.94253	GAT	.	.		0.453	PTPDC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215007.1	NM_177995, NM_152422		A	96864001	G	A	96864001	3	1	191	1	0	0	0	0	1	0	0	0	12786	942	33	3	2273	3	PTPDC1	9	96864001	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	59118560	96864001	44349430	63	28311										
GALNT12	79695	hgsc.bcm.edu	37	chr9	101570305	101570305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agattaacatctacctcagcGaccgcatctcactgcaccgc	6	16	3	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr9:101570305G>A	ENST00000375011.3	+	1	325	c.325G>A	c.(325-327)Gac>Aac	p.D109N		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	109					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				CTACCTCAGCGACCGCATCTC	0.706																																					p.D109N		Atlas-SNP	.											.	GALNT12	37	.	0			c.G325A						.						8	9	8					9																	101570305		2172	4241	6413	SO:0001583	missense	79695	exon1			CTCAGCGACCGCA	AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19877	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 12"	610290	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.325G>A	chr9.hg19:g.101570305G>A	ENSP00000364150:p.Asp109Asn	30.0	0.0		64.0	20.0	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Missense_Mutation	SNP	ENST00000375011.3	hg19	CCDS6737.1	.	.	.	.	.	.	.	.	.	.	g	28.6	4.934265	0.92458	.	.	ENSG00000119514	ENST00000375011	T	0.61274	0.12	3.91	3.0	0.34707	.	0.117349	0.56097	D	0.000036	T	0.68146	0.2969	M	0.66378	2.025	0.46458	D	0.999053	D	0.76494	0.999	D	0.75020	0.985	T	0.65857	-0.6066	10	0.41790	T	0.15	.	7.4213	0.27073	0.1223:0.0:0.8777:0.0	.	109	Q8IXK2	GLT12_HUMAN	N	109	ENSP00000364150:D109N	ENSP00000364150:D109N	D	+	1	0	GALNT12	100610126	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.006000	0.88564	0.980000	0.38523	0.450000	0.29827	GAC	.	.		0.706	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642		A	101570305	G	A	101570305	3	1	191	1	0	0	0	0	1	0	0	0	6218	1058	37	1	327	1	GALNT12	9	101570305	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	4706304	101570305	39643126	64	28312										
GALNT12	79695	hgsc.bcm.edu	37	chr9	101597550	101597550	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ggtctccaacaatggctggtGggctgtttgctgtgagtaag	15	7	1	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr9:101597550G>A	ENST00000375011.3	+	5	937	c.937G>A	c.(937-939)Ggg>Agg	p.G313R		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	313	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				AATGGCTGGTGGGCTGTTTGC	0.418																																					p.G313R		Atlas-SNP	.											.	GALNT12	37	.	0			c.G937A						.						142	150	147					9																	101597550		2203	4300	6503	SO:0001583	missense	79695	exon5			GCTGGTGGGCTGT	AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19877	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 12"	610290	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.937G>A	chr9.hg19:g.101597550G>A	ENSP00000364150:p.Gly313Arg	88.0	0.0		119.0	41.0	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Missense_Mutation	SNP	ENST00000375011.3	hg19	CCDS6737.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.670338	0.88348	.	.	ENSG00000119514	ENST00000375011	T	0.61274	0.12	5.43	5.43	0.79202	Glycosyl transferase, family 2 (1);	0.046562	0.85682	D	0.000000	D	0.82407	0.5030	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86683	0.1918	10	0.87932	D	0	.	17.0949	0.86632	0.0:0.0:1.0:0.0	.	313	Q8IXK2	GLT12_HUMAN	R	313	ENSP00000364150:G313R	ENSP00000364150:G313R	G	+	1	0	GALNT12	100637371	1.000000	0.71417	0.989000	0.46669	0.927000	0.56198	9.781000	0.99029	2.722000	0.93159	0.655000	0.94253	GGG	.	.		0.418	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642		A	101597550	G	A	101597550	3	1	191	1	0	0	0	0	1	0	0	0	6218	1348	47	3	955	3	GALNT12	9	101597550	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	27245	101597550	39615881	65	28313										
LCN9	392399	hgsc.bcm.edu	37	chr9	138556630	138556630	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gacagagaagaatggggaatActccatcaactgtaagtgga	12	6	1	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr9:138556630A>G	ENST00000277526.3	+	3	296	c.296A>G	c.(295-297)tAc>tGc	p.Y99C	LCN9_ENST00000430290.2_3'UTR	NM_001001676.1	NP_001001676.1	Q8WX39	LCN9_HUMAN	lipocalin 9	99						extracellular region (GO:0005576)	pheromone binding (GO:0005550)|transporter activity (GO:0005215)			kidney(1)|large_intestine(2)|lung(2)|urinary_tract(1)	6		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;3.43e-07)|Epithelial(140;1.97e-06)|all cancers(34;6.1e-05)		AATGGGGAATACTCCATCAAC	0.592																																					p.Y99C		Atlas-SNP	.											.	LCN9	42	.	0			c.A296G						.						61	70	67					9																	138556630		2047	4195	6242	SO:0001583	missense	392399	exon3			GGGAATACTCCAT	AY301270	CCDS56593.1	9q34	2011-11-14			ENSG00000148386	ENSG00000148386		"Lipocalins"	17442	protein-coding gene	gene with protein product	"MUP-like lipocalin", "epididymal-specific lipocalin-9"	612903				15363845	Standard	NM_001001676		Approved		uc004cgk.2	Q8WX39	OTTHUMG00000020916	ENST00000277526.3:c.296A>G	chr9.hg19:g.138556630A>G	ENSP00000277526:p.Tyr99Cys	65.0	0.0		108.0	7.0	NM_001001676	C9J5F0|Q6JVE7	Missense_Mutation	SNP	ENST00000277526.3	hg19	CCDS56593.1	.	.	.	.	.	.	.	.	.	.	A	7.015	0.557591	0.13436	.	.	ENSG00000148386	ENST00000277526	T	0.52983	0.64	3.09	-6.17	0.02091	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.344020	0.05435	N	0.546560	T	0.36826	0.0981	L	0.58669	1.825	0.09310	N	1	B	0.21905	0.062	B	0.24974	0.057	T	0.40194	-0.9576	10	0.52906	T	0.07	-60.3132	1.1993	0.01881	0.2139:0.1585:0.1245:0.5031	.	99	Q8WX39	LCN9_HUMAN	C	99	ENSP00000277526:Y99C	ENSP00000277526:Y99C	Y	+	2	0	LCN9	137696451	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	-0.710000	0.05024	-1.022000	0.03346	-0.695000	0.03696	TAC	.	.		0.592	LCN9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410711.1	NM_001001676		G	138556630	A	G	138556630	3	3	191	1	0	0	0	0	1	0	0	0	8696	391	14	2	306	2	LCN9	9	138556630	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	36959080	138556630	2656801	66	28314										
PTPLA	9200	hgsc.bcm.edu	37	chr10	17645602	17645602	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gccacaccataaagattcttGaactcacttggaccccagtc	6	14	2	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr10:17645602G>A	ENST00000361271.3	-	4	477	c.440C>T	c.(439-441)tCa>tTa	p.S147L		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	147					fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						AAAGATTCTTGAACTCACTTG	0.368																																					p.S147L		Atlas-SNP	.											.	PTPLA	34	.	0			c.C440T						.						99	92	94					10																	17645602		2203	4300	6503	SO:0001583	missense	9200	exon4			ATTCTTGAACTCA	AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"cementum attachment protein"	610467	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.440C>T	chr10.hg19:g.17645602G>A	ENSP00000355308:p.Ser147Leu	183.0	0.0		308.0	100.0	NM_014241	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Missense_Mutation	SNP	ENST00000361271.3	hg19	CCDS7121.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.937285	0.52972	.	.	ENSG00000165996	ENST00000361271	T	0.39592	1.07	4.87	4.87	0.63330	.	0.068458	0.64402	D	0.000009	T	0.77039	0.4072	H	0.96805	3.885	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.85897	0.1432	10	0.87932	D	0	-6.8978	18.4033	0.90525	0.0:0.0:1.0:0.0	.	147	B0YJ81	HACD1_HUMAN	L	147	ENSP00000355308:S147L	ENSP00000355308:S147L	S	-	2	0	PTPLA	17685608	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.795000	0.99099	2.426000	0.82243	0.460000	0.39030	TCA	.	.		0.368	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241		A	17645602	G	A	17645602	3	1	191	1	0	0	0	0	1	0	0	0	12787	1294	45	3	442	3	PTPLA	10	17645602	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10		17645602	117889145	67	28315										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26446396	26446396	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tctggaaacagcaagaattcGaagactaggattctcccatc	8	10	2	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr10:26446396G>A	ENST00000265944.5	+	26	3117	c.2951G>A	c.(2950-2952)cGa>cAa	p.R984Q	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	984	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GCAAGAATTCGAAGACTAGGA	0.363																																					p.R984Q		Atlas-SNP	.											MYO3A,NS,carcinoma,0,1	MYO3A	371	.	0			c.G2951A						.						109	106	107					10																	26446396		2203	4300	6503	SO:0001583	missense	53904	exon26			GAATTCGAAGACT	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2951G>A	chr10.hg19:g.26446396G>A	ENSP00000265944:p.Arg984Gln	86.0	1.0		130.0	15.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	35	5.426828	0.96131	.	.	ENSG00000095777	ENST00000265944	T	0.73681	-0.77	5.07	5.07	0.68467	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.91267	0.7247	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94026	0.7297	10	0.72032	D	0.01	.	18.8211	0.92097	0.0:0.0:1.0:0.0	.	984	Q8NEV4	MYO3A_HUMAN	Q	984	ENSP00000265944:R984Q	ENSP00000265944:R984Q	R	+	2	0	MYO3A	26486402	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.809000	0.99208	2.524000	0.85096	0.655000	0.94253	CGA	.	.		0.363	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26446396	G	A	26446396	3	1	191	1	0	0	0	0	1	0	0	0	10085	1058	37	1	3045	1	MYO3A	10	26446396	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	8800794	26446396	109088351	68	28316										
CDH23	64072	hgsc.bcm.edu	37	chr10	73560411	73560411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agggtgacatctatgtgctgTcttctctggaccgggagaag	14	8	3	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr10:73560411T>C	ENST00000224721.6	+	52	7401	c.7396T>C	c.(7396-7398)Tct>Cct	p.S2466P	CDH23_ENST00000475158.1_3'UTR|CDH23_ENST00000398788.3_Missense_Mutation_p.S221P	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2461	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CTATGTGCTGTCTTCTCTGGA	0.488																																					p.S2461P		Atlas-SNP	.											.	CDH23	365	.	0			c.T7381C						.						57	59	59					10																	73560411		1937	4135	6072	SO:0001583	missense	64072	exon51			GTGCTGTCTTCTC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.7396T>C	chr10.hg19:g.73560411T>C	ENSP00000224721:p.Ser2466Pro	55.0	0.0		79.0	28.0	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	T	22.3	4.266048	0.80358	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.01871	4.59	5.43	5.43	0.79202	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.07007	0.0178	L	0.29908	0.895	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.70227	0.968;0.968	T	0.41360	-0.9513	10	0.56958	D	0.05	.	15.4863	0.75571	0.0:0.0:0.0:1.0	.	2461;2461	E9PEX1;Q9H251	.;CAD23_HUMAN	P	2466;2461;2464;221	ENSP00000381768:S221P	ENSP00000224721:S2466P	S	+	1	0	CDH23	73230417	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	5.720000	0.68470	2.062000	0.61559	0.438000	0.28831	TCT	.	.		0.488	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		C	73560411	T	C	73560411	3	2	191	1	0	0	0	0	1	0	0	0	3110	1667	58	2	7932	2	CDH23	10	73560411	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	47114015	73560411	61974336	69	28317										
SLIT1	6585	hgsc.bcm.edu	37	chr10	98762647	98762647	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gcgtcttggtgaagtcctgcAgctcgttgttgatgtacagg	14	8	1	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr10:98762647A>T	ENST00000266058.4	-	35	4213	c.3968T>A	c.(3967-3969)cTg>cAg	p.L1323Q	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Missense_Mutation_p.L1323Q	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	1323	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		GAAGTCCTGCAGCTCGTTGTT	0.602																																					p.L1323Q		Atlas-SNP	.											.	SLIT1	154	.	0			c.T3968A						.						170	165	167					10																	98762647		2203	4300	6503	SO:0001583	missense	6585	exon35			TCCTGCAGCTCGT	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.3968T>A	chr10.hg19:g.98762647A>T	ENSP00000266058:p.Leu1323Gln	118.0	0.0		130.0	54.0	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	hg19	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.259060	0.80246	.	.	ENSG00000187122	ENST00000266058;ENST00000371070	T;T	0.69926	-0.44;-0.44	4.75	4.75	0.60458	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.64402	D	0.000001	T	0.77961	0.4209	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78443	-0.2202	10	0.46703	T	0.11	.	14.0816	0.64925	1.0:0.0:0.0:0.0	.	1323	O75093	SLIT1_HUMAN	Q	1323	ENSP00000266058:L1323Q;ENSP00000360109:L1323Q	ENSP00000266058:L1323Q	L	-	2	0	SLIT1	98752637	1.000000	0.71417	0.995000	0.50966	0.987000	0.75469	9.115000	0.94336	1.995000	0.58328	0.459000	0.35465	CTG	.	.		0.602	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		T	98762647	A	T	98762647	3	4	191	1	0	0	0	0	1	0	0	0	14754	188	7	4	648	4	SLIT1	10	98762647	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	25202236	98762647	36772100	70	28318										
MMP21	118856	hgsc.bcm.edu	37	chr10	127460888	127460888	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tggatcccgtcctgtaggtgTgaggcaagcccaggacatgg	15	10	0	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr10:127460888T>C	ENST00000368808.3	-	4	877	c.878A>G	c.(877-879)cAc>cGc	p.H293R		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	293					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	CCTGTAGGTGTGAGGCAAGCC	0.527																																					p.H293R		Atlas-SNP	.											.	MMP21	46	.	0			c.A878G						.						106	89	95					10																	127460888		2203	4300	6503	SO:0001583	missense	118856	exon4			TAGGTGTGAGGCA	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.878A>G	chr10.hg19:g.127460888T>C	ENSP00000357798:p.His293Arg	65.0	0.0		87.0	26.0	NM_147191	Q5VZP9|Q8NG02	Missense_Mutation	SNP	ENST00000368808.3	hg19	CCDS7647.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.944663	0.73672	.	.	ENSG00000154485	ENST00000368808	T	0.66995	-0.24	5.05	3.89	0.44902	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.86234	0.5884	H	0.96996	3.92	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.87684	0.2549	10	0.87932	D	0	-17.9828	10.161	0.42851	0.0:0.0:0.1683:0.8317	.	293	Q8N119	MMP21_HUMAN	R	293	ENSP00000357798:H293R	ENSP00000357798:H293R	H	-	2	0	MMP21	127450878	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.012000	0.64017	0.746000	0.32786	0.459000	0.35465	CAC	.	.		0.527	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			C	127460888	T	C	127460888	3	2	191	1	0	0	0	0	1	0	0	0	9669	1696	59	2	847	2	MMP21	10	127460888	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	28698241	127460888	8073859	71	28319										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1258280	1258280	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tggaagctctccccctcctgCccggacgccctggcacccaa	9	20	1	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr11:1258280C>T	ENST00000529681.1	+	25	3241	c.3183C>T	c.(3181-3183)tgC>tgT	p.C1061C	MUC5B_ENST00000447027.1_Silent_p.C1064C	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1061	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCCCCTCCTGCCCGGACGCCC	0.657																																					p.C1061C		Atlas-SNP	.											.	MUC5B	473	.	0			c.C3183T						.						41	58	52					11																	1258280		2092	4193	6285	SO:0001819	synonymous_variant	727897	exon25			CTCCTGCCCGGAC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.3183C>T	chr11.hg19:g.1258280C>T		80.0	0.0		96.0	19.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.657	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1258280	C	T	1258280	2	4	191	1	0	0	0	0	0	0	0	1	9988	747	26	3		3	MUC5B	11	1258280	Silent	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10		1258280	133748236	72	28320										
IPO7	10527	hgsc.bcm.edu	37	chr11	9446761	9446761	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aatgctgaccctcgaaaaaaAgatggagccctgcatatgat	9	9	0	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr11:9446761A>C	ENST00000379719.3	+	12	1429	c.1287A>C	c.(1285-1287)aaA>aaC	p.K429N		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	429					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		CTCGAAAAAAAGATGGAGCCC	0.348																																					p.K429N		Atlas-SNP	.											.	IPO7	72	.	0			c.A1287C						.						84	82	83					11																	9446761		2201	4295	6496	SO:0001583	missense	10527	exon12			AAAAAAAGATGGA	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.1287A>C	chr11.hg19:g.9446761A>C	ENSP00000369042:p.Lys429Asn	98.0	0.0		101.0	6.0	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	hg19	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	A	19.64	3.865484	0.71949	.	.	ENSG00000205339	ENST00000379719	T	0.69806	-0.43	5.45	3.15	0.36227	Armadillo-like helical (1);Armadillo-type fold (1);Exportin/Importin, Cse1-like (1);	0.000000	0.85682	D	0.000000	T	0.81044	0.4741	M	0.88310	2.945	0.80722	D	1	D	0.60160	0.987	D	0.66084	0.941	T	0.82222	-0.0564	10	0.87932	D	0	.	9.1753	0.37107	0.8524:0.0:0.1476:0.0	.	429	O95373	IPO7_HUMAN	N	429	ENSP00000369042:K429N	ENSP00000369042:K429N	K	+	3	2	IPO7	9403337	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.046000	0.30354	0.881000	0.35993	0.533000	0.62120	AAA	.	.		0.348	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		C	9446761	A	C	9446761	3	2	191	1	0	0	0	0	1	0	0	0	7806	69	3	5	1333	5	IPO7	11	9446761	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	8188481	9446761	125559755	73	28321										
TTC17	55761	hgsc.bcm.edu	37	chr11	43421488	43421488	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agagtatcaaaagcagcatgAccactacctgagacagcagg	10	10	1	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr11:43421488A>T	ENST00000039989.4	+	9	1123	c.1109A>T	c.(1108-1110)gAc>gTc	p.D370V	TTC17_ENST00000299240.6_Missense_Mutation_p.D370V|TTC17_ENST00000526774.1_3'UTR	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	370					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						AAGCAGCATGACCACTACCTG	0.348																																					p.D370V		Atlas-SNP	.											.	TTC17	112	.	0			c.A1109T						.						108	106	106					11																	43421488		2203	4300	6503	SO:0001583	missense	55761	exon9			AGCATGACCACTA	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"Tetratricopeptide (TTC) repeat domain containing"	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.1109A>T	chr11.hg19:g.43421488A>T	ENSP00000039989:p.Asp370Val	280.0	0.0		406.0	27.0	NM_018259	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	hg19	CCDS31466.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.533124	0.85812	.	.	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.37752	1.33;1.18	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.55970	0.1954	L	0.57536	1.79	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.79108	0.972;0.986;0.992	T	0.52924	-0.8510	10	0.36615	T	0.2	-21.9472	15.7262	0.77763	1.0:0.0:0.0:0.0	.	370;370;370	Q8NEC0;Q96AE7;G3XAB3	.;TTC17_HUMAN;.	V	370	ENSP00000299240:D370V;ENSP00000039989:D370V	ENSP00000039989:D370V	D	+	2	0	TTC17	43378064	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.108000	0.64289	0.460000	0.39030	GAC	.	.		0.348	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259		T	43421488	A	T	43421488	3	4	191	1	0	0	0	0	1	0	0	0	16699	275	10	4	1143	4	TTC17	11	43421488	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	33974727	43421488	91585028	74	28322										
SERPINH1	871	hgsc.bcm.edu	37	chr11	75280184	75280184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctgttgccatctccttgcccAagggtgtggtggaggtgacc	14	11	1	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr11:75280184A>G	ENST00000524558.1	+	4	2357	c.922A>G	c.(922-924)Aag>Gag	p.K308E	SERPINH1_ENST00000525876.1_Missense_Mutation_p.K91E|SERPINH1_ENST00000533603.1_Missense_Mutation_p.K308E|SERPINH1_ENST00000530284.1_Missense_Mutation_p.K308E|SERPINH1_ENST00000358171.3_Missense_Mutation_p.K308E			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	308					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					CTCCTTGCCCAAGGGTGTGGT	0.612																																					p.K308E		Atlas-SNP	.											.	SERPINH1	33	.	0			c.A922G						.						55	45	49					11																	75280184		2200	4293	6493	SO:0001583	missense	871	exon5			TTGCCCAAGGGTG	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"Serine (or cysteine) peptidase inhibitors"	1546	protein-coding gene	gene with protein product		600943	"serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2", "serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.922A>G	chr11.hg19:g.75280184A>G	ENSP00000434412:p.Lys308Glu	72.0	0.0		118.0	11.0	NM_001207014	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Missense_Mutation	SNP	ENST00000524558.1	hg19	CCDS8239.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.408313	0.83340	.	.	ENSG00000149257	ENST00000533603;ENST00000358171;ENST00000421448;ENST00000530284;ENST00000524558;ENST00000525876	D;D;D;D;D	0.92099	-2.97;-2.97;-2.97;-2.97;-2.97	5.54	5.54	0.83059	Serpin domain (3);	0.000000	0.85682	D	0.000000	D	0.95683	0.8596	M	0.77820	2.39	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.968	D	0.96021	0.9009	10	0.72032	D	0.01	.	13.6314	0.62198	1.0:0.0:0.0:0.0	.	308;308	E9PPV6;P50454	.;SERPH_HUMAN	E	308;308;287;308;308;91	ENSP00000434657:K308E;ENSP00000350894:K308E;ENSP00000436305:K308E;ENSP00000434412:K308E;ENSP00000433532:K91E	ENSP00000350894:K308E	K	+	1	0	SERPINH1	74957832	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.425000	0.80255	2.104000	0.64026	0.533000	0.62120	AAG	.	.		0.612	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353		G	75280184	A	G	75280184	3	3	191	1	0	0	0	0	1	0	0	0	14132	131	5	2	932	2	SERPINH1	11	75280184	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	31858696	75280184	59726332	75	28323										
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101863554	101863554	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cccatccatcaaaaatacttTacaaataataccacttctgg	2	12	2	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr11:101863554T>A	ENST00000263468.8	+	10	3560	c.3290T>A	c.(3289-3291)tTa>tAa	p.L1097*	KIAA1377_ENST00000537689.1_Nonsense_Mutation_p.L898*	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	1097										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AAAAATACTTTACAAATAATA	0.274																																					p.L1097X		Atlas-SNP	.											.	KIAA1377	111	.	0			c.T3290A						.						27	29	28					11																	101863554		2188	4263	6451	SO:0001587	stop_gained	57562	exon10			ATACTTTACAAAT	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.3290T>A	chr11.hg19:g.101863554T>A	ENSP00000263468:p.Leu1097*	273.0	0.0		378.0	111.0	NM_020802	Q4G0U6	Nonsense_Mutation	SNP	ENST00000263468.8	hg19	CCDS31658.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	45|45	12.056640|12.056640	0.99631|0.99631	.|.	.|.	ENSG00000110318|ENSG00000110318	ENST00000532077|ENST00000263468;ENST00000537689	.|.	.|.	.|.	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	.|0.133751	.|0.34200	.|N	.|0.004164	T|.	0.41834|.	0.1176|.	.|.	.|.	.|.	0.52099|0.52099	D|D	0.999949|0.999949	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.33266|.	-0.9875|.	4|.	.|0.02654	.|T	.|1	-4.7772|-4.7772	14.562|14.562	0.68148|0.68148	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	L|X	60|1097;898	.|.	.|ENSP00000263468:L1097X	F|L	+|+	3|2	2|0	KIAA1377|KIAA1377	101368764|101368764	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.954000|0.954000	0.61252|0.61252	4.773000|4.773000	0.62331|0.62331	2.149000|2.149000	0.67028|0.67028	0.477000|0.477000	0.44152|0.44152	TTT|TTA	.	.		0.274	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		A	101863554	T	A	101863554	4	1	191	1	0	0	0	0	0	1	0	0	8236	1764	61	4	3328	4	KIAA1377	11	101863554	Nonsense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	26583370	101863554	33142962	76	28324										
MLL	4297	hgsc.bcm.edu	37	chr11	118347552	118347552	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gactcatcagagacctctgtGcgaggaccccggattaaaca	10	12	3	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr11:118347552G>A	ENST00000389506.5	+	4	3189	c.3189G>A	c.(3187-3189)gtG>gtA	p.V1063V	KMT2A_ENST00000354520.4_Silent_p.V1063V|KMT2A_ENST00000534358.1_Silent_p.V1063V			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1063					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										AGACCTCTGTGCGAGGACCCC	0.468																																					p.V1063V		Atlas-SNP	.											.	MLL	548	.	0			c.G3189A						.						112	108	109					11																	118347552		2200	4296	6496	SO:0001819	synonymous_variant	4297	exon4			CTCTGTGCGAGGA	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.3189G>A	chr11.hg19:g.118347552G>A		84.0	0.0		155.0	8.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.468	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118347552	G	A	118347552	2	1	191	1	0	0	0	0	0	0	0	1	9629	1306	46	3		3	MLL	11	118347552	Silent	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	16483998	118347552	16658964	77	28325										
KCNA6	3742	hgsc.bcm.edu	37	chr12	4920420	4920420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aggctgacgatgacgattcgCtttttcccagcatcccggat	10	12	0	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr12:4920420C>T	ENST00000280684.3	+	1	2079	c.1213C>T	c.(1213-1215)Ctt>Ttt	p.L405F	KCNA6_ENST00000433855.1_Missense_Mutation_p.L405F|RP11-234B24.4_ENST00000542988.1_lincRNA			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	405					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	TGACGATTCGCTTTTTCCCAG	0.562										HNSCC(72;0.22)																											p.L405F		Atlas-SNP	.											.	KCNA6	122	.	0			c.C1213T						.						142	121	128					12																	4920420		2203	4300	6503	SO:0001583	missense	3742	exon1			GATTCGCTTTTTC	X17622	CCDS8534.1	12p13	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6225	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 96"	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.1213C>T	chr12.hg19:g.4920420C>T	ENSP00000280684:p.Leu405Phe	103.0	0.0		141.0	25.0	NM_002235		Missense_Mutation	SNP	ENST00000280684.3	hg19	CCDS8534.1	.	.	.	.	.	.	.	.	.	.	C	2.998	-0.206675	0.06180	.	.	ENSG00000151079	ENST00000433855;ENST00000280684	D;D	0.98493	-4.96;-4.96	5.18	5.18	0.71444	Ion transport (1);	0.213205	0.39475	N	0.001346	D	0.93976	0.8071	N	0.16656	0.425	0.22610	N	0.998937	B	0.13145	0.007	B	0.21546	0.035	D	0.84155	0.0425	10	0.21540	T	0.41	.	9.5211	0.39135	0.0:0.8421:0.0:0.1579	.	405	P17658	KCNA6_HUMAN	F	405	ENSP00000408321:L405F;ENSP00000280684:L405F	ENSP00000280684:L405F	L	+	1	0	KCNA6	4790681	0.000000	0.05858	0.960000	0.40013	0.710000	0.40934	-0.043000	0.12043	2.688000	0.91661	0.655000	0.94253	CTT	.	.		0.562	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235		T	4920420	C	T	4920420	3	4	191	1	0	0	0	0	1	0	0	0	8016	797	28	3	1215	3	KCNA6	12	4920420	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10		4920420	128931475	78	28326										
ARID2	196528	hgsc.bcm.edu	37	chr12	46244283	46244283	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gcactcctgttacagtaattCaacaagctgtcccacagagt	7	12	1	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr12:46244283C>A	ENST00000334344.6	+	15	2549	c.2377C>A	c.(2377-2379)Caa>Aaa	p.Q793K	ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000444670.1_Missense_Mutation_p.Q403K|ARID2_ENST00000422737.1_Missense_Mutation_p.Q644K|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	793	Gln-rich.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TACAGTAATTCAACAAGCTGT	0.453			"N, S, F"		hepatocellular carcinoma																																p.Q793K		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.C2377A						.						91	80	84					12																	46244283		2203	4300	6503	SO:0001583	missense	196528	exon15			GTAATTCAACAAG		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2377C>A	chr12.hg19:g.46244283C>A	ENSP00000335044:p.Gln793Lys	82.0	0.0		96.0	27.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.275244	0.80580	.	.	ENSG00000189079	ENST00000334344;ENST00000422737;ENST00000444670	T	0.36340	1.26	5.83	5.83	0.93111	.	0.049507	0.85682	D	0.000000	T	0.37892	0.1020	N	0.24115	0.695	0.80722	D	1	P;P;P	0.51933	0.859;0.949;0.9	P;P;B	0.50659	0.554;0.647;0.444	T	0.02860	-1.1101	10	0.24483	T	0.36	-4.521	20.1152	0.97926	0.0:1.0:0.0:0.0	.	793;403;793	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	K	793;644;403	ENSP00000335044:Q793K	ENSP00000335044:Q793K	Q	+	1	0	ARID2	44530550	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	6.776000	0.75023	2.750000	0.94351	0.655000	0.94253	CAA	.	.		0.453	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46244283	C	A	46244283	3	1	191	1	0	0	0	0	1	0	0	0	915	827	29	3	2435	3	ARID2	12	46244283	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	41323863	46244283	87607612	79	28327										
ARHGAP9	64333	hgsc.bcm.edu	37	chr12	57871256	57871256	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tctcaccgtctcgctgcgacTgcggcgcgggggcttccagg	15	15	2	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr12:57871256T>A	ENST00000356411.2	-	4	880	c.742A>T	c.(742-744)Agt>Tgt	p.S248C	ARHGAP9_ENST00000550288.1_Missense_Mutation_p.S327C|ARHGAP9_ENST00000393797.2_Missense_Mutation_p.S319C|ARHGAP9_ENST00000424809.2_Missense_Mutation_p.S248C|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.S248C|ARHGAP9_ENST00000430041.2_Missense_Mutation_p.S64C|ARHGAP9_ENST00000550454.1_5'UTR			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	248					positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			TCGCTGCGACTGCGGCGCGGG	0.587																																					p.S248C		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.A742T						.						54	61	59					12																	57871256		2203	4300	6503	SO:0001583	missense	64333	exon3			TGCGACTGCGGCG	AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.742A>T	chr12.hg19:g.57871256T>A	ENSP00000348782:p.Ser248Cys	108.0	0.0		186.0	60.0	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Missense_Mutation	SNP	ENST00000356411.2	hg19		.	.	.	.	.	.	.	.	.	.	T	13.39	2.223052	0.39300	.	.	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000430041;ENST00000548139;ENST00000552604;ENST00000551452;ENST00000552066	T;T;T;T;T;T	0.47177	3.11;3.11;1.75;3.09;2.99;0.85	3.58	2.39	0.29439	WW/Rsp5/WWP (1);	0.631054	0.15570	N	0.255515	T	0.32675	0.0837	N	0.19112	0.55	0.23978	N	0.99628	P;P;P;B;B;B	0.50369	0.934;0.79;0.845;0.32;0.41;0.291	B;B;B;B;B;B	0.43916	0.436;0.275;0.319;0.325;0.088;0.078	T	0.11891	-1.0569	10	0.72032	D	0.01	.	7.0886	0.25272	0.0:0.0:0.2299:0.7701	.	248;327;248;248;248;64	B4E248;Q6ZN13;Q9BRR9;Q9BRR9-2;E9PDX9;B4DVI3	.;.;RHG09_HUMAN;.;.;.	C	248;248;248;319;297;64;64;64;101;64	ENSP00000377380:S248C;ENSP00000348782:S248C;ENSP00000394307:S248C;ENSP00000377386:S319C;ENSP00000397950:S64C;ENSP00000449829:S64C	ENSP00000344852:S297C	S	-	1	0	ARHGAP9	56157523	0.059000	0.20769	0.005000	0.12908	0.002000	0.02628	-0.045000	0.12003	0.701000	0.31803	0.533000	0.62120	AGT	.	.		0.587	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496		A	57871256	T	A	57871256	3	1	191	1	0	0	0	0	1	0	0	0	889	1580	55	4	1513	4	ARHGAP9	12	57871256	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	11626973	57871256	75980639	80	28328										
MARS	4141	hgsc.bcm.edu	37	chr12	57892224	57892224	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tactctcgcctccgccagtgGaacaccctctatctgtgtgg	9	15	3	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr12:57892224G>C	ENST00000262027.5	+	9	1043	c.909G>C	c.(907-909)tgG>tgC	p.W303C	MARS_ENST00000447721.2_3'UTR|MARS_ENST00000315473.5_Missense_Mutation_p.W69C	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	303					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	TCCGCCAGTGGAACACCCTCT	0.587																																					p.W303C		Atlas-SNP	.											.	MARS	84	.	0			c.G909C						.						78	71	73					12																	57892224		2203	4300	6503	SO:0001583	missense	4141	exon9			CCAGTGGAACACC	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.909G>C	chr12.hg19:g.57892224G>C	ENSP00000262027:p.Trp303Cys	68.0	0.0		100.0	36.0	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	hg19	CCDS8942.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.7|22.7	4.318956|4.318956	0.81469|0.81469	.|.	.|.	ENSG00000166986|ENSG00000166986	ENST00000552371|ENST00000262027;ENST00000315473	.|T;T	.|0.42131	.|1.55;0.98	4.7|4.7	4.7|4.7	0.59300|0.59300	.|Aminoacyl-tRNA synthetase, class I (M) (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.58206|0.58206	0.2106|0.2106	L|L	0.52364|0.52364	1.645|1.645	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.71674	.|0.957;0.998;0.997	.|P;D;D	.|0.69142	.|0.719;0.962;0.962	T|T	0.59736|0.59736	-0.7398|-0.7398	5|10	.|0.52906	.|T	.|0.07	-8.4755|-8.4755	16.7833|16.7833	0.85567|0.85567	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|69;176;303	.|A6NC17;B4E0E9;P56192	.|.;.;SYMC_HUMAN	A|C	136|303;69	.|ENSP00000262027:W303C;ENSP00000314653:W69C	.|ENSP00000262027:W303C	G|W	+|+	2|3	0|0	MARS|MARS	56178491|56178491	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.318000|9.318000	0.96334|0.96334	2.325000|2.325000	0.78763|0.78763	0.561000|0.561000	0.74099|0.74099	GGA|TGG	.	.		0.587	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		C	57892224	G	C	57892224	3	2	191	1	0	0	0	0	1	0	0	0	9325	1183	41	4	943	4	MARS	12	57892224	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	20968	57892224	75959671	81	28329										
ANKRD13A	88455	hgsc.bcm.edu	37	chr12	110437503	110437503	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gcctcctcgccatgtcctcgGcctgcgacgcgggcgaccac	12	19	0	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr12:110437503G>A	ENST00000261739.4	+	1	176	c.10G>A	c.(10-12)Gcc>Acc	p.A4T	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	4						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						CATGTCCTCGGCCTGCGACGC	0.726																																					p.A4T		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.G10A						.						11	11	11					12																	110437503		1861	3508	5369	SO:0001583	missense	88455	exon1			TCCTCGGCCTGCG	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"Ankyrin repeat domain containing"	21268	protein-coding gene	gene with protein product		615123	"ankyrin repeat domain 13"	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.10G>A	chr12.hg19:g.110437503G>A	ENSP00000261739:p.Ala4Thr	89.0	0.0		112.0	11.0	NM_033121	O60736	Missense_Mutation	SNP	ENST00000261739.4	hg19	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.158000	0.38119	.	.	ENSG00000076513	ENST00000261739	T	0.56776	0.44	3.98	0.966	0.19667	.	0.888139	0.09933	N	0.736907	T	0.28532	0.0706	N	0.13235	0.315	0.80722	D	1	B;B;B	0.12013	0.0;0.005;0.002	B;B;B	0.17098	0.003;0.017;0.004	T	0.17198	-1.0377	10	0.14252	T	0.57	-15.6115	3.1807	0.06583	0.0994:0.3553:0.3849:0.1605	.	4;4;4	B4DYP5;Q3ZTS7;Q8IZ07	.;.;AN13A_HUMAN	T	4	ENSP00000261739:A4T	ENSP00000261739:A4T	A	+	1	0	ANKRD13A	108921886	0.001000	0.12720	0.992000	0.48379	0.835000	0.47333	0.141000	0.16076	0.072000	0.16694	0.563000	0.77884	GCC	.	.		0.726	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		A	110437503	G	A	110437503	3	1	191	1	0	0	0	0	1	0	0	0	641	1203	42	3	12	3	ANKRD13A	12	110437503	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	52545279	110437503	23414392	82	28330										
GPR81	27198	hgsc.bcm.edu	37	chr12	123214615	123214615	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tcatggccaacgtgaagagcCccactcggcagggaatgtcc	12	13	1	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr12:123214615C>T	ENST00000436083.2	-	1	775	c.272G>A	c.(271-273)gGg>gAg	p.G91E	HCAR1_ENST00000432564.1_Missense_Mutation_p.G91E|HCAR1_ENST00000356987.2_Missense_Mutation_p.G91E			Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	91					response to estradiol (GO:0032355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	10						CGTGAAGAGCCCCACTCGGCA	0.577																																					p.G91E		Atlas-SNP	.											.	HCAR1	21	.	0			c.G272A						.						60	55	56					12																	123214615		2203	4300	6503	SO:0001583	missense	27198	exon1			AAGAGCCCCACTC	AF411110	CCDS9236.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000196917	ENSG00000196917		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	4532	protein-coding gene	gene with protein product	"lactate receptor 1"	606923	"G protein-coupled receptor 104", "G protein-coupled receptor 81"	GPR104, GPR81		11574155, 19047060, 18952058, 21454438	Standard	NM_032554		Approved	HCA1, FKSG80, TA-GPCR, LACR1	uc001ucz.3	Q9BXC0		ENST00000436083.2:c.272G>A	chr12.hg19:g.123214615C>T	ENSP00000409980:p.Gly91Glu	66.0	0.0		92.0	34.0	NM_032554	B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	Missense_Mutation	SNP	ENST00000436083.2	hg19	CCDS9236.1	.	.	.	.	.	.	.	.	.	.	C	9.108	1.005757	0.19199	.	.	ENSG00000196917	ENST00000356987;ENST00000432564;ENST00000436083	T;T;T	0.36520	1.25;1.25;1.25	5.34	0.2	0.15181	GPCR, rhodopsin-like superfamily (1);	0.601453	0.15126	N	0.279097	T	0.20047	0.0482	N	0.08118	0	0.28458	N	0.916018	B	0.26400	0.148	B	0.35770	0.21	T	0.27191	-1.0081	10	0.45353	T	0.12	-5.4874	6.8077	0.23786	0.7579:0.1293:0.1128:0.0	.	91	Q9BXC0	HCAR1_HUMAN	E	91	ENSP00000349478:G91E;ENSP00000389255:G91E;ENSP00000409980:G91E	ENSP00000349478:G91E	G	-	2	0	HCAR1	121780568	0.000000	0.05858	0.591000	0.28745	0.241000	0.25554	-0.406000	0.07187	-0.202000	0.10268	-0.262000	0.10625	GGG	.	.		0.577	HCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401415.1			T	123214615	C	T	123214615	3	4	191	1	0	0	0	0	1	0	0	0	6719	623	22	3	772	3	GPR81	12	123214615	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	12777112	123214615	10637280	83	28331										
PSPC1	55269	hgsc.bcm.edu	37	chr13	20346623	20346623	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gaagcgaatccgtagaggtcTgctcttgagaatggtgccgt	14	8	2	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr13:20346623T>G	ENST00000338910.4	-	2	592	c.433A>C	c.(433-435)Aga>Cga	p.R145R		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	145	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.|Sufficient for paraspeckles localization.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		CGTAGAGGTCTGCTCTTGAGA	0.438																																					p.R145R		Atlas-SNP	.											.	PSPC1	61	.	0			c.A433C						.						119	114	116					13																	20346623		1929	4148	6077	SO:0001819	synonymous_variant	55269	exon3			GAGGTCTGCTCTT	AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"RNA binding motif (RRM) containing"	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.433A>C	chr13.hg19:g.20346623T>G		64.0	0.0		86.0	9.0	NM_001042414	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Silent	SNP	ENST00000338910.4	hg19	CCDS41870.1																																																																																			.	.		0.438	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2			G	20346623	T	G	20346623	2	3	191	1	0	0	0	0	0	0	0	1	12728	1588	55	5		5	PSPC1	13	20346623	Silent	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10		20346623	94823255	84	28332										
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20605572	20605572	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aaaccagaaatcctggaatgGgaggcaagttgtattttgta	11	5	0	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr13:20605572G>A	ENST00000382874.2	+	11	2155	c.1965G>A	c.(1963-1965)tgG>tgA	p.W655*	ZMYM2_ENST00000382883.3_Nonsense_Mutation_p.W137*|ZMYM2_ENST00000382871.2_Nonsense_Mutation_p.W655*|ZMYM2_ENST00000382869.3_Nonsense_Mutation_p.W655*	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	655					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		TCCTGGAATGGGAGGCAAGTT	0.353																																					p.W655X		Atlas-SNP	.											.	ZMYM2	191	.	0			c.G1965A						.						82	74	76					13																	20605572		1824	4079	5903	SO:0001587	stop_gained	7750	exon11			GGAATGGGAGGCA	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.1965G>A	chr13.hg19:g.20605572G>A	ENSP00000372327:p.Trp655*	103.0	0.0		131.0	39.0	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Nonsense_Mutation	SNP	ENST00000382874.2	hg19	CCDS45016.1	.	.	.	.	.	.	.	.	.	.	G	39	7.594909	0.98381	.	.	ENSG00000121741	ENST00000382869;ENST00000456228;ENST00000382874;ENST00000382871;ENST00000382883;ENST00000382870	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0185	19.6801	0.95958	0.0:0.0:1.0:0.0	.	.	.	.	X	655;655;655;655;137;35	.	ENSP00000372322:W655X	W	+	3	0	ZMYM2	19503572	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.444000	0.97578	2.652000	0.90054	0.655000	0.94253	TGG	.	.		0.353	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		A	20605572	G	A	20605572	4	1	191	1	0	0	0	0	0	1	0	0	17715	1241	43	3	1995	3	ZMYM2	13	20605572	Nonsense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	258949	20605572	94564306	85	28333										
PML	5371	hgsc.bcm.edu	37	chr15	74324992	74324992	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gcctatggctgtggtacagtCagtgcccggggcacaccccg	14	14	1	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr15:74324992C>G	ENST00000268058.3	+	5	1430	c.1334C>G	c.(1333-1335)tCa>tGa	p.S445*	PML_ENST00000563500.1_Intron|PML_ENST00000359928.4_Intron|PML_ENST00000395135.3_Nonsense_Mutation_p.S445*|PML_ENST00000435786.2_Nonsense_Mutation_p.S445*|PML_ENST00000569477.1_Nonsense_Mutation_p.S445*|PML_ENST00000436891.3_Nonsense_Mutation_p.S445*|PML_ENST00000567543.1_Intron|PML_ENST00000569161.1_3'UTR|PML_ENST00000569965.1_Nonsense_Mutation_p.S445*|PML_ENST00000395132.2_Intron|PML_ENST00000354026.6_Intron|PML_ENST00000268059.6_Nonsense_Mutation_p.S445*|PML_ENST00000564428.1_Intron|PML_ENST00000565898.1_Intron	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	445					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						GTGGTACAGTCAGTGCCCGGG	0.607			T	"RARA, PAX5"	"APL, ALL"																																p.S445X		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.C1334G						.						46	44	44					15																	74324992		2198	4297	6495	SO:0001587	stop_gained	5371	exon5			TACAGTCAGTGCC	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1334C>G	chr15.hg19:g.74324992C>G	ENSP00000268058:p.Ser445*	173.0	0.0		247.0	94.0	NM_033244	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Nonsense_Mutation	SNP	ENST00000268058.3	hg19	CCDS10255.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.313822	0.81358	.	.	ENSG00000140464	ENST00000395135;ENST00000435786;ENST00000436891;ENST00000268058;ENST00000268059;ENST00000417341;ENST00000418568	.	.	.	3.32	1.36	0.22044	.	3.634120	0.00875	N	0.002062	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-1.1575	3.7563	0.08586	0.2625:0.6064:0.0:0.1311	.	.	.	.	X	445;445;445;445;445;6;445	.	ENSP00000268058:S445X	S	+	2	0	PML	72112045	0.036000	0.19791	0.003000	0.11579	0.161000	0.22273	0.905000	0.28504	0.386000	0.24997	0.561000	0.74099	TCA	.	.		0.607	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		G	74324992	C	G	74324992	4	3	191	1	0	0	0	0	0	1	0	0	12144	838	29	4	1352	4	PML	15	74324992	Nonsense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10		74324992	28206400	86	28334										
CCDC33	80125	hgsc.bcm.edu	37	chr15	74588203	74588203	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aagagtcctggtccaaggacAcagtgagctccacaatggac	11	11	0	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr15:74588203A>G	ENST00000398814.3	+	11	1635	c.1204A>G	c.(1204-1206)Aca>Gca	p.T402A	CCDC33_ENST00000321288.5_Missense_Mutation_p.T605A|CCDC33_ENST00000563951.1_3'UTR	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	605										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GTCCAAGGACACAGTGAGCTC	0.522																																					p.T402A		Atlas-SNP	.											.	CCDC33	160	.	0			c.A1204G						.						68	68	68					15																	74588203		2026	4182	6208	SO:0001583	missense	80125	exon11			AAGGACACAGTGA	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"cancer/testis antigen 61"					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.1204A>G	chr15.hg19:g.74588203A>G	ENSP00000381795:p.Thr402Ala	101.0	0.0		151.0	13.0	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	hg19	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	A	9.349	1.064938	0.20067	.	.	ENSG00000140481	ENST00000321288;ENST00000398814	T;T	0.34859	1.34;2.21	4.02	-0.542	0.11854	.	1.900250	0.02565	N	0.097122	T	0.30135	0.0755	L	0.44542	1.39	0.09310	N	1	B;B	0.28291	0.028;0.206	B;B	0.31101	0.016;0.124	T	0.12451	-1.0547	10	0.25106	T	0.35	.	4.5536	0.12126	0.4581:0.3487:0.0:0.1931	.	605;402	C9JFX2;Q8N5R6-6	.;.	A	605;402	ENSP00000325012:T605A;ENSP00000381795:T402A	ENSP00000325012:T605A	T	+	1	0	CCDC33	72375256	0.000000	0.05858	0.000000	0.03702	0.200000	0.23975	-1.379000	0.02554	0.081000	0.16988	0.459000	0.35465	ACA	.	.		0.522	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791		G	74588203	A	G	74588203	3	3	191	1	0	0	0	0	1	0	0	0	2808	159	6	2	1246	2	CCDC33	15	74588203	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	263211	74588203	27943189	87	28335										
AGBL1	123624	hgsc.bcm.edu	37	chr15	86791026	86791026	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cgacggggcttgctgctctgCctcaggcacattgctgccct	12	15	2	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr15:86791026C>T	ENST00000441037.2	+	6	608	c.513C>T	c.(511-513)tgC>tgT	p.C171C	AGBL1_ENST00000421325.2_Silent_p.C171C	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	171					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TGCTGCTCTGCCTCAGGCACA	0.652																																					p.C171C		Atlas-SNP	.											.	AGBL1	151	.	0			c.C513T						.						46	48	47					15																	86791026		2154	4261	6415	SO:0001819	synonymous_variant	123624	exon6			GCTCTGCCTCAGG	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.513C>T	chr15.hg19:g.86791026C>T		61.0	0.0		71.0	25.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	hg19	CCDS58398.1																																																																																			.	.		0.652	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		T	86791026	C	T	86791026	2	4	191	1	0	0	0	0	0	0	0	1	375	747	26	3		3	AGBL1	15	86791026	Silent	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	12202823	86791026	15740366	88	28336										
ACAN	176	hgsc.bcm.edu	37	chr15	89402510	89402510	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agacccagcgccctgcagagAcgcatctagaaattgagtcc	10	13	1	4			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr15:89402510A>G	ENST00000561243.1	+	11	6694	c.6694A>G	c.(6694-6696)Acg>Gcg	p.T2232A	ACAN_ENST00000352105.7_Missense_Mutation_p.T2232A|ACAN_ENST00000439576.2_Missense_Mutation_p.T2232A|ACAN_ENST00000559004.1_Missense_Mutation_p.T2232A			P16112	PGCA_HUMAN	aggrecan	2117	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.|G3.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CCCTGCAGAGACGCATCTAGA	0.577																																					p.T2232A		Atlas-SNP	.											.	ACAN	220	.	0			c.A6694G						.						38	42	41					15																	89402510		2097	4226	6323	SO:0001583	missense	176	exon12			GCAGAGACGCATC	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.6694A>G	chr15.hg19:g.89402510A>G	ENSP00000453342:p.Thr2232Ala	75.0	0.0		133.0	44.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	hg19	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	A	0.020	-1.440852	0.01098	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02067	4.8;4.47	5.27	0.974	0.19715	.	0.850575	0.09579	N	0.783071	T	0.00754	0.0025	N	0.00621	-1.32	0.09310	N	0.999999	B;B	0.17852	0.024;0.024	B;B	0.23150	0.044;0.024	T	0.46414	-0.9193	10	0.02654	T	1	-0.9054	6.3809	0.21533	0.3009:0.1233:0.5758:0.0	.	2232;2232	E7ENV9;E7EX88	.;.	A	2232;2232;2118	ENSP00000387356:T2232A;ENSP00000341615:T2232A	ENSP00000268134:T2118A	T	+	1	0	ACAN	87203514	0.946000	0.32159	0.319000	0.25293	0.840000	0.47671	1.199000	0.32235	0.210000	0.20664	-0.262000	0.10625	ACG	.	.		0.577	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		G	89402510	A	G	89402510	3	3	191	1	0	0	0	0	1	0	0	0	117	275	10	2	6736	2	ACAN	15	89402510	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	2611484	89402510	13128882	89	28337										
THOC6	79228	hgsc.bcm.edu	37	chr16	3077415	3077415	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tcaaccagtggcagctgagcGgggagctgaaggcccaggtg	17	10	1	2	rs374499488		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr16:3077415G>A	ENST00000326266.8	+	12	1155	c.859G>A	c.(859-861)Ggg>Agg	p.G287R	THOC6_ENST00000575576.1_Missense_Mutation_p.G263R|THOC6_ENST00000253952.9_Intron|THOC6_ENST00000574549.1_Missense_Mutation_p.G263R	NM_024339.3	NP_077315.2	Q86W42	THOC6_HUMAN	THO complex 6 homolog (Drosophila)	287					apoptotic process (GO:0006915)|central nervous system development (GO:0007417)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	13						GCAGCTGAGCGGGGAGCTGAA	0.667																																					p.G287R		Atlas-SNP	.											.	THOC6	40	.	0			c.G859A						.	G	,ARG/GLY	1,4395		0,1,2197	25	28	27		,859	4.4	1	16		27	0,8600		0,0,4300	no	intron,missense	THOC6	NM_001142350.1,NM_024339.3	,125	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	,probably-damaging	,287/342	3077415	1,12995	2198	4300	6498	SO:0001583	missense	79228	exon12			CTGAGCGGGGAGC	BC050674	CCDS10491.1, CCDS45392.1	16p13.3	2013-02-11	2006-03-02	2006-03-02		ENSG00000131652		"WD repeat domain containing", "THO complex subunits"	28369	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 35"	615403	"WD repeat domain 58"	WDR58		12477932	Standard	NM_024339		Approved	MGC2655, fSAP35	uc002ctb.2	Q86W42		ENST00000326266.8:c.859G>A	chr16.hg19:g.3077415G>A	ENSP00000326531:p.Gly287Arg	22.0	0.0		32.0	5.0	NM_024339	B2RA85|Q8NBR1|Q9BTV9	Missense_Mutation	SNP	ENST00000326266.8	hg19	CCDS10491.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.238871	0.79800	2.27E-4	0.0	ENSG00000131652	ENST00000326266	T	0.35236	1.32	4.44	4.44	0.53790	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.61677	0.2366	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67565	-0.5638	10	0.72032	D	0.01	-18.3705	14.5962	0.68410	0.0:0.0:1.0:0.0	.	287	Q86W42	THOC6_HUMAN	R	287	ENSP00000326531:G287R	ENSP00000326531:G287R	G	+	1	0	THOC6	3017416	1.000000	0.71417	0.988000	0.46212	0.988000	0.76386	6.124000	0.71620	2.318000	0.78349	0.462000	0.41574	GGG	.	.		0.667	THOC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436981.1	NM_024339		A	3077415	G	A	3077415	3	1	191	1	0	0	0	0	1	0	0	0	15884	1116	39	1	905	1	THOC6	16	3077415	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10		3077415	87277338	90	28338										
CDH1	999	hgsc.bcm.edu	37	chr16	68849586	68849586	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aaaagagagtggaagtgtccGaggactttggcgtgggccag	17	6	0	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr16:68849586G>T	ENST00000261769.5	+	10	1680	c.1489G>T	c.(1489-1491)Gag>Tag	p.E497*	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Nonsense_Mutation_p.E436*|RP11-354M1.2_ENST00000563916.1_RNA	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	497	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		GGAAGTGTCCGAGGACTTTGG	0.512			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												p.E497X		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	CDH1,NS,carcinoma,0,1	CDH1	535	.	1	Unknown(1)	breast(1)	c.G1489T						.						158	140	146					16																	68849586		2198	4300	6498	SO:0001587	stop_gained	999	exon10	Familial Cancer Database	HDGC	GTGTCCGAGGACT	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1489G>T	chr16.hg19:g.68849586G>T	ENSP00000261769:p.Glu497*	136.0	0.0		104.0	57.0	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Nonsense_Mutation	SNP	ENST00000261769.5	hg19	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	G	33	5.274003	0.95459	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	.	.	.	5.5	5.5	0.81552	.	0.000000	0.51477	D	0.000086	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.9951	0.92809	0.0:0.0:1.0:0.0	.	.	.	.	X	497;515;497;436	.	ENSP00000261769:E497X	E	+	1	0	CDH1	67407087	1.000000	0.71417	0.791000	0.31998	0.335000	0.28730	9.414000	0.97362	2.588000	0.87417	0.561000	0.74099	GAG	.	.		0.512	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		T	68849586	G	T	68849586	4	4	191	1	0	0	0	0	0	1	0	0	3097	1059	37	1	1527	1	CDH1	16	68849586	Nonsense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	65772171	68849586	21505167	91	28339										
RAP1GAP2	23108	hgsc.bcm.edu	37	chr17	2868924	2868924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cagaggggatcgagtacctcCgggtcatccttaggtagggc	15	10	1	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr17:2868924C>T	ENST00000254695.8	+	8	673	c.583C>T	c.(583-585)Cgg>Tgg	p.R195W	RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.R180W|CTD-3060P21.1_ENST00000574885.1_RNA|RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.R176W|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.R195W	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	195					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CGAGTACCTCCGGGTCATCCT	0.547																																					p.R195W		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.C583T						.						50	52	51					17																	2868924		2074	4192	6266	SO:0001583	missense	23108	exon8			TACCTCCGGGTCA	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 4", "GTPase activating Rap/RanGAP domain-like 4"	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.583C>T	chr17.hg19:g.2868924C>T	ENSP00000254695:p.Arg195Trp	30.0	0.0		56.0	4.0	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	hg19	CCDS45573.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.619757	0.46736	.	.	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.94862	-3.54;-3.54;-3.54;-3.54	5.21	4.22	0.49857	.	0.054039	0.64402	D	0.000001	D	0.96608	0.8893	M	0.74546	2.27	0.50313	D	0.999864	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.987	D	0.96738	0.9544	10	0.87932	D	0	-21.4404	12.7447	0.57276	0.3145:0.6855:0.0:0.0	.	180;195	Q684P5-2;Q684P5	.;RPGP2_HUMAN	W	195;180;176;195	ENSP00000254695:R195W;ENSP00000389824:R180W;ENSP00000439688:R176W;ENSP00000444890:R195W	ENSP00000254695:R195W	R	+	1	2	RAP1GAP2	2815674	0.977000	0.34250	0.879000	0.34478	0.054000	0.15201	1.560000	0.36331	1.193000	0.43086	0.558000	0.71614	CGG	.	.		0.547	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2			T	2868924	C	T	2868924	3	4	191	1	0	0	0	0	1	0	0	0	13053	643	23	1	613	1	RAP1GAP2	17	2868924	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10		2868924	78326286	92	28340										
AIPL1	23746	hgsc.bcm.edu	37	chr17	6331740	6331740	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gcgaacatgttggccagcccGcacgtgtgcacgtgccactc	12	15	0	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr17:6331740G>A	ENST00000381129.3	-	3	443	c.363C>T	c.(361-363)tgC>tgT	p.C121C	AIPL1_ENST00000571740.1_Silent_p.C121C|AIPL1_ENST00000574506.1_Silent_p.C109C|AIPL1_ENST00000575265.1_Silent_p.C121C|AIPL1_ENST00000250087.5_Intron|AIPL1_ENST00000576307.1_Silent_p.C61C|AIPL1_ENST00000576776.1_Silent_p.C121C|AIPL1_ENST00000570466.1_Silent_p.C99C	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	121	PPIase FKBP-type.				negative regulation of apoptotic process (GO:0043066)|phototransduction, visible light (GO:0007603)|protein farnesylation (GO:0018343)|protein folding (GO:0006457)|regulation of cGMP metabolic process (GO:0030823)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)	farnesylated protein binding (GO:0001918)|unfolded protein binding (GO:0051082)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	12				COAD - Colon adenocarcinoma(228;0.141)		TGGCCAGCCCGCACGTGTGCA	0.632																																					p.C121C		Atlas-SNP	.											.	AIPL1	34	.	0			c.C363T						.						99	81	87					17																	6331740		2203	4300	6503	SO:0001819	synonymous_variant	23746	exon3			CAGCCCGCACGTG	AF148864	CCDS11075.1, CCDS32539.1, CCDS32540.1, CCDS67130.1, CCDS67131.1, CCDS67132.1, CCDS67133.1	17p13.1	2013-01-08	2001-11-29		ENSG00000129221	ENSG00000129221			359	protein-coding gene	gene with protein product		604392	"aryl hydrocarbon receptor-interacting protein-like 1"	LCA4		10615133, 14555765, 15365173	Standard	NM_001285402		Approved		uc002gcp.3	Q9NZN9	OTTHUMG00000102043	ENST00000381129.3:c.363C>T	chr17.hg19:g.6331740G>A		26.0	0.0		33.0	6.0	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Silent	SNP	ENST00000381129.3	hg19	CCDS11075.1																																																																																			.	.		0.632	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336		A	6331740	G	A	6331740	2	1	191	1	0	0	0	0	0	0	0	1	436	1079	38	1		1	AIPL1	17	6331740	Silent	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	3462816	6331740	74863470	93	28341										
PFAS	5198	hgsc.bcm.edu	37	chr17	8172487	8172487	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ccgttaggccttggcagtggGcatggcgaccccctccattt	12	14	0	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr17:8172487G>C	ENST00000314666.6	+	28	4055	c.3922G>C	c.(3922-3924)Gca>Cca	p.A1308P	PFAS_ENST00000545834.1_Missense_Mutation_p.A884P	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1308					'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	TTGGCAGTGGGCATGGCGACC	0.637																																					p.A1308P		Atlas-SNP	.											.	PFAS	91	.	0			c.G3922C						.						47	48	47					17																	8172487		2203	4300	6503	SO:0001583	missense	5198	exon28			CAGTGGGCATGGC	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"FGAR amidotransferase"	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.3922G>C	chr17.hg19:g.8172487G>C	ENSP00000313490:p.Ala1308Pro	72.0	0.0		77.0	14.0	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	hg19	CCDS11136.1	.	.	.	.	.	.	.	.	.	.	G	4.055	0.007902	0.07866	.	.	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.30182	1.54;2.29	5.46	4.48	0.54585	Glutamine amidotransferase type 1 (1);	0.130712	0.50627	D	0.000117	T	0.11750	0.0286	N	0.00801	-1.175	0.49389	D	0.999784	B	0.13594	0.008	B	0.14578	0.011	T	0.08597	-1.0714	10	0.87932	D	0	-6.0835	12.613	0.56561	0.0:0.3201:0.6799:0.0	.	1308	O15067	PUR4_HUMAN	P	884;1308;717	ENSP00000441706:A884P;ENSP00000313490:A1308P	ENSP00000313490:A1308P	A	+	1	0	PFAS	8113212	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	2.742000	0.47434	1.266000	0.44231	0.655000	0.94253	GCA	.	.		0.637	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2			C	8172487	G	C	8172487	3	2	191	1	0	0	0	0	1	0	0	0	11763	1203	42	4	4028	4	PFAS	17	8172487	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	1840747	8172487	73022723	94	28342										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11778277	11778277	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cttcaccagactcccattccAgtcaccccagccctggatcc	5	20	2	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr17:11778277A>T	ENST00000262442.4	+	53	10322	c.10254A>T	c.(10252-10254)ccA>ccT	p.P3418P	DNAH9_ENST00000454412.2_Silent_p.P3418P|RP11-628O18.1_ENST00000579621.1_RNA	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3418					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CTCCCATTCCAGTCACCCCAG	0.567																																					p.P3418P		Atlas-SNP	.											.	DNAH9	695	.	0			c.A10254T						.						100	87	91					17																	11778277		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon53			CATTCCAGTCACC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10254A>T	chr17.hg19:g.11778277A>T		43.0	0.0		79.0	34.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	hg19	CCDS11160.1																																																																																			.	.		0.567	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11778277	A	T	11778277	2	4	191	1	0	0	0	0	0	0	0	1	4610	175	7	4		4	DNAH9	17	11778277	Silent	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	3605790	11778277	69416933	95	28343										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48667882	48667882	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agcaacatcgtcttcaccagCctctttgccctggagatgct	8	14	3	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr17:48667882C>T	ENST00000359106.5	+	10	2352	c.2352C>T	c.(2350-2352)agC>agT	p.S784S	CACNA1G_ENST00000416767.4_Silent_p.S784S|CACNA1G_ENST00000507896.1_Silent_p.S784S|CACNA1G_ENST00000507609.1_Silent_p.S784S|CACNA1G_ENST00000510366.1_Silent_p.S784S|CACNA1G_ENST00000358244.5_Silent_p.S784S|CACNA1G_ENST00000515765.1_Silent_p.S784S|CACNA1G_ENST00000507336.1_Silent_p.S784S|CACNA1G_ENST00000354983.4_Silent_p.S784S|CACNA1G_ENST00000514079.1_Silent_p.S784S|CACNA1G_ENST00000510115.1_Silent_p.S784S|CACNA1G_ENST00000502264.1_Silent_p.S784S|CACNA1G_ENST00000513964.1_Silent_p.S784S|CACNA1G_ENST00000507510.2_Silent_p.S784S|CACNA1G_ENST00000515165.1_Silent_p.S784S|CACNA1G_ENST00000442258.2_Silent_p.S784S|CACNA1G_ENST00000513689.2_Silent_p.S784S|CACNA1G_ENST00000352832.5_Silent_p.S784S|CACNA1G_ENST00000503485.1_Silent_p.S784S|CACNA1G_ENST00000429973.2_Silent_p.S784S|CACNA1G_ENST00000505165.1_Silent_p.S784S|CACNA1G_ENST00000514717.1_Silent_p.S784S|CACNA1G_ENST00000515411.1_Silent_p.S784S|CACNA1G_ENST00000512389.1_Silent_p.S784S|CACNA1G_ENST00000360761.4_Silent_p.S784S|CACNA1G_ENST00000514181.1_Silent_p.S784S	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	784					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	TCTTCACCAGCCTCTTTGCCC	0.537																																					p.S784S		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C2352T						.						113	116	115					17																	48667882		2079	4210	6289	SO:0001819	synonymous_variant	8913	exon10			CACCAGCCTCTTT	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.2352C>T	chr17.hg19:g.48667882C>T		46.0	0.0		64.0	12.0	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	hg19	CCDS45730.1																																																																																			.	.		0.537	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		T	48667882	C	T	48667882	2	4	191	1	0	0	0	0	0	0	0	1	2546	738	26	3		3	CACNA1G	17	48667882	Silent	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	36889605	48667882	32527328	96	28344										
EPX	8288	hgsc.bcm.edu	37	chr17	56281642	56281642	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gcgcaaggccctgagcagaaTttccttgtctcgaattatat	9	10	1	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr17:56281642T>C	ENST00000225371.5	+	12	2116	c.2006T>C	c.(2005-2007)aTt>aCt	p.I669T		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	669					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	CTGAGCAGAATTTCCTTGTCT	0.517																																					p.I669T		Atlas-SNP	.											.	EPX	95	.	0			c.T2006C						.						116	102	106					17																	56281642		2203	4300	6503	SO:0001583	missense	8288	exon12			GCAGAATTTCCTT	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.2006T>C	chr17.hg19:g.56281642T>C	ENSP00000225371:p.Ile669Thr	60.0	0.0		98.0	30.0	NM_000502	Q4TVP3	Missense_Mutation	SNP	ENST00000225371.5	hg19	CCDS11602.1	.	.	.	.	.	.	.	.	.	.	T	9.766	1.171414	0.21621	.	.	ENSG00000121053	ENST00000225371	T	0.64085	-0.08	5.65	4.57	0.56435	.	0.388040	0.31612	N	0.007346	T	0.64702	0.2622	L	0.31157	0.91	0.09310	N	1	P	0.39903	0.694	D	0.68039	0.955	T	0.54443	-0.8293	10	0.28530	T	0.3	-4.0709	5.0829	0.14666	0.1609:0.0837:0.0:0.7555	.	669	P11678	PERE_HUMAN	T	669	ENSP00000225371:I669T	ENSP00000225371:I669T	I	+	2	0	EPX	53636641	0.001000	0.12720	0.260000	0.24451	0.374000	0.29953	0.921000	0.28718	0.950000	0.37743	0.533000	0.62120	ATT	.	.		0.517	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502		C	56281642	T	C	56281642	3	2	191	1	0	0	0	0	1	0	0	0	5202	1493	52	2	2052	2	EPX	17	56281642	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	7613760	56281642	24913568	97	28345										
MRC2	9902	hgsc.bcm.edu	37	chr17	60766907	60766907	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctccctgagcccgtccccagCagcgctgccccccgccccgg	10	24	0	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr17:60766907C>G	ENST00000303375.5	+	24	3761	c.3359C>G	c.(3358-3360)gCa>gGa	p.A1120G	MRC2_ENST00000580916.1_Intron|MRC2_ENST00000446119.2_Intron	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1120					collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						CCGTCCCCAGCAGCGCTGCCC	0.682																																					p.A1120G		Atlas-SNP	.											.	MRC2	126	.	0			c.C3359G						.						10	11	11					17																	60766907		2195	4285	6480	SO:0001583	missense	9902	exon24			CCCCAGCAGCGCT	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3359C>G	chr17.hg19:g.60766907C>G	ENSP00000307513:p.Ala1120Gly	70.0	0.0		111.0	8.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.275275	0.40194	.	.	ENSG00000011028	ENST00000303375	T	0.05855	3.38	4.61	2.39	0.29439	.	0.427081	0.25546	N	0.029921	T	0.03477	0.0100	N	0.08118	0	0.58432	D	0.999996	B	0.24483	0.104	B	0.21151	0.033	T	0.50242	-0.8851	10	0.25106	T	0.35	-9.5306	12.6815	0.56924	0.4034:0.5966:0.0:0.0	.	1120	Q9UBG0	MRC2_HUMAN	G	1120	ENSP00000307513:A1120G	ENSP00000307513:A1120G	A	+	2	0	MRC2	58120639	0.167000	0.22975	0.978000	0.43139	0.689000	0.40095	1.421000	0.34815	1.241000	0.43820	0.561000	0.74099	GCA	.	.		0.682	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			G	60766907	C	G	60766907	3	3	191	1	0	0	0	0	1	0	0	0	9767	710	25	4	3453	4	MRC2	17	60766907	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	4485265	60766907	20428303	98	28346										
FASN	2194	hgsc.bcm.edu	37	chr17	80042151	80042151	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aggaagtccggtgacagcagGacagaggtggccaggccctt	16	10	0	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr17:80042151G>T	ENST00000306749.2	-	28	5096	c.4878C>A	c.(4876-4878)gtC>gtA	p.V1626V	FASN_ENST00000579758.1_5'Flank	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1626					acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GTGACAGCAGGACAGAGGTGG	0.657																																					p.V1626V	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C4878A						.						64	61	62					17																	80042151		2193	4291	6484	SO:0001819	synonymous_variant	2194	exon28			CAGCAGGACAGAG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.4878C>A	chr17.hg19:g.80042151G>T		132.0	0.0		185.0	15.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.657	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80042151	G	T	80042151	2	4	191	1	0	0	0	0	0	0	0	1	5691	1161	41	3		3	FASN	17	80042151	Silent	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	19275244	80042151	1153059	99	28347										
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56034978	56034978	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cttctctttctcctcaaaagGgacaactacacccttcagat	4	14	4	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr18:56034978G>A	ENST00000400345.3	+	22	2347	c.2064G>A	c.(2062-2064)acG>acA	p.T688T	NEDD4L_ENST00000382850.4_Splice_Site_p.T668T|NEDD4L_ENST00000357895.5_Splice_Site_p.T680T|NEDD4L_ENST00000456986.1_Splice_Site_p.T567T|NEDD4L_ENST00000356462.6_Splice_Site_p.T624T|NEDD4L_ENST00000256830.9_Splice_Site_p.T584T|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000431212.2_Splice_Site_p.T567T|NEDD4L_ENST00000586263.1_Splice_Site_p.T660T|NEDD4L_ENST00000256832.7_Splice_Site_p.T548T|NEDD4L_ENST00000456173.2_Splice_Site_p.T547T|NEDD4L_ENST00000435432.2_Splice_Site_p.T547T	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	688	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						TCCTCAAAAGGGACAACTACA	0.423																																					p.T688T		Atlas-SNP	.											.	NEDD4L	126	.	0			c.G2064A						.						118	107	110					18																	56034978		1901	4122	6023	SO:0001630	splice_region_variant	23327	exon22			CAAAAGGGACAAC	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.2064-1G>A	chr18.hg19:g.56034978G>A		103.0	0.0		111.0	10.0	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	hg19	CCDS45872.1																																																																																			.	.		0.423	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1		Silent	A	56034978	G	A	56034978	5	1	191	1	0	0	0	0	0	0	1	0	10320	1246	43	3	2178	3	NEDD4L	18	56034978	Splice_Site	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10		56034978	22042270	100	28348										
SLC25A23	79085	hgsc.bcm.edu	37	chr19	6442104	6442104	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cccggtagaggccccgcatgCcctcctgggacaggatgtga	14	14	0	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr19:6442104C>A	ENST00000301454.4	-	10	1395	c.1289G>T	c.(1288-1290)gGc>gTc	p.G430V	SLC25A23_ENST00000414491.2_Missense_Mutation_p.G191V|SLC25A23_ENST00000601760.1_Intron	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	430					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						GCCCCGCATGCCCTCCTGGGA	0.632																																					p.G430V		Atlas-SNP	.											.	SLC25A23	43	.	0			c.G1289T						.						33	28	30					19																	6442104		2203	4300	6503	SO:0001583	missense	79085	exon10			CGCATGCCCTCCT	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"Solute carriers", "EF-hand domain containing"	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.1289G>T	chr19.hg19:g.6442104C>A	ENSP00000301454:p.Gly430Val	56.0	0.0		59.0	17.0	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Missense_Mutation	SNP	ENST00000301454.4	hg19	CCDS32882.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.693024	0.88735	.	.	ENSG00000125648	ENST00000301454;ENST00000414491	D;D	0.97688	-4.49;-4.49	5.0	5.0	0.66597	Mitochondrial carrier domain (2);	.	.	.	.	D	0.99486	0.9817	H	0.99954	5.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97526	1.0076	9	0.87932	D	0	.	17.05	0.86516	0.0:1.0:0.0:0.0	.	191;430	E7ESZ5;Q9BV35	.;SCMC3_HUMAN	V	430;191	ENSP00000301454:G430V;ENSP00000408814:G191V	ENSP00000301454:G430V	G	-	2	0	SLC25A23	6393104	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	7.264000	0.78432	2.302000	0.77476	0.448000	0.29417	GGC	.	.		0.632	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103		A	6442104	C	A	6442104	3	1	191	1	0	0	0	0	1	0	0	0	14501	739	26	3	121	3	SLC25A23	19	6442104	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10		6442104	52686879	101	28349										
ZNF557	79230	hgsc.bcm.edu	37	chr19	7075098	7075098	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gtcacaggatggcggctgtcGtcctgcccccaactgccggt	13	15	1	0	rs377018544		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr19:7075098G>T	ENST00000439035.2	+	3	253	c.13G>T	c.(13-15)Gtc>Ttc	p.V5F	ZNF557_ENST00000414706.1_Missense_Mutation_p.V5F|ZNF557_ENST00000252840.6_Missense_Mutation_p.V5F			Q8N988	ZN557_HUMAN	zinc finger protein 557	5					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17				Lung(535;0.179)		GGCGGCTGTCGTCCTGCCCCC	0.632																																					p.V5F		Atlas-SNP	.											.	ZNF557	40	.	0			c.G13T						.						52	58	56					19																	7075098		2203	4300	6503	SO:0001583	missense	79230	exon3			GCTGTCGTCCTGC	AK095524	CCDS42485.1, CCDS45945.1	19p13.2	2013-09-20			ENSG00000130544	ENSG00000130544		"Zinc fingers, C2H2-type", "-"	28632	protein-coding gene	gene with protein product						12477932	Standard	NM_024341		Approved	MGC4054	uc002mgc.3	Q8N988	OTTHUMG00000181977	ENST00000439035.2:c.13G>T	chr19.hg19:g.7075098G>T	ENSP00000398965:p.Val5Phe	30.0	0.0		47.0	18.0	NM_001044387	Q6PEJ3|Q9BTZ1	Missense_Mutation	SNP	ENST00000439035.2	hg19	CCDS45945.1	.	.	.	.	.	.	.	.	.	.	.	4.233	0.042230	0.08196	.	.	ENSG00000130544	ENST00000252840;ENST00000414706;ENST00000439035	T;T;T	0.08634	3.16;3.16;3.07	1.22	0.109	0.14578	.	.	.	.	.	T	0.03305	0.0096	N	0.14661	0.345	0.09310	N	1	P;P	0.39391	0.542;0.671	B;B	0.29524	0.048;0.103	T	0.43925	-0.9361	9	0.10111	T	0.7	.	8.4553	0.32895	0.1681:0.0:0.8319:0.0	.	5;5	Q8N988;Q8N988-2	ZN557_HUMAN;.	F	5	ENSP00000252840:V5F;ENSP00000404065:V5F;ENSP00000398965:V5F	ENSP00000252840:V5F	V	+	1	0	ZNF557	7026098	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.555000	0.05999	-0.325000	0.08577	-1.829000	0.00594	GTC	.	.		0.632	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	NM_024341		T	7075098	G	T	7075098	3	4	191	1	0	0	0	0	1	0	0	0	18003	1145	40	1	15	1	ZNF557	19	7075098	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	632994	7075098	52053885	102	28350										
RASAL3	64926	hgsc.bcm.edu	37	chr19	15565556	15565556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tggatggtctggtgccaaacCaaagaggctgggtgccagga	16	8	1	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr19:15565556C>T	ENST00000343625.7	-	12	1955	c.1870G>A	c.(1870-1872)Ggt>Agt	p.G624S	RASAL3_ENST00000608577.1_5'Flank	NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	624	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						GGTGCCAAACCAAAGAGGCTG	0.647											OREG0025322	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G624S		Atlas-SNP	.											.	RASAL3	49	.	0			c.G1870A						.						26	35	32					19																	15565556		2116	4239	6355	SO:0001583	missense	64926	exon12			CCAAACCAAAGAG		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.1870G>A	chr19.hg19:g.15565556C>T	ENSP00000341905:p.Gly624Ser	131.0	0.0	703	167.0	10.0	NM_022904	Q8N2T9|Q9H735	Missense_Mutation	SNP	ENST00000343625.7	hg19	CCDS46006.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.268600	0.59540	.	.	ENSG00000105122	ENST00000343625	D	0.84298	-1.83	4.76	4.76	0.60689	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.000000	0.34676	U	0.003775	D	0.86351	0.5912	M	0.61387	1.9	0.43540	D	0.995834	P;D	0.57899	0.952;0.981	P;P	0.54431	0.485;0.752	D	0.84070	0.0379	10	0.30078	T	0.28	.	9.3186	0.37950	0.0:0.9008:0.0:0.0992	.	624;624	Q86YV0-2;Q86YV0	.;RASL3_HUMAN	S	624	ENSP00000341905:G624S	ENSP00000341905:G624S	G	-	1	0	RASAL3	15426556	0.001000	0.12720	0.997000	0.53966	0.563000	0.35712	0.281000	0.18810	2.374000	0.81015	0.561000	0.74099	GGT	.	.		0.647	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904		T	15565556	C	T	15565556	3	4	191	1	0	0	0	0	1	0	0	0	13080	594	21	3	1193	3	RASAL3	19	15565556	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	8490458	15565556	43563427	103	28351										
OR10H1	26539	hgsc.bcm.edu	37	chr19	15918067	15918067	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctggggacttttgggcttcaGgtaaatgacggaggcaaagc	15	7	1	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr19:15918067G>A	ENST00000334920.2	-	1	869	c.781C>T	c.(781-783)Ctg>Ttg	p.L261L		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L261L(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						TTGGGCTTCAGGTAAATGACG	0.557																																					p.L261L		Atlas-SNP	.											OR10H1,NS,carcinoma,0,1	OR10H1	59	.	1	Substitution - coding silent(1)	lung(1)	c.C781T						.						123	94	104					19																	15918067		2203	4300	6503	SO:0001819	synonymous_variant	26539	exon1			GCTTCAGGTAAAT	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"GPCR / Class A : Olfactory receptors"	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.781C>T	chr19.hg19:g.15918067G>A		133.0	0.0		183.0	8.0	NM_013940	Q6IFQ2|Q96R59	Silent	SNP	ENST00000334920.2	hg19	CCDS12335.1																																																																																			.	.		0.557	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1			A	15918067	G	A	15918067	2	1	191	1	0	0	0	0	0	0	0	1	10914	991	35	3		3	OR10H1	19	15918067	Silent	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	352511	15918067	43210916	104	28352										
MAP1S	55201	hgsc.bcm.edu	37	chr19	17830385	17830385	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	cgtggtgggcagcgagttcgGgagcccggggctcctcacct	17	13	1	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr19:17830385G>A	ENST00000324096.4	+	1	225	c.74G>A	c.(73-75)gGg>gAg	p.G25E	MAP1S_ENST00000597681.1_3'UTR|MAP1S_ENST00000544059.2_5'Flank	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	25	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						AGCGAGTTCGGGAGCCCGGGG	0.751																																					p.G25E		Atlas-SNP	.											.	MAP1S	74	.	0			c.G74A						.						2	3	3					19																	17830385		1546	3239	4785	SO:0001583	missense	55201	exon1			AGTTCGGGAGCCC	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.74G>A	chr19.hg19:g.17830385G>A	ENSP00000325313:p.Gly25Glu	117.0	0.0		167.0	58.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	hg19	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	g	11.46	1.646665	0.29246	.	.	ENSG00000130479	ENST00000324096	T	0.16597	2.33	2.57	1.35	0.21983	.	0.196906	0.24128	U	0.041286	T	0.23289	0.0563	L	0.59436	1.845	0.45477	D	0.998448	D;D	0.57257	0.979;0.979	P;P	0.54026	0.461;0.74	T	0.02320	-1.1177	10	0.45353	T	0.12	-22.1755	6.5415	0.22382	0.0:0.3055:0.6945:0.0	.	25;25	A8K940;Q66K74	.;MAP1S_HUMAN	E	25	ENSP00000325313:G25E	ENSP00000325313:G25E	G	+	2	0	MAP1S	17691385	0.005000	0.15991	0.739000	0.30968	0.044000	0.14063	0.245000	0.18142	1.436000	0.47453	0.486000	0.48141	GGG	.	.		0.751	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		A	17830385	G	A	17830385	3	1	191	1	0	0	0	0	1	0	0	0	9243	1232	43	3	76	3	MAP1S	19	17830385	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	1912318	17830385	41298598	105	28353										
ZNF781	163115	hgsc.bcm.edu	37	chr19	38160112	38160112	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ttcttgcattactgacattcAtaaggtttttcattagtatg	6	6	3	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr19:38160112A>G	ENST00000590008.1	-	5	1790	c.938T>C	c.(937-939)aTg>aCg	p.M313T	ZFP30_ENST00000586732.1_Intron|ZNF781_ENST00000593040.1_5'Flank|ZNF781_ENST00000358582.4_Missense_Mutation_p.M313T			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						ACTGACATTCATAAGGTTTTT	0.393																																					p.M313T		Atlas-SNP	.											.	ZNF781	66	.	0			c.T938C						.						148	142	144					19																	38160112		2203	4300	6503	SO:0001583	missense	163115	exon4			ACATTCATAAGGT	AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"Zinc fingers, C2H2-type"	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.938T>C	chr19.hg19:g.38160112A>G	ENSP00000466370:p.Met313Thr	48.0	0.0		81.0	7.0	NM_152605	Q2VPJ8	Missense_Mutation	SNP	ENST00000590008.1	hg19	CCDS12507.1	.	.	.	.	.	.	.	.	.	.	A	1.962	-0.438675	0.04636	.	.	ENSG00000196381	ENST00000358582;ENST00000545586	T	0.07444	3.19	2.32	1.26	0.21427	.	.	.	.	.	T	0.05960	0.0155	L	0.31294	0.92	0.18873	N	0.999985	B	0.09022	0.002	B	0.08055	0.003	T	0.41875	-0.9484	9	0.27785	T	0.31	-1.5867	6.263	0.20912	0.86:0.0:0.14:0.0	.	313	Q8N8C0	ZN781_HUMAN	T	313	ENSP00000351391:M313T	ENSP00000351391:M313T	M	-	2	0	ZNF781	42851952	0.000000	0.05858	0.069000	0.20011	0.005000	0.04900	0.242000	0.18087	0.141000	0.18875	-0.410000	0.06199	ATG	.	.		0.393	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605		G	38160112	A	G	38160112	3	3	191	1	0	0	0	0	1	0	0	0	18169	217	8	2	49	2	ZNF781	19	38160112	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	20329727	38160112	20968871	106	28354										
GGN	199720	hgsc.bcm.edu	37	chr19	38876402	38876402	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ggctcagccacggtgggagcTggagccggggatggggccgg	22	10	1	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr19:38876402T>C	ENST00000334928.6	-	3	1632	c.1500A>G	c.(1498-1500)ccA>ccG	p.P500P	GGN_ENST00000591809.1_Intron|SPRED3_ENST00000587013.1_5'Flank|AC005789.9_ENST00000585411.1_RNA	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	500	Interactions with ZNF403/GGNBP2 and OAZ3. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			cggtgggagctggagccgggg	0.746																																					p.P500P		Atlas-SNP	.											.	GGN	50	.	0			c.A1500G						.						4	6	5					19																	38876402		1834	3724	5558	SO:0001819	synonymous_variant	199720	exon3			GGGAGCTGGAGCC	AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.1500A>G	chr19.hg19:g.38876402T>C		33.0	0.0		42.0	7.0	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Silent	SNP	ENST00000334928.6	hg19	CCDS12516.1																																																																																			.	.		0.746	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		C	38876402	T	C	38876402	2	2	191	1	0	0	0	0	0	0	0	1	6366	1567	55	2		2	GGN	19	38876402	Silent	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	716290	38876402	20252581	107	28355										
RYR1	6261	hgsc.bcm.edu	37	chr19	38993233	38993233	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctcatcaccaagtgtgcgccGctctttgcgggcacagaaca	10	14	3	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr19:38993233G>A	ENST00000359596.3	+	48	7701	c.7701G>A	c.(7699-7701)ccG>ccA	p.P2567P	RYR1_ENST00000360985.3_Silent_p.P2567P|RYR1_ENST00000355481.4_Silent_p.P2567P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2567	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	AGTGTGCGCCGCTCTTTGCGG	0.647																																					p.P2567P		Atlas-SNP	.											.	RYR1	708	.	0			c.G7701A						.						68	53	58					19																	38993233		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon48			TGCGCCGCTCTTT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.7701G>A	chr19.hg19:g.38993233G>A		42.0	0.0		74.0	19.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.647	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38993233	G	A	38993233	2	1	191	1	0	0	0	0	0	0	0	1	13783	1074	38	1		1	RYR1	19	38993233	Silent	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	116831	38993233	20135750	108	28356										
FPR2	2358	hgsc.bcm.edu	37	chr19	52272249	52272249	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	catcaacctctttggaagtgTcttcttgattggtttcattg	8	8	5	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr19:52272249T>C	ENST00000598776.1	+	2	1110	c.338T>C	c.(337-339)gTc>gCc	p.V113A	FPR2_ENST00000598953.1_Missense_Mutation_p.V113A|FPR2_ENST00000340023.6_Missense_Mutation_p.V113A	NM_001462.3	NP_001453.1	P25090	FPR2_HUMAN	formyl peptide receptor 2	113					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|N-formyl peptide receptor activity (GO:0004982)			endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33						TTTGGAAGTGTCTTCTTGATT	0.498																																					p.V113A		Atlas-SNP	.											.	FPR2	66	.	0			c.T338C						.						179	155	163					19																	52272249		2203	4300	6503	SO:0001583	missense	2358	exon2			GAAGTGTCTTCTT	M88107	CCDS12840.1	19q13.3-q13.4	2012-08-10	2008-04-17	2008-04-17		ENSG00000171049		"GPCR / Class A : Formyl peptide receptors", "GPCR / Class A : Leukotriene receptors"	3827	protein-coding gene	gene with protein product		136538	"formyl peptide receptor-like 1"	FPRL1		9054386	Standard	NM_001462		Approved	LXA4R, HM63, FPRH2, FMLPX, FPR2A, FMLP-R-II, ALXR	uc002pxr.3	P25090		ENST00000598776.1:c.338T>C	chr19.hg19:g.52272249T>C	ENSP00000468897:p.Val113Ala	63.0	0.0		95.0	18.0	NM_001005738	A8K3E2	Missense_Mutation	SNP	ENST00000598776.1	hg19	CCDS12840.1	.	.	.	.	.	.	.	.	.	.	.	16.66	3.185897	0.57909	.	.	ENSG00000171049	ENST00000340023	T	0.73897	-0.79	3.47	3.47	0.39725	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000005	D	0.85217	0.5646	M	0.84511	2.7	0.39781	D	0.972292	D	0.69078	0.997	D	0.72075	0.976	D	0.87427	0.2386	10	0.87932	D	0	.	10.1975	0.43062	0.0:0.0:0.0:1.0	.	113	P25090	FPR2_HUMAN	A	113	ENSP00000340191:V113A	ENSP00000340191:V113A	V	+	2	0	FPR2	56964061	1.000000	0.71417	0.978000	0.43139	0.389000	0.30415	7.204000	0.77872	1.587000	0.49959	0.402000	0.26972	GTC	.	.		0.498	FPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466912.2	NM_001005738		C	52272249	T	C	52272249	3	2	191	1	0	0	0	0	1	0	0	0	6047	1667	58	2	340	2	FPR2	19	52272249	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	13279016	52272249	6856734	109	28357										
ZNF548	147694	hgsc.bcm.edu	37	chr19	57909862	57909862	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ggtttttctgtaggagtgtcAgaggttacagcttcaaagcc	12	7	3	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr19:57909862A>T	ENST00000366197.5	+	3	457	c.207A>T	c.(205-207)tcA>tcT	p.S69S	ZNF548_ENST00000336128.7_Silent_p.S81S|AC003002.4_ENST00000597658.1_Silent_p.S72S|AC003002.6_ENST00000596400.1_Intron|ZNF548_ENST00000597400.1_3'UTR|AC003002.6_ENST00000600421.1_Intron|AC004076.7_ENST00000597410.1_Intron	NM_152909.3	NP_690873.2	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TAGGAGTGTCAGAGGTTACAG	0.512																																					p.S81S		Atlas-SNP	.											.	ZNF548	64	.	0			c.A243T						.						102	100	101					19																	57909862		2146	4283	6429	SO:0001819	synonymous_variant	147694	exon4			AGTGTCAGAGGTT	AK057494	CCDS46209.1, CCDS54324.1	19q13.43	2013-01-08				ENSG00000188785		"Zinc fingers, C2H2-type", "-"	26561	protein-coding gene	gene with protein product						12477932	Standard	NM_152909		Approved	FLJ32932	uc002qon.3	Q8NEK5		ENST00000366197.5:c.207A>T	chr19.hg19:g.57909862A>T		82.0	0.0		117.0	7.0	NM_001172773	Q96M05	Silent	SNP	ENST00000366197.5	hg19	CCDS46209.1																																																																																			.	.		0.512	ZNF548-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465937.1	NM_152909		T	57909862	A	T	57909862	2	4	191	1	0	0	0	0	0	0	0	1	17995	175	7	4		4	ZNF548	19	57909862	Silent	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	5637613	57909862	1219121	110	28358										
C20orf194	25943	hgsc.bcm.edu	37	chr20	3306871	3306871	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agactggaagttttagcataAcatgcaatgccagccaaaac	8	9	0	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr20:3306871A>G	ENST00000252032.9	-	13	1228	c.1161T>C	c.(1159-1161)tgT>tgC	p.C387C	C20orf194_ENST00000453730.2_Silent_p.C125C	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	387										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						TTTTAGCATAACATGCAATGC	0.313																																					p.C387C		Atlas-SNP	.											.	C20orf194	83	.	0			c.T1161C						.						82	80	80					20																	3306871		1887	4102	5989	SO:0001819	synonymous_variant	25943	exon13			AGCATAACATGCA	AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.1161T>C	chr20.hg19:g.3306871A>G		297.0	0.0		397.0	72.0	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Silent	SNP	ENST00000252032.9	hg19	CCDS42851.1																																																																																			.	.		0.313	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984		G	3306871	A	G	3306871	2	3	191	1	0	0	0	0	0	0	0	1	2101	41	2	2		2	C20orf194	20	3306871	Silent	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10		3306871	59718649	111	28359										
SEMG2	6407	hgsc.bcm.edu	37	chr20	43851661	43851661	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tcaagagcatggccataaggAaaataaaatgtcataccaat	7	7	2	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr20:43851661A>T	ENST00000372769.3	+	2	1478	c.1388A>T	c.(1387-1389)gAa>gTa	p.E463V		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	463	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				GGCCATAAGGAAAATAAAATG	0.383																																					p.E463V		Atlas-SNP	.											.	SEMG2	92	.	0			c.A1388T						.						78	77	77					20																	43851661		2203	4300	6503	SO:0001583	missense	6407	exon2			ATAAGGAAAATAA		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"Semenogelin 2"	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.1388A>T	chr20.hg19:g.43851661A>T	ENSP00000361855:p.Glu463Val	124.0	0.0		204.0	16.0	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Missense_Mutation	SNP	ENST00000372769.3	hg19	CCDS13346.1	.	.	.	.	.	.	.	.	.	.	A	8.748	0.920582	0.17982	.	.	ENSG00000124157	ENST00000372769	T	0.08102	3.13	1.15	-1.65	0.08291	.	.	.	.	.	T	0.05823	0.0152	N	0.22421	0.69	0.09310	N	1	P;P	0.41910	0.626;0.764	B;B	0.42087	0.255;0.375	T	0.34254	-0.9836	9	0.40728	T	0.16	.	5.3595	0.16079	0.5999:0.4001:0.0:0.0	.	463;463	A8K6Z6;Q02383	.;SEMG2_HUMAN	V	463	ENSP00000361855:E463V	ENSP00000361855:E463V	E	+	2	0	SEMG2	43285075	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.322000	0.08007	-0.433000	0.07286	-1.375000	0.01183	GAA	.	.		0.383	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		T	43851661	A	T	43851661	3	4	191	1	0	0	0	0	1	0	0	0	14060	246	9	4	1394	4	SEMG2	20	43851661	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	40544790	43851661	19173859	112	28360										
NFATC2	4773	hgsc.bcm.edu	37	chr20	50158976	50158976	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	agctcgtcttgggggctgccCccaggctcgtggcctggggc	17	14	1	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr20:50158976C>T	ENST00000396009.3	-	1	282	c.63G>A	c.(61-63)ggG>ggA	p.G21G	NFATC2_ENST00000610033.1_5'UTR|NFATC2_ENST00000609943.1_Intron|NFATC2_ENST00000414705.1_Intron|NFATC2_ENST00000371564.3_Silent_p.G21G|NFATC2_ENST00000609507.1_Intron	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	21					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GGGGGCTGCCCCCAGGCTCGT	0.697																																					p.G21G		Atlas-SNP	.											.	NFATC2	112	.	0			c.G63A						.						15	18	17					20																	50158976		2196	4290	6486	SO:0001819	synonymous_variant	4773	exon1			GCTGCCCCCAGGC	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.63G>A	chr20.hg19:g.50158976C>T		206.0	0.0		307.0	116.0	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Silent	SNP	ENST00000396009.3	hg19	CCDS13437.1																																																																																			.	.		0.697	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		T	50158976	C	T	50158976	2	4	191	1	0	0	0	0	0	0	0	1	10371	610	22	3		3	NFATC2	20	50158976	Silent	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	6307315	50158976	12866544	113	28361										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57769174	57769174	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gggacaggatggccactagcAggccagcagccagggagttg	17	10	0	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr20:57769174A>T	ENST00000371030.2	+	1	3100	c.3100A>T	c.(3100-3102)Agg>Tgg	p.R1034W		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1034							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GGCCACTAGCAGGCCAGCAGC	0.647																																					p.R1034W		Atlas-SNP	.											.	ZNF831	287	.	0			c.A3100T						.						21	26	24					20																	57769174		2057	4212	6269	SO:0001583	missense	128611	exon1			ACTAGCAGGCCAG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.3100A>T	chr20.hg19:g.57769174A>T	ENSP00000360069:p.Arg1034Trp	31.0	0.0		42.0	4.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	A	11.62	1.692064	0.30052	.	.	ENSG00000124203	ENST00000371030	T	0.04758	3.56	3.97	-0.291	0.12843	.	1.458410	0.04642	N	0.405519	T	0.04227	0.0117	N	0.08118	0	0.09310	N	1	P	0.50819	0.939	P	0.46172	0.506	T	0.42310	-0.9459	10	0.66056	D	0.02	-0.2808	7.6518	0.28352	0.6954:0.0:0.3046:0.0	.	1034	Q5JPB2	ZN831_HUMAN	W	1034	ENSP00000360069:R1034W	ENSP00000360069:R1034W	R	+	1	2	ZNF831	57202569	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.954000	0.03873	0.015000	0.14971	0.338000	0.21704	AGG	.	.		0.647	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57769174	A	T	57769174	3	4	191	1	0	0	0	0	1	0	0	0	18200	179	7	4	3102	4	ZNF831	20	57769174	Missense_Mutation	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	7610198	57769174	5256346	114	28362										
SFRS15	57466	hgsc.bcm.edu	37	chr21	33065744	33065744	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	accgagatcgagaacgtcgaTgccgagaccttcgagatcta	11	11	1	4			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr21:33065744T>C	ENST00000286835.7	-	12	1758	c.1376A>G	c.(1375-1377)cAt>cGt	p.H459R	SCAF4_ENST00000399804.1_Missense_Mutation_p.H459R|SCAF4_ENST00000434667.3_Missense_Mutation_p.H444R	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	459						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						AGAACGTCGATGCCGAGACCT	0.473																																					p.H459R		Atlas-SNP	.											.	SCAF4	142	.	0			c.A1376G						.						106	82	91					21																	33065744		2203	4300	6503	SO:0001583	missense	57466	exon12			CGTCGATGCCGAG	AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"RNA binding motif (RRM) containing"	19304	protein-coding gene	gene with protein product			"splicing factor, arginine/serine-rich 15"	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.1376A>G	chr21.hg19:g.33065744T>C	ENSP00000286835:p.His459Arg	72.0	0.0		156.0	50.0	NM_020706	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Missense_Mutation	SNP	ENST00000286835.7	hg19	CCDS33537.1	.	.	.	.	.	.	.	.	.	.	T	17.99	3.522640	0.64747	.	.	ENSG00000156304	ENST00000434667;ENST00000286835;ENST00000399804	T;T;T	0.39997	1.05;1.05;1.05	5.2	5.2	0.72013	.	0.153980	0.47852	D	0.000210	T	0.60805	0.2297	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.89917	0.999;0.981;1.0;0.999	D;D;D;D	0.83275	0.991;0.966;0.996;0.991	T	0.60042	-0.7340	10	0.09084	T	0.74	-20.1116	15.063	0.71970	0.0:0.0:0.0:1.0	.	444;459;459;459	C9JLZ0;C9J1W7;O95104-2;O95104	.;.;.;SFR15_HUMAN	R	444;459;459	ENSP00000402377:H444R;ENSP00000286835:H459R;ENSP00000382703:H459R	ENSP00000286835:H459R	H	-	2	0	SCAF4	31987615	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	7.644000	0.83416	1.954000	0.56735	0.455000	0.32223	CAT	.	.		0.473	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889		C	33065744	T	C	33065744	3	2	191	1	0	0	0	0	1	0	0	0	14186	1464	51	2	2103	2	SFRS15	21	33065744	Missense_Mutation	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10		33065744	15064151	115	28363										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885648	29885648	+	Silent	SNP	A	A	G													0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	aagtccccagtgaaggcagaAgcaaagtcccctgagaaggc					rs267607535		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr22:29885648A>G	ENST00000310624.6	+	4	2052	c.2019A>G	c.(2017-2019)gaA>gaG	p.E673E		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	679	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						TGAAGGCAGAAGCAAAGTCCC	0.567																																					p.E673E		Atlas-SNP	.											.	NEFH	178	.	0			c.A2019G						.						93	99	97					22																	29885648		2203	4299	6502	SO:0001819	synonymous_variant	4744	exon4			GGCAGAAGCAAAG		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2019A>G	chr22.hg19:g.29885648A>G		237.0	0.0		353.0	18.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.567	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		G	29885648	A	G	29885648	2	3	191	1	0	0	0	0	0	0	0	1	10323	69	3	2		2	NEFH	22	29885648	Silent	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10		29885648	21418918	116	28364	140	2								
NEFH	4744	hgsc.bcm.edu	37	chr22	29885651	29885651	+	Silent	SNP	A	A	C													0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	tccccagtgaaggcagaagcAaagtcccctgagaaggccaa					rs267607535		TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr22:29885651A>C	ENST00000310624.6	+	4	2055	c.2022A>C	c.(2020-2022)gcA>gcC	p.A674A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	680	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGCAGAAGCAAAGTCCCCTG	0.567																																					p.A674A		Atlas-SNP	.											.	NEFH	178	.	0			c.A2022C						.						92	98	96					22																	29885651		2203	4297	6500	SO:0001819	synonymous_variant	4744	exon4			AGAAGCAAAGTCC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2022A>C	chr22.hg19:g.29885651A>C		241.0	0.0		355.0	19.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.567	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		C	29885651	A	C	29885651	2	2	191	1	0	0	0	0	0	0	0	1	10323	117	5	5		5	NEFH	22	29885651	Silent	SNP	A	TCGA-DD-AADI-01A-11D-A40R-10	3	29885651	21418915	117	28365	140	2								
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40042812	40042812	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctaccaggccctgcagagccGgcgccaggccctgggcccgg	15	18	0	1			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chr22:40042812G>A	ENST00000402142.3	+	8	1388	c.1388G>A	c.(1387-1389)cGg>cAg	p.R463Q	CACNA1I_ENST00000401624.1_Missense_Mutation_p.R463Q|CACNA1I_ENST00000336649.4_Missense_Mutation_p.R463Q|CACNA1I_ENST00000400164.3_Missense_Mutation_p.R463Q|CACNA1I_ENST00000407673.1_Missense_Mutation_p.R463Q|CACNA1I_ENST00000404898.1_Missense_Mutation_p.R463Q	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	463					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	CTGCAGAGCCGGCGCCAGGCC	0.721																																					p.R463Q		Atlas-SNP	.											.	CACNA1I	264	.	0			c.G1388A						.																																			SO:0001583	missense	8911	exon8			AGAGCCGGCGCCA	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.1388G>A	chr22.hg19:g.40042812G>A	ENSP00000385019:p.Arg463Gln	93.0	0.0		114.0	11.0	NM_001003406	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	hg19	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.585266	0.46110	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.97066	-4.19;-4.17;-4.18;-4.18;-4.23;-4.14	3.55	3.55	0.40652	.	1.989150	0.02561	N	0.096703	D	0.97604	0.9215	M	0.66939	2.045	0.31726	N	0.637683	D;D;D;P	0.63880	0.979;0.957;0.993;0.804	B;P;P;B	0.50109	0.44;0.481;0.631;0.166	D	0.92301	0.5849	10	0.66056	D	0.02	.	16.0019	0.80301	0.0:0.0:1.0:0.0	.	463;463;463;463	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	Q	463	ENSP00000385019:R463Q;ENSP00000384093:R463Q;ENSP00000383887:R463Q;ENSP00000385680:R463Q;ENSP00000337829:R463Q;ENSP00000383028:R463Q	ENSP00000337829:R463Q	R	+	2	0	CACNA1I	38372758	1.000000	0.71417	1.000000	0.80357	0.507000	0.33981	4.705000	0.61838	1.926000	0.55796	0.305000	0.20034	CGG	.	.		0.721	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		A	40042812	G	A	40042812	3	1	191	1	0	0	0	0	1	0	0	0	2548	1116	39	1	1418	1	CACNA1I	22	40042812	Missense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	10157161	40042812	11261754	118	28366										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382381	24382382	+	IGR	DNP	GC	GC	AT													0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctgctgctgctattgctgctGctgctgctgctgctgctgct							TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chrX:24382381_24382382GC>AT								AC004552.1 (15358 upstream) : PDK3 (100955 downstream)																							tattgctgctgctgctgctgct	0.579																																					p.A502T|p.A502V		Atlas-SNP	.											.	.	.	.	0			c.G1504A|c.C1505T						.																																			SO:0001628	intergenic_variant	100130302	exon1			GCTGCTGCTGCTG|CTGCTGCTGCTGC																													chrX.hg19:g.24382381_24382382delinsAT		171.0|166.0	0.0		241.0|239.0	19.0	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.579									AT	24382382	GC	AT	24382381	1	1	191	0	1	0	0	0	0	0	0	0	5581	1319	46	3		3	FAM48B1	23	24382381	IGR	DNP	GC	TCGA-DD-AADI-01A-11D-A40R-10		24382381	130888179	119	28367										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382420	24382420	+	IGR	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctgctgctgctgctgctgctGctgctgctcctgctcctgct	11	16	0	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chrX:24382420G>C								AC004552.1 (15397 upstream) : PDK3 (100917 downstream)																							tgctgctgctgctgctgctcc	0.622																																					p.A515P		Atlas-SNP	.											.	.	.	.	0			c.G1543C						.						2	2	2					X																	24382420		1005	2388	3393	SO:0001628	intergenic_variant	100130302	exon1			GCTGCTGCTGCTG																													chrX.hg19:g.24382420G>C		130.0	0.0		167.0	10.0	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.622									C	24382420	G	C	24382420	1	2	191	0	1	0	0	0	0	0	0	0	5581	1319	46	4		4	FAM48B1	23	24382420	IGR	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	39	24382420	130888140	120	28368										
PHKA1	5255	hgsc.bcm.edu	37	chrX	71813017	71813017	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	actctattcagtgccccatcCagccttcttcggcgttgcca	7	16	3	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chrX:71813017C>T	ENST00000373542.4	-	29	3339	c.3180G>A	c.(3178-3180)ctG>ctA	p.L1060L	PHKA1_ENST00000339490.3_Silent_p.L1047L|PHKA1_ENST00000541944.1_Silent_p.L988L|PHKA1_ENST00000373539.3_Silent_p.L1077L|PHKA1_ENST00000373545.3_Silent_p.L1018L	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	1060	Calmodulin-binding. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					GTGCCCCATCCAGCCTTCTTC	0.433																																					p.L1060L		Atlas-SNP	.											.	PHKA1	129	.	0			c.G3180A						.						135	116	123					X																	71813017		2203	4300	6503	SO:0001819	synonymous_variant	5255	exon29			CCCATCCAGCCTT		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.3180G>A	chrX.hg19:g.71813017C>T		170.0	0.0		180.0	75.0	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Silent	SNP	ENST00000373542.4	hg19	CCDS14421.1																																																																																			.	.		0.433	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			T	71813017	C	T	71813017	2	4	191	1	0	0	0	0	0	0	0	1	11852	581	21	3		3	PHKA1	23	71813017	Silent	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	47430597	71813017	83457543	121	28369										
NRK	203447	hgsc.bcm.edu	37	chrX	105197132	105197132	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ctgaagcgcaggtcaattaaGaagctgagattcctgtgcac	11	9	1	3			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chrX:105197132G>A	ENST00000243300.9	+	28	4923	c.4620G>A	c.(4618-4620)aaG>aaA	p.K1540K	NRK_ENST00000428173.2_Silent_p.K1541K|NRK_ENST00000540278.1_Silent_p.K121K	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1540	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						GGTCAATTAAGAAGCTGAGAT	0.468										HNSCC(51;0.14)																											p.K1540K		Atlas-SNP	.											.	NRK	321	.	0			c.G4620A						.						48	47	48					X																	105197132		1878	4104	5982	SO:0001819	synonymous_variant	203447	exon28			AATTAAGAAGCTG	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.4620G>A	chrX.hg19:g.105197132G>A		254.0	0.0		309.0	51.0	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Silent	SNP	ENST00000243300.9	hg19																																																																																				.	.		0.468	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		A	105197132	G	A	105197132	2	1	191	1	0	0	0	0	0	0	0	1	10664	933	33	3		3	NRK	23	105197132	Silent	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	33384115	105197132	50073428	122	28370										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107863658	107863658	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	ggtgcctctggatttccaggTaatttgtttaaagttttctc	9	7	2	0			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chrX:107863658T>C	ENST00000361603.2	+	31	2921		c.e31+2		COL4A5_ENST00000328300.6_Splice_Site	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5						axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GATTTCCAGGTAATTTGTTTA	0.443									Alport syndrome with Diffuse Leiomyomatosis																												.		Atlas-SNP	.											.	COL4A5	262	.	0			c.2677+2T>C						.						25	25	25					X																	107863658		2203	4298	6501	SO:0001630	splice_region_variant	1287	exon31	Familial Cancer Database		TCCAGGTAATTTG	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.2677+2T>C	chrX.hg19:g.107863658T>C		121.0	0.0		175.0	21.0	NM_033380	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Splice_Site	SNP	ENST00000361603.2	hg19	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.577454	0.86645	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6831	0.77388	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL4A5	107750314	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.596000	0.74113	2.088000	0.63022	0.486000	0.48141	.	.	.		0.443	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2		Intron	C	107863658	T	C	107863658	5	2	191	1	0	0	0	0	0	0	1	0	3696	1652	57	2	2801	2	COL4A5	23	107863658	Splice_Site	SNP	T	TCGA-DD-AADI-01A-11D-A40R-10	2666526	107863658	47406902	123	28371										
DDX26B	203522	hgsc.bcm.edu	37	chrX	134711160	134711160	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	atgagtttgtagcagggccaCaaaacaaagtgaaacgtcca	10	8	0	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chrX:134711160C>A	ENST00000370752.4	+	14	2150	c.1816C>A	c.(1816-1818)Caa>Aaa	p.Q606K	DDX26B_ENST00000481908.1_3'UTR	NM_182540.4	NP_872346.3	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26B	606										large_intestine(1)|lung(8)	9	Acute lymphoblastic leukemia(192;6.56e-05)					AGCAGGGCCACAAAACAAAGT	0.403																																					p.Q606K		Atlas-SNP	.											.	DDX26B	130	.	0			c.C1816A						.						211	187	195					X																	134711160		2203	4300	6503	SO:0001583	missense	203522	exon14			GGGCCACAAAACA	AK096544	CCDS35401.1	Xq26	2008-02-05			ENSG00000165359	ENSG00000165359		"DEAD-boxes"	27334	protein-coding gene	gene with protein product							Standard	NM_182540		Approved	FLJ41215	uc004eyw.4	Q5JSJ4	OTTHUMG00000022484	ENST00000370752.4:c.1816C>A	chrX.hg19:g.134711160C>A	ENSP00000359788:p.Gln606Lys	168.0	0.0		259.0	42.0	NM_182540	Q5CZA2|Q6IPS3|Q6ZTU5|Q6ZWE4	Missense_Mutation	SNP	ENST00000370752.4	hg19	CCDS35401.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.356585	0.82243	.	.	ENSG00000165359	ENST00000370752	T	0.36878	1.23	5.2	5.2	0.72013	.	0.104565	0.64402	D	0.000003	T	0.37461	0.1004	M	0.75447	2.3	0.53688	D	0.999974	B;P	0.38048	0.346;0.616	B;B	0.35278	0.118;0.199	T	0.33059	-0.9883	10	0.08837	T	0.75	-6.7628	17.0269	0.86450	0.0:1.0:0.0:0.0	.	606;606	B9EIK3;Q5JSJ4	.;DX26B_HUMAN	K	606	ENSP00000359788:Q606K	ENSP00000359788:Q606K	Q	+	1	0	DDX26B	134538826	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.035000	0.70940	2.316000	0.78162	0.600000	0.82982	CAA	.	.		0.403	DDX26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058420.1	NM_182540		A	134711160	C	A	134711160	3	1	191	1	0	0	0	0	1	0	0	0	4355	479	17	3	1870	3	DDX26B	23	134711160	Missense_Mutation	SNP	C	TCGA-DD-AADI-01A-11D-A40R-10	26847502	134711160	20559400	124	28372										
FATE1	89885	hgsc.bcm.edu	37	chrX	150891213	150891213	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.040650406504065	5	1	0.639561677505249	1.67707284323599	0.452809667673716	1	1	0	gccagcattgccaacctgtgGctgtggatgaaccagtgatc	12	11	0	2			TCGA-DD-AADI-01A-11D-A40R-10	TCGA-DD-AADI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dba0ae12-2411-4434-99df-3c0ffe50d5b8	0c54a21e-f61a-458f-971c-33e10b96eec4	g.chrX:150891213G>A	ENST00000370350.3	+	5	619	c.534G>A	c.(532-534)tgG>tgA	p.W178*		NM_033085.2	NP_149076.1	Q969F0	FATE1_HUMAN	fetal and adult testis expressed 1	178						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					CCAACCTGTGGCTGTGGATGA	0.657																																					p.W178X		Atlas-SNP	.											.	FATE1	30	.	0			c.G534A						.						50	51	51					X																	150891213		2203	4300	6503	SO:0001587	stop_gained	89885	exon5			CCTGTGGCTGTGG	AF249872	CCDS14700.1	Xq28	2009-03-25			ENSG00000147378	ENSG00000147378			24683	protein-coding gene	gene with protein product	"cancer/testis antigen 43"	300450				11694338	Standard	NM_033085		Approved	FATE, CT43	uc004fex.3	Q969F0	OTTHUMG00000024172	ENST00000370350.3:c.534G>A	chrX.hg19:g.150891213G>A	ENSP00000359375:p.Trp178*	160.0	0.0		274.0	104.0	NM_033085		Nonsense_Mutation	SNP	ENST00000370350.3	hg19	CCDS14700.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.518970	0.44866	.	.	ENSG00000147378	ENST00000370350	.	.	.	4.39	4.39	0.52855	.	0.000000	0.42053	D	0.000768	.	.	.	.	.	.	0.37504	D	0.91686	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.5415	11.3766	0.49733	0.0:0.0:1.0:0.0	.	.	.	.	X	178	.	ENSP00000359375:W178X	W	+	3	0	FATE1	150641869	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	4.082000	0.57635	2.161000	0.67846	0.600000	0.82982	TGG	.	.		0.657	FATE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060885.1	NM_033085		A	150891213	G	A	150891213	4	1	191	1	0	0	0	0	0	1	0	0	5701	1212	42	3	552	3	FATE1	23	150891213	Nonsense_Mutation	SNP	G	TCGA-DD-AADI-01A-11D-A40R-10	16180053	150891213	4379347	125	28373										
C1orf156	92342	hgsc.bcm.edu	37	chr1	169761971	169761971	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tggtttctgaggtgagaatgAgatcatattttacaaaaagt	10	3	2	3			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr1:169761971A>C	ENST00000310392.4	-	2	1219	c.866T>G	c.(865-867)cTc>cGc	p.L289R	C1orf112_ENST00000413811.2_5'Flank|C1orf112_ENST00000286031.6_5'Flank|C1orf112_ENST00000456684.1_5'Flank|C1orf112_ENST00000498289.1_Intron|METTL18_ENST00000303469.2_Missense_Mutation_p.L289R|C1orf112_ENST00000359326.4_5'Flank	NM_033418.2	NP_219486.1	O95568	MET18_HUMAN	methyltransferase like 18	289						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			kidney(1)|large_intestine(3)|lung(4)	8						GGTGAGAATGAGATCATATTT	0.333																																					p.L289R		Atlas-SNP	.											.	METTL18	23	.	0			c.T866G						.						59	61	60					1																	169761971		2203	4299	6502	SO:0001583	missense	92342	exon2			AGAATGAGATCAT	AL035369	CCDS1284.1	1q24.2	2013-10-11	2011-03-02	2011-03-02	ENSG00000171806	ENSG00000171806			28793	protein-coding gene	gene with protein product	"histidine protein methyltransferase 1"	615255	"chromosome 1 open reading frame 156"	C1orf156		20864530	Standard	NM_033418		Approved	MGC9084, AsTP2, HPM1	uc001ggn.4	O95568	OTTHUMG00000035813	ENST00000310392.4:c.866T>G	chr1.hg19:g.169761971A>C	ENSP00000307975:p.Leu289Arg	222.0	0.0		352.0	102.0	NM_033418	B2R9T5	Missense_Mutation	SNP	ENST00000310392.4	hg19	CCDS1284.1	.	.	.	.	.	.	.	.	.	.	A	17.27	3.347780	0.61183	.	.	ENSG00000171806	ENST00000310392;ENST00000303469	T;T	0.12879	2.64;2.64	6.17	6.17	0.99709	.	0.212777	0.37577	N	0.002033	T	0.27594	0.0678	M	0.84156	2.68	0.39158	D	0.962341	D	0.59767	0.986	D	0.66497	0.944	T	0.15838	-1.0423	10	0.87932	D	0	0.0217	10.029	0.42090	0.9252:0.0:0.0748:0.0	.	289	O95568	MET18_HUMAN	R	289	ENSP00000307975:L289R;ENSP00000307077:L289R	ENSP00000307077:L289R	L	-	2	0	METTL18	168028595	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.995000	0.70631	2.371000	0.80710	0.533000	0.62120	CTC	.	.		0.333	METTL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087109.1	NM_033418		C	169761971	A	C	169761971	3	2	192	1	0	0	0	0	1	0	0	0	2008	304	11	5	256	5	C1orf156	1	169761971	Missense_Mutation	SNP	A	TCGA-DD-AADJ-01A-11D-A40R-10		169761971	79488650	1	28374										
KCTD3	51133	hgsc.bcm.edu	37	chr1	215768702	215768702	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tttattgtcatttaaggagtGttcagcctgggtgttcctgt	11	6	2	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr1:215768702G>A	ENST00000259154.4	+	10	1116	c.822G>A	c.(820-822)gtG>gtA	p.V274V		NM_016121.3	NP_057205.2	Q9Y597	KCTD3_HUMAN	potassium channel tetramerization domain containing 3	274					protein homooligomerization (GO:0051260)					breast(4)|endometrium(2)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)	33				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)		TTTAAGGAGTGTTCAGCCTGG	0.373																																					p.V274V		Atlas-SNP	.											.	KCTD3	101	.	0			c.G822A						.						160	152	155					1																	215768702		2203	4300	6503	SO:0001819	synonymous_variant	51133	exon10			AGGAGTGTTCAGC	AK024547	CCDS1515.1	1q41	2013-06-20	2013-06-20		ENSG00000136636	ENSG00000136636			21305	protein-coding gene	gene with protein product		613272	"potassium channel tetramerisation domain containing 3"			10508479	Standard	NM_016121		Approved	NY-REN-45	uc001hks.3	Q9Y597	OTTHUMG00000037019	ENST00000259154.4:c.822G>A	chr1.hg19:g.215768702G>A		77.0	0.0		113.0	36.0	NM_016121	A0AV15|D3DTA6|Q49AG7|Q504Q9|Q6PJN6|Q8ND58|Q8NDJ0|Q8WX16	Silent	SNP	ENST00000259154.4	hg19	CCDS1515.1																																																																																			.	.		0.373	KCTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089871.2	NM_016121		A	215768702	G	A	215768702	2	1	192	1	0	0	0	0	0	0	0	1	8119	1364	48	3		3	KCTD3	1	215768702	Silent	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	46006731	215768702	33481919	2	28375										
C1orf35	79169	hgsc.bcm.edu	37	chr1	228290360	228290395	+	Splice_Site	DEL	GTGGGCTGCTTCTTCACGTTCTTGTAGCCACTGCGA	GTGGGCTGCTTCTTCACGTTCTTGTAGCCACTGCGA	-													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ttacctccttgctcaggcccGtgggctgcttcttcacgttc					rs371615876|rs578122372	byFrequency	TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	GTGGGCTGCTTCTTCACGTTCTTGTAGCCACTGCGA	GTGGGCTGCTTCTTCACGTTCTTGTAGCCACTGCGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr1:228290360_228290395delGTGGGCTGCTTCTTCACGTTCTTGTAGCCACTGCGA	ENST00000272139.4	-	3	480_509	c.246_275delTCGCAGTGGCTACAAGAACGTGAAGAAGCAGCCCAC	c.(244-276)cttcgcagtggctacaagaacgtgaagaagcag>ctg	p.RSGYKNVKKQ83del	C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35	83							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				GCTCAGGCCCGTGGGCTGCTTCTTCACGTTCTTGTAGCCACTGCGAGAGGGCCGGG	0.708																																					p.82_92del		Atlas-INDEL	.											.	C1orf35	17	.	0			c.246_276del						.																																			SO:0001630	splice_region_variant	79169	exon3			.	AY137773	CCDS1566.1	1q42.13	2012-06-25			ENSG00000143793	ENSG00000143793			19032	protein-coding gene	gene with protein product	"multiple myeloma tumor-associated protein 2"					12545221	Standard	NM_024319		Approved	MGC4174, MMTAG2	uc001hrx.3	Q9BU76	OTTHUMG00000037793	ENST00000272139.4:c.246-1TCGCAGTGGCTACAAGAACGTGAAGAAGCAGCCCAC>-	chr1.hg19:g.228290360_228290395delGTGGGCTGCTTCTTCACGTTCTTGTAGCCACTGCGA		73.0	0.0		72.0	13.0	NM_024319	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	Frame_Shift_Del	DEL	ENST00000272139.4	hg19	CCDS1566.1																																																																																			.	.		0.708	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092245.1	NM_024319	In_Frame_Del	-	228290395	GTGGGCTGCTTCTTCACGTTCTTGTAGCCACTGCGA	-	228290360	8	5	192	1	0	1	0	1	0	0	1	0	2040	1145	40	0	540	0	C1orf35	1	228290360	Splice_Site	DEL	GTGGGCTGCTTCTTCACGTTCTTGTAGCCACTGCGA	TCGA-DD-AADJ-01A-11D-A40R-10	12521658	228290360	20960261	3	28376										
EML4	27436	hgsc.bcm.edu	37	chr2	42557132	42557132	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	agcccttaaatgagacagctGaagaggaaagtagaataagc	11	6	0	4			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr2:42557132G>A	ENST00000318522.5	+	23	2993	c.2731G>A	c.(2731-2733)Gaa>Aaa	p.E911K	EML4_ENST00000401738.3_Missense_Mutation_p.E922K|EML4_ENST00000402711.2_Missense_Mutation_p.E853K|EML4_ENST00000453191.2_Missense_Mutation_p.E175K	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	911					microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						TGAGACAGCTGAAGAGGAAAG	0.493			T	ALK	NSCLC																																p.E911K		Atlas-SNP	.		Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	.	EML4	92	.	0			c.G2731A						.						82	77	79					2																	42557132		2203	4300	6503	SO:0001583	missense	27436	exon23			ACAGCTGAAGAGG	AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924		"WD repeat domain containing"	1316	protein-coding gene	gene with protein product		607442		C2orf2			Standard	NM_019063		Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.2731G>A	chr2.hg19:g.42557132G>A	ENSP00000320663:p.Glu911Lys	101.0	0.0		102.0	46.0	NM_019063	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	Missense_Mutation	SNP	ENST00000318522.5	hg19	CCDS1807.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.405084	0.62288	.	.	ENSG00000143924	ENST00000318522;ENST00000402711;ENST00000401738;ENST00000453191	T;T;D;T	0.97752	1.18;1.23;-4.52;0.94	5.4	4.52	0.55395	.	1.715750	0.02481	N	0.088497	D	0.94515	0.8234	L	0.27053	0.805	0.29842	N	0.829157	B;B;P;P	0.41420	0.01;0.01;0.749;0.749	B;B;B;B	0.37731	0.008;0.008;0.257;0.257	D	0.89493	0.3758	10	0.52906	T	0.07	-24.7593	4.4452	0.11593	0.2244:0.2011:0.5745:0.0	.	853;853;922;911	A6H8Y6;B5MCW9;B5MBZ0;Q9HC35	.;.;.;EMAL4_HUMAN	K	911;853;922;175	ENSP00000320663:E911K;ENSP00000385059:E853K;ENSP00000384939:E922K;ENSP00000400590:E175K	ENSP00000320663:E911K	E	+	1	0	EML4	42410636	0.965000	0.33210	0.992000	0.48379	0.996000	0.88848	2.455000	0.44988	2.519000	0.84933	0.655000	0.94253	GAA	.	.		0.493	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250463.3	NM_019063		A	42557132	G	A	42557132	3	1	192	1	0	0	0	0	1	0	0	0	5101	1291	45	3	2821	3	EML4	2	42557132	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10		42557132	200642241	4	28377										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168105919	168105919	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ttatgcaatccaaatcagctTgcgaaattaaacaaagtcac	5	9	2	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr2:168105919T>A	ENST00000409195.1	+	9	8106	c.8017T>A	c.(8017-8019)Tgc>Agc	p.C2673S	XIRP2_ENST00000409273.1_Missense_Mutation_p.C2451S|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.C2673S|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2498					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CAAATCAGCTTGCGAAATTAA	0.403																																					p.C2673S		Atlas-SNP	.											.	XIRP2	914	.	0			c.T8017A						.						58	57	57					2																	168105919		1869	4091	5960	SO:0001583	missense	129446	exon9			TCAGCTTGCGAAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8017T>A	chr2.hg19:g.168105919T>A	ENSP00000386840:p.Cys2673Ser	328.0	1.0		389.0	197.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	T	8.326	0.825298	0.16749	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02197	4.4;4.4;4.4	6.07	-0.989	0.10242	.	0.812175	0.11931	N	0.515758	T	0.02455	0.0075	L	0.57536	1.79	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.47249	-0.9132	10	0.16420	T	0.52	0.1596	5.9177	0.19063	0.1182:0.298:0.0:0.5837	.	2498;2498;2451	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	2673;2673;2451;87	ENSP00000386840:C2673S;ENSP00000295237:C2673S;ENSP00000387255:C2451S	ENSP00000295237:C2673S	C	+	1	0	XIRP2	167814165	0.003000	0.15002	0.062000	0.19696	0.843000	0.47879	0.247000	0.18179	-0.052000	0.13311	0.533000	0.62120	TGC	.	.		0.403	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168105919	T	A	168105919	3	1	192	1	0	0	0	0	1	0	0	0	17445	1812	63	4	8047	4	XIRP2	2	168105919	Missense_Mutation	SNP	T	TCGA-DD-AADJ-01A-11D-A40R-10	125548787	168105919	75093454	5	28378										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098804	178098804	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ctgaattgggagaaattcacCtgtctcttcatctagttgta	8	8	4	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr2:178098804C>A	ENST00000397062.3	-	2	795	c.241G>T	c.(241-243)Ggt>Tgt	p.G81C	NFE2L2_ENST00000423513.1_Missense_Mutation_p.G65C|NFE2L2_ENST00000446151.2_Missense_Mutation_p.G65C|NFE2L2_ENST00000464747.1_Missense_Mutation_p.G65C|NFE2L2_ENST00000397063.4_Missense_Mutation_p.G65C	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	81					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G81S(2)|p.G81_F83delGEF(1)|p.G81C(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AGAAATTCACCTGTCTCTTCA	0.438			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.G81C		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,0,4	NFE2L2	225	.	4	Substitution - Missense(3)|Deletion - In frame(1)	lung(2)|liver(1)|endometrium(1)	c.G241T						.						143	142	142					2																	178098804		1901	4105	6006	SO:0001583	missense	4780	exon2			ATTCACCTGTCTC		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.241G>T	chr2.hg19:g.178098804C>A	ENSP00000380252:p.Gly81Cys	70.0	0.0		85.0	39.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.3|21.3	4.125375|4.125375	0.77436|0.77436	.|.	.|.	ENSG00000116044|ENSG00000116044	ENST00000449627|ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	T|T;T;T;T;T;T	0.29142|0.53423	1.58|1.18;1.18;1.18;0.62;0.62;1.18	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75110|0.75110	0.3805|0.3805	M|M	0.87180|0.87180	2.865|2.865	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|1.0;1.0;1.0;1.0	T|T	0.78563|0.78563	-0.2156|-0.2156	7|10	0.31617|0.87932	T|D	0.26|0	.|.	19.9976|19.9976	0.97389|0.97389	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|65;65;65;81	.|E9PGJ7;B4DNB0;C9JFL6;Q16236	.|.;.;.;NF2L2_HUMAN	S|C	65|65;81;65;65;65;65	ENSP00000391590:A65S|ENSP00000380253:G65C;ENSP00000380252:G81C;ENSP00000411575:G65C;ENSP00000400073:G65C;ENSP00000412191:G65C;ENSP00000410015:G65C	ENSP00000391590:A65S|ENSP00000380252:G81C	A|G	-|-	1|1	0|0	NFE2L2|NFE2L2	177807050|177807050	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.995000|0.995000	0.86356|0.86356	7.298000|7.298000	0.78815|0.78815	2.737000|2.737000	0.93849|0.93849	0.563000|0.563000	0.77884|0.77884	GCA|GGT	.	.		0.438	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		A	178098804	C	A	178098804	3	1	192	1	0	0	0	0	1	0	0	0	10377	681	24	3	1592	3	NFE2L2	2	178098804	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10	9992885	178098804	65100569	6	28379										
GULP1	51454	hgsc.bcm.edu	37	chr2	189434772	189434772	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tagatccaagacttagaaacAgaaaatatggaacttaaaaa	6	5	0	4			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr2:189434772A>G	ENST00000409580.1	+	10	1248	c.534A>G	c.(532-534)acA>acG	p.T178T	GULP1_ENST00000409843.1_Silent_p.T178T|GULP1_ENST00000409830.1_Silent_p.T178T|GULP1_ENST00000359135.3_Silent_p.T178T|GULP1_ENST00000409609.1_Silent_p.T178T|GULP1_ENST00000409805.1_Silent_p.T75T			Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing 1	178					apoptotic process (GO:0006915)|lipid transport (GO:0006869)|phagocytosis, engulfment (GO:0006911)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			ACTTAGAAACAGAAAATATGG	0.279																																					p.T178T	Pancreas(178;563 2065 20199 42378 52815)	Atlas-SNP	.											.	GULP1	35	.	0			c.A534G						.						47	53	51					2																	189434772		2183	4276	6459	SO:0001819	synonymous_variant	51454	exon9			AGAAACAGAAAAT	AF191771	CCDS2295.1, CCDS58742.1, CCDS58743.1	2q32.3-q33	2008-02-05			ENSG00000144366	ENSG00000144366			18649	protein-coding gene	gene with protein product		608165				11729193	Standard	NM_001252668		Approved	CED6, CED-6, GULP	uc010fru.3	Q9UBP9	OTTHUMG00000132647	ENST00000409580.1:c.534A>G	chr2.hg19:g.189434772A>G		395.0	0.0		516.0	167.0	NM_016315	B2RB51|B4DQ40|B8ZZ72|D3DPH1|E9PB86|Q53PC1|Q53RF3|Q9BVL3	Silent	SNP	ENST00000409580.1	hg19	CCDS2295.1	.	.	.	.	.	.	.	.	.	.	A	7.931	0.740583	0.15642	.	.	ENSG00000144366	ENST00000451191	.	.	.	5.86	2.02	0.26589	.	.	.	.	.	T	0.45577	0.1349	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29458	-1.0011	4	.	.	.	-11.8172	3.0751	0.06243	0.535:0.2219:0.0689:0.1742	.	.	.	.	R	3	.	.	Q	+	2	0	GULP1	189143017	0.964000	0.33143	1.000000	0.80357	0.996000	0.88848	0.045000	0.14013	0.570000	0.29347	0.528000	0.53228	CAG	.	.		0.279	GULP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335722.1	NM_016315		G	189434772	A	G	189434772	2	3	192	1	0	0	0	0	0	0	0	1	6910	175	7	2		2	GULP1	2	189434772	Silent	SNP	A	TCGA-DD-AADJ-01A-11D-A40R-10	11335968	189434772	53764601	7	28380										
FN1	2335	hgsc.bcm.edu	37	chr2	216299510	216299513	+	Frame_Shift_Del	DEL	ATTT	ATTT	-													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	taggtccgctcccactgttgAtttatctgatagtgttttcc							TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	ATTT	ATTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr2:216299510_216299513delATTT	ENST00000359671.1	-	2	448_451	c.183_186delAAAT	c.(181-186)ataaatfs	p.IN61fs	FN1_ENST00000443816.1_Frame_Shift_Del_p.IN61fs|FN1_ENST00000426059.1_Frame_Shift_Del_p.IN61fs|FN1_ENST00000354785.4_Frame_Shift_Del_p.IN61fs|FN1_ENST00000323926.6_Frame_Shift_Del_p.IN61fs|AC012462.1_ENST00000412951.1_RNA|FN1_ENST00000432072.2_Frame_Shift_Del_p.IN61fs|FN1_ENST00000356005.4_Frame_Shift_Del_p.IN61fs|FN1_ENST00000336916.4_Frame_Shift_Del_p.IN61fs|FN1_ENST00000346544.3_Frame_Shift_Del_p.IN61fs|FN1_ENST00000357009.2_Frame_Shift_Del_p.IN61fs|FN1_ENST00000421182.1_Frame_Shift_Del_p.IN61fs|FN1_ENST00000345488.5_Frame_Shift_Del_p.IN61fs|FN1_ENST00000357867.4_Frame_Shift_Del_p.IN61fs|FN1_ENST00000446046.1_Frame_Shift_Del_p.IN61fs			P02751	FINC_HUMAN	fibronectin 1	61	Fibrin- and heparin-binding 1.|Fibronectin type-I 1. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	CCCACTGTTGATTTATCTGATAGT	0.402																																					p.62_63del		Atlas-INDEL	.											.	FN1	521	.	0			c.184_187del						.																																			SO:0001589	frameshift_variant	2335	exon2			.		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.183_186delAAAT	chr2.hg19:g.216299510_216299513delATTT	ENSP00000352696:p.Ile61fs	93.0	0.0		77.0	36.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Frame_Shift_Del	DEL	ENST00000359671.1	hg19																																																																																				.	.		0.402	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		-	216299513	ATTT	-	216299510	7	5	192	1	0	1	0	1	0	0	0	0	5970	330	12	0	7460	0	FN1	2	216299510	Frame_Shift_Del	DEL	ATTT	TCGA-DD-AADJ-01A-11D-A40R-10	26864738	216299510	26899863	8	28381										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220493162	220493162	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gaggagccccctctaagtccAgacgtggaggaggaggacga	16	10	1	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr2:220493162A>T	ENST00000358055.3	+	3	599	c.87A>T	c.(85-87)ccA>ccT	p.P29P	SLC4A3_ENST00000273063.6_Silent_p.P29P|SLC4A3_ENST00000373760.2_Silent_p.P29P|SLC4A3_ENST00000317151.3_Silent_p.P29P|AC009955.8_ENST00000455896.1_RNA|SLC4A3_ENST00000373762.3_Silent_p.P29P			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	29					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTCTAAGTCCAGACGTGGAGG	0.652																																					p.P29P		Atlas-SNP	.											.	SLC4A3	144	.	0			c.A87T						.						44	48	47					2																	220493162		2203	4300	6503	SO:0001819	synonymous_variant	6508	exon3			AAGTCCAGACGTG		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.87A>T	chr2.hg19:g.220493162A>T		198.0	0.0		222.0	94.0	NM_005070	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Silent	SNP	ENST00000358055.3	hg19	CCDS2445.1																																																																																			.	.		0.652	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		T	220493162	A	T	220493162	2	4	192	1	0	0	0	0	0	0	0	1	14670	175	7	4		4	SLC4A3	2	220493162	Silent	SNP	A	TCGA-DD-AADJ-01A-11D-A40R-10	4193652	220493162	22706211	9	28382										
LARS2	23395	hgsc.bcm.edu	37	chr3	45557708	45557708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	agcagtatgggatcgacacgAttcggctctacatccttttt	9	10	1	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr3:45557708A>G	ENST00000415258.1	+	16	2125	c.1984A>G	c.(1984-1986)Att>Gtt	p.I662V	LARS2_ENST00000467936.1_3'UTR|LARS2_ENST00000265537.3_Missense_Mutation_p.I662V|LARS2_ENST00000414984.1_Missense_Mutation_p.I619V			Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	662					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	GATCGACACGATTCGGCTCTA	0.483																																					p.I662V		Atlas-SNP	.											.	LARS2	48	.	0			c.A1984G						.						252	201	218					3																	45557708		2203	4300	6503	SO:0001583	missense	23395	exon17			GACACGATTCGGC	AJ312685	CCDS2728.1	3p21.3	2012-10-26			ENSG00000011376	ENSG00000011376	6.1.1.4	"Aminoacyl tRNA synthetases / Class I"	17095	protein-coding gene	gene with protein product	"leucine tRNA ligase 2, mitochondrial"	604544				20194621, 15123417	Standard	NM_015340		Approved	KIAA0028, LEURS, MGC26121	uc003cop.1	Q15031	OTTHUMG00000133177	ENST00000415258.1:c.1984A>G	chr3.hg19:g.45557708A>G	ENSP00000408576:p.Ile662Val	166.0	0.0		183.0	64.0	NM_015340		Missense_Mutation	SNP	ENST00000415258.1	hg19	CCDS2728.1	.	.	.	.	.	.	.	.	.	.	A	4.520	0.096474	0.08681	.	.	ENSG00000011376	ENST00000265537;ENST00000415258;ENST00000414984	T;T;T	0.35973	1.28;1.28;1.28	5.43	-1.8	0.07907	Rossmann-like alpha/beta/alpha sandwich fold (1);Aminoacyl-tRNA synthetase, class Ia (1);	0.667620	0.15704	N	0.248787	T	0.10165	0.0249	N	0.02169	-0.655	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.37103	-0.9720	10	0.02654	T	1	-6.2613	9.181	0.37141	0.4702:0.1042:0.4256:0.0	.	619;662	E9PHM2;Q15031	.;SYLM_HUMAN	V	662;662;619	ENSP00000265537:I662V;ENSP00000408576:I662V;ENSP00000412893:I619V	ENSP00000265537:I662V	I	+	1	0	LARS2	45532712	0.000000	0.05858	0.002000	0.10522	0.831000	0.47069	-0.094000	0.11094	-0.183000	0.10585	0.455000	0.32223	ATT	.	.		0.483	LARS2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345001.1	NM_015340		G	45557708	A	G	45557708	3	3	192	1	0	0	0	0	1	0	0	0	8644	333	12	2	2042	2	LARS2	3	45557708	Missense_Mutation	SNP	A	TCGA-DD-AADJ-01A-11D-A40R-10		45557708	152464722	10	28383										
CACNA2D2	9254	hgsc.bcm.edu	37	chr3	50403525	50403525	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	atagtcataggactccttgcGggtgtagaaggagttattgt	13	5	1	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr3:50403525G>A	ENST00000479441.1	-	33	2799	c.2800C>T	c.(2800-2802)Cgc>Tgc	p.R934C	CACNA2D2_ENST00000360963.3_Missense_Mutation_p.R858C|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.R928C|XXcos-LUCA11.4_ENST00000606665.1_RNA|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.R927C|XXcos-LUCA11.4_ENST00000606259.1_RNA|XXcos-LUCA11.4_ENST00000607121.1_RNA|XXcos-LUCA11.5_ENST00000606589.1_Intron|CACNA2D2_ENST00000423994.2_Missense_Mutation_p.R935C|XXcos-LUCA11.4_ENST00000607583.1_RNA|XXcos-LUCA11.4_ENST00000607088.1_RNA|XXcos-LUCA11.4_ENST00000607362.1_RNA|CACNA2D2_ENST00000424201.2_Missense_Mutation_p.R927C|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.R934C|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.R927C			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	934					energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GACTCCTTGCGGGTGTAGAAG	0.577																																					p.R934C		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.C2800T						.						108	102	104					3																	50403525		2203	4300	6503	SO:0001583	missense	9254	exon33			CCTTGCGGGTGTA	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"Calcium channel subunits"	1400	protein-coding gene	gene with protein product	"gene 26"	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.2800C>T	chr3.hg19:g.50403525G>A	ENSP00000418081:p.Arg934Cys	90.0	0.0		76.0	29.0	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	hg19	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.109775	0.56398	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	T;T;T;T;T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8	4.97	4.08	0.47627	.	0.261790	0.32473	N	0.006041	T	0.81706	0.4879	M	0.66939	2.045	0.46609	D	0.999125	D;D	0.76494	0.998;0.999	P;P	0.61275	0.676;0.886	T	0.82550	-0.0401	10	0.62326	D	0.03	-14.0228	11.6586	0.51332	0.0:0.0:0.6809:0.3191	.	934;927	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	C	935;928;927;858;934;927;927;934	ENSP00000407393:R935C;ENSP00000404631:R928C;ENSP00000266039:R927C;ENSP00000354228:R858C;ENSP00000390526:R934C;ENSP00000378519:R927C;ENSP00000390329:R927C;ENSP00000418081:R934C	ENSP00000266039:R927C	R	-	1	0	CACNA2D2	50378529	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	2.002000	0.40835	1.059000	0.40554	0.561000	0.74099	CGC	.	.		0.577	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		A	50403525	G	A	50403525	3	1	192	1	0	0	0	0	1	0	0	0	2551	1116	39	1	686	1	CACNA2D2	3	50403525	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	4845817	50403525	147618905	11	28384										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51418626	51418626	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ctcctcggaggccccacctcGcactgacaccatggactcca	8	19	0	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr3:51418626G>A	ENST00000266037.9	+	53	5752	c.5729G>A	c.(5728-5730)cGc>cAc	p.R1910H		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1910					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		GCCCCACCTCGCACTGACACC	0.607																																					p.R1910H		Atlas-SNP	.											.	DOCK3	397	.	0			c.G5729A						.						58	71	67					3																	51418626		2187	4278	6465	SO:0001583	missense	1795	exon53			CACCTCGCACTGA	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.5729G>A	chr3.hg19:g.51418626G>A	ENSP00000266037:p.Arg1910His	75.0	0.0		100.0	44.0	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.341197	0.81911	.	.	ENSG00000088538	ENST00000266037	T	0.05081	3.5	6.17	6.17	0.99709	.	0.151595	0.49916	D	0.000132	T	0.19087	0.0458	L	0.51422	1.61	0.54753	D	0.999981	D	0.71674	0.998	D	0.72075	0.976	T	0.00020	-1.2351	10	0.45353	T	0.12	.	13.9957	0.64397	0.0685:0.0:0.9315:0.0	.	1910	Q8IZD9	DOCK3_HUMAN	H	1910	ENSP00000266037:R1910H	ENSP00000266037:R1910H	R	+	2	0	DOCK3	51393666	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.272000	0.78516	2.941000	0.99782	0.655000	0.94253	CGC	.	.		0.607	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		A	51418626	G	A	51418626	3	1	192	1	0	0	0	0	1	0	0	0	4690	1087	38	1	5939	1	DOCK3	3	51418626	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	1015101	51418626	146603804	12	28385										
C3orf63	23272	hgsc.bcm.edu	37	chr3	56674029	56674029	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cttacctgtaattggaatcaGtttccaatgtatttcagtct	6	8	3	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr3:56674029G>T	ENST00000493960.2	-	16	2759	c.2749C>A	c.(2749-2751)Ctg>Atg	p.L917M	FAM208A_ENST00000431842.2_Missense_Mutation_p.L521M|FAM208A_ENST00000355628.5_Missense_Mutation_p.L917M	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	917							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						ATTGGAATCAGTTTCCAATGT	0.363																																					p.L917M		Atlas-SNP	.											.	FAM208A	113	.	0			c.C2749A						.						91	86	88					3																	56674029		2202	4300	6502	SO:0001583	missense	23272	exon16			GAATCAGTTTCCA	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 63"	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.2749C>A	chr3.hg19:g.56674029G>T	ENSP00000417509:p.Leu917Met	104.0	0.0		147.0	27.0	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.300856	0.60195	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.29917	1.55;1.74;2.63	5.48	3.23	0.37069	.	0.000000	0.52532	D	0.000075	T	0.47135	0.1429	L	0.54323	1.7	0.36001	D	0.837403	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.988;0.999	T	0.57763	-0.7755	10	0.87932	D	0	-5.4998	10.0388	0.42144	0.1923:0.0:0.8077:0.0	.	917;917;521	Q9UK61-3;Q9UK61-4;Q9UK61-2	.;.;.	M	521;917;917	ENSP00000399410:L521M;ENSP00000417509:L917M;ENSP00000347845:L917M	ENSP00000347845:L917M	L	-	1	2	C3orf63	56649069	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	2.360000	0.44151	1.074000	0.40909	0.650000	0.86243	CTG	.	.		0.363	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		T	56674029	G	T	56674029	3	4	192	1	0	0	0	0	1	0	0	0	2241	1020	36	3	2359	3	C3orf63	3	56674029	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	5255403	56674029	141348401	13	28386										
RYBP	23429	hgsc.bcm.edu	37	chr3	72427650	72427650	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tggttctgctgttctgacccTgcactggaggtcactgtgga	13	10	3	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr3:72427650T>A	ENST00000477973.2	-	4	837	c.838A>T	c.(838-840)Agg>Tgg	p.R280W		NM_012234.5	NP_036366.3	Q8N488	RYBP_HUMAN	RING1 and YY1 binding protein	0					apoptotic process (GO:0006915)|histone H2A monoubiquitination (GO:0035518)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			prostate(1)|upper_aerodigestive_tract(1)	2		Prostate(10;0.00174)|Lung NSC(201;0.0659)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;0.000197)|Epithelial(33;0.00068)|LUSC - Lung squamous cell carcinoma(21;0.00228)|Lung(16;0.00677)|KIRC - Kidney renal clear cell carcinoma(39;0.198)|Kidney(39;0.232)		GTTCTGACCCTGCACTGGAGG	0.547																																					p.A181A		Atlas-SNP	.											.	RYBP	13	.	0			c.A543T						.						102	104	103					3																	72427650		2160	4253	6413	SO:0001583	missense	23429	exon4			TGACCCTGCACTG	AF179286		3p14.2	2008-07-18			ENSG00000163602	ENSG00000163602			10480	protein-coding gene	gene with protein product	"YY1 and E4TF1 associated factor 1", "ring1 interactor RYBP", "apoptin-associating protein 1", "death effector domain-associated factor"	607535				10369680	Standard	NM_012234		Approved	YEAF1, AAP1, DEDAF	uc003dpe.3	Q8N488	OTTHUMG00000159190	ENST00000477973.2:c.838A>T	chr3.hg19:g.72427650T>A	ENSP00000419494:p.Arg280Trp	130.0	0.0		133.0	52.0	NM_012234	Q9P2W5|Q9UMW4	Silent	SNP	ENST00000477973.2	hg19		.	.	.	.	.	.	.	.	.	.	T	7.034	0.561234	0.13498	.	.	ENSG00000163602	ENST00000477973	.	.	.	5.86	3.23	0.37069	.	.	.	.	.	T	0.50377	0.1612	.	.	.	.	.	.	.	.	.	.	.	.	T	0.57516	-0.7798	3	.	.	.	-14.0658	8.8939	0.35451	0.0:0.2184:0.0:0.7816	.	.	.	.	W	280	.	.	R	-	1	2	RYBP	72510340	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	1.214000	0.32419	0.466000	0.27193	-0.297000	0.09499	AGG	.	.		0.547	RYBP-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353762.3	NM_012234		A	72427650	T	A	72427650	3	1	192	1	0	0	0	0	1	0	0	0	13781	1567	55	4	117	4	RYBP	3	72427650	Missense_Mutation	SNP	T	TCGA-DD-AADJ-01A-11D-A40R-10	15753621	72427650	125594780	14	28387										
ACAD11	84129	hgsc.bcm.edu	37	chr3	132337613	132337613	+	Frame_Shift_Del	DEL	T	T	-													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gagaccctcgactttggccaTttcctgtcaaggtgatgaac							TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr3:132337613delT	ENST00000264990.6	-	11	2250	c.1279delA	c.(1279-1281)atgfs	p.M427fs	ACAD11_ENST00000355458.3_Frame_Shift_Del_p.M427fs|ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000481970.2_Frame_Shift_Del_p.M427fs	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	427					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)			breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						ACTTTGGCCATTTCCTGTCAA	0.408																																					p.M427fs		Atlas-INDEL	.											.	ACAD11	78	.	0			c.1280delT						.						60	57	58					3																	132337613		2203	4300	6503	SO:0001589	frameshift_variant	84129	exon11			.	BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"acyl-Coenzyme A dehydrogenase family, member 11"				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.1279delA	chr3.hg19:g.132337613delT	ENSP00000264990:p.Met427fs	188.0	0.0		227.0	94.0	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Frame_Shift_Del	DEL	ENST00000264990.6	hg19	CCDS3074.1																																																																																			.	.		0.408	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169		-	132337613	T	-	132337613	7	5	192	1	0	1	0	1	0	0	0	0	109	1493	52	0	1103	0	ACAD11	3	132337613	Frame_Shift_Del	DEL	T	TCGA-DD-AADJ-01A-11D-A40R-10	59909963	132337613	65684817	15	28388										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173996998	173996998	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ttgaaaatatagtagatagcGatgatggtatatcagctagt	10	3	1	3	rs371578371		TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr3:173996998G>A	ENST00000457714.1	+	6	1636	c.1207G>A	c.(1207-1209)Gat>Aat	p.D403N	NLGN1_ENST00000361589.4_Missense_Mutation_p.D403N|NLGN1_ENST00000401917.3_Missense_Mutation_p.D443N|NLGN1_ENST00000466350.1_3'UTR|NLGN1_ENST00000545397.1_Missense_Mutation_p.D403N	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	420					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			AGTAGATAGCGATGATGGTAT	0.338																																					p.D403N		Atlas-SNP	.											.	NLGN1	209	.	0			c.G1207A						.	G	ASN/ASP	0,4406		0,0,2203	122	130	127		1207	5.6	1	3		127	1,8599		0,1,4299	no	missense	NLGN1	NM_014932.2	23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	403/824	173996998	1,13005	2203	4300	6503	SO:0001583	missense	22871	exon6			GATAGCGATGATG	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.1207G>A	chr3.hg19:g.173996998G>A	ENSP00000392500:p.Asp403Asn	157.0	0.0		159.0	66.0	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	hg19	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.325969	0.60743	0.0	1.16E-4	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000545397;ENST00000401917	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.62	5.62	0.85841	.	0.106713	0.64402	D	0.000006	T	0.49729	0.1574	N	0.16166	0.38	0.58432	D	0.999996	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.40869	-0.9540	10	0.49607	T	0.09	.	19.6753	0.95930	0.0:0.0:1.0:0.0	.	443;403	D2X2H5;Q8N2Q7-2	.;.	N	403;403;403;443	ENSP00000392500:D403N;ENSP00000354541:D403N;ENSP00000441108:D403N;ENSP00000385750:D443N	ENSP00000354541:D403N	D	+	1	0	NLGN1	175479692	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.648000	0.89879	0.563000	0.77884	GAT	.	.		0.338	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		A	173996998	G	A	173996998	3	1	192	1	0	0	0	0	1	0	0	0	10470	1058	37	1	1221	1	NLGN1	3	173996998	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	41659385	173996998	24025432	16	28389										
CRMP1	1400	hgsc.bcm.edu	37	chr4	5841321	5841322	+	Missense_Mutation	DNP	GC	GC	TT													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gaggggaagtcacgaacgccGcagccttggcccagttcttg							TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr4:5841321_5841322GC>TT	ENST00000397890.2	-	9	1109_1110	c.895_896GC>AA	c.(895-897)GCg>AAg	p.A299K	CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000512574.1_Missense_Mutation_p.A297K|CRMP1_ENST00000324989.7_Missense_Mutation_p.A413K	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	299					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		CACGAACGCCGCAGCCTTGGCC	0.629																																					p.A413E|p.A413T		Atlas-SNP	.											.	CRMP1	118	.	0			c.C1238A|c.G1237A						.																																			SO:0001583	missense	1400	exon9			AACGCCGCAGCCT|ACGCCGCAGCCTT	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.895_896delinsTT	chr4.hg19:g.5841321_5841322delinsTT	ENSP00000380987:p.Ala299Lys	62.0|63.0	0.0		75.0|76.0	31.0|30.0	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	hg19	CCDS43207.1																																																																																			.	.		0.629	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		TT	5841322	GC	TT	5841321	3	4	192	1	0	0	0	0	1	0	0	0	3892	1087	38	1	846	1	CRMP1	4	5841321	Missense_Mutation	DNP	GC	TCGA-DD-AADJ-01A-11D-A40R-10		5841321	185312955	17	28390										
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140735877	140735877	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	acagtaattgcacttttcaaCgtgcatgacagtgactcagg	9	9	2	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr5:140735877C>T	ENST00000571252.1	+	1	1110	c.1110C>T	c.(1108-1110)aaC>aaT	p.N370N	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	370	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACTTTTCAACGTGCATGACA	0.433																																					p.N370N		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.C1110T						.						30	29	30					5																	140735877		1956	4091	6047	SO:0001819	synonymous_variant	56111	exon1			TTTCAACGTGCAT	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1110C>T	chr5.hg19:g.140735877C>T		84.0	0.0		112.0	46.0	NM_018917	Q9Y5D3	Silent	SNP	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.		0.433	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		T	140735877	C	T	140735877	2	4	192	1	0	0	0	0	0	0	0	1	11565	535	19	1		1	PCDHGA4	5	140735877	Silent	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10		140735877	40179383	18	28391										
ERVFRDE1	405754	hgsc.bcm.edu	37	chr6	11104810	11104810	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gtgtttggctctggttagctCccttggttttattttcccaa	9	9	1	0	rs558720062		TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr6:11104810C>T	ENST00000472091.1	-	2	1109	c.734G>A	c.(733-735)gGa>gAa	p.G245E	SMIM13_ENST00000416247.2_Intron|ERVFRD-1_ENST00000542862.1_Missense_Mutation_p.G245E	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	245					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						ctggttagctcccttggtttt	0.448													C|||	1	0.000199681	0	0	5008	,	,		18505	0.001		0	False		,,,				2504	0				p.G245E		Atlas-SNP	.											.	ERVFRD-1	41	.	0			c.G734A						.						27	27	27					6																	11104810		2203	4299	6502	SO:0001583	missense	405754	exon2			TTAGCTCCCTTGG	AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.734G>A	chr6.hg19:g.11104810C>T	ENSP00000420174:p.Gly245Glu	60.0	0.0		61.0	26.0	NM_207582		Missense_Mutation	SNP	ENST00000472091.1	hg19	CCDS4519.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.692817	0.48202	.	.	ENSG00000244476	ENST00000472091;ENST00000542862	T;T	0.16897	2.31;2.31	0.225	0.225	0.15325	.	422.947000	0.00797	U	0.001381	T	0.13243	0.0321	N	0.22421	0.69	0.26156	N	0.980072	D	0.76494	0.999	D	0.75484	0.986	T	0.27739	-1.0065	9	0.56958	D	0.05	.	.	.	.	.	245	P60508	EFRD1_HUMAN	E	245	ENSP00000420174:G245E;ENSP00000444461:G245E	ENSP00000420174:G245E	G	-	2	0	ERVFRD-1	11212796	0.983000	0.35010	0.929000	0.37066	0.930000	0.56654	0.305000	0.19254	0.300000	0.22699	0.305000	0.20034	GGA	.	.		0.448	ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353776.1	NM_207582		T	11104810	C	T	11104810	3	4	192	1	0	0	0	0	1	0	0	0	5248	855	30	3	886	3	ERVFRDE1	6	11104810	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10		11104810	160010257	19	28392										
OR5V1	81696	hgsc.bcm.edu	37	chr6	29323627	29323627	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	acgatcatatgccattgctgCcagtaggagacactctgatc	9	11	2	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr6:29323627C>A	ENST00000377154.1	-	4	645	c.346G>T	c.(346-348)Gca>Tca	p.A116S	OR5V1_ENST00000543825.1_Missense_Mutation_p.A116S			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	116				A -> T (in Ref. 1; CAD31042). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GCCATTGCTGCCAGTAGGAGA	0.408																																					p.A116S	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											.	OR5V1	63	.	0			c.G346T						.						66	67	67					6																	29323627		2203	4299	6502	SO:0001583	missense	81696	exon1			TTGCTGCCAGTAG		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"GPCR / Class A : Olfactory receptors"	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.346G>T	chr6.hg19:g.29323627C>A	ENSP00000366359:p.Ala116Ser	117.0	0.0		125.0	48.0	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	hg19	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	C	12.01	1.808297	0.31961	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.01998	4.51;4.51	4.37	4.37	0.52481	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32719	N	0.005724	T	0.01627	0.0052	L	0.56199	1.76	0.22656	N	0.998885	P	0.47762	0.9	B	0.43331	0.416	T	0.42258	-0.9462	10	0.54805	T	0.06	-34.1359	12.0146	0.53307	0.0:0.9118:0.0:0.0882	.	116	Q9UGF6	OR5V1_HUMAN	S	116	ENSP00000366359:A116S;ENSP00000443309:A116S	ENSP00000366356:A116S	A	-	1	0	OR5V1	29431606	0.000000	0.05858	0.972000	0.41901	0.576000	0.36127	0.249000	0.18216	2.422000	0.82143	0.543000	0.68304	GCA	.	.		0.408	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3			A	29323627	C	A	29323627	3	1	192	1	0	0	0	0	1	0	0	0	11193	739	26	3	622	3	OR5V1	6	29323627	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10	18218817	29323627	141791440	20	28393										
EHMT2	10919	hgsc.bcm.edu	37	chr6	31855974	31855974	+	Frame_Shift_Del	DEL	A	A	-													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cacagtggggacagaagaccAtcccattcagctgagacaca							TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr6:31855974delA	ENST00000375537.4	-	13	1595	c.1589delT	c.(1588-1590)atgfs	p.M530fs	EHMT2_ENST00000375530.4_Frame_Shift_Del_p.M496fs|EHMT2_ENST00000395728.3_Frame_Shift_Del_p.M587fs|EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000375528.4_Frame_Shift_Del_p.M553fs	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	530					DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						ACAGAAGACCATCCCATTCAG	0.632																																					p.M530fs		Atlas-INDEL	.											.	EHMT2	45	.	0			c.1590delG						.						71	66	68					6																	31855974		1508	2708	4216	SO:0001589	frameshift_variant	10919	exon13			.	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.1589delT	chr6.hg19:g.31855974delA	ENSP00000364687:p.Met530fs	110.0	0.0		133.0	66.0	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Frame_Shift_Del	DEL	ENST00000375537.4	hg19	CCDS4725.1																																																																																			.	.		0.632	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		-	31855974	A	-	31855974	7	5	192	1	0	1	0	1	0	0	0	0	4986	217	8	0	2107	0	EHMT2	6	31855974	Frame_Shift_Del	DEL	A	TCGA-DD-AADJ-01A-11D-A40R-10	2532347	31855974	139259093	21	28394										
PI16	221476	hgsc.bcm.edu	37	chr6	36930828	36930828	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gggtactccttcttccctagCaacggggattccggctttct	10	13	2	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr6:36930828C>A	ENST00000373674.3	+	5	1038	c.710C>A	c.(709-711)gCa>gAa	p.A237E	PI16_ENST00000491324.1_Intron	NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	237					negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TCTTCCCTAGCAACGGGGATT	0.552																																					p.A237E		Atlas-SNP	.											PI16,NS,neuroblastoma,0,1	PI16	50	.	0			c.C710A						.						103	96	99					6																	36930828		2203	4300	6503	SO:0001583	missense	221476	exon6			CCCTAGCAACGGG		CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"microseminoprotein, beta-binding protein"		"protease inhibitor 16"				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.710C>A	chr6.hg19:g.36930828C>A	ENSP00000362778:p.Ala237Glu	137.0	0.0		153.0	74.0	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	hg19	CCDS34440.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.539744	0.45176	.	.	ENSG00000164530	ENST00000373674;ENST00000539035	T	0.07567	3.18	4.47	1.71	0.24356	.	0.568577	0.16057	N	0.231657	T	0.07052	0.0179	L	0.51422	1.61	0.80722	D	1	D	0.58268	0.982	P	0.55824	0.785	T	0.27434	-1.0074	10	0.49607	T	0.09	.	6.1845	0.20490	0.0:0.6649:0.1561:0.1789	.	237	Q6UXB8	PI16_HUMAN	E	237;89	ENSP00000362778:A237E	ENSP00000362778:A237E	A	+	2	0	PI16	37038806	0.953000	0.32496	0.859000	0.33776	0.945000	0.59286	0.596000	0.24044	0.383000	0.24910	0.591000	0.81541	GCA	.	.		0.552	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370		A	36930828	C	A	36930828	3	1	192	1	0	0	0	0	1	0	0	0	11878	710	25	3	728	3	PI16	6	36930828	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10	5074854	36930828	134184239	22	28395										
KCNK17	89822	hgsc.bcm.edu	37	chr6	39271861	39271861	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gcaggaagagcaggaggcccGagaggagggcgccagagccc	19	11	0	3	rs140102103		TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr6:39271861G>T	ENST00000373231.4	-	4	792	c.560C>A	c.(559-561)tCg>tAg	p.S187*	KCNK17_ENST00000453413.2_Nonsense_Mutation_p.S187*	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	187					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						CAGGAGGCCCGAGAGGAGGGC	0.652																																					p.S187X		Atlas-SNP	.											.	KCNK17	61	.	0			c.C560A						.						49	53	52					6																	39271861		2203	4300	6503	SO:0001587	stop_gained	89822	exon4			AGGCCCGAGAGGA	AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.560C>A	chr6.hg19:g.39271861G>T	ENSP00000362328:p.Ser187*	68.0	0.0		87.0	4.0	NM_001135111	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Nonsense_Mutation	SNP	ENST00000373231.4	hg19	CCDS4842.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.882316	0.51908	.	.	ENSG00000124780	ENST00000373231;ENST00000453413	.	.	.	4.21	4.21	0.49690	.	0.281130	0.22934	N	0.053875	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	9.3161	0.37934	0.1012:0.0:0.8988:0.0	.	.	.	.	X	187	.	ENSP00000362328:S187X	S	-	2	0	KCNK17	39379839	0.016000	0.18221	0.263000	0.24496	0.006000	0.05464	1.932000	0.40143	2.166000	0.68216	0.561000	0.74099	TCG	.	G|1.000;A|0.000		0.652	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460		T	39271861	G	T	39271861	4	4	192	1	0	0	0	0	0	1	0	0	8073	1059	37	1	578	1	KCNK17	6	39271861	Nonsense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	2341033	39271861	131843206	23	28396										
PRICKLE4	29964	hgsc.bcm.edu	37	chr6	41751951	41751951	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tggacttcagaccctcctgcAgcaactccctccgcaggaca	8	17	1	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr6:41751951A>T	ENST00000394260.1	+	1	95	c.95A>T	c.(94-96)cAg>cTg	p.Q32L	PRICKLE4_ENST00000394259.1_Missense_Mutation_p.Q32L|PRICKLE4_ENST00000458694.1_Missense_Mutation_p.Q72L|PRICKLE4_ENST00000394263.1_Missense_Mutation_p.Q72L|PRICKLE4_ENST00000359201.5_Missense_Mutation_p.Q72L			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	32	PET. {ECO:0000255|PROSITE- ProRule:PRU00636}.					nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			ACCCTCCTGCAGCAACTCCCT	0.557																																					p.Q72L		Atlas-SNP	.											.	PRICKLE4	29	.	0			c.A215T						.						153	117	130					6																	41751951		2203	4300	6503	SO:0001583	missense	29964	exon4			TCCTGCAGCAACT	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"chromosome 6 open reading frame 49"	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.95A>T	chr6.hg19:g.41751951A>T	ENSP00000377803:p.Gln32Leu	87.0	0.0		104.0	47.0	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Missense_Mutation	SNP	ENST00000394260.1	hg19		.	.	.	.	.	.	.	.	.	.	A	18.73	3.687081	0.68157	.	.	ENSG00000124593	ENST00000458694;ENST00000359201;ENST00000394263;ENST00000394259;ENST00000394260	D;D;D;D;D	0.85411	-1.98;-1.98;-1.98;-1.98;-1.98	4.7	2.26	0.28386	.	0.473404	0.17933	N	0.157081	T	0.70928	0.3280	L	0.45285	1.41	0.34640	D	0.720587	P	0.49559	0.925	P	0.49752	0.621	T	0.63721	-0.6573	10	0.22706	T	0.39	-6.4371	6.2312	0.20736	0.7968:0.0:0.2032:0.0	.	72	Q2TBC4-3	.	L	72;72;72;32;32	ENSP00000404911:Q72L;ENSP00000352128:Q72L;ENSP00000377806:Q72L;ENSP00000377802:Q32L;ENSP00000377803:Q32L	ENSP00000335185:Q72L	Q	+	2	0	PRICKLE4	41859929	1.000000	0.71417	0.998000	0.56505	0.923000	0.55619	2.619000	0.46401	0.304000	0.22809	0.459000	0.35465	CAG	.	.		0.557	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397		T	41751951	A	T	41751951	3	4	192	1	0	0	0	0	1	0	0	0	12501	188	7	4	221	4	PRICKLE4	6	41751951	Missense_Mutation	SNP	A	TCGA-DD-AADJ-01A-11D-A40R-10	2480090	41751951	129363116	24	28397										
MCM3	4172	hgsc.bcm.edu	37	chr6	52141926	52141940	+	In_Frame_Del	DEL	GGTGGGGATAGCTCG	GGTGGGGATAGCTCG	-													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ccagaggagccccggccagtGgtggggatagctcggggtgc					rs150139384|rs77113422	byFrequency	TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	GGTGGGGATAGCTCG	GGTGGGGATAGCTCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr6:52141926_52141940delGGTGGGGATAGCTCG	ENST00000229854.7	-	8	1166_1180	c.1090_1104delCGAGCTATCCCCACC	c.(1090-1104)cgagctatccccaccdel	p.RAIPT364del	MCM3_ENST00000476448.1_5'UTR|MCM3_ENST00000419835.2_In_Frame_Del_p.RAIPT318del|MCM3_ENST00000596288.1_In_Frame_Del_p.RAIPT409del			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	364	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					CCCGGCCAGTGGTGGGGATAGCTCGGGGTGCAGTG	0.6																																					p.409_414del		Atlas-INDEL	.											.	MCM3	63	.	0			c.1226_1240del						.																																			SO:0001651	inframe_deletion	4172	exon8			.	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"minichromosome maintenance deficient (S. cerevisiae) 3", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.1090_1104delCGAGCTATCCCCACC	chr6.hg19:g.52141926_52141940delGGTGGGGATAGCTCG	ENSP00000229854:p.Arg364_Thr368del	53.0	0.0		66.0	13.0	NM_002388	B4DWW4|Q92660|Q9BTR3|Q9NUE7	In_Frame_Del	DEL	ENST00000229854.7	hg19																																																																																				.	.		0.6	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1			-	52141940	GGTGGGGATAGCTCG	-	52141926	7	5	192	1	0	1	0	1	0	0	0	0	9396	1335	47	0	1362	0	MCM3	6	52141926	In_Frame_Del	DEL	GGTGGGGATAGCTCG	TCGA-DD-AADJ-01A-11D-A40R-10	10389975	52141926	118973141	25	28398										
DST	667	hgsc.bcm.edu	37	chr6	56480983	56480983	+	Frame_Shift_Del	DEL	T	T	-													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	caaagaatcagcaagttctgTaagtgtgatgaggccttcct							TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr6:56480983delT	ENST00000370765.6	-	24	7389	c.7282delA	c.(7282-7284)acafs	p.T2428fs	DST_ENST00000370769.4_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000361203.3_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1728	Asp-rich.				axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GCAAGTTCTGTAAGTGTGATG	0.438																																					p.T2428fs		Atlas-INDEL	.											.	DST	1427	.	0			c.7283delC						.						93	87	89					6																	56480983		2203	4300	6503	SO:0001589	frameshift_variant	667	exon24			.	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.7282delA	chr6.hg19:g.56480983delT	ENSP00000359801:p.Thr2428fs	88.0	0.0		95.0	34.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Frame_Shift_Del	DEL	ENST00000370765.6	hg19	CCDS4959.1																																																																																			.	.		0.438	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		-	56480983	T	-	56480983	7	5	192	1	0	1	0	1	0	0	0	0	4785	1638	57	0	13117	0	DST	6	56480983	Frame_Shift_Del	DEL	T	TCGA-DD-AADJ-01A-11D-A40R-10	4339057	56480983	114634084	26	28399										
ABCB4	5244	hgsc.bcm.edu	37	chr7	87074258	87074258	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	acatggggcagcctggccaaCactgaaagctccaattagga	11	11	0	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr7:87074258C>T	ENST00000265723.4	-	10	1150	c.1039G>A	c.(1039-1041)Gtt>Att	p.V347I	ABCB4_ENST00000358400.3_Missense_Mutation_p.V347I|ABCB4_ENST00000359206.3_Missense_Mutation_p.V347I|ABCB4_ENST00000545634.1_Missense_Mutation_p.V347I|ABCB4_ENST00000453593.1_Missense_Mutation_p.V347I	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	347	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	GCCTGGCCAACACTGAAAGCT	0.333																																					p.V347I		Atlas-SNP	.											.	ABCB4	177	.	0			c.G1039A						.						65	62	63					7																	87074258		2203	4300	6503	SO:0001583	missense	5244	exon10			GGCCAACACTGAA	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.1039G>A	chr7.hg19:g.87074258C>T	ENSP00000265723:p.Val347Ile	1716.0	1.0		1941.0	856.0	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	hg19	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	c	2.233	-0.375585	0.05034	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75	5.01	0.0543	0.14310	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.355033	0.28544	N	0.014963	T	0.68265	0.2982	N	0.01424	-0.875	0.24914	N	0.99202	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.12837	0.002;0.005;0.008	T	0.60234	-0.7303	10	0.07325	T	0.83	-3.6652	7.1166	0.25421	0.0:0.4995:0.1082:0.3922	.	347;347;347	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	I	347	ENSP00000352135:V347I;ENSP00000351172:V347I;ENSP00000265723:V347I;ENSP00000392983:V347I;ENSP00000437465:V347I	ENSP00000265723:V347I	V	-	1	0	ABCB4	86912194	0.000000	0.05858	0.828000	0.32881	0.989000	0.77384	-0.531000	0.06171	-0.310000	0.08766	0.460000	0.39030	GTT	.	.		0.333	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		T	87074258	C	T	87074258	3	4	192	1	0	0	0	0	1	0	0	0	43	478	17	3	2897	3	ABCB4	7	87074258	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10		87074258	72064405	27	28400										
SAMD9	54809	hgsc.bcm.edu	37	chr7	92731597	92731597	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tagcaggacaaagtattcatCaaaaaaatcaaaggactttt	6	6	3	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr7:92731597C>A	ENST00000379958.2	-	3	4083	c.3814G>T	c.(3814-3816)Gat>Tat	p.D1272Y		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1272						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			AAGTATTCATCAAAAAAATCA	0.313																																					p.D1272Y		Atlas-SNP	.											.	SAMD9	239	.	0			c.G3814T						.						43	49	47					7																	92731597		2180	4286	6466	SO:0001583	missense	54809	exon2			ATTCATCAAAAAA	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.3814G>T	chr7.hg19:g.92731597C>A	ENSP00000369292:p.Asp1272Tyr	219.0	0.0		189.0	72.0	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	hg19	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.452743	0.43531	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.24908	1.83;2.6	4.62	2.72	0.32119	.	0.387379	0.22527	U	0.058886	T	0.20047	0.0482	L	0.40543	1.245	0.27838	N	0.941209	B	0.30914	0.3	B	0.31442	0.13	T	0.14699	-1.0463	10	0.59425	D	0.04	.	9.2369	0.37473	0.1413:0.6007:0.258:0.0	.	1272	Q5K651	SAMD9_HUMAN	Y	1272	ENSP00000369292:D1272Y;ENSP00000414529:D1272Y	ENSP00000369292:D1272Y	D	-	1	0	SAMD9	92569533	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	1.665000	0.37449	2.377000	0.81083	0.536000	0.68110	GAT	.	.		0.313	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		A	92731597	C	A	92731597	3	1	192	1	0	0	0	0	1	0	0	0	13841	826	29	3	959	3	SAMD9	7	92731597	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10	5657339	92731597	66407066	28	28401										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	146829391	146829391	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cggtgcctgtctttttcaacGctacaagttacctggaggtg	11	10	2	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr7:146829391G>A	ENST00000361727.3	+	8	1654	c.1138G>A	c.(1138-1140)Gct>Act	p.A380T		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	380					adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CTTTTTCAACGCTACAAGTTA	0.463										HNSCC(39;0.1)																											p.A380T		Atlas-SNP	.											CNTNAP2,NS,carcinoma,0,1	CNTNAP2	392	.	0			c.G1138A						.						126	121	122					7																	146829391		2203	4300	6503	SO:0001583	missense	26047	exon8			TTCAACGCTACAA	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1138G>A	chr7.hg19:g.146829391G>A	ENSP00000354778:p.Ala380Thr	79.0	0.0		109.0	38.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	hg19	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.894940	0.72639	.	.	ENSG00000174469	ENST00000361727	T	0.79247	-1.25	5.7	5.7	0.88788	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.088434	0.42420	D	0.000703	T	0.66208	0.2766	N	0.24115	0.695	0.80722	D	1	B	0.25809	0.135	B	0.23574	0.047	T	0.61564	-0.7037	10	0.13470	T	0.59	.	18.3986	0.90507	0.0:0.0:1.0:0.0	.	380	Q9UHC6	CNTP2_HUMAN	T	380	ENSP00000354778:A380T	ENSP00000354778:A380T	A	+	1	0	CNTNAP2	146460324	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	5.191000	0.65110	2.686000	0.91538	0.591000	0.81541	GCT	.	.		0.463	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			A	146829391	G	A	146829391	3	1	192	1	0	0	0	0	1	0	0	0	3649	1087	38	1	1168	1	CNTNAP2	7	146829391	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	54097794	146829391	12309272	29	28402										
LZTS1	11178	hgsc.bcm.edu	37	chr8	20112506	20112506	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cttgatgtagaagaagtcttCgctcttgcccattttggagc	10	9	2	3			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr8:20112506C>T	ENST00000381569.1	-	2	544	c.187G>A	c.(187-189)Gaa>Aaa	p.E63K	LZTS1_ENST00000522290.1_Missense_Mutation_p.E63K|LZTS1_ENST00000265801.6_Missense_Mutation_p.E63K			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	63					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		AAGAAGTCTTCGCTCTTGCCC	0.592																																					p.E63K		Atlas-SNP	.											LZTS1,NS,carcinoma,0,1	LZTS1	72	.	0			c.G187A						.						99	91	94					8																	20112506		2203	4300	6503	SO:0001583	missense	11178	exon1			AGTCTTCGCTCTT	AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"F37/Esophageal cancer-related gene-coding leucine-zipper motif"			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.187G>A	chr8.hg19:g.20112506C>T	ENSP00000370981:p.Glu63Lys	117.0	0.0		92.0	42.0	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Missense_Mutation	SNP	ENST00000381569.1	hg19	CCDS6015.1	.	.	.	.	.	.	.	.	.	.	C	33	5.245606	0.95272	.	.	ENSG00000061337	ENST00000381569;ENST00000265801;ENST00000522290;ENST00000360248	T;T;T	0.24538	2.17;2.17;1.85	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.34395	0.0896	N	0.22421	0.69	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.65684	0.937;0.912	T	0.02533	-1.1145	10	0.09843	T	0.71	-21.7579	19.022	0.92919	0.0:1.0:0.0:0.0	.	63;63	Q9Y250-4;Q9Y250	.;LZTS1_HUMAN	K	63	ENSP00000370981:E63K;ENSP00000265801:E63K;ENSP00000429263:E63K	ENSP00000265801:E63K	E	-	1	0	LZTS1	20156786	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.354000	0.79424	2.835000	0.97688	0.650000	0.86243	GAA	.	.		0.592	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		T	20112506	C	T	20112506	3	4	192	1	0	0	0	0	1	0	0	0	9147	893	31	1	1615	1	LZTS1	8	20112506	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10		20112506	126251516	30	28403										
SLC24A2	25769	hgsc.bcm.edu	37	chr9	19786033	19786033	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gacgttgaatttcatgaaaaCcacatagcaaaaataagctg	7	7	1	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr9:19786033C>T	ENST00000341998.2	-	1	893	c.832G>A	c.(832-834)Gtt>Att	p.V278I	SLC24A2_ENST00000286344.3_Missense_Mutation_p.V278I	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	278					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		TTCATGAAAACCACATAGCAA	0.398																																					p.V278I		Atlas-SNP	.											SLC24A2,NS,carcinoma,0,1	SLC24A2	93	.	0			c.G832A						.						139	132	135					9																	19786033		2203	4300	6503	SO:0001583	missense	25769	exon1			TGAAAACCACATA	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"Solute carriers"	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.832G>A	chr9.hg19:g.19786033C>T	ENSP00000344801:p.Val278Ile	93.0	0.0		125.0	49.0	NM_001193288	B7ZLL8|Q9NTN5|Q9NZQ4	Missense_Mutation	SNP	ENST00000341998.2	hg19	CCDS6493.1	.	.	.	.	.	.	.	.	.	.	C	2.242	-0.373600	0.05034	.	.	ENSG00000155886	ENST00000341998;ENST00000286344	T;T	0.67523	-0.27;-0.27	5.91	-4.95	0.03048	Sodium/calcium exchanger membrane region (1);	0.598474	0.18681	N	0.134164	T	0.40862	0.1134	N	0.10645	0.015	0.30190	N	0.799618	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.15752	-1.0426	9	.	.	.	.	17.2888	0.87150	0.0:0.119:0.0:0.881	.	278;278	Q9UI40-2;Q9UI40	.;NCKX2_HUMAN	I	278	ENSP00000344801:V278I;ENSP00000286344:V278I	.	V	-	1	0	SLC24A2	19776033	0.998000	0.40836	0.924000	0.36721	0.991000	0.79684	0.463000	0.21972	-0.834000	0.04239	-0.150000	0.13652	GTT	.	.		0.398	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344		T	19786033	C	T	19786033	3	4	192	1	0	0	0	0	1	0	0	0	14481	507	18	3	1193	3	SLC24A2	9	19786033	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10		19786033	121427398	31	28404										
ACO1	48	hgsc.bcm.edu	37	chr9	32430520	32430520	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gcctctccccccttagtaatAgcatatgcaattgctggaac	7	13	1	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr9:32430520A>T	ENST00000309951.6	+	14	1812	c.1674A>T	c.(1672-1674)atA>atT	p.I558I	ACO1_ENST00000541043.1_Silent_p.I459I|ACO1_ENST00000379923.1_Silent_p.I558I	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	558					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		CCTTAGTAATAGCATATGCAA	0.428																																					p.I558I		Atlas-SNP	.											.	ACO1	149	.	0			c.A1674T						.						124	122	123					9																	32430520		2203	4300	6503	SO:0001819	synonymous_variant	48	exon14			AGTAATAGCATAT	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1674A>T	chr9.hg19:g.32430520A>T		143.0	0.0		175.0	81.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	hg19	CCDS6525.1																																																																																			.	.		0.428	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		T	32430520	A	T	32430520	2	4	192	1	0	0	0	0	0	0	0	1	146	410	15	4		4	ACO1	9	32430520	Silent	SNP	A	TCGA-DD-AADJ-01A-11D-A40R-10	12644487	32430520	108782911	32	28405										
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88272416	88272416	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gcttttcttcccaacttgatGtttgtaacactttttaaact	4	9	1	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr9:88272416G>A	ENST00000357081.3	-	10	987	c.843C>T	c.(841-843)aaC>aaT	p.N281N	AGTPBP1_ENST00000376081.4_Intron|AGTPBP1_ENST00000376080.1_3'UTR|AGTPBP1_ENST00000491784.1_5'UTR|AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000376109.3_Silent_p.N333N|AGTPBP1_ENST00000432218.1_Silent_p.N119N|AGTPBP1_ENST00000376083.3_Silent_p.N281N			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	281					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						CCAACTTGATGTTTGTAACAC	0.328																																					p.N281N		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.C843T						.						108	97	101					9																	88272416		2202	4300	6502	SO:0001819	synonymous_variant	23287	exon10			CTTGATGTTTGTA	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.843C>T	chr9.hg19:g.88272416G>A		98.0	0.0		108.0	58.0	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Silent	SNP	ENST00000357081.3	hg19																																																																																				.	.		0.328	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		A	88272416	G	A	88272416	2	1	192	1	0	0	0	0	0	0	0	1	400	1368	48	3		3	AGTPBP1	9	88272416	Silent	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	55841896	88272416	52941015	33	28406										
FIBCD1	84929	hgsc.bcm.edu	37	chr9	133799154	133799154	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ccagccgccgccgtccgtgcGcatgtcacagtacacctgga	11	17	1	0	rs369690143		TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr9:133799154G>T	ENST00000372338.4	-	4	1068	c.826C>A	c.(826-828)Cgc>Agc	p.R276S	FIBCD1_ENST00000372337.2_Missense_Mutation_p.R118S|FIBCD1_ENST00000448616.1_Missense_Mutation_p.R276S|FIBCD1_ENST00000253018.4_Missense_Mutation_p.R118S	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	276	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		CCGTCCGTGCGCATGTCACAG	0.667																																					p.R276S		Atlas-SNP	.											.	FIBCD1	34	.	0			c.C826A						.						60	53	55					9																	133799154		2202	4300	6502	SO:0001583	missense	84929	exon5			CCGTGCGCATGTC	AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"Fibrinogen C domain containing"	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.826C>A	chr9.hg19:g.133799154G>T	ENSP00000361413:p.Arg276Ser	118.0	0.0		127.0	43.0	NM_001145106	A3KFK0|Q6UXK6|Q96SJ7	Missense_Mutation	SNP	ENST00000372338.4	hg19	CCDS6937.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.621|7.621	0.676885|0.676885	0.14841|0.14841	.|.	.|.	ENSG00000130720|ENSG00000130720	ENST00000444139|ENST00000448616;ENST00000372338;ENST00000372337;ENST00000253018;ENST00000451466	.|T;T;T;T;T	.|0.80824	.|-1.42;-1.42;-1.42;-0.99;-1.42	5.67|5.67	4.7|4.7	0.59300|0.59300	.|Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	.|0.448728	.|0.26359	.|N	.|0.024836	.|T	.|0.50360	.|0.1611	N|N	0.00996|0.00996	-1.065|-1.065	0.37914|0.37914	D|D	0.931464|0.931464	.|B	.|0.02656	.|0.0	.|B	.|0.08055	.|0.003	.|T	.|0.48433	.|-0.9036	.|10	.|0.24483	.|T	.|0.36	.|.	6.9889|6.9889	0.24743|0.24743	0.0:0.1191:0.4386:0.4422|0.0:0.1191:0.4386:0.4422	.|.	.|276	.|Q8N539	.|FBCD1_HUMAN	X|S	229|276;276;118;118;276	.|ENSP00000414501:R276S;ENSP00000361413:R276S;ENSP00000361412:R118S;ENSP00000253018:R118S;ENSP00000393894:R276S	.|ENSP00000253018:R118S	C|R	-|-	3|1	2|0	FIBCD1|FIBCD1	132788975|132788975	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.630000|0.630000	0.37929|0.37929	3.975000|3.975000	0.56859|0.56859	1.316000|1.316000	0.45131|0.45131	0.563000|0.563000	0.77884|0.77884	TGC|CGC	.	.		0.667	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843		T	133799154	G	T	133799154	3	4	192	1	0	0	0	0	1	0	0	0	5892	1087	38	1	575	1	FIBCD1	9	133799154	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	45526738	133799154	7414277	34	28407										
FAM163B	642968	hgsc.bcm.edu	37	chr9	136444248	136444248	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cccgaagccccccgggggcaGctccacgtcctcctggctca	11	20	1	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr9:136444248G>A	ENST00000496132.1	-	3	641	c.397C>T	c.(397-399)Ctg>Ttg	p.L133L	FAM163B_ENST00000356873.3_Silent_p.L133L			P0C2L3	F163B_HUMAN	family with sequence similarity 163, member B	133						integral component of membrane (GO:0016021)				large_intestine(1)	1						CCCGGGGGCAGCTCCACGTCC	0.701																																					p.L133L		Atlas-SNP	.											.	FAM163B	7	.	0			c.C397T						.						8	11	10					9																	136444248		2107	4177	6284	SO:0001819	synonymous_variant	642968	exon2			GGGGCAGCTCCAC	BX629352	CCDS35171.1	9q34.2	2008-06-05	2008-06-05	2008-06-05	ENSG00000196990	ENSG00000196990			33277	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 166"	C9orf166			Standard	NM_001080515		Approved		uc011mdm.2	P0C2L3	OTTHUMG00000159557	ENST00000496132.1:c.397C>T	chr9.hg19:g.136444248G>A		84.0	0.0		124.0	47.0	NM_001080515	B2RUZ5	Silent	SNP	ENST00000496132.1	hg19	CCDS35171.1																																																																																			.	.		0.701	FAM163B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356190.1	NM_001080515		A	136444248	G	A	136444248	2	1	192	1	0	0	0	0	0	0	0	1	5482	962	34	3		3	FAM163B	9	136444248	Silent	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	2645094	136444248	4769183	35	28408										
PHPT1	29085	hgsc.bcm.edu	37	chr9	139744507	139744507	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gggcgacatgcagaagcaagGctgcgactgtgagtgtctgg	17	8	1	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr9:139744507G>T	ENST00000247665.10	+	2	540	c.203G>T	c.(202-204)gGc>gTc	p.G68V	MAMDC4_ENST00000317446.2_5'Flank|PHPT1_ENST00000371661.1_Missense_Mutation_p.G68V|MAMDC4_ENST00000445819.1_5'Flank|PHPT1_ENST00000545326.1_Missense_Mutation_p.G68V|PHPT1_ENST00000492540.1_3'UTR	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1	68					negative regulation of ATP citrate synthase activity (GO:2000984)|negative regulation of lyase activity (GO:0051350)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-histidine dephosphorylation (GO:0035971)|positive regulation of cell motility (GO:2000147)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|protein dephosphorylation (GO:0006470)|regulation of actin cytoskeleton reorganization (GO:2000249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium channel inhibitor activity (GO:0019855)|ion channel binding (GO:0044325)|phosphohistidine phosphatase activity (GO:0008969)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|large_intestine(1)|lung(1)	3	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CAGAAGCAAGGCTGCGACTGT	0.652																																					p.G68V		Atlas-SNP	.											.	PHPT1	14	.	0			c.G203T						.						107	103	104					9																	139744507		2203	4300	6503	SO:0001583	missense	29085	exon2			AGCAAGGCTGCGA	AF131857	CCDS7009.1, CCDS48060.1	9q34.3	2008-02-05			ENSG00000054148	ENSG00000054148	3.1.3.-		30033	protein-coding gene	gene with protein product	"phosphohistidine phosphatase 14kDa", " sex-regulated protein janus-a"	610167				11042152, 8619474	Standard	NM_014172		Approved	PHP14, HSPC141, CGI-202, DKFZp564M173, bA216L13.10	uc004cjq.4	Q9NRX4	OTTHUMG00000020950	ENST00000247665.10:c.203G>T	chr9.hg19:g.139744507G>T	ENSP00000247665:p.Gly68Val	80.0	0.0		92.0	33.0	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Missense_Mutation	SNP	ENST00000247665.10	hg19	CCDS7009.1	.	.	.	.	.	.	.	.	.	.	.	18.52	3.641495	0.67244	.	.	ENSG00000054148	ENST00000371661;ENST00000545326;ENST00000247665	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	D	0.84406	0.5465	M	0.93898	3.47	0.80722	D	1	D;D	0.71674	0.986;0.998	P;D	0.71870	0.905;0.975	D	0.87665	0.2537	8	0.66056	D	0.02	0.1892	11.6657	0.51372	0.0:0.0:0.8226:0.1773	.	68;68	Q9NRX4-2;Q9NRX4	.;PHP14_HUMAN	V	68	.	ENSP00000247665:G68V	G	+	2	0	PHPT1	138864328	0.974000	0.33945	0.080000	0.20451	0.932000	0.56968	3.050000	0.49877	2.102000	0.63906	0.462000	0.41574	GGC	.	.		0.652	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172		T	139744507	G	T	139744507	3	4	192	1	0	0	0	0	1	0	0	0	11869	1203	42	3	209	3	PHPT1	9	139744507	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	3300259	139744507	1468924	36	28409										
DDB1	1642	hgsc.bcm.edu	37	chr11	61090560	61090560	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gtatgtcaagcactcagcaaTagaggtctggaagaaagtca	11	7	4	2	rs367862166		TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr11:61090560T>C	ENST00000301764.7	-	8	1325	c.928A>G	c.(928-930)Att>Gtt	p.I310V	DDB1_ENST00000450997.2_Intron|DDB1_ENST00000545930.1_5'UTR	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	310	Interaction with CDT1.|WD repeat beta-propeller A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						CACTCAGCAATAGAGGTCTGG	0.478								Nucleotide excision repair (NER)																													p.I310V		Atlas-SNP	.											.	DDB1	100	.	0			c.A928G						.	T	VAL/ILE	0,4406		0,0,2203	92	77	82		928	5.7	1	11		82	1,8597	1.2+/-3.3	0,1,4298	no	missense	DDB1	NM_001923.3	29	0,1,6501	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging	310/1141	61090560	1,13003	2203	4299	6502	SO:0001583	missense	1642	exon8			CAGCAATAGAGGT	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.928A>G	chr11.hg19:g.61090560T>C	ENSP00000301764:p.Ile310Val	140.0	0.0		133.0	57.0	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Missense_Mutation	SNP	ENST00000301764.7	hg19	CCDS31576.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.005356	0.74932	0.0	1.16E-4	ENSG00000167986	ENST00000301764;ENST00000539739;ENST00000535174;ENST00000541513	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.66	5.66	0.87406	.	0.098252	0.64402	D	0.000001	T	0.55273	0.1910	M	0.84156	2.68	0.80722	D	1	B;B;P	0.42375	0.346;0.237;0.778	B;B;P	0.51266	0.181;0.156;0.664	T	0.59295	-0.7481	10	0.02654	T	1	-16.3986	15.9004	0.79369	0.0:0.0:0.0:1.0	.	310;310;310	F5GY55;B7Z2A1;Q16531	.;.;DDB1_HUMAN	V	310;29;93;125	ENSP00000301764:I310V;ENSP00000445563:I29V;ENSP00000446044:I93V;ENSP00000442660:I125V	ENSP00000301764:I310V	I	-	1	0	DDB1	60847136	1.000000	0.71417	0.971000	0.41717	0.974000	0.67602	7.843000	0.86859	2.167000	0.68274	0.533000	0.62120	ATT	.	.		0.478	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		C	61090560	T	C	61090560	3	2	192	1	0	0	0	0	1	0	0	0	4325	1406	49	2	2574	2	DDB1	11	61090560	Missense_Mutation	SNP	T	TCGA-DD-AADJ-01A-11D-A40R-10		61090560	73915956	37	28410										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73021870	73021870	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	agcaatggggaggcaggggaGgcctacaggtccctgagtga	18	8	0	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr11:73021870G>A	ENST00000263674.3	+	1	2537	c.2187G>A	c.(2185-2187)gaG>gaA	p.E729E	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	729					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						AGGCAGGGGAGGCCTACAGGT	0.637																																					p.E729E		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G2187A						.						39	42	41					11																	73021870		2200	4293	6493	SO:0001819	synonymous_variant	9828	exon1			AGGGGAGGCCTAC	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.2187G>A	chr11.hg19:g.73021870G>A		30.0	0.0		33.0	10.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Silent	SNP	ENST00000263674.3	hg19	CCDS8221.1																																																																																			.	.		0.637	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		A	73021870	G	A	73021870	2	1	192	1	0	0	0	0	0	0	0	1	900	991	35	3		3	ARHGEF17	11	73021870	Silent	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	11931310	73021870	61984646	38	28411										
EP400	57634	hgsc.bcm.edu	37	chr12	132547105	132547105	+	Silent	SNP	G	G	A													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cagcaacaacagcagcagcaGcagcagcagcagcagcagca							TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr12:132547105G>A	ENST00000333577.4	+	48	8410	c.8301G>A	c.(8299-8301)caG>caA	p.Q2767Q	EP400_ENST00000389561.2_Silent_p.Q2731Q|EP400_ENST00000330386.6_Silent_p.Q2650Q|EP400_ENST00000332482.4_Silent_p.Q2694Q|EP400_ENST00000389562.2_Silent_p.Q2730Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2767	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcagcagcagc	0.587																																					p.Q2731Q		Atlas-SNP	.											.	EP400	370	.	0			c.G8193A						.						22	27	25					12																	132547105		2072	4019	6091	SO:0001819	synonymous_variant	57634	exon47			GCAGCAGCAGCAG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8301G>A	chr12.hg19:g.132547105G>A		55.0	0.0		111.0	22.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.		0.587	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132547105	G	A	132547105	2	1	192	1	0	0	0	0	0	0	0	1	5151	962	34	3		3	EP400	12	132547105	Silent	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10		132547105	1304790	39	28412	141	2								
EP400	57634	hgsc.bcm.edu	37	chr12	132547108	132547108	+	Silent	SNP	G	G	A													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	caacaacagcagcagcagcaGcagcagcagcagcagcagca							TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr12:132547108G>A	ENST00000333577.4	+	48	8413	c.8304G>A	c.(8302-8304)caG>caA	p.Q2768Q	EP400_ENST00000389561.2_Silent_p.Q2732Q|EP400_ENST00000330386.6_Silent_p.Q2651Q|EP400_ENST00000332482.4_Silent_p.Q2695Q|EP400_ENST00000389562.2_Silent_p.Q2731Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2768	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcagcagcagc	0.587																																					p.Q2732Q		Atlas-SNP	.											.	EP400	370	.	0			c.G8196A						.						22	26	25					12																	132547108		2047	3981	6028	SO:0001819	synonymous_variant	57634	exon47			GCAGCAGCAGCAG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8304G>A	chr12.hg19:g.132547108G>A		59.0	0.0		113.0	27.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.		0.587	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132547108	G	A	132547108	2	1	192	1	0	0	0	0	0	0	0	1	5151	962	34	3		3	EP400	12	132547108	Silent	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	3	132547108	1304787	40	28413	141	2								
TGDS	23483	hgsc.bcm.edu	37	chr13	95248352	95248352	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	acccgcttcgcaaagccgccGggaagaccccacggttcctc	10	18	0	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr13:95248352G>A	ENST00000261296.5	-	1	159	c.39C>T	c.(37-39)ccC>ccT	p.P13P	TGDS_ENST00000498294.1_5'UTR	NM_014305.2	NP_055120.1	O95455	TGDS_HUMAN	TDP-glucose 4,6-dehydratase	13					nucleotide-sugar metabolic process (GO:0009225)		coenzyme binding (GO:0050662)|dTDP-glucose 4,6-dehydratase activity (GO:0008460)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					CAAAGCCGCCGGGAAGACCCC	0.602																																					p.P13P		Atlas-SNP	.											.	TGDS	24	.	0			c.C39T						.						41	42	41					13																	95248352		2203	4300	6503	SO:0001819	synonymous_variant	23483	exon1			GCCGCCGGGAAGA	AF048686	CCDS9471.1	13q32.1	2012-02-22			ENSG00000088451	ENSG00000088451	4.2.1.46	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	20324	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 2E, member 1"					19027726	Standard	NM_014305		Approved	TDPGD, SDR2E1	uc001vlw.3	O95455	OTTHUMG00000046308	ENST00000261296.5:c.39C>T	chr13.hg19:g.95248352G>A		167.0	0.0		179.0	78.0	NM_014305	Q05DQ3|Q2TU31|Q5T3Z2|Q9H1T9	Silent	SNP	ENST00000261296.5	hg19	CCDS9471.1																																																																																			.	.		0.602	TGDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106904.2	NM_014305		A	95248352	G	A	95248352	2	1	192	1	0	0	0	0	0	0	0	1	15829	1103	39	1		1	TGDS	13	95248352	Silent	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10		95248352	19921526	41	28414										
FERMT2	10979	hgsc.bcm.edu	37	chr14	53331148	53331148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cttatacttttttagatagcGgggagacaccaaacattcag	8	8	1	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr14:53331148G>A	ENST00000395631.2	-	12	1789	c.1573C>T	c.(1573-1575)Cgc>Tgc	p.R525C	FERMT2_ENST00000399304.3_Missense_Mutation_p.R525C|FERMT2_ENST00000341590.3_Missense_Mutation_p.R525C|FERMT2_ENST00000557255.1_5'Flank|FERMT2_ENST00000553373.1_Missense_Mutation_p.R525C|FERMT2_ENST00000343279.4_Missense_Mutation_p.R525C			Q96AC1	FERM2_HUMAN	fermitin family member 2	525	FERM.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					TTTAGATAGCGGGGAGACACC	0.348																																					p.R525C		Atlas-SNP	.											.	FERMT2	59	.	0			c.C1573T						.						124	120	121					14																	53331148		2203	4300	6503	SO:0001583	missense	10979	exon12			GATAGCGGGGAGA	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"Fermitins", "Pleckstrin homology (PH) domain containing"	15767	protein-coding gene	gene with protein product	"kindlin-2"	607746	"pleckstrin homology domain containing, family C (with FERM domain) member 1", "fermitin family homolog 2 (Drosophila)"	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.1573C>T	chr14.hg19:g.53331148G>A	ENSP00000378993:p.Arg525Cys	101.0	0.0		106.0	48.0	NM_001135000	B5TJY2|Q14840|Q86TY7	Missense_Mutation	SNP	ENST00000395631.2	hg19	CCDS9713.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.27|17.27	3.347306|3.347306	0.61183|0.61183	.|.	.|.	ENSG00000073712|ENSG00000073712	ENST00000553663|ENST00000395631;ENST00000341590;ENST00000554152;ENST00000343279;ENST00000553373;ENST00000399304	T|T;T;T;T;T;T	0.80033|0.80033	-1.33|-1.33;-1.33;-1.33;-1.33;-1.33;-1.33	5.86|5.86	4.97|4.97	0.65823|0.65823	.|Band 4.1 domain (1);FERM central domain (2);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.84401|0.84401	0.5464|0.5464	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.46912	.|0.886;0.778;0.778	.|P;P;P	.|0.45406	.|0.462;0.479;0.479	D|D	0.87116|0.87116	0.2188|0.2188	6|10	.|0.72032	.|D	.|0.01	.|.	15.2048|15.2048	0.73169|0.73169	0.0:0.0:0.7445:0.2555|0.0:0.0:0.7445:0.2555	.|.	.|525;525;525	.|Q96AC1-2;Q96AC1;B5TJY2	.|.;FERM2_HUMAN;.	L|C	31|525;525;478;525;525;525	ENSP00000451134:P31L|ENSP00000378993:R525C;ENSP00000340391:R525C;ENSP00000450741:R478C;ENSP00000342858:R525C;ENSP00000451084:R525C;ENSP00000382243:R525C	.|ENSP00000340391:R525C	P|R	-|-	2|1	0|0	FERMT2|FERMT2	52400898|52400898	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.943000|0.943000	0.58893|0.58893	6.622000|6.622000	0.74233|0.74233	1.597000|1.597000	0.50072|0.50072	0.650000|0.650000	0.86243|0.86243	CCG|CGC	.	.		0.348	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832		A	53331148	G	A	53331148	3	1	192	1	0	0	0	0	1	0	0	0	5826	1116	39	1	522	1	FERMT2	14	53331148	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10		53331148	54018392	42	28415										
ATP6V1D	51382	hgsc.bcm.edu	37	chr14	67826386	67826386	+	Frame_Shift_Del	DEL	A	A	-													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tttacttacattcgcgagggAaagatttcaattcggtcttt					rs144445579		TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr14:67826386delA	ENST00000216442.7	-	1	580	c.30delT	c.(28-30)tttfs	p.F10fs	ATP6V1D_ENST00000555474.1_Frame_Shift_Del_p.F10fs|EIF2S1_ENST00000256383.4_5'Flank|ATP6V1D_ENST00000554236.1_Frame_Shift_Del_p.F10fs|ATP6V1D_ENST00000555431.1_5'UTR	NM_015994.3	NP_057078.1	Q9Y5K8	VATD_HUMAN	ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D	10					cellular iron ion homeostasis (GO:0006879)|cilium assembly (GO:0042384)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|protein localization to cilium (GO:0061512)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			lung(3)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	7				all cancers(60;0.000739)|OV - Ovarian serous cystadenocarcinoma(108;0.00597)|BRCA - Breast invasive adenocarcinoma(234;0.00957)		TTCGCGAGGGAAAGATTTCAA	0.562																																					p.P11fs		Atlas-INDEL	.											.	ATP6V1D	21	.	0			c.31delC						.						81	76	77					14																	67826386		2203	4300	6503	SO:0001589	frameshift_variant	51382	exon1			.	AF145316	CCDS9780.1	14q23-q24.2	2010-04-21	2002-08-29	2002-05-10	ENSG00000100554	ENSG00000100554		"ATPases / V-type"	13527	protein-coding gene	gene with protein product		609398	"ATPase, H+ transporting, lysosomal (vacuolar proton pump)"	ATP6M		9442887	Standard	NM_015994		Approved	VATD, VMA8	uc001xjf.3	Q9Y5K8		ENST00000216442.7:c.30delT	chr14.hg19:g.67826386delA	ENSP00000216442:p.Phe10fs	57.0	0.0		71.0	37.0	NM_015994	B2RE33|Q9Y688	Frame_Shift_Del	DEL	ENST00000216442.7	hg19	CCDS9780.1																																																																																			.	.		0.562	ATP6V1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412511.1	NM_015994		-	67826386	A	-	67826386	7	5	192	1	0	1	0	1	0	0	0	0	1182	243	9	0	749	0	ATP6V1D	14	67826386	Frame_Shift_Del	DEL	A	TCGA-DD-AADJ-01A-11D-A40R-10	14495238	67826386	39523154	43	28416										
SNW1	22938	hgsc.bcm.edu	37	chr14	78187159	78187159	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	atatcccgattttcatttctCtgaagtttcgacctattttg	5	9	2	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr14:78187159C>G	ENST00000261531.7	-	12	1205	c.1143G>C	c.(1141-1143)caG>caC	p.Q381H	SNW1_ENST00000555761.1_Missense_Mutation_p.Q381H|SLIRP_ENST00000557431.1_Intron|SNW1_ENST00000554775.1_Missense_Mutation_p.Q219H|SLIRP_ENST00000557623.1_3'UTR	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	381					cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)			NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		TTTCATTTCTCTGAAGTTTCG	0.363																																					p.Q381H		Atlas-SNP	.											.	SNW1	44	.	0			c.G1143C						.						142	132	135					14																	78187159		2203	4300	6503	SO:0001583	missense	22938	exon12			ATTTCTCTGAAGT	AF045184	CCDS9867.1	14q22.1-q22.3	2005-09-13	2005-09-13	2005-09-13		ENSG00000100603			16696	protein-coding gene	gene with protein product		603055	"SKI interacting protein"	SKIIP		8973337, 9632709	Standard	NM_012245		Approved	NCoA-62, SKIP, Prp45, PRPF45, Bx42	uc001xuf.3	Q13573		ENST00000261531.7:c.1143G>C	chr14.hg19:g.78187159C>G	ENSP00000261531:p.Gln381His	118.0	0.0		112.0	33.0	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Missense_Mutation	SNP	ENST00000261531.7	hg19	CCDS9867.1	.	.	.	.	.	.	.	.	.	.	C	16.82	3.229189	0.58777	.	.	ENSG00000100603	ENST00000261531;ENST00000554775;ENST00000555761	.	.	.	5.39	4.5	0.54988	.	0.119855	0.64402	D	0.000016	T	0.68476	0.3005	M	0.75264	2.295	0.54753	D	0.999988	D;D	0.61697	0.978;0.99	P;P	0.59221	0.854;0.585	T	0.69826	-0.5040	9	0.52906	T	0.07	.	8.5443	0.33413	0.0:0.7138:0.0:0.2862	.	381;381	G3V3A4;Q13573	.;SNW1_HUMAN	H	381;219;381	.	ENSP00000261531:Q381H	Q	-	3	2	SNW1	77256912	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.179000	0.50887	1.263000	0.44181	0.467000	0.42956	CAG	.	.		0.363	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245		G	78187159	C	G	78187159	3	3	192	1	0	0	0	0	1	0	0	0	14894	912	32	4	479	4	SNW1	14	78187159	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10	10360773	78187159	29162381	44	28417										
C14orf145	145508	hgsc.bcm.edu	37	chr14	80993294	80993294	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	accctgtatttggaatatctTccatcagttctctcagatga	6	10	4	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr14:80993294T>C	ENST00000555265.1	-	23	3366	c.2991A>G	c.(2989-2991)ggA>ggG	p.G997G	CEP128_ENST00000553717.1_5'UTR|CEP128_ENST00000281129.3_Silent_p.G997G			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	997						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TGGAATATCTTCCATCAGTTC	0.358																																					p.G997G		Atlas-SNP	.											.	CEP128	146	.	0			c.A2991G						.						76	76	76					14																	80993294		2203	4300	6503	SO:0001819	synonymous_variant	145508	exon22			ATATCTTCCATCA	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2991A>G	chr14.hg19:g.80993294T>C		51.0	0.0		56.0	17.0	NM_152446	B9EK52|Q86X97|Q96ML4	Silent	SNP	ENST00000555265.1	hg19	CCDS32130.1	.	.	.	.	.	.	.	.	.	.	T	1.090	-0.664286	0.03428	.	.	ENSG00000100629	ENST00000556061	.	.	.	5.64	-0.772	0.10998	.	.	.	.	.	T	0.50171	0.1600	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36768	-0.9734	4	.	.	.	.	5.329	0.15922	0.0:0.3623:0.2539:0.3839	.	.	.	.	E	63	.	.	K	-	1	0	CEP128	80063047	0.987000	0.35691	0.826000	0.32828	0.059000	0.15707	0.050000	0.14120	-0.194000	0.10399	-0.472000	0.04984	AAG	.	.		0.358	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		C	80993294	T	C	80993294	2	2	192	1	0	0	0	0	0	0	0	1	1751	1770	62	2		2	C14orf145	14	80993294	Silent	SNP	T	TCGA-DD-AADJ-01A-11D-A40R-10	2806135	80993294	26356246	45	28418										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105407441	105407441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	atcctcacagggagagagaaTagaagattcaaagtgaggac	12	6	2	5			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr14:105407441T>C	ENST00000333244.5	-	7	14466	c.14347A>G	c.(14347-14349)Att>Gtt	p.I4783V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4783						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGAGAGAGAATAGAAGATTCA	0.502																																					p.I4783V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A14347G						.						94	99	97					14																	105407441		1943	4136	6079	SO:0001583	missense	113146	exon7			AGAGAATAGAAGA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.14347A>G	chr14.hg19:g.105407441T>C	ENSP00000353114:p.Ile4783Val	144.0	0.0		171.0	75.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	T	2.812	-0.246726	0.05867	.	.	ENSG00000185567	ENST00000333244	T	0.00655	5.95	3.26	-5.79	0.02354	.	.	.	.	.	T	0.00440	0.0014	N	0.14661	0.345	0.09310	N	1	B	0.20988	0.05	B	0.10450	0.005	T	0.45512	-0.9256	9	0.05620	T	0.96	.	5.6943	0.17847	0.1219:0.4556:0.0:0.4225	.	4783	Q8IVF2	AHNK2_HUMAN	V	4783	ENSP00000353114:I4783V	ENSP00000353114:I4783V	I	-	1	0	AHNAK2	104478486	.	.	0.000000	0.03702	0.003000	0.03518	.	.	-1.709000	0.01399	-1.072000	0.02254	ATT	.	.		0.502	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105407441	T	C	105407441	3	2	192	1	0	0	0	0	1	0	0	0	415	1406	49	2	3044	2	AHNAK2	14	105407441	Missense_Mutation	SNP	T	TCGA-DD-AADJ-01A-11D-A40R-10	24414147	105407441	1942099	46	28419										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105408464	105408464	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gtccccctccagccgcgtacTgtccagcttggctcctgggg	12	17	0	0	rs377277155		TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr14:105408464T>C	ENST00000333244.5	-	7	13443	c.13324A>G	c.(13324-13326)Agt>Ggt	p.S4442G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4442						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			AGCCGCGTACTGTCCAGCTTG	0.592																																					p.S4442G		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A13324G						.						140	149	146					14																	105408464		2029	4167	6196	SO:0001583	missense	113146	exon7			GCGTACTGTCCAG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.13324A>G	chr14.hg19:g.105408464T>C	ENSP00000353114:p.Ser4442Gly	103.0	0.0		111.0	48.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	C	0.257	-1.002408	0.02128	.	.	ENSG00000185567	ENST00000333244	T	0.00498	6.97	1.75	0.814	0.18756	.	1.211790	0.06879	N	0.802204	T	0.00178	0.0005	N	0.00554	-1.385	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29701	-1.0003	10	0.15066	T	0.55	.	4.9993	0.14257	0.0:0.4517:0.0:0.5483	.	4442	Q8IVF2	AHNK2_HUMAN	G	4442	ENSP00000353114:S4442G	ENSP00000353114:S4442G	S	-	1	0	AHNAK2	104479509	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.095000	0.11077	-0.494000	0.06669	-1.033000	0.02402	AGT	.	.		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105408464	T	C	105408464	3	2	192	1	0	0	0	0	1	0	0	0	415	1580	55	2	4067	2	AHNAK2	14	105408464	Missense_Mutation	SNP	T	TCGA-DD-AADJ-01A-11D-A40R-10	1023	105408464	1941076	47	28420										
ACAN	176	hgsc.bcm.edu	37	chr15	89401482	89401482	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cgattccagtgggtttacatCccagactccggaattcagtg	10	11	1	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr15:89401482C>T	ENST00000561243.1	+	11	5666	c.5666C>T	c.(5665-5667)tCc>tTc	p.S1889F	ACAN_ENST00000559004.1_Missense_Mutation_p.S1889F|ACAN_ENST00000439576.2_Missense_Mutation_p.S1889F|ACAN_ENST00000352105.7_Missense_Mutation_p.S1889F			P16112	PGCA_HUMAN	aggrecan	1885	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GGGTTTACATCCCAGACTCCG	0.547																																					p.S1889F		Atlas-SNP	.											.	ACAN	220	.	0			c.C5666T						.						62	65	64					15																	89401482		2003	4184	6187	SO:0001583	missense	176	exon12			TTACATCCCAGAC	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.5666C>T	chr15.hg19:g.89401482C>T	ENSP00000453342:p.Ser1889Phe	44.0	0.0		73.0	28.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	hg19	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	C	9.591	1.126196	0.20959	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.07114	3.47;3.22	5.56	5.56	0.83823	.	0.558380	0.13630	N	0.373813	T	0.37571	0.1008	M	0.86740	2.835	0.09310	N	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.23084	-1.0198	10	0.51188	T	0.08	-8.5221	18.5131	0.90925	0.0:1.0:0.0:0.0	.	1889;1889	E7ENV9;E7EX88	.;.	F	1889;1889;1775	ENSP00000387356:S1889F;ENSP00000341615:S1889F	ENSP00000268134:S1775F	S	+	2	0	ACAN	87202486	0.296000	0.24398	0.013000	0.15412	0.047000	0.14425	4.114000	0.57858	2.618000	0.88619	0.655000	0.94253	TCC	.	.		0.547	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		T	89401482	C	T	89401482	3	4	192	1	0	0	0	0	1	0	0	0	117	855	30	3	5708	3	ACAN	15	89401482	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10		89401482	13129910	48	28421										
MTHFSD	64779	hgsc.bcm.edu	37	chr16	86582083	86582083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tacttacctgagaggtggcaCattttctcaagatgtcttta	8	8	2	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr16:86582083C>T	ENST00000360900.6	-	4	363	c.338G>A	c.(337-339)tGt>tAt	p.C113Y	MTHFSD_ENST00000322911.6_Missense_Mutation_p.C112Y|MTHFSD_ENST00000543303.2_Missense_Mutation_p.C112Y|MTHFSD_ENST00000546093.1_De_novo_Start_OutOfFrame|MTHFSD_ENST00000381214.5_Missense_Mutation_p.C113Y|MTHFSD_ENST00000568037.1_5'UTR	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	113							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						AGAGGTGGCACATTTTCTCAA	0.458																																					p.C113Y		Atlas-SNP	.											.	MTHFSD	52	.	0			c.G338A						.						143	138	140					16																	86582083		1902	4106	6008	SO:0001583	missense	64779	exon4			GTGGCACATTTTC	AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"RNA binding motif (RRM) containing"	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.338G>A	chr16.hg19:g.86582083C>T	ENSP00000354152:p.Cys113Tyr	117.0	0.0		69.0	43.0	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Missense_Mutation	SNP	ENST00000360900.6	hg19	CCDS54047.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.381718	0.82792	.	.	ENSG00000103248	ENST00000543303;ENST00000381214;ENST00000360900;ENST00000322911	T;T;T	0.38077	1.16;1.16;1.16	4.98	4.98	0.66077	5-formyltetrahydrofolate cyclo-ligase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.64472	0.2601	M	0.84511	2.7	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.71241	-0.4651	10	0.87932	D	0	-2.1684	15.4266	0.75055	0.0:1.0:0.0:0.0	.	113;112;113;112	E9PAM1;B7ZLC0;Q2M296;Q2M296-2	.;.;MTHSD_HUMAN;.	Y	111;113;113;112	ENSP00000370612:C113Y;ENSP00000354152:C113Y;ENSP00000326777:C112Y	ENSP00000326777:C112Y	C	-	2	0	MTHFSD	85139584	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.860000	0.75473	2.323000	0.78572	0.655000	0.94253	TGT	.	.		0.458	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764		T	86582083	C	T	86582083	3	4	192	1	0	0	0	0	1	0	0	0	9942	478	17	3	833	3	MTHFSD	16	86582083	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10		86582083	3772670	49	28422										
PRPF8	10594	hgsc.bcm.edu	37	chr17	1582362	1582362	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ttgaagttgtagtccaggtgCaggtagttgaggtttttgcg	15	4	0	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr17:1582362C>A	ENST00000572621.1	-	10	1813	c.1548G>T	c.(1546-1548)ctG>ctT	p.L516L	PRPF8_ENST00000304992.6_Silent_p.L516L			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	516					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		AGTCCAGGTGCAGGTAGTTGA	0.557																																					p.L516L		Atlas-SNP	.											.	PRPF8	169	.	0			c.G1548T						.						189	170	177					17																	1582362		2203	4300	6503	SO:0001819	synonymous_variant	10594	exon11			CAGGTGCAGGTAG	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.1548G>T	chr17.hg19:g.1582362C>A		56.0	0.0		55.0	29.0	NM_006445	O14547|O75965	Silent	SNP	ENST00000572621.1	hg19	CCDS11010.1																																																																																			.	.		0.557	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			A	1582362	C	A	1582362	2	1	192	1	0	0	0	0	0	0	0	1	12587	697	25	3		3	PRPF8	17	1582362	Silent	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10		1582362	79612848	50	28423										
MYH13	8735	hgsc.bcm.edu	37	chr17	10210383	10210383	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tatttatcaggcttgtgttcTacaagaagaattagatatca	7	5	3	3			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr17:10210383T>C	ENST00000418404.3	-	35	5333		c.e35-2		RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Splice_Site			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle						cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						GCTTGTGTTCTACAAGAAGAA	0.483																																					.		Atlas-SNP	.											MYH13_ENST00000252172,NS,carcinoma,0,2	MYH13	533	.	0			c.5170-2A>G						.						58	59	59					17																	10210383		2114	4236	6350	SO:0001630	splice_region_variant	8735	exon37			GTGTTCTACAAGA	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.5170-2A>G	chr17.hg19:g.10210383T>C		58.0	0.0		43.0	17.0	NM_003802	O95252|Q9P0U8	Splice_Site	SNP	ENST00000418404.3	hg19	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.663739	0.47572	.	.	ENSG00000006788	ENST00000252172	.	.	.	4.21	4.21	0.49690	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7593	0.62956	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYH13	10151108	1.000000	0.71417	0.995000	0.50966	0.445000	0.32107	7.831000	0.86748	1.895000	0.54865	0.460000	0.39030	.	.	.		0.483	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	Intron	C	10210383	T	C	10210383	5	2	192	1	0	0	0	0	0	0	1	0	10041	1536	53	2	672	2	MYH13	17	10210383	Splice_Site	SNP	T	TCGA-DD-AADJ-01A-11D-A40R-10	8628021	10210383	70984827	51	28424										
PPAN	56342	hgsc.bcm.edu	37	chr19	10220893	10220893	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ctggccgtggcaacatgcggGcccagcagagtgcagtgcgg	17	12	0	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr19:10220893G>C	ENST00000253107.7	+	8	899	c.793G>C	c.(793-795)Gcc>Ccc	p.A265P	PPAN_ENST00000393793.1_Missense_Mutation_p.A212P|PPAN_ENST00000556468.1_Missense_Mutation_p.A265P|PPAN-P2RY11_ENST00000428358.1_Missense_Mutation_p.A265P|SNORD105B_ENST00000458770.1_RNA|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.A265P|P2RY11_ENST00000321826.4_5'Flank|SNORD105_ENST00000386910.1_RNA	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	265	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|liver(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			CAACATGCGGGCCCAGCAGAG	0.697																																					p.A265P		Atlas-SNP	.											.	PPAN	43	.	0			c.G793C						.						20	25	23					19																	10220893		2203	4297	6500	SO:0001583	missense	56342	exon8			ATGCGGGCCCAGC	BC033202	CCDS12225.1	19p13.2	2008-02-05	2001-11-28		ENSG00000130810	ENSG00000130810			9227	protein-coding gene	gene with protein product		607793	"peter pan (Drosophila) homolog"			10873382	Standard	NM_020230		Approved	SSF1, SSF2, SSF, BXDC3		Q9NQ55	OTTHUMG00000156826	ENST00000253107.7:c.793G>C	chr19.hg19:g.10220893G>C	ENSP00000253107:p.Ala265Pro	103.0	0.0		106.0	43.0	NM_020230	C9J3F9|Q9BW97|Q9H170	Missense_Mutation	SNP	ENST00000253107.7	hg19	CCDS12225.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.475172	0.43942	.	.	ENSG00000243207;ENSG00000243207;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810	ENST00000428358;ENST00000393796;ENST00000253107;ENST00000556468;ENST00000342696;ENST00000393793;ENST00000446223	T;T;T;T;T	0.63096	1.43;-0.02;1.45;-0.02;1.45	4.82	4.82	0.62117	Brix domain (3);	.	.	.	.	T	0.68924	0.3054	L	0.35288	1.05	0.50813	D	0.999898	D;D;D	0.76494	0.999;0.996;0.998	D;D;D	0.70487	0.969;0.92;0.955	T	0.66272	-0.5965	9	0.28530	T	0.3	-31.3739	16.6942	0.85330	0.0:0.0:1.0:0.0	.	265;265;265	C9J3F9;C9JW41;Q9NQ55	.;.;SSF1_HUMAN	P	265;265;265;265;265;212;203	ENSP00000411918:A265P;ENSP00000377385:A265P;ENSP00000253107:A265P;ENSP00000450710:A265P;ENSP00000377382:A212P	ENSP00000253107:A265P	A	+	1	0	PPAN;PPAN-P2RY11	10081893	1.000000	0.71417	0.996000	0.52242	0.015000	0.08874	4.111000	0.57838	2.226000	0.72624	0.561000	0.74099	GCC	.	.		0.697	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230		C	10220893	G	C	10220893	3	2	192	1	0	0	0	0	1	0	0	0	12297	1203	42	4	823	4	PPAN	19	10220893	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10		10220893	48908090	52	28425										
ZNF420	147923	hgsc.bcm.edu	37	chr19	37618604	37618604	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gcctttattcgtagctcacaActtacccgacatcaaaaagt	5	12	2	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr19:37618604A>C	ENST00000337995.3	+	5	926	c.711A>C	c.(709-711)caA>caC	p.Q237H	ZNF420_ENST00000304239.7_Missense_Mutation_p.Q237H|CTC-454I21.4_ENST00000587645.1_RNA|ZNF585A_ENST00000588723.1_Intron	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	237					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTAGCTCACAACTTACCCGAC	0.358																																					p.Q237H		Atlas-SNP	.											.	ZNF420	71	.	0			c.A711C						.						58	62	61					19																	37618604		2203	4300	6503	SO:0001583	missense	147923	exon5			CTCACAACTTACC	AK056695	CCDS12498.1	19q13.12	2013-01-08			ENSG00000197050	ENSG00000197050		"Zinc fingers, C2H2-type", "-"	20649	protein-coding gene	gene with protein product							Standard	NM_144689		Approved	FLJ32191	uc002ofl.3	Q8TAQ5	OTTHUMG00000048168	ENST00000337995.3:c.711A>C	chr19.hg19:g.37618604A>C	ENSP00000338770:p.Gln237His	88.0	0.0		62.0	18.0	NM_144689	B2RDY6|Q96ML5	Missense_Mutation	SNP	ENST00000337995.3	hg19	CCDS12498.1	.	.	.	.	.	.	.	.	.	.	A	9.405	1.079001	0.20227	.	.	ENSG00000197050	ENST00000304239;ENST00000337995	T;T	0.03889	3.77;3.77	3.98	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.13352	0.335	0.09310	N	1	B	0.16166	0.016	B	0.17433	0.018	T	0.47886	-0.9082	9	0.07030	T	0.85	.	4.9572	0.14048	0.702:0.1892:0.1088:0.0	.	237	Q8TAQ5	ZN420_HUMAN	H	237	ENSP00000306102:Q237H;ENSP00000338770:Q237H	ENSP00000306102:Q237H	Q	+	3	2	ZNF420	42310444	0.000000	0.05858	0.999000	0.59377	0.984000	0.73092	-1.673000	0.01951	1.663000	0.50791	0.533000	0.62120	CAA	.	.		0.358	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109587.3	NM_144689		C	37618604	A	C	37618604	3	2	192	1	0	0	0	0	1	0	0	0	17912	40	2	5	721	5	ZNF420	19	37618604	Missense_Mutation	SNP	A	TCGA-DD-AADJ-01A-11D-A40R-10	27397711	37618604	21510379	53	28426										
CYP2B6	1555	hgsc.bcm.edu	37	chr19	41497305	41497305	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cacccatgaccgcctcccacCagggccccgccctctgcccc	7	25	1	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr19:41497305C>T	ENST00000324071.4	+	1	102	c.95C>T	c.(94-96)cCa>cTa	p.P32L		NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	32					cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	CGCCTCCCACCAGGGCCCCGC	0.567																																					p.P32L		Atlas-SNP	.											.	CYP2B6	79	.	0			c.C95T						.						164	178	173					19																	41497305		2203	4300	6503	SO:0001583	missense	1555	exon1			TCCCACCAGGGCC	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"Cytochrome P450s"	2615	protein-coding gene	gene with protein product		123930	"cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6", "cytochrome P450, family 2, subfamily B", "cytochrome P450, subfamily IIB (phenobarbital-inducible)"	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.95C>T	chr19.hg19:g.41497305C>T	ENSP00000324648:p.Pro32Leu	84.0	0.0		88.0	37.0	NM_000767	B4DWP3|Q2V565|Q9UK46	Missense_Mutation	SNP	ENST00000324071.4	hg19	CCDS12570.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344124	0.61073	.	.	ENSG00000197408	ENST00000324071	T	0.09073	3.02	3.1	3.1	0.35709	.	0.000000	0.85682	U	0.000000	T	0.37732	0.1014	H	0.96080	3.765	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.50558	-0.8814	10	0.87932	D	0	.	9.8656	0.41140	0.0:1.0:0.0:0.0	.	32	P20813	CP2B6_HUMAN	L	32	ENSP00000324648:P32L	ENSP00000324648:P32L	P	+	2	0	CYP2B6	46189145	0.295000	0.24389	0.901000	0.35422	0.142000	0.21351	3.165000	0.50778	1.746000	0.51805	0.298000	0.19748	CCA	.	.		0.567	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767		T	41497305	C	T	41497305	3	4	192	1	0	0	0	0	1	0	0	0	4166	594	21	3	97	3	CYP2B6	19	41497305	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10	3878701	41497305	17631678	54	28427										
ZNF331	55422	hgsc.bcm.edu	37	chr19	54080094	54080094	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gtacgcttgaaagaccacagCgctccagagggaggtatgtc	13	10	0	3			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr19:54080094C>A	ENST00000253144.9	+	7	1613	c.280C>A	c.(280-282)Cgc>Agc	p.R94S	ZNF331_ENST00000511154.1_Missense_Mutation_p.R94S|ZNF331_ENST00000449416.1_Missense_Mutation_p.R94S|ZNF331_ENST00000511593.2_Missense_Mutation_p.R94S|ZNF331_ENST00000411977.2_Missense_Mutation_p.R94S|ZNF331_ENST00000512387.1_Missense_Mutation_p.R94S|ZNF331_ENST00000513265.1_Missense_Mutation_p.R94S|ZNF331_ENST00000513999.1_Missense_Mutation_p.R94S	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	94					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		AAGACCACAGCGCTCCAGAGG	0.423			T	?	follicular thyroid adenoma																																p.R94S		Atlas-SNP	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	.	ZNF331	66	.	0			c.C280A						.						83	85	84					19																	54080094		2203	4300	6503	SO:0001583	missense	55422	exon5			CCACAGCGCTCCA	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"Zinc fingers, C2H2-type", "-"	15489	protein-coding gene	gene with protein product	"rearranged in thyroid adenomas"	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.280C>A	chr19.hg19:g.54080094C>A	ENSP00000253144:p.Arg94Ser	193.0	0.0		202.0	97.0	NM_001253801	Q96GJ4	Missense_Mutation	SNP	ENST00000253144.9	hg19	CCDS33102.1	.	.	.	.	.	.	.	.	.	.	C	4.582	0.108157	0.08780	.	.	ENSG00000130844	ENST00000253144;ENST00000511593;ENST00000449416;ENST00000514374;ENST00000411977;ENST00000511154;ENST00000513999;ENST00000512387;ENST00000511567;ENST00000514022;ENST00000505949;ENST00000513265	T;T;T;T;T;T;T;T;T;T;T;T	0.08008	3.3;3.3;3.3;5.2;3.3;3.3;3.3;3.3;5.23;3.36;3.14;5.18	3.55	-0.634	0.11516	.	0.779502	0.10484	N	0.669185	T	0.03477	0.0100	N	0.17474	0.49	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.46596	-0.9180	10	0.08599	T	0.76	.	1.6109	0.02693	0.1355:0.2869:0.3966:0.181	.	94	Q9NQX6	ZN331_HUMAN	S	94	ENSP00000253144:R94S;ENSP00000427439:R94S;ENSP00000393817:R94S;ENSP00000424835:R94S;ENSP00000393336:R94S;ENSP00000421014:R94S;ENSP00000423156:R94S;ENSP00000421728:R94S;ENSP00000426127:R94S;ENSP00000422471:R94S;ENSP00000427532:R94S;ENSP00000426458:R94S	ENSP00000253144:R94S	R	+	1	0	ZNF331	58771906	0.001000	0.12720	0.001000	0.08648	0.074000	0.17049	0.994000	0.29693	0.244000	0.21351	0.467000	0.42956	CGC	.	.		0.423	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555		A	54080094	C	A	54080094	3	1	192	1	0	0	0	0	1	0	0	0	17864	768	27	1	290	1	ZNF331	19	54080094	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10	12582789	54080094	5048889	55	28428										
PCSK2	5126	hgsc.bcm.edu	37	chr20	17462588	17462588	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gctgcatggcactcagagtgCcccgtacatcgaccaggtgg	13	13	1	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr20:17462588C>T	ENST00000262545.2	+	12	2105	c.1790C>T	c.(1789-1791)gCc>gTc	p.A597V	PCSK2_ENST00000377899.1_Missense_Mutation_p.A578V|PCSK2_ENST00000536609.1_Missense_Mutation_p.A562V|PCSK2_ENST00000459871.1_3'UTR	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	597					cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""Insulin(DB00071)|Insulin Regular(DB00030)"	ACTCAGAGTGCCCCGTACATC	0.622																																					p.A597V		Atlas-SNP	.											.	PCSK2	112	.	0			c.C1790T						.						33	30	31					20																	17462588		2203	4300	6503	SO:0001583	missense	5126	exon12			AGAGTGCCCCGTA	AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"neuroendocrine convertase 2", "KEX2-like endoprotease 2"	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.1790C>T	chr20.hg19:g.17462588C>T	ENSP00000262545:p.Ala597Val	101.0	0.0		98.0	29.0	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	hg19	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.196933	0.79015	.	.	ENSG00000125851	ENST00000377899;ENST00000262545;ENST00000536609	T;T;T	0.64260	-0.09;-0.09;-0.09	5.47	5.47	0.80525	Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.68063	0.2960	L	0.52573	1.65	0.80722	D	1	P;P;P	0.48230	0.907;0.82;0.515	P;P;B	0.51229	0.663;0.652;0.265	T	0.67043	-0.5770	10	0.44086	T	0.13	-35.8095	18.2492	0.89997	0.0:1.0:0.0:0.0	.	562;578;597	B4DFQ3;B1ANH9;P16519	.;.;NEC2_HUMAN	V	578;597;562	ENSP00000367131:A578V;ENSP00000262545:A597V;ENSP00000437458:A562V	ENSP00000262545:A597V	A	+	2	0	PCSK2	17410588	1.000000	0.71417	0.995000	0.50966	0.666000	0.39218	7.745000	0.85046	2.718000	0.92993	0.460000	0.39030	GCC	.	.		0.622	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		T	17462588	C	T	17462588	3	4	192	1	0	0	0	0	1	0	0	0	11610	739	26	3	1836	3	PCSK2	20	17462588	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10		17462588	45562932	56	28429										
PLTP	5360	hgsc.bcm.edu	37	chr20	44538643	44538643	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	gaggcattggtgatttgaagCatcagctcctgctgtggctg	14	8	1	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr20:44538643C>T	ENST00000477313.1	-	3	861	c.267G>A	c.(265-267)atG>atA	p.M89I	PLTP_ENST00000372431.3_Missense_Mutation_p.M89I|PLTP_ENST00000420868.2_Intron|PLTP_ENST00000542937.1_Missense_Mutation_p.M109I|PLTP_ENST00000372420.1_Start_Codon_SNP_p.M1I|PLTP_ENST00000354050.4_Missense_Mutation_p.M89I			P55058	PLTP_HUMAN	phospholipid transfer protein	89					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)			endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				TGATTTGAAGCATCAGCTCCT	0.577																																					p.M89I		Atlas-SNP	.											.	PLTP	49	.	0			c.G267A						.						78	69	72					20																	44538643		2203	4300	6503	SO:0001583	missense	5360	exon4			TTGAAGCATCAGC	L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.267G>A	chr20.hg19:g.44538643C>T	ENSP00000417138:p.Met89Ile	93.0	0.0		76.0	37.0	NM_182676	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Missense_Mutation	SNP	ENST00000477313.1	hg19	CCDS13386.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.611057	0.28712	.	.	ENSG00000100979	ENST00000372420;ENST00000372431;ENST00000354050;ENST00000477313;ENST00000542937	T;T;T;T;T	0.08720	3.06;3.54;3.54;3.54;3.54	4.83	0.0155	0.14104	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.311570	0.04496	N	0.380476	T	0.05410	0.0143	N	0.14661	0.345	0.21445	N	0.999686	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.08055	0.001;0.002;0.001;0.002;0.003	T	0.40289	-0.9571	10	0.35671	T	0.21	-0.2718	5.2344	0.15439	0.1115:0.4473:0.3514:0.0899	.	1;89;89;89;109	B4DDD5;Q53H91;P55058-2;P55058;B3KUE5	.;.;.;PLTP_HUMAN;.	I	1;89;89;89;109	ENSP00000361497:M1I;ENSP00000361508:M89I;ENSP00000335290:M89I;ENSP00000417138:M89I;ENSP00000440296:M109I	ENSP00000335290:M89I	M	-	3	0	PLTP	43972050	0.232000	0.23762	0.013000	0.15412	0.939000	0.58152	0.278000	0.18753	0.251000	0.21505	0.555000	0.69702	ATG	.	.		0.577	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		T	44538643	C	T	44538643	3	4	192	1	0	0	0	0	1	0	0	0	12123	710	25	3	1266	3	PLTP	20	44538643	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10	27076055	44538643	18486877	57	28430										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41551019	41551019	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tctctgagcagaatcccaggAgtcttttgggttttgttttt	10	7	2	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr21:41551019A>G	ENST00000400454.1	-	15	3259	c.2782T>C	c.(2782-2784)Tcc>Ccc	p.S928P		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	928	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GAATCCCAGGAGTCTTTTGGG	0.413																																					p.S928P	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.T2782C						.						123	116	119					21																	41551019		1851	4097	5948	SO:0001583	missense	1826	exon15			CCCAGGAGTCTTT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.2782T>C	chr21.hg19:g.41551019A>G	ENSP00000383303:p.Ser928Pro	95.0	0.0		126.0	47.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.525017	0.44969	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.56941	0.43;0.43	4.5	4.5	0.54988	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.061145	0.64402	D	0.000002	T	0.42154	0.1190	L	0.35793	1.09	0.44188	D	0.997005	B	0.21071	0.051	B	0.18871	0.023	T	0.26608	-1.0098	10	0.25106	T	0.35	.	13.7728	0.63036	1.0:0.0:0.0:0.0	.	928	O60469	DSCAM_HUMAN	P	928;680	ENSP00000383303:S928P;ENSP00000385342:S680P	ENSP00000383303:S928P	S	-	1	0	DSCAM	40472889	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.788000	0.62439	1.792000	0.52537	0.459000	0.35465	TCC	.	.		0.413	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		G	41551019	A	G	41551019	3	3	192	1	0	0	0	0	1	0	0	0	4770	304	11	2	3332	2	DSCAM	21	41551019	Missense_Mutation	SNP	A	TCGA-DD-AADJ-01A-11D-A40R-10		41551019	6578876	58	28431										
ARVCF	421	hgsc.bcm.edu	37	chr22	19965537	19965537	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cagggcatgcaggagcgcgtCcaccagcccttcacactccc	10	18	1	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chr22:19965537C>A	ENST00000263207.3	-	8	1933	c.1642G>T	c.(1642-1644)Gac>Tac	p.D548Y	ARVCF_ENST00000401994.1_Missense_Mutation_p.D485Y|ARVCF_ENST00000344269.3_Missense_Mutation_p.D485Y|ARVCF_ENST00000406522.1_Missense_Mutation_p.D485Y|ARVCF_ENST00000406259.1_Missense_Mutation_p.D548Y	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	548					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					AGGAGCGCGTCCACCAGCCCT	0.657																																					p.D548Y		Atlas-SNP	.											.	ARVCF	54	.	0			c.G1642T						.						59	51	54					22																	19965537		2202	4299	6501	SO:0001583	missense	421	exon8			GCGCGTCCACCAG		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"Armadillo repeat containing"	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.1642G>T	chr22.hg19:g.19965537C>A	ENSP00000263207:p.Asp548Tyr	50.0	0.0		55.0	21.0	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	hg19	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.700964	0.88924	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42;-1.42	4.03	4.03	0.46877	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.91222	0.7234	M	0.89534	3.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.982	D	0.92728	0.6197	9	.	.	.	-17.5944	17.0615	0.86548	0.0:1.0:0.0:0.0	.	548;70	O00192;E7EV58	ARVC_HUMAN;.	Y	548;485;485;485;548	ENSP00000263207:D548Y;ENSP00000342042:D485Y;ENSP00000384341:D485Y;ENSP00000384732:D485Y;ENSP00000385444:D548Y	.	D	-	1	0	ARVCF	18345537	1.000000	0.71417	0.988000	0.46212	0.849000	0.48306	7.276000	0.78559	2.541000	0.85698	0.655000	0.94253	GAC	.	.		0.657	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		A	19965537	C	A	19965537	3	1	192	1	0	0	0	0	1	0	0	0	1003	855	30	3	1294	3	ARVCF	22	19965537	Missense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10		19965537	31339029	59	28432										
TIMP1	7076	hgsc.bcm.edu	37	chrX	47445002	47445002	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ttttgtggctccctggaacaGcctgagcttagctcagcgcc	11	13	1	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chrX:47445002G>T	ENST00000218388.4	+	5	559	c.389G>T	c.(388-390)aGc>aTc	p.S130I	TIMP1_ENST00000456754.2_3'UTR|TIMP1_ENST00000377017.1_Missense_Mutation_p.S66I|TIMP1_ENST00000377018.2_Missense_Mutation_p.S124I|SYN1_ENST00000340666.4_Intron|MIR4769_ENST00000584126.1_RNA|SYN1_ENST00000295987.7_Intron	NM_003254.2	NP_003245.1	P01033	TIMP1_HUMAN	TIMP metallopeptidase inhibitor 1	130	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				aging (GO:0007568)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of trophoblast cell migration (GO:1901164)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell proliferation (GO:0008284)|regulation of integrin-mediated signaling pathway (GO:2001044)|response to cytokine (GO:0034097)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	cytokine activity (GO:0005125)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|large_intestine(2)	3						CCCTGGAACAGCCTGAGCTTA	0.577																																					p.S130I		Atlas-SNP	.											.	TIMP1	12	.	0			c.G389T						.						44	36	39					X																	47445002		2203	4299	6502	SO:0001583	missense	7076	exon5			GGAACAGCCTGAG		CCDS14281.1	Xp11.3-p11.23	2008-07-29	2005-08-08		ENSG00000102265	ENSG00000102265			11820	protein-coding gene	gene with protein product		305370	"tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor)"	TIMP, CLGI			Standard	XM_005272645		Approved	EPO	uc004dif.3	P01033	OTTHUMG00000021447	ENST00000218388.4:c.389G>T	chrX.hg19:g.47445002G>T	ENSP00000218388:p.Ser130Ile	173.0	0.0		197.0	84.0	NM_003254	Q14252|Q9UCU1	Missense_Mutation	SNP	ENST00000218388.4	hg19	CCDS14281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	14.55|14.55	2.569732|2.569732	0.45798|0.45798	.|.	.|.	ENSG00000102265|ENSG00000102265	ENST00000445623|ENST00000218388;ENST00000377018;ENST00000377017	.|D;D;D	.|0.94723	.|-3.5;-3.5;-3.5	5.29|5.29	3.5|3.5	0.40072|0.40072	.|Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);	.|0.357239	.|0.27306	.|N	.|0.019961	D|D	0.95828|0.95828	0.8642|0.8642	M|M	0.84326|0.84326	2.69|2.69	0.26318|0.26318	N|N	0.977729|0.977729	.|D;D	.|0.63046	.|0.977;0.992	.|P;P	.|0.59424	.|0.857;0.777	D|D	0.90051|0.90051	0.4149|0.4149	5|10	.|0.49607	.|T	.|0.09	.|.	6.4938|6.4938	0.22130|0.22130	0.1008:0.1792:0.72:0.0|0.1008:0.1792:0.72:0.0	.|.	.|124;130	.|B4DJK3;P01033	.|.;TIMP1_HUMAN	S|I	88|130;124;66	.|ENSP00000218388:S130I;ENSP00000366217:S124I;ENSP00000366216:S66I	.|ENSP00000218388:S130I	A|S	+|+	1|2	0|0	TIMP1|TIMP1	47329946|47329946	0.590000|0.590000	0.26815|0.26815	0.373000|0.373000	0.26003|0.26003	0.408000|0.408000	0.30992|0.30992	1.231000|1.231000	0.32624|0.32624	0.450000|0.450000	0.26774|0.26774	0.519000|0.519000	0.50382|0.50382	GCC|AGC	.	.		0.577	TIMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056423.1	NM_003254		T	47445002	G	T	47445002	3	4	192	1	0	0	0	0	1	0	0	0	15932	971	34	3	403	3	TIMP1	23	47445002	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10		47445002	107825558	60	28433										
PQBP1	10084	hgsc.bcm.edu	37	chrX	48759212	48759212	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	cctgcggccccacagcgggcTcccttactactggaatgcag	11	16	0	0			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chrX:48759212T>G	ENST00000376563.1	+	4	385	c.185T>G	c.(184-186)cTc>cGc	p.L62R	PQBP1_ENST00000447146.2_Missense_Mutation_p.L62R|PQBP1_ENST00000376566.4_Missense_Mutation_p.L62R|PQBP1_ENST00000218224.4_Missense_Mutation_p.L62R|PQBP1_ENST00000247140.4_Missense_Mutation_p.L62R|PQBP1_ENST00000473764.1_3'UTR|PQBP1_ENST00000396763.1_Missense_Mutation_p.L62R	NM_001032381.1|NM_001032382.1|NM_001032383.1|NM_001167989.1	NP_001027553.1|NP_001027554.1|NP_001027555.1|NP_001161461.1	O60828	PQBP1_HUMAN	polyglutamine binding protein 1	62	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				alternative mRNA splicing, via spliceosome (GO:0000380)|neuron projection development (GO:0031175)|regulation of dendrite morphogenesis (GO:0048814)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|neuronal ribonucleoprotein granule (GO:0071598)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ribonucleoprotein complex binding (GO:0043021)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(2)	11						CACAGCGGGCTCCCTTACTAC	0.552																																					p.L62R		Atlas-SNP	.											.	PQBP1	24	.	0			c.T185G						.						77	65	69					X																	48759212		2203	4300	6503	SO:0001583	missense	10084	exon4			GCGGGCTCCCTTA	AJ005893	CCDS14309.1, CCDS55412.1	Xp11.23	2014-01-31			ENSG00000102103	ENSG00000102103			9330	protein-coding gene	gene with protein product		300463	"Sutherland-Haan X-linked mental retardation syndrome", "mental retardation, X-linked 55", "mental retardation, X-linked 2 (non-dysmorphic)"	RENS1, MRXS8, SHS, MRX55, MRX2		9875212, 15024694, 14634649	Standard	NM_144495		Approved		uc004dlg.3	O60828	OTTHUMG00000024128	ENST00000376563.1:c.185T>G	chrX.hg19:g.48759212T>G	ENSP00000365747:p.Leu62Arg	98.0	0.0		105.0	28.0	NM_001167989	Q4VY25|Q4VY26|Q4VY27|Q4VY29|Q4VY30|Q4VY34|Q4VY35|Q4VY36|Q4VY37|Q4VY38|Q9GZP2|Q9GZU4|Q9GZZ4	Missense_Mutation	SNP	ENST00000376563.1	hg19	CCDS14309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	5.812|5.812	0.334103|0.334103	0.11013|0.11013	.|.	.|.	ENSG00000102103|ENSG00000102103	ENST00000376563;ENST00000376566;ENST00000447146;ENST00000247140;ENST00000218224;ENST00000396763;ENST00000443648|ENST00000456306	T;T;T;T;T;T;T|.	0.75477|.	-0.94;-0.94;-0.94;-0.94;-0.94;-0.94;-0.94|.	5.24|5.24	5.24|5.24	0.73138|0.73138	WW/Rsp5/WWP (5);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.38825|0.38825	0.1055|0.1055	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	D|D	1|1	D;D;D;D;D;B;D;D|.	0.89917|.	0.991;1.0;0.999;1.0;0.999;0.045;1.0;0.999|.	D;D;D;D;D;B;D;D|.	0.97110|.	0.991;1.0;0.962;0.996;0.997;0.041;1.0;0.998|.	T|T	0.28170|0.28170	-1.0052|-1.0052	10|5	0.21014|.	T|.	0.42|.	-21.4748|-21.4748	11.5564|11.5564	0.50750|0.50750	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	62;62;62;62;62;62;62;62|.	O60828-5;O60828-6;O60828-2;C9JQA1;O60828-7;O60828-4;O60828-3;O60828|.	.;.;.;.;.;.;.;PQBP1_HUMAN|.	R|A	62|51	ENSP00000365747:L62R;ENSP00000365750:L62R;ENSP00000391759:L62R;ENSP00000247140:L62R;ENSP00000218224:L62R;ENSP00000379985:L62R;ENSP00000414861:L62R|.	ENSP00000218224:L62R|.	L|S	+|+	2|1	0|0	PQBP1|PQBP1	48644156|48644156	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.981000|0.981000	0.71138|0.71138	6.723000|6.723000	0.74742|0.74742	1.928000|1.928000	0.55862|0.55862	0.486000|0.486000	0.48141|0.48141	CTC|TCC	.	.		0.552	PQBP1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060777.1	NM_001032381.1		G	48759212	T	G	48759212	3	3	192	1	0	0	0	0	1	0	0	0	12429	1551	54	5	195	5	PQBP1	23	48759212	Missense_Mutation	SNP	T	TCGA-DD-AADJ-01A-11D-A40R-10	1314210	48759212	106511348	61	28434										
CACNA1F	778	hgsc.bcm.edu	37	chrX	49072969	49072969	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ccgtgacacgtctccatctgGgtataccaggaaggagcccc	11	14	2	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chrX:49072969G>C	ENST00000376265.2	-	27	3203	c.3142C>G	c.(3142-3144)Cca>Gca	p.P1048A	CACNA1F_ENST00000323022.5_Missense_Mutation_p.P1037A|CACNA1F_ENST00000376251.1_Missense_Mutation_p.P983A	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1048					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	TCTCCATCTGGGTATACCAGG	0.572																																					p.P1048A		Atlas-SNP	.											.	CACNA1F	218	.	0			c.C3142G						.						50	40	43					X																	49072969		2202	4299	6501	SO:0001583	missense	778	exon27			CATCTGGGTATAC	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1393	protein-coding gene	gene with protein product		300110	"Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.3142C>G	chrX.hg19:g.49072969G>C	ENSP00000365441:p.Pro1048Ala	250.0	0.0		299.0	112.0	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	hg19	CCDS35253.1	.	.	.	.	.	.	.	.	.	.	.	10.64	1.408420	0.25378	.	.	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	D;D;D	0.96232	-3.95;-3.88;-3.88	4.76	4.76	0.60689	Ion transport (1);	0.469861	0.24400	N	0.038846	D	0.94830	0.8330	L	0.49640	1.575	0.32183	N	0.580176	B;B	0.32467	0.372;0.302	B;B	0.40864	0.121;0.342	D	0.96039	0.9023	10	0.62326	D	0.03	.	9.7757	0.40618	0.0:0.0:0.6597:0.3403	.	1037;1048	F5CIQ9;O60840	.;CAC1F_HUMAN	A	983;1037;1048	ENSP00000365427:P983A;ENSP00000321618:P1037A;ENSP00000365441:P1048A	ENSP00000321618:P1037A	P	-	1	0	CACNA1F	48959913	1.000000	0.71417	0.946000	0.38457	0.513000	0.34164	2.113000	0.41902	1.940000	0.56252	0.513000	0.50165	CCA	.	.		0.572	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		C	49072969	G	C	49072969	3	2	192	1	0	0	0	0	1	0	0	0	2545	1232	43	4	2879	4	CACNA1F	23	49072969	Missense_Mutation	SNP	G	TCGA-DD-AADJ-01A-11D-A40R-10	313757	49072969	106197591	62	28435										
ARMCX6	54470	hgsc.bcm.edu	37	chrX	100870760	100870760	+	Frame_Shift_Del	DEL	A	A	-													0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tgtttccatttctgataaagAgggacatgaatgagaagagc					rs111444743		TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chrX:100870760delA	ENST00000361910.4	-	3	1195	c.851delT	c.(850-852)ctcfs	p.L284fs	ARMCX6_ENST00000539247.1_Frame_Shift_Del_p.L284fs|ARMCX6_ENST00000538627.1_Frame_Shift_Del_p.L284fs|ARMCX6_ENST00000497931.1_Intron	NM_019007.3	NP_061880.2	Q7L4S7	ARMX6_HUMAN	armadillo repeat containing, X-linked 6	284						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|liver(2)|lung(3)	9						TCTGATAAAGAGGGACATGAA	0.517																																					p.L284fs		Atlas-INDEL	.											.	ARMCX6	21	.	0			c.852delC						.						1	1	1					X																	100870760		44	103	147	SO:0001589	frameshift_variant	54470	exon3			.	BC007677	CCDS14488.1	Xq21.33-q22.3	2014-03-21			ENSG00000198960	ENSG00000198960		"Armadillo repeat containing"	26094	protein-coding gene	gene with protein product						16221301, 22569362	Standard	NM_001184768		Approved	FLJ20811, GASP10	uc004ehy.3	Q7L4S7	OTTHUMG00000022034	ENST00000361910.4:c.851delT	chrX.hg19:g.100870760delA	ENSP00000354708:p.Leu284fs	125.0	0.0		158.0	25.0	NM_019007	Q9NWJ3	Frame_Shift_Del	DEL	ENST00000361910.4	hg19	CCDS14488.1																																																																																			.	.		0.517	ARMCX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057562.1	NM_019007		-	100870760	A	-	100870760	7	5	192	1	0	1	0	1	0	0	0	0	963	304	11	0	55	0	ARMCX6	23	100870760	Frame_Shift_Del	DEL	A	TCGA-DD-AADJ-01A-11D-A40R-10	51797791	100870760	54399800	63	28436										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	104984619	104984619	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	tgtggaagctgacctggcgaAttatacctgccatgttgaaa	11	8	0	2			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chrX:104984619A>T	ENST00000372582.1	+	8	1739	c.983A>T	c.(982-984)aAt>aTt	p.N328I	IL1RAPL2_ENST00000344799.4_Missense_Mutation_p.N328I	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	328	Ig-like C2-type 3.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GACCTGGCGAATTATACCTGC	0.388																																					p.N328I		Atlas-SNP	.											.	IL1RAPL2	105	.	0			c.A983T						.						71	65	67					X																	104984619		2203	4300	6503	SO:0001583	missense	26280	exon8			TGGCGAATTATAC	AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.983A>T	chrX.hg19:g.104984619A>T	ENSP00000361663:p.Asn328Ile	347.0	0.0		440.0	189.0	NM_017416	Q2M3U3|Q9NZN0	Missense_Mutation	SNP	ENST00000372582.1	hg19	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.404459	0.83230	.	.	ENSG00000189108	ENST00000372582;ENST00000344799	T;T	0.03689	3.84;3.84	5.88	5.88	0.94601	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.17152	0.0412	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00166	-1.1966	10	0.54805	T	0.06	.	14.2995	0.66336	1.0:0.0:0.0:0.0	.	328	Q9NP60	IRPL2_HUMAN	I	328	ENSP00000361663:N328I;ENSP00000344976:N328I	ENSP00000344976:N328I	N	+	2	0	IL1RAPL2	104871275	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	8.324000	0.90005	1.976000	0.57569	0.486000	0.48141	AAT	.	.		0.388	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		T	104984619	A	T	104984619	3	4	192	1	0	0	0	0	1	0	0	0	7671	101	4	4	1009	4	IL1RAPL2	23	104984619	Missense_Mutation	SNP	A	TCGA-DD-AADJ-01A-11D-A40R-10	4113859	104984619	50285941	64	28437										
CXorf56	63932	hgsc.bcm.edu	37	chrX	118699267	118699267	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	ctcgccgtcgtcatattcctCccggtcccgagtgtcagagc	10	16	2	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chrX:118699267C>A	ENST00000371594.4	-	1	130	c.52G>T	c.(52-54)Gag>Tag	p.E18*	CXorf56_ENST00000320339.4_5'UTR|CXorf56_ENST00000536133.1_Nonsense_Mutation_p.E18*	NM_022101.3	NP_071384.1	Q9H5V9	CX056_HUMAN	chromosome X open reading frame 56	18										cervix(1)|endometrium(2)|lung(7)	10						TCATATTCCTCCCGGTCCCGA	0.572																																					p.E18X		Atlas-SNP	.											.	CXorf56	26	.	0			c.G52T						.						74	68	70					X																	118699267		2203	4300	6503	SO:0001587	stop_gained	63932	exon1			ATTCCTCCCGGTC	AK026618	CCDS55484.1, CCDS55485.1	Xq24	2008-02-05			ENSG00000018610	ENSG00000018610			26239	protein-coding gene	gene with protein product						12477932	Standard	NM_022101		Approved	FLJ22965	uc004erk.2	Q9H5V9	OTTHUMG00000022276	ENST00000371594.4:c.52G>T	chrX.hg19:g.118699267C>A	ENSP00000360652:p.Glu18*	234.0	0.0		275.0	97.0	NM_001170570	A8MPX7|B4DQN2|D3DWH9|F5GWL7|O43351	Nonsense_Mutation	SNP	ENST00000371594.4	hg19	CCDS14579.1	.	.	.	.	.	.	.	.	.	.	C	38	7.077629	0.98048	.	.	ENSG00000018610	ENST00000486230;ENST00000371594;ENST00000536133;ENST00000476164	.	.	.	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-25.0086	15.521	0.75866	0.0:1.0:0.0:0.0	.	.	.	.	X	18	.	ENSP00000360652:E18X	E	-	1	0	CXorf56	118583295	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.026000	0.76455	1.848000	0.53677	0.591000	0.81541	GAG	.	.		0.572	CXorf56-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022101		A	118699267	C	A	118699267	4	1	192	1	0	0	0	0	0	1	0	0	4114	864	30	3	644	3	CXorf56	23	118699267	Nonsense_Mutation	SNP	C	TCGA-DD-AADJ-01A-11D-A40R-10	13714648	118699267	36571293	65	28438										
CD40LG	959	hgsc.bcm.edu	37	chrX	135741541	135741541	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0307692307692308	2	1	0.632222222222222	2.52888888888889	0.361269841269841	1	1	0	agccaagtgagccatggcacTggcttcacgtcctttggctt	11	12	1	1			TCGA-DD-AADJ-01A-11D-A40R-10	TCGA-DD-AADJ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	61b59c1e-a279-4c80-ab24-c01048f2a295	c1da5095-b907-4c39-a7b6-4c603e64b113	g.chrX:135741541T>C	ENST00000370629.2	+	5	809	c.753T>C	c.(751-753)acT>acC	p.T251T	CD40LG_ENST00000370628.2_Silent_p.T230T	NM_000074.2	NP_000065.1	P29965	CD40L_HUMAN	CD40 ligand	251					B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|immunoglobulin secretion (GO:0048305)|inflammatory response (GO:0006954)|isotype switching (GO:0045190)|leukocyte cell-cell adhesion (GO:0007159)|negative regulation of apoptotic process (GO:0043066)|platelet activation (GO:0030168)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of interleukin-12 production (GO:0032735)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	CD40 receptor binding (GO:0005174)			endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|skin(1)|stomach(1)	26	Acute lymphoblastic leukemia(192;0.000127)					GCCATGGCACTGGCTTCACGT	0.507									Immune Deficiency with Hyper-IgM																												p.T251T		Atlas-SNP	.											.	CD40LG	46	.	0			c.T753C						.						125	106	113					X																	135741541		2203	4300	6503	SO:0001819	synonymous_variant	959	exon5	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	TGGCACTGGCTTC	X67878	CCDS14659.1	Xq26	2014-09-17	2008-08-01	2005-01-14	ENSG00000102245	ENSG00000102245		"Tumor necrosis factor (ligand) superfamily", "CD molecules", "Endogenous ligands"	11935	protein-coding gene	gene with protein product	"CD40 antigen ligand", "tumor necrosis factor (ligand) superfamily member 5", "T-B cell-activating molecule", "TNF-related activation protein", "hyper-IgM syndrome"	300386	"tumor necrosis factor (ligand) superfamily, member 5 (hyper-IgM syndrome)"	HIGM1, IMD3, TNFSF5		1427881, 7678782	Standard	NM_000074		Approved	CD40L, TRAP, gp39, hCD40L, CD154	uc004faa.3	P29965	OTTHUMG00000022512	ENST00000370629.2:c.753T>C	chrX.hg19:g.135741541T>C		1240.0	2.0		1401.0	529.0	NM_000074		Silent	SNP	ENST00000370629.2	hg19	CCDS14659.1																																																																																			.	.		0.507	CD40LG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058501.1	NM_000074		C	135741541	T	C	135741541	2	2	192	1	0	0	0	0	0	0	0	1	3018	1567	55	2		2	CD40LG	23	135741541	Silent	SNP	T	TCGA-DD-AADJ-01A-11D-A40R-10	17042274	135741541	19529019	66	28439										
MTOR	2475	hgsc.bcm.edu	37	chr1	11184573	11184573	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	acctgaggtttttccgaagaGatgttgggtcattggccaga	13	7	1	3	rs587777894		TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:11184573G>T	ENST00000361445.4	-	47	6720	c.6644C>A	c.(6643-6645)tCt>tAt	p.S2215Y	MTOR_ENST00000376838.1_Missense_Mutation_p.S420Y	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2215	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		S -> Y (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.S2215Y(4)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TTTCCGAAGAGATGTTGGGTC	0.438																																					p.S2215Y		Atlas-SNP	.											MTOR,NS,malignant_melanoma,0,5	MTOR	327	.	4	Substitution - Missense(4)	large_intestine(2)|kidney(1)|endometrium(1)	c.C6644A						.						101	98	99					1																	11184573		2203	4300	6503	SO:0001583	missense	2475	exon47			CGAAGAGATGTTG	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6644C>A	chr1.hg19:g.11184573G>T	ENSP00000354558:p.Ser2215Tyr	124.0	0.0		111.0	16.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.903707	0.92035	.	.	ENSG00000198793	ENST00000361445;ENST00000376838	T;T	0.78364	-1.17;-1.17	5.8	5.8	0.92144	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.88862	0.6552	M	0.86651	2.83	0.80722	D	1	D	0.58970	0.984	P	0.60541	0.876	D	0.90182	0.4243	10	0.87932	D	0	-14.2436	18.2956	0.90145	0.0:0.0:1.0:0.0	.	2215	P42345	MTOR_HUMAN	Y	2215;420	ENSP00000354558:S2215Y;ENSP00000366034:S420Y	ENSP00000354558:S2215Y	S	-	2	0	MTOR	11107160	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.362000	0.97126	2.761000	0.94854	0.650000	0.86243	TCT	.	.		0.438	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		T	11184573	G	T	11184573	3	4	193	1	0	0	0	0	1	0	0	0	9963	942	33	3	1053	3	MTOR	1	11184573	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10		11184573	238066048	1	28440										
RIMKLA	284716	hgsc.bcm.edu	37	chr1	42865094	42865094	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ggcctccagctaaaccagaaGgccctcaccactttcccgga	8	17	1	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:42865094G>A	ENST00000431473.3	+	2	312	c.183G>A	c.(181-183)aaG>aaA	p.K61K		NM_173642.3	NP_775913.2	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family member A	61					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)			NS(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						TAAACCAGAAGGCCCTCACCA	0.532																																					p.K61K		Atlas-SNP	.											.	RIMKLA	32	.	0			c.G183A						.						47	38	41					1																	42865094		2203	4300	6503	SO:0001819	synonymous_variant	284716	exon2			CCAGAAGGCCCTC	BC039737	CCDS466.2	1p34.2	2011-09-21	2008-10-13	2008-10-13	ENSG00000177181	ENSG00000177181	6.3.2.N6		28725	protein-coding gene	gene with protein product	"N-acetylaspartylglutamate synthetase II"		"family with sequence similarity 80, member A"	FAM80A		20657015, 21454531	Standard	NM_173642		Approved	MGC47816, RP11-157D18.1, NAAGS-II	uc001chi.2	Q8IXN7	OTTHUMG00000007335	ENST00000431473.3:c.183G>A	chr1.hg19:g.42865094G>A		50.0	0.0		48.0	8.0	NM_173642	Q5VUS5	Silent	SNP	ENST00000431473.3	hg19	CCDS466.2																																																																																			.	.		0.532	RIMKLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019174.3	NM_173642		A	42865094	G	A	42865094	2	1	193	1	0	0	0	0	0	0	0	1	13380	991	35	3		3	RIMKLA	1	42865094	Silent	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10	31680521	42865094	206385527	2	28441										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103471625	103471625	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	aaatatgtgagctcctgaccTttgccccaggttctcctggc	9	13	1	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:103471625T>C	ENST00000370096.3	-	17	2102	c.1790A>G	c.(1789-1791)aAg>aGg	p.K597R	COL11A1_ENST00000358392.2_Splice_Site_p.K609R|COL11A1_ENST00000353414.4_Splice_Site_p.K558R|COL11A1_ENST00000512756.1_Splice_Site_p.K481R|COL11A1_ENST00000461720.1_5'UTR	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	597	Collagen-like 3.|Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GCTCCTGACCTTTGCCCCAGG	0.393																																					p.K609R		Atlas-SNP	.											.	COL11A1	972	.	0			c.A1826G						.						61	60	60					1																	103471625		2203	4300	6503	SO:0001630	splice_region_variant	1301	exon17			CTGACCTTTGCCC	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1791+1A>G	chr1.hg19:g.103471625T>C		197.0	0.0		253.0	45.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.087513	0.76642	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756	D;D;D;D	0.95588	-3.17;-3.17;-3.17;-3.75	6.06	6.06	0.98353	.	0.050491	0.85682	D	0.000000	D	0.92437	0.7599	L	0.29908	0.895	0.80722	D	1	P;P;P;P	0.47253	0.892;0.868;0.868;0.892	P;B;B;P	0.48488	0.579;0.443;0.443;0.579	D	0.93761	0.7067	10	0.62326	D	0.03	.	16.6093	0.84858	0.0:0.0:0.0:1.0	.	481;558;609;597	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	R	597;609;558;481	ENSP00000359114:K597R;ENSP00000351163:K609R;ENSP00000302551:K558R;ENSP00000426533:K481R	ENSP00000302551:K558R	K	-	2	0	COL11A1	103244213	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	7.571000	0.82399	2.324000	0.78689	0.533000	0.62120	AAG	.	.		0.393	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	Missense_Mutation	C	103471625	T	C	103471625	5	2	193	1	0	0	0	0	0	0	1	0	3669	1623	56	2	3834	2	COL11A1	1	103471625	Splice_Site	SNP	T	TCGA-DD-AADK-01A-11D-A40R-10	60606531	103471625	145778996	3	28442										
VANGL1	81839	hgsc.bcm.edu	37	chr1	116194093	116194093	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ttcaagtcattcgaaaaaatCtcacagacaagggtatgtaa	7	7	3	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:116194093C>A	ENST00000355485.2	+	2	330	c.59C>A	c.(58-60)tCt>tAt	p.S20Y	VANGL1_ENST00000369509.1_Missense_Mutation_p.S20Y|VANGL1_ENST00000369510.4_Missense_Mutation_p.S20Y|VANGL1_ENST00000310260.3_Missense_Mutation_p.S20Y	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	20					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TCGAAAAAATCTCACAGACAA	0.418																																					p.S20Y		Atlas-SNP	.											.	VANGL1	65	.	0			c.C59A						.						94	84	87					1																	116194093		2203	4300	6503	SO:0001583	missense	81839	exon2			AAAAATCTCACAG	AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)", "vang-like 1 (van gogh, Drosophila)"			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.59C>A	chr1.hg19:g.116194093C>A	ENSP00000347672:p.Ser20Tyr	49.0	0.0		45.0	13.0	NM_001172411	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	hg19	CCDS883.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.850129	0.71719	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.81821	-1.53;-1.54;-1.53;-1.53	4.92	4.92	0.64577	.	0.058434	0.64402	D	0.000001	T	0.81730	0.4884	L	0.61218	1.895	0.45035	D	0.998053	P;P	0.49559	0.925;0.877	P;P	0.54100	0.742;0.557	D	0.83925	0.0303	10	0.66056	D	0.02	-7.9245	15.1536	0.72723	0.0:1.0:0.0:0.0	.	20;20	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	Y	20	ENSP00000347672:S20Y;ENSP00000358523:S20Y;ENSP00000310800:S20Y;ENSP00000358522:S20Y	ENSP00000310800:S20Y	S	+	2	0	VANGL1	115995616	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.942000	0.63547	2.521000	0.84997	0.655000	0.94253	TCT	.	.		0.418	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			A	116194093	C	A	116194093	3	1	193	1	0	0	0	0	1	0	0	0	17134	913	32	3	61	3	VANGL1	1	116194093	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	12722468	116194093	133056528	4	28443										
SEMA6C	10500	hgsc.bcm.edu	37	chr1	151105786	151105786	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ctgggcccccaccgtggagcCgggccaaactgcggagggag	17	14	0	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:151105786C>T	ENST00000341697.3	-	19	3658	c.1967G>A	c.(1966-1968)cGg>cAg	p.R656Q	RP11-68I18.10_ENST00000563624.1_RNA|SEMA6C_ENST00000479820.1_5'Flank			Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	656					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			ACCGTGGAGCCGGGCCAAACT	0.736																																					p.R688Q		Atlas-SNP	.											.	SEMA6C	70	.	0			c.G2063A						.						8	12	11					1																	151105786		2143	4192	6335	SO:0001583	missense	10500	exon20			TGGAGCCGGGCCA	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"Semaphorins"	10740	protein-coding gene	gene with protein product	"m-Sema Y2"	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.1967G>A	chr1.hg19:g.151105786C>T	ENSP00000344148:p.Arg656Gln	101.0	0.0		176.0	30.0	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	hg19	CCDS984.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148583	0.78001	.	.	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	3.89	3.89	0.44902	.	761.094000	0.00166	N	0.000000	T	0.65026	0.2652	L	0.39898	1.24	0.28729	N	0.902586	D;D;D	0.76494	0.999;0.996;0.998	D;P;D	0.71870	0.975;0.883;0.945	T	0.51426	-0.8707	10	0.54805	T	0.06	.	7.2776	0.26294	0.0:0.8813:0.0:0.1187	.	648;688;656	Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;SEM6C_HUMAN	Q	656;648;688;656	ENSP00000357910:R656Q;ENSP00000357908:R648Q;ENSP00000357909:R688Q;ENSP00000344148:R656Q	ENSP00000344148:R656Q	R	-	2	0	SEMA6C	149372410	1.000000	0.71417	0.996000	0.52242	0.944000	0.59088	2.180000	0.42537	1.999000	0.58509	0.561000	0.74099	CGG	.	.		0.736	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		T	151105786	C	T	151105786	3	4	193	1	0	0	0	0	1	0	0	0	14056	652	23	1	829	1	SEMA6C	1	151105786	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	34911693	151105786	98144835	5	28444										
ZNF687	5298	hgsc.bcm.edu	37	chr1	151262451	151262451	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ggttccctgagcgtgatgaaTacgtggcccacatgaagaag	13	9	0	5			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:151262451T>A	ENST00000368873.1	-	0	3340				ZNF687_ENST00000368879.2_Missense_Mutation_p.Y978N			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta						phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GCGTGATGAATACGTGGCCCA	0.637																																					p.Y978N	Colon(154;765 1838 9854 28443 37492)	Atlas-SNP	.											.	ZNF687	94	.	0			c.T2932A						.						19	18	18					1																	151262451		2198	4295	6493	SO:0001628	intergenic_variant	57592	exon6			GATGAATACGTGG	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348		chr1.hg19:g.151262451T>A		49.0	0.0		66.0	11.0	NM_020832	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	Missense_Mutation	SNP	ENST00000368873.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.05|15.05	2.716944|2.716944	0.48622|0.48622	.|.	.|.	ENSG00000143373|ENSG00000143373	ENST00000426871|ENST00000336715;ENST00000324048;ENST00000368879	.|T;T;T	.|0.76968	.|-1.06;-1.06;-1.06	5.25|5.25	4.12|4.12	0.48240|0.48240	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.|0.000000	.|0.32301	.|N	.|0.006298	T|T	0.78207|0.78207	0.4247|0.4247	M|M	0.68317|0.68317	2.08|2.08	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D	.|0.57899	.|0.976;0.981	.|P;P	.|0.59357	.|0.853;0.856	T|T	0.80837|0.80837	-0.1204|-0.1204	5|10	.|0.87932	.|D	.|0	.|.	9.7566|9.7566	0.40506|0.40506	0.1545:0.0:0.0:0.8455|0.1545:0.0:0.0:0.8455	.|.	.|978;978	.|Q8N1G0-2;Q8N1G0	.|.;ZN687_HUMAN	K|N	580|978	.|ENSP00000336620:Y978N;ENSP00000319829:Y978N;ENSP00000357874:Y978N	.|ENSP00000319829:Y978N	N|Y	+|+	3|1	2|0	ZNF687|ZNF687	149529075|149529075	1.000000|1.000000	0.71417|0.71417	0.411000|0.411000	0.26484|0.26484	0.314000|0.314000	0.28054|0.28054	5.998000|5.998000	0.70653|0.70653	1.003000|1.003000	0.39130|0.39130	0.260000|0.260000	0.18958|0.18958	AAT|TAC	.	.		0.637	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651		A	151262451	T	A	151262451	1	1	193	0	1	0	0	0	0	0	0	0	18107	1406	49	4		4	ZNF687	1	151262451	IGR	SNP	T	TCGA-DD-AADK-01A-11D-A40R-10	156665	151262451	97988170	6	28445										
LCE1F	353137	hgsc.bcm.edu	37	chr1	152749026	152749027	+	In_Frame_Ins	INS	-	-	CAGCTCTGGGGGCTGCTG													0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tccagctctgggggctgctgINScagctctgggggtggtggct					rs201223178	byFrequency	TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:152749026_152749027insCAGCTCTGGGGGCTGCTG	ENST00000334371.2	+	1	179_180	c.179_180insCAGCTCTGGGGGCTGCTG	c.(178-183)tgcagc>tgCAGCTCTGGGGGCTGCTGcagc	p.60_61CS>CSSGGCCS		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	60					keratinization (GO:0031424)					kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGGGGCTGCTGCAGCTCTGGGG	0.678																																					p.C60delinsCSSGGCC		Atlas-INDEL	.											.	LCE1F	42	.	0			c.179_180insCAGCTCTGGGGGCTGCTG						.																																			SO:0001652	inframe_insertion	353137	exon1			.		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"Late cornified envelopes"	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	ENST00000334371.2:c.162_179dupCAGCTCTGGGGGCTGCTG	chr1.hg19:g.152749026_152749027insCAGCTCTGGGGGCTGCTG	ENSP00000334187:p.Ser55_Cys60dup	178.0	0.0		281.0	31.0	NM_178354		In_Frame_Ins	INS	ENST00000334371.2	hg19	CCDS1023.1																																																																																			.	.		0.678	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354		CAGCTCTGGGGGCTGCTG	152749027	-	CAGCTCTGGGGGCTGCTG	152749026	7	5	193	1	0	1	1	0	0	0	0	0	8673	1319	46	0	181	0	LCE1F	1	152749026	In_Frame_Ins	INS	-	TCGA-DD-AADK-01A-11D-A40R-10	1486575	152749026	96501595	7	28446										
CRTC2	200186	hgsc.bcm.edu	37	chr1	153924613	153924613	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tagggtaggctgtctcttcaGggtccaggggggtgggcagt	19	7	2	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:153924613G>A	ENST00000368633.1	-	10	1005	c.878C>T	c.(877-879)cCt>cTt	p.P293L	CRTC2_ENST00000476883.1_5'Flank|CRTC2_ENST00000368630.3_Intron	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	293					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGTCTCTTCAGGGTCCAGGGG	0.632																																					p.P293L		Atlas-SNP	.											.	CRTC2	58	.	0			c.C878T						.						72	75	74					1																	153924613		2203	4299	6502	SO:0001583	missense	200186	exon10			TCTTCAGGGTCCA	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.878C>T	chr1.hg19:g.153924613G>A	ENSP00000357622:p.Pro293Leu	90.0	0.0		113.0	38.0	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	hg19	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.426922	0.62733	.	.	ENSG00000160741	ENST00000368633	T	0.48836	0.8	4.05	4.05	0.47172	Transducer of regulated CREB activity, middle domain (1);	0.169992	0.40728	N	0.001025	T	0.57651	0.2068	M	0.72118	2.19	0.47037	D	0.999299	D	0.69078	0.997	D	0.69142	0.962	T	0.62272	-0.6889	10	0.56958	D	0.05	-8.4711	13.7737	0.63039	0.0:0.0:1.0:0.0	.	293	Q53ET0	CRTC2_HUMAN	L	293	ENSP00000357622:P293L	ENSP00000357622:P293L	P	-	2	0	CRTC2	152191237	0.999000	0.42202	1.000000	0.80357	0.976000	0.68499	2.904000	0.48719	2.100000	0.63781	0.450000	0.29827	CCT	.	.		0.632	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		A	153924613	G	A	153924613	3	1	193	1	0	0	0	0	1	0	0	0	3902	1000	35	3	1223	3	CRTC2	1	153924613	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10	1175587	153924613	95326008	8	28447										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167097157	167097157	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tggcagcagagttggcaaagAgatggatagcagtattaata	13	4	0	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:167097157A>G	ENST00000361200.2	+	6	2955	c.2789A>G	c.(2788-2790)gAg>gGg	p.E930G	DUSP27_ENST00000271385.5_Missense_Mutation_p.E930G|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.E930G			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	930	Ser-rich.				protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GTTGGCAAAGAGATGGATAGC	0.493																																					p.E930G		Atlas-SNP	.											.	DUSP27	235	.	0			c.A2789G						.						60	54	56					1																	167097157		2203	4300	6503	SO:0001583	missense	92235	exon5			GCAAAGAGATGGA	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2789A>G	chr1.hg19:g.167097157A>G	ENSP00000354483:p.Glu930Gly	73.0	0.0		111.0	9.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	A	14.31	2.495883	0.44352	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.04706	3.57;3.57;3.57	4.45	3.29	0.37713	.	0.131674	0.34484	N	0.003936	T	0.03695	0.0105	M	0.65975	2.015	0.29884	N	0.825797	D	0.56035	0.974	P	0.45310	0.476	T	0.15178	-1.0446	10	0.87932	D	0	-10.9628	11.0506	0.47884	0.844:0.156:0.0:0.0	.	930	Q5VZP5	DUS27_HUMAN	G	930	ENSP00000354483:E930G;ENSP00000271385:E930G;ENSP00000404874:E930G	ENSP00000271385:E930G	E	+	2	0	DUSP27	165363781	1.000000	0.71417	0.034000	0.17996	0.889000	0.51656	7.793000	0.85851	0.697000	0.31718	0.523000	0.50628	GAG	.	.		0.493	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		G	167097157	A	G	167097157	3	3	193	1	0	0	0	0	1	0	0	0	4826	304	11	2	2807	2	DUSP27	1	167097157	Missense_Mutation	SNP	A	TCGA-DD-AADK-01A-11D-A40R-10	13172544	167097157	82153464	9	28448										
FMO3	2328	hgsc.bcm.edu	37	chr1	171086300	171086302	+	In_Frame_Del	DEL	CTT	CTT	-													0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tatatggatgaactctcctcCttcattggggcaaagcccaa							TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:171086300_171086302delCTT	ENST00000367755.4	+	9	1428_1430	c.1317_1319delCTT	c.(1315-1320)tccttc>tcc	p.F440del	FMO3_ENST00000538429.1_In_Frame_Del_p.F377del|FMO3_ENST00000392085.2_In_Frame_Del_p.F440del|FMO3_ENST00000542847.1_In_Frame_Del_p.F420del	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	440					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	AACTCTCCTCCTTCATTGGGGCA	0.463																																					p.439_440del		Atlas-INDEL	.											.	FMO3	73	.	0			c.1316_1318del						.																																			SO:0001651	inframe_deletion	2328	exon9			.	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.1317_1319delCTT	chr1.hg19:g.171086300_171086302delCTT	ENSP00000356729:p.Phe440del	135.0	0.0		142.0	16.0	NM_001002294	B2R816|Q14854|Q8N5N5	In_Frame_Del	DEL	ENST00000367755.4	hg19	CCDS1292.1																																																																																			.	.		0.463	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		-	171086302	CTT	-	171086300	7	5	193	1	0	1	0	1	0	0	0	0	5964	668	24	0	1347	0	FMO3	1	171086300	In_Frame_Del	DEL	CTT	TCGA-DD-AADK-01A-11D-A40R-10	3989143	171086300	78164321	10	28449										
PPP1R12B	4660	hgsc.bcm.edu	37	chr1	202318209	202318209	+	Frame_Shift_Del	DEL	T	T	-													0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	caccgacgaggtgagaaagcTtctggcaagaggtgctgata							TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:202318209delT	ENST00000608999.1	+	1	383	c.230delT	c.(229-231)cttfs	p.L78fs	PPP1R12B_ENST00000356764.2_Frame_Shift_Del_p.L78fs|PPP1R12B_ENST00000336894.4_Frame_Shift_Del_p.L78fs|PPP1R12B_ENST00000480184.1_Frame_Shift_Del_p.L78fs	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	78					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			GTGAGAAAGCTTCTGGCAAGA	0.612																																					p.L77fs		Atlas-INDEL	.											.	PPP1R12B	100	.	0			c.229delC						.						43	39	40					1																	202318209		2203	4300	6503	SO:0001589	frameshift_variant	4660	exon1			.	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7619	protein-coding gene	gene with protein product	"myosin phosphatase regulatory subunit", "myosin phosphatase, target subunit 2"	603768	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.230delT	chr1.hg19:g.202318209delT	ENSP00000476755:p.Leu78fs	95.0	0.0		149.0	24.0	NM_001167857	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Frame_Shift_Del	DEL	ENST00000608999.1	hg19	CCDS1426.1																																																																																			.	.		0.612	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105		-	202318209	T	-	202318209	7	5	193	1	0	1	0	1	0	0	0	0	12367	1609	56	0	232	0	PPP1R12B	1	202318209	Frame_Shift_Del	DEL	T	TCGA-DD-AADK-01A-11D-A40R-10	31231909	202318209	46932412	11	28450										
CNTN2	6900	hgsc.bcm.edu	37	chr1	205027173	205027173	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ctggcatgccgcgcccgggcCagccctccagccacctatcg	11	20	0	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:205027173C>T	ENST00000331830.4	+	3	479	c.195C>T	c.(193-195)gcC>gcT	p.A65A		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	65	Ig-like C2-type 1.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GCGCCCGGGCCAGCCCTCCAG	0.642																																					p.A65A	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.C195T						.						20	22	21					1																	205027173		2202	4299	6501	SO:0001819	synonymous_variant	6900	exon3			CCGGGCCAGCCCT	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.195C>T	chr1.hg19:g.205027173C>T		120.0	0.0		173.0	83.0	NM_005076	P78432|Q5T054	Silent	SNP	ENST00000331830.4	hg19	CCDS1449.1																																																																																			.	.		0.642	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		T	205027173	C	T	205027173	2	4	193	1	0	0	0	0	0	0	0	1	3643	581	21	3		3	CNTN2	1	205027173	Silent	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	2708964	205027173	44223448	12	28451										
DYRK3	8444	hgsc.bcm.edu	37	chr1	206821451	206821451	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tgagctgattaaaaaaaataAgtttcagggttttagcgtcc	9	5	1	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr1:206821451A>T	ENST00000367109.2	+	3	1076	c.908A>T	c.(907-909)aAg>aTg	p.K303M	DYRK3_ENST00000367108.3_Missense_Mutation_p.K283M|DYRK3_ENST00000367106.1_Missense_Mutation_p.K283M|DYRK3_ENST00000489878.1_Intron	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	303	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			AAAAAAAATAAGTTTCAGGGT	0.413																																					p.K303M	Melanoma(164;427 2622 26826 51707)	Atlas-SNP	.											.	DYRK3	146	.	0			c.A908T						.						88	94	92					1																	206821451		2202	4300	6502	SO:0001583	missense	8444	exon3			AAAATAAGTTTCA	Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"regulatory erythroid kinase", "dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5", "protein kinase Dyrk3"	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.908A>T	chr1.hg19:g.206821451A>T	ENSP00000356076:p.Lys303Met	144.0	0.0		210.0	33.0	NM_003582	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Missense_Mutation	SNP	ENST00000367109.2	hg19	CCDS30999.1	.	.	.	.	.	.	.	.	.	.	A	16.17	3.046677	0.55110	.	.	ENSG00000143479	ENST00000367109;ENST00000367108;ENST00000367106	T;T;T	0.68025	-0.3;-0.3;-0.3	5.21	5.21	0.72293	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.80544	0.4643	M	0.73430	2.235	0.80722	D	1	D;D	0.76494	0.993;0.999	D;D	0.71414	0.941;0.973	T	0.82995	-0.0180	10	0.72032	D	0.01	.	14.3994	0.67031	1.0:0.0:0.0:0.0	.	303;283	O43781;O43781-2	DYRK3_HUMAN;.	M	303;283;283	ENSP00000356076:K303M;ENSP00000356075:K283M;ENSP00000356073:K283M	ENSP00000356073:K283M	K	+	2	0	DYRK3	204888074	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.104000	0.94239	2.190000	0.69967	0.391000	0.25812	AAG	.	.		0.413	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1	NM_003582		T	206821451	A	T	206821451	3	4	193	1	0	0	0	0	1	0	0	0	4859	72	3	4	939	4	DYRK3	1	206821451	Missense_Mutation	SNP	A	TCGA-DD-AADK-01A-11D-A40R-10	1794278	206821451	42429170	13	28452										
RHOB	388	hgsc.bcm.edu	37	chr2	20647230	20647230	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ccgggcccggcccgctcatgGcggccatccgcaagaagctg	14	17	1	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr2:20647230G>T	ENST00000272233.4	+	1	396	c.4G>T	c.(4-6)Gcg>Tcg	p.A2S		NM_004040.2	NP_004031.1	P62745	RHOB_HUMAN	ras homolog family member B	2					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|GTP catabolic process (GO:0006184)|negative regulation of cell cycle (GO:0045786)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|transformed cell apoptotic process (GO:0006927)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|kidney(1)|lung(2)|ovary(1)|urinary_tract(2)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)	all_epithelial(98;4.19e-09)|Lung NSC(108;0.00452)|Ovarian(717;0.0164)		OV - Ovarian serous cystadenocarcinoma(76;1.14e-22)|Epithelial(75;7.84e-19)	Botulinum Toxin Type A(DB00083)	CCCGCTCATGGCGGCCATCCG	0.711																																					p.A2S		Atlas-SNP	.											.	RHOB	18	.	0			c.G4T						.						22	30	27					2																	20647230		2198	4291	6489	SO:0001583	missense	388	exon1			CTCATGGCGGCCA		CCDS1699.1	2p24	2012-02-27	2012-02-27	2004-03-24	ENSG00000143878	ENSG00000143878			668	protein-coding gene	gene with protein product	"oncogene RHO H6"	165370	"ras homolog gene family, member B"	ARH6, ARHB		3283705, 16278215	Standard	NM_004040		Approved	RhoB, RHOH6, MST081	uc002rdv.3	P62745	OTTHUMG00000090755	ENST00000272233.4:c.4G>T	chr2.hg19:g.20647230G>T	ENSP00000272233:p.Ala2Ser	52.0	0.0		68.0	12.0	NM_004040	B2R692|P01121|Q5U0H6|Q7RTN5|Q7RTR9|Q9CUV7	Missense_Mutation	SNP	ENST00000272233.4	hg19	CCDS1699.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.637458	0.87760	.	.	ENSG00000143878	ENST00000272233	T	0.71817	-0.6	5.58	5.58	0.84498	.	0.000000	0.85682	U	0.000000	T	0.59945	0.2231	N	0.16790	0.44	0.80722	D	1	B	0.14438	0.01	B	0.20384	0.029	T	0.53802	-0.8387	10	0.40728	T	0.16	-26.4184	19.561	0.95373	0.0:0.0:1.0:0.0	.	2	P62745	RHOB_HUMAN	S	2	ENSP00000272233:A2S	ENSP00000272233:A2S	A	+	1	0	RHOB	20510711	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.565000	0.98154	2.612000	0.88384	0.643000	0.83706	GCG	.	.		0.711	RHOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207500.1	NM_004040		T	20647230	G	T	20647230	3	4	193	1	0	0	0	0	1	0	0	0	13347	1203	42	3	6	3	RHOB	2	20647230	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10		20647230	222552143	14	28453										
CAPN13	92291	hgsc.bcm.edu	37	chr2	30993223	30993223	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	cagggccagaactcttggttTtggtggcgaggacgcacaaa	14	9	1	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr2:30993223T>C	ENST00000295055.8	-	5	656	c.480A>G	c.(478-480)caA>caG	p.Q160Q	CAPN13_ENST00000465960.2_5'UTR|CAPN13_ENST00000534090.2_Silent_p.Q160Q	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	160	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					ACTCTTGGTTTTGGTGGCGAG	0.562																																					p.Q160Q		Atlas-SNP	.											.	CAPN13	70	.	0			c.A480G						.						171	182	178					2																	30993223		2146	4258	6404	SO:0001819	synonymous_variant	92291	exon5			TTGGTTTTGGTGG		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.480A>G	chr2.hg19:g.30993223T>C		125.0	0.0		122.0	23.0	NM_144575	Q17RF0|Q580X1|Q8TE80	Silent	SNP	ENST00000295055.8	hg19	CCDS46252.1																																																																																			.	.		0.562	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		C	30993223	T	C	30993223	2	2	193	1	0	0	0	0	0	0	0	1	2628	1838	64	2		2	CAPN13	2	30993223	Silent	SNP	T	TCGA-DD-AADK-01A-11D-A40R-10	10345993	30993223	212206150	15	28454										
FOXN2	3344	hgsc.bcm.edu	37	chr2	48602537	48602537	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	cgtacatgtttaggttccctAataagtactgcaaagacaca	7	9	0	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr2:48602537A>C	ENST00000340553.3	+	7	1512	c.1251A>C	c.(1249-1251)ctA>ctC	p.L417L		NM_002158.3	NP_002149.2	P32314	FOXN2_HUMAN	forkhead box N2	417					transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)			TAGGTTCCCTAATAAGTACTG	0.378																																					p.L417L		Atlas-SNP	.											.	FOXN2	39	.	0			c.A1251C						.						31	32	32					2																	48602537		2203	4300	6503	SO:0001819	synonymous_variant	3344	exon7			TTCCCTAATAAGT		CCDS1838.1	2p22-p16	2008-02-05	2006-10-02	2006-10-02	ENSG00000170802	ENSG00000170802		"Forkhead boxes"	5281	protein-coding gene	gene with protein product		143089	"human T-cell leukemia virus enhancer factor"	HTLF		1639393	Standard	NM_002158		Approved		uc002rwh.1	P32314	OTTHUMG00000129168	ENST00000340553.3:c.1251A>C	chr2.hg19:g.48602537A>C		43.0	0.0		43.0	5.0	NM_002158	Q15769|Q6P4Q2	Silent	SNP	ENST00000340553.3	hg19	CCDS1838.1																																																																																			.	.		0.378	FOXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251240.3	NM_002158		C	48602537	A	C	48602537	2	2	193	1	0	0	0	0	0	0	0	1	6028	349	13	5		5	FOXN2	2	48602537	Silent	SNP	A	TCGA-DD-AADK-01A-11D-A40R-10	17609314	48602537	194596836	16	28455										
KIAA1841	84542	hgsc.bcm.edu	37	chr2	61333780	61333780	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	atacaccatggggtcccaaaActggggagctcaatgctgtg	12	10	1	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr2:61333780A>G	ENST00000402291.1	+	14	1835	c.1594A>G	c.(1594-1596)Act>Gct	p.T532A	KIAA1841_ENST00000356719.2_Missense_Mutation_p.T532A|KIAA1841_ENST00000453873.1_Missense_Mutation_p.T532A|KIAA1841_ENST00000295031.5_Missense_Mutation_p.T532A	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	532										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			GGGTCCCAAAACTGGGGAGCT	0.358																																					p.T532A		Atlas-SNP	.											.	KIAA1841	95	.	0			c.A1594G						.						126	139	135					2																	61333780		2203	4300	6503	SO:0001583	missense	84542	exon14			CCCAAAACTGGGG	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.1594A>G	chr2.hg19:g.61333780A>G	ENSP00000385579:p.Thr532Ala	112.0	0.0		98.0	12.0	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Missense_Mutation	SNP	ENST00000402291.1	hg19	CCDS46296.1	.	.	.	.	.	.	.	.	.	.	A	12.65	2.000409	0.35320	.	.	ENSG00000162929	ENST00000402291;ENST00000295031;ENST00000356719;ENST00000453873	.	.	.	5.53	4.38	0.52667	.	0.215850	0.48286	D	0.000183	T	0.49695	0.1572	L	0.60455	1.87	0.37164	D	0.90274	B;B	0.23806	0.091;0.026	B;B	0.26693	0.072;0.022	T	0.46775	-0.9167	9	0.10377	T	0.69	-8.6994	10.5245	0.44941	0.9224:0.0:0.0776:0.0	.	532;532	Q6NSI8-2;Q6NSI8	.;K1841_HUMAN	A	532	.	ENSP00000295031:T532A	T	+	1	0	KIAA1841	61187284	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	3.604000	0.54081	1.032000	0.39892	0.477000	0.44152	ACT	.	.		0.358	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506		G	61333780	A	G	61333780	3	3	193	1	0	0	0	0	1	0	0	0	8270	43	2	2	1640	2	KIAA1841	2	61333780	Missense_Mutation	SNP	A	TCGA-DD-AADK-01A-11D-A40R-10	12731243	61333780	181865593	17	28456										
PROM2	150696	hgsc.bcm.edu	37	chr2	95943741	95943741	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ccgaggccaacttctccagcAtggtccaggaggtgagagcc	13	13	1	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr2:95943741A>G	ENST00000317620.9	+	8	1172	c.1039A>G	c.(1039-1041)Atg>Gtg	p.M347V	PROM2_ENST00000463580.1_3'UTR|PROM2_ENST00000542147.1_Missense_Mutation_p.M347V|PROM2_ENST00000317668.4_Missense_Mutation_p.M347V|PROM2_ENST00000403131.2_Missense_Mutation_p.M347V	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	347					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						CTTCTCCAGCATGGTCCAGGA	0.567																																					p.M347V		Atlas-SNP	.											.	PROM2	78	.	0			c.A1039G						.						76	59	65					2																	95943741		2203	4300	6503	SO:0001583	missense	150696	exon8			TCCAGCATGGTCC	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.1039A>G	chr2.hg19:g.95943741A>G	ENSP00000318270:p.Met347Val	57.0	0.0		49.0	13.0	NM_001165977	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Missense_Mutation	SNP	ENST00000317620.9	hg19	CCDS2012.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.392854	0.42410	.	.	ENSG00000155066	ENST00000403131;ENST00000317668;ENST00000317620;ENST00000542147	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.17	5.17	0.71159	.	0.249960	0.35525	N	0.003143	T	0.40743	0.1129	M	0.73962	2.25	0.36350	D	0.860036	B	0.17038	0.02	B	0.15870	0.014	T	0.43686	-0.9376	10	0.13853	T	0.58	-40.5868	11.3368	0.49509	1.0:0.0:0.0:0.0	.	347	Q8N271	PROM2_HUMAN	V	347	ENSP00000385716:M347V;ENSP00000318520:M347V;ENSP00000318270:M347V;ENSP00000442542:M347V	ENSP00000318270:M347V	M	+	1	0	PROM2	95307468	0.996000	0.38824	1.000000	0.80357	0.965000	0.64279	4.357000	0.59436	2.183000	0.69458	0.533000	0.62120	ATG	.	.		0.567	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707		G	95943741	A	G	95943741	3	3	193	1	0	0	0	0	1	0	0	0	12568	217	8	2	1069	2	PROM2	2	95943741	Missense_Mutation	SNP	A	TCGA-DD-AADK-01A-11D-A40R-10	34609961	95943741	147255632	18	28457										
SETD2	29072	hgsc.bcm.edu	37	chr3	47155365	47155365	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ggtaattaaaaaagaacttaCgaaggaaggtctttggcagc	11	5	1	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr3:47155365C>T	ENST00000409792.3	-	5	4758		c.e5+1			NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2						angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AAAGAACTTACGAAGGAAGGT	0.453			"N, F, S, Mis"		clear cell renal carcinoma																																.		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.4715+1G>A						.						106	107	106					3																	47155365		2203	4300	6503	SO:0001630	splice_region_variant	29072	exon6			AACTTACGAAGGA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4715+1G>A	chr3.hg19:g.47155365C>T		96.0	0.0		84.0	23.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Splice_Site	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	23.1	4.377351	0.82682	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8075	0.88606	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SETD2	47130369	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.256000	0.78350	2.518000	0.84900	0.585000	0.79938	.	.	.		0.453	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	Intron	T	47155365	C	T	47155365	5	4	193	1	0	0	0	0	0	0	1	0	14146	550	19	1	3046	1	SETD2	3	47155365	Splice_Site	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10		47155365	150867065	19	28458										
PIK3CB	5291	hgsc.bcm.edu	37	chr3	138478043	138478043	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tataagaaatggtagcttccCgaggtacctccaactggata	9	9	0	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr3:138478043C>A	ENST00000477593.1	-	2	216	c.143G>T	c.(142-144)cGg>cTg	p.R48L	PIK3CB_ENST00000289153.2_Missense_Mutation_p.R48L			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	48	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	GGTAGCTTCCCGAGGTACCTC	0.408																																					p.R48L		Atlas-SNP	.											.	PIK3CB	103	.	0			c.G143T						.						61	59	60					3																	138478043		2203	4300	6503	SO:0001583	missense	5291	exon1			GCTTCCCGAGGTA		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.143G>T	chr3.hg19:g.138478043C>A	ENSP00000418143:p.Arg48Leu	336.0	0.0		382.0	81.0	NM_006219	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	hg19	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.321471	0.81580	.	.	ENSG00000051382	ENST00000477593;ENST00000289153;ENST00000483968;ENST00000461451;ENST00000465581	T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61	5.84	5.84	0.93424	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	T	0.73418	0.3584	M	0.73962	2.25	0.80722	D	1	B	0.29646	0.253	B	0.35278	0.199	T	0.68891	-0.5289	10	0.10636	T	0.68	-15.982	20.1551	0.98106	0.0:1.0:0.0:0.0	.	48	P42338	PK3CB_HUMAN	L	48	ENSP00000418143:R48L;ENSP00000289153:R48L;ENSP00000419857:R48L;ENSP00000420399:R48L	ENSP00000289153:R48L	R	-	2	0	PIK3CB	139960733	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	5.691000	0.68249	2.760000	0.94817	0.655000	0.94253	CGG	.	.		0.408	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			A	138478043	C	A	138478043	3	1	193	1	0	0	0	0	1	0	0	0	11923	652	23	1	3155	1	PIK3CB	3	138478043	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	91322678	138478043	59544387	20	28459										
MECOM	2122	hgsc.bcm.edu	37	chr3	168806945	168806945	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tatgatctagagcagaaagtCcacttttatattcttcctct	5	9	3	3			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr3:168806945C>G	ENST00000464456.1	-	14	4037	c.2837G>C	c.(2836-2838)gGa>gCa	p.G946A	MECOM_ENST00000264674.3_Missense_Mutation_p.G1020A|MECOM_ENST00000460814.1_Missense_Mutation_p.G946A|MECOM_ENST00000392736.3_Missense_Mutation_p.G955A|MECOM_ENST00000494292.1_Missense_Mutation_p.G1134A|MECOM_ENST00000472280.1_Missense_Mutation_p.G956A|MECOM_ENST00000468789.1_Missense_Mutation_p.G955A|MECOM_ENST00000433243.2_Missense_Mutation_p.G956A	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G955E(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						AGCAGAAAGTCCACTTTTATA	0.313																																					p.G1143A		Atlas-SNP	.											MECOM,mouth,carcinoma,0,1	MECOM	216	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G3428C						.						85	84	84					3																	168806945		2203	4300	6503	SO:0001583	missense	2122	exon16			GAAAGTCCACTTT	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2837G>C	chr3.hg19:g.168806945C>G	ENSP00000419770:p.Gly946Ala	74.0	0.0		66.0	3.0	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	hg19	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.486314	0.63962	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243	T;T;T;T;T;T;T;T	0.05925	3.43;3.42;3.39;3.53;3.37;3.42;3.39;3.53	5.63	5.63	0.86233	.	0.000000	0.64402	D	0.000010	T	0.11793	0.0287	L	0.52573	1.65	0.46241	D	0.998949	P;B;P;B;B	0.43287	0.802;0.4;0.702;0.4;0.451	B;B;B;B;B	0.42495	0.389;0.173;0.217;0.173;0.137	T	0.00527	-1.1688	10	0.87932	D	0	-12.6946	20.0572	0.97657	0.0:1.0:0.0:0.0	.	1143;947;1134;1020;955	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	A	1020;955;946;956;1134;955;946;956	ENSP00000264674:G1020A;ENSP00000376493:G955A;ENSP00000419770:G946A;ENSP00000420048:G956A;ENSP00000417899:G1134A;ENSP00000419995:G955A;ENSP00000420466:G946A;ENSP00000394302:G956A	ENSP00000264674:G1020A	G	-	2	0	MECOM	170289639	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	6.786000	0.75094	2.826000	0.97356	0.655000	0.94253	GGA	.	.		0.313	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		G	168806945	C	G	168806945	3	3	193	1	0	0	0	0	1	0	0	0	9431	855	30	4	299	4	MECOM	3	168806945	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	30328902	168806945	29215485	21	28460										
KIAA0226	9711	hgsc.bcm.edu	37	chr3	197431443	197431443	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ttttctgatatactgtctatCcccgagcaggggccggagct	11	11	2	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr3:197431443C>T	ENST00000296343.5	-	4	432	c.433G>A	c.(433-435)Gat>Aat	p.D145N	KIAA0226_ENST00000389665.5_Missense_Mutation_p.D145N|KIAA0226_ENST00000273582.5_Missense_Mutation_p.D85N|KIAA0226_ENST00000467303.1_5'UTR|KIAA0226_ENST00000449205.1_Missense_Mutation_p.D145N	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	145	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		TACTGTCTATCCCCGAGCAGG	0.567																																					p.D145N	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.G433A						.						75	82	80					3																	197431443		1987	4156	6143	SO:0001583	missense	9711	exon4			GTCTATCCCCGAG	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.433G>A	chr3.hg19:g.197431443C>T	ENSP00000296343:p.Asp145Asn	139.0	0.0		144.0	22.0	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	hg19	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.02|16.02	3.005684|3.005684	0.54254|0.54254	.|.	.|.	ENSG00000145016|ENSG00000145016	ENST00000273582;ENST00000296343;ENST00000389665;ENST00000449205|ENST00000413360	T;T;T;T|T	0.11063|0.26373	2.81;2.81;2.81;2.81|1.74	6.06|6.06	6.06|6.06	0.98353|0.98353	RUN (3);|.	0.123546|.	0.53938|.	D|.	0.000042|.	T|T	0.17195|0.17195	0.0413|0.0413	N|N	0.19112|0.19112	0.55|0.55	0.33049|0.33049	D|D	0.532519|0.532519	B;B;B|.	0.26577|.	0.153;0.007;0.015|.	B;B;B|.	0.23275|.	0.045;0.006;0.01|.	T|T	0.18618|0.18618	-1.0331|-1.0331	10|7	0.21540|0.13108	T|T	0.41|0.6	.|.	7.9773|7.9773	0.30161|0.30161	0.0:0.8156:0.0:0.1844|0.0:0.8156:0.0:0.1844	.|.	145;85;145|.	E9PEM3;Q92622-2;Q92622|.	.;.;RUBIC_HUMAN|.	N|E	85;145;145;145|123	ENSP00000273582:D85N;ENSP00000296343:D145N;ENSP00000374316:D145N;ENSP00000390962:D145N|ENSP00000405115:G123E	ENSP00000273582:D85N|ENSP00000405115:G123E	D|G	-|-	1|2	0|0	KIAA0226|KIAA0226	198915840|198915840	1.000000|1.000000	0.71417|0.71417	0.900000|0.900000	0.35374|0.35374	0.985000|0.985000	0.73830|0.73830	4.056000|4.056000	0.57448|0.57448	2.885000|2.885000	0.99019|0.99019	0.643000|0.643000	0.83706|0.83706	GAT|GGA	.	.		0.567	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		T	197431443	C	T	197431443	3	4	193	1	0	0	0	0	1	0	0	0	8171	855	30	3	2602	3	KIAA0226	3	197431443	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	28624498	197431443	590987	22	28461										
HNRNPD	3184	hgsc.bcm.edu	37	chr4	83294718	83294718	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	gctccgcttcccgccgccgcCgctgccccctgtgtcgccgc	11	23	0	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr4:83294718C>T	ENST00000313899.7	-	1	391	c.114G>A	c.(112-114)gcG>gcA	p.A38A	RP11-127B20.3_ENST00000609552.1_RNA|HNRNPD_ENST00000541060.1_5'UTR|HNRNPD_ENST00000543098.1_Intron|HNRNPD_ENST00000352301.4_Silent_p.A38A|HNRNPD_ENST00000353341.4_Silent_p.A38A|RP11-127B20.3_ENST00000609575.1_RNA	NM_031370.2	NP_112738.1	Q14103	HNRPD_HUMAN	heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)	38	Ala-rich.				circadian regulation of translation (GO:0097167)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|regulation of circadian rhythm (GO:0042752)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	7						ccgccgccgccgctgccccct	0.771																																					p.A38A		Atlas-SNP	.											.	HNRNPD	23	.	0			c.G114A						.						6	5	5					4																	83294718		1776	3334	5110	SO:0001819	synonymous_variant	3184	exon1			CGCCGCCGCTGCC	AF026126	CCDS3590.1, CCDS3591.1, CCDS3592.1	4q21	2013-02-12	2002-08-29	2008-04-18	ENSG00000138668	ENSG00000138668		"RNA binding motif (RRM) containing"	5036	protein-coding gene	gene with protein product		601324	"heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA-binding protein 1, 37kD)"	AUF1, HNRPD		9615222	Standard	NM_001003810		Approved		uc003hmm.1	Q14103	OTTHUMG00000130290	ENST00000313899.7:c.114G>A	chr4.hg19:g.83294718C>T		46.0	0.0		48.0	4.0	NM_031370	A8K9J2|P07029|Q01858|Q14100|Q14101|Q14102|Q4W5A1|Q9UCE8|Q9UCE9	Silent	SNP	ENST00000313899.7	hg19	CCDS3592.1																																																																																			.	.		0.771	HNRNPD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252630.2	NM_031370		T	83294718	C	T	83294718	2	4	193	1	0	0	0	0	0	0	0	1	7273	639	23	1		1	HNRNPD	4	83294718	Silent	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10		83294718	107859558	23	28462										
GPR98	84059	hgsc.bcm.edu	37	chr5	90106600	90106600	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ccattctgcagccaaccaacGtggttgccattgttactgag	9	12	1	1	rs535921202		TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr5:90106600G>A	ENST00000405460.2	+	74	15619	c.15523G>A	c.(15523-15525)Gtg>Atg	p.V5175M	GPR98_ENST00000425867.2_Missense_Mutation_p.V836M	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5175					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GCCAACCAACGTGGTTGCCAT	0.498													G|||	1	0.000199681	0	0	5008	,	,		20381	0.001		0	False		,,,				2504	0				p.V5175M		Atlas-SNP	.											.	GPR98	605	.	0			c.G15523A						.						161	157	158					5																	90106600		2052	4205	6257	SO:0001583	missense	84059	exon74			ACCAACGTGGTTG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.15523G>A	chr5.hg19:g.90106600G>A	ENSP00000384582:p.Val5175Met	71.0	0.0		45.0	6.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	G	0.252	-1.005673	0.02112	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.29655	1.63;1.56	4.91	-1.7	0.08159	.	0.779388	0.11889	N	0.519773	T	0.18467	0.0443	L	0.36672	1.1	0.09310	N	1	B;B;B	0.12013	0.003;0.001;0.005	B;B;B	0.09377	0.002;0.001;0.004	T	0.24693	-1.0153	9	.	.	.	.	5.3672	0.16121	0.3691:0.1788:0.4521:0.0	.	836;5175;836	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	M	5175;5175;836	ENSP00000384582:V5175M;ENSP00000392618:V836M	.	V	+	1	0	GPR98	90142356	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.181000	0.16880	-0.224000	0.09928	-0.471000	0.05019	GTG	.	.		0.498	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90106600	G	A	90106600	3	1	193	1	0	0	0	0	1	0	0	0	6730	1145	40	1	15817	1	GPR98	5	90106600	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10		90106600	90808660	24	28463										
MGAT4B	11282	hgsc.bcm.edu	37	chr5	179228997	179228997	+	Intron	DEL	G	G	-													0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tggtaggcaagccgtcacgaGggggcggtctagagccaccc							TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr5:179228997delG	ENST00000292591.7	-	2	448				MGAT4B_ENST00000337755.5_Frame_Shift_Del_p.L39fs|MGAT4B_ENST00000521305.1_Intron	NM_014275.4	NP_055090.1	Q9UQ53	MGT4B_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B						cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	13	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCGTCACGAGGGGGCGGTCT	0.622											OREG0017110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L39fs	GBM(13;414 434 4098 22176 23230)	Atlas-INDEL	.											.	MGAT4B	41	.	0			c.116delT						.						64	74	71					5																	179228997		2203	4300	6503	SO:0001627	intron_variant	11282	exon1			.	AB000624	CCDS4448.1, CCDS4449.1	5q35	2013-02-25	2005-11-16		ENSG00000161013	ENSG00000161013	2.4.1.145	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7048	protein-coding gene	gene with protein product		604561	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme B"			10372966	Standard	NM_014275		Approved	GnT-Ivb	uc003mks.3	Q9UQ53	OTTHUMG00000130912	ENST00000292591.7:c.98-28C>-	chr5.hg19:g.179228997delG		123.0	0.0	1952	152.0	48.0	NM_054013	A8MPR0|Q86TF1|Q96GH4|Q9NSK6	Frame_Shift_Del	DEL	ENST00000292591.7	hg19	CCDS4448.1																																																																																			.	.		0.622	MGAT4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253503.3	NM_014275		-	179228997	G	-	179228997	6	5	193	0	1	1	0	1	0	0	0	0	9555	1000	35	0		0	MGAT4B	5	179228997	Intron	DEL	G	TCGA-DD-AADK-01A-11D-A40R-10	89122397	179228997	1686263	25	28464										
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056141	26056141	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	accttggccttctttgggctCttagccactttcttggttac	8	12	3	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr6:26056141C>G	ENST00000343677.2	-	1	558	c.516G>C	c.(514-516)aaG>aaC	p.K172N		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	172					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						TCTTTGGGCTCTTAGCCACTT	0.562																																					p.K172N		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G516C						.						98	110	106					6																	26056141		2203	4300	6503	SO:0001583	missense	3006	exon1			TGGGCTCTTAGCC	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"Histones / Replication-dependent"	4716	protein-coding gene	gene with protein product		142710	"H1 histone family, member 2", "histone 1, H1c"	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.516G>C	chr6.hg19:g.26056141C>G	ENSP00000339566:p.Lys172Asn	88.0	0.0		98.0	19.0	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	hg19	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.535886	0.27475	.	.	ENSG00000187837	ENST00000343677	T	0.21361	2.01	5.3	4.43	0.53597	.	0.182554	0.46145	D	0.000303	T	0.18087	0.0434	N	0.14661	0.345	0.58432	D	0.999997	D	0.76494	0.999	D	0.80764	0.994	T	0.12528	-1.0544	10	0.56958	D	0.05	-6.1029	13.5495	0.61723	0.0:0.924:0.0:0.076	.	172	P16403	H12_HUMAN	N	172	ENSP00000339566:K172N	ENSP00000339566:K172N	K	-	3	2	HIST1H1C	26164120	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	2.365000	0.44196	1.376000	0.46267	-0.143000	0.13931	AAG	.	.		0.562	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		G	26056141	C	G	26056141	3	3	193	1	0	0	0	0	1	0	0	0	7133	912	32	4	129	4	HIST1H1C	6	26056141	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10		26056141	145058926	26	28465										
AGR3	155465	hgsc.bcm.edu	37	chr7	16900171	16900171	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tgtacaatctgttagagtatCttccagctatgtcagctcta	7	9	4	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr7:16900171C>G	ENST00000310398.2	-	7	474	c.404G>C	c.(403-405)aGa>aCa	p.R135T	AGR3_ENST00000402239.3_Missense_Mutation_p.R135T	NM_176813.3	NP_789783.1	Q8TD06	AGR3_HUMAN	anterior gradient 3	135						extracellular region (GO:0005576)	dystroglycan binding (GO:0002162)			central_nervous_system(1)|kidney(8)|lung(2)|skin(1)|stomach(1)	13	Lung NSC(10;0.0376)|all_lung(11;0.0721)|all_epithelial(12;0.202)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		GTTAGAGTATCTTCCAGCTAT	0.378																																					p.R135T		Atlas-SNP	.											.	AGR3	19	.	0			c.G404C						.						138	139	139					7																	16900171		2203	4300	6503	SO:0001583	missense	155465	exon7			GAGTATCTTCCAG	AY069977	CCDS5365.1	7p21.1	2013-07-31	2013-07-31		ENSG00000173467	ENSG00000173467		"Protein disulfide isomerases"	24167	protein-coding gene	gene with protein product	"breast cancer membrane protein 11", "protein disulfide isomerase family A, member 18"	609482	"anterior gradient 3 homolog (Xenopus laevis)"			12592373, 12477722	Standard	NM_176813		Approved	HAG3, hAG-3, BCMP11, PDIA18	uc003sts.3	Q8TD06	OTTHUMG00000128411	ENST00000310398.2:c.404G>C	chr7.hg19:g.16900171C>G	ENSP00000308606:p.Arg135Thr	134.0	0.0		112.0	22.0	NM_176813	A4D120	Missense_Mutation	SNP	ENST00000310398.2	hg19	CCDS5365.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.81|11.81	1.749331|1.749331	0.30955|0.30955	.|.	.|.	ENSG00000173467|ENSG00000173467	ENST00000414935|ENST00000310398;ENST00000402239	.|T;T	.|0.41758	.|0.99;0.99	4.28|4.28	1.47|1.47	0.22746|0.22746	.|Thioredoxin-like fold (2);	.|0.085531	.|0.49305	.|D	.|0.000146	T|T	0.33323|0.33323	0.0859|0.0859	M|M	0.64404|0.64404	1.975|1.975	0.40241|0.40241	D|D	0.977954|0.977954	.|B	.|0.22541	.|0.071	.|B	.|0.17433	.|0.018	T|T	0.08785|0.08785	-1.0705|-1.0705	5|10	.|0.23302	.|T	.|0.38	-15.2218|-15.2218	6.4396|6.4396	0.21843|0.21843	0.1463:0.6935:0.0:0.1603|0.1463:0.6935:0.0:0.1603	.|.	.|135	.|Q8TD06	.|AGR3_HUMAN	N|T	113|135	.|ENSP00000308606:R135T;ENSP00000386016:R135T	.|ENSP00000308606:R135T	K|R	-|-	3|2	2|0	AGR3|AGR3	16866696|16866696	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.678000|0.678000	0.39670|0.39670	0.585000|0.585000	0.23879|0.23879	0.110000|0.110000	0.17919|0.17919	0.655000|0.655000	0.94253|0.94253	AAG|AGA	.	.		0.378	AGR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250191.2	NM_176813		G	16900171	C	G	16900171	3	3	193	1	0	0	0	0	1	0	0	0	396	913	32	4	104	4	AGR3	7	16900171	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10		16900171	142238492	27	28466										
GLI3	2737	hgsc.bcm.edu	37	chr7	42085105	42085105	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ccatctgatgatagtattctGctgggctgactcctgcatgg	11	10	2	3			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr7:42085105G>C	ENST00000395925.3	-	6	788	c.704C>G	c.(703-705)gCa>gGa	p.A235G	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	235					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A235G(1)		NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						ATAGTATTCTGCTGGGCTGAC	0.547									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.A235G		Atlas-SNP	.											GLI3,NS,carcinoma,0,1	GLI3	312	.	1	Substitution - Missense(1)	lung(1)	c.C704G						.						58	62	60					7																	42085105		2203	4300	6503	SO:0001583	missense	2737	exon6	Familial Cancer Database	;	TATTCTGCTGGGC		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.704C>G	chr7.hg19:g.42085105G>C	ENSP00000379258:p.Ala235Gly	49.0	0.0		47.0	6.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848284	0.91277	.	.	ENSG00000106571	ENST00000395925	T	0.67523	-0.27	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.77980	0.4212	M	0.63843	1.955	0.80722	D	1	D	0.60160	0.987	P	0.57776	0.827	T	0.78163	-0.2311	10	0.52906	T	0.07	.	19.5837	0.95482	0.0:0.0:1.0:0.0	.	235	P10071	GLI3_HUMAN	G	235	ENSP00000379258:A235G	ENSP00000379258:A235G	A	-	2	0	GLI3	42051630	1.000000	0.71417	0.894000	0.35097	0.909000	0.53808	9.464000	0.97655	2.630000	0.89119	0.655000	0.94253	GCA	.	.		0.547	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		C	42085105	G	C	42085105	3	2	193	1	0	0	0	0	1	0	0	0	6447	1319	46	4	4078	4	GLI3	7	42085105	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10	25184934	42085105	117053558	28	28467										
C7orf25	79020	hgsc.bcm.edu	37	chr7	42949496	42949496	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	aaggctggtctggtaccacaTtaattcgcttaattaacaca	7	9	1	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr7:42949496T>G	ENST00000350427.4	-	2	1279	c.1004A>C	c.(1003-1005)aAt>aCt	p.N335T	C7orf25_ENST00000447342.1_Missense_Mutation_p.N335T|C7orf25_ENST00000431882.2_Missense_Mutation_p.N393T|PSMA2_ENST00000442788.1_3'UTR|C7orf25_ENST00000438029.1_Missense_Mutation_p.N335T			Q9BPX7	CG025_HUMAN	chromosome 7 open reading frame 25	335										endometrium(6)|kidney(1)|large_intestine(7)|lung(2)|skin(1)	17						TGGTACCACATTAATTCGCTT	0.453																																					p.N393T		Atlas-SNP	.											.	C7orf25	36	.	0			c.A1178C						.						87	82	83					7																	42949496		2203	4300	6503	SO:0001583	missense	79020	exon2			ACCACATTAATTC	BC001845	CCDS5466.1, CCDS47576.1	7p14.1	2011-11-24			ENSG00000136197	ENSG00000136197			21703	protein-coding gene	gene with protein product							Standard	NM_024054		Approved	MGC2821	uc003thx.4	Q9BPX7	OTTHUMG00000128869	ENST00000350427.4:c.1004A>C	chr7.hg19:g.42949496T>G	ENSP00000343364:p.Asn335Thr	152.0	0.0		202.0	32.0	NM_001099858	A4D1V2|J3KR36|Q9H779	Missense_Mutation	SNP	ENST00000350427.4	hg19	CCDS5466.1	.	.	.	.	.	.	.	.	.	.	T	0.022	-1.410545	0.01145	.	.	ENSG00000136197	ENST00000350427;ENST00000447342;ENST00000431882;ENST00000438029	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.79	-2.75	0.05914	.	0.802027	0.12205	N	0.489902	T	0.08088	0.0202	N	0.00217	-1.83	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.41627	-0.9498	10	0.07175	T	0.84	-13.467	7.884	0.29640	0.0:0.3394:0.1895:0.4711	.	393;335	B4DQM3;Q9BPX7	.;CG025_HUMAN	T	335;335;393;335	ENSP00000343364:N335T;ENSP00000413029:N335T;ENSP00000416290:N393T;ENSP00000396597:N335T	ENSP00000343364:N335T	N	-	2	0	C7orf25	42916021	0.000000	0.05858	0.981000	0.43875	0.926000	0.56050	-0.373000	0.07494	-0.287000	0.09064	0.459000	0.35465	AAT	.	.		0.453	C7orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250814.2	NM_024054		G	42949496	T	G	42949496	3	3	193	1	0	0	0	0	1	0	0	0	2382	1493	52	5	265	5	C7orf25	7	42949496	Missense_Mutation	SNP	T	TCGA-DD-AADK-01A-11D-A40R-10	864391	42949496	116189167	29	28468										
UBE3C	9690	hgsc.bcm.edu	37	chr7	157046730	157046730	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	catccacttggtggcagactAcaggctgaacaggcagatcc	11	12	0	3			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr7:157046730A>G	ENST00000348165.5	+	20	3137	c.2777A>G	c.(2776-2778)tAc>tGc	p.Y926C		NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	926	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		GTGGCAGACTACAGGCTGAAC	0.537																																					p.Y926C		Atlas-SNP	.											.	UBE3C	124	.	0			c.A2777G						.						58	57	57					7																	157046730		2203	4300	6503	SO:0001583	missense	9690	exon20			CAGACTACAGGCT	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.2777A>G	chr7.hg19:g.157046730A>G	ENSP00000309198:p.Tyr926Cys	98.0	0.0		105.0	18.0	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	hg19	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.384710	0.82792	.	.	ENSG00000009335	ENST00000348165	T	0.61040	0.14	5.31	5.31	0.75309	HECT (4);	0.000000	0.85682	D	0.000000	T	0.81517	0.4839	M	0.92367	3.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.86419	0.1753	10	0.87932	D	0	.	15.5565	0.76200	1.0:0.0:0.0:0.0	.	926;779	Q15386;B4DHJ9	UBE3C_HUMAN;.	C	926	ENSP00000309198:Y926C	ENSP00000309198:Y926C	Y	+	2	0	UBE3C	156739491	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	8.946000	0.92992	2.143000	0.66587	0.533000	0.62120	TAC	.	.		0.537	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		G	157046730	A	G	157046730	3	3	193	1	0	0	0	0	1	0	0	0	16896	391	14	2	2855	2	UBE3C	7	157046730	Missense_Mutation	SNP	A	TCGA-DD-AADK-01A-11D-A40R-10	114097234	157046730	2091933	30	28469										
PREX2	80243	hgsc.bcm.edu	37	chr8	69020463	69020463	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	catgtcaatgtgatggaagtTtcttatcccaaaacatcaac	6	9	3	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr8:69020463T>A	ENST00000288368.4	+	24	3112	c.2835T>A	c.(2833-2835)gtT>gtA	p.V945V		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	945					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TGATGGAAGTTTCTTATCCCA	0.428																																					p.V945V		Atlas-SNP	.											.	PREX2	614	.	0			c.T2835A						.						127	114	118					8																	69020463		2203	4300	6503	SO:0001819	synonymous_variant	80243	exon24			GGAAGTTTCTTAT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2835T>A	chr8.hg19:g.69020463T>A		104.0	0.0		153.0	14.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	hg19	CCDS6201.1																																																																																			.	.		0.428	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		A	69020463	T	A	69020463	2	1	193	1	0	0	0	0	0	0	0	1	12489	1828	64	4		4	PREX2	8	69020463	Silent	SNP	T	TCGA-DD-AADK-01A-11D-A40R-10		69020463	77343559	31	28470										
NLRP6	171389	hgsc.bcm.edu	37	chr11	281308	281308	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	gcccaggaccgcggctggcgGcgttgggacactcctgcgtg	17	14	0	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr11:281308G>A	ENST00000312165.5	+	4	1574	c.1574G>A	c.(1573-1575)gGc>gAc	p.G525D	NLRP6_ENST00000534750.1_Missense_Mutation_p.G525D	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	525					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		GCGGCTGGCGGCGTTGGGACA	0.682																																					p.G525D		Atlas-SNP	.											.	NLRP6	4	.	0			c.G1574A						.						29	25	26					11																	281308		2197	4294	6491	SO:0001583	missense	171389	exon4			CTGGCGGCGTTGG	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"Nucleotide-binding domain and leucine rich repeat containing"	22944	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"	609650	"NACHT, leucine rich repeat and PYD containing 6"	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.1574G>A	chr11.hg19:g.281308G>A	ENSP00000309767:p.Gly525Asp	64.0	0.0		69.0	16.0	NM_138329	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	hg19	CCDS7693.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.773994	0.00640	.	.	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.73789	-0.78;-0.76	2.79	1.87	0.25490	.	1.041160	0.07672	N	0.935599	T	0.57242	0.2040	N	0.16567	0.415	0.09310	N	1	B;D	0.54047	0.024;0.964	B;P	0.45310	0.027;0.476	T	0.43540	-0.9385	10	0.06757	T	0.87	.	7.5797	0.27957	0.139:0.0:0.861:0.0	.	525;525	E9PJZ8;P59044	.;NALP6_HUMAN	D	525	ENSP00000433617:G525D;ENSP00000309767:G525D	ENSP00000309767:G525D	G	+	2	0	NLRP6	271308	0.000000	0.05858	0.001000	0.08648	0.213000	0.24496	0.992000	0.29667	0.718000	0.32166	0.462000	0.41574	GGC	.	.		0.682	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		A	281308	G	A	281308	3	1	193	1	0	0	0	0	1	0	0	0	10490	1203	42	3	1588	3	NLRP6	11	281308	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10		281308	134725208	32	28471										
MICALCL	84953	hgsc.bcm.edu	37	chr11	12315446	12315446	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	gctggagaagaccgggaaaaAgggagtactggagccaggaa	17	6	0	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr11:12315446A>G	ENST00000256186.2	+	3	759	c.468A>G	c.(466-468)aaA>aaG	p.K156K		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	156					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		ACCGGGAAAAAGGGAGTACTG	0.562																																					p.K156K		Atlas-SNP	.											.	MICALCL	59	.	0			c.A468G						.						61	70	67					11																	12315446		1953	4135	6088	SO:0001819	synonymous_variant	84953	exon3			GGAAAAAGGGAGT	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.468A>G	chr11.hg19:g.12315446A>G		95.0	0.0		111.0	5.0	NM_032867	Q7RTP7|Q96JU6	Silent	SNP	ENST00000256186.2	hg19	CCDS41620.1																																																																																			.	.		0.562	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867		G	12315446	A	G	12315446	2	3	193	1	0	0	0	0	0	0	0	1	9581	69	3	2		2	MICALCL	11	12315446	Silent	SNP	A	TCGA-DD-AADK-01A-11D-A40R-10	12034138	12315446	122691070	33	28472										
BBOX1	8424	hgsc.bcm.edu	37	chr11	27114762	27114762	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	agctacccactttggattttGaagatgttttaagatatgat	8	5	0	4			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr11:27114762G>A	ENST00000529202.1	+	4	721	c.382G>A	c.(382-384)Gaa>Aaa	p.E128K	BBOX1_ENST00000263182.3_Missense_Mutation_p.E128K|RP11-1L12.3_ENST00000530430.1_RNA|BBOX1_ENST00000525090.1_Missense_Mutation_p.E128K|RP11-1L12.3_ENST00000526061.1_RNA|BBOX1_ENST00000527505.1_Intron|RP11-1L12.3_ENST00000525302.1_RNA|BBOX1_ENST00000528583.1_Missense_Mutation_p.E128K			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	128					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	TTTGGATTTTGAAGATGTTTT	0.408																																					p.E128K		Atlas-SNP	.											BBOX1,right_upper_lobe,carcinoma,0,1	BBOX1	46	.	0			c.G382A						.						73	73	73					11																	27114762		2202	4298	6500	SO:0001583	missense	8424	exon5			GATTTTGAAGATG	AF082868	CCDS7862.1	11p	2008-02-01			ENSG00000129151	ENSG00000129151	1.14.11.1		964	protein-coding gene	gene with protein product		603312		BBOX		9753662	Standard	XM_005253159		Approved	gamma-BBH, G-BBH, BBH	uc001mre.1	O75936	OTTHUMG00000166121	ENST00000529202.1:c.382G>A	chr11.hg19:g.27114762G>A	ENSP00000435781:p.Glu128Lys	105.0	0.0		113.0	26.0	NM_003986	B2R8L7|D3DQZ1|Q6IBJ2	Missense_Mutation	SNP	ENST00000529202.1	hg19	CCDS7862.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.044333	0.55110	.	.	ENSG00000129151	ENST00000529202;ENST00000263182;ENST00000528583;ENST00000525090	D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58	5.5	4.58	0.56647	.	0.258585	0.43747	D	0.000524	T	0.73410	0.3583	L	0.41236	1.265	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.65619	-0.6124	10	0.14656	T	0.56	.	11.3317	0.49479	0.0872:0.0:0.9128:0.0	.	128	O75936	BODG_HUMAN	K	128	ENSP00000435781:E128K;ENSP00000263182:E128K;ENSP00000434918:E128K;ENSP00000433772:E128K	ENSP00000263182:E128K	E	+	1	0	BBOX1	27071338	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.050000	0.64251	2.576000	0.86940	0.650000	0.86243	GAA	.	.		0.408	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986		A	27114762	G	A	27114762	3	1	193	1	0	0	0	0	1	0	0	0	1334	1291	45	3	392	3	BBOX1	11	27114762	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10	14799316	27114762	107891754	34	28473										
UCP2	7351	hgsc.bcm.edu	37	chr11	73687988	73687988	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	gaatcggacctttaccacatCcgtgggctgggccacagcca	11	14	0	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr11:73687988C>A	ENST00000310473.3	-	5	1254	c.412G>T	c.(412-414)Gat>Tat	p.D138Y	UCP2_ENST00000542615.1_5'Flank|UCP2_ENST00000536983.1_Missense_Mutation_p.D138Y	NM_003355.2	NP_003346.2	P55851	UCP2_HUMAN	uncoupling protein 2 (mitochondrial, proton carrier)	138					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to amino acid starvation (GO:0034198)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|female pregnancy (GO:0007565)|liver regeneration (GO:0097421)|mitochondrial transport (GO:0006839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|positive regulation of cell death (GO:0010942)|proton transport (GO:0015992)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				large_intestine(1)|lung(3)|prostate(1)	5	Breast(11;0.000112)					TTTACCACATCCGTGGGCTGG	0.632																																					p.D138Y	Colon(191;388 2040 43557 45622 48925)	Atlas-SNP	.											.	UCP2	24	.	0			c.G412T						.						69	69	69					11																	73687988		2200	4293	6493	SO:0001583	missense	7351	exon5			CCACATCCGTGGG	U76367	CCDS8228.1	11q13	2014-02-12						"Solute carriers"	12518	protein-coding gene	gene with protein product		601693	"body mass index QTL 4", "body mass index quantitative trait 4"	BMIQ4		9196039, 11381268	Standard	NM_003355		Approved	SLC25A8	uc001oup.1	P55851		ENST00000310473.3:c.412G>T	chr11.hg19:g.73687988C>A	ENSP00000312029:p.Asp138Tyr	75.0	0.0		107.0	20.0	NM_003355	Q4PJH8|Q53HM3	Missense_Mutation	SNP	ENST00000310473.3	hg19	CCDS8228.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.028710	0.93518	.	.	ENSG00000175567	ENST00000310473;ENST00000536983;ENST00000544615;ENST00000545212	D;D;D;D	0.84660	-1.88;-1.88;-1.88;-1.88	5.92	5.92	0.95590	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.94703	0.8291	M	0.93720	3.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.95353	0.8448	10	0.87932	D	0	-24.0112	18.8845	0.92370	0.0:1.0:0.0:0.0	.	138;138	F5GX45;P55851	.;UCP2_HUMAN	Y	138;138;111;22	ENSP00000312029:D138Y;ENSP00000441147:D138Y;ENSP00000439951:D111Y;ENSP00000439706:D22Y	ENSP00000312029:D138Y	D	-	1	0	UCP2	73365636	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.813000	0.96785	0.561000	0.74099	GAT	.	.		0.632	UCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398108.1	NM_003355		A	73687988	C	A	73687988	3	1	193	1	0	0	0	0	1	0	0	0	16946	855	30	3	533	3	UCP2	11	73687988	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	46573226	73687988	61318528	35	28474										
GALNT6	11226	hgsc.bcm.edu	37	chr12	51773494	51773494	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	acatccctatgcaggaggaaGaggaagagcacaaaggcgca	13	9	0	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr12:51773494G>A	ENST00000543196.2	-	2	277	c.72C>T	c.(70-72)ctC>ctT	p.L24L	GALNT6_ENST00000603203.1_5'Flank|GALNT6_ENST00000356317.3_Silent_p.L24L			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	24					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GCAGGAGGAAGAGGAAGAGCA	0.637																																					p.L24L		Atlas-SNP	.											.	GALNT6	63	.	0			c.C72T						.						39	42	41					12																	51773494		2203	4300	6503	SO:0001819	synonymous_variant	11226	exon3			GAGGAAGAGGAAG	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.72C>T	chr12.hg19:g.51773494G>A		37.0	0.0		36.0	9.0	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Silent	SNP	ENST00000543196.2	hg19	CCDS8813.1																																																																																			.	.		0.637	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		A	51773494	G	A	51773494	2	1	193	1	0	0	0	0	0	0	0	1	6225	929	33	3		3	GALNT6	12	51773494	Silent	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10		51773494	82078401	36	28475										
OR9K2	441639	hgsc.bcm.edu	37	chr12	55524551	55524551	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tttctagagaagaaaaatatTattctttgattattatttct	4	3	3	3			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr12:55524551T>C	ENST00000305377.5	+	1	1087	c.999T>C	c.(997-999)atT>atC	p.I333I		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	333						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						AGAAAAATATTATTCTTTGAT	0.308																																					p.I333I		Atlas-SNP	.											.	OR9K2	63	.	0			c.T999C						.						23	24	24					12																	55524551		2117	4241	6358	SO:0001819	synonymous_variant	441639	exon1			AAATATTATTCTT	BK004326	CCDS31814.1	12q13.2	2012-08-09						"GPCR / Class A : Olfactory receptors"	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.999T>C	chr12.hg19:g.55524551T>C		40.0	0.0		53.0	9.0	NM_001005243	B9EH19|Q6IFD6	Silent	SNP	ENST00000305377.5	hg19	CCDS31814.1																																																																																			.	.		0.308	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1			C	55524551	T	C	55524551	2	2	193	1	0	0	0	0	0	0	0	1	11263	1742	61	2		2	OR9K2	12	55524551	Silent	SNP	T	TCGA-DD-AADK-01A-11D-A40R-10	3751057	55524551	78327344	37	28476										
ESYT1	23344	hgsc.bcm.edu	37	chr12	56532051	56532051	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	gtcccactgctgctgagttaGaggaggtagggcaggagact	16	8	0	3			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr12:56532051G>A	ENST00000394048.5	+	21	2596	c.2332G>A	c.(2332-2334)Gag>Aag	p.E778K	ESYT1_ENST00000550878.1_3'UTR|ESYT1_ENST00000541590.1_Missense_Mutation_p.E788K|ESYT1_ENST00000267113.4_Missense_Mutation_p.E788K	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	778					lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						TGCTGAGTTAGAGGAGGTAGG	0.607																																					p.E788K		Atlas-SNP	.											.	ESYT1	84	.	0			c.G2362A						.						85	86	86					12																	56532051		2203	4300	6503	SO:0001583	missense	23344	exon21			GAGTTAGAGGAGG	AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"Synaptotagmins"	29534	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member A"	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.2332G>A	chr12.hg19:g.56532051G>A	ENSP00000377612:p.Glu778Lys	78.0	0.0		108.0	14.0	NM_001184796	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Missense_Mutation	SNP	ENST00000394048.5	hg19	CCDS8904.1	.	.	.	.	.	.	.	.	.	.	G	17.98	3.521037	0.64747	.	.	ENSG00000139641	ENST00000394048;ENST00000402331;ENST00000267113;ENST00000541590	T;T;T	0.56275	0.47;0.49;0.49	5.38	5.38	0.77491	.	0.155344	0.56097	D	0.000028	T	0.34571	0.0902	N	0.05383	-0.06	0.42720	D	0.993679	B;B	0.31837	0.342;0.141	B;B	0.35413	0.202;0.019	T	0.20338	-1.0278	10	0.11485	T	0.65	-28.6595	16.9874	0.86344	0.0:0.0:1.0:0.0	.	788;778	Q9BSJ8-2;Q9BSJ8	.;ESYT1_HUMAN	K	778;732;788;788	ENSP00000377612:E778K;ENSP00000267113:E788K;ENSP00000445952:E788K	ENSP00000267113:E788K	E	+	1	0	ESYT1	54818318	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.215000	0.51169	2.682000	0.91365	0.561000	0.74099	GAG	.	.		0.607	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292		A	56532051	G	A	56532051	3	1	193	1	0	0	0	0	1	0	0	0	5266	943	33	3	2444	3	ESYT1	12	56532051	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10	1007500	56532051	77319844	38	28477										
SHMT2	6472	hgsc.bcm.edu	37	chr12	57627403	57627403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ttctgaagaatgctcgggccAtggcagatgccctgctagag	13	10	1	4			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr12:57627403A>G	ENST00000328923.3	+	9	1533	c.1081A>G	c.(1081-1083)Atg>Gtg	p.M361V	SHMT2_ENST00000449049.3_Missense_Mutation_p.M340V|SHMT2_ENST00000393827.4_Missense_Mutation_p.M265V|SHMT2_ENST00000414700.3_Missense_Mutation_p.M340V|SHMT2_ENST00000553474.1_Missense_Mutation_p.M340V|SHMT2_ENST00000557487.1_Missense_Mutation_p.M351V	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	361					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	TGCTCGGGCCATGGCAGATGC	0.607																																					p.M361V	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.A1081G						.						82	71	75					12																	57627403		2203	4300	6503	SO:0001583	missense	6472	exon9			CGGGCCATGGCAG	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.1081A>G	chr12.hg19:g.57627403A>G	ENSP00000333667:p.Met361Val	55.0	0.0		85.0	11.0	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	hg19	CCDS8934.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.56|18.56	3.649772|3.649772	0.67358|0.67358	.|.	.|.	ENSG00000182199|ENSG00000182199	ENST00000557529|ENST00000328923;ENST00000557487;ENST00000555634;ENST00000414700;ENST00000553474;ENST00000449049;ENST00000393827	.|T;T;T;T;T;T;T	.|0.42513	.|0.97;0.97;0.97;0.97;0.97;0.97;0.97	4.32|4.32	4.32|4.32	0.51571|0.51571	.|Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.56804|0.56804	0.2010|0.2010	M|M	0.80982|0.80982	2.52|2.52	0.58432|0.58432	D|D	0.999999|0.999999	.|B;P;P;B;P	.|0.49358	.|0.417;0.792;0.923;0.261;0.788	.|B;B;P;B;P	.|0.52481	.|0.374;0.411;0.7;0.42;0.447	T|T	0.63479|0.63479	-0.6628|-0.6628	5|10	.|0.56958	.|D	.|0.05	-1.5384|-1.5384	12.9188|12.9188	0.58220|0.58220	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|370;351;265;292;361	.|B4DWA7;Q8N1A5;B4DLV4;B4DP88;P34897	.|.;.;.;.;GLYM_HUMAN	R|V	160|361;351;200;340;340;340;265	.|ENSP00000333667:M361V;ENSP00000452315:M351V;ENSP00000450930:M200V;ENSP00000406881:M340V;ENSP00000452419:M340V;ENSP00000413770:M340V;ENSP00000377413:M265V	.|ENSP00000333667:M361V	H|M	+|+	2|1	0|0	SHMT2|SHMT2	55913670|55913670	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	3.453000|3.453000	0.52978|0.52978	1.953000|1.953000	0.56701|0.56701	0.459000|0.459000	0.35465|0.35465	CAT|ATG	.	.		0.607	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412		G	57627403	A	G	57627403	3	3	193	1	0	0	0	0	1	0	0	0	14301	217	8	2	1115	2	SHMT2	12	57627403	Missense_Mutation	SNP	A	TCGA-DD-AADK-01A-11D-A40R-10	1095352	57627403	76224492	39	28478										
MVK	4598	hgsc.bcm.edu	37	chr12	110029107	110029107	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	catctccctggagtgtgagcGcgtgctgggagagatggggg	19	8	1	2	rs104895352		TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr12:110029107G>A	ENST00000228510.3	+	9	906	c.830G>A	c.(829-831)cGc>cAc	p.R277H	MVK_ENST00000539575.1_Missense_Mutation_p.R225H|MVK_ENST00000541384.1_Missense_Mutation_p.R83H|MVK_ENST00000539696.1_5'UTR|MVK_ENST00000392727.3_Missense_Mutation_p.R225H	NM_000431.2|NM_001114185.1	NP_000422.1|NP_001107657.1	Q03426	KIME_HUMAN	mevalonate kinase	277					cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|negative regulation of inflammatory response (GO:0050728)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|mevalonate kinase activity (GO:0004496)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8						GAGTGTGAGCGCGTGCTGGGA	0.607																																					p.R277H		Atlas-SNP	.											.	MVK	42	.	0			c.G830A	GRCh37	CM055448	MVK	M	rs104895352	.						75	76	76					12																	110029107		2203	4300	6503	SO:0001583	missense	4598	exon9			GTGAGCGCGTGCT	M88468	CCDS9132.1, CCDS73522.1	12q24	2014-09-17	2008-01-30		ENSG00000110921	ENSG00000110921	2.7.1.36		7530	protein-coding gene	gene with protein product	"LH receptor mRNA-binding protein", "mevalonic aciduria"	251170	"mevalonate kinase (mevalonic aciduria)"			1377680	Standard	XM_005253883		Approved	LRBP, MK	uc001toy.4	Q03426	OTTHUMG00000169256	ENST00000228510.3:c.830G>A	chr12.hg19:g.110029107G>A	ENSP00000228510:p.Arg277His	73.0	0.0		88.0	9.0	NM_000431		Missense_Mutation	SNP	ENST00000228510.3	hg19	CCDS9132.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.645874	0.47258	.	.	ENSG00000110921	ENST00000228510;ENST00000392727;ENST00000539575;ENST00000541384	D;D;D;D	0.94650	-3.48;-3.48;-3.48;-3.48	4.6	1.78	0.24846	.	0.175457	0.51477	D	0.000092	D	0.91778	0.7399	M	0.79805	2.47	0.39377	D	0.966193	B;B	0.29037	0.052;0.231	B;B	0.17722	0.019;0.006	D	0.86440	0.1766	10	0.48119	T	0.1	-13.0518	6.3446	0.21343	0.3002:0.0:0.6998:0.0	.	225;277	F5H8H2;Q03426	.;KIME_HUMAN	H	277;225;225;83	ENSP00000228510:R277H;ENSP00000376487:R225H;ENSP00000443551:R225H;ENSP00000443182:R83H	ENSP00000228510:R277H	R	+	2	0	MVK	108513490	0.991000	0.36638	0.897000	0.35233	0.982000	0.71751	2.330000	0.43885	0.193000	0.20303	0.655000	0.94253	CGC	.	.		0.607	MVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403143.1	NM_000431		A	110029107	G	A	110029107	3	1	193	1	0	0	0	0	1	0	0	0	10004	1087	38	1	860	1	MVK	12	110029107	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10	52401704	110029107	23822788	40	28479										
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58938977	58938977	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ttccaggaactaactttgatGaaataatcgatgtcatacag	7	7	1	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr14:58938977G>A	ENST00000556134.1	+	19	2843	c.2569G>A	c.(2569-2571)Gaa>Aaa	p.E857K	KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000261244.5_Missense_Mutation_p.E796K|KIAA0586_ENST00000354386.6_Missense_Mutation_p.E925K|KIAA0586_ENST00000423743.3_Missense_Mutation_p.E828K	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	857					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TAACTTTGATGAAATAATCGA	0.333																																					p.E925K		Atlas-SNP	.											.	KIAA0586	180	.	0			c.G2773A						.						55	52	53					14																	58938977		1815	4064	5879	SO:0001583	missense	9786	exon20			TTTGATGAAATAA	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.2569G>A	chr14.hg19:g.58938977G>A	ENSP00000452351:p.Glu857Lys	404.0	0.0		392.0	62.0	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	hg19	CCDS58321.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.449816	0.84101	.	.	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000423743;ENST00000261244;ENST00000546216	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.76	5.76	0.90799	.	0.136929	0.51477	D	0.000092	T	0.71056	0.3295	.	.	.	0.34179	D	0.670692	D;D;D;D;D;D	0.71674	0.995;0.995;0.997;0.998;0.995;0.995	D;D;D;D;D;D	0.78314	0.92;0.965;0.921;0.991;0.976;0.945	T	0.80151	-0.1502	9	0.66056	D	0.02	.	13.0958	0.59190	0.0:0.161:0.839:0.0	.	732;732;925;796;857;828	F5GWA3;B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20	.;.;.;.;K0586_HUMAN;.	K	925;857;828;796;732	ENSP00000346359:E925K;ENSP00000452351:E857K;ENSP00000399427:E828K;ENSP00000261244:E796K	ENSP00000261244:E796K	E	+	1	0	KIAA0586	58008730	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.238000	0.58688	2.714000	0.92807	0.591000	0.81541	GAA	.	.		0.333	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		A	58938977	G	A	58938977	3	1	193	1	0	0	0	0	1	0	0	0	8195	1291	45	3	2452	3	KIAA0586	14	58938977	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10		58938977	48410563	41	28480										
TTBK2	146057	hgsc.bcm.edu	37	chr15	43038338	43038338	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ggattgtgaggagatcctggActcttgcactgagtagtgct	14	7	1	3			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr15:43038338A>T	ENST00000267890.6	-	15	3498	c.3390T>A	c.(3388-3390)agT>agA	p.S1130R	CTD-2036P10.3_ENST00000500850.2_lincRNA	NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	1130					cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		GAGATCCTGGACTCTTGCACT	0.537																																					p.S1130R		Atlas-SNP	.											.	TTBK2	82	.	0			c.T3390A						.						163	162	162					15																	43038338		1958	4133	6091	SO:0001583	missense	146057	exon15			TCCTGGACTCTTG	AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"spinocerebellar ataxia 11"	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.3390T>A	chr15.hg19:g.43038338A>T	ENSP00000267890:p.Ser1130Arg	64.0	0.0		55.0	13.0	NM_173500	O94932|Q6ZN52|Q8IVV1	Missense_Mutation	SNP	ENST00000267890.6	hg19	CCDS42029.1	.	.	.	.	.	.	.	.	.	.	A	16.51	3.143647	0.57044	.	.	ENSG00000128881	ENST00000267890;ENST00000399479;ENST00000263802	T	0.38722	1.12	5.13	2.82	0.32997	.	0.157934	0.56097	D	0.000022	T	0.44767	0.1309	N	0.25890	0.77	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.22103	-1.0226	10	0.34782	T	0.22	.	7.3879	0.26893	0.7023:0.0:0.2977:0.0	.	1061;1130	Q6IQ55-2;Q6IQ55	.;TTBK2_HUMAN	R	1130;1060;1535	ENSP00000267890:S1130R	ENSP00000263802:S1535R	S	-	3	2	TTBK2	40825630	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.114000	0.31196	0.434000	0.26340	0.533000	0.62120	AGT	.	.		0.537	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500		T	43038338	A	T	43038338	3	4	193	1	0	0	0	0	1	0	0	0	16692	272	10	4	348	4	TTBK2	15	43038338	Missense_Mutation	SNP	A	TCGA-DD-AADK-01A-11D-A40R-10		43038338	59493054	42	28481										
CRLF3	51379	hgsc.bcm.edu	37	chr17	29120592	29120592	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	gggtctatgtgcaatactatGaattcagtttcagaacctac	8	8	3	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr17:29120592G>C	ENST00000324238.6	-	5	826	c.702C>G	c.(700-702)ttC>ttG	p.F234L	CRLF3_ENST00000544695.1_Missense_Mutation_p.F118L|CRLF3_ENST00000577725.1_Intron|CTD-2349P21.9_ENST00000580085.1_lincRNA	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	234	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				GCAATACTATGAATTCAGTTT	0.458																																					p.F234L	Pancreas(30;346 881 29244 33464 41299)	Atlas-SNP	.											.	CRLF3	36	.	0			c.C702G						.						101	97	98					17																	29120592		2203	4300	6503	SO:0001583	missense	51379	exon5			TACTATGAATTCA	AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.702C>G	chr17.hg19:g.29120592G>C	ENSP00000318804:p.Phe234Leu	90.0	0.0		130.0	9.0	NM_015986	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Missense_Mutation	SNP	ENST00000324238.6	hg19	CCDS32607.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.834762	0.91036	.	.	ENSG00000176390	ENST00000324238;ENST00000544695	T;T	0.27557	1.66;1.66	5.64	4.67	0.58626	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.33933	0.0880	L	0.38175	1.15	0.80722	D	1	D	0.55385	0.971	P	0.53062	0.717	T	0.03852	-1.0998	10	0.13470	T	0.59	-15.6682	14.4272	0.67225	0.0715:0.0:0.9285:0.0	.	234	Q8IUI8	CRLF3_HUMAN	L	234;118	ENSP00000318804:F234L;ENSP00000444188:F118L	ENSP00000318804:F234L	F	-	3	2	CRLF3	26144718	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.563000	0.45922	1.377000	0.46286	0.591000	0.81541	TTC	.	.		0.458	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444354.1			C	29120592	G	C	29120592	3	2	193	1	0	0	0	0	1	0	0	0	3890	1281	45	4	642	4	CRLF3	17	29120592	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10		29120592	52074618	43	28482										
ERN1	2081	hgsc.bcm.edu	37	chr17	62125306	62125306	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ggcgtttctgaggatccatcGcaatcatcttctctatcaat	7	11	5	1	rs563941838		TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr17:62125306G>T	ENST00000433197.3	-	19	2536	c.2441C>A	c.(2440-2442)gCg>gAg	p.A814E		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						AGGATCCATCGCAATCATCTT	0.468																																					p.A814E		Atlas-SNP	.											.	ERN1	102	.	0			c.C2441A						.						86	84	85					17																	62125306		1950	4149	6099	SO:0001583	missense	2081	exon19			TCCATCGCAATCA	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"inositol-requiring enzyme 1"	604033	"ER to nucleus signalling 1"			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.2441C>A	chr17.hg19:g.62125306G>T	ENSP00000401445:p.Ala814Glu	58.0	0.0		60.0	4.0	NM_001433		Missense_Mutation	SNP	ENST00000433197.3	hg19	CCDS45762.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.853757	0.32791	.	.	ENSG00000178607	ENST00000433197	T	0.64438	-0.1	5.23	5.23	0.72850	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.240041	0.44097	D	0.000485	T	0.43100	0.1232	N	0.11154	0.105	0.18873	N	0.999988	B	0.28233	0.204	B	0.31495	0.131	T	0.31752	-0.9932	10	0.26408	T	0.33	-13.2305	12.3599	0.55197	0.0:0.0:0.7177:0.2823	.	814	O75460	ERN1_HUMAN	E	814	ENSP00000401445:A814E	ENSP00000401445:A814E	A	-	2	0	ERN1	59479038	0.993000	0.37304	0.268000	0.24571	0.573000	0.36030	3.574000	0.53863	2.600000	0.87896	0.491000	0.48974	GCG	.	.		0.468	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		T	62125306	G	T	62125306	3	4	193	1	0	0	0	0	1	0	0	0	5239	1087	38	1	508	1	ERN1	17	62125306	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10	33004714	62125306	19069904	44	28483										
RNF213	57674	hgsc.bcm.edu	37	chr17	78269372	78269372	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	atcaggtgaagagatacctgTggcaacatctgaaaaaacac	9	8	2	3			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr17:78269372T>C	ENST00000582970.1	+	10	1914	c.1771T>C	c.(1771-1773)Tgg>Cgg	p.W591R	RNF213_ENST00000508628.2_Missense_Mutation_p.W640R|RNF213_ENST00000319921.4_Missense_Mutation_p.W591R|RNF213_ENST00000456466.1_Missense_Mutation_p.W591R	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	591					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GAGATACCTGTGGCAACATCT	0.517																																					p.W591R		Atlas-SNP	.											.	RNF213	766	.	0			c.T1771C						.						70	66	67					17																	78269372		2203	4300	6503	SO:0001583	missense	57674	exon10			TACCTGTGGCAAC	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.1771T>C	chr17.hg19:g.78269372T>C	ENSP00000464087:p.Trp591Arg	95.0	0.0		116.0	12.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	T	3.718	-0.058119	0.07317	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	.	.	.	4.22	4.22	0.49857	.	0.210998	0.32430	N	0.006120	T	0.70150	0.3191	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.68522	-0.5386	9	0.33141	T	0.24	-19.945	10.307	0.43687	0.0:0.0:0.0:1.0	.	591;591	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	R	591;640;591;591	.	ENSP00000324392:W591R	W	+	1	0	RNF213	75883967	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	1.377000	0.34317	1.851000	0.53745	0.456000	0.33151	TGG	.	.		0.517	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		C	78269372	T	C	78269372	3	2	193	1	0	0	0	0	1	0	0	0	13492	1696	59	2	1956	2	RNF213	17	78269372	Missense_Mutation	SNP	T	TCGA-DD-AADK-01A-11D-A40R-10	16144066	78269372	2925838	45	28484										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5423479	5423479	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ggctcttctcgtttgcgcttGtgtcctgccactataacgaa	9	12	2	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr18:5423479G>A	ENST00000341928.2	-	11	1577	c.1237C>T	c.(1237-1239)Caa>Taa	p.Q413*	EPB41L3_ENST00000342933.3_Nonsense_Mutation_p.Q413*|EPB41L3_ENST00000540638.2_Nonsense_Mutation_p.Q413*|EPB41L3_ENST00000544123.1_Nonsense_Mutation_p.Q413*|EPB41L3_ENST00000400111.3_Nonsense_Mutation_p.Q413*|EPB41L3_ENST00000542652.2_5'UTR	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	413	Hydrophilic.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GTTTGCGCTTGTGTCCTGCCA	0.463																																					p.Q413X		Atlas-SNP	.											.	EPB41L3	222	.	0			c.C1237T						.						128	99	109					18																	5423479		2203	4300	6503	SO:0001587	stop_gained	23136	exon11			GCGCTTGTGTCCT	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.1237C>T	chr18.hg19:g.5423479G>A	ENSP00000343158:p.Gln413*	143.0	0.0		166.0	31.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Nonsense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	41	8.958766	0.99018	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	.	.	.	X	413;304;413;304;413;413	.	ENSP00000343158:Q413X	Q	-	1	0	EPB41L3	5413479	1.000000	0.71417	0.990000	0.47175	0.568000	0.35870	9.830000	0.99415	2.894000	0.99253	0.591000	0.81541	CAA	.	.		0.463	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		A	5423479	G	A	5423479	4	1	193	1	0	0	0	0	0	1	0	0	5156	1386	48	3	2074	3	EPB41L3	18	5423479	Nonsense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10		5423479	72653769	46	28485										
RPRD1A	55197	hgsc.bcm.edu	37	chr18	33607210	33607210	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	taaagaagctatcctctgatGaactgctgcatcacctgagg	9	10	2	4			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr18:33607210G>A	ENST00000399022.4	-	5	721	c.550C>T	c.(550-552)Cat>Tat	p.H184Y	RPRD1A_ENST00000590898.1_Missense_Mutation_p.H148Y|RPRD1A_ENST00000357384.4_Missense_Mutation_p.H184Y|RPRD1A_ENST00000319040.6_Missense_Mutation_p.H184Y|RPRD1A_ENST00000337059.5_Missense_Mutation_p.H148Y|RPRD1A_ENST00000588737.1_Missense_Mutation_p.H148Y	NM_018170.3	NP_060640.2	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing 1A	184					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(2)	12						ATCCTCTGATGAACTGCTGCA	0.358																																					p.H184Y		Atlas-SNP	.											.	RPRD1A	30	.	0			c.C550T						.						124	126	125					18																	33607210		2203	4300	6503	SO:0001583	missense	55197	exon5			TCTGATGAACTGC	AF419845	CCDS11917.1	18q12.2	2012-02-09	2008-08-15		ENSG00000141425	ENSG00000141425			25560	protein-coding gene	gene with protein product	"cyclin-dependent kinase 2B-inhibitor-related protein", "Cyclin-dependent kinase inhibitor 2B-related protein (p15INK4B-related protein)"	610347				12470661, 22231121	Standard	NM_018170		Approved	P15RS, FLJ10656, HsT3101	uc002kzg.3	Q96P16	OTTHUMG00000132591	ENST00000399022.4:c.550C>T	chr18.hg19:g.33607210G>A	ENSP00000381984:p.His184Tyr	208.0	0.0		204.0	46.0	NM_018170	A8KA42|B2RBA3|Q7Z5G8|Q96FY9|Q9NVL4	Missense_Mutation	SNP	ENST00000399022.4	hg19	CCDS11917.1	.	.	.	.	.	.	.	.	.	.	G	18.80	3.701162	0.68501	.	.	ENSG00000141425	ENST00000399022;ENST00000357384;ENST00000337059;ENST00000319040	.	.	.	5.22	5.22	0.72569	.	0.091610	0.85682	D	0.000000	T	0.57169	0.2035	L	0.44542	1.39	0.43043	D	0.994634	P;P;P	0.47253	0.892;0.692;0.892	P;B;P	0.45712	0.491;0.216;0.491	T	0.63088	-0.6715	9	0.72032	D	0.01	-9.3564	16.6336	0.85040	0.0:0.0:1.0:0.0	.	184;184;148	Q96P16-2;Q96P16;Q96P16-3	.;RPR1A_HUMAN;.	Y	184;184;148;184	.	ENSP00000314602:H184Y	H	-	1	0	RPRD1A	31861208	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.504000	0.81646	2.583000	0.87209	0.650000	0.86243	CAT	.	.		0.358	RPRD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255802.1	NM_018170		A	33607210	G	A	33607210	3	1	193	1	0	0	0	0	1	0	0	0	13630	1290	45	3	400	3	RPRD1A	18	33607210	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10	28183731	33607210	44470038	47	28486										
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39966766	39966766	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	aggacagtgagaaggttgtcAgcatttccagtgagcacctg	13	8	1	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr19:39966766A>G	ENST00000599117.1	+	30	3437	c.3070A>G	c.(3070-3072)Agc>Ggc	p.S1024G	SUPT5H_ENST00000432763.2_Missense_Mutation_p.S1024G|SUPT5H_ENST00000598725.1_Missense_Mutation_p.S1024G|SUPT5H_ENST00000359191.6_Missense_Mutation_p.S1020G|SUPT5H_ENST00000402194.2_Missense_Mutation_p.S1020G			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	1024					7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GAAGGTTGTCAGCATTTCCAG	0.582																																					p.S1024G		Atlas-SNP	.											.	SUPT5H	119	.	0			c.A3070G						.						96	76	83					19																	39966766		2203	4300	6503	SO:0001583	missense	6829	exon28			GTTGTCAGCATTT	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"suppressor of Ty (S.cerevisiae) 5 homolog"			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.3070A>G	chr19.hg19:g.39966766A>G	ENSP00000470252:p.Ser1024Gly	42.0	0.0		79.0	24.0	NM_003169	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	hg19	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.029905	0.54790	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.54095	0.1837	M	0.72894	2.215	0.80722	D	1	B;P	0.34546	0.415;0.456	B;B	0.31442	0.112;0.13	T	0.56341	-0.7995	8	.	.	.	-30.1885	12.7754	0.57443	1.0:0.0:0.0:0.0	.	1020;1024	O00267-2;O00267	.;SPT5H_HUMAN	G	1024;1020;1002;1024	.	.	S	+	1	0	SUPT5H	44658606	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.815000	0.91973	1.852000	0.53769	0.379000	0.24179	AGC	.	.		0.582	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		G	39966766	A	G	39966766	3	3	193	1	0	0	0	0	1	0	0	0	15414	188	7	2	3180	2	SUPT5H	19	39966766	Missense_Mutation	SNP	A	TCGA-DD-AADK-01A-11D-A40R-10		39966766	19162217	48	28487										
NRSN2	80023	hgsc.bcm.edu	37	chr20	333968	333968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	agggtgagttcctggtgttgGatcagcgggcagccgactac	16	9	1	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr20:333968G>A	ENST00000382291.3	+	4	544	c.304G>A	c.(304-306)Gat>Aat	p.D102N	NRSN2_ENST00000382285.2_Missense_Mutation_p.D102N|NRSN2_ENST00000608736.1_Intron|NRSN2_ENST00000492242.1_3'UTR	NM_024958.2	NP_079234.1	Q9GZP1	NRSN2_HUMAN	neurensin 2	102						integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				endometrium(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8		all_cancers(10;0.0834)				CCTGGTGTTGGATCAGCGGGC	0.652																																					p.D102N		Atlas-SNP	.											.	NRSN2	20	.	0			c.G304A						.						78	73	75					20																	333968		2203	4300	6503	SO:0001583	missense	80023	exon4			GTGTTGGATCAGC	AL136915	CCDS12996.1	20p13	2008-02-04	2006-07-04	2006-07-04	ENSG00000125841	ENSG00000125841			16229	protein-coding gene	gene with protein product		610666	"chromosome 20 open reading frame 98"	C20orf98		16527258	Standard	NM_024958		Approved	dJ1103G7.6	uc002wdi.4	Q9GZP1	OTTHUMG00000031628	ENST00000382291.3:c.304G>A	chr20.hg19:g.333968G>A	ENSP00000371728:p.Asp102Asn	48.0	0.0		79.0	17.0	NM_024958	A8K3B2|Q6FII5|Q9NUD3	Missense_Mutation	SNP	ENST00000382291.3	hg19	CCDS12996.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.140589	0.77775	.	.	ENSG00000125841	ENST00000382291;ENST00000382285	T;T	0.35973	1.28;1.28	4.76	3.81	0.43845	.	0.055512	0.64402	D	0.000001	T	0.54095	0.1837	M	0.73217	2.22	0.35056	D	0.761106	D	0.67145	0.996	D	0.66351	0.943	T	0.67852	-0.5563	10	0.87932	D	0	-14.1649	10.2024	0.43092	0.0:0.0:0.8016:0.1984	.	102	Q9GZP1	NRSN2_HUMAN	N	102	ENSP00000371728:D102N;ENSP00000371722:D102N	ENSP00000371722:D102N	D	+	1	0	NRSN2	281968	1.000000	0.71417	0.943000	0.38184	0.953000	0.61014	5.454000	0.66651	1.226000	0.43582	0.643000	0.83706	GAT	.	.		0.652	NRSN2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077446.1	NM_024958		A	333968	G	A	333968	3	1	193	1	0	0	0	0	1	0	0	0	10672	1174	41	3	310	3	NRSN2	20	333968	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10		333968	62691552	49	28488										
RNF114	55905	hgsc.bcm.edu	37	chr20	48553085	48553085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	cggtacaggtgccctgcggaCacgtgtaagcggcgagcccg	16	13	0	0			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr20:48553085C>T	ENST00000244061.2	+	1	138	c.136C>T	c.(136-138)Cac>Tac	p.H46Y		NM_018683.3	NP_061153.1	Q9Y508	RN114_HUMAN	ring finger protein 114	46					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)	5						GCCCTGCGGACACGTGTAAGC	0.692																																					p.H46Y		Atlas-SNP	.											.	RNF114	9	.	0			c.C136T						.						8	8	8					20																	48553085		2079	4118	6197	SO:0001583	missense	55905	exon1			TGCGGACACGTGT	AF265215	CCDS33482.1	20q13	2013-01-09	2008-06-16	2008-06-16	ENSG00000124226	ENSG00000124226		"RING-type (C3HC4) zinc fingers"	13094	protein-coding gene	gene with protein product		612451	"zinc finger protein 313"	ZNF313		18364390	Standard	NM_018683		Approved	PSORS12	uc002xux.3	Q9Y508	OTTHUMG00000032709	ENST00000244061.2:c.136C>T	chr20.hg19:g.48553085C>T	ENSP00000244061:p.His46Tyr	110.0	0.0		123.0	7.0	NM_018683	B2RDQ9|B4DWY5|E1P627|Q6N0B0	Missense_Mutation	SNP	ENST00000244061.2	hg19	CCDS33482.1	.	.	.	.	.	.	.	.	.	.	C	34	5.343975	0.95807	.	.	ENSG00000124226	ENST00000449816;ENST00000244061	D	0.99557	-6.16	4.65	4.65	0.58169	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type, conserved site (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	H	0.97852	4.09	0.58432	D	0.999999	D;D	0.76494	0.999;0.995	D;P	0.83275	0.996;0.874	D	0.96755	0.9557	10	0.87932	D	0	-24.7937	16.8046	0.85623	0.0:1.0:0.0:0.0	.	46;46	Q9Y508-2;Q9Y508	.;RN114_HUMAN	Y	46	ENSP00000244061:H46Y	ENSP00000244061:H46Y	H	+	1	0	RNF114	47986492	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.134000	0.57990	2.565000	0.86533	0.555000	0.69702	CAC	.	.		0.692	RNF114-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079663.1	NM_018683		T	48553085	C	T	48553085	3	4	193	1	0	0	0	0	1	0	0	0	13444	478	17	3	138	3	RNF114	20	48553085	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	48219117	48553085	14472435	50	28489										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58467458	58467458	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	agaggatgatttttgtttagTaagttttttatttataacaa	7	1	0	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr20:58467458T>C	ENST00000357552.3	-	24	2176	c.1951A>G	c.(1951-1953)Act>Gct	p.T651A	SYCP2_ENST00000371001.2_Missense_Mutation_p.T651A			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	651					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			TTTTGTTTAGTAAGTTTTTTA	0.224																																					p.T651A		Atlas-SNP	.											.	SYCP2	204	.	0			c.A1951G						.						33	32	32					20																	58467458		2195	4279	6474	SO:0001583	missense	10388	exon23			GTTTAGTAAGTTT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1951A>G	chr20.hg19:g.58467458T>C	ENSP00000350162:p.Thr651Ala	43.0	0.0		31.0	7.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	T	0.017	-1.495187	0.01009	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.18174	2.49;2.49;2.23	5.08	-10.2	0.00374	.	1.219660	0.05641	N	0.583361	T	0.10637	0.0260	L	0.47716	1.5	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.15665	-1.0429	10	0.24483	T	0.36	1.2526	4.6103	0.12399	0.19:0.1434:0.5184:0.1482	.	651	Q9BX26	SYCP2_HUMAN	A	651	ENSP00000360040:T651A;ENSP00000350162:T651A;ENSP00000402456:T651A	ENSP00000350162:T651A	T	-	1	0	SYCP2	57900853	0.000000	0.05858	0.000000	0.03702	0.270000	0.26580	-0.702000	0.05069	-2.296000	0.00662	0.482000	0.46254	ACT	.	.		0.224	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		C	58467458	T	C	58467458	3	2	193	1	0	0	0	0	1	0	0	0	15447	1638	57	2	2729	2	SYCP2	20	58467458	Missense_Mutation	SNP	T	TCGA-DD-AADK-01A-11D-A40R-10	9914373	58467458	4558062	51	28490										
PPARA	5465	hgsc.bcm.edu	37	chr22	46614190	46614190	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ggcgaacgattcgactcaagCtggtgtatgacaagtgcgac	13	9	1	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chr22:46614190C>G	ENST00000396000.2	+	5	665	c.400C>G	c.(400-402)Ctg>Gtg	p.L134V	PPARA_ENST00000407236.1_Missense_Mutation_p.L134V|PPARA_ENST00000402126.1_Missense_Mutation_p.L134V|PPARA_ENST00000434345.2_Missense_Mutation_p.L134V|PPARA_ENST00000262735.5_Missense_Mutation_p.L134V			Q07869	PPARA_HUMAN	peroxisome proliferator-activated receptor alpha	134					behavioral response to nicotine (GO:0035095)|cellular lipid metabolic process (GO:0044255)|circadian regulation of gene expression (GO:0032922)|enamel mineralization (GO:0070166)|epidermis development (GO:0008544)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|negative regulation of appetite (GO:0032099)|negative regulation of blood pressure (GO:0045776)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of glycolytic process (GO:0045820)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter (GO:0072366)|regulation of circadian rhythm (GO:0042752)|regulation of glycolytic by positive regulation of transcription from RNA polymerase II promoter (GO:0072363)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|lipid binding (GO:0008289)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	15		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Indomethacin(DB00328)	TCGACTCAAGCTGGTGTATGA	0.483																																					p.L134V		Atlas-SNP	.											.	PPARA	36	.	0			c.C400G						.						116	102	107					22																	46614190		2203	4300	6503	SO:0001583	missense	5465	exon5			CTCAAGCTGGTGT	L02932	CCDS33669.1	22q12-q13.1	2013-01-16	2006-10-17		ENSG00000186951	ENSG00000186951		"Nuclear hormone receptors"	9232	protein-coding gene	gene with protein product		170998	"peroxisome proliferative activated receptor, alpha"	PPAR		7684926, 10591208	Standard	XM_005261655		Approved	hPPAR, NR1C1	uc003bgx.1	Q07869	OTTHUMG00000150443	ENST00000396000.2:c.400C>G	chr22.hg19:g.46614190C>G	ENSP00000379322:p.Leu134Val	71.0	0.0		83.0	14.0	NM_001001928	B0G0X3|Q16241|Q6I9S0|Q92486|Q92689|Q9Y3N1	Missense_Mutation	SNP	ENST00000396000.2	hg19	CCDS33669.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.559141	0.86335	.	.	ENSG00000186951	ENST00000396000;ENST00000262735;ENST00000407236;ENST00000402126;ENST00000434345	D;D;D;D;D	0.96522	-4.04;-4.04;-4.04;-4.04;-4.04	5.67	4.66	0.58398	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (3);	0.000000	0.85682	D	0.000000	D	0.97445	0.9164	M	0.68317	2.08	0.80722	D	1	D;D	0.64830	0.994;0.994	D;D	0.85130	0.997;0.997	D	0.97454	1.0030	10	0.87932	D	0	.	13.1436	0.59448	0.0:0.9238:0.0:0.0762	.	134;134	F1D8S4;Q07869	.;PPARA_HUMAN	V	134	ENSP00000379322:L134V;ENSP00000262735:L134V;ENSP00000385523:L134V;ENSP00000385246:L134V;ENSP00000408149:L134V	ENSP00000262735:L134V	L	+	1	2	PPARA	44992854	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	4.804000	0.62554	2.658000	0.90341	0.591000	0.81541	CTG	.	.		0.483	PPARA-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318129.3	NM_001001928		G	46614190	C	G	46614190	3	3	193	1	0	0	0	0	1	0	0	0	12306	796	28	4	410	4	PPARA	22	46614190	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10		46614190	4690376	52	28491										
TXLNG	55787	hgsc.bcm.edu	37	chrX	16836781	16836782	+	Frame_Shift_Ins	INS	-	-	T													0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	taactctcaatcaaatgataINSttcttcaacatcaaggctca							TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chrX:16836781_16836782insT	ENST00000380122.5	+	2	248_249	c.187_188insT	c.(187-189)attfs	p.I63fs	TXLNG_ENST00000398155.4_Intron	NM_018360.2	NP_060830.2	Q9NUQ3	TXLNG_HUMAN	taxilin gamma	63					cell cycle (GO:0007049)|regulation of bone mineralization (GO:0030500)|regulation of cell cycle (GO:0051726)|regulation of cell cycle process (GO:0010564)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)	protein heterodimerization activity (GO:0046982)	p.I63S(1)		breast(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	15						ATCAAATGATATTCTTCAACAT	0.396																																					p.I63fs		Atlas-INDEL	.											.	TXLNG	40	.	1	Substitution - Missense(1)	skin(1)	c.187_188insT						.																																			SO:0001589	frameshift_variant	55787	exon2			.	AK002071	CCDS14178.1, CCDS55373.1	Xp22.2	2014-05-07	2010-04-20	2010-04-20	ENSG00000086712	ENSG00000086712			18578	protein-coding gene	gene with protein product	"lipopolysaccharide specific response-5 protein", "factor inhibiting activating transcription factor 4 (ATF4)-mediated transcription"	300677	"chromosome X open reading frame 15"	CXorf15		15911876, 15184072, 16831913	Standard	NM_018360		Approved	FLJ11209, LSR5, FIAT, MGC126621, MGC126625, TXLNGX	uc004cxq.2	Q9NUQ3	OTTHUMG00000021196	ENST00000380122.5:c.189dupT	chrX.hg19:g.16836783_16836783dupT	ENSP00000369465:p.Ile63fs	439.0	0.0		483.0	93.0	NM_018360	Q2KQ75|Q5JNZ7|Q9P0X1	Frame_Shift_Ins	INS	ENST00000380122.5	hg19	CCDS14178.1																																																																																			.	.		0.396	TXLNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055912.1	NM_018360		T	16836782	-	T	16836781	7	5	193	1	0	1	1	0	0	0	0	0	16804	449	16	0	193	0	TXLNG	23	16836781	Frame_Shift_Ins	INS	-	TCGA-DD-AADK-01A-11D-A40R-10		16836781	138433779	53	28492										
YY2	404281	hgsc.bcm.edu	37	chrX	21875452	21875452	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	tccacgggcccagagtccacGtatgtgcagaatgtggcaaa	12	11	0	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chrX:21875452G>T	ENST00000429584.2	+	1	1348	c.850G>T	c.(850-852)Gta>Tta	p.V284L	MBTPS2_ENST00000465888.1_3'UTR|MBTPS2_ENST00000379484.5_Intron|MBTPS2_ENST00000365779.2_Intron	NM_206923.3	NP_996806.2	O15391	TYY2_HUMAN	YY2 transcription factor	284	Mediates transcriptional repression.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	19						CAGAGTCCACGTATGTGCAGA	0.532																																					p.V284L		Atlas-SNP	.											.	YY2	43	.	0			c.G850T						.						148	144	146					X																	21875452		2203	4300	6503	SO:0001583	missense	404281	exon1			GTCCACGTATGTG	AK091850	CCDS14202.1	Xp22.2-p22.1	2011-02-11			ENSG00000230797	ENSG00000230797		"Zinc fingers, C2H2-type"	31684	protein-coding gene	gene with protein product	"transcription factor yin yang 2"	300570				14702039	Standard	NM_206923		Approved	ZNF631	uc011mjp.2	O15391	OTTHUMG00000021236	ENST00000429584.2:c.850G>T	chrX.hg19:g.21875452G>T	ENSP00000389381:p.Val284Leu	152.0	0.0		180.0	39.0	NM_206923	B2RP10|Q6Q1S4	Missense_Mutation	SNP	ENST00000429584.2	hg19	CCDS14202.1	.	.	.	.	.	.	.	.	.	.	G	13.80	2.346360	0.41599	.	.	ENSG00000230797	ENST00000429584	T	0.35605	1.3	4.43	1.68	0.24146	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	U	0.000000	T	0.21347	0.0514	N	0.17922	0.545	0.50467	D	0.99987	P	0.40360	0.714	B	0.38562	0.276	T	0.03364	-1.1044	10	0.66056	D	0.02	.	7.5425	0.27746	0.3024:0.0:0.6975:0.0	.	284	O15391	TYY2_HUMAN	L	284	ENSP00000389381:V284L	ENSP00000389381:V284L	V	+	1	0	YY2	21785373	1.000000	0.71417	0.015000	0.15790	0.478000	0.33099	3.401000	0.52601	0.441000	0.26529	0.600000	0.82982	GTA	.	.		0.532	YY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056025.1	NM_206923		T	21875452	G	T	21875452	3	4	193	1	0	0	0	0	1	0	0	0	17524	1145	40	1	852	1	YY2	23	21875452	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10	5038671	21875452	133395108	54	28493										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34148744	34148744	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ggtggagactggacacccgaCgactcttgggaagctccggg	16	11	1	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chrX:34148744C>T	ENST00000346193.3	-	1	1703	c.1652G>A	c.(1651-1653)cGt>cAt	p.R551H		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	551										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						GGACACCCGACGACTCTTGGG	0.602																																					p.R551H		Atlas-SNP	.											.	FAM47A	249	.	0			c.G1652A						.						52	53	53					X																	34148744		2192	4292	6484	SO:0001583	missense	158724	exon1			ACCCGACGACTCT	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1652G>A	chrX.hg19:g.34148744C>T	ENSP00000345029:p.Arg551His	73.0	0.0		109.0	5.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	c	7.547	0.661842	0.14645	.	.	ENSG00000185448	ENST00000346193	T	0.29397	1.57	0.673	-0.29	0.12847	.	.	.	.	.	T	0.34687	0.0906	L	0.34521	1.04	0.09310	N	1	D	0.69078	0.997	D	0.64237	0.923	T	0.18272	-1.0342	8	0.42905	T	0.14	.	.	.	.	.	551	Q5JRC9	FA47A_HUMAN	H	551	ENSP00000345029:R551H	ENSP00000345029:R551H	R	-	2	0	FAM47A	34058665	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	-1.671000	0.01954	-0.242000	0.09667	-0.785000	0.03343	CGT	.	.		0.602	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		T	34148744	C	T	34148744	3	4	193	1	0	0	0	0	1	0	0	0	5577	536	19	1	727	1	FAM47A	23	34148744	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	12273292	34148744	121121816	55	28494										
GRIPAP1	56850	hgsc.bcm.edu	37	chrX	48840243	48840243	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	cttctcctgccctatttcttGaagttgttccagcagtcgac	7	13	2	1			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chrX:48840243G>T	ENST00000376441.1	-	15	1250	c.1216C>A	c.(1216-1218)Caa>Aaa	p.Q406K	GRIPAP1_ENST00000376444.3_Missense_Mutation_p.Q361K|GRIPAP1_ENST00000376425.3_Missense_Mutation_p.Q375K|GRIPAP1_ENST00000376423.4_Missense_Mutation_p.Q353K|GRIPAP1_ENST00000473581.1_5'UTR	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	406						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						CCTATTTCTTGAAGTTGTTCC	0.507																																					p.Q406K		Atlas-SNP	.											.	GRIPAP1	128	.	0			c.C1216A						.						240	181	201					X																	48840243		2203	4300	6503	SO:0001583	missense	56850	exon15			TTTCTTGAAGTTG	AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.1216C>A	chrX.hg19:g.48840243G>T	ENSP00000365624:p.Gln406Lys	99.0	0.0		90.0	18.0	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	hg19	CCDS35248.1	.	.	.	.	.	.	.	.	.	.	-	15.29	2.790949	0.50102	.	.	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291;ENST00000376423	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	4.74	4.74	0.60224	.	0.166997	0.41194	D	0.000940	T	0.36936	0.0985	L	0.53249	1.67	0.28256	N	0.925037	P;P;D	0.57257	0.914;0.859;0.979	P;P;P	0.56563	0.501;0.554;0.801	T	0.25467	-1.0131	10	0.10902	T	0.67	-1.4095	15.7813	0.78264	0.0:0.0:1.0:0.0	.	353;296;406	Q4V328-2;Q4V328-3;Q4V328	.;.;GRAP1_HUMAN	K	375;361;406;375;353	ENSP00000365608:Q375K;ENSP00000365627:Q361K;ENSP00000365624:Q406K;ENSP00000365606:Q353K	ENSP00000365606:Q353K	Q	-	1	0	GRIPAP1	48725187	1.000000	0.71417	0.976000	0.42696	0.305000	0.27757	4.768000	0.62293	1.970000	0.57323	0.522000	0.50473	CAA	.	.		0.507	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672		T	48840243	G	T	48840243	3	4	193	1	0	0	0	0	1	0	0	0	6798	1299	45	3	1411	3	GRIPAP1	23	48840243	Missense_Mutation	SNP	G	TCGA-DD-AADK-01A-11D-A40R-10	14691499	48840243	106430317	56	28495										
TRO	7216	hgsc.bcm.edu	37	chrX	54949797	54949797	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	acactgagcatatagaggctCtaaatgtcactgacgcagct	9	10	2	3			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chrX:54949797C>A	ENST00000173898.7	+	3	944	c.832C>A	c.(832-834)Cta>Ata	p.L278I	TRO_ENST00000399736.1_Intron|TRO_ENST00000319167.8_Missense_Mutation_p.L278I|TRO_ENST00000375022.4_Missense_Mutation_p.L278I|TRO_ENST00000375041.2_Intron|TRO_ENST00000484031.1_Intron|TRO_ENST00000420798.2_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	278					embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						TATAGAGGCTCTAAATGTCAC	0.507																																					p.L278I		Atlas-SNP	.											.	TRO	246	.	0			c.C832A						.						32	30	30					X																	54949797		1992	4145	6137	SO:0001583	missense	7216	exon3			GAGGCTCTAAATG	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.832C>A	chrX.hg19:g.54949797C>A	ENSP00000173898:p.Leu278Ile	262.0	0.0		289.0	60.0	NM_016157	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	hg19	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.021981	0.00414	.	.	ENSG00000067445	ENST00000173898;ENST00000319167;ENST00000375022	T;T;T	0.41758	0.99;3.79;3.79	3.13	0.337	0.15966	.	.	.	.	.	T	0.18467	0.0443	N	0.08118	0	0.09310	N	1	B;B	0.16603	0.018;0.009	B;B	0.14578	0.011;0.003	T	0.25537	-1.0129	8	.	.	.	.	4.9041	0.13789	0.0:0.5741:0.1793:0.2466	.	278;278	Q96SX2;Q12816	.;TROP_HUMAN	I	278	ENSP00000173898:L278I;ENSP00000318278:L278I;ENSP00000364162:L278I	.	L	+	1	2	TRO	54966522	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.332000	0.07904	-0.342000	0.08363	-1.563000	0.00883	CTA	.	.		0.507	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		A	54949797	C	A	54949797	3	1	193	1	0	0	0	0	1	0	0	0	16589	912	32	3	838	3	TRO	23	54949797	Missense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	6109554	54949797	100320763	57	28496										
IGSF1	3547	hgsc.bcm.edu	37	chrX	130417074	130417074	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.137931034482759	8	1	2.3552	3.68	1.93684210526316	0.672768878718535	1	0	ctggaagaagaaatttgcctCattttttattgtcttcttgt	7	6	3	2			TCGA-DD-AADK-01A-11D-A40R-10	TCGA-DD-AADK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81255bf2-6aa2-4e6b-a03b-09b29c43c763	e0c3f2fd-7b5a-4c19-828c-8f89bcfc39ee	g.chrX:130417074C>A	ENST00000361420.3	-	6	911	c.832G>T	c.(832-834)Gag>Tag	p.E278*	IGSF1_ENST00000370910.1_Nonsense_Mutation_p.E269*|IGSF1_ENST00000370903.3_Nonsense_Mutation_p.E278*|IGSF1_ENST00000370904.1_Nonsense_Mutation_p.E269*			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	278	Ig-like C2-type 3.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						AAATTTGCCTCATTTTTTATT	0.398																																					p.E278X		Atlas-SNP	.											.	IGSF1	231	.	0			c.G832T						.						113	98	103					X																	130417074		2203	4300	6503	SO:0001587	stop_gained	3547	exon6			TTGCCTCATTTTT	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.832G>T	chrX.hg19:g.130417074C>A	ENSP00000355010:p.Glu278*	450.0	0.0		470.0	26.0	NM_001555	B5MEG2|H9KV64|O15070|Q9NTC8	Nonsense_Mutation	SNP	ENST00000361420.3	hg19	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	C	32	5.120958	0.94385	.	.	ENSG00000147255	ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903	.	.	.	4.64	3.71	0.42584	.	0.290655	0.24815	N	0.035365	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	8.3888	0.32516	0.2329:0.7671:0.0:0.0	.	.	.	.	X	269;278;269;278	.	ENSP00000355010:E278X	E	-	1	0	IGSF1	130244755	1.000000	0.71417	1.000000	0.80357	0.726000	0.41606	1.212000	0.32394	2.308000	0.77769	0.594000	0.82650	GAG	.	.		0.398	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			A	130417074	C	A	130417074	4	1	193	1	0	0	0	0	0	1	0	0	7605	835	29	3	3253	3	IGSF1	23	130417074	Nonsense_Mutation	SNP	C	TCGA-DD-AADK-01A-11D-A40R-10	75467277	130417074	24853486	58	28497										
PIK3CD	5293	hgsc.bcm.edu	37	chr1	9775778	9775778	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ctggtggcccgtgagggcgaCcgcgtgaagaagctcatcaa	15	11	2	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:9775778C>A	ENST00000377346.4	+	4	516	c.321C>A	c.(319-321)gaC>gaA	p.D107E	PIK3CD_ENST00000361110.2_Missense_Mutation_p.D107E|PIK3CD_ENST00000543390.1_5'Flank|PIK3CD_ENST00000536656.1_Missense_Mutation_p.D107E	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	107					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	GTGAGGGCGACCGCGTGAAGA	0.667																																					p.D107E		Atlas-SNP	.											.	PIK3CD	86	.	0			c.C321A						.						68	68	68					1																	9775778		2203	4300	6503	SO:0001583	missense	5293	exon4			GGGCGACCGCGTG		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase, catalytic, delta polypeptide", "phosphoinositide-3-kinase C"	602839	"phosphoinositide-3-kinase, catalytic, delta polypeptide"			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.321C>A	chr1.hg19:g.9775778C>A	ENSP00000366563:p.Asp107Glu	136.0	0.0		203.0	89.0	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	hg19	CCDS104.1	.	.	.	.	.	.	.	.	.	.	C	36	5.705716	0.96812	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	T;T;T	0.45276	0.9;0.9;0.9	5.95	5.95	0.96441	Phosphatidylinositol 3-kinase, p85-binding (2);	0.043393	0.85682	D	0.000000	T	0.53302	0.1788	L	0.44542	1.39	0.80722	D	1	B;P;P	0.39480	0.096;0.675;0.526	B;P;P	0.52189	0.201;0.472;0.692	T	0.47235	-0.9133	10	0.54805	T	0.06	-37.2471	18.1519	0.89677	0.0:1.0:0.0:0.0	.	107;107;107	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	E	107	ENSP00000446444:D107E;ENSP00000366563:D107E;ENSP00000354410:D107E	ENSP00000353766:D107E	D	+	3	2	PIK3CD	9698365	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	5.431000	0.66507	2.826000	0.97356	0.563000	0.77884	GAC	.	.		0.667	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		A	9775778	C	A	9775778	3	1	194	1	0	0	0	0	1	0	0	0	11924	506	18	3	327	3	PIK3CD	1	9775778	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10		9775778	239474843	1	28498										
EPB41	2035	hgsc.bcm.edu	37	chr1	29391656	29391656	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ttaacatcaatgggcaaatcCccacaggagaaggagtgagt	11	8	1	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:29391656C>A	ENST00000343067.4	+	16	2297	c.2170C>A	c.(2170-2172)Ccc>Acc	p.P724T	EPB41_ENST00000373798.1_Missense_Mutation_p.P724T|EPB41_ENST00000373797.1_Missense_Mutation_p.P710T|EPB41_ENST00000373800.3_Missense_Mutation_p.P482T|EPB41_ENST00000347529.3_Missense_Mutation_p.P635T|EPB41_ENST00000398863.2_Missense_Mutation_p.P670T|EPB41_ENST00000356093.2_Missense_Mutation_p.P691T|EPB41_ENST00000349460.4_Missense_Mutation_p.P501T	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	724	C-terminal (CTD).				actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		TGGGCAAATCCCCACAGGAGA	0.418																																					p.P724T		Atlas-SNP	.											.	EPB41	118	.	0			c.C2170A						.						86	78	80					1																	29391656		2203	4300	6503	SO:0001583	missense	2035	exon16			CAAATCCCCACAG	BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023			3377	protein-coding gene	gene with protein product		130500	"elliptocytosis 1, RH-linked"	EL1			Standard	NM_001166005		Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.2170C>A	chr1.hg19:g.29391656C>A	ENSP00000345259:p.Pro724Thr	115.0	0.0		171.0	66.0	NM_001166005	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	Missense_Mutation	SNP	ENST00000343067.4	hg19	CCDS53288.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.753390	0.49362	.	.	ENSG00000159023	ENST00000358989;ENST00000343067;ENST00000356093;ENST00000398863;ENST00000398861;ENST00000398865;ENST00000349460;ENST00000373800;ENST00000347529;ENST00000373798;ENST00000373797	D;D;D;D;D;D;D;D	0.84660	-1.87;-1.85;-1.58;-1.84;-1.82;-1.58;-1.87;-1.88	5.99	5.99	0.97316	.	0.341500	0.31246	N	0.007996	D	0.91119	0.7204	L	0.53249	1.67	0.44711	D	0.997701	B;P;P;P;P;P;P;D;B	0.89917	0.035;0.775;0.57;0.837;0.837;0.749;0.837;1.0;0.151	B;P;B;P;P;B;P;D;B	0.85130	0.013;0.665;0.334;0.535;0.637;0.334;0.535;0.997;0.037	D	0.90307	0.4334	10	0.52906	T	0.07	.	19.4659	0.94939	0.0:1.0:0.0:0.0	.	564;670;724;691;710;687;635;482;501	E9PEX0;E9PEW9;P11171;P11171-2;P11171-7;Q59F12;P11171-5;P11171-4;P11171-3	.;.;41_HUMAN;.;.;.;.;.;.	T	687;724;691;670;564;710;501;482;635;724;710	ENSP00000345259:P724T;ENSP00000348397:P691T;ENSP00000381839:P670T;ENSP00000317597:P501T;ENSP00000362906:P482T;ENSP00000290100:P635T;ENSP00000362904:P724T;ENSP00000362903:P710T	ENSP00000345259:P724T	P	+	1	0	EPB41	29264243	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	4.277000	0.58939	2.840000	0.97914	0.655000	0.94253	CCC	.	.		0.418	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010312.1	NM_203342		A	29391656	C	A	29391656	3	1	194	1	0	0	0	0	1	0	0	0	5153	623	22	3	2228	3	EPB41	1	29391656	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	19615878	29391656	219858965	2	28499										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34204803	34204803	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ccttcaggacgcaggtgatgGtctctgagccctgagtccca	12	13	2	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:34204803G>T	ENST00000373381.4	-	15	2482	c.2306C>A	c.(2305-2307)aCc>aAc	p.T769N		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	729	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GCAGGTGATGGTCTCTGAGCC	0.597																																					p.T729N		Atlas-SNP	.											.	CSMD2	946	.	0			c.C2186A						.						64	59	61					1																	34204803		2203	4300	6503	SO:0001583	missense	114784	exon15			GTGATGGTCTCTG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.2306C>A	chr1.hg19:g.34204803G>T	ENSP00000362479:p.Thr769Asn	83.0	0.0		95.0	35.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	G	24.5	4.543313	0.86022	.	.	ENSG00000121904	ENST00000373381	T	0.66815	-0.23	6.17	6.17	0.99709	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.77143	0.4087	L	0.56199	1.76	0.80722	D	1	P;P	0.47604	0.898;0.764	P;P	0.61070	0.881;0.883	T	0.68217	-0.5467	10	0.19590	T	0.45	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	729;769	Q7Z408;E7EUA6	CSMD2_HUMAN;.	N	769	ENSP00000362479:T769N	ENSP00000241312:T729N	T	-	2	0	CSMD2	33977390	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	6.590000	0.74085	2.941000	0.99782	0.655000	0.94253	ACC	.	.		0.597	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34204803	G	T	34204803	3	4	194	1	0	0	0	0	1	0	0	0	3947	1261	44	3	8497	3	CSMD2	1	34204803	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	4813147	34204803	215045818	3	28500										
CYP4A22	284541	hgsc.bcm.edu	37	chr1	47606518	47606518	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cattcccaagtgcctgtcctTattggatatggggaggcaaa	11	9	0	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:47606518T>G	ENST00000371891.3	+	2	293	c.262T>G	c.(262-264)Tat>Gat	p.Y88D	CYP4A22_ENST00000371890.3_Missense_Mutation_p.Y88D|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000294337.3_Missense_Mutation_p.Y88D|CYP4A22_ENST00000485117.1_3'UTR	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	88						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGCCTGTCCTTATTGGATATG	0.498																																					p.Y88D	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.T262G						.						183	159	167					1																	47606518		2203	4300	6503	SO:0001583	missense	284541	exon2			TGTCCTTATTGGA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"Cytochrome P450s"	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.262T>G	chr1.hg19:g.47606518T>G	ENSP00000360958:p.Tyr88Asp	70.0	0.0		138.0	49.0	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	hg19	CCDS30707.1	.	.	.	.	.	.	.	.	.	.	t	1.347	-0.592506	0.03799	.	.	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.68624	-0.3;-0.34;-0.34	1.36	-0.637	0.11504	.	0.825859	0.10596	N	0.656257	T	0.52500	0.1738	L	0.39245	1.2	0.09310	N	1	B;B	0.13145	0.007;0.005	B;B	0.24848	0.007;0.056	T	0.46596	-0.9180	10	0.51188	T	0.08	.	3.4037	0.07333	0.0:0.2973:0.2179:0.4847	.	88;88	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	D	88	ENSP00000360957:Y88D;ENSP00000360958:Y88D;ENSP00000294337:Y88D	ENSP00000294337:Y88D	Y	+	1	0	CYP4A22	47379105	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	-0.227000	0.09126	-0.220000	0.09988	-1.527000	0.00925	TAT	.	.		0.498	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213		G	47606518	T	G	47606518	3	3	194	1	0	0	0	0	1	0	0	0	4186	1754	61	5	268	5	CYP4A22	1	47606518	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	13401715	47606518	201644103	4	28501										
DOCK7	85440	hgsc.bcm.edu	37	chr1	62953084	62953084	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cctacctcccagccagtactCtgtataataaaaagtaaaaa	4	11	1	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:62953084C>A	ENST00000340370.5	-	42	5418		c.e42-1		DOCK7_ENST00000251157.5_Intron	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7						activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.?(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						AGCCAGTACTCTGTATAATAA	0.338																																					.		Atlas-SNP	.											DOCK7,NS,carcinoma,0,1	DOCK7	184	.	1	Unknown(1)	endometrium(1)	c.5401-1G>T						.						64	71	69					1																	62953084		2203	4299	6502	SO:0001630	splice_region_variant	85440	exon43			AGTACTCTGTATA		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.5401-1G>T	chr1.hg19:g.62953084C>A		190.0	0.0		274.0	15.0	NM_033407	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Splice_Site	SNP	ENST00000340370.5	hg19	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.462961	0.84425	.	.	ENSG00000116641	ENST00000340370;ENST00000454575;ENST00000395441	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5753	0.95439	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DOCK7	62725672	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.770000	0.85390	2.633000	0.89246	0.591000	0.81541	.	.	.		0.338	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	Intron	A	62953084	C	A	62953084	5	1	194	1	0	0	0	0	0	0	1	0	4694	927	32	3	961	3	DOCK7	1	62953084	Splice_Site	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	15346566	62953084	186297537	5	28502										
ANGPTL3	27329	hgsc.bcm.edu	37	chr1	63070335	63070335	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tggcatgatgagtgtggagaAaacaacctaaatggtaaata	11	4	0	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:63070335A>C	ENST00000371129.3	+	7	1310	c.1230A>C	c.(1228-1230)gaA>gaC	p.E410D	DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000404627.2_Intron|DOCK7_ENST00000251157.5_Intron	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	410	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						AGTGTGGAGAAAACAACCTAA	0.393																																					p.T410T		Atlas-SNP	.											.	ANGPTL3	42	.	0			c.C1230C						.						98	98	98					1																	63070335		2203	4300	6503	SO:0001583	missense	27329	exon7			TGGAGAAAACAAC	AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.1230A>C	chr1.hg19:g.63070335A>C	ENSP00000360170:p.Glu410Asp	369.0	1.0		443.0	165.0	NM_014495	A0JLS0|B1ALJ0|B2RCW1	Silent	SNP	ENST00000371129.3	hg19	CCDS622.1	.	.	.	.	.	.	.	.	.	.	A	10.70	1.424607	0.25639	.	.	ENSG00000132855	ENST00000371129	T	0.76968	-1.06	5.4	5.4	0.78164	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.361732	0.34652	N	0.003793	T	0.43100	0.1232	N	0.11818	0.18	0.30301	N	0.789483	B	0.15719	0.014	B	0.16722	0.016	T	0.12553	-1.0543	10	0.12766	T	0.61	.	15.7054	0.77577	1.0:0.0:0.0:0.0	.	410	Q9Y5C1	ANGL3_HUMAN	D	410	ENSP00000360170:E410D	ENSP00000360170:E410D	E	+	3	2	ANGPTL3	62842923	1.000000	0.71417	0.666000	0.29783	0.940000	0.58332	3.344000	0.52174	2.164000	0.68074	0.477000	0.44152	GAA	.	.		0.393	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		C	63070335	A	C	63070335	3	2	194	1	0	0	0	0	1	0	0	0	615	11	1	5	1256	5	ANGPTL3	1	63070335	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	117251	63070335	186180286	6	28503										
ANGPTL3	27329	hgsc.bcm.edu	37	chr1	63070357	63070357	+	Missense_Mutation	SNP	A	A	G													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	acaacctaaatggtaaatatAacaaaccaagagcaaaatct					rs4145257		TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:63070357A>G	ENST00000371129.3	+	7	1332	c.1252A>G	c.(1252-1254)Aac>Gac	p.N418D	DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000404627.2_Intron|DOCK7_ENST00000251157.5_Intron	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	418	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		N -> Y (in dbSNP:rs4145257).		acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						TGGTAAATATAACAAACCAAG	0.373																																					p.E418E		Atlas-SNP	.											.	ANGPTL3	42	.	0			c.G1252G						.						99	99	99					1																	63070357		2203	4300	6503	SO:0001583	missense	27329	exon7			AAATATAACAAAC	AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.1252A>G	chr1.hg19:g.63070357A>G	ENSP00000360170:p.Asn418Asp	371.0	0.0		451.0	159.0	NM_014495	A0JLS0|B1ALJ0|B2RCW1	Silent	SNP	ENST00000371129.3	hg19	CCDS622.1	.	.	.	.	.	.	.	.	.	.	A	12.21	1.868252	0.32977	.	.	ENSG00000132855	ENST00000371129	T	0.76578	-1.03	5.4	2.71	0.32032	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.874603	0.10458	N	0.672346	T	0.51584	0.1683	L	0.41573	1.285	0.09310	N	1	B	0.25007	0.116	B	0.28011	0.085	T	0.52852	-0.8520	10	0.72032	D	0.01	.	5.8007	0.18412	0.6999:0.1696:0.1305:0.0	.	418	Q9Y5C1	ANGL3_HUMAN	D	418	ENSP00000360170:N418D	ENSP00000360170:N418D	N	+	1	0	ANGPTL3	62842945	0.011000	0.17503	0.979000	0.43373	0.987000	0.75469	0.500000	0.22562	0.945000	0.37605	0.477000	0.44152	AAC	.	A|0.998;T|0.002		0.373	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		G	63070357	A	G	63070357	3	3	194	1	0	0	0	0	1	0	0	0	615	362	13	2	1278	2	ANGPTL3	1	63070357	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	22	63070357	186180264	7	28504	142	3								
ANGPTL3	27329	hgsc.bcm.edu	37	chr1	63070362	63070362	+	Silent	SNP	A	A	G													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ctaaatggtaaatataacaaAccaagagcaaaatctaagcc							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:63070362A>G	ENST00000371129.3	+	7	1337	c.1257A>G	c.(1255-1257)aaA>aaG	p.K419K	DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000404627.2_Intron|DOCK7_ENST00000251157.5_Intron	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	419	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						AATATAACAAACCAAGAGCAA	0.378																																					p.E419E		Atlas-SNP	.											.	ANGPTL3	42	.	0			c.G1257G						.						98	98	98					1																	63070362		2203	4300	6503	SO:0001819	synonymous_variant	27329	exon7			TAACAAACCAAGA	AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.1257A>G	chr1.hg19:g.63070362A>G		369.0	1.0		455.0	164.0	NM_014495	A0JLS0|B1ALJ0|B2RCW1	Silent	SNP	ENST00000371129.3	hg19	CCDS622.1																																																																																			.	.		0.378	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		G	63070362	A	G	63070362	2	3	194	1	0	0	0	0	0	0	0	1	615	40	2	2		2	ANGPTL3	1	63070362	Silent	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	5	63070362	186180259	8	28505	142	3								
ANGPTL3	27329	hgsc.bcm.edu	37	chr1	63070371	63070371	+	Silent	SNP	A	A	G													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aaatataacaaaccaagagcAaaatctaagccagagaggag							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:63070371A>G	ENST00000371129.3	+	7	1346	c.1266A>G	c.(1264-1266)gcA>gcG	p.A422A	DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000404627.2_Intron|DOCK7_ENST00000251157.5_Intron	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	422	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						AACCAAGAGCAAAATCTAAGC	0.373																																					p.I422M		Atlas-SNP	.											.	ANGPTL3	42	.	0			c.T1266G						.						95	96	96					1																	63070371		2203	4300	6503	SO:0001819	synonymous_variant	27329	exon7			AAGAGCAAAATCT	AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.1266A>G	chr1.hg19:g.63070371A>G		369.0	0.0		460.0	173.0	NM_014495	A0JLS0|B1ALJ0|B2RCW1	Missense_Mutation	SNP	ENST00000371129.3	hg19	CCDS622.1																																																																																			.	.		0.373	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		G	63070371	A	G	63070371	2	3	194	1	0	0	0	0	0	0	0	1	615	117	5	2		2	ANGPTL3	1	63070371	Silent	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	9	63070371	186180250	9	28506	142	3								
MIER1	57708	hgsc.bcm.edu	37	chr1	67436507	67436507	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ttagtatatgaaaatgatgaTcagctcctgtgggaccctga	10	7	1	4			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:67436507T>A	ENST00000355356.3	+	8	779	c.630T>A	c.(628-630)gaT>gaA	p.D210E	MIER1_ENST00000357692.2_Missense_Mutation_p.D227E|MIER1_ENST00000401042.3_Missense_Mutation_p.D210E|MIER1_ENST00000355977.6_Missense_Mutation_p.D147E|MIER1_ENST00000401041.1_Missense_Mutation_p.D263E|MIER1_ENST00000371016.1_Missense_Mutation_p.D227E|MIER1_ENST00000371018.3_Missense_Mutation_p.D227E|MIER1_ENST00000371014.1_Missense_Mutation_p.D263E	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	210	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interaction with HDAC1.				positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						AAAATGATGATCAGCTCCTGT	0.308																																					p.D263E		Atlas-SNP	.											.	MIER1	86	.	0			c.T789A						.						74	70	71					1																	67436507		1821	4080	5901	SO:0001583	missense	57708	exon9			TGATGATCAGCTC		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.630T>A	chr1.hg19:g.67436507T>A	ENSP00000347514:p.Asp210Glu	203.0	0.0		245.0	102.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Missense_Mutation	SNP	ENST00000355356.3	hg19	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.238259	0.79800	.	.	ENSG00000198160	ENST00000371017;ENST00000371018;ENST00000355977;ENST00000357692;ENST00000401041;ENST00000371016;ENST00000371014;ENST00000401042;ENST00000355356	T;T;T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.37	5.38	2.8	0.32819	ELM2 domain (2);	0.000000	0.85682	D	0.000000	T	0.42223	0.1193	M	0.84511	2.7	0.58432	D	0.999993	D;D;D;D;D;D;D;D;D	0.89917	0.987;1.0;1.0;0.99;0.995;1.0;1.0;0.962;0.986	D;D;D;D;D;D;D;D;D	0.87578	0.966;0.998;0.996;0.986;0.982;0.998;0.996;0.953;0.971	T	0.47661	-0.9100	10	0.20519	T	0.43	-49.7154	4.7714	0.13157	0.0:0.4339:0.0:0.5661	.	227;227;210;210;147;234;227;263;263	Q5TAD2;Q32NC4;Q8N108-3;Q8N108-6;Q08AE0;Q8N108;Q8N108-10;Q5TAD5;Q5TAD4	.;.;.;.;.;MIER1_HUMAN;.;.;.	E	231;227;147;227;263;227;263;210;210	ENSP00000360057:D227E;ENSP00000348253:D147E;ENSP00000350321:D227E;ENSP00000383820:D263E;ENSP00000360055:D227E;ENSP00000360053:D263E;ENSP00000383821:D210E;ENSP00000347514:D210E	ENSP00000347514:D210E	D	+	3	2	MIER1	67209095	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.947000	0.49058	1.005000	0.39183	0.454000	0.30748	GAT	.	.		0.308	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948		A	67436507	T	A	67436507	3	1	194	1	0	0	0	0	1	0	0	0	9589	1432	50	4	900	4	MIER1	1	67436507	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	4366136	67436507	181814114	10	28507										
FLG	2312	hgsc.bcm.edu	37	chr1	152280666	152280667	+	Missense_Mutation	DNP	CC	CC	AA													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cggggcctgcttgtcctgggCcctgatgattgtccctggcc							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:152280666_152280667CC>AA	ENST00000368799.1	-	3	6730_6731	c.6695_6696GG>TT	c.(6694-6696)gGG>gTT	p.G2232V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2232	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGTCCTGGGCCCTGATGATTG	0.584									Ichthyosis																												p.G2232G|p.G2232V		Atlas-SNP	.											.	FLG	900	.	0			c.G6696T|c.G6695T						.																																			SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCTGGGCCCTGAT|CTGGGCCCTGATG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6695_6696delinsAA	chr1.hg19:g.152280666_152280667delinsAA	ENSP00000357789:p.Gly2232Val	115.0|117.0	0.0		150.0	49.0|48.0	NM_002016	Q01720|Q5T583|Q9UC71	Silent|Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.584	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		AA	152280667	CC	AA	152280666	3	1	194	1	0	0	0	0	1	0	0	0	5930	726	26	3	5493	3	FLG	1	152280666	Missense_Mutation	DNP	CC	TCGA-DD-AADL-01A-11D-A40R-10	84844159	152280666	96969955	11	28508										
NUP210L	91181	hgsc.bcm.edu	37	chr1	154033101	154033101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aaaaataaccagatccttccAcaaggctaaatgtttcctat	4	10	0	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:154033101A>G	ENST00000368559.3	-	20	2836	c.2765T>C	c.(2764-2766)gTg>gCg	p.V922A	NUP210L_ENST00000271854.3_Missense_Mutation_p.V922A	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	922					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			AGATCCTTCCACAAGGCTAAA	0.378																																					p.V922A		Atlas-SNP	.											.	NUP210L	181	.	0			c.T2765C						.						102	93	96					1																	154033101		1866	4098	5964	SO:0001583	missense	91181	exon20			CCTTCCACAAGGC	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2765T>C	chr1.hg19:g.154033101A>G	ENSP00000357547:p.Val922Ala	75.0	0.0		109.0	37.0	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	hg19	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	A	10.70	1.423837	0.25639	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.06068	3.61;3.35	5.14	5.14	0.70334	.	0.000000	0.53938	D	0.000048	T	0.03263	0.0095	L	0.51422	1.61	0.36542	D	0.871331	P;P	0.48089	0.905;0.905	P;P	0.46026	0.501;0.501	T	0.20472	-1.0274	10	0.06494	T	0.89	-15.9844	12.5793	0.56381	1.0:0.0:0.0:0.0	.	922;922	E7EP56;Q5VU65	.;P210L_HUMAN	A	922	ENSP00000357547:V922A;ENSP00000271854:V922A	ENSP00000271854:V922A	V	-	2	0	NUP210L	152299725	0.983000	0.35010	1.000000	0.80357	0.987000	0.75469	1.689000	0.37700	2.161000	0.67846	0.533000	0.62120	GTG	.	.		0.378	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		G	154033101	A	G	154033101	3	3	194	1	0	0	0	0	1	0	0	0	10770	159	6	2	2985	2	NUP210L	1	154033101	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	1752435	154033101	95217520	12	28509										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842234	154842235	+	Missense_Mutation	DNP	CT	CT	AA													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tgctgctgctgctgctgctgCtgctgctgaagctgcggagg							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:154842234_154842235CT>AA	ENST00000271915.4	-	1	521_522	c.206_207AG>TT	c.(205-207)cAG>cTT	p.Q69L	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	69	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	gctgctgctgctgctgctgaag	0.698																																					p.Q69H|p.Q69L		Atlas-SNP	.											.	KCNN3	141	.	0			c.G207T|c.A206T						.																																			SO:0001583	missense	3782	exon1			CTGCTGCTGCTGC|TGCTGCTGCTGCT	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.206_207delinsAA	chr1.hg19:g.154842234_154842235delinsAA	ENSP00000271915:p.Gln69Leu	56.0|58.0	0.0		77.0|76.0	5.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1																																																																																			.	.		0.698	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		AA	154842235	CT	AA	154842234	3	1	194	1	0	0	0	0	1	0	0	0	8089	796	28	3	2042	3	KCNN3	1	154842234	Missense_Mutation	DNP	CT	TCGA-DD-AADL-01A-11D-A40R-10	809133	154842234	94408387	13	28510										
OR10Z1	128368	hgsc.bcm.edu	37	chr1	158576492	158576492	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ctctctggcctggctgggggGgaccaggctatctcctatgt	14	12	2	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:158576492G>T	ENST00000361284.1	+	1	264	c.264G>T	c.(262-264)ggG>ggT	p.G88G		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					TGGCTGGGGGGGACCAGGCTA	0.547																																					p.G88G		Atlas-SNP	.											.	OR10Z1	99	.	0			c.G264T						.						182	191	188					1																	158576492		2203	4300	6503	SO:0001819	synonymous_variant	128368	exon1			TGGGGGGGACCAG	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.264G>T	chr1.hg19:g.158576492G>T		61.0	0.0		83.0	33.0	NM_001004478	Q5VYL0|Q6IFR7	Silent	SNP	ENST00000361284.1	hg19	CCDS30901.1																																																																																			.	.		0.547	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		T	158576492	G	T	158576492	2	4	194	1	0	0	0	0	0	0	0	1	10932	1219	43	3		3	OR10Z1	1	158576492	Silent	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	3734258	158576492	90674129	14	28511										
FMO3	2328	hgsc.bcm.edu	37	chr1	171083272	171083272	+	Missense_Mutation	SNP	T	T	C													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	catttttgaggatgggaccaTatttgagggcattgactgtg							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:171083272T>C	ENST00000367755.4	+	7	1064	c.953T>C	c.(952-954)aTa>aCa	p.I318T	FMO3_ENST00000538429.1_Missense_Mutation_p.I255T|FMO3_ENST00000542847.1_Missense_Mutation_p.I298T|FMO3_ENST00000392085.2_Missense_Mutation_p.I318T	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	318					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	GATGGGACCATATTTGAGGGC	0.443																																					p.I318T		Atlas-SNP	.											.	FMO3	73	.	0			c.T953C						.						156	141	146					1																	171083272		2203	4300	6503	SO:0001583	missense	2328	exon7			GGACCATATTTGA	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.953T>C	chr1.hg19:g.171083272T>C	ENSP00000356729:p.Ile318Thr	57.0	0.0		90.0	33.0	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	hg19	CCDS1292.1	.	.	.	.	.	.	.	.	.	.	T	0.171	-1.071672	0.01918	.	.	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	4.73	-0.888	0.10583	.	0.560313	0.19733	N	0.107301	T	0.06096	0.0158	N	0.03238	-0.38	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.34354	-0.9832	10	0.13108	T	0.6	0.0183	2.2265	0.03985	0.1023:0.2147:0.1902:0.4927	.	255;298;318	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	T	318;318;298;255	ENSP00000356729:I318T;ENSP00000375935:I318T;ENSP00000444073:I298T;ENSP00000439500:I255T	ENSP00000356729:I318T	I	+	2	0	FMO3	169349896	0.000000	0.05858	0.043000	0.18650	0.029000	0.11900	-0.375000	0.07475	-0.318000	0.08665	-1.162000	0.01777	ATA	.	.		0.443	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		C	171083272	T	C	171083272	3	2	194	1	0	0	0	0	1	0	0	0	5964	1406	49	2	975	2	FMO3	1	171083272	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	12506780	171083272	78167349	15	28512	143	2								
FMO3	2328	hgsc.bcm.edu	37	chr1	171083276	171083276	+	Missense_Mutation	SNP	T	T	G													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tttgaggatgggaccatattTgagggcattgactgtgtaat							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:171083276T>G	ENST00000367755.4	+	7	1068	c.957T>G	c.(955-957)ttT>ttG	p.F319L	FMO3_ENST00000538429.1_Missense_Mutation_p.F256L|FMO3_ENST00000542847.1_Missense_Mutation_p.F299L|FMO3_ENST00000392085.2_Missense_Mutation_p.F319L	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	319					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	GGACCATATTTGAGGGCATTG	0.433																																					p.F319L		Atlas-SNP	.											.	FMO3	73	.	0			c.T957G						.						155	141	146					1																	171083276		2203	4300	6503	SO:0001583	missense	2328	exon7			CATATTTGAGGGC	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.957T>G	chr1.hg19:g.171083276T>G	ENSP00000356729:p.Phe319Leu	56.0	0.0		89.0	32.0	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	hg19	CCDS1292.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.706657	0.30232	.	.	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	4.73	3.51	0.40186	.	0.407958	0.27379	N	0.019629	T	0.14700	0.0355	L	0.31294	0.92	0.31710	N	0.639691	P;P;B	0.42692	0.787;0.613;0.142	B;B;B	0.39258	0.295;0.185;0.216	T	0.05801	-1.0863	10	0.08381	T	0.77	-9.3707	4.9997	0.14259	0.3344:0.0:0.1406:0.525	.	256;299;319	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	L	319;319;299;256	ENSP00000356729:F319L;ENSP00000375935:F319L;ENSP00000444073:F299L;ENSP00000439500:F256L	ENSP00000356729:F319L	F	+	3	2	FMO3	169349900	0.999000	0.42202	0.998000	0.56505	0.255000	0.26057	0.509000	0.22707	1.871000	0.54225	0.528000	0.53228	TTT	.	.		0.433	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		G	171083276	T	G	171083276	3	3	194	1	0	0	0	0	1	0	0	0	5964	1809	63	5	979	5	FMO3	1	171083276	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	4	171083276	78167345	16	28513	143	2								
MYOG	4656	hgsc.bcm.edu	37	chr1	203055032	203055032	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gtggacaggcaggtagttttCcccatcatagaagcggggtt	14	8	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:203055032C>A	ENST00000241651.4	-	1	132	c.58G>T	c.(58-60)Gaa>Taa	p.E20*		NM_002479.5	NP_002470.2	P15173	MYOG_HUMAN	myogenin (myogenic factor 4)	20					cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lithium ion (GO:0071285)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|negative regulation of cell proliferation (GO:0008285)|ossification (GO:0001503)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of muscle atrophy (GO:0014737)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myoblast fusion (GO:1901739)|regulation of satellite cell proliferation (GO:0014842)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|skeletal muscle fiber development (GO:0048741)|skeletal muscle tissue development (GO:0007519)|striated muscle atrophy (GO:0014891)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|urinary_tract(1)	12						AGGTAGTTTTCCCCATCATAG	0.617																																					p.E20X		Atlas-SNP	.											.	MYOG	28	.	0			c.G58T						.						50	44	46					1																	203055032		2203	4300	6503	SO:0001587	stop_gained	4656	exon1			AGTTTTCCCCATC	BC053899	CCDS1433.1	1q31-q41	2013-05-21			ENSG00000122180	ENSG00000122180		"Basic helix-loop-helix proteins"	7612	protein-coding gene	gene with protein product		159980		MYF4		10329008	Standard	NM_002479		Approved	bHLHc3	uc001gzd.4	P15173	OTTHUMG00000042127	ENST00000241651.4:c.58G>T	chr1.hg19:g.203055032C>A	ENSP00000241651:p.Glu20*	104.0	0.0		161.0	61.0	NM_002479	Q53XW6	Nonsense_Mutation	SNP	ENST00000241651.4	hg19	CCDS1433.1	.	.	.	.	.	.	.	.	.	.	c	37	6.134173	0.97315	.	.	ENSG00000122180	ENST00000241651	.	.	.	5.68	4.74	0.60224	.	0.397439	0.30820	N	0.008815	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	15.7728	0.78184	0.1373:0.8627:0.0:0.0	.	.	.	.	X	20	.	ENSP00000241651:E20X	E	-	1	0	MYOG	201321655	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	7.230000	0.78097	1.338000	0.45544	0.558000	0.71614	GAA	.	.		0.617	MYOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100279.1	NM_002479		A	203055032	C	A	203055032	4	1	194	1	0	0	0	0	0	1	0	0	10099	864	30	3	628	3	MYOG	1	203055032	Nonsense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	31971756	203055032	46195589	17	28514										
MOSC1	64757	hgsc.bcm.edu	37	chr1	220970004	220970004	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gagtgcacggcctggagataGagggcagggactgtggcgag	20	7	0	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:220970004G>A	ENST00000366910.5	+	3	655	c.469G>A	c.(469-471)Gag>Aag	p.E157K	MARC1_ENST00000496110.1_3'UTR	NM_022746.3	NP_073583.3	Q5VT66	MARC1_HUMAN	mitochondrial amidoxime reducing component 1	157					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										CCTGGAGATAGAGGGCAGGGA	0.572																																					p.E157K		Atlas-SNP	.											.	.	.	.	0			c.G469A						.						61	56	58					1																	220970004		2203	4300	6503	SO:0001583	missense	64757	exon3			GAGATAGAGGGCA	AK026043	CCDS1526.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000186205	ENSG00000186205			26189	protein-coding gene	gene with protein product		614126	"MOCO sulphurase C-terminal domain containing 1"	MOSC1		11886751	Standard	NM_022746		Approved	FLJ22390	uc001hms.3	Q5VT66	OTTHUMG00000037353	ENST00000366910.5:c.469G>A	chr1.hg19:g.220970004G>A	ENSP00000355877:p.Glu157Lys	86.0	0.0		126.0	45.0	NM_022746	A8K447|B2D078|Q5VVS9|Q5VVT0|Q5VVT1|Q8N9P5|Q96FN8|Q9H6C7	Missense_Mutation	SNP	ENST00000366910.5	hg19	CCDS1526.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.060|7.060	0.566198|0.566198	0.13560|0.13560	.|.	.|.	ENSG00000186205|ENSG00000186205	ENST00000366910|ENST00000407981	T|.	0.29655|.	1.56|.	4.71|4.71	2.81|2.81	0.32909|0.32909	MOSC, N-terminal beta barrel (1);Pyruvate kinase-like, insert domain (1);|.	0.207351|.	0.32120|.	N|.	0.006554|.	T|T	0.37785|0.37785	0.1016|0.1016	L|L	0.39397|0.39397	1.21|1.21	0.23186|0.23186	N|N	0.998152|0.998152	B;B|.	0.13145|.	0.007;0.003|.	B;B|.	0.15870|.	0.013;0.014|.	T|T	0.20940|0.20940	-1.0260|-1.0260	10|5	0.16420|.	T|.	0.52|.	-2.5841|-2.5841	9.7471|9.7471	0.40453|0.40453	0.0851:0.5169:0.398:0.0|0.0851:0.5169:0.398:0.0	.|.	157;157|.	Q5VT66-2;Q5VT66|.	.;MOSC1_HUMAN|.	K|K	157|65	ENSP00000355877:E157K|.	ENSP00000355877:E157K|.	E|R	+|+	1|2	0|0	MOSC1|MOSC1	219036627|219036627	0.267000|0.267000	0.24122|0.24122	0.360000|0.360000	0.25837|0.25837	0.359000|0.359000	0.29487|0.29487	0.716000|0.716000	0.25836|0.25836	0.365000|0.365000	0.24400|0.24400	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.		0.572	MARC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090904.1	NM_022746		A	220970004	G	A	220970004	3	1	194	1	0	0	0	0	1	0	0	0	9722	943	33	3	479	3	MOSC1	1	220970004	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	17914972	220970004	28280617	18	28515										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228556439	228556439	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	acagccctctaacatcctgaTggtgcatcctgcccgggaag	10	14	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:228556439T>C	ENST00000422127.1	+	89	19828	c.19784T>C	c.(19783-19785)aTg>aCg	p.M6595T	OBSCN_ENST00000570156.2_Missense_Mutation_p.M7552T|OBSCN_ENST00000366707.4_Missense_Mutation_p.M4229T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6595	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AACATCCTGATGGTGCATCCT	0.597																																					p.M7552T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T22655C						.						173	182	179					1																	228556439		2011	4177	6188	SO:0001583	missense	84033	exon100			TCCTGATGGTGCA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.19784T>C	chr1.hg19:g.228556439T>C	ENSP00000409493:p.Met6595Thr	68.0	0.0		99.0	37.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.832315	0.50845	.	.	ENSG00000154358	ENST00000422127;ENST00000366707	T;T	0.65178	-0.14;-0.14	4.37	4.37	0.52481	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.898935	0.09381	N	0.809962	T	0.74313	0.3700	L	0.46819	1.47	0.80722	D	1	D	0.76494	0.999	D	0.72338	0.977	T	0.69045	-0.5249	10	0.52906	T	0.07	.	14.0056	0.64461	0.0:0.0:0.0:1.0	.	6595	Q5VST9	OBSCN_HUMAN	T	6595;4229	ENSP00000409493:M6595T;ENSP00000355668:M4229T	ENSP00000355668:M4229T	M	+	2	0	OBSCN	226623062	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	7.748000	0.85085	1.957000	0.56846	0.379000	0.24179	ATG	.	.		0.597	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228556439	T	C	228556439	3	2	194	1	0	0	0	0	1	0	0	0	10821	1464	51	2	21344	2	OBSCN	1	228556439	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	7586435	228556439	20694182	19	28516										
OR2L2	26246	hgsc.bcm.edu	37	chr1	248202072	248202072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tgcactctgtatcccatattGcaagtccagagccatcaatc	6	13	2	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr1:248202072G>A	ENST00000366479.2	+	1	599	c.503G>A	c.(502-504)tGc>tAc	p.C168Y	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			ATCCCATATTGCAAGTCCAGA	0.423																																					p.C168Y		Atlas-SNP	.											.	OR2L2	115	.	0			c.G503A						.						196	180	186					1																	248202072		2203	4300	6503	SO:0001583	missense	26246	exon1			CATATTGCAAGTC	X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"GPCR / Class A : Olfactory receptors"	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.503G>A	chr1.hg19:g.248202072G>A	ENSP00000355435:p.Cys168Tyr	58.0	0.0		68.0	27.0	NM_001004686	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	hg19	CCDS31103.1	.	.	.	.	.	.	.	.	.	.	.	13.21	2.170073	0.38315	.	.	ENSG00000203663	ENST00000366479	T	0.00224	8.51	1.9	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35970	U	0.002877	T	0.00468	0.0015	H	0.94847	3.59	0.09310	N	1	P	0.45011	0.848	P	0.50825	0.651	T	0.16867	-1.0388	10	0.72032	D	0.01	.	7.6763	0.28488	0.0:0.0:0.6672:0.3328	.	168	Q8NH16	OR2L2_HUMAN	Y	168	ENSP00000355435:C168Y	ENSP00000355435:C168Y	C	+	2	0	OR2L2	246268695	0.945000	0.32115	0.006000	0.13384	0.419000	0.31324	3.116000	0.50399	0.897000	0.36392	0.194000	0.17425	TGC	.	.		0.423	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686		A	248202072	G	A	248202072	3	1	194	1	0	0	0	0	1	0	0	0	11016	1319	46	3	505	3	OR2L2	1	248202072	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	19645633	248202072	1048549	20	28517										
WDR35	57539	hgsc.bcm.edu	37	chr2	20173444	20173447	+	Frame_Shift_Del	DEL	CATG	CATG	-													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cactggatgcctactacgtaCatgccagtgtcaatcaaaac					rs564598017|rs547986777	byFrequency	TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	CATG	CATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:20173444_20173447delCATG	ENST00000345530.3	-	8	874_877	c.759_762delCATG	c.(757-762)ggcatgfs	p.GM253fs	WDR35_ENST00000416055.2_5'UTR|WDR35_ENST00000281405.4_Frame_Shift_Del_p.GM253fs	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	253					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTACTACGTACATGCCAGTGTCAA	0.451																																					p.254_255del		Atlas-INDEL	.											.	WDR35	92	.	0			c.760_763del						.																																			SO:0001589	frameshift_variant	57539	exon8			.	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"WD repeat domain containing", "Intraflagellar transport homologs"	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.759_762delCATG	chr2.hg19:g.20173444_20173447delCATG	ENSP00000314444:p.Gly253fs	149.0	0.0		133.0	55.0	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Frame_Shift_Del	DEL	ENST00000345530.3	hg19	CCDS33152.1																																																																																			.	.		0.451	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779		-	20173447	CATG	-	20173444	7	5	194	1	0	1	0	1	0	0	0	0	17304	478	17	0	2867	0	WDR35	2	20173444	Frame_Shift_Del	DEL	CATG	TCGA-DD-AADL-01A-11D-A40R-10		20173444	223025929	21	28518										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80101354	80101354	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cgagattatgtgttcaaacaAgtccaggaggccatcgccgg	12	10	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:80101354A>T	ENST00000402739.4	+	5	743	c.738A>T	c.(736-738)caA>caT	p.Q246H	CTNNA2_ENST00000540488.1_Missense_Mutation_p.Q246H|CTNNA2_ENST00000361291.4_Missense_Mutation_p.Q280H|CTNNA2_ENST00000466387.1_Missense_Mutation_p.Q246H|CTNNA2_ENST00000541047.1_Missense_Mutation_p.Q246H|CTNNA2_ENST00000496558.1_Missense_Mutation_p.Q246H	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	246					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						TGTTCAAACAAGTCCAGGAGG	0.587																																					p.Q246H		Atlas-SNP	.											.	CTNNA2	462	.	0			c.A738T						.						49	53	52					2																	80101354		2069	4219	6288	SO:0001583	missense	1496	exon6			CAAACAAGTCCAG		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.738A>T	chr2.hg19:g.80101354A>T	ENSP00000384638:p.Gln246His	82.0	0.0		99.0	11.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	A	23.9	4.469827	0.84533	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1	5.93	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.64327	0.2588	M	0.83012	2.62	0.58432	D	0.999999	D;D;D	0.71674	0.992;0.998;0.995	D;D;D	0.71656	0.974;0.955;0.92	T	0.69079	-0.5240	10	0.66056	D	0.02	.	11.4576	0.50191	0.9303:0.0:0.0697:0.0	.	246;246;246	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	H	246;246;280;246;246;246	ENSP00000418191:Q246H;ENSP00000419295:Q246H;ENSP00000355398:Q280H;ENSP00000384638:Q246H;ENSP00000444675:Q246H;ENSP00000441705:Q246H	ENSP00000355398:Q280H	Q	+	3	2	CTNNA2	79954862	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.307000	0.65762	2.261000	0.74972	0.528000	0.53228	CAA	.	.		0.587	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		T	80101354	A	T	80101354	3	4	194	1	0	0	0	0	1	0	0	0	4015	69	3	4	756	4	CTNNA2	2	80101354	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	59927910	80101354	163098019	22	28519										
LRRTM1	347730	hgsc.bcm.edu	37	chr2	80529914	80529914	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cgccctgtgcgtactccgggCtggcgcactgcaagttgcca	13	15	0	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:80529914C>A	ENST00000295057.3	-	2	1687	c.1031G>T	c.(1030-1032)aGc>aTc	p.S344I	CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000361291.4_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.S344I|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000496558.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	344	LRRCT.				exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						GTACTCCGGGCTGGCGCACTG	0.682										HNSCC(69;0.2)																											p.S344I		Atlas-SNP	.											.	LRRTM1	251	.	0			c.G1031T						.						24	22	23					2																	80529914		2203	4300	6503	SO:0001583	missense	347730	exon2			TCCGGGCTGGCGC	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.1031G>T	chr2.hg19:g.80529914C>A	ENSP00000295057:p.Ser344Ile	128.0	0.0		133.0	38.0	NM_178839	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	hg19	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.694137	0.48202	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.49139	0.79;0.79	5.32	5.32	0.75619	.	0.160698	0.53938	U	0.000045	T	0.48732	0.1516	M	0.78456	2.415	0.43608	D	0.995974	P	0.40398	0.716	B	0.36766	0.232	T	0.53809	-0.8386	9	.	.	.	.	13.6483	0.62294	0.0:0.7165:0.2835:0.0	.	344	Q86UE6	LRRT1_HUMAN	I	344	ENSP00000295057:S344I;ENSP00000386646:S344I	.	S	-	2	0	LRRTM1	80383425	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.170000	0.58229	2.452000	0.82932	0.655000	0.94253	AGC	.	.		0.682	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		A	80529914	C	A	80529914	3	1	194	1	0	0	0	0	1	0	0	0	9048	797	28	3	541	3	LRRTM1	2	80529914	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	428560	80529914	162669459	23	28520										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84880999	84880999	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aaattcacatgctttttgagGtaagtgtacacattactgtg	8	6	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:84880999G>A	ENST00000237449.6	+	33	5642		c.e33+1		DNAH6_ENST00000398278.2_Splice_Site|DNAH6_ENST00000389394.3_Splice_Site			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6						cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GCTTTTTGAGGTAAGTGTACA	0.353																																					.		Atlas-SNP	.											.	DNAH6	194	.	0			c.5634+1G>A						.						82	66	71					2																	84880999		692	1591	2283	SO:0001630	splice_region_variant	1768	exon34			TTTGAGGTAAGTG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.5634+1G>A	chr2.hg19:g.84880999G>A		54.0	0.0		57.0	23.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Splice_Site	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.087207	0.55968	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5984	0.88018	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAH6	84734510	1.000000	0.71417	1.000000	0.80357	0.547000	0.35210	6.746000	0.74866	2.451000	0.82905	0.544000	0.68410	.	.	.		0.353	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	Intron	A	84880999	G	A	84880999	5	1	194	1	0	0	0	0	0	0	1	0	4607	1275	44	3	5765	3	DNAH6	2	84880999	Splice_Site	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	4351085	84880999	158318374	24	28521										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125530441	125530441	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tggagcttgtagtccagtctCcttctcttctgaatgacaac	8	11	3	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:125530441C>T	ENST00000431078.1	+	17	2960	c.2596C>T	c.(2596-2598)Cct>Tct	p.P866S		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	866	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		AGTCCAGTCTCCTTCTCTTCT	0.527																																					p.P866S		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.C2596T						.						183	172	176					2																	125530441		1946	4142	6088	SO:0001583	missense	129684	exon17			CAGTCTCCTTCTC	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2596C>T	chr2.hg19:g.125530441C>T	ENSP00000399013:p.Pro866Ser	92.0	0.0		119.0	15.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	c	11.76	1.735408	0.30774	.	.	ENSG00000155052	ENST00000431078	T	0.79033	-1.23	5.63	4.76	0.60689	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.47093	D	0.000248	T	0.68044	0.2958	L	0.45581	1.43	0.09310	N	0.999998	B	0.23891	0.093	B	0.21708	0.036	T	0.53718	-0.8399	10	0.20046	T	0.44	.	9.3463	0.38111	0.0:0.78:0.1441:0.0759	.	866	Q8WYK1	CNTP5_HUMAN	S	866	ENSP00000399013:P866S	ENSP00000399013:P866S	P	+	1	0	CNTNAP5	125246911	0.021000	0.18746	0.989000	0.46669	0.799000	0.45148	1.123000	0.31308	1.397000	0.46682	0.645000	0.84053	CCT	.	.		0.527	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125530441	C	T	125530441	3	4	194	1	0	0	0	0	1	0	0	0	3652	855	30	3	2662	3	CNTNAP5	2	125530441	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	40649442	125530441	117668932	25	28522										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131520209	131520209	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aaaagcctgccctccccaggGgacccgtcagaccctggggg	13	16	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:131520209G>A	ENST00000423981.1	+	2	674	c.564G>A	c.(562-564)ggG>ggA	p.G188G	AMER3_ENST00000321420.4_Silent_p.G188G	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	188					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.G188G(1)									CCTCCCCAGGGGACCCGTCAG	0.667																																					p.G188G		Atlas-SNP	.											FAM123C,NS,carcinoma,0,1	.	.	.	1	Substitution - coding silent(1)	lung(1)	c.G564A						.						32	38	36					2																	131520209		2200	4291	6491	SO:0001819	synonymous_variant	205147	exon2			CCCAGGGGACCCG	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.564G>A	chr2.hg19:g.131520209G>A		55.0	0.0		58.0	21.0	NM_152698	B7ZLH6	Silent	SNP	ENST00000423981.1	hg19	CCDS2164.1																																																																																			.	.		0.667	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		A	131520209	G	A	131520209	2	1	194	1	0	0	0	0	0	0	0	1	5429	1219	43	3		3	FAM123C	2	131520209	Silent	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	5989768	131520209	111679164	26	28523										
YSK4	80122	hgsc.bcm.edu	37	chr2	135743849	135743849	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ttcttgctgtacatacttgtTagaattcttctcactgggca	7	9	3	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:135743849T>C	ENST00000375845.3	-	7	2623	c.2593A>G	c.(2593-2595)Aac>Gac	p.N865D	MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.N882D|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.N752D|MAP3K19_ENST00000315513.3_5'UTR	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	865							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										ACATACTTGTTAGAATTCTTC	0.408																																					p.N865D		Atlas-SNP	.											.	.	.	.	0			c.A2593G						.						115	115	115					2																	135743849		2203	4300	6503	SO:0001583	missense	80122	exon7			ACTTGTTAGAATT	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.2593A>G	chr2.hg19:g.135743849T>C	ENSP00000365005:p.Asn865Asp	71.0	0.0		95.0	23.0	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	T	1.870	-0.460465	0.04508	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915;ENST00000437365	T;T;T;T	0.72167	-0.5;-0.49;1.85;-0.63	4.86	-3.94	0.04130	.	0.869319	0.09891	N	0.742345	T	0.54447	0.1859	L	0.42245	1.32	0.09310	N	0.999999	P;B;B	0.41265	0.744;0.013;0.001	B;B;B	0.41510	0.359;0.006;0.002	T	0.48490	-0.9031	10	0.14252	T	0.57	.	4.5589	0.12151	0.4585:0.2825:0.0:0.2591	.	752;882;865	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	D	865;752;882;255	ENSP00000365005:N865D;ENSP00000351140:N752D;ENSP00000376647:N882D;ENSP00000392827:N255D	ENSP00000351140:N752D	N	-	1	0	YSK4	135460319	0.001000	0.12720	0.001000	0.08648	0.067000	0.16453	0.550000	0.23345	-0.946000	0.03677	-0.714000	0.03626	AAC	.	.		0.408	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		C	135743849	T	C	135743849	3	2	194	1	0	0	0	0	1	0	0	0	17510	1754	61	2	1409	2	YSK4	2	135743849	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	4223640	135743849	107455524	27	28524										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168107365	168107365	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	acagttatgttgaacccccaCcaagaaggcccatgtcgcaa	8	13	0	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:168107365C>T	ENST00000409195.1	+	9	9552	c.9463C>T	c.(9463-9465)Cca>Tca	p.P3155S	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.P2933S|XIRP2_ENST00000295237.9_Missense_Mutation_p.P3155S|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2980					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TGAACCCCCACCAAGAAGGCC	0.453																																					p.P3155S		Atlas-SNP	.											XIRP2,NS,carcinoma,0,1	XIRP2	914	.	0			c.C9463T						.						80	77	78					2																	168107365		1881	4101	5982	SO:0001583	missense	129446	exon9			CCCCCACCAAGAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.9463C>T	chr2.hg19:g.168107365C>T	ENSP00000386840:p.Pro3155Ser	113.0	0.0		96.0	43.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	3.547	-0.092441	0.07053	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.03889	3.79;3.79;3.77	5.35	2.45	0.29901	.	0.311996	0.33553	N	0.004787	T	0.05914	0.0154	M	0.69823	2.125	0.53688	D	0.999977	B;P;P	0.35628	0.379;0.513;0.513	B;B;B	0.29598	0.048;0.104;0.104	T	0.29088	-1.0023	10	0.42905	T	0.14	-4.7767	7.6257	0.28210	0.1332:0.7185:0.0:0.1483	.	2980;2980;2933	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	3155;3155;2933;569	ENSP00000386840:P3155S;ENSP00000295237:P3155S;ENSP00000387255:P2933S	ENSP00000295237:P3155S	P	+	1	0	XIRP2	167815611	0.015000	0.18098	0.249000	0.24280	0.127000	0.20565	2.028000	0.41088	0.776000	0.33473	0.557000	0.71058	CCA	.	.		0.453	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168107365	C	T	168107365	3	4	194	1	0	0	0	0	1	0	0	0	17445	507	18	3	9493	3	XIRP2	2	168107365	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	32363516	168107365	75092008	28	28525										
TTN	7273	hgsc.bcm.edu	37	chr2	179434324	179434324	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ttttccttagttctaggtcaAgatcaatgtctggtgcttct	8	8	5	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:179434324A>T	ENST00000591111.1	-	276	71836	c.71612T>A	c.(71611-71613)cTt>cAt	p.L23871H	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L16639H|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L16572H|TTN_ENST00000589042.1_Missense_Mutation_p.L25512H|TTN_ENST00000342992.6_Missense_Mutation_p.L22944H|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L16447H|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23871	Ig-like 120.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTAGGTCAAGATCAATGTC	0.393																																					p.L25512H		Atlas-SNP	.											.	TTN	18412	.	0			c.T76535A						.						77	66	69					2																	179434324		1855	4101	5956	SO:0001583	missense	7273	exon326			AGGTCAAGATCAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.71612T>A	chr2.hg19:g.179434324A>T	ENSP00000465570:p.Leu23871His	141.0	0.0		157.0	88.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.44	3.391287	0.62066	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.69040	-0.37;-0.31;-0.32;-0.33	5.7	5.7	0.88788	Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.86301	0.5900	M	0.93720	3.45	0.52501	D	0.999955	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.76071	0.95;0.987;0.987;0.972	D	0.89956	0.4083	9	0.87932	D	0	.	15.9541	0.79871	1.0:0.0:0.0:0.0	.	16447;16572;16639;23871	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	22944;16447;16639;16572;16445	ENSP00000343764:L22944H;ENSP00000434586:L16447H;ENSP00000340554:L16639H;ENSP00000352154:L16572H	ENSP00000340554:L16639H	L	-	2	0	TTN	179142570	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.339000	0.96797	2.163000	0.67991	0.533000	0.62120	CTT	.	.		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179434324	A	T	179434324	3	4	194	1	0	0	0	0	1	0	0	0	16750	72	3	4	31592	4	TTN	2	179434324	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	11326959	179434324	63765049	29	28526										
IDH1	3417	hgsc.bcm.edu	37	chr2	209110051	209110051	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	agtcatacataccttcaaagTtatgtaccaggtatgtcacc	6	10	3	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:209110051T>G	ENST00000415913.1	-	5	893	c.512A>C	c.(511-513)aAc>aCc	p.N171T	IDH1_ENST00000345146.2_Missense_Mutation_p.N171T|IDH1_ENST00000446179.1_Missense_Mutation_p.N171T	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	171					2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ACCTTCAAAGTTATGTACCAG	0.353			Mis		gliobastoma																																p.N171T	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	.	IDH1	6310	.	0			c.A512C						.						148	131	137					2																	209110051		2203	4300	6503	SO:0001583	missense	3417	exon5			TCAAAGTTATGTA		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.512A>C	chr2.hg19:g.209110051T>G	ENSP00000390265:p.Asn171Thr	83.0	0.0		113.0	28.0	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	hg19	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.105296	0.56291	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913	T;T;T	0.68025	-0.3;-0.3;-0.3	5.66	4.49	0.54785	Isopropylmalate dehydrogenase-like domain (2);	0.272219	0.47455	D	0.000235	T	0.55386	0.1917	L	0.33339	1.005	0.43234	D	0.995131	B	0.17852	0.024	B	0.21360	0.034	T	0.55648	-0.8108	10	0.51188	T	0.08	-1.8721	11.8784	0.52560	0.0:0.0695:0.0:0.9305	.	171	O75874	IDHC_HUMAN	T	171	ENSP00000260985:N171T;ENSP00000410513:N171T;ENSP00000390265:N171T	ENSP00000260985:N171T	N	-	2	0	IDH1	208818296	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.511000	0.60462	2.153000	0.67306	0.459000	0.35465	AAC	.	.		0.353	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			G	209110051	T	G	209110051	3	3	194	1	0	0	0	0	1	0	0	0	7503	1725	60	5	756	5	IDH1	2	209110051	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	29675727	209110051	34089322	30	28527										
ANKZF1	55139	hgsc.bcm.edu	37	chr2	220096992	220096992	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tttgtactagagggaacattAtaagcttgactggcatcggt	11	6	0	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:220096992A>G	ENST00000323348.5	+	4	446	c.272A>G	c.(271-273)tAt>tGt	p.Y91C	ATG9A_ENST00000396761.2_5'Flank|ANKZF1_ENST00000409849.1_Intron|ATG9A_ENST00000409618.1_5'Flank|ANKZF1_ENST00000410034.3_Missense_Mutation_p.Y91C|ATG9A_ENST00000361242.4_5'Flank|ATG9A_ENST00000409422.1_5'Flank|ATG9A_ENST00000488833.1_5'Flank	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	91						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGGAACATTATAAGCTTGAC	0.468																																					p.Y91C		Atlas-SNP	.											.	ANKZF1	45	.	0			c.A272G						.						125	118	120					2																	220096992		1909	4130	6039	SO:0001583	missense	55139	exon4			AACATTATAAGCT	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"Zinc fingers, C2H2-type", "Ankyrin repeat domain containing"	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.272A>G	chr2.hg19:g.220096992A>G	ENSP00000321617:p.Tyr91Cys	112.0	0.0		112.0	61.0	NM_001042410	Q9NVZ4	Missense_Mutation	SNP	ENST00000323348.5	hg19	CCDS42821.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.942092	0.73557	.	.	ENSG00000163516	ENST00000323348;ENST00000453432;ENST00000410034;ENST00000447157	T;T;T	0.50548	0.74;0.74;0.74	5.16	5.16	0.70880	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.67832	0.2935	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.72027	-0.4414	10	0.87932	D	0	-10.8476	15.1597	0.72775	1.0:0.0:0.0:0.0	.	35;91	B4DZT1;Q9H8Y5	.;ANKZ1_HUMAN	C	91;26;91;91	ENSP00000321617:Y91C;ENSP00000386337:Y91C;ENSP00000399667:Y91C	ENSP00000321617:Y91C	Y	+	2	0	ANKZF1	219805236	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.363000	0.90103	2.162000	0.67917	0.533000	0.62120	TAT	.	.		0.468	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089		G	220096992	A	G	220096992	3	3	194	1	0	0	0	0	1	0	0	0	693	449	16	2	282	2	ANKZF1	2	220096992	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	10986941	220096992	23102381	31	28528										
STK11IP	114790	hgsc.bcm.edu	37	chr2	220471465	220471465	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cttggggctcagccccatggGcccacctttgccctggccag	12	17	1	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr2:220471465G>A	ENST00000456909.1	+	12	1109	c.1019G>A	c.(1018-1020)gGc>gAc	p.G340D	STK11IP_ENST00000295641.10_Missense_Mutation_p.G351D			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	351					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCCCCATGGGCCCACCTTTG	0.637																																					p.G351D		Atlas-SNP	.											.	STK11IP	152	.	0			c.G1052A						.						72	77	75					2																	220471465		2044	4183	6227	SO:0001583	missense	114790	exon12			CCATGGGCCCACC	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"LKB1 interacting protein"	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.1019G>A	chr2.hg19:g.220471465G>A	ENSP00000389383:p.Gly340Asp	47.0	0.0		45.0	15.0	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.927	1.213718	0.22289	.	.	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.04551	3.6;3.6	4.76	0.922	0.19408	.	1.014060	0.07880	N	0.969419	T	0.03053	0.0090	N	0.08118	0	0.09310	N	1	B;B;B	0.32160	0.358;0.358;0.157	B;B;B	0.38616	0.071;0.277;0.069	T	0.50346	-0.8839	10	0.17832	T	0.49	-0.4725	4.567	0.12191	0.0:0.5482:0.1701:0.2817	.	319;351;351	B4DUE4;Q8N1F8-2;Q8N1F8	.;.;S11IP_HUMAN	D	340;319;351	ENSP00000389383:G340D;ENSP00000295641:G351D	ENSP00000295641:G351D	G	+	2	0	STK11IP	220179709	0.000000	0.05858	0.001000	0.08648	0.120000	0.20174	0.333000	0.19768	-0.014000	0.14175	-0.311000	0.09066	GGC	.	.		0.637	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		A	220471465	G	A	220471465	3	1	194	1	0	0	0	0	1	0	0	0	15303	1203	42	3	1098	3	STK11IP	2	220471465	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	374473	220471465	22727908	32	28529										
C3orf23	285343	hgsc.bcm.edu	37	chr3	44434442	44434442	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tcgtttaaaagatgaactgtCtcatcaattgcaactctcag	6	9	3	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr3:44434442C>G	ENST00000342649.4	+	6	1095	c.668C>G	c.(667-669)tCt>tGt	p.S223C	TCAIM_ENST00000417237.1_Missense_Mutation_p.S223C	NM_001282913.1|NM_173826.3	NP_001269842.1|NP_776187.2	Q8N3R3	TCAIM_HUMAN	T cell activation inhibitor, mitochondrial	223						mitochondrion (GO:0005739)											GATGAACTGTCTCATCAATTG	0.333																																					p.S223C		Atlas-SNP	.											.	.	.	.	0			c.C668G						.						100	102	102					3																	44434442		2203	4296	6499	SO:0001583	missense	285343	exon6			AACTGTCTCATCA		CCDS2712.1, CCDS43076.1	3p21.33-p21.32	2012-08-22	2012-08-22	2012-08-22	ENSG00000179152	ENSG00000179152			25241	protein-coding gene	gene with protein product	"tolerance associated gene-1"		"chromosome 3 open reading frame 23"	C3orf23		12477932	Standard	NM_001029840		Approved	DKFZp313N0621, TOAG-1	uc003cnd.4	Q8N3R3	OTTHUMG00000133049	ENST00000342649.4:c.668C>G	chr3.hg19:g.44434442C>G	ENSP00000341539:p.Ser223Cys	302.0	0.0		381.0	126.0	NM_173826	A8K9P1|Q0P5T9|Q495R1|Q495R3|Q4G0M4|Q6GMU8	Missense_Mutation	SNP	ENST00000342649.4	hg19	CCDS2712.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.978802	0.34942	.	.	ENSG00000179152	ENST00000417237;ENST00000342649	T;T	0.40476	1.03;1.03	5.57	4.7	0.59300	.	0.296354	0.40064	N	0.001182	T	0.27063	0.0663	L	0.31926	0.97	0.33298	D	0.564447	B	0.14438	0.01	B	0.13407	0.009	T	0.28427	-1.0044	10	0.05436	T	0.98	.	10.5708	0.45198	0.0:0.7947:0.1335:0.0718	.	223	Q8N3R3	CC023_HUMAN	C	223	ENSP00000402581:S223C;ENSP00000341539:S223C	ENSP00000341539:S223C	S	+	2	0	C3orf23	44409446	0.895000	0.30542	0.621000	0.29145	0.993000	0.82548	1.494000	0.35616	1.359000	0.45940	0.591000	0.81541	TCT	.	.		0.333	TCAIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256655.2	NM_173826		G	44434442	C	G	44434442	3	3	194	1	0	0	0	0	1	0	0	0	2218	913	32	4	738	4	C3orf23	3	44434442	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10		44434442	153587988	33	28530										
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48463572	48463572	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gtgagcaaggcaagatgcacAgtccaggtgctgagcacagg	15	9	0	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr3:48463572A>T	ENST00000358536.4	-	6	1731	c.1462T>A	c.(1462-1464)Tgt>Agt	p.C488S	PLXNB1_ENST00000296440.6_Missense_Mutation_p.C488S|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Missense_Mutation_p.C488S|PLXNB1_ENST00000456774.1_Missense_Mutation_p.C488S	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	488					axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CAAGATGCACAGTCCAGGTGC	0.582																																					p.C488S		Atlas-SNP	.											.	PLXNB1	150	.	0			c.T1462A						.						77	69	72					3																	48463572		2203	4300	6503	SO:0001583	missense	5364	exon6			ATGCACAGTCCAG	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.1462T>A	chr3.hg19:g.48463572A>T	ENSP00000351338:p.Cys488Ser	60.0	0.0		92.0	34.0	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	hg19	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.912312	0.92178	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.82921	0.5142	H	0.95079	3.62	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.986	D	0.88147	0.2848	10	0.87932	D	0	.	14.9872	0.71356	1.0:0.0:0.0:0.0	.	488;488	O43157;O43157-2	PLXB1_HUMAN;.	S	488	ENSP00000296440:C488S;ENSP00000351242:C488S;ENSP00000351338:C488S;ENSP00000414199:C488S	ENSP00000296440:C488S	C	-	1	0	PLXNB1	48438576	1.000000	0.71417	0.979000	0.43373	0.990000	0.78478	9.071000	0.93980	2.140000	0.66376	0.528000	0.53228	TGT	.	.		0.582	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		T	48463572	A	T	48463572	3	4	194	1	0	0	0	0	1	0	0	0	12132	188	7	4	5077	4	PLXNB1	3	48463572	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	4029130	48463572	149558858	34	28531										
GPR156	165829	hgsc.bcm.edu	37	chr3	119911830	119911830	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ggtaaacaccttgtagagtcGccagctctttcccagaatgg	10	11	1	2	rs138857726		TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr3:119911830G>A	ENST00000464295.1	-	5	875	c.430C>T	c.(430-432)Cga>Tga	p.R144*	GPR156_ENST00000315843.3_Nonsense_Mutation_p.R144*|GPR156_ENST00000461057.1_Nonsense_Mutation_p.R144*			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	144						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		TTGTAGAGTCGCCAGCTCTTT	0.517																																					p.R144X		Atlas-SNP	.											.	GPR156	85	.	0			c.C430T						.	G	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	92	95	94		430,430	1.3	1	3	dbSNP_134	94	0,8600		0,0,4300	no	stop-gained,stop-gained	GPR156	NM_001168271.1,NM_153002.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	144/811,144/815	119911830	1,13005	2203	4300	6503	SO:0001587	stop_gained	165829	exon4			AGAGTCGCCAGCT	AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"GPCR / Class C : Orphans"	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.430C>T	chr3.hg19:g.119911830G>A	ENSP00000417261:p.Arg144*	50.0	0.0		79.0	10.0	NM_001168271	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Nonsense_Mutation	SNP	ENST00000464295.1	hg19	CCDS2997.1	.	.	.	.	.	.	.	.	.	.	G	37	6.416960	0.97550	2.27E-4	0.0	ENSG00000175697	ENST00000464295;ENST00000315843;ENST00000461057	.	.	.	5.78	1.31	0.21738	.	0.000000	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.1317	14.2401	0.65952	0.0:0.0:0.2604:0.7396	.	.	.	.	X	144	.	.	R	-	1	2	GPR156	121394520	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.720000	0.25896	0.313000	0.23062	-0.311000	0.09066	CGA	.	G|1.000;A|0.000		0.517	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		A	119911830	G	A	119911830	4	1	194	1	0	0	0	0	0	1	0	0	6669	1095	38	1	2038	1	GPR156	3	119911830	Nonsense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	71448258	119911830	78110600	35	28532										
POLQ	10721	hgsc.bcm.edu	37	chr3	121168168	121168168	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	agaagataaattacctgtgtAtctggatttgaaggagtcaa	10	4	2	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr3:121168168A>T	ENST00000264233.5	-	26	7386	c.7258T>A	c.(7258-7260)Tac>Aac	p.Y2420N		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2420					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TTACCTGTGTATCTGGATTTG	0.308								DNA polymerases (catalytic subunits)																													p.Y2420N	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.T7258A						.						174	174	174					3																	121168168		2203	4300	6503	SO:0001583	missense	10721	exon26			CTGTGTATCTGGA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.7258T>A	chr3.hg19:g.121168168A>T	ENSP00000264233:p.Tyr2420Asn	116.0	0.0		159.0	72.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.441768	0.83993	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	D	0.97279	-4.32	5.41	5.41	0.78517	DNA-directed DNA polymerase, family A, palm domain (2);	0.124466	0.56097	D	0.000027	D	0.98950	0.9643	H	0.96175	3.78	0.46131	D	0.99888	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99537	1.0962	10	0.87932	D	0	.	15.0946	0.72223	1.0:0.0:0.0:0.0	.	2420;1592	O75417;O75417-2	DPOLQ_HUMAN;.	N	2043;2420;2556	ENSP00000264233:Y2420N	ENSP00000264233:Y2420N	Y	-	1	0	POLQ	122650858	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.739000	0.74827	2.041000	0.60428	0.533000	0.62120	TAC	.	.		0.308	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121168168	A	T	121168168	3	4	194	1	0	0	0	0	1	0	0	0	12217	449	16	4	534	4	POLQ	3	121168168	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	1256338	121168168	76854262	36	28533										
KPNA1	3836	hgsc.bcm.edu	37	chr3	122160952	122160952	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aagcaggagaaaccactttaTaatcattatgcctgcaaaaa	6	8	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr3:122160952T>C	ENST00000344337.6	-	10	1105	c.929A>G	c.(928-930)tAt>tGt	p.Y310C	KPNA1_ENST00000466923.1_5'UTR|RP11-299J3.8_ENST00000609469.1_RNA	NM_002264.3	NP_002255.3	P52294	IMA5_HUMAN	karyopherin alpha 1 (importin alpha 5)	310	Binding to RAG1.				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|regulation of DNA recombination (GO:0000018)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	21				GBM - Glioblastoma multiforme(114;0.0898)		AACCACTTTATAATCATTATG	0.338																																					p.Y310C	Melanoma(12;340 801 11196 19797)	Atlas-SNP	.											.	KPNA1	42	.	0			c.A929G						.						141	145	143					3																	122160952		2203	4300	6503	SO:0001583	missense	3836	exon10			ACTTTATAATCAT	S75295	CCDS3013.1	3q21	2013-02-14			ENSG00000114030	ENSG00000114030		"Importins", "Armadillo repeat containing"	6394	protein-coding gene	gene with protein product		600686				8052633	Standard	NM_002264		Approved	SRP1, RCH2, NPI-1, IPOA5	uc003efe.2	P52294	OTTHUMG00000159487	ENST00000344337.6:c.929A>G	chr3.hg19:g.122160952T>C	ENSP00000343701:p.Tyr310Cys	315.0	0.0		424.0	170.0	NM_002264	D3DN93|Q6IBQ9|Q9BQ56	Missense_Mutation	SNP	ENST00000344337.6	hg19	CCDS3013.1	.	.	.	.	.	.	.	.	.	.	T	18.13	3.555508	0.65425	.	.	ENSG00000114030	ENST00000344337;ENST00000465882	T;T	0.68624	-0.34;-0.34	5.17	5.17	0.71159	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	L	0.40543	1.245	0.80722	D	1	D	0.62365	0.991	P	0.54401	0.751	T	0.68387	-0.5422	10	0.39692	T	0.17	-13.2149	14.3589	0.66757	0.0:0.0:0.0:1.0	.	310	P52294	IMA1_HUMAN	C	310	ENSP00000343701:Y310C;ENSP00000419890:Y310C	ENSP00000343701:Y310C	Y	-	2	0	KPNA1	123643642	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.952000	0.70282	2.175000	0.68902	0.533000	0.62120	TAT	.	.		0.338	KPNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355740.1	NM_002264		C	122160952	T	C	122160952	3	2	194	1	0	0	0	0	1	0	0	0	8438	1406	49	2	707	2	KPNA1	3	122160952	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	992784	122160952	75861478	37	28534										
PARP14	54625	hgsc.bcm.edu	37	chr3	122447347	122447347	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tcaaaatcctactgacctgtAtgacactgtcacagataatg	6	10	2	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr3:122447347A>G	ENST00000474629.2	+	17	5575	c.5309A>G	c.(5308-5310)tAt>tGt	p.Y1770C		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1770	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		ACTGACCTGTATGACACTGTC	0.373																																					p.Y1770C		Atlas-SNP	.											.	PARP14	242	.	0			c.A5309G						.						166	160	162					3																	122447347		1922	4143	6065	SO:0001583	missense	54625	exon17			ACCTGTATGACAC	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.5309A>G	chr3.hg19:g.122447347A>G	ENSP00000418194:p.Tyr1770Cys	76.0	0.0		137.0	59.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	A	14.24	2.475023	0.43942	.	.	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000398157	T	0.15834	2.39	6.01	0.433	0.16534	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.321156	0.26499	N	0.024038	T	0.45458	0.1343	M	0.91090	3.175	0.49582	D	0.999808	D	0.89917	1.0	D	0.76575	0.988	T	0.53222	-0.8469	10	0.72032	D	0.01	.	11.2668	0.49114	0.5404:0.0:0.0:0.4596	.	1770	Q460N5	PAR14_HUMAN	C	1770;1689;766	ENSP00000418194:Y1770C	ENSP00000381224:Y766C	Y	+	2	0	PARP14	123930037	0.868000	0.29978	0.886000	0.34754	0.452000	0.32318	1.916000	0.39986	0.119000	0.18210	-1.407000	0.01130	TAT	.	.		0.373	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		G	122447347	A	G	122447347	3	3	194	1	0	0	0	0	1	0	0	0	11467	449	16	2	5375	2	PARP14	3	122447347	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	286395	122447347	75575083	38	28535										
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122658315	122658315	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ggctgagtctgaagaggtagTtcctgtgaaaatggaaacag	14	5	1	4			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr3:122658315T>C	ENST00000357599.3	-	5	817	c.431A>G	c.(430-432)aAc>aGc	p.N144S	SEMA5B_ENST00000451055.2_Missense_Mutation_p.N198S|SEMA5B_ENST00000195173.4_Missense_Mutation_p.N144S	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	144	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GAAGAGGTAGTTCCTGTGAAA	0.537																																					p.N198S		Atlas-SNP	.											.	SEMA5B	303	.	0			c.A593G						.						167	132	144					3																	122658315		2203	4300	6503	SO:0001583	missense	54437	exon5			AGGTAGTTCCTGT	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.431A>G	chr3.hg19:g.122658315T>C	ENSP00000350215:p.Asn144Ser	73.0	0.0		89.0	31.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	hg19	CCDS35491.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.104670	0.77096	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	5.54	4.39	0.52855	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.056401	0.64402	N	0.000002	T	0.42877	0.1222	M	0.85859	2.78	0.44380	D	0.997282	D;D;D	0.71674	0.997;0.998;0.998	D;D;D	0.80764	0.978;0.994;0.994	T	0.41270	-0.9518	10	0.72032	D	0.01	.	9.4034	0.38447	0.0:0.083:0.0:0.917	.	86;144;144	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	S	144;144;86;198;144	ENSP00000350215:N144S;ENSP00000195173:N144S;ENSP00000389588:N198S;ENSP00000377208:N144S	ENSP00000195173:N144S	N	-	2	0	SEMA5B	124141005	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.674000	0.68117	1.126000	0.42016	0.528000	0.53228	AAC	.	.		0.537	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		C	122658315	T	C	122658315	3	2	194	1	0	0	0	0	1	0	0	0	14053	1725	60	2	3100	2	SEMA5B	3	122658315	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	210968	122658315	75364115	39	28536										
ATP11B	23200	hgsc.bcm.edu	37	chr3	182554178	182554178	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	atgaaatttttcctgcagacTtggtgcttctgtcctcagat	8	9	2	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr3:182554178T>A	ENST00000323116.5	+	6	732	c.472T>A	c.(472-474)Ttg>Atg	p.L158M	ATP11B_ENST00000482794.1_3'UTR|ATP11B_ENST00000493826.1_Missense_Mutation_p.L158M	NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	158					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TCCTGCAGACTTGGTGCTTCT	0.398																																					p.L158M		Atlas-SNP	.											.	ATP11B	115	.	0			c.T472A						.						171	166	168					3																	182554178		2203	4300	6503	SO:0001583	missense	23200	exon6			GCAGACTTGGTGC	AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"ATPases / P-type"	13553	protein-coding gene	gene with protein product		605869	"ATPase, Class VI, type 11B"			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.472T>A	chr3.hg19:g.182554178T>A	ENSP00000321195:p.Leu158Met	89.0	0.0		113.0	39.0	NM_014616	Q96FN1|Q9UKK7	Missense_Mutation	SNP	ENST00000323116.5	hg19	CCDS33896.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.669596	0.67814	.	.	ENSG00000058063	ENST00000323116;ENST00000493826	D;D	0.91068	-2.78;-2.78	5.13	2.76	0.32466	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.64402	D	0.000001	D	0.92612	0.7653	M	0.65320	2	0.52501	D	0.999957	D;D	0.65815	0.995;0.987	D;D	0.72075	0.971;0.976	D	0.90048	0.4147	10	0.51188	T	0.08	.	7.0662	0.25154	0.0:0.4084:0.0:0.5916	.	158;158	Q9Y2G3;B4DKX1	AT11B_HUMAN;.	M	158	ENSP00000321195:L158M;ENSP00000419032:L158M	ENSP00000321195:L158M	L	+	1	2	ATP11B	184036872	0.963000	0.33076	0.909000	0.35828	0.994000	0.84299	0.572000	0.23684	0.374000	0.24650	0.482000	0.46254	TTG	.	.		0.398	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616		A	182554178	T	A	182554178	3	1	194	1	0	0	0	0	1	0	0	0	1120	1606	56	4	494	4	ATP11B	3	182554178	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	59895863	182554178	15468252	40	28537										
ZNF141	7700	hgsc.bcm.edu	37	chr4	366828	366828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tggagagaaaccctacacttGtgaagaatgtggcaaagcct	11	8	0	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr4:366828G>A	ENST00000240499.7	+	4	751	c.602G>A	c.(601-603)tGt>tAt	p.C201Y	ZNF141_ENST00000512994.1_Intron|ZNF141_ENST00000505939.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	201					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						CCCTACACTTGTGAAGAATGT	0.358																																					p.C201Y		Atlas-SNP	.											.	ZNF141	48	.	0			c.G602A						.						60	66	64					4																	366828		2202	4298	6500	SO:0001583	missense	7700	exon4			ACACTTGTGAAGA	L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"Zinc fingers, C2H2-type", "-"	12926	protein-coding gene	gene with protein product		194648	"zinc finger protein 141 (clone pHZ-44)"	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.602G>A	chr4.hg19:g.366828G>A	ENSP00000240499:p.Cys201Tyr	76.0	0.0		126.0	56.0	NM_003441	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	hg19	CCDS33931.1	.	.	.	.	.	.	.	.	.	.	G	15.11	2.735305	0.48939	.	.	ENSG00000131127	ENST00000240499	D	0.85088	-1.94	1.23	1.23	0.21249	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.92034	0.7476	H	0.94222	3.51	0.21604	N	0.999622	D	0.59357	0.985	P	0.58721	0.844	T	0.83007	-0.0174	8	.	.	.	.	7.8726	0.29576	0.0:0.0:1.0:0.0	.	201	Q15928	ZN141_HUMAN	Y	201	ENSP00000240499:C201Y	.	C	+	2	0	ZNF141	356828	0.911000	0.30947	0.051000	0.19133	0.297000	0.27493	1.708000	0.37899	0.585000	0.29608	0.305000	0.20034	TGT	.	.		0.358	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441		A	366828	G	A	366828	3	1	194	1	0	0	0	0	1	0	0	0	17745	1377	48	3	616	3	ZNF141	4	366828	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10		366828	190787448	41	28538										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20618809	20618810	+	Nonsense_Mutation	DNP	GC	GC	AA													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ccaacggaccaatgacccttGccttggaaataagtaagttc							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr4:20618809_20618810GC>AA	ENST00000504154.1	+	35	4376_4377	c.4124_4125GC>AA	c.(4123-4125)tGC>tAA	p.C1375*	SLIT2_ENST00000503837.1_Nonsense_Mutation_p.C1371*|SLIT2_ENST00000503823.1_Nonsense_Mutation_p.C1367*|SLIT2_ENST00000273739.5_Nonsense_Mutation_p.C1388*	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	1375					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						AATGACCCTTGCCTTGGAAATA	0.569																																					p.C1375Y|p.C1375X		Atlas-SNP	.											.	SLIT2	290	.	0			c.G4124A|c.C4125A						.																																			SO:0001587	stop_gained	9353	exon35			ACCCTTGCCTTGG|CCCTTGCCTTGGA	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	Exception_encountered	chr4.hg19:g.20618809_20618810delinsAA	ENSP00000422591:p.Cys1375*	97.0|99.0	0.0		152.0|155.0	63.0|65.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1																																																																																			.	.		0.569	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			AA	20618810	GC	AA	20618809	4	1	194	1	0	0	0	0	0	1	0	0	14755	1319	46	3	4262	3	SLIT2	4	20618809	Nonsense_Mutation	DNP	GC	TCGA-DD-AADL-01A-11D-A40R-10	20251981	20618809	170535467	42	28539										
BMP3	651	hgsc.bcm.edu	37	chr4	81952752	81952752	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cagctttcgggcggcagcagCaggtgagtgcgcgaggtgag	19	9	0	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr4:81952752C>T	ENST00000282701.2	+	1	634	c.314C>T	c.(313-315)gCa>gTa	p.A105V		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	105					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						GCGGCAGCAGCAGGTGAGTGC	0.716																																					p.A105V		Atlas-SNP	.											.	BMP3	59	.	0			c.C314T						.						8	8	8					4																	81952752		2180	4248	6428	SO:0001583	missense	651	exon1			CAGCAGCAGGTGA	M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"Bone morphogenetic proteins"	1070	protein-coding gene	gene with protein product	"osteogenin"	112263	"bone morphogenetic protein 3 (osteogenic)"				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.314C>T	chr4.hg19:g.81952752C>T	ENSP00000282701:p.Ala105Val	58.0	0.0		36.0	21.0	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	hg19	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.037948	0.54896	.	.	ENSG00000152785	ENST00000282701	T	0.65364	-0.15	5.04	5.04	0.67666	Transforming growth factor-beta, N-terminal (1);	0.543205	0.21343	N	0.076095	T	0.67144	0.2862	M	0.62723	1.935	0.39984	D	0.974959	P	0.38048	0.616	P	0.45377	0.478	T	0.65882	-0.6060	10	0.30854	T	0.27	.	16.3482	0.83171	0.0:1.0:0.0:0.0	.	105	P12645	BMP3_HUMAN	V	105	ENSP00000282701:A105V	ENSP00000282701:A105V	A	+	2	0	BMP3	82171776	1.000000	0.71417	0.985000	0.45067	0.115000	0.19883	3.850000	0.55918	2.630000	0.89119	0.655000	0.94253	GCA	.	.		0.716	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1			T	81952752	C	T	81952752	3	4	194	1	0	0	0	0	1	0	0	0	1461	710	25	3	316	3	BMP3	4	81952752	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	61333943	81952752	109201524	43	28540										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13829748	13829748	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tgacggtcaggcaccatcatGgccactgagcggaaattaat	11	10	2	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr5:13829748G>A	ENST00000265104.4	-	38	6419	c.6315C>T	c.(6313-6315)gcC>gcT	p.A2105A		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2105	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GCACCATCATGGCCACTGAGC	0.458									Kartagener syndrome																												p.A2105A		Atlas-SNP	.											.	DNAH5	868	.	0			c.C6315T						.						129	115	119					5																	13829748		2203	4300	6503	SO:0001819	synonymous_variant	1767	exon38	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CATCATGGCCACT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.6315C>T	chr5.hg19:g.13829748G>A		80.0	0.0		122.0	63.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	hg19	CCDS3882.1																																																																																			.	.		0.458	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13829748	G	A	13829748	2	1	194	1	0	0	0	0	0	0	0	1	4606	1335	47	3		3	DNAH5	5	13829748	Silent	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10		13829748	167085512	44	28541										
PDZD2	23037	hgsc.bcm.edu	37	chr5	31799600	31799600	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ggagctgggggacacagagaCtgtgggcctgagttttggga	19	6	0	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr5:31799600C>G	ENST00000438447.1	+	2	633	c.245C>G	c.(244-246)aCt>aGt	p.T82S	PDZD2_ENST00000282493.3_Missense_Mutation_p.T82S			O15018	PDZD2_HUMAN	PDZ domain containing 2	82					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GACACAGAGACTGTGGGCCTG	0.557																																					p.T82S		Atlas-SNP	.											.	PDZD2	306	.	0			c.C245G						.						112	115	114					5																	31799600		2203	4300	6503	SO:0001583	missense	23037	exon1			CAGAGACTGTGGG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.245C>G	chr5.hg19:g.31799600C>G	ENSP00000402033:p.Thr82Ser	104.0	0.0		150.0	62.0	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.574398	0.65878	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.65364	-0.15;-0.15	5.67	5.67	0.87782	PDZ/DHR/GLGF (2);	0.000000	0.46145	D	0.000316	T	0.60157	0.2247	N	0.19112	0.55	0.26511	N	0.974593	D	0.67145	0.996	P	0.62740	0.906	T	0.52975	-0.8503	10	0.21014	T	0.42	.	10.6552	0.45671	0.0:0.9134:0.0:0.0866	.	82	O15018	PDZD2_HUMAN	S	82	ENSP00000402033:T82S;ENSP00000282493:T82S	ENSP00000282493:T82S	T	+	2	0	PDZD2	31835357	0.984000	0.35163	0.995000	0.50966	0.995000	0.86356	2.957000	0.49137	2.661000	0.90470	0.655000	0.94253	ACT	.	.		0.557	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			G	31799600	C	G	31799600	3	3	194	1	0	0	0	0	1	0	0	0	11710	565	20	4	247	4	PDZD2	5	31799600	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	17969852	31799600	149115660	45	28542										
TMCO6	55374	hgsc.bcm.edu	37	chr5	140022524	140022525	+	Frame_Shift_Ins	INS	-	-	CACAG													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	agcagctccatcttggcctcINScactctccctcagcacatgc							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr5:140022524_140022525insCACAG	ENST00000394671.3	+	7	805_806	c.704_705insCACAG	c.(703-708)tccactfs	p.-236fs	NDUFA2_ENST00000510680.1_Intron|TMCO6_ENST00000537378.1_5'UTR|TMCO6_ENST00000252100.6_Frame_Shift_Ins_p.-242fs	NM_018502.3	NP_060972.3	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6						protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|urinary_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCTTGGCCTCCACTCTCCCTC	0.545																																					p.S235fs		Atlas-INDEL	.											.	TMCO6	30	.	0			c.704_705insCACAG						.																																			SO:0001589	frameshift_variant	55374	exon7			.	BC001910	CCDS4233.2, CCDS75320.1	5q31.3	2008-11-06			ENSG00000113119	ENSG00000113119			28814	protein-coding gene	gene with protein product						12477932	Standard	XM_005268476		Approved	FLJ39769, PRO1580	uc003lgl.3	Q96DC7	OTTHUMG00000129497	Exception_encountered	chr5.hg19:g.140022524_140022525insCACAG	ENSP00000378166:p.Thr236fs	61.0	0.0		97.0	24.0	NM_018502	Q9BUU0|Q9P198	Frame_Shift_Ins	INS	ENST00000394671.3	hg19	CCDS4233.2																																																																																			.	.		0.545	TMCO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251666.2	NM_018502		CACAG	140022525	-	CACAG	140022524	7	5	194	1	0	1	1	0	0	0	0	0	16015	855	30	0	730	0	TMCO6	5	140022524	Frame_Shift_Ins	INS	-	TCGA-DD-AADL-01A-11D-A40R-10	108222924	140022524	40892736	46	28543										
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229700	140229700	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	caggtgagcgcgcgcgacgcGggcgtgccgcctctgggcag	19	14	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr5:140229700G>A	ENST00000532602.1	+	1	2653	c.1620G>A	c.(1618-1620)gcG>gcA	p.A540A	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.A540A|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	540	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A540A(2)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCGCGACGCGGGCGTGCCGC	0.672																																					p.A540A	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											PCDHA9_ENST00000532602,NS,carcinoma,0,2	PCDHA9	373	.	2	Substitution - coding silent(2)	lung(2)	c.G1620A						.						60	68	65					5																	140229700		2195	4267	6462	SO:0001819	synonymous_variant	9752	exon1			CGACGCGGGCGTG	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1620G>A	chr5.hg19:g.140229700G>A		63.0	0.0		87.0	31.0	NM_031857	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	hg19	CCDS54920.1																																																																																			.	.		0.672	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140229700	G	A	140229700	2	1	194	1	0	0	0	0	0	0	0	1	11540	1103	39	1		1	PCDHA9	5	140229700	Silent	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	207176	140229700	40685560	47	28544										
FAT2	2196	hgsc.bcm.edu	37	chr5	150923055	150923055	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tctctctgttgaattttcccGatccagtttctgcagagtgg	9	10	3	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr5:150923055G>T	ENST00000261800.5	-	9	7645	c.7633C>A	c.(7633-7635)Cgg>Agg	p.R2545R		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2545	Cadherin 22. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAATTTTCCCGATCCAGTTTC	0.448																																					p.R2545R		Atlas-SNP	.											.	FAT2	465	.	0			c.C7633A						.						151	154	153					5																	150923055		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon9			TTTCCCGATCCAG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.7633C>A	chr5.hg19:g.150923055G>T		63.0	0.0		77.0	24.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1																																																																																			.	.		0.448	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150923055	G	T	150923055	2	4	194	1	0	0	0	0	0	0	0	1	5698	1057	37	1		1	FAT2	5	150923055	Silent	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	10693355	150923055	29992205	48	28545										
PWWP2A	114825	hgsc.bcm.edu	37	chr5	159519506	159519506	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ctcttcttattaaagcgtgaCtggaagttttctaaaaaggg	9	6	3	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr5:159519506C>A	ENST00000307063.7	-	2	2185	c.2151G>T	c.(2149-2151)caG>caT	p.Q717H	PWWP2A_ENST00000523662.1_Intron|PWWP2A_ENST00000456329.3_Intron	NM_001130864.1	NP_001124336.1	Q96N64	PWP2A_HUMAN	PWWP domain containing 2A	717										kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TAAAGCGTGACTGGAAGTTTT	0.498																																					p.Q717H		Atlas-SNP	.											.	PWWP2A	64	.	0			c.G2151T						.						48	44	45					5																	159519506		692	1591	2283	SO:0001583	missense	114825	exon2			GCGTGACTGGAAG		CCDS47331.1, CCDS47332.1, CCDS58990.1	5q33.3	2011-03-23			ENSG00000170234	ENSG00000170234			29406	protein-coding gene	gene with protein product							Standard	NM_052927		Approved	KIAA1935	uc011ded.2	Q96N64	OTTHUMG00000163546	ENST00000307063.7:c.2151G>T	chr5.hg19:g.159519506C>A	ENSP00000305151:p.Gln717His	67.0	0.0		97.0	4.0	NM_001130864	G5EA07|Q2HJJ2|Q8IYR3|Q96PV3	Missense_Mutation	SNP	ENST00000307063.7	hg19	CCDS47332.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.471796	0.43942	.	.	ENSG00000170234	ENST00000307063	T	0.71341	-0.56	5.49	2.62	0.31277	PWWP (1);	.	.	.	.	T	0.60457	0.2270	L	0.41824	1.3	0.48511	D	0.999662	B	0.26512	0.151	B	0.30105	0.111	T	0.61865	-0.6975	9	0.62326	D	0.03	.	8.3741	0.32432	0.0:0.7283:0.1286:0.1432	.	717	Q96N64	PWP2A_HUMAN	H	717	ENSP00000305151:Q717H	ENSP00000305151:Q717H	Q	-	3	2	PWWP2A	159452084	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.266000	0.51569	1.322000	0.45245	0.557000	0.71058	CAG	.	.		0.498	PWWP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374092.1			A	159519506	C	A	159519506	3	1	194	1	0	0	0	0	1	0	0	0	12860	564	20	3	262	3	PWWP2A	5	159519506	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	8596451	159519506	21395754	49	28546										
C5orf45	51149	hgsc.bcm.edu	37	chr5	179264710	179264710	+	Missense_Mutation	SNP	T	T	G													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cactgtccacatgtgaacttTttctaggtggcaggacaaat							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr5:179264710T>G	ENST00000292586.6	-	7	803	c.713A>C	c.(712-714)aAa>aCa	p.K238T	C5orf45_ENST00000403396.2_Intron|C5orf45_ENST00000523267.1_5'UTR|C5orf45_ENST00000518235.1_Intron|C5orf45_ENST00000521333.1_3'UTR|SQSTM1_ENST00000389805.4_3'UTR|C5orf45_ENST00000523084.1_Missense_Mutation_p.K104T|C5orf45_ENST00000376931.2_Missense_Mutation_p.K183T|C5orf45_ENST00000518219.1_3'UTR|SQSTM1_ENST00000376929.3_3'UTR|C5orf45_ENST00000520698.1_Intron	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	238										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						ATGTGAACTTTTTCTAGGTGG	0.592																																					p.K238T		Atlas-SNP	.											.	C5orf45	23	.	0			c.A713C						.						80	84	83					5																	179264710		2203	4300	6503	SO:0001583	missense	51149	exon7			GAACTTTTTCTAG		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"truncated calcium binding protein"						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.713A>C	chr5.hg19:g.179264710T>G	ENSP00000292586:p.Lys238Thr	87.0	0.0		90.0	35.0	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	hg19	CCDS34319.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.524962	0.27299	.	.	ENSG00000161010	ENST00000376931;ENST00000523084;ENST00000292586	T;T;T	0.07567	3.18;3.18;3.18	4.36	0.44	0.16572	.	0.623191	0.14607	N	0.309276	T	0.03739	0.0106	N	0.08118	0	0.09310	N	0.999999	B;B	0.10296	0.003;0.001	B;B	0.06405	0.002;0.002	T	0.37709	-0.9694	10	0.66056	D	0.02	-4.5449	3.8939	0.09131	0.0:0.2065:0.1853:0.6083	.	183;238	E9PAK6;Q6NTE8	.;CE045_HUMAN	T	183;104;238	ENSP00000366130:K183T;ENSP00000429107:K104T;ENSP00000292586:K238T	ENSP00000292586:K238T	K	-	2	0	C5orf45	179197316	0.000000	0.05858	0.002000	0.10522	0.048000	0.14542	0.555000	0.23422	-0.013000	0.14199	0.402000	0.26972	AAA	.	.		0.592	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175		G	179264710	T	G	179264710	3	3	194	1	0	0	0	0	1	0	0	0	2306	1841	64	5	322	5	C5orf45	5	179264710	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	19745204	179264710	1650550	50	28547	144	2								
C5orf45	51149	hgsc.bcm.edu	37	chr5	179264714	179264714	+	Frame_Shift_Del	DEL	T	T	-													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gtccacatgtgaactttttcTaggtggcaggacaaattgcg							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr5:179264714delT	ENST00000292586.6	-	7	799	c.709delA	c.(709-711)agafs	p.R237fs	C5orf45_ENST00000403396.2_Intron|C5orf45_ENST00000523267.1_5'UTR|C5orf45_ENST00000518235.1_Intron|C5orf45_ENST00000521333.1_3'UTR|SQSTM1_ENST00000389805.4_3'UTR|C5orf45_ENST00000523084.1_Frame_Shift_Del_p.R103fs|C5orf45_ENST00000376931.2_Frame_Shift_Del_p.R182fs|C5orf45_ENST00000518219.1_3'UTR|SQSTM1_ENST00000376929.3_3'UTR|C5orf45_ENST00000520698.1_Intron	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	237										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						GAACTTTTTCTAGGTGGCAGG	0.582																																					p.R237fs		Atlas-INDEL	.											.	C5orf45	23	.	0			c.710delG						.						79	83	82					5																	179264714		2203	4300	6503	SO:0001589	frameshift_variant	51149	exon7			.		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"truncated calcium binding protein"						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.709delA	chr5.hg19:g.179264714delT	ENSP00000292586:p.Arg237fs	88.0	0.0		92.0	34.0	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Frame_Shift_Del	DEL	ENST00000292586.6	hg19	CCDS34319.1																																																																																			.	.		0.582	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175		-	179264714	T	-	179264714	7	5	194	1	0	1	0	1	0	0	0	0	2306	1530	53	0	326	0	C5orf45	5	179264714	Frame_Shift_Del	DEL	T	TCGA-DD-AADL-01A-11D-A40R-10	4	179264714	1650546	51	28548	144	2								
OR2B3	442184	hgsc.bcm.edu	37	chr6	29054417	29054417	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ggaattagaagaattagtacActaaagaagaagagctcagc	10	5	1	5			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr6:29054417A>G	ENST00000377173.2	-	1	673	c.609T>C	c.(607-609)agT>agC	p.S203S		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|lung(17)|prostate(1)|skin(2)	24						GAATTAGTACACTAAAGAAGA	0.438																																					p.S203S		Atlas-SNP	.											.	OR2B3	44	.	0			c.T609C						.						78	73	74					6																	29054417		2203	4300	6503	SO:0001819	synonymous_variant	442184	exon1			TAGTACACTAAAG		CCDS34358.1	6p22.2-p21.31	2012-08-09	2008-10-22	2008-10-22	ENSG00000204703	ENSG00000204703		"GPCR / Class A : Olfactory receptors"	8238	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily B, member 3 pseudogene"	OR2B3P			Standard	NM_001005226		Approved	OR6-4	uc003nlx.3	O76000	OTTHUMG00000031226	ENST00000377173.2:c.609T>C	chr6.hg19:g.29054417A>G		104.0	0.0		149.0	72.0	NM_001005226	B0UYQ1|Q5ST41|Q96R13	Silent	SNP	ENST00000377173.2	hg19	CCDS34358.1																																																																																			.	.		0.438	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2			G	29054417	A	G	29054417	2	3	194	1	0	0	0	0	0	0	0	1	10999	156	6	2		2	OR2B3	6	29054417	Silent	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10		29054417	142060650	52	28549										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33157128	33157128	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tggcgagtgggtgcactgagCtgggcaggtcgtgccactcg	18	10	0	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr6:33157128C>T	ENST00000374708.4	-	2	459	c.201G>A	c.(199-201)caG>caA	p.Q67Q	COL11A2_ENST00000395197.1_Silent_p.Q67Q|COL11A2_ENST00000357486.1_Silent_p.Q67Q|COL11A2_ENST00000361917.1_Silent_p.Q67Q|COL11A2_ENST00000395194.1_Silent_p.Q67Q|COL11A2_ENST00000374712.1_Silent_p.Q67Q|COL11A2_ENST00000374714.1_Silent_p.Q67Q|COL11A2_ENST00000374713.1_Silent_p.Q67Q|COL11A2_ENST00000341947.2_Silent_p.Q67Q	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	67	Laminin G-like.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						GTGCACTGAGCTGGGCAGGTC	0.632																																					p.Q67Q	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.G201A						.						72	60	64					6																	33157128		1511	2709	4220	SO:0001819	synonymous_variant	1302	exon2			ACTGAGCTGGGCA	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.201G>A	chr6.hg19:g.33157128C>T		74.0	0.0		110.0	5.0	NM_080681	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.632	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			T	33157128	C	T	33157128	2	4	194	1	0	0	0	0	0	0	0	1	3670	796	28	3		3	COL11A2	6	33157128	Silent	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	4102711	33157128	137957939	53	28550										
MUT	4594	hgsc.bcm.edu	37	chr6	49416564	49416564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cttgtcttcgggcagcacatTcttcaattcgaagtttaggt	9	9	3	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr6:49416564T>C	ENST00000274813.3	-	7	1536	c.1409A>G	c.(1408-1410)gAa>gGa	p.E470G		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	470					cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GGCAGCACATTCTTCAATTCG	0.333																																					p.E470G		Atlas-SNP	.											.	MUT	70	.	0			c.A1409G						.						140	138	138					6																	49416564		2203	4300	6503	SO:0001583	missense	4594	exon7			GCACATTCTTCAA		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"methylmalonyl Coenzyme A mutase"			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1409A>G	chr6.hg19:g.49416564T>C	ENSP00000274813:p.Glu470Gly	126.0	0.0		184.0	81.0	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Missense_Mutation	SNP	ENST00000274813.3	hg19	CCDS4924.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.926264	0.92319	.	.	ENSG00000146085	ENST00000274813	D	0.98762	-5.12	5.95	5.95	0.96441	Cobalamin (vitamin B12)-dependent enzyme, catalytic (1);Cobalamin (vitamin B12)-dependent enzyme, catalytic subdomain (1);Methylmalonyl-CoA mutase, alpha/beta chain, catalytic (1);Methylmalonyl-CoA mutase, alpha chain, catalytic (1);	0.000000	0.85682	D	0.000000	D	0.99205	0.9724	M	0.92880	3.355	0.80722	D	1	D	0.53619	0.961	P	0.61397	0.888	D	0.99063	1.0831	10	0.87932	D	0	-6.0076	15.5927	0.76550	0.0:0.0:0.0:1.0	.	470	P22033	MUTA_HUMAN	G	470	ENSP00000274813:E470G	ENSP00000274813:E470G	E	-	2	0	MUT	49524523	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.276000	0.75962	0.528000	0.53228	GAA	.	.		0.333	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1			C	49416564	T	C	49416564	3	2	194	1	0	0	0	0	1	0	0	0	10000	1783	62	2	871	2	MUT	6	49416564	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	16259436	49416564	121698503	54	28551										
MUT	4594	hgsc.bcm.edu	37	chr6	49416604	49416604	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tattccctcagctacagcttTggccattccacccatttctt	4	15	2	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr6:49416604T>A	ENST00000274813.3	-	7	1496	c.1369A>T	c.(1369-1371)Aaa>Taa	p.K457*		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	457					cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GCTACAGCTTTGGCCATTCCA	0.318																																					p.K457X		Atlas-SNP	.											.	MUT	70	.	0			c.A1369T						.						136	136	136					6																	49416604		2203	4300	6503	SO:0001587	stop_gained	4594	exon7			CAGCTTTGGCCAT		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"methylmalonyl Coenzyme A mutase"			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1369A>T	chr6.hg19:g.49416604T>A	ENSP00000274813:p.Lys457*	107.0	0.0		173.0	76.0	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Nonsense_Mutation	SNP	ENST00000274813.3	hg19	CCDS4924.1	.	.	.	.	.	.	.	.	.	.	T	39	7.502300	0.98322	.	.	ENSG00000146085	ENST00000274813	.	.	.	5.75	5.75	0.90469	.	0.153804	0.56097	D	0.000033	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.5132	11.2628	0.49093	0.0:0.0:0.1527:0.8473	.	.	.	.	X	457	.	ENSP00000274813:K457X	K	-	1	0	MUT	49524563	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.705000	0.54823	2.192000	0.70111	0.528000	0.53228	AAA	.	.		0.318	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1			A	49416604	T	A	49416604	4	1	194	1	0	0	0	0	0	1	0	0	10000	1821	63	4	911	4	MUT	6	49416604	Nonsense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	40	49416604	121698463	55	28552										
KHDRBS2	202559	hgsc.bcm.edu	37	chr6	62442656	62442656	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	catcatattcacccccgtagCcatcatcataaccctgagac	4	16	4	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr6:62442656C>T	ENST00000281156.4	-	7	1102	c.824G>A	c.(823-825)gGc>gAc	p.G275D		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	275					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		ACCCCCGTAGCCATCATCATA	0.378																																					p.G275D		Atlas-SNP	.											.	KHDRBS2	103	.	0			c.G824A						.						152	143	146					6																	62442656		2203	4300	6503	SO:0001583	missense	202559	exon7			CCGTAGCCATCAT	BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"Sam68-like mammalian protein 1"	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.824G>A	chr6.hg19:g.62442656C>T	ENSP00000281156:p.Gly275Asp	91.0	0.0		132.0	31.0	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Missense_Mutation	SNP	ENST00000281156.4	hg19	CCDS4963.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.965183	0.74131	.	.	ENSG00000112232	ENST00000281156	T	0.47869	0.83	5.93	5.93	0.95920	.	0.237178	0.44285	D	0.000461	T	0.53254	0.1785	L	0.41236	1.265	0.48040	D	0.999577	D	0.76494	0.999	D	0.68353	0.957	T	0.52638	-0.8549	10	0.59425	D	0.04	0.6457	17.3163	0.87225	0.0:1.0:0.0:0.0	.	275	Q5VWX1	KHDR2_HUMAN	D	275	ENSP00000281156:G275D	ENSP00000281156:G275D	G	-	2	0	KHDRBS2	62500615	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	4.607000	0.61133	2.827000	0.97445	0.644000	0.83932	GGC	.	.		0.378	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688		T	62442656	C	T	62442656	3	4	194	1	0	0	0	0	1	0	0	0	8156	739	26	3	237	3	KHDRBS2	6	62442656	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	13026052	62442656	108672411	56	28553										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161455352	161455352	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aatctgatctagaagacttcTccgatgaaacaaatacagag	7	8	3	5			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr6:161455352T>A	ENST00000392142.4	+	2	362	c.214T>A	c.(214-216)Tcc>Acc	p.S72T	MAP3K4_ENST00000348824.7_Missense_Mutation_p.S72T|MAP3K4_ENST00000366919.2_Missense_Mutation_p.S72T|MAP3K4_ENST00000366920.2_Missense_Mutation_p.S72T	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	72					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AGAAGACTTCTCCGATGAAAC	0.453																																					p.S72T		Atlas-SNP	.											.	MAP3K4	364	.	0			c.T214A						.						87	83	84					6																	161455352		2203	4300	6503	SO:0001583	missense	4216	exon2			GACTTCTCCGATG	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.214T>A	chr6.hg19:g.161455352T>A	ENSP00000375986:p.Ser72Thr	103.0	0.0		79.0	21.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.556742	0.45487	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824;ENST00000544209	T;T;T;T	0.72615	-0.67;-0.65;-0.64;-0.67	5.49	1.6	0.23607	.	0.380161	0.24820	N	0.035334	T	0.39279	0.1072	L	0.51422	1.61	0.24656	N	0.993493	P;B	0.35272	0.493;0.361	B;B	0.36134	0.218;0.108	T	0.28364	-1.0046	10	0.21014	T	0.42	-3.2875	7.0369	0.24998	0.0:0.1328:0.1251:0.742	.	72;72	Q9Y6R4-2;Q9Y6R4	.;M3K4_HUMAN	T	72;72;72;72;72;51	ENSP00000355886:S72T;ENSP00000375986:S72T;ENSP00000355887:S72T;ENSP00000297332:S72T	ENSP00000297332:S72T	S	+	1	0	MAP3K4	161375342	0.998000	0.40836	0.818000	0.32626	0.660000	0.38997	1.417000	0.34770	0.100000	0.17581	0.456000	0.33151	TCC	.	.		0.453	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			A	161455352	T	A	161455352	3	1	194	1	0	0	0	0	1	0	0	0	9261	1551	54	4	220	4	MAP3K4	6	161455352	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	99012696	161455352	9659715	57	28554										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20698136	20698136	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tatttttcattagaaatttaAtacattggtaggggaaaaag	8	2	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr7:20698136A>G	ENST00000404938.2	+	14	2196	c.1544A>G	c.(1543-1545)aAt>aGt	p.N515S	ABCB5_ENST00000258738.6_Missense_Mutation_p.N70S|ABCB5_ENST00000406935.1_Missense_Mutation_p.N70S|ABCB5_ENST00000443026.2_Missense_Mutation_p.N70S	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	515	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						TAGAAATTTAATACATTGGTA	0.393																																					p.N515S		Atlas-SNP	.											.	ABCB5	357	.	0			c.A1544G						.						69	67	68					7																	20698136		2203	4300	6503	SO:0001583	missense	340273	exon14			AATTTAATACATT	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.1544A>G	chr7.hg19:g.20698136A>G	ENSP00000384881:p.Asn515Ser	39.0	0.0		46.0	25.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	A	14.38	2.518164	0.44763	.	.	ENSG00000004846	ENST00000404938;ENST00000443026;ENST00000406935;ENST00000258738	D;D;D;D	0.90444	-1.92;-2.67;-2.67;-1.92	5.86	3.5	0.40072	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.169418	0.38959	N	0.001509	D	0.87676	0.6237	N	0.20766	0.605	0.32743	N	0.507456	B;B;B;B	0.27316	0.002;0.175;0.001;0.001	B;P;B;B	0.45037	0.004;0.467;0.006;0.002	D	0.88281	0.2936	10	0.59425	D	0.04	.	9.4926	0.38969	0.8573:0.0:0.1427:0.0	.	70;515;70;70	B5MD19;A7BKA4;Q2M3G0;Q2M3G0-2	.;.;ABCB5_HUMAN;.	S	515;70;70;70	ENSP00000384881:N515S;ENSP00000406730:N70S;ENSP00000383899:N70S;ENSP00000258738:N70S	ENSP00000258738:N70S	N	+	2	0	ABCB5	20664661	1.000000	0.71417	0.999000	0.59377	0.915000	0.54546	5.144000	0.64832	1.149000	0.42402	0.528000	0.53228	AAT	.	.		0.393	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		G	20698136	A	G	20698136	3	3	194	1	0	0	0	0	1	0	0	0	44	101	4	2	1594	2	ABCB5	7	20698136	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10		20698136	138440527	58	28555										
HOXA7	3204	hgsc.bcm.edu	37	chr7	27195946	27195946	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aggttgccgtaggcgtcggcGcccaggccgtagccggacgc	17	14	0	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr7:27195946G>C	ENST00000242159.3	-	1	352	c.219C>G	c.(217-219)ggC>ggG	p.G73G	HOXA7_ENST00000523796.2_5'Flank|HOXA-AS3_ENST00000518947.2_RNA|RP1-170O19.21_ENST00000602610.1_lincRNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	73					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						AGGCGTCGGCGCCCAGGCCGT	0.672																																					p.G73G		Atlas-SNP	.											.	HOXA7	34	.	0			c.C219G						.						25	34	31					7																	27195946		2203	4296	6499	SO:0001819	synonymous_variant	3204	exon1			GTCGGCGCCCAGG		CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"Homeoboxes / ANTP class : HOXL subclass"	5108	protein-coding gene	gene with protein product		142950	"homeo box A7"	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.219C>G	chr7.hg19:g.27195946G>C		195.0	0.0		227.0	67.0	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Silent	SNP	ENST00000242159.3	hg19	CCDS5408.1																																																																																			.	.		0.672	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1			C	27195946	G	C	27195946	2	2	194	1	0	0	0	0	0	0	0	1	7306	1074	38	4		4	HOXA7	7	27195946	Silent	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	6497810	27195946	131942717	59	28556										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83640603	83640604	+	Missense_Mutation	DNP	CC	CC	AA													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tcaccagacttctgtgccctCcaaagtcattctgaaagaag							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr7:83640603_83640604CC>AA	ENST00000265362.4	-	8	1134_1135	c.820_821GG>TT	c.(820-822)GGa>TTa	p.G274L	SEMA3A_ENST00000436949.1_Missense_Mutation_p.G274L	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	274	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						TCTGTGCCCTCCAAAGTCATTC	0.376																																					p.G274V|p.G274X		Atlas-SNP	.											SEMA3A,right_upper_lobe,carcinoma,0,1|.	SEMA3A	121	.	0			c.G821T|c.G820T						.																																			SO:0001583	missense	10371	exon8			TGCCCTCCAAAGT|GCCCTCCAAAGTC	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.820_821delinsAA	chr7.hg19:g.83640603_83640604delinsAA	ENSP00000265362:p.Gly274Leu	84.0|83.0	0.0		115.0	52.0	NM_006080		Missense_Mutation|Nonsense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1																																																																																			.	.		0.376	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		AA	83640604	CC	AA	83640603	3	1	194	1	0	0	0	0	1	0	0	0	14039	855	30	3	1534	3	SEMA3A	7	83640603	Missense_Mutation	DNP	CC	TCGA-DD-AADL-01A-11D-A40R-10	56444657	83640603	75498060	60	28557										
ORC5L	5001	hgsc.bcm.edu	37	chr7	103808951	103808952	+	Missense_Mutation	DNP	TC	TC	CA													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ccccggatctgtgtcatcttTctgtagcttttcccactggg							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr7:103808951_103808952TC>CA	ENST00000297431.4	-	9	988_989	c.846_847GA>TG	c.(844-849)caGAaa>caTGaa	p.282_283QK>HE	ORC5_ENST00000545943.1_Missense_Mutation_p.150_151QK>HE|ORC5_ENST00000447452.2_Missense_Mutation_p.282_283QK>HE	NM_002553.3	NP_002544.1	O43913	ORC5_HUMAN	origin recognition complex, subunit 5	282					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			kidney(1)|large_intestine(2)|lung(9)|pancreas(1)|upper_aerodigestive_tract(1)	14						GTGTCATCTTTCTGTAGCTTTT	0.342																																					p.K283E|p.Q282H		Atlas-SNP	.											.	ORC5	48	.	0			c.A847G|c.G846T						.																																			SO:0001583	missense	5001	exon9			CATCTTTCTGTAG|ATCTTTCTGTAGC		CCDS5734.1, CCDS47681.1	7q22.1	2014-06-13	2010-10-12	2010-10-12	ENSG00000164815	ENSG00000164815			8491	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 117"	602331	"origin recognition complex, subunit 5 (yeast homolog)-like", "origin recognition complex, subunit 5-like (yeast)", "origin recognition complex, subunit 5 homolog (yeast)"	ORC5L		9417919, 9829972	Standard	NM_002553		Approved	Orc5p, ORC5T, PPP1R117	uc003vcb.3	O43913	OTTHUMG00000157275	ENST00000297431.4:c.846_847delinsCA	chr7.hg19:g.103808951_103808952delinsCA	ENSP00000297431:p.Q282_K283delinsHE	27.0|28.0	0.0		79.0|75.0	45.0|44.0	NM_002553	A4D0P8|O60590|O95268	Missense_Mutation	SNP	ENST00000297431.4	hg19	CCDS5734.1																																																																																			.	.		0.342	ORC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348286.1	NM_002553		CA	103808952	TC	CA	103808951	3	2	194	1	0	0	0	0	1	0	0	0	11274	1792	62	2	582	2	ORC5L	7	103808951	Missense_Mutation	DNP	TC	TCGA-DD-AADL-01A-11D-A40R-10	20168348	103808951	55329712	61	28558										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113518118	113518118	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gtttgttgattaaaatcattGgccctagagatttttccaca	7	7	1	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr7:113518118G>T	ENST00000284601.3	-	4	3097	c.3029C>A	c.(3028-3030)cCa>cAa	p.P1010Q		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	1010					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TAAAATCATTGGCCCTAGAGA	0.383																																					p.P1010Q		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.C3029A						.						130	129	129					7																	113518118		2203	4298	6501	SO:0001583	missense	5506	exon4			ATCATTGGCCCTA	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.3029C>A	chr7.hg19:g.113518118G>T	ENSP00000284601:p.Pro1010Gln	51.0	0.0		126.0	78.0	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	hg19	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.162074	0.38217	.	.	ENSG00000154415	ENST00000284601	T	0.60171	0.21	5.71	5.71	0.89125	.	0.192043	0.37178	N	0.002211	T	0.77143	0.4087	M	0.72894	2.215	0.41562	D	0.98863	D	0.89917	1.0	D	0.91635	0.999	T	0.78760	-0.2078	10	0.87932	D	0	-6.8891	19.8454	0.96706	0.0:0.0:1.0:0.0	.	1010	Q16821	PPR3A_HUMAN	Q	1010	ENSP00000284601:P1010Q	ENSP00000284601:P1010Q	P	-	2	0	PPP1R3A	113305354	1.000000	0.71417	0.157000	0.22605	0.242000	0.25591	6.468000	0.73551	2.680000	0.91292	0.650000	0.86243	CCA	.	.		0.383	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		T	113518118	G	T	113518118	3	4	194	1	0	0	0	0	1	0	0	0	12383	1348	47	3	343	3	PPP1R3A	7	113518118	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	9709167	113518118	45620545	62	28559										
ESYT2	57488	hgsc.bcm.edu	37	chr7	158586392	158586392	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tgtctacattttcagtgtatAccttaacaccattgatcctg	5	10	2	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr7:158586392A>G	ENST00000251527.5	-	4	742	c.677T>C	c.(676-678)gTa>gCa	p.V226A	ESYT2_ENST00000497111.1_5'UTR	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	254	Glycerophospholipid-binding barrel-like domain.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						TTCAGTGTATACCTTAACACC	0.313																																					p.V226A		Atlas-SNP	.											.	ESYT2	70	.	0			c.T677C						.						103	90	95					7																	158586392		2203	4300	6503	SO:0001583	missense	57488	exon4			GTGTATACCTTAA	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"Synaptotagmins"	22211	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member B"	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.677T>C	chr7.hg19:g.158586392A>G	ENSP00000251527:p.Val226Ala	31.0	0.0		61.0	33.0	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	hg19	CCDS34791.1	.	.	.	.	.	.	.	.	.	.	A	10.46	1.356051	0.24598	.	.	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000429474	T;T	0.20463	2.07;2.07	4.97	3.81	0.43845	.	0.120339	0.56097	D	0.000032	T	0.32406	0.0828	L	0.46157	1.445	0.80722	D	1	D;D	0.63880	0.993;0.993	D;D	0.70016	0.967;0.967	T	0.05716	-1.0868	10	0.15066	T	0.55	-23.4484	9.8762	0.41205	0.9194:0.0:0.0806:0.0	.	254;226	A0FGR8-6;A0FGR8-2	.;.	A	226;254;196;50	ENSP00000251527:V226A;ENSP00000275418:V196A	ENSP00000251527:V226A	V	-	2	0	ESYT2	158279153	1.000000	0.71417	0.811000	0.32455	0.966000	0.64601	5.679000	0.68160	0.744000	0.32741	0.460000	0.39030	GTA	.	.		0.313	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728		G	158586392	A	G	158586392	3	3	194	1	0	0	0	0	1	0	0	0	5267	391	14	2	2080	2	ESYT2	7	158586392	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	45068274	158586392	552271	63	28560										
FGFR1	2260	hgsc.bcm.edu	37	chr8	38273520	38273520	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	agccctgggggcctccgggcCtgcaggtactcccgcaggtt	15	15	0	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr8:38273520C>A	ENST00000447712.2	-	13	2663	c.1722G>T	c.(1720-1722)caG>caT	p.Q574H	FGFR1_ENST00000397108.4_Missense_Mutation_p.Q572H|FGFR1_ENST00000397103.1_Missense_Mutation_p.Q485H|FGFR1_ENST00000532791.1_Missense_Mutation_p.Q572H|FGFR1_ENST00000425967.3_Missense_Mutation_p.Q605H|FGFR1_ENST00000326324.6_Missense_Mutation_p.Q483H|FGFR1_ENST00000335922.5_Missense_Mutation_p.Q564H|FGFR1_ENST00000397091.5_Missense_Mutation_p.Q572H|FGFR1_ENST00000356207.5_Missense_Mutation_p.Q485H|FGFR1_ENST00000341462.5_Missense_Mutation_p.Q574H|FGFR1_ENST00000397113.2_Missense_Mutation_p.Q572H	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	574	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)		FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	GCCTCCGGGCCTGCAGGTACT	0.637		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"																														p.Q605H	Melanoma(146;1153 1840 21453 21841 43625)	Atlas-SNP	.		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	.	FGFR1	284	.	0			c.G1815T						.						35	41	39					8																	38273520		2041	4217	6258	SO:0001583	missense	2260	exon14			CCGGGCCTGCAGG	M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.1722G>T	chr8.hg19:g.38273520C>A	ENSP00000400162:p.Gln574His	37.0	0.0		47.0	15.0	NM_001174067	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Missense_Mutation	SNP	ENST00000447712.2	hg19	CCDS6107.2	.	.	.	.	.	.	.	.	.	.	C	19.12	3.765607	0.69878	.	.	ENSG00000077782	ENST00000397091;ENST00000425967;ENST00000447712;ENST00000341462;ENST00000310729;ENST00000532791;ENST00000397113;ENST00000356207;ENST00000335922;ENST00000326324;ENST00000397103;ENST00000397108	D;D;D;D;D;D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63	5.4	5.4	0.78164	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.054186	0.85682	D	0.000000	T	0.74635	0.3742	N	0.05534	-0.03	0.53688	D	0.99997	P;P;P;P;P	0.44659	0.84;0.84;0.787;0.747;0.747	P;P;P;P;P	0.50049	0.598;0.598;0.629;0.496;0.496	T	0.78160	-0.2312	10	0.87932	D	0	.	10.1119	0.42568	0.0:0.8508:0.0:0.1492	.	483;483;574;564;572	P11362-14;P11362-4;P11362;P11362-20;P11362-2	.;.;FGFR1_HUMAN;.;.	H	572;605;574;574;574;572;572;485;564;483;485;572	ENSP00000380280:Q572H;ENSP00000393312:Q605H;ENSP00000400162:Q574H;ENSP00000340636:Q574H;ENSP00000432972:Q572H;ENSP00000380302:Q572H;ENSP00000348537:Q485H;ENSP00000337247:Q564H;ENSP00000327229:Q483H;ENSP00000380292:Q485H;ENSP00000380297:Q572H	ENSP00000311337:Q574H	Q	-	3	2	FGFR1	38392677	0.995000	0.38212	1.000000	0.80357	0.998000	0.95712	0.455000	0.21843	2.688000	0.91661	0.655000	0.94253	CAG	.	.		0.637	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	38273520	C	A	38273520	3	1	194	1	0	0	0	0	1	0	0	0	5871	680	24	3	770	3	FGFR1	8	38273520	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10		38273520	108090502	64	28561										
SAMD12	401474	hgsc.bcm.edu	37	chr8	119391802	119391802	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aggaagcaatagggtaccttGtgtgagtaactgtagatttc	12	5	0	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr8:119391802G>A	ENST00000314727.4	-	4	596	c.460C>T	c.(460-462)Caa>Taa	p.Q154*	SAMD12_ENST00000409003.4_Nonsense_Mutation_p.Q154*|SAMD12_ENST00000527515.1_5'UTR|AC023590.1_ENST00000430457.1_Intron	NM_207506.2	NP_997389.2	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12	154										endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)	9	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			AGGGTACCTTGTGTGAGTAAC	0.483																																					p.Q154X		Atlas-SNP	.											.	SAMD12	24	.	0			c.C460T						.						159	142	148					8																	119391802		2203	4300	6503	SO:0001587	stop_gained	401474	exon4			TACCTTGTGTGAG	AK096777	CCDS6325.1, CCDS47913.1	8q24.12	2013-01-10			ENSG00000177570	ENSG00000177570		"Sterile alpha motif (SAM) domain containing"	31750	protein-coding gene	gene with protein product							Standard	NM_207506		Approved	FLJ39458	uc003yom.2	Q8N8I0	OTTHUMG00000059817	ENST00000314727.4:c.460C>T	chr8.hg19:g.119391802G>A	ENSP00000314173:p.Gln154*	80.0	0.0		145.0	20.0	NM_207506	Q0P502	Nonsense_Mutation	SNP	ENST00000314727.4	hg19	CCDS6325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.839213|5.839213	0.97009|0.97009	.|.	.|.	ENSG00000177570|ENSG00000177570	ENST00000409003;ENST00000524796;ENST00000314727;ENST00000526328|ENST00000453675	.|.	.|.	.|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.77638	.|0.4160	.|.	.|.	.|.	0.52099|0.52099	D|D	0.999941|0.999941	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73658	.|-0.3913	.|4	.|.	.|.	.|.	-16.377|-16.377	20.8794|20.8794	0.99867|0.99867	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	154;146;154;154|140	.|.	.|.	Q|T	-|-	1|2	0|0	SAMD12|SAMD12	119460983|119460983	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.787000|0.787000	0.44495|0.44495	9.476000|9.476000	0.97823|0.97823	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	CAA|ACA	.	.		0.483	SAMD12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132989.3	NM_207506		A	119391802	G	A	119391802	4	1	194	1	0	0	0	0	0	1	0	0	13832	1386	48	3	176	3	SAMD12	8	119391802	Nonsense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	81118282	119391802	26972220	65	28562										
ADCY8	114	hgsc.bcm.edu	37	chr8	131896827	131896827	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	taccttgtgctccaggctggAgtctttaaacatcagtgaga	10	9	2	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr8:131896827A>G	ENST00000286355.5	-	8	4184	c.2092T>C	c.(2092-2094)Tcc>Ccc	p.S698P	ADCY8_ENST00000377928.3_Missense_Mutation_p.S698P	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	698					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TCCAGGCTGGAGTCTTTAAAC	0.463										HNSCC(32;0.087)																											p.S698P		Atlas-SNP	.											.	ADCY8	291	.	0			c.T2092C						.						114	113	114					8																	131896827		2203	4300	6503	SO:0001583	missense	114	exon8			GGCTGGAGTCTTT	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.2092T>C	chr8.hg19:g.131896827A>G	ENSP00000286355:p.Ser698Pro	46.0	0.0		54.0	17.0	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	A	3.937	-0.014994	0.07681	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.76186	-1.0;-1.0	5.98	5.98	0.97165	.	0.102243	0.64402	D	0.000001	T	0.54175	0.1842	N	0.01242	-0.935	0.40433	D	0.97996	D;B	0.53619	0.961;0.005	P;B	0.48030	0.564;0.006	T	0.64491	-0.6395	10	0.23302	T	0.38	.	15.7096	0.77615	1.0:0.0:0.0:0.0	.	698;698	E7EVL1;P40145	.;ADCY8_HUMAN	P	698	ENSP00000286355:S698P;ENSP00000367161:S698P	ENSP00000286355:S698P	S	-	1	0	ADCY8	131966009	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.325000	0.65869	2.307000	0.77673	0.529000	0.55759	TCC	.	.		0.463	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			G	131896827	A	G	131896827	3	3	194	1	0	0	0	0	1	0	0	0	300	304	11	2	1707	2	ADCY8	8	131896827	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	12505025	131896827	14467195	66	28563										
SCRIB	23513	hgsc.bcm.edu	37	chr8	144875222	144875222	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aggcctgcttcacattggcgGgcagctcatccggagaaggc	14	12	2	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr8:144875222G>A	ENST00000320476.3	-	29	3947	c.3941C>T	c.(3940-3942)cCc>cTc	p.P1314L	SCRIB_ENST00000356994.2_Missense_Mutation_p.P1314L|SCRIB_ENST00000546337.1_5'UTR|SCRIB_ENST00000377533.3_Missense_Mutation_p.P1233L|RP11-429J17.8_ENST00000527139.1_RNA|RP11-429J17.8_ENST00000532625.1_RNA|RP11-429J17.8_ENST00000534089.1_RNA	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1314	Pro-rich.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CACATTGGCGGGCAGCTCATC	0.692																																					p.P1314L	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C3941T						.						13	13	13					8																	144875222		2091	4133	6224	SO:0001583	missense	23513	exon29			TTGGCGGGCAGCT	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.3941C>T	chr8.hg19:g.144875222G>A	ENSP00000322938:p.Pro1314Leu	70.0	0.0		92.0	33.0	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.717052	0.48622	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	T;T;T	0.41065	1.22;1.16;1.01	3.81	2.83	0.33086	.	.	.	.	.	T	0.60599	0.2281	M	0.72894	2.215	0.46028	D	0.998823	D;D;D	0.89917	1.0;0.996;1.0	D;P;D	0.91635	0.997;0.898;0.999	T	0.65142	-0.6240	9	0.72032	D	0.01	.	11.6576	0.51328	0.0:0.181:0.819:0.0	.	1314;1314;1233	Q14160;Q14160-3;Q14160-2	SCRIB_HUMAN;.;.	L	1314;1314;1233;683	ENSP00000349486:P1314L;ENSP00000322938:P1314L;ENSP00000366756:P1233L	ENSP00000322938:P1314L	P	-	2	0	SCRIB	144947210	1.000000	0.71417	0.845000	0.33349	0.215000	0.24574	4.603000	0.61105	1.862000	0.54008	0.305000	0.20034	CCC	.	.		0.692	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		A	144875222	G	A	144875222	3	1	194	1	0	0	0	0	1	0	0	0	13952	1232	43	3	1062	3	SCRIB	8	144875222	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	12978395	144875222	1488800	67	28564										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2123796	2123796	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ttaatggaggaggatgagctGccctcctggatcattaagga	13	7	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr9:2123796G>A	ENST00000382203.1	+	27	4049	c.3840G>A	c.(3838-3840)ctG>ctA	p.L1280L	SMARCA2_ENST00000382194.1_Silent_p.L1280L|SMARCA2_ENST00000357248.2_Silent_p.L1280L|SMARCA2_ENST00000349721.2_Silent_p.L1280L			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	1280					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		AGGATGAGCTGCCCTCCTGGA	0.562																																					p.L1280L		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G3840A						.						46	47	46					9																	2123796		2203	4300	6503	SO:0001819	synonymous_variant	6595	exon27			TGAGCTGCCCTCC	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.3840G>A	chr9.hg19:g.2123796G>A		87.0	0.0		112.0	8.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	hg19	CCDS34977.1																																																																																			.	.		0.562	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2123796	G	A	2123796	2	1	194	1	0	0	0	0	0	0	0	1	14784	1306	46	3		3	SMARCA2	9	2123796	Silent	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10		2123796	139089635	68	28565										
SPAG8	4882	hgsc.bcm.edu	37	chr9	35811575	35811575	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ggaccagagccagagccagaGccatggccagcacctgagct	13	14	0	4			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr9:35811575G>A	ENST00000342694.2	+	0	3686				AL133410.1_ENST00000582432.1_RNA|HINT2_ENST00000474908.1_5'Flank|SPAG8_ENST00000340291.2_Silent_p.G156G|SPAG8_ENST00000479751.1_5'Flank|SPAG8_ENST00000484764.1_Silent_p.G154G|TMEM8B_ENST00000377996.1_5'Flank|SPAG8_ENST00000396638.2_Silent_p.G156G	NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2						bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	cagagccagagccatggccag	0.602																																					p.G156G		Atlas-SNP	.											.	SPAG8	67	.	0			c.C468T						.						52	41	45					9																	35811575		2203	4300	6503	SO:0001628	intergenic_variant	26206	exon2			GCCAGAGCCATGG	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871		chr9.hg19:g.35811575G>A		63.0	0.0		65.0	28.0	NM_001039592	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	hg19	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	G	5.563	0.288698	0.10513	.	.	ENSG00000137098	ENST00000497810	.	.	.	4.52	3.52	0.40303	.	.	.	.	.	T	0.35770	0.0943	.	.	.	0.20638	N	0.999877	.	.	.	.	.	.	T	0.13602	-1.0503	4	.	.	.	-2.241	9.0247	0.36222	0.0:0.0:0.7803:0.2197	.	.	.	.	V	154	.	.	A	-	2	0	SPAG8	35801575	0.000000	0.05858	0.013000	0.15412	0.084000	0.17831	-1.130000	0.03241	2.474000	0.83562	0.655000	0.94253	GCT	.	.		0.602	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			A	35811575	G	A	35811575	1	1	194	0	1	0	0	0	0	0	0	0	14999	958	34	3		3	SPAG8	9	35811575	IGR	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	33687779	35811575	105401856	69	28566										
FAM120A	23196	hgsc.bcm.edu	37	chr9	96278439	96278439	+	Frame_Shift_Del	DEL	C	C	-													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cgctgtatgagcggtcctcgCccatcaacccggcccagagc							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr9:96278439delC	ENST00000277165.6	+	7	1500	c.1306delC	c.(1306-1308)cccfs	p.P436fs	FAM120A_ENST00000340893.4_Frame_Shift_Del_p.P436fs|FAM120A_ENST00000375389.3_Frame_Shift_Del_p.P436fs|FAM120A_ENST00000333936.5_Frame_Shift_Del_p.P436fs	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	436						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GCGGTCCTCGCCCATCAACCC	0.597																																					p.S435fs		Atlas-INDEL	.											.	FAM120A	105	.	0			c.1305delG						.						106	98	101					9																	96278439		2203	4299	6502	SO:0001589	frameshift_variant	23196	exon7			.	AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"DNA polymerase-transactivated protein 1", "oxidative stess-associated Src activator"	612265	"chromosome 9 open reading frame 10"	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.1306delC	chr9.hg19:g.96278439delC	ENSP00000277165:p.Pro436fs	304.0	0.0		359.0	175.0	NM_014612	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Frame_Shift_Del	DEL	ENST00000277165.6	hg19	CCDS6706.1																																																																																			.	.		0.597	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612		-	96278439	C	-	96278439	7	5	194	1	0	1	0	1	0	0	0	0	5420	739	26	0	1332	0	FAM120A	9	96278439	Frame_Shift_Del	DEL	C	TCGA-DD-AADL-01A-11D-A40R-10	60466864	96278439	44934992	70	28567										
TRIM32	22954	hgsc.bcm.edu	37	chr9	119461915	119461915	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ctcctaaggggcagctgctgGtcttggactgttgggatcat	14	9	2	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr9:119461915G>T	ENST00000450136.1	+	2	2055	c.1894G>T	c.(1894-1896)Gtc>Ttc	p.V632F	ASTN2_ENST00000313400.4_Intron|ASTN2_ENST00000373996.3_Intron|ASTN2_ENST00000361477.3_Intron|TRIM32_ENST00000373983.2_Missense_Mutation_p.V632F|ASTN2_ENST00000361209.2_Intron	NM_001099679.1|NM_012210.3	NP_001093149.1|NP_036342.2	Q13049	TRI32_HUMAN	tripartite motif containing 32	632					fat cell differentiation (GO:0045444)|innate immune response (GO:0045087)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of proteolysis (GO:0045862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of type I interferon production (GO:0032479)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|striated muscle myosin thick filament (GO:0005863)	ligase activity (GO:0016874)|myosin binding (GO:0017022)|protein self-association (GO:0043621)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|translation initiation factor binding (GO:0031369)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	26						GCAGCTGCTGGTCTTGGACTG	0.488																																					p.V632F	Esophageal Squamous(92;212 1916 19711 26951)	Atlas-SNP	.											.	TRIM32	67	.	0			c.G1894T						.						93	93	93					9																	119461915		2203	4300	6503	SO:0001583	missense	22954	exon2			CTGCTGGTCTTGG	U18543	CCDS6817.1	9q33.1	2014-09-17	2011-01-25		ENSG00000119401	ENSG00000119401		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16380	protein-coding gene	gene with protein product		602290	"limb girdle muscular dystrophy 2H (autosomal recessive)", "tripartite motif-containing 32"	LGMD2H		11331580, 7778269, 16606853	Standard	NM_001099679		Approved	HT2A, TATIP, BBS11	uc004bjx.2	Q13049	OTTHUMG00000021026	ENST00000450136.1:c.1894G>T	chr9.hg19:g.119461915G>T	ENSP00000408292:p.Val632Phe	72.0	0.0		98.0	46.0	NM_012210	Q9NQP8	Missense_Mutation	SNP	ENST00000450136.1	hg19	CCDS6817.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.894783	0.72639	.	.	ENSG00000119401	ENST00000450136;ENST00000373983	D;D	0.87729	-2.29;-2.29	5.69	5.69	0.88448	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000003	D	0.94182	0.8133	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93724	0.7035	9	.	.	.	-22.3703	19.8228	0.96604	0.0:0.0:1.0:0.0	.	632	Q13049	TRI32_HUMAN	F	632	ENSP00000408292:V632F;ENSP00000363095:V632F	.	V	+	1	0	TRIM32	118501736	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.434000	0.97515	2.668000	0.90789	0.650000	0.86243	GTC	.	.		0.488	TRIM32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055466.2	NM_012210		T	119461915	G	T	119461915	3	4	194	1	0	0	0	0	1	0	0	0	16521	1261	44	3	1896	3	TRIM32	9	119461915	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	23183476	119461915	21751516	71	28568										
LBX1	10660	hgsc.bcm.edu	37	chr10	102988325	102988325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cctccagcgcgcacagcggcGaggtctgcgagagcagcgcg	16	15	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr10:102988325G>A	ENST00000370193.2	-	1	1226	c.248C>T	c.(247-249)tCg>tTg	p.S83L	LBX1-AS1_ENST00000546988.1_RNA|LBX1-AS1_ENST00000547077.1_RNA	NM_006562.4	NP_006553.2	P52954	LBX1_HUMAN	ladybird homeobox 1	83					anatomical structure morphogenesis (GO:0009653)|heart looping (GO:0001947)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neuron fate determination (GO:0048664)|regulation of transcription from RNA polymerase II promoter involved in spinal cord association neuron specification (GO:0021920)|spinal cord motor neuron differentiation (GO:0021522)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(2)|lung(4)|ovary(1)	7		Colorectal(252;0.234)		Epithelial(162;3.22e-09)|all cancers(201;1.79e-07)		GCACAGCGGCGAGGTCTGCGA	0.716																																					p.S83L		Atlas-SNP	.											.	LBX1	18	.	0			c.C248T						.						8	8	8					10																	102988325		2092	4108	6200	SO:0001583	missense	10660	exon1			AGCGGCGAGGTCT	X90828	CCDS31270.1	10q24.32	2011-06-20	2007-02-15		ENSG00000138136	ENSG00000138136		"Homeoboxes / ANTP class : NKL subclass"	16960	protein-coding gene	gene with protein product		604255	"ladybird homeobox homolog 1 (Drosophila)"			8645601	Standard	XM_005269443		Approved	LBX1H, HPX6	uc001ksx.3	P52954	OTTHUMG00000018927	ENST00000370193.2:c.248C>T	chr10.hg19:g.102988325G>A	ENSP00000359212:p.Ser83Leu	41.0	0.0		36.0	27.0	NM_006562	B9EGA2|Q05BB2	Missense_Mutation	SNP	ENST00000370193.2	hg19	CCDS31270.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862142	0.91511	.	.	ENSG00000138136	ENST00000370193	D	0.94046	-3.34	4.21	4.21	0.49690	.	0.000000	0.85682	D	0.000000	D	0.96244	0.8775	M	0.80746	2.51	0.58432	D	0.999999	D	0.89917	1.0	D	0.72075	0.976	D	0.96199	0.9144	10	0.52906	T	0.07	.	14.1022	0.65065	0.0:0.0:1.0:0.0	.	83	P52954	LBX1_HUMAN	L	83	ENSP00000359212:S83L	ENSP00000359212:S83L	S	-	2	0	LBX1	102978315	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.823000	0.92018	2.203000	0.70933	0.561000	0.74099	TCG	.	.		0.716	LBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049928.3	NM_006562		A	102988325	G	A	102988325	3	1	194	1	0	0	0	0	1	0	0	0	8662	1059	37	1	605	1	LBX1	10	102988325	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10		102988325	32546422	72	28569										
PPRC1	23082	hgsc.bcm.edu	37	chr10	103898443	103898443	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tctgacggagatcttggacaAtgcagattctgagaaccttt	10	8	3	4			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr10:103898443A>G	ENST00000278070.2	+	3	449	c.410A>G	c.(409-411)aAt>aGt	p.N137S	PPRC1_ENST00000413464.2_Missense_Mutation_p.N137S|PPRC1_ENST00000370012.1_5'Flank	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	137					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		ATCTTGGACAATGCAGATTCT	0.532																																					p.N137S		Atlas-SNP	.											.	PPRC1	151	.	0			c.A410G						.						121	108	112					10																	103898443		2203	4300	6503	SO:0001583	missense	23082	exon3			TGGACAATGCAGA	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.410A>G	chr10.hg19:g.103898443A>G	ENSP00000278070:p.Asn137Ser	60.0	0.0		53.0	33.0	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	hg19	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	A	14.42	2.528710	0.44969	.	.	ENSG00000148840	ENST00000278070;ENST00000413464	T;T	0.26660	1.72;1.72	4.97	4.97	0.65823	.	0.200781	0.37136	N	0.002234	T	0.20495	0.0493	L	0.32530	0.975	0.43745	D	0.996241	P;P	0.43750	0.816;0.816	B;B	0.43225	0.412;0.412	T	0.01930	-1.1245	10	0.35671	T	0.21	.	8.1841	0.31328	0.8716:0.0:0.1284:0.0	.	137;137	E7EVG6;Q5VV67	.;PPRC1_HUMAN	S	137	ENSP00000278070:N137S;ENSP00000399743:N137S	ENSP00000278070:N137S	N	+	2	0	PPRC1	103888433	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.874000	0.75546	2.024000	0.59613	0.379000	0.24179	AAT	.	.		0.532	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		G	103898443	A	G	103898443	3	3	194	1	0	0	0	0	1	0	0	0	12422	101	4	2	420	2	PPRC1	10	103898443	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	910118	103898443	31636304	73	28570										
C10orf118	55088	hgsc.bcm.edu	37	chr10	115922915	115922915	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	atagtttggactcattttctAatttgctgctttcattgcca	6	8	3	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr10:115922915A>G	ENST00000369287.3	-	2	379	c.113T>C	c.(112-114)tTa>tCa	p.L38S	C10orf118_ENST00000369286.1_Missense_Mutation_p.L38S|C10orf118_ENST00000369285.3_Missense_Mutation_p.L38S	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		38										NS(1)|autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(2)	24		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)		CTCATTTTCTAATTTGCTGCT	0.343																																					p.L38S		Atlas-SNP	.											.	C10orf118	70	.	0			c.T113C						.						124	122	123					10																	115922915		2203	4300	6503	SO:0001583	missense	55088	exon2			TTTTCTAATTTGC																												ENST00000369287.3:c.113T>C	chr10.hg19:g.115922915A>G	ENSP00000358293:p.Leu38Ser	56.0	0.0		70.0	45.0	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Missense_Mutation	SNP	ENST00000369287.3	hg19	CCDS7587.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.281855	0.40394	.	.	ENSG00000165813	ENST00000369287;ENST00000430353;ENST00000369286;ENST00000369285	T;T;T	0.47528	1.37;0.84;0.84	5.65	4.51	0.55191	.	0.676274	0.13875	N	0.356763	T	0.49762	0.1576	L	0.50333	1.59	0.80722	D	1	P	0.45827	0.867	P	0.48030	0.564	T	0.42916	-0.9423	10	0.56958	D	0.05	.	10.1473	0.42771	0.9246:0.0:0.0754:0.0	.	38	Q7Z3E2	CJ118_HUMAN	S	38;144;38;38	ENSP00000358293:L38S;ENSP00000358292:L38S;ENSP00000358291:L38S	ENSP00000358291:L38S	L	-	2	0	C10orf118	115912905	0.977000	0.34250	0.982000	0.44146	0.680000	0.39746	3.166000	0.50785	0.983000	0.38602	0.529000	0.55759	TTA	.	.		0.343	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1			G	115922915	A	G	115922915	3	3	194	1	0	0	0	0	1	0	0	0	1589	372	13	2	2643	2	C10orf118	10	115922915	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	12024472	115922915	19611832	74	28571										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33689596	33689596	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cagaaaacgacccgtctgacGctcccctgaccaacatctcc	6	18	2	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr11:33689596G>T	ENST00000321505.4	+	20	5626	c.5446G>T	c.(5446-5448)Gct>Tct	p.A1816S	KIAA1549L_ENST00000389726.3_Missense_Mutation_p.A1822S|RP4-541C22.5_ENST00000534431.1_RNA			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1816						integral component of membrane (GO:0016021)											CCCGTCTGACGCTCCCCTGAC	0.637																																					p.A1816S		Atlas-SNP	.											.	.	.	.	0			c.G5446T						.						54	62	59					11																	33689596		2025	4182	6207	SO:0001583	missense	25758	exon20			TCTGACGCTCCCC	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.5446G>T	chr11.hg19:g.33689596G>T	ENSP00000315295:p.Ala1816Ser	72.0	0.0		93.0	50.0	NM_012194	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	hg19	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	G	10.68	1.419030	0.25552	.	.	ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000536568	.	.	.	5.67	-4.08	0.03963	.	0.487586	0.17947	N	0.156629	T	0.15219	0.0367	N	0.08118	0	0.09310	N	0.999998	B	0.31893	0.345	B	0.26517	0.07	T	0.11421	-1.0588	9	0.24483	T	0.36	-0.0232	14.4568	0.67420	0.5444:0.0:0.4556:0.0	.	1822	E9PAT2	.	S	1816;1822;1655	.	ENSP00000315295:A1816S	A	+	1	0	C11orf41	33646172	0.052000	0.20516	0.039000	0.18376	0.149000	0.21700	0.072000	0.14617	-0.596000	0.05821	-0.258000	0.10820	GCT	.	.		0.637	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		T	33689596	G	T	33689596	3	4	194	1	0	0	0	0	1	0	0	0	1642	1087	38	1	5542	1	C11orf41	11	33689596	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10		33689596	101316920	75	28572										
ZNF408	79797	hgsc.bcm.edu	37	chr11	46726573	46726573	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cggccctttgcttgtgaccaGtgtggcaaggcctttgcccg	13	13	0	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr11:46726573G>T	ENST00000311764.2	+	5	1553	c.1323G>T	c.(1321-1323)caG>caT	p.Q441H		NM_001184751.1|NM_024741.2	NP_001171680.1|NP_079017.1	Q9H9D4	ZN408_HUMAN	zinc finger protein 408	441					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTTGTGACCAGTGTGGCAAGG	0.652																																					p.Q441H	Pancreas(79;698 1390 6545 18745 34127)|Esophageal Squamous(120;1014 1625 12837 24601 49525)	Atlas-SNP	.											.	ZNF408	70	.	0			c.G1323T						.						51	48	49					11																	46726573		2201	4299	6500	SO:0001583	missense	79797	exon5			TGACCAGTGTGGC	AF346626	CCDS7923.1	11p11.2	2008-02-05			ENSG00000175213	ENSG00000175213		"Zinc fingers, C2H2-type"	20041	protein-coding gene	gene with protein product						15231747	Standard	NM_024741		Approved	FLJ12827	uc010rgw.2	Q9H9D4	OTTHUMG00000166568	ENST00000311764.2:c.1323G>T	chr11.hg19:g.46726573G>T	ENSP00000309606:p.Gln441His	66.0	0.0		87.0	29.0	NM_024741		Missense_Mutation	SNP	ENST00000311764.2	hg19	CCDS7923.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.210545	0.58343	.	.	ENSG00000175213	ENST00000311764	T	0.17054	2.3	5.68	3.8	0.43715	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42682	D	0.000672	T	0.13841	0.0335	N	0.25992	0.78	0.32639	N	0.520927	P;P	0.48503	0.911;0.911	P;P	0.45753	0.492;0.492	T	0.12837	-1.0532	10	0.62326	D	0.03	-31.9179	7.299	0.26409	0.1355:0.2493:0.6152:0.0	.	433;441	B4DXY4;Q9H9D4	.;ZN408_HUMAN	H	441	ENSP00000309606:Q441H	ENSP00000309606:Q441H	Q	+	3	2	ZNF408	46683149	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.593000	0.23999	0.847000	0.35167	0.563000	0.77884	CAG	.	.		0.652	ZNF408-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390485.2	NM_024741		T	46726573	G	T	46726573	3	4	194	1	0	0	0	0	1	0	0	0	17903	1020	36	3	1373	3	ZNF408	11	46726573	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	13036977	46726573	88279943	76	28573										
C11orf24	53838	hgsc.bcm.edu	37	chr11	68029831	68029832	+	Missense_Mutation	DNP	GC	GC	AA													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ctacagtctgagcacgtgtgGccaatgtggccagggttgct					rs567702264		TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr11:68029831_68029832GC>AA	ENST00000304271.6	-	4	1033_1034	c.631_632GC>TT	c.(631-633)GCc>TTc	p.A211F	C11orf24_ENST00000530166.1_5'Flank|C11orf24_ENST00000533310.1_Intron	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	211						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						AGCACGTGTGGCCAATGTGGCC	0.604																																					p.A211V|p.A211S	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.C632T|c.G631T						.																																			SO:0001583	missense	53838	exon4			CGTGTGGCCAATG|GTGTGGCCAATGT	AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.631_632delinsAA	chr11.hg19:g.68029831_68029832delinsAA	ENSP00000307264:p.Ala211Phe	123.0|124.0	0.0		128.0|127.0	40.0	NM_022338	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	hg19	CCDS8180.1																																																																																			.	.		0.604	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338		AA	68029832	GC	AA	68029831	3	1	194	1	0	0	0	0	1	0	0	0	1637	1203	42	3	721	3	C11orf24	11	68029831	Missense_Mutation	DNP	GC	TCGA-DD-AADL-01A-11D-A40R-10	21303258	68029831	66976685	77	28574										
DHCR7	1717	hgsc.bcm.edu	37	chr11	71146549	71146549	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cagcaggatggccatgtagaTgatgtagaagtagggcagca	15	6	0	3	rs375187933		TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr11:71146549T>C	ENST00000355527.3	-	9	1576	c.1300A>G	c.(1300-1302)Atc>Gtc	p.I434V	DHCR7_ENST00000407721.2_Missense_Mutation_p.I434V	NM_001163817.1|NM_001360.2	NP_001157289.1|NP_001351.2	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	434					blood vessel development (GO:0001568)|cell differentiation (GO:0030154)|cholesterol biosynthetic process (GO:0006695)|lung development (GO:0030324)|multicellular organism growth (GO:0035264)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|regulation of cholesterol biosynthetic process (GO:0045540)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear outer membrane (GO:0005640)	7-dehydrocholesterol reductase activity (GO:0047598)			endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(1)|skin(1)	19						GCCATGTAGATGATGTAGAAG	0.687									Smith-Lemli-Opitz syndrome																												p.I434V		Atlas-SNP	.											.	DHCR7	98	.	0			c.A1300G						.	T	VAL/ILE,VAL/ILE	1,4397	2.1+/-5.4	0,1,2198	29	33	31		1300,1300	-3.5	1	11		31	0,8586		0,0,4293	no	missense,missense	DHCR7	NM_001163817.1,NM_001360.2	29,29	0,1,6491	CC,CT,TT		0.0,0.0227,0.0077	benign,benign	434/476,434/476	71146549	1,12983	2199	4293	6492	SO:0001583	missense	1717	exon9	Familial Cancer Database	SLOS type I & II	TGTAGATGATGTA	AF034544	CCDS8200.1	11q13.4	2014-09-17	2004-02-13				1.3.1.21		2860	protein-coding gene	gene with protein product		602858	"Smith-Lemli-Opitz syndrome"	SLOS		9465114, 9634533	Standard	NM_001360		Approved		uc001oql.3	Q9UBM7		ENST00000355527.3:c.1300A>G	chr11.hg19:g.71146549T>C	ENSP00000347717:p.Ile434Val	49.0	0.0		86.0	20.0	NM_001163817	B2R6Z2|O60492|O60717	Missense_Mutation	SNP	ENST00000355527.3	hg19	CCDS8200.1	.	.	.	.	.	.	.	.	.	.	T	9.029	0.986802	0.18889	2.27E-4	0.0	ENSG00000172893	ENST00000407721;ENST00000355527;ENST00000533800	D;D;D	0.97850	-4.57;-4.57;-4.57	5.12	-3.46	0.04767	.	0.329841	0.33005	N	0.005387	D	0.89897	0.6848	N	0.11284	0.12	0.33808	D	0.62748	B	0.09022	0.002	B	0.12837	0.008	T	0.80710	-0.1261	10	0.05833	T	0.94	-26.0222	11.5442	0.50683	0.0:0.4786:0.0:0.5214	.	434	Q9UBM7	DHCR7_HUMAN	V	434;434;184	ENSP00000384739:I434V;ENSP00000347717:I434V;ENSP00000435011:I184V	ENSP00000347717:I434V	I	-	1	0	DHCR7	70824197	0.031000	0.19500	0.977000	0.42913	0.937000	0.57800	-0.262000	0.08682	-0.609000	0.05724	-0.411000	0.06167	ATC	.	.		0.687	DHCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394243.1	NM_001360		C	71146549	T	C	71146549	3	2	194	1	0	0	0	0	1	0	0	0	4479	1464	51	2	131	2	DHCR7	11	71146549	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	3116718	71146549	63859967	78	28575										
SLCO2B1	11309	hgsc.bcm.edu	37	chr11	74915600	74915600	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gctagtgtcggggccagggaAgaagccagaggattcccgag	17	9	0	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr11:74915600A>G	ENST00000289575.5	+	14	2500	c.2105A>G	c.(2104-2106)aAg>aGg	p.K702R	SLCO2B1_ENST00000532236.1_Missense_Mutation_p.K586R|SLCO2B1_ENST00000454962.2_Missense_Mutation_p.K475R|SLCO2B1_ENST00000428359.2_Missense_Mutation_p.K680R|SLCO2B1_ENST00000341411.4_Missense_Mutation_p.K475R|SLCO2B1_ENST00000525650.1_Missense_Mutation_p.K558R	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	702					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	GGGCCAGGGAAGAAGCCAGAG	0.582																																					p.K702R		Atlas-SNP	.											.	SLCO2B1	84	.	0			c.A2105G						.						69	60	63					11																	74915600		2200	4293	6493	SO:0001583	missense	11309	exon14			CAGGGAAGAAGCC	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.2105A>G	chr11.hg19:g.74915600A>G	ENSP00000289575:p.Lys702Arg	57.0	0.0		83.0	16.0	NM_007256	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	hg19	CCDS8235.1	.	.	.	.	.	.	.	.	.	.	A	13.91	2.378745	0.42207	.	.	ENSG00000137491	ENST00000289575;ENST00000341411;ENST00000532236;ENST00000525650;ENST00000454962;ENST00000428359	T;T;T;T;T;T	0.41758	1.16;1.16;1.29;0.99;1.16;1.16	5.51	3.2	0.36748	.	2.321250	0.01909	N	0.039702	T	0.25680	0.0625	N	0.08118	0	0.20873	N	0.999835	B;B;B	0.23540	0.009;0.087;0.009	B;B;B	0.22601	0.008;0.04;0.008	T	0.23762	-1.0179	10	0.18710	T	0.47	.	6.8978	0.24265	0.8166:0.0:0.1834:0.0	.	558;475;702	E9PPU8;O94956-2;O94956	.;.;SO2B1_HUMAN	R	702;475;586;558;475;680	ENSP00000289575:K702R;ENSP00000341286:K475R;ENSP00000434112:K586R;ENSP00000436324:K558R;ENSP00000389653:K475R;ENSP00000388912:K680R	ENSP00000289575:K702R	K	+	2	0	SLCO2B1	74593248	0.992000	0.36948	0.777000	0.31699	0.141000	0.21300	1.804000	0.38873	0.399000	0.25367	0.460000	0.39030	AAG	.	.		0.582	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256		G	74915600	A	G	74915600	3	3	194	1	0	0	0	0	1	0	0	0	14742	72	3	2	2159	2	SLCO2B1	11	74915600	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	3769051	74915600	60090916	79	28576										
CNTN5	53942	hgsc.bcm.edu	37	chr11	99942502	99942502	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aatcaatcagatgctggaatGtatcagtgtttggctgaaaa	10	5	3	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr11:99942502G>T	ENST00000524871.1	+	12	1655	c.1365G>T	c.(1363-1365)atG>atT	p.M455I	CNTN5_ENST00000418526.2_Missense_Mutation_p.M381I|CNTN5_ENST00000527185.1_Missense_Mutation_p.M455I|CNTN5_ENST00000528682.1_Missense_Mutation_p.M455I|CNTN5_ENST00000279463.3_Missense_Mutation_p.M455I	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	455	Ig-like C2-type 4.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		ATGCTGGAATGTATCAGTGTT	0.338																																					p.M455I		Atlas-SNP	.											.	CNTN5	324	.	0			c.G1365T						.						115	110	112					11																	99942502		1884	4147	6031	SO:0001583	missense	53942	exon11			TGGAATGTATCAG	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.1365G>T	chr11.hg19:g.99942502G>T	ENSP00000435637:p.Met455Ile	94.0	0.0		128.0	56.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.659147	0.88154	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.48	5.48	0.80851	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.71978	0.3404	L	0.37507	1.11	0.80722	D	1	D;D;D	0.69078	0.985;0.99;0.997	P;P;D	0.70487	0.905;0.886;0.969	T	0.72740	-0.4202	10	0.52906	T	0.07	.	18.3469	0.90325	0.0:0.0:1.0:0.0	.	455;381;455	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	I	455;455;455;381;455	ENSP00000433575:M455I;ENSP00000436185:M455I;ENSP00000435637:M455I;ENSP00000393229:M381I;ENSP00000279463:M455I	ENSP00000279463:M455I	M	+	3	0	CNTN5	99447712	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.444000	0.97578	2.573000	0.86826	0.655000	0.94253	ATG	.	.		0.338	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		T	99942502	G	T	99942502	3	4	194	1	0	0	0	0	1	0	0	0	3646	1377	48	3	1403	3	CNTN5	11	99942502	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	25026902	99942502	35064014	80	28577										
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120319893	120319894	+	Frame_Shift_Ins	INS	-	-	GGAG													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cagcatcctgggacccccacINSggagaccaagccgtcatgac							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr11:120319893_120319894insGGAG	ENST00000397843.2	+	21	1979_1980	c.1813_1814insGGAG	c.(1813-1815)cggfs	p.R605fs	ARHGEF12_ENST00000356641.3_Frame_Shift_Ins_p.R586fs|ARHGEF12_ENST00000532993.1_Frame_Shift_Ins_p.R502fs	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	605					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		GGGACCCCCACGGAGACCAAGC	0.455			T	MLL	AML																																p.R605fs		Atlas-INDEL	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.1813_1814insGGAG						.																																			SO:0001589	frameshift_variant	23365	exon21			.	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.1814_1817dupGGAG	chr11.hg19:g.120319894_120319897dupGGAG	ENSP00000380942:p.Arg605fs	93.0	0.0		124.0	52.0	NM_015313	O15086|Q6P526	Frame_Shift_Ins	INS	ENST00000397843.2	hg19	CCDS41727.1																																																																																			.	.		0.455	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		GGAG	120319894	-	GGAG	120319893	7	5	194	1	0	1	1	0	0	0	0	0	897	527	19	0	1895	0	ARHGEF12	11	120319893	Frame_Shift_Ins	INS	-	TCGA-DD-AADL-01A-11D-A40R-10	20377391	120319893	14686623	81	28578										
TAPBPL	55080	hgsc.bcm.edu	37	chr12	6566826	6566838	+	Frame_Shift_Del	DEL	ACTATACAGGACG	ACTATACAGGACG	-													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ccctcaccctgcccggcctcActatacaggacgaggggacc					rs368603949|rs374216855		TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	ACTATACAGGACG	ACTATACAGGACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr12:6566826_6566838delACTATACAGGACG	ENST00000266556.7	+	4	985_997	c.820_832delACTATACAGGACG	c.(820-834)actatacaggacgagfs	p.TIQDE274fs	TAPBPL_ENST00000544021.1_Splice_Site_p.TI158fs|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	274	Ig-like V-type.				negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						GCCCGGCCTCACTATACAGGACGAGGGGACCTA	0.624																																					p.273_277del		Atlas-INDEL	.											.	TAPBPL	21	.	0			c.819_831del						.																																			SO:0001589	frameshift_variant	55080	exon4			.	AK001005	CCDS8546.1	12p13.31	2013-01-11						"Immunoglobulin superfamily / C1-set domain containing"	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.820_832delACTATACAGGACG	chr12.hg19:g.6566826_6566838delACTATACAGGACG	ENSP00000266556:p.Thr274fs	106.0	0.0		111.0	35.0	NM_018009	Q9NWB8	Frame_Shift_Del	DEL	ENST00000266556.7	hg19	CCDS8546.1																																																																																			.	.		0.624	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009		-	6566838	ACTATACAGGACG	-	6566826	7	5	194	1	0	1	0	1	0	0	0	0	15568	159	6	0	834	0	TAPBPL	12	6566826	Frame_Shift_Del	DEL	ACTATACAGGACG	TCGA-DD-AADL-01A-11D-A40R-10		6566826	127285069	82	28579										
COPS7A	50813	hgsc.bcm.edu	37	chr12	6837158	6837158	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ttgcttatgggacatacgctGactacttaggtaaccagagg	11	8	0	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr12:6837158G>T	ENST00000543155.1	+	3	711	c.229G>T	c.(229-231)Gac>Tac	p.D77Y	COPS7A_ENST00000538410.1_Missense_Mutation_p.D77Y|COPS7A_ENST00000542150.1_Intron|COPS7A_ENST00000229251.3_Missense_Mutation_p.D77Y|COPS7A_ENST00000539735.1_Missense_Mutation_p.D77Y|COPS7A_ENST00000534877.1_Missense_Mutation_p.D77Y|COPS7A_ENST00000534947.1_Missense_Mutation_p.D77Y	NM_001164094.1	NP_001157566.1	Q9UBW8	CSN7A_HUMAN	COP9 signalosome subunit 7A	77	PCI.				cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	10						GACATACGCTGACTACTTAGG	0.512																																					p.D77Y		Atlas-SNP	.											.	COPS7A	26	.	0			c.G229T						.						141	117	126					12																	6837158		2203	4300	6503	SO:0001583	missense	50813	exon3			TACGCTGACTACT	AF193844	CCDS8558.1	12p13.31	2013-03-14	2013-03-14		ENSG00000111652	ENSG00000111652			16758	protein-coding gene	gene with protein product			"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7A", "COP9 constitutive photomorphogenic homolog subunit 7A (Arabidopsis)"				Standard	NM_001164093		Approved	CSN7A	uc001qqh.3	Q9UBW8	OTTHUMG00000169182	ENST00000543155.1:c.229G>T	chr12.hg19:g.6837158G>T	ENSP00000438115:p.Asp77Tyr	44.0	0.0		59.0	28.0	NM_001164094	A8K9A6|Q9NVX3|Q9UJW4	Missense_Mutation	SNP	ENST00000543155.1	hg19	CCDS8558.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.928297	0.92389	.	.	ENSG00000111652	ENST00000543155;ENST00000442593;ENST00000229251;ENST00000539735;ENST00000538410;ENST00000544725;ENST00000534947;ENST00000541866;ENST00000534877;ENST00000538753	T;T;T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51	5.88	5.88	0.94601	Proteasome component (PCI) domain (1);	0.000000	0.85682	D	0.000000	T	0.66636	0.2809	M	0.91354	3.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.993;0.994	T	0.73241	-0.4045	10	0.87932	D	0	-11.7169	19.8373	0.96661	0.0:0.0:1.0:0.0	.	77;77	F5H248;Q9UBW8	.;CSN7A_HUMAN	Y	77	ENSP00000438115:D77Y;ENSP00000229251:D77Y;ENSP00000441852:D77Y;ENSP00000439547:D77Y;ENSP00000446039:D77Y;ENSP00000442613:D77Y;ENSP00000438363:D77Y;ENSP00000440683:D77Y	ENSP00000229251:D77Y	D	+	1	0	COPS7A	6707419	1.000000	0.71417	0.992000	0.48379	0.930000	0.56654	8.717000	0.91425	2.782000	0.95742	0.655000	0.94253	GAC	.	.		0.512	COPS7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402740.1			T	6837158	G	T	6837158	3	4	194	1	0	0	0	0	1	0	0	0	3740	1290	45	3	235	3	COPS7A	12	6837158	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	270332	6837158	127014737	83	28580										
ETNK1	55500	hgsc.bcm.edu	37	chr12	22837867	22837901	+	Stop_Codon_Del	DEL	TGCATTAAAAGTGCCTGAGTAAAGAAGAGATTTAA	TGCATTAAAAGTGCCTGAGTAAAGAAGAGATTTAA	-													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aaaatgaagcctgaggttacTgcattaaaagtgcctgagta					rs138041873|rs142528168|rs377113417		TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	TGCATTAAAAGTGCCTGAGTAAAGAAGAGATTTAA	TGCATTAAAAGTGCCTGAGTAAAGAAGAGATTTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr12:22837867_22837901delTGCATTAAAAGTGCCTGAGTAAAGAAGAGATTTAA	ENST00000266517.4	+	0	1427_1461					NM_018638.4	NP_061108.2	Q9HBU6	EKI1_HUMAN	ethanolamine kinase 1						glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CTGAGGTTACTGCATTAAAAGTGCCTGAGTAAAGAAGAGATTTAATTATTCTCCA	0.315																																					p.446_453del	Esophageal Squamous(42;87 913 3224 6226 43339)	Atlas-INDEL	.											.	ETNK1	61	.	0			c.1337_1381del						.																																			SO:0001567	stop_retained_variant	55500	exon8			.	BC006111	CCDS8698.1, CCDS41760.1	12p12.2	2004-07-09			ENSG00000139163	ENSG00000139163			24649	protein-coding gene	gene with protein product		609858				11912161, 11044454	Standard	XM_005253420		Approved	EKI1, EKI	uc001rft.3	Q9HBU6	OTTHUMG00000169008	Exception_encountered	chr12.hg19:g.22837867_22837901delTGCATTAAAAGTGCCTGAGTAAAGAAGAGATTTAA		88.0	0.0		79.0	14.0	NM_018638	G5E969	Frame_Shift_Del	DEL	ENST00000266517.4	hg19	CCDS8698.1																																																																																			.	.		0.315	ETNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401926.2	NM_018638		-	22837901	TGCATTAAAAGTGCCTGAGTAAAGAAGAGATTTAA	-	22837867	7	5	194	1	0	1	0	1	0	0	0	0	5275	1567	55	0	1466	0	ETNK1	12	22837867	Stop_Codon_Del	DEL	TGCATTAAAAGTGCCTGAGTAAAGAAGAGATTTAA	TCGA-DD-AADL-01A-11D-A40R-10	16000709	22837867	111014028	84	28581										
C12orf72	254013	hgsc.bcm.edu	37	chr12	31815050	31815050	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aggctttcctggaggagaacActgaagtcaccagcagtggt	13	9	1	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr12:31815050A>T	ENST00000357721.3	+	2	378	c.163A>T	c.(163-165)Act>Tct	p.T55S	METTL20_ENST00000412352.2_Missense_Mutation_p.T55S|METTL20_ENST00000395763.3_Missense_Mutation_p.T55S|METTL20_ENST00000538463.1_Missense_Mutation_p.T55S|METTL20_ENST00000538391.1_Missense_Mutation_p.T55S	NM_001135863.1	NP_001129335.1	Q8IXQ9	MET20_HUMAN	methyltransferase like 20	55						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			lung(2)|stomach(1)	3						GGAGGAGAACACTGAAGTCAC	0.552																																					p.T55S		Atlas-SNP	.											.	METTL20	23	.	0			c.A163T						.						99	97	97					12																	31815050		2203	4300	6503	SO:0001583	missense	254013	exon2			GAGAACACTGAAG	BC039535	CCDS8724.1	12p11.21	2011-03-03	2011-03-03	2011-03-03	ENSG00000139160	ENSG00000139160			28739	protein-coding gene	gene with protein product		615256	"chromosome 12 open reading frame 72"	C12orf72			Standard	NM_173802		Approved	DKFZp451L235, MGC50559	uc001rkm.3	Q8IXQ9		ENST00000357721.3:c.163A>T	chr12.hg19:g.31815050A>T	ENSP00000350353:p.Thr55Ser	102.0	0.0		120.0	52.0	NM_173802	D3DUW3	Missense_Mutation	SNP	ENST00000357721.3	hg19	CCDS8724.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.188525	0.78789	.	.	ENSG00000139160	ENST00000412352;ENST00000395763;ENST00000538463;ENST00000357721;ENST00000539633;ENST00000538391	.	.	.	4.5	2.12	0.27331	.	0.054522	0.64402	D	0.000001	T	0.75369	0.3840	M	0.85777	2.775	0.51012	D	0.999904	D	0.69078	0.997	D	0.67548	0.952	T	0.72782	-0.4189	9	0.56958	D	0.05	-14.2507	6.589	0.22636	0.6853:0.1611:0.0:0.1536	.	55	Q8IXQ9	MET20_HUMAN	S	55	.	ENSP00000350353:T55S	T	+	1	0	METTL20	31706317	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	6.281000	0.72632	0.257000	0.21650	0.459000	0.35465	ACT	.	.		0.552	METTL20-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402196.1	NM_173802		T	31815050	A	T	31815050	3	4	194	1	0	0	0	0	1	0	0	0	1715	159	6	4	165	4	C12orf72	12	31815050	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	8977183	31815050	102036845	85	28582										
KRT5	3852	hgsc.bcm.edu	37	chr12	52911408	52911408	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aggactcggcttctgtccggCtgcggttggcaatctcctca	12	13	3	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr12:52911408C>A	ENST00000252242.4	-	5	1448	c.1058G>T	c.(1057-1059)aGc>aTc	p.S353I		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	353	Coil 2.|Rod.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		TTCTGTCCGGCTGCGGTTGGC	0.562																																					p.S353I		Atlas-SNP	.											.	KRT5	88	.	0			c.G1058T						.						145	137	140					12																	52911408		2203	4300	6503	SO:0001583	missense	3852	exon5			GTCCGGCTGCGGT		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"-", "Intermediate filaments type II, keratins (basic)"	6442	protein-coding gene	gene with protein product		148040	"epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types", "keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.1058G>T	chr12.hg19:g.52911408C>A	ENSP00000252242:p.Ser353Ile	39.0	0.0		54.0	11.0	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	hg19	CCDS8830.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.3|26.3	4.725329|4.725329	0.89298|0.89298	.|.	.|.	ENSG00000186081|ENSG00000186081	ENST00000548409;ENST00000551188|ENST00000252242;ENST00000456000	.|T	.|0.80214	.|-1.35	6.03|6.03	6.03|6.03	0.97812|0.97812	.|Filament (1);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.94341|0.94341	0.8181|0.8181	H|H	0.98068|0.98068	4.14|4.14	0.52099|0.52099	D|D	0.999949|0.999949	.|D	.|0.89917	.|1.0	.|D	.|0.83275	.|0.996	D|D	0.95548|0.95548	0.8618|0.8618	5|10	.|0.87932	.|D	.|0	.|.	20.5666|20.5666	0.99351|0.99351	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|353	.|P13647	.|K2C5_HUMAN	H|I	60;167|353;318	.|ENSP00000252242:S353I	.|ENSP00000252242:S353I	Q|S	-|-	3|2	2|0	KRT5|KRT5	51197675|51197675	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.810000|0.810000	0.45777|0.45777	3.969000|3.969000	0.56816|0.56816	2.854000|2.854000	0.98071|0.98071	0.655000|0.655000	0.94253|0.94253	CAG|AGC	.	.		0.562	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1			A	52911408	C	A	52911408	3	1	194	1	0	0	0	0	1	0	0	0	8488	797	28	3	734	3	KRT5	12	52911408	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	21096358	52911408	80940487	86	28583										
CTDSP2	10106	hgsc.bcm.edu	37	chr12	58217408	58217408	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aggggcccgcagctgcccaaGgctggtgtagacgtcctctg	15	13	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr12:58217408G>T	ENST00000398073.2	-	8	1096	c.793C>A	c.(793-795)Ctt>Att	p.L265I	CTDSP2_ENST00000547701.1_Missense_Mutation_p.L113I|CTDSP2_ENST00000548823.1_Missense_Mutation_p.L92I|MIR26A2_ENST00000385054.1_RNA	NM_005730.3	NP_005721.3	O14595	CTDS2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	265					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein dephosphorylation (GO:0006470)	nucleoplasm (GO:0005654)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(1)|prostate(2)	7	all_neural(12;0.00559)|Glioma(12;0.0143)|Melanoma(17;0.122)					AGCTGCCCAAGGCTGGTGTAG	0.587																																					p.L265I		Atlas-SNP	.											.	CTDSP2	25	.	0			c.C793A						.						31	37	35					12																	58217408		2134	4257	6391	SO:0001583	missense	10106	exon8			GCCCAAGGCTGGT	AF000152	CCDS41801.1	12q14.1	2012-06-14			ENSG00000175215	ENSG00000175215		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	17077	protein-coding gene	gene with protein product	"conserved gene amplified in osteosarcoma", "nuclear LIM interactor-interacting factor 2", "NLI-interacting factor 2", "small CTD phosphatase 2"	608711				9315096, 12721286	Standard	XM_005268556		Approved	OS4, SCP2, PSR2	uc001sqm.3	O14595	OTTHUMG00000170483	ENST00000398073.2:c.793C>A	chr12.hg19:g.58217408G>T	ENSP00000381148:p.Leu265Ile	36.0	0.0		56.0	7.0	NM_005730	A8K5H4|Q53ZR2|Q6NZY3|Q9UEX1	Missense_Mutation	SNP	ENST00000398073.2	hg19	CCDS41801.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516799	0.85495	.	.	ENSG00000175215	ENST00000398073;ENST00000548823;ENST00000549039;ENST00000547701	T;T	0.48201	1.22;0.82	5.26	5.26	0.73747	HAD-like domain (2);	0.059088	0.64402	D	0.000002	T	0.61924	0.2386	L	0.47716	1.5	0.58432	D	0.999999	B;P;P	0.48834	0.184;0.83;0.916	B;P;P	0.62184	0.376;0.646;0.899	T	0.62714	-0.6796	10	0.72032	D	0.01	-17.0957	17.7708	0.88491	0.0:0.0:1.0:0.0	.	139;92;265	B4DH48;F8W1I1;O14595	.;.;CTDS2_HUMAN	I	265;92;119;113	ENSP00000381148:L265I;ENSP00000448386:L119I	ENSP00000381148:L265I	L	-	1	0	CTDSP2	56503675	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.531000	0.73820	2.729000	0.93468	0.563000	0.77884	CTT	.	.		0.587	CTDSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409353.1	NM_005730		T	58217408	G	T	58217408	3	4	194	1	0	0	0	0	1	0	0	0	4006	1000	35	3	26	3	CTDSP2	12	58217408	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	5306000	58217408	75634487	87	28584										
KERA	11081	hgsc.bcm.edu	37	chr12	91450006	91450006	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gcctcacacttctagaccacAcagtgtctgttatgaataac	6	12	3	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr12:91450006A>G	ENST00000266719.3	-	2	300	c.53T>C	c.(52-54)gTg>gCg	p.V18A		NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan	18					carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						TCTAGACCACACAGTGTCTGT	0.418																																					p.V18A		Atlas-SNP	.											.	KERA	62	.	0			c.T53C						.						85	67	73					12																	91450006		2202	4300	6502	SO:0001583	missense	11081	exon2			GACCACACAGTGT	AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6309	protein-coding gene	gene with protein product	"keratocan proteoglycan"	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.53T>C	chr12.hg19:g.91450006A>G	ENSP00000266719:p.Val18Ala	59.0	0.0		82.0	5.0	NM_007035		Missense_Mutation	SNP	ENST00000266719.3	hg19	CCDS9037.1	.	.	.	.	.	.	.	.	.	.	A	5.651	0.304812	0.10678	.	.	ENSG00000139330	ENST00000266719	T	0.55760	0.5	5.96	2.34	0.29019	.	0.517808	0.21546	N	0.072808	T	0.32071	0.0817	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18555	-1.0333	10	0.07644	T	0.81	-10.2314	10.317	0.43743	0.748:0.0:0.252:0.0	.	18	O60938	KERA_HUMAN	A	18	ENSP00000266719:V18A	ENSP00000266719:V18A	V	-	2	0	KERA	89974137	0.051000	0.20477	0.018000	0.16275	0.436000	0.31835	1.368000	0.34216	0.525000	0.28522	0.528000	0.53228	GTG	.	.		0.418	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035		G	91450006	A	G	91450006	3	3	194	1	0	0	0	0	1	0	0	0	8152	159	6	2	1013	2	KERA	12	91450006	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	33232598	91450006	42401889	88	28585										
PRDM4	11108	hgsc.bcm.edu	37	chr12	108128174	108128174	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gggtgagatggtatttggttAgataagcctttgtacatttt	12	3	0	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr12:108128174A>G	ENST00000228437.5	-	12	2678	c.2219T>C	c.(2218-2220)cTa>cCa	p.L740P	RP11-864J10.4_ENST00000546714.1_RNA|RP11-864J10.4_ENST00000546829.1_RNA	NM_012406.3	NP_036538.3	Q9UKN5	PRDM4_HUMAN	PR domain containing 4	740					cell proliferation (GO:0008283)|negative regulation of cell cycle (GO:0045786)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|methyltransferase activity (GO:0008168)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	20						GTATTTGGTTAGATAAGCCTT	0.438																																					p.L740P		Atlas-SNP	.											.	PRDM4	64	.	0			c.T2219C						.						210	209	210					12																	108128174		2203	4300	6503	SO:0001583	missense	11108	exon12			TTGGTTAGATAAG	AF144757	CCDS9115.1	12q23-q24.1	2013-01-08				ENSG00000110851		"Zinc fingers, C2H2-type"	9348	protein-coding gene	gene with protein product		605780				10552934	Standard	NM_012406		Approved	PFM1	uc001tmp.3	Q9UKN5	OTTHUMG00000169914	ENST00000228437.5:c.2219T>C	chr12.hg19:g.108128174A>G	ENSP00000228437:p.Leu740Pro	147.0	0.0		171.0	75.0	NM_012406	Q9UFA6	Missense_Mutation	SNP	ENST00000228437.5	hg19	CCDS9115.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.714394	0.89112	.	.	ENSG00000110851	ENST00000228437	T	0.09163	3.01	6.03	6.03	0.97812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.21509	0.0518	N	0.25201	0.72	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.02553	-1.1142	10	0.41790	T	0.15	-0.3342	16.5602	0.84551	1.0:0.0:0.0:0.0	.	740	Q9UKN5	PRDM4_HUMAN	P	740	ENSP00000228437:L740P	ENSP00000228437:L740P	L	-	2	0	PRDM4	106652304	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.095000	0.94175	2.313000	0.78055	0.454000	0.30748	CTA	.	.		0.438	PRDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406546.1	NM_012406		G	108128174	A	G	108128174	3	3	194	1	0	0	0	0	1	0	0	0	12471	420	15	2	190	2	PRDM4	12	108128174	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	16678168	108128174	25723721	89	28586										
CCDC63	160762	hgsc.bcm.edu	37	chr12	111345151	111345151	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gcagtggaacagcccctggaCcacagcagccttcggcagct	12	15	0	0	rs371014584		TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr12:111345151C>A	ENST00000308208.5	+	12	1805	c.1563C>A	c.(1561-1563)gaC>gaA	p.D521E	CCDC63_ENST00000545036.1_Missense_Mutation_p.D481E|CCDC63_ENST00000552694.1_Missense_Mutation_p.D442E	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	521										NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						AGCCCCTGGACCACAGCAGCC	0.562																																					p.D521E		Atlas-SNP	.											.	CCDC63	89	.	0			c.C1563A						.						48	44	45					12																	111345151		2203	4300	6503	SO:0001583	missense	160762	exon12			CCTGGACCACAGC	AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"outer row dynein assembly 5 homolog (Chlamydomonas)"						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1563C>A	chr12.hg19:g.111345151C>A	ENSP00000312399:p.Asp521Glu	40.0	0.0		49.0	21.0	NM_152591	B4DY03|Q0P603|Q6P2E1	Missense_Mutation	SNP	ENST00000308208.5	hg19	CCDS9151.1	.	.	.	.	.	.	.	.	.	.	C	6.864	0.528684	0.13127	.	.	ENSG00000173093	ENST00000545036;ENST00000308208;ENST00000552694	T;T;T	0.32753	1.44;1.44;1.44	4.01	2.12	0.27331	.	0.449706	0.24296	N	0.039770	T	0.30386	0.0763	M	0.76574	2.34	0.25134	N	0.990546	B	0.16603	0.018	B	0.19946	0.027	T	0.26849	-1.0091	10	0.48119	T	0.1	.	6.167	0.20396	0.0:0.7095:0.1847:0.1058	.	521	Q8NA47	CCD63_HUMAN	E	481;521;442	ENSP00000445881:D481E;ENSP00000312399:D521E;ENSP00000450217:D442E	ENSP00000312399:D521E	D	+	3	2	CCDC63	109829534	1.000000	0.71417	0.999000	0.59377	0.124000	0.20399	0.960000	0.29253	0.421000	0.25980	-0.415000	0.06103	GAC	.	.		0.562	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591		A	111345151	C	A	111345151	3	1	194	1	0	0	0	0	1	0	0	0	2836	506	18	3	1605	3	CCDC63	12	111345151	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	3216977	111345151	22506744	90	28587										
EFHA1	221154	hgsc.bcm.edu	37	chr13	22069447	22069447	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gttgctactttcacagctctCttaaactccgctaaaaaaca	4	12	2	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr13:22069447C>T	ENST00000382374.4	-	11	1118	c.1053G>A	c.(1051-1053)aaG>aaA	p.K351K	MICU2_ENST00000479790.1_5'UTR	NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2	351					mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										TCACAGCTCTCTTAAACTCCG	0.308																																					p.K351K		Atlas-SNP	.											.	EFHA1	33	.	0			c.G1053A						.						87	74	79					13																	22069447		2202	4300	6502	SO:0001819	synonymous_variant	221154	exon11			AGCTCTCTTAAAC	AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"EF-hand domain containing"	31830	protein-coding gene	gene with protein product		610632	"EF hand domain family A1", "EF-hand domain family, member A1"	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.1053G>A	chr13.hg19:g.22069447C>T		89.0	0.0		90.0	24.0	NM_152726	Q8N0T6|Q8NAX8	Silent	SNP	ENST00000382374.4	hg19	CCDS9297.1																																																																																			.	.		0.308	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726		T	22069447	C	T	22069447	2	4	194	1	0	0	0	0	0	0	0	1	4945	912	32	3		3	EFHA1	13	22069447	Silent	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10		22069447	93100431	91	28588										
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26594099	26594100	+	Frame_Shift_Ins	INS	-	-	A													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tccgtgcttatgacaccaccINSaaaaagaaatccaggaagaa							TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr13:26594099_26594100insA	ENST00000381655.2	+	37	3685_3686	c.3543_3544insA	c.(3544-3546)aaafs	p.K1182fs	ATP8A2_ENST00000255283.8_Frame_Shift_Ins_p.K1117fs	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	1142					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		ATGACACCACCAAAAAGAAATC	0.406																																					p.T1181fs		Atlas-INDEL	.											.	ATP8A2	181	.	0			c.3543_3544insA						.																																			SO:0001589	frameshift_variant	51761	exon37			.	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.3548dupA	chr13.hg19:g.26594104_26594104dupA	ENSP00000371070:p.Lys1182fs	60.0	0.0		61.0	16.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Frame_Shift_Ins	INS	ENST00000381655.2	hg19	CCDS41873.1																																																																																			.	.		0.406	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		A	26594100	-	A	26594099	7	5	194	1	0	1	1	0	0	0	0	0	1193	581	21	0	3689	0	ATP8A2	13	26594099	Frame_Shift_Ins	INS	-	TCGA-DD-AADL-01A-11D-A40R-10	4524652	26594099	88575779	92	28589										
FLT1	2321	hgsc.bcm.edu	37	chr13	28963914	28963914	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	agatccgagagaaaacagccTttttgttgcagtgctcacct	9	10	1	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr13:28963914T>G	ENST00000282397.4	-	13	2221				FLT1_ENST00000541932.1_Intron	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1						blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GAAAACAGCCTTTTTGTTGCA	0.388																																					p.K663T		Atlas-SNP	.											.	FLT1	393	.	0			c.A1988C						.						119	112	114					13																	28963914		2203	4300	6503	SO:0001627	intron_variant	2321	exon13			ACAGCCTTTTTGT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1969+18A>C	chr13.hg19:g.28963914T>G		45.0	0.0		48.0	33.0	NM_001159920	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.		0.388	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			G	28963914	T	G	28963914	1	3	194	0	1	0	0	0	0	0	0	0	5949	1609	56	5		5	FLT1	13	28963914	Intron	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	2369815	28963914	86205964	93	28590										
UBL3	5412	hgsc.bcm.edu	37	chr13	30341820	30341820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tcactgttgttttgccaaaaGgaagttttaatgctatgtga	9	5	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr13:30341820G>A	ENST00000380680.4	-	4	1381	c.236C>T	c.(235-237)cCt>cTt	p.P79L		NM_007106.3	NP_009037.1	O95164	UBL3_HUMAN	ubiquitin-like 3	79	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				large_intestine(3)|lung(1)	4		Lung SC(185;0.0281)		all cancers(112;0.0598)|GBM - Glioblastoma multiforme(144;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.147)		TTTGCCAAAAGGAAGTTTTAA	0.353																																					p.P79L		Atlas-SNP	.											.,1	UBL3	13	.	0			c.C236T						.						133	114	120					13																	30341820		2203	4300	6503	SO:0001583	missense	5412	exon4			CCAAAAGGAAGTT	AF044221	CCDS9334.1	13q12-q13	2008-07-18			ENSG00000122042	ENSG00000122042			12504	protein-coding gene	gene with protein product		604711		PNSC1		10375635	Standard	NM_007106		Approved	HCG-1, DKFZP434K151, FLJ32018	uc001usp.3	O95164	OTTHUMG00000016661	ENST00000380680.4:c.236C>T	chr13.hg19:g.30341820G>A	ENSP00000370055:p.Pro79Leu	84.0	0.0		70.0	4.0	NM_007106	B2R4J1|Q5RL72|Q5VZS0|Q6FIG8|Q96SG7	Missense_Mutation	SNP	ENST00000380680.4	hg19	CCDS9334.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.873674	0.91664	.	.	ENSG00000122042	ENST00000380680	.	.	.	5.74	4.9	0.64082	Ubiquitin supergroup (1);	0.047648	0.85682	N	0.000000	T	0.77025	0.4070	M	0.84511	2.7	0.80722	D	1	D	0.64830	0.994	P	0.57152	0.814	T	0.81335	-0.0979	9	0.62326	D	0.03	-15.6777	14.055	0.64761	0.0724:0.0:0.9276:0.0	.	79	O95164	UBL3_HUMAN	L	79	.	ENSP00000370055:P79L	P	-	2	0	UBL3	29239820	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.040000	0.93783	1.557000	0.49525	0.563000	0.77884	CCT	.	.		0.353	UBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044342.1	NM_007106		A	30341820	G	A	30341820	3	1	194	1	0	0	0	0	1	0	0	0	16901	1000	35	3	125	3	UBL3	13	30341820	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	1377906	30341820	84828058	94	28591										
CCNA1	8900	hgsc.bcm.edu	37	chr13	37007255	37007255	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	agtggcccgaggtcccgatgCttgtcagatactcaccagag	12	12	2	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr13:37007255C>G	ENST00000255465.4	+	2	458	c.194C>G	c.(193-195)gCt>gGt	p.A65G	CCNA1_ENST00000463403.1_3'UTR|CCNA1_ENST00000418263.1_Missense_Mutation_p.A64G|CCNA1_ENST00000449823.1_Missense_Mutation_p.A21G|CCNA1_ENST00000440264.1_Missense_Mutation_p.A21G			P78396	CCNA1_HUMAN	cyclin A1	65					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		GGTCCCGATGCTTGTCAGATA	0.607																																					p.A65G		Atlas-SNP	.											.	CCNA1	91	.	0			c.C194G						.						92	89	90					13																	37007255		2203	4300	6503	SO:0001583	missense	8900	exon2			CCGATGCTTGTCA	U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.194C>G	chr13.hg19:g.37007255C>G	ENSP00000255465:p.Ala65Gly	78.0	0.0		43.0	31.0	NM_003914	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Missense_Mutation	SNP	ENST00000255465.4	hg19	CCDS9357.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.488805	0.44249	.	.	ENSG00000133101	ENST00000440264;ENST00000449823;ENST00000418263;ENST00000255465	T;T;T;T	0.16073	2.42;2.42;2.37;2.37	4.63	1.35	0.21983	.	1.361570	0.04561	N	0.391654	T	0.13586	0.0329	L	0.36672	1.1	0.25042	N	0.991199	B;B	0.27559	0.001;0.181	B;B	0.26969	0.003;0.075	T	0.32295	-0.9912	10	0.22706	T	0.39	.	5.1207	0.14858	0.0:0.5876:0.1704:0.2419	.	64;65	P78396-2;P78396	.;CCNA1_HUMAN	G	21;21;64;65	ENSP00000400666:A21G;ENSP00000409873:A21G;ENSP00000396479:A64G;ENSP00000255465:A65G	ENSP00000255465:A65G	A	+	2	0	CCNA1	35905255	0.534000	0.26362	0.873000	0.34254	0.925000	0.55904	-0.161000	0.10026	0.477000	0.27464	-0.263000	0.10527	GCT	.	.		0.607	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914		G	37007255	C	G	37007255	3	3	194	1	0	0	0	0	1	0	0	0	2911	797	28	4	200	4	CCNA1	13	37007255	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	6665435	37007255	78162623	95	28592										
CSNK1A1L	122011	hgsc.bcm.edu	37	chr13	37679379	37679379	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	acgagttcggctttggagccGctgttgtttgtcatcctgag	13	9	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr13:37679379G>T	ENST00000379800.3	-	1	424	c.15C>A	c.(13-15)agC>agA	p.S5R		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	5			S -> G (in dbSNP:rs56224973). {ECO:0000269|PubMed:17344846}.		cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S5S(1)		NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		CTTTGGAGCCGCTGTTGTTTG	0.607																																					p.S5R		Atlas-SNP	.											CSNK1A1L,colon,carcinoma,0,2	CSNK1A1L	69	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C15A						.						76	73	74					13																	37679379		2203	4300	6503	SO:0001583	missense	122011	exon1			GGAGCCGCTGTTG	BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.15C>A	chr13.hg19:g.37679379G>T	ENSP00000369126:p.Ser5Arg	80.0	0.0		64.0	43.0	NM_145203	Q5T2N2	Missense_Mutation	SNP	ENST00000379800.3	hg19	CCDS9363.1	.	.	.	.	.	.	.	.	.	.	G	7.439	0.640261	0.14386	.	.	ENSG00000180138	ENST00000379800	T	0.51071	0.72	0.778	-0.148	0.13424	.	0.088116	0.85682	D	0.000000	T	0.27663	0.0680	N	0.19112	0.55	0.27953	N	0.93707	P	0.38677	0.642	B	0.39935	0.314	T	0.13202	-1.0518	10	0.42905	T	0.14	.	4.9918	0.14218	0.248:0.0:0.752:0.0	.	5	Q8N752	KC1AL_HUMAN	R	5	ENSP00000369126:S5R	ENSP00000369126:S5R	S	-	3	2	CSNK1A1L	36577379	1.000000	0.71417	0.009000	0.14445	0.009000	0.06853	0.727000	0.25999	-0.112000	0.11979	-0.258000	0.10820	AGC	.	.		0.607	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203		T	37679379	G	T	37679379	3	4	194	1	0	0	0	0	1	0	0	0	3953	1078	38	1	1002	1	CSNK1A1L	13	37679379	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	672124	37679379	77490499	96	28593										
EDNRB	1910	hgsc.bcm.edu	37	chr13	78475302	78475302	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tggccaatggcaagcagaaaTagaaactgaatagccaccaa	9	9	0	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr13:78475302T>C	ENST00000334286.5	-	4	1078	c.842A>G	c.(841-843)tAt>tGt	p.Y281C	EDNRB_ENST00000446573.1_Missense_Mutation_p.Y281C|EDNRB_ENST00000377211.4_Missense_Mutation_p.Y371C	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	281					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	CAAGCAGAAATAGAAACTGAA	0.338																																					p.Y371C		Atlas-SNP	.											.	EDNRB	172	.	0			c.A1112G						.						74	77	76					13																	78475302		2203	4299	6502	SO:0001583	missense	1910	exon5			CAGAAATAGAAAC	L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.842A>G	chr13.hg19:g.78475302T>C	ENSP00000335311:p.Tyr281Cys	54.0	0.0		97.0	43.0	NM_001201397	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Missense_Mutation	SNP	ENST00000334286.5	hg19	CCDS9461.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.401948	0.83120	.	.	ENSG00000136160	ENST00000377211;ENST00000446573;ENST00000334286	T;T;T	0.71817	-0.6;-0.6;-0.6	5.69	5.69	0.88448	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.85318	0.5669	M	0.83852	2.665	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	1.0;0.97;0.999	D	0.87582	0.2485	10	0.87932	D	0	-3.7268	15.9518	0.79846	0.0:0.0:0.0:1.0	.	281;371;281	P24530-2;P24530-3;P24530	.;.;EDNRB_HUMAN	C	371;281;281	ENSP00000366416:Y371C;ENSP00000403401:Y281C;ENSP00000335311:Y281C	ENSP00000335311:Y281C	Y	-	2	0	EDNRB	77373303	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.180000	0.69256	0.533000	0.62120	TAT	.	.		0.338	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			C	78475302	T	C	78475302	3	2	194	1	0	0	0	0	1	0	0	0	4922	1406	49	2	623	2	EDNRB	13	78475302	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	40795923	78475302	36694576	97	28594										
MYH7	4625	hgsc.bcm.edu	37	chr14	23895186	23895186	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tacccacctctgccggaagtCcccgtagaggatgcggttgg	13	13	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr14:23895186C>A	ENST00000355349.3	-	19	2311	c.2149G>T	c.(2149-2151)Gac>Tac	p.D717Y		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	717	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TGCCGGAAGTCCCCGTAGAGG	0.607																																					p.D717Y		Atlas-SNP	.											.	MYH7	349	.	0			c.G2149T						.						59	59	59					14																	23895186		2203	4300	6503	SO:0001583	missense	4625	exon19			GGAAGTCCCCGTA	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.2149G>T	chr14.hg19:g.23895186C>A	ENSP00000347507:p.Asp717Tyr	66.0	0.0		89.0	32.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.761038	0.89932	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.95622	-3.76	5.03	5.03	0.67393	Myosin head, motor domain (2);	.	.	.	.	D	0.98592	0.9529	H	0.98178	4.165	0.80722	D	1	P	0.46395	0.877	P	0.60173	0.87	D	0.99593	1.0976	9	0.87932	D	0	.	18.5432	0.91037	0.0:1.0:0.0:0.0	.	717	P12883	MYH7_HUMAN	Y	717	ENSP00000347507:D717Y	ENSP00000347507:D717Y	D	-	1	0	MYH7	22965026	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.399000	0.79935	2.612000	0.88384	0.655000	0.94253	GAC	.	.		0.607	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23895186	C	A	23895186	3	1	194	1	0	0	0	0	1	0	0	0	10048	855	30	3	3746	3	MYH7	14	23895186	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10		23895186	83454354	98	28595										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68256275	68256275	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gggtctccagaggtgttgagCagcttgtcagtcacgtcaga	14	9	4	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr14:68256275C>T	ENST00000347230.4	-	16	2934	c.2796G>A	c.(2794-2796)ctG>ctA	p.L932L	ZFYVE26_ENST00000555452.1_Silent_p.L932L	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	932					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		AGGTGTTGAGCAGCTTGTCAG	0.502																																					p.L932L		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.G2796A						.						120	124	123					14																	68256275		2203	4300	6503	SO:0001819	synonymous_variant	23503	exon16			GTTGAGCAGCTTG	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.2796G>A	chr14.hg19:g.68256275C>T		51.0	0.0		48.0	36.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	hg19	CCDS9788.1																																																																																			.	.		0.502	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		T	68256275	C	T	68256275	2	4	194	1	0	0	0	0	0	0	0	1	17683	697	25	3		3	ZFYVE26	14	68256275	Silent	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	44361089	68256275	39093265	99	28596										
ZFP36L1	677	hgsc.bcm.edu	37	chr14	69256756	69256756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gtggatgaagtggcagcgggGcccgtaggggcaaaagccga	19	8	0	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr14:69256756G>A	ENST00000439696.2	-	2	812	c.511C>T	c.(511-513)Ccc>Tcc	p.P171S	ZFP36L1_ENST00000336440.3_Missense_Mutation_p.P171S|ZFP36L1_ENST00000555997.1_3'UTR	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1	171					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TGGCAGCGGGGCCCGTAGGGG	0.672											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P240S		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.C718T						.						34	41	39					14																	69256756		2203	4298	6501	SO:0001583	missense	677	exon3			AGCGGGGCCCGTA	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"RING-type (C3HC4) zinc fingers"	1107	protein-coding gene	gene with protein product		601064	"zinc finger protein, C3H type, 36-like 1", "zinc finger protein 36, C3H type-like 1"	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.511C>T	chr14.hg19:g.69256756G>A	ENSP00000388402:p.Pro171Ser	60.0	0.0	1113	35.0	23.0	NM_001244701	Q13851	Missense_Mutation	SNP	ENST00000439696.2	hg19	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.166230	0.57476	.	.	ENSG00000185650	ENST00000439696;ENST00000336440;ENST00000435246;ENST00000557086;ENST00000557022	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	4.5	2.53	0.30540	Zinc finger, CCCH-type (3);	0.137414	0.48286	D	0.000193	T	0.44371	0.1290	N	0.16567	0.415	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.36625	-0.9740	10	0.42905	T	0.14	0.7599	11.067	0.47980	0.0:0.1389:0.7169:0.1442	.	171	Q07352	TISB_HUMAN	S	171;171;154;177;149	ENSP00000388402:P171S;ENSP00000337386:P171S;ENSP00000450784:P177S;ENSP00000450600:P149S	ENSP00000337386:P171S	P	-	1	0	ZFP36L1	68326509	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.735000	0.84939	1.086000	0.41228	0.585000	0.79938	CCC	.	.		0.672	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1			A	69256756	G	A	69256756	3	1	194	1	0	0	0	0	1	0	0	0	17661	1203	42	3	509	3	ZFP36L1	14	69256756	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	1000481	69256756	38092784	100	28597										
FURIN	5045	hgsc.bcm.edu	37	chr15	91424928	91424928	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ttcgtcactgtcttcctggtCctgcagctgcgctctggctt	10	14	3	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr15:91424928C>T	ENST00000268171.3	+	16	2484	c.2205C>T	c.(2203-2205)gtC>gtT	p.V735V	FES_ENST00000414248.2_5'Flank|FES_ENST00000328850.3_5'Flank|FES_ENST00000394302.1_5'Flank	NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	735					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TCTTCCTGGTCCTGCAGCTGC	0.642																																					p.V735V		Atlas-SNP	.											.	FURIN	85	.	0			c.C2205T						.						142	126	131					15																	91424928		2198	4298	6496	SO:0001819	synonymous_variant	5045	exon16			CCTGGTCCTGCAG	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.2205C>T	chr15.hg19:g.91424928C>T		110.0	0.0		139.0	61.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	hg19	CCDS10364.1																																																																																			.	.		0.642	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		T	91424928	C	T	91424928	2	4	194	1	0	0	0	0	0	0	0	1	6107	842	30	3		3	FURIN	15	91424928	Silent	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10		91424928	11106464	101	28598										
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29889696	29889696	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gctatagctctggggccagtCgggagagaggaccacgccag	16	11	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr16:29889696C>A	ENST00000308713.5	-	10	2151	c.1624G>T	c.(1624-1626)Gac>Tac	p.D542Y	SEZ6L2_ENST00000350527.3_Missense_Mutation_p.D472Y|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.D428Y|SEZ6L2_ENST00000537485.1_Missense_Mutation_p.D498Y	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	542	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGGGGCCAGTCGGGAGAGAGG	0.597																																					p.D542Y		Atlas-SNP	.											.	SEZ6L2	137	.	0			c.G1624T						.						84	72	76					16																	29889696		2197	4300	6497	SO:0001583	missense	26470	exon10			GCCAGTCGGGAGA	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1624G>T	chr16.hg19:g.29889696C>A	ENSP00000312550:p.Asp542Tyr	37.0	0.0		58.0	49.0	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	hg19	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.547122	0.86022	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.42	5.42	0.78866	CUB (5);	0.000000	0.64402	D	0.000019	T	0.53045	0.1772	L	0.53249	1.67	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.987;1.0;1.0;1.0;1.0;1.0	T	0.53837	-0.8382	10	0.87932	D	0	.	17.99	0.89165	0.0:1.0:0.0:0.0	.	498;542;428;472;542;472	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	Y	472;542;428;498	ENSP00000310206:D472Y;ENSP00000312550:D542Y;ENSP00000319215:D428Y;ENSP00000439412:D498Y	ENSP00000312550:D542Y	D	-	1	0	SEZ6L2	29797197	0.998000	0.40836	0.945000	0.38365	0.970000	0.65996	3.758000	0.55220	2.547000	0.85894	0.655000	0.94253	GAC	.	.		0.597	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		A	29889696	C	A	29889696	3	1	194	1	0	0	0	0	1	0	0	0	14159	884	31	1	1183	1	SEZ6L2	16	29889696	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10		29889696	60465057	102	28599										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30735749	30735749	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	actatgctaccagccccggtTccgtcacctctcccgagccc	7	20	2	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr16:30735749T>C	ENST00000262518.4	+	25	5389	c.5004T>C	c.(5002-5004)gtT>gtC	p.V1668V	SRCAP_ENST00000344771.4_Silent_p.V1510V|SRCAP_ENST00000395059.2_Silent_p.V1606V	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1668	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CAGCCCCGGTTCCGTCACCTC	0.572																																					p.V1668V		Atlas-SNP	.											.	SRCAP	298	.	0			c.T5004C						.						144	150	148					16																	30735749		2197	4300	6497	SO:0001819	synonymous_variant	10847	exon25			CCCGGTTCCGTCA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.5004T>C	chr16.hg19:g.30735749T>C		97.0	0.0		74.0	57.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.		0.572	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30735749	T	C	30735749	2	2	194	1	0	0	0	0	0	0	0	1	15150	1770	62	2		2	SRCAP	16	30735749	Silent	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	846053	30735749	59619004	103	28600										
SETD1A	9739	hgsc.bcm.edu	37	chr16	30990708	30990708	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cagcctcccgcaaggctcccCggggcgtggagcggaccatc	14	17	0	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr16:30990708C>T	ENST00000262519.8	+	14	4287	c.3601C>T	c.(3601-3603)Cgg>Tgg	p.R1201W		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	1201					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CAAGGCTCCCCGGGGCGTGGA	0.711																																					p.R1201W		Atlas-SNP	.											.	SETD1A	143	.	0			c.C3601T						.						12	14	14					16																	30990708		2173	4261	6434	SO:0001583	missense	9739	exon14			GCTCCCCGGGGCG	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.3601C>T	chr16.hg19:g.30990708C>T	ENSP00000262519:p.Arg1201Trp	103.0	0.0		115.0	86.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.283251	0.23392	.	.	ENSG00000099381	ENST00000262519	D	0.94723	-3.5	5.03	5.03	0.67393	.	0.258265	0.32068	N	0.006625	D	0.93025	0.7780	L	0.27053	0.805	0.39959	D	0.974631	D	0.76494	0.999	P	0.56474	0.799	D	0.93675	0.6993	10	0.72032	D	0.01	.	11.0517	0.47894	0.1854:0.8146:0.0:0.0	.	1201	O15047	SET1A_HUMAN	W	1201	ENSP00000262519:R1201W	ENSP00000262519:R1201W	R	+	1	2	SETD1A	30898209	0.652000	0.27349	0.991000	0.47740	0.357000	0.29423	0.629000	0.24538	2.328000	0.79073	0.557000	0.71058	CGG	.	.		0.711	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		T	30990708	C	T	30990708	3	4	194	1	0	0	0	0	1	0	0	0	14145	643	23	1	3651	1	SETD1A	16	30990708	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	254959	30990708	59364045	104	28601										
PHKB	5257	hgsc.bcm.edu	37	chr16	47497889	47497889	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cagtcgtctctccgtcttccGctttcttaaggtctggtaag	9	12	4	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr16:47497889G>A	ENST00000323584.5	+	1	100				PHKB_ENST00000455779.1_Missense_Mutation_p.A14T|PHKB_ENST00000567402.1_Intron|PHKB_ENST00000299167.8_Intron|ITFG1_ENST00000320640.6_5'Flank|ITFG1_ENST00000544001.2_5'Flank|PHKB_ENST00000566044.1_Missense_Mutation_p.A14T	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta						carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.A14T(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				TCCGTCTTCCGCTTTCTTAAG	0.398																																					p.A14T		Atlas-SNP	.											PHKB_ENST00000299167,NS,carcinoma,0,1	PHKB	298	.	1	Substitution - Missense(1)	endometrium(1)	c.G40A						.						137	130	132					16																	47497889		1855	4092	5947	SO:0001627	intron_variant	5257	exon2			TCTTCCGCTTTCT		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.76+2552G>A	chr16.hg19:g.47497889G>A		73.0	0.0		78.0	23.0	NM_001031835	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	G	1.407	-0.576672	0.03854	.	.	ENSG00000102893	ENST00000299167;ENST00000455779	D	0.90788	-2.73	5.65	1.33	0.21861	.	.	.	.	.	T	0.76751	0.4031	N	0.08118	0	0.18873	N	0.999982	B;B	0.10296	0.002;0.003	B;B	0.06405	0.0;0.002	T	0.59994	-0.7349	9	0.13108	T	0.6	.	7.4646	0.27314	0.2533:0.0:0.6364:0.1103	.	14;14	B4DQ16;Q93100-4	.;.	T	14	ENSP00000414345:A14T	ENSP00000299167:A14T	A	+	1	0	PHKB	46055390	0.888000	0.30383	0.144000	0.22314	0.050000	0.14768	1.209000	0.32357	0.074000	0.16767	-1.128000	0.01989	GCT	.	.		0.398	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			A	47497889	G	A	47497889	1	1	194	0	1	0	0	0	0	0	0	0	11854	1087	38	1		1	PHKB	16	47497889	Intron	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	16507181	47497889	42856864	105	28602										
USP10	9100	hgsc.bcm.edu	37	chr16	84779047	84779047	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ccaaccaaacccgagagtgcAtcacctcctgctgacggcac	8	17	1	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr16:84779047A>G	ENST00000219473.7	+	4	1073	c.960A>G	c.(958-960)gcA>gcG	p.A320A	USP10_ENST00000570191.1_Silent_p.A324A	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	320					autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						CCGAGAGTGCATCACCTCCTG	0.572																																					p.A324A		Atlas-SNP	.											.	USP10	51	.	0			c.A972G						.						40	41	41					16																	84779047		1977	4161	6138	SO:0001819	synonymous_variant	9100	exon5			GAGTGCATCACCT	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"Ubiquitin-specific peptidases"	12608	protein-coding gene	gene with protein product		609818	"ubiquitin specific protease 10"			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.960A>G	chr16.hg19:g.84779047A>G		100.0	0.0		63.0	46.0	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	hg19	CCDS45537.1																																																																																			.	.		0.572	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1			G	84779047	A	G	84779047	2	3	194	1	0	0	0	0	0	0	0	1	17056	204	8	2		2	USP10	16	84779047	Silent	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	37281158	84779047	5575706	106	28603										
TP53	7157	hgsc.bcm.edu	37	chr17	7578235	7578235	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	aagtgtttctgtcatccaaaTactccacacgcaaatttcct	4	12	2	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr17:7578235T>C	ENST00000269305.4	-	6	803	c.614A>G	c.(613-615)tAt>tGt	p.Y205C	TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.Y205C|TP53_ENST00000413465.2_Missense_Mutation_p.Y205C|TP53_ENST00000359597.4_Missense_Mutation_p.Y205C|TP53_ENST00000455263.2_Missense_Mutation_p.Y205C|TP53_ENST00000420246.2_Missense_Mutation_p.Y205C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	205	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1459726}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in sporadic cancers; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y205C(68)|p.Y205S(14)|p.Y205F(8)|p.0?(8)|p.Y112C(5)|p.?(5)|p.Y73C(5)|p.Y73S(1)|p.Y112S(1)|p.E204fs*39(1)|p.E204_N210delEYLDDRN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTCATCCAAATACTCCACACG	0.542		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y205C	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,temporoparietal,glioma,0,24	TP53	33396	.	117	Substitution - Missense(102)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(1)|Deletion - Frameshift(1)	lung(20)|upper_aerodigestive_tract(19)|central_nervous_system(10)|large_intestine(9)|biliary_tract(8)|breast(6)|ovary(6)|haematopoietic_and_lymphoid_tissue(5)|endometrium(5)|urinary_tract(5)|bone(5)|soft_tissue(4)|oesophagus(4)|stomach(3)|liver(3)|pancreas(2)|vulva(1)|skin(1)|prostate(1)	c.A614G						.						136	121	126					17																	7578235		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TCCAAATACTCCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.614A>G	chr17.hg19:g.7578235T>C	ENSP00000269305:p.Tyr205Cys	139.0	0.0		101.0	70.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.490024	0.64074	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99872	-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36	5.41	4.33	0.51752	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88906	2.99	0.58432	D	0.999999	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.995;0.998;0.995;0.997;0.999;0.997;0.996	D	0.97320	0.9943	10	0.87932	D	0	-5.8058	9.707	0.40222	0.0:0.0827:0.0:0.9173	.	166;205;205;112;205;205;205	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	205;205;205;205;205;205;194;112;73;112;73	ENSP00000410739:Y205C;ENSP00000352610:Y205C;ENSP00000269305:Y205C;ENSP00000398846:Y205C;ENSP00000391127:Y205C;ENSP00000391478:Y205C;ENSP00000425104:Y73C;ENSP00000423862:Y112C	ENSP00000269305:Y205C	Y	-	2	0	TP53	7518960	1.000000	0.71417	0.137000	0.22149	0.045000	0.14185	7.996000	0.88334	1.001000	0.39076	-0.256000	0.11100	TAT	.	.		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578235	T	C	7578235	3	2	194	1	0	0	0	0	1	0	0	0	16396	1406	49	2	680	2	TP53	17	7578235	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10		7578235	73616975	107	28604										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11593003	11593003	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tttgaagtcaatgtccctgaCtataagcagctgaggcagtg	11	8	1	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr17:11593003C>T	ENST00000262442.4	+	20	3932	c.3864C>T	c.(3862-3864)gaC>gaT	p.D1288D	DNAH9_ENST00000454412.2_Silent_p.D1288D	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1288	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		ATGTCCCTGACTATAAGCAGC	0.527																																					p.D1288D		Atlas-SNP	.											.	DNAH9	695	.	0			c.C3864T						.						113	105	107					17																	11593003		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon20			CCCTGACTATAAG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.3864C>T	chr17.hg19:g.11593003C>T		91.0	0.0		66.0	56.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	hg19	CCDS11160.1																																																																																			.	.		0.527	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11593003	C	T	11593003	2	4	194	1	0	0	0	0	0	0	0	1	4610	564	20	3		3	DNAH9	17	11593003	Silent	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	4014768	11593003	69602207	108	28605										
GRN	2896	hgsc.bcm.edu	37	chr17	42427830	42427830	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gcttcctgctgtgaagacagGgtgcactgctgtccgcacgg	14	12	0	2	rs373703310		TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr17:42427830G>A	ENST00000053867.3	+	6	545	c.483G>A	c.(481-483)agG>agA	p.R161R	GRN_ENST00000589265.1_Intron	NM_002087.2	NP_002078.1	P28799	GRN_HUMAN	granulin	161					blastocyst hatching (GO:0001835)|cell death (GO:0008219)|embryo implantation (GO:0007566)|positive regulation of epithelial cell proliferation (GO:0050679)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	growth factor activity (GO:0008083)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GTGAAGACAGGGTGCACTGCT	0.632											OREG0024459	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R161R		Atlas-SNP	.											.	GRN	51	.	0			c.G483A						.	G		0,4406		0,0,2203	119	114	116		483	0	1	17		116	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GRN	NM_002087.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		161/594	42427830	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2896	exon6			AGACAGGGTGCAC	M75161	CCDS11483.1	17q21.32	2014-09-17				ENSG00000030582			4601	protein-coding gene	gene with protein product	"progranulin"	138945				1417868, 9826678	Standard	XM_005257253		Approved	PCDGF, PGRN, CLN11	uc002igp.1	P28799		ENST00000053867.3:c.483G>A	chr17.hg19:g.42427830G>A		50.0	0.0	908	52.0	16.0	NM_002087	D3DX55|P23781|P23782|P23783|P23784|Q53HQ8|Q53Y88|Q540U8|Q9BWE7|Q9H8S1|Q9UCH0	Silent	SNP	ENST00000053867.3	hg19	CCDS11483.1	.	.	.	.	.	.	.	.	.	.	G	7.956	0.745896	0.15710	0.0	1.16E-4	ENSG00000030582	ENST00000393566	.	.	.	4.43	0.0146	0.14101	.	.	.	.	.	T	0.23766	0.0575	.	.	.	0.20074	N	0.999937	.	.	.	.	.	.	T	0.24799	-1.0150	5	0.30854	T	0.27	-15.0016	3.7331	0.08500	0.3986:0.0:0.4352:0.1662	.	.	.	.	E	68	.	ENSP00000377196:G68E	G	+	2	0	GRN	39783356	0.000000	0.05858	0.997000	0.53966	0.760000	0.43138	-0.716000	0.04991	0.127000	0.18452	0.462000	0.41574	GGG	.	.		0.632	GRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457766.1	NM_002087		A	42427830	G	A	42427830	2	1	194	1	0	0	0	0	0	0	0	1	6813	1223	43	3		3	GRN	17	42427830	Silent	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	30834827	42427830	38767380	109	28606										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2763754	2763754	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gggaaagttagaacacttgaAttccccttcgtgaatggttc	10	8	0	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr18:2763754A>G	ENST00000320876.6	+	37	5024	c.4686A>G	c.(4684-4686)gaA>gaG	p.E1562E	SMCHD1_ENST00000261598.8_Silent_p.E1562E|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1562					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GAACACTTGAATTCCCCTTCG	0.343																																					p.E1562E		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A4686G						.						108	103	105					18																	2763754		1821	4076	5897	SO:0001819	synonymous_variant	23347	exon37			ACTTGAATTCCCC	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.4686A>G	chr18.hg19:g.2763754A>G		128.0	0.0		148.0	58.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.		0.343	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			G	2763754	A	G	2763754	2	3	194	1	0	0	0	0	0	0	0	1	14803	98	4	2		2	SMCHD1	18	2763754	Silent	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10		2763754	75313494	110	28607										
TCEB3B	51224	hgsc.bcm.edu	37	chr18	44560876	44560876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ctctcttaagcaggccccgcAtgatttctccctgatcaaag	7	14	3	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr18:44560876A>G	ENST00000332567.4	-	1	1112	c.760T>C	c.(760-762)Tgc>Cgc	p.C254R	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	254			C -> F (in dbSNP:rs2010834). {ECO:0000269|PubMed:10692460}.		regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CAGGCCCCGCATGATTTCTCC	0.582																																					p.C254R		Atlas-SNP	.											.	TCEB3B	141	.	0			c.T760C						.						48	51	50					18																	44560876		2203	4300	6503	SO:0001583	missense	51224	exon1			CCCCGCATGATTT	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.760T>C	chr18.hg19:g.44560876A>G	ENSP00000331302:p.Cys254Arg	56.0	0.0		66.0	26.0	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	hg19	CCDS11932.1	.	.	.	.	.	.	.	.	.	.	A	0.189	-1.055028	0.01965	.	.	ENSG00000206181	ENST00000332567	T	0.06068	3.35	1.52	-1.6	0.08426	.	2.949720	0.01911	U	0.039898	T	0.02970	0.0088	N	0.08118	0	0.09310	N	1	B	0.21753	0.06	B	0.15870	0.014	T	0.34329	-0.9833	10	0.12103	T	0.63	.	2.4514	0.04519	0.3098:0.2945:0.3958:0.0	.	254	Q8IYF1	ELOA2_HUMAN	R	254	ENSP00000331302:C254R	ENSP00000331302:C254R	C	-	1	0	TCEB3B	42814874	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.375000	0.20518	-0.434000	0.07275	0.379000	0.24179	TGC	.	.		0.582	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		G	44560876	A	G	44560876	3	3	194	1	0	0	0	0	1	0	0	0	15697	217	8	2	1505	2	TCEB3B	18	44560876	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	41797122	44560876	33516372	111	28608										
GPR108	56927	hgsc.bcm.edu	37	chr19	6730371	6730371	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ttgttgactttggagaggccTtcccggaacccagagtccgt	12	11	0	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:6730371T>C	ENST00000264080.7	-	18	1610	c.1584A>G	c.(1582-1584)gaA>gaG	p.E528E	GPR108_ENST00000598626.1_5'UTR|GPR108_ENST00000430424.4_Silent_p.E286E	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	528						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						TGGAGAGGCCTTCCCGGAACC	0.602																																					p.E528E		Atlas-SNP	.											.	GPR108	35	.	0			c.A1584G						.						151	162	158					19																	6730371		2030	4195	6225	SO:0001819	synonymous_variant	56927	exon18			GAGGCCTTCCCGG		CCDS42479.1	19p13.3	2014-01-30				ENSG00000125734		"GPCR / Unclassified : 7TM orphan receptors"	17829	protein-coding gene	gene with protein product							Standard	NM_001080452		Approved	LUSTR2	uc002mfp.3	Q9NPR9	OTTHUMG00000170129	ENST00000264080.7:c.1584A>G	chr19.hg19:g.6730371T>C		96.0	0.0		121.0	42.0	NM_001080452	B9EJD7	Silent	SNP	ENST00000264080.7	hg19	CCDS42479.1																																																																																			.	.		0.602	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2			C	6730371	T	C	6730371	2	2	194	1	0	0	0	0	0	0	0	1	6632	1606	56	2		2	GPR108	19	6730371	Silent	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10		6730371	52398612	112	28609										
SIN3B	23309	hgsc.bcm.edu	37	chr19	16988394	16988394	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gagcagtatgtggggaccgaGggcgcgtccagctcgcccac	16	13	0	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:16988394G>C	ENST00000248054.5	+	17	2919	c.2898G>C	c.(2896-2898)gaG>gaC	p.E966D	SIN3B_ENST00000594235.1_3'UTR|SIN3B_ENST00000379803.1_Missense_Mutation_p.E998D|SIN3B_ENST00000595541.1_Missense_Mutation_p.E556D					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						TGGGGACCGAGGGCGCGTCCA	0.617																																					p.E998D		Atlas-SNP	.											.	SIN3B	90	.	0			c.G2994C						.						83	65	71					19																	16988394		2201	4300	6501	SO:0001583	missense	23309	exon18			GACCGAGGGCGCG	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.2898G>C	chr19.hg19:g.16988394G>C	ENSP00000248054:p.Glu966Asp	43.0	0.0		48.0	18.0	NM_015260		Missense_Mutation	SNP	ENST00000248054.5	hg19		.	.	.	.	.	.	.	.	.	.	G	1.423	-0.572400	0.03882	.	.	ENSG00000127511	ENST00000379803;ENST00000248054	T;T	0.46819	0.86;0.86	4.55	3.51	0.40186	.	0.000000	0.85682	D	0.000000	T	0.20700	0.0498	N	0.11427	0.14	0.44619	D	0.997595	B;B;B	0.15141	0.012;0.001;0.004	B;B;B	0.12837	0.007;0.008;0.005	T	0.11767	-1.0574	10	0.11794	T	0.64	-39.5633	3.3092	0.07011	0.1841:0.0:0.5823:0.2337	.	556;966;998	B7Z392;O75182-2;O75182	.;.;SIN3B_HUMAN	D	998;966	ENSP00000369131:E998D;ENSP00000248054:E966D	ENSP00000248054:E966D	E	+	3	2	SIN3B	16849394	1.000000	0.71417	0.973000	0.42090	0.194000	0.23727	2.755000	0.47540	2.082000	0.62665	0.555000	0.69702	GAG	.	.		0.617	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		C	16988394	G	C	16988394	3	2	194	1	0	0	0	0	1	0	0	0	14341	991	35	4	3064	4	SIN3B	19	16988394	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	10258023	16988394	42140589	113	28610										
ANKLE1	126549	hgsc.bcm.edu	37	chr19	17396553	17396553	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gggccagtggttgcggtgttGtgtccctacattgcttccag	14	10	0	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:17396553G>T	ENST00000394458.3	+	8	1876	c.1600G>T	c.(1600-1602)Gtg>Ttg	p.V534L	ANKLE1_ENST00000404085.1_Missense_Mutation_p.V530L|ANKLE1_ENST00000594072.1_Missense_Mutation_p.V497L|ANKLE1_ENST00000433424.2_3'UTR|ANKLE1_ENST00000598347.1_Intron	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	534	GIY-YIG. {ECO:0000255|PROSITE- ProRule:PRU00977}.									large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						TTGCGGTGTTGTGTCCCTACA	0.592																																					p.V534L		Atlas-SNP	.											.	ANKLE1	27	.	0			c.G1600T						.						141	113	122					19																	17396553		2203	4300	6503	SO:0001583	missense	126549	exon8			GGTGTTGTGTCCC	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"Ankyrin repeat domain containing"	26812	protein-coding gene	gene with protein product	"LEM domain containing 6"		"ankyrin repeat domain 41"	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.1600G>T	chr19.hg19:g.17396553G>T	ENSP00000377971:p.Val534Leu	69.0	0.0		81.0	28.0	NM_152363	A8VU82|Q8N8J8	Missense_Mutation	SNP	ENST00000394458.3	hg19	CCDS12354.2	.	.	.	.	.	.	.	.	.	.	G	12.90	2.076689	0.36662	.	.	ENSG00000160117	ENST00000404261;ENST00000404085;ENST00000394458	T;T	0.73152	-0.72;-0.5	5.19	0.584	0.17422	.	0.359954	0.24904	N	0.034675	T	0.66509	0.2796	L	0.58428	1.81	0.80722	D	1	P;P;P	0.52170	0.951;0.802;0.802	P;B;B	0.46796	0.527;0.236;0.236	T	0.64188	-0.6466	10	0.66056	D	0.02	-21.2453	7.7732	0.29021	0.4474:0.0:0.5526:0.0	.	494;534;497	Q8NAG6-1;Q8NAG6;A0JLW0	.;ANKL1_HUMAN;.	L	534;530;497	ENSP00000384008:V530L;ENSP00000377971:V497L	ENSP00000377971:V497L	V	+	1	0	ANKLE1	17257553	0.027000	0.19231	0.048000	0.18961	0.237000	0.25408	0.243000	0.18106	-0.035000	0.13691	-0.339000	0.08088	GTG	.	.		0.592	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363		T	17396553	G	T	17396553	3	4	194	1	0	0	0	0	1	0	0	0	632	1377	48	3	1630	3	ANKLE1	19	17396553	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	408159	17396553	41732430	114	28611										
FXYD1	5348	hgsc.bcm.edu	37	chr19	35632088	35632088	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	atcgccgggatcctcttcatCctgggcatcctcatcgtgct	9	15	3	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:35632088C>T	ENST00000588081.1	+	3	205	c.147C>T	c.(145-147)atC>atT	p.I49I	FXYD1_ENST00000588715.1_Silent_p.I49I|FXYD7_ENST00000588265.1_5'Flank|FXYD7_ENST00000270310.2_5'Flank|CTD-2527I21.4_ENST00000592174.1_RNA|LGI4_ENST00000493050.1_Intron|FXYD1_ENST00000589209.1_Silent_p.I49I|FXYD1_ENST00000351325.4_Silent_p.I49I|FXYD1_ENST00000588607.1_Silent_p.I49I|FXYD7_ENST00000586063.1_5'Flank|FXYD1_ENST00000455515.2_Silent_p.I49I			O00168	PLM_HUMAN	FXYD domain containing ion transport regulator 1	49					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|positive regulation of sodium ion export from cell (GO:1903278)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of heart contraction (GO:0008016)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)	chloride channel activity (GO:0005254)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)			lung(3)	3	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;2.32e-21)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;2.43e-18)|LUSC - Lung squamous cell carcinoma(66;0.0849)			TCCTCTTCATCCTGGGCATCC	0.662																																					p.I49I		Atlas-SNP	.											.	FXYD1	6	.	0			c.C147T						.						100	74	83					19																	35632088		2203	4300	6503	SO:0001819	synonymous_variant	5348	exon4			CTTCATCCTGGGC		CCDS12445.1	19q13.1	2008-08-01	2008-08-01			ENSG00000266964			4025	protein-coding gene	gene with protein product		602359	"phospholemman"	PLM		9169143	Standard	NM_005031		Approved		uc002nyc.3	O00168		ENST00000588081.1:c.147C>T	chr19.hg19:g.35632088C>T		30.0	0.0		37.0	10.0	NM_005031	A8K196	Silent	SNP	ENST00000588081.1	hg19	CCDS12445.1																																																																																			.	.		0.662	FXYD1-007	KNOWN	alternative_3_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460761.1	NM_021902		T	35632088	C	T	35632088	2	4	194	1	0	0	0	0	0	0	0	1	6125	845	30	3		3	FXYD1	19	35632088	Silent	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	18235535	35632088	23496895	115	28612										
LRFN1	57622	hgsc.bcm.edu	37	chr19	39798880	39798880	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ggagcgacctggagcccttgAcgcggcggctgtccccgtcg	16	15	0	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:39798880A>T	ENST00000248668.4	-	2	1708	c.1709T>A	c.(1708-1710)gTc>gAc	p.V570D		NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	570						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GGAGCCCTTGACGCGGCGGCT	0.687																																					p.V570D		Atlas-SNP	.											.	LRFN1	59	.	0			c.T1709A						.						18	24	22					19																	39798880		2131	4243	6374	SO:0001583	missense	57622	exon2			CCCTTGACGCGGC	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.1709T>A	chr19.hg19:g.39798880A>T	ENSP00000248668:p.Val570Asp	96.0	0.0		123.0	53.0	NM_020862	Q8TBS9	Missense_Mutation	SNP	ENST00000248668.4	hg19	CCDS46071.1	.	.	.	.	.	.	.	.	.	.	A	3.009	-0.204323	0.06180	.	.	ENSG00000128011	ENST00000248668	T	0.61627	0.09	4.17	-3.59	0.04583	.	1.375180	0.05524	N	0.562529	T	0.29028	0.0721	N	0.08118	0	0.20196	N	0.999928	P	0.47841	0.901	B	0.42188	0.379	T	0.13899	-1.0492	10	0.15066	T	0.55	.	1.5832	0.02638	0.2134:0.2824:0.349:0.1552	.	570	Q9P244	LRFN1_HUMAN	D	570	ENSP00000248668:V570D	ENSP00000248668:V570D	V	-	2	0	LRFN1	44490720	0.115000	0.22152	0.073000	0.20177	0.073000	0.16967	0.347000	0.20014	-0.496000	0.06650	-0.464000	0.05259	GTC	.	.		0.687	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862		T	39798880	A	T	39798880	3	4	194	1	0	0	0	0	1	0	0	0	8946	275	10	4	610	4	LRFN1	19	39798880	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	4166792	39798880	19330103	116	28613										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41026029	41026029	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	agctcttcctgcgggatctaCgccaggcgctcgtggtgctg	14	13	2	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:41026029C>T	ENST00000352632.3	+	16	3711	c.3625C>T	c.(3625-3627)Cgc>Tgc	p.R1209C	SPTBN4_ENST00000598249.1_Missense_Mutation_p.R1209C|SPTBN4_ENST00000338932.3_Missense_Mutation_p.R1209C|SPTBN4_ENST00000595535.1_Missense_Mutation_p.R1209C|SPTBN4_ENST00000344104.3_Missense_Mutation_p.R1209C			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1209					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCGGGATCTACGCCAGGCGCT	0.647																																					p.R1209C		Atlas-SNP	.											.	SPTBN4	213	.	0			c.C3625T						.						11	13	12					19																	41026029		2147	4201	6348	SO:0001583	missense	57731	exon16			GATCTACGCCAGG	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.3625C>T	chr19.hg19:g.41026029C>T	ENSP00000263373:p.Arg1209Cys	36.0	0.0		38.0	14.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.910051	0.52439	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000344104	T;T;T	0.76448	-1.02;1.26;1.26	3.89	2.61	0.31194	.	0.228526	0.30185	N	0.010215	T	0.73674	0.3617	L	0.52573	1.65	0.80722	D	1	D;B	0.76494	0.999;0.009	P;B	0.51657	0.676;0.001	T	0.70525	-0.4848	10	0.54805	T	0.06	.	2.9946	0.05994	0.3706:0.4418:0.0:0.1876	.	1209;1209	Q9H254;Q71S06	SPTN4_HUMAN;.	C	1209	ENSP00000263373:R1209C;ENSP00000340345:R1209C;ENSP00000340741:R1209C	ENSP00000340345:R1209C	R	+	1	0	SPTBN4	45717869	0.000000	0.05858	0.589000	0.28718	0.727000	0.41649	-0.582000	0.05814	0.487000	0.27698	0.462000	0.41574	CGC	.	.		0.647	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			T	41026029	C	T	41026029	3	4	194	1	0	0	0	0	1	0	0	0	15136	536	19	1	3683	1	SPTBN4	19	41026029	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	1227149	41026029	18102954	117	28614										
CEACAM3	1084	hgsc.bcm.edu	37	chr19	42314898	42314898	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tctctccactgcccaggcccCcctacccaaccccaggacag	6	22	1	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:42314898C>G	ENST00000357396.3	+	6	897	c.656C>G	c.(655-657)cCc>cGc	p.P219R	CEACAM3_ENST00000344550.4_Silent_p.P201P|CEACAM3_ENST00000221999.4_Silent_p.P201P	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	219						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						GCCCAGGCCCCCCTACCCAAC	0.612																																					p.P219R		Atlas-SNP	.											.	CEACAM3	37	.	0			c.C656G						.						83	75	78					19																	42314898		2203	4300	6503	SO:0001583	missense	1084	exon6			AGGCCCCCCTACC	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.656C>G	chr19.hg19:g.42314898C>G	ENSP00000349971:p.Pro219Arg	88.0	0.0		101.0	47.0	NM_001815	G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	hg19	CCDS12586.2	.	.	.	.	.	.	.	.	.	.	C	11.40	1.628579	0.28978	.	.	ENSG00000170956	ENST00000357396	T	0.02890	4.12	2.0	0.934	0.19477	.	.	.	.	.	T	0.02380	0.0073	L	0.38175	1.15	0.09310	N	1	B	0.28636	0.218	B	0.16722	0.016	T	0.45600	-0.9250	9	0.32370	T	0.25	.	5.8099	0.18460	0.3151:0.6849:0.0:0.0	.	219	P40198	CEAM3_HUMAN	R	219	ENSP00000349971:P219R	ENSP00000349971:P219R	P	+	2	0	CEACAM3	47006738	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.274000	0.08537	0.414000	0.25790	-0.507000	0.04495	CCC	.	.		0.612	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815		G	42314898	C	G	42314898	3	3	194	1	0	0	0	0	1	0	0	0	3195	623	22	4	678	4	CEACAM3	19	42314898	Missense_Mutation	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	1288869	42314898	16814085	118	28615										
SULT2A1	6822	hgsc.bcm.edu	37	chr19	48389503	48389503	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	atgccttcaaaccataagaaAtcgtccgacatgatgatgac	7	10	1	4			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:48389503A>G	ENST00000222002.3	-	1	151	c.12T>C	c.(10-12)gaT>gaC	p.D4D		NM_003167.3	NP_003158.2	Q06520	ST2A1_HUMAN	sulfotransferase family, cytosolic, 2A, dehydroepiandrosterone (DHEA)-preferring, member 1	4					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|bile acid catabolic process (GO:0030573)|cellular lipid metabolic process (GO:0044255)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	bile-salt sulfotransferase activity (GO:0047704)|sulfotransferase activity (GO:0008146)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20		all_cancers(25;3.02e-09)|all_lung(116;6.48e-07)|all_epithelial(76;7.35e-07)|Lung NSC(112;1.56e-06)|all_neural(266;0.0146)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000254)|all cancers(93;0.000545)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.0552)	Abiraterone(DB05812)|Acetaminophen(DB00316)	ACCATAAGAAATCGTCCGACA	0.463																																					p.D4D		Atlas-SNP	.											.	SULT2A1	49	.	0			c.T12C						.						199	163	175					19																	48389503		2203	4300	6503	SO:0001819	synonymous_variant	6822	exon1			TAAGAAATCGTCC	X70222	CCDS12707.1	19q13.3	2014-05-21			ENSG00000105398	ENSG00000105398	2.8.2.2	"Sulfotransferases, cytosolic"	11458	protein-coding gene	gene with protein product		125263		STD		1588921, 7736787	Standard	NM_003167		Approved	DHEA-ST	uc002phr.2	Q06520	OTTHUMG00000162469	ENST00000222002.3:c.12T>C	chr19.hg19:g.48389503A>G		98.0	0.0		117.0	60.0	NM_003167		Silent	SNP	ENST00000222002.3	hg19	CCDS12707.1																																																																																			.	.		0.463	SULT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369044.1	NM_003167		G	48389503	A	G	48389503	2	3	194	1	0	0	0	0	0	0	0	1	15396	98	4	2		2	SULT2A1	19	48389503	Silent	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	6074605	48389503	10739480	119	28616										
NOSIP	51070	hgsc.bcm.edu	37	chr19	50063276	50063291	+	Frame_Shift_Del	DEL	GGGTCCCATAGCCCGA	GGGTCCCATAGCCCGA	-													0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ccggctcagtcgaatgttctGggtcccatagcccgaggccg					rs534415595		TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	GGGTCCCATAGCCCGA	GGGTCCCATAGCCCGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:50063276_50063291delGGGTCCCATAGCCCGA	ENST00000596358.1	-	3	134_149	c.76_91delTCGGGCTATGGGACCC	c.(76-93)tcgggctatgggacccagfs	p.SGYGTQ26fs	NOSIP_ENST00000391853.3_Frame_Shift_Del_p.SGYGTQ26fs|NOSIP_ENST00000339093.3_Frame_Shift_Del_p.SGYGTQ26fs	NM_001270960.1	NP_001257889.1	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein	26					negative regulation of catalytic activity (GO:0043086)|negative regulation of nitric-oxide synthase activity (GO:0051001)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|skin(2)|urinary_tract(1)	11		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)		CGAATGTTCTGGGTCCCATAGCCCGAGGCCGCTGGG	0.606																																					p.26_31del		Atlas-INDEL	.											.	NOSIP	28	.	0			c.77_92del						.																																			SO:0001589	frameshift_variant	51070	exon3			.	AF132959	CCDS12772.1	19q13.3	2008-02-05				ENSG00000142546			17946	protein-coding gene	gene with protein product						11149895, 10810093	Standard	NM_015953		Approved	CGI-25	uc002pol.4	Q9Y314		ENST00000596358.1:c.76_91delTCGGGCTATGGGACCC	chr19.hg19:g.50063276_50063291delGGGTCCCATAGCCCGA	ENSP00000470034:p.Ser26fs	92.0	0.0		112.0	27.0	NM_001270960	Q96FD2	Frame_Shift_Del	DEL	ENST00000596358.1	hg19	CCDS12772.1																																																																																			.	.		0.606	NOSIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465423.1			-	50063291	GGGTCCCATAGCCCGA	-	50063276	7	5	194	1	0	1	0	1	0	0	0	0	10554	1357	47	0	842	0	NOSIP	19	50063276	Frame_Shift_Del	DEL	GGGTCCCATAGCCCGA	TCGA-DD-AADL-01A-11D-A40R-10	1673773	50063276	9065707	120	28617										
NLRP7	199713	hgsc.bcm.edu	37	chr19	55451284	55451284	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tccctcagtgccctgggccgCgtggtgaccagcaaggctgc	14	15	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:55451284C>A	ENST00000590030.1	-	3	943	c.903G>T	c.(901-903)acG>acT	p.T301T	NLRP7_ENST00000340844.2_Silent_p.T301T|NLRP7_ENST00000588756.1_Silent_p.T301T|NLRP7_ENST00000448121.2_Silent_p.T301T|NLRP7_ENST00000446217.1_Silent_p.T329T|NLRP7_ENST00000328092.5_Silent_p.T301T|NLRP7_ENST00000592784.1_Silent_p.T301T			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	301	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		CCCTGGGCCGCGTGGTGACCA	0.627																																					p.T301T		Atlas-SNP	.											NLRP7_ENST00000328092,caecum,carcinoma,0,2	NLRP7	411	.	0			c.G903T						.						43	42	42					19																	55451284		2203	4300	6503	SO:0001819	synonymous_variant	199713	exon4			GGGCCGCGTGGTG	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.903G>T	chr19.hg19:g.55451284C>A		68.0	0.0		89.0	5.0	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	hg19	CCDS33109.1																																																																																			.	.		0.627	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55451284	C	A	55451284	2	1	194	1	0	0	0	0	0	0	0	1	10491	755	27	1		1	NLRP7	19	55451284	Silent	SNP	C	TCGA-DD-AADL-01A-11D-A40R-10	5388008	55451284	3677699	121	28618										
ZNF551	90233	hgsc.bcm.edu	37	chr19	58199257	58199257	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gagtgcagtgaatgtggcaaAtcttttagacagcgctctgg	13	7	2	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr19:58199257A>G	ENST00000282296.5	+	3	1799	c.1614A>G	c.(1612-1614)aaA>aaG	p.K538K	ZNF551_ENST00000356715.4_Silent_p.K522K|AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF551_ENST00000596085.1_Intron			Q7Z340	ZN551_HUMAN	zinc finger protein 551	538					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AATGTGGCAAATCTTTTAGAC	0.448																																					p.K538K		Atlas-SNP	.											.	ZNF551	65	.	0			c.A1614G						.						85	80	82					19																	58199257		2203	4300	6503	SO:0001819	synonymous_variant	90233	exon3			TGGCAAATCTTTT	BX538151	CCDS12959.1, CCDS12959.2	19q13.43	2013-09-20			ENSG00000204519	ENSG00000204519		"Zinc fingers, C2H2-type", "-"	25108	protein-coding gene	gene with protein product							Standard	NM_138347		Approved	DKFZp686H1038	uc002qpw.5	Q7Z340	OTTHUMG00000183470	ENST00000282296.5:c.1614A>G	chr19.hg19:g.58199257A>G		83.0	0.0		88.0	35.0	NM_138347	B4DU22|P17034|Q8N246|Q9BRY1	Silent	SNP	ENST00000282296.5	hg19	CCDS12959.2	.	.	.	.	.	.	.	.	.	.	A	7.864	0.726680	0.15439	.	.	ENSG00000228006	ENST00000541705	.	.	.	2.49	-0.904	0.10530	.	0.000000	0.46758	U	0.000269	T	0.11537	0.0281	.	.	.	0.19575	N	0.999967	.	.	.	.	.	.	T	0.34725	-0.9817	6	0.02654	T	1	.	7.1774	0.25753	0.6297:0.0:0.3703:0.0	.	.	.	.	L	50	.	ENSP00000437781:F50L	F	-	1	0	AC004017.1	62891069	0.000000	0.05858	0.003000	0.11579	0.015000	0.08874	-0.198000	0.09505	-0.134000	0.11516	0.459000	0.35465	TTT	.	.		0.448	ZNF551-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466803.2	NM_138347		G	58199257	A	G	58199257	2	3	194	1	0	0	0	0	0	0	0	1	17998	98	4	2		2	ZNF551	19	58199257	Silent	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	2747973	58199257	929726	122	28619										
CST11	140880	hgsc.bcm.edu	37	chr20	23433401	23433401	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	gggagggccatcagagtcaaTagaatggccaacaggagctg	15	8	2	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr20:23433401T>C	ENST00000377009.3	-	1	81	c.48A>G	c.(46-48)ctA>ctG	p.L16L	CST11_ENST00000377007.3_Silent_p.L16L	NM_130794.1	NP_570612.1	Q9H112	CST11_HUMAN	cystatin 11	16					defense response to bacterium (GO:0042742)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			kidney(2)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	14	Colorectal(13;0.0431)|Lung NSC(19;0.235)					TCAGAGTCAATAGAATGGCCA	0.517																																					p.L16L		Atlas-SNP	.											.	CST11	27	.	0			c.A48G						.						78	68	71					20																	23433401		2203	4300	6503	SO:0001819	synonymous_variant	140880	exon1			AGTCAATAGAATG	AL096677	CCDS13154.1, CCDS13155.1	20p11.21	2012-08-14			ENSG00000125831	ENSG00000125831			15959	protein-coding gene	gene with protein product		609731		CST8L		20565543	Standard	NM_080830		Approved	dJ322G13.6, CTES2	uc002wtf.1	Q9H112	OTTHUMG00000032060	ENST00000377009.3:c.48A>G	chr20.hg19:g.23433401T>C		94.0	0.0		121.0	55.0	NM_130794	Q0VAF2|Q0VAF3|Q8WXU5|Q8WXU6|Q9H113	Silent	SNP	ENST00000377009.3	hg19	CCDS13155.1																																																																																			.	.		0.517	CST11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078314.1	NM_130794		C	23433401	T	C	23433401	2	2	194	1	0	0	0	0	0	0	0	1	3973	1393	49	2		2	CST11	20	23433401	Silent	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10		23433401	39592119	123	28620										
C20orf118	140711	hgsc.bcm.edu	37	chr20	35507490	35507490	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	caccggccatccctggagtcTggtcttctgcacgtcaaggg	12	14	4	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr20:35507490T>A	ENST00000217320.3	+	3	280	c.236T>A	c.(235-237)cTg>cAg	p.L79Q	TLDC2_ENST00000602922.1_Missense_Mutation_p.L79Q	NM_080628.1	NP_542195.1	A0PJX2	TLDC2_HUMAN	TBC/LysM-associated domain containing 2	79	TLD.																CCCTGGAGTCTGGTCTTCTGC	0.632																																					p.L79Q		Atlas-SNP	.											.	C20orf118	21	.	0			c.T236A						.						116	90	99					20																	35507490		2203	4300	6503	SO:0001583	missense	140711	exon3			GGAGTCTGGTCTT	AL079335	CCDS33465.1	20q11.23	2013-03-14	2013-03-14	2013-03-14	ENSG00000101342	ENSG00000101342			16112	protein-coding gene	gene with protein product	"hypothetical protein LOC140711", "TLD domain containing 2"		"chromosome 20 open reading frame 118"	C20orf118			Standard	NM_080628		Approved	dJ132F21.2	uc002xgg.1	A0PJX2	OTTHUMG00000032400	ENST00000217320.3:c.236T>A	chr20.hg19:g.35507490T>A	ENSP00000217320:p.Leu79Gln	60.0	0.0		84.0	29.0	NM_080628	B3KVU8	Missense_Mutation	SNP	ENST00000217320.3	hg19	CCDS33465.1	.	.	.	.	.	.	.	.	.	.	T	16.25	3.071083	0.55646	.	.	ENSG00000101342	ENST00000217320	T	0.54071	0.59	5.09	4.0	0.46444	TLDc (2);	0.000000	0.85682	D	0.000000	T	0.76528	0.4000	H	0.94306	3.52	0.46011	D	0.998815	D	0.89917	1.0	D	0.85130	0.997	T	0.78463	-0.2194	10	0.87932	D	0	-32.8788	7.4279	0.27109	0.0:0.0961:0.0:0.9039	.	79	A0PJX2	CT118_HUMAN	Q	79	ENSP00000217320:L79Q	ENSP00000217320:L79Q	L	+	2	0	C20orf118	34940904	1.000000	0.71417	0.933000	0.37362	0.491000	0.33493	5.934000	0.70138	0.980000	0.38523	-0.250000	0.11733	CTG	.	.		0.632	TLDC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079060.2	NM_080628		A	35507490	T	A	35507490	3	1	194	1	0	0	0	0	1	0	0	0	2086	1580	55	4	246	4	C20orf118	20	35507490	Missense_Mutation	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	12074089	35507490	27518030	124	28621										
SEMG2	6407	hgsc.bcm.edu	37	chr20	43850459	43850459	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	catactaaatccaaaggcagTttttctattcaacacacata	3	10	2	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr20:43850459T>C	ENST00000372769.3	+	2	276	c.186T>C	c.(184-186)agT>agC	p.S62S		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	62					sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				CCAAAGGCAGTTTTTCTATTC	0.398																																					p.S62S		Atlas-SNP	.											.	SEMG2	92	.	0			c.T186C						.						123	117	119					20																	43850459		2203	4300	6503	SO:0001819	synonymous_variant	6407	exon2			AGGCAGTTTTTCT		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"Semenogelin 2"	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.186T>C	chr20.hg19:g.43850459T>C		202.0	0.0		264.0	33.0	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Silent	SNP	ENST00000372769.3	hg19	CCDS13346.1																																																																																			.	.		0.398	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		C	43850459	T	C	43850459	2	2	194	1	0	0	0	0	0	0	0	1	14060	1722	60	2		2	SEMG2	20	43850459	Silent	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10	8342969	43850459	19175061	125	28622										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57767217	57767217	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	ggggagggcggcccgggcccGgggccaggggtcgcaggggc	25	12	0	0			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr20:57767217G>A	ENST00000371030.2	+	1	1143	c.1143G>A	c.(1141-1143)ccG>ccA	p.P381P		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	381							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					gcccgggcccggggccagggg	0.756																																					p.P381P		Atlas-SNP	.											.	ZNF831	287	.	0			c.G1143A						.						4	6	5					20																	57767217		1493	3488	4981	SO:0001819	synonymous_variant	128611	exon1			GGGCCCGGGGCCA	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.1143G>A	chr20.hg19:g.57767217G>A		67.0	0.0		107.0	45.0	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	hg19	CCDS42894.1																																																																																			.	.		0.756	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57767217	G	A	57767217	2	1	194	1	0	0	0	0	0	0	0	1	18200	1103	39	1		1	ZNF831	20	57767217	Silent	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	13916758	57767217	5258303	126	28623										
CRYBA4	1413	hgsc.bcm.edu	37	chr22	27021475	27021475	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tttgagcatgctggcttccaAgggcagcagtacattctgga	12	9	1	1			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chr22:27021475A>C	ENST00000354760.3	+	4	224	c.189A>C	c.(187-189)caA>caC	p.Q63H	CRYBA4_ENST00000466315.1_3'UTR	NM_001886.2	NP_001877.1	P53673	CRBA4_HUMAN	crystallin, beta A4	63	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(6)|liver(1)|lung(6)|skin(3)|urinary_tract(2)	18						CTGGCTTCCAAGGGCAGCAGT	0.612																																					p.Q63H		Atlas-SNP	.											.	CRYBA4	33	.	0			c.A189C						.						118	109	112					22																	27021475		2203	4300	6503	SO:0001583	missense	1413	exon4			CTTCCAAGGGCAG		CCDS13841.1	22q12.1	2008-06-10			ENSG00000196431	ENSG00000196431			2396	protein-coding gene	gene with protein product		123631				8999933, 960806	Standard	NM_001886		Approved		uc003acz.4	P53673	OTTHUMG00000150983	ENST00000354760.3:c.189A>C	chr22.hg19:g.27021475A>C	ENSP00000346805:p.Gln63His	37.0	0.0		45.0	19.0	NM_001886	Q4VB22|Q6ICE4	Missense_Mutation	SNP	ENST00000354760.3	hg19	CCDS13841.1	.	.	.	.	.	.	.	.	.	.	A	6.390	0.440004	0.12104	.	.	ENSG00000196431	ENST00000354760	T	0.77229	-1.08	4.43	-1.83	0.07833	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.131786	0.52532	D	0.000079	T	0.71476	0.3344	M	0.71581	2.175	0.54753	D	0.999987	B	0.09022	0.002	B	0.28553	0.091	T	0.59123	-0.7513	10	0.52906	T	0.07	.	5.8464	0.18669	0.4941:0.1404:0.3655:0.0	.	63	P53673	CRBA4_HUMAN	H	63	ENSP00000346805:Q63H	ENSP00000346805:Q63H	Q	+	3	2	CRYBA4	25351475	0.968000	0.33430	0.994000	0.49952	0.106000	0.19336	0.063000	0.14410	-0.328000	0.08539	-1.202000	0.01658	CAA	.	.		0.612	CRYBA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320793.1	NM_001886		C	27021475	A	C	27021475	3	2	194	1	0	0	0	0	1	0	0	0	3911	69	3	5	199	5	CRYBA4	22	27021475	Missense_Mutation	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10		27021475	24283091	127	28624										
CXCR3	2833	hgsc.bcm.edu	37	chrX	70837372	70837372	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tggcaggaactcttttgtgaTtgagtctgatttagtctgtg	12	5	3	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chrX:70837372T>C	ENST00000373693.3	-	2	80				CXCR3_ENST00000373691.4_Missense_Mutation_p.I31V	NM_001504.1	NP_001495.1	P49682	CXCR3_HUMAN	chemokine (C-X-C motif) receptor 3						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|calcium-mediated signaling (GO:0019722)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|chemokine (C-C motif) ligand 11 production (GO:0071954)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of leukocyte migration (GO:0002685)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|chemokine binding (GO:0019956)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(2)|lung(3)|ovary(2)	10	Renal(35;0.156)					TCTTTTGTGATTGAGTCTGAT	0.552																																					p.I31V		Atlas-SNP	.											.	CXCR3	57	.	0			c.A91G						.						64	56	58					X																	70837372		692	1591	2283	SO:0001627	intron_variant	2833	exon2			TTGTGATTGAGTC	U32674	CCDS14416.1, CCDS48135.1	Xq13	2012-08-08	2002-08-22	2002-08-23	ENSG00000186810	ENSG00000186810		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	4540	protein-coding gene	gene with protein product		300574	"G protein-coupled receptor 9"	GPR9		8666380, 9064356	Standard	NM_001142797		Approved	CKR-L2, CMKAR3, IP10-R, MigR, CD183	uc011mpx.2	P49682	OTTHUMG00000033326	ENST00000373693.3:c.13-63A>G	chrX.hg19:g.70837372T>C		47.0	0.0		85.0	62.0	NM_001142797	B2R982|O15185|Q7Z710|Q9P2T4|Q9P2T5	Missense_Mutation	SNP	ENST00000373693.3	hg19	CCDS14416.1	.	.	.	.	.	.	.	.	.	.	T	0.956	-0.704724	0.03255	.	.	ENSG00000186810	ENST00000373691	T	0.70516	-0.49	3.11	-3.34	0.04943	.	9.515090	0.00659	U	0.000593	T	0.46927	0.1418	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.55360	-0.8153	9	0.02654	T	1	.	12.1564	0.54079	0.0:0.6559:0.0:0.3441	.	31	P49682-2	.	V	31	ENSP00000362795:I31V	ENSP00000362795:I31V	I	-	1	0	CXCR3	70754097	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-1.510000	0.01796	-2.111000	0.00353	ATC	.	.		0.552	CXCR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144141.1			C	70837372	T	C	70837372	1	2	194	0	1	0	0	0	0	0	0	0	4094	1493	52	2		2	CXCR3	23	70837372	Intron	SNP	T	TCGA-DD-AADL-01A-11D-A40R-10		70837372	84433188	128	28625										
ZNF711	7552	hgsc.bcm.edu	37	chrX	84526085	84526085	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tttgtgttgagtgtgggaagGgttttcgacatccttctgaa	13	5	1	2			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chrX:84526085G>T	ENST00000373165.3	+	9	1843	c.1537G>T	c.(1537-1539)Ggt>Tgt	p.G513C	ZNF711_ENST00000360700.4_Missense_Mutation_p.G559C|ZNF711_ENST00000542798.1_Missense_Mutation_p.G355C|ZNF711_ENST00000276123.3_Missense_Mutation_p.G513C|ZNF711_ENST00000395402.1_Missense_Mutation_p.G521C	NM_021998.4	NP_068838.3	Q9Y462	ZN711_HUMAN	zinc finger protein 711	513					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(3)|skin(4)	28						GTGTGGGAAGGGTTTTCGACA	0.413																																					p.G513C		Atlas-SNP	.											.	ZNF711	198	.	0			c.G1537T						.						87	70	76					X																	84526085		2203	4300	6503	SO:0001583	missense	7552	exon9			GGGAAGGGTTTTC	BC006349	CCDS35344.1	Xq21.1	2014-02-19	2006-06-29	2006-06-29	ENSG00000147180	ENSG00000147180		"Zinc fingers, C2H2-type"	13128	protein-coding gene	gene with protein product		314990	"zinc finger protein 6 (CMPX1)", "zinc finger protein 6"	ZNF6		19377476	Standard	XM_005262186		Approved	CMPX1, ZNF4, ZNF5, dJ75N13.1, Zfp711, MRX97	uc004eeo.3	Q9Y462	OTTHUMG00000021933	ENST00000373165.3:c.1537G>T	chrX.hg19:g.84526085G>T	ENSP00000362260:p.Gly513Cys	93.0	0.0		115.0	102.0	NM_021998	B4DSV4|Q6NX42|Q9Y4J6	Missense_Mutation	SNP	ENST00000373165.3	hg19	CCDS35344.1	.	.	.	.	.	.	.	.	.	.	G	16.49	3.137421	0.56936	.	.	ENSG00000147180	ENST00000395402;ENST00000373165;ENST00000276123;ENST00000360700;ENST00000542798	T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21	5.19	5.19	0.71726	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43919	D	0.000507	T	0.34513	0.0900	L	0.38175	1.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.10917	-1.0609	10	0.87932	D	0	-9.6284	17.9439	0.89034	0.0:0.0:1.0:0.0	.	559;513	Q9Y462-3;Q9Y462	.;ZN711_HUMAN	C	521;513;513;559;355	ENSP00000378798:G521C;ENSP00000362260:G513C;ENSP00000276123:G513C;ENSP00000353922:G559C;ENSP00000442071:G355C	ENSP00000276123:G513C	G	+	1	0	ZNF711	84412741	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.171000	0.68590	0.513000	0.50165	GGT	.	.		0.413	ZNF711-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057388.2	NM_021998		T	84526085	G	T	84526085	3	4	194	1	0	0	0	0	1	0	0	0	18131	1232	43	3	1563	3	ZNF711	23	84526085	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	13688713	84526085	70744475	129	28626										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117676789	117676789	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	cgagatctgcttatgttcccAatggaagatatatctgtgag	10	7	2	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chrX:117676789A>G	ENST00000276202.7	+	2	267	c.204A>G	c.(202-204)ccA>ccG	p.P68P	DOCK11_ENST00000276204.6_Silent_p.P68P	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	68	Interaction with activated CDC42. {ECO:0000250}.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TTATGTTCCCAATGGAAGATA	0.393																																					p.P68P		Atlas-SNP	.											.	DOCK11	185	.	0			c.A204G						.						130	128	129					X																	117676789		2203	4300	6503	SO:0001819	synonymous_variant	139818	exon2			GTTCCCAATGGAA	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.204A>G	chrX.hg19:g.117676789A>G		141.0	0.0		208.0	161.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	hg19	CCDS35373.1																																																																																			.	.		0.393	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		G	117676789	A	G	117676789	2	3	194	1	0	0	0	0	0	0	0	1	4688	117	5	2		2	DOCK11	23	117676789	Silent	SNP	A	TCGA-DD-AADL-01A-11D-A40R-10	33150704	117676789	37593771	130	28627										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151818238	151818238	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0236220472440945	3	1	0.581496710526316	1.05223214285714	0.475201612903226	1	1	0	tgaagacatcatattattctGggatgacaatgggaacgcca	10	7	2	3			TCGA-DD-AADL-01A-11D-A40R-10	TCGA-DD-AADL-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a2a6b995-9bef-41e2-8e57-896039e6579d	12f9780c-620f-4e1c-af89-a3905b81bc11	g.chrX:151818238G>C	ENST00000370306.2	+	6	664	c.644G>C	c.(643-645)tGg>tCg	p.W215S		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	215					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ATATTATTCTGGGATGACAAT	0.433																																					p.W215S		Atlas-SNP	.											.	GABRQ	131	.	0			c.G644C						.						164	132	143					X																	151818238		2203	4300	6503	SO:0001583	missense	55879	exon6			TATTCTGGGATGA	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.644G>C	chrX.hg19:g.151818238G>C	ENSP00000359329:p.Trp215Ser	42.0	0.0		58.0	50.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	hg19	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.249999	0.59212	.	.	ENSG00000147402	ENST00000370306	T	0.80123	-1.34	5.82	5.82	0.92795	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.46758	D	0.000268	D	0.92348	0.7572	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94050	0.7317	10	0.87932	D	0	.	16.2847	0.82712	0.0:0.0:1.0:0.0	.	215	Q9UN88	GBRT_HUMAN	S	215	ENSP00000359329:W215S	ENSP00000359329:W215S	W	+	2	0	GABRQ	151568894	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	9.564000	0.98151	2.450000	0.82876	0.600000	0.82982	TGG	.	.		0.433	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		C	151818238	G	C	151818238	3	2	194	1	0	0	0	0	1	0	0	0	6183	1357	47	4	666	4	GABRQ	23	151818238	Missense_Mutation	SNP	G	TCGA-DD-AADL-01A-11D-A40R-10	34141449	151818238	3452322	131	28628										
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1905521	1905521	+	IGR	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gggcctcctgctctctgcagAgctgctcggctgcgcgcacc	13	17	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:1905521A>T								TMEM52 (54809 upstream) : C1orf222 (14041 downstream)																							CTCTCTGCAGAGCTGCTCGGC	0.682																																					p.L206H		Atlas-SNP	.											.	KIAA1751	92	.	0			c.T617A						.						28	34	32					1																	1905521		2117	4228	6345	SO:0001628	intergenic_variant	85452	exon7			CTGCAGAGCTGCT																													chr1.hg19:g.1905521A>T		141.0	0.0		93.0	28.0	NM_001080484		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	A	14.81	2.647806	0.47258	.	.	ENSG00000142609	ENST00000270720	.	.	.	3.4	2.28	0.28536	.	0.103197	0.39615	N	0.001304	T	0.53302	0.1788	M	0.65975	2.015	0.09310	N	0.999996	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.30822	-0.9965	9	0.36615	T	0.2	-10.6382	4.5666	0.12189	0.8503:0.0:0.1497:0.0	.	206;206	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	H	206	.	ENSP00000270720:L206H	L	-	2	0	C1orf222	1895381	0.953000	0.32496	0.116000	0.21606	0.002000	0.02628	2.174000	0.42482	1.507000	0.48752	0.383000	0.25322	CTC	.	.	0	0.682									T	1905521	A	T	1905521	1	4	195	0	1	0	0	0	0	0	0	0	8265	304	11	4		4	KIAA1751	1	1905521	IGR	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10		1905521	247345100	1	28629										
ID3	3399	hgsc.bcm.edu	37	chr1	23885468	23885468	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gagtcagtggcaaaagctccTtttgtcgttggagatgacaa	12	7	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:23885468T>G	ENST00000374561.5	-	2	710	c.343A>C	c.(343-345)Agg>Cgg	p.R115R	ID3_ENST00000486541.1_5'UTR	NM_002167.4	NP_002158.3	Q02535	ID3_HUMAN	inhibitor of DNA binding 3, dominant negative helix-loop-helix protein	115					central nervous system development (GO:0007417)|epithelial cell differentiation (GO:0030855)|heart development (GO:0007507)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|notochord development (GO:0030903)|odontogenesis (GO:0042476)|positive regulation of apoptotic process (GO:0043065)|regulation of cell cycle (GO:0051726)|regulation of DNA replication (GO:0006275)|response to wounding (GO:0009611)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|lung(3)	4		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00314)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;8.83e-25)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;6.5e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0827)|LUSC - Lung squamous cell carcinoma(448;0.184)		CAAAAGCTCCTTTTGTCGTTG	0.552																																					p.R115R		Atlas-SNP	.											.	ID3	29	.	0			c.A343C						.						91	87	88					1																	23885468		2203	4300	6503	SO:0001819	synonymous_variant	3399	exon2			AGCTCCTTTTGTC	X69111	CCDS237.1	1p36.13-p36.12	2013-05-21			ENSG00000117318	ENSG00000117318		"Basic helix-loop-helix proteins"	5362	protein-coding gene	gene with protein product		600277				1628620	Standard	NM_002167		Approved	HEIR-1, bHLHb25	uc001bhh.4	Q02535	OTTHUMG00000003229	ENST00000374561.5:c.343A>C	chr1.hg19:g.23885468T>G		90.0	0.0		71.0	40.0	NM_002167	A8K1T8|O75641	Silent	SNP	ENST00000374561.5	hg19	CCDS237.1																																																																																			.	.		0.552	ID3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008904.1	NM_002167		G	23885468	T	G	23885468	2	3	195	1	0	0	0	0	0	0	0	1	7500	1608	56	5		5	ID3	1	23885468	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	21979947	23885468	225365153	2	28630										
PPP1R8	5511	hgsc.bcm.edu	37	chr1	28167686	28167686	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aaggagatgagaagatgggtGgagaggatgatgaactcaag	17	2	1	6			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:28167686G>A	ENST00000311772.5	+	4	491	c.433G>A	c.(433-435)Gga>Aga	p.G145R	PPP1R8_ENST00000236412.7_Intron|PPP1R8_ENST00000373931.4_Missense_Mutation_p.G3R	NM_014110.4	NP_054829.2	Q12972	PP1R8_HUMAN	protein phosphatase 1, regulatory subunit 8	145	Interaction with EED.				cell proliferation (GO:0008283)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|protein phosphatase type 1 regulator activity (GO:0008599)|protein serine/threonine phosphatase inhibitor activity (GO:0004865)|ribonuclease E activity (GO:0008995)|RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(2)|lung(2)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|all_lung(284;0.000129)|Lung NSC(340;0.000259)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.76e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00248)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)		GAAGATGGGTGGAGAGGATGA	0.507																																					p.G145R		Atlas-SNP	.											.	PPP1R8	17	.	0			c.G433A						.						145	129	135					1																	28167686		2203	4300	6503	SO:0001583	missense	5511	exon4			ATGGGTGGAGAGG	AF061959	CCDS311.1, CCDS312.1, CCDS313.1	1p35.3	2012-04-17	2011-10-04		ENSG00000117751	ENSG00000117751		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9296	protein-coding gene	gene with protein product	"RNase E", "nuclear subunit of PP-1", "nuclear inhibitor of protein phosphatase-1", "activator of RNA decay", "protein phosphatase 1 regulatory subunit 8"	602636	"protein phosphatase 1, regulatory (inhibitor) subunit 8"			7524097, 8473324	Standard	NM_014110		Approved	ard-1, NIPP-1, PRO2047, ARD1, NIPP1	uc001bov.2	Q12972	OTTHUMG00000003734	ENST00000311772.5:c.433G>A	chr1.hg19:g.28167686G>A	ENSP00000311677:p.Gly145Arg	225.0	0.0		145.0	30.0	NM_014110	Q5TEJ2|Q5TEJ4|Q5TIF2|Q6PKF6|Q9UBH1|Q9UBZ0	Missense_Mutation	SNP	ENST00000311772.5	hg19	CCDS311.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.681565	0.47991	.	.	ENSG00000117751	ENST00000311772;ENST00000373931;ENST00000434313;ENST00000399118;ENST00000431586	T	0.41065	1.01	5.53	5.53	0.82687	.	0.053183	0.85682	D	0.000000	T	0.36853	0.0982	L	0.53249	1.67	0.32902	D	0.513253	B	0.31485	0.325	B	0.30029	0.11	T	0.45279	-0.9272	10	0.15952	T	0.53	-8.4208	13.713	0.62680	0.0737:0.0:0.9263:0.0	.	145	Q12972	PP1R8_HUMAN	R	145;3;145;3;3	ENSP00000311677:G145R	ENSP00000311677:G145R	G	+	1	0	PPP1R8	28040273	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.317000	0.51968	2.605000	0.88082	0.655000	0.94253	GGA	.	.		0.507	PPP1R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010528.1	NM_014110		A	28167686	G	A	28167686	3	1	195	1	0	0	0	0	1	0	0	0	12389	1349	47	3	447	3	PPP1R8	1	28167686	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	4282218	28167686	221082935	3	28631										
TRIT1	54802	hgsc.bcm.edu	37	chr1	40310251	40310251	+	Frame_Shift_Del	DEL	T	T	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gcaggttcaagaacagactcTtcccacttcgagacatcaga							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:40310251delT	ENST00000316891.5	-	9	1082	c.1068delA	c.(1066-1068)gaafs	p.E357fs	TRIT1_ENST00000491865.1_5'UTR|TRIT1_ENST00000441669.2_Frame_Shift_Del_p.E275fs|TRIT1_ENST00000541099.1_5'UTR|TRIT1_ENST00000537440.1_Frame_Shift_Del_p.E53fs|TRIT1_ENST00000372818.1_Frame_Shift_Del_p.E331fs|TRIT1_ENST00000537223.1_Frame_Shift_Del_p.E53fs|TRIT1_ENST00000545233.1_Frame_Shift_Del_p.E111fs	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	357					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)			breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GAACAGACTCTTCCCACTTCG	0.428																																					p.E357fs		Atlas-Indel,Pindel	.											.	TRIT1	40	.	0			c.1069delG						.						76	72	73					1																	40310251		2203	4300	6503	SO:0001589	frameshift_variant	54802	exon9			.	AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	2.5.1.8		20286	protein-coding gene	gene with protein product						11111046, 15870694	Standard	NM_017646		Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.1068delA	chr1.hg19:g.40310251delT	ENSP00000321810:p.Glu357fs	429.0	0.0		447.0	151.0	NM_017646	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	Frame_Shift_Del	DEL	ENST00000316891.5	hg19	CCDS30681.1																																																																																			.	.		0.428	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025627.2	NM_017646		-	40310251	T	-	40310251	7	5	195	1	0	1	0	1	0	0	0	0	16575	1606	56	0	347	0	TRIT1	1	40310251	Frame_Shift_Del	DEL	T	TCGA-DD-AADM-01A-11D-A40R-10	12142565	40310251	208940370	4	28632										
STIL	6491	hgsc.bcm.edu	37	chr1	47746094	47746131	+	Frame_Shift_Del	DEL	TTGCTGTGGGGAGAACAACTGCCCATATCTCCCTGAGG	TTGCTGTGGGGAGAACAACTGCCCATATCTCCCTGAGG	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccacaggcgatggttcaataTtgctgtggggagaacaactg					rs140448154|rs375723619|rs185913484	byFrequency	TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	TTGCTGTGGGGAGAACAACTGCCCATATCTCCCTGAGG	TTGCTGTGGGGAGAACAACTGCCCATATCTCCCTGAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:47746094_47746131delTTGCTGTGGGGAGAACAACTGCCCATATCTCCCTGAGG	ENST00000360380.3	-	13	2362_2399	c.1999_2036delCCTCAGGGAGATATGGGCAGTTGTTCTCCCCACAGCAA	c.(1999-2037)cctcagggagatatgggcagttgttctccccacagcaatfs	p.PQGDMGSCSPHSN667fs	STIL_ENST00000337817.5_Frame_Shift_Del_p.PQGDMGSCSPHSN667fs|STIL_ENST00000371877.3_Frame_Shift_Del_p.PQGDMGSCSPHSN667fs|STIL_ENST00000396221.2_Frame_Shift_Del_p.PQGDMGSCSPHSN667fs|STIL_ENST00000243182.6_Frame_Shift_Del_p.PQGDMGSCSPHSN667fs	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	667	PIN1-binding. {ECO:0000250}.				cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				TGGTTCAATATTGCTGTGGGGAGAACAACTGCCCATATCTCCCTGAGGTCTCAAGGCT	0.479																																					p.667_679del		Pindel	.											.	STIL	91	.	0			c.2000_2037del						.																																			SO:0001589	frameshift_variant	6491	exon12			.	M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"TAL1 (SCL) interrupting locus"	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.1999_2036delCCTCAGGGAGATATGGGCAGTTGTTCTCCCCACAGCAA	chr1.hg19:g.47746094_47746131delTTGCTGTGGGGAGAACAACTGCCCATATCTCCCTGAGG	ENSP00000353544:p.Pro667fs	133.0	0.0		113.0	11.0	NM_003035	Q5T0C5|Q68CN9	Frame_Shift_Del	DEL	ENST00000360380.3	hg19	CCDS548.1																																																																																			.	.		0.479	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035		-	47746131	TTGCTGTGGGGAGAACAACTGCCCATATCTCCCTGAGG	-	47746094	7	5	195	1	0	1	0	1	0	0	0	0	15297	1493	52	0	1854	0	STIL	1	47746094	Frame_Shift_Del	DEL	TTGCTGTGGGGAGAACAACTGCCCATATCTCCCTGAGG	TCGA-DD-AADM-01A-11D-A40R-10	7435843	47746094	201504527	5	28633										
PTGER3	5733	hgsc.bcm.edu	37	chr1	71513044	71513044	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gcgccggtagctgcgcgacaCgagcagcatggccagtgcgt	16	13	0	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:71513044C>A	ENST00000306666.5	-	1	427	c.217G>T	c.(217-219)Gtg>Ttg	p.V73L	PTGER3_ENST00000370931.3_Missense_Mutation_p.V73L|PTGER3_ENST00000460330.1_Missense_Mutation_p.V73L|PTGER3_ENST00000356595.4_Missense_Mutation_p.V73L|PTGER3_ENST00000351052.5_Missense_Mutation_p.V73L|ZRANB2-AS1_ENST00000450461.1_RNA|PTGER3_ENST00000414819.1_Missense_Mutation_p.V73L|PTGER3_ENST00000370924.4_Missense_Mutation_p.V73L|PTGER3_ENST00000354608.5_Missense_Mutation_p.V73L|PTGER3_ENST00000370932.2_Missense_Mutation_p.V73L	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	73					cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	CTGCGCGACACGAGCAGCATG	0.657																																					p.V73L		Atlas-SNP	.											.	PTGER3	246	.	0			c.G217T						.						34	38	36					1																	71513044		2202	4300	6502	SO:0001583	missense	5733	exon1			GCGACACGAGCAG	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.217G>T	chr1.hg19:g.71513044C>A	ENSP00000302313:p.Val73Leu	262.0	0.0		253.0	74.0	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Missense_Mutation	SNP	ENST00000306666.5	hg19	CCDS657.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.741675	0.49151	.	.	ENSG00000050628	ENST00000370931;ENST00000370932;ENST00000351052;ENST00000460330;ENST00000370934;ENST00000354608;ENST00000356595;ENST00000414819;ENST00000306666;ENST00000370924	T;T;T;T;T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33	4.9	4.9	0.64082	GPCR, rhodopsin-like superfamily (1);	0.116319	0.56097	D	0.000023	T	0.21062	0.0507	N	0.04724	-0.175	0.80722	D	1	D;D;D;D;D;D;D;D	0.76494	0.999;0.992;0.999;0.999;0.999;0.99;0.995;0.996	D;P;D;D;D;P;D;D	0.71870	0.975;0.903;0.957;0.975;0.975;0.844;0.91;0.946	T	0.03728	-1.1009	10	0.02654	T	1	-32.3497	18.2589	0.90028	0.0:1.0:0.0:0.0	.	73;73;73;73;73;73;73;73	Q147U0;Q6TTN3;F5H821;B1AK19;Q147X8;P43115-3;P43115-4;P43115	.;.;.;.;.;.;.;PE2R3_HUMAN	L	73	ENSP00000359969:V73L;ENSP00000359970:V73L;ENSP00000280208:V73L;ENSP00000418073:V73L;ENSP00000346624:V73L;ENSP00000349003:V73L;ENSP00000401423:V73L;ENSP00000302313:V73L;ENSP00000359962:V73L	ENSP00000302313:V73L	V	-	1	0	PTGER3	71285632	1.000000	0.71417	0.964000	0.40570	0.935000	0.57460	5.636000	0.67848	2.537000	0.85549	0.462000	0.41574	GTG	.	.		0.657	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957		A	71513044	C	A	71513044	3	1	195	1	0	0	0	0	1	0	0	0	12757	536	19	1	1274	1	PTGER3	1	71513044	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	23766950	71513044	177737577	6	28634										
NEGR1	257194	hgsc.bcm.edu	37	chr1	72748049	72748049	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	accatcatgttgtccacggcCgcccaggggaagtccacact	10	15	1	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:72748049C>A	ENST00000357731.5	-	1	368	c.129G>T	c.(127-129)gcG>gcT	p.A43A	NEGR1_ENST00000434200.1_Silent_p.A41A	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1	43	Ig-like C2-type 1.				feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|positive regulation of neuron projection development (GO:0010976)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(4)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		TGTCCACGGCCGCCCAGGGGA	0.592																																					p.A43A		Atlas-SNP	.											.	NEGR1	60	.	0			c.G129T						.						81	82	81					1																	72748049		2203	4300	6503	SO:0001819	synonymous_variant	257194	exon1			CACGGCCGCCCAG	AK092307	CCDS661.1	1p31.1	2013-01-11			ENSG00000172260	ENSG00000172260		"Immunoglobulin superfamily / I-set domain containing"	17302	protein-coding gene	gene with protein product	"a kindred of IgLON", "neurotractin", "IgLON family member 4"	613173				10075727	Standard	NM_173808		Approved	KILON, MGC46680, Ntra, IGLON4	uc001dfw.3	Q7Z3B1	OTTHUMG00000009698	ENST00000357731.5:c.129G>T	chr1.hg19:g.72748049C>A		374.0	0.0		364.0	30.0	NM_173808	Q5VT21|Q6UY06|Q8N440|Q8NAQ3	Silent	SNP	ENST00000357731.5	hg19	CCDS661.1																																																																																			.	.		0.592	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4	NM_173808		A	72748049	C	A	72748049	2	1	195	1	0	0	0	0	0	0	0	1	10326	639	23	1		1	NEGR1	1	72748049	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	1235005	72748049	176502572	7	28635										
LPHN2	23266	hgsc.bcm.edu	37	chr1	82456669	82456669	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgagaatgaggacatttactAtaaaagcatgccaaatcttg	8	6	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:82456669A>G	ENST00000370728.1	+	25	4865	c.4220A>G	c.(4219-4221)tAt>tGt	p.Y1407C	LPHN2_ENST00000271029.4_Missense_Mutation_p.Y1379C|LPHN2_ENST00000370717.2_Missense_Mutation_p.Y1422C|LPHN2_ENST00000370725.1_Missense_Mutation_p.Y1422C|LPHN2_ENST00000370721.1_Missense_Mutation_p.Y1332C|LPHN2_ENST00000394879.1_Missense_Mutation_p.Y1409C|LPHN2_ENST00000370727.1_Missense_Mutation_p.Y1379C|LPHN2_ENST00000370723.1_Missense_Mutation_p.Y1409C|LPHN2_ENST00000319517.6_Missense_Mutation_p.Y1351C|LPHN2_ENST00000370730.1_Missense_Mutation_p.Y1364C|LPHN2_ENST00000335786.5_Missense_Mutation_p.Y1364C|LPHN2_ENST00000469377.2_3'UTR|LPHN2_ENST00000370715.1_3'UTR|LPHN2_ENST00000359929.3_Missense_Mutation_p.Y1351C|LPHN2_ENST00000370713.1_3'UTR			O95490	LPHN2_HUMAN	latrophilin 2	1407					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		Gacatttactataaaagcatg	0.473																																					p.Y1351C		Atlas-SNP	.											.	LPHN2	464	.	0			c.A4052G						.						58	55	56					1																	82456669		2203	4300	6503	SO:0001583	missense	23266	exon20			TTTACTATAAAAG	AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"-", "GPCR / Class B : Orphans"	18582	protein-coding gene	gene with protein product		607018	"latrophilin 1"	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.4220A>G	chr1.hg19:g.82456669A>G	ENSP00000359763:p.Tyr1407Cys	100.0	0.0		110.0	22.0	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.69|12.69	2.015065|2.015065	0.35511|0.35511	.|.	.|.	ENSG00000117114|ENSG00000117114	ENST00000449420|ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786	.|T;T;T;T;T;T;T;T;T;T;T;T	.|0.75050	.|-0.81;-0.83;-0.9;-0.85;-0.76;-0.71;-0.84;-0.84;-0.76;-0.71;-0.85;-0.9	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|0.067301	.|0.64402	.|D	.|0.000009	T|T	0.77638|0.77638	0.4160|0.4160	L|L	0.39898|0.39898	1.24|1.24	0.80722|0.80722	D|D	1|1	.|B;D	.|0.89917	.|0.05;1.0	.|B;D	.|0.87578	.|0.037;0.998	T|T	0.81441|0.81441	-0.0931|-0.0931	5|10	.|0.87932	.|D	.|0	.|.	15.909|15.909	0.79456|0.79456	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1351;331	.|O95490-2;B3KVU1	.|.;.	V|C	1299|1332;1407;1364;1379;1422;1409;1351;1351;1422;1409;1379;1364	.|ENSP00000359756:Y1332C;ENSP00000359763:Y1407C;ENSP00000359765:Y1364C;ENSP00000359762:Y1379C;ENSP00000359760:Y1422C;ENSP00000359758:Y1409C;ENSP00000353006:Y1351C;ENSP00000322270:Y1351C;ENSP00000359752:Y1422C;ENSP00000378344:Y1409C;ENSP00000271029:Y1379C;ENSP00000337306:Y1364C	.|ENSP00000271029:Y1379C	I|Y	+|+	1|2	0|0	LPHN2|LPHN2	82229257|82229257	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	8.730000|8.730000	0.91510|0.91510	2.155000|2.155000	0.67459|0.67459	0.459000|0.459000	0.35465|0.35465	ATA|TAT	.	.		0.473	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		G	82456669	A	G	82456669	3	3	195	1	0	0	0	0	1	0	0	0	8925	449	16	2	4126	2	LPHN2	1	82456669	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	9708620	82456669	166793952	8	28636										
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94639693	94639693	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cattccccctgatactgatgAtgggagcatgtggtttataa	10	8	0	3			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:94639693A>C	ENST00000260526.6	-	23	3700	c.3518T>G	c.(3517-3519)aTc>aGc	p.I1173S	ARHGAP29_ENST00000482481.1_5'Flank	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	1173					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		GATACTGATGATGGGAGCATG	0.532																																					p.I1173S		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.T3518G						.						84	72	76					1																	94639693		2203	4300	6503	SO:0001583	missense	9411	exon23			CTGATGATGGGAG		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.3518T>G	chr1.hg19:g.94639693A>C	ENSP00000260526:p.Ile1173Ser	106.0	0.0		90.0	15.0	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	hg19	CCDS748.1	.	.	.	.	.	.	.	.	.	.	A	5.439	0.266072	0.10294	.	.	ENSG00000137962	ENST00000260526	T	0.20200	2.09	5.49	0.999	0.19862	.	1.794900	0.03253	N	0.182068	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.31110	-0.9955	10	0.10636	T	0.68	6.0451	5.5764	0.17225	0.1433:0.104:0.6262:0.1265	.	1173	Q52LW3	RHG29_HUMAN	S	1173	ENSP00000260526:I1173S	ENSP00000260526:I1173S	I	-	2	0	ARHGAP29	94412281	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.861000	0.27885	0.290000	0.22444	-0.220000	0.12472	ATC	.	.		0.532	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		C	94639693	A	C	94639693	3	2	195	1	0	0	0	0	1	0	0	0	878	333	12	5	271	5	ARHGAP29	1	94639693	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	12183024	94639693	154610928	9	28637										
VAV3	10451	hgsc.bcm.edu	37	chr1	108322109	108322109	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gaaagtcgtgataatgtttcTataacctgagaaaagaggaa	10	4	1	3			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:108322109T>C	ENST00000370056.4	-	3	601	c.327A>G	c.(325-327)atA>atG	p.I109M	VAV3_ENST00000527011.1_Missense_Mutation_p.I109M|VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000371846.4_Missense_Mutation_p.I44M	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	109	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		ATAATGTTTCTATAACCTGAG	0.328																																					p.I109M		Atlas-SNP	.											.	VAV3	176	.	0			c.A327G						.						96	91	93					1																	108322109		2203	4300	6503	SO:0001583	missense	10451	exon3			TGTTTCTATAACC	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.327A>G	chr1.hg19:g.108322109T>C	ENSP00000359073:p.Ile109Met	142.0	0.0		152.0	21.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.03|14.03	2.415077|2.415077	0.42817|0.42817	.|.	.|.	ENSG00000134215|ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000371846|ENST00000490388	T;T;T|.	0.42131|.	0.98;0.98;0.98|.	5.66|5.66	5.66|5.66	0.87406|0.87406	Calponin homology domain (5);|.	0.100929|.	0.64402|.	D|.	0.000003|.	T|.	0.51584|.	0.1683|.	L|L	0.50993|0.50993	1.605|1.605	0.49582|0.49582	D|D	0.999808|0.999808	B;B;B|.	0.32203|.	0.011;0.005;0.36|.	B;B;P|.	0.54856|.	0.209;0.054;0.762|.	T|.	0.52366|.	-0.8585|.	10|.	0.49607|.	T|.	0.09|.	.|.	13.4171|13.4171	0.60974|0.60974	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	109;109;109|.	B7ZLR1;E9PQ97;Q9UKW4|.	.;.;VAV3_HUMAN|.	M|W	109;109;44|104	ENSP00000359073:I109M;ENSP00000432540:I109M;ENSP00000360912:I44M|.	ENSP00000359073:I109M|.	I|X	-|-	3|2	3|0	VAV3|VAV3	108123632|108123632	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	2.878000|2.878000	0.48515|0.48515	2.137000|2.137000	0.66172|0.66172	0.528000|0.528000	0.53228|0.53228	ATA|TAG	.	.		0.328	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		C	108322109	T	C	108322109	3	2	195	1	0	0	0	0	1	0	0	0	17148	1512	53	2	2341	2	VAV3	1	108322109	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	13682416	108322109	140928512	10	28638										
MOV10	4343	hgsc.bcm.edu	37	chr1	113237434	113237434	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gccatgaggcacattgttacGggcaccacccgtccagcccc	10	17	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:113237434G>A	ENST00000413052.2	+	10	1926	c.1536G>A	c.(1534-1536)acG>acA	p.T512T	RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000369644.1_Silent_p.T456T|MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369645.1_Silent_p.T512T|MOV10_ENST00000357443.2_Silent_p.T512T	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	512					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		ACATTGTTACGGGCACCACCC	0.577																																					p.T512T		Atlas-SNP	.											.	MOV10	74	.	0			c.G1536A						.						79	70	73					1																	113237434		2203	4300	6503	SO:0001819	synonymous_variant	4343	exon10			TGTTACGGGCACC	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 113"	610742	"Mov10 (Moloney leukemia virus 10, mouse) homolog", "Mov10, Moloney leukemia virus 10, homolog (mouse)"			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.1536G>A	chr1.hg19:g.113237434G>A		272.0	0.0		252.0	61.0	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	hg19	CCDS853.1																																																																																			.	.		0.577	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		A	113237434	G	A	113237434	2	1	195	1	0	0	0	0	0	0	0	1	9727	1103	39	1		1	MOV10	1	113237434	Silent	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	4915325	113237434	136013187	11	28639										
COPA	1314	hgsc.bcm.edu	37	chr1	160303442	160303442	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cactcggatggtctgatcatCggaggcactcagaatccagg	12	11	3	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:160303442C>A	ENST00000241704.7	-	5	566	c.337G>T	c.(337-339)Gat>Tat	p.D113Y	COPA_ENST00000368069.3_Missense_Mutation_p.D113Y	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	113					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GTCTGATCATCGGAGGCACTC	0.408																																					p.D113Y		Atlas-SNP	.											.	COPA	181	.	0			c.G337T						.						70	71	71					1																	160303442		2203	4300	6503	SO:0001583	missense	1314	exon5			GATCATCGGAGGC	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"WD repeat domain containing", "Endogenous ligands"	2230	protein-coding gene	gene with protein product	"proxenin", "xenin"	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.337G>T	chr1.hg19:g.160303442C>A	ENSP00000241704:p.Asp113Tyr	111.0	0.0		230.0	158.0	NM_001098398	Q5T201|Q8IXZ9	Missense_Mutation	SNP	ENST00000241704.7	hg19	CCDS1202.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.833778	0.91036	.	.	ENSG00000122218	ENST00000368069;ENST00000241704	T;T	0.60920	0.15;0.15	5.12	5.12	0.69794	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.61677	0.2366	L	0.35414	1.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.66056	-0.6018	10	0.87932	D	0	-21.1402	17.2891	0.87150	0.0:1.0:0.0:0.0	.	113;113	P53621;P53621-2	COPA_HUMAN;.	Y	113	ENSP00000357048:D113Y;ENSP00000241704:D113Y	ENSP00000241704:D113Y	D	-	1	0	COPA	158570066	1.000000	0.71417	0.900000	0.35374	0.946000	0.59487	7.369000	0.79578	2.652000	0.90054	0.655000	0.94253	GAT	.	.		0.408	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371		A	160303442	C	A	160303442	3	1	195	1	0	0	0	0	1	0	0	0	3729	884	31	1	3480	1	COPA	1	160303442	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	47066008	160303442	88947179	12	28640										
C1orf112	55732	hgsc.bcm.edu	37	chr1	169773232	169773232	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tcagaatagtgaatctgtgtAttctgggtgtttacacctag	10	6	3	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:169773232A>T	ENST00000286031.6	+	6	1029	c.329A>T	c.(328-330)tAt>tTt	p.Y110F	C1orf112_ENST00000413811.2_Missense_Mutation_p.Y81F|C1orf112_ENST00000456684.1_Missense_Mutation_p.Y168F|C1orf112_ENST00000498289.1_Intron|C1orf112_ENST00000359326.4_Missense_Mutation_p.Y110F	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	110										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GAATCTGTGTATTCTGGGTGT	0.363																																					p.Y110F		Atlas-SNP	.											.	C1orf112	74	.	0			c.A329T						.						117	112	114					1																	169773232		2203	4300	6503	SO:0001583	missense	55732	exon6			CTGTGTATTCTGG	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.329A>T	chr1.hg19:g.169773232A>T	ENSP00000286031:p.Tyr110Phe	139.0	0.0		224.0	18.0	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	hg19	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.956231	0.53293	.	.	ENSG00000000460	ENST00000413811;ENST00000359326;ENST00000456684;ENST00000286031	T;T;T	0.75704	-0.96;-0.22;-0.96	5.41	4.29	0.51040	.	0.055611	0.85682	D	0.000000	T	0.80476	0.4630	M	0.78637	2.42	0.45295	D	0.998295	D;D;D;D	0.89917	0.998;1.0;1.0;0.998	D;D;D;D	0.87578	0.994;0.998;0.998;0.994	T	0.82851	-0.0253	10	0.87932	D	0	-18.6356	10.0819	0.42395	0.9204:0.0:0.0796:0.0	.	81;52;110;168	B4E0A9;B4DGF2;Q9NSG2;B4DRP7	.;.;CA112_HUMAN;.	F	81;110;168;110	ENSP00000352276:Y110F;ENSP00000415583:Y168F;ENSP00000286031:Y110F	ENSP00000286031:Y110F	Y	+	2	0	C1orf112	168039856	1.000000	0.71417	0.996000	0.52242	0.117000	0.20001	6.675000	0.74493	0.899000	0.36444	-0.326000	0.08463	TAT	.	.		0.363	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		T	169773232	A	T	169773232	3	4	195	1	0	0	0	0	1	0	0	0	1987	449	16	4	343	4	C1orf112	1	169773232	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	9469790	169773232	79477389	13	28641										
ASTN1	460	hgsc.bcm.edu	37	chr1	176913059	176913059	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cagggtcaggggtgggctccGagatctcctctaggcattga	15	10	3	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:176913059G>T	ENST00000367654.3	-	14	2580	c.2369C>A	c.(2368-2370)tCg>tAg	p.S790*	ASTN1_ENST00000361833.2_Nonsense_Mutation_p.S782*|ASTN1_ENST00000367657.3_Nonsense_Mutation_p.S782*|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Nonsense_Mutation_p.S782*	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	790					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GGTGGGCTCCGAGATCTCCTC	0.512																																					p.S782X		Atlas-SNP	.											ASTN1,colon,carcinoma,0,1	ASTN1	314	.	0			c.C2345A						.						108	95	99					1																	176913059		2203	4300	6503	SO:0001587	stop_gained	460	exon14			GGCTCCGAGATCT	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.2369C>A	chr1.hg19:g.176913059G>T	ENSP00000356626:p.Ser790*	87.0	0.0		176.0	11.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Nonsense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	G	39	7.859027	0.98528	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.8039	18.966	0.92697	0.0:0.0:1.0:0.0	.	.	.	.	X	782;782;790;782;782	.	ENSP00000354536:S782X	S	-	2	0	ASTN1	175179682	1.000000	0.71417	0.956000	0.39512	0.970000	0.65996	8.630000	0.90987	2.576000	0.86940	0.655000	0.94253	TCG	.	.		0.512	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		T	176913059	G	T	176913059	4	4	195	1	0	0	0	0	0	1	0	0	1064	1059	37	1	1583	1	ASTN1	1	176913059	Nonsense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	7139827	176913059	72337562	14	28642										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179504037	179504037	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gagaagtaaaagaagaagaaGaacaacaagaagaagaagaa	11	2	0	9	rs200097954|rs368406759|rs6425573	byFrequency	TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:179504037G>C	ENST00000367618.3	+	25	3358	c.2971G>C	c.(2971-2973)Gaa>Caa	p.E991Q		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	991	Glu-rich.		E -> Q (in dbSNP:rs6425573).					p.E991_Q992delEQ(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agaagaagaagaacaacaaga	0.318													G|||	14	0.00279553	0	0.0058	5008	,	,		17137	0.002		0.004	False		,,,				2504	0.0041				p.E991Q		Atlas-SNP	.											.	AXDND1	142	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2971C						.						49	51	50					1																	179504037		2152	4286	6438	SO:0001583	missense	126859	exon25			GAAGAAGAACAAC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2971G>C	chr1.hg19:g.179504037G>C	ENSP00000356590:p.Glu991Gln	413.0	0.0		733.0	97.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	G	9.300	1.052898	0.19907	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.19105	2.17;2.17	4.89	-6.02	0.02192	.	0.508747	0.16499	N	0.211773	T	0.08980	0.0222	N	0.24115	0.695	0.09310	N	1	B;B	0.24186	0.099;0.099	B;B	0.10450	0.003;0.005	T	0.15838	-1.0423	10	0.28530	T	0.3	-2.8152	6.1976	0.20557	0.4456:0.3814:0.173:0.0	rs6425573	875;991	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	Q	991;875;851	ENSP00000356590:E991Q;ENSP00000391716:E851Q	ENSP00000353471:E875Q	E	+	1	0	AXDND1	177770660	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.365000	0.20348	-1.164000	0.02790	-1.047000	0.02352	GAA	.	G|1.000;|0.000		0.318	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179504037	G	C	179504037	3	2	195	1	0	0	0	0	1	0	0	0	1995	943	33	4	3065	4	C1orf125	1	179504037	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	2590978	179504037	69746584	15	28643										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186045722	186045722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gtacaaagatggccaccctcTgacctcaagtgataaagtat	8	10	2	3			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:186045722T>C	ENST00000271588.4	+	54	8682	c.8453T>C	c.(8452-8454)cTg>cCg	p.L2818P	HMCN1_ENST00000367492.2_Missense_Mutation_p.L2818P	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2818	Ig-like C2-type 26.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GGCCACCCTCTGACCTCAAGT	0.428																																					p.L2818P		Atlas-SNP	.											.	HMCN1	797	.	0			c.T8453C						.						107	96	100					1																	186045722		2203	4300	6503	SO:0001583	missense	83872	exon54			ACCCTCTGACCTC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8453T>C	chr1.hg19:g.186045722T>C	ENSP00000271588:p.Leu2818Pro	68.0	0.0		143.0	21.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.277260	0.80580	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.72725	-0.68;-0.68	4.78	4.78	0.61160	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.074796	0.56097	D	0.000039	D	0.84656	0.5520	M	0.82923	2.615	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87385	0.2359	10	0.87932	D	0	.	14.6147	0.68539	0.0:0.0:0.0:1.0	.	2818	Q96RW7	HMCN1_HUMAN	P	2818	ENSP00000271588:L2818P;ENSP00000356462:L2818P	ENSP00000271588:L2818P	L	+	2	0	HMCN1	184312345	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	7.997000	0.88414	1.896000	0.54893	0.533000	0.62120	CTG	.	.		0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186045722	T	C	186045722	3	2	195	1	0	0	0	0	1	0	0	0	7229	1580	55	2	8667	2	HMCN1	1	186045722	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	6541685	186045722	63204899	16	28644										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186135944	186135944	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	attccctctgttgcagatatTgatgagtgtgctttgggtag	12	6	1	3			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:186135944T>C	ENST00000271588.4	+	100	15673	c.15444T>C	c.(15442-15444)atT>atC	p.I5148I	HMCN1_ENST00000367492.2_Silent_p.I5148I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5148	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TTGCAGATATTGATGAGTGTG	0.498																																					p.I5148I		Atlas-SNP	.											.	HMCN1	797	.	0			c.T15444C						.						171	139	150					1																	186135944		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon100			AGATATTGATGAG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15444T>C	chr1.hg19:g.186135944T>C		106.0	0.0		184.0	13.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.498	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186135944	T	C	186135944	2	2	195	1	0	0	0	0	0	0	0	1	7229	1800	63	2		2	HMCN1	1	186135944	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	90222	186135944	63114677	17	28645										
KIF14	9928	hgsc.bcm.edu	37	chr1	200558357	200558357	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aaaattacctgttttgtagcCaatgtttccatttctaatcg	5	8	1	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:200558357C>T	ENST00000367350.4	-	18	3540	c.3102G>A	c.(3100-3102)ttG>ttA	p.L1034L		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1034	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						GTTTTGTAGCCAATGTTTCCA	0.333																																					p.L1034L		Atlas-SNP	.											.	KIF14	156	.	0			c.G3102A						.						149	143	145					1																	200558357		2202	4300	6502	SO:0001819	synonymous_variant	9928	exon18			TGTAGCCAATGTT	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.3102G>A	chr1.hg19:g.200558357C>T		74.0	0.0		126.0	9.0	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	hg19	CCDS30963.1																																																																																			.	.		0.333	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		T	200558357	C	T	200558357	2	4	195	1	0	0	0	0	0	0	0	1	8285	593	21	3		3	KIF14	1	200558357	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	14422413	200558357	48692264	18	28646										
ADIPOR1	51094	hgsc.bcm.edu	37	chr1	202920181	202920181	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ttcccctgtgccaccacagaTcctttgtgggaagacatctg	9	13	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:202920181T>A	ENST00000340990.5	-	2	316	c.18A>T	c.(16-18)ggA>ggT	p.G6G	ADIPOR1_ENST00000436244.1_Silent_p.G6G|ADIPOR1_ENST00000367254.3_Silent_p.G6G	NM_015999.4	NP_057083.2	Q96A54	ADR1_HUMAN	adiponectin receptor 1	6					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|hormone-mediated signaling pathway (GO:0009755)|leptin-mediated signaling pathway (GO:0033210)|negative regulation of cell growth (GO:0030308)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of JAK-STAT cascade (GO:0046427)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	16			BRCA - Breast invasive adenocarcinoma(75;0.141)			CCACCACAGATCCTTTGTGGG	0.582																																					p.G6G		Atlas-SNP	.											.	ADIPOR1	32	.	0			c.A18T						.						97	89	91					1																	202920181		2203	4300	6503	SO:0001819	synonymous_variant	51094	exon2			CACAGATCCTTTG		CCDS1430.1	1q32.1	2012-08-22			ENSG00000159346	ENSG00000159346		"GPCR / Unclassified : Adiponectin receptors"	24040	protein-coding gene	gene with protein product		607945				12802337	Standard	XM_006711360		Approved	PAQR1, ACDCR1	uc001gyq.5	Q96A54	OTTHUMG00000041391	ENST00000340990.5:c.18A>T	chr1.hg19:g.202920181T>A		92.0	0.0		159.0	11.0	NM_015999	B3KMB0|Q53HS7|Q53YY6|Q9Y360	Silent	SNP	ENST00000340990.5	hg19	CCDS1430.1																																																																																			.	.		0.582	ADIPOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099160.2	NM_015999		A	202920181	T	A	202920181	2	1	195	1	0	0	0	0	0	0	0	1	318	1422	50	4		4	ADIPOR1	1	202920181	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	2361824	202920181	46330440	19	28647										
TMEM81	388730	hgsc.bcm.edu	37	chr1	205053415	205053415	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gtagaaggccaaccccaggcTcccaaggacaaaactagtgg	11	12	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:205053415T>A	ENST00000367167.3	-	1	230	c.34A>T	c.(34-36)Agc>Tgc	p.S12C		NM_203376.1	NP_976310.1	Q6P7N7	TMM81_HUMAN	transmembrane protein 81	12						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9	all_cancers(21;0.144)|Breast(84;0.0437)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			AACCCCAGGCTCCCAAGGACA	0.502																																					p.S12C		Atlas-SNP	.											TMEM81,right_upper_lobe,carcinoma,+2,1	TMEM81	23	.	0			c.A34T						.						78	77	77					1																	205053415		2203	4300	6503	SO:0001583	missense	388730	exon1			CCAGGCTCCCAAG	BC061592	CCDS1450.1	1q32.1	2013-01-11			ENSG00000174529	ENSG00000174529		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	32349	protein-coding gene	gene with protein product							Standard	NM_203376		Approved	UNQ2788, MGC75217, HC3107, KVLA2788	uc001hbt.3	Q6P7N7	OTTHUMG00000037103	ENST00000367167.3:c.34A>T	chr1.hg19:g.205053415T>A	ENSP00000356135:p.Ser12Cys	190.0	0.0		336.0	21.0	NM_203376	Q6UVZ4	Missense_Mutation	SNP	ENST00000367167.3	hg19	CCDS1450.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.656407	0.67586	.	.	ENSG00000174529	ENST00000367167	T	0.33438	1.41	5.31	4.18	0.49190	.	0.355168	0.26400	N	0.024586	T	0.37598	0.1009	M	0.63428	1.95	0.09310	N	1	D	0.54964	0.969	P	0.50378	0.639	T	0.25117	-1.0141	10	0.56958	D	0.05	-6.0078	7.9779	0.30166	0.0:0.1652:0.0:0.8348	.	12	Q6P7N7	TMM81_HUMAN	C	12	ENSP00000356135:S12C	ENSP00000356135:S12C	S	-	1	0	TMEM81	203320038	0.000000	0.05858	0.048000	0.18961	0.411000	0.31082	0.767000	0.26575	0.973000	0.38340	0.455000	0.32223	AGC	.	.		0.502	TMEM81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090076.1	NM_203376		A	205053415	T	A	205053415	3	1	195	1	0	0	0	0	1	0	0	0	16220	1551	54	4	737	4	TMEM81	1	205053415	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	2133234	205053415	44197206	20	28648										
CR1L	1379	hgsc.bcm.edu	37	chr1	207870917	207870917	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	caaggacaacttttcacccgGgcaggaagtgttctacagct	10	11	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:207870917G>C	ENST00000508064.2	+	6	992	c.932G>C	c.(931-933)gGg>gCg	p.G311A	CR1L_ENST00000530905.1_Intron	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	311	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TTTTCACCCGGGCAGGAAGTG	0.552																																					p.G311A		Atlas-SNP	.											.	CR1L	97	.	0			c.G932C						.						151	149	150					1																	207870917		1896	4113	6009	SO:0001583	missense	1379	exon6			CACCCGGGCAGGA	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"Complement system"	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.932G>C	chr1.hg19:g.207870917G>C	ENSP00000421736:p.Gly311Ala	435.0	0.0		744.0	48.0	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	hg19	CCDS44310.1	.	.	.	.	.	.	.	.	.	.	.	12.21	1.868234	0.32977	.	.	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.72394	-0.65	2.53	0.426	0.16479	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	D	0.84669	0.5523	M	0.93241	3.395	0.09310	N	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.71407	-0.4602	9	0.72032	D	0.01	.	5.1339	0.14924	0.3183:0.0:0.6817:0.0	.	311	Q2VPA4	CR1L_HUMAN	A	311	ENSP00000421736:G311A	ENSP00000434864:G255A	G	+	2	0	CR1L	205937540	0.010000	0.17322	0.000000	0.03702	0.004000	0.04260	1.115000	0.31209	-0.026000	0.13895	0.298000	0.19748	GGG	.	.		0.552	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735		C	207870917	G	C	207870917	3	2	195	1	0	0	0	0	1	0	0	0	3843	1232	43	4	954	4	CR1L	1	207870917	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	2817502	207870917	41379704	21	28649										
VASH2	79805	hgsc.bcm.edu	37	chr1	213125028	213125028	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gacaaagacggcggggtgctGttccacgtcaacaagagcgg	15	10	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:213125028G>A	ENST00000517399.1	+	1	144	c.144G>A	c.(142-144)ctG>ctA	p.L48L	VASH2_ENST00000366964.3_5'UTR|VASH2_ENST00000271776.4_Intron|VASH2_ENST00000366968.4_5'UTR|VASH2_ENST00000366966.2_5'UTR|VASH2_ENST00000366965.2_Silent_p.L48L|VASH2_ENST00000366967.2_Intron			Q86V25	VASH2_HUMAN	vasohibin 2	48					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)	cytoplasm (GO:0005737)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)		GCGGGGTGCTGTTCCACGTCA	0.672																																					p.L48L		Atlas-SNP	.											.	VASH2	55	.	0			c.G144A						.						43	39	40					1																	213125028		2198	4297	6495	SO:0001819	synonymous_variant	79805	exon2			GGTGCTGTTCCAC	AK022567	CCDS1511.1, CCDS44315.1, CCDS44316.1, CCDS73026.1	1q23	2008-02-05			ENSG00000143494	ENSG00000143494			25723	protein-coding gene	gene with protein product		610471				16528006	Standard	XR_247041		Approved	FLJ12505	uc001hjw.3	Q86V25	OTTHUMG00000036925	ENST00000517399.1:c.144G>A	chr1.hg19:g.213125028G>A		108.0	0.0		170.0	62.0	NM_024749	B4DYZ5|Q2VT46|Q5VTE7|Q5VTE9|Q7Z6E3|Q8IZ24|Q9H9W5	Silent	SNP	ENST00000517399.1	hg19	CCDS1511.1																																																																																			.	.		0.672	VASH2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381686.1	NM_024749		A	213125028	G	A	213125028	2	1	195	1	0	0	0	0	0	0	0	1	17141	1364	48	3		3	VASH2	1	213125028	Silent	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	5254111	213125028	36125593	22	28650										
BPNT1	10380	hgsc.bcm.edu	37	chr1	220232311	220232311	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cttgtggtactgaagaacatTcccatggatatcggttaact	9	8	0	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:220232311T>G	ENST00000469520.2	-	10	1251	c.802A>C	c.(802-804)Aat>Cat	p.N268H	BPNT1_ENST00000414869.2_Missense_Mutation_p.N232H|BPNT1_ENST00000354807.3_Missense_Mutation_p.N283H|BPNT1_ENST00000322067.7_Missense_Mutation_p.N268H|BPNT1_ENST00000544404.1_Missense_Mutation_p.N213H			O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1	268					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|dephosphorylation (GO:0016311)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|magnesium ion binding (GO:0000287)			breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)|skin(1)	14				GBM - Glioblastoma multiforme(131;0.0558)		TGAAGAACATTCCCATGGATA	0.398																																					p.N268H		Atlas-SNP	.											.	BPNT1	29	.	0			c.A802C						.						154	143	146					1																	220232311		1918	4147	6065	SO:0001583	missense	10380	exon9			GAACATTCCCATG	AF125042	CCDS41469.1, CCDS65787.1, CCDS65788.1	1q42	2008-02-05			ENSG00000162813	ENSG00000162813	3.1.3.7		1096	protein-coding gene	gene with protein product		604053				10224133	Standard	XM_005272998		Approved		uc001hma.3	O95861	OTTHUMG00000037435	ENST00000469520.2:c.802A>C	chr1.hg19:g.220232311T>G	ENSP00000446828:p.Asn268His	91.0	0.0		153.0	21.0	NM_006085	A8K7C8|B4DPS5|B4DUS9|D3DTA9|Q8WVL5|Q9UGJ3	Missense_Mutation	SNP	ENST00000469520.2	hg19	CCDS41469.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.396540	0.62177	.	.	ENSG00000162813	ENST00000322067;ENST00000469520;ENST00000354807;ENST00000302686;ENST00000544404;ENST00000414869	D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74	5.28	5.28	0.74379	.	0.086318	0.85682	D	0.000000	D	0.90167	0.6927	M	0.75777	2.31	0.80722	D	1	P;D;P	0.89917	0.526;1.0;0.48	B;D;B	0.71414	0.412;0.973;0.154	D	0.90618	0.4557	10	0.51188	T	0.08	.	15.5126	0.75795	0.0:0.0:0.0:1.0	.	232;283;268	B4DUS9;A6NF51;O95861	.;.;BPNT1_HUMAN	H	268;268;283;268;213;232	ENSP00000318852:N268H;ENSP00000446828:N268H;ENSP00000346862:N283H;ENSP00000444398:N213H;ENSP00000410348:N232H	ENSP00000307087:N268H	N	-	1	0	BPNT1	218298934	1.000000	0.71417	0.980000	0.43619	0.802000	0.45316	7.901000	0.87382	2.136000	0.66102	0.454000	0.30748	AAT	.	.		0.398	BPNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091137.2	NM_006085		G	220232311	T	G	220232311	3	3	195	1	0	0	0	0	1	0	0	0	1496	1783	62	5	128	5	BPNT1	1	220232311	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	7107283	220232311	29018310	23	28651										
HLX	3142	hgsc.bcm.edu	37	chr1	221057792	221057792	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	agcgttctctgcaccaaacaAcagttattaaggccccggtc	8	13	1	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:221057792A>G	ENST00000366903.6	+	4	2714	c.1213A>G	c.(1213-1215)Aca>Gca	p.T405A	HLX_ENST00000549319.1_Missense_Mutation_p.T191A	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	405	Ser-rich.				cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		GCACCAAACAACAGTTATTAA	0.637																																					p.T405A		Atlas-SNP	.											.	HLX	67	.	0			c.A1213G						.						65	56	59					1																	221057792		2203	4300	6503	SO:0001583	missense	3142	exon4			CAAACAACAGTTA	BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"Homeoboxes / ANTP class : NKL subclass"	4978	protein-coding gene	gene with protein product		142995	"H2.0 (Drosophila)-like homeo box 1", "H2.0-like homeobox 1 (Drosophila)", "H2.0-like homeobox 1"	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.1213A>G	chr1.hg19:g.221057792A>G	ENSP00000355870:p.Thr405Ala	167.0	0.0		336.0	69.0	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	hg19	CCDS1527.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.521063	0.44866	.	.	ENSG00000136630	ENST00000366903;ENST00000427693;ENST00000549319	D;T;T	0.89415	-2.51;0.57;3.33	5.03	2.65	0.31530	.	0.244651	0.26058	N	0.026596	T	0.77883	0.4197	N	0.19112	0.55	0.09310	N	0.999998	B	0.02656	0.0	B	0.06405	0.002	T	0.63444	-0.6636	10	0.33940	T	0.23	-14.4255	7.1511	0.25612	0.8149:0.0:0.1851:0.0	.	405	Q14774	HLX_HUMAN	A	405;138;191	ENSP00000355870:T405A;ENSP00000408248:T138A;ENSP00000449882:T191A	ENSP00000355870:T405A	T	+	1	0	HLX	219124415	0.432000	0.25554	0.230000	0.23976	0.903000	0.53119	3.721000	0.54941	0.327000	0.23409	-0.441000	0.05720	ACA	.	.		0.637	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958		G	221057792	A	G	221057792	3	3	195	1	0	0	0	0	1	0	0	0	7225	43	2	2	1227	2	HLX	1	221057792	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	825481	221057792	28192829	24	28652										
DISC1	27185	hgsc.bcm.edu	37	chr1	231829938	231829938	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgggagtgctgggtggcagcAagagtttgcagccatggata	17	6	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:231829938A>G	ENST00000602281.1	+	2	487	c.434A>G	c.(433-435)cAa>cGa	p.Q145R	DISC1_ENST00000366636.4_Missense_Mutation_p.Q145R|DISC1_ENST00000366633.3_Missense_Mutation_p.Q145R|DISC1_ENST00000317586.4_Missense_Mutation_p.Q145R|DISC1_ENST00000537876.1_Missense_Mutation_p.Q145R|DISC1_ENST00000439617.2_Missense_Mutation_p.Q145R|DISC1_ENST00000366637.3_5'UTR|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000539444.1_Missense_Mutation_p.Q145R|DISC1_ENST00000535983.1_Missense_Mutation_p.Q145R	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	145	Interaction with MAP1A.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				GGGTGGCAGCAAGAGTTTGCA	0.627																																					p.Q145R		Atlas-SNP	.											.	DISC1	207	.	0			c.A434G						.						43	43	43					1																	231829938		2203	4300	6503	SO:0001583	missense	27185	exon2			GGCAGCAAGAGTT	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.434A>G	chr1.hg19:g.231829938A>G	ENSP00000473425:p.Gln145Arg	51.0	0.0		81.0	11.0	NM_001164541	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	hg19	CCDS59205.1	.	.	.	.	.	.	.	.	.	.	A	13.27	2.186019	0.38609	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000317586;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944	T;T;T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	4.65	-0.984	0.10259	.	0.928727	0.09182	N	0.837308	T	0.28599	0.0708	L	0.27053	0.805	0.09310	N	1	B;P;P;P;P;P;P;P;P;P;B;D;P;P;P;P;D;P;P;P;B	0.56035	0.037;0.902;0.902;0.902;0.902;0.902;0.902;0.902;0.902;0.902;0.1;0.974;0.949;0.902;0.763;0.763;0.974;0.763;0.763;0.902;0.1	B;P;B;P;B;B;P;P;B;P;B;P;P;P;B;B;P;B;B;B;B	0.53954	0.012;0.52;0.342;0.602;0.311;0.415;0.52;0.52;0.311;0.52;0.038;0.738;0.738;0.52;0.311;0.311;0.738;0.311;0.311;0.442;0.038	T	0.20273	-1.0280	10	0.59425	D	0.04	-1.9438	4.9586	0.14054	0.6538:0.1714:0.1749:0.0	.	145;145;145;145;145;145;145;145;145;145;145;145;145;145;145;145;145;145;145;145;145	C4P094;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P091;C4P0D2;C4P0D3;C4P0B1;A7E2W8;Q5T409;C4P0D0;Q9NRI5-2;Q9NRI5;Q9NRI5-3;Q9NRI5-4	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.;.	R	145	ENSP00000403888:Q145R;ENSP00000320784:Q145R;ENSP00000355596:Q145R;ENSP00000443996:Q145R;ENSP00000440909:Q145R;ENSP00000355593:Q145R;ENSP00000440953:Q145R;ENSP00000295051:Q145R;ENSP00000441193:Q145R	ENSP00000295051:Q145R	Q	+	2	0	DISC1	229896561	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.159000	0.10056	-0.162000	0.10964	0.533000	0.62120	CAA	.	.		0.627	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		G	231829938	A	G	231829938	3	3	195	1	0	0	0	0	1	0	0	0	4540	130	5	2	440	2	DISC1	1	231829938	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	10772146	231829938	17420683	25	28653										
C1orf101	257044	hgsc.bcm.edu	37	chr1	244643048	244643048	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gaacgctatttatttgtggaAagttctcatacttgctttct	7	7	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:244643048A>T	ENST00000366534.4	+	5	342	c.288A>T	c.(286-288)gaA>gaT	p.E96D	C1orf101_ENST00000366533.4_Missense_Mutation_p.E96D|C1orf101_ENST00000366531.3_De_novo_Start_InFrame|C1orf101_ENST00000473875.1_3'UTR	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	96						CatSper complex (GO:0036128)				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			TATTTGTGGAAAGTTCTCATA	0.299																																					p.E96D		Atlas-SNP	.											.	C1orf101	158	.	0			c.A288T						.						155	156	156					1																	244643048		2201	4295	6496	SO:0001583	missense	257044	exon5			TGTGGAAAGTTCT	BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.288A>T	chr1.hg19:g.244643048A>T	ENSP00000355492:p.Glu96Asp	100.0	0.0		190.0	39.0	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Missense_Mutation	SNP	ENST00000366534.4	hg19	CCDS44340.1	.	.	.	.	.	.	.	.	.	.	A	0.197	-1.047931	0.01981	.	.	ENSG00000179397	ENST00000391841;ENST00000366534;ENST00000366533;ENST00000428042	T;T;T	0.27402	1.68;1.68;1.67	4.27	-8.54	0.00912	.	0.895811	0.09385	N	0.809415	T	0.06142	0.0159	N	0.00926	-1.1	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.14896	-1.0456	10	0.11794	T	0.64	.	2.9625	0.05897	0.4949:0.1186:0.0814:0.3051	.	86;96;96	B1AQM6;Q5SY80;Q5SY80-2	.;CA101_HUMAN;.	D	96;96;96;86	ENSP00000355492:E96D;ENSP00000355491:E96D;ENSP00000395796:E86D	ENSP00000355491:E96D	E	+	3	2	C1orf101	242709671	0.000000	0.05858	0.000000	0.03702	0.289000	0.27227	-2.113000	0.01331	-3.502000	0.00151	-0.223000	0.12442	GAA	.	.		0.299	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807		T	244643048	A	T	244643048	3	4	195	1	0	0	0	0	1	0	0	0	1978	11	1	4	306	4	C1orf101	1	244643048	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	12813110	244643048	4607573	26	28654										
OR2G6	391211	hgsc.bcm.edu	37	chr1	248685500	248685500	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tctgtgaggtgccagtgctcAtcaaactggcctgtgtggat	13	9	3	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr1:248685500A>C	ENST00000343414.4	+	1	585	c.553A>C	c.(553-555)Atc>Ctc	p.I185L		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	185						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCCAGTGCTCATCAAACTGGC	0.507																																					p.I185L		Atlas-SNP	.											.	OR2G6	124	.	0			c.A553C						.						122	117	119					1																	248685500		2203	4300	6503	SO:0001583	missense	391211	exon1			GTGCTCATCAAAC		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"GPCR / Class A : Olfactory receptors"	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.553A>C	chr1.hg19:g.248685500A>C	ENSP00000341291:p.Ile185Leu	145.0	0.0		254.0	19.0	NM_001013355	B2RP33	Missense_Mutation	SNP	ENST00000343414.4	hg19	CCDS31119.1	.	.	.	.	.	.	.	.	.	.	N	2.466	-0.323102	0.05350	.	.	ENSG00000188558	ENST00000343414	T	0.00012	9.3	3.68	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	U	0.000414	T	0.00039	0.0001	N	0.04820	-0.15	0.09310	N	1	B	0.23316	0.083	B	0.27262	0.078	T	0.05954	-1.0854	10	0.05833	T	0.94	.	6.998	0.24793	0.766:0.2339:0.0:0.0	.	185	Q5TZ20	OR2G6_HUMAN	L	185	ENSP00000341291:I185L	ENSP00000341291:I185L	I	+	1	0	OR2G6	246752123	0.000000	0.05858	0.989000	0.46669	0.927000	0.56198	-0.367000	0.07553	1.523000	0.49018	0.329000	0.21502	ATC	.	.		0.507	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842		C	248685500	A	C	248685500	3	2	195	1	0	0	0	0	1	0	0	0	11009	217	8	5	555	5	OR2G6	1	248685500	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	4042452	248685500	565121	27	28655										
NT5C1B	93034	hgsc.bcm.edu	37	chr2	18757614	18757614	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	catgtctttggctccatcaaAcattgtcgcagaggcaatac	8	11	2	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:18757614A>C	ENST00000359846.2	-	9	1422	c.1345T>G	c.(1345-1347)Ttt>Gtt	p.F449V	NT5C1B_ENST00000600945.1_Missense_Mutation_p.F449V|NT5C1B-RDH14_ENST00000532967.1_Missense_Mutation_p.F449V|NT5C1B_ENST00000304081.4_Missense_Mutation_p.F389V	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	449					nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				GCTCCATCAAACATTGTCGCA	0.413																																					p.F466V		Atlas-SNP	.											.	NT5C1B	72	.	0			c.T1396G						.						92	85	87					2																	18757614		2203	4300	6503	SO:0001583	missense	93034	exon9			CATCAAACATTGT	AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.1345T>G	chr2.hg19:g.18757614A>C	ENSP00000352904:p.Phe449Val	358.0	0.0		368.0	66.0	NM_001199087	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Missense_Mutation	SNP	ENST00000359846.2	hg19	CCDS33150.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.5|20.5	4.002318|4.002318	0.74932|0.74932	.|.	.|.	ENSG00000250741;ENSG00000250741;ENSG00000185013;ENSG00000185013|ENSG00000185013	ENST00000532967;ENST00000444297;ENST00000304081;ENST00000359846|ENST00000418427	D|.	0.89196|.	-2.48|.	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	0.349704|.	0.37053|.	N|.	0.002264|.	T|T	0.63224|0.63224	0.2493|0.2493	L|L	0.48260|0.48260	1.515|1.515	0.58432|0.58432	D|D	0.999999|0.999999	P;P;P;P;P;P;P;P|.	0.48764|.	0.866;0.866;0.866;0.741;0.892;0.837;0.866;0.915|.	P;P;P;P;P;P;P;P|.	0.50896|.	0.593;0.593;0.593;0.491;0.575;0.457;0.593;0.653|.	T|T	0.60510|0.60510	-0.7249|-0.7249	10|5	0.41790|.	T|.	0.15|.	-19.8052|-19.8052	15.7698|15.7698	0.78157|0.78157	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	432;466;389;432;391;389;449;449|.	E7EXB7;B4DZ86;B4DXQ9;B4DXZ9;C9J2C7;Q96P26-2;Q96P26;Q96P26-4|.	.;.;.;.;.;.;5NT1B_HUMAN;.|.	V|G	449;391;389;449|103	ENSP00000412639:F391V|.	ENSP00000305979:F389V|.	F|V	-|-	1|2	0|0	NT5C1B-RDH14;NT5C1B|NT5C1B	18621095|18621095	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.729000|0.729000	0.41735|0.41735	9.265000|9.265000	0.95647|0.95647	2.189000|2.189000	0.69895|0.69895	0.533000|0.533000	0.62120|0.62120	TTT|GTT	.	.		0.413	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1			C	18757614	A	C	18757614	3	2	195	1	0	0	0	0	1	0	0	0	10695	43	2	5	495	5	NT5C1B	2	18757614	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10		18757614	224441759	28	28656										
CRIPT	9419	hgsc.bcm.edu	37	chr2	46846808	46846809	+	Frame_Shift_Ins	INS	-	-	A													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gaaaataaagctttgacttcINSaaaaaaagcaaggtgggtaa							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:46846808_46846809insA	ENST00000238892.3	+	3	257_258	c.125_126insA	c.(124-129)tcaaaafs	p.SK42fs	PIGF_ENST00000306465.4_5'Flank|PIGF_ENST00000495933.1_5'Flank|CRIPT_ENST00000486447.1_3'UTR|PIGF_ENST00000281382.6_5'Flank	NM_014171.4	NP_054890.1	Q9P021	CRIPT_HUMAN	cysteine-rich PDZ-binding protein	42					cytoplasmic microtubule organization (GO:0031122)|establishment of protein localization (GO:0045184)|protein localization to microtubule (GO:0035372)|regulation of postsynaptic density protein 95 clustering (GO:1902897)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)	microtubule binding (GO:0008017)|PDZ domain binding (GO:0030165)|protein complex binding (GO:0032403)			kidney(1)|large_intestine(1)|lung(2)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			GCTTTGACTTCAAAAAAAGCAA	0.322																																					p.S42fs		Pindel	.											.	CRIPT	9	.	0			c.125_126insA						.			0,4266		0,0,2133						5	1			57	1,8253		0,1,4126	no	frameshift	CRIPT	NM_014171.4		0,1,6259	A1A1,A1R,RR		0.0121,0.0,0.0080				1,12519				SO:0001589	frameshift_variant	9419	exon3			.	AA165108	CCDS1829.1	2p21	2008-02-05			ENSG00000119878	ENSG00000119878			14312	protein-coding gene	gene with protein product		604594				16091592, 11744724, 10570482, 9581762	Standard	NM_014171		Approved	HSPC139	uc002rve.3	Q9P021	OTTHUMG00000128815	ENST00000238892.3:c.132dupA	chr2.hg19:g.46846815_46846815dupA	ENSP00000238892:p.Ser42fs	630.0	0.0		652.0	61.0	NM_014171		Frame_Shift_Ins	INS	ENST00000238892.3	hg19	CCDS1829.1																																																																																			.	.		0.322	CRIPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250748.1	NM_014171		A	46846809	-	A	46846808	7	5	195	1	0	1	1	0	0	0	0	0	3880	838	29	0	135	0	CRIPT	2	46846808	Frame_Shift_Ins	INS	-	TCGA-DD-AADM-01A-11D-A40R-10	28089194	46846808	196352565	29	28657										
PUS10	150962	hgsc.bcm.edu	37	chr2	61236071	61236071	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gttcttgcagtcgaattttcTtgggaggtgggttcataact	12	6	3	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:61236071T>C	ENST00000316752.6	-	3	467	c.206A>G	c.(205-207)aAg>aGg	p.K69R	PUS10_ENST00000407787.1_Missense_Mutation_p.K69R	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	69					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			TCGAATTTTCTTGGGAGGTGG	0.368																																					p.K69R		Atlas-SNP	.											.	PUS10	49	.	0			c.A206G						.						67	65	66					2																	61236071		2203	4299	6502	SO:0001583	missense	150962	exon3			ATTTTCTTGGGAG	AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"coiled-coil domain containing 139"	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.206A>G	chr2.hg19:g.61236071T>C	ENSP00000326003:p.Lys69Arg	134.0	0.0		110.0	21.0	NM_144709	Q5JPJ5|Q96MI8	Missense_Mutation	SNP	ENST00000316752.6	hg19	CCDS1865.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.387402	0.82902	.	.	ENSG00000162927	ENST00000316752;ENST00000407787;ENST00000421319	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.79458	0.4449	M	0.84326	2.69	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79638	-0.1720	9	0.35671	T	0.21	-14.273	13.7534	0.62921	0.0:0.0:0.0:1.0	.	69	Q3MIT2	PUS10_HUMAN	R	69	.	ENSP00000326003:K69R	K	-	2	0	PUS10	61089575	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.968000	0.63728	2.142000	0.66516	0.477000	0.44152	AAG	.	.		0.368	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709		C	61236071	T	C	61236071	3	2	195	1	0	0	0	0	1	0	0	0	12846	1609	56	2	1447	2	PUS10	2	61236071	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	14389263	61236071	181963302	30	28658										
CCT4	10575	hgsc.bcm.edu	37	chr2	62107502	62107502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ggtgccatctcctgcttctaTatcttgagccttagacagct	8	12	3	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:62107502T>C	ENST00000394440.3	-	4	594	c.298A>G	c.(298-300)Ata>Gta	p.I100V	CCT4_ENST00000544185.1_Intron|CCT4_ENST00000544079.1_Missense_Mutation_p.I70V|AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000538252.1_Missense_Mutation_p.I44V	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	100					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			CCTGCTTCTATATCTTGAGCC	0.428																																					p.I100V		Atlas-SNP	.											.	CCT4	38	.	0			c.A298G						.						135	137	137					2																	62107502		2203	4300	6503	SO:0001583	missense	10575	exon4			CTTCTATATCTTG		CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"Heat Shock Proteins / Chaperonins"	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.298A>G	chr2.hg19:g.62107502T>C	ENSP00000377958:p.Ile100Val	87.0	0.0		84.0	16.0	NM_006430	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Missense_Mutation	SNP	ENST00000394440.3	hg19	CCDS33206.1	.	.	.	.	.	.	.	.	.	.	T	5.831	0.337646	0.11013	.	.	ENSG00000115484	ENST00000394440;ENST00000544079;ENST00000538252	T;T;T	0.78246	-1.16;-1.16;-1.16	5.65	4.5	0.54988	Chaperonin TCP-1, conserved site (1);	0.045054	0.85682	D	0.000000	T	0.54191	0.1843	N	0.05351	-0.065	0.80722	D	1	B;B	0.18013	0.025;0.014	B;B	0.19946	0.023;0.027	T	0.50092	-0.8868	10	0.02654	T	1	-17.0132	11.3032	0.49318	0.0:0.0719:0.0:0.9281	.	70;100	F5H5W3;P50991	.;TCPD_HUMAN	V	100;70;44	ENSP00000377958:I100V;ENSP00000443061:I70V;ENSP00000442174:I44V	ENSP00000377958:I100V	I	-	1	0	CCT4	61961006	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.145000	0.58065	0.978000	0.38470	0.533000	0.62120	ATA	.	.		0.428	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2			C	62107502	T	C	62107502	3	2	195	1	0	0	0	0	1	0	0	0	2957	1406	49	2	1365	2	CCT4	2	62107502	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	871431	62107502	181091871	31	28659										
RIF1	55183	hgsc.bcm.edu	37	chr2	152267846	152267846	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cttcctcggctgtacaaagtTttaaaggtatgtatctgttt	8	7	1	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:152267846T>G	ENST00000243326.5	+	2	660	c.177T>G	c.(175-177)gtT>gtG	p.V59V	RIF1_ENST00000453091.2_Silent_p.V59V|RIF1_ENST00000433166.2_Silent_p.V59V|RIF1_ENST00000444746.2_Silent_p.V59V|RIF1_ENST00000428287.2_Silent_p.V59V|RIF1_ENST00000430328.2_Silent_p.V59V			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TGTACAAAGTTTTAAAGGTAT	0.308																																					p.V59V		Atlas-SNP	.											.	RIF1	244	.	0			c.T177G						.						77	85	82					2																	152267846		2203	4300	6503	SO:0001819	synonymous_variant	55183	exon3			CAAAGTTTTAAAG	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.177T>G	chr2.hg19:g.152267846T>G		714.0	0.0		786.0	92.0	NM_018151	A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	hg19	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	T	1.485	-0.556207	0.03967	.	.	ENSG00000080345	ENST00000414861	.	.	.	4.93	1.05	0.20165	.	.	.	.	.	T	0.26195	0.0639	.	.	.	0.31836	N	0.624086	.	.	.	.	.	.	T	0.32640	-0.9899	4	.	.	.	-2.0877	0.2974	0.00267	0.2341:0.2015:0.147:0.4174	.	.	.	.	V	51	.	.	F	+	1	0	RIF1	151976092	0.916000	0.31088	0.836000	0.33094	0.198000	0.23893	-0.246000	0.08878	0.747000	0.32809	0.460000	0.39030	TTT	.	.		0.308	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			G	152267846	T	G	152267846	2	3	195	1	0	0	0	0	0	0	0	1	13374	1828	64	5		5	RIF1	2	152267846	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	90160344	152267846	90931527	32	28660										
KLHL23	151230	hgsc.bcm.edu	37	chr2	170597991	170597991	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctgcacctatgacaaagttcAgagctacaattccgatatca	6	11	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:170597991A>G	ENST00000392647.2	+	3	1554	c.1310A>G	c.(1309-1311)cAg>cGg	p.Q437R	KLHL23_ENST00000272797.4_Missense_Mutation_p.Q437R|KLHL23_ENST00000602521.1_5'UTR	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	437										breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						GACAAAGTTCAGAGCTACAAT	0.443																																					p.Q437R		Atlas-SNP	.											.	KLHL23	52	.	0			c.A1310G						.						166	141	150					2																	170597991		2203	4300	6503	SO:0001583	missense	151230	exon3			AAGTTCAGAGCTA	BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160		"Kelch-like", "BTB/POZ domain containing"	27506	protein-coding gene	gene with protein product			"kelch-like 23 (Drosophila)"				Standard	NM_144711		Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000392647.2:c.1310A>G	chr2.hg19:g.170597991A>G	ENSP00000376419:p.Gln437Arg	139.0	0.0		143.0	14.0	NM_144711	Q8N9B9|Q96FT8	Missense_Mutation	SNP	ENST00000392647.2	hg19	CCDS2236.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.926576	0.92319	.	.	ENSG00000213160	ENST00000272797;ENST00000392647;ENST00000437875	T;T;T	0.77750	-1.12;-1.12;-1.12	5.77	5.77	0.91146	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.89911	0.6852	M	0.89095	3.005	0.29060	N	0.883976	D	0.89917	1.0	D	0.87578	0.998	D	0.91760	0.5419	9	0.87932	D	0	.	16.0977	0.81139	1.0:0.0:0.0:0.0	.	437	Q8NBE8	KLH23_HUMAN	R	437;437;258	ENSP00000272797:Q437R;ENSP00000376419:Q437R;ENSP00000394732:Q258R	ENSP00000272797:Q437R	Q	+	2	0	KLHL23	170306237	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	9.339000	0.96797	2.216000	0.71823	0.528000	0.53228	CAG	.	.		0.443	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711		G	170597991	A	G	170597991	3	3	195	1	0	0	0	0	1	0	0	0	8387	188	7	2	1316	2	KLHL23	2	170597991	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	18330145	170597991	72601382	33	28661										
TTN	7273	hgsc.bcm.edu	37	chr2	179574355	179574355	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cattggacactttgcatgtgTacaaaccagcgtcgttcatg	9	10	1	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:179574355T>C	ENST00000591111.1	-	97	27964	c.27740A>G	c.(27739-27741)tAc>tGc	p.Y9247C	TTN_ENST00000342992.6_Missense_Mutation_p.Y8320C|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.Y9564C|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13370	Ig-like 75.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTGCATGTGTACAAACCAGC	0.438																																					p.Y9564C		Atlas-SNP	.											.	TTN	18412	.	0			c.A28691G						.						164	168	166					2																	179574355		2059	4198	6257	SO:0001583	missense	7273	exon99			CATGTGTACAAAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.27740A>G	chr2.hg19:g.179574355T>C	ENSP00000465570:p.Tyr9247Cys	121.0	0.0		148.0	25.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.36	2.513640	0.44763	.	.	ENSG00000155657	ENST00000342992	T	0.79554	-1.28	5.91	5.91	0.95273	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.93582	0.7951	H	0.97587	4.035	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95688	0.8738	9	0.87932	D	0	.	16.3483	0.83171	0.0:0.0:0.0:1.0	.	9247	Q8WZ42	TITIN_HUMAN	C	8320	ENSP00000343764:Y8320C	ENSP00000343764:Y8320C	Y	-	2	0	TTN	179282600	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	8.040000	0.89188	2.254000	0.74563	0.533000	0.62120	TAC	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179574355	T	C	179574355	3	2	195	1	0	0	0	0	1	0	0	0	16750	1638	57	2	75894	2	TTN	2	179574355	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	8976364	179574355	63625018	34	28662										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196636398	196636398	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccttaccttgattgctttttGaatatttacgcacgaatctc	5	10	1	2	rs57513754		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:196636398G>A	ENST00000312428.6	-	61	11519	c.11419C>T	c.(11419-11421)Caa>Taa	p.Q3807*	DNAH7_ENST00000409063.1_Nonsense_Mutation_p.Q290*	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3807					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						ATTGCTTTTTGAATATTTACG	0.338																																					p.Q3807X		Atlas-SNP	.											.	DNAH7	512	.	0			c.C11419T						.						175	155	161					2																	196636398		1838	4102	5940	SO:0001587	stop_gained	56171	exon61			CTTTTTGAATATT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.11419C>T	chr2.hg19:g.196636398G>A	ENSP00000311273:p.Gln3807*	112.0	0.0		107.0	45.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Nonsense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	G	36	5.771063	0.96914	.	.	ENSG00000118997	ENST00000312428;ENST00000409063	.	.	.	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	.	18.2425	0.89971	0.0:0.0:1.0:0.0	.	.	.	.	X	3807;290	.	ENSP00000311273:Q3807X	Q	-	1	0	DNAH7	196344643	1.000000	0.71417	0.998000	0.56505	0.849000	0.48306	6.695000	0.74593	2.630000	0.89119	0.655000	0.94253	CAA	.	.		0.338	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196636398	G	A	196636398	4	1	195	1	0	0	0	0	0	1	0	0	4608	1299	45	3	675	3	DNAH7	2	196636398	Nonsense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	17062043	196636398	46562975	35	28663										
RUFY4	285180	hgsc.bcm.edu	37	chr2	218939937	218939937	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	agggcttcccaggtcccagcAacaaaggcatcttcctttct	8	14	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:218939937A>G	ENST00000344321.7	+	9	1240	c.722A>G	c.(721-723)cAa>cGa	p.Q241R	RUFY4_ENST00000441828.2_3'UTR|RUFY4_ENST00000374155.3_Missense_Mutation_p.Q261R|RUFY4_ENST00000463872.1_3'UTR	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	241							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		AGGTCCCAGCAACAAAGGCAT	0.527																																					p.Q241R		Atlas-SNP	.											.	RUFY4	59	.	0			c.A722G						.						23	25	25					2																	218939937		1928	4147	6075	SO:0001583	missense	285180	exon9			CCCAGCAACAAAG	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"Zinc fingers, FYVE domain containing"	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.722A>G	chr2.hg19:g.218939937A>G	ENSP00000345900:p.Gln241Arg	311.0	0.0		341.0	77.0	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	hg19		.	.	.	.	.	.	.	.	.	.	A	10.10	1.256792	0.22965	.	.	ENSG00000188282	ENST00000344321;ENST00000374155	T;T	0.44482	1.53;0.92	4.37	-2.51	0.06365	.	0.869159	0.09610	N	0.779036	T	0.21962	0.0529	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.25363	-1.0134	10	0.19147	T	0.46	-0.0885	1.2137	0.01910	0.2746:0.369:0.2093:0.1472	.	241	Q6ZNE9	RUFY4_HUMAN	R	241;261	ENSP00000345900:Q241R;ENSP00000363270:Q261R	ENSP00000345900:Q241R	Q	+	2	0	RUFY4	218648182	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.074000	0.11450	-0.046000	0.13446	0.383000	0.25322	CAA	.	.		0.527	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483		G	218939937	A	G	218939937	3	3	195	1	0	0	0	0	1	0	0	0	13756	130	5	2	748	2	RUFY4	2	218939937	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	22303539	218939937	24259436	36	28664										
ACSL3	2181	hgsc.bcm.edu	37	chr2	223781203	223781203	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgcacaggcgtgttttatgtAtaattttcagcgtatgtaga	10	5	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:223781203A>G	ENST00000357430.3	+	5	1076	c.545A>G	c.(544-546)tAt>tGt	p.Y182C	AC097461.4_ENST00000446709.1_RNA|ACSL3_ENST00000392066.3_Missense_Mutation_p.Y182C	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	182					brain development (GO:0007420)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty acid import (GO:0044539)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)|positive regulation of phosphatidylcholine biosynthetic process (GO:2001247)|positive regulation of secretion (GO:0051047)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)|skin(2)	22		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	TGTTTTATGTATAATTTTCAG	0.378			T	ETV1	prostate																																p.Y182C		Atlas-SNP	.		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	.	ACSL3	107	.	0			c.A545G						.						135	130	132					2																	223781203		2203	4300	6503	SO:0001583	missense	2181	exon4			TTATGTATAATTT	D89053	CCDS2455.1	2q34-q35	2008-02-05	2004-02-19	2004-02-20	ENSG00000123983	ENSG00000123983		"Acyl-CoA synthetase family"	3570	protein-coding gene	gene with protein product		602371	"fatty-acid-Coenzyme A ligase, long-chain 3"	FACL3			Standard	NM_004457		Approved	ACS3, PRO2194	uc002vnj.3	O95573	OTTHUMG00000133160	ENST00000357430.3:c.545A>G	chr2.hg19:g.223781203A>G	ENSP00000350012:p.Tyr182Cys	107.0	0.0		126.0	46.0	NM_203372	Q60I92|Q8IUM9	Missense_Mutation	SNP	ENST00000357430.3	hg19	CCDS2455.1	.	.	.	.	.	.	.	.	.	.	A	13.57	2.276933	0.40294	.	.	ENSG00000123983	ENST00000357430;ENST00000392066;ENST00000540115	T;T;T	0.40476	1.03;1.03;1.03	5.07	5.07	0.68467	AMP-dependent synthetase/ligase (1);	0.125773	0.56097	D	0.000030	T	0.48554	0.1506	M	0.87758	2.905	0.58432	D	0.999993	B	0.12630	0.006	B	0.18263	0.021	T	0.54050	-0.8351	10	0.62326	D	0.03	-16.2479	9.9807	0.41811	0.9131:0.0:0.0869:0.0	.	182	O95573	ACSL3_HUMAN	C	182;182;30	ENSP00000350012:Y182C;ENSP00000375918:Y182C;ENSP00000441643:Y30C	ENSP00000350012:Y182C	Y	+	2	0	ACSL3	223489447	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.206000	0.65192	2.031000	0.59945	0.533000	0.62120	TAT	.	.		0.378	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457		G	223781203	A	G	223781203	3	3	195	1	0	0	0	0	1	0	0	0	178	449	16	2	551	2	ACSL3	2	223781203	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	4841266	223781203	19418170	37	28665										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228883428	228883428	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aacgtgaagcatatcacatcTaaaagcagttgatttgtact	7	7	2	2	rs34143542		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:228883428T>A	ENST00000392056.3	-	7	2188	c.2142A>T	c.(2140-2142)ttA>ttT	p.L714F	SPHKAP_ENST00000344657.5_Missense_Mutation_p.L714F	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	714						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		ATATCACATCTAAAAGCAGTT	0.408																																					p.L714F		Atlas-SNP	.											.	SPHKAP	750	.	0			c.A2142T						.						201	181	188					2																	228883428		2203	4300	6503	SO:0001583	missense	80309	exon7			CACATCTAAAAGC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.2142A>T	chr2.hg19:g.228883428T>A	ENSP00000375909:p.Leu714Phe	87.0	0.0		84.0	26.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	hg19	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.461283	0.01062	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.37915	1.17;1.17	5.62	0.707	0.18139	.	0.139121	0.64402	N	0.000003	T	0.05273	0.0140	N	0.00142	-2.005	0.20307	N	0.999917	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.37549	-0.9701	10	0.02654	T	1	.	2.9806	0.05952	0.3523:0.0:0.332:0.3157	.	714;714	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	F	714	ENSP00000375909:L714F;ENSP00000339886:L714F	ENSP00000339886:L714F	L	-	3	2	SPHKAP	228591672	1.000000	0.71417	0.854000	0.33618	0.456000	0.32438	1.968000	0.40500	0.119000	0.18210	-0.795000	0.03280	TTA	.	.		0.408	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228883428	T	A	228883428	3	1	195	1	0	0	0	0	1	0	0	0	15063	1519	53	4	2984	4	SPHKAP	2	228883428	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	5102225	228883428	14315945	38	28666										
NGEF	25791	hgsc.bcm.edu	37	chr2	233757625	233757626	+	Frame_Shift_Ins	INS	-	-	CG													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	acagcagctgcttataggtcINScgctcctggtaggtctgatt							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:233757625_233757626insCG	ENST00000264051.3	-	7	1402_1403	c.1124_1125insCG	c.(1123-1125)cggfs	p.R375fs	NGEF_ENST00000539537.1_Frame_Shift_Ins_p.R98fs|NGEF_ENST00000373552.4_Frame_Shift_Ins_p.R283fs	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	375	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		GCTTATAGGTCCGCTCCTGGTA	0.584																																					p.R375fs		Atlas-Indel,Pindel	.											.	NGEF	198	.	0			c.1125_1126insCG						.																																			SO:0001589	frameshift_variant	25791	exon7			.	AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"Rho guanine nucleotide exchange factors"	7807	protein-coding gene	gene with protein product	"ephexin"	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.1123_1124dupCG	chr2.hg19:g.233757626_233757627dupCG	ENSP00000264051:p.Arg375fs	101.0	0.0		114.0	17.0	NM_019850	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Frame_Shift_Ins	INS	ENST00000264051.3	hg19	CCDS2500.1																																																																																			.	.		0.584	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799		CG	233757626	-	CG	233757625	7	5	195	1	0	1	1	0	0	0	0	0	10403	842	30	0	1043	0	NGEF	2	233757625	Frame_Shift_Ins	INS	-	TCGA-DD-AADM-01A-11D-A40R-10	4874197	233757625	9441748	39	28667										
MYEOV2	150678	hgsc.bcm.edu	37	chr2	241066176	241066176	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccagccacttggattggttcTtccgtaaactgtttcttaag	8	10	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr2:241066176T>G	ENST00000307266.3	-	5	562	c.563A>C	c.(562-564)aAg>aCg	p.K188T		NM_138336.1	NP_612209.1	Q8WXC6	MYOV2_HUMAN	myeloma overexpressed 2	0										breast(1)|lung(5)|pancreas(1)	7		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)		GGATTGGTTCTTCCGTAAACT	0.478																																					p.K188T		Atlas-SNP	.											.	MYEOV2	20	.	0			c.A563C						.						251	247	248					2																	241066176		2203	4300	6503	SO:0001583	missense	150678	exon5			TGGTTCTTCCGTA	AF453951	CCDS2532.1, CCDS63183.1	2q37.3	2008-02-05			ENSG00000172428	ENSG00000172428			21314	protein-coding gene	gene with protein product							Standard	NM_138336		Approved		uc002vyu.1	Q8WXC6	OTTHUMG00000133352	ENST00000307266.3:c.563A>C	chr2.hg19:g.241066176T>G	ENSP00000304147:p.Lys188Thr	159.0	0.0		146.0	17.0	NM_138336	Q8N110	Missense_Mutation	SNP	ENST00000307266.3	hg19	CCDS2532.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.685673	0.29962	.	.	ENSG00000172428	ENST00000307266	.	.	.	1.78	-0.741	0.11112	.	.	.	.	.	T	0.46619	0.1402	.	.	.	0.09310	N	1	D	0.55172	0.97	P	0.55713	0.782	T	0.36456	-0.9747	7	0.87932	D	0	.	4.2445	0.10665	0.0:0.407:0.0:0.593	.	188	Q8WXC6-1	.	T	188	.	ENSP00000304147:K188T	K	-	2	0	MYEOV2	240714849	0.001000	0.12720	0.000000	0.03702	0.011000	0.07611	-0.140000	0.10342	-0.181000	0.10619	0.338000	0.21704	AAG	.	.		0.478	MYEOV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257182.2	NM_138336		G	241066176	T	G	241066176	3	3	195	1	0	0	0	0	1	0	0	0	10035	1609	56	5	199	5	MYEOV2	2	241066176	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	7308551	241066176	2133197	40	28668										
TTC21A	199223	hgsc.bcm.edu	37	chr3	39152495	39152495	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccgcatgctgaagatttctaGaggcttcagagaggtactta	11	8	2	4			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:39152495G>C	ENST00000431162.2	+	4	556	c.422G>C	c.(421-423)aGa>aCa	p.R141T	GORASP1_ENST00000319283.3_5'Flank|TTC21A_ENST00000301819.6_Missense_Mutation_p.R141T|TTC21A_ENST00000440121.1_Missense_Mutation_p.R141T			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	141										NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AAGATTTCTAGAGGCTTCAGA	0.522																																					p.R141T		Atlas-SNP	.											.	TTC21A	96	.	0			c.G422C						.						67	69	68					3																	39152495		1958	4165	6123	SO:0001583	missense	199223	exon4			TTTCTAGAGGCTT	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"Tetratricopeptide (TTC) repeat domain containing"	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.422G>C	chr3.hg19:g.39152495G>C	ENSP00000398211:p.Arg141Thr	70.0	0.0		86.0	11.0	NM_001105513	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	hg19	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	1.264	-0.615034	0.03663	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.63096	0.01;0.01;-0.02	5.74	-5.88	0.02290	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	1.902520	0.02061	N	0.050794	T	0.43831	0.1265	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.001;0.001	T	0.21008	-1.0258	10	0.31617	T	0.26	1.7895	6.615	0.22773	0.6378:0.1018:0.1573:0.1031	.	141;141;141;141;141	Q8NDW8-6;Q8NDW8-5;Q8NDW8-7;Q8NDW8;F5H6V8	.;.;.;TT21A_HUMAN;.	T	141	ENSP00000301819:R141T;ENSP00000398211:R141T;ENSP00000410882:R141T	ENSP00000301819:R141T	R	+	2	0	TTC21A	39127499	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.095000	0.11077	-1.530000	0.01751	-0.140000	0.14226	AGA	.	.		0.522	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		C	39152495	G	C	39152495	3	2	195	1	0	0	0	0	1	0	0	0	16702	942	33	4	436	4	TTC21A	3	39152495	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10		39152495	158869935	41	28669										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41274911	41274911	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgtctttggactctcaggaaTctttcagatgctgcaactaa	8	9	4	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:41274911T>A	ENST00000349496.5	+	8	1441	c.1161T>A	c.(1159-1161)aaT>aaA	p.N387K	CTNNB1_ENST00000396183.3_Missense_Mutation_p.N387K|CTNNB1_ENST00000396185.3_Missense_Mutation_p.N387K|CTNNB1_ENST00000453024.1_Missense_Mutation_p.N380K|CTNNB1_ENST00000405570.1_Missense_Mutation_p.N387K	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	387					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.N387K(4)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTCTCAGGAATCTTTCAGATG	0.393		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.N387K	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,5	CTNNB1	4904	.	4	Substitution - Missense(4)	large_intestine(1)|prostate(1)|liver(1)|kidney(1)	c.T1161A						.						102	93	96					3																	41274911		2203	4300	6503	SO:0001583	missense	1499	exon8	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CAGGAATCTTTCA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1161T>A	chr3.hg19:g.41274911T>A	ENSP00000344456:p.Asn387Lys	141.0	1.0		153.0	19.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	19.46	3.832364	0.71258	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79	5.72	1.33	0.21861	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.90263	0.6955	M	0.89478	3.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.88091	0.2813	10	0.54805	T	0.06	-10.1444	8.463	0.32938	0.0:0.3714:0.0:0.6286	.	315;387	B4DSW9;P35222	.;CTNB1_HUMAN	K	387;387;387;380;387	ENSP00000385604:N387K;ENSP00000379486:N387K;ENSP00000344456:N387K;ENSP00000411226:N380K;ENSP00000379488:N387K	ENSP00000344456:N387K	N	+	3	2	CTNNB1	41249915	0.995000	0.38212	0.998000	0.56505	0.998000	0.95712	0.358000	0.20216	0.227000	0.20999	0.533000	0.62120	AAT	.	.		0.393	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41274911	T	A	41274911	3	1	195	1	0	0	0	0	1	0	0	0	4018	1432	50	4	1187	4	CTNNB1	3	41274911	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	2122416	41274911	156747519	42	28670										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108380762	108380762	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	actacagactatggagaaacTgaaaaggaaaggcttgctcg	11	7	0	3			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:108380762T>A	ENST00000361582.3	+	20	2468	c.2238T>A	c.(2236-2238)acT>acA	p.T746T	DZIP3_ENST00000463306.1_Silent_p.T746T	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	746					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						ATGGAGAAACTGAAAAGGAAA	0.348																																					p.T746T		Atlas-SNP	.											.	DZIP3	111	.	0			c.T2238A						.						105	106	106					3																	108380762		2203	4300	6503	SO:0001819	synonymous_variant	9666	exon20			AGAAACTGAAAAG	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2238T>A	chr3.hg19:g.108380762T>A		428.0	1.0		425.0	163.0	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Silent	SNP	ENST00000361582.3	hg19	CCDS2952.1																																																																																			.	.		0.348	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		A	108380762	T	A	108380762	2	1	195	1	0	0	0	0	0	0	0	1	4867	1567	55	4		4	DZIP3	3	108380762	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	67105851	108380762	89641668	43	28671										
LSAMP	4045	hgsc.bcm.edu	37	chr3	115529252	115529252	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	atccatttattcctctcaccGacccaggtcctgcagagcaa	6	15	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:115529252G>A	ENST00000490035.2	-	7	1428	c.929C>T	c.(928-930)tCg>tTg	p.S310L	LSAMP_ENST00000539563.1_Missense_Mutation_p.S330L	NM_002338.3	NP_002329.2	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	310					cell adhesion (GO:0007155)|locomotory exploration behavior (GO:0035641)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(1)|large_intestine(4)|lung(14)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		TCCTCTCACCGACCCAGGTCC	0.463																																					p.S310L		Atlas-SNP	.											LSAMP,NS,carcinoma,0,1	LSAMP	62	.	0			c.C929T						.						44	44	44					3																	115529252		2203	4300	6503	SO:0001583	missense	4045	exon7			CTCACCGACCCAG	U41901	CCDS2982.1	3q13.2-q21	2013-01-11			ENSG00000185565	ENSG00000185565		"Immunoglobulin superfamily / I-set domain containing"	6705	protein-coding gene	gene with protein product	"IgLON family member 3"	603241				9615236	Standard	NM_002338		Approved	LAMP, IGLON3	uc003ebs.3	Q13449	OTTHUMG00000159308	ENST00000490035.2:c.929C>T	chr3.hg19:g.115529252G>A	ENSP00000419000:p.Ser310Leu	252.0	1.0		252.0	59.0	NM_002338	Q8IV49	Missense_Mutation	SNP	ENST00000490035.2	hg19	CCDS2982.1	.	.	.	.	.	.	.	.	.	.	G	17.22	3.334713	0.60853	.	.	ENSG00000185565	ENST00000333617;ENST00000490035;ENST00000539563	T;T;T	0.58506	0.4;0.67;0.33	6.06	6.06	0.98353	.	0.168326	0.39615	N	0.001308	T	0.42337	0.1198	N	0.08118	0	0.36650	D	0.877368	B;B	0.27140	0.021;0.169	B;B	0.17433	0.005;0.018	T	0.48433	-0.9036	10	0.72032	D	0.01	0.2826	20.6243	0.99512	0.0:0.0:1.0:0.0	.	310;310	B2RCU8;Q13449	.;LSAMP_HUMAN	L	317;310;330	ENSP00000328455:S317L;ENSP00000419000:S310L;ENSP00000443429:S330L	ENSP00000328455:S317L	S	-	2	0	LSAMP	117011942	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.385000	0.73182	2.879000	0.98667	0.650000	0.86243	TCG	.	.		0.463	LSAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354495.4	NM_002338		A	115529252	G	A	115529252	3	1	195	1	0	0	0	0	1	0	0	0	9057	1059	37	1	91	1	LSAMP	3	115529252	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	7148490	115529252	82493178	44	28672										
CCDC14	64770	hgsc.bcm.edu	37	chr3	123634282	123634283	+	Frame_Shift_Ins	INS	-	-	A													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tccatgcccctagtgttactINSattttgagggcctctggagg							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:123634282_123634283insA	ENST00000488653.2	-	13	2295_2296	c.2205_2206insT	c.(2203-2208)aatagtfs	p.S736fs	CCDC14_ENST00000433542.2_Frame_Shift_Ins_p.S695fs|CCDC14_ENST00000485727.1_Frame_Shift_Ins_p.S536fs|CCDC14_ENST00000483247.1_Intron|CCDC14_ENST00000489746.1_Frame_Shift_Ins_p.S536fs|CCDC14_ENST00000310351.4_Frame_Shift_Ins_p.S576fs			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	736					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		CTAGTGTTACTATTTTGAGGGC	0.406																																					p.S695_N696delinsX		Atlas-Indel,Pindel	.											.	CCDC14	97	.	0			c.2083_2084insT						.																																			SO:0001589	frameshift_variant	64770	exon12			.	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.2206dupT	chr3.hg19:g.123634283_123634283dupA	ENSP00000420180:p.Ser736fs	113.0	0.0		93.0	23.0	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Frame_Shift_Ins	INS	ENST00000488653.2	hg19																																																																																				.	.		0.406	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757		A	123634283	-	A	123634282	7	5	195	1	0	1	1	0	0	0	0	0	2775	1522	53	0	659	0	CCDC14	3	123634282	Frame_Shift_Ins	INS	-	TCGA-DD-AADM-01A-11D-A40R-10	8105030	123634282	74388148	45	28673										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130110508	130110508	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgagggtatggcagggaataAaaacaatactatctatgtag	11	4	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:130110508A>C	ENST00000432398.2	+	7	3397	c.2903A>C	c.(2902-2904)aAa>aCa	p.K968T	COL6A5_ENST00000265379.6_Missense_Mutation_p.K968T	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	968	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GCAGGGAATAAAAACAATACT	0.393																																					p.K968T		Atlas-SNP	.											.	COL6A5	205	.	0			c.A2903C						.						45	36	39					3																	130110508		692	1591	2283	SO:0001583	missense	256076	exon7			GGAATAAAAACAA	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.2903A>C	chr3.hg19:g.130110508A>C	ENSP00000390895:p.Lys968Thr	555.0	0.0		572.0	71.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.	.	.	.	.	.	.	.	.	.	A	7.396	0.631799	0.14322	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.77750	-1.12;-1.12	5.71	4.56	0.56223	.	.	.	.	.	T	0.66694	0.2815	L	0.35542	1.07	0.09310	N	1	B	0.32918	0.39	B	0.34824	0.19	T	0.56469	-0.7974	9	0.36615	T	0.2	.	6.954	0.24560	0.7735:0.1495:0.077:0.0	.	968	A8TX70-2	.	T	968	ENSP00000390895:K968T;ENSP00000265379:K968T	ENSP00000265379:K968T	K	+	2	0	COL6A5	131593198	0.000000	0.05858	0.025000	0.17156	0.017000	0.09413	0.712000	0.25779	1.002000	0.39104	0.528000	0.53228	AAA	.	.		0.393	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		C	130110508	A	C	130110508	3	2	195	1	0	0	0	0	1	0	0	0	3704	14	1	5	2925	5	COL6A5	3	130110508	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	6476226	130110508	67911922	46	28674										
PIK3CB	5291	hgsc.bcm.edu	37	chr3	138478168	138478168	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tctgccatagcaggaggcatTatgaaactgaagcacattca	9	9	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:138478168T>G	ENST00000477593.1	-	2	91	c.18A>C	c.(16-18)atA>atC	p.I6I	PIK3CB_ENST00000289153.2_Silent_p.I6I			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	6					activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	CAGGAGGCATTATGAAACTGA	0.428																																					p.I6I		Atlas-SNP	.											.	PIK3CB	103	.	0			c.A18C						.						86	82	83					3																	138478168		2203	4300	6503	SO:0001819	synonymous_variant	5291	exon1			AGGCATTATGAAA		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.18A>C	chr3.hg19:g.138478168T>G		391.0	0.0		353.0	47.0	NM_006219	D3DNF0|Q24JU2	Silent	SNP	ENST00000477593.1	hg19	CCDS3104.1																																																																																			.	.		0.428	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			G	138478168	T	G	138478168	2	3	195	1	0	0	0	0	0	0	0	1	11923	1744	61	5		5	PIK3CB	3	138478168	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	8367660	138478168	59544262	47	28675										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140401718	140401718	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	atcgcttacaagcgctgcatCacctgccgcctcaacctgtg	8	16	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:140401718C>A	ENST00000286349.3	+	2	947	c.756C>A	c.(754-756)atC>atA	p.I252I		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	252						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AGCGCTGCATCACCTGCCGCC	0.622																																					p.I252I		Atlas-SNP	.											.	TRIM42	143	.	0			c.C756A						.						93	85	87					3																	140401718		2203	4300	6503	SO:0001819	synonymous_variant	287015	exon2			CTGCATCACCTGC	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.756C>A	chr3.hg19:g.140401718C>A		83.0	0.0		74.0	17.0	NM_152616	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	hg19	CCDS3113.1																																																																																			.	.		0.622	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		A	140401718	C	A	140401718	2	1	195	1	0	0	0	0	0	0	0	1	16532	816	29	3		3	TRIM42	3	140401718	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	1923550	140401718	57620712	48	28676										
KPNA4	3840	hgsc.bcm.edu	37	chr3	160233335	160233335	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgtttgctcatcagttccagTaacaatgttgcccacagctc	7	12	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:160233335T>C	ENST00000334256.4	-	12	1242	c.937A>G	c.(937-939)Act>Gct	p.T313A	SCARNA7_ENST00000458797.1_RNA	NM_002268.4	NP_002259.1	O00629	IMA3_HUMAN	karyopherin alpha 4 (importin alpha 3)	313	NLS binding site (minor). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)	22			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			TCAGTTCCAGTAACAATGTTG	0.388																																					p.T313A		Atlas-SNP	.											.	KPNA4	50	.	0			c.A937G						.						114	96	102					3																	160233335		2203	4300	6503	SO:0001583	missense	3840	exon12			TTCCAGTAACAAT	AB002533	CCDS3191.1	3q25.33	2013-02-14			ENSG00000186432	ENSG00000186432		"Importins", "Armadillo repeat containing"	6397	protein-coding gene	gene with protein product		602970				9168958, 9395085	Standard	NM_002268		Approved	QIP1, SRP3, IPOA3, MGC12217, MGC26703	uc003fdn.3	O00629	OTTHUMG00000159033	ENST00000334256.4:c.937A>G	chr3.hg19:g.160233335T>C	ENSP00000334373:p.Thr313Ala	271.0	0.0		258.0	95.0	NM_002268	A8K4S6|D3DNM2|O00190	Missense_Mutation	SNP	ENST00000334256.4	hg19	CCDS3191.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.821722	0.90873	.	.	ENSG00000186432	ENST00000334256;ENST00000483437	T;T	0.29142	1.58;1.58	5.55	5.55	0.83447	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.60104	0.2243	M	0.82923	2.615	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66320	-0.5953	10	0.87932	D	0	-5.4707	15.9896	0.80193	0.0:0.0:0.0:1.0	.	313	O00629	IMA4_HUMAN	A	313;18	ENSP00000334373:T313A;ENSP00000417172:T18A	ENSP00000334373:T313A	T	-	1	0	KPNA4	161716029	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.886000	0.87288	2.238000	0.73509	0.533000	0.62120	ACT	.	.		0.388	KPNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352960.1	NM_002268		C	160233335	T	C	160233335	3	2	195	1	0	0	0	0	1	0	0	0	8441	1638	57	2	652	2	KPNA4	3	160233335	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	19831617	160233335	37789095	49	28677										
CCDC50	152137	hgsc.bcm.edu	37	chr3	191093078	191093078	+	Intron	DEL	A	A	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	acaatgagcagcatgaaaggAaacggtccactcaggagagg							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:191093078delA	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Frame_Shift_Del_p.K226fs	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		GCATGAAAGGAAACGGTCCAC	0.493																																					p.R225fs		Atlas-INDEL	.											.	CCDC50	39	.	0			c.675delG						.						80	73	75					3																	191093078		2203	4300	6503	SO:0001627	intron_variant	152137	exon6			.	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"deafness, autosomal dominant 44"	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-4870A>-	chr3.hg19:g.191093078delA		193.0	0.0		182.0	22.0	NM_178335	Q86VH7	Frame_Shift_Del	DEL	ENST00000392455.3	hg19	CCDS33913.1																																																																																			.	.		0.493	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908		-	191093078	A	-	191093078	6	5	195	0	1	1	0	1	0	0	0	0	2822	247	9	0		0	CCDC50	3	191093078	Intron	DEL	A	TCGA-DD-AADM-01A-11D-A40R-10	30859743	191093078	6929352	50	28678	145	2								
CCDC50	152137	hgsc.bcm.edu	37	chr3	191093079	191093080	+	Intron	DEL	AA	AA	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	caatgagcagcatgaaaggaAacggtccactcaggagaggc					rs2028573	byFrequency	TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr3:191093079_191093080delAA	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Frame_Shift_Del_p.K226fs	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		CATGAAAGGAAACGGTCCACTC	0.5																																					p.226_226del		Pindel	.											.	CCDC50	39	.	0			c.676_677del						.																																			SO:0001627	intron_variant	152137	exon6			.	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"deafness, autosomal dominant 44"	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-4868AA>-	chr3.hg19:g.191093079_191093080delAA		190.0	0.0		180.0	17.0	NM_178335	Q86VH7	Frame_Shift_Del	DEL	ENST00000392455.3	hg19	CCDS33913.1																																																																																			.	.		0.5	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908		-	191093080	AA	-	191093079	6	5	195	0	1	1	0	1	0	0	0	0	2822	14	1	0		0	CCDC50	3	191093079	Intron	DEL	AA	TCGA-DD-AADM-01A-11D-A40R-10	1	191093079	6929351	51	28679	145	2								
WFS1	7466	hgsc.bcm.edu	37	chr4	6303155	6303155	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tcatgtggtgtgagctctccGtggtcatcctgctggagtcc	13	11	3	1	rs201993978		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr4:6303155G>A	ENST00000226760.1	+	8	1803	c.1633G>A	c.(1633-1635)Gtg>Atg	p.V545M	WFS1_ENST00000503569.1_Missense_Mutation_p.V545M	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	545					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		TGAGCTCTCCGTGGTCATCCT	0.612																																					p.V545M		Atlas-SNP	.											.	WFS1	71	.	0			c.G1633A						.						98	100	99					4																	6303155		2203	4300	6503	SO:0001583	missense	7466	exon8			CTCTCCGTGGTCA	AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.1633G>A	chr4.hg19:g.6303155G>A	ENSP00000226760:p.Val545Met	62.0	0.0		80.0	23.0	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Missense_Mutation	SNP	ENST00000226760.1	hg19	CCDS3386.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.516793	0.44763	.	.	ENSG00000109501	ENST00000503569;ENST00000226760	D;D	0.84298	-1.83;-1.83	5.05	5.05	0.67936	.	0.140397	0.48767	D	0.000177	D	0.88347	0.6412	M	0.64997	1.995	0.49051	D	0.999749	D	0.63046	0.992	P	0.51945	0.685	D	0.89996	0.4111	10	0.87932	D	0	-22.9394	17.407	0.87476	0.0:0.0:1.0:0.0	.	545	O76024	WFS1_HUMAN	M	545	ENSP00000423337:V545M;ENSP00000226760:V545M	ENSP00000226760:V545M	V	+	1	0	WFS1	6354056	1.000000	0.71417	0.958000	0.39756	0.925000	0.55904	3.157000	0.50716	2.350000	0.79820	0.561000	0.74099	GTG	.	.		0.612	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1			A	6303155	G	A	6303155	3	1	195	1	0	0	0	0	1	0	0	0	17375	1145	40	1	1659	1	WFS1	4	6303155	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10		6303155	184851121	52	28680										
CPEB2	132864	hgsc.bcm.edu	37	chr4	15010011	15010011	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gggctcagattcactccaagAtagttggtgcactgcagccg	12	11	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr4:15010011A>G	ENST00000507071.1	+	3	770	c.683A>G	c.(682-684)gAt>gGt	p.D228G	CPEB2_ENST00000382401.3_Intron|RP11-665G4.1_ENST00000502344.1_RNA|CPEB2_ENST00000345451.3_Intron|CPEB2_ENST00000442003.2_Intron|RP11-665G4.1_ENST00000513384.1_RNA|CPEB2_ENST00000259997.5_Missense_Mutation_p.D228G|CPEB2_ENST00000382395.3_Intron|CPEB2_ENST00000538197.1_Missense_Mutation_p.D665G|CPEB2_ENST00000541112.1_Missense_Mutation_p.D665G			Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding protein 2	228					cellular response to arsenic-containing substance (GO:0071243)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to oxidative stress (GO:0034599)|negative regulation of cytoplasmic translation (GO:2000766)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of GTPase activity (GO:0034260)	cytoplasm (GO:0005737)|messenger ribonucleoprotein complex (GO:1990124)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|ribosome binding (GO:0043022)|translation repressor activity, nucleic acid binding (GO:0000900)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(3)	14						TCACTCCAAGATAGTTGGTGC	0.423																																					p.D665G		Atlas-SNP	.											.	CPEB2	77	.	0			c.A1994G						.						81	75	77					4																	15010011		2203	4300	6503	SO:0001583	missense	132864	exon3			TCCAAGATAGTTG	AY247744	CCDS56325.1, CCDS56326.1	4p15.33	2013-02-12			ENSG00000137449	ENSG00000137449		"RNA binding motif (RRM) containing"	21745	protein-coding gene	gene with protein product		610605				12672660	Standard	NM_182485		Approved		uc003gnk.2	Q7Z5Q1	OTTHUMG00000090669	ENST00000507071.1:c.683A>G	chr4.hg19:g.15010011A>G	ENSP00000424084:p.Asp228Gly	128.0	0.0		92.0	10.0	NM_001177382	E7EPM3|F5H160|Q3B8N6|Q3MI89|Q3MI90|Q3MI92|Q7Z5Q0	Missense_Mutation	SNP	ENST00000507071.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.08	3.022779	0.54683	.	.	ENSG00000137449	ENST00000538197;ENST00000541112;ENST00000507071;ENST00000259997;ENST00000382391	T;T;T;T	0.52526	0.71;0.66;0.81;0.78	5.54	5.54	0.83059	.	0.406139	0.28052	N	0.016783	T	0.46268	0.1384	N	0.08118	0	0.80722	D	1	P;P	0.52577	0.954;0.924	D;P	0.67900	0.954;0.9	T	0.49960	-0.8883	10	0.36615	T	0.2	-18.8579	12.3385	0.55081	1.0:0.0:0.0:0.0	.	665;228	F5H160;Q7Z5Q1	.;CPEB2_HUMAN	G	665;665;228;228;207	ENSP00000443985:D665G;ENSP00000437884:D665G;ENSP00000424084:D228G;ENSP00000259997:D228G	ENSP00000259997:D228G	D	+	2	0	CPEB2	14619109	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.243000	0.58721	2.223000	0.72356	0.460000	0.39030	GAT	.	.		0.423	CPEB2-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000207349.2	XM_059607		G	15010011	A	G	15010011	3	3	195	1	0	0	0	0	1	0	0	0	3803	333	12	2	2013	2	CPEB2	4	15010011	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	8706856	15010011	176144265	53	28681										
SPATA18	132671	hgsc.bcm.edu	37	chr4	52928483	52928483	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctcaacccggagtcaatgcaAccaggttcaagacgagtaag	10	11	3	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr4:52928483A>G	ENST00000295213.4	+	4	781	c.407A>G	c.(406-408)aAc>aGc	p.N136S	SPATA18_ENST00000419395.2_Missense_Mutation_p.N136S|SPATA18_ENST00000506829.1_Intron	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	136					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			AGTCAATGCAACCAGGTTCAA	0.388																																					p.N136S		Atlas-SNP	.											.	SPATA18	222	.	0			c.A407G						.						87	88	88					4																	52928483		2203	4300	6503	SO:0001583	missense	132671	exon4			AATGCAACCAGGT	BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"spermatogenesis associated 18 homolog (rat)"			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.407A>G	chr4.hg19:g.52928483A>G	ENSP00000295213:p.Asn136Ser	132.0	0.0		136.0	13.0	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	hg19	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	A	3.682	-0.065392	0.07273	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	D;D	0.87729	-2.29;-2.29	5.05	1.28	0.21552	.	0.454305	0.27336	N	0.019834	T	0.73305	0.3570	L	0.31664	0.95	0.29843	N	0.829081	B;B;B	0.17667	0.002;0.002;0.023	B;B;B	0.12156	0.005;0.003;0.007	T	0.56998	-0.7886	10	0.17832	T	0.49	-20.2316	3.541	0.07811	0.5675:0.2121:0.2203:0.0	.	136;136;136	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	S	136	ENSP00000295213:N136S;ENSP00000415309:N136S	ENSP00000295213:N136S	N	+	2	0	SPATA18	52623240	0.956000	0.32656	0.989000	0.46669	0.250000	0.25880	0.254000	0.18314	0.389000	0.25086	-0.400000	0.06385	AAC	.	.		0.388	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263		G	52928483	A	G	52928483	3	3	195	1	0	0	0	0	1	0	0	0	15018	43	2	2	421	2	SPATA18	4	52928483	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	37918472	52928483	138225793	54	28682										
AASDH	132949	hgsc.bcm.edu	37	chr4	57250358	57250358	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gaagcagcattaaccacagtCttgtaggtgtagtaaactgg	11	7	1	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr4:57250358C>G	ENST00000205214.6	-	2	288	c.108G>C	c.(106-108)aaG>aaC	p.K36N	AASDH_ENST00000602986.1_5'UTR|AASDH_ENST00000513376.1_Intron|AASDH_ENST00000510762.1_Intron|AASDH_ENST00000451613.1_Missense_Mutation_p.K36N|AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000502617.1_Missense_Mutation_p.K36N	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	36					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TAACCACAGTCTTGTAGGTGT	0.418																																					p.K36N		Atlas-SNP	.											.	AASDH	101	.	0			c.G108C						.						116	108	110					4																	57250358		2203	4300	6503	SO:0001583	missense	132949	exon2			CACAGTCTTGTAG	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.108G>C	chr4.hg19:g.57250358C>G	ENSP00000205214:p.Lys36Asn	319.0	0.0		298.0	42.0	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	hg19	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	C	9.580	1.123219	0.20959	.	.	ENSG00000157426	ENST00000205214;ENST00000451613;ENST00000502617	T;T;T	0.41758	0.99;0.99;0.99	5.92	2.22	0.28083	AMP-dependent synthetase/ligase (1);	0.828892	0.11719	N	0.536144	T	0.36524	0.0970	L	0.50333	1.59	0.09310	N	1	P;P;P;P	0.43352	0.804;0.551;0.804;0.734	P;B;B;P	0.45406	0.463;0.397;0.369;0.479	T	0.17258	-1.0375	10	0.30078	T	0.28	-0.4739	2.4899	0.04607	0.1199:0.4994:0.1168:0.2639	.	36;36;36;36	Q4L235-4;B4E2K0;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	N	36	ENSP00000205214:K36N;ENSP00000409656:K36N;ENSP00000421171:K36N	ENSP00000205214:K36N	K	-	3	2	AASDH	56945115	0.000000	0.05858	0.077000	0.20336	0.314000	0.28054	-1.302000	0.02746	0.398000	0.25338	-0.142000	0.14014	AAG	.	.		0.418	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		G	57250358	C	G	57250358	3	3	195	1	0	0	0	0	1	0	0	0	22	912	32	4	3244	4	AASDH	4	57250358	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	4321875	57250358	133903918	55	28683										
CNOT6L	246175	hgsc.bcm.edu	37	chr4	78697452	78697453	+	Frame_Shift_Ins	INS	-	-	T													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tctaattctgcccagtgagaINSttttttcccattggctacct					rs200743940		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr4:78697452_78697453insT	ENST00000504123.1	-	2	229_230	c.99_100insA	c.(97-102)aaatctfs	p.S34fs	CNOT6L_ENST00000506166.1_5'UTR|CNOT6L_ENST00000264903.4_Frame_Shift_Ins_p.S34fs			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	34	Required for interaction with CNOT1, CNOT3 and CNOT7.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						GCCCAGTGAGATTTTTTCCCAT	0.371																																					p.S34fs		Atlas-Indel,Pindel	.											.	CNOT6L	57	.	0			c.100_101insA						.																																			SO:0001589	frameshift_variant	246175	exon2			.	AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.100dupA	chr4.hg19:g.78697458_78697458dupT	ENSP00000424896:p.Ser34fs	102.0	0.0		100.0	28.0	NM_144571	Q9UF92	Frame_Shift_Ins	INS	ENST00000504123.1	hg19																																																																																				.	.		0.371	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1			T	78697453	-	T	78697452	7	5	195	1	0	1	1	0	0	0	0	0	3625	333	12	0	1611	0	CNOT6L	4	78697452	Frame_Shift_Ins	INS	-	TCGA-DD-AADM-01A-11D-A40R-10	21447094	78697452	112456824	56	28684										
TNIP3	79931	hgsc.bcm.edu	37	chr4	122078298	122078298	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ggtcgcgctgcctgtcgtccTctctctgcctgtcgtccttt	10	16	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr4:122078298T>A	ENST00000509841.1	-	7	623	c.545A>T	c.(544-546)gAg>gTg	p.E182V	TNIP3_ENST00000454328.1_Missense_Mutation_p.E105V|TNIP3_ENST00000057513.3_Missense_Mutation_p.E105V|TNIP3_ENST00000507879.1_Missense_Mutation_p.E175V	NM_001244764.1	NP_001231693.1			TNFAIP3 interacting protein 3											NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2)	24						CCTGTCGTCCTCTCTCTGCCT	0.637																																					p.E182V		Atlas-SNP	.											.	TNIP3	58	.	0			c.A545T						.						171	191	184					4																	122078298		2203	4300	6503	SO:0001583	missense	79931	exon7			TCGTCCTCTCTCT	AJ320534	CCDS3718.1, CCDS58925.1, CCDS58926.1	4q27	2008-02-05			ENSG00000050730	ENSG00000050730			19315	protein-coding gene	gene with protein product		608019				11345586	Standard	NM_024873		Approved	LIND, FLJ21162, ABIN-3	uc021xrj.1	Q96KP6	OTTHUMG00000132969	ENST00000509841.1:c.545A>T	chr4.hg19:g.122078298T>A	ENSP00000426613:p.Glu182Val	75.0	0.0		85.0	18.0	NM_001244764		Missense_Mutation	SNP	ENST00000509841.1	hg19	CCDS58926.1	.	.	.	.	.	.	.	.	.	.	T	7.750	0.703039	0.15172	.	.	ENSG00000050730	ENST00000057513;ENST00000454328;ENST00000507879;ENST00000509841	T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0	0.69	0.69	0.18039	.	0.515844	0.18289	N	0.145765	T	0.64327	0.2588	M	0.70275	2.135	0.09310	N	1	P;P;B	0.47106	0.89;0.557;0.091	P;B;B	0.49332	0.607;0.125;0.027	T	0.57487	-0.7803	9	0.87932	D	0	0.0309	.	.	.	.	175;105;105	B4DVF5;A5HU65;Q96KP6	.;.;TNIP3_HUMAN	V	105;105;175;182	ENSP00000057513:E105V;ENSP00000411817:E105V;ENSP00000427106:E175V;ENSP00000426613:E182V	ENSP00000057513:E105V	E	-	2	0	TNIP3	122297748	0.002000	0.14202	0.034000	0.17996	0.025000	0.11179	0.286000	0.18902	0.531000	0.28639	0.164000	0.16699	GAG	.	.		0.637	TNIP3-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364000.4	NM_024873		A	122078298	T	A	122078298	3	1	195	1	0	0	0	0	1	0	0	0	16331	1551	54	4	695	4	TNIP3	4	122078298	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	43380846	122078298	69075978	57	28685										
FGA	2243	hgsc.bcm.edu	37	chr4	155510651	155510651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ggcagattgatgtctttccaCaacccttgggccacgcacgc	10	14	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr4:155510651C>T	ENST00000302053.3	-	2	196	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	FGA_ENST00000403106.3_Missense_Mutation_p.V40M	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	40					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	TGTCTTTCCACAACCCTTGGG	0.498																																					p.V40M	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.G118A						.						156	147	150					4																	155510651		2203	4300	6503	SO:0001583	missense	2243	exon2			TTTCCACAACCCT		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.118G>A	chr4.hg19:g.155510651C>T	ENSP00000306361:p.Val40Met	71.0	0.0		70.0	26.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	C	14.55	2.567440	0.45694	.	.	ENSG00000171560	ENST00000302053;ENST00000403106;ENST00000457487	T;T	0.62639	0.01;2.48	5.58	1.92	0.25849	.	0.728598	0.13820	N	0.360495	T	0.53658	0.1810	L	0.53249	1.67	0.09310	N	0.999998	B;P;B	0.37207	0.068;0.587;0.451	B;B;B	0.38156	0.022;0.266;0.112	T	0.45600	-0.9250	10	0.49607	T	0.09	.	5.6402	0.17559	0.0:0.4921:0.2463:0.2617	.	40;40;40	A8K3E4;P02671-2;P02671	.;.;FIBA_HUMAN	M	40	ENSP00000306361:V40M;ENSP00000385981:V40M	ENSP00000306361:V40M	V	-	1	0	FGA	155730101	0.000000	0.05858	0.002000	0.10522	0.206000	0.24218	-0.762000	0.04745	0.306000	0.22856	0.650000	0.86243	GTG	.	.		0.498	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		T	155510651	C	T	155510651	3	4	195	1	0	0	0	0	1	0	0	0	5838	478	17	3	2546	3	FGA	4	155510651	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	33432353	155510651	35643625	58	28686										
ADCY2	108	hgsc.bcm.edu	37	chr5	7396475	7396476	+	In_Frame_Ins	INS	-	-	GGG													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccgaggaggcggcgggcggcINSggagacgggctgccgcggtc							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr5:7396475_7396476insGGG	ENST00000338316.4	+	1	155_156	c.66_67insGGG	c.(67-69)gga>GGGgga	p.23_23G>GG		NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	23					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CGGCGGGCGGCGGAGACGGGCT	0.733																																					p.G22delinsGG		Atlas-Indel,Pindel	.											.	ADCY2	337	.	0			c.66_67insGGG						.																																			SO:0001652	inframe_insertion	108	exon1			.	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	Exception_encountered	chr5.hg19:g.7396475_7396476insGGG	ENSP00000342952:p.Gly23dup	80.0	0.0		106.0	19.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	In_Frame_Ins	INS	ENST00000338316.4	hg19	CCDS3872.2																																																																																			.	.		0.733	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		GGG	7396476	-	GGG	7396475	7	5	195	1	0	1	1	0	0	0	0	0	294	755	27	0	68	0	ADCY2	5	7396475	In_Frame_Ins	INS	-	TCGA-DD-AADM-01A-11D-A40R-10		7396475	173518785	59	28687										
GPR98	84059	hgsc.bcm.edu	37	chr5	89947508	89947508	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cattttttctctggagcccaTagacaaagcagtggaagaag	10	8	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr5:89947508T>C	ENST00000405460.2	+	18	3473	c.3377T>C	c.(3376-3378)aTa>aCa	p.I1126T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1126	Calx-beta 9. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CTGGAGCCCATAGACAAAGCA	0.333																																					p.I1126T		Atlas-SNP	.											.	GPR98	605	.	0			c.T3377C						.						96	90	92					5																	89947508		1828	4083	5911	SO:0001583	missense	84059	exon18			AGCCCATAGACAA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.3377T>C	chr5.hg19:g.89947508T>C	ENSP00000384582:p.Ile1126Thr	166.0	0.0		239.0	18.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.582427	0.28180	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.26660	1.72	5.49	4.32	0.51571	.	0.457911	0.26510	N	0.023977	T	0.14614	0.0353	N	0.13098	0.295	0.28203	N	0.92725	B	0.15719	0.014	B	0.12837	0.008	T	0.13124	-1.0521	10	0.37606	T	0.19	.	9.0048	0.36104	0.0:0.2035:0.0:0.7965	.	1126	Q8WXG9	GPR98_HUMAN	T	1126	ENSP00000384582:I1126T	ENSP00000296619:I1126T	I	+	2	0	GPR98	89983264	0.952000	0.32445	0.998000	0.56505	0.962000	0.63368	1.743000	0.38258	0.916000	0.36871	0.482000	0.46254	ATA	.	.		0.333	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	89947508	T	C	89947508	3	2	195	1	0	0	0	0	1	0	0	0	6730	1406	49	2	3447	2	GPR98	5	89947508	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	82551033	89947508	90967752	60	28688										
APC	324	hgsc.bcm.edu	37	chr5	112175181	112175181	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tcagacgacacaggaagcagAttctgctaataccctgcaaa	8	11	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr5:112175181A>G	ENST00000457016.1	+	16	4270	c.3890A>G	c.(3889-3891)gAt>gGt	p.D1297G	APC_ENST00000508376.2_Missense_Mutation_p.D1297G|APC_ENST00000257430.4_Missense_Mutation_p.D1297G|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1297	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.T1293fs*2(1)|p.D1297A(1)|p.D1297fs*3(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGGAAGCAGATTCTGCTAAT	0.398		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.D1297G	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	APC,NS,carcinoma,0,1	APC	4158	.	5	Deletion - Frameshift(3)|Substitution - Missense(1)|Unknown(1)	large_intestine(3)|soft_tissue(1)|skin(1)	c.A3890G						.						55	57	56					5																	112175181		2202	4300	6502	SO:0001583	missense	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AAGCAGATTCTGC	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3890A>G	chr5.hg19:g.112175181A>G	ENSP00000413133:p.Asp1297Gly	217.0	0.0		469.0	42.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	9.925	1.213292	0.22289	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.92048	-2.67;-2.67;-2.67;-2.96	5.73	4.54	0.55810	.	0.571888	0.19199	N	0.120224	D	0.84483	0.5482	N	0.19112	0.55	0.39800	D	0.97255	B;B	0.14805	0.011;0.011	B;B	0.15870	0.007;0.014	T	0.77643	-0.2511	9	.	.	.	-4.19	11.6759	0.51430	0.8577:0.0:0.0:0.1423	.	1299;1297	Q4LE70;P25054	.;APC_HUMAN	G	1297	ENSP00000413133:D1297G;ENSP00000257430:D1297G;ENSP00000427089:D1297G;ENSP00000423828:D1297G	.	D	+	2	0	APC	112203080	0.996000	0.38824	0.972000	0.41901	0.997000	0.91878	3.430000	0.52807	1.057000	0.40506	0.533000	0.62120	GAT	.	.		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175181	A	G	112175181	3	3	195	1	0	0	0	0	1	0	0	0	763	333	12	2	3948	2	APC	5	112175181	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	22227673	112175181	68740079	61	28689										
CXCL14	9547	hgsc.bcm.edu	37	chr5	134914200	134914200	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gtcgctgtagcggatcttggGtcccttccgggagcacttgc	14	12	1	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr5:134914200G>A	ENST00000337225.5	-	2	594	c.130C>T	c.(130-132)Ccc>Tcc	p.P44S	CTC-321K16.1_ENST00000514446.1_RNA|CTC-321K16.1_ENST00000509372.1_RNA|CXCL14_ENST00000512158.1_Missense_Mutation_p.P32S	NM_004887.4	NP_004878.2	O95715	CXL14_HUMAN	chemokine (C-X-C motif) ligand 14	44					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inner ear development (GO:0048839)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	chemokine activity (GO:0008009)			large_intestine(2)|lung(2)|prostate(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CGGATCTTGGGTCCCTTCCGG	0.592																																					p.P44S		Atlas-SNP	.											.	CXCL14	13	.	0			c.C130T						.						139	131	134					5																	134914200		2203	4300	6503	SO:0001583	missense	9547	exon2			TCTTGGGTCCCTT	AF073957	CCDS4188.1	5q31	2010-04-30	2002-08-22	2002-08-23	ENSG00000145824	ENSG00000145824			10640	protein-coding gene	gene with protein product	"breast and kidney"	604186	"small inducible cytokine subfamily B (Cys-X-Cys), member 14 (BRAK)"	SCYB14		10049774	Standard	NM_004887		Approved	BRAK, NJAC, bolekine, Kec, MIP-2g, BMAC, KS1	uc003lay.3	O95715	OTTHUMG00000129139	ENST00000337225.5:c.130C>T	chr5.hg19:g.134914200G>A	ENSP00000337065:p.Pro44Ser	98.0	0.0		141.0	14.0	NM_004887	B3KQU8|Q6UW97|Q86U69|Q9BTR1|Q9NS21	Missense_Mutation	SNP	ENST00000337225.5	hg19	CCDS4188.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.971161	0.92919	.	.	ENSG00000145824	ENST00000337225;ENST00000512158	T;T	0.04194	3.68;3.68	5.12	5.12	0.69794	Chemokine interleukin-8-like domain (2);	0.000000	0.85682	D	0.000000	T	0.18257	0.0438	L	0.53249	1.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00154	-1.1981	10	0.72032	D	0.01	6.3574	16.7212	0.85410	0.0:0.0:1.0:0.0	.	44	O95715	CXL14_HUMAN	S	44;32	ENSP00000337065:P44S;ENSP00000423783:P32S	ENSP00000337065:P44S	P	-	1	0	CXCL14	134942099	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.488000	0.90458	2.380000	0.81148	0.591000	0.81541	CCC	.	.		0.592	CXCL14-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_004887		A	134914200	G	A	134914200	3	1	195	1	0	0	0	0	1	0	0	0	4084	1261	44	3	217	3	CXCL14	5	134914200	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	22739019	134914200	46001060	62	28690										
PKD2L2	27039	hgsc.bcm.edu	37	chr5	137230131	137230133	+	In_Frame_Del	DEL	CTA	CTA	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ttaaagaacagcagtcgcatCtactatgaaaatatacttct							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	CTA	CTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr5:137230131_137230133delCTA	ENST00000508883.1	+	4	383_385	c.357_359delCTA	c.(355-360)atctac>atc	p.Y121del	PKD2L2_ENST00000350250.4_In_Frame_Del_p.Y87del|PKD2L2_ENST00000508638.1_In_Frame_Del_p.Y121del|PKD2L2_ENST00000502810.1_In_Frame_Del_p.Y121del|PKD2L2_ENST00000290431.5_In_Frame_Del_p.Y121del			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	121					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GCAGTCGCATCTACTATGAAAAT	0.399																																					p.119_120del		Atlas-Indel,Pindel	.											.	PKD2L2	68	.	0			c.356_358del						.																																			SO:0001651	inframe_deletion	27039	exon4			.	AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"Voltage-gated ion channels / Transient receptor potential cation channels"	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.357_359delCTA	chr5.hg19:g.137230134_137230136delCTA	ENSP00000424725:p.Tyr121del	71.0	0.0		127.0	75.0	NM_001258448	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	In_Frame_Del	DEL	ENST00000508883.1	hg19																																																																																				.	.		0.399	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		-	137230133	CTA	-	137230131	7	5	195	1	0	1	0	1	0	0	0	0	11977	903	32	0	371	0	PKD2L2	5	137230131	In_Frame_Del	DEL	CTA	TCGA-DD-AADM-01A-11D-A40R-10	2315931	137230131	43685129	63	28691										
PCDHGB1	56104	hgsc.bcm.edu	37	chr5	140730572	140730572	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aggtatacagggttagcctcCaagaaaacgtaccgtgggga	13	8	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr5:140730572C>G	ENST00000523390.1	+	1	745	c.745C>G	c.(745-747)Caa>Gaa	p.Q249E	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	249	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTTAGCCTCCAAGAAAACGT	0.552																																					p.Q249E		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.C745G						.						89	94	93					5																	140730572		2005	4179	6184	SO:0001583	missense	56104	exon1			AGCCTCCAAGAAA	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"Cadherins / Protocadherins : Clustered"	8708	other	protocadherin	"protocadherin gamma subfamily B, 1, isoform 2"	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.745C>G	chr5.hg19:g.140730572C>G	ENSP00000429273:p.Gln249Glu	179.0	0.0		251.0	51.0	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	hg19	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	3.055	-0.194541	0.06259	.	.	ENSG00000254221	ENST00000523390	T	0.01685	4.69	5.58	3.66	0.41972	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01061	0.0035	N	0.02266	-0.62	0.09310	N	1	B;B	0.32101	0.356;0.271	B;B	0.33121	0.098;0.158	T	0.52593	-0.8555	9	0.34782	T	0.22	.	9.154	0.36980	0.462:0.4167:0.1212:0.0	.	249;249	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	E	249	ENSP00000429273:Q249E	ENSP00000429273:Q249E	Q	+	1	0	PCDHGB1	140710756	0.000000	0.05858	0.835000	0.33067	0.677000	0.39632	-1.989000	0.01480	1.464000	0.47987	0.563000	0.77884	CAA	.	.		0.552	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922		G	140730572	C	G	140730572	3	3	195	1	0	0	0	0	1	0	0	0	11571	595	21	4	747	4	PCDHGB1	5	140730572	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	3500441	140730572	40184688	64	28692										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169502981	169502981	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgggagctgggattaagatcCatgagaaaagggtgtcagat	15	4	1	3			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr5:169502981C>T	ENST00000256935.8	+	47	4839	c.4759C>T	c.(4759-4761)Cat>Tat	p.H1587Y	DOCK2_ENST00000540750.1_Missense_Mutation_p.H648Y|DOCK2_ENST00000520908.1_Missense_Mutation_p.H1079Y|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1587	DHR-2.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GATTAAGATCCATGAGAAAAG	0.532																																					p.H1587Y		Atlas-SNP	.											.	DOCK2	389	.	0			c.C4759T						.						155	159	157					5																	169502981		2203	4300	6503	SO:0001583	missense	1794	exon47			AAGATCCATGAGA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4759C>T	chr5.hg19:g.169502981C>T	ENSP00000256935:p.His1587Tyr	131.0	0.0		223.0	35.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079518	0.94050	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.19938	2.11;2.11;2.11	5.18	5.18	0.71444	Cytochrome c domain (1);	0.057139	0.64402	D	0.000001	T	0.58104	0.2099	H	0.94620	3.56	0.80722	D	1	D;D;D	0.76494	0.999;0.993;0.973	P;D;P	0.64144	0.872;0.922;0.845	T	0.70963	-0.4729	10	0.62326	D	0.03	.	19.1283	0.93394	0.0:1.0:0.0:0.0	.	1079;143;1587	E7ERW7;B3KY14;Q92608	.;.;DOCK2_HUMAN	Y	1587;1079;648	ENSP00000256935:H1587Y;ENSP00000429283:H1079Y;ENSP00000438827:H648Y	ENSP00000256935:H1587Y	H	+	1	0	DOCK2	169435559	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.726000	0.84824	2.598000	0.87819	0.650000	0.86243	CAT	.	.		0.532	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169502981	C	T	169502981	3	4	195	1	0	0	0	0	1	0	0	0	4689	594	21	3	4945	3	DOCK2	5	169502981	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	28772409	169502981	11412279	65	28693										
CDKAL1	54901	hgsc.bcm.edu	37	chr6	20846331	20846331	+	Frame_Shift_Del	DEL	A	A	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tcaatgcttgtacctactgcAaaactaaacacgccagagga							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:20846331delA	ENST00000378610.1	+	7	674	c.664delA	c.(664-666)aaafs	p.K222fs	CDKAL1_ENST00000274695.4_Frame_Shift_Del_p.K222fs|CDKAL1_ENST00000378624.4_Frame_Shift_Del_p.K152fs			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	222					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			TACCTACTGCAAAACTAAACA	0.333																																					p.C221X		Atlas-Indel,Pindel	.											.	CDKAL1	55	.	0			c.663delC						.						76	77	77					6																	20846331		2203	4300	6503	SO:0001589	frameshift_variant	54901	exon9			.	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.664delA	chr6.hg19:g.20846331delA	ENSP00000367873:p.Lys222fs	155.0	0.0		223.0	62.0	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Frame_Shift_Del	DEL	ENST00000378610.1	hg19	CCDS4546.1																																																																																			.	.		0.333	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774		-	20846331	A	-	20846331	7	5	195	1	0	1	0	1	0	0	0	0	3154	131	5	0	690	0	CDKAL1	6	20846331	Frame_Shift_Del	DEL	A	TCGA-DD-AADM-01A-11D-A40R-10		20846331	150268736	66	28694										
PPP1R10	5514	hgsc.bcm.edu	37	chr6	30569817	30569817	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gtggcggccctcgatggtcaTggcctcggtgaccagggaca	16	12	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:30569817T>A	ENST00000376511.2	-	19	3161	c.2609A>T	c.(2608-2610)cAt>cTt	p.H870L		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	870	Gly-rich.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						TCGATGGTCATGGCCTCGGTG	0.677																																					p.H870L		Atlas-SNP	.											.	PPP1R10	60	.	0			c.A2609T						.						35	37	37					6																	30569817		1508	2707	4215	SO:0001583	missense	5514	exon19			TGGTCATGGCCTC	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9284	protein-coding gene	gene with protein product	"phosphatase 1 nuclear targeting subunit", "HLA-C associated transcript 53"	603771	"protein phosphatase 1, regulatory (inhibitor) subunit 10"			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.2609A>T	chr6.hg19:g.30569817T>A	ENSP00000365694:p.His870Leu	102.0	0.0		137.0	20.0	NM_002714	O00405	Missense_Mutation	SNP	ENST00000376511.2	hg19	CCDS4681.1	.	.	.	.	.	.	.	.	.	.	t	11.62	1.693019	0.30052	.	.	ENSG00000204569	ENST00000376511	T	0.48836	0.8	4.44	4.44	0.53790	.	0.000000	0.64402	D	0.000003	T	0.11367	0.0277	N	0.08118	0	0.29280	N	0.870096	B	0.14438	0.01	B	0.06405	0.002	T	0.11591	-1.0581	10	0.21014	T	0.42	-11.0005	11.9651	0.53029	0.0:0.0:0.0:1.0	.	870	Q96QC0	PP1RA_HUMAN	L	870	ENSP00000365694:H870L	ENSP00000365694:H870L	H	-	2	0	PPP1R10	30677796	0.998000	0.40836	0.998000	0.56505	0.983000	0.72400	1.724000	0.38064	1.986000	0.57962	0.398000	0.26397	CAT	.	.		0.677	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		A	30569817	T	A	30569817	3	1	195	1	0	0	0	0	1	0	0	0	12364	1464	51	4	221	4	PPP1R10	6	30569817	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	9723486	30569817	140545250	67	28695										
C6orf47	57827	hgsc.bcm.edu	37	chr6	31627289	31627336	+	In_Frame_Del	DEL	CCAATGGGGCTCCTGGCCCAGGGACGCTCAGTCCCCCTTCAGGGGACA	CCAATGGGGCTCCTGGCCCAGGGACGCTCAGTCCCCCTTCAGGGGACA	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctcacgcctaccaggtttctCcaatggggctcctggcccag					rs529057431|rs538881383		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	CCAATGGGGCTCCTGGCCCAGGGACGCTCAGTCCCCCTTCAGGGGACA	CCAATGGGGCTCCTGGCCCAGGGACGCTCAGTCCCCCTTCAGGGGACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:31627289_31627336delCCAATGGGGCTCCTGGCCCAGGGACGCTCAGTCCCCCTTCAGGGGACA	ENST00000375911.1	-	1	1213_1260	c.389_436delTGTCCCCTGAAGGGGGACTGAGCGTCCCTGGGCCAGGAGCCCCATTGG	c.(388-438)gtgtcccctgaagggggactgagcgtccctgggccaggagccccattggag>gag	p.VSPEGGLSVPGPGAPL130del	C6orf47-AS1_ENST00000422049.1_RNA	NM_021184.3	NP_067007.3	O95873	CF047_HUMAN	chromosome 6 open reading frame 47	130						cytoplasm (GO:0005737)		p.L145L(1)		NS(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9						CCAGGTTTCTCCAATGGGGCTCCTGGCCCAGGGACGCTCAGTCCCCCTTCAGGGGACACCCCTGGTCT	0.621																																					p.130_146del		Atlas-Indel,Pindel	.											.	C6orf47	15	.	1	Substitution - coding silent(1)	kidney(1)	c.390_437del						.																																			SO:0001651	inframe_deletion	57827	exon1			.	AF129756	CCDS34399.1	6p21.3	2011-12-13			ENSG00000204439	ENSG00000204439			19076	protein-coding gene	gene with protein product						2477242	Standard	NM_021184		Approved	D6S53E, G4	uc003nvm.1	O95873	OTTHUMG00000031172	ENST00000375911.1:c.389_436delTGTCCCCTGAAGGGGGACTGAGCGTCCCTGGGCCAGGAGCCCCATTGG	chr6.hg19:g.31627289_31627336delCCAATGGGGCTCCTGGCCCAGGGACGCTCAGTCCCCCTTCAGGGGACA	ENSP00000365076:p.Val130_Leu145del	74.0	0.0		92.0	19.0	NM_021184	B0UXA1|B0UZ50|Q5SSS6|Q95IG0	In_Frame_Del	DEL	ENST00000375911.1	hg19	CCDS34399.1																																																																																			.	.		0.621	C6orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076324.1	NM_021184		-	31627336	CCAATGGGGCTCCTGGCCCAGGGACGCTCAGTCCCCCTTCAGGGGACA	-	31627289	7	5	195	1	0	1	0	1	0	0	0	0	2366	864	30	0	452	0	C6orf47	6	31627289	In_Frame_Del	DEL	CCAATGGGGCTCCTGGCCCAGGGACGCTCAGTCCCCCTTCAGGGGACA	TCGA-DD-AADM-01A-11D-A40R-10	1057472	31627289	139487778	68	28696										
TFEB	7942	hgsc.bcm.edu	37	chr6	41653841	41653841	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	accagacctggatacggagcCagagctgcttgttggtcatc	12	11	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:41653841C>A	ENST00000230323.4	-	9	1239	c.938G>T	c.(937-939)tGg>tTg	p.W313L	TFEB_ENST00000373033.1_Missense_Mutation_p.W313L|AL035588.1_ENST00000597468.1_5'Flank|TFEB_ENST00000403298.4_Missense_Mutation_p.W313L|TFEB_ENST00000358871.2_Missense_Mutation_p.W327L|TFEB_ENST00000420312.1_Missense_Mutation_p.W228L	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	313	Leucine-zipper.				autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			GATACGGAGCCAGAGCTGCTT	0.547			T	ALPHA	renal (childhood epithelioid)																																p.W327L		Atlas-SNP	.		Dom	yes		6	6p21	7942	transcription factor EB		"E,M"	.	TFEB	37	.	0			c.G980T						.						126	108	114					6																	41653841		2203	4300	6503	SO:0001583	missense	7942	exon8			CGGAGCCAGAGCT	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"Basic helix-loop-helix proteins"	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.938G>T	chr6.hg19:g.41653841C>A	ENSP00000230323:p.Trp313Leu	110.0	0.0		110.0	31.0	NM_001167827	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Missense_Mutation	SNP	ENST00000230323.4	hg19	CCDS4858.1	.	.	.	.	.	.	.	.	.	.	C	1.979	-0.434656	0.04669	.	.	ENSG00000112561	ENST00000406563;ENST00000343317;ENST00000230323;ENST00000358871;ENST00000403298;ENST00000420312;ENST00000373033	T;T;T;T;T;T;T	0.18657	2.2;2.2;2.23;2.22;2.23;2.2;2.23	4.91	3.05	0.35203	.	0.384607	0.28612	N	0.014736	T	0.01870	0.0059	N	0.01424	-0.875	0.35608	D	0.808435	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.001;0.002	T	0.44406	-0.9330	10	0.02654	T	1	-5.9744	13.2521	0.60057	0.5892:0.4108:0.0:0.0	.	327;313;228	B0QYS6;P19484;P19484-2	.;TFEB_HUMAN;.	L	171;399;313;327;313;228;313	ENSP00000383998:W171L;ENSP00000343948:W399L;ENSP00000230323:W313L;ENSP00000351742:W327L;ENSP00000384203:W313L;ENSP00000412551:W228L;ENSP00000362124:W313L	ENSP00000230323:W313L	W	-	2	0	TFEB	41761819	0.991000	0.36638	1.000000	0.80357	0.988000	0.76386	1.270000	0.33086	0.411000	0.25702	0.655000	0.94253	TGG	.	.		0.547	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3			A	41653841	C	A	41653841	3	1	195	1	0	0	0	0	1	0	0	0	15816	595	21	3	500	3	TFEB	6	41653841	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	10026552	41653841	129461226	69	28697										
PRPH2	5961	hgsc.bcm.edu	37	chr6	42689615	42689615	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gcagcatgtcgatggtcttcTtcatgaaacacctgccaggg	11	11	3	1	rs61755785		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:42689615T>C	ENST00000230381.5	-	1	697	c.458A>G	c.(457-459)aAg>aGg	p.K153R		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	153			K -> R (in RP7).|Missing (in RP7).		cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			GATGGTCTTCTTCATGAAACA	0.542																																					p.K153R		Atlas-SNP	.											.	PRPH2	47	.	0			c.A458G	GRCh37	CM941208	PRPH2	M	rs61755785	.						116	103	108					6																	42689615		2203	4300	6503	SO:0001583	missense	5961	exon1			GTCTTCTTCATGA		CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"Tetraspanins"	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"retinal degeneration, slow (retinitis pigmentosa 7)", "retinal degeneration, slow"	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.458A>G	chr6.hg19:g.42689615T>C	ENSP00000230381:p.Lys153Arg	105.0	0.0		132.0	16.0	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	hg19	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	T	32	5.118863	0.94385	.	.	ENSG00000112619	ENST00000230381	T	0.80123	-1.34	5.78	5.78	0.91487	Tetraspanin, EC2 domain (1);	0.000000	0.85682	D	0.000000	D	0.88529	0.6461	M	0.81614	2.55	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.89834	0.3998	10	0.66056	D	0.02	.	16.3979	0.83621	0.0:0.0:0.0:1.0	rs61755785	153	P23942	PRPH2_HUMAN	R	153	ENSP00000230381:K153R	ENSP00000230381:K153R	K	-	2	0	PRPH2	42797593	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.927000	0.87577	2.333000	0.79357	0.533000	0.62120	AAG	.	.		0.542	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322		C	42689615	T	C	42689615	3	2	195	1	0	0	0	0	1	0	0	0	12589	1609	56	2	594	2	PRPH2	6	42689615	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	1035774	42689615	128425452	70	28698										
CRIP3	401262	hgsc.bcm.edu	37	chr6	43276057	43276057	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cctggccaggtcttacctctGcatgcccgccaggggacagg	13	15	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:43276057G>T	ENST00000274990.4	-	2	138	c.134C>A	c.(133-135)gCa>gAa	p.A45E	CRIP3_ENST00000372569.3_Missense_Mutation_p.A45E|ZNF318_ENST00000607252.1_5'UTR			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	45	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			TCTTACCTCTGCATGCCCGCC	0.627																																					p.A45E		Atlas-SNP	.											.	CRIP3	30	.	0			c.C134A						.						63	53	56					6																	43276057		2203	4300	6503	SO:0001583	missense	401262	exon2			ACCTCTGCATGCC	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.134C>A	chr6.hg19:g.43276057G>T	ENSP00000274990:p.Ala45Glu	76.0	0.0		85.0	7.0	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	hg19		.	.	.	.	.	.	.	.	.	.	G	27.6	4.847003	0.91277	.	.	ENSG00000146215	ENST00000372569;ENST00000274990	D;D	0.87809	-2.3;-2.3	5.15	5.15	0.70609	Zinc finger, LIM-type (4);	0.067071	0.56097	D	0.000024	D	0.93785	0.8013	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.93	D	0.94474	0.7687	10	0.87932	D	0	-15.5663	16.1532	0.81636	0.0:0.0:1.0:0.0	.	45;45	Q6Q6R5;Q6Q6R5-3	CRIP3_HUMAN;.	E	45	ENSP00000361650:A45E;ENSP00000274990:A45E	ENSP00000274990:A45E	A	-	2	0	CRIP3	43384035	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	8.794000	0.91867	2.664000	0.90586	0.561000	0.74099	GCA	.	.		0.627	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			T	43276057	G	T	43276057	3	4	195	1	0	0	0	0	1	0	0	0	3878	1319	46	3	508	3	CRIP3	6	43276057	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	586442	43276057	127839010	71	28699										
CD2AP	23607	hgsc.bcm.edu	37	chr6	47548615	47548615	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aacagaaaccaaagaaaccaCcacctcctgctaaggctcca	5	15	0	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:47548615C>A	ENST00000359314.5	+	10	1480	c.1024C>A	c.(1024-1026)Cca>Aca	p.P342T		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	342	Pro-rich.				mitotic nuclear division (GO:0007067)|negative regulation of transforming growth factor beta1 production (GO:0032911)|positive regulation of protein localization to nucleus (GO:1900182)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of receptor-mediated endocytosis (GO:0048259)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|substrate-dependent cell migration, cell extension (GO:0006930)|vesicle organization (GO:0016050)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	20			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			AAAGAAACCACCACCTCCTGC	0.294																																					p.P342T		Atlas-SNP	.											.	CD2AP	43	.	0			c.C1024A						.						87	89	88					6																	47548615		2203	4298	6501	SO:0001583	missense	23607	exon10			AAACCACCACCTC	AF146277	CCDS34472.1	6p12	2008-02-05			ENSG00000198087	ENSG00000198087			14258	protein-coding gene	gene with protein product		604241				10339567	Standard	NM_012120		Approved	CMS	uc003oyw.3	Q9Y5K6	OTTHUMG00000014799	ENST00000359314.5:c.1024C>A	chr6.hg19:g.47548615C>A	ENSP00000352264:p.Pro342Thr	436.0	0.0		442.0	47.0	NM_012120	A6NL34|Q5VYA3|Q9UG97	Missense_Mutation	SNP	ENST00000359314.5	hg19	CCDS34472.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.607229	0.66558	.	.	ENSG00000198087	ENST00000359314	T	0.30448	1.53	5.42	4.55	0.56014	Src homology-3 domain (1);	0.098253	0.39146	U	0.001458	T	0.46483	0.1395	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.49476	-0.8936	10	0.34782	T	0.22	-3.8459	12.965	0.58480	0.0:0.9212:0.0:0.0788	.	342	Q9Y5K6	CD2AP_HUMAN	T	342	ENSP00000352264:P342T	ENSP00000352264:P342T	P	+	1	0	CD2AP	47656574	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.258000	0.65479	1.428000	0.47296	0.650000	0.86243	CCA	.	.		0.294	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2			A	47548615	C	A	47548615	3	1	195	1	0	0	0	0	1	0	0	0	2996	507	18	3	1062	3	CD2AP	6	47548615	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	4272558	47548615	123566452	72	28700										
RAB23	51715	hgsc.bcm.edu	37	chr6	57059644	57059644	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctttttgccagtgcctcagcTtcctcactgcacatcaattt	5	14	3	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:57059644T>A	ENST00000317483.3	-	5	1024	c.405A>T	c.(403-405)gaA>gaT	p.E135D	RAB23_ENST00000468148.1_Missense_Mutation_p.E135D	NM_016277.3	NP_057361.3	Q9ULC3	RAB23_HUMAN	RAB23, member RAS oncogene family	135					autophagic vacuole assembly (GO:0000045)|cellular defense response (GO:0006968)|cilium assembly (GO:0042384)|craniofacial suture morphogenesis (GO:0097094)|embryonic digit morphogenesis (GO:0042733)|GTP catabolic process (GO:0006184)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription factor import into nucleus (GO:0042992)|protein transport (GO:0015031)|regulation of smoothened signaling pathway (GO:0008589)|small GTPase mediated signal transduction (GO:0007264)|spinal cord dorsal/ventral patterning (GO:0021513)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	8	Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GTGCCTCAGCTTCCTCACTGC	0.308																																					p.E135D		Atlas-SNP	.											.	RAB23	22	.	0			c.A405T						.						76	71	72					6																	57059644		2202	4295	6497	SO:0001583	missense	51715	exon5			CTCAGCTTCCTCA	AB034244	CCDS4962.1	6p12.1	2008-05-15			ENSG00000112210	ENSG00000112210		"RAB, member RAS oncogene"	14263	protein-coding gene	gene with protein product		606144					Standard	NM_016277		Approved		uc003pdt.3	Q9ULC3	OTTHUMG00000014918	ENST00000317483.3:c.405A>T	chr6.hg19:g.57059644T>A	ENSP00000320413:p.Glu135Asp	203.0	0.0		220.0	68.0	NM_016277	B2R9I5|Q68DJ6|Q8NI06|Q9P023	Missense_Mutation	SNP	ENST00000317483.3	hg19	CCDS4962.1	.	.	.	.	.	.	.	.	.	.	T	17.64	3.439709	0.63067	.	.	ENSG00000112210	ENST00000317483;ENST00000468148	T;T	0.79033	-1.23;-1.23	5.89	2.16	0.27623	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.57198	0.2037	L	0.53780	1.695	0.54753	D	0.999988	B	0.28291	0.206	B	0.31337	0.128	T	0.52426	-0.8577	10	0.37606	T	0.19	-2.4056	9.4955	0.38986	0.0:0.2903:0.0:0.7097	.	135	Q9ULC3	RAB23_HUMAN	D	135	ENSP00000320413:E135D;ENSP00000417610:E135D	ENSP00000320413:E135D	E	-	3	2	RAB23	57167603	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	0.910000	0.28571	0.138000	0.18790	0.528000	0.53228	GAA	.	.		0.308	RAB23-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041042.1			A	57059644	T	A	57059644	3	1	195	1	0	0	0	0	1	0	0	0	12925	1606	56	4	320	4	RAB23	6	57059644	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	9511029	57059644	114055423	73	28701										
USP45	85015	hgsc.bcm.edu	37	chr6	99885203	99885203	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cacataagcagtgtagtggcCttctctcatcgagccactat	8	12	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:99885203C>G	ENST00000327681.6	-	17	2765	c.2233G>C	c.(2233-2235)Ggc>Cgc	p.G745R	USP45_ENST00000539675.1_Missense_Mutation_p.G38R|USP45_ENST00000392738.2_Missense_Mutation_p.G425R|USP45_ENST00000369233.2_Missense_Mutation_p.G697R|USP45_ENST00000500704.2_Missense_Mutation_p.G745R	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	745	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		GTGTAGTGGCCTTCTCTCATC	0.393																																					p.G745R		Atlas-SNP	.											.	USP45	56	.	0			c.G2233C						.						118	107	111					6																	99885203		2203	4300	6503	SO:0001583	missense	85015	exon17			AGTGGCCTTCTCT	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"Ubiquitin-specific peptidases"	20080	protein-coding gene	gene with protein product			"ubiquitin specific protease 45"			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.2233G>C	chr6.hg19:g.99885203C>G	ENSP00000333376:p.Gly745Arg	113.0	0.0		157.0	64.0	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	hg19	CCDS34501.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.014970	0.75161	.	.	ENSG00000123552	ENST00000392738;ENST00000500704;ENST00000327681;ENST00000539675;ENST00000369233	D;T;T;D;D	0.85629	-2.01;0.42;0.42;-2.01;-2.01	5.65	5.65	0.86999	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	D	0.95449	0.8522	H	0.97265	3.97	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96629	0.9465	10	0.87932	D	0	.	19.7072	0.96079	0.0:1.0:0.0:0.0	.	745;425	Q70EL2;Q70EL2-3	UBP45_HUMAN;.	R	425;745;745;38;697	ENSP00000376495:G425R;ENSP00000424372:G745R;ENSP00000333376:G745R;ENSP00000439569:G38R;ENSP00000358236:G697R	ENSP00000333376:G745R	G	-	1	0	USP45	99991924	1.000000	0.71417	0.999000	0.59377	0.134000	0.20937	7.329000	0.79170	2.662000	0.90505	0.591000	0.81541	GGC	.	.		0.393	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929		G	99885203	C	G	99885203	3	3	195	1	0	0	0	0	1	0	0	0	17091	681	24	4	219	4	USP45	6	99885203	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	42825559	99885203	71229864	74	28702										
NMBR	4829	hgsc.bcm.edu	37	chr6	142396877	142396877	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gcttttcagagatgtcatacGcaccgctgaagagctgagta	11	9	2	4			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:142396877G>A	ENST00000258042.1	-	3	1221	c.1081C>T	c.(1081-1083)Cgt>Tgt	p.R361C	NMBR_ENST00000480652.1_Intron	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	361					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)			breast(2)|central_nervous_system(3)|endometrium(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;9.93e-06)|GBM - Glioblastoma multiforme(68;0.0013)		GATGTCATACGCACCGCTGAA	0.473																																					p.R361C		Atlas-SNP	.											.	NMBR	62	.	0			c.C1081T						.						126	115	119					6																	142396877		2203	4300	6503	SO:0001583	missense	4829	exon3			TCATACGCACCGC		CCDS5196.1	6q24.1	2014-02-21			ENSG00000135577	ENSG00000135577		"GPCR / Class A : Bombesin receptors"	7843	protein-coding gene	gene with protein product	"bombesin receptor 1"	162341					Standard	NM_002511		Approved	BB1	uc003qiu.3	P28336	OTTHUMG00000015704	ENST00000258042.1:c.1081C>T	chr6.hg19:g.142396877G>A	ENSP00000258042:p.Arg361Cys	136.0	0.0		150.0	22.0	NM_002511	E9KL38|Q5VUK8	Missense_Mutation	SNP	ENST00000258042.1	hg19	CCDS5196.1	.	.	.	.	.	.	.	.	.	.	G	13.03	2.116013	0.37339	.	.	ENSG00000135577	ENST00000258042	T	0.69926	-0.44	5.28	3.31	0.37934	.	0.317119	0.34338	N	0.004056	T	0.43897	0.1268	L	0.41961	1.31	0.58432	D	0.999994	B	0.15930	0.015	B	0.13407	0.009	T	0.49624	-0.8920	10	0.46703	T	0.11	-1.0378	13.7386	0.62833	0.0:0.0:0.7121:0.2879	.	361	P28336	NMBR_HUMAN	C	361	ENSP00000258042:R361C	ENSP00000258042:R361C	R	-	1	0	NMBR	142438570	1.000000	0.71417	0.836000	0.33094	0.908000	0.53690	3.094000	0.50227	1.293000	0.44690	0.655000	0.94253	CGT	.	.		0.473	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1			A	142396877	G	A	142396877	3	1	195	1	0	0	0	0	1	0	0	0	10496	1087	38	1	95	1	NMBR	6	142396877	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	42511674	142396877	28718190	75	28703										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157405805	157405805	+	Frame_Shift_Del	DEL	G	G	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tcctttcttaggatctgtctGgctccattgatgacctcccc							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr6:157405805delG	ENST00000350026.5	+	5	2009	c.2008delG	c.(2008-2010)ggcfs	p.G670fs	ARID1B_ENST00000275248.4_Frame_Shift_Del_p.G612fs|ARID1B_ENST00000367148.1_Frame_Shift_Del_p.G670fs|ARID1B_ENST00000346085.5_Frame_Shift_Del_p.G683fs	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	670					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GGATCTGTCTGGCTCCATTGA	0.488																																					p.S682fs		Atlas-INDEL	.											.	ARID1B	320	.	0			c.2046delT						.						108	104	106					6																	157405805		2203	4300	6503	SO:0001589	frameshift_variant	57492	exon6			.	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.2008delG	chr6.hg19:g.157405805delG	ENSP00000055163:p.Gly670fs	80.0	0.0		69.0	10.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Frame_Shift_Del	DEL	ENST00000350026.5	hg19	CCDS5251.2																																																																																			.	.		0.488	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		-	157405805	G	-	157405805	7	5	195	1	0	1	0	1	0	0	0	0	914	1348	47	0	2069	0	ARID1B	6	157405805	Frame_Shift_Del	DEL	G	TCGA-DD-AADM-01A-11D-A40R-10	15008928	157405805	13709262	76	28704										
ADAP1	11033	hgsc.bcm.edu	37	chr7	959636	959636	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ggctcctgcttctccgggtaGatgaactcctgtcgctcgta	11	13	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:959636G>A	ENST00000265846.5	-	4	576	c.357C>T	c.(355-357)atC>atT	p.I119I	ADAP1_ENST00000449296.2_Silent_p.I47I|ADAP1_ENST00000463358.1_5'UTR|ADAP1_ENST00000539900.1_Silent_p.I130I	NM_001284308.1|NM_001284309.1|NM_001284311.1|NM_006869.2	NP_001271237.1|NP_001271238.1|NP_001271240.1|NP_006860	O75689	ADAP1_HUMAN	ArfGAP with dual PH domains 1	119	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cell surface receptor signaling pathway (GO:0007166)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF GTPase activity (GO:0032312)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	6						TCTCCGGGTAGATGAACTCCT	0.677																																					p.I119I		Atlas-SNP	.											.	ADAP1	23	.	0			c.C357T						.						39	36	37					7																	959636		2200	4297	6497	SO:0001819	synonymous_variant	11033	exon4			CGGGTAGATGAAC	AJ006422	CCDS5318.1, CCDS64576.1, CCDS64577.1, CCDS75558.1	7p22.3	2013-01-10	2008-09-22	2008-09-22	ENSG00000105963	ENSG00000105963		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16486	protein-coding gene	gene with protein product		608114	"centaurin, alpha 1"	CENTA1		10333475	Standard	NM_006869		Approved	GCS1L	uc003sjo.4	O75689	OTTHUMG00000023380	ENST00000265846.5:c.357C>T	chr7.hg19:g.959636G>A		24.0	0.0		37.0	13.0	NM_006869	A4D2Q2|B3KRZ4|B4DVA6|F6XZ68|H7C2Q4	Silent	SNP	ENST00000265846.5	hg19	CCDS5318.1	.	.	.	.	.	.	.	.	.	.	G	0.972	-0.699933	0.03279	.	.	ENSG00000105963	ENST00000446141;ENST00000437486;ENST00000453823	.	.	.	4.53	-7.15	0.01521	.	.	.	.	.	T	0.19287	0.0463	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.31447	-0.9943	4	.	.	.	-4.6985	5.5999	0.17347	0.1558:0.5072:0.2331:0.1038	.	.	.	.	F	102;53;62	.	.	S	-	2	0	ADAP1	926162	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.117000	0.10708	-1.009000	0.03400	0.549000	0.68633	TCT	.	.		0.677	ADAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059701.2	NM_006869		A	959636	G	A	959636	2	1	195	1	0	0	0	0	0	0	0	1	279	932	33	3		3	ADAP1	7	959636	Silent	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10		959636	158179027	77	28705										
ZNF680	340252	hgsc.bcm.edu	37	chr7	63982713	63982713	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tcaaacattggttaagttcaTtataaccttctttgaacacc	4	9	3	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:63982713T>G	ENST00000309683.6	-	4	570	c.419A>C	c.(418-420)aAt>aCt	p.N140T	ZNF680_ENST00000476563.1_5'UTR	NM_178558.4	NP_848653.2	Q8NEM1	ZN680_HUMAN	zinc finger protein 680	140					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	27		Lung NSC(55;0.118)|all_lung(88;0.243)				GTTAAGTTCATTATAACCTTC	0.308																																					p.N140T		Atlas-SNP	.											.	ZNF680	58	.	0			c.A419C						.						58	61	60					7																	63982713		2203	4291	6494	SO:0001583	missense	340252	exon4			AGTTCATTATAAC	AK074911	CCDS34644.1, CCDS47594.1	7q11.21	2013-01-08			ENSG00000173041	ENSG00000173041		"Zinc fingers, C2H2-type", "-"	26897	protein-coding gene	gene with protein product	"hypothetical protein FLJ90430"					12477932	Standard	NM_178558		Approved	FLJ90430	uc003tta.2	Q8NEM1	OTTHUMG00000156542	ENST00000309683.6:c.419A>C	chr7.hg19:g.63982713T>G	ENSP00000309330:p.Asn140Thr	190.0	0.0		213.0	47.0	NM_178558	B3KVJ4|Q6ZNF3|Q8NC79	Missense_Mutation	SNP	ENST00000309683.6	hg19	CCDS34644.1	.	.	.	.	.	.	.	.	.	.	t	6.507	0.461751	0.12342	.	.	ENSG00000173041	ENST00000309683	T	0.04917	3.53	1.09	1.09	0.20402	.	.	.	.	.	T	0.09202	0.0227	M	0.80028	2.48	0.09310	N	1	B	0.30914	0.3	B	0.29077	0.098	T	0.24941	-1.0146	9	0.62326	D	0.03	.	4.2287	0.10592	0.0:0.0:0.0:1.0	.	140	Q8NEM1	ZN680_HUMAN	T	140	ENSP00000309330:N140T	ENSP00000309330:N140T	N	-	2	0	ZNF680	63620148	0.000000	0.05858	0.068000	0.19968	0.064000	0.16182	0.197000	0.17197	0.413000	0.25759	0.402000	0.26972	AAT	.	.		0.308	ZNF680-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344568.1	NM_178558		G	63982713	T	G	63982713	3	3	195	1	0	0	0	0	1	0	0	0	18102	1493	52	5	1177	5	ZNF680	7	63982713	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	63023077	63982713	95155950	78	28706										
RHBDD2	57414	hgsc.bcm.edu	37	chr7	75511209	75511209	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tctccctgctctgcggcgctAtcatcatctggcgctttgct	9	15	5	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:75511209A>G	ENST00000006777.6	+	2	376	c.241A>G	c.(241-243)Atc>Gtc	p.I81V	RHBDD2_ENST00000318622.4_5'UTR|RHBDD2_ENST00000468304.1_Intron|RHBDD2_ENST00000428119.1_5'Flank	NM_001040456.1	NP_001035546.1	Q6NTF9	RHBD2_HUMAN	rhomboid domain containing 2	81						Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|lung(4)|prostate(1)	6						CTGCGGCGCTATCATCATCTG	0.557																																					p.I81V		Atlas-SNP	.											.	RHBDD2	49	.	0			c.A241G						.						113	120	118					7																	75511209		2066	4215	6281	SO:0001583	missense	57414	exon2			GGCGCTATCATCA	AF226732	CCDS43602.1, CCDS43603.1	7q11	2008-09-04	2006-02-22	2006-02-22	ENSG00000005486	ENSG00000005486			23082	protein-coding gene	gene with protein product		615203	"rhomboid, veinlet-like 7 (Drosophila)"	RHBDL7		12838346	Standard	XM_005250511		Approved	NPD007	uc003udw.1	Q6NTF9	OTTHUMG00000156435	ENST00000006777.6:c.241A>G	chr7.hg19:g.75511209A>G	ENSP00000006777:p.Ile81Val	123.0	0.0		135.0	27.0	NM_001040456	Q7L534|Q9H5W6|Q9HBK7|Q9UDT2	Missense_Mutation	SNP	ENST00000006777.6	hg19	CCDS43602.1	.	.	.	.	.	.	.	.	.	.	A	7.510	0.654450	0.14580	.	.	ENSG00000005486	ENST00000006777;ENST00000413229	T	0.13538	2.58	5.5	-3.23	0.05109	Peptidase S54, rhomboid domain (1);	0.877863	0.10021	N	0.725943	T	0.04634	0.0126	N	0.03608	-0.345	0.27211	N	0.959908	B	0.02656	0.0	B	0.06405	0.002	T	0.45948	-0.9226	10	0.15952	T	0.53	-9.5901	7.6913	0.28569	0.1651:0.4177:0.4171:0.0	.	81	Q6NTF9	RHBD2_HUMAN	V	81;126	ENSP00000006777:I81V	ENSP00000006777:I81V	I	+	1	0	RHBDD2	75349145	0.000000	0.05858	0.031000	0.17742	0.787000	0.44495	-0.513000	0.06305	-0.476000	0.06842	-0.371000	0.07208	ATC	.	.		0.557	RHBDD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344176.1	NM_020684		G	75511209	A	G	75511209	3	3	195	1	0	0	0	0	1	0	0	0	13332	449	16	2	247	2	RHBDD2	7	75511209	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	11528496	75511209	83627454	79	28707										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77549626	77549626	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gcaaagaattcaattgataaAtcaactgaaactgacaatgg	7	6	2	4			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:77549626A>G	ENST00000248550.7	+	9	883	c.807A>G	c.(805-807)aaA>aaG	p.K269K	PHTF2_ENST00000450574.1_Silent_p.K235K|PHTF2_ENST00000422959.2_Silent_p.K235K|PHTF2_ENST00000416283.2_Silent_p.K235K|PHTF2_ENST00000275575.7_Silent_p.K231K|PHTF2_ENST00000424760.1_Silent_p.K231K|PHTF2_ENST00000307305.8_Silent_p.K231K|PHTF2_ENST00000454592.1_3'UTR|PHTF2_ENST00000415251.2_Silent_p.K231K			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	269					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						CAATTGATAAATCAACTGAAA	0.323																																					p.K235K		Atlas-SNP	.											.	PHTF2	104	.	0			c.A705G						.						50	47	48					7																	77549626		1827	4077	5904	SO:0001819	synonymous_variant	57157	exon8			TGATAAATCAACT	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.807A>G	chr7.hg19:g.77549626A>G		101.0	0.0		118.0	25.0	NM_001127359	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Silent	SNP	ENST00000248550.7	hg19																																																																																				.	.		0.323	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		G	77549626	A	G	77549626	2	3	195	1	0	0	0	0	0	0	0	1	11872	98	4	2		2	PHTF2	7	77549626	Silent	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	2038417	77549626	81589037	80	28708										
CD36	948	hgsc.bcm.edu	37	chr7	80276132	80276132	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tggctgtgtttggaggtattCtaatgccagttggagacctg	14	6	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:80276132C>G	ENST00000435819.1	+	6	760	c.76C>G	c.(76-78)Cta>Gta	p.L26V	CD36_ENST00000309881.7_Missense_Mutation_p.L26V|CD36_ENST00000441109.2_3'UTR|CD36_ENST00000538969.1_Missense_Mutation_p.L26V|CD36_ENST00000447544.2_Missense_Mutation_p.L26V|CD36_ENST00000433696.2_Missense_Mutation_p.L26V|CD36_ENST00000534394.1_Intron|CD36_ENST00000544133.1_Missense_Mutation_p.L26V|CD36_ENST00000394788.3_Missense_Mutation_p.L26V|CD36_ENST00000432207.1_Missense_Mutation_p.L26V			P16671	CD36_HUMAN	CD36 molecule (thrombospondin receptor)	26					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular lipid metabolic process (GO:0044255)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to hydroperoxide (GO:0071447)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cGMP-mediated signaling (GO:0019934)|cholesterol transport (GO:0030301)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|lipoprotein transport (GO:0042953)|long-chain fatty acid import (GO:0044539)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle mediated signaling (GO:0055096)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitric oxide mediated signal transduction (GO:0007263)|phagocytosis, recognition (GO:0006910)|plasma lipoprotein particle clearance (GO:0034381)|plasma membrane long-chain fatty acid transport (GO:0015911)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood microparticle formation (GO:2000334)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of removal of superoxide radicals (GO:2000121)|response to stilbenoid (GO:0035634)|small molecule metabolic process (GO:0044281)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|lipoteichoic acid receptor activity (GO:0070892)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|thrombospondin receptor activity (GO:0070053)|transforming growth factor beta binding (GO:0050431)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(10)|large_intestine(1)|lung(6)|ovary(1)	21						TGGAGGTATTCTAATGCCAGT	0.438																																					p.L26V		Atlas-SNP	.											CD36_ENST00000447544,colon,carcinoma,0,4	CD36	185	.	0			c.C76G						.						197	182	187					7																	80276132		2203	4300	6503	SO:0001583	missense	948	exon1			GGTATTCTAATGC	Z32770	CCDS34673.1	7q11.2	2010-02-26	2006-03-28		ENSG00000135218	ENSG00000135218		"CD molecules"	1663	protein-coding gene	gene with protein product		173510	"CD36 antigen (collagen type I receptor, thrombospondin receptor)"			7503937	Standard	NM_001001548		Approved	SCARB3, GPIV, FAT, GP4, GP3B	uc003uhg.4	P16671	OTTHUMG00000155383	ENST00000435819.1:c.76C>G	chr7.hg19:g.80276132C>G	ENSP00000399421:p.Leu26Val	174.0	0.0		164.0	27.0	NM_001127444	D9IX66|D9IX67|D9IX68|D9IX69|Q13966|Q16093|Q8TCV7|Q9BPZ8|Q9BQC2|Q9BZM8|Q9BZN3|Q9BZN4|Q9BZN5	Missense_Mutation	SNP	ENST00000435819.1	hg19	CCDS34673.1	.	.	.	.	.	.	.	.	.	.	C	19.77	3.888412	0.72524	.	.	ENSG00000135218	ENST00000435819;ENST00000309881;ENST00000438020;ENST00000436384;ENST00000428497;ENST00000482059;ENST00000394788;ENST00000447544;ENST00000426978;ENST00000432207;ENST00000413265;ENST00000419819;ENST00000538969;ENST00000544133;ENST00000433696	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.82472	0.5044	M	0.66297	2.02	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.82018	-0.0665	9	.	.	.	-13.3208	16.194	0.82011	0.0:1.0:0.0:0.0	.	26	P16671	CD36_HUMAN	V	26	ENSP00000399421:L26V;ENSP00000308165:L26V;ENSP00000410371:L26V;ENSP00000398760:L26V;ENSP00000409762:L26V;ENSP00000433659:L26V;ENSP00000378268:L26V;ENSP00000415743:L26V;ENSP00000416388:L26V;ENSP00000411411:L26V;ENSP00000407690:L26V;ENSP00000392298:L26V;ENSP00000439543:L26V;ENSP00000441956:L26V;ENSP00000401863:L26V	.	L	+	1	2	CD36	80114068	0.995000	0.38212	0.747000	0.31113	0.830000	0.47004	2.939000	0.48995	2.552000	0.86080	0.655000	0.94253	CTA	.	.		0.438	CD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339767.6	NM_001001547		G	80276132	C	G	80276132	3	3	195	1	0	0	0	0	1	0	0	0	3009	912	32	4	78	4	CD36	7	80276132	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	2726506	80276132	78862531	81	28709										
PCLO	27445	hgsc.bcm.edu	37	chr7	82584346	82584346	+	Missense_Mutation	SNP	T	T	C													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	attttcttcttcttgccttgTtagcagactgccatctaccg							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:82584346T>C	ENST00000333891.9	-	5	6260	c.5923A>G	c.(5923-5925)Aca>Gca	p.T1975A	PCLO_ENST00000423517.2_Missense_Mutation_p.T1975A	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCTTGCCTTGTTAGCAGACTG	0.363																																					p.T1975A		Atlas-SNP	.											.	PCLO	1506	.	0			c.A5923G						.						116	119	118					7																	82584346		1877	4102	5979	SO:0001583	missense	27445	exon5			GCCTTGTTAGCAG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5923A>G	chr7.hg19:g.82584346T>C	ENSP00000334319:p.Thr1975Ala	136.0	0.0		155.0	31.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	2.254	-0.370838	0.05034	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.15718	2.4;2.4	5.57	-0.861	0.10676	.	.	.	.	.	T	0.09642	0.0237	N	0.16478	0.41	0.09310	N	1	B;B	0.11235	0.004;0.004	B;B	0.11329	0.006;0.006	T	0.31833	-0.9929	9	0.87932	D	0	.	6.0348	0.19702	0.0:0.2705:0.1251:0.6044	.	1975;1975	Q9Y6V0-5;Q9Y6V0-6	.;.	A	1906;1975;1975	ENSP00000334319:T1975A;ENSP00000388393:T1975A	ENSP00000334319:T1975A	T	-	1	0	PCLO	82422282	0.000000	0.05858	0.025000	0.17156	0.559000	0.35586	-0.151000	0.10175	-0.140000	0.11394	0.533000	0.62120	ACA	.	.		0.363	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82584346	T	C	82584346	3	2	195	1	0	0	0	0	1	0	0	0	11592	1725	60	2	9606	2	PCLO	7	82584346	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	2308214	82584346	76554317	82	28710	146	2								
PCLO	27445	hgsc.bcm.edu	37	chr7	82584348	82584348	+	Missense_Mutation	SNP	A	A	G													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tttcttcttcttgccttgttAgcagactgccatctaccgat							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:82584348A>G	ENST00000333891.9	-	5	6258	c.5921T>C	c.(5920-5922)cTa>cCa	p.L1974P	PCLO_ENST00000423517.2_Missense_Mutation_p.L1974P	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTGCCTTGTTAGCAGACTGCC	0.358																																					p.L1974P		Atlas-SNP	.											.	PCLO	1506	.	0			c.T5921C						.						115	117	117					7																	82584348		1877	4099	5976	SO:0001583	missense	27445	exon5			CTTGTTAGCAGAC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5921T>C	chr7.hg19:g.82584348A>G	ENSP00000334319:p.Leu1974Pro	138.0	0.0		153.0	30.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	1.252	-0.618246	0.03663	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17213	2.29;2.29	5.57	4.34	0.51931	.	.	.	.	.	T	0.16300	0.0392	L	0.36672	1.1	0.09310	N	0.999999	P;P	0.48503	0.911;0.911	P;P	0.44811	0.461;0.461	T	0.11446	-1.0587	9	0.87932	D	0	.	7.4764	0.27378	0.8009:0.0:0.0712:0.1279	.	1974;1974	Q9Y6V0-5;Q9Y6V0-6	.;.	P	1905;1974;1974	ENSP00000334319:L1974P;ENSP00000388393:L1974P	ENSP00000334319:L1974P	L	-	2	0	PCLO	82422284	0.003000	0.15002	0.755000	0.31263	0.554000	0.35429	1.891000	0.39738	2.116000	0.64780	0.533000	0.62120	CTA	.	.		0.358	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82584348	A	G	82584348	3	3	195	1	0	0	0	0	1	0	0	0	11592	420	15	2	9608	2	PCLO	7	82584348	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	2	82584348	76554315	83	28711	146	2								
ADAM22	53616	hgsc.bcm.edu	37	chr7	87780310	87780310	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tcctagtgtgcccctaatatTcataaaatggatggatattc	7	8	1	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:87780310T>A	ENST00000265727.7	+	19	1660	c.1581T>A	c.(1579-1581)atT>atA	p.I527I	ADAM22_ENST00000398209.3_Silent_p.I527I|ADAM22_ENST00000398201.4_Silent_p.I527I|ADAM22_ENST00000398204.4_Silent_p.I527I|ADAM22_ENST00000315984.7_Silent_p.I527I			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	527	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			CCCCTAATATTCATAAAATGG	0.338																																					p.I527I		Atlas-SNP	.											.	ADAM22	280	.	0			c.T1581A						.						198	184	188					7																	87780310		1836	4082	5918	SO:0001819	synonymous_variant	53616	exon19			TAATATTCATAAA	AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277		"ADAM metallopeptidase domain containing"	201	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2"	603709	"a disintegrin and metalloproteinase domain 22"			9693107, 10524237	Standard	NM_021723		Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.1581T>A	chr7.hg19:g.87780310T>A		155.0	0.0		210.0	21.0	NM_021722	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Silent	SNP	ENST00000265727.7	hg19	CCDS47637.1																																																																																			.	.		0.338	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723		A	87780310	T	A	87780310	2	1	195	1	0	0	0	0	0	0	0	1	244	1771	62	4		4	ADAM22	7	87780310	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	5195962	87780310	71358353	84	28712										
ZNF3	7551	hgsc.bcm.edu	37	chr7	99669473	99669494	+	Frame_Shift_Del	DEL	TTCGATTAAAGCTCTTGCTACA	TTCGATTAAAGCTCTTGCTACA	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	atgttgaataaggtctgaagTtcgattaaagctcttgctac					rs199648870		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	TTCGATTAAAGCTCTTGCTACA	TTCGATTAAAGCTCTTGCTACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:99669473_99669494delTTCGATTAAAGCTCTTGCTACA	ENST00000424697.1	-	6	919_940	c.613_634delTGTAGCAAGAGCTTTAATCGAA	c.(613-636)tgtagcaagagctttaatcgaactfs	p.CSKSFNRT205fs	ZNF3_ENST00000303915.6_Frame_Shift_Del_p.CSKSFNRT205fs|ZNF3_ENST00000299667.4_Frame_Shift_Del_p.CSKSFNRT205fs|ZNF3_ENST00000413658.2_Intron	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	205					cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)	p.S206R(1)		NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			AGGTCTGAAGTTCGATTAAAGCTCTTGCTACATTCATCACAC	0.441																																					p.205_212del		Atlas-Indel,Pindel	.											ZNF3,extremity,malignant_melanoma,0,1	ZNF3	54	.	1	Substitution - Missense(1)	lung(1)	c.614_635del						.																																			SO:0001589	frameshift_variant	7551	exon6			.	AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"Zinc fingers, C2H2-type", "-"	13089	protein-coding gene	gene with protein product		194510	"zinc finger protein 3 (A8-51)"				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.613_634delTGTAGCAAGAGCTTTAATCGAA	chr7.hg19:g.99669473_99669494delTTCGATTAAAGCTCTTGCTACA	ENSP00000415358:p.Cys205fs	92.0	0.0		157.0	17.0	NM_032924	D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Frame_Shift_Del	DEL	ENST00000424697.1	hg19	CCDS43619.1																																																																																			.	.		0.441	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	NM_017715		-	99669494	TTCGATTAAAGCTCTTGCTACA	-	99669473	7	5	195	1	0	1	0	1	0	0	0	0	17844	1725	60	0	839	0	ZNF3	7	99669473	Frame_Shift_Del	DEL	TTCGATTAAAGCTCTTGCTACA	TCGA-DD-AADM-01A-11D-A40R-10	11889163	99669473	59469190	85	28713										
RELN	5649	hgsc.bcm.edu	37	chr7	103155875	103155875	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tttagcatcaggagggagaaGgatattcacaaatctatagg	11	5	3	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:103155875G>C	ENST00000428762.1	-	50	8035	c.7876C>G	c.(7876-7878)Ctt>Gtt	p.L2626V	RELN_ENST00000424685.2_Missense_Mutation_p.L2626V|CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000343529.5_Missense_Mutation_p.L2626V	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2626					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GGAGGGAGAAGGATATTCACA	0.468																																					p.L2626V	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C7876G						.						46	49	48					7																	103155875		2203	4300	6503	SO:0001583	missense	5649	exon50			GGAGAAGGATATT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.7876C>G	chr7.hg19:g.103155875G>C	ENSP00000392423:p.Leu2626Val	61.0	0.0		95.0	46.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783825	0.49891	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000424828;ENST00000448171	T;T;T	0.24151	1.87;1.87;1.87	5.12	5.12	0.69794	Neuraminidase (2);	0.063695	0.64402	D	0.000005	T	0.24470	0.0593	L	0.36672	1.1	0.51012	D	0.999906	B;B	0.15473	0.013;0.004	B;B	0.24006	0.05;0.016	T	0.04090	-1.0978	10	0.21540	T	0.41	.	18.7499	0.91810	0.0:0.0:1.0:0.0	.	2626;2626	P78509-2;P78509	.;RELN_HUMAN	V	2626;2626;2626;143;2626	ENSP00000392423:L2626V;ENSP00000345694:L2626V;ENSP00000388446:L2626V	ENSP00000345694:L2626V	L	-	1	0	RELN	102943111	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.381000	0.79718	2.647000	0.89833	0.643000	0.83706	CTT	.	.		0.468	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103155875	G	C	103155875	3	2	195	1	0	0	0	0	1	0	0	0	13235	1000	35	4	2570	4	RELN	7	103155875	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	3486402	103155875	55982788	86	28714										
ATXN7L1	222255	hgsc.bcm.edu	37	chr7	105260694	105260694	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tctaccatggagtttagtgcGaatcgaaaacgatcccatct	8	10	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:105260694G>A	ENST00000419735.3	-	9	1515	c.1470C>T	c.(1468-1470)ttC>ttT	p.F490F	ATXN7L1_ENST00000388807.4_Silent_p.F48F|ATXN7L1_ENST00000477775.1_Silent_p.F366F|ATXN7L1_ENST00000472910.1_5'UTR	NM_020725.1	NP_065776.1	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1	490										endometrium(1)|large_intestine(4)|lung(5)	10						AGTTTAGTGCGAATCGAAAAC	0.408																																					p.F490F		Atlas-SNP	.											ATXN7L1_ENST00000419735,NS,carcinoma,0,1	ATXN7L1	56	.	0			c.C1470T						.						164	126	138					7																	105260694		692	1591	2283	SO:0001819	synonymous_variant	222255	exon9			TAGTGCGAATCGA	AB033044	CCDS34727.1, CCDS47682.1, CCDS47683.1	7q22.1	2007-11-13			ENSG00000146776	ENSG00000146776			22210	protein-coding gene	gene with protein product			"ataxin 7-like 4"	ATXN7L4		15115762	Standard	NM_152749		Approved	KIAA1218, MGC33190	uc003vde.2	Q9ULK2	OTTHUMG00000157521	ENST00000419735.3:c.1470C>T	chr7.hg19:g.105260694G>A		170.0	1.0		228.0	38.0	NM_020725	A4D0Q2|B4DTS1|Q8N2T0	Silent	SNP	ENST00000419735.3	hg19	CCDS47682.1																																																																																			.	.		0.408	ATXN7L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349037.2			A	105260694	G	A	105260694	2	1	195	1	0	0	0	0	0	0	0	1	1216	1049	37	1		1	ATXN7L1	7	105260694	Silent	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	2104819	105260694	53877969	87	28715										
GPR22	2845	hgsc.bcm.edu	37	chr7	107115516	107115516	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gttttaaataccaccattttAtgtttaggcccaagtgacct	6	9	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:107115516A>G	ENST00000304402.4	+	3	2354	c.1011A>G	c.(1009-1011)ttA>ttG	p.L337L	COG5_ENST00000393603.2_Intron|COG5_ENST00000347053.3_Intron|COG5_ENST00000297135.3_Intron|COG5_ENST00000475638.2_Intron	NM_005295.2	NP_005286.2	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	337					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(3)|lung(6)|ovary(2)|stomach(1)	12						CCACCATTTTATGTTTAGGCC	0.328																																					p.L337L		Atlas-SNP	.											.	GPR22	43	.	0			c.A1011G						.						92	95	94					7																	107115516		2203	4299	6502	SO:0001819	synonymous_variant	2845	exon3			CATTTTATGTTTA	U66581	CCDS5744.1	7q22-q31.1	2012-08-21			ENSG00000172209	ENSG00000172209		"GPCR / Class A : Orphans"	4477	protein-coding gene	gene with protein product		601910				9073069	Standard	NM_005295		Approved		uc003vef.3	Q99680	OTTHUMG00000154902	ENST00000304402.4:c.1011A>G	chr7.hg19:g.107115516A>G		297.0	0.0		392.0	33.0	NM_005295	O14554	Silent	SNP	ENST00000304402.4	hg19	CCDS5744.1																																																																																			.	.		0.328	GPR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337598.1			G	107115516	A	G	107115516	2	3	195	1	0	0	0	0	0	0	0	1	6690	446	16	2		2	GPR22	7	107115516	Silent	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	1854822	107115516	52023147	88	28716										
ZNF800	168850	hgsc.bcm.edu	37	chr7	127014269	127014269	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	caatttgcatatgtcttttaAgcattatttgtgaactatat	5	5	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:127014269A>G	ENST00000393313.1	-	5	1712	c.1121T>C	c.(1120-1122)cTt>cCt	p.L374P	ZNF800_ENST00000393312.1_Missense_Mutation_p.L374P|ZNF800_ENST00000485577.1_5'Flank|ZNF800_ENST00000265827.3_Missense_Mutation_p.L374P			Q2TB10	ZN800_HUMAN	zinc finger protein 800	374					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						ATGTCTTTTAAGCATTATTTG	0.328																																					p.L374P		Atlas-SNP	.											.	ZNF800	78	.	0			c.T1121C						.						90	96	94					7																	127014269		2203	4299	6502	SO:0001583	missense	168850	exon5			CTTTTAAGCATTA	AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"Zinc fingers, C2H2-type"	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.1121T>C	chr7.hg19:g.127014269A>G	ENSP00000376989:p.Leu374Pro	119.0	0.0		140.0	32.0	NM_176814	Q9HBN0	Missense_Mutation	SNP	ENST00000393313.1	hg19	CCDS5795.1	.	.	.	.	.	.	.	.	.	.	A	14.58	2.576874	0.45902	.	.	ENSG00000048405	ENST00000393313;ENST00000265827;ENST00000393312	T;T;T	0.42900	0.96;0.96;0.96	5.68	5.68	0.88126	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.64402	D	0.000001	T	0.49064	0.1535	N	0.19112	0.55	0.35601	D	0.807858	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.53556	-0.8422	8	.	.	.	-0.3006	15.1137	0.72380	1.0:0.0:0.0:0.0	.	277;374	B7Z4V7;Q2TB10	.;ZN800_HUMAN	P	374	ENSP00000376989:L374P;ENSP00000265827:L374P;ENSP00000376988:L374P	.	L	-	2	0	ZNF800	126801505	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.447000	0.90332	2.169000	0.68431	0.528000	0.53228	CTT	.	.		0.328	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814		G	127014269	A	G	127014269	3	3	195	1	0	0	0	0	1	0	0	0	18184	72	3	2	881	2	ZNF800	7	127014269	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	19898753	127014269	32124394	89	28717										
TRPV5	56302	hgsc.bcm.edu	37	chr7	142605697	142605697	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	taatcaaaaatggtagacctCctctccatccccctcactaa	3	15	3	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:142605697C>A	ENST00000265310.1	-	15	2521	c.2173G>T	c.(2173-2175)Gag>Tag	p.E725*		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	725	Involved in Ca(2+)-dependent inactivation. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					TGGTAGACCTCCTCTCCATCC	0.557																																					p.E725X		Atlas-SNP	.											.	TRPV5	164	.	0			c.G2173T						.						114	108	110					7																	142605697		2203	4300	6503	SO:0001587	stop_gained	56302	exon15			AGACCTCCTCTCC	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.2173G>T	chr7.hg19:g.142605697C>A	ENSP00000265310:p.Glu725*	187.0	0.0		254.0	35.0	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Nonsense_Mutation	SNP	ENST00000265310.1	hg19	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.139200	0.56936	.	.	ENSG00000127412	ENST00000265310;ENST00000439304	.	.	.	4.99	4.99	0.66335	.	0.563480	0.18473	N	0.140160	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-21.222	15.5865	0.76489	0.0:1.0:0.0:0.0	.	.	.	.	X	725;670	.	ENSP00000265310:E725X	E	-	1	0	TRPV5	142315819	0.999000	0.42202	0.979000	0.43373	0.166000	0.22503	2.606000	0.46291	2.615000	0.88500	0.655000	0.94253	GAG	.	.		0.557	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		A	142605697	C	A	142605697	4	1	195	1	0	0	0	0	0	1	0	0	16614	864	30	3	20	3	TRPV5	7	142605697	Nonsense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	15591428	142605697	16532966	90	28718										
TRPV5	56302	hgsc.bcm.edu	37	chr7	142627485	142627485	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgcagtccagtagaagttgcCtaagaacagacaggtcattt	10	8	1	3			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr7:142627485C>A	ENST00000265310.1	-	2	533	c.185G>T	c.(184-186)aGg>aTg	p.R62M	TRPV5_ENST00000442623.1_Missense_Mutation_p.R62M	NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	62					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					TAGAAGTTGCCTAAGAACAGA	0.512																																					p.R62M		Atlas-SNP	.											.	TRPV5	164	.	0			c.G185T						.						193	157	169					7																	142627485		2203	4300	6503	SO:0001583	missense	56302	exon2			AGTTGCCTAAGAA	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.185G>T	chr7.hg19:g.142627485C>A	ENSP00000265310:p.Arg62Met	115.0	0.0		176.0	27.0	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	hg19	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	C	4.871	0.161845	0.09287	.	.	ENSG00000127412	ENST00000265310;ENST00000439304;ENST00000442623	T;T;T	0.66815	0.55;-0.23;-0.22	4.56	0.491	0.16867	Ankyrin repeat-containing domain (3);	0.510188	0.22932	N	0.053884	T	0.55386	0.1917	L	0.53729	1.69	0.09310	N	1	B;B	0.16802	0.004;0.019	B;B	0.19666	0.026;0.012	T	0.48163	-0.9059	10	0.46703	T	0.11	-11.3004	5.9427	0.19201	0.0:0.3648:0.1385:0.4967	.	62;62	E9PBZ6;Q9NQA5	.;TRPV5_HUMAN	M	62;56;62	ENSP00000265310:R62M;ENSP00000406361:R56M;ENSP00000406572:R62M	ENSP00000265310:R62M	R	-	2	0	TRPV5	142337607	1.000000	0.71417	0.009000	0.14445	0.477000	0.33069	0.903000	0.28475	-0.003000	0.14444	-0.253000	0.11424	AGG	.	.		0.512	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		A	142627485	C	A	142627485	3	1	195	1	0	0	0	0	1	0	0	0	16614	681	24	3	2060	3	TRPV5	7	142627485	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	21788	142627485	16511178	91	28719										
MTUS1	57509	hgsc.bcm.edu	37	chr8	17612099	17612099	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	caagtcagtccaaatgacgaGcccaccttttgtcctggcgg	10	13	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr8:17612099G>A	ENST00000262102.6	-	2	1442	c.1218C>T	c.(1216-1218)ggC>ggT	p.G406G	MTUS1_ENST00000381862.3_Silent_p.G406G|MTUS1_ENST00000519263.1_Silent_p.G406G|MTUS1_ENST00000381869.3_Silent_p.G406G	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	406					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		CAAATGACGAGCCCACCTTTT	0.443																																					p.G406G		Atlas-SNP	.											.	MTUS1	144	.	0			c.C1218T						.						77	73	74					8																	17612099		1874	4105	5979	SO:0001819	synonymous_variant	57509	exon2			TGACGAGCCCACC	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.1218C>T	chr8.hg19:g.17612099G>A		104.0	0.0		85.0	51.0	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	hg19	CCDS43717.1																																																																																			.	.		0.443	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		A	17612099	G	A	17612099	2	1	195	1	0	0	0	0	0	0	0	1	9974	958	34	3		3	MTUS1	8	17612099	Silent	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10		17612099	128751923	92	28720										
WRN	7486	hgsc.bcm.edu	37	chr8	30958398	30958398	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgctgtggatgaggctcactGtatttctgagtgggggcatg	16	6	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr8:30958398G>A	ENST00000298139.5	+	18	2264	c.2015G>A	c.(2014-2016)tGt>tAt	p.C672Y		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	672	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		GAGGCTCACTGTATTTCTGAG	0.418			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.C672Y	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"L, E, M, O"	.	WRN	116	.	0			c.G2015A						.						98	90	93					8																	30958398		2203	4300	6503	SO:0001583	missense	7486	exon18	Familial Cancer Database	WS, Adult Progeria	CTCACTGTATTTC		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"Werner syndrome"			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.2015G>A	chr8.hg19:g.30958398G>A	ENSP00000298139:p.Cys672Tyr	110.0	0.0		61.0	16.0	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	hg19	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.388669	0.82902	.	.	ENSG00000165392	ENST00000298139	T	0.04862	3.54	5.74	5.74	0.90152	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.44138	0.1279	H	0.98155	4.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.64812	-0.6319	10	0.87932	D	0	-16.1922	19.5086	0.95132	0.0:0.0:1.0:0.0	.	82;672	Q59F09;Q14191	.;WRN_HUMAN	Y	672	ENSP00000298139:C672Y	ENSP00000298139:C672Y	C	+	2	0	WRN	31077940	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.345000	0.79337	2.711000	0.92665	0.591000	0.81541	TGT	.	.		0.418	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			A	30958398	G	A	30958398	3	1	195	1	0	0	0	0	1	0	0	0	17417	1377	48	3	2081	3	WRN	8	30958398	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	13346299	30958398	115405624	93	28721										
MYST3	7994	hgsc.bcm.edu	37	chr8	41905925	41905925	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ttcatgtggaagaagggacaCtggaggtaaacaggaaagag	15	4	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr8:41905925C>A	ENST00000396930.3	-	3	1114	c.571G>T	c.(571-573)Gtg>Ttg	p.V191L	KAT6A_ENST00000265713.2_Missense_Mutation_p.V191L|KAT6A_ENST00000485568.1_Missense_Mutation_p.V191L|KAT6A_ENST00000406337.1_Missense_Mutation_p.V191L	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	191	Interaction with PML.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										AGAAGGGACACTGGAGGTAAA	0.438																																					p.V191L		Atlas-SNP	.											.	.	.	.	0			c.G571T						.						92	90	91					8																	41905925		2203	4300	6503	SO:0001583	missense	7994	exon3			GGGACACTGGAGG	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.571G>T	chr8.hg19:g.41905925C>A	ENSP00000380136:p.Val191Leu	207.0	0.0		262.0	23.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	C	13.63	2.293843	0.40594	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000485568	T;T;T;D	0.84442	0.17;0.17;0.17;-1.85	5.45	5.45	0.79879	.	0.000000	0.64402	D	0.000010	D	0.90590	0.7050	M	0.63428	1.95	0.49687	D	0.99981	D;P	0.63880	0.993;0.894	P;B	0.60415	0.874;0.437	D	0.90878	0.4751	10	0.66056	D	0.02	-25.9317	19.6363	0.95735	0.0:1.0:0.0:0.0	.	191;191	A5PLL3;Q92794	.;KAT6A_HUMAN	L	191	ENSP00000265713:V191L;ENSP00000385888:V191L;ENSP00000380136:V191L;ENSP00000430606:V191L	ENSP00000265713:V191L	V	-	1	0	KAT6A	42025082	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	5.681000	0.68175	2.711000	0.92665	0.655000	0.94253	GTG	.	.		0.438	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		A	41905925	C	A	41905925	3	1	195	1	0	0	0	0	1	0	0	0	10113	565	20	3	5507	3	MYST3	8	41905925	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	10947527	41905925	104458097	94	28722										
PRKDC	5591	hgsc.bcm.edu	37	chr8	48774689	48774689	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ttttcaaaaataagcaagttCtgtgaatacaaagaatcata	5	5	3	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr8:48774689C>A	ENST00000523565.1	-	44	5975		c.e44-1		PRKDC_ENST00000314191.2_Splice_Site|PRKDC_ENST00000338368.3_Splice_Site			P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide						B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	TAAGCAAGTTCTGTGAATACA	0.313								Non-homologous end-joining																													.	Esophageal Squamous(79;1091 1253 12329 31680 40677)	Atlas-SNP	.											.	PRKDC	394	.	0			c.5919-1G>T						.						37	33	34					8																	48774689		1779	3994	5773	SO:0001630	splice_region_variant	5591	exon45			CAAGTTCTGTGAA		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000523565.1:c.7534-1G>T	chr8.hg19:g.48774689C>A		99.0	0.0		114.0	12.0	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Splice_Site	SNP	ENST00000523565.1	hg19		.	.	.	.	.	.	.	.	.	.	C	20.1	3.938988	0.73557	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	.	.	.	5.88	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0808	0.72113	0.0:0.9322:0.0:0.0678	.	.	.	.	.	-1	.	.	.	-	.	.	PRKDC	48937242	1.000000	0.71417	0.993000	0.49108	0.923000	0.55619	5.282000	0.65615	1.497000	0.48584	0.655000	0.94253	.	.	.		0.313	PRKDC-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000377896.1	NM_001081640	Intron	A	48774689	C	A	48774689	5	1	195	1	0	0	0	0	0	0	1	0	12533	927	32	3	6639	3	PRKDC	8	48774689	Splice_Site	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	6868764	48774689	97589333	95	28723										
PGCP	10404	hgsc.bcm.edu	37	chr8	97797311	97797311	+	Missense_Mutation	SNP	A	A	C													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tatggtaaagcccagaacagAtcctatgagcgattggcact							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr8:97797311A>C	ENST00000220763.5	+	2	396	c.186A>C	c.(184-186)agA>agC	p.R62S		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	62					peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)										CCCAGAACAGATCCTATGAGC	0.423																																					p.R62S		Atlas-SNP	.											.	.	.	.	0			c.A186C						.						122	115	117					8																	97797311		2203	4300	6503	SO:0001583	missense	10404	exon2			GAACAGATCCTAT	AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"lysosomal dipeptidase", "Ser-Met dipeptidase", "plasma glutamate carboxypeptidase"					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.186A>C	chr8.hg19:g.97797311A>C	ENSP00000220763:p.Arg62Ser	210.0	0.0		377.0	140.0	NM_016134	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Missense_Mutation	SNP	ENST00000220763.5	hg19	CCDS6273.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.411129	0.42817	.	.	ENSG00000104324	ENST00000220763;ENST00000519900;ENST00000517742;ENST00000519484;ENST00000521142	T;T	0.42131	0.98;0.99	5.28	0.0485	0.14285	.	0.000000	0.85682	D	0.000000	T	0.25644	0.0624	L	0.41906	1.305	0.41131	D	0.985882	B;B	0.29612	0.138;0.251	B;B	0.24155	0.04;0.051	T	0.10636	-1.0621	10	0.12430	T	0.62	-7.4447	8.6913	0.34269	0.644:0.0:0.356:0.0	.	62;62	B5MDX4;Q9Y646	.;PGCP_HUMAN	S	62	ENSP00000220763:R62S;ENSP00000429146:R62S	ENSP00000220763:R62S	R	+	3	2	AC010859.1	97866487	1.000000	0.71417	0.996000	0.52242	0.952000	0.60782	1.675000	0.37555	-0.215000	0.10063	0.460000	0.39030	AGA	.	.		0.423	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134		C	97797311	A	C	97797311	3	2	195	1	0	0	0	0	1	0	0	0	11795	330	12	5	188	5	PGCP	8	97797311	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	49022622	97797311	48566711	96	28724	147	2								
PGCP	10404	hgsc.bcm.edu	37	chr8	97797316	97797316	+	Missense_Mutation	SNP	A	A	G													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	taaagcccagaacagatcctAtgagcgattggcacttctgg							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr8:97797316A>G	ENST00000220763.5	+	2	401	c.191A>G	c.(190-192)tAt>tGt	p.Y64C		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	64					peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)										AACAGATCCTATGAGCGATTG	0.423																																					p.Y64C		Atlas-SNP	.											.	.	.	.	0			c.A191G						.						122	115	117					8																	97797316		2203	4300	6503	SO:0001583	missense	10404	exon2			GATCCTATGAGCG	AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"lysosomal dipeptidase", "Ser-Met dipeptidase", "plasma glutamate carboxypeptidase"					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.191A>G	chr8.hg19:g.97797316A>G	ENSP00000220763:p.Tyr64Cys	215.0	0.0		386.0	146.0	NM_016134	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Missense_Mutation	SNP	ENST00000220763.5	hg19	CCDS6273.1	.	.	.	.	.	.	.	.	.	.	A	18.42	3.619699	0.66787	.	.	ENSG00000104324	ENST00000220763;ENST00000519900;ENST00000517742;ENST00000519484;ENST00000521142	T;T	0.61274	0.58;0.12	5.28	4.07	0.47477	.	0.073633	0.56097	D	0.000028	T	0.77232	0.4100	M	0.89414	3.03	0.47819	D	0.999528	D;D	0.89917	1.0;0.999	D;D	0.74023	0.982;0.959	T	0.81453	-0.0926	10	0.72032	D	0.01	-4.6186	11.5098	0.50486	0.866:0.0:0.0:0.134	.	64;64	B5MDX4;Q9Y646	.;PGCP_HUMAN	C	64	ENSP00000220763:Y64C;ENSP00000429146:Y64C	ENSP00000220763:Y64C	Y	+	2	0	AC010859.1	97866492	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	6.832000	0.75329	2.009000	0.58944	0.460000	0.39030	TAT	.	.		0.423	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134		G	97797316	A	G	97797316	3	3	195	1	0	0	0	0	1	0	0	0	11795	449	16	2	193	2	PGCP	8	97797316	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	5	97797316	48566706	97	28725	147	2								
CYC1	1537	hgsc.bcm.edu	37	chr8	145150875	145150876	+	Frame_Shift_Ins	INS	-	-	C													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gccagtgacctggagctgcaINScccccccagctatccgtggt							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr8:145150875_145150876insC	ENST00000318911.4	+	2	342_343	c.269_270insC	c.(268-273)caccccfs	p.HP90fs		NM_001916.3	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	90					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to glucagon (GO:0033762)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|respiratory chain (GO:0070469)	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity (GO:0045155)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	15	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTGGAGCTGCACCCCCCCAGCT	0.668											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H90fs		Atlas-Indel,Pindel	.											.,1	CYC1	34	.	0			c.269_270insC						.																																			SO:0001589	frameshift_variant	1537	exon2			.	BC001006	CCDS6415.1	8q24	2011-07-04			ENSG00000179091	ENSG00000179091		"Mitochondrial respiratory chain complex / Complex III"	2579	protein-coding gene	gene with protein product		123980					Standard	NM_001916		Approved	UQCR4	uc003zaz.4	P08574	OTTHUMG00000165242	ENST00000318911.4:c.276dupC	chr8.hg19:g.145150882_145150882dupC	ENSP00000317159:p.His90fs	45.0	0.0	1692	57.0	20.0	NM_001916	Q5U062|Q6FHS7	Frame_Shift_Ins	INS	ENST00000318911.4	hg19	CCDS6415.1																																																																																			.	.		0.668	CYC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382895.1	NM_001916		C	145150876	-	C	145150875	7	5	195	1	0	1	1	0	0	0	0	0	4137	159	6	0	275	0	CYC1	8	145150875	Frame_Shift_Ins	INS	-	TCGA-DD-AADM-01A-11D-A40R-10	47353559	145150875	1213147	98	28726										
AK3	50808	hgsc.bcm.edu	37	chr9	4713077	4713077	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ggtttctgttccggagaatgTttccagcaccccttttttcc	8	12	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr9:4713077T>C	ENST00000381809.3	-	5	813	c.583A>G	c.(583-585)Aca>Gca	p.T195A	AK3_ENST00000447596.4_Missense_Mutation_p.T155A|AK3_ENST00000359883.2_Missense_Mutation_p.T125A	NM_016282.3	NP_057366.2	P27144	KAD4_HUMAN	adenylate kinase 3	193					ADP biosynthetic process (GO:0006172)|AMP metabolic process (GO:0046033)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|GTP metabolic process (GO:0046039)|liver development (GO:0001889)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|response to drug (GO:0042493)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside triphosphate adenylate kinase activity (GO:0046899)			large_intestine(2)|lung(1)|ovary(2)	5	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0302)	Adefovir Dipivoxil(DB00718)|Tenofovir(DB00300)	CCGGAGAATGTTTCCAGCACC	0.383																																					p.T195A		Atlas-SNP	.											.	AK3	16	.	0			c.A583G						.						116	110	112					9																	4713077		2203	4300	6503	SO:0001583	missense	50808	exon5			AGAATGTTTCCAG	BC013771	CCDS6455.1, CCDS56561.1, CCDS56562.1	9p24.1	2010-09-29	2004-06-11	2005-04-07	ENSG00000147853	ENSG00000147853			17376	protein-coding gene	gene with protein product		609290	"adenylate kinase 6", "adenylate kinase 3 like 1"	AK6, AK3L1		8288, 182062	Standard	NM_001199852		Approved	AKL3L1	uc003ziq.2	Q9UIJ7	OTTHUMG00000019472	ENST00000381809.3:c.583A>G	chr9.hg19:g.4713077T>C	ENSP00000371230:p.Thr195Ala	67.0	0.0		66.0	25.0	NM_016282	B2R927|D3DQ62|Q6IBH4|Q6NXQ5|Q8IUU9	Missense_Mutation	SNP	ENST00000381809.3	hg19	CCDS6455.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.638433	0.47153	.	.	ENSG00000147853	ENST00000381809;ENST00000359883;ENST00000474822;ENST00000447596	T;T;T	0.80480	1.02;-1.38;1.02	5.47	4.26	0.50523	.	0.197410	0.51477	D	0.000081	T	0.77191	0.4094	M	0.80183	2.485	0.48452	D	0.99965	B;B	0.22276	0.067;0.021	B;B	0.20577	0.03;0.009	T	0.69712	-0.5071	10	0.10902	T	0.67	-12.7637	10.0566	0.42248	0.2268:0.0:0.0:0.7732	.	155;195	E7ET30;Q9UIJ7	.;KAD3_HUMAN	A	195;125;125;155	ENSP00000371230:T195A;ENSP00000352948:T125A;ENSP00000413933:T155A	ENSP00000352948:T125A	T	-	1	0	AK3	4703077	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.749000	0.55150	2.078000	0.62432	0.533000	0.62120	ACA	.	.		0.383	AK3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051585.1	NM_016282		C	4713077	T	C	4713077	3	2	195	1	0	0	0	0	1	0	0	0	441	1725	60	2	104	2	AK3	9	4713077	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10		4713077	136500354	99	28727										
CNTLN	54875	hgsc.bcm.edu	37	chr9	17330664	17330664	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	atccttatcaagcttagaaaCgttaatggtttcacagaagt	7	7	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr9:17330664C>T	ENST00000380647.3	+	9	1460	c.1376C>T	c.(1375-1377)aCg>aTg	p.T459M	CNTLN_ENST00000262360.5_Missense_Mutation_p.T459M|CNTLN_ENST00000425824.1_Missense_Mutation_p.T459M			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	459					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AGCTTAGAAACGTTAATGGTT	0.294																																					p.T459M		Atlas-SNP	.											.	CNTLN	128	.	0			c.C1376T						.						125	122	123					9																	17330664		1807	4083	5890	SO:0001583	missense	54875	exon9			TAGAAACGTTAAT	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.1376C>T	chr9.hg19:g.17330664C>T	ENSP00000370021:p.Thr459Met	452.0	0.0		421.0	83.0	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	hg19	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.379723	0.24944	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.12465	2.68;2.68;2.68	4.85	3.88	0.44766	.	.	.	.	.	T	0.28566	0.0707	M	0.65975	2.015	0.26401	N	0.976419	D;D;D	0.89917	1.0;0.993;0.993	D;P;P	0.69824	0.966;0.834;0.742	T	0.19289	-1.0310	9	0.54805	T	0.06	.	3.707	0.08404	0.1498:0.5101:0.2493:0.0908	.	459;459;459	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	M	459	ENSP00000370021:T459M;ENSP00000392798:T459M;ENSP00000262360:T459M	ENSP00000262360:T459M	T	+	2	0	CNTLN	17320664	0.979000	0.34478	1.000000	0.80357	0.199000	0.23934	0.719000	0.25881	2.381000	0.81170	0.650000	0.86243	ACG	.	.		0.294	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		T	17330664	C	T	17330664	3	4	195	1	0	0	0	0	1	0	0	0	3641	536	19	1	1440	1	CNTLN	9	17330664	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	12617587	17330664	123882767	100	28728										
FAM154A	158297	hgsc.bcm.edu	37	chr9	18928249	18928249	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccttgggagtaaagctgatgGtgtaggtggtctggctttcc	15	7	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr9:18928249G>T	ENST00000380534.4	-	4	1505	c.1226C>A	c.(1225-1227)aCc>aAc	p.T409N	FAM154A_ENST00000542071.1_Missense_Mutation_p.T217N|FAM154A_ENST00000380530.1_3'UTR	NM_153707.2	NP_714918.2	Q8IYX7	F154A_HUMAN	family with sequence similarity 154, member A	409										breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|skin(1)	26				GBM - Glioblastoma multiforme(50;6.53e-16)		AAAGCTGATGGTGTAGGTGGT	0.527																																					p.T409N		Atlas-SNP	.											.	FAM154A	61	.	0			c.C1226A						.						112	92	99					9																	18928249		2203	4300	6503	SO:0001583	missense	158297	exon4			CTGATGGTGTAGG	BC033489	CCDS6487.1, CCDS75819.1, CCDS75820.1	9p22.1	2012-03-23	2008-02-21	2008-02-21	ENSG00000155875	ENSG00000155875			28566	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 138"	C9orf138		12477932	Standard	NM_153707		Approved	MGC35182	uc003zni.2	Q8IYX7	OTTHUMG00000019609	ENST00000380534.4:c.1226C>A	chr9.hg19:g.18928249G>T	ENSP00000369907:p.Thr409Asn	107.0	0.0		121.0	48.0	NM_153707	Q5VY58	Missense_Mutation	SNP	ENST00000380534.4	hg19	CCDS6487.1	.	.	.	.	.	.	.	.	.	.	G	8.814	0.936051	0.18206	.	.	ENSG00000155875	ENST00000380534;ENST00000542071	T;T	0.21543	2.8;2.0	4.79	1.65	0.23941	.	1.425010	0.04174	N	0.325248	T	0.17619	0.0423	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23726	-1.0180	10	0.33141	T	0.24	-0.4909	5.7627	0.18209	0.0818:0.1376:0.6394:0.1413	.	409	Q8IYX7	F154A_HUMAN	N	409;217	ENSP00000369907:T409N;ENSP00000438823:T217N	ENSP00000369907:T409N	T	-	2	0	FAM154A	18918249	0.711000	0.27906	0.468000	0.27192	0.916000	0.54674	0.994000	0.29693	0.693000	0.31634	0.650000	0.86243	ACC	.	.		0.527	FAM154A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051811.1	NM_153707		T	18928249	G	T	18928249	3	4	195	1	0	0	0	0	1	0	0	0	5468	1261	44	3	202	3	FAM154A	9	18928249	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	1597585	18928249	122285182	101	28729										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21974713	21974713	+	Frame_Shift_Del	DEL	G	G	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccgtaactattcggtgcgttGggcagcgcccccgcctccag							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr9:21974713delG	ENST00000304494.5	-	1	384	c.114delC	c.(112-114)cccfs	p.P38fs	CDKN2A_ENST00000446177.1_Frame_Shift_Del_p.P38fs|CDKN2A_ENST00000579755.1_Intron|CDKN2A_ENST00000361570.3_Intron|CDKN2A_ENST00000498124.1_Frame_Shift_Del_p.P38fs|CDKN2A_ENST00000579122.1_Frame_Shift_Del_p.P38fs|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000494262.1_Intron|CDKN2A_ENST00000498628.2_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	38					cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(23)|p.G35fs*13(1)|p.0(1)|p.V28_V51del(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		TCGGTGCGTTGGGCAGCGCCC	0.706		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.N39fs		Atlas-INDEL	.											.	CDKN2A	4810	.	1341	Whole gene deletion(1316)|Unknown(23)|Deletion - In frame(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(278)|skin(168)|central_nervous_system(163)|lung(146)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(52)|oesophagus(51)|upper_aerodigestive_tract(48)|ovary(34)|kidney(31)|breast(30)|pancreas(29)|thyroid(14)|biliary_tract(13)|NS(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.115delA						.						34	42	39					9																	21974713		2199	4289	6488	SO:0001589	frameshift_variant	1029	exon1			.	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.114delC	chr9.hg19:g.21974713delG	ENSP00000307101:p.Pro38fs	90.0	0.0		82.0	11.0	NM_058197	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Frame_Shift_Del	DEL	ENST00000304494.5	hg19	CCDS6510.1																																																																																			.	.		0.706	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		-	21974713	G	-	21974713	7	5	195	1	0	1	0	1	0	0	0	0	3163	1335	47	0	569	0	CDKN2A	9	21974713	Frame_Shift_Del	DEL	G	TCGA-DD-AADM-01A-11D-A40R-10	3046464	21974713	119238718	102	28730										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87359975	87359975	+	Frame_Shift_Del	DEL	G	G	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cgtcactgataaaaccggtcGggaacatctctcggtgagtg							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr9:87359975delG	ENST00000323115.4	+	10	1636	c.1283delG	c.(1282-1284)cggfs	p.R428fs	NTRK2_ENST00000376213.1_Frame_Shift_Del_p.R428fs|NTRK2_ENST00000376214.1_Frame_Shift_Del_p.R428fs|NTRK2_ENST00000395866.2_Frame_Shift_Del_p.R272fs|NTRK2_ENST00000395882.1_Frame_Shift_Del_p.R428fs|NTRK2_ENST00000376208.1_Frame_Shift_Del_p.R428fs|NTRK2_ENST00000304053.6_Frame_Shift_Del_p.R428fs|NTRK2_ENST00000359847.3_Frame_Shift_Del_p.R428fs|NTRK2_ENST00000277120.3_Frame_Shift_Del_p.R428fs			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	428					activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	AAAACCGGTCGGGAACATCTC	0.453										TSP Lung(25;0.17)																											p.R428fs		Pindel	.											.	NTRK2	331	.	0			c.1282delC						.						130	121	124					9																	87359975		2203	4300	6503	SO:0001589	frameshift_variant	4915	exon11			.	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.1283delG	chr9.hg19:g.87359975delG	ENSP00000314586:p.Arg428fs	157.0	0.0		188.0	17.0	NM_001018066	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Frame_Shift_Del	DEL	ENST00000323115.4	hg19	CCDS35050.1																																																																																			.	.		0.453	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			-	87359975	G	-	87359975	7	5	195	1	0	1	0	1	0	0	0	0	10716	1116	39	0	1321	0	NTRK2	9	87359975	Frame_Shift_Del	DEL	G	TCGA-DD-AADM-01A-11D-A40R-10	65385262	87359975	53853456	103	28731										
PKN3	29941	hgsc.bcm.edu	37	chr9	131468992	131468992	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cctgtgctatggctccatagGagaggaagctcctggcagct	13	11	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr9:131468992G>A	ENST00000291906.4	+	4	805	c.412G>A	c.(412-414)Gag>Aag	p.E138K		NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	138					epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						GGCTCCATAGGAGAGGAAGCT	0.632																																					p.E138K		Atlas-SNP	.											.	PKN3	62	.	0			c.G412A						.						8	10	9					9																	131468992		2168	4250	6418	SO:0001630	splice_region_variant	29941	exon4			CCATAGGAGAGGA	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.412-1G>A	chr9.hg19:g.131468992G>A		57.0	0.0		61.0	11.0	NM_013355	Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	hg19	CCDS6908.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.407949	0.83340	.	.	ENSG00000160447	ENST00000291906	T	0.34275	1.37	5.02	5.02	0.67125	.	.	.	.	.	T	0.42223	0.1193	L	0.43152	1.355	0.80722	D	1	P;P	0.45283	0.855;0.645	P;P	0.49502	0.613;0.533	T	0.14172	-1.0482	8	.	.	.	.	16.8712	0.86041	0.0:0.0:1.0:0.0	.	138;138	Q05BU1;Q6P5Z2	.;PKN3_HUMAN	K	138	ENSP00000291906:E138K	.	E	+	1	0	PKN3	130508813	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	8.966000	0.93397	2.316000	0.78162	0.561000	0.74099	GAG	.	.		0.632	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355	Missense_Mutation	A	131468992	G	A	131468992	5	1	195	1	0	0	0	0	0	0	1	0	11990	1188	41	3	426	3	PKN3	9	131468992	Splice_Site	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	44109017	131468992	9744439	104	28732										
NUP214	8021	hgsc.bcm.edu	37	chr9	134004694	134004694	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gcaaaaacgcccatttgcctAtcataagcttttgaaagatg	7	9	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr9:134004694A>G	ENST00000359428.5	+	4	566	c.422A>G	c.(421-423)tAt>tGt	p.Y141C	RNU6-881P_ENST00000516813.1_RNA|NUP214_ENST00000451030.1_Missense_Mutation_p.Y141C|NUP214_ENST00000411637.2_Missense_Mutation_p.Y141C			P35658	NU214_HUMAN	nucleoporin 214kDa	141	Seven-bladed beta propeller.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		CCATTTGCCTATCATAAGCTT	0.378			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.Y141C	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.A422G						.						141	115	124					9																	134004694		2203	4300	6503	SO:0001583	missense	8021	exon4			TTGCCTATCATAA	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.422A>G	chr9.hg19:g.134004694A>G	ENSP00000352400:p.Tyr141Cys	130.0	0.0		141.0	42.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.560333	0.65538	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000531584	D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29	5.37	5.37	0.77165	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.34879	N	0.003603	D	0.88923	0.6569	L	0.44542	1.39	0.34622	D	0.718711	B;B	0.12013	0.005;0.005	B;B	0.11329	0.006;0.006	D	0.87452	0.2402	10	0.40728	T	0.16	-11.3553	8.266	0.31815	0.8464:0.0:0.1536:0.0	.	141;141	P35658-4;P35658	.;NU214_HUMAN	C	141;141;141;141;51	ENSP00000352400:Y141C;ENSP00000396576:Y141C;ENSP00000405014:Y141C;ENSP00000435874:Y51C	ENSP00000352400:Y141C	Y	+	2	0	NUP214	132994515	0.999000	0.42202	1.000000	0.80357	0.984000	0.73092	3.169000	0.50809	2.164000	0.68074	0.533000	0.62120	TAT	.	.		0.378	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		G	134004694	A	G	134004694	3	3	195	1	0	0	0	0	1	0	0	0	10771	449	16	2	436	2	NUP214	9	134004694	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	2535702	134004694	7208737	105	28733										
QSOX2	169714	hgsc.bcm.edu	37	chr9	139100947	139100947	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctccttcactggaatcccccTggtctgcggaatacgtgtct	9	14	3	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr9:139100947T>C	ENST00000358701.5	-	12	1761	c.1724A>G	c.(1723-1725)cAg>cGg	p.Q575R		NM_181701.3	NP_859052.3	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2	575					cell redox homeostasis (GO:0045454)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	thiol oxidase activity (GO:0016972)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)		GGAATCCCCCTGGTCTGCGGA	0.577																																					p.Q575R		Atlas-SNP	.											.	QSOX2	63	.	0			c.A1724G						.						90	87	88					9																	139100947		2203	4300	6503	SO:0001583	missense	169714	exon12			TCCCCCTGGTCTG	AJ318051	CCDS35178.1	9q34.3	2008-02-05	2007-04-23	2007-04-23	ENSG00000165661	ENSG00000165661			30249	protein-coding gene	gene with protein product		612860	"quiescin Q6-like 1"	QSCN6L1		12176051	Standard	NM_181701		Approved	SOXN, DKFZp762A2013	uc010nbi.2	Q6ZRP7	OTTHUMG00000020923	ENST00000358701.5:c.1724A>G	chr9.hg19:g.139100947T>C	ENSP00000351536:p.Gln575Arg	97.0	0.0		85.0	19.0	NM_181701	A2CEE0|A6NLB0|Q5TB37|Q7Z7B6|Q86VV7|Q8N3G2	Missense_Mutation	SNP	ENST00000358701.5	hg19	CCDS35178.1	.	.	.	.	.	.	.	.	.	.	T	6.337	0.430270	0.12045	.	.	ENSG00000165661	ENST00000358701	T	0.05025	3.51	4.91	-9.82	0.00484	.	1.064250	0.07313	N	0.876153	T	0.02848	0.0085	L	0.28556	0.865	0.09310	N	1	B	0.14805	0.011	B	0.10450	0.005	T	0.42103	-0.9471	10	0.09843	T	0.71	-0.0187	2.3547	0.04293	0.2344:0.0685:0.2239:0.4733	.	575	Q6ZRP7	QSOX2_HUMAN	R	575	ENSP00000351536:Q575R	ENSP00000351536:Q575R	Q	-	2	0	QSOX2	138240768	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.584000	0.05800	-2.488000	0.00518	-0.471000	0.05019	CAG	.	.		0.577	QSOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055046.2	NM_181701		C	139100947	T	C	139100947	3	2	195	1	0	0	0	0	1	0	0	0	12899	1580	55	2	376	2	QSOX2	9	139100947	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	5096253	139100947	2112484	106	28734										
GRIN1	2902	hgsc.bcm.edu	37	chr9	140051158	140051158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctgtataccgcgcagccgcgAtgctgaacatgacgggctcc	12	14	0	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr9:140051158A>G	ENST00000371561.3	+	5	1806	c.709A>G	c.(709-711)Atg>Gtg	p.M237V	GRIN1_ENST00000471122.1_3'UTR|GRIN1_ENST00000371559.4_Missense_Mutation_p.M237V|GRIN1_ENST00000371560.3_Missense_Mutation_p.M258V|GRIN1_ENST00000371555.4_Missense_Mutation_p.M258V|GRIN1_ENST00000371546.4_Missense_Mutation_p.M258V|GRIN1_ENST00000371550.4_Missense_Mutation_p.M237V|GRIN1_ENST00000371553.3_Missense_Mutation_p.M258V|GRIN1_ENST00000315048.3_Missense_Mutation_p.M237V|GRIN1_ENST00000350902.5_Missense_Mutation_p.M237V	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	237					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CGCAGCCGCGATGCTGAACAT	0.697																																					p.M258V	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											.	GRIN1	51	.	0			c.A772G						.						32	26	28					9																	140051158		2186	4285	6471	SO:0001583	missense	2902	exon6			GCCGCGATGCTGA		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4584	protein-coding gene	gene with protein product		138249	"N-methyl-D-aspartate receptor subunit NR1"	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.709A>G	chr9.hg19:g.140051158A>G	ENSP00000360616:p.Met237Val	104.0	0.0		125.0	55.0	NM_001185091	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Missense_Mutation	SNP	ENST00000371561.3	hg19	CCDS7031.1	.	.	.	.	.	.	.	.	.	.	A	7.382	0.629043	0.14257	.	.	ENSG00000176884	ENST00000371561;ENST00000315048;ENST00000350902;ENST00000371550;ENST00000371546;ENST00000371555;ENST00000371553;ENST00000371559;ENST00000371560	D;D;D;D;D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6	4.29	3.15	0.36227	Extracellular ligand-binding receptor (1);	4.609150	0.00718	N	0.000874	T	0.63189	0.2490	N	0.01352	-0.895	0.33804	D	0.626977	B;B;B;B;B;B	0.15473	0.002;0.0;0.005;0.013;0.006;0.002	B;B;B;B;B;B	0.11329	0.005;0.001;0.004;0.006;0.006;0.002	T	0.59161	-0.7506	10	0.27785	T	0.31	.	8.0546	0.30598	0.8991:0.0:0.1009:0.0	.	258;258;237;237;237;237	Q5VSF4;Q5VSF5;Q05586-2;Q05586-3;Q05586;A2AVK2	.;.;.;.;NMDZ1_HUMAN;.	V	237;237;237;237;258;258;258;237;258	ENSP00000360616:M237V;ENSP00000316696:M237V;ENSP00000316915:M237V;ENSP00000360605:M237V;ENSP00000360601:M258V;ENSP00000360610:M258V;ENSP00000360608:M258V;ENSP00000360614:M237V;ENSP00000360615:M258V	ENSP00000316696:M237V	M	+	1	0	GRIN1	139170979	0.899000	0.30636	0.998000	0.56505	0.748000	0.42578	1.347000	0.33975	1.567000	0.49668	0.402000	0.26972	ATG	.	.		0.697	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327		G	140051158	A	G	140051158	3	3	195	1	0	0	0	0	1	0	0	0	6787	333	12	2	794	2	GRIN1	9	140051158	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	950211	140051158	1162273	107	28735										
KIN	22944	hgsc.bcm.edu	37	chr10	7822135	7822135	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	caatgttgttgtggacccttTtagtgcctgagaacaaaata	9	7	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr10:7822135T>C	ENST00000379562.4	-	4	307	c.260A>G	c.(259-261)aAa>aGa	p.K87R	KIN_ENST00000535925.1_Missense_Mutation_p.K87R|KIN_ENST00000543003.1_5'UTR	NM_012311.3	NP_036443.1			Kin17 DNA and RNA binding protein											endometrium(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(2)	19						GTGGACCCTTTTAGTGCCTGA	0.383																																					p.K87R		Atlas-SNP	.											.	KIN	39	.	0			c.A260G						.						265	234	245					10																	7822135		2203	4300	6503	SO:0001583	missense	22944	exon4			ACCCTTTTAGTGC	AJ005273	CCDS7080.1	10p15-p14	2014-07-15	2014-07-15		ENSG00000151657	ENSG00000151657			6327	protein-coding gene	gene with protein product		601720	"antigenic determinant of recA protein (mouse) homolog", "KIN, antigenic determinant of recA protein homolog (mouse)"			1923796, 24140279	Standard	NM_012311		Approved	KIN17, Rts2	uc001ijt.3	O60870	OTTHUMG00000017634	ENST00000379562.4:c.260A>G	chr10.hg19:g.7822135T>C	ENSP00000368881:p.Lys87Arg	176.0	0.0		174.0	53.0	NM_012311		Missense_Mutation	SNP	ENST00000379562.4	hg19	CCDS7080.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.458275	0.43634	.	.	ENSG00000151657	ENST00000535925;ENST00000379562	.	.	.	5.92	4.8	0.61643	DNA/RNA-binding protein Kin17, conserved domain (1);	0.000000	0.85682	D	0.000000	T	0.58892	0.2154	M	0.65677	2.01	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.14023	0.01;0.01	T	0.55256	-0.8169	9	0.40728	T	0.16	-24.0763	10.504	0.44823	0.0:0.0728:0.0:0.9272	.	87;87	B4DX32;O60870	.;KIN17_HUMAN	R	87	.	ENSP00000368881:K87R	K	-	2	0	KIN	7862141	1.000000	0.71417	0.562000	0.28370	0.585000	0.36419	7.991000	0.88244	1.079000	0.41038	0.533000	0.62120	AAA	.	.		0.383	KIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046683.2	NM_012311		C	7822135	T	C	7822135	3	2	195	1	0	0	0	0	1	0	0	0	8324	1841	64	2	961	2	KIN	10	7822135	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10		7822135	127712612	108	28736										
LDB1	8861	hgsc.bcm.edu	37	chr10	103870846	103870846	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctctgtccagttctgaagccGtttgttaagctcaaatattc	7	10	3	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr10:103870846G>A	ENST00000425280.1	-	4	571	c.229C>T	c.(229-231)Cgg>Tgg	p.R77W	LDB1_ENST00000361198.5_Missense_Mutation_p.R41W|LDB1_ENST00000490751.1_5'UTR	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	77					anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		TTCTGAAGCCGTTTGTTAAGC	0.532																																					p.R77W		Atlas-SNP	.											.	LDB1	61	.	0			c.C229T						.						155	156	156					10																	103870846		2203	4300	6503	SO:0001583	missense	8861	exon4			GAAGCCGTTTGTT	AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"carboxy terminal LIM domain protein 2"	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.229C>T	chr10.hg19:g.103870846G>A	ENSP00000392466:p.Arg77Trp	85.0	0.0		55.0	14.0	NM_001113407	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Missense_Mutation	SNP	ENST00000425280.1	hg19	CCDS44472.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.099104	0.76983	.	.	ENSG00000198728	ENST00000361198;ENST00000425280	.	.	.	5.97	5.04	0.67666	.	0.052260	0.85682	N	0.000000	T	0.80711	0.4675	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.993;1.0	T	0.83045	-0.0155	9	0.87932	D	0	-0.2368	16.2964	0.82776	0.0:0.0:0.8671:0.1329	.	77;41	Q86U70;Q86U70-3	LDB1_HUMAN;.	W	41;77	.	ENSP00000354616:R41W	R	-	1	2	LDB1	103860836	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.304000	0.43655	2.838000	0.97847	0.561000	0.74099	CGG	.	.		0.532	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407		A	103870846	G	A	103870846	3	1	195	1	0	0	0	0	1	0	0	0	8704	1144	40	1	1038	1	LDB1	10	103870846	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	96048711	103870846	31663901	109	28737										
C10orf96	374355	hgsc.bcm.edu	37	chr10	118084530	118084530	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	agccaggccctgagatgagcTtggagtccctgtttcagcac	12	12	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr10:118084530T>C	ENST00000333254.3	+	2	258	c.7T>C	c.(7-9)Ttg>Ctg	p.L3L	CCDC172_ENST00000497093.1_3'UTR	NM_198515.2	NP_940917.1	P0C7W6	CC172_HUMAN	coiled-coil domain containing 172	3																	TGAGATGAGCTTGGAGTCCCT	0.498																																					p.L3L		Atlas-SNP	.											C10orf96,NS,carcinoma,0,1	.	.	.	0			c.T7C						.						105	106	106					10																	118084530		2203	4300	6503	SO:0001819	synonymous_variant	374355	exon2			ATGAGCTTGGAGT	BC044830	CCDS31291.1	10q26.11-q26.12	2012-05-31	2012-05-31	2012-05-31	ENSG00000182645	ENSG00000182645			30524	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 96"	C10orf96		12477932	Standard	NM_198515		Approved	MGC35062	uc001lck.3	P0C7W6	OTTHUMG00000019098	ENST00000333254.3:c.7T>C	chr10.hg19:g.118084530T>C		75.0	0.0		45.0	11.0	NM_198515		Silent	SNP	ENST00000333254.3	hg19	CCDS31291.1																																																																																			.	.		0.498	CCDC172-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050516.2	NM_198515		C	118084530	T	C	118084530	2	2	195	1	0	0	0	0	0	0	0	1	1629	1606	56	2		2	C10orf96	10	118084530	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	14213684	118084530	17450217	110	28738										
MUC2	4583	hgsc.bcm.edu	37	chr11	1081111	1081111	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gatggcagtgtactgctcaaCgagctgcaggtgaacctgcc	13	11	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr11:1081111C>T	ENST00000441003.2	+	11	1434	c.1407C>T	c.(1405-1407)aaC>aaT	p.N469N	MUC2_ENST00000359061.5_Silent_p.N469N	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	469	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TACTGCTCAACGAGCTGCAGG	0.667																																					p.N469N		Atlas-SNP	.											.	MUC2	614	.	0			c.C1407T						.						37	43	41					11																	1081111		1993	4166	6159	SO:0001819	synonymous_variant	4583	exon11			GCTCAACGAGCTG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.1407C>T	chr11.hg19:g.1081111C>T		173.0	0.0		184.0	62.0	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.		0.667	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1081111	C	T	1081111	2	4	195	1	0	0	0	0	0	0	0	1	9984	535	19	1		1	MUC2	11	1081111	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10		1081111	133925405	111	28739										
ZNF215	7762	hgsc.bcm.edu	37	chr11	6953723	6953723	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gccaactctgggagctctgtCttcaatggctgagaccagag	12	11	4	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr11:6953723C>A	ENST00000278319.5	+	3	808	c.220C>A	c.(220-222)Ctt>Att	p.L74I	ZNF215_ENST00000529903.1_Missense_Mutation_p.L74I|ZNF215_ENST00000527171.1_3'UTR|ZNF215_ENST00000414517.2_Missense_Mutation_p.L74I	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	74	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		GGAGCTCTGTCTTCAATGGCT	0.473																																					p.L74I		Atlas-SNP	.											.	ZNF215	72	.	0			c.C220A						.						70	74	73					11																	6953723		2201	4296	6497	SO:0001583	missense	7762	exon3			CTCTGTCTTCAAT	AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"Zinc fingers, C2H2-type", "-", "-", "-"	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.220C>A	chr11.hg19:g.6953723C>A	ENSP00000278319:p.Leu74Ile	167.0	0.0		171.0	43.0	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	hg19	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	C	9.811	1.183218	0.21870	.	.	ENSG00000149054	ENST00000278319;ENST00000414517;ENST00000529903	T;T;T	0.05580	3.42;3.42;3.42	4.15	0.0388	0.14202	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.503504	0.14919	N	0.290787	T	0.08313	0.0207	M	0.76328	2.33	0.21105	N	0.999782	B;B;B	0.24426	0.103;0.103;0.013	B;B;B	0.22152	0.038;0.038;0.033	T	0.32877	-0.9890	10	0.23302	T	0.38	-1.3864	8.9087	0.35539	0.1583:0.3798:0.462:0.0	.	74;74;74	B4DYW9;Q96C84;Q9UL58	.;.;ZN215_HUMAN	I	74	ENSP00000278319:L74I;ENSP00000393202:L74I;ENSP00000432306:L74I	ENSP00000278319:L74I	L	+	1	0	ZNF215	6910299	0.994000	0.37717	0.928000	0.36995	0.894000	0.52154	0.682000	0.25335	0.017000	0.15025	-0.961000	0.02630	CTT	.	.		0.473	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1			A	6953723	C	A	6953723	3	1	195	1	0	0	0	0	1	0	0	0	17786	913	32	3	222	3	ZNF215	11	6953723	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	5872612	6953723	128052793	112	28740										
SOX6	55553	hgsc.bcm.edu	37	chr11	16205478	16205478	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ttttgtgctgctgttgcagaAgttgctgctgttgtctcgca	12	8	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr11:16205478A>G	ENST00000352083.6	-	6	808	c.731T>C	c.(730-732)cTt>cCt	p.L244P	SOX6_ENST00000396356.3_Missense_Mutation_p.L244P|SOX6_ENST00000527619.1_Missense_Mutation_p.L247P|SOX6_ENST00000316399.6_Missense_Mutation_p.L244P|SOX6_ENST00000528252.1_Missense_Mutation_p.L244P|SOX6_ENST00000528429.1_Missense_Mutation_p.L244P			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	244	Gln-rich.				astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						CTGTTGCAGAAGTTGCTGCTG	0.378																																					p.L257P		Atlas-SNP	.											SOX6_ENST00000527619,NS,carcinoma,0,2	SOX6	149	.	0			c.T770C						.						167	154	159					11																	16205478		2200	4294	6494	SO:0001583	missense	55553	exon6			TGCAGAAGTTGCT	AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"SRY (sex determining region Y)-boxes"	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.731T>C	chr11.hg19:g.16205478A>G	ENSP00000339876:p.Leu244Pro	103.0	0.0		74.0	10.0	NM_001145819	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Missense_Mutation	SNP	ENST00000352083.6	hg19		.	.	.	.	.	.	.	.	.	.	A	22.2	4.252963	0.80135	.	.	ENSG00000110693	ENST00000316399;ENST00000352083;ENST00000396356;ENST00000528252;ENST00000527619;ENST00000528429	D;D;D;D;D;D	0.98602	-5.02;-4.99;-5.02;-5.02;-5.02;-4.99	5.32	5.32	0.75619	.	0.129583	0.53938	D	0.000057	D	0.98751	0.9580	M	0.75085	2.285	0.80722	D	1	D;D;D	0.76494	0.973;0.966;0.999	P;P;D	0.83275	0.864;0.514;0.996	D	0.99869	1.1093	10	0.87932	D	0	.	15.2753	0.73737	1.0:0.0:0.0:0.0	.	244;244;247	P35712-3;P35712;P35712-2	.;SOX6_HUMAN;.	P	244;244;244;244;247;244	ENSP00000324948:L244P;ENSP00000339876:L244P;ENSP00000379644:L244P;ENSP00000432134:L244P;ENSP00000434455:L247P;ENSP00000433233:L244P	ENSP00000324948:L244P	L	-	2	0	SOX6	16162054	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.605000	0.90883	2.015000	0.59207	0.374000	0.22700	CTT	.	.		0.378	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326		G	16205478	A	G	16205478	3	3	195	1	0	0	0	0	1	0	0	0	14970	72	3	2	1841	2	SOX6	11	16205478	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	9251755	16205478	118801038	113	28741										
MRGPRX2	117194	hgsc.bcm.edu	37	chr11	19077740	19077740	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aggaagtcggccccggccagGctgaggacgtagacagagaa	16	10	0	3			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr11:19077740G>C	ENST00000329773.2	-	2	297	c.210C>G	c.(208-210)agC>agG	p.S70R		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	70					positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)			NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						CCCCGGCCAGGCTGAGGACGT	0.542																																					p.S70R	GBM(198;1966 2199 4849 37227 49954)	Atlas-SNP	.											.	MRGPRX2	42	.	0			c.C210G						.						85	93	91					11																	19077740		2199	4293	6492	SO:0001583	missense	117194	exon2			GGCCAGGCTGAGG		CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"GPCR / Class A : Orphans"	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.210C>G	chr11.hg19:g.19077740G>C	ENSP00000333800:p.Ser70Arg	172.0	0.0		161.0	18.0	NM_054030	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Missense_Mutation	SNP	ENST00000329773.2	hg19	CCDS7847.1	.	.	.	.	.	.	.	.	.	.	.	14.85	2.659929	0.47572	.	.	ENSG00000183695	ENST00000329773	T	0.09445	2.98	5.14	3.27	0.37495	GPCR, rhodopsin-like superfamily (1);	0.239450	0.36703	N	0.002456	T	0.15435	0.0372	L	0.43923	1.385	0.26794	N	0.969346	P	0.47191	0.891	P	0.52424	0.698	T	0.02789	-1.1110	10	0.87932	D	0	.	7.5485	0.27781	0.2594:0.0:0.7406:0.0	.	70	Q96LB1	MRGX2_HUMAN	R	70	ENSP00000333800:S70R	ENSP00000333800:S70R	S	-	3	2	MRGPRX2	19034316	1.000000	0.71417	0.997000	0.53966	0.159000	0.22180	3.776000	0.55356	0.868000	0.35678	0.655000	0.94253	AGC	.	.		0.542	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030		C	19077740	G	C	19077740	3	2	195	1	0	0	0	0	1	0	0	0	9776	1194	42	4	786	4	MRGPRX2	11	19077740	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	2872262	19077740	115928776	114	28742										
OR5AR1	219493	hgsc.bcm.edu	37	chr11	56431491	56431491	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tttgtaggttttgtggatgcTgagtgctatgtcctggcagc	14	6	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr11:56431491T>A	ENST00000302969.2	+	1	354	c.330T>A	c.(328-330)gcT>gcA	p.A110A		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						TTGTGGATGCTGAGTGCTATG	0.507																																					p.A110A		Atlas-SNP	.											.	OR5AR1	68	.	0			c.T330A						.						163	161	161					11																	56431491		2201	4296	6497	SO:0001819	synonymous_variant	219493	exon1			GGATGCTGAGTGC	AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"GPCR / Class A : Olfactory receptors"	15260	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily AR, member 1"				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.330T>A	chr11.hg19:g.56431491T>A		101.0	0.0		89.0	16.0	NM_001004730	Q6IF61	Silent	SNP	ENST00000302969.2	hg19	CCDS31535.1																																																																																			.	.		0.507	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730		A	56431491	T	A	56431491	2	1	195	1	0	0	0	0	0	0	0	1	11154	1567	55	4		4	OR5AR1	11	56431491	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	37353751	56431491	78575025	115	28743										
TMEM132A	54972	hgsc.bcm.edu	37	chr11	60703453	60703453	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aggagcctggtgccatcctgCcagctgaggagcagggtgcc	16	12	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr11:60703453C>A	ENST00000453848.2	+	11	2304	c.2146C>A	c.(2146-2148)Cca>Aca	p.P716T	TMEM132A_ENST00000005286.4_Missense_Mutation_p.P717T			Q24JP5	T132A_HUMAN	transmembrane protein 132A	716	Binds to HSPA5/GRP78. {ECO:0000250}.|Confers cellular localization similar to full-length form. {ECO:0000250}.					endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						TGCCATCCTGCCAGCTGAGGA	0.692																																					p.P717T		Atlas-SNP	.											.	TMEM132A	135	.	0			c.C2149A						.						39	37	38					11																	60703453		2203	4298	6501	SO:0001583	missense	54972	exon11			ATCCTGCCAGCTG	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.2146C>A	chr11.hg19:g.60703453C>A	ENSP00000405823:p.Pro716Thr	45.0	0.0		49.0	15.0	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	hg19	CCDS44618.1	.	.	.	.	.	.	.	.	.	.	C	9.781	1.175292	0.21704	.	.	ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286;ENST00000535480	T;T;T	0.22945	2.62;2.62;1.93	5.35	4.37	0.52481	.	0.426996	0.21729	N	0.069991	T	0.16557	0.0398	N	0.20530	0.585	0.33632	D	0.606229	B;B	0.32968	0.392;0.257	B;B	0.34093	0.172;0.175	T	0.16453	-1.0402	10	0.87932	D	0	.	8.6013	0.33747	0.1696:0.6665:0.1639:0.0	.	716;717	Q24JP5;Q24JP5-2	T132A_HUMAN;.	T	467;716;717;82	ENSP00000405823:P716T;ENSP00000005286:P717T;ENSP00000439716:P82T	ENSP00000005286:P717T	P	+	1	0	TMEM132A	60460029	0.939000	0.31865	1.000000	0.80357	0.767000	0.43475	1.250000	0.32850	2.677000	0.91161	0.561000	0.74099	CCA	.	.		0.692	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		A	60703453	C	A	60703453	3	1	195	1	0	0	0	0	1	0	0	0	16060	739	26	3	2191	3	TMEM132A	11	60703453	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	4271962	60703453	74303063	116	28744										
PPP1CA	5499	hgsc.bcm.edu	37	chr11	67166088	67166097	+	Frame_Shift_Del	DEL	CCCTTGTTCT	CCCTTGTTCT	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cactgaactgcccgtacttcCccttgttcttgtcggcgggc							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	CCCTTGTTCT	CCCTTGTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr11:67166088_67166097delCCCTTGTTCT	ENST00000376745.4	-	7	1050_1059	c.902_911delAGAACAAGGG	c.(901-912)aagaacaaggggfs	p.KNKG301fs	PPP1CA_ENST00000532446.1_5'UTR|PPP1CA_ENST00000312989.7_Frame_Shift_Del_p.KNKG312fs|PPP1CA_ENST00000358239.4_Frame_Shift_Del_p.KNKG257fs	NM_001008709.1|NM_002708.3	NP_001008709.1|NP_002699.1	P62136	PP1A_HUMAN	protein phosphatase 1, catalytic subunit, alpha isozyme	301					branching morphogenesis of an epithelial tube (GO:0048754)|cell cycle (GO:0007049)|cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|lung development (GO:0030324)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|MLL5-L complex (GO:0070688)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein phosphatase type 1 complex (GO:0000164)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)|ribonucleoprotein complex binding (GO:0043021)			breast(1)|lung(2)|pancreas(1)|urinary_tract(3)	7			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			CCCGTACTTCCCCTTGTTCTTGTCGGCGGG	0.605																																					p.312_315del		Atlas-Indel,Pindel	.											.	PPP1CA	83	.	0			c.936_945del						.																																			SO:0001589	frameshift_variant	5499	exon7			.		CCDS8160.1, CCDS8161.1, CCDS31618.1	11q13	2013-01-18	2010-03-05			ENSG00000172531	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9281	protein-coding gene	gene with protein product		176875	"protein phosphatase 1, catalytic subunit, alpha isoform"	PPP1A			Standard	NM_002708		Approved	PP1A, PP-1A, PP1alpha	uc001oku.1	P62136		ENST00000376745.4:c.902_911delAGAACAAGGG	chr11.hg19:g.67166088_67166097delCCCTTGTTCT	ENSP00000365936:p.Lys301fs	96.0	0.0		94.0	10.0	NM_001008709	A6NNR3|B2R908|P08129|P20653|P22802|Q07161	Frame_Shift_Del	DEL	ENST00000376745.4	hg19	CCDS8160.1																																																																																			.	.		0.605	PPP1CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395487.1	NM_002708		-	67166097	CCCTTGTTCT	-	67166088	7	5	195	1	0	1	0	1	0	0	0	0	12361	623	22	0	85	0	PPP1CA	11	67166088	Frame_Shift_Del	DEL	CCCTTGTTCT	TCGA-DD-AADM-01A-11D-A40R-10	6462635	67166088	67840428	117	28745										
DDI1	414301	hgsc.bcm.edu	37	chr11	103908514	103908514	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	agtgctctttctccatacttGaggatcaacccatggatatg	8	10	3	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr11:103908514G>A	ENST00000302259.3	+	1	1207	c.964G>A	c.(964-966)Gag>Aag	p.E322K	PDGFD_ENST00000393158.2_Intron|PDGFD_ENST00000302251.5_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	322							aspartic-type endopeptidase activity (GO:0004190)			central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		CTCCATACTTGAGGATCAACC	0.448																																					p.E322K		Atlas-SNP	.											.	DDI1	222	.	0			c.G964A						.						136	127	130					11																	103908514		2202	4299	6501	SO:0001583	missense	414301	exon1			ATACTTGAGGATC		CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.964G>A	chr11.hg19:g.103908514G>A	ENSP00000302805:p.Glu322Lys	117.0	0.0		120.0	37.0	NM_001001711	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	hg19	CCDS31660.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.893254	0.33442	.	.	ENSG00000170967	ENST00000302259	T	0.50001	0.76	5.21	4.29	0.51040	Peptidase aspartic (1);Peptidase aspartic, eukaryotic predicted (1);Peptidase aspartic, catalytic (1);	0.000000	0.85682	D	0.000000	T	0.51160	0.1658	M	0.81497	2.545	0.43058	D	0.994674	P	0.39326	0.668	B	0.37480	0.251	T	0.60915	-0.7168	10	0.56958	D	0.05	-13.2733	13.8723	0.63626	0.0:0.1541:0.8459:0.0	.	322	Q8WTU0	DDI1_HUMAN	K	322	ENSP00000302805:E322K	ENSP00000302805:E322K	E	+	1	0	DDI1	103413724	1.000000	0.71417	0.123000	0.21794	0.063000	0.16089	7.224000	0.78042	1.560000	0.49568	-0.175000	0.13238	GAG	.	.		0.448	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711		A	103908514	G	A	103908514	3	1	195	1	0	0	0	0	1	0	0	0	4330	1291	45	3	966	3	DDI1	11	103908514	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	36742426	103908514	31098002	118	28746										
C11orf63	79864	hgsc.bcm.edu	37	chr11	122774672	122774672	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aaatattcagacctccgctaTgacccgaactggaagagtaa	8	10	1	3			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr11:122774672T>C	ENST00000531316.1	+	2	476	c.384T>C	c.(382-384)taT>taC	p.Y128Y	C11orf63_ENST00000307257.6_Silent_p.Y128Y|C11orf63_ENST00000227349.2_Silent_p.Y128Y			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	128					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)					breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		ACCTCCGCTATGACCCGAACT	0.468																																					p.Y128Y		Atlas-SNP	.											.	C11orf63	116	.	0			c.T384C						.						147	166	159					11																	122774672		2202	4299	6501	SO:0001819	synonymous_variant	79864	exon3			CCGCTATGACCCG	BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.384T>C	chr11.hg19:g.122774672T>C		156.0	0.0		168.0	20.0	NM_024806	A8K6G0|Q96GB5|Q9H5D6	Silent	SNP	ENST00000531316.1	hg19	CCDS8438.1																																																																																			.	.		0.468	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806		C	122774672	T	C	122774672	2	2	195	1	0	0	0	0	0	0	0	1	1656	1471	51	2		2	C11orf63	11	122774672	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	18866158	122774672	12231844	119	28747										
C11orf63	79864	hgsc.bcm.edu	37	chr11	122805414	122805414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gattatgcatgcctctaacaAtgatgtacaagcctcaaggg	9	9	2	1	rs201888967		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr11:122805414A>G	ENST00000531316.1	+	4	1357	c.1265A>G	c.(1264-1266)aAt>aGt	p.N422S	C11orf63_ENST00000227349.2_Missense_Mutation_p.N422S			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	422					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)					breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		GCCTCTAACAATGATGTACAA	0.418																																					p.N422S		Atlas-SNP	.											.	C11orf63	116	.	0			c.A1265G						.						77	75	76					11																	122805414		2202	4299	6501	SO:0001583	missense	79864	exon5			CTAACAATGATGT	BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.1265A>G	chr11.hg19:g.122805414A>G	ENSP00000431669:p.Asn422Ser	174.0	0.0		200.0	73.0	NM_024806	A8K6G0|Q96GB5|Q9H5D6	Missense_Mutation	SNP	ENST00000531316.1	hg19	CCDS8438.1	.	.	.	.	.	.	.	.	.	.	A	6.911	0.537618	0.13188	.	.	ENSG00000109944	ENST00000227349;ENST00000531316	T;T	0.23147	1.92;1.92	5.25	-1.33	0.09172	.	1.157030	0.06281	N	0.697381	T	0.14614	0.0353	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.31998	-0.9923	10	0.15499	T	0.54	0.0253	4.5599	0.12154	0.3803:0.3417:0.278:0.0	.	422	Q6NUN7	CK063_HUMAN	S	422	ENSP00000227349:N422S;ENSP00000431669:N422S	ENSP00000227349:N422S	N	+	2	0	C11orf63	122310624	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.472000	0.06623	-0.247000	0.09597	-0.334000	0.08254	AAT	.	.		0.418	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806		G	122805414	A	G	122805414	3	3	195	1	0	0	0	0	1	0	0	0	1656	101	4	2	1343	2	C11orf63	11	122805414	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	30742	122805414	12201102	120	28748										
WNK1	65125	hgsc.bcm.edu	37	chr12	992147	992147	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cgagtagtagaatgtcaattAgagactcataataggaaaat	9	4	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr12:992147A>T	ENST00000315939.6	+	15	4054	c.3411A>T	c.(3409-3411)ttA>ttT	p.L1137F	WNK1_ENST00000530271.2_Missense_Mutation_p.L1635F|WNK1_ENST00000537687.1_Missense_Mutation_p.L1397F|WNK1_ENST00000340908.4_Missense_Mutation_p.L730F|WNK1_ENST00000535572.1_Missense_Mutation_p.L890F	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1137					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			AATGTCAATTAGAGACTCATA	0.358																																					p.L1397F	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.A4191T						.						118	124	122					12																	992147		2203	4300	6503	SO:0001583	missense	65125	exon15			TCAATTAGAGACT	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.3411A>T	chr12.hg19:g.992147A>T	ENSP00000313059:p.Leu1137Phe	189.0	0.0		155.0	27.0	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	hg19	CCDS8506.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.47|18.47	3.630498|3.630498	0.67015|0.67015	.|.	.|.	ENSG00000060237|ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908|ENST00000544965	T;T;T;T;T|.	0.44482|.	0.92;0.92;0.92;0.92;0.92|.	6.02|6.02	-0.255|-0.255	0.12988|0.12988	.|.	0.000000|.	0.50627|.	D|.	0.000101|.	T|.	0.66694|.	0.2815|.	M|M	0.67700|0.67700	2.07|2.07	0.53005|0.53005	D|D	0.999964|0.999964	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.997|.	T|.	0.64533|.	-0.6385|.	10|.	0.87932|.	D|.	0|.	-11.2212|-11.2212	11.0923|11.0923	0.48123|0.48123	0.5138:0.0:0.4862:0.0|0.5138:0.0:0.4862:0.0	.|.	890;890;1137|.	Q9H4A3-2;F5GWT4;Q9H4A3|.	.;.;WNK1_HUMAN|.	F|X	890;1137;1397;310;1635;730|214	ENSP00000441972:L890F;ENSP00000313059:L1137F;ENSP00000444465:L1397F;ENSP00000433548:L1635F;ENSP00000341292:L730F|.	ENSP00000252477:L310F|.	L|R	+|+	3|1	2|2	WNK1|WNK1	862408|862408	0.983000|0.983000	0.35010|0.35010	0.943000|0.943000	0.38184|0.38184	0.998000|0.998000	0.95712|0.95712	0.362000|0.362000	0.20284|0.20284	0.150000|0.150000	0.19136|0.19136	0.528000|0.528000	0.53228|0.53228	TTA|AGA	.	.		0.358	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		T	992147	A	T	992147	3	4	195	1	0	0	0	0	1	0	0	0	17392	417	15	4	4971	4	WNK1	12	992147	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10		992147	132859748	121	28749										
RND1	27289	hgsc.bcm.edu	37	chr12	49258640	49258640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctgtgtaattttcgaacacgGtgggcacataggtctgtgaa	12	7	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr12:49258640G>A	ENST00000309739.5	-	2	264	c.134C>T	c.(133-135)aCc>aTc	p.T45I		NM_014470.3	NP_055285.1	Q92730	RND1_HUMAN	Rho family GTPase 1	45					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|GTP catabolic process (GO:0006184)|negative regulation of cell adhesion (GO:0007162)|neuron remodeling (GO:0016322)|small GTPase mediated signal transduction (GO:0007264)	adherens junction (GO:0005912)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(2)|skin(1)|urinary_tract(1)	10						TTCGAACACGGTGGGCACATA	0.512																																					p.T45I		Atlas-SNP	.											.	RND1	26	.	0			c.C134T						.						186	163	171					12																	49258640		2203	4300	6503	SO:0001583	missense	27289	exon2			AACACGGTGGGCA	Y07923	CCDS8771.1	12q12	2008-01-23				ENSG00000172602			18314	protein-coding gene	gene with protein product	"ras homolog gene family, member S"	609038				9531558	Standard	NM_014470		Approved	Rho6, ARHS, RHOS	uc001rsn.3	Q92730	OTTHUMG00000170400	ENST00000309739.5:c.134C>T	chr12.hg19:g.49258640G>A	ENSP00000308461:p.Thr45Ile	167.0	0.0		196.0	40.0	NM_014470	A8K9P7	Missense_Mutation	SNP	ENST00000309739.5	hg19	CCDS8771.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.986880	0.74589	.	.	ENSG00000172602	ENST00000309739	D	0.87887	-2.31	4.14	3.25	0.37280	Small GTP-binding protein domain (1);	0.053331	0.64402	N	0.000001	D	0.93979	0.8072	M	0.92923	3.36	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.93958	0.7238	10	0.87932	D	0	-8.559	9.9628	0.41706	0.1013:0.0:0.8987:0.0	.	45	Q92730	RND1_HUMAN	I	45	ENSP00000308461:T45I	ENSP00000308461:T45I	T	-	2	0	RND1	47544907	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.135000	0.94478	1.104000	0.41587	0.449000	0.29647	ACC	.	.		0.512	RND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408915.1	NM_014470		A	49258640	G	A	49258640	3	1	195	1	0	0	0	0	1	0	0	0	13434	1261	44	3	580	3	RND1	12	49258640	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	48266493	49258640	84593255	122	28750										
GRIP1	23426	hgsc.bcm.edu	37	chr12	66786128	66786129	+	Missense_Mutation	DNP	TG	TG	GA													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tctattgcagacccatcccaTgaatccacagcactgtccac							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr12:66786128_66786129TG>GA	ENST00000398016.3	-	18	2335_2336	c.2267_2268CA>TC	c.(2266-2268)tCA>tTC	p.S756F	GRIP1_ENST00000542021.1_5'Flank|GRIP1_ENST00000359742.4_Missense_Mutation_p.S808F|GRIP1_ENST00000286445.7_Missense_Mutation_p.S808F	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		ACCCATCCCATGAATCCACAGC	0.545																																					p.S756S|p.S756L		Atlas-SNP	.											.	GRIP1	106	.	0			c.A2268C|c.C2267T						.																																			SO:0001583	missense	23426	exon18			ATCCCATGAATCC|TCCCATGAATCCA	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.2267_2268delinsGA	chr12.hg19:g.66786128_66786129delinsGA	ENSP00000381098:p.Ser756Phe	78.0|77.0	0.0		69.0|72.0	9.0|10.0	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Silent|Missense_Mutation	SNP	ENST00000398016.3	hg19	CCDS41807.1																																																																																			.	.		0.545	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			GA	66786129	TG	GA	66786128	3	3	195	1	0	0	0	0	1	0	0	0	6796	1451	51	5	990	5	GRIP1	12	66786128	Missense_Mutation	DNP	TG	TCGA-DD-AADM-01A-11D-A40R-10	17527488	66786128	67065767	123	28751										
CNOT2	4848	hgsc.bcm.edu	37	chr12	70729244	70729244	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gtgaaaatgtgacaggattgGacctttcagatttcccagca	10	8	1	3			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr12:70729244G>T	ENST00000418359.3	+	9	1127	c.676G>T	c.(676-678)Gac>Tac	p.D226Y	CNOT2_ENST00000548230.1_3'UTR|CNOT2_ENST00000229195.3_Missense_Mutation_p.D226Y|CNOT2_ENST00000551483.1_5'UTR	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	226					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription corepressor binding (GO:0001226)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(2)|urinary_tract(1)	20	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			GACAGGATTGGACCTTTCAGA	0.383																																					p.D226Y		Atlas-SNP	.											.	CNOT2	53	.	0			c.G676T						.						115	110	112					12																	70729244		2203	4300	6503	SO:0001583	missense	4848	exon9			GGATTGGACCTTT	AF180473	CCDS31857.1	12q15	2008-05-14				ENSG00000111596			7878	protein-coding gene	gene with protein product		604909		NOT2		10637334	Standard	NM_014515		Approved	CDC36, NOT2H	uc001svv.3	Q9NZN8		ENST00000418359.3:c.676G>T	chr12.hg19:g.70729244G>T	ENSP00000412091:p.Asp226Tyr	129.0	0.0		143.0	52.0	NM_001199302	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Missense_Mutation	SNP	ENST00000418359.3	hg19	CCDS31857.1	.	.	.	.	.	.	.	.	.	.	G	33	5.223156	0.95139	.	.	ENSG00000111596	ENST00000552231;ENST00000229195;ENST00000418359;ENST00000550160;ENST00000552915;ENST00000552483;ENST00000548159;ENST00000551043;ENST00000550155	T;T;T;T;T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.83894	0.5353	M	0.75615	2.305	0.80722	D	1	D	0.61697	0.99	P	0.56216	0.794	D	0.85799	0.1372	10	0.87932	D	0	-7.5889	19.484	0.95022	0.0:0.0:1.0:0.0	.	226	Q9NZN8	CNOT2_HUMAN	Y	226;226;226;89;165;80;217;226;36	ENSP00000450318:D226Y;ENSP00000229195:D226Y;ENSP00000412091:D226Y;ENSP00000448490:D89Y;ENSP00000447497:D165Y;ENSP00000450077:D80Y;ENSP00000449659:D217Y;ENSP00000449260:D226Y;ENSP00000448499:D36Y	ENSP00000229195:D226Y	D	+	1	0	CNOT2	69015511	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.777000	0.99008	2.669000	0.90835	0.650000	0.86243	GAC	.	.		0.383	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404260.1			T	70729244	G	T	70729244	3	4	195	1	0	0	0	0	1	0	0	0	3621	1174	41	3	702	3	CNOT2	12	70729244	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	3943116	70729244	63122651	124	28752										
TRPC4	7223	hgsc.bcm.edu	37	chr13	38237691	38237691	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	agtatatgaatagaaacttcAaaatgtccaggagcattctt	7	6	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr13:38237691A>G	ENST00000379705.3	-	6	2407	c.1550T>C	c.(1549-1551)tTg>tCg	p.L517S	TRPC4_ENST00000379681.3_Missense_Mutation_p.L517S|TRPC4_ENST00000379673.2_Missense_Mutation_p.L517S|TRPC4_ENST00000447043.1_Missense_Mutation_p.L517S|TRPC4_ENST00000426868.2_Intron|TRPC4_ENST00000355779.2_Missense_Mutation_p.L517S|TRPC4_ENST00000494529.1_5'UTR|TRPC4_ENST00000379679.1_Missense_Mutation_p.L344S|TRPC4_ENST00000338947.5_Missense_Mutation_p.L344S|TRPC4_ENST00000358477.2_Missense_Mutation_p.L517S			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	517					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TAGAAACTTCAAAATGTCCAG	0.398																																					p.L517S		Atlas-SNP	.											.	TRPC4	389	.	0			c.T1550C						.						85	83	83					13																	38237691		2203	4300	6503	SO:0001583	missense	7223	exon6			AACTTCAAAATGT	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.1550T>C	chr13.hg19:g.38237691A>G	ENSP00000369027:p.Leu517Ser	174.0	0.0		147.0	38.0	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	hg19	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.383135	0.82792	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	D;D;D;D;D;D;D;D	0.98567	-5.0;-5.0;-5.0;-5.0;-5.0;-5.0;-5.0;-5.0	6.08	6.08	0.98989	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98741	0.9577	M	0.71581	2.175	0.80722	D	1	P;D;D;D;P;P	0.76494	0.851;0.959;0.999;0.972;0.754;0.94	P;P;D;P;P;P	0.83275	0.55;0.835;0.996;0.891;0.55;0.897	D	0.99716	1.1008	10	0.51188	T	0.08	-15.3057	16.6438	0.85155	1.0:0.0:0.0:0.0	.	517;517;517;344;517;517	Q9UBN4-3;Q9UBN4-4;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;.;TRPC4_HUMAN	S	517;517;344;344;517;517;517;517	ENSP00000369027:L517S;ENSP00000369003:L517S;ENSP00000342580:L344S;ENSP00000369001:L344S;ENSP00000348025:L517S;ENSP00000351264:L517S;ENSP00000368995:L517S;ENSP00000414316:L517S	ENSP00000342580:L344S	L	-	2	0	TRPC4	37135691	1.000000	0.71417	0.993000	0.49108	0.975000	0.68041	9.339000	0.96797	2.333000	0.79357	0.533000	0.62120	TTG	.	.		0.398	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		G	38237691	A	G	38237691	3	3	195	1	0	0	0	0	1	0	0	0	16595	131	5	2	1422	2	TRPC4	13	38237691	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10		38237691	76932187	125	28753										
RB1	5925	hgsc.bcm.edu	37	chr13	48936988	48936988	+	Frame_Shift_Del	DEL	A	A	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	attaatggttcacctcgaacAcccaggcgaggtcagaacag							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr13:48936988delA	ENST00000267163.4	+	8	894	c.756delA	c.(754-756)acafs	p.T252fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	252					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(6)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CACCTCGAACACCCAGGCGAG	0.338		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.T252fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	21	Whole gene deletion(15)|Unknown(6)	bone(11)|breast(5)|eye(1)|soft_tissue(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.755delC						.						107	109	108					13																	48936988		2203	4300	6503	SO:0001589	frameshift_variant	5925	exon8	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.756delA	chr13.hg19:g.48936988delA	ENSP00000267163:p.Thr252fs	384.0	0.0		216.0	34.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Del	DEL	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.338	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			-	48936988	A	-	48936988	7	5	195	1	0	1	0	1	0	0	0	0	13113	146	6	0	786	0	RB1	13	48936988	Frame_Shift_Del	DEL	A	TCGA-DD-AADM-01A-11D-A40R-10	10699297	48936988	66232890	126	28754										
IRS2	8660	hgsc.bcm.edu	37	chr13	110436754	110436754	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	taggagcggccacagtggctCaggggcctgtccatggtcat	15	11	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr13:110436754C>A	ENST00000375856.3	-	1	2161	c.1647G>T	c.(1645-1647)ctG>ctT	p.L549L		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	549					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			CACAGTGGCTCAGGGGCCTGT	0.716																																					p.L549L	Melanoma(100;613 2409 40847)	Atlas-SNP	.											.	IRS2	44	.	0			c.G1647T						.						12	16	15					13																	110436754		2141	4236	6377	SO:0001819	synonymous_variant	8660	exon1			GTGGCTCAGGGGC	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"Pleckstrin homology (PH) domain containing"	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.1647G>T	chr13.hg19:g.110436754C>A		125.0	0.0		101.0	40.0	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Silent	SNP	ENST00000375856.3	hg19	CCDS9510.1																																																																																			.	.		0.716	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749		A	110436754	C	A	110436754	2	1	195	1	0	0	0	0	0	0	0	1	7850	813	29	3		3	IRS2	13	110436754	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	61499766	110436754	4733124	127	28755										
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21544595	21544595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cactgcctccagcactcattCctgccttgagccaacttcag	6	17	2	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr14:21544595C>T	ENST00000298694.4	+	6	1943	c.1816C>T	c.(1816-1818)Cct>Tct	p.P606S	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.P606S			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	606						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						AGCACTCATTCCTGCCTTGAG	0.597																																					p.P606S		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.C1816T						.						70	61	64					14																	21544595		2203	4300	6503	SO:0001583	missense	55701	exon6			CTCATTCCTGCCT		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"Rho guanine nucleotide exchange factors"	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.1816C>T	chr14.hg19:g.21544595C>T	ENSP00000298694:p.Pro606Ser	54.0	0.0		48.0	16.0	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	hg19	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	C	0.130	-1.114504	0.01799	.	.	ENSG00000165801	ENST00000298694;ENST00000298693	T;T	0.01871	4.65;4.59	5.52	3.63	0.41609	.	0.141481	0.33040	N	0.005346	T	0.02083	0.0065	L	0.27053	0.805	0.25579	N	0.986817	B	0.20261	0.043	B	0.24974	0.057	T	0.45026	-0.9289	10	0.07030	T	0.85	.	13.7699	0.63018	0.2743:0.7257:0.0:0.0	.	606	Q8TER5	ARH40_HUMAN	S	606	ENSP00000298694:P606S;ENSP00000298693:P606S	ENSP00000298693:P606S	P	+	1	0	ARHGEF40	20614435	0.885000	0.30320	0.970000	0.41538	0.054000	0.15201	0.114000	0.15520	0.708000	0.31955	-1.367000	0.01198	CCT	.	.		0.597	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			T	21544595	C	T	21544595	3	4	195	1	0	0	0	0	1	0	0	0	5934	855	30	3	1838	3	FLJ10357	14	21544595	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10		21544595	85804945	128	28756										
G2E3	55632	hgsc.bcm.edu	37	chr14	31058658	31058658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	atggttttctaatagaagatAtcaggaaggaagtgaataga	11	2	2	4			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr14:31058658A>G	ENST00000206595.6	+	4	359	c.205A>G	c.(205-207)Atc>Gtc	p.I69V	G2E3_ENST00000544007.1_3'UTR|G2E3_ENST00000438909.2_Missense_Mutation_p.I23V|G2E3_ENST00000553504.1_Missense_Mutation_p.I99V	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	69					apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						AATAGAAGATATCAGGAAGGA	0.299																																					p.I69V		Atlas-SNP	.											.	G2E3	82	.	0			c.A205G						.						106	116	113					14																	31058658		2203	4296	6499	SO:0001583	missense	55632	exon4			GAAGATATCAGGA	AK000340	CCDS9638.1	14q12	2013-01-28	2010-09-17	2009-02-03	ENSG00000092140	ENSG00000092140		"Zinc fingers, PHD-type"	20338	protein-coding gene	gene with protein product	"PHD finger protein 7B"	611299	"KIAA1333"	KIAA1333		18511420, 17239372	Standard	NM_017769		Approved	FLJ20333, PHF7B	uc001wqk.2	Q7L622	OTTHUMG00000140204	ENST00000206595.6:c.205A>G	chr14.hg19:g.31058658A>G	ENSP00000206595:p.Ile69Val	157.0	0.0		157.0	27.0	NM_017769	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Missense_Mutation	SNP	ENST00000206595.6	hg19	CCDS9638.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.315837	0.81469	.	.	ENSG00000092140	ENST00000206595;ENST00000550944;ENST00000438909;ENST00000553504;ENST00000554714;ENST00000547532;ENST00000555429	T;T;T;T;T;T;D	0.90844	-0.39;-0.39;-0.39;-0.39;-0.39;-0.39;-2.74	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.91734	0.7386	N	0.25485	0.75	0.54753	D	0.999987	D;D	0.69078	0.972;0.997	P;D	0.80764	0.779;0.994	D	0.91895	0.5527	10	0.42905	T	0.14	-8.3866	15.4936	0.75632	1.0:0.0:0.0:0.0	.	23;69	B4DIF9;Q7L622	.;G2E3_HUMAN	V	69;69;23;99;69;69;69	ENSP00000206595:I69V;ENSP00000448745:I69V;ENSP00000391068:I23V;ENSP00000451653:I99V;ENSP00000451147:I69V;ENSP00000446615:I69V;ENSP00000452275:I69V	ENSP00000206595:I69V	I	+	1	0	G2E3	30128409	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.507000	0.81676	2.134000	0.65973	0.482000	0.46254	ATC	.	.		0.299	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769		G	31058658	A	G	31058658	3	3	195	1	0	0	0	0	1	0	0	0	6148	449	16	2	215	2	G2E3	14	31058658	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	9514063	31058658	76290882	129	28757										
KIAA0391	9692	hgsc.bcm.edu	37	chr14	35649939	35649939	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ttgatgttgtcattgatggtCtcaatgttgccaaaatgttt	9	5	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr14:35649939C>G	ENST00000557565.1	+	5	1612	c.1231C>G	c.(1231-1233)Ctc>Gtc	p.L411V	KIAA0391_ENST00000605870.1_Missense_Mutation_p.L39V|KIAA0391_ENST00000603544.1_Missense_Mutation_p.L395V|KIAA0391_ENST00000321130.10_Missense_Mutation_p.L395V|KIAA0391_ENST00000250377.7_Missense_Mutation_p.L316V|KIAA0391_ENST00000604948.1_Missense_Mutation_p.L316V|KIAA0391_ENST00000534898.4_Missense_Mutation_p.L411V	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	411					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		CATTGATGGTCTCAATGTTGC	0.303																																					p.L411V		Atlas-SNP	.											.	KIAA0391	35	.	0			c.C1231G						.						174	155	162					14																	35649939		2201	4300	6501	SO:0001583	missense	9692	exon5			GATGGTCTCAATG	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 3", "proteinaceous RNase P"	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.1231C>G	chr14.hg19:g.35649939C>G	ENSP00000454657:p.Leu411Val	91.0	0.0		88.0	15.0	NM_014672	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Missense_Mutation	SNP	ENST00000557565.1	hg19	CCDS32063.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.942081	0.73557	.	.	ENSG00000100890	ENST00000554896;ENST00000250377;ENST00000321130;ENST00000534898;ENST00000556121;ENST00000556912;ENST00000557404	T;T;T;T	0.55588	0.63;0.51;0.56;1.02	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000001	T	0.74981	0.3788	M	0.87180	2.865	0.51233	D	0.999916	D;D	0.63046	0.992;0.992	D;D	0.68192	0.956;0.956	T	0.78135	-0.2322	10	0.54805	T	0.06	-3.8909	15.0838	0.72135	0.0:1.0:0.0:0.0	.	395;411	O15091-2;O15091	.;MRRP3_HUMAN	V	316;316;395;411;395;39;39	ENSP00000250377:L316V;ENSP00000324697:L395V;ENSP00000440915:L411V;ENSP00000450898:L39V	ENSP00000250377:L316V	L	+	1	0	KIAA0391	34719690	0.995000	0.38212	0.996000	0.52242	0.975000	0.68041	4.078000	0.57606	2.630000	0.89119	0.655000	0.94253	CTC	.	.		0.303	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		G	35649939	C	G	35649939	3	3	195	1	0	0	0	0	1	0	0	0	8181	913	32	4	1245	4	KIAA0391	14	35649939	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	4591281	35649939	71699601	130	28758										
SDCCAG1	9147	hgsc.bcm.edu	37	chr14	50266232	50266232	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aatgtctccggctctgtgatTtactgtcactctattaaaac	6	10	4	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr14:50266232T>G	ENST00000298310.5	-	25	2875	c.2426A>C	c.(2425-2427)aAa>aCa	p.K809T	NEMF_ENST00000545773.1_Missense_Mutation_p.K767T|NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000546046.1_Missense_Mutation_p.K788T			O60524	NEMF_HUMAN	nuclear export mediator factor	809					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						GCTCTGTGATTTACTGTCACT	0.303																																					p.K809T		Atlas-SNP	.											.	NEMF	79	.	0			c.A2426C						.						91	99	96					14																	50266232		2203	4297	6500	SO:0001583	missense	9147	exon25			TGTGATTTACTGT	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.2426A>C	chr14.hg19:g.50266232T>G	ENSP00000298310:p.Lys809Thr	312.0	0.0		297.0	46.0	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Missense_Mutation	SNP	ENST00000298310.5	hg19	CCDS9694.1	.	.	.	.	.	.	.	.	.	.	T	10.86	1.470168	0.26423	.	.	ENSG00000165525	ENST00000298310;ENST00000545773;ENST00000546046;ENST00000534912;ENST00000555970	T;T;T;T	0.49139	0.81;0.8;0.79;0.8	5.2	5.2	0.72013	.	0.123434	0.53938	D	0.000049	T	0.36580	0.0972	L	0.39245	1.2	0.80722	D	1	B;B;P;P	0.38335	0.43;0.266;0.528;0.627	B;B;B;B	0.35353	0.152;0.107;0.201;0.15	T	0.21109	-1.0255	10	0.37606	T	0.19	-7.2413	10.3455	0.43903	0.0:0.0797:0.0:0.9203	.	788;784;767;809	O60524-3;O60524-5;O60524-4;O60524	.;.;.;NEMF_HUMAN	T	809;767;788;581;767	ENSP00000298310:K809T;ENSP00000438309:K767T;ENSP00000441016:K788T;ENSP00000452540:K767T	ENSP00000298310:K809T	K	-	2	0	NEMF	49335982	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	4.380000	0.59581	1.956000	0.56807	0.383000	0.25322	AAA	.	.		0.303	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		G	50266232	T	G	50266232	3	3	195	1	0	0	0	0	1	0	0	0	13972	1841	64	5	840	5	SDCCAG1	14	50266232	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	14616293	50266232	57083308	131	28759										
SLC10A1	6554	hgsc.bcm.edu	37	chr14	70246027	70246027	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctcttccccacattgatggcAgagagaactgtgacggccac	10	13	1	4	rs375859965		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr14:70246027A>T	ENST00000216540.4	-	3	751	c.618T>A	c.(616-618)tcT>tcA	p.S206S		NM_003049.3	NP_003040.1	Q14973	NTCP_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 1	206					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)	14				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)	Bumetanide(DB00887)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Ethinyl Estradiol(DB00977)|Indomethacin(DB00328)|Liothyronine(DB00279)|Liotrix(DB01583)|Pitavastatin(DB08860)|Probenecid(DB01032)|Progesterone(DB00396)|Testosterone(DB00624)|Ursodeoxycholic acid(DB01586)	CATTGATGGCAGAGAGAACTG	0.483																																					p.S206S		Atlas-SNP	.											.	SLC10A1	32	.	0			c.T618A						.						148	103	118					14																	70246027		2203	4300	6503	SO:0001819	synonymous_variant	6554	exon3			GATGGCAGAGAGA	L21893	CCDS9797.1	14q24.2	2013-07-18	2013-07-18		ENSG00000100652	ENSG00000100652		"Solute carriers"	10905	protein-coding gene	gene with protein product		182396				8132774	Standard	NM_003049		Approved	NTCP	uc001xlr.2	Q14973	OTTHUMG00000171236	ENST00000216540.4:c.618T>A	chr14.hg19:g.70246027A>T		118.0	0.0		101.0	28.0	NM_003049	B9EGB6|Q2TU29	Silent	SNP	ENST00000216540.4	hg19	CCDS9797.1																																																																																			.	.		0.483	SLC10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412464.1			T	70246027	A	T	70246027	2	4	195	1	0	0	0	0	0	0	0	1	14388	175	7	4		4	SLC10A1	14	70246027	Silent	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	19979795	70246027	37103513	132	28760										
RIN3	79890	hgsc.bcm.edu	37	chr14	93118677	93118677	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccctgaggacacgccccgggAgagcacggagcaaggccagg	16	14	0	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr14:93118677A>G	ENST00000216487.7	+	6	1442	c.1283A>G	c.(1282-1284)gAg>gGg	p.E428G	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	428	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.E428G(1)		endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				ACGCCCCGGGAGAGCACGGAG	0.662																																					p.E428G		Atlas-SNP	.											RIN3,NS,carcinoma,0,1	RIN3	81	.	1	Substitution - Missense(1)	prostate(1)	c.A1283G						.						63	72	69					14																	93118677		2203	4300	6503	SO:0001583	missense	79890	exon6			CCCGGGAGAGCAC	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.1283A>G	chr14.hg19:g.93118677A>G	ENSP00000216487:p.Glu428Gly	218.0	1.0		151.0	20.0	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	hg19	CCDS32144.1	.	.	.	.	.	.	.	.	.	.	A	0.305	-0.971129	0.02232	.	.	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.06294	3.32	3.79	2.9	0.33743	.	1.489490	0.04233	N	0.335545	T	0.03348	0.0097	N	0.02011	-0.69	0.09310	N	0.999991	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.38672	-0.9650	10	0.29301	T	0.29	-6.1219	9.1654	0.37048	0.2456:0.0:0.7544:0.0	.	428;474;353;428	Q8TB24-4;Q86U22;Q6ZRC2;Q8TB24	.;.;.;RIN3_HUMAN	G	428;352	ENSP00000216487:E428G	ENSP00000216487:E428G	E	+	2	0	RIN3	92188430	0.018000	0.18449	0.038000	0.18304	0.003000	0.03518	0.422000	0.21296	0.731000	0.32448	-0.765000	0.03448	GAG	.	.		0.662	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			G	93118677	A	G	93118677	3	3	195	1	0	0	0	0	1	0	0	0	13388	304	11	2	1305	2	RIN3	14	93118677	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	22872650	93118677	14230863	133	28761										
MGA	23269	hgsc.bcm.edu	37	chr15	42054035	42054035	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aatattctgatacggaaagtAtcgtctctttcaggtgagat	9	6	3	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr15:42054035A>G	ENST00000570161.1	+	20	7497	c.7497A>G	c.(7495-7497)gtA>gtG	p.V2499V	MGA_ENST00000545763.1_Silent_p.V2290V|MGA_ENST00000219905.7_Silent_p.V2499V|MGA_ENST00000566586.1_Silent_p.V2290V|MGA_ENST00000389936.4_Silent_p.V2460V			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TACGGAAAGTATCGTCTCTTT	0.358																																					p.V2499V		Atlas-SNP	.											.	MGA	264	.	0			c.A7497G						.						40	34	36					15																	42054035		1832	4079	5911	SO:0001819	synonymous_variant	23269	exon21			GAAAGTATCGTCT	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7497A>G	chr15.hg19:g.42054035A>G		225.0	0.0		235.0	63.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.358	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	42054035	A	G	42054035	2	3	195	1	0	0	0	0	0	0	0	1	9549	436	16	2		2	MGA	15	42054035	Silent	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10		42054035	60477357	134	28762										
LEO1	123169	hgsc.bcm.edu	37	chr15	52258161	52258161	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cctcagatagctgttgtctcTcatcatcggaaagctgaggc	10	11	4	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr15:52258161T>A	ENST00000299601.5	-	2	659	c.599A>T	c.(598-600)gAg>gTg	p.E200V	LEO1_ENST00000315141.5_Missense_Mutation_p.E200V	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	200	Asp-rich.				endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		CTGTTGTCTCTCATCATCGGA	0.433																																					p.E200V	Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)	Atlas-SNP	.											.	LEO1	46	.	0			c.A599T						.						282	275	277					15																	52258161		2195	4293	6488	SO:0001583	missense	123169	exon2			TGTCTCTCATCAT	AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.599A>T	chr15.hg19:g.52258161T>A	ENSP00000299601:p.Glu200Val	86.0	0.0		84.0	13.0	NM_138792	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	hg19	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.796206	0.31777	.	.	ENSG00000166477	ENST00000299601;ENST00000538386;ENST00000315141	.	.	.	5.13	5.13	0.70059	.	0.408874	0.24098	N	0.041567	T	0.48390	0.1497	N	0.19112	0.55	0.80722	D	1	P;B	0.35894	0.526;0.392	B;B	0.41571	0.36;0.27	T	0.47898	-0.9081	9	0.33940	T	0.23	.	14.9417	0.70997	0.0:0.0:0.0:1.0	.	200;200	Q8WVC0-2;Q8WVC0	.;LEO1_HUMAN	V	200	.	ENSP00000299601:E200V	E	-	2	0	LEO1	50045453	1.000000	0.71417	0.472000	0.27241	0.204000	0.24138	4.208000	0.58486	1.938000	0.56188	0.533000	0.62120	GAG	.	.		0.433	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792		A	52258161	T	A	52258161	3	1	195	1	0	0	0	0	1	0	0	0	8735	1551	54	4	1445	4	LEO1	15	52258161	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	10204126	52258161	50273231	135	28763										
LMAN1L	79748	hgsc.bcm.edu	37	chr15	75111586	75111586	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tccctggaggtttctttgggGtctcagcagccaccggcacc	12	14	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr15:75111586G>T	ENST00000309664.5	+	6	830	c.691G>T	c.(691-693)Gtc>Ttc	p.V231F	LMAN1L_ENST00000379709.3_Missense_Mutation_p.V231F|RP11-414J4.2_ENST00000564823.1_RNA	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	231	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TTTCTTTGGGGTCTCAGCAGC	0.562																																					p.V231F		Atlas-SNP	.											.	LMAN1L	43	.	0			c.G691T						.						165	164	164					15																	75111586		2197	4296	6493	SO:0001583	missense	79748	exon6			TTTGGGGTCTCAG	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.691G>T	chr15.hg19:g.75111586G>T	ENSP00000310431:p.Val231Phe	66.0	0.0		78.0	25.0	NM_021819	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	hg19	CCDS10270.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.778183	0.49786	.	.	ENSG00000140506	ENST00000309664;ENST00000456603;ENST00000379709	T;T	0.65178	-0.14;-0.14	5.67	3.41	0.39046	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.366373	0.25720	N	0.028751	T	0.70544	0.3236	L	0.61218	1.895	0.44927	D	0.997949	D;D;D;D	0.63880	0.993;0.992;0.993;0.993	D;P;D;D	0.65874	0.919;0.868;0.939;0.919	T	0.67503	-0.5654	9	.	.	.	-26.1906	7.3317	0.26586	0.2438:0.0:0.7562:0.0	.	123;231;159;231	B4DGW5;Q9HAT1-3;B4DU67;Q9HAT1	.;.;.;LMA1L_HUMAN	F	231;123;231	ENSP00000310431:V231F;ENSP00000369031:V231F	.	V	+	1	0	LMAN1L	72898639	1.000000	0.71417	0.999000	0.59377	0.178000	0.23041	1.368000	0.34216	0.649000	0.30751	-0.218000	0.12543	GTC	.	.		0.562	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4			T	75111586	G	T	75111586	3	4	195	1	0	0	0	0	1	0	0	0	8846	1261	44	3	713	3	LMAN1L	15	75111586	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	22853425	75111586	27419806	136	28764										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3843532	3843532	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gcatgaagcagtagaaccagCtgctgctgtatcagtttgcg	12	9	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr16:3843532C>T	ENST00000262367.5	-	4	1880	c.1071G>A	c.(1069-1071)caG>caA	p.Q357Q	CREBBP_ENST00000382070.3_Silent_p.Q357Q	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	357	Interaction with SRCAP.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GTAGAACCAGCTGCTGCTGTA	0.498			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.Q357Q		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.G1071A						.						180	145	157					16																	3843532		2197	4300	6497	SO:0001819	synonymous_variant	1387	exon4			AACCAGCTGCTGC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.1071G>A	chr16.hg19:g.3843532C>T		141.0	0.0		136.0	60.0	NM_001079846	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.		0.498	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		T	3843532	C	T	3843532	2	4	195	1	0	0	0	0	0	0	0	1	3863	796	28	3		3	CREBBP	16	3843532	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10		3843532	86511221	137	28765										
SNX29	92017	hgsc.bcm.edu	37	chr16	12497309	12497318	+	Frame_Shift_Del	DEL	AACCGGGCGC	AACCGGGCGC	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tcttccttttggttagatcaAaccgggcgctgatcaacgtc							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	AACCGGGCGC	AACCGGGCGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr16:12497309_12497318delAACCGGGCGC	ENST00000566228.1	+	18	2029_2038	c.1960_1969delAACCGGGCGC	c.(1960-1971)aaccgggcgctgfs	p.NRAL654fs	SNX29_ENST00000323433.4_Frame_Shift_Del_p.NRAL269fs|SNX29_ENST00000306030.3_Frame_Shift_Del_p.NRAL269fs	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	654						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GGTTAGATCAAACCGGGCGCTGATCAACGT	0.424																																					p.653_656del		Atlas-Indel,Pindel	.											.	SNX29	60	.	0			c.1959_1968del						.																																			SO:0001589	frameshift_variant	92017	exon18			.	AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"Sorting nexins"	30542	protein-coding gene	gene with protein product			"RUN domain containing 2A"	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.1960_1969delAACCGGGCGC	chr16.hg19:g.12497309_12497318delAACCGGGCGC	ENSP00000456480:p.Asn654fs	140.0	0.0		93.0	29.0	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Frame_Shift_Del	DEL	ENST00000566228.1	hg19	CCDS10553.2																																																																																			.	.		0.424	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			-	12497318	AACCGGGCGC	-	12497309	7	5	195	1	0	1	0	1	0	0	0	0	14913	14	1	0	843	0	SNX29	16	12497309	Frame_Shift_Del	DEL	AACCGGGCGC	TCGA-DD-AADM-01A-11D-A40R-10	8653777	12497309	77857444	138	28766										
GSG1L	146395	hgsc.bcm.edu	37	chr16	27840137	27840137	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ggaagtacttgatggcctcaGggtctatgaaggtcggctct	14	8	3	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr16:27840137G>T	ENST00000447459.2	-	5	887	c.803C>A	c.(802-804)cCt>cAt	p.P268H	GSG1L_ENST00000380898.2_Missense_Mutation_p.P113H|GSG1L_ENST00000395724.3_Missense_Mutation_p.P217H|GSG1L_ENST00000569166.1_Missense_Mutation_p.P113H|GSG1L_ENST00000380897.3_Missense_Mutation_p.P113H	NM_001109763.1	NP_001103233.1	Q6UXU4	GSG1L_HUMAN	GSG1-like	268					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	asymmetric synapse (GO:0032279)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(4)	17						GATGGCCTCAGGGTCTATGAA	0.607																																					p.P268H		Atlas-SNP	.											GSG1L_ENST00000447459,right_upper_lobe,carcinoma,0,2	GSG1L	82	.	0			c.C803A						.						99	82	88					16																	27840137		2197	4300	6497	SO:0001583	missense	146395	exon5			GCCTCAGGGTCTA	AK128775	CCDS10631.1, CCDS45450.1	16p11.2	2014-01-20			ENSG00000169181	ENSG00000169181			28283	protein-coding gene	gene with protein product						22813734	Standard	NM_001109763		Approved	MGC18079, PRO19651, KTSR5831	uc002doz.2	Q6UXU4	OTTHUMG00000131676	ENST00000447459.2:c.803C>A	chr16.hg19:g.27840137G>T	ENSP00000394954:p.Pro268His	111.0	1.0		96.0	33.0	NM_001109763	Q7Z6F8|Q8TB81	Missense_Mutation	SNP	ENST00000447459.2	hg19	CCDS45450.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.511930	0.44660	.	.	ENSG00000169181	ENST00000447459;ENST00000395724;ENST00000380898;ENST00000380897	T;T	0.32515	1.46;1.45	5.24	5.24	0.73138	.	0.149703	0.44097	D	0.000485	T	0.23965	0.0580	L	0.31578	0.945	0.43559	D	0.995879	B;B;B	0.22003	0.063;0.013;0.027	B;B;B	0.17433	0.018;0.018;0.01	T	0.03231	-1.1058	10	0.44086	T	0.13	.	13.2596	0.60098	0.0:0.0:0.8405:0.1594	.	217;113;268	Q6UXU4-3;Q6UXU4-4;Q6UXU4	.;.;GSG1L_HUMAN	H	268;217;113;113	ENSP00000394954:P268H;ENSP00000379074:P217H	ENSP00000370282:P113H	P	-	2	0	GSG1L	27747638	1.000000	0.71417	0.972000	0.41901	0.992000	0.81027	3.185000	0.50934	2.455000	0.83008	0.650000	0.86243	CCT	.	.		0.607	GSG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433832.2	NM_144675		T	27840137	G	T	27840137	3	4	195	1	0	0	0	0	1	0	0	0	6830	1000	35	3	204	3	GSG1L	16	27840137	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	15342828	27840137	62514616	139	28767										
XPO6	23214	hgsc.bcm.edu	37	chr16	28187343	28187359	+	Frame_Shift_Del	DEL	AGTTTGGGCAGACAGCT	AGTTTGGGCAGACAGCT	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ttttatggtgagccaaaaggAgtttgggcagacagctacgg							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	AGTTTGGGCAGACAGCT	AGTTTGGGCAGACAGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr16:28187343_28187359delAGTTTGGGCAGACAGCT	ENST00000304658.5	-	4	765_781	c.265_281delAGCTGTCTGCCCAAACT	c.(265-282)agctgtctgcccaaactcfs	p.SCLPKL89fs	XPO6_ENST00000565698.1_Frame_Shift_Del_p.SCLPKL75fs	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	89	Importin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00115}.				protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						AGCCAAAAGGAGTTTGGGCAGACAGCTACGGATTTCC	0.401																																					p.89_94del		Atlas-Indel,Pindel	.											.	XPO6	177	.	0			c.266_282del						.																																			SO:0001589	frameshift_variant	23214	exon4			.	AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"Exportins"	19733	protein-coding gene	gene with protein product		608411	"RAN binding protein 20"	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.265_281delAGCTGTCTGCCCAAACT	chr16.hg19:g.28187343_28187359delAGTTTGGGCAGACAGCT	ENSP00000302790:p.Ser89fs	158.0	0.0		143.0	12.0	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Frame_Shift_Del	DEL	ENST00000304658.5	hg19	CCDS42135.1																																																																																			.	.		0.401	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		-	28187359	AGTTTGGGCAGACAGCT	-	28187343	7	5	195	1	0	1	0	1	0	0	0	0	17463	304	11	0	3180	0	XPO6	16	28187343	Frame_Shift_Del	DEL	AGTTTGGGCAGACAGCT	TCGA-DD-AADM-01A-11D-A40R-10	347206	28187343	62167410	140	28768										
RBL2	5934	hgsc.bcm.edu	37	chr16	53514601	53514602	+	Frame_Shift_Ins	INS	-	-	G													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgacatggaagaagaggagaINSggggagacctcattcagttc							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr16:53514601_53514602insG	ENST00000262133.6	+	20	3141_3142	c.3004_3005insG	c.(3004-3006)aggfs	p.R1002fs	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Intron	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	1002	Domain B.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						AGAAGAGGAGAGGGGAGACCTC	0.475																																					p.R1002fs		Atlas-Indel,Pindel	.											.	RBL2	115	.	0			c.3004_3005insG						.																																			SO:0001589	frameshift_variant	5934	exon20			.	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.3008dupG	chr16.hg19:g.53514605_53514605dupG	ENSP00000262133:p.Arg1002fs	169.0	0.0		199.0	29.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Frame_Shift_Ins	INS	ENST00000262133.6	hg19	CCDS10748.1																																																																																			.	.		0.475	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		G	53514602	-	G	53514601	7	5	195	1	0	1	1	0	0	0	0	0	13125	295	11	0	3082	0	RBL2	16	53514601	Frame_Shift_Ins	INS	-	TCGA-DD-AADM-01A-11D-A40R-10	25327258	53514601	36840152	141	28769										
IRX5	10265	hgsc.bcm.edu	37	chr16	54966798	54966798	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gcccgaggacaagggcgaccCcgagggccccgaagcaggtt	16	14	0	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr16:54966798C>G	ENST00000394636.4	+	2	975	c.638C>G	c.(637-639)cCc>cGc	p.P213R	IRX5_ENST00000560154.1_Intron|IRX5_ENST00000558597.1_Missense_Mutation_p.P147R|IRX5_ENST00000320990.5_Missense_Mutation_p.P213R|CTD-3032H12.2_ENST00000560487.1_lincRNA			P78411	IRX5_HUMAN	iroquois homeobox 5	213					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)			kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						AAGGGCGACCCCGAGGGCCCC	0.652																																					p.P213R		Atlas-SNP	.											.	IRX5	41	.	0			c.C638G						.						65	83	77					16																	54966798		2198	4300	6498	SO:0001583	missense	10265	exon2			GCGACCCCGAGGG	U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"Homeoboxes / TALE class"	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.638C>G	chr16.hg19:g.54966798C>G	ENSP00000378132:p.Pro213Arg	416.0	0.0		351.0	100.0	NM_001252197	H0YMS7|P78416|Q7Z2E1	Missense_Mutation	SNP	ENST00000394636.4	hg19	CCDS10751.1	.	.	.	.	.	.	.	.	.	.	C	0.170	-1.072352	0.01918	.	.	ENSG00000176842	ENST00000394636;ENST00000320990	T;T	0.58652	0.32;0.36	4.14	-1.35	0.09114	.	1.190180	0.06065	N	0.659125	T	0.24699	0.0599	N	0.01874	-0.695	0.20074	N	0.999933	B	0.02656	0.0	B	0.04013	0.001	T	0.13019	-1.0525	10	0.15952	T	0.53	-0.3635	3.3736	0.07229	0.2847:0.3803:0.0:0.335	.	213	P78411	IRX5_HUMAN	R	213	ENSP00000378132:P213R;ENSP00000316250:P213R	ENSP00000316250:P213R	P	+	2	0	IRX5	53524299	0.238000	0.23825	0.778000	0.31720	0.564000	0.35744	1.177000	0.31969	-0.117000	0.11872	0.655000	0.94253	CCC	.	.		0.652	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256911.2			G	54966798	C	G	54966798	3	3	195	1	0	0	0	0	1	0	0	0	7856	623	22	4	644	4	IRX5	16	54966798	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	1452197	54966798	35387955	142	28770										
KIFC3	3801	hgsc.bcm.edu	37	chr16	57805281	57805281	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	acctctaggttcagctctgaCagcatgcctttgctttccgc	8	14	3	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr16:57805281C>T	ENST00000379655.4	-	6	851	c.594G>A	c.(592-594)ctG>ctA	p.L198L	KIFC3_ENST00000445690.2_Silent_p.L198L|KIFC3_ENST00000541240.1_Silent_p.L220L|KIFC3_ENST00000566975.1_5'Flank|KIFC3_ENST00000562903.1_Silent_p.L59L|KIFC3_ENST00000465878.2_Silent_p.L59L|KIFC3_ENST00000543930.1_Silent_p.L59L|KIFC3_ENST00000539578.1_Silent_p.L140L|KIFC3_ENST00000540079.2_Silent_p.L96L|KIFC3_ENST00000421376.2_Silent_p.L59L	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	198					ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				TCAGCTCTGACAGCATGCCTT	0.617																																					p.L198L		Atlas-SNP	.											.	KIFC3	55	.	0			c.G594A						.						136	128	131					16																	57805281		2198	4300	6498	SO:0001819	synonymous_variant	3801	exon6			CTCTGACAGCATG	BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"Kinesins"	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.594G>A	chr16.hg19:g.57805281C>T		114.0	0.0		110.0	28.0	NM_001130100	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Silent	SNP	ENST00000379655.4	hg19	CCDS10789.2																																																																																			.	.		0.617	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550		T	57805281	C	T	57805281	2	4	195	1	0	0	0	0	0	0	0	1	8323	465	17	3		3	KIFC3	16	57805281	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	2838483	57805281	32549472	143	28771										
RABEP1	9135	hgsc.bcm.edu	37	chr17	5286425	5286425	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ttgtttctccaggtgcagttAgagcggatccggcaagctga	13	9	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr17:5286425A>T	ENST00000546142.2	+	18	2683	c.2496A>T	c.(2494-2496)ttA>ttT	p.L832F	NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000408982.2_Missense_Mutation_p.L799F|RABEP1_ENST00000537505.1_Missense_Mutation_p.L789F|RABEP1_ENST00000262477.6_Missense_Mutation_p.L832F|RABEP1_ENST00000341923.6_Missense_Mutation_p.L799F			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	832					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						AGGTGCAGTTAGAGCGGATCC	0.463																																					p.L832F		Atlas-SNP	.											.	RABEP1	59	.	0			c.A2496T						.						68	73	71					17																	5286425		2141	4295	6436	SO:0001583	missense	9135	exon18			GCAGTTAGAGCGG	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2496A>T	chr17.hg19:g.5286425A>T	ENSP00000437701:p.Leu832Phe	95.0	0.0		113.0	30.0	NM_004703	B2RAG7|O95369|Q8IVX3	Missense_Mutation	SNP	ENST00000546142.2	hg19	CCDS45592.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.961887	0.74016	.	.	ENSG00000029725	ENST00000262477;ENST00000408982;ENST00000546142;ENST00000341923;ENST00000537505	T;T;T;T;T	0.77358	-0.74;-1.09;-0.74;-1.09;-0.75	4.45	-2.59	0.06209	.	0.000000	0.64402	D	0.000002	T	0.76528	0.4000	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.73547	-0.3948	10	0.59425	D	0.04	-8.2226	9.1802	0.37136	0.2322:0.1505:0.6173:0.0	.	789;832;799	F5H355;Q15276;Q15276-2	.;RABE1_HUMAN;.	F	832;799;832;799;789	ENSP00000262477:L832F;ENSP00000386150:L799F;ENSP00000437701:L832F;ENSP00000339569:L799F;ENSP00000445408:L789F	ENSP00000262477:L832F	L	+	3	2	RABEP1	5227149	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	1.431000	0.34925	-0.243000	0.09653	0.460000	0.39030	TTA	.	.		0.463	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703		T	5286425	A	T	5286425	3	4	195	1	0	0	0	0	1	0	0	0	12976	417	15	4	2566	4	RABEP1	17	5286425	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10		5286425	75908785	144	28772										
TNFRSF13B	23495	hgsc.bcm.edu	37	chr17	16842939	16842939	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gggatgtgtgggcaaggctgCaggactgtggtcctggtgtg	20	6	0	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr17:16842939C>A	ENST00000261652.2	-	5	816	c.804G>T	c.(802-804)ctG>ctT	p.L268L	TNFRSF13B_ENST00000583789.1_Silent_p.L222L|TNFRSF13B_ENST00000437538.2_Intron|TNFRSF13B_ENST00000581616.2_5'Flank|TNFRSF13B_ENST00000579315.1_Intron	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	268					B cell homeostasis (GO:0001782)|cell surface receptor signaling pathway (GO:0007166)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of B cell proliferation (GO:0030889)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|skin(1)	16						GGCAAGGCTGCAGGACTGTGG	0.662									IgA Deficiency, Selective																												p.L268L		Atlas-SNP	.											.	TNFRSF13B	34	.	0			c.G804T						.						48	45	46					17																	16842939		2203	4300	6503	SO:0001819	synonymous_variant	23495	exon5	Familial Cancer Database	IGAD1, IGAD2	AGGCTGCAGGACT	AF023614	CCDS11181.1	17p11.2	2014-09-17			ENSG00000240505	ENSG00000240505		"Tumor necrosis factor receptor superfamily", "CD molecules"	18153	protein-coding gene	gene with protein product		604907				9311921	Standard	NM_012452		Approved	TACI, CD267	uc002gqs.1	O14836	OTTHUMG00000059262	ENST00000261652.2:c.804G>T	chr17.hg19:g.16842939C>A		125.0	0.0		112.0	22.0	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Silent	SNP	ENST00000261652.2	hg19	CCDS11181.1																																																																																			.	.		0.662	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2			A	16842939	C	A	16842939	2	1	195	1	0	0	0	0	0	0	0	1	16302	697	25	3		3	TNFRSF13B	17	16842939	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	11556514	16842939	64352271	145	28773										
DHRS13	147015	hgsc.bcm.edu	37	chr17	27228310	27228310	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cctcacgggtccggccacagGaactgatacctggggcagag	14	13	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr17:27228310G>A	ENST00000378895.4	-	4	506	c.380C>T	c.(379-381)tCc>tTc	p.S127F	DHRS13_ENST00000426464.2_Missense_Mutation_p.S46F|DHRS13_ENST00000581974.1_5'Flank|DHRS13_ENST00000394901.3_Missense_Mutation_p.S77F|RP11-20B24.4_ENST00000580603.1_RNA|RP11-20B24.4_ENST00000579187.1_RNA	NM_144683.3	NP_653284.2	Q6UX07	DHR13_HUMAN	dehydrogenase/reductase (SDR family) member 13	127						extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	9	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.59e-06)|all cancers(11;9.27e-06)|BRCA - Breast invasive adenocarcinoma(11;5.78e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)			CCGGCCACAGGAACTGATACC	0.572																																					p.S127F		Atlas-SNP	.											.	DHRS13	22	.	0			c.C380T						.						46	49	48					17																	27228310		2203	4300	6503	SO:0001583	missense	147015	exon4			CCACAGGAACTGA	BC015582	CCDS11246.2	17q11.2	2011-09-14			ENSG00000167536	ENSG00000167536	1.1.-.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	28326	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 5"					12975309, 19027726	Standard	NM_144683		Approved	MGC23280, SDR7C5	uc002hde.4	Q6UX07	OTTHUMG00000132678	ENST00000378895.4:c.380C>T	chr17.hg19:g.27228310G>A	ENSP00000368173:p.Ser127Phe	212.0	0.0		204.0	89.0	NM_144683	Q96BH7	Missense_Mutation	SNP	ENST00000378895.4	hg19	CCDS11246.2	.	.	.	.	.	.	.	.	.	.	G	18.38	3.610844	0.66558	.	.	ENSG00000167536	ENST00000378895;ENST00000394901;ENST00000426464	D;D;D	0.87966	-2.32;-2.32;-1.73	5.58	5.58	0.84498	NAD(P)-binding domain (1);	0.420407	0.25453	N	0.030580	T	0.82001	0.4942	N	0.04162	-0.26	0.41503	D	0.988297	D;D	0.71674	0.997;0.998	D;D	0.68943	0.931;0.961	T	0.77446	-0.2585	10	0.10111	T	0.7	.	10.8193	0.46595	0.0:0.14:0.7151:0.1449	.	46;127	B4DJC5;Q6UX07	.;DHR13_HUMAN	F	127;77;46	ENSP00000368173:S127F;ENSP00000378361:S77F;ENSP00000412826:S46F	ENSP00000368173:S127F	S	-	2	0	DHRS13	24252436	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.469000	0.45110	2.625000	0.88918	0.561000	0.74099	TCC	.	.		0.572	DHRS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255952.1	NM_144683		A	27228310	G	A	27228310	3	1	195	1	0	0	0	0	1	0	0	0	4491	1174	41	3	761	3	DHRS13	17	27228310	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	10385371	27228310	53966900	146	28774										
CACNB1	782	hgsc.bcm.edu	37	chr17	37331579	37331579	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgtcggtcagctcttcctcaTagtcttcttcctcgtcctcc	6	16	5	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr17:37331579T>C	ENST00000394303.3	-	14	1871	c.1664A>G	c.(1663-1665)tAt>tGt	p.Y555C	RP5-906A24.2_ENST00000579256.1_RNA	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit	555					axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CTCTTCCTCATAGTCTTCTTC	0.647											OREG0024371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y555C	Esophageal Squamous(5;100 366 38393 41452 45827)	Atlas-SNP	.											.	CACNB1	89	.	0			c.A1664G						.						143	160	155					17																	37331579		1895	4093	5988	SO:0001583	missense	782	exon14			TCCTCATAGTCTT		CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"Calcium channel subunits"	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.1664A>G	chr17.hg19:g.37331579T>C	ENSP00000377840:p.Tyr555Cys	62.0	0.0	869	85.0	12.0	NM_000723	A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Missense_Mutation	SNP	ENST00000394303.3	hg19	CCDS42311.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.011863	0.35511	.	.	ENSG00000067191	ENST00000539338;ENST00000394303	T	0.76578	-1.03	4.28	3.2	0.36748	.	0.890681	0.09973	N	0.731967	T	0.58552	0.2130	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.51973	-0.8637	10	0.48119	T	0.1	-1.1945	7.4332	0.27139	0.0:0.1825:0.0:0.8175	.	555	Q02641	CACB1_HUMAN	C	505;555	ENSP00000377840:Y555C	ENSP00000377840:Y555C	Y	-	2	0	CACNB1	34585105	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.120000	0.57897	0.979000	0.38497	0.459000	0.35465	TAT	.	.		0.647	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3			C	37331579	T	C	37331579	3	2	195	1	0	0	0	0	1	0	0	0	2554	1406	49	2	136	2	CACNB1	17	37331579	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	10103269	37331579	43863631	147	28775										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37872630	37872630	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gggcccacccagtgtgtcaaCtgcagccagttccttcgggg	13	14	1	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr17:37872630C>T	ENST00000269571.5	+	13	1749	c.1590C>T	c.(1588-1590)aaC>aaT	p.N530N	ERBB2_ENST00000406381.2_Silent_p.N500N|ERBB2_ENST00000584601.1_Silent_p.N500N|ERBB2_ENST00000578199.1_Silent_p.N500N|ERBB2_ENST00000540147.1_Silent_p.N500N|ERBB2_ENST00000445658.2_Silent_p.N254N|ERBB2_ENST00000541774.1_Silent_p.N515N|ERBB2_ENST00000584450.1_Silent_p.N530N|ERBB2_ENST00000540042.1_Silent_p.N500N			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	530					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	AGTGTGTCAACTGCAGCCAGT	0.692		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.N530N		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	.	ERBB2	429	.	0			c.C1590T						.						29	30	30					17																	37872630		2202	4300	6502	SO:0001819	synonymous_variant	2064	exon13			TGTCAACTGCAGC	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1590C>T	chr17.hg19:g.37872630C>T		81.0	0.0		91.0	20.0	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent	SNP	ENST00000269571.5	hg19	CCDS32642.1																																																																																			.	.		0.692	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			T	37872630	C	T	37872630	2	4	195	1	0	0	0	0	0	0	0	1	5208	564	20	3		3	ERBB2	17	37872630	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	541051	37872630	43322580	148	28776										
KRT37	8688	hgsc.bcm.edu	37	chr17	39577655	39577655	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccagaaggttccggtatgtgGcaatctcgttctccaaccgg	11	12	2	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr17:39577655G>T	ENST00000225550.3	-	6	1204	c.1205C>A	c.(1204-1206)gCc>gAc	p.A402D	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	402	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				CCGGTATGTGGCAATCTCGTT	0.557																																					p.A402D		Atlas-SNP	.											.	KRT37	61	.	0			c.C1205A						.						116	92	100					17																	39577655		2203	4300	6503	SO:0001583	missense	8688	exon6			TATGTGGCAATCT	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"-", "Intermediate filaments type I, keratins (acidic)"	6455	protein-coding gene	gene with protein product		604541	"keratin, hair, acidic, 7"	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.1205C>A	chr17.hg19:g.39577655G>T	ENSP00000225550:p.Ala402Asp	142.0	0.0		125.0	40.0	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	hg19	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.758630	0.49468	.	.	ENSG00000108417	ENST00000225550	D	0.90788	-2.73	5.61	-5.8	0.02347	Filament (1);Intermediate filament protein, conserved site (1);	1.391630	0.04988	N	0.466811	D	0.92648	0.7664	M	0.88450	2.955	0.09310	N	1	P	0.43578	0.811	B	0.43413	0.419	D	0.84087	0.0388	10	0.23891	T	0.37	.	19.685	0.95977	0.0:0.0:0.2332:0.7668	.	402	O76014	KRT37_HUMAN	D	402	ENSP00000225550:A402D	ENSP00000225550:A402D	A	-	2	0	KRT37	36831181	0.000000	0.05858	0.000000	0.03702	0.561000	0.35649	0.036000	0.13819	-1.491000	0.01840	-0.274000	0.10170	GCC	.	.		0.557	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770		T	39577655	G	T	39577655	3	4	195	1	0	0	0	0	1	0	0	0	8483	1203	42	3	152	3	KRT37	17	39577655	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	1705025	39577655	41617555	149	28777										
PSMD12	5718	hgsc.bcm.edu	37	chr17	65343347	65343347	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccagctgaatcattaaattaTagtacttcaactttaatttc	3	8	2	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr17:65343347T>C	ENST00000356126.3	-	7	787	c.680A>G	c.(679-681)tAt>tGt	p.Y227C	PSMD12_ENST00000357146.4_Missense_Mutation_p.Y207C	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	227					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					CATTAAATTATAGTACTTCAA	0.328																																					p.Y227C		Atlas-SNP	.											.	PSMD12	32	.	0			c.A680G						.						64	64	64					17																	65343347		2203	4300	6503	SO:0001583	missense	5718	exon7			AAATTATAGTACT	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.680A>G	chr17.hg19:g.65343347T>C	ENSP00000348442:p.Tyr227Cys	107.0	0.0		131.0	18.0	NM_002816	A6NP15|Q53HA2|Q6P053	Missense_Mutation	SNP	ENST00000356126.3	hg19	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.339571	0.81911	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	T;T	0.07327	3.2;3.2	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.28732	0.0712	M	0.88181	2.935	0.80722	D	1	P;P	0.42973	0.796;0.796	P;P	0.51016	0.656;0.656	T	0.04078	-1.0979	10	0.62326	D	0.03	-14.8374	16.3593	0.83251	0.0:0.0:0.0:1.0	.	207;227	A6NP15;O00232	.;PSD12_HUMAN	C	227;207	ENSP00000348442:Y227C;ENSP00000349667:Y207C	ENSP00000348442:Y227C	Y	-	2	0	PSMD12	62773809	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.680000	0.84062	2.267000	0.75376	0.383000	0.25322	TAT	.	.		0.328	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		C	65343347	T	C	65343347	3	2	195	1	0	0	0	0	1	0	0	0	12707	1406	49	2	710	2	PSMD12	17	65343347	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	25765692	65343347	15851863	150	28778										
ESCO1	114799	hgsc.bcm.edu	37	chr18	19154672	19154672	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	agatttagcctgtgattttaTagtctcctttggacctgatt	8	7	1	3	rs141644808		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr18:19154672T>C	ENST00000269214.5	-	4	1070	c.133A>G	c.(133-135)Ata>Gta	p.I45V		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	45					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)			breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						TGTGATTTTATAGTCTCCTTT	0.343																																					p.I45V		Atlas-SNP	.											.	ESCO1	89	.	0			c.A133G						.	T	VAL/ILE	0,4406		0,0,2203	171	173	172		133	-9.1	0	18	dbSNP_134	172	1,8599	1.2+/-3.3	0,1,4299	no	missense	ESCO1	NM_052911.2	29	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	45/841	19154672	1,13005	2203	4300	6503	SO:0001583	missense	114799	exon4			ATTTTATAGTCTC	AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.133A>G	chr18.hg19:g.19154672T>C	ENSP00000269214:p.Ile45Val	82.0	0.0		76.0	9.0	NM_052911	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Missense_Mutation	SNP	ENST00000269214.5	hg19	CCDS32800.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.931792	0.00053	0.0	1.16E-4	ENSG00000141446	ENST00000269214;ENST00000383276	T;T	0.56275	0.47;2.05	5.39	-9.12	0.00707	.	2.117430	0.02190	N	0.061304	T	0.22589	0.0545	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12243	-1.0555	10	0.29301	T	0.29	-26.8966	2.6763	0.05082	0.1721:0.3795:0.0851:0.3634	.	45	Q5FWF5	ESCO1_HUMAN	V	45	ENSP00000269214:I45V;ENSP00000372763:I45V	ENSP00000269214:I45V	I	-	1	0	ESCO1	17408670	0.000000	0.05858	0.002000	0.10522	0.104000	0.19210	-0.932000	0.03963	-2.140000	0.00806	-0.904000	0.02843	ATA	.	T|1.000;C|0.000		0.343	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		C	19154672	T	C	19154672	3	2	195	1	0	0	0	0	1	0	0	0	5250	1406	49	2	2425	2	ESCO1	18	19154672	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10		19154672	58922576	151	28779										
ZNF396	252884	hgsc.bcm.edu	37	chr18	32953439	32953439	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccatgtggtcttaaggactgAagctcccatgatgctccctg	10	12	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr18:32953439A>C	ENST00000589332.1	-	3	674	c.543T>G	c.(541-543)ctT>ctG	p.L181L	ZNF396_ENST00000306346.1_Silent_p.L181L|ZNF396_ENST00000586687.1_Silent_p.L181L			Q96N95	ZN396_HUMAN	zinc finger protein 396	181					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)	7						TTAAGGACTGAAGCTCCCATG	0.522																																					p.L181L		Atlas-SNP	.											.	ZNF396	28	.	0			c.T543G						.						110	100	103					18																	32953439		2203	4300	6503	SO:0001819	synonymous_variant	252884	exon3			GGACTGAAGCTCC	AK055775	CCDS11913.1	18p12	2013-01-09			ENSG00000186496	ENSG00000186496		"-", "Zinc fingers, C2H2-type"	18824	protein-coding gene	gene with protein product		609600					Standard	NM_145756		Approved	ZSCAN14, FLJ31213	uc010xcf.1	Q96N95	OTTHUMG00000132562	ENST00000589332.1:c.543T>G	chr18.hg19:g.32953439A>C		96.0	0.0		92.0	52.0	NM_145756	A1L3V0|Q8NF98|Q8TD80	Silent	SNP	ENST00000589332.1	hg19																																																																																				.	.		0.522	ZNF396-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255766.1	NM_145756		C	32953439	A	C	32953439	2	2	195	1	0	0	0	0	0	0	0	1	17897	233	9	5		5	ZNF396	18	32953439	Silent	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	13798767	32953439	45123809	152	28780										
DCC	1630	hgsc.bcm.edu	37	chr18	51057014	51057014	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cttaatgccatcacaggctcAgccttttaacatgtatttct	5	11	3	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr18:51057014A>C	ENST00000442544.2	+	29	4951	c.4335A>C	c.(4333-4335)tcA>tcC	p.S1445S	RP11-671P2.1_ENST00000582064.1_RNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1445					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TCACAGGCTCAGCCTTTTAAC	0.423																																					p.S1445S		Atlas-SNP	.											.	DCC	360	.	0			c.A4335C						.						129	118	122					18																	51057014		2203	4300	6503	SO:0001819	synonymous_variant	1630	exon29			AGGCTCAGCCTTT	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.4335A>C	chr18.hg19:g.51057014A>C		115.0	0.0		102.0	39.0	NM_005215		Silent	SNP	ENST00000442544.2	hg19	CCDS11952.1																																																																																			.	.		0.423	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		C	51057014	A	C	51057014	2	2	195	1	0	0	0	0	0	0	0	1	4284	175	7	5		5	DCC	18	51057014	Silent	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	18103575	51057014	27020234	153	28781										
SERPINB10	5273	hgsc.bcm.edu	37	chr18	61597343	61597343	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	accaggatgattctggtgaaCgccctatactttaaaggaat	9	8	1	2	rs550376818		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr18:61597343C>T	ENST00000238508.3	+	6	614	c.555C>T	c.(553-555)aaC>aaT	p.N185N		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	185					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				TTCTGGTGAACGCCCTATACT	0.393																																					p.N185N		Atlas-SNP	.											.	SERPINB10	53	.	0			c.C555T						.						84	84	84					18																	61597343		2203	4299	6502	SO:0001819	synonymous_variant	5273	exon5			GGTGAACGCCCTA	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"Serine (or cysteine) peptidase inhibitors"	8942	protein-coding gene	gene with protein product	"protease inhibitor 10 (ovalbumin type, bomapin)"	602058	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.555C>T	chr18.hg19:g.61597343C>T		130.0	0.0		122.0	32.0	NM_005024	Q4VAX4|Q4VAX7	Silent	SNP	ENST00000238508.3	hg19	CCDS11990.1																																																																																			.	.		0.393	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		T	61597343	C	T	61597343	2	4	195	1	0	0	0	0	0	0	0	1	14112	535	19	1		1	SERPINB10	18	61597343	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	10540329	61597343	16479905	154	28782										
CBLN2	147381	hgsc.bcm.edu	37	chr18	70205499	70205499	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	caagtttgagatgcactttgTcttccctttccatgagcagc	8	11	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr18:70205499T>C	ENST00000269503.4	-	5	1360	c.587A>G	c.(586-588)gAc>gGc	p.D196G	CBLN2_ENST00000584764.1_Missense_Mutation_p.D80G|CBLN2_ENST00000581073.1_Missense_Mutation_p.D82G|CBLN2_ENST00000583651.1_5'UTR|CBLN2_ENST00000585159.1_Missense_Mutation_p.D196G	NM_182511.3	NP_872317.1	Q8IUK8	CBLN2_HUMAN	cerebellin 2 precursor	196	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				positive regulation of synapse assembly (GO:0051965)	extracellular space (GO:0005615)				endometrium(2)|lung(15)	17		Esophageal squamous(42;0.131)				ATGCACTTTGTCTTCCCTTTC	0.522																																					p.D196G		Atlas-SNP	.											.	CBLN2	41	.	0			c.A587G						.						122	115	117					18																	70205499		2203	4300	6503	SO:0001583	missense	147381	exon5			ACTTTGTCTTCCC	BC035789	CCDS11999.1	18q22.3	2007-11-19			ENSG00000141668	ENSG00000141668			1544	protein-coding gene	gene with protein product		600433				7877445	Standard	NM_182511		Approved		uc002lkv.2	Q8IUK8	OTTHUMG00000132825	ENST00000269503.4:c.587A>G	chr18.hg19:g.70205499T>C	ENSP00000269503:p.Asp196Gly	141.0	0.0		136.0	19.0	NM_182511	Q53Z56	Missense_Mutation	SNP	ENST00000269503.4	hg19	CCDS11999.1	.	.	.	.	.	.	.	.	.	.	T	15.14	2.743758	0.49151	.	.	ENSG00000141668	ENST00000269503	D	0.85556	-2.0	5.52	5.52	0.82312	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.000000	0.85682	D	0.000000	D	0.95098	0.8412	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96713	0.9527	10	0.87932	D	0	-32.3275	15.938	0.79729	0.0:0.0:0.0:1.0	.	196	Q8IUK8	CBLN2_HUMAN	G	196	ENSP00000269503:D196G	ENSP00000269503:D196G	D	-	2	0	CBLN2	68356479	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.990000	0.88215	2.222000	0.72286	0.533000	0.62120	GAC	.	.		0.522	CBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256288.1	NM_182511		C	70205499	T	C	70205499	3	2	195	1	0	0	0	0	1	0	0	0	2707	1667	58	2	91	2	CBLN2	18	70205499	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	8608156	70205499	7871749	155	28783										
CLEC4G	339390	hgsc.bcm.edu	37	chr19	7795687	7795687	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctctcctgctccatcagcttCgcctgcgcctccccaagctc	6	21	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:7795687C>G	ENST00000328853.5	-	5	410	c.342G>C	c.(340-342)gcG>gcC	p.A114A	CLEC4G_ENST00000598081.1_5'Flank	NM_001244856.1|NM_198492.3	NP_001231785.1|NP_940894.1	Q6UXB4	CLC4G_HUMAN	C-type lectin domain family 4, member G	114						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(1)|large_intestine(1)|lung(1)	6						CCATCAGCTTCGCCTGCGCCT	0.766																																					p.A114A	Esophageal Squamous(146;540 1807 3349 19438 30853)	Atlas-SNP	.											.	CLEC4G	18	.	0			c.G342C						.						3	4	3					19																	7795687		1565	3031	4596	SO:0001819	synonymous_variant	339390	exon5			CAGCTTCGCCTGC	AY358431	CCDS12185.1	19p13.2	2010-04-27	2008-11-04			ENSG00000182566		"C-type lectin domain containing"	24591	protein-coding gene	gene with protein product			"C-type lectin superfamily 4, member G"			12975309	Standard	NM_198492		Approved	UNQ431, LSECtin	uc002mhp.4	Q6UXB4		ENST00000328853.5:c.342G>C	chr19.hg19:g.7795687C>G		26.0	0.0		40.0	14.0	NM_198492		Silent	SNP	ENST00000328853.5	hg19	CCDS12185.1																																																																																			.	.		0.766	CLEC4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461989.1	NM_198492		G	7795687	C	G	7795687	2	3	195	1	0	0	0	0	0	0	0	1	3519	871	31	4		4	CLEC4G	19	7795687	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10		7795687	51333296	156	28784										
ZNF561	93134	hgsc.bcm.edu	37	chr19	9721732	9721732	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aatacttaaagccttttccaCattccttacatttgtagggt	5	9	0	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:9721732C>T	ENST00000302851.3	-	6	968	c.605G>A	c.(604-606)tGt>tAt	p.C202Y	ZNF561_ENST00000354661.4_Missense_Mutation_p.C66Y|ZNF561_ENST00000326044.5_3'UTR|ZNF561_ENST00000495503.1_5'UTR|ZNF561_ENST00000424629.1_Missense_Mutation_p.C133Y	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	202					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						GCCTTTTCCACATTCCTTACA	0.383																																					p.C202Y		Atlas-SNP	.											.	ZNF561	64	.	0			c.G605A						.						63	57	59					19																	9721732		2203	4300	6503	SO:0001583	missense	93134	exon6			TTTCCACATTCCT	AK074787	CCDS12216.2	19p13.2	2013-09-20			ENSG00000171469	ENSG00000171469		"Zinc fingers, C2H2-type", "-"	28684	protein-coding gene	gene with protein product						12477932	Standard	NM_152289		Approved	MGC45408	uc002mlu.3	Q8N587	OTTHUMG00000157054	ENST00000302851.3:c.605G>A	chr19.hg19:g.9721732C>T	ENSP00000303915:p.Cys202Tyr	92.0	0.0		105.0	31.0	NM_152289	B4E2Q8|Q6PJS0	Missense_Mutation	SNP	ENST00000302851.3	hg19	CCDS12216.2	.	.	.	.	.	.	.	.	.	.	C	16.84	3.232822	0.58777	.	.	ENSG00000171469	ENST00000424629;ENST00000302851;ENST00000354661;ENST00000444611	D;D;D;D	0.99974	-10.2;-10.2;-10.2;-10.2	1.14	-0.0931	0.13652	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.99964	0.9986	M	0.88570	2.965	0.32493	N	0.539905	D	0.55385	0.971	P	0.55161	0.77	D	0.94280	0.7519	9	0.87932	D	0	.	6.089	0.19983	0.3018:0.6982:0.0:0.0	.	202	Q8N587	ZN561_HUMAN	Y	133;202;66;208	ENSP00000393074:C133Y;ENSP00000303915:C202Y;ENSP00000346687:C66Y;ENSP00000392013:C208Y	ENSP00000303915:C202Y	C	-	2	0	ZNF561	9582732	0.241000	0.23857	0.004000	0.12327	0.696000	0.40369	3.028000	0.49705	0.009000	0.14813	0.305000	0.20034	TGT	.	.		0.383	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289		T	9721732	C	T	9721732	3	4	195	1	0	0	0	0	1	0	0	0	18007	478	17	3	859	3	ZNF561	19	9721732	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	1926045	9721732	49407251	157	28785										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10602646	10602646	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gcatcacctgcgtgggcttgTgcagggtgagctcctcgaag	15	11	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:10602646T>A	ENST00000171111.5	-	3	1479	c.932A>T	c.(931-933)cAc>cTc	p.H311L	KEAP1_ENST00000393623.2_Missense_Mutation_p.H311L|CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000588024.1_5'UTR	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	311					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CGTGGGCTTGTGCAGGGTGAG	0.637																																					p.H311L		Atlas-SNP	.											.	KEAP1	182	.	0			c.A932T						.						45	50	48					19																	10602646		2203	4300	6503	SO:0001583	missense	9817	exon3			GGCTTGTGCAGGG	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.932A>T	chr19.hg19:g.10602646T>A	ENSP00000171111:p.His311Leu	106.0	0.0		102.0	54.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.241881	0.58995	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.71103	-0.54;-0.54	5.61	4.59	0.56863	.	0.048905	0.85682	D	0.000000	T	0.57007	0.2024	L	0.27053	0.805	0.80722	D	1	B	0.14805	0.011	B	0.10450	0.005	T	0.52548	-0.8561	10	0.52906	T	0.07	.	10.3323	0.43829	0.1471:0.0:0.0:0.8529	.	311	Q14145	KEAP1_HUMAN	L	311	ENSP00000171111:H311L;ENSP00000377245:H311L	ENSP00000171111:H311L	H	-	2	0	KEAP1	10463646	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.610000	0.67668	0.949000	0.37715	0.459000	0.35465	CAC	.	.		0.637	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		A	10602646	T	A	10602646	3	1	195	1	0	0	0	0	1	0	0	0	8150	1696	59	4	958	4	KEAP1	19	10602646	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	880914	10602646	48526337	158	28786										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610207	10610207	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ggaagtcactgcaggcacggAcaacgctgtcgatctggtac	13	11	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:10610207A>C	ENST00000171111.5	-	2	1050	c.503T>G	c.(502-504)gTc>gGc	p.V168G	KEAP1_ENST00000393623.2_Missense_Mutation_p.V168G|KEAP1_ENST00000588024.1_5'Flank	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	168					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GCAGGCACGGACAACGCTGTC	0.582																																					p.V168G		Atlas-SNP	.											.	KEAP1	182	.	0			c.T503G						.						162	129	140					19																	10610207		2203	4300	6503	SO:0001583	missense	9817	exon2			GCACGGACAACGC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.503T>G	chr19.hg19:g.10610207A>C	ENSP00000171111:p.Val168Gly	113.0	0.0		115.0	39.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.249198	0.80024	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.72835	-0.69;-0.69	4.81	4.81	0.61882	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.060844	0.64402	D	0.000004	T	0.80330	0.4603	M	0.76574	2.34	0.80722	D	1	D	0.61080	0.989	P	0.60012	0.867	T	0.81568	-0.0873	10	0.49607	T	0.09	.	12.3271	0.55018	1.0:0.0:0.0:0.0	.	168	Q14145	KEAP1_HUMAN	G	168	ENSP00000171111:V168G;ENSP00000377245:V168G	ENSP00000171111:V168G	V	-	2	0	KEAP1	10471207	1.000000	0.71417	0.961000	0.40146	0.813000	0.45954	4.914000	0.63348	1.811000	0.52892	0.459000	0.35465	GTC	.	.		0.582	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		C	10610207	A	C	10610207	3	2	195	1	0	0	0	0	1	0	0	0	8150	275	10	5	1391	5	KEAP1	19	10610207	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	7561	10610207	48518776	159	28787										
ZNF625	90589	hgsc.bcm.edu	37	chr19	12256356	12256356	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cagtgtgagttctttcatgaTatcgaacggaattgaaagaa	10	5	2	4			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:12256356T>C	ENST00000355738.1	-	4	1026	c.677A>G	c.(676-678)tAt>tGt	p.Y226C	ZNF625_ENST00000455799.1_3'UTR|ZNF625_ENST00000439556.2_Missense_Mutation_p.Y292C|ZNF625-ZNF20_ENST00000430024.1_Intron|ZNF625_ENST00000542938.1_Missense_Mutation_p.Y226C|CTC-359D24.3_ENST00000472362.1_RNA			Q96I27	ZN625_HUMAN	zinc finger protein 625	226					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|large_intestine(6)|lung(4)|skin(2)	14						TCTTTCATGATATCGAACGGA	0.453																																					p.Y292C		Atlas-SNP	.											.	ZNF625	37	.	0			c.A875G						.						123	117	119					19																	12256356		2203	4300	6503	SO:0001583	missense	90589	exon4			TCATGATATCGAA	BC007868	CCDS12269.1, CCDS12269.2	19p13.2	2013-01-08			ENSG00000257591	ENSG00000257591		"Zinc fingers, C2H2-type", "-"	30571	protein-coding gene	gene with protein product						12477932	Standard	NM_145233		Approved		uc010dyo.2	Q96I27	OTTHUMG00000156407	ENST00000355738.1:c.677A>G	chr19.hg19:g.12256356T>C	ENSP00000347977:p.Tyr226Cys	132.0	0.0		169.0	50.0	NM_145233	A4FU45|I3L0E9	Missense_Mutation	SNP	ENST00000355738.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.39	1.922580	0.33908	.	.	ENSG00000257591	ENST00000542938;ENST00000355738;ENST00000439556	T;T;T	0.19669	2.13;2.13;2.13	0.856	-1.71	0.08133	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22044	0.0531	L	0.27053	0.805	0.09310	N	1	P;D	0.67145	0.89;0.996	B;D	0.65443	0.279;0.935	T	0.10268	-1.0637	9	0.36615	T	0.2	.	1.862	0.03190	0.2922:0.0:0.2933:0.4145	.	226;226	A8K8U0;Q96I27	.;ZN625_HUMAN	C	226;226;292	ENSP00000438436:Y226C;ENSP00000347977:Y226C;ENSP00000394380:Y292C	ENSP00000347977:Y226C	Y	-	2	0	AC022415.5	12117356	0.000000	0.05858	0.000000	0.03702	0.882000	0.50991	-3.830000	0.00355	-1.219000	0.02597	0.260000	0.18958	TAT	.	.		0.453	ZNF625-201	KNOWN	basic	protein_coding	protein_coding		NM_145233		C	12256356	T	C	12256356	3	2	195	1	0	0	0	0	1	0	0	0	18064	1406	49	2	247	2	ZNF625	19	12256356	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	1646149	12256356	46872627	160	28788										
PTGER1	5731	hgsc.bcm.edu	37	chr19	14583393	14583393	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tagaagtggctgaggccgctGtgccgggagctgcgcagcga	18	10	0	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:14583393G>C	ENST00000292513.3	-	3	1305	c.1188C>G	c.(1186-1188)caC>caG	p.H396Q		NM_000955.2	NP_000946.2	P34995	PE2R1_HUMAN	prostaglandin E receptor 1 (subtype EP1), 42kDa	396					G-protein coupled receptor signaling pathway (GO:0007186)|response to lipopolysaccharide (GO:0032496)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)									Alprostadil(DB00770)|Bimatoprost(DB00905)|Bupivacaine(DB00297)|Carboprost Tromethamine(DB00429)|Dinoprostone(DB00917)|Iloprost(DB01088)	TGAGGCCGCTGTGCCGGGAGC	0.706																																					p.H396Q		Atlas-SNP	.											.	PTGER1	5	.	0			c.C1188G						.						11	12	12					19																	14583393		2198	4293	6491	SO:0001583	missense	5731	exon3			GCCGCTGTGCCGG		CCDS12309.1	19p13.1	2012-08-08	2002-08-29		ENSG00000160951	ENSG00000160951		"GPCR / Class A : Prostanoid receptors"	9593	protein-coding gene	gene with protein product		176802	"prostaglandin E receptor 1 (subtype EP1), 42kD"			8253813	Standard	NM_000955		Approved	EP1	uc002mys.3	P34995	OTTHUMG00000039610	ENST00000292513.3:c.1188C>G	chr19.hg19:g.14583393G>C	ENSP00000292513:p.His396Gln	59.0	0.0		65.0	13.0	NM_000955	Q5U5U4|Q86UH3|Q86VB5|Q8NHB2	Missense_Mutation	SNP	ENST00000292513.3	hg19	CCDS12309.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.481661	0.44147	.	.	ENSG00000160951	ENST00000292513	T	0.16597	2.33	4.49	2.24	0.28232	.	0.421858	0.25011	N	0.033838	T	0.11922	0.0290	L	0.27053	0.805	0.24115	N	0.995822	B	0.02656	0.0	B	0.04013	0.001	T	0.22138	-1.0225	10	0.33141	T	0.24	-16.0678	12.2205	0.54431	0.0:0.3298:0.6702:0.0	.	396	P34995	PE2R1_HUMAN	Q	396	ENSP00000292513:H396Q	ENSP00000292513:H396Q	H	-	3	2	PTGER1	14444393	1.000000	0.71417	0.995000	0.50966	0.758000	0.43043	2.094000	0.41719	0.476000	0.27440	0.561000	0.74099	CAC	.	.		0.706	PTGER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095509.1			C	14583393	G	C	14583393	3	2	195	1	0	0	0	0	1	0	0	0	12755	1368	48	4	24	4	PTGER1	19	14583393	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	2327037	14583393	44545590	161	28789										
ZNF98	148198	hgsc.bcm.edu	37	chr19	22575383	22575384	+	Missense_Mutation	DNP	GG	GG	AT													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aggtttgaggcctcattataGgctttcccacattctttaca							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:22575383_22575384GG>AT	ENST00000357774.5	-	4	774_775	c.653_654CC>AT	c.(652-654)gCC>gAT	p.A218D		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	218					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				CCTCATTATAGGCTTTCCCACA	0.376																																					p.A218A|p.A218D		Atlas-SNP	.											.	ZNF98	230	.	0			c.C654T|c.C653A						.																																			SO:0001583	missense	148198	exon4			ATTATAGGCTTTC|TTATAGGCTTTCC		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"Zinc fingers, C2H2-type", "-"	13174	protein-coding gene	gene with protein product	"zinc finger protein 739"	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.653_654delinsAT	chr19.hg19:g.22575383_22575384delinsAT	ENSP00000350418:p.Ala218Asp	456.0|449.0	0.0		535.0|531.0	171.0|170.0	NM_001098626		Silent|Missense_Mutation	SNP	ENST00000357774.5	hg19	CCDS46031.1																																																																																			.	.		0.376	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		AT	22575384	GG	AT	22575383	3	1	195	1	0	0	0	0	1	0	0	0	18218	987	35	3	1068	3	ZNF98	19	22575383	Missense_Mutation	DNP	GG	TCGA-DD-AADM-01A-11D-A40R-10	7991990	22575383	36553600	162	28790										
ZNF573	126231	hgsc.bcm.edu	37	chr19	38230022	38230022	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	aatattctgatgtcgagtaaGatttctatacaaagtaaagg	8	4	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:38230022G>T	ENST00000590414.2	-	4	1390	c.1369C>A	c.(1369-1371)Ctt>Att	p.L457I	ZNF573_ENST00000536220.1_Missense_Mutation_p.L369I|ZNF573_ENST00000339503.4_Missense_Mutation_p.L399I|ZNF573_ENST00000392138.1_Missense_Mutation_p.L370I|ZNF573_ENST00000357309.3_Missense_Mutation_p.L369I			Q86YE8	ZN573_HUMAN	zinc finger protein 573	457					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			TGTCGAGTAAGATTTCTATAC	0.353																																					p.L457I		Atlas-SNP	.											.	ZNF573	63	.	0			c.C1369A						.						78	82	80					19																	38230022		2203	4300	6503	SO:0001583	missense	126231	exon5			GAGTAAGATTTCT	AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"Zinc fingers, C2H2-type", "-"	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.1369C>A	chr19.hg19:g.38230022G>T	ENSP00000465020:p.Leu457Ile	155.0	0.0		224.0	40.0	NM_001172690	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Missense_Mutation	SNP	ENST00000590414.2	hg19	CCDS59381.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.546410	0.45383	.	.	ENSG00000189144	ENST00000392138;ENST00000536220;ENST00000357309;ENST00000339503;ENST00000427026	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	2.19	2.19	0.27852	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.74366	0.3707	M	0.91872	3.25	0.09310	N	1	P;P;P;P	0.51791	0.936;0.936;0.948;0.936	P;P;P;P	0.62740	0.847;0.847;0.906;0.847	T	0.63989	-0.6512	9	0.87932	D	0	.	11.0686	0.47989	0.0:0.0:1.0:0.0	.	370;399;437;369	Q86YE8-4;Q86YE8-3;Q86YE8;Q86YE8-2	.;.;ZN573_HUMAN;.	I	370;369;369;399;369	ENSP00000375983:L370I;ENSP00000440464:L369I;ENSP00000349861:L369I;ENSP00000340171:L399I	ENSP00000340171:L399I	L	-	1	0	ZNF573	42921862	0.009000	0.17119	0.998000	0.56505	0.985000	0.73830	0.890000	0.28295	1.045000	0.40225	0.585000	0.79938	CTT	.	.		0.353	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360		T	38230022	G	T	38230022	3	4	195	1	0	0	0	0	1	0	0	0	18020	942	33	3	632	3	ZNF573	19	38230022	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	15654639	38230022	20898961	163	28791										
GYS1	2997	hgsc.bcm.edu	37	chr19	49473108	49473108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccatgtggcgcgcagacataTagtactaggggaaaggagga	15	7	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:49473108T>C	ENST00000323798.3	-	15	2010	c.1814A>G	c.(1813-1815)tAt>tGt	p.Y605C	GYS1_ENST00000541188.1_Missense_Mutation_p.Y525C|GYS1_ENST00000263276.6_Missense_Mutation_p.Y541C|GYS1_ENST00000544287.1_Missense_Mutation_p.Y238C	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	605					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		CGCAGACATATAGTACTAGGG	0.597																																					p.Y605C		Atlas-SNP	.											.	GYS1	59	.	0			c.A1814G						.						47	45	46					19																	49473108		2203	4300	6503	SO:0001583	missense	2997	exon15			GACATATAGTACT		CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.1814A>G	chr19.hg19:g.49473108T>C	ENSP00000317904:p.Tyr605Cys	26.0	0.0		38.0	4.0	NM_002103	Q9BTT9	Missense_Mutation	SNP	ENST00000323798.3	hg19	CCDS12747.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.297981	0.60086	.	.	ENSG00000104812	ENST00000323798;ENST00000263276;ENST00000541188;ENST00000544287	T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.85712	0.5760	M	0.79614	2.46	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.87512	0.2440	10	0.87932	D	0	-18.1798	13.7359	0.62817	0.0:0.0:0.0:1.0	.	525;541;605	B7Z806;Q9BTT9;P13807	.;.;GYS1_HUMAN	C	605;541;525;238	ENSP00000317904:Y605C;ENSP00000263276:Y541C;ENSP00000437922:Y525C;ENSP00000444004:Y238C	ENSP00000263276:Y541C	Y	-	2	0	GYS1	54164920	1.000000	0.71417	0.992000	0.48379	0.163000	0.22366	7.090000	0.76916	2.197000	0.70478	0.533000	0.62120	TAT	.	.		0.597	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103		C	49473108	T	C	49473108	3	2	195	1	0	0	0	0	1	0	0	0	6921	1406	49	2	407	2	GYS1	19	49473108	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	11243086	49473108	9655875	164	28792										
ZNF577	84765	hgsc.bcm.edu	37	chr19	52375982	52375982	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gtttaacaatggcggggttcCtgaggaaggcatttctatag	13	6	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:52375982C>T	ENST00000301399.5	-	7	1626	c.1261G>A	c.(1261-1263)Gga>Aga	p.G421R	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.G362R|ZNF577_ENST00000451628.2_Missense_Mutation_p.G362R	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	421					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GGCGGGGTTCCTGAGGAAGGC	0.433																																					p.G421R		Atlas-SNP	.											.	ZNF577	63	.	0			c.G1261A						.						60	61	61					19																	52375982		2203	4300	6503	SO:0001583	missense	84765	exon7			GGGTTCCTGAGGA	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"Zinc fingers, C2H2-type", "-"	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1261G>A	chr19.hg19:g.52375982C>T	ENSP00000301399:p.Gly421Arg	122.0	0.0		152.0	12.0	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	hg19	CCDS12842.2	.	.	.	.	.	.	.	.	.	.	.	7.010	0.556663	0.13436	.	.	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.05996	3.37;3.42;3.42;3.36	2.51	0.367	0.16140	.	.	.	.	.	T	0.02571	0.0078	N	0.03608	-0.345	0.09310	N	1	B;B	0.10296	0.001;0.003	B;B	0.09377	0.002;0.004	T	0.43015	-0.9417	9	0.66056	D	0.02	.	2.3681	0.04324	0.2395:0.4756:0.0:0.2849	.	421;362	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	R	421;362;362;421	ENSP00000301399:G421R;ENSP00000413476:G362R;ENSP00000389652:G362R;ENSP00000404509:G421R	ENSP00000301399:G421R	G	-	1	0	ZNF577	57067794	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.012000	0.12699	0.142000	0.18901	-0.137000	0.14449	GGA	.	.		0.433	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		T	52375982	C	T	52375982	3	4	195	1	0	0	0	0	1	0	0	0	18024	690	24	3	200	3	ZNF577	19	52375982	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	2902874	52375982	6753001	165	28793										
TTYH1	57348	hgsc.bcm.edu	37	chr19	54947007	54947007	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	atgccccgcatcaaaccccaGtgacgactacgatgacacag	8	15	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr19:54947007G>A	ENST00000376530.3	+	12	1371		c.e12-1		AC008746.3_ENST00000457113.1_RNA|TTYH1_ENST00000301194.4_Splice_Site|TTYH1_ENST00000489425.1_Splice_Site|TTYH1_ENST00000391739.3_Splice_Site|TTYH1_ENST00000376531.3_Intron|CTD-2587H19.2_ENST00000596631.1_RNA|CTD-2587H19.3_ENST00000597355.1_lincRNA|AC008746.12_ENST00000599382.1_lincRNA	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1						cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)			endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		TCAAACCCCAGTGACGACTAC	0.662																																					.		Atlas-SNP	.											.	TTYH1	78	.	0			c.1269-1G>A						.						124	113	117					19																	54947007		2203	4300	6503	SO:0001630	splice_region_variant	57348	exon12			ACCCCAGTGACGA	AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"tweety (Drosophila) homolog 1", "tweety homolog 1 (Drosophila)"			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.1269-1G>A	chr19.hg19:g.54947007G>A		97.0	0.0		91.0	35.0	NM_020659	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Splice_Site	SNP	ENST00000376530.3	hg19	CCDS12893.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.196897	0.58126	.	.	ENSG00000167614	ENST00000301194;ENST00000376530	.	.	.	3.98	3.98	0.46160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9331	0.64007	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TTYH1	59638819	1.000000	0.71417	0.993000	0.49108	0.871000	0.50021	5.846000	0.69444	1.946000	0.56461	0.561000	0.74099	.	.	.		0.662	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1		Intron	A	54947007	G	A	54947007	5	1	195	1	0	0	0	0	0	0	1	0	16754	1043	36	3	1314	3	TTYH1	19	54947007	Splice_Site	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	2571025	54947007	4181976	166	28794										
RALGAPA2	57186	hgsc.bcm.edu	37	chr20	20505080	20505080	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	taatccagcaagggggctctGgccgaatgctgctcctctag	12	12	2	0			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr20:20505080G>A	ENST00000202677.7	-	30	3877	c.3870C>T	c.(3868-3870)gcC>gcT	p.A1290A		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1290					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						AGGGGGCTCTGGCCGAATGCT	0.542																																					p.A1290A		Atlas-SNP	.											.	RALGAPA2	274	.	0			c.C3870T						.						44	44	44					20																	20505080		1977	4160	6137	SO:0001819	synonymous_variant	57186	exon30			GGCTCTGGCCGAA	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.3870C>T	chr20.hg19:g.20505080G>A		59.0	0.0		28.0	10.0	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Silent	SNP	ENST00000202677.7	hg19	CCDS46584.1	.	.	.	.	.	.	.	.	.	.	G	5.022	0.189811	0.09547	.	.	ENSG00000188559	ENST00000430436	.	.	.	5.54	0.759	0.18438	.	.	.	.	.	T	0.35508	0.0934	.	.	.	0.29569	N	0.850053	.	.	.	.	.	.	T	0.34576	-0.9823	4	.	.	.	.	9.4696	0.38833	0.4709:0.0:0.5291:0.0	.	.	.	.	L	1107	.	.	P	-	2	0	RALGAPA2	20453080	0.998000	0.40836	0.134000	0.22075	0.598000	0.36846	0.543000	0.23237	0.252000	0.21531	0.650000	0.86243	CCA	.	.		0.542	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		A	20505080	G	A	20505080	2	1	195	1	0	0	0	0	0	0	0	1	13029	1335	47	3		3	RALGAPA2	20	20505080	Silent	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10		20505080	42520440	167	28795										
DEFB116	245930	hgsc.bcm.edu	37	chr20	29891100	29891100	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tcacatttttagaactggttAttttcacagaaagtttcagg	7	6	3	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr20:29891100A>G	ENST00000400549.1	-	2	223	c.224T>C	c.(223-225)aTa>aCa	p.I75T		NM_001037731.1	NP_001032820.1	Q30KQ4	DB116_HUMAN	defensin, beta 116	75					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				kidney(2)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	12	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			AGAACTGGTTATTTTCACAGA	0.393																																					p.I75T		Atlas-SNP	.											.	DEFB116	18	.	0			c.T224C						.						348	313	324					20																	29891100		1857	4100	5957	SO:0001583	missense	245930	exon2			CTGGTTATTTTCA	DQ012020	CCDS42860.1	20q11.21	2008-07-17			ENSG00000215545	ENSG00000215545		"Defensins, beta"	18097	protein-coding gene	gene with protein product	"defensin, beta 16"					11854508, 16033865	Standard	NM_001037731		Approved	DEFB-16	uc010ztm.2	Q30KQ4	OTTHUMG00000159285	ENST00000400549.1:c.224T>C	chr20.hg19:g.29891100A>G	ENSP00000383396:p.Ile75Thr	114.0	0.0		123.0	10.0	NM_001037731		Missense_Mutation	SNP	ENST00000400549.1	hg19	CCDS42860.1	.	.	.	.	.	.	.	.	.	.	A	6.093	0.385461	0.11524	.	.	ENSG00000215545	ENST00000400549	T	0.21031	2.03	3.32	-4.84	0.03151	.	.	.	.	.	T	0.10508	0.0257	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27839	-1.0062	9	0.39692	T	0.17	-11.8605	4.111	0.10058	0.2738:0.0:0.4129:0.3132	.	75	Q30KQ4	DB116_HUMAN	T	75	ENSP00000383396:I75T	ENSP00000383396:I75T	I	-	2	0	DEFB116	29354761	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.277000	0.02812	-1.253000	0.02488	-1.981000	0.00455	ATA	.	.		0.393	DEFB116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354403.1	NM_001037731		G	29891100	A	G	29891100	3	3	195	1	0	0	0	0	1	0	0	0	4407	449	16	2	87	2	DEFB116	20	29891100	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	9386020	29891100	33134420	168	28796										
SUN5	140732	hgsc.bcm.edu	37	chr20	31573549	31573549	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ggggagtgctcacatagatgAcgaagtccttgggggcggtg	18	7	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr20:31573549A>G	ENST00000356173.3	-	11	982	c.890T>C	c.(889-891)gTc>gCc	p.V297A	SUN5_ENST00000375523.3_Missense_Mutation_p.V272A	NM_080675.3	NP_542406.2	Q8TC36	SUN5_HUMAN	Sad1 and UNC84 domain containing 5	297	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	25						CACATAGATGACGAAGTCCTT	0.537																																					p.V297A		Atlas-SNP	.											.	SUN5	63	.	0			c.T890C						.						124	97	106					20																	31573549		2203	4300	6503	SO:0001583	missense	140732	exon11			TAGATGACGAAGT	AL121756	CCDS13209.1	20q11.21	2010-01-27	2010-01-27	2010-01-27	ENSG00000167098	ENSG00000167098			16252	protein-coding gene	gene with protein product	"testis and spermatogenesis related gene 4"	613942	"sperm associated antigen 4-like"	SPAG4L		9691178, 10373309	Standard	NM_080675		Approved	dJ726C3.1, TSARG4	uc002wyi.3	Q8TC36	OTTHUMG00000032239	ENST00000356173.3:c.890T>C	chr20.hg19:g.31573549A>G	ENSP00000348496:p.Val297Ala	110.0	0.0		155.0	28.0	NM_080675	A6NJ82|Q5T9R0	Missense_Mutation	SNP	ENST00000356173.3	hg19	CCDS13209.1	.	.	.	.	.	.	.	.	.	.	A	4.780	0.144960	0.09134	.	.	ENSG00000167098	ENST00000356173;ENST00000375523	T;T	0.40225	1.04;1.04	5.71	4.62	0.57501	Sad1/UNC-like, C-terminal (2);	0.266290	0.37261	N	0.002171	T	0.14399	0.0348	N	0.02960	-0.455	0.80722	D	1	P	0.38420	0.63	B	0.34873	0.191	T	0.18147	-1.0346	10	0.07030	T	0.85	-48.6352	7.6337	0.28253	0.9073:0.0:0.0927:0.0	.	297	Q8TC36	SUN5_HUMAN	A	297;272	ENSP00000348496:V297A;ENSP00000364673:V272A	ENSP00000348496:V297A	V	-	2	0	SUN5	31037210	0.996000	0.38824	0.998000	0.56505	0.347000	0.29111	3.781000	0.55394	2.171000	0.68590	0.533000	0.62120	GTC	.	.		0.537	SUN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078659.1	NM_080675		G	31573549	A	G	31573549	3	3	195	1	0	0	0	0	1	0	0	0	15409	275	10	2	261	2	SUN5	20	31573549	Missense_Mutation	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10	1682449	31573549	31451971	169	28797										
C20orf71	128861	hgsc.bcm.edu	37	chr20	31812207	31812207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	actgtggtgggatccagataTcattccataaggagtggttc	12	7	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr20:31812207T>C	ENST00000375454.3	+	3	535	c.325T>C	c.(325-327)Tca>Cca	p.S109P	BPIFA3_ENST00000490499.1_3'UTR|BPIFA3_ENST00000375452.3_Intron	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	109						extracellular region (GO:0005576)	lipid binding (GO:0008289)										GATCCAGATATCATTCCATAA	0.488																																					p.S109P		Atlas-SNP	.											.	.	.	.	0			c.T325C						.						172	153	159					20																	31812207		2203	4300	6503	SO:0001583	missense	128861	exon3			CAGATATCATTCC		CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"BPI fold containing"	16204	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 71"	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.325T>C	chr20.hg19:g.31812207T>C	ENSP00000364603:p.Ser109Pro	97.0	0.0		109.0	19.0	NM_178466	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	hg19	CCDS13216.2	.	.	.	.	.	.	.	.	.	.	T	12.16	1.854169	0.32791	.	.	ENSG00000131059	ENST00000375454	T	0.07327	3.2	4.35	2.03	0.26663	.	0.734404	0.12296	N	0.481572	T	0.12987	0.0315	L	0.29908	0.895	0.43959	D	0.996632	D	0.59767	0.986	D	0.63283	0.913	T	0.21586	-1.0241	10	0.72032	D	0.01	-0.2133	4.4048	0.11404	0.0:0.1063:0.2126:0.6811	.	109	Q9BQP9	BPIA3_HUMAN	P	109	ENSP00000364603:S109P	ENSP00000364603:S109P	S	+	1	0	BPIFA3	31275868	0.995000	0.38212	0.626000	0.29213	0.088000	0.18126	0.967000	0.29344	0.433000	0.26313	0.460000	0.39030	TCA	.	.		0.488	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466		C	31812207	T	C	31812207	3	2	195	1	0	0	0	0	1	0	0	0	2119	1435	50	2	335	2	C20orf71	20	31812207	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	238658	31812207	31213313	170	28798										
JAM2	58494	hgsc.bcm.edu	37	chr21	27086971	27086971	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ggatttcaagcacacaaaatCctttataatttaaagactcc	4	9	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr21:27086971C>G	ENST00000480456.1	+	10	1434	c.884C>G	c.(883-885)tCc>tGc	p.S295C	JAM2_ENST00000312957.5_Missense_Mutation_p.S295C|JAM2_ENST00000477351.1_3'UTR|JAM2_ENST00000425221.2_Missense_Mutation_p.S259C	NM_001270407.1|NM_021219.3	NP_001257336.1|NP_067042.1	P57087	JAM2_HUMAN	junctional adhesion molecule 2	295					blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|stomach(1)|urinary_tract(1)	19						CACACAAAATCCTTTATAATT	0.284																																					p.S295C		Atlas-SNP	.											.	JAM2	33	.	0			c.C884G						.						54	54	54					21																	27086971		1784	4055	5839	SO:0001583	missense	58494	exon10			CAAAATCCTTTAT	AF255910	CCDS42911.1, CCDS58787.1, CCDS58788.1	21q21.2	2013-01-11			ENSG00000154721	ENSG00000154721		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing"	14686	protein-coding gene	gene with protein product		606870		C21orf43		10779521, 10945976	Standard	NM_021219		Approved	VE-JAM, JAM-B, JAMB, CD322	uc031rvc.1	P57087	OTTHUMG00000078441	ENST00000480456.1:c.884C>G	chr21.hg19:g.27086971C>G	ENSP00000420419:p.Ser295Cys	641.0	0.0		636.0	96.0	NM_021219	B2R6T9|B4DGT9|Q6UXG6|Q6YNC1	Missense_Mutation	SNP	ENST00000480456.1	hg19	CCDS42911.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.40|18.40	3.615902|3.615902	0.66672|0.66672	.|.	.|.	ENSG00000154721|ENSG00000154721	ENST00000400533|ENST00000480456;ENST00000400537;ENST00000312957;ENST00000425221	.|D;D;D	.|0.82984	.|-1.67;-1.67;-1.67	4.87|4.87	4.87|4.87	0.63330|0.63330	.|.	.|.	.|.	.|.	.|.	D|D	0.90407|0.90407	0.6997|0.6997	M|M	0.75615|0.75615	2.305|2.305	0.58432|0.58432	D|D	0.999998|0.999998	B|D;D;D	0.19200|0.89917	0.034|1.0;1.0;1.0	B|D;D;D	0.14023|0.87578	0.01|0.998;0.997;0.998	D|D	0.91256|0.91256	0.5033|0.5033	8|9	0.87932|0.87932	D|D	0|0	.|.	15.3828|15.3828	0.74673|0.74673	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	277|259;291;295	A8MXS1|B4DGT9;A8MTB0;P57087	.|.;.;JAM2_HUMAN	A|C	277|295;291;295;259	.|ENSP00000420419:S295C;ENSP00000318416:S295C;ENSP00000392611:S259C	ENSP00000383377:P277A|ENSP00000318416:S295C	P|S	+|+	1|2	0|0	JAM2|JAM2	26008842|26008842	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.995000|0.995000	0.86356|0.86356	4.114000|4.114000	0.57858|0.57858	2.674000|2.674000	0.91012|0.91012	0.650000|0.650000	0.86243|0.86243	CCT|TCC	.	.		0.284	JAM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171347.1			G	27086971	C	G	27086971	3	3	195	1	0	0	0	0	1	0	0	0	7952	855	30	4	922	4	JAM2	21	27086971	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10		27086971	21042924	171	28799										
NCF4	4689	hgsc.bcm.edu	37	chr22	37272032	37272032	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ccaccccacaccccacttccAgcctgatgcctccttactcc	3	23	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr22:37272032A>T	ENST00000248899.6	+	9	942				NCF4_ENST00000397147.4_Missense_Mutation_p.Q322L	NM_000631.4	NP_000622.2	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4, 40kDa						antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of catalytic activity (GO:0043085)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|membrane (GO:0016020)|NADPH oxidase complex (GO:0043020)|phagolysosome (GO:0032010)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein dimerization activity (GO:0046983)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16					Dextromethorphan(DB00514)	CCCCACTTCCAGCCTGATGCC	0.592																																					p.Q322L		Atlas-SNP	.											.	NCF4	66	.	0			c.A965T						.						27	27	27					22																	37272032		2203	4300	6503	SO:0001627	intron_variant	4689	exon8			ACTTCCAGCCTGA	X77094	CCDS13934.1, CCDS13935.1	22q13.1	2014-09-17	2002-08-29		ENSG00000100365	ENSG00000100365			7662	protein-coding gene	gene with protein product	"neutrophil NADPH oxidase factor 4"	601488	"neutrophil cytosolic factor 4 (40kD)"			8839867	Standard	NM_013416		Approved	p40phox, SH3PXD4	uc003apy.4	Q15080	OTTHUMG00000150548	ENST00000248899.6:c.759-39A>T	chr22.hg19:g.37272032A>T		159.0	0.0		171.0	21.0	NM_013416	A8K4F9|O60808|Q86U56|Q9BU98|Q9NP45	Missense_Mutation	SNP	ENST00000248899.6	hg19	CCDS13934.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.303172	0.23736	.	.	ENSG00000100365	ENST00000397147	T	0.59083	0.29	4.13	-8.25	0.01025	.	2.558080	0.01337	N	0.011457	T	0.32556	0.0833	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20405	-1.0276	8	.	.	.	.	2.5763	0.04807	0.3988:0.1953:0.308:0.0979	.	322	A8K4F9	.	L	322	ENSP00000380334:Q322L	.	Q	+	2	0	NCF4	35601978	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.510000	0.02262	-2.824000	0.00342	-0.911000	0.02809	CAG	.	.		0.592	NCF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318863.1	NM_000631		T	37272032	A	T	37272032	1	4	195	0	1	0	0	0	0	0	0	0	10227	188	7	4		4	NCF4	22	37272032	Intron	SNP	A	TCGA-DD-AADM-01A-11D-A40R-10		37272032	14032534	172	28800										
CYP2D6	1565	hgsc.bcm.edu	37	chr22	42525795	42525795	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	atgggcacaggcgggcggtcGgcggtgtcctcgccgtgggt	20	11	0	0	rs200269944		TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chr22:42525795G>C	ENST00000360608.5	-	2	411	c.297C>G	c.(295-297)gcC>gcG	p.A99A	CYP2D6_ENST00000389970.3_Silent_p.A99A|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Silent_p.A99A|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000608288.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	99					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GCGGGCGGTCGGCGGTGTCCT	0.701																																					p.A99A		Atlas-SNP	.											.	CYP2D6	104	.	0			c.C297G						.						16	18	18					22																	42525795		2182	4267	6449	SO:0001819	synonymous_variant	1565	exon2			GCGGTCGGCGGTG	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"Cytochrome P450s"	2625	protein-coding gene	gene with protein product		124030	"cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6", "cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2", "cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2", "cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2", "cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.297C>G	chr22.hg19:g.42525795G>C		225.0	0.0		292.0	18.0	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Silent	SNP	ENST00000360608.5	hg19	CCDS46721.1																																																																																			.	G|0.998;A|0.002		0.701	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1			C	42525795	G	C	42525795	2	2	195	1	0	0	0	0	0	0	0	1	4171	1103	39	4		4	CYP2D6	22	42525795	Silent	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	5253763	42525795	8778771	173	28801										
ASMT	438	hgsc.bcm.edu	37	chrX	1761898	1761898	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	atttatgatgccattttagcCaggaaataactgtttcttgt	7	6	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chrX:1761898C>G	ENST00000381229.4	+	8	1065	c.1029C>G	c.(1027-1029)gcC>gcG	p.A343A	ASMT_ENST00000381233.3_Silent_p.A296A|ASMT_ENST00000381241.3_Silent_p.A371A			P46597	ASMT_HUMAN	acetylserotonin O-methyltransferase	343					cellular nitrogen compound metabolic process (GO:0034641)|indolalkylamine biosynthetic process (GO:0046219)|melatonin biosynthetic process (GO:0030187)|negative regulation of male gonad development (GO:2000019)|small molecule metabolic process (GO:0044281)|translation (GO:0006412)	cytosol (GO:0005829)	acetylserotonin O-methyltransferase activity (GO:0017096)|identical protein binding (GO:0042802)|O-methyltransferase activity (GO:0008171)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	16		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Melatonin(DB01065)	CCATTTTAGCCAGGAAATAAC	0.443																																					p.A371A		Atlas-SNP	.											.	ASMT	31	.	0			c.C1113G						.						144	136	139					X																	1761898		2203	4296	6499	SO:0001819	synonymous_variant	438	exon9			TTTAGCCAGGAAA	M83779	CCDS14117.1, CCDS55364.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000196433	ENSG00000196433	2.1.1.4	"Pseudoautosomal regions / PAR1"	750	protein-coding gene	gene with protein product		300015, 402500				8397829, 7989373	Standard	NM_004043		Approved	HIOMT, ASMTY, HIOMTY	uc010ncy.3	P46597	OTTHUMG00000021065	ENST00000381229.4:c.1029C>G	chrX.hg19:g.1761898C>G		253.0	0.0		285.0	37.0	NM_001171038	B2RC33|Q16598|Q5JQ72|Q5JQ73	Silent	SNP	ENST00000381229.4	hg19																																																																																				.	.		0.443	ASMT-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055612.1	NM_004043		G	1761898	C	G	1761898	2	3	195	1	0	0	0	0	0	0	0	1	1045	581	21	4		4	ASMT	23	1761898	Silent	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10		1761898	153508662	174	28802										
MED14	9282	hgsc.bcm.edu	37	chrX	40526045	40526045	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gggggaggagttggaacaaaTgacgctggtgatggggctct	19	5	1	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chrX:40526045T>C	ENST00000324817.1	-	24	3310	c.3192A>G	c.(3190-3192)tcA>tcG	p.S1064S		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	1064	Pro-rich.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TTGGAACAAATGACGCTGGTG	0.473																																					p.S1064S		Atlas-SNP	.											.	MED14	108	.	0			c.A3192G						.						41	35	37					X																	40526045		2203	4300	6503	SO:0001819	synonymous_variant	9282	exon24			AACAAATGACGCT	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.3192A>G	chrX.hg19:g.40526045T>C		217.0	0.0		176.0	49.0	NM_004229	Q4KMR7|Q9UNB3	Silent	SNP	ENST00000324817.1	hg19	CCDS14254.1																																																																																			.	.		0.473	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		C	40526045	T	C	40526045	2	2	195	1	0	0	0	0	0	0	0	1	9441	1451	51	2		2	MED14	23	40526045	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	38764147	40526045	114744515	175	28803										
RBM10	8241	hgsc.bcm.edu	37	chrX	47039334	47039345	+	In_Frame_Del	DEL	CCTGGCACCCTA	CCTGGCACCCTA	-													0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	atggattccatcctgggggcCctggcaccctacgcggtgct							TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	CCTGGCACCCTA	CCTGGCACCCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chrX:47039334_47039345delCCTGGCACCCTA	ENST00000377604.3	+	10	1699_1710	c.957_968delCCTGGCACCCTA	c.(955-969)gccctggcaccctac>gcc	p.LAPY320del	RBM10_ENST00000329236.7_In_Frame_Del_p.LAPY243del|RBM10_ENST00000478410.1_3'UTR|RBM10_ENST00000345781.6_In_Frame_Del_p.LAPY243del	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	320	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						TCCTGGGGGCCCTGGCACCCTACGCGGTGCTG	0.594																																					p.384_388del	Melanoma(171;120 2705 19495 39241)	Atlas-Indel,Pindel	.											.	RBM10	117	.	0			c.1151_1162del						.																																			SO:0001651	inframe_deletion	8241	exon10			.	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.957_968delCCTGGCACCCTA	chrX.hg19:g.47039334_47039345delCCTGGCACCCTA	ENSP00000366829:p.Leu320_Tyr323del	102.0	0.0		107.0	18.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	In_Frame_Del	DEL	ENST00000377604.3	hg19	CCDS14274.1																																																																																			.	.		0.594	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		-	47039345	CCTGGCACCCTA	-	47039334	7	5	195	1	0	1	0	1	0	0	0	0	13126	610	22	0	991	0	RBM10	23	47039334	In_Frame_Del	DEL	CCTGGCACCCTA	TCGA-DD-AADM-01A-11D-A40R-10	6513289	47039334	108231226	176	28804										
HDAC6	10013	hgsc.bcm.edu	37	chrX	48673109	48673109	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgcgggatgctgactacattGctgctttcctgcacgtcctg	11	12	0	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chrX:48673109G>T	ENST00000334136.5	+	12	1139	c.961G>T	c.(961-963)Gct>Tct	p.A321S	HDAC6_ENST00000376619.2_Missense_Mutation_p.A321S|HDAC6_ENST00000413163.2_Missense_Mutation_p.A266S|HDAC6_ENST00000444343.2_Missense_Mutation_p.A335S			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	321	Histone deacetylase 1.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	TGACTACATTGCTGCTTTCCT	0.627																																					p.A321S	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.G961T						.						80	68	72					X																	48673109		2203	4300	6503	SO:0001583	missense	10013	exon12			TACATTGCTGCTT	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.961G>T	chrX.hg19:g.48673109G>T	ENSP00000334061:p.Ala321Ser	42.0	0.0		34.0	25.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	hg19	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.871724	0.33069	.	.	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000413163	T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44	5.05	2.96	0.34315	Histone deacetylase domain (2);	0.516766	0.18747	N	0.132290	T	0.57007	0.2024	L	0.41961	1.31	0.31374	N	0.679836	P;P;P	0.42556	0.515;0.783;0.515	B;P;B	0.46917	0.383;0.531;0.383	T	0.60094	-0.7330	10	0.35671	T	0.21	-13.4759	1.7054	0.02881	0.1259:0.2031:0.4563:0.2146	.	311;266;321	B4DZN1;E7EUZ1;Q9UBN7	.;.;HDAC6_HUMAN	S	335;321;321;321;266	ENSP00000398566:A335S;ENSP00000334061:A321S;ENSP00000365804:A321S;ENSP00000398801:A266S	ENSP00000334061:A321S	A	+	1	0	HDAC6	48558053	0.274000	0.24191	1.000000	0.80357	0.055000	0.15305	0.375000	0.20518	2.096000	0.63516	0.529000	0.55759	GCT	.	.		0.627	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		T	48673109	G	T	48673109	3	4	195	1	0	0	0	0	1	0	0	0	7020	1319	46	3	1003	3	HDAC6	23	48673109	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	1633775	48673109	106597451	177	28805										
PHKA1	5255	hgsc.bcm.edu	37	chrX	71838613	71838613	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	tgttcctgtaagcttgaggtCtccttcaactgtaaaaccag	8	10	2	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chrX:71838613C>G	ENST00000373542.4	-	21	2475	c.2316G>C	c.(2314-2316)gaG>gaC	p.E772D	PHKA1_ENST00000373545.3_Missense_Mutation_p.E713D|PHKA1_ENST00000339490.3_Missense_Mutation_p.E772D|PHKA1_ENST00000541944.1_Missense_Mutation_p.E713D|PHKA1_ENST00000373539.3_Missense_Mutation_p.E772D	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	772					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					AGCTTGAGGTCTCCTTCAACT	0.393																																					p.E772D		Atlas-SNP	.											.	PHKA1	129	.	0			c.G2316C						.						163	135	144					X																	71838613		2203	4300	6503	SO:0001583	missense	5255	exon21			TGAGGTCTCCTTC		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.2316G>C	chrX.hg19:g.71838613C>G	ENSP00000362643:p.Glu772Asp	142.0	0.0		125.0	44.0	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	C	5.267	0.234718	0.09969	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.91124	-2.77;-2.79;-2.79;-2.77;-2.76	5.53	3.65	0.41850	Glycoside hydrolase 15-related (1);	0.181059	0.51477	D	0.000084	T	0.73297	0.3569	N	0.04203	-0.255	0.26174	N	0.979824	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.11329	0.002;0.002;0.006	T	0.58451	-0.7634	10	0.12103	T	0.63	-15.384	3.8581	0.08984	0.1926:0.6083:0.0:0.199	.	713;772;772	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	D	713;772;713;772;772	ENSP00000362646:E713D;ENSP00000362643:E772D;ENSP00000441251:E713D;ENSP00000342469:E772D;ENSP00000362640:E772D	ENSP00000342469:E772D	E	-	3	2	PHKA1	71755338	0.995000	0.38212	1.000000	0.80357	0.977000	0.68977	0.354000	0.20146	1.095000	0.41419	0.513000	0.50165	GAG	.	.		0.393	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			G	71838613	C	G	71838613	3	3	195	1	0	0	0	0	1	0	0	0	11852	912	32	4	1403	4	PHKA1	23	71838613	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	23165504	71838613	83431947	178	28806										
PHKA1	5255	hgsc.bcm.edu	37	chrX	71838663	71838663	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	gtccacctccccagactggtCtctaggaagatgtatttcta	8	12	2	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chrX:71838663C>G	ENST00000373542.4	-	21	2425	c.2266G>C	c.(2266-2268)Gac>Cac	p.D756H	PHKA1_ENST00000373545.3_Missense_Mutation_p.D697H|PHKA1_ENST00000339490.3_Missense_Mutation_p.D756H|PHKA1_ENST00000541944.1_Missense_Mutation_p.D697H|PHKA1_ENST00000373539.3_Missense_Mutation_p.D756H	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	756					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					CCAGACTGGTCTCTAGGAAGA	0.388																																					p.D756H		Atlas-SNP	.											.	PHKA1	129	.	0			c.G2266C						.						128	110	116					X																	71838663		2203	4300	6503	SO:0001583	missense	5255	exon21			ACTGGTCTCTAGG		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.2266G>C	chrX.hg19:g.71838663C>G	ENSP00000362643:p.Asp756His	121.0	0.0		106.0	37.0	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.241568	0.39598	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.92048	-2.94;-2.96;-2.96;-2.91;-2.91	5.46	1.79	0.24919	Glycoside hydrolase 15-related (1);	0.487969	0.23134	N	0.051549	D	0.95351	0.8491	M	0.87038	2.855	0.38361	D	0.944616	D;P;P	0.76494	0.999;0.691;0.736	D;B;P	0.71870	0.975;0.405;0.828	D	0.93877	0.7167	10	0.72032	D	0.01	-1.8962	8.3981	0.32570	0.0:0.6589:0.0:0.3411	.	697;756;756	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	H	697;756;697;756;756	ENSP00000362646:D697H;ENSP00000362643:D756H;ENSP00000441251:D697H;ENSP00000342469:D756H;ENSP00000362640:D756H	ENSP00000342469:D756H	D	-	1	0	PHKA1	71755388	0.949000	0.32298	0.709000	0.30452	0.714000	0.41099	2.185000	0.42584	-0.066000	0.12998	-0.281000	0.10026	GAC	.	.		0.388	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			G	71838663	C	G	71838663	3	3	195	1	0	0	0	0	1	0	0	0	11852	913	32	4	1453	4	PHKA1	23	71838663	Missense_Mutation	SNP	C	TCGA-DD-AADM-01A-11D-A40R-10	50	71838663	83431897	179	28807										
ARMCX2	9823	hgsc.bcm.edu	37	chrX	100911407	100911407	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	ctgaagcaaggcaaggacctTcctgagatcgcggacaccca	11	13	0	2			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chrX:100911407T>C	ENST00000328766.5	-	5	1621	c.1168A>G	c.(1168-1170)Aag>Gag	p.K390E	ARMCX2_ENST00000467416.1_5'Flank|ARMCX2_ENST00000330154.2_Missense_Mutation_p.K390E|ARMCX2_ENST00000356824.4_Missense_Mutation_p.K390E	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	390						integral component of membrane (GO:0016021)				NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(6)|prostate(1)|skin(1)	29						GCAAGGACCTTCCTGAGATCG	0.498																																					p.K390E		Atlas-SNP	.											.	ARMCX2	75	.	0			c.A1168G						.						104	93	97					X																	100911407		2203	4300	6503	SO:0001583	missense	9823	exon5			GGACCTTCCTGAG	AB011084	CCDS14490.1	Xq21.33-q22.2	2014-03-21			ENSG00000184867	ENSG00000184867		"Armadillo repeat containing"	16869	protein-coding gene	gene with protein product		300363				9628581, 11162520, 16221301, 22569362	Standard	XM_005278109		Approved	ALEX2, KIAA0512, GASP9	uc004eif.3	Q7L311	OTTHUMG00000022038	ENST00000328766.5:c.1168A>G	chrX.hg19:g.100911407T>C	ENSP00000331662:p.Lys390Glu	61.0	0.0		60.0	10.0	NM_014782	O60267|Q5H9D9	Missense_Mutation	SNP	ENST00000328766.5	hg19	CCDS14490.1	.	.	.	.	.	.	.	.	.	.	T	15.30	2.791396	0.50102	.	.	ENSG00000184867	ENST00000328766;ENST00000330154;ENST00000356824	T;T;T	0.38077	1.16;1.16;1.16	3.77	3.77	0.43336	Armadillo-like helical (1);Armadillo-type fold (1);	0.194986	0.52532	D	0.000080	T	0.52256	0.1723	M	0.68317	2.08	0.33997	D	0.649897	D	0.76494	0.999	D	0.81914	0.995	T	0.63413	-0.6643	10	0.44086	T	0.13	-11.4456	8.0153	0.30376	0.0:0.0:0.0:1.0	.	390	Q7L311	ARMX2_HUMAN	E	390	ENSP00000331662:K390E;ENSP00000328631:K390E;ENSP00000349281:K390E	ENSP00000331662:K390E	K	-	1	0	ARMCX2	100798063	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.791000	0.55469	1.709000	0.51313	0.345000	0.21793	AAG	.	.		0.498	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057586.1	NM_014782		C	100911407	T	C	100911407	3	2	195	1	0	0	0	0	1	0	0	0	960	1792	62	2	734	2	ARMCX2	23	100911407	Missense_Mutation	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	29072744	100911407	54359153	180	28808										
LHFPL1	340596	hgsc.bcm.edu	37	chrX	111914512	111914512	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	acactggcttccccatctggGatccaaagagccagtaaggt	10	12	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chrX:111914512G>C	ENST00000371968.3	-	2	346	c.107C>G	c.(106-108)tCc>tGc	p.S36C	LHFPL1_ENST00000478229.1_Intron|LHFPL1_ENST00000536453.1_Missense_Mutation_p.S36C	NM_178175.3	NP_835469.1	Q86WI0	LHPL1_HUMAN	lipoma HMGIC fusion partner-like 1	36						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)	13						CCCCATCTGGGATCCAAAGAG	0.557																																					p.S36C		Atlas-SNP	.											.	LHFPL1	28	.	0			c.C107G						.						152	141	144					X																	111914512		2203	4300	6503	SO:0001583	missense	340596	exon2			ATCTGGGATCCAA	AY217350	CCDS14562.1	Xq23	2008-02-05			ENSG00000182508	ENSG00000182508			6587	protein-coding gene	gene with protein product		300566				10329012	Standard	NM_178175		Approved		uc004epq.3	Q86WI0	OTTHUMG00000022214	ENST00000371968.3:c.107C>G	chrX.hg19:g.111914512G>C	ENSP00000361036:p.Ser36Cys	104.0	0.0		130.0	32.0	NM_178175	A8K1N1|Q496M9|Q496N0|Q6UXU2	Missense_Mutation	SNP	ENST00000371968.3	hg19	CCDS14562.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.425519	0.43020	.	.	ENSG00000182508	ENST00000371968;ENST00000536453	T;T	0.73897	-0.79;-0.79	5.44	4.56	0.56223	.	0.179620	0.49916	D	0.000137	T	0.76962	0.4061	M	0.72118	2.19	0.42774	D	0.993845	P;P	0.50710	0.924;0.938	P;P	0.51453	0.54;0.67	T	0.78593	-0.2144	10	0.56958	D	0.05	-27.0486	7.5263	0.27658	0.1898:0.0:0.8102:0.0	.	36;36	Q86WI0-2;Q86WI0	.;LHPL1_HUMAN	C	36	ENSP00000361036:S36C;ENSP00000444573:S36C	ENSP00000361036:S36C	S	-	2	0	LHFPL1	111801168	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.176000	0.50863	2.524000	0.85096	0.600000	0.82982	TCC	.	.		0.557	LHFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057947.1	NM_178175		C	111914512	G	C	111914512	3	2	195	1	0	0	0	0	1	0	0	0	8773	1174	41	4	567	4	LHFPL1	23	111914512	Missense_Mutation	SNP	G	TCGA-DD-AADM-01A-11D-A40R-10	11003105	111914512	43356048	181	28809										
SPRY3	10251	hgsc.bcm.edu	37	chrX	155004067	155004067	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0558659217877095	10	1	1.37505567928731	2.5329973039503	0.665349522235793	0.245077461269365	0.896214637779148	0	cagcgctgcctttgctctgcTgagagcctcctcgattatgg	11	13	1	1			TCGA-DD-AADM-01A-11D-A40R-10	TCGA-DD-AADM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3f5bd9c-15d2-40c2-8a80-2e79612b0da2	240c9f1e-b53f-41d5-a4cb-6249427390ad	g.chrX:155004067T>C	ENST00000302805.2	+	2	965	c.534T>C	c.(532-534)gcT>gcC	p.A178A		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	178	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)						all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TTTGCTCTGCTGAGAGCCTCC	0.582																																					p.A178A		Atlas-SNP	.											.	SPRY3	52	.	0			c.T534C						.						190	179	183					X																	155004067		2203	4296	6499	SO:0001819	synonymous_variant	10251	exon2			CTCTGCTGAGAGC	AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"Pseudoautosomal regions / PAR2"	11271	protein-coding gene	gene with protein product	"antagonist of FGF signaling"	300531	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.534T>C	chrX.hg19:g.155004067T>C		128.0	0.0		119.0	47.0	NM_005840	A8K0H8	Silent	SNP	ENST00000302805.2	hg19	CCDS14769.4																																																																																			.	.		0.582	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840		C	155004067	T	C	155004067	2	2	195	1	0	0	0	0	0	0	0	1	15122	1567	55	2		2	SPRY3	23	155004067	Silent	SNP	T	TCGA-DD-AADM-01A-11D-A40R-10	43089555	155004067	266493	182	28810										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12337226	12337226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gaaatatggcagaaaaattgCaactgcaagtataggtggca	11	5	0	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:12337226C>T	ENST00000358136.3	+	19	3711	c.3581C>T	c.(3580-3582)gCa>gTa	p.A1194V	VPS13D_ENST00000356315.4_Missense_Mutation_p.A1194V	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		AGAAAAATTGCAACTGCAAGT	0.423																																					p.A1194V		Atlas-SNP	.											.	VPS13D	316	.	0			c.C3581T						.						128	114	118					1																	12337226		2203	4300	6503	SO:0001583	missense	55187	exon19			AAATTGCAACTGC	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.3581C>T	chr1.hg19:g.12337226C>T	ENSP00000350854:p.Ala1194Val	114.0	0.0		82.0	30.0	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	hg19	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.3|23.3	4.403974|4.403974	0.83230|0.83230	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000356315;ENST00000358136|ENST00000011700	T;T|.	0.54071|.	0.59;0.59|.	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.73953|.	0.3653|.	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	P;P|.	0.40970|.	0.734;0.615|.	B;B|.	0.35470|.	0.203;0.1|.	T|.	0.69277|.	-0.5187|.	10|.	0.66056|.	D|.	0.02|.	.|.	20.2985|20.2985	0.98592|0.98592	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1194;1194|.	Q5THJ4-2;Q5THJ4|.	.;VP13D_HUMAN|.	V|X	1194|17	ENSP00000348666:A1194V;ENSP00000350854:A1194V|.	ENSP00000348666:A1194V|.	A|Q	+|+	2|1	0|0	VPS13D|VPS13D	12259813|12259813	1.000000|1.000000	0.71417|0.71417	0.766000|0.766000	0.31476|0.31476	0.998000|0.998000	0.95712|0.95712	7.487000|7.487000	0.81328|0.81328	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	GCA|CAA	.	.		0.423	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		T	12337226	C	T	12337226	3	4	196	1	0	0	0	0	1	0	0	0	17207	710	25	3	3651	3	VPS13D	1	12337226	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10		12337226	236913395	1	28811										
USP48	84196	hgsc.bcm.edu	37	chr1	22048144	22048144	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tgtacactgtgcaacataccCctttactgctgctttcagca	6	13	1	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:22048144C>A	ENST00000308271.9	-	13	2410	c.1762G>T	c.(1762-1764)Ggc>Tgc	p.G588C	USP48_ENST00000374732.3_Splice_Site_p.G127C|USP48_ENST00000529637.1_Splice_Site_p.G587C|USP48_ENST00000400301.1_Splice_Site_p.G588C	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	588	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		GCAACATACCCCTTTACTGCT	0.338																																					p.G588C		Atlas-SNP	.											.	USP48	91	.	0			c.G1762T						.						68	69	69					1																	22048144		2202	4300	6502	SO:0001630	splice_region_variant	84196	exon13			CATACCCCTTTAC	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.1763+1G>T	chr1.hg19:g.22048144C>A		152.0	0.0		133.0	65.0	NM_032236	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	hg19	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	C	14.98	2.698811	0.48307	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000374732;ENST00000529637	T;T;T;T	0.43688	0.94;0.94;0.97;0.94	5.47	3.6	0.41247	Peptidase C19, ubiquitin-specific peptidase, DUSP domain (1);	0.249817	0.49305	D	0.000160	T	0.53045	0.1772	L	0.54323	1.7	0.53005	D	0.999964	D;D;D;D;D;D	0.89917	1.0;0.991;0.996;0.996;0.995;0.994	D;P;P;P;P;P	0.65684	0.937;0.598;0.724;0.794;0.701;0.694	T	0.54536	-0.8279	10	0.72032	D	0.01	.	8.1685	0.31241	0.0:0.7616:0.0:0.2384	.	587;588;588;588;588;127	B7ZKS7;B7ZKS3;Q86UV5-3;Q86UV5-2;Q86UV5;Q86UV5-5	.;.;.;.;UBP48_HUMAN;.	C	588;588;127;587	ENSP00000383157:G588C;ENSP00000309262:G588C;ENSP00000363864:G127C;ENSP00000431949:G587C	ENSP00000309262:G588C	G	-	1	0	USP48	21920731	0.986000	0.35501	1.000000	0.80357	0.925000	0.55904	1.168000	0.31859	1.330000	0.45394	0.650000	0.86243	GGC	.	.		0.338	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	Missense_Mutation	A	22048144	C	A	22048144	5	1	196	1	0	0	0	0	0	0	1	0	17094	637	22	3	1405	3	USP48	1	22048144	Splice_Site	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	9710918	22048144	227202477	2	28812										
TSSK3	81629	hgsc.bcm.edu	37	chr1	32828424	32828424	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aaaagtggcaattaaagttaTagacaagatgggagggccag	13	4	0	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:32828424T>C	ENST00000373534.3	+	1	627	c.122T>C	c.(121-123)aTa>aCa	p.I41T	FAM229A_ENST00000432622.1_5'Flank|FAM229A_ENST00000415596.1_Intron	NM_052841.3	NP_443073.1	Q96PN8	TSSK3_HUMAN	testis-specific serine kinase 3	41	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|large_intestine(6)|lung(5)|skin(2)|stomach(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212)				ATTAAAGTTATAGACAAGATG	0.507																																					p.I41T		Atlas-SNP	.											.	TSSK3	22	.	0			c.T122C						.						116	124	121					1																	32828424		2203	4300	6503	SO:0001583	missense	81629	exon1			AAGTTATAGACAA	AF296450	CCDS362.1	1p35-p34	2008-02-05	2005-03-10	2005-03-12	ENSG00000162526	ENSG00000162526			15473	protein-coding gene	gene with protein product		607660	"serine/threonine kinase 22C (spermiogenesis associated)"	STK22C		11597141	Standard	NM_052841		Approved	SPOGA3	uc001bvf.3	Q96PN8	OTTHUMG00000007585	ENST00000373534.3:c.122T>C	chr1.hg19:g.32828424T>C	ENSP00000362634:p.Ile41Thr	214.0	0.0		163.0	35.0	NM_052841	Q5TEE5	Missense_Mutation	SNP	ENST00000373534.3	hg19	CCDS362.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.255596	0.59321	.	.	ENSG00000162526	ENST00000373534	T	0.28255	1.62	5.02	5.02	0.67125	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000011	T	0.55305	0.1912	M	0.85099	2.735	0.80722	D	1	D	0.65815	0.995	P	0.61722	0.893	T	0.63260	-0.6677	10	0.87932	D	0	.	12.4075	0.55449	0.0:0.0:0.0:1.0	.	41	Q96PN8	TSSK3_HUMAN	T	41	ENSP00000362634:I41T	ENSP00000362634:I41T	I	+	2	0	TSSK3	32601011	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.313000	0.72844	2.020000	0.59435	0.460000	0.39030	ATA	.	.		0.507	TSSK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020049.1			C	32828424	T	C	32828424	3	2	196	1	0	0	0	0	1	0	0	0	16685	1406	49	2	124	2	TSSK3	1	32828424	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	10780280	32828424	216422197	3	28813										
FAM40A	85369	hgsc.bcm.edu	37	chr1	110596387	110596387	+	Frame_Shift_Del	DEL	C	C	-													0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tatgaccgggcccacagcaaCcctgacttcctgccagtgga							TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:110596387delC	ENST00000369795.3	+	21	2389	c.2367delC	c.(2365-2367)aacfs	p.N789fs	STRIP1_ENST00000369796.1_Frame_Shift_Del_p.N694fs	NM_033088.3	NP_149079.2	Q5VSL9	STRP1_HUMAN	striatin interacting protein 1	789					cortical actin cytoskeleton organization (GO:0030866)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)											CCCACAGCAACCCTGACTTCC	0.582											OREG0013647	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N789fs		Atlas-Indel,Pindel	.											.	STRIP1	1	.	0			c.2366delA						.						53	51	52					1																	110596387		2203	4300	6503	SO:0001589	frameshift_variant	85369	exon21			.	AK027649	CCDS30798.1, CCDS59197.1	1p13.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000143093	ENSG00000143093			25916	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog A (yeast)"		"family with sequence similarity 40, member A"	FAM40A		11214970, 12588993, 22782902, 22298706, 18782753	Standard	NM_033088		Approved	FLJ14743, KIAA1761, FAR11A	uc001dza.2	Q5VSL9	OTTHUMG00000170607	ENST00000369795.3:c.2367delC	chr1.hg19:g.110596387delC	ENSP00000358810:p.Asn789fs	85.0	0.0	1428	56.0	25.0	NM_033088	Q0V925|Q5VSL8|Q658K2|Q6ZV31|Q8N598|Q96SN2|Q9C0A2	Frame_Shift_Del	DEL	ENST00000369795.3	hg19	CCDS30798.1																																																																																			.	.		0.582	STRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032213.1	NM_033088		-	110596387	C	-	110596387	7	5	196	1	0	1	0	1	0	0	0	0	5568	506	18	0	2449	0	FAM40A	1	110596387	Frame_Shift_Del	DEL	C	TCGA-DD-AADN-01A-11D-A40R-10	77767963	110596387	138654234	4	28814										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157494289	157494289	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cagtgaagctccagcaggtcCcccaccacagcctgggccct	10	18	0	1	rs143158449		TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:157494289C>T	ENST00000361835.3	-	10	2176	c.2019G>A	c.(2017-2019)ggG>ggA	p.G673G	FCRL5_ENST00000461387.1_5'Flank|FCRL5_ENST00000368190.3_Silent_p.G673G|FCRL5_ENST00000368191.3_Silent_p.G588G|FCRL5_ENST00000356953.4_Silent_p.G673G	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	673	Ig-like C2-type 7.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				CCAGCAGGTCCCCCACCACAG	0.552																																					p.G673G		Atlas-SNP	.											.	FCRL5	177	.	0			c.G2019A						.						47	53	51					1																	157494289		2203	4300	6503	SO:0001819	synonymous_variant	83416	exon10			CAGGTCCCCCACC	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.2019G>A	chr1.hg19:g.157494289C>T		356.0	0.0		209.0	52.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Silent	SNP	ENST00000361835.3	hg19	CCDS1165.1																																																																																			.	C|1.000;A|0.000		0.552	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		T	157494289	C	T	157494289	2	4	196	1	0	0	0	0	0	0	0	1	5806	610	22	3		3	FCRL5	1	157494289	Silent	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	46897902	157494289	91756332	5	28815										
ATP1A4	480	hgsc.bcm.edu	37	chr1	160136391	160136391	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gaacctggaggcggtggagaCgctgggctccacgtccacca	15	13	0	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:160136391C>T	ENST00000368081.4	+	8	1592	c.1121C>T	c.(1120-1122)aCg>aTg	p.T374M		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	374					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.T374M(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCGGTGGAGACGCTGGGCTCC	0.582																																					p.T374M		Atlas-SNP	.											ATP1A4,NS,carcinoma,0,1	ATP1A4	167	.	1	Substitution - Missense(1)	lung(1)	c.C1121T						.						126	104	112					1																	160136391		2203	4300	6503	SO:0001583	missense	480	exon8			TGGAGACGCTGGG	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1121C>T	chr1.hg19:g.160136391C>T	ENSP00000357060:p.Thr374Met	117.0	0.0		80.0	14.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	hg19	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.671393	0.88348	.	.	ENSG00000132681	ENST00000368081	D	0.92397	-3.03	4.35	4.35	0.52113	ATPase, P-type, cytoplasmic domain N (1);ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.97331	0.9127	H	0.97659	4.05	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98235	1.0485	10	0.87932	D	0	.	14.7749	0.69724	0.0:1.0:0.0:0.0	.	374	Q13733	AT1A4_HUMAN	M	374	ENSP00000357060:T374M	ENSP00000357060:T374M	T	+	2	0	ATP1A4	158403015	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.580000	0.82523	2.427000	0.82271	0.650000	0.86243	ACG	.	.		0.582	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		T	160136391	C	T	160136391	3	4	196	1	0	0	0	0	1	0	0	0	1131	536	19	1	1151	1	ATP1A4	1	160136391	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	2642102	160136391	89114230	6	28816										
DENND1B	163486	hgsc.bcm.edu	37	chr1	197479885	197479885	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ccagtcctgaagtagggtcaCtcacattgtcagcaccgagg	11	12	3	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:197479885C>T								CRB1 (32300 upstream) : DENND1B (41499 downstream)														p.S318T(1)|p.S242T(1)									AGTAGGGTCACTCACATTGTC	0.448																																					p.S678N		Atlas-SNP	.											.	DENND1B	108	.	2	Substitution - Missense(2)	lung(2)	c.G2033A						.						112	103	106					1																	197479885		2203	4300	6503	SO:0001628	intergenic_variant	163486	exon23			GGGTCACTCACAT																													chr1.hg19:g.197479885C>T		189.0	0.0		149.0	51.0	NM_001195215		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	C	7.124	0.578562	0.13686	.	.	ENSG00000213047	ENST00000391979;ENST00000542760;ENST00000450419	T	0.30714	1.52	5.31	0.248	0.15526	.	0.530450	0.15843	U	0.241930	T	0.19685	0.0473	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18999	-1.0319	10	0.27785	T	0.31	.	6.9673	0.24629	0.0:0.3846:0.0:0.6154	.	678	Q6P3S1-5	.	N	318;678;658	ENSP00000375839:S318N	ENSP00000375839:S318N	S	-	2	0	DENND1B	195746508	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.101000	0.10973	0.227000	0.20999	0.563000	0.77884	AGT	.	.	0	0.448									T	197479885	C	T	197479885	1	4	196	0	1	0	0	0	0	0	0	0	4429	565	20	3		3	DENND1B	1	197479885	IGR	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	37343494	197479885	51770736	7	28817										
LEFTY2	7044	hgsc.bcm.edu	37	chr1	226127110	226127110	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ctccagctggggctccccaaGcccggctggcgccccctgcg	13	20	0	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:226127110G>T	ENST00000366820.5	-	3	1036	c.688C>A	c.(688-690)Ctt>Att	p.L230I	LEFTY2_ENST00000420304.2_Missense_Mutation_p.L196I|RP4-559A3.6_ENST00000513672.1_RNA|LEFTY2_ENST00000474493.1_5'Flank	NM_003240.3	NP_003231.2	O00292	LFTY2_HUMAN	left-right determination factor 2	230					blood coagulation (GO:0007596)|cell growth (GO:0016049)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|platelet alpha granule lumen (GO:0031093)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16	Breast(184;0.197)					GGCTCCCCAAGCCCGGCTGGC	0.687																																					p.L230I	Colon(172;116 2643 9098 43333)	Atlas-SNP	.											.	LEFTY2	25	.	0			c.C688A						.						13	15	15					1																	226127110		2200	4291	6491	SO:0001583	missense	7044	exon3			CCCCAAGCCCGGC	U81523	CCDS1549.1, CCDS53479.1	1q42.1	2008-07-18	2004-11-17	2004-11-17	ENSG00000143768	ENSG00000143768			3122	protein-coding gene	gene with protein product	"transforming growth factor, beta-4 (endometrial bleeding-associated factor; LEFTY A)"	601877	"endometrial bleeding associated factor (left-right determination, factor A; transforming growth factor beta superfamily)"	TGFB4, EBAF		9153275	Standard	NM_001172425		Approved	LEFTA, LEFTYA	uc001hpt.2	O00292	OTTHUMG00000037441	ENST00000366820.5:c.688C>A	chr1.hg19:g.226127110G>T	ENSP00000355785:p.Leu230Ile	150.0	0.0		129.0	31.0	NM_003240	B3KNH4|B4E332|E9PDM4|O75611|Q5TE89|Q8NBQ9	Missense_Mutation	SNP	ENST00000366820.5	hg19	CCDS1549.1	.	.	.	.	.	.	.	.	.	.	g	6.850	0.526147	0.13066	.	.	ENSG00000143768	ENST00000420304;ENST00000366820	T;T	0.69040	-0.11;-0.37	4.47	0.109	0.14578	.	1.201010	0.05948	N	0.638279	T	0.54224	0.1845	L	0.32530	0.975	0.09310	N	1	B;B	0.30937	0.301;0.301	B;B	0.34931	0.192;0.192	T	0.45293	-0.9271	10	0.37606	T	0.19	.	4.3752	0.11267	0.0811:0.1495:0.5199:0.2495	.	196;230	E9PDM4;O00292	.;LFTY2_HUMAN	I	196;230	ENSP00000388009:L196I;ENSP00000355785:L230I	ENSP00000355785:L230I	L	-	1	0	LEFTY2	224193733	0.014000	0.17966	0.001000	0.08648	0.003000	0.03518	1.804000	0.38873	0.053000	0.16036	-0.314000	0.08810	CTT	.	.		0.687	LEFTY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091152.1	NM_003240		T	226127110	G	T	226127110	3	4	196	1	0	0	0	0	1	0	0	0	8725	971	34	3	420	3	LEFTY2	1	226127110	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	28647225	226127110	23123511	8	28818										
LYST	1130	hgsc.bcm.edu	37	chr1	235897870	235897870	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aacttcaaagcattcataagCagttctgctgtgcctagctc	7	11	3	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:235897870C>A	ENST00000389794.3	-	32	8622	c.8448G>T	c.(8446-8448)ctG>ctT	p.L2816L	LYST_ENST00000389793.2_Silent_p.L2816L|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2816					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.L2816L(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			CATTCATAAGCAGTTCTGCTG	0.383																																					p.L2816L		Atlas-SNP	.											LYST,colon,carcinoma,-1,1	LYST	370	.	1	Substitution - coding silent(1)	ovary(1)	c.G8448T						.						237	205	216					1																	235897870		2203	4300	6503	SO:0001819	synonymous_variant	1130	exon32			CATAAGCAGTTCT	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.8448G>T	chr1.hg19:g.235897870C>A		120.0	0.0		85.0	15.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.383	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235897870	C	A	235897870	2	1	196	1	0	0	0	0	0	0	0	1	9137	697	25	3		3	LYST	1	235897870	Silent	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	9770760	235897870	13352751	9	28819										
RYR2	6262	hgsc.bcm.edu	37	chr1	237889575	237889575	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	catttttatttctttcagaaGtctaaacgtgtgggtcggag	10	6	3	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:237889575G>A	ENST00000366574.2	+	75	11009	c.10692G>A	c.(10690-10692)aaG>aaA	p.K3564K	RYR2_ENST00000542537.1_Silent_p.K3548K|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Silent_p.K3562K	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3564					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TCTTTCAGAAGTCTAAACGTG	0.313																																					p.K3564K		Atlas-SNP	.											.	RYR2	1273	.	0			c.G10692A						.						56	54	55					1																	237889575		1811	4068	5879	SO:0001819	synonymous_variant	6262	exon75			TCAGAAGTCTAAA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.10692G>A	chr1.hg19:g.237889575G>A		358.0	0.0		252.0	32.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.313	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237889575	G	A	237889575	2	1	196	1	0	0	0	0	0	0	0	1	13784	1020	36	3		3	RYR2	1	237889575	Silent	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	1991705	237889575	11361046	10	28820										
TRIM58	25893	hgsc.bcm.edu	37	chr1	248039229	248039229	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aaagctggatcccgccacggCgcacccgagtctgctcttga	11	15	2	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr1:248039229C>A	ENST00000366481.3	+	6	947	c.899C>A	c.(898-900)gCg>gAg	p.A300E	OR2W3_ENST00000537741.1_5'UTR	NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	300	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			CCCGCCACGGCGCACCCGAGT	0.552																																					p.A300E		Atlas-SNP	.											TRIM58,NS,carcinoma,0,1	TRIM58	143	.	0			c.C899A						.						62	60	61					1																	248039229		2203	4300	6503	SO:0001583	missense	25893	exon6			CCACGGCGCACCC	AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	24150	protein-coding gene	gene with protein product			"tripartite motif-containing 58"				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.899C>A	chr1.hg19:g.248039229C>A	ENSP00000355437:p.Ala300Glu	83.0	0.0		52.0	11.0	NM_015431	Q6B0H9	Missense_Mutation	SNP	ENST00000366481.3	hg19	CCDS1636.1	.	.	.	.	.	.	.	.	.	.	C	15.30	2.792603	0.50102	.	.	ENSG00000162722	ENST00000366481	T	0.39406	1.08	3.95	3.03	0.35002	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.000000	0.56097	D	0.000026	T	0.73241	0.3562	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80870	-0.1189	10	0.87932	D	0	.	11.2344	0.48931	0.1846:0.8154:0.0:0.0	.	300	Q8NG06	TRI58_HUMAN	E	300	ENSP00000355437:A300E	ENSP00000355437:A300E	A	+	2	0	TRIM58	246105852	0.995000	0.38212	0.197000	0.23402	0.100000	0.18952	3.349000	0.52217	1.250000	0.43966	0.650000	0.86243	GCG	.	.		0.552	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431		A	248039229	C	A	248039229	3	1	196	1	0	0	0	0	1	0	0	0	16546	768	27	1	921	1	TRIM58	1	248039229	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	10149654	248039229	1211392	11	28821										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1926369	1926369	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tggcaaacactctcgaccggGggctcaactgctcctccagc	10	16	2	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr2:1926369G>T	ENST00000399161.2	-	10	1919	c.1172C>A	c.(1171-1173)cCc>cAc	p.P391H	MYT1L_ENST00000428368.2_Missense_Mutation_p.P391H	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	391					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TCTCGACCGGGGGCTCAACTG	0.597																																					p.P391H		Atlas-SNP	.											.	MYT1L	241	.	0			c.C1172A						.						38	40	39					2																	1926369		2121	4240	6361	SO:0001583	missense	23040	exon10			GACCGGGGGCTCA	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.1172C>A	chr2.hg19:g.1926369G>T	ENSP00000382114:p.Pro391His	74.0	0.0		70.0	9.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	G	18.39	3.613197	0.66672	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.61392	0.12;0.11	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.69735	0.3144	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.69587	-0.5105	10	0.59425	D	0.04	-34.5834	20.4387	0.99107	0.0:0.0:1.0:0.0	.	391;391	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	H	391;339;391	ENSP00000382114:P391H;ENSP00000396103:P391H	ENSP00000295067:P339H	P	-	2	0	MYT1L	1905376	1.000000	0.71417	0.863000	0.33907	0.113000	0.19764	9.781000	0.99029	2.836000	0.97738	0.655000	0.94253	CCC	.	.		0.597	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		T	1926369	G	T	1926369	3	4	196	1	0	0	0	0	1	0	0	0	10116	1232	43	3	2446	3	MYT1L	2	1926369	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10		1926369	241273004	12	28822										
CENPO	79172	hgsc.bcm.edu	37	chr2	25038488	25038488	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aaccactccggatacatcacCattcagtcccagtcttcatt	4	15	4	0	rs547353937		TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr2:25038488C>T	ENST00000380834.2	+	5	882	c.457C>T	c.(457-459)Cat>Tat	p.H153Y	CENPO_ENST00000473706.1_Missense_Mutation_p.H147Y|CENPO_ENST00000260662.1_Missense_Mutation_p.H153Y			Q9BU64	CENPO_HUMAN	centromere protein O	153					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					GATACATCACCATTCAGTCCC	0.463																																					p.H153Y		Atlas-SNP	.											.	CENPO	18	.	0			c.C457T						.						176	168	171					2																	25038488		2203	4300	6503	SO:0001583	missense	79172	exon5			CATCACCATTCAG	AK027859	CCDS1714.1, CCDS56113.1	2p23.3	2013-11-05			ENSG00000138092	ENSG00000138092			28152	protein-coding gene	gene with protein product		611504				16622420, 16622419	Standard	NM_024322		Approved	MGC11266, CENP-O	uc002rfp.2	Q9BU64	OTTHUMG00000125525	ENST00000380834.2:c.457C>T	chr2.hg19:g.25038488C>T	ENSP00000370214:p.His153Tyr	183.0	0.0		135.0	60.0	NM_024322	B2RDC0|D6W536|Q53T55|Q96JV3	Missense_Mutation	SNP	ENST00000380834.2	hg19	CCDS1714.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.437524	0.83885	.	.	ENSG00000138092	ENST00000380834;ENST00000473706;ENST00000260662	T;T;T	0.78003	-1.14;-1.13;-1.14	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.88941	0.6574	M	0.81802	2.56	0.52501	D	0.999959	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.89916	0.4055	10	0.87932	D	0	-16.1442	18.655	0.91450	0.0:1.0:0.0:0.0	.	147;153	Q9BU64-2;Q9BU64	.;CENPO_HUMAN	Y	153;147;153	ENSP00000370214:H153Y;ENSP00000417787:H147Y;ENSP00000260662:H153Y	ENSP00000260662:H153Y	H	+	1	0	CENPO	24891992	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.859000	0.62954	2.737000	0.93849	0.650000	0.86243	CAT	.	.		0.463	CENPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246856.2	NM_024322		T	25038488	C	T	25038488	3	4	196	1	0	0	0	0	1	0	0	0	3241	594	21	3	471	3	CENPO	2	25038488	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	23112119	25038488	218160885	13	28823										
HNRPLL	92906	hgsc.bcm.edu	37	chr2	38810997	38810997	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ggatattcaaccattgcttgTatcccatttctcttgaatat	5	9	2	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr2:38810997T>C	ENST00000449105.3	-	4	957	c.618A>G	c.(616-618)atA>atG	p.I206M	HNRNPLL_ENST00000378915.3_Missense_Mutation_p.I206M|HNRNPLL_ENST00000409636.1_Missense_Mutation_p.I201M|HNRNPLL_ENST00000608859.1_Missense_Mutation_p.I206M|HNRNPLL_ENST00000409328.1_Missense_Mutation_p.I206M|HNRNPLL_ENST00000410076.1_Missense_Mutation_p.I201M|HNRNPLL_ENST00000358367.4_Missense_Mutation_p.I206M			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	206	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										CCATTGCTTGTATCCCATTTC	0.313																																					p.I206M		Atlas-SNP	.											.	HNRPLL	19	.	0			c.A618G						.						64	63	63					2																	38810997		2202	4294	6496	SO:0001583	missense	92906	exon4			TGCTTGTATCCCA	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"RNA binding motif (RRM) containing"	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.618A>G	chr2.hg19:g.38810997T>C	ENSP00000390625:p.Ile206Met	385.0	0.0		356.0	72.0	NM_138394	Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Missense_Mutation	SNP	ENST00000449105.3	hg19		.	.	.	.	.	.	.	.	.	.	T	19.63	3.862695	0.71949	.	.	ENSG00000143889	ENST00000449105;ENST00000409636;ENST00000378915;ENST00000409328;ENST00000358367;ENST00000410076;ENST00000425682	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.53367	0.1792	L	0.28115	0.83	0.47183	D	0.999347	P;P	0.40332	0.713;0.713	P;P	0.45406	0.479;0.479	T	0.59484	-0.7446	9	0.72032	D	0.01	.	15.4605	0.75353	0.0:0.0:0.0:1.0	.	201;206	C9J9G0;D6W592	.;.	M	206;201;206;206;206;201;145	.	ENSP00000351136:I206M	I	-	3	3	HNRPLL	38664501	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.928000	0.48908	2.101000	0.63845	0.460000	0.39030	ATA	.	.		0.313	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394		C	38810997	T	C	38810997	3	2	196	1	0	0	0	0	1	0	0	0	7286	1628	57	2	1050	2	HNRPLL	2	38810997	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	13772509	38810997	204388376	14	28824										
TTL	150465	hgsc.bcm.edu	37	chr2	113278000	113278000	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aacggtgcccctgcatgtgcTcagtaagcctgcacgtcatt	10	13	2	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr2:113278000T>A	ENST00000233336.6	+	6	1208	c.1017T>A	c.(1015-1017)gcT>gcA	p.A339A		NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	339	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)			breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		CTGCATGTGCTCAGTAAGCCT	0.512			T	ETV6	ALL																																p.A339A		Atlas-SNP	.		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	.	TTL	27	.	0			c.T1017A						.						102	91	95					2																	113278000		2203	4300	6503	SO:0001819	synonymous_variant	150465	exon6			ATGTGCTCAGTAA		CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.1017T>A	chr2.hg19:g.113278000T>A		103.0	0.0		69.0	22.0	NM_153712	Q585T3|Q7Z302|Q8N426	Silent	SNP	ENST00000233336.6	hg19	CCDS2096.1																																																																																			.	.		0.512	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254085.2	NM_153712		A	113278000	T	A	113278000	2	1	196	1	0	0	0	0	0	0	0	1	16736	1538	54	4		4	TTL	2	113278000	Silent	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	74467003	113278000	129921373	15	28825										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141072505	141072505	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	atgacaatgaaatatttaccTagaactgatggtacgcaagt	8	6	0	4			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr2:141072505T>A	ENST00000389484.3	-	83	13775	c.12804A>T	c.(12802-12804)ctA>ctT	p.L4268L		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4268	EGF-like 18. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AATATTTACCTAGAACTGATG	0.353										TSP Lung(27;0.18)																											p.L4268L	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A12804T						.						106	103	104					2																	141072505		2203	4300	6503	SO:0001630	splice_region_variant	53353	exon83			TTTACCTAGAACT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12805+1A>T	chr2.hg19:g.141072505T>A		107.0	0.0		46.0	12.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	0.463	-0.888134	0.02511	.	.	ENSG00000168702	ENST00000437977	.	.	.	5.9	-1.52	0.08637	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.6556	0.02781	0.1312:0.2954:0.1706:0.4028	.	.	.	.	L	500	.	.	X	-	2	0	LRP1B	140788975	0.276000	0.24211	0.864000	0.33941	0.143000	0.21401	-0.357000	0.07651	-0.135000	0.11495	0.533000	0.62120	TAG	.	.		0.353	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Silent	A	141072505	T	A	141072505	5	1	196	1	0	0	0	0	0	0	1	0	8964	1536	53	4	1031	4	LRP1B	2	141072505	Splice_Site	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	27794505	141072505	102126868	16	28826										
SESTD1	91404	hgsc.bcm.edu	37	chr2	179979934	179979935	+	Frame_Shift_Ins	INS	-	-	A													0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	agtgcagcgcaaagattggcINSataacacaactgtggcctgt							TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr2:179979934_179979935insA	ENST00000428443.3	-	16	2012_2013	c.1696_1697insT	c.(1696-1698)tgcfs	p.C566fs		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	566							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			CAAAGATTGGCATAACACAACT	0.391																																					p.C566fs		Atlas-INDEL	.											SESTD1,colon,carcinoma,0,1	SESTD1	66	.	0			c.1697_1698insT						.																																			SO:0001589	frameshift_variant	91404	exon16			.	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.1697dupT	chr2.hg19:g.179979935_179979935dupA	ENSP00000415332:p.Cys566fs	90.0	0.0		76.0	10.0	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Frame_Shift_Ins	INS	ENST00000428443.3	hg19	CCDS33338.1																																																																																			.	.		0.391	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		A	179979935	-	A	179979934	7	5	196	1	0	1	1	0	0	0	0	0	14142	710	25	0	405	0	SESTD1	2	179979934	Frame_Shift_Ins	INS	-	TCGA-DD-AADN-01A-11D-A40R-10	38907429	179979934	63219439	17	28827										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187618658	187618673	+	Splice_Site	DEL	TTACATACCTTTTTAG	TTACATACCTTTTTAG	-													0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tattttttacatacctttttAggtgcttgggtaaatcatgg					rs17855085		TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	TTACATACCTTTTTAG	TTACATACCTTTTTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr2:187618658_187618673delTTACATACCTTTTTAG	ENST00000304698.5	+	6	1098_1112	c.895_909delTTACATACCTTTTTAG	c.(895-909)ttacatacctttttadel	p.LHTFL299fs		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	299						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						ATACCTTTTTAGGTGCTTGGGTAAATCATGGTCGGG	0.37																																					.		Atlas-Indel,Pindel	.											.	FAM171B	146	.	0			.						.																																			SO:0001630	splice_region_variant	165215	.			.	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.896-1TTACATACCTTTTTAG>-	chr2.hg19:g.187618658_187618673delTTACATACCTTTTTAG		98.0	0.0		58.0	18.0	.	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Splice_Site	DEL	ENST00000304698.5	hg19	CCDS33347.1																																																																																			.	.		0.37	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	Frame_Shift_Del	-	187618673	TTACATACCTTTTTAG	-	187618658	8	5	196	1	0	1	0	1	0	0	1	0	5496	434	15	0	916	0	FAM171B	2	187618658	Splice_Site	DEL	TTACATACCTTTTTAG	TCGA-DD-AADN-01A-11D-A40R-10	7638724	187618658	55580715	18	28828										
TTLL3	26140	hgsc.bcm.edu	37	chr3	9876555	9876555	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tccctcccaccgaaccttgaTttcaaggtggcacccagcat	7	16	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr3:9876555T>C	ENST00000547186.1	+	12	2103	c.1887T>C	c.(1885-1887)gaT>gaC	p.D629D	TTLL3_ENST00000383827.1_3'UTR|TTLL3_ENST00000397241.1_3'UTR|TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000430793.1_Silent_p.D417D|TTLL3_ENST00000426895.4_Silent_p.D772D|ARPC4-TTLL3_ENST00000397256.1_3'UTR	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	629					axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					CGAACCTTGATTTCAAGGTGG	0.597																																					p.D772D		Atlas-SNP	.											.	TTLL3	51	.	0			c.T2316C						.						96	96	96					3																	9876555		2203	4300	6503	SO:0001819	synonymous_variant	26140	exon12			CCTTGATTTCAAG		CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"Tubulin tyrosine ligase-like family"	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.1887T>C	chr3.hg19:g.9876555T>C		108.0	0.0		105.0	53.0	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Silent	SNP	ENST00000547186.1	hg19																																																																																				.	.		0.597	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2		C	9876555	T	C	9876555	2	2	196	1	0	0	0	0	0	0	0	1	16743	1490	52	2		2	TTLL3	3	9876555	Silent	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10		9876555	188145875	19	28829										
SLC4A7	9497	hgsc.bcm.edu	37	chr3	27436010	27436010	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ggcaataaagaaattttaccTttaggactgaagtcatgaac	8	6	1	3			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr3:27436010T>A	ENST00000295736.5	-	20	3159	c.3089A>T	c.(3088-3090)aAg>aTg	p.K1030M	SLC4A7_ENST00000446700.1_Splice_Site_p.K1022M|SLC4A7_ENST00000428386.1_Splice_Site_p.K906M|SLC4A7_ENST00000454389.1_Splice_Site_p.K1039M|SLC4A7_ENST00000437179.1_Splice_Site_p.K911M|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000435667.2_Splice_Site_p.K915M|SLC4A7_ENST00000445684.1_Splice_Site_p.K1026M|SLC4A7_ENST00000388777.4_Splice_Site_p.K580M|SLC4A7_ENST00000455077.1_Splice_Site_p.K911M|SLC4A7_ENST00000440156.1_Splice_Site_p.K1026M	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	1030					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	AAATTTTACCTTTAGGACTGA	0.323																																					p.K1030M		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A3089T						.						48	51	50					3																	27436010		2203	4300	6503	SO:0001630	splice_region_variant	9497	exon20			TTTACCTTTAGGA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"Solute carriers"	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.3090+1A>T	chr3.hg19:g.27436010T>A		124.0	0.0		115.0	61.0	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	hg19	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.373635	0.82573	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000428179	T;T;T;T;T;T;T;T;T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42	5.77	4.62	0.57501	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.89326	0.6683	M	0.83774	2.66	0.80722	D	1	D;D;D;D;D;P;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;0.725;0.999;1.0;0.999	D;D;D;D;D;P;D;D;D	0.97110	0.996;0.981;0.996;1.0;0.996;0.452;0.978;0.996;0.987	D	0.89670	0.3883	10	0.66056	D	0.02	.	11.6812	0.51458	0.0:0.0691:0.0:0.9309	.	1026;911;1022;1026;1039;580;906;1030;911	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	M	581;1030;906;1039;1026;911;1022;911;1026;915;580;926	ENSP00000411031:K581M;ENSP00000295736:K1030M;ENSP00000416368:K906M;ENSP00000390394:K1039M;ENSP00000414797:K1026M;ENSP00000394252:K911M;ENSP00000406605:K1022M;ENSP00000407382:K911M;ENSP00000406804:K1026M;ENSP00000395336:K915M;ENSP00000373429:K580M;ENSP00000388703:K926M	ENSP00000295736:K1030M	K	-	2	0	SLC4A7	27411014	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	8.040000	0.89188	1.019000	0.39547	0.482000	0.46254	AAG	.	.		0.323	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	Missense_Mutation	A	27436010	T	A	27436010	5	1	196	1	0	0	0	0	0	0	1	0	14673	1623	56	4	579	4	SLC4A7	3	27436010	Splice_Site	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	17559455	27436010	170586420	20	28830										
ZNF860	344787	hgsc.bcm.edu	37	chr3	32030993	32030994	+	In_Frame_Ins	INS	-	-	TGATCGAAGGCATCCTGGAAACAAGCCTATCAAAGATCAGCTTGG													0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	actggtagcaccgacagataINStgatcgaaggcatcctggaa					rs187640039		TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr3:32030993_32030994insTGATCGAAGGCATCCTGGAAACAAGCCTATCAAAGATCAGCTTGG	ENST00000360311.4	+	2	971_972	c.422_423insTGATCGAAGGCATCCTGGAAACAAGCCTATCAAAGATCAGCTTGG	c.(421-426)tatgat>taTGATCGAAGGCATCCTGGAAACAAGCCTATCAAAGATCAGCTTGGtgat	p.142_143insRRHPGNKPIKDQLGD		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	142					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						ACCGACAGATATGATCGAAGGC	0.396																																					p.Y141delinsYDRRHPGNKPIKDQLG		Pindel	.											.	ZNF860	96	.	0			c.422_423insTGATCGAAGGCATCCTGGAAACAAGCCTATCAAAGATCAGCTTGG						.																																			SO:0001652	inframe_insertion	344787	exon2			.	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"Zinc fingers, C2H2-type", "-"	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.423_467dupTGATCGAAGGCATCCTGGAAACAAGCCTATCAAAGATCAGCTTGG	chr3.hg19:g.32030993_32030994insTGATCGAAGGCATCCTGGAAACAAGCCTATCAAAGATCAGCTTGG	ENSP00000373274:p.Asp142_Arg143insArgArgHisProGlyAsnLysProIleLysAspGlnLeuGlyAsp	287.0	0.0		388.0	25.0	NM_001137674	B4DFA4	In_Frame_Ins	INS	ENST00000360311.4	hg19	CCDS46784.1																																																																																			.	.		0.396	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1			TGATCGAAGGCATCCTGGAAACAAGCCTATCAAAGATCAGCTTGG	32030994	-	TGATCGAAGGCATCCTGGAAACAAGCCTATCAAAGATCAGCTTGG	32030993	7	5	196	1	0	1	1	0	0	0	0	0	18209	449	16	0	424	0	ZNF860	3	32030993	In_Frame_Ins	INS	-	TCGA-DD-AADN-01A-11D-A40R-10	4594983	32030993	165991437	21	28831										
TGM4	7047	hgsc.bcm.edu	37	chr3	44926965	44926965	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cagcccctacaatcctaccaCcaactgaaactggaattcag	5	15	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr3:44926965C>A	ENST00000296125.4	+	2	236	c.168C>A	c.(166-168)caC>caA	p.H56Q		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	56					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	AATCCTACCACCAACTGAAAC	0.572																																					p.H56Q		Atlas-SNP	.											.	TGM4	82	.	0			c.C168A						.						59	60	60					3																	44926965		2203	4300	6503	SO:0001583	missense	7047	exon2			CTACCACCAACTG	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"Transglutaminases"	11780	protein-coding gene	gene with protein product		600585	"transglutaminase 4 (prostate)"			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.168C>A	chr3.hg19:g.44926965C>A	ENSP00000296125:p.His56Gln	163.0	0.0		139.0	71.0	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	hg19	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	C	8.777	0.927258	0.18056	.	.	ENSG00000163810	ENST00000296125	D	0.86164	-2.08	2.99	-1.15	0.09709	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	0.138996	0.28279	U	0.015922	T	0.73040	0.3536	L	0.27053	0.805	0.09310	N	1	B;B	0.15141	0.012;0.01	B;B	0.06405	0.002;0.002	T	0.60762	-0.7199	10	0.59425	D	0.04	.	3.2703	0.06879	0.0:0.3022:0.3775:0.3203	.	56;56	P49221;B4YUQ1	TGM4_HUMAN;.	Q	56	ENSP00000296125:H56Q	ENSP00000296125:H56Q	H	+	3	2	TGM4	44901969	0.001000	0.12720	0.000000	0.03702	0.068000	0.16541	-0.269000	0.08596	-0.125000	0.11703	0.467000	0.42956	CAC	.	.		0.572	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		A	44926965	C	A	44926965	3	1	196	1	0	0	0	0	1	0	0	0	15847	506	18	3	174	3	TGM4	3	44926965	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	12895972	44926965	153095465	22	28832										
GRAMD1C	54762	hgsc.bcm.edu	37	chr3	113588361	113588361	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tttattgttgcagatttcaaGttccacctataaagacagga	7	7	1	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr3:113588361G>T	ENST00000358160.4	+	3	674	c.182G>T	c.(181-183)aGt>aTt	p.S61I	GRAMD1C_ENST00000452134.2_5'UTR|GRAMD1C_ENST00000479212.1_3'UTR	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	61						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						CAGATTTCAAGTTCCACCTAT	0.303																																					p.S61I		Atlas-SNP	.											.	GRAMD1C	71	.	0			c.G182T						.						73	79	77					3																	113588361		2203	4294	6497	SO:0001583	missense	54762	exon3			TTTCAAGTTCCAC		CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.182G>T	chr3.hg19:g.113588361G>T	ENSP00000350881:p.Ser61Ile	477.0	0.0		455.0	35.0	NM_017577	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Missense_Mutation	SNP	ENST00000358160.4	hg19	CCDS33826.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.600393	0.46423	.	.	ENSG00000178075	ENST00000358160	T	0.36520	1.25	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000009	T	0.52821	0.1758	M	0.74467	2.265	0.80722	D	1	D	0.57257	0.979	P	0.52267	0.694	T	0.58200	-0.7678	10	0.59425	D	0.04	.	17.6656	0.88202	0.0:0.0:1.0:0.0	.	61	Q8IYS0	GRM1C_HUMAN	I	61	ENSP00000350881:S61I	ENSP00000350881:S61I	S	+	2	0	GRAMD1C	115071051	1.000000	0.71417	1.000000	0.80357	0.618000	0.37518	3.732000	0.55021	2.462000	0.83206	0.655000	0.94253	AGT	.	.		0.303	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577		T	113588361	G	T	113588361	3	4	196	1	0	0	0	0	1	0	0	0	6758	1029	36	3	192	3	GRAMD1C	3	113588361	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	68661396	113588361	84434069	23	28833										
GATA2	2624	hgsc.bcm.edu	37	chr3	128204630	128204630	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gctggaggccggtccccccaGgaagcctccggggtggaaga	17	13	0	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr3:128204630G>A	ENST00000341105.2	-	3	1142	c.811C>T	c.(811-813)Ctg>Ttg	p.L271L	GATA2_ENST00000430265.2_Silent_p.L271L|GATA2_ENST00000487848.1_Silent_p.L271L	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	271					blood coagulation (GO:0007596)|cell differentiation in hindbrain (GO:0021533)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|definitive hemopoiesis (GO:0060216)|embryonic placenta development (GO:0001892)|eosinophil fate commitment (GO:0035854)|GABAergic neuron differentiation (GO:0097154)|homeostasis of number of cells within a tissue (GO:0048873)|inner ear morphogenesis (GO:0042472)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of phagocytosis (GO:0050766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of forebrain neuron differentiation (GO:2000977)|regulation of histone acetylation (GO:0035065)|semicircular canal development (GO:0060872)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|ventral spinal cord interneuron differentiation (GO:0021514)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(58)|kidney(2)|large_intestine(3)|lung(9)|prostate(3)|skin(1)|urinary_tract(1)	79				GBM - Glioblastoma multiforme(114;0.173)		GGTCCCCCCAGGAAGCCTCCG	0.652			Mis		AML(CML blast transformation)																																p.L271L		Atlas-SNP	.		Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	.	GATA2	122	.	0			c.C811T						.						35	40	38					3																	128204630		2202	4300	6502	SO:0001819	synonymous_variant	2624	exon3			CCCCCAGGAAGCC	AF169253	CCDS3049.1, CCDS46903.1	3q21	2014-09-17	2001-11-28		ENSG00000179348	ENSG00000179348		"GATA zinc finger domain containing"	4171	protein-coding gene	gene with protein product		137295	"GATA-binding protein 2"			1714909	Standard	NM_032638		Approved	NFE1B	uc003eko.2	P23769	OTTHUMG00000159689	ENST00000341105.2:c.811C>T	chr3.hg19:g.128204630G>A		71.0	0.0		42.0	16.0	NM_001145662	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Silent	SNP	ENST00000341105.2	hg19	CCDS3049.1																																																																																			.	.		0.652	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638		A	128204630	G	A	128204630	2	1	196	1	0	0	0	0	0	0	0	1	6262	991	35	3		3	GATA2	3	128204630	Silent	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	14616269	128204630	69817800	24	28834										
RASA2	5922	hgsc.bcm.edu	37	chr3	141289753	141289753	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tcacttatatttttactttaGgtacttgctacagccaagag	6	8	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr3:141289753G>A	ENST00000452898.1	+	10	898		c.e10-1		RASA2_ENST00000286364.3_Splice_Site	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2						intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						TTTTACTTTAGGTACTTGCTA	0.343																																					.		Atlas-SNP	.											.	RASA2	169	.	0			c.864-1G>A						.						41	42	42					3																	141289753		2203	4300	6503	SO:0001630	splice_region_variant	5922	exon10			ACTTTAGGTACTT	AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"Pleckstrin homology (PH) domain containing"	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.864-1G>A	chr3.hg19:g.141289753G>A		142.0	0.0		103.0	41.0	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Splice_Site	SNP	ENST00000452898.1	hg19		.	.	.	.	.	.	.	.	.	.	G	22.2	4.256904	0.80246	.	.	ENSG00000155903	ENST00000286364;ENST00000452898	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2936	0.94112	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RASA2	142772443	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	7.312000	0.78968	2.580000	0.87095	0.650000	0.86243	.	.	.		0.343	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506	Intron	A	141289753	G	A	141289753	5	1	196	1	0	0	0	0	0	0	1	0	13076	1014	35	3	901	3	RASA2	3	141289753	Splice_Site	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	13085123	141289753	56732677	25	28835										
GRK7	131890	hgsc.bcm.edu	37	chr3	141499234	141499234	+	Frame_Shift_Del	DEL	A	A	-													0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aggtatgtgccgtccaggtgAaaaacactgggaagatgtat							TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr3:141499234delA	ENST00000264952.2	+	2	768	c.631delA	c.(631-633)aaafs	p.K211fs		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	211	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						CGTCCAGGTGAAAAACACTGG	0.458																																					p.V210fs		Atlas-Indel,Pindel	.											.	GRK7	65	.	0			c.630delG						.						54	55	54					3																	141499234		2203	4300	6503	SO:0001589	frameshift_variant	131890	exon2			.		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.631delA	chr3.hg19:g.141499234delA	ENSP00000264952:p.Lys211fs	161.0	0.0		135.0	41.0	NM_139209		Frame_Shift_Del	DEL	ENST00000264952.2	hg19	CCDS3120.1																																																																																			.	.		0.458	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209		-	141499234	A	-	141499234	7	5	196	1	0	1	0	1	0	0	0	0	6803	247	9	0	637	0	GRK7	3	141499234	Frame_Shift_Del	DEL	A	TCGA-DD-AADN-01A-11D-A40R-10	209481	141499234	56523196	26	28836										
PLSCR1	5359	hgsc.bcm.edu	37	chr3	146234891	146234891	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	agcgtctgtaaatgcctctcTcaaaattccagtccagtgct	7	12	3	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr3:146234891T>A	ENST00000342435.4	-	8	1212	c.802A>T	c.(802-804)Aga>Tga	p.R268*	PLSCR1_ENST00000484560.1_5'UTR|PLSCR1_ENST00000448787.2_Nonsense_Mutation_p.R187*|PLSCR1_ENST00000487389.1_Nonsense_Mutation_p.R261*|PLSCR1_ENST00000448205.1_5'UTR	NM_021105.2	NP_066928.1	O15162	PLS1_HUMAN	phospholipid scramblase 1	268					acute-phase response (GO:0006953)|apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|negative regulation of viral genome replication (GO:0045071)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid scrambling (GO:0017121)|platelet activation (GO:0030168)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of gene expression (GO:0010628)|positive regulation of innate immune response (GO:0045089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|regulation of mast cell activation (GO:0033003)|response to interferon-beta (GO:0035456)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|epidermal growth factor receptor binding (GO:0005154)|phospholipid scramblase activity (GO:0017128)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15						AATGCCTCTCTCAAAATTCCA	0.348																																					p.R268X		Atlas-SNP	.											.	PLSCR1	35	.	0			c.A802T						.						98	97	97					3																	146234891		2203	4300	6503	SO:0001587	stop_gained	5359	exon8			CCTCTCTCAAAAT	AF098642	CCDS3135.1	3q23	2004-02-27			ENSG00000188313	ENSG00000188313			9092	protein-coding gene	gene with protein product		604170				9218461	Standard	NM_021105		Approved	MMTRA1B	uc003evx.4	O15162	OTTHUMG00000159427	ENST00000342435.4:c.802A>T	chr3.hg19:g.146234891T>A	ENSP00000345494:p.Arg268*	285.0	0.0		180.0	70.0	NM_021105	B2R8H8|B4DTE8	Nonsense_Mutation	SNP	ENST00000342435.4	hg19	CCDS3135.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	33|33	5.279612|5.279612	0.95489|0.95489	.|.	.|.	ENSG00000188313|ENSG00000188313	ENST00000342435;ENST00000487389;ENST00000448787;ENST00000462666|ENST00000483300	.|.	.|.	.|.	4.84|4.84	4.84|4.84	0.62591|0.62591	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.21740|0.21740	N|N	0.999567|0.999567	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.02654|.	T|.	1|.	.|.	11.9267|11.9267	0.52823|0.52823	0.0:0.0:0.145:0.855|0.0:0.0:0.145:0.855	.|.	.|.	.|.	.|.	X|C	268;261;187;244|134	.|.	ENSP00000345494:R268X|.	R|X	-|-	1|3	2|0	PLSCR1|PLSCR1	147717581|147717581	0.004000|0.004000	0.15560|0.15560	0.016000|0.016000	0.15963|0.15963	0.577000|0.577000	0.36160|0.36160	1.475000|1.475000	0.35409|0.35409	1.938000|1.938000	0.56188|0.56188	0.454000|0.454000	0.30748|0.30748	AGA|TGA	.	.		0.348	PLSCR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355257.2	NM_021105		A	146234891	T	A	146234891	4	1	196	1	0	0	0	0	0	1	0	0	12118	1559	54	4	162	4	PLSCR1	3	146234891	Nonsense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	4735657	146234891	51787539	27	28837										
ZIC4	84107	hgsc.bcm.edu	37	chr3	147113964	147113964	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	agctcctgtttgatgggctgGcgcatgtagcggaagaaagc	15	8	0	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr3:147113964G>T	ENST00000383075.3	-	3	875	c.363C>A	c.(361-363)cgC>cgA	p.R121R	ZIC4_ENST00000473123.1_Silent_p.R121R|ZIC4_ENST00000484399.1_Silent_p.R121R|ZIC4_ENST00000525172.2_Silent_p.R171R|ZIC4_ENST00000491672.1_Intron|ZIC4_ENST00000425731.3_Silent_p.R159R	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	121						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						TGATGGGCTGGCGCATGTAGC	0.657																																					p.R171R		Atlas-SNP	.											.	ZIC4	174	.	0			c.C513A						.						34	39	37					3																	147113964		2200	4299	6499	SO:0001819	synonymous_variant	84107	exon3			GGGCTGGCGCATG	AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"Zinc fingers, C2H2-type"	20393	protein-coding gene	gene with protein product		608948	"zinc finger protein of the cerebellum 4"				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.363C>A	chr3.hg19:g.147113964G>T		128.0	0.0		127.0	53.0	NM_001168378	A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Silent	SNP	ENST00000383075.3	hg19	CCDS43160.1																																																																																			.	.		0.657	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1			T	147113964	G	T	147113964	2	4	196	1	0	0	0	0	0	0	0	1	17696	1190	42	3		3	ZIC4	3	147113964	Silent	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	879073	147113964	50908466	28	28838										
NCAPG	64151	hgsc.bcm.edu	37	chr4	17829968	17829968	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gttgaagcagatgtccatttCaacaggcttaagtgcaacca	9	9	1	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr4:17829968C>A	ENST00000251496.2	+	12	1897	c.1721C>A	c.(1720-1722)tCa>tAa	p.S574*		NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	574					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		ATGTCCATTTCAACAGGCTTA	0.343																																					p.S574X		Atlas-SNP	.											.	NCAPG	76	.	0			c.C1721A						.						155	148	150					4																	17829968		2203	4300	6503	SO:0001587	stop_gained	64151	exon12			CCATTTCAACAGG	AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"chromosome condensation protein G"	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.1721C>A	chr4.hg19:g.17829968C>A	ENSP00000251496:p.Ser574*	89.0	0.0		60.0	29.0	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Nonsense_Mutation	SNP	ENST00000251496.2	hg19	CCDS3424.1	.	.	.	.	.	.	.	.	.	.	C	39	7.420824	0.98272	.	.	ENSG00000109805	ENST00000251496;ENST00000510063	.	.	.	5.01	4.16	0.48862	.	0.193867	0.45606	D	0.000347	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.332	12.7885	0.57520	0.0:0.9203:0.0:0.0797	.	.	.	.	X	574;139	.	ENSP00000251496:S574X	S	+	2	0	NCAPG	17439066	1.000000	0.71417	0.963000	0.40424	0.804000	0.45430	3.753000	0.55180	2.309000	0.77851	0.585000	0.79938	TCA	.	.		0.343	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346		A	17829968	C	A	17829968	4	1	196	1	0	0	0	0	0	1	0	0	10216	838	29	3	1767	3	NCAPG	4	17829968	Nonsense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10		17829968	173324308	29	28839										
PGM2	55276	hgsc.bcm.edu	37	chr4	37848658	37848658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	atcgcagtgctctcaaagacAcgtacatgttgtccagcacc	8	13	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr4:37848658A>G	ENST00000381967.4	+	9	1214	c.1114A>G	c.(1114-1116)Acg>Gcg	p.T372A	PGM2_ENST00000544359.1_Missense_Mutation_p.T233A|PGM2_ENST00000537241.1_Missense_Mutation_p.T212A	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	372					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						TCTCAAAGACACGTACATGTT	0.498																																					p.T372A		Atlas-SNP	.											.	PGM2	45	.	0			c.A1114G						.						131	134	133					4																	37848658		2203	4300	6503	SO:0001583	missense	55276	exon9			AAAGACACGTACA	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"phosphopentomutase"	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.1114A>G	chr4.hg19:g.37848658A>G	ENSP00000371393:p.Thr372Ala	77.0	0.0		70.0	27.0	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Missense_Mutation	SNP	ENST00000381967.4	hg19	CCDS3443.1	.	.	.	.	.	.	.	.	.	.	A	8.416	0.845297	0.16963	.	.	ENSG00000169299	ENST00000381967;ENST00000544359;ENST00000537241	T;T;T	0.39406	1.08;1.08;1.08	5.78	-1.26	0.09376	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);Alpha-D-phosphohexomutase, alpha/beta/alpha domain III (1);	0.660508	0.16568	N	0.208754	T	0.14013	0.0339	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.0;0.004	T	0.14117	-1.0484	10	0.12430	T	0.62	1.0458	0.4514	0.00501	0.385:0.1291:0.2342:0.2516	.	372;233	Q96G03;B4E0G8	PGM2_HUMAN;.	A	372;233;212	ENSP00000371393:T372A;ENSP00000438025:T233A;ENSP00000437342:T212A	ENSP00000371393:T372A	T	+	1	0	PGM2	37525053	0.000000	0.05858	0.072000	0.20136	0.411000	0.31082	0.044000	0.13992	0.098000	0.17522	0.533000	0.62120	ACG	.	.		0.498	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290		G	37848658	A	G	37848658	3	3	196	1	0	0	0	0	1	0	0	0	11807	159	6	2	1148	2	PGM2	4	37848658	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	20018690	37848658	153305618	30	28840										
LARP1B	55132	hgsc.bcm.edu	37	chr4	129043173	129043173	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	taaacaagattttgattgtaActcagacaccaccttatgtg	6	8	1	3			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr4:129043173A>G	ENST00000326639.6	+	11	1565	c.1354A>G	c.(1354-1356)Act>Gct	p.T452A	LARP1B_ENST00000354456.3_5'UTR|LARP1B_ENST00000512292.1_Missense_Mutation_p.T452A|LARP1B_ENST00000441387.1_Missense_Mutation_p.T452A|LARP1B_ENST00000427266.1_Missense_Mutation_p.T452A|LARP1B_ENST00000264584.5_Missense_Mutation_p.T405A	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	452						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						TTTGATTGTAACTCAGACACC	0.363																																					p.T452A		Atlas-SNP	.											.	LARP1B	120	.	0			c.A1354G						.						95	92	93					4																	129043173		2203	4298	6501	SO:0001583	missense	55132	exon11			ATTGTAACTCAGA		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.1354A>G	chr4.hg19:g.129043173A>G	ENSP00000321997:p.Thr452Ala	244.0	0.0		196.0	74.0	NM_178043	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Missense_Mutation	SNP	ENST00000326639.6	hg19	CCDS3738.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.69|14.69	2.610270|2.610270	0.46527|0.46527	.|.	.|.	ENSG00000138709|ENSG00000138709	ENST00000507377|ENST00000326639;ENST00000512292;ENST00000508819;ENST00000264584;ENST00000441387;ENST00000427266	.|T;T;T;T;T;T	.|0.62498	.|0.58;0.04;0.05;0.81;0.55;0.02	5.27|5.27	4.1|4.1	0.47936|0.47936	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.77356|0.77356	0.4118|0.4118	M|M	0.76938|0.76938	2.355|2.355	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;0.998	.|D;D;D	.|0.91635	.|0.999;0.998;0.994	T|T	0.78966|0.78966	-0.1995|-0.1995	5|10	.|0.72032	.|D	.|0.01	.|.	11.0305|11.0305	0.47769|0.47769	0.9276:0.0:0.0723:0.0|0.9276:0.0:0.0723:0.0	.|.	.|405;452;452	.|D6RJB0;Q659C4;G3XAJ5	.|.;LAR1B_HUMAN;.	S|A	420|452;452;405;405;452;452	.|ENSP00000321997:T452A;ENSP00000422850:T452A;ENSP00000427281:T405A;ENSP00000264584:T405A;ENSP00000396521:T452A;ENSP00000403586:T452A	.|ENSP00000264584:T405A	N|T	+|+	2|1	0|0	LARP1B|LARP1B	129262623|129262623	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.052000|0.052000	0.14988|0.14988	8.794000|8.794000	0.91867|0.91867	1.030000|1.030000	0.39839|0.39839	-0.256000|-0.256000	0.11100|0.11100	AAC|ACT	.	.		0.363	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		G	129043173	A	G	129043173	3	3	196	1	0	0	0	0	1	0	0	0	8638	43	2	2	1477	2	LARP1B	4	129043173	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	91194515	129043173	62111103	31	28841										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79026111	79026111	+	Frame_Shift_Del	DEL	A	A	-													0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	agaagaaccagagaaagaagAaatagaaacttccctaccca							TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr5:79026111delA	ENST00000446378.2	+	2	1554	c.1523delA	c.(1522-1524)gaafs	p.E508fs		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	508	Glu-rich.				negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GAGAAAGAAGAAATAGAAACT	0.413																																					p.E508fs		Pindel	.											.	CMYA5	643	.	0			c.1522delG						.						112	107	109					5																	79026111		1880	4113	5993	SO:0001589	frameshift_variant	202333	exon2			.	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.1523delA	chr5.hg19:g.79026111delA	ENSP00000394770:p.Glu508fs	180.0	0.0		164.0	27.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Frame_Shift_Del	DEL	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.		0.413	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		-	79026111	A	-	79026111	7	5	196	1	0	1	0	1	0	0	0	0	3592	246	9	0	1529	0	CMYA5	5	79026111	Frame_Shift_Del	DEL	A	TCGA-DD-AADN-01A-11D-A40R-10		79026111	101889149	32	28842										
DCP2	167227	hgsc.bcm.edu	37	chr5	112339697	112339697	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	acggttctcctggtgaccagTgggtaaagcacaggcaacca	12	11	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr5:112339697T>C	ENST00000389063.2	+	8	1063	c.865T>C	c.(865-867)Tgg>Cgg	p.W289R	DCP2_ENST00000515408.1_Missense_Mutation_p.W289R|DCP2_ENST00000543319.1_Missense_Mutation_p.W78R	NM_152624.5	NP_689837	Q8IU60	DCP2_HUMAN	decapping mRNA 2	289					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)|RISC complex (GO:0016442)	exoribonuclease activity, producing 5'-phosphomonoesters (GO:0016896)|m7G(5')pppN diphosphatase activity (GO:0050072)|manganese ion binding (GO:0030145)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(6)|lung(1)	10		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		TGGTGACCAGTGGGTAAAGCA	0.393																																					p.W289R		Atlas-SNP	.											.	DCP2	34	.	0			c.T865C						.						71	67	68					5																	112339697		2202	4300	6502	SO:0001583	missense	167227	exon8			GACCAGTGGGTAA	AY135173	CCDS34210.1, CCDS56377.1	5q22	2013-05-02	2013-05-02		ENSG00000172795	ENSG00000172795	3.6.1.62	"Nudix motif containing"	24452	protein-coding gene	gene with protein product	"nudix (nucleoside diphosphate linked moiety X)-type motif 20", "M(7)GpppN-mRNA hydrolase"	609844	"DCP2 decapping enzyme homolog (S. cerevisiae)"			12218187, 12417715	Standard	NM_152624		Approved	NUDT20	uc003kqh.3	Q8IU60	OTTHUMG00000162853	ENST00000389063.2:c.865T>C	chr5.hg19:g.112339697T>C	ENSP00000373715:p.Trp289Arg	207.0	0.0		208.0	73.0	NM_152624	C9J778|Q6P2D4|Q7Z5W5|Q8NBG5	Missense_Mutation	SNP	ENST00000389063.2	hg19	CCDS34210.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.33|17.33	3.362825|3.362825	0.61403|0.61403	.|.	.|.	ENSG00000172795|ENSG00000172795	ENST00000513585|ENST00000515408;ENST00000389063;ENST00000543319	.|T;T	.|0.41400	.|1.02;1.0	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.265855	.|0.41001	.|D	.|0.000979	T|T	0.28433|0.28433	0.0703|0.0703	L|L	0.29908|0.29908	0.895|0.895	0.44188|0.44188	D|D	0.997004|0.997004	.|P;P	.|0.45283	.|0.846;0.855	.|B;B	.|0.39258	.|0.295;0.216	T|T	0.06267|0.06267	-1.0836|-1.0836	5|10	.|0.15952	.|T	.|0.53	.|.	11.2467|11.2467	0.49002|0.49002	0.1364:0.0:0.0:0.8636|0.1364:0.0:0.0:0.8636	.|.	.|289;289	.|Q8IU60-2;Q8IU60	.|.;DCP2_HUMAN	A|R	270|289;289;78	.|ENSP00000425770:W289R;ENSP00000373715:W289R	.|ENSP00000373715:W289R	V|W	+|+	2|1	0|0	DCP2|DCP2	112367596|112367596	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.895000|0.895000	0.52256|0.52256	3.356000|3.356000	0.52269|0.52269	2.202000|2.202000	0.70862|0.70862	0.523000|0.523000	0.50628|0.50628	GTG|TGG	.	.		0.393	DCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370765.3	NM_152624		C	112339697	T	C	112339697	3	2	196	1	0	0	0	0	1	0	0	0	4302	1696	59	2	895	2	DCP2	5	112339697	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	33313586	112339697	68575563	33	28843										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140431371	140431371	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ccgacccttgtgttctgcacTttgaagtagtcctggtggag	12	10	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr5:140431371T>C	ENST00000306549.3	+	1	393	c.316T>C	c.(316-318)Ttt>Ctt	p.F106L		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	106	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGTTCTGCACTTTGAAGTAGT	0.522																																					p.F106L		Atlas-SNP	.											.	PCDHB1	148	.	0			c.T316C						.						57	62	60					5																	140431371		2203	4300	6503	SO:0001583	missense	29930	exon1			CTGCACTTTGAAG	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.316T>C	chr5.hg19:g.140431371T>C	ENSP00000307234:p.Phe106Leu	123.0	0.0		108.0	42.0	NM_013340	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	hg19	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	T	10.89	1.479205	0.26511	.	.	ENSG00000171815	ENST00000306549	T	0.23147	1.92	5.81	5.81	0.92471	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.49305	D	0.000160	T	0.29783	0.0744	L	0.33093	0.98	0.35298	D	0.782752	B	0.27932	0.194	B	0.40256	0.324	T	0.39099	-0.9630	10	0.41790	T	0.15	.	16.162	0.81727	0.0:0.0:0.0:1.0	.	106	Q9Y5F3	PCDB1_HUMAN	L	106	ENSP00000307234:F106L	ENSP00000307234:F106L	F	+	1	0	PCDHB1	140411555	0.338000	0.24775	1.000000	0.80357	0.621000	0.37620	0.647000	0.24812	2.224000	0.72417	0.533000	0.62120	TTT	.	.		0.522	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		C	140431371	T	C	140431371	3	2	196	1	0	0	0	0	1	0	0	0	11543	1609	56	2	318	2	PCDHB1	5	140431371	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	28091674	140431371	40483889	34	28844										
DSP	1832	hgsc.bcm.edu	37	chr6	7568673	7568673	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tttattcaccattgcagaaaGaacgagagaaaatccttgaa	7	7	1	4			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr6:7568673G>T	ENST00000379802.3	+	11	1611	c.1270G>T	c.(1270-1272)Gaa>Taa	p.E424*	DSP_ENST00000418664.2_Nonsense_Mutation_p.E424*	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	424	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		ATTGCAGAAAGAACGAGAGAA	0.393																																					p.E424X		Atlas-SNP	.											.	DSP	306	.	0			c.G1270T						.						97	95	95					6																	7568673		2203	4300	6503	SO:0001587	stop_gained	1832	exon11			CAGAAAGAACGAG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.1270G>T	chr6.hg19:g.7568673G>T	ENSP00000369129:p.Glu424*	97.0	0.0		59.0	25.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Nonsense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	G	42	9.437047	0.99171	.	.	ENSG00000096696	ENST00000379802;ENST00000418664;ENST00000397483	.	.	.	5.9	5.9	0.94986	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	20.2789	0.98501	0.0:0.0:1.0:0.0	.	.	.	.	X	424;424;229	.	ENSP00000369129:E424X	E	+	1	0	DSP	7513672	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.961000	0.87903	2.788000	0.95919	0.650000	0.86243	GAA	.	.		0.393	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7568673	G	T	7568673	4	4	196	1	0	0	0	0	0	1	0	0	4783	943	33	3	1312	3	DSP	6	7568673	Nonsense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10		7568673	163546394	35	28845										
PPP1R10	5514	hgsc.bcm.edu	37	chr6	30571840	30571840	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cttctcccgctcagcctggaTatatcgctcctgactattgc	7	15	2	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr6:30571840T>C	ENST00000376511.2	-	14	2005	c.1453A>G	c.(1453-1455)Atc>Gtc	p.I485V		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	485	Interaction with WDR82. {ECO:0000250}.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						TCAGCCTGGATATATCGCTCC	0.582																																					p.I485V		Atlas-SNP	.											.	PPP1R10	60	.	0			c.A1453G						.						104	116	112					6																	30571840		2203	4300	6503	SO:0001583	missense	5514	exon14			CCTGGATATATCG	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9284	protein-coding gene	gene with protein product	"phosphatase 1 nuclear targeting subunit", "HLA-C associated transcript 53"	603771	"protein phosphatase 1, regulatory (inhibitor) subunit 10"			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.1453A>G	chr6.hg19:g.30571840T>C	ENSP00000365694:p.Ile485Val	89.0	0.0		45.0	17.0	NM_002714	O00405	Missense_Mutation	SNP	ENST00000376511.2	hg19	CCDS4681.1	.	.	.	.	.	.	.	.	.	.	T	8.861	0.947055	0.18356	.	.	ENSG00000204569	ENST00000376511	T	0.27104	1.69	4.71	2.33	0.28932	.	0.350989	0.31760	N	0.007113	T	0.05044	0.0135	N	0.17631	0.505	0.28869	N	0.895072	B	0.02656	0.0	B	0.04013	0.001	T	0.37056	-0.9722	10	0.27785	T	0.31	-13.2476	8.2445	0.31680	0.0:0.1949:0.0:0.8051	.	485	Q96QC0	PP1RA_HUMAN	V	485	ENSP00000365694:I485V	ENSP00000365694:I485V	I	-	1	0	PPP1R10	30679819	1.000000	0.71417	0.998000	0.56505	0.952000	0.60782	3.392000	0.52537	0.834000	0.34852	0.383000	0.25322	ATC	.	.		0.582	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		C	30571840	T	C	30571840	3	2	196	1	0	0	0	0	1	0	0	0	12364	1406	49	2	1397	2	PPP1R10	6	30571840	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	23003167	30571840	140543227	36	28846										
STK19	8859	hgsc.bcm.edu	37	chr6	31939824	31939824	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gcaatcattcagcgacagtgGcgggcaaacccctcccgggg	13	14	2	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr6:31939824G>C	ENST00000375333.2	+	1	104	c.51G>C	c.(49-51)tgG>tgC	p.W17C	STK19_ENST00000375331.2_Missense_Mutation_p.W17C|DXO_ENST00000478221.1_5'UTR|DXO_ENST00000375349.3_5'UTR|DXO_ENST00000337523.5_5'UTR|DXO_ENST00000375356.3_5'Flank	NM_032454.1	NP_115830.1	P49842	STK19_HUMAN	serine/threonine kinase 19	17					protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			skin(5)|upper_aerodigestive_tract(2)	7						AGCGACAGTGGCGGGCAAACC	0.632																																					p.W17C		Atlas-SNP	.											.	STK19	33	.	0			c.G51C						.						76	85	82					6																	31939824		2203	4300	6503	SO:0001583	missense	8859	exon1			ACAGTGGCGGGCA	X77474	CCDS4733.1, CCDS34417.1	6p21.33	2011-09-15			ENSG00000204344	ENSG00000204344			11398	protein-coding gene	gene with protein product		604977				8012361, 9812991	Standard	NM_032454		Approved	D6S60, G11, RP1	uc003nyv.3	P49842	OTTHUMG00000166424	ENST00000375333.2:c.51G>C	chr6.hg19:g.31939824G>C	ENSP00000364482:p.Trp17Cys	111.0	0.0		80.0	15.0	NM_032454	A6NF95|A6NFW8|B0QZR5|Q13159|Q31617|Q5JP77|Q5ST72|Q5ST75	Missense_Mutation	SNP	ENST00000375333.2	hg19	CCDS4733.1	.	.	.	.	.	.	.	.	.	.	G	11.54	1.669176	0.29604	.	.	ENSG00000204344	ENST00000460018;ENST00000375331;ENST00000375333	T;T;T	0.56444	0.46;1.48;1.47	4.46	0.348	0.16026	.	.	.	.	.	T	0.20373	0.0490	N	0.14661	0.345	0.09310	N	1	D;P;P	0.63046	0.992;0.867;0.79	P;B;B	0.51385	0.668;0.325;0.173	T	0.07328	-1.0778	9	0.87932	D	0	.	1.4823	0.02439	0.1951:0.1665:0.4673:0.1711	.	17;17;17	B4E0M4;P49842-2;P49842	.;.;STK19_HUMAN	C	17	ENSP00000418350:W17C;ENSP00000364480:W17C;ENSP00000364482:W17C	ENSP00000364480:W17C	W	+	3	0	STK19	32047803	0.000000	0.05858	0.000000	0.03702	0.081000	0.17604	-1.659000	0.01975	-0.056000	0.13221	0.561000	0.74099	TGG	.	.		0.632	STK19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076484.3			C	31939824	G	C	31939824	3	2	196	1	0	0	0	0	1	0	0	0	15307	1212	42	4	53	4	STK19	6	31939824	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	1367984	31939824	139175243	37	28847										
KIF6	221458	hgsc.bcm.edu	37	chr6	39387781	39387781	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ggccttggcttcagaaaatcTggaggggaaaaaaatgaaaa	12	5	2	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr6:39387781T>C	ENST00000287152.7	-	15	1849		c.e15-2		KIF6_ENST00000538893.1_Splice_Site|KIF6_ENST00000541946.1_Splice_Site|KIF6_ENST00000373213.4_Splice_Site|KIF6_ENST00000373216.3_Splice_Site|KIF6_ENST00000394362.1_Splice_Site|KIF6_ENST00000373215.3_Splice_Site|KIF6_ENST00000229913.5_Splice_Site	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6						ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						TCAGAAAATCTGGAGGGGAAA	0.323																																					.		Atlas-SNP	.											.	KIF6	233	.	0			c.1755-2A>G						.						90	94	92					6																	39387781		2203	4300	6503	SO:0001630	splice_region_variant	221458	exon16			AAAATCTGGAGGG	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.1755-2A>G	chr6.hg19:g.39387781T>C		148.0	0.0		135.0	40.0	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Splice_Site	SNP	ENST00000287152.7	hg19	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.313409	0.60414	.	.	ENSG00000164627	ENST00000287152;ENST00000458470;ENST00000394362;ENST00000373216;ENST00000373213;ENST00000229913;ENST00000373215;ENST00000538893;ENST00000541946;ENST00000540362	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6796	0.51451	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIF6	39495759	0.999000	0.42202	0.978000	0.43139	0.880000	0.50808	3.356000	0.52269	2.246000	0.74042	0.533000	0.62120	.	.	.		0.323	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	Intron	C	39387781	T	C	39387781	5	2	196	1	0	0	0	0	0	0	1	0	8317	1594	55	2	727	2	KIF6	6	39387781	Splice_Site	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	7447957	39387781	131727286	38	28848										
GPR116	221395	hgsc.bcm.edu	37	chr6	46828584	46828584	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	atgctaatagaaagatccttCaggtatgtagggagcatctc	10	7	2	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr6:46828584C>A	ENST00000283296.7	-	16	2535	c.2247G>T	c.(2245-2247)ctG>ctT	p.L749L	GPR116_ENST00000456426.2_Silent_p.L607L|GPR116_ENST00000362015.4_Silent_p.L749L|GPR116_ENST00000265417.7_Silent_p.L749L|GPR116_ENST00000545669.1_Silent_p.L178L	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	749					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			AAAGATCCTTCAGGTATGTAG	0.413																																					p.L749L	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.G2247T						.						103	101	102					6																	46828584		2203	4300	6503	SO:0001819	synonymous_variant	221395	exon16			ATCCTTCAGGTAT	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.2247G>T	chr6.hg19:g.46828584C>A		95.0	0.0		91.0	9.0	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	hg19	CCDS4919.1																																																																																			.	.		0.413	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		A	46828584	C	A	46828584	2	1	196	1	0	0	0	0	0	0	0	1	6641	813	29	3		3	GPR116	6	46828584	Silent	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	7440803	46828584	124286483	39	28849										
BAG2	9532	hgsc.bcm.edu	37	chr6	57037534	57037534	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aacgctaaagccaacgagggGcgcttctgccgctcctcctc	10	16	1	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr6:57037534G>T	ENST00000370693.5	+	1	411	c.39G>T	c.(37-39)ggG>ggT	p.G13G	RP11-203B9.4_ENST00000589394.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000586466.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000586234.1_RNA|RP11-203B9.4_ENST00000592785.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000609545.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000589263.1_RNA|RP11-203B9.4_ENST00000589312.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000588819.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000585414.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000590164.1_RNA|RP11-203B9.4_ENST00000589549.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|BAG2_ENST00000545080.1_5'Flank	NM_004282.3	NP_004273.1	O95816	BAG2_HUMAN	BCL2-associated athanogene 2	13					protein folding (GO:0006457)|protein metabolic process (GO:0019538)		identical protein binding (GO:0042802)			endometrium(1)|large_intestine(1)	2	Lung NSC(77;0.126)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			CCAACGAGGGGCGCTTCTGCC	0.692																																					p.G13G		Atlas-SNP	.											.	BAG2	10	.	0			c.G39T						.						31	27	28					6																	57037534		2200	4297	6497	SO:0001819	synonymous_variant	9532	exon1			CGAGGGGCGCTTC	AF095192	CCDS4961.1	6p12.3-p11.2	2008-02-05			ENSG00000112208	ENSG00000112208			938	protein-coding gene	gene with protein product		603882				9873016	Standard	NM_004282		Approved		uc003pdr.3	O95816	OTTHUMG00000014919	ENST00000370693.5:c.39G>T	chr6.hg19:g.57037534G>T		239.0	0.0		214.0	48.0	NM_004282	B4DXE2|Q08AS9|Q6FID0	Silent	SNP	ENST00000370693.5	hg19	CCDS4961.1																																																																																			.	.		0.692	BAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041044.2			T	57037534	G	T	57037534	2	4	196	1	0	0	0	0	0	0	0	1	1287	1190	42	3		3	BAG2	6	57037534	Silent	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	10208950	57037534	114077533	40	28850										
FHL5	9457	hgsc.bcm.edu	37	chr6	97052637	97052637	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gtctcaaaggatctttgttaCaaagaccggcactggcatga	10	9	2	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr6:97052637C>A	ENST00000326771.2	+	4	551	c.171C>A	c.(169-171)taC>taA	p.Y57*	FHL5_ENST00000541107.1_Nonsense_Mutation_p.Y57*	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	57	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		ATCTTTGTTACAAAGACCGGC	0.428																																					p.Y57X		Atlas-SNP	.											.	FHL5	73	.	0			c.C171A						.						79	74	76					6																	97052637		2203	4300	6503	SO:0001587	stop_gained	9457	exon4			TTGTTACAAAGAC	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.171C>A	chr6.hg19:g.97052637C>A	ENSP00000326022:p.Tyr57*	63.0	0.0		57.0	16.0	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Nonsense_Mutation	SNP	ENST00000326771.2	hg19	CCDS5035.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.011812	0.93346	.	.	ENSG00000112214	ENST00000541107;ENST00000326771;ENST00000450218	.	.	.	5.36	3.57	0.40892	.	0.000000	0.41001	D	0.000972	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3192	0.32119	0.0:0.7007:0.0:0.2993	.	.	.	.	X	57	.	ENSP00000326022:Y57X	Y	+	3	2	FHL5	97159358	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.789000	0.26886	0.747000	0.32809	0.655000	0.94253	TAC	.	.		0.428	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482		A	97052637	C	A	97052637	4	1	196	1	0	0	0	0	0	1	0	0	5889	489	17	3	177	3	FHL5	6	97052637	Nonsense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	40015103	97052637	74062430	41	28851										
PNLDC1	154197	hgsc.bcm.edu	37	chr6	160240288	160240288	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gcaaacttgttttggcagtgCgcggaacatcctgaaggagt	13	8	0	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr6:160240288C>T	ENST00000610273.1	+	18	1574	c.1403C>T	c.(1402-1404)gCg>gTg	p.A468V	PNLDC1_ENST00000392167.3_Missense_Mutation_p.A479V	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	468						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TTTGGCAGTGCGCGGAACATC	0.597																																					p.A468V		Atlas-SNP	.											.	PNLDC1	66	.	0			c.C1403T						.						96	74	81					6																	160240288		2203	4300	6503	SO:0001583	missense	154197	exon18			GCAGTGCGCGGAA	AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.1403C>T	chr6.hg19:g.160240288C>T	ENSP00000476448:p.Ala468Val	54.0	0.0		43.0	18.0	NM_173516	Q5TAP7|Q8N7X5	Missense_Mutation	SNP	ENST00000610273.1	hg19	CCDS5271.1	.	.	.	.	.	.	.	.	.	.	C	9.613	1.131898	0.21041	.	.	ENSG00000146453	ENST00000275275;ENST00000392167	.	.	.	5.86	3.11	0.35812	.	0.225470	0.31381	N	0.007748	T	0.04092	0.0114	N	0.04880	-0.145	0.09310	N	1	B;B	0.17667	0.023;0.009	B;B	0.09377	0.003;0.004	T	0.41179	-0.9523	9	0.07030	T	0.85	.	6.2774	0.20989	0.0:0.6582:0.0:0.3418	.	479;468	Q8NA58-2;Q8NA58	.;PNDC1_HUMAN	V	468;479	.	ENSP00000275275:A468V	A	+	2	0	PNLDC1	160160278	0.230000	0.23740	0.042000	0.18584	0.001000	0.01503	1.676000	0.37565	1.482000	0.48325	0.561000	0.74099	GCG	.	.		0.597	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516		T	160240288	C	T	160240288	3	4	196	1	0	0	0	0	1	0	0	0	12157	768	27	1	1469	1	PNLDC1	6	160240288	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	63187651	160240288	10874779	42	28852										
TAS2R60	338398	hgsc.bcm.edu	37	chr7	143141236	143141236	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ggaagaaggctctccttacaAcctcaggattccgagagccc	10	13	2	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr7:143141236A>G	ENST00000332690.1	+	1	691	c.691A>G	c.(691-693)Acc>Gcc	p.T231A	EPHA1-AS1_ENST00000429289.1_RNA	NM_177437.1	NP_803186.1	P59551	T2R60_HUMAN	taste receptor, type 2, member 60	231					sensory perception of bitter taste (GO:0050913)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(1)|large_intestine(2)|lung(17)|prostate(1)|skin(7)|urinary_tract(2)	31	Melanoma(164;0.172)					TCTCCTTACAACCTCAGGATT	0.463																																					p.T231A		Atlas-SNP	.											.	TAS2R60	55	.	0			c.A691G						.						121	124	123					7																	143141236		2203	4300	6503	SO:0001583	missense	338398	exon1			CTTACAACCTCAG	AY114094	CCDS5885.1	7q35	2014-07-10			ENSG00000185899	ENSG00000185899		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	20639	protein-coding gene	gene with protein product		613968				12584440	Standard	NM_177437		Approved	T2R60	uc011ktg.2	P59551	OTTHUMG00000154891	ENST00000332690.1:c.691A>G	chr7.hg19:g.143141236A>G	ENSP00000327724:p.Thr231Ala	77.0	0.0		42.0	26.0	NM_177437	A4D2G8|Q645W8|Q7RTR7	Missense_Mutation	SNP	ENST00000332690.1	hg19	CCDS5885.1	.	.	.	.	.	.	.	.	.	.	A	2.387	-0.340668	0.05243	.	.	ENSG00000185899	ENST00000332690	T	0.35789	1.29	5.47	-1.98	0.07480	.	1.366100	0.05290	U	0.520835	T	0.14442	0.0349	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.23332	-1.0191	10	0.02654	T	1	.	5.226	0.15396	0.3391:0.323:0.3379:0.0	.	231	P59551	T2R60_HUMAN	A	231	ENSP00000327724:T231A	ENSP00000327724:T231A	T	+	1	0	TAS2R60	142851358	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.295000	0.08298	-0.286000	0.09076	0.482000	0.46254	ACC	.	.		0.463	TAS2R60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337541.1			G	143141236	A	G	143141236	3	3	196	1	0	0	0	0	1	0	0	0	15600	43	2	2	693	2	TAS2R60	7	143141236	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10		143141236	15997427	43	28853										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3087644	3087644	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ttggcttgtccttggagctgAtagccagggtcacactggaa	13	9	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr8:3087644A>G	ENST00000520002.1	-	28	4821	c.4266T>C	c.(4264-4266)taT>taC	p.Y1422Y	CSMD1_ENST00000537824.1_Silent_p.Y1421Y|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602723.1_Silent_p.Y1422Y|CSMD1_ENST00000400186.3_Silent_p.Y1422Y|CSMD1_ENST00000542608.1_Silent_p.Y1421Y|CSMD1_ENST00000602557.1_Silent_p.Y1422Y|CSMD1_ENST00000539096.1_Silent_p.Y1421Y			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1422	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.Y1421Y(1)|p.Y1150Y(1)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CTTGGAGCTGATAGCCAGGGT	0.522																																					p.Y1421Y		Atlas-SNP	.											CSMD1_ENST00000537824,NS,carcinoma,0,2	CSMD1	1469	.	2	Substitution - coding silent(2)	kidney(2)	c.T4263C						.						92	92	92					8																	3087644		1989	4169	6158	SO:0001819	synonymous_variant	64478	exon27			GAGCTGATAGCCA			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4266T>C	chr8.hg19:g.3087644A>G		148.0	0.0		58.0	16.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.756	1.168829	0.21621	.	.	ENSG00000183117	ENST00000335551	.	.	.	6.16	-2.87	0.05700	.	.	.	.	.	T	0.64011	0.2560	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63532	-0.6616	4	.	.	.	.	14.166	0.65477	0.8398:0.0:0.1602:0.0	.	.	.	.	P	902	.	.	S	-	1	0	CSMD1	3075051	0.992000	0.36948	0.819000	0.32651	0.880000	0.50808	0.289000	0.18957	-0.354000	0.08212	0.528000	0.53228	TCA	.	.		0.522	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	3087644	A	G	3087644	2	3	196	1	0	0	0	0	0	0	0	1	3946	340	12	2		2	CSMD1	8	3087644	Silent	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10		3087644	143276378	44	28854										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3326340	3326340	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aggtcaggaacactggatccCgtgagcctgcaagaaagaga	13	9	1	3			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr8:3326340C>A	ENST00000520002.1	-	13	2013	c.1458G>T	c.(1456-1458)acG>acT	p.T486T	CSMD1_ENST00000537824.1_Silent_p.T485T|CSMD1_ENST00000602723.1_Silent_p.T486T|CSMD1_ENST00000400186.3_Silent_p.T486T|CSMD1_ENST00000542608.1_Silent_p.T485T|CSMD1_ENST00000602557.1_Silent_p.T486T|CSMD1_ENST00000539096.1_Silent_p.T485T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	486	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.T485T(2)|p.T214T(2)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CACTGGATCCCGTGAGCCTGC	0.468																																					p.T485T		Atlas-SNP	.											CSMD1_ENST00000537824,NS,lymphoid_neoplasm,0,4	CSMD1	1469	.	4	Substitution - coding silent(4)	haematopoietic_and_lymphoid_tissue(4)	c.G1455T						.						51	50	50					8																	3326340		1950	4151	6101	SO:0001819	synonymous_variant	64478	exon12			GGATCCCGTGAGC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.1458G>T	chr8.hg19:g.3326340C>A		46.0	0.0		18.0	6.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19																																																																																				.	.		0.468	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3326340	C	A	3326340	2	1	196	1	0	0	0	0	0	0	0	1	3946	639	23	1		1	CSMD1	8	3326340	Silent	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	238696	3326340	143037682	45	28855										
DLC1	10395	hgsc.bcm.edu	37	chr8	12952358	12952358	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ctgcttcagcatgtctgccaCgtcataagcagactgtcctt	8	13	3	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr8:12952358C>A	ENST00000276297.4	-	12	3845	c.3436G>T	c.(3436-3438)Gtg>Ttg	p.V1146L	DLC1_ENST00000512044.2_Missense_Mutation_p.V743L|DLC1_ENST00000510318.1_5'UTR|DLC1_ENST00000520226.1_Missense_Mutation_p.V635L|DLC1_ENST00000358919.2_Missense_Mutation_p.V709L	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	1146	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						ATGTCTGCCACGTCATAAGCA	0.483																																					p.V1146L		Atlas-SNP	.											.	DLC1	411	.	0			c.G3436T						.						95	90	92					8																	12952358		2203	4300	6503	SO:0001583	missense	10395	exon12			CTGCCACGTCATA	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.3436G>T	chr8.hg19:g.12952358C>A	ENSP00000276297:p.Val1146Leu	115.0	0.0		36.0	15.0	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	hg19	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	35	5.525498	0.96431	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000510318;ENST00000512044;ENST00000520226	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	4.97	4.97	0.65823	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.058370	0.64402	D	0.000002	T	0.53061	0.1773	M	0.76727	2.345	0.80722	D	1	P;D;P	0.76494	0.868;0.999;0.811	P;D;P	0.73380	0.654;0.98;0.654	T	0.56390	-0.7987	10	0.87932	D	0	.	18.8143	0.92071	0.0:1.0:0.0:0.0	.	1146;743;709	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	L	1146;709;85;743;635	ENSP00000276297:V1146L;ENSP00000351797:V709L;ENSP00000422595:V743L;ENSP00000428028:V635L	ENSP00000276297:V1146L	V	-	1	0	DLC1	12996729	1.000000	0.71417	0.972000	0.41901	0.995000	0.86356	7.646000	0.83445	2.761000	0.94854	0.650000	0.86243	GTG	.	.		0.483	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		A	12952358	C	A	12952358	3	1	196	1	0	0	0	0	1	0	0	0	4552	536	19	1	1178	1	DLC1	8	12952358	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	9626018	12952358	133411664	46	28856										
PSD3	23362	hgsc.bcm.edu	37	chr8	18658787	18658787	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tgtatcagattaccttgtgaAgcaatggtatctgggttaca	10	6	2	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr8:18658787A>C	ENST00000327040.8	-	7	2118	c.2016T>G	c.(2014-2016)gcT>gcG	p.A672A	PSD3_ENST00000523619.1_Silent_p.A607A|PSD3_ENST00000286485.8_Silent_p.A138A|PSD3_ENST00000440756.2_Silent_p.A672A	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	672	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		TACCTTGTGAAGCAATGGTAT	0.289																																					p.A672A		Atlas-SNP	.											.	PSD3	142	.	0			c.T2016G						.						50	55	54					8																	18658787		2200	4285	6485	SO:0001819	synonymous_variant	23362	exon7			TTGTGAAGCAATG	AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"Pleckstrin homology (PH) domain containing"	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.2016T>G	chr8.hg19:g.18658787A>C		505.0	0.0		194.0	76.0	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Silent	SNP	ENST00000327040.8	hg19	CCDS43720.1	.	.	.	.	.	.	.	.	.	.	A	7.207	0.594581	0.13875	.	.	ENSG00000156011	ENST00000520858	.	.	.	5.79	2.0	0.26442	.	.	.	.	.	T	0.52677	0.1749	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45804	-0.9236	4	.	.	.	.	5.8298	0.18574	0.6901:0.1446:0.1653:0.0	.	.	.	.	V	105	.	.	F	-	1	0	PSD3	18703067	1.000000	0.71417	1.000000	0.80357	0.583000	0.36354	0.722000	0.25925	1.029000	0.39812	0.523000	0.50628	TTC	.	.		0.289	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310		C	18658787	A	C	18658787	2	2	196	1	0	0	0	0	0	0	0	1	12660	59	3	5		5	PSD3	8	18658787	Silent	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	5706429	18658787	127705235	47	28857										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100127975	100127975	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ctttctatcacagatcaacaActgcctatgtttattcgtat	4	10	3	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr8:100127975A>G	ENST00000358544.2	+	7	921	c.810A>G	c.(808-810)caA>caG	p.Q270Q	VPS13B_ENST00000395996.1_Silent_p.Q270Q|VPS13B_ENST00000357162.2_Silent_p.Q270Q|VPS13B_ENST00000441350.2_Silent_p.Q270Q|VPS13B_ENST00000355155.1_Silent_p.Q270Q	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	270					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CAGATCAACAACTGCCTATGT	0.323																																					p.Q270Q	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A810G						.						88	89	89					8																	100127975		2203	4293	6496	SO:0001819	synonymous_variant	157680	exon7			TCAACAACTGCCT	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.810A>G	chr8.hg19:g.100127975A>G		388.0	0.0		747.0	50.0	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	hg19	CCDS6280.1																																																																																			.	.		0.323	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100127975	A	G	100127975	2	3	196	1	0	0	0	0	0	0	0	1	17205	40	2	2		2	VPS13B	8	100127975	Silent	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	81469188	100127975	46236047	48	28858										
LRP12	29967	hgsc.bcm.edu	37	chr8	105509945	105509945	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gcaattgcttccaggaggatAaaagtctggataattgggag	13	5	1	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr8:105509945A>C	ENST00000276654.5	-	5	943	c.835T>G	c.(835-837)Tat>Gat	p.Y279D	LRP12_ENST00000518375.1_5'Flank|LRP12_ENST00000424843.2_Missense_Mutation_p.Y260D	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	279	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CCAGGAGGATAAAAGTCTGGA	0.398																																					p.Y279D		Atlas-SNP	.											.	LRP12	124	.	0			c.T835G						.						63	66	65					8																	105509945		2203	4300	6503	SO:0001583	missense	29967	exon5			GAGGATAAAAGTC	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"Low density lipoprotein receptors"	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.835T>G	chr8.hg19:g.105509945A>C	ENSP00000276654:p.Tyr279Asp	146.0	0.0		240.0	192.0	NM_013437	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000276654.5	hg19	CCDS6303.1	.	.	.	.	.	.	.	.	.	.	A	19.76	3.888207	0.72524	.	.	ENSG00000147650	ENST00000424843;ENST00000276654	T;T	0.29655	1.56;1.56	5.66	5.66	0.87406	CUB (5);	0.000000	0.85682	D	0.000000	T	0.63815	0.2543	M	0.91612	3.225	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.996;0.998	T	0.69258	-0.5192	10	0.37606	T	0.19	-31.0306	15.9017	0.79384	1.0:0.0:0.0:0.0	.	260;279	Q9Y561-2;Q9Y561	.;LRP12_HUMAN	D	260;279	ENSP00000399148:Y260D;ENSP00000276654:Y279D	ENSP00000276654:Y279D	Y	-	1	0	LRP12	105579121	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.962000	0.93254	2.153000	0.67306	0.460000	0.39030	TAT	.	.		0.398	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		C	105509945	A	C	105509945	3	2	196	1	0	0	0	0	1	0	0	0	8963	362	13	5	1756	5	LRP12	8	105509945	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	5381970	105509945	40854077	49	28859										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110457250	110457250	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aatgtgaaacatcccctgctGcccaacagcttgtggatgta	9	11	0	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr8:110457250G>A	ENST00000378402.5	+	38	5256	c.5152G>A	c.(5152-5154)Gcc>Acc	p.A1718T		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1718	IPT/TIG 9.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ATCCCCTGCTGCCCAACAGCT	0.443										HNSCC(38;0.096)																											p.A1718T		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G5152A						.						201	194	196					8																	110457250		1918	4130	6048	SO:0001583	missense	93035	exon38			CCTGCTGCCCAAC	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5152G>A	chr8.hg19:g.110457250G>A	ENSP00000367655:p.Ala1718Thr	131.0	0.0		276.0	30.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	1.711	-0.498998	0.04291	.	.	ENSG00000205038	ENST00000378402	T	0.76839	-1.05	6.17	3.45	0.39498	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.560686	0.18974	N	0.126079	T	0.51398	0.1672	N	0.11756	0.17	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.35325	-0.9793	10	0.07030	T	0.85	.	2.9744	0.05933	0.1417:0.5556:0.1485:0.1542	.	1718	Q86WI1	PKHL1_HUMAN	T	1718	ENSP00000367655:A1718T	ENSP00000367655:A1718T	A	+	1	0	PKHD1L1	110526426	0.000000	0.05858	0.358000	0.25811	0.375000	0.29983	-0.201000	0.09464	0.493000	0.27837	-0.165000	0.13383	GCC	.	.		0.443	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110457250	G	A	110457250	3	1	196	1	0	0	0	0	1	0	0	0	11981	1319	46	3	5302	3	PKHD1L1	8	110457250	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	4947305	110457250	35906772	50	28860										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113249531	113249531	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tgtttccttcctttgaaattGtaagagcctttccatatata	5	8	0	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr8:113249531G>A	ENST00000297405.5	-	67	10759	c.10515C>T	c.(10513-10515)taC>taT	p.Y3505Y	CSMD3_ENST00000343508.3_Silent_p.Y3465Y|CSMD3_ENST00000352409.3_Silent_p.Y3435Y|CSMD3_ENST00000455883.2_Silent_p.Y3336Y	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3505						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CTTTGAAATTGTAAGAGCCTT	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.Y3505Y		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C10515T						.						157	144	148					8																	113249531		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon67			GAAATTGTAAGAG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10515C>T	chr8.hg19:g.113249531G>A		140.0	1.0		193.0	151.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113249531	G	A	113249531	2	1	196	1	0	0	0	0	0	0	0	1	3948	1372	48	3		3	CSMD3	8	113249531	Silent	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	2792281	113249531	33114491	51	28861										
EXT1	2131	hgsc.bcm.edu	37	chr8	119122935	119122935	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cctttttgctgtgggtatacGtagactttgaagccgttttt	10	7	0	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr8:119122935G>A	ENST00000378204.2	-	1	1157	c.351C>T	c.(349-351)taC>taT	p.Y117Y		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	117					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			GTGGGTATACGTAGACTTTGA	0.512			"Mis, N, F, S"			"exostoses, osteosarcoma"			Langer-Giedion syndrome;Hereditary Multiple Exostoses																												p.Y117Y		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	EXT1	98	.	0			c.C351T						.						78	82	81					8																	119122935		2203	4300	6503	SO:0001819	synonymous_variant	2131	exon1	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	GTATACGTAGACT	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3512	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608177	"Langer-Giedion syndrome chromosome region", "exostoses (multiple) 1", "exostosin 1"	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.351C>T	chr8.hg19:g.119122935G>A		233.0	0.0		354.0	19.0	NM_000127	B2R7V2|Q9BVI9	Silent	SNP	ENST00000378204.2	hg19	CCDS6324.1																																																																																			.	.		0.512	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127		A	119122935	G	A	119122935	2	1	196	1	0	0	0	0	0	0	0	1	5325	1140	40	1		1	EXT1	8	119122935	Silent	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	5873404	119122935	27241087	52	28862										
PTAR1	375743	hgsc.bcm.edu	37	chr9	72374805	72374805	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tgaaggcgttagtgatgtccTtcacaacccgctgcaccagc	10	13	1	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr9:72374805T>C	ENST00000340434.4	-	1	53	c.50A>G	c.(49-51)aAg>aGg	p.K17R	PTAR1_ENST00000472967.2_Missense_Mutation_p.K17R|PTAR1_ENST00000377200.5_Missense_Mutation_p.K17R	NM_001099666.1	NP_001093136.1	Q7Z6K3	PTAR1_HUMAN	protein prenyltransferase alpha subunit repeat containing 1	17					protein prenylation (GO:0018342)		protein prenyltransferase activity (GO:0008318)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)	5						AGTGATGTCCTTCACAACCCG	0.726																																					p.K17R		Atlas-SNP	.											.	PTAR1	46	.	0			c.A50G						.						15	18	17					9																	72374805		2026	4141	6167	SO:0001583	missense	375743	exon1			ATGTCCTTCACAA	BC053622	CCDS47978.1	9q21.13	2008-10-01			ENSG00000188647	ENSG00000188647		"Prenyltransferase alpha subunit repeat containing"	30449	protein-coding gene	gene with protein product						12477932	Standard	NM_001099666		Approved		uc004ahj.4	Q7Z6K3	OTTHUMG00000019982	ENST00000340434.4:c.50A>G	chr9.hg19:g.72374805T>C	ENSP00000344299:p.Lys17Arg	170.0	0.0		96.0	44.0	NM_001099666	Q5T7V5|Q5T7V6	Missense_Mutation	SNP	ENST00000340434.4	hg19	CCDS47978.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.004203	0.35320	.	.	ENSG00000188647	ENST00000377200;ENST00000340434;ENST00000472967	.	.	.	4.05	2.72	0.32119	.	0.130381	0.49916	D	0.000137	T	0.29158	0.0725	L	0.27053	0.805	0.22017	N	0.999412	B	0.27791	0.189	B	0.34991	0.193	T	0.23547	-1.0185	9	0.18710	T	0.47	-0.6132	9.0194	0.36191	0.2162:0.0:0.0:0.7838	.	17	Q7Z6K3	PTAR1_HUMAN	R	17	.	ENSP00000344299:K17R	K	-	2	0	PTAR1	71564625	1.000000	0.71417	0.960000	0.40013	0.733000	0.41908	2.881000	0.48538	0.392000	0.25172	0.240000	0.17902	AAG	.	.		0.726	PTAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052582.4	NM_001099666		C	72374805	T	C	72374805	3	2	196	1	0	0	0	0	1	0	0	0	12736	1609	56	2	1190	2	PTAR1	9	72374805	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10		72374805	68838626	53	28863										
HELLS	3070	hgsc.bcm.edu	37	chr10	96350289	96350289	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aaactgatcagtcaaatacaGccagaggtggaccgagaaag	11	8	2	3			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr10:96350289G>A	ENST00000348459.5	+	14	1713	c.1608G>A	c.(1606-1608)caG>caA	p.Q536Q	HELLS_ENST00000394036.1_3'UTR|RP11-119K6.6_ENST00000432120.1_RNA|HELLS_ENST00000239026.6_3'UTR|HELLS_ENST00000394045.1_Silent_p.Q438Q|HELLS_ENST00000371332.4_Silent_p.Q582Q	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		GTCAAATACAGCCAGAGGTGG	0.333																																					p.Q536Q		Atlas-SNP	.											.	HELLS	63	.	0			c.G1608A						.						79	80	80					10																	96350289		2203	4299	6502	SO:0001819	synonymous_variant	3070	exon14			AATACAGCCAGAG	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6", "proliferation-associated SNF2-like protein"	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.1608G>A	chr10.hg19:g.96350289G>A		330.0	0.0		183.0	36.0	NM_018063		Silent	SNP	ENST00000348459.5	hg19	CCDS7434.1																																																																																			.	.		0.333	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		A	96350289	G	A	96350289	2	1	196	1	0	0	0	0	0	0	0	1	7055	962	34	3		3	HELLS	10	96350289	Silent	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10		96350289	39184458	54	28864										
NHLRC2	374354	hgsc.bcm.edu	37	chr10	115662337	115662337	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aatttactttatgttgcagaCtcctacaatcacaaggtgag	7	8	1	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr10:115662337C>G	ENST00000369301.3	+	8	1691	c.1479C>G	c.(1477-1479)gaC>gaG	p.D493E		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	493										breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		ATGTTGCAGACTCCTACAATC	0.388																																					p.D493E		Atlas-SNP	.											.	NHLRC2	56	.	0			c.C1479G						.						101	101	101					10																	115662337		2203	4300	6503	SO:0001583	missense	374354	exon8			TGCAGACTCCTAC	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.1479C>G	chr10.hg19:g.115662337C>G	ENSP00000358307:p.Asp493Glu	254.0	0.0		126.0	17.0	NM_198514	Q8N1H1|Q8N5A6	Missense_Mutation	SNP	ENST00000369301.3	hg19	CCDS7585.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.600177	0.66332	.	.	ENSG00000196865	ENST00000369301	D	0.89939	-2.59	5.58	3.74	0.42951	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.94974	0.8374	H	0.95679	3.705	0.51767	D	0.999934	D	0.89917	1.0	D	0.97110	1.0	D	0.93837	0.7133	10	0.62326	D	0.03	-19.6535	5.7076	0.17917	0.0:0.692:0.0:0.308	.	493	Q8NBF2	NHLC2_HUMAN	E	493	ENSP00000358307:D493E	ENSP00000358307:D493E	D	+	3	2	NHLRC2	115652327	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	1.617000	0.36943	1.379000	0.46325	0.561000	0.74099	GAC	.	.		0.388	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514		G	115662337	C	G	115662337	3	3	196	1	0	0	0	0	1	0	0	0	10415	564	20	4	1509	4	NHLRC2	10	115662337	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	19312048	115662337	19872410	55	28865										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6643621	6643621	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tgcacctggcagcagcagccCtgcctttcggcccttatacc	9	17	0	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr11:6643621C>T	ENST00000299441.3	-	21	9697	c.9286G>A	c.(9286-9288)Ggg>Agg	p.G3096R	RP11-732A19.9_ENST00000545572.1_RNA|TPP1_ENST00000299427.6_5'Flank|RP11-732A19.5_ENST00000526456.1_RNA|TPP1_ENST00000528657.1_5'Flank|TPP1_ENST00000534644.1_5'Flank	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	3096					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGCAGCAGCCCTGCCTTTCGG	0.652																																					p.G3096R		Atlas-SNP	.											.	DCHS1	277	.	0			c.G9286A						.						10	10	10					11																	6643621		2185	4268	6453	SO:0001583	missense	8642	exon21			GCAGCCCTGCCTT	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.9286G>A	chr11.hg19:g.6643621C>T	ENSP00000299441:p.Gly3096Arg	91.0	0.0		68.0	22.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.685795	0.47991	.	.	ENSG00000166341	ENST00000299441	T	0.56103	0.48	5.04	5.04	0.67666	.	0.159460	0.29515	N	0.011935	T	0.44808	0.1311	N	0.22421	0.69	0.52099	D	0.999944	P	0.50943	0.94	P	0.47915	0.561	T	0.19910	-1.0291	10	0.19590	T	0.45	.	15.2361	0.73432	0.0:1.0:0.0:0.0	.	3096	Q96JQ0	PCD16_HUMAN	R	3096	ENSP00000299441:G3096R	ENSP00000299441:G3096R	G	-	1	0	DCHS1	6600197	0.993000	0.37304	1.000000	0.80357	0.946000	0.59487	1.977000	0.40589	2.613000	0.88420	0.462000	0.41574	GGG	.	.		0.652	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		T	6643621	C	T	6643621	3	4	196	1	0	0	0	0	1	0	0	0	4289	681	24	3	614	3	DCHS1	11	6643621	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10		6643621	128362895	56	28866										
TRAF6	7189	hgsc.bcm.edu	37	chr11	36520132	36520132	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	acgttttgcaaaattgtctgGaaatagttgattttccagca	8	6	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr11:36520132G>T	ENST00000526995.1	-	3	601	c.355C>A	c.(355-357)Cca>Aca	p.P119T	TRAF6_ENST00000348124.5_Missense_Mutation_p.P119T|TRAF6_ENST00000529150.1_5'Flank	NM_004620.3	NP_004611.1	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	119	Interaction with TAX1BP1.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of protein kinase activity (GO:0032147)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic signaling pathway (GO:0097190)|bone resorption (GO:0045453)|cell development (GO:0048468)|cellular response to lipopolysaccharide (GO:0071222)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein autoubiquitination (GO:0051865)|protein complex assembly (GO:0006461)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of immunoglobulin secretion (GO:0051023)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	histone deacetylase binding (GO:0042826)|ligase activity (GO:0016874)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)	27	all_lung(20;0.211)	all_hematologic(20;0.107)				AAATTGTCTGGAAATAGTTGA	0.358																																					p.P119T		Atlas-SNP	.											.	TRAF6	56	.	0			c.C355A						.						111	103	106					11																	36520132		2202	4298	6500	SO:0001583	missense	7189	exon3			TGTCTGGAAATAG		CCDS7901.1	11p12	2013-01-09	2012-02-23		ENSG00000175104	ENSG00000175104		"RING-type (C3HC4) zinc fingers"	12036	protein-coding gene	gene with protein product		602355	"TNF receptor-associated factor 6"			8837778	Standard	NM_004620		Approved	RNF85	uc001mws.2	Q9Y4K3	OTTHUMG00000166391	ENST00000526995.1:c.355C>A	chr11.hg19:g.36520132G>T	ENSP00000433623:p.Pro119Thr	102.0	0.0		55.0	13.0	NM_004620	A6NKI7|A8KAB3|D3DR16|Q8NEH5	Missense_Mutation	SNP	ENST00000526995.1	hg19	CCDS7901.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.125643	0.77436	.	.	ENSG00000175104	ENST00000526995;ENST00000348124	D;D	0.84146	-1.81;-1.81	5.43	5.43	0.79202	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.90786	0.7107	M	0.92219	3.285	0.80722	D	1	P	0.51791	0.948	P	0.45538	0.484	D	0.92974	0.6400	10	0.72032	D	0.01	-12.6803	19.6031	0.95572	0.0:0.0:1.0:0.0	.	119	Q9Y4K3	TRAF6_HUMAN	T	119	ENSP00000433623:P119T;ENSP00000337853:P119T	ENSP00000337853:P119T	P	-	1	0	TRAF6	36476708	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.708000	0.92522	0.655000	0.94253	CCA	.	.		0.358	TRAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389530.1	NM_145803		T	36520132	G	T	36520132	3	4	196	1	0	0	0	0	1	0	0	0	16460	1174	41	3	1233	3	TRAF6	11	36520132	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	29876511	36520132	98486384	57	28867										
KBTBD4	55709	hgsc.bcm.edu	37	chr11	47599068	47599068	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gtgcttggcagccgtatagaGctcaggatcactgtgccgat	13	10	2	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr11:47599068G>A	ENST00000526005.1	-	2	637	c.484C>T	c.(484-486)Ctc>Ttc	p.L162F	NDUFS3_ENST00000263774.4_5'Flank|NDUFS3_ENST00000534716.2_5'Flank|NDUFS3_ENST00000533507.1_Intron|NDUFS3_ENST00000529276.1_5'Flank|NDUFS3_ENST00000534208.1_5'Flank|KBTBD4_ENST00000395288.2_Missense_Mutation_p.L162F|KBTBD4_ENST00000525720.1_Missense_Mutation_p.L211F|RNU5E-10P_ENST00000363506.1_RNA|KBTBD4_ENST00000450908.1_5'Flank|NDUFS3_ENST00000528192.1_5'Flank|KBTBD4_ENST00000533290.1_Missense_Mutation_p.L187F|KBTBD4_ENST00000430070.2_Missense_Mutation_p.L178F			Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	162	BACK.									NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	24						GCCGTATAGAGCTCAGGATCA	0.537																																					p.L178F		Atlas-SNP	.											.	KBTBD4	55	.	0			c.C532T						.						148	144	145					11																	47599068		2201	4298	6499	SO:0001583	missense	55709	exon2			TATAGAGCTCAGG	AF151086	CCDS7940.1, CCDS44594.1	11p11.2	2013-01-08	2003-12-12	2003-12-17	ENSG00000123444	ENSG00000123444		"BTB/POZ domain containing"	23761	protein-coding gene	gene with protein product			"BTB and kelch domain containing 4"	BKLHD4		11042152	Standard	NM_018095		Approved	FLJ10450, HSPC252	uc001nfz.3	Q9NVX7	OTTHUMG00000166894	ENST00000526005.1:c.484C>T	chr11.hg19:g.47599068G>A	ENSP00000433340:p.Leu162Phe	99.0	0.0		66.0	11.0	NM_018095	D3DQS1|D3DQS2|Q6IA85|Q9BUC3|Q9NV76	Missense_Mutation	SNP	ENST00000526005.1	hg19	CCDS7940.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279711	0.80692	.	.	ENSG00000123444	ENST00000526005;ENST00000533290;ENST00000395288;ENST00000430070;ENST00000525720;ENST00000529499	D;D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5;-1.5	5.54	5.54	0.83059	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	D	0.91188	0.7224	M	0.85373	2.75	0.58432	D	0.999998	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.83275	0.994;0.996;0.996	D	0.92107	0.5693	10	0.87932	D	0	-12.1682	19.478	0.94996	0.0:0.0:1.0:0.0	.	178;162;187	Q9NVX7-2;Q9NVX7;B3KRH9	.;KBTB4_HUMAN;.	F	162;187;162;178;211;162	ENSP00000433340:L162F;ENSP00000436713:L187F;ENSP00000378703:L162F;ENSP00000415106:L178F;ENSP00000434477:L211F;ENSP00000433404:L162F	ENSP00000378703:L162F	L	-	1	0	KBTBD4	47555644	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.468000	0.60162	2.607000	0.88179	0.462000	0.41574	CTC	.	.		0.537	KBTBD4-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000391763.1	NM_016506		A	47599068	G	A	47599068	3	1	196	1	0	0	0	0	1	0	0	0	8004	971	34	3	1084	3	KBTBD4	11	47599068	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	11078936	47599068	87407448	58	28868										
OR5R1	219479	hgsc.bcm.edu	37	chr11	56185178	56185178	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aaggggaggtcatcacaataGaaatggttaattaagtttgg	12	3	2	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr11:56185178G>A	ENST00000312253.1	-	1	530	c.531C>T	c.(529-531)ttC>ttT	p.F177F		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					CATCACAATAGAAATGGTTAA	0.438																																					p.F177F		Atlas-SNP	.											.	OR5R1	83	.	0			c.C531T						.						102	96	98					11																	56185178		2201	4296	6497	SO:0001819	synonymous_variant	219479	exon1			ACAATAGAAATGG	AB065504	CCDS31530.1	11q11	2012-08-09		2004-03-10	ENSG00000174942	ENSG00000174942		"GPCR / Class A : Olfactory receptors"	14841	protein-coding gene	gene with protein product				OR5R1P			Standard	NM_001004744		Approved		uc010rji.2	Q8NH85	OTTHUMG00000154219	ENST00000312253.1:c.531C>T	chr11.hg19:g.56185178G>A		178.0	0.0		92.0	38.0	NM_001004744		Silent	SNP	ENST00000312253.1	hg19	CCDS31530.1																																																																																			.	.		0.438	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744		A	56185178	G	A	56185178	2	1	196	1	0	0	0	0	0	0	0	1	11189	933	33	3		3	OR5R1	11	56185178	Silent	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	8586110	56185178	78821338	59	28869										
TMEM223	79064	hgsc.bcm.edu	37	chr11	62558364	62558364	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	agaccggagagagaagagaaGaccagcaccgagtacgaggg	16	8	0	5			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr11:62558364G>C	ENST00000307366.7	-	2	366	c.340C>G	c.(340-342)Ctt>Gtt	p.L114V	TMEM223_ENST00000527073.1_Intron|NXF1_ENST00000533048.1_5'Flank|TMEM223_ENST00000525631.1_Intron	NM_001080501.2	NP_001073970.1	A0PJW6	TM223_HUMAN	transmembrane protein 223	114						integral component of membrane (GO:0016021)											GAGAAGAGAAGACCAGCACCG	0.597																																					p.L114V		Atlas-SNP	.											.	TMEM223	22	.	0			c.C340G						.						22	24	23					11																	62558364		2071	4201	6272	SO:0001583	missense	79064	exon2			AGAGAAGACCAGC		CCDS44628.1	11q12.3	2008-12-08				ENSG00000168569			28464	protein-coding gene	gene with protein product							Standard	NM_001080501		Approved	MGC3196	uc001nve.2	A0PJW6		ENST00000307366.7:c.340C>G	chr11.hg19:g.62558364G>C	ENSP00000303987:p.Leu114Val	125.0	0.0		65.0	32.0	NM_001080501	Q504S0|Q86YD4|Q8WUC5|Q96HG0	Missense_Mutation	SNP	ENST00000307366.7	hg19	CCDS44628.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.362788	0.24684	.	.	ENSG00000168569	ENST00000307366	T	0.46819	0.86	5.32	2.36	0.29203	.	0.601836	0.15659	N	0.250987	T	0.38585	0.1046	L	0.53249	1.67	0.18873	N	0.999989	B	0.25563	0.129	B	0.23419	0.046	T	0.28870	-1.0030	10	0.41790	T	0.15	-5.3003	5.6699	0.17717	0.1686:0.3111:0.5203:0.0	.	114	A0PJW6	TM223_HUMAN	V	114	ENSP00000303987:L114V	ENSP00000303987:L114V	L	-	1	0	TMEM223	62314940	0.991000	0.36638	0.119000	0.21687	0.605000	0.37080	1.660000	0.37397	0.220000	0.20860	0.455000	0.32223	CTT	.	.		0.597	TMEM223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395674.1			C	62558364	G	C	62558364	3	2	196	1	0	0	0	0	1	0	0	0	16161	942	33	4	272	4	TMEM223	11	62558364	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	6373186	62558364	72448152	60	28870										
PGR	5241	hgsc.bcm.edu	37	chr11	100996767	100996767	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ccctcttaaagaagaccttaCagctcccacaggtaaggaca	7	13	1	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr11:100996767C>G	ENST00000325455.5	-	2	3213	c.1760G>C	c.(1759-1761)tGt>tCt	p.C587S	PGR_ENST00000263463.5_Missense_Mutation_p.C587S|PGR_ENST00000534013.1_5'UTR	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	587					cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	GAAGACCTTACAGCTCCCACA	0.413																																					p.C587S	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.G1760C						.						102	89	93					11																	100996767		2203	4300	6503	SO:0001583	missense	5241	exon2			ACCTTACAGCTCC	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"Nuclear hormone receptors"	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.1760G>C	chr11.hg19:g.100996767C>G	ENSP00000325120:p.Cys587Ser	100.0	0.0		66.0	13.0	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	hg19	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.669204	0.88348	.	.	ENSG00000082175	ENST00000325455;ENST00000263463;ENST00000537623	D;D	0.99803	-6.82;-6.82	5.4	5.4	0.78164	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.000000	0.85682	D	0.000000	D	0.99871	0.9939	H	0.96365	3.81	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.96611	0.9452	10	0.72032	D	0.01	.	19.1896	0.93660	0.0:1.0:0.0:0.0	.	587;587	Q8TDS3;P06401	.;PRGR_HUMAN	S	587	ENSP00000325120:C587S;ENSP00000263463:C587S	ENSP00000263463:C587S	C	-	2	0	PGR	100501977	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.519000	0.84933	0.655000	0.94253	TGT	.	.		0.413	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			G	100996767	C	G	100996767	3	3	196	1	0	0	0	0	1	0	0	0	11814	478	17	4	1069	4	PGR	11	100996767	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	38438403	100996767	34009749	61	28871										
EXPH5	23086	hgsc.bcm.edu	37	chr11	108389093	108389093	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ccagaggtgaattgtatattTttgcctgctaattttaaagc	8	6	0	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr11:108389093T>G	ENST00000265843.4	-	5	610	c.500A>C	c.(499-501)aAa>aCa	p.K167T	EXPH5_ENST00000428840.1_Missense_Mutation_p.K91T|EXPH5_ENST00000525344.1_Missense_Mutation_p.K160T|EXPH5_ENST00000443411.1_5'UTR|EXPH5_ENST00000524840.1_5'UTR	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	167					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		ATTGTATATTTTTGCCTGCTA	0.433																																					p.K167T		Atlas-SNP	.											.	EXPH5	193	.	0			c.A500C						.						61	55	57					11																	108389093		2201	4298	6499	SO:0001583	missense	23086	exon5			TATATTTTTGCCT		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.500A>C	chr11.hg19:g.108389093T>G	ENSP00000265843:p.Lys167Thr	95.0	0.0		60.0	18.0	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	hg19	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.641717	0.67244	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000525344;ENST00000439956;ENST00000526312	T;T;T;T	0.03386	4.11;4.03;4.11;3.95	5.12	3.97	0.46021	.	0.312451	0.28182	N	0.016294	T	0.11367	0.0277	M	0.67953	2.075	0.80722	D	1	D	0.67145	0.996	P	0.59948	0.866	T	0.00643	-1.1630	10	0.52906	T	0.07	-18.8221	9.0827	0.36561	0.0:0.0903:0.0:0.9097	.	167	Q8NEV8	EXPH5_HUMAN	T	167;91;160;11;91	ENSP00000265843:K167T;ENSP00000391966:K91T;ENSP00000432546:K160T;ENSP00000432683:K91T	ENSP00000265843:K167T	K	-	2	0	EXPH5	107894303	1.000000	0.71417	0.989000	0.46669	0.749000	0.42624	1.961000	0.40432	2.056000	0.61249	0.533000	0.62120	AAA	.	.		0.433	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		G	108389093	T	G	108389093	3	3	196	1	0	0	0	0	1	0	0	0	5324	1841	64	5	5477	5	EXPH5	11	108389093	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	7392326	108389093	26617423	62	28872										
SIK2	23235	hgsc.bcm.edu	37	chr11	111591262	111591262	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tgtggactctgagtatgataTggggtctgttcagagggacc	15	6	3	3			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr11:111591262T>C	ENST00000304987.3	+	11	1729	c.1556T>C	c.(1555-1557)aTg>aCg	p.M519T	SIK2_ENST00000533868.1_3'UTR	NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	519					insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						GAGTATGATATGGGGTCTGTT	0.458																																					p.M519T		Atlas-SNP	.											.	SIK2	89	.	0			c.T1556C						.						113	113	113					11																	111591262		2201	4297	6498	SO:0001583	missense	23235	exon11			ATGATATGGGGTC	AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"SNF1-like kinase 2"	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.1556T>C	chr11.hg19:g.111591262T>C	ENSP00000305976:p.Met519Thr	145.0	0.0		83.0	16.0	NM_015191	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Missense_Mutation	SNP	ENST00000304987.3	hg19	CCDS8347.1	.	.	.	.	.	.	.	.	.	.	T	13.53	2.265745	0.40095	.	.	ENSG00000170145	ENST00000304987	T	0.75367	-0.93	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.70150	0.3191	L	0.57536	1.79	0.58432	D	0.999999	B	0.26002	0.139	B	0.23574	0.047	T	0.65899	-0.6056	10	0.21540	T	0.41	.	15.4975	0.75666	0.0:0.0:0.0:1.0	.	519	Q9H0K1	SIK2_HUMAN	T	519	ENSP00000305976:M519T	ENSP00000305976:M519T	M	+	2	0	SIK2	111096472	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.434000	0.80377	2.324000	0.78689	0.533000	0.62120	ATG	.	.		0.458	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191		C	111591262	T	C	111591262	3	2	196	1	0	0	0	0	1	0	0	0	14333	1464	51	2	1598	2	SIK2	11	111591262	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	3202169	111591262	23415254	63	28873										
PTPRR	5801	hgsc.bcm.edu	37	chr12	71155351	71155351	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cagagggcagagcatcagaaAttcctgtttttcggtttatg	11	7	1	3			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr12:71155351A>G	ENST00000283228.2	-	4	979	c.527T>C	c.(526-528)aTt>aCt	p.I176T	PTPRR_ENST00000342084.4_Missense_Mutation_p.I64T	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	176					ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		AGCATCAGAAATTCCTGTTTT	0.348																																					p.I176T		Atlas-SNP	.											.	PTPRR	109	.	0			c.T527C						.						132	130	131					12																	71155351		2203	4300	6503	SO:0001583	missense	5801	exon4			TCAGAAATTCCTG	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.527T>C	chr12.hg19:g.71155351A>G	ENSP00000283228:p.Ile176Thr	178.0	0.0		107.0	44.0	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	hg19	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	A	8.910	0.958480	0.18507	.	.	ENSG00000153233	ENST00000283228;ENST00000342084	T;T	0.33654	1.4;1.4	5.48	3.09	0.35607	.	0.764738	0.10983	U	0.612522	T	0.15739	0.0379	N	0.03608	-0.345	0.19300	N	0.99998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.23976	-1.0173	10	0.25106	T	0.35	-0.7167	6.751	0.23487	0.7856:0.0:0.074:0.1404	.	64;176	F5GXR7;Q15256	.;PTPRR_HUMAN	T	176;64	ENSP00000283228:I176T;ENSP00000339605:I64T	ENSP00000283228:I176T	I	-	2	0	PTPRR	69441618	0.001000	0.12720	0.117000	0.21633	0.995000	0.86356	1.306000	0.33505	0.874000	0.35823	0.368000	0.22195	ATT	.	.		0.348	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		G	71155351	A	G	71155351	3	3	196	1	0	0	0	0	1	0	0	0	12825	101	4	2	1490	2	PTPRR	12	71155351	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10		71155351	62696544	64	28874										
USP44	84101	hgsc.bcm.edu	37	chr12	95927545	95927545	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gtgattgttcaaaccatgttCgaaagattttacccattagt	7	7	1	2	rs371620070		TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr12:95927545C>A	ENST00000258499.3	-	2	776	c.488G>T	c.(487-489)cGa>cTa	p.R163L	USP44_ENST00000393091.2_Missense_Mutation_p.R163L|USP44_ENST00000552440.1_Missense_Mutation_p.R163L|USP44_ENST00000537435.2_Missense_Mutation_p.R163L	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	163					mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.R163Q(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						AAACCATGTTCGAAAGATTTT	0.373																																					p.R163L		Atlas-SNP	.											USP44,caecum,carcinoma,0,1	USP44	83	.	1	Substitution - Missense(1)	large_intestine(1)	c.G488T						.						108	107	107					12																	95927545		2203	4300	6503	SO:0001583	missense	84101	exon2			CATGTTCGAAAGA	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"Ubiquitin-specific peptidases"	20064	protein-coding gene	gene with protein product		610993	"ubiquitin specific protease 44"			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.488G>T	chr12.hg19:g.95927545C>A	ENSP00000258499:p.Arg163Leu	119.0	0.0		127.0	49.0	NM_032147	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	hg19	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.140562	0.37825	.	.	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435;ENST00000551837	T;T;T;T;T	0.50277	3.67;3.67;2.39;3.67;0.75	5.0	5.0	0.66597	.	0.059766	0.64402	D	0.000004	T	0.48502	0.1503	M	0.62723	1.935	0.58432	D	0.999998	B	0.32409	0.37	B	0.33890	0.172	T	0.44019	-0.9355	10	0.23302	T	0.38	.	18.6628	0.91477	0.0:1.0:0.0:0.0	.	163	Q9H0E7	UBP44_HUMAN	L	163	ENSP00000258499:R163L;ENSP00000376806:R163L;ENSP00000448670:R163L;ENSP00000442629:R163L;ENSP00000448601:R163L	ENSP00000258499:R163L	R	-	2	0	USP44	94451676	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	4.472000	0.60189	2.474000	0.83562	0.561000	0.74099	CGA	.	.		0.373	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		A	95927545	C	A	95927545	3	1	196	1	0	0	0	0	1	0	0	0	17090	884	31	1	1670	1	USP44	12	95927545	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	24772194	95927545	37924350	65	28875										
MYO16	23026	hgsc.bcm.edu	37	chr13	109777634	109777634	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ccgggaaaatgaccggctccGtagtgaaatgaacgctccct	11	12	0	3	rs375704783		TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr13:109777634G>A	ENST00000357550.2	+	29	3685	c.3644G>A	c.(3643-3645)cGt>cAt	p.R1215H	MYO16_ENST00000356711.2_Missense_Mutation_p.R1215H|MYO16_ENST00000457511.2_Missense_Mutation_p.R727H	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			GACCGGCTCCGTAGTGAAATG	0.463																																					p.R1237H		Atlas-SNP	.											.	MYO16	285	.	0			c.G3710A						.	G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	60	56	57		3710,3644	4.9	0.2	13		57	0,8600		0,0,4300	no	missense,missense	MYO16	NM_001198950.1,NM_015011.1	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	1237/1881,1215/1859	109777634	1,13005	2203	4300	6503	SO:0001583	missense	23026	exon30			GGCTCCGTAGTGA		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.3644G>A	chr13.hg19:g.109777634G>A	ENSP00000350160:p.Arg1215His	514.0	0.0		294.0	32.0	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	hg19	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221228	0.79464	2.27E-4	0.0	ENSG00000041515	ENST00000356711;ENST00000357550;ENST00000457511	T;T;T	0.59906	0.23;0.23;0.23	5.75	4.9	0.64082	.	0.000000	0.38959	U	0.001511	T	0.71099	0.3300	M	0.76328	2.33	0.43942	D	0.9966	D;D	0.89917	1.0;0.999	D;P	0.67382	0.951;0.894	T	0.71826	-0.4475	9	.	.	.	.	9.5836	0.39504	0.1528:0.0:0.8472:0.0	.	727;1215	F8W883;Q9Y6X6	.;MYO16_HUMAN	H	1215;1215;727	ENSP00000349145:R1215H;ENSP00000350160:R1215H;ENSP00000401633:R727H	.	R	+	2	0	MYO16	108575635	0.999000	0.42202	0.227000	0.23927	0.915000	0.54546	4.783000	0.62403	2.716000	0.92895	0.655000	0.94253	CGT	.	.		0.463	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		A	109777634	G	A	109777634	3	1	196	1	0	0	0	0	1	0	0	0	10073	1145	40	1	3758	1	MYO16	13	109777634	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10		109777634	5392244	66	28876										
PSMB5	5693	hgsc.bcm.edu	37	chr14	23503937	23503937	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	atgaagcatttcgattcctgGctcttctgggacaccccagc	9	13	2	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr14:23503937G>A	ENST00000361611.6	-	1	417	c.154C>T	c.(154-156)Cca>Tca	p.P52S	AL132780.1_ENST00000385031.1_RNA|PSMB5_ENST00000460922.2_Missense_Mutation_p.P52S|PSMB5_ENST00000493471.2_Missense_Mutation_p.P52S|PSMB5_ENST00000425762.2_Intron	NM_002797.3	NP_002788.1	P28074	PSB5_HUMAN	proteasome (prosome, macropain) subunit, beta type, 5	52					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to oxidative stress (GO:0006979)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)|Carfilzomib(DB08889)	TCGATTCCTGGCTCTTCTGGG	0.612																																					p.P52S		Atlas-SNP	.											.	PSMB5	31	.	0			c.C154T						.						51	47	48					14																	23503937		2203	4300	6503	SO:0001583	missense	5693	exon1			TTCCTGGCTCTTC	D29011	CCDS9584.1, CCDS45083.1, CCDS45084.1	14q11.2	2008-08-29			ENSG00000100804	ENSG00000100804		"Proteasome (prosome, macropain) subunits"	9542	protein-coding gene	gene with protein product		600306				8066462, 8811196	Standard	NM_001130725		Approved	X, MB1	uc001wii.3	P28074	OTTHUMG00000028713	ENST00000361611.6:c.154C>T	chr14.hg19:g.23503937G>A	ENSP00000355325:p.Pro52Ser	64.0	0.0		59.0	15.0	NM_001144932	B2R4N9|B4DUM9|D3DS43|E9PAV2|Q16242|Q6PEW2|Q7Z3B5|Q86T01|Q9TNN9	Missense_Mutation	SNP	ENST00000361611.6	hg19	CCDS9584.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.547653	0.45383	.	.	ENSG00000100804	ENST00000361611;ENST00000493471;ENST00000460922	T;T;T	0.49432	0.78;0.78;0.78	5.04	5.04	0.67666	.	0.065101	0.64402	D	0.000009	T	0.38585	0.1046	N	0.24115	0.695	0.80722	D	1	B;B	0.33171	0.4;0.016	B;B	0.36808	0.233;0.01	T	0.19976	-1.0289	10	0.29301	T	0.29	-11.1309	17.1802	0.86853	0.0:0.0:1.0:0.0	.	52;52	P28074-2;P28074	.;PSB5_HUMAN	S	52	ENSP00000355325:P52S;ENSP00000452424:P52S;ENSP00000451286:P52S	ENSP00000334973:P52S	P	-	1	0	PSMB5	22573777	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	4.432000	0.59922	2.348000	0.79779	0.555000	0.69702	CCA	.	.		0.612	PSMB5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071695.4	NM_002797		A	23503937	G	A	23503937	3	1	196	1	0	0	0	0	1	0	0	0	12692	1203	42	3	738	3	PSMB5	14	23503937	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10		23503937	83845603	67	28877										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33014464	33014464	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tgattctctaacagaagtggAtgactcaggacaattaacca	8	8	2	3			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr14:33014464A>T	ENST00000280979.4	+	4	775	c.605A>T	c.(604-606)gAt>gTt	p.D202V	AKAP6_ENST00000557272.1_Missense_Mutation_p.D202V|AKAP6_ENST00000557354.1_Missense_Mutation_p.D202V	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	202					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		ACAGAAGTGGATGACTCAGGA	0.398																																					p.D202V	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.A605T						.						147	141	143					14																	33014464		2203	4300	6503	SO:0001583	missense	9472	exon4			AAGTGGATGACTC	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.605A>T	chr14.hg19:g.33014464A>T	ENSP00000280979:p.Asp202Val	163.0	0.0		68.0	15.0	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.009664	0.75046	.	.	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272	T;T;T	0.39056	2.36;1.12;1.1	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.64538	0.2607	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.66984	-0.5785	10	0.87932	D	0	-19.4019	16.6438	0.85155	1.0:0.0:0.0:0.0	.	202;202	A7E242;Q13023	.;AKAP6_HUMAN	V	202	ENSP00000280979:D202V;ENSP00000450531:D202V;ENSP00000451247:D202V	ENSP00000280979:D202V	D	+	2	0	AKAP6	32084215	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.555000	0.90693	2.333000	0.79357	0.533000	0.62120	GAT	.	.		0.398	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33014464	A	T	33014464	3	4	196	1	0	0	0	0	1	0	0	0	455	333	12	4	615	4	AKAP6	14	33014464	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	9510527	33014464	74335076	68	28878										
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36211696	36211696	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	catgaacaaaggtttttcctCttgttggatccattcttgat	7	8	2	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr14:36211696C>T	ENST00000389698.3	-	11	1717	c.1327G>A	c.(1327-1329)Gag>Aag	p.E443K	RALGAPA1_ENST00000382366.3_Missense_Mutation_p.E443K|RALGAPA1_ENST00000554704.1_5'UTR|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.E443K|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.E443K	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	443					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GGTTTTTCCTCTTGTTGGATC	0.368																																					p.E443K		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.G1327A						.						51	50	50					14																	36211696		2201	4279	6480	SO:0001583	missense	253959	exon11			TTTCCTCTTGTTG	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.1327G>A	chr14.hg19:g.36211696C>T	ENSP00000374348:p.Glu443Lys	351.0	0.0		207.0	37.0	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.335662	0.41398	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	D;D;D;D;D	0.94138	-3.36;-3.36;-3.36;-3.36;-3.36	4.98	4.98	0.66077	.	0.054420	0.64402	D	0.000001	D	0.87861	0.6284	L	0.29908	0.895	0.42217	D	0.991832	B;B;B;B;B	0.21606	0.056;0.034;0.004;0.004;0.058	B;B;B;B;B	0.21917	0.027;0.012;0.012;0.009;0.037	D	0.83656	0.0158	10	0.25751	T	0.34	-11.8038	11.7238	0.51698	0.0:0.9188:0.0:0.0812	.	443;443;443;443;443	Q6GYQ0-6;B9EK38;Q6GYQ0-3;Q6GYQ0-2;Q6GYQ0	.;.;.;.;RGPA1_HUMAN	K	443	ENSP00000374348:E443K;ENSP00000302647:E443K;ENSP00000258840:E443K;ENSP00000371803:E443K;ENSP00000451877:E443K	ENSP00000258840:E443K	E	-	1	0	RALGAPA1	35281447	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.760000	0.55235	2.310000	0.77875	0.484000	0.47621	GAG	.	.		0.368	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		T	36211696	C	T	36211696	3	4	196	1	0	0	0	0	1	0	0	0	13028	922	32	3	5056	3	RALGAPA1	14	36211696	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	3197232	36211696	71137844	69	28879										
CATSPERB	79820	hgsc.bcm.edu	37	chr14	92076871	92076871	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ctgactgtctttatgaactcCactaatccagtcttcaaatg	5	11	3	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr14:92076871C>T	ENST00000256343.3	-	21	2707	c.2551G>A	c.(2551-2553)Gga>Aga	p.G851R		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	851					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				TTATGAACTCCACTAATCCAG	0.358																																					p.G851R		Atlas-SNP	.											.	CATSPERB	114	.	0			c.G2551A						.						88	86	86					14																	92076871		2203	4300	6503	SO:0001583	missense	79820	exon21			GAACTCCACTAAT	AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.2551G>A	chr14.hg19:g.92076871C>T	ENSP00000256343:p.Gly851Arg	75.0	0.0		40.0	8.0	NM_024764	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	hg19	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.898519	0.52227	.	.	ENSG00000133962	ENST00000256343	T	0.56776	0.44	5.75	3.87	0.44632	.	0.129707	0.34652	N	0.003785	T	0.58921	0.2156	M	0.64404	1.975	0.09310	N	0.999996	D	0.64830	0.994	P	0.56474	0.799	T	0.53229	-0.8468	10	0.72032	D	0.01	-19.2889	6.3682	0.21468	0.183:0.7264:0.0:0.0906	.	851	Q9H7T0	CTSRB_HUMAN	R	851	ENSP00000256343:G851R	ENSP00000256343:G851R	G	-	1	0	CATSPERB	91146624	0.481000	0.25941	0.056000	0.19401	0.022000	0.10575	2.425000	0.44723	1.363000	0.46019	0.563000	0.77884	GGA	.	.		0.358	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		T	92076871	C	T	92076871	3	4	196	1	0	0	0	0	1	0	0	0	2693	603	21	3	827	3	CATSPERB	14	92076871	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	55865175	92076871	15272669	70	28880										
RASGRP1	10125	hgsc.bcm.edu	37	chr15	38798090	38798090	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cataggaaagctcatagattTcatcctcagtgtagtaaaga	8	7	3	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr15:38798090T>C	ENST00000310803.5	-	10	1451	c.1274A>G	c.(1273-1275)gAa>gGa	p.E425G	RP11-102L12.2_ENST00000560231.1_RNA|RASGRP1_ENST00000450598.2_Missense_Mutation_p.E425G|RASGRP1_ENST00000559830.1_Missense_Mutation_p.E425G|RASGRP1_ENST00000539159.1_Missense_Mutation_p.E377G|RASGRP1_ENST00000561180.1_Missense_Mutation_p.E476G|RASGRP1_ENST00000558164.1_Missense_Mutation_p.E425G	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	425	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		CTCATAGATTTCATCCTCAGT	0.448																																					p.E425G		Atlas-SNP	.											.	RASGRP1	50	.	0			c.A1274G						.						84	83	83					15																	38798090		1889	4104	5993	SO:0001583	missense	10125	exon10			TAGATTTCATCCT	AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"EF-hand domain containing"	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.1274A>G	chr15.hg19:g.38798090T>C	ENSP00000310244:p.Glu425Gly	101.0	0.0		71.0	29.0	NM_001128602	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Missense_Mutation	SNP	ENST00000310803.5	hg19	CCDS45222.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.634764	0.87660	.	.	ENSG00000172575	ENST00000310803;ENST00000450598;ENST00000415523;ENST00000431814;ENST00000539159;ENST00000414708;ENST00000541438	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	4.6	4.6	0.57074	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.76737	0.4029	M	0.90542	3.125	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.998;1.0	D;D;D;D	0.83275	0.996;0.988;0.98;0.996	T	0.82581	-0.0386	10	0.87932	D	0	-19.4816	14.1614	0.65450	0.0:0.0:0.0:1.0	.	425;425;425;425	C9JM27;C9JCE5;O95267;O95267-2	.;.;GRP1_HUMAN;.	G	425;425;425;425;377;425;425	ENSP00000310244:E425G;ENSP00000388540:E425G;ENSP00000444762:E377G;ENSP00000413105:E425G	ENSP00000310244:E425G	E	-	2	0	RASGRP1	36585382	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.698000	0.84413	1.909000	0.55274	0.533000	0.62120	GAA	.	.		0.448	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739		C	38798090	T	C	38798090	3	2	196	1	0	0	0	0	1	0	0	0	13089	1783	62	2	1151	2	RASGRP1	15	38798090	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10		38798090	63733302	71	28881										
RHOV	171177	hgsc.bcm.edu	37	chr15	41165411	41165411	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cttctgcgtcaaggctgagcActcaaggtagcagcaggctc	12	12	3	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr15:41165411A>G	ENST00000220507.4	-	3	705	c.556T>C	c.(556-558)Tgc>Cgc	p.C186R	AC025166.1_ENST00000582049.1_RNA	NM_133639.3	NP_598378.3			ras homolog family member V											central_nervous_system(1)|large_intestine(1)	2		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.58e-05)|COAD - Colon adenocarcinoma(120;0.149)|BRCA - Breast invasive adenocarcinoma(123;0.163)		AAGGCTGAGCACTCAAGGTAG	0.577																																					p.C186R	Pancreas(13;103 483 3593 12123 44457)	Atlas-SNP	.											.	RHOV	6	.	0			c.T556C						.						89	91	90					15																	41165411		2203	4300	6503	SO:0001583	missense	171177	exon3			CTGAGCACTCAAG	AY059636	CCDS10068.1	15q13.3	2012-02-27	2012-02-27	2004-03-24	ENSG00000104140	ENSG00000104140			18313	protein-coding gene	gene with protein product			"ras homolog gene family, member V"	ARHV		11839775	Standard	NM_133639		Approved	Chp, WRCH2	uc001znd.3	Q96L33	OTTHUMG00000130134	ENST00000220507.4:c.556T>C	chr15.hg19:g.41165411A>G	ENSP00000220507:p.Cys186Arg	87.0	0.0		74.0	18.0	NM_133639		Missense_Mutation	SNP	ENST00000220507.4	hg19	CCDS10068.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.195131	0.78902	.	.	ENSG00000104140	ENST00000220507	T	0.71461	-0.57	5.63	5.63	0.86233	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.89217	0.6652	H	0.96175	3.78	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92595	0.6086	10	0.87932	D	0	-11.6267	15.8478	0.78905	1.0:0.0:0.0:0.0	.	186	Q96L33	RHOV_HUMAN	R	186	ENSP00000220507:C186R	ENSP00000220507:C186R	C	-	1	0	RHOV	38952703	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	9.321000	0.96353	2.157000	0.67596	0.374000	0.22700	TGC	.	.		0.577	RHOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252442.1			G	41165411	A	G	41165411	3	3	196	1	0	0	0	0	1	0	0	0	13361	159	6	2	158	2	RHOV	15	41165411	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	2367321	41165411	61365981	72	28882										
VPS18	57617	hgsc.bcm.edu	37	chr15	41191757	41191757	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gcccagggtttctcagggctCtttgcagcttacacggacca	11	13	2	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr15:41191757C>T	ENST00000220509.5	+	4	1080	c.741C>T	c.(739-741)ctC>ctT	p.L247L	VPS18_ENST00000558474.1_Intron	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	247					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		TCTCAGGGCTCTTTGCAGCTT	0.607																																					p.L247L		Atlas-SNP	.											.	VPS18	67	.	0			c.C741T						.						65	70	68					15																	41191757		2203	4300	6503	SO:0001819	synonymous_variant	57617	exon4			AGGGCTCTTTGCA	AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"vacuolar protein sorting protein 18"			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.741C>T	chr15.hg19:g.41191757C>T		25.0	0.0		24.0	12.0	NM_020857	Q8TCG0|Q96DI3|Q9H268	Silent	SNP	ENST00000220509.5	hg19	CCDS10069.1																																																																																			.	.		0.607	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2			T	41191757	C	T	41191757	2	4	196	1	0	0	0	0	0	0	0	1	17209	900	32	3		3	VPS18	15	41191757	Silent	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	26346	41191757	61339635	73	28883										
NKD1	85407	hgsc.bcm.edu	37	chr16	50667280	50667280	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ggtctcagagctccagcaacGgctccggggcacccaggacg	14	15	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr16:50667280G>T	ENST00000268459.3	+	10	1225	c.1001G>T	c.(1000-1002)cGg>cTg	p.R334L		NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	334					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of convergent extension involved in axis elongation (GO:1901233)|positive regulation of non-canonical Wnt signaling pathway via JNK cascade (GO:1901231)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|prostate(1)|urinary_tract(2)	23		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		CTCCAGCAACGGCTCCGGGGC	0.642																																					p.R334L		Atlas-SNP	.											.	NKD1	43	.	0			c.G1001T						.						82	94	90					16																	50667280		2198	4300	6498	SO:0001583	missense	85407	exon10			AGCAACGGCTCCG	AF358135	CCDS10743.1	16q12.1	2013-01-10			ENSG00000140807	ENSG00000140807		"EF-hand domain containing"	17045	protein-coding gene	gene with protein product		607851				11356022	Standard	NM_033119		Approved		uc002egg.2	Q969G9	OTTHUMG00000133169	ENST00000268459.3:c.1001G>T	chr16.hg19:g.50667280G>T	ENSP00000268459:p.Arg334Leu	309.0	0.0		232.0	67.0	NM_033119	B2RC39|Q8WZ08	Missense_Mutation	SNP	ENST00000268459.3	hg19	CCDS10743.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534299	0.64972	.	.	ENSG00000140807	ENST00000268459	T	0.70749	-0.51	4.44	2.5	0.30297	.	0.142167	0.45606	D	0.000357	T	0.75125	0.3807	M	0.79258	2.445	0.46774	D	0.999193	P	0.46064	0.872	P	0.50896	0.653	T	0.73572	-0.3940	10	0.49607	T	0.09	-12.9994	8.8198	0.35018	0.1731:0.0:0.8269:0.0	.	334	Q969G9	NKD1_HUMAN	L	334	ENSP00000268459:R334L	ENSP00000268459:R334L	R	+	2	0	NKD1	49224781	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.692000	0.54727	0.515000	0.28320	-0.203000	0.12734	CGG	.	.		0.642	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1			T	50667280	G	T	50667280	3	4	196	1	0	0	0	0	1	0	0	0	10450	1116	39	1	1039	1	NKD1	16	50667280	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10		50667280	39687473	74	28884										
CX3CL1	6376	hgsc.bcm.edu	37	chr16	57416592	57416592	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cttccaggactgggggcctgGcagcatggcccacgtctctg	14	14	1	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr16:57416592G>A	ENST00000006053.6	+	3	953	c.842G>A	c.(841-843)gGc>gAc	p.G281D	CX3CL1_ENST00000563383.1_Missense_Mutation_p.G287D|CX3CL1_ENST00000565912.1_Missense_Mutation_p.G243D	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	281	Mucin-like stalk.				angiogenesis involved in wound healing (GO:0060055)|cell adhesion (GO:0007155)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|immune response (GO:0006955)|leukocyte adhesive activation (GO:0050902)|leukocyte chemotaxis (GO:0030595)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcium-independent cell-cell adhesion (GO:0051041)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transforming growth factor beta1 production (GO:0032914)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5						TGGGGGCCTGGCAGCATGGCC	0.667																																					p.G281D		Atlas-SNP	.											.	CX3CL1	27	.	0			c.G842A						.						36	40	38					16																	57416592		2198	4300	6498	SO:0001583	missense	6376	exon3			GGCCTGGCAGCAT	U84487	CCDS10779.1	16q13	2013-02-25	2002-08-22	2002-08-23	ENSG00000006210	ENSG00000006210		"Endogenous ligands"	10647	protein-coding gene	gene with protein product		601880	"small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)"	SCYD1		9177350, 9024663	Standard	NM_002996		Approved	NTN, C3Xkine, ABCD-3, CXC3C, CXC3, fractalkine, neurotactin	uc002eli.3	P78423	OTTHUMG00000133469	ENST00000006053.6:c.842G>A	chr16.hg19:g.57416592G>A	ENSP00000006053:p.Gly281Asp	79.0	0.0		67.0	23.0	NM_002996	O00672	Missense_Mutation	SNP	ENST00000006053.6	hg19	CCDS10779.1	.	.	.	.	.	.	.	.	.	.	G	4.626	0.116295	0.08881	.	.	ENSG00000006210	ENST00000006053	T	0.03772	3.81	4.63	-0.314	0.12750	.	1.752800	0.03874	N	0.276091	T	0.02848	0.0085	N	0.05124	-0.11	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43798	-0.9369	10	0.87932	D	0	-25.7703	3.2983	0.06974	0.4146:0.211:0.3744:0.0	.	281	P78423	X3CL1_HUMAN	D	281	ENSP00000006053:G281D	ENSP00000006053:G281D	G	+	2	0	CX3CL1	55974093	0.001000	0.12720	0.000000	0.03702	0.449000	0.32228	0.694000	0.25512	0.063000	0.16370	-0.259000	0.10710	GGC	.	.		0.667	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996		A	57416592	G	A	57416592	3	1	196	1	0	0	0	0	1	0	0	0	4076	1203	42	3	852	3	CX3CL1	16	57416592	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	6749312	57416592	32938161	75	28885										
AGRP	181	hgsc.bcm.edu	37	chr16	67517252	67517252	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ccatctgggctcctcgcgtgGcaggcagtgccagcagcagg	15	14	1	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr16:67517252G>A	ENST00000290953.2	-	2	349	c.50C>T	c.(49-51)gCc>gTc	p.A17V	ATP6V0D1_ENST00000540149.1_5'Flank|ATP6V0D1_ENST00000290949.3_5'Flank|RP11-297D21.4_ENST00000602596.1_RNA	NM_001138.1	NP_001129.1	O00253	AGRP_HUMAN	agouti related neuropeptide	17					adult feeding behavior (GO:0008343)|eating behavior (GO:0042755)|feeding behavior (GO:0007631)|hormone-mediated signaling pathway (GO:0009755)|maternal process involved in female pregnancy (GO:0060135)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of feeding behavior (GO:2000253)|regulation of feeding behavior (GO:0060259)|response to insulin (GO:0032868)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)	neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			endometrium(1)	1		Acute lymphoblastic leukemia(13;0.00263)|all_hematologic(13;0.0274)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0717)|Epithelial(162;0.16)		TCCTCGCGTGGCAGGCAGTGC	0.642																																					p.A17V		Atlas-SNP	.											.	AGRP	8	.	0			c.C50T						.						29	27	28					16																	67517252		2196	4299	6495	SO:0001583	missense	181	exon2			CGCGTGGCAGGCA	U88063	CCDS10839.1	16q22	2014-07-15	2014-07-15		ENSG00000159723	ENSG00000159723		"Endogenous ligands"	330	protein-coding gene	gene with protein product		602311	"agouti (mouse) related protein", "agouti related protein homolog (mouse)"			9119224, 9311920	Standard	NM_001138		Approved	Agrt, ART, ASIP2	uc002etg.1	O00253	OTTHUMG00000137509	ENST00000290953.2:c.50C>T	chr16.hg19:g.67517252G>A	ENSP00000290953:p.Ala17Val	92.0	0.0		95.0	16.0	NM_001138	O15459|Q2TBD9	Missense_Mutation	SNP	ENST00000290953.2	hg19	CCDS10839.1	.	.	.	.	.	.	.	.	.	.	G	9.436	1.086911	0.20390	.	.	ENSG00000159723	ENST00000290953	T	0.43688	0.94	5.67	1.56	0.23342	.	1.767970	0.02185	N	0.060828	T	0.31734	0.0806	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.24905	-1.0147	10	0.46703	T	0.11	-9.8371	8.2418	0.31665	0.3188:0.0:0.6812:0.0	.	17	O00253	AGRP_HUMAN	V	17	ENSP00000290953:A17V	ENSP00000290953:A17V	A	-	2	0	AGRP	66074753	0.000000	0.05858	0.001000	0.08648	0.068000	0.16541	0.018000	0.13422	0.351000	0.24027	-0.251000	0.11542	GCC	.	.		0.642	AGRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268828.1			A	67517252	G	A	67517252	3	1	196	1	0	0	0	0	1	0	0	0	398	1203	42	3	360	3	AGRP	16	67517252	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	10100660	67517252	22837501	76	28886										
ESRP2	80004	hgsc.bcm.edu	37	chr16	68265859	68265859	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	catcaggatggcgcacaaagAgcagcccctcggtaccccca	10	16	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr16:68265859A>C	ENST00000565858.1	-	10	1261	c.1175T>G	c.(1174-1176)cTc>cGc	p.L392R	ESRP2_ENST00000473183.2_Missense_Mutation_p.L382R|RP11-96D1.11_ENST00000571197.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	392	RRM 2.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						GCGCACAAAGAGCAGCCCCTC	0.662																																					p.L382R		Atlas-SNP	.											.	ESRP2	118	.	0			c.T1145G						.						45	44	44					16																	68265859		2198	4300	6498	SO:0001583	missense	80004	exon10			ACAAAGAGCAGCC	AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"RNA binding motif (RRM) containing"	26152	protein-coding gene	gene with protein product		612960	"RNA binding motif protein 35B"	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.1175T>G	chr16.hg19:g.68265859A>C	ENSP00000454554:p.Leu392Arg	134.0	0.0		118.0	17.0	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Missense_Mutation	SNP	ENST00000565858.1	hg19		.	.	.	.	.	.	.	.	.	.	A	22.1	4.239418	0.79800	.	.	ENSG00000103067	ENST00000473183	T	0.06687	3.27	5.83	5.83	0.93111	RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	T	0.23766	0.0575	L	0.46947	1.48	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.00237	-1.1890	10	0.51188	T	0.08	-24.0184	16.1883	0.81967	1.0:0.0:0.0:0.0	.	392;382	Q9H6T0;Q9H6T0-2	ESRP2_HUMAN;.	R	382	ENSP00000418748:L382R	ENSP00000418748:L382R	L	-	2	0	ESRP2	66823360	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.281000	0.95811	2.231000	0.72958	0.454000	0.30748	CTC	.	.		0.662	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939		C	68265859	A	C	68265859	3	2	196	1	0	0	0	0	1	0	0	0	5261	304	11	5	1032	5	ESRP2	16	68265859	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	748607	68265859	22088894	77	28887										
TP53	7157	hgsc.bcm.edu	37	chr17	7578237	7578238	+	Frame_Shift_Del	DEL	CT	CT	-													0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gtgtttctgtcatccaaataCtccacacgcaaatttccttc							TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr17:7578237_7578238delCT	ENST00000269305.4	-	6	800_801	c.611_612delAG	c.(610-612)gagfs	p.E204fs	TP53_ENST00000420246.2_Frame_Shift_Del_p.E204fs|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Frame_Shift_Del_p.E204fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.E204fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.E204fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.E204fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	204	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> Q (in a sporadic cancer; somatic mutation).|E -> V (in a sporadic cancer; somatic mutation).|VE -> LV (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(5)|p.E204D(4)|p.E204E(2)|p.E204fs*5(2)|p.E204G(2)|p.E204A(1)|p.E111D(1)|p.Y205fs*43(1)|p.E204fs*4(1)|p.E72D(1)|p.E204V(1)|p.V203_E204>LV(1)|p.E204fs*39(1)|p.G199fs*42(1)|p.E204_N210delEYLDDRN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CATCCAAATACTCCACACGCAA	0.54		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.204_205del	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,temporoparietal,glioma,+1,1	TP53	33396	.	33	Substitution - Missense(10)|Whole gene deletion(8)|Unknown(5)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Substitution - coding silent(2)|Deletion - In frame(1)|Complex - compound substitution(1)	biliary_tract(5)|endometrium(5)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|central_nervous_system(2)|lung(2)|oesophagus(2)|stomach(1)|soft_tissue(1)|large_intestine(1)|urinary_tract(1)|ovary(1)|autonomic_ganglia(1)|pancreas(1)	c.612_613del						.																																			SO:0001589	frameshift_variant	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.611_612delAG	chr17.hg19:g.7578237_7578238delCT	ENSP00000269305:p.Glu204fs	163.0	0.0		114.0	63.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.54	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7578238	CT	-	7578237	7	5	196	1	0	1	0	1	0	0	0	0	16396	564	20	0	682	0	TP53	17	7578237	Frame_Shift_Del	DEL	CT	TCGA-DD-AADN-01A-11D-A40R-10		7578237	73616973	78	28888										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11660954	11660954	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tccagacagagagagccaacTtaaccattttgttcgacaag	8	10	0	3			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr17:11660954T>A	ENST00000262442.4	+	35	7008	c.6940T>A	c.(6940-6942)Tta>Ata	p.L2314I	DNAH9_ENST00000454412.2_Missense_Mutation_p.L2314I	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2314	AAA 2. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GAGAGCCAACTTAACCATTTT	0.473																																					p.L2314I		Atlas-SNP	.											.	DNAH9	695	.	0			c.T6940A						.						129	112	117					17																	11660954		2203	4300	6503	SO:0001583	missense	1770	exon35			GCCAACTTAACCA	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6940T>A	chr17.hg19:g.11660954T>A	ENSP00000262442:p.Leu2314Ile	145.0	0.0		91.0	51.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.170956	0.57584	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.28666	1.6;1.6	5.11	-1.96	0.07525	.	0.000000	0.64402	D	0.000010	T	0.54351	0.1853	H	0.94222	3.51	0.80722	D	1	D	0.63046	0.992	P	0.62184	0.899	T	0.55835	-0.8078	10	0.72032	D	0.01	.	6.4239	0.21758	0.1089:0.5031:0.0:0.388	.	2314	Q9NYC9	DYH9_HUMAN	I	2314;2314;896	ENSP00000262442:L2314I;ENSP00000414874:L2314I	ENSP00000262442:L2314I	L	+	1	2	DNAH9	11601679	0.997000	0.39634	0.936000	0.37596	0.483000	0.33249	0.709000	0.25734	-0.521000	0.06426	-1.092000	0.02172	TTA	.	.		0.473	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11660954	T	A	11660954	3	1	196	1	0	0	0	0	1	0	0	0	4610	1606	56	4	7078	4	DNAH9	17	11660954	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	4082717	11660954	69534256	79	28889										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12656632	12656632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	agaagggcacagggtctcctCgcccatcagcagccaggtgt	13	13	2	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr17:12656632C>T	ENST00000343344.4	+	10	2027	c.2027C>T	c.(2026-2028)tCg>tTg	p.S676L	AC005358.1_ENST00000609971.1_Missense_Mutation_p.S580L|MYOCD_ENST00000395988.1_3'UTR|MYOCD_ENST00000425538.1_Missense_Mutation_p.S676L			Q8IZQ8	MYCD_HUMAN	myocardin	676					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		AGGGTCTCCTCGCCCATCAGC	0.567																																					p.S676L		Atlas-SNP	.											.	MYOCD	291	.	0			c.C2027T						.						52	56	55					17																	12656632		2203	4300	6503	SO:0001583	missense	93649	exon10			TCTCCTCGCCCAT	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.2027C>T	chr17.hg19:g.12656632C>T	ENSP00000341835:p.Ser676Leu	74.0	0.0		32.0	20.0	NM_001146312	Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	hg19	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.479353	0.63849	.	.	ENSG00000141052	ENST00000395982;ENST00000425538;ENST00000343344;ENST00000395988;ENST00000443061	T;T	0.46063	0.9;0.88	5.49	5.49	0.81192	.	0.869934	0.10124	N	0.713025	T	0.49270	0.1547	L	0.57536	1.79	0.44976	D	0.99799	P;D;D;P	0.59357	0.931;0.959;0.985;0.929	B;B;P;B	0.44561	0.129;0.254;0.453;0.173	T	0.54241	-0.8323	10	0.56958	D	0.05	-4.1821	18.2062	0.89855	0.0:1.0:0.0:0.0	.	395;580;676;676	E9PEP9;Q8IZQ8-2;Q8IZQ8-3;Q8IZQ8	.;.;.;MYCD_HUMAN	L	395;676;676;580;381	ENSP00000341835:S676L;ENSP00000400148:S381L	ENSP00000341835:S676L	S	+	2	0	MYOCD	12597357	1.000000	0.71417	0.204000	0.23530	0.062000	0.15995	6.057000	0.71119	2.613000	0.88420	0.644000	0.83932	TCG	.	.		0.567	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		T	12656632	C	T	12656632	3	4	196	1	0	0	0	0	1	0	0	0	10096	893	31	1	2065	1	MYOCD	17	12656632	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	995678	12656632	68538578	80	28890										
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305699	39305699	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	acagactggcagcactggggTctgcagcagctggacacaca	13	12	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr17:39305699T>C	ENST00000343246.4	-	1	355	c.321A>G	c.(319-321)agA>agG	p.R107R		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	107	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCACTGGGGTCTgcagcagc	0.662																																					p.R107R		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.A321G						.						20	24	23					17																	39305699		2163	4217	6380	SO:0001819	synonymous_variant	85289	exon1			CTGGGGTCTGCAG	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.321A>G	chr17.hg19:g.39305699T>C		80.0	0.0		53.0	26.0	NM_033188		Silent	SNP	ENST00000343246.4	hg19	CCDS32650.1																																																																																			.	.		0.662	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			C	39305699	T	C	39305699	2	2	196	1	0	0	0	0	0	0	0	1	8563	1664	58	2		2	KRTAP4-5	17	39305699	Silent	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	26649067	39305699	41889511	81	28891										
HLF	3131	hgsc.bcm.edu	37	chr17	53345280	53345280	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ggaggagtttttgtcagaaaAtggcattccccccagcccat	10	11	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr17:53345280A>G	ENST00000226067.5	+	2	757	c.284A>G	c.(283-285)aAt>aGt	p.N95S	HLF_ENST00000573945.1_Missense_Mutation_p.N10S|HLF_ENST00000430986.2_Missense_Mutation_p.N10S|HLF_ENST00000575345.1_Missense_Mutation_p.N10S	NM_002126.4	NP_002117.1	Q16534	HLF_HUMAN	hepatic leukemia factor	95					multicellular organismal development (GO:0007275)|rhythmic process (GO:0048511)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|ovary(2)	3						TTGTCAGAAAATGGCATTCCC	0.572			T	TCF3	ALL																																p.N95S		Atlas-SNP	.		Dom	yes		17	17q22	3131	hepatic leukemia factor		L	.	HLF	39	.	0			c.A284G						.						112	109	110					17																	53345280		2203	4300	6503	SO:0001583	missense	3131	exon2			CAGAAAATGGCAT		CCDS11585.1	17q22	2011-05-19			ENSG00000108924	ENSG00000108924			4977	protein-coding gene	gene with protein product		142385				1386162	Standard	XM_005257269		Approved	MGC33822	uc002iug.1	Q16534		ENST00000226067.5:c.284A>G	chr17.hg19:g.53345280A>G	ENSP00000226067:p.Asn95Ser	155.0	0.0		124.0	38.0	NM_002126	A8K1X8|Q6FHS9	Missense_Mutation	SNP	ENST00000226067.5	hg19	CCDS11585.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.557548	0.86231	.	.	ENSG00000108924	ENST00000226067;ENST00000430986	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.81014	0.4735	M	0.84683	2.71	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	D	0.83944	0.0313	9	0.66056	D	0.02	.	15.389	0.74726	1.0:0.0:0.0:0.0	.	95	Q16534	HLF_HUMAN	S	95;10	.	ENSP00000226067:N95S	N	+	2	0	HLF	50700279	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.779000	0.91792	2.224000	0.72417	0.533000	0.62120	AAT	.	.		0.572	HLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439185.1	NM_002126		G	53345280	A	G	53345280	3	3	196	1	0	0	0	0	1	0	0	0	7223	101	4	2	290	2	HLF	17	53345280	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	14039581	53345280	27849930	82	28892										
JMJD6	23210	hgsc.bcm.edu	37	chr17	74722553	74722553	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tgcgcttcttgctcttgtggTtcattctgcggggtcgccag	13	11	4	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr17:74722553T>G	ENST00000397625.4	-	1	119	c.5A>C	c.(4-6)aAc>aCc	p.N2T	METTL23_ENST00000341249.6_5'Flank|METTL23_ENST00000588783.1_5'Flank|METTL23_ENST00000589977.1_5'Flank|METTL23_ENST00000588822.1_5'Flank|METTL23_ENST00000586200.1_5'Flank|JMJD6_ENST00000585429.1_Missense_Mutation_p.N2T|JMJD6_ENST00000445478.2_Missense_Mutation_p.N2T|METTL23_ENST00000586752.1_5'Flank|METTL23_ENST00000591571.1_5'Flank|METTL23_ENST00000586738.1_5'Flank|METTL23_ENST00000590964.1_5'Flank|METTL23_ENST00000588302.1_5'Flank	NM_015167.2	NP_055982.2	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6	2					cell surface receptor signaling pathway (GO:0007166)|erythrocyte development (GO:0048821)|heart development (GO:0007507)|histone H3-R2 demethylation (GO:0070078)|histone H4-R3 demethylation (GO:0070079)|kidney development (GO:0001822)|lung development (GO:0030324)|macrophage activation (GO:0042116)|mRNA processing (GO:0006397)|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine (GO:0018395)|recognition of apoptotic cell (GO:0043654)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|RNA splicing (GO:0008380)|sprouting angiogenesis (GO:0002040)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone demethylase activity (H3-R2 specific) (GO:0033746)|histone demethylase activity (H4-R3 specific) (GO:0033749)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)|peptidyl-lysine 5-dioxygenase activity (GO:0070815)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			endometrium(2)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|skin(2)	16						GCTCTTGTGGTTCATTCTGCG	0.672																																					p.N2T		Atlas-SNP	.											.	JMJD6	57	.	0			c.A5C						.						34	39	38					17																	74722553		2034	4192	6226	SO:0001583	missense	23210	exon1			TTGTGGTTCATTC	AB011157	CCDS42383.1, CCDS42384.1	17q25	2007-11-20	2007-02-16	2007-02-16	ENSG00000070495	ENSG00000070495			19355	protein-coding gene	gene with protein product		604914	"phosphatidylserine receptor"	PTDSR		11877474	Standard	NM_015167		Approved	PTDSR1, KIAA0585	uc002jsn.1	Q6NYC1	OTTHUMG00000169267	ENST00000397625.4:c.5A>C	chr17.hg19:g.74722553T>G	ENSP00000380750:p.Asn2Thr	60.0	0.0		56.0	32.0	NM_001081461	B3KMN8|B4DGX1|Q86VY0|Q8IUM5|Q9Y4E2	Missense_Mutation	SNP	ENST00000397625.4	hg19	CCDS42384.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.897905	0.52227	.	.	ENSG00000070495	ENST00000445478;ENST00000344991;ENST00000397625	.	.	.	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.52581	0.1743	L	0.57536	1.79	0.80722	D	1	B;P;P	0.39094	0.18;0.659;0.519	B;B;B	0.34722	0.043;0.188;0.153	T	0.59096	-0.7518	9	0.51188	T	0.08	0.2916	14.2737	0.66166	0.0:0.0:0.0:1.0	.	2;2;2	B2WTI3;Q6NYC1;Q6NYC1-3	.;JMJD6_HUMAN;.	T	2	.	ENSP00000302916:N2T	N	-	2	0	JMJD6	72234148	1.000000	0.71417	1.000000	0.80357	0.176000	0.22953	7.352000	0.79404	1.967000	0.57214	0.402000	0.26972	AAC	.	.		0.672	JMJD6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403211.1	NM_015167		G	74722553	T	G	74722553	3	3	196	1	0	0	0	0	1	0	0	0	7962	1725	60	5	1271	5	JMJD6	17	74722553	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	21377273	74722553	6472657	83	28893										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9208736	9208736	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	agttagcattctttttggttAtccactctctgagcgaaaac	7	9	2	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr18:9208736A>G	ENST00000262126.4	+	5	626	c.386A>G	c.(385-387)tAt>tGt	p.Y129C	ANKRD12_ENST00000540578.2_3'UTR|ANKRD12_ENST00000400020.3_Missense_Mutation_p.Y106C|ANKRD12_ENST00000383440.2_Missense_Mutation_p.Y106C	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	129						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CTTTTTGGTTATCCACTCTCT	0.388																																					p.Y129C		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A386G						.						191	169	176					18																	9208736		2203	4300	6503	SO:0001583	missense	23253	exon5			TTGGTTATCCACT	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.386A>G	chr18.hg19:g.9208736A>G	ENSP00000262126:p.Tyr129Cys	297.0	0.0		250.0	65.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	14.98	2.696804	0.48202	.	.	ENSG00000101745	ENST00000383440;ENST00000546007;ENST00000262126;ENST00000540578	T;T;T	0.51817	3.38;0.69;3.45	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.57829	0.2080	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.997	T	0.62440	-0.6854	10	0.87932	D	0	-21.552	16.1777	0.81874	1.0:0.0:0.0:0.0	.	129;106;129	Q6PG48;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	C	106;106;129;129	ENSP00000372932:Y106C;ENSP00000441510:Y106C;ENSP00000262126:Y129C	ENSP00000262126:Y129C	Y	+	2	0	ANKRD12	9198736	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.222000	0.72286	0.383000	0.25322	TAT	.	.		0.388	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		G	9208736	A	G	9208736	3	3	196	1	0	0	0	0	1	0	0	0	640	449	16	2	400	2	ANKRD12	18	9208736	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10		9208736	68868512	84	28894										
KATNAL2	83473	hgsc.bcm.edu	37	chr18	44580795	44580795	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	aatttaccgcaaagaagtagAgggaagaccagaaggtaaag	12	5	0	4			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr18:44580795A>T	ENST00000245121.5	+	3	296	c.102A>T	c.(100-102)agA>agT	p.R34S	KATNAL2_ENST00000356157.7_Missense_Mutation_p.R106S|KATNAL2_ENST00000592005.1_Intron	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						AAAGAAGTAGAGGGAAGACCA	0.398																																					p.R34S		Atlas-SNP	.											.	KATNAL2	64	.	0			c.A102T						.						188	200	196					18																	44580795		2203	4300	6503	SO:0001583	missense	83473	exon3			AAGTAGAGGGAAG	BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"ATPases / AAA-type"	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.102A>T	chr18.hg19:g.44580795A>T	ENSP00000245121:p.Arg34Ser	347.0	0.0		227.0	41.0	NM_031303		Missense_Mutation	SNP	ENST00000245121.5	hg19	CCDS32828.1	.	.	.	.	.	.	.	.	.	.	A	10.21	1.286809	0.23478	.	.	ENSG00000167216	ENST00000356157;ENST00000245121	D;D	0.93133	-3.17;-3.15	5.57	4.41	0.53225	.	0.116998	0.56097	N	0.000025	D	0.83018	0.5163	N	0.08118	0	0.19300	N	0.999979	.	.	.	.	.	.	T	0.69221	-0.5202	8	0.10902	T	0.67	-1.2462	10.2457	0.43339	0.8161:0.1839:0.0:0.0	.	.	.	.	S	106;34	ENSP00000348478:R106S;ENSP00000245121:R34S	ENSP00000245121:R34S	R	+	3	2	KATNAL2	42834793	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.270000	0.51600	0.943000	0.37553	0.379000	0.24179	AGA	.	.		0.398	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303		T	44580795	A	T	44580795	3	4	196	1	0	0	0	0	1	0	0	0	7995	301	11	4	108	4	KATNAL2	18	44580795	Missense_Mutation	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	35372059	44580795	33496453	85	28895										
ATP9B	374868	hgsc.bcm.edu	37	chr18	77137276	77137276	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ttatcaccaccgtgaccttcCtgtggaaagtgtcggcgatc	10	12	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr18:77137276C>A	ENST00000426216.2	+	30	3354	c.3337C>A	c.(3337-3339)Ctg>Atg	p.L1113M	ATP9B_ENST00000543761.1_Missense_Mutation_p.L423M|ATP9B_ENST00000307671.7_Missense_Mutation_p.L1102M	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	1113					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		CGTGACCTTCCTGTGGAAAGT	0.562																																					p.L1113M		Atlas-SNP	.											.	ATP9B	96	.	0			c.C3337A						.						153	129	137					18																	77137276		2203	4300	6503	SO:0001583	missense	374868	exon30			ACCTTCCTGTGGA	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"ATPases / P-type"	13541	protein-coding gene	gene with protein product		614446	"ATPase, Class II, type 9B"			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.3337C>A	chr18.hg19:g.77137276C>A	ENSP00000398076:p.Leu1113Met	71.0	0.0		39.0	9.0	NM_198531	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	hg19	CCDS12014.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.349614	0.41599	.	.	ENSG00000166377	ENST00000426216;ENST00000307671;ENST00000543761	T;T	0.41065	1.01;1.01	4.5	1.02	0.19986	.	0.082491	0.49916	D	0.000122	T	0.40222	0.1108	M	0.68728	2.09	0.54753	D	0.999982	B;B	0.27264	0.173;0.058	B;B	0.32465	0.146;0.107	T	0.22208	-1.0223	10	0.62326	D	0.03	.	8.1104	0.30911	0.0:0.6678:0.2148:0.1174	.	1113;1102	O43861;O43861-2	ATP9B_HUMAN;.	M	1102;1113;423	ENSP00000398076:L1102M;ENSP00000442015:L423M	ENSP00000304500:L1113M	L	+	1	2	ATP9B	75238264	1.000000	0.71417	0.995000	0.50966	0.888000	0.51559	1.142000	0.31540	-0.155000	0.11098	0.543000	0.68304	CTG	.	.		0.562	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531		A	77137276	C	A	77137276	3	1	196	1	0	0	0	0	1	0	0	0	1199	680	24	3	3455	3	ATP9B	18	77137276	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	32556481	77137276	939972	86	28896										
ZNF560	147741	hgsc.bcm.edu	37	chr19	9577581	9577581	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cgttacattcagaggtcttcTctgctgcatgagtttttaag	9	8	3	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr19:9577581T>C	ENST00000301480.4	-	10	2255	c.2042A>G	c.(2041-2043)gAg>gGg	p.E681G		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	681					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						AGAGGTCTTCTCTGCTGCATG	0.358																																					p.E681G		Atlas-SNP	.											.	ZNF560	162	.	0			c.A2042G						.						118	122	120					19																	9577581		2203	4300	6503	SO:0001583	missense	147741	exon10			GTCTTCTCTGCTG	AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"Zinc fingers, C2H2-type", "-"	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.2042A>G	chr19.hg19:g.9577581T>C	ENSP00000301480:p.Glu681Gly	96.0	0.0		62.0	25.0	NM_152476	Q495S9|Q495T1	Missense_Mutation	SNP	ENST00000301480.4	hg19	CCDS12214.1	.	.	.	.	.	.	.	.	.	.	T	12.26	1.883218	0.33255	.	.	ENSG00000198028	ENST00000301480	T	0.20200	2.09	1.69	1.69	0.24217	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46444	0.1393	M	0.86805	2.84	0.31694	N	0.641469	D	0.89917	1.0	D	0.85130	0.997	T	0.52902	-0.8513	9	0.66056	D	0.02	.	7.3583	0.26731	0.0:0.0:0.0:1.0	.	681	Q96MR9	ZN560_HUMAN	G	681	ENSP00000301480:E681G	ENSP00000301480:E681G	E	-	2	0	ZNF560	9438581	0.022000	0.18835	0.011000	0.14972	0.071000	0.16799	1.766000	0.38491	1.019000	0.39547	0.379000	0.24179	GAG	.	.		0.358	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476		C	9577581	T	C	9577581	3	2	196	1	0	0	0	0	1	0	0	0	18006	1551	54	2	334	2	ZNF560	19	9577581	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10		9577581	49551402	87	28897										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11145796	11145796	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	agcgactcactgacggagaaGcagtggctcaaggtacatgc	13	10	2	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr19:11145796G>T	ENST00000429416.3	+	30	4439	c.4158G>T	c.(4156-4158)aaG>aaT	p.K1386N	SMARCA4_ENST00000450717.3_Missense_Mutation_p.K1353N|SMARCA4_ENST00000444061.3_Missense_Mutation_p.K1353N|SMARCA4_ENST00000413806.3_Missense_Mutation_p.K1353N|SMARCA4_ENST00000358026.2_Missense_Mutation_p.K1386N|SMARCA4_ENST00000344626.4_Missense_Mutation_p.K1386N|SMARCA4_ENST00000590574.1_Missense_Mutation_p.K1353N|SMARCA4_ENST00000538456.3_3'UTR|SMARCA4_ENST00000541122.2_Missense_Mutation_p.K1353N|SMARCA4_ENST00000589677.1_Missense_Mutation_p.K1353N	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1386					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TGACGGAGAAGCAGTGGCTCA	0.662			"F, N, Mis"		NSCLC																																p.K1386N		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	SMARCA4_ENST00000358026,NS,carcinoma,0,2	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.G4158T						.						38	32	34					19																	11145796		2199	4300	6499	SO:0001583	missense	6597	exon29			GGAGAAGCAGTGG	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.4158G>T	chr19.hg19:g.11145796G>T	ENSP00000395654:p.Lys1386Asn	169.0	0.0		111.0	38.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	20.7|20.7	4.037129|4.037129	0.75617|0.75617	.|.	.|.	ENSG00000127616|ENSG00000127616	ENST00000538456|ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	.|D;D;D;D;D;D;D	.|0.87412	.|-2.2;-2.17;-2.2;-2.24;-2.23;-2.25;-2.24	4.59|4.59	4.59|4.59	0.56863|0.56863	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91801|0.91801	0.7406|0.7406	L|L	0.60957|0.60957	1.885|1.885	0.52099|0.52099	D|D	0.999942|0.999942	.|P;P;P;P;D;P;P	.|0.89917	.|0.944;0.944;0.944;0.944;1.0;0.788;0.944	.|P;P;P;P;D;B;P	.|0.73380	.|0.829;0.829;0.829;0.829;0.98;0.368;0.829	D|D	0.92762|0.92762	0.6225|0.6225	5|10	.|0.87932	.|D	.|0	-41.5199|-41.5199	16.3525|16.3525	0.83220|0.83220	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1353;1353;1353;1386;1353;573;1386	.|B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.|.;.;.;.;.;.;SMCA4_HUMAN	S|N	123|1386;1386;1417;1386;1353;1353;1353;1353	.|ENSP00000395654:K1386N;ENSP00000350720:K1386N;ENSP00000343896:K1386N;ENSP00000445036:K1353N;ENSP00000392837:K1353N;ENSP00000397783:K1353N;ENSP00000414727:K1353N	.|ENSP00000343896:K1386N	A|K	+|+	1|3	0|2	SMARCA4|SMARCA4	11006796|11006796	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	0.907000|0.907000	0.28531|0.28531	2.385000|2.385000	0.81259|0.81259	0.558000|0.558000	0.71614|0.71614	GCA|AAG	.	.		0.662	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		T	11145796	G	T	11145796	3	4	196	1	0	0	0	0	1	0	0	0	14785	962	34	3	4268	3	SMARCA4	19	11145796	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	1568215	11145796	47983187	88	28898										
OR10H2	26538	hgsc.bcm.edu	37	chr19	15839113	15839113	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	catgctggccgacctgctgtCcacccagcgctccatcgcct	9	19	0	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr19:15839113C>T	ENST00000305899.3	+	1	280	c.260C>T	c.(259-261)tCc>tTc	p.S87F		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	87						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					GACCTGCTGTCCACCCAGCGC	0.612																																					p.S87F		Atlas-SNP	.											.	OR10H2	59	.	0			c.C260T						.						77	65	69					19																	15839113		2203	4297	6500	SO:0001583	missense	26538	exon1			TGCTGTCCACCCA	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"GPCR / Class A : Olfactory receptors"	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.260C>T	chr19.hg19:g.15839113C>T	ENSP00000306095:p.Ser87Phe	184.0	0.0		127.0	19.0	NM_013939	Q6IFQ1|Q96R58	Missense_Mutation	SNP	ENST00000305899.3	hg19	CCDS12333.1	.	.	.	.	.	.	.	.	.	.	.	6.075	0.382065	0.11524	.	.	ENSG00000171942	ENST00000305899	T	0.78924	-1.22	3.4	3.4	0.38934	GPCR, rhodopsin-like superfamily (1);	0.141093	0.32563	N	0.005938	T	0.76205	0.3955	M	0.76170	2.325	0.09310	N	1	B	0.15719	0.014	B	0.19946	0.027	T	0.69224	-0.5201	10	0.49607	T	0.09	.	12.3469	0.55126	0.0:1.0:0.0:0.0	.	87	O60403	O10H2_HUMAN	F	87	ENSP00000306095:S87F	ENSP00000306095:S87F	S	+	2	0	OR10H2	15700113	0.000000	0.05858	0.491000	0.27477	0.069000	0.16628	0.259000	0.18405	1.446000	0.47643	0.537000	0.68136	TCC	.	.		0.612	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1			T	15839113	C	T	15839113	3	4	196	1	0	0	0	0	1	0	0	0	10915	855	30	3	262	3	OR10H2	19	15839113	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	4693317	15839113	43289870	89	28899										
LASS1	10715	hgsc.bcm.edu	37	chr19	18991094	18991094	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	accactcaccagctgaagccGaagctgaggcagcccaagtc	10	15	1	2	rs566462746		TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr19:18991094G>T	ENST00000427170.2	-	4	812	c.741C>A	c.(739-741)ttC>ttA	p.F247L	CERS1_ENST00000429504.2_Missense_Mutation_p.F247L|GDF1_ENST00000247005.6_5'UTR|AC005197.2_ENST00000597769.1_RNA|CERS1_ENST00000542296.2_Missense_Mutation_p.F149L	NM_001492.4|NM_021267.3	NP_001483.3|NP_067090.1	P27544	CERS1_HUMAN	ceramide synthase 1	247	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				cellular response to dithiothreitol (GO:0072721)|cellular response to drug (GO:0035690)|cellular response to mycotoxin (GO:0036146)|cellular response to UV-A (GO:0071492)|ceramide biosynthetic process (GO:0046513)|negative regulation of telomerase activity (GO:0051974)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	sphingosine N-acyltransferase activity (GO:0050291)			endometrium(3)|lung(2)	5						AGCTGAAGCCGAAGCTGAGGC	0.617																																					p.F247L		Atlas-SNP	.											.	CERS1	19	.	0			c.C741A						.						20	24	22					19																	18991094		2000	4105	6105	SO:0001583	missense	10715	exon4			GAAGCCGAAGCTG	AF105005	CCDS46021.1	19p12	2011-07-08	2011-07-08	2011-07-08		ENSG00000223802			14253	protein-coding gene	gene with protein product		606919	"longevity assurance (LAG1, S. cerevisiae) homolog 1", "LAG1 longevity assurance homolog 1 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 1"	LASS1		9872981, 2034669	Standard	NM_198207		Approved	LAG1, UOG1	uc002nkj.3	P27544		ENST00000427170.2:c.741C>A	chr19.hg19:g.18991094G>T	ENSP00000402697:p.Phe247Leu	41.0	0.0		31.0	14.0	NM_198207		Missense_Mutation	SNP	ENST00000427170.2	hg19	CCDS46020.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.390884	0.82902	.	.	ENSG00000223802	ENST00000427170;ENST00000429504;ENST00000542296	D;D;D	0.85773	-2.03;-2.03;-2.03	3.85	2.79	0.32731	TRAM/LAG1/CLN8 homology domain (3);	.	.	.	.	D	0.91600	0.7346	M	0.87758	2.905	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.91925	0.5550	9	0.87932	D	0	.	9.7999	0.40757	0.1067:0.0:0.8933:0.0	.	247	P27544	CERS1_HUMAN	L	247;247;149	ENSP00000402697:F247L;ENSP00000389044:F247L;ENSP00000437648:F149L	ENSP00000402697:F247L	F	-	3	2	CERS1	18852094	1.000000	0.71417	0.884000	0.34674	0.993000	0.82548	7.266000	0.78452	1.869000	0.54173	0.430000	0.28490	TTC	.	.		0.617	CERS1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	18991094	G	T	18991094	3	4	196	1	0	0	0	0	1	0	0	0	8647	1049	37	1	331	1	LASS1	19	18991094	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	3151981	18991094	40137889	90	28900										
CEBPA	1050	hgsc.bcm.edu	37	chr19	33792755	33792755	+	Missense_Mutation	SNP	G	G	T													0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ggtgcgggtgcgggtgcgagGgcggcggcggcggcggcggc							TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr19:33792755G>T	ENST00000498907.2	-	1	715	c.566C>A	c.(565-567)cCc>cAc	p.P189H	CTD-2540B15.11_ENST00000589932.1_RNA|CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.7_ENST00000587312.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	189	Poly-Pro.				acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P185_P197del(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					CGGGTGCGAGggcggcggcgg	0.751			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.P189H		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	.	CEBPA	986	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.C566A						.						1	1	1					19																	33792755		447	1075	1522	SO:0001583	missense	1050	exon1	Familial Cancer Database	Familial AML	TGCGAGGGCGGCG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.566C>A	chr19.hg19:g.33792755G>T	ENSP00000427514:p.Pro189His	209.0	0.0		226.0	25.0	NM_004364	A7LNP2|P78319|Q05CA4	Missense_Mutation	SNP	ENST00000498907.2	hg19	CCDS54243.1	.	.	.	.	.	.	.	.	.	.	G	5.519	0.280743	0.10458	.	.	ENSG00000245848	ENST00000498907	T	0.23754	1.89	3.5	1.14	0.20703	.	.	.	.	.	T	0.12263	0.0298	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30119	-0.9989	9	0.32370	T	0.25	.	8.2882	0.31941	0.0:0.0:0.3118:0.6881	.	189	P49715	CEBPA_HUMAN	H	189	ENSP00000427514:P189H	ENSP00000427514:P189H	P	-	2	0	CEBPA	38484595	0.982000	0.34865	0.123000	0.21794	0.139000	0.21198	0.311000	0.19380	0.009000	0.14813	0.064000	0.15345	CCC	.	.		0.751	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		T	33792755	G	T	33792755	3	4	196	1	0	0	0	0	1	0	0	0	3201	1232	43	3	514	3	CEBPA	19	33792755	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	14801661	33792755	25336228	91	28901	148	2								
CEBPA	1050	hgsc.bcm.edu	37	chr19	33792759	33792759	+	Missense_Mutation	SNP	G	G	A													0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cgggtgcgggtgcgagggcgGcggcggcggcggcggctggt							TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr19:33792759G>A	ENST00000498907.2	-	1	711	c.562C>T	c.(562-564)Ccg>Tcg	p.P188S	CTD-2540B15.11_ENST00000589932.1_RNA|CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.7_ENST00000587312.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	188	Poly-Pro.				acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P188del(4)|p.P185_P197del(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					TGCGAGggcggcggcggcggc	0.746			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.P188S		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	.	CEBPA	986	.	5	Deletion - In frame(5)	haematopoietic_and_lymphoid_tissue(5)	c.C562T						.						1	1	1					19																	33792759		371	891	1262	SO:0001583	missense	1050	exon1	Familial Cancer Database	Familial AML	AGGGCGGCGGCGG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.562C>T	chr19.hg19:g.33792759G>A	ENSP00000427514:p.Pro188Ser	222.0	0.0		227.0	20.0	NM_004364	A7LNP2|P78319|Q05CA4	Missense_Mutation	SNP	ENST00000498907.2	hg19	CCDS54243.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.906015	0.33628	.	.	ENSG00000245848	ENST00000498907	T	0.21932	1.98	3.67	3.67	0.42095	.	.	.	.	.	T	0.13372	0.0324	N	0.22421	0.69	0.18873	N	0.999985	B	0.21688	0.059	B	0.11329	0.006	T	0.21109	-1.0255	9	0.15499	T	0.54	.	11.04	0.47825	0.0:0.0:1.0:0.0	.	188	P49715	CEBPA_HUMAN	S	188	ENSP00000427514:P188S	ENSP00000427514:P188S	P	-	1	0	CEBPA	38484599	0.968000	0.33430	0.769000	0.31535	0.114000	0.19823	-0.017000	0.12590	1.631000	0.50456	0.064000	0.15345	CCG	.	.		0.746	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		A	33792759	G	A	33792759	3	1	196	1	0	0	0	0	1	0	0	0	3201	1203	42	3	518	3	CEBPA	19	33792759	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	4	33792759	25336224	92	28902	148	2								
NCR1	9437	hgsc.bcm.edu	37	chr19	55417692	55417692	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	agaggatcagcgcccagcagCgtgagtccttccttcaaagc	11	13	2	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr19:55417692C>T	ENST00000291890.4	+	2	108	c.70C>T	c.(70-72)Cag>Tag	p.Q24*	NCR1_ENST00000594765.1_Splice_Site_p.Q24*|NCR1_ENST00000357397.5_Intron|NCR1_ENST00000350790.5_Splice_Site_p.Q24*|NCR1_ENST00000598576.1_Intron|NCR1_ENST00000447255.1_Splice_Site_p.Q24*|NCR1_ENST00000338835.5_Splice_Site_p.Q24*	NM_004829.5	NP_004820.2	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	24					cellular defense response (GO:0006968)|intracellular signal transduction (GO:0035556)|natural killer cell activation (GO:0030101)|regulation of natural killer cell mediated cytotoxicity (GO:0042269)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|SWI/SNF complex (GO:0016514)	receptor signaling protein activity (GO:0005057)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(193;0.0449)		CGCCCAGCAGCGTGAGTCCTT	0.617																																					p.Q24X		Atlas-SNP	.											.	NCR1	60	.	0			c.C70T						.						92	78	83					19																	55417692		2203	4300	6503	SO:0001630	splice_region_variant	9437	exon2			CAGCAGCGTGAGT	AJ001383	CCDS12911.1, CCDS46181.1, CCDS46182.1, CCDS56103.1	19q13.42	2013-09-20	2002-11-13	2002-11-15	ENSG00000189430	ENSG00000189430		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6731	protein-coding gene	gene with protein product		604530	"lymphocyte antigen 94 (mouse) homolog (activating NK-receptor; NK-p46)"	LY94		9730896	Standard	NM_001145457		Approved	NK-p46, NKP46, CD335	uc002qib.2	O76036	OTTHUMG00000183212	ENST00000291890.4:c.70+1C>T	chr19.hg19:g.55417692C>T		35.0	0.0		30.0	16.0	NM_001145458	B0V3L2|B0V3L3|B0V3L4|B0V3L5|B8JL03|O76016|O76017|O76018	Nonsense_Mutation	SNP	ENST00000291890.4	hg19	CCDS12911.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.431849	0.43122	.	.	ENSG00000189430	ENST00000291890;ENST00000447255;ENST00000338835;ENST00000350790	.	.	.	3.2	-1.84	0.07809	.	1.396620	0.04740	N	0.422626	.	.	.	.	.	.	0.43835	D	0.996414	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	6.9521	0.24550	0.0:0.3578:0.5308:0.1114	.	.	.	.	X	24	.	ENSP00000291890:Q24X	Q	+	1	0	NCR1	60109504	0.000000	0.05858	0.063000	0.19743	0.195000	0.23768	-1.955000	0.01523	-0.216000	0.10048	-0.182000	0.12963	CAG;CAG;CAG;CAA	.	.		0.617	NCR1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465680.1		Nonsense_Mutation	T	55417692	C	T	55417692	5	4	196	1	0	0	0	0	0	0	1	0	10246	782	27	1	76	1	NCR1	19	55417692	Splice_Site	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	21624933	55417692	3711291	93	28903										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55493985	55493985	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tgatcgaggacatctgcgggGactgggagaagaagaagccg	17	7	1	4			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr19:55493985G>T	ENST00000543010.1	+	6	1062	c.919G>T	c.(919-921)Gac>Tac	p.D307Y	NLRP2_ENST00000339757.7_Missense_Mutation_p.D285Y|NLRP2_ENST00000537859.1_Missense_Mutation_p.D285Y|NLRP2_ENST00000263437.6_Missense_Mutation_p.D304Y|NLRP2_ENST00000448584.2_Missense_Mutation_p.D307Y|NLRP2_ENST00000427260.2_Missense_Mutation_p.D284Y|NLRP2_ENST00000391721.4_Missense_Mutation_p.D283Y|NLRP2_ENST00000538819.1_Missense_Mutation_p.D283Y	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	307	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		CATCTGCGGGGACTGGGAGAA	0.617																																					p.D307Y		Atlas-SNP	.											.	NLRP2	161	.	0			c.G919T						.						49	48	48					19																	55493985		2203	4300	6503	SO:0001583	missense	55655	exon6			TGCGGGGACTGGG	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.919G>T	chr19.hg19:g.55493985G>T	ENSP00000445135:p.Asp307Tyr	75.0	0.0		52.0	17.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.729391	0.30684	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.81330	-1.44;-1.38;-1.38;-1.44;-1.38;-1.48;-1.38;-1.43	1.55	-2.06	0.07298	NACHT nucleoside triphosphatase (1);	.	.	.	.	D	0.88142	0.6357	M	0.88979	2.995	0.18873	N	0.999982	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.995;0.999;0.992;0.999	T	0.77351	-0.2620	9	0.87932	D	0	.	5.0778	0.14640	0.5851:0.0:0.4149:0.0	.	284;285;304;283;307	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	Y	307;283;285;307;285;284;283;304	ENSP00000445135:D307Y;ENSP00000375601:D283Y;ENSP00000344074:D285Y;ENSP00000409370:D307Y;ENSP00000440601:D285Y;ENSP00000402474:D284Y;ENSP00000441133:D283Y;ENSP00000263437:D304Y	ENSP00000263437:D304Y	D	+	1	0	NLRP2	60185797	0.002000	0.14202	0.006000	0.13384	0.004000	0.04260	0.175000	0.16762	-0.521000	0.06426	-0.350000	0.07774	GAC	.	.		0.617	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		T	55493985	G	T	55493985	3	4	196	1	0	0	0	0	1	0	0	0	10486	1174	41	3	937	3	NLRP2	19	55493985	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10	76293	55493985	3634998	94	28904										
MICALL1	85377	hgsc.bcm.edu	37	chr22	38318092	38318092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	gggcccggggacacggtcggGgaccaggcctgggcccttct	18	14	1	0			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chr22:38318092G>A	ENST00000215957.6	+	6	809	c.683G>A	c.(682-684)gGg>gAg	p.G228E		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	228					endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					ACACGGTCGGGGACCAGGCCT	0.642																																					p.G228E		Atlas-SNP	.											.	MICALL1	53	.	0			c.G683A						.						33	33	33					22																	38318092		2203	4300	6503	SO:0001583	missense	85377	exon6			GGTCGGGGACCAG	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"molecule interacting with Rab13"					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.683G>A	chr22.hg19:g.38318092G>A	ENSP00000215957:p.Gly228Glu	173.0	0.0		131.0	54.0	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	hg19	CCDS13961.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.480417	0.44044	.	.	ENSG00000100139	ENST00000445494;ENST00000215957	T;T	0.72394	-0.65;0.5	4.87	2.55	0.30701	.	0.198284	0.35013	N	0.003509	T	0.52901	0.1763	L	0.48362	1.52	0.46011	D	0.998811	B	0.17852	0.024	B	0.15052	0.012	T	0.35325	-0.9793	10	0.13853	T	0.58	.	1.897	0.03260	0.2322:0.0:0.4383:0.3295	.	228	Q8N3F8	MILK1_HUMAN	E	144;228	ENSP00000404543:G144E;ENSP00000215957:G228E	ENSP00000215957:G228E	G	+	2	0	MICALL1	36648038	0.679000	0.27596	0.012000	0.15200	0.004000	0.04260	1.009000	0.29886	1.011000	0.39340	0.400000	0.26472	GGG	.	.		0.642	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		A	38318092	G	A	38318092	3	1	196	1	0	0	0	0	1	0	0	0	9582	1232	43	3	705	3	MICALL1	22	38318092	Missense_Mutation	SNP	G	TCGA-DD-AADN-01A-11D-A40R-10		38318092	12986474	95	28905										
DMD	1756	hgsc.bcm.edu	37	chrX	32862919	32862919	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cattattgttctgcaaaaccCgcagtgccttgttgacattg	8	10	1	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chrX:32862919C>A	ENST00000357033.4	-	4	451	c.245G>T	c.(244-246)cGg>cTg	p.R82L	DMD_ENST00000378677.2_Missense_Mutation_p.R78L|DMD_ENST00000288447.4_Missense_Mutation_p.R74L	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	82	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				CTGCAAAACCCGCAGTGCCTT	0.458																																					p.R82L		Atlas-SNP	.											.	DMD	2127	.	0			c.G245T	GRCh37	CM051908	DMD	M		.						190	134	153					X																	32862919		2202	4300	6502	SO:0001583	missense	1756	exon4			AAAACCCGCAGTG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.245G>T	chrX.hg19:g.32862919C>A	ENSP00000354923:p.Arg82Leu	62.0	0.0		44.0	28.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243481	0.39697	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000288447;ENST00000447523	D;D;D;D	0.94966	-3.57;-3.57;-3.57;-3.57	5.74	0.0358	0.14189	Calponin homology domain (5);	0.578074	0.12895	U	0.430300	D	0.89832	0.6829	L	0.36672	1.1	0.50171	D	0.999852	B;B;B;B	0.25235	0.121;0.061;0.008;0.075	B;B;B;B	0.25291	0.059;0.022;0.005;0.037	T	0.82178	-0.0586	10	0.87932	D	0	.	9.3333	0.38034	0.0:0.257:0.0:0.743	.	74;74;82;78	Q4G0X0;P11532-4;P11532;E9PDN5	.;.;DMD_HUMAN;.	L	74;78;82;82;74;45	ENSP00000367948:R78L;ENSP00000354923:R82L;ENSP00000288447:R74L;ENSP00000395904:R45L	ENSP00000288447:R74L	R	-	2	0	DMD	32772840	0.235000	0.23794	0.286000	0.24833	0.954000	0.61252	0.563000	0.23547	-0.052000	0.13311	-0.192000	0.12808	CGG	.	.		0.458	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32862919	C	A	32862919	3	1	196	1	0	0	0	0	1	0	0	0	4582	652	23	1	11359	1	DMD	23	32862919	Missense_Mutation	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10		32862919	122407641	96	28906										
RP2	6102	hgsc.bcm.edu	37	chrX	46713384	46713384	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	tggagccttcttccagaagaTgctgtggttcaggactatgt	12	8	2	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chrX:46713384T>C	ENST00000218340.3	+	2	737	c.576T>C	c.(574-576)gaT>gaC	p.D192D		NM_006915.2	NP_008846.2	O75695	XRP2_HUMAN	retinitis pigmentosa 2 (X-linked recessive)	192					cell morphogenesis (GO:0000902)|CTP biosynthetic process (GO:0006241)|cytoskeleton organization (GO:0007010)|GTP biosynthetic process (GO:0006183)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein transport (GO:0015031)|UTP biosynthetic process (GO:0006228)|visual perception (GO:0007601)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|periciliary membrane compartment (GO:1990075)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|nucleoside diphosphate kinase activity (GO:0004550)|unfolded protein binding (GO:0051082)			NS(1)|large_intestine(4)|lung(5)|stomach(1)	11						TTCCAGAAGATGCTGTGGTTC	0.443																																					p.D192D		Atlas-SNP	.											.	RP2	37	.	0			c.T576C						.						96	77	84					X																	46713384		2203	4300	6503	SO:0001819	synonymous_variant	6102	exon2			AGAAGATGCTGTG	AJ007590	CCDS14270.1	Xp11.3	2013-01-08			ENSG00000102218	ENSG00000102218			10274	protein-coding gene	gene with protein product		300757				6325945, 9697692, 19852809	Standard	NM_006915		Approved	TBCCD2, NME10, NM23-H10	uc004dgw.4	O75695	OTTHUMG00000021430	ENST00000218340.3:c.576T>C	chrX.hg19:g.46713384T>C		115.0	0.0		55.0	32.0	NM_006915	Q86XJ7|Q9NU67	Silent	SNP	ENST00000218340.3	hg19	CCDS14270.1																																																																																			.	.		0.443	RP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056375.1	NM_006915		C	46713384	T	C	46713384	2	2	196	1	0	0	0	0	0	0	0	1	13549	1461	51	2		2	RP2	23	46713384	Silent	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10	13850465	46713384	108557176	97	28907										
FAM133A	286499	hgsc.bcm.edu	37	chrX	92964868	92964868	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	agctctacgcatgaatcagaAtcagagagcaaggagtctgt	11	8	4	3			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chrX:92964868A>G	ENST00000355813.5	+	4	976	c.450A>G	c.(448-450)gaA>gaG	p.E150E	FAM133A_ENST00000322139.4_Silent_p.E150E|FAM133A_ENST00000332647.4_Silent_p.E150E|FAM133A_ENST00000538690.1_Silent_p.E150E	NM_001171109.1|NM_173698.2	NP_001164580.1|NP_775969.1	Q8N9E0	F133A_HUMAN	family with sequence similarity 133, member A	150	Lys-rich.|Ser-rich.									breast(2)|endometrium(2)|large_intestine(8)|lung(7)|upper_aerodigestive_tract(1)	20						ATGAATCAGAATCAGAGAGCA	0.358																																					p.E150E		Atlas-SNP	.											.	FAM133A	37	.	0			c.A450G						.						28	25	26					X																	92964868		2200	4297	6497	SO:0001819	synonymous_variant	286499	exon4			ATCAGAATCAGAG	AK094978	CCDS14466.1	Xq21.32	2010-05-04			ENSG00000179083	ENSG00000179083			26748	protein-coding gene	gene with protein product	"cancer/testis antigen 115"						Standard	NM_173698		Approved	RP1-32F7.2, FLJ37659, CT115	uc022bzv.1	Q8N9E0	OTTHUMG00000021975	ENST00000355813.5:c.450A>G	chrX.hg19:g.92964868A>G		81.0	0.0		48.0	26.0	NM_173698		Silent	SNP	ENST00000355813.5	hg19	CCDS14466.1																																																																																			.	.		0.358	FAM133A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057452.1	NM_173698		G	92964868	A	G	92964868	2	3	196	1	0	0	0	0	0	0	0	1	5448	98	4	2		2	FAM133A	23	92964868	Silent	SNP	A	TCGA-DD-AADN-01A-11D-A40R-10	46251484	92964868	62305692	98	28908										
ATP2B3	492	hgsc.bcm.edu	37	chrX	152814216	152814216	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	ccggtctatgtacaatacttCgtgaagttcttcatcattgg	8	9	4	1			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chrX:152814216C>T	ENST00000349466.2	+	9	1568	c.1242C>T	c.(1240-1242)ttC>ttT	p.F414F	ATP2B3_ENST00000263519.4_Silent_p.F414F|ATP2B3_ENST00000359149.3_Silent_p.F414F|ATP2B3_ENST00000370186.1_Silent_p.F400F|ATP2B3_ENST00000393842.1_Silent_p.F400F|ATP2B3_ENST00000370181.2_Silent_p.F400F			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	414					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TACAATACTTCGTGAAGTTCT	0.522													C|||	1	0.000264901	0	0	3775	,	,		13933	0		0	False		,,,				2504	0.001				p.F414F		Atlas-SNP	.											.	ATP2B3	552	.	0			c.C1242T						.						203	129	154					X																	152814216		2203	4300	6503	SO:0001819	synonymous_variant	492	exon8			ATACTTCGTGAAG	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"ATPases / P-type"	816	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 3", "cilia and flagella associated protein 39"	300014	"spinocerebellar ataxia, X-linked 1", "cerebellar ataxia 2 (X-linked)"	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.1242C>T	chrX.hg19:g.152814216C>T		59.0	0.0		30.0	19.0	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	hg19	CCDS35440.1																																																																																			.	.		0.522	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		T	152814216	C	T	152814216	2	4	196	1	0	0	0	0	0	0	0	1	1141	883	31	1		1	ATP2B3	23	152814216	Silent	SNP	C	TCGA-DD-AADN-01A-11D-A40R-10	59849348	152814216	2456344	99	28909										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	4967388	4967388	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0404040404040404	4	1	0.87781954887218	1.75563909774436	0.752416756176155	0.559440559440559	1	0	cagcaatgtcacagtctttgTaagcattattgatcagaatg	8	7	3	2			TCGA-DD-AADN-01A-11D-A40R-10	TCGA-DD-AADN-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b5fdeb5e-38a1-4da0-b372-045b08809738	9a4390a9-935c-4d95-aa5e-55b7dcfb8fbe	g.chrY:4967388T>C	ENST00000333703.4	+	5	2249	c.1736T>C	c.(1735-1737)gTa>gCa	p.V579A	PCDH11Y_ENST00000362095.5_Missense_Mutation_p.V590A|PCDH11Y_ENST00000215473.6_Missense_Mutation_p.V590A	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	590	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						ACAGTCTTTGTAAGCATTATT	0.368																																					p.V590A		Atlas-SNP	.											.	PCDH11Y	163	.	0			c.T1769C						.						51	42	44					Y																	4967388		696	2073	2769	SO:0001583	missense	83259	exon2			TCTTTGTAAGCAT	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000333703.4:c.1736T>C	chrY.hg19:g.4967388T>C	ENSP00000330552:p.Val579Ala	192.0	0.0		115.0	43.0	NM_032972	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000333703.4	hg19	CCDS14776.1																																																																																			.	.		0.368	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	NM_032973		C	4967388	T	C	4967388	3	2	196	1	0	0	0	0	1	0	0	0	11518	1638	57	2	1811	2	PCDH11Y	24	4967388	Missense_Mutation	SNP	T	TCGA-DD-AADN-01A-11D-A40R-10		4967388	54406178	100	28910										
CROCC	9696	hgsc.bcm.edu	37	chr1	17296811	17296811	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ccgtccagaagctgcaagacGagcggcggctgctgcaggag	16	12	0	2	rs572688461		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:17296811G>A	ENST00000375541.5	+	34	5584	c.5515G>A	c.(5515-5517)Gag>Aag	p.E1839K		NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GCTGCAAGACGAGCGGCGGCT	0.692																																					p.E1839K		Atlas-SNP	.											.	CROCC	185	.	0			c.G5515A						.						5	5	5					1																	17296811		1858	3791	5649	SO:0001583	missense	9696	exon34			CAAGACGAGCGGC	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.5515G>A	chr1.hg19:g.17296811G>A	ENSP00000364691:p.Glu1839Lys	92.0	0.0		165.0	27.0	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.661241	0.88154	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.21031	2.03	4.81	4.81	0.61882	.	.	.	.	.	T	0.49115	0.1538	M	0.80422	2.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.991;0.998;0.994	T	0.52946	-0.8507	9	0.56958	D	0.05	.	15.7617	0.78087	0.0:0.0:1.0:0.0	.	1720;1142;1839	B1AKD8;Q5TZA2-2;Q5TZA2	.;.;CROCC_HUMAN	K	1839;1720	ENSP00000364691:E1839K	ENSP00000364691:E1839K	E	+	1	0	CROCC	17169398	1.000000	0.71417	0.940000	0.37924	0.507000	0.33981	6.848000	0.75409	2.395000	0.81488	0.655000	0.94253	GAG	.	.		0.692	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		A	17296811	G	A	17296811	3	1	197	1	0	0	0	0	1	0	0	0	3895	1059	37	1	5649	1	CROCC	1	17296811	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10		17296811	231953810	1	28911										
EBNA1BP2	149465	hgsc.bcm.edu	37	chr1	43638006	43638006	+	5'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ccggcggcaaaccatacttcCggtttgtcgttgctatagga	11	11	0	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:43638006C>T	ENST00000372492.4	+	0	187				EBNA1BP2_ENST00000472982.1_5'Flank|EBNA1BP2_ENST00000431635.2_Silent_p.P29P|WDR65_ENST00000528956.1_5'UTR|EBNA1BP2_ENST00000236051.2_5'Flank	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN												NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				ACCATACTTCCGGTTTGTCGT	0.562																																					p.P29P		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.G87A						.						68	64	66					1																	43638006		692	1591	2283	SO:0001623	5_prime_UTR_variant	10969	exon1			TACTTCCGGTTTG																												ENST00000372492.4:c.-138C>T	chr1.hg19:g.43638006C>T		65.0	0.0		60.0	25.0	NM_001159936	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	hg19																																																																																				.	.		0.562	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			T	43638006	C	T	43638006	1	4	197	0	1	0	0	0	0	0	0	0	4887	639	23	1		1	EBNA1BP2	1	43638006	5'UTR	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	26341195	43638006	205612615	2	28912										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86289219	86289219	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cttaaataatttcaacttacTtcagatcctctctctccttt	1	12	4	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:86289219T>C	ENST00000370571.2	-	45	4155	c.3789A>G	c.(3787-3789)gaA>gaG	p.E1263E	COL24A1_ENST00000436319.1_Splice_Site_p.E1263E	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1263	Collagen-like 14.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TTCAACTTACTTCAGATCCTC	0.343																																					p.E1263E		Atlas-SNP	.											.	COL24A1	202	.	0			c.A3789G						.						106	100	102					1																	86289219		1856	4099	5955	SO:0001630	splice_region_variant	255631	exon45			ACTTACTTCAGAT	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.3789+1A>G	chr1.hg19:g.86289219T>C		147.0	0.0		133.0	33.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Silent	SNP	ENST00000370571.2	hg19	CCDS41353.1																																																																																			.	.		0.343	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	Silent	C	86289219	T	C	86289219	5	2	197	1	0	0	0	0	0	0	1	0	3685	1623	56	2	1419	2	COL24A1	1	86289219	Splice_Site	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	42651213	86289219	162961402	3	28913										
DPYD	1806	hgsc.bcm.edu	37	chr1	98015267	98015267	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ctacttctgggagaccccatCtgttaaattttatagggctc	8	10	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:98015267C>T	ENST00000370192.3	-	12	1473	c.1373G>A	c.(1372-1374)aGa>aAa	p.R458K		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	458					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.R458K(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	GAGACCCCATCTGTTAAATTT	0.373																																					p.R458K		Atlas-SNP	.											DPYD,acral,malignant_melanoma,0,2	DPYD	219	.	1	Substitution - Missense(1)	lung(1)	c.G1373A						.						70	65	67					1																	98015267		2203	4300	6503	SO:0001583	missense	1806	exon12			CCCCATCTGTTAA	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1373G>A	chr1.hg19:g.98015267C>T	ENSP00000359211:p.Arg458Lys	78.0	0.0		67.0	14.0	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	C	10.16	1.275007	0.23307	.	.	ENSG00000188641	ENST00000370192	D	0.92249	-3.0	6.16	3.34	0.38264	.	0.151926	0.56097	N	0.000024	T	0.68952	0.3057	N	0.17922	0.545	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.62613	-0.6817	10	0.02654	T	1	-15.0585	11.0603	0.47944	0.0:0.7682:0.0:0.2318	.	458	Q12882	DPYD_HUMAN	K	458	ENSP00000359211:R458K	ENSP00000359211:R458K	R	-	2	0	DPYD	97787855	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.466000	0.35310	0.498000	0.27948	0.650000	0.86243	AGA	.	.		0.373	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		T	98015267	C	T	98015267	3	4	197	1	0	0	0	0	1	0	0	0	4747	913	32	3	1752	3	DPYD	1	98015267	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	11726048	98015267	151235354	4	28914										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144886226	144886226	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tcaggtggagcatttcttccTgaagacacctgttactgtcc	9	11	2	2	rs139542367		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:144886226T>G	ENST00000369354.3	-	23	3197	c.3008A>C	c.(3007-3009)cAg>cCg	p.Q1003P	PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.Q1140P|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.Q1003P|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.Q1069P|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.Q1140P			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1003					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CATTTCTTCCTGAAGACACCT	0.507			T	PDGFRB	MPD																																p.Q1069P		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A3206C						.						214	214	214					1																	144886226		2203	4296	6499	SO:0001583	missense	9659	exon26			TCTTCCTGAAGAC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.3008A>C	chr1.hg19:g.144886226T>G	ENSP00000358360:p.Gln1003Pro	137.0	0.0		163.0	19.0	NM_001198832	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	10.05	1.244139	0.22796	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01647	4.71;4.79;4.79;4.79;4.78	5.56	5.56	0.83823	.	.	.	.	.	T	0.01627	0.0052	L	0.29908	0.895	0.80722	D	1	B;D	0.60575	0.119;0.988	B;P	0.53313	0.028;0.723	T	0.72487	-0.4278	9	0.36615	T	0.2	.	13.676	0.62454	0.0:0.0:0.0:1.0	.	1069;1003	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	P	1069;1003;1003;1140;1140	ENSP00000327209:Q1069P;ENSP00000358360:Q1003P;ENSP00000358363:Q1003P;ENSP00000435654:Q1140P;ENSP00000358366:Q1140P	ENSP00000327209:Q1069P	Q	-	2	0	PDE4DIP	143597583	1.000000	0.71417	1.000000	0.80357	0.080000	0.17528	1.995000	0.40767	2.128000	0.65567	0.459000	0.35465	CAG	.	.		0.507	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		G	144886226	T	G	144886226	3	3	197	1	0	0	0	0	1	0	0	0	11652	1580	55	5	4120	5	PDE4DIP	1	144886226	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	46870959	144886226	104364395	5	28915										
RFX5	5993	hgsc.bcm.edu	37	chr1	151315082	151315082	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agaggggtagaattcctttcCccacttccacctgacttttt	7	12	0	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:151315082C>T	ENST00000290524.4	-	11	1609	c.1431G>A	c.(1429-1431)ggG>ggA	p.G477G	RFX5_ENST00000478564.1_5'Flank|RP11-126K1.8_ENST00000422153.1_RNA|RFX5_ENST00000452513.2_Silent_p.G437G|RFX5_ENST00000452671.2_Silent_p.G477G|RFX5_ENST00000368870.2_Silent_p.G477G	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	477					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			AATTCCTTTCCCCACTTCCAC	0.537																																					p.G477G		Atlas-SNP	.											.	RFX5	69	.	0			c.G1431A						.						212	232	225					1																	151315082		2203	4300	6503	SO:0001819	synonymous_variant	5993	exon11			CCTTTCCCCACTT		CCDS994.1	1q21	2014-09-17			ENSG00000143390	ENSG00000143390			9986	protein-coding gene	gene with protein product		601863				9401005	Standard	XM_005245405		Approved		uc001exw.1	P48382	OTTHUMG00000012495	ENST00000290524.4:c.1431G>A	chr1.hg19:g.151315082C>T		90.0	0.0		122.0	15.0	NM_000449	B7Z848|D3DV19|E9PFU4|Q5VWC3	Silent	SNP	ENST00000290524.4	hg19	CCDS994.1																																																																																			.	.		0.537	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449		T	151315082	C	T	151315082	2	4	197	1	0	0	0	0	0	0	0	1	13281	610	22	3		3	RFX5	1	151315082	Silent	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	6428856	151315082	97935539	6	28916										
TCHH	7062	hgsc.bcm.edu	37	chr1	152083480	152083480	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cactctcccggcgccgcctcTtttcctcctgctcttggcgg	9	19	3	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:152083480T>A	ENST00000368804.1	-	2	2212	c.2213A>T	c.(2212-2214)aAg>aTg	p.K738M		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	738					keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCGCCGCCTCTTTTCCTCCTG	0.652																																					p.K738M		Atlas-SNP	.											.	TCHH	275	.	0			c.A2213T						.						83	103	97					1																	152083480		1949	4125	6074	SO:0001583	missense	7062	exon3			CGCCTCTTTTCCT	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.2213A>T	chr1.hg19:g.152083480T>A	ENSP00000357794:p.Lys738Met	52.0	0.0		91.0	6.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	t	11.21	1.572701	0.28092	.	.	ENSG00000159450	ENST00000368804	T	0.06142	3.34	4.09	0.299	0.15771	.	.	.	.	.	T	0.01627	0.0052	N	0.14661	0.345	0.09310	N	1	P	0.49961	0.93	P	0.48368	0.575	T	0.40117	-0.9580	9	0.59425	D	0.04	-1.6725	3.5021	0.07677	0.1664:0.1999:0.0:0.6338	.	738	Q07283	TRHY_HUMAN	M	738	ENSP00000357794:K738M	ENSP00000357794:K738M	K	-	2	0	TCHH	150350104	0.000000	0.05858	0.001000	0.08648	0.552000	0.35366	-0.003000	0.12901	-0.238000	0.09724	0.375000	0.23000	AAG	.	.		0.652	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		A	152083480	T	A	152083480	3	1	197	1	0	0	0	0	1	0	0	0	15715	1609	56	4	3622	4	TCHH	1	152083480	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	768398	152083480	97167141	7	28917										
FLG	2312	hgsc.bcm.edu	37	chr1	152280916	152280916	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gctcttggtgggacccctgtCttcctcctctgcttggcccc	10	17	3	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:152280916C>T	ENST00000368799.1	-	3	6481	c.6446G>A	c.(6445-6447)aGa>aAa	p.R2149K	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2149	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGACCCCTGTCTTCCTCCTCT	0.587									Ichthyosis																												p.R2149K		Atlas-SNP	.											.	FLG	900	.	0			c.G6446A						.						401	324	350					1																	152280916		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCCTGTCTTCCTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6446G>A	chr1.hg19:g.152280916C>T	ENSP00000357789:p.Arg2149Lys	91.0	0.0		162.0	24.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	c	7.808	0.715007	0.15306	.	.	ENSG00000143631	ENST00000368799	T	0.03920	3.76	2.87	0.751	0.18392	.	.	.	.	.	T	0.01905	0.0060	M	0.79805	2.47	0.09310	N	1	P	0.45531	0.86	B	0.40534	0.332	T	0.36915	-0.9728	9	0.05721	T	0.95	.	8.5764	0.33601	0.0:0.5299:0.4701:0.0	.	2149	P20930	FILA_HUMAN	K	2149	ENSP00000357789:R2149K	ENSP00000357789:R2149K	R	-	2	0	FLG	150547540	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.561000	0.05957	0.052000	0.16007	0.485000	0.47835	AGA	.	.		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152280916	C	T	152280916	3	4	197	1	0	0	0	0	1	0	0	0	5930	913	32	3	5743	3	FLG	1	152280916	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	197436	152280916	96969705	8	28918										
NTRK1	4914	hgsc.bcm.edu	37	chr1	156851354	156851354	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggcagcgggagccccagcaaCgccacagcatcaaggatgtg	14	13	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:156851354C>T	ENST00000524377.1	+	17	2352	c.2311C>T	c.(2311-2313)Cgc>Tgc	p.R771C	NTRK1_ENST00000531606.1_3'UTR|NTRK1_ENST00000392302.2_Missense_Mutation_p.R735C|NTRK1_ENST00000368196.3_Missense_Mutation_p.R765C|NTRK1_ENST00000358660.3_Missense_Mutation_p.R768C	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	771	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	GCCCCAGCAACGCCACAGCAT	0.692			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.R771C		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1	287	.	0			c.C2311T						.						27	26	26					1																	156851354		2202	4297	6499	SO:0001583	missense	4914	exon17			CAGCAACGCCACA	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.2311C>T	chr1.hg19:g.156851354C>T	ENSP00000431418:p.Arg771Cys	147.0	0.0		202.0	25.0	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	hg19	CCDS1161.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951991	0.73787	.	.	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	D;D;D;D	0.98381	-4.9;-4.9;-4.9;-4.9	4.87	4.87	0.63330	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000008	D	0.99318	0.9761	H	0.97896	4.1	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98686	1.0694	10	0.87932	D	0	.	11.911	0.52739	0.1741:0.8259:0.0:0.0	.	768;765;771;735	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	C	735;765;771;768	ENSP00000376120:R735C;ENSP00000357179:R765C;ENSP00000431418:R771C;ENSP00000351486:R768C	ENSP00000351486:R768C	R	+	1	0	NTRK1	155117978	0.995000	0.38212	0.994000	0.49952	0.863000	0.49368	3.201000	0.51059	2.518000	0.84900	0.655000	0.94253	CGC	.	.		0.692	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		T	156851354	C	T	156851354	3	4	197	1	0	0	0	0	1	0	0	0	10715	536	19	1	2507	1	NTRK1	1	156851354	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	4570438	156851354	92399267	9	28919										
KIRREL	55243	hgsc.bcm.edu	37	chr1	158061204	158061204	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	accctggaacgctatacagtGgagaggaccaactcaggcag	12	11	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:158061204G>T	ENST00000359209.6	+	11	1396	c.1329G>T	c.(1327-1329)gtG>gtT	p.V443V	KIRREL_ENST00000368173.3_Silent_p.V459V|KIRREL_ENST00000392272.2_Silent_p.V340V|KIRREL_ENST00000368172.1_Silent_p.V257V|KIRREL_ENST00000416935.2_Silent_p.V343V|KIRREL_ENST00000360089.4_Silent_p.V279V			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	443	Ig-like C2-type 5.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					GCTATACAGTGGAGAGGACCA	0.567																																					p.V443V		Atlas-SNP	.											.	KIRREL	346	.	0			c.G1329T						.						127	119	122					1																	158061204		2203	4300	6503	SO:0001819	synonymous_variant	55243	exon11			TACAGTGGAGAGG	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15734	protein-coding gene	gene with protein product	"nephrin-like protein 1"	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.1329G>T	chr1.hg19:g.158061204G>T		99.0	0.0		151.0	79.0	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Silent	SNP	ENST00000359209.6	hg19	CCDS1172.2																																																																																			.	.		0.567	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240		T	158061204	G	T	158061204	2	4	197	1	0	0	0	0	0	0	0	1	8333	1335	47	3		3	KIRREL	1	158061204	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	1209850	158061204	91189417	10	28920										
ADAMTS4	9507	hgsc.bcm.edu	37	chr1	161163059	161163059	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggcctggcaggtgagtttgcActggtcctggggggccacgc	18	11	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:161163059A>C	ENST00000367996.5	-	7	2283	c.1855T>G	c.(1855-1857)Tgc>Ggc	p.C619G	ADAMTS4_ENST00000478394.1_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	619	Cys-rich.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	GTGAGTTTGCACTGGTCCTGG	0.632																																					p.C619G		Atlas-SNP	.											.	ADAMTS4	171	.	0			c.T1855G						.						51	48	49					1																	161163059		2203	4300	6503	SO:0001583	missense	9507	exon7			GTTTGCACTGGTC	AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"ADAM metallopeptidases with thrombospondin type 1 motif"	220	protein-coding gene	gene with protein product		603876	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.1855T>G	chr1.hg19:g.161163059A>C	ENSP00000356975:p.Cys619Gly	43.0	0.0		71.0	5.0	NM_005099	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	hg19	CCDS1223.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.406768	0.83230	.	.	ENSG00000158859	ENST00000367996	T	0.74842	-0.88	4.81	4.81	0.61882	.	0.000000	0.64402	D	0.000002	D	0.90376	0.6988	H	0.98721	4.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93758	0.7064	10	0.87932	D	0	.	13.4839	0.61353	1.0:0.0:0.0:0.0	.	619	O75173	ATS4_HUMAN	G	619	ENSP00000356975:C619G	ENSP00000356975:C619G	C	-	1	0	ADAMTS4	159429683	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.139000	0.94554	2.007000	0.58848	0.455000	0.32223	TGC	.	.		0.632	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099		C	161163059	A	C	161163059	3	2	197	1	0	0	0	0	1	0	0	0	268	159	6	5	670	5	ADAMTS4	1	161163059	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	3101855	161163059	88087562	11	28921										
UAP1	6675	hgsc.bcm.edu	37	chr1	162551100	162551100	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggaatggtggtctttatcggGcacttgcagcccagaatatt	12	8	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:162551100G>A	ENST00000367925.1	+	4	717	c.685G>A	c.(685-687)Gca>Aca	p.A229T	UAP1_ENST00000367926.4_Missense_Mutation_p.A229T|UAP1_ENST00000367924.1_Missense_Mutation_p.A229T|UAP1_ENST00000271469.3_Missense_Mutation_p.A229T			Q16222	UAP1_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1	229					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|UDP-N-acetylglucosamine diphosphorylase activity (GO:0003977)			breast(2)|cervix(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)|skin(2)|stomach(1)	22	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			TCTTTATCGGGCACTTGCAGC	0.403																																					p.A229T		Atlas-SNP	.											.	UAP1	47	.	0			c.G685A						.						226	229	228					1																	162551100		2203	4300	6503	SO:0001583	missense	6675	exon5			TATCGGGCACTTG	AB011004	CCDS1240.1	1q23.2	2014-07-31	2014-07-31		ENSG00000117143	ENSG00000117143	2.7.7.23		12457	protein-coding gene	gene with protein product		602862		SPAG2		9603950, 8025165	Standard	NM_003115		Approved	AGX1, AgX	uc001gce.4	Q16222	OTTHUMG00000034419	ENST00000367925.1:c.685G>A	chr1.hg19:g.162551100G>A	ENSP00000356902:p.Ala229Thr	125.0	0.0		161.0	20.0	NM_003115	B2R6R8|Q5VTA9|Q5VTB0|Q5VTB1|Q96GM2	Missense_Mutation	SNP	ENST00000367925.1	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.446404	0.96187	.	.	ENSG00000117143	ENST00000367926;ENST00000271469;ENST00000367925;ENST00000367924	T;T;T;T	0.19806	2.12;2.12;2.12;2.12	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.50922	0.1644	M	0.92219	3.285	0.58432	D	0.999991	D	0.89917	1.0	D	0.76575	0.988	T	0.64202	-0.6463	9	0.87932	D	0	-8.6366	17.5485	0.87870	0.0:0.0:1.0:0.0	.	229	Q16222-2	.	T	229	ENSP00000356903:A229T;ENSP00000271469:A229T;ENSP00000356902:A229T;ENSP00000356901:A229T	ENSP00000271469:A229T	A	+	1	0	UAP1	160817724	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.628000	0.83189	2.548000	0.85928	0.591000	0.81541	GCA	.	.		0.403	UAP1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000083203.1	NM_003115		A	162551100	G	A	162551100	3	1	197	1	0	0	0	0	1	0	0	0	16840	1203	42	3	699	3	UAP1	1	162551100	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	1388041	162551100	86699521	12	28922										
PBX1	5087	hgsc.bcm.edu	37	chr1	164776788	164776788	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tctttacaaaggcggaagagAcggaatttcaacaagcaagc	10	8	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:164776788A>G	ENST00000420696.2	+	5	899	c.711A>G	c.(709-711)agA>agG	p.R237R	PBX1_ENST00000559240.1_Silent_p.R237R|PBX1_ENST00000540246.1_Silent_p.R132R|PBX1_ENST00000540236.1_Silent_p.R237R|PBX1_ENST00000367897.1_Silent_p.R237R|PBX1_ENST00000560641.1_Silent_p.R132R|PBX1_ENST00000401534.1_Silent_p.R237R	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	237					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						GGCGGAAGAGACGGAATTTCA	0.393			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.R237R		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1	60	.	0			c.A711G						.						102	112	109					1																	164776788		2203	4300	6503	SO:0001819	synonymous_variant	5087	exon5			GAAGAGACGGAAT	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"Homeoboxes / TALE class"	8632	protein-coding gene	gene with protein product		176310	"pre-B-cell leukemia transcription factor 1"				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.711A>G	chr1.hg19:g.164776788A>G		180.0	0.0		308.0	46.0	NM_001204963	B4DSC1|F5H4U9|Q5T488	Silent	SNP	ENST00000420696.2	hg19	CCDS1246.1																																																																																			.	.		0.393	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		G	164776788	A	G	164776788	2	3	197	1	0	0	0	0	0	0	0	1	11501	272	10	2		2	PBX1	1	164776788	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	2225688	164776788	84473833	13	28923										
UCK2	7371	hgsc.bcm.edu	37	chr1	165865569	165865569	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	acacccggctctcacgcagaGgtgcgttctaaaagcctcag	10	14	3	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:165865569G>A	ENST00000367879.4	+	4	802	c.499G>A	c.(499-501)Gta>Ata	p.V167I	UCK2_ENST00000469256.2_Splice_Site_p.V17I|UCK2_ENST00000372212.4_Intron|RP11-525G13.2_ENST00000455257.2_RNA|UCK2_ENST00000470820.1_Splice_Site_p.V17I|UCK2_ENST00000462329.1_3'UTR	NM_012474.4	NP_036606.2	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2	167					cellular response to oxygen levels (GO:0071453)|CTP salvage (GO:0044211)|feeding behavior (GO:0007631)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to axon injury (GO:0048678)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					CTCACGCAGAGGTGCGTTCTA	0.602																																					p.V167I		Atlas-SNP	.											.	UCK2	31	.	0			c.G499A						.						114	119	117					1																	165865569		2203	4300	6503	SO:0001630	splice_region_variant	7371	exon4			CGCAGAGGTGCGT	AF236637	CCDS1252.1	1p32	2012-10-02	2004-07-13	2004-07-14	ENSG00000143179	ENSG00000143179	2.7.1.48		12562	protein-coding gene	gene with protein product		609329	"uridine monophosphate kinase"	UMPK			Standard	NM_012474		Approved		uc001gdp.3	Q9BZX2	OTTHUMG00000040117	ENST00000367879.4:c.499+1G>A	chr1.hg19:g.165865569G>A		68.0	0.0		113.0	15.0	NM_012474	Q5VV91|Q7KZV3|Q92528|Q96KG5|Q9BU42	Missense_Mutation	SNP	ENST00000367879.4	hg19	CCDS1252.1	.	.	.	.	.	.	.	.	.	.	G	19.78	3.890994	0.72524	.	.	ENSG00000143179	ENST00000367879	.	.	.	4.97	4.97	0.65823	Phosphoribulokinase/uridine kinase (1);	0.060192	0.64402	D	0.000003	T	0.41465	0.1160	L	0.28556	0.865	.	.	.	D	0.67145	0.996	P	0.61132	0.884	T	0.25984	-1.0116	8	0.08599	T	0.76	-5.9114	15.7418	0.77905	0.0:0.0:1.0:0.0	.	167	Q9BZX2	UCK2_HUMAN	I	167	.	ENSP00000356853:V167I	V	+	1	0	UCK2	164132193	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.517000	0.98020	2.309000	0.77851	0.655000	0.94253	GTA	.	.		0.602	UCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096753.1	NM_012474	Missense_Mutation	A	165865569	G	A	165865569	5	1	197	1	0	0	0	0	0	0	1	0	16939	1014	35	3	513	3	UCK2	1	165865569	Splice_Site	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	1088781	165865569	83385052	14	28924										
TNFSF4	7292	hgsc.bcm.edu	37	chr1	173176191	173176191	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cagagaagtgcaggcagatgTaggtgaagcacaggagcagc	16	7	0	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:173176191T>G	ENST00000281834.3	-	1	261	c.125A>C	c.(124-126)tAc>tCc	p.Y42S	TNFSF4_ENST00000488053.1_5'Flank|TNFSF4_ENST00000367718.1_5'Flank	NM_003326.3	NP_003317.1	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily, member 4	42					acute inflammatory response (GO:0002526)|CD4-positive, alpha-beta T cell costimulation (GO:0035783)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nitrogen dioxide (GO:0035714)|cellular response to prostaglandin E stimulus (GO:0071380)|chemokine (C-C motif) ligand 11 production (GO:0071954)|cholesterol metabolic process (GO:0008203)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|memory T cell activation (GO:0035709)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell activation (GO:0050871)|positive regulation of CD4-positive, alpha-beta T cell costimulation (GO:1900281)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-4-dependent isotype switching to IgE isotypes (GO:2000572)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of memory T cell activation (GO:2000568)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T-helper 2 cell activation (GO:2000570)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of type 2 immune response (GO:0002830)|regulation of adaptive immune response (GO:0002819)|regulation of inflammatory response (GO:0050727)|response to nitrogen dioxide (GO:0035713)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|T-helper 2 cell activation (GO:0035712)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)|tumor necrosis factor receptor superfamily binding (GO:0032813)			breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	12						CAGGCAGATGTAGGTGAAGCA	0.542																																					p.Y42S		Atlas-SNP	.											.	TNFSF4	29	.	0			c.A125C						.						112	95	101					1																	173176191		2203	4300	6503	SO:0001583	missense	7292	exon1			CAGATGTAGGTGA	D90224	CCDS1306.1, CCDS72985.1	1q25	2008-07-31	2008-07-31		ENSG00000117586	ENSG00000117586		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11934	protein-coding gene	gene with protein product		603594	"tax-transcriptionally activated glycoprotein 1, 34kD"	TXGP1		1996093, 8076595	Standard	XM_005245475		Approved	OX-40L, gp34, CD252	uc001giw.3	P23510	OTTHUMG00000034838	ENST00000281834.3:c.125A>C	chr1.hg19:g.173176191T>G	ENSP00000281834:p.Tyr42Ser	86.0	0.0		107.0	57.0	NM_003326	Q5JZA5|Q8IV74|Q9HCN9	Missense_Mutation	SNP	ENST00000281834.3	hg19	CCDS1306.1	.	.	.	.	.	.	.	.	.	.	T	8.887	0.953071	0.18431	.	.	ENSG00000117586	ENST00000281834	.	.	.	5.67	1.93	0.25924	.	0.349225	0.24920	N	0.034556	T	0.37517	0.1006	M	0.71581	2.175	0.27245	N	0.959055	D	0.58268	0.982	P	0.55824	0.785	T	0.27739	-1.0065	9	0.87932	D	0	-7.8065	8.7487	0.34602	0.4457:0.0:0.0:0.5543	.	42	P23510	TNFL4_HUMAN	S	42	.	ENSP00000281834:Y42S	Y	-	2	0	TNFSF4	171442814	0.990000	0.36364	0.109000	0.21407	0.011000	0.07611	0.678000	0.25277	0.062000	0.16340	-1.385000	0.01166	TAC	.	.		0.542	TNFSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084271.1			G	173176191	T	G	173176191	3	3	197	1	0	0	0	0	1	0	0	0	16325	1638	57	5	438	5	TNFSF4	1	173176191	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	7310622	173176191	76074430	15	28925										
ZBTB37	84614	hgsc.bcm.edu	37	chr1	173839522	173839522	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aaagtggtgctggctgccagCtccccctatttccgggatca	11	13	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:173839522C>G	ENST00000367701.5	+	2	350	c.159C>G	c.(157-159)agC>agG	p.S53R	ZBTB37_ENST00000367702.1_Missense_Mutation_p.S53R|ZBTB37_ENST00000427304.1_Missense_Mutation_p.S53R|ZBTB37_ENST00000432989.1_Missense_Mutation_p.S53R|ZBTB37_ENST00000367704.1_Missense_Mutation_p.S53R|GAS5_ENST00000364084.1_RNA			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	53	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						TGGCTGCCAGCTCCCCCTATT	0.488																																					p.S53R		Atlas-SNP	.											.	ZBTB37	38	.	0			c.C159G						.						113	112	113					1																	173839522		2203	4300	6503	SO:0001583	missense	84614	exon3			TGCCAGCTCCCCC	AK057310	CCDS1312.1, CCDS44278.1	1q24.2	2013-01-08			ENSG00000185278	ENSG00000185278		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	28365	protein-coding gene	gene with protein product						12477932	Standard	NM_032522		Approved	MGC2629, ZNF908	uc009wwp.1	Q5TC79	OTTHUMG00000037274	ENST00000367701.5:c.159C>G	chr1.hg19:g.173839522C>G	ENSP00000356674:p.Ser53Arg	141.0	0.0		218.0	30.0	NM_032522	Q5TC80|Q96M87|Q9BQ88	Missense_Mutation	SNP	ENST00000367701.5	hg19	CCDS44278.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.559583	0.65538	.	.	ENSG00000185278	ENST00000367704;ENST00000427304;ENST00000432989;ENST00000367702;ENST00000367701	T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11	5.6	1.58	0.23477	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.071297	0.85682	D	0.000000	T	0.55386	0.1917	L	0.31926	0.97	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.85130	0.993;0.997	T	0.59107	-0.7516	10	0.66056	D	0.02	.	9.7332	0.40374	0.0:0.7124:0.0:0.2876	.	53;53	Q5TC79;Q5TC79-2	ZBT37_HUMAN;.	R	53	ENSP00000356677:S53R;ENSP00000415293:S53R;ENSP00000409408:S53R;ENSP00000356675:S53R;ENSP00000356674:S53R	ENSP00000356674:S53R	S	+	3	2	ZBTB37	172106145	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	2.243000	0.43115	0.039000	0.15632	0.563000	0.77884	AGC	.	.		0.488	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522		G	173839522	C	G	173839522	3	3	197	1	0	0	0	0	1	0	0	0	17553	796	28	4	161	4	ZBTB37	1	173839522	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	663331	173839522	75411099	16	28926										
TOR1AIP2	163590	hgsc.bcm.edu	37	chr1	179815788	179815788	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tgcttctggagaaacttccgTcctctctgccacaggaagga	10	12	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:179815788T>A	ENST00000367612.3	-	6	1218	c.831A>T	c.(829-831)ggA>ggT	p.G277G	TOR1AIP2_ENST00000609928.1_Silent_p.G277G	NM_145034.4	NP_659471.1	Q9H496	IFG15_HUMAN	torsin A interacting protein 2	0										cervix(1)|endometrium(3)|large_intestine(1)|lung(10)|ovary(1)|skin(2)	18						GAAACTTCCGTCCTCTCTGCC	0.517																																					p.G277G		Atlas-SNP	.											.	TOR1AIP2	38	.	0			c.A831T						.						71	71	71					1																	179815788		2203	4300	6503	SO:0001819	synonymous_variant	163590	exon7			CTTCCGTCCTCTC		CCDS1334.1	1q25.2	2012-02-09			ENSG00000169905	ENSG00000169905			24055	protein-coding gene	gene with protein product		614513				15767459	Standard	NM_145034		Approved	LULL1, NET9, IFRG15	uc001gnk.3	Q8NFQ8	OTTHUMG00000035265	ENST00000367612.3:c.831A>T	chr1.hg19:g.179815788T>A		97.0	0.0		103.0	10.0	NM_001199260	Q05BU2	Silent	SNP	ENST00000367612.3	hg19	CCDS1334.1																																																																																			.	.		0.517	TOR1AIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085304.1	NM_145034		A	179815788	T	A	179815788	2	1	197	1	0	0	0	0	0	0	0	1	16388	1654	58	4		4	TOR1AIP2	1	179815788	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	5976266	179815788	69434833	17	28927										
FAM129A	116496	hgsc.bcm.edu	37	chr1	184764664	184764664	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gctctttttcctcttcttctTcattttcttggggaacgtgg	8	10	6	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:184764664T>A	ENST00000367511.3	-	14	2427	c.2234A>T	c.(2233-2235)gAa>gTa	p.E745V	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	745	Glu-rich.				negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						CTCTTCTTCTTCATTTTCTTG	0.542																																					p.E745V		Atlas-SNP	.											.	FAM129A	98	.	0			c.A2234T						.						147	156	153					1																	184764664		2203	4300	6503	SO:0001583	missense	116496	exon14			TCTTCTTCATTTT	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"cell growth inhibiting protein 39"		"chromosome 1 open reading frame 24"	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.2234A>T	chr1.hg19:g.184764664T>A	ENSP00000356481:p.Glu745Val	61.0	0.0		87.0	11.0	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	hg19	CCDS1364.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.082091	0.36758	.	.	ENSG00000135842	ENST00000367511	T	0.11385	2.78	5.44	0.117	0.14652	.	1.131090	0.06718	N	0.774372	T	0.06735	0.0172	L	0.29908	0.895	0.09310	N	1	B	0.29646	0.253	B	0.24541	0.054	T	0.40270	-0.9572	10	0.30854	T	0.27	-3.0053	1.9748	0.03413	0.1162:0.1507:0.3094:0.4237	.	745	Q9BZQ8	NIBAN_HUMAN	V	745	ENSP00000356481:E745V	ENSP00000356481:E745V	E	-	2	0	FAM129A	183031287	0.000000	0.05858	0.017000	0.16124	0.345000	0.29048	0.246000	0.18160	0.013000	0.14918	0.402000	0.26972	GAA	.	.		0.542	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			A	184764664	T	A	184764664	3	1	197	1	0	0	0	0	1	0	0	0	5441	1783	62	4	556	4	FAM129A	1	184764664	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	4948876	184764664	64485957	18	28928										
SERTAD4	56256	hgsc.bcm.edu	37	chr1	210414923	210414923	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	accatctcaatttttgaggaAcgagcccacatcctttatat	5	11	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:210414923A>G	ENST00000367012.3	+	4	542	c.312A>G	c.(310-312)gaA>gaG	p.E104E	SERTAD4_ENST00000490620.1_3'UTR	NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	104	SERTA. {ECO:0000255|PROSITE- ProRule:PRU00396}.					nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		TTTTTGAGGAACGAGCCCACA	0.318																																					p.E104E		Atlas-SNP	.											.	SERTAD4	53	.	0			c.A312G						.						59	62	61					1																	210414923		2203	4300	6503	SO:0001819	synonymous_variant	56256	exon4			TGAGGAACGAGCC	BC012083	CCDS1494.1	1q32.1-q41	2008-02-05			ENSG00000082497	ENSG00000082497			25236	protein-coding gene	gene with protein product						12477932	Standard	NM_019605		Approved	DJ667H12.2	uc001hhy.3	Q9NUC0	OTTHUMG00000036391	ENST00000367012.3:c.312A>G	chr1.hg19:g.210414923A>G		100.0	0.0		160.0	22.0	NM_019605	B2RD32	Silent	SNP	ENST00000367012.3	hg19	CCDS1494.1																																																																																			.	.		0.318	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1	NM_019605		G	210414923	A	G	210414923	2	3	197	1	0	0	0	0	0	0	0	1	14138	40	2	2		2	SERTAD4	1	210414923	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	25650259	210414923	38835698	19	28929										
CENPF	1063	hgsc.bcm.edu	37	chr1	214814115	214814115	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gaagcatgccttcagagaggAgtgaatgtcgtttagaagca	13	6	1	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:214814115A>C	ENST00000366955.3	+	12	2602	c.2434A>C	c.(2434-2436)Agt>Cgt	p.S812R		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TTCAGAGAGGAGTGAATGTCG	0.388																																					p.S812R	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A2434C						.						51	53	52					1																	214814115		2198	4299	6497	SO:0001583	missense	1063	exon12			GAGAGGAGTGAAT	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.2434A>C	chr1.hg19:g.214814115A>C	ENSP00000355922:p.Ser812Arg	151.0	0.0		249.0	35.0	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	4.477	0.088490	0.08583	.	.	ENSG00000117724	ENST00000366955	T	0.03272	3.99	5.59	0.569	0.17340	.	0.324291	0.22475	N	0.059577	T	0.03305	0.0096	.	.	.	0.09310	N	1	D	0.54601	0.967	P	0.46629	0.522	T	0.45571	-0.9252	9	0.23302	T	0.38	.	4.7063	0.12851	0.4936:0.0:0.3555:0.1509	.	812	P49454	CENPF_HUMAN	R	812	ENSP00000355922:S812R	ENSP00000355922:S812R	S	+	1	0	CENPF	212880738	0.000000	0.05858	0.035000	0.18076	0.105000	0.19272	0.467000	0.22035	0.092000	0.17331	0.496000	0.49642	AGT	.	.		0.388	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		C	214814115	A	C	214814115	3	2	197	1	0	0	0	0	1	0	0	0	3233	304	11	5	2476	5	CENPF	1	214814115	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	4399192	214814115	34436506	20	28930										
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220364508	220364508	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggcgcatagatcacaaggaaTtgagctactcgacttggacc	11	10	1	2	rs149874983		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:220364508T>C	ENST00000358951.2	-	14	1505	c.1389A>G	c.(1387-1389)caA>caG	p.Q463Q		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	463					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		TCACAAGGAATTGAGCTACTC	0.478																																					p.Q463Q		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.A1389G						.						125	123	124					1																	220364508		2203	4300	6503	SO:0001819	synonymous_variant	25782	exon14			AAGGAATTGAGCT	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.1389A>G	chr1.hg19:g.220364508T>C		105.0	0.0		147.0	22.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Silent	SNP	ENST00000358951.2	hg19	CCDS31028.1																																																																																			.	T|1.000;G|0.000		0.478	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		C	220364508	T	C	220364508	2	2	197	1	0	0	0	0	0	0	0	1	12951	1490	52	2		2	RAB3GAP2	1	220364508	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	5550393	220364508	28886113	21	28931										
EPHX1	2052	hgsc.bcm.edu	37	chr1	226030084	226030084	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	caggctctgctctgaatgacTctcctgtgggtctggctgcc	12	13	4	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:226030084T>A	ENST00000366837.4	+	7	1145	c.949T>A	c.(949-951)Tct>Act	p.S317T	EPHX1_ENST00000272167.5_Missense_Mutation_p.S317T|RP11-285F7.2_ENST00000424332.1_RNA	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	317					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TCTGAATGACTCTCCTGTGGG	0.587																																					p.S317T		Atlas-SNP	.											.	EPHX1	57	.	0			c.T949A						.						101	108	105					1																	226030084		2203	4300	6503	SO:0001583	missense	2052	exon7			AATGACTCTCCTG	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.949T>A	chr1.hg19:g.226030084T>A	ENSP00000355802:p.Ser317Thr	52.0	0.0		74.0	9.0	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Missense_Mutation	SNP	ENST00000366837.4	hg19	CCDS1547.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.758823	0.89843	.	.	ENSG00000143819	ENST00000272167;ENST00000366837	T;T	0.62105	0.05;0.05	5.33	5.33	0.75918	Alpha/beta hydrolase fold-1 (1);	0.058311	0.64402	D	0.000001	D	0.84964	0.5589	H	0.95365	3.66	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.89568	0.3811	10	0.72032	D	0.01	-19.5836	15.5961	0.76583	0.0:0.0:0.0:1.0	.	317	P07099	HYEP_HUMAN	T	317	ENSP00000272167:S317T;ENSP00000355802:S317T	ENSP00000272167:S317T	S	+	1	0	EPHX1	224096707	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.914000	0.87478	2.137000	0.66172	0.533000	0.62120	TCT	.	.		0.587	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120		A	226030084	T	A	226030084	3	1	197	1	0	0	0	0	1	0	0	0	5181	1551	54	4	971	4	EPHX1	1	226030084	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	5665576	226030084	23220537	22	28932										
ZNF238	10472	hgsc.bcm.edu	37	chr1	244217368	244217368	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tgtatgaagggaaactccagTtcaaagacttgcccattgaa	9	8	1	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:244217368T>C	ENST00000358704.4	+	2	441	c.292T>C	c.(292-294)Ttc>Ctc	p.F98L		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	89					cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GAAACTCCAGTTCAAAGACTT	0.458																																					p.F98L		Atlas-SNP	.											.	.	.	.	0			c.T292C						.						68	69	69					1																	244217368		2203	4300	6503	SO:0001583	missense	10472	exon2			CTCCAGTTCAAAG	U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13030	protein-coding gene	gene with protein product		608433	"zinc finger protein 238"	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.292T>C	chr1.hg19:g.244217368T>C	ENSP00000351539:p.Phe98Leu	74.0	0.0		112.0	42.0	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	hg19	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	T	9.701	1.154584	0.21371	.	.	ENSG00000179456	ENST00000366538;ENST00000358704	T	0.66460	-0.21	4.98	4.98	0.66077	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.50480	0.1618	N	0.00801	-1.175	0.80722	D	1	D;B;B	0.57257	0.979;0.129;0.14	D;B;B	0.71414	0.973;0.161;0.171	T	0.57700	-0.7766	10	0.02654	T	1	.	14.6603	0.68865	0.0:0.0:0.0:1.0	.	98;89;98	B4DF20;Q99592;Q99592-2	.;ZN238_HUMAN;.	L	98	ENSP00000351539:F98L	ENSP00000351539:F98L	F	+	1	0	ZNF238	242283991	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	1.876000	0.54355	0.533000	0.62120	TTC	.	.		0.458	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768		C	244217368	T	C	244217368	3	2	197	1	0	0	0	0	1	0	0	0	17805	1725	60	2	298	2	ZNF238	1	244217368	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	18187284	244217368	5033253	23	28933										
TRIM58	25893	hgsc.bcm.edu	37	chr1	248039449	248039449	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ctgccaagaaagggggaaacCacgccatctcctgagaatgg	12	11	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr1:248039449C>T	ENST00000366481.3	+	6	1167	c.1119C>T	c.(1117-1119)acC>acT	p.T373T	OR2W3_ENST00000537741.1_Intron	NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	373	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			AGGGGGAAACCACGCCATCTC	0.557																																					p.T373T		Atlas-SNP	.											.	TRIM58	143	.	0			c.C1119T						.						116	113	114					1																	248039449		2203	4300	6503	SO:0001819	synonymous_variant	25893	exon6			GGAAACCACGCCA	AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	24150	protein-coding gene	gene with protein product			"tripartite motif-containing 58"				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.1119C>T	chr1.hg19:g.248039449C>T		114.0	0.0		169.0	23.0	NM_015431	Q6B0H9	Silent	SNP	ENST00000366481.3	hg19	CCDS1636.1																																																																																			.	.		0.557	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431		T	248039449	C	T	248039449	2	4	197	1	0	0	0	0	0	0	0	1	16546	581	21	3		3	TRIM58	1	248039449	Silent	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	3822081	248039449	1211172	24	28934										
KIDINS220	57498	hgsc.bcm.edu	37	chr2	8871439	8871439	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aatcctttttgtcaaggagcGcatccgataaatactctttg	7	9	2	0	rs202036173		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:8871439G>T	ENST00000256707.3	-	30	4908	c.4727C>A	c.(4726-4728)gCg>gAg	p.A1576E	KIDINS220_ENST00000427284.1_Missense_Mutation_p.A1557E|KIDINS220_ENST00000418530.1_Missense_Mutation_p.A1477E|KIDINS220_ENST00000473731.1_Missense_Mutation_p.A1557E	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1576					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)	p.A1576V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GTCAAGGAGCGCATCCGATAA	0.473																																					p.A1576E		Atlas-SNP	.											KIDINS220,NS,carcinoma,0,1	KIDINS220	136	.	1	Substitution - Missense(1)	lung(1)	c.C4727A						.						132	128	129					2																	8871439		1978	4174	6152	SO:0001583	missense	57498	exon30			AGGAGCGCATCCG	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4727C>A	chr2.hg19:g.8871439G>T	ENSP00000256707:p.Ala1576Glu	53.0	0.0		88.0	4.0	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.808634	0.70797	.	.	ENSG00000134313	ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731	T;T;T;T	0.69561	-0.4;-0.39;-0.41;-0.39	5.92	5.92	0.95590	.	0.227294	0.45867	D	0.000338	T	0.75170	0.3813	L	0.27053	0.805	0.44417	D	0.997338	D;D;D	0.89917	0.991;0.994;1.0	D;P;D	0.97110	0.916;0.826;1.0	T	0.76898	-0.2789	10	0.72032	D	0.01	.	20.3214	0.98679	0.0:0.0:1.0:0.0	.	1477;1576;430	Q9ULH0-2;Q9ULH0;B4DG84	.;KDIS_HUMAN;.	E	1576;1557;1477;1557	ENSP00000256707:A1576E;ENSP00000411849:A1557E;ENSP00000414923:A1477E;ENSP00000418974:A1557E	ENSP00000256707:A1576E	A	-	2	0	KIDINS220	8788890	1.000000	0.71417	0.388000	0.26195	0.768000	0.43524	4.254000	0.58798	2.804000	0.96469	0.655000	0.94253	GCG	.	.		0.473	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		T	8871439	G	T	8871439	3	4	197	1	0	0	0	0	1	0	0	0	8280	1087	38	1	592	1	KIDINS220	2	8871439	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10		8871439	234327934	25	28935										
GREB1	9687	hgsc.bcm.edu	37	chr2	11777860	11777860	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aggtgtctgataactctgccGcggtcgtgccggcccagtac	13	13	2	1	rs553020411		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:11777860G>T	ENST00000381486.2	+	31	5665	c.5365G>T	c.(5365-5367)Gcg>Tcg	p.A1789S	GREB1_ENST00000396123.1_Missense_Mutation_p.A787S|GREB1_ENST00000234142.5_Missense_Mutation_p.A1789S	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1789						integral component of membrane (GO:0016021)		p.A1789T(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TAACTCTGCCGCGGTCGTGCC	0.667																																					p.A1789S	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											GREB1_ENST00000381486,NS,carcinoma,0,1	GREB1	308	.	1	Substitution - Missense(1)	endometrium(1)	c.G5365T						.						44	50	48					2																	11777860		2065	4202	6267	SO:0001583	missense	9687	exon31			TCTGCCGCGGTCG		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.5365G>T	chr2.hg19:g.11777860G>T	ENSP00000370896:p.Ala1789Ser	38.0	0.0		48.0	3.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	G	3.342	-0.134352	0.06711	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.21734	3.33;3.33;1.99	4.75	3.78	0.43462	.	0.129539	0.53938	D	0.000050	T	0.06872	0.0175	N	0.01576	-0.805	0.34301	D	0.684343	B	0.14438	0.01	B	0.19391	0.025	T	0.19712	-1.0297	10	0.06757	T	0.87	-26.8203	11.8034	0.52141	0.0:0.0:0.6865:0.3135	.	1789	Q4ZG55	GREB1_HUMAN	S	1789;1789;787	ENSP00000370896:A1789S;ENSP00000234142:A1789S;ENSP00000379429:A787S	ENSP00000234142:A1789S	A	+	1	0	GREB1	11695311	0.820000	0.29190	0.051000	0.19133	0.125000	0.20455	1.233000	0.32648	2.186000	0.69663	0.557000	0.71058	GCG	.	.		0.667	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		T	11777860	G	T	11777860	3	4	197	1	0	0	0	0	1	0	0	0	6769	1087	38	1	5591	1	GREB1	2	11777860	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	2906421	11777860	231421513	26	28936										
NT5C1B	93034	hgsc.bcm.edu	37	chr2	18765411	18765411	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	acgttctcattggtgagctgAtactccatgtacttttccag	8	10	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:18765411A>T	ENST00000359846.2	-	6	1091	c.1014T>A	c.(1012-1014)taT>taA	p.Y338*	NT5C1B_ENST00000600945.1_Nonsense_Mutation_p.Y338*|NT5C1B-RDH14_ENST00000532967.1_Nonsense_Mutation_p.Y338*|NT5C1B_ENST00000304081.4_Nonsense_Mutation_p.Y278*|RNU6-1215P_ENST00000384441.1_RNA|NT5C1B_ENST00000460052.1_5'Flank	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	338					nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				TGGTGAGCTGATACTCCATGT	0.557																																					p.Y355X		Atlas-SNP	.											.	NT5C1B	72	.	0			c.T1065A						.						172	164	167					2																	18765411		2203	4300	6503	SO:0001587	stop_gained	93034	exon6			GAGCTGATACTCC	AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.1014T>A	chr2.hg19:g.18765411A>T	ENSP00000352904:p.Tyr338*	115.0	0.0		187.0	30.0	NM_001199087	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Nonsense_Mutation	SNP	ENST00000359846.2	hg19	CCDS33150.1	.	.	.	.	.	.	.	.	.	.	A	36	5.907847	0.97093	.	.	ENSG00000250741;ENSG00000250741;ENSG00000185013;ENSG00000185013	ENST00000532967;ENST00000444297;ENST00000304081;ENST00000359846	.	.	.	5.58	-6.4	0.01944	.	0.231990	0.46145	D	0.000310	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.1702	19.7889	0.96450	0.2169:0.0:0.7831:0.0	.	.	.	.	X	338;280;278;338	.	ENSP00000305979:Y278X	Y	-	3	2	NT5C1B-RDH14;NT5C1B	18628892	0.996000	0.38824	0.450000	0.26969	0.951000	0.60555	0.505000	0.22642	-1.173000	0.02758	-0.297000	0.09499	TAT	.	.		0.557	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1			T	18765411	A	T	18765411	4	4	197	1	0	0	0	0	0	1	0	0	10695	340	12	4	838	4	NT5C1B	2	18765411	Nonsense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	6987551	18765411	224433962	27	28937										
HADHB	3032	hgsc.bcm.edu	37	chr2	26502110	26502110	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gaacaggatgaatatgcactGcgctctcacagtctagccaa	9	11	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:26502110G>A	ENST00000317799.5	+	9	842	c.738G>A	c.(736-738)ctG>ctA	p.L246L	HADHB_ENST00000545822.1_Silent_p.L224L|HADHB_ENST00000405867.3_Intron|HADHB_ENST00000537713.1_Silent_p.L231L|HADHB_ENST00000494615.1_3'UTR	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	246					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AATATGCACTGCGCTCTCACA	0.512																																					p.L246L		Atlas-SNP	.											.	HADHB	50	.	0			c.G738A						.						108	99	102					2																	26502110		2203	4300	6503	SO:0001819	synonymous_variant	3032	exon9			TGCACTGCGCTCT		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"mitochondrial trifunctional protein, beta subunit"	143450	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.738G>A	chr2.hg19:g.26502110G>A		91.0	0.0		92.0	11.0	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Silent	SNP	ENST00000317799.5	hg19	CCDS1722.1																																																																																			.	.		0.512	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183		A	26502110	G	A	26502110	2	1	197	1	0	0	0	0	0	0	0	1	6953	1306	46	3		3	HADHB	2	26502110	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	7736699	26502110	216697263	28	28938										
KLRAQ1	129285	hgsc.bcm.edu	37	chr2	48692100	48692100	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tagtcagtacaacgctctgaAcgttccactccacaatagga	7	12	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:48692100A>C	ENST00000294952.8	+	8	876	c.719A>C	c.(718-720)aAc>aCc	p.N240T	PPP1R21_ENST00000281394.4_Missense_Mutation_p.N240T|PPP1R21_ENST00000449090.2_Missense_Mutation_p.N240T	NM_001135629.2	NP_001129101.1	Q6ZMI0	PPR21_HUMAN	protein phosphatase 1, regulatory subunit 21	240						membrane (GO:0016020)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(4)|lung(9)	15						AACGCTCTGAACGTTCCACTC	0.313																																					p.N240T		Atlas-SNP	.											.	PPP1R21	47	.	0			c.A719C						.						121	121	121					2																	48692100		2203	4300	6503	SO:0001583	missense	129285	exon8			CTCTGAACGTTCC	AY134855	CCDS1839.1, CCDS46278.1, CCDS54358.1	2p16.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000162869	ENSG00000162869		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30595	protein-coding gene	gene with protein product			"coiled-coil domain containing 128", "KLRAQ motif containing 1"	CCDC128, KLRAQ1		12477932	Standard	NM_001135629		Approved	FLJ16566	uc002rwm.3	Q6ZMI0	OTTHUMG00000129167	ENST00000294952.8:c.719A>C	chr2.hg19:g.48692100A>C	ENSP00000294952:p.Asn240Thr	241.0	0.0		291.0	29.0	NM_152994	B7ZKY5|B7ZKY7|E1B6W7|Q2TA78|Q6ZMI6|Q8IW83|Q8J029|Q96ES8	Missense_Mutation	SNP	ENST00000294952.8	hg19	CCDS46278.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.487127	0.84854	.	.	ENSG00000162869	ENST00000281394;ENST00000294952;ENST00000449090	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.76040	0.3932	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.989;0.998;0.998;0.998	T	0.77378	-0.2610	9	0.54805	T	0.06	-23.0109	15.6865	0.77415	1.0:0.0:0.0:0.0	.	240;240;240;240;240	E1B6W7;Q6ZMI0;Q6ZMI0-2;Q6ZMI0-3;Q6ZMI0-4	.;PPR21_HUMAN;.;.;.	T	240	.	ENSP00000281394:N240T	N	+	2	0	KLRAQ1	48545604	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	8.655000	0.91098	2.168000	0.68352	0.528000	0.53228	AAC	.	.		0.313	PPP1R21-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251238.4	NM_152994		C	48692100	A	C	48692100	3	2	197	1	0	0	0	0	1	0	0	0	8422	43	2	5	749	5	KLRAQ1	2	48692100	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	22189990	48692100	194507273	29	28939										
PEX13	5194	hgsc.bcm.edu	37	chr2	61258830	61258830	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agatttgttcagcaagctgaAgaaagcagcaggggtgcatt	13	6	1	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:61258830A>G	ENST00000295030.5	+	2	407	c.369A>G	c.(367-369)gaA>gaG	p.E123E	PEX13_ENST00000472678.1_3'UTR	NM_002618.3	NP_002609.1	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	123					cerebral cortex cell migration (GO:0021795)|fatty acid alpha-oxidation (GO:0001561)|locomotory behavior (GO:0007626)|microtubule-based peroxisome localization (GO:0060152)|neuron migration (GO:0001764)|protein import into peroxisome matrix, docking (GO:0016560)|suckling behavior (GO:0001967)	integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			AGCAAGCTGAAGAAAGCAGCA	0.443																																					p.E123E		Atlas-SNP	.											.	PEX13	27	.	0			c.A369G						.						148	140	143					2																	61258830		2203	4300	6503	SO:0001819	synonymous_variant	5194	exon2			AGCTGAAGAAAGC	U71374	CCDS1866.1	2p16.1	2008-08-26	2008-08-26		ENSG00000162928	ENSG00000162928			8855	protein-coding gene	gene with protein product		601789	"peroxisome biogenesis factor 13"			9878256	Standard	NM_002618		Approved		uc002sau.4	Q92968	OTTHUMG00000129422	ENST00000295030.5:c.369A>G	chr2.hg19:g.61258830A>G		91.0	0.0		102.0	34.0	NM_002618	B2RCS1	Silent	SNP	ENST00000295030.5	hg19	CCDS1866.1																																																																																			.	.		0.443	PEX13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251581.3	NM_002618		G	61258830	A	G	61258830	2	3	197	1	0	0	0	0	0	0	0	1	11750	69	3	2		2	PEX13	2	61258830	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	12566730	61258830	181940543	30	28940										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	catggccgggcgagctggagGaggaggaggaggaggaggag	24	5	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						.						3	4	4					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	124.0	0.0		168.0	10.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73613036	G	C	73613036	3	2	197	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	12354206	73613036	169586337	31	28941										
DQX1	165545	hgsc.bcm.edu	37	chr2	74752644	74752644	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtgctcttgccagaaccaggCtccccagacaccagcaccac	8	18	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:74752644C>T	ENST00000404568.3	-	2	432	c.213G>A	c.(211-213)gaG>gaA	p.E71E	DQX1_ENST00000393951.2_Silent_p.E71E|DQX1_ENST00000495597.1_5'Flank	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	71	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						CAGAACCAGGCTCCCCAGACA	0.592																																					p.E71E		Atlas-SNP	.											.	DQX1	95	.	0			c.G213A						.						29	31	31					2																	74752644		692	1591	2283	SO:0001819	synonymous_variant	165545	exon2			ACCAGGCTCCCCA	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.213G>A	chr2.hg19:g.74752644C>T		79.0	0.0		107.0	19.0	NM_133637	Q6B017|Q8NAM8	Silent	SNP	ENST00000404568.3	hg19	CCDS1949.2																																																																																			.	.		0.592	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		T	74752644	C	T	74752644	2	4	197	1	0	0	0	0	0	0	0	1	4753	796	28	3		3	DQX1	2	74752644	Silent	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	1139608	74752644	168446729	32	28942										
MGAT4A	11320	hgsc.bcm.edu	37	chr2	99242216	99242216	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	atggcccaaacagcagaattCtgaataactgaaagtcgaaa	8	8	1	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:99242216C>A	ENST00000264968.3	-	14	1914	c.1551G>T	c.(1549-1551)caG>caT	p.Q517H	MGAT4A_ENST00000414521.2_Missense_Mutation_p.Q389H|MGAT4A_ENST00000409391.1_Missense_Mutation_p.Q517H|MGAT4A_ENST00000393487.1_Missense_Mutation_p.Q517H			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	517					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						CAGCAGAATTCTGAATAACTG	0.313																																					p.Q517H		Atlas-SNP	.											.	MGAT4A	51	.	0			c.G1551T						.						73	67	69					2																	99242216		2203	4300	6503	SO:0001583	missense	11320	exon15			AGAATTCTGAATA	AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	2.4.1.145	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7047	protein-coding gene	gene with protein product		604623	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A"			10024668	Standard	NM_001160154		Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.1551G>T	chr2.hg19:g.99242216C>A	ENSP00000264968:p.Gln517His	285.0	0.0		247.0	45.0	NM_012214	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Missense_Mutation	SNP	ENST00000264968.3	hg19	CCDS2036.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.877873	0.33162	.	.	ENSG00000071073	ENST00000393487;ENST00000414521;ENST00000264968;ENST00000409391	T;T;T;T	0.23552	1.91;1.9;1.91;1.91	5.63	2.74	0.32292	.	0.201867	0.52532	N	0.000069	T	0.20333	0.0489	L	0.50333	1.59	0.43657	D	0.996075	B;B	0.10296	0.003;0.003	B;B	0.08055	0.001;0.003	T	0.07252	-1.0782	10	0.66056	D	0.02	.	4.5018	0.11867	0.1278:0.6087:0.1237:0.1398	.	389;517	E9PEN2;Q9UM21	.;MGT4A_HUMAN	H	517;389;517;517	ENSP00000377127:Q517H;ENSP00000404889:Q389H;ENSP00000264968:Q517H;ENSP00000386841:Q517H	ENSP00000264968:Q517H	Q	-	3	2	MGAT4A	98608648	0.964000	0.33143	1.000000	0.80357	0.999000	0.98932	0.065000	0.14466	0.272000	0.22027	0.655000	0.94253	CAG	.	.		0.313	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214		A	99242216	C	A	99242216	3	1	197	1	0	0	0	0	1	0	0	0	9554	912	32	3	143	3	MGAT4A	2	99242216	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	24489572	99242216	143957157	33	28943										
TBC1D8	11138	hgsc.bcm.edu	37	chr2	101650198	101650198	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ttcccgtagtaaccagggtgTgaggcaagatccgtcaccgc	12	12	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:101650198T>C	ENST00000376840.4	-	10	1580	c.1581A>G	c.(1579-1581)tcA>tcG	p.S527S	TBC1D8_ENST00000409318.1_Silent_p.S542S			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	527	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						AACCAGGGTGTGAGGCAAGAT	0.522																																					p.S527S		Atlas-SNP	.											.	TBC1D8	169	.	0			c.A1581G						.						73	81	78					2																	101650198		2181	4290	6471	SO:0001819	synonymous_variant	11138	exon10			AGGGTGTGAGGCA	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"BUB2-like protein 1", "vascular Rab-GAP/TBC-containing protein"					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.1581A>G	chr2.hg19:g.101650198T>C		117.0	0.0		109.0	24.0	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	hg19	CCDS46375.1																																																																																			.	.		0.522	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063		C	101650198	T	C	101650198	2	2	197	1	0	0	0	0	0	0	0	1	15640	1683	59	2		2	TBC1D8	2	101650198	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	2407982	101650198	141549175	34	28944										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109384438	109384438	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	accacaagagagaggacagaTgttattcagggtgatgatgt	13	5	1	5			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:109384438T>C	ENST00000283195.6	+	20	7569	c.7443T>C	c.(7441-7443)gaT>gaC	p.D2481D		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2481					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						AGAGGACAGATGTTATTCAGG	0.433																																					p.D2481D		Atlas-SNP	.											.	RANBP2	488	.	0			c.T7443C						.						111	116	114					2																	109384438		2203	4297	6500	SO:0001819	synonymous_variant	5903	exon20			GACAGATGTTATT	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.7443T>C	chr2.hg19:g.109384438T>C		98.0	0.0		131.0	25.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	hg19	CCDS2079.1																																																																																			.	.		0.433	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109384438	T	C	109384438	2	2	197	1	0	0	0	0	0	0	0	1	13043	1461	51	2		2	RANBP2	2	109384438	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	7734240	109384438	133814935	35	28945										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166243456	166243456	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tgtgtgctgaaactgatctcTcttcgttactactatttcac	6	10	3	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:166243456T>C	ENST00000375437.2	+	26	5042	c.4752T>C	c.(4750-4752)tcT>tcC	p.S1584S	SCN2A_ENST00000283256.6_Silent_p.S1584S|SCN2A_ENST00000357398.3_Silent_p.S1584S|SCN2A_ENST00000375427.2_Silent_p.S1584S	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1584					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AACTGATCTCTCTTCGTTACT	0.368																																					p.S1584S		Atlas-SNP	.											.	SCN2A	589	.	0			c.T4752C						.						237	217	224					2																	166243456		2203	4300	6503	SO:0001819	synonymous_variant	6326	exon25			GATCTCTCTTCGT	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.4752T>C	chr2.hg19:g.166243456T>C		95.0	0.0		179.0	18.0	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	hg19	CCDS33314.1																																																																																			.	.		0.368	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		C	166243456	T	C	166243456	2	2	197	1	0	0	0	0	0	0	0	1	13931	1538	54	2		2	SCN2A	2	166243456	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	56859018	166243456	76955917	36	28946										
GALNT3	2591	hgsc.bcm.edu	37	chr2	166605296	166605296	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aattttaaggaacacttaatCattttggctaagtatccatt	5	6	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:166605296C>G	ENST00000392701.3	-	11	2672	c.1897G>C	c.(1897-1899)Gat>Cat	p.D633H	GALNT3_ENST00000409882.1_Missense_Mutation_p.D371H	NM_004482.3	NP_004473.2	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	633					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(1)	20						AACACTTAATCATTTTGGCTA	0.338																																					p.D633H		Atlas-SNP	.											.	GALNT3	65	.	0			c.G1897C						.						64	63	63					2																	166605296		2203	4297	6500	SO:0001583	missense	2591	exon11			CTTAATCATTTTG		CCDS2226.1	2q24-q31	2014-03-13	2014-03-13		ENSG00000115339	ENSG00000115339	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4125	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 3"	601756	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)"			9592121, 15133511	Standard	NM_004482		Approved	GalNAc-T3, HHS, HFTC	uc010fph.1	Q14435	OTTHUMG00000132157	ENST00000392701.3:c.1897G>C	chr2.hg19:g.166605296C>G	ENSP00000376465:p.Asp633His	46.0	0.0		85.0	55.0	NM_004482	Q53TG9|Q7Z476	Missense_Mutation	SNP	ENST00000392701.3	hg19	CCDS2226.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.946986	0.34377	.	.	ENSG00000115339	ENST00000392701;ENST00000409882	T;T	0.61627	0.31;0.09	5.86	3.09	0.35607	.	0.317119	0.28683	N	0.014494	T	0.34890	0.0913	N	0.08118	0	0.27954	N	0.937043	B	0.34015	0.435	B	0.32465	0.146	T	0.32851	-0.9891	10	0.87932	D	0	.	9.8267	0.40916	0.0:0.6769:0.0:0.3231	.	633	Q14435	GALT3_HUMAN	H	633;371	ENSP00000376465:D633H;ENSP00000386955:D371H	ENSP00000376465:D633H	D	-	1	0	GALNT3	166313542	0.001000	0.12720	1.000000	0.80357	0.997000	0.91878	0.093000	0.15086	0.813000	0.34350	0.563000	0.77884	GAT	.	.		0.338	GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255205.2	NM_004482		G	166605296	C	G	166605296	3	3	197	1	0	0	0	0	1	0	0	0	6222	826	29	4	8	4	GALNT3	2	166605296	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	361840	166605296	76594077	37	28947										
GLS	2744	hgsc.bcm.edu	37	chr2	191819351	191819351	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	catggaacagcgggactatgAttctagaacagcactccatg	10	10	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:191819351A>T	ENST00000320717.3	+	16	2012	c.1754A>T	c.(1753-1755)gAt>gTt	p.D585V	GLS_ENST00000409428.1_Missense_Mutation_p.D90V	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	585					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate secretion (GO:0014047)|glutamine catabolic process (GO:0006543)|neurotransmitter secretion (GO:0007269)|protein homotetramerization (GO:0051289)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|small molecule metabolic process (GO:0044281)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamine(DB00130)	CGGGACTATGATTCTAGAACA	0.353																																					p.D585V		Atlas-SNP	.											.	GLS	47	.	0			c.A1754T						.						84	86	85					2																	191819351		2203	4300	6503	SO:0001583	missense	2744	exon16			ACTATGATTCTAG	AB020645	CCDS2308.1, CCDS58744.1	2q32-q34	2013-01-10			ENSG00000115419	ENSG00000115419	3.5.1.2	"Ankyrin repeat domain containing"	4331	protein-coding gene	gene with protein product		138280				10048485	Standard	NM_014905		Approved	KIAA0838, GLS1	uc002usf.3	O94925	OTTHUMG00000132701	ENST00000320717.3:c.1754A>T	chr2.hg19:g.191819351A>T	ENSP00000317379:p.Asp585Val	187.0	0.0		239.0	42.0	NM_014905	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	hg19	CCDS2308.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.686004	0.88639	.	.	ENSG00000115419	ENST00000320717;ENST00000457316;ENST00000409428;ENST00000412247	T;T;T;T	0.35605	1.3;1.3;1.3;1.49	5.38	5.38	0.77491	Ankyrin repeat-containing domain (4);	0.150326	0.64402	D	0.000017	T	0.63010	0.2475	M	0.80422	2.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.983;0.998;0.998	T	0.68454	-0.5404	10	0.87932	D	0	-11.345	15.566	0.76294	1.0:0.0:0.0:0.0	.	156;585;585	B7Z2P1;A8K132;O94925	.;.;GLSK_HUMAN	V	585;156;90;106	ENSP00000317379:D585V;ENSP00000395596:D156V;ENSP00000387177:D90V;ENSP00000403329:D106V	ENSP00000317379:D585V	D	+	2	0	GLS	191527596	1.000000	0.71417	0.975000	0.42487	0.987000	0.75469	8.761000	0.91691	2.254000	0.74563	0.533000	0.62120	GAT	.	.		0.353	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			T	191819351	A	T	191819351	3	4	197	1	0	0	0	0	1	0	0	0	6471	333	12	4	1816	4	GLS	2	191819351	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	25214055	191819351	51380022	38	28948										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196620956	196620956	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cacatttctggaattttgacAttcaaaatgctgctaaccac	5	10	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:196620956A>G	ENST00000312428.6	-	62	11587	c.11487T>C	c.(11485-11487)aaT>aaC	p.N3829N	DNAH7_ENST00000409063.1_Silent_p.N312N	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3829					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GAATTTTGACATTCAAAATGC	0.378																																					p.N3829N		Atlas-SNP	.											.	DNAH7	512	.	0			c.T11487C						.						115	108	110					2																	196620956		1844	4099	5943	SO:0001819	synonymous_variant	56171	exon62			TTTGACATTCAAA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.11487T>C	chr2.hg19:g.196620956A>G		236.0	0.0		314.0	47.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.378	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		G	196620956	A	G	196620956	2	3	197	1	0	0	0	0	0	0	0	1	4608	214	8	2		2	DNAH7	2	196620956	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	4801605	196620956	46578417	39	28949										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196774843	196774843	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agcttttgccaaatccttggTagtttcagtcttcccagtgc	8	11	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:196774843T>A	ENST00000312428.6	-	25	4112	c.4012A>T	c.(4012-4014)Acc>Tcc	p.T1338S		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1338	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AAATCCTTGGTAGTTTCAGTC	0.423																																					p.T1338S		Atlas-SNP	.											.	DNAH7	512	.	0			c.A4012T						.						74	73	73					2																	196774843		1876	4120	5996	SO:0001583	missense	56171	exon25			CCTTGGTAGTTTC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.4012A>T	chr2.hg19:g.196774843T>A	ENSP00000311273:p.Thr1338Ser	107.0	0.0		125.0	16.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.825853	0.90955	.	.	ENSG00000118997	ENST00000312428	T	0.39997	1.05	5.6	5.6	0.85130	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.67961	0.2949	M	0.85041	2.73	0.80722	D	1	D	0.76494	0.999	D	0.72338	0.977	T	0.72991	-0.4123	10	0.56958	D	0.05	.	15.4358	0.75146	0.0:0.0:0.0:1.0	.	1338	Q8WXX0	DYH7_HUMAN	S	1338	ENSP00000311273:T1338S	ENSP00000311273:T1338S	T	-	1	0	DNAH7	196483088	1.000000	0.71417	0.968000	0.41197	0.996000	0.88848	8.036000	0.88901	2.122000	0.65172	0.533000	0.62120	ACC	.	.		0.423	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196774843	T	A	196774843	3	1	197	1	0	0	0	0	1	0	0	0	4608	1638	57	4	8226	4	DNAH7	2	196774843	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	153887	196774843	46424530	40	28950										
PTH2R	5746	hgsc.bcm.edu	37	chr2	209353870	209353870	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtgagctcttcttcaactccTttcaggtaaagggtgctgcc	10	11	4	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:209353870T>A	ENST00000272847.2	+	11	1423	c.1210T>A	c.(1210-1212)Ttt>Att	p.F404I	PTH2R_ENST00000413482.1_3'UTR|AC019185.4_ENST00000424628.1_RNA	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	404					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	CTTCAACTCCTTTCAGGTAAA	0.468																																					p.F404I		Atlas-SNP	.											.	PTH2R	92	.	0			c.T1210A						.						170	158	162					2																	209353870		2203	4300	6503	SO:0001583	missense	5746	exon11			AACTCCTTTCAGG	BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"GPCR / Class B : Parathyroid hormone receptors"	9609	protein-coding gene	gene with protein product		601469	"parathyroid hormone receptor 2"	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1210T>A	chr2.hg19:g.209353870T>A	ENSP00000272847:p.Phe404Ile	46.0	0.0		50.0	5.0	NM_005048	Q8N429	Missense_Mutation	SNP	ENST00000272847.2	hg19	CCDS2383.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.401481	0.83120	.	.	ENSG00000144407	ENST00000272847	T	0.51071	0.72	5.6	5.6	0.85130	GPCR, family 2-like (1);	0.000000	0.49916	D	0.000140	T	0.75317	0.3833	M	0.93420	3.415	0.58432	D	0.999999	D;D	0.67145	0.996;0.996	D;D	0.70227	0.968;0.968	T	0.82329	-0.0511	9	.	.	.	.	13.7336	0.62804	0.0:0.0:0.0:1.0	.	293;404	B4DFN8;P49190	.;PTH2R_HUMAN	I	404	ENSP00000272847:F404I	.	F	+	1	0	PTH2R	209062115	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	7.618000	0.83043	2.130000	0.65690	0.482000	0.46254	TTT	.	.		0.468	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048		A	209353870	T	A	209353870	3	1	197	1	0	0	0	0	1	0	0	0	12773	1609	56	4	1252	4	PTH2R	2	209353870	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	12579027	209353870	33845503	41	28951										
ZNF142	7701	hgsc.bcm.edu	37	chr2	219508527	219508527	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	acaggttgcagagggatgggTgaatctggtctgggcaagcc	17	7	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:219508527T>C	ENST00000449707.1	-	8	3133	c.2712A>G	c.(2710-2712)tcA>tcG	p.S904S	ZNF142_ENST00000411696.2_Silent_p.S904S	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	904					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GAGGGATGGGTGAATCTGGTC	0.572																																					p.S904S	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.A2712G						.						129	136	134					2																	219508527		1991	4158	6149	SO:0001819	synonymous_variant	7701	exon8			GATGGGTGAATCT	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.2712A>G	chr2.hg19:g.219508527T>C		60.0	0.0		89.0	4.0	NM_001105537	Q92510	Silent	SNP	ENST00000449707.1	hg19	CCDS42817.1																																																																																			.	.		0.572	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		C	219508527	T	C	219508527	2	2	197	1	0	0	0	0	0	0	0	1	17746	1683	59	2		2	ZNF142	2	219508527	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	10154657	219508527	23690846	42	28952										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225642958	225642958	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	acagacctgtcagcttaggcTctttataaatatactcttta	5	9	3	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:225642958T>A	ENST00000258390.7	-	51	5766	c.5699A>T	c.(5698-5700)gAg>gTg	p.E1900V	DOCK10_ENST00000409592.3_Missense_Mutation_p.E1894V	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1900	DHR-2.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		CAGCTTAGGCTCTTTATAAAT	0.353																																					p.E1900V		Atlas-SNP	.											.	DOCK10	308	.	0			c.A5699T						.						81	72	75					2																	225642958		1815	4066	5881	SO:0001583	missense	55619	exon51			TTAGGCTCTTTAT	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.5699A>T	chr2.hg19:g.225642958T>A	ENSP00000258390:p.Glu1900Val	97.0	0.0		94.0	12.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.6|27.6	4.845847|4.845847	0.91277|0.91277	.|.	.|.	ENSG00000135905|ENSG00000135905	ENST00000409592;ENST00000258390;ENST00000373702|ENST00000535663	T;T|.	0.25085|.	1.82;1.82|.	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	0.118681|.	0.64402|.	D|.	0.000009|.	D|D	0.87184|0.87184	0.6114|0.6114	H|H	0.94503|0.94503	3.545|3.545	0.80722|0.80722	D|D	1|1	D;D;D|.	0.71674|.	0.997;0.997;0.998|.	D;D;D|.	0.69479|.	0.937;0.964;0.963|.	D|D	0.90497|0.90497	0.4471|0.4471	10|5	0.87932|.	D|.	0|.	.|.	16.8061|16.8061	0.85666|0.85666	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1900;1894;562|.	Q96BY6;B3FL70;B4DEY4|.	DOC10_HUMAN;.;.|.	V|S	1894;1900;407|49	ENSP00000386694:E1894V;ENSP00000258390:E1900V|.	ENSP00000258390:E1900V|.	E|R	-|-	2|3	0|2	DOCK10|DOCK10	225351202|225351202	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.698000|7.698000	0.84413|0.84413	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	GAG|AGA	.	.		0.353	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			A	225642958	T	A	225642958	3	1	197	1	0	0	0	0	1	0	0	0	4687	1551	54	4	885	4	DOCK10	2	225642958	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	6134431	225642958	17556415	43	28953										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225684228	225684228	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cttaaacacataccctcggtCcataaatgtaaagcagcgct	6	12	0	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr2:225684228C>T	ENST00000258390.7	-	29	3269	c.3202G>A	c.(3202-3204)Gac>Aac	p.D1068N	DOCK10_ENST00000409592.3_Missense_Mutation_p.D1062N	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1068					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TACCCTCGGTCCATAAATGTA	0.313																																					p.D1068N		Atlas-SNP	.											.	DOCK10	308	.	0			c.G3202A						.						104	98	100					2																	225684228		1824	4083	5907	SO:0001583	missense	55619	exon29			CTCGGTCCATAAA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3202G>A	chr2.hg19:g.225684228C>T	ENSP00000258390:p.Asp1068Asn	260.0	0.0		298.0	54.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156080	0.57259	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.65364	1.91;-0.15	6.15	6.15	0.99193	.	0.044610	0.85682	D	0.000000	T	0.60996	0.2312	L	0.58810	1.83	0.45867	D	0.998721	B;B	0.27594	0.146;0.182	B;B	0.30251	0.022;0.113	T	0.59679	-0.7409	10	0.59425	D	0.04	.	13.9607	0.64177	0.0:0.9313:0.0:0.0687	.	1068;1062	Q96BY6;B3FL70	DOC10_HUMAN;.	N	1062;1068	ENSP00000386694:D1062N;ENSP00000258390:D1068N	ENSP00000258390:D1068N	D	-	1	0	DOCK10	225392472	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	3.787000	0.55439	2.932000	0.99384	0.643000	0.83706	GAC	.	.		0.313	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			T	225684228	C	T	225684228	3	4	197	1	0	0	0	0	1	0	0	0	4687	855	30	3	3470	3	DOCK10	2	225684228	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	41270	225684228	17515145	44	28954										
SH3BP5	9467	hgsc.bcm.edu	37	chr3	15300443	15300443	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aggccccatggcactggagcGccgccgctcgtggatctcat	13	15	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:15300443G>C	ENST00000383791.3	-	7	1004	c.784C>G	c.(784-786)Cgc>Ggc	p.R262G	SH3BP5-AS1_ENST00000413977.1_RNA|SH3BP5-AS1_ENST00000420195.1_RNA|SH3BP5-AS1_ENST00000436602.1_RNA|SH3BP5_ENST00000426925.1_Missense_Mutation_p.R105G|SH3BP5_ENST00000408919.3_Missense_Mutation_p.R105G|SH3BP5_ENST00000253688.5_Missense_Mutation_p.R105G	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	262					intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	protein kinase inhibitor activity (GO:0004860)			NS(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	12						GCACTGGAGCGCCGCCGCTCG	0.597																																					p.R262G		Atlas-SNP	.											.	SH3BP5	32	.	0			c.C784G						.						77	70	73					3																	15300443		2203	4300	6503	SO:0001583	missense	9467	exon7			TGGAGCGCCGCCG	AB005047	CCDS2625.2, CCDS43055.1	3p24.3	2008-07-10			ENSG00000131370	ENSG00000131370			10827	protein-coding gene	gene with protein product	"SH3 binding protein"	605612				9571151, 10339589	Standard	NM_004844		Approved	Sab	uc003bzp.2	O60239	OTTHUMG00000129859	ENST00000383791.3:c.784C>G	chr3.hg19:g.15300443G>C	ENSP00000373301:p.Arg262Gly	63.0	0.0		77.0	14.0	NM_004844	B3KQW6|Q5JWV9	Missense_Mutation	SNP	ENST00000383791.3	hg19	CCDS2625.2	.	.	.	.	.	.	.	.	.	.	G	14.33	2.502387	0.44455	.	.	ENSG00000131370	ENST00000383791;ENST00000426925;ENST00000253688;ENST00000408919;ENST00000366391	.	.	.	5.47	4.59	0.56863	.	0.050281	0.85682	D	0.000000	T	0.50718	0.1632	L	0.39245	1.2	0.48632	D	0.999689	B	0.33318	0.408	B	0.39904	0.313	T	0.50162	-0.8860	9	0.42905	T	0.14	-4.3348	9.087	0.36587	0.0749:0.0:0.7797:0.1454	.	262	O60239	3BP5_HUMAN	G	262;105;105;105;105	.	ENSP00000253688:R105G	R	-	1	0	SH3BP5	15275447	1.000000	0.71417	0.999000	0.59377	0.670000	0.39368	5.429000	0.66495	1.327000	0.45338	-0.422000	0.05995	CGC	.	.		0.597	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844		C	15300443	G	C	15300443	3	2	197	1	0	0	0	0	1	0	0	0	14262	1087	38	4	595	4	SH3BP5	3	15300443	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10		15300443	182721987	45	28955										
UBE2E1	7324	hgsc.bcm.edu	37	chr3	23932096	23932096	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gaccaagagatacgctacatAaattggggtttcacaattct	8	8	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:23932096A>G	ENST00000306627.3	+	6	800	c.581A>G	c.(580-582)tAa>tGa	p.*194*	UBE2E1_ENST00000424381.1_Silent_p.*161*|UBE2E1_ENST00000346855.3_Silent_p.*177*|UBE2E1_ENST00000475680.1_3'UTR	NM_003341.4	NP_003332.1	P51965	UB2E1_HUMAN	ubiquitin-conjugating enzyme E2E 1	0					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cytokine-mediated signaling pathway (GO:0019221)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ISG15-protein conjugation (GO:0032020)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|large_intestine(4)	7						TACGCTACATAAATTGGGGTT	0.468																																					p.X194X		Atlas-SNP	.											.	UBE2E1	15	.	0			c.A581G						.						89	80	83					3																	23932096		2203	4300	6503	SO:0001819	synonymous_variant	7324	exon6			CTACATAAATTGG	X92963	CCDS2638.1, CCDS2639.1, CCDS56244.1	3p24.2	2011-05-19	2011-05-19		ENSG00000170142	ENSG00000170142		"Ubiquitin-conjugating enzymes E2"	12477	protein-coding gene	gene with protein product		602916	"ubiquitin-conjugating enzyme E2E 1 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2E 1 (UBC4/5 homolog, yeast)"			8576257	Standard	NM_003341		Approved	UbcH6	uc003cch.3	P51965	OTTHUMG00000130483	ENST00000306627.3:c.581A>G	chr3.hg19:g.23932096A>G		147.0	0.0		168.0	47.0	NM_003341	B2RBX4|C9J8K2|K4DI90	Silent	SNP	ENST00000306627.3	hg19	CCDS2638.1																																																																																			.	.		0.468	UBE2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252882.2	NM_003341		G	23932096	A	G	23932096	2	3	197	1	0	0	0	0	0	0	0	1	16867	369	13	2		2	UBE2E1	3	23932096	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	8631653	23932096	174090334	46	28956										
MLH1	4292	hgsc.bcm.edu	37	chr3	37059089	37059089	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cacacccattcctgtacctcAggtaatgtagcaccaaactc	5	15	1	0	rs587779050|rs63751598|rs267607800		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:37059089A>T	ENST00000231790.2	+	10	1099	c.883A>T	c.(883-885)Agt>Tgt	p.S295C	MLH1_ENST00000435176.1_Splice_Site_p.S197C|MLH1_ENST00000458205.2_Splice_Site_p.S54C|MLH1_ENST00000536378.1_Splice_Site_p.S54C|MLH1_ENST00000539477.1_Splice_Site_p.S54C|MLH1_ENST00000455445.2_Splice_Site_p.S54C	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	295			Missing (in HNPCC2).|S -> T (in HNPCC2). {ECO:0000269|PubMed:9399661}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						CCTGTACCTCAGGTAATGTAG	0.418		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.S295C		Atlas-SNP	.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	.	MLH1	226	.	1	Whole gene deletion(1)	ovary(1)	c.A883T	GRCh37	CS064424|CS971799	MLH1	S		.						184	162	170					3																	37059089		2203	4300	6503	SO:0001630	splice_region_variant	4292	exon10	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TACCTCAGGTAAT	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.884+1A>T	chr3.hg19:g.37059089A>T		123.0	0.0		96.0	4.0	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	hg19	CCDS2663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.7|25.7	4.661367|4.661367	0.88154|0.88154	.|.	.|.	ENSG00000076242|ENSG00000076242	ENST00000537937|ENST00000231790;ENST00000436867;ENST00000383761;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000441265;ENST00000536378	.|D;D;D;D;D;D;D	.|0.84944	.|-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92	5.35|5.35	5.35|5.35	0.76521|0.76521	.|Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	.|0.040715	.|0.85682	.|D	.|0.000000	.|D	.|0.93275	.|0.7857	M|M	0.89478|0.89478	3.035|3.035	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.999;0.999	.|D;D;D	.|0.78314	.|0.991;0.986;0.986	.|D	.|0.94521	.|0.7727	.|10	0.87932|0.87932	D|D	0|0	-14.8511|-14.8511	15.3325|15.3325	0.74226|0.74226	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|197;295;295	.|E9PCU2;Q53GX1;P40692	.|.;.;MLH1_HUMAN	X|C	261|295;261;159;54;54;54;197;54;54	.|ENSP00000231790:S295C;ENSP00000402667:S54C;ENSP00000443665:S54C;ENSP00000398272:S54C;ENSP00000402564:S197C;ENSP00000398392:S54C;ENSP00000444286:S54C	ENSP00000442802:R261X|ENSP00000231790:S295C	R|S	+|+	1|1	2|0	MLH1|MLH1	37034093|37034093	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.825000|0.825000	0.46686|0.46686	8.953000|8.953000	0.93041|0.93041	2.024000|2.024000	0.59613|0.59613	0.482000|0.482000	0.46254|0.46254	AGA|AGT	.	.		0.418	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	Missense_Mutation	T	37059089	A	T	37059089	5	4	197	1	0	0	0	0	0	0	1	0	9626	202	7	4	921	4	MLH1	3	37059089	Splice_Site	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	13126993	37059089	160963341	47	28957										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38739345	38739345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ctccagggaccaaaggcaggTccatctggatcagtatattt	10	10	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:38739345T>C	ENST00000449082.2	-	27	5365	c.5366A>G	c.(5365-5367)gAc>gGc	p.D1789G		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1789					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CAAAGGCAGGTCCATCTGGAT	0.468																																					p.D1789G		Atlas-SNP	.											.	SCN10A	359	.	0			c.A5366G						.						60	63	62					3																	38739345		2203	4300	6503	SO:0001583	missense	6336	exon27			GGCAGGTCCATCT	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.5366A>G	chr3.hg19:g.38739345T>C	ENSP00000390600:p.Asp1789Gly	86.0	0.0		80.0	24.0	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	hg19	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628743	0.67015	.	.	ENSG00000185313	ENST00000449082	D	0.96619	-4.07	5.28	4.1	0.47936	.	0.055121	0.64402	D	0.000001	D	0.98413	0.9472	M	0.93898	3.47	0.47476	D	0.999433	D	0.89917	1.0	D	0.91635	0.999	D	0.98826	1.0749	10	0.87932	D	0	.	12.4293	0.55565	0.0:0.0:0.1404:0.8596	.	1789	Q9Y5Y9	SCNAA_HUMAN	G	1789	ENSP00000390600:D1789G	ENSP00000390600:D1789G	D	-	2	0	SCN10A	38714349	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.868000	0.87116	0.995000	0.38917	0.533000	0.62120	GAC	.	.		0.468	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		C	38739345	T	C	38739345	3	2	197	1	0	0	0	0	1	0	0	0	13927	1667	58	2	508	2	SCN10A	3	38739345	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	1680256	38739345	159283085	48	28958										
SETD2	29072	hgsc.bcm.edu	37	chr3	47161750	47161751	+	Frame_Shift_Ins	INS	-	-	CCATT													0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cttggcacattccttccatcINSgctgtgggtccctgaagtca							TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:47161750_47161751insCCATT	ENST00000409792.3	-	3	4417_4418	c.4375_4376insAATGG	c.(4375-4377)cgafs	p.R1459fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1459					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTCCTTCCATCGCTGTGGGTCC	0.446			"N, F, S, Mis"		clear cell renal carcinoma																																p.R1459fs		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.4376_4377insAATGG						.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4375_4376insAATGG	chr3.hg19:g.47161750_47161751insCCATT	ENSP00000386759:p.Arg1459fs	88.0	0.0		81.0	18.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Ins	INS	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.		0.446	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		CCATT	47161751	-	CCATT	47161750	7	5	197	1	0	1	1	0	0	0	0	0	14146	884	31	0	3394	0	SETD2	3	47161750	Frame_Shift_Ins	INS	-	TCGA-DD-AADO-01A-11D-A40R-10	8422405	47161750	150860680	49	28959										
ABHD14A	25864	hgsc.bcm.edu	37	chr3	52011894	52011894	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tctccctctccagactgtggTacagacctccatgagccggt	9	15	2	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:52011894T>A	ENST00000273596.3	+	2	145	c.77T>A	c.(76-78)gTa>gAa	p.V26E	ABHD14A_ENST00000491470.1_Missense_Mutation_p.V26E|ACY1_ENST00000458031.2_5'UTR|ABHD14A-ACY1_ENST00000463937.1_Missense_Mutation_p.V26E|ABHD14B_ENST00000483233.1_Intron	NM_015407.4	NP_056222.2	Q9BUJ0	ABHEA_HUMAN	abhydrolase domain containing 14A	26						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|stomach(1)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CAGACTGTGGTACAGACCTCC	0.612																																					p.V26E		Atlas-SNP	.											.	ABHD14A	15	.	0			c.T77A						.						100	111	107					3																	52011894		2203	4300	6503	SO:0001583	missense	25864	exon2			CTGTGGTACAGAC	AY358201	CCDS2843.1	3p21.1	2011-02-14			ENSG00000248487	ENSG00000248487		"Abhydrolase domain containing"	24538	protein-coding gene	gene with protein product							Standard	NM_015407		Approved	DKFZP564O243, DORZ1	uc003dco.3	Q9BUJ0	OTTHUMG00000157818	ENST00000273596.3:c.77T>A	chr3.hg19:g.52011894T>A	ENSP00000273596:p.Val26Glu	44.0	0.0		27.0	6.0	NM_015407	Q6UXU8|Q9Y3T7	Missense_Mutation	SNP	ENST00000273596.3	hg19	CCDS2843.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.488049	0.64074	.	.	ENSG00000248487;ENSG00000248487;ENSG00000248487;ENSG00000248487;ENSG00000114786	ENST00000497864;ENST00000494478;ENST00000273596;ENST00000491470;ENST00000463937	T;T;T;T;T	0.71222	0.96;1.1;1.14;0.96;-0.55	5.09	-0.131	0.13494	.	1.364740	0.04835	N	0.439348	T	0.58552	0.2130	L	0.50333	1.59	0.09310	N	1	P;B	0.37864	0.61;0.421	B;B	0.33042	0.157;0.143	T	0.52275	-0.8597	10	0.72032	D	0.01	0.0526	0.5592	0.00676	0.1729:0.1901:0.1795:0.4574	.	26;26	C9JMV9;Q9BUJ0	.;ABHEA_HUMAN	E	91;21;26;26;26	ENSP00000418242:V91E;ENSP00000420475:V21E;ENSP00000273596:V26E;ENSP00000418824:V26E;ENSP00000420487:V26E	ENSP00000273596:V26E	V	+	2	0	RP11-155D18.11;ABHD14A	51986934	0.084000	0.21492	0.482000	0.27366	0.983000	0.72400	0.319000	0.19522	0.088000	0.17205	0.533000	0.62120	GTA	.	.		0.612	ABHD14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349689.1	NM_015407		A	52011894	T	A	52011894	3	1	197	1	0	0	0	0	1	0	0	0	79	1638	57	4	83	4	ABHD14A	3	52011894	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	4850144	52011894	146010536	50	28960										
TLR9	54106	hgsc.bcm.edu	37	chr3	52255355	52255355	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gggctggtggggccagaggaGgacactctggcggcagaggc	21	9	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:52255355G>A	ENST00000360658.2	-	2	3610	c.2977C>T	c.(2977-2979)Ctc>Ttc	p.L993F	TLR9_ENST00000494383.1_Missense_Mutation_p.P1146L|TLR9_ENST00000597542.1_Missense_Mutation_p.L1017F	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	993	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	GGCCAGAGGAGGACACTCTGG	0.677																																					p.L993F		Atlas-SNP	.											.	TLR9	72	.	0			c.C2977T						.						37	41	40					3																	52255355		2203	4299	6502	SO:0001583	missense	54106	exon2			AGAGGAGGACACT	AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"CD molecules"	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.2977C>T	chr3.hg19:g.52255355G>A	ENSP00000353874:p.Leu993Phe	113.0	0.0		89.0	25.0	NM_017442	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	hg19	CCDS2848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.85|16.85	3.235379|3.235379	0.58886|0.58886	.|.	.|.	ENSG00000239732|ENSG00000173366	ENST00000360658|ENST00000494383	T|.	0.09911|.	2.93|.	5.18|5.18	4.3|4.3	0.51218|0.51218	Toll/interleukin-1 receptor homology (TIR) domain (3);|.	0.000000|.	0.37219|.	N|.	0.002198|.	T|T	0.77075|0.77075	0.4077|0.4077	M|M	0.91038|0.91038	3.17|3.17	0.49130|0.49130	D|D	0.999751|0.999751	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.988;1.0|.	T|T	0.79070|0.79070	-0.1954|-0.1954	10|5	0.87932|.	D|.	0|.	.|.	6.4251|6.4251	0.21766|0.21766	0.0901:0.0:0.7272:0.1827|0.0901:0.0:0.7272:0.1827	.|.	1090;993|.	B4E0A1;Q9NR96|.	.;TLR9_HUMAN|.	F|L	993|1146	ENSP00000353874:L993F|.	ENSP00000353874:L993F|.	L|P	-|-	1|2	0|0	TLR9|RP11-330H6.5	52230395|52230395	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.713000|0.713000	0.41058|0.41058	2.489000|2.489000	0.45285|0.45285	1.390000|1.390000	0.46547|0.46547	0.591000|0.591000	0.81541|0.81541	CTC|CCT	.	.		0.677	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1			A	52255355	G	A	52255355	3	1	197	1	0	0	0	0	1	0	0	0	15973	1000	35	3	125	3	TLR9	3	52255355	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	243461	52255355	145767075	51	28961										
ERC2	26059	hgsc.bcm.edu	37	chr3	56468944	56468944	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cacctcccccactacttgttCttcggtggcccaaacgagga	8	16	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:56468944C>A	ENST00000288221.6	-	2	347	c.92G>T	c.(91-93)aGa>aTa	p.R31I		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	31						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		ACTACTTGTTCTTCGGTGGCC	0.502																																					p.R31I		Atlas-SNP	.											.	ERC2	221	.	0			c.G92T						.						107	103	104					3																	56468944		1938	4144	6082	SO:0001583	missense	26059	exon2			CTTGTTCTTCGGT	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.92G>T	chr3.hg19:g.56468944C>A	ENSP00000288221:p.Arg31Ile	71.0	0.0		70.0	15.0	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	hg19	CCDS46851.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.418606	0.83559	.	.	ENSG00000187672	ENST00000288221	T	0.57436	0.4	5.76	4.89	0.63831	.	0.046054	0.85682	D	0.000000	T	0.48095	0.1481	L	0.52573	1.65	0.58432	D	0.999999	P	0.44578	0.838	B	0.38655	0.278	T	0.55003	-0.8208	10	0.87932	D	0	-20.3351	14.798	0.69891	0.0:0.9311:0.0:0.0689	.	31	O15083	ERC2_HUMAN	I	31	ENSP00000288221:R31I	ENSP00000288221:R31I	R	-	2	0	ERC2	56443984	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	1.432000	0.47375	0.655000	0.94253	AGA	.	.		0.502	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		A	56468944	C	A	56468944	3	1	197	1	0	0	0	0	1	0	0	0	5213	913	32	3	2835	3	ERC2	3	56468944	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	4213589	56468944	141553486	52	28962										
POU1F1	5449	hgsc.bcm.edu	37	chr3	87313643	87313643	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtgtggtcaggaaatttataAagacaaggggttaaactacc	11	5	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:87313643A>G	ENST00000350375.2	-	3	358	c.234T>C	c.(232-234)ctT>ctC	p.L78L	POU1F1_ENST00000344265.3_Silent_p.L104L|POU1F1_ENST00000560656.1_Silent_p.L78L	NM_000306.2	NP_000297.1	P28069	PIT1_HUMAN	POU class 1 homeobox 1	78					B cell differentiation (GO:0030183)|cell fate specification (GO:0001708)|determination of adult lifespan (GO:0008340)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear transport (GO:0051169)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin-like growth factor receptor signaling pathway (GO:0043567)|somatotropin secreting cell development (GO:0060133)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(2)	18	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)		GAAATTTATAAAGACAAGGGG	0.403																																					p.L104L		Atlas-SNP	.											.	POU1F1	70	.	0			c.T312C						.						60	66	64					3																	87313643		2203	4299	6502	SO:0001819	synonymous_variant	5449	exon3			TTTATAAAGACAA	D10216	CCDS2919.1, CCDS46873.1	3p11.2	2011-06-20	2007-07-13		ENSG00000064835	ENSG00000064835		"Homeoboxes / POU class"	9210	protein-coding gene	gene with protein product	"growth hormone factor 1"	173110	"POU domain class 1, transcription factor 1"	PIT1		1956794	Standard	NM_001122757		Approved	GHF-1, POU1F1a	uc010hoj.1	P28069	OTTHUMG00000158992	ENST00000350375.2:c.234T>C	chr3.hg19:g.87313643A>G		203.0	0.0		172.0	29.0	NM_001122757	O75757|Q15132|Q15133|Q9UD34|Q9UEL3	Silent	SNP	ENST00000350375.2	hg19	CCDS2919.1																																																																																			.	.		0.403	POU1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352827.1	NM_000306		G	87313643	A	G	87313643	2	3	197	1	0	0	0	0	0	0	0	1	12278	1	1	2		2	POU1F1	3	87313643	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	30844699	87313643	110708787	53	28963										
ABHD10	55347	hgsc.bcm.edu	37	chr3	111710309	111710309	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ttataacgttcagtacagttTcattaaagaagctgaacatc	6	7	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:111710309T>A	ENST00000273359.3	+	5	689	c.662T>A	c.(661-663)tTc>tAc	p.F221Y	ABHD10_ENST00000534857.1_Missense_Mutation_p.F64Y|ABHD10_ENST00000494817.1_3'UTR	NM_018394.2	NP_060864.1	Q9NUJ1	ABHDA_HUMAN	abhydrolase domain containing 10	221					glucuronoside catabolic process (GO:0019391)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			large_intestine(2)|lung(7)|skin(1)	10						CAGTACAGTTTCATTAAAGAA	0.398																																					p.F221Y		Atlas-SNP	.											.	ABHD10	20	.	0			c.T662A						.						143	131	135					3																	111710309		2203	4300	6503	SO:0001583	missense	55347	exon5			ACAGTTTCATTAA	AL713726	CCDS2963.1, CCDS63718.1	3q13.2	2012-03-26			ENSG00000144827	ENSG00000144827		"Abhydrolase domain containing"	25656	protein-coding gene	gene with protein product						22294686	Standard	NM_018394		Approved	FLJ11342	uc003dyk.5	Q9NUJ1	OTTHUMG00000159280	ENST00000273359.3:c.662T>A	chr3.hg19:g.111710309T>A	ENSP00000273359:p.Phe221Tyr	181.0	0.0		162.0	46.0	NM_018394	B7Z6A8|C9IZX5|D3DN63|Q8TCF9	Missense_Mutation	SNP	ENST00000273359.3	hg19	CCDS2963.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.935008	0.73442	.	.	ENSG00000144827	ENST00000534857;ENST00000273359	T;T	0.66460	0.92;-0.21	5.53	4.38	0.52667	.	0.098116	0.64402	D	0.000001	T	0.73853	0.3640	M	0.79475	2.455	0.47094	D	0.999311	P	0.49447	0.924	P	0.51945	0.685	T	0.74051	-0.3789	10	0.44086	T	0.13	-5.8023	10.6179	0.45462	0.0:0.0771:0.0:0.9229	.	221	Q9NUJ1	ABHDA_HUMAN	Y	64;221	ENSP00000442932:F64Y;ENSP00000273359:F221Y	ENSP00000273359:F221Y	F	+	2	0	ABHD10	113192999	1.000000	0.71417	0.999000	0.59377	0.766000	0.43426	7.632000	0.83247	1.048000	0.40298	0.482000	0.46254	TTC	.	.		0.398	ABHD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354326.1	NM_018394		A	111710309	T	A	111710309	3	1	197	1	0	0	0	0	1	0	0	0	74	1783	62	4	680	4	ABHD10	3	111710309	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	24396666	111710309	86312121	54	28964										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112357345	112357345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tcggtggccatgttcccgccTgtccatgcggttgtcccgga	13	14	0	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:112357345T>C	ENST00000206423.3	-	2	2361	c.1408A>G	c.(1408-1410)Agg>Ggg	p.R470G	CCDC80_ENST00000475181.1_5'Flank|CCDC80_ENST00000439685.2_Missense_Mutation_p.R470G	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	470					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						TGTTCCCGCCTGTCCATGCGG	0.582																																					p.R470G		Atlas-SNP	.											.	CCDC80	100	.	0			c.A1408G						.						66	68	67					3																	112357345		2203	4300	6503	SO:0001583	missense	151887	exon2			CCCGCCTGTCCAT	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.1408A>G	chr3.hg19:g.112357345T>C	ENSP00000206423:p.Arg470Gly	91.0	0.0		71.0	32.0	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	hg19	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.065597	0.55539	.	.	ENSG00000091986	ENST00000206423;ENST00000439685;ENST00000444594	T;T	0.56103	0.48;0.48	5.15	-0.617	0.11579	.	0.323582	0.35903	N	0.002915	T	0.38026	0.1025	N	0.24115	0.695	0.32958	D	0.520627	P;P;P	0.39665	0.675;0.682;0.546	B;B;B	0.39379	0.298;0.244;0.156	T	0.53457	-0.8436	10	0.54805	T	0.06	-18.503	14.3871	0.66953	0.0:0.0:0.5171:0.4829	.	481;470;470	Q76M96-2;A3KC71;Q76M96	.;.;CCD80_HUMAN	G	470;470;98	ENSP00000206423:R470G;ENSP00000411814:R470G	ENSP00000206423:R470G	R	-	1	2	CCDC80	113840035	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	0.807000	0.27140	0.059000	0.16252	0.454000	0.30748	AGG	.	.		0.582	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		C	112357345	T	C	112357345	3	2	197	1	0	0	0	0	1	0	0	0	2856	1579	55	2	1472	2	CCDC80	3	112357345	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	647036	112357345	85665085	55	28965										
NR1I2	8856	hgsc.bcm.edu	37	chr3	119530393	119530394	+	Missense_Mutation	DNP	GT	GT	CA													0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	actgtccctgcagtgatcatGtccgacgaggccgtggagga							TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:119530393_119530394GT>CA	ENST00000337940.4	+	4	504_505	c.456_457GT>CA	c.(454-459)atGTcc>atCAcc	p.152_153MS>IT	NR1I2_ENST00000466380.1_Missense_Mutation_p.113_114MS>IT|NR1I2_ENST00000393716.2_Missense_Mutation_p.113_114MS>IT	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	113	Hinge.				drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	CAGTGATCATGTCCGACGAGGC	0.629																																					p.M152I|p.S153T		Atlas-SNP	.											.	NR1I2	44	.	0			c.G456C|c.T457A						.																																			SO:0001583	missense	8856	exon4			GATCATGTCCGAC|ATCATGTCCGACG	AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"Nuclear hormone receptors"	7968	protein-coding gene	gene with protein product	"pregnane X receptor", "orphan nuclear receptor PXR"	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	Exception_encountered	chr3.hg19:g.119530393_119530394delinsCA	ENSP00000336528:p.M152_S153delinsIT	96.0|99.0	0.0		77.0|81.0	15.0|17.0	NM_022002	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Missense_Mutation	SNP	ENST00000337940.4	hg19	CCDS2995.1																																																																																			.	.		0.629	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1			CA	119530394	GT	CA	119530393	3	2	197	1	0	0	0	0	1	0	0	0	10629	1377	48	4	470	4	NR1I2	3	119530393	Missense_Mutation	DNP	GT	TCGA-DD-AADO-01A-11D-A40R-10	7173048	119530393	78492037	56	28966										
CASR	846	hgsc.bcm.edu	37	chr3	122002614	122002614	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gcattgccaaggagatcgagTttctgtcgtggacggagccc	14	10	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:122002614T>C	ENST00000490131.1	+	7	2185	c.1813T>C	c.(1813-1815)Ttt>Ctt	p.F605L	CASR_ENST00000296154.5_Missense_Mutation_p.F605L|AC068754.1_ENST00000408547.1_RNA|CASR_ENST00000498619.1_Missense_Mutation_p.F615L	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	605					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	GGAGATCGAGTTTCTGTCGTG	0.522																																					p.F615L		Atlas-SNP	.											.	CASR	190	.	0			c.T1843C						.						151	124	133					3																	122002614		2203	4300	6503	SO:0001583	missense	846	exon7			ATCGAGTTTCTGT	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.1813T>C	chr3.hg19:g.122002614T>C	ENSP00000418685:p.Phe605Leu	74.0	0.0		72.0	8.0	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	hg19	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	T	18.57	3.652760	0.67472	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.91237	-2.78;-2.81;-2.78	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.93025	0.7780	M	0.93507	3.425	0.80722	D	1	P;B	0.35612	0.512;0.451	B;B	0.34346	0.18;0.112	D	0.93580	0.6912	10	0.87932	D	0	.	15.5237	0.75885	0.0:0.0:0.0:1.0	.	615;605	E7ENE0;P41180	.;CASR_HUMAN	L	605;615;605	ENSP00000418685:F605L;ENSP00000420194:F615L;ENSP00000296154:F605L	ENSP00000296154:F605L	F	+	1	0	CASR	123485304	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.040000	0.89188	2.263000	0.75096	0.379000	0.24179	TTT	.	.		0.522	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		C	122002614	T	C	122002614	3	2	197	1	0	0	0	0	1	0	0	0	2684	1725	60	2	1865	2	CASR	3	122002614	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	2472221	122002614	76019816	57	28967										
CCDC14	64770	hgsc.bcm.edu	37	chr3	123674900	123674900	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aaaaaaaaaaaacctgaatcTtcatttctcaaaatgtccct	2	9	3	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:123674900T>C	ENST00000488653.2	-	4	456	c.366A>G	c.(364-366)gaA>gaG	p.E122E	CCDC14_ENST00000489746.1_5'UTR|CCDC14_ENST00000433542.2_Silent_p.E122E|CCDC14_ENST00000485727.1_5'UTR|CCDC14_ENST00000483247.1_Intron			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	122					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		AACCTGAATCTTCATTTCTCA	0.308																																					p.E122E		Atlas-SNP	.											.	CCDC14	97	.	0			c.A366G						.						94	91	92					3																	123674900		692	1591	2283	SO:0001819	synonymous_variant	64770	exon4			TGAATCTTCATTT	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.366A>G	chr3.hg19:g.123674900T>C		129.0	0.0		101.0	11.0	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Silent	SNP	ENST00000488653.2	hg19																																																																																				.	.		0.308	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757		C	123674900	T	C	123674900	2	2	197	1	0	0	0	0	0	0	0	1	2775	1606	56	2		2	CCDC14	3	123674900	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	1672286	123674900	74347530	58	28968										
MSL2	55167	hgsc.bcm.edu	37	chr3	135870012	135870012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	acagtcgaatctcatgtctaTagcttcatccaaacttttat	4	10	3	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:135870012T>C	ENST00000309993.2	-	2	2443	c.1711A>G	c.(1711-1713)Ata>Gta	p.I571V	MSL2_ENST00000434835.2_Missense_Mutation_p.I497V	NM_018133.3	NP_060603.2	Q9HCI7	MSL2_HUMAN	male-specific lethal 2 homolog (Drosophila)	571					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	18						CTCATGTCTATAGCTTCATCC	0.413																																					p.I571V		Atlas-SNP	.											.	MSL2	63	.	0			c.A1711G						.						127	130	129					3																	135870012		2203	4300	6503	SO:0001583	missense	55167	exon2			TGTCTATAGCTTC	AK001408	CCDS33861.1, CCDS46922.1	3q22.2	2008-10-29	2008-10-29	2008-10-29	ENSG00000174579	ENSG00000174579		"RING-type (C3HC4) zinc fingers"	25544	protein-coding gene	gene with protein product	"male-specific lethal-2 homolog (Drosophila)"	614802	"ring finger protein 184", "male-specific lethal 2-like 1 (Drosophila)"	RNF184, MSL2L1		16227571, 16543150	Standard	NM_018133		Approved	FLJ10546, KIAA1585, msl-2	uc003eqx.1	Q9HCI7	OTTHUMG00000159793	ENST00000309993.2:c.1711A>G	chr3.hg19:g.135870012T>C	ENSP00000311827:p.Ile571Val	118.0	0.0		104.0	20.0	NM_018133	B4DYL4|G5E9I1|Q0D2P1|Q8NDB4|Q9NVS4	Missense_Mutation	SNP	ENST00000309993.2	hg19	CCDS33861.1	.	.	.	.	.	.	.	.	.	.	T	9.644	1.139723	0.21205	.	.	ENSG00000174579	ENST00000309993;ENST00000434835	.	.	.	5.33	5.33	0.75918	.	0.053759	0.85682	D	0.000000	T	0.49047	0.1534	L	0.36672	1.1	0.37956	D	0.932805	B	0.25441	0.126	B	0.22880	0.042	T	0.53655	-0.8408	9	0.52906	T	0.07	-8.2677	14.7844	0.69790	0.0:0.0:0.0:1.0	.	571	Q9HCI7	MSL2_HUMAN	V	571;497	.	ENSP00000311827:I571V	I	-	1	0	MSL2	137352702	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.901000	0.39838	2.142000	0.66516	0.383000	0.25322	ATA	.	.		0.413	MSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357347.1	NM_018133		C	135870012	T	C	135870012	3	2	197	1	0	0	0	0	1	0	0	0	9887	1406	49	2	26	2	MSL2	3	135870012	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	12195112	135870012	62152418	59	28969										
MME	4311	hgsc.bcm.edu	37	chr3	154878219	154878219	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tagtcaatgcattttactctTcaggaagaaatcagataggt	8	6	4	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:154878219T>A	ENST00000460393.1	+	17	1762	c.1642T>A	c.(1642-1644)Tca>Aca	p.S548T	MME_ENST00000360490.2_Missense_Mutation_p.S548T|MME_ENST00000493237.1_Missense_Mutation_p.S548T|MME_ENST00000462745.1_Missense_Mutation_p.S548T|MME_ENST00000492661.1_Missense_Mutation_p.S548T|MME-AS1_ENST00000484721.1_RNA	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	548					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	ATTTTACTCTTCAGGAAGAAA	0.343																																					p.S548T		Atlas-SNP	.											.	MME	133	.	0			c.T1642A						.						184	197	193					3																	154878219		2203	4300	6503	SO:0001583	missense	4311	exon17			TACTCTTCAGGAA		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.1642T>A	chr3.hg19:g.154878219T>A	ENSP00000418525:p.Ser548Thr	102.0	0.0		92.0	20.0	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	hg19	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.927939	0.34002	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	5.5	3.07	0.35406	Peptidase M13, neprilysin, C-terminal (1);Metallopeptidase, catalytic domain (1);	0.482715	0.21875	N	0.067840	T	0.66587	0.2804	L	0.28458	0.855	0.39363	D	0.965952	B	0.27765	0.188	B	0.22753	0.041	T	0.61845	-0.6979	10	0.87932	D	0	-2.3276	5.9082	0.19012	0.0:0.1541:0.3543:0.4916	.	548	P08473	NEP_HUMAN	T	548	ENSP00000420389:S548T;ENSP00000418525:S548T;ENSP00000419653:S548T;ENSP00000417079:S548T;ENSP00000353679:S548T	ENSP00000353679:S548T	S	+	1	0	MME	156360913	0.944000	0.32072	0.999000	0.59377	0.997000	0.91878	0.536000	0.23129	0.370000	0.24538	0.528000	0.53228	TCA	.	.		0.343	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		A	154878219	T	A	154878219	3	1	197	1	0	0	0	0	1	0	0	0	9654	1783	62	4	1704	4	MME	3	154878219	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	19008207	154878219	43144211	60	28970										
ST6GAL1	6480	hgsc.bcm.edu	37	chr3	186790725	186790725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cccatctgtataccactcagAtatcccaaaggtaagtgggt	8	11	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:186790725A>G	ENST00000169298.3	+	6	1468	c.794A>G	c.(793-795)gAt>gGt	p.D265G	ST6GAL1_ENST00000457772.2_Missense_Mutation_p.D34G|ST6GAL1_ENST00000448044.1_Missense_Mutation_p.D265G	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	265					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		TACCACTCAGATATCCCAAAG	0.438																																					p.D265G		Atlas-SNP	.											.	ST6GAL1	36	.	0			c.A794G						.						102	100	101					3																	186790725		2203	4300	6503	SO:0001583	missense	6480	exon5			ACTCAGATATCCC	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"ST6Gal I"	109675	"sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.794A>G	chr3.hg19:g.186790725A>G	ENSP00000169298:p.Asp265Gly	130.0	0.0		127.0	31.0	NM_003032	A8KA14|B2R513|D3DNV3	Missense_Mutation	SNP	ENST00000169298.3	hg19	CCDS3285.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.521643	0.44866	.	.	ENSG00000073849	ENST00000169298;ENST00000457772;ENST00000427315;ENST00000448044;ENST00000442023	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	4.5	4.5	0.54988	.	0.142257	0.64402	D	0.000007	T	0.33673	0.0871	M	0.83223	2.63	0.45806	D	0.998689	B	0.33777	0.425	B	0.33196	0.159	T	0.11036	-1.0604	10	0.15499	T	0.54	-14.1272	10.4944	0.44768	1.0:0.0:0.0:0.0	.	265	P15907	SIAT1_HUMAN	G	265;34;34;265;34	ENSP00000169298:D265G;ENSP00000412221:D34G;ENSP00000389337:D265G;ENSP00000403063:D34G	ENSP00000169298:D265G	D	+	2	0	ST6GAL1	188273419	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	5.022000	0.64078	2.257000	0.74773	0.459000	0.35465	GAT	.	.		0.438	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216		G	186790725	A	G	186790725	3	3	197	1	0	0	0	0	1	0	0	0	15236	333	12	2	804	2	ST6GAL1	3	186790725	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	31912506	186790725	11231705	61	28971										
ATP13A5	344905	hgsc.bcm.edu	37	chr3	192992998	192992998	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ccaggttgagtcttctgctaGcttcttttgccaagtcctat	8	11	3	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr3:192992998G>C	ENST00000342358.4	-	30	3607	c.3490C>G	c.(3490-3492)Cta>Gta	p.L1164V	ATP13A5_ENST00000495496.1_5'UTR	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	1164						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TCTTCTGCTAGCTTCTTTTGC	0.398																																					p.L1164V		Atlas-SNP	.											.	ATP13A5	171	.	0			c.C3490G						.						151	141	145					3																	192992998		2203	4300	6503	SO:0001583	missense	344905	exon30			CTGCTAGCTTCTT	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"ATPases / P-type"	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.3490C>G	chr3.hg19:g.192992998G>C	ENSP00000341942:p.Leu1164Val	91.0	0.0		83.0	20.0	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	hg19	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.945722	0.34377	.	.	ENSG00000187527	ENST00000342358	T	0.58652	0.32	5.59	2.79	0.32731	.	0.108809	0.41001	D	0.000977	T	0.32071	0.0817	N	0.14661	0.345	0.27674	N	0.946671	P	0.41041	0.736	B	0.35312	0.2	T	0.23368	-1.0190	10	0.56958	D	0.05	-8.6316	5.029	0.14400	0.2358:0.1629:0.6012:0.0	.	1164	Q4VNC0	AT135_HUMAN	V	1164	ENSP00000341942:L1164V	ENSP00000341942:L1164V	L	-	1	2	ATP13A5	194475692	0.875000	0.30112	0.981000	0.43875	0.909000	0.53808	0.231000	0.17872	1.366000	0.46076	0.563000	0.77884	CTA	.	.		0.398	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		C	192992998	G	C	192992998	3	2	197	1	0	0	0	0	1	0	0	0	1127	962	34	4	168	4	ATP13A5	3	192992998	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	6202273	192992998	5029432	62	28972										
COMMD8	54951	hgsc.bcm.edu	37	chr4	47465616	47465616	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ccctcacctgcgggcccagcTcggccggcagcttctgcagc	12	19	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr4:47465616T>A	ENST00000381571.4	-	1	120	c.53A>T	c.(52-54)gAg>gTg	p.E18V		NM_017845.3	NP_060315.1	Q9NX08	COMD8_HUMAN	COMM domain containing 8	18										large_intestine(2)|lung(5)|prostate(1)	8						CGGGCCCAGCTCGGCCGGCAG	0.741																																					p.E18V		Atlas-SNP	.											.	COMMD8	15	.	0			c.A53T						.						4	4	4					4																	47465616		1664	3187	4851	SO:0001583	missense	54951	exon1			CCCAGCTCGGCCG	AY542163	CCDS3475.1	4p12	2008-02-05			ENSG00000169019	ENSG00000169019			26036	protein-coding gene	gene with protein product						15799966	Standard	NM_017845		Approved	FLJ20502	uc003gxi.3	Q9NX08	OTTHUMG00000099435	ENST00000381571.4:c.53A>T	chr4.hg19:g.47465616T>A	ENSP00000370984:p.Glu18Val	57.0	0.0		69.0	13.0	NM_017845	Q8WUR4|Q9HC15	Missense_Mutation	SNP	ENST00000381571.4	hg19	CCDS3475.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.314639	0.81358	.	.	ENSG00000169019	ENST00000381571	T	0.09630	2.96	5.17	5.17	0.71159	.	0.387514	0.28653	N	0.014597	T	0.23965	0.0580	M	0.65498	2.005	0.41436	D	0.987898	D	0.58970	0.984	P	0.56343	0.796	T	0.00708	-1.1600	10	0.52906	T	0.07	-27.9928	11.3169	0.49396	0.0:0.0:0.0:1.0	.	18	Q9NX08	COMD8_HUMAN	V	18	ENSP00000370984:E18V	ENSP00000370984:E18V	E	-	2	0	COMMD8	47160373	0.994000	0.37717	0.970000	0.41538	0.683000	0.39861	3.299000	0.51826	2.168000	0.68352	0.533000	0.62120	GAG	.	.		0.741	COMMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216898.2	NM_017845		A	47465616	T	A	47465616	3	1	197	1	0	0	0	0	1	0	0	0	3724	1551	54	4	518	4	COMMD8	4	47465616	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10		47465616	143688660	63	28973										
FAM13A	10144	hgsc.bcm.edu	37	chr4	89689194	89689194	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tctcatgagatcgtgtggaaTtgagactttccatattctgt	9	7	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr4:89689194T>G	ENST00000264344.5	-	12	1682	c.1475A>C	c.(1474-1476)aAt>aCt	p.N492T	FAM13A_ENST00000511976.1_Missense_Mutation_p.N78T|FAM13A_ENST00000503556.1_Missense_Mutation_p.N152T|FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000395002.2_Missense_Mutation_p.N166T|FAM13A_ENST00000508369.1_Missense_Mutation_p.N166T|FAM13A_ENST00000513837.1_Missense_Mutation_p.N138T	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	492					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						TCGTGTGGAATTGAGACTTTC	0.358																																					p.N492T		Atlas-SNP	.											.	FAM13A	181	.	0			c.A1475C						.						93	87	89					4																	89689194		2203	4300	6503	SO:0001583	missense	10144	exon12			GTGGAATTGAGAC	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.1475A>C	chr4.hg19:g.89689194T>G	ENSP00000264344:p.Asn492Thr	206.0	0.0		134.0	33.0	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	hg19	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.497742	0.26861	.	.	ENSG00000138640	ENST00000395002;ENST00000264344;ENST00000503556;ENST00000511976;ENST00000508369;ENST00000513837	T;T;T;T;T;T	0.62941	-0.01;-0.01;1.46;1.53;-0.01;1.46	5.13	-7.72	0.01250	.	1.035740	0.07534	N	0.912755	T	0.49695	0.1572	L	0.43152	1.355	0.09310	N	1	B;B;B;B;B;B	0.25904	0.034;0.137;0.029;0.034;0.034;0.034	B;B;B;B;B;B	0.21917	0.036;0.037;0.006;0.023;0.023;0.023	T	0.31586	-0.9938	10	0.33141	T	0.24	.	14.5637	0.68159	0.0:0.6775:0.1983:0.1242	.	138;78;492;166;152;166	O94988-6;E9PGM7;O94988;O94988-3;O94988-5;O94988-1	.;.;FA13A_HUMAN;.;.;.	T	166;492;152;78;166;138	ENSP00000378450:N166T;ENSP00000264344:N492T;ENSP00000427189:N152T;ENSP00000421914:N78T;ENSP00000421562:N166T;ENSP00000423252:N138T	ENSP00000264344:N492T	N	-	2	0	FAM13A	89908217	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.707000	0.05041	-1.775000	0.01287	-0.924000	0.02725	AAT	.	.		0.358	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			G	89689194	T	G	89689194	3	3	197	1	0	0	0	0	1	0	0	0	5457	1493	52	5	1648	5	FAM13A	4	89689194	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	42223578	89689194	101465082	64	28974										
FSTL5	56884	hgsc.bcm.edu	37	chr4	162307147	162307147	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agagagctccacaaagagcaCatcagtttgtgtgcttgaac	10	9	1	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr4:162307147C>T	ENST00000306100.5	-	16	2732	c.2296G>A	c.(2296-2298)Gtg>Atg	p.V766M	FSTL5_ENST00000427802.2_Missense_Mutation_p.V756M|FSTL5_ENST00000536695.1_Missense_Mutation_p.V765M|RP11-234O6.2_ENST00000508189.1_RNA|FSTL5_ENST00000379164.4_Missense_Mutation_p.V765M	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	766						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		ACAAAGAGCACATCAGTTTGT	0.433																																					p.V766M		Atlas-SNP	.											.	FSTL5	207	.	0			c.G2296A						.						128	119	122					4																	162307147		2203	4300	6503	SO:0001583	missense	56884	exon16			AGAGCACATCAGT	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.2296G>A	chr4.hg19:g.162307147C>T	ENSP00000305334:p.Val766Met	145.0	0.0		84.0	26.0	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	hg19	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.443101	0.83993	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);	0.114370	0.64402	D	0.000013	T	0.56426	0.1984	M	0.71036	2.16	0.58432	D	0.99999	D;D;D	0.67145	0.978;0.996;0.987	P;D;P	0.67548	0.836;0.952;0.812	T	0.57751	-0.7757	10	0.87932	D	0	.	18.9648	0.92692	0.0:1.0:0.0:0.0	.	756;765;766	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	M	766;765;756;765	ENSP00000305334:V766M;ENSP00000368462:V765M;ENSP00000389270:V756M;ENSP00000440409:V765M	ENSP00000305334:V766M	V	-	1	0	FSTL5	162526597	1.000000	0.71417	0.962000	0.40283	0.987000	0.75469	7.380000	0.79704	2.702000	0.92279	0.655000	0.94253	GTG	.	.		0.433	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		T	162307147	C	T	162307147	3	4	197	1	0	0	0	0	1	0	0	0	6088	478	17	3	251	3	FSTL5	4	162307147	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	72617953	162307147	28847129	65	28975										
TLR3	7098	hgsc.bcm.edu	37	chr4	187004594	187004594	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agttgaggtcttcaaggattTatttgaactaaagatcatcg	9	5	3	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr4:187004594T>C	ENST00000296795.3	+	4	1858	c.1754T>C	c.(1753-1755)tTa>tCa	p.L585S	TLR3_ENST00000504367.1_Missense_Mutation_p.L308S	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	585					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		TTCAAGGATTTATTTGAACTA	0.398																																					p.L585S		Atlas-SNP	.											.	TLR3	83	.	0			c.T1754C						.						76	76	76					4																	187004594		2203	4300	6503	SO:0001583	missense	7098	exon4			AGGATTTATTTGA	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"CD molecules"	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.1754T>C	chr4.hg19:g.187004594T>C	ENSP00000296795:p.Leu585Ser	177.0	0.0		145.0	18.0	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	hg19	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.955634	0.53293	.	.	ENSG00000164342	ENST00000296795;ENST00000542020;ENST00000504367	T;T	0.70631	-0.5;-0.5	5.88	5.88	0.94601	.	0.063079	0.64402	D	0.000005	D	0.87144	0.6104	M	0.89904	3.07	0.36853	D	0.888013	D	0.89917	1.0	D	0.97110	1.0	D	0.91611	0.5303	10	0.72032	D	0.01	.	16.2948	0.82765	0.0:0.0:0.0:1.0	.	585	O15455	TLR3_HUMAN	S	585;585;308	ENSP00000296795:L585S;ENSP00000423684:L308S	ENSP00000296795:L585S	L	+	2	0	TLR3	187241588	0.996000	0.38824	0.039000	0.18376	0.556000	0.35491	8.040000	0.89188	2.253000	0.74438	0.455000	0.32223	TTA	.	.		0.398	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			C	187004594	T	C	187004594	3	2	197	1	0	0	0	0	1	0	0	0	15967	1764	61	2	1764	2	TLR3	4	187004594	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	24697447	187004594	4149682	66	28976										
NIPBL	25836	hgsc.bcm.edu	37	chr5	36986168	36986168	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tttgtcattccgaaaatcaaGagggataaagatggcaatgt	10	5	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:36986168G>A	ENST00000282516.8	+	10	3385	c.2886G>A	c.(2884-2886)aaG>aaA	p.K962K	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Silent_p.K962K	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	962					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			CGAAAATCAAGAGGGATAAAG	0.378																																					p.K962K		Atlas-SNP	.											.	NIPBL	513	.	0			c.G2886A						.						121	128	126					5																	36986168		2203	4300	6503	SO:0001819	synonymous_variant	25836	exon10			AATCAAGAGGGAT	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.2886G>A	chr5.hg19:g.36986168G>A		1313.0	2.0		1463.0	280.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.		0.378	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		A	36986168	G	A	36986168	2	1	197	1	0	0	0	0	0	0	0	1	10437	933	33	3		3	NIPBL	5	36986168	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10		36986168	143929092	67	28977										
ZNF366	167465	hgsc.bcm.edu	37	chr5	71756336	71756336	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cggcttcacctcgctgtgctGcatcatgtggcgcttcaggt	12	13	3	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:71756336G>A	ENST00000318442.5	-	2	1478	c.988C>T	c.(988-990)Cag>Tag	p.Q330*		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	330					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TCGCTGTGCTGCATCATGTGG	0.667																																					p.Q330X		Atlas-SNP	.											.	ZNF366	108	.	0			c.C988T						.						40	38	39					5																	71756336		2203	4300	6503	SO:0001587	stop_gained	167465	exon2			TGTGCTGCATCAT	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"Zinc fingers, C2H2-type"	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.988C>T	chr5.hg19:g.71756336G>A	ENSP00000313158:p.Gln330*	52.0	0.0		44.0	14.0	NM_152625	Q5HYI9|Q7RTV4	Nonsense_Mutation	SNP	ENST00000318442.5	hg19	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	G	41	8.555257	0.98861	.	.	ENSG00000178175	ENST00000318442	.	.	.	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-48.1929	19.7279	0.96172	0.0:0.0:1.0:0.0	.	.	.	.	X	330	.	ENSP00000313158:Q330X	Q	-	1	0	ZNF366	71792092	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.659000	0.90383	0.561000	0.74099	CAG	.	.		0.667	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			A	71756336	G	A	71756336	4	1	197	1	0	0	0	0	0	1	0	0	17885	1328	46	3	1262	3	ZNF366	5	71756336	Nonsense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	34770168	71756336	109158924	68	28978										
LRRTM2	26045	hgsc.bcm.edu	37	chr5	138209107	138209107	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gatgagcttattctttttgtAtattcagtggttggatctct	9	5	3	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:138209107A>G	ENST00000274711.6	-	2	1521	c.1143T>C	c.(1141-1143)taT>taC	p.Y381Y	CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000302763.7_Intron|CTNNA1_ENST00000518825.1_Intron|LRRTM2_ENST00000523537.1_5'Flank|CTNNA1_ENST00000520400.1_Intron|LRRTM2_ENST00000518785.1_3'UTR|LRRTM2_ENST00000521094.2_Intron|CTNNA1_ENST00000540387.1_5'Flank	NM_015564.2	NP_056379.1	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2	381					long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|synapse organization (GO:0050808)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|urinary_tract(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTCTTTTTGTATATTCAGTGG	0.423																																					p.Y381Y		Atlas-SNP	.											.	LRRTM2	42	.	0			c.T1143C						.						180	155	163					5																	138209107		1900	4121	6021	SO:0001819	synonymous_variant	26045	exon2			TTTTGTATATTCA	AB007876	CCDS47272.1	5q31	2008-02-05				ENSG00000146006			19409	protein-coding gene	gene with protein product		610868				12676565	Standard	NM_015564		Approved	KIAA0416	uc011cyz.1	O43300		ENST00000274711.6:c.1143T>C	chr5.hg19:g.138209107A>G		90.0	0.0		99.0	11.0	NM_015564	A0AVL3|A8K4U9|B7ZLN8|Q7L770	Silent	SNP	ENST00000274711.6	hg19	CCDS47272.1																																																																																			.	.		0.423	LRRTM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374043.2			G	138209107	A	G	138209107	2	3	197	1	0	0	0	0	0	0	0	1	9049	456	16	2		2	LRRTM2	5	138209107	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	66452771	138209107	42706153	69	28979										
UBE2D2	7322	hgsc.bcm.edu	37	chr5	138994470	138994471	+	Missense_Mutation	DNP	CA	CA	AT													0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	catttacaacaagaatttatCatccaaatattaacagtaat							TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:138994470_138994471CA>AT	ENST00000398733.3	+	5	849_850	c.223_224CA>AT	c.(223-225)CAt>ATt	p.H75I	UBE2D2_ENST00000253815.2_Missense_Mutation_p.H46I|UBE2D2_ENST00000505548.1_Missense_Mutation_p.H46I|UBE2D2_ENST00000511725.1_Missense_Mutation_p.H46I	NM_003339.2	NP_003330.1	P62837	UB2D2_HUMAN	ubiquitin-conjugating enzyme E2D 2	75					cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAGAATTTATCATCCAAATATT	0.322																																					p.H75N|p.H75L		Atlas-SNP	.											.	UBE2D2	17	.	0			c.C223A|c.A224T						.																																			SO:0001583	missense	7322	exon5			ATTTATCATCCAA|TTTATCATCCAAA	L40146	CCDS43369.1, CCDS47275.1	5q31.2	2013-10-18	2011-05-19		ENSG00000131508	ENSG00000131508		"Ubiquitin-conjugating enzymes E2"	12475	protein-coding gene	gene with protein product		602962	"ubiquitin-conjugating enzyme E2D 2 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)"			8530467	Standard	NM_181838		Approved	UbcH5B, UBC4	uc003ler.3	P62837	OTTHUMG00000163282	Exception_encountered	chr5.hg19:g.138994470_138994471delinsAT	ENSP00000381717:p.His75Ile	276.0|273.0	0.0		261.0|259.0	136.0|135.0	NM_003339	D3DQC9|P51669|Q3MN78|Q96RP6	Missense_Mutation	SNP	ENST00000398733.3	hg19	CCDS43369.1																																																																																			.	.		0.322	UBE2D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372454.3	NM_181838		AT	138994471	CA	AT	138994470	3	1	197	1	0	0	0	0	1	0	0	0	16864	826	29	3	241	3	UBE2D2	5	138994470	Missense_Mutation	DNP	CA	TCGA-DD-AADO-01A-11D-A40R-10	785363	138994470	41920790	70	28980										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139917018	139917018	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gccaaccaaaaggagtcagtGccagtcaagatcgaaagata	10	9	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:139917018G>T	ENST00000360839.2	+	31	7226	c.7072G>T	c.(7072-7074)Gcc>Tcc	p.A2358S	ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.A2358S|ANKHD1_ENST00000544120.1_Missense_Mutation_p.A682S|ANKHD1_ENST00000297183.6_Missense_Mutation_p.A2358S	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	2358						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGAGTCAGTGCCAGTCAAGA	0.542																																					p.A2358S		Atlas-SNP	.											.	ANKHD1	233	.	0			c.G7072T						.						100	96	97					5																	139917018		2203	4300	6503	SO:0001583	missense	54882	exon31			GTCAGTGCCAGTC	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.7072G>T	chr5.hg19:g.139917018G>T	ENSP00000354085:p.Ala2358Ser	137.0	0.0		137.0	67.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.46|14.46	2.542862|2.542862	0.45280|0.45280	.|.	.|.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996;ENSG00000254996|ENSG00000131503	ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000433049;ENST00000544120;ENST00000532219;ENST00000437495|ENST00000435794;ENST00000432301	T;T;T;T;T;T;T|.	0.64618|.	-0.06;-0.11;1.99;1.99;1.55;-0.11;0.97|.	5.78|5.78	4.87|4.87	0.63330|0.63330	.|.	0.256502|.	0.40385|.	N|.	0.001119|.	T|T	0.28001|0.28001	0.0690|0.0690	L|L	0.29908|0.29908	0.895|0.895	0.23546|0.23546	N|N	0.997442|0.997442	B;B;B;B;B;B|.	0.25390|.	0.077;0.01;0.125;0.001;0.001;0.02|.	B;B;B;B;B;B|.	0.28916|.	0.044;0.017;0.096;0.002;0.004;0.017|.	T|T	0.12268|0.12268	-1.0554|-1.0554	10|5	0.15952|.	T|.	0.53|.	.|.	5.4802|5.4802	0.16719|0.16719	0.1066:0.1285:0.6329:0.132|0.1066:0.1285:0.6329:0.132	.|.	682;805;682;2375;2358;2358|.	Q8IWG5;Q9H059;F6WFL0;E9PF56;Q8IWZ2;Q8IWZ3|.	.;.;.;.;.;ANKH1_HUMAN|.	S|F	2358;2358;2375;1031;897;682;2358;386|848;749	ENSP00000354085:A2358S;ENSP00000297183:A2358S;ENSP00000393204:A1031S;ENSP00000390034:A897S;ENSP00000437687:A682S;ENSP00000432016:A2358S;ENSP00000396882:A386S|.	ENSP00000396882:A386S|.	A|C	+|+	1|2	0|0	ANKHD1-EIF4EBP3;ANKHD1|ANKHD1	139897202|139897202	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	1.144000|1.144000	0.31565|0.31565	2.894000|2.894000	0.99253|0.99253	0.591000|0.591000	0.81541|0.81541	GCC|TGC	.	.		0.542	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		T	139917018	G	T	139917018	3	4	197	1	0	0	0	0	1	0	0	0	628	1319	46	3	7300	3	ANKHD1	5	139917018	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	922548	139917018	40998242	71	28981										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237595	140237595	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtgctggtgaaggaccatggCgagccgtcgctgacggccac	16	12	0	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:140237595C>G	ENST00000307360.5	+	1	1962	c.1962C>G	c.(1960-1962)ggC>ggG	p.G654G	PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	654	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGACCATGGCGAGCCGTCGC	0.682																																					p.G654G		Atlas-SNP	.											.	PCDHA10	358	.	0			c.C1962G						.						16	22	20					5																	140237595		1322	2284	3606	SO:0001819	synonymous_variant	56139	exon1			CCATGGCGAGCCG	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1962C>G	chr5.hg19:g.140237595C>G		82.0	0.0		115.0	23.0	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	hg19	CCDS54921.1																																																																																			.	.		0.682	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		G	140237595	C	G	140237595	2	3	197	1	0	0	0	0	0	0	0	1	11529	755	27	4		4	PCDHA10	5	140237595	Silent	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	320577	140237595	40677665	72	28982										
PCDHGB7	56099	hgsc.bcm.edu	37	chr5	140797663	140797663	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ctgcacttcagcgtagacgcGcagagcggggacttacttgt	13	11	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:140797663G>T	ENST00000398594.2	+	1	237	c.237G>T	c.(235-237)gcG>gcT	p.A79A	PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	79	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGTAGACGCGCAGAGCGGGG	0.537																																					p.A79A		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.G237T						.						129	134	132					5																	140797663		1950	4152	6102	SO:0001819	synonymous_variant	56099	exon1			AGACGCGCAGAGC	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.237G>T	chr5.hg19:g.140797663G>T		134.0	0.0		98.0	37.0	NM_018927	Q9UN63	Silent	SNP	ENST00000398594.2	hg19	CCDS47293.1																																																																																			.	.		0.537	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		T	140797663	G	T	140797663	2	4	197	1	0	0	0	0	0	0	0	1	11577	1074	38	1		1	PCDHGB7	5	140797663	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	560068	140797663	40117597	73	28983										
SPINK5	11005	hgsc.bcm.edu	37	chr5	147450013	147450013	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tgccacgtgcaaaatgatacTgtgagtaaaggtttctttct	9	7	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:147450013T>G	ENST00000256084.7	+	3	251	c.209T>G	c.(208-210)cTg>cGg	p.L70R	SPINK5_ENST00000398454.1_Splice_Site_p.L70R|SPINK5_ENST00000359874.3_Splice_Site_p.L70R	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	70					anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAAATGATACTGTGAGTAAAG	0.323																																					p.L70R		Atlas-SNP	.											.	SPINK5	245	.	0			c.T209G						.						75	74	74					5																	147450013		1833	4084	5917	SO:0001630	splice_region_variant	11005	exon3			TGATACTGTGAGT	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.209+1T>G	chr5.hg19:g.147450013T>G		326.0	0.0		301.0	19.0	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	hg19	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.694205	0.48202	.	.	ENSG00000133710	ENST00000521206;ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18	5.33	5.33	0.75918	.	0.000000	0.35040	N	0.003484	T	0.24084	0.0583	M	0.66939	2.045	0.33678	D	0.611786	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;D	0.97110	0.997;1.0;0.999;0.956	T	0.21518	-1.0243	10	0.23891	T	0.37	-4.2526	12.2661	0.54679	0.0:0.0:0.0:1.0	.	51;70;70;70	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	R	51;70;70;51;70	ENSP00000430264:L51R;ENSP00000381472:L70R;ENSP00000352936:L70R;ENSP00000421519:L51R;ENSP00000256084:L70R	ENSP00000256084:L70R	L	+	2	0	SPINK5	147430206	0.979000	0.34478	0.938000	0.37757	0.285000	0.27093	2.153000	0.42282	2.322000	0.78497	0.528000	0.53228	CTG	.	.		0.323	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	Missense_Mutation	G	147450013	T	G	147450013	5	3	197	1	0	0	0	0	0	0	1	0	15077	1594	55	5	219	5	SPINK5	5	147450013	Splice_Site	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	6652350	147450013	33465247	74	28984										
FOXI1	2299	hgsc.bcm.edu	37	chr5	169533520	169533520	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gcttcaagaaggtgccccgcGacgaggacgacccgggtaag	15	12	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:169533520G>A	ENST00000306268.6	+	1	620	c.559G>A	c.(559-561)Gac>Aac	p.D187N	FOXI1_ENST00000449804.2_Missense_Mutation_p.D187N			Q12951	FOXI1_HUMAN	forkhead box I1	187					embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGTGCCCCGCGACGAGGACGA	0.582									Pendred syndrome																												p.D187N		Atlas-SNP	.											.	FOXI1	70	.	0			c.G559A						.						38	41	40					5																	169533520		2203	4300	6503	SO:0001583	missense	2299	exon1	Familial Cancer Database	Goiter-Deafness syndrome	CCCCGCGACGAGG	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.559G>A	chr5.hg19:g.169533520G>A	ENSP00000304286:p.Asp187Asn	96.0	0.0		101.0	31.0	NM_012188	Q14518|Q66SR7|Q8N6L8	Missense_Mutation	SNP	ENST00000306268.6	hg19	CCDS4372.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.429315	0.43122	.	.	ENSG00000168269	ENST00000306268;ENST00000449804	D;D	0.95482	-3.72;-3.72	4.86	4.86	0.63082	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.056515	0.64402	D	0.000002	D	0.95262	0.8463	N	0.20445	0.575	0.80722	D	1	D;D	0.67145	0.995;0.996	P;D	0.64595	0.88;0.927	D	0.96440	0.9326	10	0.87932	D	0	.	18.1961	0.89822	0.0:0.0:1.0:0.0	.	187;187	Q12951-2;Q12951	.;FOXI1_HUMAN	N	187	ENSP00000304286:D187N;ENSP00000415483:D187N	ENSP00000304286:D187N	D	+	1	0	FOXI1	169466098	1.000000	0.71417	0.331000	0.25455	0.202000	0.24057	9.651000	0.98493	2.513000	0.84729	0.650000	0.86243	GAC	.	.		0.582	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		A	169533520	G	A	169533520	3	1	197	1	0	0	0	0	1	0	0	0	6017	1058	37	1	561	1	FOXI1	5	169533520	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	22083507	169533520	11381740	75	28985										
CDHR2	54825	hgsc.bcm.edu	37	chr5	176019770	176019770	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tggatgtggacaagaacagtCaggaaatcaaggcaagatgg	14	5	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:176019770C>G	ENST00000510636.1	+	31	4055	c.3781C>G	c.(3781-3783)Cag>Gag	p.Q1261E	CDHR2_ENST00000506348.1_Missense_Mutation_p.Q1261E|CDHR2_ENST00000261944.5_Missense_Mutation_p.Q1261E	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	1261					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CAAGAACAGTCAGGAAATCAA	0.547																																					p.Q1261E		Atlas-SNP	.											.	CDHR2	152	.	0			c.C3781G						.						154	128	137					5																	176019770		2203	4300	6503	SO:0001583	missense	54825	exon31			AACAGTCAGGAAA	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.3781C>G	chr5.hg19:g.176019770C>G	ENSP00000424565:p.Gln1261Glu	103.0	0.0		112.0	54.0	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	hg19	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	c	0.021	-1.422716	0.01126	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.54479	0.57;0.57;0.57	3.63	-5.51	0.02568	.	.	.	.	.	T	0.20088	0.0483	N	0.04636	-0.2	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36065	-0.9763	9	0.05721	T	0.95	-4.7353	7.2803	0.26308	0.407:0.208:0.385:0.0	.	1261	Q9BYE9	CDHR2_HUMAN	E	1261	ENSP00000424565:Q1261E;ENSP00000261944:Q1261E;ENSP00000421078:Q1261E	ENSP00000261944:Q1261E	Q	+	1	0	CDHR2	175952376	0.000000	0.05858	0.004000	0.12327	0.084000	0.17831	-1.790000	0.01759	-0.749000	0.04747	-1.533000	0.00918	CAG	.	.		0.547	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		G	176019770	C	G	176019770	3	3	197	1	0	0	0	0	1	0	0	0	3121	827	29	4	3899	4	CDHR2	5	176019770	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	6486250	176019770	4895490	76	28986										
TMED9	54732	hgsc.bcm.edu	37	chr5	177019635	177019635	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agtaccagccggccaccccgGggcttggcatgtttgtggag	15	12	0	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:177019635G>T	ENST00000332598.6	+	2	301	c.244G>T	c.(244-246)Ggg>Tgg	p.G82W		NM_017510.4	NP_059980.2	Q9BVK6	TMED9_HUMAN	transmembrane emp24 protein transport domain containing 9	82	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				COPI coating of Golgi vesicle (GO:0048205)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network transport vesicle (GO:0030140)	syntaxin binding (GO:0019905)			endometrium(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(2)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCCACCCCGGGGCTTGGCAT	0.652																																					p.G82W		Atlas-SNP	.											.	TMED9	18	.	0			c.G244T						.						26	31	29					5																	177019635		2203	4300	6503	SO:0001583	missense	54732	exon2			ACCCCGGGGCTTG	AF441399	CCDS4428.1	5q35.3	2008-02-05			ENSG00000184840	ENSG00000184840			24878	protein-coding gene	gene with protein product						12477932	Standard	NM_017510		Approved	HSGP25L2G	uc003mhx.3	Q9BVK6	OTTHUMG00000130859	ENST00000332598.6:c.244G>T	chr5.hg19:g.177019635G>T	ENSP00000330945:p.Gly82Trp	227.0	0.0		223.0	116.0	NM_017510	Q14437|Q8WZ61	Missense_Mutation	SNP	ENST00000332598.6	hg19	CCDS4428.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.316351	0.60524	.	.	ENSG00000184840	ENST00000332598	T	0.19105	2.17	5.05	4.17	0.49024	GOLD (2);	0.100180	0.64402	N	0.000002	T	0.41305	0.1153	M	0.82630	2.6	0.80722	D	1	P	0.40282	0.711	P	0.50934	0.654	T	0.41716	-0.9493	10	0.62326	D	0.03	-20.5084	13.0372	0.58879	0.0:0.0:0.8381:0.1619	.	82	Q9BVK6	TMED9_HUMAN	W	82	ENSP00000330945:G82W	ENSP00000330945:G82W	G	+	1	0	TMED9	176952241	1.000000	0.71417	0.961000	0.40146	0.966000	0.64601	7.402000	0.79972	1.216000	0.43427	0.462000	0.41574	GGG	.	.		0.652	TMED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253433.1	NM_017510		T	177019635	G	T	177019635	3	4	197	1	0	0	0	0	1	0	0	0	16027	1232	43	3	250	3	TMED9	5	177019635	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	999865	177019635	3895625	77	28987										
N4BP3	23138	hgsc.bcm.edu	37	chr5	177547301	177547301	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agcaatggcagcctgcacacGctggcctgccacccgcccct	10	19	0	0	rs374439291		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:177547301G>T	ENST00000274605.5	+	3	812	c.453G>T	c.(451-453)acG>acT	p.T151T		NM_015111.1	NP_055926.1	O15049	N4BP3_HUMAN	NEDD4 binding protein 3	151						cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)				breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCTGCACACGCTGGCCTGCC	0.697																																					p.T151T		Atlas-SNP	.											.	N4BP3	25	.	0			c.G453T						.	G		0,4406		0,0,2203	16	19	18		453	-10.3	0.3	5		18	1,8591		0,1,4295	no	coding-synonymous	N4BP3	NM_015111.1		0,1,6498	TT,TG,GG		0.0116,0.0,0.0077		151/545	177547301	1,12997	2203	4296	6499	SO:0001819	synonymous_variant	23138	exon3			GCACACGCTGGCC	AB002339	CCDS34307.1	5q35.3	2012-05-17				ENSG00000145911			29852	protein-coding gene	gene with protein product						9205841, 11717310	Standard	XM_006714834		Approved	LZTS4	uc003mik.1	O15049		ENST00000274605.5:c.453G>T	chr5.hg19:g.177547301G>T		109.0	0.0		130.0	24.0	NM_015111	B4DIL3|D3DWP3|Q6ZSQ6|Q7Z6I3	Silent	SNP	ENST00000274605.5	hg19	CCDS34307.1																																																																																			.	.		0.697	N4BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373552.2	NM_015111		T	177547301	G	T	177547301	2	4	197	1	0	0	0	0	0	0	0	1	10122	1074	38	1		1	N4BP3	5	177547301	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	527666	177547301	3367959	78	28988										
CLK4	57396	hgsc.bcm.edu	37	chr5	178043910	178043910	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gatcaatgcactctacaactTtgccaaaggctccttcaccc	5	15	3	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr5:178043910T>G	ENST00000316308.4	-	5	683	c.515A>C	c.(514-516)aAa>aCa	p.K172T	CLK4_ENST00000522749.1_5'UTR|RN7SKP70_ENST00000516655.1_RNA	NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	172	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		CTCTACAACTTTGCCAAAGGC	0.378																																					p.K172T		Atlas-SNP	.											.	CLK4	103	.	0			c.A515C						.						120	110	114					5																	178043910		2203	4300	6503	SO:0001583	missense	57396	exon5			ACAACTTTGCCAA	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.515A>C	chr5.hg19:g.178043910T>G	ENSP00000316948:p.Lys172Thr	280.0	0.0		277.0	58.0	NM_020666		Missense_Mutation	SNP	ENST00000316308.4	hg19	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	T	11.46	1.646827	0.29246	.	.	ENSG00000113240	ENST00000316308;ENST00000536763	T	0.65732	-0.17	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.71459	0.3342	L	0.39514	1.22	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.992;0.992	T	0.74506	-0.3643	10	0.87932	D	0	.	13.3639	0.60671	0.0:0.0:0.0:1.0	.	172;172;172	B7ZL31;B9EG64;Q9HAZ1	.;.;CLK4_HUMAN	T	172	ENSP00000316948:K172T	ENSP00000316948:K172T	K	-	2	0	CLK4	177976516	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.146000	0.71777	2.047000	0.60756	0.528000	0.53228	AAA	.	.		0.378	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			G	178043910	T	G	178043910	3	3	197	1	0	0	0	0	1	0	0	0	3541	1841	64	5	966	5	CLK4	5	178043910	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	496609	178043910	2871350	79	28989										
TRIM10	10107	hgsc.bcm.edu	37	chr6	30122220	30122220	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cgctggtggtcctcggacaaGaggagcttggggtgggaagt	19	7	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr6:30122220G>T	ENST00000449742.2	-	7	1047	c.972C>A	c.(970-972)ctC>ctA	p.L324L	TRIM10_ENST00000376704.3_Silent_p.L324L	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	324	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			ovary(1)	1						CCTCGGACAAGAGGAGCTTGG	0.537																																					p.L324L		Atlas-SNP	.											.	TRIM10	65	.	0			c.C972A						.						61	74	69					6																	30122220		1509	2708	4217	SO:0001819	synonymous_variant	10107	exon7			GGACAAGAGGAGC	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10072	protein-coding gene	gene with protein product		605701	"tripartite motif-containing 10"	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.972C>A	chr6.hg19:g.30122220G>T		39.0	0.0		50.0	5.0	NM_052828	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Silent	SNP	ENST00000449742.2	hg19	CCDS34375.1																																																																																			.	.		0.537	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1			T	30122220	G	T	30122220	2	4	197	1	0	0	0	0	0	0	0	1	16501	929	33	3		3	TRIM10	6	30122220	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10		30122220	140992847	80	28990										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33652240	33652240	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agaagaccaagtacggggacCgggtgagtgccctggtgggg	19	8	0	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr6:33652240C>T	ENST00000374316.5	+	38	6104	c.5044C>T	c.(5044-5046)Cgg>Tgg	p.R1682W	ITPR3_ENST00000605930.1_Missense_Mutation_p.R1682W			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1682					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GTACGGGGACCGGGTGAGTGC	0.632																																					p.R1682W		Atlas-SNP	.											.	ITPR3	409	.	0			c.C5044T						.						52	56	55					6																	33652240		2203	4300	6503	SO:0001583	missense	3710	exon37			GGGGACCGGGTGA	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.5044C>T	chr6.hg19:g.33652240C>T	ENSP00000363435:p.Arg1682Trp	94.0	0.0		138.0	11.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352482	0.82132	.	.	ENSG00000096433	ENST00000374316	D	0.90261	-2.64	5.02	4.09	0.47781	.	0.113529	0.64402	D	0.000018	D	0.86125	0.5858	L	0.34521	1.04	0.42224	D	0.991865	D	0.69078	0.997	P	0.53490	0.727	D	0.87687	0.2551	10	0.62326	D	0.03	-36.0857	10.928	0.47201	0.3833:0.6167:0.0:0.0	.	1682	Q14573	ITPR3_HUMAN	W	1682	ENSP00000363435:R1682W	ENSP00000363435:R1682W	R	+	1	2	ITPR3	33760218	0.959000	0.32827	0.998000	0.56505	0.929000	0.56500	2.197000	0.42696	2.306000	0.77630	0.650000	0.86243	CGG	.	.		0.632	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		T	33652240	C	T	33652240	3	4	197	1	0	0	0	0	1	0	0	0	7931	643	23	1	5190	1	ITPR3	6	33652240	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	3530020	33652240	137462827	81	28991										
XPO5	57510	hgsc.bcm.edu	37	chr6	43492932	43492932	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agggaattgaaggctgtaatTaatagcgctgtacaaacatc	10	6	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr6:43492932T>C	ENST00000265351.7	-	29	3297	c.3087A>G	c.(3085-3087)ttA>ttG	p.L1029L	POLR1C_ENST00000304004.3_Intron	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	1029					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			AGGCTGTAATTAATAGCGCTG	0.438																																					p.L1029L		Atlas-SNP	.											.	XPO5	79	.	0			c.A3087G						.						41	41	41					6																	43492932		1881	4115	5996	SO:0001819	synonymous_variant	57510	exon29			TGTAATTAATAGC	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.3087A>G	chr6.hg19:g.43492932T>C		70.0	0.0		72.0	12.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	hg19	CCDS47430.1																																																																																			.	.		0.438	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		C	43492932	T	C	43492932	2	2	197	1	0	0	0	0	0	0	0	1	17462	1751	61	2		2	XPO5	6	43492932	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	9840692	43492932	127622135	82	28992										
DST	667	hgsc.bcm.edu	37	chr6	56342211	56342211	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gatggagtcggggtggcagaTagccaaaacggtgtcgccca	16	9	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr6:56342211T>C	ENST00000361203.3	-	86	20654	c.20647A>G	c.(20647-20649)Atc>Gtc	p.I6883V	DST_ENST00000421834.2_Missense_Mutation_p.I4906V|DST_ENST00000370769.4_Missense_Mutation_p.I6994V|DST_ENST00000370754.5_Missense_Mutation_p.I7172V|DST_ENST00000312431.6_3'UTR|DST_ENST00000244364.6_Missense_Mutation_p.I4580V|DST_ENST00000446842.2_Missense_Mutation_p.I6668V|DST_ENST00000370788.2_Missense_Mutation_p.I4797V			Q03001	DYST_HUMAN	dystonin	6884					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GGGTGGCAGATAGCCAAAACG	0.453																																					p.I4580V		Atlas-SNP	.											.	DST	1427	.	0			c.A13738G						.						190	199	196					6																	56342211		1948	4157	6105	SO:0001583	missense	667	exon72			GGCAGATAGCCAA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.20647A>G	chr6.hg19:g.56342211T>C	ENSP00000354508:p.Ile6883Val	106.0	0.0		99.0	15.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	T	12.38	1.921875	0.33908	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.58	-1.57	0.08506	.	0.256160	0.27139	N	0.020746	T	0.14743	0.0356	N	0.08118	0	0.24783	N	0.992805	P;B;B;B;B	0.46277	0.875;0.035;0.017;0.001;0.0	P;B;B;B;B	0.48815	0.591;0.074;0.02;0.004;0.006	T	0.16041	-1.0416	9	0.28530	T	0.3	.	9.8118	0.40828	0.0:0.0642:0.4794:0.4564	.	4906;6994;7172;6992;4580	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	V	4580;7172;6994;4906;6668;4797;6883	ENSP00000244364:I4580V;ENSP00000359790:I7172V;ENSP00000359805:I6994V;ENSP00000400883:I4906V;ENSP00000393645:I6668V;ENSP00000359824:I4797V;ENSP00000354508:I6883V	ENSP00000244364:I4580V	I	-	1	0	DST	56450170	1.000000	0.71417	0.985000	0.45067	0.959000	0.62525	2.825000	0.48096	-0.387000	0.07809	-0.438000	0.05819	ATC	.	.		0.453	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56342211	T	C	56342211	3	2	197	1	0	0	0	0	1	0	0	0	4785	1406	49	2	1829	2	DST	6	56342211	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	12849279	56342211	114772856	83	28993										
ZNF451	26036	hgsc.bcm.edu	37	chr6	57012444	57012444	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtttacacatgagccggattCacggaggggcacatttaaat	11	8	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr6:57012444C>T	ENST00000370706.4	+	10	1805	c.1561C>T	c.(1561-1563)Cac>Tac	p.H521Y	RP11-203B9.4_ENST00000589549.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|ZNF451_ENST00000357489.3_Missense_Mutation_p.H521Y|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|ZNF451_ENST00000491832.2_Missense_Mutation_p.H521Y|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000589263.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	521					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GAGCCGGATTCACGGAGGGGC	0.403																																					p.H521Y		Atlas-SNP	.											.	ZNF451	181	.	0			c.C1561T						.						188	180	183					6																	57012444		2203	4300	6503	SO:0001583	missense	26036	exon10			CGGATTCACGGAG	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"Zinc fingers, C2H2-type"	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.1561C>T	chr6.hg19:g.57012444C>T	ENSP00000359740:p.His521Tyr	96.0	0.0		144.0	25.0	NM_001031623	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Missense_Mutation	SNP	ENST00000370706.4	hg19	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.226616	0.79576	.	.	ENSG00000112200	ENST00000370706;ENST00000357489;ENST00000491832	T;T;T	0.09163	3.01;3.01;3.01	5.41	5.41	0.78517	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	H	0.97806	4.08	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.85130	0.997;0.99;0.997;0.99	T	0.68625	-0.5359	10	0.87932	D	0	-15.7279	19.216	0.93778	0.0:1.0:0.0:0.0	.	521;521;521;521	Q9Y4E5-2;Q9Y4E5;E9PH99;Q4KMR5	.;ZN451_HUMAN;.;.	Y	521	ENSP00000359740:H521Y;ENSP00000350083:H521Y;ENSP00000421645:H521Y	ENSP00000350083:H521Y	H	+	1	0	ZNF451	57120403	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.142000	0.77339	2.529000	0.85273	0.650000	0.86243	CAC	.	.		0.403	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555		T	57012444	C	T	57012444	3	4	197	1	0	0	0	0	1	0	0	0	17937	826	29	3	1599	3	ZNF451	6	57012444	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	670233	57012444	114102623	84	28994										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72967920	72967920	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	atcaccgctcacgttcagtaTctcctcatcgcggcaatgat	7	14	5	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr6:72967920T>C	ENST00000521978.1	+	17	2863	c.2863T>C	c.(2863-2865)Tct>Cct	p.S955P	RIMS1_ENST00000425662.2_Missense_Mutation_p.S348P|RIMS1_ENST00000517827.1_Missense_Mutation_p.S414P|RIMS1_ENST00000520567.1_Missense_Mutation_p.S954P|RIMS1_ENST00000538414.1_5'UTR|RIMS1_ENST00000522291.1_Missense_Mutation_p.S954P|RIMS1_ENST00000348717.5_Missense_Mutation_p.S954P|RIMS1_ENST00000517960.1_Missense_Mutation_p.S954P|RIMS1_ENST00000491071.2_Missense_Mutation_p.S955P|RIMS1_ENST00000523963.1_Missense_Mutation_p.S429P|RIMS1_ENST00000264839.7_Missense_Mutation_p.S955P|RIMS1_ENST00000401910.3_Missense_Mutation_p.S428P|RIMS1_ENST00000518273.1_Missense_Mutation_p.S955P	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	955					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				ACGTTCAGTATCTCCTCATCG	0.463																																					p.S955P		Atlas-SNP	.											.	RIMS1	278	.	0			c.T2863C						.						92	87	89					6																	72967920		1992	4166	6158	SO:0001583	missense	22999	exon17			TCAGTATCTCCTC	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2863T>C	chr6.hg19:g.72967920T>C	ENSP00000428417:p.Ser955Pro	46.0	0.0		69.0	20.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.34|18.34	3.602249|3.602249	0.66445|0.66445	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.20200	.|2.35;2.35;2.37;2.35;2.43;2.44;2.44;2.35;2.38;2.48;2.45;2.4;2.45;2.09	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	.|0.000000	.|0.64402	.|D	.|0.000007	T|T	0.29355|0.29355	0.0731|0.0731	L|L	0.45137|0.45137	1.4|1.4	0.80722|0.80722	D|D	1|1	.|B;D;D;D;B;D;D;B;D;D;D;D	.|0.76494	.|0.103;0.995;0.999;0.999;0.054;0.999;0.977;0.33;0.987;0.998;0.999;0.999	.|B;D;D;D;B;D;P;B;D;D;D;D	.|0.87578	.|0.082;0.969;0.993;0.993;0.046;0.998;0.551;0.084;0.958;0.995;0.993;0.993	T|T	0.05649|0.05649	-1.0872|-1.0872	5|10	.|0.66056	.|D	.|0.02	-12.0825|-12.0825	15.0624|15.0624	0.71964|0.71964	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|414;429;955;414;428;954;207;955;954;208;955;955	.|B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5	.|.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN	T|P	528|955;955;955;954;955;954;955;954;955;954;954;955;428;429;348;348;414;180	.|ENSP00000430101:S955P;ENSP00000275037:S954P;ENSP00000264839:S955P;ENSP00000429959:S954P;ENSP00000430408:S955P;ENSP00000430502:S954P;ENSP00000430932:S954P;ENSP00000428417:S955P;ENSP00000385649:S428P;ENSP00000428328:S429P;ENSP00000411235:S348P;ENSP00000389503:S348P;ENSP00000428367:S414P;ENSP00000359448:S180P	.|ENSP00000264839:S955P	I|S	+|+	2|1	0|0	RIMS1|RIMS1	73024641|73024641	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.859000|0.859000	0.49053|0.49053	7.823000|7.823000	0.86660|0.86660	1.971000|1.971000	0.57363|0.57363	0.477000|0.477000	0.44152|0.44152	ATC|TCT	.	.		0.463	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			C	72967920	T	C	72967920	3	2	197	1	0	0	0	0	1	0	0	0	13382	1435	50	2	3092	2	RIMS1	6	72967920	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	15955476	72967920	98147147	85	28995										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75843108	75843108	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tggctgcagattcctaagaaTggcataattggtattcccgg	11	8	0	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr6:75843108T>A	ENST00000322507.8	-	34	6004	c.5695A>T	c.(5695-5697)Att>Ttt	p.I1899F	COL12A1_ENST00000416123.2_Missense_Mutation_p.I1899F|COL12A1_ENST00000483888.2_Missense_Mutation_p.I1899F|COL12A1_ENST00000345356.6_Missense_Mutation_p.I735F	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1899	Fibronectin type-III 14. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTCCTAAGAATGGCATAATTG	0.373																																					p.I1899F		Atlas-SNP	.											.	COL12A1	385	.	0			c.A5695T						.						115	105	108					6																	75843108		1856	4087	5943	SO:0001583	missense	1303	exon34			TAAGAATGGCATA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.5695A>T	chr6.hg19:g.75843108T>A	ENSP00000325146:p.Ile1899Phe	125.0	0.0		145.0	41.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.9|21.9	4.222114|4.222114	0.79464|0.79464	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000419671|ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	.|T;T;T;T	.|0.58060	.|0.36;0.36;0.36;0.36	5.4|5.4	4.24|4.24	0.50183|0.50183	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.080371	.|0.52532	.|D	.|0.000067	T|T	0.46718|0.46718	0.1407|0.1407	L|L	0.52573|0.52573	1.65|1.65	0.48571|0.48571	D|D	0.999672|0.999672	.|P;D	.|0.60575	.|0.941;0.988	.|P;P	.|0.55455	.|0.571;0.776	T|T	0.53078|0.53078	-0.8489|-0.8489	5|10	.|0.66056	.|D	.|0.02	.|.	8.3231|8.3231	0.32140|0.32140	0.0:0.149:0.0:0.851|0.0:0.149:0.0:0.851	.|.	.|735;1899	.|Q99715-2;Q99715	.|.;COCA1_HUMAN	L|F	633|1899;1899;735;1899;1899	.|ENSP00000325146:I1899F;ENSP00000305147:I735F;ENSP00000412864:I1899F;ENSP00000421216:I1899F	.|ENSP00000325146:I1899F	H|I	-|-	2|1	0|0	COL12A1|COL12A1	75899828|75899828	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.961000|0.961000	0.63080|0.63080	2.645000|2.645000	0.46621|0.46621	2.169000|2.169000	0.68431|0.68431	0.528000|0.528000	0.53228|0.53228	CAT|ATT	.	.		0.373	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75843108	T	A	75843108	3	1	197	1	0	0	0	0	1	0	0	0	3671	1464	51	4	3628	4	COL12A1	6	75843108	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	2875188	75843108	95271959	86	28996										
MYO6	4646	hgsc.bcm.edu	37	chr6	76596595	76596595	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ttaaggtgggcacactgaaaAaacgacttgataaatttaat	8	5	0	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr6:76596595A>G	ENST00000369977.3	+	25	2681	c.2542A>G	c.(2542-2544)Aaa>Gaa	p.K848E	MYO6_ENST00000369981.3_Missense_Mutation_p.K848E|MYO6_ENST00000369975.1_Missense_Mutation_p.K848E|MYO6_ENST00000369985.4_Missense_Mutation_p.K848E	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	848					actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		CACACTGAAAAAACGACTTGA	0.323																																					p.K848E		Atlas-SNP	.											.	MYO6	124	.	0			c.A2542G						.						84	89	88					6																	76596595		2203	4300	6503	SO:0001583	missense	4646	exon25			CTGAAAAAACGAC	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.2542A>G	chr6.hg19:g.76596595A>G	ENSP00000358994:p.Lys848Glu	123.0	0.0		180.0	26.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	hg19	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.568264	0.28003	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	D;D;D;T	0.89123	-2.47;-2.47;-2.45;1.99	5.93	4.71	0.59529	.	0.192580	0.53938	D	0.000057	T	0.79209	0.4407	L	0.54323	1.7	0.58432	D	0.999996	B;B	0.18741	0.007;0.03	B;B	0.18871	0.023;0.022	T	0.76152	-0.3064	10	0.26408	T	0.33	.	12.8806	0.58014	0.8644:0.1356:0.0:0.0	.	848;848	Q9UM54-2;Q9UM54-1	.;.	E	848	ENSP00000358998:K848E;ENSP00000359002:K848E;ENSP00000358994:K848E;ENSP00000358992:K848E	ENSP00000358992:K848E	K	+	1	0	MYO6	76653315	1.000000	0.71417	0.991000	0.47740	0.675000	0.39556	6.953000	0.75995	2.258000	0.74832	0.533000	0.62120	AAA	.	.		0.323	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		G	76596595	A	G	76596595	3	3	197	1	0	0	0	0	1	0	0	0	10090	15	1	2	2636	2	MYO6	6	76596595	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	753487	76596595	94518472	87	28997										
MYO6	4646	hgsc.bcm.edu	37	chr6	76599977	76599977	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agaaaggaagaggaggaaagGcggatgtgaggcatttatat	16	2	0	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr6:76599977G>A	ENST00000369977.3	+	26	3001	c.2862G>A	c.(2860-2862)agG>agA	p.R954R	MYO6_ENST00000369981.3_Silent_p.R954R|MYO6_ENST00000369975.1_Silent_p.R954R|MYO6_ENST00000369985.4_Silent_p.R954R	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	954	Glu-rich.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		AGGAGGAAAGGCGGATGTGAG	0.353																																					p.R954R		Atlas-SNP	.											.	MYO6	124	.	0			c.G2862A						.						80	98	92					6																	76599977		2201	4299	6500	SO:0001819	synonymous_variant	4646	exon26			GGAAAGGCGGATG	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.2862G>A	chr6.hg19:g.76599977G>A		501.0	0.0		601.0	88.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Silent	SNP	ENST00000369977.3	hg19	CCDS34487.1																																																																																			.	.		0.353	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		A	76599977	G	A	76599977	2	1	197	1	0	0	0	0	0	0	0	1	10090	1194	42	3		3	MYO6	6	76599977	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	3382	76599977	94515090	88	28998										
MYCT1	80177	hgsc.bcm.edu	37	chr6	153019044	153019044	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	acttatttccttttatgcgaAcacaagtatatgaggggttg	9	6	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr6:153019044A>G	ENST00000367245.5	+	1	15	c.7A>G	c.(7-9)Aca>Gca	p.T3A	MYCT1_ENST00000529453.1_Missense_Mutation_p.T3A	NM_025107.2	NP_079383.2	Q8N699	MYCT1_HUMAN	myc target 1	3						nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	20		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		TTTTATGCGAACACAAGTATA	0.328																																					p.T3A		Atlas-SNP	.											.	MYCT1	48	.	0			c.A7G						.						72	73	73					6																	153019044		2203	4297	6500	SO:0001583	missense	80177	exon1			ATGCGAACACAAG	AF527367	CCDS5239.1	6q25.1	2008-02-05			ENSG00000120279	ENSG00000120279			23172	protein-coding gene	gene with protein product						12477932	Standard	NM_025107		Approved	MTLC, FLJ21269	uc003qpc.4	Q8N699	OTTHUMG00000015850	ENST00000367245.5:c.7A>G	chr6.hg19:g.153019044A>G	ENSP00000356214:p.Thr3Ala	146.0	0.0		147.0	23.0	NM_025107	Q8N396|Q8TBE8|Q9H763	Missense_Mutation	SNP	ENST00000367245.5	hg19	CCDS5239.1	.	.	.	.	.	.	.	.	.	.	A	19.26	3.792706	0.70452	.	.	ENSG00000120279	ENST00000367245;ENST00000529453	T	0.32272	1.46	5.86	5.86	0.93980	.	0.345759	0.21124	N	0.079768	T	0.22627	0.0546	N	0.19112	0.55	0.27966	N	0.936584	D	0.69078	0.997	P	0.60789	0.879	T	0.14839	-1.0458	10	0.87932	D	0	-4.5686	11.0739	0.48019	0.8616:0.0:0.0:0.1384	.	3	Q8N699	MYCT1_HUMAN	A	3	ENSP00000356214:T3A	ENSP00000356214:T3A	T	+	1	0	MYCT1	153060737	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.452000	0.44961	2.244000	0.73946	0.528000	0.53228	ACA	.	.		0.328	MYCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042750.2	NM_025107		G	153019044	A	G	153019044	3	3	197	1	0	0	0	0	1	0	0	0	10031	43	2	2	9	2	MYCT1	6	153019044	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	76419067	153019044	18096023	89	28999										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7571326	7571326	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cttaaatgtctgcaggtcctTccaggaagaaaaaggtggat	11	7	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:7571326T>G	ENST00000399429.3	-	3	474	c.334A>C	c.(334-336)Aag>Cag	p.K112Q		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	112	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TGCAGGTCCTTCCAGGAAGAA	0.428																																					p.K112Q		Atlas-SNP	.											.	COL28A1	113	.	0			c.A334C						.						67	64	65					7																	7571326		1880	4116	5996	SO:0001583	missense	340267	exon3			GGTCCTTCCAGGA	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.334A>C	chr7.hg19:g.7571326T>G	ENSP00000382356:p.Lys112Gln	225.0	0.0		207.0	44.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	hg19	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.863256	0.51482	.	.	ENSG00000215018	ENST00000399429;ENST00000399419;ENST00000448652	D	0.83163	-1.69	4.2	4.2	0.49525	von Willebrand factor, type A (3);	0.167251	0.37955	U	0.001871	T	0.66781	0.2824	N	0.05351	-0.065	0.32474	N	0.5424	B	0.30482	0.281	B	0.31442	0.13	T	0.69397	-0.5156	10	0.20519	T	0.43	-5.9075	13.3961	0.60853	0.0:0.0:0.0:1.0	.	112	Q2UY09	COSA1_HUMAN	Q	112	ENSP00000382356:K112Q	ENSP00000382347:K112Q	K	-	1	0	COL28A1	7537851	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.543000	0.36147	1.911000	0.55334	0.533000	0.62120	AAG	.	.		0.428	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		G	7571326	T	G	7571326	3	3	197	1	0	0	0	0	1	0	0	0	3688	1792	62	5	3175	5	COL28A1	7	7571326	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10		7571326	151567337	90	29000										
FAM126A	84668	hgsc.bcm.edu	37	chr7	22985357	22985357	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	attggcatctgtcccagcccCacaaccaacagcagatgacg	8	15	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:22985357C>T	ENST00000432176.2	-	11	1649	c.1417G>A	c.(1417-1419)Ggg>Agg	p.G473R	FAM126A_ENST00000498833.1_5'Flank|FAM126A_ENST00000409923.1_3'UTR	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	473					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						GTCCCAGCCCCACAACCAACA	0.448																																					p.G473R		Atlas-SNP	.											.	FAM126A	53	.	0			c.G1417A						.						103	96	98					7																	22985357		2203	4299	6502	SO:0001583	missense	84668	exon11			CAGCCCCACAACC	BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"down regulated by Ctnnb1, a"	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.1417G>A	chr7.hg19:g.22985357C>T	ENSP00000403396:p.Gly473Arg	113.0	0.0		111.0	30.0	NM_032581	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Missense_Mutation	SNP	ENST00000432176.2	hg19	CCDS5377.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.559449	0.45590	.	.	ENSG00000122591	ENST00000432176	T	0.75938	-0.98	6.16	6.16	0.99307	.	0.430599	0.26638	N	0.023277	T	0.65228	0.2671	N	0.22421	0.69	0.80722	D	1	P	0.36733	0.567	B	0.38327	0.271	T	0.60172	-0.7315	10	0.15952	T	0.53	0.623	19.848	0.96722	0.0:1.0:0.0:0.0	.	473	Q9BYI3	HYCCI_HUMAN	R	473	ENSP00000403396:G473R	ENSP00000403396:G473R	G	-	1	0	FAM126A	22951882	0.996000	0.38824	0.999000	0.59377	0.995000	0.86356	4.188000	0.58351	2.937000	0.99478	0.650000	0.86243	GGG	.	.		0.448	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581		T	22985357	C	T	22985357	3	4	197	1	0	0	0	0	1	0	0	0	5434	594	21	3	152	3	FAM126A	7	22985357	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	15414031	22985357	136153306	91	29001										
HNRNPA2B1	3181	hgsc.bcm.edu	37	chr7	26232908	26232908	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cccatgttcctgctaccaccAaagtttccactcttcattgg	5	15	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:26232908A>G	ENST00000354667.4	-	10	1131	c.963T>C	c.(961-963)ttT>ttC	p.F321F	HNRNPA2B1_ENST00000356674.7_Silent_p.F309F|HNRNPA2B1_ENST00000476233.1_5'Flank	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	321	Gly-rich.|Nuclear targeting sequence. {ECO:0000250}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|RNA binding (GO:0003723)|single-stranded telomeric DNA binding (GO:0043047)		HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22						TGCTACCACCAAAGTTTCCAC	0.348			T	ETV1	prostate																																p.F321F		Atlas-SNP	.		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	.,2	HNRNPA2B1	70	.	0			c.T963C						.						122	118	119					7																	26232908		2203	4300	6503	SO:0001819	synonymous_variant	3181	exon10			ACCACCAAAGTTT	D28877	CCDS5397.1, CCDS43557.1	7p15	2013-02-12		2007-08-16	ENSG00000122566	ENSG00000122566		"RNA binding motif (RRM) containing"	5033	protein-coding gene	gene with protein product		600124		HNRPA2B1		8029005	Standard	NM_002137		Approved		uc003sxr.4	P22626	OTTHUMG00000023471	ENST00000354667.4:c.963T>C	chr7.hg19:g.26232908A>G		67.0	0.0		154.0	49.0	NM_031243	A8K064|P22627|Q9UC98|Q9UDJ2	Silent	SNP	ENST00000354667.4	hg19	CCDS43557.1																																																																																			.	.		0.348	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137		G	26232908	A	G	26232908	2	3	197	1	0	0	0	0	0	0	0	1	7268	127	5	2		2	HNRNPA2B1	7	26232908	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	3247551	26232908	132905755	92	29002										
HOXA3	3200	hgsc.bcm.edu	37	chr7	27149809	27149809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggggaagatttgtttggccaCtgtgggtgagttgagcaggg	19	4	0	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:27149809C>T	ENST00000396352.4	-	2	650	c.451G>A	c.(451-453)Gtg>Atg	p.V151M	HOXA-AS2_ENST00000518088.1_RNA|HOXA3_ENST00000521401.1_5'Flank|HOXA3_ENST00000317201.2_Missense_Mutation_p.V151M	NM_030661.4	NP_109377.1	O43365	HXA3_HUMAN	homeobox A3	151					angiogenesis (GO:0001525)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(18)|skin(1)	29						TGTTTGGCCACTGTGGGTGAG	0.582																																					p.V151M	Esophageal Squamous(136;1368 1743 5685 7935 50360)	Atlas-SNP	.											.	HOXA3	62	.	0			c.G451A						.						104	105	104					7																	27149809		2203	4300	6503	SO:0001583	missense	3200	exon2			TGGCCACTGTGGG		CCDS5404.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105997	ENSG00000105997		"Homeoboxes / ANTP class : HOXL subclass"	5104	protein-coding gene	gene with protein product		142954	"homeo box A3"	HOX1E, HOX1		1973146, 1358459	Standard	XM_005249730		Approved		uc011jzl.2	O43365	OTTHUMG00000023209	ENST00000396352.4:c.451G>A	chr7.hg19:g.27149809C>T	ENSP00000379640:p.Val151Met	78.0	0.0		116.0	15.0	NM_030661	A4D181	Missense_Mutation	SNP	ENST00000396352.4	hg19	CCDS5404.1	.	.	.	.	.	.	.	.	.	.	C	14.93	2.682593	0.47991	.	.	ENSG00000105997	ENST00000396352;ENST00000317201	T;T	0.07021	3.23;3.23	5.83	4.84	0.62591	.	0.230990	0.39834	N	0.001247	T	0.02267	0.0070	N	0.00538	-1.39	0.38306	D	0.94311	B	0.15473	0.013	B	0.13407	0.009	T	0.47824	-0.9087	10	0.30854	T	0.27	.	7.7092	0.28667	0.0:0.7623:0.0:0.2377	.	151	O43365	HXA3_HUMAN	M	151	ENSP00000379640:V151M;ENSP00000324884:V151M	ENSP00000324884:V151M	V	-	1	0	HOXA3	27116334	0.985000	0.35326	0.997000	0.53966	0.983000	0.72400	1.364000	0.34171	2.769000	0.95229	0.655000	0.94253	GTG	.	.		0.582	HOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358708.2			T	27149809	C	T	27149809	3	4	197	1	0	0	0	0	1	0	0	0	7302	565	20	3	888	3	HOXA3	7	27149809	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	916901	27149809	131988854	93	29003										
VPS41	27072	hgsc.bcm.edu	37	chr7	38783021	38783021	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cgtggtttgtcaatggaataTaaaatcaaatcttcccacag	7	8	3	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:38783021T>G	ENST00000310301.4	-	24	2157	c.2103A>C	c.(2101-2103)ttA>ttC	p.L701F	VPS41_ENST00000395969.2_Missense_Mutation_p.L676F	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	701					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						CAATGGAATATAAAATCAAAT	0.353																																					p.L701F		Atlas-SNP	.											.	VPS41	102	.	0			c.A2103C						.						138	131	133					7																	38783021		2203	4300	6503	SO:0001583	missense	27072	exon24			GGAATATAAAATC	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"vacuolar protein sorting 41 (yeast homolog)", "vacuolar protein sorting 41 (yeast)"			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.2103A>C	chr7.hg19:g.38783021T>G	ENSP00000309457:p.Leu701Phe	84.0	0.0		162.0	15.0	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	hg19	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.019161	0.54576	.	.	ENSG00000006715	ENST00000310301;ENST00000395969;ENST00000439468	T;T;T	0.19250	2.16;2.16;2.16	5.74	0.7	0.18099	Tetratricopeptide-like helical (1);	0.157757	0.46442	D	0.000297	T	0.16471	0.0396	L	0.29908	0.895	0.44380	D	0.997288	P;P;P	0.39883	0.693;0.693;0.693	B;B;B	0.42282	0.382;0.382;0.382	T	0.03576	-1.1023	10	0.59425	D	0.04	-9.7244	9.8084	0.40808	0.0:0.374:0.0:0.626	.	701;676;701	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	F	701;676;42	ENSP00000309457:L701F;ENSP00000379297:L676F;ENSP00000395410:L42F	ENSP00000309457:L701F	L	-	3	2	VPS41	38749546	0.621000	0.27077	0.998000	0.56505	0.915000	0.54546	-0.215000	0.09279	0.189000	0.20188	-0.263000	0.10527	TTA	.	.		0.353	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3			G	38783021	T	G	38783021	3	3	197	1	0	0	0	0	1	0	0	0	17225	1403	49	5	485	5	VPS41	7	38783021	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	11633212	38783021	120355642	94	29004										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83037794	83037794	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cactgtagagtccagcaaacAattcactacctacacgggag	8	12	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:83037794A>T	ENST00000307792.3	-	6	1027	c.560T>A	c.(559-561)tTg>tAg	p.L187*	SEMA3E_ENST00000427262.1_Nonsense_Mutation_p.L127*	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	187	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TCCAGCAAACAATTCACTACC	0.423																																					p.L187X		Atlas-SNP	.											.	SEMA3E	125	.	0			c.T560A						.						51	47	48					7																	83037794		2203	4300	6503	SO:0001587	stop_gained	9723	exon6			GCAAACAATTCAC	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.560T>A	chr7.hg19:g.83037794A>T	ENSP00000303212:p.Leu187*	104.0	0.0		125.0	23.0	NM_012431	B4E1P1|Q75M94|Q75M97	Nonsense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.446833	0.84101	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514;ENST00000442159	.	.	.	5.97	5.97	0.96955	.	0.073669	0.56097	D	0.000033	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.4383	0.83889	1.0:0.0:0.0:0.0	.	.	.	.	X	187;127;187;127	.	ENSP00000303212:L187X	L	-	2	0	SEMA3E	82875730	1.000000	0.71417	0.856000	0.33681	0.427000	0.31564	8.773000	0.91762	2.287000	0.76781	0.482000	0.46254	TTG	.	.		0.423	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		T	83037794	A	T	83037794	4	4	197	1	0	0	0	0	0	1	0	0	14043	131	5	4	1815	4	SEMA3E	7	83037794	Nonsense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	44254773	83037794	76100869	95	29005										
ASB4	51666	hgsc.bcm.edu	37	chr7	95125087	95125087	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	caggttactggttgcctagcTataaattgaagtcttcctgg	10	8	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:95125087T>C	ENST00000325885.5	+	2	276	c.205T>C	c.(205-207)Tat>Cat	p.Y69H	ASB4_ENST00000257621.4_3'UTR|ASB4_ENST00000428113.1_Missense_Mutation_p.Y69H	NM_016116.2	NP_057200.1	Q9Y574	ASB4_HUMAN	ankyrin repeat and SOCS box containing 4	69					intracellular signal transduction (GO:0035556)|positive regulation of vasculogenesis (GO:2001214)|protein autoubiquitination (GO:0051865)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|pancreas(1)|prostate(1)|skin(2)	20	all_cancers(62;2.27e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.218)|all_lung(186;0.246)		STAD - Stomach adenocarcinoma(171;0.0151)			GTTGCCTAGCTATAAATTGAA	0.408																																					p.Y69H		Atlas-SNP	.											.	ASB4	52	.	0			c.T205C						.						74	66	69					7																	95125087		2203	4300	6503	SO:0001583	missense	51666	exon2			CCTAGCTATAAAT	AF156779	CCDS5641.1, CCDS5642.1	7q21-q22	2013-01-10	2011-01-25		ENSG00000005981	ENSG00000005981		"Ankyrin repeat domain containing"	16009	protein-coding gene	gene with protein product		605761	"ankyrin repeat and SOCS box-containing 4"				Standard	NM_145872		Approved	ASB-4	uc011kij.2	Q9Y574	OTTHUMG00000153960	ENST00000325885.5:c.205T>C	chr7.hg19:g.95125087T>C	ENSP00000321388:p.Tyr69His	109.0	0.0		115.0	19.0	NM_016116	A4D1H6|O14586|Q14D68|Q8TBT2	Missense_Mutation	SNP	ENST00000325885.5	hg19	CCDS5641.1	.	.	.	.	.	.	.	.	.	.	T	19.41	3.822310	0.71028	.	.	ENSG00000005981	ENST00000325885;ENST00000428113	T;T	0.54675	0.56;0.56	5.35	4.12	0.48240	Ankyrin repeat-containing domain (1);	0.060741	0.64402	D	0.000002	T	0.55465	0.1922	L	0.27053	0.805	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.985	T	0.47649	-0.9101	10	0.19147	T	0.46	-15.2019	12.2489	0.54587	0.0:0.0:0.1417:0.8583	.	69;69	Q9Y574;Q14D68	ASB4_HUMAN;.	H	69	ENSP00000321388:Y69H;ENSP00000397070:Y69H	ENSP00000321388:Y69H	Y	+	1	0	ASB4	94963023	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	5.659000	0.68010	2.165000	0.68154	0.533000	0.62120	TAT	.	.		0.408	ASB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333225.2	NM_016116		C	95125087	T	C	95125087	3	2	197	1	0	0	0	0	1	0	0	0	1025	1522	53	2	211	2	ASB4	7	95125087	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	12087293	95125087	64013576	96	29006										
ACTL6B	51412	hgsc.bcm.edu	37	chr7	100246398	100246398	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	actggaatggccgtggtgtgGgtggctccactgtccagcac	15	11	0	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:100246398G>A	ENST00000160382.5	-	6	622	c.516C>T	c.(514-516)acC>acT	p.T172T		NM_016188.4	NP_057272.1	O94805	ACL6B_HUMAN	actin-like 6B	172					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|nervous system development (GO:0007399)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	structural constituent of cytoskeleton (GO:0005200)|transcription coactivator activity (GO:0003713)			endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					CCGTGGTGTGGGTGGCTCCAC	0.627																																					p.T172T		Atlas-SNP	.											.	ACTL6B	47	.	0			c.C516T						.						73	66	68					7																	100246398		2203	4300	6503	SO:0001819	synonymous_variant	51412	exon6			GGTGTGGGTGGCT	AB015906	CCDS5702.1	7q22	2008-02-01	2004-07-12	2004-07-14	ENSG00000077080	ENSG00000077080			160	protein-coding gene	gene with protein product		612458	"actin-like 6"	ACTL6		9799793	Standard	NM_016188		Approved	BAF53B	uc003uvy.3	O94805	OTTHUMG00000159661	ENST00000160382.5:c.516C>T	chr7.hg19:g.100246398G>A		69.0	0.0		88.0	16.0	NM_016188	A4D2D0|O75421	Silent	SNP	ENST00000160382.5	hg19	CCDS5702.1																																																																																			.	.		0.627	ACTL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356745.1	NM_016188		A	100246398	G	A	100246398	2	1	197	1	0	0	0	0	0	0	0	1	199	1219	43	3		3	ACTL6B	7	100246398	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	5121311	100246398	58892265	97	29007										
ORC5L	5001	hgsc.bcm.edu	37	chr7	103801580	103801580	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	acgatactatataatattgcTaataatctgtctagtggaaa	6	5	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:103801580T>C	ENST00000297431.4	-	12	1231	c.1089A>G	c.(1087-1089)ttA>ttG	p.L363L	ORC5_ENST00000545943.1_Silent_p.L231L	NM_002553.3	NP_002544.1	O43913	ORC5_HUMAN	origin recognition complex, subunit 5	363					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			kidney(1)|large_intestine(2)|lung(9)|pancreas(1)|upper_aerodigestive_tract(1)	14						ATAATATTGCTAATAATCTGT	0.353																																					p.L363L		Atlas-SNP	.											.	ORC5	48	.	0			c.A1089G						.						128	132	130					7																	103801580		2203	4300	6503	SO:0001819	synonymous_variant	5001	exon12			TATTGCTAATAAT		CCDS5734.1, CCDS47681.1	7q22.1	2014-06-13	2010-10-12	2010-10-12	ENSG00000164815	ENSG00000164815			8491	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 117"	602331	"origin recognition complex, subunit 5 (yeast homolog)-like", "origin recognition complex, subunit 5-like (yeast)", "origin recognition complex, subunit 5 homolog (yeast)"	ORC5L		9417919, 9829972	Standard	NM_002553		Approved	Orc5p, ORC5T, PPP1R117	uc003vcb.3	O43913	OTTHUMG00000157275	ENST00000297431.4:c.1089A>G	chr7.hg19:g.103801580T>C		113.0	0.0		121.0	25.0	NM_002553	A4D0P8|O60590|O95268	Silent	SNP	ENST00000297431.4	hg19	CCDS5734.1																																																																																			.	.		0.353	ORC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348286.1	NM_002553		C	103801580	T	C	103801580	2	2	197	1	0	0	0	0	0	0	0	1	11274	1519	53	2		2	ORC5L	7	103801580	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	3555182	103801580	55337083	98	29008										
CADPS2	93664	hgsc.bcm.edu	37	chr7	121985695	121985695	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gaatatcttggttttgccgaAcaaacataatataggtgtct	8	6	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:121985695A>T	ENST00000449022.2	-	28	3564	c.3545T>A	c.(3544-3546)gTt>gAt	p.V1182D	CADPS2_ENST00000334010.7_Missense_Mutation_p.V1180D|RP5-1101C3.1_ENST00000593910.1_RNA|RP5-1101C3.1_ENST00000591140.1_RNA|RP5-1101C3.1_ENST00000602012.1_RNA|CADPS2_ENST00000412584.2_Missense_Mutation_p.V1141D|RP5-1101C3.1_ENST00000482375.1_RNA|CADPS2_ENST00000313070.7_Missense_Mutation_p.V1141D|RP5-1101C3.1_ENST00000602199.1_RNA	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	1182					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						GTTTTGCCGAACAAACATAAT	0.368																																					p.V1186D		Atlas-SNP	.											.	CADPS2	116	.	0			c.T3557A						.						173	165	167					7																	121985695		1819	4080	5899	SO:0001583	missense	93664	exon28			TGCCGAACAAACA		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.3545T>A	chr7.hg19:g.121985695A>T	ENSP00000398481:p.Val1182Asp	63.0	0.0		56.0	11.0	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	hg19	CCDS55158.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	34|34|34	5.308313|5.308313|5.308313	0.95629|0.95629|0.95629	.|.|.	.|.|.	ENSG00000081803|ENSG00000081803|ENSG00000081803	ENST00000397721|ENST00000462699|ENST00000360097;ENST00000313070;ENST00000334010;ENST00000420900;ENST00000545465;ENST00000412584;ENST00000449022	.|.|T;T;T;T	.|.|0.36878	.|.|1.23;1.23;1.23;1.23	6.08|6.08|6.08	6.08|6.08|6.08	0.98989|0.98989|0.98989	.|.|.	.|.|0.073354	.|.|0.56097	.|.|D	.|.|0.000027	.|T|T	.|0.60881|0.60881	.|0.2303|0.2303	M|M|M	0.78637|0.78637|0.78637	2.42|2.42|2.42	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;P;D;D	.|.|0.67145	.|.|0.995;0.942;0.995;0.996	.|.|P;P;P;D	.|.|0.63877	.|.|0.883;0.786;0.883;0.919	.|T|T	.|0.65228|0.65228	.|-0.6219|-0.6219	.|5|10	.|.|0.87932	.|.|D	.|.|0	-20.8227|-20.8227|-20.8227	16.6438|16.6438|16.6438	0.85155|0.85155|0.85155	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|.|1186;1141;1182;1136	.|.|B7ZM57;Q86UW7-2;Q86UW7;Q86UW7-3	.|.|.;.;CAPS2_HUMAN;.	X|I|D	784|376|355;1141;1180;1187;1108;1141;1182	.|.|ENSP00000325581:V1141D;ENSP00000333940:V1180D;ENSP00000400401:V1141D;ENSP00000398481:V1182D	.|.|ENSP00000325581:V1141D	C|F|V	-|-|-	3|1|2	2|0|0	CADPS2|CADPS2|CADPS2	121772931|121772931|121772931	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.996000|0.996000|0.996000	0.88848|0.88848|0.88848	9.339000|9.339000|9.339000	0.96797|0.96797|0.96797	2.333000|2.333000|2.333000	0.79357|0.79357|0.79357	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	TGT|TTC|GTT	.	.		0.368	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		T	121985695	A	T	121985695	3	4	197	1	0	0	0	0	1	0	0	0	2573	43	2	4	357	4	CADPS2	7	121985695	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	18184115	121985695	37152968	99	29009										
GRM8	2918	hgsc.bcm.edu	37	chr7	126883030	126883030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aattgcataaagcatggcctCcagtctgtgaatcccctttt	7	11	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:126883030C>T	ENST00000339582.2	-	2	1037	c.229G>A	c.(229-231)Gag>Aag	p.E77K	GRM8_ENST00000444921.2_Missense_Mutation_p.E77K|GRM8_ENST00000358373.3_Missense_Mutation_p.E77K|GRM8_ENST00000405249.1_Missense_Mutation_p.E77K			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	77					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				AGCATGGCCTCCAGTCTGTGA	0.532										HNSCC(24;0.065)																											p.E77K		Atlas-SNP	.											.	GRM8	377	.	0			c.G229A						.						100	74	83					7																	126883030		2203	4300	6503	SO:0001583	missense	2918	exon1			TGGCCTCCAGTCT		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.229G>A	chr7.hg19:g.126883030C>T	ENSP00000344173:p.Glu77Lys	110.0	0.0		89.0	26.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	hg19	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.023426	0.93462	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249;ENST00000457830	T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07	6.07	6.07	0.98685	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.89560	0.6750	M	0.84326	2.69	0.80722	D	1	D;D	0.76494	0.996;0.999	D;D	0.79784	0.987;0.993	D	0.89845	0.4005	10	0.87932	D	0	.	19.6475	0.95784	0.0:1.0:0.0:0.0	.	77;77	O00222-2;O00222	.;GRM8_HUMAN	K	77	ENSP00000344173:E77K;ENSP00000409790:E77K;ENSP00000351142:E77K;ENSP00000385731:E77K;ENSP00000415522:E77K	ENSP00000344173:E77K	E	-	1	0	GRM8	126670266	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.885000	0.99019	0.655000	0.94253	GAG	.	.		0.532	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			T	126883030	C	T	126883030	3	4	197	1	0	0	0	0	1	0	0	0	6812	864	30	3	2587	3	GRM8	7	126883030	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	4897335	126883030	32255633	100	29010										
MKLN1	4289	hgsc.bcm.edu	37	chr7	131113817	131113817	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtttatttgtttggtggctgGgatggaacacaagatcttgc	13	5	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:131113817G>A	ENST00000352689.6	+	9	913	c.873G>A	c.(871-873)tgG>tgA	p.W291*	MKLN1_ENST00000421797.2_Nonsense_Mutation_p.W199*	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	291					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					TTGGTGGCTGGGATGGAACAC	0.403																																					p.W291X		Atlas-SNP	.											.	MKLN1	67	.	0			c.G873A						.						128	123	125					7																	131113817		2203	4300	6503	SO:0001587	stop_gained	4289	exon9			TGGCTGGGATGGA	AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.873G>A	chr7.hg19:g.131113817G>A	ENSP00000323527:p.Trp291*	103.0	0.0		104.0	28.0	NM_013255	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Nonsense_Mutation	SNP	ENST00000352689.6	hg19	CCDS34754.1	.	.	.	.	.	.	.	.	.	.	G	38	6.704980	0.97776	.	.	ENSG00000128585	ENST00000421797;ENST00000352689	.	.	.	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.46	19.5352	0.95251	0.0:0.0:1.0:0.0	.	.	.	.	X	199;291	.	ENSP00000323527:W291X	W	+	3	0	MKLN1	130764357	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.651000	0.98493	2.850000	0.98022	0.650000	0.86243	TGG	.	.		0.403	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255		A	131113817	G	A	131113817	4	1	197	1	0	0	0	0	0	1	0	0	9612	1241	43	3	940	3	MKLN1	7	131113817	Nonsense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	4230787	131113817	28024846	101	29011										
PODXL	5420	hgsc.bcm.edu	37	chr7	131241029	131241029	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggccactcaccattctgggaGggcgacggcgacggcgacgg	17	13	2	0	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000322985.9_Silent_p.P30P|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000541194.1_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		Atlas-SNP	.											.	PODXL	53	.	0			c.C90G						.						5	7	6					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	chr7.hg19:g.131241029G>C		86.0	0.0		93.0	7.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		C	131241029	G	C	131241029	2	2	197	1	0	0	0	0	0	0	0	1	12189	987	35	4		4	PODXL	7	131241029	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	127212	131241029	27897634	102	29012										
DOCK5	80005	hgsc.bcm.edu	37	chr8	25154121	25154121	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tgccctcttcaaggcccatgAggtggcctccaaaaggattg	11	12	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:25154121A>T	ENST00000276440.7	+	7	607	c.563A>T	c.(562-564)gAg>gTg	p.E188V	DOCK5_ENST00000481100.1_Missense_Mutation_p.E188V	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	188					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		AAGGCCCATGAGGTGGCCTCC	0.488																																					p.E188V	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.A563T						.						78	71	74					8																	25154121		2203	4300	6503	SO:0001583	missense	80005	exon7			CCCATGAGGTGGC		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.563A>T	chr8.hg19:g.25154121A>T	ENSP00000276440:p.Glu188Val	127.0	0.0		83.0	19.0	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	hg19	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	A	12.42	1.931987	0.34096	.	.	ENSG00000147459	ENST00000481100;ENST00000276440	T;T	0.58940	0.3;0.3	5.65	3.2	0.36748	.	0.058524	0.64402	N	0.000002	T	0.50188	0.1601	L	0.49778	1.585	0.58432	D	0.999996	B	0.33826	0.427	B	0.36885	0.235	T	0.34403	-0.9830	10	0.23891	T	0.37	.	11.1039	0.48190	0.7534:0.0:0.0:0.2466	.	188	Q9H7D0	DOCK5_HUMAN	V	188	ENSP00000429737:E188V;ENSP00000276440:E188V	ENSP00000276440:E188V	E	+	2	0	DOCK5	25210038	1.000000	0.71417	0.471000	0.27229	0.370000	0.29829	6.876000	0.75556	0.517000	0.28361	-0.301000	0.09380	GAG	.	.		0.488	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		T	25154121	A	T	25154121	3	4	197	1	0	0	0	0	1	0	0	0	4692	304	11	4	589	4	DOCK5	8	25154121	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10		25154121	121209901	103	29013										
ADAM18	8749	hgsc.bcm.edu	37	chr8	39564351	39564351	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtcaatgcttccctggacatAgacctccagattgtaaattc	7	11	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:39564351A>C	ENST00000265707.5	+	18	1990	c.1945A>C	c.(1945-1947)Aga>Cga	p.R649R	ADAM18_ENST00000541111.1_Silent_p.R63R|ADAM18_ENST00000379866.1_Silent_p.R625R|ADAM18_ENST00000523755.1_3'UTR	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	649	EGF-like.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			CCCTGGACATAGACCTCCAGA	0.348																																					p.R649R		Atlas-SNP	.											.	ADAM18	169	.	0			c.A1945C						.						107	108	108					8																	39564351		2203	4299	6502	SO:0001819	synonymous_variant	8749	exon18			GGACATAGACCTC	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1945A>C	chr8.hg19:g.39564351A>C		132.0	0.0		63.0	38.0	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Silent	SNP	ENST00000265707.5	hg19	CCDS6113.1																																																																																			.	.		0.348	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		C	39564351	A	C	39564351	2	2	197	1	0	0	0	0	0	0	0	1	239	412	15	5		5	ADAM18	8	39564351	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	14410230	39564351	106799671	104	29014										
VCPIP1	80124	hgsc.bcm.edu	37	chr8	67547274	67547274	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	caactgaagtttccctagctCttggatcaaggtgtgggtta	11	8	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:67547274C>T	ENST00000310421.4	-	3	3389	c.3131G>A	c.(3130-3132)aGa>aAa	p.R1044K		NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	1044					endoplasmic reticulum membrane fusion (GO:0016320)|Golgi reassembly (GO:0090168)|mitotic nuclear division (GO:0007067)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	ubiquitin-specific protease activity (GO:0004843)			breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			TTCCCTAGCTCTTGGATCAAG	0.403																																					p.R1044K	NSCLC(179;265 2915 6144 43644)	Atlas-SNP	.											.	VCPIP1	110	.	0			c.G3131A						.						169	165	166					8																	67547274		2203	4300	6503	SO:0001583	missense	80124	exon3			CTAGCTCTTGGAT	AB058753	CCDS6192.1	8q13	2014-02-24			ENSG00000175073	ENSG00000175073		"OTU domain containing"	30897	protein-coding gene	gene with protein product		611745				11347906, 12509440	Standard	NM_025054		Approved	VCIP135, KIAA1850, FLJ23132, DUBA3	uc003xwn.3	Q96JH7	OTTHUMG00000164560	ENST00000310421.4:c.3131G>A	chr8.hg19:g.67547274C>T	ENSP00000309031:p.Arg1044Lys	88.0	0.0		73.0	20.0	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Missense_Mutation	SNP	ENST00000310421.4	hg19	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.473504	0.43942	.	.	ENSG00000175073	ENST00000310421	T	0.30714	1.52	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.29716	0.0742	N	0.20986	0.625	0.37482	D	0.916034	P	0.36392	0.551	P	0.44394	0.448	T	0.15292	-1.0442	10	0.45353	T	0.12	-14.1577	13.8168	0.63297	0.0:0.9305:0.0:0.0695	.	1044	Q96JH7	VCIP1_HUMAN	K	1044	ENSP00000309031:R1044K	ENSP00000309031:R1044K	R	-	2	0	VCPIP1	67709828	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.882000	0.48546	2.894000	0.99253	0.591000	0.81541	AGA	.	.		0.403	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			T	67547274	C	T	67547274	3	4	197	1	0	0	0	0	1	0	0	0	17156	913	32	3	541	3	VCPIP1	8	67547274	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	27982923	67547274	78816748	105	29015										
TERF1	7013	hgsc.bcm.edu	37	chr8	73958317	73958317	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gacaagtgtcatgttaaaagAcagatggaggaccatgaaga	12	5	1	4			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:73958317A>G	ENST00000276603.5	+	10	1288	c.1265A>G	c.(1264-1266)gAc>gGc	p.D422G	TERF1_ENST00000276602.6_Missense_Mutation_p.D402G|RP11-531A24.7_ENST00000607665.1_RNA	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	422	HTH myb-type. {ECO:0000255|PROSITE- ProRule:PRU00625}.				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			ATGTTAAAAGACAGATGGAGG	0.368																																					p.D422G		Atlas-SNP	.											.	TERF1	48	.	0			c.A1265G						.						56	56	56					8																	73958317		2202	4296	6498	SO:0001583	missense	7013	exon10			TAAAAGACAGATG	U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.1265A>G	chr8.hg19:g.73958317A>G	ENSP00000276603:p.Asp422Gly	287.0	0.0		456.0	220.0	NM_017489	A7XP29|Q15553|Q8NHT6|Q93029	Missense_Mutation	SNP	ENST00000276603.5	hg19	CCDS6211.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.337322	0.81911	.	.	ENSG00000147601	ENST00000276603;ENST00000276602	T;T	0.45276	0.9;0.9	5.52	5.52	0.82312	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.73032	0.3535	M	0.93283	3.4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.81048	-0.1109	10	0.87932	D	0	.	14.6385	0.68706	1.0:0.0:0.0:0.0	.	402;422	P54274-2;P54274	.;TERF1_HUMAN	G	422;402	ENSP00000276603:D422G;ENSP00000276602:D402G	ENSP00000276602:D402G	D	+	2	0	TERF1	74120871	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.093000	0.76937	2.096000	0.63516	0.455000	0.32223	GAC	.	.		0.368	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		G	73958317	A	G	73958317	3	3	197	1	0	0	0	0	1	0	0	0	15776	275	10	2	1303	2	TERF1	8	73958317	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	6411043	73958317	72405705	106	29016										
NBN	4683	hgsc.bcm.edu	37	chr8	90996753	90996753	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggcttcccttctgcccttacCtcctgccgggcccgcggcgg	12	19	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:90996753C>A	ENST00000265433.3	-	1	191	c.37G>T	c.(37-39)Gga>Tga	p.G13*	NBN_ENST00000409330.1_5'Flank	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	13					blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			CTGCCCTTACCTCCTGCCGGG	0.706								Homologous recombination			OREG0018856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G13X		Atlas-SNP	.											.	NBN	86	.	0			c.G37T						.						20	23	22					8																	90996753		2201	4298	6499	SO:0001630	splice_region_variant	4683	exon1			CCTTACCTCCTGC	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"Nijmegen breakage syndrome 1 (nibrin)"	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.37+1G>T	chr8.hg19:g.90996753C>A		382.0	0.0	1279	611.0	74.0	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Nonsense_Mutation	SNP	ENST00000265433.3	hg19	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.283662	0.80803	.	.	ENSG00000104320	ENST00000265433;ENST00000452387;ENST00000519426	.	.	.	3.72	3.72	0.42706	.	0.119030	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.236	12.6752	0.56891	0.0:1.0:0.0:0.0	.	.	.	.	X	13	.	.	G	-	1	0	NBN	91065929	1.000000	0.71417	0.998000	0.56505	0.105000	0.19272	3.523000	0.53488	2.060000	0.61445	0.460000	0.39030	GGA	.	.		0.706	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	Nonsense_Mutation	A	90996753	C	A	90996753	5	1	197	1	0	0	0	0	0	0	1	0	10200	695	24	3	2291	3	NBN	8	90996753	Splice_Site	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	17038436	90996753	55367269	107	29017										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	93026961	93026961	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gattagccagagaggaggagGaagaagaggaaggcccattg	17	5	0	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:93026961G>A	ENST00000523629.1	-	4	768	c.314C>T	c.(313-315)tCc>tTc	p.S105F	RUNX1T1_ENST00000521553.1_Missense_Mutation_p.S68F|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.S105F|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.S78F|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.S78F|RUNX1T1_ENST00000522163.1_5'Flank|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.S68F|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.S68F|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.S68F|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.S116F	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	105	Poly-Ser.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			AGAGGAGGAGGAAGAAGAGGA	0.547																																					p.S164F		Atlas-SNP	.											.,3	RUNX1T1	516	.	0			c.C491T						.						59	61	60					8																	93026961		2203	4300	6503	SO:0001583	missense	862	exon4			GAGGAGGAAGAAG	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.314C>T	chr8.hg19:g.93026961G>A	ENSP00000428543:p.Ser105Phe	89.0	0.0		123.0	22.0	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	hg19	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.970520	0.92919	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844;ENST00000521553;ENST00000518992;ENST00000521054;ENST00000519847;ENST00000517792;ENST00000522467;ENST00000517919;ENST00000521733;ENST00000520556;ENST00000521319;ENST00000520583;ENST00000523168;ENST00000518823	T;T;T;T;T;T;T;T;T;T;T	0.50548	1.26;1.27;1.26;1.27;1.27;1.27;1.26;1.27;0.79;0.74;1.38	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.64907	0.2641	L	0.47190	1.495	0.80722	D	1	D;D;D;D;D	0.76494	0.997;0.999;0.992;0.999;0.992	P;D;D;D;D	0.68943	0.904;0.961;0.934;0.961;0.945	T	0.63611	-0.6598	10	0.72032	D	0.01	-15.3138	20.6013	0.99457	0.0:0.0:1.0:0.0	.	116;116;78;105;78	E7EPN4;B7Z4P4;B2R6I9;Q06455;Q06455-2	.;.;.;MTG8_HUMAN;.	F	105;78;105;68;68;68;116;78;68;105;68;105;68;105;105;78;68;68;105;105;78	ENSP00000428543:S105F;ENSP00000379520:S78F;ENSP00000265814:S105F;ENSP00000353504:S68F;ENSP00000390137:S68F;ENSP00000428742:S68F;ENSP00000402257:S116F;ENSP00000430728:S78F;ENSP00000429728:S68F;ENSP00000431094:S105F;ENSP00000427763:S68F	ENSP00000265814:S105F	S	-	2	0	RUNX1T1	93096137	1.000000	0.71417	0.994000	0.49952	0.965000	0.64279	9.823000	0.99369	2.878000	0.98634	0.650000	0.86243	TCC	.	.		0.547	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		A	93026961	G	A	93026961	3	1	197	1	0	0	0	0	1	0	0	0	13762	1174	41	3	1536	3	RUNX1T1	8	93026961	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	2030208	93026961	53337061	108	29018										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	93088272	93088272	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ctccaagtgtttcttttgacAgatatcattctccaccaatc	4	12	3	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:93088272A>T	ENST00000523629.1	-	2	463	c.9T>A	c.(7-9)tcT>tcA	p.S3S	RUNX1T1_ENST00000265814.3_Silent_p.S3S|RUNX1T1_ENST00000518844.1_5'UTR|RUNX1T1_ENST00000522163.1_5'UTR|RUNX1T1_ENST00000520724.1_Intron|RUNX1T1_ENST00000360348.2_Intron|RUNX1T1_ENST00000436581.2_Intron	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	3					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			TTCTTTTGACAGATATCATTC	0.393																																					p.S3S		Atlas-SNP	.											.	RUNX1T1	516	.	0			c.T9A						.						200	189	193					8																	93088272		2203	4299	6502	SO:0001819	synonymous_variant	862	exon2			TTTGACAGATATC	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.9T>A	chr8.hg19:g.93088272A>T		43.0	0.0		79.0	9.0	NM_001198628	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Silent	SNP	ENST00000523629.1	hg19	CCDS6256.1																																																																																			.	.		0.393	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		T	93088272	A	T	93088272	2	4	197	1	0	0	0	0	0	0	0	1	13762	175	7	4		4	RUNX1T1	8	93088272	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	61311	93088272	53275750	109	29019										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100115264	100115264	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tactaaaatatgttgaagatGatatcgtcctttccgtcaat	6	7	1	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:100115264G>T	ENST00000358544.2	+	5	607	c.496G>T	c.(496-498)Gat>Tat	p.D166Y	VPS13B_ENST00000395996.1_Missense_Mutation_p.D166Y|VPS13B_ENST00000357162.2_Missense_Mutation_p.D166Y|VPS13B_ENST00000355155.1_Missense_Mutation_p.D166Y|VPS13B_ENST00000441350.2_Missense_Mutation_p.D166Y	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	166					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TGTTGAAGATGATATCGTCCT	0.318																																					p.D166Y	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.G496T						.						132	126	128					8																	100115264		2203	4300	6503	SO:0001583	missense	157680	exon5			GAAGATGATATCG	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.496G>T	chr8.hg19:g.100115264G>T	ENSP00000351346:p.Asp166Tyr	159.0	0.0		254.0	19.0	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.212343	0.58452	.	.	ENSG00000132549	ENST00000355155;ENST00000357162;ENST00000358544;ENST00000395996;ENST00000441350	T;T;T;T;D	0.85088	-1.41;-0.74;-0.74;-0.43;-1.94	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	D	0.93177	0.7827	M	0.79693	2.465	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.998;1.0;1.0;1.0	D	0.93132	0.6534	10	0.87932	D	0	.	20.3552	0.98837	0.0:0.0:1.0:0.0	.	166;166;166;166;166	Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3;Q7Z7G8-4;Q7Z7G8-5	.;VP13B_HUMAN;.;.;.	Y	166	ENSP00000347281:D166Y;ENSP00000349685:D166Y;ENSP00000351346:D166Y;ENSP00000379318:D166Y;ENSP00000398472:D166Y	ENSP00000347281:D166Y	D	+	1	0	VPS13B	100184440	1.000000	0.71417	1.000000	0.80357	0.055000	0.15305	9.086000	0.94088	2.812000	0.96745	0.557000	0.71058	GAT	.	.		0.318	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100115264	G	T	100115264	3	4	197	1	0	0	0	0	1	0	0	0	17205	1290	45	3	510	3	VPS13B	8	100115264	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	7026992	100115264	46248758	110	29020										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100874106	100874106	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ccggcaggaggagtggcggcGgcagctccccgagagcctgg	19	13	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:100874106G>A	ENST00000358544.2	+	58	11333	c.11222G>A	c.(11221-11223)cGg>cAg	p.R3741Q	VPS13B_ENST00000357162.2_Missense_Mutation_p.R3716Q|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3741					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GAGTGGCGGCGGCAGCTCCCC	0.672																																					p.R3741Q	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.G11222A						.						26	21	22					8																	100874106		2186	4290	6476	SO:0001583	missense	157680	exon58			GGCGGCGGCAGCT	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.11222G>A	chr8.hg19:g.100874106G>A	ENSP00000351346:p.Arg3741Gln	79.0	0.0		157.0	30.0	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	37	6.070232	0.97256	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.74106	-0.81;-0.81	5.79	5.79	0.91817	Autophagy-related, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87341	0.6153	M	0.79614	2.46	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.87576	0.2481	10	0.66056	D	0.02	.	20.04	0.97581	0.0:0.0:1.0:0.0	.	3716;3741	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	Q	3716;3741	ENSP00000349685:R3716Q;ENSP00000351346:R3741Q	ENSP00000349685:R3716Q	R	+	2	0	VPS13B	100943282	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.441000	0.97557	2.733000	0.93635	0.655000	0.94253	CGG	.	.		0.672	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		A	100874106	G	A	100874106	3	1	197	1	0	0	0	0	1	0	0	0	17205	1116	39	1	11642	1	VPS13B	8	100874106	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	758842	100874106	45489916	111	29021										
SLC25A32	81034	hgsc.bcm.edu	37	chr8	104415433	104415433	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ttcatacttatatattttcaCaagtgtatcaaacattcctt	2	8	3	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:104415433C>G	ENST00000297578.4	-	4	677	c.511G>C	c.(511-513)Gtg>Ctg	p.V171L	SLC25A32_ENST00000523701.1_5'Flank|SLC25A32_ENST00000543107.1_Missense_Mutation_p.V39L	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32	171					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	TATATTTTCACAAGTGTATCA	0.318																																					p.V171L		Atlas-SNP	.											.	SLC25A32	36	.	0			c.G511C						.						76	74	75					8																	104415433		2203	4300	6503	SO:0001583	missense	81034	exon4			TTTTCACAAGTGT	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"Solute carriers"	29683	protein-coding gene	gene with protein product		610815	"solute carrier family 25, member 32"			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790	ENST00000297578.4:c.511G>C	chr8.hg19:g.104415433C>G	ENSP00000297578:p.Val171Leu	85.0	0.0		152.0	14.0	NM_030780	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	hg19	CCDS6300.1	.	.	.	.	.	.	.	.	.	.	C	7.623	0.677227	0.14841	.	.	ENSG00000164933	ENST00000297578;ENST00000424899;ENST00000543107	T;T	0.77877	-1.13;-1.13	5.91	-0.32	0.12721	Mitochondrial carrier domain (2);	0.493212	0.23065	N	0.052331	T	0.57036	0.2026	L	0.37630	1.12	0.29827	N	0.83038	B	0.06786	0.001	B	0.10450	0.005	T	0.33007	-0.9885	10	0.14656	T	0.56	-18.6451	0.8017	0.01076	0.2255:0.3303:0.22:0.2242	.	171	Q9H2D1	MFTC_HUMAN	L	171;155;39	ENSP00000297578:V171L;ENSP00000443497:V39L	ENSP00000297578:V171L	V	-	1	0	SLC25A32	104484609	0.140000	0.22579	0.943000	0.38184	0.998000	0.95712	-0.312000	0.08113	-0.372000	0.07992	0.579000	0.79373	GTG	.	.		0.318	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780		G	104415433	C	G	104415433	3	3	197	1	0	0	0	0	1	0	0	0	14511	478	17	4	452	4	SLC25A32	8	104415433	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	3541327	104415433	41948589	112	29022										
ANGPT1	284	hgsc.bcm.edu	37	chr8	108296966	108296966	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tcatactgtgaataggctcgGttcccttcccagtccattaa	7	12	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:108296966G>C	ENST00000520734.1	-	6	834	c.549C>G	c.(547-549)aaC>aaG	p.N183K	ANGPT1_ENST00000518386.1_Intron|ANGPT1_ENST00000520052.1_Missense_Mutation_p.N182K			Q15389	ANGP1_HUMAN	angiopoietin 1	383					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			AATAGGCTCGGTTCCCTTCCC	0.423																																					p.N383K		Atlas-SNP	.											.	ANGPT1	111	.	0			c.C1149G						.						151	128	136					8																	108296966		2203	4300	6503	SO:0001583	missense	284	exon7			GGCTCGGTTCCCT	D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"Fibrinogen C domain containing"	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.549C>G	chr8.hg19:g.108296966G>C	ENSP00000430750:p.Asn183Lys	136.0	0.0		177.0	9.0	NM_001146	Q5HYA0	Missense_Mutation	SNP	ENST00000520734.1	hg19		.	.	.	.	.	.	.	.	.	.	G	20.7	4.038845	0.75617	.	.	ENSG00000154188	ENST00000517746;ENST00000297450;ENST00000520734;ENST00000520052	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.73	5.73	0.89815	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.081401	0.85682	D	0.000000	T	0.41119	0.1145	M	0.62266	1.93	0.50039	D	0.999843	B;D;D	0.55800	0.031;0.973;0.973	B;P;P	0.56563	0.041;0.801;0.801	T	0.15435	-1.0437	10	0.12103	T	0.63	.	10.3271	0.43801	0.1456:0.0:0.8544:0.0	.	182;383;383	E7ERK4;Q5HYA0;Q15389	.;.;ANGP1_HUMAN	K	383;382;183;182	ENSP00000428340:N383K;ENSP00000297450:N382K;ENSP00000430750:N183K;ENSP00000429349:N182K	ENSP00000297450:N382K	N	-	3	2	ANGPT1	108366142	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	3.127000	0.50484	2.709000	0.92574	0.650000	0.86243	AAC	.	.		0.423	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290		C	108296966	G	C	108296966	3	2	197	1	0	0	0	0	1	0	0	0	610	1252	44	4	359	4	ANGPT1	8	108296966	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	3881533	108296966	38067056	113	29023										
EBAG9	9166	hgsc.bcm.edu	37	chr8	110567069	110567069	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	attctttggaacaactggaaCctgactattttaaggacatg	8	7	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr8:110567069C>A	ENST00000337573.5	+	4	574	c.274C>A	c.(274-276)Cct>Act	p.P92T	EBAG9_ENST00000529502.1_3'UTR|EBAG9_ENST00000531677.1_Missense_Mutation_p.P92T|EBAG9_ENST00000395785.2_Missense_Mutation_p.P92T	NM_001278938.1|NM_004215.3	NP_001265867.1|NP_004206.1	O00559	RCAS1_HUMAN	estrogen receptor binding site associated, antigen, 9	92					regulation of cell growth (GO:0001558)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	peptidase activator activity involved in apoptotic process (GO:0016505)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)	10			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)			ACAACTGGAACCTGACTATTT	0.383																																					p.P92T		Atlas-SNP	.											.	EBAG9	23	.	0			c.C274A						.						139	126	130					8																	110567069		2203	4300	6503	SO:0001583	missense	9166	exon4			CTGGAACCTGACT	AB007619	CCDS6313.1	8q23	2013-03-07			ENSG00000147654	ENSG00000147654			3123	protein-coding gene	gene with protein product		605772					Standard	NM_004215		Approved	EB9, RCAS1	uc003ynf.3	O00559	OTTHUMG00000165346	ENST00000337573.5:c.274C>A	chr8.hg19:g.110567069C>A	ENSP00000337675:p.Pro92Thr	117.0	0.0		178.0	52.0	NM_004215	A8K3N6|Q5Y8C7|Q6IB20|Q9BS76	Missense_Mutation	SNP	ENST00000337573.5	hg19	CCDS6313.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.197479	0.58126	.	.	ENSG00000147654	ENST00000395785;ENST00000337573;ENST00000530629;ENST00000531677	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.57021	0.2025	M	0.66939	2.045	0.80722	D	1	P	0.41848	0.763	B	0.37144	0.242	T	0.58885	-0.7557	9	0.33141	T	0.24	0.0769	18.5664	0.91118	0.0:1.0:0.0:0.0	.	92	O00559	RCAS1_HUMAN	T	92	.	ENSP00000337675:P92T	P	+	1	0	EBAG9	110636245	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.487000	0.81328	2.711000	0.92665	0.655000	0.94253	CCT	.	.		0.383	EBAG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383536.1	NM_004215		A	110567069	C	A	110567069	3	1	197	1	0	0	0	0	1	0	0	0	4881	507	18	3	284	3	EBAG9	8	110567069	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	2270103	110567069	35796953	114	29024										
RLN1	6013	hgsc.bcm.edu	37	chr9	5335511	5335511	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ttgcctctcagatagggctgCcttcagctccggtggcaaat	11	12	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr9:5335511C>T	ENST00000223862.1	-	2	424	c.298G>A	c.(298-300)Gca>Aca	p.A100T	RLN1_ENST00000487557.2_5'UTR|RLN1_ENST00000223858.4_3'UTR	NM_006911.2	NP_008842.1	P04808	REL1_HUMAN	relaxin 1	100					female pregnancy (GO:0007565)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			large_intestine(1)|lung(4)	5	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.02)|Lung(218;0.0984)		GATAGGGCTGCCTTCAGCTCC	0.363																																					p.A100T		Atlas-SNP	.											.	RLN1	16	.	0			c.G298A						.						96	92	94					9																	5335511		2203	4300	6503	SO:0001583	missense	6013	exon2			GGGCTGCCTTCAG		CCDS6462.1	9p24.1	2013-02-26	2004-11-15		ENSG00000107018	ENSG00000107018		"Endogenous ligands"	10026	protein-coding gene	gene with protein product	"prorelaxin H1"	179730	"relaxin 1 (H1)"				Standard	NM_006911		Approved	H1	uc003zjb.2	P04808	OTTHUMG00000019495	ENST00000223862.1:c.298G>A	chr9.hg19:g.5335511C>T	ENSP00000223862:p.Ala100Thr	72.0	0.0		82.0	6.0	NM_006911	Q99936|Q9UQJ1	Missense_Mutation	SNP	ENST00000223862.1	hg19	CCDS6462.1	.	.	.	.	.	.	.	.	.	.	C	7.757	0.704617	0.15172	.	.	ENSG00000107018	ENST00000223862	T	0.18502	2.21	2.46	0.258	0.15578	Insulin-like (3);	1.137210	0.06920	N	0.809100	T	0.16685	0.0401	L	0.51914	1.62	0.09310	N	1	P	0.41313	0.745	B	0.41202	0.35	T	0.25293	-1.0136	10	0.41790	T	0.15	.	4.4997	0.11858	0.0:0.6094:0.0:0.3906	.	100	P04808	REL1_HUMAN	T	100	ENSP00000223862:A100T	ENSP00000223862:A100T	A	-	1	0	RLN1	5325511	0.000000	0.05858	0.001000	0.08648	0.223000	0.24884	-0.800000	0.04555	0.083000	0.17047	0.388000	0.25769	GCA	.	.		0.363	RLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051617.1			T	5335511	C	T	5335511	3	4	197	1	0	0	0	0	1	0	0	0	13406	739	26	3	263	3	RLN1	9	5335511	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10		5335511	135877920	115	29025										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5920853	5920853	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agatgatgcaaggtgtcctgTtttcacagttgatatagcca	10	7	1	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr9:5920853T>C	ENST00000399933.3	-	8	5142	c.5143A>G	c.(5143-5145)Aca>Gca	p.T1715A	KIAA2026_ENST00000381461.2_Missense_Mutation_p.T1685A	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1715										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		AGGTGTCCTGTTTTCACAGTT	0.388																																					p.T1715A		Atlas-SNP	.											.	KIAA2026	231	.	0			c.A5143G						.						120	117	118					9																	5920853		1924	4133	6057	SO:0001583	missense	158358	exon8			GTCCTGTTTTCAC	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.5143A>G	chr9.hg19:g.5920853T>C	ENSP00000382815:p.Thr1715Ala	111.0	0.0		97.0	10.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	hg19		.	.	.	.	.	.	.	.	.	.	T	16.43	3.122139	0.56613	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	5.48	5.48	0.80851	.	0.000000	0.64402	D	0.000003	T	0.67822	0.2934	L	0.36672	1.1	0.36443	D	0.865639	D	0.89917	1.0	D	0.83275	0.996	T	0.73697	-0.3901	9	0.51188	T	0.08	-15.3411	15.7326	0.77817	0.0:0.0:0.0:1.0	.	1715	Q5HYC2	K2026_HUMAN	A	1715;1685	.	ENSP00000370870:T1685A	T	-	1	0	KIAA2026	5910853	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.733000	0.47360	2.302000	0.77476	0.477000	0.44152	ACA	.	.		0.388	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		C	5920853	T	C	5920853	3	2	197	1	0	0	0	0	1	0	0	0	8279	1725	60	2	1172	2	KIAA2026	9	5920853	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	585342	5920853	135292578	116	29026										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5968486	5968487	+	Frame_Shift_Ins	INS	-	-	T													0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	attttctttacaacaatcagINStttttttaatttcacaaggc							TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr9:5968486_5968487insT	ENST00000399933.3	-	3	1743_1744	c.1744_1745insA	c.(1744-1746)actfs	p.T582fs	KIAA2026_ENST00000381461.2_Frame_Shift_Ins_p.T582fs	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	582										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		ACAACAATCAGTTTTTTTAATT	0.356																																					p.T582fs		Atlas-INDEL	.											.	KIAA2026	231	.	0			c.1745_1746insA						.																																			SO:0001589	frameshift_variant	158358	exon3			.	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.1745dupA	chr9.hg19:g.5968493_5968493dupT	ENSP00000382815:p.Thr582fs	57.0	0.0		62.0	22.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Frame_Shift_Ins	INS	ENST00000399933.3	hg19																																																																																				.	.		0.356	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		T	5968487	-	T	5968486	7	5	197	1	0	1	1	0	0	0	0	0	8279	1029	36	0	4590	0	KIAA2026	9	5968486	Frame_Shift_Ins	INS	-	TCGA-DD-AADO-01A-11D-A40R-10	47633	5968486	135244945	117	29027										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77386661	77386661	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gttcctcacaactacaattcAcatcttccatcttctcatgg	3	14	5	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr9:77386661A>G	ENST00000360774.1	-	25	3731	c.3494T>C	c.(3493-3495)gTg>gCg	p.V1165A	TRPM6_ENST00000449912.2_Missense_Mutation_p.V1160A|TRPM6_ENST00000451710.3_Missense_Mutation_p.V1165A|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.V1165A|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Missense_Mutation_p.V1160A	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1165					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						ACTACAATTCACATCTTCCAT	0.373																																					p.V1165A		Atlas-SNP	.											.	TRPM6	377	.	0			c.T3494C						.						133	116	122					9																	77386661		2203	4300	6503	SO:0001583	missense	140803	exon25			CAATTCACATCTT	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.3494T>C	chr9.hg19:g.77386661A>G	ENSP00000354006:p.Val1165Ala	55.0	0.0		25.0	16.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	A	6.646	0.487650	0.12641	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.12039	2.72;2.72;2.72;2.72;2.72	5.37	4.2	0.49525	.	0.573276	0.18118	N	0.151144	T	0.08133	0.0203	N	0.08118	0	0.19300	N	0.999977	B;B;B	0.10296	0.001;0.003;0.002	B;B;B	0.09377	0.002;0.004;0.004	T	0.27673	-1.0067	10	0.72032	D	0.01	.	11.4845	0.50346	0.8652:0.0:0.0:0.1348	.	1165;1160;1160	Q9BX84;Q9BX84-3;Q9BX84-2	TRPM6_HUMAN;.;.	A	1165;1165;1160;1160;1165;828;828	ENSP00000354006:V1165A;ENSP00000407341:V1165A;ENSP00000396672:V1160A;ENSP00000354962:V1160A;ENSP00000366060:V1165A	ENSP00000309693:V828A	V	-	2	0	TRPM6	76576481	0.422000	0.25473	0.021000	0.16686	0.014000	0.08584	3.172000	0.50832	0.837000	0.34925	0.533000	0.62120	GTG	.	.		0.373	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		G	77386661	A	G	77386661	3	3	197	1	0	0	0	0	1	0	0	0	16605	159	6	2	2634	2	TRPM6	9	77386661	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	71418175	77386661	63826770	118	29028										
TEX10	54881	hgsc.bcm.edu	37	chr9	103092453	103092453	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aactgtgcaatgcttgatgcTagaaacaaagacacacacat	7	9	0	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr9:103092453T>C	ENST00000374902.4	-	6	1427		c.e6-2		TEX10_ENST00000535814.1_Splice_Site|TEX10_ENST00000537512.1_Splice_Site	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		TGCTTGATGCTAGAAACAAAG	0.353																																					.		Atlas-SNP	.											.	TEX10	99	.	0			c.1260-2A>G						.						123	120	121					9																	103092453		2203	4300	6503	SO:0001630	splice_region_variant	54881	exon7			TGATGCTAGAAAC	AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"testis expressed gene 10", "testis expressed sequence 10"			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.1251-2A>G	chr9.hg19:g.103092453T>C		76.0	0.0		37.0	15.0	NM_001161584	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Splice_Site	SNP	ENST00000374902.4	hg19	CCDS6748.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.016117	0.75161	.	.	ENSG00000136891	ENST00000535814;ENST00000374902;ENST00000444730;ENST00000429235;ENST00000537512	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3466	0.74343	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TEX10	102132274	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.110000	0.71535	2.084000	0.62774	0.533000	0.62120	.	.	.		0.353	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746	Intron	C	103092453	T	C	103092453	5	2	197	1	0	0	0	0	0	0	1	0	15787	1536	53	2	1580	2	TEX10	9	103092453	Splice_Site	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	25705792	103092453	38120978	119	29029										
GOLGA1	2800	hgsc.bcm.edu	37	chr9	127685404	127685404	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	attttacttagttcctgctgCtggaacccctctaattcatc	5	12	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr9:127685404C>A	ENST00000373555.4	-	8	864	c.531G>T	c.(529-531)caG>caT	p.Q177H		NM_002077.3	NP_002068	Q92805	GOGA1_HUMAN	golgin A1	177					protein targeting to Golgi (GO:0000042)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)				NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	20						GTTCCTGCTGCTGGAACCCCT	0.353																																					p.Q177H		Atlas-SNP	.											.	GOLGA1	60	.	0			c.G531T						.						168	151	157					9																	127685404		2203	4300	6503	SO:0001583	missense	2800	exon8			CTGCTGCTGGAAC	U51587	CCDS6860.1	9q34.11	2010-02-12	2010-02-12		ENSG00000136935	ENSG00000136935			4424	protein-coding gene	gene with protein product		602502	"golgi autoantigen, golgin subfamily a, 1"			9324025	Standard	NM_002077		Approved	golgin-97, MGC33154	uc004bpc.3	Q92805	OTTHUMG00000020665	ENST00000373555.4:c.531G>T	chr9.hg19:g.127685404C>A	ENSP00000362656:p.Gln177His	34.0	0.0		20.0	9.0	NM_002077	Q5T164|Q8IYZ9	Missense_Mutation	SNP	ENST00000373555.4	hg19	CCDS6860.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.922615	0.73213	.	.	ENSG00000136935	ENST00000373555	T	0.11063	2.81	5.42	4.53	0.55603	.	0.000000	0.42172	U	0.000752	T	0.30417	0.0764	M	0.76328	2.33	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.85130	0.997;0.993	T	0.01998	-1.1232	10	0.37606	T	0.19	-15.5209	11.5035	0.50451	0.0:0.8494:0.0:0.1506	.	76;177	Q59HA1;Q92805	.;GOGA1_HUMAN	H	177	ENSP00000362656:Q177H	ENSP00000362656:Q177H	Q	-	3	2	GOLGA1	126725225	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.124000	0.42006	1.294000	0.44707	0.591000	0.81541	CAG	.	.		0.353	GOLGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054049.1	NM_002077		A	127685404	C	A	127685404	3	1	197	1	0	0	0	0	1	0	0	0	6559	796	28	3	1836	3	GOLGA1	9	127685404	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	24592951	127685404	13528027	120	29030										
ADARB2	105	hgsc.bcm.edu	37	chr10	1313165	1313165	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gctacctttggtcatgacgaTtcctgccagcgctttatggc	10	12	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr10:1313165T>C	ENST00000381312.1	-	4	1502	c.1177A>G	c.(1177-1179)Atc>Gtc	p.I393V		NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	393					mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		GTCATGACGATTCCTGCCAGC	0.537																																					p.I393V		Atlas-SNP	.											.	ADARB2	95	.	0			c.A1177G						.						94	78	83					10																	1313165		2203	4300	6503	SO:0001583	missense	105	exon4			TGACGATTCCTGC	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1177A>G	chr10.hg19:g.1313165T>C	ENSP00000370713:p.Ile393Val	67.0	0.0		75.0	18.0	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	hg19	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	T	9.321	1.058168	0.19987	.	.	ENSG00000185736	ENST00000381312	T	0.27720	1.65	5.42	5.42	0.78866	Adenosine deaminase/editase (1);	0.000000	0.85682	D	0.000000	T	0.37625	0.1010	L	0.57536	1.79	0.80722	D	1	B	0.31581	0.329	B	0.40702	0.338	T	0.12502	-1.0545	10	0.19147	T	0.46	-41.0978	15.4603	0.75349	0.0:0.0:0.0:1.0	.	393	Q9NS39	RED2_HUMAN	V	393	ENSP00000370713:I393V	ENSP00000370713:I393V	I	-	1	0	ADARB2	1303165	1.000000	0.71417	0.998000	0.56505	0.511000	0.34104	4.357000	0.59436	2.056000	0.61249	0.402000	0.26972	ATC	.	.		0.537	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		C	1313165	T	C	1313165	3	2	197	1	0	0	0	0	1	0	0	0	283	1493	52	2	1070	2	ADARB2	10	1313165	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10		1313165	134221582	121	29031										
ASB13	79754	hgsc.bcm.edu	37	chr10	5683744	5683744	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtgtctcactttcgtagtacTcgaagcacttggcgggagcg	13	10	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr10:5683744T>C	ENST00000357700.6	-	5	724	c.698A>G	c.(697-699)gAg>gGg	p.E233G	ASB13_ENST00000479033.1_5'UTR	NM_024701.3	NP_078977.2	Q8WXK3	ASB13_HUMAN	ankyrin repeat and SOCS box containing 13	233	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					NS(1)|endometrium(3)|lung(3)|ovary(1)	8				GBM - Glioblastoma multiforme(2;9.59e-09)		TTCGTAGTACTCGAAGCACTT	0.637																																					p.E233G		Atlas-SNP	.											.	ASB13	26	.	0			c.A698G						.						67	65	66					10																	5683744		2203	4300	6503	SO:0001583	missense	79754	exon5			TAGTACTCGAAGC	AK091935	CCDS7070.1	10p15.1	2013-01-10	2011-01-25		ENSG00000196372	ENSG00000196372		"Ankyrin repeat domain containing"	19765	protein-coding gene	gene with protein product		615055	"ankyrin repeat and SOCS box-containing 13"			12076535	Standard	NM_024701		Approved	FLJ13134, MGC19879	uc001iig.2	Q8WXK3	OTTHUMG00000017603	ENST00000357700.6:c.698A>G	chr10.hg19:g.5683744T>C	ENSP00000350331:p.Glu233Gly	60.0	0.0		83.0	16.0	NM_024701	A8K7Q6|D3DRR2|Q96EP7|Q9H8Z1	Missense_Mutation	SNP	ENST00000357700.6	hg19	CCDS7070.1	.	.	.	.	.	.	.	.	.	.	T	9.893	1.204639	0.22205	.	.	ENSG00000196372	ENST00000357700	T	0.68624	-0.34	5.7	5.7	0.88788	.	0.046293	0.85682	D	0.000000	T	0.61413	0.2345	L	0.58354	1.805	0.47276	D	0.999379	P	0.42296	0.775	B	0.38225	0.268	T	0.60321	-0.7286	10	0.15952	T	0.53	-17.5525	15.6263	0.76859	0.0:0.0:0.0:1.0	.	233	Q8WXK3	ASB13_HUMAN	G	233	ENSP00000350331:E233G	ENSP00000350331:E233G	E	-	2	0	ASB13	5723750	1.000000	0.71417	0.997000	0.53966	0.174000	0.22865	4.644000	0.61397	2.175000	0.68902	0.383000	0.25322	GAG	.	.		0.637	ASB13-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046564.1			C	5683744	T	C	5683744	3	2	197	1	0	0	0	0	1	0	0	0	1017	1551	54	2	146	2	ASB13	10	5683744	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	4370579	5683744	129851003	122	29032										
ITGA8	8516	hgsc.bcm.edu	37	chr10	15573079	15573079	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ccttctgggagttttgctggCtgatctgtataaggcatctt	11	8	3	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr10:15573079C>T	ENST00000378076.3	-	28	3305	c.2952G>A	c.(2950-2952)caG>caA	p.Q984Q		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	984					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						GTTTTGCTGGCTGATCTGTAT	0.313																																					p.Q984Q		Atlas-SNP	.											.	ITGA8	230	.	0			c.G2952A						.						100	100	100					10																	15573079		2203	4300	6503	SO:0001819	synonymous_variant	8516	exon28			TGCTGGCTGATCT	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.2952G>A	chr10.hg19:g.15573079C>T		200.0	0.0		188.0	31.0	NM_003638	B0YJ31|Q5VX94	Silent	SNP	ENST00000378076.3	hg19	CCDS31155.1																																																																																			.	.		0.313	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		T	15573079	C	T	15573079	2	4	197	1	0	0	0	0	0	0	0	1	7891	796	28	3		3	ITGA8	10	15573079	Silent	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	9889335	15573079	119961668	123	29033										
GAD2	2572	hgsc.bcm.edu	37	chr10	26513476	26513476	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	actacatttcaggttcacctAtgaaattgctccagtatttg	6	9	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr10:26513476A>T	ENST00000376261.3	+	6	1123	c.620A>T	c.(619-621)tAt>tTt	p.Y207F	GAD2_ENST00000376248.1_Missense_Mutation_p.Y93F|GAD2_ENST00000259271.3_Missense_Mutation_p.Y207F	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	207					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						AGGTTCACCTATGAAATTGCT	0.363																																					p.Y207F		Atlas-SNP	.											.	GAD2	116	.	0			c.A620T						.						128	126	127					10																	26513476		2203	4300	6503	SO:0001583	missense	2572	exon6			TCACCTATGAAAT	AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.620A>T	chr10.hg19:g.26513476A>T	ENSP00000365437:p.Tyr207Phe	115.0	0.0		146.0	29.0	NM_000818	Q9UD87	Missense_Mutation	SNP	ENST00000376261.3	hg19	CCDS7149.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.917241	0.73098	.	.	ENSG00000136750	ENST00000376261;ENST00000259271;ENST00000376248	T;T;T	0.38722	1.12;1.12;1.12	5.21	5.21	0.72293	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.122019	0.56097	D	0.000021	T	0.41581	0.1165	L	0.48260	1.515	0.80722	D	1	B	0.19200	0.034	B	0.28709	0.093	T	0.31724	-0.9933	10	0.52906	T	0.07	-13.4372	15.1137	0.72380	1.0:0.0:0.0:0.0	.	207	Q05329	DCE2_HUMAN	F	207;207;93	ENSP00000365437:Y207F;ENSP00000259271:Y207F;ENSP00000365424:Y93F	ENSP00000259271:Y207F	Y	+	2	0	GAD2	26553482	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	1.981000	0.57761	0.533000	0.62120	TAT	.	.		0.363	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818		T	26513476	A	T	26513476	3	4	197	1	0	0	0	0	1	0	0	0	6188	449	16	4	642	4	GAD2	10	26513476	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	10940397	26513476	109021271	124	29034										
CCDC6	8030	hgsc.bcm.edu	37	chr10	61566806	61566806	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cttctctcatgtgacgttccTcctccagatactgtgccatt	6	14	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr10:61566806T>A	ENST00000263102.6	-	6	1109	c.878A>T	c.(877-879)gAg>gTg	p.E293V		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	293						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		GTGACGTTCCTCCTCCAGATA	0.443			T	RET	NSCLC																																p.E293V		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	CCDC6	44	.	0			c.A878T						.						120	103	109					10																	61566806		2203	4300	6503	SO:0001583	missense	8030	exon6			CGTTCCTCCTCCA	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"	601985	"DNA segment on chromosome 10 (unique) 170"	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.878A>T	chr10.hg19:g.61566806T>A	ENSP00000263102:p.Glu293Val	64.0	0.0		66.0	16.0	NM_005436	Q15250|Q6GSG7	Missense_Mutation	SNP	ENST00000263102.6	hg19	CCDS7257.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.920907	0.92249	.	.	ENSG00000108091	ENST00000263102	D	0.92965	-3.14	5.37	5.37	0.77165	.	0.104877	0.64402	D	0.000002	D	0.95300	0.8475	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.95723	0.8768	10	0.72032	D	0.01	-16.4066	15.4364	0.75149	0.0:0.0:0.0:1.0	.	293	Q16204	CCDC6_HUMAN	V	293	ENSP00000263102:E293V	ENSP00000263102:E293V	E	-	2	0	CCDC6	61236812	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.037000	0.88933	2.070000	0.61991	0.378000	0.23410	GAG	.	.		0.443	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436		A	61566806	T	A	61566806	3	1	197	1	0	0	0	0	1	0	0	0	2832	1551	54	4	562	4	CCDC6	10	61566806	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	35053330	61566806	73967941	125	29035										
CYP17A1	1586	hgsc.bcm.edu	37	chr10	104595084	104595084	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gccagccttcgatgcagctgCcagtgtgcgccagagtcagc	13	14	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr10:104595084C>T	ENST00000369887.3	-	2	534	c.363G>A	c.(361-363)tgG>tgA	p.W121*	CYP17A1-AS1_ENST00000369884.4_RNA|CYP17A1_ENST00000489268.1_5'UTR	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	121					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	GATGCAGCTGCCAGTGTGCGC	0.577											OREG0020487	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W121X		Atlas-SNP	.											.	CYP17A1	48	.	0			c.G363A						.						138	111	120					10																	104595084		2203	4300	6503	SO:0001587	stop_gained	1586	exon2			CAGCTGCCAGTGT	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"Cytochrome P450s"	2593	protein-coding gene	gene with protein product	"Steroid 17-alpha-monooxygenase"	609300	"cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.363G>A	chr10.hg19:g.104595084C>T	ENSP00000358903:p.Trp121*	55.0	0.0	172	74.0	28.0	NM_000102	Q5TZV7	Nonsense_Mutation	SNP	ENST00000369887.3	hg19	CCDS7541.1	.	.	.	.	.	.	.	.	.	.	C	32	5.131922	0.94473	.	.	ENSG00000148795	ENST00000369887	.	.	.	5.8	5.8	0.92144	.	0.116551	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.6542	0.95830	0.0:1.0:0.0:0.0	.	.	.	.	X	121	.	ENSP00000358903:W121X	W	-	3	0	CYP17A1	104585074	1.000000	0.71417	1.000000	0.80357	0.429000	0.31625	7.148000	0.77389	2.747000	0.94245	0.462000	0.41574	TGG	.	.		0.577	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102		T	104595084	C	T	104595084	4	4	197	1	0	0	0	0	0	1	0	0	4149	740	26	3	1191	3	CYP17A1	10	104595084	Nonsense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	43028278	104595084	30939663	126	29036										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105165833	105165833	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agcttttctgccactgctgaAagcccaggagtacatcagac	9	12	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr10:105165833A>T	ENST00000369797.3	+	6	750	c.656A>T	c.(655-657)aAa>aTa	p.K219I		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	219	S1 motif 2. {ECO:0000255|PROSITE- ProRule:PRU00180}.				mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CCACTGCTGAAAGCCCAGGAG	0.507																																					p.K219I		Atlas-SNP	.											.	PDCD11	160	.	0			c.A656T						.						131	124	126					10																	105165833		2203	4300	6503	SO:0001583	missense	22984	exon6			TGCTGAAAGCCCA	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.656A>T	chr10.hg19:g.105165833A>T	ENSP00000358812:p.Lys219Ile	113.0	0.0		129.0	28.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	hg19	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.391044	0.82902	.	.	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.17854	2.25	5.41	5.41	0.78517	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (2);	0.242700	0.48767	D	0.000171	T	0.49592	0.1566	M	0.88377	2.95	0.58432	D	0.999999	P	0.47910	0.902	D	0.72075	0.976	T	0.57189	-0.7854	10	0.72032	D	0.01	-16.79	15.1042	0.72306	1.0:0.0:0.0:0.0	.	219	Q14690	RRP5_HUMAN	I	219	ENSP00000358812:K219I	ENSP00000358812:K219I	K	+	2	0	PDCD11	105155823	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	4.548000	0.60718	2.055000	0.61198	0.459000	0.35465	AAA	.	.		0.507	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			T	105165833	A	T	105165833	3	4	197	1	0	0	0	0	1	0	0	0	11626	14	1	4	674	4	PDCD11	10	105165833	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	570749	105165833	30368914	127	29037										
NRAP	4892	hgsc.bcm.edu	37	chr10	115372164	115372164	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agatggaactgcgcctttgaGtgttcaaagcctttcttgta	10	8	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr10:115372164G>A	ENST00000359988.3	-	30	3571	c.3327C>T	c.(3325-3327)caC>caT	p.H1109H	NRAP_ENST00000360478.3_Silent_p.H1074H|NRAP_ENST00000369360.3_Silent_p.H1082H|NRAP_ENST00000369358.4_Silent_p.H1117H	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GCGCCTTTGAGTGTTCAAAGC	0.527																																					p.H1109H		Atlas-SNP	.											.	NRAP	208	.	0			c.C3327T						.						89	77	81					10																	115372164		2203	4300	6503	SO:0001819	synonymous_variant	4892	exon30			CTTTGAGTGTTCA		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3327C>T	chr10.hg19:g.115372164G>A		98.0	0.0		114.0	26.0	NM_001261463		Silent	SNP	ENST00000359988.3	hg19	CCDS7579.1																																																																																			.	.		0.527	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		A	115372164	G	A	115372164	2	1	197	1	0	0	0	0	0	0	0	1	10647	1020	36	3		3	NRAP	10	115372164	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	10206331	115372164	20162583	128	29038										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124358530	124358530	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tgtgcgctgctcaggacacgAgtcttacctgtggagctgcc	13	12	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr10:124358530A>G	ENST00000338354.3	+	26	3303	c.3197A>G	c.(3196-3198)gAg>gGg	p.E1066G	DMBT1_ENST00000368956.2_Missense_Mutation_p.E567G|DMBT1_ENST00000368909.3_Missense_Mutation_p.E1066G|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000344338.3_Missense_Mutation_p.E1056G|DMBT1_ENST00000330163.4_Missense_Mutation_p.E567G|DMBT1_ENST00000368955.3_Missense_Mutation_p.E1056G			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1066	SRCR 8. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TCAGGACACGAGTCTTACCTG	0.592																																					p.E1066G	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.A3197G						.						117	115	115					10																	124358530		1964	4142	6106	SO:0001583	missense	1755	exon26			GACACGAGTCTTA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.3197A>G	chr10.hg19:g.124358530A>G	ENSP00000342210:p.Glu1066Gly	100.0	0.0		100.0	24.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	A	20.6	4.025532	0.75390	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04;-0.04	3.57	3.57	0.40892	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.35407	U	0.003235	D	0.84665	0.5522	H	0.97186	3.955	0.80722	D	1	D;D;D;D;D	0.89917	0.989;0.999;1.0;1.0;1.0	P;D;D;D;D	0.97110	0.898;0.956;0.999;0.999;1.0	D	0.89023	0.3436	10	0.87932	D	0	.	12.5079	0.55991	1.0:0.0:0.0:0.0	.	573;1066;567;1056;1066	Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	G	1066;1066;1066;1066;1066;1066;567;1056;567;567;1066;1056;567	ENSP00000342210:E1066G;ENSP00000343175:E1056G;ENSP00000327747:E567G;ENSP00000357905:E1066G;ENSP00000357951:E1056G;ENSP00000357952:E567G	ENSP00000331522:E567G	E	+	2	0	DMBT1	124348520	1.000000	0.71417	0.520000	0.27837	0.108000	0.19459	5.663000	0.68038	1.402000	0.46780	0.456000	0.33151	GAG	.	.		0.592	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		G	124358530	A	G	124358530	3	3	197	1	0	0	0	0	1	0	0	0	4579	304	11	2	3299	2	DMBT1	10	124358530	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	8986366	124358530	11176217	129	29039										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1271184	1271184	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cacccctcctccactccggaGaccacccacacctccacagt	4	23	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:1271184G>A	ENST00000529681.1	+	31	13132	c.13074G>A	c.(13072-13074)gaG>gaA	p.E4358E	MUC5B_ENST00000447027.1_Silent_p.E4361E|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4358	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCACTCCGGAGACCACCCACA	0.662																																					p.E4358E		Atlas-SNP	.											.	MUC5B	473	.	0			c.G13074A						.						83	107	99					11																	1271184		2137	4228	6365	SO:0001819	synonymous_variant	727897	exon31			TCCGGAGACCACC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.13074G>A	chr11.hg19:g.1271184G>A		129.0	0.0		70.0	21.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.662	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1271184	G	A	1271184	2	1	197	1	0	0	0	0	0	0	0	1	9988	933	33	3		3	MUC5B	11	1271184	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10		1271184	133735332	130	29040										
SOX6	55553	hgsc.bcm.edu	37	chr11	16077382	16077382	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cctgctgtgtttggtggctgTggagttgatggcatctttgc	15	7	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:16077382T>C	ENST00000352083.6	-	10	1244	c.1167A>G	c.(1165-1167)ccA>ccG	p.P389P	SOX6_ENST00000528429.1_Silent_p.P389P|SOX6_ENST00000528252.1_Silent_p.P348P|SOX6_ENST00000316399.6_Silent_p.P389P|SOX6_ENST00000527619.1_Silent_p.P351P|SOX6_ENST00000396356.3_Silent_p.P389P			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	389					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						TTGGTGGCTGTGGAGTTGATG	0.502																																					p.P402P		Atlas-SNP	.											.	SOX6	149	.	0			c.A1206G						.						178	145	156					11																	16077382		2200	4294	6494	SO:0001819	synonymous_variant	55553	exon10			TGGCTGTGGAGTT	AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"SRY (sex determining region Y)-boxes"	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.1167A>G	chr11.hg19:g.16077382T>C		68.0	0.0		29.0	14.0	NM_001145819	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Silent	SNP	ENST00000352083.6	hg19																																																																																				.	.		0.502	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326		C	16077382	T	C	16077382	2	2	197	1	0	0	0	0	0	0	0	1	14970	1683	59	2		2	SOX6	11	16077382	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	14806198	16077382	118929134	131	29041										
OR5T2	219464	hgsc.bcm.edu	37	chr11	55999752	55999752	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtcatggtccgaagcatagcTggaacttggtctcacataca	10	10	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:55999752T>A	ENST00000313264.4	-	1	985	c.910A>T	c.(910-912)Agc>Tgc	p.S304C		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	304						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					GAAGCATAGCTGGAACTTGGT	0.418																																					p.S304C		Atlas-SNP	.											.	OR5T2	107	.	0			c.A910T						.						198	174	182					11																	55999752		2201	4296	6497	SO:0001583	missense	219464	exon1			CATAGCTGGAACT	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.910A>T	chr11.hg19:g.55999752T>A	ENSP00000323688:p.Ser304Cys	112.0	0.0		99.0	21.0	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	hg19	CCDS31523.1	.	.	.	.	.	.	.	.	.	.	T	13.93	2.383347	0.42207	.	.	ENSG00000181718	ENST00000313264	T	0.00179	8.61	5.07	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	U	0.000124	T	0.00580	0.0019	M	0.90870	3.155	0.09310	N	1	D	0.76494	0.999	D	0.76071	0.987	T	0.32587	-0.9901	10	0.87932	D	0	.	4.9638	0.14080	0.1634:0.0876:0.0:0.7491	.	304	Q8NGG2	OR5T2_HUMAN	C	304	ENSP00000323688:S304C	ENSP00000323688:S304C	S	-	1	0	OR5T2	55756328	0.000000	0.05858	0.507000	0.27676	0.608000	0.37181	0.730000	0.26043	2.041000	0.60428	0.391000	0.25812	AGC	.	.		0.418	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		A	55999752	T	A	55999752	3	1	197	1	0	0	0	0	1	0	0	0	11191	1580	55	4	168	4	OR5T2	11	55999752	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	39922370	55999752	79006764	132	29042										
OR8K1	390157	hgsc.bcm.edu	37	chr11	56114330	56114330	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ttgcaacccaagtccagtcaTactttggctattgataaaat	6	9	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:56114330T>C	ENST00000279783.2	+	1	910	c.816T>C	c.(814-816)caT>caC	p.H272H		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					AGTCCAGTCATACTTTGGCTA	0.408										HNSCC(65;0.19)																											p.H272H		Atlas-SNP	.											.	OR8K1	93	.	0			c.T816C						.						121	110	114					11																	56114330		2201	4296	6497	SO:0001819	synonymous_variant	390157	exon1			CAGTCATACTTTG	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.816T>C	chr11.hg19:g.56114330T>C		101.0	0.0		81.0	16.0	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Silent	SNP	ENST00000279783.2	hg19	CCDS31528.1																																																																																			.	.		0.408	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		C	56114330	T	C	56114330	2	2	197	1	0	0	0	0	0	0	0	1	11252	1403	49	2		2	OR8K1	11	56114330	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	114578	56114330	78892186	133	29043										
OR9Q1	219956	hgsc.bcm.edu	37	chr11	57946997	57946997	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cctgaatgggcactccctctCttcctcttgtttttatttat	5	12	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:57946997C>T	ENST00000335397.3	+	3	397	c.81C>T	c.(79-81)ctC>ctT	p.L27L		NM_001005212.3	NP_001005212.1	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q, member 1	27						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Breast(21;0.222)				CACTCCCTCTCTTCCTCTTGT	0.453																																					p.L27L		Atlas-SNP	.											.	OR9Q1	60	.	0			c.C81T						.						223	208	213					11																	57946997		2201	4296	6497	SO:0001819	synonymous_variant	219956	exon3			CCCTCTCTTCCTC	AB065734	CCDS31543.1	11q12.1	2012-08-09				ENSG00000186509		"GPCR / Class A : Olfactory receptors"	14724	protein-coding gene	gene with protein product							Standard	NM_001005212		Approved		uc001nmj.3	Q8NGQ5		ENST00000335397.3:c.81C>T	chr11.hg19:g.57946997C>T		97.0	0.0		65.0	7.0	NM_001005212	Q2TAN3|Q96RA7	Silent	SNP	ENST00000335397.3	hg19	CCDS31543.1																																																																																			.	.		0.453	OR9Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394538.2	NM_001005212		T	57946997	C	T	57946997	2	4	197	1	0	0	0	0	0	0	0	1	11264	900	32	3		3	OR9Q1	11	57946997	Silent	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	1832667	57946997	77059519	134	29044										
CABP4	57010	hgsc.bcm.edu	37	chr11	67222916	67222916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tgaccacagagcaggcaaggGggcagcagggcccaaatctg	15	11	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:67222916G>A	ENST00000325656.5	+	1	99	c.22G>A	c.(22-24)Ggg>Agg	p.G8R	CABP4_ENST00000438189.2_Intron|GPR152_ENST00000312457.2_5'Flank|CABP4_ENST00000542025.2_3'UTR	NM_145200.3	NP_660201.1	P57796	CABP4_HUMAN	calcium binding protein 4	8					photoreceptor cell morphogenesis (GO:0008594)|phototransduction (GO:0007602)|retinal bipolar neuron differentiation (GO:0060040)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytosol (GO:0005829)|extracellular region (GO:0005576)|synapse (GO:0045202)|terminal bouton (GO:0043195)	calcium ion binding (GO:0005509)			central_nervous_system(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)	11			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			GCAGGCAAGGGGGCAGCAGGG	0.612																																					p.G8R		Atlas-SNP	.											.	CABP4	33	.	0			c.G22A						.						16	19	18					11																	67222916		2162	4220	6382	SO:0001583	missense	57010	exon1			GCAAGGGGGCAGC	AC005849	CCDS8166.1, CCDS73333.1	11q13.2	2013-09-20			ENSG00000175544	ENSG00000175544		"EF-hand domain containing"	1386	protein-coding gene	gene with protein product		608965				10625670, 16960802	Standard	NM_145200		Approved	CSNB2B	uc001olo.3	P57796	OTTHUMG00000168033	ENST00000325656.5:c.22G>A	chr11.hg19:g.67222916G>A	ENSP00000324960:p.Gly8Arg	67.0	0.0		48.0	6.0	NM_145200	Q8N4Z2|Q8WWY5	Missense_Mutation	SNP	ENST00000325656.5	hg19	CCDS8166.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.945722	0.34377	.	.	ENSG00000175544	ENST00000325656	T	0.74947	-0.89	3.51	1.55	0.23275	.	3.634860	0.00848	N	0.001816	T	0.62744	0.2453	L	0.29908	0.895	0.09310	N	1	B	0.29378	0.243	B	0.21360	0.034	T	0.53927	-0.8369	10	0.66056	D	0.02	.	5.0608	0.14557	0.2862:0.0:0.7138:0.0	.	8	P57796	CABP4_HUMAN	R	8	ENSP00000324960:G8R	ENSP00000324960:G8R	G	+	1	0	CABP4	66979492	0.009000	0.17119	0.002000	0.10522	0.147000	0.21601	0.878000	0.28126	0.600000	0.29862	0.491000	0.48974	GGG	.	.		0.612	CABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397624.2			A	67222916	G	A	67222916	3	1	197	1	0	0	0	0	1	0	0	0	2535	1232	43	3	24	3	CABP4	11	67222916	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	9275919	67222916	67783600	135	29045										
WNT11	7481	hgsc.bcm.edu	37	chr11	75905679	75905679	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggatcctgtttttttcacctTcataggagcatcggaaaact	8	9	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:75905679T>A	ENST00000322563.3	-	3	653	c.529A>T	c.(529-531)Aag>Tag	p.K177*	RP11-619A14.2_ENST00000527314.1_RNA	NM_004626.2	NP_004617.2	O96014	WNT11_HUMAN	wingless-type MMTV integration site family, member 11	177					adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|bone mineralization (GO:0030282)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|cloacal septation (GO:0060197)|embryonic skeletal system development (GO:0048706)|lung-associated mesenchyme development (GO:0060484)|mesonephric duct development (GO:0072177)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of fibroblast growth factor production (GO:0090272)|negative regulation of mesenchymal cell proliferation (GO:0072201)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroendocrine cell differentiation (GO:0061101)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway (GO:0035567)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta2 production (GO:0032915)|protein localization to cell surface (GO:0034394)|protein phosphorylation (GO:0006468)|response to nutrient levels (GO:0031667)|tight junction assembly (GO:0070830)|ureteric bud morphogenesis (GO:0060675)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|protein kinase activator activity (GO:0030295)|Ras GTPase activator activity (GO:0005099)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	20						TTTTTCACCTTCATAGGAGCA	0.582																																					p.K177X		Atlas-SNP	.											.	WNT11	44	.	0			c.A529T						.						62	53	56					11																	75905679		1719	3226	4945	SO:0001587	stop_gained	7481	exon3			TCACCTTCATAGG	Y12692	CCDS8242.1	11q13.5	2008-02-05			ENSG00000085741	ENSG00000085741		"Wingless-type MMTV integration sites"	12776	protein-coding gene	gene with protein product		603699				9757009	Standard	NM_004626		Approved		uc001oxe.3	O96014	OTTHUMG00000165264	ENST00000322563.3:c.529A>T	chr11.hg19:g.75905679T>A	ENSP00000325526:p.Lys177*	94.0	0.0		94.0	24.0	NM_004626	B2R8Z6|Q14DE8|Q8WZ98	Nonsense_Mutation	SNP	ENST00000322563.3	hg19	CCDS8242.1	.	.	.	.	.	.	.	.	.	.	T	37	6.204161	0.97376	.	.	ENSG00000085741	ENST00000322563;ENST00000531317;ENST00000447195	.	.	.	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	14.1498	0.65375	0.0:0.0:0.0:1.0	.	.	.	.	X	177	.	ENSP00000325526:K177X	K	-	1	0	WNT11	75583327	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.283000	0.72646	1.939000	0.56221	0.454000	0.30748	AAG	.	.		0.582	WNT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383083.1	NM_004626		A	75905679	T	A	75905679	4	1	197	1	0	0	0	0	0	1	0	0	17399	1792	62	4	547	4	WNT11	11	75905679	Nonsense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	8682763	75905679	59100837	136	29046										
MAML2	84441	hgsc.bcm.edu	37	chr11	95712390	95712391	+	Frame_Shift_Del	DEL	AC	AC	-													0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ctgattcaaccctgttcctgActgattcaaattaggcaaaa							TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:95712390_95712391delAC	ENST00000524717.1	-	5	4476_4477	c.3192_3193delGT	c.(3190-3195)cagtcafs	p.QS1064fs		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	1064					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				CCTGTTCCTGACTGATTCAAAT	0.495			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.1065_1065del		Atlas-INDEL	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.3193_3194del						.																																			SO:0001589	frameshift_variant	84441	exon5			.	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.3192_3193delGT	chr11.hg19:g.95712390_95712391delAC	ENSP00000434552:p.Gln1064fs	64.0	0.0		65.0	17.0	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Frame_Shift_Del	DEL	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.		0.495	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			-	95712391	AC	-	95712390	7	5	197	1	0	1	0	1	0	0	0	0	9215	275	10	0	281	0	MAML2	11	95712390	Frame_Shift_Del	DEL	AC	TCGA-DD-AADO-01A-11D-A40R-10	19806711	95712390	39294126	137	29047										
SIK2	23235	hgsc.bcm.edu	37	chr11	111591239	111591239	+	Frame_Shift_Del	DEL	C	C	-													0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aatgacagcccctcccttgaCagtgtggactctgagtatga							TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:111591239delC	ENST00000304987.3	+	11	1706	c.1533delC	c.(1531-1533)gacfs	p.D511fs	SIK2_ENST00000533868.1_3'UTR	NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	511					insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						CCTCCCTTGACAGTGTGGACT	0.443																																					p.D511fs		Atlas-INDEL	.											.	SIK2	89	.	0			c.1532delA						.						100	102	101					11																	111591239		2201	4297	6498	SO:0001589	frameshift_variant	23235	exon11			.	AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"SNF1-like kinase 2"	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.1533delC	chr11.hg19:g.111591239delC	ENSP00000305976:p.Asp511fs	108.0	0.0		56.0	11.0	NM_015191	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Frame_Shift_Del	DEL	ENST00000304987.3	hg19	CCDS8347.1																																																																																			.	.		0.443	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191		-	111591239	C	-	111591239	7	5	197	1	0	1	0	1	0	0	0	0	14333	477	17	0	1575	0	SIK2	11	111591239	Frame_Shift_Del	DEL	C	TCGA-DD-AADO-01A-11D-A40R-10	15878849	111591239	23415277	138	29048										
ALG9	91893	hgsc.bcm.edu	37	chr11	111742145	111742145	+	IGR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cagcttgtccgcagccggggCgcgtatccccactgctggcc	13	17	0	0	rs10708475|rs200786242		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:111742145C>G	ENST00000260257.4	-	0	2789				ALG9_ENST00000398006.2_5'Flank|ALG9_ENST00000527228.1_5'UTR|ALG9_ENST00000524880.1_Missense_Mutation_p.R254P|ALG9_ENST00000531154.1_5'Flank|ALG9_ENST00000527377.1_5'UTR	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1						phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						GCAGCCGGGGCGCGTATCCCC	0.711																																					p.A21P		Atlas-SNP	.											.	ALG9	77	.	0			c.G61C						.						1	1	1					11																	111742145		776	1973	2749	SO:0001628	intergenic_variant	79796	exon2			CCGGGGCGCGTAT		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"hypothetical protein BC006136"						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795		chr11.hg19:g.111742145C>G		667.0	0.0		625.0	39.0	NM_001077690	A0PJW7|B4DUU2	Missense_Mutation	SNP	ENST00000260257.4	hg19	CCDS44729.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.83|11.83	1.756102|1.756102	0.31137|0.31137	.|.	.|.	ENSG00000086848|ENSG00000086848	ENST00000428306|ENST00000428306	.|.	.|.	.|.	4.98|4.98	0.976|0.976	0.19727|0.19727	.|.	.|.	.|.	.|.	.|.	.|T	.|0.17831	.|0.0428	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	0.99999|0.99999	.|B;B	.|0.21147	.|0.0;0.052	.|B;B	.|0.16722	.|0.0;0.016	.|T	.|0.23940	.|-1.0174	.|8	.|0.26408	.|T	.|0.33	.|.	4.2702|4.2702	0.10783|0.10783	0.1565:0.5847:0.0:0.2588|0.1565:0.5847:0.0:0.2588	.|.	.|21;21	.|Q9H6U8-3;Q9H6U8	.|.;ALG9_HUMAN	.|P	-1|254	.|.	.|ENSP00000387627:A254P	.|A	-|-	.|1	.|0	ALG9|ALG9	111247355|111247355	0.130000|0.130000	0.22417|0.22417	0.101000|0.101000	0.21167|0.21167	0.687000|0.687000	0.40016|0.40016	0.758000|0.758000	0.26447|0.26447	0.032000|0.032000	0.15435|0.15435	-0.291000|-0.291000	0.09656|0.09656	.|GCC	.	.		0.711	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378		G	111742145	C	G	111742145	1	3	197	0	1	0	0	0	0	0	0	0	524	768	27	4		4	ALG9	11	111742145	IGR	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	150906	111742145	23264371	139	29049										
PCSK7	9159	hgsc.bcm.edu	37	chr11	117100406	117100406	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ccaggtgcacagcccagctcGgcccccctgtgccctggcca	11	20	0	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:117100406G>A	ENST00000320934.3	-	3	785	c.155C>T	c.(154-156)cCg>cTg	p.P52L		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	52				P -> A (in Ref. 1; AAC50417 and 3; AAB03087). {ECO:0000305}.	peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		AGCCCAGCTCGGCCCCCCTGT	0.652			T	IGH@	MLCLS																																p.P52L		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	PCSK7,NS,carcinoma,0,1	PCSK7	59	.	0			c.C155T						.						32	35	34					11																	117100406		2201	4296	6497	SO:0001583	missense	9159	exon3			CAGCTCGGCCCCC	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.155C>T	chr11.hg19:g.117100406G>A	ENSP00000325917:p.Pro52Leu	114.0	1.0		110.0	22.0	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	hg19	CCDS8382.1	.	.	.	.	.	.	.	.	.	.	G	0.034	-1.315806	0.01331	.	.	ENSG00000160613	ENST00000320934;ENST00000543900;ENST00000525027;ENST00000524507;ENST00000532301;ENST00000530269	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	4.21	3.09	0.35607	Proteinase inhibitor, propeptide (1);	0.408692	0.22742	N	0.056198	T	0.13157	0.0319	N	0.00621	-1.32	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25710	-1.0124	10	0.02654	T	1	-2.276	7.9365	0.29933	0.8973:0.0:0.1027:0.0	.	52	Q16549	PCSK7_HUMAN	L	52	ENSP00000325917:P52L;ENSP00000431181:P52L;ENSP00000433841:P52L;ENSP00000436459:P52L;ENSP00000433252:P52L	ENSP00000325917:P52L	P	-	2	0	PCSK7	116605616	0.973000	0.33851	0.663000	0.29738	0.590000	0.36582	3.090000	0.50191	0.676000	0.31285	-0.379000	0.06801	CCG	.	.		0.652	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		A	117100406	G	A	117100406	3	1	197	1	0	0	0	0	1	0	0	0	11614	1116	39	1	2262	1	PCSK7	11	117100406	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	5358261	117100406	17906110	140	29050										
OR6M1	390261	hgsc.bcm.edu	37	chr11	123676433	123676433	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtaggacccagtagtgaatgCcagggagctcaggatgacaa	14	8	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:123676433C>A	ENST00000309154.2	-	1	662	c.625G>T	c.(625-627)Gca>Tca	p.A209S		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	209						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		GTAGTGAATGCCAGGGAGCTC	0.488																																					p.A209S		Atlas-SNP	.											.	OR6M1	60	.	0			c.G625T						.						66	60	62					11																	123676433		2202	4299	6501	SO:0001583	missense	390261	exon1			TGAATGCCAGGGA	AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"GPCR / Class A : Olfactory receptors"	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.625G>T	chr11.hg19:g.123676433C>A	ENSP00000311038:p.Ala209Ser	87.0	0.0		66.0	7.0	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	hg19	CCDS31696.1	.	.	.	.	.	.	.	.	.	.	C	0.777	-0.763838	0.02996	.	.	ENSG00000196099	ENST00000309154	T	0.37411	1.2	3.48	2.53	0.30540	GPCR, rhodopsin-like superfamily (1);	0.538685	0.13838	U	0.359236	T	0.17916	0.0430	N	0.05574	-0.02	0.09310	N	0.999999	B	0.15473	0.013	B	0.14023	0.01	T	0.17018	-1.0383	10	0.56958	D	0.05	.	5.8927	0.18921	0.2218:0.5623:0.216:0.0	.	209	Q8NGM8	OR6M1_HUMAN	S	209	ENSP00000311038:A209S	ENSP00000311038:A209S	A	-	1	0	OR6M1	123181643	0.000000	0.05858	0.243000	0.24186	0.008000	0.06430	-3.352000	0.00501	0.597000	0.29811	0.655000	0.94253	GCA	.	.		0.488	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325		A	123676433	C	A	123676433	3	1	197	1	0	0	0	0	1	0	0	0	11214	739	26	3	319	3	OR6M1	11	123676433	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	6576027	123676433	11330083	141	29051										
OR8G5	219865	hgsc.bcm.edu	37	chr11	124135129	124135129	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ccctgaatgcatgactcagcTctacttcttcctcgtttttg	6	13	3	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr11:124135129T>C	ENST00000524943.2	+	1	407	c.407T>C	c.(406-408)cTc>cCc	p.L136P	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		ATGACTCAGCTCTACTTCTTC	0.473																																					p.L136P	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.T407C						.						164	150	155					11																	124135129		2149	4278	6427	SO:0001583	missense	219865	exon1			CTCAGCTCTACTT	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"GPCR / Class A : Olfactory receptors"	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.407T>C	chr11.hg19:g.124135129T>C	ENSP00000477014:p.Leu136Pro	55.0	0.0		58.0	11.0	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	hg19																																																																																				.	.		0.473	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198		C	124135129	T	C	124135129	3	2	197	1	0	0	0	0	1	0	0	0	11245	1551	54	2	409	2	OR8G5	11	124135129	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	458696	124135129	10871387	142	29052										
PKP2	5318	hgsc.bcm.edu	37	chr12	33030888	33030888	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tcctcccgctggaatccacgGcgacactgggcccagcttcc	10	18	0	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr12:33030888G>A	ENST00000070846.6	-	3	950	c.926C>T	c.(925-927)gCc>gTc	p.A309V	PKP2_ENST00000340811.4_Missense_Mutation_p.A309V	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	309					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GGAATCCACGGCGACACTGGG	0.642																																					p.A309V		Atlas-SNP	.											.	PKP2	110	.	0			c.C926T						.						51	48	49					12																	33030888		2203	4300	6503	SO:0001583	missense	5318	exon3			TCCACGGCGACAC	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"Armadillo repeat containing"	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.926C>T	chr12.hg19:g.33030888G>A	ENSP00000070846:p.Ala309Val	48.0	0.0		33.0	9.0	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	hg19	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	G	9.787	1.176755	0.21704	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.80824	-1.42;-1.35	4.51	3.54	0.40534	.	436.916000	0.00166	N	0.000000	T	0.74741	0.3756	L	0.29908	0.895	0.09310	N	1	B;B;B	0.28713	0.161;0.1;0.22	B;B;B	0.24394	0.053;0.024;0.024	T	0.60403	-0.7270	10	0.34782	T	0.22	-8.9753	13.3223	0.60440	0.0:0.2136:0.7864:0.0	.	309;309;309	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	V	309	ENSP00000342800:A309V;ENSP00000070846:A309V	ENSP00000070846:A309V	A	-	2	0	PKP2	32922155	0.007000	0.16637	0.003000	0.11579	0.312000	0.27988	1.522000	0.35921	2.246000	0.74042	0.555000	0.69702	GCC	.	.		0.642	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		A	33030888	G	A	33030888	3	1	197	1	0	0	0	0	1	0	0	0	11994	1203	42	3	1767	3	PKP2	12	33030888	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10		33030888	100821007	143	29053										
KIF21A	55605	hgsc.bcm.edu	37	chr12	39756972	39756972	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aggggacatgtgtggccctcTtgctcttgtctcccaaggca	12	12	3	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr12:39756972T>A	ENST00000361418.5	-	7	962	c.947A>T	c.(946-948)aAg>aTg	p.K316M	KIF21A_ENST00000361961.3_Missense_Mutation_p.K316M|KIF21A_ENST00000544797.2_Missense_Mutation_p.K316M|KIF21A_ENST00000541463.2_Missense_Mutation_p.K316M|KIF21A_ENST00000395670.3_Missense_Mutation_p.K316M			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	316	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				TGTGGCCCTCTTGCTCTTGTC	0.393																																					p.K316M		Atlas-SNP	.											.	KIF21A	238	.	0			c.A947T						.						153	150	151					12																	39756972		2203	4300	6503	SO:0001583	missense	55605	exon7			GCCCTCTTGCTCT	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.947A>T	chr12.hg19:g.39756972T>A	ENSP00000354878:p.Lys316Met	64.0	0.0		80.0	16.0	NM_001173463	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	hg19	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.635456	0.87760	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000544797;ENST00000361418;ENST00000541463;ENST00000552908	T;T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05;-1.05	4.98	4.98	0.66077	Kinesin, motor domain (3);	0.000000	0.53938	D	0.000043	D	0.87720	0.6248	M	0.79614	2.46	0.58432	D	0.999997	D;D;D;D;D	0.89917	1.0;1.0;0.997;1.0;0.998	D;D;D;D;D	0.97110	0.982;0.998;0.963;1.0;0.97	D	0.89465	0.3739	10	0.87932	D	0	.	14.7019	0.69162	0.0:0.0:0.0:1.0	.	316;316;316;316;316	F5H219;B9EGE4;F5H0C3;Q7Z4S6;Q7Z4S6-2	.;.;.;KI21A_HUMAN;.	M	316;316;316;316;316;316;139	ENSP00000354851:K316M;ENSP00000379029:K316M;ENSP00000445606:K316M;ENSP00000354878:K316M;ENSP00000438075:K316M;ENSP00000449700:K139M	ENSP00000344501:K316M	K	-	2	0	KIF21A	38043239	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.023000	0.70848	1.880000	0.54463	0.460000	0.39030	AAG	.	.		0.393	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		A	39756972	T	A	39756972	3	1	197	1	0	0	0	0	1	0	0	0	8297	1609	56	4	4205	4	KIF21A	12	39756972	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	6726084	39756972	94094923	144	29054										
PPM1H	57460	hgsc.bcm.edu	37	chr12	63328293	63328293	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ctgcgtagccagtggcccagGgcagccgccgagtctccttg	14	15	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr12:63328293G>C	ENST00000228705.6	-	1	524	c.224C>G	c.(223-225)cCc>cGc	p.P75R	Y_RNA_ENST00000516851.1_RNA	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	75							phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		AGTGGCCCAGGGCAGCCGCCG	0.701																																					p.P75R		Atlas-SNP	.											.	PPM1H	42	.	0			c.C224G						.						4	7	6					12																	63328293		1886	3945	5831	SO:0001583	missense	57460	exon1			GCCCAGGGCAGCC	AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	18583	protein-coding gene	gene with protein product	"neurite extension-related protein phosphatase related to PP2C"		"ras homolog gene family, member C like 1", "protein phosphatase 1H (PP2C domain containing)"	ARHCL1			Standard	NM_020700		Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.224C>G	chr12.hg19:g.63328293G>C	ENSP00000228705:p.Pro75Arg	109.0	0.0		81.0	20.0	NM_020700	B1Q2A9|B2RXG4|Q6PI86	Missense_Mutation	SNP	ENST00000228705.6	hg19	CCDS44934.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.773831	0.90108	.	.	ENSG00000111110	ENST00000228705	T	0.55588	0.51	3.75	3.75	0.43078	Protein phosphatase 2C-like (3);	0.000000	0.85682	D	0.000000	T	0.73598	0.3607	M	0.84773	2.715	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.78516	-0.2174	9	.	.	.	2.9353	14.2944	0.66302	0.0:0.0:1.0:0.0	.	75	Q9ULR3	PPM1H_HUMAN	R	75	ENSP00000228705:P75R	.	P	-	2	0	PPM1H	61614560	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.219000	0.65262	1.929000	0.55896	0.561000	0.74099	CCC	.	.		0.701	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700		C	63328293	G	C	63328293	3	2	197	1	0	0	0	0	1	0	0	0	12353	1232	43	4	1360	4	PPM1H	12	63328293	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	23571321	63328293	70523602	145	29055										
UTP20	27340	hgsc.bcm.edu	37	chr12	101764273	101764273	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ctgaaaaacagctccaagttCtactggcctatgctgaggag	10	10	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr12:101764273C>G	ENST00000261637.4	+	50	6793	c.6619C>G	c.(6619-6621)Cta>Gta	p.L2207V		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2207					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						GCTCCAAGTTCTACTGGCCTA	0.433																																					p.L2207V		Atlas-SNP	.											.	UTP20	222	.	0			c.C6619G						.						190	175	180					12																	101764273		2203	4300	6503	SO:0001583	missense	27340	exon50			CAAGTTCTACTGG	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.6619C>G	chr12.hg19:g.101764273C>G	ENSP00000261637:p.Leu2207Val	73.0	0.0		87.0	11.0	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	hg19	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.722875	0.68959	.	.	ENSG00000120800	ENST00000261637	T	0.75260	-0.92	5.94	4.12	0.48240	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.86058	0.5842	M	0.90309	3.105	0.54753	D	0.999981	D	0.89917	1.0	D	0.91635	0.999	D	0.85623	0.1265	10	0.40728	T	0.16	-12.9508	8.1483	0.31126	0.0:0.7111:0.0:0.2889	.	2207	O75691	UTP20_HUMAN	V	2207	ENSP00000261637:L2207V	ENSP00000261637:L2207V	L	+	1	2	UTP20	100288404	1.000000	0.71417	0.793000	0.32043	0.988000	0.76386	3.443000	0.52907	1.524000	0.49035	-0.259000	0.10710	CTA	.	.		0.433	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		G	101764273	C	G	101764273	3	3	197	1	0	0	0	0	1	0	0	0	17114	912	32	4	6817	4	UTP20	12	101764273	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	38435980	101764273	32087622	146	29056										
NOS1	4842	hgsc.bcm.edu	37	chr12	117768235	117768235	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gctcccactggtgagaaggcTcagcacaggctctatctcct	10	14	3	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr12:117768235T>C	ENST00000338101.4	-	1	644	c.640A>G	c.(640-642)Agc>Ggc	p.S214G	NOS1_ENST00000317775.6_Missense_Mutation_p.S214G|NOS1_ENST00000549189.1_5'Flank|NOS1_ENST00000344089.3_Missense_Mutation_p.S214G			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GTGAGAAGGCTCAGCACAGGC	0.592																																					p.S214G	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.A640G						.						128	136	134					12																	117768235		2055	4205	6260	SO:0001583	missense	4842	exon2			GAAGGCTCAGCAC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.640A>G	chr12.hg19:g.117768235T>C	ENSP00000337459:p.Ser214Gly	41.0	0.0		64.0	11.0	NM_000620		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	T	10.80	1.453947	0.26161	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000344089;ENST00000338101	T;T;T	0.05717	4.97;3.4;4.97	4.65	2.26	0.28386	.	0.777994	0.13174	N	0.408005	T	0.04227	0.0117	L	0.29908	0.895	0.26070	N	0.981237	B	0.02656	0.0	B	0.01281	0.0	T	0.46275	-0.9203	10	0.17369	T	0.5	-4.2879	4.1645	0.10300	0.0:0.227:0.1776:0.5954	.	214	P29475	NOS1_HUMAN	G	214	ENSP00000320758:S214G;ENSP00000339862:S214G;ENSP00000337459:S214G	ENSP00000320758:S214G	S	-	1	0	NOS1	116252618	0.998000	0.40836	0.519000	0.27824	0.867000	0.49689	2.930000	0.48924	0.296000	0.22592	0.397000	0.26171	AGC	.	.		0.592	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			C	117768235	T	C	117768235	3	2	197	1	0	0	0	0	1	0	0	0	10550	1551	54	2	3776	2	NOS1	12	117768235	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	16003962	117768235	16083660	147	29057										
MAB21L1	4081	hgsc.bcm.edu	37	chr13	36049724	36049724	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tggggaagtggccagtgggcAgcactcctcggccagatccc	15	13	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr13:36049724A>T	ENST00000379919.4	-	1	1108	c.552T>A	c.(550-552)gcT>gcA	p.A184A	NBEA_ENST00000310336.4_Intron|NBEA_ENST00000379939.2_Intron|NBEA_ENST00000540320.1_Intron|NBEA_ENST00000537702.1_5'Flank|NBEA_ENST00000400445.3_Intron	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)	184					anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		GCCAGTGGGCAGCACTCCTCG	0.602																																					p.A184A		Atlas-SNP	.											.	MAB21L1	52	.	0			c.T552A						.						48	54	52					13																	36049724		2203	4300	6503	SO:0001819	synonymous_variant	4081	exon1			GTGGGCAGCACTC	BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"mab-21 (C. elegans)-like 1"			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.552T>A	chr13.hg19:g.36049724A>T		68.0	0.0		48.0	11.0	NM_005584	Q6I9T5	Silent	SNP	ENST00000379919.4	hg19	CCDS9353.1																																																																																			.	.		0.602	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584		T	36049724	A	T	36049724	2	4	197	1	0	0	0	0	0	0	0	1	9150	175	7	4		4	MAB21L1	13	36049724	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10		36049724	79120154	148	29058										
DCLK1	9201	hgsc.bcm.edu	37	chr13	36385016	36385016	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gccacgtatgttggggtgccAcagactgtgtacagggggcc	16	10	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr13:36385016A>G	ENST00000360631.3	-	12	1855	c.1644T>C	c.(1642-1644)tgT>tgC	p.C548C	DCLK1_ENST00000379893.1_Silent_p.C241C|DCLK1_ENST00000255448.4_Silent_p.C548C			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	548	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		TTGGGGTGCCACAGACTGTGT	0.488																																					p.C548C		Atlas-SNP	.											.	DCLK1	350	.	0			c.T1644C						.						173	168	170					13																	36385016		2203	4300	6503	SO:0001819	synonymous_variant	9201	exon12			GGTGCCACAGACT	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1644T>C	chr13.hg19:g.36385016A>G		81.0	0.0		67.0	15.0	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	hg19																																																																																				.	.		0.488	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		G	36385016	A	G	36385016	2	3	197	1	0	0	0	0	0	0	0	1	4293	157	6	2		2	DCLK1	13	36385016	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	335292	36385016	78784862	149	29059										
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46542149	46542149	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tcttcttgaactatggcttcTtgaatcctggcgatctaaaa	7	9	4	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr13:46542149T>A	ENST00000242848.4	-	15	4159	c.3811A>T	c.(3811-3813)Aga>Tga	p.R1271*	ZC3H13_ENST00000282007.3_Nonsense_Mutation_p.R1271*|ZC3H13_ENST00000378921.2_Nonsense_Mutation_p.R227*			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1271	Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		CTATGGCTTCTTGAATCCTGG	0.363																																					p.R1271X	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-SNP	.											.	ZC3H13	197	.	0			c.A3811T						.						101	102	102					13																	46542149		2203	4300	6503	SO:0001587	stop_gained	23091	exon15			GGCTTCTTGAATC	AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.3811A>T	chr13.hg19:g.46542149T>A	ENSP00000242848:p.Arg1271*	74.0	0.0		56.0	12.0	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Nonsense_Mutation	SNP	ENST00000242848.4	hg19		.	.	.	.	.	.	.	.	.	.	T	46	12.469775	0.99670	.	.	ENSG00000123200	ENST00000242848;ENST00000378921;ENST00000282007	.	.	.	5.36	4.15	0.48705	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.5356	0.56140	0.0:0.0:0.1395:0.8605	.	.	.	.	X	1271;227;1271	.	ENSP00000242848:R1271X	R	-	1	2	ZC3H13	45440150	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.711000	0.61881	0.944000	0.37579	0.482000	0.46254	AGA	.	.		0.363	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46542149	T	A	46542149	4	1	197	1	0	0	0	0	0	1	0	0	17580	1617	56	4	895	4	ZC3H13	13	46542149	Nonsense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	10157133	46542149	68627729	150	29060										
PNN	5411	hgsc.bcm.edu	37	chr14	39650465	39650470	+	In_Frame_Del	DEL	CAGGAG	CAGGAG	-													0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agccaacaccccaagttactCaggagcaagggcatttacta							TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	CAGGAG	CAGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr14:39650465_39650470delCAGGAG	ENST00000216832.4	+	9	1619_1624	c.1552_1557delCAGGAG	c.(1552-1557)caggagdel	p.QE518del	PNN_ENST00000557680.1_Intron	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	518	Gln-rich.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		CCAAGTTACTCAGGAGCAAGGGCATT	0.49																																					p.517_519del		Atlas-INDEL	.											.	PNN	67	.	0			c.1551_1556del						.																																			SO:0001651	inframe_deletion	5411	exon9			.	U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.1552_1557delCAGGAG	chr14.hg19:g.39650465_39650470delCAGGAG	ENSP00000216832:p.Gln518_Glu519del	113.0	0.0		105.0	21.0	NM_002687	B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	In_Frame_Del	DEL	ENST00000216832.4	hg19	CCDS9671.1																																																																																			.	.		0.49	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687		-	39650470	CAGGAG	-	39650465	7	5	197	1	0	1	0	1	0	0	0	0	12169	827	29	0	1586	0	PNN	14	39650465	In_Frame_Del	DEL	CAGGAG	TCGA-DD-AADO-01A-11D-A40R-10		39650465	67699075	151	29061										
SAMD4A	23034	hgsc.bcm.edu	37	chr14	55215638	55215638	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	caccgagtgccagctggaggCgcaggtatgtgcttgaggtg	17	9	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr14:55215638C>G	ENST00000554335.1	+	5	1748	c.1085C>G	c.(1084-1086)gCg>gGg	p.A362G	SAMD4A_ENST00000357634.3_Missense_Mutation_p.A361G|SAMD4A_ENST00000251091.5_Missense_Mutation_p.A274G|SAMD4A_ENST00000392067.3_Missense_Mutation_p.A362G			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	362	SAM.				negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						CAGCTGGAGGCGCAGGTATGT	0.582																																					p.A362G		Atlas-SNP	.											SAMD4A,colon,carcinoma,0,2	SAMD4A	68	.	0			c.C1085G						.						51	45	47					14																	55215638		2160	4227	6387	SO:0001583	missense	23034	exon4			TGGAGGCGCAGGT	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"Sterile alpha motif (SAM) domain containing"	23023	protein-coding gene	gene with protein product	"smaug homolog (Drosophila)"	610747	"sterile alpha motif domain containing 4"	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1085C>G	chr14.hg19:g.55215638C>G	ENSP00000452535:p.Ala362Gly	82.0	0.0		65.0	26.0	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	hg19	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233508	0.79688	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634	T;T;T	0.50813	0.73;0.73;0.73	5.32	5.32	0.75619	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.64136	0.2571	M	0.64170	1.965	0.58432	D	0.99999	P;D	0.63046	0.564;0.992	B;P	0.60117	0.343;0.869	T	0.61402	-0.7070	10	0.41790	T	0.15	-8.0339	19.1782	0.93612	0.0:1.0:0.0:0.0	.	274;362	Q9UPU9-3;Q9UPU9	.;SMAG1_HUMAN	G	362;362;274;273;361	ENSP00000452535:A362G;ENSP00000375919:A362G;ENSP00000350261:A361G	ENSP00000306381:A274G	A	+	2	0	SAMD4A	54285388	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.477000	0.66799	2.769000	0.95229	0.563000	0.77884	GCG	.	.		0.582	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		G	55215638	C	G	55215638	3	3	197	1	0	0	0	0	1	0	0	0	13836	768	27	4	1096	4	SAMD4A	14	55215638	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	15565173	55215638	52133902	152	29062										
NUMB	8650	hgsc.bcm.edu	37	chr14	73750978	73750978	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggcatgaggattgttcatctCcagagaggtcgtggcatcag	14	8	3	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr14:73750978C>A	ENST00000355058.3	-	10	1038	c.760G>T	c.(760-762)Gag>Tag	p.E254*	NUMB_ENST00000554521.2_Intron|NUMB_ENST00000544991.3_Intron|NUMB_ENST00000559312.1_Intron|NUMB_ENST00000556772.1_Nonsense_Mutation_p.E110*|NUMB_ENST00000359560.3_Nonsense_Mutation_p.E243*|NUMB_ENST00000557597.1_Nonsense_Mutation_p.E243*|NUMB_ENST00000356296.4_Nonsense_Mutation_p.E254*|NUMB_ENST00000454166.4_Intron|NUMB_ENST00000560335.1_Intron|NUMB_ENST00000555394.1_Nonsense_Mutation_p.E254*|NUMB_ENST00000554546.1_Nonsense_Mutation_p.E243*|NUMB_ENST00000555738.2_Intron|NUMB_ENST00000555238.1_Nonsense_Mutation_p.E254*|NUMB_ENST00000535282.1_Nonsense_Mutation_p.E243*			P49757	NUMB_HUMAN	numb homolog (Drosophila)	254					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		TTGTTCATCTCCAGAGAGGTC	0.532																																					p.E254X		Atlas-SNP	.											.	NUMB	56	.	0			c.G760T						.						174	165	168					14																	73750978		2203	4300	6503	SO:0001587	stop_gained	8650	exon10			TCATCTCCAGAGA	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"numb (Drosophila) homolog", "chromosome 14 open reading frame 41"	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.760G>T	chr14.hg19:g.73750978C>A	ENSP00000347169:p.Glu254*	159.0	0.0		114.0	53.0	NM_001005744	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Nonsense_Mutation	SNP	ENST00000355058.3	hg19	CCDS32116.1	.	.	.	.	.	.	.	.	.	.	C	37	6.238345	0.97403	.	.	ENSG00000133961	ENST00000554546;ENST00000356296;ENST00000557597;ENST00000555238;ENST00000556772;ENST00000355058;ENST00000359560;ENST00000555394;ENST00000535282;ENST00000326018;ENST00000555859;ENST00000555307;ENST00000554394	.	.	.	5.39	5.39	0.77823	.	0.173814	0.52532	D	0.000075	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-15.7781	19.34	0.94337	0.0:1.0:0.0:0.0	.	.	.	.	X	243;254;243;254;110;254;243;254;243;218;218;254;254	.	ENSP00000315193:E218X	E	-	1	0	NUMB	72820731	1.000000	0.71417	0.998000	0.56505	0.701000	0.40568	7.427000	0.80284	2.808000	0.96608	0.655000	0.94253	GAG	.	.		0.532	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1			A	73750978	C	A	73750978	4	1	197	1	0	0	0	0	0	1	0	0	10760	864	30	3	1211	3	NUMB	14	73750978	Nonsense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	18535340	73750978	33598562	153	29063										
ASB2	51676	hgsc.bcm.edu	37	chr14	94423206	94423206	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggccggcgaactctcaggagGtgcagtggacctggagggtg	19	9	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr14:94423206G>A	ENST00000315988.4	-	1	561	c.73C>T	c.(73-75)Cct>Tct	p.P25S	ASB2_ENST00000555019.1_Missense_Mutation_p.P73S|ASB2_ENST00000556337.1_Intron	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	25					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		CTCTCAGGAGGTGCAGTGGAC	0.577																																					p.P73S		Atlas-SNP	.											.	ASB2	71	.	0			c.C217T						.						93	94	94					14																	94423206		2203	4300	6503	SO:0001583	missense	51676	exon3			CAGGAGGTGCAGT	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"Ankyrin repeat domain containing"	16012	protein-coding gene	gene with protein product		605759	"ankyrin repeat and SOCS box-containing 2"				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.73C>T	chr14.hg19:g.94423206G>A	ENSP00000320675:p.Pro25Ser	112.0	0.0		93.0	15.0	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	hg19	CCDS9915.1	.	.	.	.	.	.	.	.	.	.	G	0.304	-0.971776	0.02215	.	.	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988	T;T	0.67171	-0.25;-0.2	5.42	-0.271	0.12922	.	0.640402	0.14988	N	0.286861	T	0.45994	0.1370	L	0.27053	0.805	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.25328	-1.0135	10	0.40728	T	0.16	-1.2658	4.6335	0.12513	0.2251:0.0:0.5221:0.2528	.	73;25	B4E166;Q96Q27	.;ASB2_HUMAN	S	73;41;25	ENSP00000451575:P73S;ENSP00000320675:P25S	ENSP00000320675:P25S	P	-	1	0	ASB2	93492959	0.063000	0.20901	0.001000	0.08648	0.005000	0.04900	0.591000	0.23969	-0.042000	0.13535	-0.136000	0.14681	CCT	.	.		0.577	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1			A	94423206	G	A	94423206	3	1	197	1	0	0	0	0	1	0	0	0	1023	1261	44	3	1722	3	ASB2	14	94423206	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	20672228	94423206	12926334	154	29064										
RYR3	6263	hgsc.bcm.edu	37	chr15	33835899	33835902	+	Frame_Shift_Del	DEL	GAAT	GAAT	-													0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	acgataccatctacagaccaGaatgattcccagcacaggta					rs538703172	byFrequency	TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	GAAT	GAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:33835899_33835902delGAAT	ENST00000389232.4	+	8	793_796	c.723_726delGAAT	c.(721-726)cagaatfs	p.QN241fs	RYR3_ENST00000415757.3_Frame_Shift_Del_p.QN241fs	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	241	MIR 3. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.Q241H(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CTACAGACCAGAATGATTCCCAGC	0.392																																					p.241_242del		Atlas-INDEL	.											.	RYR3	760	.	1	Substitution - Missense(1)	lung(1)	c.722_725del						.																																			SO:0001589	frameshift_variant	6263	exon8			.		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.723_726delGAAT	chr15.hg19:g.33835899_33835902delGAAT	ENSP00000373884:p.Gln241fs	114.0	0.0		92.0	25.0	NM_001243996	O15175|Q15412	Frame_Shift_Del	DEL	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.392	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			-	33835902	GAAT	-	33835899	7	5	197	1	0	1	0	1	0	0	0	0	13785	933	33	0	753	0	RYR3	15	33835899	Frame_Shift_Del	DEL	GAAT	TCGA-DD-AADO-01A-11D-A40R-10		33835899	68695493	155	29065										
C15orf53	400359	hgsc.bcm.edu	37	chr15	38990484	38990484	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gttgatacaagctccagctcAtgtcttcagacaatgctggg	10	10	3	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:38990484A>C	ENST00000318792.1	+	2	288	c.278A>C	c.(277-279)cAt>cCt	p.H93P		NM_207444.2	NP_997327.1	Q8NAA6	CO053_HUMAN	chromosome 15 open reading frame 53	93										endometrium(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	6		all_cancers(109;1.75e-13)|all_epithelial(112;1.02e-11)|Lung NSC(122;1.9e-09)|all_lung(180;4.04e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;8.39e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0321)		GCTCCAGCTCATGTCTTCAGA	0.502																																					p.H93P		Atlas-SNP	.											.	C15orf53	12	.	0			c.A278C						.						74	70	72					15																	38990484		2200	4297	6497	SO:0001583	missense	400359	exon2			CAGCTCATGTCTT		CCDS10048.1	15q14	2007-11-21			ENSG00000175779	ENSG00000175779			33796	protein-coding gene	gene with protein product							Standard	NM_207444		Approved	FLJ35695	uc001zkf.1	Q8NAA6	OTTHUMG00000129841	ENST00000318792.1:c.278A>C	chr15.hg19:g.38990484A>C	ENSP00000325144:p.His93Pro	110.0	0.0		83.0	19.0	NM_207444		Missense_Mutation	SNP	ENST00000318792.1	hg19	CCDS10048.1	.	.	.	.	.	.	.	.	.	.	A	8.015	0.758371	0.15846	.	.	ENSG00000175779	ENST00000318792	T	0.37411	1.2	3.29	-1.98	0.07480	.	.	.	.	.	T	0.14270	0.0345	N	0.08118	0	0.09310	N	1	P	0.39862	0.692	B	0.37304	0.246	T	0.13229	-1.0517	9	0.87932	D	0	.	0.3085	0.00284	0.3512:0.2002:0.2536:0.195	.	93	Q8NAA6	CO053_HUMAN	P	93	ENSP00000325144:H93P	ENSP00000325144:H93P	H	+	2	0	C15orf53	36777776	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.001000	0.12947	-0.405000	0.07599	0.402000	0.26972	CAT	.	.		0.502	C15orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252081.1	NM_207444		C	38990484	A	C	38990484	3	2	197	1	0	0	0	0	1	0	0	0	1803	217	8	5	284	5	C15orf53	15	38990484	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	5154585	38990484	63540908	156	29066										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42150939	42150939	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggttcttctccctcagccacGcagccacctgggcacatggg	11	16	3	0	rs372953121		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:42150939G>A	ENST00000320955.6	-	49	8314	c.8087C>T	c.(8086-8088)gCg>gTg	p.A2696V		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2696					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CCTCAGCCACGCAGCCACCTG	0.622																																					p.A2661V		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C7982T						.	G	VAL/ALA	0,4256		0,0,2128	22	25	24		7982	-5.9	0	15		24	1,8451		0,1,4225	no	missense	SPTBN5	NM_016642.2	64	0,1,6353	AA,AG,GG		0.0118,0.0,0.0079	benign	2661/3640	42150939	1,12707	2128	4226	6354	SO:0001583	missense	51332	exon49			AGCCACGCAGCCA	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8087C>T	chr15.hg19:g.42150939G>A	ENSP00000317790:p.Ala2696Val	58.0	0.0		65.0	15.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	12.33	1.904967	0.33628	0.0	1.18E-4	ENSG00000137877	ENST00000320955	T	0.52983	0.64	4.7	-5.87	0.02297	.	2.128150	0.02461	N	0.086613	T	0.40862	0.1134	L	0.41961	1.31	0.09310	N	1	B	0.26120	0.142	B	0.21546	0.035	T	0.36407	-0.9749	10	0.42905	T	0.14	.	13.5294	0.61613	0.5079:0.0:0.4921:0.0	.	2696	Q9NRC6	SPTN5_HUMAN	V	2696	ENSP00000317790:A2696V	ENSP00000317790:A2696V	A	-	2	0	SPTBN5	39938231	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.570000	0.23653	-1.279000	0.02405	-1.232000	0.01568	GCG	.	.		0.622	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		A	42150939	G	A	42150939	3	1	197	1	0	0	0	0	1	0	0	0	15137	1087	38	1	3017	1	SPTBN5	15	42150939	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	3160455	42150939	60380453	157	29067										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51772972	51772972	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtctaccatttcttcctgatCcagcagatcactctctactt	4	14	4	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:51772972C>G	ENST00000251076.5	-	24	6618	c.6331G>C	c.(6331-6333)Gat>Cat	p.D2111H	DMXL2_ENST00000449909.3_Missense_Mutation_p.D1475H|DMXL2_ENST00000543779.2_Missense_Mutation_p.D2111H|RP11-707P17.1_ENST00000561007.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2111						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TCTTCCTGATCCAGCAGATCA	0.393																																					p.D2111H		Atlas-SNP	.											DMXL2,bladder,carcinoma,0,1	DMXL2	262	.	0			c.G6331C						.						119	114	116					15																	51772972		2196	4293	6489	SO:0001583	missense	23312	exon24			CCTGATCCAGCAG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.6331G>C	chr15.hg19:g.51772972C>G	ENSP00000251076:p.Asp2111His	101.0	1.0		164.0	13.0	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	10.96	1.499195	0.26861	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	T;T;T	0.78816	-1.21;-1.21;-1.21	5.77	2.91	0.33838	.	0.334765	0.38837	N	0.001541	T	0.71736	0.3375	N	0.22421	0.69	0.46927	D	0.999256	B;D;P;B	0.60160	0.432;0.987;0.498;0.025	B;P;B;B	0.53809	0.368;0.735;0.259;0.022	T	0.68887	-0.5290	10	0.45353	T	0.12	.	9.4269	0.38586	0.0:0.7519:0.1187:0.1294	.	2111;1475;2111;2111	F5GWF1;B2RTR3;Q8TDJ6;B7ZMH3	.;.;DMXL2_HUMAN;.	H	2111;2111;1475	ENSP00000251076:D2111H;ENSP00000441858:D2111H;ENSP00000400855:D1475H	ENSP00000251076:D2111H	D	-	1	0	DMXL2	49560264	0.998000	0.40836	0.730000	0.30809	0.218000	0.24690	3.582000	0.53921	0.382000	0.24878	-0.123000	0.14984	GAT	.	.		0.393	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		G	51772972	C	G	51772972	3	3	197	1	0	0	0	0	1	0	0	0	4597	855	30	4	2862	4	DMXL2	15	51772972	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	9622033	51772972	50758420	158	29068										
PSTPIP1	9051	hgsc.bcm.edu	37	chr15	77320208	77320208	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tgcagtatgaggccgtcatgGaccgggtccagaagagcaag	15	9	1	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:77320208G>T	ENST00000558012.1	+	6	859	c.370G>T	c.(370-372)Gac>Tac	p.D124Y	PSTPIP1_ENST00000379595.3_Missense_Mutation_p.D124Y|PSTPIP1_ENST00000267939.5_Missense_Mutation_p.D123Y|PSTPIP1_ENST00000559295.1_Missense_Mutation_p.D124Y	NM_003978.3	NP_003969.2	O43586	PPIP1_HUMAN	proline-serine-threonine phosphatase interacting protein 1	124					cell adhesion (GO:0007155)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|signal transduction (GO:0007165)	actomyosin contractile ring (GO:0005826)|cell projection (GO:0042995)|cleavage furrow (GO:0032154)|cytosol (GO:0005829)|membrane (GO:0016020)|stress fiber (GO:0001725)				breast(1)|endometrium(3)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						GGCCGTCATGGACCGGGTCCA	0.672																																					p.D124Y		Atlas-SNP	.											.	PSTPIP1	50	.	0			c.G370T						.						22	26	25					15																	77320208		1996	4144	6140	SO:0001583	missense	9051	exon6			GTCATGGACCGGG	U94778	CCDS45312.1	15q24.3	2014-09-17			ENSG00000140368	ENSG00000140368			9580	protein-coding gene	gene with protein product	"CD2 cytoplasmic tail-binding protein", "CD2 antigen-binding protein 1", "PEST phosphatase-interacting protein 1"	606347				9857189	Standard	NM_003978		Approved	PSTPIP, CD2BP1L, CD2BP1, CD2BP1S, H-PIP, PAPAS	uc002bcf.2	O43586	OTTHUMG00000172594	ENST00000558012.1:c.370G>T	chr15.hg19:g.77320208G>T	ENSP00000452746:p.Asp124Tyr	282.0	0.0		352.0	121.0	NM_003978	B5BU74|B5BUK4|O43585|O95657	Missense_Mutation	SNP	ENST00000558012.1	hg19	CCDS45312.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.264821	0.80358	.	.	ENSG00000140368	ENST00000379595;ENST00000267939	T;T	0.42900	0.96;2.56	4.2	4.2	0.49525	Prismane-like (1);	0.116695	0.64402	D	0.000018	T	0.62780	0.2456	M	0.78456	2.415	0.51233	D	0.999917	D;P;D;D	0.71674	0.998;0.816;0.991;0.985	D;P;P;P	0.63381	0.914;0.574;0.73;0.781	T	0.69921	-0.5014	10	0.72032	D	0.01	-18.7755	15.3433	0.74314	0.0:0.0:1.0:0.0	.	2;124;123;124	B4DQC0;O43586-2;C9K004;O43586	.;.;.;PPIP1_HUMAN	Y	124;123	ENSP00000368914:D124Y;ENSP00000267939:D123Y	ENSP00000267939:D123Y	D	+	1	0	PSTPIP1	75107263	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.903000	0.87398	1.895000	0.54865	0.462000	0.41574	GAC	.	.		0.672	PSTPIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419373.2	NM_003978		T	77320208	G	T	77320208	3	4	197	1	0	0	0	0	1	0	0	0	12733	1174	41	3	392	3	PSTPIP1	15	77320208	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	25547236	77320208	25211184	159	29069										
CTSH	1512	hgsc.bcm.edu	37	chr15	79223830	79223830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	attgaagtcctgggcgcagtCcaccagctgctgttccgcct	11	14	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:79223830C>T	ENST00000220166.5	-	7	620	c.511G>A	c.(511-513)Gac>Aac	p.D171N	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	171					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						TGGGCGCAGTCCACCAGCTGC	0.587																																					p.D171N		Atlas-SNP	.											.	CTSH	23	.	0			c.G511A						.						123	99	107					15																	79223830		2196	4293	6489	SO:0001583	missense	1512	exon7			CGCAGTCCACCAG	X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"Cathepsins"	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.511G>A	chr15.hg19:g.79223830C>T	ENSP00000220166:p.Asp171Asn	80.0	0.0		73.0	27.0	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Missense_Mutation	SNP	ENST00000220166.5	hg19	CCDS10308.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.582774	0.86748	.	.	ENSG00000103811	ENST00000220166;ENST00000394758;ENST00000528741	T;T	0.29142	1.58;1.58	3.68	3.68	0.42216	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.59689	0.2212	M	0.89534	3.04	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.67829	-0.5569	10	0.87932	D	0	.	11.1069	0.48207	0.0:1.0:0.0:0.0	.	171;159	P09668;E9PBP2	CATH_HUMAN;.	N	171;159;95	ENSP00000220166:D171N;ENSP00000435329:D95N	ENSP00000220166:D171N	D	-	1	0	CTSH	77010885	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	5.969000	0.70422	2.073000	0.62155	0.462000	0.41574	GAC	.	.		0.587	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390		T	79223830	C	T	79223830	3	4	197	1	0	0	0	0	1	0	0	0	4038	855	30	3	520	3	CTSH	15	79223830	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	1903622	79223830	23307562	160	29070										
TMC3	342125	hgsc.bcm.edu	37	chr15	81628988	81628988	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cctttttcttatcctctgatCttgcctaaaatgcaaatgat	4	10	3	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:81628988C>G	ENST00000359440.5	-	20	2300	c.2165G>C	c.(2164-2166)aGa>aCa	p.R722T	RP11-761I4.3_ENST00000560973.1_RNA|RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.R723T|RP11-761I4.3_ENST00000559781.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						ATCCTCTGATCTTGCCTAAAA	0.368																																					p.R722T		Atlas-SNP	.											.	TMC3	112	.	0			c.G2165C						.						280	273	275					15																	81628988		1895	4102	5997	SO:0001583	missense	342125	exon20			TCTGATCTTGCCT	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.2165G>C	chr15.hg19:g.81628988C>G	ENSP00000352413:p.Arg722Thr	52.0	0.0		89.0	17.0	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	hg19	CCDS45324.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.045491	0.75846	.	.	ENSG00000188869	ENST00000359440	T	0.68479	-0.33	5.18	5.18	0.71444	.	1.874750	0.03529	N	0.222210	D	0.84813	0.5555	M	0.86028	2.79	0.41534	D	0.988474	.	.	.	.	.	.	T	0.72734	-0.4204	8	0.66056	D	0.02	-4.6803	16.8735	0.86045	0.0:1.0:0.0:0.0	.	.	.	.	T	722	ENSP00000352413:R722T	ENSP00000352413:R722T	R	-	2	0	TMC3	79416043	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	5.315000	0.65810	2.387000	0.81309	0.561000	0.74099	AGA	.	.		0.368	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		G	81628988	C	G	81628988	3	3	197	1	0	0	0	0	1	0	0	0	16001	927	32	4	1149	4	TMC3	15	81628988	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	2405158	81628988	20902404	161	29071										
AGBL1	123624	hgsc.bcm.edu	37	chr15	87097621	87097621	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aaaatccttgataagctagcAccagcattcacaatgagcag	7	10	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:87097621A>G	ENST00000441037.2	+	20	2804	c.2709A>G	c.(2707-2709)gcA>gcG	p.A903A	AGBL1_ENST00000389298.3_Silent_p.A634A|AGBL1_ENST00000421325.2_Silent_p.A903A	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	903					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						ATAAGCTAGCACCAGCATTCA	0.463																																					p.A903A		Atlas-SNP	.											.	AGBL1	151	.	0			c.A2709G						.						33	33	33					15																	87097621		1875	4105	5980	SO:0001819	synonymous_variant	123624	exon20			GCTAGCACCAGCA	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2709A>G	chr15.hg19:g.87097621A>G		99.0	0.0		111.0	21.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	hg19	CCDS58398.1																																																																																			.	.		0.463	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		G	87097621	A	G	87097621	2	3	197	1	0	0	0	0	0	0	0	1	375	146	6	2		2	AGBL1	15	87097621	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	5468633	87097621	15433771	162	29072										
DET1	55070	hgsc.bcm.edu	37	chr15	89074816	89074816	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gaagacattctgatggaacaCtcggacttggtgccagtggg	14	8	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:89074816C>T	ENST00000268148.8	-	2	266	c.121G>A	c.(121-123)Gtg>Atg	p.V41M	DET1_ENST00000444300.1_Missense_Mutation_p.V52M|DET1_ENST00000558413.1_Intron|DET1_ENST00000564406.1_Missense_Mutation_p.V52M|DET1_ENST00000559656.1_5'Flank	NM_001144074.1	NP_001137546.1	Q7L5Y6	DET1_HUMAN	de-etiolated homolog 1 (Arabidopsis)	41						nucleus (GO:0005634)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)			TGATGGAACACTCGGACTTGG	0.488																																					p.V52M		Atlas-SNP	.											.	DET1	55	.	0			c.G154A						.						161	159	159					15																	89074816		2003	4180	6183	SO:0001583	missense	55070	exon3			GGAACACTCGGAC	BC001242	CCDS45343.1, CCDS45344.1	15q25.3	2004-12-13				ENSG00000140543			25477	protein-coding gene	gene with protein product		608727				14739464	Standard	NM_001144074		Approved	FLJ10103	uc002bmq.2	Q7L5Y6		ENST00000268148.8:c.121G>A	chr15.hg19:g.89074816C>T	ENSP00000268148:p.Val41Met	134.0	0.0		182.0	17.0	NM_017996	B3KNN6|Q2VPC0|Q9NWD5	Missense_Mutation	SNP	ENST00000268148.8	hg19	CCDS45344.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.199349	0.38806	.	.	ENSG00000140543	ENST00000444300;ENST00000268148	.	.	.	5.91	5.91	0.95273	.	0.221335	0.47455	D	0.000237	T	0.43634	0.1256	N	0.22421	0.69	0.37158	D	0.90246	B;B	0.27117	0.168;0.168	B;B	0.23716	0.029;0.048	T	0.48603	-0.9021	9	0.48119	T	0.1	-19.0177	12.5706	0.56334	0.0:0.9251:0.0:0.0749	.	41;52	Q7L5Y6;B3KNN6	DET1_HUMAN;.	M	52;41	.	ENSP00000268148:V41M	V	-	1	0	DET1	86875820	0.997000	0.39634	0.973000	0.42090	0.962000	0.63368	2.912000	0.48782	2.793000	0.96121	0.655000	0.94253	GTG	.	.		0.488	DET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415442.2	NM_017996		T	89074816	C	T	89074816	3	4	197	1	0	0	0	0	1	0	0	0	4452	565	20	3	1547	3	DET1	15	89074816	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	1977195	89074816	13456576	163	29073										
MFGE8	4240	hgsc.bcm.edu	37	chr15	89453089	89453089	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtacgaggggaagacatctcCtcgcacttcttgggaaatct	11	10	3	1	rs148213281		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:89453089C>G	ENST00000566497.1	-	2	200	c.139G>C	c.(139-141)Gga>Cga	p.G47R	MFGE8_ENST00000539437.1_Missense_Mutation_p.G39R|MFGE8_ENST00000542878.1_Intron|MFGE8_ENST00000559997.1_Intron|MFGE8_ENST00000268150.8_Missense_Mutation_p.G47R|MFGE8_ENST00000268151.7_Missense_Mutation_p.G47R			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	47	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					AAGACATCTCCTCGCACTTCT	0.527													C|||	1	0.000199681	8e-04	0	5008	,	,		22778	0		0	False		,,,				2504	0				p.G47R		Atlas-SNP	.											.	MFGE8	60	.	0			c.G139C						.	C	ARG/GLY,ARG/GLY	2,4398	4.2+/-10.8	0,2,2198	185	151	163		139,139	5.4	1	15	dbSNP_134	163	0,8598		0,0,4299	no	missense,missense	MFGE8	NM_001114614.1,NM_005928.2	125,125	0,2,6497	GG,GC,CC		0.0,0.0455,0.0154	probably-damaging,probably-damaging	47/336,47/388	89453089	2,12996	2200	4299	6499	SO:0001583	missense	4240	exon2			CATCTCCTCGCAC	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"sperm surface protein hP47"	602281	"sperm associated antigen 10"	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.139G>C	chr15.hg19:g.89453089C>G	ENSP00000456281:p.Gly47Arg	168.0	0.0		190.0	23.0	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Missense_Mutation	SNP	ENST00000566497.1	hg19	CCDS10347.1	.	.	.	.	.	.	.	.	.	.	C	19.92	3.915509	0.73098	4.55E-4	0.0	ENSG00000140545	ENST00000268150;ENST00000268151;ENST00000539437	D;D;D	0.98381	-4.74;-4.9;-4.89	5.39	5.39	0.77823	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.98482	0.9494	L	0.52905	1.665	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98516	1.0621	10	0.37606	T	0.19	-44.8874	18.0846	0.89453	0.0:1.0:0.0:0.0	.	39;39;47;47	B3KTQ2;F5H7N9;Q08431-3;Q08431	.;.;.;MFGM_HUMAN	R	47;47;39	ENSP00000268150:G47R;ENSP00000268151:G47R;ENSP00000442386:G39R	ENSP00000268150:G47R	G	-	1	0	MFGE8	87254093	1.000000	0.71417	0.957000	0.39632	0.022000	0.10575	7.113000	0.77095	2.700000	0.92200	0.561000	0.74099	GGA	.	C|1.000;G|0.000		0.527	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928		G	89453089	C	G	89453089	3	3	197	1	0	0	0	0	1	0	0	0	9529	690	24	4	1052	4	MFGE8	15	89453089	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	378273	89453089	13078303	164	29074										
BLM	641	hgsc.bcm.edu	37	chr15	91293034	91293034	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	accccaaagtcactttgtaaGagtaagcactgctcagaaat	7	10	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr15:91293034G>T	ENST00000355112.3	+	3	654	c.536G>T	c.(535-537)aGa>aTa	p.R179I	BLM_ENST00000560509.1_Missense_Mutation_p.R179I	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	179					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			CACTTTGTAAGAGTAAGCACT	0.368			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.R179I		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	.	BLM	122	.	0			c.G536T						.						66	65	65					15																	91293034		2198	4298	6496	SO:0001583	missense	641	exon3	Familial Cancer Database		TTGTAAGAGTAAG	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"Bloom syndrome"			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.536G>T	chr15.hg19:g.91293034G>T	ENSP00000347232:p.Arg179Ile	142.0	0.0		189.0	22.0	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	hg19	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	G	18.28	3.590168	0.66105	.	.	ENSG00000197299	ENST00000355112	T	0.50548	0.74	6.01	3.93	0.45458	.	0.397165	0.26190	N	0.025804	T	0.41026	0.1141	L	0.34521	1.04	0.43793	D	0.996331	P;P	0.48911	0.917;0.917	P;P	0.49226	0.603;0.603	T	0.35301	-0.9794	10	0.66056	D	0.02	-26.1553	5.817	0.18497	0.2548:0.0:0.7452:0.0	.	179;179	B2RAN0;P54132	.;BLM_HUMAN	I	179	ENSP00000347232:R179I	ENSP00000347232:R179I	R	+	2	0	BLM	89094038	0.996000	0.38824	0.977000	0.42913	0.591000	0.36615	2.651000	0.46674	1.550000	0.49438	0.650000	0.86243	AGA	.	.		0.368	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			T	91293034	G	T	91293034	3	4	197	1	0	0	0	0	1	0	0	0	1445	942	33	3	542	3	BLM	15	91293034	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	1839945	91293034	11238358	165	29075										
AXIN1	8312	hgsc.bcm.edu	37	chr16	348025	348025	+	Frame_Shift_Del	DEL	G	G	-													0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tggccacgtgcccactgtccGgggagcgatggccaggccca							TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr16:348025delG	ENST00000262320.3	-	6	1852	c.1481delC	c.(1480-1482)ccgfs	p.P494fs	AXIN1_ENST00000481769.1_5'UTR|AXIN1_ENST00000354866.3_Frame_Shift_Del_p.P494fs	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	494	Interaction with CTNNB1. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CCCACTGTCCGGGGAGCGATG	0.687																																					p.P494fs		Atlas-INDEL	.											.	AXIN1	290	.	0			c.1482delG						.						26	22	23					16																	348025		2196	4291	6487	SO:0001589	frameshift_variant	8312	exon6			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1481delC	chr16.hg19:g.348025delG	ENSP00000262320:p.Pro494fs	35.0	0.0		31.0	14.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Del	DEL	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.687	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			-	348025	G	-	348025	7	5	197	1	0	1	0	1	0	0	0	0	1236	1116	39	0	1131	0	AXIN1	16	348025	Frame_Shift_Del	DEL	G	TCGA-DD-AADO-01A-11D-A40R-10		348025	90006728	166	29076										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48576816	48576816	+	Nonstop_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tcagcgctcagcacaatcttCaatccaacaccatggcagaa	6	14	4	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr16:48576816C>A	ENST00000262384.3	-	7	2926	c.2690G>T	c.(2689-2691)tGa>tTa	p.*897L	N4BP1_ENST00000565423.1_5'UTR	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	0					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				GCACAATCTTCAATCCAACAC	0.463																																					p.X897L		Atlas-SNP	.											.	N4BP1	121	.	0			c.G2690T						.						80	74	76					16																	48576816		1922	4135	6057	SO:0001578	stop_lost	9683	exon7			AATCTTCAATCCA	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.2690G>T	chr16.hg19:g.48576816C>A		71.0	0.0		51.0	26.0	NM_153029	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	hg19	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.276077	0.40294	.	.	ENSG00000102921	ENST00000262384	.	.	.	5.63	-0.075	0.13728	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.7427	0.05258	0.1174:0.5075:0.1142:0.2608	.	.	.	.	L	897	.	.	X	-	2	2	N4BP1	47134317	0.915000	0.31059	0.216000	0.23742	0.226000	0.24999	0.209000	0.17435	0.302000	0.22762	-0.225000	0.12378	TGA	.	.		0.463	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		A	48576816	C	A	48576816	4	1	197	1	0	0	0	0	0	0	0	0	10118	837	29	3	4	3	N4BP1	16	48576816	Nonstop_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	48228791	48576816	41777937	167	29077										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72991690	72991690	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gccccgcaggagctactgatAttggctgccgccgccgccgc	13	17	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr16:72991690A>G	ENST00000268489.5	-	2	3027	c.2355T>C	c.(2353-2355)aaT>aaC	p.N785N	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	785					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				AGCTACTGATATTGgctgccg	0.657																																					p.N785N		Atlas-SNP	.											.	ZFHX3	404	.	0			c.T2355C						.						29	35	33					16																	72991690		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			ACTGATATTGGCT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2355T>C	chr16.hg19:g.72991690A>G		35.0	0.0		38.0	13.0	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.657	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		G	72991690	A	G	72991690	2	3	197	1	0	0	0	0	0	0	0	1	17649	446	16	2		2	ZFHX3	16	72991690	Silent	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	24414874	72991690	17363063	168	29078										
RNMTL1	55178	hgsc.bcm.edu	37	chr17	695150	695150	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtgagcctggagtccctgcaGctggccgagagcactggtgg	17	11	0	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr17:695150G>A	ENST00000304478.4	+	4	1210	c.1104G>A	c.(1102-1104)caG>caA	p.Q368Q	RP11-676J12.8_ENST00000574560.1_RNA	NM_018146.2	NP_060616.1			RNA methyltransferase like 1											breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0219)		AGTCCCTGCAGCTGGCCGAGA	0.622																																					p.Q368Q		Atlas-SNP	.											.	RNMTL1	25	.	0			c.G1104A						.						54	53	53					17																	695150		2203	4300	6503	SO:0001819	synonymous_variant	55178	exon4			CCTGCAGCTGGCC	AF177344	CCDS10997.1	17p13.3	2008-02-05			ENSG00000171861	ENSG00000171861			18485	protein-coding gene	gene with protein product		612600				12296377	Standard	NM_018146		Approved	FLJ10581, HC90	uc002frw.3	Q9HC36	OTTHUMG00000090285	ENST00000304478.4:c.1104G>A	chr17.hg19:g.695150G>A		62.0	0.0		94.0	5.0	NM_018146		Silent	SNP	ENST00000304478.4	hg19	CCDS10997.1																																																																																			.	.		0.622	RNMTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206611.1	NM_018146		A	695150	G	A	695150	2	1	197	1	0	0	0	0	0	0	0	1	13522	962	34	3		3	RNMTL1	17	695150	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10		695150	80500060	169	29079										
NUP88	4927	hgsc.bcm.edu	37	chr17	5312086	5312086	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tgatgtatgtcaggaaagtcTctccattttcatataagatg	8	6	3	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr17:5312086T>C	ENST00000573584.1	-	5	1333	c.824A>G	c.(823-825)gAg>gGg	p.E275G		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	275					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						CAGGAAAGTCTCTCCATTTTC	0.443																																					p.E275G		Atlas-SNP	.											.	NUP88	47	.	0			c.A824G						.						139	124	129					17																	5312086		2203	4300	6503	SO:0001583	missense	4927	exon5			AAAGTCTCTCCAT	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"nucleoporin 88kD"			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.824A>G	chr17.hg19:g.5312086T>C	ENSP00000458954:p.Glu275Gly	84.0	0.0		106.0	17.0	NM_002532	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	hg19	CCDS11070.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.093697	0.76870	.	.	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	5.05	3.95	0.45737	.	0.106421	0.64402	D	0.000007	T	0.67998	0.2953	M	0.68317	2.08	0.52501	D	0.999955	D;P;P	0.57257	0.979;0.951;0.919	P;P;P	0.57846	0.828;0.675;0.686	T	0.70817	-0.4769	9	0.72032	D	0.01	-4.5841	11.5599	0.50769	0.0:0.0:0.1496:0.8504	.	275;144;275	B7Z5I6;B4DP20;Q99567	.;.;NUP88_HUMAN	G	275;144	.	ENSP00000225696:E275G	E	-	2	0	NUP88	5252810	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	6.868000	0.75516	1.026000	0.39733	0.377000	0.23210	GAG	.	.		0.443	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		C	5312086	T	C	5312086	3	2	197	1	0	0	0	0	1	0	0	0	10780	1551	54	2	1453	2	NUP88	17	5312086	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	4616936	5312086	75883124	170	29080										
ARHGEF15	22899	hgsc.bcm.edu	37	chr17	8215455	8215455	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tcgttccagggctgcccagtCcccagggcctccccacaatg	10	18	0	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr17:8215455C>T	ENST00000361926.3	+	2	208	c.98C>T	c.(97-99)tCc>tTc	p.S33F	ARHGEF15_ENST00000421050.1_Missense_Mutation_p.S33F	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	33	Pro-rich.				negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						GCTGCCCAGTCCCCAGGGCCT	0.632																																					p.S33F		Atlas-SNP	.											.	ARHGEF15	97	.	0			c.C98T						.						80	88	85					17																	8215455		2203	4300	6503	SO:0001583	missense	22899	exon2			CCCAGTCCCCAGG	AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"Rho guanine nucleotide exchange factors"	15590	protein-coding gene	gene with protein product	"Rho guanine exchange factor (GEF) 15"	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.98C>T	chr17.hg19:g.8215455C>T	ENSP00000355026:p.Ser33Phe	174.0	0.0		202.0	73.0	NM_025014	A8K6G1|Q8N449|Q9H8B4	Missense_Mutation	SNP	ENST00000361926.3	hg19	CCDS11139.1	.	.	.	.	.	.	.	.	.	.	C	6.231	0.410832	0.11812	.	.	ENSG00000198844	ENST00000361926;ENST00000421050	T;T	0.72725	-0.68;-0.68	5.0	2.96	0.34315	.	0.275100	0.26359	N	0.024835	T	0.53174	0.1780	L	0.27053	0.805	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.42832	-0.9428	10	0.38643	T	0.18	-13.2931	7.9577	0.30053	0.0:0.8079:0.0:0.1921	.	33;33	D3DTR7;O94989	.;ARHGF_HUMAN	F	33	ENSP00000355026:S33F;ENSP00000412505:S33F	ENSP00000355026:S33F	S	+	2	0	ARHGEF15	8156180	0.971000	0.33674	0.965000	0.40720	0.520000	0.34377	0.481000	0.22260	1.346000	0.45694	-0.145000	0.13849	TCC	.	.		0.632	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728		T	8215455	C	T	8215455	3	4	197	1	0	0	0	0	1	0	0	0	898	855	30	3	100	3	ARHGEF15	17	8215455	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	2903369	8215455	72979755	171	29081										
NDEL1	81565	hgsc.bcm.edu	37	chr17	8363472	8363472	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agggcatacatctttcttcgAcaaagggtaagtcctgaatg	10	8	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr17:8363472A>T	ENST00000334527.7	+	8	1135	c.938A>T	c.(937-939)gAc>gTc	p.D313V	NDEL1_ENST00000299734.7_Missense_Mutation_p.D313V|NDEL1_ENST00000402554.3_Missense_Mutation_p.D313V|NDEL1_ENST00000585098.1_Intron|NDEL1_ENST00000380025.4_Intron	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1	313	Interaction with CENPF.|Interaction with NEFL. {ECO:0000250}.				activation of Cdc42 GTPase activity (GO:0032864)|central nervous system neuron axonogenesis (GO:0021955)|centrosome localization (GO:0051642)|cerebral cortex radially oriented cell migration (GO:0021799)|chromosome segregation (GO:0007059)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|neurofilament cytoskeleton organization (GO:0060052)|neuron migration (GO:0001764)|neuron projection extension (GO:1990138)|nuclear envelope disassembly (GO:0051081)|positive regulation of axon extension (GO:0045773)|positive regulation of axon regeneration (GO:0048680)|retrograde axon cargo transport (GO:0008090)|vesicle transport along microtubule (GO:0047496)	axon hillock (GO:0043203)|cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|neurofilament cytoskeleton (GO:0060053)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)	oligopeptidase activity (GO:0070012)			large_intestine(6)|lung(4)|skin(3)	13						TCTTTCTTCGACAAAGGGTAA	0.393																																					p.D313V		Atlas-SNP	.											.	NDEL1	47	.	0			c.A938T						.						108	102	104					17																	8363472		2203	4300	6503	SO:0001583	missense	81565	exon8			TCTTCGACAAAGG	AF182078	CCDS11143.1, CCDS32564.1	17p13.1	2013-08-06	2013-08-06	2003-04-16	ENSG00000166579	ENSG00000166579			17620	protein-coding gene	gene with protein product		607538	"nudE nuclear distribution gene E homolog (A. nidulans)-like 1", "nudE nuclear distribution E homolog (A. nidulans)-like 1"			11163260, 11163259	Standard	NM_001025579		Approved	NUDEL, MITAP1, NDE1L1, NDE2	uc002glj.4	Q9GZM8	OTTHUMG00000108193	ENST00000334527.7:c.938A>T	chr17.hg19:g.8363472A>T	ENSP00000333982:p.Asp313Val	150.0	0.0		142.0	14.0	NM_001025579	B3KP93|D3DTS0|J3QT32|Q86T80|Q8TAR7|Q9UH50	Missense_Mutation	SNP	ENST00000334527.7	hg19	CCDS11143.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.305133	0.81247	.	.	ENSG00000166579	ENST00000299734;ENST00000380025;ENST00000402554;ENST00000334527	.	.	.	5.0	5.0	0.66597	NUDE protein, C-terminal (1);	0.088081	0.85682	D	0.000000	T	0.76169	0.3950	M	0.76328	2.33	0.80722	D	1	P;D	0.63046	0.863;0.992	P;P	0.62740	0.728;0.906	T	0.76921	-0.2780	9	0.41790	T	0.15	-0.682	15.151	0.72700	1.0:0.0:0.0:0.0	.	313;313	Q9GZM8;A6NIZ0	NDEL1_HUMAN;.	V	313;313;368;313	.	ENSP00000299734:D313V	D	+	2	0	NDEL1	8304197	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	8.249000	0.89833	2.227000	0.72691	0.402000	0.26972	GAC	.	.		0.393	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	NM_030808		T	8363472	A	T	8363472	3	4	197	1	0	0	0	0	1	0	0	0	10253	275	10	4	964	4	NDEL1	17	8363472	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	148017	8363472	72831738	172	29082										
PSME3	10197	hgsc.bcm.edu	37	chr17	40989684	40989684	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agcccacttataagaagcgaAggttggatgagtgtgaagaa	13	5	0	4			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr17:40989684A>T	ENST00000590720.1	+	5	495	c.262A>T	c.(262-264)Agg>Tgg	p.R88W	PSME3_ENST00000441946.2_Missense_Mutation_p.R99W|PSME3_ENST00000592169.1_Missense_Mutation_p.R32W|PSME3_ENST00000545225.1_Missense_Mutation_p.R27W|PSME3_ENST00000541124.1_3'UTR|PSME3_ENST00000293362.3_Missense_Mutation_p.R88W			P61289	PSME3_HUMAN	proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki)	88					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)			NS(1)|cervix(1)|large_intestine(3)|lung(1)	6		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		TAAGAAGCGAAGGTTGGATGA	0.493																																					p.R99W		Atlas-SNP	.											.	PSME3	11	.	0			c.A295T						.						213	176	189					17																	40989684		2203	4300	6503	SO:0001583	missense	10197	exon7			AAGCGAAGGTTGG	U11292	CCDS11442.1, CCDS45689.1, CCDS59290.1	17q12-q21	2004-02-17				ENSG00000131467		"Proteasome (prosome, macropain) subunits"	9570	protein-coding gene	gene with protein product		605129				7951316	Standard	NM_005789		Approved	Ki, PA28-gamma, REG-GAMMA, PA28G	uc002ibq.4	P61289		ENST00000590720.1:c.262A>T	chr17.hg19:g.40989684A>T	ENSP00000466794:p.Arg88Trp	127.0	0.0		149.0	25.0	NM_001267045	A8K9A3|O35563|P97373|Q12920|Q13172|Q9BQD9	Missense_Mutation	SNP	ENST00000590720.1	hg19	CCDS45689.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.955358	0.92726	.	.	ENSG00000131467	ENST00000545225;ENST00000293362;ENST00000441946;ENST00000543428	T;T;T	0.55930	1.21;1.79;0.49	5.35	5.35	0.76521	.	0.230536	0.43919	D	0.000512	T	0.38931	0.1059	N	0.08118	0	0.80722	D	1	P;P;P	0.50272	0.69;0.69;0.933	B;B;P	0.44772	0.271;0.271;0.46	T	0.50432	-0.8829	10	0.87932	D	0	-0.5881	15.503	0.75716	1.0:0.0:0.0:0.0	.	88;88;88	Q6FHK7;P61289;P61289-2	.;PSME3_HUMAN;.	W	27;88;88;88	ENSP00000441682:R27W;ENSP00000293362:R88W;ENSP00000437924:R88W	ENSP00000293362:R88W	R	+	1	2	PSME3	38243210	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.382000	0.59594	2.236000	0.73375	0.528000	0.53228	AGG	.	.		0.493	PSME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452430.1	NM_176863		T	40989684	A	T	40989684	3	4	197	1	0	0	0	0	1	0	0	0	12720	63	3	4	280	4	PSME3	17	40989684	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	32626212	40989684	40205526	173	29083										
TBX4	9496	hgsc.bcm.edu	37	chr17	59560478	59560478	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtggacgacctgcccccaccTccgctgagctgtaacatgtg	11	15	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr17:59560478T>C	ENST00000240335.1	+	8	1284	c.1239T>C	c.(1237-1239)ccT>ccC	p.P413P	TBX4_ENST00000589449.1_Intron|TBX4_ENST00000393853.4_Silent_p.P414P	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	413					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						TGCCCCCACCTCCGCTGAGCT	0.602																																					p.P413P		Atlas-SNP	.											.	TBX4	69	.	0			c.T1239C						.						91	80	83					17																	59560478		2203	4300	6503	SO:0001819	synonymous_variant	9496	exon8			CCCACCTCCGCTG	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"T-boxes"	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1239T>C	chr17.hg19:g.59560478T>C		62.0	0.0		91.0	27.0	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	hg19	CCDS11629.1																																																																																			.	.		0.602	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488		C	59560478	T	C	59560478	2	2	197	1	0	0	0	0	0	0	0	1	15675	1538	54	2		2	TBX4	17	59560478	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	18570794	59560478	21634732	174	29084										
FASN	2194	hgsc.bcm.edu	37	chr17	80043416	80043416	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aggtgaggaaggccacgatgTccccgagggggtgcccccgg	18	12	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr17:80043416T>A	ENST00000306749.2	-	23	4282	c.4064A>T	c.(4063-4065)gAc>gTc	p.D1355V	FASN_ENST00000579758.1_5'Flank	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1355				LGDI -> SGH (in Ref. 2; AAA73576). {ECO:0000305}.	acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GGCCACGATGTCCCCGAGGGG	0.701																																					p.D1355V	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.A4064T						.						14	17	16					17																	80043416		2177	4282	6459	SO:0001583	missense	2194	exon23			ACGATGTCCCCGA	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.4064A>T	chr17.hg19:g.80043416T>A	ENSP00000304592:p.Asp1355Val	198.0	0.0		251.0	32.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.499563	0.26861	.	.	ENSG00000169710	ENST00000306749;ENST00000545909	T	0.25749	1.78	4.79	4.79	0.61399	.	0.178574	0.47455	D	0.000229	T	0.15089	0.0364	N	0.08118	0	0.58432	D	0.999994	B	0.11235	0.004	B	0.10450	0.005	T	0.04796	-1.0926	10	0.42905	T	0.14	-25.8548	14.2888	0.66263	0.0:0.0:0.0:1.0	.	1355	P49327	FAS_HUMAN	V	1355;320	ENSP00000304592:D1355V	ENSP00000304592:D1355V	D	-	2	0	FASN	77636705	1.000000	0.71417	0.321000	0.25320	0.062000	0.15995	7.387000	0.79785	1.772000	0.52199	0.379000	0.24179	GAC	.	.		0.701	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80043416	T	A	80043416	3	1	197	1	0	0	0	0	1	0	0	0	5691	1667	58	4	3555	4	FASN	17	80043416	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	20482938	80043416	1151794	175	29085										
CD7	924	hgsc.bcm.edu	37	chr17	80274230	80274230	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cctgtcggtggggcagggagGgcagaggcccttggtggggc	22	9	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr17:80274230G>T	ENST00000312648.3	-	3	559	c.453C>A	c.(451-453)gcC>gcA	p.A151A	CD7_ENST00000578509.1_Silent_p.A51A|CD7_ENST00000583376.1_Silent_p.A51A|CD7_ENST00000584284.1_Silent_p.A151A	NM_006137.6	NP_006128.1	P09564	CD7_HUMAN	CD7 molecule	151	4 X 9 AA tandem repeats, potential spacer function.				homeostasis of number of cells within a tissue (GO:0048873)|immune response (GO:0006955)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)			GGGCAGGGAGGGCAGAGGCCC	0.667																																					p.A151A	Pancreas(45;804 1068 19702 28207 28798)	Atlas-SNP	.											.	CD7	25	.	0			c.C453A						.						19	24	22					17																	80274230		2191	4296	6487	SO:0001819	synonymous_variant	924	exon3			AGGGAGGGCAGAG	X06180	CCDS11807.1	17q25.2-q25.3	2013-01-11	2006-03-28			ENSG00000173762		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1695	protein-coding gene	gene with protein product	"p41 protein", "T-cell antigen CD7", "T-cell leukemia antigen"	186820	"CD7 antigen (p41)"			1695199, 3501369	Standard	NM_006137		Approved	GP40, LEU-9, TP41, Tp40	uc002kel.1	P09564		ENST00000312648.3:c.453C>A	chr17.hg19:g.80274230G>T		79.0	0.0		100.0	13.0	NM_006137		Silent	SNP	ENST00000312648.3	hg19	CCDS11807.1																																																																																			.	.		0.667	CD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442826.1	NM_006137		T	80274230	G	T	80274230	2	4	197	1	0	0	0	0	0	0	0	1	3034	1219	43	3		3	CD7	17	80274230	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	230814	80274230	920980	176	29086										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7080342	7080342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	actgtgggtttcggacgggcCgacctggcacatgctccaca	13	13	0	0	rs375547281		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr18:7080342C>T	ENST00000389658.3	-	2	269	c.176G>A	c.(175-177)cGg>cAg	p.R59Q	RP11-76K13.3_ENST00000581502.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	59	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TCGGACGGGCCGACCTGGCAC	0.547																																					p.R59Q		Atlas-SNP	.											LAMA1,colon,carcinoma,0,1	LAMA1	458	.	0			c.G176A						.	C	GLN/ARG	0,4406		0,0,2203	83	83	83		176	4.8	0	18		83	1,8599	1.2+/-3.3	0,1,4299	no	missense	LAMA1	NM_005559.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	59/3076	7080342	1,13005	2203	4300	6503	SO:0001583	missense	284217	exon2			ACGGGCCGACCTG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.176G>A	chr18.hg19:g.7080342C>T	ENSP00000374309:p.Arg59Gln	202.0	0.0		183.0	39.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.667802	0.29604	0.0	1.16E-4	ENSG00000101680	ENST00000389658	T	0.17370	2.28	5.68	4.8	0.61643	Laminin, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.21347	0.0514	N	0.20986	0.625	0.09310	N	0.999996	D	0.76494	0.999	P	0.60173	0.87	T	0.13926	-1.0491	10	0.11794	T	0.64	.	14.9131	0.70773	0.0:0.9305:0.0:0.0695	.	59	P25391	LAMA1_HUMAN	Q	59	ENSP00000374309:R59Q	ENSP00000374309:R59Q	R	-	2	0	LAMA1	7070342	0.990000	0.36364	0.011000	0.14972	0.047000	0.14425	3.486000	0.53215	2.677000	0.91161	0.650000	0.86243	CGG	.	.		0.547	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	7080342	C	T	7080342	3	4	197	1	0	0	0	0	1	0	0	0	8614	652	23	1	9299	1	LAMA1	18	7080342	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10		7080342	70996906	177	29087										
ZCCHC2	54877	hgsc.bcm.edu	37	chr18	60217605	60217618	+	Frame_Shift_Del	DEL	ACTTTTGACAAGAC	ACTTTTGACAAGAC	-													0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	caaaggaactgtcttcagagActtttgacaagaccatctta					rs200012607		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	ACTTTTGACAAGAC	ACTTTTGACAAGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr18:60217605_60217618delACTTTTGACAAGAC	ENST00000269499.5	+	5	1643_1656	c.1225_1238delACTTTTGACAAGAC	c.(1225-1239)acttttgacaagaccfs	p.TFDKT409fs	ZCCHC2_ENST00000586834.1_Frame_Shift_Del_p.TFDKT88fs	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	409						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						GTCTTCAGAGACTTTTGACAAGACCATCTTAAGA	0.407																																					p.408_413del		Atlas-INDEL	.											.	ZCCHC2	64	.	0			c.1224_1237del						.																																			SO:0001589	frameshift_variant	54877	exon5			.	AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"Zinc fingers, CCHC domain containing"	22916	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 49"	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.1225_1238delACTTTTGACAAGAC	chr18.hg19:g.60217605_60217618delACTTTTGACAAGAC	ENSP00000269499:p.Thr409fs	117.0	0.0		72.0	12.0	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Frame_Shift_Del	DEL	ENST00000269499.5	hg19	CCDS45880.1																																																																																			.	.		0.407	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742		-	60217618	ACTTTTGACAAGAC	-	60217605	7	5	197	1	0	1	0	1	0	0	0	0	17602	275	10	0	1243	0	ZCCHC2	18	60217605	Frame_Shift_Del	DEL	ACTTTTGACAAGAC	TCGA-DD-AADO-01A-11D-A40R-10	53137263	60217605	17859643	178	29088										
ZCCHC2	54877	hgsc.bcm.edu	37	chr18	60242385	60242385	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aaggtgcagctgtgggaccaAtggaaaccttcagctaaata	11	8	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr18:60242385A>T	ENST00000269499.5	+	13	3489	c.3071A>T	c.(3070-3072)aAt>aTt	p.N1024I	ZCCHC2_ENST00000586834.1_Missense_Mutation_p.N703I	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	1024						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						TGTGGGACCAATGGAAACCTT	0.507																																					p.N1024I		Atlas-SNP	.											.	ZCCHC2	64	.	0			c.A3071T						.						86	96	93					18																	60242385		2141	4249	6390	SO:0001583	missense	54877	exon13			GGACCAATGGAAA	AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"Zinc fingers, CCHC domain containing"	22916	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 49"	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.3071A>T	chr18.hg19:g.60242385A>T	ENSP00000269499:p.Asn1024Ile	79.0	0.0		71.0	20.0	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Missense_Mutation	SNP	ENST00000269499.5	hg19	CCDS45880.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.583415	0.46006	.	.	ENSG00000141664	ENST00000269499	T	0.25749	1.78	4.76	0.643	0.17770	.	0.061171	0.64402	D	0.000007	T	0.21062	0.0507	L	0.43152	1.355	0.46849	D	0.999221	P	0.47409	0.895	B	0.42851	0.4	T	0.02202	-1.1196	10	0.62326	D	0.03	-4.984	8.8979	0.35476	0.7637:0.0:0.2363:0.0	.	1024	Q9C0B9	ZCHC2_HUMAN	I	1024	ENSP00000269499:N1024I	ENSP00000269499:N1024I	N	+	2	0	ZCCHC2	58393365	1.000000	0.71417	0.994000	0.49952	0.962000	0.63368	1.883000	0.39658	0.030000	0.15379	-0.256000	0.11100	AAT	.	.		0.507	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742		T	60242385	A	T	60242385	3	4	197	1	0	0	0	0	1	0	0	0	17602	101	4	4	3121	4	ZCCHC2	18	60242385	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	24780	60242385	17834863	179	29089										
MUC16	94025	hgsc.bcm.edu	37	chr19	9076752	9076752	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tctctgtggccggggtgctgTccatggtactcatacccact	11	13	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:9076752T>A	ENST00000397910.4	-	3	10897	c.10694A>T	c.(10693-10695)gAc>gTc	p.D3565V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3566	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CGGGGTGCTGTCCATGGTACT	0.537											OREG0007306	type=TRANSCRIPTION FACTOR BINDING SITE|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.D3565V		Atlas-SNP	.											.	MUC16	4315	.	0			c.A10694T						.						203	200	201					19																	9076752		2125	4233	6358	SO:0001583	missense	94025	exon3			GTGCTGTCCATGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.10694A>T	chr19.hg19:g.9076752T>A	ENSP00000381008:p.Asp3565Val	181.0	0.0	654	160.0	28.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	2.985	-0.209550	0.06140	.	.	ENSG00000181143	ENST00000397910	T	0.03065	4.06	1.65	0.539	0.17156	.	.	.	.	.	T	0.02342	0.0072	N	0.08118	0	.	.	.	P	0.52061	0.95	P	0.45138	0.471	T	0.43294	-0.9400	8	0.87932	D	0	.	3.642	0.08170	0.3438:0.0:0.0:0.6562	.	3565	B5ME49	.	V	3565	ENSP00000381008:D3565V	ENSP00000381008:D3565V	D	-	2	0	MUC16	8937752	0.001000	0.12720	0.000000	0.03702	0.043000	0.13939	0.526000	0.22971	0.081000	0.16988	0.260000	0.18958	GAC	.	.		0.537	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9076752	T	A	9076752	3	1	197	1	0	0	0	0	1	0	0	0	9982	1667	58	4	33157	4	MUC16	19	9076752	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10		9076752	50052231	180	29090										
MUC16	94025	hgsc.bcm.edu	37	chr19	9083709	9083709	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	atgctcctatctgggttactTactgtcttaagaaccagtgc	8	10	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:9083709T>G	ENST00000397910.4	-	1	8309	c.8106A>C	c.(8104-8106)gtA>gtC	p.V2702V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2702	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGGGTTACTTACTGTCTTAA	0.483																																					p.V2702V		Atlas-SNP	.											.	MUC16	4315	.	0			c.A8106C						.						118	110	113					19																	9083709		1921	4137	6058	SO:0001819	synonymous_variant	94025	exon1			GTTACTTACTGTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8106A>C	chr19.hg19:g.9083709T>G		59.0	0.0		87.0	4.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9083709	T	G	9083709	2	3	197	1	0	0	0	0	0	0	0	1	9982	1741	61	5		5	MUC16	19	9083709	Silent	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	6957	9083709	50045274	181	29091										
PDE4C	5143	hgsc.bcm.edu	37	chr19	18327687	18327687	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gcaccgaggcgtcgttgtacAtaagcgccagctctgagtct	12	12	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:18327687A>G	ENST00000355502.3	-	16	2220	c.1349T>C	c.(1348-1350)aTg>aCg	p.M450T	PDE4C_ENST00000447275.3_Missense_Mutation_p.M344T|PDE4C_ENST00000594617.3_Missense_Mutation_p.M450T|PDE4C_ENST00000598111.2_Missense_Mutation_p.M165T|PDE4C_ENST00000597297.1_Missense_Mutation_p.M220T|PDE4C_ENST00000539010.1_Missense_Mutation_p.M219T|PDE4C_ENST00000594465.3_Missense_Mutation_p.M450T|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000262805.12_Missense_Mutation_p.M418T			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	450					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	GTCGTTGTACATAAGCGCCAG	0.567																																					p.M450T		Atlas-SNP	.											.	PDE4C	80	.	0			c.T1349C						.						73	72	72					19																	18327687		2203	4300	6503	SO:0001583	missense	5143	exon13			TTGTACATAAGCG		CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"Phosphodiesterases"	8782	protein-coding gene	gene with protein product	"phosphodiesterase E1 dunce homolog (Drosophila)"	600128	"phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.1349T>C	chr19.hg19:g.18327687A>G	ENSP00000347689:p.Met450Thr	68.0	0.0		76.0	34.0	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	hg19	CCDS12373.1	.	.	.	.	.	.	.	.	.	.	a	13.71	2.319359	0.41096	.	.	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000447275;ENST00000545961;ENST00000336173;ENST00000539010;ENST00000543547	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	4.52	4.52	0.55395	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	T	0.61185	0.2327	L	0.38531	1.155	0.37413	D	0.913311	B;B;B;B	0.25563	0.129;0.126;0.011;0.08	B;B;B;B	0.35770	0.179;0.21;0.053;0.074	T	0.67417	-0.5676	10	0.87932	D	0	.	11.8181	0.52222	1.0:0.0:0.0:0.0	.	450;418;256;165	Q08493;Q08493-3;O43850;O76104	PDE4C_HUMAN;.;.;.	T	529;450;438;418;344;256;164;219;559	ENSP00000347689:M450T;ENSP00000262805:M418T;ENSP00000402091:M344T;ENSP00000439470:M219T	ENSP00000262805:M418T	M	-	2	0	PDE4C	18188687	1.000000	0.71417	0.992000	0.48379	0.783000	0.44284	8.803000	0.91915	1.682000	0.51000	0.392000	0.25879	ATG	.	.		0.567	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1			G	18327687	A	G	18327687	3	3	197	1	0	0	0	0	1	0	0	0	11650	217	8	2	805	2	PDE4C	19	18327687	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	9243978	18327687	40801296	182	29092										
COMP	1311	hgsc.bcm.edu	37	chr19	18896571	18896571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aggccctgaagtcggtgagcGtgacttcagcgttctccgga	14	11	2	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:18896571G>A	ENST00000222271.2	-	14	1624	c.1580C>T	c.(1579-1581)aCg>aTg	p.T527M	COMP_ENST00000425807.1_Missense_Mutation_p.T474M|COMP_ENST00000542601.2_Missense_Mutation_p.T494M	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	527	Mediates cell survival and induction of the IAP family of survival proteins.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GTCGGTGAGCGTGACTTCAGC	0.627																																					p.T527M		Atlas-SNP	.											.	COMP	62	.	0			c.C1580T						.						85	71	76					19																	18896571		2203	4300	6503	SO:0001583	missense	1311	exon14			GTGAGCGTGACTT	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"thrombospondin-5"	600310	"cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1580C>T	chr19.hg19:g.18896571G>A	ENSP00000222271:p.Thr527Met	45.0	0.0		52.0	5.0	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	ENST00000222271.2	hg19	CCDS12385.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.471085	0.84533	.	.	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.98400	-4.91;-4.91;-4.91	4.54	4.54	0.55810	.	0.000000	0.85682	U	0.000000	D	0.98648	0.9547	M	0.75447	2.3	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.81914	0.905;0.995	D	0.98891	1.0773	10	0.35671	T	0.21	-29.1406	15.8171	0.78612	0.0:0.0:1.0:0.0	.	474;527	B4DKJ3;P49747	.;COMP_HUMAN	M	494;527;474;514	ENSP00000439156:T494M;ENSP00000222271:T527M;ENSP00000403792:T474M	ENSP00000222271:T527M	T	-	2	0	COMP	18757571	1.000000	0.71417	1.000000	0.80357	0.782000	0.44232	9.642000	0.98461	2.071000	0.62044	0.436000	0.28706	ACG	.	.		0.627	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095		A	18896571	G	A	18896571	3	1	197	1	0	0	0	0	1	0	0	0	3726	1145	40	1	717	1	COMP	19	18896571	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	568884	18896571	40232412	183	29093										
C19orf55	148137	hgsc.bcm.edu	37	chr19	36256011	36256011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cattccccaccagctctgatGgcctctctcccttctcggag	7	18	3	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:36256011G>A	ENST00000544099.1	+	7	766	c.703G>A	c.(703-705)Ggc>Agc	p.G235S	C19orf55_ENST00000396908.4_Missense_Mutation_p.G235S			Q2NL68	PRSR3_HUMAN		235	Ser-rich.									cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CAGCTCTGATGGCCTCTCTCC	0.627																																					p.G235S		Atlas-SNP	.											.	C19orf55	39	.	0			c.G703A						.						131	135	134					19																	36256011		2142	4254	6396	SO:0001583	missense	148137	exon7			TCTGATGGCCTCT																												ENST00000544099.1:c.703G>A	chr19.hg19:g.36256011G>A	ENSP00000467267:p.Gly235Ser	56.0	0.0		46.0	12.0	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Missense_Mutation	SNP	ENST00000544099.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.36	2.513328	0.44660	.	.	ENSG00000167595	ENST00000396908;ENST00000301165	T;T	0.46451	0.87;0.87	4.42	4.42	0.53409	.	0.000000	0.40554	N	0.001076	T	0.54631	0.1870	L	0.59436	1.845	0.30998	N	0.720598	D	0.55605	0.972	P	0.61477	0.889	T	0.56105	-0.8034	10	0.34782	T	0.22	-30.2292	12.7703	0.57417	0.0:0.0:1.0:0.0	.	235	E5RFB9	.	S	235;234	ENSP00000380116:G235S;ENSP00000301165:G234S	ENSP00000301165:G234S	G	+	1	0	C19orf55	40947851	0.994000	0.37717	0.998000	0.56505	0.002000	0.02628	4.123000	0.57917	2.460000	0.83146	0.558000	0.71614	GGC	.	.		0.627	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2			A	36256011	G	A	36256011	3	1	197	1	0	0	0	0	1	0	0	0	1939	1348	47	3	729	3	C19orf55	19	36256011	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	17359440	36256011	22872972	184	29094										
WDR62	284403	hgsc.bcm.edu	37	chr19	36592199	36592199	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggtgtcctccgacagcccaaAggaccagagcccgcctgagg	13	15	0	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:36592199A>T	ENST00000270301.7	+	24	2951	c.2951A>T	c.(2950-2952)aAg>aTg	p.K984M	WDR62_ENST00000401500.2_Missense_Mutation_p.K984M			O43379	WDR62_HUMAN	WD repeat domain 62	984					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GACAGCCCAAAGGACCAGAGC	0.647																																					p.K984M		Atlas-SNP	.											.	WDR62	102	.	0			c.A2951T						.						24	25	24					19																	36592199		2203	4300	6503	SO:0001583	missense	284403	exon24			GCCCAAAGGACCA	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"WD repeat domain containing"	24502	protein-coding gene	gene with protein product		613583	"chromosome 19 open reading frame 14", "microcephaly, primary autosomal recessive 2"	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.2951A>T	chr19.hg19:g.36592199A>T	ENSP00000270301:p.Lys984Met	161.0	0.0		194.0	44.0	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	hg19	CCDS33001.1	.	.	.	.	.	.	.	.	.	.	A	16.01	3.000646	0.54254	.	.	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.52295	0.76;0.67	5.25	5.25	0.73442	.	0.220505	0.39020	N	0.001492	T	0.62938	0.2469	M	0.68317	2.08	0.80722	D	1	D;D	0.76494	0.999;0.998	D;P	0.65987	0.94;0.872	T	0.63607	-0.6599	10	0.46703	T	0.11	-25.3009	11.7216	0.51685	1.0:0.0:0.0:0.0	.	984;984	O43379-4;O43379	.;WDR62_HUMAN	M	984	ENSP00000384792:K984M;ENSP00000270301:K984M	ENSP00000270301:K984M	K	+	2	0	WDR62	41284039	0.997000	0.39634	0.711000	0.30485	0.487000	0.33371	2.575000	0.46025	2.333000	0.79357	0.533000	0.62120	AAG	.	.		0.647	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671		T	36592199	A	T	36592199	3	4	197	1	0	0	0	0	1	0	0	0	17328	72	3	4	3045	4	WDR62	19	36592199	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	336188	36592199	22536784	185	29095										
ZNF585B	92285	hgsc.bcm.edu	37	chr19	37678065	37678065	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	actcataggatttttccccaGaataaattttttgatcttga	5	7	2	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:37678065G>A	ENST00000532828.2	-	5	625	c.374C>T	c.(373-375)tCt>tTt	p.S125F	CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000312908.5_5'Flank|ZNF585B_ENST00000527838.1_Missense_Mutation_p.S125F|ZNF585B_ENST00000531805.1_Missense_Mutation_p.S70F	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTTTCCCCAGAATAAATTTT	0.373																																					p.S125F	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.C374T						.						60	64	63					19																	37678065		2202	4300	6502	SO:0001583	missense	92285	exon5			TCCCCAGAATAAA	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.374C>T	chr19.hg19:g.37678065G>A	ENSP00000433773:p.Ser125Phe	87.0	0.0		104.0	35.0	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	hg19	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	G	2.302	-0.360046	0.05103	.	.	ENSG00000245680	ENST00000531805;ENST00000532828;ENST00000527838	T;T;T	0.08282	3.11;3.15;6.78	2.32	2.32	0.28847	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.469425	0.15734	U	0.247298	T	0.10337	0.0253	L	0.55743	1.74	0.80722	D	1	B	0.09022	0.002	B	0.13407	0.009	T	0.09930	-1.0652	10	0.87932	D	0	.	11.6544	0.51309	0.0:0.0:1.0:0.0	.	125	Q52M93	Z585B_HUMAN	F	70;125;125	ENSP00000436774:S70F;ENSP00000433773:S125F;ENSP00000435268:S125F	ENSP00000435268:S125F	S	-	2	0	ZNF585B	42369905	0.845000	0.29573	0.095000	0.20976	0.027000	0.11550	1.420000	0.34804	1.280000	0.44463	0.455000	0.32223	TCT	.	.		0.373	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		A	37678065	G	A	37678065	3	1	197	1	0	0	0	0	1	0	0	0	18033	942	33	3	1939	3	ZNF585B	19	37678065	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	1085866	37678065	21450918	186	29096										
RYR1	6261	hgsc.bcm.edu	37	chr19	39075613	39075613	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ttcacatgtacgtgggtgtcCgggctggcggaggcattggg	18	8	1	0	rs118192150		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:39075613C>T	ENST00000359596.3	+	102	14677	c.14677C>T	c.(14677-14679)Cgg>Tgg	p.R4893W	RYR1_ENST00000360985.3_Missense_Mutation_p.R4888W|RYR1_ENST00000355481.4_Missense_Mutation_p.R4888W			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4893			R -> Q (in CCD). {ECO:0000269|PubMed:12565913}.|R -> W (in CCD; release of calcium from intracellular stores in the absence of any pharmacological activator of RYR; smaller thapsigargin-sensitive intracellular calcium stores; normal sensitivity of the calcium release to the RYR inhibitor dantrolene). {ECO:0000269|PubMed:11709545, ECO:0000269|PubMed:14670767}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CGTGGGTGTCCGGGCTGGCGG	0.567																																					p.R4893W		Atlas-SNP	.											.	RYR1	708	.	0			c.C14677T	GRCh37	CM013432	RYR1	M	rs118192150	.						187	160	169					19																	39075613		2203	4300	6503	SO:0001583	missense	6261	exon102			GGTGTCCGGGCTG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14677C>T	chr19.hg19:g.39075613C>T	ENSP00000352608:p.Arg4893Trp	129.0	0.0		155.0	55.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.207908	0.39003	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.94687	-3.49;-3.49;-3.49	5.08	4.02	0.46733	Ion transport (1);	0.000000	0.64402	U	0.000015	D	0.97832	0.9288	M	0.94142	3.5	0.48511	D	0.999663	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.98640	1.0675	10	0.87932	D	0	.	13.3753	0.60734	0.2844:0.7156:0.0:0.0	.	4888;4893	P21817-2;P21817	.;RYR1_HUMAN	W	4893;4888;4888	ENSP00000352608:R4893W;ENSP00000347667:R4888W;ENSP00000354254:R4888W	ENSP00000347667:R4888W	R	+	1	2	RYR1	43767453	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.070000	0.30653	1.333000	0.45449	0.449000	0.29647	CGG	.	.		0.567	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	39075613	C	T	39075613	3	4	197	1	0	0	0	0	1	0	0	0	13783	643	23	1	15083	1	RYR1	19	39075613	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	1397548	39075613	20053370	187	29097										
GMFG	9535	hgsc.bcm.edu	37	chr19	39819668	39819668	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gctctgctgtctgcaccagcCtgtttttactccctgcatac	7	15	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:39819668C>T	ENST00000597595.1	-	6	537	c.329G>A	c.(328-330)aGg>aAg	p.R110K	GMFG_ENST00000253054.8_Missense_Mutation_p.R77K|GMFG_ENST00000595636.1_3'UTR|GMFG_ENST00000600322.1_Missense_Mutation_p.R77K|GMFG_ENST00000601387.1_Missense_Mutation_p.R69K|GMFG_ENST00000598034.1_Missense_Mutation_p.R110K|GMFG_ENST00000602185.1_Missense_Mutation_p.R61K|GMFG_ENST00000594700.1_Intron	NM_004877.2	NP_004868.1	O60234	GMFG_HUMAN	glia maturation factor, gamma	110	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				negative regulation of protein kinase activity (GO:0006469)|positive regulation of catalytic activity (GO:0043085)|protein phosphorylation (GO:0006468)	intracellular (GO:0005622)	enzyme activator activity (GO:0008047)|protein kinase inhibitor activity (GO:0004860)			breast(1)|large_intestine(2)|liver(2)|lung(3)|skin(1)|stomach(1)	10	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.15e-27)|all cancers(26;1.3e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			CTGCACCAGCCTGTTTTTACT	0.557																																					p.R110K		Atlas-SNP	.											.	GMFG	16	.	0			c.G329A						.						192	159	170					19																	39819668		2203	4300	6503	SO:0001583	missense	9535	exon6			ACCAGCCTGTTTT	AB001993	CCDS12532.1, CCDS74364.1	19q13.2	2014-08-12			ENSG00000130755	ENSG00000130755			4374	protein-coding gene	gene with protein product		604104				9545571, 9653160, 17127212	Standard	XM_005259440		Approved		uc002okz.4	O60234	OTTHUMG00000182811	ENST00000597595.1:c.329G>A	chr19.hg19:g.39819668C>T	ENSP00000472249:p.Arg110Lys	55.0	0.0		47.0	9.0	NM_004877	Q6IB37	Missense_Mutation	SNP	ENST00000597595.1	hg19	CCDS12532.1	.	.	.	.	.	.	.	.	.	.	C	6.705	0.498785	0.12762	.	.	ENSG00000130755	ENST00000253054	.	.	.	5.44	4.39	0.52855	Actin-binding, cofilin/tropomyosin type (3);	0.000000	0.85682	D	0.000000	T	0.27098	0.0664	N	0.12182	0.205	0.37693	D	0.923924	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.19811	-1.0294	9	0.05436	T	0.98	-29.8184	8.9142	0.35572	0.0:0.8286:0.0:0.1714	.	110;110	O60234;Q6IB37	GMFG_HUMAN;.	K	110	.	ENSP00000253054:R110K	R	-	2	0	GMFG	44511508	0.657000	0.27393	1.000000	0.80357	0.971000	0.66376	1.110000	0.31147	2.532000	0.85374	0.655000	0.94253	AGG	.	.		0.557	GMFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463839.1			T	39819668	C	T	39819668	3	4	197	1	0	0	0	0	1	0	0	0	6498	681	24	3	107	3	GMFG	19	39819668	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	744055	39819668	19309315	188	29098										
ZNF526	116115	hgsc.bcm.edu	37	chr19	42729783	42729783	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tctaccaccggcgcactcacGccggcaaaagcggggcacct	11	17	2	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:42729783G>T	ENST00000301215.3	+	3	1453	c.1228G>T	c.(1228-1230)Gcc>Tcc	p.A410S		NM_133444.1	NP_597701.1	Q8TF50	ZN526_HUMAN	zinc finger protein 526	410					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(3)	22		Prostate(69;0.0704)				GCGCACTCACGCCGGCAAAAG	0.677																																					p.A410S		Atlas-SNP	.											.	ZNF526	51	.	0			c.G1228T						.						33	37	36					19																	42729783		2203	4300	6503	SO:0001583	missense	116115	exon3			ACTCACGCCGGCA	AB075831	CCDS12598.1	19q13.31	2013-01-08				ENSG00000167625		"Zinc fingers, C2H2-type"	29415	protein-coding gene	gene with protein product		614387				11853319	Standard	NM_133444		Approved	KIAA1951, MGC4267	uc002osz.1	Q8TF50		ENST00000301215.3:c.1228G>T	chr19.hg19:g.42729783G>T	ENSP00000301215:p.Ala410Ser	145.0	0.0		153.0	35.0	NM_133444	B3KV29|Q69YI2|Q96E24	Missense_Mutation	SNP	ENST00000301215.3	hg19	CCDS12598.1	.	.	.	.	.	.	.	.	.	.	G	5.297	0.240203	0.10023	.	.	ENSG00000167625	ENST00000437878;ENST00000301215	T	0.14144	2.53	4.23	-0.718	0.11205	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.413227	0.22873	N	0.054607	T	0.04815	0.0130	N	0.04636	-0.2	0.09310	N	1	B	0.10296	0.003	B	0.15484	0.013	T	0.28427	-1.0044	10	0.54805	T	0.06	-3.0001	3.7137	0.08430	0.2585:0.0:0.4486:0.2929	.	410	Q8TF50	ZN526_HUMAN	S	266;410	ENSP00000301215:A410S	ENSP00000301215:A410S	A	+	1	0	ZNF526	47421623	0.000000	0.05858	0.001000	0.08648	0.368000	0.29767	0.240000	0.18042	-0.096000	0.12329	-0.319000	0.08680	GCC	.	.		0.677	ZNF526-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463681.2	XM_057401		T	42729783	G	T	42729783	3	4	197	1	0	0	0	0	1	0	0	0	17982	1087	38	1	1230	1	ZNF526	19	42729783	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	2910115	42729783	16399200	189	29099										
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47423310	47423310	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aagaggcccgtagttttattAtgaatgaggatttctaccag	10	6	1	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:47423310A>G	ENST00000404338.3	+	1	1378	c.1378A>G	c.(1378-1380)Atg>Gtg	p.M460V		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	460	FF 3.				axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										TAGTTTTATTATGAATGAGGA	0.398																																					p.M460V		Atlas-SNP	.											.	.	.	.	0			c.A1378G						.						30	30	30					19																	47423310		1821	4076	5897	SO:0001583	missense	2909	exon1			TTTATTATGAATG	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.1378A>G	chr19.hg19:g.47423310A>G	ENSP00000385720:p.Met460Val	102.0	0.0		118.0	18.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	A	11.96	1.795990	0.31777	.	.	ENSG00000160007	ENST00000317082;ENST00000501576;ENST00000404338	T	0.08896	3.04	5.95	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.12263	0.0298	M	0.72894	2.215	0.58432	D	0.99999	P	0.36789	0.57	B	0.35240	0.198	T	0.01386	-1.1368	10	0.72032	D	0.01	-47.0498	12.0417	0.53456	0.8561:0.1439:0.0:0.0	.	460	Q9NRY4-2	.	V	460	ENSP00000385720:M460V	ENSP00000324820:M460V	M	+	1	0	ARHGAP35	52115150	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	4.287000	0.59001	2.279000	0.76181	0.533000	0.62120	ATG	.	.		0.398	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		G	47423310	A	G	47423310	3	3	197	1	0	0	0	0	1	0	0	0	6804	449	16	2	1380	2	ARHGAP35	19	47423310	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	4693527	47423310	11705673	190	29100										
EHD2	30846	hgsc.bcm.edu	37	chr19	48239730	48239730	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aaactgcccgtcatctttgcGaagattcagctggaacatca	8	11	4	1	rs536783884	byFrequency	TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:48239730G>A	ENST00000263277.3	+	5	1271	c.1020G>A	c.(1018-1020)gcG>gcA	p.A340A	EHD2_ENST00000538399.1_Silent_p.A204A|EHD2_ENST00000540884.1_3'UTR	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	340					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		TCATCTTTGCGAAGATTCAGC	0.517													G|||	4	0.000798722	0	0	5008	,	,		18590	0		0	False		,,,				2504	0.0041				p.A340A		Atlas-SNP	.											EHD2,NS,carcinoma,0,1	EHD2	59	.	0			c.G1020A						.						147	127	134					19																	48239730		2203	4300	6503	SO:0001819	synonymous_variant	30846	exon5			CTTTGCGAAGATT	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"EF-hand domain containing"	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.1020G>A	chr19.hg19:g.48239730G>A		117.0	0.0		124.0	19.0	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	hg19	CCDS12704.1																																																																																			.	.		0.517	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1			A	48239730	G	A	48239730	2	1	197	1	0	0	0	0	0	0	0	1	4980	1045	37	1		1	EHD2	19	48239730	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	816420	48239730	10889253	191	29101										
LILRB5	10990	hgsc.bcm.edu	37	chr19	54759241	54759241	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tgtactggcccccgtgggagCggctcacagggcccagggtg	17	13	1	0	rs146167320		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:54759241C>G	ENST00000316219.5	-	5	967	c.860G>C	c.(859-861)cGc>cCc	p.R287P	LILRB5_ENST00000450632.1_Missense_Mutation_p.R278P|LILRB5_ENST00000345866.6_Missense_Mutation_p.R187P|LILRB5_ENST00000449561.2_Missense_Mutation_p.R287P	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	287	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCCGTGGGAGCGGCTCACAGG	0.662																																					p.R287P		Atlas-SNP	.											.	LILRB5	176	.	0			c.G860C						.						42	43	42					19																	54759241		2203	4299	6502	SO:0001583	missense	10990	exon5			TGGGAGCGGCTCA	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.860G>C	chr19.hg19:g.54759241C>G	ENSP00000320390:p.Arg287Pro	149.0	0.0		149.0	7.0	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	hg19	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	C	0.152	-1.090490	0.01873	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.11277	2.79;2.79;2.79;2.79	2.35	-4.71	0.03279	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.187420	0.01181	N	0.007095	T	0.04272	0.0118	N	0.03294	-0.36	0.09310	N	1	B;B;B;B;B	0.23185	0.012;0.081;0.034;0.066;0.003	B;B;B;B;B	0.27500	0.036;0.033;0.045;0.08;0.018	T	0.27226	-1.0080	10	0.23302	T	0.38	.	0.448	0.00497	0.3596:0.2013:0.2366:0.2026	.	278;178;187;287;287	C9JMK7;Q8NF80;O75023-2;O75023-3;O75023	.;.;.;.;LIRB5_HUMAN	P	287;278;287;187	ENSP00000320390:R287P;ENSP00000414225:R278P;ENSP00000406478:R287P;ENSP00000263430:R187P	ENSP00000320390:R287P	R	-	2	0	LILRB5	59451053	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.171000	0.00281	-3.550000	0.00142	-0.827000	0.03088	CGC	.	C|0.999;G|0.001		0.662	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			G	54759241	C	G	54759241	3	3	197	1	0	0	0	0	1	0	0	0	8803	768	27	4	951	4	LILRB5	19	54759241	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	6519511	54759241	4369742	192	29102										
LILRB1	10859	hgsc.bcm.edu	37	chr19	55144168	55144168	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ggtgcacacaacctctcctcCgagtggtcggcccccagcga	11	17	1	0	rs377724258		TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:55144168C>T	ENST00000396331.1	+	7	1272	c.915C>T	c.(913-915)tcC>tcT	p.S305S	LILRB1_ENST00000427581.2_Silent_p.S341S|LILRB1_ENST00000396315.1_Silent_p.S305S|LILRB1_ENST00000396332.4_Silent_p.S305S|LILRB1_ENST00000434867.2_Silent_p.S305S|LILRB1_ENST00000396321.2_Silent_p.S305S|LILRB1_ENST00000396317.1_Silent_p.S305S|LILRB1_ENST00000448689.1_Silent_p.S305S|LILRB1_ENST00000418536.2_Silent_p.S305S|LILRB1_ENST00000324602.7_Silent_p.S305S|LILRB1_ENST00000396327.3_Silent_p.S305S	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	305	Ig-like C2-type 3.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		ACCTCTCCTCCGAGTGGTCGG	0.692										HNSCC(37;0.09)																											p.S305S		Atlas-SNP	.											.	LILRB1	140	.	0			c.C915T						.	C	,,,	2,4404	2.1+/-5.4	0,2,2201	40	43	42		915,915,915,915	-3.8	0	19		42	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	,,,	0,2,6499	TT,TC,CC		0.0,0.0454,0.0154	,,,	305/653,305/652,305/652,305/651	55144168	2,13000	2203	4298	6501	SO:0001819	synonymous_variant	10859	exon6			CTCCTCCGAGTGG	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.915C>T	chr19.hg19:g.55144168C>T		103.0	0.0		98.0	7.0	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	hg19	CCDS42617.1																																																																																			.	.		0.692	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			T	55144168	C	T	55144168	2	4	197	1	0	0	0	0	0	0	0	1	8799	639	23	1		1	LILRB1	19	55144168	Silent	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	384927	55144168	3984815	193	29103										
SAPS1	22870	hgsc.bcm.edu	37	chr19	55743228	55743228	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gctctgagtggggaggccctGgggcacactgaggggcccct	18	12	1	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr19:55743228G>C	ENST00000412770.2	-	19	2814	c.2248C>G	c.(2248-2250)Cag>Gag	p.Q750E	TMEM86B_ENST00000327042.4_5'Flank|PPP6R1_ENST00000587283.1_Missense_Mutation_p.Q750E|AC010327.1_ENST00000581390.1_RNA	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	750	Pro-rich.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						GGGAGGCCCTGGGGCACACTG	0.682																																					p.Q750E		Atlas-SNP	.											.	PPP6R1	63	.	0			c.C2248G						.						9	12	11					19																	55743228		1913	4094	6007	SO:0001583	missense	22870	exon19			GGCCCTGGGGCAC	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	29195	protein-coding gene	gene with protein product		610875	"KIAA1115", "SAPS domain family, member 1"	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.2248C>G	chr19.hg19:g.55743228G>C	ENSP00000414202:p.Gln750Glu	49.0	0.0		66.0	22.0	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	hg19	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	G	0.017	-1.503957	0.00992	.	.	ENSG00000105063	ENST00000444538;ENST00000412770	T	0.41758	0.99	4.01	0.757	0.18427	.	2.216670	0.02914	N	0.137000	T	0.20170	0.0485	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.002;0.017	B;B	0.14023	0.003;0.01	T	0.22173	-1.0224	10	0.02654	T	1	.	5.5823	0.17256	0.3616:0.0:0.6384:0.0	.	750;112	Q9UPN7;Q96ID3	PP6R1_HUMAN;.	E	265;750	ENSP00000414202:Q750E	ENSP00000414202:Q750E	Q	-	1	0	PPP6R1	60435040	0.003000	0.15002	0.001000	0.08648	0.009000	0.06853	1.010000	0.29898	0.267000	0.21916	0.561000	0.74099	CAG	.	.		0.682	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931		C	55743228	G	C	55743228	3	2	197	1	0	0	0	0	1	0	0	0	13851	1357	47	4	421	4	SAPS1	19	55743228	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	599060	55743228	3385755	194	29104										
TMC2	117532	hgsc.bcm.edu	37	chr20	2593864	2593864	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tcatgaggctgacggtgtctGacatgctggtaacgtacatc	12	9	2	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr20:2593864G>A	ENST00000358864.1	+	14	1783	c.1768G>A	c.(1768-1770)Gac>Aac	p.D590N	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	590					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GACGGTGTCTGACATGCTGGT	0.557																																					p.D590N		Atlas-SNP	.											.	TMC2	121	.	0			c.G1768A						.						185	140	155					20																	2593864		2203	4300	6503	SO:0001583	missense	117532	exon14			GTGTCTGACATGC	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1768G>A	chr20.hg19:g.2593864G>A	ENSP00000351732:p.Asp590Asn	83.0	0.0		123.0	42.0	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	hg19	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	G	31	5.092155	0.94149	.	.	ENSG00000149488	ENST00000358864	T	0.72051	-0.62	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.82628	0.5078	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	D	0.84655	0.0703	10	0.87932	D	0	-27.6504	16.0339	0.80608	0.0:0.0:1.0:0.0	.	421;422;590;590	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	N	590	ENSP00000351732:D590N	ENSP00000351732:D590N	D	+	1	0	TMC2	2541864	1.000000	0.71417	0.960000	0.40013	0.922000	0.55478	9.544000	0.98092	2.460000	0.83146	0.655000	0.94253	GAC	.	.		0.557	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			A	2593864	G	A	2593864	3	1	197	1	0	0	0	0	1	0	0	0	16000	1290	45	3	1822	3	TMC2	20	2593864	Missense_Mutation	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10		2593864	60431656	195	29105										
FERMT1	55612	hgsc.bcm.edu	37	chr20	6100146	6100146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gctgctcttcattgggatggTcaacgcggaccacaagctcc	11	13	3	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr20:6100146T>C	ENST00000217289.4	-	2	844	c.56A>G	c.(55-57)gAc>gGc	p.D19G	FERMT1_ENST00000536936.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	19					cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						ATTGGGATGGTCAACGCGGAC	0.468																																					p.D19G		Atlas-SNP	.											.	FERMT1	106	.	0			c.A56G						.						201	140	160					20																	6100146		2203	4300	6503	SO:0001583	missense	55612	exon2			GGATGGTCAACGC	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"Fermitins", "Pleckstrin homology (PH) domain containing"	15889	protein-coding gene	gene with protein product	"kindlin-1", "kinderlin"	607900	"chromosome 20 open reading frame 42", "fermitin family homolog 1 (Drosophila)"	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.56A>G	chr20.hg19:g.6100146T>C	ENSP00000217289:p.Asp19Gly	96.0	0.0		136.0	24.0	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Missense_Mutation	SNP	ENST00000217289.4	hg19	CCDS13098.1	.	.	.	.	.	.	.	.	.	.	T	10.62	1.399942	0.25291	.	.	ENSG00000101311	ENST00000217289;ENST00000339538;ENST00000378844	T;T	0.58060	0.36;0.36	5.93	5.93	0.95920	.	0.089898	0.85682	D	0.000000	T	0.53997	0.1831	L	0.46741	1.465	0.80722	D	1	P;B	0.37824	0.609;0.262	B;B	0.43990	0.438;0.187	T	0.48801	-0.9003	10	0.27082	T	0.32	0.154	16.3756	0.83387	0.0:0.0:0.0:1.0	.	19;19	Q9BQL6-4;Q9BQL6	.;FERM1_HUMAN	G	19	ENSP00000217289:D19G;ENSP00000368121:D19G	ENSP00000217289:D19G	D	-	2	0	FERMT1	6048146	1.000000	0.71417	0.205000	0.23548	0.012000	0.07955	7.394000	0.79862	2.270000	0.75569	0.460000	0.39030	GAC	.	.		0.468	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671		C	6100146	T	C	6100146	3	2	197	1	0	0	0	0	1	0	0	0	5825	1667	58	2	2033	2	FERMT1	20	6100146	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	3506282	6100146	56925374	196	29106										
ID1	3397	hgsc.bcm.edu	37	chr20	30193892	30193892	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cggacgatcgcatcttgtgtCgctgaagcgcctcccccagg	12	15	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr20:30193892C>A	ENST00000376112.3	+	2	568	c.463C>A	c.(463-465)Cgc>Agc	p.R155S	ID1_ENST00000376105.3_3'UTR|MIR3193_ENST00000578262.1_RNA	NM_002165.3	NP_002156.2	P41134	ID1_HUMAN	inhibitor of DNA binding 1, dominant negative helix-loop-helix protein	155					angiogenesis (GO:0001525)|blood vessel endothelial cell migration (GO:0043534)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|collagen metabolic process (GO:0032963)|endothelial cell morphogenesis (GO:0001886)|heart development (GO:0007507)|lung morphogenesis (GO:0060425)|lung vasculature development (GO:0060426)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein destabilization (GO:0031648)|regulation of angiogenesis (GO:0045765)|regulation of MAPK cascade (GO:0043408)|response to antibiotic (GO:0046677)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|ovary(1)|pancreas(1)	4	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			CATCTTGTGTCGCTGAAGCGC	0.652																																					p.R155S	NSCLC(123;1618 1779 21803 28680 33854)	Atlas-SNP	.											.	ID1	12	.	0			c.C463A						.						41	41	41					20																	30193892		2203	4300	6503	SO:0001583	missense	3397	exon2			TTGTGTCGCTGAA		CCDS13185.1, CCDS13186.1	20q11	2013-05-21			ENSG00000125968	ENSG00000125968		"Basic helix-loop-helix proteins"	5360	protein-coding gene	gene with protein product	"DNA-binding protein inhibitor ID-1"	600349				8294468	Standard	NM_002165		Approved	dJ857M17.1.2, bHLHb24	uc002wwg.2	P41134	OTTHUMG00000032181	ENST00000376112.3:c.463C>A	chr20.hg19:g.30193892C>A	ENSP00000365280:p.Arg155Ser	35.0	0.0		66.0	18.0	NM_002165	A8K537|E1P5L4|O00651|O00652|Q16371|Q16377|Q5TE66|Q5TE67|Q969Z7|Q9H0Z5|Q9H109	Missense_Mutation	SNP	ENST00000376112.3	hg19	CCDS13185.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.436165	0.62955	.	.	ENSG00000125968	ENST00000376112	T	0.61510	0.1	4.76	3.81	0.43845	.	0.317846	0.34777	N	0.003699	T	0.47619	0.1455	L	0.36672	1.1	0.80722	D	1	D	0.54207	0.965	B	0.44085	0.44	T	0.51092	-0.8749	10	0.87932	D	0	.	8.9282	0.35655	0.0:0.8993:0.0:0.1007	.	155	P41134	ID1_HUMAN	S	155	ENSP00000365280:R155S	ENSP00000365280:R155S	R	+	1	0	ID1	29657553	1.000000	0.71417	1.000000	0.80357	0.409000	0.31022	1.291000	0.33330	1.232000	0.43678	-0.300000	0.09419	CGC	.	.		0.652	ID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078550.1	NM_002165		A	30193892	C	A	30193892	3	1	197	1	0	0	0	0	1	0	0	0	7498	884	31	1	493	1	ID1	20	30193892	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	24093746	30193892	32831628	197	29107										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39802780	39802780	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gaagcaggagaatggtgaccTcagtcccttcagtggtacgt	13	9	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr20:39802780T>G	ENST00000373271.1	+	31	4064	c.3659T>G	c.(3658-3660)cTc>cGc	p.L1220R	PLCG1_ENST00000608689.1_3'UTR|PLCG1_ENST00000244007.3_Missense_Mutation_p.L1221R|PLCG1_ENST00000373272.2_Missense_Mutation_p.L1221R	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	1220					activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				AATGGTGACCTCAGTCCCTTC	0.607																																					p.L1221R		Atlas-SNP	.											.	PLCG1	111	.	0			c.T3662G						.						74	78	76					20																	39802780		2203	4300	6503	SO:0001583	missense	5335	exon31			GTGACCTCAGTCC	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.3659T>G	chr20.hg19:g.39802780T>G	ENSP00000362368:p.Leu1220Arg	39.0	0.0		64.0	29.0	NM_002660	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	hg19	CCDS13314.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.454676	0.26161	.	.	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.54279	0.58;0.58;0.58	5.43	5.43	0.79202	.	0.779744	0.12162	N	0.493913	T	0.41766	0.1173	L	0.34521	1.04	0.21386	N	0.999706	B;B;B	0.21905	0.062;0.01;0.01	B;B;B	0.23150	0.044;0.014;0.014	T	0.33803	-0.9854	10	0.72032	D	0.01	.	6.7109	0.23276	0.1359:0.0741:0.0:0.79	.	1221;1220;1221	P19174-2;P19174;A2A284	.;PLCG1_HUMAN;.	R	1221;1220;1221	ENSP00000244007:L1221R;ENSP00000362368:L1220R;ENSP00000362369:L1221R	ENSP00000244007:L1221R	L	+	2	0	PLCG1	39236194	0.826000	0.29277	0.998000	0.56505	0.749000	0.42624	2.265000	0.43311	2.062000	0.61559	0.374000	0.22700	CTC	.	.		0.607	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		G	39802780	T	G	39802780	3	3	197	1	0	0	0	0	1	0	0	0	12044	1551	54	5	3784	5	PLCG1	20	39802780	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	9608888	39802780	23222740	198	29108										
TPTE	7179	hgsc.bcm.edu	37	chr21	10933910	10933910	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	agatcttgagccatccactcAtttacttccttggtgaaaac	6	11	2	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr21:10933910A>C	ENST00000361285.4	-	17	1298	c.969T>G	c.(967-969)aaT>aaG	p.N323K	TPTE_ENST00000342420.5_Missense_Mutation_p.N285K|TPTE_ENST00000298232.7_Missense_Mutation_p.N305K|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	323	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CCATCCACTCATTTACTTCCT	0.328																																					p.N323K		Atlas-SNP	.											.	TPTE	513	.	0			c.T969G						.						252	252	252					21																	10933910		2203	4297	6500	SO:0001583	missense	7179	exon17			CCACTCATTTACT	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.969T>G	chr21.hg19:g.10933910A>C	ENSP00000355208:p.Asn323Lys	946.0	0.0		1005.0	73.0	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	0.326	-0.958985	0.02267	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	T;T;T	0.26810	1.71;1.71;1.71	2.07	-0.561	0.11785	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.562019	0.18308	U	0.145211	T	0.07863	0.0197	N	0.04203	-0.255	0.22017	N	0.999416	B;B;B	0.11235	0.001;0.001;0.004	B;B;B	0.20577	0.006;0.01;0.03	T	0.31888	-0.9927	10	0.09843	T	0.71	-0.6319	2.6663	0.05053	0.6197:0.0:0.1522:0.2282	.	285;305;323	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	K	305;323;285	ENSP00000298232:N305K;ENSP00000355208:N323K;ENSP00000344441:N285K	ENSP00000298232:N305K	N	-	3	2	TPTE	9955781	0.000000	0.05858	0.006000	0.13384	0.576000	0.36127	-0.656000	0.05342	-0.125000	0.11703	0.163000	0.16589	AAT	.	.		0.328	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			C	10933910	A	C	10933910	3	2	197	1	0	0	0	0	1	0	0	0	16445	214	8	5	718	5	TPTE	21	10933910	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10		10933910	37195985	199	29109										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19715849	19715849	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tttaactgtttcatttagggTtacttgtccataattccaat	5	7	1	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr21:19715849T>A	ENST00000284885.3	-	12	1435	c.1402A>T	c.(1402-1404)Acc>Tcc	p.T468S		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	468	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TCATTTAGGGTTACTTGTCCA	0.284																																					p.T468S		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A1402T						.						79	66	71					21																	19715849		2200	4292	6492	SO:0001583	missense	5651	exon12			TTAGGGTTACTTG		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1402A>T	chr21.hg19:g.19715849T>A	ENSP00000284885:p.Thr468Ser	182.0	0.0		228.0	77.0	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	hg19	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.180688	0.78677	.	.	ENSG00000154646	ENST00000284885	T	0.02236	4.38	5.18	5.18	0.71444	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.000000	0.85682	D	0.000000	T	0.08980	0.0222	L	0.49256	1.55	0.45594	D	0.998538	D	0.89917	1.0	D	0.97110	1.0	T	0.21484	-1.0244	9	.	.	.	.	14.497	0.67694	0.0:0.0:0.0:1.0	.	468	P98073	ENTK_HUMAN	S	468	ENSP00000284885:T468S	.	T	-	1	0	TMPRSS15	18637720	1.000000	0.71417	0.981000	0.43875	0.983000	0.72400	6.029000	0.70895	2.089000	0.63090	0.455000	0.32223	ACC	.	.		0.284	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		A	19715849	T	A	19715849	3	1	197	1	0	0	0	0	1	0	0	0	16261	1725	60	4	1713	4	TMPRSS15	21	19715849	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	8781939	19715849	28414046	200	29110										
NCAM2	4685	hgsc.bcm.edu	37	chr21	22906918	22906918	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gaggatgaaagagttactaaTcacgaagatgggagcccagt	13	6	1	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr21:22906918T>A	ENST00000400546.1	+	17	2592	c.2343T>A	c.(2341-2343)aaT>aaA	p.N781K	NCAM2_ENST00000284894.7_Missense_Mutation_p.N639K	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	781					axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		GAGTTACTAATCACGAAGATG	0.398																																					p.N781K		Atlas-SNP	.											.	NCAM2	220	.	0			c.T2343A						.						119	112	115					21																	22906918		1897	4118	6015	SO:0001583	missense	4685	exon17			TACTAATCACGAA		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.2343T>A	chr21.hg19:g.22906918T>A	ENSP00000383392:p.Asn781Lys	147.0	0.0		127.0	52.0	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	hg19	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	T	15.32	2.798143	0.50208	.	.	ENSG00000154654	ENST00000400546;ENST00000284894	T;T	0.51574	0.7;0.7	5.49	-0.0574	0.13801	.	0.146598	0.64402	D	0.000016	T	0.39358	0.1075	L	0.54323	1.7	0.80722	D	1	B;B	0.24186	0.099;0.043	B;B	0.22601	0.04;0.016	T	0.30563	-0.9974	10	0.87932	D	0	-28.0276	9.6475	0.39877	0.0:0.4699:0.0:0.5301	.	639;781	B7Z5K2;O15394	.;NCAM2_HUMAN	K	781;639	ENSP00000383392:N781K;ENSP00000284894:N639K	ENSP00000284894:N639K	N	+	3	2	NCAM2	21828789	0.987000	0.35691	0.998000	0.56505	0.955000	0.61496	0.139000	0.16036	-0.014000	0.14175	0.377000	0.23210	AAT	.	.		0.398	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		A	22906918	T	A	22906918	3	1	197	1	0	0	0	0	1	0	0	0	10212	1432	50	4	2409	4	NCAM2	21	22906918	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	3191069	22906918	25222977	201	29111										
HUNK	30811	hgsc.bcm.edu	37	chr21	33370991	33370991	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cagggcccggaagcactggcAtcccccacaaggaagacccc	11	17	0	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr21:33370991A>T	ENST00000270112.2	+	11	1999	c.1639A>T	c.(1639-1641)Atc>Ttc	p.I547F		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	547					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						AAGCACTGGCATCCCCCACAA	0.607																																					p.I547F		Atlas-SNP	.											.	HUNK	74	.	0			c.A1639T						.						89	69	76					21																	33370991		2203	4300	6503	SO:0001583	missense	30811	exon11			ACTGGCATCCCCC	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"hormonally upregulated Neu-associated kinase"			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.1639A>T	chr21.hg19:g.33370991A>T	ENSP00000270112:p.Ile547Phe	96.0	0.0		83.0	27.0	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	hg19	CCDS13610.1	.	.	.	.	.	.	.	.	.	.	A	2.561	-0.301881	0.05495	.	.	ENSG00000142149	ENST00000270112	T	0.69685	-0.42	4.55	-7.31	0.01441	.	1.441670	0.04140	N	0.319368	T	0.42585	0.1209	N	0.19112	0.55	0.09310	N	1	B	0.24823	0.112	B	0.19148	0.024	T	0.31752	-0.9932	10	0.10111	T	0.7	-0.6533	7.6784	0.28499	0.3063:0.4238:0.27:0.0	.	547	P57058	HUNK_HUMAN	F	547	ENSP00000270112:I547F	ENSP00000270112:I547F	I	+	1	0	HUNK	32292862	0.000000	0.05858	0.000000	0.03702	0.172000	0.22775	-0.872000	0.04219	-1.703000	0.01409	0.402000	0.26972	ATC	.	.		0.607	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		T	33370991	A	T	33370991	3	4	197	1	0	0	0	0	1	0	0	0	7467	217	8	4	1681	4	HUNK	21	33370991	Missense_Mutation	SNP	A	TCGA-DD-AADO-01A-11D-A40R-10	10464073	33370991	14758904	202	29112										
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38850602	38850602	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	acatacaagcatattaatgaGgtaagacttgatttgttata	7	4	0	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr21:38850602G>C	ENST00000398960.2	+	3	402	c.327G>C	c.(325-327)gaG>gaC	p.E109D	DYRK1A_ENST00000451934.1_Splice_Site_p.E109D|DYRK1A_ENST00000339659.4_Splice_Site_p.E100D|DYRK1A_ENST00000398956.2_Splice_Site_p.E109D|DYRK1A_ENST00000462274.1_3'UTR|DYRK1A_ENST00000338785.3_Splice_Site_p.E109D|DYRK1A_ENST00000321219.8_Splice_Site_p.E109D	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	109					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ATATTAATGAGGTAAGACTTG	0.373																																					p.E109D	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.G327C						.						79	79	79					21																	38850602		2203	4300	6503	SO:0001630	splice_region_variant	1859	exon3			TAATGAGGTAAGA	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.327+1G>C	chr21.hg19:g.38850602G>C		94.0	0.0		71.0	13.0	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	hg19	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.881521	0.91740	.	.	ENSG00000157540	ENST00000338785;ENST00000426672;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956	T;T;T;T;T;T;T	0.59638	0.36;0.42;0.25;0.38;0.36;0.26;0.37	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.75903	0.3913	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D	0.67145	0.974;0.974;0.996;0.995;0.974	D;D;D;D;D	0.67725	0.953;0.953;0.913;0.946;0.953	T	0.76748	-0.2845	10	0.62326	D	0.03	.	19.8326	0.96642	0.0:0.0:1.0:0.0	.	109;109;109;100;109	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	D	109;109;100;109;109;109;109	ENSP00000342690:E109D;ENSP00000412269:E109D;ENSP00000340373:E100D;ENSP00000319032:E109D;ENSP00000416089:E109D;ENSP00000381932:E109D;ENSP00000381929:E109D	ENSP00000319032:E109D	E	+	3	2	DYRK1A	37772472	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.805000	0.99149	2.686000	0.91538	0.591000	0.81541	GAG	.	.		0.373	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396	Missense_Mutation	C	38850602	G	C	38850602	5	2	197	1	0	0	0	0	0	0	1	0	4856	1014	35	4	337	4	DYRK1A	21	38850602	Splice_Site	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	5479611	38850602	9279293	203	29113										
HSF2BP	11077	hgsc.bcm.edu	37	chr21	45076519	45076519	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ctccagcacctccccatttaGtattctgggtaagaagtccc	7	14	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr21:45076519G>A	ENST00000291560.2	-	3	467	c.136C>T	c.(136-138)Cta>Tta	p.L46L	RRP1B_ENST00000340648.4_5'Flank|HSF2BP_ENST00000542962.1_Intron	NM_007031.1	NP_008962.1	O75031	HSF2B_HUMAN	heat shock transcription factor 2 binding protein	46					spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)				kidney(2)|large_intestine(3)|prostate(1)|skin(1)	7				STAD - Stomach adenocarcinoma(101;0.18)		TCCCCATTTAGTATTCTGGGT	0.398																																					p.L46L		Atlas-SNP	.											.	HSF2BP	28	.	0			c.C136T						.						140	137	138					21																	45076519		2203	4300	6503	SO:0001819	synonymous_variant	11077	exon3			CATTTAGTATTCT	AB007131	CCDS13697.1	21q22.3	2008-07-31			ENSG00000160207	ENSG00000160207			5226	protein-coding gene	gene with protein product	"heat shock factor 2 binding protein"	604554				9651507	Standard	XM_005261090		Approved		uc002zdi.3	O75031	OTTHUMG00000086863	ENST00000291560.2:c.136C>T	chr21.hg19:g.45076519G>A		102.0	0.0		86.0	29.0	NM_007031	B4DX36	Silent	SNP	ENST00000291560.2	hg19	CCDS13697.1																																																																																			.	.		0.398	HSF2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195620.1	NM_007031		A	45076519	G	A	45076519	2	1	197	1	0	0	0	0	0	0	0	1	7406	1020	36	3		3	HSF2BP	21	45076519	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	6225917	45076519	3053376	204	29114										
KRTAP10-9	386676	hgsc.bcm.edu	37	chr21	46047944	46047944	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	cggcctgctacagcttctccTcaggccagaagtccagctgc	10	16	2	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr21:46047944T>A	ENST00000397911.3	+	1	905	c.856T>A	c.(856-858)Tca>Aca	p.S286T	TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	286						keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CAGCTTCTCCTCAGGCCAGAA	0.701																																					p.S286T		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.T856A						.						54	68	63					21																	46047944		2173	4280	6453	SO:0001583	missense	386676	exon1			TTCTCCTCAGGCC	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"Keratin associated proteins"	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.856T>A	chr21.hg19:g.46047944T>A	ENSP00000381009:p.Ser286Thr	55.0	0.0		50.0	9.0	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	hg19	CCDS42961.1	.	.	.	.	.	.	.	.	.	.	t	5.656	0.305714	0.10733	.	.	ENSG00000221837	ENST00000397911	T	0.00776	5.71	2.43	2.43	0.29744	.	.	.	.	.	T	0.02571	0.0078	M	0.66939	2.045	0.09310	N	1	D	0.53885	0.963	D	0.67231	0.95	T	0.44574	-0.9319	8	.	.	.	.	4.5739	0.12223	0.0:0.1709:0.0:0.8291	.	286	P60411	KR109_HUMAN	T	286	ENSP00000381009:S286T	.	S	+	1	0	KRTAP10-9	44872372	0.009000	0.17119	0.018000	0.16275	0.018000	0.09664	0.803000	0.27083	1.049000	0.40321	0.460000	0.39030	TCA	.	.		0.701	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1			A	46047944	T	A	46047944	3	1	197	1	0	0	0	0	1	0	0	0	8525	1551	54	4	858	4	KRTAP10-9	21	46047944	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10	971425	46047944	2081951	205	29115										
C21orf56	84221	hgsc.bcm.edu	37	chr21	47602716	47602716	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	aggagccggctcatcagctcGccgccttcagccatggcggg	14	15	3	0			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr21:47602716G>A	ENST00000291672.5	-	2	1076	c.15C>T	c.(13-15)ggC>ggT	p.G5G	AP001468.58_ENST00000415026.1_RNA|SPATC1L_ENST00000330205.6_Intron	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	5																	TCATCAGCTCGCCGCCTTCAG	0.662																																					p.G5G		Atlas-SNP	.											.	.	.	.	0			c.C15T						.						7	8	8					21																	47602716		684	1581	2265	SO:0001819	synonymous_variant	84221	exon2			CAGCTCGCCGCCT	BC009497	CCDS13732.1, CCDS46653.1	21q22.3	2013-01-21	2012-11-12	2012-11-12	ENSG00000160284	ENSG00000160284			1298	protein-coding gene	gene with protein product	"speriolin-like protein"	612412	"chromosome 21 open reading frame 56"	C21orf56			Standard	NM_032261		Approved		uc011afu.2	Q9H0A9	OTTHUMG00000090487	ENST00000291672.5:c.15C>T	chr21.hg19:g.47602716G>A		71.0	0.0		48.0	8.0	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Silent	SNP	ENST00000291672.5	hg19	CCDS46653.1																																																																																			.	.		0.662	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261		A	47602716	G	A	47602716	2	1	197	1	0	0	0	0	0	0	0	1	2129	1074	38	1		1	C21orf56	21	47602716	Silent	SNP	G	TCGA-DD-AADO-01A-11D-A40R-10	1554772	47602716	527179	206	29116										
GAB4	128954	hgsc.bcm.edu	37	chr22	17472883	17472883	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	actggtcttgatgtcaaacaTatagcccttctgaatctcct	6	11	4	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr22:17472883T>C	ENST00000400588.1	-	2	465	c.358A>G	c.(358-360)Atg>Gtg	p.M120V	GAB4_ENST00000523144.1_5'UTR	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	120	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				ATGTCAAACATATAGCCCTTC	0.502																																					p.M120V		Atlas-SNP	.											.	GAB4	95	.	0			c.A358G						.						258	268	264					22																	17472883		2202	4300	6502	SO:0001583	missense	128954	exon2			CAAACATATAGCC	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"Pleckstrin homology (PH) domain containing"	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.358A>G	chr22.hg19:g.17472883T>C	ENSP00000383431:p.Met120Val	112.0	0.0		110.0	19.0	NM_001037814		Missense_Mutation	SNP	ENST00000400588.1	hg19	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.447366	0.00178	.	.	ENSG00000215568	ENST00000400588	T	0.10763	2.84	1.81	0.667	0.17907	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.263614	0.31347	N	0.007801	T	0.02230	0.0069	N	0.01096	-1.015	0.29239	N	0.872775	B	0.11235	0.004	B	0.09377	0.004	T	0.41342	-0.9514	10	0.08381	T	0.77	.	4.0272	0.09693	0.0:0.4447:0.0:0.5553	.	120	Q2WGN9	GAB4_HUMAN	V	120	ENSP00000383431:M120V	ENSP00000383431:M120V	M	-	1	0	GAB4	15852883	1.000000	0.71417	0.546000	0.28166	0.123000	0.20343	2.693000	0.47027	0.206000	0.20587	0.482000	0.46254	ATG	.	.		0.502	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		C	17472883	T	C	17472883	3	2	197	1	0	0	0	0	1	0	0	0	6159	1406	49	2	1402	2	GAB4	22	17472883	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10		17472883	33831683	207	29117										
PES1	23481	hgsc.bcm.edu	37	chr22	30977601	30977601	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	gtagaactcggtgaaggtggCcatgaccctgtagtccacgt	13	10	0	3			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chr22:30977601C>G	ENST00000405677.1	-	9	1187	c.244G>C	c.(244-246)Gcc>Ccc	p.A82P	PES1_ENST00000354694.7_Missense_Mutation_p.A221P|PES1_ENST00000402281.1_Missense_Mutation_p.A82P|PES1_ENST00000335214.6_Missense_Mutation_p.A221P|PES1_ENST00000402284.3_Missense_Mutation_p.A204P	NM_001282328.1	NP_001269257.1			pescadillo ribosomal biogenesis factor 1											breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	29						GTGAAGGTGGCCATGACCCTG	0.587																																					p.A221P		Atlas-SNP	.											.	PES1	55	.	0			c.G661C						.						101	71	81					22																	30977601		2203	4300	6503	SO:0001583	missense	23481	exon7			AGGTGGCCATGAC	U78310	CCDS13880.1, CCDS58802.1, CCDS74842.1	22q12.1	2012-02-23	2012-02-23		ENSG00000100029	ENSG00000100029			8848	protein-coding gene	gene with protein product		605819	"pescadillo (zebrafish) homolog 1, containing BRCT domain", "pescadillo homolog 1, containing BRCT domain (zebrafish)"			8985183, 10591208, 17353269	Standard	NM_014303		Approved	PES	uc003aij.2	O00541	OTTHUMG00000151077	ENST00000405677.1:c.244G>C	chr22.hg19:g.30977601C>G	ENSP00000385654:p.Ala82Pro	75.0	0.0		82.0	16.0	NM_014303		Missense_Mutation	SNP	ENST00000405677.1	hg19		.	.	.	.	.	.	.	.	.	.	C	30	5.049898	0.93740	.	.	ENSG00000100029	ENST00000354694;ENST00000402281;ENST00000405677;ENST00000402284;ENST00000335214	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.62109	0.2401	M	0.69823	2.125	0.80722	D	1	D;D;D;D	0.64830	0.991;0.994;0.993;0.991	P;D;P;P	0.63597	0.876;0.916;0.801;0.876	T	0.64968	-0.6282	10	0.56958	D	0.05	-27.1835	16.3155	0.82918	0.0:1.0:0.0:0.0	.	221;204;221;221	B2RDF2;B5MCF9;O00541-2;O00541	.;.;.;PESC_HUMAN	P	221;82;82;204;221	ENSP00000346725:A221P;ENSP00000384366:A82P;ENSP00000385654:A82P;ENSP00000384252:A204P;ENSP00000334612:A221P	ENSP00000334612:A221P	A	-	1	0	PES1	29307601	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.132000	0.77251	2.388000	0.81334	0.655000	0.94253	GCC	.	.		0.587	PES1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000321189.2	NM_014303		G	30977601	C	G	30977601	3	3	197	1	0	0	0	0	1	0	0	0	11742	739	26	4	1141	4	PES1	22	30977601	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	13504718	30977601	20326965	208	29118										
TAB3	257397	hgsc.bcm.edu	37	chrX	30871043	30871043	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	tctccatccttgctcgttgaTgtaacagcaaggctacagca	8	12	1	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chrX:30871043T>C	ENST00000378933.1	-	4	1739	c.1562A>G	c.(1561-1563)cAt>cGt	p.H521R	TAB3_ENST00000378932.2_Missense_Mutation_p.H521R|TAB3_ENST00000288422.2_Missense_Mutation_p.H521R|TAB3_ENST00000378930.3_Missense_Mutation_p.H521R|TAB3-AS2_ENST00000445240.1_RNA|TAB3_ENST00000378928.1_5'Flank	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	521					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						TGCTCGTTGATGTAACAGCAA	0.408																																					p.H521R	Pancreas(164;1598 1985 29022 43301 49529)	Atlas-SNP	.											.	TAB3	82	.	0			c.A1562G						.						152	100	118					X																	30871043		2202	4300	6502	SO:0001583	missense	257397	exon7			CGTTGATGTAACA	AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"TAK1 binding protein 3"	300480	"mitogen-activated protein kinase kinase kinase 7 interacting protein 3"	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.1562A>G	chrX.hg19:g.30871043T>C	ENSP00000368215:p.His521Arg	17.0	0.0		15.0	8.0	NM_152787	A6NDD9|Q6VQR0	Missense_Mutation	SNP	ENST00000378933.1	hg19	CCDS14226.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.366911	0.82463	.	.	ENSG00000157625	ENST00000378933;ENST00000378930;ENST00000288422;ENST00000378932	T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.22	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.87962	0.6310	M	0.62723	1.935	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.78314	0.986;0.991	D	0.89192	0.3551	10	0.87932	D	0	-5.6731	14.8121	0.70003	0.0:0.0:0.0:1.0	.	521;521	Q8N5C8-2;Q8N5C8	.;TAB3_HUMAN	R	521	ENSP00000368215:H521R;ENSP00000368212:H521R;ENSP00000288422:H521R;ENSP00000368214:H521R	ENSP00000288422:H521R	H	-	2	0	TAB3	30780964	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.635000	0.83286	1.947000	0.56498	0.412000	0.27726	CAT	.	.		0.408	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787		C	30871043	T	C	30871043	3	2	197	1	0	0	0	0	1	0	0	0	15512	1464	51	2	596	2	TAB3	23	30871043	Missense_Mutation	SNP	T	TCGA-DD-AADO-01A-11D-A40R-10		30871043	124399517	209	29119										
CHM	1121	hgsc.bcm.edu	37	chrX	85218702	85218702	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	atcaatattaaatctcctgcCttctttaataatttgtgagt	4	7	3	1			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chrX:85218702C>A	ENST00000357749.2	-	5	699	c.670G>T	c.(670-672)Ggc>Tgc	p.G224C	CHM_ENST00000467744.2_Intron|CHM_ENST00000537751.1_Missense_Mutation_p.G76C	NM_000390.2	NP_000381.1	P24386	RAE1_HUMAN	choroideremia (Rab escort protein 1)	224					blood vessel development (GO:0001568)|protein geranylgeranylation (GO:0018344)|protein targeting to membrane (GO:0006612)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytosol (GO:0005829)|Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|prostate(1)	20		all_lung(315;5.41e-06)				AATCTCCTGCCTTCTTTAATA	0.338																																					p.G224C		Atlas-SNP	.											.	CHM	57	.	0			c.G670T						.						61	51	54					X																	85218702		2203	4300	6503	SO:0001583	missense	1121	exon5			TCCTGCCTTCTTT	X78121	CCDS14454.1, CCDS48139.1	Xq21.1-q21.3	2014-09-17			ENSG00000188419	ENSG00000188419			1940	protein-coding gene	gene with protein product		300390		TCD, DXS540		1373238	Standard	XM_006724615		Approved	REP-1	uc004eet.3	P24386	OTTHUMG00000021937	ENST00000357749.2:c.670G>T	chrX.hg19:g.85218702C>A	ENSP00000350386:p.Gly224Cys	33.0	0.0		31.0	12.0	NM_000390	A1L4D2|O43732	Missense_Mutation	SNP	ENST00000357749.2	hg19	CCDS14454.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.925129	0.52759	.	.	ENSG00000188419	ENST00000357749;ENST00000537751	D;D	0.86432	-2.12;-2.12	4.5	4.5	0.54988	.	0.000000	0.85682	D	0.000000	D	0.93926	0.8056	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94960	0.8107	10	0.66056	D	0.02	-7.4156	16.7714	0.85538	0.0:1.0:0.0:0.0	.	224	P24386	RAE1_HUMAN	C	224;76	ENSP00000350386:G224C;ENSP00000441728:G76C	ENSP00000350386:G224C	G	-	1	0	CHM	85105358	1.000000	0.71417	1.000000	0.80357	0.415000	0.31203	6.561000	0.73955	1.962000	0.57031	0.284000	0.19432	GGC	.	.		0.338	CHM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057396.3	NM_000390		A	85218702	C	A	85218702	3	1	197	1	0	0	0	0	1	0	0	0	3352	681	24	3	1335	3	CHM	23	85218702	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	54347659	85218702	70051858	210	29120										
CETN2	1069	hgsc.bcm.edu	37	chrX	151997125	151997125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0616113744075829	13	1	1.29798761609907	1.4453781512605	1.24171122994652	0.170446785574706	0.751940625889747	0	ctcacccaactccttggccaCgcgtttcagatttttgaacg	7	14	2	2			TCGA-DD-AADO-01A-11D-A40R-10	TCGA-DD-AADO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0a3f5ccf-b8ce-4d56-af78-c4f04b7119f1	5ca67e3d-63d5-48e4-85b6-e7df2f4497ed	g.chrX:151997125C>T	ENST00000370277.3	-	4	451	c.385G>A	c.(385-387)Gtg>Atg	p.V129M	NSDHL_ENST00000370274.3_5'Flank|NSDHL_ENST00000440023.1_5'Flank|CETN2_ENST00000493482.1_5'UTR	NM_004344.1	NP_004335.1	P41208	CETN2_HUMAN	centrin, EF-hand protein, 2	129	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)|regulation of cytokinesis (GO:0032465)|spermatogenesis (GO:0007283)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|intracellular (GO:0005622)|photoreceptor connecting cilium (GO:0032391)|XPC complex (GO:0071942)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|calcium ion binding (GO:0005509)|nucleic acid binding (GO:0003676)			breast(1)|lung(4)|prostate(1)|skin(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)					TCCTTGGCCACGCGTTTCAGA	0.423								Direct reversal of damage;Nucleotide excision repair (NER)																													p.V129M		Atlas-SNP	.											.	CETN2	23	.	0			c.G385A						.						136	118	124					X																	151997125		2203	4300	6503	SO:0001583	missense	1069	exon4			TGGCCACGCGTTT	X72964	CCDS14716.1	Xq28	2013-01-10			ENSG00000147400	ENSG00000147400		"EF-hand domain containing"	1867	protein-coding gene	gene with protein product		300006		CALT		7713520, 8597638	Standard	NM_004344		Approved	CEN2	uc004fgq.3	P41208	OTTHUMG00000024246	ENST00000370277.3:c.385G>A	chrX.hg19:g.151997125C>T	ENSP00000359300:p.Val129Met	105.0	0.0		107.0	36.0	NM_004344	B2R4T4|Q53XW1	Missense_Mutation	SNP	ENST00000370277.3	hg19	CCDS14716.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.479132	0.84747	.	.	ENSG00000147400	ENST00000370277	T	0.77877	-1.13	6.17	5.31	0.75309	EF-hand-like domain (1);	1.744950	0.03434	N	0.208355	D	0.84745	0.5540	M	0.66506	2.035	0.80722	D	1	P	0.49090	0.919	P	0.50659	0.647	T	0.69371	-0.5163	10	0.87932	D	0	.	11.9876	0.53157	0.0:0.9156:0.0:0.0844	.	129	P41208	CETN2_HUMAN	M	129	ENSP00000359300:V129M	ENSP00000359300:V129M	V	-	1	0	CETN2	151747781	1.000000	0.71417	0.715000	0.30552	0.952000	0.60782	7.664000	0.83830	1.348000	0.45733	0.600000	0.82982	GTG	.	.		0.423	CETN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061197.1	NM_004344		T	151997125	C	T	151997125	3	4	197	1	0	0	0	0	1	0	0	0	3277	536	19	1	141	1	CETN2	23	151997125	Missense_Mutation	SNP	C	TCGA-DD-AADO-01A-11D-A40R-10	66778423	151997125	3273435	211	29121										
MIB2	142678	hgsc.bcm.edu	37	chr1	1562694	1562694	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	aggtggacaccaagaaccaaGgcaggaccgctctgcaagtg	13	11	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:1562694G>T	ENST00000357210.4	+	12	1783	c.1567G>T	c.(1567-1569)Ggc>Tgc	p.G523C	MIB2_ENST00000378712.1_Missense_Mutation_p.G400C|MIB2_ENST00000360522.4_Missense_Mutation_p.G488C|MIB2_ENST00000520777.1_Missense_Mutation_p.G576C|MIB2_ENST00000378710.3_Missense_Mutation_p.G487C|MIB2_ENST00000505820.2_Missense_Mutation_p.G580C|MIB2_ENST00000504599.1_Missense_Mutation_p.G479C|MIB2_ENST00000355826.5_Missense_Mutation_p.G566C|MIB2_ENST00000518681.1_Missense_Mutation_p.G515C|MIB2_ENST00000378708.1_Missense_Mutation_p.G429C	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	523					Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CAAGAACCAAGGCAGGACCGC	0.652																																					p.G580C		Atlas-SNP	.											.	MIB2	62	.	0			c.G1738T						.						44	56	52					1																	1562694		2122	4224	6346	SO:0001583	missense	142678	exon12			AACCAAGGCAGGA	AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	30577	protein-coding gene	gene with protein product		611141	"zinc finger, ZZ type with ankyrin repeat domain 1", "mindbomb homolog 2 (Drosophila)"	ZZANK1		12761501	Standard	NM_080875		Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000357210.4:c.1567G>T	chr1.hg19:g.1562694G>T	ENSP00000349741:p.Gly523Cys	355.0	0.0		182.0	101.0	NM_080875	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	Missense_Mutation	SNP	ENST00000357210.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.62|19.62	3.862644|3.862644	0.71949|0.71949	.|.	.|.	ENSG00000197530|ENSG00000197530	ENST00000520777;ENST00000357210;ENST00000360522;ENST00000378710;ENST00000355826;ENST00000518681;ENST00000505820;ENST00000378712;ENST00000504599;ENST00000378708|ENST00000514234	D;D;D;D;D;D;D;D;D;D|.	0.88741|.	-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42|.	3.92|3.92	3.92|3.92	0.45320|0.45320	Ankyrin repeat-containing domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86489|0.86489	0.5945|0.5945	H|H	0.95402|0.95402	3.665|3.665	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D|D	0.90958|0.90958	0.4810|0.4810	10|5	0.87932|.	D|.	0|.	-13.4616|-13.4616	15.0876|15.0876	0.72167|0.72167	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	488;429;400;515;576;509;523|.	Q96AX9-5;F2Z2L2;B3KXY1;E9PHQ1;E9PGU1;Q96AX9-2;Q96AX9|.	.;.;.;.;.;.;MIB2_HUMAN|.	C|M	576;523;488;487;566;515;580;400;479;429|338	ENSP00000428660:G576C;ENSP00000349741:G523C;ENSP00000353713:G488C;ENSP00000367982:G487C;ENSP00000348081:G566C;ENSP00000428264:G515C;ENSP00000426103:G580C;ENSP00000367984:G400C;ENSP00000426128:G479C;ENSP00000367980:G429C|.	ENSP00000348081:G566C|.	G|R	+|+	1|2	0|0	MIB2|MIB2	1552557|1552557	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.827000|0.827000	0.46813|0.46813	9.459000|9.459000	0.97638|0.97638	2.011000|2.011000	0.59026|0.59026	0.455000|0.455000	0.32223|0.32223	GGC|AGG	.	.		0.652	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875		T	1562694	G	T	1562694	3	4	198	1	0	0	0	0	1	0	0	0	9576	1000	35	3	1784	3	MIB2	1	1562694	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10		1562694	247687927	1	29122										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27097800	27097809	+	Frame_Shift_Del	DEL	TCCAGCCTCC	TCCAGCCTCC	-													0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	caagaagtcccagcccaagaTccagcctccctctcctggta							TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	TCCAGCCTCC	TCCAGCCTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:27097800_27097809delTCCAGCCTCC	ENST00000324856.7	+	12	3760_3769	c.3389_3398delTCCAGCCTCC	c.(3388-3399)atccagcctcccfs	p.IQPP1130fs	ARID1A_ENST00000374152.2_Frame_Shift_Del_p.IQPP747fs|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.IQPP1130fs|ARID1A_ENST00000540690.1_5'Flank	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1130					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.Q1131*(3)|p.Q1131fs*30(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CAGCCCAAGATCCAGCCTCCCTCTCCTGGT	0.543			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.1130_1133del		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	4	Substitution - Nonsense(3)|Deletion - Frameshift(1)	skin(2)|ovary(1)|endometrium(1)	c.3388_3397del						.																																			SO:0001589	frameshift_variant	8289	exon12			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3389_3398delTCCAGCCTCC	chr1.hg19:g.27097800_27097809delTCCAGCCTCC	ENSP00000320485:p.Ile1130fs	137.0	0.0		36.0	22.0	NM_139135	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.543	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27097809	TCCAGCCTCC	-	27097800	7	5	198	1	0	1	0	1	0	0	0	0	913	1435	50	0	3435	0	ARID1A	1	27097800	Frame_Shift_Del	DEL	TCCAGCCTCC	TCGA-DD-AADP-01A-11D-A38X-10	25535106	27097800	222152821	2	29123										
ZNF644	84146	hgsc.bcm.edu	37	chr1	91382375	91382375	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ctatgaagctgcttcggccaTtagtagagaaaatgaagttt	10	6	0	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:91382375T>A	ENST00000370440.1	-	6	4181	c.3964A>T	c.(3964-3966)Atg>Ttg	p.M1322L	ZNF644_ENST00000467231.1_5'UTR|ZNF644_ENST00000337393.5_Missense_Mutation_p.M1322L|ZNF644_ENST00000347275.5_Missense_Mutation_p.M100L|ZNF644_ENST00000361321.5_Missense_Mutation_p.M100L			Q9H582	ZN644_HUMAN	zinc finger protein 644	1322					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		GCTTCGGCCATTAGTAGAGAA	0.378																																					p.M1322L		Atlas-SNP	.											.	ZNF644	120	.	0			c.A3964T						.						70	69	69					1																	91382375		2203	4300	6503	SO:0001583	missense	84146	exon6			CGGCCATTAGTAG	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.3964A>T	chr1.hg19:g.91382375T>A	ENSP00000359469:p.Met1322Leu	168.0	0.0		144.0	63.0	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	hg19	CCDS731.1	.	.	.	.	.	.	.	.	.	.	T	12.51	1.960278	0.34565	.	.	ENSG00000122482	ENST00000370440;ENST00000347275;ENST00000337393;ENST00000361321	T;T	0.00574	6.47;6.47	5.8	4.69	0.59074	.	0.228597	0.45867	D	0.000337	T	0.00241	0.0007	N	0.14661	0.345	0.35334	D	0.785894	P;B	0.40000	0.698;0.002	B;B	0.38296	0.27;0.001	T	0.73180	-0.4064	10	0.87932	D	0	-6.5633	11.2739	0.49155	0.0:0.0707:0.0:0.9293	.	1322;100	Q9H582;Q9H582-3	ZN644_HUMAN;.	L	1322;100;1322;100	ENSP00000359469:M1322L;ENSP00000337008:M1322L	ENSP00000337008:M1322L	M	-	1	0	ZNF644	91154963	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.522000	0.53480	2.216000	0.71823	0.533000	0.62120	ATG	.	.		0.378	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		A	91382375	T	A	91382375	3	1	198	1	0	0	0	0	1	0	0	0	18075	1493	52	4	23	4	ZNF644	1	91382375	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	64284575	91382375	157868246	3	29124										
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94685889	94685889	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gttctgatgtttattcattaTagactttaaaacacggagca	7	6	2	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:94685889T>C	ENST00000260526.6	-	3	447	c.265A>G	c.(265-267)Ata>Gta	p.I89V	ARHGAP29_ENST00000370217.3_Missense_Mutation_p.I89V	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	89					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		TTATTCATTATAGACTTTAAA	0.313																																					p.I89V		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.A265G						.						97	97	97					1																	94685889		2202	4298	6500	SO:0001583	missense	9411	exon3			TCATTATAGACTT		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.265A>G	chr1.hg19:g.94685889T>C	ENSP00000260526:p.Ile89Val	98.0	0.0		56.0	21.0	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	hg19	CCDS748.1	.	.	.	.	.	.	.	.	.	.	T	2.973	-0.212107	0.06140	.	.	ENSG00000137962	ENST00000260526;ENST00000370217	T;T	0.17854	2.4;2.25	5.67	-0.797	0.10909	.	0.752143	0.10886	N	0.623287	T	0.01287	0.0042	N	0.04018	-0.295	0.26110	N	0.980698	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.47995	-0.9073	10	0.02654	T	1	-8.156	5.1579	0.15044	0.1365:0.3966:0.0:0.4669	.	89;89	Q52LW3-2;Q52LW3	.;RHG29_HUMAN	V	89	ENSP00000260526:I89V;ENSP00000359237:I89V	ENSP00000260526:I89V	I	-	1	0	ARHGAP29	94458477	0.228000	0.23718	0.999000	0.59377	0.988000	0.76386	-0.415000	0.07106	0.254000	0.21573	0.533000	0.62120	ATA	.	.		0.313	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		C	94685889	T	C	94685889	3	2	198	1	0	0	0	0	1	0	0	0	878	1406	49	2	3604	2	ARHGAP29	1	94685889	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	3303514	94685889	154564732	4	29125										
YY1AP1	55249	hgsc.bcm.edu	37	chr1	155630103	155630103	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gaaaggccctggctccccttCtttttgagggtctccgtctc	10	14	3	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:155630103C>T	ENST00000295566.4	-	11	1759	c.1736G>A	c.(1735-1737)aGa>aAa	p.R579K	YY1AP1_ENST00000359205.5_Missense_Mutation_p.R522K|YY1AP1_ENST00000368339.5_Missense_Mutation_p.R671K|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000355499.4_Missense_Mutation_p.R533K|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000311573.5_Missense_Mutation_p.R502K|YY1AP1_ENST00000361831.5_Missense_Mutation_p.R522K|YY1AP1_ENST00000404643.1_Missense_Mutation_p.R513K|YY1AP1_ENST00000407221.1_Missense_Mutation_p.R502K|YY1AP1_ENST00000535662.1_Missense_Mutation_p.R379K|YY1AP1_ENST00000368330.2_Missense_Mutation_p.R533K|YY1AP1_ENST00000368340.5_Missense_Mutation_p.R651K|YY1AP1_ENST00000347088.5_Missense_Mutation_p.R533K	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	579					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					GGCTCCCCTTCTTTTTGAGGG	0.522																																					p.R671K		Atlas-SNP	.											YY1AP1_ENST00000368339,right_upper_lobe,carcinoma,0,2	YY1AP1	104	.	0			c.G2012A						.						108	105	106					1																	155630103		2203	4300	6503	SO:0001583	missense	55249	exon10			CCCCTTCTTTTTG	BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.1736G>A	chr1.hg19:g.155630103C>T	ENSP00000295566:p.Arg579Lys	222.0	2.0		231.0	69.0	NM_001198903	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	hg19	CCDS1115.1	.	.	.	.	.	.	.	.	.	.	c	10.72	1.429237	0.25726	.	.	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000535662	T;T;T;T;T;T;T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9	2.53	1.58	0.23477	.	0.558747	0.19160	N	0.121218	T	0.28797	0.0714	M	0.66939	2.045	0.53688	D	0.999979	B;B;B;B;B	0.34399	0.001;0.009;0.452;0.025;0.1	B;B;P;B;B	0.44623	0.003;0.013;0.455;0.012;0.022	T	0.10941	-1.0608	10	0.30854	T	0.27	.	6.0708	0.19887	0.0:0.652:0.0:0.348	.	671;513;579;533;651	B4DMP2;Q9H869-4;Q9H869;Q9H869-2;Q5VYZ1	.;.;YYAP1_HUMAN;.;.	K	522;533;502;533;522;651;579;533;502;513;671;379	ENSP00000352134:R522K;ENSP00000347686:R533K;ENSP00000311138:R502K;ENSP00000316079:R533K;ENSP00000355298:R522K;ENSP00000357324:R651K;ENSP00000295566:R579K;ENSP00000357314:R533K;ENSP00000385791:R502K;ENSP00000385390:R513K;ENSP00000357323:R671K;ENSP00000437926:R379K	ENSP00000295566:R579K	R	-	2	0	YY1AP1	153896727	0.952000	0.32445	0.507000	0.27676	0.828000	0.46876	0.610000	0.24253	0.388000	0.25054	0.306000	0.20318	AGA	.	.		0.522	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		T	155630103	C	T	155630103	3	4	198	1	0	0	0	0	1	0	0	0	17523	913	32	3	658	3	YY1AP1	1	155630103	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	60944214	155630103	93620518	5	29126										
PRRX1	5396	hgsc.bcm.edu	37	chr1	170633528	170633528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	cggcacaggcggatgagaacGtgggcgaggctggccggagc	20	10	0	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:170633528G>A	ENST00000239461.6	+	1	482	c.169G>A	c.(169-171)Gtg>Atg	p.V57M	PRRX1_ENST00000367760.3_Missense_Mutation_p.V57M|RP1-79C4.4_ENST00000606154.1_lincRNA|PRRX1_ENST00000497230.2_Missense_Mutation_p.V57M	NM_022716.2	NP_073207.1	P54821	PRRX1_HUMAN	paired related homeobox 1	57					artery morphogenesis (GO:0048844)|cartilage development (GO:0051216)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)	nucleolus (GO:0005730)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			large_intestine(2)|ovary(1)	3	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GGATGAGAACGTGGGCGAGGC	0.672																																					p.V57M		Atlas-SNP	.											.	PRRX1	81	.	0			c.G169A						.						29	28	28					1																	170633528		2203	4300	6503	SO:0001583	missense	5396	exon1			GAGAACGTGGGCG	M95929	CCDS1290.1, CCDS1291.1	1q24.3	2011-06-20	2003-11-12	2003-11-14	ENSG00000116132	ENSG00000116132		"Homeoboxes / PRD class"	9142	protein-coding gene	gene with protein product		167420	"paired mesoderm homeo box 1"	PMX1		1509260	Standard	NM_006902		Approved	PHOX1	uc001ghf.3	P54821	OTTHUMG00000035231	ENST00000239461.6:c.169G>A	chr1.hg19:g.170633528G>A	ENSP00000239461:p.Val57Met	369.0	1.0		390.0	109.0	NM_006902	B5BUM7|O60807	Missense_Mutation	SNP	ENST00000239461.6	hg19	CCDS1290.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.899395	0.33535	.	.	ENSG00000116132	ENST00000553786;ENST00000367760;ENST00000239461;ENST00000497230	D;D;D;D	0.91351	-2.75;-2.79;-2.83;-2.77	4.63	4.63	0.57726	.	0.126840	0.53938	D	0.000058	T	0.77961	0.4209	N	0.19112	0.55	0.80722	D	1	P;P	0.46277	0.614;0.875	B;B	0.42245	0.089;0.381	T	0.81495	-0.0907	10	0.46703	T	0.11	.	11.4545	0.50173	0.0:0.0:0.8198:0.1801	.	57;57	P54821;P54821-2	PRRX1_HUMAN;.	M	10;57;57;57	ENSP00000451943:V10M;ENSP00000356734:V57M;ENSP00000239461:V57M;ENSP00000450762:V57M	ENSP00000239461:V57M	V	+	1	0	PRRX1	168900152	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.568000	0.67385	2.399000	0.81585	0.555000	0.69702	GTG	.	.		0.672	PRRX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085236.3	NM_006902		A	170633528	G	A	170633528	3	1	198	1	0	0	0	0	1	0	0	0	12624	1145	40	1	171	1	PRRX1	1	170633528	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	15003425	170633528	78617093	6	29127										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177250089	177250089	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tggccatctacgtcaaccccTttgggggcagccactctgag	11	14	3	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:177250089T>C	ENST00000361539.4	+	8	2089	c.1777T>C	c.(1777-1779)Ttt>Ctt	p.F593L	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	593					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											CGTCAACCCCTTTGGGGGCAG	0.567																																					p.F593L		Atlas-SNP	.											.	FAM5B	191	.	0			c.T1777C						.						46	46	46					1																	177250089		2203	4300	6503	SO:0001583	missense	57795	exon8			AACCCCTTTGGGG		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1777T>C	chr1.hg19:g.177250089T>C	ENSP00000354481:p.Phe593Leu	76.0	0.0		126.0	35.0	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	hg19	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	T	15.80	2.940782	0.52972	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.18016	2.24	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.42562	0.1208	M	0.79475	2.455	0.80722	D	1	D;D	0.76494	0.999;0.993	D;D	0.80764	0.994;0.956	T	0.30534	-0.9975	10	0.38643	T	0.18	-11.8898	14.8158	0.70034	0.0:0.0:0.0:1.0	.	488;593	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	L	346;593	ENSP00000354481:F593L	ENSP00000354481:F593L	F	+	1	0	FAM5B	175516712	1.000000	0.71417	0.990000	0.47175	0.282000	0.26991	7.910000	0.87451	1.978000	0.57642	0.260000	0.18958	TTT	.	.		0.567	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		C	177250089	T	C	177250089	3	2	198	1	0	0	0	0	1	0	0	0	5601	1609	56	2	1803	2	FAM5B	1	177250089	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	6616561	177250089	72000532	7	29128										
ANGPTL1	9068	hgsc.bcm.edu	37	chr1	178834353	178834353	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gatcatcacagattggttatTgacaagatcagtcaaggaag	10	6	4	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:178834353T>G	ENST00000234816.2	-	3	1006	c.559A>C	c.(559-561)Aat>Cat	p.N187H	ANGPTL1_ENST00000367629.1_Missense_Mutation_p.N187H|RALGPS2_ENST00000367635.3_Intron|RALGPS2_ENST00000367634.2_Intron	NM_004673.3	NP_004664.1	O95841	ANGL1_HUMAN	angiopoietin-like 1	187					transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(2)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	14						GATTGGTTATTGACAAGATCA	0.443																																					p.N187H		Atlas-SNP	.											.	ANGPTL1	41	.	0			c.A559C						.						108	94	99					1																	178834353		2203	4300	6503	SO:0001583	missense	9068	exon3			GGTTATTGACAAG	AF107253	CCDS1327.1	1q25.2	2013-02-06			ENSG00000116194	ENSG00000116194		"Fibrinogen C domain containing"	489	protein-coding gene	gene with protein product	"angioarrestin"	603874		ANGPT3		10025962, 9286704	Standard	NM_004673		Approved	ANG3, AngY, ARP1	uc001gma.3	O95841	OTTHUMG00000035075	ENST00000234816.2:c.559A>C	chr1.hg19:g.178834353T>G	ENSP00000234816:p.Asn187His	148.0	0.0		168.0	89.0	NM_004673	Q5T5Z5	Missense_Mutation	SNP	ENST00000234816.2	hg19	CCDS1327.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.826399	0.50739	.	.	ENSG00000116194	ENST00000234816;ENST00000367629;ENST00000415564	T;T	0.56275	0.47;0.47	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.48409	0.1498	L	0.46741	1.465	0.80722	D	1	B	0.31989	0.35	B	0.34301	0.179	T	0.43814	-0.9368	10	0.30854	T	0.27	.	15.235	0.73422	0.0:0.0:0.0:1.0	.	187	O95841	ANGL1_HUMAN	H	187;187;151	ENSP00000234816:N187H;ENSP00000356601:N187H	ENSP00000234816:N187H	N	-	1	0	ANGPTL1	177100976	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.997000	0.88414	2.132000	0.65825	0.528000	0.53228	AAT	.	.		0.443	ANGPTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084924.1	NM_004673		G	178834353	T	G	178834353	3	3	198	1	0	0	0	0	1	0	0	0	613	1812	63	5	932	5	ANGPTL1	1	178834353	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	1584264	178834353	70416268	8	29129										
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186880516	186880516	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gtgaaggattgcattctgcaCgtgatgtgagttggaaattt	13	4	1	3	rs374028240		TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:186880516C>T	ENST00000367466.3	+	7	705	c.553C>T	c.(553-555)Cgt>Tgt	p.R185C	PLA2G4A_ENST00000442353.2_Intron|PLA2G4A_ENST00000466600.1_3'UTR	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	185	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	GCATTCTGCACGTGATGTGAG	0.353																																					p.R185C		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.C553T						.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	105	108	107		553	4.9	1	1		107	0,8600		0,0,4300	no	missense	PLA2G4A	NM_024420.2	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	185/750	186880516	1,13005	2203	4300	6503	SO:0001583	missense	5321	exon7			TCTGCACGTGATG	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.553C>T	chr1.hg19:g.186880516C>T	ENSP00000356436:p.Arg185Cys	99.0	0.0		92.0	38.0	NM_024420	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	hg19	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.937054	0.34189	2.27E-4	0.0	ENSG00000116711	ENST00000367466	T	0.04706	3.57	4.94	4.94	0.65067	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.447714	0.25981	N	0.027080	T	0.08044	0.0201	M	0.61703	1.905	0.80722	D	1	P	0.52061	0.95	B	0.43155	0.41	T	0.02983	-1.1086	10	0.59425	D	0.04	-12.3085	11.1737	0.48586	0.1839:0.8161:0.0:0.0	.	185	P47712	PA24A_HUMAN	C	185	ENSP00000356436:R185C	ENSP00000356436:R185C	R	+	1	0	PLA2G4A	185147139	0.990000	0.36364	0.996000	0.52242	0.367000	0.29736	1.898000	0.39809	2.437000	0.82529	0.650000	0.86243	CGT	.	.		0.353	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		T	186880516	C	T	186880516	3	4	198	1	0	0	0	0	1	0	0	0	12010	536	19	1	575	1	PLA2G4A	1	186880516	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	8046163	186880516	62370105	9	29130										
IARS2	55699	hgsc.bcm.edu	37	chr1	220273891	220273891	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ggctccaaaatacattttgtGcccggctgggattgtcatgg	12	9	1	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:220273891G>T	ENST00000302637.5	+	3	554	c.450G>T	c.(448-450)gtG>gtT	p.V150V	IARS2_ENST00000366922.1_Silent_p.V78V	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	150					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	TACATTTTGTGCCCGGCTGGG	0.338																																					p.V150V		Atlas-SNP	.											.	IARS2	106	.	0			c.G450T						.						62	67	65					1																	220273891		2203	4300	6503	SO:0001819	synonymous_variant	55699	exon3			TTTTGTGCCCGGC	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.450G>T	chr1.hg19:g.220273891G>T		353.0	0.0		340.0	179.0	NM_018060	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Silent	SNP	ENST00000302637.5	hg19	CCDS1523.1																																																																																			.	.		0.338	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		T	220273891	G	T	220273891	2	4	198	1	0	0	0	0	0	0	0	1	7483	1306	46	3		3	IARS2	1	220273891	Silent	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	33393375	220273891	28976730	10	29131										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370098	240370098	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tctgtccttgtcgcccttcaGgaagttgttgacatgaagtc	10	10	2	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:240370098G>A	ENST00000319653.9	+	5	2216		c.e5-1			NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2						cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TCGCCCTTCAGGAAGTTGTTG	0.393																																					.		Atlas-SNP	.											.	FMN2	451	.	0			c.1987-1G>A						.						43	44	44					1																	240370098		2201	4297	6498	SO:0001630	splice_region_variant	56776	exon5			CCTTCAGGAAGTT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1987-1G>A	chr1.hg19:g.240370098G>A		263.0	0.0		318.0	177.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Splice_Site	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	14.04	2.416696	0.42918	.	.	ENSG00000155816	ENST00000447095;ENST00000319653	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1731	0.98165	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FMN2	238436721	1.000000	0.71417	0.981000	0.43875	0.095000	0.18619	7.991000	0.88244	2.768000	0.95171	0.655000	0.94253	.	.	.		0.393	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	Intron	A	240370098	G	A	240370098	5	1	198	1	0	0	0	0	0	0	1	0	5958	1014	35	3	2004	3	FMN2	1	240370098	Splice_Site	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	20096207	240370098	8880523	11	29132										
CHML	1122	hgsc.bcm.edu	37	chr1	241797784	241797784	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	aataaaatatttagcatttaTtctttgaccaaagtgatcta	4	5	2	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr1:241797784T>C	ENST00000366553.1	-	1	1448	c.1285A>G	c.(1285-1287)Ata>Gta	p.I429V	OPN3_ENST00000469376.1_Intron|OPN3_ENST00000366554.2_Intron|OPN3_ENST00000331838.5_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	429					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			TTAGCATTTATTCTTTGACCA	0.353																																					p.I429V		Atlas-SNP	.											.	CHML	82	.	0			c.A1285G						.						76	80	79					1																	241797784		2200	4298	6498	SO:0001583	missense	1122	exon1			CATTTATTCTTTG	X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.1285A>G	chr1.hg19:g.241797784T>C	ENSP00000355511:p.Ile429Val	61.0	0.0		77.0	19.0	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	hg19	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.139700	0.56936	.	.	ENSG00000203668	ENST00000366553	T	0.59906	0.23	4.93	4.93	0.64822	.	0.047798	0.85682	U	0.000000	T	0.64159	0.2573	.	.	.	0.41886	D	0.990341	P	0.36535	0.557	P	0.52481	0.7	T	0.59252	-0.7489	9	0.20519	T	0.43	-15.9105	12.8833	0.58030	0.0:0.0:0.0:1.0	.	429	P26374	RAE2_HUMAN	V	429	ENSP00000355511:I429V	ENSP00000355511:I429V	I	-	1	0	CHML	239864407	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.302000	0.65733	2.218000	0.71995	0.533000	0.62120	ATA	.	.		0.353	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821		C	241797784	T	C	241797784	3	2	198	1	0	0	0	0	1	0	0	0	3353	1493	52	2	689	2	CHML	1	241797784	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	1427686	241797784	7452837	12	29133										
KIDINS220	57498	hgsc.bcm.edu	37	chr2	8953428	8953428	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	actctactacgtcagtacggCctttgtaacatgcccacata	6	13	2	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr2:8953428C>T	ENST00000256707.3	-	5	525	c.344G>A	c.(343-345)gGc>gAc	p.G115D	KIDINS220_ENST00000319688.5_Missense_Mutation_p.G115D|KIDINS220_ENST00000473731.1_Missense_Mutation_p.G115D|KIDINS220_ENST00000418530.1_Missense_Mutation_p.G73D|KIDINS220_ENST00000427284.1_Missense_Mutation_p.G115D	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	115					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GTCAGTACGGCCTTTGTAACA	0.378																																					p.G115D		Atlas-SNP	.											.	KIDINS220	136	.	0			c.G344A						.						162	151	154					2																	8953428		1903	4133	6036	SO:0001583	missense	57498	exon5			GTACGGCCTTTGT	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.344G>A	chr2.hg19:g.8953428C>T	ENSP00000256707:p.Gly115Asp	279.0	0.0		266.0	100.0	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.898405	0.91962	.	.	ENSG00000134313	ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T	0.74421	-0.84;-0.84;1.91;-0.84;-0.84;-0.84	6.0	6.0	0.97389	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	D	0.87426	0.6174	M	0.78049	2.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.87427	0.2386	10	0.72032	D	0.01	.	20.0896	0.97814	0.0:1.0:0.0:0.0	.	115;73;115	B4DK94;Q9ULH0-2;Q9ULH0	.;.;KDIS_HUMAN	D	115;115;73;115;115;115	ENSP00000256707:G115D;ENSP00000411849:G115D;ENSP00000414923:G73D;ENSP00000418974:G115D;ENSP00000419964:G115D;ENSP00000319947:G115D	ENSP00000256707:G115D	G	-	2	0	KIDINS220	8870879	1.000000	0.71417	1.000000	0.80357	0.699000	0.40488	7.268000	0.78473	2.846000	0.97976	0.650000	0.86243	GGC	.	.		0.378	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		T	8953428	C	T	8953428	3	4	198	1	0	0	0	0	1	0	0	0	8280	739	26	3	5075	3	KIDINS220	2	8953428	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10		8953428	234245945	13	29134										
NBAS	51594	hgsc.bcm.edu	37	chr2	15319165	15319165	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ctcgtgcagatgctcatctcGgctctcgaggagaagtttca	11	11	4	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr2:15319165G>A	ENST00000281513.5	-	51	6812	c.6787C>T	c.(6787-6789)Cga>Tga	p.R2263*	NBAS_ENST00000441750.1_Nonsense_Mutation_p.R2143*	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2263					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.R2263*(1)		NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TGCTCATCTCGGCTCTCGAGG	0.483																																					p.R2263X		Atlas-SNP	.											NBAS,NS,carcinoma,0,1	NBAS	246	.	1	Substitution - Nonsense(1)	breast(1)	c.C6787T						.						87	75	79					2																	15319165		2203	4300	6503	SO:0001587	stop_gained	51594	exon51			CATCTCGGCTCTC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.6787C>T	chr2.hg19:g.15319165G>A	ENSP00000281513:p.Arg2263*	449.0	1.0		404.0	148.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Nonsense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	G	44	10.732753	0.99458	.	.	ENSG00000151779	ENST00000441750;ENST00000281513;ENST00000423602	.	.	.	5.98	3.16	0.36331	.	1.426570	0.03665	N	0.243171	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	9.0963	0.36640	0.0:0.2389:0.3935:0.3676	.	.	.	.	X	2143;2263;117	.	ENSP00000281513:R2263X	R	-	1	2	NBAS	15236616	0.988000	0.35896	0.315000	0.25238	0.015000	0.08874	2.073000	0.41519	0.395000	0.25257	-0.230000	0.12252	CGA	.	.		0.483	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		A	15319165	G	A	15319165	4	1	198	1	0	0	0	0	0	1	0	0	10195	1124	39	1	336	1	NBAS	2	15319165	Nonsense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	6365737	15319165	227880208	14	29135										
MYCN	4613	hgsc.bcm.edu	37	chr2	16082485	16082485	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ggaggacgcgttcggcctggGgggactgggtggcctcaccc	19	12	1	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr2:16082485G>T	ENST00000281043.3	+	2	596	c.299G>T	c.(298-300)gGg>gTg	p.G100V	MYCNOS_ENST00000448719.1_RNA|MYCNOS_ENST00000419083.1_RNA|MYCNOS_ENST00000453400.1_RNA|MYCNOS_ENST00000439180.1_RNA|MYCNOS_ENST00000420452.1_RNA	NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	100					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			TTCGGCCTGGGGGGACTGGGT	0.697			A		neuroblastoma																																p.G100V		Atlas-SNP	.		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	.	MYCN	63	.	0			c.G299T						.						11	11	11					2																	16082485		2167	4254	6421	SO:0001583	missense	4613	exon2			GCCTGGGGGGACT	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.299G>T	chr2.hg19:g.16082485G>T	ENSP00000281043:p.Gly100Val	1018.0	0.0		777.0	288.0	NM_005378	Q53XS5|Q6LDT9	Missense_Mutation	SNP	ENST00000281043.3	hg19	CCDS1687.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.342692	0.61073	.	.	ENSG00000134323	ENST00000281043;ENST00000426211	T	0.19938	2.11	2.89	2.89	0.33648	Transcription regulator Myc, N-terminal (1);	0.625852	0.16639	N	0.205726	T	0.38852	0.1056	L	0.57536	1.79	0.80722	D	1	D	0.61080	0.989	D	0.65443	0.935	T	0.21348	-1.0248	10	0.49607	T	0.09	-12.5617	12.7304	0.57195	0.0:0.0:1.0:0.0	.	100	P04198	MYCN_HUMAN	V	100	ENSP00000281043:G100V	ENSP00000281043:G100V	G	+	2	0	MYCN	15999936	1.000000	0.71417	0.937000	0.37676	0.344000	0.29017	4.356000	0.59430	1.567000	0.49668	0.561000	0.74099	GGG	.	.		0.697	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		T	16082485	G	T	16082485	3	4	198	1	0	0	0	0	1	0	0	0	10030	1232	43	3	301	3	MYCN	2	16082485	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	763320	16082485	227116888	15	29136										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33588558	33588558	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	actgtaagcaagggacgtacTatgatcctgtgaaactgcag	11	8	0	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr2:33588558T>G	ENST00000404816.2	+	29	4725	c.4372T>G	c.(4372-4374)Tat>Gat	p.Y1458D	LTBP1_ENST00000418533.2_Missense_Mutation_p.Y1090D|LTBP1_ENST00000354476.3_Missense_Mutation_p.Y1459D|LTBP1_ENST00000407925.1_Missense_Mutation_p.Y1132D|LTBP1_ENST00000272273.5_Missense_Mutation_p.Y356D|LTBP1_ENST00000404525.1_Missense_Mutation_p.Y1079D|LTBP1_ENST00000402934.1_Missense_Mutation_p.Y1077D|LTBP1_ENST00000390003.4_Missense_Mutation_p.Y1133D			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1458	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AGGGACGTACTATGATCCTGT	0.393																																					p.Y1458D		Atlas-SNP	.											.	LTBP1	317	.	0			c.T4372G						.						173	162	165					2																	33588558		2203	4300	6503	SO:0001583	missense	4052	exon29			ACGTACTATGATC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.4372T>G	chr2.hg19:g.33588558T>G	ENSP00000386043:p.Tyr1458Asp	94.0	0.0		71.0	36.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	T	20.8	4.044928	0.75732	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273	D;D;D;D;D;D;D;D	0.95622	-3.76;-3.76;-3.76;-3.76;-3.76;-3.76;-3.76;-2.9	5.34	5.34	0.76211	Epidermal growth factor-like (1);	.	.	.	.	D	0.98036	0.9353	M	0.90252	3.1	0.58432	D	0.999998	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.995;0.999;0.998;1.0;0.999;0.999;1.0	D	0.99150	1.0858	9	0.87932	D	0	.	15.3253	0.74157	0.0:0.0:0.0:1.0	.	356;1458;1090;1079;1132;1133;1459	E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.;LTBP1_HUMAN;.;.;.;.;.	D	1458;1459;1133;1090;1077;1079;1132;356	ENSP00000386043:Y1458D;ENSP00000346467:Y1459D;ENSP00000374653:Y1133D;ENSP00000393057:Y1090D;ENSP00000384373:Y1077D;ENSP00000385359:Y1079D;ENSP00000384091:Y1132D;ENSP00000272273:Y356D	ENSP00000272273:Y356D	Y	+	1	0	LTBP1	33442062	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	7.846000	0.86887	2.025000	0.59659	0.460000	0.39030	TAT	.	.		0.393	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		G	33588558	T	G	33588558	3	3	198	1	0	0	0	0	1	0	0	0	9082	1522	53	5	4541	5	LTBP1	2	33588558	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	17506073	33588558	209610815	16	29137										
HK2	3099	hgsc.bcm.edu	37	chr2	75107408	75107408	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gcagttttgccaagcgtctaCataagaccgtgcggcggctg	13	11	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr2:75107408C>G	ENST00000290573.2	+	10	1882	c.1282C>G	c.(1282-1284)Cat>Gat	p.H428D	HK2_ENST00000409174.1_Missense_Mutation_p.H400D	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	428	Hexokinase type-2 1.|Regulatory.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						CAAGCGTCTACATAAGACCGT	0.587																																					p.H428D		Atlas-SNP	.											.	HK2	85	.	0			c.C1282G						.						182	204	196					2																	75107408		2202	4299	6501	SO:0001583	missense	3099	exon10			CGTCTACATAAGA		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.1282C>G	chr2.hg19:g.75107408C>G	ENSP00000290573:p.His428Asp	118.0	0.0		96.0	42.0	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	hg19	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.363212	0.24684	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.96365	-3.99;-3.99	4.89	4.89	0.63831	Hexokinase, C-terminal (1);	0.226646	0.53938	D	0.000060	D	0.96460	0.8845	L	0.58428	1.81	0.58432	D	0.999999	P	0.36733	0.567	P	0.50231	0.635	D	0.94628	0.7819	10	0.22706	T	0.39	-16.621	15.9407	0.79750	0.0:1.0:0.0:0.0	.	428	P52789	HXK2_HUMAN	D	428;428;400	ENSP00000290573:H428D;ENSP00000387140:H400D	ENSP00000290573:H428D	H	+	1	0	HK2	74960916	1.000000	0.71417	1.000000	0.80357	0.408000	0.30992	4.582000	0.60957	2.704000	0.92352	0.563000	0.77884	CAT	.	.		0.587	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189		G	75107408	C	G	75107408	3	3	198	1	0	0	0	0	1	0	0	0	7200	478	17	4	1320	4	HK2	2	75107408	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	41518850	75107408	168091965	17	29138										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185803460	185803471	+	In_Frame_Del	DEL	GCAGCTGCAGCC	GCAGCTGCAGCC	-													0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	acgctgcagctgctgcagctGcagctgcagccgcagctgca					rs151203071|rs111695281|rs143955610|rs149962176	byFrequency	TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	GCAGCTGCAGCC	GCAGCTGCAGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr2:185803460_185803471delGCAGCTGCAGCC	ENST00000302277.6	+	4	3931_3942	c.3337_3348delGCAGCTGCAGCC	c.(3337-3348)gcagctgcagccdel	p.AAAA1113del		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	1113							metal ion binding (GO:0046872)	p.A1114G(1)		NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						tgctgcagctgcagctgcagccgcagctgcag	0.524																																					p.1112_1116del		Atlas-INDEL	.											.	ZNF804A	322	.	1	Substitution - Missense(1)	lung(1)	c.3336_3347del						.																																			SO:0001651	inframe_deletion	91752	exon4			.	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.3337_3348delGCAGCTGCAGCC	chr2.hg19:g.185803460_185803471delGCAGCTGCAGCC	ENSP00000303252:p.Ala1113_Ala1116del	86.0	0.0		94.0	30.0	NM_194250	A7E253|Q6ZN26	In_Frame_Del	DEL	ENST00000302277.6	hg19	CCDS2291.1																																																																																			.	.		0.524	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		-	185803471	GCAGCTGCAGCC	-	185803460	7	5	198	1	0	1	0	1	0	0	0	0	18185	1319	46	0	3351	0	ZNF804A	2	185803460	In_Frame_Del	DEL	GCAGCTGCAGCC	TCGA-DD-AADP-01A-11D-A38X-10	110696052	185803460	57395913	18	29139										
RBMS3	27303	hgsc.bcm.edu	37	chr3	29804446	29804446	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gtggtaattcaacattttaaTggaaaatatctgaaaacacc	6	6	2	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr3:29804446T>C	ENST00000383767.2	+	6	939	c.603T>C	c.(601-603)aaT>aaC	p.N201N	RBMS3_ENST00000396583.3_Silent_p.N201N|RBMS3_ENST00000273139.9_Silent_p.N201N|RBMS3_ENST00000445033.1_Silent_p.N201N|RBMS3_ENST00000456853.1_Silent_p.N201N|RBMS3_ENST00000434693.2_Silent_p.N200N|RBMS3_ENST00000452462.1_Silent_p.N201N|RBMS3_ENST00000383766.2_Silent_p.N200N			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	201	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				AACATTTTAATGGAAAATATC	0.343																																					p.N201N		Atlas-SNP	.											.	RBMS3	62	.	0			c.T603C						.						65	65	65					3																	29804446		2203	4300	6503	SO:0001819	synonymous_variant	27303	exon6			TTTTAATGGAAAA	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"RNA binding motif (RRM) containing"	13427	protein-coding gene	gene with protein product	"RNA-binding protein"	605786	"RNA binding motif, single stranded interacting protein"			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.603T>C	chr3.hg19:g.29804446T>C		378.0	0.0		303.0	102.0	NM_001003793	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Silent	SNP	ENST00000383767.2	hg19	CCDS33724.1																																																																																			.	.		0.343	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792		C	29804446	T	C	29804446	2	2	198	1	0	0	0	0	0	0	0	1	13165	1461	51	2		2	RBMS3	3	29804446	Silent	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10		29804446	168217984	19	29140										
STT3B	201595	hgsc.bcm.edu	37	chr3	31658480	31658480	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	atctgagagaccgattaacaAaacaagagttccagaccctt	7	10	1	4			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr3:31658480A>C	ENST00000295770.2	+	7	1245	c.1036A>C	c.(1036-1038)Aaa>Caa	p.K346Q	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	346					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						CCGATTAACAAAACAAGAGTT	0.388																																					p.K346Q		Atlas-SNP	.											.	STT3B	52	.	0			c.A1036C						.						208	211	210					3																	31658480		2203	4300	6503	SO:0001583	missense	201595	exon7			TTAACAAAACAAG	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"source of immunodominant MHC associated peptides", "dolichyl-diphosphooligosaccharide protein glycotransferase"	608605	"STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.1036A>C	chr3.hg19:g.31658480A>C	ENSP00000295770:p.Lys346Gln	119.0	0.0		97.0	33.0	NM_178862	Q96JZ4|Q96KY7	Missense_Mutation	SNP	ENST00000295770.2	hg19	CCDS2650.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.483048	0.44147	.	.	ENSG00000163527	ENST00000295770	.	.	.	5.44	5.44	0.79542	.	0.050004	0.85682	D	0.000000	T	0.60157	0.2247	M	0.62088	1.915	0.40987	D	0.984829	B	0.19935	0.04	B	0.21151	0.033	T	0.57642	-0.7776	9	0.25751	T	0.34	-14.3221	15.5023	0.75709	1.0:0.0:0.0:0.0	.	346	Q8TCJ2	STT3B_HUMAN	Q	346	.	ENSP00000295770:K346Q	K	+	1	0	STT3B	31633484	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	5.846000	0.69444	2.065000	0.61736	0.459000	0.35465	AAA	.	.		0.388	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862		C	31658480	A	C	31658480	3	2	198	1	0	0	0	0	1	0	0	0	15349	15	1	5	1062	5	STT3B	3	31658480	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	1854034	31658480	166363950	20	29141										
ATRIP	84126	hgsc.bcm.edu	37	chr3	48501904	48501904	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tgcacttagcattcttcagcAcctggtgtgccacagcggag	11	12	2	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr3:48501904A>G	ENST00000320211.3	+	8	1564	c.1451A>G	c.(1450-1452)cAc>cGc	p.H484R	ATRIP_ENST00000346691.4_Missense_Mutation_p.H484R|ATRIP_ENST00000357105.6_Missense_Mutation_p.H357R|ATRIP_ENST00000412052.1_Missense_Mutation_p.H391R	NM_130384.2	NP_569055.1	Q8WXE1	ATRIP_HUMAN	ATR interacting protein	484					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)	22				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ATTCTTCAGCACCTGGTGTGC	0.562								Other conserved DNA damage response genes																													p.H484R		Atlas-SNP	.											.	ATRIP	41	.	0			c.A1451G						.						107	104	105					3																	48501904		2203	4300	6503	SO:0001583	missense	84126	exon8			TTCAGCACCTGGT	AF451323	CCDS2767.1, CCDS2768.1, CCDS59449.1, CCDS59450.1	3p24.3-p22.1	2007-06-20			ENSG00000164053	ENSG00000164053			33499	protein-coding gene	gene with protein product		606605				11721054	Standard	NM_130384		Approved	FLJ12343, MGC20625, MGC21482, MGC26740	uc003ctf.2	Q8WXE1	OTTHUMG00000133532	ENST00000320211.3:c.1451A>G	chr3.hg19:g.48501904A>G	ENSP00000323099:p.His484Arg	98.0	0.0		71.0	25.0	NM_130384	A8K6A3|A8K714|B2RCE7|B4DU92|B5MEB7|Q69YK9|Q8NHQ2|Q8WUG7|Q96CL3|Q9HA30	Missense_Mutation	SNP	ENST00000320211.3	hg19	CCDS2768.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.173050	0.78452	.	.	ENSG00000164053	ENST00000320211;ENST00000346691;ENST00000357105;ENST00000412052	T;T;T;T	0.50001	1.33;1.31;0.76;1.33	5.95	5.95	0.96441	.	0.221434	0.46145	D	0.000303	T	0.55401	0.1918	M	0.63843	1.955	0.43300	D	0.995293	D;D	0.53462	0.96;0.96	P;P	0.50537	0.643;0.643	T	0.55885	-0.8070	9	.	.	.	-10.6132	14.3757	0.66874	1.0:0.0:0.0:0.0	.	484;484	Q8WXE1-2;Q8WXE1	.;ATRIP_HUMAN	R	484;484;357;391	ENSP00000323099:H484R;ENSP00000302338:H484R;ENSP00000349620:H357R;ENSP00000400930:H391R	.	H	+	2	0	ATRIP	48476908	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.865000	0.75500	2.279000	0.76181	0.533000	0.62120	CAC	.	.		0.562	ATRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257507.2	NM_130384		G	48501904	A	G	48501904	3	3	198	1	0	0	0	0	1	0	0	0	1205	159	6	2	1481	2	ATRIP	3	48501904	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	16843424	48501904	149520526	21	29142										
QRICH1	54870	hgsc.bcm.edu	37	chr3	49070130	49070130	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tttatccttgggattagaggGgttcttctttgtctgtcgca	11	7	3	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr3:49070130G>A	ENST00000395443.2	-	8	2444	c.1972C>T	c.(1972-1974)Ccc>Tcc	p.P658S	QRICH1_ENST00000424300.1_Missense_Mutation_p.P658S|QRICH1_ENST00000357496.2_Missense_Mutation_p.P658S|RP13-131K19.6_ENST00000607245.1_RNA|QRICH1_ENST00000479449.1_5'Flank	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	658						nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		GGATTAGAGGGGTTCTTCTTT	0.498																																					p.P658S		Atlas-SNP	.											.	QRICH1	48	.	0			c.C1972T						.						127	120	122					3																	49070130		2203	4300	6503	SO:0001583	missense	54870	exon8			TAGAGGGGTTCTT		CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.1972C>T	chr3.hg19:g.49070130G>A	ENSP00000378830:p.Pro658Ser	98.0	0.0		80.0	31.0	NM_198880	Q4G0F7|Q7L621|Q8TEA5	Missense_Mutation	SNP	ENST00000395443.2	hg19	CCDS2787.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434305	0.62955	.	.	ENSG00000198218	ENST00000395443;ENST00000357496;ENST00000424300	.	.	.	5.5	4.61	0.57282	.	0.046599	0.85682	D	0.000000	T	0.50240	0.1604	L	0.35723	1.085	0.80722	D	1	B	0.33883	0.43	B	0.35859	0.212	T	0.48514	-0.9029	9	0.38643	T	0.18	-3.6025	15.4935	0.75632	0.0:0.0:0.8603:0.1396	.	658	Q2TAL8	QRIC1_HUMAN	S	658	.	ENSP00000350094:P658S	P	-	1	0	QRICH1	49045134	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.476000	0.97823	1.296000	0.44742	0.650000	0.86243	CCC	.	.		0.498	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		A	49070130	G	A	49070130	3	1	198	1	0	0	0	0	1	0	0	0	12894	1232	43	3	370	3	QRICH1	3	49070130	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	568226	49070130	148952300	22	29143										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52595942	52595942	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	catgttgattttccgtttggAgccttccttctttgcactgc	8	11	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr3:52595942A>C	ENST00000296302.7	-	25	4130	c.4129T>G	c.(4129-4131)Tcc>Gcc	p.S1377A	PBRM1_ENST00000356770.4_Missense_Mutation_p.S1345A|PBRM1_ENST00000337303.4_Missense_Mutation_p.S1377A|PBRM1_ENST00000409114.3_Missense_Mutation_p.S1392A|PBRM1_ENST00000394830.3_Missense_Mutation_p.S1325A|PBRM1_ENST00000409057.1_Missense_Mutation_p.S1377A|PBRM1_ENST00000409767.1_Missense_Mutation_p.S1392A|PBRM1_ENST00000410007.1_Missense_Mutation_p.S1352A|RNU6ATAC16P_ENST00000408591.1_RNA|SMIM4_ENST00000476842.1_Intron			Q86U86	PB1_HUMAN	polybromo 1	1377					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTCCGTTTGGAGCCTTCCTTC	0.468			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.S1325A		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.T3973G						.						167	167	167					3																	52595942		2203	4300	6503	SO:0001583	missense	55193	exon26			GTTTGGAGCCTTC	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4129T>G	chr3.hg19:g.52595942A>C	ENSP00000296302:p.Ser1377Ala	168.0	0.0		139.0	54.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	A	10.21	1.288211	0.23478	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	D;D;D;D;D;D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29;-3.29;-3.29;-3.29;-3.29;-3.29	5.89	4.73	0.59995	High mobility group, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.81884	0.4917	N	0.03608	-0.345	0.39338	D	0.96553	B;B;B;B;B;B;B;B	0.14438	0.006;0.007;0.006;0.0;0.001;0.01;0.001;0.0	B;B;B;B;B;B;B;B	0.10450	0.005;0.003;0.005;0.001;0.003;0.002;0.005;0.0	T	0.74592	-0.3614	10	0.27785	T	0.31	-9.3819	7.8835	0.29635	0.7934:0.1375:0.069:0.0	.	1352;1325;1377;1392;1392;1377;1345;1377	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;PB1_HUMAN;.;.	A	1345;1325;1377;1377;1377;1352;1392;1392;1376	ENSP00000349213:S1345A;ENSP00000378307:S1325A;ENSP00000296302:S1377A;ENSP00000338302:S1377A;ENSP00000386593:S1377A;ENSP00000386529:S1352A;ENSP00000386643:S1392A;ENSP00000386601:S1392A;ENSP00000387775:S1376A	ENSP00000296302:S1377A	S	-	1	0	PBRM1	52570982	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.690000	0.54713	1.059000	0.40554	0.455000	0.32223	TCC	.	.		0.468	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		C	52595942	A	C	52595942	3	2	198	1	0	0	0	0	1	0	0	0	11500	304	11	5	795	5	PBRM1	3	52595942	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	3525812	52595942	145426488	23	29144										
EIF2A	83939	hgsc.bcm.edu	37	chr3	150290287	150290287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	cttatagacccccagctttaAgaaataaaccaatcaccaat	3	12	1	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr3:150290287A>G	ENST00000460851.1	+	10	1463	c.1354A>G	c.(1354-1356)Aga>Gga	p.R452G	EIF2A_ENST00000482471.1_3'UTR|SERP1_ENST00000490945.1_Intron|EIF2A_ENST00000383043.3_Missense_Mutation_p.R238G|EIF2A_ENST00000406576.3_Missense_Mutation_p.R391G|EIF2A_ENST00000487799.1_Missense_Mutation_p.R427G|SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000273435.5_Missense_Mutation_p.R447G			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	452					positive regulation of signal transduction (GO:0009967)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|ribosome assembly (GO:0042255)|SREBP signaling pathway (GO:0032933)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular space (GO:0005615)	ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)|tRNA binding (GO:0000049)			cervix(1)|endometrium(2)|kidney(1)|lung(3)	7		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			CCCAGCTTTAAGAAATAAACC	0.363																																					p.R452G		Atlas-SNP	.											.	EIF2A	59	.	0			c.A1354G						.						72	71	72					3																	150290287		1824	4078	5902	SO:0001583	missense	83939	exon10			GCTTTAAGAAATA	AF212241	CCDS46935.1	3q25.1	2011-01-19	2006-01-24		ENSG00000144895	ENSG00000144895			3254	protein-coding gene	gene with protein product		609234				12133843, 1620067	Standard	NM_032025		Approved	EIF-2A	uc003eya.3	Q9BY44	OTTHUMG00000159775	ENST00000460851.1:c.1354A>G	chr3.hg19:g.150290287A>G	ENSP00000417229:p.Arg452Gly	118.0	0.0		87.0	34.0	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Missense_Mutation	SNP	ENST00000460851.1	hg19	CCDS46935.1	.	.	.	.	.	.	.	.	.	.	A	17.60	3.429572	0.62844	.	.	ENSG00000144895	ENST00000487799;ENST00000460851;ENST00000406576;ENST00000273435;ENST00000383043	T;T;T;T;T	0.54675	1.08;1.06;1.06;1.01;0.56	5.87	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.75766	0.3894	M	0.88105	2.93	0.58432	D	0.999995	D;D;D	0.89917	1.0;0.994;0.969	D;D;P	0.85130	0.997;0.918;0.814	T	0.80274	-0.1451	10	0.87932	D	0	-41.111	13.0098	0.58725	0.7476:0.2524:0.0:0.0	.	391;427;452	B4DF96;B4DQ14;Q9BY44	.;.;EIF2A_HUMAN	G	427;452;391;447;238	ENSP00000420537:R427G;ENSP00000417229:R452G;ENSP00000385292:R391G;ENSP00000273435:R447G;ENSP00000372513:R238G	ENSP00000273435:R447G	R	+	1	2	EIF2A	151772977	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.932000	0.48940	1.104000	0.41587	0.533000	0.62120	AGA	.	.		0.363	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025		G	150290287	A	G	150290287	3	3	198	1	0	0	0	0	1	0	0	0	4997	64	3	2	1392	2	EIF2A	3	150290287	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	97694345	150290287	47732143	24	29145										
PDE6B	5158	hgsc.bcm.edu	37	chr4	651192	651192	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gaacaccgacacctacgacaAgatgaacaagctggagaacc	9	12	0	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr4:651192A>T	ENST00000496514.1	+	10	1331	c.1310A>T	c.(1309-1311)aAg>aTg	p.K437M	RP11-1191J2.2_ENST00000489312.1_RNA|PDE6B_ENST00000255622.6_Missense_Mutation_p.K437M|RP11-1191J2.2_ENST00000468356.1_RNA|PDE6B_ENST00000429163.2_Missense_Mutation_p.K158M			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	437					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	ACCTACGACAAGATGAACAAG	0.612																																					p.K437M	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.A1310T						.						196	117	144					4																	651192		2203	4300	6503	SO:0001583	missense	5158	exon10			ACGACAAGATGAA	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"Phosphodiesterases"	8786	protein-coding gene	gene with protein product	"congenital stationary night blindness 3, autosomal dominant"	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.1310A>T	chr4.hg19:g.651192A>T	ENSP00000420295:p.Lys437Met	357.0	1.0		303.0	102.0	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	hg19	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.420362	0.83559	.	.	ENSG00000133256	ENST00000255622;ENST00000496514;ENST00000429163	T;T;T	0.71222	-0.55;-0.55;-0.55	4.85	4.85	0.62838	GAF (1);	0.241479	0.42420	D	0.000705	D	0.82962	0.5151	M	0.84433	2.695	0.80722	D	1	D;D	0.63880	0.988;0.993	P;P	0.61658	0.784;0.892	D	0.85936	0.1455	10	0.87932	D	0	.	12.3767	0.55283	1.0:0.0:0.0:0.0	.	437;437	P35913;P35913-2	PDE6B_HUMAN;.	M	437;437;158	ENSP00000255622:K437M;ENSP00000420295:K437M;ENSP00000406334:K158M	ENSP00000255622:K437M	K	+	2	0	PDE6B	641192	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	4.014000	0.57145	1.804000	0.52760	0.367000	0.22151	AAG	.	.		0.612	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		T	651192	A	T	651192	3	4	198	1	0	0	0	0	1	0	0	0	11655	72	3	4	1348	4	PDE6B	4	651192	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10		651192	190503084	25	29146										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46060543	46060543	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	cagttgagttccgtaaccctAcaaatgcaaactgatataat	6	9	0	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr4:46060543A>G	ENST00000295452.4	-	6	889	c.722T>C	c.(721-723)gTa>gCa	p.V241A		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	241					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CCGTAACCCTACAAATGCAAA	0.338																																					p.V241A		Atlas-SNP	.											.	GABRG1	172	.	0			c.T722C						.						93	89	90					4																	46060543		2203	4300	6503	SO:0001583	missense	2565	exon6			AACCCTACAAATG	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.722T>C	chr4.hg19:g.46060543A>G	ENSP00000295452:p.Val241Ala	223.0	0.0		145.0	61.0	NM_173536	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.694185	0.48202	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	T	0.78481	-1.18	5.83	4.65	0.58169	Neurotransmitter-gated ion-channel ligand-binding (3);	0.188463	0.45867	N	0.000337	T	0.74861	0.3772	L	0.39633	1.23	0.44890	D	0.997902	B	0.33549	0.417	B	0.43194	0.411	T	0.73424	-0.3987	10	0.51188	T	0.08	.	10.8942	0.47012	0.9269:0.0:0.0731:0.0	.	241	Q8N1C3	GBRG1_HUMAN	A	241	ENSP00000295452:V241A	ENSP00000295452:V241A	V	-	2	0	GABRG1	45755300	1.000000	0.71417	1.000000	0.80357	0.501000	0.33797	6.303000	0.72794	1.051000	0.40369	0.529000	0.55759	GTA	.	.		0.338	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		G	46060543	A	G	46060543	3	3	198	1	0	0	0	0	1	0	0	0	6179	391	14	2	691	2	GABRG1	4	46060543	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	45409351	46060543	145093733	26	29147										
UBA6	55236	hgsc.bcm.edu	37	chr4	68528881	68528881	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	catttggcttgcgactgtatTtctcctgaaactggtccaag	9	10	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr4:68528881T>G	ENST00000322244.5	-	12	1072	c.1013A>C	c.(1012-1014)aAa>aCa	p.K338T	UBA6_ENST00000420827.2_Missense_Mutation_p.K338T	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	338					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						GCGACTGTATTTCTCCTGAAA	0.323																																					p.K338T		Atlas-SNP	.											.	UBA6	98	.	0			c.A1013C						.						144	146	146					4																	68528881		2203	4300	6503	SO:0001583	missense	55236	exon12			CTGTATTTCTCCT	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"Ubiquitin-like modifier activating enzymes"	25581	protein-coding gene	gene with protein product	"UBA6, ubiquitin-activating enzyme E1"	611361	"ubiquitin-activating enzyme E1-like 2"	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.1013A>C	chr4.hg19:g.68528881T>G	ENSP00000313454:p.Lys338Thr	310.0	0.0		163.0	95.0	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Missense_Mutation	SNP	ENST00000322244.5	hg19	CCDS3516.1	.	.	.	.	.	.	.	.	.	.	T	11.58	1.680361	0.29872	.	.	ENSG00000033178	ENST00000322244;ENST00000420827	T;T	0.29917	1.55;1.55	6.03	2.3	0.28687	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.538421	0.23220	N	0.050565	T	0.20495	0.0493	L	0.38838	1.175	0.27260	N	0.958652	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.14504	-1.0470	10	0.31617	T	0.26	-7.1868	6.8878	0.24212	0.0:0.1333:0.1277:0.7391	.	338;338	A0AVT1-3;A0AVT1	.;UBA6_HUMAN	T	338	ENSP00000313454:K338T;ENSP00000399234:K338T	ENSP00000313454:K338T	K	-	2	0	UBA6	68211476	1.000000	0.71417	0.983000	0.44433	0.924000	0.55760	1.505000	0.35736	0.508000	0.28173	0.455000	0.32223	AAA	.	.		0.323	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227		G	68528881	T	G	68528881	3	3	198	1	0	0	0	0	1	0	0	0	16847	1841	64	5	2233	5	UBA6	4	68528881	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	22468338	68528881	122625395	27	29148										
MGST2	4258	hgsc.bcm.edu	37	chr4	140616397	140616397	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tattcataattacattgtggAtggctgggtggtatttcaac	10	5	2	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr4:140616397A>G	ENST00000265498.1	+	3	457	c.205A>G	c.(205-207)Atg>Gtg	p.M69V	MGST2_ENST00000515137.1_3'UTR|MGST2_ENST00000506797.1_Intron	NM_001204366.1|NM_002413.4	NP_001191295.1|NP_002404.1	Q99735	MGST2_HUMAN	microsomal glutathione S-transferase 2	69					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|leukotriene biosynthetic process (GO:0019370)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)|glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|leukotriene-C4 synthase activity (GO:0004464)			lung(1)|ovary(1)	2	all_hematologic(180;0.162)				Busulfan(DB01008)|Glutathione(DB00143)	TACATTGTGGATGGCTGGGTG	0.333																																					p.M69V		Atlas-SNP	.											.	MGST2	7	.	0			c.A205G						.						127	125	126					4																	140616397		2203	4300	6503	SO:0001583	missense	4258	exon3			TTGTGGATGGCTG	U77604	CCDS3749.1, CCDS56339.1	4q28.3	2012-06-21			ENSG00000085871	ENSG00000085871	2.5.1.18	"Glutathione S-transferases / Microsomal"	7063	protein-coding gene	gene with protein product		601733				8703034	Standard	NM_002413		Approved	MGST-II	uc003ihy.3	Q99735	OTTHUMG00000133382	ENST00000265498.1:c.205A>G	chr4.hg19:g.140616397A>G	ENSP00000265498:p.Met69Val	98.0	0.0		51.0	32.0	NM_001204366	D6RBB5|Q7Z5B8	Missense_Mutation	SNP	ENST00000265498.1	hg19	CCDS3749.1	.	.	.	.	.	.	.	.	.	.	A	1.539	-0.542373	0.04053	.	.	ENSG00000085871	ENST00000265498	T	0.54279	0.58	5.73	4.55	0.56014	Membrane associated eicosanoid/glutathione metabolism-like domain (1);	0.203950	0.44097	D	0.000500	T	0.28101	0.0693	N	0.12887	0.27	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	T	0.13308	-1.0514	10	0.02654	T	1	-18.7034	9.2087	0.37304	0.9174:0.0:0.0826:0.0	.	69	Q99735	MGST2_HUMAN	V	69	ENSP00000265498:M69V	ENSP00000265498:M69V	M	+	1	0	MGST2	140835847	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.327000	0.33746	1.008000	0.39264	0.460000	0.39030	ATG	.	.		0.333	MGST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257232.2	NM_002413		G	140616397	A	G	140616397	3	3	198	1	0	0	0	0	1	0	0	0	9570	333	12	2	215	2	MGST2	4	140616397	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	72087516	140616397	50537879	28	29149										
FYB	2533	hgsc.bcm.edu	37	chr5	39126206	39126206	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	caaaatcccccaggaccacgTattactcttctcttgaacct	4	15	2	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr5:39126206T>C	ENST00000351578.6	-	11	2098				FYB_ENST00000505428.1_Missense_Mutation_p.T647A|FYB_ENST00000515010.1_Intron|FYB_ENST00000512982.1_Missense_Mutation_p.T647A|FYB_ENST00000540520.1_Missense_Mutation_p.T657A	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein						immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			CAGGACCACGTATTACTCTTC	0.413																																					p.T657A		Atlas-SNP	.											FYB_ENST00000540520,NS,carcinoma,0,2	FYB	354	.	0			c.A1969G						.						113	102	106					5																	39126206		1914	4139	6053	SO:0001627	intron_variant	2533	exon12			ACCACGTATTACT	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1907+1636A>G	chr5.hg19:g.39126206T>C		104.0	0.0		88.0	21.0	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	hg19	CCDS47200.1	.	.	.	.	.	.	.	.	.	.	T	4.305	0.055841	0.08291	.	.	ENSG00000082074	ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542	T;T;T	0.21734	1.99;1.99;2.0	6.07	-2.6	0.06190	.	1.299270	0.04734	N	0.421711	T	0.11410	0.0278	N	0.16478	0.41	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29336	-1.0015	10	0.32370	T	0.25	-0.6544	4.1481	0.10225	0.1747:0.1536:0.0689:0.6027	.	657	B4DLN2	.	A	647;647;657;647	ENSP00000425845:T647A;ENSP00000427114:T647A;ENSP00000442840:T657A	ENSP00000427114:T647A	T	-	1	0	FYB	39161963	0.985000	0.35326	0.025000	0.17156	0.989000	0.77384	0.248000	0.18198	-0.349000	0.08274	0.477000	0.44152	ACG	.	.		0.413	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		C	39126206	T	C	39126206	1	2	198	0	1	0	0	0	0	0	0	0	6132	1638	57	2		2	FYB	5	39126206	Intron	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10		39126206	141789054	29	29150										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141038047	141038047	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gcagtcagggttggggacacCtggggtcagggcaagagcag	19	8	2	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr5:141038047C>T	ENST00000239440.4	-	25	3477		c.e25-1		ARAP3_ENST00000512390.1_Splice_Site|ARAP3_ENST00000513878.1_Splice_Site|ARAP3_ENST00000508305.1_Splice_Site	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3						cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						TTGGGGACACCTGGGGTCAGG	0.567																																					.		Atlas-SNP	.											.	ARAP3	139	.	0			c.3412-1G>A						.						103	85	91					5																	141038047		2203	4300	6503	SO:0001630	splice_region_variant	64411	exon26			GGACACCTGGGGT	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3412-1G>A	chr5.hg19:g.141038047C>T		130.0	0.0		109.0	30.0	NM_022481	B4DIT1|D3DQE3	Splice_Site	SNP	ENST00000239440.4	hg19	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.977829	0.92982	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.201	0.89838	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ARAP3	141018231	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.970000	0.76099	2.837000	0.97791	0.655000	0.94253	.	.	.		0.567	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	Intron	T	141038047	C	T	141038047	5	4	198	1	0	0	0	0	0	0	1	0	840	695	24	3	1259	3	ARAP3	5	141038047	Splice_Site	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	101911841	141038047	39877213	30	29151										
FAT2	2196	hgsc.bcm.edu	37	chr5	150887158	150887158	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gtccttctgaacaacccctcGcctccatttcacacctgcgg	6	18	2	1	rs538316910		TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr5:150887158G>A	ENST00000261800.5	-	22	12086	c.12074C>T	c.(12073-12075)gCg>gTg	p.A4025V	CTC-251D13.1_ENST00000606930.1_RNA	NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	4025					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACAACCCCTCGCCTCCATTTC	0.552													G|||	1	0.000199681	0	0	5008	,	,		17739	0		0	False		,,,				2504	0.001				p.A4025V		Atlas-SNP	.											.	FAT2	465	.	0			c.C12074T						.						31	28	29					5																	150887158		2203	4300	6503	SO:0001583	missense	2196	exon22			CCCCTCGCCTCCA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.12074C>T	chr5.hg19:g.150887158G>A	ENSP00000261800:p.Ala4025Val	33.0	0.0		36.0	10.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	9.971	1.225479	0.22457	.	.	ENSG00000086570	ENST00000261800	D	0.91237	-2.81	5.46	4.47	0.54385	Concanavalin A-like lectin/glucanase, subgroup (1);	0.219986	0.31531	N	0.007489	T	0.72661	0.3488	N	0.03209	-0.39	0.09310	N	1	P;B	0.46020	0.871;0.11	B;B	0.38428	0.273;0.026	T	0.65450	-0.6165	10	0.17369	T	0.5	.	6.1789	0.20459	0.1568:0.0:0.8432:0.0	.	4025;1130	Q9NYQ8;E9PDJ8	FAT2_HUMAN;.	V	4025	ENSP00000261800:A4025V	ENSP00000261800:A4025V	A	-	2	0	FAT2	150867351	0.008000	0.16893	0.060000	0.19600	0.223000	0.24884	1.012000	0.29924	2.548000	0.85928	0.655000	0.94253	GCG	.	.		0.552	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150887158	G	A	150887158	3	1	198	1	0	0	0	0	1	0	0	0	5698	1087	38	1	983	1	FAT2	5	150887158	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	9849111	150887158	30028102	31	29152										
MAPK9	5601	hgsc.bcm.edu	37	chr5	179707453	179707453	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tacttaccaaacaatcccttGggccccagagccaattggtt	7	13	0	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr5:179707453G>C	ENST00000452135.2	-	2	407	c.109C>G	c.(109-111)Caa>Gaa	p.Q37E	MAPK9_ENST00000347470.4_Missense_Mutation_p.Q37E|MAPK9_ENST00000539014.1_Missense_Mutation_p.Q37E|MAPK9_ENST00000343111.6_Missense_Mutation_p.Q37E|MAPK9_ENST00000455781.1_Missense_Mutation_p.Q37E|MAPK9_ENST00000393360.3_Missense_Mutation_p.Q37E|MAPK9_ENST00000397072.3_Missense_Mutation_p.Q37E|MAPK9_ENST00000425491.2_Missense_Mutation_p.Q37E			P45984	MK09_HUMAN	mitogen-activated protein kinase 9	37	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to growth factor stimulus (GO:0071363)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV (GO:0034644)|central nervous system development (GO:0007417)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neuron projection development (GO:0031175)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell morphogenesis involved in differentiation (GO:0010770)|positive regulation of chemokine production (GO:0032722)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|protein targeting to mitochondrion (GO:0006626)|regulation of JNK cascade (GO:0046328)|regulation of protein ubiquitination (GO:0031396)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to amine (GO:0014075)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|JUN kinase activity (GO:0004705)|transcription factor binding (GO:0008134)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACAATCCCTTGGGCCCCAGAG	0.393																																					p.Q37E		Atlas-SNP	.											.	MAPK9	173	.	0			c.C109G						.						140	129	133					5																	179707453		2203	4300	6503	SO:0001583	missense	5601	exon2			TCCCTTGGGCCCC	U09759	CCDS4453.1, CCDS4454.1, CCDS43409.1, CCDS43410.1, CCDS47356.1	5q35	2011-06-09			ENSG00000050748	ENSG00000050748	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6886	protein-coding gene	gene with protein product	"Jun kinase"	602896		PRKM9		8001819	Standard	NM_002752		Approved	JNK2, p54a, SAPK	uc003mls.4	P45984	OTTHUMG00000130934	ENST00000452135.2:c.109C>G	chr5.hg19:g.179707453G>C	ENSP00000394560:p.Gln37Glu	154.0	0.0		115.0	33.0	NM_002752	A8K0S3|B5BU66|B5M0B4|D3DWQ8|D3DWQ9|Q15708|Q15710|Q15711|Q8N5C5	Missense_Mutation	SNP	ENST00000452135.2	hg19	CCDS4453.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787963	0.70337	.	.	ENSG00000050748	ENST00000452135;ENST00000393360;ENST00000455781;ENST00000343111;ENST00000347470;ENST00000397072;ENST00000425491;ENST00000539014;ENST00000523583	D;D;D;D;D;T;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-0.76;-1.63;-1.63;-1.63	5.33	4.47	0.54385	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.82273	0.5001	N	0.21508	0.67	0.80722	D	1	D;D;D;D;D	0.67145	0.981;0.981;0.981;0.996;0.99	P;P;P;P;P	0.61003	0.682;0.745;0.804;0.875;0.882	T	0.80765	-0.1236	9	.	.	.	-23.7831	13.6346	0.62215	0.0739:0.0:0.9261:0.0	.	37;37;37;37;37	P45984-5;P45984-4;P45984-3;P45984-2;P45984	.;.;.;.;MK09_HUMAN	E	37	ENSP00000394560:Q37E;ENSP00000377028:Q37E;ENSP00000389338:Q37E;ENSP00000345524:Q37E;ENSP00000321410:Q37E;ENSP00000380262:Q37E;ENSP00000397422:Q37E;ENSP00000443149:Q37E;ENSP00000430608:Q37E	.	Q	-	1	0	MAPK9	179640059	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.731000	0.98807	1.251000	0.43983	0.655000	0.94253	CAA	.	.		0.393	MAPK9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253530.3			C	179707453	G	C	179707453	3	2	198	1	0	0	0	0	1	0	0	0	9296	1357	47	4	1331	4	MAPK9	5	179707453	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	28820295	179707453	1207807	32	29153										
MYLK4	340156	hgsc.bcm.edu	37	chr6	2685717	2685717	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ccacctcccacaggctgtacCttgtccttcatgcctctggt	7	17	2	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr6:2685717C>T	ENST00000274643.7	-	5	777	c.435G>A	c.(433-435)aaG>aaA	p.K145K	MYLK4_ENST00000268446.5_Splice_Site_p.K145K	NM_001012418.3	NP_001012418.2	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4	145	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23	Ovarian(93;0.0412)	all_hematologic(90;0.0897)				CAGGCTGTACCTTGTCCTTCA	0.567																																					p.K145K		Atlas-SNP	.											.	MYLK4	74	.	0			c.G435A						.						154	150	152					6																	2685717		2203	4300	6503	SO:0001630	splice_region_variant	340156	exon5			CTGTACCTTGTCC		CCDS34330.1	6p25.2	2008-01-23			ENSG00000145949	ENSG00000145949			27972	protein-coding gene	gene with protein product	"caMLCK like"						Standard	NM_001012418		Approved	SgK085	uc003mty.4	Q86YV6	OTTHUMG00000014121	ENST00000274643.7:c.435+1G>A	chr6.hg19:g.2685717C>T		95.0	0.0		98.0	26.0	NM_001012418	A2RUC0|Q5TAW2	Silent	SNP	ENST00000274643.7	hg19	CCDS34330.1																																																																																			.	.		0.567	MYLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039632.2	NM_001012418	Silent	T	2685717	C	T	2685717	5	4	198	1	0	0	0	0	0	0	1	0	10068	695	24	3	763	3	MYLK4	6	2685717	Splice_Site	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10		2685717	168429350	33	29154										
CSNK2B	1460	hgsc.bcm.edu	37	chr6	31635683	31635683	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	caggacaaatttaatcttacTggactcaatgagcaggtccc	8	10	2	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr6:31635683T>C	ENST00000375882.2	+	3	267	c.111T>C	c.(109-111)acT>acC	p.T37T	CSNK2B_ENST00000375866.2_Silent_p.T37T|CSNK2B-LY6G5B-1181_ENST00000375880.2_Silent_p.T37T|GPANK1_ENST00000375900.4_5'Flank|GPANK1_ENST00000375906.1_5'Flank|GPANK1_ENST00000375893.2_5'Flank|CSNK2B_ENST00000375865.2_Silent_p.T37T|LY6G5B_ENST00000409525.1_5'Flank|LY6G5B_ENST00000375864.4_5'Flank|GPANK1_ENST00000375895.2_5'Flank|CSNK2B_ENST00000375885.4_Silent_p.T56T|GPANK1_ENST00000375896.4_5'Flank	NM_001282385.1|NM_001320.5	NP_001269314.1|NP_001311.3	P67870	CSK2B_HUMAN	casein kinase 2, beta polypeptide	37					adiponectin-activated signaling pathway (GO:0033211)|axon guidance (GO:0007411)|cellular protein complex assembly (GO:0043623)|endothelial tube morphogenesis (GO:0061154)|mitotic cell cycle (GO:0000278)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell proliferation (GO:0008285)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|protein phosphorylation (GO:0006468)|regulation of DNA binding (GO:0051101)|regulation of protein kinase activity (GO:0045859)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein kinase CK2 complex (GO:0005956)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein kinase regulator activity (GO:0019887)|receptor binding (GO:0005102)|transcription factor binding (GO:0008134)			central_nervous_system(5)|endometrium(1)|large_intestine(2)|liver(1)|urinary_tract(1)	10						TTAATCTTACTGGACTCAATG	0.488																																					p.T37T		Atlas-SNP	.											.	CSNK2B	15	.	0			c.T111C						.						131	119	123					6																	31635683		2203	4300	6503	SO:0001819	synonymous_variant	1460	exon3			TCTTACTGGACTC	M30448	CCDS4712.1	6p21.33	2013-01-17			ENSG00000204435	ENSG00000204435	2.7.11.1		2460	protein-coding gene	gene with protein product		115441				2276748, 9503014	Standard	NM_001320		Approved		uc003nvr.1	P67870	OTTHUMG00000177888	ENST00000375882.2:c.111T>C	chr6.hg19:g.31635683T>C		70.0	0.0		82.0	30.0	NM_001320	B0UXA9|P07312|P13862|Q4VX47	Silent	SNP	ENST00000375882.2	hg19	CCDS4712.1																																																																																			.	.		0.488	CSNK2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076063.8	NM_001320		C	31635683	T	C	31635683	2	2	198	1	0	0	0	0	0	0	0	1	3961	1567	55	2		2	CSNK2B	6	31635683	Silent	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	28949966	31635683	139479384	34	29155										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33145203	33145204	+	In_Frame_Ins	INS	-	-	GCC													0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ctcacctgggtcccaggggtINSgccctgttgtccaggaggtc							TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr6:33145203_33145204insGCC	ENST00000374708.4	-	21	1956_1957	c.1698_1699insGGC	c.(1696-1701)ggcacc>ggcGGCacc	p.566_567insG	COL11A2_ENST00000341947.2_In_Frame_Ins_p.652_653insG|COL11A2_ENST00000374714.1_In_Frame_Ins_p.626_627insG|COL11A2_ENST00000374713.1_In_Frame_Ins_p.605_606insG|COL11A2_ENST00000395197.1_In_Frame_Ins_p.592_593insG|COL11A2_ENST00000374712.1_In_Frame_Ins_p.571_572insG|COL11A2_ENST00000361917.1_In_Frame_Ins_p.545_546insG|COL11A2_ENST00000477772.1_5'UTR|COL11A2_ENST00000357486.1_In_Frame_Ins_p.631_632insG	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	652	Collagen-like 3.|Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						GTCCCAGGGGTGCCCTGTTGTC	0.564																																					p.T653delinsGT	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.1957_1958insGGC						.																																			SO:0001652	inframe_insertion	1302	exon23			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.1696_1698dupGGC	chr6.hg19:g.33145204_33145206dupGCC	ENSP00000363840:p.Gly566_Gly566dup	109.0	0.0		73.0	23.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	In_Frame_Ins	INS	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.564	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			GCC	33145204	-	GCC	33145203	7	5	198	1	0	1	1	0	0	0	0	0	3670	1696	59	0	3429	0	COL11A2	6	33145203	In_Frame_Ins	INS	-	TCGA-DD-AADP-01A-11D-A38X-10	1509520	33145203	137969864	35	29156										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38897346	38897346	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gaggacagcctttccttgggCcgaccccttctcattgagga	11	13	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr6:38897346C>A	ENST00000359357.3	+	73	10781	c.10527C>A	c.(10525-10527)ggC>ggA	p.G3509G	RP1-207H1.3_ENST00000453417.1_RNA|RP1-207H1.3_ENST00000416948.1_RNA|DNAH8_ENST00000441566.1_Silent_p.G3473G|DNAH8_ENST00000449981.2_Silent_p.G3726G|RP1-207H1.3_ENST00000418399.1_RNA			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3509	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTTCCTTGGGCCGACCCCTTC	0.408																																					p.G3726G		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C11178A						.						136	132	133					6																	38897346		2203	4300	6503	SO:0001819	synonymous_variant	1769	exon75			CTTGGGCCGACCC	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.10527C>A	chr6.hg19:g.38897346C>A		94.0	0.0		65.0	28.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	hg19																																																																																				.	.		0.408	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38897346	C	A	38897346	2	1	198	1	0	0	0	0	0	0	0	1	4609	726	26	3		3	DNAH8	6	38897346	Silent	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	5752143	38897346	132217721	36	29157										
ABCC10	89845	hgsc.bcm.edu	37	chr6	43400067	43400067	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tggcctggatcagccacagcCtggccctgtgggtgttggca	15	12	1	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr6:43400067C>G	ENST00000372530.4	+	3	564	c.349C>G	c.(349-351)Ctg>Gtg	p.L117V	ABCC10_ENST00000443426.2_Intron|ABCC10_ENST00000244533.3_Missense_Mutation_p.L74V	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	117					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	CAGCCACAGCCTGGCCCTGTG	0.652																																					p.L117V		Atlas-SNP	.											.	ABCC10	118	.	0			c.C349G						.						61	61	61					6																	43400067		2203	4300	6503	SO:0001583	missense	89845	exon3			CACAGCCTGGCCC	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.349C>G	chr6.hg19:g.43400067C>G	ENSP00000361608:p.Leu117Val	38.0	0.0		34.0	5.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	hg19	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	3.628	-0.076076	0.07184	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	T;T	0.42513	0.97;0.97	5.94	1.56	0.23342	.	0.709261	0.13904	N	0.354722	T	0.11495	0.0280	L	0.29908	0.895	0.28209	N	0.927008	B;B	0.19073	0.033;0.02	B;B	0.15484	0.013;0.006	T	0.31166	-0.9953	10	0.21540	T	0.41	-1.104	9.8227	0.40891	0.0:0.687:0.1343:0.1788	.	74;117	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	V	117;74	ENSP00000361608:L117V;ENSP00000244533:L74V	ENSP00000244533:L74V	L	+	1	2	ABCC10	43508045	0.055000	0.20627	1.000000	0.80357	0.018000	0.09664	-0.450000	0.06803	0.324000	0.23333	0.561000	0.74099	CTG	.	.		0.652	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		G	43400067	C	G	43400067	3	3	198	1	0	0	0	0	1	0	0	0	50	680	24	4	222	4	ABCC10	6	43400067	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	4502721	43400067	127715000	37	29158										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51524481	51524481	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ttccccaatagaaaaaagcgCaaaacttgaggagtttgatc	8	8	0	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr6:51524481C>A	ENST00000371117.3	-	61	10718	c.10443G>T	c.(10441-10443)ttG>ttT	p.L3481F		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3481					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GAAAAAAGCGCAAAACTTGAG	0.443																																					p.L3481F		Atlas-SNP	.											.	PKHD1	927	.	0			c.G10443T						.						77	79	78					6																	51524481		2203	4300	6503	SO:0001583	missense	5314	exon61			AAAGCGCAAAACT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10443G>T	chr6.hg19:g.51524481C>A	ENSP00000360158:p.Leu3481Phe	123.0	0.0		109.0	38.0	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.452662	0.26074	.	.	ENSG00000170927	ENST00000371117	D	0.89270	-2.49	5.72	3.96	0.45880	.	0.301940	0.27577	N	0.018760	T	0.65903	0.2736	N	0.17082	0.46	0.54753	D	0.999989	B	0.25719	0.132	B	0.17098	0.017	T	0.63607	-0.6599	10	0.41790	T	0.15	.	8.0397	0.30515	0.0:0.7101:0.1406:0.1493	.	3481	P08F94	PKHD1_HUMAN	F	3481	ENSP00000360158:L3481F	ENSP00000360158:L3481F	L	-	3	2	PKHD1	51632440	0.996000	0.38824	0.610000	0.28997	0.909000	0.53808	0.439000	0.21575	0.778000	0.33520	-0.137000	0.14449	TTG	.	.		0.443	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51524481	C	A	51524481	3	1	198	1	0	0	0	0	1	0	0	0	11980	709	25	3	1809	3	PKHD1	6	51524481	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	8124414	51524481	119590586	38	29159										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121452855	121452855	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tctatccattcagtttgtttAtcagatattttgaggcataa	6	6	3	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr6:121452855A>C	ENST00000398212.2	-	25	2866	c.2817T>G	c.(2815-2817)gaT>gaG	p.D939E	TBC1D32_ENST00000275159.6_Missense_Mutation_p.D980E|TBC1D32_ENST00000398197.2_5'UTR	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	939					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										CAGTTTGTTTATCAGATATTT	0.303																																					p.D939E		Atlas-SNP	.											.	C6orf170	146	.	0			c.T2817G						.						88	81	83					6																	121452855		1798	4073	5871	SO:0001583	missense	221322	exon25			TTGTTTATCAGAT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.2817T>G	chr6.hg19:g.121452855A>C	ENSP00000381270:p.Asp939Glu	45.0	0.0		23.0	15.0	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	hg19	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.702377	0.48307	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.16597	2.33;2.33	5.37	2.95	0.34219	.	0.410154	0.27245	N	0.020260	T	0.03608	0.0103	L	0.42245	1.32	0.30354	N	0.784461	B;B	0.10296	0.003;0.002	B;B	0.11329	0.006;0.005	T	0.40850	-0.9541	10	0.14656	T	0.56	.	3.9851	0.09513	0.6674:0.1333:0.0715:0.1278	.	980;939	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	E	980;939	ENSP00000275159:D980E;ENSP00000381270:D939E	ENSP00000275159:D980E	D	-	3	2	C6orf170	121494554	0.998000	0.40836	1.000000	0.80357	0.565000	0.35776	0.444000	0.21661	0.828000	0.34709	0.477000	0.44152	GAT	.	.		0.303	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		C	121452855	A	C	121452855	3	2	198	1	0	0	0	0	1	0	0	0	2346	446	16	5	988	5	C6orf170	6	121452855	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	69928374	121452855	49662212	39	29160										
TRDN	10345	hgsc.bcm.edu	37	chr6	123658791	123658791	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tttcagaattgaagaagtctTcccagatttttcttttctaa	5	7	4	4			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr6:123658791T>C	ENST00000398178.3	-	22	1414	c.1393A>G	c.(1393-1395)Aag>Gag	p.K465E	TRDN_ENST00000334268.4_Missense_Mutation_p.K465E	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	465					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		GAAGAAGTCTTCCCAGATTTT	0.279																																					p.K465E		Atlas-SNP	.											.	TRDN	88	.	0			c.A1393G						.						24	22	23					6																	123658791		1184	2563	3747	SO:0001583	missense	10345	exon22			AAGTCTTCCCAGA	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1393A>G	chr6.hg19:g.123658791T>C	ENSP00000381240:p.Lys465Glu	187.0	0.0		103.0	6.0	NM_006073	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	hg19	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.878343	0.33162	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.18960	2.18;2.19	4.68	4.68	0.58851	.	0.000000	0.44483	D	0.000454	T	0.05456	0.0144	N	0.24115	0.695	0.80722	D	1	P	0.46784	0.884	B	0.37731	0.257	T	0.30475	-0.9977	10	0.20519	T	0.43	-1.4364	10.7071	0.45960	0.0:0.0:0.0:1.0	.	465	Q13061	TRDN_HUMAN	E	465;467;465	ENSP00000381240:K465E;ENSP00000333984:K465E	ENSP00000333984:K465E	K	-	1	0	TRDN	123700490	1.000000	0.71417	0.728000	0.30774	0.137000	0.21094	3.858000	0.55979	2.107000	0.64212	0.528000	0.53228	AAG	.	.		0.279	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	123658791	T	C	123658791	3	2	198	1	0	0	0	0	1	0	0	0	16483	1792	62	2	876	2	TRDN	6	123658791	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	2205936	123658791	47456276	40	29161										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129704303	129704303	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	cagatggcgagcagaccggaCaggatgctgagaggaccaac	15	10	0	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr6:129704303C>T	ENST00000421865.2	+	35	5045	c.4996C>T	c.(4996-4998)Cag>Tag	p.Q1666*		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1666	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GCAGACCGGACAGGATGCTGA	0.438																																					p.Q1666X		Atlas-SNP	.											.	LAMA2	481	.	0			c.C4996T						.						82	85	84					6																	129704303		2203	4300	6503	SO:0001587	stop_gained	3908	exon35			ACCGGACAGGATG	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.4996C>T	chr6.hg19:g.129704303C>T	ENSP00000400365:p.Gln1666*	166.0	0.0		66.0	38.0	NM_000426	Q14736|Q5VUM2|Q93022	Nonsense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	C	45	11.598638	0.99580	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	.	.	.	5.63	5.63	0.86233	.	0.127355	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	14.8347	0.70175	0.1439:0.8561:0.0:0.0	.	.	.	.	X	1666	.	ENSP00000346769:Q1666X	Q	+	1	0	LAMA2	129745996	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.771000	0.47670	2.814000	0.96858	0.563000	0.77884	CAG	.	.		0.438	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129704303	C	T	129704303	4	4	198	1	0	0	0	0	0	1	0	0	8615	479	17	3	5134	3	LAMA2	6	129704303	Nonsense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	6045512	129704303	41410764	41	29162										
SAMD5	389432	hgsc.bcm.edu	37	chr6	147830394	147830394	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	cagggcacccgcggggactcTcgcggccacacgaccgcccc	13	20	1	0	rs370342734		TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr6:147830394T>C	ENST00000367474.1	+	1	332	c.330T>C	c.(328-330)tcT>tcC	p.S110S		NM_001030060.2	NP_001025231.1	Q5TGI4	SAMD5_HUMAN	sterile alpha motif domain containing 5	110													Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.55e-10)|GBM - Glioblastoma multiforme(68;0.112)		gcggggACTCTCGCGGCCACA	0.756																																					p.S110S		Atlas-SNP	.											.	SAMD5	4	.	0			c.T330C						.						11	11	11					6																	147830394		2184	4277	6461	SO:0001819	synonymous_variant	389432	exon1			GGACTCTCGCGGC	AL354880	CCDS34548.1	6q24.3	2013-01-10			ENSG00000203727	ENSG00000203727		"Sterile alpha motif (SAM) domain containing"	21180	protein-coding gene	gene with protein product							Standard	NM_001030060		Approved	dJ875H10.1	uc003qmc.2	Q5TGI4	OTTHUMG00000015767	ENST00000367474.1:c.330T>C	chr6.hg19:g.147830394T>C		70.0	0.0		41.0	13.0	NM_001030060		Silent	SNP	ENST00000367474.1	hg19	CCDS34548.1																																																																																			.	.		0.756	SAMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042610.1	NM_001030060		C	147830394	T	C	147830394	2	2	198	1	0	0	0	0	0	0	0	1	13838	1538	54	2		2	SAMD5	6	147830394	Silent	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	18126091	147830394	23284673	42	29163										
RUNDC3B	154661	hgsc.bcm.edu	37	chr7	87459284	87459284	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gtctctaacaagcttaaaatCtaatgactaccttgcaagtc	5	10	2	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr7:87459284C>G	ENST00000338056.3	+	12	1772	c.1361C>G	c.(1360-1362)tCt>tGt	p.S454C	RUNDC3B_ENST00000493037.1_Missense_Mutation_p.S388C|RUNDC3B_ENST00000394654.3_Missense_Mutation_p.S437C	NM_001134405.1|NM_138290.2	NP_001127877.1|NP_612147.1	Q96NL0	RUN3B_HUMAN	RUN domain containing 3B	454										breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(2)	26	Esophageal squamous(14;0.00164)					AGCTTAAAATCTAATGACTAC	0.373																																					p.S454C		Atlas-SNP	.											.	RUNDC3B	63	.	0			c.C1361G						.						124	121	122					7																	87459284		2203	4300	6503	SO:0001583	missense	154661	exon12			TAAAATCTAATGA		CCDS5609.1, CCDS47635.1, CCDS47636.1	7q21.12	2009-01-14			ENSG00000105784	ENSG00000105784			30286	protein-coding gene	gene with protein product						12645870	Standard	NM_138290		Approved	RPIP9, RPIB9	uc003ujb.3	Q96NL0	OTTHUMG00000131035	ENST00000338056.3:c.1361C>G	chr7.hg19:g.87459284C>G	ENSP00000337732:p.Ser454Cys	123.0	0.0		117.0	39.0	NM_138290	B4DFD0|E9PBR4|Q8IWW5|Q8NB55|Q8TBG7	Missense_Mutation	SNP	ENST00000338056.3	hg19	CCDS5609.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.622580	0.87460	.	.	ENSG00000105784	ENST00000338056;ENST00000493037;ENST00000394654	T;T;T	0.36520	1.86;1.25;1.84	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.57489	0.2057	L	0.59436	1.845	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.79784	0.993;0.992;0.992;0.993	T	0.53954	-0.8365	10	0.45353	T	0.12	-7.726	17.7312	0.88378	0.0:1.0:0.0:0.0	.	437;310;388;454	E9PBR4;Q96NL0-2;Q96NL0-4;Q96NL0	.;.;.;RUN3B_HUMAN	C	454;388;437	ENSP00000337732:S454C;ENSP00000420394:S388C;ENSP00000378149:S437C	ENSP00000337732:S454C	S	+	2	0	RUNDC3B	87297220	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.539000	0.67199	2.628000	0.89032	0.585000	0.79938	TCT	.	.		0.373	RUNDC3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253679.1	NM_138290		G	87459284	C	G	87459284	3	3	198	1	0	0	0	0	1	0	0	0	13760	913	32	4	1407	4	RUNDC3B	7	87459284	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10		87459284	71679379	43	29164										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121653745	121653745	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ttctgacaagtgatgaagaaAgtggatcagggcaaggtacc	13	6	2	4			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr7:121653745A>C	ENST00000393386.2	+	12	5056	c.4645A>C	c.(4645-4647)Agt>Cgt	p.S1549R	PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1549					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TGATGAAGAAAGTGGATCAGG	0.433																																					p.S1549R		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.A4645C						.						129	121	124					7																	121653745		2203	4300	6503	SO:0001583	missense	5803	exon12			GAAGAAAGTGGAT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.4645A>C	chr7.hg19:g.121653745A>C	ENSP00000377047:p.Ser1549Arg	189.0	0.0		145.0	48.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	A	18.91	3.723460	0.68959	.	.	ENSG00000106278	ENST00000393386	T	0.57273	0.41	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.53351	0.1791	M	0.71581	2.175	0.80722	D	1	P	0.39480	0.675	B	0.35353	0.201	T	0.60000	-0.7348	10	0.56958	D	0.05	.	16.3473	0.83146	1.0:0.0:0.0:0.0	.	1549	P23471	PTPRZ_HUMAN	R	1549	ENSP00000377047:S1549R	ENSP00000377047:S1549R	S	+	1	0	PTPRZ1	121440981	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.451000	0.80668	2.320000	0.78422	0.528000	0.53228	AGT	.	.		0.433	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121653745	A	C	121653745	3	2	198	1	0	0	0	0	1	0	0	0	12829	72	3	5	4691	5	PTPRZ1	7	121653745	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	34194461	121653745	37484918	44	29165										
EGR3	1960	hgsc.bcm.edu	37	chr8	22548606	22548606	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gaagagattgctgtccaacgCcggcttggccgattggtaat	13	9	0	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr8:22548606C>A	ENST00000317216.2	-	2	901	c.544G>T	c.(544-546)Gcg>Tcg	p.A182S	EGR3_ENST00000522910.1_Missense_Mutation_p.A144S|EGR3_ENST00000519492.1_3'UTR|RP11-459E5.1_ENST00000523627.1_RNA|EGR3_ENST00000524088.1_5'UTR	NM_001199881.1|NM_004430.2	NP_001186810.1|NP_004421.2	Q06889	EGR3_HUMAN	early growth response 3	182					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|circadian rhythm (GO:0007623)|endothelial cell chemotaxis (GO:0035767)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of gamma-delta T cell differentiation (GO:0045586)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Prostate(55;0.0421)|Breast(100;0.102)		Colorectal(74;0.0145)|BRCA - Breast invasive adenocarcinoma(99;0.053)|COAD - Colon adenocarcinoma(73;0.0608)		CTGTCCAACGCCGGCTTGGCC	0.602																																					p.A182S		Atlas-SNP	.											.	EGR3	33	.	0			c.G544T						.						59	61	61					8																	22548606		2203	4300	6503	SO:0001583	missense	1960	exon2			CCAACGCCGGCTT	X63741	CCDS6033.1, CCDS56528.1	8p23-p21	2013-01-08			ENSG00000179388	ENSG00000179388		"Zinc fingers, C2H2-type"	3240	protein-coding gene	gene with protein product	"zinc finger protein pilot"	602419				1906159, 11909874	Standard	NM_004430		Approved	PILOT	uc003xcm.1	Q06889	OTTHUMG00000097825	ENST00000317216.2:c.544G>T	chr8.hg19:g.22548606C>A	ENSP00000318057:p.Ala182Ser	144.0	0.0		77.0	47.0	NM_004430	A8K8U9|B4DHJ5|E7EW38|Q2M3W2	Missense_Mutation	SNP	ENST00000317216.2	hg19	CCDS6033.1	.	.	.	.	.	.	.	.	.	.	C	5.717	0.316839	0.10845	.	.	ENSG00000179388	ENST00000317216;ENST00000522910	T;T	0.07908	3.15;3.17	5.52	4.63	0.57726	.	0.273629	0.35235	N	0.003354	T	0.05502	0.0145	N	0.19112	0.55	0.80722	D	1	B;B	0.18013	0.025;0.025	B;B	0.25506	0.061;0.036	T	0.40961	-0.9535	10	0.15952	T	0.53	-17.9063	8.8927	0.35444	0.0:0.8307:0.0:0.1693	.	144;182	E7EW38;Q06889	.;EGR3_HUMAN	S	182;144	ENSP00000318057:A182S;ENSP00000430310:A144S	ENSP00000318057:A182S	A	-	1	0	EGR3	22604551	0.902000	0.30710	0.999000	0.59377	0.989000	0.77384	1.628000	0.37060	2.586000	0.87340	0.561000	0.74099	GCG	.	.		0.602	EGR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215098.1	NM_004430		A	22548606	C	A	22548606	3	1	198	1	0	0	0	0	1	0	0	0	4975	739	26	3	623	3	EGR3	8	22548606	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10		22548606	123815416	45	29166										
SCARA5	286133	hgsc.bcm.edu	37	chr8	27824054	27824054	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gcttgcccgccgtttgtgacAtggacctggacaataagggt	13	10	0	1	rs111460095		TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr8:27824054A>G	ENST00000354914.3	-	3	603	c.118T>C	c.(118-120)Tgt>Cgt	p.C40R	SCARA5_ENST00000301906.4_Intron|SCARA5_ENST00000518030.1_Intron|SCARA5_ENST00000380385.2_Missense_Mutation_p.C40R|SCARA5_ENST00000524352.1_Missense_Mutation_p.C40R	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	40					cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)			central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		CGTTTGTGACATGGACCTGGA	0.517																																					p.C40R		Atlas-SNP	.											.	SCARA5	53	.	0			c.T118C						.						93	102	99					8																	27824054		2203	4300	6503	SO:0001583	missense	286133	exon3			TGTGACATGGACC	AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"scavenger receptor class A, member 5 (putative)"			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.118T>C	chr8.hg19:g.27824054A>G	ENSP00000346990:p.Cys40Arg	249.0	0.0		138.0	27.0	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	hg19	CCDS6064.1	.	.	.	.	.	.	.	.	.	.	A	8.173	0.792219	0.16258	.	.	ENSG00000168079	ENST00000354914;ENST00000380385;ENST00000524352	D;D;D	0.90563	-2.3;-2.29;-2.69	5.93	2.21	0.28008	.	0.293688	0.32120	N	0.006554	D	0.85712	0.5760	L	0.51422	1.61	0.26494	N	0.97489	B;B;B	0.25105	0.036;0.118;0.021	B;B;B	0.31245	0.059;0.126;0.036	T	0.74051	-0.3789	10	0.32370	T	0.25	.	6.352	0.21381	0.4588:0.4002:0.0:0.141	.	40;40;40	Q6ZMJ2-4;Q6ZMJ2-2;Q6ZMJ2	.;.;SCAR5_HUMAN	R	40	ENSP00000346990:C40R;ENSP00000369746:C40R;ENSP00000428663:C40R	ENSP00000346990:C40R	C	-	1	0	SCARA5	27879973	0.150000	0.22732	0.645000	0.29479	0.980000	0.70556	0.727000	0.25999	0.439000	0.26476	0.460000	0.39030	TGT	.	A|0.500;C|0.500		0.517	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833		G	27824054	A	G	27824054	3	3	198	1	0	0	0	0	1	0	0	0	13895	217	8	2	1397	2	SCARA5	8	27824054	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	5275448	27824054	118539968	46	29167										
MYST3	7994	hgsc.bcm.edu	37	chr8	41906233	41906233	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gtttattatccaattttccaTggttccgaggcttaggaagt	9	7	0	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr8:41906233T>A	ENST00000396930.3	-	3	806	c.263A>T	c.(262-264)cAt>cTt	p.H88L	KAT6A_ENST00000485568.1_Missense_Mutation_p.H88L|KAT6A_ENST00000265713.2_Missense_Mutation_p.H88L|KAT6A_ENST00000406337.1_Missense_Mutation_p.H88L	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	88	Required for activation of RUNX1-1.|Required for nuclear localization.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CAATTTTCCATGGTTCCGAGG	0.388																																					p.H88L		Atlas-SNP	.											.	.	.	.	0			c.A263T						.						141	143	142					8																	41906233		2203	4300	6503	SO:0001583	missense	7994	exon3			TTTCCATGGTTCC	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.263A>T	chr8.hg19:g.41906233T>A	ENSP00000380136:p.His88Leu	135.0	0.0		79.0	39.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.175641	0.38413	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000485568	T;T;T;D	0.83506	0.32;0.32;0.32;-1.73	5.81	5.81	0.92471	.	0.077427	0.56097	D	0.000038	T	0.71953	0.3401	N	0.08118	0	0.46849	D	0.999227	B;P	0.44734	0.024;0.842	B;P	0.45343	0.008;0.477	T	0.71600	-0.4544	10	0.15499	T	0.54	-17.9016	16.1637	0.81739	0.0:0.0:0.0:1.0	.	88;88	A5PLL3;Q92794	.;KAT6A_HUMAN	L	88	ENSP00000265713:H88L;ENSP00000385888:H88L;ENSP00000380136:H88L;ENSP00000430606:H88L	ENSP00000265713:H88L	H	-	2	0	KAT6A	42025390	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.206000	0.51098	2.216000	0.71823	0.533000	0.62120	CAT	.	.		0.388	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		A	41906233	T	A	41906233	3	1	198	1	0	0	0	0	1	0	0	0	10113	1464	51	4	5815	4	MYST3	8	41906233	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	14082179	41906233	104457789	47	29168										
MYBL1	4603	hgsc.bcm.edu	37	chr8	67488316	67488316	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	accaccatcgttcaatgagcCatccctaagttcgctgcctg	7	15	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr8:67488316C>A	ENST00000522677.3	-	10	1806	c.1396G>T	c.(1396-1398)Ggc>Tgc	p.G466C	MYBL1_ENST00000517885.1_Missense_Mutation_p.G124C|MYBL1_ENST00000524176.2_Missense_Mutation_p.G466C	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	466	Negative regulatory domain. {ECO:0000250}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			TTCAATGAGCCATCCCTAAGT	0.438																																					p.G466C		Atlas-SNP	.											.	MYBL1	73	.	0			c.G1396T						.						111	101	104					8																	67488316		1961	4141	6102	SO:0001583	missense	4603	exon10			ATGAGCCATCCCT	X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.1396G>T	chr8.hg19:g.67488316C>A	ENSP00000429633:p.Gly466Cys	170.0	0.0		199.0	40.0	NM_001080416	E7EW29|Q495F9	Missense_Mutation	SNP	ENST00000522677.3	hg19	CCDS47867.1	.	.	.	.	.	.	.	.	.	.	C	8.091	0.774532	0.16051	.	.	ENSG00000185697	ENST00000522677;ENST00000517885;ENST00000524176	T;T;T	0.18338	2.7;2.24;2.22	5.46	2.72	0.32119	.	0.368259	0.31233	N	0.008009	T	0.14570	0.0352	N	0.24115	0.695	0.28161	N	0.928984	B;P;P	0.49696	0.001;0.927;0.661	B;P;B	0.47673	0.002;0.554;0.285	T	0.04635	-1.0937	10	0.72032	D	0.01	-1.4465	9.1505	0.36959	0.0:0.7749:0.0:0.2251	.	466;465;466	Q495F9;Q495G0;P10243	.;.;MYBA_HUMAN	C	466;124;466	ENSP00000429633:G466C;ENSP00000428265:G124C;ENSP00000428011:G466C	ENSP00000428265:G124C	G	-	1	0	MYBL1	67650870	0.832000	0.29368	0.039000	0.18376	0.196000	0.23810	0.956000	0.29202	0.294000	0.22547	0.591000	0.81541	GGC	.	.		0.438	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		A	67488316	C	A	67488316	3	1	198	1	0	0	0	0	1	0	0	0	10018	594	21	3	890	3	MYBL1	8	67488316	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	25582083	67488316	78875706	48	29169										
KLF10	7071	hgsc.bcm.edu	37	chr8	103664417	103664417	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ctgggattgtatgaaaatcaGgtgttcccggaagcagattc	12	7	1	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr8:103664417G>C	ENST00000285407.6	-	2	545	c.245C>G	c.(244-246)cCt>cGt	p.P82R	KLF10_ENST00000395884.3_Missense_Mutation_p.P71R	NM_005655.2	NP_005646.1	Q13118	KLF10_HUMAN	Kruppel-like factor 10	82					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular response to peptide (GO:1901653)|cellular response to starvation (GO:0009267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of circadian rhythm (GO:0042752)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(3)	18	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			ATGAAAATCAGGTGTTCCCGG	0.313											OREG0018913	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P82R	Esophageal Squamous(16;495 519 2144 16528 44005)	Atlas-SNP	.											.	KLF10	44	.	0			c.C245G						.						65	65	65					8																	103664417		2203	4300	6503	SO:0001583	missense	7071	exon2			AAATCAGGTGTTC	U21847	CCDS6294.1, CCDS47905.1	8q22.3	2014-09-17	2004-11-29	2004-12-01	ENSG00000155090	ENSG00000155090		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11810	protein-coding gene	gene with protein product		601878	"TGFB inducible early growth response"	TIEG		8584037, 9721211	Standard	NM_001032282		Approved	EGRA, TIEG1	uc011lhk.1	Q13118	OTTHUMG00000164735	ENST00000285407.6:c.245C>G	chr8.hg19:g.103664417G>C	ENSP00000285407:p.Pro82Arg	94.0	0.0	1375	118.0	71.0	NM_005655	A8MVH0|B2R794|L0R4P6|L0R679|O75411|Q503B2	Missense_Mutation	SNP	ENST00000285407.6	hg19	CCDS6294.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.679879	0.29783	.	.	ENSG00000155090	ENST00000285407;ENST00000395884	T;T	0.14266	2.52;2.58	6.01	6.01	0.97437	.	0.323388	0.30930	N	0.008594	T	0.11153	0.0272	L	0.36672	1.1	0.09310	N	1	P;B	0.42409	0.779;0.309	B;B	0.33690	0.168;0.055	T	0.27872	-1.0061	10	0.49607	T	0.09	.	13.6832	0.62499	0.0701:0.0:0.9299:0.0	.	82;71	Q13118;O75411	KLF10_HUMAN;.	R	82;71	ENSP00000285407:P82R;ENSP00000379222:P71R	ENSP00000285407:P82R	P	-	2	0	KLF10	103733593	0.954000	0.32549	0.907000	0.35723	0.873000	0.50193	4.933000	0.63484	2.861000	0.98227	0.650000	0.86243	CCT	.	.		0.313	KLF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379967.1			C	103664417	G	C	103664417	3	2	198	1	0	0	0	0	1	0	0	0	8347	1000	35	4	1209	4	KLF10	8	103664417	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	36176101	103664417	42699605	49	29170										
DGAT1	8694	hgsc.bcm.edu	37	chr8	145540696	145540696	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	agcactgacctcgtggaagaAggccgaggccaggaacaccc	13	13	0	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr8:145540696A>C	ENST00000332324.4	-	15	1510	c.1237T>G	c.(1237-1239)Ttc>Gtc	p.F413V	GS1-393G12.12_ENST00000525023.1_RNA|DGAT1_ENST00000527438.1_5'UTR	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1	413					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	diacylglycerol O-acyltransferase activity (GO:0004144)|retinol O-fatty-acyltransferase activity (GO:0050252)|transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			TCGTGGAAGAAGGCCGAGGCC	0.637																																					p.F413V		Atlas-SNP	.											.	DGAT1	26	.	0			c.T1237G						.						56	56	56					8																	145540696		2203	4296	6499	SO:0001583	missense	8694	exon15			GGAAGAAGGCCGA	AF059202	CCDS6420.1	8q24.3	2014-05-06	2010-06-24	2001-11-09	ENSG00000185000	ENSG00000185000	2.3.1.20		2843	protein-coding gene	gene with protein product		604900	"diacylglycerol O-acyltransferase homolog 1 (mouse)"			9756920	Standard	NM_012079		Approved	ARGP1, DGAT	uc003zbv.3	O75907	OTTHUMG00000174606	ENST00000332324.4:c.1237T>G	chr8.hg19:g.145540696A>C	ENSP00000332258:p.Phe413Val	82.0	0.0		85.0	43.0	NM_012079	B2RWQ2|D3DWL6|Q96BB8	Missense_Mutation	SNP	ENST00000332324.4	hg19	CCDS6420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.1|23.1	4.371347|4.371347	0.82573|0.82573	.|.	.|.	ENSG00000185000|ENSG00000185000	ENST00000332324|ENST00000526479	T|.	0.68025|.	-0.3|.	4.55|4.55	4.55|4.55	0.56014|0.56014	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.50837|0.50837	0.1639|0.1639	L|L	0.28115|0.28115	0.83|0.83	0.80722|0.80722	D|D	1|1	P|D	0.52061|0.58620	0.95|0.983	P|P	0.60012|0.58331	0.867|0.837	T|T	0.39078|0.39078	-0.9631|-0.9631	10|8	0.14656|0.15499	T|T	0.56|0.54	-19.1825|-19.1825	11.8781|11.8781	0.52558|0.52558	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	413|247	O75907|E9PS80	DGAT1_HUMAN|.	V|R	413|247	ENSP00000332258:F413V|.	ENSP00000332258:F413V|ENSP00000435883:L247R	F|L	-|-	1|2	0|0	DGAT1|DGAT1	145511504|145511504	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	8.416000|8.416000	0.90244|0.90244	1.917000|1.917000	0.55516|0.55516	0.459000|0.459000	0.35465|0.35465	TTC|CTT	.	.		0.637	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	NM_012079		C	145540696	A	C	145540696	3	2	198	1	0	0	0	0	1	0	0	0	4459	72	3	5	241	5	DGAT1	8	145540696	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	41876279	145540696	823326	50	29171										
ZNF7	7553	hgsc.bcm.edu	37	chr8	146054920	146054920	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ctcgggaggagtggcagtgtCtggaccctggccagagggcc	18	11	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr8:146054920C>T	ENST00000528372.1	+	3	301	c.61C>T	c.(61-63)Ctg>Ttg	p.L21L	ZNF7_ENST00000325241.6_Silent_p.L21L|ZNF7_ENST00000325217.5_Silent_p.L32L|ZNF7_ENST00000532393.1_Intron|ZNF7_ENST00000544249.1_Intron|ZNF7_ENST00000529819.1_Silent_p.L21L|ZNF7_ENST00000528130.1_Silent_p.L21L|ZNF7_ENST00000446747.2_Silent_p.L32L|ZNF7_ENST00000525266.1_Silent_p.L21L			P17097	ZNF7_HUMAN	zinc finger protein 7	21	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		GTGGCAGTGTCTGGACCCTGG	0.612																																					p.L21L		Atlas-SNP	.											.	ZNF7	62	.	0			c.C61T						.						167	139	149					8																	146054920		2203	4300	6503	SO:0001819	synonymous_variant	7553	exon3			CAGTGTCTGGACC	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.61C>T	chr8.hg19:g.146054920C>T		156.0	0.0		169.0	45.0	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Silent	SNP	ENST00000528372.1	hg19	CCDS6435.1																																																																																			.	.		0.612	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		T	146054920	C	T	146054920	2	4	198	1	0	0	0	0	0	0	0	1	18117	912	32	3		3	ZNF7	8	146054920	Silent	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	514224	146054920	309102	51	29172										
DENND4C	55667	hgsc.bcm.edu	37	chr9	19372063	19372063	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gacaatgaatatggaattgcAtacaatagtctgtcttcaga	8	6	3	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr9:19372063A>G	ENST00000380432.2	+	28	4947	c.4914A>G	c.(4912-4914)gcA>gcG	p.A1638A	DENND4C_ENST00000602925.1_Silent_p.A1874A|RP11-513M16.7_ENST00000609609.1_RNA|DENND4C_ENST00000434457.2_Silent_p.A1923A			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1638					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						ATGGAATTGCATACAATAGTC	0.383																																					p.A1874A		Atlas-SNP	.											.	DENND4C	120	.	0			c.A5622G						.						92	101	98					9																	19372063		2203	4300	6503	SO:0001819	synonymous_variant	55667	exon32			AATTGCATACAAT	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.4914A>G	chr9.hg19:g.19372063A>G		148.0	0.0		77.0	41.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Silent	SNP	ENST00000380432.2	hg19																																																																																				.	.		0.383	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		G	19372063	A	G	19372063	2	3	198	1	0	0	0	0	0	0	0	1	4437	204	8	2		2	DENND4C	9	19372063	Silent	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10		19372063	121841368	52	29173										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32631818	32631818	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ctccttttcctggttccgctTaagccgcctcagttgctctt	7	15	2	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr9:32631818T>G	ENST00000242310.4	-	1	3849	c.3760A>C	c.(3760-3762)Aag>Cag	p.K1254Q	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1254					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TGGTTCCGCTTAAGCCGCCTC	0.458																																					p.K1254Q		Atlas-SNP	.											.	TAF1L	382	.	0			c.A3760C						.						89	89	89					9																	32631818		2203	4300	6503	SO:0001583	missense	138474	exon1			TCCGCTTAAGCCG	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3760A>C	chr9.hg19:g.32631818T>G	ENSP00000418379:p.Lys1254Gln	311.0	1.0		262.0	97.0	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	hg19	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.357001	0.61293	.	.	ENSG00000122728	ENST00000242310	T	0.64085	-0.08	1.04	-1.18	0.09617	.	0.135428	0.64402	D	0.000003	T	0.64316	0.2587	L	0.52573	1.65	0.49389	D	0.999784	D	0.89917	1.0	D	0.70935	0.971	T	0.61237	-0.7103	10	0.42905	T	0.14	.	4.6615	0.12645	0.0:0.0:0.3144:0.6856	.	1254	Q8IZX4	TAF1L_HUMAN	Q	1254	ENSP00000418379:K1254Q	ENSP00000418379:K1254Q	K	-	1	0	TAF1L	32621818	1.000000	0.71417	0.994000	0.49952	0.392000	0.30506	5.064000	0.64338	0.426000	0.26116	0.164000	0.16699	AAG	.	.		0.458	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			G	32631818	T	G	32631818	3	3	198	1	0	0	0	0	1	0	0	0	15538	1763	61	5	1724	5	TAF1L	9	32631818	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	13259755	32631818	108581613	53	29174			1	43		2	2	21	T		6.718832e-05
TAF1L	138474	hgsc.bcm.edu	37	chr9	32631838	32631838	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	taagccgcctcagttgctctTgaatcctccgccgttctttc	7	15	3	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr9:32631838T>A	ENST00000242310.4	-	1	3829	c.3740A>T	c.(3739-3741)cAa>cTa	p.Q1247L	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1247					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CAGTTGCTCTTGAATCCTCCG	0.453																																					p.Q1247L		Atlas-SNP	.											.	TAF1L	382	.	0			c.A3740T						.						93	91	92					9																	32631838		2203	4300	6503	SO:0001583	missense	138474	exon1			TGCTCTTGAATCC	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3740A>T	chr9.hg19:g.32631838T>A	ENSP00000418379:p.Gln1247Leu	320.0	1.0		275.0	98.0	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	hg19	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	15.00	2.704197	0.48412	.	.	ENSG00000122728	ENST00000242310	T	0.65178	-0.14	1.04	1.04	0.20106	.	0.000000	0.85682	D	0.000000	T	0.67822	0.2934	L	0.54323	1.7	0.58432	D	0.999998	D	0.61697	0.99	D	0.68192	0.956	T	0.65981	-0.6036	10	0.87932	D	0	.	5.8599	0.18740	0.0:0.0:0.0:1.0	.	1247	Q8IZX4	TAF1L_HUMAN	L	1247	ENSP00000418379:Q1247L	ENSP00000418379:Q1247L	Q	-	2	0	TAF1L	32621838	1.000000	0.71417	0.981000	0.43875	0.373000	0.29922	5.064000	0.64338	0.426000	0.26116	0.164000	0.16699	CAA	.	.		0.453	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32631838	T	A	32631838	3	1	198	1	0	0	0	0	1	0	0	0	15538	1812	63	4	1744	4	TAF1L	9	32631838	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	20	32631838	108581593	54	29175			1	43		2	2	21	T		6.718832e-05
ISCA1	81689	hgsc.bcm.edu	37	chr9	88889128	88889128	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tcaggcttatctttaagaagTtgttttatcttgtttactgc	7	6	3	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr9:88889128T>C	ENST00000375991.4	-	2	181	c.111A>G	c.(109-111)caA>caG	p.Q37Q	ISCA1_ENST00000311534.6_5'UTR|ISCA1_ENST00000326094.4_Silent_p.Q37Q|ISCA1_ENST00000452279.2_Silent_p.Q84Q	NM_030940.3	NP_112202.2	Q9BUE6	ISCA1_HUMAN	iron-sulfur cluster assembly 1	37					iron-sulfur cluster assembly (GO:0016226)	mitochondrion (GO:0005739)	iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(1)|lung(4)|pancreas(1)	8				OV - Ovarian serous cystadenocarcinoma(323;5.4e-34)|Lung(182;0.0375)		CTTTAAGAAGTTGTTTTATCT	0.303																																					p.Q37Q		Atlas-SNP	.											.	ISCA1	10	.	0			c.A111G						.						75	75	75					9																	88889128		2203	4297	6500	SO:0001819	synonymous_variant	81689	exon2			AAGAAGTTGTTTT	AF038186	CCDS35056.1	9q22.1	2013-08-06	2013-08-06	2007-01-18	ENSG00000135070	ENSG00000135070			28660	protein-coding gene	gene with protein product		611006	"HESB like domain containing 2", "iron-sulfur cluster assembly 1 homolog (S. cerevisiae)"	HBLD2		15262227, 22323289	Standard	NM_030940		Approved	MGC4276, ISA1, hIscA	uc004aop.3	Q9BUE6	OTTHUMG00000020135	ENST00000375991.4:c.111A>G	chr9.hg19:g.88889128T>C		82.0	0.0		59.0	30.0	NM_030940	B3KP34|B4DJI5|Q8ND75|Q9BZR2	Silent	SNP	ENST00000375991.4	hg19	CCDS35056.1																																																																																			.	.		0.303	ISCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052914.1	NM_030940		C	88889128	T	C	88889128	2	2	198	1	0	0	0	0	0	0	0	1	7858	1722	60	2		2	ISCA1	9	88889128	Silent	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	56257290	88889128	52324303	55	29176										
GLE1	2733	hgsc.bcm.edu	37	chr9	131289570	131289570	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	accaacagcaaggacagtcaGgtaggggagaggtatatggc	15	7	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr9:131289570G>T	ENST00000309971.4	+	8	1348	c.1242G>T	c.(1240-1242)caG>caT	p.Q414H	RP11-216B9.6_ENST00000434999.1_RNA|GLE1_ENST00000494417.1_3'UTR|GLE1_ENST00000372770.4_Splice_Site_p.Q414H|GLE1_ENST00000539582.1_Splice_Site_p.Q160H	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	414					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						AGGACAGTCAGGTAGGGGAGA	0.483																																					p.Q414H		Atlas-SNP	.											.	GLE1	42	.	0			c.G1242T						.						108	97	101					9																	131289570		2203	4300	6503	SO:0001630	splice_region_variant	2733	exon8			CAGTCAGGTAGGG	AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"GLE1 (yeast homolog)-like, RNA export mediator", "GLE1 RNA export mediator-like (yeast)", "GLE1 RNA export mediator (yeast)", "lethal congenital contracture syndrome 1", "GLE1 RNA export mediator homolog (yeast)"	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.1242+1G>T	chr9.hg19:g.131289570G>T		52.0	0.0		51.0	4.0	NM_001499	O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Missense_Mutation	SNP	ENST00000309971.4	hg19	CCDS35154.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.580575	0.65992	.	.	ENSG00000119392	ENST00000309971;ENST00000372770;ENST00000539582	T;T;T	0.73047	-0.71;-0.71;-0.71	5.66	5.66	0.87406	.	0.107189	0.64402	D	0.000003	D	0.82935	0.5145	M	0.69823	2.125	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.69307	0.963;0.957	D	0.83931	0.0306	10	0.62326	D	0.03	-28.5061	16.9119	0.86142	0.0:0.0:1.0:0.0	.	414;414	Q53GS7;Q53GS7-2	GLE1_HUMAN;.	H	414;414;160	ENSP00000308622:Q414H;ENSP00000361856:Q414H;ENSP00000438670:Q160H	ENSP00000308622:Q414H	Q	+	3	2	GLE1	130329391	1.000000	0.71417	1.000000	0.80357	0.113000	0.19764	9.430000	0.97488	2.671000	0.90904	0.650000	0.86243	CAG	.	.		0.483	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1	NM_001003722	Missense_Mutation	T	131289570	G	T	131289570	5	4	198	1	0	0	0	0	0	0	1	0	6443	1014	35	3	1272	3	GLE1	9	131289570	Splice_Site	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	42400442	131289570	9923861	56	29177										
KIAA0649	9858	hgsc.bcm.edu	37	chr9	138376480	138376480	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	acgagggcgtggagagcgcgTcggtgagcgcccgggtgcag	21	10	0	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr9:138376480T>A	ENST00000356818.2	+	4	673	c.124T>A	c.(124-126)Tcg>Acg	p.S42T	PPP1R26_ENST00000604351.1_Missense_Mutation_p.S42T|PPP1R26_ENST00000605660.1_Missense_Mutation_p.S42T|PPP1R26_ENST00000401470.3_Missense_Mutation_p.S42T|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605286.1_Missense_Mutation_p.S42T	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	42					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGAGAGCGCGTCGGTGAGCGC	0.682																																					p.S42T		Atlas-SNP	.											.	.	.	.	0			c.T124A						.						41	50	47					9																	138376480		2203	4299	6502	SO:0001583	missense	9858	exon4			AGCGCGTCGGTGA	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29089	protein-coding gene	gene with protein product	"DRIM/UTP20 interacting protein", "1A6/DRIM (down-regulated in metastasis) interacting protein"	614056	"KIAA0649"	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.124T>A	chr9.hg19:g.138376480T>A	ENSP00000349274:p.Ser42Thr	66.0	0.0		48.0	16.0	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	hg19	CCDS6988.1	.	.	.	.	.	.	.	.	.	.	T	6.921	0.539601	0.13250	.	.	ENSG00000196422	ENST00000356818;ENST00000401470	T;T	0.22945	1.93;1.93	5.32	-4.79	0.03200	.	0.574317	0.18009	N	0.154630	T	0.21062	0.0507	L	0.44542	1.39	0.19575	N	0.999969	B	0.26002	0.139	B	0.20184	0.028	T	0.23013	-1.0200	10	0.66056	D	0.02	-10.5474	18.3484	0.90329	0.0:0.0:0.2205:0.7795	.	42	Q5T8A7	PPR26_HUMAN	T	42	ENSP00000349274:S42T;ENSP00000385826:S42T	ENSP00000349274:S42T	S	+	1	0	KIAA0649	137516301	0.002000	0.14202	0.001000	0.08648	0.014000	0.08584	-0.012000	0.12699	-0.515000	0.06479	-1.542000	0.00909	TCG	.	.		0.682	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811		A	138376480	T	A	138376480	3	1	198	1	0	0	0	0	1	0	0	0	8196	1667	58	4	126	4	KIAA0649	9	138376480	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	7086910	138376480	2836951	57	29178										
PLXDC2	84898	hgsc.bcm.edu	37	chr10	20290907	20290907	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	atgggcaggacaataacactCagatcgaggtagataaatag	11	6	1	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr10:20290907C>T	ENST00000377252.4	+	2	1157	c.316C>T	c.(316-318)Cag>Tag	p.Q106*	PLXDC2_ENST00000377242.3_Nonsense_Mutation_p.Q106*	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	106					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						CAATAACACTCAGATCGAGGT	0.448																																					p.Q106X		Atlas-SNP	.											.	PLXDC2	108	.	0			c.C316T						.						62	58	59					10																	20290907		2203	4300	6503	SO:0001587	stop_gained	84898	exon2			AACACTCAGATCG	AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"tumor endothelial marker 7-related precursor"	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.316C>T	chr10.hg19:g.20290907C>T	ENSP00000366460:p.Gln106*	211.0	0.0		151.0	53.0	NM_032812	Q96E59|Q96PD9|Q96SU9	Nonsense_Mutation	SNP	ENST00000377252.4	hg19	CCDS7132.1	.	.	.	.	.	.	.	.	.	.	C	42	9.696264	0.99241	.	.	ENSG00000120594	ENST00000377252;ENST00000377242;ENST00000536022	.	.	.	5.79	4.87	0.63330	.	0.265356	0.44902	D	0.000407	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.454	0.75299	0.0:0.8519:0.1481:0.0	.	.	.	.	X	106;106;92	.	ENSP00000366450:Q106X	Q	+	1	0	PLXDC2	20330913	0.984000	0.35163	0.997000	0.53966	0.195000	0.23768	2.613000	0.46351	1.385000	0.46445	0.650000	0.86243	CAG	.	.		0.448	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		T	20290907	C	T	20290907	4	4	198	1	0	0	0	0	0	1	0	0	12127	827	29	3	322	3	PLXDC2	10	20290907	Nonsense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10		20290907	115243840	58	29179										
ARMC3	219681	hgsc.bcm.edu	37	chr10	23235105	23235105	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	atgattgaaagcaaaaaagcAgcaactgtggtgttaatgct	10	5	0	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr10:23235105A>T	ENST00000298032.5	+	3	165	c.81A>T	c.(79-81)gcA>gcT	p.A27A	ARMC3_ENST00000376528.4_Intron|ARMC3_ENST00000409983.3_Silent_p.A27A|ARMC3_ENST00000409049.3_Silent_p.A27A	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	27						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GCAAAAAAGCAGCAACTGTGG	0.318																																					p.A27A		Atlas-SNP	.											.	ARMC3	102	.	0			c.A81T						.						89	95	93					10																	23235105		2203	4300	6503	SO:0001819	synonymous_variant	219681	exon3			AAAAGCAGCAACT	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"Armadillo repeat containing"	30964	protein-coding gene	gene with protein product	"cancer/testis antigen 81"	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.81A>T	chr10.hg19:g.23235105A>T		91.0	0.0		83.0	24.0	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Silent	SNP	ENST00000298032.5	hg19	CCDS7142.1																																																																																			.	.		0.318	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		T	23235105	A	T	23235105	2	4	198	1	0	0	0	0	0	0	0	1	952	175	7	4		4	ARMC3	10	23235105	Silent	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	2944198	23235105	112299642	59	29180										
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38344426	38344426	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gtgacttcgcaccttaaagtAcaccagagaactcacacagg	8	12	1	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr10:38344426A>G	ENST00000458705.2	+	5	1529	c.1371A>G	c.(1369-1371)gtA>gtG	p.V457V	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000307441.9_Silent_p.V457V|ZNF33A_ENST00000432900.2_Silent_p.V464V|ZNF33A_ENST00000374618.3_Silent_p.V458V			Q06730	ZN33A_HUMAN	zinc finger protein 33A	457					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						ACCTTAAAGTACACCAGAGAA	0.408																																					p.V458V		Atlas-SNP	.											.	ZNF33A	103	.	0			c.A1374G						.						69	67	67					10																	38344426		2203	4300	6503	SO:0001819	synonymous_variant	7581	exon5			TAAAGTACACCAG	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.1371A>G	chr10.hg19:g.38344426A>G		137.0	0.0		97.0	32.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	hg19	CCDS31182.1																																																																																			.	.		0.408	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		G	38344426	A	G	38344426	2	3	198	1	0	0	0	0	0	0	0	1	17869	378	14	2		2	ZNF33A	10	38344426	Silent	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	15109321	38344426	97190321	60	29181										
TNKS2	80351	hgsc.bcm.edu	37	chr10	93619284	93619284	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ggcatgcgtacataggtggtAtgtttggagctggcatttat	14	5	0	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr10:93619284A>G	ENST00000371627.4	+	25	3539	c.3160A>G	c.(3160-3162)Atg>Gtg	p.M1054V		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	1054	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				CATAGGTGGTATGTTTGGAGC	0.383																																					p.M1054V		Atlas-SNP	.											.	TNKS2	103	.	0			c.A3160G						.						129	127	127					10																	93619284		2203	4300	6503	SO:0001583	missense	80351	exon25			GGTGGTATGTTTG	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.3160A>G	chr10.hg19:g.93619284A>G	ENSP00000360689:p.Met1054Val	121.0	0.0		94.0	30.0	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Missense_Mutation	SNP	ENST00000371627.4	hg19	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	A	17.24	3.338266	0.60963	.	.	ENSG00000107854	ENST00000371627	T	0.14766	2.48	5.75	5.75	0.90469	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.000000	0.85682	D	0.000000	T	0.36248	0.0960	M	0.65498	2.005	0.58432	D	0.999999	D	0.63046	0.992	D	0.68621	0.959	T	0.07770	-1.0755	10	0.87932	D	0	.	16.0432	0.80698	1.0:0.0:0.0:0.0	.	1054	Q9H2K2	TNKS2_HUMAN	V	1054	ENSP00000360689:M1054V	ENSP00000360689:M1054V	M	+	1	0	TNKS2	93609264	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.331000	0.96430	2.196000	0.70406	0.472000	0.43445	ATG	.	.		0.383	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		G	93619284	A	G	93619284	3	3	198	1	0	0	0	0	1	0	0	0	16336	449	16	2	3258	2	TNKS2	10	93619284	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	55274858	93619284	41915463	61	29182										
BTRC	8945	hgsc.bcm.edu	37	chr10	103292148	103292148	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tttactgtttacagtatgatGatcagaaaatagtaagcggc	9	5	1	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr10:103292148G>A	ENST00000370187.3	+	8	1055	c.937G>A	c.(937-939)Gat>Aat	p.D313N	BTRC_ENST00000393441.4_Missense_Mutation_p.D272N|BTRC_ENST00000408038.2_Missense_Mutation_p.D277N	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	313					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		ACAGTATGATGATCAGAAAAT	0.403																																					p.D313N		Atlas-SNP	.											.	BTRC	64	.	0			c.G937A						.						135	132	133					10																	103292148		2203	4300	6503	SO:0001583	missense	8945	exon8			TATGATGATCAGA	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.937G>A	chr10.hg19:g.103292148G>A	ENSP00000359206:p.Asp313Asn	84.0	0.0		46.0	11.0	NM_033637	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	hg19	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	G	35	5.475137	0.96291	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038	T;T;T	0.60424	0.19;0.19;0.19	5.96	5.96	0.96718	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.70037	0.3178	L	0.39020	1.185	0.80722	D	1	D;P;D	0.89917	0.999;0.784;1.0	D;P;D	0.91635	0.979;0.562;0.999	T	0.66787	-0.5835	10	0.42905	T	0.14	-16.559	20.4008	0.98991	0.0:0.0:1.0:0.0	.	287;277;313	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	N	313;272;277	ENSP00000359206:D313N;ENSP00000377088:D272N;ENSP00000385339:D277N	ENSP00000359206:D313N	D	+	1	0	BTRC	103282138	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	9.869000	0.99810	2.826000	0.97356	0.655000	0.94253	GAT	.	.		0.403	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		A	103292148	G	A	103292148	3	1	198	1	0	0	0	0	1	0	0	0	1571	1290	45	3	967	3	BTRC	10	103292148	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	9672864	103292148	32242599	62	29183										
F2	2147	hgsc.bcm.edu	37	chr11	46744939	46744939	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tttcctgttccagaatcaacTccactacccatcctggggcc	6	16	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr11:46744939T>C	ENST00000311907.5	+	6	486	c.430T>C	c.(430-432)Tcc>Ccc	p.S144P	F2_ENST00000530231.1_Missense_Mutation_p.S144P	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	144	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell surface receptor signaling pathway (GO:0007166)|cellular protein metabolic process (GO:0044267)|cytosolic calcium ion homeostasis (GO:0051480)|fibrinolysis (GO:0042730)|leukocyte migration (GO:0050900)|multicellular organismal development (GO:0007275)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|negative regulation of proteolysis (GO:0045861)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900738)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of blood coagulation (GO:0030193)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|thrombospondin receptor activity (GO:0070053)			endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	27		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|ART-123(DB05777)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Dabigatran etexilate(DB06695)|Drotrecogin alfa(DB00055)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Suramin(DB04786)|Ximelagatran(DB04898)	CAGAATCAACTCCACTACCCA	0.602																																					p.S144P	Esophageal Squamous(147;1147 1808 2148 38609 51144)	Atlas-SNP	.											.	F2	75	.	0			c.T430C						.						60	62	61					11																	46744939		2201	4299	6500	SO:0001583	missense	2147	exon6			ATCAACTCCACTA	M33031	CCDS31476.1	11p11.2	2013-02-28			ENSG00000180210	ENSG00000180210	3.4.21.5	"Endogenous ligands"	3535	protein-coding gene	gene with protein product	"prepro-coagulation factor II"	176930					Standard	NM_000506		Approved		uc001ndf.4	P00734	OTTHUMG00000150344	ENST00000311907.5:c.430T>C	chr11.hg19:g.46744939T>C	ENSP00000308541:p.Ser144Pro	124.0	0.0		117.0	42.0	NM_000506	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Missense_Mutation	SNP	ENST00000311907.5	hg19	CCDS31476.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.774718	0.00640	.	.	ENSG00000180210	ENST00000311907;ENST00000530231;ENST00000442468	T;T;T	0.78707	-1.2;-1.2;-1.2	4.87	2.56	0.30785	Kringle (4);Kringle-like fold (1);	0.410383	0.29424	N	0.012183	T	0.43211	0.1237	N	0.01091	-1.02	0.26513	N	0.974565	B	0.10296	0.003	B	0.09377	0.004	T	0.40590	-0.9555	10	0.87932	D	0	.	1.1333	0.01749	0.1342:0.1717:0.2143:0.4798	.	144	P00734	THRB_HUMAN	P	144;144;134	ENSP00000308541:S144P;ENSP00000433907:S144P;ENSP00000387413:S134P	ENSP00000308541:S144P	S	+	1	0	F2	46701515	0.006000	0.16342	0.926000	0.36857	0.165000	0.22458	0.034000	0.13776	0.362000	0.24319	-0.444000	0.05651	TCC	.	.		0.602	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1			C	46744939	T	C	46744939	3	2	198	1	0	0	0	0	1	0	0	0	5344	1551	54	2	452	2	F2	11	46744939	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10		46744939	88261577	63	29184										
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563878	55563878	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	cctctgtattttacacagttGtcaaccccatgctgaaccct	5	14	2	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr11:55563878G>T	ENST00000335605.1	+	1	847	c.847G>T	c.(847-849)Gtc>Ttc	p.V283F		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				TTACACAGTTGTCAACCCCAT	0.428																																					p.V283F		Atlas-SNP	.											.	OR5D14	116	.	0			c.G847T						.						63	60	61					11																	55563878		2200	4296	6496	SO:0001583	missense	219436	exon1			ACAGTTGTCAACC	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.847G>T	chr11.hg19:g.55563878G>T	ENSP00000334456:p.Val283Phe	71.0	0.0		66.0	20.0	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	hg19	CCDS31508.1	.	.	.	.	.	.	.	.	.	.	g	16.79	3.219575	0.58560	.	.	ENSG00000186113	ENST00000335605	T	0.00281	8.32	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39274	N	0.001401	T	0.00496	0.0016	M	0.82132	2.575	0.28139	N	0.92986	P	0.35226	0.491	P	0.46320	0.512	T	0.06499	-1.0823	10	0.87932	D	0	-33.8606	13.0021	0.58681	0.0:0.0:0.8381:0.1619	.	283	Q8NGL3	OR5DE_HUMAN	F	283	ENSP00000334456:V283F	ENSP00000334456:V283F	V	+	1	0	OR5D14	55320454	0.578000	0.26717	0.992000	0.48379	0.990000	0.78478	1.352000	0.34033	2.363000	0.80096	0.643000	0.83706	GTC	.	.		0.428	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		T	55563878	G	T	55563878	3	4	198	1	0	0	0	0	1	0	0	0	11164	1377	48	3	849	3	OR5D14	11	55563878	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	8818939	55563878	79442638	64	29185										
OR5I1	10798	hgsc.bcm.edu	37	chr11	55703216	55703216	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gactgagagaagaatgaaaaAgtaggagatgatgatgatga	14	1	0	9			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr11:55703216A>G	ENST00000301532.3	-	1	660	c.661T>C	c.(661-663)Ttt>Ctt	p.F221L		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	221					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						AGAATGAAAAAGTAGGAGATG	0.428																																					p.F221L		Atlas-SNP	.											.	OR5I1	110	.	0			c.T661C						.						45	47	46					11																	55703216		2201	4295	6496	SO:0001583	missense	10798	exon1			TGAAAAAGTAGGA	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"GPCR / Class A : Olfactory receptors"	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.661T>C	chr11.hg19:g.55703216A>G	ENSP00000301532:p.Phe221Leu	136.0	0.0		119.0	37.0	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	hg19	CCDS7949.1	.	.	.	.	.	.	.	.	.	.	A	0.959	-0.703875	0.03255	.	.	ENSG00000167825	ENST00000301532	T	0.00044	8.83	5.16	-0.149	0.13420	GPCR, rhodopsin-like superfamily (1);	0.627808	0.14174	N	0.336498	T	0.00039	0.0001	N	0.01529	-0.815	0.09310	N	1	B	0.16802	0.019	B	0.22152	0.038	T	0.32161	-0.9917	10	0.02654	T	1	.	3.2437	0.06789	0.338:0.4379:0.0826:0.1415	.	221	Q13606	OR5I1_HUMAN	L	221	ENSP00000301532:F221L	ENSP00000301532:F221L	F	-	1	0	OR5I1	55459792	0.000000	0.05858	0.069000	0.20011	0.805000	0.45488	-0.742000	0.04850	0.004000	0.14682	0.523000	0.50628	TTT	.	.		0.428	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637		G	55703216	A	G	55703216	3	3	198	1	0	0	0	0	1	0	0	0	11173	72	3	2	286	2	OR5I1	11	55703216	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	139338	55703216	79303300	65	29186										
GANAB	23193	hgsc.bcm.edu	37	chr11	62394101	62394101	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ccttcatacattctgaagacCgccgcactcgcatccatcga	6	16	2	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr11:62394101C>A	ENST00000356638.3	-	21	2469	c.2453G>T	c.(2452-2454)cGg>cTg	p.R818L	GANAB_ENST00000534779.1_Missense_Mutation_p.R726L|GANAB_ENST00000346178.4_Missense_Mutation_p.R840L|GANAB_ENST00000540933.1_Missense_Mutation_p.R721L	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	818					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	TTCTGAAGACCGCCGCACTCG	0.552																																					p.R840L	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											.	GANAB	110	.	0			c.G2519T						.						65	53	57					11																	62394101		2202	4299	6501	SO:0001583	missense	23193	exon22			GAAGACCGCCGCA	AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.2453G>T	chr11.hg19:g.62394101C>A	ENSP00000349053:p.Arg818Leu	98.0	0.0		80.0	4.0	NM_198335	A6NC20|Q8WTS9|Q9P0X0	Missense_Mutation	SNP	ENST00000356638.3	hg19	CCDS8026.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.652835	0.88056	.	.	ENSG00000089597	ENST00000346178;ENST00000356638;ENST00000534779;ENST00000540933	D;D;D;D	0.89617	-2.48;-2.45;-2.54;-2.49	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	D	0.94000	0.8078	M	0.94063	3.49	0.80722	D	1	P;P;B;B	0.50943	0.94;0.94;0.372;0.333	P;P;B;B	0.51806	0.68;0.68;0.169;0.318	D	0.95489	0.8567	10	0.87932	D	0	-12.6963	14.9217	0.70843	0.0:1.0:0.0:0.0	.	704;726;818;840	B4DIW2;E9PKU7;Q14697;Q14697-2	.;.;GANAB_HUMAN;.	L	840;818;726;721	ENSP00000340466:R840L;ENSP00000349053:R818L;ENSP00000435306:R726L;ENSP00000442962:R721L	ENSP00000340466:R840L	R	-	2	0	GANAB	62150677	0.048000	0.20356	0.998000	0.56505	0.977000	0.68977	2.735000	0.47377	2.360000	0.80028	0.563000	0.77884	CGG	.	.		0.552	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334		A	62394101	C	A	62394101	3	1	198	1	0	0	0	0	1	0	0	0	6241	652	23	1	397	1	GANAB	11	62394101	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	6690885	62394101	72612415	66	29187										
ATM	472	hgsc.bcm.edu	37	chr11	108205694	108205694	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	atcatgtttatacttttattAggtggaccacacaggagaat	8	6	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr11:108205694A>T	ENST00000452508.2	+	56	8199		c.e56-1		C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Splice_Site			Q13315	ATM_HUMAN	ATM serine/threonine kinase						brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TACTTTTATTAGGTGGACCAC	0.294			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											.		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.8011-2A>T	GRCh37	CS053445	ATM	S		.						67	67	67					11																	108205694		2201	4298	6499	SO:0001630	splice_region_variant	472	exon55	Familial Cancer Database	AT, Louis-Bar syndrome	TTTATTAGGTGGA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.8011-1A>T	chr11.hg19:g.108205694A>T		168.0	0.0		76.0	42.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Splice_Site	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.317094	0.81469	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9192	0.79547	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATM	107710904	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	8.624000	0.90961	2.164000	0.68074	0.533000	0.62120	.	.	.		0.294	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	Intron	T	108205694	A	T	108205694	5	4	198	1	0	0	0	0	0	0	1	0	1109	434	15	4	8223	4	ATM	11	108205694	Splice_Site	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	45811593	108205694	26800822	67	29188										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7548802	7548802	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	atcacaggaaacatcatcgaGccaaatttttccatatcctg	5	11	2	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr12:7548802G>T	ENST00000313599.3	-	8	1996	c.1939C>A	c.(1939-1941)Ctc>Atc	p.L647I	CD163L1_ENST00000416109.2_Missense_Mutation_p.L657I|CD163L1_ENST00000396630.1_Missense_Mutation_p.L647I			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	647	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.L647F(1)		breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						ACATCATCGAGCCAAATTTTT	0.483																																					p.L647I		Atlas-SNP	.											CD163L1,colon,carcinoma,0,1	CD163L1	238	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1939A						.						118	100	106					12																	7548802		2203	4300	6503	SO:0001583	missense	283316	exon8			CATCGAGCCAAAT	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.1939C>A	chr12.hg19:g.7548802G>T	ENSP00000315945:p.Leu647Ile	159.0	0.0		117.0	38.0	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	hg19	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.529455	0.44969	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630;ENST00000545926	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	2.23	1.28	0.21552	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.174679	0.25377	U	0.031119	T	0.59810	0.2221	M	0.81682	2.555	0.23820	N	0.996757	D;D	0.76494	0.998;0.999	D;D	0.72338	0.977;0.969	T	0.49194	-0.8965	10	0.72032	D	0.01	.	7.9604	0.30068	0.0:0.0:0.754:0.246	.	657;647	E7EVK4;Q9NR16	.;C163B_HUMAN	I	647;657;647;186	ENSP00000315945:L647I;ENSP00000393474:L657I;ENSP00000379871:L647I;ENSP00000439921:L186I	ENSP00000315945:L647I	L	-	1	0	CD163L1	7440069	0.992000	0.36948	0.639000	0.29394	0.124000	0.20399	0.319000	0.19522	0.446000	0.26666	0.557000	0.71058	CTC	.	.		0.483	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		T	7548802	G	T	7548802	3	4	198	1	0	0	0	0	1	0	0	0	2970	971	34	3	2470	3	CD163L1	12	7548802	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10		7548802	126303093	68	29189										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	57009334	57009334	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gagcagagttcaaaatccctGaagtagtagtgtgagataca	11	6	1	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr12:57009334G>A	ENST00000551812.1	-	3	393	c.200C>T	c.(199-201)tCa>tTa	p.S67L	BAZ2A_ENST00000379441.3_Missense_Mutation_p.S67L|BAZ2A_ENST00000179765.5_Missense_Mutation_p.S65L|BAZ2A_ENST00000549884.1_Missense_Mutation_p.S65L	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	67					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						CAAAATCCCTGAAGTAGTAGT	0.478																																					p.S67L		Atlas-SNP	.											.	BAZ2A	263	.	0			c.C200T						.						64	65	65					12																	57009334		2064	4213	6277	SO:0001583	missense	11176	exon3			ATCCCTGAAGTAG	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.200C>T	chr12.hg19:g.57009334G>A	ENSP00000446880:p.Ser67Leu	53.0	0.0		59.0	29.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.588382	0.86851	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884;ENST00000546695;ENST00000549506	T;T;T;T;T;T	0.14640	2.49;2.49;2.49;2.49;2.49;2.49	4.89	4.89	0.63831	.	0.270934	0.29908	N	0.010899	T	0.16385	0.0394	N	0.14661	0.345	0.39584	D	0.969489	P;D;P	0.56035	0.936;0.974;0.956	B;P;P	0.53861	0.445;0.736;0.549	T	0.04128	-1.0975	10	0.87932	D	0	.	15.4594	0.75342	0.0:0.0:1.0:0.0	.	67;65;67	B7Z8F7;F8VU39;Q9UIF9	.;.;BAZ2A_HUMAN	L	67;65;67;65;65;65	ENSP00000368754:S67L;ENSP00000179765:S65L;ENSP00000446880:S67L;ENSP00000447941:S65L;ENSP00000449496:S65L;ENSP00000447248:S65L	ENSP00000179765:S65L	S	-	2	0	BAZ2A	55295601	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.657000	0.67996	2.703000	0.92315	0.655000	0.94253	TCA	.	.		0.478	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		A	57009334	G	A	57009334	3	1	198	1	0	0	0	0	1	0	0	0	1331	1294	45	3	5625	3	BAZ2A	12	57009334	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	49460532	57009334	76842561	69	29190										
RDH16	8608	hgsc.bcm.edu	37	chr12	57348907	57348907	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gagcaactcattgggagccgTgggcaaggagatgccagcat	15	9	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr12:57348907T>C	ENST00000398138.3	-	2	1211	c.355A>G	c.(355-357)Acg>Gcg	p.T119A	RDH16_ENST00000360752.4_Intron	NM_003708.3	NP_003699.3	O75452	RDH16_HUMAN	retinol dehydrogenase 16 (all-trans)	119					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	electron carrier activity (GO:0009055)|retinol dehydrogenase activity (GO:0004745)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)	16						TTGGGAGCCGTGGGCAAGGAG	0.552																																					p.T119A	GBM(179;741 2921 43105 45298)	Atlas-SNP	.											.	RDH16	33	.	0			c.A355G						.						80	77	78					12																	57348907		2078	4224	6302	SO:0001583	missense	8608	exon2			GAGCCGTGGGCAA		CCDS41797.1	12q13.3	2011-09-14	2006-05-09			ENSG00000139547		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	29674	protein-coding gene	gene with protein product	"microsomal NAD+ dependent retinol dehydrogenase 4", "short chain dehydrogenase/reductase family 9C, member 8"		"retinol dehydrogenase 16 (all-trans and 13-cis)"			9677409, 10329026, 19027726	Standard	NM_003708		Approved	RODH-4, SDR9C8	uc001smi.4	O75452		ENST00000398138.3:c.355A>G	chr12.hg19:g.57348907T>C	ENSP00000381206:p.Thr119Ala	116.0	0.0		101.0	40.0	NM_003708	Q9UNV2	Missense_Mutation	SNP	ENST00000398138.3	hg19	CCDS41797.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.191656	0.00302	.	.	ENSG00000139547	ENST00000398138	D	0.87334	-2.24	5.02	-10.0	0.00425	NAD(P)-binding domain (1);	2.782010	0.00973	N	0.003261	T	0.69133	0.3077	N	0.11673	0.155	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.58317	-0.7657	10	0.16896	T	0.51	.	4.4075	0.11416	0.127:0.2436:0.0528:0.5765	.	119	O75452	RDH16_HUMAN	A	119	ENSP00000381206:T119A	ENSP00000381206:T119A	T	-	1	0	RDH16	55635174	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.716000	0.00102	-5.503000	0.00013	-3.099000	0.00064	ACG	.	.		0.552	RDH16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410898.1	NM_003708		C	57348907	T	C	57348907	3	2	198	1	0	0	0	0	1	0	0	0	13209	1696	59	2	610	2	RDH16	12	57348907	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	339573	57348907	76502988	70	29191										
TAOK3	51347	hgsc.bcm.edu	37	chr12	118588895	118588895	+	Missense_Mutation	SNP	T	T	A													0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	aaagtttcaatctctcgctcTtgcctttccaataggttctt							TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr12:118588895T>A	ENST00000392533.3	-	21	3094	c.2604A>T	c.(2602-2604)caA>caT	p.Q868H	TAOK3_ENST00000537952.1_Missense_Mutation_p.Q408H|TAOK3_ENST00000536979.1_Missense_Mutation_p.Q63H|TAOK3_ENST00000419821.2_Missense_Mutation_p.Q868H|TAOK3_ENST00000543709.1_Intron	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	868					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCTCTCGCTCTTGCCTTTCCA	0.423																																					p.Q868H		Atlas-SNP	.											.	TAOK3	151	.	0			c.A2604T						.						164	165	165					12																	118588895		2203	4300	6503	SO:0001583	missense	51347	exon21			TCGCTCTTGCCTT	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.2604A>T	chr12.hg19:g.118588895T>A	ENSP00000376317:p.Gln868His	95.0	0.0		76.0	33.0	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Missense_Mutation	SNP	ENST00000392533.3	hg19	CCDS9188.1	.	.	.	.	.	.	.	.	.	.	T	10.74	1.434950	0.25813	.	.	ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000536979;ENST00000537952	T;T;T;T	0.52983	0.64;0.64;0.64;0.64	5.34	4.19	0.49359	.	0.000000	0.85682	D	0.000000	T	0.41926	0.1180	L	0.47016	1.485	0.53688	D	0.999971	P	0.39391	0.671	B	0.44163	0.443	T	0.16453	-1.0402	10	0.20519	T	0.43	.	7.442	0.27190	0.0:0.2414:0.0:0.7586	.	868	Q9H2K8	TAOK3_HUMAN	H	868;868;63;408	ENSP00000416374:Q868H;ENSP00000376317:Q868H;ENSP00000441932:Q63H;ENSP00000443834:Q408H	ENSP00000376317:Q868H	Q	-	3	2	TAOK3	117073278	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.485000	0.45250	1.036000	0.39998	0.533000	0.62120	CAA	.	.		0.423	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281		A	118588895	T	A	118588895	3	1	198	1	0	0	0	0	1	0	0	0	15564	1606	56	4	96	4	TAOK3	12	118588895	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	61239988	118588895	15263000	71	29192	149	2								
TAOK3	51347	hgsc.bcm.edu	37	chr12	118588900	118588900	+	Missense_Mutation	SNP	T	T	A													0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ttcaatctctcgctcttgccTttccaataggttctttattc							TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr12:118588900T>A	ENST00000392533.3	-	21	3089	c.2599A>T	c.(2599-2601)Agg>Tgg	p.R867W	TAOK3_ENST00000537952.1_Missense_Mutation_p.R407W|TAOK3_ENST00000536979.1_Missense_Mutation_p.R62W|TAOK3_ENST00000419821.2_Missense_Mutation_p.R867W|TAOK3_ENST00000543709.1_5'UTR	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	867					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGCTCTTGCCTTTCCAATAGG	0.433																																					p.R867W		Atlas-SNP	.											.	TAOK3	151	.	0			c.A2599T						.						161	162	161					12																	118588900		2203	4300	6503	SO:0001583	missense	51347	exon21			CTTGCCTTTCCAA	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.2599A>T	chr12.hg19:g.118588900T>A	ENSP00000376317:p.Arg867Trp	95.0	0.0		76.0	34.0	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Missense_Mutation	SNP	ENST00000392533.3	hg19	CCDS9188.1	.	.	.	.	.	.	.	.	.	.	T	17.62	3.434824	0.62955	.	.	ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000536979;ENST00000537952	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.74935	0.3782	M	0.80183	2.485	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.78542	-0.2164	10	0.87932	D	0	.	11.377	0.49735	0.0:0.0:0.1513:0.8487	.	867	Q9H2K8	TAOK3_HUMAN	W	867;867;62;407	ENSP00000416374:R867W;ENSP00000376317:R867W;ENSP00000441932:R62W;ENSP00000443834:R407W	ENSP00000376317:R867W	R	-	1	2	TAOK3	117073283	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.339000	0.65953	2.212000	0.71576	0.533000	0.62120	AGG	.	.		0.433	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281		A	118588900	T	A	118588900	3	1	198	1	0	0	0	0	1	0	0	0	15564	1608	56	4	101	4	TAOK3	12	118588900	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	5	118588900	15262995	72	29193	149	2								
ZNF605	100289635	hgsc.bcm.edu	37	chr12	133502153	133502153	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tgtatgaattctctgatgtaTaatcagctgtgccttctcaa	7	8	3	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr12:133502153T>C	ENST00000360187.4	-	5	2080	c.1732A>G	c.(1732-1734)Ata>Gta	p.I578V	ZNF605_ENST00000331711.7_5'Flank|ZNF605_ENST00000392321.3_Missense_Mutation_p.I609V	NM_183238.3	NP_899061.1	Q86T29	ZN605_HUMAN	zinc finger protein 605	578					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(16)|large_intestine(5)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00227)|all_epithelial(31;0.142)		OV - Ovarian serous cystadenocarcinoma(86;9.24e-09)|Epithelial(86;2.11e-07)|all cancers(50;5.27e-06)		CTCTGATGTATAATCAGCTGT	0.403																																					p.I609V		Atlas-SNP	.											.	ZNF605	50	.	0			c.A1825G						.						129	120	123					12																	133502153		2203	4300	6503	SO:0001583	missense	100289635	exon5			GATGTATAATCAG	AL832623	CCDS31938.1, CCDS53850.1	12q24.33	2013-01-08	2009-09-11	2009-09-11		ENSG00000196458		"Zinc fingers, C2H2-type", "-"	28068	protein-coding gene	gene with protein product							Standard	NM_183238		Approved		uc001uli.3	Q86T29		ENST00000360187.4:c.1732A>G	chr12.hg19:g.133502153T>C	ENSP00000353314:p.Ile578Val	87.0	0.0		80.0	34.0	NM_001164715	B3KVG4|D3DXJ0|Q86T91	Missense_Mutation	SNP	ENST00000360187.4	hg19	CCDS31938.1	.	.	.	.	.	.	.	.	.	.	T	0.223	-1.027080	0.02045	.	.	ENSG00000196458	ENST00000360187;ENST00000392321	T;T	0.14766	3.12;2.48	3.72	1.26	0.21427	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.492139	0.15144	N	0.278103	T	0.04407	0.0121	N	0.02751	-0.505	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.12837	0.008;0.005	T	0.44832	-0.9302	10	0.13853	T	0.58	.	5.6193	0.17448	0.0:0.0961:0.1725:0.7314	.	609;578	B3KVG4;Q86T29	.;ZN605_HUMAN	V	578;609	ENSP00000353314:I578V;ENSP00000376135:I609V	ENSP00000353314:I578V	I	-	1	0	ZNF605	132012226	0.000000	0.05858	0.415000	0.26534	0.992000	0.81027	-0.626000	0.05527	0.149000	0.19098	0.379000	0.24179	ATA	.	.		0.403	ZNF605-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397135.2	NM_183238		C	133502153	T	C	133502153	3	2	198	1	0	0	0	0	1	0	0	0	18046	1406	49	2	197	2	ZNF605	12	133502153	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	14913253	133502153	349742	73	29194										
PCDH8	5100	hgsc.bcm.edu	37	chr13	53422433	53422433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	caggtcctcggccagggtccCgatgaccgtgccgggggcat	16	14	0	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr13:53422433C>T	ENST00000377942.3	-	1	342	c.139G>A	c.(139-141)Ggg>Agg	p.G47R	PCDH8_ENST00000338862.4_Missense_Mutation_p.G47R	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	47	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		GCCAGGGTCCCGATGACCGTG	0.602																																					p.G47R	GBM(36;25 841 9273 49207)	Atlas-SNP	.											.	PCDH8	95	.	0			c.G139A						.						96	91	93					13																	53422433		2203	4300	6503	SO:0001583	missense	5100	exon1			GGGTCCCGATGAC	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"Cadherins / Protocadherins : Non-clustered"	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.139G>A	chr13.hg19:g.53422433C>T	ENSP00000367177:p.Gly47Arg	54.0	0.0		51.0	26.0	NM_032949	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	hg19	CCDS9438.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650202	0.87958	.	.	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.45668	0.89;0.89	5.51	5.51	0.81932	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.44688	D	0.000421	T	0.77980	0.4212	H	0.97186	3.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.85611	0.1258	10	0.87932	D	0	.	19.4153	0.94694	0.0:1.0:0.0:0.0	.	47;47	O95206-2;O95206	.;PCDH8_HUMAN	R	47	ENSP00000367177:G47R;ENSP00000341350:G47R	ENSP00000341350:G47R	G	-	1	0	PCDH8	52320434	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.783000	0.85696	2.595000	0.87683	0.561000	0.74099	GGG	.	.		0.602	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590		T	53422433	C	T	53422433	3	4	198	1	0	0	0	0	1	0	0	0	11526	652	23	1	3085	1	PCDH8	13	53422433	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10		53422433	61747445	74	29195										
REC8	9985	hgsc.bcm.edu	37	chr14	24646411	24646411	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	cctgctgatcgcagaggaagAagctatcttgttagaaagta	11	7	1	4	rs370800103		TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr14:24646411A>C	ENST00000311457.3	+	9	1285	c.686A>C	c.(685-687)gAa>gCa	p.E229A	REC8_ENST00000559919.1_Missense_Mutation_p.E229A			O95072	REC8_HUMAN	REC8 meiotic recombination protein	229	Glu-rich.				double-strand break repair via homologous recombination (GO:0000724)|fertilization (GO:0009566)|linear element assembly (GO:0030999)|male meiosis I (GO:0007141)|meiotic nuclear division (GO:0007126)|oocyte maturation (GO:0001556)|reciprocal meiotic recombination (GO:0007131)|seminiferous tubule development (GO:0072520)|sister chromatid cohesion (GO:0007062)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)	condensed nuclear chromosome kinetochore (GO:0000778)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear meiotic cohesin complex (GO:0034991)|nucleus (GO:0005634)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(265;0.00839)		GCAGAGGAAGAAGCTATCTTG	0.587																																					p.E229A	NSCLC(139;1764 2537 12868 49041)	Atlas-SNP	.											.,1	REC8	47	.	0			c.A686C						.						66	71	69					14																	24646411		1927	4122	6049	SO:0001583	missense	9985	exon8			AGGAAGAAGCTAT	AF006264	CCDS41932.1	14q11.2-q12	2013-08-06	2013-08-06	2007-04-03		ENSG00000100918			16879	protein-coding gene	gene with protein product		608193	"REC8-like 1 (yeast)", "REC8 homolog (yeast)"	REC8L1		10207075, 15935783, 12759374	Standard	NM_005132		Approved	Rec8p, kleisin-alpha	uc001wms.3	O95072		ENST00000311457.3:c.686A>C	chr14.hg19:g.24646411A>C	ENSP00000308699:p.Glu229Ala	64.0	0.0		86.0	8.0	NM_001048205	A8K576|D3DS62|Q658V5|Q6IA92|Q8WUV8|Q9BTF2|Q9NVQ9	Missense_Mutation	SNP	ENST00000311457.3	hg19	CCDS41932.1	.	.	.	.	.	.	.	.	.	.	A	14.38	2.519143	0.44866	.	.	ENSG00000100918	ENST00000311457;ENST00000447460	T	0.26810	1.71	5.31	4.17	0.49024	.	0.367956	0.27715	N	0.018154	T	0.15565	0.0375	N	0.24115	0.695	0.22001	N	0.999423	B;B	0.13594	0.008;0.005	B;B	0.15052	0.012;0.005	T	0.18209	-1.0344	10	0.29301	T	0.29	-4.7435	7.7943	0.29138	0.9077:0.0:0.0923:0.0	.	230;230	O95072-2;O95072	.;REC8_HUMAN	A	229	ENSP00000308699:E229A	ENSP00000308699:E229A	E	+	2	0	REC8	23716251	0.948000	0.32251	0.794000	0.32065	0.471000	0.32888	2.087000	0.41653	1.040000	0.40099	0.459000	0.35465	GAA	.	.		0.587	REC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415889.3	NM_005132		C	24646411	A	C	24646411	3	2	198	1	0	0	0	0	1	0	0	0	13214	246	9	5	716	5	REC8	14	24646411	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10		24646411	82703129	75	29196										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33290708	33290708	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	cataagtaacaagttaattaGtttgaatgaggaatcaaatg	8	3	1	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr14:33290708G>T	ENST00000280979.4	+	13	3859	c.3689G>T	c.(3688-3690)aGt>aTt	p.S1230I	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1230					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		AAGTTAATTAGTTTGAATGAG	0.423																																					p.S1230I	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.G3689T						.						127	117	120					14																	33290708		2203	4300	6503	SO:0001583	missense	9472	exon13			TAATTAGTTTGAA	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.3689G>T	chr14.hg19:g.33290708G>T	ENSP00000280979:p.Ser1230Ile	164.0	0.0		129.0	34.0	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.578505	0.46006	.	.	ENSG00000151320	ENST00000280979	T	0.06608	3.28	6.03	5.14	0.70334	.	0.101862	0.64402	D	0.000002	T	0.23649	0.0572	M	0.65975	2.015	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.00670	-1.1617	10	0.87932	D	0	-12.48	15.2809	0.73784	0.0667:0.0:0.9333:0.0	.	1230	Q13023	AKAP6_HUMAN	I	1230	ENSP00000280979:S1230I	ENSP00000280979:S1230I	S	+	2	0	AKAP6	32360459	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.159000	0.77483	1.567000	0.49668	-0.136000	0.14681	AGT	.	.		0.423	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33290708	G	T	33290708	3	4	198	1	0	0	0	0	1	0	0	0	455	1029	36	3	3735	3	AKAP6	14	33290708	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	8644297	33290708	74058832	76	29197										
FANCM	57697	hgsc.bcm.edu	37	chr14	45658071	45658071	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	atgaagaggagtcttgcaaaGgccaatcaagtgaagaagaa	12	5	2	5			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr14:45658071G>A	ENST00000267430.5	+	20	4931	c.4846G>A	c.(4846-4848)Ggc>Agc	p.G1616S	FANCM_ENST00000542564.2_Missense_Mutation_p.G1590S	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1616					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						GTCTTGCAAAGGCCAATCAAG	0.308								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G1616S		Atlas-SNP	.											.	FANCM	225	.	0			c.G4846A						.						86	88	87					14																	45658071		2203	4298	6501	SO:0001583	missense	57697	exon20	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGCAAAGGCCAAT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.4846G>A	chr14.hg19:g.45658071G>A	ENSP00000267430:p.Gly1616Ser	202.0	0.0		174.0	59.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.212|0.212	-1.035407|-1.035407	0.02029|0.02029	.|.	.|.	ENSG00000187790|ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250|ENST00000554809	T;T;T|.	0.75938|.	-0.98;-0.98;-0.98|.	5.56|5.56	2.91|2.91	0.33838|0.33838	.|.	3.357770|.	0.00496|.	N|.	0.000143|.	T|T	0.04543|0.04543	0.0124|0.0124	N|N	0.00116|0.00116	-2.08|-2.08	0.23010|0.23010	N|N	0.998439|0.998439	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.37244|0.37244	-0.9714|-0.9714	10|5	0.08179|.	T|.	0.78|.	.|.	5.6929|5.6929	0.17839|0.17839	0.6844:0.0:0.078:0.2376|0.6844:0.0:0.078:0.2376	.|.	1590;1616|.	B2RTQ9;Q8IYD8|.	.;FANCM_HUMAN|.	S|K	1616;1590;1132|548	ENSP00000267430:G1616S;ENSP00000442493:G1590S;ENSP00000452033:G1132S|.	ENSP00000267430:G1616S|.	G|R	+|+	1|2	0|0	FANCM|FANCM	44727821|44727821	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.401000|0.401000	0.30781|0.30781	2.753000|2.753000	0.47524|0.47524	1.036000|1.036000	0.39998|0.39998	-0.300000|-0.300000	0.09419|0.09419	GGC|AGG	.	.		0.308	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		A	45658071	G	A	45658071	3	1	198	1	0	0	0	0	1	0	0	0	5679	1000	35	3	4924	3	FANCM	14	45658071	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	12367363	45658071	61691469	77	29198										
VSX2	338917	hgsc.bcm.edu	37	chr14	74727375	74727375	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	acgccaggccctgcccaagcTcgacaagatggagcaggacg	13	14	0	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr14:74727375T>C	ENST00000261980.2	+	5	929	c.839T>C	c.(838-840)cTc>cCc	p.L280P		NM_182894.2	NP_878314.1	P58304	VSX2_HUMAN	visual system homeobox 2	280					cell fate commitment (GO:0045165)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7				BRCA - Breast invasive adenocarcinoma(234;0.00154)		CTGCCCAAGCTCGACAAGATG	0.627																																					p.L280P		Atlas-SNP	.											.	VSX2	32	.	0			c.T839C						.						15	17	16					14																	74727375		2193	4295	6488	SO:0001583	missense	338917	exon5			CCAAGCTCGACAA	AC005519	CCDS9827.1	14q24.3	2011-06-20	2007-08-21	2007-08-21		ENSG00000119614		"Homeoboxes / PRD class"	1975	protein-coding gene	gene with protein product		142993	"C elegans ceh-10 homeo domain-containing homolog", "ceh-10 homeo domain containing homolog (C. elegans)", "ceh-10 homeodomain containing homolog (C. elegans)"	HOX10, CHX10		1973146	Standard	NM_182894		Approved	RET1	uc001xpq.3	P58304		ENST00000261980.2:c.839T>C	chr14.hg19:g.74727375T>C	ENSP00000261980:p.Leu280Pro	414.0	1.0		394.0	142.0	NM_182894	A1A4X6	Missense_Mutation	SNP	ENST00000261980.2	hg19	CCDS9827.1	.	.	.	.	.	.	.	.	.	.	T	7.413	0.635203	0.14322	.	.	ENSG00000119614	ENST00000261980	D	0.91068	-2.78	4.83	4.83	0.62350	.	0.419222	0.26546	N	0.023778	T	0.81202	0.4773	N	0.16478	0.41	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.75379	-0.3338	10	0.30078	T	0.28	.	9.1372	0.36881	0.0:0.0817:0.0:0.9183	.	280	P58304	VSX2_HUMAN	P	280	ENSP00000261980:L280P	ENSP00000261980:L280P	L	+	2	0	VSX2	73797128	0.324000	0.24652	0.896000	0.35187	0.325000	0.28411	0.572000	0.23684	2.017000	0.59298	0.533000	0.62120	CTC	.	.		0.627	VSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412323.1	NM_182894		C	74727375	T	C	74727375	3	2	198	1	0	0	0	0	1	0	0	0	17247	1551	54	2	857	2	VSX2	14	74727375	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	29069304	74727375	32622165	78	29199										
ESRRB	2103	hgsc.bcm.edu	37	chr14	76948999	76948999	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gacaagctctatgccatgccTccccctggtatgcctgaggg	11	14	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr14:76948999T>C	ENST00000509242.1	+	6	782	c.684T>C	c.(682-684)ccT>ccC	p.P228P	ESRRB_ENST00000380887.2_Silent_p.P228P|ESRRB_ENST00000556177.1_Silent_p.P228P|ESRRB_ENST00000261532.7_Silent_p.P228P	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	228					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		ATGCCATGCCTCCCCCTGGTA	0.552																																					p.P228P		Atlas-SNP	.											.	ESRRB	114	.	0			c.T684C						.						106	84	92					14																	76948999		2203	4300	6503	SO:0001819	synonymous_variant	2103	exon7			CATGCCTCCCCCT	X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715		"Nuclear hormone receptors"	3473	protein-coding gene	gene with protein product		602167	"deafness, autosomal recessive 35"	ESRL2, DFNB35		3267207, 9344655, 18179891	Standard	NM_004452		Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000509242.1:c.684T>C	chr14.hg19:g.76948999T>C		134.0	0.0		109.0	5.0	NM_004452	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Silent	SNP	ENST00000509242.1	hg19	CCDS9850.2																																																																																			.	.		0.552	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1			C	76948999	T	C	76948999	2	2	198	1	0	0	0	0	0	0	0	1	5263	1538	54	2		2	ESRRB	14	76948999	Silent	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	2221624	76948999	30400541	79	29200										
C14orf49	161176	hgsc.bcm.edu	37	chr14	95932451	95932451	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tggctcagctgccactgcttCtccttcaggcccagctggag	11	15	3	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr14:95932451C>T	ENST00000334258.5	-	3	458	c.444G>A	c.(442-444)gaG>gaA	p.E148E	SYNE3_ENST00000557275.1_Silent_p.E148E|SYNE3_ENST00000553340.1_Silent_p.E148E	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	148					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						GCCACTGCTTCTCCTTCAGGC	0.632																																					p.E148E		Atlas-SNP	.											.	SYNE3	130	.	0			c.G444A						.						61	60	60					14																	95932451		2203	4300	6503	SO:0001819	synonymous_variant	161176	exon3			CTGCTTCTCCTTC	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.444G>A	chr14.hg19:g.95932451C>T		69.0	0.0		52.0	19.0	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	hg19	CCDS9935.1																																																																																			.	.		0.632	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		T	95932451	C	T	95932451	2	4	198	1	0	0	0	0	0	0	0	1	1778	912	32	3		3	C14orf49	14	95932451	Silent	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	18983452	95932451	11417089	80	29201										
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40313196	40313196	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	agaaactctggacagcaggcAtcacagcagaaatcatgtac	9	10	3	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr15:40313196A>G	ENST00000263791.5	+	31	4313	c.4270A>G	c.(4270-4272)Atc>Gtc	p.I1424V	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.I1396V	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	1424	Histidyl-tRNA synthetase-like.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		GACAGCAGGCATCACAGCAGA	0.473																																					p.I1424V		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.A4270G						.						112	105	107					15																	40313196		2010	4175	6185	SO:0001583	missense	440275	exon31			GCAGGCATCACAG	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.4270A>G	chr15.hg19:g.40313196A>G	ENSP00000263791:p.Ile1424Val	182.0	0.0		165.0	68.0	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	hg19	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	A	12.31	1.898402	0.33535	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.58940	0.3;0.3	5.62	4.48	0.54585	Anticodon-binding (1);Serine/threonine-protein kinase GCN2, anticodon binding domain (1);	0.132843	0.56097	D	0.000034	T	0.43344	0.1243	L	0.27053	0.805	0.47698	D	0.999495	B;B	0.17038	0.016;0.02	B;B	0.22601	0.024;0.04	T	0.34725	-0.9817	10	0.62326	D	0.03	-17.6747	8.2194	0.31532	0.7953:0.1355:0.0692:0.0	.	1396;1424	Q9P2K8-2;Q9P2K8	.;E2AK4_HUMAN	V	1424;1396	ENSP00000263791:I1424V;ENSP00000372174:I1396V	ENSP00000263791:I1424V	I	+	1	0	EIF2AK4	38100488	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.491000	0.53252	1.043000	0.40175	0.533000	0.62120	ATC	.	.		0.473	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			G	40313196	A	G	40313196	3	3	198	1	0	0	0	0	1	0	0	0	5001	217	8	2	4392	2	EIF2AK4	15	40313196	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10		40313196	62218196	81	29202										
RFX7	64864	hgsc.bcm.edu	37	chr15	56385746	56385746	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	taaagtgttcaaatcattgaTgctgcctgagagctcagaag	10	7	3	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr15:56385746T>C	ENST00000559447.2	-	9	4160	c.3889A>G	c.(3889-3891)Atc>Gtc	p.I1297V	RFX7_ENST00000423270.1_Missense_Mutation_p.I1394V|RFX7_ENST00000317318.6_Intron|RFX7_ENST00000422057.1_Intron			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	1297					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						AAATCATTGATGCTGCCTGAG	0.448																																					p.I1394V		Atlas-SNP	.											.	RFX7	170	.	0			c.A4180G						.						80	75	76					15																	56385746		1964	4136	6100	SO:0001583	missense	64864	exon9			CATTGATGCTGCC			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.3889A>G	chr15.hg19:g.56385746T>C	ENSP00000453281:p.Ile1297Val	97.0	0.0		70.0	25.0	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.46	3.130091	0.56721	.	.	ENSG00000181827	ENST00000423270	T	0.59364	0.27	5.77	5.77	0.91146	.	0.000000	0.49916	U	0.000134	T	0.67097	0.2857	L	0.32530	0.975	0.80722	D	1	D	0.64830	0.994	D	0.72625	0.978	T	0.70249	-0.4924	10	0.87932	D	0	-10.959	15.5635	0.76269	0.0:0.0:0.0:1.0	.	1297	Q2KHR2	RFX7_HUMAN	V	1394	ENSP00000397644:I1394V	ENSP00000397644:I1394V	I	-	1	0	RFX7	54173038	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.594000	0.82698	2.326000	0.78906	0.533000	0.62120	ATC	.	.		0.448	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		C	56385746	T	C	56385746	3	2	198	1	0	0	0	0	1	0	0	0	13283	1464	51	2	206	2	RFX7	15	56385746	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	16072550	56385746	46145646	82	29203										
PRSS36	146547	hgsc.bcm.edu	37	chr16	31153852	31153852	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gtaggcagggcagagcgcgtGcggcgggtctccgggcagcg	21	11	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr16:31153852G>T	ENST00000268281.4	-	10	1529	c.1471C>A	c.(1471-1473)Cac>Aac	p.H491N	PRSS36_ENST00000418068.2_Missense_Mutation_p.H491N|PRSS36_ENST00000569305.1_Missense_Mutation_p.H491N	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	491	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						CAGAGCGCGTGCGGCGGGTCT	0.746																																					p.H491N		Atlas-SNP	.											.	PRSS36	50	.	0			c.C1471A						.						1	2	2					16																	31153852		1137	2498	3635	SO:0001583	missense	146547	exon10			GCGCGTGCGGCGG	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"Serine peptidases / Serine peptidases"	26906	protein-coding gene	gene with protein product	"polyserase 2"	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.1471C>A	chr16.hg19:g.31153852G>T	ENSP00000268281:p.His491Asn	30.0	0.0		26.0	17.0	NM_001258291	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	hg19	CCDS32436.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.633780	0.47049	.	.	ENSG00000178226	ENST00000268281;ENST00000418068	T;T	0.26067	1.76;1.76	5.42	2.17	0.27698	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (2);	.	.	.	.	T	0.13286	0.0322	N	0.10782	0.045	0.09310	N	1	B;B;B	0.25007	0.025;0.057;0.116	B;B;B	0.22152	0.026;0.01;0.038	T	0.23583	-1.0184	9	0.23302	T	0.38	.	10.9399	0.47268	0.0:0.2535:0.6168:0.1296	.	491;491;491	E7EX56;B7ZMK8;Q5K4E3	.;.;POLS2_HUMAN	N	491	ENSP00000268281:H491N;ENSP00000407160:H491N	ENSP00000268281:H491N	H	-	1	0	PRSS36	31061353	0.025000	0.19082	0.691000	0.30163	0.920000	0.55202	1.342000	0.33919	1.261000	0.44149	-0.282000	0.10007	CAC	.	.		0.746	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502		T	31153852	G	T	31153852	3	4	198	1	0	0	0	0	1	0	0	0	12637	1319	46	3	1120	3	PRSS36	16	31153852	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10		31153852	59200901	83	29204										
CRK	1398	hgsc.bcm.edu	37	chr17	1359301	1359301	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gggctggtgctcgagtcccgCaccaggaacaccccgtgccg	14	16	0	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr17:1359301C>T	ENST00000300574.2	-	1	251	c.111G>A	c.(109-111)gtG>gtA	p.V37V	CRK_ENST00000574295.1_Silent_p.V37V|CRK_ENST00000398970.5_Silent_p.V37V|CRK_ENST00000572145.1_Intron	NM_016823.3	NP_058431.2	P46108	CRK_HUMAN	v-crk avian sarcoma virus CT10 oncogene homolog	37	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPKK activity (GO:0000186)|blood coagulation (GO:0007596)|ephrin receptor signaling pathway (GO:0048013)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Rho GTPase activity (GO:0032319)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|SH2 domain binding (GO:0042169)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(2)	9				UCEC - Uterine corpus endometrioid carcinoma (25;0.083)		TCGAGTCCCGCACCAGGAACA	0.682																																					p.V37V		Atlas-SNP	.											.	CRK	14	.	0			c.G111A						.						30	33	32					17																	1359301		2201	4298	6499	SO:0001819	synonymous_variant	1398	exon1			GTCCCGCACCAGG	D10656	CCDS11002.1, CCDS45561.1	17p13	2013-07-09	2013-07-09		ENSG00000167193	ENSG00000167193		"SH2 domain containing"	2362	protein-coding gene	gene with protein product		164762				1690891	Standard	NM_005206		Approved		uc002fsl.3	P46108	OTTHUMG00000090317	ENST00000300574.2:c.111G>A	chr17.hg19:g.1359301C>T		82.0	0.0		51.0	19.0	NM_016823	A8MWE8|B0LPE8|D3DTH6|Q96GA9|Q96HJ0	Silent	SNP	ENST00000300574.2	hg19	CCDS11002.1																																																																																			.	.		0.682	CRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206679.1	NM_016823		T	1359301	C	T	1359301	2	4	198	1	0	0	0	0	0	0	0	1	3886	697	25	3		3	CRK	17	1359301	Silent	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10		1359301	79835909	84	29205										
WDR81	124997	hgsc.bcm.edu	37	chr17	1630159	1630159	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ttccaaatggagtgggccggCcagttttagaggccactccc	12	12	0	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr17:1630159C>T	ENST00000409644.1	+	1	1906	c.1906C>T	c.(1906-1908)Cca>Tca	p.P636S	WDR81_ENST00000437219.2_Intron|WDR81_ENST00000419248.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000309182.5_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	636					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGTGGGCCGGCCAGTTTTAGA	0.597																																					p.P636S		Atlas-SNP	.											.	WDR81	180	.	0			c.C1906T						.						9	10	10					17																	1630159		690	1584	2274	SO:0001583	missense	124997	exon1			GGCCGGCCAGTTT	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"WD repeat domain containing"	26600	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 166"	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.1906C>T	chr17.hg19:g.1630159C>T	ENSP00000386609:p.Pro636Ser	72.0	0.0		72.0	36.0	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	hg19	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.968417	0.00457	.	.	ENSG00000167716	ENST00000409644	T	0.48201	0.82	5.59	-0.761	0.11038	.	.	.	.	.	T	0.28134	0.0694	.	.	.	0.23956	N	0.996352	.	.	.	.	.	.	T	0.24870	-1.0148	6	0.21014	T	0.42	.	4.2563	0.10719	0.2182:0.5359:0.1067:0.1392	.	.	.	.	S	636	ENSP00000386609:P636S	ENSP00000386609:P636S	P	+	1	0	WDR81	1576909	0.019000	0.18553	0.050000	0.19076	0.040000	0.13550	0.004000	0.13106	0.028000	0.15324	0.462000	0.41574	CCA	.	.		0.597	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		T	1630159	C	T	1630159	3	4	198	1	0	0	0	0	1	0	0	0	17345	739	26	3	1970	3	WDR81	17	1630159	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	270858	1630159	79565051	85	29206										
NLRP1	22861	hgsc.bcm.edu	37	chr17	5463296	5463296	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ctggtgtgcgcctgtgggggCgttcctaccaccgctgccca	14	15	0	0	rs369131551		TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr17:5463296C>T	ENST00000572272.1	-	4	719	c.720G>A	c.(718-720)acG>acA	p.T240T	NLRP1_ENST00000577119.1_Silent_p.T240T|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000354411.3_Silent_p.T240T|NLRP1_ENST00000269280.4_Silent_p.T240T|NLRP1_ENST00000262467.5_Silent_p.T240T|NLRP1_ENST00000345221.3_Silent_p.T240T			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	240					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				CCTGTGGGGGCGTTCCTACCA	0.547																																					p.T240T		Atlas-SNP	.											.	NLRP1	358	.	0			c.G720A						.						58	64	62					17																	5463296		2203	4300	6503	SO:0001819	synonymous_variant	22861	exon4			TGGGGGCGTTCCT	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.720G>A	chr17.hg19:g.5463296C>T		95.0	0.0		82.0	30.0	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Silent	SNP	ENST00000572272.1	hg19	CCDS42246.1																																																																																			.	.		0.547	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		T	5463296	C	T	5463296	2	4	198	1	0	0	0	0	0	0	0	1	10480	755	27	1		1	NLRP1	17	5463296	Silent	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	3833137	5463296	75731914	86	29207										
PIK3R5	23533	hgsc.bcm.edu	37	chr17	8791704	8791704	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gggcccgggaagggggtgatActggttcgtccagggggctg	21	8	0	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr17:8791704A>G	ENST00000447110.1	-	10	1524	c.1400T>C	c.(1399-1401)gTa>gCa	p.V467A	PIK3R5_ENST00000581552.1_Missense_Mutation_p.V467A|PIK3R5_ENST00000584803.1_Missense_Mutation_p.V467A	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	467					blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						AGGGGGTGATACTGGTTCGTC	0.716																																					p.V467A	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.T1400C						.						8	11	10					17																	8791704		2171	4263	6434	SO:0001583	missense	23533	exon10			GGTGATACTGGTT	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.1400T>C	chr17.hg19:g.8791704A>G	ENSP00000392812:p.Val467Ala	70.0	0.0		58.0	4.0	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Missense_Mutation	SNP	ENST00000447110.1	hg19	CCDS11147.1	.	.	.	.	.	.	.	.	.	.	A	3.544	-0.093128	0.07053	.	.	ENSG00000141506	ENST00000269300;ENST00000447110	T	0.76316	-1.01	4.86	-8.76	0.00830	.	1.545490	0.03334	N	0.193745	T	0.48484	0.1502	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48896	-0.8994	10	0.07030	T	0.85	6.3151	5.3446	0.16002	0.1311:0.503:0.1793:0.1866	.	467	Q8WYR1	PI3R5_HUMAN	A	467	ENSP00000392812:V467A	ENSP00000269300:V467A	V	-	2	0	PIK3R5	8732429	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.734000	0.01848	-1.505000	0.01807	-1.586000	0.00850	GTA	.	.		0.716	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308		G	8791704	A	G	8791704	3	3	198	1	0	0	0	0	1	0	0	0	11931	391	14	2	1282	2	PIK3R5	17	8791704	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	3328408	8791704	72403506	87	29208										
KRT34	3885	hgsc.bcm.edu	37	chr17	39538463	39538463	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	cgggaggagcagctggtgcgGcagcccaggctgggcaggca	20	11	0	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr17:39538463G>C	ENST00000394001.1	-	1	192	c.162C>G	c.(160-162)tgC>tgG	p.C54W		NM_021013.3	NP_066293.2	O76011	KRT34_HUMAN	keratin 34	54	Head.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Breast(137;0.000496)				AGCTGGTGCGGCAGCCCAGGC	0.622																																					p.C54W		Atlas-SNP	.											.	KRT34	71	.	0			c.C162G						.						51	49	49					17																	39538463		2203	4300	6503	SO:0001583	missense	3885	exon1			GGTGCGGCAGCCC	Y16790	CCDS11390.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131737	ENSG00000131737		"-", "Intermediate filaments type I, keratins (acidic)"	6452	protein-coding gene	gene with protein product	"hard keratin type I 4"	602763	"keratin, hair, acidic, 4"	KRTHA4		2431943, 9756910, 16831889	Standard	NM_021013		Approved	Ha-4	uc002hwm.3	O76011	OTTHUMG00000133436	ENST00000394001.1:c.162C>G	chr17.hg19:g.39538463G>C	ENSP00000377570:p.Cys54Trp	165.0	0.0		129.0	38.0	NM_021013	Q8IUT8|Q8N4W2	Missense_Mutation	SNP	ENST00000394001.1	hg19	CCDS11390.1	.	.	.	.	.	.	.	.	.	.	g	15.79	2.937343	0.52972	.	.	ENSG00000131737	ENST00000394001;ENST00000251648	.	.	.	5.87	2.85	0.33270	.	0.262685	0.34291	N	0.004085	T	0.49525	0.1562	L	0.43923	1.385	0.48632	D	0.999684	D	0.55800	0.973	P	0.51866	0.682	T	0.37979	-0.9682	9	0.38643	T	0.18	.	6.9858	0.24727	0.2053:0.1281:0.6666:0.0	.	54	O76011	KRT34_HUMAN	W	12;54	.	ENSP00000251648:C54W	C	-	3	2	KRT34	36791989	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	3.466000	0.53071	0.406000	0.25560	0.563000	0.77884	TGC	.	.		0.622	KRT34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257304.3	NM_021013		C	39538463	G	C	39538463	3	2	198	1	0	0	0	0	1	0	0	0	8480	1195	42	4	1176	4	KRT34	17	39538463	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	30746759	39538463	41656747	88	29209										
ITGA2B	3674	hgsc.bcm.edu	37	chr17	42463044	42463044	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gcgtcttctcagcctcctcaGtcttttctaggacgttccag	8	14	5	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr17:42463044G>T	ENST00000262407.5	-	4	480	c.449C>A	c.(448-450)aCt>aAt	p.T150N	ITGA2B_ENST00000377068.3_5'Flank|ITGA2B_ENST00000353281.4_Missense_Mutation_p.T150N	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	150					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	AGCCTCCTCAGTCTTTTCTAG	0.667																																					p.T150N		Atlas-SNP	.											.	ITGA2B	88	.	0			c.C449A						.						29	37	35					17																	42463044		2199	4299	6498	SO:0001583	missense	3674	exon4			TCCTCAGTCTTTT		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"CD molecules", "Integrins"	6138	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 93"	607759	"integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.449C>A	chr17.hg19:g.42463044G>T	ENSP00000262407:p.Thr150Asn	64.0	0.0		36.0	14.0	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Missense_Mutation	SNP	ENST00000262407.5	hg19	CCDS32665.1	.	.	.	.	.	.	.	.	.	.	G	8.364	0.833800	0.16820	.	.	ENSG00000005961	ENST00000262407;ENST00000353281	D;D	0.85258	-1.96;-1.96	5.55	-2.88	0.05682	.	1.519990	0.04838	N	0.440059	T	0.70962	0.3284	L	0.28458	0.855	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.51212	-0.8734	10	0.15952	T	0.53	.	1.4616	0.02397	0.215:0.1126:0.213:0.4594	.	150	P08514	ITA2B_HUMAN	N	150	ENSP00000262407:T150N;ENSP00000340536:T150N	ENSP00000262407:T150N	T	-	2	0	ITGA2B	39818570	0.000000	0.05858	0.000000	0.03702	0.176000	0.22953	-0.376000	0.07465	-0.502000	0.06596	-0.254000	0.11334	ACT	.	.		0.667	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			T	42463044	G	T	42463044	3	4	198	1	0	0	0	0	1	0	0	0	7885	1029	36	3	2778	3	ITGA2B	17	42463044	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	2924581	42463044	38732166	89	29210										
PSMD12	5718	hgsc.bcm.edu	37	chr17	65343236	65343236	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	acgaatatattcttacctgcTgccatttttcactttctgcc	4	12	3	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr17:65343236T>A	ENST00000356126.3	-	7	898	c.791A>T	c.(790-792)cAg>cTg	p.Q264L	PSMD12_ENST00000357146.4_Missense_Mutation_p.Q244L	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	264	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					TCTTACCTGCTGCCATTTTTC	0.338																																					p.Q264L		Atlas-SNP	.											.	PSMD12	32	.	0			c.A791T						.						110	105	107					17																	65343236		2202	4297	6499	SO:0001583	missense	5718	exon7			ACCTGCTGCCATT	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.791A>T	chr17.hg19:g.65343236T>A	ENSP00000348442:p.Gln264Leu	74.0	0.0		46.0	12.0	NM_002816	A6NP15|Q53HA2|Q6P053	Missense_Mutation	SNP	ENST00000356126.3	hg19	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	T	17.12	3.307591	0.60305	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	T;T	0.05081	3.5;3.5	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.06872	0.0175	L	0.33339	1.005	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.13407	0.005;0.009	T	0.38415	-0.9662	10	0.18276	T	0.48	-19.0341	16.4484	0.83959	0.0:0.0:0.0:1.0	.	244;264	A6NP15;O00232	.;PSD12_HUMAN	L	264;244	ENSP00000348442:Q264L;ENSP00000349667:Q244L	ENSP00000348442:Q264L	Q	-	2	0	PSMD12	62773698	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.680000	0.84062	2.285000	0.76669	0.533000	0.62120	CAG	.	.		0.338	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		A	65343236	T	A	65343236	3	1	198	1	0	0	0	0	1	0	0	0	12707	1580	55	4	599	4	PSMD12	17	65343236	Missense_Mutation	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	22880192	65343236	15851974	90	29211										
LGALS3BP	3959	hgsc.bcm.edu	37	chr17	76968132	76968132	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ctggactgatagaccagttgTgacttccgtgcactccagga	11	11	0	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr17:76968132T>G	ENST00000262776.3	-	6	1592	c.1284A>C	c.(1282-1284)tcA>tcC	p.S428S	LGALS3BP_ENST00000591778.1_3'UTR	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	428					cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(5)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			AGACCAGTTGTGACTTCCGTG	0.532											OREG0024787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S428S	GBM(89;1105 1755 18102 21513)	Atlas-SNP	.											.	LGALS3BP	47	.	0			c.A1284C						.						51	55	54					17																	76968132		2203	4300	6503	SO:0001819	synonymous_variant	3959	exon6			CAGTTGTGACTTC	L13210	CCDS11759.1	17q25	2014-07-09				ENSG00000108679		"BTB/POZ domain containing", "Endogenous ligands"	6564	protein-coding gene	gene with protein product	"L3 antigen", "Mac-2-binding protein", "serum protein 90K", "transport and golgi organization 10 homolog B (Drosophila)"	600626				7698018, 8034587, 8390986	Standard	NM_005567		Approved	MAC-2-BP, 90K, BTBD17B, TANGO10B, M2BP, gp90, CyCAP	uc002jwh.3	Q08380		ENST00000262776.3:c.1284A>C	chr17.hg19:g.76968132T>G		68.0	0.0	1172	47.0	19.0	NM_005567	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Silent	SNP	ENST00000262776.3	hg19	CCDS11759.1																																																																																			.	.		0.532	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567		G	76968132	T	G	76968132	2	3	198	1	0	0	0	0	0	0	0	1	8753	1683	59	5		5	LGALS3BP	17	76968132	Silent	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	11624896	76968132	4227078	91	29212										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2697978	2697978	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ggtgtagtggaagggattatCcgttatcatccattcttata	10	6	2	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr18:2697978C>T	ENST00000320876.6	+	10	1619	c.1281C>T	c.(1279-1281)atC>atT	p.I427I	SMCHD1_ENST00000261598.8_Silent_p.I427I|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	427					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)	p.I427M(2)		NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AAGGGATTATCCGTTATCATC	0.348																																					p.I427I		Atlas-SNP	.											AP001011.3_ENST00000320876,caecum,carcinoma,0,2	SMCHD1	88	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1281T						.						167	152	157					18																	2697978		1904	4133	6037	SO:0001819	synonymous_variant	23347	exon10			GATTATCCGTTAT	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.1281C>T	chr18.hg19:g.2697978C>T		88.0	0.0		72.0	29.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.		0.348	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2697978	C	T	2697978	2	4	198	1	0	0	0	0	0	0	0	1	14803	845	30	3		3	SMCHD1	18	2697978	Silent	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10		2697978	75379270	92	29213										
TCF4	6925	hgsc.bcm.edu	37	chr18	52927189	52927189	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	aaatacactacctgagagagAtggaggagagccaacaggag	13	7	0	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr18:52927189A>G	ENST00000356073.4	-	13	1671	c.1060T>C	c.(1060-1062)Tct>Cct	p.S354P	TCF4_ENST00000565018.2_Missense_Mutation_p.S354P|TCF4_ENST00000561831.3_Missense_Mutation_p.S194P|TCF4_ENST00000354452.3_Missense_Mutation_p.S354P|TCF4_ENST00000568740.1_Missense_Mutation_p.S329P|TCF4_ENST00000537856.3_Missense_Mutation_p.S224P|TCF4_ENST00000564999.1_Missense_Mutation_p.S354P|TCF4_ENST00000398339.1_Missense_Mutation_p.S456P|TCF4_ENST00000568673.1_Missense_Mutation_p.S330P|TCF4_ENST00000540999.1_Missense_Mutation_p.S330P|TCF4_ENST00000544241.2_Missense_Mutation_p.S283P|TCF4_ENST00000567880.1_Missense_Mutation_p.S294P|TCF4_ENST00000570177.2_Missense_Mutation_p.S224P|TCF4_ENST00000570287.2_Missense_Mutation_p.S194P|TCF4_ENST00000564228.1_Missense_Mutation_p.S283P|TCF4_ENST00000563760.1_Intron|TCF4_ENST00000457482.3_Missense_Mutation_p.S194P|TCF4_ENST00000564403.2_Missense_Mutation_p.S360P|TCF4_ENST00000537578.1_Missense_Mutation_p.S330P|TCF4_ENST00000566286.1_Missense_Mutation_p.S352P|TCF4_ENST00000566279.1_Missense_Mutation_p.S294P|TCF4_ENST00000543082.1_Missense_Mutation_p.S312P|TCF4_ENST00000561992.1_Missense_Mutation_p.S224P	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	354					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		CCTGAGAGAGATGGAGGAGAG	0.373																																					p.S456P		Atlas-SNP	.											.	TCF4	178	.	0			c.T1366C						.						140	147	145					18																	52927189		2203	4300	6503	SO:0001583	missense	6925	exon14			AGAGAGATGGAGG	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1060T>C	chr18.hg19:g.52927189A>G	ENSP00000348374:p.Ser354Pro	142.0	0.0		110.0	39.0	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	A	5.592	0.294033	0.10567	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.61510	0.1;0.1;0.1;0.1;0.1;0.1;0.1;0.1;0.1	6.06	6.06	0.98353	.	0.109098	0.64402	D	0.000005	T	0.24967	0.0606	N	0.00670	-1.27	0.47276	D	0.999377	B;B;B;B;B;B;B;B;B	0.13145	0.0;0.001;0.003;0.004;0.004;0.0;0.0;0.007;0.001	B;B;B;B;B;B;B;B;B	0.17098	0.001;0.008;0.017;0.011;0.003;0.002;0.002;0.008;0.003	T	0.40590	-0.9555	10	0.05721	T	0.95	-11.5015	15.6071	0.76682	1.0:0.0:0.0:0.0	.	330;354;194;456;354;312;283;194;352	B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;ITF2_HUMAN;.;.;.;.	P	354;194;354;312;330;330;283;224;456	ENSP00000346440:S354P;ENSP00000409447:S194P;ENSP00000348374:S354P;ENSP00000439656:S312P;ENSP00000445202:S330P;ENSP00000440731:S330P;ENSP00000441562:S283P;ENSP00000439827:S224P;ENSP00000381382:S456P	ENSP00000346440:S354P	S	-	1	0	TCF4	51078187	0.994000	0.37717	0.980000	0.43619	0.847000	0.48162	2.990000	0.49401	2.323000	0.78572	0.528000	0.53228	TCT	.	.		0.373	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		G	52927189	A	G	52927189	3	3	198	1	0	0	0	0	1	0	0	0	15710	333	12	2	983	2	TCF4	18	52927189	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	50229211	52927189	25150059	93	29214										
DSEL	92126	hgsc.bcm.edu	37	chr18	65178398	65178398	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ttggtttaaactagcaggagAcaaaggaattccaagaaagg	11	5	0	2	rs535957295		TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr18:65178398A>G	ENST00000310045.7	-	2	4951	c.3478T>C	c.(3478-3480)Tct>Cct	p.S1160P	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	1150					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				CTAGCAGGAGACAAAGGAATT	0.373													A|||	1	0.000199681	0	0	5008	,	,		18370	0		0	False		,,,				2504	0.001				p.S1160P		Atlas-SNP	.											.	DSEL	196	.	0			c.T3478C						.						70	68	69					18																	65178398		2203	4300	6503	SO:0001583	missense	92126	exon2			CAGGAGACAAAGG	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.3478T>C	chr18.hg19:g.65178398A>G	ENSP00000310565:p.Ser1160Pro	164.0	0.0		106.0	37.0	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	hg19	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	A	13.07	2.126555	0.37533	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.23552	1.9	4.79	4.79	0.61399	Sulfotransferase domain (1);	0.167948	0.40469	U	0.001094	T	0.18257	0.0438	L	0.31294	0.92	0.38526	D	0.948851	B	0.11235	0.004	B	0.16289	0.015	T	0.07309	-1.0779	10	0.35671	T	0.21	-21.8807	9.5771	0.39465	0.9091:0.0:0.0909:0.0	.	1150	Q8IZU8	DSEL_HUMAN	P	1160;1150	ENSP00000310565:S1160P	ENSP00000310565:S1160P	S	-	1	0	DSEL	63329378	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.859000	0.48364	1.910000	0.55303	0.460000	0.39030	TCT	.	.		0.373	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		G	65178398	A	G	65178398	3	3	198	1	0	0	0	0	1	0	0	0	4777	275	10	2	194	2	DSEL	18	65178398	Missense_Mutation	SNP	A	TCGA-DD-AADP-01A-11D-A38X-10	12251209	65178398	12898850	94	29215										
TICAM1	148022	hgsc.bcm.edu	37	chr19	4816573	4816573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	cctggcccccaaagggcattCgagccccatagggcgcccca	11	18	0	0	rs377447415		TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr19:4816573C>T	ENST00000248244.5	-	2	2046	c.1817G>A	c.(1816-1818)cGa>cAa	p.R606Q		NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	606	Sufficient to induce apoptosis.				apoptotic signaling pathway (GO:0097190)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of protein homodimerization activity (GO:0043496)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|ripoptosome (GO:0097342)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		AAAGGGCATTCGAGCCCCATA	0.667																																					p.R606Q		Atlas-SNP	.											.	TICAM1	69	.	0			c.G1817A						.						31	32	32					19																	4816573		2203	4300	6503	SO:0001583	missense	148022	exon2			GGCATTCGAGCCC	AB086380	CCDS12136.1	19p13.3	2014-09-17				ENSG00000127666			18348	protein-coding gene	gene with protein product		607601				12539043, 12471095	Standard	NM_182919		Approved	TRIF, TICAM-1, MGC35334, PRVTIRB	uc002mbi.4	Q8IUC6		ENST00000248244.5:c.1817G>A	chr19.hg19:g.4816573C>T	ENSP00000248244:p.Arg606Gln	50.0	0.0		57.0	12.0	NM_182919	B3Y691|O75532|Q86XP8|Q96GA0	Missense_Mutation	SNP	ENST00000248244.5	hg19	CCDS12136.1	.	.	.	.	.	.	.	.	.	.	C	0.101	-1.152840	0.01700	.	.	ENSG00000127666	ENST00000248244	T	0.42513	0.97	2.87	-5.75	0.02384	.	.	.	.	.	T	0.14313	0.0346	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.29243	-1.0018	9	0.02654	T	1	0.3022	5.4632	0.16627	0.0:0.2393:0.498:0.2628	.	606	Q8IUC6	TCAM1_HUMAN	Q	606	ENSP00000248244:R606Q	ENSP00000248244:R606Q	R	-	2	0	TICAM1	4767573	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.452000	0.06787	-1.812000	0.01227	-1.474000	0.01003	CGA	.	.		0.667	TICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450435.1	NM_014261		T	4816573	C	T	4816573	3	4	198	1	0	0	0	0	1	0	0	0	15907	884	31	1	325	1	TICAM1	19	4816573	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10		4816573	54312410	95	29216										
KLHL26	55295	hgsc.bcm.edu	37	chr19	18778935	18778935	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tgacccggcccggcggccgcGcgccagccacgtgctctgcc	14	20	1	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr19:18778935G>T	ENST00000300976.4	+	3	818	c.728G>T	c.(727-729)cGc>cTc	p.R243L	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	243	BACK.									breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						cggcggccgcgcgccAGCCAC	0.677																																					p.R243L		Atlas-SNP	.											.	KLHL26	43	.	0			c.G728T						.						15	18	17					19																	18778935		2124	4161	6285	SO:0001583	missense	55295	exon3			GGCCGCGCGCCAG		CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"Kelch-like", "BTB/POZ domain containing"	25623	protein-coding gene	gene with protein product			"kelch-like 26 (Drosophila)"				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.728G>T	chr19.hg19:g.18778935G>T	ENSP00000300976:p.Arg243Leu	48.0	0.0		29.0	10.0	NM_018316	Q8TAP0|Q9NUX3	Missense_Mutation	SNP	ENST00000300976.4	hg19	CCDS12384.1	.	.	.	.	.	.	.	.	.	.	G	5.707	0.314966	0.10789	.	.	ENSG00000167487	ENST00000300976	T	0.68181	-0.31	5.04	5.04	0.67666	BTB/Kelch-associated (2);	0.627207	0.16485	N	0.212341	T	0.31071	0.0785	N	0.00560	-1.38	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.13282	-1.0515	9	.	.	.	.	10.9448	0.47294	0.0864:0.0:0.9136:0.0	.	243	Q53HC5	KLH26_HUMAN	L	243	ENSP00000300976:R243L	.	R	+	2	0	KLHL26	18639935	0.003000	0.15002	0.346000	0.25655	0.906000	0.53458	0.942000	0.29017	2.341000	0.79615	0.591000	0.81541	CGC	.	.		0.677	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316		T	18778935	G	T	18778935	3	4	198	1	0	0	0	0	1	0	0	0	8390	1087	38	1	738	1	KLHL26	19	18778935	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	13962362	18778935	40350048	96	29217										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935118	30935118	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	acaagcagctgaaaggcagcCtgctgcagccccggccggac	13	15	0	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr19:30935118C>A	ENST00000355537.3	+	2	796	c.649C>A	c.(649-651)Ctg>Atg	p.L217M		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	217					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GAAAGGCAGCCTGCTGCAGCC	0.726																																					p.L217M		Atlas-SNP	.											.	ZNF536	424	.	0			c.C649A						.						6	5	5					19																	30935118		2023	3978	6001	SO:0001583	missense	9745	exon2			GGCAGCCTGCTGC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.649C>A	chr19.hg19:g.30935118C>A	ENSP00000347730:p.Leu217Met	34.0	0.0		25.0	11.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	11.33	1.607091	0.28623	.	.	ENSG00000198597	ENST00000355537	T	0.10099	2.91	5.94	5.94	0.96194	.	0.173018	0.39146	N	0.001448	T	0.18130	0.0435	L	0.34521	1.04	0.40131	D	0.976713	D;D	0.69078	0.988;0.997	P;P	0.57679	0.758;0.825	T	0.00312	-1.1826	10	0.46703	T	0.11	-20.6272	13.5478	0.61715	0.0:0.9292:0.0:0.0708	.	217;217	A7E228;O15090	.;ZN536_HUMAN	M	217	ENSP00000347730:L217M	ENSP00000347730:L217M	L	+	1	2	ZNF536	35626958	1.000000	0.71417	1.000000	0.80357	0.493000	0.33554	3.367000	0.52350	2.826000	0.97356	0.561000	0.74099	CTG	.	.		0.726	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		A	30935118	C	A	30935118	3	1	198	1	0	0	0	0	1	0	0	0	17989	680	24	3	651	3	ZNF536	19	30935118	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	12156183	30935118	28193865	97	29218										
CEBPA	1050	hgsc.bcm.edu	37	chr19	33792731	33792731	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gggcggccaggtgcgcgggcGgcgggtgcgggtgcgggtgc	26	10	0	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr19:33792731G>T	ENST00000498907.2	-	1	739	c.590C>A	c.(589-591)cCg>cAg	p.P197Q	CTD-2540B15.11_ENST00000589932.1_RNA|CTD-2540B15.7_ENST00000587312.1_RNA|CEBPA-AS1_ENST00000592982.2_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	197					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P185_P197del(1)|p.S190_P198del(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					GTGCGCGGGCGGCGGGTGCGG	0.771			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.P197Q		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	.	CEBPA	986	.	2	Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(2)	c.C590A						.						2	2	2					19																	33792731		646	1482	2128	SO:0001583	missense	1050	exon1	Familial Cancer Database	Familial AML	GCGGGCGGCGGGT	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.590C>A	chr19.hg19:g.33792731G>T	ENSP00000427514:p.Pro197Gln	208.0	0.0		82.0	8.0	NM_004364	A7LNP2|P78319|Q05CA4	Missense_Mutation	SNP	ENST00000498907.2	hg19	CCDS54243.1	.	.	.	.	.	.	.	.	.	.	G	5.481	0.273783	0.10403	.	.	ENSG00000245848	ENST00000498907	T	0.18174	2.23	4.04	4.04	0.47022	.	.	.	.	.	T	0.07863	0.0197	N	0.08118	0	0.26767	N	0.969872	B	0.26147	0.143	B	0.17979	0.02	T	0.28776	-1.0033	9	0.14252	T	0.57	.	9.2485	0.37541	0.0:0.0:0.7839:0.2161	.	197	P49715	CEBPA_HUMAN	Q	197	ENSP00000427514:P197Q	ENSP00000427514:P197Q	P	-	2	0	CEBPA	38484571	0.997000	0.39634	0.974000	0.42286	0.061000	0.15899	3.946000	0.56644	1.799000	0.52666	0.289000	0.19496	CCG	.	.		0.771	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		T	33792731	G	T	33792731	3	4	198	1	0	0	0	0	1	0	0	0	3201	1116	39	1	490	1	CEBPA	19	33792731	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	2857613	33792731	25336252	98	29219										
SPHK2	56848	hgsc.bcm.edu	37	chr19	49132057	49132057	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ctcgggctcccgctgtttctCcttcctgtctgtggcctggg	12	15	2	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr19:49132057C>T	ENST00000245222.4	+	7	1358	c.992C>T	c.(991-993)tCc>tTc	p.S331F	SPHK2_ENST00000340932.3_Intron|SPHK2_ENST00000599748.1_Missense_Mutation_p.S295F|SPHK2_ENST00000599029.1_Missense_Mutation_p.S295F|SPHK2_ENST00000598088.1_Missense_Mutation_p.S331F|SPHK2_ENST00000600537.1_Missense_Mutation_p.S272F|SPHK2_ENST00000443164.1_Missense_Mutation_p.S393F	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	331					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		CGCTGTTTCTCCTTCCTGTCT	0.642																																					p.S331F		Atlas-SNP	.											.	SPHK2	62	.	0			c.C992T						.						78	76	77					19																	49132057		2203	4300	6503	SO:0001583	missense	56848	exon7			GTTTCTCCTTCCT	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.992C>T	chr19.hg19:g.49132057C>T	ENSP00000245222:p.Ser331Phe	74.0	0.0		61.0	18.0	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Missense_Mutation	SNP	ENST00000245222.4	hg19	CCDS12727.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.244527	0.59103	.	.	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000443164	T;T	0.08984	3.03;3.03	4.13	4.13	0.48395	.	0.063906	0.64402	D	0.000004	T	0.17023	0.0409	M	0.93062	3.375	0.80722	D	1	B;P;P	0.42409	0.271;0.651;0.779	B;B;B	0.34242	0.097;0.153;0.178	T	0.26780	-1.0093	10	0.72032	D	0.01	-66.6872	14.2586	0.66070	0.0:1.0:0.0:0.0	.	272;393;331	B4DU87;A0T4C8;Q9NRA0	.;.;SPHK2_HUMAN	F	331;304;393	ENSP00000245222:S331F;ENSP00000413369:S393F	ENSP00000245222:S331F	S	+	2	0	SPHK2	53823869	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.229000	0.78088	2.317000	0.78254	0.655000	0.94253	TCC	.	.		0.642	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1			T	49132057	C	T	49132057	3	4	198	1	0	0	0	0	1	0	0	0	15062	855	30	3	1014	3	SPHK2	19	49132057	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	15339326	49132057	9996926	99	29220										
PPFIA3	8541	hgsc.bcm.edu	37	chr19	49638145	49638145	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gatggagatcgaccagctgcGggggaggccaccatcctcct	14	13	0	1			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr19:49638145G>A	ENST00000334186.4	+	13	1842	c.1493G>A	c.(1492-1494)cGg>cAg	p.R498Q	PPFIA3_ENST00000602351.1_Missense_Mutation_p.R498Q	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	498					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GACCAGCTGCGGGGGAGGCCA	0.647																																					p.R498Q		Atlas-SNP	.											.	PPFIA3	71	.	0			c.G1493A						.						48	42	44					19																	49638145		2203	4300	6503	SO:0001583	missense	8541	exon13			AGCTGCGGGGGAG	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"Sterile alpha motif (SAM) domain containing"	9247	protein-coding gene	gene with protein product	"protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3", "liprin-alpha 3", "liprin"	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.1493G>A	chr19.hg19:g.49638145G>A	ENSP00000335614:p.Arg498Gln	110.0	0.0		80.0	33.0	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Missense_Mutation	SNP	ENST00000334186.4	hg19	CCDS12758.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.488163	0.84854	.	.	ENSG00000177380	ENST00000334186;ENST00000421230	T	0.20069	2.1	3.88	3.88	0.44766	.	0.000000	0.32068	U	0.006640	T	0.43433	0.1247	M	0.71036	2.16	0.51012	D	0.999901	D;D;P	0.76494	0.999;0.998;0.903	D;P;B	0.66497	0.944;0.905;0.34	T	0.47005	-0.9150	10	0.59425	D	0.04	-18.3502	14.9742	0.71257	0.0:0.0:1.0:0.0	.	422;498;498	B4DEU8;O75145-2;O75145	.;.;LIPA3_HUMAN	Q	498;422	ENSP00000335614:R498Q	ENSP00000335614:R498Q	R	+	2	0	PPFIA3	54329957	1.000000	0.71417	0.992000	0.48379	0.807000	0.45602	5.669000	0.68081	1.895000	0.54865	0.313000	0.20887	CGG	.	.		0.647	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660		A	49638145	G	A	49638145	3	1	198	1	0	0	0	0	1	0	0	0	12320	1116	39	1	1539	1	PPFIA3	19	49638145	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	506088	49638145	9490838	100	29221										
ASPDH	554235	hgsc.bcm.edu	37	chr19	51017056	51017056	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gccatagcccaccacgcccaCcctccacgggcccctgtcgg	9	22	0	0			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr19:51017056C>T	ENST00000389208.4	-	1	86	c.25G>A	c.(25-27)Gtg>Atg	p.V9M	JOSD2_ENST00000598418.1_5'Flank|JOSD2_ENST00000601423.1_5'Flank|ASPDH_ENST00000597030.1_Intron|ASPDH_ENST00000376916.3_Intron|JOSD2_ENST00000391815.3_5'Flank|JOSD2_ENST00000595669.1_5'Flank	NM_001114598.1	NP_001108070.1	A6ND91	ASPD_HUMAN	aspartate dehydrogenase domain containing	9					NAD biosynthetic process (GO:0009435)|NADP catabolic process (GO:0006742)		aspartate dehydrogenase activity (GO:0033735)|NADP binding (GO:0050661)			endometrium(1)|large_intestine(1)|lung(1)	3						ACCACGCCCACCCTCCACGGG	0.692																																					p.V9M		Atlas-SNP	.											.	ASPDH	22	.	0			c.G25A						.						37	46	43					19																	51017056		692	1591	2283	SO:0001583	missense	554235	exon1			CGCCCACCCTCCA		CCDS33082.1, CCDS46153.1	19q13.33	2012-10-02			ENSG00000204653	ENSG00000204653			33856	protein-coding gene	gene with protein product							Standard	NM_001024656		Approved		uc010enz.3	A6ND91		ENST00000389208.4:c.25G>A	chr19.hg19:g.51017056C>T	ENSP00000373860:p.Val9Met	340.0	0.0		257.0	14.0	NM_001114598	Q6NZ37	Missense_Mutation	SNP	ENST00000389208.4	hg19	CCDS46153.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.593862	0.66219	.	.	ENSG00000204653	ENST00000389208	T	0.60299	0.2	3.76	3.76	0.43208	NAD(P)-binding domain (1);	0.147637	0.30686	U	0.009100	T	0.58864	0.2152	M	0.62723	1.935	0.41431	D	0.987865	P	0.48162	0.906	P	0.46585	0.521	T	0.66172	-0.5990	10	0.87932	D	0	.	11.4424	0.50105	0.0:1.0:0.0:0.0	.	9	A6ND91	ASPD_HUMAN	M	9	ENSP00000373860:V9M	ENSP00000373860:V9M	V	-	1	0	ASPDH	55708868	0.261000	0.24063	0.977000	0.42913	0.759000	0.43091	2.068000	0.41471	1.829000	0.53265	0.462000	0.41574	GTG	.	.		0.692	ASPDH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464861.1	NM_001024656		T	51017056	C	T	51017056	3	4	198	1	0	0	0	0	1	0	0	0	1051	507	18	3	854	3	ASPDH	19	51017056	Missense_Mutation	SNP	C	TCGA-DD-AADP-01A-11D-A38X-10	1378911	51017056	8111927	101	29222										
ZNF578	147660	hgsc.bcm.edu	37	chr19	53013919	53013919	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	atgttgcaaagacatgaaagTtatcacactggagatttttg	9	5	1	3			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr19:53013919T>C	ENST00000421239.2	+	6	529	c.285T>C	c.(283-285)agT>agC	p.S95S	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	95	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GACATGAAAGTTATCACACTG	0.393																																					p.S95S		Atlas-SNP	.											.	.	.	.	0			c.T285C						.						114	119	117					19																	53013919		2202	4300	6502	SO:0001819	synonymous_variant	147660	exon6			TGAAAGTTATCAC	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.285T>C	chr19.hg19:g.53013919T>C		254.0	0.0		222.0	94.0	NM_001099694	B4DR51|I3L1Y6	Silent	SNP	ENST00000421239.2	hg19	CCDS54310.1																																																																																			.	.		0.393	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		C	53013919	T	C	53013919	2	2	198	1	0	0	0	0	0	0	0	1	18025	1722	60	2		2	ZNF578	19	53013919	Silent	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10	1996863	53013919	6115064	102	29223										
XRN2	22803	hgsc.bcm.edu	37	chr20	21312938	21312938	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	tagctgatctcattatgcttGgccttgccacacatgaaccg	8	12	1	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr20:21312938G>A	ENST00000377191.3	+	9	813	c.718G>A	c.(718-720)Ggc>Agc	p.G240S	XRN2_ENST00000430571.2_Missense_Mutation_p.G164S|XRN2_ENST00000539513.1_Missense_Mutation_p.G186S	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	240				GLATHE -> AFPHMN (in Ref. 1; AAQ13577). {ECO:0000305}.	cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						CATTATGCTTGGCCTTGCCAC	0.388																																					p.G240S		Atlas-SNP	.											.	XRN2	90	.	0			c.G718A						.						110	101	104					20																	21312938		2203	4300	6503	SO:0001583	missense	22803	exon9			ATGCTTGGCCTTG	AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.718G>A	chr20.hg19:g.21312938G>A	ENSP00000366396:p.Gly240Ser	102.0	0.0		80.0	33.0	NM_012255	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Missense_Mutation	SNP	ENST00000377191.3	hg19	CCDS13144.1	.	.	.	.	.	.	.	.	.	.	G	32	5.164116	0.94727	.	.	ENSG00000088930	ENST00000377191;ENST00000430571;ENST00000539513	T;T;T	0.38722	1.17;1.16;1.12	5.51	5.51	0.81932	Putative 5-3 exonuclease (1);	0.000000	0.85682	D	0.000000	T	0.64057	0.2564	M	0.62266	1.93	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.62011	-0.6944	10	0.45353	T	0.12	-10.3936	19.4218	0.94725	0.0:0.0:1.0:0.0	.	240	Q9H0D6	XRN2_HUMAN	S	240;164;186	ENSP00000366396:G240S;ENSP00000413548:G164S;ENSP00000441113:G186S	ENSP00000366396:G240S	G	+	1	0	XRN2	21260938	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.837000	0.99465	2.583000	0.87209	0.655000	0.94253	GGC	.	.		0.388	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255		A	21312938	G	A	21312938	3	1	198	1	0	0	0	0	1	0	0	0	17475	1348	47	3	752	3	XRN2	20	21312938	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10		21312938	41712582	103	29224										
PIWIL3	440822	hgsc.bcm.edu	37	chr22	25145785	25145785	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	ctgtgacaatttctttatgtTgctgctcaacaaacaagaga	7	8	2	2			TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr22:25145785T>G	ENST00000332271.5	-	10	1507	c.1091A>C	c.(1090-1092)cAa>cCa	p.Q364P	PIWIL3_ENST00000533313.1_Splice_Site_p.Q255P|PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000527701.1_Splice_Site_p.Q255P	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	364	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						TTCTTTATGTTGCTGCTCAAC	0.458																																					p.Q364P		Atlas-SNP	.											.	PIWIL3	115	.	0			c.A1091C						.						110	88	95					22																	25145785		2203	4300	6503	SO:0001630	splice_region_variant	440822	exon10			TTATGTTGCTGCT	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.1090-1A>C	chr22.hg19:g.25145785T>G		88.0	0.0		81.0	31.0	NM_001008496		Missense_Mutation	SNP	ENST00000332271.5	hg19	CCDS33623.1	.	.	.	.	.	.	.	.	.	.	T	13.77	2.337696	0.41398	.	.	ENSG00000184571	ENST00000332271;ENST00000533313;ENST00000527701	T;T;T	0.15372	2.43;2.43;2.43	2.0	-0.403	0.12400	Argonaute/Dicer protein, PAZ (4);	0.146424	0.47852	U	0.000215	T	0.34803	0.0910	M	0.81614	2.55	0.28036	N	0.933932	D;P;D	0.64830	0.977;0.952;0.994	D;D;D	0.78314	0.967;0.936;0.991	T	0.11397	-1.0589	10	0.66056	D	0.02	-0.9522	5.2577	0.15555	0.0:0.3813:0.0:0.6187	.	255;364;364	E9PIP6;B4DYF7;Q7Z3Z3	.;.;PIWL3_HUMAN	P	364;255;255	ENSP00000330031:Q364P;ENSP00000431843:Q255P;ENSP00000435718:Q255P	ENSP00000330031:Q364P	Q	-	2	0	PIWIL3	23475785	0.979000	0.34478	0.047000	0.18901	0.509000	0.34042	0.697000	0.25556	-0.137000	0.11455	0.260000	0.18958	CAA	.	.		0.458	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496	Missense_Mutation	G	25145785	T	G	25145785	5	3	198	1	0	0	0	0	0	0	1	0	11968	1826	63	5	1605	5	PIWIL3	22	25145785	Splice_Site	SNP	T	TCGA-DD-AADP-01A-11D-A38X-10		25145785	26158781	104	29225										
APOBEC3H	164668	hgsc.bcm.edu	37	chr22	39497462	39497462	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0673076923076923	7	1	1.58342245989305	1.28181818181818	1.64805194805195	0.0291375291375292	0.304738562091504	0	gccccagcagaaggggctgcGgcttctgtgtggatcccagg	16	12	1	1	rs374311513		TCGA-DD-AADP-01A-11D-A38X-10	TCGA-DD-AADP-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22a818c7-14c6-4d8e-9aeb-88d94ff13da0	f2bd6609-3c48-48a0-8e21-c0d91ed42912	g.chr22:39497462G>A	ENST00000401756.1	+	3	447	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	APOBEC3H_ENST00000442487.3_Missense_Mutation_p.R124Q|APOBEC3H_ENST00000421988.2_Missense_Mutation_p.R124Q|APOBEC3H_ENST00000348946.4_Missense_Mutation_p.R124Q	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	124					cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					AAGGGGCTGCGGCTTCTGTGT	0.592													G|||	1	0.000199681	8e-04	0	5008	,	,		6331	0		0	False		,,,				2504	0				p.R124Q		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.G371A						.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	2,4404		0,2,2201	49	47	48		371,371,371,371	-6.7	0	22		48	0,8600		0,0,4300	no	missense,missense,missense,missense	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	43,43,43,43	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign,benign,benign,benign	124/183,124/201,124/155,124/184	39497462	2,13004	2203	4300	6503	SO:0001583	missense	164668	exon3			GGCTGCGGCTTCT	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"Apolipoprotein B mRNA editing enzymes"	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.371G>A	chr22.hg19:g.39497462G>A	ENSP00000385741:p.Arg124Gln	87.0	0.0		58.0	25.0	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Missense_Mutation	SNP	ENST00000401756.1	hg19	CCDS54530.1	.	.	.	.	.	.	.	.	.	.	.	2.502	-0.314970	0.05422	4.54E-4	0.0	ENSG00000100298	ENST00000348946;ENST00000442487;ENST00000421988;ENST00000401756	T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56	3.33	-6.67	0.01783	.	.	.	.	.	T	0.46328	0.1387	N	0.16201	0.385	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.31998	-0.9923	9	0.20046	T	0.44	-24.1796	9.9638	0.41712	0.1812:0.0:0.6888:0.13	.	124	B7TQM3	.	Q	124	ENSP00000216123:R124Q;ENSP00000411754:R124Q;ENSP00000393520:R124Q;ENSP00000385741:R124Q	ENSP00000216123:R124Q	R	+	2	0	APOBEC3H	37827408	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.644000	0.05415	-2.206000	0.00741	-3.029000	0.00073	CGG	.	.		0.592	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773		A	39497462	G	A	39497462	3	1	198	1	0	0	0	0	1	0	0	0	795	1116	39	1	377	1	APOBEC3H	22	39497462	Missense_Mutation	SNP	G	TCGA-DD-AADP-01A-11D-A38X-10	14351677	39497462	11807104	105	29226										
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17318784	17318784	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	accagctccggggagcctttGacgtaggcctcgggctgagt	15	12	0	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:17318784G>T	ENST00000326735.8	-	18	1992	c.1959C>A	c.(1957-1959)gtC>gtA	p.V653V	RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000452699.1_Silent_p.V648V|ATP13A2_ENST00000341676.5_Silent_p.V648V			Q9NQ11	AT132_HUMAN	ATPase type 13A2	653					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		GGGAGCCTTTGACGTAGGCCT	0.667																																					p.V653V		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C1959A						.						15	18	17					1																	17318784		2203	4297	6500	SO:0001819	synonymous_variant	23400	exon18			GCCTTTGACGTAG	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.1959C>A	chr1.hg19:g.17318784G>T		97.0	0.0		84.0	60.0	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	hg19	CCDS175.1																																																																																			.	.		0.667	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		T	17318784	G	T	17318784	2	4	199	1	0	0	0	0	0	0	0	1	1124	1277	45	3		3	ATP13A2	1	17318784	Silent	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10		17318784	231931837	1	29227										
KDM1A	23028	hgsc.bcm.edu	37	chr1	23409732	23409732	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gtaactacccagccacagtgCatggtgctctgctgagtggg	13	11	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:23409732C>T	ENST00000356634.3	+	19	2583	c.2434C>T	c.(2434-2436)Cat>Tat	p.H812Y	RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Missense_Mutation_p.H836Y|KDM1A_ENST00000542151.1_Missense_Mutation_p.H836Y	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	812	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						AGCCACAGTGCATGGTGCTCT	0.537																																					p.H836Y		Atlas-SNP	.											.	KDM1A	49	.	0			c.C2506T						.						94	82	86					1																	23409732		2203	4300	6503	SO:0001583	missense	23028	exon21			ACAGTGCATGGTG	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.2434C>T	chr1.hg19:g.23409732C>T	ENSP00000349049:p.His812Tyr	104.0	0.0		134.0	104.0	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Missense_Mutation	SNP	ENST00000356634.3	hg19	CCDS30627.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520985	0.85495	.	.	ENSG00000004487	ENST00000356634;ENST00000400181;ENST00000542151	D;D;D	0.93488	-3.23;-3.23;-3.23	5.67	3.77	0.43336	Amine oxidase (1);	0.000000	0.85682	D	0.000000	D	0.97408	0.9152	H	0.95950	3.745	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97512	1.0067	10	0.87932	D	0	-18.6124	10.4675	0.44616	0.132:0.7976:0.0:0.0704	.	836;812	O60341-2;O60341	.;KDM1A_HUMAN	Y	812;836;836	ENSP00000349049:H812Y;ENSP00000383042:H836Y;ENSP00000439072:H836Y	ENSP00000349049:H812Y	H	+	1	0	KDM1A	23282319	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.984000	0.70548	1.382000	0.46385	0.655000	0.94253	CAT	.	.		0.537	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		T	23409732	C	T	23409732	3	4	199	1	0	0	0	0	1	0	0	0	8131	710	25	3	2588	3	KDM1A	1	23409732	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	6090948	23409732	225840889	2	29228										
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35453298	35453298	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agtcaaagttccttggagacTtaaatttaattcatttataa	5	5	2	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:35453298T>G	ENST00000357182.4	-	16	3612	c.3385A>C	c.(3385-3387)Agt>Cgt	p.S1129R	ZMYM6_ENST00000373340.2_Intron|ZMYM6NB_ENST00000373337.3_5'Flank|ZMYM6_ENST00000487874.1_Intron|ZMYM6_ENST00000493328.1_5'UTR|RP11-244H3.1_ENST00000417456.1_RNA	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	1129					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				ccttggagacttaaatttaat	0.313																																					p.S1129R		Atlas-SNP	.											.	ZMYM6	110	.	0			c.A3385C						.						18	16	17					1																	35453298		1638	3737	5375	SO:0001583	missense	9204	exon16			GGAGACTTAAATT	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"Zinc fingers, MYM type", "Zinc fingers, BED-type"	13050	protein-coding gene	gene with protein product	"zinc finger, BED-type containing 7"	613567	"zinc finger protein 258", "zinc finger, MYM-type containing 6"	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.3385A>C	chr1.hg19:g.35453298T>G	ENSP00000349708:p.Ser1129Arg	481.0	0.0		398.0	23.0	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	hg19	CCDS387.2	.	.	.	.	.	.	.	.	.	.	T	14.23	2.474524	0.43942	.	.	ENSG00000163867	ENST00000357182	T	0.42131	0.98	4.88	2.6	0.31112	Ribonuclease H-like (1);	0.049163	0.85682	D	0.000000	T	0.36991	0.0987	L	0.52759	1.655	0.80722	D	1	P	0.45348	0.856	P	0.45506	0.483	T	0.11348	-1.0591	10	0.44086	T	0.13	-17.3568	6.0116	0.19580	0.0:0.2001:0.0:0.7999	.	1129	O95789	ZMYM6_HUMAN	R	1129	ENSP00000349708:S1129R	ENSP00000349708:S1129R	S	-	1	0	ZMYM6	35225885	0.991000	0.36638	1.000000	0.80357	0.998000	0.95712	0.447000	0.21710	0.997000	0.38969	0.528000	0.53228	AGT	.	.		0.313	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		G	35453298	T	G	35453298	3	3	199	1	0	0	0	0	1	0	0	0	17719	1609	56	5	596	5	ZMYM6	1	35453298	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	12043566	35453298	213797323	3	29229										
GRIK3	2899	hgsc.bcm.edu	37	chr1	37282713	37282713	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	cagccccatactcgattttgGtttgcttggccaggtcatca	9	12	2	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:37282713G>A	ENST00000373091.3	-	13	2055	c.2039C>T	c.(2038-2040)aCc>aTc	p.T680I	GRIK3_ENST00000373093.4_Missense_Mutation_p.T680I	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	680					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CTCGATTTTGGTTTGCTTGGC	0.557																																					p.T680I		Atlas-SNP	.											.	GRIK3	195	.	0			c.C2039T						.						143	116	125					1																	37282713		2203	4300	6503	SO:0001583	missense	2899	exon13			ATTTTGGTTTGCT	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.2039C>T	chr1.hg19:g.37282713G>A	ENSP00000362183:p.Thr680Ile	162.0	0.0		147.0	14.0	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	hg19	CCDS416.1	.	.	.	.	.	.	.	.	.	.	G	32	5.125940	0.94429	.	.	ENSG00000163873	ENST00000373091;ENST00000373093	T;T	0.56103	0.48;0.48	6.16	6.16	0.99307	Ionotropic glutamate receptor (2);	0.242107	0.42548	D	0.000683	D	0.82586	0.5069	H	0.95574	3.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86176	0.1603	10	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	680;680	A9Z1Z8;Q13003	.;GRIK3_HUMAN	I	680	ENSP00000362183:T680I;ENSP00000362185:T680I	ENSP00000362183:T680I	T	-	2	0	GRIK3	37055300	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.869000	0.99810	2.937000	0.99478	0.650000	0.86243	ACC	.	.		0.557	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		A	37282713	G	A	37282713	3	1	199	1	0	0	0	0	1	0	0	0	6784	1261	44	3	736	3	GRIK3	1	37282713	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	1829415	37282713	211967908	4	29230										
EIF2B3	8891	hgsc.bcm.edu	37	chr1	45407298	45407298	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	cacaacctcatgtaaggcaaCgtctgttatcagatcacagc	7	12	4	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:45407298C>T	ENST00000360403.2	-	4	460	c.334G>A	c.(334-336)Gtt>Att	p.V112I	EIF2B3_ENST00000372183.3_Missense_Mutation_p.V112I|EIF2B3_ENST00000480675.1_5'UTR	NM_001261418.1|NM_020365.4	NP_001248347.1|NP_065098.1	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa	112					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|positive regulation of GTPase activity (GO:0043547)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	guanyl-nucleotide exchange factor activity (GO:0005085)|nucleotidyltransferase activity (GO:0016779)|translation initiation factor activity (GO:0003743)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	17	Acute lymphoblastic leukemia(166;0.155)					TGTAAGGCAACGTCTGTTATC	0.418																																					p.V112I	Colon(26;357 658 2581 11857 12657)	Atlas-SNP	.											EIF2B3,right_upper_lobe,carcinoma,0,1	EIF2B3	43	.	0			c.G334A						.						205	183	191					1																	45407298		2203	4300	6503	SO:0001583	missense	8891	exon4			AGGCAACGTCTGT	AF257077	CCDS517.1, CCDS53313.1, CCDS72775.1	1p34.1	2008-02-05	2002-08-29		ENSG00000070785	ENSG00000070785			3259	protein-coding gene	gene with protein product		606273	"eukaryotic translation initiation factor 2B, subunit 3 (gamma, 58kD)"			10900014	Standard	NM_020365		Approved	EIF2Bgamma, EIF-2B	uc001cmt.3	Q9NR50	OTTHUMG00000008585	ENST00000360403.2:c.334G>A	chr1.hg19:g.45407298C>T	ENSP00000353575:p.Val112Ile	177.0	0.0		175.0	10.0	NM_020365	B2RBH8|D3DPZ2|Q5QP89|Q5QP90|Q8NDB5|Q8WV57|Q9H850	Missense_Mutation	SNP	ENST00000360403.2	hg19	CCDS517.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.608999	0.87258	.	.	ENSG00000070785	ENST00000360403;ENST00000372183;ENST00000372182	T;T;T	0.72942	-0.7;-0.7;-0.7	5.41	5.41	0.78517	Nucleotidyl transferase (1);	0.000000	0.85682	D	0.000000	T	0.63733	0.2536	L	0.41573	1.285	0.80722	D	1	P;P;P	0.50943	0.925;0.94;0.625	B;B;B	0.43194	0.411;0.22;0.153	T	0.61332	-0.7084	10	0.09084	T	0.74	-24.9607	19.1869	0.93647	0.0:1.0:0.0:0.0	.	112;112;112	Q9NR50-2;Q9NR50-3;Q9NR50	.;.;EI2BG_HUMAN	I	112	ENSP00000353575:V112I;ENSP00000361257:V112I;ENSP00000361256:V112I	ENSP00000353575:V112I	V	-	1	0	EIF2B3	45179885	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.272000	0.78516	2.539000	0.85634	0.591000	0.81541	GTT	.	.		0.418	EIF2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023724.1	NM_020365		T	45407298	C	T	45407298	3	4	199	1	0	0	0	0	1	0	0	0	5004	536	19	1	1097	1	EIF2B3	1	45407298	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	8124585	45407298	203843323	5	29231										
PTGER3	5733	hgsc.bcm.edu	37	chr1	71512486	71512486	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	cgtggccttggcccggcagcGggacaccagggccttaatgg	16	13	0	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:71512486G>A	ENST00000306666.5	-	1	985	c.775C>T	c.(775-777)Cgc>Tgc	p.R259C	PTGER3_ENST00000414819.1_Missense_Mutation_p.R259C|PTGER3_ENST00000354608.5_Missense_Mutation_p.R259C|PTGER3_ENST00000460330.1_Missense_Mutation_p.R259C|PTGER3_ENST00000370932.2_Missense_Mutation_p.R259C|ZRANB2-AS1_ENST00000450461.1_RNA|PTGER3_ENST00000370924.4_Missense_Mutation_p.R259C|PTGER3_ENST00000370931.3_Missense_Mutation_p.R259C|PTGER3_ENST00000351052.5_Missense_Mutation_p.R259C|PTGER3_ENST00000356595.4_Missense_Mutation_p.R259C	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	259					cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	GCCCGGCAGCGGGACACCAGG	0.622																																					p.R259C		Atlas-SNP	.											.	PTGER3	246	.	0			c.C775T						.						62	64	63					1																	71512486		2203	4300	6503	SO:0001583	missense	5733	exon1			GGCAGCGGGACAC	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.775C>T	chr1.hg19:g.71512486G>A	ENSP00000302313:p.Arg259Cys	102.0	0.0		94.0	63.0	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Missense_Mutation	SNP	ENST00000306666.5	hg19	CCDS657.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.152967	0.78001	.	.	ENSG00000050628	ENST00000370931;ENST00000370932;ENST00000351052;ENST00000460330;ENST00000370934;ENST00000354608;ENST00000356595;ENST00000414819;ENST00000306666;ENST00000370924	T;T;T;T;T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11;1.11;1.11;1.11;1.11	4.87	4.87	0.63330	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.58148	0.2102	M	0.70842	2.15	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999;0.999;0.999;0.999	T	0.59434	-0.7455	10	0.51188	T	0.08	-30.2375	17.8095	0.88611	0.0:0.0:1.0:0.0	.	259;259;259;259;259;259;259;259	Q147U0;Q6TTN3;F5H821;B1AK19;Q147X8;P43115-3;P43115-4;P43115	.;.;.;.;.;.;.;PE2R3_HUMAN	C	259	ENSP00000359969:R259C;ENSP00000359970:R259C;ENSP00000280208:R259C;ENSP00000418073:R259C;ENSP00000346624:R259C;ENSP00000349003:R259C;ENSP00000401423:R259C;ENSP00000302313:R259C;ENSP00000359962:R259C	ENSP00000302313:R259C	R	-	1	0	PTGER3	71285074	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.053000	0.64269	2.530000	0.85305	0.462000	0.41574	CGC	.	.		0.622	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957		A	71512486	G	A	71512486	3	1	199	1	0	0	0	0	1	0	0	0	12757	1116	39	1	716	1	PTGER3	1	71512486	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	26105188	71512486	177738135	6	29232										
TTLL7	79739	hgsc.bcm.edu	37	chr1	84417572	84417572	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	catttgctgtaatggttcccTtctttttcttctttctgact	5	10	4	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:84417572T>A	ENST00000260505.8	-	3	490	c.113A>T	c.(112-114)aAg>aTg	p.K38M	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	38	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		AATGGTTCCCTTCTTTTTCTT	0.363																																					p.K38M		Atlas-SNP	.											.	TTLL7	93	.	0			c.A113T						.						70	73	72					1																	84417572		2203	4299	6502	SO:0001583	missense	79739	exon3			GTTCCCTTCTTTT	AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"Tubulin tyrosine ligase-like family"	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.113A>T	chr1.hg19:g.84417572T>A	ENSP00000260505:p.Lys38Met	200.0	0.0		203.0	10.0	NM_024686	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Missense_Mutation	SNP	ENST00000260505.8	hg19	CCDS690.2	.	.	.	.	.	.	.	.	.	.	T	21.5	4.157621	0.78114	.	.	ENSG00000137941	ENST00000260505;ENST00000370703	T	0.04454	3.62	5.21	4.08	0.47627	.	0.146882	0.64402	D	0.000011	T	0.02888	0.0086	L	0.29908	0.895	0.41443	D	0.987937	D	0.63880	0.993	P	0.50231	0.635	T	0.57004	-0.7885	10	0.38643	T	0.18	.	10.9898	0.47543	0.0:0.0741:0.0:0.9259	.	38	Q6ZT98	TTLL7_HUMAN	M	38	ENSP00000260505:K38M	ENSP00000260505:K38M	K	-	2	0	TTLL7	84190160	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.618000	0.61211	0.926000	0.37118	0.533000	0.62120	AAG	.	.		0.363	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686		A	84417572	T	A	84417572	3	1	199	1	0	0	0	0	1	0	0	0	16747	1609	56	4	2626	4	TTLL7	1	84417572	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	12905086	84417572	164833049	7	29233										
VAV3	10451	hgsc.bcm.edu	37	chr1	108185361	108185361	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ccagaatagttcctaatgacCtgcatctttggtaaacctga	7	10	1	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:108185361C>A	ENST00000370056.4	-	20	2068	c.1794G>T	c.(1792-1794)caG>caT	p.Q598H	VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000415432.2_Missense_Mutation_p.Q38H|VAV3_ENST00000527011.1_Missense_Mutation_p.Q598H|VAV3_ENST00000544443.1_Missense_Mutation_p.Q2H	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	598	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.|Sufficient for interaction with ROS1.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.Q598Q(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TCCTAATGACCTGCATCTTTG	0.413																																					p.Q598H		Atlas-SNP	.											VAV3,caecum,carcinoma,0,1	VAV3	176	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1794T						.						115	109	111					1																	108185361		2203	4300	6503	SO:0001583	missense	10451	exon20			AATGACCTGCATC	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1794G>T	chr1.hg19:g.108185361C>A	ENSP00000359073:p.Gln598His	142.0	0.0		110.0	6.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.26|13.26	2.182883|2.182883	0.38511|0.38511	.|.	.|.	ENSG00000134215|ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000544443;ENST00000415432|ENST00000529809	T;T;T;T|.	0.08807|.	3.05;3.05;3.05;3.05|.	5.67|5.67	4.75|4.75	0.60458|0.60458	Src homology-3 domain (3);Variant SH3 (1);|.	0.326257|.	0.34386|.	N|.	0.004018|.	T|T	0.40719|0.40719	0.1128|0.1128	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	D|D	1|1	P;P;P;P|.	0.51537|.	0.564;0.633;0.946;0.531|.	P;P;P;P|.	0.56163|.	0.54;0.637;0.793;0.482|.	T|T	0.50311|0.50311	-0.8843|-0.8843	10|6	0.44086|0.87932	T|D	0.13|0	.|.	5.75|5.75	0.18142|0.18142	0.0:0.7368:0.0:0.2632|0.0:0.7368:0.0:0.2632	.|.	598;2;598;38|.	E9PQ97;B7Z3Z5;Q9UKW4;Q9UKW4-3|.	.;.;VAV3_HUMAN;.|.	H|M	598;598;2;38|126	ENSP00000359073:Q598H;ENSP00000432540:Q598H;ENSP00000446404:Q2H;ENSP00000394897:Q38H|.	ENSP00000359073:Q598H|ENSP00000434944:R23M	Q|R	-|-	3|2	2|0	VAV3|VAV3	107986884|107986884	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.331000|2.331000	0.43894|0.43894	2.682000|2.682000	0.91365|0.91365	0.555000|0.555000	0.69702|0.69702	CAG|AGG	.	.		0.413	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		A	108185361	C	A	108185361	3	1	199	1	0	0	0	0	1	0	0	0	17148	680	24	3	781	3	VAV3	1	108185361	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	23767789	108185361	141065260	8	29234										
UBAP2L	9898	hgsc.bcm.edu	37	chr1	154226506	154226506	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	atgaacagagatccacacagActcggcggtaccccagctcc	9	15	0	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:154226506A>T	ENST00000361546.2	+	14	1837	c.1795A>T	c.(1795-1797)Act>Tct	p.T599S	AL590431.1_ENST00000517008.1_RNA|UBAP2L_ENST00000343815.6_Missense_Mutation_p.T599S|UBAP2L_ENST00000428931.1_Missense_Mutation_p.T599S|UBAP2L_ENST00000271877.7_Missense_Mutation_p.T610S			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	599					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			ATCCACACAGACTCGGCGGTA	0.502																																					p.T599S		Atlas-SNP	.											.	UBAP2L	197	.	0			c.A1795T						.						77	73	74					1																	154226506		2203	4300	6503	SO:0001583	missense	9898	exon15			ACACAGACTCGGC	BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.1795A>T	chr1.hg19:g.154226506A>T	ENSP00000355343:p.Thr599Ser	115.0	0.0		108.0	51.0	NM_001127320	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	hg19	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	A	13.97	2.394832	0.42512	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000456955;ENST00000433006;ENST00000271877;ENST00000361546	T;T;T;T	0.11277	2.83;2.86;2.79;2.86	5.05	5.05	0.67936	.	0.169187	0.51477	D	0.000091	T	0.09158	0.0226	N	0.16790	0.44	0.45390	D	0.998375	P;D;D;D;P	0.67145	0.956;0.996;0.974;0.974;0.956	P;D;D;D;P	0.73380	0.899;0.98;0.953;0.953;0.899	T	0.43048	-0.9415	10	0.20046	T	0.44	-7.603	14.1255	0.65217	1.0:0.0:0.0:0.0	.	513;610;592;599;599	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	S	599;599;95;95;610;599	ENSP00000345308:T599S;ENSP00000389445:T599S;ENSP00000271877:T610S;ENSP00000355343:T599S	ENSP00000271877:T610S	T	+	1	0	UBAP2L	152493130	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.347000	0.79356	2.119000	0.64992	0.533000	0.62120	ACT	.	.		0.502	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		T	154226506	A	T	154226506	3	4	199	1	0	0	0	0	1	0	0	0	16853	275	10	4	1849	4	UBAP2L	1	154226506	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	46041145	154226506	95024115	9	29235										
INSRR	3645	hgsc.bcm.edu	37	chr1	156816468	156816468	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggctcctgggtgcggcttagGggcagctccacatccagcag	15	13	0	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:156816468G>C	ENST00000368195.3	-	8	2049	c.1653C>G	c.(1651-1653)ccC>ccG	p.P551P	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	551	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TGCGGCTTAGGGGCAGCTCCA	0.612																																					p.P551P		Atlas-SNP	.											.	INSRR	309	.	0			c.C1653G						.						80	71	74					1																	156816468		2203	4300	6503	SO:0001819	synonymous_variant	3645	exon8			GCTTAGGGGCAGC	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.1653C>G	chr1.hg19:g.156816468G>C		122.0	0.0		124.0	48.0	NM_014215	O60724|Q5VZS3	Silent	SNP	ENST00000368195.3	hg19	CCDS1160.1																																																																																			.	.		0.612	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		C	156816468	G	C	156816468	2	2	199	1	0	0	0	0	0	0	0	1	7783	1219	43	4		4	INSRR	1	156816468	Silent	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	2589962	156816468	92434153	10	29236										
FMO3	2328	hgsc.bcm.edu	37	chr1	171076962	171076962	+	Frame_Shift_Del	DEL	A	A	-													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	catgtgtatcccaacctaccAaaagagtcctttccaggtaa							TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:171076962delA	ENST00000367755.4	+	4	579	c.468delA	c.(466-468)ccafs	p.P156fs	FMO3_ENST00000392085.2_Frame_Shift_Del_p.P156fs|FMO3_ENST00000542847.1_Frame_Shift_Del_p.P136fs|FMO3_ENST00000538429.1_Frame_Shift_Del_p.P93fs	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	156					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CCAACCTACCAAAAGAGTCCT	0.388																																					p.P156fs		Atlas-INDEL	.											.	FMO3	73	.	0			c.467delC						.						125	129	127					1																	171076962		2203	4300	6503	SO:0001589	frameshift_variant	2328	exon4			.	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.468delA	chr1.hg19:g.171076962delA	ENSP00000356729:p.Pro156fs	154.0	0.0		143.0	53.0	NM_001002294	B2R816|Q14854|Q8N5N5	Frame_Shift_Del	DEL	ENST00000367755.4	hg19	CCDS1292.1																																																																																			.	.		0.388	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		-	171076962	A	-	171076962	7	5	199	1	0	1	0	1	0	0	0	0	5964	117	5	0	478	0	FMO3	1	171076962	Frame_Shift_Del	DEL	A	TCGA-DD-AADQ-01A-11D-A40R-10	14260494	171076962	78173659	11	29237										
PRDX6	9588	hgsc.bcm.edu	37	chr1	173455515	173455515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ccagctgacagcagaaaaaaGggttgccaccccagttgatt	10	11	0	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:173455515G>A	ENST00000340385.5	+	4	653	c.521G>A	c.(520-522)aGg>aAg	p.R174K	PRDX6_ENST00000470017.1_3'UTR	NM_004905.2	NP_004896.1	P30041	PRDX6_HUMAN	peroxiredoxin 6	174					hydrogen peroxide catabolic process (GO:0042744)|phospholipid catabolic process (GO:0009395)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)	antioxidant activity (GO:0016209)|glutathione peroxidase activity (GO:0004602)|peroxiredoxin activity (GO:0051920)|phospholipase A2 activity (GO:0004623)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	12						GCAGAAAAAAGGGTTGCCACC	0.463																																					p.R174K		Atlas-SNP	.											.	PRDX6	20	.	0			c.G521A						.						129	136	134					1																	173455515		2203	4300	6503	SO:0001583	missense	9588	exon4			AAAAAAGGGTTGC	D14662	CCDS1307.1	1q24.1	2008-02-05			ENSG00000117592	ENSG00000117592			16753	protein-coding gene	gene with protein product		602316				11233154	Standard	NM_004905		Approved	AOP2, KIAA0106, 1-Cys, NSGPx, PRX, aiPLA2, MGC46173, p29	uc001giy.1	P30041	OTTHUMG00000034804	ENST00000340385.5:c.521G>A	chr1.hg19:g.173455515G>A	ENSP00000342026:p.Arg174Lys	149.0	0.0		154.0	61.0	NM_004905	A8JZY7|P32077|Q5TAH4|Q5ZEZ8	Missense_Mutation	SNP	ENST00000340385.5	hg19	CCDS1307.1	.	.	.	.	.	.	.	.	.	.	G	2.113	-0.403297	0.04832	.	.	ENSG00000117592	ENST00000340385	T	0.25250	1.81	5.63	0.844	0.18943	Peroxiredoxin, C-terminal (1);Thioredoxin-like fold (1);	0.308219	0.38381	N	0.001709	T	0.00967	0.0032	N	0.00496	-1.435	0.21719	N	0.999573	B	0.02656	0.0	B	0.04013	0.001	T	0.38564	-0.9655	10	0.02654	T	1	-2.7912	0.7002	0.00906	0.1646:0.2039:0.2544:0.3771	.	174	P30041	PRDX6_HUMAN	K	174	ENSP00000342026:R174K	ENSP00000342026:R174K	R	+	2	0	PRDX6	171722138	0.959000	0.32827	0.120000	0.21714	0.534000	0.34807	1.310000	0.33551	0.346000	0.23899	-0.182000	0.12963	AGG	.	.		0.463	PRDX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084222.1	NM_004905		A	173455515	G	A	173455515	3	1	199	1	0	0	0	0	1	0	0	0	12481	1000	35	3	535	3	PRDX6	1	173455515	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	2378553	173455515	75795106	12	29238										
LEMD1	93273	hgsc.bcm.edu	37	chr1	205388368	205388368	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	atggcggtaccttcgctgtcAtcactgtcctgcgctccatc	9	15	2	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:205388368A>G	ENST00000367153.4	-	3	297	c.195T>C	c.(193-195)gaT>gaC	p.D65D	LEMD1_ENST00000367151.2_Intron|LEMD1_ENST00000476884.1_Intron|LEMD1_ENST00000367152.1_Intron|LEMD1_ENST00000391936.2_Silent_p.D65D|LEMD1_ENST00000367149.3_Intron|LEMD1_ENST00000367154.1_Silent_p.D65D	NM_001199050.1	NP_001185979.1	Q68G75	LEMD1_HUMAN	LEM domain containing 1	65						integral component of membrane (GO:0016021)				breast(1)|lung(2)	3	Breast(84;0.247)		BRCA - Breast invasive adenocarcinoma(75;0.0938)			CTTCGCTGTCATCACTGTCCT	0.463																																					p.D65D		Atlas-SNP	.											.	LEMD1	21	.	0			c.T195C						.						140	129	133					1																	205388368		2203	4300	6503	SO:0001819	synonymous_variant	93273	exon3			GCTGTCATCACTG		CCDS30986.1, CCDS55677.1, CCDS55678.1, CCDS55679.1	1q32.1	2009-03-25			ENSG00000186007	ENSG00000186007			18725	protein-coding gene	gene with protein product	"cancer/testis antigen 50"	610480				15254688	Standard	NM_001199050		Approved	LEMP-1, CT50	uc001hcj.2	Q68G75	OTTHUMG00000037201	ENST00000367153.4:c.195T>C	chr1.hg19:g.205388368A>G		90.0	0.0		94.0	32.0	NM_001001552	Q6L9T9|Q6L9U0|Q6L9U1|Q6L9U2|Q6L9U3|Q6L9U4	Silent	SNP	ENST00000367153.4	hg19	CCDS55679.1																																																																																			.	.		0.463	LEMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090401.1	NM_001001552		G	205388368	A	G	205388368	2	3	199	1	0	0	0	0	0	0	0	1	8728	214	8	2		2	LEMD1	1	205388368	Silent	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	31932853	205388368	43862253	13	29239										
MIA3	375056	hgsc.bcm.edu	37	chr1	222801611	222801611	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	aaagtctggcgttgagaaatAtccaacagataaagagcaga	10	6	1	4			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr1:222801611A>G	ENST00000344922.5	+	4	1074	c.1049A>G	c.(1048-1050)tAt>tGt	p.Y350C	MIA3_ENST00000344507.1_Missense_Mutation_p.Y350C|MIA3_ENST00000344441.6_Missense_Mutation_p.Y350C|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	350					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		GTTGAGAAATATCCAACAGAT	0.398																																					p.Y350C		Atlas-SNP	.											.	MIA3	167	.	0			c.A1049G						.						82	77	79					1																	222801611		1839	4086	5925	SO:0001583	missense	375056	exon4			AGAAATATCCAAC		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.1049A>G	chr1.hg19:g.222801611A>G	ENSP00000340900:p.Tyr350Cys	280.0	0.0		299.0	112.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	hg19	CCDS41470.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.591555	0.66219	.	.	ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000344507	T;T;T	0.42900	0.96;0.96;1.47	5.15	1.34	0.21922	.	.	.	.	.	T	0.50034	0.1592	L	0.54323	1.7	0.09310	N	1	D;D	0.76494	0.997;0.999	P;D	0.63488	0.821;0.915	T	0.34304	-0.9834	9	0.62326	D	0.03	.	3.8254	0.08852	0.6618:0.1363:0.0715:0.1303	.	350;350	Q5JRA6-2;Q5JRA6	.;MIA3_HUMAN	C	350	ENSP00000340900:Y350C;ENSP00000340587:Y350C;ENSP00000341348:Y350C	ENSP00000325973:Y350C	Y	+	2	0	MIA3	220868234	0.000000	0.05858	0.000000	0.03702	0.564000	0.35744	0.690000	0.25451	0.033000	0.15463	0.373000	0.22412	TAT	.	.		0.398	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		G	222801611	A	G	222801611	3	3	199	1	0	0	0	0	1	0	0	0	9574	449	16	2	1063	2	MIA3	1	222801611	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	17413243	222801611	26449010	14	29240										
PXDN	7837	hgsc.bcm.edu	37	chr2	1642646	1642646	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tgaggtctgtgatggtcttcTgcatttccagaacaaactct	9	9	4	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:1642646T>C	ENST00000252804.4	-	21	4228	c.4178A>G	c.(4177-4179)cAg>cGg	p.Q1393R		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1393					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GATGGTCTTCTGCATTTCCAG	0.562																																					p.Q1393R		Atlas-SNP	.											.	PXDN	255	.	0			c.A4178G						.						138	142	141					2																	1642646		2090	4222	6312	SO:0001583	missense	7837	exon21			GTCTTCTGCATTT	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.4178A>G	chr2.hg19:g.1642646T>C	ENSP00000252804:p.Gln1393Arg	78.0	0.0		73.0	30.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	hg19	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	T	16.58	3.163565	0.57476	.	.	ENSG00000130508	ENST00000252804	T	0.60424	0.19	5.43	5.43	0.79202	.	0.119539	0.56097	D	0.000021	T	0.53948	0.1828	L	0.55990	1.75	0.43234	D	0.995136	B	0.14805	0.011	B	0.18561	0.022	T	0.51702	-0.8672	10	0.44086	T	0.13	-41.3602	14.0045	0.64453	0.0:0.0:0.0:1.0	.	1393	Q92626	PXDN_HUMAN	R	1393	ENSP00000252804:Q1393R	ENSP00000252804:Q1393R	Q	-	2	0	PXDN	1621653	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.289000	0.78701	2.185000	0.69588	0.460000	0.39030	CAG	.	.		0.562	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		C	1642646	T	C	1642646	3	2	199	1	0	0	0	0	1	0	0	0	12862	1580	55	2	273	2	PXDN	2	1642646	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10		1642646	241556727	15	29241										
C2orf53	339779	hgsc.bcm.edu	37	chr2	27360805	27360805	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agggaggagttctgaggctgGgagggagaaaaggaaggggt	22	2	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:27360805G>T	ENST00000335524.3	-	3	918	c.393C>A	c.(391-393)tcC>tcA	p.S131S		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		131	Pro-rich.									cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tctgaggctgggagggagaaa	0.622																																					p.S131S		Atlas-SNP	.											.	C2orf53	45	.	0			c.C393A						.						32	33	33					2																	27360805		2203	4300	6503	SO:0001819	synonymous_variant	339779	exon3			AGGCTGGGAGGGA																												ENST00000335524.3:c.393C>A	chr2.hg19:g.27360805G>T		86.0	0.0		88.0	34.0	NM_178553	Q86UE2	Silent	SNP	ENST00000335524.3	hg19	CCDS1739.1																																																																																			.	.		0.622	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1			T	27360805	G	T	27360805	2	4	199	1	0	0	0	0	0	0	0	1	2176	1219	43	3		3	C2orf53	2	27360805	Silent	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	25718159	27360805	215838568	16	29242										
C2orf73	129852	hgsc.bcm.edu	37	chr2	54587449	54587449	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gtcacgttcatcagaacagtCcaaaaaaacagagaaaggaa	8	8	3	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:54587449C>A	ENST00000398634.2	+	5	656	c.614C>A	c.(613-615)tCc>tAc	p.S205Y	C2orf73_ENST00000491538.1_Intron|C2orf73_ENST00000405749.1_Intron	NM_001100396.1	NP_001093866.1	Q8N5S3	CB073_HUMAN	chromosome 2 open reading frame 73	205										breast(2)	2						TCAGAACAGTCCAAAAAAACA	0.443																																					p.S205Y		Atlas-SNP	.											.	C2orf73	17	.	0			c.C614A						.						46	44	44					2																	54587449		1897	4116	6013	SO:0001583	missense	129852	exon5			AACAGTCCAAAAA	BC031669, AK097617	CCDS46285.1	2p16.2	2008-07-07			ENSG00000177994	ENSG00000177994			26861	protein-coding gene	gene with protein product						14702039	Standard	NM_001100396		Approved	FLJ40298	uc002rxt.1	Q8N5S3	OTTHUMG00000151826	ENST00000398634.2:c.614C>A	chr2.hg19:g.54587449C>A	ENSP00000381631:p.Ser205Tyr	173.0	0.0		171.0	77.0	NM_001100396	A0AV79|A0AV81|Q8N7V4	Missense_Mutation	SNP	ENST00000398634.2	hg19	CCDS46285.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.471324	0.84533	.	.	ENSG00000177994	ENST00000486488;ENST00000398634;ENST00000447328	T;T;T	0.32753	1.44;1.44;1.44	5.35	5.35	0.76521	.	0.469117	0.19565	N	0.111237	T	0.47710	0.1460	L	0.51422	1.61	0.34661	D	0.722634	D;D	0.59767	0.986;0.986	P;P	0.57152	0.742;0.814	T	0.58081	-0.7699	10	0.72032	D	0.01	-27.7261	19.4212	0.94721	0.0:1.0:0.0:0.0	.	147;205	B7ZM12;Q8N5S3	.;CB073_HUMAN	Y	211;205;147	ENSP00000417971:S211Y;ENSP00000381631:S205Y;ENSP00000389570:S147Y	ENSP00000381631:S205Y	S	+	2	0	C2orf73	54440953	0.461000	0.25783	0.976000	0.42696	0.977000	0.68977	3.871000	0.56077	2.660000	0.90430	0.650000	0.86243	TCC	.	.		0.443	C2orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324075.2	NM_001100396		A	54587449	C	A	54587449	3	1	199	1	0	0	0	0	1	0	0	0	2194	855	30	3	632	3	C2orf73	2	54587449	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	27226644	54587449	188611924	17	29243										
REV1	51455	hgsc.bcm.edu	37	chr2	100050856	100050856	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ccagctgggggttagcgccaGgacgtaaaggtgcccttcct	14	12	0	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:100050856G>A	ENST00000258428.3	-	8	1604	c.1376C>T	c.(1375-1377)cCt>cTt	p.P459L	REV1_ENST00000465835.1_5'UTR|REV1_ENST00000393445.3_Missense_Mutation_p.P459L	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	459	UmuC. {ECO:0000255|PROSITE- ProRule:PRU00216}.				DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTTAGCGCCAGGACGTAAAGG	0.443								Direct reversal of damage																													p.P459L		Atlas-SNP	.											.	REV1	100	.	0			c.C1376T						.						83	86	85					2																	100050856		2203	4300	6503	SO:0001583	missense	51455	exon8			GCGCCAGGACGTA	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.1376C>T	chr2.hg19:g.100050856G>A	ENSP00000258428:p.Pro459Leu	100.0	0.0		96.0	40.0	NM_001037872	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	hg19	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.528522	0.85706	.	.	ENSG00000135945	ENST00000393445;ENST00000258428;ENST00000450415	T;T;T	0.48836	1.54;1.54;0.8	5.58	5.58	0.84498	DNA-repair protein, UmuC-like, N-terminal (1);DNA-repair protein, UmuC-like (1);	0.099917	0.64402	D	0.000001	T	0.66197	0.2765	M	0.69358	2.11	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.73708	0.964;0.981	T	0.68269	-0.5453	10	0.72032	D	0.01	.	14.423	0.67196	0.0:0.0:0.8526:0.1474	.	459;459	Q9UBZ9;Q9UBZ9-2	REV1_HUMAN;.	L	459;459;97	ENSP00000377091:P459L;ENSP00000258428:P459L;ENSP00000414875:P97L	ENSP00000258428:P459L	P	-	2	0	REV1	99417288	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.436000	0.73417	2.626000	0.88956	0.561000	0.74099	CCT	.	.		0.443	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		A	100050856	G	A	100050856	3	1	199	1	0	0	0	0	1	0	0	0	13254	1000	35	3	2443	3	REV1	2	100050856	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	45463407	100050856	143148517	18	29244										
MYO7B	4648	hgsc.bcm.edu	37	chr2	128366406	128366406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agaaggtgttcggcttcctcCctgccatgattgggggccag	14	11	0	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:128366406C>T	ENST00000409816.2	+	21	2799	c.2767C>T	c.(2767-2769)Cct>Tct	p.P923S	MYO7B_ENST00000389524.4_Missense_Mutation_p.P923S|MYO7B_ENST00000428314.1_Missense_Mutation_p.P923S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	923						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CGGCTTCCTCCCTGCCATGAT	0.627																																					p.P923S		Atlas-SNP	.											.	MYO7B	359	.	0			c.C2767T						.						33	40	38					2																	128366406		2094	4203	6297	SO:0001583	missense	4648	exon22			TTCCTCCCTGCCA		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.2767C>T	chr2.hg19:g.128366406C>T	ENSP00000386461:p.Pro923Ser	158.0	0.0		211.0	99.0	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.975962	0.74360	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.87809	-2.3;-2.29;-2.29	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.87649	0.6230	L	0.61387	1.9	0.54753	D	0.999989	D	0.54397	0.966	P	0.45794	0.493	D	0.86403	0.1743	10	0.30854	T	0.27	.	18.8763	0.92337	0.0:1.0:0.0:0.0	.	923	Q6PIF6	MYO7B_HUMAN	S	923	ENSP00000374175:P923S;ENSP00000415090:P923S;ENSP00000386461:P923S	ENSP00000374175:P923S	P	+	1	0	MYO7B	128082876	0.046000	0.20272	0.921000	0.36526	0.955000	0.61496	0.755000	0.26405	2.548000	0.85928	0.462000	0.41574	CCT	.	.		0.627	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		T	128366406	C	T	128366406	3	4	199	1	0	0	0	0	1	0	0	0	10092	623	22	3	2849	3	MYO7B	2	128366406	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	28315550	128366406	114832967	19	29245										
NXPH2	11249	hgsc.bcm.edu	37	chr2	139429158	139429158	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gagtgcaccacgttgccgacCaacgtccctggagcatcttt	10	14	1	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:139429158C>T	ENST00000272641.3	-	2	235	c.129G>A	c.(127-129)ttG>ttA	p.L43L		NM_007226.2	NP_009157.1	O95156	NXPH2_HUMAN	neurexophilin 2	43	II.				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)|urinary_tract(3)	22				BRCA - Breast invasive adenocarcinoma(221;0.101)		CGTTGCCGACCAACGTCCCTG	0.542																																					p.L43L		Atlas-SNP	.											.	NXPH2	63	.	0			c.G129A						.						92	92	92					2																	139429158		1980	4173	6153	SO:0001819	synonymous_variant	11249	exon2			GCCGACCAACGTC	AF043467	CCDS46421.1	2q22.1	2008-05-15			ENSG00000144227	ENSG00000144227			8076	protein-coding gene	gene with protein product		604635				9570794	Standard	NM_007226		Approved	NPH2	uc002tvi.3	O95156	OTTHUMG00000153636	ENST00000272641.3:c.129G>A	chr2.hg19:g.139429158C>T		112.0	0.0		143.0	57.0	NM_007226	B7WP24|Q494R1|Q75QC3	Silent	SNP	ENST00000272641.3	hg19	CCDS46421.1																																																																																			.	.		0.542	NXPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331901.1			T	139429158	C	T	139429158	2	4	199	1	0	0	0	0	0	0	0	1	10800	593	21	3		3	NXPH2	2	139429158	Silent	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	11062752	139429158	103770215	20	29246										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141739748	141739748	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ccacaagatgccatttcatcTgtctggtcaccacagtcgtc	7	14	4	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:141739748T>A	ENST00000389484.3	-	18	3839	c.2868A>T	c.(2866-2868)acA>acT	p.T956T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	956	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCATTTCATCTGTCTGGTCAC	0.473										TSP Lung(27;0.18)																											p.T956T	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A2868T						.						147	128	134					2																	141739748		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon18			TTCATCTGTCTGG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2868A>T	chr2.hg19:g.141739748T>A		97.0	0.0		83.0	26.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.		0.473	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141739748	T	A	141739748	2	1	199	1	0	0	0	0	0	0	0	1	8964	1567	55	4		4	LRP1B	2	141739748	Silent	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	2310590	141739748	101459625	21	29247										
MBD5	55777	hgsc.bcm.edu	37	chr2	149267693	149267693	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ccatgagtgaactggacaaaAtgtctgggactgtaagttaa	11	6	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:149267693A>G	ENST00000407073.1	+	14	5399	c.4402A>G	c.(4402-4404)Atg>Gtg	p.M1468V	MBD5_ENST00000404807.1_Missense_Mutation_p.M1701V	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1468					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		ACTGGACAAAATGTCTGGGAC	0.313																																					p.M1468V		Atlas-SNP	.											.	MBD5	164	.	0			c.A4402G						.						98	101	100					2																	149267693		2203	4299	6502	SO:0001583	missense	55777	exon14			GACAAAATGTCTG	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.4402A>G	chr2.hg19:g.149267693A>G	ENSP00000386049:p.Met1468Val	399.0	0.0		368.0	144.0	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	hg19	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.856558	0.51376	.	.	ENSG00000204406	ENST00000407073;ENST00000404807	T;T	0.68903	-0.36;-0.36	5.41	5.41	0.78517	.	0.067384	0.64402	D	0.000006	T	0.63920	0.2552	L	0.53249	1.67	0.51233	D	0.999919	B;B	0.12013	0.005;0.005	B;B	0.14578	0.008;0.011	T	0.61931	-0.6961	10	0.54805	T	0.06	-6.8787	15.7403	0.77891	1.0:0.0:0.0:0.0	.	1701;1468	E9PHH0;Q9P267	.;MBD5_HUMAN	V	1468;1701	ENSP00000386049:M1468V;ENSP00000384672:M1701V	ENSP00000384672:M1701V	M	+	1	0	MBD5	148984163	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.714000	0.91412	2.173000	0.68751	0.528000	0.53228	ATG	.	.		0.313	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			G	149267693	A	G	149267693	3	3	199	1	0	0	0	0	1	0	0	0	9356	101	4	2	4436	2	MBD5	2	149267693	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	7527945	149267693	93931680	22	29248										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166868648	166868648	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	taagaagtccagccaacaccAggcattggtgaaatatgttt	9	8	0	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:166868648A>T	ENST00000303395.4	-	19	3849	c.3850T>A	c.(3850-3852)Tgg>Agg	p.W1284R	SCN1A_ENST00000375405.3_Missense_Mutation_p.W1273R|SCN1A_ENST00000409050.1_Missense_Mutation_p.W1256R|SCN1A_ENST00000423058.2_Missense_Mutation_p.W1284R|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1284					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGCCAACACCAGGCATTGGTG	0.348																																					p.W1284R		Atlas-SNP	.											.	SCN1A	641	.	0			c.T3850A						.						107	97	100					2																	166868648		2203	4299	6502	SO:0001583	missense	6323	exon19			AACACCAGGCATT	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3850T>A	chr2.hg19:g.166868648A>T	ENSP00000303540:p.Trp1284Arg	330.0	0.0		285.0	105.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.442580	0.83993	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.99176	-5.52;-5.52;-5.52;-5.52	5.38	5.38	0.77491	Ion transport (1);	0.000000	0.53938	D	0.000044	D	0.99753	0.9901	H	0.99986	5.255	0.80722	D	1	P;D;D	0.89917	0.94;0.999;1.0	P;D;D	0.97110	0.622;0.998;1.0	D	0.96409	0.9303	10	0.87932	D	0	.	15.3795	0.74641	1.0:0.0:0.0:0.0	.	1273;1256;1284	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	R	1284;1284;1273;1256	ENSP00000407030:W1284R;ENSP00000303540:W1284R;ENSP00000364554:W1273R;ENSP00000386312:W1256R	ENSP00000303540:W1284R	W	-	1	0	SCN1A	166576894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.284000	0.95882	2.029000	0.59856	0.455000	0.32223	TGG	.	.		0.348	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166868648	A	T	166868648	3	4	199	1	0	0	0	0	1	0	0	0	13929	188	7	4	2211	4	SCN1A	2	166868648	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	17600955	166868648	76330725	23	29249										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168115577	168115577	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	actttttcttttctaacaccGtgaaaatcactgcattttcc	3	11	3	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:168115577G>A	ENST00000409728.1	+	11	2709	c.2620G>A	c.(2620-2622)Gtg>Atg	p.V874M	XIRP2_ENST00000420519.1_Missense_Mutation_p.V874M|XIRP2_ENST00000409043.1_Missense_Mutation_p.V841M|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409605.1_Missense_Mutation_p.V619M|XIRP2_ENST00000409756.2_Missense_Mutation_p.V841M|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409195.1_3'UTR	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTCTAACACCGTGAAAATCAC	0.308																																					p.V874M		Atlas-SNP	.											.	XIRP2	914	.	0			c.G2620A						.						28	27	27					2																	168115577		1807	4077	5884	SO:0001583	missense	129446	exon11			AACACCGTGAAAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2620G>A	chr2.hg19:g.168115577G>A	ENSP00000386619:p.Val874Met	550.0	1.0		488.0	185.0	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	hg19	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.344134	0.24339	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	D;D;D;D;D	0.85339	-1.89;-1.88;-1.89;-1.88;-1.97	5.66	2.88	0.33553	.	.	.	.	.	T	0.70334	0.3212	.	.	.	0.80722	D	1	P;P	0.45569	0.861;0.861	B;B	0.31016	0.123;0.123	T	0.64964	-0.6283	8	0.31617	T	0.26	.	6.8616	0.24069	0.2165:0.1834:0.6001:0.0	.	841;874	A4UGR9-4;A4UGR9-6	.;.	M	841;874;841;874;619	ENSP00000386454:V841M;ENSP00000386619:V874M;ENSP00000386724:V841M;ENSP00000415541:V874M;ENSP00000386981:V619M	ENSP00000386454:V841M	V	+	1	0	XIRP2	167823823	0.272000	0.24172	0.997000	0.53966	0.940000	0.58332	0.376000	0.20535	0.757000	0.33036	0.555000	0.69702	GTG	.	.		0.308	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		A	168115577	G	A	168115577	3	1	199	1	0	0	0	0	1	0	0	0	17445	1145	40	1	11938	1	XIRP2	2	168115577	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	1246929	168115577	75083796	24	29250										
UBR3	130507	hgsc.bcm.edu	37	chr2	170806382	170806382	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggcttgatgacatagaaattTtaatccaaccagaaattcct	6	8	0	4			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:170806382T>G	ENST00000272793.5	+	23	3402	c.3352T>G	c.(3352-3354)Tta>Gta	p.L1118V	UBR3_ENST00000418381.1_Missense_Mutation_p.L1118V			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1118					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						CATAGAAATTTTAATCCAACC	0.348																																					p.L1118V		Atlas-SNP	.											.	UBR3	182	.	0			c.T3352G						.						97	81	86					2																	170806382		692	1591	2283	SO:0001583	missense	130507	exon23			GAAATTTTAATCC	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.3352T>G	chr2.hg19:g.170806382T>G	ENSP00000272793:p.Leu1118Val	253.0	0.0		289.0	138.0	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.37|17.37	3.373614|3.373614	0.61624|0.61624	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000392632|ENST00000272793;ENST00000442603;ENST00000418381	.|T;T	.|0.53857	.|0.6;0.6	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	.|.	.|.	.|.	.|.	T|T	0.53932|0.53932	0.1827|0.1827	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	.|P	.|0.52842	.|0.956	.|D	.|0.65010	.|0.931	T|T	0.51268|0.51268	-0.8727|-0.8727	5|9	.|0.27082	.|T	.|0.32	.|.	10.3543|10.3543	0.43954|0.43954	0.0:0.0727:0.0:0.9273|0.0:0.0727:0.0:0.9273	.|.	.|1118	.|Q6ZT12	.|UBR3_HUMAN	L|V	175|1118	.|ENSP00000272793:L1118V;ENSP00000396068:L1118V	.|ENSP00000272793:L1118V	F|L	+|+	3|1	2|2	UBR3|UBR3	170514628|170514628	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.253000|2.253000	0.43205|0.43205	2.191000|2.191000	0.70037|0.70037	0.528000|0.528000	0.53228|0.53228	TTT|TTA	.	.		0.348	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		G	170806382	T	G	170806382	3	3	199	1	0	0	0	0	1	0	0	0	16918	1838	64	5	3442	5	UBR3	2	170806382	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	2690805	170806382	72392991	25	29251										
OBFC2A	64859	hgsc.bcm.edu	37	chr2	192546742	192546742	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gtgaacttcaaaaaattgggGagtaagtattaaaatgcatt	9	3	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:192546742G>T	ENST00000425611.2	+	3	384	c.301G>T	c.(301-303)Gaa>Taa	p.E101*	NABP1_ENST00000410026.2_Splice_Site_p.E21*|NABP1_ENST00000409510.1_Splice_Site_p.E21*	NM_001031716.2	NP_001026886.1	Q96AH0	SOSB2_HUMAN	nucleic acid binding protein 1	101					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SOSS complex (GO:0070876)	RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)										AAAAATTGGGGAGTAAGTATT	0.318																																					p.E101X		Atlas-SNP	.											.	.	.	.	0			c.G301T						.						55	57	56					2																	192546742		2202	4295	6497	SO:0001630	splice_region_variant	64859	exon3			ATTGGGGAGTAAG	BC017114	CCDS33352.1, CCDS58745.1	2q32.3	2012-06-19	2012-06-19	2012-06-19	ENSG00000173559	ENSG00000173559			26232	protein-coding gene	gene with protein product	"single-stranded DNA-binding protein 2", "sensor of single-strand DNA complex subunit B2"	612103	"oligonucleotide/oligosaccharide-binding fold containing 2A"	OBFC2A			Standard	NM_001031716		Approved	FLJ22833, DKFZp667M1322, FLJ13624, MGC111163, SSB2, hSSB2, SOSS-B2	uc002usx.3	Q96AH0	OTTHUMG00000132720	ENST00000425611.2:c.302+1G>T	chr2.hg19:g.192546742G>T		787.0	1.0		694.0	273.0	NM_001031716	Q658Y8|Q9H5X6	Nonsense_Mutation	SNP	ENST00000425611.2	hg19	CCDS33352.1	.	.	.	.	.	.	.	.	.	.	G	37	6.151667	0.97329	.	.	ENSG00000173559	ENST00000410026;ENST00000409510;ENST00000425611	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.9813	0.97326	0.0:0.0:1.0:0.0	.	.	.	.	X	21;21;101	.	ENSP00000386605:E21X	E	+	1	0	OBFC2A	192254987	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.835000	0.99442	2.726000	0.93360	0.655000	0.94253	GAA	.	.		0.318	NABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256060.1	NM_022837	Nonsense_Mutation	T	192546742	G	T	192546742	5	4	199	1	0	0	0	0	0	0	1	0	10817	1188	41	3	311	3	OBFC2A	2	192546742	Splice_Site	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	21740360	192546742	50652631	26	29252										
AOX1	316	hgsc.bcm.edu	37	chr2	201521589	201521589	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ctgccttggttcacatttatCttgatggctctgtgctggtc	10	10	3	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:201521589C>T	ENST00000374700.2	+	27	3341	c.3100C>T	c.(3100-3102)Ctt>Ttt	p.L1034F	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1034					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TCACATTTATCTTGATGGCTC	0.408																																					p.L1034F		Atlas-SNP	.											.	AOX1	152	.	0			c.C3100T						.						111	102	105					2																	201521589		2203	4300	6503	SO:0001583	missense	316	exon27			ATTTATCTTGATG	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3100C>T	chr2.hg19:g.201521589C>T	ENSP00000363832:p.Leu1034Phe	123.0	0.0		96.0	30.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	hg19	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.082548	0.36758	.	.	ENSG00000138356	ENST00000374700	T	0.37235	1.21	5.41	2.46	0.29980	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.359640	0.29783	N	0.011218	T	0.47600	0.1454	M	0.76002	2.32	0.09310	N	0.999999	P	0.50156	0.932	P	0.57425	0.82	T	0.36939	-0.9727	10	0.56958	D	0.05	-5.4518	4.0635	0.09849	0.3376:0.4169:0.0:0.2455	.	1034	Q06278	ADO_HUMAN	F	1034	ENSP00000363832:L1034F	ENSP00000363832:L1034F	L	+	1	0	AOX1	201229834	0.928000	0.31464	0.038000	0.18304	0.588000	0.36517	2.053000	0.41326	0.324000	0.23333	-0.367000	0.07326	CTT	.	.		0.408	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		T	201521589	C	T	201521589	3	4	199	1	0	0	0	0	1	0	0	0	729	913	32	3	3206	3	AOX1	2	201521589	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	8974847	201521589	41677784	27	29253										
FN1	2335	hgsc.bcm.edu	37	chr2	216261901	216261901	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	aggagactgtgagcactccaGtgtcagggtttgcctccaga	13	10	1	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:216261901G>T	ENST00000359671.1	-	23	3828	c.3563C>A	c.(3562-3564)aCt>aAt	p.T1188N	FN1_ENST00000446046.1_Missense_Mutation_p.T1188N|FN1_ENST00000357867.4_Missense_Mutation_p.T1188N|FN1_ENST00000345488.5_Missense_Mutation_p.T1188N|FN1_ENST00000357009.2_Missense_Mutation_p.T1188N|FN1_ENST00000421182.1_Missense_Mutation_p.T1188N|FN1_ENST00000346544.3_Missense_Mutation_p.T1188N|FN1_ENST00000336916.4_Missense_Mutation_p.T1188N|FN1_ENST00000323926.6_Missense_Mutation_p.T1188N|FN1_ENST00000443816.1_Missense_Mutation_p.T1188N|FN1_ENST00000354785.4_Missense_Mutation_p.T1188N|FN1_ENST00000356005.4_Missense_Mutation_p.T1188N|FN1_ENST00000432072.2_Missense_Mutation_p.T1188N			P02751	FINC_HUMAN	fibronectin 1	1188	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	GAGCACTCCAGTGTCAGGGTT	0.473																																					p.T1188N		Atlas-SNP	.											.	FN1	521	.	0			c.C3563A						.						197	195	195					2																	216261901		2203	4300	6503	SO:0001583	missense	2335	exon23			ACTCCAGTGTCAG		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.3563C>A	chr2.hg19:g.216261901G>T	ENSP00000352696:p.Thr1188Asn	104.0	0.0		93.0	32.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.32	2.203299	0.38905	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.57273	0.45;0.41;0.41;0.45;0.41;0.41;0.45;0.41;0.41;0.41;0.45;0.41;0.45	5.62	4.73	0.59995	.	0.256048	0.33895	N	0.004442	T	0.59376	0.2189	N	0.21545	0.675	0.54753	D	0.999981	D;B;P;D;P;B;D;D;D;D	0.76494	0.984;0.14;0.79;0.998;0.932;0.136;0.999;0.985;0.992;0.998	P;B;P;D;P;B;D;D;D;D	0.79108	0.839;0.139;0.614;0.922;0.672;0.082;0.992;0.989;0.989;0.974	T	0.61103	-0.7130	10	0.40728	T	0.16	.	16.0028	0.80308	0.0:0.0:0.8643:0.1357	.	1188;1188;1188;1188;1188;1188;1188;1188;1188;1188	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	N	1188	ENSP00000394423:T1188N;ENSP00000323534:T1188N;ENSP00000338200:T1188N;ENSP00000350534:T1188N;ENSP00000346839:T1188N;ENSP00000352696:T1188N;ENSP00000265312:T1188N;ENSP00000273049:T1188N;ENSP00000349509:T1188N;ENSP00000410422:T1188N;ENSP00000415018:T1188N;ENSP00000399538:T1188N;ENSP00000348285:T1188N	ENSP00000265313:T1188N	T	-	2	0	FN1	215970146	1.000000	0.71417	0.965000	0.40720	0.083000	0.17756	5.954000	0.70298	1.469000	0.48083	0.585000	0.79938	ACT	.	.		0.473	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216261901	G	T	216261901	3	4	199	1	0	0	0	0	1	0	0	0	5970	1029	36	3	3966	3	FN1	2	216261901	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	14740312	216261901	26937472	28	29254										
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233709124	233709124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggaattctgtttggggctctAtaaatactggtcctcctaac	9	9	2	0	rs371374687		TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:233709124A>G	ENST00000409547.1	+	27	3456	c.3145A>G	c.(3145-3147)Ata>Gta	p.I1049V	GIGYF2_ENST00000409196.3_Missense_Mutation_p.I1043V|GIGYF2_ENST00000409480.1_Missense_Mutation_p.I1071V|GIGYF2_ENST00000452341.2_3'UTR|GIGYF2_ENST00000373563.4_Missense_Mutation_p.I1049V|GIGYF2_ENST00000409451.3_Missense_Mutation_p.I1070V|GIGYF2_ENST00000373566.3_Missense_Mutation_p.I1071V	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1049					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		TTGGGGCTCTATAAATACTGG	0.398																																					p.I1070V		Atlas-SNP	.											.	GIGYF2	288	.	0			c.A3208G						.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	101	100	100		3145,3127,3208,3145	2.2	1	2		100	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	GIGYF2	NM_015575.3,NM_001103148.1,NM_001103147.1,NM_001103146.1	29,29,29,29	0,2,6501	GG,GA,AA		0.0116,0.0227,0.0154	benign,benign,benign,benign	1049/1300,1043/1294,1070/1321,1049/1300	233709124	2,13004	2203	4300	6503	SO:0001583	missense	26058	exon27			GGCTCTATAAATA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3145A>G	chr2.hg19:g.233709124A>G	ENSP00000386537:p.Ile1049Val	138.0	0.0		144.0	59.0	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	A	5.324	0.245083	0.10077	2.27E-4	1.16E-4	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000426102	T;T;T;T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54;-0.54;-0.54;1.34	5.82	2.24	0.28232	.	0.205159	0.51477	D	0.000090	T	0.34366	0.0895	N	0.02011	-0.69	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.03025	-1.1081	10	0.19147	T	0.46	-13.0994	1.7782	0.03026	0.4742:0.2433:0.1743:0.1082	.	1070;1049;1043	A6H8W4;Q6Y7W6;E9PBB0	.;PERQ2_HUMAN;.	V	1071;1049;1071;1049;1043;1070;78	ENSP00000362667:I1071V;ENSP00000362664:I1049V;ENSP00000386765:I1071V;ENSP00000386537:I1049V;ENSP00000387070:I1043V;ENSP00000387170:I1070V;ENSP00000415037:I78V	ENSP00000362664:I1049V	I	+	1	0	GIGYF2	233417368	0.972000	0.33761	0.991000	0.47740	0.580000	0.36256	1.455000	0.35190	0.466000	0.27193	-0.379000	0.06801	ATA	.	.		0.398	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		G	233709124	A	G	233709124	3	3	199	1	0	0	0	0	1	0	0	0	6386	449	16	2	3305	2	GIGYF2	2	233709124	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	17447223	233709124	9490249	29	29255										
UGT1A3	54659	hgsc.bcm.edu	37	chr2	234638551	234638551	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tgtgtggctgttccgaggggActttgtgatggactacccca	14	9	0	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr2:234638551A>G	ENST00000482026.1	+	1	798	c.779A>G	c.(778-780)gAc>gGc	p.D260G	UGT1A6_ENST00000406651.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000609767.1_Missense_Mutation_p.D260G|UGT1A5_ENST00000373414.3_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A1_ENST00000373450.4_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	260					cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)			breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	TTCCGAGGGGACTTTGTGATG	0.502																																					p.D260G		Atlas-SNP	.											.	UGT1A3	91	.	0			c.A779G						.						199	197	197					2																	234638551		2203	4300	6503	SO:0001583	missense	54659	exon1			GAGGGGACTTTGT	M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"UDP glucuronosyltransferases"	12535	other	complex locus constituent		606428	"UDP glycosyltransferase 1 family, polypeptide A3"			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.779A>G	chr2.hg19:g.234638551A>G	ENSP00000418532:p.Asp260Gly	150.0	0.0		142.0	47.0	NM_019093	B8K287	Missense_Mutation	SNP	ENST00000482026.1	hg19	CCDS2509.1	.	.	.	.	.	.	.	.	.	.	a	19.77	3.888640	0.72524	.	.	ENSG00000243135	ENST00000482026	T	0.61510	0.1	3.91	3.91	0.45181	.	.	.	.	.	T	0.78515	0.4295	M	0.94021	3.485	0.48511	D	0.999669	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80585	-0.1317	9	0.12766	T	0.61	.	12.7681	0.57403	1.0:0.0:0.0:0.0	.	260;260	Q5DT01;P35503	.;UD13_HUMAN	G	260	ENSP00000418532:D260G	ENSP00000418532:D260G	D	+	2	0	UGT1A3	234303290	1.000000	0.71417	0.980000	0.43619	0.947000	0.59692	9.145000	0.94634	1.414000	0.47017	0.373000	0.22412	GAC	.	.		0.502	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093		G	234638551	A	G	234638551	3	3	199	1	0	0	0	0	1	0	0	0	16961	275	10	2	781	2	UGT1A3	2	234638551	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	929427	234638551	8560822	30	29256										
FAM116A	201627	hgsc.bcm.edu	37	chr3	57646534	57646534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gtgtaatgttttccctggcaCtggggcaggccatcgatcaa	12	10	1	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr3:57646534C>A	ENST00000311128.5	-	7	722	c.652G>T	c.(652-654)Gtg>Ttg	p.V218L		NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	218					positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										TTCCCTGGCACTGGGGCAGGC	0.303																																					p.V218L		Atlas-SNP	.											.	.	.	.	0			c.G652T						.						43	43	43					3																	57646534		2203	4300	6503	SO:0001583	missense	201627	exon7			CTGGCACTGGGGC	AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839		"DENN/MADD domain containing"	26635	protein-coding gene	gene with protein product			"family with sequence similarity 116, member A"	FAM116A		21330364	Standard	NM_152678		Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.652G>T	chr3.hg19:g.57646534C>A	ENSP00000311401:p.Val218Leu	1511.0	1.0		1369.0	553.0	NM_152678	Q7Z5T4|Q8N235|Q8TEG8	Missense_Mutation	SNP	ENST00000311128.5	hg19	CCDS33773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.02|10.02	1.236027|1.236027	0.22626|0.22626	.|.	.|.	ENSG00000174839|ENSG00000174839	ENST00000477344|ENST00000311128	.|.	.|.	.|.	5.02|5.02	2.21|2.21	0.28008|0.28008	.|.	.|0.402362	.|0.27253	.|N	.|0.020215	T|T	0.40448|0.40448	0.1117|0.1117	L|L	0.38531|0.38531	1.155|1.155	0.35302|0.35302	D|D	0.783112|0.783112	.|B	.|0.06786	.|0.001	.|B	.|0.08055	.|0.003	T|T	0.37361|0.37361	-0.9709|-0.9709	5|9	.|0.08381	.|T	.|0.77	-12.2775|-12.2775	9.9256|9.9256	0.41489|0.41489	0.0:0.7715:0.0:0.2285|0.0:0.7715:0.0:0.2285	.|.	.|218	.|Q8IWF6	.|F116A_HUMAN	I|L	7|218	.|.	.|ENSP00000311401:V218L	S|V	-|-	2|1	0|0	FAM116A|FAM116A	57621574|57621574	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	0.870000|0.870000	0.28010|0.28010	0.515000|0.515000	0.28320|0.28320	0.460000|0.460000	0.39030|0.39030	AGT|GTG	.	.		0.303	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351594.1	NM_152678		A	57646534	C	A	57646534	3	1	199	1	0	0	0	0	1	0	0	0	5412	565	20	3	1230	3	FAM116A	3	57646534	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10		57646534	140375896	31	29257										
EAF2	55840	hgsc.bcm.edu	37	chr3	121573668	121573668	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	aacatcactgtaaaaaaaacAaggtatgtggtttaatgaaa	7	4	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr3:121573668A>C	ENST00000273668.2	+	3	407	c.336A>C	c.(334-336)acA>acC	p.T112T	EAF2_ENST00000451944.2_Silent_p.T112T	NM_018456.4	NP_060926.2	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	112					apoptotic process (GO:0006915)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	ELL-EAF complex (GO:0032783)|transcription elongation factor complex (GO:0008023)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)	9				GBM - Glioblastoma multiforme(114;0.0972)		TAAAAAAAACAAGGTATGTGG	0.249																																					p.T112T	Esophageal Squamous(194;1942 2097 24663 29345 31866)	Atlas-SNP	.											.	EAF2	26	.	0			c.A336C						.						43	48	46					3																	121573668		2201	4295	6496	SO:0001819	synonymous_variant	55840	exon3			AAAAACAAGGTAT	AF517829	CCDS3006.1	3q21.1	2007-08-01			ENSG00000145088	ENSG00000145088			23115	protein-coding gene	gene with protein product		607659				12446457, 12907652	Standard	NM_018456		Approved	BM040, TRAITS, U19	uc003een.3	Q96CJ1	OTTHUMG00000159424	ENST00000273668.2:c.336A>C	chr3.hg19:g.121573668A>C		729.0	0.0		693.0	267.0	NM_018456	Q9NZ82	Silent	SNP	ENST00000273668.2	hg19	CCDS3006.1																																																																																			.	.		0.249	EAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355247.1	NM_018456		C	121573668	A	C	121573668	2	2	199	1	0	0	0	0	0	0	0	1	4878	117	5	5		5	EAF2	3	121573668	Silent	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	63927134	121573668	76448762	32	29258										
MUC13	56667	hgsc.bcm.edu	37	chr3	124635177	124635177	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tacttacaatcatagtttagAaagttgcttgagctacttct	6	7	2	2	rs370885108		TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr3:124635177A>G	ENST00000311075.3	-	6	986	c.948T>C	c.(946-948)ttT>ttC	p.F316F		NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	317	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						CATAGTTTAGAAAGTTGCTTG	0.308																																					p.F316F		Atlas-SNP	.											.	MUC13	57	.	0			c.T948C						.						95	90	92					3																	124635177		2202	4299	6501	SO:0001819	synonymous_variant	56667	exon6			GTTTAGAAAGTTG	AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"Mucins"	7511	protein-coding gene	gene with protein product		612181	"down-regulated in colon cancer 1", "mucin 13, epithelial transmembrane"	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.948T>C	chr3.hg19:g.124635177A>G		214.0	0.0		217.0	100.0	NM_033049	Q6UWD9|Q9NXT5	Silent	SNP	ENST00000311075.3	hg19																																																																																				.	.		0.308	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049		G	124635177	A	G	124635177	2	3	199	1	0	0	0	0	0	0	0	1	9980	243	9	2		2	MUC13	3	124635177	Silent	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	3061509	124635177	73387253	33	29259										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130380832	130380832	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	actaaatggagatgcttttaTtggtcatgccttacagtgga	10	6	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr3:130380832T>C	ENST00000358511.6	+	34	6213	c.6182T>C	c.(6181-6183)aTt>aCt	p.I2061T	COL6A6_ENST00000453409.2_Missense_Mutation_p.I2061T	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	2061	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GATGCTTTTATTGGTCATGCC	0.418																																					p.I2061T		Atlas-SNP	.											.	COL6A6	497	.	0			c.T6182C						.						91	89	89					3																	130380832		1896	4134	6030	SO:0001583	missense	131873	exon34			CTTTTATTGGTCA	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.6182T>C	chr3.hg19:g.130380832T>C	ENSP00000351310:p.Ile2061Thr	111.0	0.0		133.0	49.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268604	0.40095	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.81330	-1.48;-1.48	6.04	6.04	0.98038	von Willebrand factor, type A (3);	.	.	.	.	T	0.71484	0.3345	N	0.21583	0.68	0.09310	N	1	B;B	0.21520	0.027;0.057	B;B	0.28385	0.024;0.089	T	0.54330	-0.8310	9	0.11794	T	0.64	.	16.5763	0.84648	0.0:0.0:0.0:1.0	.	2061;2061	A6NMZ7;F8W6Y7	CO6A6_HUMAN;.	T	2061	ENSP00000351310:I2061T;ENSP00000399236:I2061T	ENSP00000351310:I2061T	I	+	2	0	COL6A6	131863522	0.114000	0.22134	0.007000	0.13788	0.896000	0.52359	3.251000	0.51453	2.317000	0.78254	0.459000	0.35465	ATT	.	.		0.418	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		C	130380832	T	C	130380832	3	2	199	1	0	0	0	0	1	0	0	0	3705	1493	52	2	6316	2	COL6A6	3	130380832	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	5745655	130380832	67641598	34	29260										
ESYT3	83850	hgsc.bcm.edu	37	chr3	138183192	138183192	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ttggacattttccagggggtGatcagagtgcacttgctgga	14	7	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr3:138183192G>A	ENST00000389567.4	+	9	1107	c.921G>A	c.(919-921)gtG>gtA	p.V307V		NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	307	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|organelle membrane contact site (GO:0044232)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	25						TCCAGGGGGTGATCAGAGTGC	0.587																																					p.V307V		Atlas-SNP	.											.	ESYT3	64	.	0			c.G921A						.						51	53	52					3																	138183192		2203	4300	6503	SO:0001819	synonymous_variant	83850	exon9			GGGGGTGATCAGA	AJ303366	CCDS3101.2	3q22.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000158220	ENSG00000158220		"Synaptotagmins"	24295	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member C"	FAM62C		11543631, 17672888	Standard	NM_031913		Approved	CHR3SYT	uc003esk.3	A0FGR9	OTTHUMG00000147354	ENST00000389567.4:c.921G>A	chr3.hg19:g.138183192G>A		74.0	0.0		63.0	23.0	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Silent	SNP	ENST00000389567.4	hg19	CCDS3101.2																																																																																			.	.		0.587	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913		A	138183192	G	A	138183192	2	1	199	1	0	0	0	0	0	0	0	1	5268	1277	45	3		3	ESYT3	3	138183192	Silent	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	7802360	138183192	59839238	35	29261										
CCDC39	339829	hgsc.bcm.edu	37	chr3	180377348	180377348	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tgaatcttacgaaaatcttgTgctgctttatccaattctaa	5	8	3	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr3:180377348T>C	ENST00000442201.2	-	6	749	c.630A>G	c.(628-630)gcA>gcG	p.A210A	CCDC39_ENST00000273654.4_Silent_p.A294A	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	210					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			GAAAATCTTGTGCTGCTTTAT	0.328																																					p.A210A		Atlas-SNP	.											.	CCDC39	242	.	0			c.A630G						.						246	224	231					3																	180377348		1866	4106	5972	SO:0001819	synonymous_variant	339829	exon6			ATCTTGTGCTGCT	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.630A>G	chr3.hg19:g.180377348T>C		177.0	0.0		123.0	49.0	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	hg19	CCDS46964.1																																																																																			.	.		0.328	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		C	180377348	T	C	180377348	2	2	199	1	0	0	0	0	0	0	0	1	2813	1683	59	2		2	CCDC39	3	180377348	Silent	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	42194156	180377348	17645082	36	29262										
KIAA0226	9711	hgsc.bcm.edu	37	chr3	197409349	197409349	+	Silent	SNP	T	T	A													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ctggccactcacgttggggcTggatgaacattaaaaattat							TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr3:197409349T>A	ENST00000296343.5	-	14	2117	c.2118A>T	c.(2116-2118)ccA>ccT	p.P706P	KIAA0226_ENST00000273582.5_Silent_p.P661P|KIAA0226_ENST00000389665.5_Silent_p.P731P	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	706					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		ACGTTGGGGCTGGATGAACAT	0.562																																					p.P706P	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.A2118T						.						31	37	35					3																	197409349		1970	4152	6122	SO:0001819	synonymous_variant	9711	exon14			TGGGGCTGGATGA	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.2118A>T	chr3.hg19:g.197409349T>A		165.0	0.0		129.0	54.0	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	hg19	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.06|11.06	1.526432|1.526432	0.27299|0.27299	.|.	.|.	ENSG00000145016|ENSG00000145016	ENST00000415452|ENST00000413360	.|.	.|.	.|.	5.56|5.56	0.231|0.231	0.15377|0.15377	.|.	.|.	.|.	.|.	.|.	T|T	0.40791|0.40791	0.1131|0.1131	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.27971|0.27971	-1.0058|-1.0058	4|4	.|.	.|.	.|.	.|.	1.2423|1.2423	0.01965|0.01965	0.207:0.2021:0.1064:0.4846|0.207:0.2021:0.1064:0.4846	.|.	.|.	.|.	.|.	L|C	490|668	.|.	.|.	Q|S	-|-	2|1	0|0	KIAA0226|KIAA0226	198893746|198893746	0.272000|0.272000	0.24172|0.24172	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	-0.458000|-0.458000	0.06737|0.06737	0.428000|0.428000	0.26173|0.26173	-0.258000|-0.258000	0.10820|0.10820	CAG|AGC	.	.		0.562	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		A	197409349	T	A	197409349	2	1	199	1	0	0	0	0	0	0	0	1	8171	1567	55	4		4	KIAA0226	3	197409349	Silent	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	17032001	197409349	613081	37	29263	150	2								
KIAA0226	9711	hgsc.bcm.edu	37	chr3	197409351	197409351	+	Missense_Mutation	SNP	G	G	A													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggccactcacgttggggctgGatgaacattaaaaattatct							TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr3:197409351G>A	ENST00000296343.5	-	14	2115	c.2116C>T	c.(2116-2118)Cca>Tca	p.P706S	KIAA0226_ENST00000273582.5_Missense_Mutation_p.P661S|KIAA0226_ENST00000389665.5_Missense_Mutation_p.P731S	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	706					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		GTTGGGGCTGGATGAACATTA	0.567																																					p.P706S	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.C2116T						.						32	37	36					3																	197409351		1970	4155	6125	SO:0001583	missense	9711	exon14			GGGCTGGATGAAC	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.2116C>T	chr3.hg19:g.197409351G>A	ENSP00000296343:p.Pro706Ser	166.0	0.0		135.0	54.0	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	hg19	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.52|15.52	2.858421|2.858421	0.51376|0.51376	.|.	.|.	ENSG00000145016|ENSG00000145016	ENST00000273582;ENST00000296343;ENST00000389665|ENST00000413360	.|.	.|.	.|.	5.56|5.56	4.69|4.69	0.59074|0.59074	.|.	0.123169|.	0.56097|.	N|.	0.000033|.	T|T	0.61974|0.61974	0.2390|0.2390	M|M	0.67625|0.67625	2.065|2.065	0.49130|0.49130	D|D	0.999754|0.999754	P;B;P|.	0.35348|.	0.488;0.165;0.496|.	B;B;B|.	0.37267|.	0.209;0.086;0.245|.	T|T	0.61540|0.61540	-0.7042|-0.7042	9|5	0.45353|.	T|.	0.12|.	.|.	6.7282|6.7282	0.23369|0.23369	0.146:0.0:0.7104:0.1436|0.146:0.0:0.7104:0.1436	.|.	731;661;706|.	Q92622-3;Q92622-2;Q92622|.	.;.;RUBIC_HUMAN|.	S|F	661;706;731|667	.|.	ENSP00000273582:P661S|.	P|S	-|-	1|2	0|0	KIAA0226|KIAA0226	198893748|198893748	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.467000|3.467000	0.53078|0.53078	1.360000|1.360000	0.45960|0.45960	0.655000|0.655000	0.94253|0.94253	CCA|TCC	.	.		0.567	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		A	197409351	G	A	197409351	3	1	199	1	0	0	0	0	1	0	0	0	8171	1174	41	3	830	3	KIAA0226	3	197409351	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	2	197409351	613079	38	29264	150	2								
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6865250	6865250	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tcctttgacttaagcaatccAttttcacaagttcttcatgt	4	10	3	1	rs549270762		TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr4:6865250A>G	ENST00000307659.5	+	7	3596	c.3141A>G	c.(3139-3141)ccA>ccG	p.P1047P	KIAA0232_ENST00000425103.1_Silent_p.P1047P	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	1047							ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						TAAGCAATCCATTTTCACAAG	0.388													A|||	1	0.000199681	8e-04	0	5008	,	,		20559	0		0	False		,,,				2504	0				p.P1047P		Atlas-SNP	.											.	KIAA0232	102	.	0			c.A3141G						.						78	73	75					4																	6865250		1849	4101	5950	SO:0001819	synonymous_variant	9778	exon7			CAATCCATTTTCA	D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.3141A>G	chr4.hg19:g.6865250A>G		123.0	0.0		127.0	43.0	NM_014743	A7E2D2	Silent	SNP	ENST00000307659.5	hg19	CCDS43209.1																																																																																			.	.		0.388	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		G	6865250	A	G	6865250	2	3	199	1	0	0	0	0	0	0	0	1	8172	204	8	2		2	KIAA0232	4	6865250	Silent	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10		6865250	184289026	39	29265										
NSUN7	79730	hgsc.bcm.edu	37	chr4	40809188	40809188	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	caatggttgttttctttctaTtttaacaagggaggtaagga	10	4	2	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr4:40809188T>C	ENST00000381782.2	+	11	2006	c.1511T>C	c.(1510-1512)aTt>aCt	p.I504T	NSUN7_ENST00000316607.5_Intron	NM_024677.4	NP_078953	Q8NE18	NSUN7_HUMAN	NOP2/Sun domain family, member 7	504							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|cervix(1)|large_intestine(1)|lung(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						TTTCTTTCTATTTTAACAAGG	0.343																																					p.I504T		Atlas-SNP	.											.	NSUN7	70	.	0			c.T1511C						.						88	72	77					4																	40809188		692	1591	2283	SO:0001583	missense	79730	exon11			TTTCTATTTTAAC	BC036568	CCDS3461.2	4p14	2013-10-11	2009-11-23		ENSG00000179299	ENSG00000179299		"NOP2/Sun domain containing"	25857	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family, member 7"			17442852	Standard	NM_024677		Approved	FLJ14001	uc003gvj.4	Q8NE18	OTTHUMG00000128597	ENST00000381782.2:c.1511T>C	chr4.hg19:g.40809188T>C	ENSP00000371201:p.Ile504Thr	160.0	0.0		152.0	62.0	NM_024677	C9JI19|Q8N9K8|Q9H815	Missense_Mutation	SNP	ENST00000381782.2	hg19	CCDS3461.2	.	.	.	.	.	.	.	.	.	.	T	14.24	2.476720	0.44044	.	.	ENSG00000179299	ENST00000381782	T	0.40476	1.03	5.96	5.96	0.96718	.	0.342627	0.27509	N	0.019053	T	0.31420	0.0796	N	0.22421	0.69	0.80722	D	1	B	0.31769	0.339	B	0.24701	0.055	T	0.11446	-1.0587	10	0.56958	D	0.05	-11.3479	16.4221	0.83766	0.0:0.0:0.0:1.0	.	504	Q8NE18	NSUN7_HUMAN	T	504	ENSP00000371201:I504T	ENSP00000371201:I504T	I	+	2	0	NSUN7	40503945	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	3.684000	0.54671	2.283000	0.76528	0.477000	0.44152	ATT	.	.		0.343	NSUN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250454.2	NM_024677		C	40809188	T	C	40809188	3	2	199	1	0	0	0	0	1	0	0	0	10692	1493	52	2	1549	2	NSUN7	4	40809188	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	33943938	40809188	150345088	40	29266										
ALB	213	hgsc.bcm.edu	37	chr4	74281992	74281992	+	Frame_Shift_Del	DEL	T	T	-													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gttcgatgaatttaaacctcTtgtggaagagcctcagaatt							TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr4:74281992delT	ENST00000503124.1	+	8	968	c.761delT	c.(760-762)cttfs	p.L254fs	ALB_ENST00000401494.3_Frame_Shift_Del_p.L289fs|ALB_ENST00000509063.1_Frame_Shift_Del_p.L404fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000415165.2_Frame_Shift_Del_p.L212fs|ALB_ENST00000295897.4_Frame_Shift_Del_p.L404fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTAAACCTCTTGTGGAAGAG	0.358																																					p.L404fs		Atlas-INDEL	.											.	ALB	132	.	0			c.1210delC						.						72	72	72					4																	74281992		2201	4300	6501	SO:0001589	frameshift_variant	213	exon10			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.761delT	chr4.hg19:g.74281992delT	ENSP00000421027:p.Leu254fs	350.0	0.0		335.0	150.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.358	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74281992	T	-	74281992	7	5	199	1	0	1	0	1	0	0	0	0	486	1609	56	0	1249	0	ALB	4	74281992	Frame_Shift_Del	DEL	T	TCGA-DD-AADQ-01A-11D-A40R-10	33472804	74281992	116872284	41	29267										
PRKG2	5593	hgsc.bcm.edu	37	chr4	82125912	82125912	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	caagaggcactttatctggaGaggcctgaagcgggcttcct	13	10	1	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr4:82125912G>A	ENST00000395578.1	-	2	406	c.290C>T	c.(289-291)tCt>tTt	p.S97F	PRKG2_ENST00000264399.1_Missense_Mutation_p.S97F|PRKG2_ENST00000418486.2_Missense_Mutation_p.S97F			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	97					blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						TTTATCTGGAGAGGCCTGAAG	0.562																																					p.S97F		Atlas-SNP	.											.	PRKG2	195	.	0			c.C290T						.						109	118	115					4																	82125912		2203	4300	6503	SO:0001583	missense	5593	exon1			TCTGGAGAGGCCT	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.290C>T	chr4.hg19:g.82125912G>A	ENSP00000378945:p.Ser97Phe	149.0	0.0		154.0	61.0	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Missense_Mutation	SNP	ENST00000395578.1	hg19	CCDS3589.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.871535	0.33069	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486	T;T;T	0.70749	-0.39;-0.39;-0.51	5.55	5.55	0.83447	.	0.117855	0.64402	D	0.000019	T	0.70107	0.3186	L	0.34521	1.04	0.80722	D	1	P;P	0.50819	0.855;0.939	B;P	0.48873	0.288;0.593	T	0.71679	-0.4520	10	0.54805	T	0.06	-17.0592	19.28	0.94050	0.0:0.0:1.0:0.0	.	97;97	E7EPE6;Q13237	.;KGP2_HUMAN	F	97	ENSP00000378945:S97F;ENSP00000264399:S97F;ENSP00000389038:S97F	ENSP00000264399:S97F	S	-	2	0	PRKG2	82344936	1.000000	0.71417	0.975000	0.42487	0.014000	0.08584	5.009000	0.63998	2.890000	0.99128	0.585000	0.79938	TCT	.	.		0.562	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		A	82125912	G	A	82125912	3	1	199	1	0	0	0	0	1	0	0	0	12535	942	33	3	2070	3	PRKG2	4	82125912	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	7843920	82125912	109028364	42	29268										
GYPE	2996	hgsc.bcm.edu	37	chr4	144801614	144801614	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tgactgaagaagaggttgaaGtgtgcattgccacaccagtg	13	7	0	5			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr4:144801614G>A	ENST00000358615.4	-	2	137	c.86C>T	c.(85-87)aCt>aTt	p.T29I	GYPE_ENST00000437468.2_Missense_Mutation_p.T29I	NM_198682.2	NP_941391.2	P15421	GLPE_HUMAN	glycophorin E (MNS blood group)	29						integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_hematologic(180;0.158)					AGAGGTTGAAGTGTGCATTGC	0.383																																					p.T29I		Atlas-SNP	.											.	GYPE	21	.	0			c.C86T						.						212	220	217					4																	144801614		2203	4300	6503	SO:0001583	missense	2996	exon2			GTTGAAGTGTGCA		CCDS47138.1	4q31.21	2010-01-19	2010-01-19		ENSG00000197465	ENSG00000197465		"Blood group antigens"	4705	protein-coding gene	gene with protein product		138590	"glycophorin E"				Standard	NM_198682		Approved	GPE, MNS	uc003ijj.3	P15421	OTTHUMG00000161402	ENST00000358615.4:c.86C>T	chr4.hg19:g.144801614G>A	ENSP00000351430:p.Thr29Ile	458.0	0.0		457.0	203.0	NM_198682	D3DNZ5	Missense_Mutation	SNP	ENST00000358615.4	hg19	CCDS47138.1	.	.	.	.	.	.	.	.	.	.	G	10.22	1.289554	0.23478	.	.	ENSG00000197465	ENST00000358615;ENST00000437468;ENST00000428604	T;T	0.03242	4.0;4.0	0.858	-0.0599	0.13791	.	.	.	.	.	T	0.02649	0.0080	.	.	.	0.09310	N	1	P	0.35780	0.52	B	0.30029	0.11	T	0.42699	-0.9436	8	0.87932	D	0	.	3.2532	0.06822	0.3177:0.0:0.6823:0.0	.	29	P15421	GLPE_HUMAN	I	29	ENSP00000351430:T29I;ENSP00000400698:T29I	ENSP00000351430:T29I	T	-	2	0	GYPE	145021064	0.003000	0.15002	0.001000	0.08648	0.065000	0.16274	1.419000	0.34793	-0.031000	0.13781	0.134000	0.15878	ACT	.	.		0.383	GYPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364780.1	NM_002102		A	144801614	G	A	144801614	3	1	199	1	0	0	0	0	1	0	0	0	6920	1029	36	3	158	3	GYPE	4	144801614	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	62675702	144801614	46352662	43	29269										
KLHL2	11275	hgsc.bcm.edu	37	chr4	166184404	166184404	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggatgtgaagaagacttgttGtgaatttttggaatcccagc	12	5	0	4			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr4:166184404G>T	ENST00000226725.6	+	5	696	c.437G>T	c.(436-438)tGt>tTt	p.C146F	KLHL2_ENST00000421009.2_Missense_Mutation_p.C49F|KLHL2_ENST00000514860.1_Missense_Mutation_p.C150F|KLHL2_ENST00000538127.1_Missense_Mutation_p.C58F|KLHL2_ENST00000506761.1_5'UTR	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	146					protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		AAGACTTGTTGTGAATTTTTG	0.463																																					p.C150F		Atlas-SNP	.											.	KLHL2	42	.	0			c.G449T						.						157	145	149					4																	166184404		2203	4300	6503	SO:0001583	missense	11275	exon5			CTTGTTGTGAATT	AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"Kelch-like", "BTB/POZ domain containing"	6353	protein-coding gene	gene with protein product	"mayven"	605774	"kelch (Drosophila)-like 2 (Mayven)", "kelch-like 2, Mayven (Drosophila)"			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.437G>T	chr4.hg19:g.166184404G>T	ENSP00000226725:p.Cys146Phe	263.0	0.0		225.0	109.0	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Missense_Mutation	SNP	ENST00000226725.6	hg19	CCDS34094.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.418210	0.83449	.	.	ENSG00000109466	ENST00000226725;ENST00000509704;ENST00000514860;ENST00000538127;ENST00000421009	T;T;T;T;T	0.72505	-0.24;-0.24;-0.24;-0.24;-0.66	5.42	5.42	0.78866	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.86033	0.5836	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.87612	0.2504	10	0.72032	D	0.01	.	19.2162	0.93780	0.0:0.0:1.0:0.0	.	150;146	B4DFH7;O95198	.;KLHL2_HUMAN	F	146;108;150;58;49	ENSP00000226725:C146F;ENSP00000421324:C108F;ENSP00000424198:C150F;ENSP00000437526:C58F;ENSP00000408974:C49F	ENSP00000226725:C146F	C	+	2	0	KLHL2	166403854	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.869000	0.99810	2.550000	0.86006	0.650000	0.86243	TGT	.	.		0.463	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1			T	166184404	G	T	166184404	3	4	199	1	0	0	0	0	1	0	0	0	8383	1377	48	3	497	3	KLHL2	4	166184404	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	21382790	166184404	24969872	44	29270										
SH3RF1	57630	hgsc.bcm.edu	37	chr4	170043263	170043263	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tcacttacacactggggcgaGtctgcggccgtaaatgtgca	12	11	2	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr4:170043263G>A	ENST00000284637.9	-	7	1675	c.1334C>T	c.(1333-1335)aCt>aTt	p.T445I	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	445	Interaction with AKT2. {ECO:0000250}.|SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328)	cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		ACTGGGGCGAGTCTGCGGCCG	0.547																																					p.T445I		Atlas-SNP	.											.	SH3RF1	60	.	0			c.C1334T						.						89	78	82					4																	170043263		2203	4300	6503	SO:0001583	missense	57630	exon7			GGGCGAGTCTGCG	BC033203	CCDS34099.1	4q32.3	2013-01-09	2006-02-13	2006-02-13	ENSG00000154447	ENSG00000154447		"RING-type (C3HC4) zinc fingers"	17650	protein-coding gene	gene with protein product	"plenty of SH3 domains"		"SH3 multiple domains 2"	SH3MD2		9482736	Standard	NM_020870		Approved	POSH, RNF142, KIAA1494	uc003isa.1	Q7Z6J0	OTTHUMG00000161010	ENST00000284637.9:c.1334C>T	chr4.hg19:g.170043263G>A	ENSP00000284637:p.Thr445Ile	101.0	0.0		102.0	39.0	NM_020870	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Missense_Mutation	SNP	ENST00000284637.9	hg19	CCDS34099.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.309909	0.40895	.	.	ENSG00000154447	ENST00000284637	T	0.28666	1.6	5.3	4.44	0.53790	Src homology-3 domain (2);	0.481828	0.24666	N	0.036599	T	0.14013	0.0339	N	0.03608	-0.345	0.38118	D	0.937774	B	0.34103	0.437	B	0.23852	0.049	T	0.10613	-1.0622	10	0.36615	T	0.2	-2.6297	15.7767	0.78228	0.0:0.1367:0.8632:0.0	.	445	Q7Z6J0	SH3R1_HUMAN	I	445	ENSP00000284637:T445I	ENSP00000284637:T445I	T	-	2	0	SH3RF1	170279838	0.984000	0.35163	0.882000	0.34594	0.508000	0.34012	3.887000	0.56197	1.187000	0.43000	0.585000	0.79938	ACT	.	.		0.547	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870		A	170043263	G	A	170043263	3	1	199	1	0	0	0	0	1	0	0	0	14273	1029	36	3	1356	3	SH3RF1	4	170043263	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	3858859	170043263	21111013	45	29271										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55265599	55265599	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	aatccatacatttttcctttAgcacacaaactgcagtgaaa	4	10	0	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr5:55265599A>G	ENST00000381298.2	-	4	461	c.149T>C	c.(148-150)cTa>cCa	p.L50P	IL6ST_ENST00000336909.5_Missense_Mutation_p.L50P|IL6ST_ENST00000381294.3_Missense_Mutation_p.L50P|IL6ST_ENST00000502326.3_Missense_Mutation_p.L50P|IL6ST_ENST00000536319.1_Missense_Mutation_p.L50P|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000577363.1_Intron|IL6ST_ENST00000396816.1_Intron|IL6ST_ENST00000381293.2_Missense_Mutation_p.L50P|IL6ST_ENST00000522633.2_Missense_Mutation_p.L50P|IL6ST_ENST00000381287.4_Missense_Mutation_p.L50P	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	50	Ig-like C2-type.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				TTTTTCCTTTAGCACACAAAC	0.318			O		hepatocellular ca																																p.L50P		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.T149C						.						83	83	83					5																	55265599		2203	4297	6500	SO:0001583	missense	3572	exon4			TCCTTTAGCACAC	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.149T>C	chr5.hg19:g.55265599A>G	ENSP00000370698:p.Leu50Pro	106.0	0.0		178.0	113.0	NM_175767	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	hg19	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.966791	0.74131	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294;ENST00000381287;ENST00000536319;ENST00000381293;ENST00000522633;ENST00000542298	D;D;D;D;D;D;D	0.88586	-1.6;-1.6;-1.6;-1.6;-1.6;-2.4;-1.6	5.86	5.86	0.93980	Fibronectin, type III (1);Immunoglobulin C2-set-like, ligand-binding (1);Immunoglobulin-like fold (1);	0.688458	0.14275	N	0.329899	D	0.93592	0.7954	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.89917	0.995;1.0;1.0;1.0	D;D;D;D	0.97110	0.951;1.0;1.0;0.995	D	0.93043	0.6459	10	0.72032	D	0.01	.	14.8116	0.70000	1.0:0.0:0.0:0.0	.	50;50;50;50	Q5FC05;Q5FC04;P40189-2;P40189	.;.;.;IL6RB_HUMAN	P	50	ENSP00000370698:L50P;ENSP00000338799:L50P;ENSP00000370694:L50P;ENSP00000370687:L50P;ENSP00000444456:L50P;ENSP00000370693:L50P;ENSP00000435399:L50P	ENSP00000338799:L50P	L	-	2	0	IL6ST	55301356	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.374000	0.73132	2.238000	0.73509	0.477000	0.44152	CTA	.	.		0.318	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		G	55265599	A	G	55265599	3	3	199	1	0	0	0	0	1	0	0	0	7712	420	15	2	2663	2	IL6ST	5	55265599	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10		55265599	125649661	46	29272										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71403461	71403461	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tgtcgcaccgcttccttgacAgcaagttctacttgctggtg	10	12	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr5:71403461A>C	ENST00000296755.7	+	1	401	c.103A>C	c.(103-105)Agc>Cgc	p.S35R	MAP1B_ENST00000504183.1_3'UTR	NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	35					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CTTCCTTGACAGCAAGTTCTA	0.687																																					p.S35R	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A103C						.						35	32	33					5																	71403461		2203	4300	6503	SO:0001583	missense	4131	exon1			CTTGACAGCAAGT	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.103A>C	chr5.hg19:g.71403461A>C	ENSP00000296755:p.Ser35Arg	78.0	0.0		130.0	28.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.788100	0.49997	.	.	ENSG00000131711	ENST00000512974;ENST00000296755;ENST00000511641	T;T	0.05649	3.98;3.41	5.02	5.02	0.67125	.	0.087834	0.48767	D	0.000166	T	0.04588	0.0125	N	0.22421	0.69	0.42295	D	0.992158	B	0.34103	0.437	B	0.29267	0.1	T	0.48547	-0.9026	10	0.10902	T	0.67	-11.2039	14.8997	0.70670	1.0:0.0:0.0:0.0	.	35	P46821	MAP1B_HUMAN	R	35	ENSP00000296755:S35R;ENSP00000423444:S35R	ENSP00000296755:S35R	S	+	1	0	MAP1B	71439217	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.615000	0.54167	2.105000	0.64084	0.459000	0.35465	AGC	.	.		0.687	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		C	71403461	A	C	71403461	3	2	199	1	0	0	0	0	1	0	0	0	9237	188	7	5	105	5	MAP1B	5	71403461	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	16137862	71403461	109511799	47	29273										
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121780326	121780326	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gaaaagccctcccagagcgcCgagcggcaggggcacaccct	13	16	0	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr5:121780326C>A	ENST00000261368.8	+	8	1753	c.1491C>A	c.(1489-1491)gcC>gcA	p.A497A	CTC-210G5.1_ENST00000505546.1_RNA|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000379538.3_Silent_p.A131A|CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000542191.1_Silent_p.A55A|SNCAIP_ENST00000261367.7_Silent_p.A544A|CTC-210G5.1_ENST00000509993.1_RNA|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000503116.2_3'UTR|SNCAIP_ENST00000414317.2_Silent_p.A99A|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000379536.2_Silent_p.A437A|SNCAIP_ENST00000379533.2_Silent_p.A544A	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	497					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		CCCAGAGCGCCGAGCGGCAGG	0.552																																					p.A497A		Atlas-SNP	.											SNCAIP_ENST00000379533,NS,carcinoma,0,2	SNCAIP	308	.	0			c.C1491A						.						90	86	88					5																	121780326		2203	4300	6503	SO:0001819	synonymous_variant	9627	exon8			GAGCGCCGAGCGG	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.1491C>A	chr5.hg19:g.121780326C>A		160.0	0.0		274.0	59.0	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Silent	SNP	ENST00000261368.8	hg19	CCDS4131.1																																																																																			.	.		0.552	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			A	121780326	C	A	121780326	2	1	199	1	0	0	0	0	0	0	0	1	14856	639	23	1		1	SNCAIP	5	121780326	Silent	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	50376865	121780326	59134934	48	29274										
FBN2	2201	hgsc.bcm.edu	37	chr5	127614345	127614345	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	acctcttccatcagttgtatAtcctgggccatgaggacata	8	11	2	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr5:127614345A>C	ENST00000508053.1	-	63	8301	c.7327T>G	c.(7327-7329)Tat>Gat	p.Y2443D	FBN2_ENST00000262464.4_Missense_Mutation_p.Y2443D			P35556	FBN2_HUMAN	fibrillin 2	2443					anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TCAGTTGTATATCCTGGGCCA	0.423																																					p.Y2443D		Atlas-SNP	.											.	FBN2	858	.	0			c.T7327G						.						106	102	103					5																	127614345		2203	4300	6503	SO:0001583	missense	2201	exon57			TTGTATATCCTGG	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.7327T>G	chr5.hg19:g.127614345A>C	ENSP00000424571:p.Tyr2443Asp	103.0	0.0		139.0	23.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.066581	0.76301	.	.	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.91124	-2.79;-2.79	5.08	5.08	0.68730	Matrix fibril-associated (2);	0.000000	0.50627	D	0.000115	D	0.95143	0.8426	H	0.94306	3.52	0.80722	D	1	D	0.63880	0.993	P	0.52109	0.69	D	0.96261	0.9191	10	0.66056	D	0.02	.	15.3042	0.73979	1.0:0.0:0.0:0.0	.	2443	P35556	FBN2_HUMAN	D	2443	ENSP00000262464:Y2443D;ENSP00000424571:Y2443D	ENSP00000262464:Y2443D	Y	-	1	0	FBN2	127642244	1.000000	0.71417	0.845000	0.33349	0.939000	0.58152	9.029000	0.93718	2.252000	0.74401	0.528000	0.53228	TAT	.	.		0.423	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		C	127614345	A	C	127614345	3	2	199	1	0	0	0	0	1	0	0	0	5711	449	16	5	1447	5	FBN2	5	127614345	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	5834019	127614345	53300915	49	29275										
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140772927	140772927	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	accacttctccctggacgtgCagactggagacaatggagcc	11	13	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr5:140772927C>G	ENST00000398604.2	+	1	547	c.547C>G	c.(547-549)Cag>Gag	p.Q183E	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	183	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGGACGTGCAGACTGGAGA	0.612																																					p.Q183E		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.C547G						.						52	58	56					5																	140772927		2147	4282	6429	SO:0001583	missense	9708	exon1			GACGTGCAGACTG	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.547C>G	chr5.hg19:g.140772927C>G	ENSP00000381605:p.Gln183Glu	198.0	0.0		332.0	86.0	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	hg19	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	9.532	1.110965	0.20714	.	.	ENSG00000253767	ENST00000398604	T	0.19105	2.17	5.41	5.41	0.78517	Cadherin (4);Cadherin-like (1);	0.000000	0.30118	U	0.010368	T	0.25344	0.0616	L	0.58969	1.84	0.09310	N	1	B;B	0.29988	0.164;0.264	B;B	0.33254	0.117;0.16	T	0.15636	-1.0430	10	0.46703	T	0.11	.	13.7424	0.62855	0.1539:0.8461:0.0:0.0	.	183;183	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	E	183	ENSP00000381605:Q183E	ENSP00000381605:Q183E	Q	+	1	0	PCDHGA8	140753111	0.000000	0.05858	0.859000	0.33776	0.662000	0.39071	-0.042000	0.12063	2.552000	0.86080	0.655000	0.94253	CAG	.	.		0.612	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		G	140772927	C	G	140772927	3	3	199	1	0	0	0	0	1	0	0	0	11569	711	25	4	549	4	PCDHGA8	5	140772927	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	13158582	140772927	40142333	50	29276										
PCDHGC5	56097	hgsc.bcm.edu	37	chr5	140870856	140870856	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tccagtgacttcctcatacaCcctcctgagcgttcagacct	6	16	2	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr5:140870856C>T	ENST00000252087.1	+	1	2049	c.2049C>T	c.(2047-2049)caC>caT	p.H683H	PCDHGC4_ENST00000306593.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	683					homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTCATACACCCTCCTGAGC	0.532																																					p.H683H		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.C2049T						.						205	186	193					5																	140870856		2203	4300	6503	SO:0001819	synonymous_variant	56097	exon1			CATACACCCTCCT	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"Cadherins / Protocadherins : Clustered"	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.2049C>T	chr5.hg19:g.140870856C>T		110.0	0.0		178.0	42.0	NM_018929	Q9Y5C2	Silent	SNP	ENST00000252087.1	hg19	CCDS4263.1																																																																																			.	.		0.532	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929		T	140870856	C	T	140870856	2	4	199	1	0	0	0	0	0	0	0	1	11580	506	18	3		3	PCDHGC5	5	140870856	Silent	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	97929	140870856	40044404	51	29277										
FAM71B	153745	hgsc.bcm.edu	37	chr5	156590354	156590354	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	cgccagcgctgtggtcacttGacctgggcctgcagatttgg	14	12	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr5:156590354G>A	ENST00000302938.4	-	2	1017	c.922C>T	c.(922-924)Caa>Taa	p.Q308*		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	308	Ala-rich.					nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTGGTCACTTGACCTGGGCCT	0.517																																					p.Q308X		Atlas-SNP	.											.	FAM71B	145	.	0			c.C922T						.						118	114	115					5																	156590354		2203	4300	6503	SO:0001587	stop_gained	153745	exon2			TCACTTGACCTGG		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.922C>T	chr5.hg19:g.156590354G>A	ENSP00000305596:p.Gln308*	55.0	0.0		81.0	62.0	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Nonsense_Mutation	SNP	ENST00000302938.4	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.439847	0.63067	.	.	ENSG00000170613	ENST00000302938	.	.	.	3.85	2.96	0.34315	.	0.365738	0.20136	N	0.098493	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-9.8624	9.482	0.38906	0.0:0.216:0.784:0.0	.	.	.	.	X	308	.	ENSP00000305596:Q308X	Q	-	1	0	FAM71B	156522932	0.133000	0.22466	0.016000	0.15963	0.002000	0.02628	3.753000	0.55180	1.164000	0.42652	-0.175000	0.13238	CAA	.	.		0.517	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		A	156590354	G	A	156590354	4	1	199	1	0	0	0	0	0	1	0	0	5616	1299	45	3	899	3	FAM71B	5	156590354	Nonsense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	15719498	156590354	24324906	52	29278										
TTC1	7265	hgsc.bcm.edu	37	chr5	159463724	159463724	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tagaagctgaaagttcttatAgtcgagccctcgaaatgtgc	10	8	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr5:159463724A>T	ENST00000231238.5	+	4	528	c.418A>T	c.(418-420)Agt>Tgt	p.S140C	TTC1_ENST00000522793.1_Missense_Mutation_p.S140C	NM_001282500.1|NM_003314.1	NP_001269429.1|NP_003305.1	Q99614	TTC1_HUMAN	tetratricopeptide repeat domain 1	140					protein folding (GO:0006457)	peroxisomal membrane (GO:0005778)	unfolded protein binding (GO:0051082)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|prostate(1)|skin(1)	12	Renal(175;0.00196)	all_hematologic(541;0.00014)|Breast(839;0.0101)|all_neural(177;0.0281)|Medulloblastoma(196;0.0425)|Lung NSC(249;0.119)|all_lung(500;0.163)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Epithelial(171;8.37e-05)|all cancers(165;0.000694)|OV - Ovarian serous cystadenocarcinoma(192;0.0402)		AAGTTCTTATAGTCGAGCCCT	0.388																																					p.S140C		Atlas-SNP	.											.	TTC1	26	.	0			c.A418T						.						87	85	86					5																	159463724		2203	4300	6503	SO:0001583	missense	7265	exon4			TCTTATAGTCGAG	U46570	CCDS4348.1	5q32-q33.2	2013-01-10			ENSG00000113312	ENSG00000113312		"Tetratricopeptide (TTC) repeat domain containing"	12391	protein-coding gene	gene with protein product		601963				8836031	Standard	NM_003314		Approved	TPR1	uc003lxu.3	Q99614	OTTHUMG00000130326	ENST00000231238.5:c.418A>T	chr5.hg19:g.159463724A>T	ENSP00000231238:p.Ser140Cys	95.0	0.0		112.0	23.0	NM_003314	B2RCT2|D3DQJ8|Q9BVT3	Missense_Mutation	SNP	ENST00000231238.5	hg19	CCDS4348.1	.	.	.	.	.	.	.	.	.	.	A	19.15	3.771959	0.69992	.	.	ENSG00000113312	ENST00000231238;ENST00000522793	T;T	0.61040	0.14;0.14	5.52	5.52	0.82312	Elongated TPR repeat-containing domain (1);Tetratricopeptide repeat-containing (1);	0.252132	0.42053	D	0.000770	T	0.78400	0.4277	M	0.92970	3.365	0.09310	N	0.999996	D	0.57899	0.981	P	0.59546	0.859	T	0.75614	-0.3257	10	0.87932	D	0	-15.1795	13.2989	0.60313	1.0:0.0:0.0:0.0	.	140	Q99614	TTC1_HUMAN	C	140	ENSP00000231238:S140C;ENSP00000429225:S140C	ENSP00000231238:S140C	S	+	1	0	TTC1	159396302	0.082000	0.21442	0.205000	0.23548	0.873000	0.50193	3.153000	0.50685	2.223000	0.72356	0.482000	0.46254	AGT	.	.		0.388	TTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252675.3	NM_003314		T	159463724	A	T	159463724	3	4	199	1	0	0	0	0	1	0	0	0	16693	420	15	4	428	4	TTC1	5	159463724	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	2873370	159463724	21451536	53	29279										
PRPF4B	8899	hgsc.bcm.edu	37	chr6	4060749	4060749	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	accaacgtaagaaagtacacCagctaaaggacttgttggac	9	9	0	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr6:4060749C>T	ENST00000337659.6	+	15	3023	c.2923C>T	c.(2923-2925)Cag>Tag	p.Q975*	PRPF4B_ENST00000538861.1_Nonsense_Mutation_p.Q961*|PRPF4B_ENST00000494674.1_3'UTR	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	975	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GAAAGTACACCAGCTAAAGGA	0.448																																					p.Q975X		Atlas-SNP	.											.	PRPF4B	140	.	0			c.C2923T						.						63	56	58					6																	4060749		2203	4300	6503	SO:0001587	stop_gained	8899	exon15			GTACACCAGCTAA	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.2923C>T	chr6.hg19:g.4060749C>T	ENSP00000337194:p.Gln975*	374.0	2.0		647.0	453.0	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Nonsense_Mutation	SNP	ENST00000337659.6	hg19	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.952248	0.92660	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	.	.	.	5.3	5.3	0.74995	.	0.000000	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	18.9491	0.92635	0.0:1.0:0.0:0.0	.	.	.	.	X	975;961	.	ENSP00000337194:Q975X	Q	+	1	0	PRPF4B	4005748	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.451000	0.82905	0.655000	0.94253	CAG	.	.		0.448	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			T	4060749	C	T	4060749	4	4	199	1	0	0	0	0	0	1	0	0	12585	595	21	3	2981	3	PRPF4B	6	4060749	Nonsense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10		4060749	167054318	54	29280										
ZBTB9	221504	hgsc.bcm.edu	37	chr6	33423514	33423514	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tgctgcaaattcaggtggaaGaagaagaggaggaggaggaa	17	3	1	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr6:33423514G>A	ENST00000395064.2	+	2	905	c.637G>A	c.(637-639)Gaa>Aaa	p.E213K		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	213					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E213Q(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						TCaggtggaagaagaagagga	0.547																																					p.E213K		Atlas-SNP	.											ZBTB9,larynx,carcinoma,0,1	ZBTB9	23	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G637A						.						62	63	62					6																	33423514		2203	4300	6503	SO:0001583	missense	221504	exon2			GTGGAAGAAGAAG	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.637G>A	chr6.hg19:g.33423514G>A	ENSP00000378503:p.Glu213Lys	93.0	0.0		157.0	95.0	NM_152735	A2AB19	Missense_Mutation	SNP	ENST00000395064.2	hg19	CCDS4780.1	.	.	.	.	.	.	.	.	.	.	G	6.865	0.528919	0.13127	.	.	ENSG00000213588	ENST00000395064	T	0.06933	3.24	5.22	5.22	0.72569	.	0.810441	0.09729	U	0.763381	T	0.02970	0.0088	L	0.32530	0.975	0.34650	D	0.721508	P	0.41673	0.759	B	0.37833	0.259	T	0.34875	-0.9811	10	0.07325	T	0.83	.	16.3266	0.82986	0.0:0.0:1.0:0.0	.	213	Q96C00	ZBTB9_HUMAN	K	213	ENSP00000378503:E213K	ENSP00000378503:E213K	E	+	1	0	ZBTB9	33531492	1.000000	0.71417	0.254000	0.24359	0.887000	0.51463	4.623000	0.61247	2.710000	0.92621	0.563000	0.77884	GAA	.	.		0.547	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735		A	33423514	G	A	33423514	3	1	199	1	0	0	0	0	1	0	0	0	17573	943	33	3	639	3	ZBTB9	6	33423514	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	29362765	33423514	137691553	55	29281										
CDKN1A	1026	hgsc.bcm.edu	37	chr6	36652053	36652053	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	actttgtcaccgagacaccaCtggagggtgacttcgcctgg	12	12	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr6:36652053C>T	ENST00000405375.1	+	2	410	c.175C>T	c.(175-177)Ctg>Ttg	p.L59L	CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000448526.2_Silent_p.L93L|CDKN1A_ENST00000244741.5_Silent_p.L59L|CDKN1A_ENST00000373711.2_Silent_p.L59L	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	59					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						CGAGACACCACTGGAGGGTGA	0.667																																					p.L59L		Atlas-SNP	.											.	CDKN1A	27	.	0			c.C175T						.						59	53	55					6																	36652053		2203	4300	6503	SO:0001819	synonymous_variant	1026	exon2			ACACCACTGGAGG	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.175C>T	chr6.hg19:g.36652053C>T		83.0	0.0		142.0	31.0	NM_001220778	Q14010|Q6FI05|Q9BUT4	Silent	SNP	ENST00000405375.1	hg19	CCDS4824.1																																																																																			.	.		0.667	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467		T	36652053	C	T	36652053	2	4	199	1	0	0	0	0	0	0	0	1	3160	564	20	3		3	CDKN1A	6	36652053	Silent	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	3228539	36652053	134463014	56	29282										
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117130749	117130749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ctcaatgctgtgtatcatggCaagagtttgaagaaaaactg	10	6	2	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr6:117130749C>T	ENST00000310357.3	-	2	247	c.226G>A	c.(226-228)Gcc>Acc	p.A76T	GPRC6A_ENST00000368549.3_Missense_Mutation_p.A76T|GPRC6A_ENST00000530250.1_Missense_Mutation_p.A76T	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	76					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TGTATCATGGCAAGAGTTTGA	0.368																																					p.A76T		Atlas-SNP	.											.	GPRC6A	152	.	0			c.G226A						.						98	93	94					6																	117130749		2203	4300	6503	SO:0001583	missense	222545	exon2			TCATGGCAAGAGT	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.226G>A	chr6.hg19:g.117130749C>T	ENSP00000309493:p.Ala76Thr	84.0	0.0		36.0	24.0	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	hg19	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.954544	0.92726	.	.	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.91577	-2.87;-2.87;-2.87	4.66	4.66	0.58398	Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000002	D	0.91623	0.7353	L	0.49778	1.585	0.34476	D	0.703367	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.79784	0.992;0.993;0.978	D	0.89160	0.3529	10	0.22706	T	0.39	.	17.7521	0.88438	0.0:1.0:0.0:0.0	.	76;76;76	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	T	76	ENSP00000309493:A76T;ENSP00000357537:A76T;ENSP00000433465:A76T	ENSP00000309493:A76T	A	-	1	0	GPRC6A	117237442	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.860000	0.75473	2.420000	0.82092	0.650000	0.86243	GCC	.	.		0.368	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			T	117130749	C	T	117130749	3	4	199	1	0	0	0	0	1	0	0	0	6737	710	25	3	2574	3	GPRC6A	6	117130749	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	80478696	117130749	53984318	57	29283										
UTRN	7402	hgsc.bcm.edu	37	chr6	144863929	144863929	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tctgtttgtcctgatgcggtAgatttgcagagaggtgccta	13	7	1	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr6:144863929A>G	ENST00000367545.3	+	45	6519		c.e45-1			NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin						aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		CTGATGCGGTAGATTTGCAGA	0.413																																					.		Atlas-SNP	.											.	UTRN	327	.	0			c.6520-2A>G						.						89	86	87					6																	144863929		2203	4300	6503	SO:0001630	splice_region_variant	7402	exon45			TGCGGTAGATTTG	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.6520-1A>G	chr6.hg19:g.144863929A>G		105.0	0.0		40.0	24.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Splice_Site	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	13.17	2.157780	0.38119	.	.	ENSG00000152818	ENST00000367545	.	.	.	3.69	3.69	0.42338	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6945	0.45890	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UTRN	144905622	0.998000	0.40836	0.962000	0.40283	0.468000	0.32798	4.743000	0.62110	1.911000	0.55334	0.459000	0.35465	.	.	.		0.413	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		Intron	G	144863929	A	G	144863929	5	3	199	1	0	0	0	0	0	0	1	0	17118	434	15	2	6696	2	UTRN	6	144863929	Splice_Site	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	27733180	144863929	26251138	58	29284										
TNS3	64759	hgsc.bcm.edu	37	chr7	47440020	47440020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ctcaggcgtggcagagaagaCtaattcaaccttcccatagt	9	11	2	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr7:47440020C>T	ENST00000398879.1	-	15	1255	c.889G>A	c.(889-891)Gtc>Atc	p.V297I	TNS3_ENST00000311160.9_Missense_Mutation_p.V297I|TNS3_ENST00000355730.3_Intron			Q68CZ2	TENS3_HUMAN	tensin 3	297	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						GCAGAGAAGACTAATTCAACC	0.448																																					p.V297I		Atlas-SNP	.											.	TNS3	140	.	0			c.G889A						.						76	75	75					7																	47440020		1987	4160	6147	SO:0001583	missense	64759	exon15			AGAAGACTAATTC	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.889G>A	chr7.hg19:g.47440020C>T	ENSP00000381854:p.Val297Ile	263.0	0.0		232.0	83.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	hg19	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	C	16.04	3.009347	0.54361	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000457718;ENST00000450444	D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08	5.29	4.41	0.53225	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.347490	0.29034	N	0.013345	T	0.79281	0.4419	L	0.35341	1.055	0.80722	D	1	B	0.15719	0.014	B	0.17722	0.019	T	0.71027	-0.4711	10	0.16896	T	0.51	-30.4402	11.4605	0.50208	0.0:0.9119:0.0:0.0881	.	297	Q68CZ2	TENS3_HUMAN	I	297;407;297;400;386	ENSP00000312143:V297I;ENSP00000381854:V297I;ENSP00000414358:V400I;ENSP00000396914:V386I	ENSP00000312143:V297I	V	-	1	0	TNS3	47406545	0.681000	0.27614	0.539000	0.28077	0.993000	0.82548	1.320000	0.33666	1.209000	0.43321	0.655000	0.94253	GTC	.	.		0.448	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		T	47440020	C	T	47440020	3	4	199	1	0	0	0	0	1	0	0	0	16359	565	20	3	3516	3	TNS3	7	47440020	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10		47440020	111698643	59	29285										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81593423	81593423	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gtaatatgtctgctactgatGgctataaaataaaataataa	6	4	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr7:81593423G>A	ENST00000356253.5	-	34	3020	c.2765C>T	c.(2764-2766)cCa>cTa	p.P922L	CACNA2D1_ENST00000535308.1_Splice_Site_p.P122L|CACNA2D1_ENST00000356860.3_Splice_Site_p.P910L			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	922					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TGCTACTGATGGCTATAAAAT	0.368																																					p.P910L		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.C2729T						.						45	48	47					7																	81593423		2199	4292	6491	SO:0001630	splice_region_variant	781	exon34			ACTGATGGCTATA	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2764-1C>T	chr7.hg19:g.81593423G>A		250.0	0.0		234.0	98.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	hg19		.	.	.	.	.	.	.	.	.	.	G	26.8	4.772177	0.90108	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000535308	T;T;T	0.76060	-0.99;-0.99;-0.99	5.36	5.36	0.76844	.	0.104471	0.64402	D	0.000002	D	0.87916	0.6298	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	0.966;1.0	P;D	0.87578	0.688;0.998	D	0.89123	0.3504	10	0.87932	D	0	-5.265	19.4987	0.95085	0.0:0.0:1.0:0.0	.	122;910	B7Z658;P54289-2	.;.	L	910;929;922;122	ENSP00000349320:P910L;ENSP00000348589:P922L;ENSP00000443124:P122L	ENSP00000284088:P929L	P	-	2	0	CACNA2D1	81431359	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.375000	0.97178	2.677000	0.91161	0.644000	0.83932	CCA	.	.		0.368	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			Missense_Mutation	A	81593423	G	A	81593423	5	1	199	1	0	0	0	0	0	0	1	0	2550	1362	47	3	570	3	CACNA2D1	7	81593423	Splice_Site	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	34153403	81593423	77545240	60	29286										
KIAA1324L	222223	hgsc.bcm.edu	37	chr7	86526844	86526844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gaaatcctctcttgcaggctCcctcaatctcatggaagtca	7	13	4	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr7:86526844C>T	ENST00000450689.2	-	19	2848	c.2663G>A	c.(2662-2664)gGa>gAa	p.G888E	KIAA1324L_ENST00000444627.1_Missense_Mutation_p.G817E|KIAA1324L_ENST00000297222.6_Missense_Mutation_p.G648E|KIAA1324L_ENST00000416314.1_Missense_Mutation_p.G721E	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	888						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					CTTGCAGGCTCCCTCAATCTC	0.488																																					p.G888E		Atlas-SNP	.											.	KIAA1324L	225	.	0			c.G2663A						.						100	96	97					7																	86526844		2203	4300	6503	SO:0001583	missense	222223	exon19			CAGGCTCCCTCAA	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.2663G>A	chr7.hg19:g.86526844C>T	ENSP00000413445:p.Gly888Glu	133.0	0.0		92.0	38.0	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Missense_Mutation	SNP	ENST00000450689.2	hg19	CCDS47632.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.693642	0.88735	.	.	ENSG00000164659	ENST00000450689;ENST00000297222;ENST00000444627;ENST00000416314	T;T;T;T	0.23950	2.18;1.95;1.88;1.94	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.55321	0.1913	M	0.80847	2.515	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.79784	0.982;0.993;0.993	T	0.56245	-0.8011	10	0.51188	T	0.08	.	18.5874	0.91196	0.0:1.0:0.0:0.0	.	888;648;721	A8MWY0;A8MWY0-2;B4DJV3	K132L_HUMAN;.;.	E	888;648;817;721	ENSP00000413445:G888E;ENSP00000297222:G648E;ENSP00000397377:G817E;ENSP00000402390:G721E	ENSP00000297222:G648E	G	-	2	0	KIAA1324L	86364780	1.000000	0.71417	0.994000	0.49952	0.983000	0.72400	6.089000	0.71384	2.642000	0.89623	0.650000	0.86243	GGA	.	.		0.488	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		T	86526844	C	T	86526844	3	4	199	1	0	0	0	0	1	0	0	0	8233	855	30	3	442	3	KIAA1324L	7	86526844	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	4933421	86526844	72611819	61	29287										
TAS2R16	50833	hgsc.bcm.edu	37	chr7	122634906	122634906	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	aaagcatagacaaaagcttcCcagacccataaccaacatct	4	13	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr7:122634906C>G	ENST00000249284.2	-	1	848	c.783G>C	c.(781-783)tgG>tgC	p.W261C		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	261					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	bitter taste receptor activity (GO:0033038)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CAAAAGCTTCCCAGACCCATA	0.403																																					p.W261C		Atlas-SNP	.											.	TAS2R16	57	.	0			c.G783C						.						128	126	126					7																	122634906		2203	4300	6503	SO:0001583	missense	50833	exon1			AGCTTCCCAGACC	AF227139	CCDS5785.1	7q31.1-q31.3	2012-08-22			ENSG00000128519	ENSG00000128519		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14921	protein-coding gene	gene with protein product		604867				10761934	Standard	NM_016945		Approved	T2R16	uc003vkl.1	Q9NYV7	OTTHUMG00000157090	ENST00000249284.2:c.783G>C	chr7.hg19:g.122634906C>G	ENSP00000249284:p.Trp261Cys	137.0	0.0		148.0	49.0	NM_016945	A4D0X2|Q502V3|Q549U8|Q645W1	Missense_Mutation	SNP	ENST00000249284.2	hg19	CCDS5785.1	.	.	.	.	.	.	.	.	.	.	C	7.598	0.672129	0.14776	.	.	ENSG00000128519	ENST00000249284	T	0.00695	5.83	4.77	2.89	0.33648	.	1.178150	0.06102	N	0.665669	T	0.01421	0.0046	L	0.53729	1.69	0.09310	N	0.999994	P	0.35982	0.531	B	0.37833	0.259	T	0.53885	-0.8375	10	0.25106	T	0.35	.	11.2561	0.49054	0.0:0.6251:0.3749:0.0	.	261	Q9NYV7	T2R16_HUMAN	C	261	ENSP00000249284:W261C	ENSP00000249284:W261C	W	-	3	0	TAS2R16	122422142	0.000000	0.05858	0.024000	0.17045	0.045000	0.14185	-0.320000	0.08028	0.672000	0.31204	0.655000	0.94253	TGG	.	.		0.403	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945		G	122634906	C	G	122634906	3	3	199	1	0	0	0	0	1	0	0	0	15584	624	22	4	96	4	TAS2R16	7	122634906	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	36108062	122634906	36503757	62	29288										
GPR37	2861	hgsc.bcm.edu	37	chr7	124404046	124404046	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	cttgcaggagaagtcctccaGcagccacttcttggtcagct	10	13	2	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr7:124404046G>A	ENST00000303921.2	-	1	1635	c.985C>T	c.(985-987)Ctg>Ttg	p.L329L		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	329				L -> V (in Ref. 3; AAC51281). {ECO:0000305}.	dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AAGTCCTCCAGCAGCCACTTC	0.517																																					p.L329L		Atlas-SNP	.											.	GPR37	89	.	0			c.C985T						.						139	154	149					7																	124404046		2203	4300	6503	SO:0001819	synonymous_variant	2861	exon1			CCTCCAGCAGCCA		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.985C>T	chr7.hg19:g.124404046G>A		42.0	0.0		28.0	13.0	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Silent	SNP	ENST00000303921.2	hg19	CCDS5792.1																																																																																			.	.		0.517	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		A	124404046	G	A	124404046	2	1	199	1	0	0	0	0	0	0	0	1	6699	962	34	3		3	GPR37	7	124404046	Silent	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	1769140	124404046	34734617	63	29289										
SSPO	23145	hgsc.bcm.edu	37	chr7	149524046	149524046	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ctgctccctcgttgactgtcAgggtgagatgtggctgtcca	13	11	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr7:149524046A>G	ENST00000378016.2	+	0	14768							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GTTGACTGTCAGGGTGAGATG	0.597																																					p.Q4922R		Atlas-SNP	.											.	.	.	.	0			c.A14765G						.						158	184	175					7																	149524046		2184	4277	6461			23145	exon104			ACTGTCAGGGTGA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149524046A>G		55.0	0.0		35.0	15.0	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.597	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149524046	A	G	149524046	1	3	199	0	1	0	0	0	0	0	0	0	15204	188	7	2		2	SSPO	7	149524046	RNA	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	25120000	149524046	9614617	64	29290										
ADAM2	2515	hgsc.bcm.edu	37	chr8	39678669	39678669	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gttctattccataactaacaTtttcaaactgtagtacgccc	4	11	2	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr8:39678669T>A	ENST00000265708.4	-	6	468	c.365A>T	c.(364-366)aAt>aTt	p.N122I	ADAM2_ENST00000379853.2_Missense_Mutation_p.N122I|ADAM2_ENST00000347580.4_Missense_Mutation_p.N122I|ADAM2_ENST00000523181.1_5'UTR|ADAM2_ENST00000521880.1_Missense_Mutation_p.N122I	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	122					adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		ATAACTAACATTTTCAAACTG	0.308																																					p.N122I		Atlas-SNP	.											.	ADAM2	124	.	0			c.A365T						.						38	38	38					8																	39678669		2203	4295	6498	SO:0001583	missense	2515	exon6			CTAACATTTTCAA	U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"ADAM metallopeptidase domain containing"	198	protein-coding gene	gene with protein product	"cancer/testis antigen 15"	601533	"fertilin beta"	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.365A>T	chr8.hg19:g.39678669T>A	ENSP00000265708:p.Asn122Ile	257.0	0.0		415.0	86.0	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	hg19	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.544003	0.65198	.	.	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	T;T;T;T	0.07800	3.16;3.16;3.16;3.16	5.33	4.13	0.48395	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.35158	0.0922	M	0.92880	3.355	0.36977	D	0.894127	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.999;0.991;0.998;0.999	T	0.50550	-0.8815	8	.	.	.	.	10.417	0.44327	0.0:0.0:0.1645:0.8355	.	122;122;122;122	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	I	122	ENSP00000343854:N122I;ENSP00000369182:N122I;ENSP00000265708:N122I;ENSP00000429352:N122I	.	N	-	2	0	ADAM2	39797826	1.000000	0.71417	0.999000	0.59377	0.888000	0.51559	2.432000	0.44784	0.820000	0.34516	0.533000	0.62120	AAT	.	.		0.308	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		A	39678669	T	A	39678669	3	1	199	1	0	0	0	0	1	0	0	0	241	1493	52	4	1902	4	ADAM2	8	39678669	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10		39678669	106685353	65	29291										
CNGB3	54714	hgsc.bcm.edu	37	chr8	87755757	87755757	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gtttgctgagactgattactTgggtgagagccttcttcatt	11	7	2	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr8:87755757T>G	ENST00000320005.5	-	1	146	c.99A>C	c.(97-99)ccA>ccC	p.P33P	CNGB3_ENST00000519777.1_5'UTR|RP11-386D6.1_ENST00000519041.1_RNA	NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	33					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						ACTGATTACTTGGGTGAGAGC	0.398																																					p.P33P		Atlas-SNP	.											.	CNGB3	176	.	0			c.A99C						.						329	275	293					8																	87755757		2203	4300	6503	SO:0001819	synonymous_variant	54714	exon1			ATTACTTGGGTGA	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2153	protein-coding gene	gene with protein product		605080	"achromatopsia (rod monochromacy) 3", "achromatopsia (rod monochromacy) 1"	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.99A>C	chr8.hg19:g.87755757T>G		153.0	0.0		288.0	188.0	NM_019098	C9JA51|Q9NRE9	Silent	SNP	ENST00000320005.5	hg19	CCDS6244.1																																																																																			.	.		0.398	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		G	87755757	T	G	87755757	2	3	199	1	0	0	0	0	0	0	0	1	3603	1799	63	5		5	CNGB3	8	87755757	Silent	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	48077088	87755757	58608265	66	29292										
C8orf38	137682	hgsc.bcm.edu	37	chr8	96037272	96037272	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	cacggctctgtctgggggccGttgcggcttggcatccccgg	16	14	2	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr8:96037272G>T	ENST00000396124.4	+	1	59	c.36G>T	c.(34-36)ccG>ccT	p.P12P	NDUFAF6_ENST00000542894.1_Intron|NDUFAF6_ENST00000396111.2_Intron|NDUFAF6_ENST00000396113.1_Intron|NDUFAF6_ENST00000286687.4_5'Flank	NM_152416.3	NP_689629.2	Q330K2	NDUF6_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 6	12					biosynthetic process (GO:0009058)|mitochondrial respiratory chain complex I assembly (GO:0032981)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	transferase activity (GO:0016740)										TCTGGGGGCCGTTGCGGCTTG	0.786																																					p.P12P		Atlas-SNP	.											.	.	.	.	0			c.G36T						.						3	3	3					8																	96037272		1194	2802	3996	SO:0001819	synonymous_variant	137682	exon1			GGGGCCGTTGCGG	BC028166	CCDS6266.2	8q22.1	2013-10-21	2012-05-08	2012-05-08	ENSG00000156170	ENSG00000156170		"Mitochondrial respiratory chain complex assembly factors"	28625	protein-coding gene	gene with protein product		612392	"chromosome 8 open reading frame 38"	C8orf38		22019594, 23509070	Standard	NM_152416		Approved	MGC40214	uc003yhj.3	Q330K2	OTTHUMG00000150173	ENST00000396124.4:c.36G>T	chr8.hg19:g.96037272G>T		3.0	0.0		11.0	7.0	NM_152416	A8MT28|A8MWF0|B4DQ45|Q8N6U6	Silent	SNP	ENST00000396124.4	hg19	CCDS6266.2																																																																																			.	.		0.786	NDUFAF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316700.2	NM_152416		T	96037272	G	T	96037272	2	4	199	1	0	0	0	0	0	0	0	1	2426	1132	40	1		1	C8orf38	8	96037272	Silent	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	8281515	96037272	50326750	67	29293										
DOCK8	81704	hgsc.bcm.edu	37	chr9	434898	434898	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ctgccatgtgcctggtgcacGccgctgcgttagtggctgag	15	12	0	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr9:434898G>A	ENST00000453981.1	+	39	5114	c.5002G>A	c.(5002-5004)Gcc>Acc	p.A1668T	DOCK8_ENST00000469391.1_Missense_Mutation_p.A1568T|DOCK8_ENST00000432829.2_Missense_Mutation_p.A1600T|DOCK8_ENST00000382329.1_Missense_Mutation_p.A1135T			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1668	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CCTGGTGCACGCCGCTGCGTT	0.592																																					p.A1668T		Atlas-SNP	.											.	DOCK8	401	.	0			c.G5002A						.						98	86	90					9																	434898		2203	4300	6503	SO:0001583	missense	81704	exon39			GTGCACGCCGCTG	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.5002G>A	chr9.hg19:g.434898G>A	ENSP00000408464:p.Ala1668Thr	68.0	0.0		60.0	27.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	12.13	1.844259	0.32606	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.73575	2.52;-0.76;-0.76;-0.76	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.74344	0.3704	M	0.66939	2.045	0.80722	D	1	B;B;B	0.30824	0.104;0.296;0.104	B;B;B	0.31812	0.046;0.136;0.086	T	0.72520	-0.4268	10	0.33940	T	0.23	.	18.5837	0.91181	0.0:0.0:1.0:0.0	.	1568;1135;1668	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	T	1668;1636;1600;1568;1135	ENSP00000408464:A1668T;ENSP00000394888:A1600T;ENSP00000419438:A1568T;ENSP00000371766:A1135T	ENSP00000287364:A1636T	A	+	1	0	DOCK8	424898	1.000000	0.71417	0.971000	0.41717	0.087000	0.18053	4.493000	0.60341	2.615000	0.88500	0.609000	0.83330	GCC	.	.		0.592	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		A	434898	G	A	434898	3	1	199	1	0	0	0	0	1	0	0	0	4695	1087	38	1	5156	1	DOCK8	9	434898	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10		434898	140778533	68	29294										
NOL6	65083	hgsc.bcm.edu	37	chr9	33467217	33467217	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tggctccgtcctggaaacgcCgaagctccgagcgggatccc	13	15	0	0	rs374756474		TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr9:33467217C>G	ENST00000379471.2	-	14	1856	c.1769G>C	c.(1768-1770)cGg>cCg	p.R590P	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Missense_Mutation_p.R538P			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	590					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		CTGGAAACGCCGAAGCTCCGA	0.617											OREG0019137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R590P		Atlas-SNP	.											.	NOL6	85	.	0			c.G1769C						.						50	57	54					9																	33467217		2203	4300	6503	SO:0001583	missense	65083	exon14			AAACGCCGAAGCT	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"nucleolar protein family 6 (RNA-associated)"			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.1769G>C	chr9.hg19:g.33467217C>G	ENSP00000368784:p.Arg590Pro	91.0	0.0	840	104.0	53.0	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.378085	0.95945	.	.	ENSG00000165271	ENST00000353159;ENST00000297990;ENST00000379471;ENST00000541373;ENST00000325914;ENST00000455041	T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.88526	0.6460	M	0.84846	2.72	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.89334	0.3649	10	0.87932	D	0	.	20.0609	0.97674	0.0:1.0:0.0:0.0	.	538;587;590;590;590	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4-3;Q9H6R4	.;.;.;.;NOL6_HUMAN	P	590;590;590;146;590;538	ENSP00000313978:R590P;ENSP00000297990:R590P;ENSP00000368784:R590P;ENSP00000395915:R538P	ENSP00000297990:R590P	R	-	2	0	NOL6	33457217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.428000	0.80296	2.755000	0.94549	0.655000	0.94253	CGG	.	.		0.617	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		G	33467217	C	G	33467217	3	3	199	1	0	0	0	0	1	0	0	0	10534	652	23	4	1723	4	NOL6	9	33467217	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	33032319	33467217	107746214	69	29295										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79898289	79898289	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agctttaaaactatccacaaAtgaagatatcattactttgc	4	8	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr9:79898289A>T	ENST00000360280.3	+	30	3397	c.3137A>T	c.(3136-3138)aAt>aTt	p.N1046I	VPS13A_ENST00000376634.4_Missense_Mutation_p.N1046I|VPS13A_ENST00000357409.5_Missense_Mutation_p.N1046I|VPS13A_ENST00000423463.2_3'UTR|VPS13A_ENST00000376636.3_Intron	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1046					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CTATCCACAAATGAAGATATC	0.259																																					p.N1046I		Atlas-SNP	.											.	VPS13A	735	.	0			c.A3137T						.						24	26	25					9																	79898289		2174	4265	6439	SO:0001583	missense	23230	exon30			CCACAAATGAAGA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.3137A>T	chr9.hg19:g.79898289A>T	ENSP00000353422:p.Asn1046Ile	375.0	1.0		348.0	137.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	5.513	0.279587	0.10458	.	.	ENSG00000197969	ENST00000376634;ENST00000360280;ENST00000357409	T;T;T	0.17691	2.26;2.26;2.26	5.74	1.9	0.25705	.	1.056110	0.07284	N	0.871226	T	0.08758	0.0217	N	0.08118	0	0.80722	D	1	B;B;B	0.29432	0.158;0.244;0.244	B;B;B	0.23716	0.021;0.048;0.048	T	0.16512	-1.0400	10	0.36615	T	0.2	.	7.588	0.28004	0.6598:0.2249:0.1153:0.0	.	1046;1046;1046	Q96RL7;Q96RL7-2;Q96RL7-4	VP13A_HUMAN;.;.	I	1046	ENSP00000365821:N1046I;ENSP00000353422:N1046I;ENSP00000349985:N1046I	ENSP00000349985:N1046I	N	+	2	0	VPS13A	79088109	0.998000	0.40836	0.790000	0.31976	0.280000	0.26924	0.652000	0.24888	0.982000	0.38575	-0.323000	0.08544	AAT	.	.		0.259	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		T	79898289	A	T	79898289	3	4	199	1	0	0	0	0	1	0	0	0	17204	101	4	4	3255	4	VPS13A	9	79898289	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	46431072	79898289	61315142	70	29296										
USP20	10868	hgsc.bcm.edu	37	chr9	132638408	132638408	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tctctcccaccctgggcacaGattcgggggtggccccgccg	13	17	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr9:132638408G>T	ENST00000315480.4	+	22	2458		c.e22-1		USP20_ENST00000358355.1_Splice_Site|USP20_ENST00000372429.3_Splice_Site			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20						endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				CCTGGGCACAGATTCGGGGGT	0.647																																					.		Atlas-SNP	.											.	USP20	186	.	0			c.2301-1G>T						.						22	25	24					9																	132638408		2019	4188	6207	SO:0001630	splice_region_variant	10868	exon22			GGCACAGATTCGG	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.2301-1G>T	chr9.hg19:g.132638408G>T		206.0	0.0		172.0	67.0	NM_001110303	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Splice_Site	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.068255	0.36470	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0289	0.92946	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	USP20	131678229	1.000000	0.71417	1.000000	0.80357	0.079000	0.17450	9.467000	0.97671	2.746000	0.94184	0.561000	0.74099	.	.	.		0.647	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		Intron	T	132638408	G	T	132638408	5	4	199	1	0	0	0	0	0	0	1	0	17067	956	33	3	2378	3	USP20	9	132638408	Splice_Site	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	52740119	132638408	8575023	71	29297										
GTF3C4	9329	hgsc.bcm.edu	37	chr9	135553599	135553599	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gaccatccaggcaaatctcaAcagactgcagtgggtccagc	10	13	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr9:135553599A>G	ENST00000372146.4	+	2	1157	c.593A>G	c.(592-594)aAc>aGc	p.N198S	GTF3C4_ENST00000483873.2_Intron	NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	198					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		GCAAATCTCAACAGACTGCAG	0.527																																					p.N198S	Pancreas(142;417 1875 11086 31973 47667)	Atlas-SNP	.											.	GTF3C4	53	.	0			c.A593G						.						70	68	69					9																	135553599		2203	4300	6503	SO:0001583	missense	9329	exon2			ATCTCAACAGACT	AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"Chromatin-modifying enzymes / K-acetyltransferases", "General transcription factors"	4667	protein-coding gene	gene with protein product		604892	"general transcription factor IIIC, polypeptide 4 (90kD)"			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.593A>G	chr9.hg19:g.135553599A>G	ENSP00000361219:p.Asn198Ser	153.0	0.0		129.0	46.0	NM_012204	Q5VZJ7	Missense_Mutation	SNP	ENST00000372146.4	hg19	CCDS6953.1	.	.	.	.	.	.	.	.	.	.	A	10.79	1.449064	0.26074	.	.	ENSG00000125484	ENST00000372146	T	0.40476	1.03	5.72	4.59	0.56863	Transcription factor IIIC, 90kDa subunit, N-terminal (1);	0.197602	0.52532	N	0.000077	T	0.22666	0.0547	N	0.19112	0.55	0.33217	D	0.554233	B	0.09022	0.002	B	0.10450	0.005	T	0.27806	-1.0063	10	0.02654	T	1	-33.2064	9.1267	0.36818	0.9075:0.0:0.0925:0.0	.	198	Q9UKN8	TF3C4_HUMAN	S	198	ENSP00000361219:N198S	ENSP00000361219:N198S	N	+	2	0	GTF3C4	134543420	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.727000	0.47311	0.997000	0.38969	0.459000	0.35465	AAC	.	.		0.527	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1			G	135553599	A	G	135553599	3	3	199	1	0	0	0	0	1	0	0	0	6884	43	2	2	599	2	GTF3C4	9	135553599	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	2915191	135553599	5659832	72	29298										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7659077	7659077	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gcaacgacgatcctattaccTggatgtccccaatgctctgt	8	13	1	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr10:7659077T>A	ENST00000256861.6	-	6	899	c.821A>T	c.(820-822)cAg>cTg	p.Q274L	ITIH5_ENST00000298441.6_Splice_Site_p.Q60L|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000446830.2_Splice_Site_p.Q56L|ITIH5_ENST00000397145.2_Splice_Site_p.Q274L|ITIH5_ENST00000397146.2_Splice_Site_p.Q274L	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	274					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TCCTATTACCTGGATGTCCCC	0.423																																					p.Q274L		Atlas-SNP	.											.	ITIH5	343	.	0			c.A821T						.						180	157	165					10																	7659077		2203	4300	6503	SO:0001630	splice_region_variant	80760	exon6			ATTACCTGGATGT			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.822+1A>T	chr10.hg19:g.7659077T>A		86.0	0.0		103.0	6.0	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	T	28.5	4.925231	0.92319	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06	6.08	6.08	0.98989	.	0.051461	0.85682	D	0.000000	D	0.86518	0.5952	.	.	.	0.58432	D	0.999999	P;D;D	0.65815	0.93;0.995;0.994	P;P;P	0.62014	0.762;0.848;0.897	D	0.86451	0.1773	9	0.45353	T	0.12	-24.9552	16.3246	0.82970	0.0:0.0:0.0:1.0	.	274;274;60	G5E9D8;Q86UX2;Q86UX2-3	.;ITIH5_HUMAN;.	L	274;274;60;56;274	ENSP00000256861:Q274L;ENSP00000380333:Q274L;ENSP00000298441:Q60L;ENSP00000387969:Q56L;ENSP00000380332:Q274L	ENSP00000256861:Q274L	Q	-	2	0	ITIH5	7699083	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	7.278000	0.78587	2.333000	0.79357	0.482000	0.46254	CAG	.	.		0.423	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	Missense_Mutation	A	7659077	T	A	7659077	5	1	199	1	0	0	0	0	0	0	1	0	7916	1594	55	4	2166	4	ITIH5	10	7659077	Splice_Site	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10		7659077	127875670	73	29299										
CACNB2	783	hgsc.bcm.edu	37	chr10	18828423	18828423	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	acgtggaccactatgcctcaCaccgtgaccacaaccacaga	7	16	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr10:18828423C>T	ENST00000324631.7	+	14	1813	c.1753C>T	c.(1753-1755)Cac>Tac	p.H585Y	CACNB2_ENST00000377329.4_Missense_Mutation_p.H531Y|CACNB2_ENST00000377331.2_Missense_Mutation_p.H533Y|CACNB2_ENST00000352115.6_Missense_Mutation_p.H561Y|RP11-499P20.2_ENST00000425669.1_RNA|RP11-499P20.2_ENST00000436485.1_RNA|CACNB2_ENST00000377315.4_Missense_Mutation_p.H537Y|CACNB2_ENST00000377328.1_Missense_Mutation_p.H335Y|CACNB2_ENST00000377319.3_Missense_Mutation_p.H492Y|CACNB2_ENST00000282343.8_Missense_Mutation_p.H557Y|CACNB2_ENST00000396576.2_Missense_Mutation_p.H530Y	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	585					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CTATGCCTCACACCGTGACCA	0.577																																					p.H585Y		Atlas-SNP	.											.	CACNB2	220	.	0			c.C1753T						.						114	82	93					10																	18828423		2203	4300	6503	SO:0001583	missense	783	exon14			GCCTCACACCGTG	U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995		"Calcium channel subunits"	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2		9254841, 8494331	Standard	NM_201596		Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.1753C>T	chr10.hg19:g.18828423C>T	ENSP00000320025:p.His585Tyr	206.0	0.0		202.0	78.0	NM_201596	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	Missense_Mutation	SNP	ENST00000324631.7	hg19	CCDS7125.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999929	0.74818	.	.	ENSG00000165995	ENST00000324631;ENST00000352115;ENST00000377328;ENST00000282343;ENST00000377331;ENST00000396576;ENST00000377319;ENST00000377329;ENST00000377315	D;T;D;D;T;D;D;D;D	0.83755	-1.69;1.99;-1.76;-1.68;1.99;-1.68;-1.7;-1.68;-1.69	5.91	5.91	0.95273	.	0.127596	0.64402	D	0.000001	D	0.85239	0.5651	N	0.14661	0.345	0.80722	D	1	P;D;D;D;D;D;D;P;P;D;P;D;D	0.71674	0.908;0.997;0.996;0.976;0.995;0.986;0.995;0.952;0.947;0.998;0.952;0.989;0.997	P;D;D;D;D;D;D;P;P;D;P;P;D	0.79784	0.684;0.985;0.918;0.943;0.985;0.974;0.985;0.453;0.622;0.993;0.709;0.868;0.985	D	0.86666	0.1907	10	0.54805	T	0.06	-20.9662	20.2963	0.98556	0.0:1.0:0.0:0.0	.	499;557;335;537;507;531;541;492;533;557;547;561;585	B7Z1U5;Q5QJA0;A6PVM6;Q5VVH1;Q6TME1;Q08289-3;Q59H42;Q08289-6;A6PVM7;Q08289-4;Q08289-7;Q08289-8;Q08289	.;.;.;.;.;.;.;.;.;.;.;.;CACB2_HUMAN	Y	585;561;335;557;533;530;492;531;537	ENSP00000320025:H585Y;ENSP00000344474:H561Y;ENSP00000366545:H335Y;ENSP00000282343:H557Y;ENSP00000366548:H533Y;ENSP00000379821:H530Y;ENSP00000366536:H492Y;ENSP00000366546:H531Y;ENSP00000366532:H537Y	ENSP00000282343:H557Y	H	+	1	0	CACNB2	18868429	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	4.951000	0.63610	2.813000	0.96785	0.655000	0.94253	CAC	.	.		0.577	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047072.2	NM_000724		T	18828423	C	T	18828423	3	4	199	1	0	0	0	0	1	0	0	0	2555	478	17	3	2117	3	CACNB2	10	18828423	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	11169346	18828423	116706324	74	29300										
ZNF239	8187	hgsc.bcm.edu	37	chr10	44052197	44052197	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gctggtggatgtgaaggttgGagctctggctgaagcccttc	16	8	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr10:44052197G>A	ENST00000306006.6	-	2	1983	c.1331C>T	c.(1330-1332)tCc>tTc	p.S444F	ZNF239_ENST00000426961.1_Missense_Mutation_p.S444F|ZNF239_ENST00000374446.2_Missense_Mutation_p.S444F|ZNF239_ENST00000491188.1_5'Flank|ZNF239_ENST00000535642.1_Missense_Mutation_p.S444F	NM_005674.2	NP_005665.2	Q16600	ZN239_HUMAN	zinc finger protein 239	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						GTGAAGGTTGGAGCTCTGGCT	0.488																																					p.S444F		Atlas-SNP	.											.	ZNF239	45	.	0			c.C1331T						.						64	69	67					10																	44052197		2201	4300	6501	SO:0001583	missense	8187	exon2			AGGTTGGAGCTCT	X82125	CCDS41502.1	10q11.22-q11.23	2013-01-08			ENSG00000196793	ENSG00000196793		"Zinc fingers, C2H2-type"	13031	protein-coding gene	gene with protein product		601069				8903737, 8587123	Standard	NM_005674		Approved	MOK2, HOK-2	uc009xmk.3	Q16600	OTTHUMG00000018033	ENST00000306006.6:c.1331C>T	chr10.hg19:g.44052197G>A	ENSP00000307774:p.Ser444Phe	91.0	0.0		93.0	40.0	NM_001099283	Q5T1G9|Q8TAS5	Missense_Mutation	SNP	ENST00000306006.6	hg19	CCDS41502.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.886048	0.51908	.	.	ENSG00000196793	ENST00000306006;ENST00000374446;ENST00000426961;ENST00000535642;ENST00000339962	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	3.25	3.25	0.37280	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.64305	0.2586	M	0.89478	3.035	0.30614	N	0.759207	D	0.71674	0.998	D	0.79784	0.993	T	0.66909	-0.5804	9	0.87932	D	0	-14.5011	12.8102	0.57635	0.0:0.0:1.0:0.0	.	444	Q16600	ZN239_HUMAN	F	444	ENSP00000307774:S444F;ENSP00000363569:S444F;ENSP00000398202:S444F;ENSP00000443907:S444F	ENSP00000307774:S444F	S	-	2	0	ZNF239	43372203	0.190000	0.23276	1.000000	0.80357	0.990000	0.78478	2.261000	0.43276	2.129000	0.65627	0.650000	0.86243	TCC	.	.		0.488	ZNF239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047710.1			A	44052197	G	A	44052197	3	1	199	1	0	0	0	0	1	0	0	0	17806	1174	41	3	49	3	ZNF239	10	44052197	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	25223774	44052197	91482550	75	29301										
TMEM72	643236	hgsc.bcm.edu	37	chr10	45406975	45406975	+	5'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggcaccatgcagctccaggtGttctggactgggctggaata	14	10	1	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr10:45406975G>A	ENST00000544540.1	+	0	212				TMEM72-AS1_ENST00000450287.2_RNA|RP11-285G1.2_ENST00000436877.2_RNA			A0PK05	TMM72_HUMAN	transmembrane protein 72							integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						AGCTCCAGGTGTTCTGGACTG	0.607																																					p.V5V		Atlas-SNP	.											.	TMEM72	25	.	0			c.G15A						.						18	18	18					10																	45406975		1502	3420	4922	SO:0001623	5_prime_UTR_variant	643236	exon1			CCAGGTGTTCTGG	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 127"	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.-273G>A	chr10.hg19:g.45406975G>A		39.0	0.0		32.0	12.0	NM_001123376	A1L181|Q5T740	Silent	SNP	ENST00000544540.1	hg19																																																																																				.	.		0.607	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376		A	45406975	G	A	45406975	1	1	199	0	1	0	0	0	0	0	0	0	16216	1364	48	3		3	TMEM72	10	45406975	5'UTR	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	1354778	45406975	90127772	76	29302										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108924108	108924108	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggagccctgcctggccgcccCtggtgggaaaagcccctagg	15	15	0	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr10:108924108C>A	ENST00000263054.6	-	1	184	c.177G>T	c.(175-177)caG>caT	p.Q59H	SORCS1_ENST00000344440.6_Missense_Mutation_p.Q59H	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	59					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CTGGCCGCCCCTGGTGGGAAA	0.756																																					p.Q59H		Atlas-SNP	.											.	SORCS1	534	.	0			c.G177T						.						2	3	3					10																	108924108		1734	3594	5328	SO:0001583	missense	114815	exon1			CCGCCCCTGGTGG	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.177G>T	chr10.hg19:g.108924108C>A	ENSP00000263054:p.Gln59His	72.0	0.0		67.0	7.0	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	C	2.949	-0.217203	0.06101	.	.	ENSG00000108018	ENST00000263054;ENST00000344440	T;T	0.14391	2.51;2.52	4.06	2.17	0.27698	.	0.570812	0.13469	N	0.385558	T	0.05364	0.0142	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.41698	-0.9494	9	.	.	.	-0.2343	2.782	0.05363	0.1861:0.5292:0.1809:0.1037	.	59;59;59;59;59	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	H	59	ENSP00000263054:Q59H;ENSP00000345964:Q59H	.	Q	-	3	2	SORCS1	108914098	0.548000	0.26473	0.002000	0.10522	0.183000	0.23260	1.234000	0.32660	0.348000	0.23949	0.467000	0.42956	CAG	.	.		0.756	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108924108	C	A	108924108	3	1	199	1	0	0	0	0	1	0	0	0	14945	680	24	3	3667	3	SORCS1	10	108924108	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	63517133	108924108	26610639	77	29303										
SEC23IP	11196	hgsc.bcm.edu	37	chr10	121678002	121678002	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gctaatggagttgtgaagcaGctacattttcaggaaaagca	11	6	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr10:121678002G>T	ENST00000369075.3	+	10	1923	c.1851G>T	c.(1849-1851)caG>caT	p.Q617H	SEC23IP_ENST00000543134.1_Missense_Mutation_p.Q406H	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	617					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		TTGTGAAGCAGCTACATTTTC	0.373																																					p.Q617H		Atlas-SNP	.											.	SEC23IP	100	.	0			c.G1851T						.						111	105	107					10																	121678002		2203	4300	6503	SO:0001583	missense	11196	exon10			GAAGCAGCTACAT	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.1851G>T	chr10.hg19:g.121678002G>T	ENSP00000358071:p.Gln617His	111.0	0.0		87.0	6.0	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Missense_Mutation	SNP	ENST00000369075.3	hg19	CCDS7618.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.582412	0.28180	.	.	ENSG00000107651	ENST00000369075;ENST00000543134	T;T	0.42900	0.96;0.96	5.72	-1.79	0.07932	.	0.379061	0.33875	N	0.004467	T	0.14614	0.0353	N	0.04880	-0.145	0.20873	N	0.999839	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.06303	-1.0834	10	0.41790	T	0.15	-7.7821	0.8952	0.01262	0.2986:0.0957:0.2475:0.3582	.	406;617	F5H0L8;Q9Y6Y8	.;S23IP_HUMAN	H	617;406	ENSP00000358071:Q617H;ENSP00000438773:Q406H	ENSP00000358071:Q617H	Q	+	3	2	SEC23IP	121667992	0.034000	0.19679	0.383000	0.26132	0.989000	0.77384	0.113000	0.15499	-0.069000	0.12931	-0.137000	0.14449	CAG	.	.		0.373	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			T	121678002	G	T	121678002	3	4	199	1	0	0	0	0	1	0	0	0	14008	962	34	3	1889	3	SEC23IP	10	121678002	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	12753894	121678002	13856745	78	29304										
MMP26	56547	hgsc.bcm.edu	37	chr11	5013312	5013312	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tatcacgaccctagaaccttCcagctcagtgccgatgatat	7	13	2	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr11:5013312C>T	ENST00000380390.1	+	6	930	c.714C>T	c.(712-714)ttC>ttT	p.F238F	MMP26_ENST00000300762.1_Silent_p.F238F			Q9NRE1	MMP26_HUMAN	matrix metallopeptidase 26	238					collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(3)|stomach(1)	22		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)	Marimastat(DB00786)	CTAGAACCTTCCAGCTCAGTG	0.478																																					p.F238F		Atlas-SNP	.											.	MMP26	49	.	0			c.C714T						.						86	77	80					11																	5013312		2201	4298	6499	SO:0001819	synonymous_variant	56547	exon5			AACCTTCCAGCTC	AF230354	CCDS7752.1	11p15	2008-07-18	2005-08-08		ENSG00000167346	ENSG00000167346	3.4.24.1		14249	protein-coding gene	gene with protein product	"matrilysin 2"	605470	"matrix metalloproteinase 26"			10801841, 10824119	Standard	NM_021801		Approved	endometase, MGC126590, MGC126592	uc001lzv.3	Q9NRE1	OTTHUMG00000066442	ENST00000380390.1:c.714C>T	chr11.hg19:g.5013312C>T		164.0	0.0		183.0	72.0	NM_021801	Q3MJ78|Q9GZS2|Q9NR87	Silent	SNP	ENST00000380390.1	hg19	CCDS7752.1																																																																																			.	.		0.478	MMP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142058.3	NM_021801		T	5013312	C	T	5013312	2	4	199	1	0	0	0	0	0	0	0	1	9672	854	30	3		3	MMP26	11	5013312	Silent	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10		5013312	129993204	79	29305										
RBMXL2	27288	hgsc.bcm.edu	37	chr11	7111063	7111063	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ttgccccctcgcccggagagTacacccaccgcgattacggc	10	18	0	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr11:7111063T>C	ENST00000306904.5	+	1	899	c.712T>C	c.(712-714)Tac>Cac	p.Y238H		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	238	Arg/Gly/Pro-rich.					nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GCCCGGAGAGTACACCCACCG	0.672																																					p.Y238H		Atlas-SNP	.											.	RBMXL2	47	.	0			c.T712C						.						20	22	21					11																	7111063		2193	4277	6470	SO:0001583	missense	27288	exon1			GGAGAGTACACCC	AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"RNA binding motif (RRM) containing"	17886	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein G T"	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.712T>C	chr11.hg19:g.7111063T>C	ENSP00000304139:p.Tyr238His	85.0	0.0		59.0	16.0	NM_014469	Q6PEZ2|Q9NQU0	Missense_Mutation	SNP	ENST00000306904.5	hg19	CCDS7777.1	.	.	.	.	.	.	.	.	.	.	T	13.83	2.354446	0.41700	.	.	ENSG00000170748	ENST00000306904	T	0.79749	-1.3	3.08	3.08	0.35506	.	0.075363	0.56097	U	0.000035	D	0.85826	0.5787	M	0.73962	2.25	0.43133	D	0.994873	D	0.76494	0.999	P	0.60789	0.879	D	0.87050	0.2146	10	0.87932	D	0	.	9.8477	0.41037	0.0:0.0:0.0:1.0	.	238	O75526	HNRGT_HUMAN	H	238	ENSP00000304139:Y238H	ENSP00000304139:Y238H	Y	+	1	0	RBMXL2	7067639	1.000000	0.71417	0.967000	0.41034	0.379000	0.30106	6.042000	0.70996	1.637000	0.50538	0.383000	0.25322	TAC	.	.		0.672	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469		C	7111063	T	C	7111063	3	2	199	1	0	0	0	0	1	0	0	0	13169	1638	57	2	714	2	RBMXL2	11	7111063	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	2097751	7111063	127895453	80	29306										
KCNA4	3739	hgsc.bcm.edu	37	chr11	30034089	30034089	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	cttcgacagcagctgtggccGctgcaacagcagctgctgca	12	14	0	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr11:30034089G>C	ENST00000328224.6	-	2	1370	c.137C>G	c.(136-138)gCg>gGg	p.A46G	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	46					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	AGCTGTGGCCGCTGCAACAGC	0.662																																					p.A46G		Atlas-SNP	.											.	KCNA4	158	.	0			c.C137G						.						40	41	41					11																	30034089		1806	3994	5800	SO:0001583	missense	3739	exon2			GTGGCCGCTGCAA	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.137C>G	chr11.hg19:g.30034089G>C	ENSP00000328511:p.Ala46Gly	35.0	0.0		41.0	17.0	NM_002233		Missense_Mutation	SNP	ENST00000328224.6	hg19	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	G	9.597	1.127630	0.20959	.	.	ENSG00000182255	ENST00000328224	D	0.96967	-4.19	4.84	4.84	0.62591	Potassium channel, voltage dependent, Kv1.4, tandem inactivation (2);	4.111420	0.00616	N	0.000436	D	0.92714	0.7684	N	0.12182	0.205	0.39953	D	0.974562	B	0.06786	0.001	B	0.09377	0.004	T	0.67715	-0.5599	10	0.28530	T	0.3	.	13.6829	0.62496	0.0:0.1546:0.8454:0.0	.	46	P22459	KCNA4_HUMAN	G	46	ENSP00000328511:A46G	ENSP00000328511:A46G	A	-	2	0	KCNA4	29990665	1.000000	0.71417	0.090000	0.20809	0.132000	0.20833	4.380000	0.59581	2.239000	0.73571	0.561000	0.74099	GCG	.	.		0.662	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		C	30034089	G	C	30034089	3	2	199	1	0	0	0	0	1	0	0	0	8014	1087	38	4	1828	4	KCNA4	11	30034089	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	22923026	30034089	104972427	81	29307										
PACSIN3	29763	hgsc.bcm.edu	37	chr11	47201829	47201829	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gtctgcctttgcgtggctctCcctcgtctgggcggtcttct	12	14	5	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr11:47201829C>A	ENST00000539589.1	-	6	853	c.511G>T	c.(511-513)Gag>Tag	p.E171*	PACSIN3_ENST00000298838.6_Nonsense_Mutation_p.E171*	NM_001184975.1	NP_001171904.1	Q9UKS6	PACN3_HUMAN	protein kinase C and casein kinase substrate in neurons 3	171	F-BAR domain. {ECO:0000250}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endocytosis (GO:0045806)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium channel inhibitor activity (GO:0019855)|cytoskeletal protein binding (GO:0008092)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)	11						GCGTGGCTCTCCCTCGTCTGG	0.622											OREG0020952	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E171X		Atlas-SNP	.											.	PACSIN3	28	.	0			c.G511T						.						135	108	117					11																	47201829		2201	4298	6499	SO:0001587	stop_gained	29763	exon6			GGCTCTCCCTCGT	AF130979	CCDS31481.1	11p12-p11	2008-02-05				ENSG00000165912			8572	protein-coding gene	gene with protein product	"syndapin III"	606513				10531379	Standard	NM_016223		Approved	SDPIII	uc001ndx.3	Q9UKS6		ENST00000539589.1:c.511G>T	chr11.hg19:g.47201829C>A	ENSP00000440945:p.Glu171*	45.0	0.0	945	41.0	18.0	NM_016223	A6NH84|Q9H331|Q9NWV9	Nonsense_Mutation	SNP	ENST00000539589.1	hg19	CCDS31481.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.952545	0.53293	.	.	ENSG00000165912	ENST00000298838;ENST00000415232;ENST00000539589;ENST00000528462	.	.	.	5.62	4.71	0.59529	.	0.190075	0.56097	D	0.000032	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-21.5089	14.561	0.68136	0.0:0.9296:0.0:0.0704	.	.	.	.	X	171	.	ENSP00000298838:E171X	E	-	1	0	PACSIN3	47158405	1.000000	0.71417	0.999000	0.59377	0.005000	0.04900	6.086000	0.71352	1.397000	0.46682	-0.258000	0.10820	GAG	.	.		0.622	PACSIN3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391632.1	NM_016223		A	47201829	C	A	47201829	4	1	199	1	0	0	0	0	0	1	0	0	11385	864	30	3	787	3	PACSIN3	11	47201829	Nonsense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	17167740	47201829	87804687	82	29308										
OR5D13	390142	hgsc.bcm.edu	37	chr11	55541283	55541283	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tagcagcgatggcttatgacCgttttgtggcagtttgtaaa	12	6	0	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr11:55541283C>A	ENST00000361760.1	+	1	370	c.370C>A	c.(370-372)Cgt>Agt	p.R124S		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	124			R -> H (in dbSNP:rs11230983).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				GGCTTATGACCGTTTTGTGGC	0.433																																					p.R124S		Atlas-SNP	.											.	OR5D13	96	.	0			c.C370A						.						238	231	233					11																	55541283		2200	4296	6496	SO:0001583	missense	390142	exon1			TATGACCGTTTTG	BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"GPCR / Class A : Olfactory receptors"	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.370C>A	chr11.hg19:g.55541283C>A	ENSP00000354800:p.Arg124Ser	154.0	0.0		176.0	72.0	NM_001001967	Q6IF68|Q6IFC9	Missense_Mutation	SNP	ENST00000361760.1	hg19	CCDS31507.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.511149	0.27036	.	.	ENSG00000198877	ENST00000361760	T	0.77620	-1.11	3.3	1.17	0.20885	GPCR, rhodopsin-like superfamily (1);	0.339612	0.16661	U	0.204770	D	0.84220	0.5424	H	0.97023	3.925	0.20764	N	0.999857	P	0.37985	0.613	B	0.41466	0.358	T	0.77993	-0.2378	10	0.87932	D	0	-0.0508	7.3858	0.26882	0.1802:0.4926:0.3272:0.0	.	124	Q8NGL4	OR5DD_HUMAN	S	124	ENSP00000354800:R124S	ENSP00000354800:R124S	R	+	1	0	OR5D13	55297859	0.013000	0.17824	0.131000	0.22000	0.002000	0.02628	0.316000	0.19469	0.173000	0.19788	0.486000	0.48141	CGT	.	.		0.433	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967		A	55541283	C	A	55541283	3	1	199	1	0	0	0	0	1	0	0	0	11163	652	23	1	372	1	OR5D13	11	55541283	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	8339454	55541283	79465233	83	29309										
OR8J3	81168	hgsc.bcm.edu	37	chr11	55905105	55905105	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agcacatagagcactaggaaGaccaggaagaggggaatctg	14	7	1	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr11:55905105G>T	ENST00000301529.1	-	1	89	c.90C>A	c.(88-90)gtC>gtA	p.V30V		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					GCACTAGGAAGACCAGGAAGA	0.498																																					p.V30V		Atlas-SNP	.											.	OR8J3	112	.	0			c.C90A						.						124	124	124					11																	55905105		2201	4296	6497	SO:0001819	synonymous_variant	81168	exon1			TAGGAAGACCAGG		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"GPCR / Class A : Olfactory receptors"	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.90C>A	chr11.hg19:g.55905105G>T		167.0	0.0		134.0	63.0	NM_001004064	Q6IFB6|Q96RC2	Silent	SNP	ENST00000301529.1	hg19	CCDS31520.1																																																																																			.	.		0.498	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064		T	55905105	G	T	55905105	2	4	199	1	0	0	0	0	0	0	0	1	11251	929	33	3		3	OR8J3	11	55905105	Silent	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	363822	55905105	79101411	84	29310										
SLC22A24	283238	hgsc.bcm.edu	37	chr11	62863471	62863471	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	aatggaacttacctcacaaaGcacaggccgaagactctcat	7	12	2	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr11:62863471G>C	ENST00000417740.1	-	6	1503	c.1062C>G	c.(1060-1062)tgC>tgG	p.C354W		NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	0					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						ACCTCACAAAGCACAGGCCGA	0.413																																					p.C354W		Atlas-SNP	.											.	SLC22A24	31	.	0			c.C1062G						.						111	93	98					11																	62863471		692	1591	2283	SO:0001583	missense	283238	exon6			CACAAAGCACAGG		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"Solute carriers"	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.1062C>G	chr11.hg19:g.62863471G>C	ENSP00000396586:p.Cys354Trp	171.0	0.0		171.0	70.0	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.209	1.030385	0.19512	.	.	ENSG00000197658	ENST00000417740	T	0.58652	0.32	3.68	-2.13	0.07144	.	.	.	.	.	T	0.56426	0.1984	L	0.39898	1.24	0.09310	N	1	D	0.55800	0.973	P	0.61275	0.886	T	0.48246	-0.9052	9	0.38643	T	0.18	.	4.1523	0.10244	0.4463:0.1769:0.3768:0.0	.	354	C9JC66	.	W	354	ENSP00000396586:C354W	ENSP00000396586:C354W	C	-	3	2	SLC22A24	62620047	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.158000	0.10070	-0.557000	0.06126	0.590000	0.80494	TGC	.	.		0.413	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586		C	62863471	G	C	62863471	3	2	199	1	0	0	0	0	1	0	0	0	14468	963	34	4	611	4	SLC22A24	11	62863471	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	6958366	62863471	72143045	85	29311										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78525437	78525437	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tgctggggcagttatccaccGactctggggagagaaaggag	16	8	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr11:78525437G>T	ENST00000278550.7	-	13	2147	c.1685C>A	c.(1684-1686)tCg>tAg	p.S562*		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	562	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										GTTATCCACCGACTCTGGGGA	0.522																																					p.S562X		Atlas-SNP	.											.	.	.	.	0			c.C1685A						.						71	86	81					11																	78525437		692	1591	2283	SO:0001587	stop_gained	26011	exon13			TCCACCGACTCTG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.1685C>A	chr11.hg19:g.78525437G>T	ENSP00000278550:p.Ser562*	237.0	0.0		229.0	91.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Nonsense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	G	41	9.029282	0.99042	.	.	ENSG00000149256	ENST00000278550	.	.	.	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.462	0.90741	0.0:0.0:1.0:0.0	.	.	.	.	X	562	.	.	S	-	2	0	ODZ4	78203085	1.000000	0.71417	0.828000	0.32881	0.276000	0.26787	7.826000	0.86716	2.646000	0.89796	0.655000	0.94253	TCG	.	.		0.522	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78525437	G	T	78525437	4	4	199	1	0	0	0	0	0	1	0	0	10846	1059	37	1	6712	1	ODZ4	11	78525437	Nonsense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	15661966	78525437	56481079	86	29312										
FZD4	8322	hgsc.bcm.edu	37	chr11	86663371	86663371	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tgggaatttgctgcagttcaGactctctggccaggcaaatc	11	10	2	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr11:86663371G>T	ENST00000531380.1	-	2	732	c.427C>A	c.(427-429)Ctg>Atg	p.L143M	PRSS23_ENST00000533902.2_3'UTR	NM_012193.3	NP_036325.2	Q9ULV1	FZD4_HUMAN	frizzled class receptor 4	143	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|cerebellum vasculature morphogenesis (GO:0061301)|extracellular matrix-cell signaling (GO:0035426)|locomotion involved in locomotory behavior (GO:0031987)|negative regulation of cell-substrate adhesion (GO:0010812)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal blood vessel morphogenesis (GO:0061304)|sensory perception of sound (GO:0007605)|substrate adhesion-dependent cell spreading (GO:0034446)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(6)|skin(1)	21		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTGCAGTTCAGACTCTCTGGC	0.537																																					p.L143M		Atlas-SNP	.											.	FZD4	52	.	0			c.C427A						.						92	96	95					11																	86663371		2201	4299	6500	SO:0001583	missense	8322	exon2			AGTTCAGACTCTC	AB032417	CCDS8279.1	11q14-q21	2014-01-29	2014-01-29			ENSG00000174804		"GPCR / Class F : Frizzled receptors", "CD molecules"	4042	protein-coding gene	gene with protein product		604579	"frizzled (Drosophila) homolog 4", "exudative vitreoretinopathy 1", "frizzled homolog 4 (Drosophila)", "frizzled 4, seven transmembrane spanning receptor", "frizzled family receptor 4"	EVR1		10544037, 15024691	Standard	NM_012193		Approved	CD344	uc001pce.3	Q9ULV1		ENST00000531380.1:c.427C>A	chr11.hg19:g.86663371G>T	ENSP00000434034:p.Leu143Met	175.0	0.0		144.0	51.0	NM_012193	A8K9Q3|Q14C97|Q6S9E4	Missense_Mutation	SNP	ENST00000531380.1	hg19	CCDS8279.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.678702	0.47886	.	.	ENSG00000174804	ENST00000531380	D	0.84516	-1.86	5.82	5.82	0.92795	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.89480	0.6727	L	0.58354	1.805	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.88259	0.2922	9	.	.	.	.	10.4781	0.44676	0.1435:0.0:0.8565:0.0	.	143	Q9ULV1	FZD4_HUMAN	M	143	ENSP00000434034:L143M	.	L	-	1	2	FZD4	86341019	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.996000	0.63914	2.760000	0.94817	0.655000	0.94253	CTG	.	.		0.537	FZD4-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393818.2	NM_012193		T	86663371	G	T	86663371	3	4	199	1	0	0	0	0	1	0	0	0	6140	933	33	3	1190	3	FZD4	11	86663371	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	8137934	86663371	48343145	87	29313										
VAMP1	6843	hgsc.bcm.edu	37	chr12	6574098	6574099	+	Frame_Shift_Ins	INS	-	-	GA													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gcacagatggctcccagcatINSgatcatcatctgaggaaaca							TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr12:6574098_6574099insGA	ENST00000396308.3	-	4	442_443	c.297_298insTC	c.(295-300)atcatgfs	p.M100fs	VAMP1_ENST00000535180.1_Frame_Shift_Ins_p.M100fs|VAMP1_ENST00000400911.3_Frame_Shift_Ins_p.M100fs|VAMP1_ENST00000361716.3_Frame_Shift_Ins_p.M100fs|VAMP1_ENST00000544432.1_5'UTR|TAPBPL_ENST00000545700.1_Intron	NM_014231.3|NM_199245.1	NP_055046.1|NP_954740.1	P23763	VAMP1_HUMAN	vesicle-associated membrane protein 1 (synaptobrevin 1)	100					neurotransmitter secretion (GO:0007269)|SNARE complex assembly (GO:0035493)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuron projection (GO:0043005)|synapse (GO:0045202)				endometrium(1)|large_intestine(1)|prostate(1)	3					Botulinum Toxin Type B(DB00042)	GCTCCCAGCATGATCATCATCT	0.465																																					p.M100fs		Atlas-INDEL	.											.	VAMP1	6	.	0			c.298_299insTC						.																																			SO:0001589	frameshift_variant	6843	exon4			.		CCDS31731.1, CCDS41740.1, CCDS44809.1, CCDS73422.1	12p	2013-02-13			ENSG00000139190	ENSG00000139190		"Vesicle-associated membrane proteins"	12642	protein-coding gene	gene with protein product		185880		SYB1		1976629	Standard	XM_006719011		Approved	VAMP-1	uc001qok.3	P23763	OTTHUMG00000168269	ENST00000396308.3:c.296_297dupTC	chr12.hg19:g.6574099_6574100dupGA	ENSP00000379602:p.Met100fs	78.0	0.0		63.0	16.0	NM_016830	A8MVP3|D3DUR3|O75468|Q15857|Q6FG94|Q8IVC9	Frame_Shift_Ins	INS	ENST00000396308.3	hg19	CCDS41740.1																																																																																			.	.		0.465	VAMP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399078.1			GA	6574099	-	GA	6574098	7	5	199	1	0	1	1	0	0	0	0	0	17127	1464	51	0	95	0	VAMP1	12	6574098	Frame_Shift_Ins	INS	-	TCGA-DD-AADQ-01A-11D-A40R-10		6574098	127277797	88	29314										
DDX11	1663	hgsc.bcm.edu	37	chr12	31253960	31253961	+	Splice_Site	INS	-	-	A													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ccctccctggctcttaccagINSgtcacgtgatccctccagac							TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr12:31253960_31253961insA	ENST00000407793.2	+	20	2199_2200		c.e20-1		DDX11_ENST00000228264.6_Splice_Site|DDX11_ENST00000545668.1_Splice_Site|DDX11_ENST00000350437.4_Splice_Site|DDX11_ENST00000251758.5_Splice_Site|DDX11_ENST00000542838.1_Splice_Site	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GCTCTTACCAGGTCACGTGATC	0.579										Multiple Myeloma(12;0.14)																											.		Atlas-INDEL	.											.	DDX11	188	.	0			c.1949-1->A						.																																			SO:0001630	splice_region_variant	1663	exon20			.	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1949-1->A	chr12.hg19:g.31253960_31253961insA		87.0	0.0		59.0	13.0	NM_152438	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Splice_Site	INS	ENST00000407793.2	hg19	CCDS44856.1																																																																																			.	.		0.579	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	Intron	A	31253961	-	A	31253960	8	5	199	1	0	1	1	0	0	0	1	0	4345	1014	35	0	2022	0	DDX11	12	31253960	Splice_Site	INS	-	TCGA-DD-AADQ-01A-11D-A40R-10	24679862	31253960	102597935	89	29315										
GJB2	2706	hgsc.bcm.edu	37	chr13	20763464	20763464	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tggccactaggagcgctggcGtggacacgaagatcagctgc	15	11	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr13:20763464G>A	ENST00000382844.1	-	1	455	c.257C>T	c.(256-258)aCg>aTg	p.T86M	GJB2_ENST00000382848.4_Missense_Mutation_p.T86M			P29033	CXB2_HUMAN	gap junction protein, beta 2, 26kDa	86			T -> R (in DFNB1A; does not form gap junctions since the mutated protein is confined in the cytoplasm and not transported to the cell membrane; when the mutation is coexpressed with the wild-type protein ionic and biochemical coupling is normal consistent with the recessive nature of the mutation). {ECO:0000269|PubMed:12560944, ECO:0000269|PubMed:19384972}.	T -> S (in Ref. 1; AAD21314). {ECO:0000305}.	cell-cell signaling (GO:0007267)|gap junction assembly (GO:0016264)|male genitalia development (GO:0030539)|membrane organization (GO:0061024)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	connexon complex (GO:0005922)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7		all_cancers(29;3.95e-22)|all_epithelial(30;2.36e-19)|all_lung(29;2.27e-18)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000435)|Epithelial(112;0.000722)|OV - Ovarian serous cystadenocarcinoma(117;0.0096)|Lung(94;0.0236)|LUSC - Lung squamous cell carcinoma(192;0.0738)		GAGCGCTGGCGTGGACACGAA	0.552									Keratitis, Ichthyosis and Deafness syndrome		OREG0022282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T86M		Atlas-SNP	.											.	GJB2	19	.	0			c.C257T	GRCh37	CM031189|CM065231	GJB2	M		.						104	90	95					13																	20763464		2203	4300	6503	SO:0001583	missense	2706	exon2	Familial Cancer Database	KID syndrome	GCTGGCGTGGACA	M86849	CCDS9290.1	13q11-q12	2010-01-06	2007-01-16		ENSG00000165474	ENSG00000165474		"Ion channels / Gap junction proteins (connexins)"	4284	protein-coding gene	gene with protein product	"connexin 26"	121011	"gap junction protein, beta 2, 26kD (connexin 26)", "gap junction protein, beta 2, 26kDa (connexin 26)"	DFNB1, DFNA3		9139825	Standard	NM_004004		Approved	CX26, NSRD1	uc001umy.3	P29033	OTTHUMG00000016513	ENST00000382844.1:c.257C>T	chr13.hg19:g.20763464G>A	ENSP00000372295:p.Thr86Met	64.0	0.0	743	65.0	26.0	NM_004004	Q508A5|Q508A6|Q5YLL0|Q5YLL1|Q5YLL4|Q6IPV5|Q86U88|Q96AK0|Q9H536|Q9NNY4	Missense_Mutation	SNP	ENST00000382844.1	hg19	CCDS9290.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.876910	0.91664	.	.	ENSG00000165474	ENST00000382848;ENST00000382844	D;D	0.99207	-5.56;-5.56	5.33	5.33	0.75918	Connexin, N-terminal (1);	0.057675	0.64402	D	0.000004	D	0.99423	0.9796	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99097	1.0842	10	0.87932	D	0	.	19.382	0.94540	0.0:0.0:1.0:0.0	.	86	P29033	CXB2_HUMAN	M	86	ENSP00000372299:T86M;ENSP00000372295:T86M	ENSP00000372295:T86M	T	-	2	0	GJB2	19661464	1.000000	0.71417	0.962000	0.40283	0.963000	0.63663	9.751000	0.98889	2.636000	0.89361	0.655000	0.94253	ACG	.	.		0.552	GJB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044064.1			A	20763464	G	A	20763464	3	1	199	1	0	0	0	0	1	0	0	0	6416	1145	40	1	427	1	GJB2	13	20763464	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10		20763464	94406414	90	29316										
MTMR6	9107	hgsc.bcm.edu	37	chr13	25823489	25823492	+	Frame_Shift_Del	DEL	GAAG	GAAG	-													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gctgctgccctctatagttcGaagagcatcatttacgggta							TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	GAAG	GAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr13:25823489_25823492delGAAG	ENST00000381801.5	-	14	2505_2508	c.1744_1747delCTTC	c.(1744-1749)cttcgafs	p.LR582fs	AL590787.1_ENST00000408397.1_RNA|MTMR6_ENST00000540661.1_Intron	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	582					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		TCTATAGTTCGAAGAGCATCATTT	0.431																																					p.582_583del		Atlas-INDEL	.											MTMR6,colon,carcinoma,0,1	MTMR6	75	.	0			c.1745_1748del						.																																			SO:0001589	frameshift_variant	9107	exon14			.	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.1744_1747delCTTC	chr13.hg19:g.25823489_25823492delGAAG	ENSP00000371221:p.Leu582fs	178.0	0.0		135.0	36.0	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Frame_Shift_Del	DEL	ENST00000381801.5	hg19	CCDS9313.1																																																																																			.	.		0.431	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		-	25823492	GAAG	-	25823489	7	5	199	1	0	1	0	1	0	0	0	0	9956	1066	37	0	122	0	MTMR6	13	25823489	Frame_Shift_Del	DEL	GAAG	TCGA-DD-AADQ-01A-11D-A40R-10	5060025	25823489	89346389	91	29317	151	2								
MTMR6	9107	hgsc.bcm.edu	37	chr13	25823497	25823498	+	In_Frame_Ins	INS	-	-	TTA													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ctctatagttcgaagagcatINScatttacgggtagcagagtc							TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr13:25823497_25823498insTTA	ENST00000381801.5	-	14	2499_2500	c.1738_1739insTAA	c.(1738-1740)gat>gTAAat	p.580_580D>VN	AL590787.1_ENST00000408397.1_RNA|MTMR6_ENST00000540661.1_Intron	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	580					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		TCGAAGAGCATCATTTACGGGT	0.436																																					p.D580delinsVN		Atlas-INDEL	.											.	MTMR6	75	.	0			c.1739_1740insTAA						.																																			SO:0001652	inframe_insertion	9107	exon14			.	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.1738_1739insTAA	chr13.hg19:g.25823497_25823498insTTA	ENSP00000371221:p.Asp580delinsValAsn	183.0	0.0		137.0	37.0	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	In_Frame_Ins	INS	ENST00000381801.5	hg19	CCDS9313.1																																																																																			.	.		0.436	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		TTA	25823498	-	TTA	25823497	7	5	199	1	0	1	1	0	0	0	0	0	9956	1435	50	0	130	0	MTMR6	13	25823497	In_Frame_Ins	INS	-	TCGA-DD-AADQ-01A-11D-A40R-10	8	25823497	89346381	92	29318	151	2								
GPR12	2835	hgsc.bcm.edu	37	chr13	27333433	27333433	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gtctcggaggcagttccagcCcatgacgggcagcagcccca	13	15	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr13:27333433C>A	ENST00000381436.2	-	1	994	c.532G>T	c.(532-534)Ggc>Tgc	p.G178C	GPR12_ENST00000405846.3_Missense_Mutation_p.G178C			P47775	GPR12_HUMAN	G protein-coupled receptor 12	178					cellular calcium ion homeostasis (GO:0006874)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			endometrium(7)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		CAGTTCCAGCCCATGACGGGC	0.602																																					p.G178C		Atlas-SNP	.											.	GPR12	67	.	0			c.G532T						.						52	47	49					13																	27333433		2203	4300	6503	SO:0001583	missense	2835	exon2			TCCAGCCCATGAC	U18548	CCDS9319.1	13q12	2014-06-12			ENSG00000132975	ENSG00000132975		"GPCR / Class A : Orphans"	4466	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 84"	600752				8262253, 8530049	Standard	NM_005288		Approved	GPCR21, PPP1R84	uc010aal.3	P47775	OTTHUMG00000016620	ENST00000381436.2:c.532G>T	chr13.hg19:g.27333433C>A	ENSP00000370844:p.Gly178Cys	61.0	0.0		70.0	31.0	NM_005288	Q5T8P3	Missense_Mutation	SNP	ENST00000381436.2	hg19	CCDS9319.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.532635	0.85812	.	.	ENSG00000132975	ENST00000405846;ENST00000381436	T;T	0.73681	-0.77;-0.77	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.91088	0.7195	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93607	0.6935	10	0.72032	D	0.01	.	19.0843	0.93196	0.0:1.0:0.0:0.0	.	178	P47775	GPR12_HUMAN	C	178	ENSP00000384932:G178C;ENSP00000370844:G178C	ENSP00000370844:G178C	G	-	1	0	GPR12	26231433	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.685000	0.84117	2.532000	0.85374	0.561000	0.74099	GGC	.	.		0.602	GPR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044257.2			A	27333433	C	A	27333433	3	1	199	1	0	0	0	0	1	0	0	0	6643	623	22	3	476	3	GPR12	13	27333433	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	1509936	27333433	87836445	93	29319										
PCDH9	5101	hgsc.bcm.edu	37	chr13	67799953	67799953	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agagcttttgggagacttccTtttctttcttttctttttct	6	8	4	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr13:67799953T>C	ENST00000377865.2	-	1	2754	c.2620A>G	c.(2620-2622)Agg>Ggg	p.R874G	PCDH9_ENST00000544246.1_Missense_Mutation_p.R874G|PCDH9_ENST00000328454.5_Missense_Mutation_p.R874G|PCDH9_ENST00000377861.3_Missense_Mutation_p.R874G|PCDH9_ENST00000456367.1_Missense_Mutation_p.R874G			Q9HC56	PCDH9_HUMAN	protocadherin 9	874					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GGAGACTTCCTTTTCTTTCTT	0.438																																					p.R874G		Atlas-SNP	.											.	PCDH9	252	.	0			c.A2620G						.						83	90	88					13																	67799953		2203	4300	6503	SO:0001583	missense	5101	exon2			ACTTCCTTTTCTT	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.2620A>G	chr13.hg19:g.67799953T>C	ENSP00000367096:p.Arg874Gly	141.0	0.0		168.0	69.0	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.762666	0.49574	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	5.87	5.87	0.94306	Protocadherin (1);	0.000000	0.85682	D	0.000000	T	0.31606	0.0802	N	0.17474	0.49	0.80722	D	1	P;P;P;P	0.42161	0.772;0.463;0.73;0.772	P;B;P;P	0.49192	0.602;0.296;0.467;0.602	T	0.11108	-1.0601	10	0.54805	T	0.06	.	16.2597	0.82535	0.0:0.0:0.0:1.0	.	874;874;874;874	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	G	874	ENSP00000442186:R874G;ENSP00000367096:R874G;ENSP00000401699:R874G;ENSP00000332060:R874G;ENSP00000367092:R874G	ENSP00000332060:R874G	R	-	1	2	PCDH9	66697954	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.037000	0.88933	2.243000	0.73865	0.533000	0.62120	AGG	.	.		0.438	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		C	67799953	T	C	67799953	3	2	199	1	0	0	0	0	1	0	0	0	11527	1608	56	2	1109	2	PCDH9	13	67799953	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	40466520	67799953	47369925	94	29320										
KLHL1	57626	hgsc.bcm.edu	37	chr13	70535504	70535504	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	atgccttccattttgatctcCtcttgcttggcttcacaaac	5	13	3	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr13:70535504C>G	ENST00000377844.4	-	3	1512	c.753G>C	c.(751-753)gaG>gaC	p.E251D	KLHL1_ENST00000545028.1_Missense_Mutation_p.E58D	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	251	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TTTTGATCTCCTCTTGCTTGG	0.413																																					p.E251D		Atlas-SNP	.											.	KLHL1	164	.	0			c.G753C						.						165	144	151					13																	70535504		2203	4300	6503	SO:0001583	missense	57626	exon3			GATCTCCTCTTGC	AB040923	CCDS9445.1, CCDS73582.1	13q21	2013-01-30	2013-01-30		ENSG00000150361	ENSG00000150361		"Kelch-like", "BTB/POZ domain containing"	6352	protein-coding gene	gene with protein product	"Kelch-like protein 1", "Mayven-related protein 2"	605332	"kelch (Drosophila)-like 1", "kelch-like 1 (Drosophila)"			10888605	Standard	NM_020866		Approved	KIAA1490, MRP2, FLJ30047	uc001vip.3	Q9NR64	OTTHUMG00000017056	ENST00000377844.4:c.753G>C	chr13.hg19:g.70535504C>G	ENSP00000367075:p.Glu251Asp	108.0	0.0		131.0	62.0	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Missense_Mutation	SNP	ENST00000377844.4	hg19	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	C	9.192	1.026203	0.19512	.	.	ENSG00000150361	ENST00000377844;ENST00000545028	T;T	0.67523	-0.27;-0.27	5.08	-0.334	0.12666	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.084010	0.51477	N	0.000099	T	0.46560	0.1399	L	0.28192	0.835	0.29757	N	0.835898	B;B	0.32338	0.365;0.053	B;B	0.37888	0.26;0.09	T	0.35025	-0.9805	10	0.20519	T	0.43	.	4.0138	0.09634	0.1761:0.2711:0.0:0.5528	.	251;251	Q8TBJ7;Q9NR64	.;KLHL1_HUMAN	D	251;58	ENSP00000367075:E251D;ENSP00000439602:E58D	ENSP00000367075:E251D	E	-	3	2	KLHL1	69433505	0.917000	0.31117	0.998000	0.56505	0.739000	0.42172	0.017000	0.13399	0.022000	0.15160	-2.477000	0.00200	GAG	.	.		0.413	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		G	70535504	C	G	70535504	3	3	199	1	0	0	0	0	1	0	0	0	8374	680	24	4	1529	4	KLHL1	13	70535504	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	2735551	70535504	44634374	95	29321										
CHMP4A	29082	hgsc.bcm.edu	37	chr14	24679870	24679870	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ccccaatcacctcatccacaTcatctccaaagcccataggc	3	19	4	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr14:24679870T>A	ENST00000609024.1	-	4	512	c.464A>T	c.(463-465)gAt>gTt	p.D155V	TM9SF1_ENST00000530611.1_Missense_Mutation_p.D155V|TM9SF1_ENST00000556387.1_Missense_Mutation_p.D155V|CHMP4A_ENST00000530996.1_Missense_Mutation_p.D50V|AL136419.6_ENST00000565988.1_RNA|CHMP4A_ENST00000347519.6_Missense_Mutation_p.D198V|CHMP4A_ENST00000542700.2_5'UTR			Q9BY43	CHM4A_HUMAN	charged multivesicular body protein 4A	155	Intramolecular interaction with N- terminus. {ECO:0000250}.				endosomal transport (GO:0016197)|membrane budding (GO:0006900)|membrane organization (GO:0061024)|membrane tubulation (GO:0097320)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)			NS(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9				GBM - Glioblastoma multiforme(265;0.0181)		CTCATCCACATCATCTCCAAA	0.507																																					p.D198V		Atlas-SNP	.											.	CHMP4A	20	.	0			c.A593T						.						207	165	179					14																	24679870		2203	4300	6503	SO:0001583	missense	29082	exon4			TCCACATCATCTC	AF212243	CCDS9619.1	14q12	2012-10-04	2011-09-21	2005-04-04	ENSG00000254505	ENSG00000254505		"Charged multivesicular body proteins"	20274	protein-coding gene	gene with protein product		610051	"chromosome 14 open reading frame 123", "chromatin modifying protein 4A"	C14orf123			Standard	NM_014169		Approved	HSPC134, VPS32A		Q9BY43	OTTHUMG00000167036	ENST00000609024.1:c.464A>T	chr14.hg19:g.24679870T>A	ENSP00000476412:p.Asp155Val	114.0	0.0		111.0	43.0	NM_014169	Q14D22|Q32Q79|Q86SZ8|Q96QJ9|Q9P026	Missense_Mutation	SNP	ENST00000609024.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.09	3.024946	0.54683	.	.	ENSG00000100926;ENSG00000254692;ENSG00000254505;ENSG00000254505	ENST00000556387;ENST00000530611;ENST00000347519;ENST00000533011	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	5.1	3.93	0.45458	.	0.265962	0.26598	N	0.023485	T	0.69415	0.3108	M	0.64997	1.995	0.58432	D	0.999997	B;B	0.20988	0.006;0.05	B;B	0.25140	0.018;0.058	T	0.63862	-0.6541	10	0.34782	T	0.22	-2.9262	9.4369	0.38643	0.1591:0.0:0.0:0.8409	.	155;198	Q9BY43;Q14D22	CHM4A_HUMAN;.	V	155;155;198;165	ENSP00000451949:D155V;ENSP00000433967:D155V;ENSP00000324205:D198V;ENSP00000432575:D165V	ENSP00000324205:D198V	D	-	2	0	TM9SF1;AL096870.1;RP11-468E2.1	23749710	0.992000	0.36948	0.939000	0.37840	0.997000	0.91878	3.757000	0.55212	0.928000	0.37168	0.459000	0.35465	GAT	.	.		0.507	CHMP4A-012	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471846.1	NM_014169		A	24679870	T	A	24679870	3	1	199	1	0	0	0	0	1	0	0	0	3358	1435	50	4	216	4	CHMP4A	14	24679870	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10		24679870	82669670	96	29322										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102500705	102500705	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggaatacctttccaatgctgAtgagcgtcttcgctggcagg	12	10	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr14:102500705A>T	ENST00000360184.4	+	56	10834	c.10670A>T	c.(10669-10671)gAt>gTt	p.D3557V	RP11-1017G21.4_ENST00000557242.1_RNA|RP11-1017G21.4_ENST00000553701.1_RNA|DYNC1H1_ENST00000556791.1_3'UTR|RP11-1017G21.4_ENST00000557551.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	3557	AAA 5. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TCCAATGCTGATGAGCGTCTT	0.512																																					p.D3557V		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A10670T						.						117	94	102					14																	102500705		2203	4300	6503	SO:0001583	missense	1778	exon56			ATGCTGATGAGCG	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.10670A>T	chr14.hg19:g.102500705A>T	ENSP00000348965:p.Asp3557Val	147.0	0.0		128.0	55.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.08|19.08	3.758791|3.758791	0.69763|0.69763	.|.	.|.	ENSG00000197102|ENSG00000197102	ENST00000360184|ENST00000553423	T|.	0.52295|.	0.67|.	5.17|5.17	4.01|4.01	0.46588|0.46588	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.43322|.	0.1242|.	N|N	0.20881|0.20881	0.62|0.62	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.78314|.	0.991|.	T|.	0.19877|.	-1.0292|.	10|.	0.21014|.	T|.	0.42|.	.|.	11.2|11.2	0.48736|0.48736	0.9271:0.0:0.0729:0.0|0.9271:0.0:0.0729:0.0	.|.	3557|.	Q14204|.	DYHC1_HUMAN|.	V|C	3557|32	ENSP00000348965:D3557V|.	ENSP00000348965:D3557V|.	D|X	+|+	2|3	0|0	DYNC1H1|DYNC1H1	101570458|101570458	1.000000|1.000000	0.71417|0.71417	0.630000|0.630000	0.29268|0.29268	0.667000|0.667000	0.39255|0.39255	9.232000|9.232000	0.95325|0.95325	0.912000|0.912000	0.36772|0.36772	0.482000|0.482000	0.46254|0.46254	GAT|TGA	.	.		0.512	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102500705	A	T	102500705	3	4	199	1	0	0	0	0	1	0	0	0	4843	333	12	4	10892	4	DYNC1H1	14	102500705	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	77820835	102500705	4848835	97	29323										
FMN1	342184	hgsc.bcm.edu	37	chr15	33260970	33260970	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	aggcttcatgggacaactggGctcgatggctggttttcgag	15	8	1	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr15:33260970G>C	ENST00000559047.1	-	5	2931	c.2932C>G	c.(2932-2934)Ccc>Gcc	p.P978A	SNORD77_ENST00000391113.1_RNA|FMN1_ENST00000561249.1_Missense_Mutation_p.P880A|FMN1_ENST00000334528.9_Missense_Mutation_p.P755A			Q68DA7	FMN1_HUMAN	formin 1	978	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.|Pro-rich.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GGACAACTGGGCTCGATGGCT	0.502																																					p.P755A		Atlas-SNP	.											.	FMN1	174	.	0			c.C2263G						.						127	123	124					15																	33260970		1844	4092	5936	SO:0001583	missense	342184	exon4			AACTGGGCTCGAT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2932C>G	chr15.hg19:g.33260970G>C	ENSP00000454047:p.Pro978Ala	200.0	0.0		189.0	57.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.32	2.799424	0.50208	.	.	ENSG00000248905	ENST00000334528	T	0.21191	2.02	4.42	3.49	0.39957	.	0.162214	0.56097	D	0.000028	T	0.50905	0.1643	M	0.87758	2.905	.	.	.	D	0.89917	1.0	D	0.97110	1.0	T	0.68146	-0.5486	9	0.72032	D	0.01	.	14.361	0.66771	0.0:0.1491:0.8509:0.0	.	755	Q68DA7-5	.	A	755	ENSP00000333950:P755A	ENSP00000333950:P755A	P	-	1	0	FMN1	31048262	1.000000	0.71417	0.887000	0.34795	0.523000	0.34469	9.488000	0.97947	1.039000	0.40074	0.650000	0.86243	CCC	.	.		0.502	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		C	33260970	G	C	33260970	3	2	199	1	0	0	0	0	1	0	0	0	5957	1203	42	4	1383	4	FMN1	15	33260970	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10		33260970	69270422	98	29324										
MGA	23269	hgsc.bcm.edu	37	chr15	42042688	42042688	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agggtgggagaagcagtgctGacttcactgttttggatttg	15	5	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr15:42042688G>C	ENST00000570161.1	+	16	6883	c.6883G>C	c.(6883-6885)Gac>Cac	p.D2295H	MGA_ENST00000566586.1_Missense_Mutation_p.D2086H|MGA_ENST00000389936.4_Missense_Mutation_p.D2256H|MGA_ENST00000219905.7_Missense_Mutation_p.D2295H|MGA_ENST00000545763.1_Missense_Mutation_p.D2086H			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AAGCAGTGCTGACTTCACTGT	0.408																																					p.D2295H		Atlas-SNP	.											.	MGA	264	.	0			c.G6883C						.						111	102	105					15																	42042688		1929	4134	6063	SO:0001583	missense	23269	exon17			AGTGCTGACTTCA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.6883G>C	chr15.hg19:g.42042688G>C	ENSP00000457035:p.Asp2295His	119.0	0.0		106.0	48.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.356832	0.41801	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.89343	-2.48;-2.46;-2.5	5.11	4.18	0.49190	.	1.048350	0.07489	N	0.905276	D	0.91314	0.7261	L	0.27053	0.805	0.24227	N	0.995411	D;D;D;D	0.89917	0.999;0.992;0.999;1.0	D;P;D;D	0.85130	0.927;0.875;0.936;0.997	T	0.82210	-0.0570	10	0.72032	D	0.01	.	13.1062	0.59249	0.0:0.1607:0.8393:0.0	.	911;2086;2295;2256	B4DVS1;F5H7K2;E7ENI0;Q8IWI9	.;.;.;MGAP_HUMAN	H	2295;2256;2086	ENSP00000219905:D2295H;ENSP00000374586:D2256H;ENSP00000442467:D2086H	ENSP00000219905:D2295H	D	+	1	0	MGA	39829980	1.000000	0.71417	0.994000	0.49952	0.824000	0.46624	5.873000	0.69644	1.355000	0.45865	0.591000	0.81541	GAC	.	.		0.408	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		C	42042688	G	C	42042688	3	2	199	1	0	0	0	0	1	0	0	0	9549	1290	45	4	6945	4	MGA	15	42042688	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	8781718	42042688	60488704	99	29325										
TMEM8A	58986	hgsc.bcm.edu	37	chr16	422089	422089	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tcggcgggctggtcaggtggCggcagcagcaaggctgcgct	19	11	1	0	rs141574918	byFrequency	TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr16:422089C>A	ENST00000431232.2	-	13	2374	c.2214G>T	c.(2212-2214)ccG>ccT	p.P738P	MRPL28_ENST00000389675.2_5'Flank|MRPL28_ENST00000429738.1_5'Flank|TMEM8A_ENST00000250930.3_Silent_p.P545P|MRPL28_ENST00000199706.8_5'Flank	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	738					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						GGTCAGGTGGCGGCAGCAGCA	0.602																																					p.P738P		Atlas-SNP	.											.	TMEM8A	49	.	0			c.G2214T						.						62	67	65					16																	422089		2201	4299	6500	SO:0001819	synonymous_variant	58986	exon13			AGGTGGCGGCAGC	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"transmembrane protein 6", "transmembrane protein 8 (five membrane-spanning domains)"	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.2214G>T	chr16.hg19:g.422089C>A		91.0	0.0		78.0	27.0	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	hg19	CCDS10407.1	.	.	.	.	.	.	.	.	.	.	C	2.336	-0.352223	0.05173	.	.	ENSG00000129925	ENST00000424078	.	.	.	4.3	-8.59	0.00893	.	.	.	.	.	T	0.35335	0.0928	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41680	-0.9495	4	.	.	.	-2.3796	3.1236	0.06400	0.1599:0.2948:0.0857:0.4596	.	.	.	.	L	206	.	.	R	-	2	0	TMEM8A	362090	0.000000	0.05858	0.432000	0.26747	0.098000	0.18820	-3.821000	0.00358	-1.468000	0.01892	-0.384000	0.06662	CGC	.	C|1.000;T|0.000		0.602	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259		A	422089	C	A	422089	2	1	199	1	0	0	0	0	0	0	0	1	16229	755	27	1		1	TMEM8A	16	422089	Silent	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10		422089	89932664	100	29326										
ITGAM	3684	hgsc.bcm.edu	37	chr16	31332817	31332817	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	actgagagtcaaggcaatcaTggagttcaatcccagggaag	12	8	3	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr16:31332817T>C	ENST00000287497.8	+	16	1946	c.1871T>C	c.(1870-1872)aTg>aCg	p.M624T	ITGAM_ENST00000544665.3_Missense_Mutation_p.M625T			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	624					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						AAGGCAATCATGGAGTTCAAT	0.498																																					p.M625T		Atlas-SNP	.											.	ITGAM	137	.	0			c.T1874C						.						302	301	302					16																	31332817		2084	4226	6310	SO:0001583	missense	3684	exon16			CAATCATGGAGTT	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.1871T>C	chr16.hg19:g.31332817T>C	ENSP00000287497:p.Met624Thr	173.0	0.0		159.0	66.0	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	hg19	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	T	12.13	1.844131	0.32606	.	.	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.60672	0.17;0.17	4.83	4.83	0.62350	Integrin alpha-2 (1);	.	.	.	.	T	0.74913	0.3779	M	0.83603	2.65	0.31651	N	0.646857	D;D;D	0.69078	0.997;0.978;0.978	D;P;P	0.67548	0.952;0.897;0.897	T	0.79349	-0.1840	9	0.87932	D	0	.	10.7095	0.45975	0.0:0.0:0.0:1.0	.	30;624;624	B3KXM6;Q4VAK1;P11215	.;.;ITAM_HUMAN	T	625;624	ENSP00000441691:M625T;ENSP00000287497:M624T	ENSP00000287497:M624T	M	+	2	0	ITGAM	31240318	0.997000	0.39634	0.919000	0.36401	0.064000	0.16182	3.759000	0.55227	2.006000	0.58801	0.533000	0.62120	ATG	.	.		0.498	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		C	31332817	T	C	31332817	3	2	199	1	0	0	0	0	1	0	0	0	7896	1464	51	2	1936	2	ITGAM	16	31332817	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	30910728	31332817	59021936	101	29327										
ITGAM	3684	hgsc.bcm.edu	37	chr16	31336335	31336335	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tgccaggatgacctcagcatCaccttcagtttcatgaggtg	10	11	4	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr16:31336335C>A	ENST00000287497.8	+	19	2421	c.2346C>A	c.(2344-2346)atC>atA	p.I782I	ITGAM_ENST00000544665.3_Silent_p.I783I			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	782					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						ACCTCAGCATCACCTTCAGTT	0.448																																					p.I783I		Atlas-SNP	.											.	ITGAM	137	.	0			c.C2349A						.						76	72	73					16																	31336335		1923	4137	6060	SO:0001819	synonymous_variant	3684	exon19			CAGCATCACCTTC	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2346C>A	chr16.hg19:g.31336335C>A		59.0	0.0		60.0	18.0	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Silent	SNP	ENST00000287497.8	hg19	CCDS45470.1																																																																																			.	.		0.448	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		A	31336335	C	A	31336335	2	1	199	1	0	0	0	0	0	0	0	1	7896	816	29	3		3	ITGAM	16	31336335	Silent	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	3518	31336335	59018418	102	29328										
TGFB1I1	7041	hgsc.bcm.edu	37	chr16	31485920	31485920	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	caactcagccaccggtggtgAgctccacaaatgagggctcc	11	14	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr16:31485920A>C	ENST00000394863.3	+	7	686	c.556A>C	c.(556-558)Agc>Cgc	p.S186R	TGFB1I1_ENST00000567607.1_Missense_Mutation_p.S169R|TGFB1I1_ENST00000394858.2_Missense_Mutation_p.S169R|TGFB1I1_ENST00000361773.3_Missense_Mutation_p.S169R	NM_001042454.2	NP_001035919.1	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced transcript 1	186	Interaction with PTK2B/PYK2.|Transcription activation. {ECO:0000250}.				androgen receptor signaling pathway (GO:0030521)|cell adhesion (GO:0007155)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|response to heat (GO:0009408)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|I-SMAD binding (GO:0070411)|Roundabout binding (GO:0048495)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(8)|upper_aerodigestive_tract(1)	9						ACCGGTGGTGAGCTCCACAAA	0.622																																					p.S186R		Atlas-SNP	.											.	TGFB1I1	60	.	0			c.A556C						.						27	25	26					16																	31485920		2197	4300	6497	SO:0001583	missense	7041	exon7			GTGGTGAGCTCCA	AB007836	CCDS10713.1, CCDS42156.1	16p11	2008-02-05			ENSG00000140682	ENSG00000140682			11767	protein-coding gene	gene with protein product		602353				9422762, 10075738	Standard	NM_015927		Approved	Hic-5, TSC-5, ARA55, HIC-5	uc002ecd.2	O43294	OTTHUMG00000132467	ENST00000394863.3:c.556A>C	chr16.hg19:g.31485920A>C	ENSP00000378332:p.Ser186Arg	112.0	0.0		108.0	44.0	NM_001042454	B2R8D5|Q9BPW3|Q9Y2V5	Missense_Mutation	SNP	ENST00000394863.3	hg19	CCDS42156.1	.	.	.	.	.	.	.	.	.	.	A	5.056	0.196085	0.09599	.	.	ENSG00000140682	ENST00000394863;ENST00000361773;ENST00000394858	T;T;T	0.57107	0.42;0.42;0.42	5.22	4.06	0.47325	.	0.801737	0.12152	N	0.494747	T	0.46560	0.1399	L	0.54323	1.7	0.09310	N	0.999998	B	0.09022	0.002	B	0.08055	0.003	T	0.36648	-0.9739	10	0.52906	T	0.07	.	7.9285	0.29889	0.8173:0.0:0.0:0.1827	.	186	O43294	TGFI1_HUMAN	R	186;169;169	ENSP00000378332:S186R;ENSP00000355117:S169R;ENSP00000378327:S169R	ENSP00000355117:S169R	S	+	1	0	TGFB1I1	31393421	0.533000	0.26354	0.008000	0.14137	0.061000	0.15899	2.982000	0.49337	2.099000	0.63709	0.533000	0.62120	AGC	.	.		0.622	TGFB1I1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255630.3			C	31485920	A	C	31485920	3	2	199	1	0	0	0	0	1	0	0	0	15832	304	11	5	582	5	TGFB1I1	16	31485920	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	149585	31485920	58868833	103	29329										
ESRP2	80004	hgsc.bcm.edu	37	chr16	68265386	68265401	+	Splice_Site	DEL	TGCTGGTTGAGCACCA	TGCTGGTTGAGCACCA	-													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	taccaagcagtggcttcaccTgctggttgagcaccatgtgt							TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	TGCTGGTTGAGCACCA	TGCTGGTTGAGCACCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr16:68265386_68265401delTGCTGGTTGAGCACCA	ENST00000565858.1	-	11	1612_1627	c.1526_1541delTGGTGCTCAACCAGCA	c.(1525-1542)atggtgctcaaccagcag>ag	p.MVLNQQ509fs	ESRP2_ENST00000473183.2_Splice_Site_p.MVLNQQ499fs|RP11-96D1.11_ENST00000571197.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	509	RRM 3.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						TGGCTTCACCTGCTGGTTGAGCACCATGTGTACACC	0.551																																					p.499_504del		Atlas-INDEL	.											.	ESRP2	118	.	0			c.1497_1512del						.																																			SO:0001630	splice_region_variant	80004	exon11			.	AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"RNA binding motif (RRM) containing"	26152	protein-coding gene	gene with protein product		612960	"RNA binding motif protein 35B"	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.1542+1TGGTGCTCAACCAGCA>-	chr16.hg19:g.68265386_68265401delTGCTGGTTGAGCACCA		83.0	0.0		65.0	17.0	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Frame_Shift_Del	DEL	ENST00000565858.1	hg19																																																																																				.	.		0.551	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939	Frame_Shift_Del	-	68265401	TGCTGGTTGAGCACCA	-	68265386	8	5	199	1	0	1	0	1	0	0	1	0	5261	1594	55	0	662	0	ESRP2	16	68265386	Splice_Site	DEL	TGCTGGTTGAGCACCA	TCGA-DD-AADQ-01A-11D-A40R-10	36779466	68265386	22089367	104	29330										
MYO1C	4641	hgsc.bcm.edu	37	chr17	1378257	1378257	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	acgctgtaggtcacctccccCgcatagtgcagaaggcggaa	12	13	1	1	rs551011507	byFrequency	TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr17:1378257C>A	ENST00000575158.1	-	15	1715	c.1539G>T	c.(1537-1539)gcG>gcT	p.A513A	MYO1C_ENST00000545534.2_Silent_p.A524A|MYO1C_ENST00000361007.2_Silent_p.A513A|MYO1C_ENST00000359786.5_Silent_p.A548A|MYO1C_ENST00000438665.2_Silent_p.A529A			Q12965	MYO1E_HUMAN	myosin IC	508	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TCACCTCCCCCGCATAGTGCA	0.652																																					p.A548A		Atlas-SNP	.											.	MYO1C	57	.	0			c.G1644T						.						55	49	51					17																	1378257		2198	4294	6492	SO:0001819	synonymous_variant	4641	exon15			CTCCCCCGCATAG	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"Myosins / Myosin superfamily : Class I"	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.1539G>T	chr17.hg19:g.1378257C>A		98.0	0.0		122.0	49.0	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	hg19	CCDS11003.1																																																																																			.	.		0.652	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2			A	1378257	C	A	1378257	2	1	199	1	0	0	0	0	0	0	0	1	10079	639	23	1		1	MYO1C	17	1378257	Silent	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10		1378257	79816953	105	29331										
USP43	124739	hgsc.bcm.edu	37	chr17	9604706	9604706	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ctggaagtgtcctcactgccAagtcctgcagcaggggatgg	14	11	1	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr17:9604706A>T	ENST00000285199.7	+	12	1796	c.1700A>T	c.(1699-1701)cAa>cTa	p.Q567L	USP43_ENST00000570475.1_Missense_Mutation_p.Q567L|USP43_ENST00000570827.2_3'UTR	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	567	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						CCTCACTGCCAAGTCCTGCAG	0.597																																					p.Q567L		Atlas-SNP	.											.	USP43	65	.	0			c.A1700T						.						32	34	33					17																	9604706		2170	4266	6436	SO:0001583	missense	124739	exon12			ACTGCCAAGTCCT	AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"Ubiquitin-specific peptidases"	20072	protein-coding gene	gene with protein product			"ubiquitin specific protease 43"			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.1700A>T	chr17.hg19:g.9604706A>T	ENSP00000285199:p.Gln567Leu	75.0	0.0		57.0	23.0	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	hg19	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	A	15.31	2.795517	0.50208	.	.	ENSG00000154914	ENST00000285199	T	0.02837	4.14	5.12	3.96	0.45880	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.276734	0.31897	N	0.006898	T	0.03434	0.0099	L	0.38838	1.175	0.38490	D	0.947943	P;P;B;B	0.35124	0.485;0.469;0.367;0.356	B;B;B;B	0.37550	0.253;0.158;0.216;0.138	T	0.47497	-0.9113	10	0.87932	D	0	-1.0423	9.2684	0.37657	0.8385:0.0:0.0:0.1615	.	567;256;567;79	B7ZVX5;Q70EL4-3;Q70EL4;Q70EL4-2	.;.;UBP43_HUMAN;.	L	567	ENSP00000285199:Q567L	ENSP00000285199:Q567L	Q	+	2	0	USP43	9545431	1.000000	0.71417	0.058000	0.19502	0.860000	0.49131	3.982000	0.56909	2.040000	0.60383	0.460000	0.39030	CAA	.	.		0.597	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210		T	9604706	A	T	9604706	3	4	199	1	0	0	0	0	1	0	0	0	17089	130	5	4	1746	4	USP43	17	9604706	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	8226449	9604706	71590504	106	29332										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27028455	27028455	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tcaacttttcttcccctcccAggtccaacagccatgcagcc	5	18	2	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr17:27028455A>G	ENST00000314616.6	+	37	5277		c.e37-1		PROCA1_ENST00000579650.1_5'Flank|SUPT6H_ENST00000347486.4_Splice_Site	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					TTCCCCTCCCAGGTCCAACAG	0.542																																					.		Atlas-SNP	.											.	SUPT6H	165	.	0			c.4995-2A>G						.						58	58	58					17																	27028455		2203	4300	6503	SO:0001630	splice_region_variant	6830	exon37			CCTCCCAGGTCCA	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.4995-1A>G	chr17.hg19:g.27028455A>G		70.0	0.0		66.0	34.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Splice_Site	SNP	ENST00000314616.6	hg19	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.932710	0.73442	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7254	0.77751	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SUPT6H	24052582	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	8.647000	0.91057	2.120000	0.65058	0.460000	0.39030	.	.	.		0.542	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	Intron	G	27028455	A	G	27028455	5	3	199	1	0	0	0	0	0	0	1	0	15415	202	7	2	5135	2	SUPT6H	17	27028455	Splice_Site	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	17423749	27028455	54166755	107	29333										
KRTAP17-1	83902	hgsc.bcm.edu	37	chr17	39471767	39471767	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gcagctgcccccgcagccagAgcccccgcagccagagcccc	11	22	0	2	rs572148015|rs386797077	byFrequency	TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr17:39471767A>T	ENST00000334202.3	-	1	180	c.136T>A	c.(136-138)Tct>Act	p.S46T		NM_031964.1	NP_114170.1	Q9BYP8	KR171_HUMAN	keratin associated protein 17-1	46						intermediate filament (GO:0005882)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			ccgcagccagagcccccgcag	0.687																																					p.S46T		Atlas-SNP	.											.	KRTAP17-1	14	.	0			c.T136A						.						9	14	12					17																	39471767		2165	4218	6383	SO:0001583	missense	83902	exon1			AGCCAGAGCCCCC	AJ406952	CCDS11387.1	17q21.2	2013-06-20			ENSG00000186860	ENSG00000186860		"Keratin associated proteins"	18917	protein-coding gene	gene with protein product							Standard	NM_031964		Approved	KAP17.1	uc002hwj.3	Q9BYP8	OTTHUMG00000133433	ENST00000334202.3:c.136T>A	chr17.hg19:g.39471767A>T	ENSP00000333993:p.Ser46Thr	24.0	0.0		54.0	6.0	NM_031964		Missense_Mutation	SNP	ENST00000334202.3	hg19	CCDS11387.1	.	.	.	.	.	.	.	.	.	.	A	5.663	0.306859	0.10733	.	.	ENSG00000186860	ENST00000334202	.	.	.	3.53	-5.98	0.02220	.	.	.	.	.	T	0.20659	0.0497	N	0.08118	0	0.09310	N	1	B	0.18310	0.027	B	0.23574	0.047	T	0.35076	-0.9803	8	0.87932	D	0	4.2542	8.5795	0.33619	0.2025:0.6771:0.0:0.1203	.	46	Q9BYP8	KR171_HUMAN	T	46	.	ENSP00000333993:S46T	S	-	1	0	KRTAP17-1	36725293	0.005000	0.15991	0.001000	0.08648	0.449000	0.32228	0.296000	0.19083	-1.344000	0.02216	0.369000	0.22263	TCT	.	.		0.687	KRTAP17-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257296.1			T	39471767	A	T	39471767	3	4	199	1	0	0	0	0	1	0	0	0	8536	304	11	4	185	4	KRTAP17-1	17	39471767	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	12443312	39471767	41723443	108	29334										
KRT16	3868	hgsc.bcm.edu	37	chr17	39766282	39766282	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggacgaggaggaggtgaagaCtgtgggagagagaagaggag	22	2	0	5			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr17:39766282C>T	ENST00000301653.4	-	8	1392		c.e8-1			NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16						aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				GAGGTGAAGACTGTGGGAGAG	0.617																																					.		Atlas-SNP	.											.	KRT16	45	.	0			c.1328-1G>A						.						27	27	27					17																	39766282		2203	4300	6503	SO:0001630	splice_region_variant	3868	exon9			TGAAGACTGTGGG	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"-", "Intermediate filaments type I, keratins (acidic)"	6423	protein-coding gene	gene with protein product	"focal non-epidermolytic palmoplantar keratoderma"	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.1328-1G>A	chr17.hg19:g.39766282C>T		89.0	0.0		78.0	29.0	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Splice_Site	SNP	ENST00000301653.4	hg19	CCDS11401.1	.	.	.	.	.	.	.	.	.	.	C	13.68	2.308070	0.40895	.	.	ENSG00000186832	ENST00000301653	.	.	.	4.59	-2.31	0.06765	.	.	.	.	.	.	.	.	.	.	.	0.20074	N	0.999936	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.1917	0.01866	0.3889:0.2267:0.2317:0.1526	.	.	.	.	.	-1	.	.	.	-	.	.	KRT16	37019808	0.001000	0.12720	0.001000	0.08648	0.824000	0.46624	0.575000	0.23729	-0.015000	0.14150	0.462000	0.41574	.	.	.		0.617	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557	Intron	T	39766282	C	T	39766282	5	4	199	1	0	0	0	0	0	0	1	0	8462	579	20	3	98	3	KRT16	17	39766282	Splice_Site	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	294515	39766282	41428928	109	29335										
CTAGE1	64693	hgsc.bcm.edu	37	chr18	19997418	19997418	+	5'Flank	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ttctcttcttttaactctttTtctagacagagtatttcatg	4	8	5	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr18:19997418T>A	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Missense_Mutation_p.E119D			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					TTAACTCTTTTTCTAGACAGA	0.388																																					p.E119D		Atlas-SNP	.											.	CTAGE1	146	.	0			c.A357T						.						96	106	103					18																	19997418		2166	4290	6456	SO:0001631	upstream_gene_variant	64693	exon1			CTCTTTTTCTAGA	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"cutaneous T-cell lymphoma-associated antigen 1", "cutaneous T-cell lymphoma-associated antigen 2", "cancer/testis antigen family 21, member 1", "cancer/testis antigen family 21, member 2"	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			chr18.hg19:g.19997418T>A	Exception_encountered	136.0	0.0		99.0	36.0	NM_172241	B0YIZ3	Missense_Mutation	SNP	ENST00000525417.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.58	3.162660	0.57368	.	.	ENSG00000212710	ENST00000391403	T	0.76709	-1.04	0.949	-0.479	0.12089	.	.	.	.	.	D	0.84083	0.5394	M	0.82923	2.615	0.21105	N	0.999785	D	0.69078	0.997	D	0.66847	0.947	T	0.71297	-0.4635	8	.	.	.	.	3.0429	0.06143	0.0:0.3164:0.0:0.6836	.	119	Q96RT6	CTGE2_HUMAN	D	119	ENSP00000375220:E119D	.	E	-	3	2	CTAGE1	18251416	0.001000	0.12720	0.327000	0.25402	0.698000	0.40448	-0.829000	0.04415	-0.168000	0.10853	0.374000	0.22700	GAA	.	.		0.388	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241		A	19997418	T	A	19997418	1	1	199	0	1	0	0	0	0	0	0	0	3994	1838	64	4		4	CTAGE1	18	19997418	5'Flank	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10		19997418	58079830	110	29336										
LIPG	9388	hgsc.bcm.edu	37	chr18	47101852	47101852	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	acacgcgttccttcggcttgAgcattggtattcagatgcct	10	11	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr18:47101852A>T	ENST00000261292.4	+	5	963	c.685A>T	c.(685-687)Agc>Tgc	p.S229C	LIPG_ENST00000427224.2_Intron|LIPG_ENST00000580036.1_Missense_Mutation_p.S229C|LIPG_ENST00000577628.1_Missense_Mutation_p.S265C	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial	229					cell proliferation (GO:0008283)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle remodeling (GO:0034375)|lipid metabolic process (GO:0006629)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|regulation of lipoprotein metabolic process (GO:0050746)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)	extracellular space (GO:0005615)	heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phospholipase activity (GO:0004620)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(2)	18						CTTCGGCTTGAGCATTGGTAT	0.552																																					p.S229C	Pancreas(126;280 1778 12814 26243 34948)	Atlas-SNP	.											.	LIPG	47	.	0			c.A685T						.						101	79	87					18																	47101852		2203	4300	6503	SO:0001583	missense	9388	exon5			GGCTTGAGCATTG	AF118767	CCDS11938.1	18q21.1	2006-04-22				ENSG00000101670			6623	protein-coding gene	gene with protein product		603684				10318835, 10192396	Standard	XM_005258390		Approved	EDL	uc002ldv.3	Q9Y5X9		ENST00000261292.4:c.685A>T	chr18.hg19:g.47101852A>T	ENSP00000261292:p.Ser229Cys	95.0	0.0		91.0	34.0	NM_006033	B0LPG6|Q6P9C8|Q6UW82	Missense_Mutation	SNP	ENST00000261292.4	hg19	CCDS11938.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.910730	0.92107	.	.	ENSG00000101670	ENST00000261292	D	0.91843	-2.92	5.72	5.72	0.89469	Lipase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96876	0.8980	M	0.91140	3.18	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.994	D	0.97737	1.0206	10	0.87932	D	0	-13.9412	15.9791	0.80094	1.0:0.0:0.0:0.0	.	229;229	Q9Y5X9;Q9Y5X9-2	LIPE_HUMAN;.	C	229	ENSP00000261292:S229C	ENSP00000261292:S229C	S	+	1	0	LIPG	45355850	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	9.331000	0.96430	2.182000	0.69389	0.482000	0.46254	AGC	.	.		0.552	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	NM_006033		T	47101852	A	T	47101852	3	4	199	1	0	0	0	0	1	0	0	0	8832	304	11	4	703	4	LIPG	18	47101852	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	27104434	47101852	30975396	111	29337										
CCDC68	80323	hgsc.bcm.edu	37	chr18	52604137	52604137	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tttggtagttttcaaataatCtctgggccacgtttctcaga	8	8	3	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr18:52604137C>T	ENST00000591504.1	-	6	672	c.398G>A	c.(397-399)aGa>aAa	p.R133K	CCDC68_ENST00000432185.1_Missense_Mutation_p.R133K|CCDC68_ENST00000337363.4_Missense_Mutation_p.R133K	NM_025214.2	NP_079490.1	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68	133										breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|stomach(1)	14				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)		TTCAAATAATCTCTGGGCCAC	0.433																																					p.R133K		Atlas-SNP	.											CCDC68,NS,malignant_melanoma,0,1	CCDC68	38	.	0			c.G398A						.						162	136	144					18																	52604137		2203	4300	6503	SO:0001583	missense	80323	exon6			AATAATCTCTGGG		CCDS11959.1	18q21	2006-02-07			ENSG00000166510	ENSG00000166510			24350	protein-coding gene	gene with protein product	"cutaneous T-cell lymphoma associated antigen"					11149944, 15142679	Standard	NM_025214		Approved	SE57-1	uc002lft.3	Q9H2F9	OTTHUMG00000132708	ENST00000591504.1:c.398G>A	chr18.hg19:g.52604137C>T	ENSP00000466690:p.Arg133Lys	122.0	0.0		87.0	37.0	NM_025214	B2R9I3	Missense_Mutation	SNP	ENST00000591504.1	hg19	CCDS11959.1	.	.	.	.	.	.	.	.	.	.	C	6.320	0.427144	0.11987	.	.	ENSG00000166510	ENST00000337363;ENST00000432185	T;T	0.49720	0.77;0.77	5.53	1.17	0.20885	.	0.359032	0.27586	N	0.018715	T	0.27384	0.0672	L	0.37466	1.105	0.24440	N	0.994534	B	0.06786	0.001	B	0.09377	0.004	T	0.27640	-1.0068	10	0.02654	T	1	-8.6657	6.6013	0.22703	0.0:0.5117:0.0:0.4883	.	133	Q9H2F9	CCD68_HUMAN	K	133	ENSP00000337209:R133K;ENSP00000413406:R133K	ENSP00000337209:R133K	R	-	2	0	CCDC68	50755135	0.644000	0.27277	0.980000	0.43619	0.954000	0.61252	0.131000	0.15870	0.391000	0.25143	0.650000	0.86243	AGA	.	.		0.433	CCDC68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256006.1	NM_025214		T	52604137	C	T	52604137	3	4	199	1	0	0	0	0	1	0	0	0	2842	913	32	3	637	3	CCDC68	18	52604137	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	5502285	52604137	25473111	112	29338										
SAFB2	9667	hgsc.bcm.edu	37	chr19	5594100	5594100	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gccgctggcgctggcactcgAgctgcaggcgttcccgctgt	15	15	0	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:5594100A>C	ENST00000252542.4	-	15	2273	c.2009T>G	c.(2008-2010)cTc>cGc	p.L670R		NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	670	Arg-rich.|Glu-rich.|Interacts with SAFB1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		CTGGCACTCGAGCTGCAGGCG	0.721																																					p.L670R	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.T2009G						.						8	11	10					19																	5594100		2153	4229	6382	SO:0001583	missense	9667	exon15			CACTCGAGCTGCA	D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"RNA binding motif (RRM) containing"	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.2009T>G	chr19.hg19:g.5594100A>C	ENSP00000252542:p.Leu670Arg	89.0	0.0		71.0	25.0	NM_014649	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	hg19	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.369314	0.42003	.	.	ENSG00000130254	ENST00000252542	T	0.20738	2.05	4.33	4.33	0.51752	.	0.318954	0.21251	N	0.077644	T	0.43500	0.1250	M	0.75615	2.305	0.58432	D	0.999998	D	0.76494	0.999	D	0.69307	0.963	T	0.30563	-0.9974	10	0.37606	T	0.19	-8.5728	12.688	0.56958	1.0:0.0:0.0:0.0	.	670	Q14151	SAFB2_HUMAN	R	670	ENSP00000252542:L670R	ENSP00000252542:L670R	L	-	2	0	SAFB2	5545100	0.995000	0.38212	0.174000	0.22961	0.149000	0.21700	5.241000	0.65384	1.586000	0.49944	0.358000	0.22013	CTC	.	.		0.721	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		C	5594100	A	C	5594100	3	2	199	1	0	0	0	0	1	0	0	0	13822	304	11	5	880	5	SAFB2	19	5594100	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10		5594100	53534883	113	29339										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11143970	11143970	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gcacctcttcccccaggaccTgcaagcgcaggaccgagccc	10	19	1	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:11143970T>C	ENST00000429416.3	+	27	3832	c.3551T>C	c.(3550-3552)cTg>cCg	p.L1184P	SMARCA4_ENST00000344626.4_Missense_Mutation_p.L1184P|SMARCA4_ENST00000589677.1_Missense_Mutation_p.L1184P|SMARCA4_ENST00000358026.2_Missense_Mutation_p.L1184P|SMARCA4_ENST00000450717.3_Missense_Mutation_p.L1184P|SMARCA4_ENST00000444061.3_Missense_Mutation_p.L1184P|SMARCA4_ENST00000590574.1_Missense_Mutation_p.L1184P|SMARCA4_ENST00000413806.3_Missense_Mutation_p.L1184P|SMARCA4_ENST00000541122.2_Missense_Mutation_p.L1184P	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1184	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CCCCAGGACCTGCAAGCGCAG	0.622			"F, N, Mis"		NSCLC																																p.L1184P		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.T3551C						.						43	44	44					19																	11143970		2203	4298	6501	SO:0001583	missense	6597	exon26			AGGACCTGCAAGC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3551T>C	chr19.hg19:g.11143970T>C	ENSP00000395654:p.Leu1184Pro	146.0	0.0		132.0	56.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	T	18.62	3.663223	0.67700	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05;-1.05;-1.05	4.74	4.74	0.60224	Helicase, C-terminal (3);	0.000000	0.64402	D	0.000009	D	0.92110	0.7499	H	0.98089	4.145	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0;1.0;0.999	D;D;D;D;D;D;D	0.91635	0.996;0.996;0.996;0.99;0.999;0.996;0.996	D	0.94547	0.7750	10	0.87932	D	0	-32.0752	13.3948	0.60846	0.0:0.0:0.0:1.0	.	1184;1184;1184;1184;1184;404;1184	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	P	1184;1184;1248;1184;1184;1184;1184;1184	ENSP00000395654:L1184P;ENSP00000350720:L1184P;ENSP00000343896:L1184P;ENSP00000445036:L1184P;ENSP00000392837:L1184P;ENSP00000397783:L1184P;ENSP00000414727:L1184P	ENSP00000343896:L1184P	L	+	2	0	SMARCA4	11004970	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	7.596000	0.82721	2.012000	0.59069	0.456000	0.33151	CTG	.	.		0.622	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		C	11143970	T	C	11143970	3	2	199	1	0	0	0	0	1	0	0	0	14785	1580	55	2	3649	2	SMARCA4	19	11143970	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	5549870	11143970	47985013	114	29340										
ZNF627	199692	hgsc.bcm.edu	37	chr19	11728647	11728656	+	Frame_Shift_Del	DEL	AGAGAAACCC	AGAGAAACCC	-													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	catgaaaaaattcatactggAgagaaaccctatgagaaccc					rs573622915|rs190861488	byFrequency	TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	AGAGAAACCC	AGAGAAACCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:11728647_11728656delAGAGAAACCC	ENST00000361113.5	+	4	1537_1546	c.1329_1338delAGAGAAACCC	c.(1327-1338)ggagagaaacccfs	p.GEKP443fs	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	443					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P446P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						TTCATACTGGAGAGAAACCCTATGAGAACC	0.41																																					p.443_446del	Melanoma(112;173 1614 10731 17751 23322)	Atlas-INDEL	.											.	ZNF627	43	.	1	Substitution - coding silent(1)	prostate(1)	c.1328_1337del						.																																			SO:0001589	frameshift_variant	199692	exon4			.	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"Zinc fingers, C2H2-type", "-"	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.1329_1338delAGAGAAACCC	chr19.hg19:g.11728647_11728656delAGAGAAACCC	ENSP00000354414:p.Gly443fs	29.0	0.0		27.0	13.0	NM_145295	O14846|Q4KMP9|Q6NT81|Q9BRG4	Frame_Shift_Del	DEL	ENST00000361113.5	hg19	CCDS42502.1																																																																																			.	.		0.41	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295		-	11728656	AGAGAAACCC	-	11728647	7	5	199	1	0	1	0	1	0	0	0	0	18066	291	11	0	1343	0	ZNF627	19	11728647	Frame_Shift_Del	DEL	AGAGAAACCC	TCGA-DD-AADQ-01A-11D-A40R-10	584677	11728647	47400336	115	29341										
MYO9B	4650	hgsc.bcm.edu	37	chr19	17321609	17321609	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agccggcggcgatgaggaccGggaaaaggagattctcattg	16	8	1	2	rs373618149		TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:17321609G>A	ENST00000594824.1	+	38	6029	c.5882G>A	c.(5881-5883)cGg>cAg	p.R1961Q	MYO9B_ENST00000397274.2_Missense_Mutation_p.R1961Q|MYO9B_ENST00000595618.1_Missense_Mutation_p.R1961Q|CTD-3032J10.3_ENST00000601929.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	1961	Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						GATGAGGACCGGGAAAAGGAG	0.577																																					p.R1961Q		Atlas-SNP	.											.	MYO9B	264	.	0			c.G5882A						.	G	GLN/ARG,GLN/ARG	1,4227		0,1,2113	37	49	45		5882,5882	2.9	0.5	19		45	0,8454		0,0,4227	no	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	43,43	0,1,6340	AA,AG,GG		0.0,0.0237,0.0079	probably-damaging,probably-damaging	1961/2023,1961/2158	17321609	1,12681	2114	4227	6341	SO:0001583	missense	4650	exon38			AGGACCGGGAAAA		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"Myosins / Myosin superfamily : Class IX"	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.5882G>A	chr19.hg19:g.17321609G>A	ENSP00000471367:p.Arg1961Gln	100.0	0.0		84.0	38.0	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.281	1.048246	0.19827	2.37E-4	0.0	ENSG00000099331	ENST00000397274;ENST00000319396	D	0.83419	-1.72	5.01	2.89	0.33648	.	0.000000	0.43416	D	0.000567	T	0.67135	0.2861	N	0.25380	0.74	0.31904	N	0.615594	B;B;B	0.30361	0.231;0.231;0.277	B;B;B	0.14023	0.01;0.01;0.01	T	0.62886	-0.6759	10	0.18710	T	0.47	.	9.8479	0.41039	0.1659:0.0:0.8341:0.0	.	1961;1961;1967	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	Q	1961;306	ENSP00000380444:R1961Q	ENSP00000314032:R306Q	R	+	2	0	MYO9B	17182609	0.948000	0.32251	0.509000	0.27700	0.369000	0.29798	4.006000	0.57083	0.518000	0.28383	0.561000	0.74099	CGG	.	.		0.577	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			A	17321609	G	A	17321609	3	1	199	1	0	0	0	0	1	0	0	0	10094	1116	39	1	6028	1	MYO9B	19	17321609	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	5592962	17321609	41807374	116	29342										
ZNF714	148206	hgsc.bcm.edu	37	chr19	21299777	21299777	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	aggtgtacaaaaaaggttatGaactaaaccagtgtttgaca	9	5	0	2	rs111443257		TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:21299777G>A	ENST00000596143.1	+	5	632	c.307G>A	c.(307-309)Gaa>Aaa	p.E103K	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AAAAGGTTATGAACTAAACCA	0.328																																					p.E103K		Atlas-SNP	.											.	ZNF714	121	.	0			c.G307A						.						39	38	38					19																	21299777		2190	4291	6481	SO:0001583	missense	148206	exon5			GGTTATGAACTAA	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.307G>A	chr19.hg19:g.21299777G>A	ENSP00000472368:p.Glu103Lys	435.0	0.0		457.0	25.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	0.388	-0.924824	0.02377	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.394	0.394	0.16299	.	.	.	.	.	T	0.22322	0.0538	L	0.27975	0.815	0.09310	N	1	B;P	0.37781	0.004;0.608	B;B	0.35413	0.004;0.202	T	0.14062	-1.0486	7	0.56958	D	0.05	.	.	.	.	.	104;103	Q96N38-2;A6NEM4	.;.	K	103	.	ENSP00000291770:E103K	E	+	1	0	ZNF714	21091617	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	-0.857000	0.04286	0.452000	0.26830	0.456000	0.33151	GAA	.	.		0.328	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		A	21299777	G	A	21299777	3	1	199	1	0	0	0	0	1	0	0	0	18133	1291	45	3	317	3	ZNF714	19	21299777	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	3978168	21299777	37829206	117	29343										
ZNF99	7652	hgsc.bcm.edu	37	chr19	22940876	22940876	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	tctttccagtatgaattatcTgatgttttctaagggctgag	9	6	3	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:22940876T>A	ENST00000596209.1	-	4	1925	c.1835A>T	c.(1834-1836)cAg>cTg	p.Q612L	ZNF99_ENST00000397104.3_Missense_Mutation_p.Q521L	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	612					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				ATGAATTATCTGATGTTTTCT	0.378																																					p.Q612L		Atlas-SNP	.											.	ZNF99	273	.	0			c.A1835T						.						35	39	38					19																	22940876		1966	4190	6156	SO:0001583	missense	7652	exon4			ATTATCTGATGTT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1835A>T	chr19.hg19:g.22940876T>A	ENSP00000472969:p.Gln612Leu	166.0	0.0		177.0	82.0	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	t	4.658	0.122266	0.08931	.	.	ENSG00000213973	ENST00000397104	T	0.36340	1.26	1.16	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20047	0.0482	N	0.16266	0.395	0.09310	N	1	B	0.14805	0.011	B	0.08055	0.003	T	0.21415	-1.0246	9	0.87932	D	0	.	4.2921	0.10883	0.0:0.2167:0.0:0.7833	.	521	A8MXY4	ZNF99_HUMAN	L	521	ENSP00000380293:Q521L	ENSP00000380293:Q521L	Q	-	2	0	ZNF99	22732716	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.487000	0.06505	0.501000	0.28013	0.163000	0.16589	CAG	.	.		0.378	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		A	22940876	T	A	22940876	3	1	199	1	0	0	0	0	1	0	0	0	18219	1580	55	4	1562	4	ZNF99	19	22940876	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	1641099	22940876	36188107	118	29344										
ZNF527	84503	hgsc.bcm.edu	37	chr19	37880756	37880756	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agcccttagacgacatcagaGaattcataatagagaaacgc	8	9	2	3	rs202094634		TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:37880756G>T	ENST00000436120.2	+	5	1912	c.1805G>T	c.(1804-1806)aGa>aTa	p.R602I	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	602					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CGACATCAGAGAATTCATAAT	0.348																																					p.R602I		Atlas-SNP	.											.	ZNF527	78	.	0			c.G1805T						.						53	54	54					19																	37880756		1971	4182	6153	SO:0001583	missense	84503	exon5			ATCAGAGAATTCA	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"Zinc fingers, C2H2-type", "-"	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.1805G>T	chr19.hg19:g.37880756G>T	ENSP00000390179:p.Arg602Ile	70.0	0.0		54.0	23.0	NM_032453	B4DVL5	Missense_Mutation	SNP	ENST00000436120.2	hg19	CCDS42559.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.615400	0.28801	.	.	ENSG00000189164	ENST00000356178;ENST00000317566;ENST00000436120	.	.	.	3.91	0.389	0.16269	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.229124	0.22584	N	0.058161	T	0.58878	0.2153	M	0.77712	2.385	0.80722	D	1	B;B	0.24186	0.06;0.099	B;B	0.26416	0.031;0.069	T	0.55023	-0.8205	9	0.72032	D	0.01	.	7.5375	0.27719	0.5704:0.0:0.4296:0.0	.	602;570	Q8NB42;Q8NB42-2	ZN527_HUMAN;.	I	602;570;550	.	ENSP00000325231:R570I	R	+	2	0	ZNF527	42572596	0.000000	0.05858	0.744000	0.31058	0.780000	0.44128	0.068000	0.14531	-0.084000	0.12595	0.655000	0.94253	AGA	.	G|0.999;T|0.001		0.348	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453		T	37880756	G	T	37880756	3	4	199	1	0	0	0	0	1	0	0	0	17983	942	33	3	1819	3	ZNF527	19	37880756	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	14939880	37880756	21248227	119	29345										
RYR1	6261	hgsc.bcm.edu	37	chr19	38956904	38956904	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agtgcaggacatcccagcgcGccgaaaccctcggctggtgc	13	15	0	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:38956904G>A	ENST00000359596.3	+	24	3044	c.3044G>A	c.(3043-3045)cGc>cAc	p.R1015H	RYR1_ENST00000355481.4_Missense_Mutation_p.R1015H|RYR1_ENST00000360985.3_Missense_Mutation_p.R1015H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1015	6 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.R1015H(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ATCCCAGCGCGCCGAAACCCT	0.677																																					p.R1015H		Atlas-SNP	.											RYR1,NS,carcinoma,+1,1	RYR1	708	.	1	Substitution - Missense(1)	endometrium(1)	c.G3044A						.						43	41	42					19																	38956904		2200	4299	6499	SO:0001583	missense	6261	exon24			CAGCGCGCCGAAA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.3044G>A	chr19.hg19:g.38956904G>A	ENSP00000352608:p.Arg1015His	160.0	0.0		130.0	48.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	g	11.67	1.708236	0.30322	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.91740	-2.9;-2.9;-2.9	3.8	3.8	0.43715	B30.2/SPRY domain (1);Ryanodine receptor Ryr (1);	0.206543	0.30134	U	0.010337	D	0.93936	0.8059	M	0.68952	2.095	0.31797	N	0.628888	D;D	0.76494	0.996;0.999	D;D	0.73708	0.936;0.981	D	0.92296	0.5845	10	0.54805	T	0.06	.	7.1924	0.25832	0.121:0.0:0.879:0.0	.	1015;1015	P21817-2;P21817	.;RYR1_HUMAN	H	1015	ENSP00000352608:R1015H;ENSP00000347667:R1015H;ENSP00000354254:R1015H	ENSP00000347667:R1015H	R	+	2	0	RYR1	43648744	0.951000	0.32395	0.989000	0.46669	0.294000	0.27393	1.734000	0.38166	1.988000	0.58038	0.444000	0.29173	CGC	.	.		0.677	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38956904	G	A	38956904	3	1	199	1	0	0	0	0	1	0	0	0	13783	1087	38	1	3138	1	RYR1	19	38956904	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	1076148	38956904	20172079	120	29346										
BCL3	602	hgsc.bcm.edu	37	chr19	45260629	45260629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gaacaccgagtgccaagaaaCcgtgcagctcttgctagagc	11	12	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:45260629C>T	ENST00000164227.5	+	5	1014	c.770C>T	c.(769-771)aCc>aTc	p.T257I		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	257					antimicrobial humoral response (GO:0019730)|cellular response to DNA damage stimulus (GO:0006974)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|protein import into nucleus, translocation (GO:0000060)|regulation of apoptotic process (GO:0042981)|regulation of DNA binding (GO:0051101)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to UV-C (GO:0010225)|response to virus (GO:0009615)|spleen development (GO:0048536)|T-helper 1 type immune response (GO:0042088)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	Bcl3-Bcl10 complex (GO:0032996)|Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)				TGCCAAGAAACCGTGCAGCTC	0.667			T	IGH@	CLL																																p.T257I		Atlas-SNP	.		Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	.	BCL3	28	.	0			c.C770T						.						25	19	21					19																	45260629		2203	4298	6501	SO:0001583	missense	602	exon5			AAGAAACCGTGCA	M31732	CCDS12642.2	19q13.1-q13.2	2013-01-10			ENSG00000069399	ENSG00000069399		"Ankyrin repeat domain containing"	998	protein-coding gene	gene with protein product	"B-cell lymphoma 3-encoded protein", "B-cell leukemia/lymphoma 3", "chronic lymphatic leukemia protein"	109560		D19S37, BCL4		1501714, 2180580	Standard	NM_005178		Approved		uc010xxe.2	P20749	OTTHUMG00000151517	ENST00000164227.5:c.770C>T	chr19.hg19:g.45260629C>T	ENSP00000164227:p.Thr257Ile	179.0	0.0		136.0	53.0	NM_005178		Missense_Mutation	SNP	ENST00000164227.5	hg19	CCDS12642.2	.	.	.	.	.	.	.	.	.	.	C	10.03	1.237881	0.22711	.	.	ENSG00000069399	ENST00000403534;ENST00000164227	T	0.60171	0.21	4.71	4.71	0.59529	Ankyrin repeat-containing domain (3);	0.296735	0.24091	N	0.041622	T	0.28234	0.0697	N	0.02213	-0.635	0.09310	N	0.999992	B	0.18863	0.031	B	0.17098	0.017	T	0.07539	-1.0767	10	0.06236	T	0.91	-25.5142	13.1677	0.59581	0.0:1.0:0.0:0.0	.	257	P20749	BCL3_HUMAN	I	217;257	ENSP00000164227:T257I	ENSP00000164227:T257I	T	+	2	0	BCL3	49952469	0.021000	0.18746	0.566000	0.28421	0.618000	0.37518	2.341000	0.43983	2.178000	0.69098	0.305000	0.20034	ACC	.	.		0.667	BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1	NM_005178		T	45260629	C	T	45260629	3	4	199	1	0	0	0	0	1	0	0	0	1375	507	18	3	788	3	BCL3	19	45260629	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	6303725	45260629	13868354	121	29347										
HAS1	3036	hgsc.bcm.edu	37	chr19	52216886	52216886	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	caggcccccaagcagcagcaGcgcccagagcgccaggggca	14	17	0	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:52216886G>A	ENST00000222115.1	-	5	1565	c.1531C>T	c.(1531-1533)Ctg>Ttg	p.L511L	HAS1_ENST00000601714.1_Silent_p.L518L|HAS1_ENST00000540069.2_Silent_p.L510L	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	511					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		AGCAGCAGCAGCGCCCAGAGC	0.721																																					p.L511L	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.C1531T						.						5	5	5					19																	52216886		2042	4012	6054	SO:0001819	synonymous_variant	3036	exon5			GCAGCAGCGCCCA	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.1531C>T	chr19.hg19:g.52216886G>A		118.0	0.0		117.0	46.0	NM_001523	Q14470|Q9NS49	Silent	SNP	ENST00000222115.1	hg19	CCDS12838.1																																																																																			.	.		0.721	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		A	52216886	G	A	52216886	2	1	199	1	0	0	0	0	0	0	0	1	6970	962	34	3		3	HAS1	19	52216886	Silent	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	6956257	52216886	6912097	122	29348										
ZNF578	147660	hgsc.bcm.edu	37	chr19	53014279	53014279	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gggaataattttttccattcAtcattactcacacaaaaaca	3	9	3	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:53014279A>T	ENST00000421239.2	+	6	889	c.645A>T	c.(643-645)tcA>tcT	p.S215S	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	215					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		TTTTCCATTCATCATTACTCA	0.358																																					p.S215S		Atlas-SNP	.											.	.	.	.	0			c.A645T						.						67	70	69					19																	53014279		2201	4299	6500	SO:0001819	synonymous_variant	147660	exon6			CCATTCATCATTA	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.645A>T	chr19.hg19:g.53014279A>T		299.0	0.0		308.0	116.0	NM_001099694	B4DR51|I3L1Y6	Silent	SNP	ENST00000421239.2	hg19	CCDS54310.1																																																																																			.	.		0.358	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		T	53014279	A	T	53014279	2	4	199	1	0	0	0	0	0	0	0	1	18025	204	8	4		4	ZNF578	19	53014279	Silent	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	797393	53014279	6114704	123	29349										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53644667	53644667	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	aattagctgatgccttgcaaGgtgtgaattacgcctaaaga	10	7	0	3			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr19:53644667G>A	ENST00000334197.7	-	5	1482	c.1414C>T	c.(1414-1416)Ctt>Ttt	p.L472F	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000452676.2_Missense_Mutation_p.L473F|ZNF347_ENST00000601469.2_Missense_Mutation_p.L473F	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	472					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		TGCCTTGCAAGGTGTGAATTA	0.428																																					p.L473F	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.C1417T						.						147	145	146					19																	53644667		2203	4300	6503	SO:0001583	missense	84671	exon5			TTGCAAGGTGTGA	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.1414C>T	chr19.hg19:g.53644667G>A	ENSP00000334146:p.Leu472Phe	109.0	0.0		110.0	47.0	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	hg19	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118790	0.37436	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.52057	0.68;0.68	2.61	1.52	0.23074	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.65842	0.2730	M	0.84683	2.71	0.09310	N	1	D;D	0.89917	1.0;0.991	D;P	0.97110	1.0;0.825	T	0.51228	-0.8732	9	0.49607	T	0.09	.	5.1408	0.14957	0.124:0.0:0.6749:0.2011	.	473;472	G5E9N4;Q96SE7	.;ZN347_HUMAN	F	472;473	ENSP00000334146:L472F;ENSP00000405218:L473F	ENSP00000334146:L472F	L	-	1	0	ZNF347	58336479	0.460000	0.25776	0.003000	0.11579	0.007000	0.05969	1.464000	0.35288	0.439000	0.26476	0.655000	0.94253	CTT	.	.		0.428	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		A	53644667	G	A	53644667	3	1	199	1	0	0	0	0	1	0	0	0	17876	1000	35	3	1109	3	ZNF347	19	53644667	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	630388	53644667	5484316	124	29350										
C20orf96	140680	hgsc.bcm.edu	37	chr20	270284	270284	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	aggcagagtagatggcttggTttcctgcttggactgctgcc	14	9	0	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr20:270284T>C	ENST00000360321.2	-	3	241	c.103A>G	c.(103-105)Acc>Gcc	p.T35A	C20orf96_ENST00000400269.3_Intron|C20orf96_ENST00000382369.5_Intron	NM_080571.1|NM_153269.2	NP_542138.1|NP_695001.2	Q9NUD7	CT096_HUMAN	chromosome 20 open reading frame 96	35										endometrium(3)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			GATGGCTTGGTTTCCTGCTTG	0.463																																					p.T35A		Atlas-SNP	.											.	C20orf96	28	.	0			c.A103G						.						164	137	146					20																	270284		2203	4300	6503	SO:0001583	missense	140680	exon3			GCTTGGTTTCCTG	AL034548	CCDS12994.1, CCDS74685.1	20p13	2012-10-30			ENSG00000196476	ENSG00000196476			16227	protein-coding gene	gene with protein product							Standard	NM_153269		Approved	dJ1103G7.2	uc002wde.2	Q9NUD7	OTTHUMG00000031626	ENST00000360321.2:c.103A>G	chr20.hg19:g.270284T>C	ENSP00000353470:p.Thr35Ala	168.0	0.0		140.0	61.0	NM_153269	A3KPE0|B2RPH9|Q8N840|Q8NAX5	Missense_Mutation	SNP	ENST00000360321.2	hg19	CCDS12994.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.563605	0.00903	.	.	ENSG00000196476	ENST00000360321	T	0.41065	1.01	3.95	-2.07	0.07276	.	1.078640	0.07210	N	0.858980	T	0.20536	0.0494	N	0.17082	0.46	0.09310	N	1	B	0.17038	0.02	B	0.11329	0.006	T	0.21999	-1.0229	10	0.13853	T	0.58	-10.8412	3.3819	0.07257	0.26:0.3767:0.0:0.3633	.	35	Q9NUD7	CT096_HUMAN	A	35	ENSP00000353470:T35A	ENSP00000353470:T35A	T	-	1	0	C20orf96	218284	0.000000	0.05858	0.003000	0.11579	0.358000	0.29455	-0.352000	0.07701	-0.390000	0.07774	0.374000	0.22700	ACC	.	.		0.463	C20orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077439.2	NM_153269		C	270284	T	C	270284	3	2	199	1	0	0	0	0	1	0	0	0	2124	1725	60	2	1024	2	C20orf96	20	270284	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10		270284	62755236	125	29351										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52198237	52198237	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agctttgccgcactcggagcAgtgagtgggcttctccttgc	13	12	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr20:52198237A>T	ENST00000371471.2	-	2	1554	c.1129T>A	c.(1129-1131)Tgc>Agc	p.C377S	ZNF217_ENST00000302342.3_Missense_Mutation_p.C377S|ZNF217_ENST00000540425.1_5'Flank			O75362	ZN217_HUMAN	zinc finger protein 217	377					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			CACTCGGAGCAGTGAGTGGGC	0.612																																					p.C377S		Atlas-SNP	.											.	ZNF217	227	.	0			c.T1129A						.						96	99	98					20																	52198237		2203	4300	6503	SO:0001583	missense	7764	exon1			CGGAGCAGTGAGT	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1129T>A	chr20.hg19:g.52198237A>T	ENSP00000360526:p.Cys377Ser	126.0	0.0		94.0	42.0	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	hg19	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	A	19.03	3.748109	0.69533	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.59638	0.25;0.25	5.7	5.7	0.88788	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.80654	0.4664	M	0.89658	3.05	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84958	0.0875	10	0.87932	D	0	-29.0809	15.6258	0.76855	1.0:0.0:0.0:0.0	.	377	O75362	ZN217_HUMAN	S	377	ENSP00000360526:C377S;ENSP00000304308:C377S	ENSP00000304308:C377S	C	-	1	0	ZNF217	51631644	1.000000	0.71417	0.560000	0.28344	0.343000	0.28985	8.838000	0.92115	2.170000	0.68504	0.482000	0.46254	TGC	.	.		0.612	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		T	52198237	A	T	52198237	3	4	199	1	0	0	0	0	1	0	0	0	17787	188	7	4	2033	4	ZNF217	20	52198237	Missense_Mutation	SNP	A	TCGA-DD-AADQ-01A-11D-A40R-10	51927953	52198237	10827283	126	29352										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58496502	58496502	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	agcatcatcaatgcatttttCcaactgctagagaaatatat	5	8	2	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr20:58496502C>A	ENST00000357552.3	-	4	256	c.31G>T	c.(31-33)Gaa>Taa	p.E11*	SYCP2_ENST00000476314.1_5'UTR|SYCP2_ENST00000371001.2_Nonsense_Mutation_p.E11*			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	11					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ATGCATTTTTCCAACTGCTAG	0.284																																					p.E11X		Atlas-SNP	.											.	SYCP2	204	.	0			c.G31T						.						33	32	32					20																	58496502		2200	4285	6485	SO:0001587	stop_gained	10388	exon3			ATTTTTCCAACTG	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.31G>T	chr20.hg19:g.58496502C>A	ENSP00000350162:p.Glu11*	170.0	0.0		209.0	89.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Nonsense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	C	36	5.702171	0.96812	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834;ENST00000425931	.	.	.	5.04	5.04	0.67666	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-27.6222	18.7497	0.91809	0.0:1.0:0.0:0.0	.	.	.	.	X	11;11;11;10	.	ENSP00000350162:E11X	E	-	1	0	SYCP2	57929897	1.000000	0.71417	1.000000	0.80357	0.434000	0.31775	5.156000	0.64905	2.515000	0.84797	0.467000	0.42956	GAA	.	.		0.284	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		A	58496502	C	A	58496502	4	1	199	1	0	0	0	0	0	1	0	0	15447	864	30	3	4729	3	SYCP2	20	58496502	Nonsense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	6298265	58496502	4529018	127	29353										
CDH26	60437	hgsc.bcm.edu	37	chr20	58569360	58569360	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ctcttcctgtctgacatcaaTgacaacgtcccgactctccg	6	16	4	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr20:58569360T>C	ENST00000244047.5	+	11	1793	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N	CDH26_ENST00000348616.4_Silent_p.N494N|CDH26_ENST00000497614.1_3'UTR|CDH26_ENST00000244049.3_5'Flank|CDH26_ENST00000350849.6_5'Flank			Q8IXH8	CAD26_HUMAN	cadherin 26	494	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			CTGACATCAATGACAACGTCC	0.567																																					p.N494N		Atlas-SNP	.											CDH26_ENST00000244047,caecum,carcinoma,0,2	CDH26	229	.	0			c.T1482C						.						103	88	93					20																	58569360		2203	4300	6503	SO:0001819	synonymous_variant	60437	exon11			CATCAATGACAAC	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"Cadherins / Major cadherins"	15902	protein-coding gene	gene with protein product			"cadherin-like 26"				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.1482T>C	chr20.hg19:g.58569360T>C		92.0	0.0		94.0	45.0	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Silent	SNP	ENST00000244047.5	hg19		.	.	.	.	.	.	.	.	.	.	T	5.229	0.227807	0.09916	.	.	ENSG00000124215	ENST00000370991	.	.	.	4.57	-2.33	0.06724	.	.	.	.	.	T	0.54565	0.1866	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.48352	-0.9043	4	.	.	.	.	9.911	0.41406	0.0:0.4504:0.0:0.5496	.	.	.	.	T	86	.	.	M	+	2	0	CDH26	58002755	0.731000	0.28111	0.002000	0.10522	0.609000	0.37215	-0.164000	0.09983	-0.887000	0.03961	-0.256000	0.11100	ATG	.	.		0.567	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980		C	58569360	T	C	58569360	2	2	199	1	0	0	0	0	0	0	0	1	3112	1461	51	2		2	CDH26	20	58569360	Silent	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	72858	58569360	4456160	128	29354										
STMN3	50861	hgsc.bcm.edu	37	chr20	62273597	62273597	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ccagcgccttgtgcagcaccTcgcgctcgtgctcgcgccgc	12	19	0	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr20:62273597T>C	ENST00000370053.1	-	4	428	c.347A>G	c.(346-348)gAg>gGg	p.E116G	STMN3_ENST00000540534.1_Missense_Mutation_p.E105G	NM_001276310.1|NM_015894.2	NP_001263239.1|NP_056978.2	Q9NZ72	STMN3_HUMAN	stathmin-like 3	116	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				cytoplasmic microtubule organization (GO:0031122)|negative regulation of Rac protein signal transduction (GO:0035021)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|regulation of cytoskeleton organization (GO:0051493)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of Rac GTPase activity (GO:0032314)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	protein domain specific binding (GO:0019904)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)	8	all_cancers(38;2.31e-11)|all_epithelial(29;7.76e-13)		Epithelial(9;1.9e-09)|all cancers(9;1.22e-08)|BRCA - Breast invasive adenocarcinoma(10;8.86e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.00559)			GTGCAGCACCTCGCGCTCGTG	0.682																																					p.E116G		Atlas-SNP	.											.	STMN3	19	.	0			c.A347G						.						28	25	26					20																	62273597		2200	4300	6500	SO:0001583	missense	50861	exon4			AGCACCTCGCGCT	AF069709	CCDS13529.1, CCDS63330.1	20q13.3	2007-01-22			ENSG00000197457	ENSG00000197457			15926	protein-coding gene	gene with protein product		608362				9603203, 10655513	Standard	NM_001276310		Approved	SCLIP	uc002yfr.2	Q9NZ72	OTTHUMG00000032985	ENST00000370053.1:c.347A>G	chr20.hg19:g.62273597T>C	ENSP00000359070:p.Glu116Gly	116.0	0.0		88.0	33.0	NM_015894	B3KSQ5|B7WP52|B7Z5G4|O75527|Q969Y4	Missense_Mutation	SNP	ENST00000370053.1	hg19	CCDS13529.1	.	.	.	.	.	.	.	.	.	.	t	16.42	3.117392	0.56505	.	.	ENSG00000197457	ENST00000370053;ENST00000540534	.	.	.	5.14	5.14	0.70334	.	0.281959	0.27586	U	0.018701	T	0.62405	0.2425	M	0.85630	2.765	0.58432	D	0.999995	P	0.46512	0.879	B	0.38985	0.287	T	0.72754	-0.4198	9	0.87932	D	0	-14.434	14.9715	0.71238	0.0:0.0:0.0:1.0	.	116	Q9NZ72	STMN3_HUMAN	G	116;105	.	ENSP00000359070:E116G	E	-	2	0	STMN3	61744041	1.000000	0.71417	1.000000	0.80357	0.126000	0.20510	5.970000	0.70431	1.945000	0.56424	0.393000	0.25936	GAG	.	.		0.682	STMN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080163.1	NM_015894		C	62273597	T	C	62273597	3	2	199	1	0	0	0	0	1	0	0	0	15325	1551	54	2	203	2	STMN3	20	62273597	Missense_Mutation	SNP	T	TCGA-DD-AADQ-01A-11D-A40R-10	3704237	62273597	751923	129	29355										
ICOSLG	23308	hgsc.bcm.edu	37	chr21	45655360	45655360	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	cagtacacgttgggcctgggGtagccgtttatggatgtaca	14	8	0	0			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr21:45655360G>A	ENST00000407780.3	-	4	619	c.492C>T	c.(490-492)taC>taT	p.Y164Y	ICOSLG_ENST00000344330.4_Silent_p.Y164Y|ICOSLG_ENST00000400379.3_Silent_p.Y164Y|ICOSLG_ENST00000400377.3_Silent_p.Y47Y	NM_001283052.1	NP_001269981.1	O75144	ICOSL_HUMAN	inducible T-cell co-stimulator ligand	164	Ig-like C2-type.				B cell activation (GO:0042113)|defense response (GO:0006952)|hyperosmotic response (GO:0006972)|positive regulation of activated T cell proliferation (GO:0042104)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(2)|lung(1)|stomach(1)|urinary_tract(1)	5				Colorectal(79;0.0163)|READ - Rectum adenocarcinoma(84;0.0772)		TGGGCCTGGGGTAGCCGTTTA	0.582																																					p.Y164Y		Atlas-SNP	.											.	ICOSLG	20	.	0			c.C492T						.						91	97	95					21																	45655360		2160	4271	6431	SO:0001819	synonymous_variant	23308	exon4			CCTGGGGTAGCCG	AB014553	CCDS42952.1, CCDS63377.1, CCDS63379.1	21q22.3	2014-01-30		2005-01-12	ENSG00000160223	ENSG00000160223		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Endogenous ligands"	17087	protein-coding gene	gene with protein product	"B7-related protein 1", "B7 homologue 2", "B7 homolog 2"	605717		ICOSL		9734811, 11007762	Standard	NM_001283050		Approved	KIAA0653, GL50, B7-H2, B7RP-1, B7H2, B7RP1, ICOS-L, CD275	uc002zee.3	O75144	OTTHUMG00000086920	ENST00000407780.3:c.492C>T	chr21.hg19:g.45655360G>A		113.0	0.0		64.0	43.0	NM_015259	A8MUZ1|Q9HD18|Q9NRQ1	Silent	SNP	ENST00000407780.3	hg19	CCDS42952.1																																																																																			.	.		0.582	ICOSLG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195838.1	NM_015259		A	45655360	G	A	45655360	2	1	199	1	0	0	0	0	0	0	0	1	7496	1256	44	3		3	ICOSLG	21	45655360	Silent	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10		45655360	2474535	130	29356										
POTEH	23784	hgsc.bcm.edu	37	chr22	16287870	16287870	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggaggcagccggcattgaacCagcctcagccaccatctgct	11	15	2	1	rs368142357		TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chr22:16287870C>T	ENST00000343518.6	-	1	67	c.16G>A	c.(16-18)Ggt>Agt	p.G6S		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	6										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						GGCATTGAACCAGCCTCAGCC	0.587																																					p.G6S		Atlas-SNP	.											.	POTEH	114	.	0			c.G16A						.	C	SER/GLY	0,3920		0,0,1960	50	61	57		16	-0.9	0	22		57	1,7537		0,1,3768	no	missense	POTEH	NM_001136213.1	56	0,1,5728	TT,TC,CC		0.0133,0.0,0.0087	benign	6/546	16287870	1,11457	1960	3769	5729	SO:0001583	missense	23784	exon1			TTGAACCAGCCTC	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	133	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 7"	608913	"actin, beta-like 1", "ANKRD26-like family C, member 3"	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.16G>A	chr22.hg19:g.16287870C>T	ENSP00000340610:p.Gly6Ser	682.0	0.0		633.0	178.0	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Missense_Mutation	SNP	ENST00000343518.6	hg19	CCDS46658.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.614322	0.00120	0.0	1.33E-4	ENSG00000198062	ENST00000359587;ENST00000343518;ENST00000355872	T	0.23552	1.9	0.462	-0.925	0.10458	.	.	.	.	.	T	0.06735	0.0172	N	0.01874	-0.695	0.09310	N	1	B	0.16396	0.017	B	0.12156	0.007	T	0.32666	-0.9898	8	0.08837	T	0.75	.	.	.	.	.	6	Q6S545	POTEH_HUMAN	S	6	ENSP00000340610:G6S	ENSP00000340610:G6S	G	-	1	0	POTEH	14667870	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.610000	0.05629	-0.950000	0.03659	-1.064000	0.02280	GGT	.	.		0.587	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		T	16287870	C	T	16287870	3	4	199	1	0	0	0	0	1	0	0	0	12276	594	21	3	1661	3	POTEH	22	16287870	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10		16287870	35016696	131	29357										
FAM120C	54954	hgsc.bcm.edu	37	chrX	54185860	54185862	+	In_Frame_Del	DEL	CTT	CTT	-													0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	caggcccagctgcttggctaCttcttgcatcaggaactggt							TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chrX:54185860_54185862delCTT	ENST00000375180.2	-	2	943_945	c.887_889delAAG	c.(886-891)gaagta>gta	p.E296del	FAM120C_ENST00000328235.4_In_Frame_Del_p.E296del	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	296							poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						TGCTTGGCTACTTCTTGCATCAG	0.463																																					p.296_297del		Atlas-INDEL	.											.	FAM120C	89	.	0			c.888_890del						.																																			SO:0001651	inframe_deletion	54954	exon2			.	AY150025	CCDS14356.1, CCDS55421.1, CCDS75987.1	Xp11.22	2011-04-13	2006-07-04	2006-07-04	ENSG00000184083	ENSG00000184083			16949	protein-coding gene	gene with protein product		300741	"chromosome X open reading frame 17"	CXorf17		14585507	Standard	XM_006724589		Approved	ORF34, FLJ20506	uc004dsz.4	Q9NX05	OTTHUMG00000021625	ENST00000375180.2:c.887_889delAAG	chrX.hg19:g.54185863_54185865delCTT	ENSP00000364324:p.Glu296del	152.0	0.0		127.0	97.0	NM_017848	B2RMT7	In_Frame_Del	DEL	ENST00000375180.2	hg19	CCDS14356.1																																																																																			.	.		0.463	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056795.2	NM_017848		-	54185862	CTT	-	54185860	7	5	199	1	0	1	0	1	0	0	0	0	5423	565	20	0	2461	0	FAM120C	23	54185860	In_Frame_Del	DEL	CTT	TCGA-DD-AADQ-01A-11D-A40R-10		54185860	101084700	132	29358										
CPXCR1	53336	hgsc.bcm.edu	37	chrX	88008450	88008450	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	taaagaaggaagtgatacagCtggaaatgctcacaaaaatt	9	5	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chrX:88008450C>T	ENST00000276127.4	+	3	294	c.35C>T	c.(34-36)gCt>gTt	p.A12V	CPXCR1_ENST00000373111.1_Missense_Mutation_p.A12V	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	12							metal ion binding (GO:0046872)	p.A12V(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						AGTGATACAGCTGGAAATGCT	0.353																																					p.A12V		Atlas-SNP	.											.	CPXCR1	83	.	1	Substitution - Missense(1)	large_intestine(1)	c.C35T						.						27	24	25					X																	88008450		2202	4297	6499	SO:0001583	missense	53336	exon3			ATACAGCTGGAAA	AL031116	CCDS14458.1	Xq21.3	2009-08-06			ENSG00000147183	ENSG00000147183			2332	protein-coding gene	gene with protein product	"cancer/testis antigen 77"					11499681	Standard	NM_033048		Approved	CT77	uc004efc.4	Q8N123	OTTHUMG00000021950	ENST00000276127.4:c.35C>T	chrX.hg19:g.88008450C>T	ENSP00000276127:p.Ala12Val	309.0	0.0		229.0	197.0	NM_001184771	B2R9F9|D3DTE7|Q96RS3	Missense_Mutation	SNP	ENST00000276127.4	hg19	CCDS14458.1	.	.	.	.	.	.	.	.	.	.	C	9.161	1.018624	0.19355	.	.	ENSG00000147183	ENST00000276127;ENST00000373111	T;T	0.29397	1.57;1.57	3.28	-0.711	0.11230	.	0.972892	0.08355	N	0.958693	T	0.15565	0.0375	N	0.24115	0.695	0.09310	N	1	B	0.16396	0.017	B	0.18561	0.022	T	0.31110	-0.9955	9	.	.	.	.	0.5159	0.00603	0.1986:0.358:0.1916:0.2518	.	12	Q8N123	CPXCR_HUMAN	V	12	ENSP00000276127:A12V;ENSP00000362203:A12V	.	A	+	2	0	CPXCR1	87895106	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.152000	0.16302	-0.303000	0.08856	-1.057000	0.02308	GCT	.	.		0.353	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048		T	88008450	C	T	88008450	3	4	199	1	0	0	0	0	1	0	0	0	3838	797	28	3	37	3	CPXCR1	23	88008450	Missense_Mutation	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	33822590	88008450	67262110	133	29359										
PLS3	5358	hgsc.bcm.edu	37	chrX	114863611	114863611	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	ggtggaacttcagagttgtcCagcgaaggaacacagcattc	12	9	1	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chrX:114863611C>T	ENST00000420625.2	+	4	473	c.339C>T	c.(337-339)tcC>tcT	p.S113S	PLS3_ENST00000289290.3_Silent_p.S68S|PLS3_ENST00000537301.1_Silent_p.S91S|PLS3_ENST00000539310.1_Silent_p.S68S|PLS3_ENST00000355899.3_Silent_p.S113S	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	113	Actin-binding 1.				bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						CAGAGTTGTCCAGCGAAGGAA	0.418																																					p.S113S	Colon(160;1047 1864 8490 12969 29601)	Atlas-SNP	.											.	PLS3	60	.	0			c.C339T						.						132	116	121					X																	114863611		2203	4300	6503	SO:0001819	synonymous_variant	5358	exon4			GTTGTCCAGCGAA	L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"EF-hand domain containing"	9091	protein-coding gene	gene with protein product		300131	"plastin 3 (T isoform)"			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.339C>T	chrX.hg19:g.114863611C>T		278.0	0.0		272.0	229.0	NM_005032	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Silent	SNP	ENST00000420625.2	hg19	CCDS14568.1																																																																																			.	.		0.418	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			T	114863611	C	T	114863611	2	4	199	1	0	0	0	0	0	0	0	1	12117	581	21	3		3	PLS3	23	114863611	Silent	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	26855161	114863611	40406949	134	29360										
GPR112	139378	hgsc.bcm.edu	37	chrX	135443733	135443733	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	taaaaaatgaggatggaaatGccacaagattctggtatgta	10	4	1	2			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chrX:135443733G>T	ENST00000394143.1	+	12	7555	c.7264G>T	c.(7264-7266)Gcc>Tcc	p.A2422S	GPR112_ENST00000370652.1_Missense_Mutation_p.A2422S|GPR112_ENST00000394141.1_Missense_Mutation_p.A2217S|GPR112_ENST00000412101.1_Missense_Mutation_p.A2217S|GPR112_ENST00000287534.4_Missense_Mutation_p.A2220S	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2422					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GGATGGAAATGCCACAAGATT	0.403																																					p.A2422S		Atlas-SNP	.											.	GPR112	459	.	0			c.G7264T						.						154	113	127					X																	135443733		2203	4300	6503	SO:0001583	missense	139378	exon12			GGAAATGCCACAA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.7264G>T	chrX.hg19:g.135443733G>T	ENSP00000377699:p.Ala2422Ser	218.0	0.0		222.0	179.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.349632	0.82132	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.46063	0.93;0.93;0.88;1.01;0.88	5.79	5.79	0.91817	.	.	.	.	.	T	0.54598	0.1868	L	0.34521	1.04	0.26112	N	0.980672	D;D;D	0.89917	1.0;0.999;0.995	D;D;D	0.87578	0.998;0.981;0.975	T	0.50759	-0.8790	9	0.59425	D	0.04	.	14.244	0.65975	0.0:0.0:1.0:0.0	.	2220;2217;2422	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	S	2422;2422;2217;2220;2217	ENSP00000377699:A2422S;ENSP00000359686:A2422S;ENSP00000416526:A2217S;ENSP00000287534:A2220S;ENSP00000377697:A2217S	ENSP00000287534:A2220S	A	+	1	0	GPR112	135271399	0.994000	0.37717	0.444000	0.26895	0.936000	0.57629	3.168000	0.50801	2.438000	0.82558	0.600000	0.82982	GCC	.	.		0.403	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			T	135443733	G	T	135443733	3	4	199	1	0	0	0	0	1	0	0	0	6637	1319	46	3	7298	3	GPR112	23	135443733	Missense_Mutation	SNP	G	TCGA-DD-AADQ-01A-11D-A40R-10	20580122	135443733	19826827	135	29361										
DUSP9	1852	hgsc.bcm.edu	37	chrX	152915517	152915517	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	8	1	1.15847476305929	0.836676217765043	1.22582794695809	0.0328502415458937	0.322451055174167	0	gtcaccgtcactgtggcctaCctcatgcagaagctccacct	8	16	3	1			TCGA-DD-AADQ-01A-11D-A40R-10	TCGA-DD-AADQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ad3707-975a-4455-a65c-976f9cc645ad	f1879db2-297f-44d1-b52f-3cbf282a8ecd	g.chrX:152915517C>T	ENST00000342782.3	+	4	1177	c.912C>T	c.(910-912)taC>taT	p.Y304Y	DUSP9_ENST00000370167.4_Silent_p.Y304Y			Q99956	DUS9_HUMAN	dual specificity phosphatase 9	304	Tyrosine-protein phosphatase.				inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTGTGGCCTACCTCATGCAGA	0.567																																					p.Y304Y		Atlas-SNP	.											.	DUSP9	41	.	0			c.C912T						.						271	232	245					X																	152915517		2203	4300	6503	SO:0001819	synonymous_variant	1852	exon4			GGCCTACCTCATG	Y08302	CCDS14724.1	Xq28	2011-06-09			ENSG00000130829	ENSG00000130829		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3076	protein-coding gene	gene with protein product	"map kinase phosphatase 4"	300134				9030581, 9286695	Standard	NM_001395		Approved	MKP-4, MKP4	uc004fhx.4	Q99956	OTTHUMG00000024211	ENST00000342782.3:c.912C>T	chrX.hg19:g.152915517C>T		84.0	0.0		83.0	63.0	NM_001395	D3DWU5	Silent	SNP	ENST00000342782.3	hg19	CCDS14724.1	.	.	.	.	.	.	.	.	.	.	c	10.29	1.310324	0.23821	.	.	ENSG00000130829	ENST00000433144	.	.	.	4.83	2.98	0.34508	.	.	.	.	.	T	0.56731	0.2005	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51980	-0.8636	4	.	.	.	.	8.1857	0.31337	0.1562:0.7547:0.0:0.0892	.	.	.	.	I	275	.	.	T	+	2	0	DUSP9	152568711	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.526000	0.45607	1.009000	0.39289	0.529000	0.55759	ACC	.	.		0.567	DUSP9-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061022.3	NM_001395		T	152915517	C	T	152915517	2	4	199	1	0	0	0	0	0	0	0	1	4834	518	18	3		3	DUSP9	23	152915517	Silent	SNP	C	TCGA-DD-AADQ-01A-11D-A40R-10	17471784	152915517	2355043	136	29362										
HP1BP3	50809	hgsc.bcm.edu	37	chr1	21072039	21072039	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ttttcacatgtccacaccttCtcttaggtggcggctcttca	7	13	4	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:21072039C>G	ENST00000312239.5	-	12	1503	c.1364G>C	c.(1363-1365)aGa>aCa	p.R455T	RP5-930J4.4_ENST00000413451.1_RNA|HP1BP3_ENST00000375003.2_Missense_Mutation_p.R303T	NM_016287.3	NP_057371.2	Q5SSJ5	HP1B3_HUMAN	heterochromatin protein 1, binding protein 3	455	Lys-rich.				nucleosome assembly (GO:0006334)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(2)|skin(2)|urinary_tract(1)	16		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		TCCACACCTTCTCTTAGGTGG	0.448																																					p.R455T		Atlas-SNP	.											.	HP1BP3	47	.	0			c.G1364C						.						109	96	101					1																	21072039		2203	4300	6503	SO:0001583	missense	50809	exon12			CACCTTCTCTTAG	BC053327	CCDS30621.1	1p36.12	2008-02-05			ENSG00000127483	ENSG00000127483			24973	protein-coding gene	gene with protein product						12477932	Standard	NM_016287		Approved	HP1-BP74	uc001bdw.1	Q5SSJ5	OTTHUMG00000002622	ENST00000312239.5:c.1364G>C	chr1.hg19:g.21072039C>G	ENSP00000312625:p.Arg455Thr	78.0	0.0		56.0	34.0	NM_016287	A6NI71|A8K5D7|B3KMZ8|B4E210|Q05BI0|Q5SSJ6|Q5SWC6|Q6PIM9|Q8NDF0|Q9UHY0	Missense_Mutation	SNP	ENST00000312239.5	hg19	CCDS30621.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.310845	0.60414	.	.	ENSG00000127483	ENST00000312239;ENST00000375004;ENST00000375003	T;T	0.52057	0.68;0.71	5.87	4.75	0.60458	.	0.273767	0.47093	D	0.000250	T	0.30727	0.0774	L	0.27053	0.805	0.80722	D	1	B	0.27498	0.18	B	0.24974	0.057	T	0.12016	-1.0564	10	0.41790	T	0.15	.	6.5213	0.22277	0.0:0.8336:0.0:0.1664	.	455	Q5SSJ5	HP1B3_HUMAN	T	455;417;303	ENSP00000312625:R455T;ENSP00000364142:R303T	ENSP00000312625:R455T	R	-	2	0	HP1BP3	20944626	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.517000	0.45529	2.941000	0.99782	0.655000	0.94253	AGA	.	.		0.448	HP1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007457.2	NM_016287		G	21072039	C	G	21072039	3	3	200	1	0	0	0	0	1	0	0	0	7337	913	32	4	305	4	HP1BP3	1	21072039	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10		21072039	228178582	1	29363										
ZNF436	80818	hgsc.bcm.edu	37	chr1	23689582	23689582	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gtctttctgacctatctccgCtttcaaagccctcttcactt	4	15	6	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:23689582C>T	ENST00000314011.4	-	4	429	c.293G>A	c.(292-294)aGc>aAc	p.S98N	ZNF436_ENST00000374608.3_Missense_Mutation_p.S98N	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	98					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		CCTATCTCCGCTTTCAAAGCC	0.443																																					p.S98N		Atlas-SNP	.											.	ZNF436	49	.	0			c.G293A						.						186	188	187					1																	23689582		2203	4300	6503	SO:0001583	missense	80818	exon4			TCTCCGCTTTCAA	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"Zinc fingers, C2H2-type", "-"	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.293G>A	chr1.hg19:g.23689582C>T	ENSP00000313582:p.Ser98Asn	105.0	0.0		57.0	34.0	NM_001077195	Q658I9	Missense_Mutation	SNP	ENST00000314011.4	hg19	CCDS233.1	.	.	.	.	.	.	.	.	.	.	C	1.135	-0.651148	0.03506	.	.	ENSG00000125945	ENST00000314011;ENST00000374609;ENST00000374608	T;T;T	0.06608	3.28;3.51;3.28	5.85	0.137	0.14787	.	0.751927	0.12633	N	0.452002	T	0.02807	0.0084	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47459	-0.9116	10	0.21014	T	0.42	-7.1493	5.3217	0.15885	0.0:0.3878:0.1439:0.4683	.	98	Q9C0F3	ZN436_HUMAN	N	98	ENSP00000313582:S98N;ENSP00000363737:S98N;ENSP00000363736:S98N	ENSP00000313582:S98N	S	-	2	0	ZNF436	23562169	0.000000	0.05858	0.034000	0.17996	0.769000	0.43574	-0.935000	0.03950	-0.145000	0.11294	0.655000	0.94253	AGC	.	.		0.443	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		T	23689582	C	T	23689582	3	4	200	1	0	0	0	0	1	0	0	0	17924	797	28	3	1123	3	ZNF436	1	23689582	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	2617543	23689582	225561039	2	29364										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27023388	27023388	+	Frame_Shift_Del	DEL	C	C	-													0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gtctgccgtcgccgccgccgCggccgccgtcttccaccaac							TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:27023388delC	ENST00000324856.7	+	1	865	c.494delC	c.(493-495)gcgfs	p.A167fs	RP5-968P14.2_ENST00000569378.1_RNA|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.A167fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	167					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCCGCCGCCGCGGCCGCCGTC	0.766			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.A165fs		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.493delG						.						2	3	3					1																	27023388		1260	2903	4163	SO:0001589	frameshift_variant	8289	exon1			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.494delC	chr1.hg19:g.27023388delC	ENSP00000320485:p.Ala167fs	69.0	0.0		36.0	18.0	NM_139135	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.766	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27023388	C	-	27023388	7	5	200	1	0	1	0	1	0	0	0	0	913	768	27	0	496	0	ARID1A	1	27023388	Frame_Shift_Del	DEL	C	TCGA-DD-AADR-01A-11D-A40R-10	3333806	27023388	222227233	3	29365										
TTLL7	79739	hgsc.bcm.edu	37	chr1	84386928	84386928	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tactttcttaaaactttcatAccaactcttctttccgcctc	1	14	4	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:84386928A>G	ENST00000260505.8	-	11	1668		c.e11+1		TTLL7_ENST00000477524.1_Splice_Site	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7						cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		AAACTTTCATACCAACTCTTC	0.388																																					.		Atlas-SNP	.											.	TTLL7	93	.	0			c.1290+2T>C						.						93	94	94					1																	84386928		2203	4299	6502	SO:0001630	splice_region_variant	79739	exon12			TTTCATACCAACT	AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"Tubulin tyrosine ligase-like family"	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.1290+1T>C	chr1.hg19:g.84386928A>G		107.0	0.0		108.0	41.0	NM_024686	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Splice_Site	SNP	ENST00000260505.8	hg19	CCDS690.2	.	.	.	.	.	.	.	.	.	.	A	23.5	4.423474	0.83559	.	.	ENSG00000137941	ENST00000260505;ENST00000370704;ENST00000370703	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5427	0.84406	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TTLL7	84159516	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.585000	0.90802	2.363000	0.80096	0.523000	0.50628	.	.	.		0.388	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686	Intron	G	84386928	A	G	84386928	5	3	200	1	0	0	0	0	0	0	1	0	16747	405	14	2	1415	2	TTLL7	1	84386928	Splice_Site	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	57363540	84386928	164863693	4	29366										
TMEM56	148534	hgsc.bcm.edu	37	chr1	95609526	95609526	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ttcacctttcagcttcttttCtactttgtaagttactggtt	5	9	4	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:95609526C>G	ENST00000370203.4	+	2	360	c.69C>G	c.(67-69)ttC>ttG	p.F23L	TMEM56_ENST00000463375.1_3'UTR|RP11-57H12.6_ENST00000604534.1_Missense_Mutation_p.F23L	NM_001199679.1|NM_152487.2	NP_001186608.1|NP_689700.1	Q96MV1	TMM56_HUMAN	transmembrane protein 56	23						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(2)|skin(1)|urinary_tract(1)	12		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.133)		AGCTTCTTTTCTACTTTGTAA	0.353																																					p.F23L		Atlas-SNP	.											.	TMEM56	24	.	0			c.C69G						.						110	109	109					1																	95609526		2202	4299	6501	SO:0001583	missense	148534	exon2			TCTTTTCTACTTT		CCDS753.1	1p21.3	2008-02-05			ENSG00000152078	ENSG00000152078			26477	protein-coding gene	gene with protein product							Standard	NM_152487		Approved	FLJ31842	uc001drb.3	Q96MV1	OTTHUMG00000010847	ENST00000370203.4:c.69C>G	chr1.hg19:g.95609526C>G	ENSP00000359222:p.Phe23Leu	148.0	0.0		118.0	51.0	NM_001199679	B2RPI2|D3DT48	Missense_Mutation	SNP	ENST00000370203.4	hg19	CCDS753.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.446642	0.84101	.	.	ENSG00000152078	ENST00000370203;ENST00000456991;ENST00000455656	.	.	.	5.45	5.45	0.79879	.	0.095798	0.64402	D	0.000001	T	0.78136	0.4236	M	0.82056	2.57	0.45806	D	0.998687	D;D	0.89917	1.0;0.985	D;P	0.77004	0.989;0.863	T	0.74697	-0.3578	8	0.24483	T	0.36	-24.5126	18.0671	0.89394	0.0:1.0:0.0:0.0	.	23;23	C9JJM2;Q96MV1	.;TMM56_HUMAN	L	23	.	ENSP00000359222:F23L	F	+	3	2	TMEM56	95382114	1.000000	0.71417	0.995000	0.50966	0.962000	0.63368	2.211000	0.42825	2.545000	0.85829	0.650000	0.86243	TTC	.	.		0.353	TMEM56-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029935.1	NM_152487		G	95609526	C	G	95609526	3	3	200	1	0	0	0	0	1	0	0	0	16198	912	32	4	71	4	TMEM56	1	95609526	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	11222598	95609526	153641095	5	29367										
AMPD1	270	hgsc.bcm.edu	37	chr1	115223060	115223060	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tttcaggaaggttgtctgttCggaaggggtcctctcccttc	12	10	3	0	rs149424604		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:115223060C>T	ENST00000520113.2	-	6	701	c.686G>A	c.(685-687)cGa>cAa	p.R229Q	AMPD1_ENST00000353928.6_Missense_Mutation_p.R196Q|AMPD1_ENST00000369538.3_Missense_Mutation_p.R225Q			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	229					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	GTTGTCTGTTCGGAAGGGGTC	0.423													C|||	1	0.000199681	0	0	5008	,	,		19044	0		0	False		,,,				2504	0.001				p.R229Q		Atlas-SNP	.											AMPD1_ENST00000520113,colon,carcinoma,0,4	AMPD1	223	.	0			c.G686A						.	C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	121	120	120		686,674	0.6	0.3	1	dbSNP_134	120	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	AMPD1	NM_000036.2,NM_001172626.1	43,43	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging	229/781,225/777	115223060	2,13004	2203	4300	6503	SO:0001583	missense	270	exon6			TCTGTTCGGAAGG	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.686G>A	chr1.hg19:g.115223060C>T	ENSP00000430075:p.Arg229Gln	146.0	0.0		119.0	31.0	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	hg19	CCDS876.2	.	.	.	.	.	.	.	.	.	.	C	10.79	1.450420	0.26074	2.27E-4	1.16E-4	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.86865	-2.18;-2.18;-2.18	6.07	0.651	0.17817	.	0.560054	0.20388	N	0.093306	T	0.62196	0.2408	L	0.33485	1.01	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	T	0.52866	-0.8518	10	0.20519	T	0.43	-0.3344	11.336	0.49505	0.0:0.5997:0.0:0.4003	.	225;196	Q5TF02;P23109	.;AMPD1_HUMAN	Q	229;225;196	ENSP00000430075:R229Q;ENSP00000358551:R225Q;ENSP00000316520:R196Q	ENSP00000316520:R196Q	R	-	2	0	AMPD1	115024583	0.003000	0.15002	0.273000	0.24645	0.985000	0.73830	0.135000	0.15952	-0.111000	0.12001	-0.224000	0.12420	CGA	.	C|1.000;T|0.000		0.423	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			T	115223060	C	T	115223060	3	4	200	1	0	0	0	0	1	0	0	0	585	884	31	1	1700	1	AMPD1	1	115223060	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	19613534	115223060	134027561	6	29368										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120484359	120484359	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tcactccatccatacaggaaCctccattctggcaaggatct	6	14	3	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:120484359C>A	ENST00000256646.2	-	18	2990	c.2771G>T	c.(2770-2772)gGt>gTt	p.G924V		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	924	EGF-like 24; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CATACAGGAACCTCCATTCTG	0.433			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.G924V		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.G2771T						.						59	56	57					1																	120484359		2203	4300	6503	SO:0001583	missense	4853	exon18	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CAGGAACCTCCAT	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.2771G>T	chr1.hg19:g.120484359C>A	ENSP00000256646:p.Gly924Val	268.0	0.0		280.0	109.0	NM_001200001	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	hg19	CCDS908.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.933683	0.73442	.	.	ENSG00000134250	ENST00000256646	D	0.97455	-4.39	6.08	4.16	0.48862	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.211734	0.23672	U	0.045707	D	0.98422	0.9475	H	0.95645	3.7	0.80722	D	1	P;D	0.52996	0.526;0.957	P;P	0.57324	0.61;0.818	D	0.99560	1.0968	10	0.87932	D	0	.	14.4364	0.67284	0.0:0.4895:0.5105:0.0	.	924;924	Q6IQ50;Q04721	.;NOTC2_HUMAN	V	924	ENSP00000256646:G924V	ENSP00000256646:G924V	G	-	2	0	NOTCH2	120285882	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	2.613000	0.46351	1.571000	0.49722	0.591000	0.81541	GGT	.	.		0.433	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		A	120484359	C	A	120484359	3	1	200	1	0	0	0	0	1	0	0	0	10557	507	18	3	4712	3	NOTCH2	1	120484359	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	5261299	120484359	128766262	7	29369										
PFDN2	5202	hgsc.bcm.edu	37	chr1	161070507	161070507	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ctccagctgagctggccttaGccccagccccttctgagttt	9	16	1	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:161070507G>T	ENST00000368010.3	-	4	515	c.431C>A	c.(430-432)gCt>gAt	p.A144D	PFDN2_ENST00000468311.1_5'UTR	NM_012394.3	NP_036526.2	Q9UHV9	PFD2_HUMAN	prefoldin subunit 2	144					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	unfolded protein binding (GO:0051082)			lung(1)|skin(1)	2	all_cancers(52;1.84e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			GCTGGCCTTAGCCCCAGCCCC	0.458																																					p.A144D		Atlas-SNP	.											.	PFDN2	10	.	0			c.C431A						.						110	105	107					1																	161070507		2203	4300	6503	SO:0001583	missense	5202	exon4			GCCTTAGCCCCAG	AF165883	CCDS1217.1	1q23.3	2008-02-05	2006-02-24		ENSG00000143256	ENSG00000143256			8867	protein-coding gene	gene with protein product		613466	"prefoldin 2"			10051400	Standard	NM_012394		Approved		uc001fxu.3	Q9UHV9	OTTHUMG00000031481	ENST00000368010.3:c.431C>A	chr1.hg19:g.161070507G>T	ENSP00000356989:p.Ala144Asp	140.0	0.0		128.0	6.0	NM_012394	Q9P0P7|Q9UN05	Missense_Mutation	SNP	ENST00000368010.3	hg19	CCDS1217.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.985728	0.35036	.	.	ENSG00000143256	ENST00000368010	.	.	.	5.24	5.24	0.73138	.	0.112377	0.64402	D	0.000013	T	0.29882	0.0747	N	0.22421	0.69	0.46336	D	0.99899	B	0.31893	0.345	B	0.34180	0.177	T	0.13282	-1.0515	9	0.15066	T	0.55	-5.9868	16.3815	0.83462	0.0:0.0:1.0:0.0	.	144	Q9UHV9	PFD2_HUMAN	D	144	.	ENSP00000356989:A144D	A	-	2	0	PFDN2	159337131	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.817000	0.86213	2.724000	0.93272	0.561000	0.74099	GCT	.	.		0.458	PFDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077100.1	NM_012394		T	161070507	G	T	161070507	3	4	200	1	0	0	0	0	1	0	0	0	11765	971	34	3	37	3	PFDN2	1	161070507	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	40586148	161070507	88180114	8	29370										
C1orf226	400793	hgsc.bcm.edu	37	chr1	162353116	162353116	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ctggagtatgggacagagccAtcacctgggcaggcccagga	15	11	1	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:162353116A>G	ENST00000458626.2	+	2	634	c.462A>G	c.(460-462)ccA>ccG	p.P154P	C1orf226_ENST00000426197.2_Silent_p.P197P	NM_001085375.1	NP_001078844.1	A1L170	CA226_HUMAN	chromosome 1 open reading frame 226	154										central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12						GGACAGAGCCATCACCTGGGC	0.602																																					p.P197P		Atlas-SNP	.											.	C1orf226	49	.	0			c.A591G						.						35	39	38					1																	162353116		1997	4169	6166	SO:0001819	synonymous_variant	400793	exon3			AGAGCCATCACCT	AI480219, AK023199, AK125122, AL512785, BC127743	CCDS44268.1, CCDS53422.1	1q23.3	2013-10-11			ENSG00000239887	ENSG00000239887			34351	protein-coding gene	gene with protein product						14702039	Standard	NM_001085375		Approved	FLJ13137	uc010pkt.1	A1L170	OTTHUMG00000031376	ENST00000458626.2:c.462A>G	chr1.hg19:g.162353116A>G		170.0	0.0		191.0	73.0	NM_001135240	B4DF31	Silent	SNP	ENST00000458626.2	hg19	CCDS53422.1																																																																																			.	.		0.602	C1orf226-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076793.2	NM_001085375		G	162353116	A	G	162353116	2	3	200	1	0	0	0	0	0	0	0	1	2034	204	8	2		2	C1orf226	1	162353116	Silent	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	1282609	162353116	86897505	9	29371										
NVL	4931	hgsc.bcm.edu	37	chr1	224415337	224415337	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tgctggagacatcaccggctGagggactcctgcaaacgttc	12	12	1	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:224415337G>A	ENST00000281701.6	-	23	2821	c.2562C>T	c.(2560-2562)ctC>ctT	p.L854L	NVL_ENST00000340871.4_Silent_p.L665L|NVL_ENST00000482491.1_Silent_p.L578L|NVL_ENST00000391875.2_Silent_p.L748L|NVL_ENST00000469075.1_Silent_p.L763L|RP11-365O16.6_ENST00000420350.1_RNA	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	854						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		ATCACCGGCTGAGGGACTCCT	0.547																																					p.L854L		Atlas-SNP	.											.	NVL	74	.	0			c.C2562T						.						60	56	57					1																	224415337		2203	4300	6503	SO:0001819	synonymous_variant	4931	exon23			CCGGCTGAGGGAC	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"ATPases / AAA-type"	8070	protein-coding gene	gene with protein product	"Nuclear valosin-containing protein-like", "nuclear VCP-like protein"	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.2562C>T	chr1.hg19:g.224415337G>A		420.0	0.0		362.0	103.0	NM_002533	B4DMC4|B4DP98|Q96EM7	Silent	SNP	ENST00000281701.6	hg19	CCDS1541.1	.	.	.	.	.	.	.	.	.	.	G	7.535	0.659437	0.14645	.	.	ENSG00000143748	ENST00000469968	.	.	.	4.9	1.7	0.24286	.	.	.	.	.	.	.	.	.	.	.	0.48571	D	0.99967	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.3407	6.6129	0.22761	0.0974:0.3502:0.5523:0.0	.	.	.	.	X	737	.	.	Q	-	1	0	NVL	222481960	0.360000	0.24964	0.262000	0.24481	0.302000	0.27658	0.335000	0.19806	0.560000	0.29169	0.655000	0.94253	CAG	.	.		0.547	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533		A	224415337	G	A	224415337	2	1	200	1	0	0	0	0	0	0	0	1	10789	1277	45	3		3	NVL	1	224415337	Silent	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	62062221	224415337	24835284	10	29372										
EXOC8	149371	hgsc.bcm.edu	37	chr1	231472537	231472537	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tacctcaggaacagctggttCttcttcttcgtcatcctcaa	6	13	6	0	rs144793875	byFrequency	TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:231472537C>A	ENST00000360394.2	-	1	1041	c.955G>T	c.(955-957)Gaa>Taa	p.E319*	SPRTN_ENST00000295050.7_5'Flank|SPRTN_ENST00000008440.9_5'Flank|EXOC8_ENST00000366645.1_Nonsense_Mutation_p.E315*|SPRTN_ENST00000391858.4_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	319	Poly-Glu.				cellular protein localization (GO:0034613)|cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(2)|endometrium(1)|large_intestine(2)|liver(1)|lung(5)|prostate(1)|skin(1)|stomach(1)	14	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				ACAGCTGGTTCTTCTTCTTCG	0.552																																					p.E319X		Atlas-SNP	.											.	EXOC8	42	.	0			c.G955T						.						139	122	128					1																	231472537		2203	4300	6503	SO:0001587	stop_gained	149371	exon1			CTGGTTCTTCTTC	AL117352	CCDS1593.1	1q42.2	2013-01-22			ENSG00000116903	ENSG00000116903			24659	protein-coding gene	gene with protein product		615283				12477932	Standard	NM_175876		Approved	SEC84, EXO84, Exo84p	uc001huq.3	Q8IYI6	OTTHUMG00000038025	ENST00000360394.2:c.955G>T	chr1.hg19:g.231472537C>A	ENSP00000353564:p.Glu319*	98.0	0.0		95.0	36.0	NM_175876	B3KU33|Q5TE82	Nonsense_Mutation	SNP	ENST00000360394.2	hg19	CCDS1593.1	.	.	.	.	.	.	.	.	.	.	C	36	5.960066	0.97145	.	.	ENSG00000116903	ENST00000360394;ENST00000366645	.	.	.	5.55	4.62	0.57501	.	0.268239	0.28940	N	0.013649	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-13.2016	15.9135	0.79491	0.0:0.8641:0.1359:0.0	.	.	.	.	X	319;315	.	ENSP00000353564:E319X	E	-	1	0	EXOC8	229539160	1.000000	0.71417	0.131000	0.22000	0.852000	0.48524	7.017000	0.76399	1.287000	0.44583	0.561000	0.74099	GAA	.	C|0.997;G|0.003		0.552	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876		A	231472537	C	A	231472537	4	1	200	1	0	0	0	0	0	1	0	0	5313	922	32	3	1226	3	EXOC8	1	231472537	Nonsense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	7057200	231472537	17778084	11	29373										
LYST	1130	hgsc.bcm.edu	37	chr1	235916449	235916451	+	In_Frame_Del	DEL	AGA	AGA	-													0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	aacaagaatttaaaatttggAgaagaagtaaaagagcatta							TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:235916449_235916451delAGA	ENST00000389794.3	-	26	7527_7529	c.7353_7355delTCT	c.(7351-7356)cttctc>ctc	p.2451_2452LL>L	LYST_ENST00000389793.2_In_Frame_Del_p.2451_2452LL>L			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2451	Poly-Leu.				blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TAAAATTTGGAGAAGAAGTAAAA	0.365																																					p.2452_2452del		Atlas-INDEL	.											.,1	LYST	370	.	0			c.7354_7356del						.			14,4252		7,0,2126						-2.1	1			69	29,8213		14,1,4106	no	coding	LYST	NM_000081.2		21,1,6232	A1A1,A1R,RR		0.3519,0.3282,0.3438				43,12465				SO:0001651	inframe_deletion	1130	exon26			.	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.7353_7355delTCT	chr1.hg19:g.235916452_235916454delAGA	ENSP00000374444:p.Leu2452del	381.0	0.0		375.0	118.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	In_Frame_Del	DEL	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.365	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			-	235916451	AGA	-	235916449	7	5	200	1	0	1	0	1	0	0	0	0	9137	304	11	0	4162	0	LYST	1	235916449	In_Frame_Del	DEL	AGA	TCGA-DD-AADR-01A-11D-A40R-10	4443912	235916449	13334172	12	29374										
MOGS	7841	hgsc.bcm.edu	37	chr2	74692368	74692368	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gcggcgccgccgctcgccccGagccatcctggcactgaggt	14	18	0	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:74692368G>A	ENST00000233616.4	-	1	169	c.7C>T	c.(7-9)Cgg>Tgg	p.R3W	MOGS_ENST00000535045.1_Missense_Mutation_p.R3W|MOGS_ENST00000452063.2_Intron|MOGS_ENST00000409065.1_Missense_Mutation_p.R3W|MOGS_ENST00000462443.1_Intron	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	3					cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						CGCTCGCCCCGAGCCATCCTG	0.781																																					p.R3W		Atlas-SNP	.											.	MOGS	58	.	0			c.C7T						.						5	6	5					2																	74692368		1176	2657	3833	SO:0001583	missense	7841	exon1			CGCCCCGAGCCAT	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"glucosidase I", "processing A-glucosidase I"	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.7C>T	chr2.hg19:g.74692368G>A	ENSP00000233616:p.Arg3Trp	249.0	1.0		187.0	86.0	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	hg19	CCDS42700.1	.	.	.	.	.	.	.	.	.	.	G	35	5.459894	0.96240	.	.	ENSG00000115275	ENST00000233616;ENST00000409065;ENST00000535045	T	0.42900	0.96	4.72	4.72	0.59763	.	0.154600	0.39274	N	0.001408	T	0.43277	0.1240	N	0.08118	0	0.39413	D	0.966781	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.948	T	0.54879	-0.8227	10	0.87932	D	0	-20.6456	13.0502	0.58950	0.0:0.0:1.0:0.0	.	3;3	B4E3B8;Q13724	.;MOGS_HUMAN	W	3	ENSP00000233616:R3W	ENSP00000233616:R3W	R	-	1	2	MOGS	74545876	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.432000	0.59922	2.448000	0.82819	0.643000	0.83706	CGG	.	.		0.781	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302		A	74692368	G	A	74692368	3	1	200	1	0	0	0	0	1	0	0	0	9706	1057	37	1	2522	1	MOGS	2	74692368	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10		74692368	168507005	13	29375										
C2orf65	130951	hgsc.bcm.edu	37	chr2	74842177	74842177	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gagcccatcctctactgccaGccgcagagaagcaccttgtg	10	15	1	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:74842177G>A	ENST00000290536.5	-	3	456	c.340C>T	c.(340-342)Ctg>Ttg	p.L114L	M1AP_ENST00000409585.1_Silent_p.L114L|M1AP_ENST00000358434.2_5'UTR|M1AP_ENST00000536235.1_Silent_p.L114L	NM_001281296.1|NM_138804.3	NP_001268225.1|NP_620159.2	Q8TC57	M1AP_HUMAN	meiosis 1 associated protein	114					cell differentiation (GO:0030154)|chromatin assembly (GO:0031497)|female gamete generation (GO:0007292)|male meiosis chromosome separation (GO:0051308)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											TCTACTGCCAGCCGCAGAGAA	0.512																																					p.L114L		Atlas-SNP	.											.	.	.	.	0			c.C340T						.						186	161	170					2																	74842177		2203	4300	6503	SO:0001819	synonymous_variant	130951	exon3			CTGCCAGCCGCAG		CCDS33229.1, CCDS62941.1	2p13.1	2013-02-05	2013-02-05	2013-01-16	ENSG00000159374	ENSG00000159374			25183	protein-coding gene	gene with protein product	"meiosis 1 arresting protein", "spermatogenesis associated 37"		"chromosome 2 open reading frame 65"	C2orf65		16881047, 23269666	Standard	NM_138804		Approved	D6Mm5e, SPATA37	uc002smy.3	Q8TC57	OTTHUMG00000152918	ENST00000290536.5:c.340C>T	chr2.hg19:g.74842177G>A		127.0	0.0		112.0	42.0	NM_138804	B7Z6E7|E9PGG8|Q6ZP30|Q96L07	Silent	SNP	ENST00000290536.5	hg19	CCDS33229.1																																																																																			.	.		0.512	M1AP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328569.1	NM_138804		A	74842177	G	A	74842177	2	1	200	1	0	0	0	0	0	0	0	1	2186	962	34	3		3	C2orf65	2	74842177	Silent	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	149809	74842177	168357196	14	29376										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166172100	166172100	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tccaaaagtgaaaaagagctGaaaaacagaagaaagaaaaa	8	4	0	6	rs267598958		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:166172100G>T	ENST00000375437.2	+	11	1793	c.1503G>T	c.(1501-1503)ctG>ctT	p.L501L	SCN2A_ENST00000283256.6_Silent_p.L501L|SCN2A_ENST00000375427.2_Silent_p.L501L|SCN2A_ENST00000357398.3_Silent_p.L501L	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	501					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAAAAGAGCTGAaaaacagaa	0.393																																					p.L501L		Atlas-SNP	.											.	SCN2A	589	.	0			c.G1503T						.						44	47	46					2																	166172100		2203	4300	6503	SO:0001819	synonymous_variant	6326	exon10			AGAGCTGAAAAAC	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.1503G>T	chr2.hg19:g.166172100G>T		178.0	0.0		155.0	53.0	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	hg19	CCDS33314.1																																																																																			.	.		0.393	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166172100	G	T	166172100	2	4	200	1	0	0	0	0	0	0	0	1	13931	1277	45	3		3	SCN2A	2	166172100	Silent	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	91329923	166172100	77027273	15	29377										
TTN	7273	hgsc.bcm.edu	37	chr2	179474547	179474547	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gtataggtcaggattggtacCaggtgttcattgcatctctt	11	7	3	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:179474547C>A	ENST00000591111.1	-	222	46904	c.46680G>T	c.(46678-46680)ctG>ctT	p.L15560L	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Silent_p.L14633L|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.L8328L|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Silent_p.L17201L|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Silent_p.L8261L|TTN_ENST00000460472.2_Silent_p.L8136L			Q8WZ42	TITIN_HUMAN	titin	15560	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGATTGGTACCAGGTGTTCAT	0.478																																					p.L17201L		Atlas-SNP	.											.	TTN	18412	.	0			c.G51603T						.						447	426	433					2																	179474547		1926	4144	6070	SO:0001819	synonymous_variant	7273	exon272			TGGTACCAGGTGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.46680G>T	chr2.hg19:g.179474547C>A		186.0	0.0		159.0	35.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179474547	C	A	179474547	2	1	200	1	0	0	0	0	0	0	0	1	16750	581	21	3		3	TTN	2	179474547	Silent	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	13302447	179474547	63724826	16	29378										
ABI2	10152	hgsc.bcm.edu	37	chr2	204267450	204267450	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ggaggacctttttatagccaGaatccaggttagtttttttg	10	6	0	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:204267450G>C	ENST00000422511.2	+	9	1117	c.1086G>C	c.(1084-1086)caG>caC	p.Q362H	ABI2_ENST00000261017.5_Missense_Mutation_p.Q328H|ABI2_ENST00000430418.1_Missense_Mutation_p.Q340H|ABI2_ENST00000261016.6_Missense_Mutation_p.Q283H|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000424558.1_Missense_Mutation_p.Q389H|ABI2_ENST00000430574.1_3'UTR|ABI2_ENST00000295851.5_Missense_Mutation_p.Q395H|ABI2_ENST00000261018.7_Missense_Mutation_p.Q181H			Q9NYB9	ABI2_HUMAN	abl-interactor 2	395	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						TTTATAGCCAGAATCCAGGTT	0.373																																					p.Q328H		Atlas-SNP	.											ABI2,colon,carcinoma,0,1	ABI2	44	.	0			c.G984C						.						102	100	101					2																	204267450		2203	4300	6503	SO:0001583	missense	10152	exon7			TAGCCAGAATCCA	AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443			24011	protein-coding gene	gene with protein product		606442				7590236, 10964520	Standard	XM_005246217		Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.1086G>C	chr2.hg19:g.204267450G>C	ENSP00000396249:p.Gln362His	191.0	0.0		165.0	58.0	NM_005759	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	Missense_Mutation	SNP	ENST00000422511.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.104458|4.104458	0.77096|0.77096	.|.	.|.	ENSG00000138443|ENSG00000138443	ENST00000295851;ENST00000261017;ENST00000430418;ENST00000424558;ENST00000261016;ENST00000417864;ENST00000422511;ENST00000261018|ENST00000451591;ENST00000454023	T;T;T;T;T;T;T;T|.	0.48836|.	1.02;1.08;1.16;1.02;0.93;1.25;1.07;0.8|.	5.6|5.6	4.72|4.72	0.59763|0.59763	.|.	0.050825|.	0.85682|.	D|.	0.000000|.	T|T	0.64962|0.64962	0.2646|0.2646	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	B;D;D;D;D;D;D;D;P|.	0.69078|.	0.435;0.997;0.99;0.995;0.988;0.976;0.995;0.98;0.816|.	B;D;D;P;D;D;D;D;P|.	0.77004|.	0.109;0.921;0.979;0.862;0.977;0.923;0.989;0.948;0.866|.	T|T	0.62872|0.62872	-0.6762|-0.6762	10|5	0.87932|.	D|.	0|.	-9.7717|-9.7717	12.2155|12.2155	0.54404|0.54404	0.078:0.0:0.922:0.0|0.078:0.0:0.922:0.0	.|.	181;230;120;272;389;340;283;395;328|.	B7Z5L1;B7Z612;B4DMM5;B7Z836;Q9NYB9-4;E9PEZ7;Q9NYB9-3;Q9NYB9;Q9NYB9-2|.	.;.;.;.;.;.;.;ABI2_HUMAN;.|.	H|T	395;328;340;389;283;395;362;181|199;175	ENSP00000295851:Q395H;ENSP00000261017:Q328H;ENSP00000408898:Q340H;ENSP00000391433:Q389H;ENSP00000261016:Q283H;ENSP00000414703:Q395H;ENSP00000396249:Q362H;ENSP00000261018:Q181H|.	ENSP00000261016:Q283H|.	Q|R	+|+	3|2	2|0	ABI2|ABI2	203975695|203975695	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.249000|5.249000	0.65427|0.65427	2.636000|2.636000	0.89361|0.89361	0.655000|0.655000	0.94253|0.94253	CAG|AGA	.	.		0.373	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000336179.2	NM_005759		C	204267450	G	C	204267450	3	2	200	1	0	0	0	0	1	0	0	0	89	933	33	4	1010	4	ABI2	2	204267450	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	24792903	204267450	38931923	17	29379										
PSMD1	5707	hgsc.bcm.edu	37	chr2	232028365	232028365	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tcagatgccgaaagttcagtAtaaatcgaactgtaaaccat	7	8	2	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:232028365A>G	ENST00000308696.6	+	21	2567	c.2405A>G	c.(2404-2406)tAt>tGt	p.Y802C	PSMD1_ENST00000373635.4_Intron|PSMD1_ENST00000409643.1_Intron	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	802					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	AAAGTTCAGTATAAATCGAAC	0.383																																					p.Y802C		Atlas-SNP	.											.	PSMD1	77	.	0			c.A2405G						.						110	108	108					2																	232028365		2203	4300	6503	SO:0001583	missense	5707	exon21			TTCAGTATAAATC	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.2405A>G	chr2.hg19:g.232028365A>G	ENSP00000309474:p.Tyr802Cys	122.0	0.0		81.0	33.0	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	hg19	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.130568	0.77549	.	.	ENSG00000173692	ENST00000308696	.	.	.	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.63757	0.2538	L	0.59436	1.845	0.80722	D	1	D	0.59357	0.985	P	0.51193	0.662	T	0.69379	-0.5161	9	0.87932	D	0	-13.8533	14.5377	0.67973	1.0:0.0:0.0:0.0	.	802	Q99460	PSMD1_HUMAN	C	802	.	ENSP00000309474:Y802C	Y	+	2	0	PSMD1	231736609	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.139000	0.94554	2.002000	0.58637	0.454000	0.30748	TAT	.	.		0.383	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			G	232028365	A	G	232028365	3	3	200	1	0	0	0	0	1	0	0	0	12704	449	16	2	2487	2	PSMD1	2	232028365	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	27760915	232028365	11171008	18	29380										
ALPI	248	hgsc.bcm.edu	37	chr2	233323747	233323747	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tctggagccctacacggcctGcgacctggcgcctcccgcct	11	19	1	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:233323747G>A	ENST00000295463.3	+	11	1555	c.1478G>A	c.(1477-1479)tGc>tAc	p.C493Y		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	493					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TACACGGCCTGCGACCTGGCG	0.726																																					p.C493Y		Atlas-SNP	.											.	ALPI	64	.	0			c.G1478A						.						18	18	18					2																	233323747		2136	4212	6348	SO:0001583	missense	248	exon11			CGGCCTGCGACCT	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.1478G>A	chr2.hg19:g.233323747G>A	ENSP00000295463:p.Cys493Tyr	121.0	0.0		76.0	37.0	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Missense_Mutation	SNP	ENST00000295463.3	hg19	CCDS2492.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248887	0.80024	.	.	ENSG00000163295	ENST00000295463	D	0.95690	-3.78	4.84	4.84	0.62591	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.217378	0.49305	D	0.000157	D	0.95802	0.8634	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	D	0.96792	0.9583	10	0.62326	D	0.03	.	17.9391	0.89021	0.0:0.0:1.0:0.0	.	493	P09923	PPBI_HUMAN	Y	493	ENSP00000295463:C493Y	ENSP00000295463:C493Y	C	+	2	0	ALPI	233031991	1.000000	0.71417	0.117000	0.21633	0.051000	0.14879	4.944000	0.63561	2.213000	0.71641	0.591000	0.81541	TGC	.	.		0.726	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631		A	233323747	G	A	233323747	3	1	200	1	0	0	0	0	1	0	0	0	543	1319	46	3	1520	3	ALPI	2	233323747	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	1295382	233323747	9875626	19	29381										
IL17RC	84818	hgsc.bcm.edu	37	chr3	9975230	9975230	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cggggactcccgcgccgggaCgcggggtgggaccaggcgcg	21	14	0	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:9975230C>T	ENST00000295981.3	+	19	2547	c.2329C>T	c.(2329-2331)Cgc>Tgc	p.R777C	IL17RC_ENST00000403601.3_Missense_Mutation_p.R706C|IL17RC_ENST00000416074.2_Missense_Mutation_p.R532C|RP11-1020A11.1_ENST00000602411.1_RNA|CRELD1_ENST00000397170.3_5'Flank|CRELD1_ENST00000383811.3_5'Flank|CRELD1_ENST00000326434.5_5'Flank|IL17RC_ENST00000413608.1_Missense_Mutation_p.R693C|IL17RC_ENST00000498214.1_3'UTR|CRELD1_ENST00000452070.1_5'Flank|IL17RC_ENST00000383812.4_Missense_Mutation_p.R691C|IL17RC_ENST00000455057.1_Missense_Mutation_p.R674C	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	777					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CGCGCCGGGACGCGGGGTGGG	0.672																																					p.R777C		Atlas-SNP	.											.	IL17RC	55	.	0			c.C2329T						.						6	8	8					3																	9975230		1761	3844	5605	SO:0001583	missense	84818	exon19			CCGGGACGCGGGG	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"Interleukins and interleukin receptors"	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.2329C>T	chr3.hg19:g.9975230C>T	ENSP00000295981:p.Arg777Cys	104.0	0.0		80.0	22.0	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	hg19	CCDS2590.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.928411	0.34002	.	.	ENSG00000163702	ENST00000383812;ENST00000295981;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T	0.47528	1.83;1.81;1.83;0.84;1.83	4.22	-1.66	0.08265	.	3.416830	0.01360	N	0.012212	T	0.32912	0.0845	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B;B;B	0.09022	0.001;0.001;0.001;0.001;0.001;0.001;0.002;0.001	B;B;B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.0;0.001;0.0;0.001	T	0.34079	-0.9843	10	0.72032	D	0.01	1.8744	5.5264	0.16960	0.0:0.2842:0.4943:0.2215	.	532;674;676;693;532;691;777;706	F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;B4E008;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;I17RC_HUMAN;.	C	691;777;706;532;674;693	ENSP00000373323:R691C;ENSP00000295981:R777C;ENSP00000384969:R706C;ENSP00000407894:R674C;ENSP00000396064:R693C	ENSP00000295981:R777C	R	+	1	0	IL17RC	9950230	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.088000	0.14979	-0.113000	0.11958	-0.266000	0.10368	CGC	.	.		0.672	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		T	9975230	C	T	9975230	3	4	200	1	0	0	0	0	1	0	0	0	7650	536	19	1	2403	1	IL17RC	3	9975230	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10		9975230	188047200	20	29382										
SATB1	6304	hgsc.bcm.edu	37	chr3	18390666	18390666	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	aacaaatacttttatctcagTctttcaaatcagtattaatg	3	7	4	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:18390666T>C	ENST00000338745.6	-	11	4022	c.2288A>G	c.(2287-2289)gAc>gGc	p.D763G	TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Missense_Mutation_p.D763G|SATB1_ENST00000417717.2_Missense_Mutation_p.D795G	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	763					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						TTTATCTCAGTCTTTCAAATC	0.353																																					p.D795G		Atlas-SNP	.											.	SATB1	96	.	0			c.A2384G						.						104	101	102					3																	18390666		2203	4300	6503	SO:0001583	missense	6304	exon12			TCTCAGTCTTTCA		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.2288A>G	chr3.hg19:g.18390666T>C	ENSP00000341024:p.Asp763Gly	138.0	0.0		125.0	42.0	NM_001195470	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	T	4.989	0.183690	0.09495	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	T;T;T	0.55052	0.62;0.62;0.54	5.7	5.7	0.88788	.	0.107977	0.64402	D	0.000009	T	0.41259	0.1151	N	0.19112	0.55	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.001	T	0.26677	-1.0096	10	0.66056	D	0.02	-10.4461	15.9579	0.79902	0.0:0.0:0.0:1.0	.	795;763	Q01826-2;Q01826	.;SATB1_HUMAN	G	763;763;795	ENSP00000341024:D763G;ENSP00000399708:D763G;ENSP00000399518:D795G	ENSP00000341024:D763G	D	-	2	0	SATB1	18365670	1.000000	0.71417	1.000000	0.80357	0.146000	0.21551	6.979000	0.76154	2.178000	0.69098	0.533000	0.62120	GAC	.	.		0.353	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		C	18390666	T	C	18390666	3	2	200	1	0	0	0	0	1	0	0	0	13868	1667	58	2	7	2	SATB1	3	18390666	Missense_Mutation	SNP	T	TCGA-DD-AADR-01A-11D-A40R-10	8415436	18390666	179631764	21	29383										
RNF123	63891	hgsc.bcm.edu	37	chr3	49753432	49753432	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cctctgagatgctgctgcggCgtcttgcacaggtgtggcca	14	12	2	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:49753432C>T	ENST00000327697.6	+	33	3472	c.3328C>T	c.(3328-3330)Cgt>Tgt	p.R1110C	RNF123_ENST00000433785.1_Missense_Mutation_p.R222C	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	1110					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GCTGCTGCGGCGTCTTGCACA	0.602																																					p.R1110C		Atlas-SNP	.											.	RNF123	100	.	0			c.C3328T						.						100	94	96					3																	49753432		2203	4300	6503	SO:0001583	missense	63891	exon33			CTGCGGCGTCTTG	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.3328C>T	chr3.hg19:g.49753432C>T	ENSP00000328287:p.Arg1110Cys	48.0	0.0		51.0	23.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496586	0.85069	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000433785	D	0.84730	-1.89	5.97	5.07	0.68467	.	0.051043	0.85682	D	0.000000	D	0.90899	0.7140	M	0.67700	2.07	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.91249	0.5028	10	0.87932	D	0	-13.933	14.3919	0.66986	0.2506:0.7494:0.0:0.0	.	1110	Q5XPI4	RN123_HUMAN	C	1110;1110;222	ENSP00000328287:R1110C	ENSP00000328287:R1110C	R	+	1	0	RNF123	49728436	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.474000	0.60203	2.828000	0.97474	0.655000	0.94253	CGT	.	.		0.602	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		T	49753432	C	T	49753432	3	4	200	1	0	0	0	0	1	0	0	0	13448	768	27	1	3454	1	RNF123	3	49753432	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	31362766	49753432	148268998	22	29384										
MST1R	4486	hgsc.bcm.edu	37	chr3	49932696	49932696	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cgcagagtccaggtcccttaGctggatggactctttccgca	11	13	1	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:49932696G>A	ENST00000296474.3	-	14	3202	c.3175C>T	c.(3175-3177)Cta>Tta	p.L1059L	MST1R_ENST00000344206.4_Silent_p.L1010L	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	1059					cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		AGGTCCCTTAGCTGGATGGAC	0.542																																					p.L1059L		Atlas-SNP	.											.	MST1R	205	.	0			c.C3175T						.						166	163	164					3																	49932696		2203	4300	6503	SO:0001819	synonymous_variant	4486	exon14			CCCTTAGCTGGAT	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.3175C>T	chr3.hg19:g.49932696G>A		114.0	0.0		146.0	43.0	NM_002447	B5A944|B5A945|B5A946|B5A947	Silent	SNP	ENST00000296474.3	hg19	CCDS2807.1																																																																																			.	.		0.542	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			A	49932696	G	A	49932696	2	1	200	1	0	0	0	0	0	0	0	1	9900	962	34	3		3	MST1R	3	49932696	Silent	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	179264	49932696	148089734	23	29385										
CPOX	1371	hgsc.bcm.edu	37	chr3	98299597	98299597	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ctttggaattctctgagggtGaatgcatgtactcccatcta	9	9	2	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:98299597G>A	ENST00000264193.2	-	7	1513	c.1295C>T	c.(1294-1296)tCa>tTa	p.S432L		NM_000097.5	NP_000088.3	P36551	HEM6_HUMAN	coproporphyrinogen oxidase	432					heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to arsenic-containing substance (GO:0046685)|response to insecticide (GO:0017085)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to methylmercury (GO:0051597)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	coproporphyrinogen oxidase activity (GO:0004109)|protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						CTCTGAGGGTGAATGCATGTA	0.403																																					p.S432L	Esophageal Squamous(75;7 1223 22300 43648 48951)	Atlas-SNP	.											.	CPOX	34	.	0			c.C1295T						.						82	72	76					3																	98299597		2203	4300	6503	SO:0001583	missense	1371	exon7			GAGGGTGAATGCA	BC017210	CCDS2932.1	3q12	2012-10-02		2004-01-30		ENSG00000080819	1.3.3.3		2321	protein-coding gene	gene with protein product	"coproporphyria"	612732	"coproporphyrinogen oxidase (coproporphyria, harderoporphyria)"	CPO		7757079, 8407975	Standard	NM_000097		Approved	CPX, HCP	uc003dsx.3	P36551		ENST00000264193.2:c.1295C>T	chr3.hg19:g.98299597G>A	ENSP00000264193:p.Ser432Leu	111.0	0.0		105.0	30.0	NM_000097	A8K275|B4DSD5|Q14060|Q53F08|Q8IZ45|Q96AF3	Missense_Mutation	SNP	ENST00000264193.2	hg19	CCDS2932.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.558600	0.45590	.	.	ENSG00000080819	ENST00000264193	D	0.93247	-3.19	5.62	4.75	0.60458	.	0.285416	0.39407	N	0.001363	D	0.89332	0.6685	L	0.45581	1.43	0.28967	N	0.889478	B	0.10296	0.003	B	0.12837	0.008	T	0.82546	-0.0403	10	0.44086	T	0.13	-6.4579	8.5325	0.33344	0.1742:0.0:0.8258:0.0	.	432	P36551	HEM6_HUMAN	L	432	ENSP00000264193:S432L	ENSP00000264193:S432L	S	-	2	0	CPOX	99782287	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.130000	0.50508	1.361000	0.45981	0.655000	0.94253	TCA	.	.		0.403	CPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358900.1	NM_000097		A	98299597	G	A	98299597	3	1	200	1	0	0	0	0	1	0	0	0	3823	1294	45	3	73	3	CPOX	3	98299597	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	48366901	98299597	99722833	24	29386										
POLQ	10721	hgsc.bcm.edu	37	chr3	121208342	121208342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	actagtggcctgacaagtcaCatttttactctgagatcctg	8	10	2	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:121208342C>T	ENST00000264233.5	-	16	3564	c.3436G>A	c.(3436-3438)Gtg>Atg	p.V1146M		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1146					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TGACAAGTCACATTTTTACTC	0.353								DNA polymerases (catalytic subunits)																													p.V1146M	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G3436A						.						129	128	129					3																	121208342		2203	4300	6503	SO:0001583	missense	10721	exon16			AAGTCACATTTTT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.3436G>A	chr3.hg19:g.121208342C>T	ENSP00000264233:p.Val1146Met	140.0	0.0		119.0	45.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	2.541	-0.306331	0.05458	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.51574	0.7	5.24	-2.31	0.06765	.	1.657830	0.03438	N	0.208881	T	0.29620	0.0739	N	0.14661	0.345	0.09310	N	1	B;B	0.22480	0.07;0.003	B;B	0.15870	0.014;0.009	T	0.20371	-1.0277	10	0.39692	T	0.17	.	7.3718	0.26806	0.0:0.5966:0.11:0.2934	.	1146;318	O75417;O75417-2	DPOLQ_HUMAN;.	M	769;1146;1282	ENSP00000264233:V1146M	ENSP00000264233:V1146M	V	-	1	0	POLQ	122691032	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.450000	0.06803	-0.331000	0.08501	-0.471000	0.05019	GTG	.	.		0.353	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121208342	C	T	121208342	3	4	200	1	0	0	0	0	1	0	0	0	12217	478	17	3	4396	3	POLQ	3	121208342	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	22908745	121208342	76814088	25	29387										
OSBPL11	114885	hgsc.bcm.edu	37	chr3	125271474	125271474	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gatgagacataaagtctgcaTacatttccagcaaggaacgc	9	9	1	1	rs375600104		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:125271474T>C	ENST00000296220.5	-	9	1494	c.1205A>G	c.(1204-1206)tAt>tGt	p.Y402C		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	402					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						AAAGTCTGCATACATTTCCAG	0.403																																					p.Y402C		Atlas-SNP	.											.	OSBPL11	64	.	0			c.A1205G						.	T	CYS/TYR	0,4406		0,0,2203	103	100	101		1205	3.8	1	3		101	1,8599	1.2+/-3.3	0,1,4299	no	missense	OSBPL11	NM_022776.4	194	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	402/748	125271474	1,13005	2203	4300	6503	SO:0001583	missense	114885	exon9			TCTGCATACATTT	AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.1205A>G	chr3.hg19:g.125271474T>C	ENSP00000296220:p.Tyr402Cys	127.0	0.0		133.0	40.0	NM_022776	A8K9I7	Missense_Mutation	SNP	ENST00000296220.5	hg19	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	T	17.83	3.485106	0.63962	0.0	1.16E-4	ENSG00000144909	ENST00000296220	T	0.29142	1.58	5.07	3.85	0.44370	.	0.000000	0.85682	D	0.000000	T	0.58977	0.2160	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66756	-0.5843	10	0.87932	D	0	-18.2334	11.3851	0.49780	0.1349:0.0:0.0:0.8651	.	402	Q9BXB4	OSB11_HUMAN	C	402	ENSP00000296220:Y402C	ENSP00000296220:Y402C	Y	-	2	0	OSBPL11	126754164	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.721000	0.84768	2.134000	0.65973	0.482000	0.46254	TAT	.	.		0.403	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		C	125271474	T	C	125271474	3	2	200	1	0	0	0	0	1	0	0	0	11285	1406	49	2	1058	2	OSBPL11	3	125271474	Missense_Mutation	SNP	T	TCGA-DD-AADR-01A-11D-A40R-10	4063132	125271474	72750956	26	29388										
CCDC48	79825	hgsc.bcm.edu	37	chr3	128753168	128753168	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gaccctggggacctctgaggAggaggtcagcagagcctaga	16	10	2	3			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:128753168A>G	ENST00000480450.1	+	5	1445	c.1445A>G	c.(1444-1446)gAg>gGg	p.E482G	EFCC1_ENST00000436022.2_Missense_Mutation_p.E45G			Q9HA90	EFCC1_HUMAN	EF-hand and coiled-coil domain containing 1	482							calcium ion binding (GO:0005509)										ACCTCTGAGGAGGAGGTCAGC	0.597																																					p.E482G		Atlas-SNP	.											.	.	.	.	0			c.A1445G						.						39	39	39					3																	128753168		2203	4300	6503	SO:0001583	missense	79825	exon5			CTGAGGAGGAGGT	AK022119	CCDS3054.1, CCDS3054.2	3q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000114654	ENSG00000114654		"EF-hand domain containing"	25692	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 73", "coiled-coil domain containing 48"	C3orf73, CCDC48			Standard	NM_024768		Approved	FLJ12057	uc011bkt.2	Q9HA90	OTTHUMG00000158996	ENST00000480450.1:c.1445A>G	chr3.hg19:g.128753168A>G	ENSP00000420075:p.Glu482Gly	81.0	0.0		53.0	24.0	NM_024768	A8MYE2	Missense_Mutation	SNP	ENST00000480450.1	hg19	CCDS3054.2	.	.	.	.	.	.	.	.	.	.	A	15.79	2.938030	0.52972	.	.	ENSG00000114654	ENST00000480450;ENST00000436022	T;T	0.49720	0.78;0.77	4.29	3.1	0.35709	.	0.586195	0.15359	N	0.266511	T	0.37839	0.1018	L	0.47716	1.5	0.24165	N	0.995645	B	0.11235	0.004	B	0.09377	0.004	T	0.29088	-1.0023	10	0.56958	D	0.05	.	6.7895	0.23692	0.8829:0.0:0.1171:0.0	.	482	Q9HA90	CCD48_HUMAN	G	482;45	ENSP00000420075:E482G;ENSP00000414597:E45G	ENSP00000414597:E45G	E	+	2	0	CCDC48	130235858	1.000000	0.71417	0.858000	0.33744	0.515000	0.34225	5.818000	0.69236	1.687000	0.51057	0.260000	0.18958	GAG	.	.		0.597	EFCC1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352832.1	NM_024768		G	128753168	A	G	128753168	3	3	200	1	0	0	0	0	1	0	0	0	2821	304	11	2	1463	2	CCDC48	3	128753168	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	3481694	128753168	69269262	27	29389										
MBNL1	4154	hgsc.bcm.edu	37	chr3	152173338	152173338	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gcatgatgggcaggctcaatAttgtgcatgacacccgctac	11	11	1	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:152173338A>G	ENST00000463374.1	+	7	1526				MBNL1_ENST00000282488.7_Intron|RP11-362A9.3_ENST00000463255.1_RNA|MBNL1_ENST00000324210.5_Missense_Mutation_p.I323M|MBNL1_ENST00000492948.1_Missense_Mutation_p.I323M|MBNL1_ENST00000355460.2_Intron|MBNL1_ENST00000357472.3_Missense_Mutation_p.I323M|MBNL1_ENST00000485910.1_Intron|MBNL1_ENST00000324196.5_Intron|MBNL1_ENST00000498502.1_Intron|MBNL1_ENST00000545754.1_Missense_Mutation_p.I255M|MBNL1_ENST00000282486.6_Intron|MBNL1_ENST00000485509.1_Intron|MBNL1_ENST00000493459.1_Missense_Mutation_p.I284M	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1						alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			CAGGCTCAATATTGTGCATGA	0.413																																					p.I323M		Atlas-SNP	.											.	MBNL1	100	.	0			c.A969G						.						238	212	221					3																	152173338		2203	4300	6503	SO:0001627	intron_variant	4154	exon7			CTCAATATTGTGC	Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"Zinc fingers, CCCH-type domain containing"	6923	protein-coding gene	gene with protein product		606516	"muscleblind (Drosophila)-like", "muscleblind-like (Drosophila)"	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.1016-718A>G	chr3.hg19:g.152173338A>G		104.0	0.0		97.0	30.0	NM_021038	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Missense_Mutation	SNP	ENST00000463374.1	hg19	CCDS3165.1	.	.	.	.	.	.	.	.	.	.	A	12.39	1.924937	0.34002	.	.	ENSG00000152601	ENST00000493459;ENST00000324210;ENST00000545754;ENST00000357472;ENST00000465907;ENST00000492948;ENST00000478535	.	.	.	5.7	4.49	0.54785	.	.	.	.	.	T	0.19287	0.0463	N	0.00991	-1.07	0.31524	N	0.662024	B;B;B;P	0.45715	0.066;0.009;0.356;0.865	B;B;B;P	0.46253	0.066;0.011;0.197;0.509	T	0.21177	-1.0253	8	0.48119	T	0.1	.	14.1329	0.65266	0.8669:0.133:0.0:0.0	.	255;323;284;323	Q96RE3;Q86UV8;Q86VM6;Q96P92	.;.;.;.	M	284;323;255;323;255;323;191	.	ENSP00000319429:I323M	I	+	3	3	MBNL1	153656028	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.611000	0.67674	2.168000	0.68352	0.533000	0.62120	ATA	.	.		0.413	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038		G	152173338	A	G	152173338	1	3	200	0	1	0	0	0	0	0	0	0	9362	439	16	2		2	MBNL1	3	152173338	Intron	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	23420170	152173338	45849092	28	29390										
LDB2	9079	hgsc.bcm.edu	37	chr4	16900005	16900005	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gagactgcagtctcttgttcAtctcatagattcggtactct	8	10	4	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:16900005A>G	ENST00000304523.5	-	1	427	c.104T>C	c.(103-105)aTg>aCg	p.M35T	LDB2_ENST00000502640.1_Missense_Mutation_p.M35T|LDB2_ENST00000515064.1_Missense_Mutation_p.M35T|LDB2_ENST00000441778.2_Missense_Mutation_p.M35T	NM_001290.3	NP_001281.1	O43679	LDB2_HUMAN	LIM domain binding 2	35					epithelial structure maintenance (GO:0010669)|hair follicle development (GO:0001942)|positive regulation of cellular component biogenesis (GO:0044089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell maintenance (GO:0035019)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	LIM domain binding (GO:0030274)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(23)|urinary_tract(1)	33						TCTCTTGTTCATCTCATAGAT	0.448																																					p.M35T		Atlas-SNP	.											.	LDB2	129	.	0			c.T104C						.						202	179	187					4																	16900005		2203	4300	6503	SO:0001583	missense	9079	exon1			TTGTTCATCTCAT	AF068651	CCDS3420.1, CCDS47031.1	4p16	2008-08-01			ENSG00000169744	ENSG00000169744			6533	protein-coding gene	gene with protein product		603450				9853615, 9880598, 10861853	Standard	NM_001290		Approved	CLIM1, LDB1	uc003goz.3	O43679	OTTHUMG00000048212	ENST00000304523.5:c.104T>C	chr4.hg19:g.16900005A>G	ENSP00000306772:p.Met35Thr	145.0	0.0		104.0	31.0	NM_001290	O60619|O75480	Missense_Mutation	SNP	ENST00000304523.5	hg19	CCDS3420.1	.	.	.	.	.	.	.	.	.	.	A	16.98	3.270647	0.59540	.	.	ENSG00000169744	ENST00000515064;ENST00000441778;ENST00000304523;ENST00000502640;ENST00000506732	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.57902	0.2085	L	0.47190	1.495	0.80722	D	1	B;P;P;P;B	0.40197	0.029;0.706;0.506;0.657;0.247	B;P;B;B;B	0.44921	0.085;0.464;0.333;0.409;0.247	T	0.63242	-0.6681	9	0.87932	D	0	-13.2894	13.9753	0.64268	1.0:0.0:0.0:0.0	.	1;35;35;35;35	B7Z6D0;E9PFI4;G5E9Y7;O43679-2;O43679	.;.;.;.;LDB2_HUMAN	T	35;35;35;35;11	.	ENSP00000306772:M35T	M	-	2	0	LDB2	16509103	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.790000	0.91844	1.883000	0.54544	0.377000	0.23210	ATG	.	.		0.448	LDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250321.2			G	16900005	A	G	16900005	3	3	200	1	0	0	0	0	1	0	0	0	8705	217	8	2	1158	2	LDB2	4	16900005	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10		16900005	174254271	29	29391										
MED28	80306	hgsc.bcm.edu	37	chr4	17616334	17616342	+	In_Frame_Del	DEL	CCCGCCGGG	CCCGCCGGG	-													0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ccacccggtccccctcaggcCccgccgggccttccgggcca					rs375191348		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	CCCGCCGGG	CCCGCCGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:17616334_17616342delCCCGCCGGG	ENST00000237380.7	+	1	81_89	c.57_65delCCCGCCGGG	c.(55-66)gccccgccgggc>gcc	p.PPG20del	AC006160.5_ENST00000511010.1_RNA	NM_025205.3	NP_079481.2	Q9H204	MED28_HUMAN	mediator complex subunit 28	20					negative regulation of smooth muscle cell differentiation (GO:0051151)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cortical actin cytoskeleton (GO:0030864)|mediator complex (GO:0016592)|membrane (GO:0016020)				lung(6)|skin(2)	8						CCCCTCAGGCCCCGCCGGGCCTTCCGGGC	0.612																																					p.19_22del		Atlas-INDEL	.											.	MED28	16	.	0			c.56_64del						.																																			SO:0001651	inframe_deletion	80306	exon1			.	AF317678	CCDS33963.1	4p16	2007-07-30	2007-07-30		ENSG00000118579	ENSG00000118579			24628	protein-coding gene	gene with protein product		610311	"mediator of RNA polymerase II transcription, subunit 28 homolog (S. cerevisiae)"			11779215, 15467741	Standard	NM_025205		Approved	EG1, DKFZP434N185, magicin	uc003gpi.1	Q9H204	OTTHUMG00000161980	ENST00000237380.7:c.57_65delCCCGCCGGG	chr4.hg19:g.17616334_17616342delCCCGCCGGG	ENSP00000237380:p.Pro20_Gly22del	139.0	0.0		108.0	42.0	NM_025205	Q9BZJ5	In_Frame_Del	DEL	ENST00000237380.7	hg19	CCDS33963.1																																																																																			.	.		0.612	MED28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360055.3	NM_025205		-	17616342	CCCGCCGGG	-	17616334	7	5	200	1	0	1	0	1	0	0	0	0	9455	610	22	0	59	0	MED28	4	17616334	In_Frame_Del	DEL	CCCGCCGGG	TCGA-DD-AADR-01A-11D-A40R-10	716329	17616334	173537942	30	29392										
PDS5A	23244	hgsc.bcm.edu	37	chr4	39904058	39904058	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gtgggggacaagatactgagCaaagattttctctaccaaca	10	8	1	3			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:39904058C>A	ENST00000303538.8	-	13	1947	c.1408G>T	c.(1408-1410)Gct>Tct	p.A470S	PDS5A_ENST00000503396.1_Missense_Mutation_p.A470S	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						AGATACTGAGCAAAGATTTTC	0.308																																					p.A470S		Atlas-SNP	.											.	PDS5A	114	.	0			c.G1408T						.						97	93	94					4																	39904058		1821	4079	5900	SO:0001583	missense	23244	exon13			ACTGAGCAAAGAT	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.1408G>T	chr4.hg19:g.39904058C>A	ENSP00000303427:p.Ala470Ser	271.0	0.0		197.0	72.0	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.54|14.54	2.566126|2.566126	0.45694|0.45694	.|.	.|.	ENSG00000121892|ENSG00000121892	ENST00000303538;ENST00000503396|ENST00000513798	.|.	.|.	.|.	5.47|5.47	5.47|5.47	0.80525|0.80525	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67069|0.67069	0.2854|0.2854	L|L	0.41236|0.41236	1.265|1.265	0.80722|0.80722	D|D	1|1	B;P|.	0.50272|.	0.05;0.933|.	B;P|.	0.55222|.	0.037;0.771|.	T|T	0.62324|0.62324	-0.6878|-0.6878	8|5	.|.	.|.	.|.	-12.0649|-12.0649	19.313|19.313	0.94199|0.94199	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	470;470|.	Q29RF7-3;Q29RF7|.	.;PDS5A_HUMAN|.	S|F	470|107	.|.	.|.	A|L	-|-	1|3	0|2	PDS5A|PDS5A	39580453|39580453	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.818000|7.818000	0.86416|0.86416	2.570000|2.570000	0.86706|0.86706	0.655000|0.655000	0.94253|0.94253	GCT|TTG	.	.		0.308	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		A	39904058	C	A	39904058	3	1	200	1	0	0	0	0	1	0	0	0	11700	710	25	3	2722	3	PDS5A	4	39904058	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	22287724	39904058	151250218	31	29393										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	73943157	73943157	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	caattcctgtactatctcgcTccattgcttgatgttgtgaa	7	10	1	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:73943157T>G	ENST00000358602.4	-	32	7618	c.7502A>C	c.(7501-7503)gAg>gCg	p.E2501A	ANKRD17_ENST00000330838.6_Missense_Mutation_p.E2250A|ANKRD17_ENST00000509867.2_Missense_Mutation_p.E2388A	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2501					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACTATCTCGCTCCATTGCTTG	0.458																																					p.E2501A		Atlas-SNP	.											.	ANKRD17	214	.	0			c.A7502C						.						195	175	182					4																	73943157		2203	4300	6503	SO:0001583	missense	26057	exon32			TCTCGCTCCATTG	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.7502A>C	chr4.hg19:g.73943157T>G	ENSP00000351416:p.Glu2501Ala	132.0	0.0		73.0	6.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	hg19	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	T	18.72	3.684889	0.68157	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867	T;T;T	0.75154	-0.91;-0.87;-0.87	5.65	5.65	0.86999	.	0.174226	0.39083	N	0.001469	T	0.69351	0.3101	L	0.49778	1.585	0.43014	D	0.994559	P;P;P;B	0.37330	0.59;0.59;0.455;0.319	B;B;B;B	0.33121	0.158;0.158;0.076;0.076	T	0.74160	-0.3755	10	0.87932	D	0	.	15.8801	0.79197	0.0:0.0:0.0:1.0	.	2500;2250;2501;2388	O75179-2;G5E964;O75179;E7EUV3	.;.;ANR17_HUMAN;.	A	2501;1908;2250;2388	ENSP00000351416:E2501A;ENSP00000332265:E2250A;ENSP00000427151:E2388A	ENSP00000332265:E2250A	E	-	2	0	ANKRD17	74162021	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.127000	0.77210	2.166000	0.68216	0.460000	0.39030	GAG	.	.		0.458	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		G	73943157	T	G	73943157	3	3	200	1	0	0	0	0	1	0	0	0	646	1551	54	5	321	5	ANKRD17	4	73943157	Missense_Mutation	SNP	T	TCGA-DD-AADR-01A-11D-A40R-10	34039099	73943157	117211119	32	29394										
TRPC3	7222	hgsc.bcm.edu	37	chr4	122853582	122853582	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gagtggctgaaggagtcgtgCctctgcttctccatgcagtc	13	11	2	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:122853582C>T	ENST00000379645.3	-	2	904	c.831G>A	c.(829-831)agG>agA	p.R277R	TRPC3_ENST00000264811.5_Silent_p.R204R|TRPC3_ENST00000513531.1_Silent_p.R204R	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	192					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.R204R(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						AGGAGTCGTGCCTCTGCTTCT	0.592																																					p.R277R		Atlas-SNP	.											TRPC3_ENST00000379645,NS,carcinoma,-1,1	TRPC3	201	.	1	Substitution - coding silent(1)	endometrium(1)	c.G831A						.						51	46	47					4																	122853582		2203	4300	6503	SO:0001819	synonymous_variant	7222	exon2			GTCGTGCCTCTGC	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.831G>A	chr4.hg19:g.122853582C>T		177.0	0.0		105.0	9.0	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	ENST00000379645.3	hg19	CCDS47130.1																																																																																			.	.		0.592	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		T	122853582	C	T	122853582	2	4	200	1	0	0	0	0	0	0	0	1	16594	738	26	3		3	TRPC3	4	122853582	Silent	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	48910425	122853582	68300694	33	29395										
FAT4	79633	hgsc.bcm.edu	37	chr4	126336041	126336041	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tcttccctttaatttcaggcAtcaactctcaattgacttat	3	11	4	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:126336041A>T	ENST00000394329.3	+	5	5936	c.5923A>T	c.(5923-5925)Atc>Ttc	p.I1975F	FAT4_ENST00000335110.5_Missense_Mutation_p.I273F	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1975	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AATTTCAGGCATCAACTCTCA	0.358																																					p.I1975F		Atlas-SNP	.											.	FAT4	1752	.	0			c.A5923T						.						64	68	67					4																	126336041		2203	4300	6503	SO:0001583	missense	79633	exon5			TCAGGCATCAACT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.5923A>T	chr4.hg19:g.126336041A>T	ENSP00000377862:p.Ile1975Phe	164.0	0.0		92.0	6.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	9.485	1.099278	0.20552	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.51325	0.71;0.71	5.23	-1.08	0.09936	Cadherin (4);Cadherin-like (1);	0.871371	0.09306	U	0.820226	T	0.24353	0.0590	N	0.13352	0.335	0.20703	N	0.999868	B;B	0.09022	0.0;0.002	B;B	0.09377	0.003;0.004	T	0.21075	-1.0256	10	0.56958	D	0.05	.	0.8668	0.01205	0.208:0.2089:0.3295:0.2536	.	273;1975	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	F	1975;273	ENSP00000377862:I1975F;ENSP00000335169:I273F	ENSP00000335169:I273F	I	+	1	0	FAT4	126555491	0.000000	0.05858	0.916000	0.36221	0.926000	0.56050	-0.377000	0.07456	-0.170000	0.10816	0.528000	0.53228	ATC	.	.		0.358	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126336041	A	T	126336041	3	4	200	1	0	0	0	0	1	0	0	0	5700	217	8	4	5941	4	FAT4	4	126336041	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	3482459	126336041	64818235	34	29396										
PHF17	79960	hgsc.bcm.edu	37	chr4	129778563	129778563	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cattcccagcagccggtgggCgctagtgtgcagcctctgca	13	14	1	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:129778563C>A	ENST00000226319.6	+	8	1215	c.935C>A	c.(934-936)gCg>gAg	p.A312E	PHF17_ENST00000452328.2_Missense_Mutation_p.A300E|PHF17_ENST00000511647.1_Missense_Mutation_p.A312E|PHF17_ENST00000512960.1_Missense_Mutation_p.A312E|PHF17_ENST00000413543.2_Missense_Mutation_p.A312E	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						AGCCGGTGGGCGCTAGTGTGC	0.532																																					p.A312E		Atlas-SNP	.											.	PHF17	63	.	0			c.C935A						.						157	161	160					4																	129778563		2203	4300	6503	SO:0001583	missense	79960	exon8			GGTGGGCGCTAGT																												ENST00000226319.6:c.935C>A	chr4.hg19:g.129778563C>A	ENSP00000226319:p.Ala312Glu	151.0	0.0		96.0	50.0	NM_199320		Missense_Mutation	SNP	ENST00000226319.6	hg19	CCDS34062.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.366421	0.61513	.	.	ENSG00000077684	ENST00000226319;ENST00000511647;ENST00000452328;ENST00000512960;ENST00000535321;ENST00000413543	T;T;T;T;T	0.13089	2.62;2.62;2.62;2.62;2.62	4.54	4.54	0.55810	.	0.111121	0.64402	D	0.000008	T	0.29749	0.0743	L	0.43554	1.36	0.80722	D	1	P;D;P	0.69078	0.908;0.997;0.455	P;D;B	0.74348	0.855;0.983;0.387	T	0.01099	-1.1452	9	.	.	.	.	17.8247	0.88661	0.0:1.0:0.0:0.0	.	300;312;312	Q6IE81-2;Q6IE81;Q6IE81-3	.;JADE1_HUMAN;.	E	312;312;300;312;312;312	ENSP00000226319:A312E;ENSP00000423737:A312E;ENSP00000388015:A300E;ENSP00000425730:A312E;ENSP00000404211:A312E	.	A	+	2	0	PHF17	129998013	1.000000	0.71417	0.969000	0.41365	0.114000	0.19823	6.966000	0.76073	2.496000	0.84212	0.655000	0.94253	GCG	.	.		0.532	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1			A	129778563	C	A	129778563	3	1	200	1	0	0	0	0	1	0	0	0	11837	768	27	1	961	1	PHF17	4	129778563	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	3442522	129778563	61375713	35	29397										
ABCE1	6059	hgsc.bcm.edu	37	chr4	146041189	146041189	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	agcaaatgaagaagaagttaAaaagatgtgtatgtataaat	9	1	0	4			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:146041189A>C	ENST00000296577.4	+	11	1543	c.1028A>C	c.(1027-1029)aAa>aCa	p.K343T	OTUD4_ENST00000455611.2_Intron|ABCE1_ENST00000502803.1_3'UTR	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	343	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					GAAGAAGTTAAAAAGATGTGT	0.338																																					p.K343T		Atlas-SNP	.											.	ABCE1	47	.	0			c.A1028C						.						59	63	62					4																	146041189		2202	4300	6502	SO:0001583	missense	6059	exon11			AAGTTAAAAAGAT	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"ATP binding cassette transporters / subfamily E"	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.1028A>C	chr4.hg19:g.146041189A>C	ENSP00000296577:p.Lys343Thr	253.0	1.0		156.0	77.0	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Missense_Mutation	SNP	ENST00000296577.4	hg19	CCDS34071.1	.	.	.	.	.	.	.	.	.	.	A	16.09	3.025636	0.54683	.	.	ENSG00000164163	ENST00000296577	D	0.94232	-3.38	5.31	5.31	0.75309	ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.88243	0.6384	N	0.20685	0.6	0.80722	D	1	B	0.16802	0.019	B	0.20955	0.032	D	0.84372	0.0544	10	0.41790	T	0.15	-18.4169	15.548	0.76123	1.0:0.0:0.0:0.0	.	343	P61221	ABCE1_HUMAN	T	343	ENSP00000296577:K343T	ENSP00000296577:K343T	K	+	2	0	ABCE1	146260639	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.232000	0.95325	2.120000	0.65058	0.454000	0.30748	AAA	.	.		0.338	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940		C	146041189	A	C	146041189	3	2	200	1	0	0	0	0	1	0	0	0	64	14	1	5	1066	5	ABCE1	4	146041189	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	16262626	146041189	45113087	36	29398										
PLCXD3	345557	hgsc.bcm.edu	37	chr5	41382514	41382514	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cattgtctgagtggctaaccAtttccgcatgagctttttgg	10	9	1	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr5:41382514A>T	ENST00000377801.3	-	2	300	c.226T>A	c.(226-228)Tgg>Agg	p.W76R	PLCXD3_ENST00000328457.3_Missense_Mutation_p.W76R			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	76	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GTGGCTAACCATTTCCGCATG	0.463																																					p.W76R		Atlas-SNP	.											.	PLCXD3	86	.	0			c.T226A						.						59	65	63					5																	41382514		2203	4300	6503	SO:0001583	missense	345557	exon2			CTAACCATTTCCG		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.226T>A	chr5.hg19:g.41382514A>T	ENSP00000367032:p.Trp76Arg	114.0	0.0		89.0	33.0	NM_001005473	A6NL04	Missense_Mutation	SNP	ENST00000377801.3	hg19	CCDS34150.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.178619	0.78564	.	.	ENSG00000182836	ENST00000377801;ENST00000328457	.	.	.	6.07	6.07	0.98685	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (1);	0.000000	0.85682	D	0.000000	D	0.86577	0.5966	M	0.93150	3.385	0.80722	D	1	D	0.67145	0.996	D	0.79108	0.992	D	0.89906	0.4048	9	0.87932	D	0	-3.2113	16.6406	0.85098	1.0:0.0:0.0:0.0	.	76	Q63HM9	PLCX3_HUMAN	R	76	.	ENSP00000333751:W76R	W	-	1	0	PLCXD3	41418271	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.923000	0.92808	2.326000	0.78906	0.533000	0.62120	TGG	.	.		0.463	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875		T	41382514	A	T	41382514	3	4	200	1	0	0	0	0	1	0	0	0	12052	217	8	4	747	4	PLCXD3	5	41382514	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10		41382514	139532746	37	29399										
ZNF474	133923	hgsc.bcm.edu	37	chr5	121488330	121488330	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	aagaaagcttgtagtggaacCccagcccgaccaaggactgt	11	11	0	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr5:121488330C>T	ENST00000296600.4	+	2	1028	c.645C>T	c.(643-645)acC>acT	p.T215T	ZNF474_ENST00000514925.1_Intron|CTC-441N14.2_ENST00000504829.1_RNA|CTC-441N14.1_ENST00000505209.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	215							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		GTAGTGGAACCCCAGCCCGAC	0.488																																					p.T215T		Atlas-SNP	.											.	ZNF474	43	.	0			c.C645T						.						98	97	97					5																	121488330		2203	4300	6503	SO:0001819	synonymous_variant	133923	exon2			TGGAACCCCAGCC	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"Zinc fingers, C2H2-type"	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.645C>T	chr5.hg19:g.121488330C>T		133.0	0.0		118.0	46.0	NM_207317	A8K4M0|Q96M07	Silent	SNP	ENST00000296600.4	hg19	CCDS4130.1																																																																																			.	.		0.488	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317		T	121488330	C	T	121488330	2	4	200	1	0	0	0	0	0	0	0	1	17947	610	22	3		3	ZNF474	5	121488330	Silent	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	80105816	121488330	59426930	38	29400										
HARS2	23438	hgsc.bcm.edu	37	chr5	140075365	140075365	+	Frame_Shift_Del	DEL	G	G	-													0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ttgaccctatgatccccgatGcagagtgtttgaagatcatg							TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr5:140075365delG	ENST00000230771.3	+	6	791	c.568delG	c.(568-570)gcafs	p.A190fs	HARS2_ENST00000508522.1_Frame_Shift_Del_p.A165fs|HARS2_ENST00000435019.2_Frame_Shift_Del_p.A150fs|HARS2_ENST00000437649.2_Frame_Shift_Del_p.A116fs|HARS2_ENST00000448069.2_Frame_Shift_Del_p.A51fs|HARS2_ENST00000432671.2_Frame_Shift_Del_p.A76fs	NM_012208.2	NP_036340.1	P49590	SYHM_HUMAN	histidyl-tRNA synthetase 2, mitochondrial	190					gene expression (GO:0010467)|histidyl-tRNA aminoacylation (GO:0006427)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|histidine-tRNA ligase activity (GO:0004821)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|large_intestine(5)|lung(10)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATCCCCGATGCAGAGTGTTT	0.443																																					p.D189fs		Atlas-INDEL	.											.	HARS2	41	.	0			c.567delT						.						185	177	180					5																	140075365		2203	4300	6503	SO:0001589	frameshift_variant	23438	exon6			.	U18937	CCDS4238.1, CCDS64267.1	5q31.3	2012-07-20	2012-07-20	2007-02-23	ENSG00000112855	ENSG00000112855	6.1.1.21	"Aminoacyl tRNA synthetases / Class II"	4817	protein-coding gene	gene with protein product	"histidine tRNA ligase 2, mitochondrial (putative)"	600783	"histidyl-tRNA synthetase-like"	HARSL		7755634, 21464306	Standard	NM_012208		Approved	HO3, HARSR	uc003lgx.3	P49590	OTTHUMG00000129500	ENST00000230771.3:c.568delG	chr5.hg19:g.140075365delG	ENSP00000230771:p.Ala190fs	155.0	0.0		130.0	42.0	NM_012208	B4DDY8	Frame_Shift_Del	DEL	ENST00000230771.3	hg19	CCDS4238.1																																																																																			.	.		0.443	HARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251670.2	NM_012208		-	140075365	G	-	140075365	7	5	200	1	0	1	0	1	0	0	0	0	6969	1319	46	0	590	0	HARS2	5	140075365	Frame_Shift_Del	DEL	G	TCGA-DD-AADR-01A-11D-A40R-10	18587035	140075365	40839895	39	29401										
PCDHGB4	8641	hgsc.bcm.edu	37	chr5	140768944	140768944	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cagtgacctggagcagcgggAgctgtcatcctacgtgtcca	13	12	1	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr5:140768944A>G	ENST00000519479.1	+	1	1493	c.1493A>G	c.(1492-1494)gAg>gGg	p.E498G	PCDHGA7_ENST00000518325.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	498	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCAGCGGGAGCTGTCATCC	0.617																																					p.E498G		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.A1493G						.						59	66	64					5																	140768944		2015	4167	6182	SO:0001583	missense	8641	exon1			AGCGGGAGCTGTC	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"Cadherins / Protocadherins : Clustered"	8711	other	protocadherin	"fibroblast cadherin FIB2", "cadherin 20"	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1493A>G	chr5.hg19:g.140768944A>G	ENSP00000428288:p.Glu498Gly	135.0	0.0		139.0	45.0	NM_032098	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	hg19	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	10.27	1.305186	0.23736	.	.	ENSG00000253953	ENST00000519479	T	0.61158	0.13	5.18	2.04	0.26737	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.44435	0.1293	N	0.20986	0.625	0.19575	N	0.999965	B;B	0.20368	0.035;0.044	B;B	0.29524	0.062;0.103	T	0.45745	-0.9240	9	0.87932	D	0	.	8.4986	0.33144	0.2723:0.6484:0.0:0.0794	.	498;498	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	G	498	ENSP00000428288:E498G	ENSP00000428288:E498G	E	+	2	0	PCDHGB4	140749128	0.435000	0.25577	0.499000	0.27577	0.009000	0.06853	0.922000	0.28734	0.588000	0.29660	-1.142000	0.01873	GAG	.	.		0.617	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		G	140768944	A	G	140768944	3	3	200	1	0	0	0	0	1	0	0	0	11574	304	11	2	1495	2	PCDHGB4	5	140768944	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	693579	140768944	40146316	40	29402										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30918187	30918187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	agaaaatagagaaatgacagCcaacgagaagaccacactat	8	8	0	5			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:30918187C>T	ENST00000462446.1	+	2	1974	c.1946C>T	c.(1945-1947)gCc>gTc	p.A649V	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	196						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						GAAATGACAGCCAACGAGAAG	0.488																																					p.A649V		Atlas-SNP	.											.	DPCR1	99	.	0			c.C1946T						.						181	203	196					6																	30918187		692	1591	2283	SO:0001583	missense	135656	exon2			TGACAGCCAACGA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.1946C>T	chr6.hg19:g.30918187C>T	ENSP00000417182:p.Ala649Val	158.0	0.0		114.0	47.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	-	7.090	0.571884	0.13623	.	.	ENSG00000168631	ENST00000462446	T	0.53423	0.62	1.43	-2.86	0.05717	.	.	.	.	.	T	0.15046	0.0363	L	0.27053	0.805	0.09310	N	0.999998	D	0.58620	0.983	P	0.51170	0.661	T	0.03662	-1.1015	9	0.23891	T	0.37	.	0.5364	0.00637	0.2429:0.3319:0.2406:0.1846	.	649	E9PEI6	.	V	649	ENSP00000417182:A649V	ENSP00000417182:A649V	A	+	2	0	DPCR1	31026166	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-1.035000	0.03564	-0.789000	0.04498	0.109000	0.15622	GCC	.	.		0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		T	30918187	C	T	30918187	3	4	200	1	0	0	0	0	1	0	0	0	4714	739	26	3	1952	3	DPCR1	6	30918187	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10		30918187	140196880	41	29403										
C2	717	hgsc.bcm.edu	37	chr6	31895872	31895872	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	acccatccccagcatcacggCtgtgcaagagcagcggacag	11	15	1	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:31895872C>A	ENST00000299367.5	+	2	463	c.187C>A	c.(187-189)Ctg>Atg	p.L63M	CFB_ENST00000556679.1_Missense_Mutation_p.L63M|CFB_ENST00000456570.1_Missense_Mutation_p.L63M|C2_ENST00000418949.2_Missense_Mutation_p.L63M|C2_ENST00000442278.2_Intron|C2_ENST00000452323.2_Intron|C2_ENST00000469372.1_Intron|CFB_ENST00000477310.1_Missense_Mutation_p.L63M	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	63	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		AGCATCACGGCTGTGCAAGAG	0.642																																					p.L63M		Atlas-SNP	.											.	C2	50	.	0			c.C187A						.						26	28	27					6																	31895872		2203	4300	6503	SO:0001583	missense	717	exon2			TCACGGCTGTGCA		CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"Complement system"	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.187C>A	chr6.hg19:g.31895872C>A	ENSP00000299367:p.Leu63Met	74.0	0.0		58.0	22.0	NM_000063	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	hg19	CCDS4728.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.602958	0.46423	.	.	ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000413154;ENST00000299367;ENST00000447952;ENST00000418949;ENST00000556679;ENST00000456570;ENST00000477310	T;T;T;T;T;T;T	0.50548	0.92;0.74;0.92;0.74;0.92;0.92;0.74	5.22	-2.13	0.07144	Complement control module (2);Sushi/SCR/CCP (2);	0.959111	0.08454	N	0.943421	T	0.10852	0.0265	.	.	.	0.09310	N	1	B;B;B	0.22276	0.067;0.005;0.017	B;B;B	0.21546	0.035;0.014;0.008	T	0.27297	-1.0078	9	0.41790	T	0.15	-3.6602	0.6883	0.00887	0.3716:0.1977:0.2444:0.1863	.	63;63;63	B4E1Z4;P06681;Q8N6L6	.;CO2_HUMAN;.	M	63	ENSP00000403325:L63M;ENSP00000299367:L63M;ENSP00000391354:L63M;ENSP00000406190:L63M;ENSP00000451848:L63M;ENSP00000410815:L63M;ENSP00000418996:L63M	ENSP00000299367:L63M	L	+	1	2	CFB;C2;XXbac-BPG116M5.17	32003851	0.000000	0.05858	0.057000	0.19452	0.551000	0.35334	-0.820000	0.04457	-0.277000	0.09193	0.655000	0.94253	CTG	.	.		0.642	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9			A	31895872	C	A	31895872	3	1	200	1	0	0	0	0	1	0	0	0	2076	796	28	3	270	3	C2	6	31895872	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	977685	31895872	139219195	42	29404										
ATF6B	1388	hgsc.bcm.edu	37	chr6	32085446	32085446	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tcttagtagtagctccttggCgcccccagggaaggctgtca	12	12	2	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:32085446C>T	ENST00000375203.3	-	13	1482	c.1450G>A	c.(1450-1452)Gcc>Acc	p.A484T	ATF6B_ENST00000375201.4_Missense_Mutation_p.A481T	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	484					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						AGCTCCTTGGCGCCCCCAGGG	0.562																																					p.A484T		Atlas-SNP	.											.	ATF6B	40	.	0			c.G1450A						.						53	58	56					6																	32085446		2203	4300	6503	SO:0001583	missense	1388	exon13			CCTTGGCGCCCCC		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"basic leucine zipper proteins"	2349	protein-coding gene	gene with protein product		600984	"cAMP responsive element binding protein-like 1"	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.1450G>A	chr6.hg19:g.32085446C>T	ENSP00000364349:p.Ala484Thr	89.0	0.0		92.0	4.0	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Missense_Mutation	SNP	ENST00000375203.3	hg19	CCDS4737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.365|6.365	0.435387|0.435387	0.12045|0.12045	.|.	.|.	ENSG00000213676|ENSG00000213676	ENST00000375192;ENST00000375203;ENST00000375201|ENST00000453203	T;T|.	0.55588|.	0.51;1.25|.	5.58|5.58	1.6|1.6	0.23607|0.23607	.|.	1.089090|.	0.07216|.	N|.	0.860079|.	T|T	0.14743|0.14743	0.0356|0.0356	L|L	0.31294|0.31294	0.92|0.92	0.21355|0.21355	N|N	0.999715|0.999715	B;B;B|.	0.16396|.	0.017;0.006;0.01|.	B;B;B|.	0.11329|.	0.006;0.002;0.002|.	T|T	0.28964|0.28964	-1.0027|-1.0027	9|5	.|.	.|.	.|.	-5.3948|-5.3948	9.2689|9.2689	0.37659|0.37659	0.0:0.6772:0.0:0.3228|0.0:0.6772:0.0:0.3228	.|.	481;484;484|.	Q99941-2;Q99941;Q6AZW6|.	.;ATF6B_HUMAN;.|.	T|H	87;484;481|20	ENSP00000364349:A484T;ENSP00000364347:A481T|.	.|.	A|R	-|-	1|2	0|0	ATF6B|ATF6B	32193424|32193424	0.000000|0.000000	0.05858|0.05858	0.121000|0.121000	0.21740|0.21740	0.928000|0.928000	0.56348|0.56348	-0.526000|-0.526000	0.06207|0.06207	-0.004000|-0.004000	0.14419|0.14419	-0.126000|-0.126000	0.14955|0.14955	GCC|CGC	.	.		0.562	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2			T	32085446	C	T	32085446	3	4	200	1	0	0	0	0	1	0	0	0	1085	768	27	1	685	1	ATF6B	6	32085446	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	189574	32085446	139029621	43	29405										
C6orf222	389384	hgsc.bcm.edu	37	chr6	36298079	36298079	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ccaggggctccggatgctggGagataccctccttccccctt	11	16	0	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:36298079G>A	ENST00000437635.2	-	2	566	c.389C>T	c.(388-390)tCc>tTc	p.S130F		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	130										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						CGGATGCTGGGAGATACCCTC	0.607																																					p.S130F		Atlas-SNP	.											.	C6orf222	72	.	0			c.C389T						.						73	66	68					6																	36298079		2203	4300	6503	SO:0001583	missense	389384	exon2			TGCTGGGAGATAC		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.389C>T	chr6.hg19:g.36298079G>A	ENSP00000418983:p.Ser130Phe	66.0	0.0		70.0	27.0	NM_001010903	B2RTY8	Missense_Mutation	SNP	ENST00000437635.2	hg19	CCDS34439.1	.	.	.	.	.	.	.	.	.	.	G	4.432	0.079968	0.08533	.	.	ENSG00000189325	ENST00000437635	T	0.49139	0.79	3.55	1.72	0.24424	.	0.512563	0.16611	N	0.206908	T	0.18215	0.0437	L	0.46157	1.445	0.09310	N	1	P	0.45011	0.848	B	0.37989	0.262	T	0.06180	-1.0841	10	0.87932	D	0	-28.1982	5.2395	0.15464	0.2704:0.0:0.7296:0.0	.	130	P0C671	CF222_HUMAN	F	130	ENSP00000418983:S130F	ENSP00000418983:S130F	S	-	2	0	C6orf222	36406057	0.000000	0.05858	0.003000	0.11579	0.074000	0.17049	0.087000	0.14958	0.834000	0.34852	0.289000	0.19496	TCC	.	.		0.607	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903		A	36298079	G	A	36298079	3	1	200	1	0	0	0	0	1	0	0	0	2358	1174	41	3	1613	3	C6orf222	6	36298079	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	4212633	36298079	134816988	44	29406										
KIAA0240	23506	hgsc.bcm.edu	37	chr6	42796515	42796515	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	catccttcttcatcagcatcCtttactcaggcttctaatgt	4	13	5	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:42796515C>G	ENST00000314073.5	+	6	620	c.444C>G	c.(442-444)tcC>tcG	p.S148S	GLTSCR1L_ENST00000394168.1_Silent_p.S148S			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	148																	CATCAGCATCCTTTACTCAGG	0.463																																					p.S148S		Atlas-SNP	.											.	.	.	.	0			c.C444G						.						147	134	138					6																	42796515		2203	4300	6503	SO:0001819	synonymous_variant	23506	exon5			AGCATCCTTTACT	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"KIAA0240"	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.444C>G	chr6.hg19:g.42796515C>G		121.0	0.0		105.0	41.0	NM_015349	A1L3W2|Q5TFZ3|Q92514	Silent	SNP	ENST00000314073.5	hg19	CCDS34451.1																																																																																			.	.		0.463	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		G	42796515	C	G	42796515	2	3	200	1	0	0	0	0	0	0	0	1	8173	668	24	4		4	KIAA0240	6	42796515	Silent	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	6498436	42796515	128318552	45	29407										
TBX18	9096	hgsc.bcm.edu	37	chr6	85446578	85446578	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	accccaagaaacttccttggGaagaaacaattttctcagga	7	10	1	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:85446578G>T	ENST00000369663.5	-	8	1986	c.1649C>A	c.(1648-1650)tCc>tAc	p.S550Y	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	550					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		ACTTCCTTGGGAAGAAACAAT	0.507																																					p.S550Y		Atlas-SNP	.											.	TBX18	131	.	0			c.C1649A						.						67	77	74					6																	85446578		2203	4300	6503	SO:0001583	missense	9096	exon8			CCTTGGGAAGAAA	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"T-boxes"	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1649C>A	chr6.hg19:g.85446578G>T	ENSP00000358677:p.Ser550Tyr	208.0	0.0		160.0	62.0	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Missense_Mutation	SNP	ENST00000369663.5	hg19	CCDS34495.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.554023	0.65425	.	.	ENSG00000112837	ENST00000369663	D	0.87650	-2.28	5.26	5.26	0.73747	.	0.150436	0.64402	D	0.000006	D	0.82728	0.5100	L	0.27053	0.805	0.54753	D	0.999982	D	0.61080	0.989	P	0.50708	0.648	D	0.85861	0.1410	10	0.72032	D	0.01	.	18.8443	0.92198	0.0:0.0:1.0:0.0	.	550	O95935	TBX18_HUMAN	Y	550	ENSP00000358677:S550Y	ENSP00000358677:S550Y	S	-	2	0	TBX18	85503297	1.000000	0.71417	1.000000	0.80357	0.618000	0.37518	6.968000	0.76086	2.453000	0.82957	0.585000	0.79938	TCC	.	.		0.507	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508		T	85446578	G	T	85446578	3	4	200	1	0	0	0	0	1	0	0	0	15668	1174	41	3	178	3	TBX18	6	85446578	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	42650063	85446578	85668489	46	29408										
ASF1A	25842	hgsc.bcm.edu	37	chr6	119228720	119228720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	taccttcagcatcaaagggaTggtccacatcagaaaactca	7	11	4	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:119228720T>C	ENST00000229595.5	+	4	750	c.556T>C	c.(556-558)Tgg>Cgg	p.W186R	MCM9_ENST00000316316.6_Intron	NM_014034.2	NP_054753.1	Q9Y294	ASF1A_HUMAN	anti-silencing function 1A histone chaperone	186	Required for interaction with HIRA.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|muscle cell differentiation (GO:0042692)|negative regulation of chromatin silencing (GO:0031936)|nucleosome assembly (GO:0006334)|osteoblast differentiation (GO:0001649)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|histone binding (GO:0042393)			endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0633)|OV - Ovarian serous cystadenocarcinoma(136;0.188)		ATCAAAGGGATGGTCCACATC	0.388																																					p.W186R		Atlas-SNP	.											.	ASF1A	16	.	0			c.T556C						.						113	105	107					6																	119228720		1910	4120	6030	SO:0001583	missense	25842	exon4			AAGGGATGGTCCA	AF279306	CCDS47469.1	6q22.31	2013-05-01	2013-05-01		ENSG00000111875	ENSG00000111875			20995	protein-coding gene	gene with protein product		609189	"ASF1 anti-silencing function 1 homolog A (S. cerevisiae)"			10810093, 11042152	Standard	NM_014034		Approved	DKFZP547E2110, CIA	uc011ebn.2	Q9Y294	OTTHUMG00000015470	ENST00000229595.5:c.556T>C	chr6.hg19:g.119228720T>C	ENSP00000229595:p.Trp186Arg	272.0	0.0		120.0	66.0	NM_014034	Q6IA08|Q9P014	Missense_Mutation	SNP	ENST00000229595.5	hg19	CCDS47469.1	.	.	.	.	.	.	.	.	.	.	T	12.91	2.080082	0.36662	.	.	ENSG00000111875	ENST00000229595	.	.	.	6.01	6.01	0.97437	.	0.000000	0.64402	D	0.000002	T	0.18841	0.0452	N	0.08118	0	0.58432	D	0.999999	B	0.31910	0.346	B	0.28709	0.093	T	0.11397	-1.0589	9	0.25106	T	0.35	-3.3821	16.5285	0.84344	0.0:0.0:0.0:1.0	.	186	Q9Y294	ASF1A_HUMAN	R	186	.	ENSP00000229595:W186R	W	+	1	0	ASF1A	119270419	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.435000	0.59941	2.307000	0.77673	0.528000	0.53228	TGG	.	.		0.388	ASF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361910.1	NM_014034		C	119228720	T	C	119228720	3	2	200	1	0	0	0	0	1	0	0	0	1037	1464	51	2	457	2	ASF1A	6	119228720	Missense_Mutation	SNP	T	TCGA-DD-AADR-01A-11D-A40R-10	33782142	119228720	51886347	47	29409										
SERAC1	84947	hgsc.bcm.edu	37	chr6	158535862	158535862	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ccaacgaggggaagagaagaTagcgaatattaacagagtat	12	5	0	3			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:158535862T>C	ENST00000367104.3	-	15	1774	c.1643A>G	c.(1642-1644)tAt>tGt	p.Y548C	SERAC1_ENST00000367102.2_3'UTR|SERAC1_ENST00000367101.1_3'UTR	NM_032861.3	NP_116250.3	Q96JX3	SRAC1_HUMAN	serine active site containing 1	548					extracellular matrix organization (GO:0030198)|GPI anchor metabolic process (GO:0006505)|intracellular protein transport (GO:0006886)|phospholipid biosynthetic process (GO:0008654)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	15		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)		GAAGAGAAGATAGCGAATATT	0.368																																					p.Y548C		Atlas-SNP	.											.	SERAC1	31	.	0			c.A1643G						.						163	166	165					6																	158535862		2203	4300	6503	SO:0001583	missense	84947	exon15			AGAAGATAGCGAA	BC001705	CCDS5255.1	6q25.3	2003-05-12			ENSG00000122335	ENSG00000122335			21061	protein-coding gene	gene with protein product		614725					Standard	NM_032861		Approved	FLJ14917	uc003qrc.2	Q96JX3	OTTHUMG00000015905	ENST00000367104.3:c.1643A>G	chr6.hg19:g.158535862T>C	ENSP00000356071:p.Tyr548Cys	165.0	0.0		88.0	39.0	NM_032861	Q49AT1|Q5VTX3|Q6PKF3	Missense_Mutation	SNP	ENST00000367104.3	hg19	CCDS5255.1	.	.	.	.	.	.	.	.	.	.	.	19.12	3.765764	0.69878	.	.	ENSG00000122335	ENST00000367104;ENST00000435180	D;D	0.95205	-3.64;-3.62	6.08	6.08	0.98989	.	0.114120	0.64402	D	0.000007	D	0.95909	0.8668	M	0.77616	2.38	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.95682	0.8733	10	0.48119	T	0.1	-23.1776	10.3822	0.44119	0.2517:0.0:0.0:0.7483	.	548	Q96JX3	SRAC1_HUMAN	C	548;123	ENSP00000356071:Y548C;ENSP00000391168:Y123C	ENSP00000356071:Y548C	Y	-	2	0	SERAC1	158455850	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	3.709000	0.54853	2.333000	0.79357	0.533000	0.62120	TAT	.	.		0.368	SERAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042862.1	NM_032861		C	158535862	T	C	158535862	3	2	200	1	0	0	0	0	1	0	0	0	14089	1406	49	2	333	2	SERAC1	6	158535862	Missense_Mutation	SNP	T	TCGA-DD-AADR-01A-11D-A40R-10	39307142	158535862	12579205	48	29410										
USP42	84132	hgsc.bcm.edu	37	chr7	6189723	6189723	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	aatgggattggtacgattgtGagctcccactctcccggcca	11	12	1	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:6189723G>A	ENST00000306177.5	+	13	2054	c.1896G>A	c.(1894-1896)gtG>gtA	p.V632V		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	632					cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		GTACGATTGTGAGCTCCCACT	0.582																																					p.V632V		Atlas-SNP	.											.	USP42	138	.	0			c.G1896A						.						32	39	36					7																	6189723		2032	4174	6206	SO:0001819	synonymous_variant	84132	exon13			GATTGTGAGCTCC	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"Ubiquitin-specific peptidases"	20068	protein-coding gene	gene with protein product			"ubiquitin specific protease 42"			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.1896G>A	chr7.hg19:g.6189723G>A		107.0	0.0		85.0	19.0	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Silent	SNP	ENST00000306177.5	hg19	CCDS47535.1																																																																																			.	.		0.582	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526		A	6189723	G	A	6189723	2	1	200	1	0	0	0	0	0	0	0	1	17088	1277	45	3		3	USP42	7	6189723	Silent	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10		6189723	152948940	49	29411										
DLX5	1749	hgsc.bcm.edu	37	chr7	96650094	96650094	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ccagcgggtgctgtaaggagCccggcggcggcaggtgggaa	20	10	0	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:96650094C>T	ENST00000222598.4	-	3	1297	c.824G>A	c.(823-825)gGc>gAc	p.G275D	DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	275					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					CTGTAAGGAGCCCGGCGGCGG	0.572																																					p.G275D		Atlas-SNP	.											.	DLX5	52	.	0			c.G824A						.						47	54	51					7																	96650094		2203	4300	6503	SO:0001583	missense	1749	exon3			AAGGAGCCCGGCG		CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"Homeoboxes / ANTP class : NKL subclass"	2918	protein-coding gene	gene with protein product		600028	"distal-less homeo box 5"			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.824G>A	chr7.hg19:g.96650094C>T	ENSP00000222598:p.Gly275Asp	114.0	0.0		96.0	32.0	NM_005221	B7Z4P3|Q9UPL1	Missense_Mutation	SNP	ENST00000222598.4	hg19	CCDS5647.1	.	.	.	.	.	.	.	.	.	.	C	8.944	0.966557	0.18659	.	.	ENSG00000105880	ENST00000222598	D	0.89123	-2.47	5.34	4.45	0.53987	.	0.177624	0.51477	D	0.000085	D	0.82926	0.5143	L	0.43152	1.355	0.38939	D	0.958102	B	0.21071	0.051	B	0.16722	0.016	T	0.79169	-0.1914	10	0.39692	T	0.17	-13.3977	9.004	0.36100	0.0:0.6517:0.2722:0.0761	.	275	P56178	DLX5_HUMAN	D	275	ENSP00000222598:G275D	ENSP00000222598:G275D	G	-	2	0	DLX5	96488030	1.000000	0.71417	0.996000	0.52242	0.453000	0.32348	1.942000	0.40243	2.659000	0.90383	0.655000	0.94253	GGC	.	.		0.572	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			T	96650094	C	T	96650094	3	4	200	1	0	0	0	0	1	0	0	0	4576	739	26	3	49	3	DLX5	7	96650094	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	90460371	96650094	62488569	50	29412										
AGFG2	3268	hgsc.bcm.edu	37	chr7	100160302	100160302	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gcagcacagggctggcctttGgaggtgagtcctgcctgtgg	17	10	0	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:100160302G>A	ENST00000300176.4	+	8	1206	c.1084G>A	c.(1084-1086)Gga>Aga	p.G362R	AGFG2_ENST00000262935.4_3'UTR|AGFG2_ENST00000474713.1_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	362					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCTGGCCTTTGGAGGTGAGTC	0.657																																					p.G362R		Atlas-SNP	.											.	AGFG2	44	.	0			c.G1084A						.						20	22	21					7																	100160302		2202	4300	6502	SO:0001583	missense	3268	exon8			GCCTTTGGAGGTG	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"ADP-ribosylation factor GTPase activating proteins"	5177	protein-coding gene	gene with protein product		604019	"HIV-1 Rev binding protein-like"	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1084G>A	chr7.hg19:g.100160302G>A	ENSP00000300176:p.Gly362Arg	48.0	0.0		25.0	12.0	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	hg19	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577412	0.86645	.	.	ENSG00000106351	ENST00000300176	T	0.28666	1.6	5.0	5.0	0.66597	.	0.299228	0.30830	N	0.008794	T	0.51941	0.1704	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.52147	-0.8614	10	0.66056	D	0.02	-4.2535	13.7212	0.62728	0.0:0.0:1.0:0.0	.	362	O95081	AGFG2_HUMAN	R	362	ENSP00000300176:G362R	ENSP00000300176:G362R	G	+	1	0	AGFG2	99998238	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.235000	0.58666	2.610000	0.88304	0.549000	0.68633	GGA	.	.		0.657	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076		A	100160302	G	A	100160302	3	1	200	1	0	0	0	0	1	0	0	0	381	1349	47	3	1114	3	AGFG2	7	100160302	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	3510208	100160302	58978361	51	29413										
SRRT	51593	hgsc.bcm.edu	37	chr7	100483551	100483552	+	Frame_Shift_Ins	INS	-	-	A													0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	agagatctgttggaacctgcINSagaacatccgtgtgagtgct							TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:100483551_100483552insA	ENST00000347433.4	+	12	1605_1606	c.1447_1448insA	c.(1447-1449)cagfs	p.Q483fs	SRRT_ENST00000388793.4_Frame_Shift_Ins_p.Q482fs|SRRT_ENST00000457580.2_Frame_Shift_Ins_p.Q483fs|SRRT_ENST00000432932.1_Frame_Shift_Ins_p.Q482fs			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	483					cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						TTGGAACCTGCAGAACATCCGT	0.495																																					p.Q483fs		Atlas-INDEL	.											.	SRRT	108	.	0			c.1447_1448insA						.																																			SO:0001589	frameshift_variant	51593	exon12			.		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.1448dupA	chr7.hg19:g.100483552_100483552dupA	ENSP00000314491:p.Gln483fs	141.0	0.0		100.0	36.0	NM_001128853	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Frame_Shift_Ins	INS	ENST00000347433.4	hg19	CCDS34709.1																																																																																			.	.		0.495	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		A	100483552	-	A	100483551	7	5	200	1	0	1	1	0	0	0	0	0	15187	711	25	0	1489	0	SRRT	7	100483551	Frame_Shift_Ins	INS	-	TCGA-DD-AADR-01A-11D-A40R-10	323249	100483551	58655112	52	29414										
TRIM56	81844	hgsc.bcm.edu	37	chr7	100732328	100732328	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tcatcaaccccaacggcgaaGtgcagtggcgcagggccctg	13	14	2	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:100732328G>A	ENST00000306085.6	+	3	2032	c.1735G>A	c.(1735-1737)Gtg>Atg	p.V579M		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	579					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					CAACGGCGAAGTGCAGTGGCG	0.716																																					p.V579M	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.G1735A						.						53	59	57					7																	100732328		2102	4203	6305	SO:0001583	missense	81844	exon3			GGCGAAGTGCAGT	BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19028	protein-coding gene	gene with protein product			"tripartite motif-containing 56"				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.1735G>A	chr7.hg19:g.100732328G>A	ENSP00000305161:p.Val579Met	31.0	0.0		31.0	10.0	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Missense_Mutation	SNP	ENST00000306085.6	hg19	CCDS43625.1	.	.	.	.	.	.	.	.	.	.	G	9.141	1.013807	0.19277	.	.	ENSG00000169871	ENST00000306085	T	0.32988	1.43	3.87	2.98	0.34508	Six-bladed beta-propeller, TolB-like (1);	.	.	.	.	T	0.19927	0.0479	N	0.14661	0.345	0.24224	N	0.995424	P	0.44627	0.839	B	0.43575	0.424	T	0.05886	-1.0858	9	0.56958	D	0.05	.	7.2567	0.26181	0.1196:0.0:0.8804:0.0	.	579	Q9BRZ2	TRI56_HUMAN	M	579	ENSP00000305161:V579M	ENSP00000305161:V579M	V	+	1	0	TRIM56	100519048	0.999000	0.42202	0.948000	0.38648	0.317000	0.28152	1.146000	0.31589	1.219000	0.43474	0.586000	0.80456	GTG	.	.		0.716	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961		A	100732328	G	A	100732328	3	1	200	1	0	0	0	0	1	0	0	0	16545	1029	36	3	1737	3	TRIM56	7	100732328	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	248777	100732328	58406335	53	29415										
DLD	1738	hgsc.bcm.edu	37	chr7	107558474	107558474	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tccttgggcagaaatcgacaGacagagtactgggagcacat	12	9	0	3			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:107558474G>A	ENST00000205402.5	+	12	1623	c.1342G>A	c.(1342-1344)Gac>Aac	p.D448N	DLD_ENST00000440410.1_Missense_Mutation_p.D425N|DLD_ENST00000537148.1_Missense_Mutation_p.D349N|DLD_ENST00000437604.2_Missense_Mutation_p.D400N	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	448					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	GAAATCGACAGACAGAGTACT	0.398																																					p.D448N		Atlas-SNP	.											.	DLD	72	.	0			c.G1342A						.						134	126	129					7																	107558474		2203	4300	6503	SO:0001583	missense	1738	exon12			TCGACAGACAGAG	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.1342G>A	chr7.hg19:g.107558474G>A	ENSP00000205402:p.Asp448Asn	201.0	0.0		176.0	34.0	NM_000108	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Missense_Mutation	SNP	ENST00000205402.5	hg19	CCDS5749.1	.	.	.	.	.	.	.	.	.	.	G	32	5.177864	0.94846	.	.	ENSG00000091140	ENST00000205402;ENST00000417551;ENST00000537148;ENST00000440410;ENST00000437604;ENST00000539590	D;D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08;-3.08	6.07	5.19	0.71726	FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (2);	0.000000	0.85682	D	0.000000	D	0.95408	0.8509	M	0.62088	1.915	0.80722	D	1	D;P;D	0.89917	1.0;0.853;1.0	D;P;D	0.97110	1.0;0.874;1.0	D	0.95850	0.8874	10	0.87932	D	0	-7.9006	17.4012	0.87460	0.0:0.1247:0.8753:0.0	.	425;400;448	E9PEX6;B4DT69;P09622	.;.;DLDH_HUMAN	N	448;448;349;425;400;398	ENSP00000205402:D448N;ENSP00000390667:D448N;ENSP00000442399:D349N;ENSP00000417016:D425N;ENSP00000387542:D400N	ENSP00000205402:D448N	D	+	1	0	DLD	107345710	1.000000	0.71417	0.940000	0.37924	0.982000	0.71751	9.869000	0.99810	1.556000	0.49512	0.655000	0.94253	GAC	.	.		0.398	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108		A	107558474	G	A	107558474	3	1	200	1	0	0	0	0	1	0	0	0	4553	942	33	3	1388	3	DLD	7	107558474	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	6826146	107558474	51580189	54	29416										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107818532	107818532	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tccagtgttggattcacaatCttcaaagacgagggagcact	10	9	3	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:107818532C>A	ENST00000425651.2	-	23	2876	c.2877G>T	c.(2875-2877)aaG>aaT	p.K959N	NRCAM_ENST00000379028.3_Missense_Mutation_p.K959N|NRCAM_ENST00000379024.4_Missense_Mutation_p.K940N|NRCAM_ENST00000351718.4_Missense_Mutation_p.K943N|NRCAM_ENST00000413765.2_Missense_Mutation_p.K940N|NRCAM_ENST00000379022.4_Missense_Mutation_p.K959N	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	959	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GATTCACAATCTTCAAAGACG	0.428																																					p.K959N		Atlas-SNP	.											.	NRCAM	267	.	0			c.G2877T						.						83	73	77					7																	107818532		2203	4300	6503	SO:0001583	missense	4897	exon23			CACAATCTTCAAA		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.2877G>T	chr7.hg19:g.107818532C>A	ENSP00000401244:p.Lys959Asn	176.0	0.0		154.0	53.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.033160	0.35893	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022	T;T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31;0.31	6.05	5.16	0.70880	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.195360	0.53938	D	0.000043	T	0.48095	0.1481	L	0.41492	1.28	0.42549	D	0.993103	B;B;B;B;B	0.22909	0.077;0.003;0.009;0.007;0.014	B;B;B;B;B	0.28991	0.097;0.017;0.034;0.011;0.067	T	0.43097	-0.9412	10	0.31617	T	0.26	.	9.3878	0.38354	0.1435:0.7841:0.0:0.0724	.	959;940;940;943;959	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	N	959;959;940;959;943;940;959;959	ENSP00000368314:K959N;ENSP00000407858:K940N;ENSP00000325269:K943N;ENSP00000368310:K940N;ENSP00000401244:K959N;ENSP00000368308:K959N	ENSP00000325269:K943N	K	-	3	2	NRCAM	107605768	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	0.743000	0.26231	1.533000	0.49186	0.650000	0.86243	AAG	.	.		0.428	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		A	107818532	C	A	107818532	3	1	200	1	0	0	0	0	1	0	0	0	10653	912	32	3	1099	3	NRCAM	7	107818532	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	260058	107818532	51320131	55	29417										
RALYL	138046	hgsc.bcm.edu	37	chr8	85774619	85774619	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tggcagtcacaacgactcgcAgggggaaaggagtcttttcc	13	10	2	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr8:85774619A>C	ENST00000521268.1	+	6	1607	c.502A>C	c.(502-504)Agg>Cgg	p.R168R	RALYL_ENST00000522455.1_Silent_p.R168R|RALYL_ENST00000517638.1_Silent_p.R181R|RALYL_ENST00000518566.1_Silent_p.R157R|RALYL_ENST00000521376.1_Silent_p.R79R|RALYL_ENST00000521695.1_Silent_p.R168R|RALYL_ENST00000523850.1_Silent_p.R95R	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	168							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						AACGACTCGCAGGGGGAAAGG	0.473																																					p.R181R		Atlas-SNP	.											.	RALYL	123	.	0			c.A541C						.						59	63	62					8																	85774619		1920	4138	6058	SO:0001819	synonymous_variant	138046	exon6			ACTCGCAGGGGGA		CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"RNA binding motif (RRM) containing"	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.502A>C	chr8.hg19:g.85774619A>C		71.0	0.0		119.0	16.0	NM_001100391	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Silent	SNP	ENST00000521268.1	hg19	CCDS55253.1																																																																																			.	.		0.473	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1			C	85774619	A	C	85774619	2	2	200	1	0	0	0	0	0	0	0	1	13035	179	7	5		5	RALYL	8	85774619	Silent	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10		85774619	60589403	56	29418										
CDH17	1015	hgsc.bcm.edu	37	chr8	95182668	95182668	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tcaaatacggttactggtgaCggacatgtaggtggattatc	12	6	1	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr8:95182668C>T	ENST00000027335.3	-	9	1147	c.1023G>A	c.(1021-1023)ccG>ccA	p.P341P	CDH17_ENST00000441892.2_Intron|CDH17_ENST00000450165.2_Silent_p.P341P	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	341	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			TTACTGGTGACGGACATGTAG	0.418																																					p.P341P		Atlas-SNP	.											.	CDH17	119	.	0			c.G1023A						.						158	146	150					8																	95182668		2203	4300	6503	SO:0001819	synonymous_variant	1015	exon9			TGGTGACGGACAT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1023G>A	chr8.hg19:g.95182668C>T		217.0	0.0		248.0	17.0	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	hg19	CCDS6260.1																																																																																			.	.		0.418	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		T	95182668	C	T	95182668	2	4	200	1	0	0	0	0	0	0	0	1	3104	523	19	1		1	CDH17	8	95182668	Silent	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	9408049	95182668	51181354	57	29419										
CCIN	881	hgsc.bcm.edu	37	chr9	36169649	36169649	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	aatgtgctggctgctgtctcCccactggtgaggagcctcat	12	12	2	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr9:36169649C>A	ENST00000335119.2	+	1	261	c.150C>A	c.(148-150)tcC>tcA	p.S50S		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	50	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			CTGCTGTCTCCCCACTGGTGA	0.537																																					p.S50S		Atlas-SNP	.											.	CCIN	56	.	0			c.C150A						.						132	122	125					9																	36169649		2203	4300	6503	SO:0001819	synonymous_variant	881	exon1			TGTCTCCCCACTG	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"BTB/POZ domain containing"	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.150C>A	chr9.hg19:g.36169649C>A		179.0	0.0		152.0	62.0	NM_005893	Q9BXG7	Silent	SNP	ENST00000335119.2	hg19	CCDS6599.1																																																																																			.	.		0.537	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893		A	36169649	C	A	36169649	2	1	200	1	0	0	0	0	0	0	0	1	2880	610	22	3		3	CCIN	9	36169649	Silent	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10		36169649	105043782	58	29420										
FOXB2	442425	hgsc.bcm.edu	37	chr9	79635418	79635418	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tggccgggactacaagggcgTgctgcaggctggagggctgc	19	10	0	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr9:79635418T>A	ENST00000376708.1	+	1	848	c.848T>A	c.(847-849)gTg>gAg	p.V283E		NM_001013735.1	NP_001013757.1	Q5VYV0	FOXB2_HUMAN	forkhead box B2	283					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|lung(8)|ovary(1)	10						TACAAGGGCGTGCTGCAGGCT	0.697																																					p.V283E		Atlas-SNP	.											.	FOXB2	71	.	0			c.T848A						.						42	42	42					9																	79635418		2203	4300	6503	SO:0001583	missense	442425	exon1			AGGGCGTGCTGCA		CCDS35045.1	9q21.2	2008-02-05			ENSG00000204612	ENSG00000204612		"Forkhead boxes"	23315	protein-coding gene	gene with protein product							Standard	NM_001013735		Approved	bA159H20.4	uc004ako.1	Q5VYV0	OTTHUMG00000020051	ENST00000376708.1:c.848T>A	chr9.hg19:g.79635418T>A	ENSP00000365898:p.Val283Glu	97.0	0.0		74.0	24.0	NM_001013735		Missense_Mutation	SNP	ENST00000376708.1	hg19	CCDS35045.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.064103	0.55432	.	.	ENSG00000204612	ENST00000376708	D	0.96232	-3.95	3.41	3.41	0.39046	.	0.000000	0.37178	U	0.002206	D	0.95169	0.8434	L	0.42245	1.32	0.43885	D	0.996504	D	0.65815	0.995	D	0.70487	0.969	D	0.91991	0.5603	10	0.07482	T	0.82	.	5.851	0.18694	0.2354:0.0:0.0:0.7645	.	283	Q5VYV0	FOXB2_HUMAN	E	283	ENSP00000365898:V283E	ENSP00000365898:V283E	V	+	2	0	FOXB2	78825238	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	2.523000	0.45580	1.400000	0.46741	0.379000	0.24179	GTG	.	.		0.697	FOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052745.1	NM_001013735		A	79635418	T	A	79635418	3	1	200	1	0	0	0	0	1	0	0	0	6001	1696	59	4	850	4	FOXB2	9	79635418	Missense_Mutation	SNP	T	TCGA-DD-AADR-01A-11D-A40R-10	43465769	79635418	61578013	59	29421										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79922965	79922965	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cctgctgtaacaaaagaccaAtacagtgccactagtggagt	9	10	0	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr9:79922965A>G	ENST00000360280.3	+	35	4325	c.4065A>G	c.(4063-4065)caA>caG	p.Q1355Q	VPS13A_ENST00000423463.2_3'UTR|VPS13A_ENST00000376636.3_Silent_p.Q1316Q|VPS13A_ENST00000376634.4_Silent_p.Q1355Q|VPS13A_ENST00000357409.5_Silent_p.Q1355Q	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1355					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CAAAAGACCAATACAGTGCCA	0.343																																					p.Q1355Q		Atlas-SNP	.											.	VPS13A	735	.	0			c.A4065G						.						172	169	170					9																	79922965		2203	4300	6503	SO:0001819	synonymous_variant	23230	exon35			AGACCAATACAGT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.4065A>G	chr9.hg19:g.79922965A>G		375.0	0.0		280.0	71.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	hg19	CCDS6655.1																																																																																			.	.		0.343	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		G	79922965	A	G	79922965	2	3	200	1	0	0	0	0	0	0	0	1	17204	98	4	2		2	VPS13A	9	79922965	Silent	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	287547	79922965	61290466	60	29422										
WDR38	401551	hgsc.bcm.edu	37	chr9	127619833	127619834	+	Frame_Shift_Ins	INS	-	-	A													0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	accccagatgggaaaatcttINSagtgtctggagctgccgatc							TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr9:127619833_127619834insA	ENST00000373574.1	+	9	925_926	c.869_870insA	c.(868-873)ttagtgfs	p.V291fs		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	291					hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						GGGAAAATCTTAGTGTCTGGAG	0.554																																					p.L291fs		Atlas-INDEL	.											.	WDR38	21	.	0			c.872_873insA						.																																			SO:0001589	frameshift_variant	401551	exon9			.		CCDS43876.1, CCDS75898.1, CCDS75899.1	9q33.3	2013-01-09			ENSG00000136918	ENSG00000136918		"WD repeat domain containing"	23745	protein-coding gene	gene with protein product							Standard	NM_001276375		Approved		uc011lzo.3	Q5JTN6	OTTHUMG00000020664	ENST00000373574.1:c.870dupA	chr9.hg19:g.127619834_127619834dupA	ENSP00000362677:p.Val291fs	95.0	0.0		89.0	15.0	NM_001276374	A0PK24	Frame_Shift_Ins	INS	ENST00000373574.1	hg19	CCDS43876.1																																																																																			.	.		0.554	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476		A	127619834	-	A	127619833	7	5	200	1	0	1	1	0	0	0	0	0	17307	1764	61	0	903	0	WDR38	9	127619833	Frame_Shift_Ins	INS	-	TCGA-DD-AADR-01A-11D-A40R-10	47696868	127619833	13593598	61	29423										
THNSL1	79896	hgsc.bcm.edu	37	chr10	25312662	25312662	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cgtctaaaattaatgaagacAgataggattgtaggtcagaa	10	4	2	4			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr10:25312662A>T	ENST00000524413.1	+	3	857	c.510A>T	c.(508-510)acA>acT	p.T170T	THNSL1_ENST00000376356.4_Silent_p.T170T			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	170						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	TAATGAAGACAGATAGGATTG	0.343																																					p.T170T		Atlas-SNP	.											.	THNSL1	70	.	0			c.A510T						.						56	57	56					10																	25312662		2203	4300	6503	SO:0001819	synonymous_variant	79896	exon3			GAAGACAGATAGG	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"threonine synthase-like 1 (bacterial)"			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.510A>T	chr10.hg19:g.25312662A>T		71.0	0.0		54.0	20.0	NM_024838	B3KWL1|D3DRV3|Q5VV21	Silent	SNP	ENST00000524413.1	hg19	CCDS7147.1																																																																																			.	.		0.343	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838		T	25312662	A	T	25312662	2	4	200	1	0	0	0	0	0	0	0	1	15877	175	7	4		4	THNSL1	10	25312662	Silent	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10		25312662	110222085	62	29424										
LDB3	94233	hgsc.bcm.edu	37	chr10	88428477	88428477	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cagtgtgaccctgactgggcCcgggccctggggcttccgtc	15	15	0	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr10:88428477C>A	ENST00000241891.5	+	0	2308				LDB3_ENST00000263066.6_Missense_Mutation_p.P10H|LDB3_ENST00000372066.3_Missense_Mutation_p.P10H|LDB3_ENST00000458213.2_Missense_Mutation_p.P10H|LDB3_ENST00000310944.6_Missense_Mutation_p.P10H|LDB3_ENST00000361373.4_Missense_Mutation_p.P10H|LDB3_ENST00000372056.4_Missense_Mutation_p.P10H|LDB3_ENST00000542786.1_Missense_Mutation_p.P10H|LDB3_ENST00000352360.5_Missense_Mutation_p.P10H|LDB3_ENST00000429277.2_Missense_Mutation_p.P10H	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4						phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						CTGACTGGGCCCGGGCCCTGG	0.642																																					p.P10H		Atlas-SNP	.											.	LDB3	164	.	0			c.C29A						.						52	57	55					10																	88428477		2203	4300	6503	SO:0001628	intergenic_variant	11155	exon1			CTGGGCCCGGGCC	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"GPCR / Class A : Opsin receptors"	14449	protein-coding gene	gene with protein product	"melanopsin"	606665	"opsin 4 (melanopsin)"			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654		chr10.hg19:g.88428477C>A		120.0	0.0		89.0	18.0	NM_007078	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	hg19	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888670	0.91814	.	.	ENSG00000122367	ENST00000539402;ENST00000429277;ENST00000458213;ENST00000352360;ENST00000372066;ENST00000263066;ENST00000372056;ENST00000310944;ENST00000361373;ENST00000542786	T;T;T;T;T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71	5.5	5.5	0.81552	PDZ/DHR/GLGF (3);	0.000000	0.32204	N	0.006423	T	0.65228	0.2671	H	0.94620	3.56	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;0.999;1.0;0.966	T	0.75844	-0.3174	10	0.87932	D	0	.	19.4084	0.94658	0.0:1.0:0.0:0.0	.	10;10;10;10;10;10;10	B4E3K3;F5H0C2;O75112-4;O75112;O75112-2;O75112-5;O75112-6	.;.;.;LDB3_HUMAN;.;.;.	H	10	ENSP00000401437:P10H;ENSP00000409148:P10H;ENSP00000263067:P10H;ENSP00000361136:P10H;ENSP00000263066:P10H;ENSP00000361126:P10H;ENSP00000311913:P10H;ENSP00000355296:P10H;ENSP00000438866:P10H	ENSP00000263066:P10H	P	+	2	0	LDB3	88418457	1.000000	0.71417	0.987000	0.45799	0.918000	0.54935	7.717000	0.84732	2.593000	0.87608	0.655000	0.94253	CCC	.	.		0.642	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282		A	88428477	C	A	88428477	1	1	200	0	1	0	0	0	0	0	0	0	8706	623	22	3		3	LDB3	10	88428477	IGR	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	63115815	88428477	47106270	63	29425										
IFITM3	10410	hgsc.bcm.edu	37	chr11	320798	320798	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gacaggagagaagaaggtttGgacagtgtgattcatggtgt	16	3	1	3			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:320798G>A	ENST00000399808.4	-	1	252	c.16C>T	c.(16-18)Caa>Taa	p.Q6*	RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000526811.1_Intron|IFITM3_ENST00000602735.1_Intron|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.11_ENST00000602429.1_RNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	6					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		AAGAAGGTTTGGACAGTGTGA	0.587																																					p.Q6X		Atlas-SNP	.											.	IFITM3	132	.	0			c.C16T						.						127	141	137					11																	320798		1936	4144	6080	SO:0001587	stop_gained	10410	exon1			AGGTTTGGACAGT	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"interferon induced transmembrane protein 3 (1-8U)"			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.16C>T	chr11.hg19:g.320798G>A	ENSP00000382707:p.Gln6*	42.0	0.0		30.0	7.0	NM_021034	Q53Y76|Q96HK8|Q96J15	Nonsense_Mutation	SNP	ENST00000399808.4	hg19	CCDS41585.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.709345	0.89018	.	.	ENSG00000142089	ENST00000399808	.	.	.	4.0	-0.68	0.11346	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	2.8102	0.05440	0.1039:0.3287:0.3958:0.1716	.	.	.	.	X	6	.	ENSP00000382707:Q6X	Q	-	1	0	IFITM3	310798	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.448000	0.21726	-0.188000	0.10499	0.405000	0.27470	CAA	.	.		0.587	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034		A	320798	G	A	320798	4	1	200	1	0	0	0	0	0	1	0	0	7537	1357	47	3	393	3	IFITM3	11	320798	Nonsense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10		320798	134685718	64	29426										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1275529	1275529	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cctcagcatccactacaagtCcatggatatcgtcctcactg	6	15	2	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:1275529C>A	ENST00000529681.1	+	34	15483	c.15425C>A	c.(15424-15426)tCc>tAc	p.S5142Y	MUC5B_ENST00000447027.1_Missense_Mutation_p.S5145Y	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5142	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CACTACAAGTCCATGGATATC	0.632																																					p.S5142Y		Atlas-SNP	.											.	MUC5B	473	.	0			c.C15425A						.						34	41	39					11																	1275529		2163	4263	6426	SO:0001583	missense	727897	exon34			ACAAGTCCATGGA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.15425C>A	chr11.hg19:g.1275529C>A	ENSP00000436812:p.Ser5142Tyr	47.0	0.0		49.0	16.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106012	0.37145	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.18810	2.19;2.38	4.31	3.32	0.38043	.	.	.	.	.	T	0.40423	0.1116	L	0.58101	1.795	0.09310	N	1	D;D	0.71674	0.998;0.998	D;D	0.67900	0.954;0.954	T	0.10109	-1.0644	9	0.87932	D	0	.	12.7585	0.57350	0.1639:0.836:0.0:0.0	.	5479;5145	A7Y9J9;E9PBJ0	.;.	Y	5142;5145;5086;41;4854	ENSP00000436812:S5142Y;ENSP00000415793:S5145Y	ENSP00000343037:S5086Y	S	+	2	0	MUC5B	1232105	0.008000	0.16893	0.057000	0.19452	0.716000	0.41182	1.502000	0.35704	2.119000	0.64992	0.400000	0.26472	TCC	.	.		0.632	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1275529	C	A	1275529	3	1	200	1	0	0	0	0	1	0	0	0	9988	855	30	3	15568	3	MUC5B	11	1275529	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	954731	1275529	133730987	65	29427										
ELP4	26610	hgsc.bcm.edu	37	chr11	31653846	31653846	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cgatatttgctgtgcagaaaAtggtggcaacagtcacagcc	11	9	1	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:31653846A>C	ENST00000350638.5	+	7	856	c.821A>C	c.(820-822)aAt>aCt	p.N274T	ELP4_ENST00000395934.2_Missense_Mutation_p.N274T|ELP4_ENST00000379163.5_Missense_Mutation_p.N275T	NM_019040.3	NP_061913.3	Q96EB1	ELP4_HUMAN	elongator acetyltransferase complex subunit 4	274					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)			breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)	20	Lung SC(675;0.225)					TGTGCAGAAAATGGTGGCAAC	0.418																																					p.N274T		Atlas-SNP	.											.	ELP4	78	.	0			c.A821C						.						119	115	116					11																	31653846		1910	4131	6041	SO:0001583	missense	26610	exon7			CAGAAAATGGTGG	AJ276005	CCDS7875.2, CCDS73271.1, CCDS73272.1	11p13	2012-08-14	2012-08-08	2002-05-24	ENSG00000109911	ENSG00000109911		"Elongator acetyltransferase complex subunits"	1171	protein-coding gene	gene with protein product		606985	"chromosome 11 open reading frame 19", "elongation protein 4 homolog (S. cerevisiae)"	C11orf19		11889558, 11435442	Standard	XM_005252865		Approved	PAXNEB	uc001mtb.3	Q96EB1	OTTHUMG00000142919	ENST00000350638.5:c.821A>C	chr11.hg19:g.31653846A>C	ENSP00000298937:p.Asn274Thr	118.0	0.0		110.0	30.0	NM_019040	B4E3W0|E7EPZ6|Q9H4E8|Q9NX11	Missense_Mutation	SNP	ENST00000350638.5	hg19	CCDS7875.2	.	.	.	.	.	.	.	.	.	.	A	5.186	0.219839	0.09863	.	.	ENSG00000109911	ENST00000350638;ENST00000379163;ENST00000395934	T;T;T	0.41065	1.01;1.01;1.01	5.85	2.35	0.29111	.	0.464639	0.26708	N	0.022907	T	0.20780	0.0500	N	0.16368	0.405	0.23943	N	0.996399	B;B;B	0.30914	0.3;0.062;0.028	B;B;B	0.25987	0.065;0.05;0.027	T	0.13335	-1.0513	10	0.21540	T	0.41	-5.0039	6.5047	0.22188	0.5829:0.1821:0.2349:0.0	.	275;274;274	B4E3W0;G5E9D4;Q96EB1	.;.;ELP4_HUMAN	T	274;275;274	ENSP00000298937:N274T;ENSP00000368461:N275T;ENSP00000379267:N274T	ENSP00000298937:N274T	N	+	2	0	ELP4	31610422	0.502000	0.26107	0.455000	0.27031	0.345000	0.29048	0.704000	0.25661	0.487000	0.27698	0.528000	0.53228	AAT	.	.		0.418	ELP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286640.1	NM_019040		C	31653846	A	C	31653846	3	2	200	1	0	0	0	0	1	0	0	0	5084	101	4	5	847	5	ELP4	11	31653846	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	30378317	31653846	103352670	66	29428										
ATM	472	hgsc.bcm.edu	37	chr11	108117798	108117798	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gaaagtattcttcaggatttCgtaatattgccgtcaaagaa	8	6	3	1	rs138398778		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:108117798C>T	ENST00000452508.2	+	9	1198	c.1009C>T	c.(1009-1011)Cgt>Tgt	p.R337C	ATM_ENST00000278616.4_Missense_Mutation_p.R337C			Q13315	ATM_HUMAN	ATM serine/threonine kinase	337			R -> C (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.|R -> H (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.R337C(3)|p.R337S(2)|p.F336_A340del(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TTCAGGATTTCGTAATATTGC	0.323			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.R337C		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	ATM_ENST00000278616,NS,adenocarcinoma,-1,16	ATM	1657	.	6	Substitution - Missense(5)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(3)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)	c.C1009T						.	C	CYS/ARG	0,4402		0,0,2201	60	61	61		1009	5.7	1	11	dbSNP_134	61	1,8595	1.2+/-3.3	0,1,4297	yes	missense	ATM	NM_000051.3	180	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	337/3057	108117798	1,12997	2201	4298	6499	SO:0001583	missense	472	exon8	Familial Cancer Database	AT, Louis-Bar syndrome	GGATTTCGTAATA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.1009C>T	chr11.hg19:g.108117798C>T	ENSP00000388058:p.Arg337Cys	239.0	0.0		208.0	66.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568847	0.86439	0.0	1.16E-4	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.02369	4.32;4.62;4.62	5.72	5.72	0.89469	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.15565	0.0375	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.00022	-1.2342	10	0.87932	D	0	.	19.8868	0.96915	0.0:1.0:0.0:0.0	.	337	Q13315	ATM_HUMAN	C	337	ENSP00000435747:R337C;ENSP00000278616:R337C;ENSP00000388058:R337C	ENSP00000278616:R337C	R	+	1	0	ATM	107623008	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.213000	0.58520	2.709000	0.92574	0.655000	0.94253	CGT	.	C|1.000;T|0.000		0.323	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108117798	C	T	108117798	3	4	200	1	0	0	0	0	1	0	0	0	1109	884	31	1	1035	1	ATM	11	108117798	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	76463952	108117798	26888718	67	29429										
ROBO3	64221	hgsc.bcm.edu	37	chr11	124743649	124743649	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ccagttcccctccgggggctCcctctcagccagtggtcact	10	18	2	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:124743649C>T	ENST00000397801.1	+	11	1867	c.1675C>T	c.(1675-1677)Ccc>Tcc	p.P559S	ROBO3_ENST00000538940.1_Missense_Mutation_p.P537S	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	559	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		TCCGGGGGCTCCCTCTCAGCC	0.527																																					p.P559S		Atlas-SNP	.											.	ROBO3	199	.	0			c.C1675T						.						35	38	37					11																	124743649		1864	4085	5949	SO:0001583	missense	64221	exon11			GGGGCTCCCTCTC	AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13433	protein-coding gene	gene with protein product		608630	"roundabout (axon guidance receptor, Drosophila) homolog 3", "horizontal gaze palsy with progressive scoliosis"	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.1675C>T	chr11.hg19:g.124743649C>T	ENSP00000380903:p.Pro559Ser	69.0	0.0		66.0	23.0	NM_022370		Missense_Mutation	SNP	ENST00000397801.1	hg19	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.853629	0.71719	.	.	ENSG00000154134	ENST00000397801;ENST00000538940	D;D	0.95069	-3.6;-3.6	5.71	5.71	0.89125	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41001	D	0.000976	D	0.98005	0.9343	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98715	1.0706	10	0.87932	D	0	.	18.6381	0.91385	0.0:1.0:0.0:0.0	.	559	Q96MS0	ROBO3_HUMAN	S	559;537	ENSP00000380903:P559S;ENSP00000441797:P537S	ENSP00000380903:P559S	P	+	1	0	ROBO3	124248859	1.000000	0.71417	1.000000	0.80357	0.368000	0.29767	7.721000	0.84768	2.702000	0.92279	0.563000	0.77884	CCC	.	.		0.527	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		T	124743649	C	T	124743649	3	4	200	1	0	0	0	0	1	0	0	0	13530	855	30	3	1717	3	ROBO3	11	124743649	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	16625851	124743649	10262867	68	29430										
BARX2	8538	hgsc.bcm.edu	37	chr11	129306802	129306802	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tgaggccccagggggcgaggCcctagccagcagcgagtcag	17	13	1	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:129306802C>A	ENST00000281437.4	+	2	440	c.344C>A	c.(343-345)gCc>gAc	p.A115D	BARX2_ENST00000526127.1_5'UTR	NM_003658.4	NP_003649.2	Q9UMQ3	BARX2_HUMAN	BARX homeobox 2	115					cartilage condensation (GO:0001502)|catagen (GO:0042637)|myotube differentiation (GO:0014902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	20	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)		GGGGGCGAGGCCCTAGCCAGC	0.687																																					p.A115D		Atlas-SNP	.											.	BARX2	40	.	0			c.C344A						.						35	41	39					11																	129306802		2201	4296	6497	SO:0001583	missense	8538	exon2			GCGAGGCCCTAGC	AF031924	CCDS8481.1	11q24.3	2011-06-20	2007-07-09		ENSG00000043039	ENSG00000043039		"Homeoboxes / ANTP class : NKL subclass"	956	protein-coding gene	gene with protein product		604823	"BarH-like homeobox 2"			10644443	Standard	NM_003658		Approved		uc001qfc.4	Q9UMQ3	OTTHUMG00000165776	ENST00000281437.4:c.344C>A	chr11.hg19:g.129306802C>A	ENSP00000281437:p.Ala115Asp	163.0	0.0		173.0	17.0	NM_003658	O43518|Q6NT51	Missense_Mutation	SNP	ENST00000281437.4	hg19	CCDS8481.1	.	.	.	.	.	.	.	.	.	.	C	7.481	0.648643	0.14516	.	.	ENSG00000043039	ENST00000281437	D	0.90504	-2.68	5.76	3.86	0.44501	Homeodomain-related (1);	0.371999	0.26130	N	0.026177	T	0.79125	0.4393	N	0.24115	0.695	0.80722	D	1	B	0.28713	0.22	B	0.24006	0.05	T	0.67764	-0.5586	10	0.12766	T	0.61	.	5.3255	0.15905	0.1594:0.6283:0.1364:0.076	.	115	Q9UMQ3	BARX2_HUMAN	D	115	ENSP00000281437:A115D	ENSP00000281437:A115D	A	+	2	0	BARX2	128812012	0.994000	0.37717	0.338000	0.25549	0.101000	0.19017	3.148000	0.50647	0.746000	0.32786	0.655000	0.94253	GCC	.	.		0.687	BARX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386153.1	NM_003658		A	129306802	C	A	129306802	3	1	200	1	0	0	0	0	1	0	0	0	1316	739	26	3	350	3	BARX2	11	129306802	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	4563153	129306802	5699714	69	29431										
IQSEC3	440073	hgsc.bcm.edu	37	chr12	248119	248119	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gcgggcaaggccgagcagggCgagacctctgggcgggaggc	21	11	1	1	rs548532490		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:248119C>A	ENST00000538872.1	+	4	1708	c.1590C>A	c.(1588-1590)ggC>ggA	p.G530G	IQSEC3_ENST00000382841.2_Silent_p.G227G|IQSEC3_ENST00000326261.4_Silent_p.G530G|RP11-598F7.4_ENST00000505893.2_RNA|RP11-598F7.4_ENST00000508953.2_RNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	530					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		CCGAGCAGGGCGAGACCTCTG	0.751																																					p.G530G		Atlas-SNP	.											.	IQSEC3	154	.	0			c.C1590A						.						14	13	14					12																	248119		2161	4216	6377	SO:0001819	synonymous_variant	440073	exon4			GCAGGGCGAGACC	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.1590C>A	chr12.hg19:g.248119C>A		69.0	0.0		68.0	27.0	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Silent	SNP	ENST00000538872.1	hg19	CCDS53728.1																																																																																			.	.		0.751	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		A	248119	C	A	248119	2	1	200	1	0	0	0	0	0	0	0	1	7828	755	27	1		1	IQSEC3	12	248119	Silent	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10		248119	133603776	70	29432										
SLC6A12	6539	hgsc.bcm.edu	37	chr12	301770	301770	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gggtacacatagacgttgttGtacttgaggggggtgtactt	15	5	0	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:301770G>A	ENST00000428720.1	-	15	2318	c.1575C>T	c.(1573-1575)taC>taT	p.Y525Y	SLC6A12_ENST00000397296.2_Silent_p.Y525Y|RP11-283I3.1_ENST00000544067.1_RNA|SLC6A12_ENST00000536824.1_Silent_p.Y525Y|SLC6A12_ENST00000424061.2_Silent_p.Y525Y|SLC6A12_ENST00000359674.4_Silent_p.Y525Y	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	525					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			AGACGTTGTTGTACTTGAGGG	0.572																																					p.Y525Y		Atlas-SNP	.											.	SLC6A12	60	.	0			c.C1575T						.						111	115	113					12																	301770		2203	4300	6503	SO:0001819	synonymous_variant	6539	exon15			GTTGTTGTACTTG	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"Solute carriers"	11045	protein-coding gene	gene with protein product	"betaine/GABA transporter-1"	603080	"solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.1575C>T	chr12.hg19:g.301770G>A		173.0	0.0		194.0	55.0	NM_001122848	A0AV52|B2R992|D3DUN8	Silent	SNP	ENST00000428720.1	hg19	CCDS8501.1																																																																																			.	.		0.572	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044		A	301770	G	A	301770	2	1	200	1	0	0	0	0	0	0	0	1	14690	1372	48	3		3	SLC6A12	12	301770	Silent	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	53651	301770	133550125	71	29433										
TROAP	10024	hgsc.bcm.edu	37	chr12	49725143	49725143	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ctccctcaggccccacccggGtctgcaccaaccctgtggct	9	20	2	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:49725143G>C	ENST00000257909.3	+	14	2321	c.2245G>C	c.(2245-2247)Gtc>Ctc	p.V749L	TROAP_ENST00000547923.1_Missense_Mutation_p.V428L|TROAP_ENST00000551245.1_Missense_Mutation_p.V839L	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	749					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						CCCCACCCGGGTCTGCACCAA	0.602											OREG0021792	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V749L		Atlas-SNP	.											.	TROAP	80	.	0			c.G2245C						.						52	50	50					12																	49725143		2203	4300	6503	SO:0001583	missense	10024	exon14			ACCCGGGTCTGCA	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"tastin"	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.2245G>C	chr12.hg19:g.49725143G>C	ENSP00000257909:p.Val749Leu	74.0	0.0	964	95.0	30.0	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Missense_Mutation	SNP	ENST00000257909.3	hg19	CCDS8784.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.903822	0.52333	.	.	ENSG00000135451	ENST00000551245;ENST00000257909;ENST00000547923	.	.	.	5.93	1.62	0.23740	.	0.707580	0.12780	N	0.439766	T	0.22589	0.0545	L	0.35854	1.095	0.25243	N	0.989735	B;B;B	0.33940	0.433;0.433;0.157	B;B;B	0.27887	0.084;0.084;0.05	T	0.19712	-1.0297	9	0.72032	D	0.01	-6.1667	4.072	0.09887	0.2873:0.1736:0.5391:0.0	.	839;428;749	F8W130;F8W1U0;Q12815	.;.;TROAP_HUMAN	L	839;749;428	.	ENSP00000257909:V749L	V	+	1	0	TROAP	48011410	0.983000	0.35010	0.964000	0.40570	0.961000	0.63080	0.270000	0.18607	0.848000	0.35191	0.561000	0.74099	GTC	.	.		0.602	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480		C	49725143	G	C	49725143	3	2	200	1	0	0	0	0	1	0	0	0	16590	1261	44	4	2397	4	TROAP	12	49725143	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	49423373	49725143	84126752	72	29434										
PFDN5	5204	hgsc.bcm.edu	37	chr12	53691669	53691669	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	aagctgcatgatgtggaacaCgtgctcatcgatgtgggaac	13	8	1	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:53691669C>T	ENST00000551018.1	+	4	520	c.243C>T	c.(241-243)caC>caT	p.H81H	PFDN5_ENST00000334478.4_Silent_p.H81H|C12orf10_ENST00000267103.5_5'Flank|PFDN5_ENST00000351500.3_Silent_p.H36H|PFDN5_ENST00000550846.1_Intron|C12orf10_ENST00000549488.1_5'Flank|RP11-680A11.5_ENST00000550263.1_RNA|C12orf10_ENST00000548632.1_5'Flank	NM_002624.3	NP_002615.2	Q99471	PFD5_HUMAN	prefoldin subunit 5	81					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	transcription corepressor activity (GO:0003714)			kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)	8						ATGTGGAACACGTGCTCATCG	0.512																																					p.H81H		Atlas-SNP	.											.	PFDN5	16	.	0			c.C243T						.						182	166	172					12																	53691669		2203	4300	6503	SO:0001819	synonymous_variant	5204	exon4			GGAACACGTGCTC	D89667	CCDS8853.1, CCDS8854.1	12q13.13	2008-05-14	2006-02-24						8869	protein-coding gene	gene with protein product		604899	"prefoldin 5"			9630229, 9792694	Standard	NM_002624		Approved	PFD5, MM-1	uc001scl.3	Q99471	OTTHUMG00000169675	ENST00000551018.1:c.243C>T	chr12.hg19:g.53691669C>T		119.0	0.0		105.0	11.0	NM_002624	A8K9A8|Q54AA8|Q9C083|Q9C084	Silent	SNP	ENST00000551018.1	hg19	CCDS8853.1																																																																																			.	.		0.512	PFDN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405368.2			T	53691669	C	T	53691669	2	4	200	1	0	0	0	0	0	0	0	1	11767	535	19	1		1	PFDN5	12	53691669	Silent	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	3966526	53691669	80160226	73	29435										
SP1	6667	hgsc.bcm.edu	37	chr12	53776141	53776141	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cagcaatggcagtgagtcttCcaagaatcgcacagtctctg	10	11	2	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:53776141C>T	ENST00000327443.4	+	3	508	c.410C>T	c.(409-411)tCc>tTc	p.S137F	SP1_ENST00000426431.2_Missense_Mutation_p.S130F	NM_001251825.1|NM_138473.2	NP_001238754.1|NP_612482.2	P08047	SP1_HUMAN	Sp1 transcription factor	137	Ser/Thr-rich.				cellular lipid metabolic process (GO:0044255)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|gene expression (GO:0010467)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|ossification (GO:0001503)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	bHLH transcription factor binding (GO:0043425)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|histone deacetylase binding (GO:0042826)|HMG box domain binding (GO:0071837)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.00527)		AGTGAGTCTTCCAAGAATCGC	0.537																																					p.S137F		Atlas-SNP	.											.	SP1	57	.	0			c.C410T						.						65	66	66					12																	53776141		2203	4300	6503	SO:0001583	missense	6667	exon3			AGTCTTCCAAGAA	J03133	CCDS8857.1, CCDS44898.1	12q13.1	2013-01-08						"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11205	protein-coding gene	gene with protein product	"specificity protein 1"	189906				1662663	Standard	NM_003109		Approved		uc001scw.3	P08047	OTTHUMG00000170047	ENST00000327443.4:c.410C>T	chr12.hg19:g.53776141C>T	ENSP00000329357:p.Ser137Phe	132.0	0.0		103.0	35.0	NM_138473	E4Z9M7|G5E9M8|Q86TN8|Q9H3Q5|Q9NR51|Q9NY21|Q9NYE7	Missense_Mutation	SNP	ENST00000327443.4	hg19	CCDS8857.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977718	0.53720	.	.	ENSG00000185591	ENST00000327443;ENST00000426431	T;T	0.09911	2.96;2.93	4.13	4.13	0.48395	.	0.000000	0.53938	D	0.000048	T	0.12689	0.0308	L	0.46157	1.445	0.46298	D	0.998978	D	0.54772	0.968	B	0.42062	0.374	T	0.04495	-1.0947	10	0.87932	D	0	.	15.6957	0.77494	0.0:1.0:0.0:0.0	.	137	P08047	SP1_HUMAN	F	137;130	ENSP00000329357:S137F;ENSP00000404263:S130F	ENSP00000329357:S137F	S	+	2	0	SP1	52062408	0.002000	0.14202	1.000000	0.80357	0.945000	0.59286	1.251000	0.32862	2.306000	0.77630	0.467000	0.42956	TCC	.	.		0.537	SP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407044.1			T	53776141	C	T	53776141	3	4	200	1	0	0	0	0	1	0	0	0	14974	855	30	3	420	3	SP1	12	53776141	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	84472	53776141	80075754	74	29436										
ATP2A2	488	hgsc.bcm.edu	37	chr12	110778773	110778773	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ctaaaatcgtagaatttcttCagtcttttgatgagattaca	6	6	3	3			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:110778773C>T	ENST00000539276.2	+	14	2180	c.2071C>T	c.(2071-2073)Cag>Tag	p.Q691*	ATP2A2_ENST00000395494.2_Nonsense_Mutation_p.Q664*|ATP2A2_ENST00000308664.6_Nonsense_Mutation_p.Q691*			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	691					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						AGAATTTCTTCAGTCTTTTGA	0.473																																					p.Q691X		Atlas-SNP	.											.	ATP2A2	78	.	0			c.C2071T						.						42	44	43					12																	110778773		2203	4300	6503	SO:0001587	stop_gained	488	exon14			TTTCTTCAGTCTT		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.2071C>T	chr12.hg19:g.110778773C>T	ENSP00000440045:p.Gln691*	146.0	0.0		136.0	36.0	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Nonsense_Mutation	SNP	ENST00000539276.2	hg19	CCDS9144.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.430852|6.430852	0.97559|0.97559	.|.	.|.	ENSG00000174437|ENSG00000174437	ENST00000308664;ENST00000395494;ENST00000539276|ENST00000548169	.|.	.|.	.|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.80037	.|0.4550	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77705	.|-0.2488	.|3	0.21540|.	T|.	0.41|.	.|.	20.0784|20.0784	0.97758|0.97758	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	691;664;691|581	.|.	ENSP00000311186:Q691X|.	Q|S	+|+	1|2	0|0	ATP2A2|ATP2A2	109263156|109263156	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.999000|0.999000	0.98932|0.98932	7.818000|7.818000	0.86416|0.86416	2.736000|2.736000	0.93811|0.93811	0.655000|0.655000	0.94253|0.94253	CAG|TCA	.	.		0.473	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		T	110778773	C	T	110778773	4	4	200	1	0	0	0	0	0	1	0	0	1137	827	29	3	2125	3	ATP2A2	12	110778773	Nonsense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	57002632	110778773	23073122	75	29437										
AQP9	366	hgsc.bcm.edu	37	chr15	58430833	58430833	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gtcttgaagagcagcttagcGaaagaaaccctctctgagtt	10	9	2	4	rs370186994		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr15:58430833G>A	ENST00000219919.4	+	1	439	c.69G>A	c.(67-69)gcG>gcA	p.A23A	ALDH1A2_ENST00000558231.1_Intron|AQP9_ENST00000559443.1_3'UTR|AQP9_ENST00000536493.1_Silent_p.A23A|AQP9_ENST00000558772.1_Intron	NM_020980.3	NP_066190.2	O43315	AQP9_HUMAN	aquaporin 9	23					amine transport (GO:0015837)|canalicular bile acid transport (GO:0015722)|carboxylic acid transport (GO:0046942)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|glycerol transport (GO:0015793)|immune response (GO:0006955)|metabolic process (GO:0008152)|polyol transport (GO:0015791)|purine nucleobase transport (GO:0006863)|pyrimidine nucleobase transport (GO:0015855)|pyrimidine-containing compound transmembrane transport (GO:0072531)|response to mercury ion (GO:0046689)|response to organic substance (GO:0010033)|response to osmotic stress (GO:0006970)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water homeostasis (GO:0030104)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carboxylic acid transmembrane transporter activity (GO:0046943)|glycerol channel activity (GO:0015254)|polyol transmembrane transporter activity (GO:0015166)|porin activity (GO:0015288)|purine nucleobase transmembrane transporter activity (GO:0005345)|pyrimidine nucleobase transmembrane transporter activity (GO:0005350)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)	21				GBM - Glioblastoma multiforme(80;0.16)		GCAGCTTAGCGAAAGAAACCC	0.483																																					p.A23A		Atlas-SNP	.											.	AQP9	39	.	0			c.G69A						.	G		0,4384		0,0,2192	148	148	148		69	-6.1	0.1	15		148	1,8583		0,1,4291	no	coding-synonymous	AQP9	NM_020980.3		0,1,6483	AA,AG,GG		0.0116,0.0,0.0077		23/296	58430833	1,12967	2192	4292	6484	SO:0001819	synonymous_variant	366	exon1			CTTAGCGAAAGAA	AF016495	CCDS10165.1	15q	2005-09-20			ENSG00000103569	ENSG00000103569		"Ion channels / Aquaporins"	643	protein-coding gene	gene with protein product		602914					Standard	NM_020980		Approved	SSC1, HsT17287	uc002aez.2	O43315	OTTHUMG00000132631	ENST00000219919.4:c.69G>A	chr15.hg19:g.58430833G>A		153.0	0.0		150.0	49.0	NM_020980	Q9NP32	Silent	SNP	ENST00000219919.4	hg19	CCDS10165.1																																																																																			.	.		0.483	AQP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255878.2	NM_020980		A	58430833	G	A	58430833	2	1	200	1	0	0	0	0	0	0	0	1	833	1045	37	1		1	AQP9	15	58430833	Silent	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10		58430833	44100559	76	29438										
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65702586	65702586	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	agctggcagcccttcaatgtGgcactcaaagcgagctgtcc	11	13	2	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr15:65702586G>A	ENST00000352385.2	-	3	702	c.493C>T	c.(493-495)Cac>Tac	p.H165Y		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	165	Ig-like C2-type 2.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						CCTTCAATGTGGCACTCAAAG	0.612																																					p.H165Y		Atlas-SNP	.											.	IGDCC4	95	.	0			c.C493T						.						91	78	83					15																	65702586		2201	4299	6500	SO:0001583	missense	57722	exon3			CAATGTGGCACTC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.493C>T	chr15.hg19:g.65702586G>A	ENSP00000319623:p.His165Tyr	54.0	0.0		30.0	6.0	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.947320	0.34377	.	.	ENSG00000103742	ENST00000352385	T	0.67171	-0.25	5.48	5.48	0.80851	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.253764	0.41001	D	0.000975	T	0.59676	0.2211	L	0.42744	1.35	0.37722	D	0.92495	B	0.10296	0.003	B	0.15052	0.012	T	0.57590	-0.7785	10	0.19590	T	0.45	-18.2775	17.1439	0.86761	0.0:0.0:1.0:0.0	.	165	Q8TDY8	IGDC4_HUMAN	Y	165	ENSP00000319623:H165Y	ENSP00000319623:H165Y	H	-	1	0	IGDCC4	63489639	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.072000	0.76777	2.576000	0.86940	0.655000	0.94253	CAC	.	.		0.612	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		A	65702586	G	A	65702586	3	1	200	1	0	0	0	0	1	0	0	0	7578	1348	47	3	3331	3	IGDCC4	15	65702586	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	7271753	65702586	36828806	77	29439										
DNAJA4	55466	hgsc.bcm.edu	37	chr15	78568034	78568034	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tcaagaagacgataaaaacaTtggacaatcgaattcttgtt	7	6	2	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr15:78568034T>C	ENST00000394852.3	+	5	1031	c.841T>C	c.(841-843)Ttg>Ctg	p.L281L	DNAJA4_ENST00000446172.2_Silent_p.L254L|DNAJA4_ENST00000343789.3_Silent_p.L281L|DNAJA4_ENST00000394855.3_Silent_p.L310L	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	281					negative regulation of inclusion body assembly (GO:0090084)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	8						GATAAAAACATTGGACAATCG	0.363																																					p.L310L		Atlas-SNP	.											.	DNAJA4	63	.	0			c.T928C						.						118	112	114					15																	78568034		2196	4293	6489	SO:0001819	synonymous_variant	55466	exon6			AAAACATTGGACA	AF116663	CCDS10299.2, CCDS45316.1, CCDS45317.1	15q24.1	2011-09-02			ENSG00000140403	ENSG00000140403		"Heat shock proteins / DNAJ (HSP40)"	14885	protein-coding gene	gene with protein product						11147971	Standard	NM_018602		Approved	PRO1472	uc002bdi.3	Q8WW22	OTTHUMG00000143733	ENST00000394852.3:c.841T>C	chr15.hg19:g.78568034T>C		69.0	0.0		65.0	19.0	NM_018602	E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Silent	SNP	ENST00000394852.3	hg19	CCDS45316.1																																																																																			.	.		0.363	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	NM_018602		C	78568034	T	C	78568034	2	2	200	1	0	0	0	0	0	0	0	1	4616	1490	52	2		2	DNAJA4	15	78568034	Silent	SNP	T	TCGA-DD-AADR-01A-11D-A40R-10	12865448	78568034	23963358	78	29440										
RGMA	56963	hgsc.bcm.edu	37	chr15	93588470	93588470	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ggcctggtagtacaggtcctCcaccggcagcttctccttgc	11	15	1	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr15:93588470C>A	ENST00000329082.7	-	4	1382	c.1111G>T	c.(1111-1113)Gag>Tag	p.E371*	RGMA_ENST00000557301.1_Nonsense_Mutation_p.E379*|RGMA_ENST00000425933.2_Nonsense_Mutation_p.E355*|RGMA_ENST00000542321.2_Nonsense_Mutation_p.E355*|RGMA_ENST00000556658.1_Nonsense_Mutation_p.E262*|RGMA_ENST00000557420.1_3'UTR|RGMA_ENST00000538818.1_Nonsense_Mutation_p.E262*|RGMA_ENST00000543599.1_Nonsense_Mutation_p.E355*	NM_020211.2	NP_064596	Q96B86	RGMA_HUMAN	repulsive guidance molecule family member a	371					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|neural tube closure (GO:0001843)|regulation of BMP signaling pathway (GO:0030510)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	9	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)			TACAGGTCCTCCACCGGCAGC	0.647																																					p.E379X		Atlas-SNP	.											.	RGMA	49	.	0			c.G1135T						.						34	37	36					15																	93588470		2116	4233	6349	SO:0001587	stop_gained	56963	exon4			GGTCCTCCACCGG	AL390083	CCDS45357.1, CCDS53973.1, CCDS53974.1	15q26.1	2013-11-06	2013-11-06			ENSG00000182175			30308	protein-coding gene	gene with protein product		607362	"RGM domain family, member A"			15975920	Standard	NM_020211		Approved	RGM, RGMa	uc010urc.2	Q96B86		ENST00000329082.7:c.1111G>T	chr15.hg19:g.93588470C>A	ENSP00000330005:p.Glu371*	129.0	0.0		113.0	34.0	NM_001166283	B2RTW1|B7Z5S8|F5GXQ7|F5GZU6|G3V518|Q0JV97|Q8NC80|Q9H0E6|Q9NPM3	Nonsense_Mutation	SNP	ENST00000329082.7	hg19	CCDS45357.1	.	.	.	.	.	.	.	.	.	.	C	42	9.237840	0.99110	.	.	ENSG00000182175	ENST00000543599;ENST00000425933;ENST00000329082;ENST00000542321;ENST00000538818;ENST00000557301	.	.	.	4.87	4.87	0.63330	.	0.050013	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-13.1226	17.6076	0.88042	0.0:1.0:0.0:0.0	.	.	.	.	X	355;355;371;355;262;379	.	ENSP00000330005:E371X	E	-	1	0	RGMA	91389474	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.879000	0.63100	2.240000	0.73641	0.491000	0.48974	GAG	.	.		0.647	RGMA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415091.1	NM_020211		A	93588470	C	A	93588470	4	1	200	1	0	0	0	0	0	1	0	0	13295	864	30	3	245	3	RGMA	15	93588470	Nonsense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	15020436	93588470	8942922	79	29441										
GNPTG	84572	hgsc.bcm.edu	37	chr16	1411878	1411878	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	catctgtgtccccaggtacaAgtatgagttctgcccgttcc	9	13	2	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr16:1411878A>C	ENST00000204679.4	+	5	282	c.239A>C	c.(238-240)aAg>aCg	p.K80T	LA16c-316G12.2_ENST00000569831.1_RNA	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit	80	PRKCSH.				carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				CCCAGGTACAAGTATGAGTTC	0.657																																					p.K80T		Atlas-SNP	.											.	GNPTG	18	.	0			c.A239C						.						58	54	55					16																	1411878		2199	4300	6499	SO:0001583	missense	84572	exon5			GGTACAAGTATGA	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"GlcNAc-phosphotransferase gamma-subunit"	607838	"N-acetylglucosamine-1-phosphotransferase, gamma subunit", "chromosome 16 open reading frame 27"	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835	ENST00000204679.4:c.239A>C	chr16.hg19:g.1411878A>C	ENSP00000204679:p.Lys80Thr	63.0	0.0		42.0	12.0	NM_032520	B2R556|Q6XYD7|Q96L13	Missense_Mutation	SNP	ENST00000204679.4	hg19	CCDS10436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.92|15.92	2.975758|2.975758	0.53720|0.53720	.|.	.|.	ENSG00000090581|ENSG00000090581	ENST00000204679|ENST00000529110	D|.	0.81659|.	-1.52|.	5.28|5.28	5.28|5.28	0.74379|0.74379	Mannose-6-phosphate receptor, binding (1);Glucosidase II beta subunit-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.57932|0.57932	0.2087|0.2087	L|L	0.41492|0.41492	1.28|1.28	0.52099|0.52099	D|D	0.999946|0.999946	P|.	0.51057|.	0.941|.	P|.	0.58520|.	0.84|.	T|T	0.55471|0.55471	-0.8136|-0.8136	10|5	0.41790|.	T|.	0.15|.	-50.8171|-50.8171	13.1571|13.1571	0.59524|0.59524	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	80|.	Q9UJJ9|.	GNPTG_HUMAN|.	T|H	80|102	ENSP00000204679:K80T|.	ENSP00000204679:K80T|.	K|Q	+|+	2|3	0|2	GNPTG|GNPTG	1351879|1351879	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.868000|0.868000	0.49771|0.49771	8.397000|8.397000	0.90193|0.90193	2.003000|2.003000	0.58678|0.58678	0.533000|0.533000	0.62120|0.62120	AAG|CAA	.	.		0.657	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520		C	1411878	A	C	1411878	3	2	200	1	0	0	0	0	1	0	0	0	6554	72	3	5	257	5	GNPTG	16	1411878	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10		1411878	88942875	80	29442										
GUCY2D	3000	hgsc.bcm.edu	37	chr17	7916472	7916472	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ggacccagccctggagcgccGgggaacgctggccggcgacg	18	15	0	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr17:7916472G>A	ENST00000254854.4	+	11	2315	c.2165G>A	c.(2164-2166)cGg>cAg	p.R722Q		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	722	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> W (in dbSNP:rs34331388).		intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				CTGGAGCGCCGGGGAACGCTG	0.657																																					p.R722Q		Atlas-SNP	.											.	GUCY2D	82	.	0			c.G2165A						.						37	35	36					17																	7916472		2203	4300	6503	SO:0001583	missense	3000	exon11			AGCGCCGGGGAAC	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.2165G>A	chr17.hg19:g.7916472G>A	ENSP00000254854:p.Arg722Gln	77.0	0.0		48.0	29.0	NM_000180	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	hg19	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.479356	0.44044	.	.	ENSG00000132518	ENST00000254854	T	0.62232	0.04	4.97	1.75	0.24633	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.315714	0.23211	N	0.050671	T	0.42899	0.1223	L	0.33624	1.015	0.25727	N	0.98531	B	0.24483	0.104	B	0.19391	0.025	T	0.17992	-1.0351	10	0.13470	T	0.59	.	7.4891	0.27452	0.3553:0.0:0.6447:0.0	.	722	Q02846	GUC2D_HUMAN	Q	722	ENSP00000254854:R722Q	ENSP00000254854:R722Q	R	+	2	0	GUCY2D	7857197	0.000000	0.05858	0.993000	0.49108	0.971000	0.66376	0.071000	0.14594	0.698000	0.31739	0.561000	0.74099	CGG	.	.		0.657	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			A	7916472	G	A	7916472	3	1	200	1	0	0	0	0	1	0	0	0	6906	1116	39	1	2203	1	GUCY2D	17	7916472	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10		7916472	73278738	81	29443										
CDC27	996	hgsc.bcm.edu	37	chr17	45219595	45219595	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	attaagcatttaaaacagacCtgctgctgctttttgtagat	7	7	0	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr17:45219595C>A	ENST00000066544.3	-	11	1471	c.1378G>T	c.(1378-1380)Gaa>Taa	p.E460*	CDC27_ENST00000531206.1_Splice_Site_p.E466*|CDC27_ENST00000446365.2_Splice_Site_p.E399*|CDC27_ENST00000527547.1_Splice_Site_p.G460C	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	460				Missing (in Ref. 1; AAA60471). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAAACAGACCTGCTGCTGCT	0.294																																					p.E466X		Atlas-SNP	.											.	CDC27	337	.	0			c.G1396T						.						25	25	25					17																	45219595		2199	4292	6491	SO:0001630	splice_region_variant	996	exon11			ACAGACCTGCTGC	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1378+1G>T	chr17.hg19:g.45219595C>A		276.0	0.0		272.0	78.0	NM_001114091	G3V1C4|Q16349|Q96F35	Nonsense_Mutation	SNP	ENST00000066544.3	hg19	CCDS11509.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	6.663474|6.663474	0.97743|0.97743	.|.	.|.	ENSG00000004897|ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365|ENST00000527547	.|T	.|0.75154	.|-0.91	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	0.053451|.	0.64402|.	D|.	0.000001|.	.|D	.|0.86322	.|0.5905	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	.|D	.|0.86259	.|0.1654	.|6	.|.	.|.	.|.	-0.6453|-0.6453	17.0728|17.0728	0.86579|0.86579	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|460	.|G5EA36	.|.	X|C	460;466;399|460	.|ENSP00000437339:G460C	.|.	E|G	-|-	1|1	0|0	CDC27|CDC27	42574594|42574594	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.932000|0.932000	0.56968|0.56968	7.429000|7.429000	0.80309|0.80309	2.632000|2.632000	0.89209|0.89209	0.557000|0.557000	0.71058|0.71058	GAA|GGT	.	.		0.294	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Nonsense_Mutation	A	45219595	C	A	45219595	5	1	200	1	0	0	0	0	0	0	1	0	3068	695	24	3	1132	3	CDC27	17	45219595	Splice_Site	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	37303123	45219595	35975615	82	29444										
KCNH6	81033	hgsc.bcm.edu	37	chr17	61620964	61620964	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ggggtctccactcatcccccCgacaggctcctggcagccaa	10	18	2	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr17:61620964C>T	ENST00000583023.1	+	10	2187	c.2176C>T	c.(2176-2178)Cga>Tga	p.R726*	KCNH6_ENST00000581784.1_Nonsense_Mutation_p.R673*|KCNH6_ENST00000314672.5_Nonsense_Mutation_p.R726*|KCNH6_ENST00000456941.2_Nonsense_Mutation_p.R673*	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	726					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	CTCATCCCCCCGACAGGCTCC	0.597																																					p.R726X		Atlas-SNP	.											.	KCNH6	122	.	0			c.C2176T						.						59	64	63					17																	61620964		2203	4300	6503	SO:0001587	stop_gained	81033	exon10			TCCCCCCGACAGG	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2176C>T	chr17.hg19:g.61620964C>T	ENSP00000463533:p.Arg726*	176.0	0.0		169.0	60.0	NM_030779	Q9BRD7	Nonsense_Mutation	SNP	ENST00000583023.1	hg19	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	C	31	5.081806	0.94050	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	.	.	.	4.92	3.88	0.44766	.	2.951240	0.03137	U	0.166020	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.0816	0.48064	0.1842:0.8158:0.0:0.0	.	.	.	.	X	726;673	.	ENSP00000318212:R726X	R	+	1	2	KCNH6	58974696	0.008000	0.16893	0.953000	0.39169	0.371000	0.29859	0.148000	0.16224	2.442000	0.82660	0.655000	0.94253	CGA	.	.		0.597	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		T	61620964	C	T	61620964	4	4	200	1	0	0	0	0	0	1	0	0	8045	644	23	1	2214	1	KCNH6	17	61620964	Nonsense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	16401369	61620964	19574246	83	29445										
GRIN2C	2905	hgsc.bcm.edu	37	chr17	72846852	72846852	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	aggctgcagagaggcactgtAgcgaggccacacggggtact	16	10	0	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr17:72846852A>G	ENST00000293190.5	-	5	1314	c.1168T>C	c.(1168-1170)Tac>Cac	p.Y390H	GRIN2C_ENST00000347612.4_Missense_Mutation_p.Y390H|GRIN2C_ENST00000578159.1_5'Flank	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	390					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GAGGCACTGTAGCGAGGCCAC	0.657																																					p.Y390H		Atlas-SNP	.											.	GRIN2C	144	.	0			c.T1168C						.						69	49	56					17																	72846852		2203	4300	6503	SO:0001583	missense	2905	exon5			CACTGTAGCGAGG		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.1168T>C	chr17.hg19:g.72846852A>G	ENSP00000293190:p.Tyr390His	187.0	0.0		177.0	48.0	NM_000835	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	hg19	CCDS32724.1	.	.	.	.	.	.	.	.	.	.	A	14.51	2.555626	0.45487	.	.	ENSG00000161509	ENST00000293190;ENST00000347612	T	0.07567	3.18	4.28	4.28	0.50868	.	0.069729	0.64402	D	0.000015	T	0.29749	0.0743	M	0.84433	2.695	0.47511	D	0.999449	D;D	0.76494	0.999;0.994	D;D	0.68483	0.958;0.947	T	0.07616	-1.0763	10	0.39692	T	0.17	.	13.5423	0.61681	1.0:0.0:0.0:0.0	.	424;390	Q8IW23;Q14957	.;NMDE3_HUMAN	H	390;424	ENSP00000293190:Y390H	ENSP00000293190:Y390H	Y	-	1	0	GRIN2C	70358447	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	9.079000	0.94032	1.922000	0.55676	0.454000	0.30748	TAC	.	.		0.657	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1			G	72846852	A	G	72846852	3	3	200	1	0	0	0	0	1	0	0	0	6790	420	15	2	2569	2	GRIN2C	17	72846852	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10	11225888	72846852	8348358	84	29446										
HAUS1	115106	hgsc.bcm.edu	37	chr18	43708091	43708091	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gtagacatgatggaactgtgAcaaaagccaaataaacatcc	8	8	0	3			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr18:43708091A>G	ENST00000282058.6	+	9	917	c.837A>G	c.(835-837)tgA>tgG	p.*279W	HAUS1_ENST00000588704.1_3'UTR|HAUS1_ENST00000585518.1_3'UTR	NM_138443.3	NP_612452.1	Q96CS2	HAUS1_HUMAN	HAUS augmin-like complex, subunit 1	0					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7						TGGAACTGTGACAAAAGCCAA	0.348																																					p.X279W	NSCLC(79;183 1423 5813 15597 38427)	Atlas-SNP	.											.	HAUS1	22	.	0			c.A837G						.						100	85	90					18																	43708091		2203	4297	6500	SO:0001578	stop_lost	115106	exon9			ACTGTGACAAAAG	AY360137	CCDS11928.1	18q21.1	2013-10-11	2009-04-20	2009-04-20	ENSG00000152240	ENSG00000152240		"HAUS augmin-like complex subunits"	25174	protein-coding gene	gene with protein product		608775	"coiled-coil domain containing 5 (spindle associated)"	CCDC5		19427217	Standard	NR_026978		Approved	HEI-C, HsT1461, FLJ40084	uc002lbu.3	Q96CS2	OTTHUMG00000132638	ENST00000282058.6:c.837A>G	chr18.hg19:g.43708091A>G	ENSP00000282058:p.*279Trpext*10	452.0	0.0		397.0	88.0	NM_138443	B2RDM7|Q8N837	Missense_Mutation	SNP	ENST00000282058.6	hg19	CCDS11928.1	.	.	.	.	.	.	.	.	.	.	A	8.756	0.922472	0.17982	.	.	ENSG00000152240	ENST00000282058	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4884	0.50367	1.0:0.0:0.0:0.0	.	.	.	.	W	279	.	.	X	+	3	0	HAUS1	41962089	1.000000	0.71417	0.996000	0.52242	0.145000	0.21501	4.442000	0.59988	2.026000	0.59711	0.477000	0.44152	TGA	.	.		0.348	HAUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255885.1	NM_138443		G	43708091	A	G	43708091	4	3	200	1	0	0	0	0	0	0	0	0	6974	288	10	2	871	2	HAUS1	18	43708091	Nonstop_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10		43708091	34369157	85	29447										
MBP	4155	hgsc.bcm.edu	37	chr18	74728894	74728894	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ggaggaagccatgcctggcaTggtccatggtacttgctgtg	15	9	0	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr18:74728894T>C	ENST00000397869.3	-	1	117	c.71A>G	c.(70-72)cAt>cGt	p.H24R	MBP_ENST00000397866.4_Missense_Mutation_p.H24R|MBP_ENST00000354542.4_Missense_Mutation_p.H24R|MBP_ENST00000578193.1_Missense_Mutation_p.H24R|MBP_ENST00000527041.1_Missense_Mutation_p.H24R|MBP_ENST00000355994.2_Missense_Mutation_p.H157R|MBP_ENST00000359645.3_Missense_Mutation_p.H24R|MBP_ENST00000397865.5_Missense_Mutation_p.H24R|MBP_ENST00000397863.1_Missense_Mutation_p.H157R|MBP_ENST00000580402.1_Missense_Mutation_p.H157R|MBP_ENST00000487778.1_5'Flank|MBP_ENST00000526111.1_Intron|MBP_ENST00000397875.3_Missense_Mutation_p.H24R|MBP_ENST00000579129.1_Missense_Mutation_p.H157R|MBP_ENST00000397860.3_Missense_Mutation_p.H157R|MBP_ENST00000528160.1_Missense_Mutation_p.H24R|MBP_ENST00000382582.3_Missense_Mutation_p.H24R			P13727	PRG2_HUMAN	myelin basic protein	0					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)	Sargramostim(DB00020)	ATGCCTGGCATGGTCCATGGT	0.622																																					p.H157R	NSCLC(17;72 1131 19392)	Atlas-SNP	.											.	MBP	45	.	0			c.A470G						.						112	91	98					18																	74728894		2203	4300	6503	SO:0001583	missense	4155	exon4			CTGGCATGGTCCA		CCDS12011.1, CCDS32847.1, CCDS42448.1, CCDS42449.1, CCDS42450.1	18q23	2008-08-01			ENSG00000197971	ENSG00000197971			6925	protein-coding gene	gene with protein product		159430				2425357	Standard	XM_005266699		Approved		uc010xfd.2	P02686	OTTHUMG00000132874	ENST00000397869.3:c.71A>G	chr18.hg19:g.74728894T>C	ENSP00000380967:p.His24Arg	138.0	0.0		96.0	24.0	NM_001025100	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Missense_Mutation	SNP	ENST00000397869.3	hg19		.	.	.	.	.	.	.	.	.	.	T	17.56	3.420651	0.62622	.	.	ENSG00000197971	ENST00000382582;ENST00000355994;ENST00000397875;ENST00000397866;ENST00000397865;ENST00000527041;ENST00000359645;ENST00000528160;ENST00000397869;ENST00000354542;ENST00000397868;ENST00000498683;ENST00000397863;ENST00000397860	.	.	.	5.06	5.06	0.68205	.	0.063133	0.64402	D	0.000004	T	0.75087	0.3802	L	0.55990	1.75	0.39451	D	0.967407	D;D;D;P;D;D	0.67145	0.996;0.993;0.996;0.907;0.995;0.995	D;P;D;P;D;D	0.87578	0.998;0.824;0.99;0.45;0.996;0.996	T	0.79186	-0.1907	9	0.87932	D	0	-6.6509	14.8857	0.70567	0.0:0.0:0.0:1.0	.	24;157;157;24;24;24	B7Z3Y6;P02686;P02686-2;P02686-6;P02686-4;P02686-3	.;MBP_HUMAN;.;.;.;.	R	24;157;24;24;24;24;24;24;24;24;24;24;157;157	.	ENSP00000346545:H24R	H	-	2	0	MBP	72857882	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	5.071000	0.64382	1.912000	0.55364	0.456000	0.33151	CAT	.	.		0.622	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1	NM_001025081		C	74728894	T	C	74728894	3	2	200	1	0	0	0	0	1	0	0	0	9368	1464	51	2	568	2	MBP	18	74728894	Missense_Mutation	SNP	T	TCGA-DD-AADR-01A-11D-A40R-10	31020803	74728894	3348354	86	29448										
ZNF441	126068	hgsc.bcm.edu	37	chr19	11891553	11891553	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	catgatagtgcacactggagAtgggcctcataaatgtaaga	11	7	1	3			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:11891553A>T	ENST00000357901.4	+	4	1016	c.914A>T	c.(913-915)gAt>gTt	p.D305V	ZNF441_ENST00000454339.2_Missense_Mutation_p.D238V	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	305					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CACACTGGAGATGGGCCTCAT	0.403																																					p.D305V		Atlas-SNP	.											.	ZNF441	123	.	0			c.A914T						.						100	102	101					19																	11891553		2203	4300	6503	SO:0001583	missense	126068	exon4			CTGGAGATGGGCC	AK095956	CCDS12266.2	19p13.13	2013-01-08			ENSG00000197044	ENSG00000197044		"Zinc fingers, C2H2-type", "-"	20875	protein-coding gene	gene with protein product							Standard	NM_152355		Approved	FLJ38637	uc010dyj.3	Q8N8Z8	OTTHUMG00000154449	ENST00000357901.4:c.914A>T	chr19.hg19:g.11891553A>T	ENSP00000350576:p.Asp305Val	140.0	0.0		81.0	29.0	NM_152355		Missense_Mutation	SNP	ENST00000357901.4	hg19	CCDS12266.2	.	.	.	.	.	.	.	.	.	.	-	18.46	3.629913	0.67015	.	.	ENSG00000197044	ENST00000409902;ENST00000357901;ENST00000454339	T;T	0.17691	2.26;2.26	0.998	0.998	0.19857	Zinc finger, C2H2 (1);	.	.	.	.	T	0.15652	0.0377	N	0.20610	0.595	0.45205	D	0.998217	P	0.47350	0.894	P	0.51701	0.677	T	0.06881	-1.0802	9	0.62326	D	0.03	.	7.5239	0.27643	1.0:0.0:0.0:0.0	.	305	Q8N8Z8	ZN441_HUMAN	V	261;305;238	ENSP00000350576:D305V;ENSP00000403738:D238V	ENSP00000350576:D305V	D	+	2	0	ZNF441	11752553	0.905000	0.30787	0.005000	0.12908	0.799000	0.45148	2.685000	0.46959	0.703000	0.31848	0.248000	0.18094	GAT	.	.		0.403	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355		T	11891553	A	T	11891553	3	4	200	1	0	0	0	0	1	0	0	0	17929	333	12	4	928	4	ZNF441	19	11891553	Missense_Mutation	SNP	A	TCGA-DD-AADR-01A-11D-A40R-10		11891553	47237430	87	29449										
GIPC1	10755	hgsc.bcm.edu	37	chr19	14591237	14591237	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gctctgcccgttaatggcctCgatcatgtcgcccacgctga	10	15	2	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:14591237C>A	ENST00000393033.4	-	6	804	c.535G>T	c.(535-537)Gag>Tag	p.E179*	GIPC1_ENST00000586027.1_Nonsense_Mutation_p.E179*|GIPC1_ENST00000393028.1_Nonsense_Mutation_p.E82*|GIPC1_ENST00000345425.2_Nonsense_Mutation_p.E179*|GIPC1_ENST00000591349.1_Nonsense_Mutation_p.E82*|GIPC1_ENST00000393029.3_Nonsense_Mutation_p.E82*	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	179	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.E179K(1)		endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						TTAATGGCCTCGATCATGTCG	0.667											OREG0025316	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E179X	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											GIPC1,NS,carcinoma,0,1	GIPC1	21	.	1	Substitution - Missense(1)	lung(1)	c.G535T						.						74	75	74					19																	14591237		2203	4300	6503	SO:0001587	stop_gained	10755	exon5			TGGCCTCGATCAT	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"chromosome 19 open reading frame 3", "regulator of G-protein signalling 19 interacting protein 1"	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.535G>T	chr19.hg19:g.14591237C>A	ENSP00000376753:p.Glu179*	146.0	1.0	696	122.0	40.0	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Nonsense_Mutation	SNP	ENST00000393033.4	hg19	CCDS12310.1	.	.	.	.	.	.	.	.	.	.	C	39	7.440191	0.98286	.	.	ENSG00000123159	ENST00000393033;ENST00000345425;ENST00000393029;ENST00000393028;ENST00000351277	.	.	.	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-7.024	15.6737	0.77297	0.0:1.0:0.0:0.0	.	.	.	.	X	179;179;82;82;179	.	ENSP00000340698:E179X	E	-	1	0	GIPC1	14452237	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.189000	0.77747	2.311000	0.77944	0.561000	0.74099	GAG	.	.		0.667	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2			A	14591237	C	A	14591237	4	1	200	1	0	0	0	0	0	1	0	0	6400	893	31	1	482	1	GIPC1	19	14591237	Nonsense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	2699684	14591237	44537746	88	29450										
ZNF507	22847	hgsc.bcm.edu	37	chr19	32845669	32845669	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	aacgaccctaccgttgccgcCtgtgtcactacacaagtggc	9	15	1	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:32845669C>T	ENST00000311921.4	+	2	2125	c.1933C>T	c.(1933-1935)Ctg>Ttg	p.L645L	ZNF507_ENST00000544431.1_Silent_p.L645L|ZNF507_ENST00000355898.5_Silent_p.L645L	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	645					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					CCGTTGCCGCCTGTGTCACTA	0.527																																					p.L645L		Atlas-SNP	.											.	ZNF507	92	.	0			c.C1933T						.						153	119	131					19																	32845669		2203	4300	6503	SO:0001819	synonymous_variant	22847	exon3			TGCCGCCTGTGTC	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"Zinc fingers, C2H2-type"	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.1933C>T	chr19.hg19:g.32845669C>T		168.0	0.0		135.0	35.0	NM_001136156	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Silent	SNP	ENST00000311921.4	hg19	CCDS32985.1																																																																																			.	.		0.527	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910		T	32845669	C	T	32845669	2	4	200	1	0	0	0	0	0	0	0	1	17968	680	24	3		3	ZNF507	19	32845669	Silent	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	18254432	32845669	26283314	89	29451										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40368348	40368348	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ttcgatgacaaccccagcggCctggcaggcggccacgtagg	14	14	0	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:40368348C>T	ENST00000221347.6	-	28	13007	c.13000G>A	c.(13000-13002)Gcc>Acc	p.A4334T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4334						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			ACCCCAGCGGCCTGGCAGGCG	0.647																																					p.A4334T		Atlas-SNP	.											.	FCGBP	416	.	0			c.G13000A						.						175	185	181					19																	40368348		2203	4300	6503	SO:0001583	missense	8857	exon28			CAGCGGCCTGGCA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.13000G>A	chr19.hg19:g.40368348C>T	ENSP00000221347:p.Ala4334Thr	343.0	0.0		323.0	51.0	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	9.235	1.036807	0.19669	.	.	ENSG00000090920	ENST00000221347	T	0.78003	-1.14	4.08	4.08	0.47627	Uncharacterised domain, cysteine-rich (2);	0.349619	0.25768	U	0.028439	D	0.82273	0.5001	M	0.73217	2.22	0.26109	N	0.980703	D	0.63046	0.992	P	0.62491	0.903	T	0.71646	-0.4530	10	0.17369	T	0.5	.	9.3858	0.38342	0.0:0.898:0.0:0.102	.	4334	Q9Y6R7	FCGBP_HUMAN	T	4334	ENSP00000221347:A4334T	ENSP00000221347:A4334T	A	-	1	0	FCGBP	45060188	0.000000	0.05858	0.994000	0.49952	0.123000	0.20343	-0.051000	0.11885	2.279000	0.76181	0.305000	0.20034	GCC	.	.		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40368348	C	T	40368348	3	4	200	1	0	0	0	0	1	0	0	0	5786	739	26	3	3253	3	FCGBP	19	40368348	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	7522679	40368348	18760635	90	29452										
SIGLEC9	27180	hgsc.bcm.edu	37	chr19	51633222	51633222	+	Frame_Shift_Del	DEL	G	G	-													0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gcttctgcccgctcctcagtGggggaaggagagctccagta							TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:51633222delG	ENST00000250360.3	+	7	1345	c.1278delG	c.(1276-1278)gtgfs	p.V426fs	SIGLEC9_ENST00000440804.3_Intron	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	426					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		GCTCCTCAGTGGGGGAAGGAG	0.612																																					p.V426fs		Atlas-INDEL	.											.	SIGLEC9	85	.	0			c.1277delT						.						67	68	68					19																	51633222		2203	4300	6503	SO:0001589	frameshift_variant	27180	exon7			.	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.1278delG	chr19.hg19:g.51633222delG	ENSP00000250360:p.Val426fs	73.0	0.0		67.0	21.0	NM_014441	Q6GTU4|Q9BYI9	Frame_Shift_Del	DEL	ENST00000250360.3	hg19	CCDS12825.1																																																																																			.	.		0.612	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		-	51633222	G	-	51633222	7	5	200	1	0	1	0	1	0	0	0	0	14330	1335	47	0	1304	0	SIGLEC9	19	51633222	Frame_Shift_Del	DEL	G	TCGA-DD-AADR-01A-11D-A40R-10	11264874	51633222	7495761	91	29453										
ZNF135	7694	hgsc.bcm.edu	37	chr19	58579348	58579348	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	gccctatgaatgcaatgactGcggcaaggcattcagtcaca	10	11	2	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:58579348G>A	ENST00000313434.5	+	5	1597	c.1496G>A	c.(1495-1497)tGc>tAc	p.C499Y	RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000439855.2_Missense_Mutation_p.C499Y|ZNF135_ENST00000511556.1_Missense_Mutation_p.C511Y|ZNF135_ENST00000401053.4_Missense_Mutation_p.C523Y|ZNF135_ENST00000359978.6_Intron|ZNF135_ENST00000506786.1_Missense_Mutation_p.C457Y	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	499					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		TGCAATGACTGCGGCAAGGCA	0.562																																					p.C523Y		Atlas-SNP	.											ZNF135_ENST00000401053,NS,carcinoma,0,2	ZNF135	159	.	0			c.G1568A						.						90	81	84					19																	58579348		2203	4300	6503	SO:0001583	missense	7694	exon4			ATGACTGCGGCAA	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"Zinc fingers, C2H2-type", "-"	12919	protein-coding gene	gene with protein product		604077	"zinc finger protein 61", "zinc finger protein 135 (clone pHZ-17)"	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.1496G>A	chr19.hg19:g.58579348G>A	ENSP00000321406:p.Cys499Tyr	107.0	0.0		92.0	29.0	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.49|10.49	1.365473|1.365473	0.24684|0.24684	.|.	.|.	ENSG00000176293|ENSG00000176293	ENST00000391699|ENST00000401053;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	.|D;D;D;D;D	.|0.85861	.|-2.04;-2.04;-2.04;-2.04;-2.04	3.26|3.26	2.16|2.16	0.27623|0.27623	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	D|D	0.93844|0.93844	0.8031|0.8031	H|H	0.96365|0.96365	3.81|3.81	0.34095|0.34095	D|D	0.661122|0.661122	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.998	D|D	0.94796|0.94796	0.7966|0.7966	5|9	.|0.87932	.|D	.|0	.|.	9.9698|9.9698	0.41747|0.41747	0.1088:0.0:0.8912:0.0|0.1088:0.0:0.8912:0.0	.|.	.|511;499	.|E9PEV2;P52742	.|.;ZN135_HUMAN	T|Y	517|523;499;499;511;457	.|ENSP00000441410:C523Y;ENSP00000444828:C499Y;ENSP00000321406:C499Y;ENSP00000422074:C511Y;ENSP00000427691:C457Y	.|ENSP00000321406:C499Y	A|C	+|+	1|2	0|0	ZNF135|ZNF135	63271160|63271160	1.000000|1.000000	0.71417|0.71417	0.499000|0.499000	0.27577|0.27577	0.010000|0.010000	0.07245|0.07245	4.121000|4.121000	0.57904|0.57904	0.671000|0.671000	0.31185|0.31185	0.557000|0.557000	0.71058|0.71058	GCG|TGC	.	.		0.562	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		A	58579348	G	A	58579348	3	1	200	1	0	0	0	0	1	0	0	0	17740	1319	46	3	1699	3	ZNF135	19	58579348	Missense_Mutation	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10	6946126	58579348	549635	92	29454										
ZCCHC3	85364	hgsc.bcm.edu	37	chr20	278367	278367	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	ggcccaggtggtgaagaatcTagccgagaagaagggcgaat	16	7	1	4			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr20:278367T>C	ENST00000382352.3	+	1	631	c.140T>C	c.(139-141)cTa>cCa	p.L47P		NM_033089.6	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	47							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			GTGAAGAATCTAGCCGAGAAG	0.791																																					p.L47P		Atlas-SNP	.											.	ZCCHC3	20	.	0			c.T140C						.						1	2	1					20																	278367		805	2014	2819	SO:0001583	missense	85364	exon1			AGAATCTAGCCGA	AL034548	CCDS42844.1	20p13-p12.2	2014-04-10	2004-07-14	2004-07-14	ENSG00000177764	ENSG00000247315		"Zinc fingers, CCHC domain containing"	16230	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 99"	C20orf99			Standard	NM_033089		Approved	dJ1103G7.7	uc002wdf.3	Q9NUD5	OTTHUMG00000188280	ENST00000382352.3:c.140T>C	chr20.hg19:g.278367T>C	ENSP00000371789:p.Leu47Pro	80.0	0.0		75.0	16.0	NM_033089	Q3B7J3|Q6NT79	Missense_Mutation	SNP	ENST00000382352.3	hg19	CCDS42844.1	.	.	.	.	.	.	.	.	.	.	T	13.71	2.318499	0.40996	.	.	ENSG00000177764	ENST00000382352	.	.	.	4.08	2.95	0.34219	.	0.209202	0.22922	N	0.054011	T	0.36880	0.0983	N	0.14661	0.345	0.52501	D	0.999956	D	0.61080	0.989	P	0.50825	0.651	T	0.24333	-1.0163	9	0.87932	D	0	-16.2416	8.1946	0.31389	0.1792:0.0:0.0:0.8207	.	47	Q9NUD5	ZCHC3_HUMAN	P	47	.	ENSP00000371789:L47P	L	+	2	0	ZCCHC3	226367	0.986000	0.35501	0.998000	0.56505	0.757000	0.42996	0.903000	0.28475	0.691000	0.31592	0.379000	0.24179	CTA	.	.		0.791	ZCCHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077447.1			C	278367	T	C	278367	3	2	200	1	0	0	0	0	1	0	0	0	17604	1522	53	2	142	2	ZCCHC3	20	278367	Missense_Mutation	SNP	T	TCGA-DD-AADR-01A-11D-A40R-10		278367	62747153	93	29455										
CDH4	1002	hgsc.bcm.edu	37	chr20	60448832	60448832	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cgatgctgacgacagcaccaCggccaacgggatggtgcggt	15	12	0	1			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr20:60448832C>A	ENST00000360469.5	+	7	1014	c.926C>A	c.(925-927)aCg>aAg	p.T309K	CDH4_ENST00000543233.1_Missense_Mutation_p.T235K	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	309	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GACAGCACCACGGCCAACGGG	0.602																																					p.T309K		Atlas-SNP	.											.	CDH4	172	.	0			c.C926A						.						150	116	127					20																	60448832		2203	4300	6503	SO:0001583	missense	1002	exon7			GCACCACGGCCAA	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.926C>A	chr20.hg19:g.60448832C>A	ENSP00000353656:p.Thr309Lys	91.0	0.0		85.0	35.0	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	hg19	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546761	0.86022	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.53206	0.63;0.63	4.76	4.76	0.60689	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.74176	0.3682	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79926	-0.1597	9	.	.	.	.	17.8138	0.88624	0.0:1.0:0.0:0.0	.	309	P55283	CADH4_HUMAN	K	309;217;235	ENSP00000353656:T309K;ENSP00000443301:T235K	.	T	+	2	0	CDH4	59882227	1.000000	0.71417	0.995000	0.50966	0.938000	0.57974	4.621000	0.61233	2.196000	0.70406	0.460000	0.39030	ACG	.	.		0.602	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		A	60448832	C	A	60448832	3	1	200	1	0	0	0	0	1	0	0	0	3114	536	19	1	952	1	CDH4	20	60448832	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	60170465	60448832	2576688	94	29456										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46912479	46912479	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tgagcgtgccgggacctgagGtatgtgcctgcccagcttct	14	12	1	2			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr21:46912479G>A	ENST00000359759.4	+	22	3453		c.e22+1		COL18A1_ENST00000400337.2_Splice_Site|COL18A1_ENST00000355480.5_Splice_Site			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1						angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GGGACCTGAGGTATGTGCCTG	0.607																																					.		Atlas-SNP	.											.	COL18A1	129	.	0			c.2187+1G>A						.						126	138	134					21																	46912479		1935	4129	6064	SO:0001630	splice_region_variant	80781	exon23			CCTGAGGTATGTG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3432+1G>A	chr21.hg19:g.46912479G>A		136.0	0.0		75.0	11.0	NM_130445	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Splice_Site	SNP	ENST00000359759.4	hg19		.	.	.	.	.	.	.	.	.	.	G	12.70	2.017299	0.35606	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645;ENST00000342220	.	.	.	3.15	3.15	0.36227	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0448	0.42180	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL18A1	45736907	1.000000	0.71417	0.472000	0.27241	0.011000	0.07611	3.908000	0.56355	1.795000	0.52594	0.556000	0.70494	.	.	.		0.607	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		Intron	A	46912479	G	A	46912479	5	1	200	1	0	0	0	0	0	0	1	0	3677	1275	44	3	3633	3	COL18A1	21	46912479	Splice_Site	SNP	G	TCGA-DD-AADR-01A-11D-A40R-10		46912479	1217416	95	29457										
PNPLA5	150379	hgsc.bcm.edu	37	chr22	44282291	44282291	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	cttccagcgttggtcacagcCagcatcccagtttccgtcag	9	15	2	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr22:44282291C>T	ENST00000597664.1	-	6	970	c.841G>A	c.(841-843)Ggc>Agc	p.G281S	PNPLA5_ENST00000381198.2_Missense_Mutation_p.G167S|PNPLA5_ENST00000593866.1_Missense_Mutation_p.G167S|PNPLA5_ENST00000216177.4_Missense_Mutation_p.G281S			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	281					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				TGGTCACAGCCAGCATCCCAG	0.587																																					p.G281S		Atlas-SNP	.											.	PNPLA5	46	.	0			c.G841A						.						95	83	87					22																	44282291		2203	4300	6503	SO:0001583	missense	150379	exon6			CACAGCCAGCATC	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"Patatin-like phospholipase domain containing"	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.841G>A	chr22.hg19:g.44282291C>T	ENSP00000471069:p.Gly281Ser	70.0	0.0		70.0	12.0	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.64	1.699025	0.30142	.	.	ENSG00000100341	ENST00000216177;ENST00000381198;ENST00000438734	T;T;T	0.44083	1.45;0.93;1.71	3.86	2.79	0.32731	.	1.332370	0.05078	N	0.482968	T	0.31949	0.0813	L	0.41356	1.27	0.09310	N	1	P;P;B	0.40970	0.473;0.734;0.036	B;B;B	0.35470	0.091;0.203;0.023	T	0.14896	-1.0456	10	0.14656	T	0.56	-9.7781	8.5041	0.33177	0.2318:0.7682:0.0:0.0	.	189;167;281	E9PGS4;Q7Z6Z6-2;Q7Z6Z6	.;.;PLPL5_HUMAN	S	281;167;189	ENSP00000216177:G281S;ENSP00000370595:G167S;ENSP00000405732:G189S	ENSP00000216177:G281S	G	-	1	0	PNPLA5	42613624	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	0.774000	0.26675	0.906000	0.36621	0.491000	0.48974	GGC	.	.		0.587	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814		T	44282291	C	T	44282291	3	4	200	1	0	0	0	0	1	0	0	0	12177	594	21	3	464	3	PNPLA5	22	44282291	Missense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10		44282291	7022275	96	29458										
NHS	4810	hgsc.bcm.edu	37	chrX	17745169	17745169	+	Frame_Shift_Del	DEL	A	A	-													0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	attgaatgcatcaaatctccAgagagctctgaatcccaaac							TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chrX:17745169delA	ENST00000380060.3	+	6	3218	c.2880delA	c.(2878-2880)ccafs	p.P960fs	NHS_ENST00000398097.3_Frame_Shift_Del_p.P804fs	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	981					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TCAAATCTCCAGAGAGCTCTG	0.423																																					p.P960fs		Atlas-INDEL	.											.	NHS	302	.	0			c.2879delC						.						80	78	78					X																	17745169		2203	4300	6503	SO:0001589	frameshift_variant	4810	exon6			.		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.2880delA	chrX.hg19:g.17745169delA	ENSP00000369400:p.Pro960fs	144.0	0.0		124.0	93.0	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Frame_Shift_Del	DEL	ENST00000380060.3	hg19	CCDS14181.1																																																																																			.	.		0.423	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		-	17745169	A	-	17745169	7	5	200	1	0	1	0	1	0	0	0	0	10420	175	7	0	3007	0	NHS	23	17745169	Frame_Shift_Del	DEL	A	TCGA-DD-AADR-01A-11D-A40R-10		17745169	137525391	97	29459										
SPANXC	64663	hgsc.bcm.edu	37	chrX	140336533	140336533	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0816326530612245	8	1	1.42927496580027	4.60941176470588	1.01083591331269	0.659442724458204	1	0	tcttaccgtctcattcacctCgttggattcacaggggacgc	9	13	4	0			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chrX:140336533C>A	ENST00000358993.2	-	1	96	c.58G>T	c.(58-60)Gag>Tag	p.E20*		NM_022661.2	NP_073152.1	Q9NY87	SPNXC_HUMAN	SPANX family, member C	20						cytoplasm (GO:0005737)|nucleus (GO:0005634)				large_intestine(2)|lung(3)|pancreas(1)	6	Acute lymphoblastic leukemia(192;7.65e-05)					TCATTCACCTCGTTGGATTCA	0.493																																					p.E20X		Atlas-SNP	.											.	SPANXC	8	.	0			c.G58T						.						81	115	103					X																	140336533		2173	4253	6426	SO:0001587	stop_gained	64663	exon1			TCACCTCGTTGGA	AJ238277	CCDS14673.1	Xq27.2	2009-03-25			ENSG00000198573	ENSG00000198573			14331	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 3"	300330				10626816	Standard	NM_022661		Approved	CTp11, CT11.3	uc004fbk.3	Q9NY87	OTTHUMG00000022556	ENST00000358993.2:c.58G>T	chrX.hg19:g.140336533C>A	ENSP00000351884:p.Glu20*	310.0	1.0		287.0	209.0	NM_022661	Q32WL9|Q5JX88	Nonsense_Mutation	SNP	ENST00000358993.2	hg19	CCDS14673.1	.	.	.	.	.	.	.	.	.	.	c	10.43	1.348209	0.24426	.	.	ENSG00000198573	ENST00000358993	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	.	.	.	.	.	.	.	.	X	20	.	ENSP00000351884:E20X	E	-	1	0	SPANXC	140164199	0.082000	0.21442	0.000000	0.03702	0.000000	0.00434	-1.577000	0.02127	-0.759000	0.04684	-0.773000	0.03387	GAG	.	.		0.493	SPANXC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058590.1	NM_022661		A	140336533	C	A	140336533	4	1	200	1	0	0	0	0	0	1	0	0	15002	893	31	1	243	1	SPANXC	23	140336533	Nonsense_Mutation	SNP	C	TCGA-DD-AADR-01A-11D-A40R-10	122591364	140336533	14934027	98	29460										
ANGPTL7	10218	hgsc.bcm.edu	37	chr1	11249740	11249740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gctctctaagcacaagacacCagcacagccacagctcaaag	7	15	2	1	rs554783669		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:11249740C>T	ENST00000376819.3	+	1	343	c.104C>T	c.(103-105)cCa>cTa	p.P35L	MTOR_ENST00000361445.4_Intron	NM_021146.2	NP_066969.1	O43827	ANGL7_HUMAN	angiopoietin-like 7	35					response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|stomach(1)	10	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.39e-06)|COAD - Colon adenocarcinoma(227;0.000244)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0487)		CACAAGACACCAGCACAGCCA	0.552													C|||	1	0.000199681	0	0	5008	,	,		21423	0.001		0	False		,,,				2504	0				p.P35L		Atlas-SNP	.											.	ANGPTL7	23	.	0			c.C104T						.						64	64	64					1																	11249740		2203	4300	6503	SO:0001583	missense	10218	exon1			AGACACCAGCACA	Y16132	CCDS128.1	1p36	2013-02-06			ENSG00000171819	ENSG00000171819		"Fibrinogen C domain containing"	24078	protein-coding gene	gene with protein product						9727400, 11682471	Standard	NM_021146		Approved	CDT6, AngX	uc001ase.4	O43827	OTTHUMG00000002002	ENST00000376819.3:c.104C>T	chr1.hg19:g.11249740C>T	ENSP00000366015:p.Pro35Leu	146.0	0.0		157.0	57.0	NM_021146	B2R9B2|F1T0A6|Q4ZGK4	Missense_Mutation	SNP	ENST00000376819.3	hg19	CCDS128.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.051330	0.36181	.	.	ENSG00000171819	ENST00000376819	T	0.53206	0.63	4.56	3.65	0.41850	.	1.766140	0.04043	U	0.303386	T	0.38931	0.1059	L	0.27053	0.805	0.45946	D	0.998778	B	0.09022	0.002	B	0.06405	0.002	T	0.02625	-1.1132	10	0.27785	T	0.31	.	10.4341	0.44424	0.1956:0.8044:0.0:0.0	.	35	O43827	ANGL7_HUMAN	L	35	ENSP00000366015:P35L	ENSP00000366015:P35L	P	+	2	0	ANGPTL7	11172327	0.036000	0.19791	0.956000	0.39512	0.750000	0.42670	3.098000	0.50259	1.040000	0.40099	-0.122000	0.15005	CCA	.	.		0.552	ANGPTL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005564.1	NM_021146		T	11249740	C	T	11249740	3	4	201	1	0	0	0	0	1	0	0	0	619	594	21	3	106	3	ANGPTL7	1	11249740	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10		11249740	238000881	1	29461										
STMN1	3925	hgsc.bcm.edu	37	chr1	26230232	26230232	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ggaattctggaacagattctTttgaccgagggctgagaatc	12	7	2	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:26230232T>A	ENST00000399728.1	-	3	449	c.86A>T	c.(85-87)aAa>aTa	p.K29I	STMN1_ENST00000357865.2_Missense_Mutation_p.K29I|STMN1_ENST00000426559.2_Missense_Mutation_p.K29I|STMN1_ENST00000455785.2_Missense_Mutation_p.K29I|STMN1_ENST00000465604.1_5'UTR|STMN1_ENST00000374291.1_Missense_Mutation_p.K29I|MIR3917_ENST00000580971.1_RNA	NM_203401.1	NP_981946.1	P16949	STMN1_HUMAN	stathmin 1	29	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				axonogenesis (GO:0007409)|intracellular signal transduction (GO:0035556)|microtubule depolymerization (GO:0007019)|mitotic spindle organization (GO:0007052)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of cellular component movement (GO:0051272)|response to virus (GO:0009615)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|microtubule (GO:0005874)	signal transducer activity (GO:0004871)|tubulin binding (GO:0015631)			breast(2)|large_intestine(2)|skin(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000163)|all_lung(284;0.000234)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.013)|READ - Rectum adenocarcinoma(331;0.0649)		AACAGATTCTTTTGACCGAGG	0.433																																					p.K29I		Atlas-SNP	.											.	STMN1	22	.	0			c.A86T						.						77	84	82					1																	26230232		2203	4300	6503	SO:0001583	missense	3925	exon3			GATTCTTTTGACC	J04991	CCDS269.1, CCDS44090.1	1p36.11	2011-02-09	2009-04-28	2001-07-13	ENSG00000117632	ENSG00000117632			6510	protein-coding gene	gene with protein product	"oncoprotein 18"	151442	"chromosome 1 open reading frame 215", "stathmin 1/oncoprotein 18"	LAP18, C1orf215		2917975	Standard	NM_005563		Approved	SMN, OP18, PR22, PP19, PP17, Lag, FLJ32206	uc010oev.2	P16949	OTTHUMG00000007389	ENST00000399728.1:c.86A>T	chr1.hg19:g.26230232T>A	ENSP00000382633:p.Lys29Ile	61.0	0.0		71.0	20.0	NM_005563	A2A2D1|B2R4E7|B7Z8N4|D3DPJ5	Missense_Mutation	SNP	ENST00000399728.1	hg19	CCDS269.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.621195	0.46736	.	.	ENSG00000117632	ENST00000426559;ENST00000455785;ENST00000399728;ENST00000357865;ENST00000374291;ENST00000446334	.	.	.	5.72	5.72	0.89469	.	0.229569	0.46145	D	0.000301	T	0.34803	0.0910	L	0.42245	1.32	0.21841	N	0.999514	P;P;P	0.39404	0.672;0.533;0.533	B;B;B	0.38194	0.195;0.267;0.25	T	0.30707	-0.9969	9	0.30854	T	0.27	.	10.8717	0.46887	0.1405:0.0:0.0:0.8595	.	29;29;29	P16949-2;B5BU83;P16949	.;.;STMN1_HUMAN	I	29	.	ENSP00000350531:K29I	K	-	2	0	STMN1	26102819	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.622000	0.54217	2.194000	0.70268	0.533000	0.62120	AAA	.	.		0.433	STMN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019359.1	NM_005563		A	26230232	T	A	26230232	3	1	201	1	0	0	0	0	1	0	0	0	15323	1841	64	4	526	4	STMN1	1	26230232	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	14980492	26230232	223020389	2	29462										
CYP4B1	1580	hgsc.bcm.edu	37	chr1	47279879	47279879	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	acactctgtgcttttggttcAgaccaggtcatcagggagcg	12	10	4	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:47279879A>G	ENST00000271153.4	+	7	808		c.e7-1		CYP4B1_ENST00000452782.2_Splice_Site|CYP4B1_ENST00000371919.4_Splice_Site|CYP4B1_ENST00000371923.4_Splice_Site			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1						biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	CTTTTGGTTCAGACCAGGTCA	0.577																																					.		Atlas-SNP	.											.	CYP4B1	81	.	0			c.776-2A>G						.						61	63	62					1																	47279879		2203	4300	6503	SO:0001630	splice_region_variant	1580	exon7			TGGTTCAGACCAG	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"Cytochrome P450s"	2644	protein-coding gene	gene with protein product		124075	"cytochrome P450, subfamily IVB, polypeptide 1"				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.773-1A>G	chr1.hg19:g.47279879A>G		74.0	0.0		83.0	26.0	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Splice_Site	SNP	ENST00000271153.4	hg19	CCDS542.1	.	.	.	.	.	.	.	.	.	.	A	13.47	2.246845	0.39697	.	.	ENSG00000142973	ENST00000371923;ENST00000271153;ENST00000371919;ENST00000452782;ENST00000468637	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.598	0.76602	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CYP4B1	47052466	1.000000	0.71417	0.841000	0.33234	0.263000	0.26337	8.888000	0.92464	2.100000	0.63781	0.391000	0.25812	.	.	.		0.577	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779	Intron	G	47279879	A	G	47279879	5	3	201	1	0	0	0	0	0	0	1	0	4187	202	7	2	800	2	CYP4B1	1	47279879	Splice_Site	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	21049647	47279879	201970742	3	29463										
CYP4A11	1579	hgsc.bcm.edu	37	chr1	47400132	47400132	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tacacatactcactttggccAagaggaggatatccagaaaa	8	9	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:47400132A>G	ENST00000310638.4	-	7	921	c.890T>C	c.(889-891)tTg>tCg	p.L297S	CYP4A11_ENST00000457840.2_Silent_p.L141L|CYP4A11_ENST00000462347.1_Silent_p.L245L|CYP4A11_ENST00000496519.1_5'Flank|CYP4A11_ENST00000371904.4_Missense_Mutation_p.L298S|CYP4A11_ENST00000371905.1_Missense_Mutation_p.L297S	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	297					arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	CACTTTGGCCAAGAGGAGGAT	0.498																																					p.L297S		Atlas-SNP	.											.	CYP4A11	77	.	0			c.T890C						.						120	115	117					1																	47400132		2203	4300	6503	SO:0001583	missense	1579	exon7			TTGGCCAAGAGGA	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"Cytochrome P450s"	2642	protein-coding gene	gene with protein product		601310	"cytochrome P450, subfamily IVA, polypeptide 11"	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.890T>C	chr1.hg19:g.47400132A>G	ENSP00000311095:p.Leu297Ser	115.0	0.0		181.0	47.0	NM_000778	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	hg19	CCDS543.1	.	.	.	.	.	.	.	.	.	.	N	0.562	-0.844804	0.02671	.	.	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905	T;T;T	0.69435	-0.4;-0.4;-0.4	5.23	1.73	0.24493	.	0.622767	0.18285	N	0.145912	T	0.44074	0.1276	N	0.17312	0.475	0.09310	N	1	B	0.09022	0.002	B	0.15052	0.012	T	0.21827	-1.0234	10	0.09590	T	0.72	.	9.707	0.40222	0.5497:0.3722:0.0781:0.0	.	297	Q02928	CP4AB_HUMAN	S	297;298;297	ENSP00000311095:L297S;ENSP00000360971:L298S;ENSP00000360972:L297S	ENSP00000311095:L297S	L	-	2	0	CYP4A11	47172719	0.005000	0.15991	0.025000	0.17156	0.402000	0.30811	0.683000	0.25349	0.059000	0.16252	0.528000	0.53228	TTG	.	.		0.498	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778		G	47400132	A	G	47400132	3	3	201	1	0	0	0	0	1	0	0	0	4185	131	5	2	693	2	CYP4A11	1	47400132	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	120253	47400132	201850489	4	29464										
LRP8	7804	hgsc.bcm.edu	37	chr1	53715077	53715077	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	atttgacgacaggcagctcgGaaagagggttcttcgggagt	15	7	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:53715077G>A	ENST00000306052.6	-	18	2929	c.2828C>T	c.(2827-2829)tCc>tTc	p.S943F	LRP8_ENST00000354412.3_Intron|LRP8_ENST00000465675.1_Intron|LRP8_ENST00000371454.2_Intron|LRP8_ENST00000347547.2_Missense_Mutation_p.S773F	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	943					ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						AGGCAGCTCGGAAAGAGGGTT	0.587																																					p.S943F		Atlas-SNP	.											.	LRP8	58	.	0			c.C2828T						.						80	72	75					1																	53715077		2203	4300	6503	SO:0001583	missense	7804	exon18			AGCTCGGAAAGAG	D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"Low density lipoprotein receptors"	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.2828C>T	chr1.hg19:g.53715077G>A	ENSP00000303634:p.Ser943Phe	94.0	0.0		111.0	34.0	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	hg19	CCDS578.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990386	0.54041	.	.	ENSG00000157193	ENST00000306052;ENST00000347547	D;D	0.90955	-2.76;-2.73	4.02	3.09	0.35607	.	.	.	.	.	D	0.85788	0.5778	N	0.19112	0.55	0.34984	D	0.754368	D;D	0.60575	0.97;0.988	P;P	0.49708	0.62;0.601	D	0.88243	0.2911	9	0.87932	D	0	.	9.0878	0.36592	0.0:0.0:0.7814:0.2186	.	773;943	Q14114-4;Q14114	.;LRP8_HUMAN	F	943;773	ENSP00000303634:S943F;ENSP00000334522:S773F	ENSP00000303634:S943F	S	-	2	0	LRP8	53487665	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.817000	0.55668	1.252000	0.44001	0.467000	0.42956	TCC	.	.		0.587	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		A	53715077	G	A	53715077	3	1	201	1	0	0	0	0	1	0	0	0	8972	1174	41	3	71	3	LRP8	1	53715077	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	6314945	53715077	195535544	5	29465										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144892215	144892215	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agtaaaaatgcttctgaagcTatagctacagagaataaata	7	5	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:144892215T>A	ENST00000369354.3	-	22	3094				PDE4DIP_ENST00000524974.1_Intron|PDE4DIP_ENST00000369349.3_Nonstop_Mutation_p.*970L|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000313431.9_Nonstop_Mutation_p.*1133L|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369351.3_3'UTR|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein						cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTTCTGAAGCTATAGCTACAG	0.453			T	PDGFRB	MPD																																p.X1133L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A3398T						.						65	68	67					1																	144892215		2203	4296	6499	SO:0001627	intron_variant	9659	exon19			TGAAGCTATAGCT	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.2904+285A>T	chr1.hg19:g.144892215T>A		164.0	0.0		246.0	42.0	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.396444	0.62177	.	.	ENSG00000178104	ENST00000369349;ENST00000313431	.	.	.	4.85	3.7	0.42460	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7886	0.18347	0.0:0.1208:0.0:0.8792	.	.	.	.	L	970;1133	.	.	X	-	2	0	PDE4DIP	143603572	1.000000	0.71417	0.998000	0.56505	0.811000	0.45836	1.993000	0.40747	2.060000	0.61445	0.529000	0.55759	TAG	.	.		0.453	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		A	144892215	T	A	144892215	1	1	201	0	1	0	0	0	0	0	0	0	11652	1535	53	4		4	PDE4DIP	1	144892215	Intron	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	91177138	144892215	104358406	6	29466										
FLG2	388698	hgsc.bcm.edu	37	chr1	152323287	152323287	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ctatgtgactgaaaatgactTgctctactagatctggaacc	8	9	2	4			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:152323287T>A	ENST00000388718.5	-	3	7047	c.6975A>T	c.(6973-6975)gcA>gcT	p.A2325A	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	2325					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAAAATGACTTGCTCTACTAG	0.458																																					p.A2325A		Atlas-SNP	.											.	FLG2	431	.	0			c.A6975T						.						299	275	283					1																	152323287		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			ATGACTTGCTCTA	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.6975A>T	chr1.hg19:g.152323287T>A		104.0	0.0		147.0	50.0	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	hg19	CCDS30861.1																																																																																			.	.		0.458	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152323287	T	A	152323287	2	1	201	1	0	0	0	0	0	0	0	1	5931	1799	63	4		4	FLG2	1	152323287	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	7431072	152323287	96927334	7	29467										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155319387	155319387	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ccagtgcttgccgggaagaaTctgcaaaagaatgtgaggtt	13	7	1	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:155319387T>C	ENST00000368346.3	-	18	8021	c.7382A>G	c.(7381-7383)gAt>gGt	p.D2461G	ASH1L_ENST00000392403.3_Splice_Site_p.D2456G			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2461					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CCGGGAAGAATCTGCAAAAGA	0.413																																					p.D2456G		Atlas-SNP	.											.	ASH1L	279	.	0			c.A7367G						.						44	44	44					1																	155319387		2203	4300	6503	SO:0001630	splice_region_variant	55870	exon18			GAAGAATCTGCAA	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.7382-1A>G	chr1.hg19:g.155319387T>C		218.0	0.0		252.0	86.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	T	23.5	4.420079	0.83559	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	T;T	0.34275	1.37;1.37	5.02	5.02	0.67125	Bromodomain (4);	0.047006	0.85682	D	0.000000	T	0.54175	0.1842	M	0.81614	2.55	0.80722	D	1	D;D	0.67145	0.996;0.995	D;D	0.79108	0.992;0.985	T	0.61893	-0.6969	10	0.72032	D	0.01	.	14.5653	0.68171	0.0:0.0:0.0:1.0	.	2461;2456	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	G	2461;2456	ENSP00000357330:D2461G;ENSP00000376204:D2456G	ENSP00000357330:D2461G	D	-	2	0	ASH1L	153586011	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.686000	0.74548	2.118000	0.64928	0.454000	0.30748	GAT	.	.		0.413	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	Missense_Mutation	C	155319387	T	C	155319387	5	2	201	1	0	0	0	0	0	0	1	0	1041	1449	50	2	1571	2	ASH1L	1	155319387	Splice_Site	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	2996100	155319387	93931234	8	29468										
CD5L	922	hgsc.bcm.edu	37	chr1	157805814	157805814	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agctccacagcccagctcccGgcacaacacagccacgtcct	7	20	0	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:157805814G>A	ENST00000368174.4	-	3	283	c.187C>T	c.(187-189)Cgg>Tgg	p.R63W	CD5L_ENST00000484609.1_5'UTR	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	63	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CCCAGCTCCCGGCACAACACA	0.577																																					p.R63W		Atlas-SNP	.											.	CD5L	112	.	0			c.C187T						.						128	130	130					1																	157805814		2203	4300	6503	SO:0001583	missense	922	exon3			GCTCCCGGCACAA	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.187C>T	chr1.hg19:g.157805814G>A	ENSP00000357156:p.Arg63Trp	45.0	0.0		80.0	29.0	NM_005894	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	hg19	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.666152	0.47677	.	.	ENSG00000073754	ENST00000368174	T	0.44482	0.92	4.85	1.82	0.25136	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.343624	0.21072	N	0.080652	T	0.51126	0.1656	H	0.96833	3.89	0.30263	N	0.792999	D	0.69078	0.997	P	0.56788	0.806	T	0.51228	-0.8732	10	0.72032	D	0.01	.	3.1111	0.06359	0.0872:0.1533:0.4444:0.3151	.	63	O43866	CD5L_HUMAN	W	63	ENSP00000357156:R63W	ENSP00000357156:R63W	R	-	1	2	CD5L	156072438	0.008000	0.16893	0.997000	0.53966	0.758000	0.43043	0.000000	0.12993	0.202000	0.20498	0.563000	0.77884	CGG	.	.		0.577	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		A	157805814	G	A	157805814	3	1	201	1	0	0	0	0	1	0	0	0	3029	1115	39	1	872	1	CD5L	1	157805814	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	2486427	157805814	91444807	9	29469										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158595952	158595952	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tcacctgttttgccagaagaGtgaggaagtcaccaaggtct	11	9	3	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:158595952G>T	ENST00000368147.4	-	42	6074	c.5894C>A	c.(5893-5895)aCt>aAt	p.T1965N		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1965					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGCCAGAAGAGTGAGGAAGTC	0.398																																					p.T1965N		Atlas-SNP	.											.	SPTA1	720	.	0			c.C5894A						.						119	119	119					1																	158595952		1920	4120	6040	SO:0001583	missense	6708	exon42			AGAAGAGTGAGGA	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5894C>A	chr1.hg19:g.158595952G>T	ENSP00000357129:p.Thr1965Asn	101.0	0.0		164.0	49.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.901993	0.33535	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.49139	0.79;0.79	4.93	2.91	0.33838	.	0.251551	0.20859	N	0.084397	T	0.37210	0.0995	L	0.51422	1.61	0.28046	N	0.93354	D	0.53462	0.96	P	0.57009	0.811	T	0.07083	-1.0791	10	0.36615	T	0.2	.	8.3622	0.32365	0.2082:0.0:0.7918:0.0	.	1965	P02549	SPTA1_HUMAN	N	1965;1962	ENSP00000357130:T1965N;ENSP00000357129:T1962N	ENSP00000357129:T1962N	T	-	2	0	SPTA1	156862576	0.917000	0.31117	0.023000	0.16930	0.215000	0.24574	1.594000	0.36697	1.303000	0.44873	0.563000	0.77884	ACT	.	.		0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158595952	G	T	158595952	3	4	201	1	0	0	0	0	1	0	0	0	15131	1029	36	3	1409	3	SPTA1	1	158595952	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	790138	158595952	90654669	10	29470										
FCRL6	343413	hgsc.bcm.edu	37	chr1	159772232	159772232	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cccatgctgctctggacggcTgtgctgctctttggtaagtc	12	12	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:159772232T>A	ENST00000368106.3	+	1	19	c.18T>A	c.(16-18)gcT>gcA	p.A6A	FCRL6_ENST00000321935.6_Silent_p.A13A|FCRL6_ENST00000339348.5_Silent_p.A6A|FCRL6_ENST00000392235.3_Silent_p.A6A	NM_001004310.2	NP_001004310.2	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6	6						external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	24	all_hematologic(112;0.0597)					TCTGGACGGCTGTGCTGCTCT	0.572																																					p.A6A		Atlas-SNP	.											.	FCRL6	61	.	0			c.T18A						.						80	58	65					1																	159772232		2203	4300	6503	SO:0001819	synonymous_variant	343413	exon1			GACGGCTGTGCTG	AK131201	CCDS30912.1, CCDS60312.1	1q23.2	2013-01-11			ENSG00000181036	ENSG00000181036		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31910	protein-coding gene	gene with protein product		613562					Standard	NM_001004310		Approved	IFGP6, FLJ16056, FcRH6	uc001fud.4	Q6DN72	OTTHUMG00000035351	ENST00000368106.3:c.18T>A	chr1.hg19:g.159772232T>A		42.0	0.0		62.0	17.0	NM_001004310	A1KXW6|A2A4D6|Q6DN73|Q6XRC3|Q6ZNI1	Silent	SNP	ENST00000368106.3	hg19	CCDS30912.1																																																																																			.	.		0.572	FCRL6-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276853.1	NM_001004310		A	159772232	T	A	159772232	2	1	201	1	0	0	0	0	0	0	0	1	5807	1567	55	4		4	FCRL6	1	159772232	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	1176280	159772232	89478389	11	29471										
SLC19A2	10560	hgsc.bcm.edu	37	chr1	169446983	169446983	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gtaagtccatactggataaaTttcattgaagacctggtaga	9	6	1	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:169446983T>C	ENST00000236137.5	-	2	453	c.217A>G	c.(217-219)Att>Gtt	p.I73V	SLC19A2_ENST00000367804.4_Intron	NM_006996.2	NP_008927.1	O60779	S19A2_HUMAN	solute carrier family 19 (thiamine transporter), member 2	73					folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|thiamine transport (GO:0015888)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid transporter activity (GO:0008517)|thiamine transmembrane transporter activity (GO:0015234)|thiamine uptake transmembrane transporter activity (GO:0015403)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	11	all_hematologic(923;0.208)				Thiamine(DB00152)	ACTGGATAAATTTCATTGAAG	0.363																																					p.I73V		Atlas-SNP	.											.	SLC19A2	35	.	0			c.A217G						.						29	27	27					1																	169446983		2203	4300	6503	SO:0001583	missense	10560	exon2			GATAAATTTCATT	AF135488	CCDS1280.1	1q23.3	2013-05-22			ENSG00000117479	ENSG00000117479		"Solute carriers"	10938	protein-coding gene	gene with protein product		603941		TRMA		9399900, 10391221	Standard	NM_006996		Approved	THTR1	uc001gge.4	O60779	OTTHUMG00000035452	ENST00000236137.5:c.217A>G	chr1.hg19:g.169446983T>C	ENSP00000236137:p.Ile73Val	227.0	0.0		333.0	126.0	NM_006996	B2R9H0|B4E1X4|Q8WV87|Q9UBL7|Q9UKJ2|Q9UN31|Q9UN43	Missense_Mutation	SNP	ENST00000236137.5	hg19	CCDS1280.1	.	.	.	.	.	.	.	.	.	.	T	12.30	1.895528	0.33442	.	.	ENSG00000117479	ENST00000236137;ENST00000367802	D;D	0.85013	-1.93;-1.93	4.44	4.44	0.53790	Major facilitator superfamily domain, general substrate transporter (1);	0.050436	0.85682	D	0.000000	T	0.75406	0.3845	L	0.35542	1.07	0.39660	D	0.970595	B	0.34241	0.444	P	0.47786	0.557	T	0.72754	-0.4198	9	0.09590	T	0.72	-21.0558	14.1622	0.65454	0.0:0.0:0.0:1.0	.	73	O60779	S19A2_HUMAN	V	73	ENSP00000236137:I73V;ENSP00000356776:I73V	ENSP00000236137:I73V	I	-	1	0	SLC19A2	167713607	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.315000	0.51951	1.993000	0.58246	0.455000	0.32223	ATT	.	.		0.363	SLC19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086106.1	NM_006996		C	169446983	T	C	169446983	3	2	201	1	0	0	0	0	1	0	0	0	14444	1493	52	2	1296	2	SLC19A2	1	169446983	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	9674751	169446983	79803638	12	29472										
WNT9A	7483	hgsc.bcm.edu	37	chr1	228109383	228109383	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gttcttctcacggtggcaccTacggccagcggtgcccgggg	15	14	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:228109383T>A	ENST00000272164.5	-	4	944	c.934A>T	c.(934-936)Agg>Tgg	p.R312W		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	312					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				CGGTGGCACCTACGGCCAGCG	0.672																																					p.R312W		Atlas-SNP	.											.	WNT9A	39	.	0			c.A934T						.						31	30	30					1																	228109383		2202	4300	6502	SO:0001583	missense	7483	exon4			GGCACCTACGGCC	AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"Wingless-type MMTV integration sites"	12778	protein-coding gene	gene with protein product		602863	"wingless-type MMTV integration site family, member 14"	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.934A>T	chr1.hg19:g.228109383T>A	ENSP00000272164:p.Arg312Trp	88.0	0.0		102.0	35.0	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Missense_Mutation	SNP	ENST00000272164.5	hg19	CCDS31045.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.602115	0.66445	.	.	ENSG00000143816	ENST00000272164	T	0.76578	-1.03	4.64	2.14	0.27477	.	0.112361	0.64402	D	0.000014	D	0.83922	0.5359	M	0.73319	2.225	0.34845	D	0.741081	D	0.63046	0.992	D	0.63957	0.92	D	0.86659	0.1903	10	0.66056	D	0.02	.	10.4114	0.44296	0.0:0.0:0.3149:0.685	.	312	O14904	WNT9A_HUMAN	W	312	ENSP00000272164:R312W	ENSP00000272164:R312W	R	-	1	2	WNT9A	226176006	0.749000	0.28305	0.998000	0.56505	0.862000	0.49288	2.078000	0.41567	0.243000	0.21327	0.397000	0.26171	AGG	.	.		0.672	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395		A	228109383	T	A	228109383	3	1	201	1	0	0	0	0	1	0	0	0	17413	1521	53	4	167	4	WNT9A	1	228109383	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	58662400	228109383	21141238	13	29473										
PGBD5	79605	hgsc.bcm.edu	37	chr1	230492898	230492898	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	atgtagcccaggaacgccttCatctccgtcagcgtcacctc	8	16	4	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:230492898C>G	ENST00000525115.1	-	2	317	c.294G>C	c.(292-294)atG>atC	p.M98I	PGBD5_ENST00000391860.1_Missense_Mutation_p.M52I|PGBD5_ENST00000321327.2_Missense_Mutation_p.M197I			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	98						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		GGAACGCCTTCATCTCCGTCA	0.592																																					p.M167I		Atlas-SNP	.											.	PGBD5	73	.	0			c.G501C						.						131	106	114					1																	230492898		2203	4300	6503	SO:0001583	missense	79605	exon2			CGCCTTCATCTCC	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.294G>C	chr1.hg19:g.230492898C>G	ENSP00000431404:p.Met98Ile	93.0	0.0		119.0	33.0	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Missense_Mutation	SNP	ENST00000525115.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.10	1.835669	0.32421	.	.	ENSG00000177614	ENST00000391860;ENST00000321327;ENST00000525115	T;T;T	0.13538	2.58;2.58;2.58	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.08492	0.0211	N	0.12746	0.255	0.80722	D	1	B	0.13145	0.007	B	0.14578	0.011	T	0.29852	-0.9998	10	0.11485	T	0.65	-59.592	15.6149	0.76756	0.138:0.862:0.0:0.0	.	98	Q8N414	PGBD5_HUMAN	I	52;197;98	ENSP00000375733:M52I;ENSP00000322530:M197I;ENSP00000431404:M98I	ENSP00000322530:M197I	M	-	3	0	PGBD5	228559521	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.970000	0.70431	2.746000	0.94184	0.655000	0.94253	ATG	.	.		0.592	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		G	230492898	C	G	230492898	3	3	201	1	0	0	0	0	1	0	0	0	11793	826	29	4	1097	4	PGBD5	1	230492898	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	2383515	230492898	18757723	14	29474										
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233388234	233388234	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agattatctgtctttgtctaTtgccctgaaaacttaacaca	5	9	3	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:233388234T>C	ENST00000258229.9	-	7	2228	c.1994A>G	c.(1993-1995)aAt>aGt	p.N665S	PCNXL2_ENST00000430153.1_5'UTR	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	665						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				TCTTTGTCTATTGCCCTGAAA	0.358																																					p.N665S		Atlas-SNP	.											.	PCNXL2	204	.	0			c.A1994G						.						115	108	110					1																	233388234		1834	4089	5923	SO:0001583	missense	80003	exon7			TGTCTATTGCCCT	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.1994A>G	chr1.hg19:g.233388234T>C	ENSP00000258229:p.Asn665Ser	129.0	0.0		137.0	50.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.234803	0.39498	.	.	ENSG00000135749	ENST00000258229	T	0.07327	3.2	5.49	-4.66	0.03329	.	.	.	.	.	T	0.03959	0.0111	N	0.14661	0.345	0.31695	N	0.641377	B	0.12630	0.006	B	0.08055	0.003	T	0.50415	-0.8831	9	0.02654	T	1	.	14.4351	0.67274	0.0:0.6325:0.1032:0.2643	.	665	A6NKB5	PCX2_HUMAN	S	665	ENSP00000258229:N665S	ENSP00000258229:N665S	N	-	2	0	PCNXL2	231454857	0.059000	0.20769	0.109000	0.21407	0.957000	0.61999	-0.856000	0.04290	-0.810000	0.04375	0.455000	0.32223	AAT	.	.		0.358	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		C	233388234	T	C	233388234	3	2	201	1	0	0	0	0	1	0	0	0	11601	1493	52	2	4531	2	PCNXL2	1	233388234	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	2895336	233388234	15862387	15	29475										
RYR2	6262	hgsc.bcm.edu	37	chr1	237814791	237814791	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	attaaatgaacacgcaaagaTgcctcttaaagtaagtatag	7	6	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:237814791T>A	ENST00000366574.2	+	51	8131	c.7814T>A	c.(7813-7815)aTg>aAg	p.M2605K	RYR2_ENST00000360064.6_Missense_Mutation_p.M2603K|RYR2_ENST00000542537.1_Missense_Mutation_p.M2589K	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2605	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CACGCAAAGATGCCTCTTAAA	0.323																																					p.M2605K		Atlas-SNP	.											.	RYR2	1273	.	0			c.T7814A						.						74	66	68					1																	237814791		1829	4098	5927	SO:0001583	missense	6262	exon51			CAAAGATGCCTCT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7814T>A	chr1.hg19:g.237814791T>A	ENSP00000355533:p.Met2605Lys	141.0	0.0		206.0	77.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.363850	0.82353	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96830	-4.14;-4.14;-4.14	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.97161	0.9072	M	0.68317	2.08	0.80722	D	1	D	0.65815	0.995	P	0.58721	0.844	D	0.97777	1.0230	10	0.87932	D	0	-19.6589	15.4811	0.75528	0.0:0.0:0.0:1.0	.	2605	Q92736	RYR2_HUMAN	K	2605;2603;2589	ENSP00000355533:M2605K;ENSP00000353174:M2603K;ENSP00000443798:M2589K	ENSP00000353174:M2603K	M	+	2	0	RYR2	235881414	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	7.972000	0.88022	2.113000	0.64589	0.477000	0.44152	ATG	.	.		0.323	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237814791	T	A	237814791	3	1	201	1	0	0	0	0	1	0	0	0	13784	1464	51	4	8016	4	RYR2	1	237814791	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	4426557	237814791	11435830	16	29476										
WDR64	128025	hgsc.bcm.edu	37	chr1	241912886	241912886	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gactttggcagtgggcaggaGatgaaggtgttgccggaggg	20	5	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:241912886G>A	ENST00000366552.2	+	13	1809	c.1602G>A	c.(1600-1602)gaG>gaA	p.E534E	WDR64_ENST00000437684.2_Silent_p.E534E	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	534										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GTGGGCAGGAGATGAAGGTGT	0.502																																					p.E534E		Atlas-SNP	.											.	WDR64	234	.	0			c.G1602A						.						132	134	134					1																	241912886		2203	4300	6503	SO:0001819	synonymous_variant	128025	exon13			GCAGGAGATGAAG	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1602G>A	chr1.hg19:g.241912886G>A		159.0	0.0		244.0	31.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Silent	SNP	ENST00000366552.2	hg19		.	.	.	.	.	.	.	.	.	.	G	9.797	1.179570	0.21787	.	.	ENSG00000162843	ENST00000425826	.	.	.	6.06	3.96	0.45880	.	.	.	.	.	T	0.54951	0.1890	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52495	-0.8568	4	.	.	.	-16.1446	5.696	0.17855	0.2928:0.0:0.7072:0.0	.	.	.	.	K	13	.	.	R	+	2	0	WDR64	239979509	1.000000	0.71417	0.994000	0.49952	0.943000	0.58893	1.690000	0.37711	1.545000	0.49373	0.655000	0.94253	AGA	.	.		0.502	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		A	241912886	G	A	241912886	2	1	201	1	0	0	0	0	0	0	0	1	17330	933	33	3		3	WDR64	1	241912886	Silent	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	4098095	241912886	7337735	17	29477										
OR2G2	81470	hgsc.bcm.edu	37	chr1	247752022	247752022	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agtgcgtcctcccggctgtgAtgtcctgtgaccgctatgtg	13	12	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:247752022A>T	ENST00000320065.1	+	1	361	c.361A>T	c.(361-363)Atg>Ttg	p.M121L	RP11-978I15.10_ENST00000435333.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			CCCGGCTGTGATGTCCTGTGA	0.537																																					p.M121L		Atlas-SNP	.											.	OR2G2	88	.	0			c.A361T						.						279	223	242					1																	247752022		2203	4300	6503	SO:0001583	missense	81470	exon1			GCTGTGATGTCCT	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"GPCR / Class A : Olfactory receptors"	15007	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily G, member 2", "olfactory receptor, family 2, subfamily G, member 2 pseudogene"				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.361A>T	chr1.hg19:g.247752022A>T	ENSP00000326349:p.Met121Leu	114.0	0.0		155.0	39.0	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	hg19	CCDS31092.1	.	.	.	.	.	.	.	.	.	.	A	18.66	3.671958	0.67928	.	.	ENSG00000177489	ENST00000320065	T	0.01647	4.71	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42420	U	0.000718	T	0.08447	0.0210	H	0.98507	4.25	0.31641	N	0.648085	P	0.34757	0.467	B	0.34590	0.186	T	0.03608	-1.1020	10	0.87932	D	0	.	11.4683	0.50252	1.0:0.0:0.0:0.0	.	121	Q8NGZ5	OR2G2_HUMAN	L	121	ENSP00000326349:M121L	ENSP00000326349:M121L	M	+	1	0	OR2G2	245818645	1.000000	0.71417	0.923000	0.36655	0.993000	0.82548	6.968000	0.76086	1.789000	0.52484	0.481000	0.45027	ATG	.	.		0.537	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1			T	247752022	A	T	247752022	3	4	201	1	0	0	0	0	1	0	0	0	11007	333	12	4	363	4	OR2G2	1	247752022	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	5839136	247752022	1498599	18	29478										
OR14C36	127066	hgsc.bcm.edu	37	chr1	248512548	248512548	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ttgtctatgcaggcatgcacActggcagcacattccagctg	10	12	1	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr1:248512548A>T	ENST00000317861.1	+	1	472	c.472A>T	c.(472-474)Act>Tct	p.T158S		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	158						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						AGGCATGCACACTGGCAGCAC	0.522																																					p.T158S		Atlas-SNP	.											.	OR14C36	113	.	0			c.A472T						.						133	113	120					1																	248512548		2203	4300	6503	SO:0001583	missense	127066	exon1			ATGCACACTGGCA	BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"GPCR / Class A : Olfactory receptors"	15026	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily BF, member 1"	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.472A>T	chr1.hg19:g.248512548A>T	ENSP00000324534:p.Thr158Ser	37.0	0.0		51.0	13.0	NM_001001918	Q6IEZ6	Missense_Mutation	SNP	ENST00000317861.1	hg19	CCDS31112.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.621843	0.46840	.	.	ENSG00000177174	ENST00000317861	T	0.00258	8.41	4.05	4.05	0.47172	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000190	T	0.00440	0.0014	M	0.62088	1.915	0.23271	N	0.998003	D	0.69078	0.997	D	0.74674	0.984	T	0.53493	-0.8431	10	0.51188	T	0.08	.	11.497	0.50415	1.0:0.0:0.0:0.0	.	158	Q8NHC7	O14CZ_HUMAN	S	158	ENSP00000324534:T158S	ENSP00000324534:T158S	T	+	1	0	OR14C36	246579171	0.000000	0.05858	0.187000	0.23214	0.782000	0.44232	-0.052000	0.11865	1.728000	0.51552	0.324000	0.21423	ACT	.	.		0.522	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918		T	248512548	A	T	248512548	3	4	201	1	0	0	0	0	1	0	0	0	10955	159	6	4	474	4	OR14C36	1	248512548	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	760526	248512548	738073	19	29479										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54873140	54873140	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tccagactgtgcagctgttaAtaaagaaaaatcaggtaagc	9	7	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr2:54873140A>G	ENST00000356805.4	+	22	4851	c.4570A>G	c.(4570-4572)Ata>Gta	p.I1524V	SPTBN1_ENST00000333896.5_Missense_Mutation_p.I1511V	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1524					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GCAGCTGTTAATAAAGAAAAA	0.433																																					p.I1524V		Atlas-SNP	.											.	SPTBN1	378	.	0			c.A4570G						.						91	88	89					2																	54873140		2203	4300	6503	SO:0001583	missense	6711	exon22			CTGTTAATAAAGA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.4570A>G	chr2.hg19:g.54873140A>G	ENSP00000349259:p.Ile1524Val	61.0	0.0		84.0	33.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.532848	0.64972	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.48201	1.26;0.82	5.74	5.74	0.90152	.	0.043762	0.85682	D	0.000000	T	0.57110	0.2031	M	0.83774	2.66	0.50632	D	0.999884	B;B	0.26445	0.026;0.149	B;B	0.32928	0.026;0.155	T	0.57934	-0.7725	10	0.45353	T	0.12	.	16.3305	0.83010	1.0:0.0:0.0:0.0	.	1511;1524	Q01082-3;Q01082	.;SPTB2_HUMAN	V	1524;1511	ENSP00000349259:I1524V;ENSP00000334156:I1511V	ENSP00000334156:I1511V	I	+	1	0	SPTBN1	54726644	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	9.193000	0.94954	2.317000	0.78254	0.459000	0.35465	ATA	.	.		0.433	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			G	54873140	A	G	54873140	3	3	201	1	0	0	0	0	1	0	0	0	15134	101	4	2	4765	2	SPTBN1	2	54873140	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10		54873140	188326233	20	29480										
SLC5A7	60482	hgsc.bcm.edu	37	chr2	108614395	108614395	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tggtgggagggctctattctGtggcctacactgatgtcgtt	14	8	2	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr2:108614395G>T	ENST00000264047.2	+	5	826	c.550G>T	c.(550-552)Gtg>Ttg	p.V184L	SLC5A7_ENST00000409059.1_Missense_Mutation_p.V184L|SLC5A7_ENST00000540517.1_Missense_Mutation_p.V79L	NM_021815.2	NP_068587.1	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (sodium/choline cotransporter), member 7	184					acetylcholine biosynthetic process (GO:0008292)|cell death (GO:0008219)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	choline binding (GO:0033265)|choline transmembrane transporter activity (GO:0015220)|choline:sodium symporter activity (GO:0005307)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	49					Choline(DB00122)	GCTCTATTCTGTGGCCTACAC	0.463																																					p.V184L		Atlas-SNP	.											.	SLC5A7	109	.	0			c.G550T						.						243	214	223					2																	108614395		2203	4300	6503	SO:0001583	missense	60482	exon5			TATTCTGTGGCCT	AF276871	CCDS2074.1	2q12	2013-07-19	2013-07-19		ENSG00000115665	ENSG00000115665		"Solute carriers"	14025	protein-coding gene	gene with protein product		608761	"solute carrier family 5 (choline transporter), member 7"			11027560	Standard	NM_021815		Approved	hCHT, CHT1	uc002tdv.3	Q9GZV3	OTTHUMG00000130959	ENST00000264047.2:c.550G>T	chr2.hg19:g.108614395G>T	ENSP00000264047:p.Val184Leu	132.0	0.0		162.0	59.0	NM_021815	Q53TF2	Missense_Mutation	SNP	ENST00000264047.2	hg19	CCDS2074.1	.	.	.	.	.	.	.	.	.	.	G	32	5.141610	0.94560	.	.	ENSG00000115665	ENST00000409059;ENST00000540517;ENST00000264047	D;D;D	0.89746	-2.56;-2.56;-2.56	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.96103	0.8730	M	0.93594	3.435	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.97178	0.9849	10	0.87932	D	0	0.9748	18.5601	0.91097	0.0:0.0:1.0:0.0	.	184	Q9GZV3	SC5A7_HUMAN	L	184;79;184	ENSP00000387346:V184L;ENSP00000445351:V79L;ENSP00000264047:V184L	ENSP00000264047:V184L	V	+	1	0	SLC5A7	107980827	1.000000	0.71417	0.976000	0.42696	0.913000	0.54294	9.869000	0.99810	2.390000	0.81377	0.655000	0.94253	GTG	.	.		0.463	SLC5A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253562.1			T	108614395	G	T	108614395	3	4	201	1	0	0	0	0	1	0	0	0	14685	1377	48	3	564	3	SLC5A7	2	108614395	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	53741255	108614395	134584978	21	29481										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166210790	166210790	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tgataacgaaatgaataatcTccagattgctgtgggaagga	11	5	1	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr2:166210790T>C	ENST00000375437.2	+	17	3298	c.3008T>C	c.(3007-3009)cTc>cCc	p.L1003P	SCN2A_ENST00000283256.6_Missense_Mutation_p.L1003P|SCN2A_ENST00000357398.3_Missense_Mutation_p.L1003P|SCN2A_ENST00000375427.2_Missense_Mutation_p.L1003P	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1003			L -> I (in BFIS3). {ECO:0000269|PubMed:15048894}.		intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATGAATAATCTCCAGATTGCT	0.388																																					p.L1003P		Atlas-SNP	.											.	SCN2A	589	.	0			c.T3008C						.						151	156	154					2																	166210790		2203	4300	6503	SO:0001583	missense	6326	exon16			ATAATCTCCAGAT	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.3008T>C	chr2.hg19:g.166210790T>C	ENSP00000364586:p.Leu1003Pro	157.0	0.0		179.0	70.0	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	hg19	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.251735	0.80135	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.90444	-2.67;-2.67;-2.67;-2.67	5.6	5.6	0.85130	Sodium ion transport-associated (1);	0.202030	0.35235	N	0.003345	D	0.96800	0.8955	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	0.993;1.0	D;D	0.97110	0.952;1.0	D	0.97992	1.0355	10	0.87932	D	0	.	15.7718	0.78176	0.0:0.0:0.0:1.0	.	1003;1003	Q99250-2;Q99250	.;SCN2A_HUMAN	P	1003	ENSP00000364586:L1003P;ENSP00000349973:L1003P;ENSP00000283256:L1003P;ENSP00000364576:L1003P	ENSP00000283256:L1003P	L	+	2	0	SCN2A	165919036	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.036000	0.88901	2.110000	0.64415	0.482000	0.46254	CTC	.	.		0.388	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		C	166210790	T	C	166210790	3	2	201	1	0	0	0	0	1	0	0	0	13931	1551	54	2	3166	2	SCN2A	2	166210790	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	57596395	166210790	76988583	22	29482										
TLK1	9874	hgsc.bcm.edu	37	chr2	171863315	171863315	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ttaatattcacttacgtatcTgtatccaaggagaaataatc	5	7	2	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr2:171863315T>A	ENST00000431350.2	-	16	1997	c.1593A>T	c.(1591-1593)acA>acT	p.T531T	TLK1_ENST00000521943.1_Silent_p.T483T|TLK1_ENST00000360843.3_Silent_p.T552T|TLK1_ENST00000442919.2_Silent_p.T483T|TLK1_ENST00000434911.2_Silent_p.T435T			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	531	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						CTTACGTATCTGTATCCAAGG	0.368																																					p.T531T		Atlas-SNP	.											.	TLK1	134	.	0			c.A1593T						.						104	111	109					2																	171863315		2202	4298	6500	SO:0001819	synonymous_variant	9874	exon16			CGTATCTGTATCC	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.1593A>T	chr2.hg19:g.171863315T>A		92.0	0.0		135.0	48.0	NM_012290	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Silent	SNP	ENST00000431350.2	hg19	CCDS2241.1																																																																																			.	.		0.368	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		A	171863315	T	A	171863315	2	1	201	1	0	0	0	0	0	0	0	1	15958	1567	55	4		4	TLK1	2	171863315	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	5652525	171863315	71336058	23	29483										
MAP2	4133	hgsc.bcm.edu	37	chr2	210560650	210560650	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gataaactgctcttccgctcAgacacccttcagataactga	6	13	3	3	rs185809016	byFrequency	TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr2:210560650A>T	ENST00000360351.4	+	7	4262	c.3756A>T	c.(3754-3756)tcA>tcT	p.S1252S	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000447185.1_Silent_p.S1248S|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1252					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	TCTTCCGCTCAGACACCCTTC	0.483																																					p.S1252S	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.A3756T						.						95	99	98					2																	210560650		2203	4300	6503	SO:0001819	synonymous_variant	4133	exon7			CCGCTCAGACACC		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.3756A>T	chr2.hg19:g.210560650A>T		85.0	0.0		108.0	49.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	A|0.997;C|0.003		0.483	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		T	210560650	A	T	210560650	2	4	201	1	0	0	0	0	0	0	0	1	9244	175	7	4		4	MAP2	2	210560650	Silent	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	38697335	210560650	32638723	24	29484										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215823030	215823030	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	aatgaagtttgttacccagtAgcatgtcacgccaatgcctg	9	10	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr2:215823030A>T	ENST00000272895.7	-	41	6307	c.6088T>A	c.(6088-6090)Tac>Aac	p.Y2030N	AC072062.1_ENST00000607412.1_RNA|AC072062.1_ENST00000420134.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.Y1712N	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2030					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GTTACCCAGTAGCATGTCACG	0.413																																					p.Y2030N	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.T6088A						.						225	197	206					2																	215823030		2203	4300	6503	SO:0001583	missense	26154	exon41			CCCAGTAGCATGT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.6088T>A	chr2.hg19:g.215823030A>T	ENSP00000272895:p.Tyr2030Asn	83.0	0.0		141.0	45.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.122354	0.77436	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.94497	-3.44;-3.44	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000015	D	0.97598	0.9213	M	0.89287	3.02	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98485	1.0607	10	0.87932	D	0	.	15.9507	0.79835	1.0:0.0:0.0:0.0	.	2030;1712	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	N	2030;1712	ENSP00000272895:Y2030N;ENSP00000374312:Y1712N	ENSP00000272895:Y2030N	Y	-	1	0	ABCA12	215531275	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.287000	0.95975	2.232000	0.73038	0.528000	0.53228	TAC	.	.		0.413	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215823030	A	T	215823030	3	4	201	1	0	0	0	0	1	0	0	0	30	420	15	4	1751	4	ABCA12	2	215823030	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	5262380	215823030	27376343	25	29485										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230638898	230638898	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tattgggaaaccctggcagaGtgaaatccagtcctagatct	10	9	1	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr2:230638898G>C	ENST00000283943.5	-	37	5562	c.5384C>G	c.(5383-5385)aCt>aGt	p.T1795S	TRIP12_ENST00000389045.3_Missense_Mutation_p.T1525S|TRIP12_ENST00000389044.4_Missense_Mutation_p.T1843S	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1795					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		CCCTGGCAGAGTGAAATCCAG	0.413																																					p.T1795S		Atlas-SNP	.											.	TRIP12	207	.	0			c.C5384G						.						141	136	138					2																	230638898		2203	4300	6503	SO:0001583	missense	9320	exon37			GGCAGAGTGAAAT	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.5384C>G	chr2.hg19:g.230638898G>C	ENSP00000283943:p.Thr1795Ser	74.0	0.0		105.0	42.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	hg19	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.278588	0.80692	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044;ENST00000418123	T;T;T;T	0.60424	0.19;0.19;0.19;0.99	6.08	6.08	0.98989	HECT (4);	0.000000	0.85682	D	0.000000	T	0.69646	0.3134	L	0.31926	0.97	0.80722	D	1	D;D;D	0.57257	0.979;0.979;0.979	D;D;D	0.74023	0.982;0.982;0.982	T	0.69179	-0.5213	10	0.62326	D	0.03	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	1525;1843;1795	Q14CF1;Q14CA3;Q14669	.;.;TRIPC_HUMAN	S	1795;1525;1843;93	ENSP00000283943:T1795S;ENSP00000373697:T1525S;ENSP00000373696:T1843S;ENSP00000408330:T93S	ENSP00000283943:T1795S	T	-	2	0	TRIP12	230347142	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.214000	0.95140	2.894000	0.99253	0.591000	0.81541	ACT	.	.		0.413	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		C	230638898	G	C	230638898	3	2	201	1	0	0	0	0	1	0	0	0	16571	1029	36	4	614	4	TRIP12	2	230638898	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	14815868	230638898	12560475	26	29486										
DGKD	8527	hgsc.bcm.edu	37	chr2	234299052	234299052	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tgtttgtctctttctagtcaAtcatatttgatgaggtggat	9	5	4	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr2:234299052A>G	ENST00000264057.2	+	3	283	c.271A>G	c.(271-273)Atc>Gtc	p.I91V	AC019221.4_ENST00000442524.1_RNA|DGKD_ENST00000409813.3_Missense_Mutation_p.I47V	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	91	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	TTTCTAGTCAATCATATTTGA	0.463																																					p.I91V		Atlas-SNP	.											.	DGKD	106	.	0			c.A271G						.						203	177	186					2																	234299052		2203	4300	6503	SO:0001583	missense	8527	exon3			TAGTCAATCATAT	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.271A>G	chr2.hg19:g.234299052A>G	ENSP00000264057:p.Ile91Val	75.0	0.0		95.0	43.0	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	hg19	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.864339	0.51482	.	.	ENSG00000077044	ENST00000264057;ENST00000447484;ENST00000409813	T;T;T	0.74947	-0.89;-0.89;-0.89	5.6	5.6	0.85130	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.64402	D	0.000001	T	0.48624	0.1510	N	0.04090	-0.28	0.38224	D	0.940834	B;B	0.32753	0.383;0.045	B;B	0.29716	0.106;0.098	T	0.55218	-0.8175	10	0.11794	T	0.64	.	11.1269	0.48324	0.8455:0.1544:0.0:0.0	.	47;91	Q16760-2;Q16760	.;DGKD_HUMAN	V	91;61;47	ENSP00000264057:I91V;ENSP00000395530:I61V;ENSP00000386455:I47V	ENSP00000264057:I91V	I	+	1	0	DGKD	233963791	0.996000	0.38824	0.959000	0.39883	0.868000	0.49771	3.510000	0.53393	2.274000	0.75844	0.533000	0.62120	ATC	.	.		0.463	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		G	234299052	A	G	234299052	3	3	201	1	0	0	0	0	1	0	0	0	4469	101	4	2	305	2	DGKD	2	234299052	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	3660154	234299052	8900321	27	29487										
SETMAR	6419	hgsc.bcm.edu	37	chr3	4354838	4354838	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agtggtccagaaaggtctacAgttccacttccaagtgttca	9	10	2	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr3:4354838A>C	ENST00000358065.4	+	2	480	c.413A>C	c.(412-414)cAg>cCg	p.Q138P	SUMF1_ENST00000534863.1_Intron|SETMAR_ENST00000430981.1_Missense_Mutation_p.Q138P|SETMAR_ENST00000425863.1_Missense_Mutation_p.Q138P	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	138	Histone-lysine N-methyltransferase.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		AAAGGTCTACAGTTCCACTTC	0.458								Chromatin Structure																													p.Q138P		Atlas-SNP	.											.	SETMAR	30	.	0			c.A413C						.						62	61	61					3																	4354838		2203	4300	6503	SO:0001583	missense	6419	exon2			GTCTACAGTTCCA	U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.413A>C	chr3.hg19:g.4354838A>C	ENSP00000373354:p.Gln138Pro	74.0	0.0		98.0	29.0	NM_001243723	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	hg19	CCDS2563.2	.	.	.	.	.	.	.	.	.	.	A	17.68	3.448238	0.63178	.	.	ENSG00000170364	ENST00000358065;ENST00000430981;ENST00000425863	D;D;T	0.89415	-2.51;-2.51;-1.4	5.18	4.02	0.46733	SET domain (1);	.	.	.	.	D	0.93835	0.8028	M	0.85630	2.765	0.26133	N	0.980384	D;P;P	0.71674	0.998;0.951;0.77	D;P;B	0.67231	0.95;0.692;0.408	D	0.86699	0.1928	9	0.72032	D	0.01	.	9.6681	0.39996	0.8541:0.0:0.1459:0.0	.	138;125;138	E7EN68;Q53H47;C9JHK2	.;SETMR_HUMAN;.	P	138	ENSP00000373354:Q138P;ENSP00000403000:Q138P;ENSP00000403145:Q138P	ENSP00000373354:Q138P	Q	+	2	0	SETMAR	4329838	0.998000	0.40836	0.927000	0.36925	0.850000	0.48378	3.234000	0.51320	0.809000	0.34255	0.455000	0.32223	CAG	.	.		0.458	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515		C	4354838	A	C	4354838	3	2	201	1	0	0	0	0	1	0	0	0	14155	188	7	5	419	5	SETMAR	3	4354838	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10		4354838	193667592	28	29488										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47044767	47044767	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ttgctgcaggaggaccagctCggcgaggacgagctggctga	17	10	0	1	rs201985571		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr3:47044767C>T	ENST00000450053.3	+	35	5867	c.5688C>T	c.(5686-5688)ctC>ctT	p.L1896L	NBEAL2_ENST00000292309.5_Silent_p.L1712L|NBEAL2_ENST00000383740.2_Silent_p.L175L	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1896					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		AGGACCAGCTCGGCGAGGACG	0.647																																					p.L1896L		Atlas-SNP	.											.	NBEAL2	267	.	0			c.C5688T						.	C		0,3876		0,0,1938	29	34	32		5688	-8.2	0.1	3		32	1,8255		0,1,4127	no	coding-synonymous	NBEAL2	NM_015175.1		0,1,6065	TT,TC,CC		0.0121,0.0,0.0082		1896/2755	47044767	1,12131	1938	4128	6066	SO:0001819	synonymous_variant	23218	exon35			CCAGCTCGGCGAG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.5688C>T	chr3.hg19:g.47044767C>T		95.0	0.0		122.0	41.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.283|0.283	-0.985041|-0.985041	0.02180|0.02180	0.0|0.0	1.21E-4|1.21E-4	ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000416683	.|.	.|.	.|.	5.01|5.01	-8.2|-8.2	0.01045|0.01045	.|.	.|.	.|.	.|.	.|.	T|T	0.35098|0.35098	0.0920|0.0920	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.39313|0.39313	-0.9620|-0.9620	4|4	.|.	.|.	.|.	.|.	2.6218|2.6218	0.04918|0.04918	0.403:0.2965:0.2031:0.0974|0.403:0.2965:0.2031:0.0974	.|.	.|.	.|.	.|.	W|L	265|1184	.|.	.|.	R|S	+|+	1|2	2|0	NBEAL2|NBEAL2	47019771|47019771	0.981000|0.981000	0.34729|0.34729	0.050000|0.050000	0.19076|0.19076	0.047000|0.047000	0.14425|0.14425	0.041000|0.041000	0.13927|0.13927	-1.748000|-1.748000	0.01332|0.01332	-1.762000|-1.762000	0.00668|0.00668	CGG|TCG	.	C|0.998;T|0.002		0.647	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47044767	C	T	47044767	2	4	201	1	0	0	0	0	0	0	0	1	10198	871	31	1		1	NBEAL2	3	47044767	Silent	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	42689929	47044767	150977663	29	29489										
MITF	4286	hgsc.bcm.edu	37	chr3	69788758	69788758	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	aagcgggagccatgcagtccGaatcggggatcgtgccggat	16	10	0	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr3:69788758G>T	ENST00000448226.2	+	1	137	c.10G>T	c.(10-12)Gaa>Taa	p.E4*	MITF_ENST00000352241.4_Nonsense_Mutation_p.E4*			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	4					bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		CATGCAGTCCGAATCGGGGAT	0.592			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														p.E4X	Melanoma(29;269 969 31479 41502 42961)	Atlas-SNP	.		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	.	MITF	156	.	0			c.G10T						.						37	43	42					3																	69788758		1919	4118	6037	SO:0001587	stop_gained	4286	exon1			CAGTCCGAATCGG		CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.10G>T	chr3.hg19:g.69788758G>T	ENSP00000391803:p.Glu4*	73.0	0.0		86.0	20.0	NM_198159	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Nonsense_Mutation	SNP	ENST00000448226.2	hg19		.	.	.	.	.	.	.	.	.	.	G	37	6.395046	0.97533	.	.	ENSG00000187098	ENST00000352241;ENST00000448226	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2345	0.89945	0.0:0.0:1.0:0.0	.	.	.	.	X	4	.	.	E	+	1	0	MITF	69871448	1.000000	0.71417	0.993000	0.49108	0.285000	0.27093	8.045000	0.89436	2.550000	0.86006	0.313000	0.20887	GAA	.	.		0.592	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		T	69788758	G	T	69788758	4	4	201	1	0	0	0	0	0	1	0	0	9605	1059	37	1	12	1	MITF	3	69788758	Nonsense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	22743991	69788758	128233672	30	29490										
ARL13B	200894	hgsc.bcm.edu	37	chr3	93755562	93755562	+	Frame_Shift_Del	DEL	A	A	-													0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tgaggaacaagagaaacaagAaagagctgaacgagtgcgaa							TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr3:93755562delA	ENST00000394222.3	+	5	928	c.653delA	c.(652-654)gaafs	p.E218fs	ARL13B_ENST00000471138.1_Frame_Shift_Del_p.E218fs|ARL13B_ENST00000535334.1_Frame_Shift_Del_p.E115fs|ARL13B_ENST00000303097.7_Frame_Shift_Del_p.E111fs|ARL13B_ENST00000539730.1_5'UTR|ARL13B_ENST00000486562.1_3'UTR	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	218					cilium assembly (GO:0042384)|dorsal/ventral pattern formation (GO:0009953)|formation of radial glial scaffolds (GO:0021943)|heart looping (GO:0001947)|interneuron migration from the subpallium to the cortex (GO:0021830)|left/right axis specification (GO:0070986)|neural tube patterning (GO:0021532)|nonmotile primary cilium assembly (GO:0035058)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|intracellular (GO:0005622)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(2)	10						GAGAAACAAGAAAGAGCTGAA	0.373																																					p.E218fs		Atlas-INDEL	.											.	ARL13B	52	.	0			c.652delG						.						63	61	61					3																	93755562		2203	4300	6503	SO:0001589	frameshift_variant	200894	exon5			.	AL713789	CCDS2924.1, CCDS2925.1, CCDS54615.1	3q11	2014-05-09	2005-11-18	2005-11-18	ENSG00000169379	ENSG00000169379		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	25419	protein-coding gene	gene with protein product		608922	"ADP-ribosylation factor-like 2-like 1"	ARL2L1		15314642, 18674751	Standard	NR_033427		Approved	DKFZp761H079, JBTS8	uc003drf.3	Q3SXY8	OTTHUMG00000159012	ENST00000394222.3:c.653delA	chr3.hg19:g.93755562delA	ENSP00000377769:p.Glu218fs	341.0	0.0		486.0	166.0	NM_001174150	D3DN29|G3V1S8|Q504W8|Q8TCL5	Frame_Shift_Del	DEL	ENST00000394222.3	hg19	CCDS2925.1																																																																																			.	.		0.373	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896		-	93755562	A	-	93755562	7	5	201	1	0	1	0	1	0	0	0	0	929	246	9	0	671	0	ARL13B	3	93755562	Frame_Shift_Del	DEL	A	TCGA-DD-AADS-01A-11D-A40R-10	23966804	93755562	104266868	31	29491										
CASR	846	hgsc.bcm.edu	37	chr3	121976018	121976018	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gcccttcttcccaacttgacGctgggatacaggatatttga	9	11	1	2	rs201013419		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr3:121976018G>T	ENST00000490131.1	+	3	648	c.276G>T	c.(274-276)acG>acT	p.T92T	CASR_ENST00000296154.5_Silent_p.T92T|CASR_ENST00000498619.1_Silent_p.T92T	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	92					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	CCAACTTGACGCTGGGATACA	0.443																																					p.T92T		Atlas-SNP	.											.	CASR	190	.	0			c.G276T						.						120	120	120					3																	121976018		2203	4300	6503	SO:0001819	synonymous_variant	846	exon3			CTTGACGCTGGGA	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.276G>T	chr3.hg19:g.121976018G>T		103.0	0.0		150.0	44.0	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Silent	SNP	ENST00000490131.1	hg19	CCDS3010.1																																																																																			.	G|0.999;A|0.001		0.443	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		T	121976018	G	T	121976018	2	4	201	1	0	0	0	0	0	0	0	1	2684	1074	38	1		1	CASR	3	121976018	Silent	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	28220456	121976018	76046412	32	29492										
RTP2	344892	hgsc.bcm.edu	37	chr3	187416345	187416345	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	aacaacgagcaggcagagagAggcccagaagaggcaccagc	14	11	0	4			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr3:187416345A>T	ENST00000358241.1	-	2	1047	c.619T>A	c.(619-621)Tct>Act	p.S207T		NM_001004312.2	NP_001004312.2	Q5QGT7	RTP2_HUMAN	receptor (chemosensory) transporter protein 2	207					protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)			large_intestine(3)|lung(14)|skin(1)	18	all_cancers(143;4.06e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0515)		AGGCAGAGAGAGGCCCAGAAG	0.582																																					p.S207T		Atlas-SNP	.											.	RTP2	38	.	0			c.T619A						.						85	89	88					3																	187416345		2203	4300	6503	SO:0001583	missense	344892	exon2			AGAGAGAGGCCCA	AY562236	CCDS33911.1	3q27.3	2014-02-20	2006-11-21		ENSG00000198471	ENSG00000198471		"Receptor transporter proteins"	32486	protein-coding gene	gene with protein product	"receptor transporting protein 2", "zinc finger, 3CxxC-type 2"	609138	"receptor transporter protein 2"			16271481, 15550249, 16720576	Standard	NM_001004312		Approved	MGC78665, Z3CXXC2	uc003fro.1	Q5QGT7	OTTHUMG00000156458	ENST00000358241.1:c.619T>A	chr3.hg19:g.187416345A>T	ENSP00000350976:p.Ser207Thr	75.0	0.0		112.0	38.0	NM_001004312	Q6NVH4	Missense_Mutation	SNP	ENST00000358241.1	hg19	CCDS33911.1	.	.	.	.	.	.	.	.	.	.	A	0.761	-0.769407	0.02974	.	.	ENSG00000198471	ENST00000358241	T	0.11930	2.73	3.93	1.49	0.22878	.	0.729779	0.12614	N	0.453594	T	0.04998	0.0134	N	0.11201	0.11	0.21527	N	0.999656	B	0.02656	0.0	B	0.01281	0.0	T	0.43426	-0.9392	10	0.02654	T	1	-13.1634	4.4722	0.11717	0.5976:0.2053:0.0:0.1971	.	207	Q5QGT7	RTP2_HUMAN	T	207	ENSP00000350976:S207T	ENSP00000350976:S207T	S	-	1	0	RTP2	188899039	0.041000	0.20044	0.863000	0.33907	0.891000	0.51852	-0.188000	0.09642	0.321000	0.23259	0.379000	0.24179	TCT	.	.		0.582	RTP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344259.1	NM_001004312		T	187416345	A	T	187416345	3	4	201	1	0	0	0	0	1	0	0	0	13749	304	11	4	62	4	RTP2	3	187416345	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	65440327	187416345	10606085	33	29493										
RGS12	6002	hgsc.bcm.edu	37	chr4	3318367	3318367	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ttttgaaaacccgagcctttGtgcgagcaattcagagccct	9	11	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr4:3318367G>T	ENST00000344733.5	+	2	1374	c.470G>T	c.(469-471)tGt>tTt	p.C157F	RGS12_ENST00000336727.3_Missense_Mutation_p.C157F|RGS12_ENST00000382788.3_Missense_Mutation_p.C157F|RGS12_ENST00000543385.1_Missense_Mutation_p.C157F	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	157					positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CCGAGCCTTTGTGCGAGCAAT	0.413																																					p.C157F		Atlas-SNP	.											.	RGS12	128	.	0			c.G470T						.						47	53	51					4																	3318367		2203	4300	6503	SO:0001583	missense	6002	exon2			GCCTTTGTGCGAG	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"Regulators of G-protein signaling"	9994	protein-coding gene	gene with protein product		602512	"regulator of G-protein signalling 12"			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.470G>T	chr4.hg19:g.3318367G>T	ENSP00000339381:p.Cys157Phe	50.0	0.0		87.0	4.0	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	hg19	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	G	8.524	0.869483	0.17322	.	.	ENSG00000159788	ENST00000543385;ENST00000344733;ENST00000336727;ENST00000382788	T;T;T;T	0.29655	1.56;1.67;1.66;1.66	4.72	3.88	0.44766	.	0.482216	0.23678	N	0.045649	T	0.26846	0.0657	L	0.44542	1.39	0.20074	N	0.999934	P;P;P	0.43287	0.736;0.802;0.797	B;B;P	0.45099	0.195;0.26;0.469	T	0.07462	-1.0771	10	0.14656	T	0.56	-0.0181	8.5146	0.33237	0.1777:0.0:0.8223:0.0	.	157;157;157	Q8WX97;O14924;O14924-4	.;RGS12_HUMAN;.	F	157	ENSP00000440566:C157F;ENSP00000339381:C157F;ENSP00000338509:C157F;ENSP00000372238:C157F	ENSP00000338509:C157F	C	+	2	0	RGS12	3288165	0.980000	0.34600	0.001000	0.08648	0.018000	0.09664	2.886000	0.48578	0.983000	0.38602	0.491000	0.48974	TGT	.	.		0.413	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926		T	3318367	G	T	3318367	3	4	201	1	0	0	0	0	1	0	0	0	13310	1377	48	3	472	3	RGS12	4	3318367	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10		3318367	187835909	34	29494										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46067562	46067562	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	attgaattttaaacgactgtCaaaccaggtttgggcaaaaa	8	6	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr4:46067562C>A	ENST00000295452.4	-	4	528	c.361G>T	c.(361-363)Gac>Tac	p.D121Y		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	121					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AAACGACTGTCAAACCAGGTT	0.299																																					p.D121Y		Atlas-SNP	.											.	GABRG1	172	.	0			c.G361T						.						43	44	44					4																	46067562		2203	4299	6502	SO:0001583	missense	2565	exon4			GACTGTCAAACCA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.361G>T	chr4.hg19:g.46067562C>A	ENSP00000295452:p.Asp121Tyr	62.0	0.0		70.0	18.0	NM_173536	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.438906	0.83885	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	D	0.93763	-3.28	5.08	5.08	0.68730	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.98134	0.9384	H	0.97829	4.085	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99675	1.0997	10	0.87932	D	0	.	17.8218	0.88652	0.0:1.0:0.0:0.0	.	121	Q8N1C3	GBRG1_HUMAN	Y	121	ENSP00000295452:D121Y	ENSP00000295452:D121Y	D	-	1	0	GABRG1	45762319	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.772000	0.85439	2.513000	0.84729	0.508000	0.49915	GAC	.	.		0.299	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		A	46067562	C	A	46067562	3	1	201	1	0	0	0	0	1	0	0	0	6179	826	29	3	1060	3	GABRG1	4	46067562	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	42749195	46067562	145086714	35	29495										
FRYL	285527	hgsc.bcm.edu	37	chr4	48542570	48542570	+	Frame_Shift_Del	DEL	T	T	-													0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ctgatttatccaaaggcaaaTggataagcagtttgttgaga							TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr4:48542570delT	ENST00000503238.1	-	43	6094	c.6095delA	c.(6094-6096)catfs	p.H2032fs	FRYL_ENST00000358350.4_Frame_Shift_Del_p.H2032fs|FRYL_ENST00000507873.2_5'UTR|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Frame_Shift_Del_p.H2032fs			O94915	FRYL_HUMAN	FRY-like	2032					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						CAAAGGCAAATGGATAAGCAG	0.378																																					p.H2032fs		Atlas-INDEL	.											.	FRYL	242	.	0			c.6096delT						.						100	91	94					4																	48542570		1846	4088	5934	SO:0001589	frameshift_variant	285527	exon46			.	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.6095delA	chr4.hg19:g.48542570delT	ENSP00000426064:p.His2032fs	135.0	0.0		149.0	50.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Frame_Shift_Del	DEL	ENST00000503238.1	hg19	CCDS43227.1																																																																																			.	.		0.378	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			-	48542570	T	-	48542570	7	5	201	1	0	1	0	1	0	0	0	0	6072	1464	51	0	3022	0	FRYL	4	48542570	Frame_Shift_Del	DEL	T	TCGA-DD-AADS-01A-11D-A40R-10	2475008	48542570	142611706	36	29496										
PAICS	10606	hgsc.bcm.edu	37	chr4	57325638	57325638	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gtatggagcaaactgcgagcAagcattttgaacacatggat	11	7	0	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr4:57325638A>T	ENST00000512576.1	+	9	1373	c.1212A>T	c.(1210-1212)gcA>gcT	p.A404A	PAICS_ENST00000399688.3_Silent_p.A411A|PAICS_ENST00000264221.2_Silent_p.A404A|PAICS_ENST00000514888.1_Silent_p.A312A	NM_001079524.1	NP_001072992.1	P22234	PUR6_HUMAN	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase	404	AIR carboxylase.				'de novo' IMP biosynthetic process (GO:0006189)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|phosphoribosylaminoimidazole carboxylase activity (GO:0004638)|phosphoribosylaminoimidazolesuccinocarboxamide synthase activity (GO:0004639)			endometrium(1)|kidney(2)|large_intestine(1)|urinary_tract(1)	5	Glioma(25;0.08)|all_neural(26;0.101)				L-Aspartic Acid(DB00128)	AACTGCGAGCAAGCATTTTGA	0.393																																					p.A411A	GBM(53;429 1144 8755 40726)	Atlas-SNP	.											.	PAICS	21	.	0			c.A1233T						.						70	62	64					4																	57325638		1850	4097	5947	SO:0001819	synonymous_variant	10606	exon10			GCGAGCAAGCATT	X53793	CCDS47060.1, CCDS47061.1	4q12	2012-07-13			ENSG00000128050	ENSG00000128050	4.1.1.21, 6.3.2.6		8587	protein-coding gene	gene with protein product		172439		PAIS		2253271, 8106516	Standard	NM_006452		Approved	ADE2H1, AIRC	uc003hbt.1	P22234	OTTHUMG00000160957	ENST00000512576.1:c.1212A>T	chr4.hg19:g.57325638A>T		153.0	0.0		232.0	78.0	NM_001079525	E9PDH9|Q68CQ5	Silent	SNP	ENST00000512576.1	hg19	CCDS47061.1																																																																																			.	.		0.393	PAICS-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363136.2	NM_006452		T	57325638	A	T	57325638	2	4	201	1	0	0	0	0	0	0	0	1	11404	117	5	4		4	PAICS	4	57325638	Silent	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	8783068	57325638	133828638	37	29497										
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69962793	69962793	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	acttttgaaaagcatagtggAggatttattttccctccttc	7	8	0	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr4:69962793A>G	ENST00000508661.1	+	1	582	c.555A>G	c.(553-555)ggA>ggG	p.G185G	UGT2B7_ENST00000509763.1_Intron|UGT2B7_ENST00000305231.7_Silent_p.G185G			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	185					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	AGCATAGTGGAGGATTTATTT	0.393																																					p.G185G		Atlas-SNP	.											.	UGT2B7	79	.	0			c.A555G						.						119	118	118					4																	69962793		2203	4298	6501	SO:0001819	synonymous_variant	7364	exon1			TAGTGGAGGATTT	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"UDP glucuronosyltransferases"	12554	protein-coding gene	gene with protein product		600068	"UDP glycosyltransferase 2 family, polypeptide B7"			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.555A>G	chr4.hg19:g.69962793A>G		107.0	0.0		146.0	54.0	NM_001074	B2R810|Q6GTW0	Silent	SNP	ENST00000508661.1	hg19																																																																																				.	.		0.393	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		G	69962793	A	G	69962793	2	3	201	1	0	0	0	0	0	0	0	1	16977	291	11	2		2	UGT2B7	4	69962793	Silent	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	12637155	69962793	121191483	38	29498										
FABP2	2169	hgsc.bcm.edu	37	chr4	120241841	120241841	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ttaccctgagttcagttccgTctgctagattgtaattaaag	8	8	2	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr4:120241841T>A	ENST00000274024.3	-	2	511	c.224A>T	c.(223-225)gAc>gTc	p.D75V		NM_000134.3	NP_000125.2	P12104	FABPI_HUMAN	fatty acid binding protein 2, intestinal	75					digestion (GO:0007586)	cytoplasm (GO:0005737)	fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			breast(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	8					Estradiol(DB00783)|Ibuprofen(DB01050)|Sulfinpyrazone(DB01138)	TTCAGTTCCGTCTGCTAGATT	0.318																																					p.D75V		Atlas-SNP	.											.	FABP2	21	.	0			c.A224T						.						87	93	91					4																	120241841		2201	4299	6500	SO:0001583	missense	2169	exon2			GTTCCGTCTGCTA	J03465	CCDS3712.1	4q28-q31	2013-03-01			ENSG00000145384	ENSG00000145384		"Fatty acid binding protein family"	3556	protein-coding gene	gene with protein product		134640					Standard	NM_000134		Approved	I-FABP	uc003icw.3	P12104	OTTHUMG00000132972	ENST00000274024.3:c.224A>T	chr4.hg19:g.120241841T>A	ENSP00000274024:p.Asp75Val	36.0	0.0		35.0	12.0	NM_000134	Q2NKJ1	Missense_Mutation	SNP	ENST00000274024.3	hg19	CCDS3712.1	.	.	.	.	.	.	.	.	.	.	T	16.02	3.004733	0.54254	.	.	ENSG00000145384	ENST00000274024	T	0.56611	0.45	5.71	5.71	0.89125	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.000000	0.85682	D	0.000000	T	0.72415	0.3457	M	0.74881	2.28	0.80722	D	1	D	0.60575	0.988	D	0.74023	0.982	T	0.76061	-0.3097	10	0.87932	D	0	.	15.6632	0.77206	0.0:0.0:0.0:1.0	.	75	P12104	FABPI_HUMAN	V	75	ENSP00000274024:D75V	ENSP00000274024:D75V	D	-	2	0	FABP2	120461289	1.000000	0.71417	0.893000	0.35052	0.060000	0.15804	7.496000	0.81526	2.176000	0.68965	0.528000	0.53228	GAC	.	.		0.318	FABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256531.1	NM_000134		A	120241841	T	A	120241841	3	1	201	1	0	0	0	0	1	0	0	0	5362	1667	58	4	186	4	FABP2	4	120241841	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	50279048	120241841	70912435	39	29499										
INPP4B	8821	hgsc.bcm.edu	37	chr4	143324209	143324209	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	acagtgggtcccttgttcccTgtaacagcacaagcagacaa	9	12	0	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr4:143324209T>A	ENST00000513000.1	-	8	689		c.e8-2		INPP4B_ENST00000508116.1_Splice_Site|INPP4B_ENST00000262992.4_Splice_Site|INPP4B_ENST00000506217.1_Splice_Site|INPP4B_ENST00000509777.1_Splice_Site|INPP4B_ENST00000308502.4_Splice_Site	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa						cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CCTTGTTCCCTGTAACAGCAC	0.443																																					.		Atlas-SNP	.											.	INPP4B	132	.	0			c.256-2A>T						.						144	126	132					4																	143324209		2203	4300	6503	SO:0001630	splice_region_variant	8821	exon9			GTTCCCTGTAACA	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.256-2A>T	chr4.hg19:g.143324209T>A		68.0	0.0		83.0	29.0	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Splice_Site	SNP	ENST00000513000.1	hg19	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	T	19.49	3.836521	0.71373	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000508116;ENST00000509777;ENST00000510812;ENST00000506217	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8101	0.78552	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	INPP4B	143543659	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	5.783000	0.68982	2.178000	0.69098	0.533000	0.62120	.	.	.		0.443	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	Intron	A	143324209	T	A	143324209	5	1	201	1	0	0	0	0	0	0	1	0	7762	1594	55	4	2600	4	INPP4B	4	143324209	Splice_Site	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	23082368	143324209	47830067	40	29500										
FRG1	2483	hgsc.bcm.edu	37	chr4	190878604	190878604	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gctttattagatgcaatgaaGcaggggacatagaagcaaaa	11	5	0	3	rs371189769		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr4:190878604G>A	ENST00000226798.4	+	6	706	c.484G>A	c.(484-486)Gca>Aca	p.A162T	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	162					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		ATGCAATGAAGCAGGGGACAT	0.383																																					p.A162T		Atlas-SNP	.											.	FRG1	76	.	0			c.G484A						.						36	36	36					4																	190878604		2184	4280	6464	SO:0001583	missense	2483	exon6			AATGAAGCAGGGG	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.484G>A	chr4.hg19:g.190878604G>A	ENSP00000226798:p.Ala162Thr	204.0	0.0		265.0	16.0	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	hg19	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	11.61	1.689550	0.29962	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.42900	1.94;0.96	4.19	4.19	0.49359	Actin cross-linking (1);	0.268853	0.42821	D	0.000657	T	0.36110	0.0955	L	0.47716	1.5	0.31376	N	0.679557	B	0.27951	0.195	B	0.30716	0.119	T	0.35001	-0.9806	10	0.14656	T	0.56	-21.4303	14.4711	0.67517	0.0:0.0:1.0:0.0	.	162	Q14331	FRG1_HUMAN	T	162;34;99	ENSP00000226798:A162T;ENSP00000435943:A99T	ENSP00000226798:A162T	A	+	1	0	FRG1	191115598	1.000000	0.71417	1.000000	0.80357	0.534000	0.34807	4.336000	0.59304	2.063000	0.61619	0.454000	0.30748	GCA	.	.		0.383	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477		A	190878604	G	A	190878604	3	1	201	1	0	0	0	0	1	0	0	0	6054	971	34	3	506	3	FRG1	4	190878604	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	47554395	190878604	275672	41	29501										
NKD2	85409	hgsc.bcm.edu	37	chr5	1034416	1034416	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ggacgttcacgctctatgacTttgacaactgcgggaaggtc	12	10	2	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:1034416T>A	ENST00000296849.5	+	6	626	c.397T>A	c.(397-399)Ttt>Att	p.F133I	NKD2_ENST00000537972.1_Missense_Mutation_p.F133I|NKD2_ENST00000274150.4_Missense_Mutation_p.F133I|NKD2_ENST00000382730.2_5'Flank	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	133	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.|Interaction with DVL1, DVL2 and DVL3. {ECO:0000250}.|Targeting to the basolateral cell membrane.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			GCTCTATGACTTTGACAACTG	0.627																																					p.F133I		Atlas-SNP	.											.	NKD2	39	.	0			c.T397A						.						135	100	112					5																	1034416		2202	4297	6499	SO:0001583	missense	85409	exon6			TATGACTTTGACA	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"EF-hand domain containing"	17046	protein-coding gene	gene with protein product	"naked cuticle-2", "Dvl-binding protein NKD2"	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.397T>A	chr5.hg19:g.1034416T>A	ENSP00000296849:p.Phe133Ile	88.0	0.0		95.0	25.0	NM_001271082	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	hg19	CCDS3859.1	.	.	.	.	.	.	.	.	.	.	T	17.27	3.347800	0.61183	.	.	ENSG00000145506	ENST00000296849;ENST00000274150;ENST00000537972	T;T;T	0.00597	6.31;6.31;6.31	3.65	3.65	0.41850	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.01421	0.0046	M	0.77486	2.375	0.80722	D	1	P;P	0.50156	0.932;0.872	P;P	0.50659	0.647;0.495	T	0.63616	-0.6597	10	0.52906	T	0.07	-14.1761	8.6817	0.34212	0.0:0.0:0.0:1.0	.	133;133	Q969F2-2;Q969F2	.;NKD2_HUMAN	I	133	ENSP00000296849:F133I;ENSP00000274150:F133I;ENSP00000440925:F133I	ENSP00000274150:F133I	F	+	1	0	NKD2	1087416	1.000000	0.71417	0.981000	0.43875	0.248000	0.25809	4.522000	0.60539	1.306000	0.44926	0.454000	0.30748	TTT	.	.		0.627	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		A	1034416	T	A	1034416	3	1	201	1	0	0	0	0	1	0	0	0	10451	1609	56	4	419	4	NKD2	5	1034416	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10		1034416	179880844	42	29502										
TERT	7015	hgsc.bcm.edu	37	chr5	1266629	1266629	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ggtgtcaccaacaagaaatcAtccaccaaacgcaggagcag	9	12	2	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:1266629A>G	ENST00000310581.5	-	10	2661	c.2604T>C	c.(2602-2604)gaT>gaC	p.D868D	TERT_ENST00000334602.6_Silent_p.D868D|TERT_ENST00000508104.2_Nonstop_Mutation_p.*808R|TERT_ENST00000296820.5_Nonstop_Mutation_p.*808R	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	868	Reverse transcriptase. {ECO:0000255|PROSITE-ProRule:PRU00405}.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	ACAAGAAATCATCCACCAAAC	0.498									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.D868D		Atlas-SNP	.											.	TERT	2594	.	0			c.T2604C						.						140	96	111					5																	1266629		2201	4298	6499	SO:0001819	synonymous_variant	7015	exon10	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	GAAATCATCCACC	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.2604T>C	chr5.hg19:g.1266629A>G		127.0	0.0		144.0	58.0	NM_001193376	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	hg19	CCDS3861.2	.	.	.	.	.	.	.	.	.	.	A	0.045	-1.271324	0.01421	.	.	ENSG00000164362	ENST00000296820;ENST00000508104	.	.	.	3.87	-3.87	0.04218	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.4092	9.9408	0.41578	0.5685:0.0:0.4315:0.0	.	.	.	.	R	808	.	.	X	-	1	0	TERT	1319629	0.990000	0.36364	0.835000	0.33067	0.041000	0.13682	0.251000	0.18257	-1.038000	0.03279	-0.371000	0.07208	TGA	.	.		0.498	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			G	1266629	A	G	1266629	2	3	201	1	0	0	0	0	0	0	0	1	15779	214	8	2		2	TERT	5	1266629	Silent	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	232213	1266629	179648631	43	29503										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5462373	5462374	+	Frame_Shift_Ins	INS	-	-	CA													0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agacattgtgagagaagctgINScagtgcagggagatgggcag							TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:5462373_5462374insCA	ENST00000296564.7	+	13	3148_3149	c.2926_2927insCA	c.(2926-2928)gcafs	p.A976fs		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		976					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						GAGAGAAGCTGCAGTGCAGGGA	0.47																																					p.A976fs		Atlas-INDEL	.											.	KIAA0947	301	.	0			c.2926_2927insCA						.																																			SO:0001589	frameshift_variant	23379	exon13			.																												ENST00000296564.7:c.2927_2928dupCA	chr5.hg19:g.5462374_5462375dupCA	ENSP00000296564:p.Ala976fs	103.0	0.0		128.0	39.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Frame_Shift_Ins	INS	ENST00000296564.7	hg19	CCDS47187.1																																																																																			.	.		0.47	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			CA	5462374	-	CA	5462373	7	5	201	1	0	1	1	0	0	0	0	0	8211	1319	46	0	2976	0	KIAA0947	5	5462373	Frame_Shift_Ins	INS	-	TCGA-DD-AADS-01A-11D-A40R-10	4195744	5462373	175452887	44	29504										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11098730	11098730	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tctgcagggcgcctgccgccCcttccagcgtgtctggattt	12	15	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:11098730C>A	ENST00000304623.8	-	15	2783	c.2594G>T	c.(2593-2595)gGg>gTg	p.G865V	CTNND2_ENST00000511377.1_Missense_Mutation_p.G774V|CTNND2_ENST00000458100.2_Missense_Mutation_p.G432V|CTNND2_ENST00000503622.1_Missense_Mutation_p.G528V|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000359640.2_Intron	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	865					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GCCTGCCGCCCCTTCCAGCGT	0.517																																					p.G865V		Atlas-SNP	.											.	CTNND2	289	.	0			c.G2594T						.						92	85	88					5																	11098730		2203	4300	6503	SO:0001583	missense	1501	exon15			GCCGCCCCTTCCA	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.2594G>T	chr5.hg19:g.11098730C>A	ENSP00000307134:p.Gly865Val	64.0	0.0		86.0	4.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	30	5.050037	0.93740	.	.	ENSG00000169862	ENST00000304623;ENST00000511377;ENST00000458100;ENST00000503622	D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0	6.17	6.17	0.99709	Armadillo-like helical (1);Armadillo-type fold (1);	0.049769	0.85682	D	0.000000	D	0.91236	0.7238	L	0.50333	1.59	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90766	0.4668	10	0.87932	D	0	-23.4378	20.8794	0.99867	0.0:1.0:0.0:0.0	.	528;432;865	B4DRK2;B4DG58;Q9UQB3	.;.;CTND2_HUMAN	V	865;774;432;528	ENSP00000307134:G865V;ENSP00000426510:G774V;ENSP00000391155:G432V;ENSP00000426887:G528V	ENSP00000307134:G865V	G	-	2	0	CTNND2	11151730	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GGG	.	.		0.517	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11098730	C	A	11098730	3	1	201	1	0	0	0	0	1	0	0	0	4022	623	22	3	1115	3	CTNND2	5	11098730	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	5636357	11098730	169816530	45	29505										
ITGA1	3672	hgsc.bcm.edu	37	chr5	52235677	52235677	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gacatttaaacaggactgcaAtacatgtaaatttgctacca	6	8	0	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:52235677A>G	ENST00000282588.6	+	26	3646	c.3188A>G	c.(3187-3189)aAt>aGt	p.N1063S	CTD-2175A23.1_ENST00000505701.1_RNA|CTD-2175A23.1_ENST00000503559.1_RNA	NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	1063					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				CAGGACTGCAATACATGTAAA	0.313																																					p.N1063S		Atlas-SNP	.											.	ITGA1	112	.	0			c.A3188G						.						114	97	103					5																	52235677		2203	4300	6503	SO:0001583	missense	3672	exon26			ACTGCAATACATG	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.3188A>G	chr5.hg19:g.52235677A>G	ENSP00000282588:p.Asn1063Ser	186.0	0.0		265.0	77.0	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	hg19	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	A	0.020	-1.442891	0.01089	.	.	ENSG00000213949	ENST00000282588	T	0.45668	0.89	6.05	0.239	0.15484	.	0.692454	0.15883	N	0.239946	T	0.09686	0.0238	N	0.00841	-1.15	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34502	-0.9826	10	0.02654	T	1	.	4.1856	0.10397	0.4688:0.1769:0.3543:0.0	.	1063	P56199	ITA1_HUMAN	S	1063	ENSP00000282588:N1063S	ENSP00000282588:N1063S	N	+	2	0	ITGA1	52271434	0.112000	0.22096	0.087000	0.20705	0.320000	0.28249	1.206000	0.32321	0.129000	0.18514	-0.182000	0.12963	AAT	.	.		0.313	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		G	52235677	A	G	52235677	3	3	201	1	0	0	0	0	1	0	0	0	7881	101	4	2	3290	2	ITGA1	5	52235677	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	41136947	52235677	128679583	46	29506										
ESM1	11082	hgsc.bcm.edu	37	chr5	54277844	54277844	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cccgtgagagaaacaaatctGttggaagacttggttactga	11	7	1	4			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:54277844G>T	ENST00000381405.4	-	2	577	c.432C>A	c.(430-432)aaC>aaA	p.N144K	ESM1_ENST00000381403.4_Intron|ESM1_ENST00000598310.1_Intron	NM_007036.4	NP_008967.1	Q9NQ30	ESM1_HUMAN	endothelial cell-specific molecule 1	144					angiogenesis (GO:0001525)|positive regulation of cell proliferation (GO:0008284)|positive regulation of hepatocyte growth factor receptor signaling pathway (GO:1902204)|regulation of cell growth (GO:0001558)|sprouting angiogenesis (GO:0002040)	extracellular region (GO:0005576)	hepatocyte growth factor receptor binding (GO:0005171)|integrin binding (GO:0005178)			breast(1)|kidney(1)|large_intestine(4)|lung(4)	10		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.116)	Lung(15;0.23)			AAACAAATCTGTTGGAAGACT	0.428																																					p.N144K		Atlas-SNP	.											.	ESM1	27	.	0			c.C432A						.						121	118	119					5																	54277844		2203	4300	6503	SO:0001583	missense	11082	exon2			AAATCTGTTGGAA	X89426	CCDS3963.1, CCDS47206.1	5q11	2008-02-05			ENSG00000164283	ENSG00000164283			3466	protein-coding gene	gene with protein product		601521				8702785	Standard	NM_001135604		Approved		uc003jpk.3	Q9NQ30	OTTHUMG00000097010	ENST00000381405.4:c.432C>A	chr5.hg19:g.54277844G>T	ENSP00000370812:p.Asn144Lys	99.0	0.0		138.0	48.0	NM_007036	B2R4G3|Q15330|Q3V4E3|Q96ES3	Missense_Mutation	SNP	ENST00000381405.4	hg19	CCDS3963.1	.	.	.	.	.	.	.	.	.	.	G	9.583	1.124210	0.20959	.	.	ENSG00000164283	ENST00000381405	.	.	.	5.63	2.57	0.30868	.	1.035260	0.07602	N	0.923825	T	0.44286	0.1286	N	0.24115	0.695	0.58432	D	0.999991	B	0.06786	0.001	B	0.04013	0.001	T	0.39396	-0.9616	9	0.62326	D	0.03	-24.379	8.7588	0.34661	0.0737:0.0:0.568:0.3583	.	144	Q9NQ30	ESM1_HUMAN	K	144	.	ENSP00000370812:N144K	N	-	3	2	ESM1	54313601	1.000000	0.71417	0.534000	0.28014	0.282000	0.26991	0.980000	0.29513	1.357000	0.45904	-0.309000	0.09137	AAC	.	.		0.428	ESM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214099.2	NM_007036		T	54277844	G	T	54277844	3	4	201	1	0	0	0	0	1	0	0	0	5254	1368	48	3	130	3	ESM1	5	54277844	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	2042167	54277844	126637416	47	29507										
KDM3B	51780	hgsc.bcm.edu	37	chr5	137753199	137753199	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	caatattggagacatggtacAtgctgcccggggcaagtggg	15	8	0	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:137753199A>T	ENST00000314358.5	+	13	3535	c.3335A>T	c.(3334-3336)cAt>cTt	p.H1112L	KDM3B_ENST00000394866.1_Missense_Mutation_p.H768L|KDM3B_ENST00000542866.1_Missense_Mutation_p.H144L	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1112					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						GACATGGTACATGCTGCCCGG	0.418																																					p.H1112L		Atlas-SNP	.											.	KDM3B	177	.	0			c.A3335T						.						142	129	134					5																	137753199		2203	4300	6503	SO:0001583	missense	51780	exon13			TGGTACATGCTGC	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.3335A>T	chr5.hg19:g.137753199A>T	ENSP00000326563:p.His1112Leu	75.0	0.0		110.0	5.0	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	A	31	5.092109	0.94149	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	D;D;D	0.85861	-1.5;-2.04;-1.53	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.92642	0.7662	M	0.82517	2.595	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.978	D	0.93705	0.7019	10	0.87932	D	0	-5.6809	15.6827	0.77385	1.0:0.0:0.0:0.0	.	768;1112	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	L	1112;902;768;144	ENSP00000326563:H1112L;ENSP00000378335:H768L;ENSP00000439462:H144L	ENSP00000326563:H1112L	H	+	2	0	KDM3B	137781098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.103000	0.63969	0.460000	0.39030	CAT	.	.		0.418	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		T	137753199	A	T	137753199	3	4	201	1	0	0	0	0	1	0	0	0	8136	217	8	4	3385	4	KDM3B	5	137753199	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	83475355	137753199	43162061	48	29508										
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140255480	140255480	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gaaagggaacaaaaggtaccTgtttctgaatctgcgcctct	10	9	3	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:140255480T>A	ENST00000398631.2	+	1	423	c.423T>A	c.(421-423)ccT>ccA	p.P141P	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	141	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAAAGGTACCTGTTTCTGAAT	0.502																																					p.P141P	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.T423A						.						81	94	89					5																	140255480		2203	4300	6503	SO:0001819	synonymous_variant	56137	exon1			GGTACCTGTTTCT	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.423T>A	chr5.hg19:g.140255480T>A		169.0	0.0		219.0	75.0	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	hg19	CCDS47285.1																																																																																			.	.		0.502	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140255480	T	A	140255480	2	1	201	1	0	0	0	0	0	0	0	1	11531	1567	55	4		4	PCDHA12	5	140255480	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	2502281	140255480	40659780	49	29509										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140262777	140262777	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	attaggacaaaaggcaaactAgatttcgaagaaaagaaatt	8	4	0	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:140262777A>T	ENST00000289272.2	+	1	924	c.924A>T	c.(922-924)ctA>ctT	p.L308L	PCDHA6_ENST00000527624.1_Intron|PCDHA13_ENST00000409494.1_Silent_p.L308L|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	308	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGGCAAACTAGATTTCGAAG	0.383																																					p.L308L	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.A924T						.						57	65	62					5																	140262777		2203	4300	6503	SO:0001819	synonymous_variant	56136	exon1			CAAACTAGATTTC	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.924A>T	chr5.hg19:g.140262777A>T		130.0	0.0		143.0	51.0	NM_031865	O75277	Silent	SNP	ENST00000289272.2	hg19	CCDS4240.1																																																																																			.	.		0.383	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		T	140262777	A	T	140262777	2	4	201	1	0	0	0	0	0	0	0	1	11532	407	15	4		4	PCDHA13	5	140262777	Silent	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	7297	140262777	40652483	50	29510										
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140348697	140348697	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cctcacttcattgaagttcgAgggaatggctccctcaccaa	8	13	3	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:140348697A>G	ENST00000289269.5	+	1	2878	c.2346A>G	c.(2344-2346)cgA>cgG	p.R782R	PCDHA6_ENST00000527624.1_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	782					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGAAGTTCGAGGGAATGGCT	0.512																																					p.R782R	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.A2346G						.						92	86	88					5																	140348697		2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			AGTTCGAGGGAAT	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"Cadherins / Protocadherins : Clustered"	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.2346A>G	chr5.hg19:g.140348697A>G		101.0	0.0		146.0	50.0	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	hg19	CCDS4242.1																																																																																			.	.		0.512	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		G	140348697	A	G	140348697	2	3	201	1	0	0	0	0	0	0	0	1	11542	291	11	2		2	PCDHAC2	5	140348697	Silent	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	85920	140348697	40566563	51	29511										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140564018	140564018	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ggcgaggtgcgcaccgccagGctgctgagcgagcgcgacgc	18	14	0	1	rs146665935	byFrequency	TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:140564018G>T	ENST00000361016.2	+	1	3039	c.1884G>T	c.(1882-1884)agG>agT	p.R628S		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	628	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCACCGCCAGGCTGCTGAGCG	0.692																																					p.R628S		Atlas-SNP	.											.	PCDHB16	159	.	0			c.G1884T						.						23	24	24					5																	140564018		2048	4023	6071	SO:0001583	missense	57717	exon1			CGCCAGGCTGCTG	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1884G>T	chr5.hg19:g.140564018G>T	ENSP00000354293:p.Arg628Ser	50.0	0.0		65.0	18.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	g	16.00	2.998736	0.54147	.	.	ENSG00000196963	ENST00000361016	T	0.52295	0.67	3.96	2.07	0.26955	Cadherin (4);Cadherin-like (1);	0.000000	0.35207	N	0.003380	T	0.58963	0.2159	M	0.74467	2.265	0.09310	N	1	D	0.76494	0.999	D	0.77557	0.99	T	0.50996	-0.8761	10	0.87932	D	0	.	1.4092	0.02287	0.2688:0.1443:0.4394:0.1475	.	628	Q9NRJ7	PCDBG_HUMAN	S	628	ENSP00000354293:R628S	ENSP00000354293:R628S	R	+	3	2	PCDHB16	140544202	0.001000	0.12720	0.939000	0.37840	0.814000	0.46013	0.322000	0.19576	0.629000	0.30376	0.298000	0.19748	AGG	.	G|0.999;A|0.001		0.692	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		T	140564018	G	T	140564018	3	4	201	1	0	0	0	0	1	0	0	0	11550	1194	42	3	1886	3	PCDHB16	5	140564018	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	215321	140564018	40351242	52	29512										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141334585	141334585	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tcctccacggggttccgctcGgcgaaggcagccacagacag	13	15	0	1	rs375930414		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:141334585G>A	ENST00000231484.3	-	1	4042	c.2832C>T	c.(2830-2832)gcC>gcT	p.A944A	AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	944					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTTCCGCTCGGCGAAGGCAG	0.607													G|||	1	0.000199681	0	0	5008	,	,		17283	0		0	False		,,,				2504	0.001				p.A944A		Atlas-SNP	.											.	PCDH12	133	.	0			c.C2832T						.						38	42	41					5																	141334585		2203	4300	6503	SO:0001819	synonymous_variant	51294	exon1			CCGCTCGGCGAAG	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2832C>T	chr5.hg19:g.141334585G>A		94.0	0.0		78.0	22.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	hg19	CCDS4269.1																																																																																			.	.		0.607	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141334585	G	A	141334585	2	1	201	1	0	0	0	0	0	0	0	1	11519	1103	39	1		1	PCDH12	5	141334585	Silent	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	770567	141334585	39580675	53	29513										
DPYSL3	1809	hgsc.bcm.edu	37	chr5	146780396	146780396	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ccagatagctgcagatccccGctggcaaaggagaaaagctc	11	12	0	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:146780396G>T	ENST00000398514.3	-	10	1340	c.969C>A	c.(967-969)agC>agA	p.S323R	DPYSL3_ENST00000534907.1_Intron|DPYSL3_ENST00000343218.5_Splice_Site_p.S437R|CTB-108O6.2_ENST00000607270.1_RNA	NM_001387.2	NP_001378.1	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	323					actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cell migration (GO:0030336)|negative regulation of neuron projection development (GO:0010977)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron projection development (GO:0010976)|protein homooligomerization (GO:0051260)|pyrimidine nucleobase catabolic process (GO:0006208)|response to axon injury (GO:0048678)	cell body (GO:0044297)|cytosol (GO:0005829)|extracellular space (GO:0005615)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|lamellipodium (GO:0030027)	chondroitin sulfate binding (GO:0035374)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)|SH3 domain binding (GO:0017124)			breast(2)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGATCCCCGCTGGCAAAGG	0.537																																					p.S437R		Atlas-SNP	.											DPYSL3,NS,carcinoma,0,1	DPYSL3	58	.	0			c.C1311A						.						57	62	60					5																	146780396		2148	4275	6423	SO:0001630	splice_region_variant	1809	exon10			ATCCCCGCTGGCA	D78014	CCDS43381.1, CCDS56387.1	5q32	2008-02-05							3015	protein-coding gene	gene with protein product		601168				8973361, 9115293	Standard	NM_001197294		Approved	DRP-3, ULIP, CRMP4	uc003loo.3	Q14195		ENST00000398514.3:c.969-1C>A	chr5.hg19:g.146780396G>T		45.0	1.0		60.0	12.0	NM_001197294	B3SXQ8|Q93012	Missense_Mutation	SNP	ENST00000398514.3	hg19	CCDS43381.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.233314	0.39498	.	.	ENSG00000113657	ENST00000398514;ENST00000343218	D;D	0.90844	-2.74;-2.74	5.53	-2.89	0.05665	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.90957	0.7157	L	0.45698	1.435	0.80722	D	1	D;P	0.64830	0.994;0.585	D;B	0.69307	0.963;0.21	D	0.87817	0.2635	10	0.48119	T	0.1	.	11.3928	0.49824	0.6163:0.0:0.3837:0.0	.	437;323	B3SXQ8;Q14195	.;DPYL3_HUMAN	R	323;437	ENSP00000381526:S323R;ENSP00000343690:S437R	ENSP00000343690:S437R	S	-	3	2	DPYSL3	146760589	0.999000	0.42202	0.991000	0.47740	0.280000	0.26924	0.906000	0.28517	-0.373000	0.07979	-0.956000	0.02647	AGC	.	.		0.537	DPYSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373421.2	NM_001387	Missense_Mutation	T	146780396	G	T	146780396	5	4	201	1	0	0	0	0	0	0	1	0	4750	1101	38	1	763	1	DPYSL3	5	146780396	Splice_Site	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	5445811	146780396	34134864	54	29514										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161580332	161580332	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ttcttccccactgccttctgCctgtttaatctggtctattg	6	13	4	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr5:161580332C>G	ENST00000361925.4	+	9	1582	c.1362C>G	c.(1360-1362)tgC>tgG	p.C454W	GABRG2_ENST00000414552.2_Missense_Mutation_p.C502W|GABRG2_ENST00000356592.3_Missense_Mutation_p.C462W|GABRG2_ENST00000393933.4_Missense_Mutation_p.C359W			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	454					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTGCCTTCTGCCTGTTTAATC	0.463																																					p.C502W		Atlas-SNP	.											.	GABRG2	142	.	0			c.C1506G						.						268	273	271					5																	161580332		2203	4300	6503	SO:0001583	missense	2566	exon11			CTTCTGCCTGTTT		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1362C>G	chr5.hg19:g.161580332C>G	ENSP00000354651:p.Cys454Trp	120.0	0.0		147.0	40.0	NM_198903	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	hg19	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	C	13.53	2.265804	0.40095	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933	D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76	5.95	3.2	0.36748	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.148926	0.64402	D	0.000009	D	0.82838	0.5124	L	0.29908	0.895	0.58432	D	0.999998	P;P;P	0.50272	0.933;0.532;0.663	P;P;P	0.60173	0.87;0.497;0.694	D	0.83981	0.0332	10	0.72032	D	0.01	.	10.8297	0.46652	0.0:0.7303:0.0:0.2697	.	502;454;462	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	W	462;502;454;359	ENSP00000349000:C462W;ENSP00000410732:C502W;ENSP00000354651:C454W;ENSP00000377510:C359W	ENSP00000349000:C462W	C	+	3	2	GABRG2	161512910	0.893000	0.30496	1.000000	0.80357	0.995000	0.86356	-0.031000	0.12287	1.530000	0.49136	0.655000	0.94253	TGC	.	.		0.463	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			G	161580332	C	G	161580332	3	3	201	1	0	0	0	0	1	0	0	0	6180	747	26	4	1548	4	GABRG2	5	161580332	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	14799936	161580332	19334928	55	29515										
IRF4	3662	hgsc.bcm.edu	37	chr6	393256	393256	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gatcgaccagatcgacagcgGcaagtaccccgggctggtgt	14	12	0	1	rs538907751		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr6:393256G>A	ENST00000380956.4	+	2	230	c.104G>A	c.(103-105)gGc>gAc	p.G35D	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	35					cytokine-mediated signaling pathway (GO:0019221)|defense response to protozoan (GO:0042832)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of DNA binding (GO:0043388)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of interleukin-13 biosynthetic process (GO:0045368)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of T-helper cell differentiation (GO:0045622)|T cell activation (GO:0042110)|T-helper 17 cell lineage commitment (GO:0072540)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear nucleosome (GO:0000788)|nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		ATCGACAGCGGCAAGTACCCC	0.667			T	IGH@	MM																																p.G35D		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.G104A						.						35	35	35					6																	393256		2201	4298	6499	SO:0001583	missense	3662	exon2			ACAGCGGCAAGTA	U52682	CCDS4469.1	6p25-p23	2008-08-29			ENSG00000137265	ENSG00000137265			6119	protein-coding gene	gene with protein product		601900		MUM1		8921401, 18417578	Standard	NM_002460		Approved	LSIRF	uc003msz.4	Q15306	OTTHUMG00000016294	ENST00000380956.4:c.104G>A	chr6.hg19:g.393256G>A	ENSP00000370343:p.Gly35Asp	214.0	0.0		260.0	84.0	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	hg19	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	G	34	5.294557	0.95546	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.98044	-4.68	4.58	4.58	0.56647	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.098877	0.64402	D	0.000001	D	0.98406	0.9470	M	0.79258	2.445	0.80722	D	1	D;D;P	0.56521	0.976;0.971;0.946	D;P;P	0.66602	0.945;0.908;0.775	D	0.99274	1.0894	10	0.66056	D	0.02	-28.3311	17.6301	0.88104	0.0:0.0:1.0:0.0	.	35;35;35	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	D	35;65	ENSP00000370343:G35D	ENSP00000370343:G35D	G	+	2	0	IRF4	338256	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	8.812000	0.91959	2.399000	0.81585	0.306000	0.20318	GGC	.	.		0.667	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			A	393256	G	A	393256	3	1	201	1	0	0	0	0	1	0	0	0	7841	1203	42	3	106	3	IRF4	6	393256	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10		393256	170721811	56	29516										
PHF1	5252	hgsc.bcm.edu	37	chr6	33382581	33382581	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tgcctccccctgtggagcccCctactggagatggagcactc	11	16	0	1	rs201507218		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr6:33382581C>T	ENST00000374516.3	+	11	1295	c.1024C>T	c.(1024-1026)Cct>Tct	p.P342S	PHF1_ENST00000374512.3_Missense_Mutation_p.P342S	NM_024165.2	NP_077084.1	O43189	PHF1_HUMAN	PHD finger protein 1	342					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of histone H3-K27 methylation (GO:0061087)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19		Ovarian(999;0.0443)				TGTGGAGCCCCCTACTGGAGA	0.527											OREG0017346	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P342S		Atlas-SNP	.											.	PHF1	42	.	0			c.C1024T						.						67	66	66					6																	33382581		2203	4294	6497	SO:0001583	missense	5252	exon11			GAGCCCCCTACTG	AF029678	CCDS4777.1, CCDS4778.1	6p21.3	2013-01-28			ENSG00000112511	ENSG00000112511		"Tudor domain containing", "Zinc fingers, PHD-type"	8919	protein-coding gene	gene with protein product	"tudor domain containing 19C"	602881				9545646, 18385154	Standard	NM_024165		Approved	MTF2L2, TDRD19C	uc003oeh.3	O43189	OTTHUMG00000031105	ENST00000374516.3:c.1024C>T	chr6.hg19:g.33382581C>T	ENSP00000363640:p.Pro342Ser	61.0	0.0	839	73.0	18.0	NM_024165	B1AZX2|B1AZX3|O60929|Q5SU07|Q5SU08|Q96KM7	Missense_Mutation	SNP	ENST00000374516.3	hg19	CCDS4777.1	.	.	.	.	.	.	.	.	.	.	C	13.10	2.136914	0.37728	.	.	ENSG00000112511	ENST00000374512;ENST00000374516	T;T	0.24350	1.92;1.86	4.75	4.75	0.60458	.	0.509864	0.20175	N	0.097653	T	0.05227	0.0139	N	0.02011	-0.69	0.29377	N	0.863601	P;B	0.43231	0.801;0.179	B;B	0.41571	0.36;0.197	T	0.16100	-1.0414	10	0.29301	T	0.29	-0.3061	15.279	0.73767	0.0:1.0:0.0:0.0	.	342;342	O43189-2;O43189	.;PHF1_HUMAN	S	342	ENSP00000363636:P342S;ENSP00000363640:P342S	ENSP00000363636:P342S	P	+	1	0	PHF1	33490559	0.029000	0.19370	0.348000	0.25681	0.928000	0.56348	1.846000	0.39289	2.493000	0.84123	0.555000	0.69702	CCT	.	C|1.000;G|0.000		0.527	PHF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076175.3			T	33382581	C	T	33382581	3	4	201	1	0	0	0	0	1	0	0	0	11829	623	22	3	1062	3	PHF1	6	33382581	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	32989325	33382581	137732486	57	29517										
C6orf138	442213	hgsc.bcm.edu	37	chr6	47976781	47976781	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ggctctggctgacttgacccGctgatctttgctgtttggca	12	11	2	3	rs375811446		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr6:47976781G>C	ENST00000339488.4	-	2	529	c.496C>G	c.(496-498)Cgg>Ggg	p.R166G	PTCHD4_ENST00000543600.1_Missense_Mutation_p.R149G	NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	166						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										GACTTGACCCGCTGATCTTTG	0.493																																					p.R166G		Atlas-SNP	.											.	.	.	.	0			c.C496G						.						38	38	38					6																	47976781		1973	4150	6123	SO:0001583	missense	442213	exon2			TGACCCGCTGATC		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 138"	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.496C>G	chr6.hg19:g.47976781G>C	ENSP00000341914:p.Arg166Gly	68.0	0.0		100.0	41.0	NM_001013732	B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	hg19	CCDS34473.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.07|17.07	3.295842|3.295842	0.60086|0.60086	.|.	.|.	ENSG00000244694|ENSG00000244694	ENST00000398738|ENST00000339488;ENST00000543600	.|D;D	.|0.85484	.|-1.99;-1.99	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	.|0.171773	.|0.52532	.|D	.|0.000080	T|T	0.79969|0.79969	0.4538|0.4538	L|L	0.34521|0.34521	1.04|1.04	0.50813|0.50813	D|D	0.999892|0.999892	.|P;P	.|0.52842	.|0.653;0.956	.|B;P	.|0.53722	.|0.361;0.733	T|T	0.76345|0.76345	-0.2993|-0.2993	5|10	.|0.21014	.|T	.|0.42	.|.	15.4463|15.4463	0.75232|0.75232	0.0:0.0:0.8297:0.1703|0.0:0.0:0.8297:0.1703	.|.	.|166;149	.|Q6ZW05;B0QZ29	.|CF138_HUMAN;.	G|G	165|166;149	.|ENSP00000341914:R166G;ENSP00000439864:R149G	.|ENSP00000341914:R166G	A|R	-|-	2|1	0|2	C6orf138|C6orf138	48084740|48084740	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.091000|5.091000	0.64505|0.64505	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCG|CGG	.	.		0.493	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		C	47976781	G	C	47976781	3	2	201	1	0	0	0	0	1	0	0	0	2334	1086	38	4	2052	4	C6orf138	6	47976781	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	14594200	47976781	123138286	58	29518										
B3GAT2	135152	hgsc.bcm.edu	37	chr6	71603943	71603943	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cgcccaccaaccaggcccacAggccagacggagaccttgcg	11	18	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr6:71603943A>T	ENST00000230053.6	-	2	1232	c.624T>A	c.(622-624)ccT>ccA	p.P208P		NM_080742.2	NP_542780.1	Q9NPZ5	B3GA2_HUMAN	beta-1,3-glucuronyltransferase 2	208					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						CCAGGCCCACAGGCCAGACGG	0.527																																					p.P208P		Atlas-SNP	.											.	B3GAT2	33	.	0			c.T624A						.						74	72	73					6																	71603943		2203	4300	6503	SO:0001819	synonymous_variant	135152	exon2			GCCCACAGGCCAG	AB075843	CCDS4974.1	6q12	2014-07-08	2014-07-08		ENSG00000112309	ENSG00000112309	2.4.1.135	"Beta-1,3-glucuronyltransferases"	922	protein-coding gene	gene with protein product	"glucuronosyltransferase S", "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2"	607497				12383500	Standard	NM_080742		Approved	GlcAT-S	uc003pfv.3	Q9NPZ5	OTTHUMG00000014997	ENST00000230053.6:c.624T>A	chr6.hg19:g.71603943A>T		183.0	0.0		238.0	72.0	NM_080742	Q5JS09|Q8TF38|Q96NK4	Silent	SNP	ENST00000230053.6	hg19	CCDS4974.1																																																																																			.	.		0.527	B3GAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041150.2	NM_080742		T	71603943	A	T	71603943	2	4	201	1	0	0	0	0	0	0	0	1	1254	175	7	4		4	B3GAT2	6	71603943	Silent	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	23627162	71603943	99511124	59	29519										
PHIP	55023	hgsc.bcm.edu	37	chr6	79679818	79679818	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agtatcaggatctagaaaagCaagtttaaggcagcaaaggg	12	5	2	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr6:79679818C>G	ENST00000275034.4	-	26	3237	c.3070G>C	c.(3070-3072)Gct>Cct	p.A1024P	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1024	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TCTAGAAAAGCAAGTTTAAGG	0.383																																					p.A1024P		Atlas-SNP	.											.	PHIP	177	.	0			c.G3070C						.						125	125	125					6																	79679818		2203	4300	6503	SO:0001583	missense	55023	exon26			GAAAAGCAAGTTT	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.3070G>C	chr6.hg19:g.79679818C>G	ENSP00000275034:p.Ala1024Pro	95.0	0.0		120.0	37.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.342062	0.81911	.	.	ENSG00000146247	ENST00000275034	T	0.46819	0.86	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000002	T	0.63663	0.2530	M	0.76170	2.325	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.80764	0.994;0.994	T	0.63804	-0.6554	9	.	.	.	-19.0361	18.1612	0.89708	0.0:1.0:0.0:0.0	.	1024;1024	A7J992;Q8WWQ0	.;PHIP_HUMAN	P	1024	ENSP00000275034:A1024P	.	A	-	1	0	PHIP	79736537	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.527000	0.60573	2.544000	0.85801	0.557000	0.71058	GCT	.	.		0.383	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			G	79679818	C	G	79679818	3	3	201	1	0	0	0	0	1	0	0	0	11851	710	25	4	2455	4	PHIP	6	79679818	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	8075875	79679818	91435249	60	29520										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7412740	7412740	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	atcatttttcttcaccacccCtatcacaaatatctccacat	0	15	5	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:7412740C>G	ENST00000399429.3	-	32	2937	c.2797G>C	c.(2797-2799)Ggg>Cgg	p.G933R		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	933	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TTCACCACCCCTATCACAAAT	0.398																																					p.G933R		Atlas-SNP	.											COL28A1,colon,carcinoma,0,1	COL28A1	113	.	0			c.G2797C						.						120	113	115					7																	7412740		1874	4103	5977	SO:0001583	missense	340267	exon32			CCACCCCTATCAC	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2797G>C	chr7.hg19:g.7412740C>G	ENSP00000382356:p.Gly933Arg	92.0	1.0		152.0	34.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	hg19	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.740460	0.69304	.	.	ENSG00000215018	ENST00000399429	D	0.91740	-2.9	4.09	4.09	0.47781	von Willebrand factor, type A (3);	0.000000	0.64402	U	0.000004	D	0.97396	0.9148	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98137	1.0434	10	0.49607	T	0.09	-5.903	16.8665	0.86030	0.0:1.0:0.0:0.0	.	933	Q2UY09	COSA1_HUMAN	R	933	ENSP00000382356:G933R	ENSP00000382356:G933R	G	-	1	0	COL28A1	7379265	1.000000	0.71417	1.000000	0.80357	0.602000	0.36980	7.416000	0.80143	2.284000	0.76573	0.655000	0.94253	GGG	.	.		0.398	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		G	7412740	C	G	7412740	3	3	201	1	0	0	0	0	1	0	0	0	3688	681	24	4	596	4	COL28A1	7	7412740	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10		7412740	151725923	61	29521										
NXPH1	30010	hgsc.bcm.edu	37	chr7	8791265	8791265	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agcaaacccaaagtcatgtaTcctggctctgctccaagccc	7	15	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:8791265T>A	ENST00000405863.1	+	3	1593	c.682T>A	c.(682-684)Tcc>Acc	p.S228T	NXPH1_ENST00000497400.1_3'UTR|NXPH1_ENST00000602349.1_Missense_Mutation_p.S111T	NM_152745.2	NP_689958.1	P58417	NXPH1_HUMAN	neurexophilin 1	228	V (Cys-rich).					extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|ovary(1)	17		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		AAGTCATGTATCCTGGCTCTG	0.408																																					p.S228T		Atlas-SNP	.											.	NXPH1	42	.	0			c.T682A						.						46	42	43					7																	8791265		1876	4115	5991	SO:0001583	missense	30010	exon3			CATGTATCCTGGC	AB047362	CCDS47540.1	7p22	2003-03-20			ENSG00000122584	ENSG00000122584			20693	protein-coding gene	gene with protein product		604639				9570794	Standard	NM_152745		Approved		uc003srv.3	P58417	OTTHUMG00000151941	ENST00000405863.1:c.682T>A	chr7.hg19:g.8791265T>A	ENSP00000384551:p.Ser228Thr	171.0	0.0		345.0	16.0	NM_152745	Q8NB31	Missense_Mutation	SNP	ENST00000405863.1	hg19	CCDS47540.1	.	.	.	.	.	.	.	.	.	.	T	15.91	2.973252	0.53614	.	.	ENSG00000122584	ENST00000405863;ENST00000417186	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.57095	0.2030	L	0.45051	1.395	0.80722	D	1	P	0.46395	0.877	P	0.48654	0.585	T	0.51419	-0.8708	9	0.18710	T	0.47	-12.4694	15.827	0.78718	0.0:0.0:0.0:1.0	.	228	P58417	NXPH1_HUMAN	T	228;111	.	ENSP00000384551:S228T	S	+	1	0	NXPH1	8757790	1.000000	0.71417	0.994000	0.49952	0.999000	0.98932	7.841000	0.86834	2.324000	0.78689	0.533000	0.62120	TCC	.	.		0.408	NXPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324591.1	NM_152745		A	8791265	T	A	8791265	3	1	201	1	0	0	0	0	1	0	0	0	10799	1435	50	4	688	4	NXPH1	7	8791265	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	1378525	8791265	150347398	62	29522										
BZW2	28969	hgsc.bcm.edu	37	chr7	16720989	16720989	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gaccaaccactgtgtgttttCagcaaatgaagatcatgaaa	8	8	2	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:16720989C>A	ENST00000433922.2	+	4	477	c.299C>A	c.(298-300)tCa>tAa	p.S100*	BZW2_ENST00000258761.3_Nonsense_Mutation_p.S100*|BZW2_ENST00000432311.1_3'UTR|BZW2_ENST00000452975.2_Nonsense_Mutation_p.S100*|BZW2_ENST00000405202.1_Nonsense_Mutation_p.S24*	NM_001159767.1	NP_001153239.1	Q9Y6E2	BZW2_HUMAN	basic leucine zipper and W2 domains 2	100					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	membrane (GO:0016020)				cervix(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	15	Lung NSC(10;0.0367)|all_lung(11;0.0837)			UCEC - Uterine corpus endometrioid carcinoma (126;0.199)		TGTGTGTTTTCAGCAAATGAA	0.418																																					p.S100X		Atlas-SNP	.											.	BZW2	35	.	0			c.C299A						.						145	128	134					7																	16720989		2203	4300	6503	SO:0001587	stop_gained	28969	exon4			TGTTTTCAGCAAA	AF083246	CCDS5362.1	7p21.3	2008-07-18			ENSG00000136261	ENSG00000136261			18808	protein-coding gene	gene with protein product						11042152	Standard	NM_001159767		Approved	HSPC028, MST017, MSTP017	uc003stj.2	Q9Y6E2	OTTHUMG00000130755	ENST00000433922.2:c.299C>A	chr7.hg19:g.16720989C>A	ENSP00000397249:p.Ser100*	72.0	0.0		102.0	28.0	NM_014038	A4D123|Q3B779|Q96JW5|Q9H3F7	Nonsense_Mutation	SNP	ENST00000433922.2	hg19	CCDS5362.1	.	.	.	.	.	.	.	.	.	.	C	37	6.168190	0.97343	.	.	ENSG00000136261	ENST00000415365;ENST00000258761;ENST00000433922;ENST00000452975;ENST00000405202;ENST00000446596;ENST00000438834;ENST00000430000	.	.	.	5.89	4.83	0.62350	.	0.424586	0.23718	N	0.045252	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-22.1205	13.6347	0.62215	0.0:0.885:0.0:0.115	.	.	.	.	X	100;100;100;100;24;100;100;100	.	ENSP00000258761:S100X	S	+	2	0	BZW2	16687514	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.536000	0.36072	2.788000	0.95919	0.557000	0.71058	TCA	.	.		0.418	BZW2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253256.2	NM_014038		A	16720989	C	A	16720989	4	1	201	1	0	0	0	0	0	1	0	0	1581	838	29	3	309	3	BZW2	7	16720989	Nonsense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	7929724	16720989	142417674	63	29523										
PDE1C	5137	hgsc.bcm.edu	37	chr7	31887658	31887658	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	aaggcgataagctgcacttaAatggtgattctccagtacag	10	8	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:31887658A>C	ENST00000396191.1	-	9	1359	c.904T>G	c.(904-906)Tta>Gta	p.L302V	PDE1C_ENST00000396182.2_Missense_Mutation_p.L302V|PDE1C_ENST00000321453.7_Missense_Mutation_p.L302V|PDE1C_ENST00000396193.1_Missense_Mutation_p.L362V|PDE1C_ENST00000396184.3_Missense_Mutation_p.L302V	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	302	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GCTGCACTTAAATGGTGATTC	0.383																																					p.L362V		Atlas-SNP	.											.	PDE1C	465	.	0			c.T1084G						.						111	103	106					7																	31887658		2203	4300	6503	SO:0001583	missense	5137	exon10			CACTTAAATGGTG	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.904T>G	chr7.hg19:g.31887658A>C	ENSP00000379494:p.Leu302Val	92.0	0.0		110.0	18.0	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	hg19	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	A	5.757	0.324146	0.10900	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12	5.92	0.593	0.17478	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.123681	0.53938	D	0.000058	T	0.49029	0.1533	N	0.11064	0.09	0.37526	D	0.917734	B;B;B	0.10296	0.0;0.003;0.001	B;B;B	0.21546	0.003;0.035;0.007	T	0.15867	-1.0422	10	0.11485	T	0.65	.	1.4002	0.02269	0.3821:0.2603:0.2388:0.1188	.	302;362;302	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	V	362;302;302;302;302	ENSP00000379496:L362V;ENSP00000379494:L302V;ENSP00000318105:L302V;ENSP00000379487:L302V;ENSP00000379485:L302V	ENSP00000318105:L302V	L	-	1	2	PDE1C	31854183	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	3.045000	0.49838	0.461000	0.27071	0.528000	0.53228	TTA	.	.		0.383	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			C	31887658	A	C	31887658	3	2	201	1	0	0	0	0	1	0	0	0	11644	11	1	5	1036	5	PDE1C	7	31887658	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	15166669	31887658	127251005	64	29524										
ZNF679	168417	hgsc.bcm.edu	37	chr7	63726440	63726440	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	caaaaaggaggttgtaatgaAgttaaccaatgtttgtcaac	9	5	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:63726440A>T	ENST00000421025.1	+	5	698	c.429A>T	c.(427-429)gaA>gaT	p.E143D	ZNF679_ENST00000255746.4_Missense_Mutation_p.E143D	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	143					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						GTTGTAATGAAGTTAACCAAT	0.328																																					p.E143D		Atlas-SNP	.											.	ZNF679	80	.	0			c.A429T						.						198	175	182					7																	63726440		692	1591	2283	SO:0001583	missense	168417	exon5			TAATGAAGTTAAC	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"Zinc fingers, C2H2-type", "-"	28650	protein-coding gene	gene with protein product	"hypothetical protein MGC42415"					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.429A>T	chr7.hg19:g.63726440A>T	ENSP00000416809:p.Glu143Asp	172.0	0.0		337.0	79.0	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	hg19	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	A	5.935	0.356624	0.11239	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.06371	3.31;3.31	1.03	-2.06	0.07298	.	.	.	.	.	T	0.05593	0.0147	L	0.53561	1.675	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.41910	-0.9482	9	0.39692	T	0.17	.	1.3855	0.02239	0.3407:0.0:0.314:0.3453	.	143	Q8IYX0	ZN679_HUMAN	D	143	ENSP00000416809:E143D;ENSP00000255746:E143D	ENSP00000255746:E143D	E	+	3	2	ZNF679	63363875	0.001000	0.12720	0.005000	0.12908	0.246000	0.25737	0.735000	0.26115	-0.694000	0.05113	0.163000	0.16589	GAA	.	.		0.328	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		T	63726440	A	T	63726440	3	4	201	1	0	0	0	0	1	0	0	0	18101	69	3	4	443	4	ZNF679	7	63726440	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	31838782	63726440	95412223	65	29525										
CD36	948	hgsc.bcm.edu	37	chr7	80302699	80302699	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agaatctgaagaggaactatAttgtgcctattctttggctt	9	6	2	3	rs550565800	byFrequency	TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:80302699A>C	ENST00000435819.1	+	16	1912	c.1228A>C	c.(1228-1230)Att>Ctt	p.I410L	CD36_ENST00000432207.1_Missense_Mutation_p.I410L|CD36_ENST00000534394.1_Missense_Mutation_p.I334L|CD36_ENST00000544133.1_3'UTR|CD36_ENST00000538969.1_Missense_Mutation_p.I350L|CD36_ENST00000309881.7_Missense_Mutation_p.I410L|CD36_ENST00000447544.2_Missense_Mutation_p.I410L|CD36_ENST00000394788.3_Missense_Mutation_p.I410L|CD36_ENST00000433696.2_Missense_Mutation_p.I371L			P16671	CD36_HUMAN	CD36 molecule (thrombospondin receptor)	410					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular lipid metabolic process (GO:0044255)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to hydroperoxide (GO:0071447)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cGMP-mediated signaling (GO:0019934)|cholesterol transport (GO:0030301)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|lipoprotein transport (GO:0042953)|long-chain fatty acid import (GO:0044539)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle mediated signaling (GO:0055096)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitric oxide mediated signal transduction (GO:0007263)|phagocytosis, recognition (GO:0006910)|plasma lipoprotein particle clearance (GO:0034381)|plasma membrane long-chain fatty acid transport (GO:0015911)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood microparticle formation (GO:2000334)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of removal of superoxide radicals (GO:2000121)|response to stilbenoid (GO:0035634)|small molecule metabolic process (GO:0044281)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|lipoteichoic acid receptor activity (GO:0070892)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|thrombospondin receptor activity (GO:0070053)|transforming growth factor beta binding (GO:0050431)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(10)|large_intestine(1)|lung(6)|ovary(1)	21						GAGGAACTATATTGTGCCTAT	0.254																																					p.I410L		Atlas-SNP	.											.	CD36	185	.	0			c.A1228C	GRCh37	CD012238	CD36	D		.						73	75	75					7																	80302699		2202	4268	6470	SO:0001583	missense	948	exon11			AACTATATTGTGC	Z32770	CCDS34673.1	7q11.2	2010-02-26	2006-03-28		ENSG00000135218	ENSG00000135218		"CD molecules"	1663	protein-coding gene	gene with protein product		173510	"CD36 antigen (collagen type I receptor, thrombospondin receptor)"			7503937	Standard	NM_001001548		Approved	SCARB3, GPIV, FAT, GP4, GP3B	uc003uhg.4	P16671	OTTHUMG00000155383	ENST00000435819.1:c.1228A>C	chr7.hg19:g.80302699A>C	ENSP00000399421:p.Ile410Leu	141.0	0.0		352.0	23.0	NM_001127444	D9IX66|D9IX67|D9IX68|D9IX69|Q13966|Q16093|Q8TCV7|Q9BPZ8|Q9BQC2|Q9BZM8|Q9BZN3|Q9BZN4|Q9BZN5	Missense_Mutation	SNP	ENST00000435819.1	hg19	CCDS34673.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.52|10.52	1.373800|1.373800	0.24857|0.24857	.|.	.|.	ENSG00000135218|ENSG00000135218	ENST00000435819;ENST00000309881;ENST00000534394;ENST00000394788;ENST00000447544;ENST00000432207;ENST00000419819;ENST00000538969;ENST00000433696|ENST00000488048	T;T;T;T;T;T;T;T;T|T	0.72051|0.71817	-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62|-0.6	5.83|5.83	-11.7|-11.7	0.00046|0.00046	.|.	0.663319|.	0.15051|.	N|.	0.283281|.	T|T	0.53932|0.53932	0.1827|0.1827	L|L	0.31294|0.31294	0.92|0.92	0.54753|0.54753	D|D	0.999989|0.999989	B|.	0.14012|.	0.009|.	B|.	0.15870|.	0.014|.	T|T	0.56195|0.56195	-0.8019|-0.8019	9|6	.|.	.|.	.|.	-1.671|-1.671	9.3781|9.3781	0.38295|0.38295	0.1122:0.6218:0.0529:0.2131|0.1122:0.6218:0.0529:0.2131	.|.	410|.	P16671|.	CD36_HUMAN|.	L|S	410;410;334;410;410;410;410;350;371|3	ENSP00000399421:I410L;ENSP00000308165:I410L;ENSP00000431296:I334L;ENSP00000378268:I410L;ENSP00000415743:I410L;ENSP00000411411:I410L;ENSP00000392298:I410L;ENSP00000439543:I350L;ENSP00000401863:I371L|ENSP00000435698:Y3S	.|.	I|Y	+|+	1|2	0|0	CD36|CD36	80140635|80140635	0.000000|0.000000	0.05858|0.05858	0.016000|0.016000	0.15963|0.15963	0.118000|0.118000	0.20060|0.20060	-1.319000|-1.319000	0.02702|0.02702	-1.425000|-1.425000	0.01997|0.01997	-1.096000|-1.096000	0.02151|0.02151	ATT|TAT	.	.		0.254	CD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339767.6	NM_001001547		C	80302699	A	C	80302699	3	2	201	1	0	0	0	0	1	0	0	0	3009	449	16	5	1270	5	CD36	7	80302699	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	16576259	80302699	78835964	66	29526										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83610774	83610774	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agctgggcaaccccagccgtTgaaccaatatatagttgttg	10	10	0	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:83610774T>C	ENST00000265362.4	-	14	1829	c.1515A>G	c.(1513-1515)tcA>tcG	p.S505S	SEMA3A_ENST00000436949.1_Silent_p.S505S	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	505	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CCCCAGCCGTTGAACCAATAT	0.433																																					p.S505S		Atlas-SNP	.											.	SEMA3A	121	.	0			c.A1515G						.						55	56	55					7																	83610774		2203	4300	6503	SO:0001819	synonymous_variant	10371	exon14			AGCCGTTGAACCA	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1515A>G	chr7.hg19:g.83610774T>C		88.0	0.0		203.0	9.0	NM_006080		Silent	SNP	ENST00000265362.4	hg19	CCDS5599.1																																																																																			.	.		0.433	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		C	83610774	T	C	83610774	2	2	201	1	0	0	0	0	0	0	0	1	14039	1799	63	2		2	SEMA3A	7	83610774	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	3308075	83610774	75527889	67	29527										
KIAA1324L	222223	hgsc.bcm.edu	37	chr7	86574266	86574266	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tactggtactcaaagaagacAtagcctgacttcttaaggtg	9	8	2	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:86574266A>T	ENST00000450689.2	-	4	788	c.603T>A	c.(601-603)taT>taA	p.Y201*	KIAA1324L_ENST00000416314.1_Nonsense_Mutation_p.Y34*|KIAA1324L_ENST00000444627.1_Nonsense_Mutation_p.Y201*	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	201						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					CAAAGAAGACATAGCCTGACT	0.393																																					p.Y201X		Atlas-SNP	.											.	KIAA1324L	225	.	0			c.T603A						.						133	119	123					7																	86574266		692	1591	2283	SO:0001587	stop_gained	222223	exon4			GAAGACATAGCCT	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.603T>A	chr7.hg19:g.86574266A>T	ENSP00000413445:p.Tyr201*	269.0	0.0		427.0	117.0	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Nonsense_Mutation	SNP	ENST00000450689.2	hg19	CCDS47632.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	34|34	5.304548|5.304548	0.95601|0.95601	.|.	.|.	ENSG00000164659|ENSG00000164659	ENST00000423294|ENST00000450689;ENST00000444627;ENST00000416314;ENST00000398276;ENST00000425689	.|.	.|.	.|.	5.66|5.66	2.03|2.03	0.26663|0.26663	.|.	.|20.081800	.|0.03009	.|U	.|0.149243	T|.	0.57286|.	0.2043|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.16453|.	-1.0402|.	4|.	.|.	.|.	.|.	.|.	8.72|8.72	0.34434|0.34434	0.7847:0.0:0.2153:0.0|0.7847:0.0:0.2153:0.0	.|.	.|.	.|.	.|.	S|X	162|201;201;34;87;87	.|.	.|.	C|Y	-|-	1|3	0|2	KIAA1324L|KIAA1324L	86412202|86412202	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.653000|0.653000	0.24902|0.24902	0.172000|0.172000	0.19760|0.19760	0.533000|0.533000	0.62120|0.62120	TGT|TAT	.	.		0.393	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		T	86574266	A	T	86574266	4	4	201	1	0	0	0	0	0	1	0	0	8233	224	8	4	2562	4	KIAA1324L	7	86574266	Nonsense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	2963492	86574266	72564397	68	29528										
SGCE	8910	hgsc.bcm.edu	37	chr7	94259029	94259029	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tttttcctcacaaagaacatAccaggttttgggtaaggtgg	10	7	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:94259029A>G	ENST00000265735.7	-	2	343		c.e2+1		SGCE_ENST00000445866.2_Splice_Site|SGCE_ENST00000437425.2_Intron|SGCE_ENST00000447873.1_Splice_Site|SGCE_ENST00000428696.2_Splice_Site|SGCE_ENST00000415788.2_Splice_Site	NM_003919.2	NP_003910.1	O43556	SGCE_HUMAN	sarcoglycan, epsilon						cell-matrix adhesion (GO:0007160)|muscle organ development (GO:0007517)	cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|dystrophin-associated glycoprotein complex (GO:0016010)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	14	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			CAAAGAACATACCAGGTTTTG	0.318																																					.		Atlas-SNP	.											.	SGCE	68	.	0			c.232+2T>C	GRCh37	CS062103	SGCE	S		.						103	115	111					7																	94259029		2203	4299	6502	SO:0001630	splice_region_variant	8910	exon3			GAACATACCAGGT	AF036364	CCDS5637.1, CCDS47642.1, CCDS47643.1, CCDS75634.1	7q21.3	2014-09-17			ENSG00000127990	ENSG00000127990			10808	protein-coding gene	gene with protein product		604149		DYT11		9475163, 9405466	Standard	NM_001099401		Approved		uc003unn.2	O43556	OTTHUMG00000022828	ENST00000265735.7:c.232+1T>C	chr7.hg19:g.94259029A>G		256.0	0.0		476.0	233.0	NM_001099400	B2R8N2|D6W5Q8|E9PF60|G5E9K6|Q6L8P0|Q75MH8|Q8NFG8|Q8WW28	Splice_Site	SNP	ENST00000265735.7	hg19	CCDS5637.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.454778	0.84209	.	.	ENSG00000127990	ENST00000265735;ENST00000445866;ENST00000447873;ENST00000428696;ENST00000415788	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.187	0.81960	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SGCE	94096965	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.962000	0.93254	2.285000	0.76669	0.533000	0.62120	.	.	.		0.318	SGCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255251.2		Intron	G	94259029	A	G	94259029	5	3	201	1	0	0	0	0	0	0	1	0	14217	405	14	2	1271	2	SGCE	7	94259029	Splice_Site	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	7684763	94259029	64879634	69	29529										
LMTK2	22853	hgsc.bcm.edu	37	chr7	97770825	97770825	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gtaccaaatatttcactcccAgctccctcgcaattccagcc	4	17	1	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:97770825A>T	ENST00000297293.5	+	3	641	c.348A>T	c.(346-348)ccA>ccT	p.P116P	LMTK2_ENST00000493372.1_3'UTR	NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	116					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					TTTCACTCCCAGCTCCCTCGC	0.468																																					p.P116P		Atlas-SNP	.											.	LMTK2	228	.	0			c.A348T						.						166	164	165					7																	97770825		2203	4300	6503	SO:0001819	synonymous_variant	22853	exon3			ACTCCCAGCTCCC	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 100"	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.348A>T	chr7.hg19:g.97770825A>T		97.0	0.0		158.0	27.0	NM_014916	A4D272|Q75MG7|Q9UPS3	Silent	SNP	ENST00000297293.5	hg19	CCDS5654.1																																																																																			.	.		0.468	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		T	97770825	A	T	97770825	2	4	201	1	0	0	0	0	0	0	0	1	8868	175	7	4		4	LMTK2	7	97770825	Silent	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	3511796	97770825	61367838	70	29530										
SLC37A3	84255	hgsc.bcm.edu	37	chr7	140055481	140055481	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tacctacctcataaccatacTgaagaacagaagaagctagg	7	10	1	4			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:140055481T>A	ENST00000326232.9	-	7	808	c.605A>T	c.(604-606)cAg>cTg	p.Q202L	SLC37A3_ENST00000447932.2_Missense_Mutation_p.Q202L|SLC37A3_ENST00000429996.2_Silent_p.S153S|SLC37A3_ENST00000340308.3_Missense_Mutation_p.Q202L|SLC37A3_ENST00000461089.1_5'Flank	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	202					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					ATAACCATACTGAAGAACAGA	0.433																																					p.Q202L	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.A605T						.						171	141	151					7																	140055481		2203	4300	6503	SO:0001583	missense	84255	exon7			CCATACTGAAGAA	AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"Solute carriers"	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.605A>T	chr7.hg19:g.140055481T>A	ENSP00000321498:p.Gln202Leu	64.0	0.0		160.0	29.0	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	hg19	CCDS5859.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	10.22|10.22	1.290405|1.290405	0.23478|0.23478	.|.	.|.	ENSG00000157800|ENSG00000157800	ENST00000340308;ENST00000447932;ENST00000326232;ENST00000539816|ENST00000485861	T;T;T|.	0.56444|.	0.46;0.46;0.46|.	5.28|5.28	2.81|2.81	0.32909|0.32909	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.055692|.	0.64402|.	D|.	0.000001|.	T|T	0.53932|0.53932	0.1827|0.1827	L|L	0.41824|0.41824	1.3|1.3	0.80722|0.80722	D|D	1|1	B;B;B;P;B|.	0.34587|.	0.042;0.03;0.129;0.458;0.257|.	B;B;B;B;B|.	0.36186|.	0.103;0.062;0.138;0.219;0.216|.	T|T	0.41787|0.41787	-0.9489|-0.9489	10|5	0.33141|.	T|.	0.24|.	-13.1658|-13.1658	10.6547|10.6547	0.45667|0.45667	0.2561:0.0:0.0:0.7439|0.2561:0.0:0.0:0.7439	.|.	174;202;202;202;202|.	B4DKF5;F5H743;Q8NCC5-2;Q8NCC5-3;Q8NCC5|.	.;.;.;.;SPX3_HUMAN|.	L|C	202|127	ENSP00000343358:Q202L;ENSP00000397481:Q202L;ENSP00000321498:Q202L|.	ENSP00000321498:Q202L|.	Q|S	-|-	2|1	0|0	SLC37A3|SLC37A3	139701950|139701950	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.175000|0.175000	0.22909|0.22909	4.082000|4.082000	0.57635|0.57635	0.364000|0.364000	0.24374|0.24374	-0.357000|-0.357000	0.07601|0.07601	CAG|AGT	.	.		0.433	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295		A	140055481	T	A	140055481	3	1	201	1	0	0	0	0	1	0	0	0	14614	1580	55	4	1064	4	SLC37A3	7	140055481	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	42284656	140055481	19083182	71	29531										
UBE3C	9690	hgsc.bcm.edu	37	chr7	156932031	156932031	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ccttggcggcgcgagcaggaAggtgagggccgggctggcgg	22	10	0	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr7:156932031A>G	ENST00000348165.5	+	1	425	c.65A>G	c.(64-66)aAg>aGg	p.K22R	UBE3C_ENST00000389103.4_Splice_Site_p.K22R	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	22	Cis-determinant of acceptor ubiquitin- binding.				protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		GCGAGCAGGAAGGTGAGGGCC	0.756																																					p.K22R		Atlas-SNP	.											.	UBE3C	124	.	0			c.A65G						.						9	11	10					7																	156932031		2153	4223	6376	SO:0001630	splice_region_variant	9690	exon1			GCAGGAAGGTGAG	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.66+1A>G	chr7.hg19:g.156932031A>G		32.0	0.0		44.0	9.0	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	hg19	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	a	9.715	1.158001	0.21454	.	.	ENSG00000009335	ENST00000348165;ENST00000389103	T	0.50813	0.73	3.92	3.92	0.45320	.	0.000000	0.85682	U	0.000000	T	0.36110	0.0955	L	0.38838	1.175	0.09310	N	0.999995	B;B;B	0.24132	0.001;0.098;0.0	B;B;B	0.29785	0.001;0.107;0.0	T	0.19451	-1.0305	10	0.21014	T	0.42	.	9.4521	0.38731	1.0:0.0:0.0:0.0	.	22;22;22	Q15386;Q15386-2;Q15386-3	UBE3C_HUMAN;.;.	R	22	ENSP00000309198:K22R	ENSP00000309198:K22R	K	+	2	0	UBE3C	156624792	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	4.808000	0.62583	1.523000	0.49018	0.398000	0.26397	AAG	.	.		0.756	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671	Missense_Mutation	G	156932031	A	G	156932031	5	3	201	1	0	0	0	0	0	0	1	0	16896	86	3	2	67	2	UBE3C	7	156932031	Splice_Site	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	16876550	156932031	2206632	72	29532										
NEFM	4741	hgsc.bcm.edu	37	chr8	24775019	24775019	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agtcagaccaagccgaagagGgaggatccgagaaggaaggc	16	8	1	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr8:24775019G>C	ENST00000221166.5	+	3	2433	c.1651G>C	c.(1651-1653)Gga>Cga	p.G551R	NEFM_ENST00000518131.1_Missense_Mutation_p.G551R|NEFM_ENST00000521540.1_Intron|GS1-72M22.1_ENST00000607058.1_RNA|NEFM_ENST00000437366.2_Missense_Mutation_p.G551R|NEFM_ENST00000433454.2_Missense_Mutation_p.G175R			P07197	NFM_HUMAN	neurofilament, medium polypeptide	551	Tail.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		AGCCGAAGAGGGAGGATCCGA	0.493																																					p.G551R		Atlas-SNP	.											.	NEFM	115	.	0			c.G1651C						.						34	38	36					8																	24775019		2189	4254	6443	SO:0001583	missense	4741	exon3			GAAGAGGGAGGAT	BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"Intermediate filaments type IV"	7734	protein-coding gene	gene with protein product		162250	"neurofilament, medium polypeptide 150kDa"	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.1651G>C	chr8.hg19:g.24775019G>C	ENSP00000221166:p.Gly551Arg	149.0	0.0		179.0	58.0	NM_005382	B4DGN2|E9PBF7|Q4QRK6	Missense_Mutation	SNP	ENST00000221166.5	hg19	CCDS6046.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.030565	0.35797	.	.	ENSG00000104722	ENST00000221166;ENST00000518131;ENST00000437366;ENST00000433454	D;D;D;D	0.94758	-1.76;-1.72;-1.72;-3.51	4.41	4.41	0.53225	.	0.000000	0.46145	D	0.000319	D	0.95443	0.8520	M	0.81682	2.555	0.40553	D	0.981136	P;D	0.55800	0.731;0.973	B;P	0.48873	0.231;0.593	D	0.95944	0.8949	10	0.49607	T	0.09	.	16.9666	0.86287	0.0:0.0:1.0:0.0	.	551;551	E7EMV2;P07197	.;NFM_HUMAN	R	551;551;551;175	ENSP00000221166:G551R;ENSP00000427872:G551R;ENSP00000410137:G551R;ENSP00000412295:G175R	ENSP00000221166:G551R	G	+	1	0	NEFM	24830924	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.104000	0.77024	2.152000	0.67230	0.313000	0.20887	GGA	.	.		0.493	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382		C	24775019	G	C	24775019	3	2	201	1	0	0	0	0	1	0	0	0	10325	1233	43	4	1661	4	NEFM	8	24775019	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10		24775019	121589003	73	29533										
ST18	9705	hgsc.bcm.edu	37	chr8	53055540	53055540	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tgaagcttgggtttagggctTggtatagaggcctctccagg	15	7	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr8:53055540T>A	ENST00000276480.7	-	17	2801	c.2118A>T	c.(2116-2118)ccA>ccT	p.P706P		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	706					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				GTTTAGGGCTTGGTATAGAGG	0.403																																					p.P706P		Atlas-SNP	.											.	ST18	212	.	0			c.A2118T						.						155	145	149					8																	53055540		2203	4300	6503	SO:0001819	synonymous_variant	9705	exon17			AGGGCTTGGTATA	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2118A>T	chr8.hg19:g.53055540T>A		85.0	0.0		118.0	42.0	NM_014682	Q17RY1	Silent	SNP	ENST00000276480.7	hg19	CCDS6149.1																																																																																			.	.		0.403	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			A	53055540	T	A	53055540	2	1	201	1	0	0	0	0	0	0	0	1	15227	1799	63	4		4	ST18	8	53055540	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	28280521	53055540	93308482	74	29534										
STAU2	27067	hgsc.bcm.edu	37	chr8	74464277	74464277	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tgaatccttgctaaatattcCagttgttttgaaggttgtac	8	6	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr8:74464277C>A	ENST00000521451.1	-	8	1216	c.840G>T	c.(838-840)ctG>ctT	p.L280L	STAU2_ENST00000524300.1_Silent_p.L500L|STAU2_ENST00000522695.1_Silent_p.L468L|STAU2_ENST00000521727.1_Silent_p.L480L|STAU2_ENST00000355780.5_Silent_p.L468L|STAU2_ENST00000522509.1_Silent_p.L468L|STAU2_ENST00000517542.1_Silent_p.L462L|STAU2_ENST00000523558.1_Silent_p.L328L|STAU2_ENST00000519961.1_Silent_p.L500L|STAU2_ENST00000521210.1_Silent_p.L396L			Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	500					transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)	19	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			CTAAATATTCCAGTTGTTTTG	0.358																																					p.L500L		Atlas-SNP	.											.	STAU2	148	.	0			c.G1500T						.						60	65	63					8																	74464277		2203	4297	6500	SO:0001819	synonymous_variant	27067	exon13			ATATTCCAGTTGT	Y19062	CCDS6214.1, CCDS55244.1, CCDS55245.1, CCDS55246.1, CCDS55247.1, CCDS55248.1	8q21.11	2013-06-05	2013-06-05		ENSG00000040341	ENSG00000040341			11371	protein-coding gene	gene with protein product		605920	"staufen (Drosophila, RNA-binding protein) homolog 2", "staufen, RNA binding protein, homolog 2 (Drosophila)"			10585778	Standard	NM_014393		Approved	39K2	uc003xzm.3	Q9NUL3	OTTHUMG00000164499	ENST00000521451.1:c.840G>T	chr8.hg19:g.74464277C>A		163.0	0.0		236.0	20.0	NM_001164380	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	Silent	SNP	ENST00000521451.1	hg19																																																																																				.	.		0.358	STAU2-006	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000379006.4	NM_001164380		A	74464277	C	A	74464277	2	1	201	1	0	0	0	0	0	0	0	1	15288	581	21	3		3	STAU2	8	74464277	Silent	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	21408737	74464277	71899745	75	29535										
PLEC	5339	hgsc.bcm.edu	37	chr8	145001727	145001727	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cagctggcggcccagttgctCgagctcgcgctgccgcacgt	14	16	0	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr8:145001727C>T	ENST00000322810.4	-	27	4187	c.4018G>A	c.(4018-4020)Gag>Aag	p.E1340K	PLEC_ENST00000357649.2_Missense_Mutation_p.E1207K|PLEC_ENST00000398774.2_Missense_Mutation_p.E1171K|PLEC_ENST00000354958.2_Missense_Mutation_p.E1181K|PLEC_ENST00000354589.3_Missense_Mutation_p.E1203K|PLEC_ENST00000356346.3_Missense_Mutation_p.E1189K|PLEC_ENST00000436759.2_Missense_Mutation_p.E1230K|PLEC_ENST00000345136.3_Missense_Mutation_p.E1203K|PLEC_ENST00000527096.1_Missense_Mutation_p.E1226K	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1340	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CCCAGTTGCTCGAGCTCGCGC	0.716																																					p.E1340K		Atlas-SNP	.											.	PLEC	1144	.	0			c.G4018A						.						6	7	7					8																	145001727		1801	3847	5648	SO:0001583	missense	5339	exon27			GTTGCTCGAGCTC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.4018G>A	chr8.hg19:g.145001727C>T	ENSP00000323856:p.Glu1340Lys	26.0	0.0		48.0	17.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396421	0.42512	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06;1.06;1.06	5.17	5.17	0.71159	.	0.267312	0.28098	U	0.016607	T	0.42832	0.1220	L	0.54323	1.7	0.52099	D	0.999941	B;B;B;B;B;B;B;B	0.22211	0.066;0.014;0.014;0.014;0.014;0.014;0.024;0.024	B;B;B;B;B;B;B;B	0.15870	0.014;0.014;0.014;0.006;0.014;0.014;0.014;0.014	T	0.38001	-0.9681	10	0.66056	D	0.02	.	18.2525	0.90009	0.0:1.0:0.0:0.0	.	1230;1189;1181;1340;1171;1203;1207;1203	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	K	1203;1207;1203;1171;1340;1181;1189;1230;1226	ENSP00000344848:E1203K;ENSP00000350277:E1207K;ENSP00000346602:E1203K;ENSP00000381756:E1171K;ENSP00000323856:E1340K;ENSP00000347044:E1181K;ENSP00000348702:E1189K;ENSP00000388180:E1230K;ENSP00000434583:E1226K	ENSP00000323856:E1340K	E	-	1	0	PLEC	145073715	0.986000	0.35501	0.992000	0.48379	0.540000	0.34992	2.910000	0.48766	2.393000	0.81446	0.551000	0.68910	GAG	.	.		0.716	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	145001727	C	T	145001727	3	4	201	1	0	0	0	0	1	0	0	0	12061	893	31	1	10060	1	PLEC	8	145001727	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	70537450	145001727	1362295	76	29536										
RFK	55312	hgsc.bcm.edu	37	chr9	79002393	79002393	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ttcaaatgttctggtaactcTagtcgtttcttagcttcttc	6	9	5	0	rs188158713		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr9:79002393T>A	ENST00000376736.1	-	4	723	c.390A>T	c.(388-390)ctA>ctT	p.L130L	RFK_ENST00000479197.1_5'Flank	NM_018339.5	NP_060809.3	Q969G6	RIFK_HUMAN	riboflavin kinase	130					apoptotic process (GO:0006915)|FMN biosynthetic process (GO:0009398)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|reactive oxygen species metabolic process (GO:0072593)|riboflavin biosynthetic process (GO:0009231)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|riboflavin kinase activity (GO:0008531)			pancreas(1)|prostate(1)|urinary_tract(1)	3					Riboflavin(DB00140)	CTGGTAACTCTAGTCGTTTCT	0.308																																					p.L130L		Atlas-SNP	.											.	RFK	13	.	0			c.A390T						.						113	116	115					9																	79002393		2203	4299	6502	SO:0001819	synonymous_variant	55312	exon4			TAACTCTAGTCGT	AK002011	CCDS35044.1, CCDS35044.2	9q21.31	2010-11-16			ENSG00000135002	ENSG00000135002			30324	protein-coding gene	gene with protein product		613010				14580199	Standard	NM_018339		Approved	FLJ11149, RIFK	uc004akd.2	Q969G6	OTTHUMG00000020040	ENST00000376736.1:c.390A>T	chr9.hg19:g.79002393T>A		34.0	0.0		52.0	18.0	NM_018339	Q5JSG9|Q9NUT7	Silent	SNP	ENST00000376736.1	hg19	CCDS35044.2																																																																																			.	T|1.000;C|0.000		0.308	RFK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052720.1	NM_018339		A	79002393	T	A	79002393	2	1	201	1	0	0	0	0	0	0	0	1	13266	1509	53	4		4	RFK	9	79002393	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10		79002393	62211038	77	29537										
DENND1A	57706	hgsc.bcm.edu	37	chr9	126439003	126439003	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ttaaaaaggtaaatacctgtCtttttgtcgtgtaatctgcc	7	7	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr9:126439003C>A	ENST00000373624.2	-	6	569	c.368G>T	c.(367-369)aGa>aTa	p.R123I	DENND1A_ENST00000394219.3_Missense_Mutation_p.R91I|DENND1A_ENST00000473039.1_Intron|DENND1A_ENST00000373620.3_Missense_Mutation_p.R123I|DENND1A_ENST00000373618.1_Missense_Mutation_p.R91I|DENND1A_ENST00000394215.2_Missense_Mutation_p.R93I	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	123	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						AAATACCTGTCTTTTTGTCGT	0.303																																					p.R123I		Atlas-SNP	.											.	DENND1A	112	.	0			c.G368T						.						71	72	72					9																	126439003		2203	4300	6503	SO:0001583	missense	57706	exon6			ACCTGTCTTTTTG	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"DENN/MADD domain containing"	29324	protein-coding gene	gene with protein product		613633	"KIAA1608"	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.368G>T	chr9.hg19:g.126439003C>A	ENSP00000362727:p.Arg123Ile	60.0	0.0		92.0	34.0	NM_024820	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	hg19	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.367285	0.41902	.	.	ENSG00000119522	ENST00000373624;ENST00000394219;ENST00000373620;ENST00000394215;ENST00000373618	T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75	5.99	4.12	0.48240	DENN (3);	0.106591	0.64402	D	0.000004	T	0.08980	0.0222	L	0.31664	0.95	0.42362	D	0.992412	B;B;B;B;B	0.27140	0.018;0.015;0.169;0.038;0.009	B;B;B;B;B	0.29077	0.062;0.037;0.06;0.098;0.063	T	0.19257	-1.0311	10	0.41790	T	0.15	0.009	9.8722	0.41182	0.0:0.7881:0.0:0.2119	.	91;91;93;123;123	Q8TEH3-6;Q8TEH3-4;Q8TEH3-5;Q8TEH3-2;Q8TEH3	.;.;.;.;DEN1A_HUMAN	I	123;91;123;93;91	ENSP00000362727:R123I;ENSP00000377766:R91I;ENSP00000362722:R123I;ENSP00000377763:R93I;ENSP00000362720:R91I	ENSP00000362720:R91I	R	-	2	0	DENND1A	125478824	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.248000	0.32827	0.827000	0.34685	0.655000	0.94253	AGA	.	.		0.303	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		A	126439003	C	A	126439003	3	1	201	1	0	0	0	0	1	0	0	0	4428	913	32	3	2836	3	DENND1A	9	126439003	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	47436610	126439003	14774428	78	29538										
GTF3C5	9328	hgsc.bcm.edu	37	chr9	135929323	135929323	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tccgaatccgttgtggaatgAaacacggtaaaaattcctga	9	8	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr9:135929323A>C	ENST00000372097.5	+	6	1305	c.982A>C	c.(982-984)Aaa>Caa	p.K328Q	GTF3C5_ENST00000372095.5_Missense_Mutation_p.K203Q|GTF3C5_ENST00000342018.8_Missense_Mutation_p.K259Q|GTF3C5_ENST00000372108.5_Missense_Mutation_p.K328Q|GTF3C5_ENST00000372099.6_Missense_Mutation_p.K319Q	NM_012087.3	NP_036219.2	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5, 63kDa	328					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)		TTGTGGAATGAAACACGGTAA	0.423																																					p.K328Q		Atlas-SNP	.											.	GTF3C5	46	.	0			c.A982C						.						66	63	64					9																	135929323		2203	4300	6503	SO:0001583	missense	9328	exon6			GGAATGAAACACG	AF133124	CCDS6958.1, CCDS48050.1, CCDS75927.1	9q34.13	2010-03-23	2002-08-29		ENSG00000148308	ENSG00000148308		"General transcription factors"	4668	protein-coding gene	gene with protein product	"transcription factor IIIC, 63 kD"	604890	"general transcription factor IIIC, polypeptide 5 (63kD)"			10373544	Standard	NM_012087		Approved	TFiiiC2-63, TFIIIC63, TFIIICepsilon	uc004ccj.4	Q9Y5Q8	OTTHUMG00000020856	ENST00000372097.5:c.982A>C	chr9.hg19:g.135929323A>C	ENSP00000361169:p.Lys328Gln	109.0	0.0		135.0	49.0	NM_012087	A6NI44|A6NJB9|Q5T7U2|Q5T7U3|Q8N2U7|Q8N857|Q96GD9|Q9H4P2	Missense_Mutation	SNP	ENST00000372097.5	hg19	CCDS6958.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.5|26.5	4.739835|4.739835	0.89573|0.89573	.|.	.|.	ENSG00000148308|ENSG00000148308	ENST00000372097;ENST00000372099;ENST00000372095;ENST00000372089;ENST00000372108;ENST00000342018;ENST00000439697|ENST00000434175;ENST00000435745	T;T;T;T;T;T|.	0.48836|.	0.8;0.8;0.8;0.8;0.8;0.8|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	0.042371|.	0.85682|.	D|.	0.000000|.	T|.	0.75466|.	0.3853|.	M|M	0.77820|0.77820	2.39|2.39	0.53688|0.53688	D|D	0.999973|0.999973	D;D;D|.	0.89917|.	1.0;0.995;1.0|.	D;D;D|.	0.76071|.	0.987;0.909;0.974|.	T|.	0.76788|.	-0.2830|.	10|.	0.32370|.	T|.	0.25|.	-0.356|-0.356	14.7944|14.7944	0.69868|0.69868	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	203;328;328|.	B7Z1V3;Q9Y5Q8-3;Q9Y5Q8|.	.;.;TF3C5_HUMAN|.	Q|C	328;319;203;178;328;259;203|99;6	ENSP00000361169:K328Q;ENSP00000361171:K319Q;ENSP00000361167:K203Q;ENSP00000361180:K328Q;ENSP00000339530:K259Q;ENSP00000393207:K203Q|.	ENSP00000339530:K259Q|.	K|X	+|+	1|3	0|0	GTF3C5|GTF3C5	134919144|134919144	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.947000|0.947000	0.59692|0.59692	8.535000|8.535000	0.90623|0.90623	2.085000|2.085000	0.62840|0.62840	0.533000|0.533000	0.62120|0.62120	AAA|TGA	.	.		0.423	GTF3C5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054826.1	NM_001122823		C	135929323	A	C	135929323	3	2	201	1	0	0	0	0	1	0	0	0	6885	247	9	5	1004	5	GTF3C5	9	135929323	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	9490320	135929323	5284108	79	29539										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7627891	7627891	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gggtgacatatggtgaatgtAcactttcccatccctgatgc	10	10	0	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr10:7627891A>T	ENST00000256861.6	-	8	1159	c.1081T>A	c.(1081-1083)Tac>Aac	p.Y361N	ITIH5_ENST00000397145.2_Missense_Mutation_p.Y361N|ITIH5_ENST00000397146.2_Missense_Mutation_p.Y361N|ITIH5_ENST00000446830.2_Missense_Mutation_p.Y143N|ITIH5_ENST00000298441.6_Missense_Mutation_p.Y147N|ITIH5_ENST00000434980.1_5'UTR	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	361	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TGGTGAATGTACACTTTCCCA	0.393																																					p.Y361N		Atlas-SNP	.											.	ITIH5	343	.	0			c.T1081A						.						183	145	158					10																	7627891		2203	4300	6503	SO:0001583	missense	80760	exon8			GAATGTACACTTT			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.1081T>A	chr10.hg19:g.7627891A>T	ENSP00000256861:p.Tyr361Asn	103.0	0.0		141.0	48.0	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	A	19.38	3.817403	0.70912	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15	5.3	4.17	0.49024	von Willebrand factor, type A (3);	0.054481	0.64402	D	0.000001	D	0.86740	0.6005	.	.	.	0.42256	D	0.99199	D;P;P	0.54397	0.966;0.856;0.826	D;B;B	0.69307	0.963;0.424;0.299	D	0.87329	0.2323	9	0.87932	D	0	-25.7311	10.9471	0.47306	0.9265:0.0:0.0735:0.0	.	361;361;147	G5E9D8;Q86UX2;Q86UX2-3	.;ITIH5_HUMAN;.	N	361;361;147;143;361	ENSP00000256861:Y361N;ENSP00000380333:Y361N;ENSP00000298441:Y147N;ENSP00000387969:Y143N;ENSP00000380332:Y361N	ENSP00000256861:Y361N	Y	-	1	0	ITIH5	7667897	1.000000	0.71417	0.987000	0.45799	0.849000	0.48306	5.847000	0.69451	0.862000	0.35528	0.459000	0.35465	TAC	.	.		0.393	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7627891	A	T	7627891	3	4	201	1	0	0	0	0	1	0	0	0	7916	391	14	4	1898	4	ITIH5	10	7627891	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10		7627891	127906856	80	29540										
TRDMT1	1787	hgsc.bcm.edu	37	chr10	17191063	17191063	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tcatataagattttgattagTttagctactacatgcacgtt	6	6	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr10:17191063T>C	ENST00000377799.3	-	11	1199	c.1152A>G	c.(1150-1152)aaA>aaG	p.K384K	TRDMT1_ENST00000351358.4_Silent_p.K338K|TRDMT1_ENST00000358282.7_3'UTR|TRDMT1_ENST00000412821.3_Silent_p.K360K|TRDMT1_ENST00000377766.5_3'UTR|TRDMT1_ENST00000457442.2_Silent_p.K303K|TRDMT1_ENST00000452380.2_5'Flank	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	384	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	TTTTGATTAGTTTAGCTACTA	0.303																																					p.K384K		Atlas-SNP	.											.	TRDMT1	46	.	0			c.A1152G						.						58	59	58					10																	17191063		2202	4297	6499	SO:0001819	synonymous_variant	1787	exon11			GATTAGTTTAGCT	AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"DNA (cytosine-5-)-methyltransferase 2"	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.1152A>G	chr10.hg19:g.17191063T>C		52.0	0.0		61.0	21.0	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Silent	SNP	ENST00000377799.3	hg19	CCDS7114.1																																																																																			.	.		0.303	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412		C	17191063	T	C	17191063	2	2	201	1	0	0	0	0	0	0	0	1	16482	1722	60	2		2	TRDMT1	10	17191063	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	9563172	17191063	118343684	81	29541										
FZD8	8325	hgsc.bcm.edu	37	chr10	35930122	35930122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	acttgagatcgggcgagcacTggatctccaccagcggccag	13	13	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr10:35930122T>C	ENST00000374694.1	-	1	240	c.236A>G	c.(235-237)cAg>cGg	p.Q79R	MIR4683_ENST00000579659.1_RNA	NM_031866.2	NP_114072.1	Q9H461	FZD8_HUMAN	frizzled class receptor 8	79	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	11						GGGCGAGCACTGGATCTCCAC	0.602																																					p.Q79R		Atlas-SNP	.											.	FZD8	41	.	0			c.A236G						.						115	94	101					10																	35930122		2203	4300	6503	SO:0001583	missense	8325	exon1			GAGCACTGGATCT	AB043703	CCDS7192.1	10p11.2	2014-01-29	2014-01-29		ENSG00000177283	ENSG00000177283		"GPCR / Class F : Frizzled receptors"	4046	protein-coding gene	gene with protein product		606146	"frizzled (Drosophila) homolog 8", "frizzled homolog 8 (Drosophila)", "frizzled 8, seven transmembrane spanning receptor", "frizzled family receptor 8"			11295046	Standard	NM_031866		Approved		uc001iyz.1	Q9H461	OTTHUMG00000017956	ENST00000374694.1:c.236A>G	chr10.hg19:g.35930122T>C	ENSP00000363826:p.Gln79Arg	53.0	0.0		86.0	24.0	NM_031866		Missense_Mutation	SNP	ENST00000374694.1	hg19	CCDS7192.1	.	.	.	.	.	.	.	.	.	.	T	14.08	2.428992	0.43122	.	.	ENSG00000177283	ENST00000374694	T	0.53423	0.62	3.74	3.74	0.42951	Frizzled domain (5);	0.165679	0.40908	U	0.000983	T	0.37945	0.1022	L	0.37897	1.145	0.44789	D	0.997791	B	0.20052	0.041	B	0.25405	0.06	T	0.17715	-1.0360	10	0.27082	T	0.32	.	12.7482	0.57293	0.0:0.0:0.0:1.0	.	79	Q9H461	FZD8_HUMAN	R	79	ENSP00000363826:Q79R	ENSP00000363826:Q79R	Q	-	2	0	FZD8	35970128	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.989000	0.63870	1.489000	0.48450	0.368000	0.22195	CAG	.	.		0.602	FZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047575.2	NM_031866		C	35930122	T	C	35930122	3	2	201	1	0	0	0	0	1	0	0	0	6144	1580	55	2	1852	2	FZD8	10	35930122	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	18739059	35930122	99604625	82	29542										
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46998926	46998926	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gtccctgggcacccctgagcCcccgccttcagcccctgtcc	9	22	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr10:46998926C>T	ENST00000374317.1	+	3	319	c.46C>T	c.(46-48)Ccc>Tcc	p.P16S	GPRIN2_ENST00000374314.4_Missense_Mutation_p.P16S	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	16										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						ACCCCTGAGCCCCCGCCTTCA	0.672																																					p.P16S		Atlas-SNP	.											.	GPRIN2	94	.	0			c.C46T						.						45	63	57					10																	46998926		2197	4292	6489	SO:0001583	missense	9721	exon3			CTGAGCCCCCGCC	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"KIAA0514"	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.46C>T	chr10.hg19:g.46998926C>T	ENSP00000363436:p.Pro16Ser	104.0	0.0		109.0	11.0	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	hg19	CCDS31192.1	.	.	.	.	.	.	.	.	.	.	C	7.099	0.573722	0.13623	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03580	3.88;3.88	5.33	4.42	0.53409	.	0.483057	0.17726	N	0.164073	T	0.05364	0.0142	L	0.57536	1.79	0.23113	N	0.998272	P	0.44044	0.825	B	0.40066	0.318	T	0.33343	-0.9872	10	0.16896	T	0.51	-6.6732	12.3625	0.55211	0.0:0.8302:0.1698:0.0	.	16	O60269	GRIN2_HUMAN	S	16	ENSP00000363436:P16S;ENSP00000363433:P16S	ENSP00000363433:P16S	P	+	1	0	GPRIN2	46418932	0.014000	0.17966	0.192000	0.23308	0.501000	0.33797	1.430000	0.34914	1.377000	0.46286	0.655000	0.94253	CCC	.	.		0.672	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		T	46998926	C	T	46998926	3	4	201	1	0	0	0	0	1	0	0	0	6739	623	22	3	48	3	GPRIN2	10	46998926	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	11068804	46998926	88535821	83	29543										
CDH23	64072	hgsc.bcm.edu	37	chr10	73560473	73560473	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gccttggccaaagacaacccTggggatgtagccagcaaccg	12	13	0	1	rs34911784		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr10:73560473T>A	ENST00000224721.6	+	52	7463	c.7458T>A	c.(7456-7458)ccT>ccA	p.P2486P	CDH23_ENST00000398788.3_Silent_p.P241P|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2481	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						AAGACAACCCTGGGGATGTAG	0.572																																					p.P2481P		Atlas-SNP	.											.	CDH23	365	.	0			c.T7443A						.						66	69	68					10																	73560473		1961	4147	6108	SO:0001819	synonymous_variant	64072	exon51			CAACCCTGGGGAT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.7458T>A	chr10.hg19:g.73560473T>A		69.0	0.0		93.0	35.0	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	hg19																																																																																				.	.		0.572	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73560473	T	A	73560473	2	1	201	1	0	0	0	0	0	0	0	1	3110	1567	55	4		4	CDH23	10	73560473	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	26561547	73560473	61974274	84	29544										
ENTPD7	57089	hgsc.bcm.edu	37	chr10	101439111	101439111	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gactgtggcagcagtggttcCcggatttttgtttatttctg	12	7	1	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr10:101439111C>G	ENST00000370489.4	+	4	463	c.285C>G	c.(283-285)tcC>tcG	p.S95S		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	95						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		GCAGTGGTTCCCGGATTTTTG	0.463																																					p.S95S		Atlas-SNP	.											.	ENTPD7	44	.	0			c.C285G						.						95	99	97					10																	101439111		2203	4300	6503	SO:0001819	synonymous_variant	57089	exon4			TGGTTCCCGGATT	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.285C>G	chr10.hg19:g.101439111C>G		126.0	0.0		164.0	51.0	NM_020354	B2RB83|B3KP21|D3DR64	Silent	SNP	ENST00000370489.4	hg19	CCDS7480.1																																																																																			.	.		0.463	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354		G	101439111	C	G	101439111	2	3	201	1	0	0	0	0	0	0	0	1	5146	610	22	4		4	ENTPD7	10	101439111	Silent	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	27878638	101439111	34095636	85	29545										
PWWP2B	170394	hgsc.bcm.edu	37	chr10	134219298	134219298	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gcgacagcctggacgaggccAgatcgtccggctcggaaggg	17	12	0	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr10:134219298A>G	ENST00000305233.5	+	2	1353	c.1294A>G	c.(1294-1296)Aga>Gga	p.R432G	PWWP2B_ENST00000368609.4_Missense_Mutation_p.R432G	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	432										central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)		GGACGAGGCCAGATCGTCCGG	0.687																																					p.R432G		Atlas-SNP	.											PWWP2B,colon,carcinoma,0,1	PWWP2B	33	.	0			c.A1294G						.						29	28	28					10																	134219298		2195	4297	6492	SO:0001583	missense	170394	exon2			GAGGCCAGATCGT	AK128663	CCDS7667.2	10q26.3	2009-06-03	2007-10-22	2007-10-22	ENSG00000171813	ENSG00000171813			25150	protein-coding gene	gene with protein product			"PWWP domain containing 2"	PWWP2			Standard	NM_001098637		Approved	bA432J24.1, FLJ46823	uc001lll.4	Q6NUJ5	OTTHUMG00000019286	ENST00000305233.5:c.1294A>G	chr10.hg19:g.134219298A>G	ENSP00000306324:p.Arg432Gly	32.0	0.0		44.0	16.0	NM_001098637	A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Missense_Mutation	SNP	ENST00000305233.5	hg19	CCDS7667.2	.	.	.	.	.	.	.	.	.	.	A	12.81	2.049899	0.36181	.	.	ENSG00000171813	ENST00000305233;ENST00000368609	T;T	0.56444	0.46;1.48	3.59	3.59	0.41128	.	0.064956	0.64402	U	0.000014	T	0.30070	0.0753	N	0.08118	0	0.30022	N	0.814229	B	0.31769	0.339	B	0.23716	0.048	T	0.41448	-0.9508	10	0.87932	D	0	-8.545	12.3972	0.55391	1.0:0.0:0.0:0.0	.	432	Q6NUJ5	PWP2B_HUMAN	G	432	ENSP00000306324:R432G;ENSP00000357598:R432G	ENSP00000306324:R432G	R	+	1	2	PWWP2B	134069288	1.000000	0.71417	0.087000	0.20705	0.404000	0.30871	5.203000	0.65174	1.880000	0.54463	0.460000	0.39030	AGA	.	.		0.687	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499		G	134219298	A	G	134219298	3	3	201	1	0	0	0	0	1	0	0	0	12861	180	7	2	1300	2	PWWP2B	10	134219298	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	32780187	134219298	1315449	86	29546										
C10orf125	282969	hgsc.bcm.edu	37	chr10	135169315	135169315	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ctctatctttgccagggctcTctggaagacaaaatggcagg	11	10	3	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr10:135169315T>C	ENST00000368552.3	-	5	342	c.325A>G	c.(325-327)Aga>Gga	p.R109G	FUOM_ENST00000368551.1_Splice_Site_p.R64G|FUOM_ENST00000465384.1_5'UTR|FUOM_ENST00000278025.4_Splice_Site_p.R109G|FUOM_ENST00000447176.1_Splice_Site_p.R65G	NM_001098483.1	NP_001091953.1	A2VDF0	FUCM_HUMAN	fucose mutarotase	109					female mating behavior (GO:0060180)|fucose metabolic process (GO:0006004)|fucosylation (GO:0036065)|negative regulation of neuron differentiation (GO:0045665)		fucose binding (GO:0042806)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)										GCCAGGGCTCTCTGGAAGACA	0.572																																					p.R109G		Atlas-SNP	.											.	.	.	.	0			c.A325G						.						84	101	95					10																	135169315		2203	4300	6503	SO:0001630	splice_region_variant	282969	exon5			GGGCTCTCTGGAA	AK129527	CCDS7680.1	10q26.3	2012-07-10	2012-07-10	2012-07-10	ENSG00000148803	ENSG00000148803	5.1.3.n2		24733	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 125"	C10orf125		17602138	Standard	NM_001098483		Approved	FLJ26016, FucU, FucM	uc001lmt.2	A2VDF0	OTTHUMG00000019315	ENST00000368552.3:c.325-1A>G	chr10.hg19:g.135169315T>C		77.0	0.0		89.0	32.0	NM_001098483	A1L300|Q5VWY2|Q5VWY3|Q6ZPD2	Missense_Mutation	SNP	ENST00000368552.3	hg19	CCDS44499.1	.	.	.	.	.	.	.	.	.	.	T	5.581	0.292087	0.10567	.	.	ENSG00000148803	ENST00000278025;ENST00000447176;ENST00000368551;ENST00000368552	.	.	.	4.09	0.219	0.15274	D-ribose pyranase RbsD-like (2);	1.395380	0.04609	N	0.399908	T	0.13713	0.0332	N	0.02539	-0.55	0.09310	N	0.999994	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.16837	-1.0389	9	0.22109	T	0.4	0.1997	2.2049	0.03933	0.2285:0.2903:0.0:0.4812	.	109;109	A2VDF0;A2VDF0-2	FUCM_HUMAN;.	G	109;65;64;109	.	ENSP00000278025:R109G	R	-	1	2	C10orf125	135019305	0.010000	0.17322	0.276000	0.24689	0.638000	0.38207	-0.287000	0.08388	0.148000	0.19059	0.383000	0.25322	AGA	.	.		0.572	FUOM-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198472	Missense_Mutation	C	135169315	T	C	135169315	5	2	201	1	0	0	0	0	0	0	1	0	1593	1565	54	2	158	2	C10orf125	10	135169315	Splice_Site	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	950017	135169315	365432	87	29547										
PDDC1	347862	hgsc.bcm.edu	37	chr11	770992	770992	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tgcccaccctggtgccctcaCcggctgccacagaggaagag	12	16	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr11:770992C>A	ENST00000319863.8	-	7	678		c.e7+1		PDDC1_ENST00000442059.2_Splice_Site|PDDC1_ENST00000524550.1_Splice_Site|PDDC1_ENST00000526325.1_Intron|PDDC1_ENST00000529966.1_Splice_Site|PDDC1_ENST00000397472.2_Intron	NM_182612.2	NP_872418.1	Q8NB37	PDDC1_HUMAN	Parkinson disease 7 domain containing 1							extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(3)|urinary_tract(1)	5		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;3.66e-26)|Epithelial(43;2.43e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-19)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGTGCCCTCACCGGCTGCCAC	0.622																																					.		Atlas-SNP	.											.	PDDC1	16	.	0			c.656+1G>T						.						56	55	56					11																	770992		2203	4300	6503	SO:0001630	splice_region_variant	347862	exon8			CCCTCACCGGCTG	AK128653	CCDS7713.1	11p15.5	2005-10-26			ENSG00000177225	ENSG00000177225			26616	protein-coding gene	gene with protein product							Standard	XM_005252898		Approved	FLJ34283	uc001lrc.3	Q8NB37	OTTHUMG00000133315	ENST00000319863.8:c.656+1G>T	chr11.hg19:g.770992C>A		60.0	0.0		66.0	26.0	NM_182612	B7ZKW5|Q2NL76|Q6ZQY0|Q8NAE0	Splice_Site	SNP	ENST00000319863.8	hg19	CCDS7713.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.201541	0.58234	.	.	ENSG00000177225	ENST00000465313;ENST00000319863;ENST00000442059;ENST00000524550	.	.	.	4.55	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4372	0.83880	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDDC1	760992	1.000000	0.71417	0.998000	0.56505	0.894000	0.52154	4.483000	0.60264	2.250000	0.74265	0.462000	0.41574	.	.	.		0.622	PDDC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258051.2	NM_182612	Intron	A	770992	C	A	770992	5	1	201	1	0	0	0	0	0	0	1	0	11638	521	18	3	13	3	PDDC1	11	770992	Splice_Site	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10		770992	134235524	88	29548										
BBOX1	8424	hgsc.bcm.edu	37	chr11	27114795	27114795	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gatatgatgaacacgcatacAagtggctctccaccctcaag	8	12	2	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr11:27114795A>T	ENST00000529202.1	+	4	754	c.415A>T	c.(415-417)Aag>Tag	p.K139*	RP11-1L12.3_ENST00000530430.1_RNA|RP11-1L12.3_ENST00000525302.1_RNA|BBOX1_ENST00000527505.1_Intron|BBOX1_ENST00000528583.1_Nonsense_Mutation_p.K139*|RP11-1L12.3_ENST00000526061.1_RNA|BBOX1_ENST00000525090.1_Nonsense_Mutation_p.K139*|BBOX1_ENST00000263182.3_Nonsense_Mutation_p.K139*			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	139					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	ACACGCATACAAGTGGCTCTC	0.428																																					p.K139X		Atlas-SNP	.											.	BBOX1	46	.	0			c.A415T						.						100	99	99					11																	27114795		2202	4298	6500	SO:0001587	stop_gained	8424	exon5			GCATACAAGTGGC	AF082868	CCDS7862.1	11p	2008-02-01			ENSG00000129151	ENSG00000129151	1.14.11.1		964	protein-coding gene	gene with protein product		603312		BBOX		9753662	Standard	XM_005253159		Approved	gamma-BBH, G-BBH, BBH	uc001mre.1	O75936	OTTHUMG00000166121	ENST00000529202.1:c.415A>T	chr11.hg19:g.27114795A>T	ENSP00000435781:p.Lys139*	145.0	0.0		176.0	60.0	NM_003986	B2R8L7|D3DQZ1|Q6IBJ2	Nonsense_Mutation	SNP	ENST00000529202.1	hg19	CCDS7862.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.468958	0.84533	.	.	ENSG00000129151	ENST00000529202;ENST00000263182;ENST00000528583;ENST00000525090	.	.	.	5.29	1.51	0.23008	.	0.580480	0.20309	N	0.094879	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.5756	0.27933	0.4013:0.4619:0.0:0.1368	.	.	.	.	X	139	.	ENSP00000263182:K139X	K	+	1	0	BBOX1	27071371	0.999000	0.42202	0.980000	0.43619	0.285000	0.27093	2.049000	0.41288	-0.010000	0.14271	0.528000	0.53228	AAG	.	.		0.428	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986		T	27114795	A	T	27114795	4	4	201	1	0	0	0	0	0	1	0	0	1334	131	5	4	425	4	BBOX1	11	27114795	Nonsense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	26343803	27114795	107891721	89	29549										
MYBPC3	4607	hgsc.bcm.edu	37	chr11	47361216	47361216	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cagtacctgcgtgatagcctTctgccagatcacagtgggag	12	11	2	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr11:47361216T>A	ENST00000545968.1	-	21	2107	c.2053A>T	c.(2053-2055)Aag>Tag	p.K685*	MYBPC3_ENST00000399249.2_Nonsense_Mutation_p.K685*|MYBPC3_ENST00000256993.4_Nonsense_Mutation_p.K684*	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	685	Ig-like C2-type 5.				cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		GTGATAGCCTTCTGCCAGATC	0.572																																					p.K685X		Atlas-SNP	.											.	MYBPC3	102	.	0			c.A2053T						.						68	72	71					11																	47361216		2005	4164	6169	SO:0001587	stop_gained	4607	exon20			TAGCCTTCTGCCA	X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7551	protein-coding gene	gene with protein product		600958	"myosin-binding protein C, cardiac"	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.2053A>T	chr11.hg19:g.47361216T>A	ENSP00000442795:p.Lys685*	82.0	0.0		82.0	39.0	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Nonsense_Mutation	SNP	ENST00000545968.1	hg19	CCDS53621.1	.	.	.	.	.	.	.	.	.	.	T	37	6.145888	0.97324	.	.	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.6842	0.69037	0.0:0.0:0.0:1.0	.	.	.	.	X	685;685;684	.	ENSP00000256993:K684X	K	-	1	0	MYBPC3	47317792	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	7.318000	0.79029	2.054000	0.61138	0.459000	0.35465	AAG	.	.		0.572	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3			A	47361216	T	A	47361216	4	1	201	1	0	0	0	0	0	1	0	0	10022	1792	62	4	1827	4	MYBPC3	11	47361216	Nonsense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	20246421	47361216	87645300	90	29550										
GANAB	23193	hgsc.bcm.edu	37	chr11	62402314	62402314	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agaccctaggggccctctgaTgctcaaactccaagagtcct	9	14	2	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr11:62402314T>C	ENST00000356638.3	-	5	555	c.539A>G	c.(538-540)cAt>cGt	p.H180R	GANAB_ENST00000534779.1_Missense_Mutation_p.H66R|GANAB_ENST00000534422.1_5'UTR|GANAB_ENST00000346178.4_Missense_Mutation_p.H180R|GANAB_ENST00000540933.1_Missense_Mutation_p.H83R	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	180					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	GGCCCTCTGATGCTCAAACTC	0.547																																					p.H180R	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											GANAB,NS,carcinoma,0,1	GANAB	110	.	0			c.A539G						.						124	103	110					11																	62402314		2202	4299	6501	SO:0001583	missense	23193	exon5			CTCTGATGCTCAA	AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.539A>G	chr11.hg19:g.62402314T>C	ENSP00000349053:p.His180Arg	87.0	0.0		122.0	48.0	NM_198334	A6NC20|Q8WTS9|Q9P0X0	Missense_Mutation	SNP	ENST00000356638.3	hg19	CCDS8026.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.554093	0.27739	.	.	ENSG00000089597	ENST00000346178;ENST00000356638;ENST00000534779;ENST00000540933;ENST00000525994	D;D;D;D;T	0.89681	-2.52;-2.38;-2.55;-2.53;0.99	5.67	5.67	0.87782	Glycoside hydrolase-type carbohydrate-binding (1);	0.100301	0.64402	D	0.000002	D	0.93452	0.7911	M	0.86502	2.82	0.80722	D	1	B;D;B;P	0.59357	0.378;0.985;0.225;0.679	B;P;B;B	0.55112	0.168;0.769;0.087;0.43	D	0.94404	0.7625	10	0.87932	D	0	-24.9071	13.8725	0.63629	0.0:0.0:0.0:1.0	.	66;66;180;180	B4DIW2;E9PKU7;Q14697;Q14697-2	.;.;GANAB_HUMAN;.	R	180;180;66;83;66	ENSP00000340466:H180R;ENSP00000349053:H180R;ENSP00000435306:H66R;ENSP00000442962:H83R;ENSP00000434805:H66R	ENSP00000340466:H180R	H	-	2	0	GANAB	62158890	1.000000	0.71417	1.000000	0.80357	0.038000	0.13279	7.161000	0.77505	2.174000	0.68829	0.533000	0.62120	CAT	.	.		0.547	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334		C	62402314	T	C	62402314	3	2	201	1	0	0	0	0	1	0	0	0	6241	1464	51	2	2445	2	GANAB	11	62402314	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	15041098	62402314	72604202	91	29551										
ZBTB44	29068	hgsc.bcm.edu	37	chr11	130131553	130131587	+	Frame_Shift_Del	DEL	CAACACATTCTTGTTCTCATCCTCGGCTTGGCCTA	CAACACATTCTTGTTCTCATCCTCGGCTTGGCCTA	-													0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	actgtaacatgatgcagatcCaacacattcttgttctcatc					rs529557692|rs373677642|rs146574096	byFrequency	TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	CAACACATTCTTGTTCTCATCCTCGGCTTGGCCTA	CAACACATTCTTGTTCTCATCCTCGGCTTGGCCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr11:130131553_130131587delCAACACATTCTTGTTCTCATCCTCGGCTTGGCCTA	ENST00000357899.4	-	2	454_488	c.182_216delTAGGCCAAGCCGAGGATGAGAACAAGAATGTGTTG	c.(181-216)gtaggccaagccgaggatgagaacaagaatgtgttgfs	p.VGQAEDENKNVL61fs	ZBTB44_ENST00000530205.1_Frame_Shift_Del_p.VGQAEDENKNVL61fs|ZBTB44_ENST00000525842.1_Frame_Shift_Del_p.VGQAEDENKNVL61fs|ZBTB44_ENST00000397753.1_Frame_Shift_Del_p.VGQAEDENKNVL61fs			Q8NCP5	ZBT44_HUMAN	zinc finger and BTB domain containing 44	61	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)		GATGCAGATCCAACACATTCTTGTTCTCATCCTCGGCTTGGCCTACAAGTTTGGT	0.404																																					p.61_73del		Atlas-INDEL	.											.	ZBTB44	41	.	0			c.183_217del						.																																			SO:0001589	frameshift_variant	29068	exon2			.	AK024659	CCDS44776.1, CCDS73414.1, CCDS73415.1	11q24.3	2013-01-08	2006-09-19	2006-09-19		ENSG00000196323		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	25001	protein-coding gene	gene with protein product			"BTB (POZ) domain containing 15"	BTBD15		11042152	Standard	NM_014155		Approved	HSPC063, ZNF851	uc001qgb.4	Q8NCP5		ENST00000357899.4:c.182_216delTAGGCCAAGCCGAGGATGAGAACAAGAATGTGTTG	chr11.hg19:g.130131553_130131587delCAACACATTCTTGTTCTCATCCTCGGCTTGGCCTA	ENSP00000350574:p.Val61fs	111.0	0.0		142.0	12.0	NM_014155	Q6IPT8|Q86VJ7|Q86XX5	Frame_Shift_Del	DEL	ENST00000357899.4	hg19																																																																																				.	.		0.404	ZBTB44-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000386126.1	NM_014155		-	130131587	CAACACATTCTTGTTCTCATCCTCGGCTTGGCCTA	-	130131553	7	5	201	1	0	1	0	1	0	0	0	0	17560	593	21	0	1165	0	ZBTB44	11	130131553	Frame_Shift_Del	DEL	CAACACATTCTTGTTCTCATCCTCGGCTTGGCCTA	TCGA-DD-AADS-01A-11D-A40R-10	67729239	130131553	4874963	92	29552										
SLC6A13	6540	hgsc.bcm.edu	37	chr12	351921	351936	+	Splice_Site	DEL	CTGCGGGGAAACTGCA	CTGCGGGGAAACTGCA	-													0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ctgggaggcatagccaatgcCtgcggggaaactgcagaatt					rs372831595	byFrequency	TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	CTGCGGGGAAACTGCA	CTGCGGGGAAACTGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr12:351921_351936delCTGCGGGGAAACTGCA	ENST00000343164.4	-	4	390		c.e4-1		SLC6A13_ENST00000445055.2_Intron	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13						neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			TAGCCAATGCCTGCGGGGAAACTGCAGAATTGGGCT	0.546																																					p.113_113del		Atlas-INDEL	.											.	SLC6A13	62	.	0			c.338_338del						.																																			SO:0001630	splice_region_variant	6540	exon4			.	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.338-1TGCAGTTTCCCCGCAG>-	chr12.hg19:g.351921_351936delCTGCGGGGAAACTGCA		54.0	0.0		58.0	19.0	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Frame_Shift_Del	DEL	ENST00000343164.4	hg19	CCDS8502.1																																																																																			.	.		0.546	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615	Intron	-	351936	CTGCGGGGAAACTGCA	-	351921	8	5	201	1	0	1	0	1	0	0	1	0	14691	695	24	0	1519	0	SLC6A13	12	351921	Splice_Site	DEL	CTGCGGGGAAACTGCA	TCGA-DD-AADS-01A-11D-A40R-10		351921	133499974	93	29553										
SLC2A3	6515	hgsc.bcm.edu	37	chr12	8085600	8085600	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tacctgccaaagcggttgacGaagagtccgacggaaaagga	13	9	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr12:8085600G>A	ENST00000075120.7	-	3	492	c.252C>T	c.(250-252)ttC>ttT	p.F84F		NM_006931.2	NP_008862.1	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 3	84					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(14)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				Kidney(36;0.0866)		AGCGGTTGACGAAGAGTCCGA	0.552											OREG0021656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F84F	Colon(96;424 1461 14416 20933 23688)	Atlas-SNP	.											.	SLC2A3	83	.	0			c.C252T						.						89	82	85					12																	8085600		2203	4300	6503	SO:0001819	synonymous_variant	6515	exon3			GTTGACGAAGAGT	M20681	CCDS8586.1	12p13.3	2013-05-22			ENSG00000059804	ENSG00000059804		"Solute carriers"	11007	protein-coding gene	gene with protein product		138170		GLUT3			Standard	NM_006931		Approved		uc001qtr.3	P11169	OTTHUMG00000133685	ENST00000075120.7:c.252C>T	chr12.hg19:g.8085600G>A		114.0	0.0	646	174.0	65.0	NM_006931	B2R606|D3DUU6|Q6I9U2|Q9UG15	Silent	SNP	ENST00000075120.7	hg19	CCDS8586.1																																																																																			.	.		0.552	SLC2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257914.1	NM_006931		A	8085600	G	A	8085600	2	1	201	1	0	0	0	0	0	0	0	1	14560	1049	37	1		1	SLC2A3	12	8085600	Silent	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	7733679	8085600	125766295	94	29554										
A2ML1	144568	hgsc.bcm.edu	37	chr12	8998818	8998818	+	Splice_Site	DEL	G	G	-													0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gagatgtgctttgacaatcaGgtaaaatgatagcggagaag							TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr12:8998818delG	ENST00000299698.7	+	14	1863	c.1683delG	c.(1681-1683)cag>ca	p.Q561fs	A2ML1_ENST00000539547.1_Splice_Site_p.Q70fs|A2ML1_ENST00000540049.1_3'UTR	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						TTGACAATCAGGTAAAATGAT	0.448																																					p.Q561fs		Atlas-INDEL	.											.	A2ML1	199	.	0			c.1682delA						.						106	92	96					12																	8998818		1910	4133	6043	SO:0001630	splice_region_variant	144568	exon14			.	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.1683+1G>-	chr12.hg19:g.8998818delG		100.0	0.0		132.0	47.0	NM_144670		Frame_Shift_Del	DEL	ENST00000299698.7	hg19	CCDS8596.2																																																																																			.	.		0.448	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	Frame_Shift_Del	-	8998818	G	-	8998818	8	5	201	1	0	1	0	1	0	0	1	0	5	1014	35	0	1737	0	A2ML1	12	8998818	Splice_Site	DEL	G	TCGA-DD-AADS-01A-11D-A40R-10	913218	8998818	124853077	95	29555										
KLRC2	3823	hgsc.bcm.edu	37	chr12	10588437	10588437	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tatcaatcccttgatgattcAgggaaggattttgaagattt	9	5	2	4			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr12:10588437A>T	ENST00000539033.1	-	1	163	c.149T>A	c.(148-150)cTg>cAg	p.L50Q	KLRC2_ENST00000381901.1_Missense_Mutation_p.L50Q|KLRC2_ENST00000536833.2_Intron|KLRC2_ENST00000381902.2_Missense_Mutation_p.L50Q																							TTGATGATTCAGGGAAGGATT	0.358																																					p.L50Q		Atlas-SNP	.											.	KLRC2	29	.	0			c.T149A						.						127	137	134					12																	10588437		2110	4201	6311	SO:0001583	missense	3822	exon1			TGATTCAGGGAAG																												ENST00000539033.1:c.149T>A	chr12.hg19:g.10588437A>T	ENSP00000437563:p.Leu50Gln	94.0	0.0		115.0	38.0	NM_002260		Missense_Mutation	SNP	ENST00000539033.1	hg19		.	.	.	.	.	.	.	.	.	.	A	0	-2.739580	0.00088	.	.	ENSG00000255641;ENSG00000205809;ENSG00000205809	ENST00000539033;ENST00000381902;ENST00000381901	T;T;T	0.05081	3.5;3.5;3.5	1.71	-3.24	0.05094	.	0.772167	0.11399	N	0.567988	T	0.01421	0.0046	N	0.02120	-0.675	0.09310	N	1	B;B;B	0.11235	0.001;0.0;0.004	B;B;B	0.14578	0.002;0.0;0.011	T	0.41378	-0.9512	10	0.02654	T	1	.	0.1483	0.00090	0.238:0.1683:0.2364:0.3574	.	36;50;50	Q3KQS7;P26717;F5H6K3	.;NKG2C_HUMAN;.	Q	50	ENSP00000437563:L50Q;ENSP00000371327:L50Q;ENSP00000371326:L50Q	ENSP00000371326:L50Q	L	-	2	0	KLRC2;RP11-277P12.6	10479704	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.977000	0.03782	-0.727000	0.04888	-1.194000	0.01681	CTG	.	.		0.358	NKG2-E-001	KNOWN	basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000400274.1			T	10588437	A	T	10588437	3	4	201	1	0	0	0	0	1	0	0	0	8425	188	7	4	570	4	KLRC2	12	10588437	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	1589619	10588437	123263458	96	29556										
GYS2	2998	hgsc.bcm.edu	37	chr12	21713357	21713357	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tgcttgtcctttcagggtttCcacgttgaaattatttgtct	8	8	2	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr12:21713357C>T	ENST00000261195.2	-	8	1386	c.1132G>A	c.(1132-1134)Gaa>Aaa	p.E378K		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	378					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TTCAGGGTTTCCACGTTGAAA	0.373																																					p.E378K	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											.	GYS2	110	.	0			c.G1132A						.						207	187	194					12																	21713357		2203	4300	6503	SO:0001583	missense	2998	exon8			GGGTTTCCACGTT		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1132G>A	chr12.hg19:g.21713357C>T	ENSP00000261195:p.Glu378Lys	68.0	0.0		81.0	7.0	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	hg19	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	C	36	5.689631	0.96784	.	.	ENSG00000111713	ENST00000261195	T	0.69306	-0.39	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	D	0.85831	0.5788	M	0.90870	3.155	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.89195	0.3553	10	0.87932	D	0	-26.5301	18.1927	0.89812	0.0:1.0:0.0:0.0	.	378	P54840	GYS2_HUMAN	K	378	ENSP00000261195:E378K	ENSP00000261195:E378K	E	-	1	0	GYS2	21604624	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.638000	0.83328	2.530000	0.85305	0.563000	0.77884	GAA	.	.		0.373	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		T	21713357	C	T	21713357	3	4	201	1	0	0	0	0	1	0	0	0	6922	864	30	3	1015	3	GYS2	12	21713357	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	11124920	21713357	112138538	97	29557										
HOXC11	3227	hgsc.bcm.edu	37	chr12	54367150	54367150	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cagttgcacttactacatgcCcgagttctccacggtctcct	7	15	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr12:54367150C>A	ENST00000546378.1	+	1	241	c.125C>A	c.(124-126)cCc>cAc	p.P42H	HOTAIR_ENST00000455246.1_RNA|HOTAIR_ENST00000424518.1_RNA|HOXC11_ENST00000243082.4_Missense_Mutation_p.P42H			O43248	HXC11_HUMAN	homeobox C11	42					anterior/posterior pattern specification (GO:0009952)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal joint morphogenesis (GO:0060272)|endoderm development (GO:0007492)|metanephros development (GO:0001656)|organ induction (GO:0001759)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			large_intestine(1)|ovary(1)	2						TACTACATGCCCGAGTTCTCC	0.632			T	NUP98	AML																																p.P42H		Atlas-SNP	.		Dom	yes		12	12q13.3	3227	homeo box C11		L	.	HOXC11	32	.	0			c.C125A						.						115	119	118					12																	54367150		2203	4300	6503	SO:0001583	missense	3227	exon1			ACATGCCCGAGTT		CCDS8867.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123388	ENSG00000123388		"Homeoboxes / ANTP class : HOXL subclass"	5123	protein-coding gene	gene with protein product		605559	"homeo box C11"	HOX3H		1973146, 1358459	Standard	NM_014212		Approved		uc001sem.3	O43248	OTTHUMG00000160011	ENST00000546378.1:c.125C>A	chr12.hg19:g.54367150C>A	ENSP00000446680:p.Pro42His	60.0	0.0		91.0	30.0	NM_014212	A8K7D1|Q96DH2	Missense_Mutation	SNP	ENST00000546378.1	hg19	CCDS8867.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.709630	0.68730	.	.	ENSG00000123388	ENST00000546378;ENST00000243082	T;T	0.46819	0.86;0.86	4.47	4.47	0.54385	Domain of unknown function DUF3528, homeobox protein, eukaryotic (1);	0.000000	0.85682	D	0.000000	T	0.66036	0.2749	M	0.62088	1.915	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.70048	-0.4979	10	0.87932	D	0	.	16.4268	0.83817	0.0:1.0:0.0:0.0	.	42	O43248	HXC11_HUMAN	H	42	ENSP00000446680:P42H;ENSP00000243082:P42H	ENSP00000243082:P42H	P	+	2	0	HOXC11	52653417	1.000000	0.71417	0.999000	0.59377	0.962000	0.63368	7.292000	0.78731	2.471000	0.83476	0.561000	0.74099	CCC	.	.		0.632	HOXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358869.2			A	54367150	C	A	54367150	3	1	201	1	0	0	0	0	1	0	0	0	7319	623	22	3	127	3	HOXC11	12	54367150	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	32653793	54367150	79484745	98	29558										
NUP37	79023	hgsc.bcm.edu	37	chr12	102512230	102512230	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	attctcaaagggattaaattCtaccacatgcacataatctt	4	9	3	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr12:102512230C>T	ENST00000552283.1	-	2	206	c.67G>A	c.(67-69)Gaa>Aaa	p.E23K	PARPBP_ENST00000541394.1_5'Flank|PARPBP_ENST00000358383.5_5'Flank|PARPBP_ENST00000392911.2_5'Flank|PARPBP_ENST00000327680.2_5'Flank|NUP37_ENST00000251074.1_Missense_Mutation_p.E23K|NUP37_ENST00000543021.1_5'UTR|PARPBP_ENST00000543784.1_5'Flank|PARPBP_ENST00000378128.3_5'Flank|PARPBP_ENST00000537257.1_5'Flank			Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	23					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(10)|ovary(1)	17						GGATTAAATTCTACCACATGC	0.388																																					p.E23K		Atlas-SNP	.											NUP37,NS,carcinoma,0,1	NUP37	26	.	0			c.G67A						.						230	205	213					12																	102512230		2203	4300	6503	SO:0001583	missense	79023	exon1			TAAATTCTACCAC	AF514994	CCDS9089.1	12q23.2	2014-08-12			ENSG00000075188	ENSG00000075188		"WD repeat domain containing"	29929	protein-coding gene	gene with protein product		609264				12196509	Standard	NM_024057		Approved	MGC5585, FLJ22618	uc001tjc.3	Q8NFH4	OTTHUMG00000170478	ENST00000552283.1:c.67G>A	chr12.hg19:g.102512230C>T	ENSP00000448054:p.Glu23Lys	74.0	0.0		109.0	27.0	NM_024057	Q9H644	Missense_Mutation	SNP	ENST00000552283.1	hg19	CCDS9089.1	.	.	.	.	.	.	.	.	.	.	C	17.22	3.333640	0.60853	.	.	ENSG00000075188	ENST00000552283;ENST00000251074;ENST00000551744;ENST00000550459	T;T;T	0.27890	1.64;1.64;2.83	5.3	5.3	0.74995	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.046533	0.85682	D	0.000000	T	0.25044	0.0608	L	0.58583	1.82	0.58432	D	0.999994	P;B	0.38110	0.618;0.105	B;B	0.32211	0.142;0.018	T	0.04650	-1.0936	10	0.08837	T	0.75	-18.3705	12.7622	0.57372	0.0:0.9141:0.0:0.0859	.	23;23	B4DKV8;Q8NFH4	.;NUP37_HUMAN	K	23	ENSP00000448054:E23K;ENSP00000251074:E23K;ENSP00000448086:E23K	ENSP00000251074:E23K	E	-	1	0	NUP37	101036360	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.256000	0.58810	2.471000	0.83476	0.650000	0.86243	GAA	.	.		0.388	NUP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409330.1	NM_024057		T	102512230	C	T	102512230	3	4	201	1	0	0	0	0	1	0	0	0	10773	922	32	3	949	3	NUP37	12	102512230	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	48145080	102512230	31339665	99	29559										
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123472076	123472076	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	acctgaccaccatcttgataGggtagacacccacgcccagg	9	15	1	3			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr12:123472076G>T	ENST00000542749.1	-	20	3308	c.3245C>A	c.(3244-3246)cCt>cAt	p.P1082H	PITPNM2_ENST00000320201.4_Missense_Mutation_p.P1082H|PITPNM2_ENST00000392428.1_Missense_Mutation_p.P803H|PITPNM2_ENST00000280562.5_Missense_Mutation_p.P1076H			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	1082					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CATCTTGATAGGGTAGACACC	0.622																																					p.P1082H		Atlas-SNP	.											.	PITPNM2	105	.	0			c.C3245A						.						107	95	99					12																	123472076		2203	4300	6503	SO:0001583	missense	57605	exon21			TTGATAGGGTAGA	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.3245C>A	chr12.hg19:g.123472076G>T	ENSP00000437611:p.Pro1082His	79.0	0.0		98.0	4.0	NM_020845	Q9P271	Missense_Mutation	SNP	ENST00000542749.1	hg19	CCDS9242.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.252243	0.80135	.	.	ENSG00000090975	ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749	D;D;D;D	0.95377	-3.69;-3.69;-3.69;-3.69	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.97926	0.9318	M	0.84585	2.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98440	1.0586	10	0.59425	D	0.04	-37.0685	18.7781	0.91920	0.0:0.0:1.0:0.0	.	1076;1082	Q9BZ72-2;Q9BZ72	.;PITM2_HUMAN	H	1076;1082;803;1082	ENSP00000280562:P1076H;ENSP00000322218:P1082H;ENSP00000376223:P803H;ENSP00000437611:P1082H	ENSP00000280562:P1076H	P	-	2	0	PITPNM2	122038029	1.000000	0.71417	0.998000	0.56505	0.840000	0.47671	9.781000	0.99029	2.434000	0.82447	0.561000	0.74099	CCT	.	.		0.622	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		T	123472076	G	T	123472076	3	4	201	1	0	0	0	0	1	0	0	0	11960	1000	35	3	824	3	PITPNM2	12	123472076	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	20959846	123472076	10379819	100	29560										
GJB6	10804	hgsc.bcm.edu	37	chr13	20797574	20797574	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cttcccgatgctggtggagtGtttgttgacacccccgatga	12	11	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr13:20797574G>A	ENST00000356192.6	-	5	666	c.46C>T	c.(46-48)Cac>Tac	p.H16Y	GJB6_ENST00000400066.3_Missense_Mutation_p.H16Y|GJB6_ENST00000400065.3_Missense_Mutation_p.H16Y|GJB6_ENST00000241124.6_Missense_Mutation_p.H16Y	NM_001110219.2	NP_001103689.1	O95452	CXB6_HUMAN	gap junction protein, beta 6, 30kDa	16					apoptotic process (GO:0006915)|cell communication (GO:0007154)|ear morphogenesis (GO:0042471)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|sensory perception of sound (GO:0007605)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)				biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	9		all_cancers(29;2.04e-22)|all_epithelial(30;1.19e-19)|all_lung(29;2.27e-18)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;2.17e-05)|Epithelial(112;0.00075)|OV - Ovarian serous cystadenocarcinoma(117;0.00978)|Lung(94;0.0238)|GBM - Glioblastoma multiforme(144;0.0323)|LUSC - Lung squamous cell carcinoma(192;0.0744)		CTGGTGGAGTGTTTGTTGACA	0.507																																					p.H16Y		Atlas-SNP	.											.	GJB6	33	.	0			c.C46T						.						134	122	126					13																	20797574		2203	4300	6503	SO:0001583	missense	10804	exon4			TGGAGTGTTTGTT	AJ005585	CCDS9291.1	13q12	2010-01-06	2007-11-06		ENSG00000121742	ENSG00000121742		"Ion channels / Gap junction proteins (connexins)"	4288	protein-coding gene	gene with protein product	"connexin 30"	604418	"ectodermal dysplasia 2, hidrotic (Clouston syndrome)", "gap junction protein, beta 6 (connexin 30)", "gap junction protein, beta 6"	DFNA3, ED2		10471490, 8845850	Standard	NM_006783		Approved	EDH, HED, CX30	uc001und.4	O95452	OTTHUMG00000016515	ENST00000356192.6:c.46C>T	chr13.hg19:g.20797574G>A	ENSP00000348521:p.His16Tyr	71.0	0.0		116.0	33.0	NM_001110220	B3KQN2|Q5Q1H9|Q5Q1I0|Q5Q1I1|Q5T5U0|Q8IUP0	Missense_Mutation	SNP	ENST00000356192.6	hg19	CCDS9291.1	.	.	.	.	.	.	.	.	.	.	G	1.233	-0.623550	0.03636	.	.	ENSG00000121742	ENST00000241124;ENST00000400065;ENST00000400066;ENST00000356192	D;D;D;D	0.99143	-5.48;-5.48;-5.48;-5.48	5.38	4.53	0.55603	Connexin, N-terminal (1);	0.129929	0.49916	D	0.000129	D	0.96207	0.8763	L	0.35341	1.055	0.46131	D	0.998889	B	0.22983	0.078	B	0.25614	0.062	D	0.93492	0.6836	10	0.13470	T	0.59	.	9.8206	0.40880	0.1519:0.0:0.8481:0.0	.	16	O95452	CXB6_HUMAN	Y	16	ENSP00000241124:H16Y;ENSP00000382938:H16Y;ENSP00000382939:H16Y;ENSP00000348521:H16Y	ENSP00000241124:H16Y	H	-	1	0	GJB6	19695574	1.000000	0.71417	0.985000	0.45067	0.806000	0.45545	4.163000	0.58183	2.507000	0.84556	0.655000	0.94253	CAC	.	.		0.507	GJB6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272906.1			A	20797574	G	A	20797574	3	1	201	1	0	0	0	0	1	0	0	0	6420	1377	48	3	743	3	GJB6	13	20797574	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10		20797574	94372304	101	29561										
SERPINE3	647174	hgsc.bcm.edu	37	chr13	51936118	51936118	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gtccactatcccctcaaaaaTaagcattctttctagctgtt	4	12	3	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr13:51936118T>C	ENST00000521255.1	+	7	1320	c.1260T>C	c.(1258-1260)aaT>aaC	p.N420N	RP11-24B19.3_ENST00000602636.1_RNA|RP11-24B19.4_ENST00000602881.1_RNA|SERPINE3_ENST00000524365.1_Intron|SERPINE3_ENST00000400389.4_Intron	NM_001101320.1	NP_001094790.1	A8MV23	SERP3_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3	420					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(2)	2						CCCTCAAAAATAAGCATTCTT	0.373																																					p.N420N		Atlas-SNP	.											.	SERPINE3	37	.	0			c.T1260C						.						124	111	115					13																	51936118		1844	4083	5927	SO:0001819	synonymous_variant	647174	exon7			CAAAAATAAGCAT	AX772926	CCDS53870.1	13q14.3	2014-02-18			ENSG00000253309	ENSG00000253309		"Serine (or cysteine) peptidase inhibitors"	24774	protein-coding gene	gene with protein product						24172014	Standard	NM_001101320		Approved		uc001vfh.2	A8MV23	OTTHUMG00000016943	ENST00000521255.1:c.1260T>C	chr13.hg19:g.51936118T>C		142.0	0.0		192.0	9.0	NM_001101320	B1V8P3	Silent	SNP	ENST00000521255.1	hg19	CCDS53870.1																																																																																			.	.		0.373	SERPINE3-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045021.2	NM_001101320		C	51936118	T	C	51936118	2	2	201	1	0	0	0	0	0	0	0	1	14128	1403	49	2		2	SERPINE3	13	51936118	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	31138544	51936118	63233760	102	29562										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23548222	23548222	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cagtatagctggtgctgctgTccctggagactccagggctc	13	12	0	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr14:23548222T>C	ENST00000262710.1	-	7	2315	c.1988A>G	c.(1987-1989)gAc>gGc	p.D663G	ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000457657.1_Missense_Mutation_p.D623G|ACIN1_ENST00000605057.1_Missense_Mutation_p.D605G|ACIN1_ENST00000555053.1_Missense_Mutation_p.D663G	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	663	Ser-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		GGTGCTGCTGTCCCTGGAGAC	0.448																																					p.D663G		Atlas-SNP	.											.	ACIN1	147	.	0			c.A1988G						.						87	81	83					14																	23548222		2203	4300	6503	SO:0001583	missense	22985	exon7			CTGCTGTCCCTGG	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1988A>G	chr14.hg19:g.23548222T>C	ENSP00000262710:p.Asp663Gly	66.0	0.0		94.0	32.0	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.297565	0.81025	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.29655	2.36;1.56;2.36	6.07	6.07	0.98685	.	0.000000	0.43260	D	0.000590	T	0.41351	0.1155	L	0.27053	0.805	0.46774	D	0.999192	D;D;D	0.71674	0.998;0.997;0.997	D;D;D	0.78314	0.991;0.98;0.98	T	0.20907	-1.0261	10	0.38643	T	0.18	-15.3039	13.0325	0.58851	0.0:0.0:0.0:1.0	.	663;663;623	G3V3M7;Q9UKV3;E7EQT4	.;ACINU_HUMAN;.	G	663;623;663	ENSP00000262710:D663G;ENSP00000405677:D623G;ENSP00000451328:D663G	ENSP00000262710:D663G	D	-	2	0	ACIN1	22618062	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.612000	0.54142	2.326000	0.78906	0.533000	0.62120	GAC	.	.		0.448	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23548222	T	C	23548222	3	2	201	1	0	0	0	0	1	0	0	0	142	1667	58	2	2236	2	ACIN1	14	23548222	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10		23548222	83801318	103	29563										
PTGR2	145482	hgsc.bcm.edu	37	chr14	74343770	74343770	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	taggtatgcctggtttgactTccttgattgggatacaggaa	12	6	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr14:74343770T>A	ENST00000555661.1	+	5	563	c.418T>A	c.(418-420)Tcc>Acc	p.S140T	PTGR2_ENST00000553813.1_Missense_Mutation_p.S6T|PTGR2_ENST00000267568.4_Missense_Mutation_p.S140T|RP5-1021I20.4_ENST00000556551.2_Missense_Mutation_p.S140T|PTGR2_ENST00000555228.1_Missense_Mutation_p.S140T			Q8N8N7	PTGR2_HUMAN	prostaglandin reductase 2	140					prostaglandin metabolic process (GO:0006693)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)			NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(2)	9					Indomethacin(DB00328)	TGGTTTGACTTCCTTGATTGG	0.423																																					p.S140T	Esophageal Squamous(98;1155 1417 16452 47043 47872)	Atlas-SNP	.											.	PTGR2	21	.	0			c.T418A						.						140	129	133					14																	74343770		2203	4300	6503	SO:0001583	missense	145482	exon5			TTGACTTCCTTGA	AK096410	CCDS9820.1	14q24.1-q24.2	2008-06-04	2008-06-02	2008-06-03		ENSG00000140043			20149	protein-coding gene	gene with protein product		608642	"zinc binding alcohol dehydrogenase domain containing 1"	ZADH1		17449869	Standard	NM_152444		Approved	FLJ39091	uc001xow.3	Q8N8N7		ENST00000555661.1:c.418T>A	chr14.hg19:g.74343770T>A	ENSP00000452280:p.Ser140Thr	94.0	0.0		133.0	33.0	NM_152444	Q3L8A4|Q6MZH8	Missense_Mutation	SNP	ENST00000555661.1	hg19	CCDS9820.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.946619	0.73672	.	.	ENSG00000140043;ENSG00000140043;ENSG00000140043;ENSG00000140043;ENSG00000258653	ENST00000555228;ENST00000555661;ENST00000267568;ENST00000554885;ENST00000553813	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	5.79	4.61	0.57282	GroES-like (1);	0.098371	0.64402	D	0.000002	T	0.33818	0.0876	L	0.42245	1.32	0.43579	D	0.995917	P	0.35745	0.518	B	0.28991	0.097	T	0.16158	-1.0412	10	0.87932	D	0	-1.504	12.6545	0.56780	0.0:0.0:0.3971:0.6028	.	140	Q8N8N7	PTGR2_HUMAN	T	140;140;140;91;6	ENSP00000450975:S140T;ENSP00000452280:S140T;ENSP00000267568:S140T;ENSP00000451158:S91T;ENSP00000450824:S6T	ENSP00000267568:S140T	S	+	1	0	RP5-1021I20.4;PTGR2	73413523	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.303000	0.51858	0.954000	0.37851	0.477000	0.44152	TCC	.	.		0.423	PTGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412575.1			A	74343770	T	A	74343770	3	1	201	1	0	0	0	0	1	0	0	0	12767	1783	62	4	432	4	PTGR2	14	74343770	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	50795548	74343770	33005770	104	29564										
TTLL5	23093	hgsc.bcm.edu	37	chr14	76135787	76135787	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	catgcatcatgtggactggaGgctgcaggagaattccagtt	13	8	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr14:76135787G>A	ENST00000298832.9	+	3	308	c.103G>A	c.(103-105)Ggc>Agc	p.G35S	TTLL5_ENST00000286650.5_Missense_Mutation_p.G35S|TTLL5_ENST00000557636.1_Missense_Mutation_p.G35S|TTLL5_ENST00000556977.1_Missense_Mutation_p.G35S	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	35					fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		GTGGACTGGAGGCTGCAGGAG	0.418																																					p.G35S		Atlas-SNP	.											.	TTLL5	102	.	0			c.G103A						.						184	178	180					14																	76135787		2203	4300	6503	SO:0001583	missense	23093	exon3			ACTGGAGGCTGCA	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"Tubulin tyrosine ligase-like family"	19963	protein-coding gene	gene with protein product		612268	"KIAA0998"	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.103G>A	chr14.hg19:g.76135787G>A	ENSP00000298832:p.Gly35Ser	77.0	0.0		122.0	11.0	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	hg19	CCDS32124.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.118614	0.77323	.	.	ENSG00000119685	ENST00000557003;ENST00000556977;ENST00000557636;ENST00000286650;ENST00000298832	T;T;T	0.06687	3.89;3.27;3.95	5.39	5.39	0.77823	.	0.109437	0.64402	D	0.000015	T	0.09862	0.0242	L	0.50333	1.59	0.80722	D	1	P;B;P	0.43352	0.488;0.369;0.804	B;B;B	0.37833	0.259;0.132;0.163	T	0.22906	-1.0203	10	0.24483	T	0.36	.	16.0699	0.80919	0.0:0.0:1.0:0.0	.	35;35;35	G3V2J9;Q6EMB2;Q6EMB2-3	.;TTLL5_HUMAN;.	S	35	ENSP00000450713:G35S;ENSP00000286650:G35S;ENSP00000298832:G35S	ENSP00000286650:G35S	G	+	1	0	TTLL5	75205540	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.896000	0.69822	2.520000	0.84964	0.467000	0.42956	GGC	.	.		0.418	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072		A	76135787	G	A	76135787	3	1	201	1	0	0	0	0	1	0	0	0	16745	1000	35	3	109	3	TTLL5	14	76135787	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	1792017	76135787	31213753	105	29565										
TTC7B	145567	hgsc.bcm.edu	37	chr14	91044612	91044612	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gcagcttcttgggtacaggcTgtggcttctgcaggcttccc	13	12	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr14:91044612T>A	ENST00000328459.6	-	19	2269	c.2148A>T	c.(2146-2148)acA>acT	p.T716T	TTC7B_ENST00000554654.1_5'UTR|TTC7B_ENST00000357056.2_Silent_p.T733T	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	716										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				GGGTACAGGCTGTGGCTTCTG	0.597																																					p.T716T		Atlas-SNP	.											.	TTC7B	93	.	0			c.A2148T						.						109	95	100					14																	91044612		2203	4300	6503	SO:0001819	synonymous_variant	145567	exon19			ACAGGCTGTGGCT	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"Tetratricopeptide (TTC) repeat domain containing"	19858	protein-coding gene	gene with protein product			"tetratricopeptide repeat domain 7 like 1"	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.2148A>T	chr14.hg19:g.91044612T>A		94.0	0.0		141.0	48.0	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	hg19	CCDS32140.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.502153	0.26949	.	.	ENSG00000165914	ENST00000557292	.	.	.	5.39	-8.05	0.01106	.	.	.	.	.	T	0.37376	0.1001	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41124	-0.9526	4	.	.	.	-12.7696	4.0022	0.09585	0.0924:0.1835:0.4351:0.2889	.	.	.	.	C	144	.	.	S	-	1	0	TTC7B	90114365	0.143000	0.22626	0.839000	0.33178	0.983000	0.72400	-0.538000	0.06120	-1.791000	0.01261	-1.236000	0.01555	AGC	.	.		0.597	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2			A	91044612	T	A	91044612	2	1	201	1	0	0	0	0	0	0	0	1	16728	1567	55	4		4	TTC7B	14	91044612	Silent	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	14908825	91044612	16304928	106	29566										
INO80	54617	hgsc.bcm.edu	37	chr15	41313274	41313274	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ccttcagaactcgcctttcaTattctgcacttcggtcattg	6	13	4	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr15:41313274T>A	ENST00000361937.3	-	26	3522	c.3098A>T	c.(3097-3099)tAt>tTt	p.Y1033F	RP11-540O11.4_ENST00000558967.1_RNA|INO80_ENST00000401393.3_Missense_Mutation_p.Y1033F			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1033	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TCGCCTTTCATATTCTGCACT	0.488																																					p.Y1033F		Atlas-SNP	.											.	INO80	122	.	0			c.A3098T						.						89	81	84					15																	41313274		2203	4300	6503	SO:0001583	missense	54617	exon26			CTTTCATATTCTG	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.3098A>T	chr15.hg19:g.41313274T>A	ENSP00000355205:p.Tyr1033Phe	57.0	0.0		59.0	18.0	NM_017553	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	hg19	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.566724	0.86439	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.91577	-2.87;-2.87	5.14	5.14	0.70334	.	0.062420	0.64402	D	0.000003	D	0.83519	0.5272	L	0.47190	1.495	0.58432	D	0.999999	P	0.49783	0.928	B	0.32090	0.14	T	0.82896	-0.0230	10	0.15066	T	0.55	.	15.1111	0.72359	0.0:0.0:0.0:1.0	.	1033	Q9ULG1	INO80_HUMAN	F	1033	ENSP00000355205:Y1033F;ENSP00000384686:Y1033F	ENSP00000355205:Y1033F	Y	-	2	0	INO80	39100566	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.047000	0.76599	2.150000	0.67090	0.533000	0.62120	TAT	.	.		0.488	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		A	41313274	T	A	41313274	3	1	201	1	0	0	0	0	1	0	0	0	7755	1406	49	4	1616	4	INO80	15	41313274	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10		41313274	61218118	107	29567										
RPAP1	26015	hgsc.bcm.edu	37	chr15	41812892	41812892	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cggaacagctcactgtccacCaggaacacacacatgagccg	9	15	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr15:41812892C>T	ENST00000304330.4	-	22	3608	c.3492G>A	c.(3490-3492)ctG>ctA	p.L1164L	RPAP1_ENST00000561603.1_Intron	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	1164	Leu-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CACTGTCCACCAGGAACACAC	0.642																																					p.L1164L		Atlas-SNP	.											.	RPAP1	111	.	0			c.G3492A						.						74	76	76					15																	41812892		2203	4300	6503	SO:0001819	synonymous_variant	26015	exon22			GTCCACCAGGAAC	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.3492G>A	chr15.hg19:g.41812892C>T		63.0	0.0		90.0	29.0	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	ENST00000304330.4	hg19	CCDS10079.1																																																																																			.	.		0.642	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		T	41812892	C	T	41812892	2	4	201	1	0	0	0	0	0	0	0	1	13556	581	21	3		3	RPAP1	15	41812892	Silent	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	499618	41812892	60718500	108	29568										
VPS39	23339	hgsc.bcm.edu	37	chr15	42458405	42458405	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agcacccacactgagtaggaGaaaatcaaatgcaggttttc	9	9	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr15:42458405G>C	ENST00000348544.4	-	17	1664	c.1665C>G	c.(1663-1665)ttC>ttG	p.F555L	VPS39_ENST00000318006.5_Missense_Mutation_p.F544L			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	555					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		CTGAGTAGGAGAAAATCAAAT	0.512																																					p.F544L		Atlas-SNP	.											VPS39,NS,carcinoma,0,2	VPS39	53	.	0			c.C1632G						.						102	97	99					15																	42458405		2203	4299	6502	SO:0001583	missense	23339	exon16			GTAGGAGAAAATC	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.1665C>G	chr15.hg19:g.42458405G>C	ENSP00000335193:p.Phe555Leu	119.0	0.0		134.0	45.0	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Missense_Mutation	SNP	ENST00000348544.4	hg19	CCDS10083.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.414770	0.42817	.	.	ENSG00000166887	ENST00000318006;ENST00000348544	T;T	0.38560	1.13;1.14	5.89	2.29	0.28610	Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.21267	0.0512	N	0.05574	-0.02	0.80722	D	1	B;B	0.27286	0.174;0.148	B;B	0.36092	0.217;0.079	T	0.09509	-1.0671	10	0.05620	T	0.96	-13.8211	9.5364	0.39224	0.7295:0.0:0.2705:0.0	.	555;544	Q96JC1;Q96JC1-2	VPS39_HUMAN;.	L	544;555	ENSP00000326534:F544L;ENSP00000335193:F555L	ENSP00000326534:F544L	F	-	3	2	VPS39	40245697	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.104000	0.31074	0.492000	0.27815	-0.302000	0.09304	TTC	.	.		0.512	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		C	42458405	G	C	42458405	3	2	201	1	0	0	0	0	1	0	0	0	17224	933	33	4	1035	4	VPS39	15	42458405	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	645513	42458405	60072987	109	29569										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48055213	48055213	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gtttttaatttttctttcagAgccacactttcttcatgcca	4	10	4	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr15:48055213A>T	ENST00000316364.5	+	9	1098	c.659A>T	c.(658-660)gAg>gTg	p.E220V	SEMA6D_ENST00000389428.3_Splice_Site_p.E220V|SEMA6D_ENST00000358066.4_Splice_Site_p.E220V|SEMA6D_ENST00000389432.2_Splice_Site_p.E220V|SEMA6D_ENST00000389433.2_Splice_Site_p.E220V|SEMA6D_ENST00000355997.3_Splice_Site_p.E220V|SEMA6D_ENST00000558816.1_Splice_Site_p.E220V|SEMA6D_ENST00000558014.1_Splice_Site_p.E220V|SEMA6D_ENST00000354744.4_Splice_Site_p.E220V|SEMA6D_ENST00000389425.3_Splice_Site_p.E220V|SEMA6D_ENST00000536845.2_Splice_Site_p.E220V|SEMA6D_ENST00000537942.1_Splice_Site_p.E220V	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	220	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TTTCTTTCAGAGCCACACTTT	0.358																																					p.E220V		Atlas-SNP	.											.	SEMA6D	322	.	0			c.A659T						.						61	58	59					15																	48055213		2198	4296	6494	SO:0001630	splice_region_variant	80031	exon9			TTTCAGAGCCACA	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.659-1A>T	chr15.hg19:g.48055213A>T		58.0	0.0		47.0	22.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	A	31	5.078560	0.94050	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.26518	1.73;1.73;1.73;1.73;1.73;1.73;1.73;1.73;1.73;1.73	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.60792	0.2296	M	0.91038	3.17	0.80722	D	1	D;D;D;P;D	0.89917	1.0;1.0;1.0;0.688;1.0	D;D;D;P;D	0.97110	0.999;1.0;0.999;0.872;0.999	T	0.70055	-0.4977	9	.	.	.	.	16.1596	0.81693	1.0:0.0:0.0:0.0	.	220;220;220;220;220	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	V	220	ENSP00000442040:E220V;ENSP00000446152:E220V;ENSP00000324857:E220V;ENSP00000374084:E220V;ENSP00000374083:E220V;ENSP00000346786:E220V;ENSP00000350770:E220V;ENSP00000374079:E220V;ENSP00000348276:E220V;ENSP00000374076:E220V	.	E	+	2	0	SEMA6D	45842505	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	8.962000	0.93254	2.216000	0.71823	0.533000	0.62120	GAG	.	.		0.358	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	Missense_Mutation	T	48055213	A	T	48055213	5	4	201	1	0	0	0	0	0	0	1	0	14057	318	11	4	689	4	SEMA6D	15	48055213	Splice_Site	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	5596808	48055213	54476179	110	29570										
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81225646	81225646	+	Frame_Shift_Del	DEL	G	G	-													0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tcaaccagctggacatggatGgggataagacatctgtgttc							TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr15:81225646delG	ENST00000394685.3	+	23	3273	c.2854delG	c.(2854-2856)gggfs	p.G952fs	KIAA1199_ENST00000356249.5_Frame_Shift_Del_p.G952fs|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Frame_Shift_Del_p.G952fs			Q8WUJ3	CEMIP_HUMAN		952					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GGACATGGATGGGGATAAGAC	0.557																																					p.D951fs		Atlas-INDEL	.											.	KIAA1199	118	.	0			c.2853delT						.						121	109	113					15																	81225646		2203	4300	6503	SO:0001589	frameshift_variant	57214	exon22			.																												ENST00000394685.3:c.2854delG	chr15.hg19:g.81225646delG	ENSP00000378177:p.Gly952fs	128.0	0.0		156.0	41.0	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Frame_Shift_Del	DEL	ENST00000394685.3	hg19	CCDS10315.1																																																																																			.	.		0.557	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			-	81225646	G	-	81225646	7	5	201	1	0	1	0	1	0	0	0	0	8222	1348	47	0	2936	0	KIAA1199	15	81225646	Frame_Shift_Del	DEL	G	TCGA-DD-AADS-01A-11D-A40R-10	33170433	81225646	21305746	111	29571										
SLCO3A1	28232	hgsc.bcm.edu	37	chr15	92647605	92647605	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	actcttcttctcttccctctTgatgtttgggtttccacagt	6	12	4	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr15:92647605T>A	ENST00000318445.6	+	4	1056	c.842T>A	c.(841-843)tTg>tAg	p.L281*	SLCO3A1_ENST00000555549.1_3'UTR|SLCO3A1_ENST00000424469.2_Nonsense_Mutation_p.L281*	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	281					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	TCTTCCCTCTTGATGTTTGGG	0.597																																					p.L281X		Atlas-SNP	.											.	SLCO3A1	84	.	0			c.T842A						.						189	160	170					15																	92647605		2198	4298	6496	SO:0001587	stop_gained	28232	exon4			CCCTCTTGATGTT	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"Solute carriers"	10952	protein-coding gene	gene with protein product		612435	"solute carrier family 21 (organic anion transporter), member 11"	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.842T>A	chr15.hg19:g.92647605T>A	ENSP00000320634:p.Leu281*	50.0	0.0		64.0	18.0	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Nonsense_Mutation	SNP	ENST00000318445.6	hg19	CCDS10371.1	.	.	.	.	.	.	.	.	.	.	T	38	6.927826	0.97940	.	.	ENSG00000176463	ENST00000318445;ENST00000424469;ENST00000556649	.	.	.	5.12	3.98	0.46160	.	0.236375	0.35235	N	0.003352	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	5.5318	0.16989	0.0:0.1149:0.1706:0.7146	.	.	.	.	X	281;281;74	.	ENSP00000320634:L281X	L	+	2	0	SLCO3A1	90448609	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.725000	0.54970	0.755000	0.32990	0.533000	0.62120	TTG	.	.		0.597	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272		A	92647605	T	A	92647605	4	1	201	1	0	0	0	0	0	1	0	0	14743	1821	63	4	856	4	SLCO3A1	15	92647605	Nonsense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	11421959	92647605	9883787	112	29572										
AXIN1	8312	hgsc.bcm.edu	37	chr16	347192	347192	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cttccccgactcagccttctTggcatttcttttgcacgcca	6	16	3	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr16:347192T>A	ENST00000262320.3	-	7	2190	c.1819A>T	c.(1819-1821)Aag>Tag	p.K607*	AXIN1_ENST00000354866.3_Nonsense_Mutation_p.K607*|AXIN1_ENST00000481769.1_5'Flank	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	607	Interaction with PPP2CA.|Interaction with RNF111.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				TCAGCCTTCTTGGCATTTCTT	0.622																																					p.K607X		Atlas-SNP	.											.	AXIN1	290	.	0			c.A1819T						.						175	172	173					16																	347192		2203	4300	6503	SO:0001587	stop_gained	8312	exon7			CCTTCTTGGCATT	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1819A>T	chr16.hg19:g.347192T>A	ENSP00000262320:p.Lys607*	14.0	0.0		13.0	6.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Nonsense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	T	38	7.197489	0.98129	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	5.16	5.16	0.70880	.	0.179987	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.082	14.9761	0.71273	0.0:0.0:0.0:1.0	.	.	.	.	X	607	.	ENSP00000262320:K607X	K	-	1	0	AXIN1	287193	1.000000	0.71417	0.921000	0.36526	0.296000	0.27459	4.580000	0.60942	1.959000	0.56917	0.391000	0.25812	AAG	.	.		0.622	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	347192	T	A	347192	4	1	201	1	0	0	0	0	0	1	0	0	1236	1821	63	4	789	4	AXIN1	16	347192	Nonsense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10		347192	90007561	113	29573										
RAB26	25837	hgsc.bcm.edu	37	chr16	2203207	2203207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gcctcaacgtggacttggccTtcacagccatagcaaagtaa	9	12	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr16:2203207T>C	ENST00000210187.6	+	8	812	c.652T>C	c.(652-654)Ttc>Ctc	p.F218L	RAB26_ENST00000541451.1_Missense_Mutation_p.F152L|SNORD60_ENST00000383903.1_RNA|TRAF7_ENST00000326181.6_5'Flank|RP11-304L19.5_ENST00000563192.1_lincRNA	NM_014353.4	NP_055168.2	Q9ULW5	RAB26_HUMAN	RAB26, member RAS oncogene family	218					exocrine system development (GO:0035272)|Golgi to plasma membrane protein transport (GO:0043001)|regulated secretory pathway (GO:0045055)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	Golgi membrane (GO:0000139)|intrinsic component of plasma membrane (GO:0031226)|secretory granule membrane (GO:0030667)	GMP binding (GO:0019002)|GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(3)	5						GGACTTGGCCTTCACAGCCAT	0.607																																					p.F218L		Atlas-SNP	.											.	RAB26	9	.	0			c.T652C						.						60	56	57					16																	2203207		2197	4300	6497	SO:0001583	missense	25837	exon8			TTGGCCTTCACAG	AB027137	CCDS10460.1	16p13.3	2008-07-28			ENSG00000167964	ENSG00000167964		"RAB, member RAS oncogene"	14259	protein-coding gene	gene with protein product		605455				11043516	Standard	NM_014353		Approved		uc002cou.3	Q9ULW5	OTTHUMG00000128829	ENST00000210187.6:c.652T>C	chr16.hg19:g.2203207T>C	ENSP00000210187:p.Phe218Leu	126.0	0.0		141.0	50.0	NM_014353	B2RAA6|Q3L6K5|Q6NXS7	Missense_Mutation	SNP	ENST00000210187.6	hg19	CCDS10460.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.648179	0.87958	.	.	ENSG00000167964	ENST00000541451;ENST00000210187	D;D	0.82526	-1.62;-1.62	4.22	4.22	0.49857	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	D	0.92189	0.7523	M	0.92077	3.27	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.93348	0.6716	10	0.87932	D	0	.	11.2799	0.49188	0.0:0.0:0.0:1.0	.	218	Q9ULW5	RAB26_HUMAN	L	152;218	ENSP00000441580:F152L;ENSP00000210187:F218L	ENSP00000210187:F218L	F	+	1	0	RAB26	2143208	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	7.519000	0.81809	1.775000	0.52247	0.260000	0.18958	TTC	.	.		0.607	RAB26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250767.2			C	2203207	T	C	2203207	3	2	201	1	0	0	0	0	1	0	0	0	12928	1609	56	2	682	2	RAB26	16	2203207	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	1856015	2203207	88151546	114	29574										
USP7	7874	hgsc.bcm.edu	37	chr16	8989502	8989502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gtatcggggacagatacctcTattcgaaacgtccggctcgt	11	11	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr16:8989502T>C	ENST00000344836.4	-	27	3114	c.2916A>G	c.(2914-2916)atA>atG	p.I972M	USP7_ENST00000535863.1_Missense_Mutation_p.I873M|USP7_ENST00000381886.4_Missense_Mutation_p.I956M	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	972					maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						CAGATACCTCTATTCGAAACG	0.408																																					p.I972M		Atlas-SNP	.											.	USP7	116	.	0			c.A2916G						.						75	74	74					16																	8989502		2197	4300	6497	SO:0001583	missense	7874	exon27			TACCTCTATTCGA	Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"Ubiquitin-specific peptidases"	12630	protein-coding gene	gene with protein product		602519	"ubiquitin specific protease 7 (herpes virus-associated)"	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.2916A>G	chr16.hg19:g.8989502T>C	ENSP00000343535:p.Ile972Met	71.0	0.0		92.0	25.0	NM_003470	A6NMY8|B7Z815|H0Y3G8	Missense_Mutation	SNP	ENST00000344836.4	hg19	CCDS32385.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.077420	0.76528	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863	T;T	0.08282	3.11;3.13	5.5	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.24160	0.0585	M	0.66939	2.045	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.64776	0.929;0.929	T	0.00470	-1.1720	10	0.66056	D	0.02	.	12.6896	0.56966	0.0:0.0:0.1379:0.8621	.	972;956	Q93009;B7Z815	UBP7_HUMAN;.	M	972;980;873	ENSP00000343535:I972M;ENSP00000443646:I873M	ENSP00000343535:I972M	I	-	3	3	USP7	8897003	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	5.048000	0.64238	0.904000	0.36572	0.454000	0.30748	ATA	.	.		0.408	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			C	8989502	T	C	8989502	3	2	201	1	0	0	0	0	1	0	0	0	17103	1512	53	2	412	2	USP7	16	8989502	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	6786295	8989502	81365251	115	29575										
MYO1C	4641	hgsc.bcm.edu	37	chr17	1384146	1384146	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cactcgtgacttttccaggaGgtaactgaggatgtggccac	12	10	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr17:1384146G>C	ENST00000575158.1	-	6	732	c.556C>G	c.(556-558)Ctc>Gtc	p.L186V	MYO1C_ENST00000361007.2_Missense_Mutation_p.L186V|MYO1C_ENST00000573198.1_5'UTR|MYO1C_ENST00000545534.2_Missense_Mutation_p.L197V|MYO1C_ENST00000359786.5_Missense_Mutation_p.L221V|MYO1C_ENST00000438665.2_Missense_Mutation_p.L202V			Q12965	MYO1E_HUMAN	myosin IC	193	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TTTTCCAGGAGGTAACTGAGG	0.627																																					p.L221V		Atlas-SNP	.											.	MYO1C	57	.	0			c.C661G						.						89	88	89					17																	1384146		2203	4300	6503	SO:0001583	missense	4641	exon6			CCAGGAGGTAACT	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"Myosins / Myosin superfamily : Class I"	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.556C>G	chr17.hg19:g.1384146G>C	ENSP00000459174:p.Leu186Val	48.0	0.0		71.0	18.0	NM_001080779	Q14778	Missense_Mutation	SNP	ENST00000575158.1	hg19	CCDS11003.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.671955	0.88348	.	.	ENSG00000197879	ENST00000359786;ENST00000438665;ENST00000535856;ENST00000361007;ENST00000545534;ENST00000535421	T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11	4.96	4.96	0.65561	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.92570	0.7640	H	0.98089	4.145	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.72982	0.951;0.979;0.919	D	0.95199	0.8315	10	0.87932	D	0	.	17.366	0.87364	0.0:0.0:1.0:0.0	.	197;221;202	B7Z3E5;O00159;O00159-3	.;MYO1C_HUMAN;.	V	221;202;202;186;197;186	ENSP00000352834:L221V;ENSP00000412197:L202V;ENSP00000354283:L186V;ENSP00000437685:L197V	ENSP00000352834:L221V	L	-	1	0	MYO1C	1330896	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.608000	0.74168	2.575000	0.86900	0.462000	0.41574	CTC	.	.		0.627	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2			C	1384146	G	C	1384146	3	2	201	1	0	0	0	0	1	0	0	0	10079	1000	35	4	2638	4	MYO1C	17	1384146	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10		1384146	79811064	116	29576										
MYH13	8735	hgsc.bcm.edu	37	chr17	10216060	10216060	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cctctgcttcctggagcctcTgggccagttttttcctacga	9	14	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr17:10216060T>A	ENST00000418404.3	-	30	4359	c.4196A>T	c.(4195-4197)cAg>cTg	p.Q1399L	RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Missense_Mutation_p.Q1399L			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1399					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CTGGAGCCTCTGGGCCAGTTT	0.493																																					p.Q1399L		Atlas-SNP	.											.	MYH13	533	.	0			c.A4196T						.						39	41	40					17																	10216060		2128	4267	6395	SO:0001583	missense	8735	exon31			AGCCTCTGGGCCA	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.4196A>T	chr17.hg19:g.10216060T>A	ENSP00000404570:p.Gln1399Leu	56.0	0.0		99.0	28.0	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	hg19	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.963096	0.53507	.	.	ENSG00000006788	ENST00000252172	T	0.78924	-1.22	3.96	3.96	0.45880	Myosin tail (1);	.	.	.	.	T	0.73094	0.3543	M	0.62154	1.92	0.36937	D	0.892184	B	0.06786	0.001	B	0.17979	0.02	T	0.71111	-0.4687	9	0.18276	T	0.48	.	13.3004	0.60321	0.0:0.0:0.0:1.0	.	1399	Q9UKX3	MYH13_HUMAN	L	1399	ENSP00000252172:Q1399L	ENSP00000252172:Q1399L	Q	-	2	0	MYH13	10156785	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.023000	0.70848	1.792000	0.52537	0.379000	0.24179	CAG	.	.		0.493	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		A	10216060	T	A	10216060	3	1	201	1	0	0	0	0	1	0	0	0	10041	1580	55	4	1664	4	MYH13	17	10216060	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	8831914	10216060	70979150	117	29577										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27448104	27448104	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gtggtcttgccactgccactActgcccaggaggatgattga	12	11	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr17:27448104A>G	ENST00000527372.1	-	6	1677	c.1497T>C	c.(1495-1497)agT>agC	p.S499S	MYO18A_ENST00000354329.4_Silent_p.S499S|MYO18A_ENST00000531253.1_Silent_p.S499S|MYO18A_ENST00000533112.1_Silent_p.S499S	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	499	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CACTGCCACTACTGCCCAGGA	0.607																																					p.S499S	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.T1497C						.						48	50	49					17																	27448104		2123	4243	6366	SO:0001819	synonymous_variant	399687	exon6			GCCACTACTGCCC	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.1497T>C	chr17.hg19:g.27448104A>G		56.0	0.0		62.0	22.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	hg19	CCDS45642.1																																																																																			.	.		0.607	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		G	27448104	A	G	27448104	2	3	201	1	0	0	0	0	0	0	0	1	10074	388	14	2		2	MYO18A	17	27448104	Silent	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	17232044	27448104	53747106	118	29578										
ACCN1	40	hgsc.bcm.edu	37	chr17	31618817	31618817	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tgagccagtagagcaagcggTtcgaggaccaggacagcagc	15	10	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr17:31618817T>C	ENST00000359872.6	-	2	1317				ASIC2_ENST00000448983.1_5'Flank|ASIC2_ENST00000225823.2_Missense_Mutation_p.N106S	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2						central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	GAGCAAGCGGTTCGAGGACCA	0.667																																					p.N106S		Atlas-SNP	.											.	.	.	.	0			c.A317G						.						36	36	36					17																	31618817		2203	4297	6500	SO:0001627	intron_variant	40	exon1			AAGCGGTTCGAGG	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.556-179732A>G	chr17.hg19:g.31618817T>C		39.0	0.0		78.0	23.0	NM_183377	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Missense_Mutation	SNP	ENST00000359872.6	hg19	CCDS42296.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.534177	0.27475	.	.	ENSG00000108684	ENST00000225823	T	0.62639	0.01	4.73	4.73	0.59995	.	0.461095	0.23722	N	0.045219	T	0.48447	0.1500	L	0.39085	1.19	0.80722	D	1	B	0.09022	0.002	B	0.11329	0.006	T	0.38478	-0.9659	10	0.09590	T	0.72	-27.1555	12.1572	0.54083	0.0:0.0:0.0:1.0	.	106	E9PBX2	.	S	106	ENSP00000225823:N106S	ENSP00000225823:N106S	N	-	2	0	ACCN1	28642930	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	4.905000	0.63286	1.744000	0.51775	0.260000	0.18958	AAC	.	.		0.667	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		C	31618817	T	C	31618817	1	2	201	0	1	0	0	0	0	0	0	0	128	1725	60	2		2	ACCN1	17	31618817	Intron	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	4170713	31618817	49576393	119	29579										
KRT32	3882	hgsc.bcm.edu	37	chr17	39623382	39623382	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ctggcaggaactggatagatAggttttggagaggcagctgg	17	5	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr17:39623382A>T	ENST00000225899.3	-	1	299	c.196T>A	c.(196-198)Tat>Aat	p.Y66N	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	66	Head.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				CTGGATAGATAGGTTTTGGAG	0.627																																					p.Y66N		Atlas-SNP	.											.	KRT32	57	.	0			c.T196A						.						36	40	39					17																	39623382		2203	4300	6503	SO:0001583	missense	3882	exon1			ATAGATAGGTTTT	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"-", "Intermediate filaments type I, keratins (acidic)"	6449	protein-coding gene	gene with protein product	"hard keratin type I"	602760	"keratin, hair, acidic, 2"	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.196T>A	chr17.hg19:g.39623382A>T	ENSP00000225899:p.Tyr66Asn	83.0	0.0		124.0	52.0	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	hg19	CCDS11393.1	.	.	.	.	.	.	.	.	.	.	A	6.574	0.474274	0.12521	.	.	ENSG00000108759	ENST00000225899	D	0.88975	-2.45	5.26	1.73	0.24493	.	0.223489	0.22850	N	0.054868	D	0.83917	0.5358	M	0.64404	1.975	0.27161	N	0.961166	B	0.26400	0.148	B	0.22601	0.04	T	0.70400	-0.4882	10	0.28530	T	0.3	.	7.8978	0.29717	0.7555:0.0:0.2445:0.0	.	66	Q14532	K1H2_HUMAN	N	66	ENSP00000225899:Y66N	ENSP00000225899:Y66N	Y	-	1	0	KRT32	36876908	0.119000	0.22226	0.180000	0.23079	0.178000	0.23041	1.687000	0.37680	0.064000	0.16427	0.460000	0.39030	TAT	.	.		0.627	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278		T	39623382	A	T	39623382	3	4	201	1	0	0	0	0	1	0	0	0	8477	420	15	4	1178	4	KRT32	17	39623382	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	8004565	39623382	41571828	120	29580										
KRT15	3866	hgsc.bcm.edu	37	chr17	39670928	39670928	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gatggcaatgccagccatccTgaaagaaagagggaagctga	13	8	0	4			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr17:39670928T>A	ENST00000254043.3	-	7	4833		c.e7-2		KRT15_ENST00000393974.3_Splice_Site|KRT15_ENST00000393981.3_3'UTR|KRT15_ENST00000393976.2_Splice_Site	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15						epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				CCAGCCATCCTGAAAGAAAGA	0.517																																					.		Atlas-SNP	.											.	KRT15	60	.	0			c.1248-2A>T						.						84	67	73					17																	39670928		2203	4300	6503	SO:0001630	splice_region_variant	3866	exon8			CCATCCTGAAAGA		CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"-", "Intermediate filaments type I, keratins (acidic)"	6421	protein-coding gene	gene with protein product	"keratin-15, basic", "keratin-15, beta", "type I cytoskeletal 15", "cytokeratin 15"	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.1248-2A>T	chr17.hg19:g.39670928T>A		94.0	0.0		98.0	34.0	NM_002275	B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	Splice_Site	SNP	ENST00000254043.3	hg19	CCDS11398.1	.	.	.	.	.	.	.	.	.	.	T	12.18	1.860716	0.32884	.	.	ENSG00000171346	ENST00000254043;ENST00000393974;ENST00000393976	.	.	.	4.22	4.22	0.49857	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0071	0.41964	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KRT15	36924454	1.000000	0.71417	1.000000	0.80357	0.425000	0.31504	3.093000	0.50217	2.119000	0.64992	0.528000	0.53228	.	.	.		0.517	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1	NM_002275	Intron	A	39670928	T	A	39670928	5	1	201	1	0	0	0	0	0	0	1	0	8461	1594	55	4	132	4	KRT15	17	39670928	Splice_Site	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	47546	39670928	41524282	121	29581										
SPATA20	64847	hgsc.bcm.edu	37	chr17	48627450	48627450	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ccctgaaaatgatggctaacGggggcatccgggaccatgtg	14	10	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr17:48627450G>A	ENST00000356488.4	+	7	1002	c.919G>A	c.(919-921)Ggg>Agg	p.G307R	SPATA20_ENST00000006658.6_Missense_Mutation_p.G323R|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000393244.3_Missense_Mutation_p.G263R	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	307					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)	p.G323W(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			GATGGCTAACGGGGGCATCCG	0.642																																					p.G323R		Atlas-SNP	.											.	SPATA20	59	.	1	Substitution - Missense(1)	lung(1)	c.G967A						.						111	121	118					17																	48627450		2203	4300	6503	SO:0001583	missense	64847	exon8			GCTAACGGGGGCA		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.919G>A	chr17.hg19:g.48627450G>A	ENSP00000348878:p.Gly307Arg	42.0	0.0		52.0	20.0	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	hg19	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	G	31	5.083012	0.94050	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.32272	1.46;1.46;1.46	5.53	5.53	0.82687	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.000000	0.85682	D	0.000000	T	0.67363	0.2885	M	0.92738	3.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.75838	-0.3176	10	0.87932	D	0	-7.5395	19.4936	0.95062	0.0:0.0:1.0:0.0	.	333;307;323	B4DZC5;Q8TB22;Q8TB22-2	.;SPT20_HUMAN;.	R	323;307;263	ENSP00000006658:G323R;ENSP00000348878:G307R;ENSP00000376935:G263R	ENSP00000006658:G323R	G	+	1	0	SPATA20	45982449	1.000000	0.71417	0.967000	0.41034	0.983000	0.72400	9.869000	0.99810	2.605000	0.88082	0.655000	0.94253	GGG	.	.		0.642	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48627450	G	A	48627450	3	1	201	1	0	0	0	0	1	0	0	0	15021	1116	39	1	997	1	SPATA20	17	48627450	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	8956522	48627450	32567760	122	29582										
SDK2	54549	hgsc.bcm.edu	37	chr17	71429982	71429982	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gcctctggtgatgttaggggCgatgcctgcaaacagagaag	15	8	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr17:71429982C>T	ENST00000392650.3	-	10	1201	c.1201G>A	c.(1201-1203)Gcc>Acc	p.A401T	SDK2_ENST00000388726.3_Missense_Mutation_p.A401T	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	401					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						ATGTTAGGGGCGATGCCTGCA	0.647																																					p.A401T		Atlas-SNP	.											.	SDK2	219	.	0			c.G1201A						.						43	34	37					17																	71429982		2203	4300	6503	SO:0001583	missense	54549	exon10			TAGGGGCGATGCC	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.1201G>A	chr17.hg19:g.71429982C>T	ENSP00000376421:p.Ala401Thr	72.0	0.0		90.0	25.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.3|22.3	4.265838|4.265838	0.80358|0.80358	.|.	.|.	ENSG00000069188|ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000316893|ENST00000416616	D;D|.	0.96427|.	-4.01;-4.01|.	4.8|4.8	4.8|4.8	0.61643|0.61643	Immunoglobulin-like fold (1);|.	0.195205|.	0.43747|.	D|.	0.000521|.	T|T	0.74989|0.74989	0.3789|0.3789	M|M	0.71920|0.71920	2.185|2.185	0.80722|0.80722	D|D	1|1	P;P|.	0.45396|.	0.857;0.776|.	B;B|.	0.42462|.	0.388;0.217|.	T|T	0.75311|0.75311	-0.3362|-0.3362	10|5	0.72032|.	D|.	0.01|.	.|.	17.8294|17.8294	0.88676|0.88676	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	401;401|.	Q58EX2-2;Q58EX2|.	.;SDK2_HUMAN|.	T|H	25;401;401;401|305	ENSP00000376421:A401T;ENSP00000373378:A401T|.	ENSP00000324967:A401T|.	A|R	-|-	1|2	0|0	SDK2|SDK2	68941577|68941577	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.939000|0.939000	0.58152|0.58152	6.685000|6.685000	0.74543|0.74543	2.375000|2.375000	0.81037|0.81037	0.462000|0.462000	0.41574|0.41574	GCC|CGC	.	.		0.647	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		T	71429982	C	T	71429982	3	4	201	1	0	0	0	0	1	0	0	0	13984	768	27	1	5461	1	SDK2	17	71429982	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	22802532	71429982	9765228	123	29583										
COLEC12	81035	hgsc.bcm.edu	37	chr18	335067	335067	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gagcctttagatcctttgccGccacgctctccggggggacc	12	15	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr18:335067G>A	ENST00000400256.3	-	6	1698	c.1491C>T	c.(1489-1491)ggC>ggT	p.G497G		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	497	Collagen-like 2.				carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				ATCCTTTGCCGCCACGCTCTC	0.692																																					p.G497G		Atlas-SNP	.											.	COLEC12	121	.	0			c.C1491T						.						27	30	29					18																	335067		2186	4263	6449	SO:0001819	synonymous_variant	81035	exon6			TTTGCCGCCACGC	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"Collectins"	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.1491C>T	chr18.hg19:g.335067G>A		53.0	0.0		71.0	32.0	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Silent	SNP	ENST00000400256.3	hg19	CCDS32782.1																																																																																			.	.		0.692	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			A	335067	G	A	335067	2	1	201	1	0	0	0	0	0	0	0	1	3714	1074	38	1		1	COLEC12	18	335067	Silent	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10		335067	77742181	124	29584										
COLEC12	81035	hgsc.bcm.edu	37	chr18	346985	346985	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gaggttcctctgctgcacctGggtcaggttcaggttgttga	14	9	3	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr18:346985G>T	ENST00000400256.3	-	5	844	c.637C>A	c.(637-639)Cag>Aag	p.Q213K		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	213					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				TGCTGCACCTGGGTCAGGTTC	0.493																																					p.Q213K		Atlas-SNP	.											.	COLEC12	121	.	0			c.C637A						.						117	117	117					18																	346985		2203	4300	6503	SO:0001583	missense	81035	exon5			GCACCTGGGTCAG	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"Collectins"	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.637C>A	chr18.hg19:g.346985G>T	ENSP00000383115:p.Gln213Lys	48.0	0.0		76.0	26.0	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000400256.3	hg19	CCDS32782.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.476247	0.63737	.	.	ENSG00000158270	ENST00000400256	D	0.97161	-4.27	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.96833	0.8966	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	D	0.92617	0.6104	10	0.02654	T	1	-14.6472	20.6634	0.99662	0.0:0.0:1.0:0.0	.	213	Q5KU26	COL12_HUMAN	K	213	ENSP00000383115:Q213K	ENSP00000383115:Q213K	Q	-	1	0	COLEC12	336985	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.414000	0.97362	2.894000	0.99253	0.655000	0.94253	CAG	.	.		0.493	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			T	346985	G	T	346985	3	4	201	1	0	0	0	0	1	0	0	0	3714	1357	47	3	1615	3	COLEC12	18	346985	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	11918	346985	77730263	125	29585										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9255216	9255216	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ataaagaaggtaaaacattaAaaaaacataaattgaagcat	5	3	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr18:9255216A>G	ENST00000262126.4	+	9	2191	c.1951A>G	c.(1951-1953)Aaa>Gaa	p.K651E	ANKRD12_ENST00000400020.3_Missense_Mutation_p.K628E|ANKRD12_ENST00000383440.2_Missense_Mutation_p.K628E	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	651						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						taaaacattaaaaaaacataa	0.279																																					p.K651E		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A1951G						.						33	37	36					18																	9255216		2192	4281	6473	SO:0001583	missense	23253	exon9			ACATTAAAAAAAC	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.1951A>G	chr18.hg19:g.9255216A>G	ENSP00000262126:p.Lys651Glu	264.0	0.0		397.0	125.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.190666	0.58017	.	.	ENSG00000101745	ENST00000383440;ENST00000262126;ENST00000359158	D;D	0.92397	-3.03;-3.03	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.94771	0.8312	M	0.78637	2.42	0.58432	D	0.999999	P;P;P	0.51537	0.946;0.946;0.911	P;P;B	0.55667	0.781;0.636;0.432	D	0.95405	0.8493	10	0.87932	D	0	-0.7563	15.4212	0.75011	1.0:0.0:0.0:0.0	.	278;628;651	Q9NXU3;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	E	628;651;358	ENSP00000372932:K628E;ENSP00000262126:K651E	ENSP00000262126:K651E	K	+	1	0	ANKRD12	9245216	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.910000	0.92685	2.110000	0.64415	0.377000	0.23210	AAA	.	.		0.279	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		G	9255216	A	G	9255216	3	3	201	1	0	0	0	0	1	0	0	0	640	15	1	2	1981	2	ANKRD12	18	9255216	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	8908231	9255216	68822032	126	29586										
MOCOS	55034	hgsc.bcm.edu	37	chr18	33846710	33846710	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tgttttccttctcacctgccAggttttggggccttgtcaca	9	12	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr18:33846710A>T	ENST00000261326.5	+	14	2430		c.e14-1		MOCOS_ENST00000588132.1_Splice_Site	NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CTCACCTGCCAGGTTTTGGGG	0.498																																					.		Atlas-SNP	.											.	MOCOS	84	.	0			c.2410-2A>T						.						87	77	80					18																	33846710		2203	4300	6503	SO:0001630	splice_region_variant	55034	exon14			CCTGCCAGGTTTT	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.2410-1A>T	chr18.hg19:g.33846710A>T		62.0	0.0		91.0	4.0	NM_017947		Splice_Site	SNP	ENST00000261326.5	hg19	CCDS11919.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.857716	0.71834	.	.	ENSG00000075643	ENST00000261326	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6765	0.56897	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MOCOS	32100708	1.000000	0.71417	0.994000	0.49952	0.788000	0.44548	5.511000	0.67024	2.242000	0.73789	0.528000	0.53228	.	.	.		0.498	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1		Intron	T	33846710	A	T	33846710	5	4	201	1	0	0	0	0	0	0	1	0	9698	202	7	4	2462	4	MOCOS	18	33846710	Splice_Site	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	24591494	33846710	44230538	127	29587										
HAUS1	115106	hgsc.bcm.edu	37	chr18	43703316	43703316	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ctctgtctcatcagtccttaGtagcactatcagaggtgagc	9	11	4	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr18:43703316G>T	ENST00000282058.6	+	6	732	c.652G>T	c.(652-654)Gta>Tta	p.V218L	HAUS1_ENST00000588704.1_3'UTR|HAUS1_ENST00000585518.1_Missense_Mutation_p.S86I|RNU6-1278P_ENST00000516130.1_RNA	NM_138443.3	NP_612452.1	Q96CS2	HAUS1_HUMAN	HAUS augmin-like complex, subunit 1	218					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7						TCAGTCCTTAGTAGCACTATC	0.333																																					p.V218L	NSCLC(79;183 1423 5813 15597 38427)	Atlas-SNP	.											.	HAUS1	22	.	0			c.G652T						.						101	108	106					18																	43703316		2203	4300	6503	SO:0001583	missense	115106	exon6			TCCTTAGTAGCAC	AY360137	CCDS11928.1	18q21.1	2013-10-11	2009-04-20	2009-04-20	ENSG00000152240	ENSG00000152240		"HAUS augmin-like complex subunits"	25174	protein-coding gene	gene with protein product		608775	"coiled-coil domain containing 5 (spindle associated)"	CCDC5		19427217	Standard	NR_026978		Approved	HEI-C, HsT1461, FLJ40084	uc002lbu.3	Q96CS2	OTTHUMG00000132638	ENST00000282058.6:c.652G>T	chr18.hg19:g.43703316G>T	ENSP00000282058:p.Val218Leu	242.0	0.0		320.0	86.0	NM_138443	B2RDM7|Q8N837	Missense_Mutation	SNP	ENST00000282058.6	hg19	CCDS11928.1	.	.	.	.	.	.	.	.	.	.	G	4.461	0.085435	0.08583	.	.	ENSG00000152240	ENST00000282058	.	.	.	5.28	0.983	0.19767	.	0.424643	0.25352	N	0.031289	T	0.25644	0.0624	L	0.31420	0.93	0.09310	N	1	B	0.12630	0.006	B	0.13407	0.009	T	0.20338	-1.0278	9	0.16420	T	0.52	-0.6034	9.0297	0.36252	0.0:0.2588:0.477:0.2643	.	218	Q96CS2	HAUS1_HUMAN	L	218	.	ENSP00000282058:V218L	V	+	1	0	HAUS1	41957314	0.999000	0.42202	0.023000	0.16930	0.286000	0.27126	1.331000	0.33793	0.258000	0.21686	0.563000	0.77884	GTA	.	.		0.333	HAUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255885.1	NM_138443		T	43703316	G	T	43703316	3	4	201	1	0	0	0	0	1	0	0	0	6974	1029	36	3	674	3	HAUS1	18	43703316	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	9856606	43703316	34373932	128	29588										
HMSD	284293	hgsc.bcm.edu	37	chr18	61627540	61627540	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	attgttattctatttcgataAtattttaaacagttttatag	4	3	1	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr18:61627540A>G	ENST00000408945.3	+	4	573	c.371A>G	c.(370-372)aAt>aGt	p.N124S	HMSD_ENST00000481726.1_Intron	NM_001123366.1	NP_001116838.1	A8MTL9	HMSD_HUMAN	histocompatibility (minor) serpin domain containing	124						extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(2)|lung(2)|stomach(1)	6						TATTTCGATAATATTTTAAAC	0.294																																					p.N124S		Atlas-SNP	.											.	HMSD	16	.	0			c.A371G						.						40	38	38					18																	61627540		1567	3580	5147	SO:0001583	missense	284293	exon4			TCGATAATATTTT	AC009802	CCDS42441.1	18q21.33	2008-02-04			ENSG00000221887	ENSG00000221887			23037	protein-coding gene	gene with protein product		612086		C18orf53		17409267	Standard	NM_001123366		Approved	ACC-6	uc010dqj.3	A8MTL9	OTTHUMG00000060593	ENST00000408945.3:c.371A>G	chr18.hg19:g.61627540A>G	ENSP00000386207:p.Asn124Ser	105.0	0.0		158.0	75.0	NM_001123366		Missense_Mutation	SNP	ENST00000408945.3	hg19	CCDS42441.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.150598	0.00328	.	.	ENSG00000221887	ENST00000408945	T	0.80304	-1.36	1.57	0.297	0.15762	.	.	.	.	.	T	0.52386	0.1731	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.42481	-0.9449	9	0.02654	T	1	.	3.3694	0.07215	0.7507:0.0:0.2493:0.0	.	124	A8MTL9	HMSD_HUMAN	S	124	ENSP00000386207:N124S	ENSP00000386207:N124S	N	+	2	0	HMSD	59778520	0.001000	0.12720	0.004000	0.12327	0.008000	0.06430	-0.130000	0.10498	-0.077000	0.12752	0.260000	0.18958	AAT	.	.		0.294	HMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134010.2	XM_209104		G	61627540	A	G	61627540	3	3	201	1	0	0	0	0	1	0	0	0	7255	101	4	2	381	2	HMSD	18	61627540	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	17924224	61627540	16449708	129	29589										
BRD4	23476	hgsc.bcm.edu	37	chr19	15355195	15355195	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gacgctgcctgggagctgggGctccaggacgggcacctggg	19	12	0	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr19:15355195G>A	ENST00000263377.2	-	13	2649	c.2428C>T	c.(2428-2430)Ccc>Tcc	p.P810S		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	810					cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			GGGAGCTGGGGCTCCAGGACG	0.721			T	C15orf55	lethal midline carcinoma of young people																																p.P810S		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.C2428T						.						13	17	16					19																	15355195		2193	4295	6488	SO:0001583	missense	23476	exon13			GCTGGGGCTCCAG	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.2428C>T	chr19.hg19:g.15355195G>A	ENSP00000263377:p.Pro810Ser	56.0	0.0		75.0	28.0	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	hg19	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.753235	0.31046	.	.	ENSG00000141867	ENST00000263377	T	0.28069	1.63	4.43	4.43	0.53597	.	0.111296	0.39687	N	0.001286	T	0.16981	0.0408	N	0.08118	0	0.80722	D	1	B	0.17038	0.02	B	0.17433	0.018	T	0.06445	-1.0826	10	0.26408	T	0.33	-12.9085	13.977	0.64279	0.0:0.0:1.0:0.0	.	810	O60885	BRD4_HUMAN	S	810	ENSP00000263377:P810S	ENSP00000263377:P810S	P	-	1	0	BRD4	15216195	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.677000	0.46892	2.020000	0.59435	0.561000	0.74099	CCC	.	.		0.721	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		A	15355195	G	A	15355195	3	1	201	1	0	0	0	0	1	0	0	0	1506	1203	42	3	1692	3	BRD4	19	15355195	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10		15355195	43773788	130	29590										
ZNF506	440515	hgsc.bcm.edu	37	chr19	19905366	19905366	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tctctccagtatgaattatcTtatgcttattaagggttgag	8	6	2	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr19:19905366T>C	ENST00000540806.2	-	4	1418	c.1330A>G	c.(1330-1332)Aga>Gga	p.R444G	CTC-559E9.6_ENST00000591884.1_RNA|CTC-559E9.6_ENST00000589657.1_RNA|ZNF506_ENST00000450683.2_Missense_Mutation_p.R412G|ZNF506_ENST00000587461.1_Intron|CTC-559E9.4_ENST00000590274.1_lincRNA|ZNF506_ENST00000443905.2_Missense_Mutation_p.R444G			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						ATGAATTATCTTATGCTTATT	0.338																																					p.R444G		Atlas-SNP	.											.	ZNF506	36	.	0			c.A1330G						.						57	62	60					19																	19905366		2089	4248	6337	SO:0001583	missense	440515	exon4			ATTATCTTATGCT	AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"Zinc fingers, C2H2-type", "-"	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.1330A>G	chr19.hg19:g.19905366T>C	ENSP00000440625:p.Arg444Gly	80.0	0.0		87.0	25.0	NM_001099269	B3KTH6	Missense_Mutation	SNP	ENST00000540806.2	hg19	CCDS42531.1	.	.	.	.	.	.	.	.	.	.	t	9.845	1.192068	0.21954	.	.	ENSG00000081665	ENST00000443905;ENST00000540806;ENST00000450683	T;T;T	0.06371	3.38;3.38;3.31	1.01	1.01	0.19927	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.22531	N	0.999018	B;P	0.44344	0.198;0.833	B;B	0.32022	0.007;0.139	T	0.43637	-0.9379	9	0.87932	D	0	.	5.7935	0.18373	0.0:0.0:0.0:1.0	.	444;412	Q5JVG8;Q5JVG8-2	ZN506_HUMAN;.	G	444;444;412	ENSP00000393835:R444G;ENSP00000440625:R444G;ENSP00000408892:R412G	ENSP00000393835:R444G	R	-	1	2	ZNF506	19766366	0.000000	0.05858	0.269000	0.24586	0.236000	0.25371	-0.621000	0.05559	0.363000	0.24346	0.352000	0.21897	AGA	.	.		0.338	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218		C	19905366	T	C	19905366	3	2	201	1	0	0	0	0	1	0	0	0	17967	1617	56	2	8	2	ZNF506	19	19905366	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	4550171	19905366	39223617	131	29591										
ZNF714	148206	hgsc.bcm.edu	37	chr19	21300669	21300669	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gaaaccttacaaatgtgaagAatgtggcaaagcttttaacc	8	7	0	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr19:21300669A>T	ENST00000596143.1	+	5	1524	c.1199A>T	c.(1198-1200)gAa>gTa	p.E400V	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	400					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AAATGTGAAGAATGTGGCAAA	0.353																																					p.E400V		Atlas-SNP	.											.	ZNF714	121	.	0			c.A1199T						.						36	39	38					19																	21300669		2154	4272	6426	SO:0001583	missense	148206	exon5			GTGAAGAATGTGG	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"Zinc fingers, C2H2-type"	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.1199A>T	chr19.hg19:g.21300669A>T	ENSP00000472368:p.Glu400Val	48.0	0.0		58.0	16.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	6.544	0.468560	0.12461	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	1.05	1.05	0.20165	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32346	0.0826	N	0.10618	0.005	0.09310	N	1	B;D;B	0.55800	0.144;0.973;0.073	B;D;B	0.62955	0.206;0.909;0.089	T	0.16012	-1.0417	8	0.59425	D	0.04	.	7.01	0.24857	1.0:0.0:0.0:0.0	.	401;400;401	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	V	400	.	ENSP00000291770:E400V	E	+	2	0	ZNF714	21092509	0.012000	0.17670	0.802000	0.32245	0.779000	0.44077	1.171000	0.31896	0.389000	0.25086	0.379000	0.24179	GAA	.	.		0.353	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515		T	21300669	A	T	21300669	3	4	201	1	0	0	0	0	1	0	0	0	18133	246	9	4	1209	4	ZNF714	19	21300669	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	1395303	21300669	37828314	132	29592										
CEACAM16	388551	hgsc.bcm.edu	37	chr19	45209000	45209000	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	agtatgtgtggaccttcaacGggcaggccctaaagaacggc	13	10	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr19:45209000G>C	ENST00000405314.2	+	4	899	c.802G>C	c.(802-804)Ggg>Cgg	p.G268R	CTB-171A8.1_ENST00000590796.1_RNA|CEACAM16_ENST00000587331.1_Missense_Mutation_p.G268R			Q2WEN9	CEA16_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 16	268	Ig-like C2-type 2.				sensory perception of sound (GO:0007605)	extracellular region (GO:0005576)|stereocilium bundle tip (GO:0032426)				endometrium(3)|large_intestine(2)|lung(3)|ovary(1)	9	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)				GACCTTCAACGGGCAGGCCCT	0.582																																					p.G268R		Atlas-SNP	.											.	CEACAM16	56	.	0			c.G802C						.						91	101	98					19																	45209000		2122	4240	6362	SO:0001583	missense	388551	exon5			TTCAACGGGCAGG		CCDS54278.1	19q13.31	2014-01-27			ENSG00000213892	ENSG00000213892		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31948	protein-coding gene	gene with protein product		614591				21368133	Standard	NM_001039213		Approved	DFNA4B	uc010xxd.2	Q2WEN9	OTTHUMG00000151519	ENST00000405314.2:c.802G>C	chr19.hg19:g.45209000G>C	ENSP00000385576:p.Gly268Arg	119.0	0.0		171.0	57.0	NM_001039213	A7LI12	Missense_Mutation	SNP	ENST00000405314.2	hg19	CCDS54278.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.061686	0.76187	.	.	ENSG00000213892	ENST00000396750;ENST00000405314	T	0.55588	0.51	5.21	5.21	0.72293	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.31760	U	0.007107	T	0.74053	0.3666	M	0.83312	2.635	0.37763	D	0.926391	D	0.89917	1.0	D	0.85130	0.997	T	0.80677	-0.1276	10	0.87932	D	0	-33.0405	14.3179	0.66465	0.0:0.0:1.0:0.0	.	327	Q2WEN9	CEA16_HUMAN	R	333;268	ENSP00000385576:G268R	ENSP00000379974:G333R	G	+	1	0	CEACAM16	49900840	1.000000	0.71417	0.997000	0.53966	0.900000	0.52787	4.752000	0.62176	2.436000	0.82500	0.555000	0.69702	GGG	.	.		0.582	CEACAM16-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		XM_371177		C	45209000	G	C	45209000	3	2	201	1	0	0	0	0	1	0	0	0	3190	1116	39	4	816	4	CEACAM16	19	45209000	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	23908331	45209000	13919983	133	29593										
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305519	48305519	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ctgggattgggcctgggatcAggcctgggttcgggcctgag	19	9	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr19:48305519A>G	ENST00000322175.3	-	2	904	c.749T>C	c.(748-750)cTg>cCg	p.L250P	TPRX1_ENST00000543508.1_Missense_Mutation_p.L240P|TPRX1_ENST00000535759.1_Missense_Mutation_p.L347P	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	250	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		gcctgggatcaggcctgggtt	0.672																																					p.L250P	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.T749C						.																																			SO:0001583	missense	284355	exon2			GGGATCAGGCCTG		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"Homeoboxes / PRD class"	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.749T>C	chr19.hg19:g.48305519A>G	ENSP00000323455:p.Leu250Pro	54.0	0.0		93.0	7.0	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	hg19	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	a	0.003	-2.494356	0.00159	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	D;D	0.91237	-1.66;-2.81	0.557	-1.11	0.09840	.	.	.	.	.	T	0.69815	0.3153	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49551	-0.8928	8	0.08179	T	0.78	.	.	.	.	.	250	Q8N7U7	TPRX1_HUMAN	P	250;347;240	ENSP00000323455:L250P;ENSP00000438832:L347P	ENSP00000323455:L250P	L	-	2	0	TPRX1	52997331	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.179000	0.00569	-3.493000	0.00153	-3.917000	0.00016	CTG	.	.		0.672	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		G	48305519	A	G	48305519	3	3	201	1	0	0	0	0	1	0	0	0	16437	188	7	2	490	2	TPRX1	19	48305519	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	3096519	48305519	10823464	134	29594										
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305570	48305570	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ggatcgggcctgggttcgggCctgagattgggcctgggatt	19	8	0	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr19:48305570C>A	ENST00000322175.3	-	2	853	c.698G>T	c.(697-699)gGc>gTc	p.G233V	TPRX1_ENST00000543508.1_Missense_Mutation_p.G223V|TPRX1_ENST00000535759.1_Missense_Mutation_p.G330V	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	233	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		tgggttcgggcctgagattgg	0.652																																					p.G233V	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.G698T						.						10	8	9					19																	48305570		2038	4017	6055	SO:0001583	missense	284355	exon2			TTCGGGCCTGAGA		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"Homeoboxes / PRD class"	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.698G>T	chr19.hg19:g.48305570C>A	ENSP00000323455:p.Gly233Val	70.0	0.0		75.0	6.0	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	hg19	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	c	0.438	-0.900130	0.02472	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	D;D	0.91894	-1.78;-2.93	0.401	-0.802	0.10889	.	.	.	.	.	T	0.80412	0.4618	N	0.14661	0.345	0.09310	N	1	B	0.19817	0.039	B	0.11329	0.006	T	0.64236	-0.6455	8	0.26408	T	0.33	.	.	.	.	.	233	Q8N7U7	TPRX1_HUMAN	V	233;330;223	ENSP00000323455:G233V;ENSP00000438832:G330V	ENSP00000323455:G233V	G	-	2	0	TPRX1	52997382	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-1.696000	0.01912	-0.668000	0.05296	-0.694000	0.03704	GGC	.	.		0.652	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		A	48305570	C	A	48305570	3	1	201	1	0	0	0	0	1	0	0	0	16437	739	26	3	541	3	TPRX1	19	48305570	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	51	48305570	10823413	135	29595										
MYH14	79784	hgsc.bcm.edu	37	chr19	50766619	50766619	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cgccctgagggtgatgcagcGgaactgcgcggcctacctca	14	14	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr19:50766619G>T	ENST00000596571.1	+	19	2513	c.2513G>T	c.(2512-2514)cGg>cTg	p.R838L	MYH14_ENST00000262269.8_Missense_Mutation_p.R879L|MYH14_ENST00000598205.1_Missense_Mutation_p.R846L|MYH14_ENST00000425460.1_Missense_Mutation_p.R846L|MYH14_ENST00000376970.2_Missense_Mutation_p.R871L|MYH14_ENST00000601313.1_Missense_Mutation_p.R879L|MYH14_ENST00000440075.2_Missense_Mutation_p.R879L			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	838					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GTGATGCAGCGGAACTGCGCG	0.657																																					p.R879L		Atlas-SNP	.											.	MYH14	261	.	0			c.G2636T						.						20	24	22					19																	50766619		2189	4294	6483	SO:0001583	missense	79784	exon22			TGCAGCGGAACTG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.2513G>T	chr19.hg19:g.50766619G>T	ENSP00000472819:p.Arg838Leu	99.0	0.0		117.0	44.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.059632	0.76074	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66	3.43	3.43	0.39272	.	.	.	.	.	D	0.86142	0.5862	H	0.95950	3.745	0.58432	D	0.999998	D;P;D	0.61697	0.99;0.954;0.973	P;P;P	0.61003	0.882;0.64;0.803	D	0.88474	0.3064	9	0.39692	T	0.17	.	12.7358	0.57222	0.0:0.0:1.0:0.0	.	879;838;846	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	L	838;879;871;846;838;879	ENSP00000406273:R879L;ENSP00000366169:R871L;ENSP00000407879:R846L;ENSP00000262269:R879L	ENSP00000262269:R879L	R	+	2	0	MYH14	55458431	1.000000	0.71417	0.993000	0.49108	0.696000	0.40369	9.440000	0.97547	1.924000	0.55735	0.313000	0.20887	CGG	.	.		0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50766619	G	T	50766619	3	4	201	1	0	0	0	0	1	0	0	0	10042	1116	39	1	2718	1	MYH14	19	50766619	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	2461049	50766619	8362364	136	29596										
KLK7	5650	hgsc.bcm.edu	37	chr19	51485634	51485634	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tagcagtaagatctgcagggGcaggagaagggatcttgcca	15	7	2	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr19:51485634G>T	ENST00000391807.1	-	2	123	c.22C>A	c.(22-24)Ccc>Acc	p.P8T	KLK7_ENST00000595638.1_5'UTR|KLK7_ENST00000597707.1_Intron|KLK7_ENST00000595820.1_Missense_Mutation_p.P8T|CTB-147C22.9_ENST00000594512.1_RNA|KLK7_ENST00000336317.4_5'UTR	NM_139277.2	NP_644806.1	P49862	KLK7_HUMAN	kallikrein-related peptidase 7	8					epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(2)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895)		ATCTGCAGGGGCAGGAGAAGG	0.587																																					p.A50D		Atlas-SNP	.											.	KLK7	40	.	0			c.C149A						.						55	42	47					19																	51485634		2203	4297	6500	SO:0001583	missense	5650	exon2			GCAGGGGCAGGAG	L33404	CCDS12812.1, CCDS59414.1	19q13.33	2011-09-07	2006-10-27			ENSG00000169035		"Kallikreins", "Serine peptidases / Serine peptidases"	6368	protein-coding gene	gene with protein product		604438	"kallikrein 7 (chymotryptic, stratum corneum)"	PRSS6		8034709, 16800724, 16800723	Standard	NM_005046		Approved	SCCE	uc021uyj.1	P49862		ENST00000391807.1:c.22C>A	chr19.hg19:g.51485634G>T	ENSP00000375683:p.Pro8Thr	42.0	0.0		61.0	16.0	NM_001243126	A8K0U5|Q8N5N9|Q8NFV7	Missense_Mutation	SNP	ENST00000391807.1	hg19	CCDS12812.1	.	.	.	.	.	.	.	.	.	.	g	9.416	1.081784	0.20309	.	.	ENSG00000169035	ENST00000304045;ENST00000391807	D	0.87650	-2.28	3.43	-4.3	0.03710	.	.	.	.	.	T	0.66346	0.2780	N	0.08118	0	0.21445	N	0.999681	B	0.06786	0.001	B	0.08055	0.003	T	0.53472	-0.8434	9	0.17832	T	0.49	.	3.8095	0.08791	0.1027:0.4442:0.3011:0.1519	.	8	P49862	KLK7_HUMAN	T	8	ENSP00000375683:P8T	ENSP00000304791:P8T	P	-	1	0	KLK7	56177446	0.000000	0.05858	0.000000	0.03702	0.320000	0.28249	-2.201000	0.01236	-0.815000	0.04346	-0.163000	0.13421	CCC	.	.		0.587	KLK7-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464344.1	NM_005046		T	51485634	G	T	51485634	3	4	201	1	0	0	0	0	1	0	0	0	8418	1203	42	3	759	3	KLK7	19	51485634	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	719015	51485634	7643349	137	29597										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54314495	54314495	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gcgcgcattgcggtcttccaTgagccggaatttcctgcgga	13	12	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr19:54314495T>A	ENST00000324134.6	-	3	586	c.418A>T	c.(418-420)Atg>Ttg	p.M140L	NLRP12_ENST00000354278.3_Missense_Mutation_p.M140L|NLRP12_ENST00000391775.3_Missense_Mutation_p.M140L|NLRP12_ENST00000535162.1_Missense_Mutation_p.M140L|NLRP12_ENST00000345770.5_Missense_Mutation_p.M140L|NLRP12_ENST00000351894.4_Missense_Mutation_p.M140L|NLRP12_ENST00000391773.1_Missense_Mutation_p.M140L|NLRP12_ENST00000391772.1_Missense_Mutation_p.M140L	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	140					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		CGGTCTTCCATGAGCCGGAAT	0.557																																					p.R140C		Atlas-SNP	.											.	NLRP12	236	.	0			c.C418T						.						90	88	89					19																	54314495		2203	4300	6503	SO:0001583	missense	91662	exon3			CTTCCATGAGCCG	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.418A>T	chr19.hg19:g.54314495T>A	ENSP00000319377:p.Met140Leu	86.0	0.0		98.0	31.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	hg19	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.448917	0.26074	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	D;D;D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04	4.47	3.37	0.38596	.	0.125142	0.36555	N	0.002522	T	0.80160	0.4572	M	0.71581	2.175	0.58432	D	0.999997	B;B;B;B	0.24533	0.085;0.085;0.085;0.105	B;B;B;B	0.15870	0.006;0.01;0.01;0.014	T	0.77568	-0.2539	10	0.48119	T	0.1	.	4.9088	0.13811	0.1835:0.0:0.1902:0.6263	.	140;140;140;140	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	L	140	ENSP00000319377:M140L;ENSP00000438030:M140L;ENSP00000340473:M140L;ENSP00000346231:M140L;ENSP00000375655:M140L;ENSP00000375653:M140L;ENSP00000375652:M140L	ENSP00000319377:M140L	M	-	1	0	NLRP12	59006307	0.001000	0.12720	0.996000	0.52242	0.919000	0.55068	0.047000	0.14056	1.808000	0.52836	0.254000	0.18369	ATG	.	.		0.557	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		A	54314495	T	A	54314495	3	1	201	1	0	0	0	0	1	0	0	0	10483	1464	51	4	2895	4	NLRP12	19	54314495	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	2828861	54314495	4814488	138	29598										
C20orf54	113278	hgsc.bcm.edu	37	chr20	746252	746252	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gatggagcagggtgaccaggAggggcccgatgttggccagc	19	9	0	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr20:746252A>C	ENST00000217254.7	-	2	408	c.167T>G	c.(166-168)cTc>cGc	p.L56R	SLC52A3_ENST00000473664.1_5'UTR|SLC52A3_ENST00000381944.3_Missense_Mutation_p.L56R	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	56					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										GGTGACCAGGAGGGGCCCGAT	0.632																																					p.L56R		Atlas-SNP	.											.	.	.	.	0			c.T167G						.						40	35	37					20																	746252		2199	4299	6498	SO:0001583	missense	113278	exon2			ACCAGGAGGGGCC	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"Solute carriers"	16187	protein-coding gene	gene with protein product	"hypothetical protein LOC113278"	613350	"chromosome 20 open reading frame 54"	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.167T>G	chr20.hg19:g.746252A>C	ENSP00000217254:p.Leu56Arg	83.0	0.0		211.0	134.0	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	hg19	CCDS13007.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.737964	0.89573	.	.	ENSG00000101276	ENST00000217254;ENST00000381944	T;T	0.79352	-1.26;-1.26	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.89276	0.6669	M	0.87456	2.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.982	D	0.91048	0.4876	10	0.87932	D	0	-23.016	14.9652	0.71184	1.0:0.0:0.0:0.0	.	56;56	Q9NQ40-2;Q9NQ40	.;RFT2_HUMAN	R	56	ENSP00000217254:L56R;ENSP00000371370:L56R	ENSP00000217254:L56R	L	-	2	0	C20orf54	694252	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.267000	0.95665	2.218000	0.71995	0.533000	0.62120	CTC	.	.		0.632	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409		C	746252	A	C	746252	3	2	201	1	0	0	0	0	1	0	0	0	2116	304	11	5	1258	5	C20orf54	20	746252	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10		746252	62279268	139	29599										
NKX2-4	644524	hgsc.bcm.edu	37	chr20	21377078	21377078	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ctgccgccgccgccgcgtgcAgcgggcccagcgacttggcg	16	18	0	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr20:21377078A>C	ENST00000351817.4	-	2	1164	c.536T>G	c.(535-537)cTg>cGg	p.L179R	RP11-227D2.3_ENST00000552439.1_RNA|RP11-227D2.3_ENST00000419666.2_RNA	NM_033176.1	NP_149416.1	Q9H2Z4	NKX24_HUMAN	NK2 homeobox 4	179					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(2)|upper_aerodigestive_tract(1)	3						CGCCGCGTGCAGCGGGCCCAG	0.721																																					p.L179R		Atlas-SNP	.											.	NKX2-4	7	.	0			c.T536G						.						2	3	3					20																	21377078		1708	3550	5258	SO:0001583	missense	644524	exon2			GCGTGCAGCGGGC		CCDS42855.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125816	ENSG00000125816		"Homeoboxes / ANTP class : NKL subclass"	7837	protein-coding gene	gene with protein product		607808	"NK-2 (Drosophila) homolog D", "NK2 transcription factor related, locus 4 (Drosophila)"	NKX2D		1346742, 10818213	Standard	NM_033176		Approved	NKX2.4	uc010gcz.3	Q9H2Z4	OTTHUMG00000032022	ENST00000351817.4:c.536T>G	chr20.hg19:g.21377078A>C	ENSP00000345147:p.Leu179Arg	38.0	0.0		78.0	39.0	NM_033176	Q5VZV8	Missense_Mutation	SNP	ENST00000351817.4	hg19	CCDS42855.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.581905	0.28180	.	.	ENSG00000125816	ENST00000351817	D	0.92249	-3.0	3.41	2.25	0.28309	Homeodomain-like (1);	0.000000	0.48286	U	0.000194	D	0.92828	0.7719	M	0.64170	1.965	0.43355	D	0.995426	D	0.65815	0.995	D	0.66602	0.945	D	0.88518	0.3094	10	0.13853	T	0.58	.	8.6391	0.33966	0.8055:0.1944:0.0:0.0	.	179	Q9H2Z4	NKX24_HUMAN	R	179	ENSP00000345147:L179R	ENSP00000345147:L179R	L	-	2	0	NKX2-4	21325078	0.997000	0.39634	0.385000	0.26158	0.216000	0.24613	5.550000	0.67268	0.195000	0.20347	0.341000	0.21757	CTG	.	.		0.721	NKX2-4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078270.2			C	21377078	A	C	21377078	3	2	201	1	0	0	0	0	1	0	0	0	10461	188	7	5	532	5	NKX2-4	20	21377078	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	20630826	21377078	41648442	140	29600										
COX4I2	84701	hgsc.bcm.edu	37	chr20	30227900	30227900	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cccacgccgaaaaggtggccTgtaagtgtcagggtggggct	16	10	1	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr20:30227900T>A	ENST00000376075.3	+	3	322	c.247T>A	c.(247-249)Ttg>Atg	p.L83M	COX4I2_ENST00000490030.1_3'UTR	NM_032609.2	NP_115998.2	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2 (lung)	83					cellular respiration (GO:0045333)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	11	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			AAAGGTGGCCTGTAAGTGTCA	0.597																																					p.L83M		Atlas-SNP	.											.	COX4I2	18	.	0			c.T247A						.						29	21	24					20																	30227900		2203	4299	6502	SO:0001630	splice_region_variant	84701	exon3			GTGGCCTGTAAGT	AF257180	CCDS13187.1	20q11.21	2011-07-04	2004-08-11		ENSG00000131055	ENSG00000131055		"Mitochondrial respiratory chain complex / Complex IV"	16232	protein-coding gene	gene with protein product	"cytochrome c oxidase subunit IV-like 2"	607976	"cytochrome c oxidase subunit IV isoform 2"	COX4L2		11311561, 17937768	Standard	NM_032609		Approved	COXIV-2, COX4B, dJ857M17.2, COX4-2	uc002wwj.1	Q96KJ9	OTTHUMG00000032180	ENST00000376075.3:c.247+1T>A	chr20.hg19:g.30227900T>A		873.0	0.0		1684.0	344.0	NM_032609	Q6GTF4|Q9H0Z4	Missense_Mutation	SNP	ENST00000376075.3	hg19	CCDS13187.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.651643	0.29336	.	.	ENSG00000131055	ENST00000376075	T	0.63096	-0.02	4.74	-3.43	0.04810	.	0.090669	0.43260	D	0.000595	T	0.76090	0.3939	M	0.89658	3.05	0.42482	D	0.992862	D	0.76494	0.999	D	0.77557	0.99	T	0.73678	-0.3907	10	0.72032	D	0.01	-7.9709	7.1919	0.25831	0.0:0.4269:0.1298:0.4433	.	83	Q96KJ9	COX42_HUMAN	M	83	ENSP00000365243:L83M	ENSP00000365243:L83M	L	+	1	2	COX4I2	29691561	0.854000	0.29725	0.955000	0.39395	0.009000	0.06853	-0.276000	0.08514	-0.955000	0.03636	-2.547000	0.00178	TTG	.	.		0.597	COX4I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078548.1	NM_032609	Missense_Mutation	A	30227900	T	A	30227900	5	1	201	1	0	0	0	0	0	0	1	0	3772	1594	55	4	253	4	COX4I2	20	30227900	Splice_Site	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	8850822	30227900	32797620	141	29601										
DHX35	60625	hgsc.bcm.edu	37	chr20	37597805	37597806	+	Frame_Shift_Ins	INS	-	-	T													0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	acaacggttgtttacaacccINSttatgctgccctttccatag							TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr20:37597805_37597806insT	ENST00000252011.3	+	2	155_156	c.122_123insT	c.(121-126)ccttatfs	p.Y42fs	DHX35_ENST00000373325.2_Frame_Shift_Ins_p.Y42fs|DHX35_ENST00000373323.4_Frame_Shift_Ins_p.Y42fs	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	42					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				GTTTACAACCCTTATGCTGCCC	0.48																																					p.P41fs		Atlas-INDEL	.											.	DHX35	82	.	0			c.122_123insT						.																																			SO:0001589	frameshift_variant	60625	exon2			.	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.124dupT	chr20.hg19:g.37597807_37597807dupT	ENSP00000252011:p.Tyr42fs	82.0	0.0		156.0	23.0	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Frame_Shift_Ins	INS	ENST00000252011.3	hg19	CCDS13310.1																																																																																			.	.		0.48	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		T	37597806	-	T	37597805	7	5	201	1	0	1	1	0	0	0	0	0	4510	681	24	0	128	0	DHX35	20	37597805	Frame_Shift_Ins	INS	-	TCGA-DD-AADS-01A-11D-A40R-10	7369905	37597805	25427715	142	29602										
TOP1	7150	hgsc.bcm.edu	37	chr20	39709835	39709835	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	aaacctaagaaaattaaaacAgaagataccaagaaggagaa	7	5	0	5			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr20:39709835A>G	ENST00000361337.2	+	7	712	c.462A>G	c.(460-462)acA>acG	p.T154T		NM_003286.2	NP_003277.1	P11387	TOP1_HUMAN	topoisomerase (DNA) I	154	Lys-rich.				chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|DNA topological change (GO:0006265)|embryonic cleavage (GO:0040016)|phosphorylation (GO:0016310)|programmed cell death (GO:0012501)|response to drug (GO:0042493)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|replication fork protection complex (GO:0031298)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|poly(A) RNA binding (GO:0044822)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Sodium stibogluconate(DB05630)|Topotecan(DB01030)	AAATTAAAACAGAAGATACCA	0.368			T	NUP98	AML*																																p.T154T		Atlas-SNP	.		Dom	yes		20	20q12-q13.1	7150	topoisomerase (DNA) I		L	.	TOP1	71	.	0			c.A462G						.						79	84	82					20																	39709835		2203	4300	6503	SO:0001819	synonymous_variant	7150	exon7			TAAAACAGAAGAT		CCDS13312.1	20q12-q13.1	1990-06-22			ENSG00000198900	ENSG00000198900	5.99.1.2		11986	protein-coding gene	gene with protein product		126420					Standard	NM_003286		Approved		uc010ggd.1	P11387	OTTHUMG00000033057	ENST00000361337.2:c.462A>G	chr20.hg19:g.39709835A>G		175.0	0.0		498.0	84.0	NM_003286	A8KA78|E1P5W3|O43256|Q12855|Q12856|Q15610|Q5TFY3|Q9UJN0	Silent	SNP	ENST00000361337.2	hg19	CCDS13312.1																																																																																			.	.		0.368	TOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080397.2			G	39709835	A	G	39709835	2	3	201	1	0	0	0	0	0	0	0	1	16378	175	7	2		2	TOP1	20	39709835	Silent	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	2112030	39709835	23315685	143	29603										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58468254	58468254	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gtataacatcctggagttcaCctaaataaaacaaatattat	4	7	1	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr20:58468254C>G	ENST00000357552.3	-	22	1961	c.1736G>C	c.(1735-1737)aGt>aCt	p.S579T	SYCP2_ENST00000371001.2_Splice_Site_p.S579T			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	579					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			CTGGAGTTCACCtaaataaaa	0.328																																					p.S579T		Atlas-SNP	.											.	SYCP2	204	.	0			c.G1736C						.						73	68	70					20																	58468254		2201	4295	6496	SO:0001630	splice_region_variant	10388	exon21			AGTTCACCTAAAT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1736-1G>C	chr20.hg19:g.58468254C>G		43.0	0.0		91.0	5.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	C	11.41	1.630458	0.28978	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.17528	2.53;2.53;2.27	5.77	-4.28	0.03732	.	0.655321	0.15182	N	0.276047	T	0.09423	0.0232	L	0.29908	0.895	0.09310	N	1	B	0.18310	0.027	B	0.13407	0.009	T	0.18272	-1.0342	10	0.35671	T	0.21	.	7.3728	0.26810	0.1247:0.4707:0.0:0.4046	.	579	Q9BX26	SYCP2_HUMAN	T	579	ENSP00000360040:S579T;ENSP00000350162:S579T;ENSP00000402456:S579T	ENSP00000350162:S579T	S	-	2	0	SYCP2	57901649	0.928000	0.31464	0.019000	0.16419	0.801000	0.45260	-0.058000	0.11750	-1.024000	0.03338	-0.324000	0.08512	AGT	.	.		0.328	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	Missense_Mutation	G	58468254	C	G	58468254	5	3	201	1	0	0	0	0	0	0	1	0	15447	521	18	4	2952	4	SYCP2	20	58468254	Splice_Site	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10	18758419	58468254	4557266	144	29604										
BAGE2	85319	hgsc.bcm.edu	37	chr21	11058295	11058295	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cttcacagcatttgatagtgGctccaaagtgcttacaaaat	7	9	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr21:11058295G>T	ENST00000470054.1	-	0	352							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TTTGATAGTGGCTCCAAAGTG	0.408																																					p.P49T		Atlas-SNP	.											.	.	.	.	0			c.C145A						.						132	98	109					21																	11058295		692	1591	2283			85318	exon3			ATAGTGGCTCCAA	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"cancer/testis antigen family 2, member 2"					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		chr21.hg19:g.11058295G>T		281.0	0.0		334.0	18.0	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	hg19																																																																																				.	.		0.408	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		T	11058295	G	T	11058295	1	4	201	0	1	0	0	0	0	0	0	0	1292	1203	42	3		3	BAGE2	21	11058295	RNA	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10		11058295	37071600	145	29605										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19666622	19666622	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gcggcggacaccagccagtcActgctgacgagagatgcgcc	14	14	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr21:19666622A>T	ENST00000284885.3	-	21	2484	c.2451T>A	c.(2449-2451)agT>agA	p.S817R		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	817	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CCAGCCAGTCACTGCTGACGA	0.582																																					p.S817R		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.T2451A						.						70	71	71					21																	19666622		2203	4300	6503	SO:0001583	missense	5651	exon21			CCAGTCACTGCTG		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.2451T>A	chr21.hg19:g.19666622A>T	ENSP00000284885:p.Ser817Arg	75.0	0.0		85.0	31.0	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	hg19	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	A	6.139	0.393914	0.11638	.	.	ENSG00000154646	ENST00000284885	D	0.93019	-3.15	5.79	-11.6	0.00059	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.061660	0.07143	N	0.847745	D	0.82953	0.5149	L	0.39326	1.205	0.20196	N	0.999924	B	0.06786	0.001	B	0.10450	0.005	T	0.66650	-0.5870	9	.	.	.	.	0.3432	0.00337	0.232:0.255:0.193:0.3199	.	817	P98073	ENTK_HUMAN	R	817	ENSP00000284885:S817R	.	S	-	3	2	TMPRSS15	18588493	0.000000	0.05858	0.001000	0.08648	0.905000	0.53344	-2.453000	0.01005	-2.252000	0.00699	-0.332000	0.08345	AGT	.	.		0.582	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		T	19666622	A	T	19666622	3	4	201	1	0	0	0	0	1	0	0	0	16261	156	6	4	628	4	TMPRSS15	21	19666622	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	8608327	19666622	28463273	146	29606										
SMARCB1	6598	hgsc.bcm.edu	37	chr22	24135767	24135767	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tcacggatacacgactctagCcaccagtgtgaccctgttaa	8	13	2	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr22:24135767C>A	ENST00000263121.7	+	3	450	c.254C>A	c.(253-255)gCc>gAc	p.A85D	SMARCB1_ENST00000407422.3_Missense_Mutation_p.A76D|SMARCB1_ENST00000407082.3_Missense_Mutation_p.A85D|SMARCB1_ENST00000344921.6_Missense_Mutation_p.A76D	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	85					ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				ACGACTCTAGCCACCAGTGTG	0.547			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.A85D		Atlas-SNP	.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	.	SMARCB1	586	.	2	Unknown(2)	soft_tissue(2)	c.C254A						.						186	165	172					22																	24135767		2203	4300	6503	SO:0001583	missense	6598	exon3			CTCTAGCCACCAG	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.254C>A	chr22.hg19:g.24135767C>A	ENSP00000263121:p.Ala85Asp	87.0	0.0		73.0	38.0	NM_003073	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Missense_Mutation	SNP	ENST00000263121.7	hg19	CCDS13817.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.030608	0.75504	.	.	ENSG00000099956	ENST00000417137;ENST00000344921;ENST00000263121;ENST00000407422;ENST00000407082	D;D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25;-3.25	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.96349	0.8809	M	0.67953	2.075	0.80722	D	1	D;D;P;P;B;B;D	0.89917	1.0;0.997;0.946;0.454;0.148;0.399;0.999	D;D;P;B;B;B;D	0.91635	0.999;0.933;0.809;0.36;0.147;0.147;0.991	D	0.95811	0.8841	10	0.54805	T	0.06	-35.2187	19.2602	0.93964	0.0:1.0:0.0:0.0	.	76;85;35;76;76;85;85	B4E117;B4DRT1;Q86WI7;G5E975;Q17S11;Q12824;C9JTA6	.;.;.;.;.;SNF5_HUMAN;.	D	85;76;85;76;85	ENSP00000388489:A85D;ENSP00000340883:A76D;ENSP00000263121:A85D;ENSP00000383984:A76D;ENSP00000385226:A85D	ENSP00000263121:A85D	A	+	2	0	SMARCB1	22465767	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	7.729000	0.84864	2.875000	0.98604	0.644000	0.83932	GCC	.	.		0.547	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		A	24135767	C	A	24135767	3	1	201	1	0	0	0	0	1	0	0	0	14789	739	26	3	264	3	SMARCB1	22	24135767	Missense_Mutation	SNP	C	TCGA-DD-AADS-01A-11D-A40R-10		24135767	27168799	147	29607										
NF2	4771	hgsc.bcm.edu	37	chr22	30035159	30035160	+	Nonsense_Mutation	DNP	GG	GG	TT													0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tatcctgagaatgctgaagaGgagctggttcaggagatcac							TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr22:30035159_30035160GG>TT	ENST00000338641.4	+	3	762_763	c.321_322GG>TT	c.(319-324)gaGGag>gaTTag	p.107_108EE>D*	NF2_ENST00000403999.3_Nonsense_Mutation_p.107_108EE>D*|NF2_ENST00000397789.3_Nonsense_Mutation_p.107_108EE>D*|NF2_ENST00000361452.4_Intron|NF2_ENST00000413209.2_Nonsense_Mutation_p.107_108EE>D*|NF2_ENST00000361166.4_Nonsense_Mutation_p.107_108EE>D*|NF2_ENST00000353887.4_Intron|NF2_ENST00000361676.4_Nonsense_Mutation_p.65_66EE>D*|NF2_ENST00000334961.7_Intron|NF2_ENST00000403435.1_Nonsense_Mutation_p.107_108EE>D*|NF2_ENST00000347330.5_Intron	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	107	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.H95fs*3(1)|p.V86_Q111>E(1)|p.A105fs*20(1)|p.L97fs*17(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						ATGCTGAAGAGGAGCTGGTTCA	0.45			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.E107D|p.E108X		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2	1312	.	7	Unknown(3)|Deletion - Frameshift(3)|Complex - deletion inframe(1)	soft_tissue(3)|stomach(1)|large_intestine(1)|lung(1)|kidney(1)	c.G321T|c.G322T						.																																			SO:0001587	stop_gained	4771	exon3	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	TGAAGAGGAGCTG|GAAGAGGAGCTGG	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	Exception_encountered	chr22.hg19:g.30035159_30035160delinsTT	ENSP00000344666:p.E107_E108delinsD*	81.0|79.0	0.0		80.0|77.0	47.0|46.0	NM_000268	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000338641.4	hg19	CCDS13861.1																																																																																			.	.		0.45	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		TT	30035160	GG	TT	30035159	4	4	201	1	0	0	0	0	0	1	0	0	10366	991	35	3	331	3	NF2	22	30035159	Nonsense_Mutation	DNP	GG	TCGA-DD-AADS-01A-11D-A40R-10	5899392	30035159	21269407	148	29608										
WNT7B	7477	hgsc.bcm.edu	37	chr22	46327010	46327010	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	ctcattgttatgcaggttcaTgaggcgccgcgcgttcttct	11	11	4	1	rs200797257		TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chr22:46327010T>A	ENST00000339464.4	-	3	912	c.538A>T	c.(538-540)Atg>Ttg	p.M180L	WNT7B_ENST00000409496.3_Missense_Mutation_p.M184L|WNT7B_ENST00000410058.1_Missense_Mutation_p.M180L|WNT7B_ENST00000410089.1_Missense_Mutation_p.M164L	NM_058238.2	NP_478679.1	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family, member 7B	180					activation of JUN kinase activity (GO:0007257)|anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular metabolic process (GO:0044237)|cellular response to retinoic acid (GO:0071300)|central nervous system vasculogenesis (GO:0022009)|chorio-allantoic fusion (GO:0060710)|developmental growth involved in morphogenesis (GO:0060560)|embryonic organ development (GO:0048568)|embryonic placenta morphogenesis (GO:0060669)|establishment or maintenance of polarity of embryonic epithelium (GO:0016332)|fibroblast proliferation (GO:0048144)|forebrain regionalization (GO:0021871)|homeostatic process (GO:0042592)|in utero embryonic development (GO:0001701)|inner medullary collecting duct development (GO:0072061)|lens fiber cell development (GO:0070307)|lobar bronchus development (GO:0060482)|lung development (GO:0030324)|lung epithelium development (GO:0060428)|lung morphogenesis (GO:0060425)|lung-associated mesenchyme development (GO:0060484)|mammary gland epithelium development (GO:0061180)|metanephric collecting duct development (GO:0072205)|metanephric epithelium development (GO:0072207)|metanephric loop of Henle development (GO:0072236)|metanephros morphogenesis (GO:0003338)|negative regulation of smoothened signaling pathway (GO:0045879)|neuron differentiation (GO:0030182)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|outer medullary collecting duct development (GO:0072060)|oxygen homeostasis (GO:0032364)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of cell projection size (GO:0032536)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|response to glucocorticoid (GO:0051384)|smooth muscle cell differentiation (GO:0051145)|stem cell proliferation (GO:0072089)|synapse organization (GO:0050808)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	19		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)		TGCAGGTTCATGAGGCGCCGC	0.662																																					p.M180L		Atlas-SNP	.											.	WNT7B	45	.	0			c.A538T						.						32	32	32					22																	46327010		2203	4300	6503	SO:0001583	missense	7477	exon3			GGTTCATGAGGCG	AF416743	CCDS33667.1	22q13	2013-02-28			ENSG00000188064	ENSG00000188064		"Wingless-type MMTV integration sites", "Endogenous ligands"	12787	protein-coding gene	gene with protein product		601967				8168088, 9284940, 11562755	Standard	NM_058238		Approved		uc003bgo.2	P56706	OTTHUMG00000154636	ENST00000339464.4:c.538A>T	chr22.hg19:g.46327010T>A	ENSP00000341032:p.Met180Leu	19.0	0.0		12.0	7.0	NM_058238	B8A596|Q96Q12	Missense_Mutation	SNP	ENST00000339464.4	hg19	CCDS33667.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.612380	0.87258	.	.	ENSG00000188064	ENST00000339464;ENST00000410089;ENST00000409496;ENST00000410058	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	3.16	3.16	0.36331	.	0.000000	0.85682	U	0.000000	D	0.83714	0.5314	M	0.80028	2.48	0.58432	D	0.999999	P;P	0.44816	0.752;0.844	P;P	0.53518	0.519;0.728	D	0.85183	0.1005	10	0.66056	D	0.02	.	10.7516	0.46213	0.0:0.0:0.0:1.0	.	184;180	A8K0G1;P56706	.;WNT7B_HUMAN	L	180;164;184;180	ENSP00000341032:M180L;ENSP00000386781:M164L;ENSP00000386546:M184L;ENSP00000387217:M180L	ENSP00000341032:M180L	M	-	1	0	WNT7B	44705674	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.480000	0.81109	1.314000	0.45095	0.260000	0.18958	ATG	.	T|1.000;C|0.000		0.662	WNT7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336418.1	NM_058238		A	46327010	T	A	46327010	3	1	201	1	0	0	0	0	1	0	0	0	17410	1464	51	4	519	4	WNT7B	22	46327010	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	16291851	46327010	4977556	149	29609										
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53272572	53272572	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cctgggacacatggtcatcgTtggtccgcagttcacgcccc	11	15	2	0			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chrX:53272572T>A	ENST00000375368.5	-	8	3001	c.2801A>T	c.(2800-2802)aAc>aTc	p.N934I	IQSEC2_ENST00000396435.3_Missense_Mutation_p.N944I|IQSEC2_ENST00000375365.2_Missense_Mutation_p.N739I			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	934					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						ATGGTCATCGTTGGTCCGCAG	0.597																																					p.N944I		Atlas-SNP	.											.	IQSEC2	195	.	0			c.A2831T						.						81	51	61					X																	53272572		2173	4210	6383	SO:0001583	missense	23096	exon9			TCATCGTTGGTCC	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.2801A>T	chrX.hg19:g.53272572T>A	ENSP00000364517:p.Asn934Ile	46.0	0.0		66.0	50.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	T	26.4	4.730092	0.89390	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	T;T;T	0.13778	2.56;2.56;2.61	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.26629	0.0651	L	0.58101	1.795	0.80722	D	1	B;P	0.44478	0.274;0.836	B;P	0.52343	0.242;0.696	T	0.00986	-1.1490	10	0.87932	D	0	.	13.4239	0.61013	0.0:0.0:0.0:1.0	.	944;739	Q5JU85-2;Q5JU85-3	.;.	I	944;934;739	ENSP00000379712:N944I;ENSP00000364517:N934I;ENSP00000364514:N739I	ENSP00000364514:N739I	N	-	2	0	IQSEC2	53289297	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.123000	0.64703	1.882000	0.54519	0.477000	0.44152	AAC	.	.		0.597	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		A	53272572	T	A	53272572	3	1	201	1	0	0	0	0	1	0	0	0	7827	1725	60	4	1663	4	IQSEC2	23	53272572	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10		53272572	101997988	150	29610										
EDA	1896	hgsc.bcm.edu	37	chrX	69255445	69255445	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	gggccatcaggctgggtgaaGcccctgcatcctagattccc	12	14	1	2			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chrX:69255445G>T	ENST00000374552.4	+	8	1404	c.1162G>T	c.(1162-1164)Gcc>Tcc	p.A388S	EDA_ENST00000374553.2_Missense_Mutation_p.A386S|EDA_ENST00000524573.1_Missense_Mutation_p.A383S	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A	388					cell differentiation (GO:0030154)|cell-matrix adhesion (GO:0007160)|ectoderm development (GO:0007398)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|immune response (GO:0006955)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|salivary gland cavitation (GO:0060662)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	apical part of cell (GO:0045177)|collagen trimer (GO:0005581)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						GCTGGGTGAAGCCCCTGCATC	0.587																																					p.A388S		Atlas-SNP	.											.	EDA	61	.	0			c.G1162T						.						125	95	105					X																	69255445		2203	4300	6503	SO:0001583	missense	1896	exon8			GGTGAAGCCCCTG	U59227	CCDS14394.1, CCDS35318.1, CCDS35319.1, CCDS43966.1, CCDS35318.2, CCDS35319.2, CCDS55436.1	Xq12-q13.1	2013-05-22	2004-08-09	2004-08-12	ENSG00000158813	ENSG00000158813		"Tumor necrosis factor (ligand) superfamily"	3157	protein-coding gene	gene with protein product		300451	"ectodermal dysplasia 1, anhidrotic", "oligodontia 1"	ED1, EDA2, ODT1		8696334, 18657636, 16583127	Standard	NM_001005612		Approved	EDA1, XLHED, HED, XHED, ED1-A1, ED1-A2, EDA-A1, EDA-A2	uc004dxs.3	Q92838	OTTHUMG00000021764	ENST00000374552.4:c.1162G>T	chrX.hg19:g.69255445G>T	ENSP00000363680:p.Ala388Ser	53.0	0.0		66.0	39.0	NM_001399	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	Missense_Mutation	SNP	ENST00000374552.4	hg19	CCDS14394.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.013923	0.93404	.	.	ENSG00000158813	ENST00000374552;ENST00000374553;ENST00000524573	D;D;D	0.99462	-5.94;-5.94;-5.94	5.42	5.42	0.78866	Tumour necrosis factor-like (2);	0.000000	0.85682	D	0.000000	D	0.98998	0.9658	N	0.24115	0.695	0.80722	D	1	D;P;D	0.55605	0.972;0.953;0.972	D;D;D	0.77557	0.99;0.978;0.99	D	0.99936	1.1365	10	0.87932	D	0	-10.1592	17.1546	0.86787	0.0:0.0:1.0:0.0	.	383;388;386	Q92838-9;Q92838;Q92838-3	.;EDA_HUMAN;.	S	388;386;383	ENSP00000363680:A388S;ENSP00000363681:A386S;ENSP00000432585:A383S	ENSP00000363680:A388S	A	+	1	0	EDA	69172170	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.125000	0.94402	2.261000	0.74972	0.529000	0.55759	GCC	.	.		0.587	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057048.2	NM_001399		T	69255445	G	T	69255445	3	4	201	1	0	0	0	0	1	0	0	0	4905	971	34	3	1328	3	EDA	23	69255445	Missense_Mutation	SNP	G	TCGA-DD-AADS-01A-11D-A40R-10	15982873	69255445	86015115	151	29611										
ATG4A	115201	hgsc.bcm.edu	37	chrX	107381369	107381369	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	tttaagatgccacagtctttAggggcattaggaggaaaacc	11	7	1	1			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chrX:107381369A>T	ENST00000372232.3	+	9	921	c.762A>T	c.(760-762)ttA>ttT	p.L254F	ATG4A_ENST00000545696.1_Intron|ATG4A_ENST00000372254.3_Missense_Mutation_p.L230F|ATG4A_ENST00000345734.3_Intron	NM_052936.3	NP_443168.2	Q8WYN0	ATG4A_HUMAN	autophagy related 4A, cysteine peptidase	254					autophagy (GO:0006914)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)			endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)	11						CACAGTCTTTAGGGGCATTAG	0.458																																					p.L254F		Atlas-SNP	.											.	ATG4A	68	.	0			c.A762T						.						202	178	186					X																	107381369		2203	4300	6503	SO:0001583	missense	115201	exon9			GTCTTTAGGGGCA	AJ320508	CCDS14538.1, CCDS14539.1	Xq22.1-q22.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000101844	ENSG00000101844			16489	protein-coding gene	gene with protein product		300663	"AUT-like 2, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog A (S. cerevisiae)", "ATG4 autophagy related 4 homolog A (S. cerevisiae)"	AUTL2, APG4A		12446702, 12473658	Standard	NM_052936		Approved		uc004enr.3	Q8WYN0	OTTHUMG00000022176	ENST00000372232.3:c.762A>T	chrX.hg19:g.107381369A>T	ENSP00000361306:p.Leu254Phe	125.0	0.0		198.0	54.0	NM_052936	A6NCH2|B2RAZ7|D3DUY0|O95534|Q5JYY9|Q5JYZ0|Q86VE5|Q96KQ0|Q96KQ1	Missense_Mutation	SNP	ENST00000372232.3	hg19	CCDS14538.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.46|17.46	3.395185|3.395185	0.62066|0.62066	.|.	.|.	ENSG00000101844|ENSG00000101844	ENST00000372232;ENST00000372254;ENST00000457035|ENST00000394892	T;T|.	0.50813|.	0.73;0.74|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.180131|.	0.38605|.	N|.	0.001638|.	T|.	0.77260|.	0.4104|.	M|M	0.90369|0.90369	3.11|3.11	0.80722|0.80722	D|D	1|1	P|.	0.44986|.	0.847|.	P|.	0.58077|.	0.832|.	T|.	0.80507|.	-0.1352|.	10|.	0.72032|.	D|.	0.01|.	-6.9712|-6.9712	7.2132|7.2132	0.25945|0.25945	0.8535:0.0:0.1465:0.0|0.8535:0.0:0.1465:0.0	.|.	254|.	Q8WYN0|.	ATG4A_HUMAN|.	F|L	254;230;177|227	ENSP00000361306:L254F;ENSP00000361328:L230F|.	ENSP00000361306:L254F|.	L|X	+|+	3|2	2|0	ATG4A|ATG4A	107268025|107268025	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.775000|2.775000	0.47702|0.47702	1.796000|1.796000	0.52611|0.52611	0.451000|0.451000	0.29950|0.29950	TTA|TAG	.	.		0.458	ATG4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057860.1	NM_052936		T	107381369	A	T	107381369	3	4	201	1	0	0	0	0	1	0	0	0	1096	417	15	4	796	4	ATG4A	23	107381369	Missense_Mutation	SNP	A	TCGA-DD-AADS-01A-11D-A40R-10	38125924	107381369	47889191	152	29612										
MCF2	4168	hgsc.bcm.edu	37	chrX	138733894	138733894	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261437908496732	4	1	0.897811865553801	1.23449131513648	0.705423608649415	1	1	0	cttaccagacaagaaggcgaTgtcttgcattaagaaatgac	9	8	1	4			TCGA-DD-AADS-01A-11D-A40R-10	TCGA-DD-AADS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7d7b0cb1-f476-4c50-91ab-d79564809fb8	7d48f285-d87c-41ed-881c-9dd20e9953dc	g.chrX:138733894T>C	ENST00000519895.1	-	2	175	c.10A>G	c.(10-12)Atc>Gtc	p.I4V	MCF2_ENST00000414978.1_Missense_Mutation_p.I4V|MCF2_ENST00000520602.1_Missense_Mutation_p.I4V|MCF2_ENST00000370578.4_Missense_Mutation_p.I89V	NM_001171876.1	NP_001165347.1	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	0	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					AAGAAGGCGATGTCTTGCATT	0.353																																					p.I4V		Atlas-SNP	.											.	MCF2	432	.	0			c.A10G						.						72	63	66					X																	138733894		1841	3996	5837	SO:0001583	missense	4168	exon2			AGGCGATGTCTTG		CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"Rho guanine nucleotide exchange factors"	6940	protein-coding gene	gene with protein product	"Oncogene MCF2 (oncogene DBL)"	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000519895.1:c.10A>G	chrX.hg19:g.138733894T>C	ENSP00000430276:p.Ile4Val	317.0	2.0		429.0	313.0	NM_001171876	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000519895.1	hg19	CCDS55517.1	.	.	.	.	.	.	.	.	.	.	T	8.094	0.775064	0.16051	.	.	ENSG00000101977	ENST00000520602;ENST00000370578;ENST00000414978;ENST00000519895	T;T;T;T	0.31247	1.5;1.55;1.5;1.55	4.3	3.01	0.34805	.	0.503584	0.19821	N	0.105309	T	0.10723	0.0262	N	0.04880	-0.145	0.24048	N	0.996055	B;B;B	0.22746	0.074;0.061;0.06	B;B;B	0.21917	0.037;0.026;0.03	T	0.31724	-0.9933	10	0.07325	T	0.83	.	3.9056	0.09180	0.2117:0.0:0.2151:0.5731	.	4;89;89	E9PH77;B7Z3Z2;Q5JYJ7	.;.;.	V	4;89;4;4	ENSP00000427745:I4V;ENSP00000359610:I89V;ENSP00000397055:I4V;ENSP00000430276:I4V	ENSP00000359610:I89V	I	-	1	0	MCF2	138561560	1.000000	0.71417	0.925000	0.36789	0.750000	0.42670	1.042000	0.30303	1.662000	0.50781	0.430000	0.28490	ATC	.	.		0.353	MCF2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377602.1	NM_005369		C	138733894	T	C	138733894	3	2	201	1	0	0	0	0	1	0	0	0	9387	1464	51	2	3190	2	MCF2	23	138733894	Missense_Mutation	SNP	T	TCGA-DD-AADS-01A-11D-A40R-10	31352525	138733894	16536666	153	29613										
KIF17	57576	hgsc.bcm.edu	37	chr1	21011489	21011489	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgtccgcaccacctctaaggCcacttccgaggccagatcta	8	16	2	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr1:21011489C>A	ENST00000247986.2	-	10	2354	c.2044G>T	c.(2044-2046)Gcc>Tcc	p.A682S	KIF17_ENST00000490034.1_5'UTR|KIF17_ENST00000375044.1_Missense_Mutation_p.A582S|KIF17_ENST00000400463.3_Missense_Mutation_p.A682S			Q9P2E2	KIF17_HUMAN	kinesin family member 17	682					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		ACCTCTAAGGCCACTTCCGAG	0.672																																					p.A682S		Atlas-SNP	.											.	KIF17	130	.	0			c.G2044T						.						30	27	28					1																	21011489		2203	4299	6502	SO:0001583	missense	57576	exon10			CTAAGGCCACTTC	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"Kinesins"	19167	protein-coding gene	gene with protein product	"kinesin-like protein KIF17", "KIF3-related motor protein", "KIF17 variant protein"	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.2044G>T	chr1.hg19:g.21011489C>A	ENSP00000247986:p.Ala682Ser	193.0	0.0		151.0	50.0	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	hg19	CCDS213.1	.	.	.	.	.	.	.	.	.	.	C	8.992	0.977947	0.18812	.	.	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986;ENST00000321188	T;T;T	0.71341	-0.56;-0.44;-0.44	4.01	-1.17	0.09648	.	0.636018	0.12020	U	0.507021	T	0.50309	0.1608	L	0.36672	1.1	0.09310	N	1	B;B;B	0.29301	0.067;0.241;0.118	B;B;B	0.28011	0.027;0.085;0.018	T	0.31668	-0.9935	10	0.14656	T	0.56	.	3.3664	0.07204	0.1805:0.4086:0.0:0.4109	.	682;682;682	B0I1R5;Q9P2E2-3;Q9P2E2	.;.;KIF17_HUMAN	S	582;682;682;63	ENSP00000364184:A582S;ENSP00000383311:A682S;ENSP00000247986:A682S	ENSP00000247986:A682S	A	-	1	0	KIF17	20884076	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.533000	0.06157	-0.216000	0.10048	0.655000	0.94253	GCC	.	.		0.672	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816		A	21011489	C	A	21011489	3	1	202	1	0	0	0	0	1	0	0	0	8288	739	26	3	1069	3	KIF17	1	21011489	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10		21011489	228239132	1	29614										
DOCK7	85440	hgsc.bcm.edu	37	chr1	62923216	62923216	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaaataagcatacctgtggcAggtgacaggcaatactgcct	10	9	0	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr1:62923216A>C	ENST00000340370.5	-	48	6297	c.6280T>G	c.(6280-6282)Tgc>Ggc	p.C2094G	DOCK7_ENST00000251157.5_Missense_Mutation_p.C2114G	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	2125	DHR-2.				activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TACCTGTGGCAGGTGACAGGC	0.413																																					p.C2114G		Atlas-SNP	.											.	DOCK7	184	.	0			c.T6340G						.						132	126	128					1																	62923216		2203	4300	6503	SO:0001583	missense	85440	exon48			TGTGGCAGGTGAC		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.6280T>G	chr1.hg19:g.62923216A>C	ENSP00000340742:p.Cys2094Gly	112.0	0.0		87.0	31.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	hg19	CCDS30734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.33|12.33	1.904386|1.904386	0.33628|0.33628	.|.	.|.	ENSG00000116641|ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370|ENST00000454575	T;T|.	0.13307|.	2.6;2.6|.	5.99|5.99	3.48|3.48	0.39840|0.39840	.|.	0.234704|.	0.34338|.	N|.	0.004043|.	T|T	0.32436|0.32436	0.0829|0.0829	N|N	0.03608|0.03608	-0.345|-0.345	0.54753|0.54753	D|D	0.999983|0.999983	B;B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0;0.0;0.0|.	T|T	0.11060|0.11060	-1.0603|-1.0603	10|5	0.27082|.	T|.	0.32|.	.|.	14.0669|14.0669	0.64837|0.64837	0.7521:0.2479:0.0:0.0|0.7521:0.2479:0.0:0.0	.|.	2125;2114;2094;2083;2085;2116|.	Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6|.	DOCK7_HUMAN;.;.;.;.;.|.	G|R	2125;2114;2094|1287	ENSP00000251157:C2114G;ENSP00000340742:C2094G|.	ENSP00000251157:C2114G|.	C|L	-|-	1|2	0|0	DOCK7|DOCK7	62695804|62695804	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.761000|5.761000	0.68801|0.68801	1.054000|1.054000	0.40438|0.40438	0.533000|0.533000	0.62120|0.62120	TGC|CTG	.	.		0.413	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		C	62923216	A	C	62923216	3	2	202	1	0	0	0	0	1	0	0	0	4694	188	7	5	57	5	DOCK7	1	62923216	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	41911727	62923216	186327405	2	29615										
FLG	2312	hgsc.bcm.edu	37	chr1	152277558	152277558	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctgattgtctggagcggtcTgcagagtgcccgtgaccggc	15	12	2	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr1:152277558T>A	ENST00000368799.1	-	3	9839	c.9804A>T	c.(9802-9804)gcA>gcT	p.A3268A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3268	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGAGCGGTCTGCAGAGTGCC	0.577									Ichthyosis																												p.A3268A		Atlas-SNP	.											.	FLG	900	.	0			c.A9804T						.						286	286	286					1																	152277558		2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCGGTCTGCAGAG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9804A>T	chr1.hg19:g.152277558T>A		120.0	0.0		103.0	41.0	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152277558	T	A	152277558	2	1	202	1	0	0	0	0	0	0	0	1	5930	1567	55	4		4	FLG	1	152277558	Silent	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	89354342	152277558	96973063	3	29616										
NOS1AP	9722	hgsc.bcm.edu	37	chr1	162302830	162302830	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cttctatgtctctcatgattCccaagacttgaagatcttca	5	11	5	4			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr1:162302830C>A	ENST00000361897.5	+	5	770	c.368C>A	c.(367-369)tCc>tAc	p.S123Y	NOS1AP_ENST00000530878.1_Missense_Mutation_p.S118Y	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	123	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			TCTCATGATTCCCAAGACTTG	0.413																																					p.S123Y		Atlas-SNP	.											.	NOS1AP	139	.	0			c.C368A						.						119	111	114					1																	162302830		2203	4300	6503	SO:0001583	missense	9722	exon5			ATGATTCCCAAGA	AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"C-terminal PDZ domain ligand of neuronal nitric oxide synthase"	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.368C>A	chr1.hg19:g.162302830C>A	ENSP00000355133:p.Ser123Tyr	126.0	0.0		145.0	27.0	NM_014697	B7ZLF5|O43564|Q3T551|Q5VU95	Missense_Mutation	SNP	ENST00000361897.5	hg19	CCDS1237.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.673183	0.88445	.	.	ENSG00000198929	ENST00000530878;ENST00000361897	T;T	0.15139	2.45;2.45	5.42	5.42	0.78866	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.049412	0.85682	D	0.000000	T	0.42607	0.1210	M	0.89214	3.015	.	.	.	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.997	T	0.51880	-0.8649	9	0.72032	D	0.01	.	16.7056	0.85371	0.0:1.0:0.0:0.0	.	118;118;123	E9PSG0;B7ZLF5;O75052	.;.;CAPON_HUMAN	Y	118;123	ENSP00000431586:S118Y;ENSP00000355133:S123Y	ENSP00000355133:S123Y	S	+	2	0	NOS1AP	160569454	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.028000	0.76470	2.520000	0.84964	0.655000	0.94253	TCC	.	.		0.413	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697		A	162302830	C	A	162302830	3	1	202	1	0	0	0	0	1	0	0	0	10551	855	30	3	386	3	NOS1AP	1	162302830	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	10025272	162302830	86947791	4	29617										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179497542	179497542	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gttcattccaaacctctattTgaaacagatgtgttgtcttc	6	9	3	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr1:179497542T>A	ENST00000367618.3	+	23	3078	c.2691T>A	c.(2689-2691)ttT>ttA	p.F897L		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	897	Glu-rich.									NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						AACCTCTATTTGAAACAGATG	0.363																																					p.F897L		Atlas-SNP	.											.	AXDND1	142	.	0			c.T2691A						.						115	103	107					1																	179497542		2203	4300	6503	SO:0001583	missense	126859	exon23			TCTATTTGAAACA	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2691T>A	chr1.hg19:g.179497542T>A	ENSP00000356590:p.Phe897Leu	86.0	0.0		102.0	20.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.821552	0.32237	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000359183;ENST00000434088	T;T	0.21361	2.01;2.01	4.12	-3.53	0.04667	.	1.091970	0.07137	N	0.846623	T	0.12774	0.0310	L	0.44542	1.39	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.38023	-0.9680	10	0.26408	T	0.33	1.2625	0.0912	0.00040	0.3115:0.1974:0.1597:0.3314	.	781;897	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	L	897;781;129;757	ENSP00000356590:F897L;ENSP00000391716:F757L	ENSP00000352107:F129L	F	+	3	2	AXDND1	177764165	0.003000	0.15002	0.000000	0.03702	0.126000	0.20510	0.013000	0.13310	-0.364000	0.08088	-0.327000	0.08410	TTT	.	.		0.363	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		A	179497542	T	A	179497542	3	1	202	1	0	0	0	0	1	0	0	0	1995	1809	63	4	2777	4	C1orf125	1	179497542	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	17194712	179497542	69753079	5	29618										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190195446	190195446	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtctgggagaagtacttgaaGcccttgaagaacaaacaaag	11	7	1	4			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr1:190195446G>T	ENST00000367462.3	-	6	958	c.727C>A	c.(727-729)Ctt>Att	p.L243I	BRINP3_ENST00000463404.1_5'Flank|BRINP3_ENST00000534846.1_Missense_Mutation_p.L141I	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	243	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											AGTACTTGAAGCCCTTGAAGA	0.299																																					p.L243I		Atlas-SNP	.											.	FAM5C	343	.	0			c.C727A						.						52	50	51					1																	190195446		2203	4300	6503	SO:0001583	missense	339479	exon6			CTTGAAGCCCTTG	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.727C>A	chr1.hg19:g.190195446G>T	ENSP00000356432:p.Leu243Ile	77.0	0.0		78.0	56.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.492434	0.44352	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.27104	1.92;1.69	5.81	4.9	0.64082	Membrane attack complex component/perforin (MACPF) domain (1);	0.065493	0.64402	D	0.000011	T	0.47746	0.1462	M	0.69358	2.11	0.47374	D	0.999408	D;D	0.67145	0.996;0.993	D;D	0.72625	0.978;0.952	T	0.49093	-0.8975	10	0.66056	D	0.02	.	12.723	0.57152	0.0792:0.0:0.9208:0.0	.	141;243	B7Z260;Q76B58	.;FAM5C_HUMAN	I	243;141	ENSP00000356432:L243I;ENSP00000438022:L141I	ENSP00000356432:L243I	L	-	1	0	FAM5C	188462069	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.490000	0.53245	1.461000	0.47929	0.655000	0.94253	CTT	.	.		0.299	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190195446	G	T	190195446	3	4	202	1	0	0	0	0	1	0	0	0	5602	971	34	3	1585	3	FAM5C	1	190195446	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	10697904	190195446	59055175	6	29619										
RGS18	64407	hgsc.bcm.edu	37	chr1	192127859	192127859	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aatacatggttcaggaaaagAagaaacaagcaaagaagcca	9	6	1	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr1:192127859A>G	ENST00000367460.3	+	1	273	c.92A>G	c.(91-93)gAa>gGa	p.E31G	RGS18_ENST00000481707.1_3'UTR	NM_130782.2	NP_570138.1	Q9NS28	RGS18_HUMAN	regulator of G-protein signaling 18	31					G-protein coupled receptor signaling pathway (GO:0007186)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			kidney(1)|large_intestine(2)|lung(15)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TCAGGAAAAGAAGAAACAAGC	0.289																																					p.E31G		Atlas-SNP	.											.	RGS18	54	.	0			c.A92G						.						48	52	51					1																	192127859		2202	4290	6492	SO:0001583	missense	64407	exon1			GAAAAGAAGAAAC	AF268036	CCDS1374.1	1q31.2	2008-02-05	2007-08-14		ENSG00000150681	ENSG00000150681		"Regulators of G-protein signaling"	14261	protein-coding gene	gene with protein product		607192	"regulator of G-protein signalling 18"			11042171	Standard	NM_130782		Approved	RGS13	uc001gsg.3	Q9NS28	OTTHUMG00000035592	ENST00000367460.3:c.92A>G	chr1.hg19:g.192127859A>G	ENSP00000356430:p.Glu31Gly	818.0	0.0		1014.0	225.0	NM_130782	B2RD23	Missense_Mutation	SNP	ENST00000367460.3	hg19	CCDS1374.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.053198	0.55218	.	.	ENSG00000150681	ENST00000367460	T	0.53423	0.62	6.06	4.94	0.65067	.	0.258414	0.45867	D	0.000340	T	0.45856	0.1363	M	0.65975	2.015	0.46654	D	0.999146	B	0.16603	0.018	B	0.17722	0.019	T	0.40346	-0.9568	10	0.51188	T	0.08	.	9.8871	0.41268	0.9227:0.0:0.0773:0.0	.	31	Q9NS28	RGS18_HUMAN	G	31	ENSP00000356430:E31G	ENSP00000356430:E31G	E	+	2	0	RGS18	190394482	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.752000	0.55172	1.119000	0.41883	0.528000	0.53228	GAA	.	.		0.289	RGS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086382.1	NM_130782		G	192127859	A	G	192127859	3	3	202	1	0	0	0	0	1	0	0	0	13315	246	9	2	94	2	RGS18	1	192127859	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	1932413	192127859	57122762	7	29620										
TPO	7173	hgsc.bcm.edu	37	chr2	1437364	1437364	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcaacctgaaaactcaacaaTcacagcatccaacgggtaat	5	12	3	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr2:1437364T>C	ENST00000345913.4	+	4	425	c.334T>C	c.(334-336)Tca>Cca	p.S112P	TPO_ENST00000329066.4_Missense_Mutation_p.S112P|TPO_ENST00000382269.3_Missense_Mutation_p.S112P|TPO_ENST00000346956.3_Missense_Mutation_p.S112P|TPO_ENST00000539820.1_Missense_Mutation_p.S112P|TPO_ENST00000349624.3_Missense_Mutation_p.S112P|TPO_ENST00000497517.2_Intron|TPO_ENST00000382198.1_Missense_Mutation_p.S112P|TPO_ENST00000382201.3_Missense_Mutation_p.S112P|TPO_ENST00000337415.3_Missense_Mutation_p.S112P	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	112					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	AACTCAACAATCACAGCATCC	0.517																																					p.S112P		Atlas-SNP	.											.	TPO	224	.	0			c.T334C						.						95	80	85					2																	1437364		2203	4300	6503	SO:0001583	missense	7173	exon4			CAACAATCACAGC		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.334T>C	chr2.hg19:g.1437364T>C	ENSP00000318820:p.Ser112Pro	290.0	0.0		226.0	66.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	T	7.773	0.707798	0.15239	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36	4.26	-1.21	0.09524	.	1.528620	0.04080	N	0.309399	T	0.49779	0.1577	L	0.36672	1.1	0.09310	N	1	P;P;D;P;P	0.56035	0.89;0.899;0.974;0.89;0.725	P;P;P;P;B	0.55391	0.527;0.571;0.775;0.527;0.327	T	0.36456	-0.9747	10	0.31617	T	0.26	-0.7739	0.8062	0.01084	0.1611:0.1911:0.1665:0.4813	.	112;112;112;112;112	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	P	112;112;112;112;112;112;112;112;112;112;41	ENSP00000371704:S112P;ENSP00000337263:S112P;ENSP00000318820:S112P;ENSP00000263886:S112P;ENSP00000332044:S112P;ENSP00000444840:S112P;ENSP00000329869:S112P;ENSP00000371636:S112P;ENSP00000390994:S112P;ENSP00000371633:S112P;ENSP00000405788:S41P	ENSP00000329869:S112P	S	+	1	0	TPO	1416371	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.374000	0.20501	-0.150000	0.11195	0.460000	0.39030	TCA	.	.		0.517	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		C	1437364	T	C	1437364	3	2	202	1	0	0	0	0	1	0	0	0	16425	1435	50	2	344	2	TPO	2	1437364	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10		1437364	241762009	8	29621										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1844609	1844609	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttctttgctcttgggcaaccTgaaaggctaaataagaaaca	8	8	2	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr2:1844609T>A	ENST00000399161.2	-	20	3528	c.2781A>T	c.(2779-2781)tcA>tcT	p.S927S	MYT1L_ENST00000407844.1_5'UTR|MYT1L_ENST00000428368.2_Silent_p.S925S|MYT1L_ENST00000471668.1_5'UTR	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	927					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TTGGGCAACCTGAAAGGCTAA	0.408																																					p.S925S		Atlas-SNP	.											.	MYT1L	241	.	0			c.A2775T						.						137	122	127					2																	1844609		1728	3731	5459	SO:0001819	synonymous_variant	23040	exon20			GCAACCTGAAAGG	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.2781A>T	chr2.hg19:g.1844609T>A		57.0	0.0		44.0	13.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	hg19																																																																																				.	.		0.408	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1844609	T	A	1844609	2	1	202	1	0	0	0	0	0	0	0	1	10116	1567	55	4		4	MYT1L	2	1844609	Silent	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	407245	1844609	241354764	9	29622										
DTNB	1838	hgsc.bcm.edu	37	chr2	25656837	25656837	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgtttgttggcatcaaagtTaaagctcaagtcagtgggag	12	5	3	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr2:25656837T>A	ENST00000406818.3	-	13	1534	c.1285A>T	c.(1285-1287)Aac>Tac	p.N429Y	DTNB_ENST00000404103.3_Missense_Mutation_p.N429Y|DTNB_ENST00000545439.1_Missense_Mutation_p.N225Y|DTNB_ENST00000407186.1_Missense_Mutation_p.N399Y|DTNB_ENST00000407038.3_Missense_Mutation_p.N399Y|DTNB_ENST00000407661.3_Missense_Mutation_p.N429Y|DTNB_ENST00000496972.2_Missense_Mutation_p.N372Y|DTNB_ENST00000405222.1_Missense_Mutation_p.N399Y|DTNB_ENST00000288642.8_Missense_Mutation_p.N429Y	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	429	Syntrophin-binding region.					cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCATCAAAGTTAAAGCTCAAG	0.423																																					p.N429Y		Atlas-SNP	.											.	DTNB	43	.	0			c.A1285T						.						217	204	208					2																	25656837		1876	4111	5987	SO:0001583	missense	1838	exon13			CAAAGTTAAAGCT	AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.1285A>T	chr2.hg19:g.25656837T>A	ENSP00000384084:p.Asn429Tyr	135.0	0.0		100.0	36.0	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Missense_Mutation	SNP	ENST00000406818.3	hg19	CCDS46237.1	.	.	.	.	.	.	.	.	.	.	T	17.89	3.499072	0.64298	.	.	ENSG00000138101	ENST00000496972;ENST00000406818;ENST00000404103;ENST00000407661;ENST00000407038;ENST00000405222;ENST00000407186;ENST00000288642;ENST00000545439;ENST00000535791	T;T;T;T;T;T;T;T;T	0.46819	2.18;2.17;2.17;2.18;2.19;2.2;2.2;2.17;0.86	5.74	5.74	0.90152	.	0.198714	0.56097	D	0.000034	T	0.40743	0.1129	L	0.34521	1.04	0.80722	D	1	B;B;B;B;B;B;B;B;B;B;B;B;B	0.13594	0.003;0.005;0.008;0.008;0.005;0.005;0.001;0.002;0.002;0.008;0.008;0.001;0.005	B;B;B;B;B;B;B;B;B;B;B;B;B	0.20184	0.005;0.008;0.019;0.028;0.008;0.008;0.004;0.005;0.007;0.019;0.019;0.003;0.008	T	0.23619	-1.0183	10	0.56958	D	0.05	-16.8472	14.8548	0.70329	0.0:0.0:0.0:1.0	.	429;225;372;429;429;372;399;399;399;429;429;429;429	E7EVB6;B7Z202;F5GZG4;O60941-3;B7Z6A9;B7Z733;E9PEY4;Q96AW0;O60941-2;O60941-4;G5E9F6;O60941;Q86VR4	.;.;.;.;.;.;.;.;.;.;.;DTNB_HUMAN;.	Y	372;429;429;429;399;399;399;429;225;282	ENSP00000444463:N372Y;ENSP00000384084:N429Y;ENSP00000385482:N429Y;ENSP00000385193:N429Y;ENSP00000384767:N399Y;ENSP00000384787:N399Y;ENSP00000385784:N399Y;ENSP00000288642:N429Y;ENSP00000444961:N225Y	ENSP00000288642:N429Y	N	-	1	0	DTNB	25510341	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.670000	0.83925	2.180000	0.69256	0.533000	0.62120	AAC	.	.		0.423	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147		A	25656837	T	A	25656837	3	1	202	1	0	0	0	0	1	0	0	0	4791	1754	61	4	630	4	DTNB	2	25656837	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	23812228	25656837	217542536	10	29623										
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40656383	40656383	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acttggtagttagctaattcTattaattgctctatttcttt	5	6	3	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr2:40656383T>C	ENST00000403092.1	-	2	1071	c.1038A>G	c.(1036-1038)atA>atG	p.I346M	SLC8A1_ENST00000405269.1_Missense_Mutation_p.I346M|SLC8A1_ENST00000406785.2_Missense_Mutation_p.I346M|SLC8A1_ENST00000408028.2_Missense_Mutation_p.I346M|SLC8A1_ENST00000405901.3_Missense_Mutation_p.I346M|SLC8A1_ENST00000332839.4_Missense_Mutation_p.I346M|SLC8A1_ENST00000406391.2_Missense_Mutation_p.I346M|SLC8A1_ENST00000542756.1_Missense_Mutation_p.I346M|SLC8A1_ENST00000402441.1_Missense_Mutation_p.I346M|SLC8A1_ENST00000542024.1_Missense_Mutation_p.I346M			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	346					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.I346M(1)		NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	TAGCTAATTCTATTAATTGCT	0.403																																					p.I346M		Atlas-SNP	.											SLC8A1,NS,carcinoma,0,1	SLC8A1	221	.	1	Substitution - Missense(1)	lung(1)	c.A1038G						.						165	166	166					2																	40656383		2203	4300	6503	SO:0001583	missense	6546	exon1			TAATTCTATTAAT		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.1038A>G	chr2.hg19:g.40656383T>C	ENSP00000384763:p.Ile346Met	101.0	1.0		113.0	62.0	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	hg19	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	T	8.898	0.955541	0.18507	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.28666	1.6;1.64;1.65;1.64;1.6;1.6;1.65;1.61;1.6;1.6	6.17	-0.778	0.10977	Heat shock protein DnaJ, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.33381	0.0861	L	0.28014	0.82	0.58432	D	0.999995	B;D;B;B;B	0.65815	0.41;0.995;0.41;0.196;0.124	B;D;B;B;B	0.80764	0.257;0.994;0.257;0.072;0.031	T	0.06058	-1.0848	10	0.45353	T	0.12	.	6.7316	0.23387	0.4667:0.0:0.2404:0.293	.	346;346;346;346;346	P32418-4;P32418-2;P32418-3;F6VPY9;P32418	.;.;.;.;NAC1_HUMAN	M	346	ENSP00000383886:I346M;ENSP00000440727:I346M;ENSP00000384763:I346M;ENSP00000385678:I346M;ENSP00000385188:I346M;ENSP00000385535:I346M;ENSP00000332931:I346M;ENSP00000384908:I346M;ENSP00000385811:I346M;ENSP00000443515:I346M	ENSP00000332931:I346M	I	-	3	3	SLC8A1	40509887	0.006000	0.16342	0.949000	0.38748	0.996000	0.88848	-1.357000	0.02607	-0.343000	0.08351	0.533000	0.62120	ATA	.	.		0.403	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		C	40656383	T	C	40656383	3	2	202	1	0	0	0	0	1	0	0	0	14721	1512	53	2	2031	2	SLC8A1	2	40656383	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	14999546	40656383	202542990	11	29624										
PCBP1	5093	hgsc.bcm.edu	37	chr2	70314990	70314990	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaggggagtcggttaagaggAtccgcgaggagagtggcgcg	20	6	0	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr2:70314990A>C	ENST00000303577.5	+	1	406	c.115A>C	c.(115-117)Atc>Ctc	p.I39L	PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000439670.2_RNA|PCBP1-AS1_ENST00000437019.1_RNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000596665.1_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	39	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						GGTTAAGAGGATCCGCGAGGA	0.517																																					p.I39L	Colon(85;1146 1307 3484 18706 25380)	Atlas-SNP	.											.	PCBP1	28	.	0			c.A115C						.						112	115	114					2																	70314990		2203	4300	6503	SO:0001583	missense	5093	exon1			AAGAGGATCCGCG		CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.115A>C	chr2.hg19:g.70314990A>C	ENSP00000305556:p.Ile39Leu	169.0	0.0		222.0	58.0	NM_006196	Q13157|Q14975	Missense_Mutation	SNP	ENST00000303577.5	hg19	CCDS1898.1	.	.	.	.	.	.	.	.	.	.	A	12.63	1.996869	0.35226	.	.	ENSG00000169564	ENST00000303577	T	0.48836	0.8	4.22	4.22	0.49857	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.204106	0.49305	D	0.000160	T	0.30103	0.0754	N	0.25992	0.78	0.36171	D	0.848796	B	0.10296	0.003	B	0.20577	0.03	T	0.18681	-1.0329	10	0.02654	T	1	.	11.9582	0.52993	1.0:0.0:0.0:0.0	.	39	Q15365	PCBP1_HUMAN	L	39	ENSP00000305556:I39L	ENSP00000305556:I39L	I	+	1	0	PCBP1	70168494	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.003000	0.63959	2.145000	0.66743	0.529000	0.55759	ATC	.	.		0.517	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		C	70314990	A	C	70314990	3	2	202	1	0	0	0	0	1	0	0	0	11509	333	12	5	117	5	PCBP1	2	70314990	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	29658607	70314990	172884383	12	29625										
POTEF	728378	hgsc.bcm.edu	37	chr2	130832582	130832582	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgaaggtctcaaacatgatCtgggtcatcttctcgcggtt	10	9	5	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr2:130832582C>A	ENST00000409914.2	-	17	2862	c.2463G>T	c.(2461-2463)caG>caT	p.Q821H	POTEF_ENST00000357462.5_Missense_Mutation_p.Q821H	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	821	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						CAAACATGATCTGGGTCATCT	0.592																																					p.Q821H		Atlas-SNP	.											.	POTEF	140	.	0			c.G2463T						.						112	127	122					2																	130832582		2203	4299	6502	SO:0001583	missense	728378	exon17			CATGATCTGGGTC	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33905	protein-coding gene	gene with protein product			"ANKRD26-like family C, member 1B"	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2463G>T	chr2.hg19:g.130832582C>A	ENSP00000386786:p.Gln821His	196.0	1.0		251.0	143.0	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	hg19	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	15.81	2.943980	0.53079	.	.	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.97688	-4.49;-4.49	.	.	.	.	.	.	.	.	D	0.98476	0.9492	H	0.99940	5	0.26212	N	0.979286	B	0.27192	0.171	B	0.30782	0.12	D	0.96697	0.9515	8	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	.	821	A5A3E0	POTEF_HUMAN	H	821	ENSP00000350052:Q821H;ENSP00000386786:Q821H	ENSP00000350052:Q821H	Q	-	3	2	POTEF	130549052	1.000000	0.71417	0.366000	0.25914	0.368000	0.29767	5.244000	0.65400	0.119000	0.18210	0.121000	0.15741	CAG	.	.		0.592	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		A	130832582	C	A	130832582	3	1	202	1	0	0	0	0	1	0	0	0	12274	912	32	3	768	3	POTEF	2	130832582	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	60517592	130832582	112366791	13	29626										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148674942	148674942	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agttcattggtgcagaaaaaCgaggcaccagtgttgatgtg	13	6	1	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr2:148674942C>T	ENST00000241416.7	+	6	1399	c.763C>T	c.(763-765)Cga>Tga	p.R255*	ACVR2A_ENST00000535787.1_Nonsense_Mutation_p.R147*|ACVR2A_ENST00000404590.1_Nonsense_Mutation_p.R255*	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	255	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TGCAGAAAAACGAGGCACCAG	0.398																																					p.R255X		Atlas-SNP	.											ACVR2A,caecum,carcinoma,0,1	ACVR2A	125	.	0			c.C763T						.						116	96	103					2																	148674942		2202	4299	6501	SO:0001587	stop_gained	92	exon6			GAAAAACGAGGCA		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.763C>T	chr2.hg19:g.148674942C>T	ENSP00000241416:p.Arg255*	265.0	0.0		294.0	80.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Nonsense_Mutation	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	C	41	9.153642	0.99084	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	.	.	.	5.68	2.53	0.30540	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0985	0.65039	0.501:0.499:0.0:0.0	.	.	.	.	X	255;147;255	.	ENSP00000241416:R255X	R	+	1	2	ACVR2A	148391412	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.544000	0.36158	1.360000	0.45960	0.655000	0.94253	CGA	.	.		0.398	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		T	148674942	C	T	148674942	4	4	202	1	0	0	0	0	0	1	0	0	223	528	19	1	785	1	ACVR2A	2	148674942	Nonsense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	17842360	148674942	94524431	14	29627										
RAD18	56852	hgsc.bcm.edu	37	chr3	8988966	8988966	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttatttttcagatccggctcTgtgacagtctagaaaaaaca	7	8	3	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr3:8988966T>A	ENST00000264926.2	-	4	320	c.204A>T	c.(202-204)acA>acT	p.T68T	RAD18_ENST00000495087.1_5'UTR	NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase	68					DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		GATCCGGCTCTGTGACAGTCT	0.338								Rad6 pathway																													p.T68T		Atlas-SNP	.											.	RAD18	52	.	0			c.A204T						.						164	173	170					3																	8988966		2202	4300	6502	SO:0001819	synonymous_variant	56852	exon4			CGGCTCTGTGACA		CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950		"RING-type (C3HC4) zinc fingers"	18278	protein-coding gene	gene with protein product		605256	"RAD18 homolog (S. cerevisiae)"			10884424, 10908344	Standard	NM_020165		Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.204A>T	chr3.hg19:g.8988966T>A		136.0	0.0		138.0	33.0	NM_020165	Q58F55|Q9NRT6	Silent	SNP	ENST00000264926.2	hg19	CCDS2571.1																																																																																			.	.		0.338	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207071.2	NM_020165		A	8988966	T	A	8988966	2	1	202	1	0	0	0	0	0	0	0	1	12995	1567	55	4		4	RAD18	3	8988966	Silent	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10		8988966	189033464	15	29628										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10392219	10392219	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtcgccagtgaccatgcggaCcgtgatgcctgcccgctggc	14	15	0	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr3:10392219C>A	ENST00000352432.4	-	14	2248	c.2179G>T	c.(2179-2181)Gtc>Ttc	p.V727F	ATP2B2_ENST00000360273.2_Missense_Mutation_p.V727F|ATP2B2_ENST00000343816.4_Missense_Mutation_p.V713F|ATP2B2_ENST00000397077.1_Missense_Mutation_p.V682F|ATP2B2_ENST00000383800.4_Missense_Mutation_p.V682F			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	727					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						ACCATGCGGACCGTGATGCCT	0.647																																					p.V727F	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.G2179T						.						96	85	89					3																	10392219		2203	4300	6503	SO:0001583	missense	491	exon15			TGCGGACCGTGAT	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.2179G>T	chr3.hg19:g.10392219C>A	ENSP00000324172:p.Val727Phe	41.0	0.0		44.0	27.0	NM_001001331	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.768671	0.90020	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.97041	-4.22;-4.22;-4.22;-4.22;-4.22;-4.22	4.18	4.18	0.49190	HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.99158	0.9709	H	0.99425	4.56	0.80722	D	1	D;D;D	0.67145	0.996;0.979;0.992	P;P;D	0.64776	0.89;0.867;0.929	D	0.98722	1.0709	10	0.87932	D	0	-42.772	16.8604	0.86016	0.0:1.0:0.0:0.0	.	662;694;727	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	F	727;682;682;727;713;662;583;727	ENSP00000324172:V727F;ENSP00000373311:V682F;ENSP00000380267:V682F;ENSP00000353414:V727F;ENSP00000344677:V713F;ENSP00000414854:V583F	ENSP00000342954:V727F	V	-	1	0	ATP2B2	10367219	1.000000	0.71417	0.822000	0.32727	0.981000	0.71138	7.808000	0.86044	2.022000	0.59522	0.491000	0.48974	GTC	.	.		0.647	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10392219	C	A	10392219	3	1	202	1	0	0	0	0	1	0	0	0	1140	507	18	3	1588	3	ATP2B2	3	10392219	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	1403253	10392219	187630211	16	29629										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266124	41266124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaatccattctggtgccactAccacagctccttctctgagt	7	14	2	1	rs121913412		TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr3:41266124A>G	ENST00000349496.5	+	3	401	c.121A>G	c.(121-123)Acc>Gcc	p.T41A	CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34A|CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41A|CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	41			T -> A (in hepatoblastoma and hepatocellular carcinoma; also in a desmoid tumor; strongly reduces phosphorylation and degradation; abolishes phosphorylation on Ser-33 and Ser-37 and enhances transactivation of target genes). {ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10398436, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10655994, ECO:0000269|PubMed:9927029}.|T -> I (in PTR, hepatocellular carcinoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T41A(550)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41P(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.A39_T42del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGTGCCACTACCACAGCTCC	0.507	T41A(CCK81_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.T41A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	681	Substitution - Missense(559)|Deletion - In frame(96)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)	soft_tissue(387)|liver(158)|large_intestine(61)|endometrium(17)|kidney(11)|stomach(8)|biliary_tract(7)|ovary(6)|small_intestine(4)|lung(4)|prostate(4)|adrenal_gland(3)|haematopoietic_and_lymphoid_tissue(3)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|salivary_gland(1)|pituitary(1)|pancreas(1)	c.A121G						.						89	77	81					3																	41266124		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCCACTACCACAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.121A>G	chr3.hg19:g.41266124A>G	ENSP00000344456:p.Thr41Ala	177.0	0.0		167.0	97.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449381	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.63117	0.2484	M	0.79258	2.445	0.80722	D	1	P	0.50943	0.94	P	0.52267	0.694	T	0.68561	-0.5376	10	0.87932	D	0	-8.9189	16.3453	0.83126	1.0:0.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	A	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34A;ENSP00000385604:T41A;ENSP00000412219:T41A;ENSP00000379486:T41A;ENSP00000344456:T41A;ENSP00000411226:T34A;ENSP00000379488:T41A;ENSP00000409302:T41A;ENSP00000401599:T41A	ENSP00000344456:T41A	T	+	1	0	CTNNB1	41241128	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	ACC	.	.		0.507	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266124	A	G	41266124	3	3	202	1	0	0	0	0	1	0	0	0	4018	391	14	2	127	2	CTNNB1	3	41266124	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	30873905	41266124	156756306	17	29630										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49161489	49161489	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctgcagtgacctgtgaagcGgtgacactgaggtgtatcta	14	8	1	4			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr3:49161489G>A	ENST00000418109.1	-	25	3633	c.3469C>T	c.(3469-3471)Cgc>Tgc	p.R1157C	LAMB2_ENST00000305544.4_Missense_Mutation_p.R1157C|LAMB2_ENST00000464891.1_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1157	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCTGTGAAGCGGTGACACTGA	0.572																																					p.R1157C		Atlas-SNP	.											.	LAMB2	156	.	0			c.C3469T						.						69	69	69					3																	49161489		2203	4300	6503	SO:0001583	missense	3913	exon24			TGAAGCGGTGACA		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.3469C>T	chr3.hg19:g.49161489G>A	ENSP00000388325:p.Arg1157Cys	43.0	0.0		55.0	12.0	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	hg19	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.322275	0.60634	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.62364	0.03;0.03	5.84	4.95	0.65309	EGF-like, laminin (3);	0.108012	0.64402	D	0.000009	T	0.80849	0.4702	M	0.92219	3.285	0.80722	D	1	D	0.76494	0.999	P	0.61201	0.885	D	0.84883	0.0832	10	0.72032	D	0.01	.	11.7847	0.52034	0.0:0.1334:0.7279:0.1388	.	1157	P55268	LAMB2_HUMAN	C	1157	ENSP00000388325:R1157C;ENSP00000307156:R1157C	ENSP00000307156:R1157C	R	-	1	0	LAMB2	49136493	1.000000	0.71417	0.945000	0.38365	0.976000	0.68499	3.663000	0.54518	1.454000	0.47793	0.561000	0.74099	CGC	.	.		0.572	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		A	49161489	G	A	49161489	3	1	202	1	0	0	0	0	1	0	0	0	8620	1116	39	1	1963	1	LAMB2	3	49161489	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	7895365	49161489	148860941	18	29631										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111993747	111993747	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttaaaaatatacttacctaAggtatggtttcttttacttt	4	5	1	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr3:111993747A>T	ENST00000305815.5	-	6	862	c.610T>A	c.(610-612)Tta>Ata	p.L204I	SLC9C1_ENST00000487372.1_Missense_Mutation_p.L204I	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	204					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TACTTACCTAAGGTATGGTTT	0.269																																					p.L204I		Atlas-SNP	.											.	.	.	.	0			c.T610A						.						33	38	36					3																	111993747		2169	4263	6432	SO:0001583	missense	285335	exon6			TACCTAAGGTATG	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.610T>A	chr3.hg19:g.111993747A>T	ENSP00000306627:p.Leu204Ile	309.0	0.0		286.0	92.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	A	6.320	0.427209	0.11987	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.15139	2.45;2.45	5.16	-10.3	0.00346	Cation/H+ exchanger (1);	0.969423	0.08432	N	0.946751	T	0.07143	0.0181	N	0.25647	0.755	0.09310	N	1	B;B	0.19817	0.01;0.039	B;B	0.25506	0.011;0.061	T	0.22695	-1.0209	10	0.19147	T	0.46	.	1.6945	0.02859	0.2835:0.0888:0.1853:0.4423	.	204;204	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	I	204	ENSP00000306627:L204I;ENSP00000420688:L204I	ENSP00000306627:L204I	L	-	1	2	SLC9A10	113476437	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.698000	0.05092	-2.934000	0.00299	-1.685000	0.00733	TTA	.	.		0.269	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		T	111993747	A	T	111993747	3	4	202	1	0	0	0	0	1	0	0	0	14725	69	3	4	3019	4	SLC9A10	3	111993747	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	62832258	111993747	86028683	19	29632										
SEC61A1	29927	hgsc.bcm.edu	37	chr3	127788431	127788431	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggatcctgctcgcagtcacaAtcatctaccagtactttgag	8	12	3	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr3:127788431A>G	ENST00000243253.3	+	12	1541	c.1357A>G	c.(1357-1359)Atc>Gtc	p.I453V	SEC61A1_ENST00000464451.1_Missense_Mutation_p.I459V|SEC61A1_ENST00000424880.2_Missense_Mutation_p.I333V|SEC61A1_ENST00000483956.1_3'UTR|RUVBL1_ENST00000464873.1_Intron	NM_013336.3	NP_037468.1	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit (S. cerevisiae)	453					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell growth (GO:0016049)|endoplasmic reticulum organization (GO:0007029)|posttranslational protein targeting to membrane (GO:0006620)|protein targeting to ER (GO:0045047)|response to interferon-gamma (GO:0034341)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)			central_nervous_system(1)|kidney(1)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|prostate(4)	21						CGCAGTCACAATCATCTACCA	0.602																																					p.I453V		Atlas-SNP	.											.	SEC61A1	39	.	0			c.A1357G						.						105	113	110					3																	127788431		2203	4300	6503	SO:0001583	missense	29927	exon12			GTCACAATCATCT	AF077032	CCDS3046.1	3q21.3	2008-02-05			ENSG00000058262	ENSG00000058262			18276	protein-coding gene	gene with protein product		609213					Standard	NM_013336		Approved		uc003ekb.3	P61619	OTTHUMG00000159624	ENST00000243253.3:c.1357A>G	chr3.hg19:g.127788431A>G	ENSP00000243253:p.Ile453Val	88.0	0.0		73.0	44.0	NM_013336	P38378|P57726|Q5JPF8|Q8N0Z4|Q8N3U3|Q8NC71|Q9BU16|Q9Y2R3	Missense_Mutation	SNP	ENST00000243253.3	hg19	CCDS3046.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.489634	0.44249	.	.	ENSG00000058262	ENST00000464451;ENST00000243253;ENST00000424880	.	.	.	5.96	5.96	0.96718	SecY subunit domain (2);	0.000000	0.85682	D	0.000000	T	0.70979	0.3286	M	0.71036	2.16	0.80722	D	1	B	0.12630	0.006	B	0.31547	0.132	T	0.68424	-0.5412	9	0.54805	T	0.06	.	16.4343	0.83869	1.0:0.0:0.0:0.0	.	453	P61619	S61A1_HUMAN	V	459;453;333	.	ENSP00000243253:I453V	I	+	1	0	SEC61A1	129271121	1.000000	0.71417	0.958000	0.39756	0.002000	0.02628	9.339000	0.96797	2.285000	0.76669	0.528000	0.53228	ATC	.	.		0.602	SEC61A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356541.2	NM_013336		G	127788431	A	G	127788431	3	3	202	1	0	0	0	0	1	0	0	0	14015	101	4	2	1403	2	SEC61A1	3	127788431	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	15794684	127788431	70233999	20	29633										
MBD4	8930	hgsc.bcm.edu	37	chr3	129150366	129150366	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aagatagacttaatttttcaTgattttcccaaagccagtca	5	8	2	3	rs370417942		TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr3:129150366T>A	ENST00000249910.1	-	8	1896	c.1721A>T	c.(1720-1722)cAt>cTt	p.H574L	EFCAB12_ENST00000326085.3_5'Flank|MBD4_ENST00000503197.1_3'UTR|EFCAB12_ENST00000505956.1_5'Flank|MBD4_ENST00000429544.2_Missense_Mutation_p.H568L|MBD4_ENST00000393278.2_Missense_Mutation_p.H256L|MBD4_ENST00000509587.1_5'Flank	NM_003925.1	NP_003916.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	574					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						TAATTTTTCATGATTTTCCCA	0.358								Base excision repair (BER), DNA glycosylases																													p.H574L		Atlas-SNP	.											.	MBD4	53	.	0			c.A1721T						.	T	LEU/HIS	0,4406		0,0,2203	192	202	198		1721	5.1	1	3		198	1,8599	1.2+/-3.3	0,1,4299	no	missense	MBD4	NM_003925.1	99	0,1,6502	AA,AT,TT		0.0116,0.0,0.0077	possibly-damaging	574/581	129150366	1,13005	2203	4300	6503	SO:0001583	missense	8930	exon8			TTTTCATGATTTT	AF072250	CCDS3058.1, CCDS63766.1, CCDS63767.1, CCDS63768.1, CCDS63769.1	3q21.3	2004-03-02			ENSG00000129071	ENSG00000129071			6919	protein-coding gene	gene with protein product		603574				9774669, 10097147	Standard	NM_003925		Approved	MED1	uc003emh.2	O95243	OTTHUMG00000159463	ENST00000249910.1:c.1721A>T	chr3.hg19:g.129150366T>A	ENSP00000249910:p.His574Leu	63.0	0.0		57.0	6.0	NM_003925	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000249910.1	hg19	CCDS3058.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.225794	0.58668	0.0	1.16E-4	ENSG00000129071	ENST00000429544;ENST00000249910;ENST00000393278	T;T;T	0.42131	0.98;0.98;0.98	5.12	5.12	0.69794	DNA glycosylase (2);	0.107611	0.64402	D	0.000007	T	0.35364	0.0929	L	0.39898	1.24	0.53005	D	0.999967	P;P;P	0.39847	0.536;0.691;0.565	B;B;B	0.39771	0.251;0.309;0.163	T	0.20405	-1.0276	10	0.51188	T	0.08	-6.5319	10.4915	0.44754	0.0:0.0787:0.0:0.9213	.	256;568;574	Q2MD36;O95243-2;O95243	.;.;MBD4_HUMAN	L	568;574;256	ENSP00000394080:H568L;ENSP00000249910:H574L;ENSP00000376959:H256L	ENSP00000249910:H574L	H	-	2	0	MBD4	130633056	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.739000	0.55075	2.078000	0.62432	0.529000	0.55759	CAT	.	.		0.358	MBD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355529.1	NM_003925		A	129150366	T	A	129150366	3	1	202	1	0	0	0	0	1	0	0	0	9355	1464	51	4	25	4	MBD4	3	129150366	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	1361935	129150366	68872064	21	29634										
UBA5	79876	hgsc.bcm.edu	37	chr3	132389819	132389819	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctttgactagtaatggtgggTtagaagaaggaaaacctgtt	12	4	0	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr3:132389819T>G	ENST00000356232.4	+	6	1577	c.505T>G	c.(505-507)Tta>Gta	p.L169V	UBA5_ENST00000494238.2_Missense_Mutation_p.L113V|UBA5_ENST00000264991.4_Missense_Mutation_p.L113V|UBA5_ENST00000493720.2_Missense_Mutation_p.L169V|UBA5_ENST00000473651.1_Missense_Mutation_p.L169V	NM_024818.3	NP_079094.1	Q9GZZ9	UBA5_HUMAN	ubiquitin-like modifier activating enzyme 5	169					protein ufmylation (GO:0071569)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|UFM1 activating enzyme activity (GO:0071566)			breast(2)|endometrium(4)|kidney(4)|large_intestine(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						TAATGGTGGGTTAGAAGAAGG	0.338																																					p.L169V		Atlas-SNP	.											.	UBA5	33	.	0			c.T505G						.						181	179	180					3																	132389819		2203	4300	6503	SO:0001583	missense	79876	exon6			GGTGGGTTAGAAG	AY253672	CCDS3076.1, CCDS3077.1	3q22	2007-11-30	2007-11-30	2007-11-30	ENSG00000081307	ENSG00000081307		"Ubiquitin-like modifier activating enzymes"	23230	protein-coding gene	gene with protein product	"UBA5, ubiquitin-activating enzyme E1 homolog (yeast)"	610552	"ubiquitin-activating enzyme E1-domain containing 1"	UBE1DC1		11230166, 15071506	Standard	NM_198329		Approved	FLJ23251	uc003epa.4	Q9GZZ9	OTTHUMG00000159759	ENST00000356232.4:c.505T>G	chr3.hg19:g.132389819T>G	ENSP00000348565:p.Leu169Val	107.0	0.0		122.0	61.0	NM_024818	A6NJL3|D3DNC8|Q96ST1	Missense_Mutation	SNP	ENST00000356232.4	hg19	CCDS3076.1	.	.	.	.	.	.	.	.	.	.	T	11.73	1.725365	0.30593	.	.	ENSG00000081307	ENST00000264991;ENST00000356232;ENST00000493720;ENST00000473651;ENST00000494238;ENST00000464068	D;D;D;D;D	0.85339	-1.9;-1.94;-1.97;-1.97;-1.9	5.58	3.01	0.34805	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.134693	0.50627	D	0.000117	T	0.77505	0.4140	L	0.55103	1.725	0.50813	D	0.999894	B;B	0.12013	0.005;0.005	B;B	0.14578	0.01;0.011	T	0.69394	-0.5157	10	0.36615	T	0.2	-5.278	3.8234	0.08845	0.2821:0.14:0.0:0.578	.	169;169	E7EWE1;Q9GZZ9	.;UBA5_HUMAN	V	113;169;169;169;113;79	ENSP00000264991:L113V;ENSP00000348565:L169V;ENSP00000417879:L169V;ENSP00000424984:L169V;ENSP00000418807:L113V	ENSP00000264991:L113V	L	+	1	2	UBA5	133872509	0.060000	0.20803	0.998000	0.56505	0.996000	0.88848	0.372000	0.20467	0.901000	0.36495	0.533000	0.62120	TTA	.	.		0.338	UBA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357187.2	NM_024818		G	132389819	T	G	132389819	3	3	202	1	0	0	0	0	1	0	0	0	16845	1722	60	5	527	5	UBA5	3	132389819	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	3239453	132389819	65632611	22	29635										
ALB	213	hgsc.bcm.edu	37	chr4	74275109	74275109	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccagaagacatccttactttTatgccccggaactccttttc	5	14	0	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr4:74275109T>C	ENST00000503124.1	+	3	277	c.70T>C	c.(70-72)Tat>Cat	p.Y24H	ALB_ENST00000401494.3_Missense_Mutation_p.Y59H|ALB_ENST00000509063.1_Missense_Mutation_p.Y174H|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000415165.2_Intron|ALB_ENST00000295897.4_Missense_Mutation_p.Y174H			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCCTTACTTTTATGCCCCGGA	0.348																																					p.Y174H		Atlas-SNP	.											.	ALB	132	.	0			c.T520C						.						67	72	71					4																	74275109		2203	4299	6502	SO:0001583	missense	213	exon5			TACTTTTATGCCC	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.70T>C	chr4.hg19:g.74275109T>C	ENSP00000421027:p.Tyr24His	307.0	0.0		184.0	66.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.0|24.0	4.479187|4.479187	0.84747|0.84747	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000511370|ENST00000441319;ENST00000295897;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202	.|T;T;T;T;T	.|0.74737	.|-0.87;-0.87;0.87;-0.87;0.87	5.55|5.55	5.55|5.55	0.83447|0.83447	.|Serum albumin-like (1);Serum albumin, N-terminal (3);	.|0.159919	.|0.44097	.|D	.|0.000493	D|D	0.87517|0.87517	0.6197|0.6197	M|M	0.86953|0.86953	2.85|2.85	0.44055|0.44055	D|D	0.996798|0.996798	.|D;D;P;D	.|0.76494	.|0.998;0.999;0.861;0.968	.|D;D;P;D	.|0.77557	.|0.99;0.99;0.831;0.931	D|D	0.89592|0.89592	0.3828|0.3828	5|10	.|0.87932	.|D	.|0	-32.146|-32.146	14.6717|14.6717	0.68948|0.68948	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|59;24;174;174	.|B7WNR0;D6RHD5;A6NBZ8;P02768	.|.;.;.;ALBU_HUMAN	S|H	18|176;174;24;174;59;183	.|ENSP00000392541:Y176H;ENSP00000295897:Y174H;ENSP00000421027:Y24H;ENSP00000422784:Y174H;ENSP00000384695:Y59H	.|ENSP00000295897:Y174H	L|Y	+|+	2|1	0|0	ALB|ALB	74493973|74493973	0.996000|0.996000	0.38824|0.38824	0.997000|0.997000	0.53966|0.53966	0.938000|0.938000	0.57974|0.57974	2.327000|2.327000	0.43858|0.43858	2.333000|2.333000	0.79357|0.79357	0.482000|0.482000	0.46254|0.46254	TTA|TAT	.	.		0.348	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		C	74275109	T	C	74275109	3	2	202	1	0	0	0	0	1	0	0	0	486	1754	61	2	538	2	ALB	4	74275109	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10		74275109	116879167	23	29636										
DSPP	1834	hgsc.bcm.edu	37	chr4	88533640	88533640	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tacatattccacattagcaaAcgaagaggggaatattgagg	10	6	0	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr4:88533640A>T	ENST00000282478.7	+	3	335	c.302A>T	c.(301-303)aAc>aTc	p.N101I	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.N101I			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	101					biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		ACATTAGCAAACGAAGAGGGG	0.438																																					p.N101I		Atlas-SNP	.											.	DSPP	174	.	0			c.A302T						.						95	93	93					4																	88533640		1913	4124	6037	SO:0001583	missense	1834	exon4			TAGCAAACGAAGA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.302A>T	chr4.hg19:g.88533640A>T	ENSP00000282478:p.Asn101Ile	449.0	0.0		328.0	123.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	12.91	2.078154	0.36662	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.91407	-2.84;-2.84	5.24	2.85	0.33270	.	0.486802	0.15166	N	0.276902	D	0.85283	0.5661	L	0.34521	1.04	0.09310	N	1	B	0.32467	0.372	B	0.36989	0.238	T	0.77940	-0.2399	10	0.87932	D	0	-11.2723	7.4067	0.26995	0.8187:0.0:0.1813:0.0	.	101	Q9NZW4	DSPP_HUMAN	I	101	ENSP00000382213:N101I;ENSP00000282478:N101I	ENSP00000282478:N101I	N	+	2	0	DSPP	88752664	0.023000	0.18921	0.002000	0.10522	0.035000	0.12851	2.741000	0.47426	0.837000	0.34925	0.377000	0.23210	AAC	.	.		0.438	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88533640	A	T	88533640	3	4	202	1	0	0	0	0	1	0	0	0	4784	43	2	4	312	4	DSPP	4	88533640	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	14258531	88533640	102620636	24	29637										
ADH1A	124	hgsc.bcm.edu	37	chr4	100201407	100201407	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acgatgacacttgtgccacaTgcctcatgacaacataacag	7	12	1	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr4:100201407T>C	ENST00000209668.2	-	7	971	c.858A>G	c.(856-858)gcA>gcG	p.A286A	RP11-696N14.1_ENST00000500358.2_RNA|RP11-696N14.1_ENST00000506160.1_RNA	NM_000667.3	NP_000658.1	P07327	ADH1A_HUMAN	alcohol dehydrogenase 1A (class I), alpha polypeptide	286					alcohol metabolic process (GO:0006066)|drug metabolic process (GO:0017144)|ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)	25				OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Ethanol(DB00898)|Fomepizole(DB01213)	TTGTGCCACATGCCTCATGAC	0.448																																					p.A286A		Atlas-SNP	.											.	ADH1A	49	.	0			c.A858G						.						251	221	231					4																	100201407		2203	4300	6503	SO:0001819	synonymous_variant	124	exon7			GCCACATGCCTCA	M12963	CCDS3648.1	4q23	2009-12-04			ENSG00000187758	ENSG00000187758	1.1.1.1	"Alcohol dehydrogenases"	249	protein-coding gene	gene with protein product		103700		ADH1		3006456	Standard	NM_000667		Approved		uc003hur.2	P07327	OTTHUMG00000131026	ENST00000209668.2:c.858A>G	chr4.hg19:g.100201407T>C		137.0	0.0		80.0	22.0	NM_000667	A8K3E3|Q17R68	Silent	SNP	ENST00000209668.2	hg19	CCDS3648.1																																																																																			.	.		0.448	ADH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253669.1	NM_000667		C	100201407	T	C	100201407	2	2	202	1	0	0	0	0	0	0	0	1	307	1451	51	2		2	ADH1A	4	100201407	Silent	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	11667767	100201407	90952869	25	29638										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155411056	155411056	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggaaaaatacccctgggggGccgccgggtagcaacgcgaa	15	11	0	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr4:155411056G>A	ENST00000339452.1	-	1	1812	c.1452C>T	c.(1450-1452)ggC>ggT	p.G484G	DCHS2_ENST00000456341.2_Silent_p.G477G|DCHS2_ENST00000443500.1_Silent_p.G484G	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1643	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CCCCTGGGGGGCCGCCGGGTA	0.632																																					p.G484G		Atlas-SNP	.											.	DCHS2	594	.	0			c.C1452T						.						17	22	21					4																	155411056		692	1591	2283	SO:0001819	synonymous_variant	54798	exon1			TGGGGGGCCGCCG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.1452C>T	chr4.hg19:g.155411056G>A		53.0	0.0		51.0	24.0	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000339452.1	hg19	CCDS47150.1																																																																																			.	.		0.632	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552		A	155411056	G	A	155411056	2	1	202	1	0	0	0	0	0	0	0	1	4290	1190	42	3		3	DCHS2	4	155411056	Silent	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	55209649	155411056	35743220	26	29639										
WDR17	116966	hgsc.bcm.edu	37	chr4	177056301	177056301	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	actgcaaattcaaacctgacGatcctaatcttttagcaaca	4	11	2	1	rs140987021		TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr4:177056301G>A	ENST00000280190.4	+	9	1369	c.1213G>A	c.(1213-1215)Gat>Aat	p.D405N	WDR17_ENST00000393643.2_Missense_Mutation_p.D381N|WDR17_ENST00000508596.1_Missense_Mutation_p.D381N|WDR17_ENST00000507824.2_Missense_Mutation_p.D388N			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	405										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CAAACCTGACGATCCTAATCT	0.353																																					p.D405N		Atlas-SNP	.											.	WDR17	198	.	0			c.G1213A						.	G	ASN/ASP,ASN/ASP	0,4406		0,0,2203	121	122	122		1213,1141	2.4	1	4	dbSNP_134	122	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	WDR17	NM_170710.4,NM_181265.3	23,23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	405/1323,381/1284	177056301	1,13005	2203	4300	6503	SO:0001583	missense	116966	exon9			CCTGACGATCCTA	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.1213G>A	chr4.hg19:g.177056301G>A	ENSP00000280190:p.Asp405Asn	341.0	0.0		296.0	107.0	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	hg19	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	G	10.35	1.326502	0.24080	0.0	1.16E-4	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.58652	0.35;3.58;0.32	5.5	2.42	0.29668	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.265065	0.38164	N	0.001790	T	0.30324	0.0761	N	0.13198	0.31	0.48571	D	0.999678	B;B	0.19445	0.036;0.036	B;B	0.18871	0.023;0.023	T	0.15150	-1.0447	10	0.05525	T	0.97	-17.5458	6.7154	0.23300	0.433:0.0:0.567:0.0	.	381;405	E7EQX0;Q8IZU2	.;WDR17_HUMAN	N	381;381;405;388	ENSP00000422763:D381N;ENSP00000377258:D381N;ENSP00000280190:D405N	ENSP00000280190:D405N	D	+	1	0	WDR17	177293295	1.000000	0.71417	0.998000	0.56505	0.740000	0.42216	3.339000	0.52135	0.703000	0.31848	0.650000	0.86243	GAT	.	G|1.000;A|0.000		0.353	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			A	177056301	G	A	177056301	3	1	202	1	0	0	0	0	1	0	0	0	17292	1058	37	1	1243	1	WDR17	4	177056301	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	21645245	177056301	14097975	27	29640										
ZFP42	132625	hgsc.bcm.edu	37	chr4	188924482	188924482	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctcgcagaatttgctagaaAgaagccccccataaataaag	8	10	0	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr4:188924482A>T	ENST00000326866.4	+	4	929	c.521A>T	c.(520-522)aAg>aTg	p.K174M	ZFP42_ENST00000509524.1_Missense_Mutation_p.K174M	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	174					female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		TTTGCTAGAAAGAAGCCCCCC	0.468																																					p.K174M		Atlas-SNP	.											.	ZFP42	87	.	0			c.A521T						.						97	110	106					4																	188924482		2203	4300	6503	SO:0001583	missense	132625	exon4			CTAGAAAGAAGCC	AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059		"Zinc fingers, C2H2-type"	30949	protein-coding gene	gene with protein product		614572	"zinc finger protein 42 homolog (mouse)", "zinc finger protein 42"			12110702	Standard	NM_174900		Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.521A>T	chr4.hg19:g.188924482A>T	ENSP00000317686:p.Lys174Met	77.0	0.0		66.0	34.0	NM_174900	D3DP65|Q8WXE2	Missense_Mutation	SNP	ENST00000326866.4	hg19	CCDS3849.1	.	.	.	.	.	.	.	.	.	.	A	7.168	0.587067	0.13812	.	.	ENSG00000179059	ENST00000326866;ENST00000509524	T;T	0.63744	-0.06;-0.06	4.27	0.326	0.15908	.	0.051145	0.85682	U	0.000000	T	0.36276	0.0961	N	0.21194	0.64	0.20196	N	0.999921	B	0.34103	0.437	B	0.23716	0.048	T	0.14282	-1.0478	10	0.36615	T	0.2	.	5.3096	0.15823	0.4679:0.3591:0.0:0.173	.	174	Q96MM3	ZFP42_HUMAN	M	174	ENSP00000317686:K174M;ENSP00000424662:K174M	ENSP00000317686:K174M	K	+	2	0	ZFP42	189161476	0.000000	0.05858	0.124000	0.21820	0.126000	0.20510	-0.423000	0.07034	0.070000	0.16634	0.533000	0.62120	AAG	.	.		0.468	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900		T	188924482	A	T	188924482	3	4	202	1	0	0	0	0	1	0	0	0	17665	72	3	4	523	4	ZFP42	4	188924482	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	11868181	188924482	2229794	28	29641										
ZCCHC9	84240	hgsc.bcm.edu	37	chr5	80604841	80604841	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcttgtcctgataatcccaaAggactctatgctgatggtaa	8	9	2	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr5:80604841A>G	ENST00000254037.2	+	3	3767	c.612A>G	c.(610-612)aaA>aaG	p.K204K	ZCCHC9_ENST00000380199.5_Silent_p.K204K|ZCCHC9_ENST00000407610.3_Silent_p.K204K|ZCCHC9_ENST00000438268.2_Silent_p.K204K|ZCCHC9_ENST00000506458.1_3'UTR			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	204					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		ATAATCCCAAAGGACTCTATG	0.383																																					p.K204K		Atlas-SNP	.											.	ZCCHC9	26	.	0			c.A612G						.						116	103	107					5																	80604841		2203	4300	6503	SO:0001819	synonymous_variant	84240	exon4			TCCCAAAGGACTC	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"Zinc fingers, CCHC domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25424	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 41"					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.612A>G	chr5.hg19:g.80604841A>G		147.0	0.0		117.0	68.0	NM_001131036	B2RAE7|Q9H027	Silent	SNP	ENST00000254037.2	hg19	CCDS4054.1																																																																																			.	.		0.383	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280		G	80604841	A	G	80604841	2	3	202	1	0	0	0	0	0	0	0	1	17610	69	3	2		2	ZCCHC9	5	80604841	Silent	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10		80604841	100310419	29	29642										
PKD2L2	51306	hgsc.bcm.edu	37	chr5	137275835	137275835	+	3'UTR	DEL	A	A	-													0	0	1	0	0	0	1	1	0	gtgcctgacaaaacgaatttAagtaccagccaagtacacac							TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr5:137275835delA	ENST00000033079.3	-	0	3278				PKD2L2_ENST00000502810.1_3'UTR|PKD2L2_ENST00000508638.1_3'UTR|PKD2L2_ENST00000290431.5_Stop_Codon_Del|PKD2L2_ENST00000508883.1_Intron	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B						regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						AAACGAATTTAAGTACCAGCC	0.378																																					p.X614K		Atlas-INDEL	.											.	PKD2L2	68	.	0			c.1840delT						.						137	137	137					5																	137275835		2203	4300	6503	SO:0001624	3_prime_UTR_variant	27039	exon14			.	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.*79T>-	chr5.hg19:g.137275835delA		170.0	0.0		232.0	86.0	NM_014386	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Frame_Shift_Del	DEL	ENST00000033079.3	hg19	CCDS4195.1																																																																																			.	.		0.378	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			-	137275835	A	-	137275835	6	5	202	0	1	1	0	1	0	0	0	0	11977	369	13	0		0	PKD2L2	5	137275835	3'UTR	DEL	A	TCGA-DD-AADU-01A-11D-A40R-10	56670994	137275835	43639425	30	29643										
PSD2	84249	hgsc.bcm.edu	37	chr5	139213348	139213348	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cttggaccagctgaatgatgGccaagactttgccaaagacc	10	11	0	4			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr5:139213348G>A	ENST00000274710.3	+	8	1536	c.1331G>A	c.(1330-1332)gGc>gAc	p.G444D		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	444	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGAATGATGGCCAAGACTTT	0.493																																					p.G444D		Atlas-SNP	.											.	PSD2	88	.	0			c.G1331A						.						227	201	210					5																	139213348		2203	4300	6503	SO:0001583	missense	84249	exon8			ATGATGGCCAAGA	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1331G>A	chr5.hg19:g.139213348G>A	ENSP00000274710:p.Gly444Asp	78.0	0.0		111.0	30.0	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.656086	0.88056	.	.	ENSG00000146005	ENST00000274710	T	0.35605	1.3	5.07	5.07	0.68467	SEC7-like, alpha orthogonal bundle (1);SEC7-like (4);	0.000000	0.85682	D	0.000000	T	0.66528	0.2798	M	0.89287	3.02	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.74016	-0.3800	10	0.87932	D	0	.	16.9996	0.86378	0.0:0.0:1.0:0.0	.	444	Q9BQI7	PSD2_HUMAN	D	444	ENSP00000274710:G444D	ENSP00000274710:G444D	G	+	2	0	PSD2	139193532	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.671000	0.91174	2.518000	0.84900	0.542000	0.68232	GGC	.	.		0.493	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		A	139213348	G	A	139213348	3	1	202	1	0	0	0	0	1	0	0	0	12659	1203	42	3	1357	3	PSD2	5	139213348	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	1937513	139213348	41701912	31	29644										
C4A	720	hgsc.bcm.edu	37	chr6	31951924	31951925	+	Frame_Shift_Ins	INS	-	-	T													0	0	1	0	0	0	1	1	0	gatgaggatggtaagaagacINStttctttcgggggctggaga							TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr6:31951924_31951925insT	ENST00000428956.2	+	8	965_966	c.881_882insT	c.(880-885)actttcfs	p.TF294fs	C4A_ENST00000537134.1_Frame_Shift_Ins_p.TF214fs|C4A_ENST00000498271.1_Frame_Shift_Ins_p.TF294fs|C4A_ENST00000467948.1_Intron	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	294					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	GGTAAGAAGACTTTCTTTCGGG	0.579																																					p.T294fs		Atlas-INDEL	.											.	C4A	15	.	0			c.881_882insT						.																																			SO:0001589	frameshift_variant	720	exon8			.	L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731		"Blood group antigens", "Complement system"	1323	protein-coding gene	gene with protein product		120810	"complement component 4A"				Standard	NM_001252204		Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.884dupT	chr6.hg19:g.31951927_31951927dupT	ENSP00000396688:p.Thr294fs	163.0	0.0		149.0	27.0	NM_007293	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	Frame_Shift_Ins	INS	ENST00000428956.2	hg19	CCDS47404.1																																																																																			.	.		0.579	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293		T	31951925	-	T	31951924	7	5	202	1	0	1	1	0	0	0	0	0	2249	565	20	0	911	0	C4A	6	31951924	Frame_Shift_Ins	INS	-	TCGA-DD-AADU-01A-11D-A40R-10		31951924	139163143	32	29645										
C4A	721	hgsc.bcm.edu	37	chr6	31984662	31984663	+	Frame_Shift_Ins	INS	-	-	T													0	0	1	0	0	0	1	1	0	gatgaggatggtaagaagacINStttctttcgggggctggaga							TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr6:31984662_31984663insT	ENST00000435363.2	+	8	965_966	c.881_882insT	c.(880-885)actttcfs	p.TF294fs	C4B_ENST00000485543.1_Intron|C4B_ENST00000425700.2_Frame_Shift_Ins_p.TF294fs	NM_001002029.3	NP_001002029.3	P0C0L5	CO4B_HUMAN	complement component 4B (Chido blood group)	294					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|detection of molecule of bacterial origin (GO:0032490)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|complement binding (GO:0001848)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	GGTAAGAAGACTTTCTTTCGGG	0.579																																					p.T294fs		Atlas-INDEL	.											.	C4A	15	.	0			c.881_882insT						.																																			SO:0001589	frameshift_variant	720	exon8			.	AF019413	CCDS47405.1	6p21.3	2014-09-17	2009-01-06		ENSG00000224389	ENSG00000224389		"Blood group antigens", "Complement system"	1324	protein-coding gene	gene with protein product		120820	"complement component 4B"				Standard	NM_001002029		Approved	CPAMD3, C4F, CO4, C4B1, C4B3, CH	uc011jpm.2	P0C0L5	OTTHUMG00000031187	ENST00000435363.2:c.884dupT	chr6.hg19:g.31984665_31984665dupT	ENSP00000415941:p.Thr294fs	191.0	0.0		136.0	19.0	NM_007293	A2BHY4|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q6U2E9|Q6U2G1|Q6U2I5|Q6U2L1|Q6U2L7|Q6U2L9|Q6U2M5|Q6VCV8|Q96SA7|Q9NPK5|Q9UIP5	Frame_Shift_Ins	INS	ENST00000435363.2	hg19	CCDS47405.1																																																																																			.	.		0.579	C4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076368.5	NM_001002029		T	31984663	-	T	31984662	7	5	202	1	0	1	1	0	0	0	0	0	2249	565	20	0	5973	0	C4A	6	31984662	Frame_Shift_Ins	INS	-	TCGA-DD-AADU-01A-11D-A40R-10	32738	31984662	139130405	33	29646										
IKZF1	10320	hgsc.bcm.edu	37	chr7	50455094	50455094	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccgaagctataaacagcgaaGctctttagaggaacataaag	9	8	1	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr7:50455094G>T	ENST00000331340.3	+	6	796	c.641G>T	c.(640-642)aGc>aTc	p.S214I	IKZF1_ENST00000346667.4_Intron|IKZF1_ENST00000438033.1_Missense_Mutation_p.S127I|IKZF1_ENST00000349824.4_Intron|IKZF1_ENST00000439701.1_Intron|IKZF1_ENST00000357364.4_Intron|IKZF1_ENST00000440768.2_Intron|IKZF1_ENST00000359197.5_Intron|IKZF1_ENST00000343574.5_Missense_Mutation_p.S127I	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	214				S -> T (in Ref. 2; AAB50683). {ECO:0000305}.	B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(131)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				AAACAGCGAAGCTCTTTAGAG	0.498			"D,T"	BCL6	"ALL, DLBCL"																																p.S214I		Atlas-SNP	.		"Rec,Dom"	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	131	Unknown(131)	haematopoietic_and_lymphoid_tissue(131)	c.G641T						.						46	48	48					7																	50455094		1868	4100	5968	SO:0001583	missense	10320	exon6			AGCGAAGCTCTTT	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13176	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 92"	603023	"zinc finger protein, subfamily 1A, 1 (Ikaros)"	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.641G>T	chr7.hg19:g.50455094G>T	ENSP00000331614:p.Ser214Ile	415.0	1.0		278.0	110.0	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	hg19		.	.	.	.	.	.	.	.	.	.	G	32	5.171940	0.94807	.	.	ENSG00000185811	ENST00000343574;ENST00000331340;ENST00000438033	T;T;T	0.62788	2.22;0.0;2.22	5.77	5.77	0.91146	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.71484	0.3345	.	.	.	0.80722	D	1	P;P	0.50819	0.939;0.831	P;B	0.49361	0.608;0.235	T	0.74627	-0.3602	9	0.87932	D	0	-7.2507	19.9886	0.97358	0.0:0.0:1.0:0.0	.	127;214	Q13422-2;Q13422	.;IKZF1_HUMAN	I	127;214;127	ENSP00000342750:S127I;ENSP00000331614:S214I;ENSP00000396554:S127I	ENSP00000331614:S214I	S	+	2	0	IKZF1	50422588	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.823000	0.99369	2.726000	0.93360	0.655000	0.94253	AGC	.	.		0.498	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060		T	50455094	G	T	50455094	3	4	202	1	0	0	0	0	1	0	0	0	7623	971	34	3	659	3	IKZF1	7	50455094	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10		50455094	108683569	34	29647										
PCLO	27445	hgsc.bcm.edu	37	chr7	82584094	82584094	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ataggcagcatcagcatctaGtagtttcctttcttcttctg	7	10	5	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr7:82584094G>C	ENST00000333891.9	-	5	6512	c.6175C>G	c.(6175-6177)Cta>Gta	p.L2059V	PCLO_ENST00000423517.2_Missense_Mutation_p.L2059V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCAGCATCTAGTAGTTTCCTT	0.438																																					p.L2059V		Atlas-SNP	.											.	PCLO	1506	.	0			c.C6175G						.						92	86	88					7																	82584094		1907	4118	6025	SO:0001583	missense	27445	exon5			CATCTAGTAGTTT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.6175C>G	chr7.hg19:g.82584094G>C	ENSP00000334319:p.Leu2059Val	90.0	0.0		75.0	27.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	1.998	-0.430087	0.04701	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.26067	1.76;1.77	5.64	-2.76	0.05896	.	.	.	.	.	T	0.37073	0.0990	L	0.54323	1.7	0.36908	D	0.890731	D;D	0.65815	0.99;0.995	P;P	0.59825	0.864;0.864	T	0.43669	-0.9377	9	0.87932	D	0	.	12.274	0.54724	0.4997:0.0:0.5003:0.0	.	2059;2059	Q9Y6V0-5;Q9Y6V0-6	.;.	V	1990;2059;2059	ENSP00000334319:L2059V;ENSP00000388393:L2059V	ENSP00000334319:L2059V	L	-	1	2	PCLO	82422030	0.963000	0.33076	0.003000	0.11579	0.619000	0.37552	1.756000	0.38390	-0.790000	0.04492	0.561000	0.74099	CTA	.	.		0.438	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82584094	G	C	82584094	3	2	202	1	0	0	0	0	1	0	0	0	11592	1020	36	4	9354	4	PCLO	7	82584094	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	32129000	82584094	76554569	35	29648										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83037763	83037763	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cggaagatcgcagcgtctctGctccagtagtcactgtagag	12	11	2	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr7:83037763G>C	ENST00000307792.3	-	6	1058	c.591C>G	c.(589-591)agC>agG	p.S197R	SEMA3E_ENST00000427262.1_Missense_Mutation_p.S137R	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	197	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				CAGCGTCTCTGCTCCAGTAGT	0.453																																					p.S197R		Atlas-SNP	.											.	SEMA3E	125	.	0			c.C591G						.						58	53	55					7																	83037763		2203	4300	6503	SO:0001583	missense	9723	exon6			GTCTCTGCTCCAG	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.591C>G	chr7.hg19:g.83037763G>C	ENSP00000303212:p.Ser197Arg	174.0	0.0		112.0	41.0	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.945456	0.34377	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514;ENST00000442159	T;T;T	0.23754	1.89;1.89;1.89	5.9	1.59	0.23543	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.157402	0.56097	D	0.000023	T	0.17874	0.0429	L	0.38175	1.15	0.23515	N	0.997512	B	0.18610	0.029	B	0.30495	0.116	T	0.20605	-1.0270	10	0.87932	D	0	.	2.1226	0.03730	0.1541:0.1013:0.4231:0.3215	.	197	O15041	SEM3E_HUMAN	R	197;137;197;137	ENSP00000303212:S197R;ENSP00000405052:S137R;ENSP00000412867:S137R	ENSP00000303212:S197R	S	-	3	2	SEMA3E	82875699	0.895000	0.30542	0.993000	0.49108	0.145000	0.21501	-0.038000	0.12144	0.850000	0.35239	0.591000	0.81541	AGC	.	.		0.453	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		C	83037763	G	C	83037763	3	2	202	1	0	0	0	0	1	0	0	0	14043	1310	46	4	1784	4	SEMA3E	7	83037763	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	453669	83037763	76100900	36	29649										
CNOT4	4850	hgsc.bcm.edu	37	chr7	135080633	135080633	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaaggcgtatcactgttagaTatctgaataaaaaaggaaaa	9	4	2	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr7:135080633T>A	ENST00000315544.5	-	9	1161	c.882A>T	c.(880-882)atA>atT	p.I294I	CNOT4_ENST00000423368.2_Silent_p.I294I|CNOT4_ENST00000361528.4_Silent_p.I291I|CNOT4_ENST00000541284.1_Silent_p.I294I|CNOT4_ENST00000414802.1_Silent_p.I294I|CNOT4_ENST00000356162.4_Silent_p.I294I|CNOT4_ENST00000428680.2_Silent_p.I291I|CNOT4_ENST00000451834.1_Silent_p.I291I	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	294					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						CACTGTTAGATATCTGAATAA	0.348																																					p.I294I	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.A882T						.						137	122	127					7																	135080633		1860	4097	5957	SO:0001819	synonymous_variant	4850	exon9			GTTAGATATCTGA	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"RNA binding motif (RRM) containing"	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.882A>T	chr7.hg19:g.135080633T>A		110.0	0.0		87.0	30.0	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Silent	SNP	ENST00000315544.5	hg19	CCDS55166.1																																																																																			.	.		0.348	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		A	135080633	T	A	135080633	2	1	202	1	0	0	0	0	0	0	0	1	3623	1396	49	4		4	CNOT4	7	135080633	Silent	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	52042870	135080633	24058030	37	29650										
TBXAS1	6916	hgsc.bcm.edu	37	chr7	139719869	139719869	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctgccctaggtccaaaaaaTggtgtctatatcaagatcgt	8	9	3	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr7:139719869T>C	ENST00000336425.5	+	17	1961	c.1572T>C	c.(1570-1572)aaT>aaC	p.N524N	TBXAS1_ENST00000458722.1_Silent_p.N570N|TBXAS1_ENST00000263552.6_Silent_p.N525N|TBXAS1_ENST00000425687.1_Silent_p.N457N|TBXAS1_ENST00000411653.1_3'UTR|TBXAS1_ENST00000448866.1_Silent_p.N524N|TBXAS1_ENST00000436047.2_Silent_p.N525N|TBXAS1_ENST00000416849.2_Silent_p.N571N|TBXAS1_ENST00000414508.2_3'UTR			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	524					arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	GTCCAAAAAATGGTGTCTATA	0.443																																					p.N571N		Atlas-SNP	.											.	TBXAS1	121	.	0			c.T1713C						.						86	88	87					7																	139719869		2203	4300	6503	SO:0001819	synonymous_variant	6916	exon14			AAAAAATGGTGTC	L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"Cytochrome P450s"	11609	protein-coding gene	gene with protein product	"cytochrome P450, family 5, subfamily A, polypeptide 1"	274180	"thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000336425.5:c.1572T>C	chr7.hg19:g.139719869T>C		61.0	0.0		50.0	25.0	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Silent	SNP	ENST00000336425.5	hg19																																																																																				.	.		0.443	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1			C	139719869	T	C	139719869	2	2	202	1	0	0	0	0	0	0	0	1	15679	1461	51	2		2	TBXAS1	7	139719869	Silent	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	4639236	139719869	19418794	38	29651										
C7orf29	113763	hgsc.bcm.edu	37	chr7	150027750	150027750	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgcttcaaggggaagattgAggccatcctgccatgggggc	15	9	1	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr7:150027750A>C	ENST00000343855.4	+	1	813	c.257A>C	c.(256-258)gAg>gCg	p.E86A	LRRC61_ENST00000493307.1_Intron|LRRC61_ENST00000323078.7_Intron|LRRC61_ENST00000359623.4_Intron	NM_138434.2	NP_612443.1	Q96FA7	ZB6CL_HUMAN	ZBED6 C-terminal like	86																	GGGAAGATTGAGGCCATCCTG	0.557																																					p.E86A		Atlas-SNP	.											.	C7orf29	18	.	0			c.A257C						.						77	77	77					7																	150027750		2203	4300	6503	SO:0001583	missense	113763	exon1			AGATTGAGGCCAT	BC011406	CCDS5900.1	7q35	2013-05-03	2013-05-03	2013-05-03	ENSG00000188707	ENSG00000188707			21720	protein-coding gene	gene with protein product		615252	"chromosome 7 open reading frame 29"	C7orf29		23533661	Standard	NM_138434		Approved			Q96FA7	OTTHUMG00000158328	ENST00000343855.4:c.257A>C	chr7.hg19:g.150027750A>C	ENSP00000343242:p.Glu86Ala	64.0	0.0		70.0	24.0	NM_138434		Missense_Mutation	SNP	ENST00000343855.4	hg19	CCDS5900.1	.	.	.	.	.	.	.	.	.	.	A	15.12	2.738198	0.49045	.	.	ENSG00000188707	ENST00000343855	.	.	.	3.75	3.75	0.43078	.	0.000000	0.43260	U	0.000598	T	0.43700	0.1259	L	0.32530	0.975	0.26147	N	0.980192	D	0.57257	0.979	P	0.54924	0.764	T	0.29243	-1.0018	9	0.66056	D	0.02	.	11.1273	0.48325	1.0:0.0:0.0:0.0	.	86	Q96FA7	CG029_HUMAN	A	86	.	ENSP00000343242:E86A	E	+	2	0	C7orf29	149658683	0.997000	0.39634	0.940000	0.37924	0.385000	0.30292	2.125000	0.42016	1.674000	0.50907	0.456000	0.33151	GAG	.	.		0.557	ZBED6CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350702.1	NM_138434		C	150027750	A	C	150027750	3	2	202	1	0	0	0	0	1	0	0	0	2387	304	11	5	259	5	C7orf29	7	150027750	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	10307881	150027750	9110913	39	29652										
TOX	9760	hgsc.bcm.edu	37	chr8	59851985	59851985	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tatggttcatggggtgacacAgagaatggtaaccagactca	12	7	2	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr8:59851985A>T	ENST00000361421.1	-	3	507	c.287T>A	c.(286-288)cTg>cAg	p.L96Q		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	96						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				GGGGTGACACAGAGAATGGTA	0.488																																					p.L96Q	Pancreas(161;610 1969 17913 21374 22725)	Atlas-SNP	.											.	TOX	83	.	0			c.T287A						.						153	131	139					8																	59851985		2203	4300	6503	SO:0001583	missense	9760	exon3			TGACACAGAGAAT		CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.287T>A	chr8.hg19:g.59851985A>T	ENSP00000354842:p.Leu96Gln	189.0	0.0		313.0	111.0	NM_014729	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	hg19	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.067270	0.76301	.	.	ENSG00000198846	ENST00000361421	T	0.59906	0.23	5.51	5.51	0.81932	.	0.072542	0.56097	D	0.000025	T	0.64627	0.2615	M	0.73598	2.24	0.58432	D	0.999998	D	0.61080	0.989	P	0.47573	0.55	T	0.68379	-0.5424	9	.	.	.	.	15.6313	0.76912	1.0:0.0:0.0:0.0	.	96	O94900	TOX_HUMAN	Q	96	ENSP00000354842:L96Q	.	L	-	2	0	TOX	60014539	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.726000	0.84824	2.105000	0.64084	0.482000	0.46254	CTG	.	.		0.488	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		T	59851985	A	T	59851985	3	4	202	1	0	0	0	0	1	0	0	0	16392	188	7	4	1321	4	TOX	8	59851985	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10		59851985	86512037	40	29653										
EEF1D	1936	hgsc.bcm.edu	37	chr8	144663449	144663449	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gactggcaatccggacgacgAgctcaccgtggtctccgctg	13	14	2	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr8:144663449A>G	ENST00000529272.1	-	4	639	c.239T>C	c.(238-240)cTc>cCc	p.L80P	NAPRT1_ENST00000426292.3_5'Flank|EEF1D_ENST00000317198.6_Missense_Mutation_p.L80P|EEF1D_ENST00000419152.2_Missense_Mutation_p.L80P|EEF1D_ENST00000442189.2_Missense_Mutation_p.L446P|EEF1D_ENST00000423316.2_Missense_Mutation_p.L446P|EEF1D_ENST00000528610.1_Missense_Mutation_p.L56P|EEF1D_ENST00000531621.1_Intron|EEF1D_ENST00000532400.1_Intron|RP11-661A12.7_ENST00000529247.1_RNA|EEF1D_ENST00000532741.1_Missense_Mutation_p.L496P|NAPRT1_ENST00000449291.2_5'Flank|EEF1D_ENST00000526838.1_Intron|EEF1D_ENST00000524624.1_Missense_Mutation_p.L56P|NAPRT1_ENST00000276844.7_5'Flank|NAPRT1_ENST00000435154.3_5'Flank|EEF1D_ENST00000395119.3_Missense_Mutation_p.L80P			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	80	Leucine-zipper.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			CCGGACGACGAGCTCACCGTG	0.692																																					p.L446P		Atlas-SNP	.											.	EEF1D	48	.	0			c.T1337C						.						28	27	27					8																	144663449		2202	4293	6495	SO:0001583	missense	1936	exon6			ACGACGAGCTCAC	AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.239T>C	chr8.hg19:g.144663449A>G	ENSP00000434872:p.Leu80Pro	90.0	0.0		269.0	143.0	NM_001130053	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	hg19	CCDS6405.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.009247	0.54361	.	.	ENSG00000104529	ENST00000419152;ENST00000532741;ENST00000442189;ENST00000528610;ENST00000395119;ENST00000529272;ENST00000423316;ENST00000356793;ENST00000317198;ENST00000337369;ENST00000524624;ENST00000534380;ENST00000534377;ENST00000533204;ENST00000530191;ENST00000531218;ENST00000533494;ENST00000530445;ENST00000533749	.	.	.	4.64	4.64	0.57946	.	0.066972	0.56097	D	0.000023	T	0.76442	0.3988	M	0.66378	2.025	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.999;0.999;0.999;0.999	T	0.79533	-0.1764	9	0.87932	D	0	.	13.5304	0.61619	1.0:0.0:0.0:0.0	.	446;374;80;496;446	D3DWK1;F8W934;P29692;E9PRY8;P29692-2	.;.;EF1D_HUMAN;.;.	P	80;496;446;56;80;80;446;374;80;446;56;80;56;80;80;80;80;80;96	.	ENSP00000317399:L80P	L	-	2	0	EEF1D	144734592	1.000000	0.71417	0.847000	0.33407	0.008000	0.06430	6.529000	0.73812	1.861000	0.53984	0.443000	0.29094	CTC	.	.		0.692	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		G	144663449	A	G	144663449	3	3	202	1	0	0	0	0	1	0	0	0	4928	304	11	2	626	2	EEF1D	8	144663449	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	84811464	144663449	1700573	41	29654										
ZNF7	7553	hgsc.bcm.edu	37	chr8	146067920	146067920	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaatgtgatgagtgtggcaaAggctttgttcagggctcaca	13	6	2	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr8:146067920A>C	ENST00000528372.1	+	5	1668	c.1428A>C	c.(1426-1428)aaA>aaC	p.K476N	ZNF7_ENST00000446747.2_Missense_Mutation_p.K487N|ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Missense_Mutation_p.K380N|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000325241.6_Missense_Mutation_p.K476N			P17097	ZNF7_HUMAN	zinc finger protein 7	476					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		AGTGTGGCAAAGGCTTTGTTC	0.443																																					p.K476N		Atlas-SNP	.											.	ZNF7	62	.	0			c.A1428C						.						82	73	76					8																	146067920		2203	4300	6503	SO:0001583	missense	7553	exon5			TGGCAAAGGCTTT	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.1428A>C	chr8.hg19:g.146067920A>C	ENSP00000432724:p.Lys476Asn	121.0	0.0		265.0	76.0	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Missense_Mutation	SNP	ENST00000528372.1	hg19	CCDS6435.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.561310	0.65538	.	.	ENSG00000147789	ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	T;T;T;T	0.35973	1.28;3.15;3.15;1.28	4.93	-3.21	0.05140	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000136	T	0.63546	0.2520	M	0.93638	3.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.72004	-0.4421	9	.	.	.	-26.092	13.3195	0.60424	0.3947:0.0:0.6053:0.0	.	487;476	B4DT08;P17097	.;ZNF7_HUMAN	N	476;487;380;476	ENSP00000320627:K476N;ENSP00000393260:K487N;ENSP00000439424:K380N;ENSP00000432724:K476N	.	K	+	3	2	ZNF7	146038724	0.013000	0.17824	0.867000	0.34043	0.967000	0.64934	-0.419000	0.07071	-0.455000	0.07054	0.533000	0.62120	AAA	.	.		0.443	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		C	146067920	A	C	146067920	3	2	202	1	0	0	0	0	1	0	0	0	18117	69	3	5	1442	5	ZNF7	8	146067920	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	1404471	146067920	296102	42	29655										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79321163	79321163	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctgtggcaatgcttgaattTgtcatctcacctaggtatga	9	8	3	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr9:79321163T>C	ENST00000376718.3	-	8	6150	c.6027A>G	c.(6025-6027)acA>acG	p.T2009T	PRUNE2_ENST00000428286.1_Silent_p.T1650T	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2009					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TGCTTGAATTTGTCATCTCAC	0.418																																					p.T2009T		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A6027G						.						111	97	101					9																	79321163		1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			TGAATTTGTCATC	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.6027A>G	chr9.hg19:g.79321163T>C		150.0	0.0		121.0	44.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.710157	0.00712	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.74	2.04	0.26737	.	.	.	.	.	T	0.31389	0.0795	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.21895	-1.0232	4	.	.	.	-1.8315	6.0531	0.19796	0.1215:0.1328:0.0:0.7457	.	.	.	.	E	1331	.	.	K	-	1	0	PRUNE2	78510983	0.004000	0.15560	0.001000	0.08648	0.021000	0.10359	0.944000	0.29043	0.156000	0.19299	0.459000	0.35465	AAA	.	.		0.418	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		C	79321163	T	C	79321163	2	2	202	1	0	0	0	0	0	0	0	1	12653	1799	63	2		2	PRUNE2	9	79321163	Silent	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10		79321163	61892268	43	29656										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123239658	123239658	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctgcagagatttgaccagaTgggtatagatgtcctgctct	11	9	1	4			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr9:123239658T>C	ENST00000349780.4	-	15	1876	c.1697A>G	c.(1696-1698)cAt>cGt	p.H566R	CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.H566R|CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.H566R|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.H566R	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	566					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TTTGACCAGATGGGTATAGAT	0.433											OREG0019439	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H566R		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.A1697G						.						241	194	210					9																	123239658		2203	4300	6503	SO:0001583	missense	55755	exon15			ACCAGATGGGTAT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.1697A>G	chr9.hg19:g.123239658T>C	ENSP00000343818:p.His566Arg	45.0	0.0	1525	44.0	15.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	hg19	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	T	9.546	1.114769	0.20795	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000345313	T;T;T;T	0.03801	3.91;3.8;3.91;3.82	5.91	2.39	0.29439	.	0.881349	0.09865	N	0.745673	T	0.02970	0.0088	N	0.17082	0.46	0.18873	N	0.999982	B;B;B;B	0.15473	0.002;0.001;0.013;0.001	B;B;B;B	0.13407	0.003;0.003;0.009;0.001	T	0.48885	-0.8995	10	0.09843	T	0.71	.	6.2371	0.20768	0.0:0.3166:0.0:0.6834	.	367;566;566;566	Q6MZT4;Q96SN8-2;Q96SN8-4;Q96SN8	.;.;.;CK5P2_HUMAN	R	566;566;566;566;568	ENSP00000354065:H566R;ENSP00000352258:H566R;ENSP00000343818:H566R;ENSP00000353317:H566R	ENSP00000341695:H568R	H	-	2	0	CDK5RAP2	122279479	0.836000	0.29430	0.748000	0.31131	0.995000	0.86356	0.986000	0.29590	0.501000	0.28013	0.533000	0.62120	CAT	.	.		0.433	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		C	123239658	T	C	123239658	3	2	202	1	0	0	0	0	1	0	0	0	3148	1464	51	2	4080	2	CDK5RAP2	9	123239658	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	43918495	123239658	17973773	44	29657										
FCN1	2219	hgsc.bcm.edu	37	chr9	137804942	137804942	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caggtagatggtgtgccagcCgctcaggaaatacccccggt	13	12	1	1	rs143987379		TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr9:137804942C>A	ENST00000371806.3	-	6	479	c.388G>T	c.(388-390)Ggc>Tgc	p.G130C		NM_002003.3	NP_001994.2	O00602	FCN1_HUMAN	ficolin (collagen/fibrinogen domain containing) 1	130	A domain; contributes to trimerization.|Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell surface pattern recognition receptor signaling pathway (GO:0002752)|complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of interleukin-8 secretion (GO:2000484)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extrinsic component of external side of plasma membrane (GO:0031232)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|G-protein coupled receptor binding (GO:0001664)|signaling pattern recognition receptor activity (GO:0008329)			endometrium(3)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	37		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		GTGTGCCAGCCGCTCAGGAAA	0.677																																					p.G130C		Atlas-SNP	.											.	FCN1	62	.	0			c.G388T						.						44	43	43					9																	137804942		2203	4300	6503	SO:0001583	missense	2219	exon6			GCCAGCCGCTCAG	D83920	CCDS6985.1	9q34	2013-02-06	2002-01-14		ENSG00000085265	ENSG00000085265		"Fibrinogen C domain containing"	3623	protein-coding gene	gene with protein product		601252	"ficolin (collagen/fibrinogen domain-containing) 1"			8573080, 8884275	Standard	NM_002003		Approved	FCNM	uc004cfi.3	O00602	OTTHUMG00000020895	ENST00000371806.3:c.388G>T	chr9.hg19:g.137804942C>A	ENSP00000360871:p.Gly130Cys	119.0	0.0		83.0	23.0	NM_002003	Q5VYV5|Q92596	Missense_Mutation	SNP	ENST00000371806.3	hg19	CCDS6985.1	.	.	.	.	.	.	.	.	.	.	C	8.367	0.834333	0.16820	.	.	ENSG00000085265	ENST00000371807;ENST00000371806;ENST00000308299	T	0.37584	1.19	3.39	1.5	0.22942	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	.	.	.	.	T	0.71550	0.3353	H	0.99312	4.51	0.40125	D	0.976645	D	0.89917	1.0	D	0.97110	1.0	T	0.73780	-0.3875	9	0.87932	D	0	.	7.7609	0.28951	0.0:0.7863:0.0:0.2137	.	130	O00602	FCN1_HUMAN	C	130;130;118	ENSP00000360871:G130C	ENSP00000308877:G118C	G	-	1	0	FCN1	136944763	0.938000	0.31826	0.294000	0.24946	0.000000	0.00434	1.907000	0.39897	0.249000	0.21456	-1.114000	0.02060	GGC	.	C|1.000;T|0.000		0.677	FCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054963.1	NM_002003		A	137804942	C	A	137804942	3	1	202	1	0	0	0	0	1	0	0	0	5799	652	23	1	608	1	FCN1	9	137804942	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	14565284	137804942	3408489	45	29658										
MAT1A	4143	hgsc.bcm.edu	37	chr10	82036146	82036146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atgcacctggggacctccgaTgacaaaccgcccactgggct	11	15	0	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr10:82036146T>C	ENST00000372213.3	-	6	1014	c.754A>G	c.(754-756)Atc>Gtc	p.I252V	MAT1A_ENST00000485270.1_5'Flank	NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	252					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	GGACCTCCGATGACAAACCGC	0.567																																					p.I252V		Atlas-SNP	.											.	MAT1A	52	.	0			c.A754G						.						84	80	81					10																	82036146		2203	4300	6503	SO:0001583	missense	4143	exon6			CTCCGATGACAAA		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"S-adenosylmethionine synthetase"	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.754A>G	chr10.hg19:g.82036146T>C	ENSP00000361287:p.Ile252Val	98.0	0.0		83.0	27.0	NM_000429	D3DWD5|Q5QP09	Missense_Mutation	SNP	ENST00000372213.3	hg19	CCDS7365.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.097254	0.56075	.	.	ENSG00000151224	ENST00000372213;ENST00000372206	D	0.98012	-4.66	4.84	4.84	0.62591	S-adenosylmethionine synthetase, C-terminal (1);S-adenosylmethionine synthetase superfamily (1);	0.045801	0.85682	D	0.000000	D	0.95677	0.8594	L	0.50333	1.59	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	D	0.93686	0.7003	10	0.59425	D	0.04	-26.2772	12.7009	0.57032	0.0:0.0:0.0:1.0	.	252	Q00266	METK1_HUMAN	V	252	ENSP00000361287:I252V	ENSP00000361280:I252V	I	-	1	0	MAT1A	82026126	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	5.799000	0.69101	2.164000	0.68074	0.533000	0.62120	ATC	.	.		0.567	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429		C	82036146	T	C	82036146	3	2	202	1	0	0	0	0	1	0	0	0	9338	1464	51	2	449	2	MAT1A	10	82036146	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10		82036146	53498601	46	29659										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1270921	1270921	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gatccacggccaccccgtccTccaccccgggaacagctccc	8	22	0	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr11:1270921T>A	ENST00000529681.1	+	31	12869	c.12811T>A	c.(12811-12813)Tcc>Acc	p.S4271T	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.S4274T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4271	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CACCCCGTCCTCCACCCCGGG	0.647																																					p.S4271T		Atlas-SNP	.											.	MUC5B	473	.	0			c.T12811A						.						121	139	133					11																	1270921		2088	4186	6274	SO:0001583	missense	727897	exon31			CCGTCCTCCACCC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.12811T>A	chr11.hg19:g.1270921T>A	ENSP00000436812:p.Ser4271Thr	155.0	0.0		148.0	53.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	t	3.957	-0.011147	0.07727	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000535652	T;T	0.16324	2.35;2.54	2.45	-4.9	0.03094	.	.	.	.	.	T	0.11410	0.0278	L	0.46157	1.445	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.01281	0.0;0.0	T	0.32955	-0.9887	9	0.87932	D	0	.	0.9881	0.01451	0.4119:0.2771:0.1154:0.1956	.	4744;4274	A7Y9J9;E9PBJ0	.;.	T	4271;4274;4215;4121;50	ENSP00000436812:S4271T;ENSP00000415793:S4274T	ENSP00000343037:S4215T	S	+	1	0	MUC5B	1227497	0.000000	0.05858	0.000000	0.03702	0.221000	0.24807	-5.990000	0.00086	-2.221000	0.00728	0.055000	0.15244	TCC	.	.		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1270921	T	A	1270921	3	1	202	1	0	0	0	0	1	0	0	0	9988	1551	54	4	12942	4	MUC5B	11	1270921	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10		1270921	133735595	47	29660										
OR51I2	390064	hgsc.bcm.edu	37	chr11	5475217	5475217	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctttcttattaagaggctgCctatctgcagatccaatgtt	7	10	2	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr11:5475217C>A	ENST00000341449.2	+	1	580	c.499C>A	c.(499-501)Cct>Act	p.P167T	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	167					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TAAGAGGCTGCCTATCTGCAG	0.478																																					p.P167T		Atlas-SNP	.											.	OR51I2	76	.	0			c.C499A						.						169	154	159					11																	5475217		2201	4297	6498	SO:0001583	missense	390064	exon1			AGGCTGCCTATCT	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"GPCR / Class A : Olfactory receptors"	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.499C>A	chr11.hg19:g.5475217C>A	ENSP00000341987:p.Pro167Thr	57.0	0.0		22.0	13.0	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	hg19	CCDS31383.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.405677	0.42715	.	.	ENSG00000187918	ENST00000341449	T	0.37915	1.17	5.58	4.68	0.58851	GPCR, rhodopsin-like superfamily (1);	0.095559	0.47093	D	0.000252	T	0.57080	0.2029	M	0.76727	2.345	0.28427	N	0.917453	D	0.89917	1.0	D	0.91635	0.999	T	0.54761	-0.8245	10	0.51188	T	0.08	.	10.3938	0.44188	0.0:0.844:0.0:0.156	.	167	Q9H344	O51I2_HUMAN	T	167	ENSP00000341987:P167T	ENSP00000341987:P167T	P	+	1	0	OR51I2	5431793	0.001000	0.12720	0.999000	0.59377	0.634000	0.38068	0.500000	0.22562	1.602000	0.50124	-0.140000	0.14226	CCT	.	.		0.478	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754		A	5475217	C	A	5475217	3	1	202	1	0	0	0	0	1	0	0	0	11110	739	26	3	501	3	OR51I2	11	5475217	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	4204296	5475217	129531299	48	29661										
PTPN5	84867	hgsc.bcm.edu	37	chr11	18751293	18751293	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caggtgcaggagtgggggggCccggtctggggtcttctggt	21	8	3	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr11:18751293C>A	ENST00000358540.2	-	13	1832	c.1402G>T	c.(1402-1404)Gcc>Tcc	p.A468S	PTPN5_ENST00000396168.1_Missense_Mutation_p.A444S|PTPN5_ENST00000396171.4_Missense_Mutation_p.A468S|RP11-1081L13.4_ENST00000527285.1_RNA|PTPN5_ENST00000396167.2_Missense_Mutation_p.A436S|PTPN5_ENST00000396170.1_Missense_Mutation_p.A436S|PTPN5_ENST00000396166.3_Missense_Mutation_p.A74S|PTPN5_ENST00000477854.1_Missense_Mutation_p.A272S	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	468	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						AGTGGGGGGGCCCGGTCTGGG	0.677																																					p.A468S		Atlas-SNP	.											.	PTPN5	163	.	0			c.G1402T						.						38	48	45					11																	18751293		2115	4250	6365	SO:0001583	missense	84867	exon13			GGGGGGCCCGGTC	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.1402G>T	chr11.hg19:g.18751293C>A	ENSP00000351342:p.Ala468Ser	53.0	0.0		52.0	12.0	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Missense_Mutation	SNP	ENST00000358540.2	hg19	CCDS7845.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354673	0.82243	.	.	ENSG00000110786	ENST00000477854;ENST00000358540;ENST00000396166;ENST00000396170;ENST00000396171;ENST00000396167;ENST00000396168	D;D;T;D;D;D;D	0.83250	-1.7;-1.7;2.54;-1.7;-1.7;-1.7;-1.7	4.26	4.26	0.50523	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.88713	0.6511	L	0.52011	1.625	0.80722	D	1	P;D	0.65815	0.805;0.995	D;D	0.83275	0.914;0.996	D	0.90226	0.4275	10	0.87932	D	0	-10.1039	16.8635	0.86024	0.0:1.0:0.0:0.0	.	468;436	P54829;B3KXG7	PTN5_HUMAN;.	S	272;468;74;436;468;436;444	ENSP00000435056:A272S;ENSP00000351342:A468S;ENSP00000379469:A74S;ENSP00000379473:A436S;ENSP00000379474:A468S;ENSP00000379470:A436S;ENSP00000379471:A444S	ENSP00000351342:A468S	A	-	1	0	PTPN5	18707869	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	5.674000	0.68117	2.210000	0.71456	0.655000	0.94253	GCC	.	.		0.677	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970		A	18751293	C	A	18751293	3	1	202	1	0	0	0	0	1	0	0	0	12806	739	26	3	307	3	PTPN5	11	18751293	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	13276076	18751293	116255223	49	29662										
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26714081	26714081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	cagcttgtcggagagatgagGaaaacagctcttgacaaaat	11	7	1	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr11:26714081G>A	ENST00000396005.3	-	9	1417	c.1108C>T	c.(1108-1110)Cct>Tct	p.P370S	SLC5A12_ENST00000280467.6_Missense_Mutation_p.P370S	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	370					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						GAGAGATGAGGAAAACAGCTC	0.438																																					p.P370S		Atlas-SNP	.											.	SLC5A12	134	.	0			c.C1108T						.						122	106	111					11																	26714081		2203	4299	6502	SO:0001583	missense	159963	exon9			GATGAGGAAAACA	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1108C>T	chr11.hg19:g.26714081G>A	ENSP00000379326:p.Pro370Ser	104.0	0.0		91.0	31.0	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	hg19	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	G	16.56	3.157459	0.57259	.	.	ENSG00000148942	ENST00000396005;ENST00000280467	D;D	0.88431	-2.38;-2.38	5.88	5.88	0.94601	.	0.123303	0.53938	D	0.000042	D	0.88658	0.6496	L	0.42632	1.34	0.36380	D	0.86188	B;P	0.37276	0.185;0.589	B;P	0.46208	0.281;0.507	D	0.90535	0.4498	10	0.51188	T	0.08	.	13.9114	0.63869	0.0:0.0:0.8476:0.1524	.	370;370	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	S	370	ENSP00000379326:P370S;ENSP00000280467:P370S	ENSP00000280467:P370S	P	-	1	0	SLC5A12	26670657	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	2.049000	0.41288	2.789000	0.95967	0.591000	0.81541	CCT	.	.		0.438	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		A	26714081	G	A	26714081	3	1	202	1	0	0	0	0	1	0	0	0	14679	1174	41	3	776	3	SLC5A12	11	26714081	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	7962788	26714081	108292435	50	29663										
EXT2	2132	hgsc.bcm.edu	37	chr11	44193161	44193161	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cagcattattttctttatagGcccggtggttctgggaagcg	12	8	2	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr11:44193161G>C	ENST00000343631.3	+	8	1303	c.1174G>C	c.(1174-1176)Gcc>Ccc	p.A392P	EXT2_ENST00000533608.1_Splice_Site_p.A392P|EXT2_ENST00000395673.3_Splice_Site_p.A425P|EXT2_ENST00000358681.4_Intron			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	392					carbohydrate metabolic process (GO:0005975)|cell differentiation (GO:0030154)|cellular polysaccharide biosynthetic process (GO:0033692)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm formation (GO:0001707)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|lung(17)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	32						TTCTTTATAGGCCCGGTGGTT	0.443			"Mis, N, F, S"			"exostoses, osteosarcoma"			Hereditary Multiple Exostoses																												p.A425P		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	.	EXT2	129	.	0			c.G1273C	GRCh37	CS063301	EXT2	S		.						98	99	99					11																	44193161		2203	4299	6502	SO:0001630	splice_region_variant	2132	exon8	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	TTATAGGCCCGGT		CCDS7908.1, CCDS53618.1, CCDS53619.1	11p12-p11	2014-09-17	2013-03-01		ENSG00000151348	ENSG00000151348	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3513	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608210	"exostoses (multiple) 2", "exostosin 2"			8162019, 9576285	Standard	NM_000401		Approved	SOTV	uc001mya.3	Q93063	OTTHUMG00000166498	ENST00000343631.3:c.1174-1G>C	chr11.hg19:g.44193161G>C		74.0	0.0		56.0	29.0	NM_000401	B2R5Z6|C9JU51|J3KPT2|O15288	Missense_Mutation	SNP	ENST00000343631.3	hg19	CCDS7908.1	.	.	.	.	.	.	.	.	.	.	G	19.06	3.753082	0.69648	.	.	ENSG00000151348	ENST00000533608;ENST00000395673;ENST00000343631	D;D;D	0.95069	-3.59;-3.6;-3.59	5.5	5.5	0.81552	.	.	.	.	.	D	0.91764	0.7395	L	0.48642	1.525	0.80722	D	1	B;B;P	0.35821	0.303;0.232;0.523	B;B;B	0.31547	0.132;0.125;0.125	D	0.90257	0.4298	8	.	.	.	0.8123	19.405	0.94644	0.0:0.0:1.0:0.0	.	392;392;405	Q6NUL1;Q93063;D3DR24	.;EXT2_HUMAN;.	P	392;425;392	ENSP00000431173:A392P;ENSP00000379032:A425P;ENSP00000342656:A392P	.	A	+	1	0	EXT2	44149737	1.000000	0.71417	0.999000	0.59377	0.804000	0.45430	9.624000	0.98398	2.579000	0.87056	0.655000	0.94253	GCC	.	.		0.443	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401	Missense_Mutation	C	44193161	G	C	44193161	5	2	202	1	0	0	0	0	0	0	1	0	5326	1217	42	4	1400	4	EXT2	11	44193161	Splice_Site	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	17479080	44193161	90813355	51	29664										
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563595	55563595	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gagtatactgctctcatctcTgtgtctggctctgatatact	8	10	4	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr11:55563595T>A	ENST00000335605.1	+	1	564	c.564T>A	c.(562-564)tcT>tcA	p.S188S		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	188						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S188S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				CTCTCATCTCTGTGTCTGGCT	0.448																																					p.S188S		Atlas-SNP	.											OR5D14,NS,carcinoma,0,1	OR5D14	116	.	1	Substitution - coding silent(1)	prostate(1)	c.T564A						.						220	215	217					11																	55563595		2200	4296	6496	SO:0001819	synonymous_variant	219436	exon1			CATCTCTGTGTCT	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.564T>A	chr11.hg19:g.55563595T>A		125.0	0.0		94.0	28.0	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Silent	SNP	ENST00000335605.1	hg19	CCDS31508.1																																																																																			.	.		0.448	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		A	55563595	T	A	55563595	2	1	202	1	0	0	0	0	0	0	0	1	11164	1567	55	4		4	OR5D14	11	55563595	Silent	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	11370434	55563595	79442921	52	29665										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103325984	103325984	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctatcagaacttttccatcCagacacatttcttaatgctc	3	13	2	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr11:103325984C>T	ENST00000375735.2	+	86	12671	c.12527C>T	c.(12526-12528)cCa>cTa	p.P4176L	DYNC2H1_ENST00000334267.7_Missense_Mutation_p.P789L|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.P4183L	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4176					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CTTTTCCATCCAGACACATTT	0.368																																					p.P4183L		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.C12548T						.						91	85	87					11																	103325984		1828	4082	5910	SO:0001583	missense	79659	exon87			TCCATCCAGACAC	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.12527C>T	chr11.hg19:g.103325984C>T	ENSP00000364887:p.Pro4176Leu	91.0	0.0		59.0	16.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.936953	0.92458	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093;ENST00000540621;ENST00000533197	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	5.84	5.84	0.93424	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.52917	0.1764	M	0.89534	3.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.994;0.999	T	0.60172	-0.7315	10	0.72032	D	0.01	.	19.7245	0.96157	0.0:1.0:0.0:0.0	.	789;4176;4183	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	L	4176;789;4183;422;93	ENSP00000364887:P4176L;ENSP00000334021:P789L;ENSP00000381167:P4183L;ENSP00000436736:P93L	ENSP00000334021:P789L	P	+	2	0	DYNC2H1	102831194	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	6.895000	0.75660	2.758000	0.94735	0.591000	0.81541	CCA	.	.		0.368	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103325984	C	T	103325984	3	4	202	1	0	0	0	0	1	0	0	0	4848	594	21	3	12894	3	DYNC2H1	11	103325984	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	47762389	103325984	31680532	53	29666										
PANX3	116337	hgsc.bcm.edu	37	chr11	124482989	124482989	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	agcaggacgggcctggccagGacaaaatgaaatctctctgg	13	10	2	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr11:124482989G>A	ENST00000284288.2	+	2	362	c.295G>A	c.(295-297)Gac>Aac	p.D99N		NM_052959.2	NP_443191.1	Q96QZ0	PANX3_HUMAN	pannexin 3	99					cell-cell signaling (GO:0007267)|ion transport (GO:0006811)|protein hexamerization (GO:0034214)|transmembrane transport (GO:0055085)	gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|urinary_tract(1)	26	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)		GCCTGGCCAGGACAAAATGAA	0.557																																					p.D99N		Atlas-SNP	.											.	PANX3	52	.	0			c.G295A						.						64	59	60					11																	124482989		2201	4299	6500	SO:0001583	missense	116337	exon2			GGCCAGGACAAAA	AF406650	CCDS8447.1	11q24.2	2011-12-02			ENSG00000154143	ENSG00000154143		"Ion channels / Pannexins"	20573	protein-coding gene	gene with protein product		608422					Standard	NM_052959		Approved	Px3	uc001qah.3	Q96QZ0	OTTHUMG00000165925	ENST00000284288.2:c.295G>A	chr11.hg19:g.124482989G>A	ENSP00000284288:p.Asp99Asn	54.0	0.0		51.0	13.0	NM_052959		Missense_Mutation	SNP	ENST00000284288.2	hg19	CCDS8447.1	.	.	.	.	.	.	.	.	.	.	G	5.606	0.296592	0.10622	.	.	ENSG00000154143	ENST00000284288	T	0.28666	1.6	5.31	-2.59	0.06209	.	1.185740	0.05722	N	0.597974	T	0.12050	0.0293	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17410	-1.0370	10	0.26408	T	0.33	-0.5417	0.0165	0.00002	0.3028:0.1926:0.2128:0.2918	.	99	Q96QZ0	PANX3_HUMAN	N	99	ENSP00000284288:D99N	ENSP00000284288:D99N	D	+	1	0	PANX3	123988199	0.000000	0.05858	0.003000	0.11579	0.387000	0.30353	-0.307000	0.08167	-0.660000	0.05352	-1.334000	0.01262	GAC	.	.		0.557	PANX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387064.1			A	124482989	G	A	124482989	3	1	202	1	0	0	0	0	1	0	0	0	11431	1174	41	3	301	3	PANX3	11	124482989	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	21157005	124482989	10523527	54	29667										
FGF23	8074	hgsc.bcm.edu	37	chr12	4479524	4479524	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	cgaccctagatgaacttggcGaaggggcggcagccttccgg	15	12	0	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr12:4479524G>C	ENST00000237837.1	-	3	886	c.741C>G	c.(739-741)ttC>ttG	p.F247L		NM_020638.2	NP_065689.1	Q9GZV9	FGF23_HUMAN	fibroblast growth factor 23	247					cell differentiation (GO:0030154)|cellular phosphate ion homeostasis (GO:0030643)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of bone mineralization (GO:0030502)|negative regulation of hormone secretion (GO:0046888)|negative regulation of osteoblast differentiation (GO:0045668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphate ion homeostasis (GO:0055062)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|regulation of phosphate transport (GO:0010966)|vitamin D catabolic process (GO:0042369)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.F247F(1)		NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	22			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)|STAD - Stomach adenocarcinoma(119;0.206)			TGAACTTGGCGAAGGGGCGGC	0.627																																					p.F247L		Atlas-SNP	.											FGF23,NS,carcinoma,0,1	FGF23	57	.	1	Substitution - coding silent(1)	prostate(1)	c.C741G						.						60	67	64					12																	4479524		2203	4300	6503	SO:0001583	missense	8074	exon3			CTTGGCGAAGGGG	AF263537	CCDS8526.1	12p13	2008-07-04			ENSG00000118972	ENSG00000118972			3680	protein-coding gene	gene with protein product		605380				11032749, 18310961	Standard	NM_020638		Approved		uc001qmq.1	Q9GZV9	OTTHUMG00000168241	ENST00000237837.1:c.741C>G	chr12.hg19:g.4479524G>C	ENSP00000237837:p.Phe247Leu	160.0	0.0		117.0	26.0	NM_020638	Q4V758	Missense_Mutation	SNP	ENST00000237837.1	hg19	CCDS8526.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.800786	0.70567	.	.	ENSG00000118972	ENST00000237837	T	0.80824	-1.42	4.58	0.437	0.16555	.	0.533484	0.17200	N	0.183163	T	0.64494	0.2603	L	0.29908	0.895	0.09310	N	1	B	0.26258	0.145	B	0.20955	0.032	T	0.55082	-0.8196	10	0.59425	D	0.04	-0.3054	4.4985	0.11853	0.2943:0.1638:0.5418:0.0	.	247	Q9GZV9	FGF23_HUMAN	L	247	ENSP00000237837:F247L	ENSP00000237837:F247L	F	-	3	2	FGF23	4349785	0.858000	0.29795	0.047000	0.18901	0.180000	0.23129	0.827000	0.27421	0.143000	0.18926	0.549000	0.68633	TTC	.	.		0.627	FGF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398936.1			C	4479524	G	C	4479524	3	2	202	1	0	0	0	0	1	0	0	0	5860	1049	37	4	18	4	FGF23	12	4479524	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10		4479524	129372371	55	29668										
NDUFA9	4704	hgsc.bcm.edu	37	chr12	4794433	4794433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttctctttccagatgggtagCaagagtctttgaaataagcc	9	8	2	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr12:4794433C>T	ENST00000266544.5	+	10	925	c.905C>T	c.(904-906)gCa>gTa	p.A302V	RP11-234B24.6_ENST00000544741.2_Missense_Mutation_p.A61V|NDUFA9_ENST00000540688.1_Missense_Mutation_p.A61V	NM_005002.4	NP_004993.1	Q16795	NDUA9_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa	302					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|sodium ion transport (GO:0006814)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21						AGATGGGTAGCAAGAGTCTTT	0.468																																					p.A302V	Colon(75;996 1244 23946 25294 29232)	Atlas-SNP	.											.	NDUFA9	45	.	0			c.C905T						.						124	113	117					12																	4794433		2203	4300	6503	SO:0001583	missense	4704	exon10			GGGTAGCAAGAGT	AF050641	CCDS8532.1	12p13.3	2011-09-14	2002-08-29		ENSG00000139180	ENSG00000139180		"Mitochondrial respiratory chain complex / Complex I", "Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	7693	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 22E, member 1", "complex I 39kDa subunit"	603834	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9 (39kD)"	NDUFS2L		8486360, 19027726	Standard	NM_005002		Approved	SDR22E1, CI-39k	uc001qnc.3	Q16795		ENST00000266544.5:c.905C>T	chr12.hg19:g.4794433C>T	ENSP00000266544:p.Ala302Val	159.0	0.0		106.0	29.0	NM_005002	Q14076|Q2NKX0	Missense_Mutation	SNP	ENST00000266544.5	hg19	CCDS8532.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.279405	0.59758	.	.	ENSG00000139180	ENST00000266544;ENST00000540688	T;D	0.83755	-1.42;-1.76	5.06	-0.223	0.13118	.	0.159674	0.56097	D	0.000035	T	0.77519	0.4142	M	0.69463	2.115	0.21386	N	0.999701	B	0.33883	0.43	B	0.29267	0.1	T	0.67241	-0.5720	10	0.51188	T	0.08	-12.09	11.8854	0.52600	0.0:0.4152:0.5143:0.0705	.	302	Q16795	NDUA9_HUMAN	V	302;61	ENSP00000266544:A302V;ENSP00000439818:A61V	ENSP00000266544:A302V	A	+	2	0	NDUFA9	4664694	0.273000	0.24181	0.004000	0.12327	0.070000	0.16714	0.780000	0.26760	-0.253000	0.09514	-0.122000	0.15005	GCA	.	.		0.468	NDUFA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398900.2	NM_005002		T	4794433	C	T	4794433	3	4	202	1	0	0	0	0	1	0	0	0	10281	710	25	3	943	3	NDUFA9	12	4794433	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	314909	4794433	129057462	56	29669										
NR4A1	3164	hgsc.bcm.edu	37	chr12	52452485	52452485	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cccgcagaccggcatgggctGcaggagccgcggcgggtgga	19	13	0	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr12:52452485G>A	ENST00000243050.1	+	8	1868	c.1554G>A	c.(1552-1554)ctG>ctA	p.L518L	NR4A1_ENST00000545748.1_Silent_p.L572L|NR4A1_ENST00000394825.1_Silent_p.L518L|RP11-1100L3.8_ENST00000564363.1_lincRNA|NR4A1_ENST00000550082.1_Silent_p.L531L|NR4A1_ENST00000394824.2_Silent_p.L518L|NR4A1_ENST00000360284.3_Silent_p.L531L	NM_002135.4	NP_002126.2	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	518					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell chemotaxis (GO:0035767)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)	16				BRCA - Breast invasive adenocarcinoma(357;0.0967)		GGCATGGGCTGCAGGAGCCGC	0.682																																					p.L531L		Atlas-SNP	.											.	NR4A1	77	.	0			c.G1593A						.						7	8	8					12																	52452485		2065	4101	6166	SO:0001819	synonymous_variant	3164	exon8			TGGGCTGCAGGAG	L13740	CCDS8818.1, CCDS55828.1, CCDS73471.1	12q13	2013-01-16			ENSG00000123358	ENSG00000123358		"Nuclear hormone receptors"	7980	protein-coding gene	gene with protein product		139139		HMR, GFRP1		2626032	Standard	NM_002135		Approved	TR3, N10, NAK-1, NGFIB, NUR77	uc001rzt.3	P22736	OTTHUMG00000150393	ENST00000243050.1:c.1554G>A	chr12.hg19:g.52452485G>A		93.0	0.0		65.0	4.0	NM_001202233	B4DML7|Q15627|Q53Y00|Q6IBU8	Silent	SNP	ENST00000243050.1	hg19	CCDS8818.1																																																																																			.	.		0.682	NR4A1-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317922.2			A	52452485	G	A	52452485	2	1	202	1	0	0	0	0	0	0	0	1	10641	1306	46	3		3	NR4A1	12	52452485	Silent	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	47658052	52452485	81399410	57	29670										
KNTC1	9735	hgsc.bcm.edu	37	chr12	123106426	123106426	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttctgctttgatttttctctAgaattttctgggttcctgtg	8	7	3	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr12:123106426A>T	ENST00000333479.7	+	61	6456		c.e61-1		HCAR1_ENST00000356987.2_Intron|KNTC1_ENST00000537348.1_Splice_Site|KNTC1_ENST00000534995.1_Splice_Site|KNTC1_ENST00000450485.2_Splice_Site|KNTC1_ENST00000436959.3_Splice_Site	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1						mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		ATTTTTCTCTAGAATTTTCTG	0.373																																					.		Atlas-SNP	.											.	KNTC1	182	.	0			c.6280-2A>T						.						40	37	38					12																	123106426		1794	4064	5858	SO:0001630	splice_region_variant	9735	exon61			TTCTCTAGAATTT		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.6280-1A>T	chr12.hg19:g.123106426A>T		146.0	0.0		86.0	30.0	NM_014708	A7E2C4|B3KSG2	Splice_Site	SNP	ENST00000333479.7	hg19	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.466323	0.63625	.	.	ENSG00000184445	ENST00000450485;ENST00000333479;ENST00000436959;ENST00000534995	.	.	.	5.69	5.69	0.88448	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9059	0.63836	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KNTC1	121672379	1.000000	0.71417	0.932000	0.37286	0.686000	0.39977	7.258000	0.78371	2.163000	0.67991	0.533000	0.62120	.	.	.		0.373	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		Intron	T	123106426	A	T	123106426	5	4	202	1	0	0	0	0	0	0	1	0	8437	434	15	4	6516	4	KNTC1	12	123106426	Splice_Site	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	70653941	123106426	10745469	58	29671										
SMAD9	4093	hgsc.bcm.edu	37	chr13	37453684	37453684	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctcgtccatggctcccttcTtcttctttaacttcttcact	4	15	5	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr13:37453684T>A	ENST00000399275.2	-	1	282	c.143A>T	c.(142-144)aAg>aTg	p.K48M	SMAD9_ENST00000350148.5_Missense_Mutation_p.K48M|SMAD9_ENST00000379826.4_Missense_Mutation_p.K48M|SMAD9_ENST00000483941.1_5'UTR			O15198	SMAD9_HUMAN	SMAD family member 9	48	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.|Poly-Lys.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cartilage development (GO:0051216)|cellular response to organic cyclic compound (GO:0071407)|hindbrain development (GO:0030902)|intracellular signal transduction (GO:0035556)|midbrain development (GO:0030901)|Mullerian duct regression (GO:0001880)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)	18		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)		GGCTCCCTTCTTCTTCTTTAA	0.592																																					p.K48M		Atlas-SNP	.											.	SMAD9	91	.	0			c.A143T						.						82	88	86					13																	37453684		2203	4300	6503	SO:0001583	missense	4093	exon2			CCCTTCTTCTTCT		CCDS9360.1, CCDS45032.1	13q12-q14	2014-09-17	2006-11-06	2004-05-26	ENSG00000120693	ENSG00000120693		"SMADs"	6774	protein-coding gene	gene with protein product		603295	"MAD, mothers against decapentaplegic homolog 9 (Drosophila)", "SMAD, mothers against DPP homolog 9 (Drosophila)"	MADH6, MADH9		9205116	Standard	NM_001127217		Approved		uc001uvw.3	O15198	OTTHUMG00000016740	ENST00000399275.2:c.143A>T	chr13.hg19:g.37453684T>A	ENSP00000382216:p.Lys48Met	66.0	0.0		63.0	25.0	NM_005905	A2A2Y6|O14989|Q5TBA1	Missense_Mutation	SNP	ENST00000399275.2	hg19	CCDS45032.1	.	.	.	.	.	.	.	.	.	.	T	18.75	3.691371	0.68271	.	.	ENSG00000120693	ENST00000399275;ENST00000350148;ENST00000379826	T;T;T	0.79554	-1.28;-1.28;-1.28	5.47	5.47	0.80525	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.91157	0.7215	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;0.994	D;D	0.76071	0.959;0.987	D	0.92935	0.6367	10	0.87932	D	0	.	14.7184	0.69286	0.0:0.0:0.0:1.0	.	48;48	O15198-2;O15198	.;SMAD9_HUMAN	M	48	ENSP00000382216:K48M;ENSP00000239885:K48M;ENSP00000369154:K48M	ENSP00000239885:K48M	K	-	2	0	SMAD9	36351684	1.000000	0.71417	1.000000	0.80357	0.470000	0.32858	6.247000	0.72411	2.073000	0.62155	0.421000	0.28195	AAG	.	.		0.592	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905		A	37453684	T	A	37453684	3	1	202	1	0	0	0	0	1	0	0	0	14779	1609	56	4	1284	4	SMAD9	13	37453684	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10		37453684	77716194	59	29672										
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23890781	23890781	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gagcccaggggaaaatttgcCgctgctaccgggggtccggg	17	11	0	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr15:23890781C>T	ENST00000532292.1	-	1	394	c.300G>A	c.(298-300)gcG>gcA	p.A100A		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	0					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		GAAAATTTGCCGCTGCTACCG	0.627																																					p.A703A		Atlas-SNP	.											MAGEL2_ENST00000532292,NS,carcinoma,0,1	MAGEL2	108	.	0			c.G2109A						.						13	14	14					15																	23890781		1848	4080	5928	SO:0001819	synonymous_variant	54551	exon1			ATTTGCCGCTGCT	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.300G>A	chr15.hg19:g.23890781C>T		149.0	1.0		200.0	56.0	NM_019066		Silent	SNP	ENST00000532292.1	hg19		.	.	.	.	.	.	.	.	.	.	c	0.603	-0.828333	0.02734	.	.	ENSG00000254585	ENST00000532292	T	0.05580	3.42	3.42	-0.854	0.10705	.	.	.	.	.	T	0.03348	0.0097	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.44128	-0.9348	5	.	.	.	.	0.5344	0.00634	0.1778:0.2978:0.1744:0.3501	.	.	.	.	Q	132	ENSP00000433433:R132Q	.	R	-	2	0	MAGEL2	21441874	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.426000	0.02443	-0.161000	0.10983	0.486000	0.48141	CGG	.	.		0.627	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		T	23890781	C	T	23890781	2	4	202	1	0	0	0	0	0	0	0	1	9198	639	23	1		1	MAGEL2	15	23890781	Silent	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10		23890781	78640611	60	29673										
ACTC1	70	hgsc.bcm.edu	37	chr15	35084456	35084456	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gacatagcacagcttctcttTaatgtcacggacaatttcac	6	11	3	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr15:35084456T>A	ENST00000290378.4	-	5	1298	c.643A>T	c.(643-645)Aaa>Taa	p.K215*	RP11-814P5.1_ENST00000558707.1_RNA|ACTC1_ENST00000557860.1_5'UTR|RP11-814P5.1_ENST00000503496.1_RNA	NM_005159.4	NP_005150.1	P68032	ACTC_HUMAN	actin, alpha, cardiac muscle 1	215					actin filament-based movement (GO:0030048)|actin-myosin filament sliding (GO:0033275)|actomyosin structure organization (GO:0031032)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|heart contraction (GO:0060047)|muscle filament sliding (GO:0030049)|negative regulation of apoptotic process (GO:0043066)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|skeletal muscle thin filament assembly (GO:0030240)	actin filament (GO:0005884)|actomyosin, actin portion (GO:0042643)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|I band (GO:0031674)|membrane (GO:0016020)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|myosin binding (GO:0017022)			central_nervous_system(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	31		all_lung(180;2.3e-08)		all cancers(64;5.83e-19)|GBM - Glioblastoma multiforme(113;1.98e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		AGCTTCTCTTTAATGTCACGG	0.473																																					p.K215X		Atlas-SNP	.											.	ACTC1	75	.	0			c.A643T						.						71	68	69					15																	35084456		2201	4298	6499	SO:0001587	stop_gained	70	exon5			TCTCTTTAATGTC	BC009978	CCDS10041.1	15q14	2014-09-17	2006-08-24	2006-08-24	ENSG00000159251	ENSG00000159251			143	protein-coding gene	gene with protein product		102540	"actin, alpha, cardiac muscle"	ACTC		1639426	Standard	NM_005159		Approved	CMD1R	uc001ziu.1	P68032	OTTHUMG00000129675	ENST00000290378.4:c.643A>T	chr15.hg19:g.35084456T>A	ENSP00000290378:p.Lys215*	145.0	0.0		126.0	72.0	NM_005159	P04270	Nonsense_Mutation	SNP	ENST00000290378.4	hg19	CCDS10041.1	.	.	.	.	.	.	.	.	.	.	T	44	10.905651	0.99486	.	.	ENSG00000159251	ENST00000290378;ENST00000544062	.	.	.	4.94	4.94	0.65067	.	0.000000	0.56097	U	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.0473	0.71838	0.0:0.0:0.0:1.0	.	.	.	.	X	215;180	.	ENSP00000290378:K215X	K	-	1	0	ACTC1	32871748	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.868000	0.87116	2.206000	0.71126	0.533000	0.62120	AAA	.	.		0.473	ACTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251876.3	NM_005159		A	35084456	T	A	35084456	4	1	202	1	0	0	0	0	0	1	0	0	195	1763	61	4	502	4	ACTC1	15	35084456	Nonsense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	11193675	35084456	67446936	61	29674										
UBR1	197131	hgsc.bcm.edu	37	chr15	43269020	43269020	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgaagaaggctgcagatcaaCagggtcatcccaatacaagg	11	9	2	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr15:43269020C>A	ENST00000290650.4	-	39	4342	c.4264G>T	c.(4264-4266)Gtt>Ttt	p.V1422F	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1422					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		TGCAGATCAACAGGGTCATCC	0.393																																					p.V1422F		Atlas-SNP	.											.	UBR1	124	.	0			c.G4264T						.						138	114	122					15																	43269020		2203	4299	6502	SO:0001583	missense	197131	exon39			GATCAACAGGGTC		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.4264G>T	chr15.hg19:g.43269020C>A	ENSP00000290650:p.Val1422Phe	195.0	0.0		172.0	47.0	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	hg19	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.670624	0.88348	.	.	ENSG00000159459	ENST00000290650	T	0.49720	0.77	5.2	5.2	0.72013	.	0.059779	0.64402	D	0.000003	T	0.63379	0.2506	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.55786	-0.8086	10	0.10111	T	0.7	-12.0873	18.6835	0.91556	0.0:1.0:0.0:0.0	.	1422	Q8IWV7	UBR1_HUMAN	F	1422	ENSP00000290650:V1422F	ENSP00000290650:V1422F	V	-	1	0	UBR1	41056312	1.000000	0.71417	0.943000	0.38184	0.884000	0.51177	4.148000	0.58085	2.576000	0.86940	0.585000	0.79938	GTT	.	.		0.393	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		A	43269020	C	A	43269020	3	1	202	1	0	0	0	0	1	0	0	0	16916	478	17	3	1021	3	UBR1	15	43269020	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	8184564	43269020	59262372	62	29675										
GATM	2628	hgsc.bcm.edu	37	chr15	45661556	45661556	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aatcaggagttttatacttcAatgaccagtcaatggggtca	9	7	4	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr15:45661556A>G	ENST00000396659.3	-	3	791	c.452T>C	c.(451-453)tTg>tCg	p.L151S	GATM_ENST00000558336.1_Missense_Mutation_p.L151S	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	151					cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|embryo development (GO:0009790)|response to mercury ion (GO:0046689)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	glycine amidinotransferase activity (GO:0015068)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines (GO:0016813)			biliary_tract(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	15		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Glycine(DB00145)|L-Ornithine(DB00129)	TTTATACTTCAATGACCAGTC	0.378																																					p.L151S		Atlas-SNP	.											.	GATM	34	.	0			c.T452C						.						109	106	107					15																	45661556		2198	4298	6496	SO:0001583	missense	2628	exon3			TACTTCAATGACC	S68805	CCDS10122.1	15q15.1	2007-12-06			ENSG00000171766	ENSG00000171766	2.1.4.1		4175	protein-coding gene	gene with protein product		602360				8313955	Standard	NM_001482		Approved	AGAT	uc001zvc.3	P50440	OTTHUMG00000131427	ENST00000396659.3:c.452T>C	chr15.hg19:g.45661556A>G	ENSP00000379895:p.Leu151Ser	158.0	0.0		112.0	36.0	NM_001482	B4DH99|B4DPI3|Q53EQ4	Missense_Mutation	SNP	ENST00000396659.3	hg19	CCDS10122.1	.	.	.	.	.	.	.	.	.	.	A	6.102	0.387150	0.11581	.	.	ENSG00000171766	ENST00000396659	T	0.09911	2.93	6.07	4.93	0.64822	.	0.903013	0.09674	N	0.770774	T	0.08447	0.0210	L	0.28115	0.83	0.29918	N	0.822997	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.32903	-0.9889	10	0.09843	T	0.71	1.1468	10.8433	0.46728	0.8586:0.0:0.0:0.1414	.	151;151	P50440-3;P50440	.;GATM_HUMAN	S	151	ENSP00000379895:L151S	ENSP00000379895:L151S	L	-	2	0	GATM	43448848	0.806000	0.28996	0.124000	0.21820	0.976000	0.68499	5.828000	0.69307	1.067000	0.40740	0.533000	0.62120	TTG	.	.		0.378	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482		G	45661556	A	G	45661556	3	3	202	1	0	0	0	0	1	0	0	0	6271	131	5	2	847	2	GATM	15	45661556	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	2392536	45661556	56869836	63	29676										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54308039	54308039	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agaagcagctttaagggcctAtaaaaagcaaatggcagagt	11	6	0	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr15:54308039A>T	ENST00000260323.11	+	1	2939	c.2939A>T	c.(2938-2940)tAt>tTt	p.Y980F	UNC13C_ENST00000537900.1_Missense_Mutation_p.Y980F|UNC13C_ENST00000545554.1_Missense_Mutation_p.Y980F	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	980					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TTAAGGGCCTATAAAAAGCAA	0.388																																					p.Y980F		Atlas-SNP	.											.	UNC13C	674	.	0			c.A2939T						.						56	55	56					15																	54308039		1843	4095	5938	SO:0001583	missense	440279	exon1			GGGCCTATAAAAA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.2939A>T	chr15.hg19:g.54308039A>T	ENSP00000260323:p.Tyr980Phe	196.0	0.0		192.0	114.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	A	19.00	3.742735	0.69418	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.82526	-1.62;-1.51;-1.62	5.58	5.58	0.84498	.	.	.	.	.	D	0.85526	0.5717	L	0.29908	0.895	0.45129	D	0.99814	D	0.69078	0.997	D	0.75020	0.985	D	0.85251	0.1044	9	0.38643	T	0.18	.	14.9285	0.70898	1.0:0.0:0.0:0.0	.	980	Q8NB66	UN13C_HUMAN	F	980	ENSP00000260323:Y980F;ENSP00000438156:Y980F;ENSP00000442569:Y980F	ENSP00000260323:Y980F	Y	+	2	0	UNC13C	52095331	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.962000	0.93254	2.128000	0.65567	0.528000	0.53228	TAT	.	.		0.388	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54308039	A	T	54308039	3	4	202	1	0	0	0	0	1	0	0	0	17001	449	16	4	2941	4	UNC13C	15	54308039	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	8646483	54308039	48223353	64	29677										
RHCG	51458	hgsc.bcm.edu	37	chr15	90016014	90016014	+	Frame_Shift_Del	DEL	G	G	-													0	0	1	0	0	0	1	1	0	atgggtagtggggacaccatGggtactgagggtactgaggg					rs562119923	byFrequency	TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr15:90016014delG	ENST00000268122.4	-	10	1460	c.1392delC	c.(1390-1392)cccfs	p.P464fs	RHCG_ENST00000544600.1_Intron	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	464					amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					GGGACACCATgggtactgagg	0.592																																					p.M465fs		Atlas-INDEL	.											.	RHCG	49	.	0			c.1393delA						.						130	92	105					15																	90016014		2199	4294	6493	SO:0001589	frameshift_variant	51458	exon10			.	AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"Solute carriers"	18140	protein-coding gene	gene with protein product		605381	"chromosome 15 open reading frame 6", "Rhesus blood group, C glycoprotein"	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.1392delC	chr15.hg19:g.90016014delG	ENSP00000268122:p.Pro464fs	129.0	0.0		129.0	31.0	NM_016321	A8K4D4|Q6X3Y4	Frame_Shift_Del	DEL	ENST00000268122.4	hg19	CCDS10351.1																																																																																			.	.		0.592	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321		-	90016014	G	-	90016014	7	5	202	1	0	1	0	1	0	0	0	0	13341	1335	47	0	51	0	RHCG	15	90016014	Frame_Shift_Del	DEL	G	TCGA-DD-AADU-01A-11D-A40R-10	35707975	90016014	12515378	65	29678										
TBC1D10B	26000	hgsc.bcm.edu	37	chr16	30380742	30380742	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccctcgaggcccagagatgcCaggtcccaggctggacgtgg	15	14	0	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr16:30380742C>A	ENST00000409939.3	-	1	843	c.763G>T	c.(763-765)Ggc>Tgc	p.G255C		NM_015527.3	NP_056342.3	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	255					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(1)|lung(2)|urinary_tract(1)	6			Colorectal(24;0.193)			CCAGAGATGCCAGGTCCCAGG	0.627																																					p.G255C		Atlas-SNP	.											.	TBC1D10B	32	.	0			c.G763T						.						31	36	34					16																	30380742		692	1591	2283	SO:0001583	missense	26000	exon1			AGATGCCAGGTCC	BC063112	CCDS10676.2	16p11.2	2013-07-09			ENSG00000169221	ENSG00000169221			24510	protein-coding gene	gene with protein product		613620				20404108	Standard	NM_015527		Approved	DKFZP434P1750, Rab27A-GAPbeta, FLJ13130, EPI64B	uc002dxt.3	Q4KMP7	OTTHUMG00000132396	ENST00000409939.3:c.763G>T	chr16.hg19:g.30380742C>A	ENSP00000386538:p.Gly255Cys	59.0	0.0		46.0	22.0	NM_015527	B9A6L0|Q6IN54|Q6P530|Q71RG7|Q86VC5|Q9H8Z2|Q9NUN6|Q9UFP2	Missense_Mutation	SNP	ENST00000409939.3	hg19	CCDS10676.2	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695014	0.68386	.	.	ENSG00000169221	ENST00000409939	T	0.06933	3.24	3.91	2.91	0.33838	.	.	.	.	.	T	0.15522	0.0374	L	0.43152	1.355	0.30844	N	0.735383	D	0.69078	0.997	P	0.56865	0.808	T	0.03957	-1.0989	9	0.62326	D	0.03	.	10.514	0.44879	0.0:0.8018:0.1981:0.0	.	255	Q4KMP7	TB10B_HUMAN	C	255	ENSP00000386538:G255C	ENSP00000386538:G255C	G	-	1	0	TBC1D10B	30288243	0.995000	0.38212	0.998000	0.56505	0.992000	0.81027	2.306000	0.43673	0.810000	0.34279	0.491000	0.48974	GGC	.	.		0.627	TBC1D10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255527.3	NM_015527		A	30380742	C	A	30380742	3	1	202	1	0	0	0	0	1	0	0	0	15614	594	21	3	1699	3	TBC1D10B	16	30380742	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10		30380742	59974011	66	29679										
HAS3	54921	hgsc.bcm.edu	37	chr16	69152319	69152344	+	3'UTR	DEL	CGGAAGCATGGTCCGTTCACCAACGC	CGGAAGCATGGTCCGTTCACCAACGC	-													0	0	1	0	0	0	1	1	0	agctgcccaggtcagagctaCggaagcatggtccgttcacc					rs113161750|rs375441522|rs533106531|rs368710507	byFrequency	TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	CGGAAGCATGGTCCGTTCACCAACGC	CGGAAGCATGGTCCGTTCACCAACGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr16:69152319_69152344delCGGAAGCATGGTCCGTTCACCAACGC	ENST00000448552.2	-	0	2471_2496				CHTF8_ENST00000523421.1_3'UTR|HAS3_ENST00000219322.3_Frame_Shift_Del_p.TEAWSVHQR267fs|CHTF8_ENST00000518041.1_3'UTR|CHTF8_ENST00000306585.6_3'UTR	NM_001039690.3|NM_001040146.3	NP_001034779.1|NP_001035236.1	P0CG13	CTF8_HUMAN	CTF8, chromosome transmission fidelity factor 8 homolog (S. cerevisiae)						cell cycle (GO:0007049)|DNA replication (GO:0006260)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T267M(1)									GTCAGAGCTACGGAAGCATGGTCCGTTCACCAACGCCACGTTTCTA	0.54																																					p.267_275del		Atlas-INDEL	.											.	HAS3	61	.	1	Substitution - Missense(1)	large_intestine(1)	c.799_824del						.																																			SO:0001624	3_prime_UTR_variant	3038	exon4			.		CCDS42185.1	16q22.1	2009-01-14				ENSG00000168802			24353	protein-coding gene	gene with protein product		613202				12766176	Standard	NM_001039690		Approved	FLJ20400, CTF8, DERPC	uc002ewo.2	P0CG12		ENST00000448552.2:c.*2009GCGTTGGTGAACGGACCATGCTTCCG>-	chr16.hg19:g.69152319_69152344delCGGAAGCATGGTCCGTTCACCAACGC		112.0	0.0		104.0	32.0	NM_138612	A8MYX8|Q71E72|Q8NDH8|Q8WV66|Q9NX73	Frame_Shift_Del	DEL	ENST00000448552.2	hg19	CCDS42185.1																																																																																			.	.		0.54	CHTF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376352.2	NM_017804		-	69152344	CGGAAGCATGGTCCGTTCACCAACGC	-	69152319	6	5	202	0	1	1	0	1	0	0	0	0	6972	536	19	0		0	HAS3	16	69152319	3'UTR	DEL	CGGAAGCATGGTCCGTTCACCAACGC	TCGA-DD-AADU-01A-11D-A40R-10	38771577	69152319	21202434	67	29680										
USP6	9098	hgsc.bcm.edu	37	chr17	5041492	5041492	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttcgatacctgggccatgaaCgatgacaccgtgctcaagca	10	12	1	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr17:5041492C>T	ENST00000574788.1	+	21	3232	c.1002C>T	c.(1000-1002)aaC>aaT	p.N334N	USP6_ENST00000332776.4_Silent_p.N334N|USP6_ENST00000250066.6_Silent_p.N334N|USP6_ENST00000304328.5_5'UTR			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	334					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GGGCCATGAACGATGACACCG	0.577			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																p.N334N		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	USP6_ENST00000250066,caecum,carcinoma,0,4	USP6	213	.	0			c.C1002T						.						146	143	144					17																	5041492		2203	4300	6503	SO:0001819	synonymous_variant	9098	exon13			CATGAACGATGAC	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.1002C>T	chr17.hg19:g.5041492C>T		77.0	0.0		58.0	11.0	NM_004505	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	hg19	CCDS11069.2																																																																																			.	.		0.577	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		T	5041492	C	T	5041492	2	4	202	1	0	0	0	0	0	0	0	1	17101	535	19	1		1	USP6	17	5041492	Silent	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10		5041492	76153718	68	29681										
PPP1R1B	84152	hgsc.bcm.edu	37	chr17	37791909	37791909	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctggaagggccctgggagcgCccaccccctctggatgagtc	14	15	1	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr17:37791909C>T	ENST00000254079.4	+	6	964	c.495C>T	c.(493-495)cgC>cgT	p.R165R	STARD3_ENST00000544210.2_5'Flank|STARD3_ENST00000394250.4_5'Flank|PPP1R1B_ENST00000580825.1_Silent_p.R165R|STARD3_ENST00000580611.1_5'Flank|PPP1R1B_ENST00000579000.1_Silent_p.R132R|PPP1R1B_ENST00000394267.2_Silent_p.R129R|PPP1R1B_ENST00000394265.1_Silent_p.R129R|STARD3_ENST00000336308.5_5'Flank	NM_032192.3	NP_115568.2	Q9UD71	PPR1B_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1B	165					intracellular signal transduction (GO:0035556)|negative regulation of catalytic activity (GO:0043086)|negative regulation of female receptivity (GO:0007621)|negative regulation of protein kinase activity (GO:0006469)|regulation of catalytic activity (GO:0050790)|response to amphetamine (GO:0001975)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	protein kinase inhibitor activity (GO:0004860)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 1 regulator activity (GO:0008599)			kidney(1)|large_intestine(1)|liver(1)|lung(2)	5	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCTGGGAGCGCCCACCCCCTC	0.582																																					p.R165R		Atlas-SNP	.											.	PPP1R1B	9	.	0			c.C495T						.						67	76	73					17																	37791909		2203	4300	6503	SO:0001819	synonymous_variant	84152	exon6			GGAGCGCCCACCC	AI124650	CCDS11339.1, CCDS11340.1	17q12	2012-04-17	2008-07-31		ENSG00000131771	ENSG00000131771	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9287	protein-coding gene	gene with protein product	"dopamine and cAMP regulated phosphoprotein"	604399				8120638	Standard	NM_032192		Approved	DARPP-32, FLJ20940	uc002hrz.3	Q9UD71	OTTHUMG00000133210	ENST00000254079.4:c.495C>T	chr17.hg19:g.37791909C>T		125.0	0.0		127.0	69.0	NM_032192	Q547V9|Q547W0|Q9H7G1	Silent	SNP	ENST00000254079.4	hg19	CCDS11339.1																																																																																			.	.		0.582	PPP1R1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256925.2	NM_032192		T	37791909	C	T	37791909	2	4	202	1	0	0	0	0	0	0	0	1	12380	726	26	3		3	PPP1R1B	17	37791909	Silent	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	32750417	37791909	43403301	69	29682										
GFAP	2670	hgsc.bcm.edu	37	chr17	42992812	42992812	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	catcatctcccctgaggagaCgtaggagcggcgagcagcgg	15	12	2	2	rs146698039		TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr17:42992812C>T	ENST00000253408.5	-	1	108	c.43G>A	c.(43-45)Gtc>Atc	p.V15I	GFAP_ENST00000435360.2_Missense_Mutation_p.V15I|GFAP_ENST00000586793.1_Missense_Mutation_p.V15I|GFAP_ENST00000588735.1_Missense_Mutation_p.V15I|GFAP_ENST00000591327.1_5'UTR	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein	15	Head.				astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				CCTGAGGAGACGTAGGAGCGG	0.667																																					p.V15I		Atlas-SNP	.											.	GFAP	88	.	0			c.G43A						.	C	ILE/VAL,ILE/VAL,ILE/VAL	1,4387		0,1,2193	14	16	16		43,43,43	-2.1	0	17	dbSNP_134	16	0,8566		0,0,4283	no	missense,missense,missense	GFAP	NM_001131019.2,NM_001242376.1,NM_002055.4	29,29,29	0,1,6476	TT,TC,CC		0.0,0.0228,0.0077	benign,benign,benign	15/432,15/439,15/433	42992812	1,12953	2194	4283	6477	SO:0001583	missense	2670	exon1			AGGAGACGTAGGA	S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"Intermediate filaments type III"	4235	protein-coding gene	gene with protein product	"intermediate filament protein"	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.43G>A	chr17.hg19:g.42992812C>T	ENSP00000253408:p.Val15Ile	117.0	0.0		127.0	68.0	NM_001131019	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Missense_Mutation	SNP	ENST00000253408.5	hg19	CCDS11491.1	.	.	.	.	.	.	.	.	.	.	C	2.850	-0.238536	0.05944	2.28E-4	0.0	ENSG00000131095	ENST00000253408;ENST00000435360;ENST00000376990	D;D;D	0.87491	-1.82;-1.76;-2.26	4.9	-2.12	0.07165	.	1.415560	0.04661	N	0.408830	T	0.73908	0.3647	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.57705	-0.7765	10	0.11794	T	0.64	.	5.0585	0.14546	0.0:0.3589:0.1553:0.4859	.	15;15	E9PAX3;P14136	.;GFAP_HUMAN	I	15	ENSP00000253408:V15I;ENSP00000403962:V15I;ENSP00000366189:V15I	ENSP00000253408:V15I	V	-	1	0	GFAP	40348338	0.000000	0.05858	0.003000	0.11579	0.067000	0.16453	-0.095000	0.11077	-0.537000	0.06290	-1.134000	0.01955	GTC	.	C|1.000;T|0.000		0.667	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055		T	42992812	C	T	42992812	3	4	202	1	0	0	0	0	1	0	0	0	6345	536	19	1	1420	1	GFAP	17	42992812	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	5200903	42992812	38202398	70	29683										
LRRC37A3	374819	hgsc.bcm.edu	37	chr17	62892812	62892812	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggctaccgggatacggtgtAtctgtactggaatattcatt	11	7	2	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr17:62892812A>G	ENST00000584306.1	-	3	1094	c.564T>C	c.(562-564)gaT>gaC	p.D188D	RP11-927P21.1_ENST00000584131.1_RNA|LRRC37A3_ENST00000319651.5_Silent_p.D188D|RP11-927P21.1_ENST00000584959.1_RNA|LRRC37A3_ENST00000339474.5_Intron|RP11-927P21.1_ENST00000577938.1_RNA|LRRC37A3_ENST00000577487.1_5'Flank|LRRC37A3_ENST00000400877.3_Intron	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	188						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GATACGGTGTATCTGTACTGG	0.488																																					p.D188D		Atlas-SNP	.											.	LRRC37A3	75	.	0			c.T564C						.						57	98	85					17																	62892812		1417	3199	4616	SO:0001819	synonymous_variant	374819	exon3			CGGTGTATCTGTA	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.564T>C	chr17.hg19:g.62892812A>G		233.0	0.0		239.0	55.0	NM_199340	Q49A01|Q49A80|Q8NB33	Silent	SNP	ENST00000584306.1	hg19	CCDS32708.1																																																																																			.	.		0.488	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340		G	62892812	A	G	62892812	2	3	202	1	0	0	0	0	0	0	0	1	9002	446	16	2		2	LRRC37A3	17	62892812	Silent	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	19900000	62892812	18302398	71	29684										
GNA13	10672	hgsc.bcm.edu	37	chr17	63014400	63014400	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aagtttatccaagttatccaGgaaatattttacagattcac	5	7	1	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr17:63014400G>A	ENST00000439174.2	-	3	777	c.532C>T	c.(532-534)Ctg>Ttg	p.L178L	GNA13_ENST00000541118.1_Silent_p.L83L	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	178					activation of phospholipase D activity (GO:0031584)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|in utero embryonic development (GO:0001701)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(14)|kidney(2)|large_intestine(4)|lung(6)|urinary_tract(1)	34						AAGTTATCCAGGAAATATTTT	0.328																																					p.L178L		Atlas-SNP	.											.	GNA13	69	.	0			c.C532T						.						122	128	126					17																	63014400		2202	4299	6501	SO:0001819	synonymous_variant	10672	exon3			TATCCAGGAAATA	L22075	CCDS11661.1, CCDS62302.1	17q24.1	2014-09-04			ENSG00000120063	ENSG00000120063			4381	protein-coding gene	gene with protein product		604406				7791744	Standard	NM_006572		Approved	G13, MGC46138	uc002jfc.3	Q14344	OTTHUMG00000179316	ENST00000439174.2:c.532C>T	chr17.hg19:g.63014400G>A		372.0	0.0		415.0	106.0	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Silent	SNP	ENST00000439174.2	hg19	CCDS11661.1																																																																																			.	.		0.328	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572		A	63014400	G	A	63014400	2	1	202	1	0	0	0	0	0	0	0	1	6509	991	35	3		3	GNA13	17	63014400	Silent	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	121588	63014400	18180810	72	29685										
HELZ	9931	hgsc.bcm.edu	37	chr17	65174838	65174838	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggtcatgtaaccgtgactgaTagttgctcttggtcaatgat	11	7	3	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr17:65174838T>C	ENST00000358691.5	-	13	1533	c.1367A>G	c.(1366-1368)tAt>tGt	p.Y456C	HELZ_ENST00000580168.1_Missense_Mutation_p.Y456C	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	456						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					CCGTGACTGATAGTTGCTCTT	0.368																																					p.Y456C		Atlas-SNP	.											.	HELZ	160	.	0			c.A1367G						.						134	127	129					17																	65174838		1851	4101	5952	SO:0001583	missense	9931	exon13			GACTGATAGTTGC	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.1367A>G	chr17.hg19:g.65174838T>C	ENSP00000351524:p.Tyr456Cys	136.0	0.0		137.0	36.0	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	T	14.29	2.492146	0.44352	.	.	ENSG00000198265	ENST00000358691	D	0.91740	-2.9	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.96030	0.8707	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.99;0.998	D	0.96377	0.9278	10	0.87932	D	0	-17.6497	16.635	0.85050	0.0:0.0:0.0:1.0	.	456;456	B7ZLW2;P42694	.;HELZ_HUMAN	C	456	ENSP00000351524:Y456C	ENSP00000351524:Y456C	Y	-	2	0	HELZ	62605300	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.618000	0.83043	2.330000	0.79161	0.477000	0.44152	TAT	.	.		0.368	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		C	65174838	T	C	65174838	3	2	202	1	0	0	0	0	1	0	0	0	7058	1406	49	2	4545	2	HELZ	17	65174838	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	2160438	65174838	16020372	73	29686										
PSMD12	5718	hgsc.bcm.edu	37	chr17	65340883	65340883	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caactccattgtggtaaaaaGctttaaaagatccctgaaaa	6	8	0	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr17:65340883G>C	ENST00000356126.3	-	9	1029	c.922C>G	c.(922-924)Ctt>Gtt	p.L308V	PSMD12_ENST00000357146.4_Missense_Mutation_p.L288V	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	308	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					GTGGTAAAAAGCTTTAAAAGA	0.323																																					p.L308V		Atlas-SNP	.											.	PSMD12	32	.	0			c.C922G						.						52	50	51					17																	65340883		2203	4300	6503	SO:0001583	missense	5718	exon9			TAAAAAGCTTTAA	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.922C>G	chr17.hg19:g.65340883G>C	ENSP00000348442:p.Leu308Val	425.0	0.0		407.0	97.0	NM_002816	A6NP15|Q53HA2|Q6P053	Missense_Mutation	SNP	ENST00000356126.3	hg19	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.895874	0.52121	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	T;T	0.30182	1.54;1.54	5.72	4.75	0.60458	Proteasome component (PCI) domain (1);	0.055741	0.64402	D	0.000001	T	0.33469	0.0864	L	0.49778	1.585	0.54753	D	0.999981	B;B	0.25850	0.013;0.136	B;B	0.37731	0.133;0.257	T	0.07177	-1.0786	10	0.26408	T	0.33	-14.4196	12.4585	0.55718	0.132:0.0:0.868:0.0	.	288;308	A6NP15;O00232	.;PSD12_HUMAN	V	308;288	ENSP00000348442:L308V;ENSP00000349667:L288V	ENSP00000348442:L308V	L	-	1	0	PSMD12	62771345	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.522000	0.60539	2.693000	0.91896	0.585000	0.79938	CTT	.	.		0.323	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		C	65340883	G	C	65340883	3	2	202	1	0	0	0	0	1	0	0	0	12707	971	34	4	460	4	PSMD12	17	65340883	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	166045	65340883	15854327	74	29687										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48575189	48575189	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaaatgtgatagtgtctgtgTgaatccatatcactacgaac	8	7	2	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr18:48575189T>C	ENST00000342988.3	+	3	921	c.383T>C	c.(382-384)gTg>gCg	p.V128A	RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000398417.2_Missense_Mutation_p.V128A|SMAD4_ENST00000588745.1_Missense_Mutation_p.V128A|SMAD4_ENST00000452201.2_Missense_Mutation_p.V128A	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	128	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(4)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		AGTGTCTGTGTGAATCCATAT	0.373																																					p.V128A		Atlas-SNP	.											SMAD4,rectum,carcinoma,0,1	SMAD4	822	.	40	Whole gene deletion(36)|Unknown(4)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|NS(1)	c.T383C						.						152	136	141					18																	48575189		2203	4300	6503	SO:0001583	missense	4089	exon3			TCTGTGTGAATCC	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.383T>C	chr18.hg19:g.48575189T>C	ENSP00000341551:p.Val128Ala	172.0	1.0		97.0	43.0	NM_005359	A8K405	Missense_Mutation	SNP	ENST00000342988.3	hg19	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.855079	0.91355	.	.	ENSG00000141646	ENST00000452201;ENST00000342988;ENST00000544926;ENST00000398417	T;T;T	0.80566	-1.39;-1.39;-1.39	5.48	5.48	0.80851	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.90410	0.6998	M	0.88377	2.95	0.58432	D	0.999999	D	0.63046	0.992	D	0.66196	0.942	D	0.92229	0.5791	10	0.87932	D	0	.	14.5339	0.67947	0.0:0.0:0.0:1.0	.	128	Q13485	SMAD4_HUMAN	A	128	ENSP00000409551:V128A;ENSP00000341551:V128A;ENSP00000381452:V128A	ENSP00000341551:V128A	V	+	2	0	SMAD4	46829187	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.014000	0.88676	2.053000	0.61076	0.477000	0.44152	GTG	.	.		0.373	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		C	48575189	T	C	48575189	3	2	202	1	0	0	0	0	1	0	0	0	14775	1696	59	2	389	2	SMAD4	18	48575189	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10		48575189	29502059	75	29688										
C18orf26	284254	hgsc.bcm.edu	37	chr18	52258515	52258515	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgatactggcagctcaagaaTggacagaaagcatggaaaat	11	6	1	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr18:52258515T>C	ENST00000321600.1	+	1	126	c.80T>C	c.(79-81)aTg>aCg	p.M27T	DYNAP_ENST00000585973.1_Missense_Mutation_p.M30T	NM_173629.1	NP_775900.1	Q8N1N2	DYNAP_HUMAN	dynactin associated protein	27					activation of protein kinase B activity (GO:0032148)|cellular response to ergosterol (GO:1901625)|positive regulation of cell proliferation (GO:0008284)|regulation of apoptotic process (GO:0042981)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											AGCTCAAGAATGGACAGAAAG	0.383																																					p.M27T		Atlas-SNP	.											.	.	.	.	0			c.T80C						.						131	131	131					18																	52258515		2203	4300	6503	SO:0001583	missense	284254	exon1			CAAGAATGGACAG	AK096425	CCDS11957.1	18q21.2	2012-10-24	2012-10-24	2012-10-24	ENSG00000178690	ENSG00000178690			26808	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 26"	C18orf26		20978158	Standard	NM_173629		Approved	FLJ39106	uc002lfq.1	Q8N1N2	OTTHUMG00000132709	ENST00000321600.1:c.80T>C	chr18.hg19:g.52258515T>C	ENSP00000315265:p.Met27Thr	136.0	0.0		93.0	38.0	NM_173629		Missense_Mutation	SNP	ENST00000321600.1	hg19	CCDS11957.1	.	.	.	.	.	.	.	.	.	.	.	14.54	2.564726	0.45694	.	.	ENSG00000178690	ENST00000321600	T	0.22539	1.95	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000003	T	0.40347	0.1113	L	0.55481	1.735	0.30285	N	0.790906	D	0.76494	0.999	D	0.85130	0.997	T	0.40040	-0.9584	10	0.87932	D	0	-9.2421	11.7662	0.51933	0.0:0.0:0.0:1.0	.	27	Q8N1N2	CR026_HUMAN	T	27	ENSP00000315265:M27T	ENSP00000315265:M27T	M	+	2	0	C18orf26	50409513	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	3.531000	0.53546	2.097000	0.63578	0.496000	0.49642	ATG	.	.		0.383	DYNAP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256007.1	NM_173629		C	52258515	T	C	52258515	3	2	202	1	0	0	0	0	1	0	0	0	1902	1464	51	2	82	2	C18orf26	18	52258515	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	3683326	52258515	25818733	76	29689										
SALL3	27164	hgsc.bcm.edu	37	chr18	76757080	76757080	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agtatgctgcagccatcactAacgggctcgccatgaagaac	10	12	1	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr18:76757080A>T	ENST00000537592.2	+	3	3661	c.3661A>T	c.(3661-3663)Aac>Tac	p.N1221Y	SALL3_ENST00000536229.3_Missense_Mutation_p.N1016Y|SALL3_ENST00000575389.2_Missense_Mutation_p.N1149Y	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1221					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		AGCCATCACTAACGGGCTCGC	0.592																																					p.N1221Y		Atlas-SNP	.											.	SALL3	162	.	0			c.A3661T						.						107	98	101					18																	76757080		2203	4300	6503	SO:0001583	missense	27164	exon3			ATCACTAACGGGC	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.3661A>T	chr18.hg19:g.76757080A>T	ENSP00000441823:p.Asn1221Tyr	180.0	0.0		151.0	10.0	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	hg19	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	A	5.766	0.325731	0.10900	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.54866	0.55	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000010	T	0.74435	0.3716	M	0.84433	2.695	0.52099	D	0.999941	D;D	0.89917	0.999;1.0	D;D	0.71184	0.969;0.972	T	0.79667	-0.1708	10	0.72032	D	0.01	-29.8556	14.8958	0.70644	1.0:0.0:0.0:0.0	.	881;1221	F5GXY4;Q9BXA9	.;SALL3_HUMAN	Y	1221;1149;881	ENSP00000441823:N1221Y	ENSP00000299466:N1221Y	N	+	1	0	SALL3	74858068	1.000000	0.71417	0.251000	0.24312	0.134000	0.20937	7.398000	0.79919	1.906000	0.55180	0.459000	0.35465	AAC	.	.		0.592	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		T	76757080	A	T	76757080	3	4	202	1	0	0	0	0	1	0	0	0	13827	362	13	4	3671	4	SALL3	18	76757080	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	24498565	76757080	1320168	77	29690										
MUC16	94025	hgsc.bcm.edu	37	chr19	9086539	9086539	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgccccctatgaattccacaTcaggagttgtaggagatgag	11	9	1	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr19:9086539T>A	ENST00000397910.4	-	1	5479	c.5276A>T	c.(5275-5277)gAt>gTt	p.D1759V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1759	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAATTCCACATCAGGAGTTGT	0.502																																					p.D1759V		Atlas-SNP	.											.	MUC16	4315	.	0			c.A5276T						.						117	109	111					19																	9086539		1968	4148	6116	SO:0001583	missense	94025	exon1			TCCACATCAGGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5276A>T	chr19.hg19:g.9086539T>A	ENSP00000381008:p.Asp1759Val	119.0	0.0		87.0	28.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	1.752	-0.488950	0.04352	.	.	ENSG00000181143	ENST00000397910	T	0.03065	4.06	1.33	-0.964	0.10326	.	.	.	.	.	T	0.01695	0.0054	N	0.08118	0	.	.	.	P	0.50710	0.938	B	0.37451	0.25	T	0.46091	-0.9216	8	0.87932	D	0	.	4.2255	0.10579	0.0:0.4969:0.0:0.5031	.	1759	B5ME49	.	V	1759	ENSP00000381008:D1759V	ENSP00000381008:D1759V	D	-	2	0	MUC16	8947539	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	-1.804000	0.01738	-0.417000	0.07461	0.260000	0.18958	GAT	.	.		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9086539	T	A	9086539	3	1	202	1	0	0	0	0	1	0	0	0	9982	1435	50	4	38583	4	MUC16	19	9086539	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10		9086539	50042444	78	29691										
ZNF253	56242	hgsc.bcm.edu	37	chr19	20003048	20003048	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctctaaccttactatacataAgagaattcatacaggagaga	6	8	2	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr19:20003048A>G	ENST00000589717.1	+	4	1084	c.992A>G	c.(991-993)aAg>aGg	p.K331R	AC011477.1_ENST00000578823.1_RNA|ZNF253_ENST00000355650.4_Missense_Mutation_p.K255R|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	331				Missing (in Ref. 1; AAC26844). {ECO:0000305}.	negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACTATACATAAGAGAATTCAT	0.388																																					p.K331R		Atlas-SNP	.											.	ZNF253	99	.	0			c.A992G						.						40	45	43					19																	20003048		2145	4271	6416	SO:0001583	missense	56242	exon4			TACATAAGAGAAT	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"Zinc fingers, C2H2-type", "-"	13497	protein-coding gene	gene with protein product		606954	"zinc finger protein 411"	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.992A>G	chr19.hg19:g.20003048A>G	ENSP00000468720:p.Lys331Arg	135.0	0.0		123.0	64.0	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Missense_Mutation	SNP	ENST00000589717.1	hg19	CCDS42532.1	.	.	.	.	.	.	.	.	.	.	a	11.12	1.544823	0.27563	.	.	ENSG00000256771	ENST00000355650	.	.	.	0.876	0.876	0.19138	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.26122	0.0637	N	0.04260	-0.245	0.21984	N	0.999437	D	0.89917	1.0	D	0.83275	0.996	T	0.15896	-1.0421	7	.	.	.	.	5.5788	0.17238	1.0:0.0:0.0:0.0	.	331	O75346	ZN253_HUMAN	R	331	.	.	K	+	2	0	ZNF253	19864048	0.000000	0.05858	0.129000	0.21949	0.128000	0.20619	-0.190000	0.09615	0.251000	0.21505	0.248000	0.18094	AAG	.	.		0.388	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047		G	20003048	A	G	20003048	3	3	202	1	0	0	0	0	1	0	0	0	17812	72	3	2	1006	2	ZNF253	19	20003048	Missense_Mutation	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10	10916509	20003048	39125935	79	29692										
ZNF99	7652	hgsc.bcm.edu	37	chr19	22940398	22940398	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttctaagggctgagaaatgCttaaaagctttgccacattc	8	8	1	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr19:22940398C>T	ENST00000596209.1	-	4	2403	c.2313G>A	c.(2311-2313)aaG>aaA	p.K771K	CTC-451A6.4_ENST00000442497.2_lincRNA|ZNF99_ENST00000397104.3_Silent_p.K680K	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	771					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				CTGAGAAATGCTTAAAAGCTT	0.358																																					p.K771K		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	.	0			c.G2313A						.						30	32	32					19																	22940398		1951	4133	6084	SO:0001819	synonymous_variant	7652	exon4			GAAATGCTTAAAA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2313G>A	chr19.hg19:g.22940398C>T		35.0	1.0		27.0	4.0	NM_001080409	M0R335	Silent	SNP	ENST00000596209.1	hg19	CCDS59369.1																																																																																			.	.		0.358	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		T	22940398	C	T	22940398	2	4	202	1	0	0	0	0	0	0	0	1	18219	796	28	3		3	ZNF99	19	22940398	Silent	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	2937350	22940398	36188585	80	29693										
DMKN	93099	hgsc.bcm.edu	37	chr19	36003608	36003608	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggggtatccgtggacccacgGagtccccagacctccaggat	13	14	0	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr19:36003608G>T	ENST00000339686.3	-	2	687	c.511C>A	c.(511-513)Ccg>Acg	p.P171T	DMKN_ENST00000418261.1_Missense_Mutation_p.P171T|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.P171T|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000429837.1_Missense_Mutation_p.P171T|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.P171T|DMKN_ENST00000419602.1_Missense_Mutation_p.P171T|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.P171T|DMKN_ENST00000424570.2_Missense_Mutation_p.P171T|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000414866.2_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	171	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TGGACCCACGGAGTCCCCAGA	0.582																																					p.P171T		Atlas-SNP	.											.	DMKN	116	.	0			c.C511A						.						53	56	55					19																	36003608		2203	4300	6503	SO:0001583	missense	93099	exon2			CCCACGGAGTCCC	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.511C>A	chr19.hg19:g.36003608G>T	ENSP00000342012:p.Pro171Thr	58.0	0.0		51.0	18.0	NM_001190347	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	hg19	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195756	0.38806	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000429837;ENST00000419602;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T;T;T	0.46063	1.59;1.45;1.37;0.88;0.99;1.01;1.0;1.07	4.22	0.547	0.17202	.	0.195238	0.25657	N	0.029177	T	0.48840	0.1522	L	0.49126	1.545	0.09310	N	1	P;D;D;P;B;B;B	0.76494	0.582;0.999;0.999;0.582;0.192;0.192;0.324	B;D;D;B;B;B;B	0.80764	0.225;0.994;0.994;0.225;0.135;0.135;0.225	T	0.21415	-1.0246	10	0.46703	T	0.11	-3.2671	4.6633	0.12653	0.1057:0.0:0.5129:0.3814	.	171;171;171;171;171;171;171	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;C9J4P6;Q6E0U4-4;Q6E0U4	.;.;.;.;.;.;DMKN_HUMAN	T	171	ENSP00000342012:P171T;ENSP00000405503:P171T;ENSP00000391036:P171T;ENSP00000394908:P171T;ENSP00000415277:P171T;ENSP00000414743:P171T;ENSP00000388404:P171T;ENSP00000409513:P171T	ENSP00000342012:P171T	P	-	1	0	DMKN	40695448	0.054000	0.20591	0.002000	0.10522	0.016000	0.09150	1.098000	0.31000	0.508000	0.28173	0.655000	0.94253	CCG	.	.		0.582	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		T	36003608	G	T	36003608	3	4	202	1	0	0	0	0	1	0	0	0	4584	1174	41	3	1296	3	DMKN	19	36003608	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	13063210	36003608	23125375	81	29694										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36348363	36348363	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tagttcagtggactaagagtGggctggccctagggggccaa	16	8	1	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr19:36348363G>A	ENST00000360202.5	+	2	376	c.178G>A	c.(178-180)Ggg>Agg	p.G60R	KIRREL2_ENST00000592409.1_Missense_Mutation_p.G60R|KIRREL2_ENST00000262625.7_Missense_Mutation_p.G60R|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Intron	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	60	Ig-like C2-type 1.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GACTAAGAGTGGGCTGGCCCT	0.652																																					p.G60R		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G178A						.						46	54	52					19																	36348363		2203	4299	6502	SO:0001583	missense	84063	exon2			AAGAGTGGGCTGG	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.178G>A	chr19.hg19:g.36348363G>A	ENSP00000353331:p.Gly60Arg	183.0	0.0		157.0	63.0	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	hg19	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.958270	0.92726	.	.	ENSG00000126259	ENST00000262625;ENST00000360202;ENST00000341658	T;T	0.71461	-0.57;-0.57	5.35	5.35	0.76521	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.48767	D	0.000177	D	0.85737	0.5766	M	0.86502	2.82	0.48511	D	0.999667	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.87838	0.2649	10	0.87932	D	0	-20.4166	14.9787	0.71296	0.0:0.0:1.0:0.0	.	60;60;60	F1T0I2;Q6UWL6;Q6UWL6-2	.;KIRR2_HUMAN;.	R	60	ENSP00000262625:G60R;ENSP00000353331:G60R	ENSP00000262625:G60R	G	+	1	0	KIRREL2	41040203	1.000000	0.71417	0.999000	0.59377	0.904000	0.53231	7.901000	0.87382	2.672000	0.90937	0.650000	0.86243	GGG	.	.		0.652	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		A	36348363	G	A	36348363	3	1	202	1	0	0	0	0	1	0	0	0	8334	1348	47	3	184	3	KIRREL2	19	36348363	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	344755	36348363	22780620	82	29695										
GGN	199720	hgsc.bcm.edu	37	chr19	38876402	38876402	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggctcagccacggtgggagcTggagccggggatggggccgg	22	10	1	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr19:38876402T>C	ENST00000334928.6	-	3	1632	c.1500A>G	c.(1498-1500)ccA>ccG	p.P500P	GGN_ENST00000591809.1_Intron|AC005789.9_ENST00000585411.1_RNA|SPRED3_ENST00000587013.1_5'Flank	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	500	Interactions with ZNF403/GGNBP2 and OAZ3. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			cggtgggagctggagccgggg	0.746																																					p.P500P		Atlas-SNP	.											.	GGN	50	.	0			c.A1500G						.						4	6	5					19																	38876402		1834	3724	5558	SO:0001819	synonymous_variant	199720	exon3			GGGAGCTGGAGCC	AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.1500A>G	chr19.hg19:g.38876402T>C		47.0	0.0		55.0	7.0	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Silent	SNP	ENST00000334928.6	hg19	CCDS12516.1																																																																																			.	.		0.746	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		C	38876402	T	C	38876402	2	2	202	1	0	0	0	0	0	0	0	1	6366	1567	55	2		2	GGN	19	38876402	Silent	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	2528039	38876402	20252581	83	29696										
PNMAL1	55228	hgsc.bcm.edu	37	chr19	46973527	46973527	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcctttgggttttttccaggGcactgcttcctgcctggagt	12	11	0	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr19:46973527G>T	ENST00000313683.10	-	2	1071	c.766C>A	c.(766-768)Ccc>Acc	p.P256T	PNMAL1_ENST00000438932.2_Missense_Mutation_p.P256T|PNMAL1_ENST00000602246.1_Intron	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	256										cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		TTTTTCCAGGGCACTGCTTCC	0.522																																					p.P256T		Atlas-SNP	.											.	PNMAL1	87	.	0			c.C766A						.						97	100	99					19																	46973527		2203	4300	6503	SO:0001583	missense	55228	exon2			TCCAGGGCACTGC	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"Paraneoplastic Ma antigens"	25578	protein-coding gene	gene with protein product			"PNMA-like 1"			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.766C>A	chr19.hg19:g.46973527G>T	ENSP00000318131:p.Pro256Thr	54.0	0.0		28.0	9.0	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Missense_Mutation	SNP	ENST00000313683.10	hg19	CCDS33059.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.606520	0.28623	.	.	ENSG00000182013	ENST00000438932;ENST00000313683	T;T	0.09163	3.01;3.01	3.94	-6.07	0.02158	.	1.605380	0.03609	N	0.234529	T	0.07279	0.0184	L	0.27053	0.805	0.09310	N	1	B;B	0.28636	0.218;0.218	B;B	0.28139	0.086;0.086	T	0.33624	-0.9861	10	0.45353	T	0.12	-5.1354	6.0109	0.19575	0.4279:0.4008:0.1713:0.0	.	256;256	Q86V59-2;Q86V59	.;PNML1_HUMAN	T	256	ENSP00000410273:P256T;ENSP00000318131:P256T	ENSP00000318131:P256T	P	-	1	0	PNMAL1	51665367	0.002000	0.14202	0.000000	0.03702	0.293000	0.27360	-0.069000	0.11542	-1.137000	0.02888	-0.136000	0.14681	CCC	.	.		0.522	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215		T	46973527	G	T	46973527	3	4	202	1	0	0	0	0	1	0	0	0	12166	1203	42	3	583	3	PNMAL1	19	46973527	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	8097125	46973527	12155456	84	29697										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53652039	53652039	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgctccaacatagagataaTactgaggtcaaaacaagaga	8	7	1	3			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr19:53652039T>C	ENST00000334197.7	-	4	234	c.166A>G	c.(166-168)Att>Gtt	p.I56V	ZNF347_ENST00000452676.2_Missense_Mutation_p.I57V|ZNF347_ENST00000601469.2_Missense_Mutation_p.I57V|ZNF347_ENST00000601804.1_5'UTR	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	56	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		ATAGAGATAATACTGAGGTCA	0.433																																					p.I57V	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.A169G						.						174	163	167					19																	53652039		2203	4300	6503	SO:0001583	missense	84671	exon4			AGATAATACTGAG	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.166A>G	chr19.hg19:g.53652039T>C	ENSP00000334146:p.Ile56Val	169.0	0.0		128.0	45.0	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	hg19	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	T	0.117	-1.130250	0.01756	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.00737	5.76;5.76	1.82	-3.63	0.04529	Krueppel-associated box (3);	.	.	.	.	T	0.00356	0.0011	N	0.02247	-0.625	0.09310	N	1	B;B	0.13145	0.007;0.003	B;B	0.06405	0.002;0.0	T	0.40887	-0.9539	9	0.02654	T	1	.	7.2768	0.26290	0.0:0.6547:0.0:0.3453	.	57;56	G5E9N4;Q96SE7	.;ZN347_HUMAN	V	56;57	ENSP00000334146:I56V;ENSP00000405218:I57V	ENSP00000334146:I56V	I	-	1	0	ZNF347	58343851	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.818000	0.04467	-1.195000	0.02680	-0.334000	0.08254	ATT	.	.		0.433	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		C	53652039	T	C	53652039	3	2	202	1	0	0	0	0	1	0	0	0	17876	1406	49	2	2361	2	ZNF347	19	53652039	Missense_Mutation	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	6678512	53652039	5476944	85	29698										
BACH1	571	hgsc.bcm.edu	37	chr21	30698823	30698823	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgccttctttatgccccaaAtacagaaaattccaaaaagc	4	11	1	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr21:30698823A>G	ENST00000399921.1	+	3	921	c.678A>G	c.(676-678)aaA>aaG	p.K226K	BACH1_ENST00000286800.3_Silent_p.K226K	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						TATGCCCCAAATACAGAAAAT	0.453																																					p.K226K		Atlas-SNP	.											.	BACH1	66	.	0			c.A678G						.						92	94	93					21																	30698823		2203	4300	6503	SO:0001819	synonymous_variant	571	exon3			CCCCAAATACAGA	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"BTB/POZ domain containing", "basic leucine zipper proteins"	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.678A>G	chr21.hg19:g.30698823A>G		137.0	0.0		97.0	33.0	NM_206866	Q3MJE2|Q8NCI5	Silent	SNP	ENST00000399921.1	hg19	CCDS13585.1																																																																																			.	.		0.453	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		G	30698823	A	G	30698823	2	3	202	1	0	0	0	0	0	0	0	1	1283	98	4	2		2	BACH1	21	30698823	Silent	SNP	A	TCGA-DD-AADU-01A-11D-A40R-10		30698823	17431072	86	29699										
COL6A1	1291	hgsc.bcm.edu	37	chr21	47412121	47412121	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccccggagagaaaggagaggCgggcgacgaggtgagtgagg	21	7	0	4			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr21:47412121C>T	ENST00000361866.3	+	17	1340	c.1226C>T	c.(1225-1227)gCg>gTg	p.A409V		NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	409	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		AAAGGAGAGGCGGGCGACGAG	0.637																																					p.A409V		Atlas-SNP	.											.	COL6A1	101	.	0			c.C1226T						.						47	57	53					21																	47412121		2201	4300	6501	SO:0001583	missense	1291	exon17			GAGAGGCGGGCGA	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"Collagens"	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.1226C>T	chr21.hg19:g.47412121C>T	ENSP00000355180:p.Ala409Val	86.0	0.0		69.0	25.0	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	hg19	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	C	8.164	0.790074	0.16258	.	.	ENSG00000142156	ENST00000361866;ENST00000538397	D	0.93712	-3.27	4.7	2.66	0.31614	.	0.456851	0.21370	N	0.075656	D	0.84692	0.5528	N	0.25380	0.74	0.09310	N	1	B	0.34313	0.448	B	0.29440	0.102	T	0.75539	-0.3282	10	0.35671	T	0.21	-21.1888	6.855	0.24036	0.2251:0.6731:0.0:0.1017	.	409	P12109	CO6A1_HUMAN	V	409	ENSP00000355180:A409V	ENSP00000355180:A409V	A	+	2	0	COL6A1	46236549	0.820000	0.29190	0.849000	0.33467	0.054000	0.15201	1.441000	0.35035	2.162000	0.67917	0.467000	0.42956	GCG	.	.		0.637	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		T	47412121	C	T	47412121	3	4	202	1	0	0	0	0	1	0	0	0	3701	768	27	1	1292	1	COL6A1	21	47412121	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10	16713298	47412121	717774	87	29700										
RFPL3	10738	hgsc.bcm.edu	37	chr22	32754272	32754272	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	attcgctgcagaaggagcccCatggggaggatctgctttgc	14	10	1	1			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chr22:32754272C>A	ENST00000249007.4	+	1	419	c.214C>A	c.(214-216)Cat>Aat	p.H72N	RFPL3_ENST00000397468.1_Missense_Mutation_p.H43N|RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000382088.3_Missense_Mutation_p.H43N	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	72							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GAAGGAGCCCCATGGGGAGGA	0.537																																					p.H72N		Atlas-SNP	.											.	RFPL3	91	.	0			c.C214A						.						122	115	117					22																	32754272		2203	4300	6503	SO:0001583	missense	10738	exon1			GAGCCCCATGGGG	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.214C>A	chr22.hg19:g.32754272C>A	ENSP00000249007:p.His72Asn	160.0	0.0		125.0	50.0	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	hg19	CCDS43011.1	.	.	.	.	.	.	.	.	.	.	C	0.045	-1.268673	0.01433	.	.	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	D;T;D	0.92699	-3.09;2.37;-3.09	0.851	-1.7	0.08159	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);RDM domain, Ret finger protein-like (1);	.	.	.	.	T	0.76912	0.4054	N	0.04880	-0.145	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.61874	-0.6973	9	0.17832	T	0.49	.	2.7544	0.05289	0.3012:0.3977:0.3011:0.0	.	72	O75679	RFPL3_HUMAN	N	43;72;43	ENSP00000380609:H43N;ENSP00000249007:H72N;ENSP00000371520:H43N	ENSP00000249007:H72N	H	+	1	0	RFPL3	31084272	0.001000	0.12720	0.002000	0.10522	0.100000	0.18952	0.253000	0.18296	-1.117000	0.02965	0.194000	0.17425	CAT	.	.		0.537	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604		A	32754272	C	A	32754272	3	1	202	1	0	0	0	0	1	0	0	0	13270	594	21	3	216	3	RFPL3	22	32754272	Missense_Mutation	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10		32754272	18550294	88	29701										
DDX53	168400	hgsc.bcm.edu	37	chrX	23018432	23018432	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	actaaaatacagatcataaaCggggaatctgaagcaaaagt	8	6	2	2			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chrX:23018432C>T	ENST00000327968.5	+	1	346	c.258C>T	c.(256-258)aaC>aaT	p.N86N	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	86	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						AGATCATAAACGGGGAATCTG	0.338																																					p.N86N		Atlas-SNP	.											.	DDX53	76	.	0			c.C258T						.						71	75	74					X																	23018432		2203	4300	6503	SO:0001819	synonymous_variant	168400	exon1			CATAAACGGGGAA	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"DEAD-boxes"	20083	protein-coding gene	gene with protein product	"cancer associated gene", "cancer/testis antigen 26"						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.258C>T	chrX.hg19:g.23018432C>T		203.0	0.0		147.0	118.0	NM_182699	Q0D2N2|Q6NVV4	Silent	SNP	ENST00000327968.5	hg19	CCDS35214.1																																																																																			.	.		0.338	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699		T	23018432	C	T	23018432	2	4	202	1	0	0	0	0	0	0	0	1	4373	535	19	1		1	DDX53	23	23018432	Silent	SNP	C	TCGA-DD-AADU-01A-11D-A40R-10		23018432	132252128	89	29702										
RBM41	55285	hgsc.bcm.edu	37	chrX	106359256	106359256	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	gggcttgtacatagtaccagGagcaaagctctctttcttag	10	9	2	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chrX:106359256G>A	ENST00000372479.3	-	3	184	c.154C>T	c.(154-156)Cct>Tct	p.P52S	RBM41_ENST00000203616.8_Missense_Mutation_p.P52S|RBM41_ENST00000372487.1_Missense_Mutation_p.P52S|RBM41_ENST00000471079.1_5'UTR	NM_018301.3	NP_060771.3	Q96IZ5	RBM41_HUMAN	RNA binding motif protein 41	52							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	13						ATAGTACCAGGAGCAAAGCTC	0.448																																					p.P52S		Atlas-SNP	.											.	RBM41	34	.	0			c.C154T						.						74	64	67					X																	106359256		2203	4300	6503	SO:0001583	missense	55285	exon3			TACCAGGAGCAAA	BC006986	CCDS14526.1, CCDS55472.1	Xq22.3	2013-02-12			ENSG00000089682	ENSG00000089682		"RNA binding motif (RRM) containing"	25617	protein-coding gene	gene with protein product						12477932	Standard	NM_001171080		Approved	FLJ11016	uc004emz.3	Q96IZ5	OTTHUMG00000022156	ENST00000372479.3:c.154C>T	chrX.hg19:g.106359256G>A	ENSP00000361557:p.Pro52Ser	187.0	1.0		138.0	115.0	NM_001171080	Q5JSN7|Q5JSN8|Q9H8F7|Q9NV04	Missense_Mutation	SNP	ENST00000372479.3	hg19	CCDS14526.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.12|17.12	3.307170|3.307170	0.60305|0.60305	.|.	.|.	ENSG00000089682|ENSG00000089682	ENST00000372487;ENST00000372479;ENST00000203616;ENST00000372482|ENST00000434854	T;T|.	0.25250|.	1.81;1.82|.	5.5|5.5	4.64|4.64	0.57946|0.57946	.|.	0.115218|.	0.64402|.	N|.	0.000012|.	T|T	0.39253|0.39253	0.1071|0.1071	N|N	0.17082|0.17082	0.46|0.46	0.45690|0.45690	D|D	0.998605|0.998605	D|.	0.89917|.	1.0|.	D|.	0.72075|.	0.976|.	T|T	0.17137|0.17137	-1.0379|-1.0379	10|5	0.40728|.	T|.	0.16|.	.|.	9.2521|9.2521	0.37562|0.37562	0.1016:0.0:0.8984:0.0|0.1016:0.0:0.8984:0.0	.|.	52|.	Q96IZ5|.	RBM41_HUMAN|.	S|F	52|49	ENSP00000361565:P52S;ENSP00000361557:P52S|.	ENSP00000203616:P52S|.	P|S	-|-	1|2	0|0	RBM41|RBM41	106245912|106245912	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	8.431000|8.431000	0.90285|0.90285	1.089000|1.089000	0.41292|0.41292	0.468000|0.468000	0.43344|0.43344	CCT|TCC	.	.		0.448	RBM41-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057819.1	NM_018301		A	106359256	G	A	106359256	3	1	202	1	0	0	0	0	1	0	0	0	13150	1174	41	3	1116	3	RBM41	23	106359256	Missense_Mutation	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	83340824	106359256	48911304	90	29703										
RNF113A	7737	hgsc.bcm.edu	37	chrX	119005199	119005199	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atggcttgtgcatcgcgctcTttctctgtgtccagctcata	9	12	3	0			TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chrX:119005199T>C	ENST00000371442.2	-	1	592	c.378A>G	c.(376-378)aaA>aaG	p.K126K	NDUFA1_ENST00000371437.4_5'Flank	NM_006978.2	NP_008909.1	O15541	R113A_HUMAN	ring finger protein 113A	126							zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(6)	15						CATCGCGCTCTTTCTCTGTGT	0.542																																					p.K126K		Atlas-SNP	.											.	RNF113A	39	.	0			c.A378G						.						259	246	250					X																	119005199		2203	4300	6503	SO:0001819	synonymous_variant	7737	exon1			GCGCTCTTTCTCT	X98253	CCDS14589.1	Xq24	2013-10-22	2005-03-22	2005-03-22	ENSG00000125352	ENSG00000125352		"RING-type (C3HC4) zinc fingers"	12974	protein-coding gene	gene with protein product			"zinc finger protein 183 (RING finger, C3HC4 type)"	ZNF183		9224902	Standard	NM_006978		Approved	RNF113, Cwc24	uc004esb.3	O15541	OTTHUMG00000022283	ENST00000371442.2:c.378A>G	chrX.hg19:g.119005199T>C		34.0	0.0		25.0	20.0	NM_006978	B2RBR7	Silent	SNP	ENST00000371442.2	hg19	CCDS14589.1																																																																																			.	.		0.542	RNF113A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058071.1	NM_006978		C	119005199	T	C	119005199	2	2	202	1	0	0	0	0	0	0	0	1	13442	1606	56	2		2	RNF113A	23	119005199	Silent	SNP	T	TCGA-DD-AADU-01A-11D-A40R-10	12645943	119005199	36265361	91	29704										
ATP2B3	492	hgsc.bcm.edu	37	chrX	152801801	152801801	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggctttgggtgcacgctggcGgagctgcgcaccctcatgga	16	12	1	0	rs202115287		TCGA-DD-AADU-01A-11D-A40R-10	TCGA-DD-AADU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d049bc2-80dc-4a61-b310-2c0eb6e10e9d	8e8307fc-2b03-455d-9aa9-83626768011c	g.chrX:152801801G>T	ENST00000349466.2	+	2	422	c.96G>T	c.(94-96)gcG>gcT	p.A32A	ATP2B3_ENST00000370186.1_Silent_p.A32A|ATP2B3_ENST00000393842.1_Silent_p.A32A|ATP2B3_ENST00000359149.3_Silent_p.A32A|ATP2B3_ENST00000263519.4_Silent_p.A32A|ATP2B3_ENST00000370181.2_Silent_p.A32A			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	32					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCACGCTGGCGGAGCTGCGCA	0.667																																					p.A32A		Atlas-SNP	.											.	ATP2B3	552	.	0			c.G96T						.						35	29	31					X																	152801801		2188	4289	6477	SO:0001819	synonymous_variant	492	exon1			GCTGGCGGAGCTG	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"ATPases / P-type"	816	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 3", "cilia and flagella associated protein 39"	300014	"spinocerebellar ataxia, X-linked 1", "cerebellar ataxia 2 (X-linked)"	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.96G>T	chrX.hg19:g.152801801G>T		127.0	0.0		80.0	65.0	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	hg19	CCDS35440.1																																																																																			.	G|0.999;A|0.001		0.667	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		T	152801801	G	T	152801801	2	4	202	1	0	0	0	0	0	0	0	1	1141	1103	39	1		1	ATP2B3	23	152801801	Silent	SNP	G	TCGA-DD-AADU-01A-11D-A40R-10	33796602	152801801	2468759	92	29705										
FBXO42	54455	hgsc.bcm.edu	37	chr1	16577701	16577701	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ggcactggccacgtgaggtgGggtatgcacaccatttgtct	14	10	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:16577701G>C	ENST00000375592.3	-	10	1834	c.1618C>G	c.(1618-1620)Cca>Gca	p.P540A		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	540										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		ACGTGAGGTGGGGTATGCACA	0.587																																					p.P540A		Atlas-SNP	.											.	FBXO42	53	.	0			c.C1618G						.						95	68	77					1																	16577701		2203	4300	6503	SO:0001583	missense	54455	exon10			GAGGTGGGGTATG	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"F-boxes /  "other""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.1618C>G	chr1.hg19:g.16577701G>C	ENSP00000364742:p.Pro540Ala	92.0	0.0		74.0	39.0	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Missense_Mutation	SNP	ENST00000375592.3	hg19	CCDS30613.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.817680	0.71028	.	.	ENSG00000037637	ENST00000375592;ENST00000456164;ENST00000444116	T;T;T	0.69926	3.28;-0.44;-0.44	5.51	5.51	0.81932	.	0.050466	0.85682	D	0.000000	T	0.72277	0.3440	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.70568	-0.4836	10	0.34782	T	0.22	-11.0311	18.7669	0.91876	0.0:0.0:1.0:0.0	.	540	Q6P3S6	FBX42_HUMAN	A	540;258;258	ENSP00000364742:P540A;ENSP00000415663:P258A;ENSP00000412416:P258A	ENSP00000364742:P540A	P	-	1	0	FBXO42	16450288	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.874000	0.92363	2.763000	0.94921	0.650000	0.86243	CCA	.	.		0.587	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			C	16577701	G	C	16577701	3	2	203	1	0	0	0	0	1	0	0	0	5759	1232	43	4	539	4	FBXO42	1	16577701	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10		16577701	232672920	1	29706										
RCC2	55920	hgsc.bcm.edu	37	chr1	17743015	17743015	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gccacgtctcgtacaaccacGtttggtacaggcagaatctg	10	12	2	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:17743015G>A	ENST00000375436.4	-	8	1174	c.987C>T	c.(985-987)aaC>aaT	p.N329N	AC004824.1_ENST00000583469.1_RNA|RCC2_ENST00000375433.3_Silent_p.N329N	NM_018715.3	NP_061185.1	Q9P258	RCC2_HUMAN	regulator of chromosome condensation 2	329					chromosome passenger complex localization to kinetochore (GO:0072356)|endosome organization (GO:0007032)|focal adhesion assembly (GO:0048041)|integrin-mediated signaling pathway (GO:0007229)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of GTPase activity (GO:0034260)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|regulation of cell migration (GO:0030334)	chromosome, centromeric core domain (GO:0034506)|cytosol (GO:0005829)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|Rac GTPase binding (GO:0048365)	p.N329N(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(7)|lung(4)	17		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)		GTACAACCACGTTTGGTACAG	0.552																																					p.N329N		Atlas-SNP	.											RCC2,NS,carcinoma,0,1	RCC2	46	.	1	Substitution - coding silent(1)	endometrium(1)	c.C987T						.						118	92	101					1																	17743015		2203	4300	6503	SO:0001819	synonymous_variant	55920	exon7			AACCACGTTTGGT		CCDS181.1	1p36.13	2010-05-05			ENSG00000179051	ENSG00000179051			30297	protein-coding gene	gene with protein product		609587				10819331, 12919680	Standard	NM_018715		Approved	TD-60	uc001bal.3	Q9P258	OTTHUMG00000002513	ENST00000375436.4:c.987C>T	chr1.hg19:g.17743015G>A		74.0	0.0		88.0	24.0	NM_001136204	Q8IVL9|Q9BSN6|Q9NPV8	Silent	SNP	ENST00000375436.4	hg19	CCDS181.1																																																																																			.	.		0.552	RCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007144.1	NM_018715		A	17743015	G	A	17743015	2	1	203	1	0	0	0	0	0	0	0	1	13189	1136	40	1		1	RCC2	1	17743015	Silent	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	1165314	17743015	231507606	2	29707										
KIF17	57576	hgsc.bcm.edu	37	chr1	21036196	21036196	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cgtgaggaatccttgttcatCagcgtgtagccgaccgaacg	12	11	2	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:21036196C>G	ENST00000247986.2	-	4	916	c.606G>C	c.(604-606)ctG>ctC	p.L202L	KIF17_ENST00000400463.3_Silent_p.L202L|KIF17_ENST00000375044.1_Silent_p.L102L			Q9P2E2	KIF17_HUMAN	kinesin family member 17	202	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CCTTGTTCATCAGCGTGTAGC	0.582																																					p.L202L		Atlas-SNP	.											.	KIF17	130	.	0			c.G606C						.						180	115	137					1																	21036196		2203	4300	6503	SO:0001819	synonymous_variant	57576	exon4			GTTCATCAGCGTG	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"Kinesins"	19167	protein-coding gene	gene with protein product	"kinesin-like protein KIF17", "KIF3-related motor protein", "KIF17 variant protein"	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.606G>C	chr1.hg19:g.21036196C>G		126.0	0.0		147.0	8.0	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	hg19	CCDS213.1																																																																																			.	.		0.582	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816		G	21036196	C	G	21036196	2	3	203	1	0	0	0	0	0	0	0	1	8288	813	29	4		4	KIF17	1	21036196	Silent	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	3293181	21036196	228214425	3	29708										
PDIK1L	149420	hgsc.bcm.edu	37	chr1	26449068	26449068	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gatagcagctgggaaacgtgAcacatattatttgcaaatac	9	7	0	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:26449068A>G	ENST00000374271.4	+	4	1313	c.1026A>G	c.(1024-1026)tgA>tgG	p.*342W	PDIK1L_ENST00000374269.1_Nonstop_Mutation_p.*342W	NM_001243532.1|NM_001243533.1|NM_152835.4	NP_001230461.1|NP_001230462.1|NP_690048.1	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like	0						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)		GGGAAACGTGACACATATTAT	0.383																																					p.X342W		Atlas-SNP	.											.	PDIK1L	19	.	0			c.A1026G						.						51	52	52					1																	26449068		2203	4300	6503	SO:0001578	stop_lost	149420	exon3			AACGTGACACATA	AF411102	CCDS274.1	1p35.1	2008-02-05			ENSG00000175087	ENSG00000175087			18981	protein-coding gene	gene with protein product		610785				14631099	Standard	NM_152835		Approved	CLIK1L	uc009vsb.3	Q8N165	OTTHUMG00000007511	ENST00000374271.4:c.1026A>G	chr1.hg19:g.26449068A>G	ENSP00000363389:p.*342Trpext*24	67.0	0.0		82.0	23.0	NM_001243532	B2R777|D3DPK2|Q5T2I0|Q8NDB3	Missense_Mutation	SNP	ENST00000374271.4	hg19	CCDS274.1	.	.	.	.	.	.	.	.	.	.	A	15.67	2.903486	0.52333	.	.	ENSG00000175087	ENST00000374271;ENST00000374269	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0365	0.80635	1.0:0.0:0.0:0.0	.	.	.	.	W	342	.	.	X	+	3	0	PDIK1L	26321655	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.923000	0.92808	2.266000	0.75297	0.533000	0.62120	TGA	.	.		0.383	PDIK1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019752.1	NM_152835		G	26449068	A	G	26449068	4	3	203	1	0	0	0	0	0	0	0	0	11682	288	10	2	1032	2	PDIK1L	1	26449068	Nonstop_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	5412872	26449068	222801553	4	29709										
ORC1L	4998	hgsc.bcm.edu	37	chr1	52863529	52863529	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cacgtttcttaggaggaggaTcagagtctagaaagaatttg	12	5	3	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:52863529T>A	ENST00000371568.3	-	4	448	c.230A>T	c.(229-231)gAt>gTt	p.D77V	ORC1_ENST00000371566.1_Missense_Mutation_p.D77V	NM_001190818.1|NM_001190819.1|NM_004153.3	NP_001177747.1|NP_001177748.1|NP_004144.2	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	77	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear origin of replication recognition complex (GO:0005664)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						AGGAGGAGGATCAGAGTCTAG	0.483																																					p.D77V		Atlas-SNP	.											.	ORC1	79	.	0			c.A230T						.						83	84	83					1																	52863529		2203	4300	6503	SO:0001583	missense	4998	exon4			GGAGGATCAGAGT		CCDS566.1	1p32	2010-10-12	2010-10-12	2010-10-12	ENSG00000085840	ENSG00000085840		"ATPases / AAA-type"	8487	protein-coding gene	gene with protein product	"origin recognition complex, subunit 1, S. cerevisiae, homolog-like", "origin recognition complex 1", "replication control protein 1"	601902	"origin recognition complex, subunit 1 (yeast homolog)-like", "origin recognition complex, subunit 1-like (yeast)", "origin recognition complex, subunit 1 homolog (S. cerevisiae)"	ORC1L		8884289	Standard	NM_004153		Approved	HSORC1, PARC1	uc001ctu.3	Q13415	OTTHUMG00000008104	ENST00000371568.3:c.230A>T	chr1.hg19:g.52863529T>A	ENSP00000360623:p.Asp77Val	185.0	0.0		228.0	103.0	NM_004153	D3DQ34|Q13471|Q5T0F5	Missense_Mutation	SNP	ENST00000371568.3	hg19	CCDS566.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.330032	0.60743	.	.	ENSG00000085840	ENST00000371568;ENST00000371566	D;D	0.86164	-2.08;-2.08	5.24	5.24	0.73138	Bromo adjacent homology (BAH) domain (3);	0.539341	0.21488	N	0.073721	D	0.83640	0.5298	L	0.34521	1.04	0.24694	N	0.993296	P;P	0.40731	0.525;0.728	B;B	0.42959	0.215;0.403	T	0.78952	-0.2001	10	0.62326	D	0.03	-4.548	14.3229	0.66499	0.0:0.0:0.0:1.0	.	77;77	B7Z8H0;Q13415	.;ORC1_HUMAN	V	77	ENSP00000360623:D77V;ENSP00000360621:D77V	ENSP00000360621:D77V	D	-	2	0	ORC1	52636117	0.008000	0.16893	0.144000	0.22314	0.110000	0.19582	1.774000	0.38573	1.989000	0.58080	0.377000	0.23210	GAT	.	.		0.483	ORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022202.1	NM_004153		A	52863529	T	A	52863529	3	1	203	1	0	0	0	0	1	0	0	0	11270	1435	50	4	2411	4	ORC1L	1	52863529	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	26414461	52863529	196387092	5	29710										
RAVER2	55225	hgsc.bcm.edu	37	chr1	65278505	65278505	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	atccatacttgaatttggcaAgtgtgttgcccagtgtgtgc	11	8	0	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:65278505A>G	ENST00000294428.3	+	10	1843	c.1765A>G	c.(1765-1767)Agt>Ggt	p.S589G	RAVER2_ENST00000371072.4_Missense_Mutation_p.S576G|RAVER2_ENST00000430964.2_Missense_Mutation_p.S128G			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	589						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						GAATTTGGCAAGTGTGTTGCC	0.353																																					p.S576G		Atlas-SNP	.											.	RAVER2	56	.	0			c.A1726G						.						128	116	120					1																	65278505		1830	4088	5918	SO:0001583	missense	55225	exon10			TTGGCAAGTGTGT	AB046799	CCDS41345.1	1p31.3	2013-02-12			ENSG00000162437	ENSG00000162437		"RNA binding motif (RRM) containing"	25577	protein-coding gene	gene with protein product		609953				16051233	Standard	NM_018211		Approved	KIAA1579, FLJ10770	uc001dbs.2	Q9HCJ3	OTTHUMG00000009102	ENST00000294428.3:c.1765A>G	chr1.hg19:g.65278505A>G	ENSP00000294428:p.Ser589Gly	85.0	0.0		74.0	35.0	NM_018211	Q6P141|Q9NPV7	Missense_Mutation	SNP	ENST00000294428.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.75	3.690788	0.68271	.	.	ENSG00000162437	ENST00000371072;ENST00000294428;ENST00000430964	T;T;T	0.80393	-1.37;-1.37;-1.37	5.49	5.49	0.81192	.	0.095343	0.64402	D	0.000001	D	0.84624	0.5513	M	0.64404	1.975	0.43088	D	0.994755	D;D	0.71674	0.997;0.998	D;D	0.80764	0.985;0.994	D	0.85604	0.1254	10	0.48119	T	0.1	-26.8996	13.8151	0.63287	1.0:0.0:0.0:0.0	.	589;576	Q9HCJ3;Q9HCJ3-2	RAVR2_HUMAN;.	G	576;589;128	ENSP00000360112:S576G;ENSP00000294428:S589G;ENSP00000408950:S128G	ENSP00000294428:S589G	S	+	1	0	RAVER2	65051093	1.000000	0.71417	0.998000	0.56505	0.665000	0.39181	5.524000	0.67105	2.068000	0.61886	0.472000	0.43445	AGT	.	.		0.353	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211		G	65278505	A	G	65278505	3	3	203	1	0	0	0	0	1	0	0	0	13110	72	3	2	1764	2	RAVER2	1	65278505	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	12414976	65278505	183972116	6	29711										
JAK1	3716	hgsc.bcm.edu	37	chr1	65332551	65332551	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ctgccaacagccacttacatTtggtttatgcctccactgga	7	13	0	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:65332551T>A	ENST00000342505.4	-	7	1236	c.988A>T	c.(988-990)Aat>Tat	p.N330Y		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	330	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CCACTTACATTTGGTTTATGC	0.443			Mis		ALL																																p.N330Y		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A988T						.						114	103	107					1																	65332551		2020	4181	6201	SO:0001583	missense	3716	exon7			TTACATTTGGTTT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.988A>T	chr1.hg19:g.65332551T>A	ENSP00000343204:p.Asn330Tyr	65.0	0.0		73.0	31.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	T	13.16	2.152862	0.38021	.	.	ENSG00000162434	ENST00000342505	T	0.75477	-0.94	5.59	4.45	0.53987	FERM domain (1);	.	.	.	.	T	0.41465	0.1160	N	0.19112	0.55	0.32045	N	0.597667	B	0.06786	0.001	B	0.04013	0.001	T	0.30794	-0.9966	9	0.62326	D	0.03	-6.9504	8.7874	0.34830	0.1268:0.0:0.1328:0.7404	.	330	P23458	JAK1_HUMAN	Y	330	ENSP00000343204:N330Y	ENSP00000343204:N330Y	N	-	1	0	JAK1	65105139	0.994000	0.37717	0.998000	0.56505	0.824000	0.46624	1.548000	0.36201	1.039000	0.40074	0.533000	0.62120	AAT	.	.		0.443	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		A	65332551	T	A	65332551	3	1	203	1	0	0	0	0	1	0	0	0	7946	1841	64	4	2552	4	JAK1	1	65332551	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	54046	65332551	183918070	7	29712										
C1orf173	127254	hgsc.bcm.edu	37	chr1	75112352	75112352	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	aataagtatatatttttaccTccatatcaagaactttatga	3	6	1	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:75112352T>G	ENST00000326665.5	-	3	460	c.242A>C	c.(241-243)gAg>gCg	p.E81A		NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		81										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						tatttttaCCTCCATATCAAG	0.269																																					p.E81A		Atlas-SNP	.											.	C1orf173	380	.	0			c.A242C						.						20	19	19					1																	75112352		1859	3494	5353	SO:0001630	splice_region_variant	127254	exon3			TTTACCTCCATAT																												ENST00000326665.5:c.243+1A>C	chr1.hg19:g.75112352T>G		345.0	0.0		414.0	182.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	hg19	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.176172	0.78564	.	.	ENSG00000178965	ENST00000326665	T	0.46063	0.88	5.71	5.71	0.89125	.	.	.	.	.	T	0.55417	0.1919	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60515	-0.7248	9	0.66056	D	0.02	-20.5177	14.9681	0.71210	0.0:0.0:0.0:1.0	.	81	Q5RHP9	CA173_HUMAN	A	81	ENSP00000322609:E81A	ENSP00000322609:E81A	E	-	2	0	C1orf173	74884940	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	6.944000	0.75940	2.179000	0.69175	0.528000	0.53228	GAG	.	.		0.269	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		Missense_Mutation	G	75112352	T	G	75112352	5	3	203	1	0	0	0	0	0	0	1	0	2016	1565	54	5	4398	5	C1orf173	1	75112352	Splice_Site	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	9779801	75112352	174138269	8	29713										
MSH4	4438	hgsc.bcm.edu	37	chr1	76345739	76345739	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tttaatctccaagcagatttCtaaagtgaaaaattcttaca	4	7	3	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:76345739C>T	ENST00000263187.3	+	13	1786	c.1682C>T	c.(1681-1683)tCt>tTt	p.S561F		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	561					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						AAGCAGATTTCTAAAGTGAAA	0.279								Mismatch excision repair (MMR)																													p.S561F		Atlas-SNP	.											.	MSH4	147	.	0			c.C1682T						.						54	53	54					1																	76345739		2194	4267	6461	SO:0001583	missense	4438	exon13			AGATTTCTAAAGT	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.1682C>T	chr1.hg19:g.76345739C>T	ENSP00000263187:p.Ser561Phe	381.0	0.0		443.0	115.0	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	hg19	CCDS670.1	.	.	.	.	.	.	.	.	.	.	C	7.608	0.674107	0.14841	.	.	ENSG00000057468	ENST00000263187	D	0.90844	-2.74	5.51	5.51	0.81932	DNA mismatch repair protein MutS, clamp (1);DNA mismatch repair protein MutS, core (3);	0.110333	0.64402	D	0.000011	T	0.82195	0.4984	N	0.24115	0.695	0.43508	D	0.995765	B	0.32365	0.367	B	0.33568	0.166	D	0.83865	0.0270	10	0.72032	D	0.01	0.0486	19.415	0.94690	0.0:1.0:0.0:0.0	.	561	O15457	MSH4_HUMAN	F	561	ENSP00000263187:S561F	ENSP00000263187:S561F	S	+	2	0	MSH4	76118327	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	4.231000	0.58639	2.600000	0.87896	0.650000	0.86243	TCT	.	.		0.279	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		T	76345739	C	T	76345739	3	4	203	1	0	0	0	0	1	0	0	0	9881	913	32	3	1732	3	MSH4	1	76345739	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	1233387	76345739	172904882	9	29714										
SYDE2	84144	hgsc.bcm.edu	37	chr1	85624884	85624884	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gataattcagagaagacttcTgctctgggaataaattgtct	9	6	4	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:85624884T>A	ENST00000341460.5	-	7	3183	c.3134A>T	c.(3133-3135)cAg>cTg	p.Q1045L		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	1045					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		AGAAGACTTCTGCTCTGGGAA	0.363																																					p.Q1045L		Atlas-SNP	.											.	SYDE2	135	.	0			c.A3134T						.						68	66	67					1																	85624884		1812	4074	5886	SO:0001583	missense	84144	exon7			GACTTCTGCTCTG	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.3134A>T	chr1.hg19:g.85624884T>A	ENSP00000340594:p.Gln1045Leu	94.0	0.0		117.0	55.0	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	hg19	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	T	14.62	2.588701	0.46110	.	.	ENSG00000097096	ENST00000341460	T	0.07908	3.15	6.17	4.99	0.66335	.	0.285087	0.32357	N	0.006202	T	0.05823	0.0152	M	0.69823	2.125	0.34799	D	0.736485	P	0.44986	0.847	B	0.36464	0.225	T	0.10064	-1.0646	10	0.66056	D	0.02	.	13.2634	0.60120	0.0:0.0:0.132:0.868	.	1045	Q5VT97	SYDE2_HUMAN	L	1045	ENSP00000340594:Q1045L	ENSP00000340594:Q1045L	Q	-	2	0	SYDE2	85397472	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.318000	0.51975	2.371000	0.80710	0.533000	0.62120	CAG	.	.		0.363	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			A	85624884	T	A	85624884	3	1	203	1	0	0	0	0	1	0	0	0	15451	1580	55	4	454	4	SYDE2	1	85624884	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	9279145	85624884	163625737	10	29715										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86904629	86904629	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gattgttgaaattcatacctTcgtgggcattgccagtttcg	10	8	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:86904629T>A	ENST00000370565.4	+	7	1205	c.1043T>A	c.(1042-1044)tTc>tAc	p.F348Y		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	348	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		ATTCATACCTTCGTGGGCATT	0.423																																					p.F348Y	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.T1043A						.						108	101	103					1																	86904629		2203	4300	6503	SO:0001583	missense	9635	exon7			ATACCTTCGTGGG		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1043T>A	chr1.hg19:g.86904629T>A	ENSP00000359596:p.Phe348Tyr	102.0	0.0		117.0	6.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	T	11.49	1.654340	0.29425	.	.	ENSG00000137975	ENST00000370565	T	0.66460	-0.21	5.92	2.09	0.27110	von Willebrand factor, type A (3);	0.267481	0.38492	N	0.001678	T	0.11965	0.0291	N	0.05554	-0.025	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.31696	-0.9934	10	0.02654	T	1	-8.8915	1.0996	0.01681	0.3035:0.0873:0.2301:0.3792	.	348	Q9UQC9	CLCA2_HUMAN	Y	348	ENSP00000359596:F348Y	ENSP00000359596:F348Y	F	+	2	0	CLCA2	86677217	0.397000	0.25270	0.974000	0.42286	0.741000	0.42261	0.779000	0.26746	0.482000	0.27582	0.533000	0.62120	TTC	.	.		0.423	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		A	86904629	T	A	86904629	3	1	203	1	0	0	0	0	1	0	0	0	3460	1783	62	4	1069	4	CLCA2	1	86904629	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	1279745	86904629	162345992	11	29716										
INSRR	3645	hgsc.bcm.edu	37	chr1	156814633	156814633	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tcctggaataccatcagcctCtcctgcgggaaggggcatcc	11	14	2	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:156814633C>T	ENST00000368195.3	-	13	2836	c.2440G>A	c.(2440-2442)Gag>Aag	p.E814K	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	814					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCATCAGCCTCTCCTGCGGGA	0.587																																					p.E814K		Atlas-SNP	.											.	INSRR	309	.	0			c.G2440A						.						42	45	44					1																	156814633		2203	4300	6503	SO:0001583	missense	3645	exon13			CAGCCTCTCCTGC	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2440G>A	chr1.hg19:g.156814633C>T	ENSP00000357178:p.Glu814Lys	80.0	0.0		112.0	56.0	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	C	5.097	0.203551	0.09704	.	.	ENSG00000027644	ENST00000368195	T	0.52983	0.64	4.73	4.73	0.59995	.	0.000000	0.44097	D	0.000488	T	0.10680	0.0261	.	.	.	0.38663	D	0.952139	B	0.21520	0.057	B	0.17979	0.02	T	0.10064	-1.0646	9	0.02654	T	1	.	13.1984	0.59752	0.0:1.0:0.0:0.0	.	814	P14616	INSRR_HUMAN	K	814	ENSP00000357178:E814K	ENSP00000357178:E814K	E	-	1	0	INSRR	155081257	0.996000	0.38824	1.000000	0.80357	0.972000	0.66771	1.799000	0.38824	2.181000	0.69327	0.467000	0.42956	GAG	.	.		0.587	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		T	156814633	C	T	156814633	3	4	203	1	0	0	0	0	1	0	0	0	7783	922	32	3	1492	3	INSRR	1	156814633	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	69910004	156814633	92435988	12	29717										
SLAMF7	57823	hgsc.bcm.edu	37	chr1	160721146	160721146	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tgcttttagagtacattgaaGagaagaagagagtggacatt	12	3	0	5			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:160721146G>C	ENST00000368043.3	+	5	818	c.781G>C	c.(781-783)Gag>Cag	p.E261Q	SLAMF7_ENST00000458104.2_Intron|SLAMF7_ENST00000444090.2_Intron|SLAMF7_ENST00000368042.3_Missense_Mutation_p.E154Q|SLAMF7_ENST00000359331.4_Intron|SLAMF7_ENST00000441662.2_Missense_Mutation_p.E130Q|SLAMF7_ENST00000458602.2_Missense_Mutation_p.E114Q	NM_001282595.1|NM_021181.3	NP_001269524.1|NP_067004.3	Q9NQ25	SLAF7_HUMAN	SLAM family member 7	261					cell adhesion (GO:0007155)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of natural killer cell activation (GO:0032814)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(4)	24	all_cancers(52;2.63e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GTACATTGAAGAGAAGAAGAG	0.478																																					p.E261Q		Atlas-SNP	.											.	SLAMF7	54	.	0			c.G781C						.						156	145	149					1																	160721146		2203	4300	6503	SO:0001583	missense	57823	exon5			ATTGAAGAGAAGA	AB027233	CCDS1209.1, CCDS60321.1, CCDS60322.1, CCDS60323.1, CCDS60324.1, CCDS60325.1, CCDS72956.1, CCDS72957.1	1q23.1-q24.1	2013-01-11			ENSG00000026751	ENSG00000026751		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	21394	protein-coding gene	gene with protein product		606625				11802771, 11220635	Standard	XM_005245386		Approved	CRACC, 19A, CS1, CD319	uc001fwq.3	Q9NQ25	OTTHUMG00000024008	ENST00000368043.3:c.781G>C	chr1.hg19:g.160721146G>C	ENSP00000357022:p.Glu261Gln	102.0	0.0		146.0	6.0	NM_021181	A8K3U1|B4DPU4|B4DPY3|B4DWA3|Q8N6Y8|Q8ND32|Q9NY08|Q9NY23	Missense_Mutation	SNP	ENST00000368043.3	hg19	CCDS1209.1	.	.	.	.	.	.	.	.	.	.	G	9.468	1.094882	0.20471	.	.	ENSG00000026751	ENST00000441662;ENST00000368043;ENST00000368042;ENST00000458602	T;T;T;T	0.56103	1.82;0.48;0.48;0.99	3.95	0.0437	0.14223	.	1.442040	0.04096	N	0.312094	T	0.18002	0.0432	N	0.19112	0.55	0.09310	N	1	B;P;P;P;P	0.42203	0.275;0.718;0.634;0.773;0.501	B;B;B;B;B	0.43274	0.159;0.159;0.277;0.414;0.109	T	0.07731	-1.0757	10	0.18710	T	0.47	-0.202	6.1186	0.20139	0.4498:0.0:0.5502:0.0	.	114;130;167;154;261	B4DWA3;B4DPU4;B4DW98;Q9NQ25-2;Q9NQ25	.;.;.;.;SLAF7_HUMAN	Q	130;261;154;114	ENSP00000405605:E130Q;ENSP00000357022:E261Q;ENSP00000357021:E154Q;ENSP00000409965:E114Q	ENSP00000357021:E154Q	E	+	1	0	SLAMF7	158987770	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.491000	0.22419	0.015000	0.14971	-0.142000	0.14014	GAG	.	.		0.478	SLAMF7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060464.1	NM_021181		C	160721146	G	C	160721146	3	2	203	1	0	0	0	0	1	0	0	0	14384	943	33	4	799	4	SLAMF7	1	160721146	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	3906513	160721146	88529475	13	29718										
LAX1	54900	hgsc.bcm.edu	37	chr1	203743135	203743135	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ctccctcggcacactgcatcAatgtcagagcttccagagac	8	15	2	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr1:203743135A>G	ENST00000442561.2	+	5	913	c.523A>G	c.(523-525)Aat>Gat	p.N175D	LAX1_ENST00000367215.1_3'UTR|LAX1_ENST00000367217.5_Missense_Mutation_p.N159D	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	175					antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)			central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			ACACTGCATCAATGTCAGAGC	0.522																																					p.N175D		Atlas-SNP	.											.	LAX1	48	.	0			c.A523G						.						102	93	96					1																	203743135		2203	4300	6503	SO:0001583	missense	54900	exon5			TGCATCAATGTCA	AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188			26005	protein-coding gene	gene with protein product	"LAT-like membrane associated protein", "linker for activation of x cells"					12359715	Standard	NM_017773		Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.523A>G	chr1.hg19:g.203743135A>G	ENSP00000406970:p.Asn175Asp	105.0	0.0		174.0	60.0	NM_017773	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	Missense_Mutation	SNP	ENST00000442561.2	hg19	CCDS1441.2	.	.	.	.	.	.	.	.	.	.	A	16.66	3.184482	0.57800	.	.	ENSG00000122188	ENST00000442561;ENST00000367217	.	.	.	5.48	0.356	0.16074	.	0.389572	0.24544	N	0.037617	T	0.31451	0.0797	L	0.58101	1.795	0.09310	N	1	B;B	0.25563	0.129;0.129	B;B	0.30572	0.117;0.117	T	0.16630	-1.0396	9	0.26408	T	0.33	-8.3646	1.8891	0.03244	0.4279:0.3188:0.0883:0.1651	.	159;175	B7Z744;Q8IWV1	.;LAX1_HUMAN	D	175;159	.	ENSP00000356186:N159D	N	+	1	0	LAX1	202009758	0.638000	0.27225	0.006000	0.13384	0.219000	0.24729	1.260000	0.32968	0.020000	0.15106	-0.316000	0.08728	AAT	.	.		0.522	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087468.3	NM_017773		G	203743135	A	G	203743135	3	3	203	1	0	0	0	0	1	0	0	0	8657	130	5	2	586	2	LAX1	1	203743135	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	43021989	203743135	45507486	14	29719										
KIDINS220	57498	hgsc.bcm.edu	37	chr2	8871742	8871742	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tttcatcttcttcagtgataGgatccaggggggaagcatcg	12	8	4	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr2:8871742G>C	ENST00000256707.3	-	30	4605	c.4424C>G	c.(4423-4425)cCt>cGt	p.P1475R	KIDINS220_ENST00000427284.1_Missense_Mutation_p.P1456R|KIDINS220_ENST00000473731.1_Missense_Mutation_p.P1456R|KIDINS220_ENST00000418530.1_Missense_Mutation_p.P1376R	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1475					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTCAGTGATAGGATCCAGGGG	0.463																																					p.P1475R		Atlas-SNP	.											.	KIDINS220	136	.	0			c.C4424G						.						76	74	74					2																	8871742		1892	4104	5996	SO:0001583	missense	57498	exon30			GTGATAGGATCCA	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4424C>G	chr2.hg19:g.8871742G>C	ENSP00000256707:p.Pro1475Arg	171.0	0.0		184.0	8.0	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.369784	0.82573	.	.	ENSG00000134313	ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731	T;T;T;T	0.73681	-0.69;-0.7;-0.77;-0.7	5.92	5.92	0.95590	.	0.050955	0.85682	D	0.000000	T	0.82029	0.4948	L	0.34521	1.04	0.58432	D	0.999999	D;D;D	0.89917	0.998;0.997;1.0	D;D;D	0.97110	0.962;0.964;1.0	T	0.82942	-0.0207	10	0.87932	D	0	.	20.3214	0.98679	0.0:0.0:1.0:0.0	.	1376;1475;329	Q9ULH0-2;Q9ULH0;B4DG84	.;KDIS_HUMAN;.	R	1475;1456;1376;1456	ENSP00000256707:P1475R;ENSP00000411849:P1456R;ENSP00000414923:P1376R;ENSP00000418974:P1456R	ENSP00000256707:P1475R	P	-	2	0	KIDINS220	8789193	1.000000	0.71417	0.998000	0.56505	0.901000	0.52897	7.228000	0.78079	2.804000	0.96469	0.655000	0.94253	CCT	.	.		0.463	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		C	8871742	G	C	8871742	3	2	203	1	0	0	0	0	1	0	0	0	8280	1000	35	4	895	4	KIDINS220	2	8871742	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10		8871742	234327631	15	29720										
C2orf39	92749	hgsc.bcm.edu	37	chr2	26667692	26667692	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gatgtggacaggatcatccaCacccatcatctggggcttcc	10	13	3	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr2:26667692C>T	ENST00000288710.2	+	10	1346	c.1272C>T	c.(1270-1272)caC>caT	p.H424H	DRC1_ENST00000483675.1_3'UTR	NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	424					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											ggatcatccacacccatcatc	0.502																																					p.H424H		Atlas-SNP	.											.	CCDC164	84	.	0			c.C1272T						.						105	87	93					2																	26667692		2203	4300	6503	SO:0001819	synonymous_variant	92749	exon10			CATCCACACCCAT	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"chromosome 2 open reading frame 39", "coiled-coil domain containing 164", "dynein regulatory complex subunit 1 homolog (Chlamydomonas)"	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.1272C>T	chr2.hg19:g.26667692C>T		96.0	0.0		93.0	21.0	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Silent	SNP	ENST00000288710.2	hg19	CCDS1723.1																																																																																			.	.		0.502	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038		T	26667692	C	T	26667692	2	4	203	1	0	0	0	0	0	0	0	1	2166	477	17	3		3	C2orf39	2	26667692	Silent	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	17795950	26667692	216531681	16	29721										
LHCGR	3973	hgsc.bcm.edu	37	chr2	48915497	48915497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	taatcagaatggcatgtcttAatcgcagcttttggtccagg	10	8	2	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr2:48915497A>G	ENST00000294954.7	-	11	1460	c.1439T>C	c.(1438-1440)tTa>tCa	p.L480S	STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000401907.1_Intron|LHCGR_ENST00000344775.3_Missense_Mutation_p.L418S|LHCGR_ENST00000405626.1_Missense_Mutation_p.L453S|LHCGR_ENST00000403273.1_3'UTR	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	480					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)	p.L480S(1)		NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	GGCATGTCTTAATCGCAGCTT	0.443																																					p.L480S		Atlas-SNP	.											LHCGR,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	LHCGR	154	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.T1439C						.						140	117	125					2																	48915497		2203	4300	6503	SO:0001583	missense	3973	exon11			TGTCTTAATCGCA		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"GPCR / Class A : Gonadotropin and TSH receptors"	6585	protein-coding gene	gene with protein product		152790	"hypergonadotropic hypogonadism"	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.1439T>C	chr2.hg19:g.48915497A>G	ENSP00000294954:p.Leu480Ser	89.0	0.0		88.0	37.0	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	hg19	CCDS1842.1	.	.	.	.	.	.	.	.	.	.	A	18.39	3.613301	0.66672	.	.	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000405626	T;T;T	0.72051	-0.62;-0.62;-0.62	5.79	5.79	0.91817	GPCR, rhodopsin-like superfamily (1);	0.130231	0.51477	D	0.000086	D	0.86822	0.6025	M	0.89785	3.06	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89139	0.3515	9	.	.	.	.	15.3114	0.74035	1.0:0.0:0.0:0.0	.	480	P22888	LSHR_HUMAN	S	418;480;453	ENSP00000344301:L418S;ENSP00000294954:L480S;ENSP00000386033:L453S	.	L	-	2	0	LHCGR	48769001	0.943000	0.32029	0.208000	0.23602	0.993000	0.82548	7.521000	0.81832	2.218000	0.71995	0.533000	0.62120	TTA	.	.		0.443	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3		G	48915497	A	G	48915497	3	3	203	1	0	0	0	0	1	0	0	0	8771	372	13	2	664	2	LHCGR	2	48915497	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	22247805	48915497	194283876	17	29722										
SLC20A1	6574	hgsc.bcm.edu	37	chr2	113404985	113404985	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tgttggtgcaactattggttTctccctcgtggcaaaggggc	13	9	1	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr2:113404985T>G	ENST00000272542.3	+	3	958	c.419T>G	c.(418-420)tTc>tGc	p.F140C	AC079922.3_ENST00000457336.1_lincRNA	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	140					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						ACTATTGGTTTCTCCCTCGTG	0.428																																					p.F140C		Atlas-SNP	.											.	SLC20A1	59	.	0			c.T419G						.						199	204	202					2																	113404985		2203	4300	6503	SO:0001583	missense	6574	exon3			TTGGTTTCTCCCT		CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"Solute carriers"	10946	protein-coding gene	gene with protein product	"gibbon ape leukemia virus receptor 1"	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.419T>G	chr2.hg19:g.113404985T>G	ENSP00000272542:p.Phe140Cys	226.0	0.0		200.0	72.0	NM_005415	Q08344|Q6DHX8|Q9UQ82	Missense_Mutation	SNP	ENST00000272542.3	hg19	CCDS2099.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.627463	0.87560	.	.	ENSG00000144136	ENST00000272542	D	0.90900	-2.75	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.96670	0.8913	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97672	1.0167	10	0.87932	D	0	-8.6166	13.9767	0.64277	0.0:0.0:0.0:1.0	.	140	Q8WUM9	S20A1_HUMAN	C	140	ENSP00000272542:F140C	ENSP00000272542:F140C	F	+	2	0	SLC20A1	113121456	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.034000	0.64152	2.175000	0.68902	0.533000	0.62120	TTC	.	.		0.428	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		G	113404985	T	G	113404985	3	3	203	1	0	0	0	0	1	0	0	0	14453	1783	62	5	425	5	SLC20A1	2	113404985	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	64489488	113404985	129794388	18	29723										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168096409	168096409	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ggcacttcaagaagcagccaGgaaatggcaagaaatgaaca	11	8	1	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr2:168096409G>T	ENST00000409728.1	+	7	1091	c.1002G>T	c.(1000-1002)caG>caT	p.Q334H	XIRP2_ENST00000409195.1_Missense_Mutation_p.Q301H|XIRP2_ENST00000295237.9_Missense_Mutation_p.Q301H|XIRP2_ENST00000409273.1_Missense_Mutation_p.Q79H|XIRP2_ENST00000409756.2_Missense_Mutation_p.Q301H|XIRP2_ENST00000420519.1_Missense_Mutation_p.Q334H|XIRP2_ENST00000409605.1_Missense_Mutation_p.Q79H|XIRP2_ENST00000409043.1_Missense_Mutation_p.Q301H	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	126					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GAAGCAGCCAGGAAATGGCAA	0.383																																					p.Q334H		Atlas-SNP	.											.	XIRP2	914	.	0			c.G1002T						.						88	90	90					2																	168096409		1874	4117	5991	SO:0001583	missense	129446	exon7			CAGCCAGGAAATG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.1002G>T	chr2.hg19:g.168096409G>T	ENSP00000386619:p.Gln334His	644.0	0.0		389.0	23.0	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	hg19	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.150619	0.37923	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409195;ENST00000409756;ENST00000420519;ENST00000295237;ENST00000409273;ENST00000409605	T;T;T;T;T;T;T;T	0.78126	-1.15;-1.15;4.15;-1.15;-1.15;4.15;4.16;-1.15	5.9	2.01	0.26516	.	0.435723	0.22988	N	0.053235	D	0.82370	0.5022	L	0.61218	1.895	0.09310	N	0.999993	D;D;D;D;D	0.67145	0.981;0.994;0.996;0.989;0.986	P;D;D;P;P	0.74674	0.635;0.984;0.929;0.859;0.742	T	0.70292	-0.4912	10	0.59425	D	0.04	-5.036	6.02	0.19625	0.5254:0.0:0.4746:0.0	.	126;301;334;126;79	A4UGR9;A4UGR9-4;A4UGR9-6;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.;.;.	H	301;334;301;301;334;301;79;79	ENSP00000386454:Q301H;ENSP00000386619:Q334H;ENSP00000386840:Q301H;ENSP00000386724:Q301H;ENSP00000415541:Q334H;ENSP00000295237:Q301H;ENSP00000387255:Q79H;ENSP00000386981:Q79H	ENSP00000295237:Q301H	Q	+	3	2	XIRP2	167804655	0.844000	0.29557	0.962000	0.40283	0.057000	0.15508	0.316000	0.19469	0.554000	0.29061	-0.157000	0.13467	CAG	.	.		0.383	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		T	168096409	G	T	168096409	3	4	203	1	0	0	0	0	1	0	0	0	17445	991	35	3	921	3	XIRP2	2	168096409	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	54691424	168096409	75102964	19	29724										
ORMDL1	94101	hgsc.bcm.edu	37	chr2	190636618	190636618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	atacttcgtatagaaacttgCcagaaaatatctgtagagat	7	6	1	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr2:190636618C>T	ENST00000325795.3	-	3	1123	c.337G>A	c.(337-339)Gca>Aca	p.A113T	ORMDL1_ENST00000392349.4_Missense_Mutation_p.A113T|ORMDL1_ENST00000392350.3_Missense_Mutation_p.A113T|ORMDL1_ENST00000496543.1_5'UTR			Q9P0S3	ORML1_HUMAN	ORMDL sphingolipid biosynthesis regulator 1	113					ceramide metabolic process (GO:0006672)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(1)|urinary_tract(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00177)|Epithelial(96;0.0317)|all cancers(119;0.0889)			TAGAAACTTGCCAGAAAATAT	0.328																																					p.A113T		Atlas-SNP	.											.	ORMDL1	8	.	0			c.G337A						.						56	57	56					2																	190636618		2203	4300	6503	SO:0001583	missense	94101	exon5			AACTTGCCAGAAA		CCDS2301.1	2q32	2014-06-16	2014-06-16		ENSG00000128699	ENSG00000128699			16036	protein-coding gene	gene with protein product		610073	"ORM1 (S. cerevisiae)-like 1", "ORM1-like 1 (S. cerevisiae)"			12093374, 23066021	Standard	NM_016467		Approved		uc002ure.4	Q9P0S3	OTTHUMG00000132661	ENST00000325795.3:c.337G>A	chr2.hg19:g.190636618C>T	ENSP00000326869:p.Ala113Thr	94.0	0.0		111.0	52.0	NM_016467	B2R8W3|D3DPH9	Missense_Mutation	SNP	ENST00000325795.3	hg19	CCDS2301.1	.	.	.	.	.	.	.	.	.	.	C	6.906	0.536702	0.13188	.	.	ENSG00000128699	ENST00000392350;ENST00000325795;ENST00000392349	.	.	.	5.21	5.21	0.72293	.	0.052491	0.85682	D	0.000000	T	0.39145	0.1067	N	0.19112	0.55	0.80722	D	1	B	0.10296	0.003	B	0.12156	0.007	T	0.21415	-1.0246	9	0.17832	T	0.49	-22.2973	10.5252	0.44943	0.0:0.8508:0.0:0.1492	.	113	Q9P0S3	ORML1_HUMAN	T	113	.	ENSP00000326869:A113T	A	-	1	0	ORMDL1	190344863	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.247000	0.51422	2.707000	0.92482	0.655000	0.94253	GCA	.	.		0.328	ORMDL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335275.1	NM_016467		T	190636618	C	T	190636618	3	4	203	1	0	0	0	0	1	0	0	0	11278	739	26	3	128	3	ORMDL1	2	190636618	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	22540209	190636618	52562755	20	29725										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198266800	198266800	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gagttgctgcttcagccaagGcagcaatggccaaagcactg	12	11	1	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr2:198266800G>A	ENST00000335508.6	-	15	2223	c.2132C>T	c.(2131-2133)gCc>gTc	p.A711V	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'UTR	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	711					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TTCAGCCAAGGCAGCAATGGC	0.443			Mis		myelodysplastic syndrome																																p.A711V		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	SF3B1,NS,haematopoietic_neoplasm,0,1	SF3B1	1038	.	0			c.C2132T						.						94	90	91					2																	198266800		2203	4300	6503	SO:0001583	missense	23451	exon15			GCCAAGGCAGCAA	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2132C>T	chr2.hg19:g.198266800G>A	ENSP00000335321:p.Ala711Val	282.0	0.0		327.0	146.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	37	6.028906	0.97216	.	.	ENSG00000115524	ENST00000335508	T	0.66280	-0.2	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85265	0.5657	H	0.95224	3.64	0.80722	D	1	D	0.67145	0.996	P	0.62184	0.899	D	0.88622	0.3163	10	0.87932	D	0	.	20.5373	0.99239	0.0:0.0:1.0:0.0	.	711	O75533	SF3B1_HUMAN	V	711	ENSP00000335321:A711V	ENSP00000335321:A711V	A	-	2	0	SF3B1	197975045	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.287000	0.95975	2.857000	0.98124	0.650000	0.86243	GCC	.	.		0.443	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			A	198266800	G	A	198266800	3	1	203	1	0	0	0	0	1	0	0	0	14164	1203	42	3	1826	3	SF3B1	2	198266800	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	7630182	198266800	44932573	21	29726										
HSPD1	3329	hgsc.bcm.edu	37	chr2	198358073	198358073	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	caagacgagtgtacttagagCttctccatcaacatcttcag	7	11	4	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr2:198358073C>G	ENST00000388968.3	-	7	1111	c.844G>C	c.(844-846)Gct>Cct	p.A282P	HSPD1_ENST00000345042.2_Missense_Mutation_p.A282P	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	282					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			GTACTTAGAGCTTCTCCATCA	0.368																																					p.A282P		Atlas-SNP	.											.	HSPD1	68	.	0			c.G844C						.						144	146	145					2																	198358073		2203	4300	6503	SO:0001583	missense	3329	exon7			TTAGAGCTTCTCC	M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"Heat Shock Proteins / Chaperonins"	5261	protein-coding gene	gene with protein product		118190	"heat shock 60kD protein 1 (chaperonin)", "spastic paraplegia 13 (autosomal dominant)"	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.844G>C	chr2.hg19:g.198358073C>G	ENSP00000373620:p.Ala282Pro	187.0	0.0		164.0	47.0	NM_002156	B2R5M6|B7Z712|Q38L19|Q9UCR6	Missense_Mutation	SNP	ENST00000388968.3	hg19	CCDS33357.1	.	.	.	.	.	.	.	.	.	.	C	34	5.396637	0.96009	.	.	ENSG00000144381	ENST00000388968;ENST00000345042;ENST00000536745	D;D	0.82433	-1.61;-1.61	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.94145	0.8122	H	0.97077	3.935	0.80722	D	1	P;P;D	0.60160	0.774;0.726;0.987	P;P;D	0.65874	0.67;0.714;0.939	D	0.95997	0.8990	10	0.87932	D	0	-14.4411	18.8471	0.92212	0.0:1.0:0.0:0.0	.	273;282;282	B7Z597;B3GQS7;P10809	.;.;CH60_HUMAN	P	282;282;138	ENSP00000373620:A282P;ENSP00000340019:A282P	ENSP00000340019:A282P	A	-	1	0	HSPD1	198066318	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.722000	0.84778	2.532000	0.85374	0.585000	0.79938	GCT	.	.		0.368	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156		G	198358073	C	G	198358073	3	3	203	1	0	0	0	0	1	0	0	0	7437	797	28	4	901	4	HSPD1	2	198358073	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	91273	198358073	44841300	22	29727										
FANCD2	2177	hgsc.bcm.edu	37	chr3	10074603	10074603	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tgacagcatctttgtaaagcTtcttaagatatcaggaatta	7	6	3	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr3:10074603T>G	ENST00000419585.1	+	3	313	c.152T>G	c.(151-153)cTt>cGt	p.L51R	FANCD2_ENST00000431693.1_Missense_Mutation_p.L51R|FANCD2_ENST00000287647.3_Missense_Mutation_p.L51R|FANCD2_ENST00000383806.1_Missense_Mutation_p.L51R|FANCD2_ENST00000383807.1_Missense_Mutation_p.L51R			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	51	Interaction with FANCE.				DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		TTTGTAAAGCTTCTTAAGATA	0.303			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.L51R		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.T152G						.						80	84	83					3																	10074603		2202	4294	6496	SO:0001583	missense	2177	exon3	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TAAAGCTTCTTAA	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.152T>G	chr3.hg19:g.10074603T>G	ENSP00000398754:p.Leu51Arg	223.0	0.0		259.0	16.0	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	hg19	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.330040	0.60743	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585;ENST00000431693	T;T;T;T;T	0.59224	0.28;0.28;0.28;0.28;0.28	6.15	6.15	0.99193	.	0.107332	0.64402	D	0.000003	T	0.74222	0.3688	M	0.70595	2.14	0.40036	D	0.975598	D;D;D	0.89917	0.999;1.0;1.0	D;D;P	0.68943	0.961;0.961;0.906	T	0.77643	-0.2511	10	0.72032	D	0.01	.	14.7406	0.69451	0.0:0.0:0.0:1.0	.	51;51;51	Q9BXW9-2;Q9BXW9;Q9BXW9-4	.;FACD2_HUMAN;.	R	51	ENSP00000287647:L51R;ENSP00000373318:L51R;ENSP00000373317:L51R;ENSP00000398754:L51R;ENSP00000399354:L51R	ENSP00000287647:L51R	L	+	2	0	FANCD2	10049603	1.000000	0.71417	0.989000	0.46669	0.291000	0.27294	4.995000	0.63908	2.363000	0.80096	0.523000	0.50628	CTT	.	.		0.303	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			G	10074603	T	G	10074603	3	3	203	1	0	0	0	0	1	0	0	0	5673	1609	56	5	158	5	FANCD2	3	10074603	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10		10074603	187947827	23	29728										
STAB1	23166	hgsc.bcm.edu	37	chr3	52553292	52553292	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gcccccagggcagcatatacCtcaatgacttcgcgcgcgtg	11	15	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr3:52553292C>T	ENST00000321725.6	+	49	5123	c.5047C>T	c.(5047-5049)Ctc>Ttc	p.L1683F		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1683	FAS1 5. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CAGCATATACCTCAATGACTT	0.642																																					p.L1683F		Atlas-SNP	.											.	STAB1	178	.	0			c.C5047T						.						107	115	112					3																	52553292		2203	4300	6503	SO:0001583	missense	23166	exon49			ATATACCTCAATG	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.5047C>T	chr3.hg19:g.52553292C>T	ENSP00000312946:p.Leu1683Phe	89.0	0.0		96.0	9.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.781729	0.70222	.	.	ENSG00000010327	ENST00000321725	D	0.91180	-2.8	5.5	-10.4	0.00318	FAS1 domain (5);	0.332572	0.29707	N	0.011411	D	0.85982	0.5824	L	0.54863	1.705	0.22292	N	0.999229	P	0.49307	0.922	P	0.46850	0.529	D	0.83852	0.0263	10	0.72032	D	0.01	.	12.7463	0.57283	0.135:0.7407:0.057:0.0673	.	1683	Q9NY15	STAB1_HUMAN	F	1683	ENSP00000312946:L1683F	ENSP00000312946:L1683F	L	+	1	0	STAB1	52528332	0.000000	0.05858	0.010000	0.14722	0.828000	0.46876	-1.043000	0.03535	-2.086000	0.00863	-1.028000	0.02416	CTC	.	.		0.642	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52553292	C	T	52553292	3	4	203	1	0	0	0	0	1	0	0	0	15252	681	24	3	5241	3	STAB1	3	52553292	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	42478689	52553292	145469138	24	29729										
TOMM70A	9868	hgsc.bcm.edu	37	chr3	100086936	100086936	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cataggcaaaatcacatttaTtgtcaatttcaatagccttg	5	8	3	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr3:100086936T>C	ENST00000284320.5	-	11	2073	c.1625A>G	c.(1624-1626)aAt>aGt	p.N542S		NM_014820.4	NP_055635.3	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70 homolog A (S. cerevisiae)	542					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			endometrium(11)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	32						ATCACATTTATTGTCAATTTC	0.358																																					p.N542S		Atlas-SNP	.											.	TOMM70A	65	.	0			c.A1625G						.						119	113	115					3																	100086936		2203	4300	6503	SO:0001583	missense	9868	exon11			CATTTATTGTCAA	AB018262	CCDS33807.1	3q12.2	2013-01-10	2006-04-04		ENSG00000154174	ENSG00000154174		"Tetratricopeptide (TTC) repeat domain containing"	11985	protein-coding gene	gene with protein product		606081	"translocase of outer mitochondrial membrane 70 (yeast) homolog A", "translocase of outer mitochondrial membrane 70 homolog A (yeast)"			10582581	Standard	NM_014820		Approved	KIAA0719	uc003dtw.3	O94826	OTTHUMG00000159065	ENST00000284320.5:c.1625A>G	chr3.hg19:g.100086936T>C	ENSP00000284320:p.Asn542Ser	100.0	0.0		90.0	25.0	NM_014820	D3DN48	Missense_Mutation	SNP	ENST00000284320.5	hg19	CCDS33807.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.740810	0.49151	.	.	ENSG00000154174	ENST00000284320;ENST00000544924	T	0.52057	0.68	5.88	5.88	0.94601	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.27419	0.0673	N	0.02916	-0.46	0.80722	D	1	B	0.23735	0.09	B	0.23150	0.044	T	0.12041	-1.0563	10	0.37606	T	0.19	-22.2088	16.2879	0.82732	0.0:0.0:0.0:1.0	.	542	O94826	TOM70_HUMAN	S	542;435	ENSP00000284320:N542S	ENSP00000284320:N542S	N	-	2	0	TOMM70A	101569626	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.974000	0.70465	2.242000	0.73789	0.533000	0.62120	AAT	.	.		0.358	TOMM70A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353141.2			C	100086936	T	C	100086936	3	2	203	1	0	0	0	0	1	0	0	0	16377	1493	52	2	209	2	TOMM70A	3	100086936	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	47533644	100086936	97935494	25	29730										
CD80	941	hgsc.bcm.edu	37	chr3	119263535	119263535	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ggagaggttattagtgatatCaaagatggtccggttcttgt	13	4	2	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr3:119263535C>T	ENST00000264246.3	-	3	642	c.280G>A	c.(280-282)Gat>Aat	p.D94N	CD80_ENST00000383669.3_Missense_Mutation_p.D94N|CD80_ENST00000383668.3_Missense_Mutation_p.D94N|CD80_ENST00000478182.1_Missense_Mutation_p.D94N	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	94	Ig-like V-type.				cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of signal transduction (GO:0009967)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	12					Abatacept(DB01281)|Belatacept(DB06681)	TTAGTGATATCAAAGATGGTC	0.453																																					p.D94N	Melanoma(132;135 1764 1806 5833 14593)	Atlas-SNP	.											.	CD80	35	.	0			c.G280A						.						156	148	151					3																	119263535		2203	4300	6503	SO:0001583	missense	941	exon3			TGATATCAAAGAT		CCDS2989.1	3q13.3-q21	2013-01-11	2006-03-31		ENSG00000121594	ENSG00000121594		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	1700	protein-coding gene	gene with protein product	"B-lymphocyte activation antigen B7"	112203	"CD80 antigen (CD28 antigen ligand 1, B7-1 antigen)", "CD80 molecule "	CD28LG, CD28LG1		1370389	Standard	NM_005191		Approved	B7.1, B7-1	uc003ecq.3	P33681	OTTHUMG00000159419	ENST00000264246.3:c.280G>A	chr3.hg19:g.119263535C>T	ENSP00000264246:p.Asp94Asn	122.0	0.0		146.0	8.0	NM_005191	Q5DTA9|Q5DTB0	Missense_Mutation	SNP	ENST00000264246.3	hg19	CCDS2989.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.269963	0.59540	.	.	ENSG00000121594	ENST00000264246;ENST00000478182;ENST00000383669;ENST00000383668	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	5.13	3.29	0.37713	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.899101	0.09455	N	0.799881	T	0.71693	0.3370	M	0.79805	2.47	0.09310	N	1	P;P;P;P	0.47762	0.875;0.9;0.9;0.9	P;P;P;P	0.52514	0.58;0.701;0.701;0.701	T	0.58951	-0.7545	10	0.66056	D	0.02	-12.7963	6.0456	0.19758	0.1868:0.718:0.0:0.0953	.	94;94;94;94	Q5DTA9;Q5DTB0;A0N0P2;P33681	.;.;.;CD80_HUMAN	N	94	ENSP00000264246:D94N;ENSP00000418364:D94N;ENSP00000373165:D94N;ENSP00000373164:D94N	ENSP00000264246:D94N	D	-	1	0	CD80	120746225	0.032000	0.19561	0.019000	0.16419	0.044000	0.14063	0.564000	0.23563	0.703000	0.31848	0.650000	0.86243	GAT	.	.		0.453	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191		T	119263535	C	T	119263535	3	4	203	1	0	0	0	0	1	0	0	0	3040	826	29	3	602	3	CD80	3	119263535	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	19176599	119263535	78758895	26	29731										
SMC4	10051	hgsc.bcm.edu	37	chr3	160148414	160148414	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	caaaaggcacaagactctgtCttgcgtacagagaaagaaat	9	8	2	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr3:160148414C>G	ENST00000357388.3	+	19	3274	c.2823C>G	c.(2821-2823)gtC>gtG	p.V941V	RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000360111.2_Silent_p.V941V|SMC4_ENST00000462787.1_Silent_p.V941V|SMC4_ENST00000469762.1_Silent_p.V916V|SMC4_ENST00000344722.5_Silent_p.V941V	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	941					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AAGACTCTGTCTTGCGTACAG	0.378																																					p.V941V		Atlas-SNP	.											.	SMC4	135	.	0			c.C2823G						.						79	82	81					3																	160148414		2203	4300	6503	SO:0001819	synonymous_variant	10051	exon18			CTCTGTCTTGCGT	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.2823C>G	chr3.hg19:g.160148414C>G		258.0	0.0		278.0	107.0	NM_005496	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Silent	SNP	ENST00000357388.3	hg19	CCDS3189.1																																																																																			.	.		0.378	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			G	160148414	C	G	160148414	2	3	203	1	0	0	0	0	0	0	0	1	14800	900	32	4		4	SMC4	3	160148414	Silent	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	40884879	160148414	37874016	27	29732										
TMEM128	85013	hgsc.bcm.edu	37	chr4	4248013	4248014	+	Frame_Shift_Ins	INS	-	-	A													0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tgccaaaatccagaatccagINSaatggatattaagtcttgga							TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr4:4248013_4248014insA	ENST00000382753.4	-	2	163_164	c.154_155insT	c.(154-156)tctfs	p.S52fs	TMEM128_ENST00000540397.1_Frame_Shift_Ins_p.S52fs|TMEM128_ENST00000254742.2_Frame_Shift_Ins_p.S28fs|TMEM128_ENST00000538516.1_Frame_Shift_Ins_p.S52fs			Q5BJH2	TM128_HUMAN	transmembrane protein 128	52						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)		CCAGAATCCAGAATGGATATTA	0.342																																					p.S28fs		Atlas-INDEL	.											.	TMEM128	12	.	0			c.83_84insT						.																																			SO:0001589	frameshift_variant	85013	exon2			.	BC007729	CCDS3373.1, CCDS75099.1	4p16.3	2008-02-05			ENSG00000132406	ENSG00000132406			28201	protein-coding gene	gene with protein product							Standard	XM_005248034		Approved	MGC13159	uc003ghq.1	Q5BJH2	OTTHUMG00000125475	ENST00000382753.4:c.155dupT	chr4.hg19:g.4248015_4248015dupA	ENSP00000372201:p.Ser52fs	171.0	0.0		128.0	48.0	NM_032927	B4DHS7|D3DVS3|Q5H9U6|Q96I94	Frame_Shift_Ins	INS	ENST00000382753.4	hg19																																																																																				.	.		0.342	TMEM128-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000246798.2	NM_032927		A	4248014	-	A	4248013	7	5	203	1	0	1	1	0	0	0	0	0	16056	942	33	0	354	0	TMEM128	4	4248013	Frame_Shift_Ins	INS	-	TCGA-DD-AADV-01A-11D-A38X-10		4248013	186906263	28	29733										
CSN1S1	1446	hgsc.bcm.edu	37	chr4	70804905	70804905	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ttcttttagaagatggaatcCagcatcagttcatcgagtga	9	7	3	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr4:70804905C>A	ENST00000246891.4	+	10	304	c.255C>A	c.(253-255)tcC>tcA	p.S85S	CSN1S1_ENST00000507772.1_Silent_p.S85S|CSN1S1_ENST00000507763.1_Silent_p.S84S|CSN1S1_ENST00000444405.3_Silent_p.S84S|CSN1S1_ENST00000505782.1_Silent_p.S77S	NM_001890.1	NP_001881.1	P47710	CASA1_HUMAN	casein alpha s1	85						extracellular region (GO:0005576)|extracellular space (GO:0005615)	transporter activity (GO:0005215)			lung(5)|prostate(1)|upper_aerodigestive_tract(1)	7						AGATGGAATCCAGCATCAGTT	0.318																																					p.S85S		Atlas-SNP	.											.	CSN1S1	20	.	0			c.C255A						.						87	86	86					4																	70804905		1798	4063	5861	SO:0001819	synonymous_variant	1446	exon10			GGAATCCAGCATC	X78416	CCDS47067.1, CCDS54769.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000126545	ENSG00000126545			2445	protein-coding gene	gene with protein product		115450	"casein, alpha"	CASA, CSN1		9050925, 7619062	Standard	NM_001890		Approved		uc003hep.1	P47710	OTTHUMG00000160843	ENST00000246891.4:c.255C>A	chr4.hg19:g.70804905C>A		185.0	0.0		141.0	32.0	NM_001890	A1A510|A1A511|E9PB60|Q4PNR5	Silent	SNP	ENST00000246891.4	hg19	CCDS47067.1																																																																																			.	.		0.318	CSN1S1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362629.1			A	70804905	C	A	70804905	2	1	203	1	0	0	0	0	0	0	0	1	3949	581	21	3		3	CSN1S1	4	70804905	Silent	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	66556892	70804905	120349371	29	29734										
PPEF2	5470	hgsc.bcm.edu	37	chr4	76805789	76805789	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	catggtttcctctgttaagaTggaactctttggggtaaacc	10	8	2	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr4:76805789T>C	ENST00000286719.7	-	8	1060	c.704A>G	c.(703-705)cAt>cGt	p.H235R		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	235	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TCTGTTAAGATGGAACTCTTT	0.388																																					p.H235R	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.A704G						.						180	182	181					4																	76805789		2203	4300	6503	SO:0001583	missense	5470	exon8			TTAAGATGGAACT	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9244	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, beta isozyme"	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.704A>G	chr4.hg19:g.76805789T>C	ENSP00000286719:p.His235Arg	94.0	0.0		63.0	34.0	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	hg19	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.821816	0.50633	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	D	0.85258	-1.96	4.84	3.65	0.41850	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);Metallophosphoesterase domain (1);	0.095854	0.64402	N	0.000001	D	0.83376	0.5241	M	0.76574	2.34	0.47819	D	0.999527	B;B	0.23058	0.079;0.028	B;B	0.26202	0.067;0.026	T	0.80051	-0.1544	10	0.59425	D	0.04	-15.3668	8.7177	0.34421	0.0:0.0901:0.0:0.9099	.	235;235	O14830-2;O14830	.;PPE2_HUMAN	R	235	ENSP00000286719:H235R	ENSP00000286719:H235R	H	-	2	0	PPEF2	77024813	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.511000	0.67024	0.873000	0.35799	0.533000	0.62120	CAT	.	.		0.388	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		C	76805789	T	C	76805789	3	2	203	1	0	0	0	0	1	0	0	0	12317	1464	51	2	1597	2	PPEF2	4	76805789	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	6000884	76805789	114348487	30	29735										
SPOCK3	50859	hgsc.bcm.edu	37	chr4	167658664	167658664	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gatcccatgacttcatttccAtatctgtcaacacaccagca	4	14	3	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr4:167658664A>G	ENST00000357154.3	-	11	1232	c.1095T>C	c.(1093-1095)taT>taC	p.Y365Y	SPOCK3_ENST00000541637.1_Silent_p.Y267Y|SPOCK3_ENST00000535728.1_Silent_p.Y233Y|SPOCK3_ENST00000511269.1_Silent_p.Y362Y|SPOCK3_ENST00000541354.1_Silent_p.Y245Y|SPOCK3_ENST00000512681.1_Silent_p.Y267Y|SPOCK3_ENST00000510741.1_Silent_p.Y322Y|SPOCK3_ENST00000511531.1_Silent_p.Y365Y|SPOCK3_ENST00000504953.1_Silent_p.Y362Y|SPOCK3_ENST00000421836.2_Silent_p.Y314Y|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Silent_p.Y362Y|SPOCK3_ENST00000502330.1_Silent_p.Y365Y|SPOCK3_ENST00000534949.1_Silent_p.Y269Y|SPOCK3_ENST00000506886.1_Silent_p.Y365Y	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	365	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		CTTCATTTCCATATCTGTCAA	0.403																																					p.Y365Y		Atlas-SNP	.											.	SPOCK3	90	.	0			c.T1095C						.						291	263	273					4																	167658664		2203	4300	6503	SO:0001819	synonymous_variant	50859	exon11			ATTTCCATATCTG	AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1095T>C	chr4.hg19:g.167658664A>G		60.0	0.0		34.0	14.0	NM_016950	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Silent	SNP	ENST00000357154.3	hg19	CCDS54817.1																																																																																			.	.		0.403	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			G	167658664	A	G	167658664	2	3	203	1	0	0	0	0	0	0	0	1	15096	224	8	2		2	SPOCK3	4	167658664	Silent	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	90852875	167658664	23495612	31	29736										
MIER3	166968	hgsc.bcm.edu	37	chr5	56226567	56226567	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ttacacttgagaagttcataTaatgcctgggatggatattc	9	6	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr5:56226567T>C	ENST00000381199.3	-	9	763	c.753A>G	c.(751-753)ttA>ttG	p.L251L	MIER3_ENST00000381226.3_Silent_p.L256L|MIER3_ENST00000381213.3_Silent_p.L251L|CTD-2310F14.1_ENST00000606813.1_RNA|MIER3_ENST00000409421.1_Silent_p.L188L			Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family member 3	251	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(2)|urinary_tract(1)	19		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)		GAAGTTCATATAATGCCTGGG	0.338																																					p.L251L		Atlas-SNP	.											.	MIER3	33	.	0			c.A753G						.						158	149	152					5																	56226567		2203	4300	6503	SO:0001819	synonymous_variant	166968	exon9			TTCATATAATGCC	BX537798	CCDS3973.2, CCDS75248.1	5q11.2	2009-03-19			ENSG00000155545	ENSG00000155545			26678	protein-coding gene	gene with protein product						12477932	Standard	XM_005248448		Approved	FLJ35954, DKFZp686L09111, DKFZp781I1119	uc003jra.1	Q7Z3K6	OTTHUMG00000059589	ENST00000381199.3:c.753A>G	chr5.hg19:g.56226567T>C		55.0	0.0		66.0	33.0	NM_152622	B4DRI9|B8ZZQ0|Q5CZI0|Q68CS3|Q6MZS7|Q86YG8|Q8NA13	Silent	SNP	ENST00000381199.3	hg19																																																																																				.	.		0.338	MIER3-004	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000132523.2	NM_152622		C	56226567	T	C	56226567	2	2	203	1	0	0	0	0	0	0	0	1	9591	1403	49	2		2	MIER3	5	56226567	Silent	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10		56226567	124688693	32	29737										
MAST4	375449	hgsc.bcm.edu	37	chr5	66391445	66391445	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gactgatggacgccgctggtCgttggcttctctcccttcct	11	14	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr5:66391445C>G	ENST00000403625.2	+	7	1149	c.854C>G	c.(853-855)tCg>tGg	p.S285W	MAST4_ENST00000490016.2_Missense_Mutation_p.S96W|MAST4_ENST00000405643.1_Missense_Mutation_p.S106W|MAST4_ENST00000261569.7_Missense_Mutation_p.S91W|MAST4_ENST00000404260.3_Missense_Mutation_p.S288W|MAST4_ENST00000403666.1_Missense_Mutation_p.S96W	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	288						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CGCCGCTGGTCGTTGGCTTCT	0.473																																					p.S285W		Atlas-SNP	.											.	MAST4	218	.	0			c.C854G						.						81	87	85					5																	66391445		1975	4165	6140	SO:0001583	missense	375449	exon7			GCTGGTCGTTGGC	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.854C>G	chr5.hg19:g.66391445C>G	ENSP00000385727:p.Ser285Trp	91.0	0.0		97.0	27.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732024	0.89390	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000490016;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000436277;ENST00000432399	T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92	6.04	6.04	0.98038	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.000000	0.50627	U	0.000113	T	0.75148	0.3810	M	0.92459	3.31	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999	T	0.79820	-0.1642	10	0.87932	D	0	-11.1109	20.5948	0.99439	0.0:1.0:0.0:0.0	.	106;288;91;96;96	E7EWQ5;O15021;O15021-2;O15021-3;D6RAK1	.;MAST4_HUMAN;.;.;.	W	288;285;96;96;106;106;91;91;91	ENSP00000385048:S288W;ENSP00000385727:S285W;ENSP00000421739:S96W;ENSP00000384313:S96W;ENSP00000384099:S106W;ENSP00000261569:S91W;ENSP00000392478:S91W	ENSP00000261569:S91W	S	+	2	0	MAST4	66427201	1.000000	0.71417	0.970000	0.41538	0.930000	0.56654	7.487000	0.81328	2.873000	0.98535	0.563000	0.77884	TCG	.	.		0.473	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			G	66391445	C	G	66391445	3	3	203	1	0	0	0	0	1	0	0	0	9336	893	31	4	1010	4	MAST4	5	66391445	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	10164878	66391445	114523815	33	29738										
F2RL1	2150	hgsc.bcm.edu	37	chr5	76129080	76129080	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tatgtcgtgaagcagaccatCttcattcctgccctgaacat	7	12	2	3	rs535468564		TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr5:76129080C>T	ENST00000296677.4	+	2	854	c.648C>T	c.(646-648)atC>atT	p.I216I		NM_005242.4	NP_005233	P55085	PAR2_HUMAN	coagulation factor II (thrombin) receptor-like 1	216					blood coagulation (GO:0007596)|chemokine (C-C motif) ligand 2 secretion (GO:0035926)|chemokine secretion (GO:0090195)|defense response to virus (GO:0051607)|establishment of endothelial barrier (GO:0061028)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|interleukin-1 beta secretion (GO:0050702)|interleukin-10 secretion (GO:0072608)|leukocyte migration (GO:0050900)|leukocyte proliferation (GO:0070661)|mature dendritic cell differentiation (GO:0097029)|negative regulation of chemokine secretion (GO:0090198)|negative regulation of JNK cascade (GO:0046329)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neutrophil activation (GO:0042119)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of cell migration (GO:0030335)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of eosinophil degranulation (GO:0043311)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JNK cascade (GO:0046330)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of neutrophil mediated killing of gram-negative bacterium (GO:0070963)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasodilation (GO:0045909)|regulation of blood coagulation (GO:0030193)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of JNK cascade (GO:0046328)|T cell activation involved in immune response (GO:0002286)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	13		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;7.7e-51)|Epithelial(54;2.77e-45)|all cancers(79;3.47e-41)		AGCAGACCATCTTCATTCCTG	0.498																																					p.I216I		Atlas-SNP	.											.	F2RL1	46	.	0			c.C648T						.						128	112	117					5																	76129080		2203	4300	6503	SO:0001819	synonymous_variant	2150	exon2			GACCATCTTCATT	BC018130	CCDS4033.1	5q13	2012-08-08			ENSG00000164251	ENSG00000164251		"GPCR / Class A : Protease activated receptors"	3538	protein-coding gene	gene with protein product	"proteinase-activated receptor-2"	600933		GPR11		7937743, 7556175	Standard	NM_005242		Approved	PAR2	uc003keo.3	P55085	OTTHUMG00000102118	ENST00000296677.4:c.648C>T	chr5.hg19:g.76129080C>T		113.0	0.0		105.0	42.0	NM_005242	Q13317|Q13346|Q53XJ8	Silent	SNP	ENST00000296677.4	hg19	CCDS4033.1																																																																																			.	.		0.498	F2RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219957.2			T	76129080	C	T	76129080	2	4	203	1	0	0	0	0	0	0	0	1	5346	903	32	3		3	F2RL1	5	76129080	Silent	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	9737635	76129080	104786180	34	29739										
RASGRF2	5924	hgsc.bcm.edu	37	chr5	80513281	80513281	+	Frame_Shift_Del	DEL	A	A	-													0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	aaggccttgtcaatttctccAaaatgagaatggtaggtata							TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr5:80513281delA	ENST00000265080.4	+	25	3608	c.3541delA	c.(3541-3543)aaafs	p.K1181fs	CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000503483.2_RNA	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	1181	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		CAATTTCTCCAAAATGAGAAT	0.378																																					p.S1180fs		Atlas-INDEL	.											.	RASGRF2	165	.	0			c.3540delC						.						108	111	110					5																	80513281		2203	4300	6503	SO:0001589	frameshift_variant	5924	exon25			.	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.3541delA	chr5.hg19:g.80513281delA	ENSP00000265080:p.Lys1181fs	105.0	0.0		82.0	25.0	NM_006909	B9EG89|Q9UK56	Frame_Shift_Del	DEL	ENST00000265080.4	hg19	CCDS4052.1																																																																																			.	.		0.378	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		-	80513281	A	-	80513281	7	5	203	1	0	1	0	1	0	0	0	0	13088	131	5	0	3639	0	RASGRF2	5	80513281	Frame_Shift_Del	DEL	A	TCGA-DD-AADV-01A-11D-A38X-10	4384201	80513281	100401979	35	29740	152	2								
RASGRF2	5924	hgsc.bcm.edu	37	chr5	80513290	80513290	+	Missense_Mutation	SNP	A	A	C													0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tcaatttctccaaaatgagaAtggtaggtataatttcataa							TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr5:80513290A>C	ENST00000265080.4	+	25	3617	c.3550A>C	c.(3550-3552)Atg>Ctg	p.M1184L	CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000503483.2_RNA	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	1184	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		CAAAATGAGAATGGTAGGTAT	0.353																																					p.M1184L		Atlas-SNP	.											.	RASGRF2	165	.	0			c.A3550C						.						102	104	104					5																	80513290		2203	4300	6503	SO:0001583	missense	5924	exon25			ATGAGAATGGTAG	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.3550A>C	chr5.hg19:g.80513290A>C	ENSP00000265080:p.Met1184Leu	96.0	0.0		80.0	25.0	NM_006909	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	hg19	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.598716	0.87055	.	.	ENSG00000113319	ENST00000265080	T	0.29397	1.57	6.03	6.03	0.97812	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.29684	0.0741	L	0.45470	1.425	0.58432	D	0.999999	B	0.31655	0.334	B	0.27262	0.078	T	0.03374	-1.1043	10	0.44086	T	0.13	.	16.2196	0.82251	1.0:0.0:0.0:0.0	.	1184	O14827	RGRF2_HUMAN	L	1184	ENSP00000265080:M1184L	ENSP00000265080:M1184L	M	+	1	0	RASGRF2	80549046	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.339000	0.96797	2.308000	0.77769	0.533000	0.62120	ATG	.	.		0.353	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		C	80513290	A	C	80513290	3	2	203	1	0	0	0	0	1	0	0	0	13088	101	4	5	3648	5	RASGRF2	5	80513290	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	9	80513290	100401970	36	29741	152	2								
ARRDC3	57561	hgsc.bcm.edu	37	chr5	90670042	90670042	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tagaggaatggtaccgatgaCaagtggcaaattaagaaata	11	4	0	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr5:90670042C>T	ENST00000265138.3	-	6	1188	c.922G>A	c.(922-924)Gtc>Atc	p.V308I	ARRDC3_ENST00000503192.1_5'Flank	NM_020801.2	NP_065852.1	Q96B67	ARRD3_HUMAN	arrestin domain containing 3	308					fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659)	endosome (GO:0005768)|plasma membrane (GO:0005886)	beta-3 adrenergic receptor binding (GO:0031699)			breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	18		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		GTACCGATGACAAGTGGCAAA	0.373																																					p.V308I		Atlas-SNP	.											.	ARRDC3	56	.	0			c.G922A						.						153	148	150					5																	90670042		2203	4300	6503	SO:0001583	missense	57561	exon6			CGATGACAAGTGG	AB037797	CCDS34202.1	5q14.3	2013-10-11			ENSG00000113369	ENSG00000113369			29263	protein-coding gene	gene with protein product	"alpha-arrestin 3"	612464				10718198, 19605364	Standard	NM_020801		Approved	KIAA1376	uc003kjz.2	Q96B67	OTTHUMG00000162616	ENST00000265138.3:c.922G>A	chr5.hg19:g.90670042C>T	ENSP00000265138:p.Val308Ile	276.0	0.0		259.0	76.0	NM_020801	A8K6T8|Q9P2H1	Missense_Mutation	SNP	ENST00000265138.3	hg19	CCDS34202.1	.	.	.	.	.	.	.	.	.	.	C	35	5.551442	0.96501	.	.	ENSG00000113369	ENST00000265138	T	0.06528	3.29	6.02	6.02	0.97574	Immunoglobulin E-set (1);Arrestin-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.24198	0.0586	L	0.58428	1.81	0.80722	D	1	D	0.63046	0.992	D	0.77004	0.989	T	0.00010	-1.2456	10	0.40728	T	0.16	-26.8126	20.5373	0.99239	0.0:1.0:0.0:0.0	.	308	Q96B67	ARRD3_HUMAN	I	308	ENSP00000265138:V308I	ENSP00000265138:V308I	V	-	1	0	ARRDC3	90705798	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.857000	0.98124	0.650000	0.86243	GTC	.	.		0.373	ARRDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369763.2	NM_020801		T	90670042	C	T	90670042	3	4	203	1	0	0	0	0	1	0	0	0	984	478	17	3	334	3	ARRDC3	5	90670042	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	10156752	90670042	90245218	37	29742										
MYOT	9499	hgsc.bcm.edu	37	chr5	137221803	137221803	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	caaaaaagttttagagggagAttcagtgaaactagaatgcc	10	5	1	4			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr5:137221803A>G	ENST00000239926.4	+	8	1465	c.1091A>G	c.(1090-1092)gAt>gGt	p.D364G	MYOT_ENST00000421631.2_Missense_Mutation_p.D180G|RP11-381K20.2_ENST00000508281.2_RNA|MYOT_ENST00000515645.1_Missense_Mutation_p.D249G|RP11-381K20.2_ENST00000514616.1_RNA	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	364	Ig-like C2-type 2.|Necessary for interaction with ACTA1.|Necessary for interaction with FLNC.				muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)			cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTAGAGGGAGATTCAGTGAAA	0.333																																					p.D364G		Atlas-SNP	.											.	MYOT	50	.	0			c.A1091G						.						74	80	78					5																	137221803		2203	4300	6503	SO:0001583	missense	9499	exon8			AGGGAGATTCAGT	AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"Immunoglobulin superfamily / I-set domain containing"	12399	protein-coding gene	gene with protein product		604103	"titin immunoglobulin domain protein (myotilin)", "limb-girdle muscular dystrophy 1A (autosomal dominant)"	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.1091A>G	chr5.hg19:g.137221803A>G	ENSP00000239926:p.Asp364Gly	443.0	0.0		586.0	244.0	NM_006790	A0A4R6|B4DT79	Missense_Mutation	SNP	ENST00000239926.4	hg19	CCDS4194.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.391477	0.62066	.	.	ENSG00000120729	ENST00000239926;ENST00000421631;ENST00000515645	T;T;T	0.42900	0.96;0.96;0.96	5.0	5.0	0.66597	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.640625	0.14933	N	0.289971	T	0.40145	0.1105	N	0.25647	0.755	0.45239	D	0.998243	P	0.44044	0.825	P	0.46362	0.514	T	0.32929	-0.9888	10	0.56958	D	0.05	.	14.9908	0.71387	1.0:0.0:0.0:0.0	.	364	Q9UBF9	MYOTI_HUMAN	G	364;180;249	ENSP00000239926:D364G;ENSP00000391185:D180G;ENSP00000426281:D249G	ENSP00000239926:D364G	D	+	2	0	MYOT	137249702	1.000000	0.71417	0.899000	0.35326	0.870000	0.49936	4.638000	0.61353	2.007000	0.58848	0.482000	0.46254	GAT	.	.		0.333	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	NM_006790		G	137221803	A	G	137221803	3	3	203	1	0	0	0	0	1	0	0	0	10103	333	12	2	1117	2	MYOT	5	137221803	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	46551761	137221803	43693457	38	29743										
GNPDA1	10007	hgsc.bcm.edu	37	chr5	141385881	141385881	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tggtaactctccgggtggtcTcgaggaaggcctgtggggcc	17	10	2	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr5:141385881T>C	ENST00000508177.1	-	3	995	c.237A>G	c.(235-237)cgA>cgG	p.R79R	GNPDA1_ENST00000503794.1_Silent_p.R79R|GNPDA1_ENST00000513454.1_Silent_p.R79R|GNPDA1_ENST00000311337.6_Silent_p.R79R|GNPDA1_ENST00000500692.2_Silent_p.R79R|GNPDA1_ENST00000542860.1_Intron|GNPDA1_ENST00000458112.2_Silent_p.R45R			P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1	79					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucosamine catabolic process (GO:0006043)|N-acetylglucosamine metabolic process (GO:0006044)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glucosamine-6-phosphate deaminase activity (GO:0004342)|hydrolase activity (GO:0016787)			central_nervous_system(1)|lung(1)|skin(3)|stomach(1)	6		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGGGTGGTCTCGAGGAAGGC	0.542																																					p.R79R		Atlas-SNP	.											.	GNPDA1	16	.	0			c.A237G						.						155	141	145					5																	141385881		2203	4300	6503	SO:0001819	synonymous_variant	10007	exon4			GTGGTCTCGAGGA	AF048826	CCDS4272.1	5q21	2008-02-05	2003-10-17	2003-10-22	ENSG00000113552	ENSG00000113552	3.5.99.6		4417	protein-coding gene	gene with protein product	"glucosamine-6-phosphate deaminase", "oscillin"	601798	"glucosamine-6-phosphate isomerase"	GNPI		9714720, 9438414	Standard	NM_005471		Approved	GNPDA, HLN, GPI, KIAA0060	uc010jgh.3	P46926	OTTHUMG00000129657	ENST00000508177.1:c.237A>G	chr5.hg19:g.141385881T>C		56.0	0.0		84.0	43.0	NM_005471	B7Z3X4|D3DQE7	Silent	SNP	ENST00000508177.1	hg19	CCDS4272.1																																																																																			.	.		0.542	GNPDA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370631.1	NM_005471		C	141385881	T	C	141385881	2	2	203	1	0	0	0	0	0	0	0	1	6550	1538	54	2		2	GNPDA1	5	141385881	Silent	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	4164078	141385881	39529379	39	29744										
DSP	1832	hgsc.bcm.edu	37	chr6	7583810	7583810	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ccattttcaggcaagacagtAtctgtttcagaagccatcaa	7	10	4	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr6:7583810A>G	ENST00000379802.3	+	24	6656	c.6315A>G	c.(6313-6315)gtA>gtG	p.V2105V	DSP_ENST00000418664.2_Silent_p.V1506V	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2105	4.5 X 38 AA tandem repeats (Domain A).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GCAAGACAGTATCTGTTTCAG	0.458																																					p.V2105V		Atlas-SNP	.											.	DSP	306	.	0			c.A6315G						.						97	104	101					6																	7583810		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon24			GACAGTATCTGTT	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.6315A>G	chr6.hg19:g.7583810A>G		98.0	0.0		139.0	9.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.458	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		G	7583810	A	G	7583810	2	3	203	1	0	0	0	0	0	0	0	1	4783	436	16	2		2	DSP	6	7583810	Silent	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10		7583810	163531257	40	29745										
HIST1H2AG	8969	hgsc.bcm.edu	37	chr6	27100855	27100855	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gtgagttgcgctcgctatgtCtggacgtggcaagcagggag	17	8	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr6:27100855C>G	ENST00000359193.2	+	1	24	c.5C>G	c.(4-6)tCt>tGt	p.S2C	HIST1H2BJ_ENST00000607124.1_5'Flank|HIST1H2BJ_ENST00000541790.1_5'Flank|HIST1H2BJ_ENST00000339812.2_5'Flank	NM_021064.4	NP_066408.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ag	2						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	17						CTCGCTATGTCTGGACGTGGC	0.577																																					p.S2C		Atlas-SNP	.											.	HIST1H2AG	37	.	0			c.C5G						.						41	47	45					6																	27100855		2198	4299	6497	SO:0001583	missense	8969	exon1			CTATGTCTGGACG	L19778	CCDS4619.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000196787	ENSG00000196787		"Histones / Replication-dependent"	4737	protein-coding gene	gene with protein product		615012	"H2A histone family, member P", "histone 1, H2ag"	H2AFP		8179821, 12408966	Standard	NM_021064		Approved	pH2A/f, H2A/p, H2A.1b	uc003niw.3	P0C0S8	OTTHUMG00000014469	ENST00000359193.2:c.5C>G	chr6.hg19:g.27100855C>G	ENSP00000352119:p.Ser2Cys	89.0	0.0		113.0	74.0	NM_021064	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000359193.2	hg19	CCDS4619.1	.	.	.	.	.	.	.	.	.	.	C	5.514	0.279826	0.10458	.	.	ENSG00000196787	ENST00000359193	D	0.92965	-3.14	4.08	4.08	0.47627	Histone-fold (2);	0.000000	0.39834	N	0.001245	D	0.82421	0.5033	.	.	.	0.23865	N	0.996624	B	0.33583	0.418	B	0.28553	0.091	T	0.79909	-0.1604	9	0.87932	D	0	.	14.6102	0.68510	0.0:1.0:0.0:0.0	.	2	P0C0S8	H2A1_HUMAN	C	2	ENSP00000352119:S2C	ENSP00000352119:S2C	S	+	2	0	HIST1H2AG	27208834	0.979000	0.34478	1.000000	0.80357	0.167000	0.22549	2.541000	0.45735	2.217000	0.71921	0.655000	0.94253	TCT	.	.		0.577	HIST1H2AG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040137.1	NM_021064		G	27100855	C	G	27100855	3	3	203	1	0	0	0	0	1	0	0	0	7142	913	32	4	7	4	HIST1H2AG	6	27100855	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	19517045	27100855	144014212	41	29746										
ANKS1A	23294	hgsc.bcm.edu	37	chr6	34935067	34935067	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gacagcactggctacacaccCctgcaccatgctgctttgaa	8	15	0	1	rs147758055	byFrequency	TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr6:34935067C>A	ENST00000360359.3	+	2	387	c.249C>A	c.(247-249)ccC>ccA	p.P83P	ANKS1A_ENST00000535627.1_Silent_p.P83P	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	83					ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						GCTACACACCCCTGCACCATG	0.458																																					p.P83P		Atlas-SNP	.											.	ANKS1A	123	.	0			c.C249A						.						239	204	216					6																	34935067		2203	4300	6503	SO:0001819	synonymous_variant	23294	exon2			CACACCCCTGCAC	D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20961	protein-coding gene	gene with protein product		608994	"ankyrin repeat and SAM domain containing 1", "ankyrin repeat and sterile alpha motif domain containing 1"	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.249C>A	chr6.hg19:g.34935067C>A		65.0	0.0		130.0	7.0	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Silent	SNP	ENST00000360359.3	hg19	CCDS4798.1																																																																																			.	C|0.998;G|0.002		0.458	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		A	34935067	C	A	34935067	2	1	203	1	0	0	0	0	0	0	0	1	688	610	22	3		3	ANKS1A	6	34935067	Silent	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	7834212	34935067	136180000	42	29747										
TINAG	27283	hgsc.bcm.edu	37	chr6	54219431	54219431	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gacacatgcagtcaaactcaCtgggtaaggcaattaaacaa	8	9	2	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr6:54219431C>T	ENST00000259782.4	+	9	1343	c.1247C>T	c.(1246-1248)aCt>aTt	p.T416I		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	416					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			GTCAAACTCACTGGGTAAGGC	0.323																																					p.T416I		Atlas-SNP	.											.	TINAG	102	.	0			c.C1247T						.						46	46	46					6																	54219431		2200	4296	6496	SO:0001583	missense	27283	exon9			AACTCACTGGGTA	AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.1247C>T	chr6.hg19:g.54219431C>T	ENSP00000259782:p.Thr416Ile	300.0	0.0		385.0	196.0	NM_014464	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	hg19	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	C	0.978	-0.697870	0.03279	.	.	ENSG00000137251	ENST00000339741;ENST00000259782;ENST00000370865	D	0.82433	-1.61	5.54	4.63	0.57726	Peptidase C1A, papain C-terminal (2);	0.769005	0.12491	N	0.464255	T	0.49098	0.1537	N	0.05012	-0.13	0.80722	D	1	B	0.24043	0.096	B	0.28385	0.089	T	0.41070	-0.9529	10	0.11794	T	0.64	.	11.5766	0.50864	0.0:0.9072:0.0:0.0928	.	416	Q9UJW2	TINAG_HUMAN	I	275;416;95	ENSP00000259782:T416I	ENSP00000259782:T416I	T	+	2	0	TINAG	54327390	1.000000	0.71417	0.995000	0.50966	0.368000	0.29767	2.746000	0.47467	1.379000	0.46325	-0.345000	0.07892	ACT	.	.		0.323	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		T	54219431	C	T	54219431	3	4	203	1	0	0	0	0	1	0	0	0	15936	565	20	3	1281	3	TINAG	6	54219431	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	19284364	54219431	116895636	43	29748										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84269885	84269885	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	catgggctgtgcaaacatgaCcggctgctgaggcatcatgg	14	10	1	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr6:84269885C>T	ENST00000439399.2	-	28	2885	c.2569G>A	c.(2569-2571)Gtc>Atc	p.V857I	SNAP91_ENST00000428679.2_Missense_Mutation_p.V857I|SNAP91_ENST00000369694.2_Missense_Mutation_p.V857I|SNAP91_ENST00000437520.1_Missense_Mutation_p.V550I|SNAP91_ENST00000521743.1_Missense_Mutation_p.V857I|SNAP91_ENST00000195649.6_Missense_Mutation_p.V852I|SNAP91_ENST00000520302.1_Missense_Mutation_p.V827I|SNAP91_ENST00000520213.1_Missense_Mutation_p.V550I|SNAP91_ENST00000521485.1_Missense_Mutation_p.V852I	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	857	Pro-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		GCAAACATGACCGGCTGCTGA	0.547																																					p.V857I		Atlas-SNP	.											.	SNAP91	199	.	0			c.G2569A						.						70	71	70					6																	84269885		1978	4160	6138	SO:0001583	missense	9892	exon27			ACATGACCGGCTG	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.2569G>A	chr6.hg19:g.84269885C>T	ENSP00000400459:p.Val857Ile	216.0	0.0		172.0	93.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.291387	0.59976	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000437520;ENST00000520302;ENST00000521743;ENST00000520213;ENST00000523448	T;T;T;T;T;T;T;T;T;T	0.25250	2.38;2.39;2.39;2.38;2.39;2.41;2.39;2.39;2.41;1.81	5.75	5.75	0.90469	.	0.167400	0.50627	D	0.000102	T	0.30665	0.0772	L	0.52573	1.65	0.20196	N	0.999926	B;P;P;P;P	0.50156	0.363;0.902;0.932;0.932;0.932	B;D;P;P;P	0.64595	0.138;0.927;0.891;0.891;0.891	T	0.10200	-1.0640	10	0.62326	D	0.03	-14.8755	12.2765	0.54739	0.0:0.9232:0.0:0.0768	.	733;550;827;857;855	B7Z2N2;O60641-3;E5RI02;O60641;E1P549	.;.;.;AP180_HUMAN;.	I	852;857;857;852;857;550;827;857;550;198	ENSP00000429776:V852I;ENSP00000358708:V857I;ENSP00000400459:V857I;ENSP00000195649:V852I;ENSP00000412492:V857I;ENSP00000413277:V550I;ENSP00000428511:V827I;ENSP00000428215:V857I;ENSP00000428026:V550I;ENSP00000430255:V198I	ENSP00000195649:V852I	V	-	1	0	SNAP91	84326604	0.999000	0.42202	0.964000	0.40570	0.805000	0.45488	4.222000	0.58580	2.719000	0.93026	0.655000	0.94253	GTC	.	.		0.547	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			T	84269885	C	T	84269885	3	4	203	1	0	0	0	0	1	0	0	0	14848	507	18	3	162	3	SNAP91	6	84269885	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	30050454	84269885	86845182	44	29749										
SDK1	221935	hgsc.bcm.edu	37	chr7	4153005	4153005	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cagaccctgcaggccccaccCgacgtggctccaaccagcgt	10	19	0	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr7:4153005C>G	ENST00000404826.2	+	24	3658	c.3519C>G	c.(3517-3519)ccC>ccG	p.P1173P	SDK1_ENST00000389531.3_Silent_p.P1173P	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1173					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AGGCCCCACCCGACGTGGCTC	0.607																																					p.P1173P		Atlas-SNP	.											.	SDK1	361	.	0			c.C3519G						.						118	126	123					7																	4153005		2203	4300	6503	SO:0001819	synonymous_variant	221935	exon24			CCCACCCGACGTG	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.3519C>G	chr7.hg19:g.4153005C>G		30.0	0.0		55.0	15.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	hg19	CCDS34590.1																																																																																			.	.		0.607	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		G	4153005	C	G	4153005	2	3	203	1	0	0	0	0	0	0	0	1	13983	639	23	4		4	SDK1	7	4153005	Silent	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10		4153005	154985658	45	29750										
OCM	654231	hgsc.bcm.edu	37	chr7	5923521	5923521	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ggatctttattatcctgtagGtttttcctccagaagtttga	8	7	1	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr7:5923521G>T	ENST00000242104.5	+	3	287	c.195G>T	c.(193-195)aaG>aaT	p.K65N	OCM_ENST00000416608.1_Splice_Site_p.K65N	NM_001097622.1	NP_001091091.1	P0CE72	ONCO_HUMAN	oncomodulin	65	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(2)	6		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0978)|OV - Ovarian serous cystadenocarcinoma(56;2.11e-14)		TATCCTGTAGGTTTTTCCTCC	0.428																																					p.K65N		Atlas-SNP	.											.	OCM	13	.	0			c.G195T						.						39	39	39					7																	5923521		2203	4300	6503	SO:0001630	splice_region_variant	654231	exon3			CTGTAGGTTTTTC	BC069468	CCDS43548.1	7p22.1	2013-01-10						"EF-hand domain containing"	8105	protein-coding gene	gene with protein product	"oncomodulin 1"	164795				1559707, 8354278	Standard	NM_001097622		Approved	OCM1	uc003spe.4	P0CE72		ENST00000242104.5:c.195-1G>T	chr7.hg19:g.5923521G>T		143.0	0.0		159.0	62.0	NM_001097622	B9EJH7|P32930|Q6ISI5|Q75MW0	Missense_Mutation	SNP	ENST00000242104.5	hg19	CCDS43548.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.831328	0.71258	.	.	ENSG00000122543	ENST00000416608;ENST00000242104	T;T	0.72725	-0.68;-0.68	4.21	4.21	0.49690	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.82226	0.4991	M	0.87758	2.905	0.47621	D	0.999471	D	0.57257	0.979	P	0.55222	0.771	D	0.85881	0.1422	9	.	.	.	.	15.5278	0.75925	0.0:0.0:1.0:0.0	.	65	P0CE72	ONCO_HUMAN	N	65	ENSP00000401365:K65N;ENSP00000242104:K65N	.	K	+	3	2	OCM	5890047	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.145000	0.50623	2.065000	0.61736	0.502000	0.49764	AAG	.	.		0.428	OCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340372.1	NM_001097622	Missense_Mutation	T	5923521	G	T	5923521	5	4	203	1	0	0	0	0	0	0	1	0	10830	1275	44	3	205	3	OCM	7	5923521	Splice_Site	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	1770516	5923521	153215142	46	29751										
C1GALT1	56913	hgsc.bcm.edu	37	chr7	7278123	7278123	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	aacaattaaagcttttcagtAtgttcatgaacattatttag	5	5	2	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr7:7278123A>G	ENST00000223122.3	+	2	520	c.458A>G	c.(457-459)tAt>tGt	p.Y153C	C1GALT1_ENST00000402468.3_Missense_Mutation_p.Y153C|C1GALT1_ENST00000436587.2_Missense_Mutation_p.Y153C			Q9NS00	C1GLT_HUMAN	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1	153					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|kidney development (GO:0001822)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity (GO:0016263)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|lung(3)|prostate(1)|urinary_tract(1)	7				UCEC - Uterine corpus endometrioid carcinoma (126;0.177)		GCTTTTCAGTATGTTCATGAA	0.348																																					p.Y153C		Atlas-SNP	.											.	C1GALT1	24	.	0			c.A458G						.						68	69	69					7																	7278123		2203	4299	6502	SO:0001583	missense	56913	exon3			TTCAGTATGTTCA	AF155582	CCDS5355.1	7p21.3	2014-06-24	2014-06-24		ENSG00000106392	ENSG00000106392	2.4.1.122	"Beta 3-glycosyltransferases"	24337	protein-coding gene	gene with protein product	"core 1 beta3-Gal-T"	610555				10580128, 11677243	Standard	NM_020156		Approved	C1GALT, T-synthase	uc003srb.3	Q9NS00	OTTHUMG00000151912	ENST00000223122.3:c.458A>G	chr7.hg19:g.7278123A>G	ENSP00000223122:p.Tyr153Cys	200.0	0.0		224.0	98.0	NM_020156	Q96QH4|Q9BTU1	Missense_Mutation	SNP	ENST00000223122.3	hg19	CCDS5355.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.401907	0.62288	.	.	ENSG00000106392	ENST00000436587;ENST00000223122;ENST00000402468	T;T;T	0.62941	-0.01;-0.01;-0.01	5.42	5.42	0.78866	.	0.113557	0.64402	D	0.000008	T	0.81475	0.4830	H	0.95224	3.64	0.58432	D	0.999999	P;P	0.35908	0.471;0.527	P;P	0.48552	0.5;0.581	D	0.84725	0.0742	9	.	.	.	-14.7763	15.7732	0.78187	1.0:0.0:0.0:0.0	.	153;153	Q9NS00-2;Q9NS00	.;C1GLT_HUMAN	C	153	ENSP00000389176:Y153C;ENSP00000223122:Y153C;ENSP00000384550:Y153C	.	Y	+	2	0	C1GALT1	7244648	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.339000	0.96797	2.193000	0.70182	0.528000	0.53228	TAT	.	.		0.348	C1GALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324379.2	NM_020156		G	7278123	A	G	7278123	3	3	203	1	0	0	0	0	1	0	0	0	1954	449	16	2	464	2	C1GALT1	7	7278123	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	1354602	7278123	151860540	47	29752										
PPP1R9A	55607	hgsc.bcm.edu	37	chr7	94897973	94897973	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	accctctaggacaagactgtAtgatagtgttagttccacag	9	9	1	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr7:94897973A>G	ENST00000433881.1	+	12	3243	c.2711A>G	c.(2710-2712)tAt>tGt	p.Y904C	PPP1R9A_ENST00000289495.5_Missense_Mutation_p.Y904C|PPP1R9A_ENST00000424654.1_Missense_Mutation_p.Y904C|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.Y926C|PPP1R9A_ENST00000456331.2_Missense_Mutation_p.Y904C|PPP1R9A_ENST00000340694.4_Missense_Mutation_p.Y904C			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	904	Interacts with TGN38. {ECO:0000250}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			ACAAGACTGTATGATAGTGTT	0.493										HNSCC(28;0.073)																											p.Y926C		Atlas-SNP	.											.	PPP1R9A	264	.	0			c.A2777G						.						107	91	97					7																	94897973		2203	4300	6503	SO:0001583	missense	55607	exon13			GACTGTATGATAG	AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Sterile alpha motif (SAM) domain containing"	14946	protein-coding gene	gene with protein product		602468	"protein phosphatase 1, regulatory (inhibitor) subunit 9A"			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.2711A>G	chr7.hg19:g.94897973A>G	ENSP00000398870:p.Tyr904Cys	118.0	0.0		133.0	50.0	NM_001166160	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Missense_Mutation	SNP	ENST00000433881.1	hg19	CCDS34683.1	.	.	.	.	.	.	.	.	.	.	A	7.782	0.709635	0.15239	.	.	ENSG00000158528	ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331	T;T;T;T;T;T	0.15017	2.49;2.5;2.46;2.5;2.46;2.46	5.58	4.44	0.53790	.	0.361985	0.26553	N	0.023730	T	0.06690	0.0171	N	0.02011	-0.69	0.35225	D	0.776395	B;B;B;B;B	0.23490	0.003;0.044;0.086;0.028;0.016	B;B;B;B;B	0.23419	0.005;0.025;0.046;0.014;0.006	T	0.19192	-1.0313	10	0.39692	T	0.17	.	8.7217	0.34445	0.8551:0.0:0.1449:0.0	.	904;904;926;904;904	B7ZLX4;F8W7J9;E9PDX1;E9PCK6;Q9ULJ8	.;.;.;.;NEB1_HUMAN	C	926;904;904;904;904;904	ENSP00000405514:Y926C;ENSP00000344524:Y904C;ENSP00000411342:Y904C;ENSP00000398870:Y904C;ENSP00000289495:Y904C;ENSP00000402893:Y904C	ENSP00000289495:Y904C	Y	+	2	0	PPP1R9A	94735909	1.000000	0.71417	0.999000	0.59377	0.017000	0.09413	5.223000	0.65283	1.070000	0.40811	0.533000	0.62120	TAT	.	.		0.493	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160		G	94897973	A	G	94897973	3	3	203	1	0	0	0	0	1	0	0	0	12390	449	16	2	2823	2	PPP1R9A	7	94897973	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	87619850	94897973	64240690	48	29753										
MCM7	4176	hgsc.bcm.edu	37	chr7	99695366	99695366	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cagcttttcgtagaaatcctCctctgtagagaagttaaggt	9	8	1	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr7:99695366C>G	ENST00000303887.5	-	9	1633	c.988G>C	c.(988-990)Gag>Cag	p.E330Q	MCM7_ENST00000343023.6_Intron|MCM7_ENST00000354230.3_Missense_Mutation_p.E154Q	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	330					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TAGAAATCCTCCTCTGTAGAG	0.493																																					p.E330Q		Atlas-SNP	.											.	MCM7	136	.	0			c.G988C						.						164	163	163					7																	99695366		2203	4300	6503	SO:0001583	missense	4176	exon9			AATCCTCCTCTGT		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.988G>C	chr7.hg19:g.99695366C>G	ENSP00000307288:p.Glu330Gln	60.0	0.0		94.0	54.0	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	hg19	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.847375	0.32606	.	.	ENSG00000166508	ENST00000303887;ENST00000542483;ENST00000362082;ENST00000354230	T;T	0.06849	3.25;3.25	4.88	4.88	0.63580	.	0.056300	0.64402	D	0.000001	T	0.13543	0.0328	L	0.56124	1.755	0.80722	D	1	B	0.25235	0.121	B	0.35971	0.215	T	0.05419	-1.0886	10	0.34782	T	0.22	-18.9757	15.5729	0.76354	0.0:1.0:0.0:0.0	.	330	P33993	MCM7_HUMAN	Q	330;267;223;154	ENSP00000307288:E330Q;ENSP00000346171:E154Q	ENSP00000307288:E330Q	E	-	1	0	MCM7	99533302	1.000000	0.71417	1.000000	0.80357	0.058000	0.15608	3.759000	0.55227	2.548000	0.85928	0.655000	0.94253	GAG	.	.		0.493	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			G	99695366	C	G	99695366	3	3	203	1	0	0	0	0	1	0	0	0	9401	864	30	4	1199	4	MCM7	7	99695366	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	4797393	99695366	59443297	49	29754										
C7orf43	55262	hgsc.bcm.edu	37	chr7	99755553	99755553	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gtggacacaatcggttcctcCacaggcagctggggttggga	15	10	0	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr7:99755553C>A	ENST00000316937.3	-	2	605	c.420G>T	c.(418-420)gtG>gtT	p.V140V	C7orf43_ENST00000498638.1_5'Flank|MIR4658_ENST00000584344.1_RNA|C7orf43_ENST00000457641.1_5'UTR|C7orf43_ENST00000419841.1_5'Flank|C7orf43_ENST00000394035.2_5'Flank	NM_018275.3	NP_060745.3	Q8WVR3	CG043_HUMAN	chromosome 7 open reading frame 43	140										breast(1)|endometrium(3)|large_intestine(3)|lung(2)|prostate(1)	10	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TCGGTTCCTCCACAGGCAGCT	0.562																																					p.V140V		Atlas-SNP	.											.	C7orf43	28	.	0			c.G420T						.						58	54	55					7																	99755553		2203	4300	6503	SO:0001819	synonymous_variant	55262	exon2			TTCCTCCACAGGC		CCDS5687.1	7q22.1	2011-11-25			ENSG00000146826	ENSG00000146826			25604	protein-coding gene	gene with protein product						12477932	Standard	NM_018275		Approved	FLJ10925	uc003utr.3	Q8WVR3	OTTHUMG00000154862	ENST00000316937.3:c.420G>T	chr7.hg19:g.99755553C>A		122.0	0.0		120.0	57.0	NM_018275	A4D2A9|D6W5U4|Q9BQJ1|Q9BUB6|Q9NV47	Silent	SNP	ENST00000316937.3	hg19	CCDS5687.1	.	.	.	.	.	.	.	.	.	.	C	9.711	1.156988	0.21454	.	.	ENSG00000146826	ENST00000456769	.	.	.	5.66	4.78	0.61160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.5687	7.4627	0.27304	0.1646:0.7513:0.0:0.0841	.	.	.	.	X	46	.	.	G	-	1	0	C7orf43	99593489	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.226000	0.42963	1.397000	0.46682	0.462000	0.41574	GGA	.	.		0.562	C7orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337395.2	NM_018275		A	99755553	C	A	99755553	2	1	203	1	0	0	0	0	0	0	0	1	2395	581	21	3		3	C7orf43	7	99755553	Silent	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	60187	99755553	59383110	50	29755										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	146536812	146536812	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cccatcttcaggtgctggggGatggtctccatcagacagcg	13	12	4	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr7:146536812G>A	ENST00000361727.3	+	3	734	c.218G>A	c.(217-219)gGa>gAa	p.G73E		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	73	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			GGTGCTGGGGGATGGTCTCCA	0.428										HNSCC(39;0.1)																											p.G73E		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.G218A						.						73	64	67					7																	146536812		2203	4300	6503	SO:0001583	missense	26047	exon3			CTGGGGGATGGTC	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.218G>A	chr7.hg19:g.146536812G>A	ENSP00000354778:p.Gly73Glu	75.0	0.0		103.0	53.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	hg19	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.922169	0.92319	.	.	ENSG00000174469	ENST00000361727	D	0.97480	-4.4	5.83	5.83	0.93111	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.000000	0.53938	D	0.000046	D	0.98918	0.9633	M	0.93328	3.405	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99537	1.0962	10	0.87932	D	0	.	18.6885	0.91574	0.0:0.0:1.0:0.0	.	73	Q9UHC6	CNTP2_HUMAN	E	73	ENSP00000354778:G73E	ENSP00000354778:G73E	G	+	2	0	CNTNAP2	146167745	1.000000	0.71417	0.990000	0.47175	0.982000	0.71751	9.869000	0.99810	2.760000	0.94817	0.650000	0.86243	GGA	.	.		0.428	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			A	146536812	G	A	146536812	3	1	203	1	0	0	0	0	1	0	0	0	3649	1174	41	3	228	3	CNTNAP2	7	146536812	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	46781259	146536812	12601851	51	29756										
PTPRN2	5799	hgsc.bcm.edu	37	chr7	158109583	158109583	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cgacacctcgtagcggtaaaAgtccattgccggaaccttct	9	13	1	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr7:158109583A>T	ENST00000389418.4	-	3	214	c.205T>A	c.(205-207)Ttt>Att	p.F69I	PTPRN2_ENST00000389413.3_Missense_Mutation_p.F69I|PTPRN2_ENST00000409483.1_Intron|PTPRN2_ENST00000404321.2_Missense_Mutation_p.F92I|PTPRN2_ENST00000389416.4_Missense_Mutation_p.F52I	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	69					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TAGCGGTAAAAGTCCATTGCC	0.597																																					p.F69I		Atlas-SNP	.											.	PTPRN2	243	.	0			c.T205A						.						76	65	69					7																	158109583		2202	4300	6502	SO:0001583	missense	5799	exon3			GGTAAAAGTCCAT	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.205T>A	chr7.hg19:g.158109583A>T	ENSP00000374069:p.Phe69Ile	71.0	0.0		101.0	17.0	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	hg19	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	A	0.025	-1.380117	0.01204	.	.	ENSG00000155093	ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T	0.02737	4.22;4.22;4.22;4.18	4.82	-9.64	0.00541	.	.	.	.	.	T	0.01287	0.0042	N	0.08118	0	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.48990	-0.8985	9	0.18710	T	0.47	.	8.5094	0.33208	0.2125:0.5318:0.0:0.2556	.	92;69;52;69	Q92932-3;Q92932-2;E9PC57;Q92932	.;.;.;PTPR2_HUMAN	I	69;52;69;92	ENSP00000374064:F69I;ENSP00000374067:F52I;ENSP00000374069:F69I;ENSP00000385464:F92I	ENSP00000374064:F69I	F	-	1	0	PTPRN2	157802344	0.003000	0.15002	0.000000	0.03702	0.007000	0.05969	-0.175000	0.09825	-2.043000	0.00913	-1.670000	0.00746	TTT	.	.		0.597	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			T	158109583	A	T	158109583	3	4	203	1	0	0	0	0	1	0	0	0	12823	72	3	4	2926	4	PTPRN2	7	158109583	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	11572771	158109583	1029080	52	29757										
ADAM18	8749	hgsc.bcm.edu	37	chr8	39564320	39564320	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ctgtttcagatatgtaataaTtttggtaattgtcaatgctt	7	4	2	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr8:39564320T>C	ENST00000265707.5	+	18	1959	c.1914T>C	c.(1912-1914)aaT>aaC	p.N638N	ADAM18_ENST00000541111.1_Silent_p.N52N|ADAM18_ENST00000379866.1_Silent_p.N614N|ADAM18_ENST00000523755.1_3'UTR	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	638	EGF-like.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TATGTAATAATTTTGGTAATT	0.333																																					p.N638N		Atlas-SNP	.											.	ADAM18	169	.	0			c.T1914C						.						97	97	97					8																	39564320		2203	4300	6503	SO:0001819	synonymous_variant	8749	exon18			TAATAATTTTGGT	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1914T>C	chr8.hg19:g.39564320T>C		103.0	0.0		68.0	20.0	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Silent	SNP	ENST00000265707.5	hg19	CCDS6113.1																																																																																			.	.		0.333	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		C	39564320	T	C	39564320	2	2	203	1	0	0	0	0	0	0	0	1	239	1490	52	2		2	ADAM18	8	39564320	Silent	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10		39564320	106799702	53	29758										
ADCY8	114	hgsc.bcm.edu	37	chr8	131833593	131833593	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gaaatgttagattacctgctGtccatggtagaacacagcca	9	9	0	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr8:131833593G>A	ENST00000286355.5	-	13	4841	c.2749C>T	c.(2749-2751)Cag>Tag	p.Q917*	ADCY8_ENST00000377928.3_Nonsense_Mutation_p.Q786*	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	917					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			ATTACCTGCTGTCCATGGTAG	0.448										HNSCC(32;0.087)																											p.Q917X		Atlas-SNP	.											.	ADCY8	291	.	0			c.C2749T						.						104	80	88					8																	131833593		2203	4300	6503	SO:0001587	stop_gained	114	exon13			CCTGCTGTCCATG	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.2749C>T	chr8.hg19:g.131833593G>A	ENSP00000286355:p.Gln917*	103.0	0.0		100.0	50.0	NM_001115		Nonsense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	55	24.036052	0.99958	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	.	.	.	5.92	5.92	0.95590	.	0.055436	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	17.4903	0.87701	0.0:0.0:1.0:0.0	.	.	.	.	X	917;786	.	ENSP00000286355:Q917X	Q	-	1	0	ADCY8	131902775	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.315000	0.96313	2.822000	0.97130	0.650000	0.86243	CAG	.	.		0.448	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	131833593	G	A	131833593	4	1	203	1	0	0	0	0	0	1	0	0	300	1386	48	3	1030	3	ADCY8	8	131833593	Nonsense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	92269273	131833593	14530429	54	29759										
CUBN	8029	hgsc.bcm.edu	37	chr10	17147481	17147481	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	attgtccatttagacaggggTgacttaggcaaatattactg	10	6	0	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr10:17147481T>A	ENST00000377833.4	-	11	1270	c.1205A>T	c.(1204-1206)cAc>cTc	p.H402L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	402	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TAGACAGGGGTGACTTAGGCA	0.438																																					p.H402L		Atlas-SNP	.											.	CUBN	515	.	0			c.A1205T						.						166	147	153					10																	17147481		2203	4300	6503	SO:0001583	missense	8029	exon11			CAGGGGTGACTTA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1205A>T	chr10.hg19:g.17147481T>A	ENSP00000367064:p.His402Leu	98.0	0.0		100.0	16.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	11.59	1.685444	0.29872	.	.	ENSG00000107611	ENST00000377833	D	0.91945	-2.94	5.5	-0.839	0.10759	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.544198	0.15554	N	0.256275	D	0.82765	0.5108	L	0.27975	0.815	0.80722	D	1	P	0.35226	0.491	B	0.25614	0.062	T	0.72616	-0.4239	10	0.72032	D	0.01	.	9.8631	0.41127	0.0:0.3395:0.0:0.6605	.	402	O60494	CUBN_HUMAN	L	402	ENSP00000367064:H402L	ENSP00000367064:H402L	H	-	2	0	CUBN	17187487	0.993000	0.37304	0.071000	0.20095	0.388000	0.30384	0.627000	0.24506	-0.400000	0.07656	0.482000	0.46254	CAC	.	.		0.438	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	17147481	T	A	17147481	3	1	203	1	0	0	0	0	1	0	0	0	4053	1696	59	4	9894	4	CUBN	10	17147481	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10		17147481	118387266	55	29760										
KIAA0913	23053	hgsc.bcm.edu	37	chr10	75558879	75558879	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ttctggctgtatgagcaaacTgcaggtggctcatccacagc	11	11	2	1	rs35762168		TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr10:75558879T>C	ENST00000605216.1	+	21	4498	c.4281T>C	c.(4279-4281)acT>acC	p.T1427T	ZSWIM8_ENST00000604524.1_Intron|ZSWIM8_ENST00000603114.1_Silent_p.T1394T|ZSWIM8_ENST00000604729.1_Silent_p.T1432T|ZSWIM8-AS1_ENST00000456638.2_RNA|ZSWIM8_ENST00000398706.2_Silent_p.T1432T|RP11-574K11.31_ENST00000603027.1_Intron	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	1427							zinc ion binding (GO:0008270)										ATGAGCAAACTGCAGGTGGCT	0.597																																					p.T1432T		Atlas-SNP	.											.	.	.	.	0			c.T4296C						.						62	68	66					10																	75558879		2018	4174	6192	SO:0001819	synonymous_variant	23053	exon21			GCAAACTGCAGGT	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"Zinc fingers, SWIM-type"	23528	protein-coding gene	gene with protein product			"KIAA0913"	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.4281T>C	chr10.hg19:g.75558879T>C		131.0	0.0		121.0	54.0	NM_015037	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Silent	SNP	ENST00000605216.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.261|8.261	0.811139|0.811139	0.16537|0.16537	.|.	.|.	ENSG00000214655|ENSG00000214655	ENST00000433366|ENST00000412198	.|.	.|.	.|.	5.59|5.59	2.91|2.91	0.33838|0.33838	.|.	.|.	.|.	.|.	.|.	T|T	0.47116|0.47116	0.1428|0.1428	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.36016|0.36016	-0.9765|-0.9765	4|4	.|.	.|.	.|.	-4.6427|-4.6427	3.9776|3.9776	0.09481|0.09481	0.4765:0.0:0.1504:0.373|0.4765:0.0:0.1504:0.373	.|.	.|.	.|.	.|.	R|P	1143|702	.|.	.|.	C|L	+|+	1|2	0|0	KIAA0913|KIAA0913	75228885|75228885	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	0.729000|0.729000	0.26028|0.26028	0.945000|0.945000	0.37605|0.37605	-0.339000|-0.339000	0.08088|0.08088	TGC|CTG	.	.		0.597	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		C	75558879	T	C	75558879	2	2	203	1	0	0	0	0	0	0	0	1	8209	1567	55	2		2	KIAA0913	10	75558879	Silent	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	58411398	75558879	59975868	56	29761										
DLG5	9231	hgsc.bcm.edu	37	chr10	79581096	79581096	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ccacgtcagggggcagggcgCtcgggggactagtggatggg	21	9	1	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr10:79581096C>A	ENST00000372391.2	-	15	3151	c.3146G>T	c.(3145-3147)aGc>aTc	p.S1049I	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Intron	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1049	Pro-rich.				apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			GGGCAGGGCGCTCGGGGGACT	0.637																																					p.S1049I		Atlas-SNP	.											.	DLG5	154	.	0			c.G3146T						.						20	23	22					10																	79581096		2198	4283	6481	SO:0001583	missense	9231	exon15			AGGGCGCTCGGGG	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"discs, large (Drosophila) homolog 5"			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.3146G>T	chr10.hg19:g.79581096C>A	ENSP00000361467:p.Ser1049Ile	42.0	0.0		62.0	9.0	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	hg19	CCDS7353.2	.	.	.	.	.	.	.	.	.	.	C	5.211	0.224455	0.09863	.	.	ENSG00000151208	ENST00000372391;ENST00000372392	T	0.04406	3.63	5.87	2.69	0.31865	.	0.528240	0.16043	N	0.232354	T	0.05593	0.0147	L	0.44542	1.39	0.09310	N	0.999999	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.29822	-0.9999	10	0.62326	D	0.03	.	9.6128	0.39674	0.128:0.3243:0.5478:0.0	.	939;1049	Q8TDM6-4;Q8TDM6	.;DLG5_HUMAN	I	1049;598	ENSP00000361467:S1049I	ENSP00000361467:S1049I	S	-	2	0	DLG5	79251102	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	1.010000	0.29898	0.335000	0.23614	0.655000	0.94253	AGC	.	.		0.637	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			A	79581096	C	A	79581096	3	1	203	1	0	0	0	0	1	0	0	0	4560	797	28	3	2685	3	DLG5	10	79581096	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	4022217	79581096	55953651	57	29762										
CALHM1	255022	hgsc.bcm.edu	37	chr10	105215375	105215375	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gcacgtctcgtcgaagagctTgcgctcgatgtcgatatagt	12	10	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr10:105215375T>A	ENST00000329905.5	-	2	821	c.685A>T	c.(685-687)Aag>Tag	p.K229*	RP11-225H22.4_ENST00000411906.1_RNA|CALHM2_ENST00000393235.1_5'Flank	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	229					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						TCGAAGAGCTTGCGCTCGATG	0.592																																					p.K229X		Atlas-SNP	.											.	CALHM1	33	.	0			c.A685T						.						81	67	72					10																	105215375		2203	4300	6503	SO:0001587	stop_gained	255022	exon2			AGAGCTTGCGCTC	BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"family with sequence similarity 26, member C"	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.685A>T	chr10.hg19:g.105215375T>A	ENSP00000329926:p.Lys229*	86.0	0.0		91.0	35.0	NM_001001412	Q5W091	Nonsense_Mutation	SNP	ENST00000329905.5	hg19	CCDS7550.1	.	.	.	.	.	.	.	.	.	.	T	37	6.213133	0.97380	.	.	ENSG00000185933	ENST00000329905	.	.	.	5.43	5.43	0.79202	.	0.100065	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.1553	15.4612	0.75359	0.0:0.0:0.0:1.0	.	.	.	.	X	229	.	ENSP00000329926:K229X	K	-	1	0	CALHM1	105205365	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	7.539000	0.82063	2.054000	0.61138	0.379000	0.24179	AAG	.	.		0.592	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412		A	105215375	T	A	105215375	4	1	203	1	0	0	0	0	0	1	0	0	2584	1821	63	4	359	4	CALHM1	10	105215375	Nonsense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	25634279	105215375	30319372	58	29763										
FANCF	2188	hgsc.bcm.edu	37	chr11	22646708	22646708	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ttccaactcttcttggggccGacgagacaaaggcggctgca	12	12	2	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr11:22646708G>A	ENST00000327470.3	-	1	679	c.649C>T	c.(649-651)Cgg>Tgg	p.R217W	AC103801.2_ENST00000428556.2_5'Flank	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	217					DNA repair (GO:0006281)|ovarian follicle development (GO:0001541)|spermatogenesis (GO:0007283)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						TCTTGGGGCCGACGAGACAAA	0.592			"N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R217W		Atlas-SNP	.	yes	Rec		Fanconi anaemia F	11	11p15	2188	"Fanconi anemia, complementation group F"		L	.	FANCF	24	.	0			c.C649T						.						57	66	63					11																	22646708		2203	4300	6503	SO:0001583	missense	2188	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGGGCCGACGAGA		CCDS7857.1	11p15	2014-09-17				ENSG00000183161		"Fanconi anemia, complementation groups"	3587	protein-coding gene	gene with protein product		613897				9382107	Standard	NM_022725		Approved	FAF	uc001mql.1	Q9NPI8		ENST00000327470.3:c.649C>T	chr11.hg19:g.22646708G>A	ENSP00000330875:p.Arg217Trp	60.0	0.0	757	72.0	21.0	NM_022725	Q52LM0	Missense_Mutation	SNP	ENST00000327470.3	hg19	CCDS7857.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.176960	0.38413	.	.	ENSG00000183161	ENST00000327470	T	0.33654	1.4	4.88	-3.52	0.04682	.	0.914236	0.09103	U	0.848160	T	0.37348	0.1000	N	0.19112	0.55	0.09310	N	1	D	0.76494	0.999	P	0.60886	0.88	T	0.47611	-0.9104	10	0.66056	D	0.02	.	11.9193	0.52783	0.0:0.4936:0.3135:0.1929	.	217	Q9NPI8	FANCF_HUMAN	W	217	ENSP00000330875:R217W	ENSP00000330875:R217W	R	-	1	2	FANCF	22603284	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-0.481000	0.06552	-0.409000	0.07553	0.561000	0.74099	CGG	.	.		0.592	FANCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387712.2	NM_022725		A	22646708	G	A	22646708	3	1	203	1	0	0	0	0	1	0	0	0	5675	1057	37	1	479	1	FANCF	11	22646708	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10		22646708	112359808	59	29764										
FANCF	2188	hgsc.bcm.edu	37	chr11	22647195	22647195	+	Frame_Shift_Del	DEL	A	A	-													0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cgccgctccagagccgtgcgAatggggccatgccgaccaaa							TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr11:22647195delA	ENST00000327470.3	-	1	192	c.162delT	c.(160-162)attfs	p.I54fs	AC103801.2_ENST00000428556.2_3'UTR	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	54					DNA repair (GO:0006281)|ovarian follicle development (GO:0001541)|spermatogenesis (GO:0007283)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						GAGCCGTGCGAATGGGGCCAT	0.692			"N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R55fs		Atlas-INDEL	.	yes	Rec		Fanconi anaemia F	11	11p15	2188	"Fanconi anemia, complementation group F"		L	.	FANCF	24	.	0			c.163delC						.						23	27	26					11																	22647195		2203	4298	6501	SO:0001589	frameshift_variant	2188	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.		CCDS7857.1	11p15	2014-09-17				ENSG00000183161		"Fanconi anemia, complementation groups"	3587	protein-coding gene	gene with protein product		613897				9382107	Standard	NM_022725		Approved	FAF	uc001mql.1	Q9NPI8		ENST00000327470.3:c.162delT	chr11.hg19:g.22647195delA	ENSP00000330875:p.Ile54fs	161.0	0.0		150.0	40.0	NM_022725	Q52LM0	Frame_Shift_Del	DEL	ENST00000327470.3	hg19	CCDS7857.1																																																																																			.	.		0.692	FANCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387712.2	NM_022725		-	22647195	A	-	22647195	7	5	203	1	0	1	0	1	0	0	0	0	5675	242	9	0	966	0	FANCF	11	22647195	Frame_Shift_Del	DEL	A	TCGA-DD-AADV-01A-11D-A38X-10	487	22647195	112359321	60	29765										
CD44	960	hgsc.bcm.edu	37	chr11	35232954	35232954	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cctttggagttactgcagttActgttggagattccaactct	9	9	1	1	rs373762543		TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr11:35232954A>G	ENST00000428726.2	+	14	1891	c.1768A>G	c.(1768-1770)Act>Gct	p.T590A	CD44_ENST00000433892.2_Missense_Mutation_p.T341A|CD44_ENST00000415148.2_Missense_Mutation_p.T547A|CD44_ENST00000526669.2_Intron|CD44_ENST00000360158.4_Intron|RP1-68D18.4_ENST00000528869.1_RNA|RP1-68D18.2_ENST00000510619.2_RNA|CD44_ENST00000263398.6_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000449691.2_Missense_Mutation_p.T547A|CD44_ENST00000278386.6_Intron|CD44_ENST00000433354.2_Missense_Mutation_p.T562A|CD44_ENST00000434472.2_Missense_Mutation_p.T277A|CD44_ENST00000437706.2_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	590	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	TACTGCAGTTACTGTTGGAGA	0.398																																					p.T590A		Atlas-SNP	.											.	CD44	48	.	0			c.A1768G						.						219	201	207					11																	35232954		2202	4298	6500	SO:0001583	missense	960	exon14			GCAGTTACTGTTG	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"CD molecules", "Blood group antigens", "Proteoglycans / Cell surface : Other"	1681	protein-coding gene	gene with protein product	"hematopoietic cell E- and L-selectin ligand", "chondroitin sulfate proteoglycan 8"	107269	"CD44 antigen (homing function and Indian blood group system)"	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.1768A>G	chr11.hg19:g.35232954A>G	ENSP00000398632:p.Thr590Ala	165.0	0.0		173.0	44.0	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Missense_Mutation	SNP	ENST00000428726.2	hg19	CCDS7897.1	.	.	.	.	.	.	.	.	.	.	A	7.923	0.738910	0.15642	.	.	ENSG00000026508	ENST00000415148;ENST00000433354;ENST00000449691;ENST00000428726;ENST00000433892;ENST00000434472;ENST00000526000	T;T;T;T;T;T;T	0.25085	1.82;1.82;1.82;1.82;1.82;1.82;1.82	5.65	1.96	0.26148	.	0.769234	0.12088	N	0.500731	T	0.24084	0.0583	M	0.64997	1.995	0.19300	N	0.99998	B;B;B;B	0.14805	0.011;0.005;0.004;0.002	B;B;B;B	0.17722	0.019;0.009;0.004;0.003	T	0.28713	-1.0035	10	0.46703	T	0.11	-13.7741	4.7447	0.13031	0.6696:0.161:0.1694:0.0	.	277;341;547;590	P16070-11;P16070-10;P16070-4;P16070	.;.;.;CD44_HUMAN	A	547;562;547;590;341;277;224	ENSP00000389830:T547A;ENSP00000414567:T562A;ENSP00000391008:T547A;ENSP00000398632:T590A;ENSP00000392331:T341A;ENSP00000404447:T277A;ENSP00000434465:T224A	ENSP00000389830:T547A	T	+	1	0	CD44	35189530	0.453000	0.25721	0.015000	0.15790	0.012000	0.07955	0.772000	0.26647	0.075000	0.16796	0.533000	0.62120	ACT	.	.		0.398	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610		G	35232954	A	G	35232954	3	3	203	1	0	0	0	0	1	0	0	0	3019	391	14	2	1822	2	CD44	11	35232954	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	12585759	35232954	99773562	61	29766										
LRRC4C	57689	hgsc.bcm.edu	37	chr11	40137179	40137179	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cccagaaagatccagctcatCtagttttatgagcggtgtga	10	9	2	4			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr11:40137179C>A	ENST00000278198.2	-	2	2627	c.664G>T	c.(664-666)Gat>Tat	p.D222Y	LRRC4C_ENST00000527150.1_Missense_Mutation_p.D222Y|LRRC4C_ENST00000530763.1_Missense_Mutation_p.D222Y|LRRC4C_ENST00000528697.1_Missense_Mutation_p.D222Y			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	222					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)		p.D222Y(1)		NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TCCAGCTCATCTAGTTTTATG	0.468																																					p.D222Y		Atlas-SNP	.											LRRC4C,NS,carcinoma,0,1	LRRC4C	190	.	1	Substitution - Missense(1)	lung(1)	c.G664T						.						83	82	82					11																	40137179		2203	4300	6503	SO:0001583	missense	57689	exon7			GCTCATCTAGTTT	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.664G>T	chr11.hg19:g.40137179C>A	ENSP00000278198:p.Asp222Tyr	121.0	1.0		142.0	60.0	NM_001258419	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	hg19	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.287319	0.59867	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.04360	3.64;3.64;3.64;3.64	5.44	5.44	0.79542	.	0.049235	0.85682	D	0.000000	T	0.09555	0.0235	N	0.16266	0.395	0.80722	D	1	D	0.69078	0.997	P	0.57425	0.82	T	0.19418	-1.0306	10	0.87932	D	0	.	18.2645	0.90048	0.0:1.0:0.0:0.0	.	222	Q9HCJ2	LRC4C_HUMAN	Y	222	ENSP00000278198:D222Y;ENSP00000436976:D222Y;ENSP00000437132:D222Y;ENSP00000434761:D222Y	ENSP00000278198:D222Y	D	-	1	0	LRRC4C	40093755	1.000000	0.71417	0.993000	0.49108	0.925000	0.55904	7.818000	0.86416	2.561000	0.86390	0.650000	0.86243	GAT	.	.		0.468	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		A	40137179	C	A	40137179	3	1	203	1	0	0	0	0	1	0	0	0	9017	913	32	3	1262	3	LRRC4C	11	40137179	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	4904225	40137179	94869337	62	29767										
SDHAF2	54949	hgsc.bcm.edu	37	chr11	61205156	61205156	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ctcagtgtgacatcattcagAcgcttctacagaggtgacag	10	10	4	4			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr11:61205156A>C	ENST00000543265.1	+	2	99	c.96A>C	c.(94-96)agA>agC	p.R32S	SDHAF2_ENST00000537782.1_Missense_Mutation_p.R32S|SDHAF2_ENST00000301761.2_Missense_Mutation_p.R32S|SDHAF2_ENST00000534878.1_Missense_Mutation_p.R32S|RP11-286N22.8_ENST00000544880.1_3'UTR|RP11-286N22.8_ENST00000543044.1_Missense_Mutation_p.R20S|SDHAF2_ENST00000542074.1_Intron					succinate dehydrogenase complex assembly factor 2											large_intestine(3)|lung(4)|ovary(2)	9						CATCATTCAGACGCTTCTACA	0.438																																					p.R32S		Atlas-SNP	.											.	SDHAF2	26	.	0			c.A96C						.						194	191	192					11																	61205156		2202	4299	6501	SO:0001583	missense	54949	exon2			ATTCAGACGCTTC	AK000494	CCDS8007.1	11q12.2	2014-09-17	2009-08-10	2009-08-10	ENSG00000167985	ENSG00000167985		"Mitochondrial respiratory chain complex assembly factors"	26034	protein-coding gene	gene with protein product		613019	"paraganglioma or familial glomus tumors 2", "chromosome 11 open reading frame 79"	PGL2, C11orf79		19628817	Standard	NM_017841		Approved	FLJ20487, SDH5	uc001nrt.3	Q9NX18	OTTHUMG00000168279	ENST00000543265.1:c.96A>C	chr11.hg19:g.61205156A>C	ENSP00000443660:p.Arg32Ser	100.0	0.0		112.0	55.0	NM_017841		Missense_Mutation	SNP	ENST00000543265.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.473	1.096020	0.20552	.	.	ENSG00000256591;ENSG00000167985;ENSG00000167985	ENST00000541135;ENST00000301761;ENST00000543265	T;T;T	0.77750	-1.12;-1.07;-1.02	5.91	1.01	0.19927	.	0.451244	0.26620	N	0.023369	T	0.62696	0.2449	L	0.39898	1.24	0.20638	N	0.99987	B	0.06786	0.001	B	0.06405	0.002	T	0.44003	-0.9356	10	0.22109	T	0.4	-4.6152	6.227	0.20714	0.4059:0.4421:0.152:0.0	.	32	Q9NX18	SDHF2_HUMAN	S	32	ENSP00000443130:R32S;ENSP00000301761:R32S;ENSP00000443660:R32S	ENSP00000440939:R32S	R	+	3	2	SDHAF2;RP11-286N22.8	60961732	0.244000	0.23889	0.272000	0.24630	0.364000	0.29643	0.120000	0.15647	-0.072000	0.12864	0.533000	0.62120	AGA	.	.		0.438	SDHAF2-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000398484.1	NM_017841		C	61205156	A	C	61205156	3	2	203	1	0	0	0	0	1	0	0	0	13979	272	10	5	102	5	SDHAF2	11	61205156	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	21067977	61205156	73801360	63	29768										
MMP1	4312	hgsc.bcm.edu	37	chr11	102661252	102661252	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	catgaaagaaatagaaaaatCctagaaacaaaacaaaagag	6	5	0	5	rs181629882		TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr11:102661252C>T	ENST00000315274.6	-	10	1368	c.1301G>A	c.(1300-1302)gGa>gAa	p.G434E	WTAPP1_ENST00000525739.2_RNA	NM_001145938.1|NM_002421.3	NP_001139410.1|NP_002412.1	P03956	MMP1_HUMAN	matrix metallopeptidase 1 (interstitial collagenase)	434					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|proteolysis (GO:0006508)|viral process (GO:0016032)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G434E(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)	Marimastat(DB00786)	ATAGAAAAATCCTAGAAACAA	0.323																																					p.G434E		Atlas-SNP	.											MMP1,NS,carcinoma,0,1	MMP1	74	.	1	Substitution - Missense(1)	lung(1)	c.G1301A						.						68	65	66					11																	102661252		2203	4296	6499	SO:0001630	splice_region_variant	4312	exon10			AAAAATCCTAGAA	X54925	CCDS8322.1	11q21-q22	2014-01-30	2005-08-08		ENSG00000196611	ENSG00000196611	3.4.24.7	"Endogenous ligands"	7155	protein-coding gene	gene with protein product		120353	"matrix metalloproteinase 1 (interstitial collagenase)"	CLG			Standard	NM_002421		Approved		uc001phi.2	P03956	OTTHUMG00000048192	ENST00000315274.6:c.1301-1G>A	chr11.hg19:g.102661252C>T		102.0	0.0		127.0	54.0	NM_002421	P08156	Missense_Mutation	SNP	ENST00000315274.6	hg19	CCDS8322.1	.	.	.	.	.	.	.	.	.	.	c	17.82	3.483506	0.63962	.	.	ENSG00000196611	ENST00000315274	T	0.03553	3.89	6.17	1.59	0.23543	Hemopexin/matrixin (2);	0.563488	0.17181	N	0.183896	T	0.08582	0.0213	M	0.86953	2.85	0.47778	D	0.999513	B	0.28378	0.209	B	0.35510	0.204	T	0.02104	-1.1213	10	0.62326	D	0.03	.	6.1893	0.20516	0.128:0.6335:0.0:0.2385	.	434	P03956	MMP1_HUMAN	E	434	ENSP00000322788:G434E	ENSP00000322788:G434E	G	-	2	0	MMP1	102166462	0.310000	0.24527	0.911000	0.35937	0.983000	0.72400	0.565000	0.23578	0.659000	0.30945	0.655000	0.94253	GGA	.	C|1.000;A|0.000		0.323	MMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109632.1	NM_002421	Missense_Mutation	T	102661252	C	T	102661252	5	4	203	1	0	0	0	0	0	0	1	0	9657	869	30	3	112	3	MMP1	11	102661252	Splice_Site	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	41456096	102661252	32345264	64	29769										
BUD13	84811	hgsc.bcm.edu	37	chr11	116633446	116633446	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tctttctggggctttaccacTtttggttctgggcagggaat	12	8	3	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr11:116633446T>C	ENST00000260210.4	-	4	882	c.859A>G	c.(859-861)Agt>Ggt	p.S287G	BUD13_ENST00000375445.3_Intron	NM_032725.3	NP_116114.1	Q9BRD0	BUD13_HUMAN	BUD13 homolog (S. cerevisiae)	287					mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)	nucleus (GO:0005634)|RES complex (GO:0070274)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|pancreas(2)|skin(1)|urinary_tract(1)	22	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)		GCTTTACCACTTTTGGTTCTG	0.493																																					p.S287G		Atlas-SNP	.											.	BUD13	41	.	0			c.A859G						.						118	124	122					11																	116633446		2201	4296	6497	SO:0001583	missense	84811	exon4			TACCACTTTTGGT	BC006350	CCDS8374.1, CCDS53712.1	11q23.3	2012-06-07	2007-01-12		ENSG00000137656	ENSG00000137656			28199	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 71"		"BUD13 homolog (yeast)"			12477932	Standard	NM_032725		Approved	MGC13125, fSAP71, Cwc26	uc001ppn.3	Q9BRD0	OTTHUMG00000045136	ENST00000260210.4:c.859A>G	chr11.hg19:g.116633446T>C	ENSP00000260210:p.Ser287Gly	124.0	0.0		122.0	53.0	NM_032725	A8K0S0|Q96LS7	Missense_Mutation	SNP	ENST00000260210.4	hg19	CCDS8374.1	.	.	.	.	.	.	.	.	.	.	T	13.13	2.144402	0.37825	.	.	ENSG00000137656	ENST00000260210	T	0.18174	2.23	3.95	3.95	0.45737	.	0.240159	0.36002	N	0.002848	T	0.19967	0.0480	M	0.76002	2.32	0.36576	D	0.873282	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.003	T	0.17107	-1.0380	10	0.87932	D	0	-10.0641	7.8676	0.29545	0.0:0.0988:0.0:0.9012	.	287;287	A8K4Z6;Q9BRD0	.;BUD13_HUMAN	G	287	ENSP00000260210:S287G	ENSP00000260210:S287G	S	-	1	0	BUD13	116138656	0.934000	0.31675	1.000000	0.80357	0.248000	0.25809	1.811000	0.38942	2.017000	0.59298	0.533000	0.62120	AGT	.	.		0.493	BUD13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000104864.1	NM_032725		C	116633446	T	C	116633446	3	2	203	1	0	0	0	0	1	0	0	0	1575	1609	56	2	1028	2	BUD13	11	116633446	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	13972194	116633446	18373070	65	29770										
ETS1	2113	hgsc.bcm.edu	37	chr11	128332286	128332286	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gcatctggcttgacgtccagCatggcgtgcagctcctcagg	13	13	2	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr11:128332286C>G	ENST00000319397.6	-	8	1605	c.1296G>C	c.(1294-1296)atG>atC	p.M432I	ETS1_ENST00000526145.2_Missense_Mutation_p.M345I|ETS1_ENST00000345075.4_Missense_Mutation_p.M345I|ETS1_ENST00000535549.1_Missense_Mutation_p.M216I|ETS1_ENST00000531611.1_3'UTR|ETS1_ENST00000392668.4_Missense_Mutation_p.M476I	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	432					angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		TGACGTCCAGCATGGCGTGCA	0.577																																					p.M476I		Atlas-SNP	.											.	ETS1	123	.	0			c.G1428C						.						99	85	90					11																	128332286		2201	4297	6498	SO:0001583	missense	2113	exon10			GTCCAGCATGGCG		CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1", "ets protein"	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.1296G>C	chr11.hg19:g.128332286C>G	ENSP00000324578:p.Met432Ile	114.0	0.0		134.0	64.0	NM_001143820	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Missense_Mutation	SNP	ENST00000319397.6	hg19	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.276038	0.80580	.	.	ENSG00000134954	ENST00000345075;ENST00000535549;ENST00000392668;ENST00000319397;ENST00000526145	T;T;T;T;T	0.13420	2.59;2.59;2.59;2.59;2.59	5.96	5.96	0.96718	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.24661	0.0598	L	0.41573	1.285	0.80722	D	1	B;B;D	0.55605	0.005;0.006;0.972	B;B;P	0.54026	0.003;0.009;0.74	T	0.00070	-1.2134	10	0.33940	T	0.23	.	20.4082	0.99013	0.0:1.0:0.0:0.0	.	432;216;476	P14921;F5GYX9;Q6N087	ETS1_HUMAN;.;.	I	345;216;476;432;345	ENSP00000340485:M345I;ENSP00000441430:M216I;ENSP00000376436:M476I;ENSP00000324578:M432I;ENSP00000433500:M345I	ENSP00000324578:M432I	M	-	3	0	ETS1	127837496	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.441000	0.80485	2.814000	0.96858	0.655000	0.94253	ATG	.	.		0.577	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238		G	128332286	C	G	128332286	3	3	203	1	0	0	0	0	1	0	0	0	5277	710	25	4	33	4	ETS1	11	128332286	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	11698840	128332286	6674230	66	29771										
KIF21A	55605	hgsc.bcm.edu	37	chr12	39726081	39726081	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	actgtcattgatgtaatcgaTattagcagtcagtgactcca	8	8	2	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr12:39726081T>C	ENST00000361418.5	-	21	3001	c.2986A>G	c.(2986-2988)Atc>Gtc	p.I996V	KIF21A_ENST00000395670.3_Missense_Mutation_p.I996V|KIF21A_ENST00000361961.3_Missense_Mutation_p.I983V|KIF21A_ENST00000541463.2_Missense_Mutation_p.I960V|KIF21A_ENST00000544797.2_Missense_Mutation_p.I983V			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	996					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				ATGTAATCGATATTAGCAGTC	0.353																																					p.I996V		Atlas-SNP	.											.	KIF21A	238	.	0			c.A2986G						.						204	184	191					12																	39726081		2203	4300	6503	SO:0001583	missense	55605	exon21			AATCGATATTAGC	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.2986A>G	chr12.hg19:g.39726081T>C	ENSP00000354878:p.Ile996Val	100.0	0.0		106.0	8.0	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	hg19	CCDS53776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.93|14.93	2.682080|2.682080	0.47991|0.47991	.|.	.|.	ENSG00000139116|ENSG00000139116	ENST00000552961|ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463;ENST00000551066	.|D;D;D;D;D;D;D	.|0.86694	.|-2.16;-2.16;-2.16;-2.16;-2.16;-2.16;-2.16	5.8|5.8	5.8|5.8	0.92144|0.92144	.|Prefoldin (1);	0.000000|0.000000	0.64402|0.64402	D|D	0.000014|0.000014	D|D	0.91932|0.91932	0.7445|0.7445	L|L	0.56769|0.56769	1.78|1.78	0.58432|0.58432	D|D	0.999994|0.999994	.|B;P;B;B;B;P	.|0.51791	.|0.003;0.948;0.029;0.003;0.008;0.645	.|B;D;B;B;B;P	.|0.67103	.|0.011;0.949;0.032;0.011;0.034;0.58	D|D	0.92560|0.92560	0.6057|0.6057	6|10	.|0.72032	.|D	.|0.01	.|.	16.1506|16.1506	0.81618|0.81618	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|983;960;996;983;996;50	.|F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2;Q7Z4S6-3;F5H0V8	.|.;.;KI21A_HUMAN;.;.;.	M|V	343|983;996;996;50;44;983;996;960;17	.|ENSP00000354851:I983V;ENSP00000379029:I996V;ENSP00000448792:I44V;ENSP00000445606:I983V;ENSP00000354878:I996V;ENSP00000438075:I960V;ENSP00000447070:I17V	.|ENSP00000344501:I996V	I|I	-|-	3|1	3|0	KIF21A|KIF21A	38012348|38012348	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.448000|0.448000	0.32197|0.32197	7.880000|7.880000	0.87243|0.87243	2.206000|2.206000	0.71126|0.71126	0.528000|0.528000	0.53228|0.53228	ATA|ATC	.	.		0.353	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		C	39726081	T	C	39726081	3	2	203	1	0	0	0	0	1	0	0	0	8297	1406	49	2	2110	2	KIF21A	12	39726081	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10		39726081	94125814	67	29772										
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46320992	46320992	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cattcttaggagatggtgatTgagacttcctgctttctttc	9	8	2	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr12:46320992T>G	ENST00000369367.3	-	11	2725	c.2492A>C	c.(2491-2493)cAa>cCa	p.Q831P	SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000465950.1_Missense_Mutation_p.Q516P|SCAF11_ENST00000419565.2_Missense_Mutation_p.Q831P|SCAF11_ENST00000549162.1_Missense_Mutation_p.Q639P	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	831					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						AGATGGTGATTGAGACTTCCT	0.473																																					p.Q831P		Atlas-SNP	.											.	SCAF11	145	.	0			c.A2492C						.						112	113	113					12																	46320992		2203	4300	6503	SO:0001583	missense	9169	exon11			GGTGATTGAGACT	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"RING-type (C3HC4) zinc fingers"	10784	protein-coding gene	gene with protein product		603668	"splicing factor, arginine/serine-rich 2, interacting protein", "serine/arginine-rich splicing factor 2, interacting protein"	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.2492A>C	chr12.hg19:g.46320992T>G	ENSP00000358374:p.Gln831Pro	69.0	0.0		73.0	5.0	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	hg19	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	T	9.710	1.156925	0.21454	.	.	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565;ENST00000547018	T;T;T;T;T	0.47528	1.45;2.18;1.45;2.18;0.84	5.93	-11.9	0.00025	.	1.797880	0.02620	N	0.103170	T	0.34861	0.0912	L	0.52573	1.65	0.20307	N	0.999917	B;P	0.52842	0.002;0.956	B;B	0.41619	0.004;0.361	T	0.56817	-0.7916	10	0.72032	D	0.01	6.9181	6.2382	0.20774	0.0747:0.0872:0.2255:0.6126	.	639;831	F8VXG7;Q99590	.;SCAFB_HUMAN	P	516;831;639;831;771	ENSP00000449812:Q516P;ENSP00000358374:Q831P;ENSP00000448864:Q639P;ENSP00000413036:Q831P;ENSP00000446746:Q771P	ENSP00000358374:Q831P	Q	-	2	0	SCAF11	44607259	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-2.310000	0.01129	-2.583000	0.00461	-0.290000	0.09829	CAA	.	.		0.473	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		G	46320992	T	G	46320992	3	3	203	1	0	0	0	0	1	0	0	0	14192	1812	63	5	1919	5	SFRS2IP	12	46320992	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	6594911	46320992	87530903	68	29773										
LLPH	84298	hgsc.bcm.edu	37	chr12	66522717	66522717	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	attgcattttctcttggcaaTgtttgggtttgggtaccacc	10	8	1	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr12:66522717T>C	ENST00000266604.2	-	2	240	c.170A>G	c.(169-171)cAt>cGt	p.H57R	TMBIM4_ENST00000539652.1_3'UTR|LLPH_ENST00000446587.2_Missense_Mutation_p.H57R|RP11-745O10.2_ENST00000510317.2_RNA|TMBIM4_ENST00000556010.1_3'UTR	NM_032338.3	NP_115714.1	Q9BRT6	LLPH_HUMAN	LLP homolog, long-term synaptic facilitation (Aplysia)	57	Lys-rich.						poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|skin(1)	5						CTCTTGGCAATGTTTGGGTTT	0.378																																					p.H57R		Atlas-SNP	.											.	LLPH	25	.	0			c.A170G						.						124	117	119					12																	66522717		2203	4298	6501	SO:0001583	missense	84298	exon2			TGGCAATGTTTGG	AK057947	CCDS8974.1	12q14.3	2014-05-09	2008-10-02	2008-10-02	ENSG00000139233	ENSG00000139233			28229	protein-coding gene	gene with protein product	"human LAPS18-like protein"		"chromosome 12 open reading frame 31"	C12orf31		12477932	Standard	NM_032338		Approved	MGC14817, hLLP	uc010ssw.2	Q9BRT6	OTTHUMG00000168959	ENST00000266604.2:c.170A>G	chr12.hg19:g.66522717T>C	ENSP00000266604:p.His57Arg	301.0	0.0		313.0	91.0	NM_032338	Q3B766	Missense_Mutation	SNP	ENST00000266604.2	hg19	CCDS8974.1	.	.	.	.	.	.	.	.	.	.	T	4.211	0.037931	0.08148	.	.	ENSG00000139233	ENST00000266604;ENST00000446587	.	.	.	4.0	1.53	0.23141	.	0.905533	0.09721	N	0.764480	T	0.13970	0.0338	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31586	-0.9938	8	.	.	.	-21.1146	4.1527	0.10245	0.0:0.1126:0.2082:0.6792	.	57	Q9BRT6	LLPH_HUMAN	R	57	.	.	H	-	2	0	LLPH	64808984	0.157000	0.22836	0.003000	0.11579	0.441000	0.31987	0.523000	0.22925	0.190000	0.20209	0.260000	0.18958	CAT	.	.		0.378	LLPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401752.1	NM_032338		C	66522717	T	C	66522717	3	2	203	1	0	0	0	0	1	0	0	0	8844	1464	51	2	227	2	LLPH	12	66522717	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	20201725	66522717	67329178	69	29774										
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72004331	72004331	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gttttacctccttctgatgcTtcaaacaagagttgctgtaa	7	9	2	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr12:72004331T>C	ENST00000378743.3	-	35	6205	c.5847A>G	c.(5845-5847)gaA>gaG	p.E1949E		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1949					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						CTTCTGATGCTTCAAACAAGA	0.378																																					p.E1949E		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.A5847G						.						106	96	100					12																	72004331		1872	4097	5969	SO:0001819	synonymous_variant	196441	exon35			TGATGCTTCAAAC	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.5847A>G	chr12.hg19:g.72004331T>C		82.0	0.0		87.0	20.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Silent	SNP	ENST00000378743.3	hg19	CCDS41813.1																																																																																			.	.		0.378	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		C	72004331	T	C	72004331	2	2	203	1	0	0	0	0	0	0	0	1	17648	1606	56	2		2	ZFC3H1	12	72004331	Silent	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	5481614	72004331	61847564	70	29775										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23532224	23532224	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gactgggtcatcaatggtaaTggaaactccggacttctgct	11	9	3	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr14:23532224T>C	ENST00000262710.1	-	14	3298	c.2971A>G	c.(2971-2973)Att>Gtt	p.I991V	ACIN1_ENST00000555053.1_Missense_Mutation_p.I978V|ACIN1_ENST00000605057.1_Missense_Mutation_p.I933V|ACIN1_ENST00000457657.1_Missense_Mutation_p.I951V|ACIN1_ENST00000338631.6_Missense_Mutation_p.I264V|ACIN1_ENST00000397341.3_Missense_Mutation_p.I233V|ACIN1_ENST00000357481.2_Missense_Mutation_p.I233V|ACIN1_ENST00000557515.1_Missense_Mutation_p.I232V	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	991					apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		TCAATGGTAATGGAAACTCCG	0.473																																					p.I991V		Atlas-SNP	.											.	ACIN1	147	.	0			c.A2971G						.						180	166	171					14																	23532224		2203	4300	6503	SO:0001583	missense	22985	exon14			TGGTAATGGAAAC	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.2971A>G	chr14.hg19:g.23532224T>C	ENSP00000262710:p.Ile991Val	109.0	0.0		141.0	47.0	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	T	13.66	2.303292	0.40795	.	.	ENSG00000100813	ENST00000557515;ENST00000338631;ENST00000357481;ENST00000262710;ENST00000457657;ENST00000397341;ENST00000555053	T;T;T;T;T;T	0.18174	3.46;3.46;2.24;2.26;3.46;2.23	5.5	5.5	0.81552	.	0.000000	0.41605	D	0.000849	T	0.14313	0.0346	L	0.35341	1.055	0.46437	D	0.999041	B;B;B;B;B	0.32526	0.323;0.217;0.374;0.234;0.234	B;B;B;B;B	0.39119	0.192;0.094;0.291;0.061;0.061	T	0.13442	-1.0509	10	0.13470	T	0.59	-8.1994	9.2121	0.37324	0.0:0.0809:0.0:0.9191	.	978;991;951;264;233	G3V3M7;Q9UKV3;E7EQT4;Q9UKV3-2;Q9UKV3-3	.;ACINU_HUMAN;.;.;.	V	232;264;233;991;951;233;978	ENSP00000345541:I264V;ENSP00000350073:I233V;ENSP00000262710:I991V;ENSP00000405677:I951V;ENSP00000380502:I233V;ENSP00000451328:I978V	ENSP00000262710:I991V	I	-	1	0	ACIN1	22602064	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.195000	0.42677	2.308000	0.77769	0.533000	0.62120	ATT	.	.		0.473	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23532224	T	C	23532224	3	2	203	1	0	0	0	0	1	0	0	0	142	1464	51	2	1078	2	ACIN1	14	23532224	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10		23532224	83817316	71	29776										
FSCB	84075	hgsc.bcm.edu	37	chr14	44974177	44974177	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ggcctcctcagctggtggagGctgaacttcagcgggggcct	16	12	2	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr14:44974177G>T	ENST00000340446.4	-	1	2305	c.2014C>A	c.(2014-2016)Cct>Act	p.P672T	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	672	Ala-rich.			P -> PPPAEEAPSEVQP (in Ref. 1; CAB66709/ CAI45927/CAI45935). {ECO:0000305}.		sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		GCTGGTGGAGGCTGAACTTCA	0.617																																					p.P672T		Atlas-SNP	.											.	FSCB	173	.	0			c.C2014A						.						16	19	18					14																	44974177		2194	4294	6488	SO:0001583	missense	84075	exon1			GTGGAGGCTGAAC	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"chromosome 14 open reading frame 155"	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.2014C>A	chr14.hg19:g.44974177G>T	ENSP00000344579:p.Pro672Thr	74.0	0.0		67.0	14.0	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	hg19	CCDS9679.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.488197	0.26686	.	.	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.13420	2.59	3.29	-6.51	0.01878	.	.	.	.	.	T	0.07999	0.0200	L	0.48642	1.525	0.09310	N	1	B	0.24823	0.112	B	0.20767	0.031	T	0.39014	-0.9634	9	0.15066	T	0.55	0.1574	3.1445	0.06467	0.5689:0.1174:0.1956:0.118	.	672	Q5H9T9	FSCB_HUMAN	T	672;565	ENSP00000344579:P672T	ENSP00000344579:P672T	P	-	1	0	FSCB	44043927	0.000000	0.05858	0.000000	0.03702	0.319000	0.28217	-1.716000	0.01878	-1.602000	0.01599	-0.450000	0.05554	CCT	.	.		0.617	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		T	44974177	G	T	44974177	3	4	203	1	0	0	0	0	1	0	0	0	6074	1203	42	3	467	3	FSCB	14	44974177	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	21441953	44974177	62375363	72	29777										
TRMT5	145389	hgsc.bcm.edu	37	chr14	61446462	61446462	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tgagaatctttttctttgacCcaataagaaaataccaggtg	7	7	2	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr14:61446462C>T	ENST00000267488.4	+	0	0				SLC38A6_ENST00000456840.2_5'Flank|TRMT5_ENST00000261249.6_Missense_Mutation_p.G52S|RP11-193F5.1_ENST00000553946.1_RNA|SLC38A6_ENST00000354886.2_5'Flank	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6						amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		TTTCTTTGACCCAATAAGAAA	0.413																																					p.G52S		Atlas-SNP	.											.	TRMT5	44	.	0			c.G154A						.						112	111	111					14																	61446462		2203	4300	6503	SO:0001631	upstream_gene_variant	57570	exon2			TTTGACCCAATAA	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"Solute carriers"	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335		chr14.hg19:g.61446462C>T	Exception_encountered	97.0	0.0		78.0	16.0	NM_020810	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000267488.4	hg19	CCDS9751.1	.	.	.	.	.	.	.	.	.	.	C	4.349	0.064159	0.08388	.	.	ENSG00000126814	ENST00000261249;ENST00000553903;ENST00000555420	T	0.20738	2.05	4.59	-0.592	0.11671	.	1.008970	0.07936	N	0.978328	T	0.07279	0.0184	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36939	-0.9727	10	0.02654	T	1	-25.6944	6.2232	0.20693	0.1215:0.5925:0.0:0.286	.	52	Q32P41	TRM5_HUMAN	S	52;80;79	ENSP00000261249:G52S	ENSP00000261249:G52S	G	-	1	0	TRMT5	60516215	0.000000	0.05858	0.015000	0.15790	0.022000	0.10575	0.725000	0.25970	-0.004000	0.14419	-0.136000	0.14681	GGT	.	.		0.413	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1			T	61446462	C	T	61446462	1	4	203	0	1	0	0	0	0	0	0	0	16582	623	22	3		3	TRMT5	14	61446462	5'Flank	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	16472285	61446462	45903078	73	29778										
CEP152	22995	hgsc.bcm.edu	37	chr15	49031451	49031451	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tcatttctttttgattttttAactgcaatcagcatctctga	4	8	4	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr15:49031451A>G	ENST00000380950.2	-	27	4315	c.4128T>C	c.(4126-4128)gtT>gtC	p.V1376V	CEP152_ENST00000399334.3_Silent_p.V1320V	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1376					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TTGATTTTTTAACTGCAATCA	0.338																																					p.V1376V		Atlas-SNP	.											.	CEP152	145	.	0			c.T4128C						.						72	66	68					15																	49031451		1837	4076	5913	SO:0001819	synonymous_variant	22995	exon27			TTTTTTAACTGCA	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.4128T>C	chr15.hg19:g.49031451A>G		67.0	0.0		71.0	29.0	NM_001194998	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.		0.338	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		G	49031451	A	G	49031451	2	3	203	1	0	0	0	0	0	0	0	1	3250	349	13	2		2	CEP152	15	49031451	Silent	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10		49031451	53499941	74	29779										
MESP2	145873	hgsc.bcm.edu	37	chr15	90320448	90320448	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gacgcagtcgtccccagagcCccggaacccaccagtgccct	10	19	0	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr15:90320448C>T	ENST00000341735.3	+	1	860	c.860C>T	c.(859-861)cCc>cTc	p.P287L	MESP2_ENST00000560219.1_Intron|MESP2_ENST00000558723.1_Intron	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	287					mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			TCCCCAGAGCCCCGGAACCCA	0.647																																					p.P287L		Atlas-SNP	.											.	MESP2	20	.	0			c.C860T						.						13	15	14					15																	90320448		1881	4094	5975	SO:0001583	missense	145873	exon1			CAGAGCCCCGGAA		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"Basic helix-loop-helix proteins"	29659	protein-coding gene	gene with protein product		605195	"mesoderm posterior 2 homolog (mouse)"			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.860C>T	chr15.hg19:g.90320448C>T	ENSP00000342392:p.Pro287Leu	97.0	0.0		95.0	4.0	NM_001039958	Q7RTU2	Missense_Mutation	SNP	ENST00000341735.3	hg19	CCDS42078.1	.	.	.	.	.	.	.	.	.	.	C	9.598	1.127958	0.20959	.	.	ENSG00000188095	ENST00000341735	D	0.88896	-2.44	4.35	3.43	0.39272	.	.	.	.	.	D	0.90031	0.6887	L	0.53249	1.67	0.09310	N	0.999998	D	0.59357	0.985	P	0.55055	0.767	T	0.81516	-0.0897	9	0.87932	D	0	-10.4457	9.4535	0.38741	0.2117:0.7883:0.0:0.0	.	287	Q0VG99	MESP2_HUMAN	L	287	ENSP00000342392:P287L	ENSP00000342392:P287L	P	+	2	0	MESP2	88121452	0.001000	0.12720	0.014000	0.15608	0.200000	0.23975	0.666000	0.25097	1.036000	0.39998	0.462000	0.41574	CCC	.	.		0.647	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		T	90320448	C	T	90320448	3	4	203	1	0	0	0	0	1	0	0	0	9492	623	22	3	862	3	MESP2	15	90320448	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	41288997	90320448	12210944	75	29780										
MEF2A	4205	hgsc.bcm.edu	37	chr15	100185917	100185917	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ggacaaagttcttctcaagtAtacagaatataatgaacctc	6	8	2	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr15:100185917A>G	ENST00000557785.1	+	4	555	c.206A>G	c.(205-207)tAt>tGt	p.Y69C	MEF2A_ENST00000558856.1_Intron|MEF2A_ENST00000557942.1_Missense_Mutation_p.Y69C|MEF2A_ENST00000449277.2_Intron|MEF2A_ENST00000354410.5_Missense_Mutation_p.Y69C|MEF2A_ENST00000558812.1_Intron|MEF2A_ENST00000338042.6_Missense_Mutation_p.Y69C|MEF2A_ENST00000453228.2_Missense_Mutation_p.Y69C	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	69					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			CTTCTCAAGTATACAGAATAT	0.348																																					p.Y69C		Atlas-SNP	.											.	MEF2A	138	.	0			c.A206G						.						84	78	80					15																	100185917		1885	4112	5997	SO:0001583	missense	4205	exon3			TCAAGTATACAGA		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"Myocyte enhancer factors"	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.206A>G	chr15.hg19:g.100185917A>G	ENSP00000453441:p.Tyr69Cys	186.0	0.0		200.0	83.0	NM_001130926	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Missense_Mutation	SNP	ENST00000557785.1	hg19	CCDS53978.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.422650	0.83559	.	.	ENSG00000068305	ENST00000453228;ENST00000354410;ENST00000338042	D;D;D	0.85861	-2.04;-2.04;-2.04	5.19	5.19	0.71726	Transcription factor, MADS-box (1);	0.000000	0.85682	D	0.000000	D	0.91788	0.7402	M	0.75264	2.295	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.91635	0.995;0.986;0.998;0.999	D	0.92844	0.6291	10	0.87932	D	0	-12.6218	15.0324	0.71717	1.0:0.0:0.0:0.0	.	69;69;69;69	Q02078;Q02078-6;Q02078-5;Q02078-2	MEF2A_HUMAN;.;.;.	C	69	ENSP00000404110:Y69C;ENSP00000346389:Y69C;ENSP00000337202:Y69C	ENSP00000337202:Y69C	Y	+	2	0	MEF2A	98003440	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	9.339000	0.96797	1.951000	0.56629	0.482000	0.46254	TAT	.	.		0.348	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1			G	100185917	A	G	100185917	3	3	203	1	0	0	0	0	1	0	0	0	9464	449	16	2	212	2	MEF2A	15	100185917	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	9865469	100185917	2345475	76	29781										
WDR90	197335	hgsc.bcm.edu	37	chr16	712038	712038	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gccgctgcttcttgtcctggGaggcggatgacggtggcatt	16	10	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr16:712038G>T	ENST00000293879.4	+	32	4012	c.4012G>T	c.(4012-4014)Gag>Tag	p.E1338*	WDR90_ENST00000549091.1_Nonsense_Mutation_p.E1338*			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1338										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CTTGTCCTGGGAGGCGGATGA	0.652																																					p.E1338X		Atlas-SNP	.											.	WDR90	107	.	0			c.G4012T						.						37	43	41					16																	712038		2086	4200	6286	SO:0001587	stop_gained	197335	exon32			TCCTGGGAGGCGG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.4012G>T	chr16.hg19:g.712038G>T	ENSP00000293879:p.Glu1338*	34.0	0.0		39.0	15.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Nonsense_Mutation	SNP	ENST00000293879.4	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	G	42	9.483677	0.99184	.	.	ENSG00000161996	ENST00000549091;ENST00000293879	.	.	.	5.18	4.16	0.48862	.	0.070578	0.53938	U	0.000044	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	14.2624	0.66094	0.0:0.1496:0.8504:0.0	.	.	.	.	X	1338	.	ENSP00000293879:E1338X	E	+	1	0	WDR90	652039	1.000000	0.71417	0.994000	0.49952	0.324000	0.28378	5.027000	0.64109	2.413000	0.81919	0.561000	0.74099	GAG	.	.		0.652	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		T	712038	G	T	712038	4	4	203	1	0	0	0	0	0	1	0	0	17352	1175	41	3	4138	3	WDR90	16	712038	Nonsense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10		712038	89642715	77	29782										
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15125629	15125629	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gaggatgtggatcagctcgtAgcctgcatagaaagcaaact	12	8	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr16:15125629A>T	ENST00000396410.4	+	17	1534	c.1437A>T	c.(1435-1437)gtA>gtT	p.V479V	PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000450288.2_Silent_p.V451V|PDXDC1_ENST00000447912.2_Silent_p.V388V|PDXDC1_ENST00000569715.1_Silent_p.V452V|PDXDC1_ENST00000563679.1_Silent_p.V497V|PDXDC1_ENST00000325823.7_Silent_p.V464V	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	479					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ATCAGCTCGTAGCCTGCATAG	0.502																																					p.V479V		Atlas-SNP	.											.	PDXDC1	59	.	0			c.A1437T						.						116	102	107					16																	15125629		2197	4300	6497	SO:0001819	synonymous_variant	23042	exon17			GCTCGTAGCCTGC	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.1437A>T	chr16.hg19:g.15125629A>T		97.0	0.0		116.0	12.0	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	hg19	CCDS32393.1																																																																																			.	.		0.502	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		T	15125629	A	T	15125629	2	4	203	1	0	0	0	0	0	0	0	1	11705	407	15	4		4	PDXDC1	16	15125629	Silent	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	14413591	15125629	75229124	78	29783										
ERN2	10595	hgsc.bcm.edu	37	chr16	23713784	23713784	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gcagtgctgggtgagccctcTcgctctcctgagacttggag	14	12	2	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr16:23713784T>C	ENST00000457008.2	-	10	1046	c.1008A>G	c.(1006-1008)cgA>cgG	p.R336R	ERN2_ENST00000256797.4_Silent_p.R384R					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		GTGAGCCCTCTCGCTCTCCTG	0.597																																					p.R384R		Atlas-SNP	.											.	ERN2	131	.	0			c.A1152G						.						112	117	116					16																	23713784		2197	4300	6497	SO:0001819	synonymous_variant	10595	exon10			GCCCTCTCGCTCT	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"ER to nucleus signalling 2"			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.1008A>G	chr16.hg19:g.23713784T>C		40.0	0.0		40.0	6.0	NM_033266		Silent	SNP	ENST00000457008.2	hg19																																																																																				.	.		0.597	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1			C	23713784	T	C	23713784	2	2	203	1	0	0	0	0	0	0	0	1	5240	1538	54	2		2	ERN2	16	23713784	Silent	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	8588155	23713784	66640969	79	29784										
PMFBP1	83449	hgsc.bcm.edu	37	chr16	72170637	72170637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	cgacacggcctctagttccaCgcgcagatccttcaccaggt	9	16	2	1	rs144745394		TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr16:72170637C>T	ENST00000237353.10	-	8	1261	c.1000G>A	c.(1000-1002)Gtg>Atg	p.V334M	PMFBP1_ENST00000355636.6_Missense_Mutation_p.V189M|PMFBP1_ENST00000537465.1_Missense_Mutation_p.V334M	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	334						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TCTAGTTCCACGCGCAGATCC	0.552																																					p.V334M		Atlas-SNP	.											.	PMFBP1	101	.	0			c.G1000A						.	T	MET/VAL,MET/VAL	1,4395	825.2+/-416.5	0,1,2197	100	82	88		565,1000	1.2	0.9	16	dbSNP_134	88	0,8600		0,0,4300	no	missense,missense	PMFBP1	NM_001160213.1,NM_031293.2	21,21	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	189/883,334/1008	72170637	1,12995	2198	4300	6498	SO:0001583	missense	83449	exon8			GTTCCACGCGCAG	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.1000G>A	chr16.hg19:g.72170637C>T	ENSP00000237353:p.Val334Met	90.0	0.0		88.0	25.0	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	hg19	CCDS32483.1	.	.	.	.	.	.	.	.	.	.	T	4.876	0.162874	0.09287	2.27E-4	0.0	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.11712	2.75;2.75;2.75	4.85	1.22	0.21188	.	0.527792	0.15935	N	0.237496	T	0.03178	0.0093	N	0.02247	-0.625	0.09310	N	1	B;B;B	0.16396	0.017;0.005;0.017	B;B;B	0.09377	0.004;0.002;0.004	T	0.39522	-0.9610	10	0.44086	T	0.13	-1.2124	0.4596	0.00514	0.2727:0.1617:0.1408:0.4247	.	334;334;334	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	M	334;334;189	ENSP00000443817:V334M;ENSP00000237353:V334M;ENSP00000347854:V189M	ENSP00000237353:V334M	V	-	1	0	PMFBP1	70728138	0.978000	0.34361	0.918000	0.36340	0.619000	0.37552	0.116000	0.15561	-0.395000	0.07715	-1.326000	0.01283	GTG	.	C|1.000;T|0.000		0.552	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293		T	72170637	C	T	72170637	3	4	203	1	0	0	0	0	1	0	0	0	12143	536	19	1	2139	1	PMFBP1	16	72170637	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	48456853	72170637	18184116	80	29785										
TP53	7157	hgsc.bcm.edu	37	chr17	7579369	7579369	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	aagcccagacggaaaccgtaGctgccctggtaggttttctg	12	11	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr17:7579369G>C	ENST00000269305.4	-	4	507	c.318C>G	c.(316-318)agC>agG	p.S106R	TP53_ENST00000420246.2_Missense_Mutation_p.S106R|TP53_ENST00000455263.2_Missense_Mutation_p.S106R|TP53_ENST00000359597.4_Missense_Mutation_p.S106R|TP53_ENST00000445888.2_Missense_Mutation_p.S106R|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.S106R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	106	Interaction with HIPK1. {ECO:0000250}.|Interaction with WWOX.|Required for interaction with ZNF385A.		S -> G (in a sporadic cancer; somatic mutation).|S -> R (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.Q100fs*37(3)|p.G59fs*23(3)|p.S106R(3)|p.V73fs*9(1)|p.S106_Y107delSY(1)|p.G105_T125del21(1)|p.Y107fs*44(1)|p.W91fs*13(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y103_L111>L(1)|p.Y103fs*15(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGAAACCGTAGCTGCCCTGGT	0.617		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.S106R	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000413465,colon,carcinoma,-2,6	TP53	33396	.	27	Deletion - Frameshift(12)|Whole gene deletion(8)|Substitution - Missense(3)|Complex - deletion inframe(2)|Deletion - In frame(2)	upper_aerodigestive_tract(5)|bone(4)|large_intestine(3)|ovary(3)|breast(3)|central_nervous_system(2)|lung(2)|liver(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	c.C318G	GRCh37	CM013441	TP53	M		.						58	57	57					17																	7579369		2203	4300	6503	SO:0001583	missense	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ACCGTAGCTGCCC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.318C>G	chr17.hg19:g.7579369G>C	ENSP00000269305:p.Ser106Arg	221.0	0.0		109.0	79.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	9.949	1.219579	0.22373	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99760	-6.66;-6.66;-6.66;-6.66;-6.66;-6.66;-6.66;-6.66	4.75	2.77	0.32553	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	1.175280	0.05775	N	0.607434	D	0.99133	0.9701	L	0.38175	1.15	0.28839	N	0.896688	B;P;B;B;B;B;B	0.34615	0.305;0.459;0.042;0.005;0.086;0.029;0.313	B;B;B;B;B;B;B	0.43103	0.107;0.408;0.117;0.007;0.186;0.186;0.061	D	0.99992	1.4503	10	0.40728	T	0.16	-0.4975	9.0942	0.36629	0.1857:0.0:0.8143:0.0	.	67;106;106;106;106;106;106	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	106	ENSP00000410739:S106R;ENSP00000352610:S106R;ENSP00000269305:S106R;ENSP00000398846:S106R;ENSP00000391127:S106R;ENSP00000391478:S106R;ENSP00000424104:S106R;ENSP00000426252:S106R	ENSP00000269305:S106R	S	-	3	2	TP53	7520094	0.247000	0.23920	0.636000	0.29352	0.532000	0.34746	0.437000	0.21543	1.364000	0.46038	0.655000	0.94253	AGC	.	.		0.617	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7579369	G	C	7579369	3	2	203	1	0	0	0	0	1	0	0	0	16396	962	34	4	984	4	TP53	17	7579369	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10		7579369	73615841	81	29786										
NF1	4763	hgsc.bcm.edu	37	chr17	29654655	29654655	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	agaaccagttcaccttaaccAttgcaaaccagggcacgccg	8	14	1	1	rs559910904	byFrequency	TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr17:29654655A>G	ENST00000358273.4	+	38	5790	c.5407A>G	c.(5407-5409)Att>Gtt	p.I1803V	NF1_ENST00000356175.3_Missense_Mutation_p.I1782V|NF1_ENST00000581113.2_3'UTR	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1803	Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CACCTTAACCATTGCAAACCA	0.463			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			A|||	2	0.000399361	0	0	5008	,	,		17323	0		0	False		,,,				2504	0.002				p.I1803V		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.A5407G						.						137	129	132					17																	29654655		2203	4300	6503	SO:0001583	missense	4763	exon38	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	TTAACCATTGCAA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.5407A>G	chr17.hg19:g.29654655A>G	ENSP00000351015:p.Ile1803Val	164.0	0.0		104.0	55.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	A	15.76	2.930032	0.52759	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;D;D	0.85258	-1.96;-1.96;-1.96	5.99	5.99	0.97316	Armadillo-type fold (1);	0.053328	0.85682	D	0.000000	D	0.83069	0.5174	L	0.54323	1.7	0.80722	D	1	B;B;B	0.12013	0.001;0.005;0.003	B;B;B	0.20184	0.004;0.028;0.023	T	0.78262	-0.2272	10	0.38643	T	0.18	.	15.7142	0.77655	1.0:0.0:0.0:0.0	.	832;1782;1803	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	V	1803;1782;1448	ENSP00000351015:I1803V;ENSP00000348498:I1782V;ENSP00000389907:I1448V	ENSP00000348498:I1782V	I	+	1	0	NF1	26678781	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.923000	0.92808	2.295000	0.77249	0.524000	0.50904	ATT	.	.		0.463	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29654655	A	G	29654655	3	3	203	1	0	0	0	0	1	0	0	0	10365	217	8	2	5618	2	NF1	17	29654655	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	22075286	29654655	51540555	82	29787										
KRT40	125115	hgsc.bcm.edu	37	chr17	39140078	39140078	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ctagggcaacaggacacagaCcttttgttggagatcttcaa	10	9	2	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr17:39140078C>T	ENST00000398486.2	-	3	608		c.e3+1		KRT40_ENST00000377755.4_Splice_Site	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40							intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				AGGACACAGACCTTTTGTTGG	0.458																																					.		Atlas-SNP	.											.	KRT40	27	.	0			c.447+1G>A						.						154	145	148					17																	39140078		2082	4228	6310	SO:0001630	splice_region_variant	125115	exon4			CACAGACCTTTTG	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"-", "Intermediate filaments type I, keratins (acidic)"	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.447+1G>A	chr17.hg19:g.39140078C>T		69.0	0.0		74.0	5.0	NM_182497	Q6IFU5	Splice_Site	SNP	ENST00000398486.2	hg19	CCDS42320.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.928726	0.34002	.	.	ENSG00000204889	ENST00000377755;ENST00000398486	.	.	.	4.77	4.77	0.60923	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4557	0.75311	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KRT40	36393604	1.000000	0.71417	0.998000	0.56505	0.226000	0.24999	7.242000	0.78210	2.634000	0.89283	0.591000	0.81541	.	.	.		0.458	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	Intron	T	39140078	C	T	39140078	5	4	203	1	0	0	0	0	0	0	1	0	8487	521	18	3	875	3	KRT40	17	39140078	Splice_Site	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	9485423	39140078	42055132	83	29788										
ATXN7L3	56970	hgsc.bcm.edu	37	chr17	42275081	42275081	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tcctcgaccaggtccgcgtaTatctcctgagcgatggcctg	11	14	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr17:42275081T>C	ENST00000454077.2	-	2	68	c.69A>G	c.(67-69)atA>atG	p.I23M	ATXN7L3_ENST00000389384.4_Missense_Mutation_p.I23M|ATXN7L3_ENST00000593073.1_Intron|CTB-175E5.7_ENST00000586560.1_RNA	NM_020218.1	NP_064603.1			ataxin 7-like 3											kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	12		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GGTCCGCGTATATCTCCTGAG	0.562																																					p.I23M		Atlas-SNP	.											.	ATXN7L3	31	.	0			c.A69G						.						103	102	103					17																	42275081		1993	4161	6154	SO:0001583	missense	56970	exon2			CGCGTATATCTCC	AK056002	CCDS42345.1, CCDS45697.1	17q21	2010-03-10			ENSG00000087152	ENSG00000087152			25416	protein-coding gene	gene with protein product						15115762	Standard	NM_001098833		Approved	DKFZp761G2113	uc002ifz.3	Q14CW9		ENST00000454077.2:c.69A>G	chr17.hg19:g.42275081T>C	ENSP00000397259:p.Ile23Met	76.0	0.0		155.0	58.0	NM_020218		Missense_Mutation	SNP	ENST00000454077.2	hg19	CCDS45697.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.481561	0.26598	.	.	ENSG00000087152	ENST00000454077;ENST00000389384	.	.	.	4.47	-3.01	0.05463	.	0.071871	0.56097	U	0.000033	T	0.48409	0.1498	L	0.53249	1.67	0.32499	N	0.539157	P;D	0.57571	0.93;0.98	P;P	0.58331	0.564;0.837	T	0.56232	-0.8013	9	0.72032	D	0.01	.	5.1777	0.15143	0.5195:0.0:0.2576:0.2228	.	23;23	Q14CW9;Q14CW9-2	AT7L3_HUMAN;.	M	23	.	ENSP00000374035:I23M	I	-	3	3	ATXN7L3	39630607	0.935000	0.31712	0.500000	0.27589	0.031000	0.12232	-0.044000	0.12023	-0.221000	0.09973	-0.333000	0.08304	ATA	.	.		0.562	ATXN7L3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457724.1			C	42275081	T	C	42275081	3	2	203	1	0	0	0	0	1	0	0	0	1218	1396	49	2	1039	2	ATXN7L3	17	42275081	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	3135003	42275081	38920129	84	29789										
NPEPPS	9520	hgsc.bcm.edu	37	chr17	45682765	45682765	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	aggcttttgtgaatgagcccAattatactgtatggagcgac	11	7	0	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr17:45682765A>C	ENST00000322157.4	+	17	2179	c.1942A>C	c.(1942-1944)Aat>Cat	p.N648H	NPEPPS_ENST00000544660.1_Missense_Mutation_p.N568H|RP11-580I16.2_ENST00000582066.1_RNA|NPEPPS_ENST00000530173.1_Missense_Mutation_p.N644H|RP11-580I16.2_ENST00000582389.1_RNA	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	648					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						GAATGAGCCCAATTATACTGT	0.433																																					p.N648H		Atlas-SNP	.											.	NPEPPS	59	.	0			c.A1942C						.						85	77	79					17																	45682765		1851	4094	5945	SO:0001583	missense	9520	exon17			GAGCCCAATTATA	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"puromycin-sensitive aminopeptidase", "metalloproteinase MP100"	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1942A>C	chr17.hg19:g.45682765A>C	ENSP00000320324:p.Asn648His	140.0	0.0		130.0	59.0	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Missense_Mutation	SNP	ENST00000322157.4	hg19	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.836761	0.91117	.	.	ENSG00000141279	ENST00000530173;ENST00000322157;ENST00000544660	T;T;T	0.05382	3.45;3.45;3.45	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.23330	0.0564	M	0.62266	1.93	0.80722	D	1	D;P;P	0.89917	1.0;0.799;0.949	D;P;P	0.74674	0.984;0.665;0.665	T	0.00071	-1.2132	10	0.51188	T	0.08	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	644;331;648	E9PLK3;B7Z1H4;P55786	.;.;PSA_HUMAN	H	644;648;568	ENSP00000433287:N644H;ENSP00000320324:N648H;ENSP00000442461:N568H	ENSP00000320324:N648H	N	+	1	0	NPEPPS	43037764	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.367000	0.80283	0.528000	0.53228	AAT	.	.		0.433	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310		C	45682765	A	C	45682765	3	2	203	1	0	0	0	0	1	0	0	0	10584	130	5	5	2008	5	NPEPPS	17	45682765	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	3407684	45682765	35512445	85	29790										
FAM117A	81558	hgsc.bcm.edu	37	chr17	47797246	47797246	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gggaccctgaggggaagctgGgaggggacgcctgaggaaga	21	7	0	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr17:47797246G>C	ENST00000240364.2	-	5	663	c.584C>G	c.(583-585)cCc>cGc	p.P195R	FAM117A_ENST00000513602.1_5'UTR|RP11-613C6.2_ENST00000512720.1_RNA|FAM117A_ENST00000514018.1_5'UTR	NM_030802.3	NP_110429.1	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A	195										haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	17						GGGGAAGCTGGGAGGGGACGC	0.572																																					p.P195R		Atlas-SNP	.											.	FAM117A	45	.	0			c.C584G						.						39	42	41					17																	47797246		2203	4300	6503	SO:0001583	missense	81558	exon5			AAGCTGGGAGGGG	BC037572	CCDS11553.1	17q21.33	2006-04-26				ENSG00000121104			24179	protein-coding gene	gene with protein product	"C/EBP induced protein"					12477932	Standard	NM_030802		Approved		uc002ipk.3	Q9C073		ENST00000240364.2:c.584C>G	chr17.hg19:g.47797246G>C	ENSP00000240364:p.Pro195Arg	17.0	0.0		20.0	12.0	NM_030802	B7Z7Q3	Missense_Mutation	SNP	ENST00000240364.2	hg19	CCDS11553.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.794226	0.70452	.	.	ENSG00000121104	ENST00000240364;ENST00000511743;ENST00000506156	.	.	.	5.27	5.27	0.74061	.	0.171334	0.40144	N	0.001165	T	0.66479	0.2793	L	0.43152	1.355	0.80722	D	1	D	0.71674	0.998	D	0.69142	0.962	T	0.57780	-0.7752	9	0.15066	T	0.55	-10.6021	16.8994	0.86109	0.0:0.0:1.0:0.0	.	195	Q9C073	F117A_HUMAN	R	195;85;163	.	ENSP00000240364:P195R	P	-	2	0	FAM117A	45152245	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.957000	0.56730	2.764000	0.94973	0.556000	0.70494	CCC	.	.		0.572	FAM117A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365736.1	NM_030802		C	47797246	G	C	47797246	3	2	203	1	0	0	0	0	1	0	0	0	5414	1232	43	4	793	4	FAM117A	17	47797246	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	2114481	47797246	33397964	86	29791										
ABCC3	8714	hgsc.bcm.edu	37	chr17	48746768	48746768	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ccagaactgcactcttcaggAaaacgtgcttttcggcaaag	9	11	2	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr17:48746768A>G	ENST00000285238.8	+	17	2200	c.2120A>G	c.(2119-2121)gAa>gGa	p.E707G		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	707	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	ACTCTTCAGGAAAACGTGCTT	0.602																																					p.E707G		Atlas-SNP	.											.	ABCC3	138	.	0			c.A2120G						.						93	87	89					17																	48746768		2203	4300	6503	SO:0001583	missense	8714	exon17			TTCAGGAAAACGT	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"ATP binding cassette transporters / subfamily C"	54	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter 2"	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.2120A>G	chr17.hg19:g.48746768A>G	ENSP00000285238:p.Glu707Gly	99.0	0.0		107.0	6.0	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	hg19	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	A	19.43	3.825576	0.71143	.	.	ENSG00000108846	ENST00000285238	D	0.95272	-3.66	4.36	4.36	0.52297	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.121261	0.52532	D	0.000064	D	0.95478	0.8531	M	0.89214	3.015	0.53688	D	0.999979	P	0.47409	0.895	P	0.45343	0.477	D	0.96228	0.9166	10	0.87932	D	0	-14.8594	14.0203	0.64550	1.0:0.0:0.0:0.0	.	707	O15438	MRP3_HUMAN	G	707	ENSP00000285238:E707G	ENSP00000285238:E707G	E	+	2	0	ABCC3	46101767	1.000000	0.71417	0.997000	0.53966	0.588000	0.36517	9.139000	0.94554	1.972000	0.57404	0.260000	0.18958	GAA	.	.		0.602	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		G	48746768	A	G	48746768	3	3	203	1	0	0	0	0	1	0	0	0	54	246	9	2	2270	2	ABCC3	17	48746768	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	949522	48746768	32448442	87	29792										
DNAI2	64446	hgsc.bcm.edu	37	chr17	72285824	72285824	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tggcatactcctgcttggatTttcagcgggcacctgtgggc	13	11	1	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr17:72285824T>A	ENST00000311014.6	+	5	626	c.559T>A	c.(559-561)Ttt>Att	p.F187I	DNAI2_ENST00000446837.2_Missense_Mutation_p.F187I|DNAI2_ENST00000307504.5_Missense_Mutation_p.F44I|DNAI2_ENST00000579490.1_Missense_Mutation_p.F244I|DNAI2_ENST00000582036.1_Missense_Mutation_p.F187I			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	187					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						CTGCTTGGATTTTCAGCGGGC	0.627									Kartagener syndrome																												p.F187I		Atlas-SNP	.											.	DNAI2	102	.	0			c.T559A						.						69	67	68					17																	72285824		2203	4300	6503	SO:0001583	missense	64446	exon5	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TTGGATTTTCAGC	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"Axonemal dyneins", "WD repeat domain containing"	18744	protein-coding gene	gene with protein product	"dynein intermediate chain 2"	605483	"dynein, axonemal, intermediate polypeptide 2"			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.559T>A	chr17.hg19:g.72285824T>A	ENSP00000308312:p.Phe187Ile	96.0	0.0		104.0	43.0	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Missense_Mutation	SNP	ENST00000311014.6	hg19	CCDS11697.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.567727	0.86439	.	.	ENSG00000171595	ENST00000311014;ENST00000307504;ENST00000446837	T;T;T	0.19250	2.16;2.16;2.16	5.01	3.93	0.45458	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.49081	0.1536	M	0.87900	2.915	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.53070	-0.8490	10	0.87932	D	0	-15.0622	10.4697	0.44629	0.0:0.0771:0.0:0.9229	.	187	Q9GZS0	DNAI2_HUMAN	I	187;44;187	ENSP00000308312:F187I;ENSP00000302929:F44I;ENSP00000400252:F187I	ENSP00000302929:F44I	F	+	1	0	DNAI2	69797419	1.000000	0.71417	0.603000	0.28903	0.955000	0.61496	7.275000	0.78548	0.769000	0.33313	0.260000	0.18958	TTT	.	.		0.627	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036		A	72285824	T	A	72285824	3	1	203	1	0	0	0	0	1	0	0	0	4612	1841	64	4	573	4	DNAI2	17	72285824	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	23539056	72285824	8909386	88	29793										
RNF126	55658	hgsc.bcm.edu	37	chr19	651657	651657	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ccggccggtggcccgccgcgTggtgaggcgggcgcggggct	22	14	0	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr19:651657T>A	ENST00000292363.5	-	4	552	c.397A>T	c.(397-399)Acg>Tcg	p.T133S		NM_194460.2	NP_919442.1			ring finger protein 126											lung(1)	1		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCCGCCGCGTGGTGAGGCGG	0.771																																					p.T133S		Atlas-SNP	.											.	RNF126	15	.	0			c.A397T						.						4	5	5					19																	651657		1648	3353	5001	SO:0001583	missense	55658	exon4			GCCGCGTGGTGAG	BC025374	CCDS12039.1	19p13.3	2013-01-09				ENSG00000070423		"RING-type (C3HC4) zinc fingers"	21151	protein-coding gene	gene with protein product		615177					Standard	NM_194460		Approved	FLJ20552	uc010drs.3	Q9BV68		ENST00000292363.5:c.397A>T	chr19.hg19:g.651657T>A	ENSP00000292363:p.Thr133Ser	72.0	0.0		72.0	32.0	NM_194460		Missense_Mutation	SNP	ENST00000292363.5	hg19	CCDS12039.1	.	.	.	.	.	.	.	.	.	.	t	2.200	-0.383196	0.04966	.	.	ENSG00000070423	ENST00000292363;ENST00000340092	T	0.13657	2.57	4.42	2.23	0.28157	.	0.419028	0.24377	N	0.039060	T	0.06462	0.0166	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.42292	-0.9460	10	0.08837	T	0.75	.	5.6165	0.17434	0.0:0.6451:0.1626:0.1923	.	133	Q9BV68-2	.	S	133	ENSP00000292363:T133S	ENSP00000292363:T133S	T	-	1	0	RNF126	602657	0.054000	0.20591	0.009000	0.14445	0.982000	0.71751	0.336000	0.19823	0.376000	0.24707	-0.464000	0.05259	ACG	.	.		0.771	RNF126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452104.2	NM_017876		A	651657	T	A	651657	3	1	203	1	0	0	0	0	1	0	0	0	13450	1696	59	4	562	4	RNF126	19	651657	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10		651657	58477326	89	29794										
MUC16	94025	hgsc.bcm.edu	37	chr19	9057497	9057497	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ctaggaggaacagttgagtgGgtccttgccaagggggctgt	17	7	0	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr19:9057497G>A	ENST00000397910.4	-	3	30152	c.29949C>T	c.(29947-29949)acC>acT	p.T9983T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9985	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGTTGAGTGGGTCCTTGCCA	0.458																																					p.T9983T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C29949T						.						182	178	179					19																	9057497		1948	4143	6091	SO:0001819	synonymous_variant	94025	exon3			TGAGTGGGTCCTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29949C>T	chr19.hg19:g.9057497G>A		122.0	0.0		170.0	68.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9057497	G	A	9057497	2	1	203	1	0	0	0	0	0	0	0	1	9982	1219	43	3		3	MUC16	19	9057497	Silent	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	8405840	9057497	50071486	90	29795										
ZNF799	90576	hgsc.bcm.edu	37	chr19	12502155	12502155	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gtgagttctttcatgactttTcagtgaactaggacaatcaa	8	7	4	3	rs201335235		TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr19:12502155T>G	ENST00000430385.3	-	4	1257	c.1057A>C	c.(1057-1059)Aaa>Caa	p.K353Q	ZNF799_ENST00000419318.1_Missense_Mutation_p.K321Q|CTD-3105H18.14_ENST00000435033.1_Intron	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	353					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						TCATGACTTTTCAGTGAACTA	0.413																																					p.K353Q		Atlas-SNP	.											.	ZNF799	111	.	0			c.A1057C						.						160	156	157					19																	12502155		2203	4300	6503	SO:0001583	missense	90576	exon4			GACTTTTCAGTGA	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"Zinc fingers, C2H2-type", "-"	28071	protein-coding gene	gene with protein product			"zinc finger protein 842"	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1057A>C	chr19.hg19:g.12502155T>G	ENSP00000411084:p.Lys353Gln	60.0	0.0		82.0	8.0	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	hg19	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.323810	0.01309	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.04406	3.63;3.63	1.31	-1.61	0.08399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.12527	0.23	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49041	-0.8980	9	0.14252	T	0.57	.	6.8386	0.23951	0.0:0.0:0.2963:0.7037	.	353	Q96GE5	ZN799_HUMAN	Q	321;353	ENSP00000415278:K321Q;ENSP00000411084:K353Q	ENSP00000415278:K321Q	K	-	1	0	ZNF799	12363155	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.687000	0.05156	-0.936000	0.03723	-1.919000	0.00516	AAA	.	.		0.413	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		G	12502155	T	G	12502155	3	3	203	1	0	0	0	0	1	0	0	0	18181	1792	62	5	878	5	ZNF799	19	12502155	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	3444658	12502155	46626828	91	29796										
PRKACA	5566	hgsc.bcm.edu	37	chr19	14208652	14208652	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tgagatccagcgagtgcagaTactcaaaggtcaggacgatc	12	9	2	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr19:14208652T>C	ENST00000308677.4	-	6	666	c.470A>G	c.(469-471)tAt>tGt	p.Y157C	PRKACA_ENST00000589994.1_Missense_Mutation_p.Y149C|PRKACA_ENST00000590853.1_Intron|PRKACA_ENST00000350356.3_5'UTR	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	157	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						CGAGTGCAGATACTCAAAGGT	0.587																																					p.Y157C		Atlas-SNP	.											.	PRKACA	65	.	0			c.A470G						.						87	85	85					19																	14208652		2203	4300	6503	SO:0001583	missense	5566	exon6			TGCAGATACTCAA		CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	2.7.11.1		9380	protein-coding gene	gene with protein product		601639				8884279	Standard	NM_002730		Approved	PKACa	uc002myc.3	P17612		ENST00000308677.4:c.470A>G	chr19.hg19:g.14208652T>C	ENSP00000309591:p.Tyr157Cys	128.0	0.0		173.0	46.0	NM_002730	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Missense_Mutation	SNP	ENST00000308677.4	hg19	CCDS12304.1	.	.	.	.	.	.	.	.	.	.	T	19.67	3.871272	0.72065	.	.	ENSG00000072062	ENST00000308677;ENST00000350356;ENST00000535695;ENST00000536649	T	0.75260	-0.92	4.76	4.76	0.60689	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.39985	N	0.001215	D	0.86016	0.5832	M	0.84219	2.685	0.49213	D	0.999769	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.87946	0.2720	10	0.87932	D	0	.	12.2331	0.54499	0.0:0.0:0.0:1.0	.	99;140;157;149	B7Z708;Q15136;P17612;P17612-2	.;.;KAPCA_HUMAN;.	C	157;149;157;99	ENSP00000309591:Y157C	ENSP00000309591:Y157C	Y	-	2	0	PRKACA	14069652	1.000000	0.71417	0.965000	0.40720	0.850000	0.48378	7.867000	0.87062	1.780000	0.52325	0.472000	0.43445	TAT	.	.		0.587	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730		C	14208652	T	C	14208652	3	2	203	1	0	0	0	0	1	0	0	0	12509	1406	49	2	605	2	PRKACA	19	14208652	Missense_Mutation	SNP	T	TCGA-DD-AADV-01A-11D-A38X-10	1706497	14208652	44920331	92	29797										
MAP1S	55201	hgsc.bcm.edu	37	chr19	17837405	17837405	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ctgcacccgccctccgccggCgccgagcgcacgctggcctc	12	22	0	0	rs374141963		TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr19:17837405C>T	ENST00000324096.4	+	5	1363	c.1212C>T	c.(1210-1212)ggC>ggT	p.G404G	MAP1S_ENST00000544059.2_Silent_p.G378G|MAP1S_ENST00000597681.1_Intron|CTD-3149D2.4_ENST00000595363.1_RNA	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	404	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CCTCCGCCGGCGCCGAGCGCA	0.731													C|||	1	0.000199681	8e-04	0	5008	,	,		12383	0		0	False		,,,				2504	0				p.G404G		Atlas-SNP	.											.	MAP1S	74	.	0			c.C1212T						.	C		2,4144		0,2,2071	6	6	6		1212	-2.9	0	19		6	0,8122		0,0,4061	no	coding-synonymous	MAP1S	NM_018174.4		0,2,6132	TT,TC,CC		0.0,0.0482,0.0163		404/1060	17837405	2,12266	2073	4061	6134	SO:0001819	synonymous_variant	55201	exon5			CGCCGGCGCCGAG	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.1212C>T	chr19.hg19:g.17837405C>T		75.0	0.0		70.0	16.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Silent	SNP	ENST00000324096.4	hg19	CCDS32954.1																																																																																			.	.		0.731	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		T	17837405	C	T	17837405	2	4	203	1	0	0	0	0	0	0	0	1	9243	755	27	1		1	MAP1S	19	17837405	Silent	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	3628753	17837405	41291578	93	29798										
ZNF99	7652	hgsc.bcm.edu	37	chr19	22952081	22952081	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	catgtccaggcattgccactCctccagagcgaattctatgg	9	13	1	1	rs149345966	byFrequency	TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr19:22952081C>A	ENST00000596209.1	-	2	139	c.49G>T	c.(49-51)Gag>Tag	p.E17*	ZNF99_ENST00000397104.3_Nonsense_Mutation_p.E38*	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	17	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				CATTGCCACTCCTCCAGAGCG	0.403																																					p.E17X		Atlas-SNP	.											.	ZNF99	273	.	0			c.G49T						.						79	85	83					19																	22952081		2198	4300	6498	SO:0001587	stop_gained	7652	exon2			GCCACTCCTCCAG	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.49G>T	chr19.hg19:g.22952081C>A	ENSP00000472969:p.Glu17*	219.0	0.0		261.0	96.0	NM_001080409	M0R335	Nonsense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	c	14.42	2.529080	0.44969	.	.	ENSG00000213973	ENST00000397104	.	.	.	1.05	1.05	0.20165	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	5.3627	0.16098	0.0:1.0:0.0:0.0	.	.	.	.	X	38	.	ENSP00000380293:E38X	E	-	1	0	ZNF99	22743921	0.948000	0.32251	0.094000	0.20943	0.091000	0.18340	2.310000	0.43708	0.482000	0.27582	0.485000	0.47835	GAG	.	C|0.995;T|0.005		0.403	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		A	22952081	C	A	22952081	4	1	203	1	0	0	0	0	0	1	0	0	18219	864	30	3	3024	3	ZNF99	19	22952081	Nonsense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	5114676	22952081	36176902	94	29799										
LRFN1	57622	hgsc.bcm.edu	37	chr19	39805143	39805143	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tagcggtcggtgaggtgttcGggcgtggcgcaggtctctaa	18	8	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr19:39805143G>A	ENST00000248668.4	-	1	833	c.834C>T	c.(832-834)ccC>ccT	p.P278P	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	278	LRRCT.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			TGAGGTGTTCGGGCGTGGCGC	0.692																																					p.P278P		Atlas-SNP	.											.	LRFN1	59	.	0			c.C834T						.						25	32	30					19																	39805143		2186	4285	6471	SO:0001819	synonymous_variant	57622	exon1			GTGTTCGGGCGTG	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.834C>T	chr19.hg19:g.39805143G>A		82.0	0.0		87.0	43.0	NM_020862	Q8TBS9	Silent	SNP	ENST00000248668.4	hg19	CCDS46071.1																																																																																			.	.		0.692	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862		A	39805143	G	A	39805143	2	1	203	1	0	0	0	0	0	0	0	1	8946	1103	39	1		1	LRFN1	19	39805143	Silent	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10	16853062	39805143	19323840	95	29800										
MYBPC2	4606	hgsc.bcm.edu	37	chr19	50958529	50958529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gggtctcccagcccagcatgAacaccaagccttttatgcct	8	15	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr19:50958529A>G	ENST00000357701.5	+	19	2230	c.2179A>G	c.(2179-2181)Aac>Gac	p.N727D		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	727	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		GCCCAGCATGAACACCAAGCC	0.507																																					p.N727D		Atlas-SNP	.											.	MYBPC2	103	.	0			c.A2179G						.						163	162	162					19																	50958529		2041	4190	6231	SO:0001583	missense	4606	exon19			AGCATGAACACCA		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7550	protein-coding gene	gene with protein product	"fast-type muscle myosin-binding-protein C"	160793	"myosin-binding protein C, fast-type"			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.2179A>G	chr19.hg19:g.50958529A>G	ENSP00000350332:p.Asn727Asp	97.0	0.0		101.0	33.0	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	hg19	CCDS46152.1	.	.	.	.	.	.	.	.	.	.	a	13.30	2.196586	0.38806	.	.	ENSG00000086967	ENST00000357701	T	0.53640	0.61	4.27	3.25	0.37280	Fibronectin, type III (2);Immunoglobulin-like fold (1);	2.187960	0.03455	U	0.211213	T	0.51058	0.1652	M	0.69823	2.125	0.30689	N	0.751504	B	0.23540	0.087	B	0.25759	0.063	T	0.39683	-0.9602	10	0.36615	T	0.2	.	8.2545	0.31746	0.8224:0.0:0.0:0.1776	.	727	Q14324	MYPC2_HUMAN	D	727	ENSP00000350332:N727D	ENSP00000350332:N727D	N	+	1	0	MYBPC2	55650341	0.028000	0.19301	0.992000	0.48379	0.915000	0.54546	0.732000	0.26072	0.624000	0.30286	-0.557000	0.04193	AAC	.	.		0.507	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533		G	50958529	A	G	50958529	3	3	203	1	0	0	0	0	1	0	0	0	10021	246	9	2	2253	2	MYBPC2	19	50958529	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	11153386	50958529	8170454	96	29801										
XRN2	22803	hgsc.bcm.edu	37	chr20	21329027	21329027	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tatttccagctgcaagtggtAattttctacctccatcatgg	7	10	2	0			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr20:21329027A>T	ENST00000377191.3	+	19	1917	c.1822A>T	c.(1822-1824)Aat>Tat	p.N608Y	XRN2_ENST00000430571.2_Missense_Mutation_p.N532Y|XRN2_ENST00000539513.1_Missense_Mutation_p.N554Y	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	608					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						TGCAAGTGGTAATTTTCTACC	0.363																																					p.N608Y		Atlas-SNP	.											.	XRN2	90	.	0			c.A1822T						.						107	113	111					20																	21329027		2203	4300	6503	SO:0001583	missense	22803	exon19			AGTGGTAATTTTC	AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.1822A>T	chr20.hg19:g.21329027A>T	ENSP00000366396:p.Asn608Tyr	83.0	0.0		93.0	26.0	NM_012255	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Missense_Mutation	SNP	ENST00000377191.3	hg19	CCDS13144.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.546687	0.86022	.	.	ENSG00000088930	ENST00000377191;ENST00000430571;ENST00000539513	T;T;T	0.74842	-0.88;-0.88;-0.88	5.7	5.7	0.88788	.	0.040148	0.85682	D	0.000000	T	0.78162	0.4240	L	0.55834	1.745	0.80722	D	1	D	0.60575	0.988	P	0.51615	0.675	T	0.79303	-0.1859	10	0.49607	T	0.09	-12.3154	15.9504	0.79830	1.0:0.0:0.0:0.0	.	608	Q9H0D6	XRN2_HUMAN	Y	608;532;554	ENSP00000366396:N608Y;ENSP00000413548:N532Y;ENSP00000441113:N554Y	ENSP00000366396:N608Y	N	+	1	0	XRN2	21277027	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.735000	0.91549	2.163000	0.67991	0.482000	0.46254	AAT	.	.		0.363	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255		T	21329027	A	T	21329027	3	4	203	1	0	0	0	0	1	0	0	0	17475	362	13	4	1896	4	XRN2	20	21329027	Missense_Mutation	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10		21329027	41696493	97	29802										
MPPED1	758	hgsc.bcm.edu	37	chr22	43898542	43898542	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	aggcttcctggactgggtccCcaagaagatgcagcgggtgg	16	10	0	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chr22:43898542C>T	ENST00000417669.2	+	6	1211	c.767C>T	c.(766-768)cCc>cTc	p.P256L	MPPED1_ENST00000538182.1_Missense_Mutation_p.P289L|MPPED1_ENST00000439548.1_Missense_Mutation_p.P98L|MPPED1_ENST00000542779.1_Missense_Mutation_p.P256L|MPPED1_ENST00000443721.1_Missense_Mutation_p.P256L|MPPED1_ENST00000414469.2_Missense_Mutation_p.P150L			O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1	256							hydrolase activity (GO:0016787)			endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|skin(1)	13		all_neural(38;0.0244)|Ovarian(80;0.0694)				GACTGGGTCCCCAAGAAGATG	0.632																																					p.P256L		Atlas-SNP	.											.	MPPED1	59	.	0			c.C767T						.						63	76	72					22																	43898542		2181	4292	6473	SO:0001583	missense	758	exon6			GGGTCCCCAAGAA	U84894	CCDS46723.1	22q13.2	2013-09-20	2005-10-10	2005-10-10	ENSG00000186732	ENSG00000186732			1306	protein-coding gene	gene with protein product		602112	"chromosome 22 open reading frame 1"	C22orf1		9266672, 10591208	Standard	NM_001044370		Approved	239AB, FAM1A	uc011apv.2	O15442	OTTHUMG00000150566	ENST00000417669.2:c.767C>T	chr22.hg19:g.43898542C>T	ENSP00000388137:p.Pro256Leu	46.0	0.0		85.0	34.0	NM_001044370	A8K159|B7Z2S9|Q8N361	Missense_Mutation	SNP	ENST00000417669.2	hg19	CCDS46723.1	.	.	.	.	.	.	.	.	.	.	C	6.713	0.500199	0.12762	.	.	ENSG00000186732	ENST00000417669;ENST00000443721;ENST00000545165;ENST00000414469;ENST00000439548;ENST00000542779;ENST00000538182	T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16	4.27	4.27	0.50696	Metallophosphoesterase domain (1);	.	.	.	.	T	0.32645	0.0836	L	0.35487	1.065	0.80722	D	1	P;P	0.50443	0.935;0.817	P;B	0.46917	0.531;0.291	T	0.04855	-1.0922	9	0.10902	T	0.67	.	17.1345	0.86735	0.0:1.0:0.0:0.0	.	289;256	B7Z2S9;O15442	.;MPPD1_HUMAN	L	256;256;234;150;98;256;289	ENSP00000388137:P256L;ENSP00000400686:P256L;ENSP00000388245:P150L;ENSP00000390379:P98L;ENSP00000444532:P256L;ENSP00000438335:P289L	ENSP00000388245:P150L	P	+	2	0	MPPED1	42229871	1.000000	0.71417	1.000000	0.80357	0.055000	0.15305	7.090000	0.76916	2.126000	0.65437	0.399000	0.26434	CCC	.	.		0.632	MPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318938.2	NM_001044370		T	43898542	C	T	43898542	3	4	203	1	0	0	0	0	1	0	0	0	9750	623	22	3	665	3	MPPED1	22	43898542	Missense_Mutation	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10		43898542	7406024	98	29803										
SFRS17A	8227	hgsc.bcm.edu	37	chrX	1720179	1720179	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ggggccgggccaccggagacGggcttgctgaccggcacaag	18	13	0	2			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chrX:1720179G>C	ENST00000313871.3	+	5	1976	c.1780G>C	c.(1780-1782)Ggg>Cgg	p.G594R		NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	594	Arg-rich.				B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						CACCGGAGACGGGCTTGCTGA	0.701																																					p.G594R		Atlas-SNP	.											.	AKAP17A	46	.	0			c.G1780C						.						25	33	31					X																	1720179		2201	4292	6493	SO:0001583	missense	8227	exon5			GGAGACGGGCTTG	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"Pseudoautosomal regions / PAR1", "A-kinase anchor proteins"	18783	protein-coding gene	gene with protein product		312095, 465000	"chromosome X and Y open reading frame 3", "splicing factor, arginine/serine-rich 17A"	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.1780G>C	chrX.hg19:g.1720179G>C	ENSP00000324827:p.Gly594Arg	54.0	0.0		73.0	26.0	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Missense_Mutation	SNP	ENST00000313871.3	hg19	CCDS14116.1	.	.	.	.	.	.	.	.	.	.	g	0.064	-1.216320	0.01542	.	.	ENSG00000197976	ENST00000313871	T	0.13089	2.62	1.41	0.269	0.15631	.	0.695830	0.10406	N	0.678588	T	0.15435	0.0372	.	.	.	0.09310	N	1	P	0.51449	0.945	P	0.54706	0.759	T	0.27331	-1.0077	9	0.16420	T	0.52	.	5.8575	0.18728	0.4609:0.0:0.5391:0.0	.	594	Q02040	AK17A_HUMAN	R	594	ENSP00000324827:G594R	ENSP00000324827:G594R	G	+	1	0	AKAP17A	1680179	0.013000	0.17824	0.008000	0.14137	0.007000	0.05969	1.090000	0.30902	0.367000	0.24454	0.367000	0.22151	GGG	.	G|1.000;A|0.000		0.701	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		C	1720179	G	C	1720179	3	2	203	1	0	0	0	0	1	0	0	0	14188	1116	39	4	1794	4	SFRS17A	23	1720179	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10		1720179	153550381	99	29804										
SYN1	6853	hgsc.bcm.edu	37	chrX	47479089	47479089	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	ccatttggcagattggccatAaagttgctgtccgacaggcg	12	10	0	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chrX:47479089A>G	ENST00000295987.7	-	1	163	c.39T>C	c.(37-39)ttT>ttC	p.F13F	SYN1_ENST00000340666.4_Silent_p.F13F	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	13	A.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						GATTGGCCATAAAGTTGCTGT	0.706																																					p.F13F		Atlas-SNP	.											.	SYN1	84	.	0			c.T39C						.						9	7	7					X																	47479089		2078	4063	6141	SO:0001819	synonymous_variant	6853	exon1			GGCCATAAAGTTG		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.39T>C	chrX.hg19:g.47479089A>G		649.0	0.0		722.0	85.0	NM_006950	B1AJQ1|O75825|Q5H9A9	Silent	SNP	ENST00000295987.7	hg19	CCDS14280.1																																																																																			.	.		0.706	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950		G	47479089	A	G	47479089	2	3	203	1	0	0	0	0	0	0	0	1	15455	359	13	2		2	SYN1	23	47479089	Silent	SNP	A	TCGA-DD-AADV-01A-11D-A38X-10	45758910	47479089	107791471	100	29805										
ARMCX3	51566	hgsc.bcm.edu	37	chrX	100880299	100880299	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	gctgtccagaaacgggcttcCcccaattcagatgataccgt	9	13	1	3			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chrX:100880299C>T	ENST00000341189.4	+	5	1196	c.330C>T	c.(328-330)tcC>tcT	p.S110S	ARMCX3-AS1_ENST00000454228.1_RNA|RP4-545K15.5_ENST00000564612.1_RNA|ARMCX3_ENST00000471229.2_Silent_p.S110S|ARMCX3_ENST00000537169.1_Silent_p.S110S	NM_016607.3	NP_057691.1	Q9UH62	ARMX3_HUMAN	armadillo repeat containing, X-linked 3	110					cellular protein localization (GO:0034613)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of mitochondrial outer membrane (GO:0031307)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11						AACGGGCTTCCCCCAATTCAG	0.532																																					p.S110S		Atlas-SNP	.											.	ARMCX3	33	.	0			c.C330T						.						57	52	54					X																	100880299		2202	4299	6501	SO:0001819	synonymous_variant	51566	exon5			GGCTTCCCCCAAT	AY359079	CCDS14489.1	Xq22.1	2014-03-21			ENSG00000102401	ENSG00000102401		"Armadillo repeat containing"	24065	protein-coding gene	gene with protein product		300364				11162520, 11042152, 19304657, 16221301, 22569362	Standard	NM_016607		Approved	ALEX3, GASP6	uc004eia.1	Q9UH62	OTTHUMG00000022035	ENST00000341189.4:c.330C>T	chrX.hg19:g.100880299C>T		83.0	0.0		82.0	42.0	NM_016607	Q53HC6|Q7LCF5|Q9NPE4	Silent	SNP	ENST00000341189.4	hg19	CCDS14489.1																																																																																			.	.		0.532	ARMCX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057568.2	NM_016607		T	100880299	C	T	100880299	2	4	203	1	0	0	0	0	0	0	0	1	961	610	22	3		3	ARMCX3	23	100880299	Silent	SNP	C	TCGA-DD-AADV-01A-11D-A38X-10	53401210	100880299	54390261	101	29806										
DDX3Y	8653	hgsc.bcm.edu	37	chrY	15029320	15029320	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0891089108910891	9	1	1.50810810810811	2.23423423423423	1.07243243243243	1	1	0	tatttttgcttacagtaataGattcagtggaggatttggtg	11	3	1	1			TCGA-DD-AADV-01A-11D-A38X-10	TCGA-DD-AADV-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4a967238-8845-4088-bf2c-df021fad1a5e	7fedcbf5-4417-4700-b02a-a4d71e5e7e33	g.chrY:15029320G>C	ENST00000336079.3	+	16	1875	c.1769G>C	c.(1768-1770)aGa>aCa	p.R590T	DDX3Y_ENST00000360160.4_Missense_Mutation_p.R590T	NM_001122665.1|NM_004660.3	NP_001116137.1|NP_004651.2	O15523	DDX3Y_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, Y-linked	590						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			kidney(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	5						TACAGTAATAGATTCAGTGGA	0.428																																					p.R590T		Atlas-SNP	.											.	DDX3Y	13	.	0			c.G1769C						.						97	89	91					Y																	15029320		618	1977	2595	SO:0001583	missense	8653	exon16			GTAATAGATTCAG	AF000984	CCDS14782.1	Yq11	2013-07-16	2013-07-16	2003-06-20	ENSG00000067048	ENSG00000067048		"DEAD-boxes"	2699	protein-coding gene	gene with protein product		400010	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide, Y chromosome", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked"	DBY		9381176	Standard	NM_004660		Approved		uc004fsv.2	O15523	OTTHUMG00000036324	ENST00000336079.3:c.1769G>C	chrY.hg19:g.15029320G>C	ENSP00000336725:p.Arg590Thr	91.0	0.0		129.0	76.0	NM_004660	B4DK29|B4DXX7|Q8IYV7	Missense_Mutation	SNP	ENST00000336079.3	hg19	CCDS14782.1																																																																																			.	.		0.428	DDX3Y-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088407.1	NM_004660		C	15029320	G	C	15029320	3	2	203	1	0	0	0	0	1	0	0	0	4361	942	33	4	1831	4	DDX3Y	24	15029320	Missense_Mutation	SNP	G	TCGA-DD-AADV-01A-11D-A38X-10		15029320	44344246	102	29807										
PADI3	51702	hgsc.bcm.edu	37	chr1	17586227	17586227	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	tcatcgtggtcatgaactccCccagcaatgacctcaacgac	7	15	3	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr1:17586227C>G	ENST00000375460.3	+	2	287	c.247C>G	c.(247-249)Ccc>Gcc	p.P83A		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	83					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CATGAACTCCCCCAGCAATGA	0.597																																					p.P83A		Atlas-SNP	.											.	PADI3	81	.	0			c.C247G						.						71	56	61					1																	17586227		2203	4300	6503	SO:0001583	missense	51702	exon2			AACTCCCCCAGCA	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"Peptidyl arginine deiminases"	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.247C>G	chr1.hg19:g.17586227C>G	ENSP00000364609:p.Pro83Ala	150.0	0.0		77.0	7.0	NM_016233	Q58EY7|Q70SX5	Missense_Mutation	SNP	ENST00000375460.3	hg19	CCDS179.1	.	.	.	.	.	.	.	.	.	.	C	6.456	0.452311	0.12283	.	.	ENSG00000142619	ENST00000375460	T	0.09073	3.02	5.2	5.2	0.72013	Cupredoxin (1);Protein-arginine deiminase (PAD) N-terminal (1);	0.134229	0.51477	D	0.000094	T	0.06826	0.0174	L	0.28274	0.84	0.31970	N	0.607346	P	0.43788	0.817	P	0.44673	0.457	T	0.01679	-1.1297	10	0.05436	T	0.98	-28.0261	11.4191	0.49971	0.18:0.82:0.0:0.0	.	83	Q9ULW8	PADI3_HUMAN	A	83	ENSP00000364609:P83A	ENSP00000364609:P83A	P	+	1	0	PADI3	17458814	0.991000	0.36638	0.998000	0.56505	0.990000	0.78478	3.854000	0.55949	2.421000	0.82119	0.563000	0.77884	CCC	.	.		0.597	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1			G	17586227	C	G	17586227	3	3	204	1	0	0	0	0	1	0	0	0	11388	623	22	4	253	4	PADI3	1	17586227	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10		17586227	231664394	1	29808										
COL8A2	1296	hgsc.bcm.edu	37	chr1	36563771	36563771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	cccctgggggccccgtgggcCcagccgtgccaggttcccct	14	19	0	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr1:36563771C>T	ENST00000397799.1	-	4	1735	c.1511G>A	c.(1510-1512)gGg>gAg	p.G504E	COL8A2_ENST00000481785.1_Missense_Mutation_p.G439E|COL8A2_ENST00000303143.4_Missense_Mutation_p.G504E			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	504	Triple-helical region.				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCCCGTGGGCCCAGCCGTGCC	0.766																																					p.G504E		Atlas-SNP	.											.	COL8A2	41	.	0			c.G1511A						.						2	2	2					1																	36563771		1406	3161	4567	SO:0001583	missense	1296	exon2			GTGGGCCCAGCCG	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"Collagens"	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.1511G>A	chr1.hg19:g.36563771C>T	ENSP00000380901:p.Gly504Glu	58.0	0.0		53.0	22.0	NM_005202	Q5JV31|Q8TEJ5	Missense_Mutation	SNP	ENST00000397799.1	hg19	CCDS403.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.167659	0.57476	.	.	ENSG00000171812	ENST00000303143;ENST00000397799;ENST00000481785	D;D;D	0.99532	-6.1;-6.1;-6.1	4.08	4.08	0.47627	.	0.000000	0.85682	D	0.000000	D	0.99725	0.9893	H	0.94306	3.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97044	0.9759	10	0.87932	D	0	.	16.824	0.85926	0.0:1.0:0.0:0.0	.	504	P25067	CO8A2_HUMAN	E	504;504;439	ENSP00000305913:G504E;ENSP00000380901:G504E;ENSP00000436433:G439E	ENSP00000305913:G504E	G	-	2	0	COL8A2	36336358	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	7.561000	0.82288	2.279000	0.76181	0.462000	0.41574	GGG	.	.		0.766	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202		T	36563771	C	T	36563771	3	4	204	1	0	0	0	0	1	0	0	0	3708	623	22	3	604	3	COL8A2	1	36563771	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	18977544	36563771	212686850	2	29809										
NEGR1	257194	hgsc.bcm.edu	37	chr1	71873213	71873213	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	taccagcaggagaaaagaacAtcagcgctcccggtaattcc	9	12	1	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr1:71873213A>T	ENST00000357731.5	-	7	1220	c.981T>A	c.(979-981)gaT>gaA	p.D327E	ZRANB2-AS2_ENST00000587066.1_RNA|ZRANB2-AS2_ENST00000585415.1_RNA|ZRANB2-AS2_ENST00000586006.1_RNA|ZRANB2-AS2_ENST00000608579.1_RNA|ZRANB2-AS2_ENST00000585499.1_RNA|ZRANB2-AS2_ENST00000590186.1_RNA|ZRANB2-AS2_ENST00000430605.1_RNA|ZRANB2-AS2_ENST00000587306.1_RNA|NEGR1_ENST00000306821.3_Missense_Mutation_p.D199E|NEGR1_ENST00000434200.1_Missense_Mutation_p.D281E	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1	327					feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|positive regulation of neuron projection development (GO:0010976)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(4)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		AGAAAAGAACATCAGCGCTCC	0.403																																					p.D327E		Atlas-SNP	.											.	NEGR1	60	.	0			c.T981A						.						85	84	84					1																	71873213		2203	4299	6502	SO:0001583	missense	257194	exon7			AAGAACATCAGCG	AK092307	CCDS661.1	1p31.1	2013-01-11			ENSG00000172260	ENSG00000172260		"Immunoglobulin superfamily / I-set domain containing"	17302	protein-coding gene	gene with protein product	"a kindred of IgLON", "neurotractin", "IgLON family member 4"	613173				10075727	Standard	NM_173808		Approved	KILON, MGC46680, Ntra, IGLON4	uc001dfw.3	Q7Z3B1	OTTHUMG00000009698	ENST00000357731.5:c.981T>A	chr1.hg19:g.71873213A>T	ENSP00000350364:p.Asp327Glu	564.0	0.0		470.0	42.0	NM_173808	Q5VT21|Q6UY06|Q8N440|Q8NAQ3	Missense_Mutation	SNP	ENST00000357731.5	hg19	CCDS661.1	.	.	.	.	.	.	.	.	.	.	A	3.241	-0.155261	0.06544	.	.	ENSG00000172260	ENST00000357731;ENST00000306821;ENST00000434200	T;T;T	0.70986	0.75;0.89;-0.53	5.85	-9.14	0.00701	.	0.387563	0.26995	N	0.021454	T	0.10294	0.0252	N	0.08118	0	0.20074	N	0.999933	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47837	-0.9086	10	0.02654	T	1	-0.4235	0.8647	0.01201	0.3544:0.1566:0.1173:0.3717	.	281;327	B4DI94;Q7Z3B1	.;NEGR1_HUMAN	E	327;199;281	ENSP00000350364:D327E;ENSP00000305938:D199E;ENSP00000413294:D281E	ENSP00000305938:D199E	D	-	3	2	NEGR1	71645801	0.008000	0.16893	0.013000	0.15412	0.986000	0.74619	-0.492000	0.06467	-1.294000	0.02360	0.533000	0.62120	GAT	.	.		0.403	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4	NM_173808		T	71873213	A	T	71873213	3	4	204	1	0	0	0	0	1	0	0	0	10326	214	8	4	87	4	NEGR1	1	71873213	Missense_Mutation	SNP	A	TCGA-DD-AADW-01A-11D-A38X-10	35309442	71873213	177377408	3	29810										
KPRP	448834	hgsc.bcm.edu	37	chr1	152733003	152733003	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	agtcgctgtcctcgccgcccCatttcaagctgctctcagag	9	16	2	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr1:152733003C>T	ENST00000606109.1	+	1	967	c.939C>T	c.(937-939)ccC>ccT	p.P313P	KPRP_ENST00000368773.1_Silent_p.P313P			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	313	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCGCCGCCCCATTTCAAGCT	0.592																																					p.P313P		Atlas-SNP	.											.	KPRP	152	.	0			c.C939T						.						48	47	48					1																	152733003		2203	4300	6503	SO:0001819	synonymous_variant	448834	exon2			CCGCCCCATTTCA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.939C>T	chr1.hg19:g.152733003C>T		63.0	0.0		131.0	25.0	NM_001025231		Silent	SNP	ENST00000606109.1	hg19	CCDS30862.1																																																																																			.	.		0.592	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		T	152733003	C	T	152733003	2	4	204	1	0	0	0	0	0	0	0	1	8445	581	21	3		3	KPRP	1	152733003	Silent	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	80859790	152733003	96517618	4	29811										
ATP8B2	57198	hgsc.bcm.edu	37	chr1	154310110	154310110	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gaagatgaagtccttgagaaGtaacgagaagtcctcttctt	10	7	2	4			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr1:154310110G>T	ENST00000368487.3	+	12	1311	c.1124G>T	c.(1123-1125)aGt>aTt	p.S375I	ATP8B2_ENST00000368489.3_Intron|ATP8B2_ENST00000426445.1_Intron|ATP8B2_ENST00000341822.2_Intron|RNU7-57P_ENST00000459540.1_RNA	NM_001005855.1	NP_001005855.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	418					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TCCTTGAGAAGTAACGAGAAG	0.438																																					p.S375I		Atlas-SNP	.											.	ATP8B2	158	.	0			c.G1124T						.						97	101	99					1																	154310110		2203	4300	6503	SO:0001583	missense	57198	exon12			TGAGAAGTAACGA	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368487.3:c.1124G>T	chr1.hg19:g.154310110G>T	ENSP00000357472:p.Ser375Ile	133.0	0.0		373.0	78.0	NM_001005855	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368487.3	hg19	CCDS41405.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.604660	0.46423	.	.	ENSG00000143515	ENST00000368487	T	0.04317	3.65	5.17	0.808	0.18719	.	.	.	.	.	T	0.01905	0.0060	.	.	.	0.09310	N	1	P	0.41848	0.763	B	0.41988	0.372	T	0.45026	-0.9289	8	0.56958	D	0.05	.	7.7606	0.28951	0.3748:0.0:0.6252:0.0	.	375	P98198-4	.	I	375	ENSP00000357472:S375I	ENSP00000357472:S375I	S	+	2	0	ATP8B2	152576734	0.000000	0.05858	0.003000	0.11579	0.039000	0.13416	-0.036000	0.12185	0.261000	0.21753	0.655000	0.94253	AGT	.	.		0.438	ATP8B2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087903.2	NM_020452		T	154310110	G	T	154310110	3	4	204	1	0	0	0	0	1	0	0	0	1195	1029	36	3	1269	3	ATP8B2	1	154310110	Missense_Mutation	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10	1577107	154310110	94940511	5	29812										
CDK18	5129	hgsc.bcm.edu	37	chr1	205495307	205495307	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	cctgcactgccatccgagagGgtacagcatcctaggctccc	10	16	0	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr1:205495307G>A	ENST00000360066.2	+	6	872	c.571G>A	c.(571-573)Gtg>Atg	p.V191M	CDK18_ENST00000506784.1_Splice_Site_p.V221M|CDK18_ENST00000429964.2_Splice_Site_p.V191M|CDK18_ENST00000509056.1_3'UTR	NM_002596.3|NM_212502.2|NM_212503.2	NP_002587.2|NP_997667.1|NP_997668.1	Q07002	CDK18_HUMAN	cyclin-dependent kinase 18	189	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|endometrium(2)|large_intestine(2)|lung(10)|stomach(2)|urinary_tract(1)	19						CATCCGAGAGGGTACAGCATC	0.627																																					p.V221M	Pancreas(180;489 2072 28461 40831 44265)	Atlas-SNP	.											.	CDK18	75	.	0			c.G661A						.						43	39	40					1																	205495307		2202	4300	6502	SO:0001630	splice_region_variant	5129	exon6			CGAGAGGGTACAG	X66362	CCDS1454.1, CCDS44300.1	1q31-q32	2011-11-08	2009-12-16	2009-12-16	ENSG00000117266	ENSG00000117266		"Cyclin-dependent kinases"	8751	protein-coding gene	gene with protein product		169190	"PCTAIRE protein kinase 3"	PCTK3		1437147, 19884882	Standard	NM_002596		Approved	PCTAIRE3	uc010pri.2	Q07002	OTTHUMG00000037203	ENST00000360066.2:c.571+1G>A	chr1.hg19:g.205495307G>A		160.0	0.0		331.0	25.0	NM_212503	Q5VXQ2|Q6V3A2|Q6V3A3|Q96F90	Missense_Mutation	SNP	ENST00000360066.2	hg19	CCDS44300.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.762777	0.89932	.	.	ENSG00000117266	ENST00000429964;ENST00000506784;ENST00000360066;ENST00000478560;ENST00000419301	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	4.63	4.63	0.57726	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.79118	0.4392	L	0.60957	1.885	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.83275	0.996;0.996;0.996;0.993	T	0.81881	-0.0729	10	0.87932	D	0	-14.1556	16.0754	0.80965	0.0:0.0:1.0:0.0	.	153;189;221;191	Q59G02;Q07002;Q07002-3;Q07002-2	.;CDK18_HUMAN;.;.	M	191;221;191;102;221	ENSP00000399082:V191M;ENSP00000423665:V221M;ENSP00000353176:V191M;ENSP00000423408:V102M;ENSP00000391324:V221M	ENSP00000353176:V191M	V	+	1	0	CDK18	203761930	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.980000	0.88113	2.123000	0.65237	0.561000	0.74099	GTG	.	.		0.627	CDK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090407.2	NM_002596	Missense_Mutation	A	205495307	G	A	205495307	5	1	204	1	0	0	0	0	0	0	1	0	3136	1246	43	3	679	3	CDK18	1	205495307	Splice_Site	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10	51185197	205495307	43755314	6	29813										
TMEM206	55248	hgsc.bcm.edu	37	chr1	212558750	212558750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gctgagcaactgggcctgacCggggtacaaggcaatacctg	14	11	0	2	rs369443875		TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr1:212558750C>T	ENST00000261455.4	-	4	498	c.361G>A	c.(361-363)Ggt>Agt	p.G121S	TMEM206_ENST00000471937.1_5'UTR|TMEM206_ENST00000535273.1_Missense_Mutation_p.G182S	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	121						cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.G121C(1)		breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		TGGGCCTGACCGGGGTACAAG	0.532																																					p.G182S		Atlas-SNP	.											.	TMEM206	41	.	1	Substitution - Missense(1)	kidney(1)	c.G544A						.	C	SER/GLY,SER/GLY	0,4406		0,0,2203	89	83	85		544,361	5.4	0.7	1		85	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TMEM206	NM_001198862.1,NM_018252.2	56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	182/412,121/351	212558750	1,13005	2203	4300	6503	SO:0001583	missense	55248	exon5			CCTGACCGGGGTA	AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 75"	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.361G>A	chr1.hg19:g.212558750C>T	ENSP00000261455:p.Gly121Ser	126.0	0.0		199.0	17.0	NM_001198862	B7Z4D6|Q6IA87|Q9NV85	Missense_Mutation	SNP	ENST00000261455.4	hg19	CCDS1504.1	.	.	.	.	.	.	.	.	.	.	C	33	5.205822	0.95033	0.0	1.16E-4	ENSG00000065600	ENST00000261455;ENST00000535273	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.72637	0.3485	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.75531	-0.3285	9	0.87932	D	0	-25.2915	19.2273	0.93822	0.0:1.0:0.0:0.0	.	182;121	B7Z4D6;Q9H813	.;TM206_HUMAN	S	121;182	.	ENSP00000261455:G121S	G	-	1	0	TMEM206	210625373	1.000000	0.71417	0.667000	0.29798	0.761000	0.43186	6.922000	0.75811	2.531000	0.85337	0.655000	0.94253	GGT	.	.		0.532	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252		T	212558750	C	T	212558750	3	4	204	1	0	0	0	0	1	0	0	0	16146	652	23	1	711	1	TMEM206	1	212558750	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	7063443	212558750	36691871	7	29814										
MBD5	55777	hgsc.bcm.edu	37	chr2	149240972	149240972	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	agcatctcctaaaccagaatCtattaaatatcctccagcct	3	13	2	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr2:149240972C>G	ENST00000407073.1	+	10	3809	c.2812C>G	c.(2812-2814)Cta>Gta	p.L938V	MBD5_ENST00000404807.1_Missense_Mutation_p.L938V	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	938					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		AAACCAGAATCTATTAAATAT	0.458																																					p.L938V		Atlas-SNP	.											.	MBD5	164	.	0			c.C2812G						.						130	135	133					2																	149240972		2203	4300	6503	SO:0001583	missense	55777	exon10			CAGAATCTATTAA	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.2812C>G	chr2.hg19:g.149240972C>G	ENSP00000386049:p.Leu938Val	65.0	0.0		64.0	21.0	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	hg19	CCDS33302.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.52|14.52	2.559832|2.559832	0.45590|0.45590	.|.	.|.	ENSG00000204406|ENSG00000204406	ENST00000416015|ENST00000407073;ENST00000404807	.|T;T	.|0.62941	.|-0.01;0.76	5.95|5.95	5.06|5.06	0.68205|0.68205	.|.	.|0.000000	.|0.47093	.|D	.|0.000243	T|T	0.49167|0.49167	0.1541|0.1541	N|N	0.19112|0.19112	0.55|0.55	0.35829|0.35829	D|D	0.825199|0.825199	.|B	.|0.19817	.|0.039	.|B	.|0.20384	.|0.029	T|T	0.56456|0.56456	-0.7976|-0.7976	5|10	.|0.66056	.|D	.|0.02	-6.4653|-6.4653	14.1266|14.1266	0.65225|0.65225	0.2735:0.7265:0.0:0.0|0.2735:0.7265:0.0:0.0	.|.	.|938	.|Q9P267	.|MBD5_HUMAN	M|V	677|938	.|ENSP00000386049:L938V;ENSP00000384672:L938V	.|ENSP00000384672:L938V	I|L	+|+	3|1	3|2	MBD5|MBD5	148957442|148957442	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.139000|2.139000	0.42149|0.42149	1.495000|1.495000	0.48549|0.48549	0.563000|0.563000	0.77884|0.77884	ATC|CTA	.	.		0.458	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			G	149240972	C	G	149240972	3	3	204	1	0	0	0	0	1	0	0	0	9356	912	32	4	2830	4	MBD5	2	149240972	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10		149240972	93958401	8	29815										
SERPINE2	5270	hgsc.bcm.edu	37	chr2	224847396	224847399	+	Splice_Site	DEL	TACT	TACT	-													0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	atacattttaaattgaacatActtgttatttttgcaaaatt							TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	TACT	TACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr2:224847396_224847399delTACT	ENST00000258405.4	-	6	1226_1228	c.984_986delAGTA	c.(982-987)acagta>aca	p.V329fs	SERPINE2_ENST00000447280.2_Splice_Site_p.V341fs|SERPINE2_ENST00000409840.3_Splice_Site_p.V329fs|SERPINE2_ENST00000409304.1_Splice_Site_p.V329fs	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	329					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		AATTGAACATACTTGTTATTTTTG	0.353																																					.		Atlas-INDEL	.											.	SERPINE2	103	.	0			.						.																																			SO:0001630	splice_region_variant	5270	.			.	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"Serine (or cysteine) peptidase inhibitors"	8951	protein-coding gene	gene with protein product	"glial-derived nexin 1"	177010	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.985+1AGTA>-	chr2.hg19:g.224847396_224847399delTACT		79.0	0.0		92.0	14.0	.	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Splice_Site	DEL	ENST00000258405.4	hg19	CCDS2460.1																																																																																			.	.		0.353	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216	Frame_Shift_Del	-	224847399	TACT	-	224847396	8	5	204	1	0	1	0	1	0	0	1	0	14127	405	14	0	225	0	SERPINE2	2	224847396	Splice_Site	DEL	TACT	TCGA-DD-AADW-01A-11D-A38X-10	75606424	224847396	18351977	9	29816										
UBE2K	3093	hgsc.bcm.edu	37	chr4	39780035	39780035	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	ggatgtagagactgcaacagAattgcttctgagtaactgag	12	6	1	4			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr4:39780035A>G	ENST00000261427.5	+	7	868	c.584A>G	c.(583-585)gAa>gGa	p.E195G	UBE2K_ENST00000295963.6_Missense_Mutation_p.E134G|UBE2K_ENST00000503368.1_Missense_Mutation_p.E144G|UBE2K_ENST00000445950.2_Missense_Mutation_p.E152G|UBE2K_ENST00000438068.2_3'UTR	NM_001111112.1|NM_005339.4	NP_001104582.1|NP_005330.1	P61086	UBE2K_HUMAN	ubiquitin-conjugating enzyme E2K	195	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein K48-linked ubiquitination (GO:0070936)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)			large_intestine(1)|lung(1)|ovary(2)	4						ACTGCAACAGAATTGCTTCTG	0.408																																					p.E195G	NSCLC(101;689 1592 16105 29682 31745)	Atlas-SNP	.											.	UBE2K	16	.	0			c.A584G						.						138	131	133					4																	39780035		2203	4300	6503	SO:0001583	missense	3093	exon7			CAACAGAATTGCT	U58522	CCDS33976.1, CCDS47043.1, CCDS47044.1	4p14	2011-05-19	2011-05-19	2007-12-04	ENSG00000078140	ENSG00000078140		"Ubiquitin-conjugating enzymes E2"	4914	protein-coding gene	gene with protein product		602846	"huntingtin interacting protein 2", "ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)"	HIP2		8702625, 17873885	Standard	NM_005339		Approved	HYPG, UBC1	uc003guu.4	P61086	OTTHUMG00000160543	ENST00000261427.5:c.584A>G	chr4.hg19:g.39780035A>G	ENSP00000261427:p.Glu195Gly	54.0	0.0		62.0	26.0	NM_005339	A6NJC1|A8K5Y9|B2RDF8|C9JGP1|O54806|P27924|Q16721|Q9CVV9|Q9Y2D3	Missense_Mutation	SNP	ENST00000261427.5	hg19	CCDS33976.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.229955	0.79688	.	.	ENSG00000078140	ENST00000261427;ENST00000295963;ENST00000503368;ENST00000445950	T;T;T;T	0.56611	1.59;1.59;1.59;0.45	5.57	5.57	0.84162	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.68430	0.3000	L	0.56199	1.76	0.80722	D	1	D;D;P;P	0.62365	0.991;0.959;0.954;0.851	D;P;P;P	0.74023	0.982;0.75;0.837;0.775	T	0.71009	-0.4716	10	0.72032	D	0.01	-13.4433	16.0169	0.80445	1.0:0.0:0.0:0.0	.	134;195;144;152	B4DIZ2;P61086;P61086-2;C9JGP1	.;UBE2K_HUMAN;.;.	G	195;134;144;152	ENSP00000261427:E195G;ENSP00000295963:E134G;ENSP00000421203:E144G;ENSP00000390483:E152G	ENSP00000261427:E195G	E	+	2	0	UBE2K	39456430	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.283000	0.95860	2.233000	0.73108	0.482000	0.46254	GAA	.	.		0.408	UBE2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361061.1	NM_005339		G	39780035	A	G	39780035	3	3	204	1	0	0	0	0	1	0	0	0	16877	246	9	2	610	2	UBE2K	4	39780035	Missense_Mutation	SNP	A	TCGA-DD-AADW-01A-11D-A38X-10		39780035	151374241	10	29817										
ANK2	287	hgsc.bcm.edu	37	chr4	114278698	114278698	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	tgaagacgttgtagtggcaaGctcctctagtggaactgttt	12	7	1	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr4:114278698G>T	ENST00000357077.4	+	38	8977	c.8924G>T	c.(8923-8925)aGc>aTc	p.S2975I	ANK2_ENST00000264366.6_Missense_Mutation_p.S2942I|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2975					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GTAGTGGCAAGCTCCTCTAGT	0.413																																					p.S2975I		Atlas-SNP	.											.	ANK2	576	.	0			c.G8924T						.						153	152	152					4																	114278698		2203	4300	6503	SO:0001583	missense	287	exon38			TGGCAAGCTCCTC	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.8924G>T	chr4.hg19:g.114278698G>T	ENSP00000349588:p.Ser2975Ile	153.0	0.0		135.0	69.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.506893	0.44558	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.70631	-0.5;-0.5	5.58	0.566	0.17317	.	0.637131	0.15035	N	0.284210	T	0.64349	0.2590	L	0.59436	1.845	0.09310	N	1	P;P	0.49559	0.8;0.925	B;P	0.44990	0.276;0.466	T	0.55412	-0.8145	9	.	.	.	.	6.0031	0.19531	0.2739:0.2459:0.4802:0.0	.	2942;2975	Q01484;Q01484-4	ANK2_HUMAN;.	I	2975;2942	ENSP00000349588:S2975I;ENSP00000264366:S2942I	.	S	+	2	0	ANK2	114498147	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.213000	0.17521	0.028000	0.15324	-0.910000	0.02820	AGC	.	.		0.413	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114278698	G	T	114278698	3	4	204	1	0	0	0	0	1	0	0	0	621	971	34	3	9139	3	ANK2	4	114278698	Missense_Mutation	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10	74498663	114278698	76875578	11	29818										
FGA	2243	hgsc.bcm.edu	37	chr4	155506805	155506805	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	ttgctttcaaatgtggagtcTcctctgttgtaactcgtgct	9	9	3	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr4:155506805T>C	ENST00000302053.3	-	5	1854	c.1776A>G	c.(1774-1776)ggA>ggG	p.G592G	FGA_ENST00000403106.3_Silent_p.G592G	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	592					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	ATGTGGAGTCTCCTCTGTTGT	0.443																																					p.G592G	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.A1776G						.						135	130	131					4																	155506805		2203	4300	6503	SO:0001819	synonymous_variant	2243	exon5			GGAGTCTCCTCTG		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1776A>G	chr4.hg19:g.155506805T>C		92.0	0.0		42.0	28.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Silent	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	T	5.825	0.336432	0.11013	.	.	ENSG00000171560	ENST00000457487	.	.	.	5.31	1.64	0.23874	.	.	.	.	.	T	0.36936	0.0985	.	.	.	0.32951	D	0.51975	.	.	.	.	.	.	T	0.44205	-0.9343	4	.	.	.	.	4.0332	0.09717	0.148:0.2208:0.0:0.6311	.	.	.	.	G	234	.	.	E	-	2	0	FGA	155726255	0.987000	0.35691	0.008000	0.14137	0.013000	0.08279	0.057000	0.14279	0.510000	0.28216	0.533000	0.62120	GAG	.	.		0.443	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		C	155506805	T	C	155506805	2	2	204	1	0	0	0	0	0	0	0	1	5838	1538	54	2		2	FGA	4	155506805	Silent	SNP	T	TCGA-DD-AADW-01A-11D-A38X-10	41228107	155506805	35647471	12	29819										
LIFR	3977	hgsc.bcm.edu	37	chr5	38523562	38523562	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	ctctttacgtagaactttaaTttcccagataacatttgagc	5	9	1	3			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr5:38523562T>C	ENST00000263409.4	-	5	682	c.520A>G	c.(520-522)Att>Gtt	p.I174V	LIFR_ENST00000453190.2_Missense_Mutation_p.I174V|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	174					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					AGAACTTTAATTTCCCAGATA	0.333			T	PLAG1	salivary adenoma																																p.I174V	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.A520G						.						88	96	93					5																	38523562		2203	4300	6503	SO:0001583	missense	3977	exon5			CTTTAATTTCCCA	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.520A>G	chr5.hg19:g.38523562T>C	ENSP00000263409:p.Ile174Val	593.0	0.0		615.0	272.0	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	T	12.85	2.060901	0.36373	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.26957	1.7;1.7	5.53	3.1	0.35709	Immunoglobulin-like fold (1);	0.333098	0.34906	N	0.003599	T	0.19644	0.0472	L	0.43152	1.355	0.36696	D	0.879867	B	0.09022	0.002	B	0.10450	0.005	T	0.09335	-1.0679	10	0.45353	T	0.12	-20.6729	6.6947	0.23193	0.0:0.1853:0.0:0.8147	.	174	P42702	LIFR_HUMAN	V	174	ENSP00000263409:I174V;ENSP00000398368:I174V	ENSP00000263409:I174V	I	-	1	0	LIFR	38559319	0.993000	0.37304	0.820000	0.32676	0.948000	0.59901	0.250000	0.18235	0.876000	0.35872	0.533000	0.62120	ATT	.	.		0.333	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		C	38523562	T	C	38523562	3	2	204	1	0	0	0	0	1	0	0	0	8789	1493	52	2	2837	2	LIFR	5	38523562	Missense_Mutation	SNP	T	TCGA-DD-AADW-01A-11D-A38X-10		38523562	142391698	13	29820										
HIST1H3A	8350	hgsc.bcm.edu	37	chr6	26021005	26021005	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gtgatggctctgcaggaggcGtgcgaggcctacttggtagg	18	8	1	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr6:26021005G>C	ENST00000357647.3	+	1	288	c.288G>C	c.(286-288)gcG>gcC	p.A96A	HIST1H1A_ENST00000244573.3_5'Flank|HIST1H4A_ENST00000359907.3_5'Flank	NM_003529.2	NP_003520.1	P68431	H31_HUMAN	histone cluster 1, H3a	96					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			endometrium(1)|lung(3)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						TGCAGGAGGCGTGCGAGGCCT	0.582																																					p.A96A		Atlas-SNP	.											.	HIST1H3A	14	.	0			c.G288C						.						46	47	47					6																	26021005		2203	4300	6503	SO:0001819	synonymous_variant	8350	exon1			GGAGGCGTGCGAG	Z46261	CCDS4570.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000198366	ENSG00000275714		"Histones / Replication-dependent"	4766	protein-coding gene	gene with protein product		602810	"H3 histone family, member A", "histone 1, H3a"	H3FA		9119399, 12408966	Standard	NM_003529		Approved	H3/A	uc003nfp.1	P68431	OTTHUMG00000014418	ENST00000357647.3:c.288G>C	chr6.hg19:g.26021005G>C		145.0	0.0		126.0	41.0	NM_003529	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000357647.3	hg19	CCDS4570.1																																																																																			.	.		0.582	HIST1H3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040080.1	NM_003529		C	26021005	G	C	26021005	2	2	204	1	0	0	0	0	0	0	0	1	7164	1132	40	4		4	HIST1H3A	6	26021005	Silent	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10		26021005	145094062	14	29821										
C6orf15	29113	hgsc.bcm.edu	37	chr6	31079471	31079471	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	ttccccaaccagtcccagggCctccacctccccaggacaca	6	21	0	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr6:31079471C>T	ENST00000259870.3	-	2	668	c.665G>A	c.(664-666)gGc>gAc	p.G222D		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	222	Gly-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						AGTCCCAGGGCCTCCACCTCC	0.577																																					p.G222D		Atlas-SNP	.											.	C6orf15	29	.	0			c.G665A						.						35	35	35					6																	31079471		1720	3330	5050	SO:0001583	missense	29113	exon2			CCAGGGCCTCCAC	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.665G>A	chr6.hg19:g.31079471C>T	ENSP00000259870:p.Gly222Asp	87.0	0.0		99.0	10.0	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	hg19	CCDS4693.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.082517	0.76528	.	.	ENSG00000204542	ENST00000259870	T	0.09817	2.94	4.4	4.4	0.53042	.	0.577244	0.15647	N	0.251585	T	0.20455	0.0492	M	0.67953	2.075	0.33144	D	0.544789	D	0.71674	0.998	D	0.67548	0.952	T	0.01048	-1.1469	10	0.87932	D	0	0.2134	14.4911	0.67651	0.0:1.0:0.0:0.0	.	222	Q6UXA7	CF015_HUMAN	D	222	ENSP00000259870:G222D	ENSP00000259870:G222D	G	-	2	0	C6orf15	31187450	0.000000	0.05858	0.993000	0.49108	0.978000	0.69477	0.323000	0.19593	2.266000	0.75297	0.643000	0.83706	GGC	.	.		0.577	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070		T	31079471	C	T	31079471	3	4	204	1	0	0	0	0	1	0	0	0	2338	739	26	3	316	3	C6orf15	6	31079471	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	5058466	31079471	140035596	15	29822										
TCP11	6954	hgsc.bcm.edu	37	chr6	35088734	35088734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	tttagcccgttcatactgaaTggaatgttcctgcaggtggg	12	8	1	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr6:35088734T>C	ENST00000512012.1	-	5	823	c.667A>G	c.(667-669)Att>Gtt	p.I223V	TCP11_ENST00000444780.2_Missense_Mutation_p.I231V|TCP11_ENST00000244645.3_Missense_Mutation_p.I161V|TCP11_ENST00000412155.2_Missense_Mutation_p.I185V|TCP11_ENST00000311875.5_Missense_Mutation_p.I236V|TCP11_ENST00000373979.2_Missense_Mutation_p.I161V|TCP11_ENST00000418521.2_Missense_Mutation_p.I160V|TCP11_ENST00000373974.4_Missense_Mutation_p.I190V			Q8WWU5	TCP11_HUMAN	t-complex 11, testis-specific	223					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				breast(1)|kidney(5)|large_intestine(3)|lung(10)|ovary(3)|prostate(1)|skin(4)	27						TCATACTGAATGGAATGTTCC	0.488																																					p.I236V		Atlas-SNP	.											.	TCP11	94	.	0			c.A706G						.						259	261	260					6																	35088734		2203	4300	6503	SO:0001583	missense	6954	exon6			ACTGAATGGAATG		CCDS4799.1, CCDS47413.1, CCDS59015.1, CCDS59016.1, CCDS59017.1, CCDS59018.1	6p21.31	2012-09-20	2012-09-20		ENSG00000124678	ENSG00000124678			11658	protein-coding gene	gene with protein product	"fertilization-promoting peptide receptor"	186982	"t-complex 11 (a murine tcp homolog)", "t-complex 11 homolog (mouse)"	D6S230E		1427894, 11756566, 21597245	Standard	NM_001093728		Approved	KIAA0229, FPPR	uc003okd.2	Q8WWU5	OTTHUMG00000014560	ENST00000512012.1:c.667A>G	chr6.hg19:g.35088734T>C	ENSP00000425995:p.Ile223Val	211.0	0.0		246.0	101.0	NM_001093728	B2RCE9|B3KQ27|B7Z7B5|B7Z7G1|B7Z7H4|B7Z7S8|E7EP29|J3KNG1|Q8NF85|Q9NQZ9|Q9NR39	Missense_Mutation	SNP	ENST00000512012.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.561|0.561	-0.845408|-0.845408	0.02671|0.02671	.|.	.|.	ENSG00000124678|ENSG00000124678	ENST00000502480|ENST00000373979;ENST00000412155;ENST00000244645;ENST00000373977;ENST00000311875;ENST00000444780;ENST00000373974;ENST00000418521;ENST00000512012;ENST00000486638	.|T;T;T;T;T;T;T;T;T	.|0.05855	.|3.38;3.38;3.38;3.38;3.38;3.38;3.38;3.38;3.38	4.32|4.32	0.415|0.415	0.16411|0.16411	.|.	.|0.238433	.|0.35235	.|N	.|0.003357	T|T	0.00608|0.00608	0.0020|0.0020	N|N	0.03209|0.03209	-0.39|-0.39	0.27488|0.27488	N|N	0.952382|0.952382	.|B;B;B;B;B;B	.|0.19935	.|0.005;0.005;0.01;0.04;0.01;0.001	.|B;B;B;B;B;B	.|0.23275	.|0.018;0.018;0.026;0.045;0.026;0.011	T|T	0.44590|0.44590	-0.9318|-0.9318	5|10	.|0.02654	.|T	.|1	.|.	8.5665|8.5665	0.33543|0.33543	0.0:0.5085:0.0:0.4915|0.0:0.5085:0.0:0.4915	.|.	.|190;185;231;296;223;161	.|B7Z7G1;E7EP29;B7Z7B5;Q5TB88;Q8WWU5;Q8WWU5-2	.|.;.;.;.;TCP11_HUMAN;.	R|V	30|161;185;161;185;236;231;190;160;223;82	.|ENSP00000363091:I161V;ENSP00000402816:I185V;ENSP00000244645:I161V;ENSP00000308708:I236V;ENSP00000404479:I231V;ENSP00000363085:I190V;ENSP00000415320:I160V;ENSP00000425995:I223V;ENSP00000421103:I82V	.|ENSP00000244645:I161V	H|I	-|-	2|1	0|0	TCP11|TCP11	35196712|35196712	0.937000|0.937000	0.31787|0.31787	0.995000|0.995000	0.50966|0.50966	0.767000|0.767000	0.43475|0.43475	0.595000|0.595000	0.24029|0.24029	-0.004000|-0.004000	0.14419|0.14419	-0.371000|-0.371000	0.07208|0.07208	CAT|ATT	.	.		0.488	TCP11-014	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000370354.1	NM_001093728		C	35088734	T	C	35088734	3	2	204	1	0	0	0	0	1	0	0	0	15728	1464	51	2	864	2	TCP11	6	35088734	Missense_Mutation	SNP	T	TCGA-DD-AADW-01A-11D-A38X-10	4009263	35088734	136026333	16	29823										
SMPD2	6610	hgsc.bcm.edu	37	chr6	109764480	109764480	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	cttttcctaggcagtttctgGgttttacatctcctgtaaga	8	9	2	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr6:109764480G>T	ENST00000258052.3	+	9	1099	c.740G>T	c.(739-741)gGg>gTg	p.G247V	PPIL6_ENST00000424445.2_5'Flank|PPIL6_ENST00000521072.2_5'Flank|PPIL6_ENST00000440797.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	247					apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		GCAGTTTCTGGGTTTTACATC	0.512																																					p.G247V		Atlas-SNP	.											.	SMPD2	25	.	0			c.G740T						.						89	98	95					6																	109764480		2203	4300	6503	SO:0001583	missense	6610	exon9			TTTCTGGGTTTTA	AJ222801	CCDS5075.1	6q21	2009-10-23			ENSG00000135587	ENSG00000135587	3.1.4.12		11121	protein-coding gene	gene with protein product		603498				9520418	Standard	XM_005267109		Approved	nSMase, ISC1	uc003pti.3	O60906	OTTHUMG00000015348	ENST00000258052.3:c.740G>T	chr6.hg19:g.109764480G>T	ENSP00000258052:p.Gly247Val	98.0	0.0		81.0	11.0	NM_003080	Q5TED1|Q9BWR3	Missense_Mutation	SNP	ENST00000258052.3	hg19	CCDS5075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.76|13.76	2.333130|2.333130	0.41297|0.41297	.|.	.|.	ENSG00000135587|ENSG00000135587	ENST00000458487|ENST00000258052	T|T	0.33216|0.29142	1.42|1.58	5.95|5.95	4.15|4.15	0.48705|0.48705	.|Endonuclease/exonuclease/phosphatase (2);	0.458485|0.458485	0.26738|0.26738	N|N	0.022743|0.022743	T|T	0.17789|0.17789	0.0427|0.0427	N|N	0.16903|0.16903	0.455|0.455	0.53688|0.53688	D|D	0.999975|0.999975	.|D	.|0.55385	.|0.971	.|P	.|0.60012	.|0.867	T|T	0.03493|0.03493	-1.1031|-1.1031	8|10	0.56958|0.25751	D|T	0.05|0.34	-14.1198|-14.1198	8.5917|8.5917	0.33690|0.33690	0.1718:0.0:0.8282:0.0|0.1718:0.0:0.8282:0.0	.|.	.|247	.|O60906	.|NSMA_HUMAN	C|V	144|247	ENSP00000399731:G144C|ENSP00000258052:G247V	ENSP00000399731:G144C|ENSP00000258052:G247V	G|G	+|+	1|2	0|0	SMPD2|SMPD2	109871173|109871173	0.953000|0.953000	0.32496|0.32496	0.823000|0.823000	0.32752|0.32752	0.734000|0.734000	0.41952|0.41952	2.828000|2.828000	0.48120|0.48120	1.495000|1.495000	0.48549|0.48549	0.655000|0.655000	0.94253|0.94253	GGT|GGG	.	.		0.512	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1			T	109764480	G	T	109764480	3	4	204	1	0	0	0	0	1	0	0	0	14820	1232	43	3	774	3	SMPD2	6	109764480	Missense_Mutation	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10	74675746	109764480	61350587	17	29824										
TULP4	56995	hgsc.bcm.edu	37	chr6	158922879	158922890	+	In_Frame_Del	DEL	GACAGCTGTAGG	GACAGCTGTAGG	-													0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gatgtcctgaccaaccagacGacagctgtagggacagcaga					rs377659848		TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	GACAGCTGTAGG	GACAGCTGTAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr6:158922879_158922890delGACAGCTGTAGG	ENST00000367097.3	+	13	3541_3552	c.2184_2195delGACAGCTGTAGG	c.(2182-2196)acgacagctgtaggg>acg	p.TAVG729del	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	729					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CCAACCAGACGACAGCTGTAGGGACAGCAGAA	0.575																																					p.728_732del		Atlas-INDEL	.											TULP4,NS,carcinoma,0,1	TULP4	137	.	0			c.2183_2194del						.																																			SO:0001651	inframe_deletion	56995	exon13			.		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"WD repeat domain containing"	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.2184_2195delGACAGCTGTAGG	chr6.hg19:g.158922879_158922890delGACAGCTGTAGG	ENSP00000356064:p.Thr729_Gly732del	105.0	0.0		97.0	27.0	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	In_Frame_Del	DEL	ENST00000367097.3	hg19	CCDS34561.1																																																																																			.	.		0.575	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		-	158922890	GACAGCTGTAGG	-	158922879	7	5	204	1	0	1	0	1	0	0	0	0	16791	1045	37	0	2234	0	TULP4	6	158922879	In_Frame_Del	DEL	GACAGCTGTAGG	TCGA-DD-AADW-01A-11D-A38X-10	49158399	158922879	12192188	18	29825										
ANLN	54443	hgsc.bcm.edu	37	chr7	36461497	36461497	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	cgaaataaatatgcaacagaCagtgatctatcaagctagcc	7	9	2	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr7:36461497C>T	ENST00000265748.2	+	13	2416	c.2195C>T	c.(2194-2196)aCa>aTa	p.T732I	ANLN_ENST00000396068.2_Missense_Mutation_p.T695I	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	732	Localization to the cleavage furrow.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						ATGCAACAGACAGTGATCTAT	0.338																																					p.T732I		Atlas-SNP	.											.	ANLN	101	.	0			c.C2195T						.						83	83	83					7																	36461497		2203	4300	6503	SO:0001583	missense	54443	exon13			AACAGACAGTGAT	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.2195C>T	chr7.hg19:g.36461497C>T	ENSP00000265748:p.Thr732Ile	267.0	0.0		267.0	29.0	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	hg19	CCDS5447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.2|28.2	4.900246|4.900246	0.92035|0.92035	.|.	.|.	ENSG00000011426|ENSG00000011426	ENST00000446635|ENST00000265748;ENST00000396068	.|T;T	.|0.15256	.|2.44;2.5	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.42314	.|0.1197	L|L	0.58428|0.58428	1.81|1.81	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.91635	.|0.999;0.988;0.996;0.991	.|T	.|0.12192	.|-1.0557	.|10	.|0.87932	.|D	.|0	-23.6929|-23.6929	20.0313|20.0313	0.97540|0.97540	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|609;694;695;732	.|B4DSL6;A8K5D9;Q9NQW6-2;Q9NQW6	.|.;.;.;ANLN_HUMAN	X|I	86|732;695	.|ENSP00000265748:T732I;ENSP00000379380:T695I	.|ENSP00000265748:T732I	Q|T	+|+	1|2	0|0	ANLN|ANLN	36428022|36428022	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.989000|0.989000	0.77384|0.77384	4.896000|4.896000	0.63222|0.63222	2.746000|2.746000	0.94184|0.94184	0.655000|0.655000	0.94253|0.94253	CAG|ACA	.	.		0.338	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		T	36461497	C	T	36461497	3	4	204	1	0	0	0	0	1	0	0	0	694	478	17	3	2245	3	ANLN	7	36461497	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10		36461497	122677166	19	29826										
MLXIPL	51085	hgsc.bcm.edu	37	chr7	73008624	73008624	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	ttggccggagagcgggcagaGagcagtactggtccagccag	17	10	0	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr7:73008624G>C	ENST00000313375.3	-	16	2467	c.2420C>G	c.(2419-2421)tCt>tGt	p.S807C	MLXIPL_ENST00000395189.1_Missense_Mutation_p.S714C|MLXIPL_ENST00000429400.2_Missense_Mutation_p.S788C|MLXIPL_ENST00000414749.2_Missense_Mutation_p.S805C|MLXIPL_ENST00000434326.1_Missense_Mutation_p.S713C|MLXIPL_ENST00000354613.1_Missense_Mutation_p.S786C	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	807					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				AGCGGGCAGAGAGCAGTACTG	0.632																																					p.S807C		Atlas-SNP	.											.	MLXIPL	54	.	0			c.C2420G						.						83	75	77					7																	73008624		2203	4300	6503	SO:0001583	missense	51085	exon16			GGCAGAGAGCAGT	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"carbohydrate response element binding protein"	605678	"Williams Beuren syndrome chromosome region 14"	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.2420C>G	chr7.hg19:g.73008624G>C	ENSP00000320886:p.Ser807Cys	32.0	0.0		40.0	13.0	NM_032951	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Missense_Mutation	SNP	ENST00000313375.3	hg19	CCDS5553.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.409768	0.83340	.	.	ENSG00000009950	ENST00000414749;ENST00000429400;ENST00000313375;ENST00000354613;ENST00000395189;ENST00000434326	T;T;T;T;T;T	0.35236	2.08;2.11;2.06;2.12;1.44;1.32	4.53	4.53	0.55603	.	0.000000	0.64402	D	0.000001	T	0.59998	0.2235	M	0.74467	2.265	0.46586	D	0.999112	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.975;0.97;0.987;0.991;0.996	T	0.65220	-0.6221	10	0.87932	D	0	-38.0824	14.8039	0.69938	0.0:0.0:1.0:0.0	.	714;807;788;805;786	Q9NP71-6;Q9NP71;Q9NP71-2;Q9NP71-3;Q9NP71-4	.;MLXPL_HUMAN;.;.;.	C	805;788;807;786;714;713	ENSP00000412330:S805C;ENSP00000406296:S788C;ENSP00000320886:S807C;ENSP00000346629:S786C;ENSP00000378616:S714C;ENSP00000392636:S713C	ENSP00000320886:S807C	S	-	2	0	MLXIPL	72646560	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.620000	0.98373	2.345000	0.79718	0.561000	0.74099	TCT	.	.		0.632	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951		C	73008624	G	C	73008624	3	2	204	1	0	0	0	0	1	0	0	0	9646	942	33	4	146	4	MLXIPL	7	73008624	Missense_Mutation	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10	36547127	73008624	86130039	20	29827										
MCM7	4176	hgsc.bcm.edu	37	chr7	99693609	99693609	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gagatggtctgctgctccatGacctcgtggatggctgtgcg	15	10	1	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr7:99693609G>T	ENST00000303887.5	-	11	2028	c.1383C>A	c.(1381-1383)gtC>gtA	p.V461V	MIR93_ENST00000385024.1_RNA|MCM7_ENST00000343023.6_Intron|MCM7_ENST00000354230.3_Silent_p.V285V|MIR25_ENST00000384816.1_RNA|MIR106B_ENST00000385301.1_RNA	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	461	MCM.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCTGCTCCATGACCTCGTGGA	0.627																																					p.V461V		Atlas-SNP	.											.	MCM7	136	.	0			c.C1383A						.						96	78	84					7																	99693609		2203	4300	6503	SO:0001819	synonymous_variant	4176	exon11			CTCCATGACCTCG		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.1383C>A	chr7.hg19:g.99693609G>T		52.0	0.0		82.0	8.0	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Silent	SNP	ENST00000303887.5	hg19	CCDS5683.1																																																																																			.	.		0.627	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			T	99693609	G	T	99693609	2	4	204	1	0	0	0	0	0	0	0	1	9401	1277	45	3		3	MCM7	7	99693609	Silent	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10	26684985	99693609	59445054	21	29828										
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68179424	68179424	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	tatattggctgcatttaagtCacagtcatagtttacataaa	6	6	2	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr8:68179424C>G	ENST00000262215.3	-	12	2103	c.1714G>C	c.(1714-1716)Gac>Cac	p.D572H	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.D26H	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	572	HUS; DCB:HUS domain interaction.				endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			GCATTTAAGTCACAGTCATAG	0.338																																					p.D572H		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.G1714C						.						73	73	73					8																	68179424		2202	4293	6495	SO:0001583	missense	10565	exon12			TTAAGTCACAGTC	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.1714G>C	chr8.hg19:g.68179424C>G	ENSP00000262215:p.Asp572His	100.0	0.0		90.0	9.0	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	hg19	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.355273	0.82243	.	.	ENSG00000066777	ENST00000520381;ENST00000262215	T;T	0.65732	0.69;-0.17	5.64	5.64	0.86602	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.79986	0.4541	M	0.92649	3.33	0.80722	D	1	P;P	0.50066	0.931;0.529	P;B	0.50825	0.651;0.443	D	0.84718	0.0738	10	0.66056	D	0.02	.	19.7032	0.96063	0.0:1.0:0.0:0.0	.	572;26	Q9Y6D6;E5RIF2	BIG1_HUMAN;.	H	26;572	ENSP00000428429:D26H;ENSP00000262215:D572H	ENSP00000262215:D572H	D	-	1	0	ARFGEF1	68341978	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.743000	0.85020	2.663000	0.90544	0.650000	0.86243	GAC	.	.		0.338	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		G	68179424	C	G	68179424	3	3	204	1	0	0	0	0	1	0	0	0	852	826	29	4	3947	4	ARFGEF1	8	68179424	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10		68179424	78184598	22	29829										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77617394	77617394	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	acaaacctcataggacccgaTccaaccttccgcggtttatg	7	14	1	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr8:77617394T>G	ENST00000521891.2	+	2	1519	c.1071T>G	c.(1069-1071)gaT>gaG	p.D357E	ZFHX4_ENST00000050961.6_Missense_Mutation_p.D357E|ZFHX4_ENST00000518282.1_Missense_Mutation_p.D357E|ZFHX4_ENST00000455469.2_Missense_Mutation_p.D357E|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	357					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TAGGACCCGATCCAACCTTCC	0.453										HNSCC(33;0.089)																											p.D357E		Atlas-SNP	.											.	ZFHX4	878	.	0			c.T1071G						.						99	91	94					8																	77617394		1831	4093	5924	SO:0001583	missense	79776	exon2			ACCCGATCCAACC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.1071T>G	chr8.hg19:g.77617394T>G	ENSP00000430497:p.Asp357Glu	70.0	0.0		75.0	34.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	T	11.45	1.643876	0.29246	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.53640	0.61;0.66;0.62;0.62	5.53	-1.45	0.08828	.	0.000000	0.45867	U	0.000329	T	0.50565	0.1623	L	0.36672	1.1	0.49798	D	0.999826	D;D;D;D	0.67145	0.994;0.996;0.996;0.98	D;D;D;P	0.77557	0.978;0.99;0.99;0.668	T	0.37641	-0.9697	10	0.30854	T	0.27	.	10.3143	0.43727	0.0:0.3704:0.0:0.6296	.	357;357;357;357	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	E	357	ENSP00000430497:D357E;ENSP00000399605:D357E;ENSP00000050961:D357E;ENSP00000430848:D357E	ENSP00000050961:D357E	D	+	3	2	ZFHX4	77779949	1.000000	0.71417	0.988000	0.46212	0.997000	0.91878	1.366000	0.34193	-0.367000	0.08052	0.533000	0.62120	GAT	.	.		0.453	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		G	77617394	T	G	77617394	3	3	204	1	0	0	0	0	1	0	0	0	17650	1432	50	5	1073	5	ZFHX4	8	77617394	Missense_Mutation	SNP	T	TCGA-DD-AADW-01A-11D-A38X-10	9437970	77617394	68746628	23	29830										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77763751	77763752	+	Frame_Shift_Ins	INS	-	-	AA													0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	agggcccaattttacgatggINSaaaaattccttgatccatct							TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr8:77763751_77763752insAA	ENST00000521891.2	+	10	5042_5043	c.4594_4595insAA	c.(4594-4596)gaafs	p.E1532fs	ZFHX4_ENST00000050961.6_Frame_Shift_Ins_p.E1487fs|ZFHX4_ENST00000518282.1_Frame_Shift_Ins_p.E1506fs|ZFHX4_ENST00000455469.2_Frame_Shift_Ins_p.E1487fs	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1487					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TTTTACGATGGAAAAATTCCTT	0.406										HNSCC(33;0.089)																											p.E1532fs		Atlas-INDEL	.											.	ZFHX4	878	.	0			c.4594_4595insAA						.																																			SO:0001589	frameshift_variant	79776	exon10			.		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.4597_4598dupAA	chr8.hg19:g.77763754_77763755dupAA	ENSP00000430497:p.Glu1532fs	176.0	0.0		167.0	18.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Frame_Shift_Ins	INS	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.406	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		AA	77763752	-	AA	77763751	7	5	204	1	0	1	1	0	0	0	0	0	17650	1175	41	0	4628	0	ZFHX4	8	77763751	Frame_Shift_Ins	INS	-	TCGA-DD-AADW-01A-11D-A38X-10	146357	77763751	68600271	24	29831										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100832349	100832349	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	tattattcctcctaattttcAggtactataacttttttaac	2	8	1	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr8:100832349A>T	ENST00000358544.2	+	49	9179	c.9068A>T	c.(9067-9069)cAg>cTg	p.Q3023L	VPS13B_ENST00000357162.2_Splice_Site_p.Q2998L|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3023					protein transport (GO:0015031)			p.Q3023R(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CCTAATTTTCAGGTACTATAA	0.328																																					p.Q3023L	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											VPS13B,NS,carcinoma,0,1	VPS13B	811	.	1	Substitution - Missense(1)	prostate(1)	c.A9068T						.						57	63	61					8																	100832349		2202	4298	6500	SO:0001630	splice_region_variant	157680	exon49			ATTTTCAGGTACT	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.9069+1A>T	chr8.hg19:g.100832349A>T		79.0	0.0		63.0	4.0	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	18.17	3.564282	0.65651	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.77877	-1.13;-1.13	5.92	5.92	0.95590	.	0.198278	0.43747	D	0.000537	T	0.67211	0.2869	L	0.27053	0.805	0.80722	D	1	P;P	0.41848	0.763;0.454	B;B	0.35971	0.215;0.073	T	0.72587	-0.4248	10	0.66056	D	0.02	.	16.3634	0.83296	1.0:0.0:0.0:0.0	.	2998;3023	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	L	2998;3023	ENSP00000349685:Q2998L;ENSP00000351346:Q3023L	ENSP00000349685:Q2998L	Q	+	2	0	VPS13B	100901525	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	5.945000	0.70226	2.270000	0.75569	0.459000	0.35465	CAG	.	.		0.328	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	Missense_Mutation	T	100832349	A	T	100832349	5	4	204	1	0	0	0	0	0	0	1	0	17205	202	7	4	9452	4	VPS13B	8	100832349	Splice_Site	SNP	A	TCGA-DD-AADW-01A-11D-A38X-10	23068598	100832349	45531673	25	29832										
IFNA8	3445	hgsc.bcm.edu	37	chr9	21409229	21409229	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gtggtgctcagctacaagtcAttcagctctctgggctgtga	12	10	4	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr9:21409229A>T	ENST00000380205.1	+	1	84	c.54A>T	c.(52-54)tcA>tcT	p.S18S		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	18					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		GCTACAAGTCATTCAGCTCTC	0.502																																					p.S18S		Atlas-SNP	.											.	IFNA8	19	.	0			c.A54T						.						150	143	146					9																	21409229		2203	4300	6503	SO:0001819	synonymous_variant	3445	exon1			CAAGTCATTCAGC		CCDS6507.1	9p22	2010-08-24			ENSG00000120242	ENSG00000120242		"Interferons"	5429	protein-coding gene	gene with protein product	"interferon alpha-B''", "interferon alpha type 201"	147568				1385305	Standard	NM_002170		Approved	IFN-alphaB	uc003zpc.1	P32881	OTTHUMG00000019677	ENST00000380205.1:c.54A>T	chr9.hg19:g.21409229A>T		49.0	0.0		75.0	29.0	NM_002170	P01565|P09236|Q5VWV7|Q5VYQ3	Silent	SNP	ENST00000380205.1	hg19	CCDS6507.1																																																																																			.	.		0.502	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1	NM_002170		T	21409229	A	T	21409229	2	4	204	1	0	0	0	0	0	0	0	1	7552	204	8	4		4	IFNA8	9	21409229	Silent	SNP	A	TCGA-DD-AADW-01A-11D-A38X-10		21409229	119804202	26	29833										
RFK	55312	hgsc.bcm.edu	37	chr9	79009045	79009045	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	cttggagccgcggccgaagcCccgcaccacttgaccccggc	12	19	0	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr9:79009045C>T	ENST00000376736.1	-	1	376	c.43G>A	c.(43-45)Ggc>Agc	p.G15S	RFK_ENST00000479197.1_5'UTR	NM_018339.5	NP_060809.3	Q969G6	RIFK_HUMAN	riboflavin kinase	15					apoptotic process (GO:0006915)|FMN biosynthetic process (GO:0009398)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|reactive oxygen species metabolic process (GO:0072593)|riboflavin biosynthetic process (GO:0009231)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|riboflavin kinase activity (GO:0008531)			pancreas(1)|prostate(1)|urinary_tract(1)	3					Riboflavin(DB00140)	CGGCCGAAGCCCCGCACCACT	0.721																																					p.G15S		Atlas-SNP	.											.	RFK	13	.	0			c.G43A						.						10	11	11					9																	79009045		2182	4248	6430	SO:0001583	missense	55312	exon1			CGAAGCCCCGCAC	AK002011	CCDS35044.1, CCDS35044.2	9q21.31	2010-11-16			ENSG00000135002	ENSG00000135002			30324	protein-coding gene	gene with protein product		613010				14580199	Standard	NM_018339		Approved	FLJ11149, RIFK	uc004akd.2	Q969G6	OTTHUMG00000020040	ENST00000376736.1:c.43G>A	chr9.hg19:g.79009045C>T	ENSP00000365926:p.Gly15Ser	127.0	0.0		139.0	56.0	NM_018339	Q5JSG9|Q9NUT7	Missense_Mutation	SNP	ENST00000376736.1	hg19	CCDS35044.2	.	.	.	.	.	.	.	.	.	.	c	36	5.675328	0.96764	.	.	ENSG00000135002	ENST00000376736;ENST00000257452;ENST00000490113	.	.	.	4.17	4.17	0.49024	Riboflavin kinase domain (1);Riboflavin kinase domain, bacterial/eukaryotic (3);	0.000000	0.85682	D	0.000000	D	0.90239	0.6948	H	0.98407	4.225	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.77557	0.99;0.987	D	0.94511	0.7718	9	0.87932	D	0	-6.3925	16.8446	0.85977	0.0:1.0:0.0:0.0	.	22;15	B2RDZ2;Q969G6	.;RIFK_HUMAN	S	15;22;2	.	ENSP00000257452:G22S	G	-	1	0	RFK	78198865	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.554000	0.73923	2.044000	0.60594	0.479000	0.44913	GGC	.	.		0.721	RFK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052720.1	NM_018339		T	79009045	C	T	79009045	3	4	204	1	0	0	0	0	1	0	0	0	13266	623	22	3	440	3	RFK	9	79009045	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	57599816	79009045	62204386	27	29834										
LOC645961	645961	hgsc.bcm.edu	37	chr9	90748542	90748542	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gtttttcatcctgcctctggGcctccccctccgccctgctg	8	19	2	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr9:90748542G>A								U6 (135292 upstream) : U3 (240641 downstream)																							CTGCCTCTGGGCCTCCCCCTC	0.592																																					p.P78S		Atlas-SNP	.											.	.	.	.	0			c.C232T						.						82	81	82					9																	90748542		692	1591	2283	SO:0001628	intergenic_variant	645961	exon2			CTCTGGGCCTCCC																													chr9.hg19:g.90748542G>A		353.0	0.0		412.0	58.0	NM_001166137		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.592									A	90748542	G	A	90748542	1	1	204	0	1	0	0	0	0	0	0	0	8892	1203	42	3		3	LOC645961	9	90748542	IGR	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10	11739497	90748542	50464889	28	29835										
C10orf140	387640	hgsc.bcm.edu	37	chr10	21805720	21805720	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	tggtggtggtggtggtggtgAtggtggtggtggtggtggtg	26	0	0	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr10:21805720A>G	ENST00000449193.2	-	4	3284	c.1032T>C	c.(1030-1032)caT>caC	p.H344H	SKIDA1_ENST00000444772.3_Silent_p.H265H|SKIDA1_ENST00000487107.1_5'Flank	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	263	Glu-rich.|Ser-rich.					nucleus (GO:0005634)											ggtggtggtgatggtggtggt	0.716																																					p.H344H		Atlas-SNP	.											.	.	.	.	0			c.T1032C						.						4	6	5					10																	21805720		1658	3602	5260	SO:0001819	synonymous_variant	387640	exon4			GTGGTGATGGTGG	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 140"	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.1032T>C	chr10.hg19:g.21805720A>G		55.0	0.0		96.0	4.0	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	ENST00000449193.2	hg19	CCDS44363.1																																																																																			.	.		0.716	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		G	21805720	A	G	21805720	2	3	204	1	0	0	0	0	0	0	0	1	1597	330	12	2		2	C10orf140	10	21805720	Silent	SNP	A	TCGA-DD-AADW-01A-11D-A38X-10		21805720	113729027	29	29836										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117075120	117075120	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	ctagtaatacaggaagaggaCattgcattgaaggttcttca	10	6	2	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr10:117075120C>T	ENST00000355044.3	+	18	3037	c.2911C>T	c.(2911-2913)Cat>Tat	p.H971Y	ATRNL1_ENST00000423111.2_Missense_Mutation_p.H68Y|ATRNL1_ENST00000303745.7_5'UTR	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	971	PSI 5.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		AGGAAGAGGACATTGCATTGA	0.453																																					p.H971Y		Atlas-SNP	.											.	ATRNL1	219	.	0			c.C2911T						.						153	133	140					10																	117075120		2203	4300	6503	SO:0001583	missense	26033	exon18			AGAGGACATTGCA	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2911C>T	chr10.hg19:g.117075120C>T	ENSP00000347152:p.His971Tyr	89.0	0.0		87.0	38.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.368|1.368	-0.586994|-0.586994	0.03827|0.03827	.|.	.|.	ENSG00000107518|ENSG00000107518	ENST00000355044;ENST00000423111|ENST00000526373	T;T|.	0.17528|.	2.27;2.27|.	5.34|5.34	3.41|3.41	0.39046|0.39046	.|.	0.455833|.	0.26627|.	N|.	0.023334|.	T|T	0.29620|0.29620	0.0739|0.0739	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.03969|0.03969	-1.0988|-1.0988	10|5	0.14656|.	T|.	0.56|.	-5.1853|-5.1853	5.5388|5.5388	0.17026|0.17026	0.1564:0.6718:0.0:0.1718|0.1564:0.6718:0.0:0.1718	.|.	68;971|.	B4DH41;Q5VV63|.	.;ATRN1_HUMAN|.	Y|I	971;68|100	ENSP00000347152:H971Y;ENSP00000409624:H68Y|.	ENSP00000347152:H971Y|.	H|T	+|+	1|2	0|0	ATRNL1|ATRNL1	117065110|117065110	0.231000|0.231000	0.23751|0.23751	0.990000|0.990000	0.47175|0.47175	0.845000|0.845000	0.48019|0.48019	0.892000|0.892000	0.28322|0.28322	0.576000|0.576000	0.29452|0.29452	0.455000|0.455000	0.32223|0.32223	CAT|ACA	.	.		0.453	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		T	117075120	C	T	117075120	3	4	204	1	0	0	0	0	1	0	0	0	1207	478	17	3	2981	3	ATRNL1	10	117075120	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	95269400	117075120	18459627	30	29837										
HMX3	340784	hgsc.bcm.edu	37	chr10	124895890	124895890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	aggtttgccctgcccgcgcaCtacctggagcgctccccagc	11	18	0	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr10:124895890C>T	ENST00000357878.5	+	1	413	c.324C>T	c.(322-324)caC>caT	p.H108H		NM_001105574.1	NP_001099044.1	A6NHT5	HMX3_HUMAN	H6 family homeobox 3	108					brain development (GO:0007420)|cell differentiation (GO:0030154)|embryo implantation (GO:0007566)|inner ear morphogenesis (GO:0042472)|maternal process involved in female pregnancy (GO:0060135)|neuromuscular process controlling balance (GO:0050885)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(4)	4		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.122)|COAD - Colon adenocarcinoma(40;0.141)		TGCCCGCGCACTACCTGGAGC	0.697																																					p.H108H		Atlas-SNP	.											.	HMX3	24	.	0			c.C324T						.						11	15	14					10																	124895890		1964	4128	6092	SO:0001819	synonymous_variant	340784	exon1			CGCGCACTACCTG		CCDS41575.1	10q26.13	2011-06-20	2007-07-09		ENSG00000188620	ENSG00000188620		"Homeoboxes / ANTP class : NKL subclass"	5019	protein-coding gene	gene with protein product		613380	"homeo box (H6 family) 3"				Standard	NM_001105574		Approved	NKX5-1	uc010quc.2	A6NHT5	OTTHUMG00000019199	ENST00000357878.5:c.324C>T	chr10.hg19:g.124895890C>T		106.0	0.0		143.0	58.0	NM_001105574	A8MU06	Silent	SNP	ENST00000357878.5	hg19	CCDS41575.1																																																																																			.	.		0.697	HMX3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050842.4	XM_291716		T	124895890	C	T	124895890	2	4	204	1	0	0	0	0	0	0	0	1	7257	564	20	3		3	HMX3	10	124895890	Silent	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	7820770	124895890	10638857	31	29838										
SLC35C1	55343	hgsc.bcm.edu	37	chr11	45832352	45832352	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	ttctggcttggtgtggaccaGgagggggcagaaggcaccct	17	9	1	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr11:45832352G>C	ENST00000314134.3	+	2	1957	c.561G>C	c.(559-561)caG>caC	p.Q187H	CTD-2210P24.6_ENST00000534128.1_lincRNA|SLC35C1_ENST00000442528.2_Missense_Mutation_p.Q174H|SLC35C1_ENST00000456334.1_Missense_Mutation_p.Q174H	NM_018389.4	NP_060859.4	Q96A29	FUCT1_HUMAN	solute carrier family 35 (GDP-fucose transporter), member C1	187					carbohydrate transport (GO:0008643)|lipid glycosylation (GO:0030259)|negative regulation of Notch signaling pathway (GO:0045746)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10				GBM - Glioblastoma multiforme(35;0.227)		GTGTGGACCAGGAGGGGGCAG	0.632																																					p.Q187H		Atlas-SNP	.											.	SLC35C1	23	.	0			c.G561C						.						41	44	43					11																	45832352		2203	4299	6502	SO:0001583	missense	55343	exon2			GGACCAGGAGGGG		CCDS7914.1, CCDS44575.1	11p11.2	2014-09-17	2013-07-17			ENSG00000181830		"Solute carriers"	20197	protein-coding gene	gene with protein product		605881	"solute carrier family 35, member C1"			11326279, 11326280	Standard	NM_018389		Approved	FUCT1, FLJ11320	uc010rgm.2	Q96A29		ENST00000314134.3:c.561G>C	chr11.hg19:g.45832352G>C	ENSP00000313318:p.Gln187His	50.0	0.0		47.0	4.0	NM_018389	B2RDB2|Q9BV76|Q9NUJ8	Missense_Mutation	SNP	ENST00000314134.3	hg19	CCDS7914.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.630484	0.67015	.	.	ENSG00000181830	ENST00000442528;ENST00000456334;ENST00000530670;ENST00000314134;ENST00000540685	T;T;T	0.64803	-0.11;-0.11;-0.12	6.08	3.13	0.36017	.	0.000000	0.85682	D	0.000000	T	0.78175	0.4242	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.79200	-0.1901	10	0.49607	T	0.09	-19.4468	11.4901	0.50377	0.2008:0.0:0.7992:0.0	.	187	Q96A29	FUCT1_HUMAN	H	174;174;108;187;187	ENSP00000412408:Q174H;ENSP00000399779:Q174H;ENSP00000313318:Q187H	ENSP00000313318:Q187H	Q	+	3	2	SLC35C1	45788928	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.600000	0.46240	0.865000	0.35603	0.655000	0.94253	CAG	.	.		0.632	SLC35C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390139.1	NM_018389		C	45832352	G	C	45832352	3	2	204	1	0	0	0	0	1	0	0	0	14594	991	35	4	567	4	SLC35C1	11	45832352	Missense_Mutation	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10		45832352	89174164	32	29839										
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579749	55579749	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	agttcaggcaatagtggagaTgctgacaaagtggccaccgt	13	8	1	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr11:55579749T>C	ENST00000333973.2	+	1	896	c.807T>C	c.(805-807)gaT>gaC	p.D269D		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	269						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				ATAGTGGAGATGCTGACAAAG	0.473																																					p.D269D		Atlas-SNP	.											.	OR5L1	145	.	0			c.T807C						.						95	84	88					11																	55579749		2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			TGGAGATGCTGAC	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.807T>C	chr11.hg19:g.55579749T>C		104.0	0.0		109.0	12.0	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	hg19	CCDS31509.1																																																																																			.	.		0.473	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		C	55579749	T	C	55579749	2	2	204	1	0	0	0	0	0	0	0	1	11179	1461	51	2		2	OR5L1	11	55579749	Silent	SNP	T	TCGA-DD-AADW-01A-11D-A38X-10	9747397	55579749	79426767	33	29840										
CATSPER1	117144	hgsc.bcm.edu	37	chr11	65789252	65789252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	cccacccaaattgttccagaAgtcaaagaagtacgagaggc	9	11	1	3			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr11:65789252A>G	ENST00000312106.5	-	3	1665	c.1528T>C	c.(1528-1530)Ttc>Ctc	p.F510L		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	510					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						TTGTTCCAGAAGTCAAAGAAG	0.587																																					p.F510L		Atlas-SNP	.											.	CATSPER1	101	.	0			c.T1528C						.						123	112	116					11																	65789252		2201	4296	6497	SO:0001583	missense	117144	exon3			TCCAGAAGTCAAA	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"Voltage-gated ion channels / Cation channels, sperm associated"	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.1528T>C	chr11.hg19:g.65789252A>G	ENSP00000309052:p.Phe510Leu	155.0	0.0		204.0	19.0	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	hg19	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.133183	0.37630	.	.	ENSG00000175294	ENST00000312106	D	0.98234	-4.81	4.58	-4.99	0.03010	Ion transport (1);	1.380240	0.05245	N	0.512954	D	0.92753	0.7696	N	0.11023	0.085	0.09310	N	1	B	0.25955	0.138	B	0.33196	0.159	D	0.87664	0.2536	10	0.40728	T	0.16	-3.075	1.2359	0.01953	0.3118:0.2732:0.2807:0.1343	.	510	Q8NEC5	CTSR1_HUMAN	L	510	ENSP00000309052:F510L	ENSP00000309052:F510L	F	-	1	0	CATSPER1	65545828	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.208000	0.03005	-0.699000	0.05077	0.247000	0.18012	TTC	.	.		0.587	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		G	65789252	A	G	65789252	3	3	204	1	0	0	0	0	1	0	0	0	2689	72	3	2	854	2	CATSPER1	11	65789252	Missense_Mutation	SNP	A	TCGA-DD-AADW-01A-11D-A38X-10	10209503	65789252	69217264	34	29841										
RNF169	254225	hgsc.bcm.edu	37	chr11	74547698	74547698	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	agcgcatgttcgacaatgagAggcggactgtgagccggcga	16	9	0	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr11:74547698A>G	ENST00000299563.4	+	6	2063	c.2050A>G	c.(2050-2052)Agg>Ggg	p.R684G		NM_001098638.1	NP_001092108.1	Q8NCN4	RN169_HUMAN	ring finger protein 169	684					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of double-strand break repair (GO:2000780)|protein ubiquitination (GO:0016567)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|site of double-strand break (GO:0035861)	K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	15						CGACAATGAGAGGCGGACTGT	0.542																																					p.R684G		Atlas-SNP	.											.	RNF169	36	.	0			c.A2050G						.						75	77	77					11																	74547698		1964	4145	6109	SO:0001583	missense	254225	exon6			AATGAGAGGCGGA	AB082522	CCDS41691.1	11q13.4	2008-02-05			ENSG00000166439	ENSG00000166439		"RING-type (C3HC4) zinc fingers"	26961	protein-coding gene	gene with protein product						12056414	Standard	NM_001098638		Approved	KIAA1991	uc001ovl.4	Q8NCN4	OTTHUMG00000165516	ENST00000299563.4:c.2050A>G	chr11.hg19:g.74547698A>G	ENSP00000299563:p.Arg684Gly	56.0	0.0		68.0	5.0	NM_001098638	Q6N015	Missense_Mutation	SNP	ENST00000299563.4	hg19	CCDS41691.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.790260	0.31685	.	.	ENSG00000166439	ENST00000299563	T	0.48522	0.81	5.53	1.54	0.23209	.	0.273555	0.36815	N	0.002399	T	0.39118	0.1066	M	0.65975	2.015	0.80722	D	1	P	0.39782	0.688	B	0.28849	0.095	T	0.39313	-0.9620	10	0.48119	T	0.1	-3.7219	11.7531	0.51859	0.5342:0.4658:0.0:0.0	.	684	Q8NCN4	RN169_HUMAN	G	684	ENSP00000299563:R684G	ENSP00000299563:R684G	R	+	1	2	RNF169	74225346	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	2.012000	0.40932	0.438000	0.26450	0.533000	0.62120	AGG	.	.		0.542	RNF169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384741.1	XM_495886		G	74547698	A	G	74547698	3	3	204	1	0	0	0	0	1	0	0	0	13475	295	11	2	2072	2	RNF169	11	74547698	Missense_Mutation	SNP	A	TCGA-DD-AADW-01A-11D-A38X-10	8758446	74547698	60458818	35	29842										
OR10G4	390264	hgsc.bcm.edu	37	chr11	123886338	123886338	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	acaggccttccccatgccccAgggctggacgccctcctctt	9	19	1	0	rs539322343		TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr11:123886338A>T	ENST00000320891.4	+	1	57	c.57A>T	c.(55-57)ccA>ccT	p.P19P		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CCCATGCCCCAGGGCTGGACG	0.567																																					p.P19P		Atlas-SNP	.											.	OR10G4	77	.	0			c.A57T						.						151	105	121					11																	123886338		2202	4298	6500	SO:0001819	synonymous_variant	390264	exon1			TGCCCCAGGGCTG	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"GPCR / Class A : Olfactory receptors"	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.57A>T	chr11.hg19:g.123886338A>T		156.0	0.0		232.0	21.0	NM_001004462	Q6IEW0	Silent	SNP	ENST00000320891.4	hg19	CCDS31702.1																																																																																			.	.		0.567	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462		T	123886338	A	T	123886338	2	4	204	1	0	0	0	0	0	0	0	1	10910	175	7	4		4	OR10G4	11	123886338	Silent	SNP	A	TCGA-DD-AADW-01A-11D-A38X-10	49338640	123886338	11120178	36	29843										
KRT83	3889	hgsc.bcm.edu	37	chr12	52710776	52710776	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gcttgacaaccacggaggtgTctgagatgtgggattggaga	16	6	1	3			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr12:52710776T>A	ENST00000293670.3	-	5	844	c.782A>T	c.(781-783)gAc>gTc	p.D261V		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	261	Linker 12.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CACGGAGGTGTCTGAGATGTG	0.537																																					p.D261V	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											.	KRT83	64	.	0			c.A782T						.						145	127	133					12																	52710776		2203	4300	6503	SO:0001583	missense	3889	exon5			GAGGTGTCTGAGA	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"-", "Intermediate filaments type II, keratins (basic)"	6460	protein-coding gene	gene with protein product	"hard keratin type II"	602765	"keratin, hair, basic, 3"	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.782A>T	chr12.hg19:g.52710776T>A	ENSP00000293670:p.Asp261Val	66.0	0.0		82.0	32.0	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Missense_Mutation	SNP	ENST00000293670.3	hg19	CCDS8823.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.255186	0.80135	.	.	ENSG00000170523	ENST00000293670	T	0.80304	-1.36	3.9	3.9	0.45041	Filament (1);	0.000000	0.43747	U	0.000539	D	0.89427	0.6712	M	0.86651	2.83	0.80722	D	1	D	0.58620	0.983	D	0.65323	0.934	D	0.91217	0.5003	10	0.87932	D	0	.	13.0274	0.58823	0.0:0.0:0.0:1.0	.	261	P78385	KRT83_HUMAN	V	261	ENSP00000293670:D261V	ENSP00000293670:D261V	D	-	2	0	KRT83	50997043	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.904000	0.87408	1.544000	0.49359	0.459000	0.35465	GAC	.	.		0.537	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282		A	52710776	T	A	52710776	3	1	204	1	0	0	0	0	1	0	0	0	8506	1667	58	4	719	4	KRT83	12	52710776	Missense_Mutation	SNP	T	TCGA-DD-AADW-01A-11D-A38X-10		52710776	81141119	37	29844										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58131312	58131312	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	ccctcccccggcggcggcggCggtggcggcggcagagaccg	19	17	0	1	rs561812307		TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr12:58131312C>T	ENST00000547588.1	-	1	717	c.718G>A	c.(718-720)Gcc>Acc	p.A240T	AGAP2_ENST00000257897.3_Intron	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	240					axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						gcggcggcggcggtggcggcg	0.706																																					p.A240T		Atlas-SNP	.											AGAP2_ENST00000547588,NS,carcinoma,0,1	AGAP2	167	.	0			c.G718A						.						4	6	5					12																	58131312		1428	3301	4729	SO:0001583	missense	116986	exon1			CGGCGGCGGTGGC	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.718G>A	chr12.hg19:g.58131312C>T	ENSP00000449241:p.Ala240Thr	80.0	0.0		75.0	4.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	hg19	CCDS44932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.24|10.24	1.294811|1.294811	0.23564|0.23564	.|.	.|.	ENSG00000135439|ENSG00000135439	ENST00000547588|ENST00000328568	T|.	0.39997|.	1.05|.	3.81|3.81	-1.14|-1.14	0.09741|0.09741	.|.	1.354790|.	0.05448|.	N|.	0.548952|.	T|T	0.10508|0.10508	0.0257|0.0257	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.14012|.	0.009;0.005|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.24548|0.24548	-1.0157|-1.0157	10|5	0.56958|.	D|.	0.05|.	.|.	0.5619|0.5619	0.00680|0.00680	0.1874:0.3561:0.184:0.2724|0.1874:0.3561:0.184:0.2724	.|.	240;240|.	F8VVT9;Q99490|.	.;AGAP2_HUMAN|.	T|H	240|103	ENSP00000449241:A240T|.	ENSP00000449241:A240T|.	A|R	-|-	1|2	0|0	AGAP2|AGAP2	56417579|56417579	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	0.086000|0.086000	0.14935|0.14935	-0.555000|-0.555000	0.06142|0.06142	0.455000|0.455000	0.32223|0.32223	GCC|CGC	.	.		0.706	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		T	58131312	C	T	58131312	3	4	204	1	0	0	0	0	1	0	0	0	368	768	27	1	2936	1	AGAP2	12	58131312	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	5420536	58131312	75720583	38	29845										
MSRB3	253827	hgsc.bcm.edu	37	chr12	65672604	65672604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gctctgcctctccctctgccTctgcctctgcctggccgcgg	10	20	5	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr12:65672604T>C	ENST00000355192.3	+	1	182	c.56T>C	c.(55-57)cTc>cCc	p.L19P	MSRB3_ENST00000540804.1_Missense_Mutation_p.L19P|MSRB3_ENST00000535664.1_5'UTR|MSRB3_ENST00000308259.5_5'UTR|RP11-305O6.3_ENST00000545709.1_RNA|MSRB3_ENST00000538725.1_3'UTR	NM_198080.3	NP_932346.1	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3	19					protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		tccctctgcctctgcctctgc	0.731																																					p.L19P		Atlas-SNP	.											.	MSRB3	80	.	0			c.T56C						.						19	18	18					12																	65672604		2166	4244	6410	SO:0001583	missense	253827	exon1			TCTGCCTCTGCCT	BX640871	CCDS8973.1, CCDS31853.1	12q14.3	2011-11-29			ENSG00000174099	ENSG00000174099			27375	protein-coding gene	gene with protein product		613719	"deafness, autosomal recessive 74"	DFNB74		21185009	Standard	NM_198080		Approved	FLJ36866, DKFZp686C1178	uc021qzy.1	Q8IXL7	OTTHUMG00000168866	ENST00000355192.3:c.56T>C	chr12.hg19:g.65672604T>C	ENSP00000347324:p.Leu19Pro	148.0	0.0		160.0	14.0	NM_198080	B4DR19|B7ZAQ0|Q6UXS2	Missense_Mutation	SNP	ENST00000355192.3	hg19	CCDS8973.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.817614	0.90790	.	.	ENSG00000174099	ENST00000355192;ENST00000540804	T;T	0.67345	-0.23;-0.26	3.83	3.83	0.44106	.	7741.500000	0.00166	N	0.000000	T	0.54695	0.1874	N	0.08118	0	0.80722	D	1	P	0.36959	0.575	B	0.42214	0.38	T	0.43180	-0.9407	9	.	.	.	.	9.0152	0.36166	0.0:0.0:0.0:1.0	.	19	Q8IXL7	MSRB3_HUMAN	P	19	ENSP00000347324:L19P;ENSP00000437623:L19P	.	L	+	2	0	MSRB3	63958871	0.637000	0.27216	0.960000	0.40013	0.836000	0.47400	1.097000	0.30988	1.371000	0.46172	0.164000	0.16699	CTC	.	.		0.731	MSRB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401421.1	NM_198080		C	65672604	T	C	65672604	3	2	204	1	0	0	0	0	1	0	0	0	9898	1551	54	2	58	2	MSRB3	12	65672604	Missense_Mutation	SNP	T	TCGA-DD-AADW-01A-11D-A38X-10	7541292	65672604	68179291	39	29846										
HSPH1	10808	hgsc.bcm.edu	37	chr13	31724104	31724104	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	aaagtacctgtaatgcacatCctctggctactgcttcatct	6	12	3	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr13:31724104C>A	ENST00000320027.5	-	8	1468	c.1124G>T	c.(1123-1125)gGa>gTa	p.G375V	HSPH1_ENST00000380406.5_Missense_Mutation_p.G334V|HSPH1_ENST00000380405.4_Missense_Mutation_p.G375V|HSPH1_ENST00000445273.2_Missense_Mutation_p.G377V|HSPH1_ENST00000429785.2_Missense_Mutation_p.G194V	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	375					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		TAATGCACATCCTCTGGCTAC	0.428																																					p.G375V		Atlas-SNP	.											.	HSPH1	65	.	0			c.G1124T						.						110	104	106					13																	31724104		2203	4300	6503	SO:0001583	missense	10808	exon8			GCACATCCTCTGG	AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"Heat shock proteins / HSP70"	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.1124G>T	chr13.hg19:g.31724104C>A	ENSP00000318687:p.Gly375Val	118.0	0.0		68.0	56.0	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Missense_Mutation	SNP	ENST00000320027.5	hg19	CCDS9340.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939361	0.73557	.	.	ENSG00000120694	ENST00000320027;ENST00000380405;ENST00000380406;ENST00000445273;ENST00000429785;ENST00000438061	D;D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11;-2.11	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	D	0.96194	0.8759	H	0.96805	3.885	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.97154	0.9833	10	0.87932	D	0	-26.0178	19.7842	0.96430	0.0:1.0:0.0:0.0	.	194;334;377;375;375	B4DY72;Q92598-3;B4DYH1;Q92598-2;Q92598	.;.;.;.;HS105_HUMAN	V	375;375;334;377;194;426	ENSP00000318687:G375V;ENSP00000369768:G375V;ENSP00000369769:G334V;ENSP00000396090:G377V;ENSP00000388778:G194V	ENSP00000318687:G375V	G	-	2	0	HSPH1	30622104	1.000000	0.71417	0.919000	0.36401	0.546000	0.35178	7.487000	0.81328	2.676000	0.91093	0.591000	0.81541	GGA	.	.		0.428	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1			A	31724104	C	A	31724104	3	1	204	1	0	0	0	0	1	0	0	0	7440	855	30	3	1496	3	HSPH1	13	31724104	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10		31724104	83445774	40	29847										
RB1	5925	hgsc.bcm.edu	37	chr13	48878060	48878103	+	Frame_Shift_Del	DEL	AACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	AACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	-													0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	aaaggcgtcatgccgcccaaAaccccccgaaaaacggccgc					rs564137727|rs587778638|rs564059250|rs530961288|rs572454921|rs148980395|rs587778852|rs528218090	byFrequency	TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	AACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	AACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr13:48878060_48878103delAACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	ENST00000267163.4	+	1	150_193	c.12_55delAACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	c.(10-57)aaaaccccccgaaaaacggccgccaccgccgccgctgccgccgcggaafs	p.TPRKTAATAAAAAAE5fs	LINC00441_ENST00000433480.2_lincRNA	NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	5					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.A14A(1)|p.?(1)|p.A16fs*3(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TGCCGCCCAAAACCCCCCGAAAAACGgccgccaccgccgccgctgccgccgcggaacccccggc	0.762		6	"D, Mis, N, F, S"		"retinoblastoma, sarcoma, breast, small cell lung"	"retinoblastoma, sarcoma, breast, small cell lung"			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.4_18del		Atlas-INDEL	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	18	Whole gene deletion(15)|Unknown(1)|Substitution - coding silent(1)|Deletion - Frameshift(1)	bone(10)|eye(2)|breast(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|lung(1)	c.11_54del	GRCh37	CD067560|CD071388|CI030631|CX034947	RB1	D|I|X		.																																			SO:0001589	frameshift_variant	5925	exon1	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.12_55delAACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	chr13.hg19:g.48878060_48878103delAACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	ENSP00000267163:p.Thr5fs	977.0	0.0		429.0	235.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Del	DEL	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.762	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			-	48878103	AACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	-	48878060	7	5	204	1	0	1	0	1	0	0	0	0	13113	11	1	0	14	0	RB1	13	48878060	Frame_Shift_Del	DEL	AACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	TCGA-DD-AADW-01A-11D-A38X-10	17153956	48878060	66291818	41	29848										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77842001	77842001	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	aacatcacagtaccatcttgCtccagtgtttcagggcttat	7	11	3	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr13:77842001C>A	ENST00000544440.2	-	8	1235	c.1218G>T	c.(1216-1218)gaG>gaT	p.E406D	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000407578.2_Missense_Mutation_p.E444D|MYCBP2_ENST00000357337.6_Missense_Mutation_p.E406D					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TACCATCTTGCTCCAGTGTTT	0.343																																					p.E444D		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.G1332T						.						155	137	143					13																	77842001		2203	4300	6503	SO:0001583	missense	23077	exon8			ATCTTGCTCCAGT	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.1218G>T	chr13.hg19:g.77842001C>A	ENSP00000444596:p.Glu406Asp	100.0	0.0		191.0	72.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	C	13.26	2.185356	0.38609	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.48201	0.82;0.82;0.82	5.79	-1.8	0.07907	.	0.064478	0.64402	D	0.000012	T	0.33323	0.0859	L	0.36672	1.1	0.40880	D	0.983982	B	0.06786	0.001	B	0.08055	0.003	T	0.12142	-1.0559	10	0.24483	T	0.36	.	13.6375	0.62230	0.0:0.4937:0.0:0.5063	.	406	O75592	MYCB2_HUMAN	D	406;444;406	ENSP00000349892:E406D;ENSP00000384288:E444D;ENSP00000444596:E406D	ENSP00000349892:E406D	E	-	3	2	MYCBP2	76740002	0.882000	0.30256	0.941000	0.38009	0.992000	0.81027	-0.017000	0.12590	-0.534000	0.06315	-0.469000	0.05056	GAG	.	.		0.343	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		A	77842001	C	A	77842001	3	1	204	1	0	0	0	0	1	0	0	0	10027	796	28	3	13008	3	MYCBP2	13	77842001	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	28963941	77842001	37327877	42	29849										
TP53	7157	hgsc.bcm.edu	37	chr17	7578402	7578402	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gagcagcgctcatggtggggGcagcgcctcacaacctccgt	14	14	2	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr17:7578402G>C	ENST00000269305.4	-	5	717	c.528C>G	c.(526-528)tgC>tgG	p.C176W	TP53_ENST00000413465.2_Missense_Mutation_p.C176W|TP53_ENST00000359597.4_Missense_Mutation_p.C176W|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Missense_Mutation_p.C176W|TP53_ENST00000420246.2_Missense_Mutation_p.C176W|TP53_ENST00000445888.2_Missense_Mutation_p.C176W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	176	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:8829627, ECO:0000269|PubMed:9450901}.|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in sporadic cancers; somatic mutation).|CP -> FS (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C176*(12)|p.C176W(11)|p.0?(8)|p.C176_R181delCPHHER(3)|p.R174fs*24(3)|p.H178fs*69(3)|p.R175_E180delRCPHHE(3)|p.C83*(2)|p.V173fs*59(2)|p.C44*(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.C176F(1)|p.C176fs*65(1)|p.C176_P177delCP(1)|p.V173fs*69(1)|p.C176fs*68(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R42fs*24(1)|p.P177fs*4(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.C176del(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.H178fs*3(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CATGGTGGGGGCAGCGCCTCA	0.647		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.C176W	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,-1,1	TP53	33396	.	75	Deletion - Frameshift(21)|Substitution - Nonsense(16)|Deletion - In frame(13)|Substitution - Missense(12)|Whole gene deletion(8)|Complex - deletion inframe(3)|Insertion - Frameshift(2)	breast(15)|large_intestine(12)|upper_aerodigestive_tract(8)|lung(8)|oesophagus(8)|haematopoietic_and_lymphoid_tissue(5)|ovary(4)|bone(4)|stomach(2)|central_nervous_system(2)|liver(2)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|skin(1)|pancreas(1)	c.C528G						.						48	48	48					17																	7578402		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GTGGGGGCAGCGC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.528C>G	chr17.hg19:g.7578402G>C	ENSP00000269305:p.Cys176Trp	132.0	1.0		72.0	8.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.640435	0.67244	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99982	-10.62;-10.62;-10.62;-10.62;-10.62;-10.62;-10.62;-10.62	5.59	-1.32	0.09201	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.092184	0.85682	D	0.000000	D	0.99972	0.9991	M	0.92923	3.36	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;1.0;0.999;0.998	D	0.94683	0.7867	10	0.87932	D	0	-18.1821	6.7443	0.23453	0.3734:0.1173:0.5093:0.0	.	137;176;176;83;176;176;176	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	W	176;176;176;176;176;176;165;83;44;83;44	ENSP00000410739:C176W;ENSP00000352610:C176W;ENSP00000269305:C176W;ENSP00000398846:C176W;ENSP00000391127:C176W;ENSP00000391478:C176W;ENSP00000425104:C44W;ENSP00000423862:C83W	ENSP00000269305:C176W	C	-	3	2	TP53	7519127	1.000000	0.71417	0.991000	0.47740	0.860000	0.49131	0.743000	0.26231	-0.094000	0.12374	-0.126000	0.14955	TGC	.	.		0.647	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578402	G	C	7578402	3	2	204	1	0	0	0	0	1	0	0	0	16396	1195	42	4	770	4	TP53	17	7578402	Missense_Mutation	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10		7578402	73616808	43	29850										
RICH2	9912	hgsc.bcm.edu	37	chr17	12883408	12883408	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	aaggaactttctccaggctcTgcacagaaaggaagtccagg	11	10	2	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr17:12883408T>C	ENST00000379672.5	+	19	2097	c.1797T>C	c.(1795-1797)tcT>tcC	p.S599S	ARHGAP44_ENST00000262444.9_Silent_p.S599S|ARHGAP44_ENST00000578087.1_3'UTR|ARHGAP44_ENST00000340825.3_Silent_p.S593S	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	599					exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						CTCCAGGCTCTGCACAGAAAG	0.587																																					p.S599S		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.T1797C						.						33	37	36					17																	12883408		1931	4149	6080	SO:0001819	synonymous_variant	9912	exon19			AGGCTCTGCACAG		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"Rho GTPase activating proteins"	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.1797T>C	chr17.hg19:g.12883408T>C		149.0	0.0		116.0	40.0	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Silent	SNP	ENST00000379672.5	hg19	CCDS45616.1																																																																																			.	.		0.587	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859		C	12883408	T	C	12883408	2	2	204	1	0	0	0	0	0	0	0	1	13372	1567	55	2		2	RICH2	17	12883408	Silent	SNP	T	TCGA-DD-AADW-01A-11D-A38X-10	5305006	12883408	68311802	44	29851										
ATAD5	79915	hgsc.bcm.edu	37	chr17	29159374	29159374	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gaagcggggagtatggtgggGgtcctggccatggcggctgc	21	8	0	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr17:29159374G>A	ENST00000321990.4	+	1	387	c.9G>A	c.(7-9)ggG>ggA	p.G3G	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	3					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				GTATGGTGGGGGTCCTGGCCA	0.642																																					p.G3G		Atlas-SNP	.											.	ATAD5	150	.	0			c.G9A						.						64	71	69					17																	29159374		2203	4300	6503	SO:0001819	synonymous_variant	79915	exon1			GGTGGGGGTCCTG		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.9G>A	chr17.hg19:g.29159374G>A		52.0	0.0		76.0	24.0	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	hg19	CCDS11260.1																																																																																			.	.		0.642	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		A	29159374	G	A	29159374	2	1	204	1	0	0	0	0	0	0	0	1	1076	1219	43	3		3	ATAD5	17	29159374	Silent	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10	16275966	29159374	52035836	45	29852										
LRRC37A3	374819	hgsc.bcm.edu	37	chr17	62856309	62856309	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	tggactctttttgaccttggGtgttctgtgggtcatgcggg	15	7	3	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr17:62856309G>T	ENST00000584306.1	-	11	4485	c.3955C>A	c.(3955-3957)Ccc>Acc	p.P1319T	LRRC37A3_ENST00000400877.3_Missense_Mutation_p.P357T|LRRC37A3_ENST00000339474.5_Missense_Mutation_p.P437T|LRRC37A3_ENST00000334962.5_Missense_Mutation_p.P296T|LRRC37A3_ENST00000319651.5_Missense_Mutation_p.P1319T	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1319						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						TTGACCTTGGGTGTTCTGTGG	0.428																																					p.P1319T		Atlas-SNP	.											.	LRRC37A3	75	.	0			c.C3955A						.						202	211	208					17																	62856309		2203	4298	6501	SO:0001583	missense	374819	exon11			CCTTGGGTGTTCT	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.3955C>A	chr17.hg19:g.62856309G>T	ENSP00000464535:p.Pro1319Thr	82.0	0.0		191.0	49.0	NM_199340	Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	ENST00000584306.1	hg19	CCDS32708.1	.	.	.	.	.	.	.	.	.	.	.	7.591	0.670751	0.14776	.	.	ENSG00000176809	ENST00000339474;ENST00000400877;ENST00000334962;ENST00000319651	T;T;T	0.59224	1.44;1.43;0.28	2.1	1.07	0.20283	.	.	.	.	.	T	0.55878	0.1948	L	0.52573	1.65	0.09310	N	1	D;P	0.54964	0.969;0.759	P;B	0.52159	0.691;0.143	T	0.44174	-0.9345	9	0.46703	T	0.11	.	4.8767	0.13660	0.1959:0.0:0.8041:0.0	.	437;1319	B4DG20;O60309	.;L37A3_HUMAN	T	400;357;296;1319	ENSP00000383674:P357T;ENSP00000335617:P296T;ENSP00000325713:P1319T	ENSP00000325713:P1319T	P	-	1	0	LRRC37A3	60286771	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	0.546000	0.23284	0.211000	0.20683	0.184000	0.17185	CCC	.	.		0.428	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340		T	62856309	G	T	62856309	3	4	204	1	0	0	0	0	1	0	0	0	9002	1261	44	3	965	3	LRRC37A3	17	62856309	Missense_Mutation	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10	33696935	62856309	18338901	46	29853										
CD7	924	hgsc.bcm.edu	37	chr17	80275365	80275365	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	cagcaggagcctcggaggccCggccatgttccccacaccca	11	18	0	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr17:80275365C>G	ENST00000312648.3	-	1	113	c.7G>C	c.(7-9)Ggg>Cgg	p.G3R	CD7_ENST00000583376.1_5'UTR|CD7_ENST00000578509.1_5'UTR|CD7_ENST00000584284.1_Missense_Mutation_p.G3R	NM_006137.6	NP_006128.1	P09564	CD7_HUMAN	CD7 molecule	3					homeostasis of number of cells within a tissue (GO:0048873)|immune response (GO:0006955)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)			CTCGGAGGCCCGGCCATGTTC	0.687																																					p.G3R	Pancreas(45;804 1068 19702 28207 28798)	Atlas-SNP	.											.	CD7	25	.	0			c.G7C						.						11	13	12					17																	80275365		2118	4205	6323	SO:0001583	missense	924	exon1			GAGGCCCGGCCAT	X06180	CCDS11807.1	17q25.2-q25.3	2013-01-11	2006-03-28			ENSG00000173762		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1695	protein-coding gene	gene with protein product	"p41 protein", "T-cell antigen CD7", "T-cell leukemia antigen"	186820	"CD7 antigen (p41)"			1695199, 3501369	Standard	NM_006137		Approved	GP40, LEU-9, TP41, Tp40	uc002kel.1	P09564		ENST00000312648.3:c.7G>C	chr17.hg19:g.80275365C>G	ENSP00000312027:p.Gly3Arg	182.0	0.0		317.0	18.0	NM_006137		Missense_Mutation	SNP	ENST00000312648.3	hg19	CCDS11807.1	.	.	.	.	.	.	.	.	.	.	C	4.181	0.032231	0.08101	.	.	ENSG00000173762	ENST00000312648	T	0.26067	1.76	1.98	-3.95	0.04118	.	.	.	.	.	T	0.13670	0.0331	N	0.22421	0.69	0.20196	N	0.999923	B;B;B	0.17667	0.004;0.023;0.023	B;B;B	0.06405	0.001;0.002;0.001	T	0.23226	-1.0194	9	0.49607	T	0.09	-0.0154	5.7535	0.18160	0.0:0.2446:0.5846:0.1708	.	3;3;3	B4DNW9;Q29VG3;P09564	.;.;CD7_HUMAN	R	3	ENSP00000312027:G3R	ENSP00000312027:G3R	G	-	1	0	CD7	77868654	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-3.653000	0.00402	-0.993000	0.03467	-0.802000	0.03209	GGG	.	.		0.687	CD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442826.1	NM_006137		G	80275365	C	G	80275365	3	3	204	1	0	0	0	0	1	0	0	0	3034	652	23	4	731	4	CD7	17	80275365	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	17419056	80275365	919845	47	29854										
TTC39C	125488	hgsc.bcm.edu	37	chr18	21644129	21644129	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	atagcccactaatgagttttGgagccagctttgtcagtttt	9	8	1	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr18:21644129G>A	ENST00000317571.3	+	2	429	c.193G>A	c.(193-195)Gga>Aga	p.G65R	TTC39C_ENST00000578150.1_3'UTR|TTC39C_ENST00000304621.6_Missense_Mutation_p.G4R	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	65										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						AATGAGTTTTGGAGCCAGCTT	0.313																																					p.G65R		Atlas-SNP	.											.	TTC39C	83	.	0			c.G193A						.						155	157	156					18																	21644129		2203	4300	6503	SO:0001583	missense	125488	exon2			AGTTTTGGAGCCA	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"Tetratricopeptide (TTC) repeat domain containing"	26595	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 17"	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.193G>A	chr18.hg19:g.21644129G>A	ENSP00000323645:p.Gly65Arg	92.0	0.0		73.0	38.0	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Missense_Mutation	SNP	ENST00000317571.3	hg19	CCDS45839.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.044878	0.93685	.	.	ENSG00000168234	ENST00000304621;ENST00000317571	T;T	0.54866	0.55;0.55	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.75561	0.3866	M	0.80422	2.495	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77403	-0.2601	10	0.56958	D	0.05	-3.4008	19.3708	0.94484	0.0:0.0:1.0:0.0	.	65	Q8N584	TT39C_HUMAN	R	4;65	ENSP00000306598:G4R;ENSP00000323645:G65R	ENSP00000306598:G4R	G	+	1	0	TTC39C	19898127	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.368000	0.97152	2.580000	0.87095	0.650000	0.86243	GGA	.	.		0.313	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211		A	21644129	G	A	21644129	3	1	204	1	0	0	0	0	1	0	0	0	16724	1349	47	3	199	3	TTC39C	18	21644129	Missense_Mutation	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10		21644129	56433119	48	29855										
WDR7	23335	hgsc.bcm.edu	37	chr18	54426112	54426112	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	taaggccacctagaccaagcAccccagacctttctaaggca	7	15	1	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr18:54426112A>G	ENST00000254442.3	+	16	2987	c.2776A>G	c.(2776-2778)Acc>Gcc	p.T926A	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Missense_Mutation_p.T926A	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	926					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TAGACCAAGCACCCCAGACCT	0.318																																					p.T926A		Atlas-SNP	.											.	WDR7	166	.	0			c.A2776G						.						63	66	65					18																	54426112		2203	4300	6503	SO:0001583	missense	23335	exon16			CCAAGCACCCCAG	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"WD repeat domain containing"	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.2776A>G	chr18.hg19:g.54426112A>G	ENSP00000254442:p.Thr926Ala	81.0	0.0		70.0	10.0	NM_052834	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Missense_Mutation	SNP	ENST00000254442.3	hg19	CCDS11962.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.370610	0.42003	.	.	ENSG00000091157	ENST00000254442;ENST00000357574;ENST00000444065;ENST00000398311	T;T	0.66815	-0.22;-0.23	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.45438	0.1342	N	0.11427	0.14	0.47659	D	0.999489	B;B	0.26363	0.143;0.147	B;B	0.22152	0.028;0.038	T	0.44221	-0.9342	10	0.23891	T	0.37	.	11.3973	0.49849	0.865:0.0:0.0:0.135	.	926;926	Q9Y4E6-2;Q9Y4E6	.;WDR7_HUMAN	A	926;926;251;926	ENSP00000254442:T926A;ENSP00000350187:T926A	ENSP00000254442:T926A	T	+	1	0	WDR7	52577110	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.485000	0.66850	2.326000	0.78906	0.533000	0.62120	ACC	.	.		0.318	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			G	54426112	A	G	54426112	3	3	204	1	0	0	0	0	1	0	0	0	17335	159	6	2	2834	2	WDR7	18	54426112	Missense_Mutation	SNP	A	TCGA-DD-AADW-01A-11D-A38X-10	32781983	54426112	23651136	49	29856										
ZNF781	163115	hgsc.bcm.edu	37	chr19	38160324	38160324	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	tctctgatgtctattaaaatCagaaacacaagtgaaagcct	6	8	3	3			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr19:38160324C>A	ENST00000590008.1	-	5	1578	c.726G>T	c.(724-726)ctG>ctT	p.L242L	ZFP30_ENST00000586732.1_Intron|ZNF781_ENST00000593040.1_5'Flank|ZNF781_ENST00000358582.4_Silent_p.L242L			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	242					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						CTATTAAAATCAGAAACACAA	0.353																																					p.L242L		Atlas-SNP	.											.	ZNF781	66	.	0			c.G726T						.						59	63	61					19																	38160324		2203	4300	6503	SO:0001819	synonymous_variant	163115	exon4			TAAAATCAGAAAC	AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"Zinc fingers, C2H2-type"	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.726G>T	chr19.hg19:g.38160324C>A		55.0	0.0		72.0	41.0	NM_152605	Q2VPJ8	Silent	SNP	ENST00000590008.1	hg19	CCDS12507.1																																																																																			.	.		0.353	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605		A	38160324	C	A	38160324	2	1	204	1	0	0	0	0	0	0	0	1	18169	813	29	3		3	ZNF781	19	38160324	Silent	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10		38160324	20968659	50	29857										
YIF1B	90522	hgsc.bcm.edu	37	chr19	38798281	38798281	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gccaccaggtcgatggtggtGaggtcggtgttgacagtgac	17	8	0	3			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr19:38798281G>T	ENST00000339413.6	-	6	696	c.651C>A	c.(649-651)ctC>ctA	p.L217L	YIF1B_ENST00000591755.1_Silent_p.L214L|YIF1B_ENST00000329420.8_Silent_p.L202L|YIF1B_ENST00000592246.1_Silent_p.L151L|YIF1B_ENST00000592694.1_Silent_p.L186L|YIF1B_ENST00000392124.3_Silent_p.L186L|YIF1B_ENST00000587361.1_5'Flank|YIF1B_ENST00000591784.1_Silent_p.L186L|YIF1B_ENST00000337679.8_Silent_p.L214L	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	217						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CGATGGTGGTGAGGTCGGTGT	0.632																																					p.L217L		Atlas-SNP	.											.	YIF1B	47	.	0			c.C651A						.						96	86	89					19																	38798281		2203	4300	6503	SO:0001819	synonymous_variant	90522	exon6			GGTGGTGAGGTCG	AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05							30511	protein-coding gene	gene with protein product						12975309	Standard	NM_001039672		Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.651C>A	chr19.hg19:g.38798281G>T		144.0	0.0		142.0	7.0	NM_001039672	H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	Silent	SNP	ENST00000339413.6	hg19	CCDS33010.1																																																																																			.	.		0.632	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460511.1	NM_033557		T	38798281	G	T	38798281	2	4	204	1	0	0	0	0	0	0	0	1	17491	1277	45	3		3	YIF1B	19	38798281	Silent	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10	637957	38798281	20330702	51	29858										
SLC8A2	6543	hgsc.bcm.edu	37	chr19	47951333	47951333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	gccgccccttgggccgcccgCcgccgtccggctcgaacatg	13	20	0	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr19:47951333C>T	ENST00000236877.6	-	4	1891	c.1496G>A	c.(1495-1497)gGc>gAc	p.G499D	SLC8A2_ENST00000539381.1_Intron|SLC8A2_ENST00000542837.1_Missense_Mutation_p.G255D|SLC8A2_ENST00000601757.1_5'Flank	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	499					blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		GGGCCGCCCGCCGCCGTCCGG	0.682																																					p.G499D		Atlas-SNP	.											.	SLC8A2	77	.	0			c.G1496A						.						11	12	12					19																	47951333		2162	4213	6375	SO:0001583	missense	6543	exon4			CGCCCGCCGCCGT	AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"Solute carriers"	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.1496G>A	chr19.hg19:g.47951333C>T	ENSP00000236877:p.Gly499Asp	96.0	0.0		117.0	44.0	NM_015063	B4DYQ9	Missense_Mutation	SNP	ENST00000236877.6	hg19	CCDS33065.1	.	.	.	.	.	.	.	.	.	.	C	11.87	1.768777	0.31320	.	.	ENSG00000118160	ENST00000391903;ENST00000236877;ENST00000542837	T;T	0.37752	1.32;1.18	4.05	4.05	0.47172	.	0.384236	0.23427	N	0.048300	T	0.21881	0.0527	L	0.34521	1.04	0.80722	D	1	B;B	0.30763	0.294;0.038	B;B	0.22152	0.038;0.016	T	0.06698	-1.0812	10	0.34782	T	0.22	.	5.9322	0.19144	0.0:0.6986:0.1968:0.1045	.	327;499	E9PGS7;Q9UPR5	.;NAC2_HUMAN	D	327;499;255	ENSP00000236877:G499D;ENSP00000437536:G255D	ENSP00000236877:G499D	G	-	2	0	SLC8A2	52643145	0.000000	0.05858	1.000000	0.80357	0.317000	0.28152	0.416000	0.21198	2.259000	0.74868	0.561000	0.74099	GGC	.	.		0.682	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1			T	47951333	C	T	47951333	3	4	204	1	0	0	0	0	1	0	0	0	14722	739	26	3	1297	3	SLC8A2	19	47951333	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10	9153052	47951333	11177650	52	29859										
RRBP1	6238	hgsc.bcm.edu	37	chr20	17640636	17640636	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	catcggcacctccttgggagCagtttccaagatggcagcct	11	13	0	1	rs141391805		TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr20:17640636C>A	ENST00000377813.1	-	3	820	c.517G>T	c.(517-519)Gct>Tct	p.A173S	RRBP1_ENST00000246043.4_Missense_Mutation_p.A173S|RRBP1_ENST00000377807.2_Missense_Mutation_p.A173S|RRBP1_ENST00000455029.2_Intron|RRBP1_ENST00000360807.4_Missense_Mutation_p.A173S			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	173					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						TCCTTGGGAGCAGTTTCCAAG	0.547																																					p.A173S		Atlas-SNP	.											.	RRBP1	157	.	0			c.G517T						.						61	50	54					20																	17640636		2203	4300	6503	SO:0001583	missense	6238	exon2			TGGGAGCAGTTTC	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"ribosome binding protein 1 (dog 180kD homolog)", "ribosome binding protein 1 homolog 180kDa (dog)"			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.517G>T	chr20.hg19:g.17640636C>A	ENSP00000367044:p.Ala173Ser	70.0	0.0		77.0	29.0	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Missense_Mutation	SNP	ENST00000377813.1	hg19		.	.	.	.	.	.	.	.	.	.	C	4.214	0.038548	0.08148	.	.	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000398782	T;T;T;T	0.48836	0.8;1.87;0.8;1.87	4.73	-0.274	0.12910	.	0.524045	0.14343	N	0.325611	T	0.26955	0.0660	L	0.36672	1.1	0.25708	N	0.985518	B	0.15473	0.013	B	0.09377	0.004	T	0.17379	-1.0371	10	0.13853	T	0.58	-1.0574	1.5506	0.02574	0.3093:0.3157:0.2281:0.1469	.	173	Q9P2E9-3	.	S	173	ENSP00000354045:A173S;ENSP00000367044:A173S;ENSP00000367038:A173S;ENSP00000246043:A173S	ENSP00000246043:A173S	A	-	1	0	RRBP1	17588636	0.388000	0.25197	0.005000	0.12908	0.034000	0.12701	0.973000	0.29422	-0.217000	0.10033	-0.311000	0.09066	GCT	.	C|1.000;T|0.000		0.547	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576		A	17640636	C	A	17640636	3	1	204	1	0	0	0	0	1	0	0	0	13693	710	25	3	2512	3	RRBP1	20	17640636	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10		17640636	45384884	53	29860										
N6AMT1	29104	hgsc.bcm.edu	37	chr21	30257545	30257545	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	tcctcgcaccctgccagttcGgcagccgctgcctccagcgc	10	20	0	0			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chr21:30257545G>T	ENST00000303775.5	-	1	148	c.123C>A	c.(121-123)gcC>gcA	p.A41A	N6AMT1_ENST00000351429.3_Silent_p.A41A	NM_013240.4	NP_037372	Q9Y5N5	HEMK2_HUMAN	N-6 adenine-specific DNA methyltransferase 1 (putative)	41					positive regulation of cell growth (GO:0030307)|protein methylation (GO:0006479)	protein complex (GO:0043234)	nucleic acid binding (GO:0003676)|protein methyltransferase activity (GO:0008276)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)	12						CTGCCAGTTCGGCAGCCGCTG	0.672																																					p.A41A		Atlas-SNP	.											.	N6AMT1	31	.	0			c.C123A						.						45	59	54					21																	30257545		2195	4276	6471	SO:0001819	synonymous_variant	29104	exon1			CAGTTCGGCAGCC	AF139682	CCDS33525.1, CCDS33526.1	21q21.3	2006-12-14	2006-12-14	2006-12-14	ENSG00000156239	ENSG00000156239	2.1.1.72		16021	protein-coding gene	gene with protein product		614553	"chromosome 21 open reading frame 127", "HemK methyltransferase family member 2"	C21orf127, HEMK2			Standard	NM_013240		Approved	PRED28, N6AMT, MTQ2	uc002ymo.2	Q9Y5N5	OTTHUMG00000078750	ENST00000303775.5:c.123C>A	chr21.hg19:g.30257545G>T		191.0	0.0		226.0	15.0	NM_182749	Q96F73	Silent	SNP	ENST00000303775.5	hg19	CCDS33526.1																																																																																			.	.		0.672	N6AMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171738.1	NM_013240		T	30257545	G	T	30257545	2	4	204	1	0	0	0	0	0	0	0	1	10123	1103	39	1		1	N6AMT1	21	30257545	Silent	SNP	G	TCGA-DD-AADW-01A-11D-A38X-10		30257545	17872350	54	29861										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53603872	53603872	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	ccacataccttcctctggagCatggtatgcagccagagcat	9	13	1	1			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chrX:53603872C>T	ENST00000342160.3	-	43	6329	c.5872G>A	c.(5872-5874)Gct>Act	p.A1958T	HUWE1_ENST00000262854.6_Missense_Mutation_p.A1958T			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	1958					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TCCTCTGGAGCATGGTATGCA	0.507																																					p.A1958T		Atlas-SNP	.											.	HUWE1	724	.	0			c.G5872A						.						85	65	72					X																	53603872		2203	4300	6503	SO:0001583	missense	10075	exon44			CTGGAGCATGGTA	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.5872G>A	chrX.hg19:g.53603872C>T	ENSP00000340648:p.Ala1958Thr	85.0	0.0		85.0	70.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.8|22.8	4.330857|4.330857	0.81690|0.81690	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000342160;ENST00000262854|ENST00000427052	T;T|.	0.37584|.	1.19;1.19|.	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.55257|0.55257	0.1909|0.1909	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	D;D|.	0.67145|.	0.993;0.996|.	D;D|.	0.79784|.	0.971;0.993|.	T|T	0.50215|0.50215	-0.8854|-0.8854	10|5	0.02654|.	T|.	1|.	.|.	17.9896|17.9896	0.89164|0.89164	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1958;1958|.	Q7Z6Z7;Q7Z6Z7-2|.	HUWE1_HUMAN;.|.	T|Y	1958|991	ENSP00000340648:A1958T;ENSP00000262854:A1958T|.	ENSP00000262854:A1958T|.	A|C	-|-	1|2	0|0	HUWE1|HUWE1	53620597|53620597	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.435000|7.435000	0.80391|0.80391	2.524000|2.524000	0.85096|0.85096	0.600000|0.600000	0.82982|0.82982	GCT|TGC	.	.		0.507	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53603872	C	T	53603872	3	4	204	1	0	0	0	0	1	0	0	0	7470	710	25	3	7416	3	HUWE1	23	53603872	Missense_Mutation	SNP	C	TCGA-DD-AADW-01A-11D-A38X-10		53603872	101666688	55	29862										
RGAG1	57529	hgsc.bcm.edu	37	chrX	109697300	109697300	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0535714285714286	3	1	1.20323559150657	3.4593023255814	0	0.181818181818182	0.751940625889747	0	cccagcactctgctacctctTagaagagcaggaagcagccc	9	15	2	2			TCGA-DD-AADW-01A-11D-A38X-10	TCGA-DD-AADW-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40648214-724a-4710-b3d8-5ec9cd6d5fe9	d1383588-3279-4d21-b931-75e2df11adc8	g.chrX:109697300T>C	ENST00000465301.2	+	3	3701	c.3455T>C	c.(3454-3456)tTa>tCa	p.L1152S	RGAG1_ENST00000540313.1_Missense_Mutation_p.L1152S	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	1152										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						TGCTACCTCTTAGAAGAGCAG	0.522																																					p.L1152S		Atlas-SNP	.											.	RGAG1	168	.	0			c.T3455C						.						110	102	105					X																	109697300		2203	4300	6503	SO:0001583	missense	57529	exon3			ACCTCTTAGAAGA	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.3455T>C	chrX.hg19:g.109697300T>C	ENSP00000419786:p.Leu1152Ser	178.0	0.0		258.0	21.0	NM_020769	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	hg19	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.824757	0.50739	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.60548	0.18;0.18	4.26	4.26	0.50523	.	0.000000	0.31554	N	0.007452	T	0.60766	0.2294	L	0.29908	0.895	0.32317	N	0.562871	D	0.89917	1.0	D	0.87578	0.998	T	0.64993	-0.6276	9	.	.	.	-11.8684	8.7451	0.34580	0.0:0.0:0.0:1.0	.	1152	Q8NET4	RGAG1_HUMAN	S	1152;1152;713	ENSP00000419786:L1152S;ENSP00000441452:L1152S	.	L	+	2	0	RGAG1	109583956	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.552000	0.53705	1.885000	0.54596	0.486000	0.48141	TTA	.	.		0.522	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		C	109697300	T	C	109697300	3	2	204	1	0	0	0	0	1	0	0	0	13289	1764	61	2	3457	2	RGAG1	23	109697300	Missense_Mutation	SNP	T	TCGA-DD-AADW-01A-11D-A38X-10	56093428	109697300	45573260	56	29863										
FLG	2312	hgsc.bcm.edu	37	chr1	152285002	152285002	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ggaaagaccctgaacgtcgaGacctttcccctgaccggtca	10	14	1	4	rs77032592	byFrequency	TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr1:152285002G>T	ENST00000368799.1	-	3	2395	c.2360C>A	c.(2359-2361)tCt>tAt	p.S787Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	787	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGAACGTCGAGACCTTTCCCC	0.562									Ichthyosis																												p.S787Y		Atlas-SNP	.											.	FLG	900	.	0			c.C2360A						.						319	304	309					1																	152285002		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGTCGAGACCTTT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2360C>A	chr1.hg19:g.152285002G>T	ENSP00000357789:p.Ser787Tyr	123.0	0.0		191.0	143.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	4.850	0.157990	0.09236	.	.	ENSG00000143631	ENST00000368799	T	0.02280	4.36	2.95	0.716	0.18191	.	.	.	.	.	T	0.03915	0.0110	M	0.82323	2.585	0.09310	N	1	D	0.63046	0.992	P	0.62813	0.907	T	0.28618	-1.0038	9	0.66056	D	0.02	.	5.2187	0.15356	0.0:0.2274:0.54:0.2326	.	787	P20930	FILA_HUMAN	Y	787	ENSP00000357789:S787Y	ENSP00000357789:S787Y	S	-	2	0	FLG	150551626	0.097000	0.21791	0.001000	0.08648	0.029000	0.11900	1.696000	0.37773	0.416000	0.25844	0.479000	0.44913	TCT	.	G|0.988;A|0.012		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152285002	G	T	152285002	3	4	205	1	0	0	0	0	1	0	0	0	5930	942	33	3	9829	3	FLG	1	152285002	Missense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10		152285002	96965619	1	29864										
CEP350	9857	hgsc.bcm.edu	37	chr1	180023062	180023063	+	Frame_Shift_Ins	INS	-	-	A													0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	attggcctggttagagcatcINSaaaaaaagtaagttcttttg							TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr1:180023062_180023063insA	ENST00000367607.3	+	24	5585_5586	c.5167_5168insA	c.(5167-5169)caafs	p.Q1723fs		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1723					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						GTTAGAGCATCAAAAAAAGTAA	0.371																																					p.Q1723fs		Atlas-INDEL	.											.	CEP350	418	.	0			c.5167_5168insA						.																																			SO:0001589	frameshift_variant	9857	exon24			.	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.5175dupA	chr1.hg19:g.180023069_180023069dupA	ENSP00000356579:p.Gln1723fs	183.0	0.0		310.0	64.0	NM_014810	O75068|Q8TDK3|Q8WY20	Frame_Shift_Ins	INS	ENST00000367607.3	hg19	CCDS1336.1																																																																																			.	.		0.371	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		A	180023063	-	A	180023062	7	5	205	1	0	1	1	0	0	0	0	0	3256	827	29	0	5257	0	CEP350	1	180023062	Frame_Shift_Ins	INS	-	TCGA-DD-AADY-01A-11D-A40R-10	27738060	180023062	69227559	2	29865										
LGTN	1939	hgsc.bcm.edu	37	chr1	206775799	206775799	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gcattgctgtaacagctcatCcatttgttctgcagggaaaa	9	9	2	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr1:206775799C>A	ENST00000271764.2	-	7	1001	c.793G>T	c.(793-795)Gat>Tat	p.D265Y	EIF2D_ENST00000367114.3_Intron	NM_006893.2	NP_008824.2	P41214	EIF2D_HUMAN	eukaryotic translation initiation factor 2D	265					formation of translation preinitiation complex (GO:0001731)|intracellular protein transport (GO:0006886)|IRES-dependent translational initiation (GO:0002192)|ribosome disassembly (GO:0032790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor activity (GO:0004872)|translation initiation factor activity (GO:0003743)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						AACAGCTCATCCATTTGTTCT	0.498																																					p.D265Y		Atlas-SNP	.											.	EIF2D	42	.	0			c.G793T						.						154	131	139					1																	206775799		2203	4300	6503	SO:0001583	missense	1939	exon7			GCTCATCCATTTG	BC001585	CCDS1465.1, CCDS55680.1	1q32.1	2014-05-06	2011-01-19	2011-01-19	ENSG00000143486	ENSG00000143486			6583	protein-coding gene	gene with protein product		613709				20566627	Standard	NM_001201478		Approved	LGTN	uc001heh.2	P41214	OTTHUMG00000184619	ENST00000271764.2:c.793G>T	chr1.hg19:g.206775799C>A	ENSP00000271764:p.Asp265Tyr	52.0	0.0		96.0	20.0	NM_006893	Q5SY40|Q8IXV3|Q96DG3|Q96TG7|Q9NR27|Q9NSN0|Q9NV18|Q9NZ21	Missense_Mutation	SNP	ENST00000271764.2	hg19	CCDS1465.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.992117	0.93167	.	.	ENSG00000143486	ENST00000271764;ENST00000367111;ENST00000437518	T;T	0.61980	0.06;0.06	6.11	6.11	0.99139	.	0.000000	0.85682	D	0.000000	T	0.81574	0.4851	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82364	-0.0494	10	0.87932	D	0	-19.9229	19.3123	0.94195	0.0:1.0:0.0:0.0	.	265	P41214	EIF2D_HUMAN	Y	265;237;237	ENSP00000271764:D265Y;ENSP00000394685:D237Y	ENSP00000271764:D265Y	D	-	1	0	EIF2D	204842422	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.786000	0.85741	2.906000	0.99361	0.655000	0.94253	GAT	.	.		0.498	EIF2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088475.1	NM_006893		A	206775799	C	A	206775799	3	1	205	1	0	0	0	0	1	0	0	0	8769	855	30	3	997	3	LGTN	1	206775799	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	26752737	206775799	42474822	3	29866										
LAMB3	3914	hgsc.bcm.edu	37	chr1	209799342	209799342	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	tgccttgtcgcagcccgggcCctctgttccccggaaatcac	10	17	2	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr1:209799342C>A	ENST00000356082.4	-	14	1761	c.1627G>T	c.(1627-1629)Ggc>Tgc	p.G543C	LAMB3_ENST00000367030.3_Missense_Mutation_p.G543C|MIR4260_ENST00000583107.1_RNA|LAMB3_ENST00000391911.1_Missense_Mutation_p.G543C	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	543	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		CAGCCCGGGCCCTCTGTTCCC	0.632																																					p.G543C		Atlas-SNP	.											.	LAMB3	136	.	0			c.G1627T						.						24	28	27					1																	209799342		2203	4300	6503	SO:0001583	missense	3914	exon14			CCGGGCCCTCTGT	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.1627G>T	chr1.hg19:g.209799342C>A	ENSP00000348384:p.Gly543Cys	102.0	0.0		183.0	44.0	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	hg19	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.168245	0.57476	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.62498	0.02;0.02;0.02	5.0	4.09	0.47781	EGF-like, laminin (3);	0.510205	0.22798	N	0.055511	T	0.77592	0.4153	M	0.82923	2.615	0.29345	N	0.865768	D	0.67145	0.996	P	0.62649	0.905	T	0.75286	-0.3371	10	0.59425	D	0.04	.	12.8623	0.57920	0.0:0.9201:0.0:0.0799	.	543	Q13751	LAMB3_HUMAN	C	543	ENSP00000375778:G543C;ENSP00000348384:G543C;ENSP00000355997:G543C	ENSP00000348384:G543C	G	-	1	0	LAMB3	207865965	0.000000	0.05858	0.901000	0.35422	0.685000	0.39939	0.314000	0.19432	1.134000	0.42165	0.456000	0.33151	GGC	.	.		0.632	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		A	209799342	C	A	209799342	3	1	205	1	0	0	0	0	1	0	0	0	8621	623	22	3	1931	3	LAMB3	1	209799342	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	3023543	209799342	39451279	4	29867										
TTC13	79573	hgsc.bcm.edu	37	chr1	231044767	231044767	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	tgaccgagtaagcaattacaCtatttaaataaagaacaaag	6	6	0	2			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr1:231044767C>T	ENST00000366661.4	-	21	2317		c.e21-1		TTC13_ENST00000366662.4_Splice_Site|TTC13_ENST00000414259.1_Splice_Site	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13											central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		AGCAATTACACTATTTAAATA	0.408																																					.		Atlas-SNP	.											.	TTC13	74	.	0			c.2148-1G>A						.						95	99	98					1																	231044767		2203	4300	6503	SO:0001630	splice_region_variant	79573	exon20			ATTACACTATTTA		CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"Tetratricopeptide (TTC) repeat domain containing"	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.2310-1G>A	chr1.hg19:g.231044767C>T		78.0	0.0		155.0	11.0	NM_001122835	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Splice_Site	SNP	ENST00000366661.4	hg19	CCDS1588.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.725231	0.89298	.	.	ENSG00000143643	ENST00000366661;ENST00000366662;ENST00000414259	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3045	0.94155	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TTC13	229111390	1.000000	0.71417	0.906000	0.35671	0.964000	0.63967	7.055000	0.76656	2.561000	0.86390	0.609000	0.83330	.	.	.		0.408	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525	Intron	T	231044767	C	T	231044767	5	4	205	1	0	0	0	0	0	0	1	0	16695	579	20	3	285	3	TTC13	1	231044767	Splice_Site	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	21245425	231044767	18205854	5	29868										
PXDN	7837	hgsc.bcm.edu	37	chr2	1647159	1647159	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ccttcacagcagtcctgccaCacccggaggtctaccctggg	10	17	2	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr2:1647159C>T	ENST00000252804.4	-	19	3983	c.3933G>A	c.(3931-3933)gtG>gtA	p.V1311V		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1311					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		AGTCCTGCCACACCCGGAGGT	0.607																																					p.V1311V		Atlas-SNP	.											.	PXDN	255	.	0			c.G3933A						.						62	71	68					2																	1647159		2114	4216	6330	SO:0001819	synonymous_variant	7837	exon19			CTGCCACACCCGG	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.3933G>A	chr2.hg19:g.1647159C>T		56.0	0.0		58.0	20.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	hg19	CCDS46221.1																																																																																			.	.		0.607	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1647159	C	T	1647159	2	4	205	1	0	0	0	0	0	0	0	1	12862	465	17	3		3	PXDN	2	1647159	Silent	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10		1647159	241552214	6	29869										
AFTPH	54812	hgsc.bcm.edu	37	chr2	64779985	64779985	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	caagattcaatgagtgatgcCacttttgaagagtcttcaga	9	7	3	6			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr2:64779985C>G	ENST00000422803.1	+	2	1691	c.1377C>G	c.(1375-1377)gcC>gcG	p.A459A	AFTPH_ENST00000409933.1_Silent_p.A459A|AFTPH_ENST00000238856.4_Silent_p.A459A|AFTPH_ENST00000238855.7_Silent_p.A459A|AFTPH_ENST00000409183.1_Silent_p.A90A			Q6ULP2	AFTIN_HUMAN	aftiphilin	459					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						TGAGTGATGCCACTTTTGAAG	0.408																																					p.A459A		Atlas-SNP	.											.	AFTPH	117	.	0			c.C1377G						.						161	155	157					2																	64779985		2203	4300	6503	SO:0001819	synonymous_variant	54812	exon2			TGATGCCACTTTT	AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.1377C>G	chr2.hg19:g.64779985C>G		108.0	0.0		98.0	38.0	NM_017657	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Silent	SNP	ENST00000422803.1	hg19																																																																																				.	.		0.408	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657		G	64779985	C	G	64779985	2	3	205	1	0	0	0	0	0	0	0	1	364	581	21	4		4	AFTPH	2	64779985	Silent	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	63132826	64779985	178419388	7	29870										
C2orf51	200523	hgsc.bcm.edu	37	chr2	88828588	88828588	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	agcaggcaaagctcgatgctCaactccgggacaaagagttt	11	10	1	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr2:88828588C>T	ENST00000303254.3	+	4	281	c.139C>T	c.(139-141)Caa>Taa	p.Q47*		NM_152670.2	NP_689883.1	Q96LM6	TEX37_HUMAN	testis expressed 37	47						nucleus (GO:0005634)											GCTCGATGCTCAACTCCGGGA	0.488																																					p.Q47X		Atlas-SNP	.											.	.	.	.	0			c.C139T						.						75	73	74					2																	88828588		2203	4300	6503	SO:0001587	stop_gained	200523	exon4			GATGCTCAACTCC	AK058098	CCDS2003.1	2p11.2	2014-01-28	2012-09-14	2012-09-14	ENSG00000172073	ENSG00000172073			26341	protein-coding gene	gene with protein product	"Testis-Specific Conserved gene 21kDa"		"chromosome 2 open reading frame 51"	C2orf51		17091336	Standard	NM_152670		Approved	FLJ25369, TSC21	uc002stb.2	Q96LM6	OTTHUMG00000130332	ENST00000303254.3:c.139C>T	chr2.hg19:g.88828588C>T	ENSP00000307142:p.Gln47*	295.0	0.0		273.0	134.0	NM_152670		Nonsense_Mutation	SNP	ENST00000303254.3	hg19	CCDS2003.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599711	0.46318	.	.	ENSG00000172073	ENST00000303254	.	.	.	4.61	4.61	0.57282	.	0.000000	0.46145	D	0.000315	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.9811	13.1466	0.59465	0.0:1.0:0.0:0.0	.	.	.	.	X	47	.	ENSP00000307142:Q47X	Q	+	1	0	C2orf51	88609703	0.335000	0.24748	0.073000	0.20177	0.184000	0.23303	1.738000	0.38207	2.561000	0.86390	0.462000	0.41574	CAA	.	.		0.488	TEX37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252682.1	NM_152670		T	88828588	C	T	88828588	4	4	205	1	0	0	0	0	0	1	0	0	2175	827	29	3	149	3	C2orf51	2	88828588	Nonsense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	24048603	88828588	154370785	8	29871										
GCC2	9648	hgsc.bcm.edu	37	chr2	109088333	109088333	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	taaggaaagagttagaagaaAtacagtcagaaaaagaggcc	11	4	1	5			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr2:109088333A>T	ENST00000309863.6	+	6	3262	c.2548A>T	c.(2548-2550)Ata>Tta	p.I850L		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	850					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						GTTAGAAGAAATACAGTCAGA	0.353																																					p.I850L		Atlas-SNP	.											.	GCC2	129	.	0			c.A2548T						.						41	45	44					2																	109088333		2198	4298	6496	SO:0001583	missense	9648	exon6			GAAGAAATACAGT	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.2548A>T	chr2.hg19:g.109088333A>T	ENSP00000307939:p.Ile850Leu	409.0	0.0		387.0	173.0	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	hg19	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.847416	0.32606	.	.	ENSG00000135968	ENST00000309863;ENST00000409896;ENST00000393318	T	0.27256	1.68	5.45	-1.38	0.09027	.	1.158890	0.06206	N	0.684125	T	0.13030	0.0316	N	0.22421	0.69	0.09310	N	0.999998	B	0.17465	0.022	B	0.09377	0.004	T	0.29458	-1.0011	10	0.02654	T	1	.	6.6789	0.23110	0.4597:0.0:0.4201:0.1203	.	850	Q8IWJ2	GCC2_HUMAN	L	850;813;594	ENSP00000307939:I850L	ENSP00000307939:I850L	I	+	1	0	GCC2	108454765	0.108000	0.22018	0.673000	0.29887	0.981000	0.71138	0.044000	0.13992	-0.070000	0.12908	0.528000	0.53228	ATA	.	.		0.353	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		T	109088333	A	T	109088333	3	4	205	1	0	0	0	0	1	0	0	0	6294	101	4	4	2570	4	GCC2	2	109088333	Missense_Mutation	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10	20259745	109088333	134111040	9	29872										
TTN	7273	hgsc.bcm.edu	37	chr2	179426149	179426149	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	aagatttactgcatttaccaAttccagcaatattttcagca	4	9	1	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr2:179426149A>G	ENST00000591111.1	-	276	80011	c.79787T>C	c.(79786-79788)aTt>aCt	p.I26596T	TTN_ENST00000342992.6_Missense_Mutation_p.I25669T|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I28237T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I19364T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I19172T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I19297T|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26596	Fibronectin type-III 93. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCATTTACCAATTCCAGCAAT	0.403																																					p.I28237T		Atlas-SNP	.											.	TTN	18412	.	0			c.T84710C						.						186	170	175					2																	179426149		1900	4141	6041	SO:0001583	missense	7273	exon326			TTACCAATTCCAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.79787T>C	chr2.hg19:g.179426149A>G	ENSP00000465570:p.Ile26596Thr	62.0	0.0		78.0	22.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	11.08	1.533555	0.27387	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.78	4.62	0.57501	Fibronectin, type III (5);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.43322	0.1242	L	0.50993	1.605	0.58432	D	0.999996	B;B;B;B	0.15719	0.014;0.014;0.014;0.014	B;B;B;B	0.17722	0.019;0.019;0.019;0.019	T	0.35822	-0.9773	9	0.87932	D	0	.	11.4785	0.50312	0.9298:0.0:0.0702:0.0	.	19172;19297;19364;26596	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	25669;19172;19364;19297;19170	ENSP00000343764:I25669T;ENSP00000434586:I19172T;ENSP00000340554:I19364T;ENSP00000352154:I19297T	ENSP00000340554:I19364T	I	-	2	0	TTN	179134395	1.000000	0.71417	0.908000	0.35775	0.932000	0.56968	7.530000	0.81962	1.027000	0.39758	0.397000	0.26171	ATT	.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179426149	A	G	179426149	3	3	205	1	0	0	0	0	1	0	0	0	16750	101	4	2	23417	2	TTN	2	179426149	Missense_Mutation	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10	70337816	179426149	63773224	10	29873										
SPATS2L	26010	hgsc.bcm.edu	37	chr2	201337678	201337678	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ccgaaaatcatccactcacaAtaagccctctgaaggcaaag	6	13	3	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr2:201337678A>G	ENST00000358677.5	+	12	1431	c.1184A>G	c.(1183-1185)aAt>aGt	p.N395S	SPATS2L_ENST00000409718.1_Missense_Mutation_p.N395S|SPATS2L_ENST00000460095.1_3'UTR|SPATS2L_ENST00000409755.3_Missense_Mutation_p.N425S|SPATS2L_ENST00000409385.1_Missense_Mutation_p.N335S|SPATS2L_ENST00000409140.3_Missense_Mutation_p.N395S|SPATS2L_ENST00000409151.1_Missense_Mutation_p.N403S|SPATS2L_ENST00000451764.2_Missense_Mutation_p.N395S|SPATS2L_ENST00000409988.3_Missense_Mutation_p.N395S|SPATS2L_ENST00000360760.5_Missense_Mutation_p.N326S	NM_001282735.1|NM_001282743.1|NM_001282744.1|NM_015535.2	NP_001269664.1|NP_001269672.1|NP_001269673.1|NP_056350.2	Q9NUQ6	SPS2L_HUMAN	spermatogenesis associated, serine-rich 2-like	395						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	10						TCCACTCACAATAAGCCCTCT	0.562																																					p.N395S		Atlas-SNP	.											SPATS2L_ENST00000409755,NS,carcinoma,0,3	SPATS2L	88	.	0			c.A1184G						.						55	61	59					2																	201337678		1975	4150	6125	SO:0001583	missense	26010	exon12			CTCACAATAAGCC	AF193059	CCDS46483.1, CCDS46484.1, CCDS74621.1, CCDS74622.1	2q33.1	2009-06-12			ENSG00000196141	ENSG00000196141			24574	protein-coding gene	gene with protein product	"DNA polymerase transactivated protein 6"	613817				11230166	Standard	NM_001100422		Approved	DNAPTP6	uc002uvr.4	Q9NUQ6	OTTHUMG00000154589	ENST00000358677.5:c.1184A>G	chr2.hg19:g.201337678A>G	ENSP00000351503:p.Asn395Ser	118.0	0.0		116.0	46.0	NM_001100423	A8K381|B4DRE6|B4DT67|B7WNZ7|Q53T22|Q8WV53|Q8WYG1|Q9NTW4	Missense_Mutation	SNP	ENST00000358677.5	hg19	CCDS46483.1	.	.	.	.	.	.	.	.	.	.	A	10.69	1.420023	0.25552	.	.	ENSG00000196141	ENST00000409718;ENST00000358677;ENST00000409988;ENST00000409385;ENST00000451764;ENST00000360760;ENST00000409140;ENST00000409755;ENST00000409151	.	.	.	5.39	-0.175	0.13315	.	0.766887	0.12514	N	0.462277	T	0.22399	0.0540	N	0.14661	0.345	0.26159	N	0.980031	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.15896	-1.0421	9	0.56958	D	0.05	-3.7213	5.6071	0.17385	0.4042:0.3382:0.2576:0.0	.	425;326;395	B4DT67;Q9NUQ6-2;Q9NUQ6	.;.;SPS2L_HUMAN	S	395;395;395;335;395;326;395;425;403	.	ENSP00000351503:N395S	N	+	2	0	SPATS2L	201045923	0.307000	0.24500	0.963000	0.40424	0.723000	0.41478	-0.285000	0.08410	-0.145000	0.11294	0.533000	0.62120	AAT	.	.		0.562	SPATS2L-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336208.3	NM_015535		G	201337678	A	G	201337678	3	3	205	1	0	0	0	0	1	0	0	0	15035	101	4	2	1222	2	SPATS2L	2	201337678	Missense_Mutation	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10	21911529	201337678	41861695	11	29874										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207172127	207172127	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gtgtttttgaaacaagtttgGattctgatgtccctcttcag	9	7	3	2			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr2:207172127G>A	ENST00000374423.3	+	5	3261	c.2875G>A	c.(2875-2877)Gat>Aat	p.D959N		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	959							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AACAAGTTTGGATTCTGATGT	0.393																																					p.D959N		Atlas-SNP	.											.	ZDBF2	531	.	0			c.G2875A						.						60	60	60					2																	207172127		1874	4104	5978	SO:0001583	missense	57683	exon5			AGTTTGGATTCTG	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.2875G>A	chr2.hg19:g.207172127G>A	ENSP00000363545:p.Asp959Asn	100.0	0.0		133.0	53.0	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.666904	0.47677	.	.	ENSG00000204186	ENST00000374423	T	0.53423	0.62	4.28	-6.18	0.02085	.	1.042200	0.07649	N	0.931524	T	0.33644	0.0870	L	0.54323	1.7	0.09310	N	1	B	0.15719	0.014	B	0.12156	0.007	T	0.27297	-1.0078	10	0.38643	T	0.18	.	2.4688	0.04559	0.4796:0.2305:0.1729:0.117	.	959	Q9HCK1	ZDBF2_HUMAN	N	959	ENSP00000363545:D959N	ENSP00000363545:D959N	D	+	1	0	ZDBF2	206880372	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.794000	0.04584	-1.577000	0.01650	-0.768000	0.03414	GAT	.	.		0.393	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207172127	G	A	207172127	3	1	205	1	0	0	0	0	1	0	0	0	17614	1174	41	3	2885	3	ZDBF2	2	207172127	Missense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10	5834449	207172127	36027246	12	29875										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52668670	52668671	+	Frame_Shift_Ins	INS	-	-	T													0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	tgctggtaataatcagggtaINSttttttctttgaaggcaaat							TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr3:52668670_52668671insT	ENST00000296302.7	-	11	1249_1250	c.1248_1249insA	c.(1246-1251)aaatacfs	p.Y417fs	PBRM1_ENST00000337303.4_Frame_Shift_Ins_p.Y417fs|PBRM1_ENST00000409767.1_Frame_Shift_Ins_p.Y417fs|PBRM1_ENST00000410007.1_Frame_Shift_Ins_p.Y417fs|PBRM1_ENST00000356770.4_Frame_Shift_Ins_p.Y385fs|PBRM1_ENST00000409114.3_Frame_Shift_Ins_p.Y417fs|PBRM1_ENST00000394830.3_Frame_Shift_Ins_p.Y417fs|PBRM1_ENST00000409057.1_Frame_Shift_Ins_p.Y417fs			Q86U86	PB1_HUMAN	polybromo 1	417	Bromo 3. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TAATCAGGGTATTTTTTCTTTG	0.347			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.Y417fs		Atlas-INDEL	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.1249_1250insA						.																																			SO:0001589	frameshift_variant	55193	exon12			.	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1249dupA	chr3.hg19:g.52668676_52668676dupT	ENSP00000296302:p.Tyr417fs	135.0	0.0		73.0	55.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Ins	INS	ENST00000296302.7	hg19																																																																																				.	.		0.347	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52668671	-	T	52668670	7	5	205	1	0	1	1	0	0	0	0	0	11500	449	16	0	3731	0	PBRM1	3	52668670	Frame_Shift_Ins	INS	-	TCGA-DD-AADY-01A-11D-A40R-10		52668670	145353760	13	29876										
ABTB1	80325	hgsc.bcm.edu	37	chr3	127398864	127398864	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	cctatgatgtgctgagcgtcGccgacatgtacctgctgcca	11	13	0	2	rs376513209		TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr3:127398864G>A	ENST00000232744.8	+	11	1152	c.1066G>A	c.(1066-1068)Gcc>Acc	p.A356T	ABTB1_ENST00000453791.2_Missense_Mutation_p.A214T|ABTB1_ENST00000393363.3_Missense_Mutation_p.A214T|ABTB1_ENST00000468137.1_Missense_Mutation_p.A214T					ankyrin repeat and BTB (POZ) domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	10						GCTGAGCGTCGCCGACATGTA	0.647																																					p.A356T		Atlas-SNP	.											.	ABTB1	36	.	0			c.G1066A						.	G	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	109	109	109		640,1066	4.9	1	3		109	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ABTB1	NM_032548.3,NM_172027.2	58,58	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	214/337,356/479	127398864	2,13004	2203	4300	6503	SO:0001583	missense	80325	exon11			AGCGTCGCCGACA	AB053324	CCDS3045.1, CCDS46901.1	3q21	2013-01-10			ENSG00000114626	ENSG00000114626		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	18275	protein-coding gene	gene with protein product		608308				10891360, 11494141	Standard	NM_172027		Approved	BPOZ, EF1ABP, Btb3, BTBD21	uc003ejt.3	Q969K4	OTTHUMG00000159636	ENST00000232744.8:c.1066G>A	chr3.hg19:g.127398864G>A	ENSP00000232744:p.Ala356Thr	43.0	0.0		50.0	6.0	NM_172027		Missense_Mutation	SNP	ENST00000232744.8	hg19	CCDS3045.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964409	0.74131	2.27E-4	1.16E-4	ENSG00000114626	ENST00000361019;ENST00000393363;ENST00000232744;ENST00000453791;ENST00000468137	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	4.95	4.95	0.65309	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.83464	0.5260	H	0.95816	3.725	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.991;0.973;0.966	D	0.89096	0.3486	10	0.87932	D	0	-32.2173	18.1914	0.89808	0.0:0.0:1.0:0.0	.	192;356;331	C9JBQ0;Q969K4;Q969K4-3	.;ABTB1_HUMAN;.	T	192;214;356;214;214	ENSP00000377030:A214T;ENSP00000232744:A356T;ENSP00000412684:A214T;ENSP00000417366:A214T	ENSP00000232744:A356T	A	+	1	0	ABTB1	128881554	1.000000	0.71417	0.982000	0.44146	0.066000	0.16364	9.844000	0.99494	2.289000	0.77006	0.467000	0.42956	GCC	.	.		0.647	ABTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356595.1	NM_172027		A	127398864	G	A	127398864	3	1	205	1	0	0	0	0	1	0	0	0	102	1087	38	1	1108	1	ABTB1	3	127398864	Missense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10	74730194	127398864	70623566	14	29877										
PCDHA1	9752	hgsc.bcm.edu	37	chr5	140389296	140389296	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	taaatacggaccaggcaaccCcaaacaatccggtcccggtg	9	14	0	0	rs575518914		TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr5:140389296C>T	ENST00000532602.1	+	4	3660	c.2627C>T	c.(2626-2628)cCc>cTc	p.P876L	PCDHAC1_ENST00000253807.2_Missense_Mutation_p.P889L|PCDHA10_ENST00000307360.5_Missense_Mutation_p.P874L|PCDHA5_ENST00000529859.1_Missense_Mutation_p.P862L|PCDHA6_ENST00000527624.1_Missense_Mutation_p.P612L|PCDHA12_ENST00000398631.2_Missense_Mutation_p.P867L|PCDHA13_ENST00000409494.1_Missense_Mutation_p.P876L|PCDHA8_ENST00000531613.1_Missense_Mutation_p.P876L|PCDHAC2_ENST00000289269.5_Missense_Mutation_p.P933L|PCDHA6_ENST00000529310.1_Missense_Mutation_p.P876L|PCDHA13_ENST00000289272.2_Missense_Mutation_p.P876L|PCDHA2_ENST00000526136.1_Missense_Mutation_p.P874L|PCDHA1_ENST00000504120.2_Missense_Mutation_p.P876L|PCDHA11_ENST00000398640.2_Missense_Mutation_p.P875L|PCDHA4_ENST00000512229.2_Missense_Mutation_p.P873L|PCDHA7_ENST00000525929.1_Missense_Mutation_p.P863L|PCDHA3_ENST00000522353.2_Missense_Mutation_p.P876L|PCDHA4_ENST00000530339.1_Missense_Mutation_p.P873L|PCDHA5_ENST00000529619.1_Missense_Mutation_p.P862L|PCDHA1_ENST00000394633.3_Missense_Mutation_p.P612L|PCDHA10_ENST00000506939.2_Missense_Mutation_p.P611L	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	876	5 X 4 AA repeats of P-X-X-P.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAGGCAACCCCAAACAATCC	0.522																																					p.P933L	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.C2798T						.						70	74	73					5																	140389296		2203	4300	6503	SO:0001583	missense	56134	exon4			GCAACCCCAAACA	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.2627C>T	chr5.hg19:g.140389296C>T	ENSP00000436042:p.Pro876Leu	209.0	0.0		194.0	90.0	NM_018899	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	hg19	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.218894	0.79464	.	.	ENSG00000204970;ENSG00000204970;ENSG00000204969;ENSG00000255408;ENSG00000204967;ENSG00000204967;ENSG00000204965;ENSG00000204965;ENSG00000081842;ENSG00000081842;ENSG00000204963;ENSG00000204962;ENSG00000204961;ENSG00000250120;ENSG00000250120;ENSG00000249158;ENSG00000251664;ENSG00000239389;ENSG00000239389;ENSG00000248383;ENSG00000243232	ENST00000504120;ENST00000394633;ENST00000526136;ENST00000522353;ENST00000512229;ENST00000530339;ENST00000529619;ENST00000529859;ENST00000529310;ENST00000527624;ENST00000525929;ENST00000531613;ENST00000532602;ENST00000506939;ENST00000307360;ENST00000398640;ENST00000398631;ENST00000409494;ENST00000289272;ENST00000253807;ENST00000289269	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61392	0.47;0.14;0.52;0.5;0.74;0.52;0.66;0.33;0.5;0.11;0.29;0.57;0.55;0.11;0.41;0.49;0.42;0.75;0.63;0.39;0.65	5.77	5.77	0.91146	.	0.000000	0.40302	N	0.001136	T	0.70448	0.3225	L	0.42245	1.32	0.49798	D	0.999824	P;B;D;D;D;D;D;P;P;D;P;P;B;P;D;P;D;D;D;D;D	0.69078	0.651;0.315;0.991;0.957;0.991;0.997;0.997;0.867;0.866;0.991;0.599;0.79;0.057;0.901;0.995;0.701;0.982;0.991;0.997;0.997;0.992	B;B;P;P;P;D;P;P;P;P;B;B;B;P;P;B;P;P;P;D;P	0.65140	0.15;0.109;0.806;0.558;0.806;0.91;0.87;0.463;0.598;0.806;0.206;0.318;0.113;0.627;0.897;0.285;0.852;0.887;0.887;0.932;0.866	T	0.71034	-0.4709	10	0.87932	D	0	.	20.3473	0.98799	0.0:1.0:0.0:0.0	.	933;889;876;876;867;875;874;611;876;876;863;876;612;862;862;873;873;876;874;876;612	Q9Y5I4;Q9H158;Q9Y5I0;C9JA99;Q9UN75;Q9Y5I1;Q9Y5I2;Q9Y5I2-2;Q9Y5H5;Q9Y5H6;Q9UN72;Q9UN73;Q9UN73-2;Q9Y5H7;Q9Y5H7-3;Q9UN74;D6RA20;Q9Y5H8;Q9Y5H9;Q9Y5I3;Q9Y5I3-2	PCDC2_HUMAN;PCDC1_HUMAN;PCDAD_HUMAN;.;PCDAC_HUMAN;PCDAB_HUMAN;PCDAA_HUMAN;.;PCDA9_HUMAN;PCDA8_HUMAN;PCDA7_HUMAN;PCDA6_HUMAN;.;PCDA5_HUMAN;.;PCDA4_HUMAN;.;PCDA3_HUMAN;PCDA2_HUMAN;PCDA1_HUMAN;.	L	876;612;874;876;873;873;862;862;876;612;863;876;876;611;874;875;867;876;876;889;933	ENSP00000420840:P876L;ENSP00000378129:P612L;ENSP00000431748:P874L;ENSP00000429808:P876L;ENSP00000423470:P873L;ENSP00000435300:P873L;ENSP00000433416:P862L;ENSP00000436557:P862L;ENSP00000433378:P876L;ENSP00000434113:P612L;ENSP00000436426:P863L;ENSP00000434655:P876L;ENSP00000436042:P876L;ENSP00000421030:P611L;ENSP00000304234:P874L;ENSP00000381636:P875L;ENSP00000381628:P867L;ENSP00000386821:P876L;ENSP00000289272:P876L;ENSP00000253807:P889L;ENSP00000289269:P933L	ENSP00000304234:P874L	P	+	2	0	PCDHA6;PCDHA7;PCDHA8;PCDHA9;PCDHA2;PCDHA3;PCDHA4;PCDHA5;PCDHA10;PCDHA11;PCDHA12;PCDHA1;PCDHA13;PCDHAC2;PCDHAC1	140369480	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.431000	0.80335	2.884000	0.98904	0.655000	0.94253	CCC	.	.		0.522	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		T	140389296	C	T	140389296	3	4	205	1	0	0	0	0	1	0	0	0	11528	623	22	3	2671	3	PCDHA1	5	140389296	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10		140389296	40525964	15	29878										
GIGYF1	64599	hgsc.bcm.edu	37	chr7	100279816	100279816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ggatataatcgtggacatcaTagggggattccacctccttg	11	9	1	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr7:100279816T>C	ENST00000275732.5	-	22	4013	c.2804A>G	c.(2803-2805)tAt>tGt	p.Y935C	GIGYF1_ENST00000471340.2_5'Flank	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	935					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					GTGGACATCATAGGGGGATTC	0.597																																					p.Y935C		Atlas-SNP	.											.	GIGYF1	113	.	0			c.A2804G						.						74	79	77					7																	100279816		2203	4300	6503	SO:0001583	missense	64599	exon22			ACATCATAGGGGG	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"GYF domain containing 1"	612064	"PERQ amino acid rich, with GYF domain 1"	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.2804A>G	chr7.hg19:g.100279816T>C	ENSP00000275732:p.Tyr935Cys	24.0	0.0		25.0	13.0	NM_022574	Q6Y7W7|Q8WZ38	Missense_Mutation	SNP	ENST00000275732.5	hg19	CCDS34708.1	.	.	.	.	.	.	.	.	.	.	.	15.43	2.832660	0.50845	.	.	ENSG00000146830	ENST00000539430;ENST00000275732	T	0.76060	-0.99	5.14	5.14	0.70334	.	0.144148	0.48767	D	0.000171	D	0.86117	0.5856	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.87372	0.2351	10	0.54805	T	0.06	-8.3937	12.9594	0.58449	0.0:0.0:0.0:1.0	.	935	O75420	PERQ1_HUMAN	C	654;935	ENSP00000275732:Y935C	ENSP00000275732:Y935C	Y	-	2	0	GIGYF1	100117752	1.000000	0.71417	0.964000	0.40570	0.912000	0.54170	5.798000	0.69095	2.159000	0.67721	0.454000	0.30748	TAT	.	.		0.597	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		C	100279816	T	C	100279816	3	2	205	1	0	0	0	0	1	0	0	0	6385	1406	49	2	315	2	GIGYF1	7	100279816	Missense_Mutation	SNP	T	TCGA-DD-AADY-01A-11D-A40R-10		100279816	58858847	16	29879										
STMN4	81551	hgsc.bcm.edu	37	chr8	27094373	27094373	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	cctctaggctttacctggagGcctcttccttcagctccttg	8	15	3	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr8:27094373G>T	ENST00000265770.7	-	6	696	c.560C>A	c.(559-561)gCc>gAc	p.A187D	STMN4_ENST00000523048.1_3'UTR|STMN4_ENST00000350889.4_Missense_Mutation_p.A214D|STMN4_ENST00000519997.1_3'UTR			Q9H169	STMN4_HUMAN	stathmin-like 4	187	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				regulation of microtubule polymerization or depolymerization (GO:0031110)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	11		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)	Lomustine(DB01206)	TTACCTGGAGGCCTCTTCCTT	0.627																																					p.A214D		Atlas-SNP	.											.	STMN4	28	.	0			c.C641A						.						80	67	71					8																	27094373		2203	4300	6503	SO:0001583	missense	81551	exon7			CTGGAGGCCTCTT		CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1	8p21.2	2006-12-09			ENSG00000015592	ENSG00000015592			16078	protein-coding gene	gene with protein product						11230166	Standard	NM_001283054		Approved	RB3	uc003xfj.3	Q9H169	OTTHUMG00000099461	ENST00000265770.7:c.560C>A	chr8.hg19:g.27094373G>T	ENSP00000265770:p.Ala187Asp	64.0	0.0		53.0	22.0	NM_030795	B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9	Missense_Mutation	SNP	ENST00000265770.7	hg19		.	.	.	.	.	.	.	.	.	.	G	19.70	3.876199	0.72180	.	.	ENSG00000015592	ENST00000350889;ENST00000265770	.	.	.	5.03	5.03	0.67393	.	0.049977	0.85682	D	0.000000	T	0.66896	0.2836	.	.	.	0.80722	D	1	P;D	0.64830	0.7;0.994	B;D	0.66351	0.244;0.943	T	0.59490	-0.7445	8	0.13470	T	0.59	-10.1118	15.8843	0.79232	0.0:0.0:1.0:0.0	.	187;214	Q9H169;Q9H169-2	STMN4_HUMAN;.	D	214;187	.	ENSP00000265770:A187D	A	-	2	0	STMN4	27150290	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.598000	0.54038	2.614000	0.88457	0.655000	0.94253	GCC	.	.		0.627	STMN4-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000375941.1	NM_030795		T	27094373	G	T	27094373	3	4	205	1	0	0	0	0	1	0	0	0	15326	1203	42	3	13	3	STMN4	8	27094373	Missense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10		27094373	119269649	17	29880										
PLEC	5339	hgsc.bcm.edu	37	chr8	145003368	145003368	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gggggccgcaggcgatggctCtggtagggccaagaccttct	17	11	2	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr8:145003368C>G	ENST00000322810.4	-	25	3743	c.3574G>C	c.(3574-3576)Gag>Cag	p.E1192Q	PLEC_ENST00000436759.2_Missense_Mutation_p.E1082Q|PLEC_ENST00000354958.2_Missense_Mutation_p.E1033Q|PLEC_ENST00000345136.3_Missense_Mutation_p.E1055Q|PLEC_ENST00000527096.1_Missense_Mutation_p.E1078Q|PLEC_ENST00000356346.3_Missense_Mutation_p.E1041Q|PLEC_ENST00000398774.2_Missense_Mutation_p.E1023Q|PLEC_ENST00000354589.3_Missense_Mutation_p.E1055Q|PLEC_ENST00000357649.2_Missense_Mutation_p.E1059Q	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1192	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GGCGATGGCTCTGGTAGGGCC	0.677																																					p.E1192Q		Atlas-SNP	.											.	PLEC	1144	.	0			c.G3574C						.						11	15	13					8																	145003368		2001	4168	6169	SO:0001583	missense	5339	exon25			ATGGCTCTGGTAG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.3574G>C	chr8.hg19:g.145003368C>G	ENSP00000323856:p.Glu1192Gln	71.0	0.0		66.0	18.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.183235	0.38511	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.76709	-1.0;-1.0;-1.04;-1.03;-1.02;-1.0;-1.0;-1.0;-1.0	5.25	5.25	0.73442	.	0.090990	0.44902	U	0.000404	T	0.63402	0.2508	N	0.08118	0	0.39366	D	0.966007	B;B;B;B;B;B;B;B	0.20052	0.041;0.041;0.041;0.024;0.041;0.041;0.041;0.041	B;B;B;B;B;B;B;B	0.20384	0.029;0.029;0.029;0.013;0.029;0.029;0.029;0.029	T	0.60647	-0.7222	10	0.39692	T	0.17	.	18.4442	0.90678	0.0:1.0:0.0:0.0	.	1082;1041;1033;1192;1023;1055;1059;1055	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	Q	1055;1059;1055;1023;1192;1033;1041;1082;1078	ENSP00000344848:E1055Q;ENSP00000350277:E1059Q;ENSP00000346602:E1055Q;ENSP00000381756:E1023Q;ENSP00000323856:E1192Q;ENSP00000347044:E1033Q;ENSP00000348702:E1041Q;ENSP00000388180:E1082Q;ENSP00000434583:E1078Q	ENSP00000323856:E1192Q	E	-	1	0	PLEC	145075356	0.996000	0.38824	0.978000	0.43139	0.630000	0.37929	3.030000	0.49720	2.444000	0.82710	0.551000	0.68910	GAG	.	.		0.677	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		G	145003368	C	G	145003368	3	3	205	1	0	0	0	0	1	0	0	0	12061	922	32	4	10512	4	PLEC	8	145003368	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	117908995	145003368	1360654	18	29881										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131378105	131378121	+	Splice_Site	DEL	GGAGTCCTGGATCAAGT	GGAGTCCTGGATCAAGT	-													0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ttccgggacatggatgacgaGgagtcctggatcaagtatgt							TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	GGAGTCCTGGATCAAGT	GGAGTCCTGGATCAAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr9:131378105_131378121delGGAGTCCTGGATCAAGT	ENST00000372731.4	+	40	5438_5452	c.5328_5342delGGAGTCCTGGATCAAGT	c.(5326-5343)gaggagtcctggatcaag>gag	p.ESWIK1777fs	SPTAN1_ENST00000372739.3_Splice_Site_p.ESWIK1782fs|SPTAN1_ENST00000358161.5_Splice_Site_p.ESWIK1782fs	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1777					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						TGGATGACGAGGAGTCCTGGATCAAGTATGTCTTCTC	0.576																																					p.1781_1786del	NSCLC(120;833 1744 2558 35612 37579)	Atlas-INDEL	.											.	SPTAN1	266	.	0			c.5342_5357del						.																																			SO:0001630	splice_region_variant	6709	exon41			.	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.5342+1GGAGTCCTGGATCAAGT>-	chr9.hg19:g.131378105_131378121delGGAGTCCTGGATCAAGT		69.0	0.0		71.0	21.0	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Frame_Shift_Del	DEL	ENST00000372731.4	hg19	CCDS6905.1																																																																																			.	.		0.576	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	Frame_Shift_Del	-	131378121	GGAGTCCTGGATCAAGT	-	131378105	8	5	205	1	0	1	0	1	0	0	1	0	15132	991	35	0	5501	0	SPTAN1	9	131378105	Splice_Site	DEL	GGAGTCCTGGATCAAGT	TCGA-DD-AADY-01A-11D-A40R-10		131378105	9835326	19	29882										
RHOBTB1	9886	hgsc.bcm.edu	37	chr10	62637748	62637748	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	tccagatccaagttaggagaCaactgcttggtatagagata	10	7	0	3			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr10:62637748C>A	ENST00000337910.5	-	8	1981	c.1644G>T	c.(1642-1644)ttG>ttT	p.L548F	RHOBTB1_ENST00000490827.1_5'Flank|RHOBTB1_ENST00000357917.4_Missense_Mutation_p.L548F	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	548	BTB 2. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					AGTTAGGAGACAACTGCTTGG	0.413																																					p.L548F		Atlas-SNP	.											.	RHOBTB1	61	.	0			c.G1644T						.						134	125	128					10																	62637748		2203	4300	6503	SO:0001583	missense	9886	exon8			AGGAGACAACTGC	AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"BTB/POZ domain containing"	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.1644G>T	chr10.hg19:g.62637748C>A	ENSP00000338671:p.Leu548Phe	129.0	0.0		90.0	75.0	NM_014836		Missense_Mutation	SNP	ENST00000337910.5	hg19	CCDS7261.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.083977	0.36758	.	.	ENSG00000072422	ENST00000357917;ENST00000337910	T;T	0.71579	-0.58;-0.58	6.17	6.17	0.99709	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.64402	D	0.000013	T	0.61912	0.2385	L	0.39326	1.205	0.58432	D	0.999996	B	0.16603	0.018	B	0.25405	0.06	T	0.54337	-0.8309	10	0.22109	T	0.4	.	12.1306	0.53940	0.0:0.8119:0.1221:0.066	.	548	O94844	RHBT1_HUMAN	F	548	ENSP00000350595:L548F;ENSP00000338671:L548F	ENSP00000338671:L548F	L	-	3	2	RHOBTB1	62307754	0.988000	0.35896	1.000000	0.80357	0.971000	0.66376	0.325000	0.19628	2.941000	0.99782	0.655000	0.94253	TTG	.	.		0.413	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			A	62637748	C	A	62637748	3	1	205	1	0	0	0	0	1	0	0	0	13348	477	17	3	462	3	RHOBTB1	10	62637748	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10		62637748	72896999	20	29883										
BTAF1	9044	hgsc.bcm.edu	37	chr10	93699785	93699785	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	tgttgaagctatagtgaaaaAtgtacctgagtggaatccag	11	5	0	3			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr10:93699785A>T	ENST00000265990.6	+	3	523	c.215A>T	c.(214-216)aAt>aTt	p.N72I		NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	72					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				ATAGTGAAAAATGTACCTGAG	0.338																																					p.N72I		Atlas-SNP	.											.	BTAF1	148	.	0			c.A215T						.						66	68	67					10																	93699785		2203	4300	6503	SO:0001583	missense	9044	exon3			TGAAAAATGTACC	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.215A>T	chr10.hg19:g.93699785A>T	ENSP00000265990:p.Asn72Ile	157.0	0.0		94.0	81.0	NM_003972	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	hg19	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.747275	0.89663	.	.	ENSG00000095564	ENST00000265990	D	0.91237	-2.81	5.42	5.42	0.78866	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.94689	0.8287	M	0.78456	2.415	0.80722	D	1	D	0.71674	0.998	D	0.65987	0.94	D	0.94822	0.7988	10	0.52906	T	0.07	-4.2471	15.4551	0.75308	1.0:0.0:0.0:0.0	.	72	O14981	BTAF1_HUMAN	I	72	ENSP00000265990:N72I	ENSP00000265990:N72I	N	+	2	0	BTAF1	93689765	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.164000	0.94755	2.063000	0.61619	0.533000	0.62120	AAT	.	.		0.338	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		T	93699785	A	T	93699785	3	4	205	1	0	0	0	0	1	0	0	0	1538	101	4	4	225	4	BTAF1	10	93699785	Missense_Mutation	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10	31062037	93699785	41834962	21	29884										
SEC23IP	11196	hgsc.bcm.edu	37	chr10	121677401	121677401	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	tcgatttcgtcactttaccaAtgaaactttgctagatattt	5	8	1	2	rs371628667		TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr10:121677401A>T	ENST00000369075.3	+	9	1670	c.1598A>T	c.(1597-1599)aAt>aTt	p.N533I	SEC23IP_ENST00000543134.1_Missense_Mutation_p.N322I	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	533					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		CACTTTACCAATGAAACTTTG	0.343																																					p.N533I		Atlas-SNP	.											.	SEC23IP	100	.	0			c.A1598T						.						54	57	56					10																	121677401		2203	4300	6503	SO:0001583	missense	11196	exon9			TTACCAATGAAAC	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.1598A>T	chr10.hg19:g.121677401A>T	ENSP00000358071:p.Asn533Ile	99.0	0.0		52.0	40.0	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Missense_Mutation	SNP	ENST00000369075.3	hg19	CCDS7618.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.702532	0.88924	.	.	ENSG00000107651	ENST00000369075;ENST00000543134	T;T	0.60424	0.19;0.19	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.82508	0.5052	M	0.94142	3.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87762	0.2599	10	0.87932	D	0	-28.7726	15.5763	0.76392	1.0:0.0:0.0:0.0	.	322;533	F5H0L8;Q9Y6Y8	.;S23IP_HUMAN	I	533;322	ENSP00000358071:N533I;ENSP00000438773:N322I	ENSP00000358071:N533I	N	+	2	0	SEC23IP	121667391	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.071000	0.93980	2.139000	0.66308	0.533000	0.62120	AAT	.	.		0.343	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			T	121677401	A	T	121677401	3	4	205	1	0	0	0	0	1	0	0	0	14008	101	4	4	1632	4	SEC23IP	10	121677401	Missense_Mutation	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10	27977616	121677401	13857346	22	29885										
C10orf90	118611	hgsc.bcm.edu	37	chr10	128153427	128153427	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gtctctagacagacagtcatCgcttggagagctatccccaa	9	12	2	3			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr10:128153427C>T	ENST00000284694.7	-	4	1492	c.1372G>A	c.(1372-1374)Gat>Aat	p.D458N	C10orf90_ENST00000544758.1_Missense_Mutation_p.D555N|C10orf90_ENST00000356858.3_Missense_Mutation_p.D411N|C10orf90_ENST00000480379.1_5'Flank|C10orf90_ENST00000454341.1_Intron	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	458					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		AGACAGTCATCGCTTGGAGAG	0.488																																					p.D458N		Atlas-SNP	.											.	C10orf90	121	.	0			c.G1372A						.						114	110	111					10																	128153427		2203	4300	6503	SO:0001583	missense	118611	exon4			AGTCATCGCTTGG	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.1372G>A	chr10.hg19:g.128153427C>T	ENSP00000284694:p.Asp458Asn	130.0	0.0		83.0	61.0	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	hg19	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	C	0.019	-1.449358	0.01080	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000544758;ENST00000432642	T;T;T	0.17854	2.25;2.25;2.25	4.44	1.36	0.22044	.	0.995724	0.08138	N	0.992091	T	0.04952	0.0133	N	0.02539	-0.55	0.09310	N	1	B;B	0.14012	0.004;0.009	B;B	0.09377	0.004;0.002	T	0.39643	-0.9604	10	0.02654	T	1	-0.2384	3.4459	0.07481	0.0:0.3332:0.2417:0.4251	.	555;458	F5GZL2;Q96M02	.;CJ090_HUMAN	N	411;458;555;458	ENSP00000284694:D458N;ENSP00000444369:D555N;ENSP00000405995:D458N	ENSP00000284694:D458N	D	-	1	0	C10orf90	128143417	0.000000	0.05858	0.000000	0.03702	0.395000	0.30598	-0.094000	0.11094	0.075000	0.16796	0.637000	0.83480	GAT	.	.		0.488	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		T	128153427	C	T	128153427	3	4	205	1	0	0	0	0	1	0	0	0	1625	884	31	1	751	1	C10orf90	10	128153427	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	6476026	128153427	7381320	23	29886										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6643315	6643315	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gaggggtggtgggtcgatacGgggagctgggggacatggcc	23	6	0	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr11:6643315G>A	ENST00000299441.3	-	21	10003	c.9592C>T	c.(9592-9594)Cgt>Tgt	p.R3198C	TPP1_ENST00000534644.1_5'Flank|RP11-732A19.5_ENST00000526456.1_RNA|TPP1_ENST00000528657.1_5'Flank|TPP1_ENST00000299427.6_5'Flank|TPP1_ENST00000533371.1_5'Flank|RP11-732A19.9_ENST00000545572.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	3198					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGTCGATACGGGGAGCTGGG	0.637																																					p.R3198C		Atlas-SNP	.											.	DCHS1	277	.	0			c.C9592T						.						45	50	48					11																	6643315		2201	4296	6497	SO:0001583	missense	8642	exon21			CGATACGGGGAGC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.9592C>T	chr11.hg19:g.6643315G>A	ENSP00000299441:p.Arg3198Cys	42.0	0.0		31.0	16.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.973264	0.53614	.	.	ENSG00000166341	ENST00000299441	T	0.56444	0.46	4.88	4.88	0.63580	.	0.000000	0.43260	D	0.000597	T	0.63792	0.2541	L	0.40543	1.245	0.80722	D	1	D	0.89917	1.0	D	0.65987	0.94	T	0.67090	-0.5758	10	0.87932	D	0	.	16.7719	0.85539	0.0:0.0:1.0:0.0	.	3198	Q96JQ0	PCD16_HUMAN	C	3198	ENSP00000299441:R3198C	ENSP00000299441:R3198C	R	-	1	0	DCHS1	6599891	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.760000	0.62235	2.531000	0.85337	0.313000	0.20887	CGT	.	.		0.637	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6643315	G	A	6643315	3	1	205	1	0	0	0	0	1	0	0	0	4289	1116	39	1	308	1	DCHS1	11	6643315	Missense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10		6643315	128363201	24	29887										
CELF1	10658	hgsc.bcm.edu	37	chr11	47506044	47506044	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	tcagtgcacttcttggaaatCataccaataaacagcttcct	5	11	3	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr11:47506044C>A	ENST00000358597.3	-	4	341	c.342G>T	c.(340-342)atG>atT	p.M114I	CELF1_ENST00000531165.1_Missense_Mutation_p.M141I|CELF1_ENST00000361904.3_Missense_Mutation_p.M114I|CELF1_ENST00000395292.2_Missense_Mutation_p.M114I|CELF1_ENST00000310513.5_Missense_Mutation_p.M114I|AC090559.1_ENST00000578625.1_RNA|CELF1_ENST00000395290.2_Missense_Mutation_p.M113I|CELF1_ENST00000532048.1_Missense_Mutation_p.M140I			Q92879	CELF1_HUMAN	CUGBP, Elav-like family member 1	114	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of translation (GO:0017148)|positive regulation of multicellular organism growth (GO:0040018)|regulation of RNA splicing (GO:0043484)|RNA interference (GO:0016246)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation repressor activity, nucleic acid binding (GO:0000900)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(2)	18						TCTTGGAAATCATACCAATAA	0.433																																					p.M140I	Pancreas(163;1949 1966 9906 43218 43785)	Atlas-SNP	.											.	CELF1	43	.	0			c.G420T						.						96	98	97					11																	47506044		2201	4298	6499	SO:0001583	missense	10658	exon7			GGAAATCATACCA	U63289	CCDS7938.1, CCDS7939.1, CCDS31482.1, CCDS53622.1, CCDS53623.1	11p11	2013-02-12	2010-02-19	2010-02-19				"RNA binding motif (RRM) containing"	2549	protein-coding gene	gene with protein product	"CUG RNA-binding protein", "nuclear polyadenylated RNA-binding protein, 50-kD", "bruno-like 2", "embryo deadenylation element binding protein"	601074	"CUG triplet repeat, RNA-binding protein 1", "CUG triplet repeat, RNA binding protein 1"	CUGBP1		8948631, 9371827	Standard	NM_006560		Approved	CUG-BP, hNab50, BRUNOL2, NAB50, CUGBP, NAPOR, EDEN-BP	uc001nfl.3	Q92879		ENST00000358597.3:c.342G>T	chr11.hg19:g.47506044C>A	ENSP00000351409:p.Met114Ile	178.0	0.0		184.0	78.0	NM_001172639	B4E2U5|D3DQS0|F8W940|Q4LE52|Q9NP83|Q9NR06	Missense_Mutation	SNP	ENST00000358597.3	hg19	CCDS31482.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.251644	0.80135	.	.	ENSG00000149187	ENST00000395290;ENST00000358597;ENST00000395292;ENST00000310513;ENST00000361904;ENST00000531165;ENST00000532048	T;T;T;T;T;T;T	0.05855	3.38;3.38;3.38;3.38;3.38;3.38;3.38	5.78	5.78	0.91487	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.16041	0.0386	L	0.47716	1.5	0.80722	D	1	B;B;P;P;B;P	0.36222	0.001;0.06;0.488;0.488;0.015;0.544	B;B;B;B;B;P	0.47891	0.004;0.071;0.424;0.424;0.061;0.56	T	0.00313	-1.1825	10	0.87932	D	0	-11.6269	20.0118	0.97458	0.0:1.0:0.0:0.0	.	113;141;140;114;114;114	F8W940;G5EA30;Q92879-4;Q92879-2;Q92879-3;Q92879	.;.;.;.;.;CELF1_HUMAN	I	113;114;114;114;114;141;140	ENSP00000378705:M113I;ENSP00000351409:M114I;ENSP00000378706:M114I;ENSP00000308386:M114I;ENSP00000354639:M114I;ENSP00000436864:M141I;ENSP00000435926:M140I	ENSP00000308386:M114I	M	-	3	0	CELF1	47462620	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.767000	0.85331	2.742000	0.94016	0.650000	0.86243	ATG	.	.		0.433	CELF1-024	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398352.1	NM_006560		A	47506044	C	A	47506044	3	1	205	1	0	0	0	0	1	0	0	0	3217	826	29	3	1157	3	CELF1	11	47506044	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	40862729	47506044	87500472	25	29888										
TUT1	64852	hgsc.bcm.edu	37	chr11	62343081	62343081	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ctgcccagggctctgcatggCccagtcctgcaccatctctc	9	18	2	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr11:62343081C>T	ENST00000476907.1	-	9	2801	c.2110G>A	c.(2110-2112)Gcc>Acc	p.A704T	EEF1G_ENST00000378019.3_5'Flank|EEF1G_ENST00000532986.1_5'Flank|MIR3654_ENST00000496634.2_Intron|EEF1G_ENST00000329251.4_5'Flank|TUT1_ENST00000308436.7_Missense_Mutation_p.A742T			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	704					mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CTCTGCATGGCCCAGTCCTGC	0.632																																					p.A742T		Atlas-SNP	.											.	TUT1	122	.	0			c.G2224A						.						244	232	236					11																	62343081		2202	4299	6501	SO:0001583	missense	64852	exon9			GCATGGCCCAGTC	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"RNA binding motif (RRM) containing"	26184	protein-coding gene	gene with protein product	"RNA uridylyltransferase", "U6 TUTase", "TUTase 6"	610641	"RNA binding motif protein 21"	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.2110G>A	chr11.hg19:g.62343081C>T	ENSP00000419607:p.Ala704Thr	62.0	0.0		126.0	31.0	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Missense_Mutation	SNP	ENST00000476907.1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.459	1.092687	0.20471	.	.	ENSG00000149016	ENST00000308436;ENST00000476907	T;T	0.41400	1.0;1.03	5.1	4.2	0.49525	.	0.565316	0.18533	N	0.138424	T	0.30417	0.0764	L	0.27053	0.805	0.20563	N	0.999887	B;B	0.18610	0.015;0.029	B;B	0.17098	0.017;0.011	T	0.18272	-1.0342	10	0.41790	T	0.15	-8.005	11.3336	0.49490	0.0:0.9126:0.0:0.0874	.	704;742	Q9H6E5;F5H0R1	STPAP_HUMAN;.	T	742;704	ENSP00000308000:A742T;ENSP00000419607:A704T	ENSP00000308000:A742T	A	-	1	0	TUT1	62099657	0.005000	0.15991	0.946000	0.38457	0.160000	0.22226	0.729000	0.26028	1.398000	0.46701	-0.136000	0.14681	GCC	.	.		0.632	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		T	62343081	C	T	62343081	3	4	205	1	0	0	0	0	1	0	0	0	16795	739	26	3	518	3	TUT1	11	62343081	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	14837037	62343081	72663435	26	29889										
SIPA1	6494	hgsc.bcm.edu	37	chr11	65414996	65414996	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	agacggcggggctgcggcccGgggcgcgcctcctgcgcgtg	20	15	0	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr11:65414996G>A	ENST00000394224.3	+	9	2469	c.2173G>A	c.(2173-2175)Ggg>Agg	p.G725R	MIR4489_ENST00000578869.1_RNA|SIPA1_ENST00000534313.1_Missense_Mutation_p.G725R|SIPA1_ENST00000527525.1_Missense_Mutation_p.G623R|SIPA1_ENST00000394227.3_Missense_Mutation_p.G623R	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	725	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582)			cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	10						GCTGCGGCCCGGGGCGCGCCT	0.746																																					p.G725R		Atlas-SNP	.											.	SIPA1	45	.	0			c.G2173A						.						4	4	4					11																	65414996		1748	3420	5168	SO:0001583	missense	6494	exon9			CGGCCCGGGGCGC	AH006363, BC010492, BM677738	CCDS8108.1	11q13.3	2008-09-12	2008-09-12		ENSG00000213445	ENSG00000213445			10885	protein-coding gene	gene with protein product		602180				9027487	Standard	NM_006747		Approved	SPA1	uc001ofb.2	Q96FS4	OTTHUMG00000166541	ENST00000394224.3:c.2173G>A	chr11.hg19:g.65414996G>A	ENSP00000377771:p.Gly725Arg	7.0	0.0		17.0	11.0	NM_006747	O14518|O60484|O60618|Q2YD83	Missense_Mutation	SNP	ENST00000394224.3	hg19	CCDS8108.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.683105	0.88542	.	.	ENSG00000213445	ENST00000534313;ENST00000527525;ENST00000394224;ENST00000394227	T;T;T;T	0.59364	0.27;0.27;0.27;0.27	4.09	3.16	0.36331	PDZ/DHR/GLGF (4);	0.108513	0.40064	U	0.001190	T	0.53110	0.1776	M	0.64170	1.965	0.32413	N	0.550449	B;B	0.26041	0.14;0.074	B;B	0.25987	0.026;0.065	T	0.62941	-0.6747	10	0.87932	D	0	-19.7828	10.2141	0.43158	0.1029:0.0:0.8971:0.0	.	623;725	F6RY50;Q96FS4	.;SIPA1_HUMAN	R	725;623;725;623	ENSP00000436269:G725R;ENSP00000433686:G623R;ENSP00000377771:G725R;ENSP00000377774:G623R	ENSP00000377771:G725R	G	+	1	0	SIPA1	65171572	1.000000	0.71417	0.992000	0.48379	0.818000	0.46254	4.980000	0.63812	0.833000	0.34828	0.297000	0.19635	GGG	.	.		0.746	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747		A	65414996	G	A	65414996	3	1	205	1	0	0	0	0	1	0	0	0	14343	1116	39	1	2203	1	SIPA1	11	65414996	Missense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10	3071915	65414996	69591520	27	29890										
PPP2R1B	5519	hgsc.bcm.edu	37	chr11	111622945	111622945	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gcggaccctccatttggcatCttctgccagctccactatgg	9	15	2	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr11:111622945C>G	ENST00000527614.1	-	10	1341	c.1276G>C	c.(1276-1278)Gat>Cat	p.D426H	PPP2R1B_ENST00000427203.2_Missense_Mutation_p.D265H|PPP2R1B_ENST00000393055.2_Missense_Mutation_p.D299H|PPP2R1B_ENST00000341980.6_Missense_Mutation_p.D381H|PPP2R1B_ENST00000426998.2_Missense_Mutation_p.D362H|PPP2R1B_ENST00000311129.5_Missense_Mutation_p.D426H	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	426					apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		CATTTGGCATCTTCTGCCAGC	0.502																																					p.D426H		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.G1276C						.						121	110	114					11																	111622945		2201	4297	6498	SO:0001583	missense	5519	exon10			TGGCATCTTCTGC	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9303	protein-coding gene	gene with protein product	"PP2A-A-beta", "protein phosphatase 2A, regulatory subunit A, beta isoform"	603113	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741	ENST00000527614.1:c.1276G>C	chr11.hg19:g.111622945C>G	ENSP00000437193:p.Asp426His	130.0	0.0		72.0	58.0	NM_002716	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	hg19	CCDS8349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.8|24.8	4.569155|4.569155	0.86439|0.86439	.|.	.|.	ENSG00000137713|ENSG00000137713	ENST00000311129;ENST00000412902;ENST00000426998;ENST00000527614;ENST00000427203;ENST00000341980;ENST00000393055|ENST00000531890	T;T;T;T;T;T|.	0.40225|.	1.6;1.6;1.6;1.6;1.04;1.6|.	5.71|5.71	4.8|4.8	0.61643|0.61643	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87838|0.87838	0.6278|0.6278	H|H	0.97415|0.97415	4|4	0.80722|0.80722	D|D	1|1	D;D;D;D;P;P|.	0.89917|.	1.0;0.999;0.957;1.0;0.873;0.938|.	D;D;P;D;P;D|.	0.97110|.	0.993;0.979;0.679;1.0;0.835;0.919|.	D|D	0.91895|0.91895	0.5527|0.5527	10|5	0.87932|.	D|.	0|.	-22.0496|-22.0496	14.2082|14.2082	0.65748|0.65748	0.1507:0.8493:0.0:0.0|0.1507:0.8493:0.0:0.0	.|.	299;381;265;362;426;426|.	A8MY67;F8W8G1;B7Z1G3;B4DWW5;P30154;P30154-2|.	.;.;.;.;2AAB_HUMAN;.|.	H|T	426;299;362;426;265;381;299|126	ENSP00000311344:D426H;ENSP00000410671:D362H;ENSP00000437193:D426H;ENSP00000415759:D265H;ENSP00000343317:D381H;ENSP00000376775:D299H|.	ENSP00000311344:D426H|.	D|R	-|-	1|2	0|0	PPP2R1B|PPP2R1B	111128155|111128155	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	5.794000|5.794000	0.69067|0.69067	1.531000|1.531000	0.49152|0.49152	0.643000|0.643000	0.83706|0.83706	GAT|AGA	.	.		0.502	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716		G	111622945	C	G	111622945	3	3	205	1	0	0	0	0	1	0	0	0	12395	913	32	4	776	4	PPP2R1B	11	111622945	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	46207949	111622945	23383571	28	29891										
KCNA6	3742	hgsc.bcm.edu	37	chr12	4920655	4920655	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gtatacccacgtcacttgtgGgcagcctgcgccggacctga	12	14	1	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr12:4920655G>C	ENST00000280684.3	+	1	2314	c.1448G>C	c.(1447-1449)gGg>gCg	p.G483A	KCNA6_ENST00000433855.1_Missense_Mutation_p.G483A|RP11-234B24.4_ENST00000542988.1_lincRNA			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	483					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	GTCACTTGTGGGCAGCCTGCG	0.602										HNSCC(72;0.22)																											p.G483A		Atlas-SNP	.											.	KCNA6	122	.	0			c.G1448C						.						110	106	107					12																	4920655		2203	4300	6503	SO:0001583	missense	3742	exon1			CTTGTGGGCAGCC	X17622	CCDS8534.1	12p13	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6225	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 96"	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.1448G>C	chr12.hg19:g.4920655G>C	ENSP00000280684:p.Gly483Ala	80.0	0.0		69.0	30.0	NM_002235		Missense_Mutation	SNP	ENST00000280684.3	hg19	CCDS8534.1	.	.	.	.	.	.	.	.	.	.	G	3.364	-0.129935	0.06753	.	.	ENSG00000151079	ENST00000433855;ENST00000280684	D;D	0.97328	-4.34;-4.34	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.94125	0.8116	L	0.44542	1.39	0.41768	D	0.98975	B	0.18610	0.029	B	0.12837	0.008	D	0.91268	0.5042	10	0.07813	T	0.8	.	17.6514	0.88165	0.0:0.0:1.0:0.0	.	483	P17658	KCNA6_HUMAN	A	483	ENSP00000408321:G483A;ENSP00000280684:G483A	ENSP00000280684:G483A	G	+	2	0	KCNA6	4790916	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.244000	0.78228	2.641000	0.89580	0.591000	0.81541	GGG	.	.		0.602	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235		C	4920655	G	C	4920655	3	2	205	1	0	0	0	0	1	0	0	0	8016	1232	43	4	1450	4	KCNA6	12	4920655	Missense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10		4920655	128931240	29	29892										
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21353510	21353510	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	tgtttgtgcttttgacgttgTtacaagtaagcagctatatt	9	5	0	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr12:21353510T>G	ENST00000256958.2	+	9	1135	c.1039T>G	c.(1039-1041)Tta>Gta	p.L347V		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	347					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	TTTGACGTTGTTACAAGTAAG	0.328																																					p.L347V		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.T1039G						.						119	108	112					12																	21353510		2202	4299	6501	SO:0001583	missense	10599	exon9			ACGTTGTTACAAG		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1039T>G	chr12.hg19:g.21353510T>G	ENSP00000256958:p.Leu347Val	98.0	0.0		88.0	41.0	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	hg19	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	T	3.845	-0.032961	0.07543	.	.	ENSG00000134538	ENST00000256958	T	0.61392	0.11	3.34	-0.296	0.12824	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.594341	0.16545	N	0.209747	T	0.44973	0.1319	L	0.57536	1.79	0.09310	N	1	B	0.16396	0.017	B	0.26864	0.074	T	0.30679	-0.9970	10	0.22109	T	0.4	.	2.5553	0.04758	0.3729:0.3427:0.0:0.2844	.	347	Q9Y6L6	SO1B1_HUMAN	V	347	ENSP00000256958:L347V	ENSP00000256958:L347V	L	+	1	2	SLCO1B1	21244777	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-1.046000	0.03525	-0.209000	0.10156	0.402000	0.26972	TTA	.	.		0.328	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		G	21353510	T	G	21353510	3	3	205	1	0	0	0	0	1	0	0	0	14738	1722	60	5	1069	5	SLCO1B1	12	21353510	Missense_Mutation	SNP	T	TCGA-DD-AADY-01A-11D-A40R-10	16432855	21353510	112498385	30	29893										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48373812	48373812	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	cggggggccttgggcacctcGggctcctttaggaccagtca	15	13	1	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr12:48373812G>A	ENST00000380518.3	-	40	2823	c.2659C>T	c.(2659-2661)Cga>Tga	p.R887*	COL2A1_ENST00000337299.6_Nonsense_Mutation_p.R818*|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	887	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	TGGGCACCTCGGGCTCCTTTA	0.642																																					p.R887X		Atlas-SNP	.											.	COL2A1	368	.	0			c.C2659T	GRCh37	CM062564	COL2A1	M		.						16	15	15					12																	48373812		2155	4233	6388	SO:0001587	stop_gained	1280	exon40			CACCTCGGGCTCC	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.2659C>T	chr12.hg19:g.48373812G>A	ENSP00000369889:p.Arg887*	170.0	0.0		184.0	85.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Nonsense_Mutation	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	G	42	9.591689	0.99214	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	.	.	.	4.99	4.09	0.47781	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3633	0.66787	0.0:0.0:0.8506:0.1494	.	.	.	.	X	887;818;818	.	ENSP00000338213:R818X	R	-	1	2	COL2A1	46660079	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.561000	0.67339	1.080000	0.41073	0.462000	0.41574	CGA	.	.		0.642	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		A	48373812	G	A	48373812	4	1	205	1	0	0	0	0	0	1	0	0	3689	1124	39	1	1864	1	COL2A1	12	48373812	Nonsense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10	27020302	48373812	85478083	31	29894										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58131312	58131312	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ccctcccccggcggcggcggCggtggcggcggcagagaccg	19	17	0	1	rs561812307		TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr12:58131312C>T	ENST00000547588.1	-	1	717	c.718G>A	c.(718-720)Gcc>Acc	p.A240T	AGAP2_ENST00000257897.3_Intron	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	240					axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						gcggcggcggcggtggcggcg	0.706																																					p.A240T		Atlas-SNP	.											AGAP2_ENST00000547588,NS,carcinoma,0,1	AGAP2	167	.	0			c.G718A						.						4	6	5					12																	58131312		1428	3301	4729	SO:0001583	missense	116986	exon1			CGGCGGCGGTGGC	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.718G>A	chr12.hg19:g.58131312C>T	ENSP00000449241:p.Ala240Thr	75.0	0.0		66.0	4.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	hg19	CCDS44932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.24|10.24	1.294811|1.294811	0.23564|0.23564	.|.	.|.	ENSG00000135439|ENSG00000135439	ENST00000547588|ENST00000328568	T|.	0.39997|.	1.05|.	3.81|3.81	-1.14|-1.14	0.09741|0.09741	.|.	1.354790|.	0.05448|.	N|.	0.548952|.	T|T	0.10508|0.10508	0.0257|0.0257	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.14012|.	0.009;0.005|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.24548|0.24548	-1.0157|-1.0157	10|5	0.56958|.	D|.	0.05|.	.|.	0.5619|0.5619	0.00680|0.00680	0.1874:0.3561:0.184:0.2724|0.1874:0.3561:0.184:0.2724	.|.	240;240|.	F8VVT9;Q99490|.	.;AGAP2_HUMAN|.	T|H	240|103	ENSP00000449241:A240T|.	ENSP00000449241:A240T|.	A|R	-|-	1|2	0|0	AGAP2|AGAP2	56417579|56417579	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	0.086000|0.086000	0.14935|0.14935	-0.555000|-0.555000	0.06142|0.06142	0.455000|0.455000	0.32223|0.32223	GCC|CGC	.	.		0.706	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		T	58131312	C	T	58131312	3	4	205	1	0	0	0	0	1	0	0	0	368	768	27	1	2936	1	AGAP2	12	58131312	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	9757500	58131312	75720583	32	29895										
CUX2	23316	hgsc.bcm.edu	37	chr12	111471987	111471987	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	tcgatagcccccaagatggcCgccaatgtgggatcgatgtt	12	11	0	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr12:111471987C>T	ENST00000261726.6	+	1	160	c.6C>T	c.(4-6)gcC>gcT	p.A2A		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	2					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						CCAAGATGGCCGCCAATGTGG	0.622																																					p.A2A		Atlas-SNP	.											.	CUX2	145	.	0			c.C6T						.						65	71	69					12																	111471987		2203	4300	6503	SO:0001819	synonymous_variant	23316	exon1			GATGGCCGCCAAT	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.6C>T	chr12.hg19:g.111471987C>T		71.0	0.0		60.0	52.0	NM_015267	A7E2Y4	Silent	SNP	ENST00000261726.6	hg19	CCDS41837.1																																																																																			.	.		0.622	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		T	111471987	C	T	111471987	2	4	205	1	0	0	0	0	0	0	0	1	4067	639	23	1		1	CUX2	12	111471987	Silent	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	53340675	111471987	22379908	33	29896										
SKA3	221150	hgsc.bcm.edu	37	chr13	21742126	21742126	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ccttttaacagagctgcttaCcttttattattcctcgcatt	4	11	0	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr13:21742126C>A	ENST00000314759.5	-	4	868		c.e4+1		SKA3_ENST00000400018.3_Splice_Site	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3						chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GAGCTGCTTACCTTTTATTAT	0.284																																					.		Atlas-SNP	.											.	SKA3	76	.	0			c.743+1G>T						.						63	58	60					13																	21742126		2203	4297	6500	SO:0001630	splice_region_variant	221150	exon5			TGCTTACCTTTTA	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 3"	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.743+1G>T	chr13.hg19:g.21742126C>A		72.0	0.0		53.0	8.0	NM_001166017	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Splice_Site	SNP	ENST00000314759.5	hg19	CCDS31946.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.052163	0.36181	.	.	ENSG00000165480	ENST00000314759;ENST00000400018	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6803	0.77364	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SKA3	20640126	1.000000	0.71417	1.000000	0.80357	0.302000	0.27658	4.395000	0.59678	2.777000	0.95525	0.655000	0.94253	.	.	.		0.284	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	Intron	A	21742126	C	A	21742126	5	1	205	1	0	0	0	0	0	0	1	0	14369	521	18	3	565	3	SKA3	13	21742126	Splice_Site	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10		21742126	93427752	34	29897										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64686099	64686099	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	agcctccctctgatatccagGaaatagaactgagagtgaag	10	9	1	4			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr14:64686099G>T	ENST00000344113.4	+	109	19974	c.19762G>T	c.(19762-19764)Gaa>Taa	p.E6588*	SYNE2_ENST00000554805.1_Nonsense_Mutation_p.E371*|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Nonsense_Mutation_p.E3245*|SYNE2_ENST00000358025.3_Nonsense_Mutation_p.E6611*|SYNE2_ENST00000357395.3_Nonsense_Mutation_p.E2973*|SYNE2_ENST00000394768.2_Nonsense_Mutation_p.E2973*|SYNE2_ENST00000555022.1_Nonsense_Mutation_p.E466*|SYNE2_ENST00000554584.1_Nonsense_Mutation_p.E6504*|SYNE2_ENST00000441438.2_Nonsense_Mutation_p.E119*|SYNE2_ENST00000458046.2_Nonsense_Mutation_p.E245*	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6588					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGATATCCAGGAAATAGAACT	0.473																																					p.E6611X		Atlas-SNP	.											.	SYNE2	577	.	0			c.G19831T						.						75	71	73					14																	64686099		2203	4300	6503	SO:0001587	stop_gained	23224	exon110			ATCCAGGAAATAG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.19762G>T	chr14.hg19:g.64686099G>T	ENSP00000341781:p.Glu6588*	136.0	0.0		171.0	79.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Nonsense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	57	30.002811	0.99976	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768;ENST00000555022;ENST00000554805;ENST00000458046;ENST00000441438	.	.	.	5.53	5.53	0.82687	.	0.132141	0.33610	N	0.004734	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	19.4629	0.94924	0.0:0.0:1.0:0.0	.	.	.	.	X	6611;2973;6588;6504;6510;3245;2973;466;371;245;119	.	ENSP00000261678:E6510X	E	+	1	0	SYNE2	63755852	0.019000	0.18553	0.950000	0.38849	0.337000	0.28794	1.166000	0.31834	2.600000	0.87896	0.655000	0.94253	GAA	.	.		0.473	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64686099	G	T	64686099	4	4	205	1	0	0	0	0	0	1	0	0	15461	1175	41	3	20265	3	SYNE2	14	64686099	Nonsense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10		64686099	42663441	35	29898										
HDC	3067	hgsc.bcm.edu	37	chr15	50535066	50535066	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	atgagattccagtctctcagGatgtcatccctagtggtaaa	9	9	3	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr15:50535066G>A	ENST00000267845.3	-	12	1782	c.1380C>T	c.(1378-1380)atC>atT	p.I460I	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Silent_p.I427I	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		AGTCTCTCAGGATGTCATCCC	0.517																																					p.I460I	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.C1380T						.						41	46	44					15																	50535066		2195	4294	6489	SO:0001819	synonymous_variant	3067	exon12			TCTCAGGATGTCA		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1380C>T	chr15.hg19:g.50535066G>A		97.0	0.0		96.0	8.0	NM_002112		Silent	SNP	ENST00000267845.3	hg19	CCDS10134.1																																																																																			.	.		0.517	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			A	50535066	G	A	50535066	2	1	205	1	0	0	0	0	0	0	0	1	7024	1164	41	3		3	HDC	15	50535066	Silent	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10		50535066	51996326	36	29899										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62207992	62207992	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	agacagacagcaccatccggCtgccaattctcctgacgtgg	10	14	1	3			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr15:62207992C>T	ENST00000261517.5	-	61	8358	c.8285G>A	c.(8284-8286)aGc>aAc	p.S2762N	VPS13C_ENST00000395896.4_Missense_Mutation_p.S2762N|VPS13C_ENST00000249837.3_Missense_Mutation_p.S2719N|VPS13C_ENST00000395898.3_Missense_Mutation_p.S2719N|RN7SL613P_ENST00000584412.1_RNA	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CACCATCCGGCTGCCAATTCT	0.458																																					p.S2762N		Atlas-SNP	.											.	VPS13C	506	.	0			c.G8285A						.						87	82	84					15																	62207992		2203	4300	6503	SO:0001583	missense	54832	exon61			ATCCGGCTGCCAA	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.8285G>A	chr15.hg19:g.62207992C>T	ENSP00000261517:p.Ser2762Asn	127.0	0.0		106.0	8.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.871888	0.33069	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.47528	0.84;0.84;1.01	5.54	3.64	0.41730	.	0.353649	0.37761	N	0.001942	T	0.35828	0.0945	L	0.40543	1.245	0.33127	D	0.542626	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.001;0.0	B;B;B;B;B	0.15870	0.009;0.009;0.014;0.009;0.006	T	0.40136	-0.9579	10	0.54805	T	0.06	.	6.7102	0.23272	0.145:0.7098:0.0:0.1452	.	2762;2719;2762;2719;2762	F5GZG8;Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;.;VP13C_HUMAN	N	2719;2762;2762;2762	ENSP00000249837:S2719N;ENSP00000261517:S2762N;ENSP00000379233:S2762N	ENSP00000249837:S2719N	S	-	2	0	VPS13C	59995284	0.996000	0.38824	0.928000	0.36995	0.523000	0.34469	2.498000	0.45363	0.667000	0.31107	0.557000	0.71058	AGC	.	.		0.458	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		T	62207992	C	T	62207992	3	4	205	1	0	0	0	0	1	0	0	0	17206	797	28	3	3104	3	VPS13C	15	62207992	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	11672926	62207992	40323400	37	29900										
HERC1	8925	hgsc.bcm.edu	37	chr15	64067763	64067763	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gattcactgtcctctgtaatCcaggagctgttcaagtgttc	9	10	3	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr15:64067763C>A	ENST00000443617.2	-	2	147	c.60G>T	c.(58-60)tgG>tgT	p.W20C		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	20					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCTCTGTAATCCAGGAGCTGT	0.433																																					p.W20C		Atlas-SNP	.											.	HERC1	624	.	0			c.G60T						.						120	116	117					15																	64067763		1915	4141	6056	SO:0001583	missense	8925	exon2			TGTAATCCAGGAG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.60G>T	chr15.hg19:g.64067763C>A	ENSP00000390158:p.Trp20Cys	124.0	0.0		124.0	58.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.468098	0.43839	.	.	ENSG00000103657	ENST00000443617;ENST00000425434	T	0.00520	6.85	5.65	4.72	0.59763	.	0.000000	0.64402	U	0.000001	T	0.01661	0.0053	M	0.66939	2.045	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.992	D;D;P	0.81914	0.947;0.995;0.707	T	0.64219	-0.6459	10	0.87932	D	0	.	16.4755	0.84131	0.0:0.8687:0.1313:0.0	.	20;20;20	B4DKS2;C9JUT5;Q15751	.;.;HERC1_HUMAN	C	20	ENSP00000390158:W20C	ENSP00000389613:W20C	W	-	3	0	HERC1	61854816	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.762000	0.85270	1.336000	0.45506	0.561000	0.74099	TGG	.	.		0.433	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	64067763	C	A	64067763	3	1	205	1	0	0	0	0	1	0	0	0	7066	856	30	3	14833	3	HERC1	15	64067763	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	1859771	64067763	38463629	38	29901										
MYH2	4620	hgsc.bcm.edu	37	chr17	10447311	10447311	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gacacgcttggtgttcacagTcttccctgcaccagattctc	8	14	3	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr17:10447311T>G	ENST00000245503.5	-	7	940	c.556A>C	c.(556-558)Act>Cct	p.T186P	CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000532183.2_Missense_Mutation_p.T186P|MYH2_ENST00000397183.2_Missense_Mutation_p.T186P	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	186	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						GTGTTCACAGTCTTCCCTGCA	0.413																																					p.T186P		Atlas-SNP	.											.	MYH2	390	.	0			c.A556C						.						133	121	125					17																	10447311		2203	4300	6503	SO:0001583	missense	4620	exon7			TCACAGTCTTCCC		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.556A>C	chr17.hg19:g.10447311T>G	ENSP00000245503:p.Thr186Pro	136.0	0.0		96.0	78.0	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	hg19	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.573356	0.45902	.	.	ENSG00000125414	ENST00000532183;ENST00000245503;ENST00000397183	D;D;D	0.84146	-1.81;-1.81;-1.81	4.76	4.76	0.60689	Myosin head, motor domain (3);	0.000000	0.40385	U	0.001103	D	0.96074	0.8721	H	0.99800	4.79	0.80722	D	1	D;B	0.67145	0.996;0.004	D;B	0.87578	0.998;0.217	D	0.97498	1.0058	10	0.72032	D	0.01	.	13.6203	0.62134	0.0:0.0:0.0:1.0	.	186;186	Q567P6;Q9UKX2	.;MYH2_HUMAN	P	186	ENSP00000433944:T186P;ENSP00000245503:T186P;ENSP00000380367:T186P	ENSP00000245503:T186P	T	-	1	0	MYH2	10388036	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.868000	0.87116	2.001000	0.58596	0.533000	0.62120	ACT	.	.		0.413	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		G	10447311	T	G	10447311	3	3	205	1	0	0	0	0	1	0	0	0	10044	1667	58	5	5405	5	MYH2	17	10447311	Missense_Mutation	SNP	T	TCGA-DD-AADY-01A-11D-A40R-10		10447311	70747899	39	29902										
NCOR1	9611	hgsc.bcm.edu	37	chr17	16029456	16029457	+	Frame_Shift_Ins	INS	-	-	T													0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ttcttcttcttttttttctgINSttttttctgctttatcctct							TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr17:16029456_16029457insT	ENST00000268712.3	-	15	1830_1831	c.1573_1574insA	c.(1573-1575)acafs	p.T525fs	NCOR1_ENST00000395851.1_Frame_Shift_Ins_p.T525fs|NCOR1_ENST00000395848.1_Frame_Shift_Ins_p.T416fs	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	525					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ttttttttctgttttttctgct	0.297																																					p.T525fs		Atlas-INDEL	.											.,1	NCOR1	240	.	0			c.1574_1575insA						.																																			SO:0001589	frameshift_variant	9611	exon14			.	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.1574dupA	chr17.hg19:g.16029462_16029462dupT	ENSP00000268712:p.Thr525fs	163.0	0.0		117.0	90.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Frame_Shift_Ins	INS	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.		0.297	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		T	16029457	-	T	16029456	7	5	205	1	0	1	1	0	0	0	0	0	10244	1377	48	0	5876	0	NCOR1	17	16029456	Frame_Shift_Ins	INS	-	TCGA-DD-AADY-01A-11D-A40R-10	5582145	16029456	65165754	40	29903										
NCOR1	9611	hgsc.bcm.edu	37	chr17	16042476	16042476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	cataggtggaatcacagagaGctgccgcatttgtttctcat	10	9	2	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr17:16042476G>A	ENST00000268712.3	-	12	1455	c.1198C>T	c.(1198-1200)Ctc>Ttc	p.L400F	NCOR1_ENST00000395851.1_Missense_Mutation_p.L400F|RNU6-862P_ENST00000362804.1_RNA|NCOR1_ENST00000395848.1_Missense_Mutation_p.L291F	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	400					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ATCACAGAGAGCTGCCGCATT	0.358																																					p.L400F		Atlas-SNP	.											.	NCOR1	240	.	0			c.C1198T						.						57	54	55					17																	16042476		2203	4300	6503	SO:0001583	missense	9611	exon11			CAGAGAGCTGCCG	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.1198C>T	chr17.hg19:g.16042476G>A	ENSP00000268712:p.Leu400Phe	255.0	0.0		138.0	106.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	12.88	2.071784	0.36566	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000458113;ENST00000395848;ENST00000411510;ENST00000436828	T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.87545	0.6204	L	0.51422	1.61	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;0.998;0.998;0.963;0.996;1.0	D;D;D;P;D;D	0.91635	0.946;0.973;0.973;0.849;0.973;0.999	D	0.88234	0.2905	10	0.66056	D	0.02	-6.8873	18.1509	0.89674	0.0:0.0:1.0:0.0	.	409;400;400;291;400;400	E7EU93;E7EV02;E7EW50;E9PGV6;O75376;O75376-2	.;.;.;.;NCOR1_HUMAN;.	F	400;400;291;409;291;400;409	ENSP00000268712:L400F;ENSP00000379192:L400F;ENSP00000379189:L291F;ENSP00000407998:L400F;ENSP00000387727:L409F	ENSP00000268712:L400F	L	-	1	0	NCOR1	15983201	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.703000	0.74633	2.515000	0.84797	0.655000	0.94253	CTC	.	.		0.358	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		A	16042476	G	A	16042476	3	1	205	1	0	0	0	0	1	0	0	0	10244	971	34	3	6264	3	NCOR1	17	16042476	Missense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10	13020	16042476	65152734	41	29904										
RAI1	10743	hgsc.bcm.edu	37	chr17	17700212	17700212	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ccagggggccatgaagaccaAggtgctgccaccccggaagg	15	13	0	2			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr17:17700212A>G	ENST00000353383.1	+	3	4419	c.3950A>G	c.(3949-3951)aAg>aGg	p.K1317R	RAI1_ENST00000261641.6_Missense_Mutation_p.K1317R	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1317					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ATGAAGACCAAGGTGCTGCCA	0.657																																					p.K1317R		Atlas-SNP	.											.	RAI1	121	.	0			c.A3950G						.						51	62	58					17																	17700212		2203	4300	6503	SO:0001583	missense	10743	exon3			AGACCAAGGTGCT	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"Smith-Magenis syndrome chromosome region"	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.3950A>G	chr17.hg19:g.17700212A>G	ENSP00000323074:p.Lys1317Arg	56.0	0.0		40.0	33.0	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	A	19.35	3.810368	0.70797	.	.	ENSG00000108557	ENST00000353383;ENST00000395776;ENST00000261641;ENST00000315321	D;T	0.85088	-1.94;-1.46	4.44	4.44	0.53790	.	0.000000	0.64402	D	0.000009	D	0.90950	0.7155	M	0.70275	2.135	0.38225	D	0.94087	D	0.69078	0.997	D	0.75020	0.985	D	0.92980	0.6405	10	0.72032	D	0.01	.	13.8441	0.63457	1.0:0.0:0.0:0.0	.	1317	Q7Z5J4	RAI1_HUMAN	R	1317;1317;1317;1269	ENSP00000323074:K1317R;ENSP00000261641:K1317R	ENSP00000261641:K1317R	K	+	2	0	RAI1	17640937	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.099000	0.89542	1.866000	0.54105	0.260000	0.18958	AAG	.	.		0.657	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		G	17700212	A	G	17700212	3	3	205	1	0	0	0	0	1	0	0	0	13022	72	3	2	3952	2	RAI1	17	17700212	Missense_Mutation	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10	1657736	17700212	63494998	42	29905										
GGN	199720	hgsc.bcm.edu	37	chr19	38876399	38876399	+	Silent	SNP	A	A	G													0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gagggctcagccacggtgggAgctggagccggggatggggc							TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr19:38876399A>G	ENST00000334928.6	-	3	1635	c.1503T>C	c.(1501-1503)gcT>gcC	p.A501A	GGN_ENST00000591809.1_Intron|AC005789.9_ENST00000585411.1_RNA|SPRED3_ENST00000587013.1_5'Flank	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	501	Interactions with ZNF403/GGNBP2 and OAZ3. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			ccacggtgggagctggagccg	0.746																																					p.A501A		Atlas-SNP	.											.	GGN	50	.	0			c.T1503C						.						4	6	6					19																	38876399		1869	3766	5635	SO:0001819	synonymous_variant	199720	exon3			GGTGGGAGCTGGA	AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.1503T>C	chr19.hg19:g.38876399A>G		43.0	0.0		51.0	5.0	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Silent	SNP	ENST00000334928.6	hg19	CCDS12516.1																																																																																			.	.		0.746	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		G	38876399	A	G	38876399	2	3	205	1	0	0	0	0	0	0	0	1	6366	291	11	2		2	GGN	19	38876399	Silent	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10		38876399	20252584	43	29906	153	2								
GGN	199720	hgsc.bcm.edu	37	chr19	38876402	38876402	+	Silent	SNP	T	T	C													0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ggctcagccacggtgggagcTggagccggggatggggccgg							TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr19:38876402T>C	ENST00000334928.6	-	3	1632	c.1500A>G	c.(1498-1500)ccA>ccG	p.P500P	GGN_ENST00000591809.1_Intron|AC005789.9_ENST00000585411.1_RNA|SPRED3_ENST00000587013.1_5'Flank	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	500	Interactions with ZNF403/GGNBP2 and OAZ3. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			cggtgggagctggagccgggg	0.746																																					p.P500P		Atlas-SNP	.											.	GGN	50	.	0			c.A1500G						.						4	6	5					19																	38876402		1834	3724	5558	SO:0001819	synonymous_variant	199720	exon3			GGGAGCTGGAGCC	AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.1500A>G	chr19.hg19:g.38876402T>C		42.0	0.0		52.0	5.0	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Silent	SNP	ENST00000334928.6	hg19	CCDS12516.1																																																																																			.	.		0.746	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		C	38876402	T	C	38876402	2	2	205	1	0	0	0	0	0	0	0	1	6366	1567	55	2		2	GGN	19	38876402	Silent	SNP	T	TCGA-DD-AADY-01A-11D-A40R-10	3	38876402	20252581	44	29907	153	2								
BAX	581	hgsc.bcm.edu	37	chr19	49464086	49464086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ggccctgtgcaccaaggtgcCggaactgatcagaaccatca	11	13	2	2	rs369660551		TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr19:49464086C>T	ENST00000345358.7	+	5	441	c.389C>T	c.(388-390)cCg>cTg	p.P130L	BAX_ENST00000391871.3_3'UTR|BAX_ENST00000293288.8_Missense_Mutation_p.P130L|BAX_ENST00000354470.3_Missense_Mutation_p.P81L|BAX_ENST00000415969.2_Missense_Mutation_p.P130L|BAX_ENST00000539787.1_Missense_Mutation_p.R163W	NM_138761.3|NM_138764.4	NP_620116.1|NP_620119.2	Q07812	BAX_HUMAN	BCL2-associated X protein	130					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell homeostatic proliferation (GO:0002358)|B cell negative selection (GO:0002352)|B cell receptor apoptotic signaling pathway (GO:1990117)|blood vessel remodeling (GO:0001974)|cellular response to organic substance (GO:0071310)|cellular response to UV (GO:0034644)|cerebral cortex development (GO:0021987)|development of secondary sexual characteristics (GO:0045136)|ectopic germ cell programmed cell death (GO:0035234)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells within a tissue (GO:0048873)|hypothalamus development (GO:0021854)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein binding (GO:0032091)|neuron apoptotic process (GO:0051402)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic DNA fragmentation (GO:1902512)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of developmental pigmentation (GO:0048087)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-embryonic camera-type eye morphogenesis (GO:0048597)|protein homooligomerization (GO:0051260)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)|protein oligomerization (GO:0051259)|regulation of cell cycle (GO:0051726)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|release of matrix enzymes from mitochondria (GO:0032976)|response to axon injury (GO:0048678)|response to gamma radiation (GO:0010332)|response to salt stress (GO:0009651)|response to toxic substance (GO:0009636)|retina development in camera-type eye (GO:0060041)|retinal cell apoptotic process (GO:1990009)|retinal cell programmed cell death (GO:0046666)|Sertoli cell proliferation (GO:0060011)|spermatid differentiation (GO:0048515)|T cell homeostatic proliferation (GO:0001777)|thymocyte apoptotic process (GO:0070242)|transformed cell apoptotic process (GO:0006927)|vagina development (GO:0060068)|viral process (GO:0016032)	BAX complex (GO:0097144)|Bcl-2 family protein complex (GO:0097136)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrial permeability transition pore complex (GO:0005757)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(4)	17		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)		ACCAAGGTGCCGGAACTGATC	0.592																																					p.P130L		Atlas-SNP	.											.	BAX	69	.	0			c.C389T						.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	110	95	100		389,389,242,389	2	0.9	19		100	0,8600		0,0,4300	no	missense,missense,missense,missense	BAX	NM_004324.3,NM_138761.3,NM_138763.3,NM_138764.4	98,98,98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	130/219,130/193,81/144,130/180	49464086	1,13005	2203	4300	6503	SO:0001583	missense	581	exon5			AGGTGCCGGAACT		CCDS12742.1, CCDS12743.1, CCDS12744.1, CCDS12745.1, CCDS12745.2	19q13.3-q13.4	2014-03-07			ENSG00000087088	ENSG00000087088			959	protein-coding gene	gene with protein product		600040				8358790	Standard	NM_138761		Approved	BCL2L4	uc002plf.1	Q07812	OTTHUMG00000160476	ENST00000345358.7:c.389C>T	chr19.hg19:g.49464086C>T	ENSP00000263262:p.Pro130Leu	55.0	0.0		60.0	32.0	NM_004324	A8K4W1|P55269|Q07814|Q07815|Q8WZ49|Q9NR76|Q9NYG7|Q9UCZ6|Q9UCZ7|Q9UQD6	Missense_Mutation	SNP	ENST00000345358.7	hg19	CCDS12742.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.362|9.362	1.068359|1.068359	0.20067|0.20067	2.27E-4|2.27E-4	0.0|0.0	ENSG00000087088|ENSG00000087088	ENST00000345358;ENST00000415969;ENST00000354470;ENST00000293288|ENST00000539787;ENST00000506183	T;T;T;T|T	0.34667|0.12039	1.35;2.73;1.35;2.73|2.72	3.1|3.1	2.03|2.03	0.26663|0.26663	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.20700|0.20700	0.0498|0.0498	L|L	0.56340|0.56340	1.77|1.77	0.80722|0.80722	D|D	1|1	P;D;D;D|.	0.71674|.	0.912;0.996;0.986;0.998|.	B;P;B;P|.	0.55577|.	0.158;0.707;0.394;0.779|.	T|T	0.01909|0.01909	-1.1249|-1.1249	10|7	0.19147|0.87932	T|D	0.46|0	-8.9341|-8.9341	8.1459|8.1459	0.31110|0.31110	0.0:0.751:0.249:0.0|0.0:0.751:0.249:0.0	.|.	81;130;130;130|.	Q07812-4;Q07812;Q07812-8;Q07812-2|.	.;BAX_HUMAN;.;.|.	L|W	130;130;81;130|163;64	ENSP00000263262:P130L;ENSP00000389971:P130L;ENSP00000346461:P81L;ENSP00000293288:P130L|ENSP00000441413:R163W	ENSP00000293288:P130L|ENSP00000348871:R163W	P|R	+|+	2|1	0|2	BAX|BAX	54155898|54155898	0.999000|0.999000	0.42202|0.42202	0.929000|0.929000	0.37066|0.37066	0.161000|0.161000	0.22273|0.22273	5.205000|5.205000	0.65186|0.65186	0.835000|0.835000	0.34877|0.34877	-0.333000|-0.333000	0.08304|0.08304	CCG|CGG	.	.		0.592	BAX-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360767.1	NM_138763		T	49464086	C	T	49464086	3	4	205	1	0	0	0	0	1	0	0	0	1328	652	23	1	407	1	BAX	19	49464086	Missense_Mutation	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	10587684	49464086	9664897	45	29908										
ZNF175	7728	hgsc.bcm.edu	37	chr19	52090771	52090771	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	actctatgaatgcagtgaatGtggcaaaggcttctcccaaa	9	9	2	2			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr19:52090771G>T	ENST00000262259.2	+	5	1545	c.1187G>T	c.(1186-1188)tGt>tTt	p.C396F	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	396					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C396F(1)		NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		TGCAGTGAATGTGGCAAAGGC	0.403																																					p.C396F		Atlas-SNP	.											ZNF175,NS,carcinoma,0,1	ZNF175	65	.	1	Substitution - Missense(1)	prostate(1)	c.G1187T						.						82	83	83					19																	52090771		2203	4300	6503	SO:0001583	missense	7728	exon5			GTGAATGTGGCAA	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"Zinc fingers, C2H2-type", "-"	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.1187G>T	chr19.hg19:g.52090771G>T	ENSP00000262259:p.Cys396Phe	119.0	0.0		131.0	62.0	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	hg19	CCDS12837.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.095932	0.56075	.	.	ENSG00000105497	ENST00000262259	D	0.85861	-2.04	2.26	2.26	0.28386	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94466	0.8219	H	0.97962	4.115	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94732	0.7910	9	0.87932	D	0	.	10.6252	0.45504	0.0:0.0:1.0:0.0	.	396	Q9Y473	ZN175_HUMAN	F	396	ENSP00000262259:C396F	ENSP00000262259:C396F	C	+	2	0	ZNF175	56782583	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.756000	0.85195	1.588000	0.49971	0.655000	0.94253	TGT	.	.		0.403	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147		T	52090771	G	T	52090771	3	4	205	1	0	0	0	0	1	0	0	0	17760	1377	48	3	1201	3	ZNF175	19	52090771	Missense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10	2626685	52090771	7038212	46	29909										
GZF1	64412	hgsc.bcm.edu	37	chr20	23345920	23345920	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	aaagcagggccggaggaggaAgaggaggaggaggaggagga	23	3	0	1	rs547594353|rs146870841	byFrequency	TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr20:23345920A>G	ENST00000338121.5	+	2	977	c.900A>G	c.(898-900)gaA>gaG	p.E300E	GZF1_ENST00000544236.1_Intron|GZF1_ENST00000542987.1_Intron|GZF1_ENST00000461789.1_3'UTR|GZF1_ENST00000377051.2_Silent_p.E300E			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	300					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					Cggaggaggaagaggaggagg	0.527																																					p.E300E		Atlas-SNP	.											.,1	GZF1	61	.	0			c.A900G						.	A		0,4406		0,0,2203	48	53	52		900	-8	0	20	dbSNP_134	52	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous	GZF1	NM_022482.3		0,3,6500	GG,GA,AA		0.0349,0.0,0.0231		300/712	23345920	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	64412	exon1			GGAGGAAGAGGAG	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	15808	protein-coding gene	gene with protein product		613842	"zinc finger protein 336"	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.900A>G	chr20.hg19:g.23345920A>G		98.0	0.0		93.0	4.0	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Silent	SNP	ENST00000338121.5	hg19	CCDS13151.1																																																																																			.	A|1.000;G|0.000		0.527	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482		G	23345920	A	G	23345920	2	3	205	1	0	0	0	0	0	0	0	1	6923	69	3	2		2	GZF1	20	23345920	Silent	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10		23345920	39679600	47	29910										
POFUT1	23509	hgsc.bcm.edu	37	chr20	30803116	30803116	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ttcaagctggagcccctccaGgcttaccatcgggtcatcag	10	14	3	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr20:30803116G>A	ENST00000375749.3	+	3	353	c.291G>A	c.(289-291)caG>caA	p.Q97Q	POFUT1_ENST00000375730.3_Silent_p.Q97Q|POFUT1_ENST00000486717.1_3'UTR|POFUT1_ENST00000539210.1_Intron	NM_015352.1	NP_056167.1	Q9H488	OFUT1_HUMAN	protein O-fucosyltransferase 1	97					angiogenesis (GO:0001525)|embryo development (GO:0009790)|fucose metabolic process (GO:0006004)|heart development (GO:0007507)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|O-glycan processing (GO:0016266)|protein O-linked fucosylation (GO:0036066)|protein O-linked glycosylation (GO:0006493)|regulation of transcription, DNA-templated (GO:0006355)|somitogenesis (GO:0001756)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	6			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			AGCCCCTCCAGGCTTACCATC	0.577																																					p.Q97Q		Atlas-SNP	.											.	POFUT1	52	.	0			c.G291A						.						69	71	71					20																	30803116		2203	4300	6503	SO:0001819	synonymous_variant	23509	exon3			CCTCCAGGCTTAC	AF375884	CCDS13198.1, CCDS13199.1	20q11	2013-03-06			ENSG00000101346	ENSG00000101346	2.4.1.221	"Fucosyltransferases"	14988	protein-coding gene	gene with protein product	"peptide-O-fucosyltransferase", "GDP-fucose protein O-fucosyltransferase 1"	607491				9023546, 9525914	Standard	NM_015352		Approved	O-FUT, O-Fuc-T, KIAA0180, FUT12	uc002wxp.3	Q9H488	OTTHUMG00000133268	ENST00000375749.3:c.291G>A	chr20.hg19:g.30803116G>A		91.0	0.0		96.0	32.0	NM_172236	A8K4R8|E1P5M4|Q14685|Q5W185|Q9BW76	Silent	SNP	ENST00000375749.3	hg19	CCDS13198.1																																																																																			.	.		0.577	POFUT1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078613.1	NM_015352		A	30803116	G	A	30803116	2	1	205	1	0	0	0	0	0	0	0	1	12192	991	35	3		3	POFUT1	20	30803116	Silent	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10	7457196	30803116	32222404	48	29911										
SIM2	6493	hgsc.bcm.edu	37	chr21	38098520	38098520	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ggggctggtggccgtgggccAgtcgctgccacccagtgcca	17	14	0	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr21:38098520A>G	ENST00000290399.6	+	6	1257	c.644A>G	c.(643-645)cAg>cGg	p.Q215R	SIM2_ENST00000430056.3_Missense_Mutation_p.Q215R	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	215					cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						GCCGTGGGCCAGTCGCTGCCA	0.547																																					p.Q215R		Atlas-SNP	.											.	SIM2	55	.	0			c.A644G						.						117	100	106					21																	38098520		2203	4300	6503	SO:0001583	missense	6493	exon6			TGGGCCAGTCGCT		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"Basic helix-loop-helix proteins"	10883	protein-coding gene	gene with protein product	"transcription factor SIM2"	600892	"single-minded (Drosophila) homolog 2", "single-minded homolog 2 (Drosophila)"	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.644A>G	chr21.hg19:g.38098520A>G	ENSP00000290399:p.Gln215Arg	33.0	0.0		24.0	17.0	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Missense_Mutation	SNP	ENST00000290399.6	hg19	CCDS13646.1	.	.	.	.	.	.	.	.	.	.	A	18.93	3.728607	0.69074	.	.	ENSG00000159263	ENST00000290399;ENST00000430056	T;T	0.71341	-0.56;-0.56	5.44	5.44	0.79542	.	0.050554	0.85682	D	0.000000	T	0.65354	0.2683	N	0.16368	0.405	0.49299	D	0.999777	P;P	0.50943	0.94;0.868	P;P	0.49752	0.621;0.572	T	0.71573	-0.4552	10	0.72032	D	0.01	.	15.804	0.78477	1.0:0.0:0.0:0.0	.	215;215	Q14190;Q14190-2	SIM2_HUMAN;.	R	215	ENSP00000290399:Q215R;ENSP00000404176:Q215R	ENSP00000290399:Q215R	Q	+	2	0	SIM2	37020390	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.732000	0.91534	2.193000	0.70182	0.533000	0.62120	CAG	.	.		0.547	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586		G	38098520	A	G	38098520	3	3	205	1	0	0	0	0	1	0	0	0	14339	188	7	2	666	2	SIM2	21	38098520	Missense_Mutation	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10		38098520	10031375	49	29912										
MX2	4600	hgsc.bcm.edu	37	chr21	42770888	42770888	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gaaggcgaccgaggagctgcGgcgttgcggggctgacatcc	18	11	0	1	rs368866145		TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chr21:42770888G>A	ENST00000330714.3	+	9	1398	c.1214G>A	c.(1213-1215)cGg>cAg	p.R405Q	MX2_ENST00000496774.1_3'UTR	NM_002463.1	NP_002454.1	P20592	MX2_HUMAN	MX dynamin-like GTPase 2	405					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|GTP catabolic process (GO:0006184)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of nucleocytoplasmic transport (GO:0046822)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	34		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				GAGGAGCTGCGGCGTTGCGGG	0.527																																					p.R405Q		Atlas-SNP	.											.	MX2	84	.	0			c.G1214A						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	81	86	85		1214	-1.2	0	21		85	0,8600		0,0,4300	no	missense	MX2	NM_002463.1	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	405/716	42770888	1,13005	2203	4300	6503	SO:0001583	missense	4600	exon9			AGCTGCGGCGTTG		CCDS13672.1	21q22.3	2014-07-15	2014-07-15		ENSG00000183486	ENSG00000183486			7533	protein-coding gene	gene with protein product	"interferon-regulated resistance GTP-binding protein MXB", "second interferon-induced protein p78"	147890	"myxovirus (influenza) resistance 2, homolog of murine", "myxovirus (influenza virus) resistance 2 (mouse)"			2481229, 8798556	Standard	NM_002463		Approved	MXB	uc002yzf.1	P20592	OTTHUMG00000086753	ENST00000330714.3:c.1214G>A	chr21.hg19:g.42770888G>A	ENSP00000333657:p.Arg405Gln	87.0	0.0		55.0	5.0	NM_002463	B7Z5D3|D3DSI7	Missense_Mutation	SNP	ENST00000330714.3	hg19	CCDS13672.1	.	.	.	.	.	.	.	.	.	.	G	1.743	-0.491252	0.04322	2.27E-4	0.0	ENSG00000183486	ENST00000330714	T	0.72051	-0.62	4.09	-1.23	0.09465	Dynamin central domain (1);	0.433164	0.24688	N	0.036403	T	0.40743	0.1129	N	0.11023	0.085	0.21762	N	0.999556	B	0.19331	0.035	B	0.19148	0.024	T	0.37009	-0.9724	10	0.02654	T	1	-8.565	9.0138	0.36157	0.6122:0.0:0.3878:0.0	.	405	P20592	MX2_HUMAN	Q	405	ENSP00000333657:R405Q	ENSP00000333657:R405Q	R	+	2	0	MX2	41692758	0.001000	0.12720	0.017000	0.16124	0.023000	0.10783	-0.185000	0.09684	-0.402000	0.07633	0.591000	0.81541	CGG	.	.		0.527	MX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195147.1	NM_002463		A	42770888	G	A	42770888	3	1	205	1	0	0	0	0	1	0	0	0	10007	1116	39	1	1244	1	MX2	21	42770888	Missense_Mutation	SNP	G	TCGA-DD-AADY-01A-11D-A40R-10	4672368	42770888	5359007	50	29913										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	6069247	6069247	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gggggttctgggggctgaaaCcgcctctctccagtgggggg	19	10	2	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chrX:6069247C>G	ENST00000381095.3	-	2	888	c.261G>C	c.(259-261)cgG>cgC	p.R87R	NLGN4X_ENST00000381093.2_Silent_p.R87R|NLGN4X_ENST00000538097.1_Silent_p.R87R|NLGN4X_ENST00000469740.1_5'UTR|NLGN4X_ENST00000381092.1_Silent_p.R87R|NLGN4X_ENST00000275857.6_Silent_p.R87R	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	87					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						GGGGCTGAAACCGCCTCTCTC	0.577																																					p.R87R		Atlas-SNP	.											.	NLGN4X	191	.	0			c.G261C						.						68	63	65					X																	6069247		2203	4300	6503	SO:0001819	synonymous_variant	57502	exon2			CTGAAACCGCCTC	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.261G>C	chrX.hg19:g.6069247C>G		203.0	0.0		176.0	73.0	NM_181332	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	hg19	CCDS14126.1																																																																																			.	.		0.577	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		G	6069247	C	G	6069247	2	3	205	1	0	0	0	0	0	0	0	1	10473	494	18	4		4	NLGN4X	23	6069247	Silent	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10		6069247	149201313	51	29914										
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27766594	27766594	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	cccacccttacctacctgtgTtggcgtgcagtggcctagat	10	14	0	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chrX:27766594T>C	ENST00000451261.2	+	5	1981	c.1582T>C	c.(1582-1584)Ttg>Ctg	p.L528L		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	528										central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						CCTACCTGTGTTGGCGTGCAG	0.468																																					p.L528L		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.T1582C						.						155	115	127					X																	27766594		692	1591	2283	SO:0001819	synonymous_variant	347442	exon1			CCTGTGTTGGCGT		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1582T>C	chrX.hg19:g.27766594T>C		227.0	0.0		214.0	97.0	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.468	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		C	27766594	T	C	27766594	2	2	205	1	0	0	0	0	0	0	0	1	4280	1722	60	2		2	DCAF8L2	23	27766594	Silent	SNP	T	TCGA-DD-AADY-01A-11D-A40R-10	21697347	27766594	127503966	52	29915										
AR	367	hgsc.bcm.edu	37	chrX	66765173	66765173	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	gctgctgcagcagcagcagcAgcagcagcagcagcagcagc	14	14	0	0			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chrX:66765173A>T	ENST00000374690.3	+	1	709	c.185A>T	c.(184-186)cAg>cTg	p.Q62L	AR_ENST00000504326.1_Missense_Mutation_p.Q62L|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q62L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	62	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q62L		Atlas-SNP	.											.	AR	249	.	0			c.A185T						.						5	9	7					X																	66765173		1734	3384	5118	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.185A>T	chrX.hg19:g.66765173A>T	ENSP00000363822:p.Gln62Leu	171.0	0.0		155.0	14.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	13.85	2.358892	0.41801	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.69306	-0.39;-0.39;-0.39	.	.	.	.	1.296110	0.05656	N	0.585987	T	0.58850	0.2151	N	0.19112	0.55	0.09310	N	0.999999	P;P;.	0.43431	0.807;0.458;.	P;B;.	0.53518	0.728;0.245;.	T	0.51180	-0.8738	8	0.11485	T	0.65	.	.	.	.	.	62;62;60	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	62	ENSP00000363822:Q62L;ENSP00000421155:Q62L;ENSP00000379359:Q62L	ENSP00000363822:Q62L	Q	+	2	0	AR	66681898	0.984000	0.35163	0.863000	0.33907	0.539000	0.34962	1.220000	0.32491	0.000000	0.14550	0.000000	0.15137	CAG	.	.		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765173	A	T	66765173	3	4	205	1	0	0	0	0	1	0	0	0	836	188	7	4	187	4	AR	23	66765173	Missense_Mutation	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10	38998579	66765173	88505387	53	29916										
ATP2B3	492	hgsc.bcm.edu	37	chrX	152825344	152825344	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ctcccgcaccatgatgaagaAcattctgggccacgccgtgt	10	14	1	3			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chrX:152825344A>T	ENST00000349466.2	+	17	3109	c.2783A>T	c.(2782-2784)aAc>aTc	p.N928I	ATP2B3_ENST00000393842.1_Missense_Mutation_p.N914I|ATP2B3_ENST00000359149.3_Missense_Mutation_p.N928I|ATP2B3_ENST00000263519.4_Missense_Mutation_p.N928I|ATP2B3_ENST00000370186.1_Missense_Mutation_p.N914I|ATP2B3_ENST00000370181.2_Missense_Mutation_p.N914I|ATP2B3_ENST00000460549.1_3'UTR			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	928					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ATGATGAAGAACATTCTGGGC	0.642																																					p.N928I		Atlas-SNP	.											.	ATP2B3	552	.	0			c.A2783T						.						109	81	91					X																	152825344		2203	4300	6503	SO:0001583	missense	492	exon16			TGAAGAACATTCT	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"ATPases / P-type"	816	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 3", "cilia and flagella associated protein 39"	300014	"spinocerebellar ataxia, X-linked 1", "cerebellar ataxia 2 (X-linked)"	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.2783A>T	chrX.hg19:g.152825344A>T	ENSP00000343886:p.Asn928Ile	110.0	0.0		93.0	10.0	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Missense_Mutation	SNP	ENST00000349466.2	hg19	CCDS35440.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443766	0.83993	.	.	ENSG00000067842	ENST00000370186;ENST00000349466;ENST00000393842;ENST00000359149;ENST00000263519;ENST00000370181	D;D;D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89;-3.89;-3.89	5.32	5.32	0.75619	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.98632	0.9542	H	0.98866	4.355	0.58432	D	0.999999	D;D	0.65815	0.992;0.995	D;D	0.68192	0.935;0.956	D	0.99191	1.0870	10	0.87932	D	0	-46.4032	13.2544	0.60070	1.0:0.0:0.0:0.0	.	928;928	Q16720;Q16720-2	AT2B3_HUMAN;.	I	914;928;914;928;928;914	ENSP00000359205:N914I;ENSP00000343886:N928I;ENSP00000377425:N914I;ENSP00000352062:N928I;ENSP00000263519:N928I;ENSP00000359200:N914I	ENSP00000263519:N928I	N	+	2	0	ATP2B3	152478538	1.000000	0.71417	0.998000	0.56505	0.830000	0.47004	9.252000	0.95491	1.771000	0.52183	0.430000	0.28490	AAC	.	.		0.642	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		T	152825344	A	T	152825344	3	4	205	1	0	0	0	0	1	0	0	0	1141	43	2	4	2845	4	ATP2B3	23	152825344	Missense_Mutation	SNP	A	TCGA-DD-AADY-01A-11D-A40R-10	86060171	152825344	2445216	54	29917										
UBL4A	8266	hgsc.bcm.edu	37	chrX	153714302	153714302	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	1.03370078740157	3.44566929133858	0.430708661417323	1	1	0	ttgggcccgatgctataatcCgagagtcgtttcccatctgc	10	12	1	1			TCGA-DD-AADY-01A-11D-A40R-10	TCGA-DD-AADY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	43286c0b-a477-4ef8-91a6-7a6703b6d1d8	2ffa15b7-17be-48ce-a5af-e25e022f0bb2	g.chrX:153714302C>T	ENST00000369660.4	-	3	256	c.171G>A	c.(169-171)tcG>tcA	p.S57S	UBL4A_ENST00000477777.1_5'UTR|UBL4A_ENST00000369653.4_Silent_p.S57S	NM_014235.3	NP_055050.1	P11441	UBL4A_HUMAN	ubiquitin-like 4A	57	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				cellular protein modification process (GO:0006464)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)	small conjugating protein ligase activity (GO:0019787)			endometrium(5)|lung(1)|urinary_tract(1)	7	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGCTATAATCCGAGAGTCGTT	0.647																																					p.S57S	Esophageal Squamous(74;88 1215 11149 34177 46777)	Atlas-SNP	.											.	UBL4A	12	.	0			c.G171A						.						81	76	78					X																	153714302		2202	4300	6502	SO:0001819	synonymous_variant	8266	exon3			ATAATCCGAGAGT	J03589	CCDS14754.1	Xq28	2010-08-05	2005-09-27	2005-09-27	ENSG00000102178	ENSG00000102178			12505	protein-coding gene	gene with protein product		312070	"ubiquitin-like 4"	UBL4		2829204, 16872915	Standard	NM_014235		Approved	GDX, DXS254E, GET5, MDY2, TMA24	uc004flo.3	P11441	OTTHUMG00000013370	ENST00000369660.4:c.171G>A	chrX.hg19:g.153714302C>T		45.0	0.0		42.0	23.0	NM_014235	Q5HY80	Silent	SNP	ENST00000369660.4	hg19	CCDS14754.1																																																																																			.	.		0.647	UBL4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037238.2	NM_014235		T	153714302	C	T	153714302	2	4	205	1	0	0	0	0	0	0	0	1	16902	639	23	1		1	UBL4A	23	153714302	Silent	SNP	C	TCGA-DD-AADY-01A-11D-A40R-10	888958	153714302	1556258	55	29918										
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21183930	21183930	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ggaattttgaggggtccagtAcccgactgttcttggcccct	12	11	1	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr1:21183930A>G	ENST00000264211.8	-	19	3331	c.3137T>C	c.(3136-3138)gTa>gCa	p.V1046A	EIF4G3_ENST00000602326.1_Missense_Mutation_p.V1052A|EIF4G3_ENST00000374937.3_Missense_Mutation_p.V1052A|EIF4G3_ENST00000400422.1_Missense_Mutation_p.V1046A|EIF4G3_ENST00000537738.1_Missense_Mutation_p.V536A|EIF4G3_ENST00000374935.3_Missense_Mutation_p.V766A|EIF4G3_ENST00000536266.1_Missense_Mutation_p.V650A	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1046					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		GGGGTCCAGTACCCGACTGTT	0.458																																					p.V1082A		Atlas-SNP	.											.	EIF4G3	300	.	0			c.T3245C						.						264	264	264					1																	21183930		2203	4300	6503	SO:0001583	missense	8672	exon23			TCCAGTACCCGAC	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.3137T>C	chr1.hg19:g.21183930A>G	ENSP00000264211:p.Val1046Ala	88.0	0.0		74.0	24.0	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	hg19	CCDS214.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.548365	0.65311	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266	T;T;T;T;T;T	0.06449	3.87;3.87;3.69;3.3;3.87;3.56	5.84	5.84	0.93424	.	0.119534	0.64402	D	0.000020	T	0.07413	0.0187	N	0.22421	0.69	0.80722	D	1	D;B;P;P;P	0.54047	0.964;0.406;0.73;0.905;0.575	P;B;B;B;B	0.50162	0.633;0.108;0.406;0.292;0.195	T	0.19192	-1.0313	10	0.05525	T	0.97	-12.0631	16.2159	0.82217	1.0:0.0:0.0:0.0	.	1241;766;650;1052;1046	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	A	1046;1242;1046;766;536;1052;650	ENSP00000264211:V1046A;ENSP00000383274:V1046A;ENSP00000364071:V766A;ENSP00000442010:V536A;ENSP00000364073:V1052A;ENSP00000444693:V650A	ENSP00000264211:V1046A	V	-	2	0	EIF4G3	21056517	1.000000	0.71417	0.948000	0.38648	0.988000	0.76386	5.170000	0.64990	2.243000	0.73865	0.533000	0.62120	GTA	.	.		0.458	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		G	21183930	A	G	21183930	3	3	206	1	0	0	0	0	1	0	0	0	5040	391	14	2	1672	2	EIF4G3	1	21183930	Missense_Mutation	SNP	A	TCGA-DD-AAE0-01A-11D-A40R-10		21183930	228066691	1	29919										
AHDC1	27245	hgsc.bcm.edu	37	chr1	27877569	27877569	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ccagtgggcagtgccccaggGgctgctggggctccagacgg	18	13	0	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr1:27877569G>A	ENST00000247087.5	-	5	1654	c.1058C>T	c.(1057-1059)cCc>cTc	p.P353L	AHDC1_ENST00000374011.2_Missense_Mutation_p.P353L			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	353	Pro-rich.						DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GTGCCCCAGGGGCTGCTGGGG	0.711																																					p.P353L		Atlas-SNP	.											.	AHDC1	98	.	0			c.C1058T						.						6	6	6					1																	27877569		1972	3949	5921	SO:0001583	missense	27245	exon6			CCCAGGGGCTGCT	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.1058C>T	chr1.hg19:g.27877569G>A	ENSP00000247087:p.Pro353Leu	88.0	0.0		70.0	16.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	hg19	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.425948	0.62733	.	.	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.44482	0.92;0.92	5.05	5.05	0.67936	.	0.414010	0.17632	U	0.167352	T	0.29556	0.0737	N	0.14661	0.345	0.44061	D	0.996806	P	0.50819	0.939	P	0.47206	0.541	T	0.04885	-1.0920	10	0.02654	T	1	-3.7732	15.4245	0.75041	0.0:0.0:1.0:0.0	.	353	Q5TGY3	AHDC1_HUMAN	L	353	ENSP00000247087:P353L;ENSP00000363123:P353L	ENSP00000247087:P353L	P	-	2	0	AHDC1	27750156	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	2.750000	0.47500	2.630000	0.89119	0.591000	0.81541	CCC	.	.		0.711	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			A	27877569	G	A	27877569	3	1	206	1	0	0	0	0	1	0	0	0	412	1232	43	3	3757	3	AHDC1	1	27877569	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	6693639	27877569	221373052	2	29920										
IFI44L	10964	hgsc.bcm.edu	37	chr1	79095456	79095456	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gactataggccctatgcagaCttggtttcagaaattcgtat	9	8	1	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr1:79095456C>A	ENST00000370751.5	+	4	758	c.579C>A	c.(577-579)gaC>gaA	p.D193E	IFI44L_ENST00000342282.3_De_novo_Start_InFrame|IFI44L_ENST00000476521.1_3'UTR	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	193					defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)				endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						CCTATGCAGACTTGGTTTCAG	0.398																																					p.D193E		Atlas-SNP	.											.	IFI44L	93	.	0			c.C579A						.						124	123	123					1																	79095456		2203	4300	6503	SO:0001583	missense	10964	exon4			TGCAGACTTGGTT	AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"chromosome 1 open reading frame 29"	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.579C>A	chr1.hg19:g.79095456C>A	ENSP00000359787:p.Asp193Glu	54.0	0.0		68.0	28.0	NM_006820	Q86TE1|Q96B64|Q99984	Missense_Mutation	SNP	ENST00000370751.5	hg19	CCDS687.2	.	.	.	.	.	.	.	.	.	.	C	9.473	1.096031	0.20552	.	.	ENSG00000137959	ENST00000370751;ENST00000450498	T;T	0.13307	2.79;2.6	2.95	-0.198	0.13224	.	0.993614	0.08173	N	0.986682	T	0.02767	0.0083	L	0.36672	1.1	0.09310	N	0.999998	B	0.24258	0.1	B	0.18263	0.021	T	0.45483	-0.9258	10	0.36615	T	0.2	-0.0486	3.224	0.06725	0.0:0.3998:0.2142:0.386	.	193	Q53G44	IF44L_HUMAN	E	193;170	ENSP00000359787:D193E;ENSP00000400784:D170E	ENSP00000359787:D193E	D	+	3	2	IFI44L	78868044	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	-0.388000	0.07352	-0.030000	0.13804	-0.362000	0.07510	GAC	.	.		0.398	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820		A	79095456	C	A	79095456	3	1	206	1	0	0	0	0	1	0	0	0	7527	564	20	3	589	3	IFI44L	1	79095456	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	51217887	79095456	170155165	3	29921										
SLC22A15	55356	hgsc.bcm.edu	37	chr1	116574049	116574049	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	actgagtgaggctgaagaggCgctgtacctcattgccaaga	13	9	1	5			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr1:116574049C>T	ENST00000369503.4	+	6	921	c.791C>T	c.(790-792)gCg>gTg	p.A264V	SLC22A15_ENST00000369502.1_3'UTR	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	264					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		GCTGAAGAGGCGCTGTACCTC	0.483																																					p.A264V		Atlas-SNP	.											.	SLC22A15	65	.	0			c.C791T						.						93	94	93					1																	116574049		1997	4174	6171	SO:0001583	missense	55356	exon6			AAGAGGCGCTGTA	AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"Solute carriers"	20301	protein-coding gene	gene with protein product		608275	"solute carrier family 22 (organic cation transporter), member 15"			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.791C>T	chr1.hg19:g.116574049C>T	ENSP00000358515:p.Ala264Val	116.0	0.0		81.0	24.0	NM_018420	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Missense_Mutation	SNP	ENST00000369503.4	hg19	CCDS44198.1	.	.	.	.	.	.	.	.	.	.	C	3.565	-0.088817	0.07097	.	.	ENSG00000163393	ENST00000369503	T	0.58940	0.3	4.81	4.81	0.61882	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.174931	0.51477	D	0.000084	T	0.12050	0.0293	N	0.00152	-1.975	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.11470	-1.0586	10	0.41790	T	0.15	.	18.0583	0.89369	0.0:1.0:0.0:0.0	.	264	Q8IZD6	S22AF_HUMAN	V	264	ENSP00000358515:A264V	ENSP00000358515:A264V	A	+	2	0	SLC22A15	116375572	0.994000	0.37717	0.091000	0.20842	0.575000	0.36095	3.396000	0.52565	2.498000	0.84270	0.655000	0.94253	GCG	.	.		0.483	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420		T	116574049	C	T	116574049	3	4	206	1	0	0	0	0	1	0	0	0	14461	768	27	1	813	1	SLC22A15	1	116574049	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	37478593	116574049	132676572	4	29922										
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156521882	156521882	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gcaatttcagcagggcatcgAagtaactggcagtggggtga	15	7	1	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr1:156521882A>G	ENST00000361170.2	-	14	1464	c.1454T>C	c.(1453-1455)tTc>tCc	p.F485S		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	485					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAGGGCATCGAAGTAACTGGC	0.542																																					p.F485S		Atlas-SNP	.											.	IQGAP3	146	.	0			c.T1454C						.						84	68	74					1																	156521882		2203	4300	6503	SO:0001583	missense	128239	exon14			GCATCGAAGTAAC	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.1454T>C	chr1.hg19:g.156521882A>G	ENSP00000354451:p.Phe485Ser	49.0	0.0		127.0	16.0	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	hg19	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.807783	0.50421	.	.	ENSG00000183856	ENST00000361170	T	0.06768	3.26	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.15565	0.0375	M	0.73598	2.24	0.50813	D	0.999891	D	0.71674	0.998	D	0.75484	0.986	T	0.05886	-1.0858	10	0.22109	T	0.4	-10.4453	12.688	0.56958	1.0:0.0:0.0:0.0	.	485	Q86VI3	IQGA3_HUMAN	S	485	ENSP00000354451:F485S	ENSP00000354451:F485S	F	-	2	0	IQGAP3	154788506	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	7.779000	0.85648	1.867000	0.54127	0.379000	0.24179	TTC	.	.		0.542	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		G	156521882	A	G	156521882	3	3	206	1	0	0	0	0	1	0	0	0	7825	246	9	2	3541	2	IQGAP3	1	156521882	Missense_Mutation	SNP	A	TCGA-DD-AAE0-01A-11D-A40R-10	39947833	156521882	92728739	5	29923										
ADCY10	55811	hgsc.bcm.edu	37	chr1	167830128	167830128	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	cctgaacatggaaaatgtcaTtaagaagacagtagaacttt	8	6	1	4			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr1:167830128T>C	ENST00000367851.4	-	15	1974	c.1790A>G	c.(1789-1791)aAt>aGt	p.N597S	ADCY10_ENST00000545172.1_Missense_Mutation_p.N444S|ADCY10_ENST00000367848.1_Missense_Mutation_p.N505S	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	597					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						GAAAATGTCATTAAGAAGACA	0.408																																					p.N597S		Atlas-SNP	.											.	ADCY10	175	.	0			c.A1790G						.						187	172	177					1																	167830128		2203	4300	6503	SO:0001583	missense	55811	exon15			ATGTCATTAAGAA	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.1790A>G	chr1.hg19:g.167830128T>C	ENSP00000356825:p.Asn597Ser	103.0	0.0		221.0	40.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	hg19	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	T	15.11	2.736613	0.49045	.	.	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	T;T;T	0.37411	1.2;1.23;1.22	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000002	T	0.46521	0.1397	M	0.76328	2.33	0.29253	N	0.871829	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.83275	0.994;0.996;0.991	T	0.47824	-0.9087	9	0.22109	T	0.4	-31.5119	12.3958	0.55384	0.0:0.0:0.0:1.0	.	444;505;597	F5GWS5;Q96PN6-2;Q96PN6	.;.;ADCYA_HUMAN	S	444;597;505	ENSP00000441992:N444S;ENSP00000356825:N597S;ENSP00000356822:N505S	ENSP00000356822:N505S	N	-	2	0	ADCY10	166096752	1.000000	0.71417	0.719000	0.30619	0.214000	0.24535	3.942000	0.56614	2.237000	0.73441	0.460000	0.39030	AAT	.	.		0.408	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		C	167830128	T	C	167830128	3	2	206	1	0	0	0	0	1	0	0	0	293	1493	52	2	3118	2	ADCY10	1	167830128	Missense_Mutation	SNP	T	TCGA-DD-AAE0-01A-11D-A40R-10	11308246	167830128	81420493	6	29924										
LRRN2	10446	hgsc.bcm.edu	37	chr1	204589034	204589034	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tggcaggcacactgagggggGcagggaacatgccagggtac	18	9	0	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr1:204589034G>A	ENST00000367175.1	-	1	2299	c.87C>T	c.(85-87)tgC>tgT	p.C29C	LRRN2_ENST00000367176.3_Silent_p.C29C|LRRN2_ENST00000496057.1_5'UTR|LRRN2_ENST00000367177.3_Silent_p.C29C			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	29	LRRNT.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			ACTGAGGGGGGCAGGGAACAT	0.647																																					p.C29C		Atlas-SNP	.											.	LRRN2	81	.	0			c.C87T						.						24	27	26					1																	204589034		2203	4300	6503	SO:0001819	synonymous_variant	10446	exon3			AGGGGGGCAGGGA	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"Immunoglobulin superfamily / I-set domain containing"	16914	protein-coding gene	gene with protein product	"leucine rich and ankyrin repeats 1", "fibronectin type III, immunoglobulin and leucine rich repeat domain 7"	605492	"leucine rich repeat neuronal 5"	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.87C>T	chr1.hg19:g.204589034G>A		90.0	0.0		139.0	25.0	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Silent	SNP	ENST00000367175.1	hg19	CCDS1448.1																																																																																			.	.		0.647	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338		A	204589034	G	A	204589034	2	1	206	1	0	0	0	0	0	0	0	1	9044	1195	42	3		3	LRRN2	1	204589034	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	36758906	204589034	44661587	7	29925										
ADI1	55256	hgsc.bcm.edu	37	chr2	3523232	3523232	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tgccgcgggtcgcccggggcGtcgtccatataccaggcctg	15	15	0	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr2:3523232G>A	ENST00000327435.6	-	1	275	c.27C>T	c.(25-27)gaC>gaT	p.D9D	AC142528.1_ENST00000450917.1_RNA|ADI1_ENST00000382093.5_5'Flank	NM_018269.3	NP_060739.2			acireductone dioxygenase 1											breast(2)|large_intestine(2)|lung(4)|ovary(1)|stomach(1)	10	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0729)|Epithelial(75;0.173)|all cancers(51;0.228)		CGCCCGGGGCGTCGTCCATAT	0.721																																					p.D9D		Atlas-SNP	.											.	ADI1	12	.	0			c.C27T						.						3	4	4					2																	3523232		1891	3818	5709	SO:0001819	synonymous_variant	55256	exon1			CGGGGCGTCGTCC		CCDS1653.1	2p25.2	2013-05-29			ENSG00000182551	ENSG00000182551	1.13.11.54		30576	protein-coding gene	gene with protein product	"membrane-type 1 matrix metalloproteinase cytoplasmic tail binding protein-1"	613400				14718544, 15938715	Standard	NM_018269		Approved	SIPL, MTCBP-1, ARD, APL1, FLJ10913, HMFT1638, mtnD	uc002qxp.4	Q9BV57	OTTHUMG00000112441	ENST00000327435.6:c.27C>T	chr2.hg19:g.3523232G>A		95.0	0.0		64.0	15.0	NM_018269		Silent	SNP	ENST00000327435.6	hg19	CCDS1653.1																																																																																			.	.		0.721	ADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000231914.6	NM_018269		A	3523232	G	A	3523232	2	1	206	1	0	0	0	0	0	0	0	1	315	1136	40	1		1	ADI1	2	3523232	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10		3523232	239676141	8	29926										
C2orf39	92749	hgsc.bcm.edu	37	chr2	26652600	26652600	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gaacaggtgaagaatgtgatGaaaacctttcgtgaggagct	13	5	0	5			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr2:26652600G>A	ENST00000288710.2	+	5	719	c.645G>A	c.(643-645)atG>atA	p.M215I		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	215					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											AGAATGTGATGAAAACCTTTC	0.468																																					p.M215I		Atlas-SNP	.											.	CCDC164	84	.	0			c.G645A						.						115	114	115					2																	26652600		2203	4300	6503	SO:0001583	missense	92749	exon5			TGTGATGAAAACC	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"chromosome 2 open reading frame 39", "coiled-coil domain containing 164", "dynein regulatory complex subunit 1 homolog (Chlamydomonas)"	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.645G>A	chr2.hg19:g.26652600G>A	ENSP00000288710:p.Met215Ile	102.0	0.0		99.0	28.0	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	hg19	CCDS1723.1	.	.	.	.	.	.	.	.	.	.	G	6.623	0.483423	0.12581	.	.	ENSG00000157856	ENST00000288710	T	0.14144	2.53	5.35	2.97	0.34412	.	0.547632	0.21139	N	0.079515	T	0.06096	0.0158	N	0.04043	-0.29	0.09310	N	0.999995	B	0.10296	0.003	B	0.11329	0.006	T	0.29640	-1.0005	10	0.37606	T	0.19	-26.4115	9.1544	0.36983	0.0871:0.2939:0.619:0.0	.	215	Q96MC2	CC164_HUMAN	I	215	ENSP00000288710:M215I	ENSP00000288710:M215I	M	+	3	0	CCDC164	26506104	0.980000	0.34600	0.450000	0.26969	0.673000	0.39480	0.508000	0.22692	2.506000	0.84524	0.563000	0.77884	ATG	.	.		0.468	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038		A	26652600	G	A	26652600	3	1	206	1	0	0	0	0	1	0	0	0	2166	1290	45	3	663	3	C2orf39	2	26652600	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	23129368	26652600	216546773	9	29927										
C2orf28	8884	hgsc.bcm.edu	37	chr2	27435079	27435079	+	5'UTR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	agggctagggcgcatgaagaCcagcgcagagctccacgagc	15	12	0	3			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr2:27435079C>G	ENST00000310574.3	-	0	75				ATRAID_ENST00000405489.3_5'Flank|ATRAID_ENST00000380171.3_Missense_Mutation_p.T3S|ATRAID_ENST00000606999.1_5'Flank|SLC5A6_ENST00000408041.1_5'Flank	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6						biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	CGCATGAAGACCAGCGCAGAG	0.687																																					p.T3S		Atlas-SNP	.											.	.	.	.	0			c.C8G						.						5	7	7					2																	27435079		2097	4100	6197	SO:0001623	5_prime_UTR_variant	51374	exon1			TGAAGACCAGCGC	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.-399G>C	chr2.hg19:g.27435079C>G		254.0	0.0		272.0	21.0	NM_080592	B2RB85|D6W549|Q969Y5	Missense_Mutation	SNP	ENST00000310574.3	hg19	CCDS1740.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995925	0.35226	.	.	ENSG00000138085	ENST00000380171	T	0.47528	0.84	4.37	-6.28	0.02020	.	1.080330	0.07297	N	0.873370	T	0.25344	0.0616	N	0.19112	0.55	0.09310	N	0.999995	B	0.18610	0.029	B	0.18871	0.023	T	0.26985	-1.0087	10	0.87932	D	0	-0.3751	2.4066	0.04414	0.361:0.1478:0.3724:0.1188	.	3	Q6UW56-3	.	S	3	ENSP00000369518:T3S	ENSP00000369518:T3S	T	+	2	0	C2orf28	27288583	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.582000	0.02117	-1.325000	0.02269	-0.367000	0.07326	ACC	.	.		0.687	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095		G	27435079	C	G	27435079	1	3	206	0	1	0	0	0	0	0	0	0	2162	507	18	4		4	C2orf28	2	27435079	5'UTR	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	782479	27435079	215764294	10	29928										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141200109	141200109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tgatgcatctgcacagtctgGatcctcgtcacaaacccaca	7	14	3	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr2:141200109G>A	ENST00000389484.3	-	66	11349	c.10378C>T	c.(10378-10380)Cca>Tca	p.P3460S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3460	LDL-receptor class A 24. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GCACAGTCTGGATCCTCGTCA	0.478										TSP Lung(27;0.18)																											p.P3460S	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C10378T						.						157	144	149					2																	141200109		2203	4300	6503	SO:0001583	missense	53353	exon66			AGTCTGGATCCTC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.10378C>T	chr2.hg19:g.141200109G>A	ENSP00000374135:p.Pro3460Ser	102.0	0.0		93.0	18.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.280604	0.59758	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.95518	-3.73	5.33	4.45	0.53987	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.144839	0.47093	U	0.000253	D	0.90010	0.6881	L	0.28608	0.87	0.39828	D	0.972933	P	0.39352	0.669	B	0.38378	0.272	D	0.86729	0.1947	10	0.18710	T	0.47	.	8.8307	0.35082	0.0754:0.0:0.7758:0.1488	.	3460	Q9NZR2	LRP1B_HUMAN	S	3460;3398	ENSP00000374135:P3460S	ENSP00000374135:P3460S	P	-	1	0	LRP1B	140916579	1.000000	0.71417	0.976000	0.42696	0.996000	0.88848	5.446000	0.66600	1.238000	0.43771	0.557000	0.71058	CCA	.	.		0.478	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141200109	G	A	141200109	3	1	206	1	0	0	0	0	1	0	0	0	8964	1174	41	3	3525	3	LRP1B	2	141200109	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	113765030	141200109	101999264	11	29929										
KIF5C	3800	hgsc.bcm.edu	37	chr2	149806841	149806841	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	taaatagaaaacacatgtgcCataccgggacagcaagatga	9	8	0	3			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr2:149806841C>T	ENST00000435030.1	+	10	1201	c.833C>T	c.(832-834)cCa>cTa	p.P278L	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000414838.2_Missense_Mutation_p.P183L|KIF5C_ENST00000397413.1_Missense_Mutation_p.P46L			O60282	KIF5C_HUMAN	kinesin family member 5C	278	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		ACACATGTGCCATACCGGGAC	0.448																																					p.P278L		Atlas-SNP	.											.	KIF5C	166	.	0			c.C833T						.						104	101	102					2																	149806841		1898	4134	6032	SO:0001583	missense	3800	exon10			ATGTGCCATACCG	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.833C>T	chr2.hg19:g.149806841C>T	ENSP00000393379:p.Pro278Leu	45.0	0.0		62.0	5.0	NM_004522	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	hg19		.	.	.	.	.	.	.	.	.	.	C	32	5.178799	0.94846	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	D;D;D	0.83335	-1.71;-1.71;-1.71	5.65	5.65	0.86999	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.91935	0.7446	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92016	0.5622	9	0.87932	D	0	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	278	O60282	KIF5C_HUMAN	L	278;183;181;46	ENSP00000393379:P278L;ENSP00000410115:P183L;ENSP00000380560:P46L	ENSP00000334176:P181L	P	+	2	0	KIF5C	149515087	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	7.651000	0.83577	2.941000	0.99782	0.655000	0.94253	CCA	.	.		0.448	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		T	149806841	C	T	149806841	3	4	206	1	0	0	0	0	1	0	0	0	8316	594	21	3	793	3	KIF5C	2	149806841	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	8606732	149806841	93392532	12	29930										
FEZF2	55079	hgsc.bcm.edu	37	chr3	62358214	62358215	+	In_Frame_Ins	INS	-	-	CCGCCG													0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ccccgccgccgccgccgccaINSccgccgccgccgcctccgcc							TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr3:62358214_62358215insCCGCCG	ENST00000283268.3	-	2	623_624	c.329_330insCGGCGG	c.(328-330)ggt>ggCGGCGGt	p.110_110G>GGG	FEZF2_ENST00000475839.1_In_Frame_Ins_p.110_110G>GGG|FEZF2_ENST00000486811.1_In_Frame_Ins_p.110_110G>GGG	NM_018008.3	NP_060478.3	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2	110	Gly-rich.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cerebral cortex GABAergic interneuron migration (GO:0021853)|dendrite development (GO:0016358)|dentate gyrus development (GO:0021542)|forebrain anterior/posterior pattern specification (GO:0021797)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|lung(8)|skin(1)	20		Lung SC(41;0.0262)		BRCA - Breast invasive adenocarcinoma(55;0.000221)|KIRC - Kidney renal clear cell carcinoma(15;0.00834)|Kidney(15;0.00957)		cgccgccgccaccgccgccgcc	0.728																																					p.G110delinsGGG	NSCLC(170;1772 2053 12525 15604 23984)	Atlas-INDEL	.											.	FEZF2	46	.	0			c.330_331insCGGCGG						.																																			SO:0001652	inframe_insertion	55079	exon2			.	AF064845	CCDS2897.1	3p21.1	2013-01-08	2006-08-15	2006-08-15	ENSG00000153266	ENSG00000153266		"Zinc fingers, C2H2-type"	13506	protein-coding gene	gene with protein product		607414	"zinc finger protein 312"	ZNF312			Standard	NM_018008		Approved	FLJ10142, FKSG36, TOF, FEZL, Zfp312	uc003dli.2	Q8TBJ5	OTTHUMG00000158705	ENST00000283268.3:c.324_329dupCGGCGG	chr3.hg19:g.62358215_62358220dupCCGCCG	ENSP00000283268:p.GlyGly116dup	33.0	0.0		46.0	16.0	NM_018008	A8K349|Q9BZ91|Q9NWB9	In_Frame_Ins	INS	ENST00000283268.3	hg19	CCDS2897.1																																																																																			.	.		0.728	FEZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351813.1	NM_018008		CCGCCG	62358215	-	CCGCCG	62358214	7	5	206	1	0	1	1	0	0	0	0	0	5834	146	6	0	1065	0	FEZF2	3	62358214	In_Frame_Ins	INS	-	TCGA-DD-AAE0-01A-11D-A40R-10		62358214	135664216	13	29931										
ZNF148	7707	hgsc.bcm.edu	37	chr3	124951547	124951547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	accaactattagtccaaagtGggacttatctggagttgttc	9	8	1	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr3:124951547G>A	ENST00000360647.4	-	9	2508	c.2023C>T	c.(2023-2025)Cac>Tac	p.H675Y	ZNF148_ENST00000497929.1_5'UTR|ZNF148_ENST00000468369.1_Intron|ZNF148_ENST00000492394.1_Missense_Mutation_p.H675Y|ZNF148_ENST00000485866.1_Missense_Mutation_p.H675Y|ZNF148_ENST00000484491.1_Missense_Mutation_p.H675Y|ZNF148_ENST00000544464.1_Intron|SLC12A8_ENST00000423114.2_Intron	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	675					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						AGTCCAAAGTGGGACTTATCT	0.438																																					p.H675Y		Atlas-SNP	.											.	ZNF148	84	.	0			c.C2023T						.						189	173	178					3																	124951547		2203	4300	6503	SO:0001583	missense	7707	exon9			CAAAGTGGGACTT	U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"Zinc fingers, C2H2-type"	12933	protein-coding gene	gene with protein product		601897	"zinc finger protein 148 (pHZ-52)"			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.2023C>T	chr3.hg19:g.124951547G>A	ENSP00000353863:p.His675Tyr	86.0	0.0		92.0	51.0	NM_021964	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Missense_Mutation	SNP	ENST00000360647.4	hg19	CCDS3031.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.514902	0.44763	.	.	ENSG00000163848	ENST00000360647;ENST00000484491;ENST00000492394;ENST00000485866	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.14	5.14	0.70334	.	0.047476	0.85682	D	0.000000	T	0.46444	0.1393	L	0.52573	1.65	0.80722	D	1	B	0.32573	0.376	B	0.31614	0.133	T	0.50056	-0.8872	10	0.62326	D	0.03	-8.9776	18.7876	0.91961	0.0:0.0:1.0:0.0	.	675	Q9UQR1	ZN148_HUMAN	Y	675	ENSP00000353863:H675Y;ENSP00000420335:H675Y;ENSP00000419322:H675Y;ENSP00000420448:H675Y	ENSP00000353863:H675Y	H	-	1	0	ZNF148	126434237	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.045000	0.71020	2.673000	0.90976	0.591000	0.81541	CAC	.	.		0.438	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964		A	124951547	G	A	124951547	3	1	206	1	0	0	0	0	1	0	0	0	17749	1348	47	3	365	3	ZNF148	3	124951547	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	62593333	124951547	73070883	14	29932										
MGLL	11343	hgsc.bcm.edu	37	chr3	127414028	127414028	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	agggggtctgagttataaatGtcgacctggaggaagaagga	16	4	1	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr3:127414028G>A	ENST00000434178.2	-	7	1472	c.576C>T	c.(574-576)gaC>gaT	p.D192D	MGLL_ENST00000453507.2_Silent_p.D172D|MGLL_ENST00000476682.1_5'UTR|MGLL_ENST00000398104.1_Silent_p.D192D|MGLL_ENST00000398101.3_Silent_p.D166D|MGLL_ENST00000265052.5_Silent_p.D202D			Q99685	MGLL_HUMAN	monoglyceride lipase	192					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						AGTTATAAATGTCGACCTGGA	0.582																																					p.D202D		Atlas-SNP	.											.	MGLL	19	.	0			c.C606T						.						36	39	38					3																	127414028		2003	4168	6171	SO:0001819	synonymous_variant	11343	exon7			ATAAATGTCGACC	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.576C>T	chr3.hg19:g.127414028G>A		159.0	0.0		137.0	29.0	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	ENST00000434178.2	hg19	CCDS43148.1	.	.	.	.	.	.	.	.	.	.	G	8.059	0.767785	0.15983	.	.	ENSG00000074416	ENST00000496306	.	.	.	5.02	2.78	0.32641	.	.	.	.	.	T	0.46927	0.1418	.	.	.	0.47441	D	0.999428	.	.	.	.	.	.	T	0.37079	-0.9721	4	.	.	.	-46.3044	3.7869	0.08704	0.1224:0.3846:0.3614:0.1315	.	.	.	.	I	98	.	.	T	-	2	0	MGLL	128896718	0.012000	0.17670	0.235000	0.24058	0.419000	0.31324	0.032000	0.13732	1.056000	0.40484	0.591000	0.81541	ACA	.	.		0.582	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283		A	127414028	G	A	127414028	2	1	206	1	0	0	0	0	0	0	0	1	9565	1368	48	3		3	MGLL	3	127414028	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	2462481	127414028	70608402	15	29933										
MED12L	116931	hgsc.bcm.edu	37	chr3	151107778	151107778	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	atgttgaaggaatatccacaGagcaacatataccgagtgcc	9	9	0	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr3:151107778G>T	ENST00000474524.1	+	36	5396	c.5358G>T	c.(5356-5358)caG>caT	p.Q1786H	MED12L_ENST00000273432.4_Missense_Mutation_p.Q1646H	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1786						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AATATCCACAGAGCAACATAT	0.423																																					p.Q1786H		Atlas-SNP	.											.	MED12L	271	.	0			c.G5358T						.						139	130	133					3																	151107778		2203	4300	6503	SO:0001583	missense	116931	exon36			TCCACAGAGCAAC	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5358G>T	chr3.hg19:g.151107778G>T	ENSP00000417235:p.Gln1786His	64.0	0.0		63.0	7.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	G	8.970	0.972808	0.18736	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.60797	0.39;0.16	5.63	4.67	0.58626	.	0.225303	0.38111	N	0.001808	T	0.60274	0.2256	N	0.19112	0.55	0.37475	D	0.915769	P;D	0.57571	0.699;0.98	B;D	0.66979	0.192;0.948	T	0.67684	-0.5607	10	0.62326	D	0.03	-5.0896	12.1613	0.54105	0.0866:0.0:0.9134:0.0	.	1646;1786	F8WAE6;Q86YW9	.;MD12L_HUMAN	H	1786;1646	ENSP00000417235:Q1786H;ENSP00000273432:Q1646H	ENSP00000273432:Q1646H	Q	+	3	2	MED12L	152590468	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.800000	0.47900	1.223000	0.43536	0.561000	0.74099	CAG	.	.		0.423	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		T	151107778	G	T	151107778	3	4	206	1	0	0	0	0	1	0	0	0	9438	933	33	3	5500	3	MED12L	3	151107778	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	23693750	151107778	46914652	16	29934										
ABCC5	10057	hgsc.bcm.edu	37	chr3	183667774	183667774	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	atttacctggagacaatgtgCaggactgaaaagaggatgac	12	6	0	4			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr3:183667774C>A	ENST00000334444.6	-	21	3324	c.3084G>T	c.(3082-3084)ctG>ctT	p.L1028L	ABCC5_ENST00000265586.6_Silent_p.L1028L	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	1028	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	AGACAATGTGCAGGACTGAAA	0.537																																					p.L1028L		Atlas-SNP	.											.	ABCC5	142	.	0			c.G3084T						.						64	71	68					3																	183667774		2096	4225	6321	SO:0001819	synonymous_variant	10057	exon21			AATGTGCAGGACT	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.3084G>T	chr3.hg19:g.183667774C>A		157.0	0.0		151.0	34.0	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	hg19	CCDS43176.1																																																																																			.	.		0.537	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		A	183667774	C	A	183667774	2	1	206	1	0	0	0	0	0	0	0	1	56	697	25	3		3	ABCC5	3	183667774	Silent	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	32559996	183667774	14354656	17	29935										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20533635	20533635	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ataataatgaatttaccgtgTtggaagccacaggaatcttt	8	6	1	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr4:20533635T>C	ENST00000504154.1	+	17	1894	c.1642T>C	c.(1642-1644)Ttg>Ctg	p.L548L	SLIT2_ENST00000503823.1_Silent_p.L540L|SLIT2_ENST00000273739.5_Silent_p.L552L|SLIT2_ENST00000503837.1_Silent_p.L544L	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	548					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						ATTTACCGTGTTGGAAGCCAC	0.303																																					p.L548L		Atlas-SNP	.											.	SLIT2	290	.	0			c.T1642C						.						49	49	49					4																	20533635		2203	4295	6498	SO:0001819	synonymous_variant	9353	exon17			ACCGTGTTGGAAG	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1642T>C	chr4.hg19:g.20533635T>C		374.0	0.0		265.0	88.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	hg19	CCDS3426.1																																																																																			.	.		0.303	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			C	20533635	T	C	20533635	2	2	206	1	0	0	0	0	0	0	0	1	14755	1722	60	2		2	SLIT2	4	20533635	Silent	SNP	T	TCGA-DD-AAE0-01A-11D-A40R-10		20533635	170620641	18	29936										
PALLD	23022	hgsc.bcm.edu	37	chr4	169602487	169602487	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tttaatactttcccaggtgcCagttcaacagattctgacag	7	10	2	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr4:169602487C>T	ENST00000505667.1	+	4	1265	c.1092C>T	c.(1090-1092)gcC>gcT	p.A364A	PALLD_ENST00000333488.4_Silent_p.A241A|PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000512127.1_5'UTR|PALLD_ENST00000261509.6_Silent_p.A364A			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	364					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		TCCCAGGTGCCAGTTCAACAG	0.323									Pancreatic Cancer, Familial Clustering of																												p.A364A	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C1092T						.						83	82	83					4																	169602487		2203	4300	6503	SO:0001819	synonymous_variant	23022	exon4	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	AGGTGCCAGTTCA	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"Immunoglobulin superfamily / I-set domain containing"	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.1092C>T	chr4.hg19:g.169602487C>T		53.0	0.0		29.0	13.0	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	hg19	CCDS54818.1																																																																																			.	.		0.323	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		T	169602487	C	T	169602487	2	4	206	1	0	0	0	0	0	0	0	1	11416	581	21	3		3	PALLD	4	169602487	Silent	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	149068852	169602487	21551789	19	29937										
RXFP3	51289	hgsc.bcm.edu	37	chr5	33937055	33937055	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	catcccccgggcagcggcggGgcagagagcgcggacacaga	17	14	0	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr5:33937055G>A	ENST00000330120.3	+	1	565	c.210G>A	c.(208-210)ggG>ggA	p.G70G		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	70					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)			endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						GCAGCGGCGGGGCAGAGAGCG	0.697																																					p.G70G		Atlas-SNP	.											.	RXFP3	114	.	0			c.G210A						.						39	51	47					5																	33937055		2201	4297	6498	SO:0001819	synonymous_variant	51289	exon1			CGGCGGGGCAGAG	D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"GPCR / Class A : Relaxin family peptide receptors"	24883	protein-coding gene	gene with protein product		609445	"relaxin 3 receptor 1", "relaxin family peptide receptor 3"	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.210G>A	chr5.hg19:g.33937055G>A		92.0	0.0		104.0	7.0	NM_016568	Q14DA5	Silent	SNP	ENST00000330120.3	hg19	CCDS3900.1																																																																																			.	.		0.697	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568		A	33937055	G	A	33937055	2	1	206	1	0	0	0	0	0	0	0	1	13776	1219	43	3		3	RXFP3	5	33937055	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10		33937055	146978205	20	29938										
RAD50	10111	hgsc.bcm.edu	37	chr5	131893023	131893023	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	aaacgtttgcaaacatgtccCggatcgaaaagatgagcatt	9	8	0	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr5:131893023C>G	ENST00000265335.6	+	1	394	c.7C>G	c.(7-9)Cgg>Ggg	p.R3G	RAD50_ENST00000378823.3_5'UTR			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	3					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AAACATGTCCCGGATCGAAAA	0.502								Homologous recombination																													p.R3G		Atlas-SNP	.											.	RAD50	246	.	0			c.C7G						.						96	98	97					5																	131893023		2203	4300	6503	SO:0001583	missense	10111	exon1			ATGTCCCGGATCG	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.7C>G	chr5.hg19:g.131893023C>G	ENSP00000265335:p.Arg3Gly	168.0	0.0		178.0	50.0	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	hg19	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.013975	0.54468	.	.	ENSG00000113522	ENST00000265335;ENST00000453394	T;T	0.07567	3.18;3.18	5.72	3.73	0.42828	.	0.098210	0.64402	D	0.000002	T	0.06962	0.0177	L	0.32530	0.975	0.80722	D	1	B	0.27932	0.194	B	0.22386	0.039	T	0.29640	-1.0005	10	0.39692	T	0.17	-11.9627	10.9171	0.47142	0.5095:0.4905:0.0:0.0	.	3	Q92878	RAD50_HUMAN	G	3	ENSP00000265335:R3G;ENSP00000400049:R3G	ENSP00000265335:R3G	R	+	1	2	RAD50	131920922	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.755000	0.47540	1.377000	0.46286	0.655000	0.94253	CGG	.	.		0.502	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		G	131893023	C	G	131893023	3	3	206	1	0	0	0	0	1	0	0	0	12999	643	23	4	9	4	RAD50	5	131893023	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	97955968	131893023	49022237	21	29939										
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140711458	140711458	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	agttagttgataattattacCgtttagtgactgaaagaaca	8	4	0	4			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr5:140711458C>T	ENST00000517417.1	+	1	1207	c.1207C>T	c.(1207-1209)Cgt>Tgt	p.R403C	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Missense_Mutation_p.R403C	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	403	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R403C(2)		breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAATTATTACCGTTTAGTGAC	0.398																																					p.R403C		Atlas-SNP	.											PCDHGA1_ENST00000517417,NS,carcinoma,-1,4	PCDHGA1	397	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1207T						.						74	72	73					5																	140711458		2203	4300	6503	SO:0001583	missense	56114	exon1			TATTACCGTTTAG	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1207C>T	chr5.hg19:g.140711458C>T	ENSP00000431083:p.Arg403Cys	91.0	0.0		95.0	21.0	NM_018912	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	hg19	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	C	10.00	1.233128	0.22626	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.01787	4.64;4.64	3.85	1.97	0.26223	Cadherin (4);Cadherin-like (1);	0.789993	0.10576	U	0.658525	T	0.03390	0.0098	M	0.79926	2.475	0.09310	N	1	B;B	0.32893	0.133;0.389	B;B	0.30646	0.073;0.118	T	0.30090	-0.9990	10	0.87932	D	0	.	6.4861	0.22089	0.3189:0.5898:0.0:0.0913	.	403;403	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	C	403	ENSP00000431083:R403C;ENSP00000367345:R403C	ENSP00000367345:R403C	R	+	1	0	PCDHGA1	140691642	0.000000	0.05858	0.998000	0.56505	0.992000	0.81027	-0.112000	0.10791	0.925000	0.37094	0.650000	0.86243	CGT	.	.		0.398	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		T	140711458	C	T	140711458	3	4	206	1	0	0	0	0	1	0	0	0	11559	652	23	1	1209	1	PCDHGA1	5	140711458	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	8818435	140711458	40203802	22	29940										
PDGFRB	5159	hgsc.bcm.edu	37	chr5	149504387	149504387	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ccaaaggccccagagccgagGgtgcgtcctggtgcagagat	15	12	0	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr5:149504387G>A	ENST00000261799.4	-	13	2284	c.1815C>T	c.(1813-1815)acC>acT	p.T605T		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	605	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGAGCCGAGGGTGCGTCCTG	0.647			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"																																p.T605T		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	.	PDGFRB	142	.	0			c.C1815T						.						39	38	38					5																	149504387		2203	4300	6503	SO:0001819	synonymous_variant	5159	exon13			GCCGAGGGTGCGT	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.1815C>T	chr5.hg19:g.149504387G>A		21.0	0.0		25.0	13.0	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	hg19	CCDS4303.1																																																																																			.	.		0.647	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		A	149504387	G	A	149504387	2	1	206	1	0	0	0	0	0	0	0	1	11671	1219	43	3		3	PDGFRB	5	149504387	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	8792929	149504387	31410873	23	29941										
BAT2	7916	hgsc.bcm.edu	37	chr6	31600194	31600194	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	aggaggcgacatgggagggcTcagcagcaggataaaccgcc	16	10	1	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr6:31600194T>G	ENST00000376033.2	+	16	3978	c.3744T>G	c.(3742-3744)gcT>gcG	p.A1248A	PRRC2A_ENST00000376007.4_Silent_p.A1248A	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1248	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						ATGGGAGGGCTCAGCAGCAGG	0.642																																					p.A1248A		Atlas-SNP	.											.	PRRC2A	152	.	0			c.T3744G						.						74	76	75					6																	31600194		1511	2709	4220	SO:0001819	synonymous_variant	7916	exon16			GAGGGCTCAGCAG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3744T>G	chr6.hg19:g.31600194T>G		54.0	0.0		69.0	16.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	hg19	CCDS4708.1																																																																																			.	.		0.642	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		G	31600194	T	G	31600194	2	3	206	1	0	0	0	0	0	0	0	1	1319	1538	54	5		5	BAT2	6	31600194	Silent	SNP	T	TCGA-DD-AAE0-01A-11D-A40R-10		31600194	139514873	24	29942										
PRDM13	59336	hgsc.bcm.edu	37	chr6	100061211	100061211	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tcaagcgcgaggcctcttccGcgccctcggccacctcgccg	11	20	2	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr6:100061211G>A	ENST00000369215.4	+	4	1005	c.700G>A	c.(700-702)Gcg>Acg	p.A234T		NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	234					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1)	17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		GGCCTCTTCCGCGCCCTCGGC	0.726																																					p.A234T		Atlas-SNP	.											.	PRDM13	65	.	0			c.G700A						.						5	7	7					6																	100061211		1908	3999	5907	SO:0001583	missense	59336	exon4			TCTTCCGCGCCCT	AY004253	CCDS43487.1	6q16.2	2012-03-28			ENSG00000112238	ENSG00000112238			13998	protein-coding gene	gene with protein product							Standard	NM_021620		Approved		uc003pqg.1	Q9H4Q3	OTTHUMG00000015269	ENST00000369215.4:c.700G>A	chr6.hg19:g.100061211G>A	ENSP00000358217:p.Ala234Thr	43.0	0.0		54.0	10.0	NM_021620	Q5TGC1|Q5TGC2	Missense_Mutation	SNP	ENST00000369215.4	hg19	CCDS43487.1	.	.	.	.	.	.	.	.	.	.	G	8.017	0.758807	0.15846	.	.	ENSG00000112238	ENST00000369215;ENST00000369214	T;T	0.06142	3.34;3.35	4.59	2.63	0.31362	.	0.222694	0.22930	N	0.053909	T	0.00998	0.0033	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.48222	-0.9054	10	0.13853	T	0.58	-3.8548	4.8876	0.13710	0.1098:0.0:0.6658:0.2244	.	234	Q9H4Q3	PRD13_HUMAN	T	234;244	ENSP00000358217:A234T;ENSP00000358216:A244T	ENSP00000358216:A244T	A	+	1	0	PRDM13	100167932	.	.	0.001000	0.08648	0.220000	0.24768	.	.	1.143000	0.42306	0.462000	0.41574	GCG	.	.		0.726	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2			A	100061211	G	A	100061211	3	1	206	1	0	0	0	0	1	0	0	0	12466	1087	38	1	714	1	PRDM13	6	100061211	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	68461017	100061211	71053856	25	29943										
FIG4	9896	hgsc.bcm.edu	37	chr6	110085143	110085143	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tttatttttaaacacaggtgGaatgaactaggaggatgtgt	11	3	0	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr6:110085143G>A	ENST00000230124.3	+	13	1516	c.1392G>A	c.(1390-1392)tgG>tgA	p.W464*	FIG4_ENST00000441478.2_Nonsense_Mutation_p.W187*	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	464	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		AACACAGGTGGAATGAACTAG	0.328																																					p.W464X		Atlas-SNP	.											.	FIG4	77	.	0			c.G1392A						.						89	88	88					6																	110085143		2203	4300	6503	SO:0001587	stop_gained	9896	exon13			CAGGTGGAATGAA	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"KIAA0274", "FIG4 homolog (S. cerevisiae)", "FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.1392G>A	chr6.hg19:g.110085143G>A	ENSP00000230124:p.Trp464*	90.0	0.0		131.0	55.0	NM_014845	Q53H49|Q5TCS6	Nonsense_Mutation	SNP	ENST00000230124.3	hg19	CCDS5078.1	.	.	.	.	.	.	.	.	.	.	G	38	6.966328	0.97967	.	.	ENSG00000112367	ENST00000441478;ENST00000230124	.	.	.	5.12	4.25	0.50352	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-9.7436	13.354	0.60617	0.0761:0.0:0.9239:0.0	.	.	.	.	X	187;464	.	ENSP00000230124:W464X	W	+	3	0	FIG4	110191836	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	6.155000	0.71833	1.156000	0.42514	0.551000	0.68910	TGG	.	.		0.328	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845		A	110085143	G	A	110085143	4	1	206	1	0	0	0	0	0	1	0	0	5896	1183	41	3	1442	3	FIG4	6	110085143	Nonsense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	10023932	110085143	61029924	26	29944										
THEMIS	387357	hgsc.bcm.edu	37	chr6	128134119	128134119	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ctgaggggtgtttcggagggCgaggtgggggatgtgaggct	23	4	0	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr6:128134119C>T	ENST00000368248.2	-	4	1815	c.1667G>A	c.(1666-1668)cGc>cAc	p.R556H	THEMIS_ENST00000368250.1_Missense_Mutation_p.R477H|THEMIS_ENST00000537166.1_Missense_Mutation_p.R521H|THEMIS_ENST00000543064.1_Missense_Mutation_p.R556H	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	556					negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						TTTCGGAGGGCGAGGTGGGGG	0.493																																					p.R556H		Atlas-SNP	.											.	THEMIS	168	.	0			c.G1667A						.						111	114	113					6																	128134119		2203	4300	6503	SO:0001583	missense	387357	exon4			GGAGGGCGAGGTG	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.1667G>A	chr6.hg19:g.128134119C>T	ENSP00000357231:p.Arg556His	75.0	0.0		93.0	18.0	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	hg19	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.294707	0.60086	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166	T;T;T;T	0.32988	1.43;1.58;1.48;1.44	5.83	2.91	0.33838	.	0.258158	0.36482	N	0.002576	T	0.38904	0.1058	M	0.65498	2.005	0.36638	D	0.876665	D;D	0.89917	1.0;0.999	D;P	0.63597	0.916;0.763	T	0.46261	-0.9204	10	0.72032	D	0.01	-0.4145	14.6116	0.68519	0.3819:0.6181:0.0:0.0	.	556;556	F5H1J9;Q8N1K5	.;THMS1_HUMAN	H	477;556;556;521	ENSP00000357233:R477H;ENSP00000439594:R556H;ENSP00000357231:R556H;ENSP00000439863:R521H	ENSP00000357231:R556H	R	-	2	0	THEMIS	128175812	0.985000	0.35326	0.907000	0.35723	0.898000	0.52572	2.713000	0.47194	0.293000	0.22520	0.563000	0.77884	CGC	.	.		0.493	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		T	128134119	C	T	128134119	3	4	206	1	0	0	0	0	1	0	0	0	15875	768	27	1	391	1	THEMIS	6	128134119	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	18048976	128134119	42980948	27	29945										
THEMIS	387357	hgsc.bcm.edu	37	chr6	128135074	128135074	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gatgcggattatatcttttcGaactaaaaagaaaaaataaa	6	4	1	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr6:128135074G>A	ENST00000368248.2	-	4	860	c.712C>T	c.(712-714)Cga>Tga	p.R238*	THEMIS_ENST00000368250.1_Nonsense_Mutation_p.R159*|THEMIS_ENST00000537166.1_Nonsense_Mutation_p.R203*|THEMIS_ENST00000543064.1_Nonsense_Mutation_p.R238*	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	238	CABIT 1.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						ATATCTTTTCGAACTAAAAAG	0.333																																					p.R238X		Atlas-SNP	.											THEMIS,NS,carcinoma,0,3	THEMIS	168	.	0			c.C712T						.						58	63	61					6																	128135074		2128	4283	6411	SO:0001587	stop_gained	387357	exon4			CTTTTCGAACTAA	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.712C>T	chr6.hg19:g.128135074G>A	ENSP00000357231:p.Arg238*	59.0	0.0		60.0	18.0	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Nonsense_Mutation	SNP	ENST00000368248.2	hg19	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	G	37	6.242014	0.97408	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166;ENST00000434358	.	.	.	5.73	1.82	0.25136	.	0.466331	0.22107	N	0.064531	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.6297	16.0043	0.80349	0.0:0.0:0.6002:0.3998	.	.	.	.	X	159;238;238;203;6	.	ENSP00000357231:R238X	R	-	1	2	THEMIS	128176767	0.924000	0.31332	0.030000	0.17652	0.941000	0.58515	2.332000	0.43903	0.042000	0.15717	0.557000	0.71058	CGA	.	.		0.333	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		A	128135074	G	A	128135074	4	1	206	1	0	0	0	0	0	1	0	0	15875	1066	37	1	1346	1	THEMIS	6	128135074	Nonsense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	955	128135074	42979993	28	29946										
KDELR2	11014	hgsc.bcm.edu	37	chr7	6509351	6509351	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	taaatttcaggtagatcaggTacactgtggcataggagcag	12	6	2	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr7:6509351T>C	ENST00000258739.4	-	3	411	c.227A>G	c.(226-228)tAc>tGc	p.Y76C	KDELR2_ENST00000490996.1_Missense_Mutation_p.Y76C|DAGLB_ENST00000436575.1_Intron|KDELR2_ENST00000463747.1_Intron	NM_006854.3	NP_006845.1	P33947	ERD22_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	76					intracellular protein transport (GO:0006886)|protein retention in ER lumen (GO:0006621)|vesicle-mediated transport (GO:0016192)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	KDEL sequence binding (GO:0005046)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		GTAGATCAGGTACACTGTGGC	0.458																																					p.Y76C		Atlas-SNP	.											.	KDELR2	31	.	0			c.A227G						.						87	82	84					7																	6509351		2203	4300	6503	SO:0001583	missense	11014	exon3			ATCAGGTACACTG	X63745	CCDS5351.1, CCDS43550.1	7p	2008-05-02			ENSG00000136240	ENSG00000136240			6305	protein-coding gene	gene with protein product		609024				1316805, 1325562	Standard	NM_006854		Approved	ELP-1, ERD2.2	uc003sqe.4	P33947	OTTHUMG00000023103	ENST00000258739.4:c.227A>G	chr7.hg19:g.6509351T>C	ENSP00000258739:p.Tyr76Cys	150.0	0.0		246.0	18.0	NM_001100603	A4D2P4|Q6IPC5|Q96E30	Missense_Mutation	SNP	ENST00000258739.4	hg19	CCDS5351.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.915870	0.73098	.	.	ENSG00000136240	ENST00000258739;ENST00000490996	T	0.52526	0.66	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.74756	0.3758	H	0.94385	3.53	0.80722	D	1	D;D	0.76494	0.999;0.994	D;D	0.74023	0.982;0.928	T	0.81152	-0.1063	10	0.87932	D	0	-0.3987	10.4834	0.44706	0.0:0.0726:0.0:0.9274	.	76;76	P33947-2;P33947	.;ERD22_HUMAN	C	76	ENSP00000258739:Y76C	ENSP00000258739:Y76C	Y	-	2	0	KDELR2	6475876	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.197000	0.58413	2.268000	0.75426	0.455000	0.32223	TAC	.	.		0.458	KDELR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059424.2			C	6509351	T	C	6509351	3	2	206	1	0	0	0	0	1	0	0	0	8129	1638	57	2	598	2	KDELR2	7	6509351	Missense_Mutation	SNP	T	TCGA-DD-AAE0-01A-11D-A40R-10		6509351	152629312	29	29947										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20689688	20689688	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	aattaagtctggagagacagTcgccttggtcggtctcaatg	12	8	2	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr7:20689688T>A	ENST00000404938.2	+	12	1902	c.1250T>A	c.(1249-1251)gTc>gAc	p.V417D	ABCB5_ENST00000406935.1_5'UTR|ABCB5_ENST00000258738.6_5'UTR|ABCB5_ENST00000477094.1_3'UTR|ABCB5_ENST00000443026.2_5'UTR	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	417	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						GGAGAGACAGTCGCCTTGGTC	0.438																																					p.V417D		Atlas-SNP	.											.	ABCB5	357	.	0			c.T1250A						.						87	76	80					7																	20689688		1568	3582	5150	SO:0001583	missense	340273	exon12			AGACAGTCGCCTT	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.1250T>A	chr7.hg19:g.20689688T>A	ENSP00000384881:p.Val417Asp	88.0	0.0		116.0	25.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.517602	0.64634	.	.	ENSG00000004846	ENST00000404938	D	0.95069	-3.6	5.14	5.14	0.70334	.	.	.	.	.	D	0.97974	0.9333	H	0.96365	3.81	0.52099	D	0.999946	D	0.56035	0.974	D	0.65233	0.933	D	0.99215	1.0877	9	0.87932	D	0	.	14.8407	0.70220	0.0:0.0:0.0:1.0	.	417	A7BKA4	.	D	417	ENSP00000384881:V417D	ENSP00000384881:V417D	V	+	2	0	ABCB5	20656213	0.730000	0.28100	0.782000	0.31804	0.787000	0.44495	2.124000	0.42006	2.239000	0.73571	0.528000	0.53228	GTC	.	.		0.438	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		A	20689688	T	A	20689688	3	1	206	1	0	0	0	0	1	0	0	0	44	1667	58	4	1292	4	ABCB5	7	20689688	Missense_Mutation	SNP	T	TCGA-DD-AAE0-01A-11D-A40R-10	14180337	20689688	138448975	30	29948										
C7orf51	222950	hgsc.bcm.edu	37	chr7	100086313	100086313	+	Frame_Shift_Del	DEL	C	C	-													0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	aagaccactccttgtgaaatCcccccgcccttccccaacct							TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr7:100086313delC	ENST00000300179.2	+	4	1128	c.969delC	c.(967-969)atcfs	p.I323fs	NYAP1_ENST00000423930.1_Frame_Shift_Del_p.I323fs|NYAP1_ENST00000454988.1_Frame_Shift_Del_p.I266fs	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	323	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CTTGTGAAATCCCCCCGCCCT	0.682																																					p.I323fs		Atlas-INDEL	.											.	.	.	.	0			c.968delT						.						51	50	51					7																	100086313		2201	4298	6499	SO:0001589	frameshift_variant	222950	exon4			.	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.969delC	chr7.hg19:g.100086313delC	ENSP00000300179:p.Ile323fs	98.0	0.0		94.0	21.0	NM_173564	Q6U9Y3|Q8N1V0	Frame_Shift_Del	DEL	ENST00000300179.2	hg19	CCDS5696.1																																																																																			.	.		0.682	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		-	100086313	C	-	100086313	7	5	206	1	0	1	0	1	0	0	0	0	2402	845	30	0	979	0	C7orf51	7	100086313	Frame_Shift_Del	DEL	C	TCGA-DD-AAE0-01A-11D-A40R-10	79396625	100086313	59052350	31	29949										
MUC17	140453	hgsc.bcm.edu	37	chr7	100681533	100681533	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	aactcttagtgaaggaacgaCtccattaacaagtatacctg	7	9	1	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr7:100681533C>A	ENST00000306151.4	+	3	6900	c.6836C>A	c.(6835-6837)aCt>aAt	p.T2279N		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2279	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GAAGGAACGACTCCATTAACA	0.478																																					p.T2279N		Atlas-SNP	.											.	MUC17	804	.	0			c.C6836A						.																																			SO:0001583	missense	140453	exon3			GAACGACTCCATT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.6836C>A	chr7.hg19:g.100681533C>A	ENSP00000302716:p.Thr2279Asn	58.0	0.0		67.0	7.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	2.491	-0.317530	0.05386	.	.	ENSG00000169876	ENST00000306151	T	0.02472	4.28	0.762	0.762	0.18454	.	.	.	.	.	T	0.03390	0.0098	N	0.19112	0.55	0.09310	N	1	P	0.51933	0.949	P	0.51297	0.665	T	0.49679	-0.8914	9	0.35671	T	0.21	.	6.9517	0.24548	0.0:0.9999:0.0:1.0E-4	.	2279	Q685J3	MUC17_HUMAN	N	2279	ENSP00000302716:T2279N	ENSP00000302716:T2279N	T	+	2	0	MUC17	100468253	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.068000	0.14531	0.132000	0.18615	0.134000	0.15878	ACT	.	.		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100681533	C	A	100681533	3	1	206	1	0	0	0	0	1	0	0	0	9983	565	20	3	6846	3	MUC17	7	100681533	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	595220	100681533	58457130	32	29950										
RBM28	55131	hgsc.bcm.edu	37	chr7	127979340	127979340	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	atctgccactttggctttttTagccttcggctccttctttg	7	12	2	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr7:127979340T>C	ENST00000223073.2	-	3	427	c.313A>G	c.(313-315)Aaa>Gaa	p.K105E	RBM28_ENST00000415472.2_Intron	NM_018077.2	NP_060547.2	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	105					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						TTGGCTTTTTTAGCCTTCGGC	0.393																																					p.K105E		Atlas-SNP	.											.	RBM28	71	.	0			c.A313G						.						193	201	198					7																	127979340		2202	4300	6502	SO:0001583	missense	55131	exon3			CTTTTTTAGCCTT	AK001239	CCDS5801.1, CCDS55159.1	7q32.2	2013-02-12			ENSG00000106344	ENSG00000106344		"RNA binding motif (RRM) containing"	21863	protein-coding gene	gene with protein product		612074					Standard	NM_018077		Approved	FLJ10377	uc003vmp.2	Q9NW13	OTTHUMG00000157711	ENST00000223073.2:c.313A>G	chr7.hg19:g.127979340T>C	ENSP00000223073:p.Lys105Glu	58.0	0.0		48.0	11.0	NM_018077	A4D100|B4DU52|E9PDD9|Q53H65|Q96CV3	Missense_Mutation	SNP	ENST00000223073.2	hg19	CCDS5801.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.712690	0.89112	.	.	ENSG00000106344	ENST00000223073;ENST00000478061;ENST00000459726	T;T;T	0.31510	2.98;2.19;1.49	5.86	4.68	0.58851	Nucleotide-binding, alpha-beta plait (1);	0.362222	0.33515	N	0.004835	T	0.29458	0.0734	L	0.32530	0.975	0.80722	D	1	P	0.39535	0.677	P	0.47673	0.554	T	0.03706	-1.1011	10	0.19147	T	0.46	-6.6855	9.9242	0.41483	0.0:0.0:0.1712:0.8288	.	105	Q9NW13	RBM28_HUMAN	E	105;105;139	ENSP00000223073:K105E;ENSP00000418071:K105E;ENSP00000420503:K139E	ENSP00000223073:K105E	K	-	1	0	RBM28	127766576	0.999000	0.42202	0.321000	0.25320	0.875000	0.50365	3.001000	0.49488	1.014000	0.39417	0.477000	0.44152	AAA	.	.		0.393	RBM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349442.2	NM_018077		C	127979340	T	C	127979340	3	2	206	1	0	0	0	0	1	0	0	0	13143	1763	61	2	2034	2	RBM28	7	127979340	Missense_Mutation	SNP	T	TCGA-DD-AAE0-01A-11D-A40R-10	27297807	127979340	31159323	33	29951										
CYP11B1	1584	hgsc.bcm.edu	37	chr8	143961168	143961168	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ctctcgtgcccagtgcctgtGccctttgcagggacagccag	12	15	1	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr8:143961168G>A	ENST00000292427.4	-	1	94	c.62C>T	c.(61-63)gCa>gTa	p.A21V	CYP11B1_ENST00000517471.1_Missense_Mutation_p.A21V|CYP11B1_ENST00000377675.3_Missense_Mutation_p.A21V	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	21					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	CAGTGCCTGTGCCCTTTGCAG	0.637									Familial Hyperaldosteronism type I																												p.A21V		Atlas-SNP	.											.	CYP11B1	128	.	0			c.C62T						.						96	94	95					8																	143961168		2203	4300	6503	SO:0001583	missense	1584	exon1	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	GCCTGTGCCCTTT	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"Cytochrome P450s"	2591	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	610613	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.62C>T	chr8.hg19:g.143961168G>A	ENSP00000292427:p.Ala21Val	48.0	0.0		98.0	22.0	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	ENST00000292427.4	hg19	CCDS6392.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.747966	0.30955	.	.	ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675	T;D;T	0.83837	-1.0;-1.77;-1.34	2.96	2.06	0.26882	.	0.550372	0.13718	N	0.367597	T	0.75910	0.3914	L	0.54323	1.7	0.09310	N	1	B;B;P	0.44734	0.018;0.209;0.842	B;B;B	0.40982	0.012;0.03;0.345	T	0.62909	-0.6754	10	0.30078	T	0.28	.	6.32	0.21213	0.1561:0.0:0.8439:0.0	.	21;21;21	Q4VAR0;Q4VAQ9;P15538	.;.;C11B1_HUMAN	V	21	ENSP00000292427:A21V;ENSP00000428043:A21V;ENSP00000366903:A21V	ENSP00000292427:A21V	A	-	2	0	CYP11B1	143958170	0.001000	0.12720	0.001000	0.08648	0.011000	0.07611	0.386000	0.20702	0.514000	0.28300	0.305000	0.20034	GCA	.	.		0.637	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			A	143961168	G	A	143961168	3	1	206	1	0	0	0	0	1	0	0	0	4147	1319	46	3	1485	3	CYP11B1	8	143961168	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10		143961168	2402854	34	29952										
FOXE1	2304	hgsc.bcm.edu	37	chr9	100616728	100616728	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ccgccgccgccgccgccgccGccgccatcttcccaggcgcg	12	24	1	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr9:100616728G>A	ENST00000375123.3	+	1	1193	c.532G>A	c.(532-534)Gcc>Acc	p.A178T		NM_004473.3	NP_004464.2	O00358	FOXE1_HUMAN	forkhead box E1 (thyroid transcription factor 2)	178	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|cell migration (GO:0016477)|embryonic organ morphogenesis (GO:0048562)|hair follicle morphogenesis (GO:0031069)|hard palate development (GO:0060022)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pharynx development (GO:0060465)|positive regulation of transcription, DNA-templated (GO:0045893)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(62;0.158)				cgccgccgccgccgccATCTT	0.791																																					p.A178T		Atlas-SNP	.											.	FOXE1	19	.	0			c.G532A						.						2	2	2					9																	100616728		529	1359	1888	SO:0001583	missense	2304	exon1			GCCGCCGCCGCCA	U89995	CCDS35078.1	9q22	2008-09-05			ENSG00000178919	ENSG00000178919		"Forkhead boxes"	3806	protein-coding gene	gene with protein product		602617	"forkhead box E2"	FKHL15, TITF2, FOXE2		9169137, 9697705	Standard	NM_004473		Approved	TTF-2, HFKH4	uc004axu.3	O00358	OTTHUMG00000020333	ENST00000375123.3:c.532G>A	chr9.hg19:g.100616728G>A	ENSP00000364265:p.Ala178Thr	162.0	0.0		211.0	15.0	NM_004473	O75765|Q5T109|Q99526	Missense_Mutation	SNP	ENST00000375123.3	hg19	CCDS35078.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.930555	0.52866	.	.	ENSG00000178919	ENST00000375123	D	0.93953	-3.32	3.94	3.02	0.34903	.	0.612880	0.14474	U	0.317365	D	0.83087	0.5178	L	0.34521	1.04	0.22571	N	0.998979	P	0.47253	0.892	B	0.30251	0.113	T	0.72969	-0.4130	10	0.13108	T	0.6	.	6.9037	0.24297	0.0993:0.1791:0.7216:0.0	.	178	O00358	FOXE1_HUMAN	T	178	ENSP00000364265:A178T	ENSP00000364265:A178T	A	+	1	0	FOXE1	99656549	0.087000	0.21565	0.898000	0.35279	0.822000	0.46500	0.422000	0.21296	0.758000	0.33059	0.557000	0.71058	GCC	.	.		0.791	FOXE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053341.1			A	100616728	G	A	100616728	3	1	206	1	0	0	0	0	1	0	0	0	6011	1087	38	1	534	1	FOXE1	9	100616728	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10		100616728	40596703	35	29953										
SGPL1	8879	hgsc.bcm.edu	37	chr10	72633292	72633292	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gatgcacttcggtgagaacgGctatgttgaagctaccaaac	11	9	0	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr10:72633292G>A	ENST00000373202.3	+	12	1444	c.1244G>A	c.(1243-1245)gGc>gAc	p.G415D		NM_003901.3	NP_003892.2	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	415					androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|ceramide metabolic process (GO:0006672)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|fatty acid metabolic process (GO:0006631)|fibroblast migration (GO:0010761)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|regulation of multicellular organism growth (GO:0040014)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid catabolic process (GO:0030149)|sphingolipid metabolic process (GO:0006665)|vasculogenesis (GO:0001570)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)|sphinganine-1-phosphate aldolase activity (GO:0008117)			large_intestine(4)	4						GGTGAGAACGGCTATGTTGAA	0.522																																					p.G415D	Colon(151;1054 2458 6676 40971)	Atlas-SNP	.											.	SGPL1	37	.	0			c.G1244A						.						142	126	132					10																	72633292		2203	4300	6503	SO:0001583	missense	8879	exon12			AGAACGGCTATGT	AI128825	CCDS31216.1	10q21	2008-08-01			ENSG00000166224	ENSG00000166224			10817	protein-coding gene	gene with protein product		603729				9464245, 17090686	Standard	NM_003901		Approved	SPL	uc001jrm.3	O95470	OTTHUMG00000018421	ENST00000373202.3:c.1244G>A	chr10.hg19:g.72633292G>A	ENSP00000362298:p.Gly415Asp	49.0	0.0		65.0	14.0	NM_003901	B2RBD4|Q7Z732|Q9ULG8|Q9UN89	Missense_Mutation	SNP	ENST00000373202.3	hg19	CCDS31216.1	.	.	.	.	.	.	.	.	.	.	G	34	5.316187	0.95655	.	.	ENSG00000166224	ENST00000373202	T	0.45276	0.9	5.73	5.73	0.89815	Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.79173	0.4401	H	0.97783	4.075	0.80722	D	1	D	0.71674	0.998	D	0.73380	0.98	D	0.86721	0.1942	10	0.87932	D	0	-19.149	19.9064	0.97008	0.0:0.0:1.0:0.0	.	415	O95470	SGPL1_HUMAN	D	415	ENSP00000362298:G415D	ENSP00000362298:G415D	G	+	2	0	SGPL1	72303298	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.615000	0.83006	2.693000	0.91896	0.655000	0.94253	GGC	.	.		0.522	SGPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048533.1	NM_003901		A	72633292	G	A	72633292	3	1	206	1	0	0	0	0	1	0	0	0	14233	1203	42	3	1286	3	SGPL1	10	72633292	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10		72633292	62901455	36	29954										
TCTN3	26123	hgsc.bcm.edu	37	chr10	97442541	97442541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	aaatctcctgctgcaagtggCtgcagtctgccttcttcaac	8	13	4	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr10:97442541C>T	ENST00000371217.5	-	12	1342	c.1319G>A	c.(1318-1320)aGc>aAc	p.S440N	TCTN3_ENST00000265993.9_Missense_Mutation_p.S458N|TCTN3_ENST00000430368.2_Missense_Mutation_p.S292N			Q6NUS6	TECT3_HUMAN	tectonic family member 3	440					apoptotic process (GO:0006915)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(3)|endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		CTGCAAGTGGCTGCAGTCTGC	0.443																																					p.S440N		Atlas-SNP	.											.	TCTN3	66	.	0			c.G1319A						.						162	162	162					10																	97442541		2203	4300	6503	SO:0001583	missense	26123	exon12			AAGTGGCTGCAGT	AK098295	CCDS31258.2, CCDS44461.1	10q24.1	2014-01-28	2007-08-20	2007-08-20	ENSG00000119977	ENSG00000119977		"Tectonic proteins"	24519	protein-coding gene	gene with protein product		613847	"chromosome 10 open reading frame 61"	C10orf61		12975309	Standard	NM_015631		Approved	DKFZP564D116, TECT3, JBTS18	uc001klb.4	Q6NUS6	OTTHUMG00000018814	ENST00000371217.5:c.1319G>A	chr10.hg19:g.97442541C>T	ENSP00000360261:p.Ser440Asn	46.0	0.0		45.0	22.0	NM_015631	A6NIC8|B0QZ90|B4DR81|Q6P7P3|Q6UW27|Q6ZQQ0|Q8N7K1|Q8NBQ0|Q96GF7|Q9Y3U1	Missense_Mutation	SNP	ENST00000371217.5	hg19	CCDS31258.2	.	.	.	.	.	.	.	.	.	.	C	11.85	1.760209	0.31137	.	.	ENSG00000119977	ENST00000265993;ENST00000430368;ENST00000371217;ENST00000343162	D	0.84146	-1.81	5.64	2.26	0.28386	.	0.784973	0.12599	N	0.454872	T	0.78246	0.4253	M	0.66506	2.035	0.09310	N	1	P;B;B	0.45176	0.852;0.012;0.069	B;B;B	0.34180	0.177;0.009;0.056	T	0.66956	-0.5792	10	0.36615	T	0.2	-26.1162	6.1477	0.20294	0.0:0.649:0.16:0.1911	.	292;440;262	B4DR81;Q6NUS6;Q6NUS6-3	.;TECT3_HUMAN;.	N	440;292;458;262	ENSP00000265993:S440N	ENSP00000265993:S440N	S	-	2	0	TCTN3	97432531	0.529000	0.26322	0.335000	0.25508	0.792000	0.44763	0.777000	0.26718	0.711000	0.32018	0.563000	0.77884	AGC	.	.		0.443	TCTN3-009	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000471858.1	NM_015631		T	97442541	C	T	97442541	3	4	206	1	0	0	0	0	1	0	0	0	15739	797	28	3	516	3	TCTN3	10	97442541	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	24809249	97442541	38092206	37	29955										
OR5AP2	338675	hgsc.bcm.edu	37	chr11	56409796	56409796	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	cccaccatgtttgccatataGatcaacagaaacaatgcaaa	5	11	1	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr11:56409796G>T	ENST00000302981.1	-	1	119	c.120C>A	c.(118-120)atC>atA	p.I40I	OR5AP2_ENST00000544374.1_Silent_p.I41I	NM_001002925.1	NP_001002925.1	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP, member 2	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	29						TTGCCATATAGATCAACAGAA	0.408																																					p.I40I		Atlas-SNP	.											.	OR5AP2	69	.	0			c.C120A						.						104	96	99					11																	56409796		2201	4296	6497	SO:0001819	synonymous_variant	338675	exon1			CATATAGATCAAC	AB065854	CCDS31534.1	11q11	2012-08-09			ENSG00000172464	ENSG00000172464		"GPCR / Class A : Olfactory receptors"	15258	protein-coding gene	gene with protein product							Standard	NM_001002925		Approved		uc001njb.1	Q8NGF4	OTTHUMG00000166865	ENST00000302981.1:c.120C>A	chr11.hg19:g.56409796G>T		62.0	0.0		100.0	43.0	NM_001002925	B2RNM8	Silent	SNP	ENST00000302981.1	hg19	CCDS31534.1																																																																																			.	.		0.408	OR5AP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391613.1	NM_001002925		T	56409796	G	T	56409796	2	4	206	1	0	0	0	0	0	0	0	1	11153	932	33	3		3	OR5AP2	11	56409796	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10		56409796	78596720	38	29956										
SLC25A45	283130	hgsc.bcm.edu	37	chr11	65147644	65147644	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tcccaggaccaagcccagagCgcctgtggtgacaagagggt	14	12	0	3			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr11:65147644C>T	ENST00000527174.1	-	2	95	c.40G>A	c.(40-42)Gct>Act	p.A14T	SLC25A45_ENST00000360662.3_Missense_Mutation_p.A14T|SLC25A45_ENST00000294187.6_5'UTR|SLC25A45_ENST00000417511.2_5'UTR|SLC25A45_ENST00000526432.1_Missense_Mutation_p.A14T|SLC25A45_ENST00000398802.1_Missense_Mutation_p.A14T|SLC25A45_ENST00000534028.1_Missense_Mutation_p.A14T|SLC25A45_ENST00000377152.2_5'UTR			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	14					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14						AAGCCCAGAGCGCCTGTGGTG	0.567																																					p.A14T		Atlas-SNP	.											.	SLC25A45	23	.	0			c.G40A						.						113	120	118					11																	65147644		1995	4177	6172	SO:0001583	missense	283130	exon3			CCAGAGCGCCTGT	BC041100	CCDS41670.1, CCDS41671.1, CCDS60850.1	11q13.1	2013-05-22			ENSG00000162241	ENSG00000162241		"Solute carriers"	27442	protein-coding gene	gene with protein product		610825				16949250	Standard	XM_006718507		Approved		uc001odr.1	Q8N413	OTTHUMG00000166255	ENST00000527174.1:c.40G>A	chr11.hg19:g.65147644C>T	ENSP00000435489:p.Ala14Thr	94.0	0.0		108.0	55.0	NM_182556	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	hg19	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	C	33	5.265812	0.95399	.	.	ENSG00000162241	ENST00000527174;ENST00000534028;ENST00000398802;ENST00000360662;ENST00000526432;ENST00000530936	T;T;T;T;T;T	0.81163	-1.46;-1.28;-1.46;-1.28;-1.46;-1.46	4.38	4.38	0.52667	Mitochondrial carrier domain (2);	0.263149	0.28989	N	0.013500	D	0.84665	0.5522	L	0.47716	1.5	0.80722	D	1	D;D;P	0.89917	1.0;0.991;0.951	D;P;P	0.69142	0.962;0.856;0.819	D	0.85095	0.0954	10	0.54805	T	0.06	-0.0071	12.3081	0.54914	0.0:1.0:0.0:0.0	.	14;14;14	E9PJQ3;Q8N413-4;Q8N413	.;.;S2545_HUMAN	T	14	ENSP00000435489:A14T;ENSP00000431769:A14T;ENSP00000381782:A14T;ENSP00000353879:A14T;ENSP00000435547:A14T;ENSP00000431642:A14T	ENSP00000353879:A14T	A	-	1	0	SLC25A45	64904220	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	5.091000	0.64505	2.251000	0.74343	0.561000	0.74099	GCT	.	.		0.567	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556		T	65147644	C	T	65147644	3	4	206	1	0	0	0	0	1	0	0	0	14525	768	27	1	846	1	SLC25A45	11	65147644	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	8737848	65147644	69858872	39	29957										
OR10S1	219873	hgsc.bcm.edu	37	chr11	123847876	123847876	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gagcaggcggaaggtgagggAggtgtggattgcagcgtgcg	22	5	0	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr11:123847876A>C	ENST00000531945.1	-	1	612	c.523T>G	c.(523-525)Tcc>Gcc	p.S175A		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		AAGGTGAGGGAGGTGTGGATT	0.567																																					p.S175A		Atlas-SNP	.											.	OR10S1	78	.	0			c.T523G						.						109	95	100					11																	123847876		2202	4299	6501	SO:0001583	missense	219873	exon1			TGAGGGAGGTGTG	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"GPCR / Class A : Olfactory receptors"	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.523T>G	chr11.hg19:g.123847876A>C	ENSP00000431914:p.Ser175Ala	76.0	0.0		115.0	28.0	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	hg19	CCDS31701.1	.	.	.	.	.	.	.	.	.	.	A	2.309	-0.358464	0.05138	.	.	ENSG00000196248	ENST00000531945	T	0.36699	1.24	4.71	0.886	0.19194	GPCR, rhodopsin-like superfamily (1);	0.181219	0.26680	U	0.023059	T	0.17619	0.0423	N	0.20610	0.595	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.26121	-1.0112	10	0.12430	T	0.62	-16.6409	6.7698	0.23587	0.3981:0.3651:0.0:0.2367	.	175	Q8NGN2	O10S1_HUMAN	A	175	ENSP00000431914:S175A	ENSP00000431914:S175A	S	-	1	0	OR10S1	123353086	0.000000	0.05858	0.525000	0.27900	0.669000	0.39330	-0.899000	0.04101	-0.008000	0.14320	-0.511000	0.04467	TCC	.	.		0.567	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474		C	123847876	A	C	123847876	3	2	206	1	0	0	0	0	1	0	0	0	10927	304	11	5	476	5	OR10S1	11	123847876	Missense_Mutation	SNP	A	TCGA-DD-AAE0-01A-11D-A40R-10	58700232	123847876	11158640	40	29958										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133816010	133816010	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gccaaacttgatgaagatagGgatggggaccccgaacttga	13	8	0	4			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr11:133816010G>C	ENST00000321016.8	-	2	438	c.208C>G	c.(208-210)Cct>Gct	p.P70A	IGSF9B_ENST00000533871.2_Missense_Mutation_p.P70A			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	70	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		ATGAAGATAGGGATGGGGACC	0.617																																					p.P70A		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C208G						.						54	65	61					11																	133816010		2100	4207	6307	SO:0001583	missense	22997	exon2			AGATAGGGATGGG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.208C>G	chr11.hg19:g.133816010G>C	ENSP00000317980:p.Pro70Ala	110.0	0.0		140.0	64.0	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	G	23.0	4.360763	0.82353	.	.	ENSG00000080854	ENST00000321016;ENST00000527648;ENST00000533160;ENST00000526663	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.68	4.77	0.60923	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.081500	0.48767	D	0.000164	T	0.81370	0.4808	M	0.77486	2.375	0.58432	D	0.999994	D	0.64830	0.994	D	0.78314	0.991	D	0.83727	0.0196	10	0.66056	D	0.02	.	14.3176	0.66463	0.0722:0.0:0.9278:0.0	.	70	Q9UPX0	TUTLB_HUMAN	A	70;70;60;117	ENSP00000317980:P70A;ENSP00000436576:P70A;ENSP00000434026:P60A;ENSP00000435989:P117A	ENSP00000317980:P70A	P	-	1	0	IGSF9B	133321220	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	9.738000	0.98835	1.415000	0.47037	0.655000	0.94253	CCT	.	.		0.617	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		C	133816010	G	C	133816010	3	2	206	1	0	0	0	0	1	0	0	0	7615	1232	43	4	3913	4	IGSF9B	11	133816010	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	9968134	133816010	1190506	41	29959										
CS	1431	hgsc.bcm.edu	37	chr12	56676233	56676233	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	cttggttcggctgataccctGtgcatatgctcgggcaaagt	12	10	0	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr12:56676233G>A	ENST00000351328.3	-	6	749	c.559C>T	c.(559-561)Cag>Tag	p.Q187*	CS_ENST00000548567.1_Nonsense_Mutation_p.Q121*|CS_ENST00000542324.2_Nonsense_Mutation_p.Q174*	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	187				Q -> R (in Ref. 1; AAC25560). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		CTGATACCCTGTGCATATGCT	0.507																																					p.Q187X		Atlas-SNP	.											.	CS	44	.	0			c.C559T						.						102	77	86					12																	56676233		2203	4300	6503	SO:0001587	stop_gained	1431	exon6			TACCCTGTGCATA		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.559C>T	chr12.hg19:g.56676233G>A	ENSP00000342056:p.Gln187*	103.0	0.0		132.0	8.0	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Nonsense_Mutation	SNP	ENST00000351328.3	hg19	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444473	0.83993	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000542324;ENST00000549221;ENST00000546930;ENST00000551936;ENST00000550734;ENST00000551253;ENST00000552688;ENST00000546554	.	.	.	4.79	2.95	0.34219	.	0.098661	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.4858	14.6063	0.68481	0.0:0.7188:0.2812:0.0	.	.	.	.	X	121;187;174;112;121;121;121;121;151;137	.	ENSP00000342056:Q187X	Q	-	1	0	CS	54962500	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.603000	0.61105	0.695000	0.31675	-0.139000	0.14373	CAG	.	.		0.507	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077		A	56676233	G	A	56676233	4	1	206	1	0	0	0	0	0	1	0	0	3926	1386	48	3	865	3	CS	12	56676233	Nonsense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10		56676233	77175662	42	29960										
RNF17	56163	hgsc.bcm.edu	37	chr13	25433221	25433221	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gagccttatttctggaaaaaAggagaagcatgtgcagtaag	12	5	1	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr13:25433221A>G	ENST00000255324.5	+	26	3745	c.3693A>G	c.(3691-3693)aaA>aaG	p.K1231K	RNF17_ENST00000339524.3_Silent_p.K283K|RNF17_ENST00000381921.1_Silent_p.K1231K	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1231	Tudor 3. {ECO:0000255|PROSITE- ProRule:PRU00211}.				multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		TCTGGAAAAAAGGAGAAGCAT	0.368																																					p.K1231K		Atlas-SNP	.											.	RNF17	259	.	0			c.A3693G						.						100	98	99					13																	25433221		2203	4300	6503	SO:0001819	synonymous_variant	56163	exon26			GAAAAAAGGAGAA	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.3693A>G	chr13.hg19:g.25433221A>G		107.0	0.0		78.0	4.0	NM_031277	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	hg19	CCDS9308.2																																																																																			.	.		0.368	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		G	25433221	A	G	25433221	2	3	206	1	0	0	0	0	0	0	0	1	13476	69	3	2		2	RNF17	13	25433221	Silent	SNP	A	TCGA-DD-AAE0-01A-11D-A40R-10		25433221	89736657	43	29961										
FLT1	2321	hgsc.bcm.edu	37	chr13	29012442	29012442	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tcagtcatgtgtataatttcGgggatttcactgtacatctc	8	8	4	0	rs537466636		TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr13:29012442G>A	ENST00000282397.4	-	4	680	c.429C>T	c.(427-429)ccC>ccT	p.P143P	FLT1_ENST00000539099.1_Silent_p.P143P|FLT1_ENST00000541932.1_Silent_p.P143P	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	143					blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GTATAATTTCGGGGATTTCAC	0.378																																					p.P143P		Atlas-SNP	.											.	FLT1	393	.	0			c.C429T						.						114	97	103					13																	29012442		2203	4300	6503	SO:0001819	synonymous_variant	2321	exon4			AATTTCGGGGATT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.429C>T	chr13.hg19:g.29012442G>A		55.0	0.0		39.0	15.0	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.		0.378	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			A	29012442	G	A	29012442	2	1	206	1	0	0	0	0	0	0	0	1	5949	1103	39	1		1	FLT1	13	29012442	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	3579221	29012442	86157436	44	29962										
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21541244	21541244	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ctgtgtgcagagcactctcgCcgccctgtatccaccctttg	9	16	1	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr14:21541244C>T	ENST00000298694.4	+	2	171	c.44C>T	c.(43-45)gCc>gTc	p.A15V	NDRG2_ENST00000403829.3_5'Flank|ARHGEF40_ENST00000298693.3_Missense_Mutation_p.A15V			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	15						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						AGCACTCTCGCCGCCCTGTAT	0.592																																					p.A15V		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.C44T						.						112	97	102					14																	21541244		2203	4300	6503	SO:0001583	missense	55701	exon2			CTCTCGCCGCCCT		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"Rho guanine nucleotide exchange factors"	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.44C>T	chr14.hg19:g.21541244C>T	ENSP00000298694:p.Ala15Val	55.0	0.0		46.0	9.0	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	hg19	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	C	33	5.200573	0.94997	.	.	ENSG00000165801	ENST00000298694;ENST00000555038;ENST00000298693	T;T	0.02890	4.17;4.12	5.03	5.03	0.67393	.	0.144353	0.31949	N	0.006808	T	0.09113	0.0225	L	0.52573	1.65	0.40116	D	0.976549	P;D	0.55605	0.792;0.972	B;P	0.56398	0.326;0.797	T	0.01448	-1.1352	10	0.72032	D	0.01	.	15.8973	0.79344	0.0:1.0:0.0:0.0	.	15;15	Q8TER5;G3V3N2	ARH40_HUMAN;.	V	15	ENSP00000298694:A15V;ENSP00000298693:A15V	ENSP00000298693:A15V	A	+	2	0	ARHGEF40	20611084	0.766000	0.28496	0.237000	0.24090	0.948000	0.59901	3.986000	0.56937	2.627000	0.88993	0.455000	0.32223	GCC	.	.		0.592	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			T	21541244	C	T	21541244	3	4	206	1	0	0	0	0	1	0	0	0	5934	739	26	3	50	3	FLJ10357	14	21541244	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10		21541244	85808296	45	29963										
HERC2	8924	hgsc.bcm.edu	37	chr15	28421672	28421672	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tttagtctctcaatgttctgGggaatgttacagccttcact	8	9	4	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr15:28421672G>A	ENST00000261609.7	-	63	9696	c.9588C>T	c.(9586-9588)ccC>ccT	p.P3196P		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CAATGTTCTGGGGAATGTTAC	0.502																																					p.P3196P		Atlas-SNP	.											.	HERC2	501	.	0			c.C9588T						.						82	86	85					15																	28421672		2203	4300	6503	SO:0001819	synonymous_variant	8924	exon63			GTTCTGGGGAATG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9588C>T	chr15.hg19:g.28421672G>A		153.0	0.0		118.0	26.0	NM_004667		Silent	SNP	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.502	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28421672	G	A	28421672	2	1	206	1	0	0	0	0	0	0	0	1	7067	1219	43	3		3	HERC2	15	28421672	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10		28421672	74109720	46	29964										
HDC	3067	hgsc.bcm.edu	37	chr15	50549685	50549685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	aagtgctctggaagtcccagCatttttgccaaccagtccat	8	12	1	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr15:50549685C>T	ENST00000267845.3	-	4	780	c.378G>A	c.(376-378)atG>atA	p.M126I	HDC_ENST00000543581.1_Missense_Mutation_p.M126I	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		GAAGTCCCAGCATTTTTGCCA	0.582																																					p.M126I	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.G378A						.						140	117	125					15																	50549685		2196	4295	6491	SO:0001583	missense	3067	exon4			TCCCAGCATTTTT		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.378G>A	chr15.hg19:g.50549685C>T	ENSP00000267845:p.Met126Ile	42.0	0.0		44.0	28.0	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	hg19	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.393593	0.42410	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.37411	1.2;1.2	5.13	5.13	0.70059	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.094456	0.64402	D	0.000001	T	0.55178	0.1904	M	0.69248	2.105	0.49299	D	0.999777	P;D	0.54047	0.909;0.964	P;P	0.56278	0.795;0.769	T	0.58747	-0.7582	10	0.87932	D	0	-31.9222	18.7731	0.91900	0.0:1.0:0.0:0.0	.	126;126	B7ZM01;P19113	.;DCHS_HUMAN	I	126	ENSP00000267845:M126I;ENSP00000440252:M126I	ENSP00000267845:M126I	M	-	3	0	HDC	48336977	1.000000	0.71417	1.000000	0.80357	0.217000	0.24651	2.305000	0.43664	2.675000	0.91044	0.655000	0.94253	ATG	.	.		0.582	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			T	50549685	C	T	50549685	3	4	206	1	0	0	0	0	1	0	0	0	7024	710	25	3	1646	3	HDC	15	50549685	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	22128013	50549685	51981707	47	29965										
ZSCAN10	84891	hgsc.bcm.edu	37	chr16	3139523	3139523	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gctgaagccctcaccgcactCgctgcagcggcagggcttct	12	16	2	1	rs540283059		TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr16:3139523C>A	ENST00000252463.2	-	5	1834	c.1747G>T	c.(1747-1749)Gag>Tag	p.E583*	RP11-473M20.9_ENST00000571404.1_lincRNA|ZSCAN10_ENST00000575108.1_Nonsense_Mutation_p.E244*|ZSCAN10_ENST00000538082.2_Nonsense_Mutation_p.E501*	NM_032805.1	NP_116194.1	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	583					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(3)|endometrium(3)|kidney(1)|lung(8)|ovary(2)|prostate(1)|skin(4)|urinary_tract(1)	24						TCACCGCACTCGCTGCAGCGG	0.706																																					p.E583X		Atlas-SNP	.											.	ZSCAN10	63	.	0			c.G1747T						.						14	15	15					16																	3139523		2187	4279	6466	SO:0001587	stop_gained	84891	exon5			CGCACTCGCTGCA	AA206569	CCDS10493.1, CCDS61813.1, CCDS61814.1	16p13.3	2013-01-08	2007-02-20	2007-02-20		ENSG00000130182		"-", "Zinc fingers, C2H2-type"	12997	protein-coding gene	gene with protein product			"zinc finger protein 206"	ZNF206		9653642	Standard	NM_032805		Approved		uc002ctv.1	Q96SZ4		ENST00000252463.2:c.1747G>T	chr16.hg19:g.3139523C>A	ENSP00000252463:p.Glu583*	74.0	0.0		44.0	15.0	NM_032805	B3KQD3|H0YFS6|Q1WWM2	Nonsense_Mutation	SNP	ENST00000252463.2	hg19	CCDS10493.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.739384	0.89573	.	.	ENSG00000130182	ENST00000538082;ENST00000252463	.	.	.	5.34	2.17	0.27698	.	0.275958	0.25813	N	0.028126	.	.	.	.	.	.	0.44985	D	0.998	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-16.2039	14.5971	0.68415	0.0:0.544:0.456:0.0	.	.	.	.	X	516;583	.	ENSP00000252463:E583X	E	-	1	0	ZSCAN10	3079524	0.000000	0.05858	0.978000	0.43139	0.875000	0.50365	-0.103000	0.10940	0.201000	0.20466	0.561000	0.74099	GAG	.	.		0.706	ZSCAN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437124.2	NM_032805		A	3139523	C	A	3139523	4	1	206	1	0	0	0	0	0	1	0	0	18242	893	31	1	434	1	ZSCAN10	16	3139523	Nonsense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10		3139523	87215230	48	29966										
TRAP1	10131	hgsc.bcm.edu	37	chr16	3713465	3713465	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ttctcctccttgtagtgatcCacgactatgtccgtctccac	6	15	2	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr16:3713465C>T	ENST00000246957.5	-	14	1756	c.1668G>A	c.(1666-1668)gtG>gtA	p.V556V	DNASE1_ENST00000414110.2_Intron|TRAP1_ENST00000538171.1_Silent_p.V503V|TRAP1_ENST00000573872.1_5'Flank|DNASE1_ENST00000575152.1_3'UTR|TRAP1_ENST00000575671.1_Silent_p.V347V	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	556					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				TGTAGTGATCCACGACTATGT	0.557																																					p.V556V		Atlas-SNP	.											.	TRAP1	53	.	0			c.G1668A						.						144	130	135					16																	3713465		2197	4300	6497	SO:0001819	synonymous_variant	10131	exon14			GTGATCCACGACT	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"Heat shock proteins / HSPC"	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.1668G>A	chr16.hg19:g.3713465C>T		64.0	0.0		39.0	19.0	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Silent	SNP	ENST00000246957.5	hg19	CCDS10508.1																																																																																			.	.		0.557	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292		T	3713465	C	T	3713465	2	4	206	1	0	0	0	0	0	0	0	1	16470	581	21	3		3	TRAP1	16	3713465	Silent	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	573942	3713465	86641288	49	29967										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31422687	31422687	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gcagggccacccctggggccGctttggggcagccctgacag	16	15	0	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr16:31422687G>A	ENST00000389202.2	+	14	1605	c.1556G>A	c.(1555-1557)cGc>cAc	p.R519H		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	519					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CCCTGGGGCCGCTTTGGGGCA	0.632																																					p.R519H		Atlas-SNP	.											.	ITGAD	154	.	0			c.G1556A						.						106	108	108					16																	31422687		2197	4300	6497	SO:0001583	missense	3681	exon14			GGGGCCGCTTTGG	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.1556G>A	chr16.hg19:g.31422687G>A	ENSP00000373854:p.Arg519His	110.0	0.0		81.0	23.0	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.066233	0.55539	.	.	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.26518	1.73	4.41	4.41	0.53225	.	.	.	.	.	T	0.34948	0.0915	M	0.87971	2.92	0.48830	D	0.999716	P;P	0.41159	0.74;0.74	B;B	0.37422	0.249;0.249	T	0.48007	-0.9072	9	0.87932	D	0	.	12.4936	0.55914	0.0:0.0:1.0:0.0	.	535;519	Q59H14;Q13349	.;ITAD_HUMAN	H	535;519	ENSP00000373854:R519H	ENSP00000373854:R519H	R	+	2	0	ITGAD	31330188	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	4.641000	0.61375	1.979000	0.57680	0.407000	0.27541	CGC	.	.		0.632	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		A	31422687	G	A	31422687	3	1	206	1	0	0	0	0	1	0	0	0	7893	1087	38	1	1610	1	ITGAD	16	31422687	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	27709222	31422687	58932066	50	29968										
PMFBP1	83449	hgsc.bcm.edu	37	chr16	72198723	72198723	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tcctgcaaggtcttcctctgTctcttgcagacatcgtgcag	9	13	3	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr16:72198723T>C	ENST00000237353.10	-	3	366	c.105A>G	c.(103-105)agA>agG	p.R35R	PMFBP1_ENST00000537465.1_Silent_p.R35R|PMFBP1_ENST00000543746.1_5'UTR|PMFBP1_ENST00000355636.6_5'UTR	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	35						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TCTTCCTCTGTCTCTTGCAGA	0.552																																					p.R35R		Atlas-SNP	.											.	PMFBP1	101	.	0			c.A105G						.						118	98	105					16																	72198723		2198	4300	6498	SO:0001819	synonymous_variant	83449	exon3			CCTCTGTCTCTTG	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.105A>G	chr16.hg19:g.72198723T>C		45.0	0.0		37.0	29.0	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Silent	SNP	ENST00000237353.10	hg19	CCDS32483.1																																																																																			.	.		0.552	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293		C	72198723	T	C	72198723	2	2	206	1	0	0	0	0	0	0	0	1	12143	1664	58	2		2	PMFBP1	16	72198723	Silent	SNP	T	TCGA-DD-AAE0-01A-11D-A40R-10	40776036	72198723	18156030	51	29969										
CDT1	81620	hgsc.bcm.edu	37	chr16	88871218	88871218	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tgcaacgggcccgggagctgGgggcaagagtccgggcgctg	20	11	0	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr16:88871218G>C	ENST00000301019.4	+	3	1019	c.400G>C	c.(400-402)Ggg>Cgg	p.G134R		NM_030928.3	NP_112190.2			chromatin licensing and DNA replication factor 1											central_nervous_system(1)|endometrium(2)|kidney(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(80;0.0476)		CCGGGAGCTGGGGGCAAGAGT	0.697																																					p.G134R	Melanoma(159;511 3380 30971)	Atlas-SNP	.											.	CDT1	30	.	0			c.G400C						.						24	26	26					16																	88871218		2192	4296	6488	SO:0001583	missense	81620	exon3			GAGCTGGGGGCAA	AF070552	CCDS32510.1	16q24.3	2014-08-12			ENSG00000167513	ENSG00000167513			24576	protein-coding gene	gene with protein product		605525				11896191, 11555648	Standard	NM_030928		Approved	DUP, RIS2	uc002flu.3	Q9H211	OTTHUMG00000173467	ENST00000301019.4:c.400G>C	chr16.hg19:g.88871218G>C	ENSP00000301019:p.Gly134Arg	88.0	0.0		87.0	66.0	NM_030928		Missense_Mutation	SNP	ENST00000301019.4	hg19	CCDS32510.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.588602	0.46110	.	.	ENSG00000167513	ENST00000301019	T	0.61392	0.11	4.26	4.26	0.50523	.	0.642546	0.15873	N	0.240431	T	0.64360	0.2591	M	0.69823	2.125	0.30075	N	0.809704	D	0.61697	0.99	P	0.50754	0.649	T	0.62859	-0.6765	10	0.17369	T	0.5	.	15.6733	0.77295	0.0:0.0:1.0:0.0	.	134	Q9H211	CDT1_HUMAN	R	134	ENSP00000301019:G134R	ENSP00000301019:G134R	G	+	1	0	CDT1	87398719	0.997000	0.39634	0.935000	0.37517	0.055000	0.15305	2.272000	0.43373	2.106000	0.64143	0.449000	0.29647	GGG	.	.		0.697	CDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423215.1	NM_030928		C	88871218	G	C	88871218	3	2	206	1	0	0	0	0	1	0	0	0	3182	1232	43	4	410	4	CDT1	16	88871218	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	16672495	88871218	1483535	52	29970										
TP53	7157	hgsc.bcm.edu	37	chr17	7577524	7577524	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gtcttccagtgtgatgatggTgaggatgggcctccggttca	15	8	2	3			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr17:7577524T>C	ENST00000269305.4	-	7	946	c.757A>G	c.(757-759)Acc>Gcc	p.T253A	TP53_ENST00000420246.2_Missense_Mutation_p.T253A|TP53_ENST00000455263.2_Missense_Mutation_p.T253A|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.T253A|TP53_ENST00000413465.2_Missense_Mutation_p.T253A|TP53_ENST00000445888.2_Missense_Mutation_p.T253A	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	253	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		T -> A (in sporadic cancers; somatic mutation).|T -> I (in sporadic cancers; somatic mutation).|T -> N (in sporadic cancers; somatic mutation).|T -> P (in sporadic cancers; somatic mutation).|T -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.T253S(5)|p.L252_I254delLTI(4)|p.I251_T253delILT(4)|p.T253P(3)|p.T253A(3)|p.T253fs*91(2)|p.T253_I255del(2)|p.L252_T253delLT(1)|p.?(1)|p.P250_T253delPILT(1)|p.T253del(1)|p.T253fs*11(1)|p.R249_T256delRPILTIIT(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGATGATGGTGAGGATGGGC	0.582		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.T253A	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000413465,NS,carcinoma,+1,1	TP53	33396	.	37	Deletion - In frame(14)|Substitution - Missense(11)|Whole gene deletion(8)|Deletion - Frameshift(2)|Insertion - Frameshift(1)|Unknown(1)	large_intestine(9)|upper_aerodigestive_tract(6)|breast(4)|bone(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|skin(2)|stomach(1)|small_intestine(1)|kidney(1)|peritoneum(1)|lung(1)|ovary(1)	c.A757G						.						151	109	123					17																	7577524		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TGATGGTGAGGAT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.757A>G	chr17.hg19:g.7577524T>C	ENSP00000269305:p.Thr253Ala	77.0	0.0		62.0	38.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.957685	0.53400	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99771	-6.71;-6.71;-6.71;-6.71;-6.71;-6.71;-6.71	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.050471	0.85682	D	0.000000	D	0.99579	0.9848	L	0.59436	1.845	0.49051	D	0.999748	P;B;P;D;D	0.89917	0.936;0.017;0.948;0.999;1.0	P;B;D;D;D	0.97110	0.813;0.082;0.95;1.0;0.997	D	0.97646	1.0151	10	0.72032	D	0.01	-33.513	12.3101	0.54924	0.0:0.0:0.0:1.0	.	253;253;253;253;253	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	A	253;253;253;253;253;253;242;121	ENSP00000410739:T253A;ENSP00000352610:T253A;ENSP00000269305:T253A;ENSP00000398846:T253A;ENSP00000391127:T253A;ENSP00000391478:T253A;ENSP00000425104:T121A	ENSP00000269305:T253A	T	-	1	0	TP53	7518249	1.000000	0.71417	1.000000	0.80357	0.375000	0.29983	4.030000	0.57260	2.074000	0.62210	0.379000	0.24179	ACC	.	.		0.582	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577524	T	C	7577524	3	2	206	1	0	0	0	0	1	0	0	0	16396	1696	59	2	533	2	TP53	17	7577524	Missense_Mutation	SNP	T	TCGA-DD-AAE0-01A-11D-A40R-10		7577524	73617686	53	29971										
KRT10	3858	hgsc.bcm.edu	37	chr17	38975319	38975319	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gccggaactgccgccgtggcCgccgccgtggccgccgccgg	17	19	0	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr17:38975319C>T	ENST00000269576.5	-	7	1477	c.1468G>A	c.(1468-1470)Ggc>Agc	p.G490S	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ccgccgtggccgccgccgtgg	0.791																																					p.G490S		Atlas-SNP	.											.	KRT10	56	.	0			c.G1468A						.																																			SO:0001583	missense	3858	exon7			CGTGGCCGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1468G>A	chr17.hg19:g.38975319C>T	ENSP00000269576:p.Gly490Ser	62.0	0.0		143.0	9.0	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546565	0.86022	.	.	ENSG00000186395	ENST00000269576	D	0.96587	-4.06	4.38	4.38	0.52667	.	0.845686	0.09879	N	0.743932	D	0.94778	0.8314	N	0.08118	0	0.27860	N	0.940431	D	0.89917	1.0	D	0.76071	0.987	D	0.87790	0.2618	10	0.18710	T	0.47	.	12.7512	0.57310	0.0:1.0:0.0:0.0	.	490	P13645	K1C10_HUMAN	S	490	ENSP00000269576:G490S	ENSP00000269576:G490S	G	-	1	0	KRT10	36228845	0.019000	0.18553	0.876000	0.34364	0.184000	0.23303	0.448000	0.21726	2.739000	0.93911	0.603000	0.83216	GGC	.	.		0.791	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		T	38975319	C	T	38975319	3	4	206	1	0	0	0	0	1	0	0	0	8457	652	23	1	294	1	KRT10	17	38975319	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	31397795	38975319	42219891	54	29972										
KRT9	3857	hgsc.bcm.edu	37	chr17	39726179	39726179	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	atactgcatctccaggtcagActtctccatggtcagattgt	8	11	4	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr17:39726179A>T	ENST00000246662.4	-	3	879	c.814T>A	c.(814-816)Tct>Act	p.S272T	KRT9_ENST00000588431.1_Missense_Mutation_p.S39T	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	272	Coil 1B.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				TCCAGGTCAGACTTCTCCATG	0.542																																					p.S272T		Atlas-SNP	.											.	KRT9	78	.	0			c.T814A						.						90	92	91					17																	39726179		2203	4300	6503	SO:0001583	missense	3857	exon3			GGTCAGACTTCTC		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"-", "Intermediate filaments type I, keratins (acidic)"	6447	protein-coding gene	gene with protein product	"cytokeratin 9", "type I cytoskeletal 9", "epidermolytic palmoplantar keratoderma"	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.814T>A	chr17.hg19:g.39726179A>T	ENSP00000246662:p.Ser272Thr	66.0	0.0		86.0	47.0	NM_000226	O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	hg19	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.695699	0.30052	.	.	ENSG00000171403	ENST00000246662	D	0.88509	-2.39	4.96	-1.29	0.09288	Filament (1);	0.282712	0.19284	N	0.118085	T	0.77565	0.4149	N	0.21545	0.675	0.09310	N	1	B	0.22080	0.064	B	0.28553	0.091	T	0.62714	-0.6796	10	0.21540	T	0.41	.	7.2841	0.26328	0.4118:0.3829:0.0:0.2053	.	272	P35527	K1C9_HUMAN	T	272	ENSP00000246662:S272T	ENSP00000246662:S272T	S	-	1	0	KRT9	36979705	0.000000	0.05858	0.411000	0.26484	0.828000	0.46876	-1.554000	0.02172	-0.094000	0.12374	0.402000	0.26972	TCT	.	.		0.542	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		T	39726179	A	T	39726179	3	4	206	1	0	0	0	0	1	0	0	0	8510	275	10	4	1077	4	KRT9	17	39726179	Missense_Mutation	SNP	A	TCGA-DD-AAE0-01A-11D-A40R-10	750860	39726179	41469031	55	29973										
ARHGAP27	201176	hgsc.bcm.edu	37	chr17	43480082	43480082	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	cccaaccccgccactcacctCcagcacattcttcctactgg	4	21	2	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr17:43480082C>T	ENST00000428638.1	-	9	1740	c.1741G>A	c.(1741-1743)Gag>Aag	p.E581K	ARHGAP27_ENST00000528384.1_Missense_Mutation_p.E213K|ARHGAP27_ENST00000532891.2_Missense_Mutation_p.E559K|ARHGAP27_ENST00000582826.1_5'UTR|ARHGAP27_ENST00000442348.1_Missense_Mutation_p.E554K|ARHGAP27_ENST00000532038.1_Missense_Mutation_p.E359K|ARHGAP27_ENST00000455881.1_Missense_Mutation_p.E240K|ARHGAP27_ENST00000376922.2_Missense_Mutation_p.E240K			Q6ZUM4	RHG27_HUMAN	Rho GTPase activating protein 27	581	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of Rac GTPase activity (GO:0032855)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|SH3 domain binding (GO:0017124)			endometrium(4)|large_intestine(9)|lung(3)|skin(1)	17	Renal(3;0.0405)					CCACTCACCTCCAGCACATTC	0.567																																					p.E240K		Atlas-SNP	.											.	ARHGAP27	37	.	0			c.G718A						.						66	66	66					17																	43480082		2203	4300	6503	SO:0001583	missense	201176	exon9			TCACCTCCAGCAC	AK125535	CCDS11498.1, CCDS74082.1	17q21.31	2013-01-10			ENSG00000159314	ENSG00000159314		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	31813	protein-coding gene	gene with protein product		610591	"SH3 domain containing 20"	SH3D20		15147912	Standard	NM_199282		Approved	CAMGAP1, FLJ43547, SH3P20	uc002iix.3	Q6ZUM4	OTTHUMG00000166982	ENST00000428638.1:c.1741G>A	chr17.hg19:g.43480082C>T	ENSP00000403323:p.Glu581Lys	32.0	0.0		61.0	19.0	NM_199282	A4FU35|A8K3N5|C9JTF3|Q494U0|Q6NWZ8|Q8WY58	Missense_Mutation	SNP	ENST00000428638.1	hg19		.	.	.	.	.	.	.	.	.	.	C	29.2	4.981708	0.93044	.	.	ENSG00000159314	ENST00000532038;ENST00000376922;ENST00000528384;ENST00000532891;ENST00000428638;ENST00000442348;ENST00000455881	T;T;T;T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93;-0.93;-0.93;-0.93	5.01	3.99	0.46301	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.78451	0.4285	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.993;0.996	T	0.78250	-0.2277	10	0.48119	T	0.1	.	13.3841	0.60785	0.0:0.8419:0.1581:0.0	.	359;554;581	B7Z6T0;F8WBX1;Q6ZUM4	.;.;RHG27_HUMAN	K	359;240;213;559;581;554;240	ENSP00000432762:E359K;ENSP00000366121:E240K;ENSP00000431591:E213K;ENSP00000433942:E559K;ENSP00000403323:E581K;ENSP00000409330:E554K;ENSP00000408235:E240K	ENSP00000366121:E240K	E	-	1	0	ARHGAP27	40835865	0.998000	0.40836	1.000000	0.80357	0.899000	0.52679	3.757000	0.55212	2.603000	0.88011	0.455000	0.32223	GAG	.	.		0.567	ARHGAP27-202	KNOWN	basic	protein_coding	protein_coding		NM_199282		T	43480082	C	T	43480082	3	4	206	1	0	0	0	0	1	0	0	0	876	864	30	3	964	3	ARHGAP27	17	43480082	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	3753903	43480082	37715128	56	29974										
NACA2	342538	hgsc.bcm.edu	37	chr17	59668029	59668029	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	acttctacacctgtttcatcGacctcttcctcttcactctc	2	17	6	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr17:59668029G>A	ENST00000521764.1	-	1	534	c.513C>T	c.(511-513)gtC>gtT	p.V171V		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	171					myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					CTGTTTCATCGACCTCTTCCT	0.448																																					p.V171V		Atlas-SNP	.											.	NACA2	33	.	0			c.C513T						.						300	271	281					17																	59668029		2203	4300	6503	SO:0001819	synonymous_variant	342538	exon1			TTCATCGACCTCT	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"alpha-NAC protein"	609274	"nascent-polypeptide-associated complex alpha polypeptide-like"	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.513C>T	chr17.hg19:g.59668029G>A		67.0	0.0		63.0	7.0	NM_199290	Q2VIR9	Silent	SNP	ENST00000521764.1	hg19	CCDS11630.1																																																																																			.	.		0.448	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290		A	59668029	G	A	59668029	2	1	206	1	0	0	0	0	0	0	0	1	10143	1045	37	1		1	NACA2	17	59668029	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	16187947	59668029	21527181	57	29975										
SLMO1	10650	hgsc.bcm.edu	37	chr18	12427045	12427045	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ttttttctttttaagatcacActcacaaatttggtgtcagt	5	7	4	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr18:12427045A>G	ENST00000440960.1	+	4	377	c.297A>G	c.(295-297)acA>acG	p.T99T	SLMO1_ENST00000590956.1_Silent_p.T9T|SLMO1_ENST00000587735.1_Silent_p.T9T|SLMO1_ENST00000592149.1_Silent_p.T78T|SLMO1_ENST00000336990.4_Silent_p.T99T	NM_001142405.1	NP_001135877.1	Q96N28	SLMO1_HUMAN	slowmo homolog 1 (Drosophila)	99	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)			endometrium(1)	1						TTAAGATCACACTCACAAATT	0.393																																					p.T99T		Atlas-SNP	.											.	SLMO1	11	.	0			c.A297G						.						64	59	60					18																	12427045		2203	4300	6503	SO:0001819	synonymous_variant	10650	exon4			GATCACACTCACA	AK056046	CCDS11860.1	18p11.21	2007-02-20	2007-02-06	2007-02-06	ENSG00000141391	ENSG00000141391			24639	protein-coding gene	gene with protein product	"erythroid differentiation and denucleation factor 1"		"chromosome 18 open reading frame 43"	C18orf43			Standard	NM_006553		Approved	HFL-EDDG1, FLJ31484, PRELID3A	uc010wzu.2	Q96N28	OTTHUMG00000131694	ENST00000440960.1:c.297A>G	chr18.hg19:g.12427045A>G		110.0	0.0		105.0	52.0	NM_001142405	B0YJ10|B4E0C9|D3DUJ1|Q6AHX2	Silent	SNP	ENST00000440960.1	hg19	CCDS11860.1																																																																																			.	.		0.393	SLMO1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254602.2	NM_006553		G	12427045	A	G	12427045	2	3	206	1	0	0	0	0	0	0	0	1	14765	146	6	2		2	SLMO1	18	12427045	Silent	SNP	A	TCGA-DD-AAE0-01A-11D-A40R-10		12427045	65650203	58	29976										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22804905	22804905	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	actctggagaggcatcttgcAaatccggcagtttccagtat	10	10	2	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr18:22804905A>T	ENST00000361524.3	-	4	3125	c.2977T>A	c.(2977-2979)Tgc>Agc	p.C993S	ZNF521_ENST00000538137.2_Missense_Mutation_p.C993S|ZNF521_ENST00000584787.1_Missense_Mutation_p.C773S|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	993					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GGCATCTTGCAAATCCGGCAG	0.483			T	PAX5	ALL																																p.C993S		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.T2977A						.						63	62	62					18																	22804905		2203	4300	6503	SO:0001583	missense	25925	exon4			TCTTGCAAATCCG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2977T>A	chr18.hg19:g.22804905A>T	ENSP00000354794:p.Cys993Ser	43.0	0.0		50.0	19.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	A	11.79	1.743010	0.30865	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.39056	1.1;1.4	5.97	5.97	0.96955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.54581	0.1867	L	0.29908	0.895	0.48511	D	0.999665	D	0.89917	1.0	D	0.85130	0.997	T	0.58120	-0.7692	10	0.87932	D	0	-25.0859	16.4473	0.83942	1.0:0.0:0.0:0.0	.	993	Q96K83	ZN521_HUMAN	S	993;1027;993	ENSP00000354794:C993S;ENSP00000382352:C993S	ENSP00000354794:C993S	C	-	1	0	ZNF521	21058903	1.000000	0.71417	0.982000	0.44146	0.998000	0.95712	8.962000	0.93254	2.281000	0.76405	0.533000	0.62120	TGC	.	.		0.483	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		T	22804905	A	T	22804905	3	4	206	1	0	0	0	0	1	0	0	0	17980	130	5	4	978	4	ZNF521	18	22804905	Missense_Mutation	SNP	A	TCGA-DD-AAE0-01A-11D-A40R-10	10377860	22804905	55272343	59	29977										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48575093	48575093	+	Frame_Shift_Del	DEL	C	C	-													0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	atttcctcatgtgatctatgCccgtctctggaggtggcctg							TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr18:48575093delC	ENST00000342988.3	+	3	825	c.287delC	c.(286-288)gccfs	p.A96fs	SMAD4_ENST00000452201.2_Frame_Shift_Del_p.A96fs|SMAD4_ENST00000588745.1_Frame_Shift_Del_p.A96fs|SMAD4_ENST00000398417.2_Frame_Shift_Del_p.A96fs|RP11-729L2.2_ENST00000590722.2_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	96	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(4)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GTGATCTATGCCCGTCTCTGG	0.368																																					p.A96fs		Atlas-INDEL	.											.	SMAD4	822	.	40	Whole gene deletion(36)|Unknown(4)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|NS(1)	c.286delG						.						155	142	147					18																	48575093		2203	4300	6503	SO:0001589	frameshift_variant	4089	exon3			.	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.287delC	chr18.hg19:g.48575093delC	ENSP00000341551:p.Ala96fs	107.0	0.0		74.0	12.0	NM_005359	A8K405	Frame_Shift_Del	DEL	ENST00000342988.3	hg19	CCDS11950.1																																																																																			.	.		0.368	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		-	48575093	C	-	48575093	7	5	206	1	0	1	0	1	0	0	0	0	14775	739	26	0	293	0	SMAD4	18	48575093	Frame_Shift_Del	DEL	C	TCGA-DD-AAE0-01A-11D-A40R-10	25770188	48575093	29502155	60	29978										
SMAD4	4089	hgsc.bcm.edu	37	chr18	48591919	48591919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ggacccttctggaggagatcGcttttgtttgggtcaactct	12	9	3	1	rs377767347		TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr18:48591919G>A	ENST00000342988.3	+	9	1620	c.1082G>A	c.(1081-1083)cGc>cAc	p.R361H	SMAD4_ENST00000588745.1_Missense_Mutation_p.R265H|SMAD4_ENST00000398417.2_Missense_Mutation_p.R361H	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	361	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		R -> C (in JPS; dbSNP:rs80338963). {ECO:0000269|PubMed:9811934}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.R361H(12)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GGAGGAGATCGCTTTTGTTTG	0.413																																					p.R361H		Atlas-SNP	.											SMAD4,caecum,carcinoma,+1,22	SMAD4	822	.	50	Whole gene deletion(36)|Substitution - Missense(12)|Unknown(2)	pancreas(26)|large_intestine(13)|lung(3)|breast(3)|upper_aerodigestive_tract(2)|stomach(2)|oesophagus(1)	c.G1082A	GRCh37	CM004254	SMAD4	M		.						167	138	148					18																	48591919		2203	4300	6503	SO:0001583	missense	4089	exon9			GAGATCGCTTTTG	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1082G>A	chr18.hg19:g.48591919G>A	ENSP00000341551:p.Arg361His	85.0	0.0		57.0	21.0	NM_005359	A8K405	Missense_Mutation	SNP	ENST00000342988.3	hg19	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	35	5.477304	0.96291	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.98120	-4.73;-4.73	5.86	5.86	0.93980	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98852	0.9612	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99741	1.1015	10	0.87932	D	0	.	18.9646	0.92691	0.0:0.0:1.0:0.0	.	361	Q13485	SMAD4_HUMAN	H	361	ENSP00000341551:R361H;ENSP00000381452:R361H	ENSP00000341551:R361H	R	+	2	0	SMAD4	46845917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.828000	0.86729	2.771000	0.95319	0.563000	0.77884	CGC	.	.		0.413	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48591919	G	A	48591919	3	1	206	1	0	0	0	0	1	0	0	0	14775	1087	38	1	1112	1	SMAD4	18	48591919	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	16826	48591919	29485329	61	29979										
CCDC102B	79839	hgsc.bcm.edu	37	chr18	66504069	66504069	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	cagatgcaacaatcatcaatTaagtcacgcggcgacatggt	9	10	3	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr18:66504069T>A	ENST00000360242.5	+	2	186	c.69T>A	c.(67-69)atT>atA	p.I23I	CCDC102B_ENST00000584156.1_Silent_p.I23I|CCDC102B_ENST00000319445.6_Silent_p.I23I|CCDC102B_ENST00000577772.1_3'UTR|CCDC102B_ENST00000358653.5_Silent_p.I23I	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	23										breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				AATCATCAATTAAGTCACGCG	0.423																																					p.I23I		Atlas-SNP	.											.	CCDC102B	92	.	0			c.T69A						.						62	63	63					18																	66504069		1948	4115	6063	SO:0001819	synonymous_variant	79839	exon4			ATCAATTAAGTCA	AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 14", "aminoacylase 1-like"	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.69T>A	chr18.hg19:g.66504069T>A		69.0	0.0		36.0	5.0	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Silent	SNP	ENST00000360242.5	hg19	CCDS11996.2																																																																																			.	.		0.423	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781		A	66504069	T	A	66504069	2	1	206	1	0	0	0	0	0	0	0	1	2739	1742	61	4		4	CCDC102B	18	66504069	Silent	SNP	T	TCGA-DD-AAE0-01A-11D-A40R-10	17912150	66504069	11573179	62	29980										
CD97	976	hgsc.bcm.edu	37	chr19	14501784	14501784	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	agtgtcatgcggaaaattctCggactgctggaacacagagg	13	8	2	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr19:14501784C>T	ENST00000242786.5	+	4	319	c.239C>T	c.(238-240)tCg>tTg	p.S80L	CD97_ENST00000587728.1_3'UTR|CD97_ENST00000357355.3_Missense_Mutation_p.S80L|CD97_ENST00000358600.3_Missense_Mutation_p.S80L	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	80	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GGAAAATTCTCGGACTGCTGG	0.522																																					p.S80L		Atlas-SNP	.											.	CD97	86	.	0			c.C239T						.						132	102	113					19																	14501784		2203	4300	6503	SO:0001583	missense	976	exon4			AATTCTCGGACTG		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.239C>T	chr19.hg19:g.14501784C>T	ENSP00000242786:p.Ser80Leu	111.0	0.0		160.0	31.0	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Missense_Mutation	SNP	ENST00000242786.5	hg19	CCDS32929.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.590001	0.46214	.	.	ENSG00000123146	ENST00000242786;ENST00000357355;ENST00000358600;ENST00000393059	D;D;D	0.92149	-2.98;-2.98;-2.98	4.39	4.39	0.52855	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.91616	0.7351	L	0.41961	1.31	0.09310	N	1	D;B;D	0.54397	0.966;0.441;0.96	B;B;P	0.51895	0.382;0.124;0.683	D	0.85321	0.1084	9	0.87932	D	0	.	12.3432	0.55105	0.0:1.0:0.0:0.0	.	80;80;80	P48960-2;P48960-3;P48960	.;.;CD97_HUMAN	L	80;80;80;79	ENSP00000242786:S80L;ENSP00000349918:S80L;ENSP00000351413:S80L	ENSP00000242786:S80L	S	+	2	0	CD97	14362784	0.294000	0.24380	0.019000	0.16419	0.002000	0.02628	3.269000	0.51592	2.288000	0.76882	0.563000	0.77884	TCG	.	.		0.522	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		T	14501784	C	T	14501784	3	4	206	1	0	0	0	0	1	0	0	0	3051	893	31	1	253	1	CD97	19	14501784	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10		14501784	44627199	63	29981										
HPN	3249	hgsc.bcm.edu	37	chr19	35540393	35540393	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ctgcagtggctgttctcctcAggagtgaccaggagccgctg	14	12	2	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr19:35540393A>T	ENST00000262626.2	+	4	958	c.133A>T	c.(133-135)Agg>Tgg	p.R45W	HPN_ENST00000597419.1_Intron|HPN_ENST00000392226.1_Missense_Mutation_p.R45W	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin	45					basement membrane disassembly (GO:0034769)|cholesterol homeostasis (GO:0042632)|cochlea morphogenesis (GO:0090103)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|epithelium development (GO:0060429)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pilomotor reflex (GO:0097195)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|positive regulation of gene expression (GO:0010628)|positive regulation of hepatocyte proliferation (GO:2000347)|positive regulation of plasminogen activation (GO:0010756)|positive regulation of thyroid hormone generation (GO:2000611)|potassium ion transmembrane transport (GO:0071805)|proteolysis (GO:0006508)|regulation of cell shape (GO:0008360)|response to thyroid hormone (GO:0097066)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	TGTTCTCCTCAGGAGTGACCA	0.657																																					p.R45W		Atlas-SNP	.											.	HPN	45	.	0			c.A133T						.						26	24	24					19																	35540393		2202	4294	6496	SO:0001583	missense	3249	exon4			CTCCTCAGGAGTG		CCDS32993.1	19q13.12	2013-04-25	2008-12-08		ENSG00000105707	ENSG00000105707		"Serine peptidases / Transmembrane"	5155	protein-coding gene	gene with protein product	"transmembrane protease, serine 1"	142440				2835076	Standard	NM_182983		Approved	TMPRSS1	uc002nxq.2	P05981	OTTHUMG00000182474	ENST00000262626.2:c.133A>T	chr19.hg19:g.35540393A>T	ENSP00000262626:p.Arg45Trp	39.0	0.0		42.0	8.0	NM_182983	B2RDS4	Missense_Mutation	SNP	ENST00000262626.2	hg19	CCDS32993.1	.	.	.	.	.	.	.	.	.	.	A	14.79	2.641344	0.47153	.	.	ENSG00000105707	ENST00000262626;ENST00000392226	D;D	0.88586	-2.4;-2.4	4.33	2.07	0.26955	.	1.069870	0.07249	N	0.865552	T	0.79405	0.4440	N	0.19112	0.55	0.80722	D	1	P	0.39831	0.69	B	0.32393	0.145	T	0.67745	-0.5591	10	0.72032	D	0.01	.	8.3089	0.32060	0.6337:0.3663:0.0:0.0	.	45	P05981	HEPS_HUMAN	W	45	ENSP00000262626:R45W;ENSP00000376060:R45W	ENSP00000262626:R45W	R	+	1	2	HPN	40232233	0.847000	0.29606	0.945000	0.38365	0.967000	0.64934	1.512000	0.35812	0.243000	0.21327	0.260000	0.18958	AGG	.	.		0.657	HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1	NM_002151		T	35540393	A	T	35540393	3	4	206	1	0	0	0	0	1	0	0	0	7345	179	7	4	143	4	HPN	19	35540393	Missense_Mutation	SNP	A	TCGA-DD-AAE0-01A-11D-A40R-10	21038609	35540393	23588590	64	29982										
LRFN3	79414	hgsc.bcm.edu	37	chr19	36431682	36431682	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gccggatcagcggcctatccCgggcatccgcatgtaccaga	12	15	1	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr19:36431682C>G	ENST00000588831.1	+	3	2409	c.1355C>G	c.(1354-1356)cCg>cGg	p.P452R	LRFN3_ENST00000246529.3_Missense_Mutation_p.P452R			Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III domain containing 3	452	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	12	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CGGCCTATCCCGGGCATCCGC	0.642																																					p.P452R		Atlas-SNP	.											.	LRFN3	43	.	0			c.C1355G						.						29	27	28					19																	36431682		2203	4300	6503	SO:0001583	missense	79414	exon2			CTATCCCGGGCAT	BC003578	CCDS12483.1	19q13.13	2013-02-11				ENSG00000126243		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28370	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 1"	612809				12975309, 16495444, 16828986	Standard	NM_024509		Approved	MGC2656, SALM4, FIGLER1	uc002oco.3	Q9BTN0		ENST00000588831.1:c.1355C>G	chr19.hg19:g.36431682C>G	ENSP00000466989:p.Pro452Arg	73.0	0.0		92.0	36.0	NM_024509	Q6UY10	Missense_Mutation	SNP	ENST00000588831.1	hg19	CCDS12483.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.802005	0.70682	.	.	ENSG00000126243	ENST00000246529	T	0.54866	0.55	4.77	4.77	0.60923	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.32952	N	0.005448	T	0.73466	0.3590	M	0.87547	2.89	0.58432	D	0.999996	D	0.60160	0.987	D	0.63597	0.916	T	0.76953	-0.2768	10	0.42905	T	0.14	.	15.3027	0.73966	0.0:1.0:0.0:0.0	.	452	Q9BTN0	LRFN3_HUMAN	R	452	ENSP00000246529:P452R	ENSP00000246529:P452R	P	+	2	0	LRFN3	41123522	0.993000	0.37304	0.986000	0.45419	0.982000	0.71751	3.970000	0.56824	2.204000	0.70986	0.591000	0.81541	CCG	.	.		0.642	LRFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457403.2	NM_024509		G	36431682	C	G	36431682	3	3	206	1	0	0	0	0	1	0	0	0	8948	652	23	4	1357	4	LRFN3	19	36431682	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	891289	36431682	22697301	65	29983										
CYP2A13	1553	hgsc.bcm.edu	37	chr19	41599545	41599545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ctccctgcaggaggagaagaAccccaacacagagttctact	9	13	1	3			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr19:41599545A>G	ENST00000330436.3	+	6	842	c.842A>G	c.(841-843)aAc>aGc	p.N281S		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	281					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	GAGGAGAAGAACCCCAACACA	0.552																																					p.N281S		Atlas-SNP	.											.	CYP2A13	90	.	0			c.A842G						.						99	83	89					19																	41599545		2203	4300	6503	SO:0001583	missense	1553	exon6			AGAAGAACCCCAA	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"Cytochrome P450s"	2608	protein-coding gene	gene with protein product		608055	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.842A>G	chr19.hg19:g.41599545A>G	ENSP00000332679:p.Asn281Ser	116.0	0.0		150.0	32.0	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	hg19	CCDS12571.1	.	.	.	.	.	.	.	.	.	.	.	9.708	1.156267	0.21454	.	.	ENSG00000197838	ENST00000330436	T	0.69306	-0.39	4.58	4.58	0.56647	.	0.587256	0.16530	N	0.210418	T	0.54886	0.1886	N	0.17922	0.545	0.09310	N	1	B	0.29886	0.26	B	0.34931	0.192	T	0.52953	-0.8506	10	0.45353	T	0.12	.	13.1064	0.59249	1.0:0.0:0.0:0.0	.	281	Q16696	CP2AD_HUMAN	S	281	ENSP00000332679:N281S	ENSP00000332679:N281S	N	+	2	0	CYP2A13	46291385	0.001000	0.12720	0.527000	0.27925	0.434000	0.31775	1.754000	0.38369	1.945000	0.56424	0.397000	0.26171	AAC	.	.		0.552	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		G	41599545	A	G	41599545	3	3	206	1	0	0	0	0	1	0	0	0	4163	43	2	2	864	2	CYP2A13	19	41599545	Missense_Mutation	SNP	A	TCGA-DD-AAE0-01A-11D-A40R-10	5167863	41599545	17529438	66	29984										
ATP1A3	478	hgsc.bcm.edu	37	chr19	42485722	42485722	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gcgttcacgcatcagcttcaCggagccagaggacagctcga	12	13	3	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr19:42485722C>T	ENST00000302102.5	-	11	1519	c.1369G>A	c.(1369-1371)Gtg>Atg	p.V457M	ATP1A3_ENST00000545399.1_Missense_Mutation_p.V470M|ATP1A3_ENST00000602133.1_Missense_Mutation_p.V427M|ATP1A3_ENST00000543770.1_Missense_Mutation_p.V468M	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	457					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						ATCAGCTTCACGGAGCCAGAG	0.557																																					p.V470M		Atlas-SNP	.											.	ATP1A3	117	.	0			c.G1408A						.						105	88	93					19																	42485722		2203	4300	6503	SO:0001583	missense	478	exon11			GCTTCACGGAGCC		CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"ATPases / P-type"	801	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-3", "sodium pump subunit alpha-3", "sodium-potassium ATPase catalytic subunit alpha-3"	182350	"dystonia 12"	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.1369G>A	chr19.hg19:g.42485722C>T	ENSP00000302397:p.Val457Met	60.0	0.0		80.0	33.0	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	hg19	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.992148	0.74703	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000535899;ENST00000543770	D;D;D;D	0.96265	-3.96;-3.96;-3.96;-3.96	3.88	3.88	0.44766	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.97542	0.9195	M	0.69523	2.12	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.993;0.996;0.998;0.996	D	0.97776	1.0229	10	0.87932	D	0	.	14.1403	0.65316	0.0:1.0:0.0:0.0	.	470;468;457;457	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	M	457;457;470;427;201;468	ENSP00000302397:V457M;ENSP00000411503:V457M;ENSP00000444688:V470M;ENSP00000437577:V468M	ENSP00000302397:V457M	V	-	1	0	ATP1A3	47177562	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.852000	0.69488	2.449000	0.82847	0.561000	0.74099	GTG	.	.		0.557	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		T	42485722	C	T	42485722	3	4	206	1	0	0	0	0	1	0	0	0	1130	536	19	1	1724	1	ATP1A3	19	42485722	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	886177	42485722	16643261	67	29985										
IGFL2	147920	hgsc.bcm.edu	37	chr19	46663963	46663963	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	agcagtgctgttacaatgacGccatcgtgtccctgagcgag	12	11	0	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr19:46663963G>A	ENST00000377693.4	+	3	202	c.166G>A	c.(166-168)Gcc>Acc	p.A56T	AC007193.6_ENST00000597989.1_lincRNA|IGFL2_ENST00000600243.1_3'UTR|IGFL2_ENST00000434646.2_Missense_Mutation_p.A67T	NM_001135113.1	NP_001128585.1	Q6UWQ7	IGFL2_HUMAN	IGF-like family member 2	56						extracellular region (GO:0005576)				cervix(1)|lung(5)	6		Ovarian(192;0.0908)|all_neural(266;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(486;0.031)|Epithelial(262;0.247)		TTACAATGACGCCATCGTGTC	0.592																																					p.A67T		Atlas-SNP	.											.	IGFL2	15	.	0			c.G199A						.						177	187	184					19																	46663963		2201	4299	6500	SO:0001583	missense	147920	exon4			AATGACGCCATCG	AY672112	CCDS46121.1, CCDS46122.1	19q13.32	2006-07-14							32929	protein-coding gene	gene with protein product		610545				14702039	Standard	NM_001002915		Approved	UNQ645	uc010xxv.2	Q6UWQ7		ENST00000377693.4:c.166G>A	chr19.hg19:g.46663963G>A	ENSP00000366922:p.Ala56Thr	61.0	0.0		71.0	19.0	NM_001002915	E9PAV1|Q6B9Z3	Missense_Mutation	SNP	ENST00000377693.4	hg19	CCDS46121.1	.	.	.	.	.	.	.	.	.	.	G	0.023	-1.405869	0.01155	.	.	ENSG00000204866	ENST00000434646;ENST00000377693	T;T	0.21734	1.99;1.99	2.83	-0.555	0.11807	.	.	.	.	.	T	0.06645	0.0170	N	0.04636	-0.2	0.09310	N	1	B;B	0.28178	0.1;0.202	B;B	0.14578	0.011;0.008	T	0.39623	-0.9605	9	0.10377	T	0.69	-24.227	5.7655	0.18224	0.567:0.0:0.433:0.0	.	56;67	Q6UWQ7;Q6UWQ7-2	IGFL2_HUMAN;.	T	67;56	ENSP00000395219:A67T;ENSP00000366922:A56T	ENSP00000366922:A56T	A	+	1	0	IGFL2	51355803	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.282000	0.08445	-0.193000	0.10415	-0.491000	0.04670	GCC	.	.		0.592	IGFL2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000461705.1	NM_001002915		A	46663963	G	A	46663963	3	1	206	1	0	0	0	0	1	0	0	0	7596	1087	38	1	232	1	IGFL2	19	46663963	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	4178241	46663963	12465020	68	29986										
SBK2	646643	hgsc.bcm.edu	37	chr19	56041657	56041657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ggcggaggccagctgggcggCgcagcggtgcaccgcgggct	21	13	0	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr19:56041657C>T	ENST00000413299.1	-	4	527	c.490G>A	c.(490-492)Gcc>Acc	p.A164T	SBK2_ENST00000344158.3_Missense_Mutation_p.A164T	NM_001101401.2	NP_001094871.2	P0C263	SBK2_HUMAN	SH3 domain binding kinase family, member 2	164	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9						AGCTGGGCGGCGCAGCGGTGC	0.746																																					p.A164T		Atlas-SNP	.											.	SBK2	26	.	0			c.G490A						.						2	2	2					19																	56041657		1484	2983	4467	SO:0001583	missense	646643	exon4			GGGCGGCGCAGCG		CCDS42631.1	19q13.42	2013-09-27	2013-09-27		ENSG00000187550	ENSG00000187550			34416	protein-coding gene	gene with protein product			"SH3-binding domain kinase family, member 2"				Standard	NM_001101401		Approved	SGK069	uc010ygc.2	P0C263	OTTHUMG00000155830	ENST00000413299.1:c.490G>A	chr19.hg19:g.56041657C>T	ENSP00000389015:p.Ala164Thr	31.0	0.0		42.0	11.0	NM_001101401		Missense_Mutation	SNP	ENST00000413299.1	hg19	CCDS42631.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.155645	0.38021	.	.	ENSG00000187550	ENST00000413299;ENST00000344158	T;T	0.67698	-0.28;-0.28	3.95	2.89	0.33648	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.120890	0.53938	D	0.000041	T	0.49779	0.1577	L	0.39085	1.19	0.25420	N	0.988275	P	0.35959	0.53	B	0.34180	0.177	T	0.34079	-0.9843	10	0.28530	T	0.3	-24.1753	6.919	0.24376	0.2008:0.6045:0.1947:0.0	.	164	P0C263	SBK2_HUMAN	T	164	ENSP00000389015:A164T;ENSP00000345044:A164T	ENSP00000345044:A164T	A	-	1	0	SBK2	60733469	0.043000	0.20138	0.052000	0.19188	0.785000	0.44390	2.939000	0.48995	0.975000	0.38392	0.462000	0.41574	GCC	.	.		0.746	SBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341919.1	NM_001101401		T	56041657	C	T	56041657	3	4	206	1	0	0	0	0	1	0	0	0	13876	768	27	1	559	1	SBK2	19	56041657	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	9377694	56041657	3087326	69	29987										
CHD6	84181	hgsc.bcm.edu	37	chr20	40050514	40050514	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ttcagcccatgtttggcagtGccgatgagcaggtctcgatc	12	11	2	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr20:40050514G>A	ENST00000373233.3	-	31	4938	c.4761C>T	c.(4759-4761)ggC>ggT	p.G1587G		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1587					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GTTTGGCAGTGCCGATGAGCA	0.557																																					p.G1587G		Atlas-SNP	.											.	CHD6	312	.	0			c.C4761T						.						110	74	86					20																	40050514		2203	4300	6503	SO:0001819	synonymous_variant	84181	exon31			GGCAGTGCCGATG	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.4761C>T	chr20.hg19:g.40050514G>A		67.0	0.0		155.0	21.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	hg19	CCDS13317.1																																																																																			.	.		0.557	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40050514	G	A	40050514	2	1	206	1	0	0	0	0	0	0	0	1	3331	1306	46	3		3	CHD6	20	40050514	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10		40050514	22975006	70	29988										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57769145	57769145	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	aaaaggggcacagttgggggGggacaagggggacaggatgg	22	4	0	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr20:57769145G>A	ENST00000371030.2	+	1	3071	c.3071G>A	c.(3070-3072)gGg>gAg	p.G1024E		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1024							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CAGTTGGGGGGGGACAAGGGG	0.677																																					p.G1024E		Atlas-SNP	.											.	ZNF831	287	.	0			c.G3071A						.						19	23	22					20																	57769145		2004	4182	6186	SO:0001583	missense	128611	exon1			TGGGGGGGGACAA	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.3071G>A	chr20.hg19:g.57769145G>A	ENSP00000360069:p.Gly1024Glu	21.0	0.0		59.0	9.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	3.188	-0.166469	0.06461	.	.	ENSG00000124203	ENST00000371030	T	0.03745	3.82	4.49	-4.43	0.03568	.	1.727610	0.02789	N	0.121858	T	0.02304	0.0071	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43702	-0.9375	10	0.13853	T	0.58	-0.2863	0.4471	0.00495	0.3612:0.2516:0.1321:0.2551	.	1024	Q5JPB2	ZN831_HUMAN	E	1024	ENSP00000360069:G1024E	ENSP00000360069:G1024E	G	+	2	0	ZNF831	57202540	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.418000	0.07080	-0.313000	0.08728	0.411000	0.27672	GGG	.	.		0.677	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57769145	G	A	57769145	3	1	206	1	0	0	0	0	1	0	0	0	18200	1232	43	3	3073	3	ZNF831	20	57769145	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	17718631	57769145	5256375	71	29989										
IL2RB	3560	hgsc.bcm.edu	37	chr22	37524403	37524403	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	tgggggtcccagtctctgggGactctttcttgcaaagaagg	14	9	3	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr22:37524403G>T	ENST00000216223.5	-	10	1587	c.1389C>A	c.(1387-1389)gtC>gtA	p.V463V		NM_000878.3	NP_000869.1	P14784	IL2RB_HUMAN	interleukin 2 receptor, beta	463					cytokine-mediated signaling pathway (GO:0019221)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of apoptotic process (GO:0043066)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-2 binding (GO:0019976)|interleukin-2 receptor activity (GO:0004911)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(5)	23					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	AGTCTCTGGGGACTCTTTCTT	0.677																																					p.V463V		Atlas-SNP	.											.	IL2RB	44	.	0			c.C1389A						.						12	16	15					22																	37524403		2080	4100	6180	SO:0001819	synonymous_variant	3560	exon10			TCTGGGGACTCTT	M26062	CCDS13942.1	22q13	2011-02-15			ENSG00000100385	ENSG00000100385		"Interleukins and interleukin receptors", "CD molecules"	6009	protein-coding gene	gene with protein product		146710	"interleukin 15 receptor, beta"	IL15RB			Standard	NM_000878		Approved	CD122	uc003aqv.1	P14784	OTTHUMG00000150534	ENST00000216223.5:c.1389C>A	chr22.hg19:g.37524403G>T		57.0	0.0		96.0	13.0	NM_000878	B2R765	Silent	SNP	ENST00000216223.5	hg19	CCDS13942.1																																																																																			.	.		0.677	IL2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318792.1			T	37524403	G	T	37524403	2	4	206	1	0	0	0	0	0	0	0	1	7696	1161	41	3		3	IL2RB	22	37524403	Silent	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10		37524403	13780163	72	29990										
EP300	2033	hgsc.bcm.edu	37	chr22	41547912	41547912	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gtagcacagaagtgaattctCaggccattgctgagaagcag	12	8	1	3			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chr22:41547912C>G	ENST00000263253.7	+	15	4112	c.2893C>G	c.(2893-2895)Cag>Gag	p.Q965E		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	965					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AGTGAATTCTCAGGCCATTGC	0.478			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.Q965E		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.C2893G						.						120	121	120					22																	41547912		2203	4300	6503	SO:0001583	missense	2033	exon15	Familial Cancer Database	Broad Thumb-Hallux syndrome	AATTCTCAGGCCA	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.2893C>G	chr22.hg19:g.41547912C>G	ENSP00000263253:p.Gln965Glu	115.0	0.0		208.0	39.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.898112	0.72639	.	.	ENSG00000100393	ENST00000263253	D	0.83419	-1.72	5.52	5.52	0.82312	.	0.000000	0.46442	D	0.000298	T	0.82204	0.4986	M	0.66939	2.045	0.40698	D	0.982455	P	0.38535	0.635	B	0.36464	0.225	T	0.81017	-0.1123	10	0.25751	T	0.34	-6.5865	19.4296	0.94759	0.0:1.0:0.0:0.0	.	965	Q09472	EP300_HUMAN	E	965	ENSP00000263253:Q965E	ENSP00000263253:Q965E	Q	+	1	0	EP300	39877858	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.084000	0.76866	2.587000	0.87381	0.557000	0.71058	CAG	.	.		0.478	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41547912	C	G	41547912	3	3	206	1	0	0	0	0	1	0	0	0	5150	827	29	4	2951	4	EP300	22	41547912	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	4023509	41547912	9756654	73	29991										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34149816	34149816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gaggagatgggacaccggagTctcgggaggcttcaggcaga	18	8	2	2			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chrX:34149816T>C	ENST00000346193.3	-	1	631	c.580A>G	c.(580-582)Act>Gct	p.T194A		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	194	Pro-rich.									NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						GACACCGGAGTCTCGGGAGGC	0.617																																					p.T194A		Atlas-SNP	.											.	FAM47A	249	.	0			c.A580G						.						57	60	59					X																	34149816		2199	4295	6494	SO:0001583	missense	158724	exon1			CCGGAGTCTCGGG	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.580A>G	chrX.hg19:g.34149816T>C	ENSP00000345029:p.Thr194Ala	105.0	0.0		80.0	28.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	T	7.059	0.566003	0.13560	.	.	ENSG00000185448	ENST00000346193	T	0.17691	2.26	0.603	0.603	0.17541	.	.	.	.	.	T	0.28400	0.0702	L	0.61218	1.895	0.09310	N	1	D	0.56521	0.976	P	0.59012	0.85	T	0.12811	-1.0533	8	0.30854	T	0.27	.	.	.	.	.	194	Q5JRC9	FA47A_HUMAN	A	194	ENSP00000345029:T194A	ENSP00000345029:T194A	T	-	1	0	FAM47A	34059737	0.622000	0.27085	0.013000	0.15412	0.013000	0.08279	0.461000	0.21940	0.451000	0.26802	0.441000	0.28932	ACT	.	.		0.617	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		C	34149816	T	C	34149816	3	2	206	1	0	0	0	0	1	0	0	0	5577	1667	58	2	1799	2	FAM47A	23	34149816	Missense_Mutation	SNP	T	TCGA-DD-AAE0-01A-11D-A40R-10		34149816	121120744	74	29992										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86887268	86887268	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	agttggctacatattggcacCatgaatggccgtaggcttca	11	9	1	1			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chrX:86887268C>T	ENST00000373119.4	+	7	1528	c.1383C>T	c.(1381-1383)acC>acT	p.T461T	KLHL4_ENST00000373114.4_Silent_p.T461T	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	461						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						ATATTGGCACCATGAATGGCC	0.388																																					p.T461T		Atlas-SNP	.											.	KLHL4	263	.	0			c.C1383T						.						98	83	88					X																	86887268		2203	4300	6503	SO:0001819	synonymous_variant	56062	exon7			TGGCACCATGAAT	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1383C>T	chrX.hg19:g.86887268C>T		278.0	0.0		204.0	30.0	NM_019117	B2RTW2|Q9Y3J5	Silent	SNP	ENST00000373119.4	hg19	CCDS14457.1																																																																																			.	.		0.388	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			T	86887268	C	T	86887268	2	4	206	1	0	0	0	0	0	0	0	1	8400	581	21	3		3	KLHL4	23	86887268	Silent	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	52737452	86887268	68383292	75	29993										
RNF128	79589	hgsc.bcm.edu	37	chrX	105970508	105970508	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	ttggttggccctcatccaacGcggcgggggctgcaccttcg	14	14	1	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chrX:105970508G>A	ENST00000255499.2	+	1	615	c.365G>A	c.(364-366)cGc>cAc	p.R122H	RNF128_ENST00000324342.3_Intron	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase	122	PA.				negative regulation of cytokine biosynthetic process (GO:0042036)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						CTCATCCAACGCGGCGGGGGC	0.617																																					p.R122H		Atlas-SNP	.											.	RNF128	74	.	0			c.G365A						.						39	38	38					X																	105970508		2203	4300	6503	SO:0001583	missense	79589	exon1			TCCAACGCGGCGG	AK027169	CCDS14520.1, CCDS14521.1	Xq22.3	2013-01-09	2012-02-23		ENSG00000133135	ENSG00000133135		"RING-type (C3HC4) zinc fingers"	21153	protein-coding gene	gene with protein product		300439	"ring finger protein 128"				Standard	NM_024539		Approved	FLJ23516, GRAIL	uc004eml.3	Q8TEB7	OTTHUMG00000022151	ENST00000255499.2:c.365G>A	chrX.hg19:g.105970508G>A	ENSP00000255499:p.Arg122His	222.0	0.0		169.0	44.0	NM_194463	A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Missense_Mutation	SNP	ENST00000255499.2	hg19	CCDS14521.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.744402	0.89663	.	.	ENSG00000133135	ENST00000255499	T	0.10099	2.91	4.31	4.31	0.51392	Protease-associated domain, PA (1);	0.000000	0.85682	D	0.000000	T	0.37293	0.0998	M	0.92026	3.265	0.58432	D	0.999998	D	0.69078	0.997	P	0.62740	0.906	T	0.49283	-0.8956	10	0.72032	D	0.01	.	13.1327	0.59391	0.0:0.0:1.0:0.0	.	122	Q8TEB7	RN128_HUMAN	H	122	ENSP00000255499:R122H	ENSP00000255499:R122H	R	+	2	0	RNF128	105857164	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.017000	0.76399	1.907000	0.55213	0.513000	0.50165	CGC	.	.		0.617	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539		A	105970508	G	A	105970508	3	1	206	1	0	0	0	0	1	0	0	0	13451	1087	38	1	777	1	RNF128	23	105970508	Missense_Mutation	SNP	G	TCGA-DD-AAE0-01A-11D-A40R-10	19083240	105970508	49300052	76	29994										
STAG2	10735	hgsc.bcm.edu	37	chrX	123205074	123205074	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gagggcgtgacatgttagagCcattagtgtatacccctgat	12	8	0	3			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chrX:123205074C>T	ENST00000371160.1	+	25	2724	c.2434C>T	c.(2434-2436)Cca>Tca	p.P812S	STAG2_ENST00000371144.3_Missense_Mutation_p.P812S|STAG2_ENST00000371145.3_Missense_Mutation_p.P812S|STAG2_ENST00000371157.3_Missense_Mutation_p.P812S|STAG2_ENST00000354548.5_Missense_Mutation_p.P743S|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.P812S	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	812					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						CATGTTAGAGCCATTAGTGTA	0.373																																					p.P812S		Atlas-SNP	.											.	STAG2	309	.	0			c.C2434T						.						226	198	207					X																	123205074		2203	4300	6503	SO:0001583	missense	10735	exon25			TTAGAGCCATTAG	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.2434C>T	chrX.hg19:g.123205074C>T	ENSP00000360202:p.Pro812Ser	87.0	0.0		79.0	13.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.809530	0.50421	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.30417	0.0764	L	0.55103	1.725	0.80722	D	1	B;P	0.36282	0.016;0.546	B;B	0.34873	0.02;0.191	T	0.07462	-1.0771	10	0.12766	T	0.61	-11.7106	18.3649	0.90388	0.0:1.0:0.0:0.0	.	812;812	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	S	812;743;812;812;812;812	ENSP00000218089:P812S;ENSP00000346555:P743S;ENSP00000360202:P812S;ENSP00000360199:P812S;ENSP00000360187:P812S;ENSP00000360186:P812S	ENSP00000218089:P812S	P	+	1	0	STAG2	123032755	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	6.003000	0.70701	2.278000	0.76064	0.538000	0.68166	CCA	.	.		0.373	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		T	123205074	C	T	123205074	3	4	206	1	0	0	0	0	1	0	0	0	15258	739	26	3	2524	3	STAG2	23	123205074	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	17234566	123205074	32065486	77	29995										
AFF2	2334	hgsc.bcm.edu	37	chrX	147919196	147919196	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.341503435545072	1.39447236180905	0.194577538857076	1	1	0	gacccattcctggcctactcCtctcacttccatgcatactg	5	17	1	0			TCGA-DD-AAE0-01A-11D-A40R-10	TCGA-DD-AAE0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2a18f024-178d-46d9-880b-a751edf71b67	42e0aa56-bad8-4d28-adb6-4f956cbaf658	g.chrX:147919196C>T	ENST00000370460.2	+	5	1591	c.1112C>T	c.(1111-1113)cCt>cTt	p.P371L	AFF2_ENST00000342251.3_Intron|AFF2_ENST00000370457.5_Intron|AFF2_ENST00000370458.1_Intron|AFF2_ENST00000286437.5_Intron	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	371					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					TGGCCTACTCCTCTCACTTCC	0.418																																					p.P371L		Atlas-SNP	.											.	AFF2	679	.	0			c.C1112T						.						171	135	147					X																	147919196		2203	4300	6503	SO:0001583	missense	2334	exon5			CTACTCCTCTCAC	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1112C>T	chrX.hg19:g.147919196C>T	ENSP00000359489:p.Pro371Leu	82.0	0.0		65.0	17.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	hg19	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.346685	0.82022	.	.	ENSG00000155966	ENST00000370460	D	0.82619	-1.63	5.42	5.42	0.78866	.	0.065748	0.64402	D	0.000010	D	0.85146	0.5630	L	0.43152	1.355	0.80722	D	1	D;D	0.56968	0.973;0.978	P;P	0.54590	0.642;0.756	D	0.86287	0.1671	10	0.56958	D	0.05	.	16.5254	0.84329	0.0:1.0:0.0:0.0	.	367;371	P51816-5;P51816	.;AFF2_HUMAN	L	371	ENSP00000359489:P371L	ENSP00000359489:P371L	P	+	2	0	AFF2	147726888	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	5.494000	0.66905	2.273000	0.75805	0.600000	0.82982	CCT	.	.		0.418	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		T	147919196	C	T	147919196	3	4	206	1	0	0	0	0	1	0	0	0	357	681	24	3	1185	3	AFF2	23	147919196	Missense_Mutation	SNP	C	TCGA-DD-AAE0-01A-11D-A40R-10	24714122	147919196	7351364	78	29996										
EBNA1BP2	10969	hgsc.bcm.edu	37	chr1	43637724	43637724	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	cgagctcggctgacacctacCtctctgtctgtgacaaggga	11	13	2	2			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr1:43637724C>T	ENST00000236051.2	-	1	207	c.66G>A	c.(64-66)gaG>gaA	p.E22E	EBNA1BP2_ENST00000431635.2_Splice_Site_p.E77E|WDR65_ENST00000372492.4_5'Flank|WDR65_ENST00000528956.1_5'Flank|EBNA1BP2_ENST00000472982.1_5'UTR	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	22					ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)	16	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGACACCTACCTCTCTGTCTG	0.607																																					p.E77E		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.G231A						.						64	55	58					1																	43637724		2203	4300	6503	SO:0001630	splice_region_variant	10969	exon2			ACCTACCTCTCTG	U86602	CCDS478.1, CCDS53308.1	1p35-p33	2011-02-10	2001-11-28		ENSG00000117395	ENSG00000117395			15531	protein-coding gene	gene with protein product		614443	"EBNA1-binding protein 2"			10074103, 11438656	Standard	NM_001159936		Approved	NOBP, EBP2, P40	uc010ojx.2	Q99848	OTTHUMG00000007284	ENST00000236051.2:c.66+1G>A	chr1.hg19:g.43637724C>T		75.0	0.0		48.0	31.0	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	hg19	CCDS478.1																																																																																			.	.		0.607	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1		Silent	T	43637724	C	T	43637724	5	4	207	1	0	0	0	0	0	0	1	0	4887	695	24	3	890	3	EBNA1BP2	1	43637724	Splice_Site	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10		43637724	205612897	1	29997										
OLFML2B	25903	hgsc.bcm.edu	37	chr1	161989734	161989734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	agtcctggctgtctgcctccCgcagcttctggagcctgaag	12	14	2	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr1:161989734C>T	ENST00000294794.3	-	2	836	c.413G>A	c.(412-414)cGg>cAg	p.R138Q	OLFML2B_ENST00000367940.2_Missense_Mutation_p.R138Q	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	138					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			GTCTGCCTCCCGCAGCTTCTG	0.582																																					p.R138Q		Atlas-SNP	.											.	OLFML2B	114	.	0			c.G413A						.						51	51	51					1																	161989734		2203	4300	6503	SO:0001583	missense	25903	exon2			GCCTCCCGCAGCT	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.413G>A	chr1.hg19:g.161989734C>T	ENSP00000294794:p.Arg138Gln	73.0	0.0		164.0	107.0	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	hg19	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.819074	0.50633	.	.	ENSG00000162745	ENST00000294794;ENST00000367940	T;T	0.42900	0.96;0.96	4.64	3.72	0.42706	.	.	.	.	.	T	0.13586	0.0329	L	0.34521	1.04	0.41621	D	0.988967	P;P	0.45044	0.669;0.849	B;B	0.31442	0.076;0.13	T	0.03374	-1.1043	8	0.36615	T	0.2	.	12.8355	0.57771	0.0:0.8344:0.1656:0.0	.	138;138	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	Q	138	ENSP00000294794:R138Q;ENSP00000356917:R138Q	ENSP00000294794:R138Q	R	-	2	0	OLFML2B	160256358	1.000000	0.71417	0.993000	0.49108	0.891000	0.51852	3.485000	0.53208	1.303000	0.44873	0.561000	0.74099	CGG	.	.		0.582	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		T	161989734	C	T	161989734	3	4	207	1	0	0	0	0	1	0	0	0	10867	652	23	1	1867	1	OLFML2B	1	161989734	Missense_Mutation	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	118352010	161989734	87260887	2	29998										
CFHR4	3080	hgsc.bcm.edu	37	chr1	196881942	196881942	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ttcctctatttatattttaaAtaaagaaatacaatataaat	1	4	1	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr1:196881942A>T	ENST00000367421.3	+	2	135				CFHR4_ENST00000251424.4_Missense_Mutation_p.N110I|CFHR4_ENST00000608469.1_Missense_Mutation_p.N39I|CFHR4_ENST00000367416.2_Missense_Mutation_p.N356I|CFHR4_ENST00000367418.2_Missense_Mutation_p.N110I			P36980	FHR2_HUMAN	complement factor H-related 2							extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						tatattttaaataaagaaata	0.289																																					p.N357I		Atlas-SNP	.											.	CFHR4	141	.	0			c.A1070T						.						23	27	25					1																	196881942		2113	4247	6360	SO:0001627	intron_variant	10877	exon7			TTTTAAATAAAGA	X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"Complement system"	4890	protein-coding gene	gene with protein product		600889	"H factor (complement)-like 3"	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367421.3:c.59-36643A>T	chr1.hg19:g.196881942A>T		571.0	0.0		1144.0	198.0	NM_001201550	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367421.3	hg19		.	.	.	.	.	.	.	.	.	.	A	13.37	2.216141	0.39201	.	.	ENSG00000134365	ENST00000367416;ENST00000367418;ENST00000251424;ENST00000538553	T;T;T	0.66995	-0.24;-0.24;-0.24	2.11	2.11	0.27256	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.81616	0.4860	M	0.89601	3.045	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.78314	0.989;0.991;0.972	T	0.67296	-0.5706	9	0.87932	D	0	.	6.1801	0.20465	1.0:0.0:0.0:0.0	.	356;357;110	C9J7J7;Q5DVJ7;Q92496	.;.;FHR4_HUMAN	I	356;110;110;110	ENSP00000356386:N356I;ENSP00000356388:N110I;ENSP00000251424:N110I	ENSP00000251424:N110I	N	+	2	0	CFHR4	195148565	0.025000	0.19082	0.024000	0.17045	0.370000	0.29829	2.161000	0.42358	1.210000	0.43336	0.172000	0.16884	AAT	.	.		0.289	CFHR2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005666		T	196881942	A	T	196881942	1	4	207	0	1	0	0	0	0	0	0	0	3289	101	4	4		4	CFHR4	1	196881942	Intron	SNP	A	TCGA-DD-AAE1-01A-11D-A40R-10	34892208	196881942	52368679	3	29999										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201018205	201018205	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ccttctcagcagggtcaccaCgtccaggtgtttgattctcc	9	14	3	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr1:201018205C>T	ENST00000362061.3	-	35	4490	c.4264G>A	c.(4264-4266)Gtg>Atg	p.V1422M	CACNA1S_ENST00000367338.3_Missense_Mutation_p.V1403M	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1422					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AGGGTCACCACGTCCAGGTGT	0.577																																					p.V1422M		Atlas-SNP	.											.	CACNA1S	249	.	0			c.G4264A						.						39	37	37					1																	201018205		2203	4300	6503	SO:0001583	missense	779	exon35			TCACCACGTCCAG	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.4264G>A	chr1.hg19:g.201018205C>T	ENSP00000355192:p.Val1422Met	25.0	0.0		80.0	42.0	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	22.7	4.322536	0.81580	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	T;T	0.10005	2.92;2.92	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.23171	0.0560	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.02026	-1.1227	10	0.31617	T	0.26	.	18.8773	0.92343	0.0:1.0:0.0:0.0	.	1422	Q13698	CAC1S_HUMAN	M	1422;1403	ENSP00000355192:V1422M;ENSP00000356307:V1403M	ENSP00000355192:V1422M	V	-	1	0	CACNA1S	199284828	1.000000	0.71417	0.994000	0.49952	0.930000	0.56654	7.773000	0.85462	2.520000	0.84964	0.655000	0.94253	GTG	.	.		0.577	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		T	201018205	C	T	201018205	3	4	207	1	0	0	0	0	1	0	0	0	2549	536	19	1	1397	1	CACNA1S	1	201018205	Missense_Mutation	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	4136263	201018205	48232416	4	30000										
ZNF678	339500	hgsc.bcm.edu	37	chr1	227843476	227843476	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	caatccatagtaagtataagAgaatttatactggagaggaa	9	4	0	2			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr1:227843476A>C	ENST00000343776.5	+	4	1870	c.1525A>C	c.(1525-1527)Aga>Cga	p.R509R	ZNF678_ENST00000397097.3_Silent_p.R564R|ZNF678_ENST00000608949.1_Intron	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	509					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				TAAGTATAAGAGAATTTATAC	0.323																																					p.R564R		Atlas-SNP	.											.	ZNF678	137	.	0			c.A1690C						.						43	48	46					1																	227843476		2201	4295	6496	SO:0001819	synonymous_variant	339500	exon4			TATAAGAGAATTT	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"Zinc fingers, C2H2-type", "-"	28652	protein-coding gene	gene with protein product	"hypothetical protein MGC42493"					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.1525A>C	chr1.hg19:g.227843476A>C		253.0	0.0		404.0	82.0	NM_178549	Q8IVQ9	Silent	SNP	ENST00000343776.5	hg19																																																																																				.	.		0.323	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		C	227843476	A	C	227843476	2	2	207	1	0	0	0	0	0	0	0	1	18100	296	11	5		5	ZNF678	1	227843476	Silent	SNP	A	TCGA-DD-AAE1-01A-11D-A40R-10	26825271	227843476	21407145	5	30001										
VIT	5212	hgsc.bcm.edu	37	chr2	36982071	36982071	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tttctcttcatagtggtgtgCttgataattcaggagggaaa	11	5	3	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr2:36982071C>A	ENST00000389975.3	+	5	585	c.283C>A	c.(283-285)Ctt>Att	p.L95I	VIT_ENST00000404084.1_Missense_Mutation_p.L73I|VIT_ENST00000401530.1_Missense_Mutation_p.L95I|VIT_ENST00000379242.3_Missense_Mutation_p.L95I|VIT_ENST00000379241.3_Missense_Mutation_p.L95I|VIT_ENST00000457137.2_Missense_Mutation_p.L95I|VIT_ENST00000497382.1_De_novo_Start_OutOfFrame	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	95	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				TAGTGGTGTGCTTGATAATTC	0.393																																					p.L95I		Atlas-SNP	.											.	VIT	138	.	0			c.C283A						.						151	141	145					2																	36982071		2203	4300	6503	SO:0001583	missense	5212	exon5			GGTGTGCTTGATA	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.283C>A	chr2.hg19:g.36982071C>A	ENSP00000374625:p.Leu95Ile	78.0	0.0		89.0	49.0	NM_001177969	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	hg19	CCDS54347.1	.	.	.	.	.	.	.	.	.	.	C	2.304	-0.359469	0.05138	.	.	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000402257;ENST00000457137;ENST00000404084;ENST00000379241;ENST00000401530	D;D;D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33;-2.33;-2.33	5.63	2.71	0.32032	LCCL (5);	0.222388	0.44483	N	0.000452	T	0.55737	0.1939	N	0.00436	-1.5	0.32797	N	0.500406	B;B;B;B;B;B	0.26400	0.057;0.07;0.025;0.017;0.057;0.148	B;B;B;B;B;B	0.27380	0.045;0.078;0.046;0.078;0.046;0.079	T	0.62407	-0.6861	10	0.02654	T	1	-9.3344	7.8166	0.29263	0.402:0.2966:0.3014:0.0	.	95;95;95;95;95;95	B4DRU4;E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4;Q6UXI7-3	.;.;.;VITRN_HUMAN;.;.	I	95;95;95;95;73;95;95	ENSP00000368544:L95I;ENSP00000374625:L95I;ENSP00000393561:L95I;ENSP00000384154:L73I;ENSP00000368543:L95I;ENSP00000385658:L95I	ENSP00000368543:L95I	L	+	1	0	VIT	36835575	1.000000	0.71417	0.979000	0.43373	0.802000	0.45316	1.296000	0.33389	0.700000	0.31782	0.655000	0.94253	CTT	.	.		0.393	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				A	36982071	C	A	36982071	3	1	207	1	0	0	0	0	1	0	0	0	17186	797	28	3	297	3	VIT	2	36982071	Missense_Mutation	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10		36982071	206217302	6	30002										
AOX1	316	hgsc.bcm.edu	37	chr2	201526345	201526345	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	cattaacctttcagctgttgGatacttcaggtaaatactcc	6	10	2	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr2:201526345G>C	ENST00000374700.2	+	30	3660	c.3419G>C	c.(3418-3420)gGa>gCa	p.G1140A	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1140					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TCAGCTGTTGGATACTTCAGG	0.423																																					p.G1140A		Atlas-SNP	.											.	AOX1	152	.	0			c.G3419C						.						139	131	134					2																	201526345		2203	4300	6503	SO:0001583	missense	316	exon30			CTGTTGGATACTT	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3419G>C	chr2.hg19:g.201526345G>C	ENSP00000363832:p.Gly1140Ala	80.0	0.0		74.0	33.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	hg19	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290947	0.59976	.	.	ENSG00000138356	ENST00000374700;ENST00000260930	T;T	0.35048	1.33;1.33	5.35	4.47	0.54385	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.113680	0.64402	D	0.000012	T	0.61261	0.2333	M	0.84683	2.71	0.80722	D	1	D	0.57257	0.979	P	0.62491	0.903	T	0.69837	-0.5037	10	0.87932	D	0	-47.6364	14.6375	0.68699	0.0699:0.0:0.9301:0.0	.	1140	Q06278	ADO_HUMAN	A	1140;26	ENSP00000363832:G1140A;ENSP00000260930:G26A	ENSP00000260930:G26A	G	+	2	0	AOX1	201234590	1.000000	0.71417	0.983000	0.44433	0.417000	0.31264	5.884000	0.69729	1.626000	0.50381	0.655000	0.94253	GGA	.	.		0.423	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		C	201526345	G	C	201526345	3	2	207	1	0	0	0	0	1	0	0	0	729	1174	41	4	3537	4	AOX1	2	201526345	Missense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10	164544274	201526345	41673028	7	30003										
PTPRN	5798	hgsc.bcm.edu	37	chr2	220172166	220172166	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ccagtgcacccagaccttacCttgggacatgagttgtcgga	11	12	0	2			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr2:220172166C>A	ENST00000295718.2	-	3	520	c.280G>T	c.(280-282)Gga>Tga	p.G94*	PTPRN_ENST00000409251.3_Splice_Site_p.G94*|PTPRN_ENST00000423636.2_Splice_Site_p.G4*	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	94					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CAGACCTTACCTTGGGACATG	0.547																																					p.G94X		Atlas-SNP	.											.	PTPRN	138	.	0			c.G280T						.						63	60	61					2																	220172166		2203	4300	6503	SO:0001630	splice_region_variant	5798	exon3			CCTTACCTTGGGA		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.280+1G>T	chr2.hg19:g.220172166C>A		49.0	0.0		54.0	17.0	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Nonsense_Mutation	SNP	ENST00000295718.2	hg19	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	C	36	5.846029	0.97016	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666;ENST00000536579;ENST00000412847;ENST00000446182;ENST00000440552;ENST00000442029;ENST00000451506	.	.	.	5.24	5.24	0.73138	.	0.000000	0.52532	D	0.000070	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7372	0.77853	0.0:1.0:0.0:0.0	.	.	.	.	X	94;94;94;4;94;4;4;61;4;4	.	.	G	-	1	0	PTPRN	219880410	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	4.933000	0.63484	2.436000	0.82500	0.460000	0.39030	GGA	.	.		0.547	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2		Nonsense_Mutation	A	220172166	C	A	220172166	5	1	207	1	0	0	0	0	0	0	1	0	12822	695	24	3	2743	3	PTPRN	2	220172166	Splice_Site	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	18645821	220172166	23027207	8	30004										
IRS1	3667	hgsc.bcm.edu	37	chr2	227661977	227661994	+	In_Frame_Del	DEL	CGGTGGCCATTGCCACCC	CGGTGGCCATTGCCACCC	-													0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	agcctgttcctggggtgcagCggtggccattgccaccccga							TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	CGGTGGCCATTGCCACCC	CGGTGGCCATTGCCACCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr2:227661977_227661994delCGGTGGCCATTGCCACCC	ENST00000305123.5	-	1	2481_2498	c.1461_1478delGGGTGGCAATGGCCACCG	c.(1459-1479)cggggtggcaatggccaccgc>cgc	p.487_493RGGNGHR>R	IRS1_ENST00000498335.1_5'Flank|RP11-395N3.2_ENST00000607970.1_lincRNA	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	487					cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		TGGGGTGCAGCGGTGGCCATTGCCACCCCGAGACAAAA	0.606											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.488_493del		Atlas-INDEL	.											.	IRS1	141	.	0			c.1462_1479del						.																																			SO:0001651	inframe_deletion	3667	exon1			.		CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"Pleckstrin homology (PH) domain containing"	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.1461_1478delGGGTGGCAATGGCCACCG	chr2.hg19:g.227661977_227661994delCGGTGGCCATTGCCACCC	ENSP00000304895:p.Arg487_His492del	77.0	0.0	2321	71.0	19.0	NM_005544		In_Frame_Del	DEL	ENST00000305123.5	hg19	CCDS2463.1																																																																																			.	.		0.606	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		-	227661994	CGGTGGCCATTGCCACCC	-	227661977	7	5	207	1	0	1	0	1	0	0	0	0	7849	768	27	0	2254	0	IRS1	2	227661977	In_Frame_Del	DEL	CGGTGGCCATTGCCACCC	TCGA-DD-AAE1-01A-11D-A40R-10	7489811	227661977	15537396	9	30005										
LAP3	51056	hgsc.bcm.edu	37	chr4	17586622	17586622	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	caggaggcctggcagaaaggAgtcctgtttgcttctgggca	15	9	1	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr4:17586622A>T	ENST00000226299.4	+	6	841	c.567A>T	c.(565-567)ggA>ggT	p.G189G	AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000606142.1_Silent_p.G158G	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	189					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						GGCAGAAAGGAGTCCTGTTTG	0.493																																					p.G189G		Atlas-SNP	.											.	LAP3	50	.	0			c.A567T						.						70	65	67					4																	17586622		2203	4300	6503	SO:0001819	synonymous_variant	51056	exon6			GAAAGGAGTCCTG	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"peptidase S"	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.567A>T	chr4.hg19:g.17586622A>T		97.0	0.0		73.0	33.0	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Silent	SNP	ENST00000226299.4	hg19	CCDS3422.1																																																																																			.	.		0.493	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			T	17586622	A	T	17586622	2	4	207	1	0	0	0	0	0	0	0	1	8632	291	11	4		4	LAP3	4	17586622	Silent	SNP	A	TCGA-DD-AAE1-01A-11D-A40R-10		17586622	173567654	10	30006										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11732327	11732327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tggaggtgtttaagccggggCtcagggaactcgtcttctct	14	9	3	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr5:11732327C>T	ENST00000304623.8	-	2	284	c.95G>A	c.(94-96)aGc>aAc	p.S32N	CTNND2_ENST00000458100.2_5'UTR|CTNND2_ENST00000359640.2_Missense_Mutation_p.S32N	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	32					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						TAAGCCGGGGCTCAGGGAACT	0.502																																					p.S32N		Atlas-SNP	.											.	CTNND2	289	.	0			c.G95A						.						128	128	128					5																	11732327		2203	4300	6503	SO:0001583	missense	1501	exon2			CCGGGGCTCAGGG	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.95G>A	chr5.hg19:g.11732327C>T	ENSP00000307134:p.Ser32Asn	74.0	0.0		51.0	24.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.838180	0.91117	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000502551;ENST00000508761	T;T	0.77358	-1.03;-1.09	5.91	5.91	0.95273	.	0.000000	0.52532	D	0.000061	T	0.64940	0.2644	N	0.08118	0	0.80722	D	1	P	0.42827	0.791	B	0.40782	0.34	T	0.72377	-0.4312	10	0.72032	D	0.01	-18.3546	17.7899	0.88548	0.0:1.0:0.0:0.0	.	32	Q9UQB3	CTND2_HUMAN	N	32;32;18;18	ENSP00000307134:S32N;ENSP00000352661:S32N	ENSP00000307134:S32N	S	-	2	0	CTNND2	11785327	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.517000	0.53443	2.796000	0.96246	0.643000	0.83706	AGC	.	.		0.502	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		T	11732327	C	T	11732327	3	4	207	1	0	0	0	0	1	0	0	0	4022	797	28	3	3666	3	CTNND2	5	11732327	Missense_Mutation	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10		11732327	169182933	11	30007										
AP3B1	8546	hgsc.bcm.edu	37	chr5	77471662	77471662	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	aggacaatatactgcacctcCctagaaatcaaaagataatt	5	9	1	2			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr5:77471662C>A	ENST00000255194.6	-	10	1216	c.1041G>T	c.(1039-1041)agG>agT	p.R347S	AP3B1_ENST00000519295.1_Splice_Site_p.R298S	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	347					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		ACTGCACCTCCCTAGAAATCA	0.308									Hermansky-Pudlak syndrome																												p.R347S		Atlas-SNP	.											.	AP3B1	94	.	0			c.G1041T						.						127	136	133					5																	77471662		2202	4296	6498	SO:0001630	splice_region_variant	8546	exon10	Familial Cancer Database	HPS, HPS1-8	CACCTCCCTAGAA	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1041-1G>T	chr5.hg19:g.77471662C>A		135.0	0.0		138.0	55.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530675	0.27387	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.25579	1.79;1.79	4.82	4.82	0.62117	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.20292	0.0488	L	0.38175	1.15	0.53688	D	0.999977	P	0.42123	0.771	B	0.41135	0.348	T	0.01874	-1.1256	10	0.30854	T	0.27	.	9.0996	0.36660	0.1479:0.7728:0.0:0.0793	.	347	O00203	AP3B1_HUMAN	S	347;298;347;251	ENSP00000255194:R347S;ENSP00000430597:R298S	ENSP00000255194:R347S	R	-	3	2	AP3B1	77507418	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.253000	0.43205	2.214000	0.71695	0.467000	0.42956	AGG	.	.		0.308	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		Missense_Mutation	A	77471662	C	A	77471662	5	1	207	1	0	0	0	0	0	0	1	0	744	637	22	3	2315	3	AP3B1	5	77471662	Splice_Site	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	65739335	77471662	103443598	12	30008										
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140589015	140589015	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	aaatccgaactctcatttccAcgttaaaataagagtcaatc	4	10	2	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr5:140589015A>T	ENST00000239450.2	+	1	725	c.536A>T	c.(535-537)cAc>cTc	p.H179L	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	179	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCTCATTTCCACGTTAAAATA	0.423																																					p.H179L		Atlas-SNP	.											.	PCDHB12	179	.	0			c.A536T						.						69	70	70					5																	140589015		2203	4300	6503	SO:0001583	missense	56124	exon1			ATTTCCACGTTAA	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"Cadherins / Protocadherins : Clustered"	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.536A>T	chr5.hg19:g.140589015A>T	ENSP00000239450:p.His179Leu	116.0	0.0		130.0	58.0	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	hg19	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	A	0.980	-0.697271	0.03279	.	.	ENSG00000120328	ENST00000239450	T	0.50548	0.74	4.16	-1.3	0.09259	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.39835	0.1093	L	0.51422	1.61	0.09310	N	1	P	0.41848	0.763	B	0.42163	0.378	T	0.31251	-0.9950	9	0.54805	T	0.06	.	5.9815	0.19409	0.4081:0.3506:0.2413:0.0	.	179	Q9Y5F1	PCDBC_HUMAN	L	179	ENSP00000239450:H179L	ENSP00000239450:H179L	H	+	2	0	PCDHB12	140569199	0.000000	0.05858	0.068000	0.19968	0.001000	0.01503	-1.625000	0.02036	-0.139000	0.11414	-0.415000	0.06103	CAC	.	.		0.423	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		T	140589015	A	T	140589015	3	4	207	1	0	0	0	0	1	0	0	0	11546	159	6	4	538	4	PCDHB12	5	140589015	Missense_Mutation	SNP	A	TCGA-DD-AAE1-01A-11D-A40R-10	63117353	140589015	40326245	13	30009										
KIAA0141	9812	hgsc.bcm.edu	37	chr5	141318088	141318088	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tctcacctcttcttgtagccCcggggcccagcgacctgaca	9	17	3	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr5:141318088C>T	ENST00000432126.2	+	12	1446	c.1312C>T	c.(1312-1314)Ccg>Tcg	p.P438S	KIAA0141_ENST00000194118.4_Missense_Mutation_p.P438S	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	438					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTGTAGCCCCGGGGCCCAG	0.547																																					p.P438S		Atlas-SNP	.											.	KIAA0141	44	.	0			c.C1312T						.						80	85	83					5																	141318088		2203	4300	6503	SO:0001583	missense	9812	exon12			GTAGCCCCGGGGC	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"death ligand signal enhancer"	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.1312C>T	chr5.hg19:g.141318088C>T	ENSP00000396225:p.Pro438Ser	58.0	0.0		60.0	25.0	NM_001142603	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	hg19	CCDS4268.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.527415	0.44969	.	.	ENSG00000081791	ENST00000432126;ENST00000194118	T;T	0.13538	2.58;2.58	4.97	0.899	0.19271	.	0.989048	0.08213	N	0.980326	T	0.08179	0.0204	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.43956	-0.9359	10	0.14252	T	0.57	3.0E-4	6.1209	0.20151	0.0:0.5348:0.0:0.4652	.	438	Q14154	DELE_HUMAN	S	438	ENSP00000396225:P438S;ENSP00000194118:P438S	ENSP00000194118:P438S	P	+	1	0	KIAA0141	141298272	0.005000	0.15991	0.004000	0.12327	0.040000	0.13550	-0.026000	0.12392	0.289000	0.22422	0.561000	0.74099	CCG	.	.		0.547	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773		T	141318088	C	T	141318088	3	4	207	1	0	0	0	0	1	0	0	0	8165	623	22	3	1358	3	KIAA0141	5	141318088	Missense_Mutation	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	729073	141318088	39597172	14	30010										
KCTD20	222658	hgsc.bcm.edu	37	chr6	36454686	36454694	+	In_Frame_Del	DEL	AAGAGAAGG	AAGAGAAGG	-													0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ctacctgtaaagaaaaaattAagagaaggcctggcggccgg					rs149081694		TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	AAGAGAAGG	AAGAGAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr6:36454686_36454694delAAGAGAAGG	ENST00000373731.2	+	8	1385_1393	c.994_1002delAAGAGAAGG	c.(994-1002)aagagaaggdel	p.KRR332del	KCTD20_ENST00000474988.1_3'UTR|KCTD20_ENST00000536244.1_In_Frame_Del_p.KRR187del|KCTD20_ENST00000449081.2_In_Frame_Del_p.KRR166del|KCTD20_ENST00000544295.1_In_Frame_Del_p.KRR86del	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	332					protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						AGAAAAAATTAAGAGAAGGCCTGGCGGCC	0.445																																					p.331_334del		Atlas-INDEL	.											.	KCTD20	37	.	0			c.993_1001del						.																																			SO:0001651	inframe_deletion	222658	exon8			.	BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"chromosome 6 open reading frame 69", "potassium channel tetramerisation domain containing 20"	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.994_1002delAAGAGAAGG	chr6.hg19:g.36454686_36454694delAAGAGAAGG	ENSP00000362836:p.Lys332_Arg334del	94.0	0.0		89.0	25.0	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	In_Frame_Del	DEL	ENST00000373731.2	hg19	CCDS4821.1																																																																																			.	.		0.445	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562		-	36454694	AAGAGAAGG	-	36454686	7	5	207	1	0	1	0	1	0	0	0	0	8117	363	13	0	1020	0	KCTD20	6	36454686	In_Frame_Del	DEL	AAGAGAAGG	TCGA-DD-AAE1-01A-11D-A40R-10		36454686	134660381	15	30011	154	2								
KCTD20	222658	hgsc.bcm.edu	37	chr6	36454696	36454698	+	In_Frame_Del	DEL	CTG	CTG	-													0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	agaaaaaattaagagaaggcCtggcggccggtctgaagtca							TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr6:36454696_36454698delCTG	ENST00000373731.2	+	8	1395_1397	c.1004_1006delCTG	c.(1003-1008)cctggc>cgc	p.335_336PG>R	KCTD20_ENST00000474988.1_3'UTR|KCTD20_ENST00000536244.1_In_Frame_Del_p.190_191PG>R|KCTD20_ENST00000449081.2_In_Frame_Del_p.169_170PG>R|KCTD20_ENST00000544295.1_In_Frame_Del_p.89_90PG>R	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	335					protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						AAGAGAAGGCCTGGCGGCCGGTC	0.448																																					p.335_335del		Atlas-INDEL	.											.	KCTD20	37	.	0			c.1003_1005del						.																																			SO:0001651	inframe_deletion	222658	exon8			.	BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"chromosome 6 open reading frame 69", "potassium channel tetramerisation domain containing 20"	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.1004_1006delCTG	chr6.hg19:g.36454696_36454698delCTG	ENSP00000362836:p.Pro335_Gly336delinsArg	95.0	0.0		88.0	25.0	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	In_Frame_Del	DEL	ENST00000373731.2	hg19	CCDS4821.1																																																																																			.	.		0.448	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562		-	36454698	CTG	-	36454696	7	5	207	1	0	1	0	1	0	0	0	0	8117	681	24	0	1030	0	KCTD20	6	36454696	In_Frame_Del	DEL	CTG	TCGA-DD-AAE1-01A-11D-A40R-10	10	36454696	134660371	16	30012	154	2								
PAQR8	85315	hgsc.bcm.edu	37	chr6	52268597	52268611	+	In_Frame_Del	DEL	TATGCCAAATATCGT	TATGCCAAATATCGT	-													0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tatcttgtgctggctgttgcTatgccaaatatcgttaccgg					rs17852802		TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	TATGCCAAATATCGT	TATGCCAAATATCGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr6:52268597_52268611delTATGCCAAATATCGT	ENST00000442253.2	+	2	760_774	c.586_600delTATGCCAAATATCGT	c.(586-600)tatgccaaatatcgtdel	p.YAKYR196del	PAQR8_ENST00000360726.3_In_Frame_Del_p.YAKYR196del	NM_133367.4	NP_588608.1	Q8TEZ7	MPRB_HUMAN	progestin and adipoQ receptor family member VIII	196					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)			endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(2)	17	Lung NSC(77;0.0875)					TGGCTGTTGCTATGCCAAATATCGTTACCGGAGGC	0.53																																					p.195_200del		Atlas-INDEL	.											.	PAQR8	31	.	0			c.585_599del						.																																			SO:0001651	inframe_deletion	85315	exon2			.	AF347029	CCDS4941.1	6p12	2012-08-10	2005-05-20	2005-05-20	ENSG00000170915	ENSG00000170915			15708	protein-coding gene	gene with protein product		607780	"chromosome 6 open reading frame 33"	C6orf33		11676489, 12574519	Standard	NM_133367		Approved	LMPB1, MPRB	uc003pao.4	Q8TEZ7	OTTHUMG00000014846	ENST00000442253.2:c.586_600delTATGCCAAATATCGT	chr6.hg19:g.52268597_52268611delTATGCCAAATATCGT	ENSP00000406197:p.Tyr196_Arg200del	78.0	0.0		86.0	25.0	NM_133367	B2RCF6|Q86WL0|Q8N6D3|Q9HD02	In_Frame_Del	DEL	ENST00000442253.2	hg19	CCDS4941.1																																																																																			.	.		0.53	PAQR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040903.2	NM_133367		-	52268611	TATGCCAAATATCGT	-	52268597	7	5	207	1	0	1	0	1	0	0	0	0	11450	1522	53	0	588	0	PAQR8	6	52268597	In_Frame_Del	DEL	TATGCCAAATATCGT	TCGA-DD-AAE1-01A-11D-A40R-10	15813901	52268597	118846470	17	30013										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20683148	20683148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tgttgtttcaaaacatgtctActttttcgattggcctggca	8	8	2	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr7:20683148A>G	ENST00000404938.2	+	7	1223	c.571A>G	c.(571-573)Act>Gct	p.T191A		NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	191	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						AAACATGTCTACTTTTTCGAT	0.418																																					p.T191A		Atlas-SNP	.											.	ABCB5	357	.	0			c.A571G						.						200	175	182					7																	20683148		1568	3582	5150	SO:0001583	missense	340273	exon7			ATGTCTACTTTTT	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.571A>G	chr7.hg19:g.20683148A>G	ENSP00000384881:p.Thr191Ala	160.0	0.0		124.0	47.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	A	10.10	1.258598	0.23051	.	.	ENSG00000004846	ENST00000404938	D	0.90900	-2.75	3.85	2.71	0.32032	.	.	.	.	.	D	0.84183	0.5416	L	0.48260	1.515	0.80722	D	1	P	0.36125	0.538	B	0.33121	0.158	T	0.79105	-0.1940	9	0.37606	T	0.19	.	6.9932	0.24767	0.8838:0.0:0.1162:0.0	.	191	A7BKA4	.	A	191	ENSP00000384881:T191A	ENSP00000384881:T191A	T	+	1	0	ABCB5	20649673	1.000000	0.71417	0.998000	0.56505	0.233000	0.25261	5.254000	0.65457	0.849000	0.35215	0.460000	0.39030	ACT	.	.		0.418	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		G	20683148	A	G	20683148	3	3	207	1	0	0	0	0	1	0	0	0	44	391	14	2	593	2	ABCB5	7	20683148	Missense_Mutation	SNP	A	TCGA-DD-AAE1-01A-11D-A40R-10		20683148	138455515	18	30014										
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145668159	145668159	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tgagatagaggcgggtcctcAtctcattcagctctccctgg	11	12	4	2			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr8:145668159A>G	ENST00000409379.3	-	5	508	c.479T>C	c.(478-480)aTg>aCg	p.M160T	AC084125.4_ENST00000442850.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	160					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						GCGGGTCCTCATCTCATTCAG	0.572																																					p.M160T		Atlas-SNP	.											.	TONSL	128	.	0			c.T479C						.						91	88	89					8																	145668159		2203	4300	6503	SO:0001583	missense	4796	exon5			GTCCTCATCTCAT		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.479T>C	chr8.hg19:g.145668159A>G	ENSP00000386239:p.Met160Thr	59.0	0.0		127.0	37.0	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	hg19	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	A	19.49	3.837127	0.71373	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.75260	-0.92	4.92	4.92	0.64577	.	0.078660	0.85682	D	0.000000	D	0.86230	0.5883	M	0.85542	2.76	0.80722	D	1	D	0.71674	0.998	D	0.72338	0.977	D	0.88017	0.2766	10	0.62326	D	0.03	-29.1779	12.5443	0.56190	1.0:0.0:0.0:0.0	.	160	Q96HA7	TONSL_HUMAN	T	160	ENSP00000386239:M160T	ENSP00000386239:M160T	M	-	2	0	TONSL	145638967	1.000000	0.71417	1.000000	0.80357	0.565000	0.35776	8.802000	0.91910	1.854000	0.53819	0.533000	0.62120	ATG	.	.		0.572	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		G	145668159	A	G	145668159	3	3	207	1	0	0	0	0	1	0	0	0	10391	217	8	2	3745	2	NFKBIL2	8	145668159	Missense_Mutation	SNP	A	TCGA-DD-AAE1-01A-11D-A40R-10		145668159	695863	19	30015										
KIAA0020	9933	hgsc.bcm.edu	37	chr9	2810431	2810431	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	aggatgttctgcaatgtgaaGctatgaagggtcaagaacag	13	5	2	3			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr9:2810431G>T	ENST00000397885.2	-	16	1842	c.1636C>A	c.(1636-1638)Ctt>Att	p.L546I		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	546						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		GCAATGTGAAGCTATGAAGGG	0.338																																					p.L546I		Atlas-SNP	.											KIAA0020,NS,carcinoma,0,1	KIAA0020	56	.	0			c.C1636A						.						160	142	148					9																	2810431		2203	4300	6503	SO:0001630	splice_region_variant	9933	exon16			TGTGAAGCTATGA	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"penguin homolog (Drosophila)", "minor histocompatibility antigen HA-8"	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1636-1C>A	chr9.hg19:g.2810431G>T		69.0	0.0		53.0	3.0	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	hg19	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	G	15.39	2.818191	0.50633	.	.	ENSG00000080608	ENST00000397885	T	0.14893	2.47	5.95	5.05	0.67936	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.111432	0.64402	D	0.000010	T	0.27900	0.0687	M	0.80183	2.485	0.54753	D	0.999984	B;B	0.30727	0.292;0.24	B;B	0.38921	0.237;0.285	T	0.02313	-1.1178	10	0.22706	T	0.39	-0.9536	13.7718	0.63029	0.0716:0.0:0.9284:0.0	.	406;546	B2RDG4;Q15397	.;K0020_HUMAN	I	546	ENSP00000380982:L546I	ENSP00000380982:L546I	L	-	1	0	KIAA0020	2800431	1.000000	0.71417	1.000000	0.80357	0.452000	0.32318	6.182000	0.71995	2.827000	0.97445	0.650000	0.86243	CTT	.	.		0.338	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	Missense_Mutation	T	2810431	G	T	2810431	5	4	207	1	0	0	0	0	0	0	1	0	8161	985	34	3	322	3	KIAA0020	9	2810431	Splice_Site	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10		2810431	138403000	20	30016										
BICD2	23299	hgsc.bcm.edu	37	chr9	95481421	95481421	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	accttctttagctccttctcCagccgggccagcagctcgcg	9	17	2	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr9:95481421C>T	ENST00000375512.3	-	5	1573	c.1506G>A	c.(1504-1506)ctG>ctA	p.L502L	BICD2_ENST00000356884.6_Silent_p.L502L	NM_015250.3	NP_056065.1	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 (Drosophila)	502					cell death (GO:0008219)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase binding (GO:0017137)			cervix(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23						GCTCCTTCTCCAGCCGGGCCA	0.652																																					p.L502L		Atlas-SNP	.											.	BICD2	68	.	0			c.G1506A						.						57	56	56					9																	95481421		2203	4300	6503	SO:0001819	synonymous_variant	23299	exon5			CTTCTCCAGCCGG	AB014599	CCDS6700.1, CCDS35064.1	9q22.32	2008-02-05			ENSG00000185963	ENSG00000185963			17208	protein-coding gene	gene with protein product		609797				9734811	Standard	NM_001003800		Approved	KIAA0699	uc004asp.1	Q8TD16	OTTHUMG00000021036	ENST00000375512.3:c.1506G>A	chr9.hg19:g.95481421C>T		38.0	0.0		45.0	23.0	NM_001003800	O75181|Q5TBQ2|Q5TBQ3|Q96LH2|Q9BT84|Q9H561	Silent	SNP	ENST00000375512.3	hg19	CCDS6700.1																																																																																			.	.		0.652	BICD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055508.1	NM_015250		T	95481421	C	T	95481421	2	4	207	1	0	0	0	0	0	0	0	1	1429	581	21	3		3	BICD2	9	95481421	Silent	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	92670990	95481421	45732010	21	30017										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113137745	113137746	+	Splice_Site	INS	-	-	AAAAAA													0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	agggaagaatgcagattgctINSaaaaaaaaaaaaaaaaaaaa					rs386415855|rs71373993		TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr9:113137745_113137746insAAAAAA	ENST00000401783.2	-	46	10841		c.e46-2		SVEP1_ENST00000297826.5_Splice_Site|SVEP1_ENST00000374469.1_Splice_Site	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1						cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TGCAGATTGCTaaaaaaaaaaa	0.46																																					.		Atlas-INDEL	.											.	SVEP1	326	.	0			c.10505-2->TTTTTT						.																																			SO:0001630	splice_region_variant	79987	exon47			.	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.10505-2->TTTTTT	chr9.hg19:g.113137746_113137751dupAAAAAA		119.0	0.0		154.0	11.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Splice_Site	INS	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.		0.46	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Intron	AAAAAA	113137746	-	AAAAAA	113137745	8	5	207	1	0	1	1	0	0	0	1	0	15435	1536	53	0	224	0	SVEP1	9	113137745	Splice_Site	INS	-	TCGA-DD-AAE1-01A-11D-A40R-10	17656324	113137745	28075686	22	30018										
OGDHL	55753	hgsc.bcm.edu	37	chr10	50950948	50950948	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ttcagcagggagccaaaggcCatgtactctgccaacgccca	10	14	2	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr10:50950948C>A	ENST00000374103.4	-	15	2023	c.1938G>T	c.(1936-1938)atG>atT	p.M646I	OGDHL_ENST00000419399.1_Missense_Mutation_p.M589I|OGDHL_ENST00000432695.1_Missense_Mutation_p.M437I	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	646					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						AGCCAAAGGCCATGTACTCTG	0.642																																					p.M646I		Atlas-SNP	.											OGDHL,NS,carcinoma,0,1	OGDHL	149	.	0			c.G1938T						.						99	75	83					10																	50950948		2203	4300	6503	SO:0001583	missense	55753	exon15			AAAGGCCATGTAC	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.1938G>T	chr10.hg19:g.50950948C>A	ENSP00000363216:p.Met646Ile	35.0	0.0		53.0	19.0	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	hg19	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	c	22.7	4.321244	0.81580	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	D;D;D	0.91521	-2.86;-2.86;-2.86	5.22	5.22	0.72569	Transketolase-like, pyrimidine-binding domain (2);	0.000000	0.85682	D	0.000000	D	0.89347	0.6689	L	0.51853	1.615	0.80722	D	1	B;B;B	0.10296	0.003;0.002;0.001	B;B;B	0.20384	0.029;0.008;0.021	D	0.85868	0.1414	10	0.87932	D	0	.	19.1492	0.93481	0.0:1.0:0.0:0.0	.	589;437;646	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	I	646;589;437	ENSP00000363216:M646I;ENSP00000401356:M589I;ENSP00000390240:M437I	ENSP00000363216:M646I	M	-	3	0	OGDHL	50620954	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.009000	0.57110	2.583000	0.87209	0.651000	0.88453	ATG	.	.		0.642	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		A	50950948	C	A	50950948	3	1	207	1	0	0	0	0	1	0	0	0	10849	594	21	3	1130	3	OGDHL	10	50950948	Missense_Mutation	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10		50950948	84583799	23	30019										
ZNF143	7702	hgsc.bcm.edu	37	chr11	9522758	9522758	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ttattactgcacagagccagGatgtgggagggcatttgcca	13	8	0	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr11:9522758G>A	ENST00000396602.2	+	11	1207	c.1088G>A	c.(1087-1089)gGa>gAa	p.G363E	ZNF143_ENST00000530463.1_Missense_Mutation_p.G362E|ZNF143_ENST00000396604.1_Missense_Mutation_p.G362E|ZNF143_ENST00000299606.2_Missense_Mutation_p.G335E|ZNF143_ENST00000396597.3_Missense_Mutation_p.G332E	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	363					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		ACAGAGCCAGGATGTGGGAGG	0.438																																					p.G363E		Atlas-SNP	.											.	ZNF143	38	.	0			c.G1088A						.						156	144	148					11																	9522758		2201	4294	6495	SO:0001583	missense	7702	exon11			AGCCAGGATGTGG	U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"Zinc fingers, C2H2-type"	12928	protein-coding gene	gene with protein product		603433	"zinc finger protein 143 (clone pHZ-1)"				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.1088G>A	chr11.hg19:g.9522758G>A	ENSP00000379847:p.Gly363Glu	81.0	0.0		112.0	56.0	NM_003442	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Missense_Mutation	SNP	ENST00000396602.2	hg19	CCDS7799.2	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111644	0.77210	.	.	ENSG00000166478	ENST00000396604;ENST00000396602;ENST00000530463;ENST00000396597;ENST00000299606	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	5.66	5.66	0.87406	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000001	T	0.53706	0.1813	L	0.36672	1.1	0.80722	D	1	D;D;D	0.58620	0.979;0.983;0.983	P;P;P	0.52793	0.675;0.709;0.709	T	0.52786	-0.8529	10	0.52906	T	0.07	.	19.7617	0.96321	0.0:0.0:1.0:0.0	.	332;362;363	P52747-2;E7ER34;P52747	.;.;ZN143_HUMAN	E	362;363;362;332;335	ENSP00000379849:G362E;ENSP00000379847:G363E;ENSP00000432154:G362E;ENSP00000379843:G332E;ENSP00000299606:G335E	ENSP00000299606:G335E	G	+	2	0	ZNF143	9479334	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.631000	0.83237	2.671000	0.90904	0.655000	0.94253	GGA	.	.		0.438	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442		A	9522758	G	A	9522758	3	1	207	1	0	0	0	0	1	0	0	0	17747	1174	41	3	1126	3	ZNF143	11	9522758	Missense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10		9522758	125483758	24	30020										
DCDC1	341019	hgsc.bcm.edu	37	chr11	31312362	31312362	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	gtaggaagcatcaacccattCattgtccaagttactttctt	6	10	3	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr11:31312362C>T	ENST00000452803.1	-	7	993	c.792G>A	c.(790-792)atG>atA	p.M264I	DCDC1_ENST00000597505.1_Missense_Mutation_p.M264I	NM_181807.3	NP_861523.2	P59894	DCDC1_HUMAN	doublecortin domain containing 1	264					intracellular signal transduction (GO:0035556)					central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|pancreas(2)|prostate(1)|skin(1)|stomach(1)	31	Lung SC(675;0.225)					TCAACCCATTCATTGTCCAAG	0.338																																					p.M264I		Atlas-SNP	.											.	DCDC1	74	.	0			c.G792A						.						84	83	84					11																	31312362		2202	4299	6501	SO:0001583	missense	341019	exon7			CCCATTCATTGTC	AY247970	CCDS7872.1	11p14.1	2013-05-22			ENSG00000170959	ENSG00000170959			20625	protein-coding gene	gene with protein product		608062				12820024	Standard	NM_181807		Approved		uc001msv.3	P59894	OTTHUMG00000150144	ENST00000452803.1:c.792G>A	chr11.hg19:g.31312362C>T	ENSP00000389792:p.Met264Ile	174.0	0.0		194.0	83.0	NM_181807	A6PVL6|B7WNX6|Q6ZU04	Missense_Mutation	SNP	ENST00000452803.1	hg19	CCDS7872.1	.	.	.	.	.	.	.	.	.	.	C	13.10	2.135286	0.37728	.	.	ENSG00000188682	ENST00000452803	T	0.31769	1.48	5.78	4.87	0.63330	Doublecortin domain (1);	0.106346	0.41605	D	0.000848	T	0.32882	0.0844	M	0.65975	2.015	0.26534	N	0.974205	B	0.25904	0.137	B	0.28011	0.085	T	0.19484	-1.0304	10	0.21014	T	0.42	-2.9769	13.4351	0.61079	0.0:0.9272:0.0:0.0728	.	264	P59894	DCDC1_HUMAN	I	264	ENSP00000389792:M264I	ENSP00000389792:M264I	M	-	3	0	DCDC1	31268938	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.859000	0.48364	1.434000	0.47414	0.655000	0.94253	ATG	.	.		0.338	DCDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316531.1	NM_181807		T	31312362	C	T	31312362	3	4	207	1	0	0	0	0	1	0	0	0	4286	826	29	3	284	3	DCDC1	11	31312362	Missense_Mutation	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	21789604	31312362	103694154	25	30021										
PGA5	5222	hgsc.bcm.edu	37	chr11	61017209	61017209	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	cattgttgacaccggcacctCtctgctgaccggcccaacca	8	17	1	2			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr11:61017209C>G	ENST00000312403.5	+	7	1027	c.842C>G	c.(841-843)tCt>tGt	p.S281C	CTD-2331C18.5_ENST00000537594.1_RNA|PGA5_ENST00000541528.1_Missense_Mutation_p.S21C|PGA5_ENST00000451616.2_Missense_Mutation_p.S127C|PGA4_ENST00000422676.2_Missense_Mutation_p.S281C	NM_014224.2	NP_055039.1	P0DJD9	PEPA5_HUMAN	pepsinogen 5, group I (pepsinogen A)	281					digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			large_intestine(1)|skin(1)	2						ACCGGCACCTCTCTGCTGACC	0.607																																					p.S281C		Atlas-SNP	.											.	PGA5	20	.	0			c.C842G						.						131	134	133					11																	61017209		2202	4299	6501	SO:0001583	missense	5222	exon7			GCACCTCTCTGCT	BC029055	CCDS8001.1	11q13	2012-10-02			ENSG00000256713	ENSG00000256713	3.4.23.1		8887	protein-coding gene	gene with protein product		169730					Standard	NM_014224		Approved		uc001nqz.3	P0DJD9	OTTHUMG00000168075	ENST00000312403.5:c.842C>G	chr11.hg19:g.61017209C>G	ENSP00000309542:p.Ser281Cys	168.0	0.0		178.0	65.0	NM_014224	A8K749|B7ZW62|B7ZW75|P00790|Q7M4R0|Q8N1E3	Missense_Mutation	SNP	ENST00000312403.5	hg19	CCDS8001.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.956258	0.92726	.	.	ENSG00000229183;ENSG00000256713;ENSG00000256713;ENSG00000256713;ENSG00000256713;ENSG00000256713	ENST00000422676;ENST00000312403;ENST00000537359;ENST00000544083;ENST00000451616;ENST00000541528	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	2.91	2.91	0.33838	.	0.000000	0.64402	D	0.000002	D	0.87708	0.6245	H	0.99740	4.74	0.38447	D	0.946869	D	0.89917	1.0	D	0.91635	0.999	D	0.93319	0.6691	10	0.87932	D	0	.	13.8637	0.63576	0.0:1.0:0.0:0.0	.	281	B7ZW62	.	C	281;281;238;140;127;21	ENSP00000395402:S281C;ENSP00000309542:S281C;ENSP00000408739:S127C;ENSP00000441981:S21C	ENSP00000395402:S281C	S	+	2	0	PGA4;PGA5	60773785	1.000000	0.71417	0.533000	0.28001	0.966000	0.64601	6.051000	0.71072	1.991000	0.58162	0.420000	0.28162	TCT	.	.		0.607	PGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397972.1	NM_014224		G	61017209	C	G	61017209	3	3	207	1	0	0	0	0	1	0	0	0	11781	913	32	4	868	4	PGA5	11	61017209	Missense_Mutation	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	29704847	61017209	73989307	26	30022										
ZNF202	7753	hgsc.bcm.edu	37	chr11	123600489	123600489	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ggctccactcctaaatgcacCgtctcctctgacaggacttc	7	16	2	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr11:123600489C>T	ENST00000529691.1	-	3	666	c.447G>A	c.(445-447)acG>acA	p.T149T	ZNF202_ENST00000530393.1_Silent_p.T149T|ZNF202_ENST00000336139.4_Silent_p.T149T			O95125	ZN202_HUMAN	zinc finger protein 202	149					lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		CTAAATGCACCGTCTCCTCTG	0.542																																					p.T149T		Atlas-SNP	.											.	ZNF202	72	.	0			c.G447A						.						79	72	74					11																	123600489		2202	4299	6501	SO:0001819	synonymous_variant	7753	exon5			ATGCACCGTCTCC	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"Zinc fingers, C2H2-type", "-", "-", "-"	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.447G>A	chr11.hg19:g.123600489C>T		41.0	0.0		55.0	10.0	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Silent	SNP	ENST00000529691.1	hg19	CCDS8443.1																																																																																			.	.		0.542	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		T	123600489	C	T	123600489	2	4	207	1	0	0	0	0	0	0	0	1	17778	639	23	1		1	ZNF202	11	123600489	Silent	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	62583280	123600489	11406027	27	30023										
A2M	2	hgsc.bcm.edu	37	chr12	9227372	9227384	+	Splice_Site	DEL	AGAGTTGTCTTAA	AGAGTTGTCTTAA	-													0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tgagggcgctcccaatggacAgagttgtcttaaagatgaga							TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	AGAGTTGTCTTAA	AGAGTTGTCTTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr12:9227372_9227384delAGAGTTGTCTTAA	ENST00000318602.7	-	29	3840_3847	c.3533_3540delTTAAGACAACTCT	c.(3532-3540)gttaagaca>g	p.VKT1178fs	A2M_ENST00000542567.1_5'Flank	NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	1178					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	CCCAATGGACAGAGTTGTCTTAAAGATGAGAAA	0.441																																					p.1178_1181del		Atlas-INDEL	.											.	A2M	180	.	0			c.3533_3541del						.																																			SO:0001630	splice_region_variant	2	exon29			.	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.3533-1TTAAGACAACTCT>-	chr12.hg19:g.9227372_9227384delAGAGTTGTCTTAA		116.0	0.0		112.0	33.0	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	In_Frame_Del	DEL	ENST00000318602.7	hg19	CCDS44827.1																																																																																			.	.		0.441	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	Frame_Shift_Del	-	9227384	AGAGTTGTCTTAA	-	9227372	8	5	207	1	0	1	0	1	0	0	1	0	4	175	7	0	916	0	A2M	12	9227372	Splice_Site	DEL	AGAGTTGTCTTAA	TCGA-DD-AAE1-01A-11D-A40R-10		9227372	124624523	28	30024										
FGD4	121512	hgsc.bcm.edu	37	chr12	32751494	32751494	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tgcttactgaaagagcttatGtcaaccgacttgacctctta	7	10	2	3	rs528790143	byFrequency	TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr12:32751494G>A	ENST00000427716.2	+	5	1088	c.664G>A	c.(664-666)Gtc>Atc	p.V222I	FGD4_ENST00000534526.2_Missense_Mutation_p.V359I|FGD4_ENST00000266482.3_5'UTR|FGD4_ENST00000531134.1_Missense_Mutation_p.V307I|FGD4_ENST00000525053.1_Missense_Mutation_p.V334I|FGD4_ENST00000546442.1_Missense_Mutation_p.V129I|FGD4_ENST00000381025.3_5'UTR	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	222	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					AAGAGCTTATGTCAACCGACT	0.299													G|||	2	0.000399361	0	0	5008	,	,		18345	0		0	False		,,,				2504	0.002				p.V222I		Atlas-SNP	.											.	FGD4	86	.	0			c.G664A						.						90	89	89					12																	32751494		2203	4299	6502	SO:0001583	missense	121512	exon5			GCTTATGTCAACC	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.664G>A	chr12.hg19:g.32751494G>A	ENSP00000394487:p.Val222Ile	91.0	0.0		97.0	40.0	NM_139241	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	hg19	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327431	0.81690	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000427716;ENST00000546442;ENST00000525053	T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46	4.91	4.91	0.64330	Dbl homology (DH) domain (5);	0.000000	0.46758	D	0.000267	D	0.83622	0.5294	M	0.82193	2.58	0.80722	D	1	D;D;D	0.89917	0.995;0.995;1.0	D;D;D	0.87578	0.98;0.98;0.998	D	0.86446	0.1770	10	0.87932	D	0	-15.6004	18.4768	0.90795	0.0:0.0:1.0:0.0	.	334;307;222	E9PJX4;B7Z493;Q96M96	.;.;FGD4_HUMAN	I	359;307;222;129;334	ENSP00000449273:V359I;ENSP00000431323:V307I;ENSP00000394487:V222I;ENSP00000446695:V129I;ENSP00000433666:V334I	ENSP00000379089:V222I	V	+	1	0	FGD4	32642761	1.000000	0.71417	0.987000	0.45799	0.853000	0.48598	7.219000	0.78000	2.426000	0.82243	0.655000	0.94253	GTC	.	.		0.299	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		A	32751494	G	A	32751494	3	1	207	1	0	0	0	0	1	0	0	0	5843	1377	48	3	674	3	FGD4	12	32751494	Missense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10	23524122	32751494	101100401	29	30025										
ACACB	32	hgsc.bcm.edu	37	chr12	109614034	109614034	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	gaagggaatccggaaggctgAgagtgcggaggacttcccga	17	8	0	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr12:109614034A>T	ENST00000338432.7	+	9	1522	c.1403A>T	c.(1402-1404)gAg>gTg	p.E468V	ACACB_ENST00000377854.5_Missense_Mutation_p.E468V|ACACB_ENST00000377848.3_Missense_Mutation_p.E468V|ACACB_ENST00000543080.1_3'UTR			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	468	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	CGGAAGGCTGAGAGTGCGGAG	0.493																																					p.E468V		Atlas-SNP	.											.	ACACB	330	.	0			c.A1403T						.						225	234	231					12																	109614034		2203	4300	6503	SO:0001583	missense	32	exon8			AGGCTGAGAGTGC	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.1403A>T	chr12.hg19:g.109614034A>T	ENSP00000341044:p.Glu468Val	118.0	0.0		151.0	54.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.465504	0.63513	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	D;D;D	0.97831	-4.56;-4.56;-4.56	5.91	5.91	0.95273	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.046253	0.85682	D	0.000000	D	0.98185	0.9400	M	0.64404	1.975	0.80722	D	1	D	0.61697	0.99	D	0.66497	0.944	D	0.98485	1.0607	10	0.44086	T	0.13	.	16.3512	0.83208	1.0:0.0:0.0:0.0	.	468	O00763	ACACB_HUMAN	V	468	ENSP00000341044:E468V;ENSP00000367079:E468V;ENSP00000367085:E468V	ENSP00000341044:E468V	E	+	2	0	ACACB	108098417	1.000000	0.71417	0.992000	0.48379	0.991000	0.79684	7.252000	0.78309	2.266000	0.75297	0.533000	0.62120	GAG	.	.		0.493	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109614034	A	T	109614034	3	4	207	1	0	0	0	0	1	0	0	0	107	304	11	4	1433	4	ACACB	12	109614034	Missense_Mutation	SNP	A	TCGA-DD-AAE1-01A-11D-A40R-10	76862540	109614034	24237861	30	30026										
PCCA	5095	hgsc.bcm.edu	37	chr13	100861682	100861682	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tattagctaagaaagcagagGttaatacaatccctggcttt	8	7	0	2			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr13:100861682G>T	ENST00000376285.1	+	7	603	c.565G>T	c.(565-567)Gtt>Ttt	p.V189F	PCCA_ENST00000376279.3_Missense_Mutation_p.V189F|PCCA_ENST00000376286.4_Missense_Mutation_p.V163F	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	189	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	GAAAGCAGAGGTTAATACAAT	0.373																																					p.V189F		Atlas-SNP	.											.	PCCA	59	.	0			c.G565T						.						146	132	137					13																	100861682		2203	4300	6503	SO:0001583	missense	5095	exon7			GCAGAGGTTAATA	X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"propionyl Coenzyme A carboxylase, alpha polypeptide"			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.565G>T	chr13.hg19:g.100861682G>T	ENSP00000365462:p.Val189Phe	90.0	0.0		112.0	44.0	NM_001178004	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	hg19	CCDS9496.2	.	.	.	.	.	.	.	.	.	.	G	25.8	4.672029	0.88348	.	.	ENSG00000175198	ENST00000376286;ENST00000376279;ENST00000376285	D;D;D	0.98044	-4.68;-4.68;-4.68	5.02	5.02	0.67125	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.000000	0.85682	D	0.000000	D	0.99381	0.9782	H	0.99104	4.43	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.995;0.999	D	0.98196	1.0465	10	0.87932	D	0	.	18.3367	0.90290	0.0:0.0:1.0:0.0	.	189;163;189	C9JPQ8;P05165-2;P05165	.;.;PCCA_HUMAN	F	163;189;189	ENSP00000365463:V163F;ENSP00000365456:V189F;ENSP00000365462:V189F	ENSP00000365456:V189F	V	+	1	0	PCCA	99659683	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.617000	0.98361	2.323000	0.78572	0.655000	0.94253	GTT	.	.		0.373	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2			T	100861682	G	T	100861682	3	4	207	1	0	0	0	0	1	0	0	0	11513	1261	44	3	591	3	PCCA	13	100861682	Missense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10		100861682	14308196	31	30027										
TEP1	7011	hgsc.bcm.edu	37	chr14	20852626	20852626	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	actcctccagcccgccaacaTagggccggccagctgccaca	9	19	0	0	rs201494870		TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr14:20852626T>C	ENST00000262715.5	-	23	3303	c.3263A>G	c.(3262-3264)tAt>tGt	p.Y1088C	TEP1_ENST00000556935.1_Missense_Mutation_p.Y980C|TEP1_ENST00000545983.1_5'Flank	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1088					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CCCGCCAACATAGGGCCGGCC	0.587																																					p.Y1088C		Atlas-SNP	.											.	TEP1	224	.	0			c.A3263G						.	T	CYS/TYR	0,4406		0,0,2203	111	131	124		3263	4	1	14		124	3,8597	3.0+/-9.4	0,3,4297	no	missense	TEP1	NM_007110.4	194	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	probably-damaging	1088/2628	20852626	3,13003	2203	4300	6503	SO:0001583	missense	7011	exon23			CCAACATAGGGCC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.3263A>G	chr14.hg19:g.20852626T>C	ENSP00000262715:p.Tyr1088Cys	42.0	0.0		63.0	26.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	T	12.08	1.829857	0.32329	0.0	3.49E-4	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.16897	2.31;2.31	5.21	3.99	0.46301	.	0.190149	0.47455	D	0.000233	T	0.35566	0.0936	M	0.74881	2.28	0.80722	D	1	D;B;D	0.89917	1.0;0.009;1.0	D;B;D	0.74023	0.982;0.022;0.956	T	0.09335	-1.0679	10	0.52906	T	0.07	-5.2177	6.5259	0.22301	0.1534:0.0:0.1591:0.6875	.	980;438;1088	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	C	1088;1088;980	ENSP00000262715:Y1088C;ENSP00000452574:Y980C	ENSP00000262715:Y1088C	Y	-	2	0	TEP1	19922466	1.000000	0.71417	0.995000	0.50966	0.851000	0.48451	3.314000	0.51943	1.971000	0.57363	0.379000	0.24179	TAT	.	T|0.999;C|0.001		0.587	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		C	20852626	T	C	20852626	3	2	207	1	0	0	0	0	1	0	0	0	15774	1406	49	2	4752	2	TEP1	14	20852626	Missense_Mutation	SNP	T	TCGA-DD-AAE1-01A-11D-A40R-10		20852626	86496914	32	30028										
ZNF219	51222	hgsc.bcm.edu	37	chr14	21561409	21561409	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	cgccgtcgaaagccggcggcGacggcgctaagtggccgctc	16	15	0	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr14:21561409G>A	ENST00000360947.3	-	3	458	c.47C>T	c.(46-48)tCg>tTg	p.S16L	ZNF219_ENST00000451119.2_Missense_Mutation_p.S16L|RP11-998D10.7_ENST00000554733.2_lincRNA|ZNF219_ENST00000556101.1_5'Flank|ZNF219_ENST00000421093.2_Missense_Mutation_p.S16L	NM_016423.2	NP_057507.2	Q9P2Y4	ZN219_HUMAN	zinc finger protein 219	16					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurotransmitter levels (GO:0001505)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histamine receptor activity (GO:0004969)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(2)	8	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;9.86e-11)|Epithelial(56;1.27e-08)|all cancers(55;6.06e-08)	GBM - Glioblastoma multiforme(265;0.0191)		AGCCGGCGGCGACGGCGCTAA	0.652											OREG0022565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S16L		Atlas-SNP	.											.	ZNF219	28	.	0			c.C47T						.						10	12	11					14																	21561409		2157	4192	6349	SO:0001583	missense	51222	exon3			GGCGGCGACGGCG	AB015427	CCDS9568.1	14q11	2013-01-08			ENSG00000165804	ENSG00000165804		"Zinc fingers, C2H2-type"	13011	protein-coding gene	gene with protein product		605036				10819330	Standard	NM_016423		Approved		uc001vzs.2	Q9P2Y4	OTTHUMG00000029647	ENST00000360947.3:c.47C>T	chr14.hg19:g.21561409G>A	ENSP00000354206:p.Ser16Leu	25.0	0.0	749	18.0	10.0	NM_001102454	D3DS16|Q53Y57|Q8IYC1|Q9BW28	Missense_Mutation	SNP	ENST00000360947.3	hg19	CCDS9568.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176369	0.78564	.	.	ENSG00000165804	ENST00000360947;ENST00000451119;ENST00000421093;ENST00000555270;ENST00000554478;ENST00000556174;ENST00000554923;ENST00000553296;ENST00000555697	T;T;T;T;T;T;T;T	0.10477	3.16;3.16;3.16;3.5;2.96;3.11;2.87;3.03	4.84	4.84	0.62591	.	0.377447	0.21121	N	0.079804	T	0.06554	0.0168	N	0.14661	0.345	0.18873	N	0.999981	B	0.26363	0.147	B	0.17979	0.02	T	0.21552	-1.0242	10	0.72032	D	0.01	-14.0205	8.9496	0.35781	0.0979:0.0:0.9021:0.0	.	16	Q9P2Y4	ZN219_HUMAN	L	16;16;16;16;62;16;53;16;16	ENSP00000354206:S16L;ENSP00000388558:S16L;ENSP00000392401:S16L;ENSP00000450803:S16L;ENSP00000451212:S62L;ENSP00000450609:S16L;ENSP00000451890:S53L;ENSP00000450900:S16L	ENSP00000354206:S16L	S	-	2	0	ZNF219	20631249	0.076000	0.21285	0.810000	0.32431	0.995000	0.86356	2.223000	0.42936	2.520000	0.84964	0.655000	0.94253	TCG	.	.		0.652	ZNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073931.2			A	21561409	G	A	21561409	3	1	207	1	0	0	0	0	1	0	0	0	17788	1059	37	1	2133	1	ZNF219	14	21561409	Missense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10	708783	21561409	85788131	33	30029										
EML5	161436	hgsc.bcm.edu	37	chr14	89202828	89202828	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	aaggtttatttctttcttgcAccacaatttcaaaaatttca	3	8	4	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr14:89202828A>G	ENST00000380664.5	-	7	928	c.929T>C	c.(928-930)gTg>gCg	p.V310A	EML5_ENST00000352093.5_Missense_Mutation_p.V310A|EML5_ENST00000554922.1_Missense_Mutation_p.V310A			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	310						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						TCTTTCTTGCACCACAATTTC	0.403																																					p.V310A		Atlas-SNP	.											.	EML5	141	.	0			c.T929C						.						163	162	162					14																	89202828		1904	4105	6009	SO:0001583	missense	161436	exon7			TCTTGCACCACAA	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.929T>C	chr14.hg19:g.89202828A>G	ENSP00000370039:p.Val310Ala	167.0	0.0		202.0	89.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	A	17.36	3.370939	0.61624	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.01369	4.97;4.97;4.98	5.15	5.15	0.70609	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.072805	0.53938	D	0.000042	T	0.02929	0.0087	L	0.39633	1.23	0.58432	D	0.999996	D	0.61080	0.989	P	0.52343	0.696	T	0.70371	-0.4890	10	0.15952	T	0.53	-13.2347	15.1382	0.72586	1.0:0.0:0.0:0.0	.	310	Q05BV3	EMAL5_HUMAN	A	310	ENSP00000451998:V310A;ENSP00000298315:V310A;ENSP00000370039:V310A	ENSP00000298315:V310A	V	-	2	0	EML5	88272581	1.000000	0.71417	0.976000	0.42696	0.983000	0.72400	8.761000	0.91691	2.166000	0.68216	0.533000	0.62120	GTG	.	.		0.403	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			G	89202828	A	G	89202828	3	3	207	1	0	0	0	0	1	0	0	0	5102	159	6	2	5152	2	EML5	14	89202828	Missense_Mutation	SNP	A	TCGA-DD-AAE1-01A-11D-A40R-10	67641419	89202828	18146712	34	30030										
RYR3	6263	hgsc.bcm.edu	37	chr15	34021159	34021159	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tttatggcattaaggatcaaActtttctgctccacttgctg	7	9	2	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr15:34021159A>G	ENST00000389232.4	+	47	7205	c.7135A>G	c.(7135-7137)Act>Gct	p.T2379A	RYR3_ENST00000415757.3_Missense_Mutation_p.T2379A	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2379	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TAAGGATCAAACTTTTCTGCT	0.448																																					p.T2379A		Atlas-SNP	.											.	RYR3	760	.	0			c.A7135G						.						78	77	78					15																	34021159		1866	4093	5959	SO:0001583	missense	6263	exon47			GATCAAACTTTTC		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.7135A>G	chr15.hg19:g.34021159A>G	ENSP00000373884:p.Thr2379Ala	84.0	0.0		60.0	10.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.324018	0.41096	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.96265	-3.96;-3.96	4.85	1.19	0.21007	.	0.109027	0.64402	D	0.000014	D	0.88695	0.6506	N	0.14661	0.345	0.25400	N	0.988452	B;B	0.19706	0.038;0.007	B;B	0.17979	0.02;0.002	T	0.78758	-0.2079	10	0.32370	T	0.25	.	5.1189	0.14851	0.6363:0.1421:0.2216:0.0	.	2379;2379	Q15413-2;Q15413	.;RYR3_HUMAN	A	2379	ENSP00000373884:T2379A;ENSP00000399610:T2379A	ENSP00000354735:T2379A	T	+	1	0	RYR3	31808451	0.993000	0.37304	0.992000	0.48379	0.986000	0.74619	1.732000	0.38146	0.097000	0.17492	0.460000	0.39030	ACT	.	.		0.448	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			G	34021159	A	G	34021159	3	3	207	1	0	0	0	0	1	0	0	0	13785	43	2	2	7321	2	RYR3	15	34021159	Missense_Mutation	SNP	A	TCGA-DD-AAE1-01A-11D-A40R-10		34021159	68510233	35	30031										
AXIN1	8312	hgsc.bcm.edu	37	chr16	396740	396740	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	gaacaggcttatcccatcttGgtcatccagcagggaatgca	10	11	2	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr16:396740G>A	ENST00000262320.3	-	2	657	c.286C>T	c.(286-288)Caa>Taa	p.Q96*	AXIN1_ENST00000354866.3_Nonsense_Mutation_p.Q96*|AXIN1_ENST00000481769.1_Intron	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	96	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				ATCCCATCTTGGTCATCCAGC	0.592											OREG0003698	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.Q96X		Atlas-SNP	.											.	AXIN1	290	.	0			c.C286T						.						42	38	39					16																	396740		2203	4300	6503	SO:0001587	stop_gained	8312	exon2			CATCTTGGTCATC	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.286C>T	chr16.hg19:g.396740G>A	ENSP00000262320:p.Gln96*	54.0	0.0	588	28.0	21.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Nonsense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	G	38	6.685887	0.97764	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-17.008	19.4141	0.94688	0.0:0.0:1.0:0.0	.	.	.	.	X	96	.	ENSP00000262320:Q96X	Q	-	1	0	AXIN1	336741	1.000000	0.71417	0.992000	0.48379	0.803000	0.45373	9.726000	0.98782	2.605000	0.88082	0.655000	0.94253	CAA	.	.		0.592	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	396740	G	A	396740	4	1	207	1	0	0	0	0	0	1	0	0	1236	1357	47	3	2342	3	AXIN1	16	396740	Nonsense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10		396740	89958013	36	30032										
KRT17	3872	hgsc.bcm.edu	37	chr17	39777023	39777023	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ctgctgctccatctcgcagcGaagctgggccagctgctcct	11	16	1	0	rs374932182		TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr17:39777023G>A	ENST00000311208.8	-	6	1136	c.1069C>T	c.(1069-1071)Cgc>Tgc	p.R357C	JUP_ENST00000540235.1_Missense_Mutation_p.R516C	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	357	Coil 2.|Rod.			R -> L (in Ref. 4; AL353997/AC022596). {ECO:0000305}.	epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinization (GO:0031424)|morphogenesis of an epithelium (GO:0002009)|positive regulation of cell growth (GO:0030307)|positive regulation of hair follicle development (GO:0051798)|positive regulation of translation (GO:0045727)|signal transduction (GO:0007165)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	MHC class II protein binding (GO:0042289)|MHC class II receptor activity (GO:0032395)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12		Breast(137;0.000307)				ATCTCGCAGCGAAGCTGGGCC	0.627																																					p.R357C	Pancreas(92;1242 2086 39193 50508)	Atlas-SNP	.											KRT17,right_upper_lobe,carcinoma,0,1	KRT17	57	.	0			c.C1069T						.	G	CYS/ARG	0,4406		0,0,2203	57	59	58		1069	4	1	17		58	1,8599	1.2+/-3.3	0,1,4299	no	missense	KRT17	NM_000422.2	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	357/433	39777023	1,13005	2203	4300	6503	SO:0001583	missense	3872	exon6			CGCAGCGAAGCTG	X62571	CCDS11402.1	17q21.2	2014-06-12			ENSG00000128422	ENSG00000128422		"-", "Intermediate filaments type I, keratins (acidic)"	6427	protein-coding gene	gene with protein product		148069		PCHC1		7539673, 1281771, 16831889	Standard	NM_000422		Approved		uc002hxh.2	Q04695	OTTHUMG00000133505	ENST00000311208.8:c.1069C>T	chr17.hg19:g.39777023G>A	ENSP00000308452:p.Arg357Cys	136.0	0.0		130.0	52.0	NM_000422	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	Missense_Mutation	SNP	ENST00000311208.8	hg19	CCDS11402.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799287	0.70567	0.0	1.16E-4	ENSG00000128422;ENSG00000173801	ENST00000311208;ENST00000540235	D;D	0.91521	-2.86;-2.86	4.02	4.02	0.46733	Filament (1);	0.000000	0.47852	D	0.000202	D	0.94594	0.8258	H	0.98738	4.315	0.45528	D	0.998482	B	0.24963	0.115	B	0.30316	0.114	D	0.94808	0.7976	10	0.87932	D	0	.	12.6993	0.57022	0.0:0.0:0.8349:0.1651	.	357	Q04695	K1C17_HUMAN	C	357;516	ENSP00000308452:R357C;ENSP00000441751:R516C	ENSP00000441751:R516C	R	-	1	0	JUP;KRT17	37030549	0.821000	0.29204	1.000000	0.80357	0.807000	0.45602	1.433000	0.34947	2.246000	0.74042	0.561000	0.74099	CGC	.	.		0.627	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422		A	39777023	G	A	39777023	3	1	207	1	0	0	0	0	1	0	0	0	8463	1058	37	1	241	1	KRT17	17	39777023	Missense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10		39777023	41418187	37	30033										
ITGB3	3690	hgsc.bcm.edu	37	chr17	45367587	45367591	+	Frame_Shift_Del	DEL	GTTCT	GTTCT	-													0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tcccagggaccacagttgggGttctgtccatggattccagc							TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	GTTCT	GTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr17:45367587_45367591delGTTCT	ENST00000559488.1	+	8	1088_1092	c.1072_1076delGTTCT	c.(1072-1077)gttctgfs	p.VL358fs	ITGB3_ENST00000571680.1_Frame_Shift_Del_p.VL358fs|ITGB3_ENST00000435993.2_Frame_Shift_Del_p.VL311fs|ITGB3_ENST00000560629.1_Frame_Shift_Del_p.GS346fs	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	358	VWFA.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	CACAGTTGGGGTTCTGTCCATGGAT	0.502																																					p.357_359del		Atlas-INDEL	.											.	ITGB3	157	.	0			c.1071_1075del						.																																			SO:0001589	frameshift_variant	3690	exon8			.		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.1072_1076delGTTCT	chr17.hg19:g.45367587_45367591delGTTCT	ENSP00000452786:p.Val358fs	68.0	0.0		59.0	29.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Frame_Shift_Del	DEL	ENST00000559488.1	hg19	CCDS11511.1																																																																																			.	.		0.502	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		-	45367591	GTTCT	-	45367587	7	5	207	1	0	1	0	1	0	0	0	0	7904	1261	44	0	1102	0	ITGB3	17	45367587	Frame_Shift_Del	DEL	GTTCT	TCGA-DD-AAE1-01A-11D-A40R-10	5590564	45367587	35827623	38	30034										
SDK2	54549	hgsc.bcm.edu	37	chr17	71390374	71390374	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	gcccagcacgagcccgttgcGatcagcctcggggacctcgc	13	17	1	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr17:71390374G>T	ENST00000392650.3	-	26	3682	c.3682C>A	c.(3682-3684)Cgc>Agc	p.R1228S	SDK2_ENST00000388726.3_Missense_Mutation_p.R1228S	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1228	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						AGCCCGTTGCGATCAGCCTCG	0.657																																					p.R1228S		Atlas-SNP	.											.	SDK2	219	.	0			c.C3682A						.						42	37	38					17																	71390374		2203	4300	6503	SO:0001583	missense	54549	exon26			CGTTGCGATCAGC	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.3682C>A	chr17.hg19:g.71390374G>T	ENSP00000376421:p.Arg1228Ser	42.0	0.0		58.0	24.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.219981	0.39201	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893	T;T;T	0.56776	0.44;0.44;0.44	5.19	5.19	0.71726	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.055776	0.64402	D	0.000001	T	0.51176	0.1659	L	0.42245	1.32	0.48632	D	0.999681	P;P;P	0.44309	0.795;0.832;0.798	P;P;B	0.46796	0.515;0.527;0.392	T	0.47509	-0.9112	10	0.35671	T	0.21	.	13.0785	0.59100	0.0799:0.0:0.9201:0.0	.	1228;1228;1228	Q58EX2-2;Q58EX2;Q58EX2-3	.;SDK2_HUMAN;.	S	852;1228;1228;404;1228	ENSP00000376421:R1228S;ENSP00000373378:R1228S;ENSP00000407098:R404S	ENSP00000324967:R1228S	R	-	1	0	SDK2	68901969	0.665000	0.27466	0.951000	0.38953	0.024000	0.10985	2.830000	0.48136	2.426000	0.82243	0.313000	0.20887	CGC	.	.		0.657	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		T	71390374	G	T	71390374	3	4	207	1	0	0	0	0	1	0	0	0	13984	1058	37	1	2916	1	SDK2	17	71390374	Missense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10	26022787	71390374	9804836	39	30035										
SLC38A10	124565	hgsc.bcm.edu	37	chr17	79257223	79257223	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ccttacctgaaacccgaacaGccgggcaaagaagttggacc	10	13	0	2	rs138694564	byFrequency	TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr17:79257223G>A	ENST00000374759.3	-	4	726	c.343C>T	c.(343-345)Ctg>Ttg	p.L115L	SLC38A10_ENST00000288439.5_Silent_p.L115L|SLC38A10_ENST00000546352.1_5'Flank	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	115					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			AACCCGAACAGCCGGGCAAAG	0.607																																					p.L115L		Atlas-SNP	.											.	SLC38A10	133	.	0			c.C343T						.						83	57	66					17																	79257223		2201	4299	6500	SO:0001819	synonymous_variant	124565	exon4			CGAACAGCCGGGC	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.343C>T	chr17.hg19:g.79257223G>A		96.0	0.0		74.0	15.0	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	hg19	CCDS42397.1																																																																																			.	G|0.999;T|0.001		0.607	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		A	79257223	G	A	79257223	2	1	207	1	0	0	0	0	0	0	0	1	14617	962	34	3		3	SLC38A10	17	79257223	Silent	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10	7866849	79257223	1937987	40	30036										
MC4R	4160	hgsc.bcm.edu	37	chr18	58039334	58039334	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tcagccacagccaagctgcaGatgaaaaagtacatgggtga	11	9	1	3			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr18:58039334G>T	ENST00000299766.3	-	1	667	c.249C>A	c.(247-249)atC>atA	p.I83I		NM_005912.2	NP_005903.2	P32245	MC4R_HUMAN	melanocortin 4 receptor	83					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|diet induced thermogenesis (GO:0002024)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|insulin secretion (GO:0030073)|negative regulation of feeding behavior (GO:2000252)|positive regulation of bone resorption (GO:0045780)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of grooming behavior (GO:2000821)|response to insulin (GO:0032868)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(73;0.0946)				CCAAGCTGCAGATGAAAAAGT	0.428																																					p.I83I		Atlas-SNP	.											.	MC4R	49	.	0			c.C249A						.						101	98	99					18																	58039334		2203	4300	6503	SO:0001819	synonymous_variant	4160	exon1			GCTGCAGATGAAA	AY236539	CCDS11976.1	18q22	2012-08-10			ENSG00000166603	ENSG00000166603		"GPCR / Class A : Melanocortin receptors"	6932	protein-coding gene	gene with protein product		155541				7949735, 9763669	Standard	NM_005912		Approved		uc002lie.1	P32245	OTTHUMG00000132766	ENST00000299766.3:c.249C>A	chr18.hg19:g.58039334G>T		92.0	0.0		72.0	5.0	NM_005912	B2RAC3|Q16317|Q3MIJ6	Silent	SNP	ENST00000299766.3	hg19	CCDS11976.1																																																																																			.	.		0.428	MC4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256139.1	NM_005912		T	58039334	G	T	58039334	2	4	207	1	0	0	0	0	0	0	0	1	9375	932	33	3		3	MC4R	18	58039334	Silent	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10		58039334	20037914	41	30037										
CBLN2	147381	hgsc.bcm.edu	37	chr18	70209069	70209069	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	tagatggtcatggtgcggttGctcatctcggacggctcgtg	15	9	3	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr18:70209069G>A	ENST00000269503.4	-	3	1100	c.327C>T	c.(325-327)agC>agT	p.S109S	CBLN2_ENST00000585159.1_Silent_p.S109S|CBLN2_ENST00000581073.1_Intron|CBLN2_ENST00000584764.1_Intron|CBLN2_ENST00000583651.1_Intron	NM_182511.3	NP_872317.1	Q8IUK8	CBLN2_HUMAN	cerebellin 2 precursor	109	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				positive regulation of synapse assembly (GO:0051965)	extracellular space (GO:0005615)				endometrium(2)|lung(15)	17		Esophageal squamous(42;0.131)				TGGTGCGGTTGCTCATCTCGG	0.721																																					p.S109S		Atlas-SNP	.											.	CBLN2	41	.	0			c.C327T						.						41	33	36					18																	70209069		2203	4300	6503	SO:0001819	synonymous_variant	147381	exon3			GCGGTTGCTCATC	BC035789	CCDS11999.1	18q22.3	2007-11-19			ENSG00000141668	ENSG00000141668			1544	protein-coding gene	gene with protein product		600433				7877445	Standard	NM_182511		Approved		uc002lkv.2	Q8IUK8	OTTHUMG00000132825	ENST00000269503.4:c.327C>T	chr18.hg19:g.70209069G>A		29.0	0.0		34.0	9.0	NM_182511	Q53Z56	Silent	SNP	ENST00000269503.4	hg19	CCDS11999.1																																																																																			.	.		0.721	CBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256288.1	NM_182511		A	70209069	G	A	70209069	2	1	207	1	0	0	0	0	0	0	0	1	2707	1310	46	3		3	CBLN2	18	70209069	Silent	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10	12169735	70209069	7868179	42	30038										
MBP	4155	hgsc.bcm.edu	37	chr18	74817196	74817196	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	cttctcggcatttaattctcGtttgcctgcgtggtttccca	8	12	2	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr18:74817196G>A	ENST00000397860.3	-	2	236	c.22C>T	c.(22-24)Cga>Tga	p.R8*	MBP_ENST00000487778.1_5'UTR|MBP_ENST00000579129.1_Nonsense_Mutation_p.R8*|MBP_ENST00000397863.1_Nonsense_Mutation_p.R8*|MBP_ENST00000580402.1_Nonsense_Mutation_p.R8*|MBP_ENST00000355994.2_Nonsense_Mutation_p.R8*	NM_001025100.1	NP_001020271.1	P13727	PRG2_HUMAN	myelin basic protein	0					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)	Sargramostim(DB00020)	TTTAATTCTCGTTTGCCTGCG	0.448																																					p.R8X	NSCLC(17;72 1131 19392)	Atlas-SNP	.											.	MBP	45	.	0			c.C22T						.						238	182	201					18																	74817196		2203	4300	6503	SO:0001587	stop_gained	4155	exon2			ATTCTCGTTTGCC		CCDS12011.1, CCDS32847.1, CCDS42448.1, CCDS42449.1, CCDS42450.1	18q23	2008-08-01			ENSG00000197971	ENSG00000197971			6925	protein-coding gene	gene with protein product		159430				2425357	Standard	XM_005266699		Approved		uc010xfd.2	P02686	OTTHUMG00000132874	ENST00000397860.3:c.22C>T	chr18.hg19:g.74817196G>A	ENSP00000380958:p.Arg8*	100.0	0.0		83.0	30.0	NM_001025100	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Nonsense_Mutation	SNP	ENST00000397860.3	hg19	CCDS42450.1	.	.	.	.	.	.	.	.	.	.	G	38	6.950281	0.97956	.	.	ENSG00000197971	ENST00000355994;ENST00000397863;ENST00000397860	.	.	.	3.26	1.37	0.22104	.	0.000000	0.47093	D	0.000244	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.0652	8.0449	0.30542	0.0:0.0:0.5636:0.4364	.	.	.	.	X	8	.	ENSP00000348273:R8X	R	-	1	2	MBP	72946184	0.978000	0.34361	0.167000	0.22817	0.006000	0.05464	0.767000	0.26575	0.362000	0.24319	0.563000	0.77884	CGA	.	.		0.448	MBP-005	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267945.1	NM_001025081		A	74817196	G	A	74817196	4	1	207	1	0	0	0	0	0	1	0	0	9368	1153	40	1	1024	1	MBP	18	74817196	Nonsense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10	4608127	74817196	3260052	43	30039										
WIZ	58525	hgsc.bcm.edu	37	chr19	15538111	15538111	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	acctgcgccgcccatcatctTggccagggcttttgggcttg	12	14	2	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr19:15538111T>C	ENST00000389282.4	-	6	3547	c.3334A>G	c.(3334-3336)Aag>Gag	p.K1112E	WIZ_ENST00000599910.2_Missense_Mutation_p.K429E|WIZ_ENST00000545156.1_Missense_Mutation_p.K426E|WIZ_ENST00000263381.7_Missense_Mutation_p.K255E|WIZ_ENST00000599686.3_Missense_Mutation_p.K296E			O95785	WIZ_HUMAN	widely interspaced zinc finger motifs	1112	Pro-rich.				positive regulation of nuclear cell cycle DNA replication (GO:0010571)|protein heterotrimerization (GO:0070208)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	24						CCCATCATCTTGGCCAGGGCT	0.657																																					p.K255E		Atlas-SNP	.											.	WIZ	152	.	0			c.A763G						.						27	31	29					19																	15538111		1988	4156	6144	SO:0001583	missense	58525	exon4			TCATCTTGGCCAG	AK091183	CCDS42516.1	19p13.12	2012-10-05	2007-01-18		ENSG00000011451	ENSG00000011451		"Zinc fingers, C2H2-type"	30917	protein-coding gene	gene with protein product			"WIZ zinc finger"			9795207, 12226707	Standard	NM_021241		Approved	ZNF803	uc002nbb.4	O95785		ENST00000389282.4:c.3334A>G	chr19.hg19:g.15538111T>C	ENSP00000373933:p.Lys1112Glu	78.0	0.0		79.0	35.0	NM_021241	B3KVH1|B7ZM82|M0QY21|Q4G0E0|Q6P6B0|Q6ZN24|Q7LDY6|Q7LDZ1|Q96IG5|Q96SQ6|Q9BUR8|Q9NPT1	Missense_Mutation	SNP	ENST00000389282.4	hg19		.	.	.	.	.	.	.	.	.	.	T	13.73	2.325004	0.41197	.	.	ENSG00000011451	ENST00000389282;ENST00000263381;ENST00000416927;ENST00000545156	T	0.02709	4.19	5.67	5.67	0.87782	.	0.192780	0.45126	D	0.000400	T	0.04634	0.0126	N	0.24115	0.695	0.28153	N	0.929293	P;D;P	0.60575	0.462;0.988;0.918	B;P;P	0.56163	0.091;0.793;0.53	T	0.45571	-0.9252	10	0.15499	T	0.54	-32.7876	11.397	0.49847	0.0:0.0:0.1512:0.8488	.	1112;255;296	O95785;O95785-2;B3KVH1	WIZ_HUMAN;.;.	E	1112;255;296;426	ENSP00000373933:K1112E	ENSP00000263381:K255E	K	-	1	0	WIZ	15399111	1.000000	0.71417	1.000000	0.80357	0.355000	0.29361	4.629000	0.61290	2.155000	0.67459	0.459000	0.35465	AAG	.	.		0.657	WIZ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021241		C	15538111	T	C	15538111	3	2	207	1	0	0	0	0	1	0	0	0	17390	1821	63	2	1641	2	WIZ	19	15538111	Missense_Mutation	SNP	T	TCGA-DD-AAE1-01A-11D-A40R-10		15538111	43590872	44	30040										
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36351887	36351887	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	gcttccttcagctgcgcctgGcgcgggaacccgcttccacg	12	17	1	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr19:36351887G>A	ENST00000360202.5	+	8	1203	c.1005G>A	c.(1003-1005)tgG>tgA	p.W335*	KIRREL2_ENST00000347900.6_Nonsense_Mutation_p.W285*|KIRREL2_ENST00000592409.1_Nonsense_Mutation_p.W335*|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000262625.7_Nonsense_Mutation_p.W335*	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	335	Ig-like C2-type 4.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCTGCGCCTGGCGCGGGAACC	0.662																																					p.W335X		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G1005A						.						12	15	14					19																	36351887		2189	4283	6472	SO:0001587	stop_gained	84063	exon8			CGCCTGGCGCGGG	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.1005G>A	chr19.hg19:g.36351887G>A	ENSP00000353331:p.Trp335*	45.0	0.0		62.0	32.0	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Nonsense_Mutation	SNP	ENST00000360202.5	hg19	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	g	39	7.551198	0.98352	.	.	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	.	.	.	4.5	4.5	0.54988	.	0.000000	0.44688	D	0.000422	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.156	12.6669	0.56848	0.0:0.0:1.0:0.0	.	.	.	.	X	335;285;335;315	.	ENSP00000262625:W335X	W	+	3	0	KIRREL2	41043727	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	8.354000	0.90080	2.362000	0.80069	0.494000	0.49563	TGG	.	.		0.662	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		A	36351887	G	A	36351887	4	1	207	1	0	0	0	0	0	1	0	0	8334	1212	42	3	1035	3	KIRREL2	19	36351887	Nonsense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10	20813776	36351887	22777096	45	30041										
CA11	770	hgsc.bcm.edu	37	chr19	49143044	49143044	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ctgaatctcgcctccgctcaCgttgacaaagaggctgagaa	10	12	2	4			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr19:49143044C>T	ENST00000084798.4	-	5	1247		c.e5+1		DBP_ENST00000222122.5_5'Flank|SEC1P_ENST00000430145.2_RNA|DBP_ENST00000601104.1_5'Flank	NM_001217.3	NP_001208.2	O75493	CAH11_HUMAN	carbonic anhydrase XI							basolateral plasma membrane (GO:0016323)|extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	14		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000103)|all cancers(93;0.000119)|GBM - Glioblastoma multiforme(486;0.00634)|Epithelial(262;0.016)	Zonisamide(DB00909)	CCTCCGCTCACGTTGACAAAG	0.632																																					.		Atlas-SNP	.											CA11,NS,carcinoma,0,1	CA11	29	.	0			c.567+1G>A						.						58	62	61					19																	49143044		2203	4300	6503	SO:0001630	splice_region_variant	770	exon6			CGCTCACGTTGAC	AF067662	CCDS12729.1	19q13.3	2012-07-02			ENSG00000063180	ENSG00000063180		"Carbonic anhydrases"	1370	protein-coding gene	gene with protein product	"CA-RP XI", "carbonic anhydrase-related protein XI", "carbonic anhydrase-related protein 2"	604644				9878252	Standard	XR_243956		Approved	CARP2, CARPX1	uc002pjz.1	O75493		ENST00000084798.4:c.567+1G>A	chr19.hg19:g.49143044C>T		92.0	0.0		106.0	45.0	NM_001217	O60596|Q6FHI1|Q9UEC4	Splice_Site	SNP	ENST00000084798.4	hg19	CCDS12729.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.058724	0.55325	.	.	ENSG00000063180	ENST00000084798	.	.	.	3.63	3.63	0.41609	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0057	0.47633	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CA11	53834856	1.000000	0.71417	0.998000	0.56505	0.687000	0.40016	3.235000	0.51328	2.055000	0.61198	0.462000	0.41574	.	.	.		0.632	CA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466172.1	NM_001217	Intron	T	49143044	C	T	49143044	5	4	207	1	0	0	0	0	0	0	1	0	2514	550	19	1	438	1	CA11	19	49143044	Splice_Site	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	12791157	49143044	9985939	46	30042										
ZNF329	79673	hgsc.bcm.edu	37	chr19	58639289	58639289	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	caggtgtgctctttgatgtcGaacaagggatgagctctttt	12	7	2	2	rs143513293	byFrequency	TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr19:58639289G>T	ENST00000598312.1	-	4	1815	c.1582C>A	c.(1582-1584)Cga>Aga	p.R528R	ZNF329_ENST00000358067.4_Silent_p.R528R	NM_024620.3	NP_078896.3	Q86UD4	ZN329_HUMAN	zinc finger protein 329	528					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|large_intestine(10)|lung(5)|skin(3)|urinary_tract(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)		CTTTGATGTCGAACAAGGGAT	0.522																																					p.R528R		Atlas-SNP	.											ZNF329,caecum,carcinoma,0,1	ZNF329	70	.	0			c.C1582A						.						185	160	168					19																	58639289		2203	4300	6503	SO:0001819	synonymous_variant	79673	exon4			GATGTCGAACAAG	AK022648	CCDS12972.1	19q13.43	2013-01-08				ENSG00000181894		"Zinc fingers, C2H2-type"	14209	protein-coding gene	gene with protein product							Standard	XM_006723381		Approved	FLJ12586	uc002qrn.3	Q86UD4		ENST00000598312.1:c.1582C>A	chr19.hg19:g.58639289G>T		98.0	0.0		116.0	39.0	NM_024620	B3KR32|Q9H9R7	Silent	SNP	ENST00000598312.1	hg19	CCDS12972.1																																																																																			.	G|1.000;A|0.000		0.522	ZNF329-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466724.1	NM_024620		T	58639289	G	T	58639289	2	4	207	1	0	0	0	0	0	0	0	1	17862	1066	37	1		1	ZNF329	19	58639289	Silent	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10	9496245	58639289	489694	47	30043										
C20orf70	140683	hgsc.bcm.edu	37	chr20	31767467	31767467	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	atgtgaatgtcattcagcagGtcgtcggtaagtcaatgggg	14	6	3	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr20:31767467G>T	ENST00000253362.2	+	7	849	c.703G>T	c.(703-705)Gtc>Ttc	p.V235F	BPIFA2_ENST00000354932.5_Missense_Mutation_p.V235F			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	235						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										CATTCAGCAGGTCGTCGGTAA	0.557																																					p.V235F		Atlas-SNP	.											.	.	.	.	0			c.G703T						.						154	148	150					20																	31767467		2203	4300	6503	SO:0001583	missense	140683	exon7			CAGCAGGTCGTCG	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"BPI fold containing"	16203	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 70"	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.703G>T	chr20.hg19:g.31767467G>T	ENSP00000253362:p.Val235Phe	50.0	0.0		65.0	25.0	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	hg19	CCDS13214.1	.	.	.	.	.	.	.	.	.	.	G	2.546	-0.305279	0.05495	.	.	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.04502	3.61;3.61	3.31	-6.62	0.01813	.	2.312150	0.02219	N	0.063839	T	0.03959	0.0111	N	0.14661	0.345	0.09310	N	1	B	0.29716	0.255	B	0.25405	0.06	T	0.38972	-0.9636	10	0.72032	D	0.01	-19.194	12.7692	0.57410	0.1092:0.5034:0.3874:0.0	.	235	Q96DR5	BPIA2_HUMAN	F	235	ENSP00000253362:V235F;ENSP00000347012:V235F	ENSP00000253362:V235F	V	+	1	0	BPIFA2	31231128	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.940000	0.00329	-4.847000	0.00029	-2.230000	0.00291	GTC	.	.		0.557	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574		T	31767467	G	T	31767467	3	4	207	1	0	0	0	0	1	0	0	0	2118	1261	44	3	725	3	C20orf70	20	31767467	Missense_Mutation	SNP	G	TCGA-DD-AAE1-01A-11D-A40R-10		31767467	31258053	48	30044										
C20orf134	170487	hgsc.bcm.edu	37	chr20	32255993	32255993	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	cgccgctggataactcgggcCatgtaccaggagtgtggctc	14	12	0	0			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr20:32255993C>T	ENST00000330271.4	+	1	1690	c.690C>T	c.(688-690)gcC>gcT	p.A230A	NECAB3_ENST00000375238.4_Intron|NECAB3_ENST00000246190.6_Intron	NM_001024675.1	NP_001019846.1	Q5JWF8	ACL10_HUMAN	actin-like 10	230																	TAACTCGGGCCATGTACCAGG	0.642																																					p.A230A		Atlas-SNP	.											.	.	.	.	0			c.C690T						.						25	29	28					20																	32255993		2203	4300	6503	SO:0001819	synonymous_variant	170487	exon1			TCGGGCCATGTAC	AL121906	CCDS33463.1	20q11.22	2011-11-24	2011-11-24	2011-11-24	ENSG00000182584	ENSG00000182584			16127	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 134"	C20orf134			Standard	NM_001024675		Approved		uc002wzt.3	Q5JWF8	OTTHUMG00000032262	ENST00000330271.4:c.690C>T	chr20.hg19:g.32255993C>T		64.0	0.0		82.0	38.0	NM_001024675	B9EH76	Silent	SNP	ENST00000330271.4	hg19	CCDS33463.1																																																																																			.	.		0.642	ACTL10-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078713.1			T	32255993	C	T	32255993	2	4	207	1	0	0	0	0	0	0	0	1	2089	581	21	3		3	C20orf134	20	32255993	Silent	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	488526	32255993	30769527	49	30045										
RALY	22913	hgsc.bcm.edu	37	chr20	32664877	32664877	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	ggtggcgccggcggcggcggCggtggtggtggcagcggtgg	26	9	0	0	rs539352667	byFrequency	TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr20:32664877C>T	ENST00000246194.3	+	8	1204	c.702C>T	c.(700-702)ggC>ggT	p.G234G	RALY_ENST00000375114.3_Silent_p.G218G	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	234	Epitope (recognized by BKRF1 antibodies).|Poly-Gly.				mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						gcggcggcggcggtggtggtg	0.667																																					p.G234G		Atlas-SNP	.											.	RALY	44	.	0			c.C702T						.						5	7	7					20																	32664877		2080	4086	6166	SO:0001819	synonymous_variant	22913	exon8			CGGCGGCGGTGGT	AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"RNA binding motif (RRM) containing"	15921	protein-coding gene	gene with protein product		614663	"RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)", "RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	ENST00000246194.3:c.702C>T	chr20.hg19:g.32664877C>T		110.0	0.0		127.0	6.0	NM_016732	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	Silent	SNP	ENST00000246194.3	hg19	CCDS13230.1																																																																																			.	.		0.667	RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1			T	32664877	C	T	32664877	2	4	207	1	0	0	0	0	0	0	0	1	13034	755	27	1		1	RALY	20	32664877	Silent	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10	408884	32664877	30360643	50	30046										
ZNF280B	140883	hgsc.bcm.edu	37	chr22	22842492	22842492	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	catcagcaaagaccgacgatCtataatggcaaacctggcac	8	12	2	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chr22:22842492C>A	ENST00000406426.1	-	4	1974	c.1232G>T	c.(1231-1233)aGa>aTa	p.R411I	ZNF280B_ENST00000360412.2_Missense_Mutation_p.R411I			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	411					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		GACCGACGATCTATAATGGCA	0.398																																					p.R411I		Atlas-SNP	.											.	ZNF280B	67	.	0			c.G1232T						.						130	121	124					22																	22842492		2203	4300	6503	SO:0001583	missense	140883	exon4			GACGATCTATAAT	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"zinc finger protein 279", "suppressor of hairy wing homolog 2 (Drosophila)"	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.1232G>T	chr22.hg19:g.22842492C>A	ENSP00000385998:p.Arg411Ile	148.0	0.0		173.0	77.0	NM_080764		Missense_Mutation	SNP	ENST00000406426.1	hg19	CCDS13799.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.482626	0.63962	.	.	ENSG00000198477	ENST00000406426;ENST00000360412	T;T	0.28255	1.62;1.62	4.85	3.83	0.44106	Zinc finger, C2H2-like (1);	.	.	.	.	T	0.57242	0.2040	M	0.85542	2.76	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.64032	-0.6502	9	0.87932	D	0	-20.0009	11.4142	0.49943	0.0:0.9114:0.0:0.0886	.	411	Q86YH2	Z280B_HUMAN	I	411	ENSP00000385998:R411I;ENSP00000353586:R411I	ENSP00000353586:R411I	R	-	2	0	ZNF280B	21172492	1.000000	0.71417	0.981000	0.43875	0.534000	0.34807	6.799000	0.75160	1.410000	0.46936	0.655000	0.94253	AGA	.	.		0.398	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764		A	22842492	C	A	22842492	3	1	207	1	0	0	0	0	1	0	0	0	17830	913	32	3	403	3	ZNF280B	22	22842492	Missense_Mutation	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10		22842492	28462074	51	30047										
CXorf40A	91966	hgsc.bcm.edu	37	chrX	148627336	148627336	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.727886056971514	4.18534482758621	0.398604269293924	1	1	0	actgggaaggcgatgcctggCgggagctgctggtggagaga	20	7	0	1			TCGA-DD-AAE1-01A-11D-A40R-10	TCGA-DD-AAE1-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	55f49128-beb9-408f-8a1b-737659403573	9109a16c-3ae7-492e-8de3-bece8e8322d0	g.chrX:148627336C>T	ENST00000441248.1	+	3	1747	c.160C>T	c.(160-162)Cgg>Tgg	p.R54W	CXorf40A_ENST00000359293.5_Missense_Mutation_p.R54W|RP5-937E21.8_ENST00000431993.1_RNA|CXorf40A_ENST00000434353.2_Missense_Mutation_p.R54W|CXorf40A_ENST00000428236.1_5'UTR|CXorf40A_ENST00000422892.2_Missense_Mutation_p.R54W|CXorf40A_ENST00000423540.2_Missense_Mutation_p.R54W|CXorf40A_ENST00000423421.1_Missense_Mutation_p.R54W|CXorf40A_ENST00000514208.1_Missense_Mutation_p.R54W|CXorf40A_ENST00000450602.2_Missense_Mutation_p.R54W|CXorf40A_ENST00000393985.3_Missense_Mutation_p.R54W			Q8TE69	CX04A_HUMAN	chromosome X open reading frame 40A	54										breast(1)|endometrium(3)|large_intestine(1)|lung(2)	7	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					CGATGCCTGGCGGGAGCTGCT	0.597																																					p.R54W		Atlas-SNP	.											.	CXorf40A	15	.	0			c.C160T						.						87	58	68					X																	148627336		2203	4299	6502	SO:0001583	missense	91966	exon4			GCCTGGCGGGAGC	AF011889	CCDS14687.1, CCDS55522.1	Xq28	2010-03-16	2005-09-13	2005-09-13	ENSG00000197620	ENSG00000197620			28089	protein-coding gene	gene with protein product	"endothelial-overexpressed lipopolysaccharide-associated factor 1"		"chromosome X open reading frame 40"	CXorf40		8717057, 9147653, 16383041	Standard	XM_005278212		Approved	EOLA1	uc004fdg.3	Q8TE69	OTTHUMG00000022622	ENST00000441248.1:c.160C>T	chrX.hg19:g.148627336C>T	ENSP00000423099:p.Arg54Trp	232.0	0.0		274.0	234.0	NM_178124	A8K784|B7Z6H6|B7ZL96|D6RA72|E7ENU3|Q2M3E9	Missense_Mutation	SNP	ENST00000441248.1	hg19	CCDS14687.1	.	.	.	.	.	.	.	.	.	.	C	5.916	0.353153	0.11182	.	.	ENSG00000197620	ENST00000450602;ENST00000441248;ENST00000393985;ENST00000423421;ENST00000423540;ENST00000434353;ENST00000514208;ENST00000422892;ENST00000359293	D;D;D;D;D;D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02	3.71	-5.12	0.02893	PUA-like domain (1);	0.670247	0.14108	N	0.340893	D	0.84938	0.5583	L	0.46157	1.445	0.19300	N	0.999975	B;B;B	0.15141	0.012;0.012;0.001	B;B;B	0.12837	0.008;0.008;0.001	T	0.71487	-0.4578	10	0.54805	T	0.06	.	6.1611	0.20364	0.516:0.2898:0.0:0.1942	.	54;54;54	Q8TE69;E7ENU3;D6RA72	CX04A_HUMAN;.;.	W	54	ENSP00000427540:R54W;ENSP00000423099:R54W;ENSP00000421745:R54W;ENSP00000422512:R54W;ENSP00000425520:R54W;ENSP00000423160:R54W;ENSP00000423708:R54W;ENSP00000422312:R54W;ENSP00000420882:R54W	ENSP00000420882:R54W	R	+	1	2	CXorf40A	148435241	0.004000	0.15560	0.001000	0.08648	0.005000	0.04900	0.006000	0.13152	-0.959000	0.03618	0.455000	0.32223	CGG	.	.		0.597	CXorf40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058699.3	NM_178124		T	148627336	C	T	148627336	3	4	207	1	0	0	0	0	1	0	0	0	4110	759	27	1	162	1	CXorf40A	23	148627336	Missense_Mutation	SNP	C	TCGA-DD-AAE1-01A-11D-A40R-10		148627336	6643224	52	30048										
CALML6	163688	hgsc.bcm.edu	37	chr1	1848609	1848609	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ttgtggccatgatgacggggGagtccttcaagctgatccag	14	9	1	3			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr1:1848609G>T	ENST00000307786.3	+	6	977	c.523G>T	c.(523-525)Gag>Tag	p.E175*		NM_138705.2	NP_619650.2	Q8TD86	CALL6_HUMAN	calmodulin-like 6	175	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(1)|prostate(2)	7	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.94e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.83e-23)|GBM - Glioblastoma multiforme(42;3.23e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		GATGACGGGGGAGTCCTTCAA	0.701																																					p.E175X		Atlas-SNP	.											.	CALML6	18	.	0			c.G523T						.						30	29	30					1																	1848609		2192	4295	6487	SO:0001587	stop_gained	163688	exon6			ACGGGGGAGTCCT	AF490905	CCDS30566.1	1p36.33	2013-01-10			ENSG00000169885	ENSG00000169885		"EF-hand domain containing"	24193	protein-coding gene	gene with protein product		610171					Standard	NM_138705		Approved	CAGLP	uc001aih.1	Q8TD86	OTTHUMG00000000943	ENST00000307786.3:c.523G>T	chr1.hg19:g.1848609G>T	ENSP00000304643:p.Glu175*	89.0	0.0		82.0	35.0	NM_138705	A2A2M3|Q6Q2C4	Nonsense_Mutation	SNP	ENST00000307786.3	hg19	CCDS30566.1	.	.	.	.	.	.	.	.	.	.	.	14.20	2.465376	0.43839	.	.	ENSG00000169885	ENST00000307786;ENST00000378604	.	.	.	3.43	1.52	0.23074	.	.	.	.	.	.	.	.	.	.	.	0.40228	D	0.977814	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.5098	0.16874	0.2675:0.0:0.7325:0.0	.	.	.	.	X	175;158	.	ENSP00000304643:E175X	E	+	1	0	CALML6	1838469	1.000000	0.71417	0.928000	0.36995	0.174000	0.22865	1.203000	0.32284	0.278000	0.22164	0.313000	0.20887	GAG	.	.		0.701	CALML6-004	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276929.1	NM_138705		T	1848609	G	T	1848609	4	4	208	1	0	0	0	0	0	1	0	0	2592	1175	41	3	545	3	CALML6	1	1848609	Nonsense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10		1848609	247402012	1	30049										
KIF1B	23095	hgsc.bcm.edu	37	chr1	10316355	10316355	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ctccaaagtccttcagcttcGactattcctactggtctcat	5	14	2	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr1:10316355G>A	ENST00000377086.1	+	3	359	c.157G>A	c.(157-159)Gac>Aac	p.D53N	KIF1B_ENST00000377081.1_Missense_Mutation_p.D53N|KIF1B_ENST00000263934.6_Missense_Mutation_p.D53N|KIF1B_ENST00000377083.1_Missense_Mutation_p.D53N|KIF1B_ENST00000377093.4_Missense_Mutation_p.D53N			O60333	KIF1B_HUMAN	kinesin family member 1B	53	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CTTCAGCTTCGACTATTCCTA	0.413																																					p.D53N		Atlas-SNP	.											.	KIF1B	242	.	0			c.G157A						.						121	106	111					1																	10316355		2203	4300	6503	SO:0001583	missense	23095	exon3			AGCTTCGACTATT	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.157G>A	chr1.hg19:g.10316355G>A	ENSP00000366290:p.Asp53Asn	50.0	0.0		64.0	9.0	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.675438	0.96764	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	5.31	5.31	0.75309	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.93517	0.7931	M	0.92555	3.32	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.999;0.995;0.998;0.987;0.984;0.993	D	0.94668	0.7854	10	0.87932	D	0	.	19.3421	0.94347	0.0:0.0:1.0:0.0	.	53;53;53;53;53;53;53	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2;O60333-3	.;.;.;.;KIF1B_HUMAN;.;.	N	53	ENSP00000263934:D53N;ENSP00000366297:D53N;ENSP00000366290:D53N;ENSP00000366287:D53N;ENSP00000366284:D53N	ENSP00000263934:D53N	D	+	1	0	KIF1B	10238942	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.642000	0.89623	0.650000	0.86243	GAC	.	.		0.413	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			A	10316355	G	A	10316355	3	1	208	1	0	0	0	0	1	0	0	0	8293	1058	37	1	163	1	KIF1B	1	10316355	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	8467746	10316355	238934266	2	30050										
FAM46B	115572	hgsc.bcm.edu	37	chr1	27333377	27333377	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ctctcagggtgcagcacgtgGctggcagctgaaccatgcag	14	12	1	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr1:27333377G>A	ENST00000289166.5	-	2	501	c.336C>T	c.(334-336)agC>agT	p.S112S		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	112										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		GCAGCACGTGGCTGGCAGCTG	0.632																																					p.S112S		Atlas-SNP	.											.	FAM46B	44	.	0			c.C336T						.						79	68	72					1																	27333377		2203	4300	6503	SO:0001819	synonymous_variant	115572	exon2			CACGTGGCTGGCA	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.336C>T	chr1.hg19:g.27333377G>A		84.0	0.0		112.0	51.0	NM_052943		Silent	SNP	ENST00000289166.5	hg19	CCDS294.2																																																																																			.	.		0.632	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943		A	27333377	G	A	27333377	2	1	208	1	0	0	0	0	0	0	0	1	5574	1194	42	3		3	FAM46B	1	27333377	Silent	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	17017022	27333377	221917244	3	30051										
EIF2B3	8891	hgsc.bcm.edu	37	chr1	45345676	45345676	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gcttcttttataaaactgtaGatatcttcagaacaaacacc	4	9	3	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr1:45345676G>A	ENST00000360403.2	-	8	915	c.789C>T	c.(787-789)atC>atT	p.I263I	EIF2B3_ENST00000372183.3_Silent_p.I263I	NM_001261418.1|NM_020365.4	NP_001248347.1|NP_065098.1	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa	263					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|positive regulation of GTPase activity (GO:0043547)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	guanyl-nucleotide exchange factor activity (GO:0005085)|nucleotidyltransferase activity (GO:0016779)|translation initiation factor activity (GO:0003743)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	17	Acute lymphoblastic leukemia(166;0.155)					TAAAACTGTAGATATCTTCAG	0.408																																					p.I263I	Colon(26;357 658 2581 11857 12657)	Atlas-SNP	.											.	EIF2B3	43	.	0			c.C789T						.						51	52	52					1																	45345676		2203	4300	6503	SO:0001819	synonymous_variant	8891	exon8			ACTGTAGATATCT	AF257077	CCDS517.1, CCDS53313.1, CCDS72775.1	1p34.1	2008-02-05	2002-08-29		ENSG00000070785	ENSG00000070785			3259	protein-coding gene	gene with protein product		606273	"eukaryotic translation initiation factor 2B, subunit 3 (gamma, 58kD)"			10900014	Standard	NM_020365		Approved	EIF2Bgamma, EIF-2B	uc001cmt.3	Q9NR50	OTTHUMG00000008585	ENST00000360403.2:c.789C>T	chr1.hg19:g.45345676G>A		117.0	0.0		124.0	49.0	NM_020365	B2RBH8|D3DPZ2|Q5QP89|Q5QP90|Q8NDB5|Q8WV57|Q9H850	Silent	SNP	ENST00000360403.2	hg19	CCDS517.1	.	.	.	.	.	.	.	.	.	.	G	7.460	0.644566	0.14451	.	.	ENSG00000070785	ENST00000439363	.	.	.	5.56	4.44	0.53790	.	.	.	.	.	T	0.59335	0.2186	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55648	-0.8108	4	.	.	.	-10.0142	8.6969	0.34301	0.8526:0.0:0.1474:0.0	.	.	.	.	F	84	.	.	S	-	2	0	EIF2B3	45118263	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	1.204000	0.32296	0.950000	0.37743	-0.361000	0.07541	TCT	.	.		0.408	EIF2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023724.1	NM_020365		A	45345676	G	A	45345676	2	1	208	1	0	0	0	0	0	0	0	1	5004	932	33	3		3	EIF2B3	1	45345676	Silent	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	18012299	45345676	203904945	4	30052										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103496781	103496781	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ccttgggatcacctgtgatcAaaaactgctgaatgtccccc	8	13	2	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr1:103496781A>G	ENST00000370096.3	-	5	983	c.671T>C	c.(670-672)tTg>tCg	p.L224S	COL11A1_ENST00000358392.2_Missense_Mutation_p.L224S|COL11A1_ENST00000512756.1_Missense_Mutation_p.L224S|COL11A1_ENST00000353414.4_Missense_Mutation_p.L224S	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	224	Laminin G-like.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		ACCTGTGATCAAAAACTGCTG	0.423																																					p.L224S		Atlas-SNP	.											.,2	COL11A1	972	.	0			c.T671C						.						71	65	67					1																	103496781		2203	4300	6503	SO:0001583	missense	1301	exon5			GTGATCAAAAACT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.671T>C	chr1.hg19:g.103496781A>G	ENSP00000359114:p.Leu224Ser	46.0	0.0		25.0	7.0	NM_001854	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	A	18.40	3.615497	0.66672	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239;ENST00000447608	T;T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08;-1.08	5.59	5.59	0.84812	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);Laminin G, subdomain 2 (1);	0.000000	0.64402	D	0.000003	D	0.88358	0.6415	M	0.90145	3.09	0.58432	D	0.999994	D;D;D;D	0.89917	0.997;0.999;1.0;0.999	D;D;D;D	0.87578	0.995;0.996;0.997;0.998	D	0.90023	0.4129	10	0.52906	T	0.07	.	15.7618	0.78087	1.0:0.0:0.0:0.0	.	224;224;224;224	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	S	224;224;224;224;224;151	ENSP00000359114:L224S;ENSP00000351163:L224S;ENSP00000302551:L224S;ENSP00000426533:L224S;ENSP00000408640:L224S;ENSP00000410177:L151S	ENSP00000302551:L224S	L	-	2	0	COL11A1	103269369	1.000000	0.71417	0.976000	0.42696	0.996000	0.88848	8.820000	0.92003	2.125000	0.65367	0.450000	0.29827	TTG	.	.		0.423	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		G	103496781	A	G	103496781	3	3	208	1	0	0	0	0	1	0	0	0	3669	131	5	2	5158	2	COL11A1	1	103496781	Missense_Mutation	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	58151105	103496781	145753840	5	30053										
CRB1	23418	hgsc.bcm.edu	37	chr1	197313448	197313448	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gaaattgacgaatgttggtcCcagccttgtttaaatggtgc	11	7	0	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr1:197313448C>T	ENST00000367400.3	+	3	825	c.690C>T	c.(688-690)tcC>tcT	p.S230S	CRB1_ENST00000538660.1_Silent_p.S230S|CRB1_ENST00000367399.2_Intron|CRB1_ENST00000535699.1_Silent_p.S161S|CRB1_ENST00000543483.1_5'UTR	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	230	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						AATGTTGGTCCCAGCCTTGTT	0.423																																					p.S230S		Atlas-SNP	.											.	CRB1	284	.	0			c.C690T						.						221	217	219					1																	197313448		2203	4300	6503	SO:0001819	synonymous_variant	23418	exon3			TTGGTCCCAGCCT		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.690C>T	chr1.hg19:g.197313448C>T		126.0	0.0		80.0	52.0	NM_001257966	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Silent	SNP	ENST00000367400.3	hg19	CCDS1390.1																																																																																			.	.		0.423	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		T	197313448	C	T	197313448	2	4	208	1	0	0	0	0	0	0	0	1	3850	610	22	3		3	CRB1	1	197313448	Silent	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	93816667	197313448	51937173	6	30054										
TMEM206	55248	hgsc.bcm.edu	37	chr1	212548579	212548580	+	Frame_Shift_Ins	INS	-	-	A													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tctttccattcaaagaccacINSaaaaaacaattgagcacttt							TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr1:212548579_212548580insA	ENST00000261455.4	-	7	983_984	c.846_847insT	c.(844-849)tttgtgfs	p.V283fs	TMEM206_ENST00000535273.1_Frame_Shift_Ins_p.V344fs	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	283						cell surface (GO:0009986)|integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		TCAAAGACCACAAAAAACAATT	0.356																																					p.V344fs		Atlas-INDEL	.											.	TMEM206	41	.	0			c.1030_1031insT						.																																			SO:0001589	frameshift_variant	55248	exon8			.	AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 75"	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.847dupT	chr1.hg19:g.212548585_212548585dupA	ENSP00000261455:p.Val283fs	173.0	0.0		223.0	74.0	NM_001198862	B7Z4D6|Q6IA87|Q9NV85	Frame_Shift_Ins	INS	ENST00000261455.4	hg19	CCDS1504.1																																																																																			.	.		0.356	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252		A	212548580	-	A	212548579	7	5	208	1	0	1	1	0	0	0	0	0	16146	478	17	0	213	0	TMEM206	1	212548579	Frame_Shift_Ins	INS	-	TCGA-DD-AAE2-01A-11D-A40R-10	15235131	212548579	36702042	7	30055										
WNT9A	7483	hgsc.bcm.edu	37	chr1	228111870	228111870	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cgaggttgttgtggaagtccAcacgggctcgcagatccttg	14	10	0	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr1:228111870A>C	ENST00000272164.5	-	3	594	c.584T>G	c.(583-585)gTg>gGg	p.V195G		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	195					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				GTGGAAGTCCACACGGGCTCG	0.627																																					p.V195G		Atlas-SNP	.											.	WNT9A	39	.	0			c.T584G						.						77	71	73					1																	228111870		2203	4300	6503	SO:0001583	missense	7483	exon3			AAGTCCACACGGG	AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"Wingless-type MMTV integration sites"	12778	protein-coding gene	gene with protein product		602863	"wingless-type MMTV integration site family, member 14"	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.584T>G	chr1.hg19:g.228111870A>C	ENSP00000272164:p.Val195Gly	185.0	0.0		197.0	73.0	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Missense_Mutation	SNP	ENST00000272164.5	hg19	CCDS31045.1	.	.	.	.	.	.	.	.	.	.	A	17.22	3.333593	0.60853	.	.	ENSG00000143816	ENST00000272164	T	0.78246	-1.16	4.78	4.78	0.61160	.	0.069953	0.64402	D	0.000020	T	0.78233	0.4251	M	0.74546	2.27	0.80722	D	1	B	0.13145	0.007	B	0.23574	0.047	T	0.77621	-0.2519	10	0.87932	D	0	.	13.503	0.61469	1.0:0.0:0.0:0.0	.	195	O14904	WNT9A_HUMAN	G	195	ENSP00000272164:V195G	ENSP00000272164:V195G	V	-	2	0	WNT9A	226178493	1.000000	0.71417	0.990000	0.47175	0.955000	0.61496	9.194000	0.94962	1.782000	0.52362	0.402000	0.26972	GTG	.	.		0.627	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395		C	228111870	A	C	228111870	3	2	208	1	0	0	0	0	1	0	0	0	17413	159	6	5	521	5	WNT9A	1	228111870	Missense_Mutation	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	15563291	228111870	21138751	8	30056										
FMN2	56776	hgsc.bcm.edu	37	chr1	240256917	240256917	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gggaggctccgcgcacctgcTggagcgcggggtggcgagtg	21	11	0	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr1:240256917T>A	ENST00000319653.9	+	1	1738	c.1508T>A	c.(1507-1509)cTg>cAg	p.L503Q		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	503					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GCGCACCTGCTGGAGCGCGGG	0.771																																					p.L503Q		Atlas-SNP	.											.	FMN2	451	.	0			c.T1508A						.						3	4	4					1																	240256917		1646	3506	5152	SO:0001583	missense	56776	exon1			ACCTGCTGGAGCG	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1508T>A	chr1.hg19:g.240256917T>A	ENSP00000318884:p.Leu503Gln	41.0	0.0		39.0	4.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	T	11.30	1.598778	0.28445	.	.	ENSG00000155816	ENST00000319653	D	0.81579	-1.51	4.72	1.1	0.20463	.	0.489196	0.16737	N	0.201597	T	0.79191	0.4404	L	0.29908	0.895	0.80722	D	1	D	0.64830	0.994	P	0.60173	0.87	T	0.75476	-0.3304	10	0.62326	D	0.03	.	8.7195	0.34432	0.0:0.2224:0.0:0.7776	.	503	Q9NZ56	FMN2_HUMAN	Q	503	ENSP00000318884:L503Q	ENSP00000318884:L503Q	L	+	2	0	FMN2	238323540	1.000000	0.71417	0.450000	0.26969	0.831000	0.47069	3.614000	0.54160	0.017000	0.15025	-0.371000	0.07208	CTG	.	.		0.771	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240256917	T	A	240256917	3	1	208	1	0	0	0	0	1	0	0	0	5958	1580	55	4	1510	4	FMN2	1	240256917	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	12145047	240256917	8993704	9	30057										
FMN2	56776	hgsc.bcm.edu	37	chr1	240371332	240371332	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cccctctacccggagcgggcAtaccccctccgcccccactt	7	23	1	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr1:240371332A>T	ENST00000319653.9	+	5	3450	c.3220A>T	c.(3220-3222)Ata>Tta	p.I1074L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1074	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGAGCGGGCATACCCCCTCC	0.726																																					p.I1074L		Atlas-SNP	.											.	FMN2	451	.	0			c.A3220T						.						2	3	3					1																	240371332		1343	2760	4103	SO:0001583	missense	56776	exon5			GCGGGCATACCCC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3220A>T	chr1.hg19:g.240371332A>T	ENSP00000318884:p.Ile1074Leu	122.0	0.0		143.0	28.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	a	8.983	0.975887	0.18736	.	.	ENSG00000155816	ENST00000319653	T	0.60040	0.22	3.04	-2.66	0.06077	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (2);	0.499468	0.18421	N	0.141758	T	0.47192	0.1432	M	0.82056	2.57	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39563	-0.9608	9	.	.	.	.	1.0252	0.01526	0.3297:0.2818:0.2496:0.1389	.	1074	Q9NZ56	FMN2_HUMAN	L	1074	ENSP00000318884:I1074L	.	I	+	1	0	FMN2	238437955	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.084000	0.14891	-0.417000	0.07461	0.397000	0.26171	ATA	.	.		0.726	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371332	A	T	240371332	3	4	208	1	0	0	0	0	1	0	0	0	5958	217	8	4	3238	4	FMN2	1	240371332	Missense_Mutation	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	114415	240371332	8879289	10	30058										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1893081	1893081	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ggtgtagtctacgggcaagtCccagcagtcgccctcgccca	12	15	1	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr2:1893081C>A	ENST00000399161.2	-	16	3199	c.2452G>T	c.(2452-2454)Gac>Tac	p.D818Y	MYT1L_ENST00000428368.2_Missense_Mutation_p.D816Y	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	818					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		ACGGGCAAGTCCCAGCAGTCG	0.567																																					p.D816Y		Atlas-SNP	.											.	MYT1L	241	.	0			c.G2446T						.						82	87	86					2																	1893081		2013	4156	6169	SO:0001583	missense	23040	exon16			GCAAGTCCCAGCA	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.2452G>T	chr2.hg19:g.1893081C>A	ENSP00000382114:p.Asp818Tyr	55.0	0.0		52.0	23.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	c	21.1	4.100877	0.76983	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.54479	0.57;0.57	4.77	3.88	0.44766	Myelin transcription factor 1 (1);	0.090356	0.85682	D	0.000000	T	0.70465	0.3227	M	0.76574	2.34	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.68943	0.961;0.912	T	0.74708	-0.3574	10	0.62326	D	0.03	-25.9023	14.7817	0.69772	0.0:0.8543:0.1457:0.0	.	818;816	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	Y	818;764;816	ENSP00000382114:D818Y;ENSP00000396103:D816Y	ENSP00000295067:D764Y	D	-	1	0	MYT1L	1872088	1.000000	0.71417	0.995000	0.50966	0.943000	0.58893	7.713000	0.84693	1.113000	0.41760	-0.290000	0.09829	GAC	.	.		0.567	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1893081	C	A	1893081	3	1	208	1	0	0	0	0	1	0	0	0	10116	855	30	3	1148	3	MYT1L	2	1893081	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10		1893081	241306292	11	30059										
SCN5A	6331	hgsc.bcm.edu	37	chr3	38651412	38651412	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	aggaccatcacatcagccagCttcttcacagactggatcag	8	13	5	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr3:38651412C>G	ENST00000333535.4	-	7	896	c.747G>C	c.(745-747)aaG>aaC	p.K249N	SCN5A_ENST00000425664.1_Missense_Mutation_p.K249N|SCN5A_ENST00000443581.1_Missense_Mutation_p.K249N|SCN5A_ENST00000455624.2_Missense_Mutation_p.K249N|SCN5A_ENST00000423572.2_Missense_Mutation_p.K249N|SCN5A_ENST00000414099.2_Missense_Mutation_p.K249N|SCN5A_ENST00000450102.2_Missense_Mutation_p.K249N|SCN5A_ENST00000413689.1_Missense_Mutation_p.K249N|SCN5A_ENST00000451551.2_Missense_Mutation_p.K249N|SCN5A_ENST00000449557.2_Missense_Mutation_p.K249N			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	249					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CATCAGCCAGCTTCTTCACAG	0.602																																					p.K249N		Atlas-SNP	.											.	SCN5A	634	.	0			c.G747C						.						85	92	89					3																	38651412		2185	4290	6475	SO:0001583	missense	6331	exon7			AGCCAGCTTCTTC	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.747G>C	chr3.hg19:g.38651412C>G	ENSP00000328968:p.Lys249Asn	144.0	0.0		139.0	40.0	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	hg19	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.527921	0.64860	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557;ENST00000399254	D;D;D;D;D;D;D;D;D;D	0.98585	-5.01;-5.01;-5.01;-5.01;-5.01;-5.01;-5.01;-5.01;-5.01;-5.01	5.34	3.53	0.40419	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97688	0.9242	L	0.46741	1.465	0.41869	D	0.990269	D;D;D;D;D;D;D	0.89917	0.998;1.0;1.0;0.999;0.998;1.0;0.999	D;D;D;D;D;D;D	0.91635	0.947;0.996;0.998;0.947;0.947;0.999;0.913	D	0.95788	0.8822	10	0.33141	T	0.24	.	6.4426	0.21859	0.0:0.6098:0.0:0.3902	.	249;249;249;249;249;249;249	E9PEF3;Q14524-3;E9PHB6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	N	249;249;249;249;249;249;249;249;249;249;59	ENSP00000398962:K249N;ENSP00000398266:K249N;ENSP00000410257:K249N;ENSP00000388797:K249N;ENSP00000397915:K249N;ENSP00000416634:K249N;ENSP00000328968:K249N;ENSP00000399524:K249N;ENSP00000403355:K249N;ENSP00000413996:K249N	ENSP00000328968:K249N	K	-	3	2	SCN5A	38626416	0.995000	0.38212	1.000000	0.80357	0.997000	0.91878	0.458000	0.21892	0.800000	0.34041	0.655000	0.94253	AAG	.	.		0.602	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		G	38651412	C	G	38651412	3	3	208	1	0	0	0	0	1	0	0	0	13937	796	28	4	5391	4	SCN5A	3	38651412	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10		38651412	159371018	12	30060										
MCM2	4171	hgsc.bcm.edu	37	chr3	127338035	127338035	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tgaagaagtacatcatctacGccaaggagagggtccacccg	11	11	2	3	rs2307313	byFrequency	TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr3:127338035G>T	ENST00000265056.7	+	13	2423	c.2179G>T	c.(2179-2181)Gcc>Tcc	p.A727S	MCM2_ENST00000468414.1_3'UTR	NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	727			A -> T (in dbSNP:rs2307313). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						CATCATCTACGCCAAGGAGAG	0.602																																					p.A727S		Atlas-SNP	.											.	MCM2	79	.	0			c.G2179T						.						105	83	90					3																	127338035		2203	4300	6503	SO:0001583	missense	4171	exon13			ATCTACGCCAAGG	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"mitotin"	116945	"minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)", "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.2179G>T	chr3.hg19:g.127338035G>T	ENSP00000265056:p.Ala727Ser	168.0	0.0		168.0	74.0	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	hg19	CCDS3043.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110380	0.77210	.	.	ENSG00000073111	ENST00000265056;ENST00000539922;ENST00000543142	T	0.10099	2.91	5.61	5.61	0.85477	.	0.048197	0.85682	D	0.000000	T	0.23572	0.0570	M	0.79123	2.44	0.80722	D	1	B;B;P	0.34684	0.347;0.272;0.463	B;B;B	0.43331	0.074;0.416;0.372	T	0.00662	-1.1621	10	0.54805	T	0.06	-35.0091	14.4675	0.67494	0.0:0.0:0.8529:0.1471	.	777;597;727	F5H1E9;B4DSV5;P49736	.;.;MCM2_HUMAN	S	727;631;777	ENSP00000265056:A727S	ENSP00000265056:A727S	A	+	1	0	MCM2	128820725	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.327000	0.79147	2.640000	0.89533	0.591000	0.81541	GCC	.	G|0.994;A|0.006		0.602	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			T	127338035	G	T	127338035	3	4	208	1	0	0	0	0	1	0	0	0	9395	1087	38	1	2229	1	MCM2	3	127338035	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	88686623	127338035	70684395	13	30061										
PRR23A	729627	hgsc.bcm.edu	37	chr3	138724398	138724398	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gacctggactccccacgcgcGgagagggaggtagaggttgg	18	10	0	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr3:138724398G>A	ENST00000383163.2	-	1	712	c.713C>T	c.(712-714)cCg>cTg	p.P238L	MRPS22_ENST00000495075.1_5'Flank	NM_001134659.1	NP_001128131.1	A6NEV1	PR23A_HUMAN	proline rich 23A	238	Pro-rich.									endometrium(3)|kidney(1)|lung(7)	11						CCCCACGCGCGGAGAGGGAGG	0.657																																					p.P238L		Atlas-SNP	.											.	PRR23A	35	.	0			c.C713T						.						22	24	24					3																	138724398		692	1591	2283	SO:0001583	missense	729627	exon1			ACGCGCGGAGAGG		CCDS46923.1	3q22.3	2014-06-03				ENSG00000206260			37172	protein-coding gene	gene with protein product							Standard	NM_001134659		Approved		uc011bms.2	A6NEV1		ENST00000383163.2:c.713C>T	chr3.hg19:g.138724398G>A	ENSP00000372649:p.Pro238Leu	158.0	0.0		191.0	11.0	NM_001134659		Missense_Mutation	SNP	ENST00000383163.2	hg19	CCDS46923.1	.	.	.	.	.	.	.	.	.	.	G	11.81	1.749066	0.30955	.	.	ENSG00000206260	ENST00000383163	.	.	.	3.23	2.35	0.29111	.	0.000000	0.41823	D	0.000820	T	0.36552	0.0971	M	0.68593	2.085	0.09310	N	1	P	0.52061	0.95	P	0.45946	0.498	T	0.23368	-1.0190	9	0.54805	T	0.06	.	6.4995	0.22160	0.1346:0.0:0.8654:0.0	.	238	A6NEV1	PR23A_HUMAN	L	238	.	ENSP00000372649:P238L	P	-	2	0	PRR23A	140207088	0.246000	0.23909	0.008000	0.14137	0.002000	0.02628	1.117000	0.31234	0.943000	0.37553	0.591000	0.81541	CCG	.	.		0.657	PRR23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361503.1	NM_001134659		A	138724398	G	A	138724398	3	1	208	1	0	0	0	0	1	0	0	0	12606	1116	39	1	91	1	PRR23A	3	138724398	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	11386363	138724398	59298032	14	30062										
GYG1	2992	hgsc.bcm.edu	37	chr3	148714621	148714621	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tgcttcaattccggagtcttCgtttatcagccttcagttga	8	10	4	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr3:148714621C>T	ENST00000345003.4	+	4	711	c.411C>T	c.(409-411)ttC>ttT	p.F137F	GYG1_ENST00000483267.1_Silent_p.F137F|GYG1_ENST00000484197.1_Silent_p.F137F|GYG1_ENST00000296048.6_Silent_p.F137F	NM_004130.3	NP_004121.2	P46976	GLYG_HUMAN	glycogenin 1	137					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogenin glucosyltransferase activity (GO:0008466)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(3)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CCGGAGTCTTCGTTTATCAGC	0.418																																					p.F137F		Atlas-SNP	.											.	GYG1	29	.	0			c.C411T						.						80	76	77					3																	148714621		2203	4300	6503	SO:0001819	synonymous_variant	2992	exon4			AGTCTTCGTTTAT	AF087942	CCDS3139.1, CCDS54654.1, CCDS54655.1	3q24-q25.1	2013-02-22	2005-11-04	2005-11-04	ENSG00000163754	ENSG00000163754	2.4.1.186	"Glycosyltransferase family 8 domain containing"	4699	protein-coding gene	gene with protein product	"glycogenin glucosyltransferase"	603942	"glycogenin"	GYG		8602861	Standard	NM_004130		Approved		uc003ewn.3	P46976	OTTHUMG00000159533	ENST00000345003.4:c.411C>T	chr3.hg19:g.148714621C>T		69.0	0.0		83.0	5.0	NM_004130	D3DNH0|D3DNH1|D3DNH2|Q6FHZ1|Q9UNV0	Silent	SNP	ENST00000345003.4	hg19	CCDS3139.1																																																																																			.	.		0.418	GYG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356046.1	NM_004130		T	148714621	C	T	148714621	2	4	208	1	0	0	0	0	0	0	0	1	6914	883	31	1		1	GYG1	3	148714621	Silent	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	9990223	148714621	49307809	15	30063										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151161667	151161667	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ctgtttcctcttagataaatCaagtcctgagaagaaaaaaa	6	7	2	3			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr3:151161667C>T	ENST00000282466.3	-	5	5067	c.5068G>A	c.(5068-5070)Gat>Aat	p.D1690N		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1690	Ig-like C2-type 3.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.D1690H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TTAGATAAATCAAGTCCTGAG	0.398																																					p.D1690N		Atlas-SNP	.											IGSF10,NS,carcinoma,0,1	IGSF10	279	.	1	Substitution - Missense(1)	prostate(1)	c.G5068A						.						34	33	33					3																	151161667		2203	4300	6503	SO:0001583	missense	285313	exon5			ATAAATCAAGTCC	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5068G>A	chr3.hg19:g.151161667C>T	ENSP00000282466:p.Asp1690Asn	93.0	0.0		104.0	34.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.768630	0.49680	.	.	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.68181	-0.31	5.25	4.36	0.52297	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.654694	0.13322	N	0.396619	T	0.54351	0.1853	N	0.14661	0.345	0.09310	N	1	P	0.41080	0.737	P	0.45971	0.499	T	0.41893	-0.9483	9	.	.	.	.	10.4078	0.44274	0.0:0.9077:0.0:0.0923	.	1690	Q6WRI0	IGS10_HUMAN	N	1690;317	ENSP00000282466:D1690N	.	D	-	1	0	IGSF10	152644357	0.073000	0.21202	0.980000	0.43619	0.967000	0.64934	1.982000	0.40638	2.458000	0.83093	0.585000	0.79938	GAT	.	.		0.398	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		T	151161667	C	T	151161667	3	4	208	1	0	0	0	0	1	0	0	0	7606	826	29	3	2859	3	IGSF10	3	151161667	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	2447046	151161667	46860763	16	30064										
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15482406	15482406	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	aggagcctgtgcaggaggagCccaagacccgcctcctgagt	14	13	0	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr4:15482406C>G	ENST00000503292.1	+	5	382	c.202C>G	c.(202-204)Ccc>Gcc	p.P68A	CC2D2A_ENST00000438599.2_Missense_Mutation_p.A103G|CC2D2A_ENST00000511544.1_Missense_Mutation_p.A103G|CC2D2A_ENST00000507954.1_Missense_Mutation_p.P68A|CC2D2A_ENST00000413206.1_Missense_Mutation_p.P68A|CC2D2A_ENST00000424120.1_Missense_Mutation_p.P68A|CC2D2A_ENST00000503658.1_Missense_Mutation_p.A103G|CC2D2A_ENST00000389652.5_Missense_Mutation_p.P19A|CC2D2A_ENST00000515124.1_Missense_Mutation_p.P68A|CC2D2A_ENST00000513811.1_3'UTR	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	68					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						GCAGGAGGAGCCCAAGACCCG	0.572																																					p.A103G		Atlas-SNP	.											.	CC2D2A	158	.	0			c.C308G						.						30	33	32					4																	15482406		1900	4107	6007	SO:0001583	missense	57545	exon6			GAGGAGCCCAAGA	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.202C>G	chr4.hg19:g.15482406C>G	ENSP00000421809:p.Pro68Ala	292.0	0.0		347.0	119.0	NM_020785	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Missense_Mutation	SNP	ENST00000503292.1	hg19	CCDS47026.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.615|9.615	1.132257|1.132257	0.21041|0.21041	.|.	.|.	ENSG00000048342|ENSG00000048342	ENST00000438599;ENST00000511544;ENST00000503658|ENST00000424120;ENST00000413206;ENST00000426932;ENST00000510333;ENST00000512702;ENST00000507954;ENST00000515124;ENST00000503292;ENST00000389652	T;T;T|T;T;T;T;T;T;T	0.67865|0.21734	-0.29;-0.29;-0.29|1.99;1.99;1.99;1.99;1.99;1.99;1.99	4.66|4.66	0.838|0.838	0.18902|0.18902	.|.	.|0.389572	.|0.19244	.|N	.|0.119086	T|T	0.14570|0.14570	0.0352|0.0352	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	P;P|B;B;P;P	0.46512|0.46912	0.879;0.782|0.0;0.03;0.573;0.886	B;B|B;B;B;B	0.42738|0.42555	0.396;0.199|0.001;0.015;0.272;0.391	T|T	0.11299|0.11299	-1.0593|-1.0593	9|10	0.87932|0.49607	D|T	0|0.09	.|.	6.5476|6.5476	0.22414|0.22414	0.0:0.5676:0.0:0.4324|0.0:0.5676:0.0:0.4324	.|.	64;103|68;19;68;68	Q8WVL8;E7EP21|Q9P2K1;Q9P2K1-2;C9JKY6;D6RB72	.;.|C2D2A_HUMAN;.;.;.	G|A	103|68;68;19;19;68;68;68;68;19	ENSP00000401154:A103G;ENSP00000426109:A103G;ENSP00000426846:A103G|ENSP00000403465:P68A;ENSP00000398391:P68A;ENSP00000422875:P68A;ENSP00000427221:P68A;ENSP00000424368:P68A;ENSP00000421809:P68A;ENSP00000374303:P19A	ENSP00000401154:A103G|ENSP00000374303:P19A	A|P	+|+	2|1	0|0	CC2D2A|CC2D2A	15091504|15091504	0.001000|0.001000	0.12720|0.12720	0.004000|0.004000	0.12327|0.12327	0.047000|0.047000	0.14425|0.14425	-0.031000|-0.031000	0.12287|0.12287	0.246000|0.246000	0.21394|0.21394	-0.254000|-0.254000	0.11334|0.11334	GCC|CCC	.	.		0.572	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		G	15482406	C	G	15482406	3	3	208	1	0	0	0	0	1	0	0	0	2730	739	26	4	322	4	CC2D2A	4	15482406	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10		15482406	175671870	17	30065										
TBC1D1	23216	hgsc.bcm.edu	37	chr4	38055878	38055878	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gtgggactcctgtgaagaccCggaggcattcctggaggcag	16	10	0	2	rs140253816		TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr4:38055878C>T	ENST00000261439.4	+	12	2324	c.1969C>T	c.(1969-1971)Cgg>Tgg	p.R657W	TBC1D1_ENST00000508802.1_Missense_Mutation_p.R751W	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	657					membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						TGTGAAGACCCGGAGGCATTC	0.488																																					p.R751W		Atlas-SNP	.											.	TBC1D1	94	.	0			c.C2251T						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	106	117	113		1969	4.8	0.7	4	dbSNP_134	113	0,8600		0,0,4300	yes	missense	TBC1D1	NM_015173.2	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	657/1169	38055878	1,13005	2203	4300	6503	SO:0001583	missense	23216	exon14			AAGACCCGGAGGC	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.1969C>T	chr4.hg19:g.38055878C>T	ENSP00000261439:p.Arg657Trp	92.0	0.0		99.0	31.0	NM_001253912	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	hg19	CCDS33972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.1|22.1	4.245743|4.245743	0.80024|0.80024	2.27E-4|2.27E-4	0.0|0.0	ENSG00000065882|ENSG00000065882	ENST00000510573|ENST00000508802;ENST00000261439;ENST00000446803;ENST00000421339	.|T;T;T;T	.|0.54675	.|3.28;0.56;0.56;0.56	5.64|5.64	4.77|4.77	0.60923|0.60923	.|.	.|0.000000	.|0.52532	.|D	.|0.000079	T|T	0.73737|0.73737	0.3625|0.3625	M|M	0.79926|0.79926	2.475|2.475	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.76575	.|0.978;0.964;0.988;0.978	T|T	0.78550|0.78550	-0.2161|-0.2161	5|10	.|0.87932	.|D	.|0	-26.7085|-26.7085	15.5654|15.5654	0.76287|0.76287	0.139:0.861:0.0:0.0|0.139:0.861:0.0:0.0	.|.	.|657;751;389;657	.|B9A6J6;E9PGH8;Q6PJJ8;Q86TI0	.|.;.;.;TBCD1_HUMAN	L|W	344|751;657;528;125	.|ENSP00000423651:R751W;ENSP00000261439:R657W;ENSP00000396877:R528W;ENSP00000410167:R125W	.|ENSP00000261439:R657W	P|R	+|+	2|1	0|2	TBC1D1|TBC1D1	37732273|37732273	0.955000|0.955000	0.32602|0.32602	0.735000|0.735000	0.30896|0.30896	0.786000|0.786000	0.44442|0.44442	5.556000|5.556000	0.67307|0.67307	1.312000|1.312000	0.45043|0.45043	0.655000|0.655000	0.94253|0.94253	CCG|CGG	.	C|1.000;G|0.000		0.488	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173		T	38055878	C	T	38055878	3	4	208	1	0	0	0	0	1	0	0	0	15612	643	23	1	2011	1	TBC1D1	4	38055878	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	22573472	38055878	153098398	18	30066										
ADAD1	132612	hgsc.bcm.edu	37	chr4	123301299	123301299	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	atgctgaaaaagaacctgccAgttcaaccagcgacaaagac	8	11	1	3			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr4:123301299A>T	ENST00000296513.2	+	3	260	c.75A>T	c.(73-75)ccA>ccT	p.P25P	ADAD1_ENST00000388725.2_Silent_p.P7P|ADAD1_ENST00000388724.2_Silent_p.P25P	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	25					multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						AGAACCTGCCAGTTCAACCAG	0.483																																					p.P25P		Atlas-SNP	.											.	ADAD1	94	.	0			c.A75T						.						91	76	81					4																	123301299		2203	4300	6503	SO:0001819	synonymous_variant	132612	exon3			CCTGCCAGTTCAA	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.75A>T	chr4.hg19:g.123301299A>T		186.0	0.0		197.0	83.0	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Silent	SNP	ENST00000296513.2	hg19	CCDS34058.1																																																																																			.	.		0.483	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		T	123301299	A	T	123301299	2	4	208	1	0	0	0	0	0	0	0	1	231	175	7	4		4	ADAD1	4	123301299	Silent	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	85245421	123301299	67852977	19	30067										
ADAD1	132612	hgsc.bcm.edu	37	chr4	123305084	123305084	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gctcttgatgagcttctacaActggatgaacctgaaccacg	9	11	2	4			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr4:123305084A>G	ENST00000296513.2	+	5	677	c.492A>G	c.(490-492)caA>caG	p.Q164Q	ADAD1_ENST00000492454.1_3'UTR|ADAD1_ENST00000388725.2_Silent_p.Q146Q|ADAD1_ENST00000388724.2_Silent_p.Q164Q	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	164	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						AGCTTCTACAACTGGATGAAC	0.363																																					p.Q164Q		Atlas-SNP	.											.	ADAD1	94	.	0			c.A492G						.						90	89	89					4																	123305084		2203	4300	6503	SO:0001819	synonymous_variant	132612	exon5			TCTACAACTGGAT	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.492A>G	chr4.hg19:g.123305084A>G		236.0	0.0		227.0	92.0	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Silent	SNP	ENST00000296513.2	hg19	CCDS34058.1																																																																																			.	.		0.363	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		G	123305084	A	G	123305084	2	3	208	1	0	0	0	0	0	0	0	1	231	40	2	2		2	ADAD1	4	123305084	Silent	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	3785	123305084	67849192	20	30068										
BBS12	166379	hgsc.bcm.edu	37	chr4	123663998	123663998	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gacatttcaagaattttcacTtgctgtctaccaggcttacc	6	11	3	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr4:123663998T>A	ENST00000314218.3	+	2	1144	c.951T>A	c.(949-951)acT>acA	p.T317T	BBS12_ENST00000542236.1_Silent_p.T317T	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	317					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						GAATTTTCACTTGCTGTCTAC	0.378									Bardet-Biedl syndrome																												p.T317T		Atlas-SNP	.											.	BBS12	63	.	0			c.T951A						.						82	70	74					4																	123663998		2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TTTCACTTGCTGT	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"Heat Shock Proteins / Chaperonins"	26648	protein-coding gene	gene with protein product		610683	"chromosome 4 open reading frame 24"	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.951T>A	chr4.hg19:g.123663998T>A		152.0	0.0		159.0	57.0	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	hg19	CCDS3728.1																																																																																			.	.		0.378	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618		A	123663998	T	A	123663998	2	1	208	1	0	0	0	0	0	0	0	1	1337	1596	56	4		4	BBS12	4	123663998	Silent	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	358914	123663998	67490278	21	30069										
FAM198B	51313	hgsc.bcm.edu	37	chr4	159048727	159048727	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tgaagaagtttctgccgtaaGtgctggctcttcaaaacaga	10	8	3	3			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr4:159048727G>C	ENST00000296530.8	-	5	2013	c.1392C>G	c.(1390-1392)caC>caG	p.H464Q	FAM198B_ENST00000393807.5_Missense_Mutation_p.H472Q|FAM198B_ENST00000585682.1_Missense_Mutation_p.H464Q	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	464						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(14)|skin(2)|urinary_tract(1)	26						TCTGCCGTAAGTGCTGGCTCT	0.373																																					p.H472Q		Atlas-SNP	.											.	FAM198B	134	.	0			c.C1416G						.						70	70	70					4																	159048727		2203	4300	6503	SO:0001583	missense	51313	exon6			CCGTAAGTGCTGG		CCDS3798.1, CCDS34087.1	4q32.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000164125	ENSG00000164125			25312	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 18"	C4orf18		12975309	Standard	NM_001031700		Approved	FLJ38155, DKFZp434L142	uc003ipr.4	Q6UWH4	OTTHUMG00000161537	ENST00000296530.8:c.1392C>G	chr4.hg19:g.159048727G>C	ENSP00000296530:p.His464Gln	89.0	0.0		119.0	55.0	NM_001031700	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Missense_Mutation	SNP	ENST00000296530.8	hg19	CCDS3798.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.278114	0.40294	.	.	ENSG00000164125	ENST00000337222;ENST00000296530;ENST00000393807;ENST00000505460	T;T	0.28454	1.61;1.61	5.67	4.83	0.62350	.	0.162849	0.53938	D	0.000051	T	0.31827	0.0809	L	0.54323	1.7	0.80722	D	1	P;P	0.49090	0.919;0.839	P;P	0.49252	0.604;0.497	T	0.11275	-1.0594	10	0.25751	T	0.34	-11.4025	5.2163	0.15344	0.205:0.1663:0.6288:0.0	.	472;464	Q6UWH4-2;Q6UWH4	.;F198B_HUMAN	Q	464;464;472;170	ENSP00000296530:H464Q;ENSP00000377396:H472Q	ENSP00000296530:H464Q	H	-	3	2	FAM198B	159268177	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.760000	0.26475	1.423000	0.47198	0.650000	0.86243	CAC	.	.		0.373	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613		C	159048727	G	C	159048727	3	2	208	1	0	0	0	0	1	0	0	0	5534	1020	36	4	171	4	FAM198B	4	159048727	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	35384729	159048727	32105549	22	30070										
GALNT7	51809	hgsc.bcm.edu	37	chr4	174223196	174223196	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ttgcagtgtttctttttcttAggtccccagccatggctggg	11	10	2	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr4:174223196A>T	ENST00000265000.4	+	7	1231		c.e7-1			NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7						carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		TCTTTTTCTTAGGTCCCCAGC	0.438																																					.		Atlas-SNP	.											.	GALNT7	61	.	0			c.1149-2A>T						.						220	224	223					4																	174223196		2203	4300	6503	SO:0001630	splice_region_variant	51809	exon7			TTTCTTAGGTCCC	AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"Glycosyltransferase family 2 domain containing"	4129	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 7"	605005	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.1149-1A>T	chr4.hg19:g.174223196A>T		89.0	0.0		104.0	38.0	NM_017423	B3KQU3|Q7Z5W7|Q9UJ28	Splice_Site	SNP	ENST00000265000.4	hg19	CCDS3815.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.489052	0.84962	.	.	ENSG00000109586	ENST00000265000;ENST00000505308;ENST00000458613	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4473	0.83942	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GALNT7	174459771	1.000000	0.71417	0.963000	0.40424	0.937000	0.57800	9.228000	0.95250	2.281000	0.76405	0.533000	0.62120	.	.	.		0.438	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2	NM_017423	Intron	T	174223196	A	T	174223196	5	4	208	1	0	0	0	0	0	0	1	0	6226	434	15	4	1173	4	GALNT7	4	174223196	Splice_Site	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	15174469	174223196	16931080	23	30071										
MAST4	375449	hgsc.bcm.edu	37	chr5	66386029	66386029	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tccaagaaatttctcccccaGtgcctcagcccatttttcat	4	15	3	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr5:66386029G>C	ENST00000403625.2	+	6	1098	c.803G>C	c.(802-804)aGt>aCt	p.S268T	MAST4_ENST00000405643.1_Missense_Mutation_p.S86T|MAST4_ENST00000261569.7_Missense_Mutation_p.S74T|MAST4_ENST00000490016.2_Missense_Mutation_p.S79T|MAST4_ENST00000404260.3_Missense_Mutation_p.S268T|MAST4_ENST00000403666.1_Missense_Mutation_p.S79T	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	268						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TTCTCCCCCAGTGCCTCAGCC	0.413																																					p.S268T		Atlas-SNP	.											.	MAST4	218	.	0			c.G803C						.						80	74	76					5																	66386029		1844	4094	5938	SO:0001583	missense	375449	exon6			CCCCCAGTGCCTC	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.803G>C	chr5.hg19:g.66386029G>C	ENSP00000385727:p.Ser268Thr	68.0	0.0		72.0	29.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.852748	0.91355	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000490016;ENST00000403666;ENST00000405643;ENST00000432426;ENST00000380908;ENST00000261569;ENST00000436277;ENST00000432399	T;T;T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45;1.45;1.45	5.82	5.82	0.92795	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.160309	0.38381	U	0.001702	T	0.62792	0.2457	M	0.85099	2.735	0.37734	D	0.925364	D;D;D;D;P	0.67145	0.987;0.996;0.984;0.984;0.542	D;D;P;D;P	0.72338	0.95;0.977;0.888;0.932;0.489	T	0.69101	-0.5234	10	0.66056	D	0.02	-3.6989	20.0958	0.97842	0.0:0.0:1.0:0.0	.	86;268;74;79;79	E7EWQ5;O15021;O15021-2;O15021-3;D6RAK1	.;MAST4_HUMAN;.;.;.	T	268;268;79;79;86;59;86;74;74;74	ENSP00000385048:S268T;ENSP00000385727:S268T;ENSP00000421739:S79T;ENSP00000384313:S79T;ENSP00000384099:S86T;ENSP00000261569:S74T;ENSP00000392478:S74T	ENSP00000261569:S74T	S	+	2	0	MAST4	66421785	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.274000	0.78538	2.759000	0.94783	0.637000	0.83480	AGT	.	.		0.413	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			C	66386029	G	C	66386029	3	2	208	1	0	0	0	0	1	0	0	0	9336	1029	36	4	955	4	MAST4	5	66386029	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10		66386029	114529231	24	30072										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135693062	135693062	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gctgcatgtttttgaaggtgCtgttcctcaacctatgggac	11	9	1	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr5:135693062C>G	ENST00000513104.1	-	2	296	c.14G>C	c.(13-15)aGc>aCc	p.S5T	TRPC7_ENST00000355180.3_Missense_Mutation_p.S5T|TRPC7_ENST00000426057.2_Missense_Mutation_p.S5T	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	5					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTTGAAGGTGCTGTTCCTCAA	0.537																																					p.S5T		Atlas-SNP	.											TRPC7,NS,carcinoma,0,2	TRPC7	126	.	0			c.G14C						.						28	31	30					5																	135693062		2073	4209	6282	SO:0001583	missense	57113	exon2			AAGGTGCTGTTCC	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.14G>C	chr5.hg19:g.135693062C>G	ENSP00000426070:p.Ser5Thr	12.0	0.0		25.0	6.0	NM_001167576	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	hg19	CCDS47267.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.624|7.624	0.677419|0.677419	0.14841|0.14841	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753|ENST00000355180;ENST00000426057;ENST00000513104;ENST00000265193	.|T;T;T	.|0.78126	.|-0.97;-1.15;-1.07	5.38|5.38	0.433|0.433	0.16534|0.16534	.|.	.|0.557442	.|0.22250	.|N	.|0.062569	T|T	0.58666|0.58666	0.2138|0.2138	N|N	0.19112|0.19112	0.55|0.55	0.20638|0.20638	N|N	0.999872|0.999872	.|B	.|0.09022	.|0.002	.|B	.|0.06405	.|0.002	T|T	0.39502|0.39502	-0.9611|-0.9611	5|10	.|0.20519	.|T	.|0.43	-6.311|-6.311	9.9072|9.9072	0.41384|0.41384	0.0:0.5753:0.0:0.4247|0.0:0.5753:0.0:0.4247	.|.	.|5	.|Q9HCX4	.|TRPC7_HUMAN	H|T	4|5	.|ENSP00000347312:S5T;ENSP00000441628:S5T;ENSP00000426070:S5T	.|ENSP00000265193:S5T	Q|S	-|-	3|2	2|0	TRPC7|TRPC7	135720961|135720961	0.969000|0.969000	0.33509|0.33509	0.985000|0.985000	0.45067|0.45067	0.971000|0.971000	0.66376|0.66376	0.241000|0.241000	0.18065|0.18065	-0.113000|-0.113000	0.11958|0.11958	0.655000|0.655000	0.94253|0.94253	CAG|AGC	.	.		0.537	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		G	135693062	C	G	135693062	3	3	208	1	0	0	0	0	1	0	0	0	16599	797	28	4	2618	4	TRPC7	5	135693062	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	69307033	135693062	45222198	25	30073										
CDC25C	995	hgsc.bcm.edu	37	chr5	137627755	137627755	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	acctgcttcagtcttggcctGttcaagttctctggcatcga	9	12	4	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr5:137627755G>T	ENST00000323760.6	-	8	944	c.666C>A	c.(664-666)aaC>aaA	p.N222K	CDC25C_ENST00000348983.3_Missense_Mutation_p.N149K|CDC25C_ENST00000356505.3_Missense_Mutation_p.N192K|CDC25C_ENST00000514555.1_Missense_Mutation_p.N192K|CDC25C_ENST00000415130.2_Missense_Mutation_p.N149K|CDC25C_ENST00000513970.1_Missense_Mutation_p.N222K|CDC25C_ENST00000357274.3_Missense_Mutation_p.N179K	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	222					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)			endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GTCTTGGCCTGTTCAAGTTCT	0.438																																					p.N222K		Atlas-SNP	.											.	CDC25C	37	.	0			c.C666A						.						149	155	153					5																	137627755		2203	4300	6503	SO:0001583	missense	995	exon8			TGGCCTGTTCAAG	M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"Protein tyrosine phosphatases / Class III Cys-based PTPs", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1727	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 60"	157680	"cell division cycle 25C", "cell division cycle 25 homolog C (S. cerevisiae)", "cell division cycle 25 homolog C (S. pombe)"	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.666C>A	chr5.hg19:g.137627755G>T	ENSP00000321656:p.Asn222Lys	108.0	0.0		121.0	48.0	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	hg19	CCDS4202.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.138|0.138	-1.105629|-1.105629	0.01828|0.01828	.|.	.|.	ENSG00000158402|ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000357274;ENST00000348983;ENST00000415130;ENST00000513970;ENST00000534892;ENST00000514555;ENST00000503022|ENST00000514017	T;T;T;T;T;T;T;T|.	0.22336|.	1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96|.	3.09|3.09	0.0358|0.0358	0.14189|0.14189	.|.	0.375132|.	0.25192|.	N|.	0.032454|.	T|T	0.39358|0.39358	0.1075|0.1075	L|L	0.46157|0.46157	1.445|1.445	0.24654|0.24654	N|N	0.993506|0.993506	B;B;D;B|.	0.64830|.	0.187;0.187;0.994;0.224|.	B;B;P;B|.	0.57425|.	0.058;0.058;0.82;0.096|.	T|T	0.34378|0.34378	-0.9831|-0.9831	10|5	0.07325|.	T|.	0.83|.	-14.8135|-14.8135	9.974|9.974	0.41772|0.41772	0.2308:0.0:0.7692:0.0|0.2308:0.0:0.7692:0.0	.|.	239;192;149;222|.	G3V1P6;P30307-2;P30307-4;P30307|.	.;.;.;MPIP3_HUMAN|.	K|K	222;192;179;149;149;222;239;192;222|17	ENSP00000321656:N222K;ENSP00000348898:N192K;ENSP00000349821:N179K;ENSP00000345205:N149K;ENSP00000392631:N149K;ENSP00000424795:N222K;ENSP00000425470:N192K;ENSP00000427251:N222K|.	ENSP00000321656:N222K|.	N|Q	-|-	3|1	2|0	CDC25C|CDC25C	137655654|137655654	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.413000|0.413000	0.31143|0.31143	0.784000|0.784000	0.26816|0.26816	-0.024000|-0.024000	0.13941|0.13941	-1.334000|-1.334000	0.01262|0.01262	AAC|CAG	.	.		0.438	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1			T	137627755	G	T	137627755	3	4	208	1	0	0	0	0	1	0	0	0	3066	1368	48	3	783	3	CDC25C	5	137627755	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	1934693	137627755	43287505	26	30074										
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138223237	138223237	+	Missense_Mutation	SNP	T	T	C													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cctggaaaccaatgttccacTtttggtattgattgaagctg							TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr5:138223237T>C	ENST00000302763.7	+	9	1292	c.1202T>C	c.(1201-1203)cTt>cCt	p.L401P	CTNNA1_ENST00000520400.1_3'UTR|CTNNA1_ENST00000540387.1_Missense_Mutation_p.L31P|CTNNA1_ENST00000355078.5_Missense_Mutation_p.L298P|CTNNA1_ENST00000518825.1_Missense_Mutation_p.L401P	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	401					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AATGTTCCACTTTTGGTATTG	0.358																																					p.L401P		Atlas-SNP	.											.	CTNNA1	114	.	0			c.T1202C						.						123	121	122					5																	138223237		2203	4300	6503	SO:0001583	missense	1495	exon9			TTCCACTTTTGGT	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.1202T>C	chr5.hg19:g.138223237T>C	ENSP00000304669:p.Leu401Pro	202.0	0.0		190.0	89.0	NM_001903	Q12795|Q8N1C0	Missense_Mutation	SNP	ENST00000302763.7	hg19	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.513295	0.85389	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000518381;ENST00000522013;ENST00000520260;ENST00000523298;ENST00000520865;ENST00000519634;ENST00000517533;ENST00000523685;ENST00000517656;ENST00000521683;ENST00000521640;ENST00000519116;ENST00000540387;ENST00000520522	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.56611	0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.73729	0.3624	M	0.81341	2.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.78290	-0.2261	10	0.87932	D	0	-8.9879	14.8558	0.70335	0.0:0.0:0.0:1.0	.	401;278;401	G3XAM7;B4DKT9;P35221	.;.;CTNA1_HUMAN	P	298;401;401;386;401;31;31;31;31;31;31;31;31;31;31;31;31;31;31	ENSP00000347190:L298P;ENSP00000304669:L401P;ENSP00000427821:L401P;ENSP00000429738:L31P;ENSP00000430379:L31P;ENSP00000429569:L31P;ENSP00000428044:L31P;ENSP00000430841:L31P;ENSP00000428088:L31P;ENSP00000431118:L31P;ENSP00000430240:L31P;ENSP00000430177:L31P;ENSP00000430981:L31P;ENSP00000430623:L31P;ENSP00000428894:L31P;ENSP00000438476:L31P;ENSP00000428710:L31P	ENSP00000304669:L401P	L	+	2	0	CTNNA1	138251136	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	1.994000	0.58287	0.533000	0.62120	CTT	.	.		0.358	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		C	138223237	T	C	138223237	3	2	208	1	0	0	0	0	1	0	0	0	4014	1609	56	2	1232	2	CTNNA1	5	138223237	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	595482	138223237	42692023	27	30075	155	2								
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138223240	138223240	+	Nonsense_Mutation	SNP	T	T	A													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ggaaaccaatgttccactttTggtattgattgaagctgcaa							TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr5:138223240T>A	ENST00000302763.7	+	9	1295	c.1205T>A	c.(1204-1206)tTg>tAg	p.L402*	CTNNA1_ENST00000520400.1_3'UTR|CTNNA1_ENST00000540387.1_Nonsense_Mutation_p.L32*|CTNNA1_ENST00000355078.5_Nonsense_Mutation_p.L299*|CTNNA1_ENST00000518825.1_Nonsense_Mutation_p.L402*	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	402					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GTTCCACTTTTGGTATTGATT	0.363																																					p.L402X		Atlas-SNP	.											.	CTNNA1	114	.	0			c.T1205A						.						123	122	122					5																	138223240		2203	4300	6503	SO:0001587	stop_gained	1495	exon9			CACTTTTGGTATT	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.1205T>A	chr5.hg19:g.138223240T>A	ENSP00000304669:p.Leu402*	203.0	0.0		194.0	91.0	NM_001903	Q12795|Q8N1C0	Nonsense_Mutation	SNP	ENST00000302763.7	hg19	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	T	36	5.906240	0.97087	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000518381;ENST00000522013;ENST00000520260;ENST00000523298;ENST00000520865;ENST00000519634;ENST00000517533;ENST00000523685;ENST00000517656;ENST00000521683;ENST00000521640;ENST00000519116;ENST00000540387;ENST00000520522	.	.	.	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-5.0133	14.8558	0.70335	0.0:0.0:0.0:1.0	.	.	.	.	X	299;402;402;387;402;32;32;32;32;32;32;32;32;32;32;32;32;32;32	.	ENSP00000304669:L402X	L	+	2	0	CTNNA1	138251139	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.040000	0.89188	1.994000	0.58287	0.533000	0.62120	TTG	.	.		0.363	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		A	138223240	T	A	138223240	4	1	208	1	0	0	0	0	0	1	0	0	4014	1821	63	4	1235	4	CTNNA1	5	138223240	Nonsense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	3	138223240	42692020	28	30076	155	2								
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140482111	140482111	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cacaatggcgaagtgcgcacCgccaggctgctgagcgagcg	15	13	0	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr5:140482111C>T	ENST00000231130.2	+	1	1878	c.1878C>T	c.(1876-1878)acC>acT	p.T626T	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	626	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AAGTGCGCACCGCCAGGCTGC	0.701																																					p.T626T		Atlas-SNP	.											PCDHB3,NS,carcinoma,0,1	PCDHB3	208	.	0			c.C1878T						.						30	32	31					5																	140482111		2145	4158	6303	SO:0001819	synonymous_variant	56132	exon1			GCGCACCGCCAGG	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1878C>T	chr5.hg19:g.140482111C>T		54.0	0.0		60.0	5.0	NM_018937	B2R8P2	Silent	SNP	ENST00000231130.2	hg19	CCDS4245.1																																																																																			.	.		0.701	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		T	140482111	C	T	140482111	2	4	208	1	0	0	0	0	0	0	0	1	11552	639	23	1		1	PCDHB3	5	140482111	Silent	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	2258871	140482111	40433149	29	30077										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140574260	140574260	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ctcggtgctcctgttcgtggCggtgcggctgtgcaggagga	18	10	0	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr5:140574260C>T	ENST00000239446.4	+	1	2319	c.2135C>T	c.(2134-2136)gCg>gTg	p.A712V		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	712					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGTTCGTGGCGGTGCGGCTG	0.692																																					p.A712V		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C2135T						.						39	49	46					5																	140574260		2081	4055	6136	SO:0001583	missense	56126	exon1			TCGTGGCGGTGCG	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.2135C>T	chr5.hg19:g.140574260C>T	ENSP00000239446:p.Ala712Val	60.0	0.0		70.0	30.0	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	hg19	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	c	16.09	3.025734	0.54683	.	.	ENSG00000120324	ENST00000239446	T	0.15603	2.41	3.18	1.2	0.21068	.	.	.	.	.	T	0.26629	0.0651	M	0.91768	3.24	0.09310	N	1	P	0.48162	0.906	B	0.40506	0.331	T	0.19418	-1.0306	9	0.44086	T	0.13	.	8.9805	0.35961	0.0:0.5249:0.4751:0.0	.	712	Q9UN67	PCDBA_HUMAN	V	712	ENSP00000239446:A712V	ENSP00000239446:A712V	A	+	2	0	PCDHB10	140554444	0.000000	0.05858	0.854000	0.33618	0.880000	0.50808	-2.879000	0.00716	0.149000	0.19098	0.298000	0.19748	GCG	.	.		0.692	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		T	140574260	C	T	140574260	3	4	208	1	0	0	0	0	1	0	0	0	11544	768	27	1	2137	1	PCDHB10	5	140574260	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	92149	140574260	40341000	30	30078										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140794696	140794696	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gcctcgtagtggccgtccagGaccacggccagccccctctc	11	19	1	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr5:140794696G>T	ENST00000398610.2	+	1	1954	c.1954G>T	c.(1954-1956)Gac>Tac	p.D652Y	PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB7_ENST00000398594.2_5'Flank|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	652	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCCGTCCAGGACCACGGCCA	0.701																																					p.D652Y		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.G1954T						.						40	50	47					5																	140794696		2199	4295	6494	SO:0001583	missense	56106	exon1			GTCCAGGACCACG		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.1954G>T	chr5.hg19:g.140794696G>T	ENSP00000381611:p.Asp652Tyr	135.0	0.0		146.0	12.0	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	hg19	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	g	22.2	4.259825	0.80246	.	.	ENSG00000253846	ENST00000398610	T	0.68903	-0.36	5.39	5.39	0.77823	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.91088	0.7195	H	0.99855	4.85	0.47659	D	0.999483	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.95258	0.8366	9	0.87932	D	0	.	18.8436	0.92194	0.0:0.0:1.0:0.0	.	652;652	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	Y	652	ENSP00000381611:D652Y	ENSP00000381611:D652Y	D	+	1	0	PCDHGA10	140774880	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	9.498000	0.97972	2.548000	0.85928	0.556000	0.70494	GAC	.	.		0.701	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		T	140794696	G	T	140794696	3	4	208	1	0	0	0	0	1	0	0	0	11560	1174	41	3	1956	3	PCDHGA10	5	140794696	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	220436	140794696	40120564	31	30079										
PHF3	23469	hgsc.bcm.edu	37	chr6	64395611	64395611	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ggaagaggataaactgaaacTgaaaaaacctgagaagaacc	10	6	0	5			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr6:64395611T>A	ENST00000262043.3	+	4	2328	c.1988T>A	c.(1987-1989)cTg>cAg	p.L663Q	PHF3_ENST00000393387.1_Missense_Mutation_p.L663Q|PHF3_ENST00000509330.1_Missense_Mutation_p.L663Q			Q92576	PHF3_HUMAN	PHD finger protein 3	663					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			AAACTGAAACTGAAAAAACCT	0.438																																					p.L663Q	GBM(135;136 1820 29512 34071 46235)	Atlas-SNP	.											.	PHF3	191	.	0			c.T1988A						.						69	72	71					6																	64395611		2203	4300	6503	SO:0001583	missense	23469	exon3			TGAAACTGAAAAA	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.1988T>A	chr6.hg19:g.64395611T>A	ENSP00000262043:p.Leu663Gln	192.0	0.0		166.0	70.0	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	hg19	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	T	4.313	0.057488	0.08339	.	.	ENSG00000118482	ENST00000506783;ENST00000481385;ENST00000262043;ENST00000494284;ENST00000509330;ENST00000393387	T;T;T;T;T;T	0.50813	2.16;1.8;2.16;1.82;0.73;2.16	5.55	1.72	0.24424	.	0.976716	0.08285	N	0.969314	T	0.14056	0.0340	L	0.29908	0.895	0.09310	N	1	B;B	0.28350	0.067;0.208	B;B	0.25291	0.013;0.059	T	0.30357	-0.9981	10	0.52906	T	0.07	-0.0249	3.9807	0.09493	0.2612:0.157:0.0:0.5818	.	663;663	Q92576;D6R9X2	PHF3_HUMAN;.	Q	477;575;663;616;663;663	ENSP00000424694:L477Q;ENSP00000425227:L575Q;ENSP00000262043:L663Q;ENSP00000424078:L616Q;ENSP00000422841:L663Q;ENSP00000377048:L663Q	ENSP00000262043:L663Q	L	+	2	0	PHF3	64453570	0.097000	0.21791	0.245000	0.24217	0.855000	0.48748	1.612000	0.36889	0.052000	0.16007	0.482000	0.46254	CTG	.	.		0.438	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			A	64395611	T	A	64395611	3	1	208	1	0	0	0	0	1	0	0	0	11845	1580	55	4	1998	4	PHF3	6	64395611	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10		64395611	106719456	32	30080										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128540089	128540089	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ctcacaataagttgagcaaaAttggacacaccggaacctcg	8	11	1	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr6:128540089A>G	ENST00000368215.3	-	6	845	c.846T>C	c.(844-846)aaT>aaC	p.N282N	PTPRK_ENST00000368210.3_Silent_p.N282N|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368207.3_Silent_p.N282N|PTPRK_ENST00000368213.5_Silent_p.N282N|PTPRK_ENST00000368226.4_Silent_p.N282N|PTPRK_ENST00000368227.3_Silent_p.N282N|PTPRK_ENST00000532331.1_Silent_p.N282N			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	282					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		GTTGAGCAAAATTGGACACAC	0.398																																					p.N282N		Atlas-SNP	.											PTPRK_ENST00000368213,caecum,carcinoma,0,2	PTPRK	330	.	0			c.T846C						.						148	132	137					6																	128540089		2203	4300	6503	SO:0001819	synonymous_variant	5796	exon6			AGCAAAATTGGAC	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.846T>C	chr6.hg19:g.128540089A>G		133.0	0.0		114.0	50.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Silent	SNP	ENST00000368215.3	hg19		.	.	.	.	.	.	.	.	.	.	A	9.789	1.177495	0.21787	.	.	ENSG00000152894	ENST00000490332	.	.	.	4.89	3.57	0.40892	.	.	.	.	.	T	0.44393	0.1291	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37220	-0.9715	4	.	.	.	.	8.7167	0.34416	0.7636:0.0:0.2364:0.0	.	.	.	.	T	99	.	.	I	-	2	0	PTPRK	128581782	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.961000	0.49168	0.600000	0.29862	0.374000	0.22700	ATT	.	.		0.398	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			G	128540089	A	G	128540089	2	3	208	1	0	0	0	0	0	0	0	1	12820	98	4	2		2	PTPRK	6	128540089	Silent	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	64144478	128540089	42574978	33	30081										
EPDR1	54749	hgsc.bcm.edu	37	chr7	37989827	37989827	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	acctggattggcatctatacAgtcaaggattgctatcctgt	9	9	2	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr7:37989827A>T	ENST00000199448.4	+	3	883	c.504A>T	c.(502-504)acA>acT	p.T168T	EPDR1_ENST00000476620.1_Silent_p.T66T|EPDR1_ENST00000559325.1_Silent_p.T288T|EPDR1_ENST00000425345.1_Silent_p.T107T|EPDR1_ENST00000423717.1_3'UTR	NM_017549.4	NP_060019.2	Q9UM22	EPDR1_HUMAN	ependymin related 1	168					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	22						GCATCTATACAGTCAAGGATT	0.368																																					p.T168T		Atlas-SNP	.											.	EPDR1	48	.	0			c.A504T						.						55	57	56					7																	37989827		2203	4300	6503	SO:0001819	synonymous_variant	54749	exon3			CTATACAGTCAAG	BC018299	CCDS5454.1, CCDS5454.2, CCDS59051.1, CCDS59052.1	7p14.1	2013-07-31	2013-07-31		ENSG00000086289	ENSG00000086289			17572	protein-coding gene	gene with protein product			"ependymin related protein 1 (zebrafish)"			11749721, 11248421	Standard	NM_001242946		Approved	MERP-1, MERP1, UCC1, EPDR	uc003tfp.4	Q9UM22	OTTHUMG00000102187	ENST00000199448.4:c.504A>T	chr7.hg19:g.37989827A>T		165.0	0.0		131.0	48.0	NM_017549	A8K4C0|C9JYS3|Q06BL0|Q99M77	Silent	SNP	ENST00000199448.4	hg19	CCDS5454.2																																																																																			.	.		0.368	EPDR1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220037.3	NM_017549		T	37989827	A	T	37989827	2	4	208	1	0	0	0	0	0	0	0	1	5165	175	7	4		4	EPDR1	7	37989827	Silent	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10		37989827	121148836	34	30082										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48313535	48313535	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	caaaatattttggggaatttCagagatatagaaaacaaaat	7	3	1	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr7:48313535C>A	ENST00000435803.1	+	17	4296	c.4272C>A	c.(4270-4272)ttC>ttA	p.F1424L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1424					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TGGGGAATTTCAGAGATATAG	0.284																																					p.F1424L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C4272A						.						32	31	31					7																	48313535		1793	4057	5850	SO:0001583	missense	154664	exon17			GAATTTCAGAGAT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4272C>A	chr7.hg19:g.48313535C>A	ENSP00000411096:p.Phe1424Leu	165.0	0.0		150.0	51.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	5.620	0.299056	0.10622	.	.	ENSG00000179869	ENST00000435803	D	0.86562	-2.14	5.04	3.2	0.36748	.	0.264539	0.26840	N	0.022226	T	0.79064	0.4383	L	0.39397	1.21	0.20403	N	0.9999	B	0.22080	0.064	B	0.17722	0.019	T	0.63269	-0.6675	9	.	.	.	.	8.2588	0.31773	0.0:0.8129:0.0:0.1871	.	1424	Q86UQ4	ABCAD_HUMAN	L	1424	ENSP00000411096:F1424L	.	F	+	3	2	ABCA13	48284081	0.005000	0.15991	0.012000	0.15200	0.115000	0.19883	0.214000	0.17541	0.615000	0.30124	0.462000	0.41574	TTC	.	.		0.284	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48313535	C	A	48313535	3	1	208	1	0	0	0	0	1	0	0	0	31	825	29	3	4167	3	ABCA13	7	48313535	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	10323708	48313535	110825128	35	30083										
VKORC1L1	154807	hgsc.bcm.edu	37	chr7	65338522	65338522	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cctctgcgacctggggccctGggtgaagtgctccgccgccc	14	17	1	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr7:65338522G>T	ENST00000360768.3	+	1	269	c.164G>T	c.(163-165)tGg>tTg	p.W55L	VKORC1L1_ENST00000434382.2_Missense_Mutation_p.W55L	NM_001284342.1|NM_173517.4	NP_001271271.1|NP_775788.2	Q8N0U8	VKORL_HUMAN	vitamin K epoxide reductase complex, subunit 1-like 1	55					cellular response to oxidative stress (GO:0034599)|peptidyl-glutamic acid carboxylation (GO:0017187)|vitamin K metabolic process (GO:0042373)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	quinone binding (GO:0048038)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			large_intestine(1)|prostate(1)	2		Lung NSC(55;0.197)			Menadione(DB00170)	CTGGGGCCCTGGGTGAAGTGC	0.726																																					p.W55L		Atlas-SNP	.											.	VKORC1L1	14	.	0			c.G164T						.						8	11	10					7																	65338522		2186	4269	6455	SO:0001583	missense	154807	exon1			GGCCCTGGGTGAA		CCDS5529.1, CCDS64663.1	7q11.21	2013-10-07			ENSG00000196715	ENSG00000196715			21492	protein-coding gene	gene with protein product		608838				23928358	Standard	NM_001284342		Approved		uc003tul.3	Q8N0U8	OTTHUMG00000129449	ENST00000360768.3:c.164G>T	chr7.hg19:g.65338522G>T	ENSP00000353998:p.Trp55Leu	65.0	0.0		75.0	26.0	NM_173517	B4E222|E7ETM5|Q6AHW9|Q6TEK6	Missense_Mutation	SNP	ENST00000360768.3	hg19	CCDS5529.1	.	.	.	.	.	.	.	.	.	.	G	9.265	1.044246	0.19748	.	.	ENSG00000196715	ENST00000360768;ENST00000434382	D;D	0.97831	-4.56;-4.56	2.09	1.15	0.20763	Vitamin K epoxide reductase (2);	0.333535	0.29212	U	0.012803	D	0.93562	0.7945	L	0.36672	1.1	0.34352	D	0.690028	P;B	0.43826	0.818;0.013	B;B	0.41374	0.355;0.026	D	0.91614	0.5305	10	0.11182	T	0.66	.	9.5774	0.39465	0.0:0.2172:0.7828:0.0	.	55;55	E7ETM5;Q8N0U8	.;VKORL_HUMAN	L	55	ENSP00000353998:W55L;ENSP00000403077:W55L	ENSP00000353998:W55L	W	+	2	0	VKORC1L1	64975957	1.000000	0.71417	1.000000	0.80357	0.393000	0.30537	4.401000	0.59716	0.202000	0.20498	-0.914000	0.02751	TGG	.	.		0.726	VKORC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251612.3	NM_173517		T	65338522	G	T	65338522	3	4	208	1	0	0	0	0	1	0	0	0	17188	1357	47	3	166	3	VKORC1L1	7	65338522	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	17024987	65338522	93800141	36	30084										
CYP3A5	1577	hgsc.bcm.edu	37	chr7	99247819	99247819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ccagttccaaagggtgtgtaTatgtaaggatctatgctgtc	11	7	1	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr7:99247819T>C	ENST00000222982.4	-	12	1389	c.1290A>G	c.(1288-1290)atA>atG	p.I430M	CYP3A5_ENST00000343703.5_Missense_Mutation_p.I420M|CYP3A5_ENST00000339843.2_3'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	430					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	AGGGTGTGTATATGTAAGGAT	0.388																																					p.I430M		Atlas-SNP	.											.	CYP3A5	46	.	0			c.A1290G						.						317	274	289					7																	99247819		2203	4300	6503	SO:0001583	missense	1577	exon12			TGTGTATATGTAA	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"Cytochrome P450s"	2638	protein-coding gene	gene with protein product		605325	"cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.1290A>G	chr7.hg19:g.99247819T>C	ENSP00000222982:p.Ile430Met	197.0	0.0		194.0	50.0	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Missense_Mutation	SNP	ENST00000222982.4	hg19	CCDS5672.1	.	.	.	.	.	.	.	.	.	.	T	9.903	1.207392	0.22205	.	.	ENSG00000106258	ENST00000222982;ENST00000343703	T;T	0.68331	-0.32;-0.32	4.73	-2.44	0.06502	.	0.843399	0.10613	N	0.654227	T	0.46308	0.1386	L	0.29908	0.895	0.58432	D	0.999997	B;B;B	0.19331	0.028;0.009;0.035	B;B;B	0.27887	0.051;0.052;0.084	T	0.39057	-0.9632	10	0.34782	T	0.22	.	1.1507	0.01785	0.141:0.275:0.2885:0.2955	.	420;430;430	F5H4S0;B2R9K2;P20815	.;.;CP3A5_HUMAN	M	430;420	ENSP00000222982:I430M;ENSP00000342969:I420M	ENSP00000222982:I430M	I	-	3	3	CYP3A5	99085755	0.000000	0.05858	0.036000	0.18154	0.983000	0.72400	-4.100000	0.00295	-0.077000	0.12752	0.459000	0.35465	ATA	.	.		0.388	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1			C	99247819	T	C	99247819	3	2	208	1	0	0	0	0	1	0	0	0	4182	1396	49	2	226	2	CYP3A5	7	99247819	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	33909297	99247819	59890844	37	30085										
HBP1	26959	hgsc.bcm.edu	37	chr7	106827063	106827063	+	Silent	SNP	T	T	G													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	aataaggaatggcaagatgtTgaagattttgctagagctga							TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr7:106827063T>G	ENST00000222574.4	+	6	888	c.702T>G	c.(700-702)gtT>gtG	p.V234V	HBP1_ENST00000461963.1_3'UTR|HBP1_ENST00000468410.1_Silent_p.V234V|HBP1_ENST00000485846.1_Silent_p.V234V	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	234	AXH. {ECO:0000255|PROSITE- ProRule:PRU00496}.				cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						GGCAAGATGTTGAAGATTTTG	0.363																																					p.V244V		Atlas-SNP	.											.	HBP1	31	.	0			c.T732G						.						146	143	144					7																	106827063		2203	4300	6503	SO:0001819	synonymous_variant	26959	exon6			AGATGTTGAAGAT	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.702T>G	chr7.hg19:g.106827063T>G		230.0	0.0		216.0	99.0	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Silent	SNP	ENST00000222574.4	hg19	CCDS5741.1																																																																																			.	.		0.363	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		G	106827063	T	G	106827063	2	3	208	1	0	0	0	0	0	0	0	1	6994	1799	63	5		5	HBP1	7	106827063	Silent	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	7579244	106827063	52311600	38	30086	156	3								
HBP1	26959	hgsc.bcm.edu	37	chr7	106827072	106827072	+	Missense_Mutation	SNP	T	T	G													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tggcaagatgttgaagatttTgctagagctgaaggctgtga							TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr7:106827072T>G	ENST00000222574.4	+	6	897	c.711T>G	c.(709-711)ttT>ttG	p.F237L	HBP1_ENST00000461963.1_3'UTR|HBP1_ENST00000468410.1_Missense_Mutation_p.F237L|HBP1_ENST00000485846.1_Missense_Mutation_p.F237L	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	237	AXH. {ECO:0000255|PROSITE- ProRule:PRU00496}.				cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						TTGAAGATTTTGCTAGAGCTG	0.358																																					p.F247L		Atlas-SNP	.											.	HBP1	31	.	0			c.T741G						.						149	145	146					7																	106827072		2203	4300	6503	SO:0001583	missense	26959	exon6			AGATTTTGCTAGA	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.711T>G	chr7.hg19:g.106827072T>G	ENSP00000222574:p.Phe237Leu	239.0	0.0		218.0	98.0	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Missense_Mutation	SNP	ENST00000222574.4	hg19	CCDS5741.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.143703	0.37825	.	.	ENSG00000105856	ENST00000468410;ENST00000222574;ENST00000485846;ENST00000498408	D;D;D	0.98249	-4.82;-4.82;-4.82	5.95	5.95	0.96441	Ataxin, AXH domain (1);Ataxin-1/HBP1 module (AXH) (3);	0.092388	0.85682	D	0.000000	D	0.93370	0.7886	N	0.04132	-0.27	0.58432	D	0.999999	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.12837	0.008;0.003;0.004	D	0.90952	0.4806	10	0.13470	T	0.59	-3.2057	16.4323	0.83853	0.0:0.0:0.0:1.0	.	247;237;237	B4DJ36;O60381-3;O60381	.;.;HBP1_HUMAN	L	237;237;237;229	ENSP00000420500:F237L;ENSP00000222574:F237L;ENSP00000418738:F237L	ENSP00000222574:F237L	F	+	3	2	HBP1	106614308	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.503000	0.53340	2.281000	0.76405	0.528000	0.53228	TTT	.	.		0.358	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		G	106827072	T	G	106827072	3	3	208	1	0	0	0	0	1	0	0	0	6994	1809	63	5	729	5	HBP1	7	106827072	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	9	106827072	52311591	39	30087	156	3								
HBP1	26959	hgsc.bcm.edu	37	chr7	106827075	106827075	+	Silent	SNP	T	T	C													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	caagatgttgaagattttgcTagagctgaaggctgtgataa							TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr7:106827075T>C	ENST00000222574.4	+	6	900	c.714T>C	c.(712-714)gcT>gcC	p.A238A	HBP1_ENST00000461963.1_3'UTR|HBP1_ENST00000468410.1_Silent_p.A238A|HBP1_ENST00000485846.1_Silent_p.A238A	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	238	AXH. {ECO:0000255|PROSITE- ProRule:PRU00496}.				cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						AAGATTTTGCTAGAGCTGAAG	0.358																																					p.A248A		Atlas-SNP	.											.	HBP1	31	.	0			c.T744C						.						150	146	147					7																	106827075		2203	4300	6503	SO:0001819	synonymous_variant	26959	exon6			TTTTGCTAGAGCT	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.714T>C	chr7.hg19:g.106827075T>C		243.0	0.0		214.0	96.0	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Silent	SNP	ENST00000222574.4	hg19	CCDS5741.1																																																																																			.	.		0.358	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		C	106827075	T	C	106827075	2	2	208	1	0	0	0	0	0	0	0	1	6994	1509	53	2		2	HBP1	7	106827075	Silent	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	3	106827075	52311588	40	30088	156	3								
COG5	10466	hgsc.bcm.edu	37	chr7	106843989	106843989	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gagcagacatagccttttgaAgcagctgaaccattatggga	11	8	0	3			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr7:106843989A>T	ENST00000347053.3	-	21	2542	c.2492T>A	c.(2491-2493)cTt>cAt	p.L831H	COG5_ENST00000297135.3_Missense_Mutation_p.L852H	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	831					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						AGCCTTTTGAAGCAGCTGAAC	0.403																																					p.L852H		Atlas-SNP	.											.	COG5	78	.	0			c.T2555A						.						146	131	136					7																	106843989		2203	4300	6503	SO:0001583	missense	10466	exon22			TTTTGAAGCAGCT	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"Components of oligomeric golgi complex"	14857	protein-coding gene	gene with protein product		606821	"golgi transport complex 1 (90 kDa subunit)"	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.2492T>A	chr7.hg19:g.106843989A>T	ENSP00000334703:p.Leu831His	93.0	0.0		88.0	27.0	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	hg19	CCDS5743.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.583591	0.86748	.	.	ENSG00000164597	ENST00000347053;ENST00000297135	T;T	0.34275	1.45;1.37	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.64046	0.2563	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.68484	-0.5396	10	0.87932	D	0	-15.5482	16.5582	0.84512	1.0:0.0:0.0:0.0	.	831;852	Q9UP83;Q9UP83-2	COG5_HUMAN;.	H	831;852	ENSP00000334703:L831H;ENSP00000297135:L852H	ENSP00000297135:L852H	L	-	2	0	COG5	106631225	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.160000	0.89653	2.308000	0.77769	0.533000	0.62120	CTT	.	.		0.403	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			T	106843989	A	T	106843989	3	4	208	1	0	0	0	0	1	0	0	0	3663	72	3	4	31	4	COG5	7	106843989	Missense_Mutation	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	16914	106843989	52294674	41	30089										
TUSC3	7991	hgsc.bcm.edu	37	chr8	15508269	15508269	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tattcatctgctttttgtaaCaagctcttcttcagtatggt	6	8	5	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr8:15508269C>G	ENST00000503731.1	+	3	520	c.372C>G	c.(370-372)aaC>aaG	p.N124K	TUSC3_ENST00000382020.4_Missense_Mutation_p.N124K|TUSC3_ENST00000503191.1_Intron|TUSC3_ENST00000506802.1_Missense_Mutation_p.N124K|TUSC3_ENST00000509380.1_Missense_Mutation_p.N124K	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	124	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		CTTTTTGTAACAAGCTCTTCT	0.383																																					p.N124K		Atlas-SNP	.											.	TUSC3	98	.	0			c.C372G						.						247	241	243					8																	15508269		2203	4300	6503	SO:0001583	missense	7991	exon3			TTGTAACAAGCTC	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.372C>G	chr8.hg19:g.15508269C>G	ENSP00000424544:p.Asn124Lys	97.0	0.0		91.0	46.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.223332	0.79464	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.37411	1.2;1.2;1.2;1.2	5.22	4.34	0.51931	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.040366	0.85682	D	0.000000	T	0.51312	0.1667	L	0.58302	1.8	0.54753	D	0.999985	D;D;D;B;P;D	0.61080	0.969;0.988;0.989;0.198;0.943;0.98	D;D;D;B;P;P	0.72982	0.968;0.95;0.979;0.304;0.867;0.76	T	0.45425	-0.9262	10	0.15066	T	0.55	-11.5749	13.0719	0.59066	0.0:0.9221:0.0:0.0779	.	124;124;124;124;124;124	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	K	124	ENSP00000371450:N124K;ENSP00000425777:N124K;ENSP00000423426:N124K;ENSP00000424544:N124K	ENSP00000221167:N124K	N	+	3	2	TUSC3	15552640	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.777000	0.55364	1.327000	0.45338	0.655000	0.94253	AAC	.	.		0.383	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		G	15508269	C	G	15508269	3	3	208	1	0	0	0	0	1	0	0	0	16793	477	17	4	382	4	TUSC3	8	15508269	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10		15508269	130855753	42	30090										
IMPA1	3612	hgsc.bcm.edu	37	chr8	82598148	82598148	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	acaggacctgggcgctgcccCatcacttagagtgactacct	10	14	1	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr8:82598148C>T	ENST00000256108.5	-	1	442				IMPA1_ENST00000311489.4_Intron|IMPA1_ENST00000449740.2_Start_Codon_SNP_p.M1I|IMPA1_ENST00000523710.1_Intron	NM_005536.3	NP_005527.1	P29218	IMPA1_HUMAN	inositol(myo)-1(or 4)-monophosphatase 1						inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|inositol monophosphate phosphatase activity (GO:0052834)|lithium ion binding (GO:0031403)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|stomach(1)	18					Lithium(DB01356)	GGCGCTGCCCCATCACTTAGA	0.587																																					p.M1I		Atlas-SNP	.											.	IMPA1	46	.	0			c.G3A						.						34	30	31					8																	82598148		692	1591	2283	SO:0001627	intron_variant	3612	exon2			CTGCCCCATCACT		CCDS6231.1, CCDS47883.1, CCDS47884.1	8q21.1-q21.3	2008-01-28			ENSG00000133731	ENSG00000133731	3.1.3.25		6050	protein-coding gene	gene with protein product		602064		IMPA		1377913	Standard	NM_005536		Approved		uc011lfq.1	P29218	OTTHUMG00000164682	ENST00000256108.5:c.23+338G>A	chr8.hg19:g.82598148C>T		140.0	0.0		144.0	53.0	NM_001144878	B2R733|B4DLN3|B7Z6Q4|J3KQT7|Q9UK71	Missense_Mutation	SNP	ENST00000256108.5	hg19	CCDS6231.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.757120	0.31137	.	.	ENSG00000133731	ENST00000449740;ENST00000522997	T;T	0.31769	1.52;1.48	2.61	-0.624	0.11552	.	.	.	.	.	T	0.24314	0.0589	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08889	-1.0700	8	0.87932	D	0	.	10.0238	0.42059	0.0:0.4069:0.5931:0.0	.	1	B7Z6Q4	.	I	1	ENSP00000408526:M1I;ENSP00000430081:M1I	ENSP00000408526:M1I	M	-	3	0	IMPA1	82760703	0.000000	0.05858	0.000000	0.03702	0.198000	0.23893	-0.735000	0.04888	-0.147000	0.11254	0.555000	0.69702	ATG	.	.		0.587	IMPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379723.1			T	82598148	C	T	82598148	1	4	208	0	1	0	0	0	0	0	0	0	7731	594	21	3		3	IMPA1	8	82598148	Intron	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	67089879	82598148	63765874	43	30091										
DCAF13	81034	hgsc.bcm.edu	37	chr8	104427489	104427489	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gcacagctaaagaaccgcccCttgctaacgtttgccggcaa	9	14	0	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr8:104427489C>T	ENST00000297578.4	-	0	0				SLC25A32_ENST00000543107.1_5'Flank|DCAF13_ENST00000521971.1_5'Flank|DCAF13_ENST00000297579.5_Missense_Mutation_p.L91F|DCAF13_ENST00000521716.1_5'Flank|DCAF13_ENST00000519682.1_5'Flank	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32						folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	AGAACCGCCCCTTGCTAACGT	0.642																																					p.L91F		Atlas-SNP	.											.	DCAF13	66	.	0			c.C271T						.						61	72	68					8																	104427489		2203	4300	6503	SO:0001631	upstream_gene_variant	25879	exon1			CCGCCCCTTGCTA	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"Solute carriers"	29683	protein-coding gene	gene with protein product		610815	"solute carrier family 25, member 32"			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790		chr8.hg19:g.104427489C>T	Exception_encountered	181.0	0.0		173.0	10.0	NM_015420	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	hg19	CCDS6300.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.371761	0.42003	.	.	ENSG00000164934	ENST00000297579	T	0.78364	-1.17	4.3	2.42	0.29668	.	2.440800	0.02262	N	0.067632	T	0.81361	0.4806	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65047	-0.6263	7	0.72032	D	0.01	0.1487	8.1959	0.31396	0.1897:0.6474:0.1629:0.0	.	.	.	.	F	91	ENSP00000297579:L91F	ENSP00000297579:L91F	L	+	1	0	DCAF13	104496665	0.095000	0.21747	0.758000	0.31321	0.009000	0.06853	0.654000	0.24918	0.525000	0.28522	-0.257000	0.10917	CTT	.	.		0.642	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780		T	104427489	C	T	104427489	1	4	208	0	1	0	0	0	0	0	0	0	4268	681	24	3		3	DCAF13	8	104427489	5'Flank	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	21829341	104427489	41936533	44	30092										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121228707	121228707	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tcgaattgtatataacaatgCagatgggactgaaatcaatg	9	5	1	2	rs150549316		TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr8:121228707C>A	ENST00000297848.3	+	14	1985	c.1715C>A	c.(1714-1716)gCa>gAa	p.A572E	COL14A1_ENST00000537875.1_3'UTR|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000247781.3_Missense_Mutation_p.A477E|COL14A1_ENST00000309791.4_Missense_Mutation_p.A572E	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.A572G(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			TATAACAATGCAGATGGGACT	0.388																																					p.A572E		Atlas-SNP	.											COL14A1,NS,carcinoma,0,1	COL14A1	292	.	1	Substitution - Missense(1)	lung(1)	c.C1715A						.						117	110	113					8																	121228707		2203	4300	6503	SO:0001583	missense	7373	exon14			ACAATGCAGATGG		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.1715C>A	chr8.hg19:g.121228707C>A	ENSP00000297848:p.Ala572Glu	121.0	0.0		131.0	35.0	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	hg19	CCDS34938.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.335|1.335	-0.595712|-0.595712	0.03771|0.03771	.|.	.|.	ENSG00000187955|ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620|ENST00000523142	T;T;T;T|.	0.56444|.	0.46;0.46;0.46;0.46|.	5.29|5.29	0.286|0.286	0.15710|0.15710	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.295671|.	0.35495|.	N|.	0.003169|.	T|.	0.31575|.	0.0801|.	L|L	0.37630|0.37630	1.12|1.12	0.26804|0.26804	N|N	0.969144|0.969144	P;B|.	0.35684|.	0.515;0.324|.	B;B|.	0.38954|.	0.286;0.174|.	T|.	0.27971|.	-1.0058|.	10|.	0.25751|.	T|.	0.34|.	.|.	5.2277|5.2277	0.15404|0.15404	0.299:0.5183:0.1097:0.0729|0.299:0.5183:0.1097:0.0729	.|.	572;572|.	Q05707-2;Q05707|.	.;COEA1_HUMAN|.	E|X	572;572;477;385|328	ENSP00000311809:A572E;ENSP00000297848:A572E;ENSP00000247781:A477E;ENSP00000409461:A385E|.	ENSP00000247781:A477E|.	A|C	+|+	2|3	0|2	COL14A1|COL14A1	121297888|121297888	0.675000|0.675000	0.27558|0.27558	0.127000|0.127000	0.21898|0.21898	0.095000|0.095000	0.18619|0.18619	1.551000|1.551000	0.36233|0.36233	0.141000|0.141000	0.18875|0.18875	0.655000|0.655000	0.94253|0.94253	GCA|TGC	.	C|1.000;T|0.000		0.388	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121228707	C	A	121228707	3	1	208	1	0	0	0	0	1	0	0	0	3673	710	25	3	1765	3	COL14A1	8	121228707	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	16801218	121228707	25135315	45	30093										
CNTLN	54875	hgsc.bcm.edu	37	chr9	17416135	17416135	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	agttaatgaaaagctcctccAtcaacagcaagtatccgatc	6	11	1	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr9:17416135A>G	ENST00000380647.3	+	18	3146	c.3062A>G	c.(3061-3063)cAt>cGt	p.H1021R	CNTLN_ENST00000262360.5_Missense_Mutation_p.H1021R|CNTLN_ENST00000425824.1_Missense_Mutation_p.H1021R			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	1021					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AAGCTCCTCCATCAACAGCAA	0.333																																					p.H1021R		Atlas-SNP	.											.	CNTLN	128	.	0			c.A3062G						.						85	80	81					9																	17416135		1829	4086	5915	SO:0001583	missense	54875	exon18			TCCTCCATCAACA	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.3062A>G	chr9.hg19:g.17416135A>G	ENSP00000370021:p.His1021Arg	276.0	0.0		274.0	112.0	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	hg19	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	A	8.148	0.786759	0.16189	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.16897	2.31;2.31;2.57	5.13	5.13	0.70059	.	.	.	.	.	T	0.17365	0.0417	L	0.54323	1.7	0.26237	N	0.97893	B;B;B	0.20988	0.05;0.034;0.034	B;B;B	0.22601	0.037;0.04;0.025	T	0.16394	-1.0404	9	0.20519	T	0.43	.	9.9837	0.41828	0.7784:0.2216:0.0:0.0	.	1021;1021;1021	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	R	1021	ENSP00000370021:H1021R;ENSP00000392798:H1021R;ENSP00000262360:H1021R	ENSP00000262360:H1021R	H	+	2	0	CNTLN	17406135	0.977000	0.34250	1.000000	0.80357	0.990000	0.78478	1.796000	0.38794	2.051000	0.60960	0.383000	0.25322	CAT	.	.		0.333	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		G	17416135	A	G	17416135	3	3	208	1	0	0	0	0	1	0	0	0	3641	217	8	2	3162	2	CNTLN	9	17416135	Missense_Mutation	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10		17416135	123797296	46	30094										
STXBP1	6812	hgsc.bcm.edu	37	chr9	130434340	130434340	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tcccttacagaccaccatgcGggacctgtcccagatgctga	9	15	0	3			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr9:130434340G>A	ENST00000373299.1	+	12	1089	c.974G>A	c.(973-975)cGg>cAg	p.R325Q	STXBP1_ENST00000373302.3_Missense_Mutation_p.R325Q|STXBP1_ENST00000481942.1_3'UTR	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	325					axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)			breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						ACCACCATGCGGGACCTGTCC	0.498																																					p.R325Q		Atlas-SNP	.											.	STXBP1	99	.	0			c.G974A						.						124	114	117					9																	130434340		2203	4300	6503	SO:0001583	missense	6812	exon12			CCATGCGGGACCT	AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"syntaxin-binding protein 1"	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.974G>A	chr9.hg19:g.130434340G>A	ENSP00000362396:p.Arg325Gln	73.0	0.0		89.0	43.0	NM_001032221	B1AM97|Q28208|Q62759|Q64320|Q96TG8	Missense_Mutation	SNP	ENST00000373299.1	hg19	CCDS35146.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.537102	0.85812	.	.	ENSG00000136854	ENST00000535154;ENST00000373302;ENST00000541198;ENST00000373299	T;T	0.79845	-1.31;-1.31	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.83275	0.5219	M	0.64404	1.975	0.58432	D	0.999999	D;D	0.55800	0.973;0.967	P;P	0.49276	0.605;0.469	D	0.85083	0.0947	10	0.62326	D	0.03	-21.1243	17.0456	0.86501	0.0:0.0:1.0:0.0	.	325;325	P61764;P61764-2	STXB1_HUMAN;.	Q	279;325;157;325	ENSP00000362399:R325Q;ENSP00000362396:R325Q	ENSP00000362396:R325Q	R	+	2	0	STXBP1	129474161	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.687000	0.68219	2.689000	0.91719	0.561000	0.74099	CGG	.	.		0.498	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165		A	130434340	G	A	130434340	3	1	208	1	0	0	0	0	1	0	0	0	15367	1116	39	1	1020	1	STXBP1	9	130434340	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	113018205	130434340	10779091	47	30095										
AKR1C2	1646	hgsc.bcm.edu	37	chr10	5032215	5032216	+	Frame_Shift_Ins	INS	-	-	G													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	catcagaaaatggataattaINSggggggccagcaaaactgga							TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr10:5032215_5032216insG	ENST00000380753.4	-	9	1131_1132	c.944_945insC	c.(943-945)cctfs	p.P315fs	AKR1C2_ENST00000407674.1_Frame_Shift_Ins_p.P315fs|AKR1C2_ENST00000421196.3_Frame_Shift_Ins_p.P289fs	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	315					cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	ATGGATAATTAGGGGGGCCAGC	0.485																																					p.P315fs		Atlas-INDEL	.											.	AKR1C2	68	.	0			c.945_946insC						.																																			SO:0001589	frameshift_variant	1646	exon11			.	L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1.3.1.20, 1.1.1.213	"Aldo-keto reductases"	385	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III"	600450	"aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)", "testicular 17,20-desmolase deficiency"	DDH2, TDD		9716498, 21802064	Standard	NM_001354		Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.945dupC	chr10.hg19:g.5032221_5032221dupG	ENSP00000370129:p.Pro315fs	546.0	0.0		532.0	132.0	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Frame_Shift_Ins	INS	ENST00000380753.4	hg19	CCDS7062.1																																																																																			.	.		0.485	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354		G	5032216	-	G	5032215	7	5	208	1	0	1	1	0	0	0	0	0	470	407	15	0	30	0	AKR1C2	10	5032215	Frame_Shift_Ins	INS	-	TCGA-DD-AAE2-01A-11D-A40R-10		5032215	130502532	48	30096										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26359123	26359123	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gacttaggatatcaatctatGataacatataattcagatca	5	6	4	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr10:26359123G>A	ENST00000265944.5	+	13	1420	c.1254G>A	c.(1252-1254)atG>atA	p.M418I	MYO3A_ENST00000543632.1_Missense_Mutation_p.M418I	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	418	Myosin motor.			M -> I (in Ref. 1 and 2). {ECO:0000305}.	ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ATCAATCTATGATAACATATA	0.333																																					p.M418I		Atlas-SNP	.											.	MYO3A	371	.	0			c.G1254A						.						61	63	62					10																	26359123		2203	4297	6500	SO:0001583	missense	53904	exon13			ATCTATGATAACA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1254G>A	chr10.hg19:g.26359123G>A	ENSP00000265944:p.Met418Ile	199.0	0.0		237.0	18.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.025320	0.93518	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	D;D	0.89343	-2.5;-2.5	5.79	5.79	0.91817	Myosin head, motor domain (2);	0.034508	0.85682	D	0.000000	D	0.95918	0.8671	M	0.91196	3.185	0.80722	D	1	D;D;D	0.59767	0.97;0.976;0.986	D;D;D	0.72338	0.961;0.977;0.93	D	0.96081	0.9054	10	0.72032	D	0.01	.	20.0275	0.97527	0.0:0.0:1.0:0.0	.	418;418;418	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	I	418	ENSP00000265944:M418I;ENSP00000445909:M418I	ENSP00000265944:M418I	M	+	3	0	MYO3A	26399129	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.649000	0.83500	2.727000	0.93392	0.650000	0.86243	ATG	.	.		0.333	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26359123	G	A	26359123	3	1	208	1	0	0	0	0	1	0	0	0	10085	1290	45	3	1296	3	MYO3A	10	26359123	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	21326908	26359123	109175624	49	30097										
PTEN	5728	hgsc.bcm.edu	37	chr10	89717669	89717674	+	In_Frame_Del	DEL	ACACGA	ACACGA	-													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	attcctccaattcaggacccAcacgacgggaagacaagttc					rs121909219		TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	ACACGA	ACACGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr10:89717669_89717674delACACGA	ENST00000371953.3	+	7	2051_2056	c.694_699delACACGA	c.(694-699)acacgadel	p.TR232del	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	232	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R233*(77)|p.0?(37)|p.R55fs*1(5)|p.R233fs*10(4)|p.R234fs*11(3)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.R233fs*12(1)|p.R233fs*20(1)|p.R233fs*25(1)|p.R233fs*23(1)|p.R233R(1)|p.R234fs*26(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TTCAGGACCCACACGACGGGAAGACA	0.413	R233*(HEC59_ENDOMETRIUM)|R233*(JHUEM1_ENDOMETRIUM)|R233*(NCIH1155_LUNG)|R233*(SF295_CENTRAL_NERVOUS_SYSTEM)|R233*(SW1783_CENTRAL_NERVOUS_SYSTEM)	31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.231_233del		Atlas-INDEL	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.	PTEN	3652	.	138	Substitution - Nonsense(77)|Whole gene deletion(37)|Deletion - Frameshift(11)|Complex - frameshift(7)|Insertion - Frameshift(3)|Deletion - In frame(1)|Unknown(1)|Substitution - coding silent(1)	endometrium(48)|central_nervous_system(21)|prostate(17)|haematopoietic_and_lymphoid_tissue(15)|lung(9)|large_intestine(6)|skin(6)|ovary(5)|cervix(3)|soft_tissue(3)|breast(3)|urinary_tract(2)	c.693_698del	GRCh37	CD982916|CM971277	PTEN	D|M	rs121909219	.																																			SO:0001651	inframe_deletion	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.694_699delACACGA	chr10.hg19:g.89717669_89717674delACACGA	ENSP00000361021:p.Thr232_Arg233del	161.0	0.0		63.0	27.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	In_Frame_Del	DEL	ENST00000371953.3	hg19	CCDS31238.1																																																																																			.	.		0.413	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		-	89717674	ACACGA	-	89717669	7	5	208	1	0	1	0	1	0	0	0	0	12750	159	6	0	720	0	PTEN	10	89717669	In_Frame_Del	DEL	ACACGA	TCGA-DD-AAE2-01A-11D-A40R-10	63358546	89717669	45817078	50	30098										
CPEB3	22849	hgsc.bcm.edu	37	chr10	94000049	94000049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ggggctgctgctgctgccgcTgctgctgctggggctggggc	20	12	0	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr10:94000049T>C	ENST00000265997.4	-	2	231	c.59A>G	c.(58-60)cAg>cGg	p.Q20R	CPEB3_ENST00000412050.4_Missense_Mutation_p.Q20R	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	20	Gln-rich.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				ctgctgccgctgctgctgctg	0.587																																					p.Q20R		Atlas-SNP	.											.	CPEB3	43	.	0			c.A59G						.						7	7	7					10																	94000049		1886	3756	5642	SO:0001583	missense	22849	exon2			TGCCGCTGCTGCT	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.59A>G	chr10.hg19:g.94000049T>C	ENSP00000265997:p.Gln20Arg	134.0	0.0		120.0	6.0	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	hg19	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	T	4.523	0.097129	0.08681	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.45668	0.89;0.9	2.23	-0.797	0.10909	.	0.992584	0.08182	N	0.985229	T	0.36193	0.0958	L	0.39898	1.24	0.29270	N	0.870753	P;P;P	0.42039	0.659;0.659;0.769	B;B;P	0.49332	0.403;0.403;0.607	T	0.34229	-0.9837	10	0.09590	T	0.72	-0.8246	4.7766	0.13182	0.0:0.3177:0.0:0.6823	.	20;20;20	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	R	20	ENSP00000398310:Q20R;ENSP00000265997:Q20R	ENSP00000265997:Q20R	Q	-	2	0	CPEB3	93990029	0.982000	0.34865	0.981000	0.43875	0.924000	0.55760	0.234000	0.17930	-0.200000	0.10300	0.254000	0.18369	CAG	.	.		0.587	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		C	94000049	T	C	94000049	3	2	208	1	0	0	0	0	1	0	0	0	3804	1580	55	2	2100	2	CPEB3	10	94000049	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	4282380	94000049	41534698	51	30099										
FAM196A	642938	hgsc.bcm.edu	37	chr10	128974496	128974496	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tgtccctctgctcattctgtGcctcgcagatatccttaaac	6	14	3	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr10:128974496G>A	ENST00000522781.1	-	4	719	c.164C>T	c.(163-165)gCa>gTa	p.A55V	DOCK1_ENST00000280333.6_Intron|FAM196A_ENST00000424811.2_Missense_Mutation_p.A55V	NM_001039762.2	NP_001034851.1	Q6ZSG2	F196A_HUMAN	family with sequence similarity 196, member A	55										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CTCATTCTGTGCCTCGCAGAT	0.592																																					p.A55V		Atlas-SNP	.											.	FAM196A	55	.	0			c.C164T						.						118	116	117					10																	128974496		2203	4300	6503	SO:0001583	missense	642938	exon4			TTCTGTGCCTCGC		CCDS31312.1	10q26.2	2009-09-11	2009-09-11	2009-09-11		ENSG00000188916			33859	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 141"	C10orf141			Standard	NM_001039762		Approved	FLJ45557	uc001ljv.1	Q6ZSG2		ENST00000522781.1:c.164C>T	chr10.hg19:g.128974496G>A	ENSP00000429763:p.Ala55Val	78.0	0.0		46.0	37.0	NM_001039762	B2RNT4|B7ZME7	Missense_Mutation	SNP	ENST00000522781.1	hg19	CCDS31312.1	.	.	.	.	.	.	.	.	.	.	G	32	5.172041	0.94807	.	.	ENSG00000188916	ENST00000522781;ENST00000424811	T;T	0.52295	0.67;0.67	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.61098	0.2320	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.63265	-0.6676	10	0.66056	D	0.02	.	19.3815	0.94540	0.0:0.0:1.0:0.0	.	55;55	B7ZME7;Q6ZSG2	.;F196A_HUMAN	V	55	ENSP00000429763:A55V;ENSP00000428730:A55V	ENSP00000428730:A55V	A	-	2	0	FAM196A	128864486	1.000000	0.71417	0.982000	0.44146	0.855000	0.48748	9.476000	0.97823	2.655000	0.90218	0.462000	0.41574	GCA	.	.		0.592	FAM196A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050978.2	NM_001039762		A	128974496	G	A	128974496	3	1	208	1	0	0	0	0	1	0	0	0	5533	1319	46	3	1287	3	FAM196A	10	128974496	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	34974447	128974496	6560251	52	30100										
PSMC3	5702	hgsc.bcm.edu	37	chr11	47441913	47441913	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cggtcaaggcggcccgagcgGaggagggcggggtccaggat	21	10	1	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr11:47441913G>A	ENST00000298852.3	-	10	1186	c.1029C>T	c.(1027-1029)ctC>ctT	p.L343L	PSMC3_ENST00000530912.1_Silent_p.L301L|PSMC3_ENST00000602866.1_Silent_p.L327L	NM_002804.4	NP_002795.2	P17980	PRS6A_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 3	343					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of RNA biosynthetic process (GO:2001141)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(4)|urinary_tract(1)	17				Lung(87;0.0932)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GGCCCGAGCGGAGGAGGGCGG	0.572																																					p.L343L		Atlas-SNP	.											.	PSMC3	35	.	0			c.C1029T						.						42	46	45					11																	47441913		2201	4298	6499	SO:0001819	synonymous_variant	5702	exon10			CGAGCGGAGGAGG	M34079	CCDS7935.1	11p11.2	2010-04-21			ENSG00000165916	ENSG00000165916		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9549	protein-coding gene	gene with protein product		186852				9048938, 9473509	Standard	NM_002804		Approved	TBP1, TBP-1	uc001nfh.2	P17980	OTTHUMG00000167692	ENST00000298852.3:c.1029C>T	chr11.hg19:g.47441913G>A		54.0	0.0		50.0	20.0	NM_002804	B2R8V1|Q3B757|Q3B865|Q53HU5|Q6GPG8|Q6IBS1|Q96HD3	Silent	SNP	ENST00000298852.3	hg19	CCDS7935.1																																																																																			.	.		0.572	PSMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395660.2	NM_002804		A	47441913	G	A	47441913	2	1	208	1	0	0	0	0	0	0	0	1	12699	1161	41	3		3	PSMC3	11	47441913	Silent	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10		47441913	87564603	53	30101										
DAGLA	747	hgsc.bcm.edu	37	chr11	61511629	61511629	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	agagcagctccttccaagacCtctactgcatggtggtgccc	10	14	1	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr11:61511629C>G	ENST00000257215.5	+	20	2913	c.2797C>G	c.(2797-2799)Ctc>Gtc	p.L933V	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	933					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		CTTCCAAGACCTCTACTGCAT	0.632																																					p.L933V		Atlas-SNP	.											.	DAGLA	109	.	0			c.C2797G						.						70	63	65					11																	61511629		2202	4298	6500	SO:0001583	missense	747	exon20			CAAGACCTCTACT	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"neural stem cell-derived dendrite regulator"	614015	"chromosome 11 open reading frame 11"	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.2797C>G	chr11.hg19:g.61511629C>G	ENSP00000257215:p.Leu933Val	98.0	0.0		142.0	61.0	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	hg19	CCDS31578.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.092162	0.36952	.	.	ENSG00000134780	ENST00000257215	T	0.34275	1.37	3.97	3.97	0.46021	.	0.072132	0.56097	D	0.000028	T	0.25494	0.0620	N	0.24115	0.695	0.42799	D	0.99392	B	0.15473	0.013	B	0.13407	0.009	T	0.11131	-1.0600	10	0.72032	D	0.01	-28.411	11.6837	0.51472	0.2274:0.7726:0.0:0.0	.	933	Q9Y4D2	DGLA_HUMAN	V	933	ENSP00000257215:L933V	ENSP00000257215:L933V	L	+	1	0	DAGLA	61268205	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.229000	0.32600	1.942000	0.56320	0.462000	0.41574	CTC	.	.		0.632	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		G	61511629	C	G	61511629	3	3	208	1	0	0	0	0	1	0	0	0	4228	681	24	4	2871	4	DAGLA	11	61511629	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	14069716	61511629	73494887	54	30102										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73824881	73824881	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cctcagtgatcaaagctgtcTttcccaatccgctttccgaa	6	14	3	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr11:73824881T>A	ENST00000334126.7	-	11	2013	c.1787A>T	c.(1786-1788)aAg>aTg	p.K596M	C2CD3_ENST00000313663.7_Missense_Mutation_p.K596M			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	596					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					CAAAGCTGTCTTTCCCAATCC	0.373																																					p.K596M		Atlas-SNP	.											.	C2CD3	288	.	0			c.A1787T						.						124	121	122					11																	73824881		2200	4293	6493	SO:0001583	missense	26005	exon11			GCTGTCTTTCCCA	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1787A>T	chr11.hg19:g.73824881T>A	ENSP00000334379:p.Lys596Met	93.0	0.0		92.0	22.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	T	23.0	4.368627	0.82463	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.11821	2.74;2.75	5.49	5.49	0.81192	C2 calcium-dependent membrane targeting (1);	0.353444	0.32868	N	0.005555	T	0.32224	0.0822	L	0.57536	1.79	0.36827	D	0.886714	D;D	0.89917	0.998;1.0	D;D	0.67548	0.922;0.952	T	0.26849	-1.0091	10	0.72032	D	0.01	-16.6348	13.821	0.63320	0.0:0.0:0.0:1.0	.	596;596	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	M	596	ENSP00000334379:K596M;ENSP00000323339:K596M	ENSP00000323339:K596M	K	-	2	0	C2CD3	73502529	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.064000	0.57506	2.089000	0.63090	0.374000	0.22700	AAG	.	.		0.373	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		A	73824881	T	A	73824881	3	1	208	1	0	0	0	0	1	0	0	0	2156	1609	56	4	4188	4	C2CD3	11	73824881	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	12313252	73824881	61181635	55	30103										
CREBZF	58487	hgsc.bcm.edu	37	chr11	85375725	85375725	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ccgccgcggctccccctcccGgcttccaactctccttcgtc	7	23	1	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr11:85375725G>A	ENST00000527447.1	-	1	421	c.195C>T	c.(193-195)gcC>gcT	p.A65A	CREBZF_ENST00000398294.2_5'Flank|CREBZF_ENST00000531515.1_Intron|CREBZF_ENST00000534224.1_Intron	NM_001039618.2	NP_001034707.1	Q9NS37	ZHANG_HUMAN	CREB/ATF bZIP transcription factor	65					negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)				TCCCCCTCCCGGCTTCCAACT	0.731																																					p.A65A	NSCLC(172;674 2044 9050 18334 41735)	Atlas-SNP	.											.	CREBZF	26	.	0			c.C195T						.						22	26	25					11																	85375725		1834	4052	5886	SO:0001819	synonymous_variant	58487	exon1			CCTCCCGGCTTCC	AF039942	CCDS41697.1	11q14.1	2013-01-10			ENSG00000137504	ENSG00000137504		"basic leucine zipper proteins"	24905	protein-coding gene	gene with protein product	"Zhangfei"	606444				10871379	Standard	NM_001039618		Approved	ZF	uc001pas.2	Q9NS37	OTTHUMG00000133648	ENST00000527447.1:c.195C>T	chr11.hg19:g.85375725G>A		118.0	0.0		101.0	43.0	NM_001039618	B2R8Q9|Q0P5U9|Q52LT3	Silent	SNP	ENST00000527447.1	hg19	CCDS41697.1																																																																																			.	.		0.731	CREBZF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390191.2	NM_001039618		A	85375725	G	A	85375725	2	1	208	1	0	0	0	0	0	0	0	1	3865	1103	39	1		1	CREBZF	11	85375725	Silent	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	11550844	85375725	49630791	56	30104										
CNTN5	53942	hgsc.bcm.edu	37	chr11	99715619	99715619	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ggccagtttttgtgcaagaaCcagatgatattatttttcca	8	7	0	3			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr11:99715619C>A	ENST00000524871.1	+	5	603	c.313C>A	c.(313-315)Cca>Aca	p.P105T	CNTN5_ENST00000527185.1_Missense_Mutation_p.P105T|CNTN5_ENST00000528682.1_Missense_Mutation_p.P105T|CNTN5_ENST00000418526.2_Missense_Mutation_p.P31T|CNTN5_ENST00000279463.3_Missense_Mutation_p.P105T	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	105	Ig-like C2-type 1.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TGTGCAAGAACCAGATGATAT	0.353																																					p.P105T		Atlas-SNP	.											.	CNTN5	324	.	0			c.C313A						.						157	144	148					11																	99715619		1839	4083	5922	SO:0001583	missense	53942	exon4			CAAGAACCAGATG	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.313C>A	chr11.hg19:g.99715619C>A	ENSP00000435637:p.Pro105Thr	179.0	0.0		152.0	56.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	C	19.72	3.880447	0.72294	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76	5.33	5.33	0.75918	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75606	0.3872	M	0.90425	3.115	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.80917	-0.1168	10	0.87932	D	0	.	18.3699	0.90403	0.0:1.0:0.0:0.0	.	105;31;105	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	T	105;105;105;31;105	ENSP00000433575:P105T;ENSP00000436185:P105T;ENSP00000435637:P105T;ENSP00000393229:P31T;ENSP00000279463:P105T	ENSP00000279463:P105T	P	+	1	0	CNTN5	99220829	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.330000	0.65899	2.653000	0.90120	0.650000	0.86243	CCA	.	.		0.353	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		A	99715619	C	A	99715619	3	1	208	1	0	0	0	0	1	0	0	0	3646	507	18	3	323	3	CNTN5	11	99715619	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	14339894	99715619	35290897	57	30105										
CAPRIN2	65981	hgsc.bcm.edu	37	chr12	30863221	30863221	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tagaggttctggctgctgagAaggcaactcgcatctgctga	13	9	2	3			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr12:30863221A>C	ENST00000298892.5	-	17	3599	c.2849T>G	c.(2848-2850)tTc>tGc	p.F950C	CAPRIN2_ENST00000251071.5_Missense_Mutation_p.F1000C|CAPRIN2_ENST00000308433.5_Missense_Mutation_p.F666C|CAPRIN2_ENST00000395805.2_3'UTR	NM_023925.3	NP_076414.2			caprin family member 2											breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					GGCTGCTGAGAAGGCAACTCG	0.498																																					p.F1000C		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.T2999G						.						152	153	153					12																	30863221		2203	4300	6503	SO:0001583	missense	65981	exon18			GCTGAGAAGGCAA	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000298892.5:c.2849T>G	chr12.hg19:g.30863221A>C	ENSP00000298892:p.Phe950Cys	155.0	0.0		126.0	48.0	NM_001002259		Missense_Mutation	SNP	ENST00000298892.5	hg19	CCDS8720.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.389397	0.82902	.	.	ENSG00000110888	ENST00000298892;ENST00000251071;ENST00000308433	D;D;D	0.98585	-5.01;-5.01;-5.01	5.7	5.7	0.88788	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.000000	0.85682	D	0.000000	D	0.99312	0.9759	H	0.96175	3.78	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98745	1.0718	10	0.87932	D	0	-9.0122	15.9561	0.79889	1.0:0.0:0.0:0.0	.	1000;950	Q6IMN6;Q6IMN6-2	CAPR2_HUMAN;.	C	950;1000;666	ENSP00000298892:F950C;ENSP00000251071:F1000C;ENSP00000309785:F666C	ENSP00000251071:F1000C	F	-	2	0	CAPRIN2	30754488	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.097000	0.94193	2.166000	0.68216	0.533000	0.62120	TTC	.	.		0.498	CAPRIN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402778.1	NM_023925		C	30863221	A	C	30863221	3	2	208	1	0	0	0	0	1	0	0	0	2638	246	9	5	388	5	CAPRIN2	12	30863221	Missense_Mutation	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10		30863221	102988674	58	30106										
KRT5	3852	hgsc.bcm.edu	37	chr12	52908953	52908953	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tccaccgaggccgccgccaaGacctccaccgaggccaccgc	10	21	0	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr12:52908953G>A	ENST00000252242.4	-	9	1936	c.1546C>T	c.(1546-1548)Ctt>Ttt	p.L516F		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	516	Tail.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		ccgccgccaagacctccaccg	0.622																																					p.L516F		Atlas-SNP	.											KRT5,NS,carcinoma,0,1	KRT5	88	.	0			c.C1546T						.						37	35	36					12																	52908953		2203	4300	6503	SO:0001583	missense	3852	exon9			CGCCAAGACCTCC		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"-", "Intermediate filaments type II, keratins (basic)"	6442	protein-coding gene	gene with protein product		148040	"epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types", "keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.1546C>T	chr12.hg19:g.52908953G>A	ENSP00000252242:p.Leu516Phe	1390.0	1.0		1449.0	550.0	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	hg19	CCDS8830.1	.	.	.	.	.	.	.	.	.	.	g	4.947	0.175944	0.09443	.	.	ENSG00000186081	ENST00000252242;ENST00000456000	D	0.87412	-2.25	5.56	-2.58	0.06228	.	7739.210000	0.00166	N	0.000002	T	0.74145	0.3678	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60244	-0.7301	10	0.11182	T	0.66	.	2.4696	0.04561	0.3299:0.2581:0.3175:0.0945	.	516	P13647	K2C5_HUMAN	F	516;481	ENSP00000252242:L516F	ENSP00000252242:L516F	L	-	1	0	KRT5	51195220	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.265000	0.01172	-0.172000	0.10779	-0.119000	0.15052	CTT	.	.		0.622	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1			A	52908953	G	A	52908953	3	1	208	1	0	0	0	0	1	0	0	0	8488	942	33	3	230	3	KRT5	12	52908953	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	22045732	52908953	80942942	59	30107										
HSD17B6	8630	hgsc.bcm.edu	37	chr12	57180920	57180920	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tgtatacagtttacaatatcAtgaaggaagggctgttgaat	10	4	1	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr12:57180920A>G	ENST00000554643.1	+	6	1097	c.748A>G	c.(748-750)Atg>Gtg	p.M250V	HSD17B6_ENST00000555159.1_Missense_Mutation_p.M250V|HSD17B6_ENST00000554150.1_Missense_Mutation_p.M250V|HSD17B6_ENST00000322165.1_Missense_Mutation_p.M250V|HSD17B6_ENST00000555805.1_Missense_Mutation_p.M250V			O14756	H17B6_HUMAN	hydroxysteroid (17-beta) dehydrogenase 6	250					androgen biosynthetic process (GO:0006702)|androgen catabolic process (GO:0006710)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|intracellular (GO:0005622)|membrane (GO:0016020)	catalytic activity (GO:0003824)|electron carrier activity (GO:0009055)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|oxidoreductase activity (GO:0016491)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			endometrium(1)|large_intestine(2)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10					Succinic acid(DB00139)	TTACAATATCATGAAGGAAGG	0.398																																					p.M250V		Atlas-SNP	.											.	HSD17B6	26	.	0			c.A748G						.						104	100	101					12																	57180920		2203	4300	6503	SO:0001583	missense	8630	exon5			AATATCATGAAGG	AF016509	CCDS8925.1	12q13.3	2012-12-07	2012-12-07		ENSG00000025423	ENSG00000025423	1.1.1.62, 1.1.1.63, 1.1.1.105	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	23316	protein-coding gene	gene with protein product	"oxidative 3-alpha-hydroxysteroid-dehydrogenase", "3(alpha->beta)-hydroxysteroid epimerasel", "retinol dehydrogenase", "oxidoreductase", "NAD+ -dependent 3 alpha-hydroxysteroid dehydrogenase", "3-hydroxysteroid epimerase", "short chain dehydrogenase/reductase family 9C, member 6"	606623	"hydroxysteroid (17-beta) dehydrogenase 6", "hydroxysteroid (17-beta) dehydrogenase 6 homolog (mouse)"			11165032, 19027726	Standard	XM_005269207		Approved	HSE, RODH, SDR9C6	uc001smg.1	O14756	OTTHUMG00000170854	ENST00000554643.1:c.748A>G	chr12.hg19:g.57180920A>G	ENSP00000451406:p.Met250Val	74.0	0.0		120.0	23.0	NM_003725	O43275	Missense_Mutation	SNP	ENST00000554643.1	hg19	CCDS8925.1	.	.	.	.	.	.	.	.	.	.	a	1.679	-0.506891	0.04231	.	.	ENSG00000025423	ENST00000555159;ENST00000555805;ENST00000554643;ENST00000554150;ENST00000322165	D;D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82;-1.82	4.34	-6.18	0.02085	NAD(P)-binding domain (1);	3.604020	0.00664	N	0.000617	T	0.63070	0.2480	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.56980	-0.7889	10	0.17369	T	0.5	.	3.3838	0.07264	0.3233:0.4237:0.1473:0.1057	.	250	O14756	H17B6_HUMAN	V	250	ENSP00000450698:M250V;ENSP00000451753:M250V;ENSP00000451406:M250V;ENSP00000452273:M250V;ENSP00000318631:M250V	ENSP00000318631:M250V	M	+	1	0	HSD17B6	55467187	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.014000	0.13333	-0.836000	0.04229	0.529000	0.55759	ATG	.	.		0.398	HSD17B6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410714.1	NM_003725		G	57180920	A	G	57180920	3	3	208	1	0	0	0	0	1	0	0	0	7396	217	8	2	762	2	HSD17B6	12	57180920	Missense_Mutation	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	4271967	57180920	76670975	60	30108										
WSCD2	9671	hgsc.bcm.edu	37	chr12	108600076	108600076	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ttccccaaagccaagtacatCggctgctacctggatgacac	8	14	0	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr12:108600076C>A	ENST00000332082.4	+	4	1211	c.393C>A	c.(391-393)atC>atA	p.I131I	WSCD2_ENST00000547525.1_Silent_p.I131I|WSCD2_ENST00000549903.1_Silent_p.I131I|WSCD2_ENST00000261400.3_Silent_p.I131I			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	131	WSC 1. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)		p.I131I(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						CCAAGTACATCGGCTGCTACC	0.517																																					p.I131I		Atlas-SNP	.											WSCD2,NS,haematopoietic_neoplasm,+2,1	WSCD2	125	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C393A						.						81	80	80					12																	108600076		1936	4142	6078	SO:0001819	synonymous_variant	9671	exon3			GTACATCGGCTGC		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.393C>A	chr12.hg19:g.108600076C>A		90.0	0.0		107.0	44.0	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Silent	SNP	ENST00000332082.4	hg19	CCDS41828.1																																																																																			.	.		0.517	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		A	108600076	C	A	108600076	2	1	208	1	0	0	0	0	0	0	0	1	17422	874	31	1		1	WSCD2	12	108600076	Silent	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	51419156	108600076	25251819	61	30109										
ATXN2	6311	hgsc.bcm.edu	37	chr12	111951302	111951302	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cccagcagaaactctgtgatTtcgaggatgtcgctgggcct	12	11	1	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr12:111951302T>A	ENST00000377617.3	-	11	2058	c.1897A>T	c.(1897-1899)Aat>Tat	p.N633Y	ATXN2_ENST00000608853.1_Missense_Mutation_p.N473Y|ATXN2_ENST00000542287.2_Missense_Mutation_p.N368Y|ATXN2_ENST00000550104.1_Missense_Mutation_p.N633Y|ATXN2_ENST00000389153.4_Missense_Mutation_p.N368Y|ATXN2_ENST00000535949.1_Missense_Mutation_p.N344Y	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	633	Pro-rich.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						ACTCTGTGATTTCGAGGATGT	0.483																																					p.N633Y		Atlas-SNP	.											.	ATXN2	99	.	0			c.A1897T						.						74	64	68					12																	111951302		2203	4300	6503	SO:0001583	missense	6311	exon11			TGTGATTTCGAGG	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.1897A>T	chr12.hg19:g.111951302T>A	ENSP00000366843:p.Asn633Tyr	108.0	0.0		118.0	7.0	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Missense_Mutation	SNP	ENST00000377617.3	hg19	CCDS31902.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.27|18.27	3.586768|3.586768	0.66105|0.66105	.|.	.|.	ENSG00000204842|ENSG00000204842	ENST00000481331|ENST00000389153;ENST00000377617;ENST00000550104;ENST00000542287;ENST00000535949;ENST00000492467;ENST00000550236	.|T;T	.|0.65178	.|-0.12;-0.14	5.53|5.53	4.4|4.4	0.53042|0.53042	.|.	.|0.338965	.|0.34291	.|N	.|0.004087	T|T	0.39911|0.39911	0.1096|0.1096	N|N	0.14661|0.14661	0.345|0.345	0.32238|0.32238	N|N	0.573072|0.573072	.|P;P;B;P	.|0.48162	.|0.761;0.906;0.327;0.875	.|B;B;B;B	.|0.39771	.|0.123;0.188;0.087;0.309	T|T	0.52609|0.52609	-0.8553|-0.8553	6|10	0.87932|0.41790	D|T	0|0.15	-13.0562|-13.0562	7.3836|7.3836	0.26870|0.26870	0.0:0.184:0.0:0.816|0.0:0.184:0.0:0.816	.|.	.|368;633;344;368	.|B3KT59;Q99700;Q24JQ7;F8VQP2	.|.;ATX2_HUMAN;.;.	D|Y	16|368;633;633;368;344;23;48	.|ENSP00000366843:N633Y;ENSP00000446576:N633Y	ENSP00000449850:E16D|ENSP00000366843:N633Y	E|N	-|-	3|1	2|0	ATXN2|ATXN2	110435685|110435685	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.119000|1.119000	0.31258|0.31258	2.105000|2.105000	0.64084|0.64084	0.528000|0.528000	0.53228|0.53228	GAA|AAT	.	.		0.483	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		A	111951302	T	A	111951302	3	1	208	1	0	0	0	0	1	0	0	0	1211	1841	64	4	2104	4	ATXN2	12	111951302	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	3351226	111951302	21900593	62	30110										
MAPKAPK5	8550	hgsc.bcm.edu	37	chr12	112308139	112308139	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cagagacctcaagcctgaaaAtctgctttttaaggataact	7	9	2	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr12:112308139A>G	ENST00000551404.2	+	6	566	c.458A>G	c.(457-459)aAt>aGt	p.N153S	MAPKAPK5_ENST00000550735.2_Missense_Mutation_p.N153S			Q8IW41	MAPK5_HUMAN	mitogen-activated protein kinase-activated protein kinase 5	153	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|MAPK cascade (GO:0000165)|negative regulation of TOR signaling (GO:0032007)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)|stress-induced premature senescence (GO:0090400)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(11)|ovary(1)	13						AAGCCTGAAAATCTGCTTTTT	0.423																																					p.N153S		Atlas-SNP	.											.	MAPKAPK5	56	.	0			c.A458G						.						131	119	123					12																	112308139		1886	4106	5992	SO:0001583	missense	8550	exon6			CTGAAAATCTGCT	AF032437	CCDS44975.1, CCDS44976.1	12q24.13	2012-05-30			ENSG00000089022	ENSG00000089022			6889	protein-coding gene	gene with protein product		606723				9628874	Standard	NM_003668		Approved	PRAK	uc001tta.4	Q8IW41	OTTHUMG00000169605	ENST00000551404.2:c.458A>G	chr12.hg19:g.112308139A>G	ENSP00000449381:p.Asn153Ser	109.0	0.0		131.0	45.0	NM_139078	B3KVA5|O60491|Q86X46|Q9BVX9|Q9UG86	Missense_Mutation	SNP	ENST00000551404.2	hg19	CCDS44975.1	.	.	.	.	.	.	.	.	.	.	A	31	5.088999	0.94100	.	.	ENSG00000089022	ENST00000550735;ENST00000202788;ENST00000428907;ENST00000551404	D;D	0.91945	-2.94;-2.94	5.6	5.6	0.85130	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97698	0.9245	H	0.98005	4.125	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.974	D;D;D	0.97110	1.0;0.998;0.953	D	0.99289	1.0898	10	0.87932	D	0	.	15.8035	0.78473	1.0:0.0:0.0:0.0	.	147;153;153	C9J458;Q8IW41;Q8IW41-2	.;MAPK5_HUMAN;.	S	153	ENSP00000449667:N153S;ENSP00000449381:N153S	ENSP00000202788:N153S	N	+	2	0	MAPKAPK5	110792522	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.320000	0.96346	2.130000	0.65690	0.482000	0.46254	AAT	.	.		0.423	MAPKAPK5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405019.2	NM_139078		G	112308139	A	G	112308139	3	3	208	1	0	0	0	0	1	0	0	0	9300	101	4	2	480	2	MAPKAPK5	12	112308139	Missense_Mutation	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	356837	112308139	21543756	63	30111										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120616729	120616729	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ggagccacccagcacctccaGcaagagcaggcactgcactt	10	16	0	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr12:120616729G>T	ENST00000300648.6	-	6	463	c.451C>A	c.(451-453)Ctg>Atg	p.L151M		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	151					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGCACCTCCAGCAAGAGCAGG	0.592																																					p.L151M		Atlas-SNP	.											.	GCN1L1	207	.	0			c.C451A						.						38	42	40					12																	120616729		2131	4239	6370	SO:0001583	missense	10985	exon6			CCTCCAGCAAGAG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.451C>A	chr12.hg19:g.120616729G>T	ENSP00000300648:p.Leu151Met	44.0	0.0		33.0	11.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.536881	0.27475	.	.	ENSG00000089154	ENST00000300648	T	0.15834	2.39	5.79	-3.67	0.04476	Armadillo-like helical (1);Armadillo-type fold (1);	0.356004	0.29403	N	0.012243	T	0.06188	0.0160	N	0.12182	0.205	0.26124	N	0.98052	B	0.19817	0.039	B	0.09377	0.004	T	0.13150	-1.0520	10	0.42905	T	0.14	-0.0228	3.5793	0.07946	0.3794:0.3567:0.1734:0.0905	.	151	Q92616	GCN1L_HUMAN	M	151	ENSP00000300648:L151M	ENSP00000300648:L151M	L	-	1	2	GCN1L1	119101112	0.011000	0.17503	0.900000	0.35374	0.683000	0.39861	-0.080000	0.11339	-0.759000	0.04684	-0.251000	0.11542	CTG	.	.		0.592	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			T	120616729	G	T	120616729	3	4	208	1	0	0	0	0	1	0	0	0	6307	962	34	3	7776	3	GCN1L1	12	120616729	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	8308590	120616729	13235166	64	30112										
FARP1	10160	hgsc.bcm.edu	37	chr13	99040698	99040698	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gaagctgagcttcaagaggaAgcgctttctcatcaagctcc	10	11	3	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr13:99040698A>G	ENST00000319562.6	+	9	1086	c.821A>G	c.(820-822)aAg>aGg	p.K274R	FARP1_ENST00000376586.2_Missense_Mutation_p.K274R|FARP1_ENST00000595437.1_Missense_Mutation_p.K274R	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	274	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			TTCAAGAGGAAGCGCTTTCTC	0.537																																					p.K274R		Atlas-SNP	.											.	FARP1	207	.	0			c.A821G						.						84	76	79					13																	99040698		2203	4300	6503	SO:0001583	missense	10160	exon9			AGAGGAAGCGCTT	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.821A>G	chr13.hg19:g.99040698A>G	ENSP00000322926:p.Lys274Arg	83.0	0.0		102.0	40.0	NM_005766	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	hg19	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.932456	0.92458	.	.	ENSG00000152767	ENST00000376586;ENST00000319562	D;D	0.91792	-2.91;-2.91	6.17	6.17	0.99709	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.048155	0.85682	D	0.000000	D	0.94155	0.8125	L	0.48174	1.505	0.80722	D	1	B;D	0.55605	0.219;0.972	B;D	0.64877	0.054;0.93	D	0.93642	0.6965	10	0.42905	T	0.14	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	274;274	Q9Y4F1;C9JME2	FARP1_HUMAN;.	R	274	ENSP00000365771:K274R;ENSP00000322926:K274R	ENSP00000322926:K274R	K	+	2	0	FARP1	97838699	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.537	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		G	99040698	A	G	99040698	3	3	208	1	0	0	0	0	1	0	0	0	5684	72	3	2	1074	2	FARP1	13	99040698	Missense_Mutation	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10		99040698	16129180	65	30113										
TM9SF1	10548	hgsc.bcm.edu	37	chr14	24661413	24661413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ggtgagaatgatgttccacaCccaacgctcgcctccaatct	8	14	1	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr14:24661413C>T	ENST00000261789.4	-	4	1475	c.1117G>A	c.(1117-1119)Gtg>Atg	p.V373M	TM9SF1_ENST00000556387.1_Missense_Mutation_p.V582M|TM9SF1_ENST00000396854.4_Missense_Mutation_p.V373M|TM9SF1_ENST00000528669.1_Missense_Mutation_p.V373M|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000524835.1_Missense_Mutation_p.V286M|TM9SF1_ENST00000530611.1_Missense_Mutation_p.V582M	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	373					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		ATGTTCCACACCCAACGCTCG	0.532																																					p.V373M		Atlas-SNP	.											.	TM9SF1	58	.	0			c.G1117A						.						151	146	148					14																	24661413		2203	4300	6503	SO:0001583	missense	10548	exon4			TCCACACCCAACG	U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.1117G>A	chr14.hg19:g.24661413C>T	ENSP00000261789:p.Val373Met	244.0	0.0		221.0	70.0	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	hg19	CCDS9617.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.345819	0.82022	.	.	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000530611	T;T;T;T;D;T	0.81908	0.93;0.93;0.93;0.3;-1.55;0.93	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	D	0.89880	0.6843	M	0.75150	2.29	0.80722	D	1	D;P;P	0.56287	0.975;0.8;0.514	D;P;B	0.64410	0.925;0.474;0.326	D	0.89477	0.3747	10	0.46703	T	0.11	-10.5377	16.1986	0.82053	0.0:1.0:0.0:0.0	.	373;373;373	E9PJM1;Q86SZ6;O15321	.;.;TM9S1_HUMAN	M	373;373;582;286;373;582	ENSP00000261789:V373M;ENSP00000432997:V373M;ENSP00000451949:V582M;ENSP00000434387:V286M;ENSP00000380063:V373M;ENSP00000433967:V582M	ENSP00000433967:V582M	V	-	1	0	TM9SF1;RP11-468E2.1	23731253	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.915000	0.75770	2.699000	0.92147	0.655000	0.94253	GTG	.	.		0.532	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405		T	24661413	C	T	24661413	3	4	208	1	0	0	0	0	1	0	0	0	15992	507	18	3	758	3	TM9SF1	14	24661413	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10		24661413	82688127	66	30114										
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36017745	36017745	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cagaactgatatttaatgatCtaaagagggaaaataaatga	8	3	1	5			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr14:36017745C>A	ENST00000389698.3	-	40	6494		c.e40-1		RALGAPA1_ENST00000258840.6_Splice_Site|RALGAPA1_ENST00000307138.6_Intron|RALGAPA1_ENST00000382366.3_Splice_Site	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)						activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						ATTTAATGATCTAAAGAGGGA	0.328																																					.		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.6104-1G>T						.						81	87	85					14																	36017745		2203	4299	6502	SO:0001630	splice_region_variant	253959	exon41			AATGATCTAAAGA	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.6104-1G>T	chr14.hg19:g.36017745C>A		109.0	0.0		69.0	30.0	NM_014990	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Splice_Site	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.368716	0.61624	.	.	ENSG00000174373	ENST00000389698;ENST00000258840;ENST00000382366;ENST00000553892	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2786	0.98501	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RALGAPA1	35087496	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.138000	0.58017	2.868000	0.98415	0.557000	0.71058	.	.	.		0.328	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	Intron	A	36017745	C	A	36017745	5	1	208	1	0	0	0	0	0	0	1	0	13028	927	32	3	164	3	RALGAPA1	14	36017745	Splice_Site	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	11356332	36017745	71331795	67	30115										
TBPL2	387332	hgsc.bcm.edu	37	chr14	55907152	55907152	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	caggtagagctccaggtaggTctcctcctgctccatggacc	11	14	1	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr14:55907152T>C	ENST00000247219.5	-	1	182	c.112A>G	c.(112-114)Acc>Gcc	p.T38A		NM_199047.2	NP_950248.1			TATA box binding protein like 2											endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8						TCCAGGTAGGTCTCCTCCTGC	0.682																																					p.T38A		Atlas-SNP	.											.	TBPL2	27	.	0			c.A112G						.						43	44	44					14																	55907152		2186	4277	6463	SO:0001583	missense	387332	exon1			GGTAGGTCTCCTC	AY457923	CCDS9724.1	14q22.2	2004-06-03			ENSG00000182521	ENSG00000182521			19841	protein-coding gene	gene with protein product		608964				14634207	Standard	NM_199047		Approved	TRF3, TBP2	uc001xby.3	Q6SJ96	OTTHUMG00000140313	ENST00000247219.5:c.112A>G	chr14.hg19:g.55907152T>C	ENSP00000247219:p.Thr38Ala	175.0	0.0		174.0	61.0	NM_199047		Missense_Mutation	SNP	ENST00000247219.5	hg19	CCDS9724.1	.	.	.	.	.	.	.	.	.	.	t	12.22	1.872330	0.33069	.	.	ENSG00000182521	ENST00000247219	T	0.41758	0.99	4.93	-4.48	0.03515	.	0.777902	0.12141	N	0.495828	T	0.21590	0.0520	L	0.36672	1.1	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.21552	-1.0242	10	0.20519	T	0.43	0.6616	1.449	0.02371	0.1948:0.2517:0.3574:0.1961	.	38	Q6SJ96	TBPL2_HUMAN	A	38	ENSP00000247219:T38A	ENSP00000247219:T38A	T	-	1	0	TBPL2	54976905	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.534000	0.06150	-0.349000	0.08274	-0.520000	0.04383	ACC	.	.		0.682	TBPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276916.1	NM_199047		C	55907152	T	C	55907152	3	2	208	1	0	0	0	0	1	0	0	0	15661	1667	58	2	1043	2	TBPL2	14	55907152	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	19889407	55907152	51442388	68	30116										
ARID4A	5926	hgsc.bcm.edu	37	chr14	58830925	58830925	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	agtgaaacagaagatgctttAgaaaagaatttaataaatga	8	2	0	6			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr14:58830925A>C	ENST00000355431.3	+	20	2491	c.2118A>C	c.(2116-2118)ttA>ttC	p.L706F	ARID4A_ENST00000348476.3_Missense_Mutation_p.L706F|ARID4A_ENST00000395168.3_Missense_Mutation_p.L706F|ARID4A_ENST00000431317.2_Missense_Mutation_p.L706F	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	706					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						AAGATGCTTTAGAAAAGAATT	0.239																																					p.L706F		Atlas-SNP	.											.	ARID4A	222	.	0			c.A2118C						.						18	19	19					14																	58830925		1876	4046	5922	SO:0001583	missense	5926	exon20			TGCTTTAGAAAAG	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2118A>C	chr14.hg19:g.58830925A>C	ENSP00000347602:p.Leu706Phe	390.0	0.0		382.0	154.0	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	hg19	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	A	11.48	1.652507	0.29336	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.15718	2.46;2.46;2.46;2.46;2.4	5.8	-2.49	0.06403	Chromo domain-like (1);	0.354280	0.29646	N	0.011578	T	0.07908	0.0198	N	0.19112	0.55	0.29904	N	0.824135	P;P;P	0.45474	0.859;0.498;0.859	B;B;B	0.42422	0.387;0.146;0.387	T	0.20907	-1.0261	10	0.56958	D	0.05	-2.1234	1.0552	0.01589	0.3591:0.0968:0.2706:0.2735	.	706;706;706	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	F	706;706;706;706;384	ENSP00000347602:L706F;ENSP00000344556:L706F;ENSP00000378597:L706F;ENSP00000397368:L706F;ENSP00000416053:L384F	ENSP00000344556:L706F	L	+	3	2	ARID4A	57900678	0.994000	0.37717	0.974000	0.42286	0.931000	0.56810	0.182000	0.16900	-0.326000	0.08564	0.528000	0.53228	TTA	.	.		0.239	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		C	58830925	A	C	58830925	3	2	208	1	0	0	0	0	1	0	0	0	919	417	15	5	2192	5	ARID4A	14	58830925	Missense_Mutation	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	2923773	58830925	48518615	69	30117										
CATSPERB	79820	hgsc.bcm.edu	37	chr14	92185810	92185810	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	aatatcaaccaaccacaaaaTccgatcactgaacttgaata	3	11	2	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr14:92185810T>G	ENST00000256343.3	-	5	478	c.322A>C	c.(322-324)Att>Ctt	p.I108L		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	108					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				AACCACAAAATCCGATCACTG	0.318																																					p.I108L		Atlas-SNP	.											.	CATSPERB	114	.	0			c.A322C						.						79	69	73					14																	92185810		2203	4299	6502	SO:0001583	missense	79820	exon5			ACAAAATCCGATC	AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.322A>C	chr14.hg19:g.92185810T>G	ENSP00000256343:p.Ile108Leu	100.0	0.0		118.0	40.0	NM_024764	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	hg19	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	T	0.245	-1.010944	0.02095	.	.	ENSG00000133962	ENST00000256343;ENST00000553329	T	0.41758	0.99	3.62	-6.09	0.02145	.	1.359100	0.05149	N	0.495740	T	0.19485	0.0468	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.14839	-1.0458	10	0.15066	T	0.55	-0.9497	1.5037	0.02482	0.1194:0.3043:0.2371:0.3392	.	108	Q9H7T0	CTSRB_HUMAN	L	108;61	ENSP00000256343:I108L	ENSP00000256343:I108L	I	-	1	0	CATSPERB	91255563	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	-1.012000	0.03649	-1.542000	0.01725	-1.245000	0.01525	ATT	.	.		0.318	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		G	92185810	T	G	92185810	3	3	208	1	0	0	0	0	1	0	0	0	2693	1435	50	5	3120	5	CATSPERB	14	92185810	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	33354885	92185810	15163730	70	30118										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92470139	92470139	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tctcctttagctgcttgattTctgaatcggtttgttcgtgt	9	8	2	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr14:92470139T>A	ENST00000267622.4	-	11	4554	c.4181A>T	c.(4180-4182)gAa>gTa	p.E1394V		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1394					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		CTGCTTGATTTCTGAATCGGT	0.373			T	PDGFRB	AML																																p.E1394V	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.A4181T						.						112	111	111					14																	92470139		2203	4300	6503	SO:0001583	missense	9321	exon11			TTGATTTCTGAAT	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.4181A>T	chr14.hg19:g.92470139T>A	ENSP00000267622:p.Glu1394Val	144.0	0.0		101.0	36.0	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	hg19	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.81|13.81	2.348803|2.348803	0.41599|0.41599	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.11495|.	2.77|.	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	0.127973|.	0.49916|.	D|.	0.000124|.	T|T	0.62332|0.62332	0.2419|0.2419	L|L	0.59436|0.59436	1.845|1.845	0.44523|0.44523	D|D	0.997471|0.997471	D;D|.	0.89917|.	0.996;1.0|.	P;D|.	0.77004|.	0.885;0.989|.	T|T	0.61768|0.61768	-0.6995|-0.6995	10|5	0.49607|.	T|.	0.09|.	.|.	9.8053|9.8053	0.40789|0.40789	0.0:0.0773:0.0:0.9227|0.0:0.0773:0.0:0.9227	.|.	1130;1394|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	V|S	1394;1130|1109	ENSP00000267622:E1394V|.	ENSP00000267622:E1394V|.	E|R	-|-	2|3	0|2	TRIP11|TRIP11	91539892|91539892	1.000000|1.000000	0.71417|0.71417	0.080000|0.080000	0.20451|0.20451	0.152000|0.152000	0.21847|0.21847	7.747000|7.747000	0.85070|0.85070	2.018000|2.018000	0.59344|0.59344	0.379000|0.379000	0.24179|0.24179	GAA|AGA	.	.		0.373	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			A	92470139	T	A	92470139	3	1	208	1	0	0	0	0	1	0	0	0	16570	1783	62	4	1802	4	TRIP11	14	92470139	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	284329	92470139	14879401	71	30119										
CHP	11261	hgsc.bcm.edu	37	chr15	41571555	41571555	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ttttggagaaggtggatgtaGaacagaaaatgagcatccga	13	4	0	4			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr15:41571555G>A	ENST00000334660.5	+	7	796	c.556G>A	c.(556-558)Gaa>Aaa	p.E186K	CHP1_ENST00000560397.1_Missense_Mutation_p.E145K|CHP1_ENST00000558351.1_3'UTR	NM_007236.4	NP_009167.1	Q99653	CHP1_HUMAN	calcineurin-like EF-hand protein 1	186	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion-dependent exocytosis (GO:0017156)|cellular response to acidic pH (GO:0071468)|cytoplasmic microtubule organization (GO:0031122)|membrane docking (GO:0022406)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|microtubule bundle formation (GO:0001578)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of protein glycosylation (GO:0060050)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of protein transport (GO:0051222)|positive regulation of sodium:proton antiporter activity (GO:0032417)|potassium ion transport (GO:0006813)|protein export from nucleus (GO:0006611)|protein oligomerization (GO:0051259)|protein stabilization (GO:0050821)|regulation of intracellular pH (GO:0051453)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|kinase binding (GO:0019900)|microtubule binding (GO:0008017)|potassium channel regulator activity (GO:0015459)|protein kinase inhibitor activity (GO:0004860)|transporter activity (GO:0005215)										GGTGGATGTAGAACAGAAAAT	0.403																																					p.E186K		Atlas-SNP	.											.	.	.	.	0			c.G556A						.						118	103	108					15																	41571555		2203	4300	6503	SO:0001583	missense	11261	exon7			GATGTAGAACAGA		CCDS10073.1	15q13.3	2013-01-11	2013-01-11		ENSG00000187446	ENSG00000187446		"EF-hand domain containing"	17433	protein-coding gene	gene with protein product	"calcineurin homologous protein"	606988				15987692, 20720019	Standard	NM_007236		Approved	Sid470p, CHP, SLC9A1BP, p22, p24	uc001znl.3	Q99653	OTTHUMG00000130233	ENST00000334660.5:c.556G>A	chr15.hg19:g.41571555G>A	ENSP00000335632:p.Glu186Lys	101.0	0.0		125.0	54.0	NM_007236	B2R6H9|Q6FHZ9	Missense_Mutation	SNP	ENST00000334660.5	hg19	CCDS10073.1	.	.	.	.	.	.	.	.	.	.	G	36	5.720743	0.96839	.	.	ENSG00000187446	ENST00000334660	T	0.67171	-0.25	5.51	5.51	0.81932	EF-hand-like domain (1);	0.110399	0.64402	D	0.000003	T	0.77968	0.4210	L	0.50333	1.59	0.80722	D	1	D	0.69078	0.997	D	0.68039	0.955	T	0.79361	-0.1835	10	0.72032	D	0.01	-16.4974	18.1792	0.89772	0.0:0.0:1.0:0.0	.	186	Q99653	CHP1_HUMAN	K	186	ENSP00000335632:E186K	ENSP00000335632:E186K	E	+	1	0	AC012652.1	39358847	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.488000	0.97947	2.583000	0.87209	0.591000	0.81541	GAA	.	.		0.403	CHP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252554.2	NM_007236		A	41571555	G	A	41571555	3	1	208	1	0	0	0	0	1	0	0	0	3368	943	33	3	582	3	CHP	15	41571555	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10		41571555	60959837	72	30120										
RAB11FIP3	9727	hgsc.bcm.edu	37	chr16	532669	532669	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	acagtgccggcggctcggccGtgccctctgagtgcctggac	15	15	1	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr16:532669G>A	ENST00000262305.4	+	4	1436	c.1048G>A	c.(1048-1050)Gtg>Atg	p.V350M	RAB11FIP3_ENST00000457159.1_Missense_Mutation_p.V350M|RAB11FIP3_ENST00000450428.1_Missense_Mutation_p.V54M	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	350					cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				CGGCTCGGCCGTGCCCTCTGA	0.677																																					p.V350M	Melanoma(160;2366 2595 4474 8099)	Atlas-SNP	.											.	RAB11FIP3	31	.	0			c.G1048A						.						43	36	39					16																	532669		2200	4300	6500	SO:0001583	missense	9727	exon4			TCGGCCGTGCCCT	AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"EF-hand domain containing"	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.1048G>A	chr16.hg19:g.532669G>A	ENSP00000262305:p.Val350Met	87.0	0.0		86.0	4.0	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Missense_Mutation	SNP	ENST00000262305.4	hg19	CCDS32351.1	.	.	.	.	.	.	.	.	.	.	G	5.053	0.195423	0.09599	.	.	ENSG00000090565	ENST00000262305;ENST00000457159;ENST00000434585;ENST00000450428;ENST00000452814;ENST00000449879;ENST00000448401;ENST00000412256	.	.	.	5.12	2.02	0.26589	.	.	.	.	.	T	0.22975	0.0555	L	0.36672	1.1	0.09310	N	1	P;B;B	0.36048	0.534;0.087;0.342	B;B;B	0.28305	0.088;0.01;0.029	T	0.09465	-1.0673	8	0.41790	T	0.15	-27.6558	6.4594	0.21948	0.1631:0.148:0.6889:0.0	.	350;54;350	O75154-3;O75154-2;O75154	.;.;RFIP3_HUMAN	M	350;350;226;54;40;54;54;5	.	ENSP00000262305:V350M	V	+	1	0	RAB11FIP3	472670	0.995000	0.38212	0.186000	0.23195	0.042000	0.13812	2.535000	0.45685	0.171000	0.19730	-0.126000	0.14955	GTG	.	.		0.677	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700		A	532669	G	A	532669	3	1	208	1	0	0	0	0	1	0	0	0	12910	1145	40	1	1081	1	RAB11FIP3	16	532669	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10		532669	89822084	73	30121										
GLYR1	84656	hgsc.bcm.edu	37	chr16	4861735	4861735	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cagggtcagcccctcggcaaTagtggccatgaagctccctt	11	14	1	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr16:4861735T>C	ENST00000321919.9	-	14	1427	c.1351A>G	c.(1351-1353)Att>Gtt	p.I451V	GLYR1_ENST00000591451.1_Missense_Mutation_p.I445V|GLYR1_ENST00000436648.5_Missense_Mutation_p.I370V|GLYR1_ENST00000381983.3_Missense_Mutation_p.I434V	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	451					pentose-phosphate shunt (GO:0006098)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	19						CCCTCGGCAATAGTGGCCATG	0.582																																					p.I451V		Atlas-SNP	.											.	GLYR1	49	.	0			c.A1351G						.						80	72	75					16																	4861735		2197	4300	6497	SO:0001583	missense	84656	exon14			CGGCAATAGTGGC	AF244907	CCDS10524.1	16p13.3	2010-02-17			ENSG00000140632	ENSG00000140632			24434	protein-coding gene	gene with protein product	"nuclear protein 60kDa"	610660				16352664	Standard	NM_032569		Approved	BM045, HIBDL, NP60, N-PAC	uc002cxx.4	Q49A26	OTTHUMG00000129530	ENST00000321919.9:c.1351A>G	chr16.hg19:g.4861735T>C	ENSP00000322716:p.Ile451Val	59.0	0.0		69.0	28.0	NM_032569	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	Missense_Mutation	SNP	ENST00000321919.9	hg19	CCDS10524.1	.	.	.	.	.	.	.	.	.	.	T	12.26	1.885947	0.33348	.	.	ENSG00000140632	ENST00000321919;ENST00000381983;ENST00000436648	T;T;T	0.27104	1.69;1.69;1.69	5.85	5.85	0.93711	Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.045987	0.85682	D	0.000000	T	0.16041	0.0386	N	0.12182	0.205	0.54753	D	0.999982	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.002;0.004;0.002;0.001	T	0.09487	-1.0672	10	0.23302	T	0.38	-12.9502	15.2169	0.73274	0.0:0.0:0.0:1.0	.	370;445;434;451	Q49A26-5;Q49A26-3;Q49A26-2;Q49A26	.;.;.;GLYR1_HUMAN	V	451;434;370	ENSP00000322716:I451V;ENSP00000371413:I434V;ENSP00000390276:I370V	ENSP00000322716:I451V	I	-	1	0	GLYR1	4801736	1.000000	0.71417	0.923000	0.36655	0.886000	0.51366	5.881000	0.69706	2.234000	0.73211	0.533000	0.62120	ATT	.	.		0.582	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251717.2	NM_032569		C	4861735	T	C	4861735	3	2	208	1	0	0	0	0	1	0	0	0	6491	1406	49	2	322	2	GLYR1	16	4861735	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	4329066	4861735	85493018	74	30122										
CDH11	1009	hgsc.bcm.edu	37	chr16	65025837	65025837	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ggtagggctgttctgatgatAcctggacaggtaagcaggca	15	7	1	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr16:65025837A>T	ENST00000268603.4	-	6	1260	c.645T>A	c.(643-645)ggT>ggA	p.G215G	CDH11_ENST00000566827.1_Splice_Site_p.G89G|CDH11_ENST00000394156.3_Splice_Site_p.G215G	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	215	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TTCTGATGATACCTGGACAGG	0.478			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.G215G		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	.	CDH11	260	.	0			c.T645A						.						181	123	143					16																	65025837		2203	4300	6503	SO:0001630	splice_region_variant	1009	exon6			GATGATACCTGGA	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.644-1T>A	chr16.hg19:g.65025837A>T		98.0	0.0		129.0	51.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	hg19	CCDS10803.1																																																																																			.	.		0.478	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	Silent	T	65025837	A	T	65025837	5	4	208	1	0	0	0	0	0	0	1	0	3099	405	14	4	1777	4	CDH11	16	65025837	Splice_Site	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10	60164102	65025837	25328916	75	30123										
CDH13	1012	hgsc.bcm.edu	37	chr16	83704424	83704424	+	Frame_Shift_Del	DEL	G	G	-													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	acagtcgaggaaggagctgtGggagttattgtcaatttgac							TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr16:83704424delG	ENST00000566620.1	+	9	1421	c.1131delG	c.(1129-1131)gtgfs	p.V377fs	CDH13_ENST00000428848.3_Frame_Shift_Del_p.V338fs|CDH13_ENST00000268613.10_Frame_Shift_Del_p.V424fs	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	377	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		AAGGAGCTGTGGGAGTTATTG	0.463																																					p.V424fs		Atlas-INDEL	.											.	CDH13	97	.	0			c.1271delT						.						76	75	76					16																	83704424		1948	4136	6084	SO:0001589	frameshift_variant	1012	exon10			.	U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"Cadherins / Major cadherins"	1753	protein-coding gene	gene with protein product	"T-cadherin", "H-cadherin (heart)"	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.1131delG	chr16.hg19:g.83704424delG	ENSP00000454435:p.Val377fs	136.0	0.0		153.0	62.0	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Frame_Shift_Del	DEL	ENST00000566620.1	hg19	CCDS58486.1																																																																																			.	.		0.463	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		-	83704424	G	-	83704424	7	5	208	1	0	1	0	1	0	0	0	0	3101	1335	47	0	1165	0	CDH13	16	83704424	Frame_Shift_Del	DEL	G	TCGA-DD-AAE2-01A-11D-A40R-10	18678587	83704424	6650329	76	30124										
EIF1	10209	hgsc.bcm.edu	37	chr17	39847045	39847045	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tcttttcagattggactggcTaaggacgatcagctgaaggt	12	7	3	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr17:39847045T>C	ENST00000469257.1	+	4	455	c.309T>C	c.(307-309)gcT>gcC	p.A103A	EIF1_ENST00000310837.4_3'UTR|JUP_ENST00000540235.1_Intron|EIF1_ENST00000591776.1_Silent_p.A103A			P41567	EIF1_HUMAN	eukaryotic translation initiation factor 1	103					dosage compensation by inactivation of X chromosome (GO:0009048)|regulation of translational initiation (GO:0006446)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|skin(1)	5		Breast(137;0.000307)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			TTGGACTGGCTAAGGACGATC	0.448																																					p.A103A	Pancreas(176;1692 2837 16734 17588)	Atlas-SNP	.											.	EIF1	10	.	0			c.T309C						.						158	142	147					17																	39847045		2203	4300	6503	SO:0001819	synonymous_variant	10209	exon4			ACTGGCTAAGGAC	AF083441	CCDS11403.1	17q21.2	2006-02-02			ENSG00000173812	ENSG00000173812			3249	protein-coding gene	gene with protein product						7904817, 10347211	Standard	NM_005801		Approved	EIF-1, ISO1, A121, SUI1, EIF1A	uc002hxj.3	P41567	OTTHUMG00000133492	ENST00000469257.1:c.309T>C	chr17.hg19:g.39847045T>C		88.0	0.0		89.0	28.0	NM_005801	Q9UNQ9	Silent	SNP	ENST00000469257.1	hg19	CCDS11403.1																																																																																			.	.		0.448	EIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257390.1	NM_005801		C	39847045	T	C	39847045	2	2	208	1	0	0	0	0	0	0	0	1	4992	1509	53	2		2	EIF1	17	39847045	Silent	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10		39847045	41348165	77	30125										
G6PC	2538	hgsc.bcm.edu	37	chr17	41056040	41056040	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	gataaagcagttccctgtaaCctgtgagactggaccaggta	11	9	0	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr17:41056040C>T	ENST00000253801.2	+	2	402	c.323C>T	c.(322-324)aCc>aTc	p.T108I	G6PC_ENST00000585489.1_Missense_Mutation_p.T108I|G6PC_ENST00000592383.1_Missense_Mutation_p.T108I	NM_000151.3	NP_000142.2	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit	108			T -> I (in GSD1A). {ECO:0000269|PubMed:10447271, ECO:0000269|PubMed:11058903}.		carbohydrate metabolic process (GO:0005975)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|hexose transport (GO:0008645)|multicellular organism growth (GO:0035264)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)|urate metabolic process (GO:0046415)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)|phosphate ion binding (GO:0042301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		TTCCCTGTAACCTGTGAGACT	0.507																																					p.T108I		Atlas-SNP	.											.	G6PC	48	.	0			c.C323T	GRCh37	CM990607	G6PC	M		.						128	110	116					17																	41056040		2203	4300	6503	SO:0001583	missense	2538	exon2			CTGTAACCTGTGA	U01120	CCDS11446.1, CCDS59291.1	17q21	2014-09-17	2006-06-28			ENSG00000131482	3.1.3.9		4056	protein-coding gene	gene with protein product	"glycogen storage disease type I, von Gierke disease"	613742	"glucose-6-phosphatase, catalytic (glycogen storage disease type I, von Gierke disease)"	G6PT		7774924	Standard	NM_000151		Approved	GSD1a	uc002icb.2	P35575		ENST00000253801.2:c.323C>T	chr17.hg19:g.41056040C>T	ENSP00000253801:p.Thr108Ile	100.0	0.0		89.0	40.0	NM_001270397	A1L4C0|B4E1C3|K7EL82	Missense_Mutation	SNP	ENST00000253801.2	hg19	CCDS11446.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.390114	0.82902	.	.	ENSG00000131482	ENST00000253801	D	0.83837	-1.77	4.74	4.74	0.60224	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.89646	0.6775	L	0.59967	1.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.90777	0.4676	10	0.87932	D	0	.	17.9027	0.88909	0.0:1.0:0.0:0.0	.	110;108	E7ENG5;P35575	.;G6PC_HUMAN	I	108	ENSP00000253801:T108I	ENSP00000253801:T108I	T	+	2	0	G6PC	38309566	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	7.604000	0.82830	2.455000	0.83008	0.491000	0.48974	ACC	.	.		0.507	G6PC-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452451.1	NM_000151		T	41056040	C	T	41056040	3	4	208	1	0	0	0	0	1	0	0	0	6151	507	18	3	329	3	G6PC	17	41056040	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	1208995	41056040	40139170	78	30126										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73738423	73738423	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ccttccaccctcgacccaggCaagaccacaccattgtggac	7	18	0	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr17:73738423C>A	ENST00000200181.3	+	24	2822	c.2635C>A	c.(2635-2637)Caa>Aaa	p.Q879K	ITGB4_ENST00000339591.3_Splice_Site_p.Q879K|ITGB4_ENST00000579662.1_Splice_Site_p.Q879K|ITGB4_ENST00000449880.2_Splice_Site_p.Q879K|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000450894.3_Splice_Site_p.Q879K	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	879					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCGACCCAGGCAAGACCACAC	0.642																																					p.Q879K		Atlas-SNP	.											.	ITGB4	165	.	0			c.C2635A						.						33	30	31					17																	73738423		2203	4300	6503	SO:0001630	splice_region_variant	3691	exon24			CCCAGGCAAGACC		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.2634-1C>A	chr17.hg19:g.73738423C>A		95.0	0.0		140.0	75.0	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.879802	0.51801	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.75821	-0.97;-0.91;-0.91	5.64	5.64	0.86602	.	0.065848	0.64402	D	0.000006	T	0.81763	0.4891	L	0.34521	1.04	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.83275	0.996;0.991;0.991	T	0.83289	-0.0034	10	0.87932	D	0	.	19.7154	0.96115	0.0:1.0:0.0:0.0	.	879;879;879	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	K	879	ENSP00000200181:Q879K;ENSP00000344079:Q879K;ENSP00000400217:Q879K	ENSP00000200181:Q879K	Q	+	1	0	ITGB4	71250018	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.890000	0.63178	2.664000	0.90586	0.655000	0.94253	CAA	.	.		0.642	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		Missense_Mutation	A	73738423	C	A	73738423	5	1	208	1	0	0	0	0	0	0	1	0	7906	724	25	3	2725	3	ITGB4	17	73738423	Splice_Site	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	32682383	73738423	7456787	79	30127										
FASN	2194	hgsc.bcm.edu	37	chr17	80038617	80038617	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	atgctgagccgggaggccagGctgtggaacacggtggtgga	19	8	0	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr17:80038617G>A	ENST00000306749.2	-	39	6995	c.6777C>T	c.(6775-6777)agC>agT	p.S2259S	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2259	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GGGAGGCCAGGCTGTGGAACA	0.687																																					p.S2259S	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C6777T						.						44	45	45					17																	80038617		2191	4290	6481	SO:0001819	synonymous_variant	2194	exon39			GGCCAGGCTGTGG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6777C>T	chr17.hg19:g.80038617G>A		121.0	0.0		187.0	47.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.687	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80038617	G	A	80038617	2	1	208	1	0	0	0	0	0	0	0	1	5691	1194	42	3		3	FASN	17	80038617	Silent	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	6300194	80038617	1156593	80	30128										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5410602	5410602	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ccccgtcggctgcggtgtccGtgcgctcactgtcagtctgt	13	15	3	0	rs373780287		TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr18:5410602G>T	ENST00000341928.2	-	14	2424	c.2084C>A	c.(2083-2085)aCg>aAg	p.T695K	EPB41L3_ENST00000427684.2_5'UTR|EPB41L3_ENST00000544123.1_Missense_Mutation_p.T526K|EPB41L3_ENST00000542146.1_5'UTR|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000540638.2_Missense_Mutation_p.T526K|EPB41L3_ENST00000342933.3_Missense_Mutation_p.T695K|EPB41L3_ENST00000400111.3_Missense_Mutation_p.T526K	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	695	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.T695M(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						TGCGGTGTCCGTGCGCTCACT	0.557																																					p.T695K		Atlas-SNP	.											EPB41L3,NS,carcinoma,0,1	EPB41L3	222	.	1	Substitution - Missense(1)	kidney(1)	c.C2084A						.						103	67	79					18																	5410602		2203	4300	6503	SO:0001583	missense	23136	exon14			GTGTCCGTGCGCT	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2084C>A	chr18.hg19:g.5410602G>T	ENSP00000343158:p.Thr695Lys	93.0	0.0		75.0	47.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.879968	0.72294	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	D;D;D;D	0.83992	-1.66;-1.79;-1.66;-1.78	5.24	5.24	0.73138	.	0.058714	0.64402	D	0.000002	D	0.84388	0.5461	N	0.19112	0.55	0.80722	D	1	D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.994;0.995;0.995;0.998;0.999	T	0.80821	-0.1211	10	0.15952	T	0.53	.	18.8177	0.92084	0.0:0.0:1.0:0.0	.	526;87;417;526;695	F5GX05;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2	.;.;.;.;E41L3_HUMAN	K	695;417;526;417;695;526	ENSP00000343158:T695K;ENSP00000441174:T526K;ENSP00000341138:T695K;ENSP00000382981:T526K	ENSP00000343158:T695K	T	-	2	0	EPB41L3	5400602	1.000000	0.71417	0.939000	0.37840	0.949000	0.60115	9.138000	0.94501	2.453000	0.82957	0.591000	0.81541	ACG	.	.		0.557	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		T	5410602	G	T	5410602	3	4	208	1	0	0	0	0	1	0	0	0	5156	1145	40	1	1215	1	EPB41L3	18	5410602	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10		5410602	72666646	81	30129										
THOP1	7064	hgsc.bcm.edu	37	chr19	2810300	2810337	+	Splice_Site	DEL	CCTGGGCACTCTGAGGCTCTGCCCCATCCCTGCAGGCG	CCTGGGCACTCTGAGGCTCTGCCCCATCCCTGCAGGCG	-													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	aggctctgccccatccctgcAggcggagttcgccatgttca					rs113316866|rs113612949|rs151055831	byFrequency	TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	CCTGGGCACTCTGAGGCTCTGCCCCATCCCTGCAGGCG	CCTGGGCACTCTGAGGCTCTGCCCCATCCCTGCAGGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr19:2810300_2810337delCCTGGGCACTCTGAGGCTCTGCCCCATCCCTGCAGGCG	ENST00000307741.6	+	10	1658_1694	c.1455_1491delCCTGGGCACTCTGAGGCTCTGCCCCATCCCTGCAGGCG	c.(1453-1491)cacctgggcactctgaggctctgccccatccctgcaggc>ca	p.HLGTLRLCPIPAG485fs	THOP1_ENST00000586677.1_Splice_Site_p.HLGTLRLCPIPAG364fs|THOP1_ENST00000591149.1_3'UTR|THOP1_ENST00000395212.4_Start_Codon_Del	NM_003249.3	NP_003240.1	P52888	THOP1_HUMAN	thimet oligopeptidase 1	485					intracellular signal transduction (GO:0035556)|peptide metabolic process (GO:0006518)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			NS(1)|central_nervous_system(1)|endometrium(1)|lung(8)|ovary(2)|skin(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCATCCCTGCAGGCGGAGTTCGCCATGTTCAGCGGGACCCACGTGGAGCGGGACTTTG	0.685																																					p.486_486del		Atlas-INDEL	.											.	THOP1	49	.	0			c.1456_1457del						.																																			SO:0001630	splice_region_variant	7064	exon10			.		CCDS12095.1	19p13.3	2008-02-05				ENSG00000172009	3.4.24.15		11793	protein-coding gene	gene with protein product		601117				9790774	Standard	NM_003249		Approved		uc002lwj.3	P52888		ENST00000307741.6:c.1456-1CCTGGGCACTCTGAGGCTCTGCCCCATCCCTGCAGGCG>-	chr19.hg19:g.2810300_2810337delCCTGGGCACTCTGAGGCTCTGCCCCATCCCTGCAGGCG		69.0	0.0		67.0	19.0	NM_003249	B3KSE2|Q9UCB3	Frame_Shift_Del	DEL	ENST00000307741.6	hg19	CCDS12095.1																																																																																			.	.		0.685	THOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451587.2		Frame_Shift_Del	-	2810337	CCTGGGCACTCTGAGGCTCTGCCCCATCCCTGCAGGCG	-	2810300	8	5	208	1	0	1	0	1	0	0	1	0	15886	202	7	0	1492	0	THOP1	19	2810300	Splice_Site	DEL	CCTGGGCACTCTGAGGCTCTGCCCCATCCCTGCAGGCG	TCGA-DD-AAE2-01A-11D-A40R-10		2810300	56318683	82	30130										
SLC35E1	79939	hgsc.bcm.edu	37	chr19	16664490	16664490	+	Nonstop_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ctggtcctgtcctttggactCtacacatcatagcggttcaa	8	12	3	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr19:16664490C>A	ENST00000595753.1	-	6	1250	c.1233G>T	c.(1231-1233)taG>taT	p.*411Y	CTD-3222D19.2_ENST00000409035.1_Intron|CTD-3222D19.11_ENST00000597357.1_RNA|SLC35E1_ENST00000593812.1_5'Flank	NM_024881.4	NP_079157.3	Q96K37	S35E1_HUMAN	solute carrier family 35, member E1	0					transport (GO:0006810)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(2)|ovary(1)	15						CCTTTGGACTCTACACATCAT	0.517																																					p.X411Y		Atlas-SNP	.											.	SLC35E1	48	.	0			c.G1233T						.						176	156	163					19																	16664490		2203	4300	6503	SO:0001578	stop_lost	79939	exon6			TGGACTCTACACA	AK024313	CCDS12346.2	19p13.11	2013-05-22			ENSG00000127526	ENSG00000127526		"Solute carriers"	20803	protein-coding gene	gene with protein product							Standard	NM_024881		Approved	FLJ14251	uc010xph.2	Q96K37	OTTHUMG00000152575	ENST00000595753.1:c.1233G>T	chr19.hg19:g.16664490C>A		110.0	0.0		122.0	10.0	NM_024881	Q8NBQ2|Q96JV7	Missense_Mutation	SNP	ENST00000595753.1	hg19	CCDS12346.2	.	.	.	.	.	.	.	.	.	.	C	11.79	1.744666	0.30865	.	.	ENSG00000127526	ENST00000409648	.	.	.	4.96	3.93	0.45458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3586	0.32346	0.0:0.8273:0.0:0.1727	.	.	.	.	Y	411	.	.	X	-	3	2	SLC35E1	16525490	0.996000	0.38824	0.990000	0.47175	0.571000	0.35966	2.463000	0.45058	2.307000	0.77673	0.561000	0.74099	TAG	.	.		0.517	SLC35E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326809.2	NM_024881		A	16664490	C	A	16664490	4	1	208	1	0	0	0	0	0	0	0	0	14599	924	32	3	3	3	SLC35E1	19	16664490	Nonstop_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	13854190	16664490	42464493	83	30131										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935445	30935445	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tggagaaggcacacatcacgGccgagtcggcccagggccag	15	13	1	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr19:30935445G>T	ENST00000355537.3	+	2	1123	c.976G>T	c.(976-978)Gcc>Tcc	p.A326S		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	326					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					ACACATCACGGCCGAGTCGGC	0.652																																					p.A326S		Atlas-SNP	.											.	ZNF536	424	.	0			c.G976T						.						88	100	96					19																	30935445		2203	4300	6503	SO:0001583	missense	9745	exon2			ATCACGGCCGAGT		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.976G>T	chr19.hg19:g.30935445G>T	ENSP00000347730:p.Ala326Ser	51.0	0.0		56.0	4.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.813411	0.32053	.	.	ENSG00000198597	ENST00000355537	T	0.09350	2.99	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.19167	0.0460	N	0.16098	0.37	0.50813	D	0.999892	D;D	0.89917	0.999;1.0	D;D	0.83275	0.957;0.996	T	0.22034	-1.0228	10	0.23302	T	0.38	-27.943	19.5661	0.95393	0.0:0.0:1.0:0.0	.	326;326	A7E228;O15090	.;ZN536_HUMAN	S	326	ENSP00000347730:A326S	ENSP00000347730:A326S	A	+	1	0	ZNF536	35627285	1.000000	0.71417	0.985000	0.45067	0.909000	0.53808	8.024000	0.88770	2.631000	0.89168	0.491000	0.48974	GCC	.	.		0.652	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30935445	G	T	30935445	3	4	208	1	0	0	0	0	1	0	0	0	17989	1203	42	3	978	3	ZNF536	19	30935445	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	14270955	30935445	28193538	84	30132										
ANKRD27	84079	hgsc.bcm.edu	37	chr19	33108518	33108518	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ttctagatctccatcagcaaCtgctctcaaaagtttttcta	4	11	5	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr19:33108518C>A	ENST00000306065.4	-	21	2187	c.2029G>T	c.(2029-2031)Gtt>Ttt	p.V677F		NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	677					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					CCATCAGCAACTGCTCTCAAA	0.289																																					p.V677F		Atlas-SNP	.											.	ANKRD27	86	.	0			c.G2029T						.						28	32	30					19																	33108518		2200	4299	6499	SO:0001583	missense	84079	exon21			CAGCAACTGCTCT	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"Ankyrin repeat domain containing"	25310	protein-coding gene	gene with protein product	"Vps9 domain and ankyrin-repeat-containing protein"					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.2029G>T	chr19.hg19:g.33108518C>A	ENSP00000304292:p.Val677Phe	507.0	0.0		560.0	189.0	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	hg19	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065904	0.76187	.	.	ENSG00000105186	ENST00000306065	T	0.72615	-0.67	5.71	3.58	0.41010	Ankyrin repeat-containing domain (3);	0.128573	0.34750	N	0.003701	T	0.80065	0.4555	M	0.63208	1.945	0.80722	D	1	D	0.65815	0.995	D	0.71656	0.974	T	0.81665	-0.0830	10	0.66056	D	0.02	-19.7631	12.1502	0.54046	0.0:0.8605:0.0:0.1395	.	677	Q96NW4	ANR27_HUMAN	F	677	ENSP00000304292:V677F	ENSP00000304292:V677F	V	-	1	0	ANKRD27	37800358	0.994000	0.37717	0.961000	0.40146	0.979000	0.70002	2.940000	0.49003	1.414000	0.47017	0.655000	0.94253	GTT	.	.		0.289	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		A	33108518	C	A	33108518	3	1	208	1	0	0	0	0	1	0	0	0	655	565	20	3	1159	3	ANKRD27	19	33108518	Missense_Mutation	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	2173073	33108518	26020465	85	30133										
MAMSTR	284358	hgsc.bcm.edu	37	chr19	49217263	49217263	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ccccggggtatccgcggcacGtggaagaggtggcctgtgag	18	11	0	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr19:49217263G>A	ENST00000318083.6	-	8	826	c.763C>T	c.(763-765)Cgt>Tgt	p.R255C	MAMSTR_ENST00000419611.1_Missense_Mutation_p.R152C|MAMSTR_ENST00000377367.3_Missense_Mutation_p.R87C|MAMSTR_ENST00000594582.1_Missense_Mutation_p.R87C|MAMSTR_ENST00000356751.4_Missense_Mutation_p.R152C			Q6ZN01	MASTR_HUMAN	MEF2 activating motif and SAP domain containing transcriptional regulator	255	Pro-rich.|Transcription activation. {ECO:0000250}.				positive regulation of myotube differentiation (GO:0010831)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)			endometrium(1)|ovary(1)	2						TCCGCGGCACGTGGAAGAGGT	0.697																																					p.R255C		Atlas-SNP	.											.	MAMSTR	36	.	0			c.C763T						.						21	21	21					19																	49217263		2203	4298	6501	SO:0001583	missense	284358	exon8			CGGCACGTGGAAG	AK093389	CCDS12730.1, CCDS46137.1, CCDS74415.1	19q13.33	2009-07-09			ENSG00000176909	ENSG00000176909			26689	protein-coding gene	gene with protein product	"MEF2-activating SAP transcriptional regulator"	610349				16818234	Standard	NM_182574		Approved	MASTR, FLJ36070	uc002pkg.2	Q6ZN01		ENST00000318083.6:c.763C>T	chr19.hg19:g.49217263G>A	ENSP00000324175:p.Arg255Cys	71.0	0.0		99.0	15.0	NM_001130915	B7ZKX4|Q3KQU9|Q8N9Y3	Missense_Mutation	SNP	ENST00000318083.6	hg19	CCDS46137.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.427550	0.43122	.	.	ENSG00000176909	ENST00000318083;ENST00000419611;ENST00000377367;ENST00000356751	.	.	.	4.2	-2.46	0.06461	.	1.173220	0.06373	N	0.713813	T	0.29028	0.0721	L	0.47716	1.5	0.09310	N	1	D	0.63880	0.993	B	0.44315	0.446	T	0.30238	-0.9985	9	0.36615	T	0.2	3.8991	3.9466	0.09350	0.0952:0.4417:0.3008:0.1622	.	255	Q6ZN01	MASTR_HUMAN	C	255;152;87;152	.	ENSP00000324175:R255C	R	-	1	0	MAMSTR	53909075	0.001000	0.12720	0.000000	0.03702	0.025000	0.11179	0.287000	0.18920	-0.255000	0.09486	-0.425000	0.05940	CGT	.	.		0.697	MAMSTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466179.1	NM_182574		A	49217263	G	A	49217263	3	1	208	1	0	0	0	0	1	0	0	0	9218	1145	40	1	496	1	MAMSTR	19	49217263	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	16108745	49217263	9911720	86	30134										
NUCB1	4924	hgsc.bcm.edu	37	chr19	49407702	49407702	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ctgcaggctgccaatgcggaGgacatcaaggtgcggctggg	17	10	1	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr19:49407702G>A	ENST00000405315.4	+	3	568	c.234G>A	c.(232-234)gaG>gaA	p.E78E	NUCB1_ENST00000407032.1_Silent_p.E78E|NUCB1_ENST00000485798.1_Intron|NUCB1_ENST00000263273.5_Silent_p.E78E	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	78						endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		CCAATGCGGAGGACATCAAGG	0.572																																					p.E78E		Atlas-SNP	.											.	NUCB1	44	.	0			c.G234A						.						53	43	46					19																	49407702		2203	4300	6503	SO:0001819	synonymous_variant	4924	exon3			TGCGGAGGACATC	BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"EF-hand domain containing"	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.234G>A	chr19.hg19:g.49407702G>A		68.0	0.0		61.0	24.0	NM_006184	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Silent	SNP	ENST00000405315.4	hg19	CCDS12740.1	.	.	.	.	.	.	.	.	.	.	g	0.336	-0.953283	0.02285	.	.	ENSG00000104805	ENST00000424608	.	.	.	4.23	3.19	0.36642	.	.	.	.	.	T	0.54062	0.1835	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48581	-0.9023	4	.	.	.	.	5.4936	0.16789	0.1059:0.0:0.6976:0.1965	.	.	.	.	K	78	.	.	R	+	2	0	NUCB1	54099514	1.000000	0.71417	0.998000	0.56505	0.013000	0.08279	0.890000	0.28295	0.936000	0.37367	0.283000	0.19423	AGG	.	.		0.572	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184		A	49407702	G	A	49407702	2	1	208	1	0	0	0	0	0	0	0	1	10727	991	35	3		3	NUCB1	19	49407702	Silent	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	190439	49407702	9721281	87	30135										
SIGLEC6	946	hgsc.bcm.edu	37	chr19	52033118	52033118	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	tgggggtggcgttcagggcgGggaagccctggaaccagctc	19	10	1	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr19:52033118G>T	ENST00000425629.3	-	5	1026	c.872C>A	c.(871-873)cCc>cAc	p.P291H	SIGLEC6_ENST00000346477.3_Missense_Mutation_p.P275H|SIGLEC6_ENST00000391797.3_Missense_Mutation_p.P280H|SIGLEC6_ENST00000343300.4_Missense_Mutation_p.P291H|SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000359982.4_Missense_Mutation_p.P302H|SIGLEC6_ENST00000436458.1_Missense_Mutation_p.P239H	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	291	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GTTCAGGGCGGGGAAGCCCTG	0.632																																					p.P302H		Atlas-SNP	.											.	SIGLEC6	142	.	0			c.C905A						.						65	74	71					19																	52033118		2198	4296	6494	SO:0001583	missense	946	exon5			AGGGCGGGGAAGC	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.872C>A	chr19.hg19:g.52033118G>T	ENSP00000401502:p.Pro291His	130.0	0.0		123.0	42.0	NM_001177548	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	hg19	CCDS12834.3	.	.	.	.	.	.	.	.	.	.	G	8.581	0.882386	0.17467	.	.	ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000359982;ENST00000436458;ENST00000343300	T;T;T;T;T	0.66460	1.56;-0.21;-0.21;-0.21;-0.21	3.71	-2.77	0.05877	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.525480	0.04431	N	0.369326	T	0.71962	0.3402	L	0.53249	1.67	0.09310	N	1	P;D;P;B;B;B	0.65815	0.531;0.995;0.659;0.019;0.014;0.069	P;D;P;B;B;B	0.66602	0.482;0.945;0.669;0.049;0.039;0.063	T	0.60826	-0.7186	10	0.45353	T	0.12	.	3.3912	0.07290	0.534:0.0:0.2709:0.1951	.	302;239;280;291;275;291	F8WA78;C9JBE5;O43699-4;O43699-2;O43699-3;O43699	.;.;.;.;.;SIGL6_HUMAN	H	264;275;291;302;239;291	ENSP00000344064:P264H;ENSP00000401502:P291H;ENSP00000353071:P302H;ENSP00000410679:P239H;ENSP00000345907:P291H	ENSP00000345907:P291H	P	-	2	0	SIGLEC6	56724930	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.133000	0.10451	-0.179000	0.10654	-0.351000	0.07748	CCC	.	.		0.632	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245		T	52033118	G	T	52033118	3	4	208	1	0	0	0	0	1	0	0	0	14327	1232	43	3	505	3	SIGLEC6	19	52033118	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10	2625416	52033118	7095865	88	30136										
TSEN34	79042	hgsc.bcm.edu	37	chr19	54695356	54695356	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cgccagaactcgcgcctgggCctcccgctgctgctgatgcc	12	18	0	2			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr19:54695356C>T	ENST00000396383.1	+	2	452	c.141C>T	c.(139-141)ggC>ggT	p.G47G	MBOAT7_ENST00000338624.6_5'Flank|MBOAT7_ENST00000431666.2_5'Flank|TSEN34_ENST00000396388.2_Silent_p.G47G|MBOAT7_ENST00000391754.1_5'Flank|CTD-3093M3.1_ENST00000594382.1_lincRNA|TSEN34_ENST00000302937.4_Silent_p.G47G|TSEN34_ENST00000429671.2_Silent_p.G47G|MBOAT7_ENST00000474910.1_5'Flank|MBOAT7_ENST00000245615.1_5'Flank			Q9BSV6	SEN34_HUMAN	TSEN34 tRNA splicing endonuclease subunit	47					mRNA processing (GO:0006397)|tRNA-type intron splice site recognition and cleavage (GO:0000379)	tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	10	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CGCGCCTGGGCCTCCCGCTGC	0.766																																					p.G47G	Esophageal Squamous(37;841 964 4869 42824)	Atlas-SNP	.											.	TSEN34	17	.	0			c.C141T						.						5	6	6					19																	54695356		1597	3632	5229	SO:0001819	synonymous_variant	79042	exon2			CCTGGGCCTCCCG	AF211970	CCDS42609.1, CCDS74446.1	19q13.4	2013-08-06	2013-08-06	2005-03-12	ENSG00000170892	ENSG00000170892		"tRNA splicing endonuclease subunits"	15506	protein-coding gene	gene with protein product		608754	"leukocyte receptor cluster (LRC) member 5", "tRNA splicing endonuclease 34 homolog (SEN34, S. cerevisiae)", "tRNA splicing endonuclease 34 homolog (S. cerevisiae)"	LENG5		10941842, 15109492	Standard	NM_024075		Approved	SEN34, SEN34L	uc002qdw.3	Q9BSV6	OTTHUMG00000066515	ENST00000396383.1:c.141C>T	chr19.hg19:g.54695356C>T		45.0	0.0		44.0	18.0	NM_024075	A6NNB1|B0V3J1|Q9BVT1|Q9H6H5	Silent	SNP	ENST00000396383.1	hg19	CCDS42609.1																																																																																			.	.		0.766	TSEN34-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142200.1	NM_024075		T	54695356	C	T	54695356	2	4	208	1	0	0	0	0	0	0	0	1	16628	726	26	3		3	TSEN34	19	54695356	Silent	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	2662238	54695356	4433627	89	30137										
LILRA1	11024	hgsc.bcm.edu	37	chr19	55106839	55106839	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ccccatgtgtggtctctaccCagtgatctcctggagctcct	9	15	2	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr19:55106839C>A	ENST00000251372.3	+	5	815	c.633C>A	c.(631-633)ccC>ccA	p.P211P	LILRB1_ENST00000396321.2_Intron|LILRA1_ENST00000453777.1_Silent_p.P211P|LILRB1_ENST00000418536.2_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000448689.1_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	211	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		GGTCTCTACCCAGTGATCTCC	0.597																																					p.P211P		Atlas-SNP	.											.	LILRA1	105	.	0			c.C633A						.						138	147	144					19																	55106839		2203	4300	6503	SO:0001819	synonymous_variant	11024	exon5			TCTACCCAGTGAT	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.633C>A	chr19.hg19:g.55106839C>A		108.0	0.0		104.0	41.0	NM_006863	O75018|Q3MJA6	Silent	SNP	ENST00000251372.3	hg19	CCDS12901.1																																																																																			.	.		0.597	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863		A	55106839	C	A	55106839	2	1	208	1	0	0	0	0	0	0	0	1	8793	581	21	3		3	LILRA1	19	55106839	Silent	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	411483	55106839	4022144	90	30138										
TTPAL	79183	hgsc.bcm.edu	37	chr20	43108747	43108747	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ggctatgtgtgctcactgacAgaagacctggtcaccaaagc	11	11	2	3			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr20:43108747A>T	ENST00000372904.3	+	3	251	c.108A>T	c.(106-108)acA>acT	p.T36T	TTPAL_ENST00000262605.4_Silent_p.T36T|TTPAL_ENST00000372906.2_Silent_p.T36T	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	36						intracellular (GO:0005622)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|skin(5)	18						GCTCACTGACAGAAGACCTGG	0.562																																					p.T36T		Atlas-SNP	.											.	TTPAL	31	.	0			c.A108T						.						78	68	72					20																	43108747		2203	4300	6503	SO:0001819	synonymous_variant	79183	exon2			ACTGACAGAAGAC	BC003071	CCDS13332.2	20q13.12	2008-06-23	2008-06-23	2008-06-23	ENSG00000124120	ENSG00000124120			16114	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 121"	C20orf121			Standard	NM_024331		Approved	dJ179M20.3	uc002xmd.2	Q9BTX7	OTTHUMG00000032536	ENST00000372904.3:c.108A>T	chr20.hg19:g.43108747A>T		179.0	0.0		155.0	58.0	NM_001039199	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Silent	SNP	ENST00000372904.3	hg19	CCDS13332.2																																																																																			.	.		0.562	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331		T	43108747	A	T	43108747	2	4	208	1	0	0	0	0	0	0	0	1	16752	175	7	4		4	TTPAL	20	43108747	Silent	SNP	A	TCGA-DD-AAE2-01A-11D-A40R-10		43108747	19916773	91	30139										
KRTAP13-2	337959	hgsc.bcm.edu	37	chr21	31744028	31744028	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	caagttgatctgcagaaggtTgatccataggctggtctgta	12	7	2	3			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr21:31744028T>A	ENST00000399889.2	-	1	529	c.504A>T	c.(502-504)tcA>tcT	p.S168S		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	168						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						TGCAGAAGGTTGATCCATAGG	0.493																																					p.S168S		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.A504T						.						77	73	74					21																	31744028		2203	4300	6503	SO:0001819	synonymous_variant	337959	exon1			GAAGGTTGATCCA	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"Keratin associated proteins"	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.504A>T	chr21.hg19:g.31744028T>A		157.0	0.0		145.0	55.0	NM_181621		Silent	SNP	ENST00000399889.2	hg19	CCDS13589.1																																																																																			.	.		0.493	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1			A	31744028	T	A	31744028	2	1	208	1	0	0	0	0	0	0	0	1	8532	1799	63	4		4	KRTAP13-2	21	31744028	Silent	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10		31744028	16385867	92	30140										
PISD	23761	hgsc.bcm.edu	37	chr22	32019822	32019822	+	Intron	DEL	G	G	-													0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	cctccgcctcagggccagctGggggaagtgcaacctgcagg							TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr22:32019822delG	ENST00000439502.2	-	4	545				PISD_ENST00000397500.1_Frame_Shift_Del_p.Q23fs|PISD_ENST00000382151.2_Frame_Shift_Del_p.Q23fs|PISD_ENST00000478893.1_5'UTR|PISD_ENST00000336566.4_Intron|PISD_ENST00000266095.5_Frame_Shift_Del_p.Q23fs			Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase						glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylserine decarboxylase activity (GO:0004609)			central_nervous_system(3)|endometrium(2)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12					Phosphatidylserine(DB00144)	AGGGCCAGCTGGGGGAAGTGC	0.672																																					p.Q23fs		Atlas-INDEL	.											.	PISD	53	.	0			c.68delA						.						52	42	46					22																	32019822		2203	4300	6503	SO:0001627	intron_variant	23761	exon4			.		CCDS13899.1	22q12.2	2011-01-25			ENSG00000241878	ENSG00000241878	4.1.1.65		8999	protein-coding gene	gene with protein product		612770				10591208	Standard	NM_014338		Approved	dJ858B16.2, PSDC	uc003alk.2	Q9UG56	OTTHUMG00000030252	ENST00000439502.2:c.322-1951C>-	chr22.hg19:g.32019822delG		145.0	0.0		128.0	49.0	NM_014338	B1AKM7|O43207|O95535|Q6IC28|Q96GQ2|Q9UGA9	Frame_Shift_Del	DEL	ENST00000439502.2	hg19																																																																																				.	.		0.672	PISD-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000075106.4			-	32019822	G	-	32019822	6	5	208	0	1	1	0	1	0	0	0	0	11955	1357	47	0		0	PISD	22	32019822	Intron	DEL	G	TCGA-DD-AAE2-01A-11D-A40R-10		32019822	19284744	93	30141										
LDOC1L	84247	hgsc.bcm.edu	37	chr22	44892922	44892922	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	acttgtaggttctccgcaacTctgccaggaacccctgatag	9	13	2	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr22:44892922T>C	ENST00000341255.3	-	2	1024	c.515A>G	c.(514-516)gAg>gGg	p.E172G		NM_032287.2	NP_115663.2	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	172										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(3)|prostate(2)	11		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)		TCTCCGCAACTCTGCCAGGAA	0.592																																					p.E172G		Atlas-SNP	.											.	LDOC1L	24	.	0			c.A515G						.						41	43	42					22																	44892922		2203	4300	6503	SO:0001583	missense	84247	exon2			CGCAACTCTGCCA	CR456439	CCDS33662.1	22q13.3	2006-09-06			ENSG00000188636	ENSG00000188636			13343	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_032287		Approved	dJ1033E15.2, DKFZp761O17121, Mart6, Mar6	uc003beu.1	Q6ICC9	OTTHUMG00000150465	ENST00000341255.3:c.515A>G	chr22.hg19:g.44892922T>C	ENSP00000340434:p.Glu172Gly	57.0	0.0		69.0	33.0	NM_032287	Q6ZTR1	Missense_Mutation	SNP	ENST00000341255.3	hg19	CCDS33662.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.962990	0.74016	.	.	ENSG00000188636	ENST00000341255	T	0.22336	1.96	3.2	3.2	0.36748	.	0.387478	0.19383	N	0.115602	T	0.32346	0.0826	L	0.41492	1.28	0.31740	N	0.635906	D	0.76494	0.999	D	0.75484	0.986	T	0.21008	-1.0258	10	0.54805	T	0.06	-16.6304	8.1706	0.31252	0.0:0.0:0.0:1.0	.	172	Q6ICC9	LDOCL_HUMAN	G	172	ENSP00000340434:E172G	ENSP00000340434:E172G	E	-	2	0	LDOC1L	43271586	0.597000	0.26874	0.988000	0.46212	0.997000	0.91878	1.811000	0.38942	1.717000	0.51406	0.482000	0.46254	GAG	.	.		0.592	LDOC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318222.1	NM_032287		C	44892922	T	C	44892922	3	2	208	1	0	0	0	0	1	0	0	0	8719	1551	54	2	208	2	LDOC1L	22	44892922	Missense_Mutation	SNP	T	TCGA-DD-AAE2-01A-11D-A40R-10	12873100	44892922	6411644	94	30142										
ADM2	79924	hgsc.bcm.edu	37	chr22	50921204	50921204	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ggacccaagcccagctcctgCgagtgggctgtgtgctgggc	16	13	0	0			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chr22:50921204C>A	ENST00000395738.2	+	2	611	c.319C>A	c.(319-321)Cga>Aga	p.R107R	ADM2_ENST00000362068.2_Nonsense_Mutation_p.C23*|ADM2_ENST00000395737.1_Silent_p.R107R	NM_001253845.1|NM_024866.5	NP_001240774.1|NP_079142.2	Q7Z4H4	ADM2_HUMAN	adrenomedullin 2	107					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|digestion (GO:0007586)|feeding behavior (GO:0007631)|negative regulation of blood pressure (GO:0045776)|positive regulation of angiogenesis (GO:0045766)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)	extracellular region (GO:0005576)	protein complex binding (GO:0032403)			breast(1)|kidney(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCAGCTCCTGCGAGTGGGCTG	0.692																																					p.R107R		Atlas-SNP	.											.	ADM2	15	.	0			c.C319A						.						8	10	10					22																	50921204		2061	4090	6151	SO:0001819	synonymous_variant	79924	exon2			CTCCTGCGAGTGG	AF529213	CCDS33682.1	22q13.33	2013-02-25			ENSG00000128165	ENSG00000128165		"Endogenous ligands"	28898	protein-coding gene	gene with protein product		608682				14706825	Standard	NM_024866		Approved	AM2, FLJ21135	uc003blj.3	Q7Z4H4	OTTHUMG00000150202	ENST00000395738.2:c.319C>A	chr22.hg19:g.50921204C>A		108.0	0.0		125.0	50.0	NM_024866	Q3LFQ0	Silent	SNP	ENST00000395738.2	hg19	CCDS33682.1	.	.	.	.	.	.	.	.	.	.	C	39	7.415909	0.98269	.	.	ENSG00000128165	ENST00000362068	.	.	.	4.62	0.634	0.17718	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.5448	0.56193	0.4295:0.5705:0.0:0.0	.	.	.	.	X	23	.	ENSP00000354955:C23X	C	+	3	2	ADM2	49268070	1.000000	0.71417	0.996000	0.52242	0.769000	0.43574	1.046000	0.30354	0.340000	0.23745	0.448000	0.29417	TGC	.	.		0.692	ADM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316816.1	NM_024866		A	50921204	C	A	50921204	2	1	208	1	0	0	0	0	0	0	0	1	322	760	27	1		1	ADM2	22	50921204	Silent	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	6028282	50921204	383362	95	30143										
MAGEB2	4113	hgsc.bcm.edu	37	chrX	30237136	30237136	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	ttgttggcaaaaggttcaggGagcacttccctgagatcctc	11	10	1	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chrX:30237136G>C	ENST00000378988.4	+	2	540	c.439G>C	c.(439-441)Gag>Cag	p.E147Q		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	147	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						AAGGTTCAGGGAGCACTTCCC	0.458																																					p.E147Q		Atlas-SNP	.											.	MAGEB2	133	.	0			c.G439C						.						62	58	59					X																	30237136		2202	4300	6502	SO:0001583	missense	4113	exon2			TTCAGGGAGCACT	AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"DSS/AHC critical interval MAGE superfamily 6", "melanoma-associated antigen B2", "cancer/testis antigen family 3, member 2"	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.439G>C	chrX.hg19:g.30237136G>C	ENSP00000368273:p.Glu147Gln	105.0	0.0		91.0	76.0	NM_002364	O75860	Missense_Mutation	SNP	ENST00000378988.4	hg19	CCDS14219.1	.	.	.	.	.	.	.	.	.	.	G	9.964	1.223686	0.22457	.	.	ENSG00000099399	ENST00000378988	T	0.04917	3.53	3.27	-0.661	0.11417	.	0.531761	0.19970	N	0.102007	T	0.05593	0.0147	M	0.66560	2.04	0.09310	N	1	B	0.33637	0.42	B	0.29077	0.098	T	0.33445	-0.9868	10	0.25106	T	0.35	.	3.506	0.07691	0.3619:0.1972:0.441:0.0	.	147	O15479	MAGB2_HUMAN	Q	147	ENSP00000368273:E147Q	ENSP00000368273:E147Q	E	+	1	0	MAGEB2	30147057	0.000000	0.05858	0.000000	0.03702	0.527000	0.34593	-0.087000	0.11215	-0.284000	0.09102	0.436000	0.28706	GAG	.	.		0.458	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364		C	30237136	G	C	30237136	3	2	208	1	0	0	0	0	1	0	0	0	9185	1175	41	4	441	4	MAGEB2	23	30237136	Missense_Mutation	SNP	G	TCGA-DD-AAE2-01A-11D-A40R-10		30237136	125033424	96	30144										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53672263	53672263	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0531914893617021	5	1	1.07974756167527	0	1.39967276513461	0.0256410256410257	0.304738562091504	0	actcttcacccaagactcacCtctgccaaatgttgtagccg	6	15	4	1			TCGA-DD-AAE2-01A-11D-A40R-10	TCGA-DD-AAE2-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66c712a0-e797-4c8f-9f9b-ff7706b87d78	318f2f81-2c67-4132-aeb5-4179b9cc568a	g.chrX:53672263C>T	ENST00000342160.3	-	6	961	c.504G>A	c.(502-504)gaG>gaA	p.E168E	HUWE1_ENST00000262854.6_Splice_Site_p.E168E|HUWE1_ENST00000218328.8_Splice_Site_p.E168E			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	168					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CAAGACTCACCTCTGCCAAAT	0.423																																					p.E168E		Atlas-SNP	.											.	HUWE1	724	.	0			c.G504A						.						65	59	61					X																	53672263		2203	4300	6503	SO:0001630	splice_region_variant	10075	exon7			ACTCACCTCTGCC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.504+1G>A	chrX.hg19:g.53672263C>T		47.0	0.0		37.0	29.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1																																																																																			.	.		0.423	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	Silent	T	53672263	C	T	53672263	5	4	208	1	0	0	0	0	0	0	1	0	7470	695	24	3	12932	3	HUWE1	23	53672263	Splice_Site	SNP	C	TCGA-DD-AAE2-01A-11D-A40R-10	23435127	53672263	101598297	97	30145										
FAM132A	388581	hgsc.bcm.edu	37	chr1	1179473	1179473	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ccagaagccctgagaaccggCgctccgtggcctctgtgggg	15	14	1	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:1179473C>T	ENST00000330388.2	-	4	423	c.392G>A	c.(391-393)cGc>cAc	p.R131H		NM_001014980.2	NP_001014980.1	Q5T7M4	ADIPL_HUMAN	family with sequence similarity 132, member A	131					negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of glucose import (GO:0046324)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|lung(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TGAGAACCGGCGCTCCGTGGC	0.736																																					p.R131H		Atlas-SNP	.											.	FAM132A	12	.	0			c.G392A						.						12	15	14					1																	1179473		2158	4267	6425	SO:0001583	missense	388581	exon4			AACCGGCGCTCCG	BC089443	CCDS30554.1	1p36.33	2012-03-26	2007-03-27	2007-03-27	ENSG00000184163	ENSG00000184163			32308	protein-coding gene	gene with protein product	"adipolin", "adipose-derived insulin-sensitizing factor"		"C1q domain containing 2"	C1QDC2		21849507	Standard	NM_001014980		Approved	MGC105127, C1QTNF12, CTRP12	uc001adl.2	Q5T7M4	OTTHUMG00000001412	ENST00000330388.2:c.392G>A	chr1.hg19:g.1179473C>T	ENSP00000329137:p.Arg131His	92.0	0.0		90.0	27.0	NM_001014980	Q5EBL5	Missense_Mutation	SNP	ENST00000330388.2	hg19	CCDS30554.1	.	.	.	.	.	.	.	.	.	.	c	11.83	1.756571	0.31137	.	.	ENSG00000184163	ENST00000330388	T	0.47177	0.85	3.94	-4.3	0.03710	.	0.218660	0.34676	N	0.003769	T	0.24624	0.0597	L	0.28115	0.83	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.04723	-1.0931	10	0.33141	T	0.24	.	5.2556	0.15546	0.1388:0.4392:0.0:0.422	.	131	Q5T7M4	F132A_HUMAN	H	131	ENSP00000329137:R131H	ENSP00000329137:R131H	R	-	2	0	FAM132A	1169336	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.553000	0.06012	-1.066000	0.03164	-0.635000	0.03985	CGC	.	.		0.736	FAM132A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004080.4	XM_371208		T	1179473	C	T	1179473	3	4	209	1	0	0	0	0	1	0	0	0	5447	768	27	1	536	1	FAM132A	1	1179473	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10		1179473	248071148	1	30146										
SPSB1	80176	hgsc.bcm.edu	37	chr1	9416228	9416228	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tatcaggggcaaagtcgggtAtacccgtgggctgcacgtgt	15	9	1	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:9416228A>G	ENST00000328089.6	+	2	619	c.278A>G	c.(277-279)tAt>tGt	p.Y93C	SPSB1_ENST00000357898.3_Missense_Mutation_p.Y93C|SPSB1_ENST00000377399.2_Missense_Mutation_p.Y93C	NM_025106.3	NP_079382.2	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box containing 1	93	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(2)|lung(5)|prostate(2)	13	all_lung(157;0.194)	all_epithelial(116;4.38e-15)|all_lung(118;0.000156)|Lung NSC(185;0.000446)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.72e-07)|COAD - Colon adenocarcinoma(227;9.12e-05)|Kidney(185;0.000296)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00193)|BRCA - Breast invasive adenocarcinoma(304;0.00202)|READ - Rectum adenocarcinoma(331;0.0419)		AAAGTCGGGTATACCCGTGGG	0.637																																					p.Y93C		Atlas-SNP	.											.	SPSB1	22	.	0			c.A278G						.						118	122	121					1																	9416228		2203	4300	6503	SO:0001583	missense	80176	exon2			TCGGGTATACCCG		CCDS102.1	1p36.22	2008-02-05			ENSG00000171621	ENSG00000171621			30628	protein-coding gene	gene with protein product		611657				15713673, 12076535	Standard	NM_025106		Approved	SSB-1	uc010oae.2	Q96BD6	OTTHUMG00000001279	ENST00000328089.6:c.278A>G	chr1.hg19:g.9416228A>G	ENSP00000330221:p.Tyr93Cys	94.0	0.0		81.0	24.0	NM_025106	A2A275|Q59FA1|Q5TIH9|Q9BRY9|Q9H6C5	Missense_Mutation	SNP	ENST00000328089.6	hg19	CCDS102.1	.	.	.	.	.	.	.	.	.	.	A	19.89	3.911203	0.72983	.	.	ENSG00000171621	ENST00000328089;ENST00000450402;ENST00000357898;ENST00000377399	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.22	5.22	0.72569	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.000000	0.85682	D	0.000000	T	0.69333	0.3099	M	0.90145	3.09	0.80722	D	1	D	0.89917	1.0	D	0.68192	0.956	T	0.76926	-0.2778	10	0.72032	D	0.01	-6.0998	14.2914	0.66281	1.0:0.0:0.0:0.0	.	93	Q96BD6	SPSB1_HUMAN	C	93	ENSP00000330221:Y93C;ENSP00000409235:Y93C;ENSP00000350573:Y93C;ENSP00000366616:Y93C	ENSP00000330221:Y93C	Y	+	2	0	SPSB1	9338815	1.000000	0.71417	0.998000	0.56505	0.865000	0.49528	7.263000	0.78421	1.966000	0.57179	0.533000	0.62120	TAT	.	.		0.637	SPSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003727.2	NM_025106		G	9416228	A	G	9416228	3	3	209	1	0	0	0	0	1	0	0	0	15127	449	16	2	280	2	SPSB1	1	9416228	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	8236755	9416228	239834393	2	30147										
UBE4B	10277	hgsc.bcm.edu	37	chr1	10190648	10190648	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cttacttaggggctttctttAgcttctcagtctttgcagaa	8	9	3	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:10190648A>T	ENST00000253251.8	+	12	2238	c.1399A>T	c.(1399-1401)Agc>Tgc	p.S467C	UBE4B_ENST00000343090.6_Missense_Mutation_p.S596C|UBE4B_ENST00000475795.1_3'UTR|UBE4B_ENST00000377157.3_Missense_Mutation_p.S351C					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GGCTTTCTTTAGCTTCTCAGT	0.448																																					p.S596C		Atlas-SNP	.											.	UBE4B	233	.	0			c.A1786T						.						163	161	162					1																	10190648		2203	4300	6503	SO:0001583	missense	10277	exon13			TTCTTTAGCTTCT	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.1399A>T	chr1.hg19:g.10190648A>T	ENSP00000253251:p.Ser467Cys	102.0	0.0		74.0	20.0	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.810377	0.90707	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.52526	0.66;0.66;0.66	5.93	5.93	0.95920	Ubiquitin conjugation factor E4, core (1);	0.000000	0.85682	D	0.000000	T	0.69205	0.3085	M	0.79258	2.445	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.68943	0.961;0.935	T	0.71593	-0.4546	10	0.52906	T	0.07	-22.247	16.3943	0.83563	1.0:0.0:0.0:0.0	.	596;467	O95155;O95155-2	UBE4B_HUMAN;.	C	467;351;596	ENSP00000253251:S467C;ENSP00000366362:S351C;ENSP00000343001:S596C	ENSP00000253251:S467C	S	+	1	0	UBE4B	10113235	1.000000	0.71417	0.946000	0.38457	0.960000	0.62799	6.108000	0.71522	2.281000	0.76405	0.533000	0.62120	AGC	.	.		0.448	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		T	10190648	A	T	10190648	3	4	209	1	0	0	0	0	1	0	0	0	16898	420	15	4	1836	4	UBE4B	1	10190648	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	774420	10190648	239059973	3	30148										
ERMAP	114625	hgsc.bcm.edu	37	chr1	43300793	43300793	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	acttctcatcatggtgtgccTttgccttatctggaagcaaa	8	10	3	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:43300793T>G	ENST00000372517.2	+	5	762	c.518T>G	c.(517-519)cTt>cGt	p.L173R	ERMAP_ENST00000487556.1_3'UTR|RP11-342M1.3_ENST00000414798.1_RNA|ERMAP_ENST00000328249.3_Missense_Mutation_p.L83R|RP11-342M1.3_ENST00000416809.2_RNA|ERMAP_ENST00000372514.3_Missense_Mutation_p.L173R	NM_001017922.1	NP_001017922.1	Q96PL5	ERMAP_HUMAN	erythroblast membrane-associated protein (Scianna blood group)	173			Missing (in Sc-3 allele).			cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ATGGTGTGCCTTTGCCTTATC	0.532																																					p.L173R		Atlas-SNP	.											.	ERMAP	30	.	0			c.T518G						.						157	122	134					1																	43300793		2203	4300	6503	SO:0001583	missense	114625	exon5			TGTGCCTTTGCCT	AF311284	CCDS475.1	1p34	2014-07-19	2006-02-23		ENSG00000164010	ENSG00000164010		"Blood group antigens", "Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	15743	protein-coding gene	gene with protein product		609017	"Radin blood group", "Scianna blood group", "erythroblast membrane-associated protein", "erythroblast membrane-associated protein (RD and SC blood groups)"	RD, SC		11549310	Standard	XM_005270415		Approved	BTN5	uc001cie.1	Q96PL5	OTTHUMG00000007619	ENST00000372517.2:c.518T>G	chr1.hg19:g.43300793T>G	ENSP00000361595:p.Leu173Arg	125.0	0.0		79.0	23.0	NM_001017922	D3DPW8|Q5VV53|Q6DUE0|Q7Z3X0|Q8NCV8|Q8NCW2|Q8NCW3|Q96PL6	Missense_Mutation	SNP	ENST00000372517.2	hg19	CCDS475.1	.	.	.	.	.	.	.	.	.	.	T	8.470	0.857328	0.17106	.	.	ENSG00000164010	ENST00000372517;ENST00000372514;ENST00000328249	T;T;T	0.57107	0.66;0.66;0.42	5.47	3.03	0.35002	.	0.753572	0.11833	N	0.525035	T	0.51890	0.1701	L	0.45352	1.415	0.09310	N	1	D;P	0.61697	0.99;0.761	P;B	0.53649	0.731;0.276	T	0.37103	-0.9720	10	0.49607	T	0.09	.	4.938	0.13950	0.0:0.0947:0.1875:0.7178	.	234;173	B7Z3C6;Q96PL5	.;ERMAP_HUMAN	R	173;173;83	ENSP00000361595:L173R;ENSP00000361592:L173R;ENSP00000332439:L83R	ENSP00000332439:L83R	L	+	2	0	ERMAP	43073380	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.749000	0.26320	0.914000	0.36822	0.482000	0.46254	CTT	.	.		0.532	ERMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020180.1	NM_018538		G	43300793	T	G	43300793	3	3	209	1	0	0	0	0	1	0	0	0	5236	1609	56	5	528	5	ERMAP	1	43300793	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	33110145	43300793	205949828	4	30149										
SLC1A7	6512	hgsc.bcm.edu	37	chr1	53580429	53580429	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ggtgtgggtggcaatagttaCcggatgaggtccaacagggc	17	7	0	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:53580429C>A	ENST00000371494.4	-	3	559		c.e3+1		SLC1A7_ENST00000371491.4_Splice_Site|RP11-334A14.8_ENST00000439621.1_RNA	NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7						dicarboxylic acid transport (GO:0006835)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Colorectal(1306;0.234)		GCAATAGTTACCGGATGAGGT	0.652																																					.	NSCLC(128;80 1811 21245 38490 51715)	Atlas-SNP	.											.	SLC1A7	65	.	0			c.431+1G>T						.						124	105	111					1																	53580429		2203	4300	6503	SO:0001630	splice_region_variant	6512	exon4			TAGTTACCGGATG	U76362	CCDS574.1, CCDS72796.1, CCDS72797.1, CCDS72798.1	1p32.3	2013-05-22			ENSG00000162383	ENSG00000162383		"Solute carriers"	10945	protein-coding gene	gene with protein product		604471				9108121	Standard	NM_001287597		Approved	EAAT5	uc001cuy.3	O00341	OTTHUMG00000008937	ENST00000371494.4:c.431+1G>T	chr1.hg19:g.53580429C>A		79.0	0.0		61.0	38.0	NM_006671	Q5VVZ0|Q969Z8|Q9BW45	Splice_Site	SNP	ENST00000371494.4	hg19	CCDS574.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.475421	0.63737	.	.	ENSG00000162383	ENST00000371494;ENST00000371491	.	.	.	5.42	4.51	0.55191	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2111	0.65764	0.0:0.9282:0.0:0.0718	.	.	.	.	.	-1	.	.	.	-	.	.	SLC1A7	53353017	1.000000	0.71417	0.999000	0.59377	0.776000	0.43924	5.782000	0.68973	1.303000	0.44873	0.655000	0.94253	.	.	.		0.652	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1	NM_006671	Intron	A	53580429	C	A	53580429	5	1	209	1	0	0	0	0	0	0	1	0	14452	521	18	3	1286	3	SLC1A7	1	53580429	Splice_Site	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	10279636	53580429	195670192	5	30150										
PALMD	54873	hgsc.bcm.edu	37	chr1	100155039	100155039	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ttccctgcctccagacataaAtgatacagaaccggtgacaa	7	12	0	4			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:100155039A>G	ENST00000263174.4	+	7	1598	c.1223A>G	c.(1222-1224)aAt>aGt	p.N408S	PALMD_ENST00000605497.1_Missense_Mutation_p.N408S	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	408					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		CCAGACATAAATGATACAGAA	0.418																																					p.N408S		Atlas-SNP	.											.	PALMD	64	.	0			c.A1223G						.						65	58	60					1																	100155039		2203	4299	6502	SO:0001583	missense	54873	exon7			ACATAAATGATAC	AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.1223A>G	chr1.hg19:g.100155039A>G	ENSP00000263174:p.Asn408Ser	128.0	0.0		75.0	15.0	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Missense_Mutation	SNP	ENST00000263174.4	hg19	CCDS758.1	.	.	.	.	.	.	.	.	.	.	A	9.477	1.097101	0.20552	.	.	ENSG00000099260	ENST00000263174	T	0.15372	2.43	5.66	0.352	0.16051	.	0.896444	0.09773	N	0.757662	T	0.01489	0.0048	N	0.02916	-0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.49062	-0.8978	10	0.12103	T	0.63	-0.0299	6.4985	0.22155	0.6094:0.2575:0.133:0.0	.	408;328	Q9NP74;Q9NP74-2	PALMD_HUMAN;.	S	408	ENSP00000263174:N408S	ENSP00000263174:N408S	N	+	2	0	PALMD	99927627	0.934000	0.31675	0.002000	0.10522	0.684000	0.39900	1.986000	0.40677	0.086000	0.17137	0.460000	0.39030	AAT	.	.		0.418	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734		G	100155039	A	G	100155039	3	3	209	1	0	0	0	0	1	0	0	0	11420	101	4	2	1249	2	PALMD	1	100155039	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	46574610	100155039	149095582	6	30151										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103385871	103385871	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tcactaacatatttacctttTctccaacaccaccaactgaa	1	14	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:103385871T>A	ENST00000370096.3	-	49	4070	c.3758A>T	c.(3757-3759)gAa>gTa	p.E1253V	COL11A1_ENST00000512756.1_Missense_Mutation_p.E1137V|COL11A1_ENST00000353414.4_Missense_Mutation_p.E1214V|COL11A1_ENST00000358392.2_Missense_Mutation_p.E1265V	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1253	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		ATTTACCTTTTCTCCAACACC	0.363																																					p.E1265V		Atlas-SNP	.											.	COL11A1	972	.	0			c.A3794T						.						176	183	181					1																	103385871		2203	4300	6503	SO:0001583	missense	1301	exon49			ACCTTTTCTCCAA	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3758A>T	chr1.hg19:g.103385871T>A	ENSP00000359114:p.Glu1253Val	71.0	0.0		56.0	13.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.964729	0.74131	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	6.06	6.06	0.98353	.	0.106801	0.64402	D	0.000006	D	0.87888	0.6291	N	0.21373	0.66	0.58432	D	0.999999	B;P;B;B;B	0.41131	0.18;0.739;0.441;0.314;0.275	B;P;B;B;B	0.45232	0.147;0.474;0.326;0.206;0.194	D	0.90128	0.4204	10	0.56958	D	0.05	.	15.8056	0.78506	0.0:0.0:0.0:1.0	.	1137;1214;1265;1253;473	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	V	1253;1265;1214;473;1137	ENSP00000359114:E1253V;ENSP00000351163:E1265V;ENSP00000302551:E1214V;ENSP00000426533:E1137V	ENSP00000302551:E1214V	E	-	2	0	COL11A1	103158459	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.293000	0.78740	2.323000	0.78572	0.528000	0.53228	GAA	.	.		0.363	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103385871	T	A	103385871	3	1	209	1	0	0	0	0	1	0	0	0	3669	1783	62	4	1738	4	COL11A1	1	103385871	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	3230832	103385871	145864750	7	30152										
GSTM5	2949	hgsc.bcm.edu	37	chr1	110256136	110256136	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tgattgatggggctcacaagAtcacccagagcaatgccatc	10	11	2	4	rs146232109	byFrequency	TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:110256136A>C	ENST00000256593.3	+	4	266	c.208A>C	c.(208-210)Atc>Ctc	p.I70L	GSTM5_ENST00000369812.5_Missense_Mutation_p.I89L|GSTM5_ENST00000369813.1_Missense_Mutation_p.I29L	NM_000851.3	NP_000842.2	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5	70	GST N-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)			NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	GGCTCACAAGATCACCCAGAG	0.587																																					p.I70L		Atlas-SNP	.											.	GSTM5	89	.	0			c.A208C						.						336	256	283					1																	110256136		2203	4300	6503	SO:0001583	missense	2949	exon4			CACAAGATCACCC	L02321	CCDS811.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134201	ENSG00000134201	2.5.1.18	"Glutathione S-transferases / Soluble"	4637	protein-coding gene	gene with protein product		138385	"glutathione S-transferase M5"			8473333	Standard	NM_000851		Approved		uc001dyn.3	P46439	OTTHUMG00000011644	ENST00000256593.3:c.208A>C	chr1.hg19:g.110256136A>C	ENSP00000256593:p.Ile70Leu	177.0	0.0		175.0	7.0	NM_000851	A8K0V8|Q6PD78	Missense_Mutation	SNP	ENST00000256593.3	hg19	CCDS811.1	.	.	.	.	.	.	.	.	.	.	A	2.484	-0.318884	0.05386	.	.	ENSG00000134201	ENST00000256593;ENST00000369813;ENST00000369812	T;T;T	0.31247	1.5;3.57;1.5	4.33	-5.35	0.02697	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.231648	0.31922	N	0.006858	T	0.03348	0.0097	N	0.03253	-0.375	0.31558	N	0.657878	B;B	0.09022	0.002;0.0	B;B	0.33196	0.159;0.038	T	0.32134	-0.9918	10	0.05620	T	0.96	.	11.6882	0.51499	0.2101:0.7058:0.0842:0.0	.	29;70	Q5T8Q9;P46439	.;GSTM5_HUMAN	L	70;29;89	ENSP00000256593:I70L;ENSP00000358828:I29L;ENSP00000358827:I89L	ENSP00000256593:I70L	I	+	1	0	GSTM5	110057659	0.648000	0.27313	0.577000	0.28562	0.531000	0.34715	-0.185000	0.09684	-0.664000	0.05324	0.413000	0.27773	ATC	.	A|1.000;G|0.000		0.587	GSTM5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032200.1	NM_000851		C	110256136	A	C	110256136	3	2	209	1	0	0	0	0	1	0	0	0	6850	333	12	5	222	5	GSTM5	1	110256136	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	6870265	110256136	138994485	8	30153										
TXNIP	10628	hgsc.bcm.edu	37	chr1	145439791	145439791	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gacacaggcctctgggaacaTccttcaaaggaaaatatggg	11	9	2	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:145439791T>A	ENST00000369317.4	+	3	671	c.337T>A	c.(337-339)Tcc>Acc	p.S113T	TXNIP_ENST00000475171.1_Intron	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	113					cell cycle (GO:0007049)|cellular response to tumor cell (GO:0071228)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|negative regulation of cell division (GO:0051782)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|protein import into nucleus (GO:0006606)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TCTGGGAACATCCTTCAAAGG	0.413																																					p.S113T		Atlas-SNP	.											.	TXNIP	51	.	0			c.T337A						.						90	93	92					1																	145439791		2203	4300	6503	SO:0001583	missense	10628	exon3			GGAACATCCTTCA	S73591	CCDS72876.1	1q11	2008-07-18			ENSG00000117289	ENSG00000265972			16952	protein-coding gene	gene with protein product	"upregulated by 1,25-dihydroxyvitamin D-3", "thioredoxin binding protein 2"	606599				8086474	Standard	NM_006472		Approved	VDUP1, EST01027, HHCPA78, THIF	uc001enn.4	Q9H3M7	OTTHUMG00000013755	ENST00000369317.4:c.337T>A	chr1.hg19:g.145439791T>A	ENSP00000358323:p.Ser113Thr	128.0	0.0		130.0	30.0	NM_006472	B4E3D3|Q16226|Q6PML0|Q9BXG9	Missense_Mutation	SNP	ENST00000369317.4	hg19	CCDS913.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.494485	0.44352	.	.	ENSG00000117289	ENST00000369317;ENST00000425134	T;T	0.42513	0.97;0.97	4.84	4.84	0.62591	Immunoglobulin E-set (1);Arrestin-like, N-terminal (1);	0.118609	0.64402	D	0.000016	T	0.36166	0.0957	M	0.77712	2.385	0.52099	D	0.999947	P;B	0.34826	0.471;0.181	B;B	0.39465	0.3;0.047	T	0.37033	-0.9723	10	0.44086	T	0.13	1.8577	12.6817	0.56926	0.0:0.0:0.0:1.0	.	58;113	B4E3D3;Q9H3M7	.;TXNIP_HUMAN	T	113;58	ENSP00000358323:S113T;ENSP00000396322:S58T	ENSP00000358323:S113T	S	+	1	0	TXNIP	144151148	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	2.923000	0.48868	2.168000	0.68352	0.456000	0.33151	TCC	.	.		0.413	TXNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038547.1	NM_006472		A	145439791	T	A	145439791	3	1	209	1	0	0	0	0	1	0	0	0	16818	1435	50	4	347	4	TXNIP	1	145439791	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	35183655	145439791	103810830	9	30154										
C1orf55	163859	hgsc.bcm.edu	37	chr1	226180658	226180658	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gacaagcttctcgattggttGtcttctcaatctgagcacca	8	11	4	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:226180658G>A	ENST00000272091.7	-	3	302	c.284C>T	c.(283-285)aCa>aTa	p.T95I		NM_152608.3	NP_689821.3	Q6IQ49	SDE2_HUMAN	SDE2 telomere maintenance homolog (S. pombe)	95																	TCGATTGGTTGTCTTCTCAAT	0.428																																					p.T95I		Atlas-SNP	.											.	.	.	.	0			c.C284T						.						90	80	83					1																	226180658		1867	4108	5975	SO:0001583	missense	163859	exon3			TTGGTTGTCTTCT	BC071563	CCDS41473.1	1q42.12	2012-06-26	2012-06-26	2012-06-26	ENSG00000143751	ENSG00000143751			26643	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 55"	C1orf55		21333630	Standard	NM_152608		Approved	FLJ35382	uc001hpu.4	Q6IQ49	OTTHUMG00000037504	ENST00000272091.7:c.284C>T	chr1.hg19:g.226180658G>A	ENSP00000272091:p.Thr95Ile	126.0	0.0		102.0	17.0	NM_152608	A8K4P3|Q5TD36|Q6ZS26|Q8NAG7	Missense_Mutation	SNP	ENST00000272091.7	hg19	CCDS41473.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	7.111089|7.111089	0.98070|0.98070	.|.	.|.	ENSG00000143751|ENSG00000143751	ENST00000366817|ENST00000272091;ENST00000366818	.|T	.|0.56776	.|0.44	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	.|0.044133	.|0.85682	.|D	.|0.000000	.|T	.|0.80778	.|0.4688	M|M	0.92268|0.92268	3.29|3.29	0.80722|0.80722	A|A	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.991	.|D	.|0.84210	.|0.0455	.|9	0.08837|0.72032	T|D	0.75|0.01	-17.1607|-17.1607	20.242|20.242	0.98377|0.98377	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|83;95	.|Q6IQ49-2;Q6IQ49	.|.;CA055_HUMAN	X|I	44|95;83	.|ENSP00000272091:T95I	ENSP00000355782:Q44X|ENSP00000272091:T95I	Q|T	-|-	1|2	0|0	C1orf55|C1orf55	224247281|224247281	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.750000|9.750000	0.98875|0.98875	2.788000|2.788000	0.95919|0.95919	0.650000|0.650000	0.86243|0.86243	CAA|ACA	.	.		0.428	SDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091310.1	NM_152608		A	226180658	G	A	226180658	3	1	209	1	0	0	0	0	1	0	0	0	2049	1377	48	3	1091	3	C1orf55	1	226180658	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	80740867	226180658	23069963	10	30155										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227222414	227222414	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agatgcttttccttcagcaaTatcgtacagaaagagtttga	8	7	1	4			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:227222414T>C	ENST00000366769.3	-	25	4604	c.3313A>G	c.(3313-3315)Att>Gtt	p.I1105V	CDC42BPA_ENST00000366767.3_Missense_Mutation_p.I1024V|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.I1085V|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.I1077V|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.I1105V|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.I1140V|CDC42BPA_ENST00000366765.3_Missense_Mutation_p.I1118V	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				CCTTCAGCAATATCGTACAGA	0.393																																					p.I1105V		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.A3313G						.						146	135	139					1																	227222414		2203	4300	6503	SO:0001583	missense	8476	exon25			CAGCAATATCGTA	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.3313A>G	chr1.hg19:g.227222414T>C	ENSP00000355731:p.Ile1105Val	73.0	0.0		76.0	6.0	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	hg19	CCDS1558.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.397|9.397	1.077082|1.077082	0.20227|0.20227	.|.	.|.	ENSG00000143776|ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765|ENST00000448940;ENST00000442054;ENST00000429440;ENST00000441725	T;T;T;T;T;T;T|.	0.41400|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	5.72|5.72	3.31|3.31	0.37934|0.37934	.|.	0.151874|.	0.64402|.	N|.	0.000018|.	T|T	0.33673|0.33673	0.0871|0.0871	N|N	0.10809|0.10809	0.05|0.05	0.36560|0.36560	D|D	0.872345|0.872345	B;B;B;B;B;B;B|.	0.13145|.	0.0;0.007;0.0;0.001;0.002;0.0;0.0|.	B;B;B;B;B;B;B|.	0.13407|.	0.001;0.007;0.001;0.003;0.009;0.007;0.001|.	T|T	0.22591|0.22591	-1.0212|-1.0212	10|5	0.07482|.	T|.	0.82|.	.|.	9.6681|9.6681	0.39996|0.39996	0.0:0.1938:0.0:0.8061|0.0:0.1938:0.0:0.8061	.|.	1085;1077;420;1024;1105;1140;307|.	F5H5N0;Q5VT25-4;E9PEF7;Q5VT25-3;Q5VT25-5;Q5VT25-2;Q5T799|.	.;.;.;.;.;.;.|.	V|C	1105;1024;1105;1140;1077;420;1085;1118|307;433;2;329	ENSP00000355731:I1105V;ENSP00000355729:I1024V;ENSP00000335341:I1105V;ENSP00000355728:I1140V;ENSP00000355726:I1077V;ENSP00000443275:I1085V;ENSP00000355727:I1118V|.	ENSP00000335341:I1105V|.	I|Y	-|-	1|2	0|0	CDC42BPA|CDC42BPA	225289037|225289037	0.931000|0.931000	0.31567|0.31567	0.734000|0.734000	0.30879|0.30879	0.839000|0.839000	0.47603|0.47603	1.441000|1.441000	0.35035|0.35035	0.403000|0.403000	0.25479|0.25479	0.528000|0.528000	0.53228|0.53228	ATT|TAT	.	.		0.393	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		C	227222414	T	C	227222414	3	2	209	1	0	0	0	0	1	0	0	0	3074	1406	49	2	1894	2	CDC42BPA	1	227222414	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	1041756	227222414	22028207	11	30156										
B3GALNT2	148789	hgsc.bcm.edu	37	chr1	235617616	235617628	+	Splice_Site	DEL	TTCAGTCTGAAAC	TTCAGTCTGAAAC	-													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cggttcggtcaactgcccaaTtcagtctgaaactgagatga							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	TTCAGTCTGAAAC	TTCAGTCTGAAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:235617616_235617628delTTCAGTCTGAAAC	ENST00000366600.3	-	10	1380_1391	c.1152_1163delGTTTCAGACTGAA	c.(1150-1164)aagtttcagactgaa>aaa	p.FQTE385fs		NM_152490.2	NP_689703.1	Q8NCR0	B3GL2_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 2	385					protein glycosylation (GO:0006486)|protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|acetylglucosaminyltransferase activity (GO:0008375)|galactosyltransferase activity (GO:0008378)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)			AACTGCCCAATTCAGTCTGAAACTGAGATGAAA	0.46																																					p.384_388del		Atlas-INDEL	.											.	B3GALNT2	36	.	0			c.1152_1164del						.																																			SO:0001630	splice_region_variant	148789	exon10			.	BC029564	CCDS1606.1, CCDS60453.1	1q42.3	2013-02-19	2006-06-14		ENSG00000162885	ENSG00000162885		"Beta 3-glycosyltransferases"	28596	protein-coding gene	gene with protein product		610194	"UDP-GalNAc:betaGlcNAc beta-1,3-galactosaminyltransferase, polypeptide 2"			14724282	Standard	NM_001277155		Approved	MGC39558	uc001hxc.3	Q8NCR0	OTTHUMG00000040468	ENST00000366600.3:c.1152-1GTTTCAGACTGAA>-	chr1.hg19:g.235617616_235617628delTTCAGTCTGAAAC		199.0	0.0		173.0	18.0	NM_152490	Q59GR3|Q5TCI3|Q96AL7	Frame_Shift_Del	DEL	ENST00000366600.3	hg19	CCDS1606.1																																																																																			.	.		0.46	B3GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097376.1	NM_152490	Frame_Shift_Del	-	235617628	TTCAGTCTGAAAC	-	235617616	8	5	209	1	0	1	0	1	0	0	1	0	1246	1493	52	0	351	0	B3GALNT2	1	235617616	Splice_Site	DEL	TTCAGTCTGAAAC	TCGA-DD-AAE3-01A-11D-A40R-10	8395202	235617616	13633005	12	30157										
LYST	1130	hgsc.bcm.edu	37	chr1	235922871	235922871	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agcatatgggcggccatctgTtgtggaataatattagagga	13	5	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:235922871T>C	ENST00000389794.3	-	23	6456	c.6282A>G	c.(6280-6282)caA>caG	p.Q2094Q	LYST_ENST00000536965.1_3'UTR|LYST_ENST00000389793.2_Silent_p.Q2094Q			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2094					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			CGGCCATCTGTTGTGGAATAA	0.383																																					p.Q2094Q		Atlas-SNP	.											.	LYST	370	.	0			c.A6282G						.						46	47	47					1																	235922871		2203	4300	6503	SO:0001819	synonymous_variant	1130	exon23			CATCTGTTGTGGA	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.6282A>G	chr1.hg19:g.235922871T>C		70.0	0.0		39.0	6.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.383	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			C	235922871	T	C	235922871	2	2	209	1	0	0	0	0	0	0	0	1	9137	1722	60	2		2	LYST	1	235922871	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	305255	235922871	13327750	13	30158										
ERO1LB	56605	hgsc.bcm.edu	37	chr1	236415384	236415384	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cagcttttattccaaccggaAttttactcttaaaaaaacaa	3	9	1	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:236415384A>C	ENST00000354619.5	-	4	515	c.314T>G	c.(313-315)aTt>aGt	p.I105S	ERO1LB_ENST00000327333.8_Missense_Mutation_p.I105S	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	105					4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	TCCAACCGGAATTTTACTCTT	0.318																																					p.I105S		Atlas-SNP	.											.	ERO1LB	48	.	0			c.T314G						.						80	83	82					1																	236415384		2203	4300	6503	SO:0001583	missense	56605	exon4			ACCGGAATTTTAC	AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.314T>G	chr1.hg19:g.236415384A>C	ENSP00000346635:p.Ile105Ser	442.0	0.0		284.0	49.0	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	hg19	CCDS31064.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.490759	0.84962	.	.	ENSG00000086619	ENST00000354619;ENST00000327333	D;T	0.82893	-1.66;0.62	5.77	5.77	0.91146	.	0.224693	0.46145	D	0.000319	D	0.88786	0.6531	M	0.78456	2.415	0.58432	D	0.999998	D;P	0.58970	0.984;0.872	P;P	0.55303	0.773;0.653	D	0.90269	0.4306	10	0.87932	D	0	-20.4477	15.0816	0.72119	1.0:0.0:0.0:0.0	.	105;105	B4DF57;Q86YB8	.;ERO1B_HUMAN	S	105	ENSP00000346635:I105S;ENSP00000377574:I105S	ENSP00000377574:I105S	I	-	2	0	ERO1LB	234482007	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.714000	0.84703	2.203000	0.70933	0.533000	0.62120	ATT	.	.		0.318	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891		C	236415384	A	C	236415384	3	2	209	1	0	0	0	0	1	0	0	0	5242	101	4	5	1141	5	ERO1LB	1	236415384	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	492513	236415384	12835237	14	30159										
OR2B11	127623	hgsc.bcm.edu	37	chr1	247615038	247615038	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	catgttgaccagcatctgagGgactgtcgtggtggtgtagc	15	8	1	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr1:247615038G>C	ENST00000318749.6	-	1	270	c.247C>G	c.(247-249)Cct>Gct	p.P83A		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	83						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			AGCATCTGAGGGACTGTCGTG	0.567																																					p.P83A		Atlas-SNP	.											.	OR2B11	102	.	0			c.C247G						.						146	139	142					1																	247615038		2203	4300	6503	SO:0001583	missense	127623	exon1			TCTGAGGGACTGT		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"GPCR / Class A : Olfactory receptors"	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.247C>G	chr1.hg19:g.247615038G>C	ENSP00000325682:p.Pro83Ala	64.0	0.0		52.0	7.0	NM_001004492	B2RP03	Missense_Mutation	SNP	ENST00000318749.6	hg19	CCDS31090.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.086798	0.55861	.	.	ENSG00000177535	ENST00000318749	T	0.25414	1.8	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000083	T	0.56543	0.1992	H	0.98769	4.325	0.39054	D	0.960387	P	0.48694	0.914	P	0.46452	0.517	T	0.77632	-0.2515	10	0.87932	D	0	.	16.1133	0.81278	0.0:0.0:1.0:0.0	.	83	Q5JQS5	OR2BB_HUMAN	A	83	ENSP00000325682:P83A	ENSP00000325682:P83A	P	-	1	0	OR2B11	245681661	1.000000	0.71417	0.532000	0.27989	0.639000	0.38242	6.719000	0.74718	2.749000	0.94314	0.551000	0.68910	CCT	.	.		0.567	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492		C	247615038	G	C	247615038	3	2	209	1	0	0	0	0	1	0	0	0	10997	1232	43	4	709	4	OR2B11	1	247615038	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	11199654	247615038	1635583	15	30160										
TSSC1	7260	hgsc.bcm.edu	37	chr2	3193108	3193108	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	taacccaggcccgggagtcaTagcaggatgtggtacttcag	13	10	2	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr2:3193108T>G	ENST00000382125.4	-	9	1353	c.1161A>C	c.(1159-1161)ctA>ctC	p.L387L	TSSC1_ENST00000478754.1_5'UTR|TSSC1_ENST00000398659.4_Silent_p.L414L	NM_003310.2	NP_003301.1	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	387										breast(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		CCGGGAGTCATAGCAGGATGT	0.577																																					p.L387L	Colon(140;1261 1762 4183 34270 49743)	Atlas-SNP	.											.	TSSC1	39	.	0			c.A1161C						.						38	36	36					2																	3193108		2192	4292	6484	SO:0001819	synonymous_variant	7260	exon9			GAGTCATAGCAGG	AF019952	CCDS1651.1	2p25.3	2013-01-10			ENSG00000032389	ENSG00000032389		"WD repeat domain containing"	12383	protein-coding gene	gene with protein product		608998				9403053, 9925925	Standard	NM_003310		Approved		uc002qxj.2	Q53HC9	OTTHUMG00000090329	ENST00000382125.4:c.1161A>C	chr2.hg19:g.3193108T>G		131.0	0.0		155.0	37.0	NM_003310	D6W4Y1|O43179|Q53S19|Q53SG2	Silent	SNP	ENST00000382125.4	hg19	CCDS1651.1																																																																																			.	.		0.577	TSSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206694.2	NM_003310		G	3193108	T	G	3193108	2	3	209	1	0	0	0	0	0	0	0	1	16681	1393	49	5		5	TSSC1	2	3193108	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10		3193108	240006265	16	30161										
SOX11	6664	hgsc.bcm.edu	37	chr2	5832874	5832874	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	atggtgcagcaggcggagagCttggaagcggagagcaacct	17	8	0	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr2:5832874C>T	ENST00000322002.3	+	1	76	c.21C>T	c.(19-21)agC>agT	p.S7S	AC108025.2_ENST00000420221.1_RNA|AC107057.2_ENST00000458264.1_RNA|AC108025.2_ENST00000453678.1_RNA	NM_003108.3	NP_003099.1	P35716	SOX11_HUMAN	SRY (sex determining region Y)-box 11	7					cardiac ventricle formation (GO:0003211)|closure of optic fissure (GO:0061386)|cornea development in camera-type eye (GO:0061303)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|eyelid development in camera-type eye (GO:0061029)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|hard palate development (GO:0060022)|kidney development (GO:0001822)|lens morphogenesis in camera-type eye (GO:0002089)|limb bud formation (GO:0060174)|lung morphogenesis (GO:0060425)|negative regulation of cell death (GO:0060548)|negative regulation of gene expression (GO:0010629)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural crest cell development (GO:0014032)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|neuron differentiation (GO:0030182)|noradrenergic neuron differentiation (GO:0003357)|oligodendrocyte development (GO:0014003)|outflow tract morphogenesis (GO:0003151)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of hippo signaling (GO:0035332)|positive regulation of hormone secretion (GO:0046887)|positive regulation of lens epithelial cell proliferation (GO:2001111)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|signal transduction involved in cell cycle checkpoint (GO:0072395)|skeletal muscle cell differentiation (GO:0035914)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)|somite development (GO:0061053)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|translation (GO:0006412)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|translation factor activity, nucleic acid binding (GO:0008135)			central_nervous_system(5)|cervix(1)|endometrium(1)|liver(1)|lung(4)|stomach(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)		AGGCGGAGAGCTTGGAAGCGG	0.701																																					p.S7S		Atlas-SNP	.											.	SOX11	69	.	0			c.C21T						.						20	22	21					2																	5832874		2202	4298	6500	SO:0001819	synonymous_variant	6664	exon1			GGAGAGCTTGGAA		CCDS1654.1	2p25	2008-05-21			ENSG00000176887	ENSG00000176887		"SRY (sex determining region Y)-boxes"	11191	protein-coding gene	gene with protein product	"SRY-related HMG-box gene 11"	600898				8666406, 12637543	Standard	NM_003108		Approved		uc002qyj.3	P35716	OTTHUMG00000090333	ENST00000322002.3:c.21C>T	chr2.hg19:g.5832874C>T		166.0	0.0		155.0	27.0	NM_003108	Q4ZFV8	Silent	SNP	ENST00000322002.3	hg19	CCDS1654.1																																																																																			.	.		0.701	SOX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206698.1	NM_003108		T	5832874	C	T	5832874	2	4	209	1	0	0	0	0	0	0	0	1	14957	796	28	3		3	SOX11	2	5832874	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	2639766	5832874	237366499	17	30162										
CEP68	23177	hgsc.bcm.edu	37	chr2	65305030	65305030	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gaaagatatagatgaacatcAgtctctgacggagagtgtct	11	6	3	5			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr2:65305030A>C	ENST00000377990.2	+	5	2239	c.2036A>C	c.(2035-2037)cAg>cCg	p.Q679P	CEP68_ENST00000546106.1_Intron|RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000260569.4_Missense_Mutation_p.Q542P	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	679					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						GATGAACATCAGTCTCTGACG	0.398																																					p.Q679P		Atlas-SNP	.											.	CEP68	69	.	0			c.A2036C						.						87	88	88					2																	65305030		2203	4300	6503	SO:0001583	missense	23177	exon5			AACATCAGTCTCT	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"KIAA0582"	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.2036A>C	chr2.hg19:g.65305030A>C	ENSP00000367229:p.Gln679Pro	76.0	0.0		59.0	11.0	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	hg19	CCDS1880.2	.	.	.	.	.	.	.	.	.	.	A	14.82	2.648389	0.47258	.	.	ENSG00000011523	ENST00000377990;ENST00000260569	T;T	0.80123	-1.34;-1.34	5.86	5.86	0.93980	.	0.075145	0.53938	D	0.000046	D	0.86138	0.5861	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.989	D	0.83863	0.0269	10	0.25106	T	0.35	-16.7968	10.7736	0.46338	0.9268:0.0:0.0732:0.0	.	679;542	Q76N32;Q76N32-2	CEP68_HUMAN;.	P	679;542	ENSP00000367229:Q679P;ENSP00000260569:Q542P	ENSP00000260569:Q542P	Q	+	2	0	CEP68	65158534	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	3.696000	0.54757	2.237000	0.73441	0.460000	0.39030	CAG	.	.		0.398	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		C	65305030	A	C	65305030	3	2	209	1	0	0	0	0	1	0	0	0	3260	188	7	5	2050	5	CEP68	2	65305030	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	59472156	65305030	177894343	18	30163										
ASTL	431705	hgsc.bcm.edu	37	chr2	96789942	96789942	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cctggattccgccgacagtgCctccaaaagccgctgcagag	11	15	0	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr2:96789942C>A	ENST00000342380.2	-	9	942	c.943G>T	c.(943-945)Gca>Tca	p.A315S		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						GCCGACAGTGCCTCCAAAAGC	0.657																																					p.A315S		Atlas-SNP	.											.	ASTL	59	.	0			c.G943T						.						15	18	17					2																	96789942		2193	4274	6467	SO:0001583	missense	431705	exon9			ACAGTGCCTCCAA	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"sperm acrosomal SLLP1 binding"	608860	"astacin-like metalloendopeptidase (M12 family)"			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.943G>T	chr2.hg19:g.96789942C>A	ENSP00000343674:p.Ala315Ser	179.0	0.0		203.0	9.0	NM_001002036		Missense_Mutation	SNP	ENST00000342380.2	hg19	CCDS33249.1	.	.	.	.	.	.	.	.	.	.	C	19.86	3.906036	0.72868	.	.	ENSG00000188886	ENST00000342380	T	0.66280	-0.2	4.74	4.74	0.60224	.	0.388428	0.19528	N	0.112113	T	0.60958	0.2309	L	0.34521	1.04	0.20638	N	0.999876	D	0.56968	0.978	P	0.53224	0.721	T	0.53041	-0.8494	10	0.27785	T	0.31	-6.4598	13.6286	0.62181	0.0:1.0:0.0:0.0	.	315	Q6HA08	ASTL_HUMAN	S	315	ENSP00000343674:A315S	ENSP00000343674:A315S	A	-	1	0	ASTL	96153669	0.012000	0.17670	0.236000	0.24074	0.054000	0.15201	2.408000	0.44574	2.357000	0.79964	0.456000	0.33151	GCA	.	.		0.657	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			A	96789942	C	A	96789942	3	1	209	1	0	0	0	0	1	0	0	0	1063	739	26	3	355	3	ASTL	2	96789942	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	31484912	96789942	146409431	19	30164										
C1QL2	165257	hgsc.bcm.edu	37	chr2	119915526	119915526	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gccgccccgagtcgcccttcTctcccggagggcccctgggt	13	19	1	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr2:119915526T>G	ENST00000272520.3	-	1	939	c.320A>C	c.(319-321)gAg>gCg	p.E107A		NM_182528.3	NP_872334.2	Q7Z5L3	C1QL2_HUMAN	complement component 1, q subcomponent-like 2	107	Collagen-like.				protein oligomerization (GO:0051259)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)				NS(1)|endometrium(1)|large_intestine(3)|pancreas(1)|prostate(1)	7						GTCGCCCTTCTCTCCCGGAGG	0.806										HNSCC(49;0.14)																											p.E107A		Atlas-SNP	.											.	C1QL2	25	.	0			c.A320C						.						2	2	2					2																	119915526		1041	2564	3605	SO:0001583	missense	165257	exon1			CCCTTCTCTCCCG	AF525315	CCDS42737.1	2q14.2	2009-05-20			ENSG00000144119	ENSG00000144119			24181	protein-coding gene	gene with protein product	"C1q and tumor necrosis factor related protein 10"	614330				18783346	Standard	NM_182528		Approved	CTRP10, C1QTNF10	uc002tlo.2	Q7Z5L3	OTTHUMG00000153271	ENST00000272520.3:c.320A>C	chr2.hg19:g.119915526T>G	ENSP00000272520:p.Glu107Ala	108.0	0.0		149.0	29.0	NM_182528		Missense_Mutation	SNP	ENST00000272520.3	hg19	CCDS42737.1	.	.	.	.	.	.	.	.	.	.	T	11.51	1.659756	0.29515	.	.	ENSG00000144119	ENST00000272520	D	0.93547	-3.24	4.29	4.29	0.51040	.	0.442010	0.20859	N	0.084395	D	0.90604	0.7054	L	0.52905	1.665	0.35683	D	0.814263	B	0.24186	0.099	B	0.28916	0.096	D	0.89724	0.3921	9	.	.	.	.	11.4065	0.49900	0.0:0.0:0.0:1.0	.	107	Q7Z5L3	C1QL2_HUMAN	A	107	ENSP00000272520:E107A	.	E	-	2	0	C1QL2	119631996	0.440000	0.25618	0.992000	0.48379	0.470000	0.32858	1.682000	0.37628	1.801000	0.52704	0.459000	0.35465	GAG	.	.		0.806	C1QL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330527.2	NM_182528		G	119915526	T	G	119915526	3	3	209	1	0	0	0	0	1	0	0	0	1961	1551	54	5	551	5	C1QL2	2	119915526	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	23125584	119915526	123283847	20	30165										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198273248	198273248	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tcggtgtttcaccaatagaaTctccacctcgatctgttcga	7	12	3	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr2:198273248T>A	ENST00000335508.6	-	8	1053	c.962A>T	c.(961-963)gAt>gTt	p.D321V		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	321	Interaction with PPP1R8.|U2AF homology region; mediates interaction with RMB39.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ACCAATAGAATCTCCACCTCG	0.463			Mis		myelodysplastic syndrome																																p.D321V		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.A962T						.						81	84	83					2																	198273248		2203	4300	6503	SO:0001583	missense	23451	exon8			ATAGAATCTCCAC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.962A>T	chr2.hg19:g.198273248T>A	ENSP00000335321:p.Asp321Val	88.0	0.0		57.0	25.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	15.89	2.965255	0.53507	.	.	ENSG00000115524	ENST00000335508	.	.	.	4.67	4.67	0.58626	Splicing factor 3B subunit 1 (1);	0.112135	0.64402	D	0.000014	T	0.41766	0.1173	N	0.16790	0.44	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.25117	-1.0141	9	0.29301	T	0.29	.	14.5576	0.68113	0.0:0.0:0.0:1.0	.	321	O75533	SF3B1_HUMAN	V	321	.	ENSP00000335321:D321V	D	-	2	0	SF3B1	197981493	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.732000	0.84908	2.087000	0.62958	0.459000	0.35465	GAT	.	.		0.463	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			A	198273248	T	A	198273248	3	1	209	1	0	0	0	0	1	0	0	0	14164	1435	50	4	3024	4	SF3B1	2	198273248	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	78357722	198273248	44926125	21	30166										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215901702	215901702	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gctggggagtccagagtgtaCagcagatgtttaacagactt	13	7	0	3	rs375880439		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr2:215901702C>G	ENST00000272895.7	-	8	1179	c.960G>C	c.(958-960)ctG>ctC	p.L320L	AC072062.3_ENST00000437897.3_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	320					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CCAGAGTGTACAGCAGATGTT	0.418																																					p.L320L	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.G960C						.						108	109	108					2																	215901702		2203	4300	6503	SO:0001819	synonymous_variant	26154	exon8			AGTGTACAGCAGA	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.960G>C	chr2.hg19:g.215901702C>G		102.0	0.0		81.0	19.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	hg19	CCDS33372.1																																																																																			.	.		0.418	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215901702	C	G	215901702	2	3	209	1	0	0	0	0	0	0	0	1	30	465	17	4		4	ABCA12	2	215901702	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	17628454	215901702	27297671	22	30167			1	44		3	2	17	N	G_C	8.165913e-05
ABCA12	26154	hgsc.bcm.edu	37	chr2	215901716	215901716	+	Missense_Mutation	SNP	C	C	A													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agtgtacagcagatgtttaaCagacttctggagggttctga							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr2:215901716C>A	ENST00000272895.7	-	8	1165	c.946G>T	c.(946-948)Gtt>Ttt	p.V316F	AC072062.3_ENST00000437897.3_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	316					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AGATGTTTAACAGACTTCTGG	0.403																																					p.V316F	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											ABCA12,NS,carcinoma,0,1	ABCA12	368	.	0			c.G946T						.						108	109	109					2																	215901716		2203	4300	6503	SO:0001583	missense	26154	exon8			GTTTAACAGACTT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.946G>T	chr2.hg19:g.215901716C>A	ENSP00000272895:p.Val316Phe	114.0	2.0		80.0	20.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.106314	0.77096	.	.	ENSG00000144452	ENST00000272895	T	0.56941	0.43	5.43	5.43	0.79202	.	0.364119	0.23142	N	0.051456	T	0.42381	0.1200	L	0.27053	0.805	0.80722	D	1	B	0.31680	0.335	B	0.30495	0.116	T	0.44757	-0.9307	10	0.87932	D	0	.	15.0898	0.72185	0.0:1.0:0.0:0.0	.	316	Q86UK0	ABCAC_HUMAN	F	316	ENSP00000272895:V316F	ENSP00000272895:V316F	V	-	1	0	ABCA12	215609961	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.273000	0.43381	2.699000	0.92147	0.655000	0.94253	GTT	.	.		0.403	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		A	215901716	C	A	215901716	3	1	209	1	0	0	0	0	1	0	0	0	30	478	17	3	7056	3	ABCA12	2	215901716	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	14	215901716	27297657	23	30168	157	2	1	44		3	2	17	N	G_C	8.165913e-05
ABCA12	26154	hgsc.bcm.edu	37	chr2	215901718	215901718	+	Missense_Mutation	SNP	G	G	T													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tgtacagcagatgtttaacaGacttctggagggttctgaaa							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr2:215901718G>T	ENST00000272895.7	-	8	1163	c.944C>A	c.(943-945)tCt>tAt	p.S315Y	AC072062.3_ENST00000437897.3_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	315					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ATGTTTAACAGACTTCTGGAG	0.408																																					p.S315Y	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C944A						.						108	109	109					2																	215901718		2203	4300	6503	SO:0001583	missense	26154	exon8			TTAACAGACTTCT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.944C>A	chr2.hg19:g.215901718G>T	ENSP00000272895:p.Ser315Tyr	114.0	0.0		79.0	19.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176668	0.78564	.	.	ENSG00000144452	ENST00000272895	T	0.57907	0.37	5.43	5.43	0.79202	.	0.366617	0.24022	N	0.042272	T	0.38639	0.1048	N	0.24115	0.695	0.80722	D	1	P	0.41748	0.761	B	0.35413	0.202	T	0.43458	-0.9390	10	0.66056	D	0.02	.	15.0898	0.72185	0.0:0.0:1.0:0.0	.	315	Q86UK0	ABCAC_HUMAN	Y	315	ENSP00000272895:S315Y	ENSP00000272895:S315Y	S	-	2	0	ABCA12	215609963	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.083000	0.50136	2.699000	0.92147	0.655000	0.94253	TCT	.	.		0.408	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215901718	G	T	215901718	3	4	209	1	0	0	0	0	1	0	0	0	30	942	33	3	7058	3	ABCA12	2	215901718	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	2	215901718	27297655	24	30169	157	2	1	44		3	2	17	N	G_C	8.165913e-05
KLHL30	377007	hgsc.bcm.edu	37	chr2	239049437	239049437	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctggatttccacctgccctcGcatgcccaggacatgctgga	10	15	0	0	rs374999323		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr2:239049437G>A	ENST00000409223.1	+	2	149	c.42G>A	c.(40-42)tcG>tcA	p.S14S	KLHL30_ENST00000305959.4_5'UTR			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	14										lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		ACCTGCCCTCGCATGCCCAGG	0.662																																					p.S14S		Atlas-SNP	.											.	KLHL30	79	.	0			c.G42A						.	G		0,4296		0,0,2148	13	14	13		42	-9.3	0.6	2		13	1,8467		0,1,4233	no	coding-synonymous	KLHL30	NM_198582.3		0,1,6381	AA,AG,GG		0.0118,0.0,0.0078		14/579	239049437	1,12763	2148	4234	6382	SO:0001819	synonymous_variant	377007	exon2			GCCCTCGCATGCC		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"Kelch-like", "BTB/POZ domain containing"	24770	protein-coding gene	gene with protein product			"kelch-like 30 (Drosophila)"				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.42G>A	chr2.hg19:g.239049437G>A		100.0	0.0		104.0	21.0	NM_198582	Q6ZUS1	Silent	SNP	ENST00000409223.1	hg19	CCDS46555.2																																																																																			.	.		0.662	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582		A	239049437	G	A	239049437	2	1	209	1	0	0	0	0	0	0	0	1	8393	1074	38	1		1	KLHL30	2	239049437	Silent	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	23147719	239049437	4149936	25	30170										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266101	41266101	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gcaacagtcttacctggactCtggaatccattctggtgcca	9	12	3	0	rs121913416|rs121913400		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr3:41266101C>G	ENST00000349496.5	+	3	378	c.98C>G	c.(97-99)tCt>tGt	p.S33C	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33C|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26C|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33C|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33C	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33C	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,359	CTNNB1	4904	.	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98G						.						92	77	82					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>G	chr3.hg19:g.41266101C>G	ENSP00000344456:p.Ser33Cys	125.0	0.0		98.0	14.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.381716	0.82792	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	C	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26C;ENSP00000385604:S33C;ENSP00000412219:S33C;ENSP00000379486:S33C;ENSP00000344456:S33C;ENSP00000411226:S26C;ENSP00000379488:S33C;ENSP00000409302:S33C;ENSP00000401599:S33C	ENSP00000344456:S33C	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266101	C	G	41266101	3	3	209	1	0	0	0	0	1	0	0	0	4018	913	32	4	104	4	CTNNB1	3	41266101	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10		41266101	156756329	26	30171										
KCTD6	200845	hgsc.bcm.edu	37	chr3	58487086	58487086	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	acgcaactaaccatcaccacTaaggtccattccttactaga	4	14	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr3:58487086T>G	ENST00000355076.6	+	2	1424	c.441T>G	c.(439-441)acT>acG	p.T147T	KCTD6_ENST00000404589.3_Silent_p.T147T|KCTD6_ENST00000490264.1_Silent_p.T147T	NM_153331.3	NP_699162.3	Q8NC69	KCTD6_HUMAN	potassium channel tetramerization domain containing 6	147					protein homooligomerization (GO:0051260)		ankyrin binding (GO:0030506)			endometrium(1)|large_intestine(2)|lung(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(55;0.000177)|Kidney(10;0.00229)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.148)		CCATCACCACTAAGGTCCATT	0.428																																					p.T147T		Atlas-SNP	.											.	KCTD6	14	.	0			c.T441G						.						130	116	120					3																	58487086		2203	4300	6503	SO:0001819	synonymous_variant	200845	exon3			CACCACTAAGGTC	AK074934	CCDS2891.1	3p21.2	2013-06-20	2013-06-20		ENSG00000168301	ENSG00000168301			22235	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 6"			21472142	Standard	NM_153331		Approved	MGC27385, KCASH3	uc003dkj.4	Q8NC69	OTTHUMG00000159161	ENST00000355076.6:c.441T>G	chr3.hg19:g.58487086T>G		162.0	0.0		135.0	29.0	NM_001128214	B3KNI5|Q8NBS6|Q8TCA6	Silent	SNP	ENST00000355076.6	hg19	CCDS2891.1																																																																																			.	.		0.428	KCTD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353591.1	NM_153331		G	58487086	T	G	58487086	2	3	209	1	0	0	0	0	0	0	0	1	8122	1509	53	5		5	KCTD6	3	58487086	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	17220985	58487086	139535344	27	30172										
CRYBG3	131544	hgsc.bcm.edu	37	chr3	97660086	97660086	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cagggcaacatctgtgtgcaTttctccctatagtggaaaga	10	9	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr3:97660086T>C	ENST00000182096.4	+	17	2820	c.2756T>C	c.(2755-2757)aTt>aCt	p.I919T	CRYBG3_ENST00000485253.1_3'UTR|CRYBG3_ENST00000389622.2_Missense_Mutation_p.I126T	NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2867							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TCTGTGTGCATTTCTCCCTAT	0.458																																					p.I2867T		Atlas-SNP	.											.	CRYBG3	86	.	0			c.T8600C						.						125	119	121					3																	97660086		1881	4103	5984	SO:0001583	missense	131544	exon20			TGTGCATTTCTCC			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.2756T>C	chr3.hg19:g.97660086T>C	ENSP00000182096:p.Ile919Thr	121.0	0.0		80.0	15.0	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000182096.4	hg19		.	.	.	.	.	.	.	.	.	.	T	7.900	0.734189	0.15574	.	.	ENSG00000080200	ENST00000182096;ENST00000495403;ENST00000389622	T;D;T	0.81659	1.67;-1.52;1.67	6.07	4.92	0.64577	Ricin B-related lectin (1);Ricin B lectin (3);	0.629153	0.15531	N	0.257492	T	0.75803	0.3899	L	0.49699	1.58	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.67476	-0.5661	10	0.72032	D	0.01	.	10.7055	0.45952	0.0:0.1313:0.0:0.8687	.	919	Q68DQ2	CRBG3_HUMAN	T	919;125;126	ENSP00000182096:I919T;ENSP00000418420:I125T;ENSP00000374273:I126T	ENSP00000182096:I919T	I	+	2	0	CRYBG3	99142776	0.081000	0.21417	0.006000	0.13384	0.307000	0.27823	2.594000	0.46189	1.121000	0.41925	0.477000	0.44152	ATT	.	.		0.458	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605		C	97660086	T	C	97660086	3	2	209	1	0	0	0	0	1	0	0	0	3915	1493	52	2	2822	2	CRYBG3	3	97660086	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	39173000	97660086	100362344	28	30173										
OR5K1	26339	hgsc.bcm.edu	37	chr3	98188512	98188512	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gactctgctgtttgtggtgtTctttgccatctatctgatca	9	9	5	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr3:98188512T>A	ENST00000332650.5	+	1	189	c.92T>A	c.(91-93)tTc>tAc	p.F31Y		NM_001004736.2	NP_001004736.2	Q8NHB7	OR5K1_HUMAN	olfactory receptor, family 5, subfamily K, member 1	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(4)|lung(21)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTTGTGGTGTTCTTTGCCATC	0.433																																					p.F31Y		Atlas-SNP	.											.	OR5K1	51	.	0			c.T92A						.						126	125	126					3																	98188512		2203	4296	6499	SO:0001583	missense	26339	exon1			TGGTGTTCTTTGC	X64984	CCDS43115.1	3q11.2	2013-09-23			ENSG00000232382	ENSG00000232382		"GPCR / Class A : Olfactory receptors"	8349	protein-coding gene	gene with protein product						1370859	Standard	NM_001004736		Approved	HTPCRX10, HSHTPCRX10	uc003dsm.3	Q8NHB7	OTTHUMG00000160048	ENST00000332650.5:c.92T>A	chr3.hg19:g.98188512T>A	ENSP00000373193:p.Phe31Tyr	135.0	0.0		110.0	23.0	NM_001004736	B9EGY5|Q6IF46	Missense_Mutation	SNP	ENST00000332650.5	hg19	CCDS43115.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.590468	0.86851	.	.	ENSG00000232382	ENST00000332650	T	0.04360	3.64	5.05	5.05	0.67936	.	0.000000	0.43747	D	0.000534	T	0.23846	0.0577	M	0.89658	3.05	0.27284	N	0.95804	D	0.67145	0.996	D	0.63113	0.911	T	0.17899	-1.0354	10	0.87932	D	0	-15.8746	12.7429	0.57264	0.0:0.0:0.0:1.0	.	31	Q8NHB7	OR5K1_HUMAN	Y	31	ENSP00000373193:F31Y	ENSP00000373193:F31Y	F	+	2	0	OR5K1	99671202	0.996000	0.38824	0.472000	0.27241	0.902000	0.53008	6.293000	0.72731	1.902000	0.55061	0.383000	0.25322	TTC	.	.		0.433	OR5K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359019.1			A	98188512	T	A	98188512	3	1	209	1	0	0	0	0	1	0	0	0	11175	1783	62	4	94	4	OR5K1	3	98188512	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	528426	98188512	99833918	29	30174										
EPHB3	2049	hgsc.bcm.edu	37	chr3	184290389	184290389	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ccagaacaactggcttcgcaCggggttcatctggcggcggg	15	12	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr3:184290389C>T	ENST00000330394.2	+	3	733	c.281C>T	c.(280-282)aCg>aTg	p.T94M	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	94	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TGGCTTCGCACGGGGTTCATC	0.587																																					p.T94M		Atlas-SNP	.											EPHB3,colon,carcinoma,0,1	EPHB3	114	.	0			c.C281T						.						63	59	60					3																	184290389		2203	4300	6503	SO:0001583	missense	2049	exon3			TTCGCACGGGGTT	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3394	protein-coding gene	gene with protein product		601839	"EphB3"	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.281C>T	chr3.hg19:g.184290389C>T	ENSP00000332118:p.Thr94Met	75.0	0.0		89.0	10.0	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.672767	0.67928	.	.	ENSG00000182580	ENST00000330394	T	0.18960	2.18	5.53	5.53	0.82687	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.111469	0.64402	D	0.000014	T	0.58764	0.2145	H	0.94620	3.56	0.58432	D	0.999992	D	0.89917	1.0	D	0.65874	0.939	T	0.71494	-0.4576	10	0.87932	D	0	.	18.4651	0.90752	0.0:1.0:0.0:0.0	.	94	P54753	EPHB3_HUMAN	M	94	ENSP00000332118:T94M	ENSP00000332118:T94M	T	+	2	0	EPHB3	185773083	1.000000	0.71417	0.956000	0.39512	0.925000	0.55904	3.899000	0.56288	2.591000	0.87537	0.655000	0.94253	ACG	.	.		0.587	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		T	184290389	C	T	184290389	3	4	209	1	0	0	0	0	1	0	0	0	5178	536	19	1	291	1	EPHB3	3	184290389	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	86101877	184290389	13732041	30	30175										
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6598950	6598950	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agtccatgttcacacgctacCtgtggccggccccccgtggg	12	16	1	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr4:6598950C>T	ENST00000285599.3	+	8	1204	c.1168C>T	c.(1168-1170)Ctg>Ttg	p.L390L	MAN2B2_ENST00000504248.1_Silent_p.L339L	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	390					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CACACGCTACCTGTGGCCGGC	0.672																																					p.L390L		Atlas-SNP	.											.	MAN2B2	80	.	0			c.C1168T						.						65	74	71					4																	6598950		2203	4300	6503	SO:0001819	synonymous_variant	23324	exon8			CGCTACCTGTGGC	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"core-specific lysosomal alpha-1,6-Mannosidase"					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1168C>T	chr4.hg19:g.6598950C>T		92.0	0.0		135.0	24.0	NM_015274	Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	hg19	CCDS33951.1																																																																																			.	.		0.672	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		T	6598950	C	T	6598950	2	4	209	1	0	0	0	0	0	0	0	1	9226	680	24	3		3	MAN2B2	4	6598950	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10		6598950	184555326	31	30176										
CPZ	8532	hgsc.bcm.edu	37	chr4	8607787	8607787	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gccgggagatgctcatctacCtagcccagtacctgtgctct	10	14	3	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr4:8607787C>T	ENST00000360986.4	+	5	955	c.781C>T	c.(781-783)Cta>Tta	p.L261L	CPZ_ENST00000429646.2_5'UTR|CPZ_ENST00000315782.6_Silent_p.L250L|CPZ_ENST00000382480.2_Silent_p.L124L	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	261					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GCTCATCTACCTAGCCCAGTA	0.602																																					p.L261L		Atlas-SNP	.											.	CPZ	95	.	0			c.C781T						.						146	114	125					4																	8607787		2203	4300	6503	SO:0001819	synonymous_variant	8532	exon5			ATCTACCTAGCCC	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.781C>T	chr4.hg19:g.8607787C>T		115.0	0.0		82.0	32.0	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	hg19	CCDS33953.1																																																																																			.	.		0.602	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		T	8607787	C	T	8607787	2	4	209	1	0	0	0	0	0	0	0	1	3841	680	24	3		3	CPZ	4	8607787	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	2008837	8607787	182546489	32	30177										
REST	5978	hgsc.bcm.edu	37	chr4	57797908	57797908	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	caagagagaatctcactggtAtaaattcaacagttgaagaa	8	6	2	4			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr4:57797908A>G	ENST00000309042.7	+	4	3198	c.2884A>G	c.(2884-2886)Ata>Gta	p.I962V		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	962					cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					TCTCACTGGTATAAATTCAAC	0.428																																					p.I962V		Atlas-SNP	.											.	REST	104	.	0			c.A2884G						.						71	69	70					4																	57797908		2203	4300	6503	SO:0001583	missense	5978	exon4			ACTGGTATAAATT	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.2884A>G	chr4.hg19:g.57797908A>G	ENSP00000311816:p.Ile962Val	187.0	0.0		166.0	32.0	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	hg19	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	A	0.019	-1.450712	0.01080	.	.	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.06849	3.25	5.38	2.91	0.33838	.	0.685951	0.13240	N	0.402958	T	0.03095	0.0091	N	0.08118	0	0.09310	N	1	B;B	0.18741	0.03;0.009	B;B	0.15870	0.014;0.006	T	0.45891	-0.9230	10	0.06757	T	0.87	-5.9837	3.064	0.06209	0.5336:0.0:0.1623:0.3041	.	939;962	F8WAN5;Q13127	.;REST_HUMAN	V	962;939	ENSP00000311816:I962V	ENSP00000311816:I962V	I	+	1	0	REST	57492665	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.024000	0.13555	0.464000	0.27142	-0.250000	0.11733	ATA	.	.		0.428	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		G	57797908	A	G	57797908	3	3	209	1	0	0	0	0	1	0	0	0	13249	449	16	2	2894	2	REST	4	57797908	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	49190121	57797908	133356368	33	30178										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79204050	79204050	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ggtaacttgctacgagccctCttgcccaccatgtccagtgg	10	14	1	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr4:79204050C>T	ENST00000325942.6	+	12	1624	c.1184C>T	c.(1183-1185)tCt>tTt	p.S395F	FRAS1_ENST00000264899.6_Missense_Mutation_p.S395F|FRAS1_ENST00000264895.6_Missense_Mutation_p.S395F	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	395	VWFC 6. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TACGAGCCCTCTTGCCCACCA	0.557																																					p.S395F		Atlas-SNP	.											.	FRAS1	779	.	0			c.C1184T						.						77	82	80					4																	79204050		2007	4166	6173	SO:0001583	missense	80144	exon12			AGCCCTCTTGCCC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1184C>T	chr4.hg19:g.79204050C>T	ENSP00000326330:p.Ser395Phe	84.0	0.0		82.0	37.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.85|16.85	3.237702|3.237702	0.58886|0.58886	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000502446|ENST00000325942;ENST00000264895;ENST00000264899;ENST00000534913	.|T;T;T	.|0.59364	.|0.27;0.27;0.27	5.6|5.6	5.6|5.6	0.85130|0.85130	.|von Willebrand factor, type C (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75496|0.75496	0.3857|0.3857	M|M	0.65320|0.65320	2|2	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|0.999;1.0;1.0;1.0	.|D;D;D;D	.|0.91635	.|0.995;0.993;0.999;0.999	T|T	0.76677|0.76677	-0.2871|-0.2871	5|10	.|0.72032	.|D	.|0.01	.|.	19.612|19.612	0.95610|0.95610	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|395;395;395;395	.|E9PHH6;Q86XX4;E7EWM9;A2RRR8	.|.;FRAS1_HUMAN;.;.	F|F	324|395;395;395;135	.|ENSP00000326330:S395F;ENSP00000264895:S395F;ENSP00000264899:S395F	.|ENSP00000264895:S395F	L|S	+|+	1|2	0|0	FRAS1|FRAS1	79423074|79423074	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.141000|0.141000	0.21300|0.21300	4.514000|4.514000	0.60482|0.60482	2.632000|2.632000	0.89209|0.89209	0.563000|0.563000	0.77884|0.77884	CTT|TCT	.	.		0.557	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			T	79204050	C	T	79204050	3	4	209	1	0	0	0	0	1	0	0	0	6050	913	32	3	1230	3	FRAS1	4	79204050	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	21406142	79204050	111950226	34	30179										
ADH4	127	hgsc.bcm.edu	37	chr4	100047761	100047761	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gtacctttttccttggttcaTtaggtcaaatgcctcactga	7	10	3	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr4:100047761T>C	ENST00000265512.7	-	8	1176	c.1102A>G	c.(1102-1104)Atg>Gtg	p.M368V	ADH4_ENST00000423445.1_Missense_Mutation_p.M387V|ADH4_ENST00000505590.1_Missense_Mutation_p.M387V|ADH4_ENST00000508393.1_Missense_Mutation_p.M387V|RP11-696N14.1_ENST00000500358.2_RNA	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	368					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		CCTTGGTTCATTAGGTCAAAT	0.363																																					p.M368V		Atlas-SNP	.											.	ADH4	35	.	0			c.A1102G						.						141	138	139					4																	100047761		2203	4300	6503	SO:0001583	missense	127	exon8			GGTTCATTAGGTC	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"Alcohol dehydrogenases"	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.1102A>G	chr4.hg19:g.100047761T>C	ENSP00000265512:p.Met368Val	57.0	0.0		39.0	10.0	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Missense_Mutation	SNP	ENST00000265512.7	hg19	CCDS34032.1	.	.	.	.	.	.	.	.	.	.	T	11.12	1.545053	0.27652	.	.	ENSG00000198099	ENST00000508393;ENST00000265512;ENST00000423445;ENST00000505590	T;T;T;T	0.10860	2.83;2.83;2.83;2.83	4.75	-2.85	0.05734	GroES-like (1);	0.128136	0.47455	U	0.000239	T	0.10380	0.0254	M	0.77486	2.375	0.09310	N	0.999999	P;B	0.48998	0.918;0.028	B;B	0.36378	0.223;0.013	T	0.23190	-1.0195	10	0.87932	D	0	-3.668	8.954	0.35807	0.1814:0.0:0.5216:0.2969	.	387;368	P08319-2;P08319	.;ADH4_HUMAN	V	387;368;387;387	ENSP00000424630:M387V;ENSP00000265512:M368V;ENSP00000397939:M387V;ENSP00000425416:M387V	ENSP00000265512:M368V	M	-	1	0	ADH4	100266784	0.000000	0.05858	0.009000	0.14445	0.947000	0.59692	-0.937000	0.03942	-0.258000	0.09446	0.533000	0.62120	ATG	.	.		0.363	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670		C	100047761	T	C	100047761	3	2	209	1	0	0	0	0	1	0	0	0	310	1493	52	2	48	2	ADH4	4	100047761	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	20843711	100047761	91106515	35	30180										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183721241	183721241	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	acgtgcgctacggcatgaccCtggacgaggagaaggcgcgc	16	12	0	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr4:183721241C>T	ENST00000511685.1	+	28	7960	c.7837C>T	c.(7837-7839)Ctg>Ttg	p.L2613L	TENM3_ENST00000406950.2_Silent_p.L2613L			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2613					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CGGCATGACCCTGGACGAGGA	0.741																																					p.L2613L		Atlas-SNP	.											.	.	.	.	0			c.C7837T						.						12	15	14					4																	183721241		2146	4243	6389	SO:0001819	synonymous_variant	55714	exon27			ATGACCCTGGACG	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.7837C>T	chr4.hg19:g.183721241C>T		59.0	0.0		74.0	15.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.		0.741	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183721241	C	T	183721241	2	4	209	1	0	0	0	0	0	0	0	1	10845	680	24	3		3	ODZ3	4	183721241	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	83673480	183721241	7433035	36	30181										
CCT5	22948	hgsc.bcm.edu	37	chr5	10258287	10258287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ccgtcctcactgtagcagatAtggagcggagagacgttgac	13	10	1	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:10258287A>G	ENST00000280326.4	+	5	1015	c.595A>G	c.(595-597)Atg>Gtg	p.M199V	CCT5_ENST00000515390.1_Missense_Mutation_p.M144V|CCT5_ENST00000515676.1_Missense_Mutation_p.M161V|CCT5_ENST00000506600.1_Missense_Mutation_p.M106V|CCT5_ENST00000503026.1_Missense_Mutation_p.M178V	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	199					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						TGTAGCAGATATGGAGCGGAG	0.478																																					p.M199V		Atlas-SNP	.											.	CCT5	49	.	0			c.A595G						.						109	92	97					5																	10258287		2203	4300	6503	SO:0001583	missense	22948	exon5			GCAGATATGGAGC	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"Heat Shock Proteins / Chaperonins"	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.595A>G	chr5.hg19:g.10258287A>G	ENSP00000280326:p.Met199Val	87.0	0.0		111.0	16.0	NM_012073	A8JZY8|A8K2X8|B4DYD8	Missense_Mutation	SNP	ENST00000280326.4	hg19	CCDS3877.1	.	.	.	.	.	.	.	.	.	.	A	11.28	1.592343	0.28357	.	.	ENSG00000150753	ENST00000280326;ENST00000503026;ENST00000515390;ENST00000440011;ENST00000515676;ENST00000506600	T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16	5.59	2.97	0.34412	.	0.036522	0.85682	D	0.000000	T	0.57227	0.2039	N	0.11560	0.145	0.58432	D	0.999995	B;B;B;B;B;B	0.10296	0.001;0.001;0.003;0.001;0.001;0.001	B;B;B;B;B;B	0.14578	0.001;0.006;0.011;0.006;0.006;0.006	T	0.54296	-0.8315	10	0.30854	T	0.27	-45.2411	10.4869	0.44729	0.7748:0.0:0.0:0.2252	.	106;144;48;197;199;199	B4DYD8;E7ENZ3;B4DZY9;Q9BU08;A8K2X8;P48643	.;.;.;.;.;TCPE_HUMAN	V	199;178;144;172;161;106	ENSP00000280326:M199V;ENSP00000423318:M178V;ENSP00000426923:M144V;ENSP00000427297:M161V;ENSP00000423052:M106V	ENSP00000280326:M199V	M	+	1	0	CCT5	10311287	1.000000	0.71417	0.962000	0.40283	0.401000	0.30781	4.592000	0.61027	2.141000	0.66446	0.529000	0.55759	ATG	.	.		0.478	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2			G	10258287	A	G	10258287	3	3	209	1	0	0	0	0	1	0	0	0	2958	449	16	2	613	2	CCT5	5	10258287	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10		10258287	170656973	37	30182										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13870897	13870898	+	Frame_Shift_Ins	INS	-	-	A													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	caataggtcctacttgaaagINStcaatggagatttgctcctc							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:13870897_13870898insA	ENST00000265104.4	-	24	3916_3917	c.3812_3813insT	c.(3811-3813)gacfs	p.D1271fs	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1271	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTACTTGAAAGTCAATGGAGAT	0.361									Kartagener syndrome																												p.D1271fs		Atlas-INDEL	.											.	DNAH5	868	.	0			c.3813_3814insT						.																																			SO:0001589	frameshift_variant	1767	exon24	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	.	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3812_3813insT	chr5.hg19:g.13870897_13870898insA	ENSP00000265104:p.Asp1271fs	78.0	0.0		113.0	13.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Frame_Shift_Ins	INS	ENST00000265104.4	hg19	CCDS3882.1																																																																																			.	.		0.361	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13870898	-	A	13870897	7	5	209	1	0	1	1	0	0	0	0	0	4606	1020	36	0	10285	0	DNAH5	5	13870897	Frame_Shift_Ins	INS	-	TCGA-DD-AAE3-01A-11D-A40R-10	3612610	13870897	167044363	38	30183										
RAI14	26064	hgsc.bcm.edu	37	chr5	34823676	34823676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agccacctgtggaagagtacGaggaaatgaaaagttcatat	11	6	1	2	rs565597265		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:34823676G>A	ENST00000265109.3	+	15	2016	c.1729G>A	c.(1729-1731)Gag>Aag	p.E577K	RAI14_ENST00000503673.1_Missense_Mutation_p.E577K|RAI14_ENST00000428746.2_Missense_Mutation_p.E577K|RAI14_ENST00000506376.1_Missense_Mutation_p.E569K|RAI14_ENST00000515799.1_Missense_Mutation_p.E580K|RAI14_ENST00000397449.1_Missense_Mutation_p.E570K|RAI14_ENST00000512629.1_Missense_Mutation_p.E548K	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	577						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GGAAGAGTACGAGGAAATGAA	0.358																																					p.E580K		Atlas-SNP	.											.	RAI14	100	.	0			c.G1738A						.						58	59	59					5																	34823676		2203	4300	6503	SO:0001583	missense	26064	exon17			GAGTACGAGGAAA	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.1729G>A	chr5.hg19:g.34823676G>A	ENSP00000265109:p.Glu577Lys	219.0	0.0		259.0	59.0	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	hg19	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.979144	0.74360	.	.	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.50001	0.78;0.76;0.78;0.78;0.78;0.82;0.82	5.42	5.42	0.78866	.	.	.	.	.	T	0.59742	0.2216	L	0.29908	0.895	0.48452	D	0.999658	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.80764	0.994;0.986;0.915;0.986	T	0.61992	-0.6948	9	0.59425	D	0.04	-25.9427	19.2253	0.93816	0.0:0.0:1.0:0.0	.	569;548;580;577	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	K	577;548;577;577;580;569;570	ENSP00000265109:E577K;ENSP00000422377:E548K;ENSP00000388725:E577K;ENSP00000422942:E577K;ENSP00000427123:E580K;ENSP00000423854:E569K;ENSP00000380591:E570K	ENSP00000265109:E577K	E	+	1	0	RAI14	34859433	1.000000	0.71417	0.952000	0.39060	0.709000	0.40893	6.416000	0.73332	2.555000	0.86185	0.555000	0.69702	GAG	.	.		0.358	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		A	34823676	G	A	34823676	3	1	209	1	0	0	0	0	1	0	0	0	13023	1059	37	1	1848	1	RAI14	5	34823676	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	20952779	34823676	146091584	39	30184										
NUP155	9631	hgsc.bcm.edu	37	chr5	37292009	37292009	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tatatcacagtaattaatgaAgccgttctaatttagcttga	6	6	2	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:37292009A>C	ENST00000231498.3	-	35	4372	c.4169T>G	c.(4168-4170)cTt>cGt	p.L1390R	NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000513532.1_Missense_Mutation_p.L1326R|NUP155_ENST00000381843.2_Missense_Mutation_p.L1331R	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	1390					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TAATTAATGAAGCCGTTCTAA	0.368																																					p.L1390R		Atlas-SNP	.											.	NUP155	116	.	0			c.T4169G						.						76	81	79					5																	37292009		2203	4300	6503	SO:0001583	missense	9631	exon35			TAATGAAGCCGTT	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.4169T>G	chr5.hg19:g.37292009A>C	ENSP00000231498:p.Leu1390Arg	318.0	0.0		385.0	52.0	NM_153485	Q9UBE9|Q9UFL5	Missense_Mutation	SNP	ENST00000231498.3	hg19	CCDS3921.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.392520	0.83011	.	.	ENSG00000113569	ENST00000231498;ENST00000381843;ENST00000434056;ENST00000513532	D;D;D	0.82526	-1.62;-1.6;-1.57	5.05	5.05	0.67936	.	0.065619	0.64402	D	0.000007	D	0.88377	0.6420	L	0.50333	1.59	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.76071	0.987;0.958	D	0.89609	0.3840	10	0.87932	D	0	.	14.9693	0.71220	1.0:0.0:0.0:0.0	.	1326;1390	E9PF10;O75694	.;NU155_HUMAN	R	1390;1331;1352;1326	ENSP00000231498:L1390R;ENSP00000371265:L1331R;ENSP00000422019:L1326R	ENSP00000231498:L1390R	L	-	2	0	NUP155	37327766	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.967000	0.87967	2.119000	0.64992	0.477000	0.44152	CTT	.	.		0.368	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		C	37292009	A	C	37292009	3	2	209	1	0	0	0	0	1	0	0	0	10765	72	3	5	10	5	NUP155	5	37292009	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	2468333	37292009	143623251	40	30185										
GHR	2690	hgsc.bcm.edu	37	chr5	42688998	42688998	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tttttattctgcagattcttCtaaggagcctaaattcacca	5	9	4	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:42688998C>T	ENST00000230882.4	+	4	333	c.143C>T	c.(142-144)tCt>tTt	p.S48F	GHR_ENST00000537449.1_Intron|GHR_ENST00000357703.3_Missense_Mutation_p.S26F	NM_000163.4|NM_001242399.2|NM_001242400.2|NM_001242401.3|NM_001242402.2|NM_001242403.2|NM_001242404.2|NM_001242405.2|NM_001242406.2	NP_000154.1|NP_001229328.1|NP_001229329.1|NP_001229330.1|NP_001229331.1|NP_001229332.1|NP_001229333.1|NP_001229334.1|NP_001229335.1	P10912	GHR_HUMAN	growth hormone receptor	48					2-oxoglutarate metabolic process (GO:0006103)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPK activity (GO:0000187)|allantoin metabolic process (GO:0000255)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|endocytosis (GO:0006897)|fatty acid metabolic process (GO:0006631)|growth hormone receptor signaling pathway (GO:0060396)|insulin-like growth factor receptor signaling pathway (GO:0048009)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|multicellular organismal metabolic process (GO:0044236)|oxaloacetate metabolic process (GO:0006107)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|receptor internalization (GO:0031623)|regulation of multicellular organism growth (GO:0040014)|response to cycloheximide (GO:0046898)|response to estradiol (GO:0032355)|succinate metabolic process (GO:0006105)|taurine metabolic process (GO:0019530)|valine metabolic process (GO:0006573)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|growth hormone receptor complex (GO:0070195)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine receptor activity (GO:0004896)|growth factor binding (GO:0019838)|peptide hormone binding (GO:0017046)|proline-rich region binding (GO:0070064)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			NS(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	GCAGATTCTTCTAAGGAGCCT	0.428																																					p.S55F		Atlas-SNP	.											.	GHR	94	.	0			c.C164T						.						241	229	233					5																	42688998		2203	4300	6503	SO:0001583	missense	2690	exon4			ATTCTTCTAAGGA		CCDS3940.1, CCDS56364.1, CCDS75239.1, CCDS75240.1	5p14-p12	2013-03-25			ENSG00000112964	ENSG00000112964		"Fibronectin type III domain containing"	4263	protein-coding gene	gene with protein product	"growth hormone binding protein"	600946					Standard	NM_001242460		Approved	GHBP	uc003jmt.3	P10912	OTTHUMG00000094791	ENST00000230882.4:c.143C>T	chr5.hg19:g.42688998C>T	ENSP00000230882:p.Ser48Phe	86.0	0.0		99.0	11.0	NM_001242399	Q9HCX2	Missense_Mutation	SNP	ENST00000230882.4	hg19	CCDS3940.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.703116	0.68501	.	.	ENSG00000112964	ENST00000230882;ENST00000357703;ENST00000356276	D;D	0.83163	-1.69;-1.69	5.66	5.66	0.87406	Growth hormone/erythropoietin receptor, ligand binding (1);	0.294159	0.38164	N	0.001796	D	0.88489	0.6450	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.87832	0.2645	10	0.48119	T	0.1	-16.5512	8.9645	0.35867	0.1494:0.7746:0.0:0.0759	.	48	P10912	GHR_HUMAN	F	48;26;48	ENSP00000230882:S48F;ENSP00000350335:S26F	ENSP00000230882:S48F	S	+	2	0	GHR	42724755	0.911000	0.30947	0.998000	0.56505	0.951000	0.60555	1.420000	0.34804	2.657000	0.90304	0.655000	0.94253	TCT	.	.		0.428	GHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211605.2	NM_000163		T	42688998	C	T	42688998	3	4	209	1	0	0	0	0	1	0	0	0	6379	913	32	3	153	3	GHR	5	42688998	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	5396989	42688998	138226262	41	30186										
HCN1	348980	hgsc.bcm.edu	37	chr5	45262400	45262400	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctgcgtgctcttgtgcacttCatttttcggcgtggagctgc	12	11	2	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:45262400C>T	ENST00000303230.4	-	8	2353	c.2296G>A	c.(2296-2298)Gaa>Aaa	p.E766K		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	766					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						TTGTGCACTTCATTTTTCGGC	0.657																																					p.E766K		Atlas-SNP	.											.	HCN1	298	.	0			c.G2296A						.						74	73	73					5																	45262400		2203	4300	6503	SO:0001583	missense	348980	exon8			GCACTTCATTTTT	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.2296G>A	chr5.hg19:g.45262400C>T	ENSP00000307342:p.Glu766Lys	43.0	0.0		70.0	6.0	NM_021072		Missense_Mutation	SNP	ENST00000303230.4	hg19	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.385835	0.25031	.	.	ENSG00000164588	ENST00000303230	D	0.97352	-4.35	5.32	4.42	0.53409	.	0.266202	0.30686	N	0.009087	D	0.93674	0.7979	L	0.44542	1.39	0.40232	D	0.977864	B	0.18013	0.025	B	0.15870	0.014	D	0.90146	0.4217	10	0.06365	T	0.9	.	16.0422	0.80694	0.0:0.8662:0.1338:0.0	.	766	O60741	HCN1_HUMAN	K	766	ENSP00000307342:E766K	ENSP00000307342:E766K	E	-	1	0	HCN1	45298157	1.000000	0.71417	0.981000	0.43875	0.988000	0.76386	4.551000	0.60740	2.491000	0.84063	0.655000	0.94253	GAA	.	.		0.657	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		T	45262400	C	T	45262400	3	4	209	1	0	0	0	0	1	0	0	0	7005	835	29	3	380	3	HCN1	5	45262400	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	2573402	45262400	135652860	42	30187										
PJA2	9867	hgsc.bcm.edu	37	chr5	108714751	108714751	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cactacaagctcctggaataTactctccctcagagtgatta	6	12	2	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:108714751T>C	ENST00000361189.2	-	4	676	c.437A>G	c.(436-438)tAt>tGt	p.Y146C	PJA2_ENST00000361557.3_Missense_Mutation_p.Y146C|PJA2_ENST00000511624.1_5'Flank	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	146					long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		TCCTGGAATATACTCTCCCTC	0.423																																					p.Y146C		Atlas-SNP	.											.	PJA2	53	.	0			c.A437G						.						106	106	106					5																	108714751		2202	4300	6502	SO:0001583	missense	9867	exon4			GGAATATACTCTC	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"RING-type (C3HC4) zinc fingers"	17481	protein-coding gene	gene with protein product			"ring finger protein 131", "praja ring finger 2"	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.437A>G	chr5.hg19:g.108714751T>C	ENSP00000354775:p.Tyr146Cys	79.0	0.0		120.0	9.0	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	hg19	CCDS4099.1	.	.	.	.	.	.	.	.	.	.	T	7.107	0.575261	0.13623	.	.	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.05447	3.44;3.44	5.65	-4.77	0.03219	.	1.001280	0.08053	N	0.996953	T	0.05090	0.0136	N	0.19112	0.55	0.09310	N	1	B	0.15473	0.013	B	0.19391	0.025	T	0.38457	-0.9660	10	0.36615	T	0.2	0.8583	14.7344	0.69406	0.0:0.534:0.0:0.466	.	146	O43164	PJA2_HUMAN	C	146	ENSP00000354775:Y146C;ENSP00000355284:Y146C	ENSP00000354775:Y146C	Y	-	2	0	PJA2	108742650	0.000000	0.05858	0.000000	0.03702	0.589000	0.36550	-0.291000	0.08343	-1.003000	0.03425	-0.408000	0.06270	TAT	.	.		0.423	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819		C	108714751	T	C	108714751	3	2	209	1	0	0	0	0	1	0	0	0	11971	1406	49	2	1717	2	PJA2	5	108714751	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	63452351	108714751	72200509	43	30188										
APC	324	hgsc.bcm.edu	37	chr5	112175960	112175960	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agaaagaggcagaaaaaactAttgattctgaaaaggaccta	9	5	1	5			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:112175960A>G	ENST00000457016.1	+	16	5049	c.4669A>G	c.(4669-4671)Att>Gtt	p.I1557V	APC_ENST00000508376.2_Missense_Mutation_p.I1557V|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.I1557V			P25054	APC_HUMAN	adenomatous polyposis coli	1557	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.I1557fs*2(3)|p.I1557fs*1(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAAAAACTATTGATTCTGA	0.343		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.I1557V	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.,1	APC	4158	.	6	Insertion - Frameshift(3)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(4)|soft_tissue(1)|skin(1)	c.A4669G	GRCh37	CD041153	APC	D		.						82	89	87					5																	112175960		2202	4300	6502	SO:0001583	missense	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AAAACTATTGATT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4669A>G	chr5.hg19:g.112175960A>G	ENSP00000413133:p.Ile1557Val	200.0	0.0		291.0	38.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	0.092	-1.165756	0.01673	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.87809	-2.3;-2.3;-2.3	5.79	-3.91	0.04168	.	0.658116	0.16858	N	0.196638	T	0.58163	0.2103	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.55872	-0.8072	9	.	.	.	0.0445	3.073	0.06237	0.4728:0.0827:0.2918:0.1526	.	1559;1557	Q4LE70;P25054	.;APC_HUMAN	V	1557	ENSP00000413133:I1557V;ENSP00000257430:I1557V;ENSP00000427089:I1557V	.	I	+	1	0	APC	112203859	0.000000	0.05858	0.059000	0.19551	0.515000	0.34225	-0.445000	0.06845	-0.944000	0.03686	-1.080000	0.02220	ATT	.	.		0.343	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175960	A	G	112175960	3	3	209	1	0	0	0	0	1	0	0	0	763	449	16	2	4727	2	APC	5	112175960	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	3461209	112175960	68739300	44	30189										
DDX46	9879	hgsc.bcm.edu	37	chr5	134116885	134116885	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	accaaaaaagcagttgtggaTtctgataagaagaaaggtga	11	4	1	4			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:134116885T>G	ENST00000354283.4	+	7	963	c.828T>G	c.(826-828)gaT>gaG	p.D276E	DDX46_ENST00000452510.2_Missense_Mutation_p.D276E			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	276					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CAGTTGTGGATTCTGATAAGA	0.368																																					p.D276E	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.T828G						.						95	101	99					5																	134116885		2203	4300	6503	SO:0001583	missense	9879	exon7			TGTGGATTCTGAT		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.828T>G	chr5.hg19:g.134116885T>G	ENSP00000346236:p.Asp276Glu	90.0	0.0		164.0	28.0	NM_014829	O94894|Q96EI0|Q9Y658	Missense_Mutation	SNP	ENST00000354283.4	hg19	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	T	6.053	0.378131	0.11466	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	T;T	0.49720	2.99;0.77	5.05	-0.774	0.10991	.	0.381640	0.31290	N	0.007908	T	0.12050	0.0293	N	0.02011	-0.69	0.26580	N	0.973396	B	0.02656	0.0	B	0.04013	0.001	T	0.23797	-1.0178	10	0.02654	T	1	-23.8049	1.6248	0.02721	0.1164:0.1851:0.3107:0.3878	.	276	Q7L014	DDX46_HUMAN	E	276	ENSP00000416534:D276E;ENSP00000346236:D276E	ENSP00000346236:D276E	D	+	3	2	DDX46	134144784	0.168000	0.22989	0.955000	0.39395	0.905000	0.53344	-0.225000	0.09151	0.210000	0.20664	0.260000	0.18958	GAT	.	.		0.368	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		G	134116885	T	G	134116885	3	3	209	1	0	0	0	0	1	0	0	0	4366	1490	52	5	854	5	DDX46	5	134116885	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	21940925	134116885	46798375	45	30190										
KDM3B	51780	hgsc.bcm.edu	37	chr5	137733999	137733999	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	atagatctagagacctcaaaAtacatcctggccaatgttgg	8	9	2	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:137733999A>G	ENST00000314358.5	+	10	3164	c.2964A>G	c.(2962-2964)aaA>aaG	p.K988K	KDM3B_ENST00000394866.1_Silent_p.K644K|KDM3B_ENST00000542866.1_Silent_p.K20K	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	988					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						AGACCTCAAAATACATCCTGG	0.517																																					p.K988K		Atlas-SNP	.											.	KDM3B	177	.	0			c.A2964G						.						134	127	129					5																	137733999		2203	4300	6503	SO:0001819	synonymous_variant	51780	exon10			CTCAAAATACATC	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.2964A>G	chr5.hg19:g.137733999A>G		132.0	0.0		164.0	21.0	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	hg19	CCDS34242.1																																																																																			.	.		0.517	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		G	137733999	A	G	137733999	2	3	209	1	0	0	0	0	0	0	0	1	8136	98	4	2		2	KDM3B	5	137733999	Silent	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	3617114	137733999	43181261	46	30191										
AFAP1L1	134265	hgsc.bcm.edu	37	chr5	148719573	148719573	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctctttctgtgcttcaggaaTgggaaatgaagaagacctag	11	7	3	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:148719573T>A	ENST00000296721.4	+	19	2385	c.2287T>A	c.(2287-2289)Tgg>Agg	p.W763R	AFAP1L1_ENST00000515000.1_Missense_Mutation_p.W720R	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	763						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTTCAGGAATGGGAAATGAA	0.413																																					p.W763R		Atlas-SNP	.											.	AFAP1L1	86	.	0			c.T2287A						.						112	102	105					5																	148719573		2203	4300	6503	SO:0001583	missense	134265	exon19			CAGGAATGGGAAA	AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"Pleckstrin homology (PH) domain containing"	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.2287T>A	chr5.hg19:g.148719573T>A	ENSP00000296721:p.Trp763Arg	68.0	0.0		94.0	38.0	NM_152406	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	hg19	CCDS34274.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.123551	0.77436	.	.	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.61392	0.11;2.64	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.76421	0.3985	M	0.78049	2.395	0.30253	N	0.793947	D;D	0.89917	1.0;0.994	D;P	0.87578	0.998;0.807	T	0.78003	-0.2374	10	0.87932	D	0	-9.184	14.6128	0.68526	0.0:0.0:0.0:1.0	.	720;763	Q8TED9-2;Q8TED9	.;AF1L1_HUMAN	R	763;720	ENSP00000296721:W763R;ENSP00000424427:W720R	ENSP00000296721:W763R	W	+	1	0	AFAP1L1	148699766	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	4.318000	0.59190	2.271000	0.75665	0.459000	0.35465	TGG	.	.		0.413	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		A	148719573	T	A	148719573	3	1	209	1	0	0	0	0	1	0	0	0	354	1464	51	4	2361	4	AFAP1L1	5	148719573	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	10985574	148719573	32195687	47	30192										
GEMIN5	25929	hgsc.bcm.edu	37	chr5	154311736	154311736	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctatggagtggatttcatcaTcatggcctcgaagcctatga	10	9	3	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:154311736T>C	ENST00000285873.7	-	4	659	c.584A>G	c.(583-585)gAt>gGt	p.D195G		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	195					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GATTTCATCATCATGGCCTCG	0.393																																					p.D195G		Atlas-SNP	.											GEMIN5,colon,carcinoma,0,1	GEMIN5	120	.	0			c.A584G						.						144	143	144					5																	154311736		2203	4300	6503	SO:0001583	missense	25929	exon4			TCATCATCATGGC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.584A>G	chr5.hg19:g.154311736T>C	ENSP00000285873:p.Asp195Gly	142.0	0.0		192.0	21.0	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	hg19	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	T	19.21	3.783108	0.70222	.	.	ENSG00000082516	ENST00000285873	T	0.60299	0.2	5.42	5.42	0.78866	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.152705	0.56097	D	0.000024	T	0.59252	0.2180	N	0.16098	0.37	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.65773	0.938;0.938	T	0.62483	-0.6845	10	0.39692	T	0.17	-14.2776	15.4924	0.75619	0.0:0.0:0.0:1.0	.	195;195	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	G	195	ENSP00000285873:D195G	ENSP00000285873:D195G	D	-	2	0	GEMIN5	154291929	1.000000	0.71417	0.978000	0.43139	0.999000	0.98932	7.431000	0.80335	2.057000	0.61298	0.528000	0.53228	GAT	.	.		0.393	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			C	154311736	T	C	154311736	3	2	209	1	0	0	0	0	1	0	0	0	6339	1435	50	2	4042	2	GEMIN5	5	154311736	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	5592163	154311736	26603524	48	30193										
ITK	3702	hgsc.bcm.edu	37	chr5	156649918	156649918	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctgtggtcattgccttatatGactaccaaaccaatgatcct	6	11	1	2	rs369289895		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:156649918G>C	ENST00000422843.3	+	6	693	c.541G>C	c.(541-543)Gac>Cac	p.D181H	CTB-4E7.1_ENST00000519375.1_RNA	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	181	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	TGCCTTATATGACTACCAAAC	0.483			T	SYK	peripheral T-cell lymphoma																																p.D181H	Esophageal Squamous(70;1378 1469 8785 19883)	Atlas-SNP	.		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	.	ITK	136	.	0			c.G541C						.						109	102	104					5																	156649918		2203	4300	6503	SO:0001583	missense	3702	exon6			TTATATGACTACC	D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.541G>C	chr5.hg19:g.156649918G>C	ENSP00000398655:p.Asp181His	125.0	0.0		138.0	15.0	NM_005546	B2R752|Q32ML7	Missense_Mutation	SNP	ENST00000422843.3	hg19	CCDS4336.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.290953	0.80914	.	.	ENSG00000113263	ENST00000521769;ENST00000422843	D;T	0.93953	-3.32;-0.28	5.81	5.81	0.92471	Src homology-3 domain (4);	0.096082	0.64402	D	0.000001	D	0.97626	0.9222	H	0.94423	3.535	0.51012	D	0.9999	D	0.76494	0.999	D	0.70487	0.969	D	0.98380	1.0558	10	0.87932	D	0	.	17.008	0.86398	0.0:0.0:1.0:0.0	.	181	Q08881	ITK_HUMAN	H	56;181	ENSP00000430327:D56H;ENSP00000398655:D181H	ENSP00000398655:D181H	D	+	1	0	ITK	156582496	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	6.554000	0.73923	2.746000	0.94184	0.591000	0.81541	GAC	.	.		0.483	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2			C	156649918	G	C	156649918	3	2	209	1	0	0	0	0	1	0	0	0	7918	1290	45	4	563	4	ITK	5	156649918	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	2338182	156649918	24265342	49	30194										
ZNF346	23567	hgsc.bcm.edu	37	chr5	176449747	176449747	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gtttgcggggaagatggagtAtcccgcgccggccacggtgc	17	11	0	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr5:176449747A>G	ENST00000358149.3	+	1	51	c.8A>G	c.(7-9)tAt>tGt	p.Y3C	ZNF346_ENST00000506693.1_Missense_Mutation_p.Y3C|ZNF346_ENST00000503039.1_Missense_Mutation_p.Y3C|ZNF346_ENST00000261948.4_Missense_Mutation_p.Y3C|ZNF346_ENST00000512315.1_Missense_Mutation_p.Y3C|ZNF346_ENST00000511834.1_Missense_Mutation_p.Y3C|ZNF346_ENST00000503425.1_Missense_Mutation_p.Y3C	NM_012279.2	NP_036411.1	Q9UL40	ZN346_HUMAN	zinc finger protein 346	3					positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	14	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGATGGAGTATCCCGCGCCG	0.667																																					p.Y3C		Atlas-SNP	.											.	ZNF346	24	.	0			c.A8G						.						5	6	6					5																	176449747		2040	4168	6208	SO:0001583	missense	23567	exon1			TGGAGTATCCCGC	AF083340	CCDS4409.1	5q35.3	2012-10-05			ENSG00000113761	ENSG00000113761			16403	protein-coding gene	gene with protein product		605308				10488071	Standard	NM_012279		Approved	JAZ, Zfp346	uc003mfi.3	Q9UL40	OTTHUMG00000130848	ENST00000358149.3:c.8A>G	chr5.hg19:g.176449747A>G	ENSP00000350869:p.Tyr3Cys	64.0	0.0		159.0	19.0	NM_012279	B7Z367|Q68CV9|Q6ZMW1	Missense_Mutation	SNP	ENST00000358149.3	hg19	CCDS4409.1	.	.	.	.	.	.	.	.	.	.	A	2.001	-0.429389	0.04701	.	.	ENSG00000113761	ENST00000358149;ENST00000506693;ENST00000512315;ENST00000503425;ENST00000261948;ENST00000511834;ENST00000503039	T;T;T;T;T;T;T	0.50813	0.83;0.73;0.79;0.79;0.78;0.82;0.78	3.27	-2.3	0.06785	.	1.280230	0.05805	N	0.612872	T	0.26448	0.0646	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.11235	0.001;0.001;0.004;0.0;0.001	B;B;B;B;B	0.09377	0.001;0.001;0.004;0.001;0.001	T	0.21552	-1.0242	10	0.39692	T	0.17	.	8.3451	0.32268	0.375:0.0:0.625:0.0	.	3;3;3;3;3	B7Z4J8;B7Z367;Q9UL40-2;B7Z4N4;Q9UL40	.;.;.;.;ZN346_HUMAN	C	3	ENSP00000350869:Y3C;ENSP00000423515:Y3C;ENSP00000421089:Y3C;ENSP00000421212:Y3C;ENSP00000261948:Y3C;ENSP00000425725:Y3C;ENSP00000424495:Y3C	ENSP00000261948:Y3C	Y	+	2	0	ZNF346	176382353	0.154000	0.22792	0.005000	0.12908	0.001000	0.01503	0.046000	0.14035	-0.500000	0.06614	-0.379000	0.06801	TAT	.	.		0.667	ZNF346-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253415.2	NM_012279		G	176449747	A	G	176449747	3	3	209	1	0	0	0	0	1	0	0	0	17875	449	16	2	10	2	ZNF346	5	176449747	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	19799829	176449747	4465513	50	30195										
ZBTB12	221527	hgsc.bcm.edu	37	chr6	31868471	31868472	+	In_Frame_Ins	INS	-	-	TCCTCA													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cgatgcagatgtcagacacgINStcctcatcctcatcctcatc							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr6:31868471_31868472insTCCTCA	ENST00000375527.2	-	2	786_787	c.611_612insTGAGGA	c.(610-612)gac>gaTGAGGAc	p.204_204D>DED	C2_ENST00000469372.1_Intron|C2_ENST00000452323.2_5'Flank	NM_181842.2	NP_862825.1	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	204					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(5)|prostate(1)|skin(1)	10						TGTCAGACACGTCCTCATCCTC	0.614																																					p.D204delinsDED		Atlas-INDEL	.											.	ZBTB12	25	.	0			c.612_613insTGAGGA						.																																			SO:0001652	inframe_insertion	221527	exon2			.	BC043609	CCDS4727.1	6p21.31	2013-01-08	2004-04-15	2004-04-16	ENSG00000204366	ENSG00000204366		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	19066	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 46"	C6orf46		9545376	Standard	NM_181842		Approved	G10, NG35, D6S59E	uc003nyd.1	Q9Y330	OTTHUMG00000031169	ENST00000375527.2:c.606_611dupTGAGGA	chr6.hg19:g.31868472_31868477dupTCCTCA	ENSP00000364677:p.GluAsp204dup	29.0	0.0		48.0	12.0	NM_181842	B0UY00|Q5JQ98	In_Frame_Ins	INS	ENST00000375527.2	hg19	CCDS4727.1																																																																																			.	.		0.614	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842		TCCTCA	31868472	-	TCCTCA	31868471	7	5	209	1	0	1	1	0	0	0	0	0	17540	1136	40	0	771	0	ZBTB12	6	31868471	In_Frame_Ins	INS	-	TCGA-DD-AAE3-01A-11D-A40R-10		31868471	139246596	51	30196										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33651106	33651106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ccagctacaaggcaaccacgCgggccttcccccgcgtcacc	9	20	1	0	rs531158838		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr6:33651106C>T	ENST00000374316.5	+	36	5780	c.4720C>T	c.(4720-4722)Cgg>Tgg	p.R1574W	ITPR3_ENST00000605930.1_Missense_Mutation_p.R1574W			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1574					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GGCAACCACGCGGGCCTTCCC	0.652													C|||	1	0.000199681	8e-04	0	5008	,	,		16915	0		0	False		,,,				2504	0				p.R1574W		Atlas-SNP	.											.	ITPR3	409	.	0			c.C4720T						.						23	20	21					6																	33651106		2195	4297	6492	SO:0001583	missense	3710	exon35			ACCACGCGGGCCT	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.4720C>T	chr6.hg19:g.33651106C>T	ENSP00000363435:p.Arg1574Trp	129.0	0.0		188.0	70.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760342	0.69763	.	.	ENSG00000096433	ENST00000374316	T	0.64085	-0.08	4.71	1.79	0.24919	.	0.000000	0.85682	D	0.000000	T	0.65913	0.2737	M	0.76574	2.34	0.53005	D	0.999964	D	0.89917	1.0	D	0.83275	0.996	T	0.67369	-0.5688	10	0.87932	D	0	-34.3961	7.4903	0.27458	0.4463:0.4778:0.0:0.0759	.	1574	Q14573	ITPR3_HUMAN	W	1574	ENSP00000363435:R1574W	ENSP00000363435:R1574W	R	+	1	2	ITPR3	33759084	0.952000	0.32445	0.751000	0.31187	0.822000	0.46500	2.218000	0.42889	0.042000	0.15717	-0.268000	0.10319	CGG	.	.		0.652	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		T	33651106	C	T	33651106	3	4	209	1	0	0	0	0	1	0	0	0	7931	759	27	1	4858	1	ITPR3	6	33651106	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	1782635	33651106	137463961	52	30197										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33654876	33654876	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tcatcagcctgcggccccagGagctggtgaggctgggcagg	17	12	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr6:33654876G>C	ENST00000374316.5	+	45	7130	c.6070G>C	c.(6070-6072)Gag>Cag	p.E2024Q	ITPR3_ENST00000605930.1_Missense_Mutation_p.E2024Q			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2024					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GCGGCCCCAGGAGCTGGTGAG	0.647																																					p.E2024Q		Atlas-SNP	.											.	ITPR3	409	.	0			c.G6070C						.						37	38	38					6																	33654876		2201	4290	6491	SO:0001583	missense	3710	exon44			CCCCAGGAGCTGG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.6070G>C	chr6.hg19:g.33654876G>C	ENSP00000363435:p.Glu2024Gln	80.0	0.0		101.0	9.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.469347	0.43839	.	.	ENSG00000096433	ENST00000374316	D	0.91237	-2.81	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.85470	0.5704	N	0.16130	0.375	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.986	T	0.82792	-0.0282	10	0.02654	T	1	-39.143	18.2503	0.90000	0.0:0.0:1.0:0.0	.	2024;1694	Q14573;Q59ES2	ITPR3_HUMAN;.	Q	2024	ENSP00000363435:E2024Q	ENSP00000363435:E2024Q	E	+	1	0	ITPR3	33762854	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.701000	0.98710	2.304000	0.77564	0.561000	0.74099	GAG	.	.		0.647	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		C	33654876	G	C	33654876	3	2	209	1	0	0	0	0	1	0	0	0	7931	1175	41	4	6244	4	ITPR3	6	33654876	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	3770	33654876	137460191	53	30198										
TREML4	285852	hgsc.bcm.edu	37	chr6	41196730	41196730	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tggtgtggaatctacaacgcTtccgaaaacatcatcactgt	8	10	3	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr6:41196730T>C	ENST00000341495.2	+	2	446	c.342T>C	c.(340-342)gcT>gcC	p.A114A	TREML4_ENST00000448827.2_Silent_p.A114A	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	114	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					TCTACAACGCTTCCGAAAACA	0.488																																					p.A114A		Atlas-SNP	.											.	TREML4	25	.	0			c.T342C						.						85	81	82					6																	41196730		2203	4300	6503	SO:0001819	synonymous_variant	285852	exon2			CAACGCTTCCGAA	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"Immunoglobulin superfamily / V-set domain containing"	30807	protein-coding gene	gene with protein product	"TREM like transcript 4"	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.342T>C	chr6.hg19:g.41196730T>C		62.0	0.0		49.0	38.0	NM_198153	B7ZL92	Silent	SNP	ENST00000341495.2	hg19	CCDS34446.1																																																																																			.	.		0.488	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2			C	41196730	T	C	41196730	2	2	209	1	0	0	0	0	0	0	0	1	16489	1596	56	2		2	TREML4	6	41196730	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	7541854	41196730	129918337	54	30199										
SUPT3H	8464	hgsc.bcm.edu	37	chr6	45289589	45289589	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	taacaatagggaaaaactgaTtttccaattatttctataga	5	5	1	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr6:45289589T>A	ENST00000371460.1	-	4	395	c.78A>T	c.(76-78)aaA>aaT	p.K26N	SUPT3H_ENST00000306867.5_Intron|SUPT3H_ENST00000459689.1_Intron|SUPT3H_ENST00000371459.1_Intron|SUPT3H_ENST00000371461.2_Missense_Mutation_p.K26N	NM_181356.2	NP_852001.1	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog (S. cerevisiae)	0					chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	transcription coactivator activity (GO:0003713)			breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	12						GAAAAACTGATTTTCCAATTA	0.313																																					p.K26N		Atlas-SNP	.											.	SUPT3H	75	.	0			c.A78T						.						41	41	41					6																	45289589		2201	4295	6496	SO:0001583	missense	8464	exon4			AACTGATTTTCCA	AF069734	CCDS34465.1, CCDS34466.1, CCDS75464.1	6p21.1-p12.3	2008-05-15	2001-11-28		ENSG00000196284	ENSG00000196284			11466	protein-coding gene	gene with protein product		602947	"suppressor of Ty (S.cerevisiae) 3 homolog"			9674425, 9726987	Standard	NM_003599		Approved	SPT3, SPT3L	uc003oxp.4	O75486	OTTHUMG00000014773	ENST00000371460.1:c.78A>T	chr6.hg19:g.45289589T>A	ENSP00000360515:p.Lys26Asn	74.0	0.0		103.0	18.0	NM_181356	A6NKG9|B2R9Q5|O76066|Q5TAV9|Q86VN7	Missense_Mutation	SNP	ENST00000371460.1	hg19	CCDS34466.1	.	.	.	.	.	.	.	.	.	.	T	11.41	1.631544	0.29068	.	.	ENSG00000196284	ENST00000371460;ENST00000371461	T;T	0.50001	0.76;0.76	4.92	-2.32	0.06745	.	0.977903	0.08360	N	0.957895	T	0.11410	0.0278	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26985	-1.0087	9	0.52906	T	0.07	.	0.6557	0.00834	0.3068:0.1292:0.1599:0.404	.	26	O75486-3	.	N	26	ENSP00000360515:K26N;ENSP00000360516:K26N	ENSP00000360515:K26N	K	-	3	2	SUPT3H	45397567	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.134000	0.15932	-0.451000	0.07097	-0.646000	0.03943	AAA	.	.		0.313	SUPT3H-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106910.3	NM_181356		A	45289589	T	A	45289589	3	1	209	1	0	0	0	0	1	0	0	0	15412	1490	52	4	948	4	SUPT3H	6	45289589	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	4092859	45289589	125825478	55	30200										
GPR115	221393	hgsc.bcm.edu	37	chr6	47681896	47681896	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ggggctatcctgagagaagcCcacttgcaaaatgtgagtct	12	9	1	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr6:47681896C>T	ENST00000283303.2	+	6	1173	c.915C>T	c.(913-915)gcC>gcT	p.A305A	GPR115_ENST00000371220.1_Silent_p.A362A|RN7SKP116_ENST00000516902.1_RNA|GPR115_ENST00000327753.3_Silent_p.A305A	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	305					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						TGAGAGAAGCCCACTTGCAAA	0.473																																					p.A305A	GBM(22;431 510 9010 26644 32828)	Atlas-SNP	.											.	GPR115	140	.	0			c.C915T						.						60	65	63					6																	47681896		2203	4300	6503	SO:0001819	synonymous_variant	221393	exon6			AGAAGCCCACTTG	AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.915C>T	chr6.hg19:g.47681896C>T		104.0	0.0		147.0	23.0	NM_153838	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Silent	SNP	ENST00000283303.2	hg19	CCDS4922.2																																																																																			.	.		0.473	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		T	47681896	C	T	47681896	2	4	209	1	0	0	0	0	0	0	0	1	6640	610	22	3		3	GPR115	6	47681896	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	2392307	47681896	123433171	56	30201										
RIMS1	22999	hgsc.bcm.edu	37	chr6	73102484	73102484	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ggaccagcccagcttgttggCcgccaaacccttgccacccc	9	19	0	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr6:73102484C>A	ENST00000521978.1	+	31	4590	c.4590C>A	c.(4588-4590)ggC>ggA	p.G1530G	RIMS1_ENST00000538414.1_Silent_p.G336G|RIMS1_ENST00000425662.2_Silent_p.G598G|RIMS1_ENST00000264839.7_Silent_p.G1379G|RIMS1_ENST00000491071.2_Silent_p.G1353G|RIMS1_ENST00000401910.3_Silent_p.G850G|RIMS1_ENST00000414192.2_Silent_p.G57G|RIMS1_ENST00000431478.2_3'UTR|RIMS1_ENST00000517960.1_Silent_p.G1313G|RIMS1_ENST00000520567.1_Silent_p.G1180G|RIMS1_ENST00000522291.1_Silent_p.G1129G|RIMS1_ENST00000518273.1_Silent_p.G1209G|RIMS1_ENST00000517827.1_Silent_p.G664G|RIMS1_ENST00000348717.5_Silent_p.G1313G|RIMS1_ENST00000523963.1_Silent_p.G655G	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1530					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				AGCTTGTTGGCCGCCAAACCC	0.388																																					p.G1530G		Atlas-SNP	.											.	RIMS1	278	.	0			c.C4590A						.						87	82	84					6																	73102484		1842	4103	5945	SO:0001819	synonymous_variant	22999	exon31			TGTTGGCCGCCAA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.4590C>A	chr6.hg19:g.73102484C>A		93.0	0.0		113.0	11.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Silent	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.293|9.293	1.051193|1.051193	0.19827|0.19827	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000522211|ENST00000517433	.|.	.|.	.|.	5.5|5.5	1.03|1.03	0.20045|0.20045	.|.	.|.	.|.	.|.	.|.	T|T	0.46619|0.46619	0.1402|0.1402	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.44236|0.44236	-0.9341|-0.9341	4|4	.|.	.|.	.|.	-16.1788|-16.1788	11.6351|11.6351	0.51198|0.51198	0.4883:0.4495:0.0:0.0622|0.4883:0.4495:0.0:0.0622	.|.	.|.	.|.	.|.	D|T	448|876	.|.	.|.	A|P	+|+	2|1	0|0	RIMS1|RIMS1	73159205|73159205	0.432000|0.432000	0.25554|0.25554	0.998000|0.998000	0.56505|0.56505	0.985000|0.985000	0.73830|0.73830	-0.232000|-0.232000	0.09055|0.09055	0.259000|0.259000	0.21709|0.21709	-0.189000|-0.189000	0.12847|0.12847	GCC|CCG	.	.		0.388	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			A	73102484	C	A	73102484	2	1	209	1	0	0	0	0	0	0	0	1	13382	726	26	3		3	RIMS1	6	73102484	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	25420588	73102484	98012583	57	30202										
RWDD2A	112611	hgsc.bcm.edu	37	chr6	83905923	83905923	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gccaattcttagaatttctcAagaagcacaaaagtgagcat	7	8	2	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr6:83905923A>T	ENST00000369724.4	+	3	1016	c.811A>T	c.(811-813)Aag>Tag	p.K271*	RWDD2A_ENST00000539997.1_Nonsense_Mutation_p.K217*|PGM3_ENST00000506587.1_5'Flank|PGM3_ENST00000513973.1_5'Flank|PGM3_ENST00000512866.1_5'Flank|PGM3_ENST00000283977.4_5'Flank	NM_033411.3	NP_219479.2	Q9UIY3	RWD2A_HUMAN	RWD domain containing 2A	271										cervix(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	5		all_cancers(76;2.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00217)		BRCA - Breast invasive adenocarcinoma(397;0.045)		AGAATTTCTCAAGAAGCACAA	0.368																																					p.K271X		Atlas-SNP	.											RWDD2A,NS,carcinoma,0,1	RWDD2A	12	.	0			c.A811T						.						72	74	73					6																	83905923		2203	4300	6503	SO:0001587	stop_gained	112611	exon3			TTTCTCAAGAAGC	BC010930	CCDS4998.1	6q15	2012-12-07	2007-07-17	2007-07-17	ENSG00000013392	ENSG00000013392			21385	protein-coding gene	gene with protein product			"RWD domain containing 2"	RWDD2			Standard	NM_033411		Approved	MGC13523, dJ747H23.2	uc003pjx.4	Q9UIY3	OTTHUMG00000015109	ENST00000369724.4:c.811A>T	chr6.hg19:g.83905923A>T	ENSP00000358739:p.Lys271*	128.0	1.0		178.0	76.0	NM_033411	B4DIQ3|E1P548|Q2M3R3|Q96FH1	Nonsense_Mutation	SNP	ENST00000369724.4	hg19	CCDS4998.1	.	.	.	.	.	.	.	.	.	.	A	45	12.058760	0.99631	.	.	ENSG00000013392	ENST00000369724;ENST00000539997	.	.	.	5.65	5.65	0.86999	.	0.214637	0.40818	N	0.001017	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.6986	16.0399	0.80667	1.0:0.0:0.0:0.0	.	.	.	.	X	271;217	.	ENSP00000358739:K271X	K	+	1	0	RWDD2A	83962642	1.000000	0.71417	0.871000	0.34182	0.872000	0.50106	7.957000	0.87870	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.368	RWDD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041348.2	NM_033411		T	83905923	A	T	83905923	4	4	209	1	0	0	0	0	0	1	0	0	13770	131	5	4	817	4	RWDD2A	6	83905923	Nonsense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	10803439	83905923	87209144	58	30203										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128540097	128540097	+	Frame_Shift_Del	DEL	C	C	-													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	aagttgagcaaaattggacaCaccggaacctcgttctgact							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr6:128540097delC	ENST00000368215.3	-	6	837	c.838delG	c.(838-840)gtgfs	p.V280fs	PTPRK_ENST00000532331.1_Frame_Shift_Del_p.V280fs|PTPRK_ENST00000368226.4_Frame_Shift_Del_p.V280fs|PTPRK_ENST00000368227.3_Frame_Shift_Del_p.V280fs|PTPRK_ENST00000368210.3_Frame_Shift_Del_p.V280fs|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368207.3_Frame_Shift_Del_p.V280fs|PTPRK_ENST00000368213.5_Frame_Shift_Del_p.V280fs			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	280	Ig-like C2-type.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		AAATTGGACACACCGGAACCT	0.398																																					p.V280fs		Atlas-INDEL	.											.	PTPRK	330	.	0			c.839delT						.						153	136	141					6																	128540097		2203	4300	6503	SO:0001589	frameshift_variant	5796	exon6			.	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.838delG	chr6.hg19:g.128540097delC	ENSP00000357198:p.Val280fs	125.0	0.0		64.0	22.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Frame_Shift_Del	DEL	ENST00000368215.3	hg19																																																																																				.	.		0.398	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			-	128540097	C	-	128540097	7	5	209	1	0	1	0	1	0	0	0	0	12820	478	17	0	3606	0	PTPRK	6	128540097	Frame_Shift_Del	DEL	C	TCGA-DD-AAE3-01A-11D-A40R-10	44634174	128540097	42574970	59	30204										
MICALL2	79778	hgsc.bcm.edu	37	chr7	1479677	1479694	+	In_Frame_Del	DEL	GCCCTCGGCTCTGCCAGG	GCCCTCGGCTCTGCCAGG	-													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ccttcctgggggcctcccccGccctcggctctgccagggcc					rs375638403|rs143197912	byFrequency	TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	GCCCTCGGCTCTGCCAGG	GCCCTCGGCTCTGCCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr7:1479677_1479694delGCCCTCGGCTCTGCCAGG	ENST00000297508.7	-	9	2008_2025	c.1833_1850delCCTGGCAGAGCCGAGGGC	c.(1831-1851)gccctggcagagccgagggcg>gcg	p.611_617ALAEPRA>A	MICALL2_ENST00000471899.1_5'Flank|MICALL2_ENST00000405088.4_In_Frame_Del_p.399_405ALAEPRA>A	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	611	Mediates targeting to the cell plasma membrane. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)	p.P615L(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		GGCCTCCCCCGCCCTCGGCTCTGCCAGGGCCCGTGGTT	0.697																																					p.612_617del		Atlas-INDEL	.											.	MICALL2	63	.	1	Substitution - Missense(1)	breast(1)	c.1834_1851del						.																																			SO:0001651	inframe_deletion	79778	exon9			.	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"junctional Rab13-binding protein"					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.1833_1850delCCTGGCAGAGCCGAGGGC	chr7.hg19:g.1479677_1479694delGCCCTCGGCTCTGCCAGG	ENSP00000297508:p.Ala611_Arg616del	133.0	0.0		130.0	29.0	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	In_Frame_Del	DEL	ENST00000297508.7	hg19	CCDS5324.1																																																																																			.	.		0.697	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924		-	1479694	GCCCTCGGCTCTGCCAGG	-	1479677	7	5	209	1	0	1	0	1	0	0	0	0	9583	1087	38	0	900	0	MICALL2	7	1479677	In_Frame_Del	DEL	GCCCTCGGCTCTGCCAGG	TCGA-DD-AAE3-01A-11D-A40R-10		1479677	157658986	60	30205										
EGFR	1956	hgsc.bcm.edu	37	chr7	55242460	55242460	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	aagttaaaattcccgtcgctAtcaaggaattaagagaagca	8	7	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr7:55242460A>G	ENST00000275493.2	+	19	2407	c.2230A>G	c.(2230-2232)Atc>Gtc	p.I744V	EGFR_ENST00000455089.1_Missense_Mutation_p.I699V|EGFR_ENST00000454757.2_Missense_Mutation_p.I691V|EGFR_ENST00000442591.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	744	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.I744_A750>VK(1)|p.I744_E749>LKR(1)|p.I744V(1)|p.E746_T751>I(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TCCCGTCGCTATCAAGGAATT	0.473		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.I744V		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	EGFR,NS,carcinoma,-1,1	EGFR	20426	.	4	Complex - deletion inframe(3)|Substitution - Missense(1)	lung(4)	c.A2230G						.						113	109	111					7																	55242460		2203	4300	6503	SO:0001583	missense	1956	exon19	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GTCGCTATCAAGG		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2230A>G	chr7.hg19:g.55242460A>G	ENSP00000275493:p.Ile744Val	79.0	0.0		99.0	12.0	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	hg19	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.287834	0.80803	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	T;T;T	0.78481	-1.18;-1.18;-1.18	5.67	5.67	0.87782	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73063	0.3539	N	0.02960	-0.455	0.58432	D	0.99999	P;D	0.69078	0.845;0.997	B;D	0.65684	0.403;0.937	T	0.81754	-0.0788	10	0.87932	D	0	.	14.73	0.69374	1.0:0.0:0.0:0.0	.	699;744	Q504U8;P00533	.;EGFR_HUMAN	V	699;614;744;691	ENSP00000415559:I699V;ENSP00000275493:I744V;ENSP00000395243:I691V	ENSP00000275493:I744V	I	+	1	0	EGFR	55209954	1.000000	0.71417	0.998000	0.56505	0.892000	0.51952	9.236000	0.95360	2.161000	0.67846	0.459000	0.35465	ATC	.	.		0.473	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55242460	A	G	55242460	3	3	209	1	0	0	0	0	1	0	0	0	4969	449	16	2	2568	2	EGFR	7	55242460	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	53762783	55242460	103896203	61	30206										
SLC25A40	55972	hgsc.bcm.edu	37	chr7	87477196	87477196	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	acaattccagcaacaattggTatgcaggtttcattttctcc	6	10	2	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr7:87477196T>C	ENST00000341119.5	-	7	775	c.429A>G	c.(427-429)atA>atG	p.I143M		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40	143					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.I143I(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	17	Esophageal squamous(14;0.00202)					CAACAATTGGTATGCAGGTTT	0.348																																					p.I143M		Atlas-SNP	.											SLC25A40,NS,carcinoma,0,1	SLC25A40	32	.	1	Substitution - coding silent(1)	lung(1)	c.A429G						.						55	54	54					7																	87477196		2203	4300	6503	SO:0001583	missense	55972	exon7			AATTGGTATGCAG	AF125531	CCDS5610.1	7q21.12	2013-05-22			ENSG00000075303	ENSG00000075303		"Solute carriers"	29680	protein-coding gene	gene with protein product		610821				16949250	Standard	NM_018843		Approved	MCFP	uc003uje.3	Q8TBP6	OTTHUMG00000131033	ENST00000341119.5:c.429A>G	chr7.hg19:g.87477196T>C	ENSP00000344831:p.Ile143Met	152.0	0.0		154.0	30.0	NM_018843	A8K483|D6W5P6|Q53GB1|Q9UHR1	Missense_Mutation	SNP	ENST00000341119.5	hg19	CCDS5610.1	.	.	.	.	.	.	.	.	.	.	T	13.90	2.375060	0.42105	.	.	ENSG00000075303	ENST00000341119	T	0.78707	-1.2	5.13	3.94	0.45596	Mitochondrial carrier domain (2);	0.160905	0.64402	D	0.000020	T	0.80417	0.4619	L	0.61036	1.89	0.31432	N	0.673039	P	0.42993	0.797	P	0.55667	0.781	T	0.78043	-0.2358	10	0.33940	T	0.23	.	5.878	0.18840	0.2835:0.0:0.1248:0.5917	.	143	Q8TBP6	S2540_HUMAN	M	143	ENSP00000344831:I143M	ENSP00000344831:I143M	I	-	3	3	SLC25A40	87315132	1.000000	0.71417	0.993000	0.49108	0.598000	0.36846	1.072000	0.30678	0.875000	0.35847	0.482000	0.46254	ATA	.	.		0.348	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	NM_018843		C	87477196	T	C	87477196	3	2	209	1	0	0	0	0	1	0	0	0	14520	1628	57	2	611	2	SLC25A40	7	87477196	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	32234736	87477196	71661467	62	30207										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98513492	98513492	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tatcaggagttcttgcctctCcttccaaacctcctgcaagg	7	14	3	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr7:98513492C>A	ENST00000359863.4	+	19	2555	c.2346C>A	c.(2344-2346)ctC>ctA	p.L782L	TRRAP_ENST00000355540.3_Silent_p.L782L|TRRAP_ENST00000446306.3_Silent_p.L781L	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	782					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TCTTGCCTCTCCTTCCAAACC	0.498																																					p.L782L		Atlas-SNP	.											.	TRRAP	863	.	0			c.C2346A						.						136	117	123					7																	98513492		2203	4300	6503	SO:0001819	synonymous_variant	8295	exon19			GCCTCTCCTTCCA	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.2346C>A	chr7.hg19:g.98513492C>A		103.0	0.0		75.0	11.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	hg19	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	9.382	1.073344	0.20147	.	.	ENSG00000196367	ENST00000456197	.	.	.	5.7	1.66	0.24008	.	.	.	.	.	T	0.55752	0.1940	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47446	-0.9117	4	.	.	.	.	8.1337	0.31041	0.0:0.3804:0.4599:0.1597	.	.	.	.	Y	497	.	.	S	+	2	0	TRRAP	98351428	0.996000	0.38824	0.963000	0.40424	0.991000	0.79684	0.264000	0.18497	0.337000	0.23665	0.655000	0.94253	TCC	.	.		0.498	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		A	98513492	C	A	98513492	2	1	209	1	0	0	0	0	0	0	0	1	16616	842	30	3		3	TRRAP	7	98513492	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	11036296	98513492	60625171	63	30208										
EXOC4	60412	hgsc.bcm.edu	37	chr7	132990717	132990720	+	Missense_Mutation	ONP	GAAC	GAAC	TTTT													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gagcttcacagcaagaagatGaaccttcacttggttctcat							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G|A|A|C	G|A|A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr7:132990717_132990720GAAC>TTTT	ENST00000253861.4	+	4	587_590	c.558_561GAAC>TTTT	c.(556-561)atGAAC>atTTTT	p.186_187MN>IF	EXOC4_ENST00000539845.1_Missense_Mutation_p.85_86MN>IF|EXOC4_ENST00000393161.2_Missense_Mutation_p.186_187MN>IF	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	186					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				GCAAGAAGATGAACCTTCACTTGG	0.475																																					p.M186I|p.N187Y|p.N187I|p.N187N		Atlas-SNP	.											.	EXOC4	118	.	0			c.G558T|c.A559T|c.A560T|c.C561T						.																																			SO:0001583	missense	60412	exon4			GAAGATGAACCTT|AAGATGAACCTTC|AGATGAACCTTCA|GATGAACCTTCAC	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"SEC8-like 1 (S. cerevisiae)"	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.558_561GAAC>TTTT	chr7.hg19:g.132990717GAAC>TTTT	ENSP00000253861:p.M186_N187delinsIF	93.0|93.0|93.0|94.0	0.0		90.0|89.0|89.0|88.0	15.0|14.0|14.0|14.0	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation|Missense_Mutation|Missense_Mutation|Silent	SNP	ENST00000253861.4	hg19	CCDS5829.1																																																																																			.	.		0.475	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		TTTT	132990720	GAAC	TTTT	132990717	3	4	209	1	0	0	0	0	1	0	0	0	5308	1290	45	3	572	3	EXOC4	7	132990717	Missense_Mutation	ONP	GAAC	TCGA-DD-AAE3-01A-11D-A40R-10	34477225	132990717	26147946	64	30209										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	146829531	146829531	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ggcaatgtggagattgacctCactgaaagcaaagtgggtgt	14	6	1	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr7:146829531C>A	ENST00000361727.3	+	8	1794	c.1278C>A	c.(1276-1278)ctC>ctA	p.L426L		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	426	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			AGATTGACCTCACTGAAAGCA	0.443										HNSCC(39;0.1)																											p.L426L		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.C1278A						.						128	111	117					7																	146829531		2203	4300	6503	SO:0001819	synonymous_variant	26047	exon8			TGACCTCACTGAA	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1278C>A	chr7.hg19:g.146829531C>A		120.0	0.0		102.0	25.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	hg19	CCDS5889.1																																																																																			.	.		0.443	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			A	146829531	C	A	146829531	2	1	209	1	0	0	0	0	0	0	0	1	3649	813	29	3		3	CNTNAP2	7	146829531	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	13838814	146829531	12309132	65	30210										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	147259228	147259228	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	taggatattttgtttgttctAgctatctacgagccttcctg	8	8	2	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr7:147259228A>G	ENST00000361727.3	+	12	2293		c.e12-1			NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2						adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TGTTTGTTCTAGCTATCTACG	0.453										HNSCC(39;0.1)																											.		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.1778-2A>G						.						109	101	104					7																	147259228		2203	4300	6503	SO:0001630	splice_region_variant	26047	exon12			TGTTCTAGCTATC	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1778-1A>G	chr7.hg19:g.147259228A>G		80.0	0.0		76.0	18.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Splice_Site	SNP	ENST00000361727.3	hg19	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.126805	0.77549	.	.	ENSG00000174469	ENST00000361727	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2071	0.73186	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNTNAP2	146890161	1.000000	0.71417	0.989000	0.46669	0.700000	0.40528	9.145000	0.94634	2.257000	0.74773	0.533000	0.62120	.	.	.		0.453	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1		Intron	G	147259228	A	G	147259228	5	3	209	1	0	0	0	0	0	0	1	0	3649	434	15	2	1822	2	CNTNAP2	7	147259228	Splice_Site	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	429697	147259228	11879435	66	30211										
MLL3	58508	hgsc.bcm.edu	37	chr7	151842365	151842365	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gaaggtataattttcacatgCctcaaccccaggaagctgaa	8	10	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr7:151842365C>G	ENST00000262189.6	-	54	14265	c.14047G>C	c.(14047-14049)Gca>Cca	p.A4683P	KMT2C_ENST00000485655.2_5'Flank|KMT2C_ENST00000355193.2_Missense_Mutation_p.A4740P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4683	FYR C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00876}.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTTTCACATGCCTCAACCCCA	0.488																																					p.A4683P		Atlas-SNP	.											.	MLL3	1564	.	0			c.G14047C						.						73	64	67					7																	151842365		2203	4300	6503	SO:0001583	missense	58508	exon54			CACATGCCTCAAC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.14047G>C	chr7.hg19:g.151842365C>G	ENSP00000262189:p.Ala4683Pro	68.0	0.0		56.0	10.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.65|16.65	3.182237|3.182237	0.57800|0.57800	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	T;T;T|.	0.44482|.	0.92;0.92;0.92|.	5.23|5.23	5.23|5.23	0.72850|0.72850	FY-rich, C-terminal (1);FY-rich, C-terminal subgroup (1);|.	0.000000|.	0.44285|.	U|.	0.000467|.	T|T	0.72510|0.72510	0.3469|0.3469	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;1.0;1.0|.	D;D;D|.	0.81914|.	0.995;0.984;0.984|.	T|T	0.69680|0.69680	-0.5080|-0.5080	10|5	0.66056|.	D|.	0.02|.	.|.	19.161|19.161	0.93531|0.93531	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4683;3801;4740|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	P|A	4683;4740;1300|2243	ENSP00000262189:A4683P;ENSP00000347325:A4740P;ENSP00000410411:A1300P|.	ENSP00000262189:A4683P|.	A|G	-|-	1|2	0|0	MLL3|MLL3	151473298|151473298	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.995000|0.995000	0.86356|0.86356	3.929000|3.929000	0.56514|0.56514	2.607000|2.607000	0.88179|0.88179	0.655000|0.655000	0.94253|0.94253	GCA|GGC	.	.		0.488	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			G	151842365	C	G	151842365	3	3	209	1	0	0	0	0	1	0	0	0	9631	739	26	4	712	4	MLL3	7	151842365	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	4583137	151842365	7296298	67	30212										
GNRH1	2796	hgsc.bcm.edu	37	chr8	25276942	25276942	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tggcccaatggatttaaatcTtcttctgcccagtttcctct	6	12	4	0	rs185185508		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr8:25276942T>G	ENST00000276414.4	-	3	1595	c.272A>C	c.(271-273)aAg>aCg	p.K91T	GNRH1_ENST00000421054.2_Missense_Mutation_p.K91T	NM_000825.3	NP_000816.4	P01148	GON1_HUMAN	gonadotropin-releasing hormone 1 (luteinizing-releasing hormone)	91					cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|ovulation cycle (GO:0042698)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|response to corticosteroid (GO:0031960)|response to ethanol (GO:0045471)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	gonadotropin hormone-releasing hormone activity (GO:0005183)|hormone activity (GO:0005179)			large_intestine(1)	1		all_cancers(63;0.0423)|Ovarian(32;0.000626)|all_epithelial(46;0.0186)|Hepatocellular(4;0.114)|Breast(100;0.14)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0201)|Epithelial(17;1.25e-12)|Colorectal(74;0.0113)|COAD - Colon adenocarcinoma(73;0.0385)		GATTTAAATCTTCTTCTGCCC	0.313																																					p.K95T		Atlas-SNP	.											.	GNRH1	8	.	0			c.A284C						.						122	113	116					8																	25276942		1823	4075	5898	SO:0001583	missense	2796	exon3			TAAATCTTCTTCT	X01059	CCDS43725.1	8p21-p11.2	2013-02-26	2004-10-13		ENSG00000147437	ENSG00000147437		"Endogenous ligands"	4419	protein-coding gene	gene with protein product		152760	"gonadotropin-releasing hormone 1 (leutinizing-releasing hormone)"	GRH, GNRH, LHRH		6090951	Standard	NM_000825		Approved		uc003xem.4	P01148	OTTHUMG00000163852	ENST00000276414.4:c.272A>C	chr8.hg19:g.25276942T>G	ENSP00000276414:p.Lys91Thr	79.0	0.0		86.0	12.0	NM_000825	A0AVP0	Missense_Mutation	SNP	ENST00000276414.4	hg19	CCDS43725.1	.	.	.	.	.	.	.	.	.	.	T	14.86	2.660399	0.47572	.	.	ENSG00000147437	ENST00000421054;ENST00000276414	T;T	0.53423	0.62;0.62	4.65	2.21	0.28008	.	0.187257	0.36234	N	0.002704	T	0.36771	0.0979	.	.	.	0.28712	N	0.903461	P	0.37781	0.608	B	0.37943	0.261	T	0.27536	-1.0071	9	0.56958	D	0.05	-10.301	7.1698	0.25712	0.0:0.1862:0.0:0.8138	.	91	P01148	GON1_HUMAN	T	91	ENSP00000391280:K91T;ENSP00000276414:K91T	ENSP00000276414:K91T	K	-	2	0	GNRH1	25332859	1.000000	0.71417	0.997000	0.53966	0.917000	0.54804	2.674000	0.46867	0.243000	0.21327	0.254000	0.18369	AAG	.	T|1.000;A|0.000		0.313	GNRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375982.1	NM_001083111		G	25276942	T	G	25276942	3	3	209	1	0	0	0	0	1	0	0	0	6555	1609	56	5	10	5	GNRH1	8	25276942	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10		25276942	121087080	68	30213										
GNRH1	2796	hgsc.bcm.edu	37	chr8	25276963	25276963	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tcttctgcccagtttcctctTcaatcagactttcctgaaaa	4	13	5	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr8:25276963T>G	ENST00000276414.4	-	3	1574	c.251A>C	c.(250-252)gAa>gCa	p.E84A	GNRH1_ENST00000421054.2_Missense_Mutation_p.E84A	NM_000825.3	NP_000816.4	P01148	GON1_HUMAN	gonadotropin-releasing hormone 1 (luteinizing-releasing hormone)	84					cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|ovulation cycle (GO:0042698)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|response to corticosteroid (GO:0031960)|response to ethanol (GO:0045471)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	gonadotropin hormone-releasing hormone activity (GO:0005183)|hormone activity (GO:0005179)			large_intestine(1)	1		all_cancers(63;0.0423)|Ovarian(32;0.000626)|all_epithelial(46;0.0186)|Hepatocellular(4;0.114)|Breast(100;0.14)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0201)|Epithelial(17;1.25e-12)|Colorectal(74;0.0113)|COAD - Colon adenocarcinoma(73;0.0385)		AGTTTCCTCTTCAATCAGACT	0.294																																					p.E88A		Atlas-SNP	.											.	GNRH1	8	.	0			c.A263C						.						105	99	101					8																	25276963		1807	4074	5881	SO:0001583	missense	2796	exon3			TCCTCTTCAATCA	X01059	CCDS43725.1	8p21-p11.2	2013-02-26	2004-10-13		ENSG00000147437	ENSG00000147437		"Endogenous ligands"	4419	protein-coding gene	gene with protein product		152760	"gonadotropin-releasing hormone 1 (leutinizing-releasing hormone)"	GRH, GNRH, LHRH		6090951	Standard	NM_000825		Approved		uc003xem.4	P01148	OTTHUMG00000163852	ENST00000276414.4:c.251A>C	chr8.hg19:g.25276963T>G	ENSP00000276414:p.Glu84Ala	78.0	0.0		93.0	10.0	NM_000825	A0AVP0	Missense_Mutation	SNP	ENST00000276414.4	hg19	CCDS43725.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.112481	0.77210	.	.	ENSG00000147437	ENST00000421054;ENST00000276414	T;T	0.56103	0.48;0.48	5.22	5.22	0.72569	.	0.081226	0.51477	D	0.000091	T	0.70894	0.3276	.	.	.	0.42689	D	0.993571	D	0.76494	0.999	D	0.69654	0.965	T	0.75516	-0.3290	9	0.72032	D	0.01	-20.5306	12.776	0.57448	0.0:0.0:0.0:1.0	.	84	P01148	GON1_HUMAN	A	84	ENSP00000391280:E84A;ENSP00000276414:E84A	ENSP00000276414:E84A	E	-	2	0	GNRH1	25332880	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.291000	0.59025	2.109000	0.64355	0.377000	0.23210	GAA	.	.		0.294	GNRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375982.1	NM_001083111		G	25276963	T	G	25276963	3	3	209	1	0	0	0	0	1	0	0	0	6555	1783	62	5	31	5	GNRH1	8	25276963	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	21	25276963	121087059	69	30214										
SLC20A2	6575	hgsc.bcm.edu	37	chr8	42297137	42297137	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ttactgaggctttcgtcagaTactcgtgataaagcaccttc	8	10	1	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr8:42297137T>C	ENST00000342228.3	-	7	1134	c.765A>G	c.(763-765)gtA>gtG	p.V255V	SLC20A2_ENST00000520262.1_Silent_p.V255V|SLC20A2_ENST00000520179.1_Silent_p.V255V	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	255					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|sodium:phosphate symporter activity (GO:0005436)|virus receptor activity (GO:0001618)			breast(1)|endometrium(6)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|stomach(1)	26	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			TTTCGTCAGATACTCGTGATA	0.408																																					p.V255V		Atlas-SNP	.											.	SLC20A2	64	.	0			c.A765G						.						139	129	132					8																	42297137		2203	4300	6503	SO:0001819	synonymous_variant	6575	exon7			GTCAGATACTCGT		CCDS6132.1	8p11.21	2013-05-22			ENSG00000168575	ENSG00000168575		"Solute carriers"	10947	protein-coding gene	gene with protein product		158378		MLVAR, GLVR2		7745689, 16790504	Standard	NM_001257180		Approved	PiT-2, Glvr-2	uc010lxm.4	Q08357	OTTHUMG00000164169	ENST00000342228.3:c.765A>G	chr8.hg19:g.42297137T>C		59.0	0.0		104.0	18.0	NM_001257181		Silent	SNP	ENST00000342228.3	hg19	CCDS6132.1																																																																																			.	.		0.408	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1			C	42297137	T	C	42297137	2	2	209	1	0	0	0	0	0	0	0	1	14454	1393	49	2		2	SLC20A2	8	42297137	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	17020174	42297137	104066885	70	30215										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53540718	53540719	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gatgatgagtaccaaatctcCcacctgaaaactgaataaag							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr8:53540718_53540719CC>AA	ENST00000025008.5	-	22	5032_5033	c.4509_4510GG>TT	c.(4507-4512)gtGGga>gtTTga	p.G1504*	RB1CC1_ENST00000435644.2_Nonsense_Mutation_p.G1504*|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Nonsense_Mutation_p.G1504*	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1504					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				ACCAAATCTCCCACCTGAAAAC	0.342																																					p.G1504X|p.V1503V	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.G4510T|c.G4509T						.																																			SO:0001587	stop_gained	9821	exon22			AATCTCCCACCTG|ATCTCCCACCTGA	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.4509_4510delinsAA	chr8.hg19:g.53540718_53540719delinsAA	ENSP00000025008:p.Gly1504*	105.0|104.0	0.0		106.0|105.0	54.0	NM_001083617	Q86YR4|Q8WVU9|Q92601	Nonsense_Mutation|Silent	SNP	ENST00000025008.5	hg19	CCDS34892.1																																																																																			.	.		0.342	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		AA	53540719	CC	AA	53540718	4	1	209	1	0	0	0	0	0	1	0	0	13114	632	22	3	286	3	RB1CC1	8	53540718	Nonsense_Mutation	DNP	CC	TCGA-DD-AAE3-01A-11D-A40R-10	11243581	53540718	92823304	71	30216										
SLC26A7	115111	hgsc.bcm.edu	37	chr8	92330492	92330492	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gtgccacatttgtggtcacaGagcctgtgatcagcgcaatg	12	10	2	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr8:92330492G>T	ENST00000276609.3	+	5	765	c.526G>T	c.(526-528)Gag>Tag	p.E176*	SLC26A7_ENST00000523719.1_Nonsense_Mutation_p.E176*|SLC26A7_ENST00000309536.2_Nonsense_Mutation_p.E176*	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			TGTGGTCACAGAGCCTGTGAT	0.488																																					p.E176X		Atlas-SNP	.											.	SLC26A7	207	.	0			c.G526T						.						128	118	121					8																	92330492		2203	4300	6503	SO:0001587	stop_gained	115111	exon5			GTCACAGAGCCTG	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"Solute carriers"	14467	protein-coding gene	gene with protein product		608479	"solute carrier family 26, member 7"			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.526G>T	chr8.hg19:g.92330492G>T	ENSP00000276609:p.Glu176*	77.0	0.0		72.0	13.0	NM_134266		Nonsense_Mutation	SNP	ENST00000276609.3	hg19	CCDS6254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.86|14.86	2.662572|2.662572	0.47572|0.47572	.|.	.|.	ENSG00000147606|ENSG00000147606	ENST00000522862;ENST00000523719;ENST00000276609;ENST00000309536|ENST00000520818	.|.	.|.	.|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	.|T	.|0.80341	.|0.4605	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77736	.|-0.2476	.|3	0.52906|.	T|.	0.07|.	.|.	20.3921|20.3921	0.98947|0.98947	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|H	176|43	.|.	ENSP00000276609:E176X|.	E|Q	+|+	1|3	0|2	SLC26A7|SLC26A7	92399668|92399668	1.000000|1.000000	0.71417|0.71417	0.969000|0.969000	0.41365|0.41365	0.357000|0.357000	0.29423|0.29423	6.408000|6.408000	0.73285|0.73285	2.822000|2.822000	0.97130|0.97130	0.650000|0.650000	0.86243|0.86243	GAG|CAG	.	.		0.488	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1			T	92330492	G	T	92330492	4	4	209	1	0	0	0	0	0	1	0	0	14537	943	33	3	540	3	SLC26A7	8	92330492	Nonsense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	38789774	92330492	54033530	72	30217										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100115280	100115280	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agatgatatcgtcctttccgTcaatatcacttctgcagaat	6	10	3	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr8:100115280T>A	ENST00000358544.2	+	5	623	c.512T>A	c.(511-513)gTc>gAc	p.V171D	VPS13B_ENST00000357162.2_Missense_Mutation_p.V171D|VPS13B_ENST00000395996.1_Missense_Mutation_p.V171D|VPS13B_ENST00000355155.1_Missense_Mutation_p.V171D|VPS13B_ENST00000441350.2_Missense_Mutation_p.V171D	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	171					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GTCCTTTCCGTCAATATCACT	0.328																																					p.V171D	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.T512A						.						146	136	140					8																	100115280		2203	4300	6503	SO:0001583	missense	157680	exon5			TTTCCGTCAATAT	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.512T>A	chr8.hg19:g.100115280T>A	ENSP00000351346:p.Val171Asp	150.0	0.0		160.0	22.0	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.294697	0.60086	.	.	ENSG00000132549	ENST00000355155;ENST00000357162;ENST00000358544;ENST00000395996;ENST00000441350	T;T;T;T;D	0.85088	-1.37;-0.71;-0.7;-0.39;-1.94	5.94	5.94	0.96194	.	0.000000	0.64402	D	0.000002	D	0.91026	0.7177	L	0.56769	1.78	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;0.998	D;D;D;D;D	0.85130	0.997;0.996;0.974;0.991;0.969	D	0.91798	0.5449	10	0.87932	D	0	.	16.3908	0.83537	0.0:0.0:0.0:1.0	.	171;171;171;171;171	Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3;Q7Z7G8-4;Q7Z7G8-5	.;VP13B_HUMAN;.;.;.	D	171	ENSP00000347281:V171D;ENSP00000349685:V171D;ENSP00000351346:V171D;ENSP00000379318:V171D;ENSP00000398472:V171D	ENSP00000347281:V171D	V	+	2	0	VPS13B	100184456	1.000000	0.71417	1.000000	0.80357	0.129000	0.20672	7.384000	0.79751	2.269000	0.75478	0.455000	0.32223	GTC	.	.		0.328	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		A	100115280	T	A	100115280	3	1	209	1	0	0	0	0	1	0	0	0	17205	1667	58	4	526	4	VPS13B	8	100115280	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	7784788	100115280	46248742	73	30218										
MRPL13	28998	hgsc.bcm.edu	37	chr8	121455467	121455467	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	atgtaatccctgaagtcttaTagatgccatagcagcaagtt	8	8	1	2	rs145547223		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr8:121455467T>C	ENST00000306185.3	-	2	400	c.109A>G	c.(109-111)Ata>Gta	p.I37V	MTBP_ENST00000305949.1_5'Flank	NM_014078.5	NP_054797.2	Q9BYD1	RM13_HUMAN	mitochondrial ribosomal protein L13	37					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	6	Lung NSC(37;1.69e-07)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TGAAGTCTTATAGATGCCATA	0.403																																					p.I37V		Atlas-SNP	.											.	MRPL13	18	.	0			c.A109G						.	T	VAL/ILE	0,4406		0,0,2203	141	132	135		109	-3.3	0	8	dbSNP_134	135	1,8599	1.2+/-3.3	0,1,4299	no	missense	MRPL13	NM_014078.5	29	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	37/179	121455467	1,13005	2203	4300	6503	SO:0001583	missense	28998	exon2			GTCTTATAGATGC	AB049640	CCDS6332.1	8q22.1-q22.3	2012-09-13			ENSG00000172172	ENSG00000172172		"Mitochondrial ribosomal proteins / large subunits"	14278	protein-coding gene	gene with protein product		610200				11543634	Standard	NM_014078		Approved	L13, RPL13, L13mt, RPML13, L13A	uc003ypa.3	Q9BYD1	OTTHUMG00000165039	ENST00000306185.3:c.109A>G	chr8.hg19:g.121455467T>C	ENSP00000306548:p.Ile37Val	118.0	0.0		129.0	20.0	NM_014078	B2R4R8|Q9UI04	Missense_Mutation	SNP	ENST00000306185.3	hg19	CCDS6332.1	.	.	.	.	.	.	.	.	.	.	T	5.074	0.199258	0.09652	0.0	1.16E-4	ENSG00000172172	ENST00000306185;ENST00000518918	.	.	.	5.74	-3.26	0.05064	Ribosomal protein L13 domain (2);	0.675472	0.15469	N	0.260683	T	0.15998	0.0385	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19614	-1.0300	9	0.27082	T	0.32	-1.3597	14.0231	0.64568	0.0:0.5308:0.0:0.4692	.	37	Q9BYD1	RM13_HUMAN	V	37;13	.	ENSP00000306548:I37V	I	-	1	0	MRPL13	121524648	0.000000	0.05858	0.000000	0.03702	0.324000	0.28378	-0.509000	0.06336	-0.429000	0.07329	0.443000	0.29094	ATA	.	T|1.000;C|0.000		0.403	MRPL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381523.1	NM_014078		C	121455467	T	C	121455467	3	2	209	1	0	0	0	0	1	0	0	0	9787	1406	49	2	451	2	MRPL13	8	121455467	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	21340187	121455467	24908555	74	30219										
KIAA0020	9933	hgsc.bcm.edu	37	chr9	2837227	2837227	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ttctcttcttgttgaatttaTttgccggctggaatttgttc	8	7	2	1	rs552128111		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr9:2837227T>C	ENST00000397885.2	-	3	463	c.257A>G	c.(256-258)aAt>aGt	p.N86S		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	86						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		GTTGAATTTATTTGCCGGCTG	0.418																																					p.N86S		Atlas-SNP	.											.	KIAA0020	56	.	0			c.A257G						.						246	239	241					9																	2837227		1864	4101	5965	SO:0001583	missense	9933	exon3			AATTTATTTGCCG	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"penguin homolog (Drosophila)", "minor histocompatibility antigen HA-8"	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.257A>G	chr9.hg19:g.2837227T>C	ENSP00000380982:p.Asn86Ser	101.0	0.0		60.0	12.0	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	hg19	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	T	10.45	1.353142	0.24512	.	.	ENSG00000080608	ENST00000397885	D	0.86230	-2.09	4.55	0.661	0.17874	.	0.592256	0.18106	N	0.151512	T	0.64649	0.2617	N	0.08118	0	0.23546	N	0.997444	B	0.28378	0.209	B	0.18263	0.021	T	0.52102	-0.8620	10	0.19147	T	0.46	-7.2252	1.9376	0.03340	0.1301:0.1587:0.1339:0.5772	.	86	Q15397	K0020_HUMAN	S	86	ENSP00000380982:N86S	ENSP00000380982:N86S	N	-	2	0	KIAA0020	2827227	0.188000	0.23250	0.991000	0.47740	0.981000	0.71138	0.854000	0.27791	0.360000	0.24265	0.528000	0.53228	AAT	.	.		0.418	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878		C	2837227	T	C	2837227	3	2	209	1	0	0	0	0	1	0	0	0	8161	1493	52	2	1753	2	KIAA0020	9	2837227	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10		2837227	138376204	75	30220										
RUSC2	9853	hgsc.bcm.edu	37	chr9	35557957	35557957	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gtggacctcattgtggctcaTtttggcacaagccgggatcc	12	11	2	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr9:35557957T>C	ENST00000455600.1	+	6	3599	c.3030T>C	c.(3028-3030)caT>caC	p.H1010H		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1010						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			TTGTGGCTCATTTTGGCACAA	0.557																																					p.H1010H		Atlas-SNP	.											.	RUSC2	88	.	0			c.T3030C						.						156	134	141					9																	35557957		2203	4300	6503	SO:0001819	synonymous_variant	9853	exon6			GGCTCATTTTGGC	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.3030T>C	chr9.hg19:g.35557957T>C		61.0	0.0		59.0	17.0	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Silent	SNP	ENST00000455600.1	hg19	CCDS35008.1																																																																																			.	.		0.557	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		C	35557957	T	C	35557957	2	2	209	1	0	0	0	0	0	0	0	1	13766	1490	52	2		2	RUSC2	9	35557957	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	32720730	35557957	105655474	76	30221										
RNF20	56254	hgsc.bcm.edu	37	chr9	104314807	104314807	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ggcatctcaggaggatgccaAtgaaatcaagtctaaacggg	12	8	3	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr9:104314807A>G	ENST00000389120.3	+	13	1763	c.1673A>G	c.(1672-1674)aAt>aGt	p.N558S	AL591377.1_ENST00000584534.1_RNA	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	558					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		GAGGATGCCAATGAAATCAAG	0.498																																					p.N558S		Atlas-SNP	.											.	RNF20	110	.	0			c.A1673G						.						83	94	90					9																	104314807		2203	4300	6503	SO:0001583	missense	56254	exon13			ATGCCAATGAAAT	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.1673A>G	chr9.hg19:g.104314807A>G	ENSP00000373772:p.Asn558Ser	117.0	0.0		104.0	19.0	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	hg19	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	A	1.303	-0.604250	0.03717	.	.	ENSG00000155827	ENST00000389120	T	0.28895	1.59	5.8	-6.42	0.01932	.	0.781535	0.13039	N	0.418652	T	0.11410	0.0278	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37056	-0.9722	10	0.12766	T	0.61	-5.2158	11.1987	0.48728	0.229:0.2066:0.5643:0.0	.	558	Q5VTR2	BRE1A_HUMAN	S	558	ENSP00000373772:N558S	ENSP00000373772:N558S	N	+	2	0	RNF20	103354628	0.000000	0.05858	0.019000	0.16419	0.415000	0.31203	-0.730000	0.04915	-1.073000	0.03137	-0.274000	0.10170	AAT	.	.		0.498	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		G	104314807	A	G	104314807	3	3	209	1	0	0	0	0	1	0	0	0	13488	101	4	2	1719	2	RNF20	9	104314807	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	68756850	104314807	36898624	77	30222										
FAM69B	138311	hgsc.bcm.edu	37	chr9	139617509	139617509	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	aaccgggtgtccctggcggaAgccaagtccgtgtgggccct	15	13	0	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr9:139617509A>G	ENST00000371692.4	+	5	675	c.579A>G	c.(577-579)gaA>gaG	p.E193E	FAM69B_ENST00000371691.1_Silent_p.E106E|SNHG7_ENST00000436596.1_RNA|SNHG7_ENST00000414282.1_RNA|SNHG7_ENST00000447221.1_RNA|SNHG7_ENST00000416970.1_RNA	NM_152421.3	NP_689634.2	Q5VUD6	FA69B_HUMAN	family with sequence similarity 69, member B	193						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|large_intestine(2)|lung(1)|prostate(1)	8	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.03e-05)|Epithelial(140;0.00013)		CCCTGGCGGAAGCCAAGTCCG	0.652																																					p.E193E		Atlas-SNP	.											.	FAM69B	22	.	0			c.A579G						.						48	46	47					9																	139617509		2203	4300	6503	SO:0001819	synonymous_variant	138311	exon5			GGCGGAAGCCAAG		CCDS7004.1	9q34.3	2012-08-03			ENSG00000165716	ENSG00000165716			28290	protein-coding gene	gene with protein product		614543				21334309	Standard	NM_152421		Approved	MGC20262, C9orf136	uc004cik.3	Q5VUD6	OTTHUMG00000020940	ENST00000371692.4:c.579A>G	chr9.hg19:g.139617509A>G		83.0	0.0		97.0	5.0	NM_152421	Q5VUD7|Q8N5N0|Q8WYU5	Silent	SNP	ENST00000371692.4	hg19	CCDS7004.1																																																																																			.	.		0.652	FAM69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055102.1	NM_152421		G	139617509	A	G	139617509	2	3	209	1	0	0	0	0	0	0	0	1	5611	69	3	2		2	FAM69B	9	139617509	Silent	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	35302702	139617509	1595922	78	30223										
GDI2	2665	hgsc.bcm.edu	37	chr10	5808025	5808025	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	catttcctcaaagtcaaactCtgatcctgtcatcctcttat	3	13	5	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr10:5808025C>A	ENST00000380191.4	-	11	1572	c.1282G>T	c.(1282-1284)Gag>Tag	p.E428*	GDI2_ENST00000479928.1_5'UTR|GDI2_ENST00000380181.3_Nonsense_Mutation_p.E383*|GDI2_ENST00000380132.4_Nonsense_Mutation_p.E432*	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2	428					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|Rab GDP-dissociation inhibitor activity (GO:0005093)|Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|large_intestine(1)|lung(6)|urinary_tract(1)	10						AAGTCAAACTCTGATCCTGTC	0.358																																					p.E428X		Atlas-SNP	.											.	GDI2	26	.	0			c.G1282T						.						218	192	201					10																	5808025		2203	4300	6503	SO:0001587	stop_gained	2665	exon11			CAAACTCTGATCC	D13988	CCDS7071.1, CCDS44352.1	10p15	2010-03-16			ENSG00000057608	ENSG00000057608			4227	protein-coding gene	gene with protein product	"rab GDP-dissociation"	600767				9434952	Standard	NM_001494		Approved	RABGDIB	uc001iil.4	P50395	OTTHUMG00000017607	ENST00000380191.4:c.1282G>T	chr10.hg19:g.5808025C>A	ENSP00000369538:p.Glu428*	94.0	0.0		99.0	17.0	NM_001494	O43928|Q5SX88|Q9UQM6	Nonsense_Mutation	SNP	ENST00000380191.4	hg19	CCDS7071.1	.	.	.	.	.	.	.	.	.	.	C	35	5.448373	0.96205	.	.	ENSG00000057608	ENST00000380191;ENST00000380132;ENST00000380181	.	.	.	5.93	5.03	0.67393	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-19.128	14.7569	0.69572	0.0:0.9302:0.0:0.0698	.	.	.	.	X	428;432;383	.	ENSP00000369475:E432X	E	-	1	0	GDI2	5848031	1.000000	0.71417	0.988000	0.46212	0.399000	0.30720	7.666000	0.83877	1.520000	0.48965	0.557000	0.71058	GAG	.	.		0.358	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	NM_001494		A	5808025	C	A	5808025	4	1	209	1	0	0	0	0	0	1	0	0	6329	922	32	3	59	3	GDI2	10	5808025	Nonsense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10		5808025	129726722	79	30224										
SGMS1	259230	hgsc.bcm.edu	37	chr10	52071136	52071136	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gccacctccagcaatgagctTcattattcttcgcagttggg	9	12	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr10:52071136T>G	ENST00000361781.2	-	9	1740	c.781A>C	c.(781-783)Aag>Cag	p.K261Q	SGMS1_ENST00000429490.1_Missense_Mutation_p.K92Q	NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	267					apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GCAATGAGCTTCATTATTCTT	0.458																																					p.K261Q		Atlas-SNP	.											.	SGMS1	40	.	0			c.A781C						.						107	76	86					10																	52071136		2203	4300	6503	SO:0001583	missense	259230	exon9			TGAGCTTCATTAT	AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	2.7.8.27	"Sterile alpha motif (SAM) domain containing"	29799	protein-coding gene	gene with protein product		611573	"transmembrane protein 23"	TMEM23		11841947, 14976195	Standard	NM_147156		Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.781A>C	chr10.hg19:g.52071136T>G	ENSP00000354829:p.Lys261Gln	64.0	0.0		42.0	10.0	NM_147156	Q68U43|Q6EKK0|Q75SP1	Missense_Mutation	SNP	ENST00000361781.2	hg19	CCDS7240.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.721495	0.48728	.	.	ENSG00000198964	ENST00000412547;ENST00000361781;ENST00000429490	T	0.46063	0.88	5.87	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.22666	0.0547	N	0.11064	0.09	0.80722	D	1	B;B	0.25441	0.126;0.112	B;B	0.24006	0.021;0.05	T	0.05649	-1.0872	10	0.14252	T	0.57	-8.3248	11.6948	0.51538	0.0:0.0:0.1483:0.8517	.	92;267	B4DJU2;Q86VZ5	.;SMS1_HUMAN	Q	61;261;92	ENSP00000354829:K261Q	ENSP00000354829:K261Q	K	-	1	0	SGMS1	51741142	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.229000	0.72294	1.124000	0.41980	0.533000	0.62120	AAG	.	.		0.458	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048074.2	NM_147156		G	52071136	T	G	52071136	3	3	209	1	0	0	0	0	1	0	0	0	14229	1792	62	5	472	5	SGMS1	10	52071136	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	46263111	52071136	83463611	80	30225										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64936130	64936130	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gagtacaggttctgactccaTattcttcaagcagcctttga	8	10	3	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr10:64936130T>C	ENST00000399262.2	-	24	7546	c.7328A>G	c.(7327-7329)tAt>tGt	p.Y2443C	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000402544.1_Missense_Mutation_p.Y2206C|JMJD1C_ENST00000542921.1_Missense_Mutation_p.Y2261C	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2443	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					TCTGACTCCATATTCTTCAAG	0.398																																					p.Y2443C		Atlas-SNP	.											.	JMJD1C	347	.	0			c.A7328G						.						112	107	108					10																	64936130		1871	4096	5967	SO:0001583	missense	221037	exon24			ACTCCATATTCTT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.7328A>G	chr10.hg19:g.64936130T>C	ENSP00000382204:p.Tyr2443Cys	166.0	0.0		156.0	36.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.675370	0.88445	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	T;T;T	0.71934	-0.61;-0.61;-0.61	5.75	5.75	0.90469	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.117745	0.64402	D	0.000016	D	0.82595	0.5071	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;0.976	D;P	0.74023	0.982;0.852	D	0.84556	0.0647	10	0.87932	D	0	-10.4747	15.7237	0.77736	0.0:0.0:0.0:1.0	.	2443;2261	Q15652;A0T124	JHD2C_HUMAN;.	C	2443;2206;2261	ENSP00000382204:Y2443C;ENSP00000384990:Y2206C;ENSP00000444682:Y2261C	ENSP00000382204:Y2443C	Y	-	2	0	JMJD1C	64606136	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.027000	0.88791	2.195000	0.70347	0.533000	0.62120	TAT	.	.		0.398	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		C	64936130	T	C	64936130	3	2	209	1	0	0	0	0	1	0	0	0	7959	1406	49	2	306	2	JMJD1C	10	64936130	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	12864994	64936130	70598617	81	30226										
GHITM	27069	hgsc.bcm.edu	37	chr10	85909910	85909910	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cattgtgggaggcctctccaCtgtggccatgtgtgcgccca	13	13	1	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr10:85909910C>T	ENST00000372134.3	+	7	885	c.692C>T	c.(691-693)aCt>aTt	p.T231I		NM_014394.2	NP_055209.2	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein	231					apoptotic process (GO:0006915)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(2)	10						GGCCTCTCCACTGTGGCCATG	0.567																																					p.T231I		Atlas-SNP	.											.	GHITM	30	.	0			c.C692T						.						115	123	120					10																	85909910		2068	4220	6288	SO:0001583	missense	27069	exon7			TCTCCACTGTGGC	AB009685	CCDS41542.1	10q23.1	2008-02-01			ENSG00000165678	ENSG00000165678			17281	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 5"					8619474, 9110174	Standard	NM_014394		Approved	HSPC282, PTD010, DERP2, My021, TMBIM5	uc001kcs.1	Q9H3K2	OTTHUMG00000018637	ENST00000372134.3:c.692C>T	chr10.hg19:g.85909910C>T	ENSP00000361207:p.Thr231Ile	74.0	0.0		83.0	40.0	NM_014394	A8K9Z9|D3DWE0|O95894|Q5VT95|Q9H0P2	Missense_Mutation	SNP	ENST00000372134.3	hg19	CCDS41542.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.608852	0.66558	.	.	ENSG00000165678	ENST00000372134;ENST00000538477;ENST00000436406;ENST00000339736	T	0.41400	1.0	6.03	6.03	0.97812	.	0.098369	0.64402	D	0.000001	T	0.39410	0.1077	L	0.46157	1.445	0.80722	D	1	B;B	0.26318	0.146;0.055	B;B	0.27380	0.079;0.029	T	0.10917	-1.0609	10	0.20519	T	0.43	-16.6221	17.4736	0.87653	0.0:1.0:0.0:0.0	.	162;231	B4DNL0;Q9H3K2	.;GHITM_HUMAN	I	231;218;231;211	ENSP00000361207:T231I	ENSP00000342214:T211I	T	+	2	0	GHITM	85899890	0.998000	0.40836	0.992000	0.48379	0.921000	0.55340	5.612000	0.67681	2.861000	0.98227	0.655000	0.94253	ACT	.	.		0.567	GHITM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049125.1	NM_014394		T	85909910	C	T	85909910	3	4	209	1	0	0	0	0	1	0	0	0	6378	565	20	3	714	3	GHITM	10	85909910	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	20973780	85909910	49624837	82	30227										
CDHR1	92211	hgsc.bcm.edu	37	chr10	85958825	85958825	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gatcctggtgaccgatgccaAtgatgaggcgcccaggttca	13	11	1	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr10:85958825A>G	ENST00000372117.3	+	5	489	c.386A>G	c.(385-387)aAt>aGt	p.N129S	CDHR1_ENST00000332904.3_Missense_Mutation_p.N129S|CDHR1_ENST00000440770.2_5'Flank	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	129	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						ACCGATGCCAATGATGAGGCG	0.557																																					p.N129S		Atlas-SNP	.											.	CDHR1	122	.	0			c.A386G						.						89	73	78					10																	85958825		2049	3918	5967	SO:0001583	missense	92211	exon5			ATGCCAATGATGA	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.386A>G	chr10.hg19:g.85958825A>G	ENSP00000361189:p.Asn129Ser	94.0	0.0		66.0	13.0	NM_001171971	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	hg19	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.344928	0.82022	.	.	ENSG00000148600	ENST00000332904;ENST00000372117	T;T	0.70631	-0.5;-0.5	5.09	5.09	0.68999	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.90000	0.6878	H	0.99404	4.55	0.80722	D	1	D;D	0.55172	0.965;0.97	P;P	0.61201	0.885;0.77	D	0.93869	0.7160	10	0.87932	D	0	-20.0667	13.8713	0.63622	1.0:0.0:0.0:0.0	.	129;129	Q96JP9-2;Q96JP9	.;CDHR1_HUMAN	S	129	ENSP00000331063:N129S;ENSP00000361189:N129S	ENSP00000331063:N129S	N	+	2	0	CDHR1	85948805	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	8.418000	0.90250	1.917000	0.55516	0.459000	0.35465	AAT	.	.		0.557	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		G	85958825	A	G	85958825	3	3	209	1	0	0	0	0	1	0	0	0	3120	101	4	2	404	2	CDHR1	10	85958825	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	48915	85958825	49575922	83	30228										
IDE	3416	hgsc.bcm.edu	37	chr10	94239137	94239137	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tgaggagctcaaggtacaaaTaggccatgttacagtgcaag	12	7	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr10:94239137T>C	ENST00000265986.6	-	15	1837	c.1781A>G	c.(1780-1782)tAt>tGt	p.Y594C	IDE_ENST00000496903.1_Intron|IDE_ENST00000371581.5_Missense_Mutation_p.Y39C	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	594					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	AAGGTACAAATAGGCCATGTT	0.423																																					p.Y594C		Atlas-SNP	.											.	IDE	77	.	0			c.A1781G						.						169	144	152					10																	94239137		2203	4300	6503	SO:0001583	missense	3416	exon15			TACAAATAGGCCA	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.1781A>G	chr10.hg19:g.94239137T>C	ENSP00000265986:p.Tyr594Cys	122.0	0.0		90.0	21.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	13.52	2.260477	0.39995	.	.	ENSG00000119912	ENST00000265986;ENST00000371581	T;T	0.29655	1.56;1.56	5.62	5.62	0.85841	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.31104	0.0786	L	0.54323	1.7	0.80722	D	1	B	0.28419	0.211	B	0.20767	0.031	T	0.06445	-1.0826	10	0.52906	T	0.07	-12.9568	15.4934	0.75629	0.0:0.0:0.0:1.0	.	594	P14735	IDE_HUMAN	C	594;39	ENSP00000265986:Y594C;ENSP00000360637:Y39C	ENSP00000265986:Y594C	Y	-	2	0	IDE	94229117	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.150000	0.67090	0.533000	0.62120	TAT	.	.		0.423	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		C	94239137	T	C	94239137	3	2	209	1	0	0	0	0	1	0	0	0	7502	1406	49	2	1322	2	IDE	10	94239137	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	8280312	94239137	41295610	84	30229										
COPB1	1315	hgsc.bcm.edu	37	chr11	14490346	14490346	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	catttcattcttagcagttaGttgcatgaaggaaatggggt	11	5	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr11:14490346G>C	ENST00000249923.3	-	16	2326	c.2026C>G	c.(2026-2028)Cta>Gta	p.L676V	COPB1_ENST00000439561.2_Missense_Mutation_p.L676V	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	676					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						TTAGCAGTTAGTTGCATGAAG	0.408																																					p.L676V		Atlas-SNP	.											.	COPB1	81	.	0			c.C2026G						.						222	201	208					11																	14490346		2200	4294	6494	SO:0001583	missense	1315	exon16			CAGTTAGTTGCAT	BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"coatomer protein complex, subunit beta"	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.2026C>G	chr11.hg19:g.14490346G>C	ENSP00000249923:p.Leu676Val	81.0	0.0		36.0	12.0	NM_001144062	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	hg19	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.115231	0.77210	.	.	ENSG00000129083	ENST00000249923;ENST00000439561	T;T	0.61158	0.13;0.13	5.32	5.32	0.75619	Coatomer, beta subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.82499	0.5050	H	0.94264	3.515	0.80722	D	1	D	0.64830	0.994	D	0.64595	0.927	D	0.87676	0.2544	10	0.87932	D	0	.	18.996	0.92813	0.0:0.0:1.0:0.0	.	676	P53618	COPB_HUMAN	V	676	ENSP00000249923:L676V;ENSP00000397873:L676V	ENSP00000249923:L676V	L	-	1	2	COPB1	14446922	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.455000	0.73497	2.494000	0.84150	0.650000	0.86243	CTA	.	.		0.408	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451		C	14490346	G	C	14490346	3	2	209	1	0	0	0	0	1	0	0	0	3730	1020	36	4	863	4	COPB1	11	14490346	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10		14490346	120516170	85	30230										
OR9I1	219954	hgsc.bcm.edu	37	chr11	57886028	57886028	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctttctgaaggcgtcttttaCatctttgtttcttaagctgt	7	8	4	1	rs372541402		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr11:57886028C>T	ENST00000302610.1	-	1	888	c.889G>A	c.(889-891)Gta>Ata	p.V297I	OR9Q1_ENST00000335397.3_Intron	NM_001005211.1	NP_001005211.1	Q8NGQ6	OR9I1_HUMAN	olfactory receptor, family 9, subfamily I, member 1	297						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|liver(1)|lung(15)|pancreas(1)|skin(1)|urinary_tract(1)	23		Breast(21;0.0589)				GCGTCTTTTACATCTTTGTTT	0.448																																					p.V297I		Atlas-SNP	.											.	OR9I1	53	.	0			c.G889A						.						122	126	125					11																	57886028		2201	4296	6497	SO:0001583	missense	219954	exon1			CTTTTACATCTTT	AB065733	CCDS31542.1	11q12.1	2012-08-09			ENSG00000172377	ENSG00000172377		"GPCR / Class A : Olfactory receptors"	14718	protein-coding gene	gene with protein product							Standard	NM_001005211		Approved		uc021qjl.1	Q8NGQ6	OTTHUMG00000167404	ENST00000302610.1:c.889G>A	chr11.hg19:g.57886028C>T	ENSP00000302606:p.Val297Ile	36.0	0.0		36.0	13.0	NM_001005211	Q6IFH0|Q96RA8	Missense_Mutation	SNP	ENST00000302610.1	hg19	CCDS31542.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.057940	0.36277	.	.	ENSG00000172377	ENST00000302610	T	0.37235	1.21	4.97	4.06	0.47325	.	0.000000	0.41605	D	0.000850	T	0.38161	0.1030	N	0.17872	0.535	0.28175	N	0.928437	D	0.64830	0.994	D	0.72625	0.978	T	0.15435	-1.0437	10	0.72032	D	0.01	-23.8747	4.9574	0.14048	0.1691:0.6594:0.0:0.1715	.	297	Q8NGQ6	OR9I1_HUMAN	I	297	ENSP00000302606:V297I	ENSP00000302606:V297I	V	-	1	0	OR9I1	57642604	0.413000	0.25400	0.998000	0.56505	0.025000	0.11179	0.778000	0.26732	1.478000	0.48253	-0.363000	0.07495	GTA	.	.		0.448	OR9I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394539.1	NM_001005211		T	57886028	C	T	57886028	3	4	209	1	0	0	0	0	1	0	0	0	11262	478	17	3	59	3	OR9I1	11	57886028	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	43395682	57886028	77120488	86	30231										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62291791	62291791	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cctttgacatccacttcaggTgtctgaactttagagcccga	8	12	2	3	rs541565103		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr11:62291791T>A	ENST00000378024.4	-	5	10372	c.10098A>T	c.(10096-10098)acA>acT	p.T3366T	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3366					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CCACTTCAGGTGTCTGAACTT	0.393																																					p.T3366T		Atlas-SNP	.											.	AHNAK	532	.	0			c.A10098T						.						55	58	57					11																	62291791		2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			TTCAGGTGTCTGA	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.10098A>T	chr11.hg19:g.62291791T>A		71.0	0.0		56.0	19.0	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.393	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62291791	T	A	62291791	2	1	209	1	0	0	0	0	0	0	0	1	414	1683	59	4		4	AHNAK	11	62291791	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	4405763	62291791	72714725	87	30232										
C11orf80	79703	hgsc.bcm.edu	37	chr11	66512287	66512287	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gttccaagcccgggctgaggAgggggcggcggcggcggcgg	23	11	0	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr11:66512287A>C	ENST00000360962.4	+	1	81	c.74A>C	c.(73-75)gAg>gCg	p.E25A	C11orf80_ENST00000540737.1_5'UTR|C11orf80_ENST00000532565.2_5'Flank|C11orf80_ENST00000346672.4_5'UTR|C11orf80_ENST00000527634.1_5'UTR|C11orf80_ENST00000527368.1_3'UTR	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	25										autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						CGGGCTGAGGAGGGggcggcg	0.791																																					p.E25A		Atlas-SNP	.											.	C11orf80	31	.	0			c.A74C						.						1	1	1					11																	66512287		258	821	1079	SO:0001583	missense	79703	exon1			CTGAGGAGGGGGC			11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.74A>C	chr11.hg19:g.66512287A>C	ENSP00000354227:p.Glu25Ala	35.0	0.0		36.0	6.0	NM_024650	Q9H677	Missense_Mutation	SNP	ENST00000360962.4	hg19	CCDS53664.1	.	.	.	.	.	.	.	.	.	.	A	16.29	3.080343	0.55753	.	.	ENSG00000173715	ENST00000360962	T	0.34275	1.37	2.37	-2.8	0.05823	.	.	.	.	.	T	0.19005	0.0456	.	.	.	0.24707	N	0.99323	.	.	.	.	.	.	T	0.28427	-1.0044	6	0.22109	T	0.4	.	3.4329	0.07434	0.328:0.4124:0.0:0.2596	.	.	.	.	A	25	ENSP00000354227:E25A	ENSP00000354227:E25A	E	+	2	0	C11orf80	66268863	0.366000	0.25014	0.017000	0.16124	0.392000	0.30506	0.135000	0.15952	-0.581000	0.05937	0.379000	0.24179	GAG	.	.		0.791	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024650		C	66512287	A	C	66512287	3	2	209	1	0	0	0	0	1	0	0	0	1666	304	11	5	76	5	C11orf80	11	66512287	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	4220496	66512287	68494229	88	30233										
MED17	9440	hgsc.bcm.edu	37	chr11	93521276	93521276	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gatgttctcagtattgttagGgataaaaaatttatgactct	8	4	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr11:93521276G>C	ENST00000251871.3	+	2	647	c.360G>C	c.(358-360)agG>agC	p.R120S	MED17_ENST00000530819.1_Missense_Mutation_p.R120S	NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	120					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			large_intestine(2)|lung(11)|ovary(1)	14		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GTATTGTTAGGGATAAAAAAT	0.363																																					p.R120S		Atlas-SNP	.											.	MED17	37	.	0			c.G360C						.						108	105	106					11																	93521276		2201	4298	6499	SO:0001583	missense	9440	exon2			TGTTAGGGATAAA	AF104254	CCDS8295.1	11q21	2007-07-30	2007-07-30	2007-07-30	ENSG00000042429	ENSG00000042429			2375	protein-coding gene	gene with protein product		603810	"cofactor required for Sp1 transcriptional activation, subunit 6 (77kD)", "cofactor required for Sp1 transcriptional activation, subunit 6, 77kDa"	CRSP6		9989412, 10198638	Standard	NM_004268		Approved	CRSP77, TRAP80, DRIP80	uc001pem.4	Q9NVC6	OTTHUMG00000167497	ENST00000251871.3:c.360G>C	chr11.hg19:g.93521276G>C	ENSP00000251871:p.Arg120Ser	61.0	0.0		53.0	11.0	NM_004268	B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Missense_Mutation	SNP	ENST00000251871.3	hg19	CCDS8295.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.802769	0.50315	.	.	ENSG00000042429	ENST00000251871;ENST00000530819;ENST00000427225;ENST00000533359;ENST00000528786	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.44	-0.0965	0.13637	.	0.091108	0.64402	D	0.000002	T	0.20170	0.0485	N	0.08118	0	0.40009	D	0.975266	B;B	0.32467	0.003;0.372	B;B	0.24394	0.01;0.053	T	0.04017	-1.0984	10	0.62326	D	0.03	-11.0694	5.8718	0.18807	0.2683:0.2339:0.4978:0.0	.	120;120	Q9NVC6;Q9NVC6-2	MED17_HUMAN;.	S	120;120;90;120;12	ENSP00000251871:R120S;ENSP00000434459:R120S;ENSP00000431524:R120S;ENSP00000433626:R12S	ENSP00000251871:R120S	R	+	3	2	MED17	93160924	1.000000	0.71417	0.948000	0.38648	0.997000	0.91878	1.228000	0.32588	0.007000	0.14760	0.650000	0.86243	AGG	.	.		0.363	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268		C	93521276	G	C	93521276	3	2	209	1	0	0	0	0	1	0	0	0	9444	1223	43	4	366	4	MED17	11	93521276	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	27008989	93521276	41485240	89	30234										
DDI1	414301	hgsc.bcm.edu	37	chr11	103908223	103908223	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tccggcagcaaaacattgaaGaaaacatgaatatagcgata	8	7	0	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr11:103908223G>C	ENST00000302259.3	+	1	916	c.673G>C	c.(673-675)Gaa>Caa	p.E225Q	PDGFD_ENST00000393158.2_Intron|PDGFD_ENST00000302251.5_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	225							aspartic-type endopeptidase activity (GO:0004190)			central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		AAACATTGAAGAAAACATGAA	0.473																																					p.E225Q		Atlas-SNP	.											.	DDI1	222	.	0			c.G673C						.						105	118	113					11																	103908223		2202	4299	6501	SO:0001583	missense	414301	exon1			ATTGAAGAAAACA		CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.673G>C	chr11.hg19:g.103908223G>C	ENSP00000302805:p.Glu225Gln	96.0	0.0		92.0	18.0	NM_001001711	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	hg19	CCDS31660.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814256	0.70912	.	.	ENSG00000170967	ENST00000302259	T	0.49432	0.78	5.02	5.02	0.67125	Peptidase aspartic, eukaryotic predicted (1);	0.000000	0.85682	D	0.000000	T	0.63022	0.2476	L	0.49571	1.57	0.54753	D	0.999984	D	0.89917	1.0	D	0.97110	1.0	T	0.59941	-0.7359	10	0.42905	T	0.14	-11.0943	16.2348	0.82365	0.0:0.0:1.0:0.0	.	225	Q8WTU0	DDI1_HUMAN	Q	225	ENSP00000302805:E225Q	ENSP00000302805:E225Q	E	+	1	0	DDI1	103413433	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	9.016000	0.93645	2.781000	0.95711	0.655000	0.94253	GAA	.	.		0.473	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711		C	103908223	G	C	103908223	3	2	209	1	0	0	0	0	1	0	0	0	4330	943	33	4	675	4	DDI1	11	103908223	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	10386947	103908223	31098293	90	30235										
OPCML	4978	hgsc.bcm.edu	37	chr11	132812840	132812840	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cctgagggtggcgctctcccCctgccggaccgtcacgttgt	13	16	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr11:132812840C>G	ENST00000331898.7	-	1	726	c.148G>C	c.(148-150)Ggg>Cgg	p.G50R	OPCML_ENST00000529038.1_Intron|OPCML_ENST00000541867.1_Missense_Mutation_p.G50R|OPCML_ENST00000374778.4_Missense_Mutation_p.G9R|OPCML_ENST00000524381.1_Missense_Mutation_p.G43R	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	50	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GCGCTCTCCCCCTGCCGGACC	0.672																																					p.G50R		Atlas-SNP	.											.	OPCML	166	.	0			c.G148C						.						67	69	68					11																	132812840		2201	4297	6498	SO:0001583	missense	4978	exon1			TCTCCCCCTGCCG	BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.148G>C	chr11.hg19:g.132812840C>G	ENSP00000330862:p.Gly50Arg	68.0	0.0		55.0	25.0	NM_002545	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	hg19	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.936304	0.92458	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48	5.71	5.71	0.89125	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.387835	0.23973	N	0.042747	D	0.93054	0.7789	H	0.94886	3.595	0.80722	D	1	D;P;D;D	0.89917	1.0;0.942;1.0;1.0	D;D;D;D	0.79784	0.993;0.955;0.993;0.993	D	0.94297	0.7534	10	0.87932	D	0	-12.1022	19.8557	0.96758	0.0:1.0:0.0:0.0	.	50;43;50;50	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	R	50;43;9;43;50	ENSP00000330862:G50R;ENSP00000434750:G43R;ENSP00000363910:G9R;ENSP00000445496:G50R	ENSP00000330862:G50R	G	-	1	0	OPCML	132318050	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.398000	0.79919	2.707000	0.92482	0.655000	0.94253	GGG	.	.		0.672	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		G	132812840	C	G	132812840	3	3	209	1	0	0	0	0	1	0	0	0	10883	623	22	4	917	4	OPCML	11	132812840	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	28904617	132812840	2193676	91	30236										
SLCO1B3	28234	hgsc.bcm.edu	37	chr12	21013982	21013982	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctaaagaaacccatattaatCcatcagaaaattcaacatca	2	10	3	2	rs374152690		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr12:21013982C>A	ENST00000381545.3	+	6	610	c.391C>A	c.(391-393)Cca>Aca	p.P131T	LST3_ENST00000540229.1_Missense_Mutation_p.P131T|SLCO1B3_ENST00000553473.1_Missense_Mutation_p.P131T|SLCO1B7_ENST00000554957.1_Intron|LST3_ENST00000381541.3_Intron|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.P131T|SLCO1B3_ENST00000545880.1_3'UTR	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	131					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	CCATATTAATCCATCAGAAAA	0.289																																					p.P131T		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.C391A						.	C	THR/PRO	1,4391	2.1+/-5.4	0,1,2195	51	48	49		391	0.5	0	12		49	0,8560		0,0,4280	no	missense	SLCO1B3	NM_019844.2	38	0,1,6475	AA,AC,CC		0.0,0.0228,0.0077	benign	131/703	21013982	1,12951	2196	4280	6476	SO:0001583	missense	28234	exon6			ATTAATCCATCAG		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.391C>A	chr12.hg19:g.21013982C>A	ENSP00000370956:p.Pro131Thr	338.0	1.0		247.0	180.0	NM_019844	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	hg19	CCDS8684.1	.	.	.	.	.	.	.	.	.	.	C	9.332	1.060884	0.19987	2.28E-4	0.0	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046	ENST00000540853;ENST00000261196;ENST00000381545;ENST00000553473;ENST00000540229	T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23	3.53	0.48	0.16804	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.713131	0.14630	N	0.307854	T	0.23766	0.0575	L	0.37897	1.145	0.09310	N	1	B;B	0.19200	0.034;0.008	B;B	0.26310	0.068;0.023	T	0.21861	-1.0233	10	0.38643	T	0.18	.	2.6183	0.04909	0.396:0.3571:0.0:0.2469	.	131;131	Q5JAR4;Q9NPD5	.;SO1B3_HUMAN	T	131	ENSP00000442000:P131T;ENSP00000261196:P131T;ENSP00000370956:P131T;ENSP00000451758:P131T;ENSP00000441269:P131T	ENSP00000441269:P131T	P	+	1	0	SLCO1B3;RP11-545J16.1	20905249	0.000000	0.05858	0.000000	0.03702	0.615000	0.37417	0.092000	0.15066	-0.105000	0.12132	-0.373000	0.07131	CCA	.	.		0.289	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		A	21013982	C	A	21013982	3	1	209	1	0	0	0	0	1	0	0	0	14739	855	30	3	405	3	SLCO1B3	12	21013982	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10		21013982	112837913	92	30237										
SLC38A2	54407	hgsc.bcm.edu	37	chr12	46754959	46754959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	caaggccatgcttccggtcaTcaccagtacaccacttaaca	6	15	2	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr12:46754959T>C	ENST00000256689.5	-	16	1900	c.1456A>G	c.(1456-1458)Atg>Gtg	p.M486V	SLC38A2_ENST00000551374.1_Missense_Mutation_p.M324V	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	486					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		CTTCCGGTCATCACCAGTACA	0.408																																					p.M486V	Ovarian(9;448 492 8335 28722 40361)	Atlas-SNP	.											.	SLC38A2	36	.	0			c.A1456G						.						98	84	88					12																	46754959		2203	4299	6502	SO:0001583	missense	54407	exon16			CGGTCATCACCAG	AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"Solute carriers"	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.1456A>G	chr12.hg19:g.46754959T>C	ENSP00000256689:p.Met486Val	101.0	0.0		46.0	10.0	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Missense_Mutation	SNP	ENST00000256689.5	hg19	CCDS8749.1	.	.	.	.	.	.	.	.	.	.	T	17.26	3.344864	0.61073	.	.	ENSG00000134294	ENST00000256689;ENST00000551374	T;T	0.02121	4.44;4.44	6.05	6.05	0.98169	.	0.034017	0.85682	D	0.000000	T	0.15046	0.0363	M	0.88450	2.955	0.80722	D	1	P;D;D	0.65815	0.923;0.995;0.983	P;D;P	0.66196	0.561;0.942;0.874	T	0.01484	-1.1343	10	0.35671	T	0.21	-29.8604	16.5993	0.84807	0.0:0.0:0.0:1.0	.	324;386;486	F8VQW8;Q96QD8-2;Q96QD8	.;.;S38A2_HUMAN	V	486;324	ENSP00000256689:M486V;ENSP00000450406:M324V	ENSP00000256689:M486V	M	-	1	0	SLC38A2	45041226	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	7.368000	0.79567	2.311000	0.77944	0.528000	0.53228	ATG	.	.		0.408	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1			C	46754959	T	C	46754959	3	2	209	1	0	0	0	0	1	0	0	0	14619	1435	50	2	68	2	SLC38A2	12	46754959	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	25740977	46754959	87096936	93	30238										
DNAJC22	79962	hgsc.bcm.edu	37	chr12	49742904	49742904	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agtcccattcgctttgctgcCcaggtgatagttggcatcta	10	11	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr12:49742904C>G	ENST00000549441.2	+	3	1453	c.249C>G	c.(247-249)gcC>gcG	p.A83A	DNAJC22_ENST00000395069.3_Silent_p.A83A			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	83						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						GCTTTGCTGCCCAGGTGATAG	0.552																																					p.A83A		Atlas-SNP	.											.	DNAJC22	29	.	0			c.C249G						.						137	145	143					12																	49742904		2203	4300	6503	SO:0001819	synonymous_variant	79962	exon2			TGCTGCCCAGGTG	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"Heat shock proteins / DNAJ (HSP40)"	25802	protein-coding gene	gene with protein product	"wurst homolog (Drosophila)"					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.249C>G	chr12.hg19:g.49742904C>G		51.0	0.0		35.0	28.0	NM_024902	B3KP54	Silent	SNP	ENST00000549441.2	hg19	CCDS8785.1																																																																																			.	.		0.552	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902		G	49742904	C	G	49742904	2	3	209	1	0	0	0	0	0	0	0	1	4643	610	22	4		4	DNAJC22	12	49742904	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	2987945	49742904	84108991	94	30239										
KRT5	3852	hgsc.bcm.edu	37	chr12	52912936	52912936	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	accttgttctgctgctccagGaaccgcacctggaggggagc	13	13	1	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr12:52912936G>T	ENST00000252242.4	-	2	954	c.564C>A	c.(562-564)ttC>ttA	p.F188L		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	188	Coil 1A.|Rod.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCTGCTCCAGGAACCGCACCT	0.547																																					p.F188L		Atlas-SNP	.											.	KRT5	88	.	0			c.C564A						.						54	49	50					12																	52912936		2203	4300	6503	SO:0001583	missense	3852	exon2			CTCCAGGAACCGC		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"-", "Intermediate filaments type II, keratins (basic)"	6442	protein-coding gene	gene with protein product		148040	"epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types", "keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.564C>A	chr12.hg19:g.52912936G>T	ENSP00000252242:p.Phe188Leu	112.0	0.0		90.0	63.0	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	hg19	CCDS8830.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.322769	0.81580	.	.	ENSG00000186081	ENST00000252242;ENST00000456000;ENST00000549420	T;T	0.75477	-0.94;-0.94	5.31	5.31	0.75309	Filament (1);	0.000000	0.64402	D	0.000016	D	0.87593	0.6216	M	0.93939	3.475	0.49915	D	0.999835	D	0.89917	1.0	D	0.85130	0.997	D	0.88733	0.3238	10	0.87932	D	0	.	7.0291	0.24956	0.1459:0.1497:0.7044:0.0	.	188	P13647	K2C5_HUMAN	L	188;153;78	ENSP00000252242:F188L;ENSP00000447209:F78L	ENSP00000252242:F188L	F	-	3	2	KRT5	51199203	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.288000	0.43514	2.764000	0.94973	0.655000	0.94253	TTC	.	.		0.547	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1			T	52912936	G	T	52912936	3	4	209	1	0	0	0	0	1	0	0	0	8488	1165	41	3	1240	3	KRT5	12	52912936	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	3170032	52912936	80938959	95	30240										
ANKRD52	283373	hgsc.bcm.edu	37	chr12	56641954	56641954	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cttgtggtcccttacgtccaGattcaccagcgtctccgcca	8	16	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr12:56641954G>A	ENST00000267116.7	-	18	1952	c.1831C>T	c.(1831-1833)Ctg>Ttg	p.L611L		NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	611										endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						CTTACGTCCAGATTCACCAGC	0.632																																					p.L611L		Atlas-SNP	.											.	ANKRD52	81	.	0			c.C1831T						.						80	83	82					12																	56641954		2128	4227	6355	SO:0001819	synonymous_variant	283373	exon18			CGTCCAGATTCAC	AK091555	CCDS44920.1	12q13.3	2013-01-10			ENSG00000139645	ENSG00000139645		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	26614	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit C"						Standard	NM_173595		Approved	FLJ34236, PP6-ARS-C	uc001skm.4	Q8NB46	OTTHUMG00000170329	ENST00000267116.7:c.1831C>T	chr12.hg19:g.56641954G>A		33.0	0.0		34.0	7.0	NM_173595	A6NE79|B1Q2K2	Silent	SNP	ENST00000267116.7	hg19	CCDS44920.1																																																																																			.	.		0.632	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595		A	56641954	G	A	56641954	2	1	209	1	0	0	0	0	0	0	0	1	678	933	33	3		3	ANKRD52	12	56641954	Silent	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	3729018	56641954	77209941	96	30241										
LRP1	4035	hgsc.bcm.edu	37	chr12	57532258	57532258	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctagcccctaagacttgcagCcccaagcagtttgcctgcag	9	15	0	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr12:57532258C>G	ENST00000243077.3	+	2	550	c.84C>G	c.(82-84)agC>agG	p.S28R	LRP1_ENST00000553277.1_Missense_Mutation_p.S28R|LRP1_ENST00000554174.1_Missense_Mutation_p.S28R|LRP1_ENST00000338962.4_Missense_Mutation_p.S28R	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	28	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	AGACTTGCAGCCCCAAGCAGT	0.542																																					p.S28R		Atlas-SNP	.											.	LRP1	428	.	0			c.C84G						.						148	149	149					12																	57532258		2203	4300	6503	SO:0001583	missense	4035	exon2			TTGCAGCCCCAAG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.84C>G	chr12.hg19:g.57532258C>G	ENSP00000243077:p.Ser28Arg	109.0	0.0		94.0	13.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.690581	0.88735	.	.	ENSG00000123384	ENST00000553277;ENST00000243077;ENST00000338962;ENST00000554174	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.53384	0.1793	L	0.41824	1.3	0.51767	D	0.999935	D;D;D;D	0.76494	0.999;0.997;0.998;0.967	D;D;D;P	0.87578	0.998;0.992;0.958;0.76	T	0.32877	-0.9890	10	0.13470	T	0.59	.	16.8396	0.85965	0.0:1.0:0.0:0.0	.	28;28;28;28	Q86SW0;Q07954;Q6PJ72;Q7Z7K9	.;LRP1_HUMAN;.;.	R	28	ENSP00000451449:S28R;ENSP00000243077:S28R;ENSP00000341264:S28R;ENSP00000451737:S28R	ENSP00000243077:S28R	S	+	3	2	LRP1	55818525	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.563000	0.67352	2.768000	0.95171	0.561000	0.74099	AGC	.	.		0.542	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		G	57532258	C	G	57532258	3	3	209	1	0	0	0	0	1	0	0	0	8960	738	26	4	90	4	LRP1	12	57532258	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	890304	57532258	76319637	97	30242										
GLIPR1	11010	hgsc.bcm.edu	37	chr12	75892688	75892688	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tctcattgttaattcagtaaTtctaatactgtctgttataa	4	6	4	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr12:75892688T>C	ENST00000266659.3	+	6	932	c.731T>C	c.(730-732)aTt>aCt	p.I244T	KRR1_ENST00000229214.4_3'UTR	NM_006851.2	NP_006842.2	P48060	GLIP1_HUMAN	GLI pathogenesis-related 1	244					cellular lipid metabolic process (GO:0044255)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	14						AATTCAGTAATTCTAATACTG	0.338																																					p.I244T		Atlas-SNP	.											.	GLIPR1	33	.	0			c.T731C						.						145	131	136					12																	75892688		2203	4300	6503	SO:0001583	missense	11010	exon6			CAGTAATTCTAAT	U16307	CCDS9011.1	12q14.1	2008-08-15	2008-08-15			ENSG00000139278			17001	protein-coding gene	gene with protein product		602692	"GLI pathogenesis-related 1 (glioma)"			7607567, 8973356	Standard	NM_006851		Approved	RTVP1, GliPR	uc001sxs.3	P48060	OTTHUMG00000169757	ENST00000266659.3:c.731T>C	chr12.hg19:g.75892688T>C	ENSP00000266659:p.Ile244Thr	70.0	0.0		60.0	14.0	NM_006851	A7YET6|F8VUC2|Q15409|Q969K2	Missense_Mutation	SNP	ENST00000266659.3	hg19	CCDS9011.1	.	.	.	.	.	.	.	.	.	.	T	4.841	0.156435	0.09236	.	.	ENSG00000139278	ENST00000266659	T	0.06768	3.26	5.27	4.11	0.48088	.	0.527824	0.20411	N	0.092844	T	0.08223	0.0205	L	0.57536	1.79	0.19300	N	0.999976	B	0.30482	0.281	B	0.24848	0.056	T	0.31806	-0.9930	10	0.15499	T	0.54	.	8.3748	0.32436	0.1741:0.0:0.0:0.8259	.	244	P48060	GLIP1_HUMAN	T	244	ENSP00000266659:I244T	ENSP00000266659:I244T	I	+	2	0	GLIPR1	74178955	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	0.620000	0.24403	1.001000	0.39076	0.459000	0.35465	ATT	.	.		0.338	GLIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405722.1	NM_006851		C	75892688	T	C	75892688	3	2	209	1	0	0	0	0	1	0	0	0	6449	1493	52	2	753	2	GLIPR1	12	75892688	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	18360430	75892688	57959207	98	30243										
ERP29	10961	hgsc.bcm.edu	37	chr12	112460383	112460383	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	caagatgagtgacgggaagaAggaggagctccagaagagct	16	6	0	6			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr12:112460383A>C	ENST00000261735.3	+	3	863	c.713A>C	c.(712-714)aAg>aCg	p.K238T	ERP29_ENST00000546477.1_Missense_Mutation_p.K137T|ERP29_ENST00000455836.1_3'UTR	NM_006817.3	NP_006808.1	P30040	ERP29_HUMAN	endoplasmic reticulum protein 29	238					intracellular protein transport (GO:0006886)|protein folding (GO:0006457)|protein secretion (GO:0009306)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	5						GACGGGAAGAAGGAGGAGCTC	0.507																																					p.K238T		Atlas-SNP	.											.	ERP29	17	.	0			c.A713C						.						84	88	87					12																	112460383		2203	4300	6503	SO:0001583	missense	10961	exon3			GGAAGAAGGAGGA	X94910	CCDS9158.1, CCDS44977.1	12q24.13	2011-10-19	2005-10-05	2005-10-05		ENSG00000089248		"Protein disulfide isomerases"	13799	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 9"	602287	"chromosome 12 open reading frame 8"	C12orf8		9738895, 9037184	Standard	NM_006817		Approved	ERp28, ERp31, ERp29, PDI-DB, PDIA9	uc001ttk.1	P30040	OTTHUMG00000169637	ENST00000261735.3:c.713A>C	chr12.hg19:g.112460383A>C	ENSP00000261735:p.Lys238Thr	53.0	0.0		59.0	13.0	NM_006817	C9J183|Q3MJC3|Q6FHT4	Missense_Mutation	SNP	ENST00000261735.3	hg19	CCDS9158.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.992472	0.74703	.	.	ENSG00000089248	ENST00000261735;ENST00000546477	.	.	.	5.75	4.59	0.56863	Endoplasmic reticulum, protein ERp29, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.73682	0.3618	M	0.71581	2.175	0.53005	D	0.999964	D	0.76494	0.999	D	0.77004	0.989	T	0.70139	-0.4954	9	0.15066	T	0.55	-14.0229	12.0223	0.53350	0.9313:0.0:0.0687:0.0	.	238	P30040	ERP29_HUMAN	T	238;137	.	ENSP00000261735:K238T	K	+	2	0	ERP29	110944766	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.599000	0.61076	2.185000	0.69588	0.459000	0.35465	AAG	.	.		0.507	ERP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405200.1			C	112460383	A	C	112460383	3	2	209	1	0	0	0	0	1	0	0	0	5244	72	3	5	723	5	ERP29	12	112460383	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	36567695	112460383	21391512	99	30244										
SPPL3	121665	hgsc.bcm.edu	37	chr12	121206182	121206182	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gaggaacatcacgcccaacaTtgggccccaggtggagcttc	12	13	1	0	rs150882911	byFrequency	TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr12:121206182T>G	ENST00000353487.2	-	8	1222	c.719A>C	c.(718-720)aAt>aCt	p.N240T		NM_139015.4	NP_620584.2	Q8TCT6	SPPL3_HUMAN	signal peptide peptidase like 3	241						Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|rough endoplasmic reticulum (GO:0005791)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|protein homodimerization activity (GO:0042803)					all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ACGCCCAACATTGGGCCCCAG	0.547																																					p.N240T		Atlas-SNP	.											.	.	.	.	0			c.A719C						.						133	125	127					12																	121206182		2203	4300	6503	SO:0001583	missense	121665	exon8			CCAACATTGGGCC		CCDS9208.1	12q24.31	2012-02-21			ENSG00000157837	ENSG00000157837			30424	protein-coding gene	gene with protein product	"intramembrane protease 2", "presenilin-like protein 4"	608240				12139484	Standard	NM_139015		Approved	IMP2, PSL4, MGC90402, MGC126674, MGC126676, DKFZP586C1324	uc001tzd.3	Q8TCT6	OTTHUMG00000169232	ENST00000353487.2:c.719A>C	chr12.hg19:g.121206182T>G	ENSP00000288680:p.Asn240Thr	59.0	0.0		44.0	10.0	NM_139015	Q3MJ04|Q8TAU4|Q96DD9	Missense_Mutation	SNP	ENST00000353487.2	hg19	CCDS9208.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.811083	0.50421	.	.	ENSG00000157837	ENST00000353487;ENST00000405631	T	0.16743	2.32	5.34	4.2	0.49525	.	0.143208	0.64402	D	0.000007	T	0.12732	0.0309	L	0.29908	0.895	0.46131	D	0.998889	B;B	0.24675	0.109;0.011	B;B	0.27380	0.079;0.024	T	0.10291	-1.0636	10	0.19590	T	0.45	-5.7361	11.082	0.48066	0.0:0.0724:0.0:0.9276	.	241;240	Q8TCT6;Q3MJ04	PSL4_HUMAN;.	T	240;239	ENSP00000288680:N240T	ENSP00000288680:N240T	N	-	2	0	AC069214.1	119690565	0.998000	0.40836	0.988000	0.46212	0.990000	0.78478	3.131000	0.50515	0.877000	0.35895	0.477000	0.44152	AAT	.	T|0.999;C|0.001		0.547	SPPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402980.2	NM_139015		G	121206182	T	G	121206182	3	3	209	1	0	0	0	0	1	0	0	0	15105	1493	52	5	451	5	SPPL3	12	121206182	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	8745799	121206182	12645713	100	30245										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88330117	88330117	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ggaggaggagaggcgggaaaGccaccacttgcggagccccg	18	11	0	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr13:88330117G>T	ENST00000325089.6	+	2	2693	c.2474G>T	c.(2473-2475)aGc>aTc	p.S825I	SLITRK5_ENST00000400028.3_Missense_Mutation_p.S584I	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	825					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					AGGCGGGAAAGCCACCACTTG	0.716																																					p.S825I		Atlas-SNP	.											.	SLITRK5	192	.	0			c.G2474T						.						10	12	12					13																	88330117		2197	4284	6481	SO:0001583	missense	26050	exon2			GGGAAAGCCACCA	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.2474G>T	chr13.hg19:g.88330117G>T	ENSP00000366283:p.Ser825Ile	121.0	0.0		163.0	23.0	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	hg19	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	G	11.98	1.800282	0.31869	.	.	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.61980	0.06;0.34	5.57	5.57	0.84162	.	0.271778	0.40222	N	0.001145	T	0.51753	0.1693	L	0.36672	1.1	0.40595	D	0.981521	B;B	0.20052	0.041;0.012	B;B	0.15484	0.013;0.006	T	0.46386	-0.9195	9	.	.	.	-6.9536	15.0578	0.71927	0.0:0.0:1.0:0.0	.	584;825	B4DSH5;O94991	.;SLIK5_HUMAN	I	825;584	ENSP00000366283:S825I;ENSP00000442244:S584I	.	S	+	2	0	SLITRK5	87128118	0.058000	0.20735	1.000000	0.80357	0.985000	0.73830	0.385000	0.20685	2.618000	0.88619	0.561000	0.74099	AGC	.	.		0.716	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			T	88330117	G	T	88330117	3	4	209	1	0	0	0	0	1	0	0	0	14761	971	34	3	2476	3	SLITRK5	13	88330117	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10		88330117	26839761	101	30246										
GPR18	2841	hgsc.bcm.edu	37	chr13	99908040	99908040	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ccaattatgaagatacagctAtagaagacaagggctgcaat	9	7	0	4	rs371441036	byFrequency	TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr13:99908040A>G	ENST00000340807.3	-	3	643	c.87T>C	c.(85-87)taT>taC	p.Y29Y	UBAC2_ENST00000403766.3_Intron|GPR18_ENST00000397470.2_Silent_p.Y29Y|GPR18_ENST00000397473.2_Silent_p.Y29Y|UBAC2_ENST00000376440.2_Intron			Q14330	GPR18_HUMAN	G protein-coupled receptor 18	29					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)	10	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Glycine(DB00145)	AGATACAGCTATAGAAGACAA	0.378													A|||	61	0.0121805	0	0	5008	,	,		18179	0		0	False		,,,				2504	0.0624				p.Y29Y		Atlas-SNP	.											.	GPR18	23	.	0			c.T87C						.						127	127	127					13																	99908040		2203	4300	6503	SO:0001819	synonymous_variant	2841	exon2			ACAGCTATAGAAG	L42324	CCDS9491.1	13q32	2014-01-30			ENSG00000125245	ENSG00000125245		"GPCR / Class A : Orphans"	4472	protein-coding gene	gene with protein product		602042				9205118	Standard	NM_005292		Approved		uc010afv.3	Q14330	OTTHUMG00000017266	ENST00000340807.3:c.87T>C	chr13.hg19:g.99908040A>G		110.0	0.0		121.0	15.0	NM_001098200	Q6GTM3|Q96HI6|Q9H2L2	Silent	SNP	ENST00000340807.3	hg19	CCDS9491.1																																																																																			.	.		0.378	GPR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045585.1			G	99908040	A	G	99908040	2	3	209	1	0	0	0	0	0	0	0	1	6683	456	16	2		2	GPR18	13	99908040	Silent	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	11577923	99908040	15261838	102	30247										
ANKRD10	55608	hgsc.bcm.edu	37	chr13	111567223	111567223	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gcagcgggaaacggagcgagAgcagctcctcgctggagaag	17	10	0	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr13:111567223A>C	ENST00000267339.2	-	1	193	c.59T>G	c.(58-60)cTc>cGc	p.L20R	ANKRD10_ENST00000310847.4_Missense_Mutation_p.L20R|ANKRD10_ENST00000375758.5_Missense_Mutation_p.L20R	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	20										central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)	9	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			ACGGAGCGAGAGCAGCTCCTC	0.736																																					p.L20R		Atlas-SNP	.											.	ANKRD10	24	.	0			c.T59G						.						10	14	13					13																	111567223		2111	4177	6288	SO:0001583	missense	55608	exon1			AGCGAGAGCAGCT	AK000100	CCDS9520.1, CCDS66580.1	13q33.3	2013-01-10			ENSG00000088448	ENSG00000088448		"Ankyrin repeat domain containing"	20265	protein-coding gene	gene with protein product							Standard	NM_017664		Approved	FLJ20093	uc001vrn.3	Q9NXR5	OTTHUMG00000017349	ENST00000267339.2:c.59T>G	chr13.hg19:g.111567223A>C	ENSP00000267339:p.Leu20Arg	73.0	0.0		129.0	18.0	NM_017664	Q5VW12|Q9BV12	Missense_Mutation	SNP	ENST00000267339.2	hg19	CCDS9520.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.457442	0.63401	.	.	ENSG00000088448	ENST00000267339;ENST00000375758;ENST00000310847	T;T;T	0.72615	-0.67;0.66;0.66	4.0	4.0	0.46444	Ankyrin repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.79082	0.4386	L	0.58101	1.795	0.58432	D	0.999997	D;D;D	0.76494	0.999;0.996;0.998	D;P;D	0.85130	0.977;0.907;0.997	T	0.76016	-0.3113	10	0.25106	T	0.35	-0.0256	12.5463	0.56201	1.0:0.0:0.0:0.0	.	20;20;20	Q8IUW1;Q9NXR5-2;Q9NXR5	.;.;ANR10_HUMAN	R	20	ENSP00000267339:L20R;ENSP00000364911:L20R;ENSP00000312534:L20R	ENSP00000267339:L20R	L	-	2	0	ANKRD10	110365224	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.549000	0.82163	1.433000	0.47394	0.402000	0.26972	CTC	.	.		0.736	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1			C	111567223	A	C	111567223	3	2	209	1	0	0	0	0	1	0	0	0	638	304	11	5	1227	5	ANKRD10	13	111567223	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	11659183	111567223	3602655	103	30248										
TEP1	7011	hgsc.bcm.edu	37	chr14	20876563	20876563	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ttctccaaggagaggatgtcTggatgggcagacacatgccc	13	10	2	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:20876563T>A	ENST00000262715.5	-	2	76	c.36A>T	c.(34-36)ccA>ccT	p.P12P	TEP1_ENST00000556935.1_Silent_p.P12P	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	12					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AGAGGATGTCTGGATGGGCAG	0.507																																					p.P12P		Atlas-SNP	.											TEP1,right_upper_lobe,carcinoma,0,1	TEP1	224	.	0			c.A36T						.						75	73	74					14																	20876563		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon2			GATGTCTGGATGG		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.36A>T	chr14.hg19:g.20876563T>A		38.0	0.0		61.0	7.0	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	.		0.507	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		A	20876563	T	A	20876563	2	1	209	1	0	0	0	0	0	0	0	1	15774	1567	55	4		4	TEP1	14	20876563	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10		20876563	86472977	104	30249										
HNRNPC	3183	hgsc.bcm.edu	37	chr14	21702133	21702133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	taaaacctggccagcaatcaTtctgccatcctctcctgcta	5	15	3	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:21702133T>C	ENST00000320084.7	-	2	459	c.220A>G	c.(220-222)Atg>Gtg	p.M74V	HNRNPC_ENST00000556628.1_Intron|HNRNPC_ENST00000553753.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000336053.6_Missense_Mutation_p.M74V|HNRNPC_ENST00000555883.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000420743.2_Missense_Mutation_p.M74V|HNRNPC_ENST00000556513.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000556142.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000554455.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000553300.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000556897.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000449098.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000557201.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000555914.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000554969.1_Missense_Mutation_p.M74V|HNRNPC_ENST00000430246.2_Missense_Mutation_p.M74V|HNRNPC_ENST00000555309.1_Missense_Mutation_p.M74V	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	74	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		CCAGCAATCATTCTGCCATCC	0.413																																					p.M74V	NSCLC(108;607 2244 12726 38757)	Atlas-SNP	.											.	HNRNPC	31	.	0			c.A220G						.						56	56	56					14																	21702133		2071	4235	6306	SO:0001583	missense	3183	exon2			CAATCATTCTGCC		CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"RNA binding motif (RRM) containing"	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.220A>G	chr14.hg19:g.21702133T>C	ENSP00000319690:p.Met74Val	204.0	0.0		227.0	27.0	NM_001077443	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Missense_Mutation	SNP	ENST00000320084.7	hg19	CCDS41915.1	.	.	.	.	.	.	.	.	.	.	T	9.434	1.086192	0.20390	.	.	ENSG00000092199	ENST00000336053;ENST00000320084;ENST00000449098;ENST00000554969;ENST00000556142;ENST00000554455;ENST00000430246;ENST00000553753;ENST00000555914;ENST00000555309;ENST00000452166;ENST00000555883;ENST00000556513;ENST00000557201;ENST00000553300;ENST00000556897;ENST00000420743;ENST00000445284;ENST00000554383;ENST00000555215;ENST00000555137;ENST00000554891;ENST00000556226;ENST00000555176	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.15372	2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43;2.43	5.43	5.43	0.79202	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.062854	0.64402	U	0.000012	T	0.08758	0.0217	N	0.05078	-0.115	0.48696	D	0.999694	B;B;P;B;B	0.39831	0.027;0.029;0.69;0.073;0.022	B;B;B;B;B	0.38264	0.038;0.018;0.269;0.065;0.01	T	0.34875	-0.9811	10	0.11182	T	0.66	.	14.4601	0.67442	0.0:0.0:0.0:1.0	.	74;74;74;74;74	B4DY08;P07910-4;G3V4C1;P07910;P07910-2	.;.;.;HNRPC_HUMAN;.	V	74	ENSP00000338095:M74V;ENSP00000319690:M74V;ENSP00000404559:M74V;ENSP00000450725:M74V;ENSP00000451187:M74V;ENSP00000451291:M74V;ENSP00000442816:M74V;ENSP00000450548:M74V;ENSP00000451708:M74V;ENSP00000450790:M74V;ENSP00000450629:M74V;ENSP00000452214:M74V;ENSP00000452276:M74V;ENSP00000450544:M74V;ENSP00000451176:M74V;ENSP00000404848:M74V;ENSP00000452021:M74V;ENSP00000452213:M74V;ENSP00000452185:M74V;ENSP00000450467:M74V;ENSP00000451292:M74V;ENSP00000452573:M74V	ENSP00000319690:M74V	M	-	1	0	HNRNPC	20771973	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.228000	0.72288	2.066000	0.61787	0.533000	0.62120	ATG	.	.		0.413	HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1			C	21702133	T	C	21702133	3	2	209	1	0	0	0	0	1	0	0	0	7271	1493	52	2	728	2	HNRNPC	14	21702133	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	825570	21702133	85647407	105	30250										
NGDN	25983	hgsc.bcm.edu	37	chr14	23945267	23945267	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gaggatgaggaggaagatgaAgcagaagatgaccagtctga	16	4	1	7			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:23945267A>C	ENST00000408901.3	+	7	478	c.450A>C	c.(448-450)gaA>gaC	p.E150D	NGDN_ENST00000556580.1_5'Flank|NGDN_ENST00000397154.3_Missense_Mutation_p.E150D	NM_001042635.1|NM_015514.1	NP_001036100.1|NP_056329.1	Q8NEJ9	NGDN_HUMAN	neuroguidin, EIF4E binding protein	150	Necessary for interaction with EIF4E. {ECO:0000250}.				regulation of translation (GO:0006417)	cell projection (GO:0042995)|chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	12	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		AGGAAGATGAAGCAGAAGATG	0.418																																					p.E150D		Atlas-SNP	.											.	NGDN	49	.	0			c.A450C						.						102	102	102					14																	23945267		2203	4300	6503	SO:0001583	missense	25983	exon7			AGATGAAGCAGAA	AK022215	CCDS32051.1, CCDS41926.1	14q11.2	2014-06-13	2006-08-02	2006-08-02	ENSG00000129460	ENSG00000129460			20271	protein-coding gene	gene with protein product		610777	"chromosome 14 open reading frame 120"	C14orf120		16705177	Standard	NM_001042635		Approved	DKFZP564O092, LCP5, lpd-2, NGD	uc001wjy.3	Q8NEJ9	OTTHUMG00000171501	ENST00000408901.3:c.450A>C	chr14.hg19:g.23945267A>C	ENSP00000386134:p.Glu150Asp	61.0	0.0		108.0	13.0	NM_015514	A8K760|Q9Y400	Missense_Mutation	SNP	ENST00000408901.3	hg19	CCDS41926.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.846|3.846	-0.032748|-0.032748	0.07543|0.07543	.|.	.|.	ENSG00000129460|ENSG00000129460	ENST00000408901;ENST00000397154;ENST00000555128|ENST00000556483	T;T|.	0.34472|.	1.36;1.36|.	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	0.246987|.	0.46758|.	D|.	0.000262|.	T|T	0.34571|0.34571	0.0902|0.0902	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B;B|.	0.06786|.	0.001;0.0|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.29212|0.29212	-1.0019|-1.0019	10|5	0.15499|.	T|.	0.54|.	-8.6696|-8.6696	9.7474|9.7474	0.40455|0.40455	0.9223:0.0:0.0777:0.0|0.9223:0.0:0.0777:0.0	.|.	150;150|.	Q8NEJ9-2;Q8NEJ9|.	.;NGDN_HUMAN|.	D|R	150;150;125|98	ENSP00000386134:E150D;ENSP00000380340:E150D|.	ENSP00000380340:E150D|.	E|S	+|+	3|1	2|0	NGDN|NGDN	23015107|23015107	0.989000|0.989000	0.36119|0.36119	0.947000|0.947000	0.38551|0.38551	0.175000|0.175000	0.22909|0.22909	1.702000|1.702000	0.37836|0.37836	2.257000|2.257000	0.74773|0.74773	0.460000|0.460000	0.39030|0.39030	GAA|AGC	.	.		0.418	NGDN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413782.3	NM_001042635		C	23945267	A	C	23945267	3	2	209	1	0	0	0	0	1	0	0	0	10402	69	3	5	476	5	NGDN	14	23945267	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	2243134	23945267	83404273	106	30251										
NOVA1	4857	hgsc.bcm.edu	37	chr14	26917256	26917256	+	Frame_Shift_Del	DEL	G	G	-													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gagcagcctgtgttgcagctGgtgttccagtaatggttacc							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:26917256delG	ENST00000539517.2	-	5	1750	c.1433delC	c.(1432-1434)ccafs	p.P478fs	NOVA1_ENST00000465357.2_Frame_Shift_Del_p.P454fs|NOVA1_ENST00000267422.7_Frame_Shift_Del_p.P356fs	NM_002515.2	NP_002506.2	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	481	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		TGTTGCAGCTGGTGTTCCAGT	0.473																																					p.P478fs		Atlas-INDEL	.											.	NOVA1	146	.	0			c.1434delA						.						153	130	138					14																	26917256		2203	4300	6503	SO:0001589	frameshift_variant	4857	exon5			.	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000539517.2:c.1433delC	chr14.hg19:g.26917256delG	ENSP00000438875:p.Pro478fs	146.0	0.0		219.0	27.0	NM_002515	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Frame_Shift_Del	DEL	ENST00000539517.2	hg19	CCDS32061.1																																																																																			.	.		0.473	NOVA1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000073261.3	NM_006491		-	26917256	G	-	26917256	7	5	209	1	0	1	0	1	0	0	0	0	10563	1348	47	0	94	0	NOVA1	14	26917256	Frame_Shift_Del	DEL	G	TCGA-DD-AAE3-01A-11D-A40R-10	2971989	26917256	80432284	107	30252										
BAZ1A	11177	hgsc.bcm.edu	37	chr14	35331372	35331372	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tgggtaaggctggtcaagtaTaaaactggaataattagtgg	13	3	1	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:35331372T>C	ENST00000382422.2	-	2	597	c.270A>G	c.(268-270)ttA>ttG	p.L90L	BAZ1A_ENST00000358716.4_Silent_p.L90L|BAZ1A_ENST00000360310.1_Silent_p.L90L|BAZ1A_ENST00000553853.1_5'UTR			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	90	Required for association with the CHRAC1/POLE3 complex.|Required for interaction with NCOR1.|WAC. {ECO:0000255|PROSITE- ProRule:PRU00475}.				chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		TGGTCAAGTATAAAACTGGAA	0.403																																					p.L90L		Atlas-SNP	.											.	BAZ1A	128	.	0			c.A270G						.						195	197	196					14																	35331372		2203	4300	6503	SO:0001819	synonymous_variant	11177	exon3			CAAGTATAAAACT	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.270A>G	chr14.hg19:g.35331372T>C		148.0	0.0		187.0	22.0	NM_182648	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	hg19	CCDS9651.1																																																																																			.	.		0.403	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			C	35331372	T	C	35331372	2	2	209	1	0	0	0	0	0	0	0	1	1329	1403	49	2		2	BAZ1A	14	35331372	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	8414116	35331372	72018168	108	30253										
PLEKHG3	26030	hgsc.bcm.edu	37	chr14	65208353	65208353	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tcttcctgcaagaagaaggaAtcagcactctccacccgaga	8	13	3	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:65208353A>G	ENST00000394691.1	+	16	2265	c.2118A>G	c.(2116-2118)gaA>gaG	p.E706E	PLEKHG3_ENST00000247226.7_Silent_p.E650E|PLEKHG3_ENST00000471182.2_Silent_p.E239E|PLEKHG3_ENST00000492928.1_3'UTR|PLEKHG3_ENST00000484731.2_Silent_p.E211E			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	706							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		AGAAGAAGGAATCAGCACTCT	0.577																																					p.E650E		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.A1950G						.						55	58	57					14																	65208353		2198	4284	6482	SO:0001819	synonymous_variant	26030	exon14			GAAGGAATCAGCA	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20364	protein-coding gene	gene with protein product			"KIAA0599"	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.2118A>G	chr14.hg19:g.65208353A>G		56.0	0.0		80.0	14.0	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Silent	SNP	ENST00000394691.1	hg19																																																																																				.	.		0.577	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549		G	65208353	A	G	65208353	2	3	209	1	0	0	0	0	0	0	0	1	12079	98	4	2		2	PLEKHG3	14	65208353	Silent	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	29876981	65208353	42141187	109	30254										
PCNX	22990	hgsc.bcm.edu	37	chr14	71413714	71413714	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tgttctgaagatggtcaactAtcgactacacagagcacttg	9	9	2	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:71413714A>G	ENST00000304743.2	+	2	682	c.236A>G	c.(235-237)tAt>tGt	p.Y79C	PCNX_ENST00000439984.3_Missense_Mutation_p.Y79C|PCNX_ENST00000238570.5_Missense_Mutation_p.Y79C	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	79						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		ATGGTCAACTATCGACTACAC	0.418																																					p.Y79C		Atlas-SNP	.											.	PCNX	198	.	0			c.A236G						.						125	107	113					14																	71413714		2203	4300	6503	SO:0001583	missense	22990	exon2			TCAACTATCGACT	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.236A>G	chr14.hg19:g.71413714A>G	ENSP00000304192:p.Tyr79Cys	93.0	0.0		120.0	14.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.326200	0.60743	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.45276	0.9;0.9;0.9	6.05	6.05	0.98169	.	0.061535	0.64402	D	0.000003	T	0.64283	0.2584	M	0.68317	2.08	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.996;0.999	T	0.65623	-0.6123	10	0.59425	D	0.04	.	16.6	0.84812	1.0:0.0:0.0:0.0	.	79;79;79	B2RTR6;Q96RV3;Q96RV3-2	.;PCX1_HUMAN;.	C	79	ENSP00000304192:Y79C;ENSP00000238570:Y79C;ENSP00000396617:Y79C	ENSP00000238570:Y79C	Y	+	2	0	PCNX	70483467	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.450000	0.80656	2.323000	0.78572	0.533000	0.62120	TAT	.	.		0.418	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		G	71413714	A	G	71413714	3	3	209	1	0	0	0	0	1	0	0	0	11600	449	16	2	242	2	PCNX	14	71413714	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	6205361	71413714	35935826	110	30255										
C14orf115	55237	hgsc.bcm.edu	37	chr14	74824495	74824495	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tgccacttcagcagttcctcCagcggttcccggagatctcc	9	16	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:74824495C>G	ENST00000256362.4	+	2	1250	c.1009C>G	c.(1009-1011)Cag>Gag	p.Q337E		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	337					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						GCAGTTCCTCCAGCGGTTCCC	0.667																																					p.Q337E		Atlas-SNP	.											.	VRTN	79	.	0			c.C1009G						.						53	58	56					14																	74824495		2203	4300	6503	SO:0001583	missense	55237	exon2			TTCCTCCAGCGGT	AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 115", "vertebrae development homolog (pig)"	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.1009C>G	chr14.hg19:g.74824495C>G	ENSP00000256362:p.Gln337Glu	48.0	0.0		83.0	44.0	NM_018228	Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	hg19	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.061167	0.36373	.	.	ENSG00000133980	ENST00000256362	T	0.46451	0.87	5.02	5.02	0.67125	.	0.221700	0.38326	N	0.001735	T	0.25827	0.0629	N	0.17082	0.46	0.29668	N	0.842703	B	0.30236	0.274	B	0.24848	0.056	T	0.13124	-1.0521	10	0.29301	T	0.29	-9.0505	12.6328	0.56667	0.165:0.835:0.0:0.0	.	337	Q9H8Y1	VRTN_HUMAN	E	337	ENSP00000256362:Q337E	ENSP00000256362:Q337E	Q	+	1	0	VRTN	73894248	0.996000	0.38824	0.993000	0.49108	0.714000	0.41099	2.124000	0.42006	2.602000	0.87976	0.561000	0.74099	CAG	.	.		0.667	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228		G	74824495	C	G	74824495	3	3	209	1	0	0	0	0	1	0	0	0	1742	595	21	4	1011	4	C14orf115	14	74824495	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	3410781	74824495	32525045	111	30256										
FAM164C	79696	hgsc.bcm.edu	37	chr14	75537802	75537802	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agccgagagagttttcatctAggaactttggtgtgaggaac	13	6	2	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:75537802A>G	ENST00000524913.1	+	2	1015	c.526A>G	c.(526-528)Agg>Ggg	p.R176G	ZC2HC1C_ENST00000526748.1_Intron|ACYP1_ENST00000555463.1_5'Flank|ZC2HC1C_ENST00000439583.2_Missense_Mutation_p.R176G|ZC2HC1C_ENST00000238686.8_Missense_Mutation_p.R176G	NM_024643.2	NP_078919.2	Q53FD0	ZC21C_HUMAN	zinc finger, C2HC-type containing 1C	176							metal ion binding (GO:0046872)										GTTTTCATCTAGGAACTTTGG	0.552																																					p.R176G		Atlas-SNP	.											.	.	.	.	0			c.A526G						.						127	127	127					14																	75537802		1925	4126	6051	SO:0001583	missense	79696	exon2			TCATCTAGGAACT	AK026746	CCDS41972.1, CCDS45138.1	14q24.3	2013-01-10	2012-02-03	2012-02-03	ENSG00000119703	ENSG00000119703		"Zinc fingers, C2HC-type containing"	20354	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 140", "family with sequence similarity 164, member C"	C14orf140, FAM164C			Standard	XM_005268062		Approved		uc001xrh.3	Q53FD0	OTTHUMG00000167439	ENST00000524913.1:c.526A>G	chr14.hg19:g.75537802A>G	ENSP00000435550:p.Arg176Gly	84.0	0.0		144.0	27.0	NM_024643	E9PJQ0|Q9BTA8|Q9H5S9	Missense_Mutation	SNP	ENST00000524913.1	hg19	CCDS41972.1	.	.	.	.	.	.	.	.	.	.	A	7.327	0.618162	0.14129	.	.	ENSG00000119703	ENST00000524913;ENST00000238686;ENST00000439583	T	0.44482	0.92	4.72	4.72	0.59763	.	0.695175	0.13395	N	0.391060	T	0.31451	0.0797	N	0.22421	0.69	0.09310	N	1	B;B	0.19817	0.039;0.013	B;B	0.16289	0.015;0.007	T	0.18116	-1.0347	10	0.48119	T	0.1	-1.7992	12.9707	0.58511	1.0:0.0:0.0:0.0	.	176;176	Q53FD0;E9PJQ0	F164C_HUMAN;.	G	176	ENSP00000435550:R176G	ENSP00000238686:R176G	R	+	1	2	FAM164C	74607555	0.002000	0.14202	0.029000	0.17559	0.018000	0.09664	1.354000	0.34056	1.995000	0.58328	0.455000	0.32223	AGG	.	.		0.552	ZC2HC1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394616.4	NM_001042430		G	75537802	A	G	75537802	3	3	209	1	0	0	0	0	1	0	0	0	5484	411	15	2	528	2	FAM164C	14	75537802	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	713307	75537802	31811738	112	30257										
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493779	77493780	+	In_Frame_Ins	INS	-	-	TGCTGCTGT													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gttgctgctgctgctgctgcINStgctgctgctgctgttgctg							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:77493779_77493780insTGCTGCTGT	ENST00000238647.3	-	1	1254_1255	c.356_357insACAGCAGCA	c.(355-357)cag>caACAGCAGCAg	p.119_119Q>QQQQ		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	119	Poly-Gln.				development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						gctgctgctgctgctgctgctg	0.693																																					p.Q119delinsQQQQ		Atlas-INDEL	.											.	IRF2BPL	40	.	0			c.357_358insACAGCAGCA						.																																			SO:0001652	inframe_insertion	64207	exon1			.	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.356_357insACAGCAGCA	chr14.hg19:g.77493779_77493780insTGCTGCTGT	ENSP00000238647:p.GlnGlnGln125dup	29.0	0.0		70.0	46.0	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	In_Frame_Ins	INS	ENST00000238647.3	hg19	CCDS9854.1																																																																																			.	CTG|1.000;|0.000		0.693	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		TGCTGCTGT	77493780	-	TGCTGCTGT	77493779	7	5	209	1	0	1	1	0	0	0	0	0	1775	796	28	0	2037	0	C14orf4	14	77493779	In_Frame_Ins	INS	-	TCGA-DD-AAE3-01A-11D-A40R-10	1955977	77493779	29855761	113	30258										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96770845	96770845	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	atcttaccttgcttagctgtAtttccattaaaaagtcatgg	6	8	2	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr14:96770845A>G	ENST00000359933.4	-	32	5722	c.4829T>C	c.(4828-4830)aTa>aCa	p.I1610T	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1610					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		GCTTAGCTGTATTTCCATTAA	0.453																																					p.I1610T		Atlas-SNP	.											.	ATG2B	169	.	0			c.T4829C						.						150	136	140					14																	96770845		2203	4300	6503	SO:0001583	missense	55102	exon32			AGCTGTATTTCCA	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.4829T>C	chr14.hg19:g.96770845A>G	ENSP00000353010:p.Ile1610Thr	105.0	0.0		124.0	16.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	21.9	4.211952	0.79240	.	.	ENSG00000066739	ENST00000359933	T	0.13901	2.55	5.18	5.18	0.71444	.	0.086607	0.85682	D	0.000000	T	0.39279	0.1072	M	0.77486	2.375	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.32052	-0.9921	10	0.72032	D	0.01	.	15.3344	0.74241	1.0:0.0:0.0:0.0	.	1610	Q96BY7	ATG2B_HUMAN	T	1610	ENSP00000353010:I1610T	ENSP00000261834:I254T	I	-	2	0	ATG2B	95840598	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	8.477000	0.90424	2.071000	0.62044	0.460000	0.39030	ATA	.	.		0.453	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96770845	A	G	96770845	3	3	209	1	0	0	0	0	1	0	0	0	1094	449	16	2	1451	2	ATG2B	14	96770845	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	19277066	96770845	10578695	114	30259										
SNRPN	6638	hgsc.bcm.edu	37	chr15	25222034	25222034	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cttgtttcagactggcattgCtcgggtaccacttgctggag	12	10	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr15:25222034C>A	ENST00000400100.1	+	10	1168	c.278C>A	c.(277-279)gCt>gAt	p.A93D	SNRPN_ENST00000444203.2_Missense_Mutation_p.A97D|SNRPN_ENST00000390687.4_Missense_Mutation_p.A93D|SNRPN_ENST00000554227.2_Missense_Mutation_p.A97D|SNRPN_ENST00000400098.1_Missense_Mutation_p.A93D|SNHG14_ENST00000551631.2_RNA|SNRPN_ENST00000400097.1_Missense_Mutation_p.A93D|SNRPN_ENST00000346403.6_Missense_Mutation_p.A93D|SNRPN_ENST00000577565.1_Missense_Mutation_p.A93D|SNURF_ENST00000338094.6_3'UTR|SNURF_ENST00000551312.2_Intron	NM_022807.2	NP_073718.1	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	93					response to hormone (GO:0009725)|RNA splicing (GO:0008380)	small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U2 snRNP (GO:0005686)	RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(2)	24		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		ACTGGCATTGCTCGGGTACCA	0.488									Prader-Willi syndrome																												p.A93D		Atlas-SNP	.											.	SNRPN	58	.	0			c.C278A						.						87	89	89					15																	25222034		1946	4149	6095	SO:0001583	missense	6638	exon10	Familial Cancer Database	Prader-Labhart-Willi syndrome	GCATTGCTCGGGT	L80005	CCDS10017.1	15q11.2	2013-07-16			ENSG00000128739	ENSG00000128739			11164	protein-coding gene	gene with protein product	"tissue-specific splicing protein", "SM protein N", "small nuclear ribonucleoprotein N"	182279	"Prader-Willi syndrome chromosome region"	PWCR		1533223	Standard	NM_022805		Approved	SMN, SM-D, HCERN3, SNRNP-N, SNURF-SNRPN, RT-LI	uc001ywt.1	P63162	OTTHUMG00000129180	ENST00000400100.1:c.278C>A	chr15.hg19:g.25222034C>A	ENSP00000382972:p.Ala93Asp	51.0	0.0		91.0	9.0	NM_022807	B3KVR1|P14648|P17135|Q0D2Q5	Missense_Mutation	SNP	ENST00000400100.1	hg19	CCDS10017.1	.	.	.	.	.	.	.	.	.	.	C	17.64	3.440195	0.63067	.	.	ENSG00000128739	ENST00000400100;ENST00000400098;ENST00000400097;ENST00000554227;ENST00000390687;ENST00000444203	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	3.79	3.79	0.43588	.	0.180238	0.48286	D	0.000194	T	0.45935	0.1367	M	0.65498	2.005	0.80722	D	1	P;P	0.49961	0.93;0.868	P;B	0.45310	0.476;0.328	T	0.52449	-0.8574	10	0.49607	T	0.09	-8.1156	13.963	0.64193	0.0:1.0:0.0:0.0	.	97;93	B3KVR1;P63162	.;RSMN_HUMAN	D	93;93;93;97;93;97	ENSP00000382972:A93D;ENSP00000382970:A93D;ENSP00000382969:A93D;ENSP00000452342:A97D;ENSP00000375105:A93D;ENSP00000408767:A97D	ENSP00000375105:A93D	A	+	2	0	SNRPN	22773127	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.437000	0.73421	2.409000	0.81822	0.561000	0.74099	GCT	.	.		0.488	SNRPN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413849.10	NM_003097		A	25222034	C	A	25222034	3	1	209	1	0	0	0	0	1	0	0	0	14885	797	28	3	292	3	SNRPN	15	25222034	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10		25222034	77309358	115	30260										
FAM98B	283742	hgsc.bcm.edu	37	chr15	38766446	38766446	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agtgccgccgacgaatgttaAtgaaacgattagatgtgact	11	7	0	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr15:38766446A>G	ENST00000491535.1	+	6	684	c.676A>G	c.(676-678)Atg>Gtg	p.M226V	FAM98B_ENST00000397609.2_Missense_Mutation_p.M226V	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B	226						cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		ACGAATGTTAATGAAACGATT	0.378																																					p.M226V		Atlas-SNP	.											.	FAM98B	53	.	0			c.A676G						.						222	197	205					15																	38766446		2200	4297	6497	SO:0001583	missense	283742	exon6			ATGTTAATGAAAC		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831	ENST00000491535.1:c.676A>G	chr15.hg19:g.38766446A>G	ENSP00000453166:p.Met226Val	91.0	0.0		75.0	14.0	NM_001042429	A8MUW5|Q8N935	Missense_Mutation	SNP	ENST00000491535.1	hg19	CCDS42015.1	.	.	.	.	.	.	.	.	.	.	A	9.424	1.083878	0.20309	.	.	ENSG00000171262	ENST00000397609;ENST00000305752	T	0.39592	1.07	4.92	1.31	0.21738	.	0.174068	0.64402	N	0.000003	T	0.24928	0.0605	N	0.26042	0.785	0.36575	D	0.873204	B;B	0.31769	0.339;0.155	B;B	0.33254	0.16;0.05	T	0.10177	-1.0641	10	0.31617	T	0.26	-12.817	5.3283	0.15918	0.7249:0.0:0.1444:0.1307	.	226;226	A8MUW5;Q52LJ0	.;FA98B_HUMAN	V	226	ENSP00000380734:M226V	ENSP00000303412:M226V	M	+	1	0	FAM98B	36553738	0.989000	0.36119	0.998000	0.56505	0.963000	0.63663	0.375000	0.20518	0.111000	0.17947	-0.503000	0.04515	ATG	.	.		0.378	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		G	38766446	A	G	38766446	3	3	209	1	0	0	0	0	1	0	0	0	5665	101	4	2	698	2	FAM98B	15	38766446	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	13544412	38766446	63764946	116	30261										
MGA	23269	hgsc.bcm.edu	37	chr15	41988901	41988901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	acagcattagcacagaaagaAtactcgacgattcaaaggat	8	8	1	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr15:41988901A>G	ENST00000570161.1	+	2	1693	c.1693A>G	c.(1693-1695)Ata>Gta	p.I565V	MGA_ENST00000389936.4_Missense_Mutation_p.I565V|MGA_ENST00000566586.1_Missense_Mutation_p.I565V|MGA_ENST00000545763.1_Missense_Mutation_p.I565V|MGA_ENST00000219905.7_Missense_Mutation_p.I565V			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CACAGAAAGAATACTCGACGA	0.403																																					p.I565V		Atlas-SNP	.											.	MGA	264	.	0			c.A1693G						.						64	57	59					15																	41988901		1868	4114	5982	SO:0001583	missense	23269	exon3			GAAAGAATACTCG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1693A>G	chr15.hg19:g.41988901A>G	ENSP00000457035:p.Ile565Val	147.0	0.0		144.0	17.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	A	0.692	-0.793965	0.02862	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.83163	-1.68;-1.69;-1.69	5.44	1.77	0.24775	.	2.341720	0.01261	N	0.009164	T	0.70133	0.3189	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.53563	-0.8421	10	0.29301	T	0.29	.	1.4579	0.02389	0.5204:0.1287:0.2112:0.1398	.	565;565	F5H7K2;E7ENI0	.;.	V	565	ENSP00000219905:I565V;ENSP00000374586:I565V;ENSP00000442467:I565V	ENSP00000219905:I565V	I	+	1	0	MGA	39776193	0.199000	0.23386	0.016000	0.15963	0.062000	0.15995	0.119000	0.15626	0.328000	0.23435	0.379000	0.24179	ATA	.	.		0.403	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	41988901	A	G	41988901	3	3	209	1	0	0	0	0	1	0	0	0	9549	101	4	2	1699	2	MGA	15	41988901	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	3222455	41988901	60542491	117	30262										
MAPK6	5597	hgsc.bcm.edu	37	chr15	52356215	52356215	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cactgatgaagaagaagtacAagttgatccccgaaaatatt	8	7	0	5			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr15:52356215A>G	ENST00000261845.5	+	6	1991	c.1184A>G	c.(1183-1185)cAa>cGa	p.Q395R	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	395					cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		GAAGAAGTACAAGTTGATCCC	0.408																																					p.Q395R		Atlas-SNP	.											.	MAPK6	70	.	0			c.A1184G						.						99	92	95					15																	52356215		2195	4293	6488	SO:0001583	missense	5597	exon6			AAGTACAAGTTGA	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"Mitogen-activated protein kinase cascade / Kinases"	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.1184A>G	chr15.hg19:g.52356215A>G	ENSP00000261845:p.Gln395Arg	43.0	0.0		44.0	10.0	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	hg19	CCDS10147.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.615171	0.87359	.	.	ENSG00000069956	ENST00000261845	T	0.45668	0.89	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.59729	0.2215	L	0.61218	1.895	0.80722	D	1	D	0.54601	0.967	P	0.62382	0.901	T	0.63857	-0.6542	10	0.87932	D	0	-15.6519	15.228	0.73364	1.0:0.0:0.0:0.0	.	395	Q16659	MK06_HUMAN	R	395	ENSP00000261845:Q395R	ENSP00000261845:Q395R	Q	+	2	0	MAPK6	50143507	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.713000	0.91408	2.023000	0.59567	0.524000	0.50904	CAA	.	.		0.408	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748		G	52356215	A	G	52356215	3	3	209	1	0	0	0	0	1	0	0	0	9290	130	5	2	1202	2	MAPK6	15	52356215	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	10367314	52356215	50175177	118	30263										
CGNL1	84952	hgsc.bcm.edu	37	chr15	57734582	57734582	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctttttcagaagcactgataAtgacgatgctactaaaagga	8	7	1	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr15:57734582A>G	ENST00000281282.5	+	4	1787	c.1709A>G	c.(1708-1710)aAt>aGt	p.N570S		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	570						myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		AGCACTGATAATGACGATGCT	0.433																																					p.N570S		Atlas-SNP	.											.	CGNL1	125	.	0			c.A1709G						.						86	79	81					15																	57734582		2192	4292	6484	SO:0001583	missense	84952	exon5			CTGATAATGACGA	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.1709A>G	chr15.hg19:g.57734582A>G	ENSP00000281282:p.Asn570Ser	64.0	0.0		62.0	10.0	NM_001252335	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	hg19	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	A	9.540	1.113239	0.20795	.	.	ENSG00000128849	ENST00000281282	T	0.41065	1.01	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000017	T	0.35828	0.0945	L	0.37507	1.11	0.45607	D	0.998547	B	0.18968	0.032	B	0.19391	0.025	T	0.09422	-1.0675	10	0.31617	T	0.26	-25.6651	15.5325	0.75974	1.0:0.0:0.0:0.0	.	570	Q0VF96	CGNL1_HUMAN	S	570	ENSP00000281282:N570S	ENSP00000281282:N570S	N	+	2	0	CGNL1	55521874	1.000000	0.71417	0.994000	0.49952	0.308000	0.27856	5.599000	0.67592	2.065000	0.61736	0.455000	0.32223	AAT	.	.		0.433	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		G	57734582	A	G	57734582	3	3	209	1	0	0	0	0	1	0	0	0	3306	101	4	2	1719	2	CGNL1	15	57734582	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	5378367	57734582	44796810	119	30264										
DENND4A	10260	hgsc.bcm.edu	37	chr15	65995317	65995317	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cttcaggtctttcaaataaaTtgttcctaagaactggaaat	6	7	3	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr15:65995317T>C	ENST00000431932.2	-	16	2325	c.2117A>G	c.(2116-2118)aAt>aGt	p.N706S	DENND4A_ENST00000443035.3_Missense_Mutation_p.N706S	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	706					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						TTCAAATAAATTGTTCCTAAG	0.338																																					p.N706S		Atlas-SNP	.											.	DENND4A	217	.	0			c.A2117G						.						110	100	103					15																	65995317		1795	4065	5860	SO:0001583	missense	10260	exon16			AATAAATTGTTCC	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.2117A>G	chr15.hg19:g.65995317T>C	ENSP00000396830:p.Asn706Ser	67.0	0.0		57.0	13.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	hg19	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	T	12.80	2.046012	0.36085	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.04603	3.6;3.59	5.72	4.6	0.57074	.	0.294964	0.41605	N	0.000860	T	0.02119	0.0066	N	0.01576	-0.805	0.33722	D	0.617128	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.32188	-0.9916	10	0.33940	T	0.23	.	10.6112	0.45423	0.0:0.0727:0.0:0.9273	.	706;706	E7EPL3;Q7Z401	.;MYCPP_HUMAN	S	706	ENSP00000391167:N706S;ENSP00000396830:N706S	ENSP00000396830:N706S	N	-	2	0	DENND4A	63782371	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.895000	0.56258	1.101000	0.41535	0.528000	0.53228	AAT	.	.		0.338	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		C	65995317	T	C	65995317	3	2	209	1	0	0	0	0	1	0	0	0	4435	1493	52	2	3675	2	DENND4A	15	65995317	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	8260735	65995317	36536075	120	30265										
IREB2	3658	hgsc.bcm.edu	37	chr15	78782771	78782771	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	actgtattcacagatggggaAtaaacggtggaattccttag	11	6	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr15:78782771A>G	ENST00000258886.8	+	17	2233	c.2084A>G	c.(2083-2085)aAt>aGt	p.N695S		NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	695					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		CAGATGGGGAATAAACGGTGG	0.363																																					p.N695S	NSCLC(200;764 2208 35157 49871 50830)	Atlas-SNP	.											.	IREB2	106	.	0			c.A2084G						.						81	77	78					15																	78782771		2196	4293	6489	SO:0001583	missense	3658	exon17			TGGGGAATAAACG	M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.2084A>G	chr15.hg19:g.78782771A>G	ENSP00000258886:p.Asn695Ser	193.0	0.0		183.0	30.0	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	hg19	CCDS10302.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.319535	0.41096	.	.	ENSG00000136381	ENST00000258886	T	0.16897	2.31	5.84	5.84	0.93424	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (1);	0.296708	0.42821	D	0.000653	T	0.13415	0.0325	L	0.33189	0.99	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08597	-1.0714	10	0.32370	T	0.25	.	10.2762	0.43512	0.926:0.0:0.074:0.0	.	695	P48200	IREB2_HUMAN	S	695	ENSP00000258886:N695S	ENSP00000258886:N695S	N	+	2	0	IREB2	76569826	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.478000	0.66806	2.234000	0.73211	0.459000	0.35465	AAT	.	.		0.363	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		G	78782771	A	G	78782771	3	3	209	1	0	0	0	0	1	0	0	0	7835	101	4	2	2150	2	IREB2	15	78782771	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	12787454	78782771	23748621	121	30266										
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81199078	81199078	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cggaggttgggcttctgagcCggaacatcatagtgatgggg	17	7	2	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr15:81199078C>A	ENST00000394685.3	+	13	1905	c.1486C>A	c.(1486-1488)Cgg>Agg	p.R496R	KIAA1199_ENST00000220244.3_Silent_p.R496R|RP11-351M8.1_ENST00000560560.1_Intron|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_Silent_p.R496R			Q8WUJ3	CEMIP_HUMAN		496	Necessary for its endoplasmic reticulum (ER) retention and interaction with HSPA5.				hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GCTTCTGAGCCGGAACATCAT	0.532																																					p.R496R		Atlas-SNP	.											.	KIAA1199	118	.	0			c.C1486A						.						166	145	152					15																	81199078		2203	4300	6503	SO:0001819	synonymous_variant	57214	exon12			CTGAGCCGGAACA																												ENST00000394685.3:c.1486C>A	chr15.hg19:g.81199078C>A		141.0	0.0		119.0	38.0	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	hg19	CCDS10315.1																																																																																			.	.		0.532	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			A	81199078	C	A	81199078	2	1	209	1	0	0	0	0	0	0	0	1	8222	643	23	1		1	KIAA1199	15	81199078	Silent	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	2416307	81199078	21332314	122	30267										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88690618	88690618	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ccacgagagtgtggtgagccGgttacttgacaggtttctgc	14	9	1	3	rs149623569		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr15:88690618G>T	ENST00000360948.2	-	5	573	c.412C>A	c.(412-414)Cgg>Agg	p.R138R	NTRK3_ENST00000558676.1_Silent_p.R138R|NTRK3_ENST00000540489.2_Silent_p.R138R|NTRK3_ENST00000542733.2_Silent_p.R40R|NTRK3_ENST00000357724.2_Silent_p.R138R|NTRK3_ENST00000557856.1_Silent_p.R138R|NTRK3_ENST00000317501.3_Silent_p.R138R|NTRK3_ENST00000355254.2_Silent_p.R138R|NTRK3_ENST00000394480.2_Silent_p.R138R	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	138					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			GTGGTGAGCCGGTTACTTGAC	0.428			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.R138R		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.C412A						.						66	60	62					15																	88690618		2201	4299	6500	SO:0001819	synonymous_variant	4916	exon6			TGAGCCGGTTACT	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.412C>A	chr15.hg19:g.88690618G>T		122.0	0.0		110.0	35.0	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	ENST00000360948.2	hg19	CCDS32322.1																																																																																			.	G|1.000;A|0.000		0.428	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				T	88690618	G	T	88690618	2	4	209	1	0	0	0	0	0	0	0	1	10717	1115	39	1		1	NTRK3	15	88690618	Silent	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	7491540	88690618	13840774	123	30268										
DNASE1L2	1775	hgsc.bcm.edu	37	chr16	2287636	2287636	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tgtacctggacgtgatcgacAagtggggcaccgacgtaagc	14	10	0	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr16:2287636A>C	ENST00000564065.1	+	4	1578	c.577A>C	c.(577-579)Aag>Cag	p.K193Q	DNASE1L2_ENST00000382437.4_Missense_Mutation_p.K172Q|DNASE1L2_ENST00000567494.1_Missense_Mutation_p.K193Q|DNASE1L2_ENST00000320700.5_Missense_Mutation_p.K193Q|RP11-304L19.11_ENST00000565709.1_RNA|RP11-304L19.12_ENST00000564055.1_lincRNA			Q92874	DNSL2_HUMAN	deoxyribonuclease I-like 2	193					corneocyte development (GO:0003335)|DNA metabolic process (GO:0006259)|hair follicle development (GO:0001942)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			endometrium(1)|prostate(1)|skin(2)	4						CGTGATCGACAAGTGGGGCAC	0.697																																					p.K193Q		Atlas-SNP	.											.	DNASE1L2	14	.	0			c.A577C						.						17	20	19					16																	2287636		1990	4138	6128	SO:0001583	missense	1775	exon5			ATCGACAAGTGGG	U62647	CCDS42105.1	16p13.3	2008-02-05				ENSG00000167968			2958	protein-coding gene	gene with protein product		602622				9205125, 1577479	Standard	NM_001374		Approved	DNAS1L2	uc002cpp.3	Q92874		ENST00000564065.1:c.577A>C	chr16.hg19:g.2287636A>C	ENSP00000454562:p.Lys193Gln	158.0	0.0		200.0	43.0	NM_001374	E9PBY4|Q6JVM2|Q6JVM3	Missense_Mutation	SNP	ENST00000564065.1	hg19	CCDS42105.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.335665	0.41398	.	.	ENSG00000167968	ENST00000541838;ENST00000320700;ENST00000382437	T;T	0.80480	-1.38;-1.38	4.35	4.35	0.52113	Endonuclease/exonuclease/phosphatase (2);	0.069954	0.56097	D	0.000033	T	0.79639	0.4480	L	0.58583	1.82	0.30521	N	0.768425	D;D	0.65815	0.995;0.979	P;P	0.50314	0.637;0.484	T	0.76280	-0.3017	10	0.24483	T	0.36	-10.5877	9.8706	0.41170	1.0:0.0:0.0:0.0	.	193;172	Q92874;Q6JVM2	DNSL2_HUMAN;.	Q	193;193;172	ENSP00000316938:K193Q;ENSP00000371874:K172Q	ENSP00000316938:K193Q	K	+	1	0	DNASE1L2	2227637	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	2.608000	0.46308	1.826000	0.53198	0.408000	0.27601	AAG	.	.		0.697	DNASE1L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435236.1	NM_001374		C	2287636	A	C	2287636	3	2	209	1	0	0	0	0	1	0	0	0	4664	131	5	5	591	5	DNASE1L2	16	2287636	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10		2287636	88067117	124	30269										
COG7	91949	hgsc.bcm.edu	37	chr16	23430073	23430073	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tgctctcttccatgtcgccaTacttcagctggtagggtttg	10	11	2	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr16:23430073T>A	ENST00000307149.5	-	8	1270	c.1085A>T	c.(1084-1086)tAt>tTt	p.Y362F		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	362					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		CATGTCGCCATACTTCAGCTG	0.483																																					p.Y362F		Atlas-SNP	.											.	COG7	62	.	0			c.A1085T						.						144	105	118					16																	23430073		2197	4300	6497	SO:0001583	missense	91949	exon8			TCGCCATACTTCA	AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"Components of oligomeric golgi complex"	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1085A>T	chr16.hg19:g.23430073T>A	ENSP00000305442:p.Tyr362Phe	80.0	0.0		85.0	21.0	NM_153603	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	hg19	CCDS10610.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.710203	0.89018	.	.	ENSG00000168434	ENST00000307149	T	0.68765	-0.35	5.73	5.73	0.89815	.	0.106321	0.64402	D	0.000003	T	0.79678	0.4487	M	0.72118	2.19	0.80722	D	1	D	0.65815	0.995	D	0.70935	0.971	T	0.78003	-0.2374	10	0.31617	T	0.26	-12.577	15.1912	0.73047	0.0:0.0:0.0:1.0	.	362	P83436	COG7_HUMAN	F	362	ENSP00000305442:Y362F	ENSP00000305442:Y362F	Y	-	2	0	COG7	23337574	1.000000	0.71417	0.967000	0.41034	0.805000	0.45488	7.999000	0.88496	2.185000	0.69588	0.533000	0.62120	TAT	.	.		0.483	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1			A	23430073	T	A	23430073	3	1	209	1	0	0	0	0	1	0	0	0	3665	1406	49	4	1267	4	COG7	16	23430073	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	21142437	23430073	66924680	125	30270										
UBFD1	56061	hgsc.bcm.edu	37	chr16	23578364	23578364	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	atgtggtcagtgaacctatcGaaggacatgaagactaccac	10	9	1	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr16:23578364G>T	ENST00000395878.3	+	6	1174	c.793G>T	c.(793-795)Gaa>Taa	p.E265*	UBFD1_ENST00000567212.1_Nonsense_Mutation_p.E256*|UBFD1_ENST00000219638.4_Nonsense_Mutation_p.E489*|CTD-2196E14.6_ENST00000568262.2_RNA	NM_019116.2	NP_061989.2	O14562	UBFD1_HUMAN	ubiquitin family domain containing 1	265							poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7				GBM - Glioblastoma multiforme(48;0.0331)		TGAACCTATCGAAGGACATGA	0.483																																					p.E265X	Melanoma(22;290 1069 22358 48158)	Atlas-SNP	.											.	UBFD1	16	.	0			c.G793T						.						118	117	117					16																	23578364		1941	4143	6084	SO:0001587	stop_gained	56061	exon6			CCTATCGAAGGAC	AK124139	CCDS10613.2	16p12.1	2008-11-05			ENSG00000103353	ENSG00000103353			30565	protein-coding gene	gene with protein product	"ubiquitin-binding protein homolog"					10493829	Standard	XM_006721064		Approved	FLJ42145, FLJ38870, UBPH	uc002dlv.3	O14562	OTTHUMG00000128855	ENST00000395878.3:c.793G>T	chr16.hg19:g.23578364G>T	ENSP00000379217:p.Glu265*	53.0	0.0		72.0	16.0	NM_019116	A8MW58|D3DWF2	Nonsense_Mutation	SNP	ENST00000395878.3	hg19	CCDS10613.2	.	.	.	.	.	.	.	.	.	.	G	36	5.760107	0.96898	.	.	ENSG00000103353	ENST00000219638;ENST00000395878;ENST00000399462	.	.	.	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-6.6309	17.4351	0.87549	0.0:0.0:1.0:0.0	.	.	.	.	X	489;265;142	.	ENSP00000219638:E489X	E	+	1	0	UBFD1	23485865	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.393000	0.97256	2.446000	0.82766	0.561000	0.74099	GAA	.	.		0.483	UBFD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250795.2	NM_019116		T	23578364	G	T	23578364	4	4	209	1	0	0	0	0	0	1	0	0	16899	1059	37	1	815	1	UBFD1	16	23578364	Nonsense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	148291	23578364	66776389	126	30271										
CDH1	999	hgsc.bcm.edu	37	chr16	68856096	68856096	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agaactaacacacggggcgaGtgccaactggaccattcagt	11	11	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr16:68856096G>T	ENST00000261769.5	+	12	2095	c.1904G>T	c.(1903-1905)aGt>aTt	p.S635I	RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.S574I	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	635	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.			ASA -> RVP (in Ref. 3; AAA61259). {ECO:0000305}.	adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CACGGGGCGAGTGCCAACTGG	0.498			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												p.S635I		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	.	CDH1	535	.	0			c.G1904T						.						95	79	84					16																	68856096		2198	4300	6498	SO:0001583	missense	999	exon12	Familial Cancer Database	HDGC	GGGCGAGTGCCAA	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1904G>T	chr16.hg19:g.68856096G>T	ENSP00000261769:p.Ser635Ile	118.0	0.0		91.0	59.0	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	hg19	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852494	0.71719	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000422392	T;T	0.53857	0.6;0.6	5.68	5.68	0.88126	Cadherin (2);Cadherin-like (1);	0.313291	0.27636	N	0.018490	T	0.69984	0.3172	M	0.80183	2.485	0.41524	D	0.988411	D;P	0.58970	0.984;0.823	P;P	0.61132	0.884;0.607	T	0.73534	-0.3952	10	0.62326	D	0.03	.	12.7648	0.57386	0.0754:0.0:0.9246:0.0	.	574;635	Q9UII8;P12830	.;CADH1_HUMAN	I	635;653;574	ENSP00000261769:S635I;ENSP00000414946:S574I	ENSP00000261769:S635I	S	+	2	0	CDH1	67413597	0.962000	0.33011	0.999000	0.59377	0.893000	0.52053	3.745000	0.55119	2.697000	0.92050	0.632000	0.83419	AGT	.	.		0.498	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		T	68856096	G	T	68856096	3	4	209	1	0	0	0	0	1	0	0	0	3097	1029	36	3	1950	3	CDH1	16	68856096	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	45277732	68856096	21498657	127	30272										
MVD	4597	hgsc.bcm.edu	37	chr16	88721693	88721693	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gaggtaagagatgggcgggaAggtgtcgaggcaggtggcgt	22	4	0	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr16:88721693A>C	ENST00000301012.3	-	7	840	c.811T>G	c.(811-813)Ttc>Gtc	p.F271V	MVD_ENST00000568709.1_5'Flank	NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	271					cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		ATGGGCGGGAAGGTGTCGAGG	0.652																																					p.F271V		Atlas-SNP	.											.	MVD	27	.	0			c.T811G						.						263	197	219					16																	88721693		2188	4294	6482	SO:0001583	missense	4597	exon7			GCGGGAAGGTGTC	U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4.1.1.33		7529	protein-coding gene	gene with protein product	"mevalonate pyrophosphate decarboxylase"	603236				8626466	Standard	NM_002461		Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.811T>G	chr16.hg19:g.88721693A>C	ENSP00000301012:p.Phe271Val	53.0	0.0		56.0	11.0	NM_002461	Q53Y65	Missense_Mutation	SNP	ENST00000301012.3	hg19	CCDS10968.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.87|13.87	2.365789|2.365789	0.41902|0.41902	.|.	.|.	ENSG00000167508|ENSG00000167508	ENST00000301012|ENST00000378400	T|.	0.29655|.	1.56|.	4.53|4.53	4.53|4.53	0.55603|0.55603	.|.	0.056069|.	0.64402|.	D|.	0.000001|.	T|T	0.65523|0.65523	0.2699|0.2699	L|L	0.54323|0.54323	1.7|1.7	0.52501|0.52501	D|D	0.999953|0.999953	B|.	0.22346|.	0.068|.	B|.	0.19391|.	0.025|.	T|T	0.69235|0.69235	-0.5198|-0.5198	10|6	0.49607|0.66056	T|D	0.09|0.02	-16.2233|-16.2233	14.1603|14.1603	0.65443|0.65443	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	271|.	P53602|.	MVD1_HUMAN|.	V|R	271|99	ENSP00000301012:F271V|.	ENSP00000301012:F271V|ENSP00000367653:L99R	F|L	-|-	1|2	0|0	MVD|MVD	87249194|87249194	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.823000|0.823000	0.46562|0.46562	6.475000|6.475000	0.73582|0.73582	1.821000|1.821000	0.53095|0.53095	0.402000|0.402000	0.26972|0.26972	TTC|CTT	.	.		0.652	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269547.2	NM_002461		C	88721693	A	C	88721693	3	2	209	1	0	0	0	0	1	0	0	0	10003	72	3	5	407	5	MVD	16	88721693	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	19865597	88721693	1633060	128	30273										
CDRT1	374286	hgsc.bcm.edu	37	chr17	15516062	15516062	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tttcacacgcatgctcttccCgtcatctaccattttaggaa	5	13	4	0	rs151267443	byFrequency	TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr17:15516062C>A	ENST00000395906.3	-	5	1074	c.1075G>T	c.(1075-1077)Ggg>Tgg	p.G359W	RP11-385D13.1_ENST00000455584.2_Missense_Mutation_p.G669W	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	359								p.G359W(2)		endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		ATGCTCTTCCCGTCATCTACC	0.428																																					p.G359W		Atlas-SNP	.											.	CDRT1	83	.	2	Substitution - Missense(2)	lung(2)	c.G1075T						.						168	170	169					17																	15516062		2203	4300	6503	SO:0001583	missense	374286	exon5			TCTTCCCGTCATC	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"F-boxes / WD-40 domains", "WD repeat domain containing"	14379	protein-coding gene	gene with protein product		604596	"F-box and WD repeat domain containing 10 pseudogene 1", "F-box and WD-40 domain protein 10 pseudogene 1"	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1075G>T	chr17.hg19:g.15516062C>A	ENSP00000379242:p.Gly359Trp	88.0	0.0		76.0	13.0	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	hg19	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	C	14.93	2.681572	0.47991	.	.	ENSG00000251537	ENST00000261644;ENST00000395906	T	0.16324	2.35	5.34	4.36	0.52297	F-box domain, Skp2-like (1);	0.396565	0.17829	U	0.160581	T	0.41119	0.1145	M	0.72894	2.215	0.37324	D	0.909667	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.956	T	0.48692	-0.9013	10	0.87932	D	0	.	13.139	0.59424	0.1613:0.8387:0.0:0.0	.	359;683	O95170;Q59EB2	CDRT1_HUMAN;.	W	389;359	ENSP00000379242:G359W	ENSP00000261644:G389W	G	-	1	0	RP11-385D13.1	15456787	0.003000	0.15002	0.034000	0.17996	0.002000	0.02628	1.214000	0.32419	1.238000	0.43771	-0.324000	0.08512	GGG	.	C|0.998;T|0.002		0.428	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382		A	15516062	C	A	15516062	3	1	209	1	0	0	0	0	1	0	0	0	3176	652	23	1	1215	1	CDRT1	17	15516062	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10		15516062	65679148	129	30274										
TOP3A	7156	hgsc.bcm.edu	37	chr17	18193904	18193904	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctccatgagggcaatgaggtCggcctcggtgagcagcttgg	16	10	0	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr17:18193904C>G	ENST00000321105.5	-	13	1778	c.1564G>C	c.(1564-1566)Gac>Cac	p.D522H	TOP3A_ENST00000540524.1_Missense_Mutation_p.D52H|TOP3A_ENST00000542570.1_Missense_Mutation_p.D427H	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	522					DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						GCAATGAGGTCGGCCTCGGTG	0.567																																					p.D522H		Atlas-SNP	.											.	TOP3A	85	.	0			c.G1564C						.						77	57	64					17																	18193904		2203	4300	6503	SO:0001583	missense	7156	exon13			TGAGGTCGGCCTC	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 7"	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.1564G>C	chr17.hg19:g.18193904C>G	ENSP00000321636:p.Asp522His	45.0	0.0		61.0	8.0	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Missense_Mutation	SNP	ENST00000321105.5	hg19	CCDS11194.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.358811	0.61403	.	.	ENSG00000177302	ENST00000321105;ENST00000540524;ENST00000542570	T;T;T	0.23552	1.9;1.9;1.9	5.66	5.66	0.87406	DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central (1);DNA topoisomerase, type IA, DNA-binding (1);DNA topoisomerase, type IA, central region, subdomain 1 (1);	0.000000	0.85682	D	0.000000	T	0.64605	0.2613	M	0.93462	3.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.74034	-0.3794	10	0.87932	D	0	-35.4812	19.7417	0.96234	0.0:1.0:0.0:0.0	.	427;522	B4DK80;Q13472	.;TOP3A_HUMAN	H	522;52;427	ENSP00000321636:D522H;ENSP00000446425:D52H;ENSP00000442336:D427H	ENSP00000321636:D522H	D	-	1	0	TOP3A	18134629	1.000000	0.71417	0.975000	0.42487	0.992000	0.81027	7.745000	0.85046	2.667000	0.90743	0.563000	0.77884	GAC	.	.		0.567	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			G	18193904	C	G	18193904	3	3	209	1	0	0	0	0	1	0	0	0	16382	884	31	4	1469	4	TOP3A	17	18193904	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	2677842	18193904	63001306	130	30275										
KRT26	353288	hgsc.bcm.edu	37	chr17	38926350	38926350	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cacgttcacgttccccccagCtgtatattgcaagacttcca	6	15	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr17:38926350C>A	ENST00000335552.4	-	4	754	c.706G>T	c.(706-708)Gct>Tct	p.A236S		NM_181539.4	NP_853517.2			keratin 26											central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				TTCCCCCCAGCTGTATATTGC	0.478																																					p.A236S		Atlas-SNP	.											.	KRT26	49	.	0			c.G706T						.						132	125	127					17																	38926350		2203	4300	6503	SO:0001583	missense	353288	exon4			CCCCAGCTGTATA	AJ564205	CCDS11374.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000186393	ENSG00000186393		"-", "Intermediate filaments type I, keratins (acidic)"	30840	protein-coding gene	gene with protein product			"keratin 25B"	KRT25B		16831889	Standard	NM_181539		Approved		uc002hvf.3	Q7Z3Y9	OTTHUMG00000133370	ENST00000335552.4:c.706G>T	chr17.hg19:g.38926350C>A	ENSP00000334798:p.Ala236Ser	81.0	0.0		70.0	17.0	NM_181539		Missense_Mutation	SNP	ENST00000335552.4	hg19	CCDS11374.1	.	.	.	.	.	.	.	.	.	.	C	3.138	-0.176925	0.06380	.	.	ENSG00000186393	ENST00000335552	D	0.88741	-2.42	5.02	2.93	0.34026	Filament (1);	0.213952	0.32836	N	0.005596	T	0.78773	0.4336	N	0.21617	0.685	0.09310	N	1	B	0.13594	0.008	B	0.21360	0.034	T	0.61222	-0.7106	10	0.18710	T	0.47	.	8.6284	0.33904	0.3295:0.5949:0.0:0.0756	.	236	Q7Z3Y9	K1C26_HUMAN	S	236	ENSP00000334798:A236S	ENSP00000334798:A236S	A	-	1	0	KRT26	36179876	0.000000	0.05858	0.004000	0.12327	0.311000	0.27955	-1.112000	0.03299	0.506000	0.28125	0.655000	0.94253	GCT	.	.		0.478	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539		A	38926350	C	A	38926350	3	1	209	1	0	0	0	0	1	0	0	0	8472	797	28	3	720	3	KRT26	17	38926350	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	20732446	38926350	42268860	131	30276										
KPNB1	3837	hgsc.bcm.edu	37	chr17	45752005	45752005	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	actcttactcatttcacagaAtgttcttcggaaagtgcaac	6	10	4	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr17:45752005A>G	ENST00000290158.4	+	15	2176	c.1769A>G	c.(1768-1770)aAt>aGt	p.N590S	KPNB1_ENST00000537679.1_Splice_Site_p.N374S|KPNB1_ENST00000535458.2_Splice_Site_p.N445S|KPNB1_ENST00000540627.1_Splice_Site_p.N445S	NM_001276453.1|NM_002265.4	NP_001263382.1|NP_002256.2	Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	590					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|protein import into nucleus (GO:0006606)|protein import into nucleus, translocation (GO:0000060)|ribosomal protein import into nucleus (GO:0006610)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|ovary(1)|pancreas(1)|skin(1)	4						ATTTCACAGAATGTTCTTCGG	0.398																																					p.D590G		Atlas-SNP	.											.	KPNB1	58	.	0			c.A1769G						.						153	146	149					17																	45752005		2203	4300	6503	SO:0001630	splice_region_variant	3837	exon15			CACAGAATGTTCT	L39793	CCDS11513.1, CCDS62228.1	17q21.32	2013-02-14			ENSG00000108424	ENSG00000108424		"Importins", "Armadillo repeat containing"	6400	protein-coding gene	gene with protein product	"importin 1"	602738				7615630, 7627554	Standard	NM_002265		Approved	NTF97, IPOB, MGC2155, MGC2156, MGC2157, IMB1, Impnb, IPO1	uc002ilt.2	Q14974	OTTHUMG00000036957	ENST00000290158.4:c.1768-1A>G	chr17.hg19:g.45752005A>G		50.0	0.0		46.0	7.0	NM_002265	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	Missense_Mutation	SNP	ENST00000290158.4	hg19	CCDS11513.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.621702	0.46736	.	.	ENSG00000108424	ENST00000535458;ENST00000290158;ENST00000540627;ENST00000537679	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	5.13	5.13	0.70059	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.25827	0.0629	N	0.00104	-2.125	0.37095	D	0.899642	B;B	0.11235	0.004;0.0	B;B	0.04013	0.001;0.0	T	0.46247	-0.9205	9	0.06494	T	0.89	-22.0706	15.2502	0.73539	1.0:0.0:0.0:0.0	.	374;590	F5H4R7;Q14974	.;IMB1_HUMAN	S	445;590;445;374	ENSP00000438253:N445S;ENSP00000290158:N590S;ENSP00000438964:N445S;ENSP00000445006:N374S	ENSP00000290158:N590S	N	+	2	0	KPNB1	43107004	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.287000	0.95975	2.072000	0.62099	0.459000	0.35465	AAT	.	.		0.398	KPNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089755.2	NM_002265	Missense_Mutation	G	45752005	A	G	45752005	5	3	209	1	0	0	0	0	0	0	1	0	8444	115	4	2	1827	2	KPNB1	17	45752005	Splice_Site	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	6825655	45752005	35443205	132	30277										
COX11	1353	hgsc.bcm.edu	37	chr17	53040188	53040188	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	caactttaatcattcttggaTcttcagcaaattcaggatca	5	9	6	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr17:53040188T>G	ENST00000299335.3	-	4	875	c.737A>C	c.(736-738)gAt>gCt	p.D246A	COX11_ENST00000573912.1_5'Flank	NM_004375.3	NP_004366.1	Q9Y6N1	COX11_HUMAN	cytochrome c oxidase assembly homolog 11 (yeast)	246					hydrogen ion transmembrane transport (GO:1902600)|negative regulation of glucokinase activity (GO:0033132)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|prostate(1)	9						CATTCTTGGATCTTCAGCAAA	0.363																																					p.D246A		Atlas-SNP	.											.	COX11	16	.	0			c.A737C						.						99	96	97					17																	53040188		2203	4300	6503	SO:0001583	missense	1353	exon4			CTTGGATCTTCAG	AF044321	CCDS11583.1, CCDS58579.1	17q22	2012-10-15	2012-10-15			ENSG00000166260		"Mitochondrial respiratory chain complex assembly factors"	2261	protein-coding gene	gene with protein product	"cytochrome c oxidase subunit 11", "cytochrome c oxidase assembly protein COX11"	603648	"COX11 (yeast) homolog, cytochrome c oxidase assembly protein", "COX11 cytochrome c oxidase assembly homolog (yeast)"			9878253	Standard	NM_004375		Approved	COX11P	uc010wng.1	Q9Y6N1		ENST00000299335.3:c.737A>C	chr17.hg19:g.53040188T>G	ENSP00000299335:p.Asp246Ala	197.0	0.0		187.0	29.0	NM_004375	D3DTY5|I3L220|Q6FHB7|Q9BRX0|Q9UME8	Missense_Mutation	SNP	ENST00000299335.3	hg19	CCDS11583.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.499842	0.85176	.	.	ENSG00000166260	ENST00000299335	T	0.64085	-0.08	5.33	5.33	0.75918	Cytochrome c oxidase assembly protein CtaG/Cox11, domain (2);	0.000000	0.85682	D	0.000000	T	0.79885	0.4523	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83017	-0.0169	9	0.87932	D	0	1.766	14.7737	0.69699	0.0:0.0:0.0:1.0	.	246	Q9Y6N1	COX11_HUMAN	A	246	ENSP00000299335:D246A	ENSP00000299335:D246A	D	-	2	0	COX11	50395187	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	7.941000	0.87700	2.134000	0.65973	0.528000	0.53228	GAT	.	.		0.363	COX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439182.1	NM_004375		G	53040188	T	G	53040188	3	3	209	1	0	0	0	0	1	0	0	0	3765	1435	50	5	163	5	COX11	17	53040188	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	7288183	53040188	28155022	133	30278										
KPNA2	3838	hgsc.bcm.edu	37	chr17	66040111	66040111	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gtggacaatgtcaaacatcaCagccggccgccaggaccaga	11	13	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr17:66040111C>G	ENST00000537025.2	+	8	1708	c.1088C>G	c.(1087-1089)aCa>aGa	p.T363R	KPNA2_ENST00000330459.3_Missense_Mutation_p.T363R			P52292	IMA1_HUMAN	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	363	NLS binding site (minor). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|DNA metabolic process (GO:0006259)|NLS-bearing protein import into nucleus (GO:0006607)|regulation of DNA recombination (GO:0000018)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|kidney(2)|lung(9)|prostate(1)|urinary_tract(2)	22	all_cancers(12;1.18e-09)		BRCA - Breast invasive adenocarcinoma(8;1.03e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			TCAAACATCACAGCCGGCCGC	0.478																																					p.T363R		Atlas-SNP	.											.	KPNA2	55	.	0			c.C1088G						.						194	201	199					17																	66040111		2203	4296	6499	SO:0001583	missense	3838	exon8			ACATCACAGCCGG	U09559	CCDS32713.1	17q24.2	2013-02-14						"Importins", "Armadillo repeat containing"	6395	protein-coding gene	gene with protein product		600685		RCH1		8016130, 7754385	Standard	NM_002266		Approved	SRP1alpha, IPOA1, QIP2	uc002jgk.3	P52292		ENST00000537025.2:c.1088C>G	chr17.hg19:g.66040111C>G	ENSP00000438483:p.Thr363Arg	243.0	0.0		330.0	148.0	NM_002266	B9EJD6|Q53YE3|Q9BRU5	Missense_Mutation	SNP	ENST00000537025.2	hg19	CCDS32713.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.687997	0.68271	.	.	ENSG00000182481	ENST00000330459;ENST00000537025	T;T	0.71341	-0.56;-0.56	5.51	5.51	0.81932	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	U	0.000000	D	0.90167	0.6927	H	0.96996	3.92	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93148	0.6547	10	0.87932	D	0	.	19.4797	0.95005	0.0:1.0:0.0:0.0	.	363	P52292	IMA2_HUMAN	R	363	ENSP00000332455:T363R;ENSP00000438483:T363R	ENSP00000332455:T363R	T	+	2	0	KPNA2	63470573	1.000000	0.71417	0.988000	0.46212	0.052000	0.14988	7.680000	0.84062	2.591000	0.87537	0.552000	0.68991	ACA	.	.		0.478	KPNA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448111.1	NM_002266		G	66040111	C	G	66040111	3	3	209	1	0	0	0	0	1	0	0	0	8439	478	17	4	1114	4	KPNA2	17	66040111	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	12999923	66040111	15155099	134	30279										
TAF4B	6875	hgsc.bcm.edu	37	chr18	23872237	23872237	+	Frame_Shift_Del	DEL	G	G	-													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agcagccttcaggaggcaatGaaaaacaagtgaccacaatt							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr18:23872237delG	ENST00000269142.5	+	8	2616	c.1618delG	c.(1618-1620)gaafs	p.E540fs	TAF4B_ENST00000578121.1_Frame_Shift_Del_p.E545fs|TAF4B_ENST00000400466.2_Frame_Shift_Del_p.E540fs	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	540	Nuclear export signal.				gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			AGGAGGCAATGAAAAACAAGT	0.368																																					p.N539fs		Atlas-INDEL	.											.	TAF4B	71	.	0			c.1617delT						.						137	123	128					18																	23872237		1905	4135	6040	SO:0001589	frameshift_variant	6875	exon8			.	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1618delG	chr18.hg19:g.23872237delG	ENSP00000269142:p.Glu540fs	104.0	0.0		91.0	28.0	NM_005640	Q29YA4|Q29YA5	Frame_Shift_Del	DEL	ENST00000269142.5	hg19	CCDS42421.1																																																																																			.	.		0.368	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		-	23872237	G	-	23872237	7	5	209	1	0	1	0	1	0	0	0	0	15542	1291	45	0	1648	0	TAF4B	18	23872237	Frame_Shift_Del	DEL	G	TCGA-DD-AAE3-01A-11D-A40R-10		23872237	54205011	135	30280										
MEX3D	399664	hgsc.bcm.edu	37	chr19	1555353	1555353	+	3'UTR	SNP	A	A	C													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	atactgtcgttgaagggctgAggcgccgccgggctgcgggg					rs200558166		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:1555353A>C	ENST00000402693.4	-	0	2164				AC027307.1_ENST00000410788.1_RNA|MEX3D_ENST00000388824.6_Missense_Mutation_p.S660A|AC027307.2_ENST00000581992.1_RNA	NM_203304.3	NP_976049.3	Q86XN8	MEX3D_HUMAN	mex-3 RNA binding family member D						mRNA destabilization (GO:0061157)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|lung(3)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGAAGGGCTGAGGCGCCGCCG	0.572																																					p.S660A		Atlas-SNP	.											.	MEX3D	11	.	0			c.T1978G						.						34	40	38					19																	1555353		2200	4298	6498	SO:0001624	3_prime_UTR_variant	399664	exon3			GGGCTGAGGCGCC	AB107353	CCDS32865.2	19p13.3	2013-08-21	2013-08-21	2007-07-18	ENSG00000181588	ENSG00000181588		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	16734	protein-coding gene	gene with protein product	"bcl-2 ARE RNA binding protein"	611009	"ring finger and KH domain containing 1", "mex-3 homolog D (C. elegans)"	RKHD1		17267406	Standard	NM_203304		Approved	Tino, KIAA2031, OK/SW-cl.4, RNF193	uc010dsn.3	Q86XN8	OTTHUMG00000150369	ENST00000402693.4:c.*209T>G	chr19.hg19:g.1555353A>C		194.0	0.0		214.0	12.0	NM_001174118	A0PJL8|A1L023|E9PAL6|Q71M49	Missense_Mutation	SNP	ENST00000402693.4	hg19	CCDS32865.2	.	.	.	.	.	.	.	.	.	.	A	10.78	1.446194	0.25987	.	.	ENSG00000181588	ENST00000388824	T	0.43688	0.94	4.76	-1.8	0.07907	.	.	.	.	.	T	0.28566	0.0707	N	0.22421	0.69	0.09310	N	1	.	.	.	.	.	.	T	0.30060	-0.9991	7	0.87932	D	0	.	5.5486	0.17078	0.2983:0.0:0.3212:0.3805	.	.	.	.	A	660	ENSP00000373476:S660A	ENSP00000373476:S660A	S	-	1	0	MEX3D	1506353	0.021000	0.18746	0.000000	0.03702	0.094000	0.18550	-0.100000	0.10990	-0.953000	0.03645	-0.421000	0.06004	TCA	.	A|0.998;C|0.002		0.572	MEX3D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317870.2	NM_203304		C	1555353	A	C	1555353	1	2	209	0	1	0	0	0	0	0	0	0	9521	304	11	5		5	MEX3D	19	1555353	3'UTR	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10		1555353	57573630	136	30281	158	5								
MEX3D	399664	hgsc.bcm.edu	37	chr19	1555356	1555356	+	3'UTR	SNP	C	C	G													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctgtcgttgaagggctgaggCgccgccgggctgcggggtct					rs201107400		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:1555356C>G	ENST00000402693.4	-	0	2161				AC027307.1_ENST00000410788.1_RNA|MEX3D_ENST00000388824.6_Missense_Mutation_p.A659P|AC027307.2_ENST00000581992.1_RNA	NM_203304.3	NP_976049.3	Q86XN8	MEX3D_HUMAN	mex-3 RNA binding family member D						mRNA destabilization (GO:0061157)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|lung(3)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGGCTGAGGCGCCGCCGGGC	0.572																																					p.A659P		Atlas-SNP	.											.	MEX3D	11	.	0			c.G1975C						.						34	40	38					19																	1555356		2201	4298	6499	SO:0001624	3_prime_UTR_variant	399664	exon3			CTGAGGCGCCGCC	AB107353	CCDS32865.2	19p13.3	2013-08-21	2013-08-21	2007-07-18	ENSG00000181588	ENSG00000181588		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	16734	protein-coding gene	gene with protein product	"bcl-2 ARE RNA binding protein"	611009	"ring finger and KH domain containing 1", "mex-3 homolog D (C. elegans)"	RKHD1		17267406	Standard	NM_203304		Approved	Tino, KIAA2031, OK/SW-cl.4, RNF193	uc010dsn.3	Q86XN8	OTTHUMG00000150369	ENST00000402693.4:c.*206G>C	chr19.hg19:g.1555356C>G		187.0	0.0		208.0	13.0	NM_001174118	A0PJL8|A1L023|E9PAL6|Q71M49	Missense_Mutation	SNP	ENST00000402693.4	hg19	CCDS32865.2	.	.	.	.	.	.	.	.	.	.	C	14.35	2.509474	0.44660	.	.	ENSG00000181588	ENST00000388824	T	0.49139	0.79	4.61	-3.83	0.04269	.	.	.	.	.	T	0.21468	0.0517	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.25398	-1.0133	7	0.87932	D	0	.	0.8792	0.01230	0.1882:0.1562:0.2369:0.4187	.	.	.	.	P	659	ENSP00000373476:A659P	ENSP00000373476:A659P	A	-	1	0	MEX3D	1506356	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-0.809000	0.04510	-0.209000	0.10156	-0.373000	0.07131	GCC	.	C|0.998;G|0.002		0.572	MEX3D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317870.2	NM_203304		G	1555356	C	G	1555356	1	3	209	0	1	0	0	0	0	0	0	0	9521	768	27	4		4	MEX3D	19	1555356	3'UTR	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	3	1555356	57573627	137	30282	158	5								
MEX3D	399664	hgsc.bcm.edu	37	chr19	1555358	1555358	+	3'UTR	SNP	C	C	T													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gtcgttgaagggctgaggcgCcgccgggctgcggggtctcc					rs202194196		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:1555358C>T	ENST00000402693.4	-	0	2159				AC027307.1_ENST00000410788.1_RNA|MEX3D_ENST00000388824.6_Missense_Mutation_p.G658D|AC027307.2_ENST00000581992.1_RNA	NM_203304.3	NP_976049.3	Q86XN8	MEX3D_HUMAN	mex-3 RNA binding family member D						mRNA destabilization (GO:0061157)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|lung(3)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCTGAGGCGCCGCCGGGCTG	0.572													C|||	1	0.000199681	0	0	5008	,	,		6241	0		0	False		,,,				2504	0.001				p.G658D		Atlas-SNP	.											.	MEX3D	11	.	0			c.G1973A						.						33	39	37					19																	1555358		2201	4298	6499	SO:0001624	3_prime_UTR_variant	399664	exon3			GAGGCGCCGCCGG	AB107353	CCDS32865.2	19p13.3	2013-08-21	2013-08-21	2007-07-18	ENSG00000181588	ENSG00000181588		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	16734	protein-coding gene	gene with protein product	"bcl-2 ARE RNA binding protein"	611009	"ring finger and KH domain containing 1", "mex-3 homolog D (C. elegans)"	RKHD1		17267406	Standard	NM_203304		Approved	Tino, KIAA2031, OK/SW-cl.4, RNF193	uc010dsn.3	Q86XN8	OTTHUMG00000150369	ENST00000402693.4:c.*204G>A	chr19.hg19:g.1555358C>T		181.0	0.0		205.0	13.0	NM_001174118	A0PJL8|A1L023|E9PAL6|Q71M49	Missense_Mutation	SNP	ENST00000402693.4	hg19	CCDS32865.2	.	.	.	.	.	.	.	.	.	.	C	13.78	2.339416	0.41398	.	.	ENSG00000181588	ENST00000388824	T	0.46063	0.88	4.61	-0.27	0.12926	.	.	.	.	.	T	0.29126	0.0724	N	0.22421	0.69	0.09310	N	1	.	.	.	.	.	.	T	0.30149	-0.9988	7	0.87932	D	0	.	5.1147	0.14829	0.0:0.4785:0.2795:0.242	.	.	.	.	D	658	ENSP00000373476:G658D	ENSP00000373476:G658D	G	-	2	0	MEX3D	1506358	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	0.441000	0.21611	-0.174000	0.10743	0.478000	0.44815	GGC	.	C|0.998;T|0.002		0.572	MEX3D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317870.2	NM_203304		T	1555358	C	T	1555358	1	4	209	0	1	0	0	0	0	0	0	0	9521	739	26	3		3	MEX3D	19	1555358	3'UTR	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	2	1555358	57573625	138	30283	158	5								
MEX3D	399664	hgsc.bcm.edu	37	chr19	1555360	1555360	+	3'UTR	SNP	G	G	T													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cgttgaagggctgaggcgccGccgggctgcggggtctccgt							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:1555360G>T	ENST00000402693.4	-	0	2157				AC027307.1_ENST00000410788.1_RNA|MEX3D_ENST00000388824.6_Silent_p.G657G|AC027307.2_ENST00000581992.1_RNA	NM_203304.3	NP_976049.3	Q86XN8	MEX3D_HUMAN	mex-3 RNA binding family member D						mRNA destabilization (GO:0061157)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|lung(3)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGAGGCGCCGCCGGGCTGCG	0.577																																					p.G657G		Atlas-SNP	.											.	MEX3D	11	.	0			c.C1971A						.						32	38	36					19																	1555360		2201	4298	6499	SO:0001624	3_prime_UTR_variant	399664	exon3			GGCGCCGCCGGGC	AB107353	CCDS32865.2	19p13.3	2013-08-21	2013-08-21	2007-07-18	ENSG00000181588	ENSG00000181588		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	16734	protein-coding gene	gene with protein product	"bcl-2 ARE RNA binding protein"	611009	"ring finger and KH domain containing 1", "mex-3 homolog D (C. elegans)"	RKHD1		17267406	Standard	NM_203304		Approved	Tino, KIAA2031, OK/SW-cl.4, RNF193	uc010dsn.3	Q86XN8	OTTHUMG00000150369	ENST00000402693.4:c.*202C>A	chr19.hg19:g.1555360G>T		173.0	0.0		202.0	13.0	NM_001174118	A0PJL8|A1L023|E9PAL6|Q71M49	Silent	SNP	ENST00000402693.4	hg19	CCDS32865.2																																																																																			.	.		0.577	MEX3D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317870.2	NM_203304		T	1555360	G	T	1555360	1	4	209	0	1	0	0	0	0	0	0	0	9521	1074	38	1		1	MEX3D	19	1555360	3'UTR	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	2	1555360	57573623	139	30284	158	5								
MEX3D	399664	hgsc.bcm.edu	37	chr19	1555363	1555363	+	3'UTR	DEL	G	G	-													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tgaagggctgaggcgccgccGggctgcggggtctccgtctc					rs538833811	byFrequency	TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:1555363delG	ENST00000402693.4	-	0	2154				AC027307.1_ENST00000410788.1_RNA|MEX3D_ENST00000388824.6_Frame_Shift_Del_p.P656fs|AC027307.2_ENST00000581992.1_RNA	NM_203304.3	NP_976049.3	Q86XN8	MEX3D_HUMAN	mex-3 RNA binding family member D						mRNA destabilization (GO:0061157)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|lung(3)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGCGCCGCCGGGCTGCGGGG	0.577													GGG|GGG|GG|deletion	3	0.000599042	0	0	5008	,	,		6277	0.002		0.001	False		,,,				2504	0				p.G657fs		Atlas-INDEL	.											.	MEX3D	11	.	0			c.1969delG						.						31	37	35					19																	1555363		2201	4298	6499	SO:0001624	3_prime_UTR_variant	399664	exon3			.	AB107353	CCDS32865.2	19p13.3	2013-08-21	2013-08-21	2007-07-18	ENSG00000181588	ENSG00000181588		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	16734	protein-coding gene	gene with protein product	"bcl-2 ARE RNA binding protein"	611009	"ring finger and KH domain containing 1", "mex-3 homolog D (C. elegans)"	RKHD1		17267406	Standard	NM_203304		Approved	Tino, KIAA2031, OK/SW-cl.4, RNF193	uc010dsn.3	Q86XN8	OTTHUMG00000150369	ENST00000402693.4:c.*199C>-	chr19.hg19:g.1555363delG		171.0	0.0		193.0	13.0	NM_001174118	A0PJL8|A1L023|E9PAL6|Q71M49	Frame_Shift_Del	DEL	ENST00000402693.4	hg19	CCDS32865.2																																																																																			.	.		0.577	MEX3D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317870.2	NM_203304		-	1555363	G	-	1555363	6	5	209	0	1	1	0	1	0	0	0	0	9521	1103	39	0		0	MEX3D	19	1555363	3'UTR	DEL	G	TCGA-DD-AAE3-01A-11D-A40R-10	3	1555363	57573620	140	30285	158	5								
MEX3D	399664	hgsc.bcm.edu	37	chr19	1555380	1555380	+	3'UTR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gccgggctgcggggtctccgTctccacgcctgaggcggcag	17	15	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:1555380T>G	ENST00000402693.4	-	0	2137				AC027307.1_ENST00000410788.1_RNA|MEX3D_ENST00000388824.6_Missense_Mutation_p.T651P|AC027307.2_ENST00000581992.1_RNA	NM_203304.3	NP_976049.3	Q86XN8	MEX3D_HUMAN	mex-3 RNA binding family member D						mRNA destabilization (GO:0061157)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|lung(3)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGGTCTCCGTCTCCACGCCT	0.637																																					p.T651P		Atlas-SNP	.											MEX3D,NS,carcinoma,0,1	MEX3D	11	.	0			c.A1951C						.						32	37	35					19																	1555380		2200	4299	6499	SO:0001624	3_prime_UTR_variant	399664	exon3			TCTCCGTCTCCAC	AB107353	CCDS32865.2	19p13.3	2013-08-21	2013-08-21	2007-07-18	ENSG00000181588	ENSG00000181588		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	16734	protein-coding gene	gene with protein product	"bcl-2 ARE RNA binding protein"	611009	"ring finger and KH domain containing 1", "mex-3 homolog D (C. elegans)"	RKHD1		17267406	Standard	NM_203304		Approved	Tino, KIAA2031, OK/SW-cl.4, RNF193	uc010dsn.3	Q86XN8	OTTHUMG00000150369	ENST00000402693.4:c.*182A>C	chr19.hg19:g.1555380T>G		140.0	0.0		189.0	38.0	NM_001174118	A0PJL8|A1L023|E9PAL6|Q71M49	Missense_Mutation	SNP	ENST00000402693.4	hg19	CCDS32865.2	.	.	.	.	.	.	.	.	.	.	T	15.51	2.855272	0.51376	.	.	ENSG00000181588	ENST00000388824	T	0.45668	0.89	4.61	-1.13	0.09775	.	0.296636	0.32987	U	0.005411	T	0.24084	0.0583	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.31888	-0.9927	8	0.87932	D	0	.	10.6308	0.45534	0.0:0.6741:0.0:0.3259	.	.	.	.	P	651	ENSP00000373476:T651P	ENSP00000373476:T651P	T	-	1	0	MEX3D	1506380	0.000000	0.05858	0.022000	0.16811	0.447000	0.32167	-0.028000	0.12350	-0.060000	0.13132	0.454000	0.30748	ACG	.	.		0.637	MEX3D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317870.2	NM_203304		G	1555380	T	G	1555380	1	3	209	0	1	0	0	0	0	0	0	0	9521	1667	58	5		5	MEX3D	19	1555380	3'UTR	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	17	1555380	57573603	141	30286										
C3	718	hgsc.bcm.edu	37	chr19	6713480	6713480	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gccatcctggatcccgaagaTgacaaaggcagttccctcca	9	14	0	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:6713480T>C	ENST00000245907.6	-	8	906	c.814A>G	c.(814-816)Atc>Gtc	p.I272V		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	272					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	ATCCCGAAGATGACAAAGGCA	0.572																																					p.I272V		Atlas-SNP	.											.	C3	192	.	0			c.A814G						.						107	93	97					19																	6713480		2203	4300	6503	SO:0001583	missense	718	exon8			CGAAGATGACAAA	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.814A>G	chr19.hg19:g.6713480T>C	ENSP00000245907:p.Ile272Val	80.0	0.0		90.0	10.0	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	T	3.914	-0.019583	0.07634	.	.	ENSG00000125730	ENST00000245907	T	0.29917	1.55	4.59	2.22	0.28083	.	0.282477	0.36519	N	0.002560	T	0.18718	0.0449	L	0.36672	1.1	0.24807	N	0.992661	B	0.14805	0.011	B	0.17722	0.019	T	0.23013	-1.0200	10	0.12766	T	0.61	.	6.315	0.21186	0.0:0.0945:0.4861:0.4194	.	272	P01024	CO3_HUMAN	V	272	ENSP00000245907:I272V	ENSP00000245907:I272V	I	-	1	0	C3	6664480	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	2.066000	0.41452	0.681000	0.31386	0.397000	0.26171	ATC	.	.		0.572	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		C	6713480	T	C	6713480	3	2	209	1	0	0	0	0	1	0	0	0	2206	1464	51	2	4313	2	C3	19	6713480	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	5158100	6713480	52415503	142	30287										
PPAN	56342	hgsc.bcm.edu	37	chr19	10218695	10218695	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ccggcaccgcatgcacgagcAgcagtttgcccacccacccc	9	20	0	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:10218695A>T	ENST00000253107.7	+	5	504	c.398A>T	c.(397-399)cAg>cTg	p.Q133L	PPAN-P2RY11_ENST00000428358.1_Missense_Mutation_p.Q133L|PPAN_ENST00000393793.1_Missense_Mutation_p.Q80L|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.Q133L|SNORD105_ENST00000386910.1_RNA|SNORD105B_ENST00000458770.1_RNA|PPAN_ENST00000556468.1_Missense_Mutation_p.Q133L	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	133	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|liver(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			ATGCACGAGCAGCAGTTTGCC	0.602																																					p.Q133L		Atlas-SNP	.											.	PPAN	43	.	0			c.A398T						.						139	102	114					19																	10218695		2203	4300	6503	SO:0001583	missense	56342	exon5			ACGAGCAGCAGTT	BC033202	CCDS12225.1	19p13.2	2008-02-05	2001-11-28		ENSG00000130810	ENSG00000130810			9227	protein-coding gene	gene with protein product		607793	"peter pan (Drosophila) homolog"			10873382	Standard	NM_020230		Approved	SSF1, SSF2, SSF, BXDC3		Q9NQ55	OTTHUMG00000156826	ENST00000253107.7:c.398A>T	chr19.hg19:g.10218695A>T	ENSP00000253107:p.Gln133Leu	80.0	0.0		103.0	22.0	NM_020230	C9J3F9|Q9BW97|Q9H170	Missense_Mutation	SNP	ENST00000253107.7	hg19	CCDS12225.1	.	.	.	.	.	.	.	.	.	.	A	29.9	5.043611	0.93685	.	.	ENSG00000243207;ENSG00000243207;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810	ENST00000428358;ENST00000393796;ENST00000253107;ENST00000556468;ENST00000342696;ENST00000393793;ENST00000446223;ENST00000430370	T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.5	5.5	0.81552	Brix domain (3);	.	.	.	.	T	0.54303	0.1850	L	0.60455	1.87	0.58432	D	0.999999	D;D;D	0.58970	0.984;0.967;0.967	P;P;P	0.57204	0.815;0.702;0.702	T	0.51988	-0.8635	9	0.35671	T	0.21	-46.803	14.5666	0.68182	1.0:0.0:0.0:0.0	.	133;133;133	C9J3F9;C9JW41;Q9NQ55	.;.;SSF1_HUMAN	L	133;133;133;133;133;80;71;71	ENSP00000411918:Q133L;ENSP00000377385:Q133L;ENSP00000253107:Q133L;ENSP00000450710:Q133L;ENSP00000377382:Q80L;ENSP00000410485:Q71L;ENSP00000415988:Q71L	ENSP00000253107:Q133L	Q	+	2	0	PPAN;PPAN-P2RY11	10079695	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.643000	0.91040	2.089000	0.63090	0.459000	0.35465	CAG	.	.		0.602	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230		T	10218695	A	T	10218695	3	4	209	1	0	0	0	0	1	0	0	0	12297	188	7	4	416	4	PPAN	19	10218695	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	3505215	10218695	48910288	143	30288										
ZNF763	284390	hgsc.bcm.edu	37	chr19	12089392	12089392	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tctcagattatatcttatccAtgaaagaactcacactggag	6	9	3	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:12089392A>G	ENST00000358987.3	+	4	780	c.653A>G	c.(652-654)cAt>cGt	p.H218R	ZNF763_ENST00000538752.1_Missense_Mutation_p.H238R|ZNF763_ENST00000343949.5_Missense_Mutation_p.H221R|ZNF763_ENST00000590798.1_Missense_Mutation_p.H238R|ZNF763_ENST00000545530.1_Missense_Mutation_p.H96R			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	218					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						TATCTTATCCATGAAAGAACT	0.388																																					p.H221R		Atlas-SNP	.											.	ZNF763	31	.	0			c.A662G						.						83	85	84					19																	12089392		2203	4300	6503	SO:0001583	missense	284390	exon4			TTATCCATGAAAG	AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"Zinc fingers, C2H2-type", "-"	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.653A>G	chr19.hg19:g.12089392A>G	ENSP00000402017:p.His218Arg	129.0	0.0		143.0	38.0	NM_001012753	B3KRU3|B4DRE7	Missense_Mutation	SNP	ENST00000358987.3	hg19		.	.	.	.	.	.	.	.	.	.	a	11.27	1.590610	0.28357	.	.	ENSG00000197054	ENST00000538752;ENST00000343949;ENST00000545530;ENST00000358987	D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18	0.149	0.149	0.14863	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94453	0.8215	H	0.95982	3.75	0.09310	N	0.999999	D;D;D	0.89917	0.992;1.0;0.978	D;D;P	0.83275	0.954;0.996;0.731	D	0.85306	0.1076	8	0.87932	D	0	.	.	.	.	.	238;218;221	F5H0A9;Q0D2J5;Q0D2J5-2	.;ZN763_HUMAN;.	R	238;221;96;218	ENSP00000438117:H238R;ENSP00000369774:H221R;ENSP00000446166:H96R;ENSP00000402017:H218R	ENSP00000369774:H221R	H	+	2	0	ZNF763	11950392	0.952000	0.32445	0.002000	0.10522	0.276000	0.26787	4.282000	0.58971	0.166000	0.19597	0.164000	0.16699	CAT	.	.		0.388	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753		G	12089392	A	G	12089392	3	3	209	1	0	0	0	0	1	0	0	0	18152	217	8	2	676	2	ZNF763	19	12089392	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	1870697	12089392	47039591	144	30289										
ZNF563	147837	hgsc.bcm.edu	37	chr19	12430381	12430381	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cacgcgactgaaaggagtgaTggtaactgaaggctttccca	12	9	0	3			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:12430381T>C	ENST00000293725.5	-	4	663	c.458A>G	c.(457-459)cAt>cGt	p.H153R	ZNF563_ENST00000595977.1_Missense_Mutation_p.H153R	NM_145276.2	NP_660319.1	Q8TA94	ZN563_HUMAN	zinc finger protein 563	153					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						AAAGGAGTGATGGTAACTGAA	0.448																																					p.H153R	GBM(39;623 795 5132 29510 31476)	Atlas-SNP	.											.	ZNF563	77	.	0			c.A458G						.						335	282	300					19																	12430381		2203	4300	6503	SO:0001583	missense	147837	exon4			GAGTGATGGTAAC	BC022523	CCDS12270.1	19p13.2	2013-09-20			ENSG00000188868	ENSG00000188868		"Zinc fingers, C2H2-type", "-"	30498	protein-coding gene	gene with protein product							Standard	NM_145276		Approved	FLJ34797	uc002mtp.3	Q8TA94	OTTHUMG00000156413	ENST00000293725.5:c.458A>G	chr19.hg19:g.12430381T>C	ENSP00000293725:p.His153Arg	105.0	0.0		122.0	23.0	NM_145276	B2R9E7|Q8NAT7	Missense_Mutation	SNP	ENST00000293725.5	hg19	CCDS12270.1	.	.	.	.	.	.	.	.	.	.	T	0.477	-0.881713	0.02530	.	.	ENSG00000188868	ENST00000293725;ENST00000318168	T	0.14022	2.54	1.0	-2.0	0.07433	.	.	.	.	.	T	0.04407	0.0121	N	0.03948	-0.315	0.09310	N	1	B;B	0.17038	0.02;0.009	B;B	0.18561	0.009;0.022	T	0.42103	-0.9471	9	0.19590	T	0.45	.	3.1614	0.06521	0.2437:0.0:0.1951:0.5612	.	153;153	Q8TA94-2;Q8TA94	.;ZN563_HUMAN	R	153	ENSP00000293725:H153R	ENSP00000293725:H153R	H	-	2	0	ZNF563	12291381	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	-2.930000	0.00689	-0.816000	0.04340	0.260000	0.18958	CAT	.	.		0.448	ZNF563-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344114.1	NM_145276		C	12430381	T	C	12430381	3	2	209	1	0	0	0	0	1	0	0	0	18009	1464	51	2	976	2	ZNF563	19	12430381	Missense_Mutation	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	340989	12430381	46698602	145	30290										
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19767906	19767906	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ccaccagcatggatagcgtaAagacgctgtagtaccagtac	10	11	0	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:19767906A>C	ENST00000357324.6	-	5	829	c.803T>G	c.(802-804)tTt>tGt	p.F268C	ATP13A1_ENST00000291503.5_Missense_Mutation_p.F150C|ATP13A1_ENST00000496082.1_5'Flank	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	268						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GGATAGCGTAAAGACGCTGTA	0.587																																					p.F268C	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.T803G						.						47	43	45					19																	19767906		2203	4300	6503	SO:0001583	missense	57130	exon5			AGCGTAAAGACGC	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"ATPases / P-type"	24215	protein-coding gene	gene with protein product	"cation transporting ATPase"		"ATPase type 13A"	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.803T>G	chr19.hg19:g.19767906A>C	ENSP00000349877:p.Phe268Cys	47.0	0.0		53.0	4.0	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Missense_Mutation	SNP	ENST00000357324.6	hg19	CCDS32970.2	.	.	.	.	.	.	.	.	.	.	A	19.50	3.838616	0.71373	.	.	ENSG00000105726	ENST00000291503;ENST00000357324	D;D	0.89123	-2.47;-2.47	4.89	4.89	0.63831	ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.92401	0.7588	H	0.95539	3.685	0.80722	D	1	P;P	0.47841	0.901;0.734	P;B	0.45276	0.475;0.382	D	0.92139	0.5719	10	0.27785	T	0.31	-38.5603	12.456	0.55704	1.0:0.0:0.0:0.0	.	268;150	Q9HD20;Q9HD20-2	AT131_HUMAN;.	C	150;268	ENSP00000291503:F150C;ENSP00000349877:F268C	ENSP00000291503:F150C	F	-	2	0	ATP13A1	19628906	1.000000	0.71417	1.000000	0.80357	0.637000	0.38172	8.877000	0.92386	1.847000	0.53656	0.383000	0.25322	TTT	.	.		0.587	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		C	19767906	A	C	19767906	3	2	209	1	0	0	0	0	1	0	0	0	1123	14	1	5	2899	5	ATP13A1	19	19767906	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	7337525	19767906	39361077	146	30291										
ZNF85	7639	hgsc.bcm.edu	37	chr19	21132307	21132307	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tttaagcagtcctcaaacctTactacacataagataattca	3	10	2	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:21132307T>C	ENST00000328178.8	+	4	1100	c.987T>C	c.(985-987)ctT>ctC	p.L329L	ZNF85_ENST00000601023.1_Silent_p.L270L|ZNF85_ENST00000345030.6_Silent_p.L296L	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	329					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						CCTCAAACCTTACTACACATA	0.383																																					p.L359L		Atlas-SNP	.											.	ZNF85	72	.	0			c.T1077C						.						44	49	47					19																	21132307		2201	4297	6498	SO:0001819	synonymous_variant	7639	exon5			AAACCTTACTACA	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"Zinc fingers, C2H2-type", "-"	13160	protein-coding gene	gene with protein product		603899	"zinc finger protein 85 (HPF4, HTF1)"			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.987T>C	chr19.hg19:g.21132307T>C		99.0	0.0		82.0	32.0	NM_001256171	B9ZVP4|Q6NVI0	Silent	SNP	ENST00000328178.8	hg19	CCDS32977.1																																																																																			.	.		0.383	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		C	21132307	T	C	21132307	2	2	209	1	0	0	0	0	0	0	0	1	18208	1741	61	2		2	ZNF85	19	21132307	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	1364401	21132307	37996676	147	30292										
TGFB1	7040	hgsc.bcm.edu	37	chr19	41850715	41850715	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	agataaccactctggcgagtCgctgggtgccagcagccggt	14	12	1	1	rs201383660		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:41850715C>T	ENST00000221930.5	-	3	1437	c.571G>A	c.(571-573)Gac>Aac	p.D191N		NM_000660.4	NP_000651.3	P01137	TGFB1_HUMAN	transforming growth factor, beta 1	191	Arm domain. {ECO:0000250}.				active induction of host immune response by virus (GO:0046732)|adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains (GO:0002460)|aging (GO:0007568)|ATP biosynthetic process (GO:0006754)|blood coagulation (GO:0007596)|branch elongation involved in mammary gland duct branching (GO:0060751)|cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cell-cell junction organization (GO:0045216)|cellular calcium ion homeostasis (GO:0006874)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation (GO:0002062)|common-partner SMAD protein phosphorylation (GO:0007182)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|defense response to fungus, incompatible interaction (GO:0009817)|digestive tract development (GO:0048565)|embryo development (GO:0009790)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|evasion or tolerance of host defenses by virus (GO:0019049)|extracellular matrix assembly (GO:0085029)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|face morphogenesis (GO:0060325)|female pregnancy (GO:0007565)|frontal suture morphogenesis (GO:0060364)|germ cell migration (GO:0008354)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|lens fiber cell differentiation (GO:0070306)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymph node development (GO:0048535)|macrophage derived foam cell differentiation (GO:0010742)|mammary gland branching involved in thelarche (GO:0060744)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|modulation by virus of host morphology or physiology (GO:0019048)|mononuclear cell proliferation (GO:0032943)|myelination (GO:0042552)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA replication (GO:0008156)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of extracellular matrix disassembly (GO:0010716)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of ossification (GO:0030279)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|ossification involved in bone remodeling (GO:0043932)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|phosphate-containing compound metabolic process (GO:0006796)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NAD+ ADP-ribosyltransferase activity (GO:1901666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of odontogenesis (GO:0042482)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein secretion (GO:0050714)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein export from nucleus (GO:0006611)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|receptor catabolic process (GO:0032801)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of binding (GO:0051098)|regulation of blood vessel remodeling (GO:0060312)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of cartilage development (GO:0061035)|regulation of cell migration (GO:0030334)|regulation of DNA binding (GO:0051101)|regulation of miRNA metabolic process (GO:2000628)|regulation of protein import into nucleus (GO:0042306)|regulation of sodium ion transport (GO:0002028)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulatory T cell differentiation (GO:0045066)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to laminar fluid shear stress (GO:0034616)|response to progesterone (GO:0032570)|response to radiation (GO:0009314)|response to vitamin D (GO:0033280)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|T cell homeostasis (GO:0043029)|tolerance induction to self antigen (GO:0002513)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|viral life cycle (GO:0019058)	axon (GO:0030424)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	antigen binding (GO:0003823)|cytokine activity (GO:0005125)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)	8					Hyaluronidase(DB00070)	TCTGGCGAGTCGCTGGGTGCC	0.547																																					p.D191N		Atlas-SNP	.											.	TGFB1	27	.	0			c.G571A						.						94	64	74					19																	41850715		2203	4300	6503	SO:0001583	missense	7040	exon3			GCGAGTCGCTGGG	X02812	CCDS33031.1	19q13.1	2014-01-30	2007-02-16			ENSG00000105329		"Endogenous ligands"	11766	protein-coding gene	gene with protein product	"Camurati-Engelmann disease", "prepro-transforming growth factor beta-1"	190180		TGFB, DPD1		10631145, 10843814	Standard	NM_000660		Approved	CED, TGFbeta	uc002oqh.2	P01137		ENST00000221930.5:c.571G>A	chr19.hg19:g.41850715C>T	ENSP00000221930:p.Asp191Asn	89.0	0.0		86.0	14.0	NM_000660	A8K792|Q9UCG4	Missense_Mutation	SNP	ENST00000221930.5	hg19	CCDS33031.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.283437	0.23392	.	.	ENSG00000105329	ENST00000221930	T	0.64803	-0.12	5.44	2.02	0.26589	Transforming growth factor-beta, N-terminal (1);	0.834073	0.11189	N	0.590129	T	0.45756	0.1358	L	0.38531	1.155	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.25916	-1.0118	10	0.20046	T	0.44	-18.7748	5.0438	0.14473	0.0:0.6264:0.1859:0.1877	.	191	P01137	TGFB1_HUMAN	N	191	ENSP00000221930:D191N	ENSP00000221930:D191N	D	-	1	0	TGFB1	46542555	0.020000	0.18652	0.172000	0.22920	0.901000	0.52897	1.240000	0.32731	0.870000	0.35726	0.655000	0.94253	GAC	.	.		0.547	TGFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463500.2			T	41850715	C	T	41850715	3	4	209	1	0	0	0	0	1	0	0	0	15831	884	31	1	621	1	TGFB1	19	41850715	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	20718408	41850715	17278268	148	30293										
CEACAM4	1089	hgsc.bcm.edu	37	chr19	42128109	42128109	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cccagtcacgatgccagcgaCggcccccacaggaaggcctg	12	17	1	0	rs368076616		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:42128109C>T	ENST00000221954.2	-	3	567	c.457G>A	c.(457-459)Gtc>Atc	p.V153I	CEACAM4_ENST00000600925.1_Missense_Mutation_p.V153I	NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	153						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						ATGCCAGCGACGGCCCCCACA	0.587																																					p.V153I		Atlas-SNP	.											CEACAM4,NS,carcinoma,0,1	CEACAM4	42	.	0			c.G457A						.	C	ILE/VAL	0,4406		0,0,2203	62	56	58		457	1	0	19		58	1,8599	1.2+/-3.3	0,1,4299	no	missense	CEACAM4	NM_001817.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	153/245	42128109	1,13005	2203	4300	6503	SO:0001583	missense	1089	exon3			CAGCGACGGCCCC	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"Immunoglobulin superfamily / V-set domain containing"	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.457G>A	chr19.hg19:g.42128109C>T	ENSP00000221954:p.Val153Ile	219.0	0.0		167.0	67.0	NM_001817	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	hg19	CCDS33033.1	.	.	.	.	.	.	.	.	.	.	C	0.036	-1.304766	0.01353	0.0	1.16E-4	ENSG00000105352	ENST00000221954	T	0.00882	5.58	3.29	1.02	0.19986	.	.	.	.	.	T	0.00440	0.0014	N	0.03209	-0.39	0.09310	N	1	B;B	0.16802	0.019;0.007	B;B	0.06405	0.002;0.002	T	0.45205	-0.9277	9	0.02654	T	1	.	2.686	0.05107	0.2243:0.1383:0.0:0.6374	.	153;153	E7EMX3;O75871	.;CEAM4_HUMAN	I	153	ENSP00000221954:V153I	ENSP00000221954:V153I	V	-	1	0	CEACAM4	46819949	0.009000	0.17119	0.000000	0.03702	0.078000	0.17371	-0.163000	0.09997	-0.080000	0.12685	-0.436000	0.05848	GTC	.	.		0.587	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817		T	42128109	C	T	42128109	3	4	209	1	0	0	0	0	1	0	0	0	3196	536	19	1	297	1	CEACAM4	19	42128109	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	277394	42128109	17000874	149	30294										
SYMPK	8189	hgsc.bcm.edu	37	chr19	46326692	46326692	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tggcagtcgcttgtggtagaGatcccggacccgcttcacca	12	13	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr19:46326692G>C	ENST00000245934.7	-	20	2882	c.2638C>G	c.(2638-2640)Ctc>Gtc	p.L880V	SYMPK_ENST00000598155.1_5'UTR	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	880					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		TTGTGGTAGAGATCCCGGACC	0.637																																					p.L880V		Atlas-SNP	.											.	SYMPK	104	.	0			c.C2638G						.						73	67	69					19																	46326692		2203	4300	6503	SO:0001583	missense	8189	exon20			GGTAGAGATCCCG	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.2638C>G	chr19.hg19:g.46326692G>C	ENSP00000245934:p.Leu880Val	75.0	0.0		50.0	13.0	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Missense_Mutation	SNP	ENST00000245934.7	hg19	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	G	27.0	4.789002	0.90367	.	.	ENSG00000125755	ENST00000245934	T	0.68765	-0.35	4.67	4.67	0.58626	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81997	0.4941	M	0.84683	2.71	0.80722	D	1	D;D	0.71674	0.998;0.974	D;P	0.65010	0.931;0.829	D	0.85471	0.1173	10	0.87932	D	0	.	15.1866	0.73006	0.0:0.0:1.0:0.0	.	895;880	Q4LE61;Q92797	.;SYMPK_HUMAN	V	880	ENSP00000245934:L880V	ENSP00000245934:L880V	L	-	1	0	SYMPK	51018532	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.061000	0.76699	2.425000	0.82216	0.650000	0.86243	CTC	.	.		0.637	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		C	46326692	G	C	46326692	3	2	209	1	0	0	0	0	1	0	0	0	15454	942	33	4	1218	4	SYMPK	19	46326692	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	4198583	46326692	12802291	150	30295										
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3675089	3675089	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ggagcagccgcagctgggccGgagggtcactgtccacacgg	17	13	1	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr20:3675089G>A	ENST00000344754.4	-	12	3034	c.3035C>T	c.(3034-3036)cCg>cTg	p.P1012L	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.P1012L	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1012	Ig-like C2-type 10.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CAGCTGGGCCGGAGGGTCACT	0.667																																					p.P1012L		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C3035T						.																																			SO:0001583	missense	6614	exon12			TGGGCCGGAGGGT	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.3035C>T	chr20.hg19:g.3675089G>A	ENSP00000341141:p.Pro1012Leu	70.0	0.0		127.0	12.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	hg19	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.427799	0.25726	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.67171	-0.25;-0.25	5.15	1.63	0.23807	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.213642	0.24559	N	0.037499	T	0.56247	0.1972	L	0.57536	1.79	0.33991	D	0.649081	B;B	0.15719	0.014;0.011	B;B	0.16289	0.015;0.012	T	0.58165	-0.7684	10	0.42905	T	0.14	.	5.7965	0.18389	0.1798:0.0:0.6326:0.1876	.	1012;1012	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	L	1012	ENSP00000341141:P1012L;ENSP00000202578:P1012L	ENSP00000202578:P1012L	P	-	2	0	SIGLEC1	3623089	0.005000	0.15991	0.846000	0.33378	0.819000	0.46315	0.135000	0.15952	0.690000	0.31570	0.561000	0.74099	CCG	.	.		0.667	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		A	3675089	G	A	3675089	3	1	209	1	0	0	0	0	1	0	0	0	14320	1116	39	1	2134	1	SIGLEC1	20	3675089	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10		3675089	59350431	151	30296										
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51871290	51871292	+	In_Frame_Del	DEL	GTT	GTT	-													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gcagtggagaaaatgcagtcGttgtctgaggccccaaacag							TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr20:51871290_51871292delGTT	ENST00000371497.5	+	2	2180_2182	c.1293_1295delGTT	c.(1291-1296)tcgttg>tcg	p.L432del	TSHZ2_ENST00000603338.2_In_Frame_Del_p.L429del|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_In_Frame_Del_p.L429del	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	432					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			AAATGCAGTCGTTGTCTGAGGCC	0.478																																					p.431_432del		Atlas-INDEL	.											TSHZ2,NS,carcinoma,+1,1	TSHZ2	209	.	0			c.1292_1294del						.																																			SO:0001651	inframe_deletion	128553	exon2			.	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.1293_1295delGTT	chr20.hg19:g.51871290_51871292delGTT	ENSP00000360552:p.Leu432del	130.0	0.0		155.0	15.0	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	In_Frame_Del	DEL	ENST00000371497.5	hg19	CCDS33490.1																																																																																			.	.		0.478	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		-	51871292	GTT	-	51871290	7	5	209	1	0	1	0	1	0	0	0	0	16639	1132	40	0	1299	0	TSHZ2	20	51871290	In_Frame_Del	DEL	GTT	TCGA-DD-AAE3-01A-11D-A40R-10	48196201	51871290	11154230	152	30297										
PCK1	5105	hgsc.bcm.edu	37	chr20	56138214	56138214	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctcgggaagaagtgctttgcTctcaggatggccagccggct	14	11	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr20:56138214T>G	ENST00000319441.4	+	5	905	c.741T>G	c.(739-741)gcT>gcG	p.A247A	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Silent_p.A115A	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	247					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			AGTGCTTTGCTCTCAGGATGG	0.632																																					p.A247A		Atlas-SNP	.											.	PCK1	95	.	0			c.T741G						.						58	66	63					20																	56138214		2203	4300	6503	SO:0001819	synonymous_variant	5105	exon5			CTTTGCTCTCAGG		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.741T>G	chr20.hg19:g.56138214T>G		60.0	0.0		76.0	38.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	.		0.632	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			G	56138214	T	G	56138214	2	3	209	1	0	0	0	0	0	0	0	1	11590	1538	54	5		5	PCK1	20	56138214	Silent	SNP	T	TCGA-DD-AAE3-01A-11D-A40R-10	4266924	56138214	6887306	153	30298										
TH1L	51497	hgsc.bcm.edu	37	chr20	57569232	57569250	+	Frame_Shift_Del	DEL	ATGACAGCATCGCAGGTAC	ATGACAGCATCGCAGGTAC	-													0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tttcctccccatcctggagaAtgacagcatcgcaggtacca					rs150954057|rs188308685	byFrequency	TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	ATGACAGCATCGCAGGTAC	ATGACAGCATCGCAGGTAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr20:57569232_57569250delATGACAGCATCGCAGGTAC	ENST00000344018.3	+	14	1703_1721	c.1676_1694delATGACAGCATCGCAGGTAC	c.(1675-1695)aatgacagcatcgcaggtaccfs	p.NDSIAGT559fs	NELFCD_ENST00000479207.1_3'UTR|NELFCD_ENST00000602795.1_Frame_Shift_Del_p.NDSIAGT568fs			Q8IXH7	NELFD_HUMAN	negative elongation factor complex member C/D	559					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	membrane (GO:0016020)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)											ATCCTGGAGAATGACAGCATCGCAGGTACCATCAAAACG	0.548																																					p.568_574del		Atlas-INDEL	.											.	.	.	.	0			c.1702_1720del						.																																			SO:0001589	frameshift_variant	51497	exon14			.	AF161479	CCDS13473.1, CCDS13473.2	20q13	2013-01-31	2013-01-31	2013-01-31	ENSG00000101158	ENSG00000101158			15934	protein-coding gene	gene with protein product	"trihydrophobin 1"	605297	"TH1-like (Drosophila homolog)", "TH1-like (Drosophila)"	TH1L		11030415, 11042152	Standard	NM_198976		Approved	HSPC130, TH1, NELF-C, NELF-D	uc002yag.4	Q8IXH7	OTTHUMG00000032861	ENST00000344018.3:c.1676_1694delATGACAGCATCGCAGGTAC	chr20.hg19:g.57569232_57569250delATGACAGCATCGCAGGTAC	ENSP00000342300:p.Asn559fs	97.0	0.0		138.0	13.0	NM_198976	B4DE06|Q9BYL2|Q9H405|Q9H888|Q9H8T3|Q9NVX5|Q9P029|Q9UGN1|Q9UGN2|Q9UGN3	Frame_Shift_Del	DEL	ENST00000344018.3	hg19																																																																																				.	.		0.548	NELFCD-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198976		-	57569250	ATGACAGCATCGCAGGTAC	-	57569232	7	5	209	1	0	1	0	1	0	0	0	0	15854	101	4	0	1730	0	TH1L	20	57569232	Frame_Shift_Del	DEL	ATGACAGCATCGCAGGTAC	TCGA-DD-AAE3-01A-11D-A40R-10	1431018	57569232	5456288	154	30299										
KRTAP24-1	643803	hgsc.bcm.edu	37	chr21	31654629	31654629	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cctgtagcttgaatagtgatAatttctcactaaatagcttt	6	7	1	2	rs529683700		TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr21:31654629A>T	ENST00000340345.4	-	1	647	c.622T>A	c.(622-624)Tat>Aat	p.Y208N		NM_001085455.1	NP_001078924.1	Q3LI83	KR241_HUMAN	keratin associated protein 24-1	208	6 X 10 AA repeats of Y-[ILR]-[SVPC]- [NRTS]-[SNTG]-X-[QHRP]-[PSY]-[QSL]-[SRK].					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|large_intestine(3)|lung(7)|urinary_tract(3)	14						GAATAGTGATAATTTCTCACT	0.423																																					p.Y208N		Atlas-SNP	.											.	KRTAP24-1	44	.	0			c.T622A						.						107	103	104					21																	31654629		1860	4097	5957	SO:0001583	missense	643803	exon1			AGTGATAATTTCT	AB096935	CCDS42915.1	21q22.11	2007-11-23			ENSG00000188694	ENSG00000188694		"Keratin associated proteins"	33902	protein-coding gene	gene with protein product							Standard	NM_001085455		Approved	KAP24.1	uc002ynv.3	Q3LI83	OTTHUMG00000125483	ENST00000340345.4:c.622T>A	chr21.hg19:g.31654629A>T	ENSP00000339238:p.Tyr208Asn	97.0	0.0		55.0	11.0	NM_001085455	Q1XDX0	Missense_Mutation	SNP	ENST00000340345.4	hg19	CCDS42915.1	.	.	.	.	.	.	.	.	.	.	A	4.532	0.098691	0.08681	.	.	ENSG00000188694	ENST00000340345	T	0.30981	1.51	4.45	1.94	0.25998	.	0.863754	0.10047	N	0.722667	T	0.17408	0.0418	N	0.19112	0.55	0.09310	N	1	B	0.26775	0.159	B	0.19391	0.025	T	0.22661	-1.0210	10	0.45353	T	0.12	0.6461	4.6313	0.12502	0.6986:0.1954:0.1059:0.0	.	208	Q3LI83	KR241_HUMAN	N	208	ENSP00000339238:Y208N	ENSP00000339238:Y208N	Y	-	1	0	KRTAP24-1	30576500	0.000000	0.05858	0.136000	0.22124	0.005000	0.04900	0.277000	0.18734	0.267000	0.21916	0.460000	0.39030	TAT	.	.		0.423	KRTAP24-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246806.2	NM_001085455		T	31654629	A	T	31654629	3	4	209	1	0	0	0	0	1	0	0	0	8551	362	13	4	146	4	KRTAP24-1	21	31654629	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10		31654629	16475266	155	30300										
SDF2L1	23753	hgsc.bcm.edu	37	chr22	21996797	21996797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tgcggctgcactcgcacgacAtcaaatacggatccggtgcg	12	13	1	0			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr22:21996797A>G	ENST00000248958.4	+	1	248	c.172A>G	c.(172-174)Atc>Gtc	p.I58V	KB-1440D3.14_ENST00000609038.1_lincRNA	NM_022044.2	NP_071327.2	Q9HCN8	SDF2L_HUMAN	stromal cell-derived factor 2-like 1	58	MIR 1. {ECO:0000255|PROSITE- ProRule:PRU00131}.					endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				prostate(1)	1	Colorectal(54;0.105)					CTCGCACGACATCAAATACGG	0.682																																					p.I58V		Atlas-SNP	.											.	SDF2L1	5	.	0			c.A172G						.						16	13	14					22																	21996797		2018	3910	5928	SO:0001583	missense	23753	exon1			CACGACATCAAAT		CCDS13792.1	22q11.21	2008-07-01			ENSG00000128228	ENSG00000128228			10676	protein-coding gene	gene with protein product	"dihydropyrimidinase-like 2", "PWP1-interacting protein 8"	607551				10591208, 11162531	Standard	NM_022044		Approved	AP000553.C22.4, OTTHUMT00000075032	uc002zvf.3	Q9HCN8	OTTHUMG00000150820	ENST00000248958.4:c.172A>G	chr22.hg19:g.21996797A>G	ENSP00000248958:p.Ile58Val	100.0	0.0		71.0	15.0	NM_022044	A2RUD3|Q9BRI5	Missense_Mutation	SNP	ENST00000248958.4	hg19	CCDS13792.1	.	.	.	.	.	.	.	.	.	.	A	8.244	0.807527	0.16467	.	.	ENSG00000128228	ENST00000248958	D	0.83755	-1.76	4.86	2.75	0.32379	MIR motif (2);MIR (2);	0.112881	0.64402	N	0.000014	T	0.41003	0.1140	N	0.00175	-1.925	0.36896	D	0.890171	B	0.12013	0.005	B	0.10450	0.005	T	0.53479	-0.8433	10	0.02654	T	1	-18.3334	5.6446	0.17582	0.7134:0.0:0.2866:0.0	.	58	Q9HCN8	SDF2L_HUMAN	V	58	ENSP00000248958:I58V	ENSP00000248958:I58V	I	+	1	0	SDF2L1	20326797	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.637000	0.67854	0.989000	0.38761	0.533000	0.62120	ATC	.	.		0.682	SDF2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320197.1	NM_022044		G	21996797	A	G	21996797	3	3	209	1	0	0	0	0	1	0	0	0	13976	217	8	2	174	2	SDF2L1	22	21996797	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10		21996797	29307769	156	30301										
TFIP11	24144	hgsc.bcm.edu	37	chr22	26902861	26902861	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	cctttcttgagccctgcgctGatgaagttgactggcgcaga	12	11	1	5			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr22:26902861G>A	ENST00000407690.1	-	5	526	c.243C>T	c.(241-243)atC>atT	p.I81I	TFIP11_ENST00000407431.1_Silent_p.I81I|TFIP11_ENST00000496523.1_5'Flank|TFIP11_ENST00000407148.1_Silent_p.I81I|TFIP11_ENST00000405938.1_Silent_p.I81I	NM_012143.2	NP_036275.1	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	81					biomineral tissue development (GO:0031214)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|spliceosomal complex disassembly (GO:0000390)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	DNA binding (GO:0003677)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25						GCCCTGCGCTGATGAAGTTGA	0.517																																					p.I81I		Atlas-SNP	.											.	TFIP11	72	.	0			c.C243T						.						66	62	63					22																	26902861		2203	4300	6503	SO:0001819	synonymous_variant	24144	exon6			TGCGCTGATGAAG	AL050258	CCDS13838.1	22q12.1	2013-01-28			ENSG00000100109	ENSG00000100109		"G patch domain containing"	17165	protein-coding gene	gene with protein product		612747				10806191, 11230166	Standard	NM_012143		Approved	TIP39, DKFZP434B194, Spp382	uc003acs.2	Q9UBB9	OTTHUMG00000150883	ENST00000407690.1:c.243C>T	chr22.hg19:g.26902861G>A		79.0	0.0		54.0	16.0	NM_001008697	O95908|Q20WL0|Q5H8V8|Q9UGV7|Q9Y2Q8	Silent	SNP	ENST00000407690.1	hg19	CCDS13838.1																																																																																			.	.		0.517	TFIP11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320750.1	NM_001008697		A	26902861	G	A	26902861	2	1	209	1	0	0	0	0	0	0	0	1	15822	1280	45	3		3	TFIP11	22	26902861	Silent	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	4906064	26902861	24401705	157	30302										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32215183	32215183	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	atgaagcttacgtccaacagAaggcgctggatgcacacttt	10	10	0	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr22:32215183A>G	ENST00000382112.3	+	21	1912	c.1842A>G	c.(1840-1842)agA>agG	p.R614R	DEPDC5_ENST00000536766.1_Silent_p.R586R|DEPDC5_ENST00000400248.2_Silent_p.R614R|DEPDC5_ENST00000400246.1_Silent_p.R614R|DEPDC5_ENST00000535622.1_Silent_p.R614R|DEPDC5_ENST00000266091.3_Silent_p.R614R|DEPDC5_ENST00000382105.2_Silent_p.R614R|DEPDC5_ENST00000400249.2_Silent_p.R614R|DEPDC5_ENST00000382111.2_Silent_p.R614R	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	614					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CGTCCAACAGAAGGCGCTGGA	0.547																																					p.R614R		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A1842G						.						117	115	116					22																	32215183		2020	4183	6203	SO:0001819	synonymous_variant	9681	exon22			CAACAGAAGGCGC	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.1842A>G	chr22.hg19:g.32215183A>G		86.0	0.0		45.0	8.0	NM_001242897	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Silent	SNP	ENST00000382112.3	hg19	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	11.24	1.581064	0.28180	.	.	ENSG00000100150	ENST00000433147	.	.	.	5.8	1.29	0.21616	.	.	.	.	.	T	0.53658	0.1810	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41680	-0.9495	4	.	.	.	.	6.4357	0.21821	0.3923:0.2331:0.3746:0.0	.	.	.	.	E	12	.	.	K	+	1	0	DEPDC5	30545183	0.983000	0.35010	1.000000	0.80357	0.992000	0.81027	0.274000	0.18680	0.147000	0.19030	0.533000	0.62120	AAG	.	.		0.547	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		G	32215183	A	G	32215183	2	3	209	1	0	0	0	0	0	0	0	1	4444	243	9	2		2	DEPDC5	22	32215183	Silent	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	5312322	32215183	19089383	158	30303										
PNPLA5	150379	hgsc.bcm.edu	37	chr22	44282314	44282314	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	catcccagtttccgtcagccGgggctgggggttccttagac	13	13	1	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chr22:44282314G>A	ENST00000597664.1	-	6	947	c.818C>T	c.(817-819)cCg>cTg	p.P273L	PNPLA5_ENST00000593866.1_Missense_Mutation_p.P159L|PNPLA5_ENST00000381198.2_Missense_Mutation_p.P159L|PNPLA5_ENST00000216177.4_Missense_Mutation_p.P273L			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	273					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				TCCGTCAGCCGGGGCTGGGGG	0.587																																					p.P273L		Atlas-SNP	.											.	PNPLA5	46	.	0			c.C818T						.						80	74	76					22																	44282314		2203	4300	6503	SO:0001583	missense	150379	exon6			TCAGCCGGGGCTG	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"Patatin-like phospholipase domain containing"	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.818C>T	chr22.hg19:g.44282314G>A	ENSP00000471069:p.Pro273Leu	53.0	0.0		43.0	12.0	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.92	1.487901	0.26686	.	.	ENSG00000100341	ENST00000216177;ENST00000381198;ENST00000438734	T;T;T	0.76186	-1.0;0.95;1.68	4.43	0.925	0.19424	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.554792	0.15658	N	0.251022	T	0.45617	0.1351	N	0.16743	0.435	0.09310	N	1	P;P;B	0.37141	0.499;0.584;0.066	B;B;B	0.25405	0.06;0.054;0.006	T	0.27297	-1.0078	10	0.26408	T	0.33	-10.5946	2.9635	0.05900	0.2343:0.0:0.5467:0.219	.	181;159;273	E9PGS4;Q7Z6Z6-2;Q7Z6Z6	.;.;PLPL5_HUMAN	L	273;159;181	ENSP00000216177:P273L;ENSP00000370595:P159L;ENSP00000405732:P181L	ENSP00000216177:P273L	P	-	2	0	PNPLA5	42613647	0.022000	0.18835	0.003000	0.11579	0.065000	0.16274	0.823000	0.27366	0.580000	0.29522	0.491000	0.48974	CCG	.	.		0.587	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814		A	44282314	G	A	44282314	3	1	209	1	0	0	0	0	1	0	0	0	12177	1116	39	1	487	1	PNPLA5	22	44282314	Missense_Mutation	SNP	G	TCGA-DD-AAE3-01A-11D-A40R-10	12067131	44282314	7022252	159	30304										
GLRA2	2742	hgsc.bcm.edu	37	chrX	14550455	14550455	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tggacaagttaatgggaaggAcatcaggatatgatgcaaga	13	4	1	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chrX:14550455A>T	ENST00000218075.4	+	2	693	c.163A>T	c.(163-165)Aca>Tca	p.T55S	GLRA2_ENST00000443437.2_5'UTR|GLRA2_ENST00000355020.4_Missense_Mutation_p.T55S	NM_002063.3	NP_002054.1	P23416	GLRA2_HUMAN	glycine receptor, alpha 2	55					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)|synapse assembly (GO:0007416)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(22)|ovary(1)|prostate(1)|skin(2)	37	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)|Lindane(DB00431)	AATGGGAAGGACATCAGGATA	0.398																																					p.T55S		Atlas-SNP	.											.	GLRA2	140	.	0			c.A163T						.						125	119	121					X																	14550455		2203	4300	6503	SO:0001583	missense	2742	exon3			GGAAGGACATCAG		CCDS14160.1, CCDS48085.1, CCDS55371.1	Xp22.2	2012-02-07			ENSG00000101958	ENSG00000101958		"Ligand-gated ion channels / Glycine receptors"	4327	protein-coding gene	gene with protein product		305990		GLR			Standard	NM_002063		Approved		uc010nep.3	P23416	OTTHUMG00000021166	ENST00000218075.4:c.163A>T	chrX.hg19:g.14550455A>T	ENSP00000218075:p.Thr55Ser	246.0	0.0		168.0	81.0	NM_001118885	A8K0J6|B2R6I8|B7Z4F5|J3KQ59|Q53YX7|Q6ICQ0|Q99862	Missense_Mutation	SNP	ENST00000218075.4	hg19	CCDS14160.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.764386	0.49574	.	.	ENSG00000101958	ENST00000218075;ENST00000355020;ENST00000415367	T;T;T	0.80123	-1.34;-1.34;0.44	5.08	5.08	0.68730	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.76983	0.4064	N	0.03281	-0.365	0.80722	D	1	D;P;B	0.55800	0.973;0.941;0.082	P;D;B	0.71414	0.887;0.973;0.098	T	0.82760	-0.0298	10	0.62326	D	0.03	.	13.2275	0.59922	1.0:0.0:0.0:0.0	.	39;55;55	B7Z4E9;P23416;P23416-2	.;GLRA2_HUMAN;.	S	55;55;39	ENSP00000218075:T55S;ENSP00000347123:T55S;ENSP00000391606:T39S	ENSP00000218075:T55S	T	+	1	0	GLRA2	14460376	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.276000	0.65580	1.785000	0.52413	0.481000	0.45027	ACA	.	.		0.398	GLRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055829.1			T	14550455	A	T	14550455	3	4	209	1	0	0	0	0	1	0	0	0	6463	275	10	4	169	4	GLRA2	23	14550455	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10		14550455	140720105	160	30305										
MED12	9968	hgsc.bcm.edu	37	chrX	70352248	70352248	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	tctctagagcgctctggtgtAtggctggtggcccccctcat	12	13	3	1			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chrX:70352248A>G	ENST00000374080.3	+	31	4307	c.4275A>G	c.(4273-4275)gtA>gtG	p.V1425V	MED12_ENST00000374102.1_Silent_p.V1425V|MED12_ENST00000333646.6_Silent_p.V1425V			Q93074	MED12_HUMAN	mediator complex subunit 12	1425					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					GCTCTGGTGTATGGCTGGTGG	0.562			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.V1425V		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.A4275G						.						66	61	62					X																	70352248		2000	4154	6154	SO:0001819	synonymous_variant	9968	exon31			TGGTGTATGGCTG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.4275A>G	chrX.hg19:g.70352248A>G		77.0	0.0		78.0	22.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	hg19	CCDS43970.1																																																																																			.	.		0.562	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		G	70352248	A	G	70352248	2	3	209	1	0	0	0	0	0	0	0	1	9437	436	16	2		2	MED12	23	70352248	Silent	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	55801793	70352248	84918312	161	30306										
ATRX	546	hgsc.bcm.edu	37	chrX	76776919	76776919	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	ctcaagaggttgaatcctcaCtgctgtcacactgtttgttg	9	10	3	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chrX:76776919C>T	ENST00000373344.5	-	33	7247	c.7033G>A	c.(7033-7035)Gtg>Atg	p.V2345M	ATRX_ENST00000395603.3_Missense_Mutation_p.V2307M|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2345					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TGAATCCTCACTGCTGTCACA	0.398			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.V2345M		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	0			c.G7033A						.						183	150	161					X																	76776919		2203	4296	6499	SO:0001583	missense	546	exon33			TCCTCACTGCTGT	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.7033G>A	chrX.hg19:g.76776919C>T	ENSP00000362441:p.Val2345Met	62.0	0.0		19.0	9.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	hg19	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	C	9.694	1.152651	0.21371	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	D;D	0.92858	-3.11;-3.12	5.06	5.06	0.68205	.	0.178870	0.38548	N	0.001644	D	0.86669	0.5988	N	0.02539	-0.55	0.80722	D	1	P;P	0.47677	0.899;0.493	P;B	0.51355	0.667;0.107	D	0.89768	0.3952	10	0.44086	T	0.13	.	17.6044	0.88034	0.0:1.0:0.0:0.0	.	2307;2345	P46100-4;P46100	.;ATRX_HUMAN	M	2345;2307	ENSP00000362441:V2345M;ENSP00000378967:V2307M	ENSP00000362441:V2345M	V	-	1	0	ATRX	76663575	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.453000	0.44970	2.086000	0.62901	0.513000	0.50165	GTG	.	.		0.398	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		T	76776919	C	T	76776919	3	4	209	1	0	0	0	0	1	0	0	0	1208	565	20	3	457	3	ATRX	23	76776919	Missense_Mutation	SNP	C	TCGA-DD-AAE3-01A-11D-A40R-10	6424671	76776919	78493641	162	30307										
FMR1	2332	hgsc.bcm.edu	37	chrX	147011692	147011692	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0569620253164557	9	1	1.50433010697911	1.62969094922737	1.41712256454554	1	1	0	gagcacatatgctgattgacAtgcactttcggagtctgcgc	11	10	1	2			TCGA-DD-AAE3-01A-11D-A40R-10	TCGA-DD-AAE3-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	56734b6f-386f-4da6-b5de-8321f1231570	a236100b-e8a3-4ffa-99db-6332dada6d98	g.chrX:147011692A>T	ENST00000370475.4	+	7	687	c.559A>T	c.(559-561)Atg>Ttg	p.M187L	FMR1_ENST00000334557.6_Missense_Mutation_p.M187L|FMR1_ENST00000218200.8_Missense_Mutation_p.M187L|FMR1_ENST00000440235.2_5'Flank|FMR1_ENST00000439526.2_Missense_Mutation_p.M187L|FMR1_ENST00000370471.3_Missense_Mutation_p.M187L|FMR1_ENST00000370470.1_Missense_Mutation_p.M187L|FMR1_ENST00000370477.1_Missense_Mutation_p.M187L	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	187					central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					GCTGATTGACATGCACTTTCG	0.398									Fragile X syndrome																												p.M187L		Atlas-SNP	.											.	FMR1	93	.	0			c.A559T						.						145	120	128					X																	147011692		2203	4300	6503	SO:0001583	missense	2332	exon7	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	ATTGACATGCACT	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"premature ovarian failure 1"	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.559A>T	chrX.hg19:g.147011692A>T	ENSP00000359506:p.Met187Leu	90.0	0.0		51.0	19.0	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Missense_Mutation	SNP	ENST00000370475.4	hg19	CCDS14682.1	.	.	.	.	.	.	.	.	.	.	A	16.51	3.142381	0.57044	.	.	ENSG00000102081	ENST00000218200;ENST00000370471;ENST00000370477;ENST00000370475;ENST00000334557;ENST00000439526;ENST00000370470	T;T;T;T;T;T;T	0.57752	1.12;0.38;1.16;1.13;1.46;1.16;1.18	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.69611	0.3130	M	0.80982	2.52	0.80722	D	1	B;B;B;D;P	0.58620	0.009;0.131;0.131;0.983;0.858	B;B;B;P;P	0.59357	0.026;0.106;0.121;0.841;0.856	T	0.73480	-0.3969	10	0.52906	T	0.07	-32.1723	13.4918	0.61399	1.0:0.0:0.0:0.0	.	187;187;103;187;187	Q8IXW7;Q06787;Q59GC1;Q06787-8;G3V0J0	.;FMR1_HUMAN;.;.;.	L	187	ENSP00000218200:M187L;ENSP00000359502:M187L;ENSP00000359508:M187L;ENSP00000359506:M187L;ENSP00000355115:M187L;ENSP00000395923:M187L;ENSP00000359501:M187L	ENSP00000218200:M187L	M	+	1	0	FMR1	146819384	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.162000	0.94745	1.850000	0.53721	0.486000	0.48141	ATG	.	.		0.398	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		T	147011692	A	T	147011692	3	4	209	1	0	0	0	0	1	0	0	0	5968	217	8	4	585	4	FMR1	23	147011692	Missense_Mutation	SNP	A	TCGA-DD-AAE3-01A-11D-A40R-10	70234773	147011692	8258868	163	30308										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7725035	7725036	+	Frame_Shift_Del	DEL	GC	GC	-													0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tctcacagtcagaggacgggGcgcgggcccccttcacccag							TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr1:7725035_7725036delGC	ENST00000303635.7	+	9	2635_2636	c.2428_2429delGC	c.(2428-2430)gcgfs	p.A810fs	CAMTA1_ENST00000439411.2_Frame_Shift_Del_p.A810fs	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	810					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A810V(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		AGAGGACGGGGCGCGGGCCCCC	0.678			T	WWTR1	epitheliod hemangioendothelioma																																p.809_810del		Atlas-INDEL	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	1	Substitution - Missense(1)	endometrium(1)	c.2427_2428del						.																																			SO:0001589	frameshift_variant	23261	exon9			.	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.2428_2429delGC	chr1.hg19:g.7725037_7725038delGC	ENSP00000306522:p.Ala810fs	104.0	0.0		149.0	48.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Frame_Shift_Del	DEL	ENST00000303635.7	hg19	CCDS30576.1																																																																																			.	.		0.678	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		-	7725036	GC	-	7725035	7	5	210	1	0	1	0	1	0	0	0	0	2615	1203	42	0	2462	0	CAMTA1	1	7725035	Frame_Shift_Del	DEL	GC	TCGA-DD-AAE4-01A-11D-A40R-10		7725035	241525586	1	30309										
FBXO42	54455	hgsc.bcm.edu	37	chr1	16579610	16579610	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	cagcattgggaccgccacacCctccgaggattaagatagtt	10	12	0	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr1:16579610C>T	ENST00000375592.3	-	8	1118	c.902G>A	c.(901-903)gGg>gAg	p.G301E		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	301										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		ACCGCCACACCCTCCGAGGAT	0.438																																					p.G301E		Atlas-SNP	.											.	FBXO42	53	.	0			c.G902A						.						66	59	61					1																	16579610		2203	4300	6503	SO:0001583	missense	54455	exon8			CCACACCCTCCGA	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"F-boxes /  "other""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.902G>A	chr1.hg19:g.16579610C>T	ENSP00000364742:p.Gly301Glu	173.0	0.0		316.0	16.0	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Missense_Mutation	SNP	ENST00000375592.3	hg19	CCDS30613.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.762432	0.89932	.	.	ENSG00000037637	ENST00000375592;ENST00000456164;ENST00000444116	D;D;D	0.95821	-3.46;-3.82;-3.82	5.86	5.86	0.93980	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.97620	0.9220	M	0.74467	2.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97574	1.0106	10	0.56958	D	0.05	-12.7863	19.1901	0.93663	0.0:1.0:0.0:0.0	.	301	Q6P3S6	FBX42_HUMAN	E	301;19;19	ENSP00000364742:G301E;ENSP00000415663:G19E;ENSP00000412416:G19E	ENSP00000364742:G301E	G	-	2	0	FBXO42	16452197	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.456000	0.73501	2.776000	0.95493	0.655000	0.94253	GGG	.	.		0.438	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			T	16579610	C	T	16579610	3	4	210	1	0	0	0	0	1	0	0	0	5759	623	22	3	1263	3	FBXO42	1	16579610	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	8854575	16579610	232671011	2	30310										
AKR7A3	22977	hgsc.bcm.edu	37	chr1	19612450	19612450	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gatctcggccacttcccaggCtgcatagttggagaggccaa	12	12	1	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr1:19612450C>A	ENST00000361640.4	-	3	979	c.439G>T	c.(439-441)Gcc>Tcc	p.A147S		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	147					cellular aldehyde metabolic process (GO:0006081)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)	13		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ACTTCCCAGGCTGCATAGTTG	0.607																																					p.A147S		Atlas-SNP	.											.	AKR7A3	30	.	0			c.G439T						.						71	66	67					1																	19612450		2199	4300	6499	SO:0001583	missense	22977	exon3			CCCAGGCTGCATA	AF040639	CCDS193.1	1p36.13	2008-05-14			ENSG00000162482	ENSG00000162482		"Aldo-keto reductases"	390	protein-coding gene	gene with protein product		608477				10383892	Standard	NM_012067		Approved		uc001bbv.1	O95154	OTTHUMG00000002523	ENST00000361640.4:c.439G>T	chr1.hg19:g.19612450C>A	ENSP00000355377:p.Ala147Ser	135.0	0.0		180.0	68.0	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Missense_Mutation	SNP	ENST00000361640.4	hg19	CCDS193.1	.	.	.	.	.	.	.	.	.	.	.	2.427	-0.331643	0.05314	.	.	ENSG00000162482	ENST00000361640	T	0.04970	3.52	3.04	-6.08	0.02151	NADP-dependent oxidoreductase domain (3);	0.311843	0.35096	N	0.003451	T	0.05547	0.0146	L	0.38175	1.15	0.27070	N	0.963339	B	0.18013	0.025	B	0.38655	0.278	T	0.39210	-0.9625	10	0.25751	T	0.34	.	6.815	0.23824	0.5751:0.3173:0.0:0.1076	.	147	O95154	ARK73_HUMAN	S	147	ENSP00000355377:A147S	ENSP00000355377:A147S	A	-	1	0	AKR7A3	19485037	0.001000	0.12720	0.350000	0.25708	0.116000	0.19942	-0.119000	0.10676	-1.111000	0.02988	-1.031000	0.02408	GCC	.	.		0.607	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067		A	19612450	C	A	19612450	3	1	210	1	0	0	0	0	1	0	0	0	476	797	28	3	576	3	AKR7A3	1	19612450	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	3032840	19612450	229638171	3	30311										
AHDC1	27245	hgsc.bcm.edu	37	chr1	27878204	27878206	+	In_Frame_Del	DEL	ACT	ACT	-													0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ccacagtccaggtgtacaccActgtgctgcaggtcctggga							TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	ACT	ACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr1:27878204_27878206delACT	ENST00000247087.5	-	5	1017_1019	c.421_423delAGT	c.(421-423)agtdel	p.S141del	AHDC1_ENST00000374011.2_In_Frame_Del_p.S141del			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	141	Pro-rich.						DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GGTGTACACCACTGTGCTGCAGG	0.635																																					p.141_142del		Atlas-INDEL	.											.	AHDC1	98	.	0			c.422_424del						.																																			SO:0001651	inframe_deletion	27245	exon6			.	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.421_423delAGT	chr1.hg19:g.27878204_27878206delACT	ENSP00000247087:p.Ser141del	123.0	0.0		173.0	48.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	In_Frame_Del	DEL	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.		0.635	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			-	27878206	ACT	-	27878204	7	5	210	1	0	1	0	1	0	0	0	0	412	156	6	0	4392	0	AHDC1	1	27878204	In_Frame_Del	DEL	ACT	TCGA-DD-AAE4-01A-11D-A40R-10	8265754	27878204	221372417	4	30312										
CHRNB2	1141	hgsc.bcm.edu	37	chr1	154548297	154548297	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	cgcctcttcctctggatcttTgtctttgtctgtgtctttgg	9	11	6	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr1:154548297T>C	ENST00000368476.3	+	6	1662	c.1398T>C	c.(1396-1398)ttT>ttC	p.F466F		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	466					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	TCTGGATCTTTGTCTTTGTCT	0.567																																					p.F466F		Atlas-SNP	.											.	CHRNB2	74	.	0			c.T1398C						.						337	243	275					1																	154548297		2203	4300	6503	SO:0001819	synonymous_variant	1141	exon6			GATCTTTGTCTTT	U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1962	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 2 (neuronal)"	118507	"cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.1398T>C	chr1.hg19:g.154548297T>C		61.0	0.0		120.0	33.0	NM_000748	Q9UEH9	Silent	SNP	ENST00000368476.3	hg19	CCDS1070.1																																																																																			.	.		0.567	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748		C	154548297	T	C	154548297	2	2	210	1	0	0	0	0	0	0	0	1	3393	1809	63	2		2	CHRNB2	1	154548297	Silent	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10	126670093	154548297	94702324	5	30313										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179504037	179504037	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gagaagtaaaagaagaagaaGaacaacaagaagaagaagaa	11	2	0	9	rs200097954|rs368406759|rs6425573	byFrequency	TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr1:179504037G>C	ENST00000367618.3	+	25	3358	c.2971G>C	c.(2971-2973)Gaa>Caa	p.E991Q		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	991	Glu-rich.		E -> Q (in dbSNP:rs6425573).					p.E991_Q992delEQ(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agaagaagaagaacaacaaga	0.318													G|||	14	0.00279553	0	0.0058	5008	,	,		17137	0.002		0.004	False		,,,				2504	0.0041				p.E991Q		Atlas-SNP	.											.	AXDND1	142	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2971C						.						49	51	50					1																	179504037		2152	4286	6438	SO:0001583	missense	126859	exon25			GAAGAAGAACAAC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2971G>C	chr1.hg19:g.179504037G>C	ENSP00000356590:p.Glu991Gln	332.0	0.0		583.0	31.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	G	9.300	1.052898	0.19907	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.19105	2.17;2.17	4.89	-6.02	0.02192	.	0.508747	0.16499	N	0.211773	T	0.08980	0.0222	N	0.24115	0.695	0.09310	N	1	B;B	0.24186	0.099;0.099	B;B	0.10450	0.003;0.005	T	0.15838	-1.0423	10	0.28530	T	0.3	-2.8152	6.1976	0.20557	0.4456:0.3814:0.173:0.0	rs6425573	875;991	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	Q	991;875;851	ENSP00000356590:E991Q;ENSP00000391716:E851Q	ENSP00000353471:E875Q	E	+	1	0	AXDND1	177770660	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.365000	0.20348	-1.164000	0.02790	-1.047000	0.02352	GAA	.	G|1.000;|0.000		0.318	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179504037	G	C	179504037	3	2	210	1	0	0	0	0	1	0	0	0	1995	943	33	4	3065	4	C1orf125	1	179504037	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	24955740	179504037	69746584	6	30314										
FMN2	56776	hgsc.bcm.edu	37	chr1	240371477	240371477	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	agcgggcataccccctcctcCccctctacccggagcgggca	10	20	1	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr1:240371477C>T	ENST00000319653.9	+	5	3595	c.3365C>T	c.(3364-3366)cCc>cTc	p.P1122L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1122	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCCCCTCCTCCCCCTCTACCC	0.721																																					p.P1122L		Atlas-SNP	.											.	FMN2	451	.	0			c.C3365T						.						8	10	9					1																	240371477		2102	4124	6226	SO:0001583	missense	56776	exon5			CTCCTCCCCCTCT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3365C>T	chr1.hg19:g.240371477C>T	ENSP00000318884:p.Pro1122Leu	87.0	0.0		136.0	42.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	c	10.27	1.302837	0.23736	.	.	ENSG00000155816	ENST00000319653	T	0.65549	-0.16	3.11	2.17	0.27698	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (2);	0.226724	0.29987	U	0.010689	T	0.68256	0.2981	M	0.90369	3.11	0.80722	D	1	P	0.35714	0.517	B	0.40565	0.333	T	0.68224	-0.5465	9	.	.	.	.	9.1994	0.37249	0.0:0.8851:0.0:0.1149	.	1122	Q9NZ56	FMN2_HUMAN	L	1122	ENSP00000318884:P1122L	.	P	+	2	0	FMN2	238438100	0.882000	0.30256	0.003000	0.11579	0.007000	0.05969	4.731000	0.62022	0.639000	0.30564	0.484000	0.47621	CCC	.	.		0.721	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371477	C	T	240371477	3	4	210	1	0	0	0	0	1	0	0	0	5958	623	22	3	3383	3	FMN2	1	240371477	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	60867440	240371477	8879144	7	30315										
CHML	1122	hgsc.bcm.edu	37	chr1	241798135	241798135	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	cctgaaagcttggtattcatCaggatgttgttcatactcta	8	8	4	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr1:241798135C>T	ENST00000366553.1	-	1	1097	c.934G>A	c.(934-936)Gat>Aat	p.D312N	OPN3_ENST00000331838.5_Intron|OPN3_ENST00000366554.2_Intron|OPN3_ENST00000469376.1_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	312					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			TGGTATTCATCAGGATGTTGT	0.348																																					p.D312N		Atlas-SNP	.											.	CHML	82	.	0			c.G934A						.						97	97	97					1																	241798135		2203	4299	6502	SO:0001583	missense	1122	exon1			ATTCATCAGGATG	X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.934G>A	chr1.hg19:g.241798135C>T	ENSP00000355511:p.Asp312Asn	109.0	0.0		197.0	78.0	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	hg19	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.534808	0.27475	.	.	ENSG00000203668	ENST00000366553	D	0.84873	-1.91	4.96	4.05	0.47172	.	1.245710	0.05436	U	0.546919	T	0.81475	0.4830	.	.	.	0.38070	D	0.93635	B	0.06786	0.001	B	0.12156	0.007	T	0.65565	-0.6137	9	0.45353	T	0.12	-0.6382	11.5362	0.50639	0.0:0.9128:0.0:0.0872	.	312	P26374	RAE2_HUMAN	N	312	ENSP00000355511:D312N	ENSP00000355511:D312N	D	-	1	0	CHML	239864758	1.000000	0.71417	0.980000	0.43619	0.465000	0.32709	3.089000	0.50183	1.468000	0.48064	0.655000	0.94253	GAT	.	.		0.348	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821		T	241798135	C	T	241798135	3	4	210	1	0	0	0	0	1	0	0	0	3353	826	29	3	1040	3	CHML	1	241798135	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	1426658	241798135	7452486	8	30316										
PSME4	23198	hgsc.bcm.edu	37	chr2	54163923	54163923	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	cctcccattgtgggagatttTgcactgaaacccaaaggcca	9	12	0	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr2:54163923T>A	ENST00000404125.1	-	6	792	c.737A>T	c.(736-738)cAa>cTa	p.Q246L	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	246					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			TGGGAGATTTTGCACTGAAAC	0.368																																					p.Q246L		Atlas-SNP	.											.	PSME4	247	.	0			c.A737T						.						112	120	117					2																	54163923		2203	4300	6503	SO:0001583	missense	23198	exon6			AGATTTTGCACTG	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.737A>T	chr2.hg19:g.54163923T>A	ENSP00000384211:p.Gln246Leu	469.0	0.0		646.0	249.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	13.41	2.227961	0.39399	.	.	ENSG00000068878	ENST00000404125	T	0.23147	1.92	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.22859	0.0552	L	0.42245	1.32	0.80722	D	1	B	0.29115	0.233	B	0.22601	0.04	T	0.02736	-1.1117	10	0.34782	T	0.22	.	14.9019	0.70687	0.0:0.0:0.0:1.0	.	246	Q14997	PSME4_HUMAN	L	246	ENSP00000384211:Q246L	ENSP00000374643:Q246L	Q	-	2	0	PSME4	54017427	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	7.831000	0.86748	1.931000	0.55961	0.254000	0.18369	CAA	.	.		0.368	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		A	54163923	T	A	54163923	3	1	210	1	0	0	0	0	1	0	0	0	12721	1812	63	4	4958	4	PSME4	2	54163923	Missense_Mutation	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10		54163923	189035450	9	30317										
ARHGEF4	50649	hgsc.bcm.edu	37	chr2	131785570	131785570	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tgcgctgacgaagtggggagCgaggaggacctgtatgatga	18	6	0	3	rs372979735		TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr2:131785570C>T	ENST00000326016.5	+	5	999	c.480C>T	c.(478-480)agC>agT	p.S160S	ARHGEF4_ENST00000409303.1_Silent_p.S160S|ARHGEF4_ENST00000355771.3_Silent_p.S89S|ARHGEF4_ENST00000392953.3_Silent_p.S160S|ARHGEF4_ENST00000428230.2_Intron|ARHGEF4_ENST00000525839.1_Silent_p.S160S	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	160					apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.S160R(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		AAGTGGGGAGCGAGGAGGACC	0.632																																					p.S160S		Atlas-SNP	.											ARHGEF4,colon,carcinoma,0,2	ARHGEF4	89	.	1	Substitution - Missense(1)	ovary(1)	c.C480T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	48	43	45		480,480	-4.5	0.7	2		45	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ARHGEF4	NM_015320.2,NM_032995.1	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	160/691,160/671	131785570	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	50649	exon5			GGGGAGCGAGGAG	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	684	protein-coding gene	gene with protein product	"APC-stimulated guanine nucleotide exchange factor"	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.480C>T	chr2.hg19:g.131785570C>T		144.0	0.0		121.0	76.0	NM_032995	Q9HDC6|Q9UPP0	Silent	SNP	ENST00000326016.5	hg19	CCDS2165.1																																																																																			.	.		0.632	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			T	131785570	C	T	131785570	2	4	210	1	0	0	0	0	0	0	0	1	908	767	27	1		1	ARHGEF4	2	131785570	Silent	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	77621647	131785570	111413803	10	30318										
NCL	4691	hgsc.bcm.edu	37	chr2	232320222	232320222	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gacccccgaagccaccttcaCccttaggtttggcccagtcc	8	18	1	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr2:232320222C>A	ENST00000322723.4	-	13	2186	c.1946G>T	c.(1945-1947)gGt>gTt	p.G649V	SNORA75_ENST00000384158.1_RNA|SNORD20_ENST00000384550.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	649	Arg/Gly/Phe-rich.				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		GCCACCTTCACCCTTAGGTTT	0.577																																					p.G649V		Atlas-SNP	.											.	NCL	80	.	0			c.G1946T						.						206	218	214					2																	232320222		2203	4300	6503	SO:0001583	missense	4691	exon13			CCTTCACCCTTAG		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.1946G>T	chr2.hg19:g.232320222C>A	ENSP00000318195:p.Gly649Val	66.0	0.0		95.0	35.0	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	hg19	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.436245	0.62955	.	.	ENSG00000115053	ENST00000322723;ENST00000392033;ENST00000322732;ENST00000356936	T;T	0.74632	0.76;-0.86	5.91	4.02	0.46733	Nucleotide-binding, alpha-beta plait (1);	0.102981	0.64402	D	0.000003	T	0.74313	0.3700	M	0.75777	2.31	0.80722	D	1	P	0.34462	0.454	B	0.37780	0.258	T	0.77024	-0.2741	10	0.72032	D	0.01	-14.0143	10.6857	0.45841	0.0:0.7966:0.1322:0.0713	.	649	P19338	NUCL_HUMAN	V	649;541;421;274	ENSP00000318195:G649V;ENSP00000349410:G274V	ENSP00000318195:G649V	G	-	2	0	NCL	232028466	1.000000	0.71417	0.972000	0.41901	0.903000	0.53119	4.492000	0.60334	1.524000	0.49035	-0.151000	0.13558	GGT	.	.		0.577	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		A	232320222	C	A	232320222	3	1	210	1	0	0	0	0	1	0	0	0	10235	507	18	3	194	3	NCL	2	232320222	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	100534652	232320222	10879151	11	30319										
PDCD6IP	10015	hgsc.bcm.edu	37	chr3	33866810	33866811	+	Frame_Shift_Ins	INS	-	-	T													0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tggcacaggctcaagaagtaINSttttttttaaaagccacaag							TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr3:33866810_33866811insT	ENST00000307296.3	+	5	971_972	c.594_595insT	c.(595-597)tttfs	p.F199fs	PDCD6IP_ENST00000457054.2_Frame_Shift_Ins_p.F199fs			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	199	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.|Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						CTCAAGAAGTATTTTTTTTAAA	0.366																																					p.V198fs		Atlas-INDEL	.											.	PDCD6IP	62	.	0			c.594_595insT						.																																			SO:0001589	frameshift_variant	10015	exon5			.	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.602dupT	chr3.hg19:g.33866818_33866818dupT	ENSP00000307387:p.Phe199fs	107.0	0.0		174.0	11.0	NM_001256192	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Frame_Shift_Ins	INS	ENST00000307296.3	hg19	CCDS2660.1																																																																																			.	.		0.366	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			T	33866811	-	T	33866810	7	5	210	1	0	1	1	0	0	0	0	0	11633	436	16	0	612	0	PDCD6IP	3	33866810	Frame_Shift_Ins	INS	-	TCGA-DD-AAE4-01A-11D-A40R-10		33866810	164155620	12	30320										
SLC22A14	9389	hgsc.bcm.edu	37	chr3	38354541	38354541	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	atgaaagggaaggtgaaggaGgccaagcaggtgctgtgcta	17	5	0	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr3:38354541G>A	ENST00000273173.4	+	5	1087	c.996G>A	c.(994-996)gaG>gaA	p.E332E	SLC22A14_ENST00000448498.1_Silent_p.E332E	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	332					organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		AGGTGAAGGAGGCCAAGCAGG	0.582																																					p.E332E		Atlas-SNP	.											.	SLC22A14	64	.	0			c.G996A						.						70	66	68					3																	38354541		2203	4299	6502	SO:0001819	synonymous_variant	9389	exon5			GAAGGAGGCCAAG	AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"Solute carriers"	8495	protein-coding gene	gene with protein product		604048	"organic cationic transporter-like 4", "solute carrier family 22 (organic cation transporter), member 14"	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.996G>A	chr3.hg19:g.38354541G>A		94.0	0.0		163.0	60.0	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Silent	SNP	ENST00000273173.4	hg19	CCDS2677.1																																																																																			.	.		0.582	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803		A	38354541	G	A	38354541	2	1	210	1	0	0	0	0	0	0	0	1	14460	991	35	3		3	SLC22A14	3	38354541	Silent	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	4487731	38354541	159667889	13	30321										
CYP8B1	1582	hgsc.bcm.edu	37	chr3	42917206	42917206	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gggcacggtacccttgtccaGagggggctcccatggcctgc	15	14	0	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr3:42917206G>T	ENST00000316161.4	-	1	427	c.103C>A	c.(103-105)Ctg>Atg	p.L35M	CYP8B1_ENST00000437102.1_Missense_Mutation_p.L35M|RP11-141M3.5_ENST00000471537.1_RNA|KRBOX1_ENST00000426937.1_Intron	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	35					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		CCCTTGTCCAGAGGGGGCTCC	0.582																																					p.L35M		Atlas-SNP	.											CYP8B1,middle_lobe,carcinoma,0,1	CYP8B1	59	.	0			c.C103A						.						46	46	46					3																	42917206		2202	4300	6502	SO:0001583	missense	1582	exon1			TGTCCAGAGGGGG	AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"Cytochrome P450s"	2653	protein-coding gene	gene with protein product		602172	"cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.103C>A	chr3.hg19:g.42917206G>T	ENSP00000318867:p.Leu35Met	52.0	0.0		113.0	83.0	NM_004391	B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	hg19	CCDS2707.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.322754	0.60634	.	.	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.01335	5.0;5.0	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000003	T	0.08846	0.0219	M	0.85945	2.785	0.46654	D	0.999141	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.00050	-1.2196	10	0.87932	D	0	-15.5713	11.1275	0.48328	0.0891:0.0:0.9109:0.0	.	35;35	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	M	35	ENSP00000404499:L35M;ENSP00000318867:L35M	ENSP00000318867:L35M	L	-	1	2	CYP8B1	42892210	0.998000	0.40836	1.000000	0.80357	0.915000	0.54546	2.667000	0.46808	2.553000	0.86117	0.561000	0.74099	CTG	.	.		0.582	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391		T	42917206	G	T	42917206	3	4	210	1	0	0	0	0	1	0	0	0	4200	933	33	3	1406	3	CYP8B1	3	42917206	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	4562665	42917206	155105224	14	30322										
DHX30	22907	hgsc.bcm.edu	37	chr3	47882619	47882619	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ggaccatagatgttaccgacTtcttgtccatgacccagcag	9	12	1	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr3:47882619T>G	ENST00000445061.1	+	7	1026	c.619T>G	c.(619-621)Ttc>Gtc	p.F207V	DHX30_ENST00000348968.4_Missense_Mutation_p.F179V|DHX30_ENST00000457607.1_Missense_Mutation_p.F235V|DHX30_ENST00000446256.2_Missense_Mutation_p.F168V	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	207						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		TGTTACCGACTTCTTGTCCAT	0.587																																					p.F207V		Atlas-SNP	.											.	DHX30	101	.	0			c.T619G						.						57	58	58					3																	47882619		2203	4300	6503	SO:0001583	missense	22907	exon7			ACCGACTTCTTGT	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.619T>G	chr3.hg19:g.47882619T>G	ENSP00000405620:p.Phe207Val	95.0	0.0		173.0	67.0	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Missense_Mutation	SNP	ENST00000445061.1	hg19	CCDS2759.1	.	.	.	.	.	.	.	.	.	.	T	14.45	2.539589	0.45176	.	.	ENSG00000132153	ENST00000446256;ENST00000445061;ENST00000348968;ENST00000457607	T;T;T;T	0.03330	4.02;4.0;4.01;3.97	5.17	3.99	0.46301	.	0.256592	0.34088	N	0.004268	T	0.04003	0.0112	L	0.36672	1.1	0.33815	D	0.628325	B;B;B	0.12013	0.005;0.001;0.001	B;B;B	0.12156	0.007;0.003;0.003	T	0.12941	-1.0528	10	0.46703	T	0.11	.	10.1475	0.42774	0.0:0.0:0.168:0.832	.	207;168;235	Q7L2E3;Q7L2E3-3;Q7L2E3-2	DHX30_HUMAN;.;.	V	168;207;179;235	ENSP00000392601:F168V;ENSP00000405620:F207V;ENSP00000343442:F179V;ENSP00000394682:F235V	ENSP00000343442:F179V	F	+	1	0	DHX30	47857623	0.999000	0.42202	0.897000	0.35233	0.966000	0.64601	4.753000	0.62183	0.777000	0.33496	0.533000	0.62120	TTC	.	.		0.587	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		G	47882619	T	G	47882619	3	3	210	1	0	0	0	0	1	0	0	0	4506	1609	56	5	648	5	DHX30	3	47882619	Missense_Mutation	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10	4965413	47882619	150139811	15	30323										
STAB1	23166	hgsc.bcm.edu	37	chr3	52535661	52535661	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	cctctgcccccagctacgaaGtacagctggggggctctatg	12	14	2	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr3:52535661G>C	ENST00000321725.6	+	3	299	c.223G>C	c.(223-225)Gta>Cta	p.V75L		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	75					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CAGCTACGAAGTACAGCTGGG	0.657																																					p.V75L		Atlas-SNP	.											.	STAB1	178	.	0			c.G223C						.						13	15	14					3																	52535661		2174	4264	6438	SO:0001583	missense	23166	exon3			TACGAAGTACAGC	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.223G>C	chr3.hg19:g.52535661G>C	ENSP00000312946:p.Val75Leu	124.0	0.0		186.0	57.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	1.872	-0.459981	0.04508	.	.	ENSG00000010327	ENST00000321725	T	0.02787	4.16	4.72	1.69	0.24217	.	0.283555	0.27912	N	0.017360	T	0.01592	0.0051	N	0.13043	0.29	0.29746	N	0.836693	B;B	0.25169	0.084;0.119	B;B	0.24269	0.033;0.052	T	0.44406	-0.9330	10	0.13470	T	0.59	-6.2017	5.372	0.16144	0.0992:0.0:0.5353:0.3655	.	75;75	Q9NY15;Q9NY15-2	STAB1_HUMAN;.	L	75	ENSP00000312946:V75L	ENSP00000312946:V75L	V	+	1	0	STAB1	52510701	1.000000	0.71417	0.987000	0.45799	0.587000	0.36485	2.189000	0.42621	0.387000	0.25024	0.563000	0.77884	GTA	.	.		0.657	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		C	52535661	G	C	52535661	3	2	210	1	0	0	0	0	1	0	0	0	15252	1029	36	4	233	4	STAB1	3	52535661	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	4653042	52535661	145486769	16	30324										
HGFAC	3083	hgsc.bcm.edu	37	chr4	3446146	3446146	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gtgcttcgggggccggacctGgtgcgaaggcacccgacata	16	12	0	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr4:3446146G>A	ENST00000382774.3	+	6	822	c.707G>A	c.(706-708)tGg>tAg	p.W236*	HGFAC_ENST00000511533.1_Nonsense_Mutation_p.W236*	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	236	Fibronectin type-I. {ECO:0000255|PROSITE- ProRule:PRU00478}.				proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGCCGGACCTGGTGCGAAGGC	0.687																																					p.W236X		Atlas-SNP	.											.	HGFAC	69	.	0			c.G707A						.						10	12	12					4																	3446146		2171	4278	6449	SO:0001587	stop_gained	3083	exon6			GGACCTGGTGCGA	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.707G>A	chr4.hg19:g.3446146G>A	ENSP00000372224:p.Trp236*	150.0	0.0		215.0	75.0	NM_001528	Q14726|Q2M1W7|Q53X47	Nonsense_Mutation	SNP	ENST00000382774.3	hg19	CCDS3369.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476004	0.44044	.	.	ENSG00000109758	ENST00000382774;ENST00000511533	.	.	.	3.74	-4.02	0.04034	.	1.599760	0.03691	N	0.247004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	6.4023	0.21646	0.6164:0.1521:0.2316:0.0	.	.	.	.	X	236	.	ENSP00000372224:W236X	W	+	2	0	HGFAC	3415944	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.581000	0.05820	-0.599000	0.05798	-0.362000	0.07510	TGG	.	.		0.687	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			A	3446146	G	A	3446146	4	1	210	1	0	0	0	0	0	1	0	0	7095	1357	47	3	729	3	HGFAC	4	3446146	Nonsense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10		3446146	187708130	17	30325										
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15517558	15517559	+	Frame_Shift_Ins	INS	-	-	G													0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	aagatgaaggcctttacaccINSggggtaagaccagaggtggc					rs201439700|rs188018643	byFrequency	TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr4:15517558_15517559insG	ENST00000503292.1	+	11	1128_1129	c.948_949insG	c.(949-951)gggfs	p.G317fs	CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000389652.5_Frame_Shift_Ins_p.G268fs|CC2D2A_ENST00000413206.1_Frame_Shift_Ins_p.G317fs|CC2D2A_ENST00000424120.1_Frame_Shift_Ins_p.G317fs	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	317					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)		p.G268R(1)|p.T267T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						GCCTTTACACCGGGGTAAGACC	0.455																																					p.T316fs		Atlas-INDEL	.											CC2D2A,caecum,carcinoma,0,1	CC2D2A	158	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	c.948_949insG						.																																			SO:0001589	frameshift_variant	57545	exon11			.	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.952dupG	chr4.hg19:g.15517562_15517562dupG	ENSP00000421809:p.Gly317fs	106.0	0.0		146.0	53.0	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Frame_Shift_Ins	INS	ENST00000503292.1	hg19	CCDS47026.1																																																																																			.	.		0.455	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		G	15517559	-	G	15517558	7	5	210	1	0	1	1	0	0	0	0	0	2730	639	23	0	1185	0	CC2D2A	4	15517558	Frame_Shift_Ins	INS	-	TCGA-DD-AAE4-01A-11D-A40R-10	12071412	15517558	175636718	18	30326										
KIT	3815	hgsc.bcm.edu	37	chr4	55573355	55573355	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ttgattgttgaatatgaagcAttccccaaacctgaacacca	6	10	0	4			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr4:55573355A>T	ENST00000288135.5	+	6	1114	c.1017A>T	c.(1015-1017)gcA>gcT	p.A339A		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	339	Ig-like C2-type 4.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AATATGAAGCATTCCCCAAAC	0.343		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.A339A		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT	7396	.	0			c.A1017T						.						108	97	101					4																	55573355		2203	4300	6503	SO:0001819	synonymous_variant	3815	exon6	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	TGAAGCATTCCCC	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1017A>T	chr4.hg19:g.55573355A>T		237.0	0.0		347.0	141.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	hg19	CCDS3496.1																																																																																			.	.		0.343	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55573355	A	T	55573355	2	4	210	1	0	0	0	0	0	0	0	1	8338	204	8	4		4	KIT	4	55573355	Silent	SNP	A	TCGA-DD-AAE4-01A-11D-A40R-10	40055797	55573355	135580921	19	30327										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155411569	155411569	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gcgcgcacgcgacagacctcGgcgcccggctgggcgtcctc	15	18	0	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr4:155411569G>A	ENST00000339452.1	-	1	1299	c.939C>T	c.(937-939)gcC>gcT	p.A313A	DCHS2_ENST00000443500.1_Silent_p.A313A|DCHS2_ENST00000456341.2_Silent_p.A306A	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1495	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GACAGACCTCGGCGCCCGGCT	0.731																																					p.A313A		Atlas-SNP	.											.	DCHS2	594	.	0			c.C939T						.						3	5	5					4																	155411569		614	1444	2058	SO:0001819	synonymous_variant	54798	exon1			GACCTCGGCGCCC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.939C>T	chr4.hg19:g.155411569G>A		32.0	0.0		52.0	21.0	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000339452.1	hg19	CCDS47150.1																																																																																			.	.		0.731	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552		A	155411569	G	A	155411569	2	1	210	1	0	0	0	0	0	0	0	1	4290	1103	39	1		1	DCHS2	4	155411569	Silent	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	99838214	155411569	35742707	20	30328										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37224832	37224832	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tttgtacagtattctccagaGaataagcaatctgcacataa	6	8	2	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr5:37224832G>T	ENST00000508244.1	-	12	2395	c.2302C>A	c.(2302-2304)Ctc>Atc	p.L768I	C5orf42_ENST00000274258.7_5'UTR|C5orf42_ENST00000425232.2_Missense_Mutation_p.L768I			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	768						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			ATTCTCCAGAGAATAAGCAAT	0.328																																					p.L768I		Atlas-SNP	.											.	C5orf42	422	.	0			c.C2302A						.						155	127	135					5																	37224832		692	1591	2283	SO:0001583	missense	65250	exon13			TCCAGAGAATAAG		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.2302C>A	chr5.hg19:g.37224832G>T	ENSP00000421690:p.Leu768Ile	123.0	0.0		137.0	15.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	16.86	3.239270	0.58995	.	.	ENSG00000197603	ENST00000508244;ENST00000425232	T;T	0.27402	1.67;1.67	5.58	4.7	0.59300	.	0.103529	0.40818	U	0.001020	T	0.50137	0.1598	M	0.73598	2.24	0.80722	D	1	D	0.65815	0.995	P	0.60415	0.874	T	0.49844	-0.8896	10	0.36615	T	0.2	-4.0837	13.4237	0.61013	0.0:0.1575:0.8425:0.0	.	768	E9PH94	.	I	768	ENSP00000421690:L768I;ENSP00000389014:L768I	ENSP00000389014:L768I	L	-	1	0	C5orf42	37260589	0.998000	0.40836	0.944000	0.38274	0.755000	0.42902	2.966000	0.49208	1.314000	0.45095	0.650000	0.86243	CTC	.	.		0.328	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37224832	G	T	37224832	3	4	210	1	0	0	0	0	1	0	0	0	2303	942	33	3	7451	3	C5orf42	5	37224832	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10		37224832	143690428	21	30329										
RICTOR	253260	hgsc.bcm.edu	37	chr5	39074458	39074458	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tcggaggttcttcagagagcGgccgcggccgatcgccgcca	15	14	2	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr5:39074458G>A	ENST00000357387.3	-	1	52	c.22C>T	c.(22-24)Cgc>Tgc	p.R8C	RICTOR_ENST00000296782.5_Missense_Mutation_p.R8C	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					TTCAGAGAGCGGCCGCGGCCG	0.697																																					p.R8C		Atlas-SNP	.											.	RICTOR	182	.	0			c.C22T						.						15	15	15					5																	39074458		1972	3885	5857	SO:0001583	missense	253260	exon1			GAGAGCGGCCGCG		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.22C>T	chr5.hg19:g.39074458G>A	ENSP00000349959:p.Arg8Cys	105.0	0.0		165.0	62.0	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.552943	0.86127	.	.	ENSG00000164327	ENST00000357387;ENST00000296782;ENST00000514735	T;T	0.55413	0.52;0.53	4.06	3.19	0.36642	.	0.179846	0.49916	D	0.000137	T	0.39009	0.1062	L	0.34521	1.04	0.58432	D	0.999999	B;B;D;B	0.60160	0.0;0.059;0.987;0.003	B;B;B;B	0.40741	0.001;0.005;0.339;0.001	T	0.35674	-0.9779	10	0.87932	D	0	-6.553	9.9823	0.41821	0.0972:0.0:0.9028:0.0	.	8;8;8;8	Q8N6M7;E7ETT0;Q6R327;Q6R327-3	.;.;RICTR_HUMAN;.	C	8	ENSP00000349959:R8C;ENSP00000296782:R8C	ENSP00000296782:R8C	R	-	1	0	RICTOR	39110215	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.869000	0.75521	0.919000	0.36945	-0.214000	0.12660	CGC	.	.		0.697	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		A	39074458	G	A	39074458	3	1	210	1	0	0	0	0	1	0	0	0	13373	1116	39	1	5256	1	RICTOR	5	39074458	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	1849626	39074458	141840802	22	30330										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222700	140222700	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gcgaaggtgcgcgcagtggaCgccgactcgggctacaacgc	16	13	0	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr5:140222700C>T	ENST00000531613.1	+	1	1794	c.1794C>T	c.(1792-1794)gaC>gaT	p.D598D	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000378123.3_Silent_p.D598D|PCDHA5_ENST00000529859.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	598	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCAGTGGACGCCGACTCGG	0.687																																					p.D598D		Atlas-SNP	.											PCDHA8_ENST00000531613,NS,carcinoma,0,2	PCDHA8	366	.	0			c.C1794T						.						73	74	73					5																	140222700		2197	4265	6462	SO:0001819	synonymous_variant	56140	exon1			AGTGGACGCCGAC	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1794C>T	chr5.hg19:g.140222700C>T		84.0	0.0		137.0	48.0	NM_031856	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	hg19	CCDS54919.1																																																																																			.	.		0.687	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		T	140222700	C	T	140222700	2	4	210	1	0	0	0	0	0	0	0	1	11539	535	19	1		1	PCDHA8	5	140222700	Silent	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	101148242	140222700	40692560	23	30331										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141036195	141036195	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gccccacccgtgggctctcaCgtcggatacctgggcataga	12	15	1	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr5:141036195C>T	ENST00000239440.4	-	27	3730	c.3665G>A	c.(3664-3666)cGt>cAt	p.R1222H	ARAP3_ENST00000513878.1_Missense_Mutation_p.R884H|ARAP3_ENST00000508305.1_Missense_Mutation_p.R1053H|ARAP3_ENST00000512390.1_5'UTR	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1222					cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						TGGGCTCTCACGTCGGATACC	0.637																																					p.R1222H		Atlas-SNP	.											.	ARAP3	139	.	0			c.G3665A						.						25	25	25					5																	141036195		2203	4300	6503	SO:0001583	missense	64411	exon27			CTCTCACGTCGGA	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3665G>A	chr5.hg19:g.141036195C>T	ENSP00000239440:p.Arg1222His	114.0	0.0		209.0	67.0	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	hg19	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.433504	0.83776	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.12569	2.67;2.67;2.67	5.64	5.64	0.86602	.	0.051053	0.85682	D	0.000000	T	0.32224	0.0822	L	0.47716	1.5	0.53688	D	0.99997	D;D;D	0.89917	0.99;1.0;0.996	P;D;P	0.70716	0.513;0.97;0.65	T	0.00331	-1.1811	10	0.40728	T	0.16	.	19.2624	0.93973	0.0:1.0:0.0:0.0	.	884;1053;1222	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	H	1053;1222;884	ENSP00000421826:R1053H;ENSP00000239440:R1222H;ENSP00000421468:R884H	ENSP00000239440:R1222H	R	-	2	0	ARAP3	141016379	0.938000	0.31826	0.993000	0.49108	0.970000	0.65996	5.229000	0.65316	2.662000	0.90505	0.591000	0.81541	CGT	.	.		0.637	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		T	141036195	C	T	141036195	3	4	210	1	0	0	0	0	1	0	0	0	840	536	19	1	997	1	ARAP3	5	141036195	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	813495	141036195	39879065	24	30332										
OR10C1	442194	hgsc.bcm.edu	37	chr6	29408146	29408146	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tgcctcctggcagccatggcCtatgaccgctatgcagccat	10	15	0	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr6:29408146C>T	ENST00000444197.2	+	1	1064	c.354C>T	c.(352-354)gcC>gcT	p.A118A	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CAGCCATGGCCTATGACCGCT	0.622																																					p.A118A		Atlas-SNP	.											.	OR10C1	58	.	0			c.C354T						.						67	71	70					6																	29408146		1510	2708	4218	SO:0001819	synonymous_variant	442194	exon1			CATGGCCTATGAC		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"GPCR / Class A : Olfactory receptors"	8165	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily C, member 2", "olfactory receptor, family 10, subfamily C, member 1"	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.354C>T	chr6.hg19:g.29408146C>T		61.0	0.0		75.0	34.0	NM_013941	Q5SUN7|Q96R18	Silent	SNP	ENST00000444197.2	hg19	CCDS34364.1																																																																																			.	.		0.622	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			T	29408146	C	T	29408146	2	4	210	1	0	0	0	0	0	0	0	1	10907	668	24	3		3	OR10C1	6	29408146	Silent	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10		29408146	141706921	25	30333										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128388773	128388773	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tgtcacccacagtgaacgggGcaggctcaggtaggtttccc	13	12	2	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr6:128388773G>C	ENST00000368215.3	-	12	2047	c.2048C>G	c.(2047-2049)gCc>gGc	p.A683G	PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368210.3_Missense_Mutation_p.A683G|PTPRK_ENST00000368227.3_Missense_Mutation_p.A683G|PTPRK_ENST00000368226.4_Missense_Mutation_p.A683G|PTPRK_ENST00000532331.1_Missense_Mutation_p.A683G|PTPRK_ENST00000368213.5_Missense_Mutation_p.A683G|RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000368207.3_Missense_Mutation_p.A683G			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	683					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A683V(1)	PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		AGTGAACGGGGCAGGCTCAGG	0.537																																					p.A683G		Atlas-SNP	.											PTPRK,NS,neuroblastoma,0,1	PTPRK	330	.	1	Substitution - Missense(1)	autonomic_ganglia(1)	c.C2048G						.						105	102	103					6																	128388773		2203	4300	6503	SO:0001583	missense	5796	exon12			AACGGGGCAGGCT	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2048C>G	chr6.hg19:g.128388773G>C	ENSP00000357198:p.Ala683Gly	85.0	0.0		108.0	38.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	hg19		.	.	.	.	.	.	.	.	.	.	G	13.71	2.319089	0.41096	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000427676	T;T;T;T;T;T;T	0.08546	3.1;3.09;3.09;3.1;3.09;3.1;3.08	5.73	5.73	0.89815	.	0.249500	0.41938	D	0.000790	T	0.02494	0.0076	N	0.08118	0	0.37342	D	0.91041	B;B;B;B;B;B	0.32101	0.231;0.147;0.23;0.356;0.035;0.058	B;B;B;B;B;B	0.30943	0.039;0.045;0.098;0.122;0.018;0.04	T	0.54357	-0.8306	10	0.26408	T	0.33	.	19.9002	0.96983	0.0:0.0:1.0:0.0	.	683;683;683;540;683;683	B4DHC3;B7ZMG0;Q15262-3;F5GWP2;Q15262;Q15262-2	.;.;.;.;PTPRK_HUMAN;.	G	683;683;683;683;683;683;683;540	ENSP00000357209:A683G;ENSP00000357210:A683G;ENSP00000432973:A683G;ENSP00000357196:A683G;ENSP00000357193:A683G;ENSP00000357198:A683G;ENSP00000357190:A683G	ENSP00000357190:A683G	A	-	2	0	PTPRK	128430466	0.038000	0.19896	1.000000	0.80357	0.902000	0.53008	1.492000	0.35594	2.709000	0.92574	0.655000	0.94253	GCC	.	.		0.537	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			C	128388773	G	C	128388773	3	2	210	1	0	0	0	0	1	0	0	0	12820	1203	42	4	2372	4	PTPRK	6	128388773	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	98980627	128388773	42726294	26	30334										
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	10	12	0	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000230354.6_Silent_p.Q60Q|TBP_ENST00000540980.1_Silent_p.Q40Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		54.0	0.0		67.0	5.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	210	1	0	0	0	0	0	0	0	1	15659	962	34	3		3	TBP	6	170871004	Silent	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	42482231	170871004	244063	27	30335										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77558460	77558460	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gggtactagttgcagctctcGctgttcaagttccagacagg	12	10	2	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr7:77558460G>T	ENST00000248550.7	+	11	1230	c.1154G>T	c.(1153-1155)cGc>cTc	p.R385L	PHTF2_ENST00000275575.7_Missense_Mutation_p.R347L|PHTF2_ENST00000416283.2_Missense_Mutation_p.R351L|PHTF2_ENST00000424760.1_Missense_Mutation_p.R347L|PHTF2_ENST00000307305.8_Missense_Mutation_p.R347L|PHTF2_ENST00000454592.1_3'UTR|PHTF2_ENST00000422959.2_Missense_Mutation_p.R351L			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						TGCAGCTCTCGCTGTTCAAGT	0.403																																					p.R351L		Atlas-SNP	.											.	PHTF2	104	.	0			c.G1052T						.						71	65	67					7																	77558460		1854	4092	5946	SO:0001583	missense	57157	exon10			GCTCTCGCTGTTC	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1154G>T	chr7.hg19:g.77558460G>T	ENSP00000248550:p.Arg385Leu	140.0	0.0		182.0	73.0	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	hg19		.	.	.	.	.	.	.	.	.	.	G	33	5.281965	0.95489	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000275575;ENST00000416283;ENST00000248550	.	.	.	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.73860	0.3641	L	0.36672	1.1	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.998;0.997;1.0	D;D;D;D;D;P;D	0.87578	0.998;0.998;0.998;0.996;0.985;0.885;0.984	T	0.71672	-0.4522	9	0.48119	T	0.1	-7.9149	20.6208	0.99490	0.0:0.0:1.0:0.0	.	189;347;210;351;385;347;347	Q8WVD6;Q8N3S3-4;Q8N5I6;Q8N3S3-2;Q8N3S3;Q8N3S3-3;B3KQZ2	.;.;.;.;PHTF2_HUMAN;.;.	L	351;351;347;347;347;351;385	.	ENSP00000248550:R385L	R	+	2	0	PHTF2	77396396	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.230000	0.95299	2.882000	0.98803	0.655000	0.94253	CGC	.	.		0.403	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		T	77558460	G	T	77558460	3	4	210	1	0	0	0	0	1	0	0	0	11872	1087	38	1	1144	1	PHTF2	7	77558460	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10		77558460	81580203	28	30336										
WDR60	55112	hgsc.bcm.edu	37	chr7	158734820	158734820	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	atctgggtcctgtcgccaaaCagcaggtctcccccaacagg	10	15	2	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr7:158734820C>T	ENST00000407559.3	+	24	3141	c.2983C>T	c.(2983-2985)Cag>Tag	p.Q995*		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	995					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		TGTCGCCAAACAGCAGGTCTC	0.602																																					p.Q995X		Atlas-SNP	.											.	WDR60	94	.	0			c.C2983T						.						47	47	47					7																	158734820		1949	4145	6094	SO:0001587	stop_gained	55112	exon24			GCCAAACAGCAGG		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"WD repeat domain containing"	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.2983C>T	chr7.hg19:g.158734820C>T	ENSP00000384290:p.Gln995*	34.0	0.0		25.0	17.0	NM_018051	Q9NW58	Nonsense_Mutation	SNP	ENST00000407559.3	hg19	CCDS47757.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.333871	0.41297	.	.	ENSG00000126870	ENST00000407559	.	.	.	5.71	5.71	0.89125	.	0.060489	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-19.591	14.4479	0.67364	0.0:0.8531:0.1469:0.0	.	.	.	.	X	995	.	ENSP00000384290:Q995X	Q	+	1	0	WDR60	158427581	0.999000	0.42202	0.035000	0.18076	0.006000	0.05464	4.334000	0.59291	2.688000	0.91661	0.655000	0.94253	CAG	.	.		0.602	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051		T	158734820	C	T	158734820	4	4	210	1	0	0	0	0	0	1	0	0	17326	479	17	3	3077	3	WDR60	7	158734820	Nonsense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	81176360	158734820	403843	29	30337										
ADAM7	8756	hgsc.bcm.edu	37	chr8	24339683	24339683	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	aaccttaaacatccatgtgaCgttggttggcattgaaatat	8	7	0	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr8:24339683C>T	ENST00000175238.6	+	9	817	c.734C>T	c.(733-735)aCg>aTg	p.T245M	RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000380789.1_Missense_Mutation_p.T245M|ADAM7_ENST00000520720.1_Missense_Mutation_p.T17M|RP11-624C23.1_ENST00000523578.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	245	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		ATCCATGTGACGTTGGTTGGC	0.299																																					p.T245M		Atlas-SNP	.											.	ADAM7	165	.	0			c.C734T						.						91	88	89					8																	24339683		2203	4299	6502	SO:0001583	missense	8756	exon9			ATGTGACGTTGGT	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"ADAM metallopeptidase domain containing"	214	protein-coding gene	gene with protein product		607310	"a disintegrin and metalloproteinase domain 7"				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.734C>T	chr8.hg19:g.24339683C>T	ENSP00000175238:p.Thr245Met	140.0	0.0		160.0	28.0	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	hg19	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	C	13.27	2.187701	0.38609	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.63744	-0.06;-0.06;-0.06	5.63	3.59	0.41128	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.237899	0.29737	N	0.011340	T	0.65790	0.2725	L	0.45744	1.44	0.24901	N	0.992106	D;D	0.69078	0.994;0.997	P;D	0.63033	0.88;0.91	T	0.55842	-0.8077	10	0.56958	D	0.05	.	5.6793	0.17765	0.0:0.732:0.0:0.268	.	17;245	E5RK87;Q9H2U9	.;ADAM7_HUMAN	M	245;245;17;60	ENSP00000175238:T245M;ENSP00000370166:T245M;ENSP00000430400:T17M	ENSP00000175238:T245M	T	+	2	0	ADAM7	24395573	0.982000	0.34865	0.965000	0.40720	0.287000	0.27160	0.969000	0.29370	1.381000	0.46364	0.655000	0.94253	ACG	.	.		0.299	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		T	24339683	C	T	24339683	3	4	210	1	0	0	0	0	1	0	0	0	251	536	19	1	768	1	ADAM7	8	24339683	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10		24339683	122024339	30	30338										
CPA6	57094	hgsc.bcm.edu	37	chr8	68536486	68536486	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ataaatcttatcactttatcActacaagataagaaaagaaa	3	6	3	3			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr8:68536486A>T	ENST00000297770.4	-	2	332	c.117T>A	c.(115-117)ggT>ggA	p.G39G	CPA6_ENST00000518549.1_Splice_Site_p.G39G|CPA6_ENST00000297769.4_5'UTR	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	39						proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			TCACTTTATCACTACAAGATA	0.299																																					p.G39G		Atlas-SNP	.											.	CPA6	69	.	0			c.T117A						.						127	113	118					8																	68536486		2202	4298	6500	SO:0001630	splice_region_variant	57094	exon2			TTTATCACTACAA	AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.117-1T>A	chr8.hg19:g.68536486A>T		81.0	0.0		105.0	34.0	NM_020361	Q8NEX8|Q8TDE8|Q9NRI9	Silent	SNP	ENST00000297770.4	hg19	CCDS6200.1																																																																																			.	.		0.299	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361	Silent	T	68536486	A	T	68536486	5	4	210	1	0	0	0	0	0	0	1	0	3796	173	6	4	1236	4	CPA6	8	68536486	Splice_Site	SNP	A	TCGA-DD-AAE4-01A-11D-A40R-10	44196803	68536486	77827536	31	30339										
C8orf85	441376	hgsc.bcm.edu	37	chr8	117954908	117954908	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	aaattacatcagactcccaaAgcccaaaagatgatgctgcg	7	11	1	3			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr8:117954908A>T	ENST00000378279.3	+	2	481	c.436A>T	c.(436-438)Agc>Tgc	p.S146C	AARD_ENST00000523536.1_3'UTR	NM_001025357.2	NP_001020528.1	Q4LEZ3	AARD_HUMAN	alanine and arginine rich domain containing protein	146					lung development (GO:0030324)												AGACTCCCAAAGCCCAAAAGA	0.488																																					p.S146C		Atlas-SNP	.											.	.	.	.	0			c.A436T						.						75	70	72					8																	117954908		2203	4300	6503	SO:0001583	missense	441376	exon2			TCCCAAAGCCCAA	AB181519, BC140924	CCDS34935.1	8q24.11	2012-04-19	2012-04-19	2012-04-19	ENSG00000205002	ENSG00000205002			33842	protein-coding gene	gene with protein product	"Alanine and arginine-rich domain-containing protein"		"chromosome 8 open reading frame 85"	C8orf85			Standard	NM_001025357		Approved	LOC441376	uc003yof.3	Q4LEZ3	OTTHUMG00000164961	ENST00000378279.3:c.436A>T	chr8.hg19:g.117954908A>T	ENSP00000367528:p.Ser146Cys	81.0	0.0		137.0	10.0	NM_001025357	A5PKU8	Missense_Mutation	SNP	ENST00000378279.3	hg19	CCDS34935.1	.	.	.	.	.	.	.	.	.	.	A	16.10	3.026479	0.54683	.	.	ENSG00000205002	ENST00000378279	T	0.32753	1.44	5.24	-0.325	0.12702	.	0.856276	0.09975	N	0.731820	T	0.35364	0.0929	L	0.32530	0.975	0.09310	N	1	D	0.76494	0.999	D	0.66847	0.947	T	0.19976	-1.0289	10	0.72032	D	0.01	0.0385	3.0078	0.06034	0.5125:0.0:0.1868:0.3007	.	146	Q4LEZ3	AARD_HUMAN	C	146	ENSP00000367528:S146C	ENSP00000367528:S146C	S	+	1	0	C8orf85	118024089	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.009000	0.12765	0.086000	0.17137	0.533000	0.62120	AGC	.	.		0.488	AARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381195.1	NM_001025357		T	117954908	A	T	117954908	3	4	210	1	0	0	0	0	1	0	0	0	2443	72	3	4	442	4	C8orf85	8	117954908	Missense_Mutation	SNP	A	TCGA-DD-AAE4-01A-11D-A40R-10	49418422	117954908	28409114	32	30340										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77362825	77362825	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tgtcaactccaattgaacttTtcagcctgtttgaaaaaaaa	5	8	2	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr9:77362825T>C	ENST00000360774.1	-	31	5300	c.5063A>G	c.(5062-5064)aAa>aGa	p.K1688R	TRPM6_ENST00000361255.3_Missense_Mutation_p.K1683R|TRPM6_ENST00000449912.2_Missense_Mutation_p.K1683R|TRPM6_ENST00000451710.3_Intron|TRPM6_ENST00000376864.4_Intron|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376872.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1688					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						AATTGAACTTTTCAGCCTGTT	0.294																																					p.K1688R		Atlas-SNP	.											.	TRPM6	377	.	0			c.A5063G						.						71	77	75					9																	77362825		2202	4294	6496	SO:0001583	missense	140803	exon31			GAACTTTTCAGCC	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.5063A>G	chr9.hg19:g.77362825T>C	ENSP00000354006:p.Lys1688Arg	39.0	0.0		76.0	30.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	T	3.226	-0.158409	0.06544	.	.	ENSG00000119121	ENST00000360774;ENST00000449912;ENST00000361255	T;T;T	0.51071	0.72;0.72;0.72	5.48	3.63	0.41609	.	.	.	.	.	T	0.26557	0.0649	N	0.24115	0.695	0.80722	D	1	B;B;B;B;B	0.21309	0.0;0.054;0.0;0.0;0.0	B;B;B;B;B	0.16722	0.0;0.016;0.0;0.001;0.001	T	0.09952	-1.0651	9	0.02654	T	1	.	8.3054	0.32038	0.0:0.7464:0.0:0.2536	.	521;639;1688;1683;1683	Q9BX84-6;Q9BX84-5;Q9BX84;Q9BX84-3;Q9BX84-2	.;.;TRPM6_HUMAN;.;.	R	1688;1683;1683	ENSP00000354006:K1688R;ENSP00000396672:K1683R;ENSP00000354962:K1683R	ENSP00000354006:K1688R	K	-	2	0	TRPM6	76552645	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	0.597000	0.24059	0.773000	0.33404	-0.462000	0.05337	AAA	.	.		0.294	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		C	77362825	T	C	77362825	3	2	210	1	0	0	0	0	1	0	0	0	16605	1841	64	2	1041	2	TRPM6	9	77362825	Missense_Mutation	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10		77362825	63850606	33	30341										
C10orf140	387640	hgsc.bcm.edu	37	chr10	21805720	21805720	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tggtggtggtggtggtggtgAtggtggtggtggtggtggtg	26	0	0	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr10:21805720A>G	ENST00000449193.2	-	4	3284	c.1032T>C	c.(1030-1032)caT>caC	p.H344H	SKIDA1_ENST00000487107.1_5'Flank|SKIDA1_ENST00000444772.3_Silent_p.H265H	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	263	Glu-rich.|Ser-rich.					nucleus (GO:0005634)											ggtggtggtgatggtggtggt	0.716																																					p.H344H		Atlas-SNP	.											.	.	.	.	0			c.T1032C						.						4	6	5					10																	21805720		1658	3602	5260	SO:0001819	synonymous_variant	387640	exon4			GTGGTGATGGTGG	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 140"	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.1032T>C	chr10.hg19:g.21805720A>G		28.0	0.0		62.0	5.0	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	ENST00000449193.2	hg19	CCDS44363.1																																																																																			.	.		0.716	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		G	21805720	A	G	21805720	2	3	210	1	0	0	0	0	0	0	0	1	1597	330	12	2		2	C10orf140	10	21805720	Silent	SNP	A	TCGA-DD-AAE4-01A-11D-A40R-10		21805720	113729027	34	30342										
GJD4	219770	hgsc.bcm.edu	37	chr10	35897262	35897262	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tgcacgcgccggaggggaggGggctggcagccccaggcgta	20	12	0	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr10:35897262G>C	ENST00000321660.1	+	2	979	c.821G>C	c.(820-822)gGg>gCg	p.G274A	RP11-425A6.5_ENST00000609313.1_RNA	NM_153368.2	NP_699199.2	Q96KN9	CXD4_HUMAN	gap junction protein, delta 4, 40.1kDa	274					cell communication (GO:0007154)|regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014717)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						GGAGGGGAGGGGGCTGGCAGC	0.706																																					p.G274A		Atlas-SNP	.											.	GJD4	38	.	0			c.G821C						.						10	10	10					10																	35897262		2116	4136	6252	SO:0001583	missense	219770	exon2			GGGAGGGGGCTGG	AJ414564	CCDS7191.1	10p11.22	2007-11-27			ENSG00000177291	ENSG00000177291		"Ion channels / Gap junction proteins (connexins)"	23296	protein-coding gene	gene with protein product	"connexin 40.1"	611922				12477932	Standard	NM_153368		Approved	CX40.1, FLJ90023	uc001iyy.1	Q96KN9	OTTHUMG00000017957	ENST00000321660.1:c.821G>C	chr10.hg19:g.35897262G>C	ENSP00000315070:p.Gly274Ala	49.0	0.0		56.0	19.0	NM_153368	Q8N2R7	Missense_Mutation	SNP	ENST00000321660.1	hg19	CCDS7191.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.724625	0.48833	.	.	ENSG00000177291	ENST00000321660	D	0.97710	-4.5	5.49	-2.53	0.06326	.	4.715010	0.00628	N	0.000470	D	0.91690	0.7373	L	0.27053	0.805	0.09310	N	1	B	0.29909	0.261	B	0.21546	0.035	D	0.87833	0.2646	10	0.07990	T	0.79	.	0.3734	0.00383	0.3311:0.1309:0.2708:0.2673	.	274	Q96KN9	CXD4_HUMAN	A	274	ENSP00000315070:G274A	ENSP00000315070:G274A	G	+	2	0	GJD4	35937268	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.267000	0.08619	-0.108000	0.12066	-0.192000	0.12808	GGG	.	.		0.706	GJD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047576.1	NM_153368		C	35897262	G	C	35897262	3	2	210	1	0	0	0	0	1	0	0	0	6427	1232	43	4	827	4	GJD4	10	35897262	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	14091542	35897262	99637485	35	30343										
A1CF	29974	hgsc.bcm.edu	37	chr10	52573658	52573658	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ttggggttttaatgtgacagGattcattggggtgagctcca	14	5	1	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr10:52573658G>A	ENST00000373993.1	-	8	1350	c.1306C>T	c.(1306-1308)Cct>Tct	p.P436S	A1CF_ENST00000493415.1_5'UTR|A1CF_ENST00000373997.3_Missense_Mutation_p.P428S|A1CF_ENST00000374001.2_Missense_Mutation_p.P428S|A1CF_ENST00000282641.2_Missense_Mutation_p.P436S|ASAH2B_ENST00000483649.1_Intron|A1CF_ENST00000373995.3_Missense_Mutation_p.P436S|A1CF_ENST00000395495.1_Missense_Mutation_p.P381S|A1CF_ENST00000395489.2_Missense_Mutation_p.P429S			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	436					cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.P428S(1)|p.P436S(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						AATGTGACAGGATTCATTGGG	0.438																																					p.P444S		Atlas-SNP	.											A1CF,NS,carcinoma,0,1	A1CF	190	.	2	Substitution - Missense(2)	lung(2)	c.C1330T						.						151	153	152					10																	52573658		2203	4300	6503	SO:0001583	missense	29974	exon12			TGACAGGATTCAT	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"RNA binding motif (RRM) containing"	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.1306C>T	chr10.hg19:g.52573658G>A	ENSP00000363105:p.Pro436Ser	117.0	0.0		154.0	52.0	NM_001198819	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	hg19	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	G	9.509	1.105132	0.20632	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489	T;T;T;T;T;T;T	0.14766	2.75;2.73;2.75;2.71;2.73;2.48;2.73	5.87	4.95	0.65309	.	0.266360	0.43260	D	0.000600	T	0.15609	0.0376	L	0.47190	1.495	0.32852	D	0.506769	B;B;B;B	0.31949	0.348;0.061;0.073;0.123	B;B;B;B	0.36244	0.22;0.045;0.053;0.062	T	0.12915	-1.0529	10	0.48119	T	0.1	-7.5986	11.6903	0.51512	0.0:0.0:0.6671:0.3329	.	429;436;428;436	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	S	428;436;428;436;436;381;411;429	ENSP00000363113:P428S;ENSP00000363105:P436S;ENSP00000363109:P428S;ENSP00000363107:P436S;ENSP00000282641:P436S;ENSP00000378873:P381S;ENSP00000378868:P429S	ENSP00000282641:P436S	P	-	1	0	A1CF	52243664	1.000000	0.71417	1.000000	0.80357	0.360000	0.29518	4.058000	0.57463	1.426000	0.47256	0.655000	0.94253	CCT	.	.		0.438	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576		A	52573658	G	A	52573658	3	1	210	1	0	0	0	0	1	0	0	0	2	1174	41	3	494	3	A1CF	10	52573658	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	16676396	52573658	82961089	36	30344										
PRDX3	10935	hgsc.bcm.edu	37	chr10	120938299	120938299	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	caaccgtcctacagcagccgCcatcttcagtgcactcgggc	9	17	2	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr10:120938299C>G	ENST00000298510.2	-	1	46	c.4G>C	c.(4-6)Gcg>Ccg	p.A2P	PRDX3_ENST00000356951.3_Missense_Mutation_p.A2P	NM_006793.2	NP_006784.1	P30048	PRDX3_HUMAN	peroxiredoxin 3	2					cellular response to oxidative stress (GO:0034599)|cellular response to reactive oxygen species (GO:0034614)|hydrogen peroxide catabolic process (GO:0042744)|maternal placenta development (GO:0001893)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of kinase activity (GO:0033673)|peptidyl-cysteine oxidation (GO:0018171)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of mitochondrial membrane potential (GO:0051881)|response to hydrogen peroxide (GO:0042542)|response to lipopolysaccharide (GO:0032496)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	alkyl hydroperoxide reductase activity (GO:0008785)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|kinase binding (GO:0019900)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|thioredoxin peroxidase activity (GO:0008379)			endometrium(1)|lung(2)	3		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0245)		ACAGCAGCCGCCATCTTCAGT	0.721																																					p.A2P	Pancreas(36;562 1096 2447 42526)	Atlas-SNP	.											.	PRDX3	15	.	0			c.G4C						.						13	9	10					10																	120938299		2070	4069	6139	SO:0001583	missense	10935	exon1			CAGCCGCCATCTT	D49396	CCDS7611.1	10q25-q26	2010-11-24			ENSG00000165672	ENSG00000165672			9354	protein-coding gene	gene with protein product		604769	"antioxidant protein 1"	AOP1		7733872, 9363753	Standard	NM_006793		Approved	MER5, AOP-1, SP-22	uc001lec.3	P30048	OTTHUMG00000019146	ENST00000298510.2:c.4G>C	chr10.hg19:g.120938299C>G	ENSP00000298510:p.Ala2Pro	117.0	0.0		162.0	60.0	NM_006793	B2R7Z0|D3DRC9|E9PH29|P35690|Q0D2H1|Q13776|Q5T5V2|Q96HK4	Missense_Mutation	SNP	ENST00000298510.2	hg19	CCDS7611.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.586234	0.86851	.	.	ENSG00000165672	ENST00000356951;ENST00000298510	T;T	0.18502	2.21;2.41	5.16	5.16	0.70880	.	0.268030	0.40222	N	0.001154	T	0.16811	0.0404	N	0.08118	0	0.58432	D	0.999998	P	0.48016	0.904	P	0.51866	0.682	T	0.08269	-1.0730	10	0.87932	D	0	-19.1078	15.4979	0.75669	0.0:1.0:0.0:0.0	.	2	P30048	PRDX3_HUMAN	P	2	ENSP00000349432:A2P;ENSP00000298510:A2P	ENSP00000298510:A2P	A	-	1	0	PRDX3	120928289	1.000000	0.71417	1.000000	0.80357	0.262000	0.26303	4.468000	0.60162	2.676000	0.91093	0.655000	0.94253	GCG	.	.		0.721	PRDX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050639.1	NM_006793		G	120938299	C	G	120938299	3	3	210	1	0	0	0	0	1	0	0	0	12478	739	26	4	794	4	PRDX3	10	120938299	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	68364641	120938299	14596448	37	30345										
GPR123	84435	hgsc.bcm.edu	37	chr10	134941950	134941950	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	cagctgcggcgccacccaggGcgcaggtacgagctgcgcac	15	16	0	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr10:134941950G>A	ENST00000392607.3	+	7	1054	c.618G>A	c.(616-618)ggG>ggA	p.G206G	GPR123_ENST00000607359.1_Silent_p.G925G|GPR123_ENST00000392606.2_Silent_p.G109G	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	206					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		GCCACCCAGGGCGCAGGTACG	0.716																																					p.G206G		Atlas-SNP	.											.	GPR123	118	.	0			c.G618A						.						11	11	11					10																	134941950		2167	4247	6414	SO:0001819	synonymous_variant	84435	exon7			CCCAGGGCGCAGG	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"-", "GPCR / Class B : Orphans"	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.618G>A	chr10.hg19:g.134941950G>A		70.0	0.0		113.0	47.0	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	hg19	CCDS41580.1																																																																																			.	.		0.716	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2			A	134941950	G	A	134941950	2	1	210	1	0	0	0	0	0	0	0	1	6645	1190	42	3		3	GPR123	10	134941950	Silent	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	14003651	134941950	592797	38	30346										
ACP2	53	hgsc.bcm.edu	37	chr11	47267056	47267056	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	aactctcattctgatactctGgtgtctgccgggtctcgttc	9	12	5	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr11:47267056G>C	ENST00000256997.3	-	5	634	c.518C>G	c.(517-519)cCa>cGa	p.P173R	ACP2_ENST00000533929.1_Missense_Mutation_p.P145R|ACP2_ENST00000529444.1_Intron|ACP2_ENST00000530453.1_Intron|ACP2_ENST00000537863.1_Intron|ACP2_ENST00000525230.1_5'Flank|ACP2_ENST00000527256.1_Missense_Mutation_p.P141R	NM_001610.2	NP_001601.1	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal	173					dephosphorylation (GO:0016311)|lysosome organization (GO:0007040)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)	acid phosphatase activity (GO:0003993)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)	10						CTGATACTCTGGTGTCTGCCG	0.587																																					p.P173R	Melanoma(90;262 1440 11488 44828 48531)	Atlas-SNP	.											.	ACP2	36	.	0			c.C518G						.						114	100	105					11																	47267056		2201	4298	6499	SO:0001583	missense	53	exon5			TACTCTGGTGTCT	X15525	CCDS7928.1, CCDS44583.1	11p11.2	2008-02-05			ENSG00000134575	ENSG00000134575	3.1.3.2		123	protein-coding gene	gene with protein product		171650				975882	Standard	NM_001610		Approved		uc001nei.3	P11117	OTTHUMG00000166949	ENST00000256997.3:c.518C>G	chr11.hg19:g.47267056G>C	ENSP00000256997:p.Pro173Arg	100.0	0.0		162.0	33.0	NM_001610	E9PCI1|Q561W5|Q9BTU7	Missense_Mutation	SNP	ENST00000256997.3	hg19	CCDS7928.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.123555	0.37436	.	.	ENSG00000134575	ENST00000256997;ENST00000527256;ENST00000540414;ENST00000533929	T;T;T	0.46063	0.88;0.88;0.88	5.16	5.16	0.70880	.	0.397062	0.29080	N	0.013205	T	0.50240	0.1604	M	0.82517	2.595	0.80722	D	1	P;B;B	0.35155	0.487;0.427;0.208	B;B;B	0.35770	0.181;0.21;0.195	T	0.52653	-0.8547	10	0.25751	T	0.34	.	18.6425	0.91400	0.0:0.0:1.0:0.0	.	141;145;173	B7Z7D2;E9PQY3;P11117	.;.;PPAL_HUMAN	R	173;141;163;145	ENSP00000256997:P173R;ENSP00000432205:P141R;ENSP00000432439:P145R	ENSP00000256997:P173R	P	-	2	0	ACP2	47223632	0.954000	0.32549	0.948000	0.38648	0.697000	0.40408	3.991000	0.56973	2.392000	0.81423	0.462000	0.41574	CCA	.	.		0.587	ACP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392022.2	NM_001610		C	47267056	G	C	47267056	3	2	210	1	0	0	0	0	1	0	0	0	163	1348	47	4	781	4	ACP2	11	47267056	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10		47267056	87739460	39	30347										
TMEM179B	374395	hgsc.bcm.edu	37	chr11	62554934	62554934	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	cctggctgcagcgcgtcgagCttgcgctctttgctgccgcc	13	16	1	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr11:62554934C>A	ENST00000333449.4	+	1	36	c.31C>A	c.(31-33)Ctt>Att	p.L11I	TMEM223_ENST00000527073.1_Intron|RP11-727F15.12_ENST00000601484.1_RNA|TMEM179B_ENST00000533861.1_Missense_Mutation_p.L11I	NM_199337.2	NP_955369.1	Q7Z7N9	T179B_HUMAN	transmembrane protein 179B	11						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|liver(1)|lung(1)	4						GCGCGTCGAGCTTGCGCTCTT	0.736											OREG0021030	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L11I		Atlas-SNP	.											.	TMEM179B	13	.	0			c.C31A						.						6	7	7					11																	62554934		2142	4204	6346	SO:0001583	missense	374395	exon1			GTCGAGCTTGCGC	BC051355	CCDS8036.1	11q12.3	2007-11-26			ENSG00000185475	ENSG00000185475			33744	protein-coding gene	gene with protein product							Standard	NM_199337		Approved		uc001nvd.4	Q7Z7N9	OTTHUMG00000167611	ENST00000333449.4:c.31C>A	chr11.hg19:g.62554934C>A	ENSP00000333697:p.Leu11Ile	14.0	0.0	1062	35.0	12.0	NM_199337		Missense_Mutation	SNP	ENST00000333449.4	hg19	CCDS8036.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752879	0.69648	.	.	ENSG00000185475	ENST00000533861;ENST00000333449	.	.	.	4.85	2.98	0.34508	.	0.000000	0.64402	D	0.000002	T	0.47210	0.1433	M	0.64997	1.995	0.34583	D	0.714624	P	0.36633	0.562	B	0.38500	0.275	T	0.55560	-0.8122	9	0.35671	T	0.21	.	7.3187	0.26515	0.0:0.8019:0.0:0.1981	.	11	Q7Z7N9	T179B_HUMAN	I	11	.	ENSP00000333697:L11I	L	+	1	0	TMEM179B	62311510	1.000000	0.71417	0.842000	0.33263	0.723000	0.41478	2.162000	0.42367	0.657000	0.30906	0.555000	0.69702	CTT	.	.		0.736	TMEM179B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395362.2	NM_199337		A	62554934	C	A	62554934	3	1	210	1	0	0	0	0	1	0	0	0	16112	797	28	3	33	3	TMEM179B	11	62554934	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	15287878	62554934	72451582	40	30348										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105842662	105842662	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	actcctgtaaaccttgccgtTttgaaactcagtgaggcagg	10	10	1	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr11:105842662T>A	ENST00000530497.1	+	14	2316	c.2316T>A	c.(2314-2316)gtT>gtA	p.V772V	GRIA4_ENST00000533094.1_Intron|GRIA4_ENST00000525187.1_Intron|GRIA4_ENST00000393127.2_Intron|RNU6-277P_ENST00000516272.1_RNA|GRIA4_ENST00000282499.5_Silent_p.V772V			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	772					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		ACCTTGCCGTTTTGAAACTCA	0.378																																					p.V772V		Atlas-SNP	.											.	GRIA4	380	.	0			c.T2316A						.						89	87	88					11																	105842662		2201	4299	6500	SO:0001819	synonymous_variant	2893	exon15			TGCCGTTTTGAAA	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.2316T>A	chr11.hg19:g.105842662T>A		143.0	0.0		205.0	78.0	NM_000829	Q86XE8	Silent	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	T	6.700	0.497864	0.12762	.	.	ENSG00000152578	ENST00000539249	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	T	0.75831	0.3903	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.78560	-0.2157	5	0.62326	D	0.03	.	15.7049	0.77569	0.0:0.0:0.0:1.0	.	.	.	.	I	116	.	ENSP00000440835:F116I	F	+	1	0	GRIA4	105347872	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.618000	0.46393	2.117000	0.64856	0.533000	0.62120	TTT	.	.		0.378	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			A	105842662	T	A	105842662	2	1	210	1	0	0	0	0	0	0	0	1	6779	1828	64	4		4	GRIA4	11	105842662	Silent	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10	43287728	105842662	29163854	41	30349										
ALX1	8092	hgsc.bcm.edu	37	chr12	85695157	85695157	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gcaaccaatggacatgcattTgaaacaaagccagagtttga	9	8	0	3			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr12:85695157T>C	ENST00000316824.3	+	4	1040	c.885T>C	c.(883-885)ttT>ttC	p.F295F		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	295					anterior/posterior pattern specification (GO:0009952)|brain development (GO:0007420)|cartilage condensation (GO:0001502)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|mesenchymal cell development (GO:0014031)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1)	26				GBM - Glioblastoma multiforme(134;0.134)		GACATGCATTTGAAACAAAGC	0.463																																					p.F295F		Atlas-SNP	.											.	ALX1	61	.	0			c.T885C						.						105	102	103					12																	85695157		2203	4300	6503	SO:0001819	synonymous_variant	8092	exon4			TGCATTTGAAACA	U31986	CCDS9028.1	12q21.31	2011-06-20	2007-07-26	2007-07-26		ENSG00000180318		"Homeoboxes / PRD class"	1494	protein-coding gene	gene with protein product		601527	"cartilage paired-class homeoprotein 1"	CART1		8756334, 7592751	Standard	NM_006982		Approved		uc001tae.4	Q15699	OTTHUMG00000169820	ENST00000316824.3:c.885T>C	chr12.hg19:g.85695157T>C		128.0	0.0		138.0	55.0	NM_006982	Q546C8|Q96FH4	Silent	SNP	ENST00000316824.3	hg19	CCDS9028.1																																																																																			.	.		0.463	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982		C	85695157	T	C	85695157	2	2	210	1	0	0	0	0	0	0	0	1	556	1809	63	2		2	ALX1	12	85695157	Silent	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10		85695157	48156738	42	30350										
ZNF140	7699	hgsc.bcm.edu	37	chr12	133682847	133682847	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	atccatacaaccaaaaccccGtatgaatgtaatgaatgtag	6	9	0	2	rs529439392		TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr12:133682847G>A	ENST00000355557.2	+	5	2267	c.984G>A	c.(982-984)ccG>ccA	p.P328P	ZNF140_ENST00000544426.1_Silent_p.P225P|ZNF140_ENST00000440550.2_3'UTR	NM_003440.2	NP_003431.2	P52738	ZN140_HUMAN	zinc finger protein 140	328					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.114)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CCAAAACCCCGTATGAATGTA	0.398													G|||	1	0.000199681	0	0	5008	,	,		22726	0		0	False		,,,				2504	0.001				p.P328P		Atlas-SNP	.											.	ZNF140	18	.	0			c.G984A						.						121	113	116					12																	133682847		2203	4300	6503	SO:0001819	synonymous_variant	7699	exon5			AACCCCGTATGAA	U09368	CCDS9282.1, CCDS73550.1	12q24.33	2013-01-08	2006-06-13		ENSG00000196387	ENSG00000196387		"Zinc fingers, C2H2-type", "-"	12925	protein-coding gene	gene with protein product		604082	"zinc finger protein 140 (clone pHZ-39)"			7557990	Standard	XR_245353		Approved	pHZ-39	uc001ulo.3	P52738	OTTHUMG00000167942	ENST00000355557.2:c.984G>A	chr12.hg19:g.133682847G>A		115.0	0.0		154.0	78.0	NM_003440	D3DXJ3|Q05CP6|Q8IV75	Silent	SNP	ENST00000355557.2	hg19	CCDS9282.1																																																																																			.	.		0.398	ZNF140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397169.1	NM_003440		A	133682847	G	A	133682847	2	1	210	1	0	0	0	0	0	0	0	1	17744	1132	40	1		1	ZNF140	12	133682847	Silent	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	47987690	133682847	169048	43	30351										
NBEA	26960	hgsc.bcm.edu	37	chr13	36242504	36242505	+	Splice_Site	DNP	GG	GG	TT													0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tttgttttaccttttctgaaGgccattctcctgagcagtga							TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr13:36242504_36242505GG>TT	ENST00000400445.3	+	57	9132_9133	c.8598_8599GG>TT	c.(8596-8601)cgGGcc>cgTTcc	p.A2867S	NBEA_ENST00000537702.1_Splice_Site_p.A660S|NBEA_ENST00000310336.4_Splice_Site_p.A2867S|NBEA_ENST00000379922.3_Splice_Site_p.A445S|NBEA_ENST00000540320.1_Splice_Site_p.A2867S|NBEA_ENST00000379939.2_Splice_Site_p.A2864S	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2867					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CTTTTCTGAAGGCCATTCTCCT	0.411																																					.|p.A2867S		Atlas-SNP	.											.	NBEA	340	.	0			c.8599-1G>T|c.G8599T						.																																			SO:0001630	splice_region_variant	26960	exon57			TCTGAAGGCCATT|CTGAAGGCCATTC	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	Exception_encountered	chr13.hg19:g.36242504_36242505delinsTT		82.0|83.0	0.0		68.0|67.0	35.0|34.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Splice_Site|Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.411	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	Missense_Mutation	TT	36242505	GG	TT	36242504	5	4	210	1	0	0	0	0	0	0	1	0	10196	1014	35	3	8824	3	NBEA	13	36242504	Splice_Site	DNP	GG	TCGA-DD-AAE4-01A-11D-A40R-10		36242504	78927374	44	30352										
SLC10A2	6555	hgsc.bcm.edu	37	chr13	103718590	103718590	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	attgtccacacagctgttcgGatcattcattgctgggtctg	10	10	3	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr13:103718590G>T	ENST00000245312.3	-	1	606	c.10C>A	c.(10-12)Ccg>Acg	p.P4T		NM_000452.2	NP_000443	Q12908	NTCP2_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 2	4					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	bile acid:sodium symporter activity (GO:0008508)			breast(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)				Aciclovir(DB00787)|Cyclosporine(DB00091)|Ursodeoxycholic acid(DB01586)|Valaciclovir(DB00577)	CAGCTGTTCGGATCATTCATT	0.512																																					p.P4T		Atlas-SNP	.											.	SLC10A2	67	.	0			c.C10A						.						101	97	98					13																	103718590		2203	4300	6503	SO:0001583	missense	6555	exon1			TGTTCGGATCATT	U10417	CCDS9506.1	13q33	2013-07-18	2013-07-18		ENSG00000125255	ENSG00000125255		"Solute carriers"	10906	protein-coding gene	gene with protein product		601295		ASBT, ISBT		8661017	Standard	NM_000452		Approved		uc001vpy.4	Q12908	OTTHUMG00000017313	ENST00000245312.3:c.10C>A	chr13.hg19:g.103718590G>T	ENSP00000245312:p.Pro4Thr	48.0	0.0		65.0	24.0	NM_000452	A1L4F4|Q13839	Missense_Mutation	SNP	ENST00000245312.3	hg19	CCDS9506.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.719938	0.00700	.	.	ENSG00000125255	ENST00000245312	T	0.07327	3.2	5.67	-5.84	0.02318	.	2.004560	0.01754	N	0.030138	T	0.03348	0.0097	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34279	-0.9835	10	0.22706	T	0.39	-25.5519	1.034	0.01544	0.3822:0.1138:0.284:0.2201	.	4	Q12908	NTCP2_HUMAN	T	4	ENSP00000245312:P4T	ENSP00000245312:P4T	P	-	1	0	SLC10A2	102516591	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.614000	0.24314	-1.386000	0.02098	-0.345000	0.07892	CCG	.	.		0.512	SLC10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045716.1			T	103718590	G	T	103718590	3	4	210	1	0	0	0	0	1	0	0	0	14389	1174	41	3	1060	3	SLC10A2	13	103718590	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	67476086	103718590	11451288	45	30353										
SEC23A	10484	hgsc.bcm.edu	37	chr14	39517887	39517887	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gggagaaagtttctgaaaatCtgaaggaacttgggtcatct	12	5	4	3			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr14:39517887C>T	ENST00000307712.6	-	15	2223	c.1706G>A	c.(1705-1707)aGa>aAa	p.R569K	SEC23A_ENST00000536508.1_Missense_Mutation_p.R443K|SEC23A_ENST00000537403.1_Missense_Mutation_p.R367K|SEC23A_ENST00000545328.2_Missense_Mutation_p.R540K	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	569					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		TTCTGAAAATCTGAAGGAACT	0.313																																					p.R569K		Atlas-SNP	.											.	SEC23A	73	.	0			c.G1706A						.						72	81	78					14																	39517887		2203	4300	6503	SO:0001583	missense	10484	exon15			GAAAATCTGAAGG	X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"Sec23 (S. cerevisiae) homolog A"			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.1706G>A	chr14.hg19:g.39517887C>T	ENSP00000306881:p.Arg569Lys	89.0	0.0		99.0	37.0	NM_006364	B2R5P4|B3KXI2|Q8NE16	Missense_Mutation	SNP	ENST00000307712.6	hg19	CCDS9668.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.849660	0.71603	.	.	ENSG00000100934	ENST00000537403;ENST00000307712;ENST00000536508;ENST00000545328	D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59	5.5	5.5	0.81552	Sec23/Sec24, helical domain (2);	0.048926	0.85682	D	0.000000	D	0.89539	0.6744	M	0.86097	2.795	0.58432	D	0.999999	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.12156	0.004;0.007;0.005	D	0.86481	0.1791	10	0.49607	T	0.09	-11.0348	12.7104	0.57086	0.0:0.9247:0.0:0.0753	.	540;443;569	F5H365;F5H6C4;Q15436	.;.;SC23A_HUMAN	K	367;569;443;540	ENSP00000444193:R367K;ENSP00000306881:R569K;ENSP00000437715:R443K;ENSP00000445393:R540K	ENSP00000306881:R569K	R	-	2	0	SEC23A	38587638	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.963000	0.63694	2.593000	0.87608	0.655000	0.94253	AGA	.	.		0.313	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2			T	39517887	C	T	39517887	3	4	210	1	0	0	0	0	1	0	0	0	14006	913	32	3	615	3	SEC23A	14	39517887	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10		39517887	67831653	46	30354										
MIA2	117153	hgsc.bcm.edu	37	chr14	39716435	39716435	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	catgtcccaccatcttcagcTgtgtctggagtcaaagaatg	9	11	4	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr14:39716435T>A	ENST00000280082.3	+	4	856	c.657T>A	c.(655-657)gcT>gcA	p.A219A	RP11-407N17.3_ENST00000553728.1_Silent_p.A219A|MIA2_ENST00000556784.1_Silent_p.A218A	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	219					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		CATCTTCAGCTGTGTCTGGAG	0.423																																					p.A219A		Atlas-SNP	.											.	MIA2	82	.	0			c.T657A						.						85	86	86					14																	39716435		2203	4300	6503	SO:0001819	synonymous_variant	117153	exon4			TTCAGCTGTGTCT	BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.657T>A	chr14.hg19:g.39716435T>A		171.0	0.0		258.0	107.0	NM_054024	A1L4H0|Q9H6C1	Silent	SNP	ENST00000280082.3	hg19	CCDS9672.1																																																																																			.	.		0.423	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024		A	39716435	T	A	39716435	2	1	210	1	0	0	0	0	0	0	0	1	9573	1567	55	4		4	MIA2	14	39716435	Silent	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10	198548	39716435	67633105	47	30355										
ZBTB25	7597	hgsc.bcm.edu	37	chr14	64954457	64954457	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gacaactgcaactgggggtgGtcaccctggacagcagctct	13	12	2	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr14:64954457G>A	ENST00000608382.1	-	3	683	c.492C>T	c.(490-492)gaC>gaT	p.D164D	ZBTB25_ENST00000555220.1_Intron|ZBTB25_ENST00000394715.1_Silent_p.D164D|ZBTB25_ENST00000555424.1_Intron	NM_006977.2	NP_008908.2	P24278	ZBT25_HUMAN	zinc finger and BTB domain containing 25	164					gene expression (GO:0010467)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(2)|skin(2)	10				all cancers(60;0.00865)|OV - Ovarian serous cystadenocarcinoma(108;0.0102)|BRCA - Breast invasive adenocarcinoma(234;0.0469)		ACTGGGGGTGGTCACCCTGGA	0.537																																					p.D164D		Atlas-SNP	.											.	ZBTB25	27	.	0			c.C492T						.						156	159	158					14																	64954457		2203	4300	6503	SO:0001819	synonymous_variant	7597	exon3			GGGGTGGTCACCC	X16576	CCDS9765.1	14q23-q24	2013-01-08	2005-05-22	2005-05-22	ENSG00000089775	ENSG00000089775		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13112	protein-coding gene	gene with protein product		194541	"zinc finger protein 46 (KUP)", "chromosome 14 open reading frame 51"	ZNF46, C14orf51			Standard	NM_006977		Approved	KUP	uc001xhf.3	P24278	OTTHUMG00000141310	ENST00000608382.1:c.492C>T	chr14.hg19:g.64954457G>A		121.0	0.0		156.0	26.0	NM_006977	B3KUX6|Q8IYH9	Silent	SNP	ENST00000608382.1	hg19	CCDS9765.1																																																																																			.	.		0.537	ZBTB25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280649.2	NM_006977		A	64954457	G	A	64954457	2	1	210	1	0	0	0	0	0	0	0	1	17547	1252	44	3		3	ZBTB25	14	64954457	Silent	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	25238022	64954457	42395083	48	30356										
DAPK2	23604	hgsc.bcm.edu	37	chr15	64204312	64204312	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	caaccctggacacaccttccAccgcctgcggacatactgct	7	18	0	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr15:64204312A>T	ENST00000457488.1	-	10	973	c.943T>A	c.(943-945)Tgg>Agg	p.W315R	DAPK2_ENST00000261891.3_Missense_Mutation_p.W315R	NM_014326.3	NP_055141.2	Q9UIK4	DAPK2_HUMAN	death-associated protein kinase 2	315	Calmodulin-binding.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	11				LUAD - Lung adenocarcinoma(2;0.215)		CACACCTTCCACCGCCTGCGG	0.617																																					p.W315R		Atlas-SNP	.											.	DAPK2	31	.	0			c.T943A						.						55	45	48					15																	64204312		2203	4300	6503	SO:0001583	missense	23604	exon10			CCTTCCACCGCCT	AB018001	CCDS10188.1	15q22.1	2008-07-18			ENSG00000035664	ENSG00000035664			2675	protein-coding gene	gene with protein product						10376525	Standard	XM_005254265		Approved	DRP-1, MGC119312	uc002amr.3	Q9UIK4	OTTHUMG00000132947	ENST00000457488.1:c.943T>A	chr15.hg19:g.64204312A>T	ENSP00000408277:p.Trp315Arg	79.0	0.0		134.0	45.0	NM_014326	E9JGM7|O75892|Q24JS1	Missense_Mutation	SNP	ENST00000457488.1	hg19	CCDS10188.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.186806	0.78789	.	.	ENSG00000035664	ENST00000261891;ENST00000457488	T;T	0.68025	-0.3;-0.3	5.15	5.15	0.70609	Protein kinase-like domain (1);	0.000000	0.56097	D	0.000034	T	0.79028	0.4377	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.81320	-0.0986	10	0.87932	D	0	.	12.3647	0.55222	1.0:0.0:0.0:0.0	.	315	Q9UIK4	DAPK2_HUMAN	R	315	ENSP00000261891:W315R;ENSP00000408277:W315R	ENSP00000261891:W315R	W	-	1	0	DAPK2	61991365	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	7.348000	0.79366	1.940000	0.56252	0.496000	0.49642	TGG	.	.		0.617	DAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256479.1	NM_014326		T	64204312	A	T	64204312	3	4	210	1	0	0	0	0	1	0	0	0	4238	159	6	4	181	4	DAPK2	15	64204312	Missense_Mutation	SNP	A	TCGA-DD-AAE4-01A-11D-A40R-10		64204312	38327080	49	30357										
ABCC6	368	hgsc.bcm.edu	37	chr16	16248764	16248764	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tgatcctggagcgcagtgtgTgcagccccacgtgggcaatg	15	11	0	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr16:16248764T>G	ENST00000205557.7	-	28	4036	c.4007A>C	c.(4006-4008)cAc>cCc	p.H1336P		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1336	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	GCGCAGTGTGTGCAGCCCCAC	0.682																																					p.H1336P		Atlas-SNP	.											.	ABCC6	110	.	0			c.A4007C						.						31	28	29					16																	16248764		2197	4299	6496	SO:0001583	missense	368	exon28			AGTGTGTGCAGCC	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.4007A>C	chr16.hg19:g.16248764T>G	ENSP00000205557:p.His1336Pro	99.0	0.0		189.0	53.0	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	hg19	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.272779	0.80580	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.93488	-3.23	4.8	4.8	0.61643	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.49305	U	0.000149	D	0.94268	0.8159	L	0.33624	1.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95046	0.8182	10	0.87932	D	0	.	14.0557	0.64767	0.0:0.0:0.0:1.0	.	1336;1336	O95255;A8Y988	MRP6_HUMAN;.	P	1336;274	ENSP00000205557:H1336P	ENSP00000205557:H1336P	H	-	2	0	ABCC6	16156265	1.000000	0.71417	0.970000	0.41538	0.963000	0.63663	5.106000	0.64597	1.797000	0.52628	0.381000	0.24937	CAC	.	.		0.682	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			G	16248764	T	G	16248764	3	3	210	1	0	0	0	0	1	0	0	0	57	1696	59	5	520	5	ABCC6	16	16248764	Missense_Mutation	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10		16248764	74105989	50	30358										
ABCC6	368	hgsc.bcm.edu	37	chr16	16255355	16255356	+	Missense_Mutation	DNP	CA	CA	AC													0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ctgaggtgggctttgctcagCacagcacacgtggcagctgc							TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr16:16255355_16255356CA>AC	ENST00000205557.7	-	25	3601_3602	c.3572_3573TG>GT	c.(3571-3573)gTG>gGT	p.V1191G		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1191	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CTTTGCTCAGCACAGCACACGT	0.609																																					p.V1191V|p.V1191G		Atlas-SNP	.											.	ABCC6	110	.	0			c.G3573T|c.T3572G						.																																			SO:0001583	missense	368	exon25			GCTCAGCACAGCA|CTCAGCACAGCAC	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"ATP binding cassette transporters / subfamily C"	57	protein-coding gene	gene with protein product		603234	"pseudoxanthoma elasticum"	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3572_3573delinsAC	chr16.hg19:g.16255355_16255356delinsAC	ENSP00000205557:p.Val1191Gly	127.0|128.0	0.0		275.0|274.0	136.0|134.0	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Silent|Missense_Mutation	SNP	ENST00000205557.7	hg19	CCDS10568.1																																																																																			.	.		0.609	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			AC	16255356	CA	AC	16255355	3	1	210	1	0	0	0	0	1	0	0	0	57	697	25	3	966	3	ABCC6	16	16255355	Missense_Mutation	DNP	CA	TCGA-DD-AAE4-01A-11D-A40R-10	6591	16255355	74099398	51	30359										
MAZ	4150	hgsc.bcm.edu	37	chr16	29821424	29821444	+	In_Frame_Del	DEL	GCGGCAGCGGCAGCGGCGGCA	GCGGCAGCGGCAGCGGCGGCA	-													0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gtgaggtttgtccaatggcgGcggcagcggcagcggcggca					rs370462022|rs374878500|rs372208027|rs530039776|rs532656391|rs368894015|rs370548510|rs75194070|rs201662748|rs199924629	byFrequency	TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	GCGGCAGCGGCAGCGGCGGCA	GCGGCAGCGGCAGCGGCGGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr16:29821424_29821444delGCGGCAGCGGCAGCGGCGGCA	ENST00000322945.6	+	5	1471_1491	c.1306_1326delGCGGCAGCGGCAGCGGCGGCA	c.(1306-1326)gcggcagcggcagcggcggcadel	p.AAAAAAA436del	PRRT2_ENST00000567659.1_5'Flank|PRRT2_ENST00000358758.7_5'Flank|MAZ_ENST00000562337.1_In_Frame_Del_p.AAAAAAA131del|PRRT2_ENST00000300797.6_5'Flank|AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000568282.1_3'UTR|MAZ_ENST00000568544.1_In_Frame_Del_p.AAAAAAA37del|MAZ_ENST00000566906.2_Splice_Site_p.94_97GGSG>G|AC009133.20_ENST00000569039.1_RNA|AC009133.14_ENST00000569981.1_RNA|MAZ_ENST00000563402.1_Splice_Site_p.94_99GGSGSG>G|MAZ_ENST00000219782.6_3'UTR|MAZ_ENST00000545521.1_In_Frame_Del_p.AAAAAAA413del|AC009133.14_ENST00000563806.1_RNA	NM_002383.2	NP_002374.2	P56270	MAZ_HUMAN	MYC-associated zinc finger protein (purine-binding transcription factor)	436	Poly-Ala.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|termination of RNA polymerase II transcription (GO:0006369)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						TCCAATggcggcggcagcggcagcggcggcagcggcagcag	0.665																																					p.435_442del	Colon(72;875 1167 15364 30899 37091)	Atlas-INDEL	.											.	MAZ	48	.	0			c.1305_1325del						.																																			SO:0001651	inframe_deletion	4150	exon5			.	M93339	CCDS42143.1, CCDS42144.1, CCDS61902.1, CCDS61903.1	16p11.2	2013-01-08			ENSG00000103495	ENSG00000103495		"Zinc fingers, C2H2-type"	6914	protein-coding gene	gene with protein product		600999				1567856, 1502157	Standard	NM_001276275		Approved	ZF87, Pur-1, Zif87, ZNF801	uc002dtx.4	P56270	OTTHUMG00000132119	ENST00000322945.6:c.1306_1326delGCGGCAGCGGCAGCGGCGGCA	chr16.hg19:g.29821424_29821444delGCGGCAGCGGCAGCGGCGGCA	ENSP00000313362:p.Ala436_Ala442del	66.0	0.0		141.0	44.0	NM_002383	A8QJL9|C6G496|G5E927|H3BQD6|Q15703|Q8NFN7|Q99443	In_Frame_Del	DEL	ENST00000322945.6	hg19	CCDS42143.1																																																																																			.	.		0.665	MAZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435536.1	NM_002383		-	29821444	GCGGCAGCGGCAGCGGCGGCA	-	29821424	7	5	210	1	0	1	0	1	0	0	0	0	9349	1203	42	0	1531	0	MAZ	16	29821424	In_Frame_Del	DEL	GCGGCAGCGGCAGCGGCGGCA	TCGA-DD-AAE4-01A-11D-A40R-10	13566069	29821424	60533329	52	30360										
KATNB1	3801	hgsc.bcm.edu	37	chr16	57790767	57790767	+	IGR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ctacaagcagcttaagagcaTcagcggcctggtcaagagca	11	11	2	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr16:57790767T>G	ENST00000379655.4	-	0	3427				KATNB1_ENST00000379661.3_Missense_Mutation_p.I626S	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3						ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				CTTAAGAGCATCAGCGGCCTG	0.622																																					p.I626S		Atlas-SNP	.											.	KATNB1	35	.	0			c.T1877G						.						31	24	27					16																	57790767		2193	4300	6493	SO:0001628	intergenic_variant	10300	exon20			AGAGCATCAGCGG	BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"Kinesins"	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455		chr16.hg19:g.57790767T>G		66.0	0.0		132.0	34.0	NM_005886	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Missense_Mutation	SNP	ENST00000379655.4	hg19	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	T	21.5	4.165581	0.78339	.	.	ENSG00000140854	ENST00000379661	T	0.61980	0.06	4.97	4.97	0.65823	.	0.068463	0.64402	D	0.000013	T	0.66257	0.2771	M	0.82630	2.6	0.48135	D	0.999597	P	0.41748	0.761	B	0.39562	0.303	T	0.73968	-0.3815	10	0.87932	D	0	0.0853	13.8555	0.63524	0.0:0.0:0.0:1.0	.	626	Q9BVA0	KTNB1_HUMAN	S	626	ENSP00000368982:I626S	ENSP00000368982:I626S	I	+	2	0	KATNB1	56348268	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	5.896000	0.69822	1.880000	0.54463	0.459000	0.35465	ATC	.	.		0.622	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550		G	57790767	T	G	57790767	1	3	210	0	1	0	0	0	0	0	0	0	7996	1435	50	5		5	KATNB1	16	57790767	IGR	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10	27969343	57790767	32563986	53	30361										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70954810	70954810	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ggtcgtcgggctcatggggcGcttcctccatccctgcagga	14	14	1	0	rs367546874		TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr16:70954810G>A	ENST00000393567.2	-	46	7619	c.7469C>T	c.(7468-7470)gCg>gTg	p.A2490V		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2490					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CTCATGGGGCGCTTCCTCCAT	0.617																																					p.A2490V		Atlas-SNP	.											.	HYDIN	788	.	0			c.C7469T						.	G	VAL/ALA	0,4038		0,0,2019	39	34	35		7466	-6.6	0	16		35	1,8289		0,1,4144	no	missense	HYDIN	NM_032821.2	64	0,1,6163	AA,AG,GG		0.0121,0.0,0.0081	benign	2489/5121	70954810	1,12327	2019	4145	6164	SO:0001583	missense	54768	exon46			TGGGGCGCTTCCT	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.7469C>T	chr16.hg19:g.70954810G>A	ENSP00000377197:p.Ala2490Val	31.0	0.0		41.0	16.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	hg19	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	4.291	0.053133	0.08291	0.0	1.21E-4	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00848	5.62	5.88	-6.59	0.01830	.	0.982876	0.08241	U	0.976108	T	0.00496	0.0016	N	0.03608	-0.345	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.48536	-0.9027	10	0.28530	T	0.3	.	8.2928	0.31967	0.2287:0.0999:0.5734:0.098	.	2489	F8WD23	.	V	2490;2489	ENSP00000377197:A2490V	ENSP00000313052:A2489V	A	-	2	0	HYDIN	69512311	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-1.624000	0.02038	-1.078000	0.03117	-0.199000	0.12753	GCG	.	.		0.617	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70954810	G	A	70954810	3	1	210	1	0	0	0	0	1	0	0	0	7476	1087	38	1	8060	1	HYDIN	16	70954810	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	13164043	70954810	19399943	54	30362										
METT10D	79066	hgsc.bcm.edu	37	chr17	2380980	2380980	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	aagaatttaaaatgatatacCtatgtcaattcctcttcgga	5	7	2	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr17:2380980C>T	ENST00000263092.6	-	3	455	c.328G>A	c.(328-330)Ggc>Agc	p.G110S	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_5'UTR	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	110							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						AATGATATACCTATGTCAATT	0.358																																					p.G110S		Atlas-SNP	.											.	METTL16	75	.	0			c.G328A						.						79	76	77					17																	2380980		1805	4065	5870	SO:0001630	splice_region_variant	79066	exon3			ATATACCTATGTC	AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"methyltransferase 10 domain containing"	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.328+1G>A	chr17.hg19:g.2380980C>T		129.0	0.0		169.0	7.0	NM_024086	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	hg19	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	C	35	5.569941	0.96540	.	.	ENSG00000127804	ENST00000263092;ENST00000399834	T	0.47869	0.83	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.78648	0.4316	H	0.94385	3.53	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.996	D	0.83610	0.0133	9	.	.	.	-7.6779	18.1573	0.89696	0.0:1.0:0.0:0.0	.	110;110	Q86W50-2;Q86W50	.;MET16_HUMAN	S	110	ENSP00000263092:G110S	.	G	-	1	0	METTL16	2327730	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.777000	0.68931	2.894000	0.99253	0.655000	0.94253	GGC	.	.		0.358	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086	Missense_Mutation	T	2380980	C	T	2380980	5	4	210	1	0	0	0	0	0	0	1	0	9499	695	24	3	1392	3	METT10D	17	2380980	Splice_Site	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10		2380980	78814230	55	30363										
LPO	4025	hgsc.bcm.edu	37	chr17	56344913	56344913	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ctctcctggcctgcctcttgGgcaagcagttccagcagatc	10	15	2	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr17:56344913G>A	ENST00000262290.4	+	12	2213	c.1897G>A	c.(1897-1899)Ggc>Agc	p.G633S	LPO_ENST00000582328.1_Missense_Mutation_p.G550S|LPO_ENST00000543544.1_Missense_Mutation_p.G574S|LPO_ENST00000421678.2_Missense_Mutation_p.G550S	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	633					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						CTGCCTCTTGGGCAAGCAGTT	0.632																																					p.G633S		Atlas-SNP	.											.	LPO	73	.	0			c.G1897A						.						48	50	49					17																	56344913		2203	4300	6503	SO:0001583	missense	4025	exon12			CTCTTGGGCAAGC	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1897G>A	chr17.hg19:g.56344913G>A	ENSP00000262290:p.Gly633Ser	71.0	0.0		124.0	49.0	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Missense_Mutation	SNP	ENST00000262290.4	hg19	CCDS32689.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.655115	0.67472	.	.	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576	T;T;T	0.68181	-0.31;-0.31;-0.31	4.83	4.83	0.62350	.	0.108147	0.64402	D	0.000008	T	0.76601	0.4010	L	0.58510	1.815	0.38293	D	0.942753	P;D	0.59767	0.853;0.986	P;P	0.61722	0.566;0.893	T	0.78165	-0.2310	10	0.37606	T	0.19	-24.5275	16.9436	0.86225	0.0:0.0:1.0:0.0	.	550;633	E7EMJ3;P22079	.;PERL_HUMAN	S	633;550;574;378	ENSP00000262290:G633S;ENSP00000400245:G550S;ENSP00000445344:G574S	ENSP00000262290:G633S	G	+	1	0	LPO	53699912	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	4.713000	0.61895	2.232000	0.73038	0.557000	0.71058	GGC	.	.		0.632	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1			A	56344913	G	A	56344913	3	1	210	1	0	0	0	0	1	0	0	0	8931	1232	43	3	1939	3	LPO	17	56344913	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	53963933	56344913	24850297	56	30364										
EVPL	2125	hgsc.bcm.edu	37	chr17	74005570	74005570	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	gcttctgggcccgcaggaccTccaggtcgggcagcagcttc	14	15	1	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr17:74005570T>A	ENST00000301607.3	-	22	3969	c.3716A>T	c.(3715-3717)gAg>gTg	p.E1239V	EVPL_ENST00000586740.1_Missense_Mutation_p.E1261V	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1239	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CCGCAGGACCTCCAGGTCGGG	0.647																																					p.E1239V		Atlas-SNP	.											.	EVPL	155	.	0			c.A3716T						.						108	85	93					17																	74005570		2203	4300	6503	SO:0001583	missense	2125	exon22			AGGACCTCCAGGT	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.3716A>T	chr17.hg19:g.74005570T>A	ENSP00000301607:p.Glu1239Val	36.0	0.0		79.0	9.0	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	hg19	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	T	5.958	0.360792	0.11296	.	.	ENSG00000167880	ENST00000301607	T	0.66460	-0.21	5.2	-3.06	0.05379	.	0.867405	0.10221	N	0.700900	T	0.45597	0.1350	N	0.24115	0.695	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.002	T	0.29427	-1.0012	10	0.49607	T	0.09	-6.6621	5.5331	0.16995	0.0693:0.1283:0.2782:0.5241	.	1261;1239	B7ZLH8;Q92817	.;EVPL_HUMAN	V	1239	ENSP00000301607:E1239V	ENSP00000301607:E1239V	E	-	2	0	EVPL	71517165	0.109000	0.22037	0.004000	0.12327	0.320000	0.28249	0.481000	0.22260	-0.451000	0.07097	0.449000	0.29647	GAG	.	.		0.647	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		A	74005570	T	A	74005570	3	1	210	1	0	0	0	0	1	0	0	0	5294	1551	54	4	2389	4	EVPL	17	74005570	Missense_Mutation	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10	17660657	74005570	7189640	57	30365										
TSHZ1	10194	hgsc.bcm.edu	37	chr18	73000060	73000060	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	acccgcagcaccttctcatcCtgcaggcccagttcgcctcg	8	19	1	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr18:73000060C>T	ENST00000580243.1	+	2	3046	c.2698C>T	c.(2698-2700)Ctg>Ttg	p.L900L	TSHZ1_ENST00000322038.5_Silent_p.L855L			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	900					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		CCTTCTCATCCTGCAGGCCCA	0.607																																					p.L855L		Atlas-SNP	.											.	TSHZ1	104	.	0			c.C2563T						.						45	43	44					18																	73000060		2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			CTCATCCTGCAGG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	10669	protein-coding gene	gene with protein product		614427	"serologically defined colon cancer antigen 33", "teashirt zinc finger 1", "teashirt family zinc finger 1"	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2698C>T	chr18.hg19:g.73000060C>T		46.0	0.0		66.0	21.0	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	hg19																																																																																				.	.		0.607	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		T	73000060	C	T	73000060	2	4	210	1	0	0	0	0	0	0	0	1	16638	680	24	3		3	TSHZ1	18	73000060	Silent	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10		73000060	5077188	58	30366										
ZNF516	9658	hgsc.bcm.edu	37	chr18	74154504	74154504	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	cactggaccgctgccttggcCtcccccggggcgcatgcgga	14	17	0	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr18:74154504C>A	ENST00000443185.2	-	3	824	c.507G>T	c.(505-507)gaG>gaT	p.E169D	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		CTGCCTTGGCCTCCCCCGGGG	0.677																																					p.E169D		Atlas-SNP	.											.	ZNF516	102	.	0			c.G507T						.						12	15	14					18																	74154504		2047	4159	6206	SO:0001583	missense	9658	exon3			CTTGGCCTCCCCC	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"Zinc fingers, C2H2-type"	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.507G>T	chr18.hg19:g.74154504C>A	ENSP00000394757:p.Glu169Asp	19.0	0.0		37.0	16.0	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	hg19		.	.	.	.	.	.	.	.	.	.	C	0.540	-0.853986	0.02630	.	.	ENSG00000101493	ENST00000443185	T	0.10192	2.9	4.41	0.156	0.14910	.	2.655290	0.01405	N	0.013770	T	0.05364	0.0142	.	.	.	0.09310	N	0.999993	B	0.10296	0.003	B	0.06405	0.002	T	0.30995	-0.9959	9	0.10902	T	0.67	-31.5803	4.2166	0.10537	0.258:0.3087:0.358:0.0753	.	169	Q92618	ZN516_HUMAN	D	169	ENSP00000394757:E169D	ENSP00000394757:E169D	E	-	3	2	ZNF516	72283492	0.000000	0.05858	0.004000	0.12327	0.038000	0.13279	-0.786000	0.04623	-0.088000	0.12506	0.655000	0.94253	GAG	.	.		0.677	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		A	74154504	C	A	74154504	3	1	210	1	0	0	0	0	1	0	0	0	17975	680	24	3	3005	3	ZNF516	18	74154504	Missense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	1154444	74154504	3922744	59	30367										
HMHA1	23526	hgsc.bcm.edu	37	chr19	1080975	1080975	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ggggctgtccaaggcggcccGtactcaccggctccggaagc	15	15	1	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr19:1080975G>A	ENST00000313093.2	+	17	2333	c.2102G>A	c.(2101-2103)cGt>cAt	p.R701H	HMHA1_ENST00000543365.1_Missense_Mutation_p.R584H|HMHA1_ENST00000590577.1_Missense_Mutation_p.R336H|HMHA1_ENST00000536472.1_Missense_Mutation_p.R569H|HMHA1_ENST00000590214.1_Missense_Mutation_p.R728H|HMHA1_ENST00000586866.1_Missense_Mutation_p.R705H|HMHA1_ENST00000539243.2_Missense_Mutation_p.R717H	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	701					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGGCGGCCCGTACTCACCGG	0.682																																					p.R717H		Atlas-SNP	.											.	HMHA1	78	.	0			c.G2150A						.						17	19	18					19																	1080975		2189	4290	6479	SO:0001583	missense	23526	exon17			CGGCCCGTACTCA	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"Rho GTPase activating proteins"	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.2102G>A	chr19.hg19:g.1080975G>A	ENSP00000316772:p.Arg701His	121.0	0.0		203.0	48.0	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	hg19	CCDS32863.1	.	.	.	.	.	.	.	.	.	.	g	13.68	2.309260	0.40895	.	.	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000544746;ENST00000536472;ENST00000412039;ENST00000543365	D;D;D;D	0.84442	-1.85;-1.85;-1.85;-1.85	4.19	1.79	0.24919	Protein kinase C-like, phorbol ester/diacylglycerol binding (1);	0.432253	0.24999	N	0.033932	T	0.79787	0.4506	L	0.28274	0.84	0.29586	N	0.848821	D;D;B;D;D	0.64830	0.994;0.986;0.283;0.986;0.977	P;P;B;P;P	0.57283	0.817;0.742;0.03;0.742;0.556	T	0.71761	-0.4495	10	0.39692	T	0.17	-4.7806	2.0599	0.03590	0.368:0.0:0.3823:0.2497	.	569;717;336;584;701	F5H4A3;F6QP70;B3KVA9;F5H1R4;Q92619	.;.;.;.;HMHA1_HUMAN	H	717;701;701;569;695;584	ENSP00000439601:R717H;ENSP00000316772:R701H;ENSP00000445109:R569H;ENSP00000438979:R584H	ENSP00000316772:R701H	R	+	2	0	HMHA1	1031975	0.912000	0.30974	0.056000	0.19401	0.162000	0.22319	2.156000	0.42310	0.752000	0.32923	-0.320000	0.08662	CGT	.	.		0.682	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1			A	1080975	G	A	1080975	3	1	210	1	0	0	0	0	1	0	0	0	7249	1145	40	1	2168	1	HMHA1	19	1080975	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10		1080975	58048008	60	30368										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15291624	15291624	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ttgacaaggctggcggctgcAccaatccaccagcgtctgga	12	13	1	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr19:15291624A>C	ENST00000263388.2	-	19	3085	c.3010T>G	c.(3010-3012)Tgc>Ggc	p.C1004G		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1004	EGF-like 26. {ECO:0000255|PROSITE- ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TGGCGGCTGCACCAATCCACC	0.617																																					p.C1004G		Atlas-SNP	.											.	NOTCH3	340	.	0			c.T3010G						.						29	28	28					19																	15291624		2203	4299	6502	SO:0001583	missense	4854	exon19			GGCTGCACCAATC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.3010T>G	chr19.hg19:g.15291624A>C	ENSP00000263388:p.Cys1004Gly	64.0	0.0		74.0	33.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.098801	0.56183	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.99992	-12.4	5.13	5.13	0.70059	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.34986	N	0.003536	D	0.99994	0.9999	H	0.98426	4.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99989	1.3860	10	0.87932	D	0	.	13.9468	0.64089	1.0:0.0:0.0:0.0	.	955;1004	Q59FL3;Q9UM47	.;NOTC3_HUMAN	G	1004;954	ENSP00000263388:C1004G	ENSP00000263388:C1004G	C	-	1	0	NOTCH3	15152624	1.000000	0.71417	1.000000	0.80357	0.089000	0.18198	7.063000	0.76714	1.941000	0.56285	0.460000	0.39030	TGC	.	.		0.617	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		C	15291624	A	C	15291624	3	2	210	1	0	0	0	0	1	0	0	0	10559	159	6	5	4015	5	NOTCH3	19	15291624	Missense_Mutation	SNP	A	TCGA-DD-AAE4-01A-11D-A40R-10	14210649	15291624	43837359	61	30369										
ZFP82	284406	hgsc.bcm.edu	37	chr19	36884752	36884752	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	atagggtttatcaacaaaatGaagtctctgatgtggagtaa	10	4	2	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr19:36884752G>T	ENST00000392161.3	-	5	732	c.490C>A	c.(490-492)Cat>Aat	p.H164N	ZFP82_ENST00000392171.1_Missense_Mutation_p.H164N	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	164					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TCAACAAAATGAAGTCTCTGA	0.423																																					p.H164N		Atlas-SNP	.											.	ZFP82	71	.	0			c.C490A						.						110	101	104					19																	36884752		2203	4300	6503	SO:0001583	missense	284406	exon5			CAAAATGAAGTCT	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"Zinc fingers, C2H2-type", "-"	28682	protein-coding gene	gene with protein product			"zinc finger protein 545", "zinc finger protein 82 homolog (mouse)", "zinc finger protein 82"	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.490C>A	chr19.hg19:g.36884752G>T	ENSP00000431265:p.His164Asn	121.0	0.0		145.0	47.0	NM_133466	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	hg19	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.382627	0.25031	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.67345	-0.26;-0.26	3.9	2.86	0.33363	.	0.578072	0.14403	N	0.321742	T	0.71384	0.3333	M	0.92412	3.305	0.30660	N	0.754552	B	0.06786	0.001	B	0.14578	0.011	T	0.71721	-0.4507	10	0.46703	T	0.11	.	9.2543	0.37573	0.112:0.0:0.888:0.0	.	164	Q8N141	ZFP82_HUMAN	N	164	ENSP00000431265:H164N;ENSP00000446080:H164N	ENSP00000431265:H164N	H	-	1	0	ZFP82	41576592	0.999000	0.42202	0.989000	0.46669	0.909000	0.53808	3.385000	0.52485	2.196000	0.70406	0.650000	0.86243	CAT	.	.		0.423	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		T	36884752	G	T	36884752	3	4	210	1	0	0	0	0	1	0	0	0	17668	1290	45	3	1112	3	ZFP82	19	36884752	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	21593128	36884752	22244231	62	30370										
SARS2	54938	hgsc.bcm.edu	37	chr19	39421215	39421215	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tctatgtccagctgagggagTgcgctgtagccctcgcgcgc	14	13	1	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr19:39421215T>C	ENST00000221431.6	-	1	321	c.162A>G	c.(160-162)gcA>gcG	p.A54A	SARS2_ENST00000600042.1_Silent_p.A54A|MRPS12_ENST00000407800.2_5'Flank|SARS2_ENST00000448145.2_Intron|MRPS12_ENST00000308018.4_5'UTR|MRPS12_ENST00000402029.3_5'Flank|SARS2_ENST00000594171.1_5'Flank|SARS2_ENST00000430193.3_Silent_p.A54A|CTC-360G5.8_ENST00000599996.1_Intron	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	54					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			GCTGAGGGAGTGCGCTGTAGC	0.627											OREG0025455	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A54A		Atlas-SNP	.											.	SARS2	33	.	0			c.A162G						.						91	80	84					19																	39421215		2203	4300	6503	SO:0001819	synonymous_variant	54938	exon1			AGGGAGTGCGCTG	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"Aminoacyl tRNA synthetases / Class II"	17697	protein-coding gene	gene with protein product	"serine tRNA ligase 2, mitochondrial"	612804	"serine-tRNA ligase, mitochondrial", "seryl-tRNA synthetase 2"	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.162A>G	chr19.hg19:g.39421215T>C		46.0	0.0	885	80.0	30.0	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	hg19	CCDS33017.1																																																																																			.	.		0.627	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827		C	39421215	T	C	39421215	2	2	210	1	0	0	0	0	0	0	0	1	13860	1683	59	2		2	SARS2	19	39421215	Silent	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10	2536463	39421215	19707768	63	30371										
SAMD4B	55095	hgsc.bcm.edu	37	chr19	39867144	39867144	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ctcttctcacagatgagctaCgaggagatgatgacactgac	10	10	2	6			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr19:39867144C>T	ENST00000314471.6	+	8	2010	c.975C>T	c.(973-975)taC>taT	p.Y325Y	SAMD4B_ENST00000596368.1_Intron|SAMD4B_ENST00000598913.1_Silent_p.Y325Y	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	325	SAM.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(5)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(2)	15	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			AGATGAGCTACGAGGAGATGA	0.557																																					p.Y325Y		Atlas-SNP	.											.	SAMD4B	48	.	0			c.C975T						.						72	60	64					19																	39867144		2203	4300	6503	SO:0001819	synonymous_variant	55095	exon8			GAGCTACGAGGAG		CCDS33020.1	19q13.2	2013-01-10				ENSG00000179134		"Sterile alpha motif (SAM) domain containing"	25492	protein-coding gene	gene with protein product	"smaug homolog B (Drosophila)"					16221671	Standard	XM_005259029		Approved	FLJ10211, MGC99832, SMGB, hSmaug2	uc002olb.3	Q5PRF9		ENST00000314471.6:c.975C>T	chr19.hg19:g.39867144C>T		47.0	0.0		74.0	28.0	NM_018028	A5Z0M6|Q6P194	Silent	SNP	ENST00000314471.6	hg19	CCDS33020.1																																																																																			.	.		0.557	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028		T	39867144	C	T	39867144	2	4	210	1	0	0	0	0	0	0	0	1	13837	547	19	1		1	SAMD4B	19	39867144	Silent	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	445929	39867144	19261839	64	30372										
IRF2BP1	26145	hgsc.bcm.edu	37	chr19	46388496	46388496	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ctcaagccgggtgccagcgtCaggcctcggcttcccaggcc	13	17	2	0			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr19:46388496C>A	ENST00000302165.3	-	1	880	c.537G>T	c.(535-537)ctG>ctT	p.L179L		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	179					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		GTGCCAGCGTCAGGCCTCGGC	0.647																																					p.L179L		Atlas-SNP	.											.	IRF2BP1	23	.	0			c.G537T						.						29	36	34					19																	46388496		2199	4289	6488	SO:0001819	synonymous_variant	26145	exon1			CAGCGTCAGGCCT	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.537G>T	chr19.hg19:g.46388496C>A		35.0	0.0		62.0	28.0	NM_015649	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Silent	SNP	ENST00000302165.3	hg19	CCDS12678.1																																																																																			.	.		0.647	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649		A	46388496	C	A	46388496	2	1	210	1	0	0	0	0	0	0	0	1	7838	813	29	3		3	IRF2BP1	19	46388496	Silent	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	6521352	46388496	12740487	65	30373										
CD93	22918	hgsc.bcm.edu	37	chr20	23066284	23066284	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	cggcacatgcctttgaagctGaacttgcacacgaagccctc	9	14	0	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr20:23066284G>T	ENST00000246006.4	-	1	693	c.546C>A	c.(544-546)ttC>ttA	p.F182L		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	182					macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					CTTTGAAGCTGAACTTGCACA	0.657																																					p.F182L		Atlas-SNP	.											.	CD93	84	.	0			c.C546A						.						45	52	50					20																	23066284		2203	4300	6503	SO:0001583	missense	22918	exon1			GAAGCTGAACTTG	U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"CD molecules"	15855	protein-coding gene	gene with protein product		120577	"matrix-remodelling associated 4", "complement component 1, q subcomponent, receptor 1", "CD93 antigen"	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.546C>A	chr20.hg19:g.23066284G>T	ENSP00000246006:p.Phe182Leu	49.0	0.0		79.0	31.0	NM_012072	O00274	Missense_Mutation	SNP	ENST00000246006.4	hg19	CCDS13149.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.269777	0.80469	.	.	ENSG00000125810	ENST00000246006;ENST00000413585	T	0.40756	1.02	5.52	4.58	0.56647	C-type lectin fold (1);C-type lectin-like (1);	0.000000	0.64402	D	0.000005	T	0.64057	0.2564	M	0.80422	2.495	0.40964	D	0.984641	D	0.67145	0.996	D	0.65443	0.935	T	0.71122	-0.4684	10	0.72032	D	0.01	-44.2406	13.7324	0.62797	0.0741:0.0:0.9259:0.0	.	182	Q9NPY3	C1QR1_HUMAN	L	182	ENSP00000246006:F182L	ENSP00000246006:F182L	F	-	3	2	CD93	23014284	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.988000	0.49386	1.469000	0.48083	-0.136000	0.14681	TTC	.	.		0.657	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		T	23066284	G	T	23066284	3	4	210	1	0	0	0	0	1	0	0	0	3049	1281	45	3	1420	3	CD93	20	23066284	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10		23066284	39959236	66	30374										
ACTR5	79913	hgsc.bcm.edu	37	chr20	37378813	37378813	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	ccacaataagccaaagaactCgatgtgcagtgggctaatca	9	10	1	1			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr20:37378813C>A	ENST00000243903.4	+	2	573	c.536C>A	c.(535-537)tCg>tAg	p.S179*		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	179					DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|UV-damage excision repair (GO:0070914)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)				kidney(2)|large_intestine(2)|liver(1)|lung(5)|skin(2)	12		Myeloproliferative disorder(115;0.00878)				CCAAAGAACTCGATGTGCAGT	0.453																																					p.S179X		Atlas-SNP	.											.	ACTR5	44	.	0			c.C536A						.						146	131	136					20																	37378813		2203	4300	6503	SO:0001587	stop_gained	79913	exon2			AGAACTCGATGTG	AK022847	CCDS13308.1	20q12	2011-07-06	2001-11-28		ENSG00000101442	ENSG00000101442		"INO80 complex subunits"	14671	protein-coding gene	gene with protein product	"INO80 complex subunit M"		"ARP5 (actin-related protein 5, yeast) homolog"			16230350	Standard	NM_024855		Approved	FLJ12785, Arp5, INO80M	uc002xjd.2	Q9H9F9	OTTHUMG00000032456	ENST00000243903.4:c.536C>A	chr20.hg19:g.37378813C>A	ENSP00000243903:p.Ser179*	122.0	0.0		192.0	77.0	NM_024855	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Nonsense_Mutation	SNP	ENST00000243903.4	hg19	CCDS13308.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.859025	0.71834	.	.	ENSG00000101442	ENST00000243903	.	.	.	4.4	-0.149	0.13420	.	0.700022	0.14102	N	0.341300	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-0.2407	5.8	0.18408	0.0:0.2642:0.3542:0.3815	.	.	.	.	X	179	.	ENSP00000243903:S179X	S	+	2	0	ACTR5	36812227	0.006000	0.16342	0.004000	0.12327	0.628000	0.37860	0.416000	0.21198	0.069000	0.16605	0.467000	0.42956	TCG	.	.		0.453	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855		A	37378813	C	A	37378813	4	1	210	1	0	0	0	0	0	1	0	0	215	893	31	1	542	1	ACTR5	20	37378813	Nonsense_Mutation	SNP	C	TCGA-DD-AAE4-01A-11D-A40R-10	14312529	37378813	25646707	67	30375										
KRTAP10-3	386682	hgsc.bcm.edu	37	chr21	45978509	45978509	+	Frame_Shift_Del	DEL	G	G	-													0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	cagcagctggtggcgcagcaGgggggctcacagcagctctc					rs587665364	byFrequency	TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chr21:45978509delG	ENST00000391620.1	-	1	134	c.90delC	c.(88-90)cccfs	p.P30fs	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	30	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						TGGCGCAGCAGGGGGGCTCAC	0.697													GGGGGG|GGGGGG|GGGGG|deletion	6	0.00119808	0	0	5008	,	,		16049	0		0	False		,,,				2504	0.0061				p.C31fs		Atlas-INDEL	.											.	KRTAP10-3	17	.	0			c.91delT						.						29	31	30					21																	45978509		2165	4257	6422	SO:0001589	frameshift_variant	386682	exon1			.	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"Keratin associated proteins"	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.90delC	chr21.hg19:g.45978509delG	ENSP00000375478:p.Pro30fs	39.0	0.0		79.0	29.0	NM_198696	A3KN67|Q70LJ4	Frame_Shift_Del	DEL	ENST00000391620.1	hg19	CCDS42956.1																																																																																			.	.		0.697	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1			-	45978509	G	-	45978509	7	5	210	1	0	1	0	1	0	0	0	0	8519	987	35	0	579	0	KRTAP10-3	21	45978509	Frame_Shift_Del	DEL	G	TCGA-DD-AAE4-01A-11D-A40R-10		45978509	2151386	68	30376										
GPR143	4935	hgsc.bcm.edu	37	chrX	9709456	9709456	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	atatctgtttgcatctcaagAtagaataaaaggctttcatt	6	6	3	2			TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chrX:9709456A>C	ENST00000467482.1	-	7	953	c.807T>G	c.(805-807)taT>taG	p.Y269*	GPR143_ENST00000487206.1_5'Flank|GPR143_ENST00000380929.2_Nonsense_Mutation_p.Y289*			P51810	GP143_HUMAN	G protein-coupled receptor 143	269					calcium-mediated signaling using intracellular calcium source (GO:0035584)|eye pigment biosynthetic process (GO:0006726)|G-protein coupled receptor signaling pathway (GO:0007186)|melanosome localization (GO:0032400)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|neuropeptide signaling pathway (GO:0007218)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of calcium-mediated signaling (GO:0050848)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|G-protein coupled receptor activity (GO:0004930)|L-DOPA binding (GO:0072544)|L-DOPA receptor activity (GO:0035643)|tyrosine binding (GO:0072545)			endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Hepatocellular(5;0.000888)				GCATCTCAAGATAGAATAAAA	0.353																																					p.Y269X		Atlas-SNP	.											.	GPR143	37	.	0			c.T807G						.						70	63	66					X																	9709456		2203	4300	6503	SO:0001587	stop_gained	4935	exon7			CTCAAGATAGAAT	Z48804	CCDS14134.1, CCDS14134.2	Xp22.3	2013-09-27	2003-12-01		ENSG00000101850	ENSG00000101850		"GPCR / Unclassified : 7TM orphan receptors"	20145	protein-coding gene	gene with protein product	"ocular albinism 1"	300808	"ocular albinism 1 (Nettleship-Falls)"	OA1		7647783, 10471510	Standard	NM_000273		Approved		uc004cst.2	P51810	OTTHUMG00000021118	ENST00000467482.1:c.807T>G	chrX.hg19:g.9709456A>C	ENSP00000417161:p.Tyr269*	473.0	0.0		601.0	228.0	NM_000273	Q6NTI7	Nonsense_Mutation	SNP	ENST00000467482.1	hg19	CCDS14134.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	35|35	5.493393|5.493393	0.96339|0.96339	.|.	.|.	ENSG00000101850|ENSG00000101850	ENST00000447366|ENST00000467482;ENST00000380929	.|.	.|.	.|.	4.91|4.91	-0.52|-0.52	0.11935|0.11935	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.23649|.	0.0572|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.41662|.	-0.9496|.	3|.	.|0.02654	.|T	.|1	-4.2142|-4.2142	11.9238|11.9238	0.52808|0.52808	0.1933:0.0:0.8067:0.0|0.1933:0.0:0.8067:0.0	.|.	.|.	.|.	.|.	A|X	205|269;289	.|.	.|ENSP00000370316:Y289X	S|Y	-|-	1|3	0|2	GPR143|GPR143	9669456|9669456	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.997000|0.997000	0.91878|0.91878	1.565000|1.565000	0.36386|0.36386	-0.142000|-0.142000	0.11354|0.11354	0.486000|0.486000	0.48141|0.48141	TCT|TAT	.	.		0.353	GPR143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055714.2	NM_000273		C	9709456	A	C	9709456	4	2	210	1	0	0	0	0	0	1	0	0	6659	340	12	5	419	5	GPR143	23	9709456	Nonsense_Mutation	SNP	A	TCGA-DD-AAE4-01A-11D-A40R-10		9709456	145561104	69	30377										
ZC3H12B	340554	hgsc.bcm.edu	37	chrX	64722582	64722582	+	Silent	SNP	T	T	A													0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	catgcccagcacccatcaacTggaacacgttccagctgtcc							TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chrX:64722582T>A	ENST00000338957.4	+	5	2071	c.2004T>A	c.(2002-2004)acT>acA	p.T668T	ZC3H12B_ENST00000423889.3_Silent_p.T657T	NM_001010888.3	NP_001010888.3	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	668							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ACCCATCAACTGGAACACGTT	0.592																																					p.T668T		Atlas-SNP	.											.	ZC3H12B	144	.	0			c.T2004A						.						59	60	60					X																	64722582		2000	4148	6148	SO:0001819	synonymous_variant	340554	exon5			ATCAACTGGAACA	BX647241	CCDS48131.1, CCDS48131.2	Xq12	2012-07-05	2005-06-14	2005-06-14	ENSG00000102053	ENSG00000102053		"Zinc fingers, CCCH-type domain containing"	17407	protein-coding gene	gene with protein product	"MCP induced protein 2"	300889	"chromosome X open reading frame 32"	CXorf32		18178554	Standard	NM_001010888		Approved	MCPIP2	uc010nko.3	Q5HYM0	OTTHUMG00000021719	ENST00000338957.4:c.2004T>A	chrX.hg19:g.64722582T>A		92.0	0.0		152.0	14.0	NM_001010888	B2RTQ3|E9PAJ6|Q5H9C0	Silent	SNP	ENST00000338957.4	hg19	CCDS48131.2																																																																																			.	.		0.592	ZC3H12B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378734.2	XM_293334		A	64722582	T	A	64722582	2	1	210	1	0	0	0	0	0	0	0	1	17577	1567	55	4		4	ZC3H12B	23	64722582	Silent	SNP	T	TCGA-DD-AAE4-01A-11D-A40R-10	55013126	64722582	90547978	70	30378	159	2								
ZC3H12B	340554	hgsc.bcm.edu	37	chrX	64722584	64722584	+	Missense_Mutation	SNP	G	G	A													0.0428571428571429	3	1	0.854941442366961	1.4723991507431	0.706751592356688	1	1	0	tgcccagcacccatcaactgGaacacgttccagctgtcctg							TCGA-DD-AAE4-01A-11D-A40R-10	TCGA-DD-AAE4-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef673fe7-a934-4041-8258-a4af537977c6	ff5a3218-ca2c-4eac-a8cb-c88524c95f7b	g.chrX:64722584G>A	ENST00000338957.4	+	5	2073	c.2006G>A	c.(2005-2007)gGa>gAa	p.G669E	ZC3H12B_ENST00000423889.3_Missense_Mutation_p.G658E	NM_001010888.3	NP_001010888.3	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	669							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCATCAACTGGAACACGTTCC	0.582																																					p.G669E		Atlas-SNP	.											.	ZC3H12B	144	.	0			c.G2006A						.						59	60	60					X																	64722584		2008	4153	6161	SO:0001583	missense	340554	exon5			CAACTGGAACACG	BX647241	CCDS48131.1, CCDS48131.2	Xq12	2012-07-05	2005-06-14	2005-06-14	ENSG00000102053	ENSG00000102053		"Zinc fingers, CCCH-type domain containing"	17407	protein-coding gene	gene with protein product	"MCP induced protein 2"	300889	"chromosome X open reading frame 32"	CXorf32		18178554	Standard	NM_001010888		Approved	MCPIP2	uc010nko.3	Q5HYM0	OTTHUMG00000021719	ENST00000338957.4:c.2006G>A	chrX.hg19:g.64722584G>A	ENSP00000340839:p.Gly669Glu	94.0	0.0		151.0	14.0	NM_001010888	B2RTQ3|E9PAJ6|Q5H9C0	Missense_Mutation	SNP	ENST00000338957.4	hg19	CCDS48131.2	.	.	.	.	.	.	.	.	.	.	G	18.34	3.602132	0.66445	.	.	ENSG00000102053	ENST00000338957;ENST00000423889;ENST00000218172	T;T	0.25579	1.79;1.8	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	M	0.66939	2.045	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.52968	-0.8504	10	0.87932	D	0	-40.2415	15.9994	0.80280	0.0:0.0:1.0:0.0	.	658	Q5HYM0	ZC12B_HUMAN	E	669;658;605	ENSP00000340839:G669E;ENSP00000408077:G658E	ENSP00000218172:G605E	G	+	2	0	ZC3H12B	64639309	1.000000	0.71417	0.939000	0.37840	0.983000	0.72400	7.341000	0.79300	2.346000	0.79739	0.506000	0.49869	GGA	.	.		0.582	ZC3H12B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378734.2	XM_293334		A	64722584	G	A	64722584	3	1	210	1	0	0	0	0	1	0	0	0	17577	1174	41	3	2024	3	ZC3H12B	23	64722584	Missense_Mutation	SNP	G	TCGA-DD-AAE4-01A-11D-A40R-10	2	64722584	90547976	71	30379	159	2								
VWA1	64856	hgsc.bcm.edu	37	chr1	1372593	1372593	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ggcctggcgctggtctatgcCaaggaacagctgtttgctga	14	10	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:1372593C>T	ENST00000476993.1	+	2	438	c.360C>T	c.(358-360)gcC>gcT	p.A120A	VWA1_ENST00000338660.5_Intron|RP4-758J18.10_ENST00000417917.1_lincRNA|VWA1_ENST00000404702.3_Intron	NM_022834.4	NP_073745.2	Q6PCB0	VWA1_HUMAN	von Willebrand factor A domain containing 1	120	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				behavioral response to pain (GO:0048266)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interstitial matrix (GO:0005614)				NS(1)|breast(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	8	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TGGTCTATGCCAAGGAACAGC	0.667																																					p.A120A		Atlas-SNP	.											.	VWA1	15	.	0			c.C360T						.						34	32	33					1																	1372593		2193	4287	6480	SO:0001819	synonymous_variant	64856	exon2			CTATGCCAAGGAA	BC059409	CCDS27.1, CCDS28.1, CCDS28.2	1p36.33	2013-02-11			ENSG00000179403	ENSG00000179403		"Fibronectin type III domain containing"	30910	protein-coding gene	gene with protein product		611901				14527666, 12062410	Standard	NM_022834		Approved	FLJ22215, VWA-1, WARP	uc001afs.3	Q6PCB0	OTTHUMG00000002975	ENST00000476993.1:c.360C>T	chr1.hg19:g.1372593C>T		106.0	0.0		90.0	53.0	NM_022834	A8K692|B3KUA1|E9PB53|Q7L5D7|Q9H6J5	Silent	SNP	ENST00000476993.1	hg19	CCDS27.1																																																																																			.	.		0.667	VWA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008291.1	NM_022834		T	1372593	C	T	1372593	2	4	211	1	0	0	0	0	0	0	0	1	17253	581	21	3		3	VWA1	1	1372593	Silent	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10		1372593	247878028	1	30380										
EXOSC10	5394	hgsc.bcm.edu	37	chr1	11128719	11128719	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	taccttgccagacggggtctGtttatttggatcaaactgag	11	8	2	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:11128719G>T	ENST00000376936.4	-	23	2582	c.2533C>A	c.(2533-2535)Cag>Aag	p.Q845K	EXOSC10_ENST00000304457.7_Missense_Mutation_p.Q820K|EXOSC10_ENST00000544779.1_3'UTR|RP4-635E18.7_ENST00000452378.1_RNA	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	845					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		GACGGGGTCTGTTTATTTGGA	0.498																																					p.Q845K	Colon(179;105 1987 14326 27364 29542)	Atlas-SNP	.											.	EXOSC10	59	.	0			c.C2533A						.						150	143	146					1																	11128719		2203	4300	6503	SO:0001583	missense	5394	exon23			GGGTCTGTTTATT	BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 2 (100kD)"	605960	"polymyositis/scleroderma autoantigen 2, 100kDa"	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.2533C>A	chr1.hg19:g.11128719G>T	ENSP00000366135:p.Gln845Lys	133.0	0.0		143.0	77.0	NM_001001998	B1AKQ0|B1AKQ1|Q15158	Missense_Mutation	SNP	ENST00000376936.4	hg19	CCDS30584.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.814679	0.32053	.	.	ENSG00000171824	ENST00000376936;ENST00000304457	.	.	.	4.83	3.9	0.45041	.	0.110220	0.64402	D	0.000006	T	0.46737	0.1408	L	0.34521	1.04	0.80722	D	1	P;B	0.35684	0.515;0.381	B;B	0.41440	0.357;0.195	T	0.38023	-0.9680	9	0.02654	T	1	-6.4652	14.301	0.66352	0.0:0.1494:0.8506:0.0	.	820;845	Q01780-2;Q01780	.;EXOSX_HUMAN	K	845;820	.	ENSP00000307307:Q820K	Q	-	1	0	EXOSC10	11051306	1.000000	0.71417	0.969000	0.41365	0.272000	0.26649	5.199000	0.65152	1.135000	0.42183	0.557000	0.71058	CAG	.	.		0.498	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998		T	11128719	G	T	11128719	3	4	211	1	0	0	0	0	1	0	0	0	5316	1386	48	3	136	3	EXOSC10	1	11128719	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	9756126	11128719	238121902	2	30381										
KIF17	57576	hgsc.bcm.edu	37	chr1	21016719	21016719	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tctcctccagcgtggacagcCtgacgtcatatgagttgcgc	11	13	2	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:21016719C>T	ENST00000247986.2	-	7	1653	c.1343G>A	c.(1342-1344)aGg>aAg	p.R448K	KIF17_ENST00000400463.3_Missense_Mutation_p.R448K|KIF17_ENST00000375044.1_Missense_Mutation_p.R348K|KIF17_ENST00000490034.1_5'UTR			Q9P2E2	KIF17_HUMAN	kinesin family member 17	448					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CGTGGACAGCCTGACGTCATA	0.642																																					p.R448K		Atlas-SNP	.											.	KIF17	130	.	0			c.G1343A						.						59	52	54					1																	21016719		2203	4300	6503	SO:0001583	missense	57576	exon7			GACAGCCTGACGT	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"Kinesins"	19167	protein-coding gene	gene with protein product	"kinesin-like protein KIF17", "KIF3-related motor protein", "KIF17 variant protein"	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1343G>A	chr1.hg19:g.21016719C>T	ENSP00000247986:p.Arg448Lys	89.0	0.0		134.0	76.0	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	hg19	CCDS213.1	.	.	.	.	.	.	.	.	.	.	C	0.869	-0.732708	0.03135	.	.	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986	T;T;T	0.68903	-0.36;-0.25;-0.25	4.87	3.75	0.43078	.	0.234822	0.21448	N	0.074378	T	0.22244	0.0536	N	0.00210	-1.845	0.23449	N	0.997656	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.37454	-0.9705	10	0.02654	T	1	.	7.1053	0.25360	0.0:0.1917:0.0:0.8083	.	448;448	Q9P2E2-3;Q9P2E2	.;KIF17_HUMAN	K	348;448;448	ENSP00000364184:R348K;ENSP00000383311:R448K;ENSP00000247986:R448K	ENSP00000247986:R448K	R	-	2	0	KIF17	20889306	1.000000	0.71417	0.897000	0.35233	0.423000	0.31445	1.093000	0.30939	0.726000	0.32339	-0.339000	0.08088	AGG	.	.		0.642	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816		T	21016719	C	T	21016719	3	4	211	1	0	0	0	0	1	0	0	0	8288	681	24	3	1782	3	KIF17	1	21016719	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	9888000	21016719	228233902	3	30382										
HCRTR1	3061	hgsc.bcm.edu	37	chr1	32084909	32084909	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ccgctatctgtggcgcgattAtctgtacccaaaacagtatg	9	11	2	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:32084909A>G	ENST00000373706.5	+	1	269	c.116A>G	c.(115-117)tAt>tGt	p.Y39C	HCRTR1_ENST00000403528.2_Missense_Mutation_p.Y39C|HCRTR1_ENST00000373705.1_Missense_Mutation_p.Y39C|HCRTR1_ENST00000468521.1_3'UTR			O43613	OX1R_HUMAN	hypocretin (orexin) receptor 1	39					feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|orexin receptor activity (GO:0016499)|peptide hormone binding (GO:0017046)			breast(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	7		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)		TGGCGCGATTATCTGTACCCA	0.607																																					p.Y39C		Atlas-SNP	.											.	HCRTR1	20	.	0			c.A116G						.						154	154	154					1																	32084909		2203	4300	6503	SO:0001583	missense	3061	exon3			GCGATTATCTGTA	AF041243	CCDS344.1	1p33	2012-08-08			ENSG00000121764	ENSG00000121764		"GPCR / Class A : Hypocretin (orexin) receptors"	4848	protein-coding gene	gene with protein product		602392				9491897	Standard	NM_001525		Approved	OX1R	uc009vtx.2	O43613	OTTHUMG00000003876	ENST00000373706.5:c.116A>G	chr1.hg19:g.32084909A>G	ENSP00000362810:p.Tyr39Cys	62.0	0.0		71.0	22.0	NM_001525	A8K3A6|Q9HBV6	Missense_Mutation	SNP	ENST00000373706.5	hg19	CCDS344.1	.	.	.	.	.	.	.	.	.	.	A	18.73	3.687146	0.68157	.	.	ENSG00000121764	ENST00000403528;ENST00000373706;ENST00000373705	T;T;T	0.37584	1.19;1.19;1.19	3.82	3.82	0.43975	.	0.000000	0.64402	D	0.000003	T	0.49081	0.1536	L	0.47190	1.495	0.50813	D	0.999894	D;D	0.89917	0.999;1.0	D;D	0.72075	0.976;0.969	T	0.44174	-0.9345	10	0.44086	T	0.13	.	11.176	0.48598	1.0:0.0:0.0:0.0	.	39;39	A6NMV7;O43613	.;OX1R_HUMAN	C	39	ENSP00000384387:Y39C;ENSP00000362810:Y39C;ENSP00000362809:Y39C	ENSP00000362809:Y39C	Y	+	2	0	HCRTR1	31857496	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	5.648000	0.67930	1.665000	0.50811	0.482000	0.46254	TAT	.	.		0.607	HCRTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011042.1	NM_001525		G	32084909	A	G	32084909	3	3	211	1	0	0	0	0	1	0	0	0	7010	449	16	2	118	2	HCRTR1	1	32084909	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	11068190	32084909	217165712	4	30383										
CDCP2	200008	hgsc.bcm.edu	37	chr1	54618578	54618578	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	actgccagcagcaggcaagcCccccactctgccagcatctc	8	19	2	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:54618578C>G	ENST00000371330.1	-	1	865	c.18G>C	c.(16-18)ggG>ggC	p.G6G	RP11-446E24.4_ENST00000525949.1_Intron|RP11-446E24.4_ENST00000311841.7_3'UTR	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	6						extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						GCAGGCAAGCCCCCCACTCTG	0.642																																					p.G6G		Atlas-SNP	.											.	CDCP2	52	.	0			c.G18C						.						53	58	56					1																	54618578		2203	4300	6503	SO:0001819	synonymous_variant	200008	exon1			GCAAGCCCCCCAC		CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.18G>C	chr1.hg19:g.54618578C>G		51.0	0.0		62.0	11.0	NM_201546	Q6ZWJ3	Silent	SNP	ENST00000371330.1	hg19	CCDS588.2																																																																																			.	.		0.642	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546		G	54618578	C	G	54618578	2	3	211	1	0	0	0	0	0	0	0	1	3096	610	22	4		4	CDCP2	1	54618578	Silent	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	22533669	54618578	194632043	5	30384										
CYP2J2	1573	hgsc.bcm.edu	37	chr1	60377391	60377391	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ccgaaggtgatggagcaaatGatattggaaactgcattgtt	12	5	0	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:60377391G>A	ENST00000371204.3	-	4	616	c.573C>T	c.(571-573)atC>atT	p.I191I	CYP2J2_ENST00000492633.1_5'UTR	NM_000775.2	NP_000766.2	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J, polypeptide 2	191					arachidonic acid metabolic process (GO:0019369)|epoxygenase P450 pathway (GO:0019373)|icosanoid metabolic process (GO:0006690)|linoleic acid metabolic process (GO:0043651)|regulation of heart contraction (GO:0008016)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	arachidonic acid 11,12-epoxygenase activity (GO:0008405)|arachidonic acid 14,15-epoxygenase activity (GO:0008404)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|linoleic acid epoxygenase activity (GO:0071614)			NS(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|skin(1)	26	all_cancers(7;0.000396)				Apixaban(DB06605)|Astemizole(DB00637)|Cholecalciferol(DB00169)|Levomilnacipran(DB08918)|Masoprocol(DB00179)|Rivaroxaban(DB06228)	TGGAGCAAATGATATTGGAAA	0.448																																					p.I191I		Atlas-SNP	.											.	CYP2J2	34	.	0			c.C573T						.						170	160	163					1																	60377391		2203	4300	6503	SO:0001819	synonymous_variant	1573	exon4			GCAAATGATATTG	BC032594	CCDS613.1	1p31.3-p31.2	2008-02-05	2003-01-14		ENSG00000134716	ENSG00000134716		"Cytochrome P450s"	2634	protein-coding gene	gene with protein product		601258	"cytochrome P450, subfamily IIJ (arachidonic acid epoxygenase) polypeptide 2"			9570962	Standard	NM_000775		Approved		uc001czq.3	P51589	OTTHUMG00000008991	ENST00000371204.3:c.573C>T	chr1.hg19:g.60377391G>A		122.0	0.0		107.0	17.0	NM_000775	B2RD33|Q8TF13	Silent	SNP	ENST00000371204.3	hg19	CCDS613.1																																																																																			.	.		0.448	CYP2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024940.1	NM_000775		A	60377391	G	A	60377391	2	1	211	1	0	0	0	0	0	0	0	1	4174	1280	45	3		3	CYP2J2	1	60377391	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	5758813	60377391	188873230	6	30385										
SSX2IP	117178	hgsc.bcm.edu	37	chr1	85116058	85116058	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	caaatacctatgttcagataTgcaggaacgtgtctggcaaa	9	8	2	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:85116058T>A	ENST00000342203.3	-	13	1920	c.1657A>T	c.(1657-1659)Ata>Tta	p.I553L	SSX2IP_ENST00000437941.2_Missense_Mutation_p.I526L|SSX2IP_ENST00000370612.4_Missense_Mutation_p.I553L|SSX2IP_ENST00000605755.1_Missense_Mutation_p.I526L|SSX2IP_ENST00000603677.1_Missense_Mutation_p.I72L	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	553					cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TGTTCAGATATGCAGGAACGT	0.403																																					p.I553L		Atlas-SNP	.											.	SSX2IP	53	.	0			c.A1657T						.						130	128	129					1																	85116058		2203	4300	6503	SO:0001583	missense	117178	exon14			CAGATATGCAGGA		CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.1657A>T	chr1.hg19:g.85116058T>A	ENSP00000340279:p.Ile553Leu	92.0	0.0		81.0	32.0	NM_001166417	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	hg19	CCDS699.1	.	.	.	.	.	.	.	.	.	.	T	8.445	0.851655	0.17034	.	.	ENSG00000117155	ENST00000342203;ENST00000437941;ENST00000370612	T;T	0.50277	0.75;0.75	5.67	1.2	0.21068	.	0.497800	0.21853	N	0.068152	T	0.13884	0.0336	L	0.39898	1.24	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.32079	-0.9920	10	0.15952	T	0.53	-0.0301	8.3313	0.32189	0.0:0.6298:0.0:0.3702	.	553;553;526	Q9Y2D8-2;Q9Y2D8;B4DFE3	.;ADIP_HUMAN;.	L	553;526;553	ENSP00000340279:I553L;ENSP00000412781:I526L	ENSP00000340279:I553L	I	-	1	0	SSX2IP	84888646	0.150000	0.22732	0.282000	0.24776	0.051000	0.14879	0.254000	0.18314	0.348000	0.23949	-0.766000	0.03442	ATA	.	.		0.403	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021		A	85116058	T	A	85116058	3	1	211	1	0	0	0	0	1	0	0	0	15219	1464	51	4	195	4	SSX2IP	1	85116058	Missense_Mutation	SNP	T	TCGA-DD-AAE6-01A-11D-A40R-10	24738667	85116058	164134563	7	30386										
PSMA5	5686	hgsc.bcm.edu	37	chr1	109957891	109957891	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	caatctctacaattttctcaAtgctgctgggctccatcagt	6	12	3	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:109957891A>G	ENST00000271308.4	-	3	211	c.191T>C	c.(190-192)aTt>aCt	p.I64T	PSMA5_ENST00000538610.1_Missense_Mutation_p.I6T|PSMA5_ENST00000490870.1_5'UTR	NM_002790.3	NP_002781.2	P28066	PSA5_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 5	64					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)	5		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.045)|Colorectal(144;0.116)|Epithelial(280;0.187)|all cancers(265;0.196)|LUSC - Lung squamous cell carcinoma(189;0.235)		AATTTTCTCAATGCTGCTGGG	0.463																																					p.I64T		Atlas-SNP	.											.	PSMA5	14	.	0			c.T191C						.						168	136	146					1																	109957891		2203	4300	6503	SO:0001583	missense	5686	exon3			TTCTCAATGCTGC	X61970	CCDS799.1, CCDS55619.1	1p13	2008-02-05			ENSG00000143106	ENSG00000143106		"Proteasome (prosome, macropain) subunits"	9534	protein-coding gene	gene with protein product		176844				1888762	Standard	NM_002790		Approved	ZETA	uc001dxn.3	P28066	OTTHUMG00000012001	ENST00000271308.4:c.191T>C	chr1.hg19:g.109957891A>G	ENSP00000271308:p.Ile64Thr	67.0	0.0		66.0	30.0	NM_002790	B2R8F6|B4E2V4|Q3T1C1|Q6IBF7	Missense_Mutation	SNP	ENST00000271308.4	hg19	CCDS799.1	.	.	.	.	.	.	.	.	.	.	a	16.49	3.137848	0.56936	.	.	ENSG00000143106	ENST00000538610;ENST00000271308	T;T	0.24538	1.85;1.85	5.89	3.52	0.40303	.	0.044629	0.85682	D	0.000000	T	0.20495	0.0493	M	0.65975	2.015	0.53688	D	0.999973	B	0.29766	0.256	B	0.42087	0.375	T	0.02391	-1.1166	9	.	.	.	-13.6216	12.1983	0.54311	0.7298:0.2702:0.0:0.0	.	64	P28066	PSA5_HUMAN	T	6;64	ENSP00000440618:I6T;ENSP00000271308:I64T	.	I	-	2	0	PSMA5	109759414	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	7.452000	0.80683	0.456000	0.26937	-0.447000	0.05616	ATT	.	.		0.463	PSMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033192.2	NM_002790		G	109957891	A	G	109957891	3	3	211	1	0	0	0	0	1	0	0	0	12682	101	4	2	562	2	PSMA5	1	109957891	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	24841833	109957891	139292730	8	30387										
RHOC	389	hgsc.bcm.edu	37	chr1	113245243	113245243	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	cttgcctcaggtccttcttaTtccccaccaggatgatgggc	9	14	2	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:113245243T>C	ENST00000285735.2	-	5	1559	c.350A>G	c.(349-351)aAt>aGt	p.N117S	RHOC_ENST00000339083.7_Missense_Mutation_p.N117S|RP11-426L16.10_ENST00000471038.2_5'UTR|RHOC_ENST00000369638.2_Missense_Mutation_p.N117S|RHOC_ENST00000369642.3_Missense_Mutation_p.N117S|RHOC_ENST00000369632.2_Missense_Mutation_p.N117S|RHOC_ENST00000369633.2_Missense_Mutation_p.N117S|RHOC_ENST00000369637.1_Missense_Mutation_p.N117S|RHOC_ENST00000369636.2_Missense_Mutation_p.N117S			P08134	RHOC_HUMAN	ras homolog family member C	117					apical junction assembly (GO:0043297)|axon guidance (GO:0007411)|cytokinesis (GO:0000910)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTCCTTCTTATTCCCCACCAG	0.572																																					p.N117S		Atlas-SNP	.											.	RHOC	15	.	0			c.A350G						.						137	127	131					1																	113245243		2203	4300	6503	SO:0001583	missense	389	exon5			TTCTTATTCCCCA	BC052808	CCDS854.1	1p13.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000155366	ENSG00000155366			669	protein-coding gene	gene with protein product		165380	"ras homolog gene family, member C"	ARH9, ARHC		3283705	Standard	NM_001042678		Approved	RhoC	uc001ecp.1	P08134	OTTHUMG00000011905	ENST00000285735.2:c.350A>G	chr1.hg19:g.113245243T>C	ENSP00000285735:p.Asn117Ser	66.0	0.0		81.0	40.0	NM_001042679	B3KSW1|Q6ICN3	Missense_Mutation	SNP	ENST00000285735.2	hg19	CCDS854.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.056969	0.55325	.	.	ENSG00000155366	ENST00000339083;ENST00000369633;ENST00000369642;ENST00000285735;ENST00000369638;ENST00000369637;ENST00000369636;ENST00000369632;ENST00000484054;ENST00000425265;ENST00000534717;ENST00000436685	T;T;T;T;T;T;T;T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15;-1.15;-1.15;-1.15;-1.15;-1.15;-1.15;-1.15	5.21	5.21	0.72293	Small GTP-binding protein domain (1);	7739.210000	0.00166	N	0.000010	T	0.66297	0.2775	L	0.53561	1.675	0.80722	D	1	B	0.28378	0.209	B	0.28139	0.086	T	0.36163	-0.9759	10	0.22706	T	0.39	-7.9771	14.7852	0.69796	0.0:0.0:0.0:1.0	.	117	P08134	RHOC_HUMAN	S	117;117;117;117;117;117;117;117;154;117;117;117	ENSP00000345236:N117S;ENSP00000358647:N117S;ENSP00000358656:N117S;ENSP00000285735:N117S;ENSP00000358652:N117S;ENSP00000358651:N117S;ENSP00000358650:N117S;ENSP00000358646:N117S;ENSP00000434877:N154S;ENSP00000390823:N117S;ENSP00000436240:N117S;ENSP00000399424:N117S	ENSP00000285735:N117S	N	-	2	0	RHOC	113046766	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.245000	0.72398	1.972000	0.57404	0.444000	0.29173	AAT	.	.		0.572	RHOC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032904.2	NM_175744		C	113245243	T	C	113245243	3	2	211	1	0	0	0	0	1	0	0	0	13351	1493	52	2	239	2	RHOC	1	113245243	Missense_Mutation	SNP	T	TCGA-DD-AAE6-01A-11D-A40R-10	3287352	113245243	136005378	9	30388										
LCE2B	26239	hgsc.bcm.edu	37	chr1	152659435	152659435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	cctgccccagtgcccagctcCatgttcccctgcagtctctt	7	19	1	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:152659435C>T	ENST00000368780.3	+	2	170	c.116C>T	c.(115-117)cCa>cTa	p.P39L	LCE2B_ENST00000417924.2_Missense_Mutation_p.P39L	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	39	Cys-rich.|Pro-rich.				epidermis development (GO:0008544)|keratinization (GO:0031424)					endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	11	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCCCAGCTCCATGTTCCCCT	0.622																																					p.P39L		Atlas-SNP	.											.	LCE2B	40	.	0			c.C116T						.						146	151	149					1																	152659435		2203	4300	6503	SO:0001583	missense	26239	exon2			CAGCTCCATGTTC	BI670514	CCDS1020.1	1q21	2008-02-05	2004-10-11	2004-10-15	ENSG00000159455	ENSG00000159455		"Late cornified envelopes"	16610	protein-coding gene	gene with protein product		612610	"small proline rich-like (epidermal differentiation complex) 1B"	SPRL1B		11698679, 9344646	Standard	NM_014357		Approved	LEP10, XP5	uc001fai.3	O14633	OTTHUMG00000012404	ENST00000368780.3:c.116C>T	chr1.hg19:g.152659435C>T	ENSP00000357769:p.Pro39Leu	147.0	0.0		263.0	25.0	NM_014357	Q5TA80	Missense_Mutation	SNP	ENST00000368780.3	hg19	CCDS1020.1	.	.	.	.	.	.	.	.	.	.	C	0.033	-1.323675	0.01309	.	.	ENSG00000159455	ENST00000417924;ENST00000368780	T;T	0.03607	3.87;3.87	2.11	-0.333	0.12671	.	.	.	.	.	T	0.00845	0.0028	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47586	-0.9106	9	0.87932	D	0	.	2.8171	0.05459	0.2664:0.5558:0.0:0.1779	.	39	O14633	LCE2B_HUMAN	L	39	ENSP00000414043:P39L;ENSP00000357769:P39L	ENSP00000357769:P39L	P	+	2	0	LCE2B	150926059	0.063000	0.20901	0.003000	0.11579	0.054000	0.15201	1.336000	0.33850	-0.245000	0.09625	0.313000	0.20887	CCA	.	.		0.622	LCE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034524.1	NM_014357		T	152659435	C	T	152659435	3	4	211	1	0	0	0	0	1	0	0	0	8675	594	21	3	118	3	LCE2B	1	152659435	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	39414192	152659435	96591186	10	30389										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158621155	158621155	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gaatggagggagccttagttAcctgccggatttgagctcct	13	9	0	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:158621155A>T	ENST00000368147.4	-	24	3658		c.e24+1			NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1						actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGCCTTAGTTACCTGCCGGAT	0.458																																					.		Atlas-SNP	.											.	SPTA1	720	.	0			c.3477+2T>A						.						176	176	176					1																	158621155		1885	4111	5996	SO:0001630	splice_region_variant	6708	exon25			TTAGTTACCTGCC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3477+1T>A	chr1.hg19:g.158621155A>T		115.0	0.0		200.0	33.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Splice_Site	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	A	14.58	2.579287	0.46006	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	.	.	.	4.66	4.66	0.58398	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3863	0.55335	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SPTA1	156887779	1.000000	0.71417	0.999000	0.59377	0.366000	0.29705	6.280000	0.72626	2.081000	0.62600	0.533000	0.62120	.	.	.		0.458	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	Intron	T	158621155	A	T	158621155	5	4	211	1	0	0	0	0	0	0	1	0	15131	405	14	4	3896	4	SPTA1	1	158621155	Splice_Site	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	5961720	158621155	90629466	11	30390										
OR10J3	441911	hgsc.bcm.edu	37	chr1	159283710	159283710	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	catagtggatgatgaccactGtgaggtgggaggcgcaggtg	18	6	0	3	rs569041098		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:159283710G>A	ENST00000332217.5	-	1	739	c.740C>T	c.(739-741)aCa>aTa	p.T247I		NM_001004467.1	NP_001004467.1	Q5JRS4	O10J3_HUMAN	olfactory receptor, family 10, subfamily J, member 3	247						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T247R(1)		breast(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(19)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	47	all_hematologic(112;0.0429)					GATGACCACTGTGAGGTGGGA	0.517																																					p.T247I		Atlas-SNP	.											OR10J3,NS,carcinoma,0,1	OR10J3	86	.	1	Substitution - Missense(1)	kidney(1)	c.C740T						.						134	115	122					1																	159283710		2203	4300	6503	SO:0001583	missense	441911	exon1			ACCACTGTGAGGT		CCDS30909.1	1q23.2	2012-08-09		2004-03-10	ENSG00000196266	ENSG00000196266		"GPCR / Class A : Olfactory receptors"	14992	protein-coding gene	gene with protein product				OR10J3P			Standard	NM_001004467		Approved		uc010piu.2	Q5JRS4	OTTHUMG00000037233	ENST00000332217.5:c.740C>T	chr1.hg19:g.159283710G>A	ENSP00000331789:p.Thr247Ile	70.0	0.0		136.0	20.0	NM_001004467		Missense_Mutation	SNP	ENST00000332217.5	hg19	CCDS30909.1	.	.	.	.	.	.	.	.	.	.	G	6.284	0.420521	0.11928	.	.	ENSG00000196266	ENST00000332217	T	0.36157	1.27	5.34	2.48	0.30137	GPCR, rhodopsin-like superfamily (1);	0.244417	0.20970	U	0.082414	T	0.14098	0.0341	L	0.41632	1.29	0.09310	N	0.999998	B	0.27823	0.19	B	0.39840	0.311	T	0.38090	-0.9677	10	0.20046	T	0.44	.	7.236	0.26070	0.1566:0.1402:0.7032:0.0	.	247	Q5JRS4	O10J3_HUMAN	I	247	ENSP00000331789:T247I	ENSP00000331789:T247I	T	-	2	0	OR10J3	157550334	0.000000	0.05858	0.375000	0.26029	0.536000	0.34869	0.033000	0.13754	0.390000	0.25115	-0.137000	0.14449	ACA	.	.		0.517	OR10J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090629.1			A	159283710	G	A	159283710	3	1	211	1	0	0	0	0	1	0	0	0	10920	1377	48	3	251	3	OR10J3	1	159283710	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	662555	159283710	89966911	12	30391										
GPR161	23432	hgsc.bcm.edu	37	chr1	168056873	168056873	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tcaccgagctccttctcttgGgtgggcaagtgcagtgagag	14	10	2	1	rs371331680		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:168056873G>T	ENST00000367838.1	-	7	1587	c.1274C>A	c.(1273-1275)cCc>cAc	p.P425H	GPR161_ENST00000361697.2_Missense_Mutation_p.P425H|GPR161_ENST00000537209.1_Missense_Mutation_p.P445H|GPR161_ENST00000539777.1_Missense_Mutation_p.P347H|GPR161_ENST00000367835.1_Missense_Mutation_p.P425H|GPR161_ENST00000271357.5_Missense_Mutation_p.P425H|GPR161_ENST00000367836.1_Missense_Mutation_p.P293H|GPR161_ENST00000546300.1_Missense_Mutation_p.P311H	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	425					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					CCTTCTCTTGGGTGGGCAAGT	0.468																																					p.P445H		Atlas-SNP	.											.	GPR161	56	.	0			c.C1334A						.	G	HIS/PRO	1,4405	2.1+/-5.4	0,1,2202	182	173	176		1274	5.6	1	1		176	0,8600		0,0,4300	no	missense	GPR161	NM_153832.1	77	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	benign	425/530	168056873	1,13005	2203	4300	6503	SO:0001583	missense	23432	exon6			CTCTTGGGTGGGC	AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"GPCR / Class A : Orphans"	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.1274C>A	chr1.hg19:g.168056873G>T	ENSP00000356812:p.Pro425His	83.0	0.0		185.0	75.0	NM_001267609	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Missense_Mutation	SNP	ENST00000367838.1	hg19	CCDS1268.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.906769	0.52333	2.27E-4	0.0	ENSG00000143147	ENST00000367838;ENST00000271357;ENST00000367836;ENST00000367835;ENST00000546300;ENST00000539777;ENST00000537209;ENST00000361697	T;T;D;T;T;T;T;T	0.81821	-0.08;-0.08;-1.54;-0.08;-1.07;-1.06;0.0;-0.08	5.61	5.61	0.85477	.	0.455799	0.24359	N	0.039209	T	0.64864	0.2637	L	0.44542	1.39	0.30087	N	0.808677	B;B;B;B;B	0.33777	0.425;0.07;0.27;0.299;0.13	B;B;B;B;B	0.28465	0.061;0.024;0.09;0.028;0.016	T	0.73043	-0.4107	9	0.72032	D	0.01	-37.6914	14.9068	0.70727	0.0:0.0:0.856:0.144	.	445;311;347;445;425	F5GXD6;B7Z5E8;F5H6J7;B7Z5Z6;Q8N6U8	.;.;.;.;GP161_HUMAN	H	425;425;293;425;311;347;445;425	ENSP00000356812:P425H;ENSP00000271357:P425H;ENSP00000356810:P293H;ENSP00000356809:P425H;ENSP00000444348:P311H;ENSP00000437576:P347H;ENSP00000441039:P445H;ENSP00000355194:P425H	ENSP00000271357:P425H	P	-	2	0	GPR161	166323497	1.000000	0.71417	0.992000	0.48379	0.968000	0.65278	3.878000	0.56130	2.628000	0.89032	0.561000	0.74099	CCC	.	.		0.468	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369		T	168056873	G	T	168056873	3	4	211	1	0	0	0	0	1	0	0	0	6673	1232	43	3	323	3	GPR161	1	168056873	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	8773163	168056873	81193748	13	30392										
TNR	7143	hgsc.bcm.edu	37	chr1	175348809	175348809	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	acttcggcttcactgttatcCcactcgaggtcaaggctggt	10	12	2	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:175348809C>T	ENST00000367674.2	-	9	2550	c.1842G>A	c.(1840-1842)tgG>tgA	p.W614*	TNR_ENST00000263525.2_Nonsense_Mutation_p.W614*			Q92752	TENR_HUMAN	tenascin R	614	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					CACTGTTATCCCACTCGAGGT	0.517																																					p.W614X		Atlas-SNP	.											.	TNR	399	.	0			c.G1842A						.						115	87	97					1																	175348809		2203	4300	6503	SO:0001587	stop_gained	7143	exon9			GTTATCCCACTCG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.1842G>A	chr1.hg19:g.175348809C>T	ENSP00000356646:p.Trp614*	75.0	0.0		141.0	21.0	NM_003285	C9J563|Q15568|Q5R3G0	Nonsense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	C	46	12.439282	0.99668	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8373	0.92168	0.0:1.0:0.0:0.0	.	.	.	.	X	614	.	ENSP00000263525:W614X	W	-	3	0	TNR	173615432	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.797000	0.75150	2.534000	0.85438	0.650000	0.86243	TGG	.	.		0.517	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		T	175348809	C	T	175348809	4	4	211	1	0	0	0	0	0	1	0	0	16353	624	22	3	2294	3	TNR	1	175348809	Nonsense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	7291936	175348809	73901812	14	30393										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186024781	186024781	+	Frame_Shift_Del	DEL	C	C	-													0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	aatgtagcaggaatgactgaCaaaaaatatgacttaagtgt							TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:186024781delC	ENST00000271588.4	+	45	7348	c.7119delC	c.(7117-7119)gacfs	p.D2373fs	HMCN1_ENST00000367492.2_Frame_Shift_Del_p.D2373fs	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2373	Ig-like C2-type 21.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GAATGACTGACAAAAAATATG	0.418																																					p.D2373fs		Atlas-INDEL	.											.	HMCN1	797	.	0			c.7118delA						.						140	129	133					1																	186024781		2203	4300	6503	SO:0001589	frameshift_variant	83872	exon45			.	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7119delC	chr1.hg19:g.186024781delC	ENSP00000271588:p.Asp2373fs	149.0	0.0		221.0	89.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Frame_Shift_Del	DEL	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.418	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		-	186024781	C	-	186024781	7	5	211	1	0	1	0	1	0	0	0	0	7229	477	17	0	7297	0	HMCN1	1	186024781	Frame_Shift_Del	DEL	C	TCGA-DD-AAE6-01A-11D-A40R-10	10675972	186024781	63225840	15	30394										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214585026	214585026	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gaaaaatgaaattacacttaCcataggaaatagcacatact	5	7	0	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:214585026C>T	ENST00000366956.5	-	5	705		c.e5+1		PTPN14_ENST00000543945.1_Splice_Site	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14						lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		ATTACACTTACCATAGGAAAT	0.323																																					.	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											.	PTPN14	168	.	0			c.510+1G>A						.						51	55	54					1																	214585026		2203	4291	6494	SO:0001630	splice_region_variant	5784	exon6			CACTTACCATAGG	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.510+1G>A	chr1.hg19:g.214585026C>T		458.0	0.0		832.0	106.0	NM_005401	Q5VSI0	Splice_Site	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.855832	0.71834	.	.	ENSG00000152104	ENST00000366956;ENST00000543945	.	.	.	4.71	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8542	0.78965	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PTPN14	212651649	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	6.716000	0.74702	2.158000	0.67659	0.557000	0.71058	.	.	.		0.323	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401	Intron	T	214585026	C	T	214585026	5	4	211	1	0	0	0	0	0	0	1	0	12796	521	18	3	3112	3	PTPN14	1	214585026	Splice_Site	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	28560245	214585026	34665595	16	30395										
PSEN2	5664	hgsc.bcm.edu	37	chr1	227076565	227076566	+	Frame_Shift_Ins	INS	-	-	C													0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tacaatgtggccatggactaINSccccaccctcttgctgactg							TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:227076565_227076566insC	ENST00000366783.3	+	8	1038_1039	c.602_603insC	c.(601-606)taccccfs	p.YP201fs	PSEN2_ENST00000340188.4_Frame_Shift_Ins_p.YP201fs|PSEN2_ENST00000366782.1_Frame_Shift_Ins_p.YP234fs|PSEN2_ENST00000422240.2_Frame_Shift_Ins_p.YP201fs|PSEN2_ENST00000391872.2_Frame_Shift_Ins_p.YP234fs|PSEN2_ENST00000472139.2_Frame_Shift_Ins_p.YP57fs	NM_000447.2|NM_012486.2	NP_000438.2|NP_036618.2	P49810	PSN2_HUMAN	presenilin 2	201					amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|brain morphogenesis (GO:0048854)|calcium ion transport (GO:0006816)|cardiac muscle contraction (GO:0060048)|cell fate specification (GO:0001708)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|forebrain development (GO:0030900)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|locomotion (GO:0040011)|lung alveolus development (GO:0048286)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|memory (GO:0007613)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of protein phosphorylation (GO:0001933)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of synaptic plasticity (GO:0048167)|response to hypoxia (GO:0001666)|somitogenesis (GO:0001756)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear inner membrane (GO:0005637)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|urinary_tract(1)	20		Prostate(94;0.0771)				GCCATGGACTACCCCACCCTCT	0.579																																					p.Y201fs		Atlas-INDEL	.											.	PSEN2	55	.	0			c.602_603insC						.																																			SO:0001589	frameshift_variant	5664	exon8			.	BC006365	CCDS1556.1, CCDS44324.1	1q42.13	2014-09-17	2014-02-24		ENSG00000143801	ENSG00000143801			9509	protein-coding gene	gene with protein product		600759	"Alzheimer disease 4"	AD4		7638621	Standard	NM_000447		Approved	AD3L, STM2, PS2	uc009xeo.1	P49810	OTTHUMG00000037563	ENST00000366783.3:c.606dupC	chr1.hg19:g.227076569_227076569dupC	ENSP00000355747:p.Tyr201fs	83.0	0.0		122.0	26.0	NM_012486	A8K8D4|B1AP21|Q96P32	Frame_Shift_Ins	INS	ENST00000366783.3	hg19	CCDS1556.1																																																																																			.	.		0.579	PSEN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091539.1	NM_000447		C	227076566	-	C	227076565	7	5	211	1	0	1	1	0	0	0	0	0	12663	391	14	0	620	0	PSEN2	1	227076565	Frame_Shift_Ins	INS	-	TCGA-DD-AAE6-01A-11D-A40R-10	12491539	227076565	22174056	17	30396										
OR2G3	81469	hgsc.bcm.edu	37	chr1	247769166	247769166	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	agaccaaagaagacgatcacTtacggtggttgtgtggcgca	13	8	1	3			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:247769166T>G	ENST00000320002.2	+	1	311	c.279T>G	c.(277-279)acT>acG	p.T93T	RNU6-691P_ENST00000516585.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(31)|skin(5)	50	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			AGACGATCACTTACGGTGGTT	0.468																																					p.T93T		Atlas-SNP	.											.	OR2G3	108	.	0			c.T279G						.						298	266	277					1																	247769166		2203	4300	6503	SO:0001819	synonymous_variant	81469	exon1			GATCACTTACGGT	BK004417	CCDS31093.1	1q44	2012-08-09			ENSG00000177476	ENSG00000177476		"GPCR / Class A : Olfactory receptors"	15008	protein-coding gene	gene with protein product							Standard	NM_001001914		Approved		uc010pyz.2	Q8NGZ4	OTTHUMG00000040576	ENST00000320002.2:c.279T>G	chr1.hg19:g.247769166T>G		107.0	0.0		178.0	48.0	NM_001001914	B2RN64|Q5JQT1|Q6IF45	Silent	SNP	ENST00000320002.2	hg19	CCDS31093.1																																																																																			.	.		0.468	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1			G	247769166	T	G	247769166	2	3	211	1	0	0	0	0	0	0	0	1	11008	1596	56	5		5	OR2G3	1	247769166	Silent	SNP	T	TCGA-DD-AAE6-01A-11D-A40R-10	20692601	247769166	1481455	18	30397										
OR2T10	127069	hgsc.bcm.edu	37	chr1	248756758	248756758	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tctgcacctcccaactgcagGtagaagtacatctgggtgcc	10	13	2	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr1:248756758G>A	ENST00000330500.2	-	1	342	c.312C>T	c.(310-312)taC>taT	p.Y104Y	Y_RNA_ENST00000364732.1_RNA	NM_001004693.1	NP_001004693.1	Q8NGZ9	O2T10_HUMAN	olfactory receptor, family 2, subfamily T, member 10	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(17)|skin(3)|upper_aerodigestive_tract(1)	26	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCAACTGCAGGTAGAAGTACA	0.537																																					p.Y104Y		Atlas-SNP	.											.	OR2T10	58	.	0			c.C312T						.						68	76	74					1																	248756758		2046	4235	6281	SO:0001819	synonymous_variant	127069	exon1			CTGCAGGTAGAAG		CCDS31121.1	1q44	2012-08-09			ENSG00000184022	ENSG00000184022		"GPCR / Class A : Olfactory receptors"	19573	protein-coding gene	gene with protein product							Standard	NM_001004693		Approved		uc010pzn.2	Q8NGZ9	OTTHUMG00000040388	ENST00000330500.2:c.312C>T	chr1.hg19:g.248756758G>A		164.0	0.0		209.0	27.0	NM_001004693	B2RNK7	Silent	SNP	ENST00000330500.2	hg19	CCDS31121.1																																																																																			.	.		0.537	OR2T10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097139.1	NM_001004693		A	248756758	G	A	248756758	2	1	211	1	0	0	0	0	0	0	0	1	11026	1256	44	3		3	OR2T10	1	248756758	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	987592	248756758	493863	19	30398										
RASGRP3	25780	hgsc.bcm.edu	37	chr2	33764196	33764196	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	acgacgcccaacaagcctgtGgtacccctggagtgggcatt	12	13	0	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr2:33764196G>A	ENST00000403687.3	+	12	1937	c.1197G>A	c.(1195-1197)gtG>gtA	p.V399V	RASGRP3_ENST00000407811.1_Silent_p.V398V|RASGRP3_ENST00000402538.3_Silent_p.V399V	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	399					MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)			large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					ACAAGCCTGTGGTACCCCTGG	0.443																																					p.V399V		Atlas-SNP	.											.	RASGRP3	87	.	0			c.G1197A						.						44	41	42					2																	33764196		1857	4097	5954	SO:0001819	synonymous_variant	25780	exon13			GCCTGTGGTACCC	AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"EF-hand domain containing"	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.1197G>A	chr2.hg19:g.33764196G>A		331.0	0.0		299.0	145.0	NM_170672	D6W583|O94931|Q53SD7	Silent	SNP	ENST00000403687.3	hg19	CCDS46256.1																																																																																			.	.		0.443	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376		A	33764196	G	A	33764196	2	1	211	1	0	0	0	0	0	0	0	1	13091	1335	47	3		3	RASGRP3	2	33764196	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10		33764196	209435177	20	30399										
LOXL3	84695	hgsc.bcm.edu	37	chr2	74776519	74776519	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tagaaggccgcgttgaccctCttttcgctggggaagcccag	13	12	1	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr2:74776519C>T	ENST00000264094.3	-	4	740	c.669G>A	c.(667-669)aaG>aaA	p.K223K	LOXL3_ENST00000409249.1_Silent_p.K223K|LOXL3_ENST00000484369.1_5'UTR|LOXL3_ENST00000409986.1_Intron|LOXL3_ENST00000393937.2_Intron|DOK1_ENST00000409429.1_Intron|LOXL3_ENST00000409549.1_Silent_p.K223K	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	223	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						CGTTGACCCTCTTTTCGCTGG	0.647																																					p.K223K		Atlas-SNP	.											.	LOXL3	73	.	0			c.G669A						.						18	19	19					2																	74776519		2203	4300	6503	SO:0001819	synonymous_variant	84695	exon4			GACCCTCTTTTCG	AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.669G>A	chr2.hg19:g.74776519C>T		61.0	0.0		73.0	10.0	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Silent	SNP	ENST00000264094.3	hg19	CCDS1953.1	.	.	.	.	.	.	.	.	.	.	C	19.28	3.798190	0.70567	.	.	ENSG00000115318	ENST00000420535	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	T	0.71937	0.3399	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70310	-0.4907	4	.	.	.	.	16.0841	0.81025	0.0:1.0:0.0:0.0	.	.	.	.	K	23	.	.	R	-	2	0	LOXL3	74630027	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	3.852000	0.55934	2.646000	0.89796	0.563000	0.77884	AGA	.	.		0.647	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		T	74776519	C	T	74776519	2	4	211	1	0	0	0	0	0	0	0	1	8910	912	32	3		3	LOXL3	2	74776519	Silent	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	41012323	74776519	168422854	21	30400										
EPB41L5	57669	hgsc.bcm.edu	37	chr2	120834878	120834878	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tagaaatgtatggggttgatAtgcatgtggtcaaggtaagc	14	3	1	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr2:120834878A>G	ENST00000263713.5	+	9	914	c.700A>G	c.(700-702)Atg>Gtg	p.M234V	EPB41L5_ENST00000443124.1_Missense_Mutation_p.M234V|EPB41L5_ENST00000331393.4_Missense_Mutation_p.M234V|EPB41L5_ENST00000443902.2_Missense_Mutation_p.M234V|EPB41L5_ENST00000452780.1_Missense_Mutation_p.M234V	NM_020909.3	NP_065960.2	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	234	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actomyosin structure organization (GO:0031032)|apical constriction (GO:0003383)|axial mesoderm morphogenesis (GO:0048319)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ectoderm development (GO:0007398)|embryonic foregut morphogenesis (GO:0048617)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|in utero embryonic development (GO:0001701)|left/right axis specification (GO:0070986)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of protein binding (GO:0032091)|neural plate morphogenesis (GO:0001839)|paraxial mesoderm development (GO:0048339)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein binding (GO:0032092)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of establishment of protein localization (GO:0070201)|somite rostral/caudal axis specification (GO:0032525)|substrate-dependent cell migration, cell attachment to substrate (GO:0006931)|unidimensional cell growth (GO:0009826)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(12)|ovary(1)	26						TGGGGTTGATATGCATGTGGT	0.368																																					p.M234V		Atlas-SNP	.											.	EPB41L5	98	.	0			c.A700G						.						101	106	104					2																	120834878		2203	4300	6503	SO:0001583	missense	57669	exon9			GTTGATATGCATG	AK023019	CCDS2130.1, CCDS54392.1, CCDS54393.1	2q14.2	2009-07-28			ENSG00000115109	ENSG00000115109			19819	protein-coding gene	gene with protein product		611730					Standard	NM_001184937		Approved	KIAA1548, FLJ12957, BE37, YMO1	uc002tmg.3	Q9HCM4	OTTHUMG00000131433	ENST00000263713.5:c.700A>G	chr2.hg19:g.120834878A>G	ENSP00000263713:p.Met234Val	489.0	1.0		411.0	265.0	NM_020909	Q7Z5S1|Q8IZ12|Q9H975	Missense_Mutation	SNP	ENST00000263713.5	hg19	CCDS2130.1	.	.	.	.	.	.	.	.	.	.	A	17.57	3.423657	0.62733	.	.	ENSG00000115109	ENST00000263713;ENST00000443902;ENST00000331393;ENST00000443124;ENST00000452780	T;T;T;T;T	0.75704	-0.96;-0.96;-0.96;-0.96;-0.96	5.18	5.18	0.71444	Band 4.1 domain (1);FERM central domain (1);FERM domain (1);Pleckstrin homology-type (1);FERM conserved site (1);	0.000000	0.85682	D	0.000000	D	0.84061	0.5389	M	0.62154	1.92	0.80722	D	1	P;D;P;D	0.76494	0.725;0.999;0.729;0.999	B;D;B;D	0.83275	0.439;0.994;0.413;0.996	D	0.85825	0.1388	10	0.72032	D	0.01	.	14.6954	0.69118	1.0:0.0:0.0:0.0	.	234;234;234;234	Q9HCM4-3;Q9HCM4-4;Q9HCM4-2;Q9HCM4	.;.;.;E41L5_HUMAN	V	234	ENSP00000263713:M234V;ENSP00000393856:M234V;ENSP00000329687:M234V;ENSP00000393722:M234V;ENSP00000390439:M234V	ENSP00000263713:M234V	M	+	1	0	EPB41L5	120551348	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	8.978000	0.93450	1.965000	0.57142	0.459000	0.35465	ATG	.	.		0.368	EPB41L5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254230.2	NM_020909		G	120834878	A	G	120834878	3	3	211	1	0	0	0	0	1	0	0	0	5159	449	16	2	730	2	EPB41L5	2	120834878	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	46058359	120834878	122364495	22	30401										
CCDC74B	91409	hgsc.bcm.edu	37	chr2	130897517	130897517	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gggaaatgcgtggcttcttgGtccctgggtgaaggaagagt	17	6	1	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr2:130897517G>A	ENST00000310463.6	-	7	1091	c.954C>T	c.(952-954)gaC>gaT	p.D318D	CCDC74B_ENST00000409943.3_Silent_p.D252D|CCDC74B_ENST00000392984.3_Silent_p.D420D|MED15P9_ENST00000427638.1_RNA	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	318										endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					TGGCTTCTTGGTCCCTGGGTG	0.617																																					p.D318D		Atlas-SNP	.											.	CCDC74B	27	.	0			c.C954T						.						41	43	42					2																	130897517		2201	4296	6497	SO:0001819	synonymous_variant	91409	exon7			TTCTTGGTCCCTG		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.954C>T	chr2.hg19:g.130897517G>A		185.0	0.0		141.0	31.0	NM_207310	Q6NW18	Silent	SNP	ENST00000310463.6	hg19	CCDS2155.1	.	.	.	.	.	.	.	.	.	.	.	14.42	2.531439	0.45073	.	.	ENSG00000152076	ENST00000409488	.	.	.	3.78	-0.487	0.12060	.	.	.	.	.	T	0.49474	0.1559	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51228	-0.8732	5	0.72032	D	0.01	.	1.5157	0.02505	0.1155:0.2071:0.3247:0.3527	.	.	.	.	I	216	.	ENSP00000386250:T216I	T	-	2	0	CCDC74B	130613987	0.998000	0.40836	0.998000	0.56505	0.719000	0.41307	0.559000	0.23485	0.011000	0.14865	0.450000	0.29827	ACC	.	.		0.617	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310		A	130897517	G	A	130897517	2	1	211	1	0	0	0	0	0	0	0	1	2850	1252	44	3		3	CCDC74B	2	130897517	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	10062639	130897517	112301856	23	30402										
ZEB2	9839	hgsc.bcm.edu	37	chr2	145156639	145156639	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gagcttctttccagggatggGgacctggaatttgagtactg	14	7	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr2:145156639G>A	ENST00000558170.2	-	8	3299	c.2115C>T	c.(2113-2115)tcC>tcT	p.S705S	ZEB2_ENST00000303660.4_Silent_p.S705S|ZEB2_ENST00000539609.3_Silent_p.S681S|ZEB2_ENST00000409487.3_Silent_p.S705S	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	705					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		CCAGGGATGGGGACCTGGAAT	0.458																																					p.S705S	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											.	ZEB2	218	.	0			c.C2115T						.						160	168	165					2																	145156639		2203	4300	6503	SO:0001819	synonymous_variant	9839	exon8			GGATGGGGACCTG	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.2115C>T	chr2.hg19:g.145156639G>A		143.0	0.0		125.0	41.0	NM_014795	A0JP09|B7Z2P2|F5H814|Q9UED1	Silent	SNP	ENST00000558170.2	hg19	CCDS2186.1																																																																																			.	.		0.458	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		A	145156639	G	A	145156639	2	1	211	1	0	0	0	0	0	0	0	1	17639	1219	43	3		3	ZEB2	2	145156639	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	14259122	145156639	98042734	24	30403										
SLC11A1	6556	hgsc.bcm.edu	37	chr2	219249062	219249062	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gaaacatcgagtcagatcttCaggctggcgccgtggcggga	15	10	3	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr2:219249062C>T	ENST00000233202.6	+	3	587	c.247C>T	c.(247-249)Cag>Tag	p.Q83*	SLC11A1_ENST00000539932.1_5'UTR|SLC11A1_ENST00000473367.1_3'UTR	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	83					activation of protein kinase activity (GO:0032147)|antigen processing and presentation of peptide antigen (GO:0048002)|cadmium ion transmembrane transport (GO:0070574)|cellular cadmium ion homeostasis (GO:0006876)|cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|divalent metal ion export (GO:0070839)|inflammatory response (GO:0006954)|interaction with host (GO:0051701)|interleukin-2 production (GO:0032623)|interleukin-3 production (GO:0032632)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|L-arginine import (GO:0043091)|macrophage activation (GO:0042116)|manganese ion transport (GO:0006828)|MHC class II biosynthetic process (GO:0045342)|mRNA stabilization (GO:0048255)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cytokine production (GO:0001818)|nitrite transport (GO:0015707)|phagocytosis (GO:0006909)|phagosome maturation (GO:0090382)|positive regulation of cytokine production (GO:0001819)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of gene expression (GO:0010628)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus, translocation (GO:0000060)|respiratory burst (GO:0045730)|response to bacterium (GO:0009617)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|T cell cytokine production (GO:0002369)|T cell proliferation involved in immune response (GO:0002309)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|wound healing (GO:0042060)	cell outer membrane (GO:0009279)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|tertiary granule membrane (GO:0070821)	manganese ion transmembrane transporter activity (GO:0005384)|metal ion:proton antiporter activity (GO:0051139)|protein homodimerization activity (GO:0042803)|transition metal ion transmembrane transporter activity (GO:0046915)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTCAGATCTTCAGGCTGGCGC	0.582																																					p.Q83X		Atlas-SNP	.											.	SLC11A1	41	.	0			c.C247T						.						111	110	110					2																	219249062		2203	4300	6503	SO:0001587	stop_gained	6556	exon3			GATCTTCAGGCTG	D38171	CCDS2415.1	2q35	2013-07-18	2013-07-18		ENSG00000018280	ENSG00000018280		"Solute carriers"	10907	protein-coding gene	gene with protein product	"natural resistance-associated macrophage protein 1"	600266		LSH, NRAMP, NRAMP1		7964458, 7980580	Standard	NM_000578		Approved		uc002vhv.3	P49279	OTTHUMG00000086747	ENST00000233202.6:c.247C>T	chr2.hg19:g.219249062C>T	ENSP00000233202:p.Gln83*	86.0	0.0		100.0	11.0	NM_000578	C0H5Y3	Nonsense_Mutation	SNP	ENST00000233202.6	hg19	CCDS2415.1	.	.	.	.	.	.	.	.	.	.	C	36	5.975222	0.97162	.	.	ENSG00000018280	ENST00000233202	.	.	.	5.06	5.06	0.68205	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-24.476	18.6237	0.91330	0.0:1.0:0.0:0.0	.	.	.	.	X	83	.	ENSP00000233202:Q83X	Q	+	1	0	SLC11A1	218957306	1.000000	0.71417	0.964000	0.40570	0.806000	0.45545	7.404000	0.79996	2.620000	0.88729	0.561000	0.74099	CAG	.	.		0.582	SLC11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195076.2	NM_000578		T	219249062	C	T	219249062	4	4	211	1	0	0	0	0	0	1	0	0	14395	827	29	3	257	3	SLC11A1	2	219249062	Nonsense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	74092423	219249062	23950311	25	30404										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222347320	222347320	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	cattataggaaatgtcctggCggccacctgtattctgaggg	12	9	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr2:222347320C>T	ENST00000281821.2	-	5	1111	c.1070G>A	c.(1069-1071)cGc>cAc	p.R357H	EPHA4_ENST00000392071.4_Missense_Mutation_p.R306H|EPHA4_ENST00000409854.1_Missense_Mutation_p.R357H|EPHA4_ENST00000409938.1_Missense_Mutation_p.R357H	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	357	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)	p.R357H(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		AATGTCCTGGCGGCCACCTGT	0.522																																					p.R357H		Atlas-SNP	.											EPHA4_ENST00000281821,colon,carcinoma,0,2	EPHA4	263	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1070A						.						142	155	151					2																	222347320		2203	4300	6503	SO:0001583	missense	2043	exon5			TCCTGGCGGCCAC	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.1070G>A	chr2.hg19:g.222347320C>T	ENSP00000281821:p.Arg357His	88.0	1.0		111.0	28.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.610380|5.610380	0.96637|0.96637	.|.	.|.	ENSG00000116106|ENSG00000116106	ENST00000441679|ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071;ENST00000443796	.|T;T;T;T;T	.|0.58506	.|0.33;0.33;0.33;0.33;0.33	6.06|6.06	6.06|6.06	0.98353|0.98353	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.82226|0.82226	0.4991|0.4991	M|M	0.90650|0.90650	3.135|3.135	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.84334|0.84334	0.0523|0.0523	5|10	.|0.87932	.|D	.|0	.|.	20.6208|20.6208	0.99490|0.99490	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|357	.|P54764	.|EPHA4_HUMAN	T|H	94|357;357;357;306;61	.|ENSP00000281821:R357H;ENSP00000386276:R357H;ENSP00000386829:R357H;ENSP00000375923:R306H;ENSP00000395917:R61H	.|ENSP00000281821:R357H	A|R	-|-	1|2	0|0	EPHA4|EPHA4	222055564|222055564	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.818000|7.818000	0.86416|0.86416	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.		0.522	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222347320	C	T	222347320	3	4	211	1	0	0	0	0	1	0	0	0	5171	768	27	1	1942	1	EPHA4	2	222347320	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	3098258	222347320	20852053	26	30405										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222436897	222436897	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ccttcattcgcggggtatacCctggaacctgtgacagcgtc	11	13	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr2:222436897C>T	ENST00000281821.2	-	1	113	c.72G>A	c.(70-72)agG>agA	p.R24R	EPHA4_ENST00000392071.4_5'UTR|EPHA4_ENST00000409854.1_Silent_p.R24R|EPHA4_ENST00000409938.1_Silent_p.R24R|CTD-2308L22.1_ENST00000609776.1_RNA	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	24					adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		CGGGGTATACCCTGGAACCTG	0.617																																					p.R24R		Atlas-SNP	.											.	EPHA4	263	.	0			c.G72A						.						95	91	92					2																	222436897		2203	4300	6503	SO:0001819	synonymous_variant	2043	exon1			GTATACCCTGGAA	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.72G>A	chr2.hg19:g.222436897C>T		75.0	0.0		118.0	47.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Silent	SNP	ENST00000281821.2	hg19	CCDS2447.1																																																																																			.	.		0.617	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222436897	C	T	222436897	2	4	211	1	0	0	0	0	0	0	0	1	5171	622	22	3		3	EPHA4	2	222436897	Silent	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	89577	222436897	20762476	27	30406										
PPP1R7	5510	hgsc.bcm.edu	37	chr2	242092994	242092994	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	cagagcctgaaggatggggaGgagcggggggaggaggaccc	22	7	0	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr2:242092994G>C	ENST00000234038.6	+	2	630	c.156G>C	c.(154-156)gaG>gaC	p.E52D	PPP1R7_ENST00000401987.1_Intron|PPP1R7_ENST00000407025.1_Missense_Mutation_p.E52D|PPP1R7_ENST00000402734.1_Intron|PPP1R7_ENST00000404405.3_Missense_Mutation_p.E52D|PPP1R7_ENST00000272983.8_Intron|PPP1R7_ENST00000406106.3_Missense_Mutation_p.E52D	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	52					positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		AGGATGGGGAGGAGCGGGGGG	0.627																																					p.E52D	NSCLC(62;446 1299 5417 11238 27640)	Atlas-SNP	.											.	PPP1R7	35	.	0			c.G156C						.						80	77	78					2																	242092994		2203	4300	6503	SO:0001583	missense	5510	exon2			TGGGGAGGAGCGG	AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9295	protein-coding gene	gene with protein product		602877	"protein phosphatase 1, regulatory (inhibitor) subunit 7"			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.156G>C	chr2.hg19:g.242092994G>C	ENSP00000234038:p.Glu52Asp	49.0	0.0		79.0	33.0	NM_002712	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Missense_Mutation	SNP	ENST00000234038.6	hg19	CCDS2546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.17|10.17	1.275838|1.275838	0.23307|0.23307	.|.	.|.	ENSG00000115685|ENSG00000115685	ENST00000438799;ENST00000407025;ENST00000234038;ENST00000404405;ENST00000439916;ENST00000406106;ENST00000427172|ENST00000450367	T;T;T;T;T;T;T|.	0.49432|.	0.88;0.78;0.78;0.93;1.24;1.07;1.42|.	4.61|4.61	1.71|1.71	0.24356|0.24356	.|.	0.931323|.	0.08998|.	N|.	0.863444|.	T|T	0.30759|0.30759	0.0775|0.0775	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.23316|.	0.01;0.083;0.017;0.01|.	B;B;B;B|.	0.18561|.	0.007;0.011;0.022;0.01|.	T|T	0.03374|0.03374	-1.1043|-1.1043	10|5	0.33940|.	T|.	0.23|.	-12.5099|-12.5099	8.0951|8.0951	0.30824|0.30824	0.2533:0.0:0.7467:0.0|0.2533:0.0:0.7467:0.0	.|.	36;52;52;52|.	C9JD73;Q15435;Q15435-3;B5MBZ8|.	.;PP1R7_HUMAN;.;.|.	D|T	36;52;52;52;52;52;61|33	ENSP00000396376:E36D;ENSP00000385657:E52D;ENSP00000234038:E52D;ENSP00000385498:E52D;ENSP00000409719:E52D;ENSP00000385022:E52D;ENSP00000397985:E61D|.	ENSP00000234038:E52D|.	E|R	+|+	3|2	2|0	PPP1R7|PPP1R7	241741667|241741667	1.000000|1.000000	0.71417|0.71417	0.931000|0.931000	0.37212|0.37212	0.943000|0.943000	0.58893|0.58893	1.295000|1.295000	0.33377|0.33377	0.368000|0.368000	0.24481|0.24481	0.561000|0.561000	0.74099|0.74099	GAG|AGG	.	.		0.627	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712		C	242092994	G	C	242092994	3	2	211	1	0	0	0	0	1	0	0	0	12388	991	35	4	162	4	PPP1R7	2	242092994	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	19656097	242092994	1106379	28	30407										
SETMAR	6419	hgsc.bcm.edu	37	chr3	4354904	4354904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tcgtaccttggaatttatacCgaaaggaaggtttgtctgtg	11	6	1	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr3:4354904C>T	ENST00000358065.4	+	2	546	c.479C>T	c.(478-480)cCg>cTg	p.P160L	SETMAR_ENST00000425863.1_Missense_Mutation_p.P160L|SETMAR_ENST00000430981.1_Missense_Mutation_p.P160L|SUMF1_ENST00000534863.1_Intron	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	160	Histone-lysine N-methyltransferase.|SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		GAATTTATACCGAAAGGAAGG	0.413								Chromatin Structure																													p.P160L		Atlas-SNP	.											.	SETMAR	30	.	0			c.C479T						.						49	52	51					3																	4354904		2203	4299	6502	SO:0001583	missense	6419	exon2			TTATACCGAAAGG	U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.479C>T	chr3.hg19:g.4354904C>T	ENSP00000373354:p.Pro160Leu	72.0	0.0		79.0	28.0	NM_001243723	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	hg19	CCDS2563.2	.	.	.	.	.	.	.	.	.	.	C	16.98	3.271328	0.59649	.	.	ENSG00000170364	ENST00000358065;ENST00000430981;ENST00000425863	D;D;D	0.83673	-1.75;-1.75;-1.56	5.18	5.18	0.71444	SET domain (3);	.	.	.	.	D	0.90232	0.6946	M	0.61703	1.905	0.58432	D	0.999992	D;D;D	0.89917	1.0;0.992;0.964	D;P;B	0.91635	0.999;0.756;0.402	D	0.91177	0.4973	9	0.87932	D	0	.	18.7279	0.91722	0.0:1.0:0.0:0.0	.	160;147;160	E7EN68;Q53H47;C9JHK2	.;SETMR_HUMAN;.	L	160	ENSP00000373354:P160L;ENSP00000403000:P160L;ENSP00000403145:P160L	ENSP00000373354:P160L	P	+	2	0	SETMAR	4329904	0.997000	0.39634	0.405000	0.26409	0.133000	0.20885	4.199000	0.58426	2.412000	0.81896	0.557000	0.71058	CCG	.	.		0.413	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515		T	4354904	C	T	4354904	3	4	211	1	0	0	0	0	1	0	0	0	14155	652	23	1	485	1	SETMAR	3	4354904	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10		4354904	193667526	29	30408										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112324389	112324389	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	atcttctgggcagcgcatccCcagtgactgctgaatcgcca	10	14	2	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr3:112324389C>G	ENST00000206423.3	-	8	3681	c.2728G>C	c.(2728-2730)Ggg>Cgg	p.G910R	CCDC80_ENST00000439685.2_Missense_Mutation_p.G910R	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	910					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						CAGCGCATCCCCAGTGACTGC	0.483																																					p.G910R		Atlas-SNP	.											.	CCDC80	100	.	0			c.G2728C						.						122	101	108					3																	112324389		2203	4300	6503	SO:0001583	missense	151887	exon8			GCATCCCCAGTGA	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.2728G>C	chr3.hg19:g.112324389C>G	ENSP00000206423:p.Gly910Arg	111.0	0.0		132.0	28.0	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	hg19	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.852356	0.91355	.	.	ENSG00000091986	ENST00000206423;ENST00000439685;ENST00000444594;ENST00000479368	T;T;T	0.70869	-0.52;-0.52;0.62	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.78861	0.4350	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80139	-0.1507	10	0.72032	D	0.01	-31.8097	20.1099	0.97909	0.0:1.0:0.0:0.0	.	921;910	Q76M96-2;Q76M96	.;CCD80_HUMAN	R	910;910;511;188	ENSP00000206423:G910R;ENSP00000411814:G910R;ENSP00000418188:G188R	ENSP00000206423:G910R	G	-	1	0	CCDC80	113807079	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.753000	0.94483	0.585000	0.79938	GGG	.	.		0.483	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		G	112324389	C	G	112324389	3	3	211	1	0	0	0	0	1	0	0	0	2856	623	22	4	128	4	CCDC80	3	112324389	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	107969485	112324389	85698041	30	30409										
C3orf30	152405	hgsc.bcm.edu	37	chr3	118867141	118867141	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	aagtttcactccaatacatgGaaaaacaccacattctgcaa	4	11	2	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr3:118867141G>A	ENST00000295622.1	+	2	1553	c.1513G>A	c.(1513-1515)Gaa>Aaa	p.E505K	IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|RP11-484M3.5_ENST00000490594.1_Intron|IGSF11_ENST00000441144.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	505										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		CCAATACATGGAAAAACACCA	0.333																																					p.E505K		Atlas-SNP	.											.	C3orf30	64	.	0			c.G1513A						.						66	70	69					3																	118867141		2203	4300	6503	SO:0001583	missense	152405	exon2			TACATGGAAAAAC	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.1513G>A	chr3.hg19:g.118867141G>A	ENSP00000295622:p.Glu505Lys	393.0	1.0		477.0	171.0	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	hg19	CCDS2984.1	.	.	.	.	.	.	.	.	.	.	G	33	5.205185	0.95033	.	.	ENSG00000163424	ENST00000295622;ENST00000470341;ENST00000473121	T	0.76316	-1.01	4.74	4.74	0.60224	.	0.000000	0.49305	D	0.000147	D	0.85066	0.5612	L	0.59436	1.845	0.39884	D	0.973677	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86781	0.1979	10	0.87932	D	0	-29.9735	13.4162	0.60970	0.0:0.0:1.0:0.0	.	505;505	E9PFE5;Q96M34	.;CC030_HUMAN	K	505;505;272	ENSP00000295622:E505K	ENSP00000295622:E505K	E	+	1	0	C3orf30	120349831	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.670000	0.61583	2.609000	0.88269	0.655000	0.94253	GAA	.	.		0.333	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539		A	118867141	G	A	118867141	3	1	211	1	0	0	0	0	1	0	0	0	2222	1175	41	3	1519	3	C3orf30	3	118867141	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	6542752	118867141	79155289	31	30410										
CD80	941	hgsc.bcm.edu	37	chr3	119263423	119263423	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ctgataacgtcacttcagccAggtgttcccgcttgaaagcg	10	12	2	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr3:119263423A>G	ENST00000264246.3	-	3	754	c.392T>C	c.(391-393)cTg>cCg	p.L131P	CD80_ENST00000383668.3_Missense_Mutation_p.L131P|CD80_ENST00000478182.1_Missense_Mutation_p.L131P|CD80_ENST00000383669.3_Missense_Mutation_p.L131P	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	131	Ig-like V-type.				cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of signal transduction (GO:0009967)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	12					Abatacept(DB01281)|Belatacept(DB06681)	CACTTCAGCCAGGTGTTCCCG	0.463																																					p.L131P	Melanoma(132;135 1764 1806 5833 14593)	Atlas-SNP	.											.	CD80	35	.	0			c.T392C						.						91	93	93					3																	119263423		2203	4300	6503	SO:0001583	missense	941	exon3			TCAGCCAGGTGTT		CCDS2989.1	3q13.3-q21	2013-01-11	2006-03-31		ENSG00000121594	ENSG00000121594		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	1700	protein-coding gene	gene with protein product	"B-lymphocyte activation antigen B7"	112203	"CD80 antigen (CD28 antigen ligand 1, B7-1 antigen)", "CD80 molecule "	CD28LG, CD28LG1		1370389	Standard	NM_005191		Approved	B7.1, B7-1	uc003ecq.3	P33681	OTTHUMG00000159419	ENST00000264246.3:c.392T>C	chr3.hg19:g.119263423A>G	ENSP00000264246:p.Leu131Pro	106.0	0.0		102.0	37.0	NM_005191	Q5DTA9|Q5DTB0	Missense_Mutation	SNP	ENST00000264246.3	hg19	CCDS2989.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.694635	0.48202	.	.	ENSG00000121594	ENST00000264246;ENST00000478182;ENST00000383669;ENST00000383668	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.13	-2.1	0.07210	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.077590	0.07311	N	0.875910	T	0.58032	0.2094	M	0.76002	2.32	0.21290	N	0.99973	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.76575	0.988;0.941;0.982;0.982	T	0.50792	-0.8786	10	0.66056	D	0.02	-0.2705	4.9992	0.14255	0.3372:0.2687:0.0:0.3941	.	131;131;131;131	Q5DTA9;Q5DTB0;A0N0P2;P33681	.;.;.;CD80_HUMAN	P	131	ENSP00000264246:L131P;ENSP00000418364:L131P;ENSP00000373165:L131P;ENSP00000373164:L131P	ENSP00000264246:L131P	L	-	2	0	CD80	120746113	0.002000	0.14202	0.000000	0.03702	0.011000	0.07611	0.456000	0.21859	-0.208000	0.10171	0.528000	0.53228	CTG	.	.		0.463	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191		G	119263423	A	G	119263423	3	3	211	1	0	0	0	0	1	0	0	0	3040	188	7	2	490	2	CD80	3	119263423	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	396282	119263423	78759007	32	30411										
TBC1D19	55296	hgsc.bcm.edu	37	chr4	26719629	26719629	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	agtgcctcgccaccaaaatcAtacataagaggtaaattttt	6	9	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr4:26719629A>G	ENST00000264866.4	+	14	1307	c.1029A>G	c.(1027-1029)tcA>tcG	p.S343S	TBC1D19_ENST00000511789.1_Silent_p.S278S	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	343	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				CACCAAAATCATACATAAGAG	0.313																																					p.S343S		Atlas-SNP	.											.	TBC1D19	53	.	0			c.A1029G						.						94	90	92					4																	26719629		2202	4299	6501	SO:0001819	synonymous_variant	55296	exon14			AAAATCATACATA	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.1029A>G	chr4.hg19:g.26719629A>G		64.0	0.0		42.0	17.0	NM_018317	B9A6M0|Q9NUX1	Silent	SNP	ENST00000264866.4	hg19	CCDS3439.1																																																																																			.	.		0.313	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317		G	26719629	A	G	26719629	2	3	211	1	0	0	0	0	0	0	0	1	15622	204	8	2		2	TBC1D19	4	26719629	Silent	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10		26719629	164434647	33	30412										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90856478	90856478	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	actgagtacatgtctactttAcatgaaaatataaagaagca	6	6	1	3			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr4:90856478A>G	ENST00000394980.1	+	7	1966	c.1647A>G	c.(1645-1647)ttA>ttG	p.L549L	MMRN1_ENST00000264790.2_Silent_p.L549L|MMRN1_ENST00000508372.1_Silent_p.L291L|MMRN1_ENST00000394981.1_Intron			Q13201	MMRN1_HUMAN	multimerin 1	549					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		TGTCTACTTTACATGAAAATA	0.378																																					p.L549L		Atlas-SNP	.											.	MMRN1	174	.	0			c.A1647G						.						77	78	78					4																	90856478		2203	4300	6503	SO:0001819	synonymous_variant	22915	exon6			TACTTTACATGAA	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.1647A>G	chr4.hg19:g.90856478A>G		163.0	0.0		74.0	72.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Silent	SNP	ENST00000394980.1	hg19	CCDS3635.1																																																																																			.	.		0.378	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		G	90856478	A	G	90856478	2	3	211	1	0	0	0	0	0	0	0	1	9679	388	14	2		2	MMRN1	4	90856478	Silent	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	64136849	90856478	100297798	34	30413										
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1219041	1219041	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gtggagggcacaggcctggcCttcatcgtcttcaccgaggc	14	13	3	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr5:1219041C>G	ENST00000304460.10	+	9	1253	c.1197C>G	c.(1195-1197)gcC>gcG	p.A399A		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	399					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CAGGCCTGGCCTTCATCGTCT	0.622																																					p.A399A		Atlas-SNP	.											.	SLC6A19	99	.	0			c.C1197G						.						301	228	253					5																	1219041		2203	4300	6503	SO:0001819	synonymous_variant	340024	exon9			CCTGGCCTTCATC	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1197C>G	chr5.hg19:g.1219041C>G		37.0	0.0		98.0	10.0	NM_001003841	A8K446	Silent	SNP	ENST00000304460.10	hg19	CCDS34130.1																																																																																			.	.		0.622	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		G	1219041	C	G	1219041	2	3	211	1	0	0	0	0	0	0	0	1	14697	668	24	4		4	SLC6A19	5	1219041	Silent	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10		1219041	179696219	35	30414										
HMGCR	3156	hgsc.bcm.edu	37	chr5	74646733	74646733	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gatgaaaatgtgtccaagagAattgaaccaagtgtttccct	9	7	0	3			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr5:74646733A>T	ENST00000287936.4	+	9	1056	c.900A>T	c.(898-900)agA>agT	p.R300S	HMGCR_ENST00000343975.5_Missense_Mutation_p.R300S|HMGCR_ENST00000511206.1_Missense_Mutation_p.R300S	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	300					aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	TGTCCAAGAGAATTGAACCAA	0.363																																					p.R300S		Atlas-SNP	.											.	HMGCR	53	.	0			c.A900T						.						107	106	106					5																	74646733		2203	4300	6503	SO:0001583	missense	3156	exon9			CAAGAGAATTGAA		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"hydroxymethylglutaryl-CoA reductase", "3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"	142910	"3-hydroxy-3-methylglutaryl-Coenzyme A reductase"				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.900A>T	chr5.hg19:g.74646733A>T	ENSP00000287936:p.Arg300Ser	119.0	0.0		95.0	17.0	NM_001130996	B7Z3Y9|Q8N190	Missense_Mutation	SNP	ENST00000287936.4	hg19	CCDS4027.1	.	.	.	.	.	.	.	.	.	.	A	14.71	2.615796	0.46631	.	.	ENSG00000113161	ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975	T;T;T	0.43688	0.96;0.96;0.94	5.92	3.53	0.40419	.	0.040191	0.85682	D	0.000000	T	0.34250	0.0891	M	0.72118	2.19	0.58432	D	0.999999	P;P;P;P	0.49253	0.698;0.835;0.921;0.514	B;B;B;B	0.38500	0.155;0.275;0.213;0.115	T	0.37641	-0.9697	10	0.06891	T	0.86	-23.9061	10.1126	0.42572	0.8647:0.0:0.1353:0.0	.	300;300;300;300	B2R649;A8KA27;P04035-2;P04035	.;.;.;HMDH_HUMAN	S	300;231;300;300	ENSP00000426745:R300S;ENSP00000287936:R300S;ENSP00000340816:R300S	ENSP00000287936:R300S	R	+	3	2	HMGCR	74682489	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.350000	0.44063	0.497000	0.27926	0.533000	0.62120	AGA	.	.		0.363	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			T	74646733	A	T	74646733	3	4	211	1	0	0	0	0	1	0	0	0	7240	243	9	4	930	4	HMGCR	5	74646733	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	73427692	74646733	106268527	36	30415										
DDX46	9879	hgsc.bcm.edu	37	chr5	134121267	134121267	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gtttacggaggaacaggaatCagtgagcaggtagttatata	13	4	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr5:134121267C>T	ENST00000354283.4	+	11	1590	c.1455C>T	c.(1453-1455)atC>atT	p.I485I	DDX46_ENST00000452510.2_Silent_p.I485I|DDX46_ENST00000509178.1_3'UTR			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	485	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GAACAGGAATCAGTGAGCAGG	0.353																																					p.I485I	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.C1455T						.						148	153	151					5																	134121267		2203	4300	6503	SO:0001819	synonymous_variant	9879	exon11			AGGAATCAGTGAG		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.1455C>T	chr5.hg19:g.134121267C>T		89.0	0.0		93.0	18.0	NM_014829	O94894|Q96EI0|Q9Y658	Silent	SNP	ENST00000354283.4	hg19	CCDS34240.1																																																																																			.	.		0.353	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		T	134121267	C	T	134121267	2	4	211	1	0	0	0	0	0	0	0	1	4366	816	29	3		3	DDX46	5	134121267	Silent	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	59474534	134121267	46793993	37	30416										
PCDHGA11	56105	hgsc.bcm.edu	37	chr5	140802419	140802419	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	acgtgacagcggggacccgcCcctcagcagcaacgtgtcgc	13	16	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr5:140802419C>T	ENST00000398587.2	+	1	1658	c.1625C>T	c.(1624-1626)cCc>cTc	p.P542L	PCDHGB4_ENST00000519479.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Missense_Mutation_p.P542L|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	542	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGGACCCGCCCCTCAGCAGC	0.577																																					p.P542L		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.C1625T						.						142	164	157					5																	140802419		2203	4300	6503	SO:0001583	missense	56105	exon1			ACCCGCCCCTCAG	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"Cadherins / Protocadherins : Clustered"	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.1625C>T	chr5.hg19:g.140802419C>T	ENSP00000381589:p.Pro542Leu	114.0	0.0		115.0	25.0	NM_032091	B7ZVY8|Q9Y5D8|Q9Y5D9	Missense_Mutation	SNP	ENST00000398587.2	hg19	CCDS47294.1	.	.	.	.	.	.	.	.	.	.	c	13.53	2.264175	0.39995	.	.	ENSG00000253873	ENST00000398587;ENST00000518882	T;T	0.56941	0.43;0.43	5.72	4.84	0.62591	Cadherin (4);Cadherin-like (1);	0.354182	0.15011	U	0.285535	T	0.76758	0.4032	M	0.92219	3.285	0.37025	D	0.896408	D;P;D	0.55385	0.959;0.861;0.971	P;P;P	0.58721	0.809;0.492;0.844	D	0.84864	0.0821	10	0.87932	D	0	.	15.8788	0.79185	0.1366:0.8634:0.0:0.0	.	542;542;542	Q9Y5H2;Q9Y5H2-3;Q9Y5H2-2	PCDGB_HUMAN;.;.	L	542	ENSP00000381589:P542L;ENSP00000428333:P542L	ENSP00000381589:P542L	P	+	2	0	PCDHGA11	140782603	0.601000	0.26907	0.664000	0.29753	0.027000	0.11550	5.683000	0.68189	1.385000	0.46445	0.655000	0.94253	CCC	.	.		0.577	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914		T	140802419	C	T	140802419	3	4	211	1	0	0	0	0	1	0	0	0	11561	623	22	3	1627	3	PCDHGA11	5	140802419	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	6681152	140802419	40112841	38	30417										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148408005	148408005	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tctgaggtggccgagaggagCtcctcctccaggctggagtc	15	12	1	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr5:148408005C>A	ENST00000515425.1	-	11	1391	c.1290G>T	c.(1288-1290)gaG>gaT	p.E430D	SH3TC2_ENST00000513340.1_5'UTR|SH3TC2_ENST00000538184.1_5'UTR|SH3TC2_ENST00000394358.2_Missense_Mutation_p.E315D|SH3TC2_ENST00000512049.1_Missense_Mutation_p.E423D	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	430					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGAGAGGAGCTCCTCCTCCA	0.622																																					p.E430D		Atlas-SNP	.											.	SH3TC2	178	.	0			c.G1290T						.						38	42	40					5																	148408005		2203	4299	6502	SO:0001583	missense	79628	exon11			GAGGAGCTCCTCC	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.1290G>T	chr5.hg19:g.148408005C>A	ENSP00000423660:p.Glu430Asp	60.0	0.0		45.0	21.0	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	C	13.66	2.304268	0.40795	.	.	ENSG00000169247	ENST00000515425;ENST00000512049;ENST00000394358	T;T;T	0.77229	-1.08;-1.08;-0.71	5.73	2.76	0.32466	.	0.139235	0.45867	N	0.000329	T	0.75796	0.3898	N	0.22421	0.69	0.33744	D	0.619768	D;D;D;D	0.76494	0.999;0.997;0.997;0.999	D;D;D;D	0.78314	0.991;0.978;0.978;0.991	T	0.77305	-0.2637	10	0.38643	T	0.18	.	6.6655	0.23039	0.2331:0.5901:0.0:0.1769	.	315;423;430;430	C9JLC3;Q14CC0;E9PDF1;Q8TF17	.;.;.;S3TC2_HUMAN	D	430;423;315	ENSP00000423660:E430D;ENSP00000421860:E423D;ENSP00000377886:E315D	ENSP00000377886:E315D	E	-	3	2	SH3TC2	148388198	0.941000	0.31946	1.000000	0.80357	0.599000	0.36880	0.184000	0.16939	0.832000	0.34804	0.655000	0.94253	GAG	.	.		0.622	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		A	148408005	C	A	148408005	3	1	211	1	0	0	0	0	1	0	0	0	14277	796	28	3	2604	3	SH3TC2	5	148408005	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	7605586	148408005	32507255	39	30418										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157222615	157222615	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	cgcacctcccaccccaggcgCagtatctgccgtcccagtcc	8	21	1	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr6:157222615C>T	ENST00000350026.5	+	3	1844	c.1843C>T	c.(1843-1845)Cag>Tag	p.Q615*	ARID1B_ENST00000275248.4_Nonsense_Mutation_p.Q557*|ARID1B_ENST00000346085.5_Nonsense_Mutation_p.Q628*|ARID1B_ENST00000367148.1_Nonsense_Mutation_p.Q615*	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	615	Gln-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		ACCCCAGGCGCAGTATCTGCC	0.642																																					p.Q628X		Atlas-SNP	.											.	ARID1B	320	.	0			c.C1882T						.						34	34	34					6																	157222615		2203	4300	6503	SO:0001587	stop_gained	57492	exon4			CAGGCGCAGTATC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.1843C>T	chr6.hg19:g.157222615C>T	ENSP00000055163:p.Gln615*	35.0	0.0		33.0	10.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Nonsense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	C	39	7.675290	0.98425	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000354354;ENST00000414678;ENST00000319584	.	.	.	5.95	5.95	0.96441	.	0.449637	0.20067	N	0.099945	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	20.3697	0.98890	0.0:1.0:0.0:0.0	.	.	.	.	X	628;615;615;557;36;114;37	.	ENSP00000275248:Q557X	Q	+	1	0	ARID1B	157264307	0.998000	0.40836	0.997000	0.53966	0.951000	0.60555	4.410000	0.59774	2.811000	0.96726	0.655000	0.94253	CAG	.	.		0.642	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		T	157222615	C	T	157222615	4	4	211	1	0	0	0	0	0	1	0	0	914	711	25	3	1896	3	ARID1B	6	157222615	Nonsense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10		157222615	13892452	40	30419										
SYNJ2	8871	hgsc.bcm.edu	37	chr6	158490577	158490577	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tcttccagtactaccaacaaGaagatgtggggtgaacagct	10	9	1	3			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr6:158490577G>T	ENST00000355585.4	+	14	1887	c.1812G>T	c.(1810-1812)aaG>aaT	p.K604N	SYNJ2_ENST00000367122.2_Missense_Mutation_p.K604N|SYNJ2_ENST00000367121.3_Missense_Mutation_p.K604N	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	604					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		CTACCAACAAGAAGATGTGGG	0.463																																					p.K604N		Atlas-SNP	.											.	SYNJ2	111	.	0			c.G1812T						.						143	123	130					6																	158490577		2203	4300	6503	SO:0001583	missense	8871	exon14			CAACAAGAAGATG	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.1812G>T	chr6.hg19:g.158490577G>T	ENSP00000347792:p.Lys604Asn	53.0	0.0		53.0	30.0	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	hg19	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.577748	0.45902	.	.	ENSG00000078269	ENST00000367122;ENST00000367121;ENST00000355585	T;T;T	0.39056	1.1;1.1;1.1	5.15	1.88	0.25563	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.085060	0.51477	D	0.000096	T	0.17066	0.0410	L	0.33339	1.005	0.80722	D	1	P;B	0.39044	0.656;0.012	B;B	0.36608	0.229;0.028	T	0.11179	-1.0598	10	0.66056	D	0.02	.	9.0331	0.36271	0.3524:0.0:0.6476:0.0	.	604;604	O15056;O15056-3	SYNJ2_HUMAN;.	N	604	ENSP00000356089:K604N;ENSP00000356088:K604N;ENSP00000347792:K604N	ENSP00000347792:K604N	K	+	3	2	SYNJ2	158410565	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.636000	0.46545	2.078000	0.62432	0.529000	0.55759	AAG	.	.		0.463	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			T	158490577	G	T	158490577	3	4	211	1	0	0	0	0	1	0	0	0	15468	933	33	3	1866	3	SYNJ2	6	158490577	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	1267962	158490577	12624490	41	30420										
ANKMY2	57037	hgsc.bcm.edu	37	chr7	16644410	16644410	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	aggtagtgcaaaattccacaTccacaaaacccacctggcca	6	14	0	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr7:16644410T>A	ENST00000306999.2	-	8	1190	c.947A>T	c.(946-948)gAt>gTt	p.D316V		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	316						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		AAATTCCACATCCACAAAACC	0.433																																					p.D316V		Atlas-SNP	.											.	ANKMY2	46	.	0			c.A947T						.						108	102	104					7																	16644410		2203	4300	6503	SO:0001583	missense	57037	exon8			TCCACATCCACAA	AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.947A>T	chr7.hg19:g.16644410T>A	ENSP00000303570:p.Asp316Val	154.0	0.0		189.0	75.0	NM_020319	A4D124|Q659G1|Q96BL3	Missense_Mutation	SNP	ENST00000306999.2	hg19	CCDS5361.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.806125	0.70682	.	.	ENSG00000106524	ENST00000306999	D	0.85484	-1.99	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.82751	0.5105	M	0.64676	1.99	0.80722	D	1	B	0.31581	0.329	B	0.24155	0.051	T	0.80516	-0.1348	10	0.35671	T	0.21	-15.2592	16.6093	0.84858	0.0:0.0:0.0:1.0	.	316	Q8IV38	ANKY2_HUMAN	V	316	ENSP00000303570:D316V	ENSP00000303570:D316V	D	-	2	0	ANKMY2	16610935	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.698000	0.84413	2.324000	0.78689	0.533000	0.62120	GAT	.	.		0.433	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319		A	16644410	T	A	16644410	3	1	211	1	0	0	0	0	1	0	0	0	635	1435	50	4	390	4	ANKMY2	7	16644410	Missense_Mutation	SNP	T	TCGA-DD-AAE6-01A-11D-A40R-10		16644410	142494253	42	30421										
MPP6	51678	hgsc.bcm.edu	37	chr7	24718945	24718945	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gacttgcattctggatgtcaAcccacaagtaagctgcttgg	10	10	2	0	rs74407305		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr7:24718945A>G	ENST00000222644.5	+	10	1560	c.1310A>G	c.(1309-1311)aAc>aGc	p.N437S	MPP6_ENST00000409761.1_Missense_Mutation_p.N325S|MPP6_ENST00000396475.2_Missense_Mutation_p.N437S			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						CTGGATGTCAACCCACAAGTA	0.393																																					p.N437S		Atlas-SNP	.											.	MPP6	62	.	0			c.A1310G						.						100	92	95					7																	24718945		2203	4300	6503	SO:0001583	missense	51678	exon11			ATGTCAACCCACA	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.1310A>G	chr7.hg19:g.24718945A>G	ENSP00000222644:p.Asn437Ser	102.0	0.0		124.0	60.0	NM_016447	B2RAF0	Missense_Mutation	SNP	ENST00000222644.5	hg19	CCDS5388.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.547417	0.65311	.	.	ENSG00000105926	ENST00000222644;ENST00000409761;ENST00000396475	T;T;T	0.39406	1.08;1.08;1.08	5.97	4.8	0.61643	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.099771	0.42964	D	0.000634	T	0.37348	0.1000	L	0.31752	0.955	0.80722	D	1	P	0.36683	0.565	B	0.42882	0.401	T	0.09143	-1.0688	10	0.30078	T	0.28	.	13.2867	0.60247	0.8676:0.1324:0.0:0.0	.	437	Q9NZW5	MPP6_HUMAN	S	437;325;437	ENSP00000222644:N437S;ENSP00000386262:N325S;ENSP00000379737:N437S	ENSP00000222644:N437S	N	+	2	0	MPP6	24685470	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.339000	0.96797	1.055000	0.40461	0.533000	0.62120	AAC	.	.		0.393	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4			G	24718945	A	G	24718945	3	3	211	1	0	0	0	0	1	0	0	0	9747	43	2	2	1344	2	MPP6	7	24718945	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	8074535	24718945	134419718	43	30422										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83095918	83095918	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	acataatttgcacattcaccCtaaagcaggaaaaaaaggga	7	8	1	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr7:83095918C>A	ENST00000307792.3	-	4	804		c.e4-1		SEMA3E_ENST00000427262.1_Splice_Site	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E						axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				CACATTCACCCTAAAGCAGGA	0.388																																					.		Atlas-SNP	.											.	SEMA3E	125	.	0			c.337-1G>T						.						109	95	100					7																	83095918		2203	4300	6503	SO:0001630	splice_region_variant	9723	exon5			TTCACCCTAAAGC	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.337-1G>T	chr7.hg19:g.83095918C>A		78.0	0.0		83.0	34.0	NM_012431	B4E1P1|Q75M94|Q75M97	Splice_Site	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.722140	0.48728	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514;ENST00000442159	.	.	.	5.48	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4471	0.61146	0.0:0.9231:0.0:0.0769	.	.	.	.	.	-1	.	.	.	-	.	.	SEMA3E	82933854	1.000000	0.71417	0.986000	0.45419	0.491000	0.33493	4.761000	0.62243	1.332000	0.45431	0.650000	0.86243	.	.	.		0.388	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	Intron	A	83095918	C	A	83095918	5	1	211	1	0	0	0	0	0	0	1	0	14043	695	24	3	2047	3	SEMA3E	7	83095918	Splice_Site	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	58376973	83095918	76042745	44	30423										
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100454563	100454563	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ctgctgtatggctccctgctGctgggccttgtgggtggggt	17	10	0	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr7:100454563G>A	ENST00000354161.3	+	5	647	c.522G>A	c.(520-522)ctG>ctA	p.L174L	SLC12A9_ENST00000415287.1_Silent_p.L85L|SLC12A9_ENST00000275729.3_Silent_p.L85L|SLC12A9_ENST00000540482.1_Silent_p.L174L|SLC12A9_ENST00000428758.1_Silent_p.L174L	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	174					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					GCTCCCTGCTGCTGGGCCTTG	0.657																																					p.L174L		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G522A						.						62	58	59					7																	100454563		2203	4300	6503	SO:0001819	synonymous_variant	56996	exon5			CCTGCTGCTGGGC	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"Solute carriers"	17435	protein-coding gene	gene with protein product	"cation-chloride cotransporter-interacting protein"					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.522G>A	chr7.hg19:g.100454563G>A		29.0	0.0		64.0	12.0	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	hg19	CCDS5707.1																																																																																			.	.		0.657	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		A	100454563	G	A	100454563	2	1	211	1	0	0	0	0	0	0	0	1	14405	1306	46	3		3	SLC12A9	7	100454563	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	17358645	100454563	58684100	45	30424										
ZDHHC2	51201	hgsc.bcm.edu	37	chr8	17043874	17043874	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gcctatcatctactttttgcAatgtttgtctggtcatactg	7	9	4	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr8:17043874A>G	ENST00000262096.8	+	3	887	c.192A>G	c.(190-192)gcA>gcG	p.A64A		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	64					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|recycling endosome membrane (GO:0055038)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|pancreas(1)|stomach(1)	8				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		TACTTTTTGCAATGTTTGTCT	0.269																																					p.A64A		Atlas-SNP	.											.	ZDHHC2	25	.	0			c.A192G						.						125	110	115					8																	17043874		1828	4077	5905	SO:0001819	synonymous_variant	51201	exon3			TTTTGCAATGTTT	AB023584	CCDS47810.1	8p22	2008-05-15			ENSG00000104219	ENSG00000104219		"Zinc fingers, DHHC-type"	18469	protein-coding gene	gene with protein product						10918388	Standard	NM_016353		Approved	ZNF372	uc003wxe.3	Q9UIJ5	OTTHUMG00000163860	ENST00000262096.8:c.192A>G	chr8.hg19:g.17043874A>G		194.0	0.0		102.0	95.0	NM_016353	D3DSP5	Silent	SNP	ENST00000262096.8	hg19	CCDS47810.1																																																																																			.	.		0.269	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	NM_016353		G	17043874	A	G	17043874	2	3	211	1	0	0	0	0	0	0	0	1	17625	117	5	2		2	ZDHHC2	8	17043874	Silent	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10		17043874	129320148	46	30425										
MYST3	7994	hgsc.bcm.edu	37	chr8	41798614	41798614	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	aaggtcaggtttcccgtcctGgcttggctgctcctcagaag	12	12	2	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr8:41798614G>A	ENST00000396930.3	-	16	3328	c.2785C>T	c.(2785-2787)Cag>Tag	p.Q929*	KAT6A_ENST00000265713.2_Nonsense_Mutation_p.Q929*|KAT6A_ENST00000406337.1_Nonsense_Mutation_p.Q929*	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	929					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										TTCCCGTCCTGGCTTGGCTGC	0.527																																					p.Q929X		Atlas-SNP	.											.	.	.	.	0			c.C2785T						.						86	83	84					8																	41798614		2203	4300	6503	SO:0001587	stop_gained	7994	exon16			CGTCCTGGCTTGG	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.2785C>T	chr8.hg19:g.41798614G>A	ENSP00000380136:p.Gln929*	63.0	0.0		83.0	34.0	NM_001099412	Q76L81	Nonsense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	G	40	8.083108	0.98646	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000418721	.	.	.	5.19	4.23	0.50019	.	0.394126	0.21108	N	0.080036	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-4.6247	5.9275	0.19120	0.1016:0.0:0.577:0.3214	.	.	.	.	X	929;929;929;509	.	ENSP00000265713:Q929X	Q	-	1	0	KAT6A	41917771	1.000000	0.71417	0.964000	0.40570	0.004000	0.04260	2.217000	0.42880	2.411000	0.81874	0.655000	0.94253	CAG	.	.		0.527	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		A	41798614	G	A	41798614	4	1	211	1	0	0	0	0	0	1	0	0	10113	1357	47	3	3241	3	MYST3	8	41798614	Nonsense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	24754740	41798614	104565408	47	30426										
PPP1R16A	84988	hgsc.bcm.edu	37	chr8	145724197	145724197	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tcagccctgacttggccaacGaggacggcctgacggccctg	13	15	1	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr8:145724197G>A	ENST00000292539.4	+	3	1221	c.304G>A	c.(304-306)Gag>Aag	p.E102K	PPP1R16A_ENST00000435887.1_Missense_Mutation_p.E102K|CTD-2517M22.14_ENST00000532766.1_RNA|CTD-2517M14.5_ENST00000569326.1_RNA			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	102						plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CTTGGCCAACGAGGACGGCCT	0.667																																					p.E102K		Atlas-SNP	.											.	PPP1R16A	25	.	0			c.G304A						.						55	50	52					8																	145724197		2201	4300	6501	SO:0001583	missense	84988	exon2			GCCAACGAGGACG		CCDS6429.1	8q24.3	2013-01-10	2011-10-04		ENSG00000160972	ENSG00000160972		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14941	protein-coding gene	gene with protein product		609172	"protein phosphatase 1, regulatory (inhibitor) subunit 16A"			11948623	Standard	NM_032902		Approved	MGC14333, MYPT3	uc003zdf.3	Q96I34	OTTHUMG00000165173	ENST00000292539.4:c.304G>A	chr8.hg19:g.145724197G>A	ENSP00000292539:p.Glu102Lys	48.0	0.0		65.0	10.0	NM_032902	D3DWM5	Missense_Mutation	SNP	ENST00000292539.4	hg19	CCDS6429.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337522	0.81911	.	.	ENSG00000160972	ENST00000292539;ENST00000435887	T;T	0.52295	0.67;0.67	4.65	4.65	0.58169	Ankyrin repeat-containing domain (4);	0.062472	0.64402	D	0.000006	T	0.43433	0.1247	N	0.04636	-0.2	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.37798	-0.9690	10	0.12103	T	0.63	.	15.3956	0.74790	0.0:0.0:1.0:0.0	.	102	Q96I34	PP16A_HUMAN	K	102	ENSP00000292539:E102K;ENSP00000391126:E102K	ENSP00000292539:E102K	E	+	1	0	PPP1R16A	145695005	1.000000	0.71417	0.999000	0.59377	0.086000	0.17979	5.150000	0.64869	2.306000	0.77630	0.462000	0.41574	GAG	.	.		0.667	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382459.1	NM_032902		A	145724197	G	A	145724197	3	1	211	1	0	0	0	0	1	0	0	0	12377	1059	37	1	310	1	PPP1R16A	8	145724197	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	103925583	145724197	639825	48	30427										
ZBTB5	9925	hgsc.bcm.edu	37	chr9	37441538	37441538	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ctcacttcatcctgaggctcAggtgagctcaggggctcaga	12	12	5	3			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr9:37441538A>G	ENST00000307750.4	-	2	1199	c.1011T>C	c.(1009-1011)ccT>ccC	p.P337P		NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	337					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		CCTGAGGCTCAGGTGAGCTCA	0.517																																					p.P337P		Atlas-SNP	.											.	ZBTB5	43	.	0			c.T1011C						.						101	91	94					9																	37441538		2203	4300	6503	SO:0001819	synonymous_variant	9925	exon2			AGGCTCAGGTGAG	AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23836	protein-coding gene	gene with protein product						9205841	Standard	NM_014872		Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.1011T>C	chr9.hg19:g.37441538A>G		41.0	0.0		28.0	18.0	NM_014872		Silent	SNP	ENST00000307750.4	hg19	CCDS6610.1																																																																																			.	.		0.517	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052462.1	NM_014872		G	37441538	A	G	37441538	2	3	211	1	0	0	0	0	0	0	0	1	17566	175	7	2		2	ZBTB5	9	37441538	Silent	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10		37441538	103771893	49	30428										
FAM75C1	441452	hgsc.bcm.edu	37	chr9	90536200	90536200	+	RNA	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ctgaactctggagacaactgGagcaatacatggggcaacgt	12	9	1	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr9:90536200G>T	ENST00000602681.1	+	0	1927							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GAGACAACTGGAGCAATACAT	0.517																																					p.E460X		Atlas-SNP	.											.	.	.	.	0			c.G1378T						.						55	51	52					9																	90536200		692	1591	2283			441452	exon4			CAACTGGAGCAAT	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"family with sequence similarity 75, member C1"	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		chr9.hg19:g.90536200G>T		222.0	0.0		239.0	112.0	NM_001145124		Nonsense_Mutation	SNP	ENST00000602681.1	hg19																																																																																				.	.		0.517	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124		T	90536200	G	T	90536200	1	4	211	0	1	0	0	0	0	0	0	0	5631	1175	41	3		3	FAM75C1	9	90536200	RNA	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	53094662	90536200	50677231	50	30429										
PAPPA	5069	hgsc.bcm.edu	37	chr9	119115123	119115123	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gtgccgagagaataagcacaAggtgggctccttctgcaaat	12	9	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr9:119115123A>G	ENST00000328252.3	+	16	4472	c.4103A>G	c.(4102-4104)aAg>aGg	p.K1368R	PAPPA_ENST00000534838.1_Missense_Mutation_p.K406R	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1368	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						AATAAGCACAAGGTGGGCTCC	0.547																																					p.K1368R		Atlas-SNP	.											.	PAPPA	243	.	0			c.A4103G						.						75	67	69					9																	119115123		2203	4300	6503	SO:0001583	missense	5069	exon16			AGCACAAGGTGGG		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.4103A>G	chr9.hg19:g.119115123A>G	ENSP00000330658:p.Lys1368Arg	79.0	0.0		97.0	23.0	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	hg19	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.983862	0.93044	.	.	ENSG00000182752	ENST00000328252;ENST00000534838	T;T	0.63913	-0.07;-0.07	5.85	5.85	0.93711	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.78000	0.4215	M	0.68317	2.08	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.87578	0.994;0.998	T	0.79443	-0.1801	10	0.59425	D	0.04	-24.2944	16.2343	0.82363	1.0:0.0:0.0:0.0	.	406;1368	F5GZ19;Q13219	.;PAPP1_HUMAN	R	1368;406	ENSP00000330658:K1368R;ENSP00000441461:K406R	ENSP00000330658:K1368R	K	+	2	0	PAPPA	118154944	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.300000	0.96151	2.234000	0.73211	0.533000	0.62120	AAG	.	.		0.547	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		G	119115123	A	G	119115123	3	3	211	1	0	0	0	0	1	0	0	0	11441	72	3	2	4165	2	PAPPA	9	119115123	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	28578923	119115123	22098308	51	30430										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138660719	138660719	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tgggccgtgaaggacttcgcCcccaactgccccctctacgt	10	17	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr9:138660719C>T	ENST00000263604.3	+	15	1389	c.1389C>T	c.(1387-1389)gcC>gcT	p.A463A	KCNT1_ENST00000486577.2_Silent_p.A443A|KCNT1_ENST00000490355.2_Silent_p.A463A|KCNT1_ENST00000371757.2_Silent_p.A482A|KCNT1_ENST00000298480.5_Silent_p.A482A|KCNT1_ENST00000491806.2_Silent_p.A449A|KCNT1_ENST00000487664.1_Silent_p.A437A|KCNT1_ENST00000488444.2_Silent_p.A463A			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	463					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		AGGACTTCGCCCCCAACTGCC	0.622																																					p.A482A		Atlas-SNP	.											KCNT1,NS,neuroblastoma,0,1	KCNT1	139	.	0			c.C1446T						.						115	98	104					9																	138660719		2202	4300	6502	SO:0001819	synonymous_variant	57582	exon15			CTTCGCCCCCAAC	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.1389C>T	chr9.hg19:g.138660719C>T		38.0	0.0		53.0	17.0	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Silent	SNP	ENST00000263604.3	hg19																																																																																				.	.		0.622	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		T	138660719	C	T	138660719	2	4	211	1	0	0	0	0	0	0	0	1	8100	610	22	3		3	KCNT1	9	138660719	Silent	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	19545596	138660719	2552712	52	30431										
ABCA2	20	hgsc.bcm.edu	37	chr9	139907958	139907958	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	cgtaggggatgaaattgccaCggggctgggtgtagttgtgg	19	5	0	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr9:139907958C>T	ENST00000371605.3	-	28	4649	c.4502G>A	c.(4501-4503)cGt>cAt	p.R1501H	ABCA2_ENST00000265662.5_Missense_Mutation_p.R1502H|ABCA2_ENST00000341511.6_Missense_Mutation_p.R1502H			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1501					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GAAATTGCCACGGGGCTGGGT	0.677																																					p.R1532H		Atlas-SNP	.											.	ABCA2	113	.	0			c.G4595A						.						52	60	57					9																	139907958		1999	4140	6139	SO:0001583	missense	20	exon29			TTGCCACGGGGCT	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.4502G>A	chr9.hg19:g.139907958C>T	ENSP00000360666:p.Arg1501His	42.0	0.0		50.0	28.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Missense_Mutation	SNP	ENST00000371605.3	hg19		.	.	.	.	.	.	.	.	.	.	C	20.7	4.036739	0.75617	.	.	ENSG00000107331	ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	D;D;D	0.87256	-2.23;-2.23;-2.23	4.86	4.86	0.63082	.	0.840660	0.10192	U	0.704486	D	0.84629	0.5514	L	0.44542	1.39	0.37658	D	0.922673	D;D	0.60160	0.976;0.987	B;P	0.47744	0.379;0.556	D	0.83777	0.0223	10	0.66056	D	0.02	.	6.3671	0.21461	0.0:0.7615:0.0:0.2385	.	1501;1532	Q9BZC7;E7ETC3	ABCA2_HUMAN;.	H	1502;1501;1532;1502	ENSP00000265662:R1502H;ENSP00000360666:R1501H;ENSP00000344155:R1502H	ENSP00000265662:R1502H	R	-	2	0	ABCA2	139027779	0.996000	0.38824	0.987000	0.45799	0.980000	0.70556	3.199000	0.51043	2.235000	0.73313	0.484000	0.47621	CGT	.	.		0.677	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		T	139907958	C	T	139907958	3	4	211	1	0	0	0	0	1	0	0	0	32	536	19	1	2889	1	ABCA2	9	139907958	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	1247239	139907958	1305473	53	30432										
BTRC	8945	hgsc.bcm.edu	37	chr10	103239157	103239157	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tgtgccagactctgcttaaaCcaagaaacagtatgtttagc	8	9	1	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr10:103239157C>G	ENST00000370187.3	+	4	385	c.267C>G	c.(265-267)aaC>aaG	p.N89K	BTRC_ENST00000408038.2_Missense_Mutation_p.N53K|BTRC_ENST00000393441.4_Missense_Mutation_p.N48K	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	89					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		TCTGCTTAAACCAAGAAACAG	0.348																																					p.N89K		Atlas-SNP	.											.	BTRC	64	.	0			c.C267G						.						111	102	105					10																	103239157		2203	4300	6503	SO:0001583	missense	8945	exon4			CTTAAACCAAGAA	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.267C>G	chr10.hg19:g.103239157C>G	ENSP00000359206:p.Asn89Lys	95.0	0.0		93.0	20.0	NM_033637	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	hg19	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872075	0.51695	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038;ENST00000539411;ENST00000370183	T;T;T	0.60424	0.33;0.37;0.19	5.35	4.43	0.53597	.	0.000000	0.64402	D	0.000002	T	0.34513	0.0900	N	0.14661	0.345	0.34495	D	0.705432	B;B;B	0.27732	0.0;0.187;0.002	B;B;B	0.22386	0.0;0.039;0.002	T	0.39143	-0.9628	10	0.05833	T	0.94	-16.8582	13.0951	0.59187	0.0:0.9204:0.0:0.0796	.	63;53;89	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	K	89;48;53;27;71	ENSP00000359206:N89K;ENSP00000377088:N48K;ENSP00000385339:N53K	ENSP00000359202:N71K	N	+	3	2	BTRC	103229147	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.850000	0.39328	1.330000	0.45394	0.655000	0.94253	AAC	.	.		0.348	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		G	103239157	C	G	103239157	3	3	211	1	0	0	0	0	1	0	0	0	1571	506	18	4	281	4	BTRC	10	103239157	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10		103239157	32295590	54	30433										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117075138	117075138	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gacattgcattgaaggttctTcacggggaccaatgaagctt	11	8	2	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr10:117075138T>A	ENST00000355044.3	+	18	3055	c.2929T>A	c.(2929-2931)Tca>Aca	p.S977T	ATRNL1_ENST00000303745.7_5'UTR|ATRNL1_ENST00000423111.2_Missense_Mutation_p.S74T	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	977	PSI 5.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TGAAGGTTCTTCACGGGGACC	0.453																																					p.S977T		Atlas-SNP	.											.	ATRNL1	219	.	0			c.T2929A						.						153	136	142					10																	117075138		2203	4300	6503	SO:0001583	missense	26033	exon18			GGTTCTTCACGGG	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2929T>A	chr10.hg19:g.117075138T>A	ENSP00000347152:p.Ser977Thr	75.0	0.0		75.0	37.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.39|13.39	2.221977|2.221977	0.39300|0.39300	.|.	.|.	ENSG00000107518|ENSG00000107518	ENST00000526373|ENST00000355044;ENST00000423111	.|T;T	.|0.21932	.|2.56;1.98	5.34|5.34	5.34|5.34	0.76211|0.76211	.|.	.|0.059923	.|0.64402	.|D	.|0.000002	T|T	0.21267|0.21267	0.0512|0.0512	L|L	0.39898|0.39898	1.24|1.24	0.80722|0.80722	D|D	1|1	.|B;P	.|0.37573	.|0.447;0.6	.|B;B	.|0.39299	.|0.171;0.296	T|T	0.02417|0.02417	-1.1162|-1.1162	5|10	.|0.29301	.|T	.|0.29	-11.3344|-11.3344	15.3184|15.3184	0.74102|0.74102	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|74;977	.|B4DH41;Q5VV63	.|.;ATRN1_HUMAN	Y|T	106|977;74	.|ENSP00000347152:S977T;ENSP00000409624:S74T	.|ENSP00000347152:S977T	F|S	+|+	2|1	0|0	ATRNL1|ATRNL1	117065128|117065128	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.969000|0.969000	0.65631|0.65631	6.081000|6.081000	0.71309|0.71309	2.031000|2.031000	0.59945|0.59945	0.374000|0.374000	0.22700|0.22700	TTC|TCA	.	.		0.453	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		A	117075138	T	A	117075138	3	1	211	1	0	0	0	0	1	0	0	0	1207	1783	62	4	2999	4	ATRNL1	10	117075138	Missense_Mutation	SNP	T	TCGA-DD-AAE6-01A-11D-A40R-10	13835981	117075138	18459609	55	30434										
SPTY2D1	144108	hgsc.bcm.edu	37	chr11	18636133	18636133	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gggcagctctgtagccagatAggggaggcttcattccattc	13	10	2	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr11:18636133A>T	ENST00000336349.5	-	3	1923	c.1688T>A	c.(1687-1689)cTa>cAa	p.L563Q	SPTY2D1_ENST00000543776.1_5'Flank	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	563										breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						GTAGCCAGATAGGGGAGGCTT	0.413																																					p.L563Q		Atlas-SNP	.											.	SPTY2D1	72	.	0			c.T1688A						.						96	102	100					11																	18636133		2199	4293	6492	SO:0001583	missense	144108	exon3			CCAGATAGGGGAG	BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.1688T>A	chr11.hg19:g.18636133A>T	ENSP00000337991:p.Leu563Gln	84.0	0.0		73.0	27.0	NM_194285	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Missense_Mutation	SNP	ENST00000336349.5	hg19	CCDS31441.1	.	.	.	.	.	.	.	.	.	.	A	13.83	2.354252	0.41700	.	.	ENSG00000179119	ENST00000336349	T	0.23754	1.89	6.08	3.78	0.43462	.	0.859036	0.09529	N	0.789839	T	0.32496	0.0831	L	0.57536	1.79	0.09310	N	1	D	0.60575	0.988	P	0.52514	0.701	T	0.13202	-1.0518	10	0.23891	T	0.37	-0.826	5.0287	0.14398	0.6708:0.0:0.3292:0.0	.	563	Q68D10	SPT2_HUMAN	Q	563	ENSP00000337991:L563Q	ENSP00000337991:L563Q	L	-	2	0	SPTY2D1	18592709	0.019000	0.18553	0.001000	0.08648	0.935000	0.57460	2.588000	0.46137	1.131000	0.42111	0.533000	0.62120	CTA	.	.		0.413	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285		T	18636133	A	T	18636133	3	4	211	1	0	0	0	0	1	0	0	0	15141	420	15	4	385	4	SPTY2D1	11	18636133	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10		18636133	116370383	56	30435										
OR4C12	283093	hgsc.bcm.edu	37	chr11	50003316	50003316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ataagacaactactatgatgTgagaaatacaggtggagagg	12	4	0	4			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr11:50003316T>C	ENST00000335238.4	-	1	755	c.722A>G	c.(721-723)cAc>cGc	p.H241R		NM_001005270.2	NP_001005270.2	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C, member 12	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(4)|large_intestine(3)|liver(1)|lung(19)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	36						TACTATGATGTGAGAAATACA	0.403																																					p.H241R		Atlas-SNP	.											.	OR4C12	82	.	0			c.A722G						.						78	71	74					11																	50003316		2201	4296	6497	SO:0001583	missense	283093	exon1			ATGATGTGAGAAA	BK004413	CCDS31496.1	11p11.12	2012-08-09			ENSG00000221954	ENSG00000221954		"GPCR / Class A : Olfactory receptors"	15168	protein-coding gene	gene with protein product							Standard	NM_001005270		Approved		uc010ria.2	Q96R67	OTTHUMG00000166687	ENST00000335238.4:c.722A>G	chr11.hg19:g.50003316T>C	ENSP00000334418:p.His241Arg	88.0	0.0		60.0	29.0	NM_001005270	B2RNF0|Q6IF49	Missense_Mutation	SNP	ENST00000335238.4	hg19	CCDS31496.1	.	.	.	.	.	.	.	.	.	.	.	12.80	2.045079	0.36085	.	.	ENSG00000221954	ENST00000335238	T	0.00311	8.15	2.98	1.8	0.24995	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44097	U	0.000484	T	0.00936	0.0031	H	0.97564	4.03	0.32749	N	0.506648	D	0.89917	1.0	D	0.97110	1.0	T	0.13737	-1.0498	10	0.87932	D	0	.	6.7627	0.23550	0.2098:0.0:0.0:0.7902	.	241	Q96R67	OR4CC_HUMAN	R	241	ENSP00000334418:H241R	ENSP00000334418:H241R	H	-	2	0	OR4C12	49959892	1.000000	0.71417	0.996000	0.52242	0.367000	0.29736	4.180000	0.58296	0.356000	0.24157	0.325000	0.21440	CAC	.	.		0.403	OR4C12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391104.1	NM_001005270		C	50003316	T	C	50003316	3	2	211	1	0	0	0	0	1	0	0	0	11055	1696	59	2	211	2	OR4C12	11	50003316	Missense_Mutation	SNP	T	TCGA-DD-AAE6-01A-11D-A40R-10	31367183	50003316	85003200	57	30436										
OR8K3	219473	hgsc.bcm.edu	37	chr11	56086555	56086555	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tgggactttgcttttcatgtAcgtgcagcccaagtccagtc	10	11	1	0	rs139467696	byFrequency	TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr11:56086555A>T	ENST00000312711.1	+	1	773	c.773A>T	c.(772-774)tAc>tTc	p.Y258F		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	258						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					CTTTTCATGTACGTGCAGCCC	0.438																																					p.Y258F		Atlas-SNP	.											.	OR8K3	92	.	0			c.A773T						.						115	102	107					11																	56086555		2201	4296	6497	SO:0001583	missense	219473	exon1			TCATGTACGTGCA	AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"GPCR / Class A : Olfactory receptors"	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.773A>T	chr11.hg19:g.56086555A>T	ENSP00000323555:p.Tyr258Phe	95.0	0.0		102.0	27.0	NM_001005202	Q6IFC4	Missense_Mutation	SNP	ENST00000312711.1	hg19	CCDS31527.1	.	.	.	.	.	.	.	.	.	.	A	16.29	3.080550	0.55753	.	.	ENSG00000181689	ENST00000312711	T	0.00291	8.27	4.28	4.28	0.50868	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000091	T	0.00754	0.0025	H	0.96861	3.895	0.25816	N	0.98435	P	0.49961	0.93	P	0.51079	0.658	T	0.07712	-1.0758	10	0.87932	D	0	.	13.0251	0.58810	1.0:0.0:0.0:0.0	.	258	Q8NH51	OR8K3_HUMAN	F	258	ENSP00000323555:Y258F	ENSP00000323555:Y258F	Y	+	2	0	OR8K3	55843131	0.991000	0.36638	1.000000	0.80357	0.719000	0.41307	3.829000	0.55760	1.917000	0.55516	0.386000	0.25728	TAC	.	A|0.999;G|0.001		0.438	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	NM_001005202		T	56086555	A	T	56086555	3	4	211	1	0	0	0	0	1	0	0	0	11253	391	14	4	775	4	OR8K3	11	56086555	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	6083239	56086555	78919961	58	30437										
CLP1	10978	hgsc.bcm.edu	37	chr11	57427365	57427365	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	cttctgctcaactacgcagtGcgtttgggccgccgtcccac	10	16	2	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr11:57427365G>A	ENST00000533682.1	+	2	1142	c.417G>A	c.(415-417)gtG>gtA	p.V139V	CLP1_ENST00000525602.1_Silent_p.V139V|CLP1_ENST00000302731.4_Intron|CLP1_ENST00000529430.1_Silent_p.V150V			Q5KU26	COL12_HUMAN	cleavage and polyadenylation factor I subunit 1	0					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|stomach(1)	15						ACTACGCAGTGCGTTTGGGCC	0.602																																					p.V139V		Atlas-SNP	.											.	CLP1	40	.	0			c.G417A						.						100	81	87					11																	57427365		2201	4296	6497	SO:0001819	synonymous_variant	10978	exon2			CGCAGTGCGTTTG	BC000446	CCDS7964.1, CCDS44600.1	11q12.1	2012-10-02	2012-10-02		ENSG00000172409	ENSG00000172409	2.7.1.78		16999	protein-coding gene	gene with protein product	"ATP/GTPbinding protein", "polyribonucleotide 5'-hydroxyl-kinase"	608757	"CLP1, cleavage and polyadenylation factor I subunit, homolog (S. cerevisiae)"			8896421, 11060040	Standard	NM_006831		Approved	HEAB, hClp1	uc001nkw.3	Q92989	OTTHUMG00000167146	ENST00000533682.1:c.417G>A	chr11.hg19:g.57427365G>A		94.0	0.0		100.0	42.0	NM_006831	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Silent	SNP	ENST00000533682.1	hg19	CCDS7964.1																																																																																			.	.		0.602	CLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393462.3	NM_006831		A	57427365	G	A	57427365	2	1	211	1	0	0	0	0	0	0	0	1	3552	1306	46	3		3	CLP1	11	57427365	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	1340810	57427365	77579151	59	30438										
SCGB1D2	10647	hgsc.bcm.edu	37	chr11	62012145	62012145	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ttcttttcctattttaggtgAaaatattgaagaaatgtagt	7	3	1	3			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr11:62012145A>C	ENST00000244926.3	+	3	345	c.247A>C	c.(247-249)Aaa>Caa	p.K83Q	RP11-703H8.9_ENST00000529875.1_RNA	NM_006551.3	NP_006542.1	O95969	SG1D2_HUMAN	secretoglobin, family 1D, member 2	83						extracellular space (GO:0005615)				breast(1)|endometrium(1)|lung(1)	3						ATTTTAGGTGAAAATATTGAA	0.433																																					p.K83Q		Atlas-SNP	.											.	SCGB1D2	11	.	0			c.A247C						.						123	116	118					11																	62012145		2201	4299	6500	SO:0001583	missense	10647	exon3			TAGGTGAAAATAT	AJ224172	CCDS8017.1	11q13	2011-12-14			ENSG00000124935	ENSG00000124935		"Secretoglobins"	18396	protein-coding gene	gene with protein product	"prostatein-like lipophilin B", "lipophilin B (uteroglobin family member), prostatein-like"	615061				10066439, 9720917, 22155607	Standard	XM_006718422		Approved	LPHB, LIPB	uc001ntb.3	O95969	OTTHUMG00000167508	ENST00000244926.3:c.247A>C	chr11.hg19:g.62012145A>C	ENSP00000244926:p.Lys83Gln	34.0	0.0		43.0	16.0	NM_006551	Q2M3N9	Missense_Mutation	SNP	ENST00000244926.3	hg19	CCDS8017.1	.	.	.	.	.	.	.	.	.	.	A	10.59	1.393634	0.25205	.	.	ENSG00000124935	ENST00000244926	T	0.16743	2.32	2.87	-2.8	0.05823	.	3.378730	0.01520	U	0.018313	T	0.14356	0.0347	.	.	.	0.09310	N	1	P	0.47841	0.901	P	0.48770	0.589	T	0.10683	-1.0619	9	0.23891	T	0.37	.	0.3499	0.00347	0.3683:0.1936:0.2492:0.1889	.	83	O95969	SG1D2_HUMAN	Q	83	ENSP00000244926:K83Q	ENSP00000244926:K83Q	K	+	1	0	SCGB1D2	61768721	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.191000	0.09601	-0.606000	0.05746	-0.815000	0.03128	AAA	.	.		0.433	SCGB1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394859.1	NM_006551		C	62012145	A	C	62012145	3	2	211	1	0	0	0	0	1	0	0	0	13912	247	9	5	257	5	SCGB1D2	11	62012145	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	4584780	62012145	72994371	60	30439										
NXF1	10482	hgsc.bcm.edu	37	chr11	62563804	62563804	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tctgctatccttgaaatactCggctaagctgcttctggggg	11	10	2	1	rs367975743		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr11:62563804C>A	ENST00000532297.1	-	16	1929	c.1300G>T	c.(1300-1302)Gag>Tag	p.E434*	NXF1_ENST00000294172.2_Nonsense_Mutation_p.E434*|NXF1_ENST00000531709.2_3'UTR|NXF1_ENST00000533048.1_5'UTR			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	434	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear inclusion body (GO:0042405)|nuclear pore (GO:0005643)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TTGAAATACTCGGCTAAGCTG	0.483																																					p.E434X		Atlas-SNP	.											.	NXF1	67	.	0			c.G1300T						.						183	183	183					11																	62563804		2201	4299	6500	SO:0001587	stop_gained	10482	exon15			AATACTCGGCTAA	AF112880	CCDS8037.1, CCDS44629.1	11q12-q13	2008-07-21			ENSG00000162231	ENSG00000162231			8071	protein-coding gene	gene with protein product	"tip associating protein"	602647				9175835, 9660949	Standard	NM_001081491		Approved	TAP, Mex67, DKFZp667O0311	uc001nvf.1	Q9UBU9	OTTHUMG00000167612	ENST00000532297.1:c.1300G>T	chr11.hg19:g.62563804C>A	ENSP00000436679:p.Glu434*	144.0	0.0		129.0	63.0	NM_006362	B4E269|Q99799|Q9UQL2	Nonsense_Mutation	SNP	ENST00000532297.1	hg19	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	C	39	7.782608	0.98486	.	.	ENSG00000162231	ENST00000294172;ENST00000532297;ENST00000530875	.	.	.	5.28	3.4	0.38934	.	0.147941	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-23.3521	10.1072	0.42541	0.0:0.8351:0.0:0.1649	.	.	.	.	X	434;434;477	.	ENSP00000294172:E434X	E	-	1	0	NXF1	62320380	0.999000	0.42202	0.672000	0.29872	0.235000	0.25334	4.332000	0.59279	0.789000	0.33779	-0.266000	0.10368	GAG	.	.		0.483	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362		A	62563804	C	A	62563804	4	1	211	1	0	0	0	0	0	1	0	0	10791	893	31	1	587	1	NXF1	11	62563804	Nonsense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	551659	62563804	72442712	61	30440										
SHANK2	22941	hgsc.bcm.edu	37	chr11	70333713	70333713	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gaaggtggtggtggggacggGggcacagactgcggtggagg	24	5	0	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr11:70333713G>A	ENST00000423696.2	-	15	1584	c.1548C>T	c.(1546-1548)ccC>ccT	p.P516P	SHANK2_ENST00000409161.1_Silent_p.P299P|SHANK2_ENST00000449833.2_Silent_p.P300P|SHANK2_ENST00000338508.4_Silent_p.P896P			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	516	Pro-rich.				adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			GTGGGGACGGGGGCACAGACT	0.577																																					p.P307P		Atlas-SNP	.											.	SHANK2	340	.	0			c.C921T						.						41	39	40					11																	70333713		2200	4294	6494	SO:0001819	synonymous_variant	22941	exon10			GGACGGGGGCACA	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14295	protein-coding gene	gene with protein product		603290	"cortactin binding protein 1"	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.1548C>T	chr11.hg19:g.70333713G>A		114.0	0.0		63.0	27.0	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Silent	SNP	ENST00000423696.2	hg19																																																																																				.	.		0.577	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		A	70333713	G	A	70333713	2	1	211	1	0	0	0	0	0	0	0	1	14280	1219	43	3		3	SHANK2	11	70333713	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	7769909	70333713	64672803	62	30441										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73768566	73768566	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	acaacaactgggtatcgataCtttccgctctgtcaaggggc	10	11	2	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr11:73768566C>T	ENST00000334126.7	-	25	5201	c.4975G>A	c.(4975-4977)Gta>Ata	p.V1659I	C2CD3_ENST00000313663.7_Missense_Mutation_p.V1659I			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1659	C2 2.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GGTATCGATACTTTCCGCTCT	0.453																																					p.V1659I		Atlas-SNP	.											C2CD3_ENST00000334126,colon,carcinoma,0,2	C2CD3	288	.	0			c.G4975A						.						109	109	109					11																	73768566		2200	4293	6493	SO:0001583	missense	26005	exon25			TCGATACTTTCCG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.4975G>A	chr11.hg19:g.73768566C>T	ENSP00000334379:p.Val1659Ile	96.0	0.0		54.0	50.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	16.16	3.045277	0.55110	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.68765	-0.35;-0.35;-0.35	5.03	5.03	0.67393	.	0.118234	0.56097	D	0.000022	T	0.64305	0.2586	L	0.51422	1.61	0.39036	D	0.96004	B	0.06786	0.001	B	0.11329	0.006	T	0.64236	-0.6455	10	0.59425	D	0.04	-7.4087	18.3221	0.90242	0.0:1.0:0.0:0.0	.	1659	Q4AC94-1	.	I	1659;1659;1640;467	ENSP00000334379:V1659I;ENSP00000323339:V1659I;ENSP00000388750:V467I	ENSP00000323339:V1659I	V	-	1	0	C2CD3	73446214	1.000000	0.71417	0.994000	0.49952	0.773000	0.43773	6.389000	0.73199	2.505000	0.84491	0.650000	0.86243	GTA	.	.		0.453	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		T	73768566	C	T	73768566	3	4	211	1	0	0	0	0	1	0	0	0	2156	565	20	3	944	3	C2CD3	11	73768566	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	3434853	73768566	61237950	63	30442										
MRPS35	60488	hgsc.bcm.edu	37	chr12	27872748	27872748	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ttctctatttaagattcccaAttttctgcatttgactcctg	4	10	2	2	rs370001683		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr12:27872748A>G	ENST00000081029.3	+	4	400	c.329A>G	c.(328-330)aAt>aGt	p.N110S	MRPS35_ENST00000538315.1_Missense_Mutation_p.N110S	NM_021821.3	NP_068593.2	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S35	0						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	6	Lung SC(9;0.0873)					AAGATTCCCAATTTTCTGCAT	0.274																																					p.N110S		Atlas-SNP	.											.	MRPS35	26	.	0			c.A329G						.						44	50	48					12																	27872748		2193	4286	6479	SO:0001583	missense	60488	exon4			TTCCCAATTTTCT	AF182422	CCDS8714.1, CCDS53769.1	12p11	2012-09-13			ENSG00000061794	ENSG00000061794		"Mitochondrial ribosomal proteins / small subunits"	16635	protein-coding gene	gene with protein product		611995				11279123	Standard	NM_021821		Approved	MRPS28, MDS023	uc001rih.3	P82673	OTTHUMG00000169215	ENST00000081029.3:c.329A>G	chr12.hg19:g.27872748A>G	ENSP00000081029:p.Asn110Ser	36.0	0.0		29.0	11.0	NM_001190864	B2RDZ7|Q96Q21	Missense_Mutation	SNP	ENST00000081029.3	hg19	CCDS8714.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.507660	0.85282	.	.	ENSG00000061794	ENST00000081029;ENST00000321446;ENST00000538315	T;T	0.59502	0.3;0.26	6.08	6.08	0.98989	.	0.042765	0.85682	D	0.000000	T	0.75532	0.3862	M	0.78916	2.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.977	T	0.77381	-0.2609	10	0.52906	T	0.07	-2.3497	14.0274	0.64594	1.0:0.0:0.0:0.0	.	110;110	P82673-2;P82673	.;RT35_HUMAN	S	110	ENSP00000081029:N110S;ENSP00000445390:N110S	ENSP00000081029:N110S	N	+	2	0	MRPS35	27764015	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	8.037000	0.88933	2.333000	0.79357	0.533000	0.62120	AAT	.	.		0.274	MRPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402897.1	NM_021821		G	27872748	A	G	27872748	3	3	211	1	0	0	0	0	1	0	0	0	9853	101	4	2	343	2	MRPS35	12	27872748	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10		27872748	105979147	64	30443										
KRT84	3890	hgsc.bcm.edu	37	chr12	52779057	52779057	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	actgccagctccaaagcccaGaccaacacagctgtcagccc	7	18	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr12:52779057G>C	ENST00000257951.3	-	1	379	c.313C>G	c.(313-315)Ctg>Gtg	p.L105V	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	105	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CCAAAGCCCAGACCAACACAG	0.592																																					p.L105V		Atlas-SNP	.											.	KRT84	61	.	0			c.C313G						.						182	170	174					12																	52779057		2203	4300	6503	SO:0001583	missense	3890	exon1			AGCCCAGACCAAC	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"-", "Intermediate filaments type II, keratins (basic)"	6461	protein-coding gene	gene with protein product	"hard keratin type II 4"	602766	"keratin, hair, basic, 4"	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.313C>G	chr12.hg19:g.52779057G>C	ENSP00000257951:p.Leu105Val	102.0	0.0		91.0	42.0	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	hg19	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	G	0.055	-1.237816	0.01493	.	.	ENSG00000161849	ENST00000257951	D	0.85556	-2.0	5.01	1.13	0.20643	.	0.000000	0.38778	N	0.001577	T	0.76673	0.4020	L	0.45581	1.43	0.09310	N	1	B	0.26195	0.144	B	0.21708	0.036	T	0.60321	-0.7286	10	0.20519	T	0.43	.	10.4716	0.44640	0.3887:0.0:0.6113:0.0	.	105	Q9NSB2	KRT84_HUMAN	V	105	ENSP00000257951:L105V	ENSP00000257951:L105V	L	-	1	2	KRT84	51065324	0.000000	0.05858	0.923000	0.36655	0.022000	0.10575	-0.089000	0.11180	0.377000	0.24735	-0.192000	0.12808	CTG	.	.		0.592	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		C	52779057	G	C	52779057	3	2	211	1	0	0	0	0	1	0	0	0	8507	933	33	4	1525	4	KRT84	12	52779057	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	24906309	52779057	81072838	65	30444										
TMPO	7112	hgsc.bcm.edu	37	chr12	98921777	98921777	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gtgaaatacggagtgaatccTggtcctattgtgggtaagtt	13	5	0	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr12:98921777T>G	ENST00000556029.1	+	2	749	c.393T>G	c.(391-393)ccT>ccG	p.P131P	TMPO_ENST00000393053.2_Silent_p.P131P|TMPO_ENST00000261210.5_Silent_p.P131P|TMPO_ENST00000266732.4_Silent_p.P131P|TMPO_ENST00000343315.5_Silent_p.P131P	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	131	LEM. {ECO:0000255|PROSITE- ProRule:PRU00313}.|Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GAGTGAATCCTGGTCCTATTG	0.353																																					p.P131P		Atlas-SNP	.											.	TMPO	111	.	0			c.T393G						.						145	151	149					12																	98921777		2203	4300	6503	SO:0001819	synonymous_variant	7112	exon2			GAATCCTGGTCCT		CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.393T>G	chr12.hg19:g.98921777T>G		113.0	0.0		103.0	41.0	NM_003276	A2T926|Q14861	Silent	SNP	ENST00000556029.1	hg19	CCDS31879.1																																																																																			.	.		0.353	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		G	98921777	T	G	98921777	2	3	211	1	0	0	0	0	0	0	0	1	16252	1567	55	5		5	TMPO	12	98921777	Silent	SNP	T	TCGA-DD-AAE6-01A-11D-A40R-10	46142720	98921777	34930118	66	30445										
VSIG10	54621	hgsc.bcm.edu	37	chr12	118506351	118506351	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tcctcctcctcctcctcctcCtcttcctcttctgaatccac	1	22	3	1	rs373328738		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr12:118506351C>T	ENST00000359236.5	-	8	1674	c.1398G>A	c.(1396-1398)gaG>gaA	p.E466E		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	466	Glu-rich.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						cctcctcctcctcttcctctt	0.458																																					p.E466E		Atlas-SNP	.											.	VSIG10	41	.	0			c.G1398A						.						96	91	92					12																	118506351		2045	4191	6236	SO:0001819	synonymous_variant	54621	exon8			CTCCTCCTCTTCC		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1398G>A	chr12.hg19:g.118506351C>T		78.0	0.0		117.0	6.0	NM_019086	Q9NWQ7	Silent	SNP	ENST00000359236.5	hg19	CCDS44992.1																																																																																			.	.		0.458	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086		T	118506351	C	T	118506351	2	4	211	1	0	0	0	0	0	0	0	1	17238	680	24	3		3	VSIG10	12	118506351	Silent	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	19584574	118506351	15345544	67	30446										
CCDC60	160777	hgsc.bcm.edu	37	chr12	119909909	119909909	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gaaactgaaagaggaggaaaGaaataaattccagccagccg	11	7	0	3			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr12:119909909G>A	ENST00000327554.2	+	3	746	c.281G>A	c.(280-282)aGa>aAa	p.R94K	RP11-768F21.1_ENST00000509470.2_lincRNA|CCDC60_ENST00000546345.1_3'UTR	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	94										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		GAGGAGGAAAGAAATAAATTC	0.433																																					p.R94K		Atlas-SNP	.											.	CCDC60	84	.	0			c.G281A						.						135	141	139					12																	119909909		2203	4300	6503	SO:0001583	missense	160777	exon3			AGGAAAGAAATAA	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.281G>A	chr12.hg19:g.119909909G>A	ENSP00000333374:p.Arg94Lys	134.0	0.0		82.0	32.0	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	hg19	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	G	5.558	0.287872	0.10513	.	.	ENSG00000183273	ENST00000327554	T	0.28069	1.63	5.22	-0.0987	0.13627	.	0.491502	0.19327	N	0.116982	T	0.17365	0.0417	L	0.35723	1.085	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.17684	-1.0361	9	.	.	.	-2.5914	3.4579	0.07522	0.2602:0.0:0.4283:0.3116	.	94	Q8IWA6	CCD60_HUMAN	K	94	ENSP00000333374:R94K	.	R	+	2	0	CCDC60	118394292	0.003000	0.15002	0.002000	0.10522	0.295000	0.27426	-0.126000	0.10563	-0.334000	0.08463	0.407000	0.27541	AGA	.	.		0.433	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		A	119909909	G	A	119909909	3	1	211	1	0	0	0	0	1	0	0	0	2833	942	33	3	291	3	CCDC60	12	119909909	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	1403558	119909909	13941986	68	30447										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	125900204	125900204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ccctcacctgcatgggccatCgcccggacacgcagagcagg	12	17	1	1	rs372738030		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr12:125900204C>T	ENST00000299308.3	+	3	1080	c.1072C>T	c.(1072-1074)Cgc>Tgc	p.R358C		NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	358						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CATGGGCCATCGCCCGGACAC	0.592																																					p.R358C		Atlas-SNP	.											.	TMEM132B	207	.	0			c.C1072T						.						48	56	53					12																	125900204		2176	4265	6441	SO:0001583	missense	114795	exon3			GGCCATCGCCCGG	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.1072C>T	chr12.hg19:g.125900204C>T	ENSP00000299308:p.Arg358Cys	205.0	0.0		262.0	90.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	hg19	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	C	13.37	2.218412	0.39201	.	.	ENSG00000139364	ENST00000299308	T	0.14640	2.49	5.63	4.66	0.58398	.	.	.	.	.	T	0.06781	0.0173	N	0.08118	0	0.19575	N	0.999966	P	0.42078	0.77	B	0.36885	0.235	T	0.13202	-1.0518	9	0.56958	D	0.05	.	7.5367	0.27714	0.2032:0.5927:0.2041:0.0	.	358	Q14DG7	T132B_HUMAN	C	358	ENSP00000299308:R358C	ENSP00000299308:R358C	R	+	1	0	TMEM132B	124466157	0.011000	0.17503	0.036000	0.18154	0.968000	0.65278	2.133000	0.42093	2.670000	0.90874	0.655000	0.94253	CGC	.	.		0.592	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		T	125900204	C	T	125900204	3	4	211	1	0	0	0	0	1	0	0	0	16061	884	31	1	1082	1	TMEM132B	12	125900204	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	5990295	125900204	7951691	69	30448										
RAB2B	84932	hgsc.bcm.edu	37	chr14	21943061	21943061	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	cagtttgatttgttttccatCaatgttgaccatacgagctc	7	9	1	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr14:21943061C>T	ENST00000397762.1	-	3	251	c.151G>A	c.(151-153)Gat>Aat	p.D51N	TOX4_ENST00000405508.1_5'Flank|TOX4_ENST00000262709.3_5'Flank|RAB2B_ENST00000461909.1_5'UTR|TOX4_ENST00000448790.2_5'Flank	NM_001163380.1|NM_032846.3	NP_001156852.1|NP_116235.2	Q8WUD1	RAB2B_HUMAN	RAB2B, member RAS oncogene family	51					positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			NS(1)|central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	6	all_cancers(95;0.000858)		Epithelial(56;1.53e-06)|all cancers(55;1.44e-05)	GBM - Glioblastoma multiforme(265;0.00391)		TGTTTTCCATCAATGTTGACC	0.428																																					p.D51N	Melanoma(131;1007 1750 28652 34486 42672)	Atlas-SNP	.											.	RAB2B	19	.	0			c.G151A						.						175	157	163					14																	21943061		2203	4300	6503	SO:0001583	missense	84932	exon3			TTCCATCAATGTT	AK027730	CCDS9570.1	14q11.1	2006-12-18			ENSG00000129472	ENSG00000129472		"RAB, member RAS oncogene"	20246	protein-coding gene	gene with protein product		607466				12376746	Standard	NM_032846		Approved	FLJ14824	uc010tlt.2	Q8WUD1	OTTHUMG00000029693	ENST00000397762.1:c.151G>A	chr14.hg19:g.21943061C>T	ENSP00000380869:p.Asp51Asn	42.0	0.0		121.0	9.0	NM_032846	B2RD03|D3DS24|Q6NZ33	Missense_Mutation	SNP	ENST00000397762.1	hg19	CCDS9570.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.338225	0.60963	.	.	ENSG00000129472	ENST00000397762;ENST00000304034	T	0.80909	-1.43	5.81	5.81	0.92471	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	T	0.73418	0.3584	L	0.37800	1.135	0.80722	D	1	B	0.09022	0.002	B	0.17433	0.018	T	0.68804	-0.5312	10	0.54805	T	0.06	.	12.8928	0.58082	0.0:0.9222:0.0:0.0778	.	51	Q8WUD1	RAB2B_HUMAN	N	51	ENSP00000380869:D51N	ENSP00000302005:D51N	D	-	1	0	RAB2B	21012901	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.580000	0.67464	2.756000	0.94617	0.655000	0.94253	GAT	.	.		0.428	RAB2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074053.4			T	21943061	C	T	21943061	3	4	211	1	0	0	0	0	1	0	0	0	12933	826	29	3	523	3	RAB2B	14	21943061	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10		21943061	85406479	70	30449										
RPS6KA5	9252	hgsc.bcm.edu	37	chr14	91338567	91338567	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	actggaactgctgcgcgtctCggtactggtgctagtctttt	12	10	2	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr14:91338567C>A	ENST00000261991.3	-	17	2433	c.2260G>T	c.(2260-2262)Gag>Tag	p.E754*	RPS6KA5_ENST00000536315.2_Nonsense_Mutation_p.E675*	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	754					axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		CTGCGCGTCTCGGTACTGGTG	0.478																																					p.E754X		Atlas-SNP	.											RPS6KA5_ENST00000261991,colon,carcinoma,0,2	RPS6KA5	135	.	0			c.G2260T						.						138	120	126					14																	91338567		2203	4300	6503	SO:0001587	stop_gained	9252	exon17			GCGTCTCGGTACT	AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"ribosomal protein S6 kinase, 90kD, polypeptide 5"			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.2260G>T	chr14.hg19:g.91338567C>A	ENSP00000261991:p.Glu754*	143.0	0.0		63.0	57.0	NM_004755	O95316|Q96AF7	Nonsense_Mutation	SNP	ENST00000261991.3	hg19	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	C	39	7.699005	0.98441	.	.	ENSG00000100784	ENST00000261991;ENST00000536315	.	.	.	5.25	5.25	0.73442	.	0.050091	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	19.2225	0.93803	0.0:1.0:0.0:0.0	.	.	.	.	X	754;675	.	ENSP00000261991:E754X	E	-	1	0	RPS6KA5	90408320	1.000000	0.71417	0.959000	0.39883	0.945000	0.59286	7.776000	0.85560	2.611000	0.88343	0.655000	0.94253	GAG	.	.		0.478	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		A	91338567	C	A	91338567	4	1	211	1	0	0	0	0	0	1	0	0	13669	893	31	1	152	1	RPS6KA5	14	91338567	Nonsense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	69395506	91338567	16010973	71	30450										
IREB2	3658	hgsc.bcm.edu	37	chr15	78778141	78778141	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	agtgggatggttacacattaCctcagttcaagtggagtatt	11	6	2	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr15:78778141C>T	ENST00000258886.8	+	13	1817	c.1668C>T	c.(1666-1668)taC>taT	p.Y556Y		NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	556					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		TTACACATTACCTCAGTTCAA	0.413																																					p.Y556Y	NSCLC(200;764 2208 35157 49871 50830)	Atlas-SNP	.											.	IREB2	106	.	0			c.C1668T						.						172	159	164					15																	78778141		2196	4293	6489	SO:0001819	synonymous_variant	3658	exon13			ACATTACCTCAGT	M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.1668C>T	chr15.hg19:g.78778141C>T		76.0	0.0		128.0	22.0	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Silent	SNP	ENST00000258886.8	hg19	CCDS10302.1																																																																																			.	.		0.413	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		T	78778141	C	T	78778141	2	4	211	1	0	0	0	0	0	0	0	1	7835	518	18	3		3	IREB2	15	78778141	Silent	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10		78778141	23753251	72	30451										
PLIN1	5346	hgsc.bcm.edu	37	chr15	90210270	90210270	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ttgaggagacagcaggggctGgtgtgaggtgcagcaccctc	17	9	0	3			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr15:90210270G>A	ENST00000300055.5	-	8	1271	c.1106C>T	c.(1105-1107)cCa>cTa	p.P369L	PLIN1_ENST00000430628.2_Missense_Mutation_p.P369L	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	369					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						AGCAGGGGCTGGTGTGAGGTG	0.607																																					p.P369L		Atlas-SNP	.											.	PLIN1	36	.	0			c.C1106T						.						75	62	66					15																	90210270		2200	4299	6499	SO:0001583	missense	5346	exon8			GGGGCTGGTGTGA	AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"Perilipins"	9076	protein-coding gene	gene with protein product		170290	"perilipin"	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.1106C>T	chr15.hg19:g.90210270G>A	ENSP00000300055:p.Pro369Leu	110.0	0.0		155.0	59.0	NM_001145311	Q8N5Y6	Missense_Mutation	SNP	ENST00000300055.5	hg19	CCDS10353.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.078987	0.36662	.	.	ENSG00000166819	ENST00000300055;ENST00000430628	T;T	0.07567	3.18;3.18	5.13	4.19	0.49359	.	2.061150	0.02074	N	0.051778	T	0.20292	0.0488	M	0.71581	2.175	0.09310	N	0.999999	P	0.40000	0.698	B	0.43413	0.419	T	0.37502	-0.9703	10	0.49607	T	0.09	-3.9652	12.2025	0.54335	0.0:0.0:0.8291:0.1709	.	369	O60240	PLIN1_HUMAN	L	369	ENSP00000300055:P369L;ENSP00000402167:P369L	ENSP00000300055:P369L	P	-	2	0	PLIN1	88011274	0.098000	0.21812	0.010000	0.14722	0.220000	0.24768	2.995000	0.49441	1.113000	0.41760	0.561000	0.74099	CCA	.	.		0.607	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313424.2	NM_002666		A	90210270	G	A	90210270	3	1	211	1	0	0	0	0	1	0	0	0	12098	1348	47	3	470	3	PLIN1	15	90210270	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	11432129	90210270	12321122	73	30452										
AXIN1	8312	hgsc.bcm.edu	37	chr16	396164	396164	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tcacctgaactctctgccttCgctgtaccgtctactggagg	9	14	3	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr16:396164C>A	ENST00000262320.3	-	2	1233	c.862G>T	c.(862-864)Gaa>Taa	p.E288*	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Nonsense_Mutation_p.E288*	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	288	Interaction with TP53. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				TCTCTGCCTTCGCTGTACCGT	0.617																																					p.E288X		Atlas-SNP	.											.	AXIN1	290	.	0			c.G862T						.						35	37	37					16																	396164		2203	4300	6503	SO:0001587	stop_gained	8312	exon2			TGCCTTCGCTGTA	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.862G>T	chr16.hg19:g.396164C>A	ENSP00000262320:p.Glu288*	28.0	0.0		36.0	35.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Nonsense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	C	42	9.582994	0.99211	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	5.4	5.4	0.78164	.	0.104367	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	19.173	0.93588	0.0:1.0:0.0:0.0	.	.	.	.	X	288	.	ENSP00000262320:E288X	E	-	1	0	AXIN1	336165	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.679000	0.84048	2.516000	0.84829	0.655000	0.94253	GAA	.	.		0.617	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	396164	C	A	396164	4	1	211	1	0	0	0	0	0	1	0	0	1236	893	31	1	1766	1	AXIN1	16	396164	Nonsense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10		396164	89958589	74	30453										
KIF22	3835	hgsc.bcm.edu	37	chr16	29816289	29816289	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ccgcagtcttcagcgcattgGcccgaagaaggcccagctaa	11	14	2	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr16:29816289G>T	ENST00000160827.4	+	12	1872	c.1832G>T	c.(1831-1833)gGc>gTc	p.G611V	KIF22_ENST00000400751.5_Missense_Mutation_p.G543V|MAZ_ENST00000545521.1_5'Flank|KIF22_ENST00000561482.1_Missense_Mutation_p.G543V|KIF22_ENST00000569382.2_Missense_Mutation_p.G557V|MAZ_ENST00000563402.1_5'Flank|MAZ_ENST00000219782.6_5'Flank|MAZ_ENST00000322945.6_5'Flank|MAZ_ENST00000566906.2_5'Flank|MAZ_ENST00000562337.1_5'Flank|AC009133.15_ENST00000566537.1_RNA	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22	611					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA repair (GO:0006281)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)			endometrium(1)|large_intestine(1)|lung(11)|skin(1)	14						CAGCGCATTGGCCCGAAGAAG	0.642																																					p.G611V		Atlas-SNP	.											.	KIF22	29	.	0			c.G1832T						.						41	43	42					16																	29816289		2197	4295	6492	SO:0001583	missense	3835	exon12			GCATTGGCCCGAA	D38751	CCDS10653.1, CCDS58444.1	16p11.2	2008-03-03	2003-01-09	2003-01-10	ENSG00000079616	ENSG00000079616		"Kinesins"	6391	protein-coding gene	gene with protein product		603213	"kinesin-like 4"	KNSL4		8599929, 11416179	Standard	NM_007317		Approved	Kid, OBP-1, OBP-2	uc002dts.4	Q14807	OTTHUMG00000097771	ENST00000160827.4:c.1832G>T	chr16.hg19:g.29816289G>T	ENSP00000160827:p.Gly611Val	42.0	0.0		51.0	26.0	NM_007317	B2R5M0|B7Z265|O60845|O94814|Q53F58|Q9BT46	Missense_Mutation	SNP	ENST00000160827.4	hg19	CCDS10653.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.562918	0.65538	.	.	ENSG00000079616	ENST00000160827;ENST00000400751	D;D	0.84442	-1.8;-1.85	5.64	5.64	0.86602	Helix-hairpin-helix DNA-binding motif, class 1 (1);	.	.	.	.	D	0.95726	0.8610	H	0.98407	4.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97274	0.9913	9	0.87932	D	0	.	17.189	0.86874	0.0:0.0:1.0:0.0	.	543;611	B7Z265;Q14807	.;KIF22_HUMAN	V	611;543	ENSP00000160827:G611V;ENSP00000383562:G543V	ENSP00000160827:G611V	G	+	2	0	KIF22	29723790	1.000000	0.71417	1.000000	0.80357	0.088000	0.18126	5.726000	0.68515	2.659000	0.90383	0.561000	0.74099	GGC	.	.		0.642	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2			T	29816289	G	T	29816289	3	4	211	1	0	0	0	0	1	0	0	0	8299	1203	42	3	1878	3	KIF22	16	29816289	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	29420125	29816289	60538464	75	30454										
BRD7	29117	hgsc.bcm.edu	37	chr16	50354273	50354273	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	cctgagcaatctggtggtctCatcaagtttcttctggaata	9	9	5	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr16:50354273C>A	ENST00000394688.3	-	15	1801	c.1642G>T	c.(1642-1644)Gag>Tag	p.E548*	BRD7_ENST00000394689.2_Nonsense_Mutation_p.E549*			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	548					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				CTGGTGGTCTCATCAAGTTTC	0.478																																					p.E549X		Atlas-SNP	.											.	BRD7	61	.	0			c.G1645T						.						107	102	104					16																	50354273		2198	4300	6498	SO:0001587	stop_gained	29117	exon15			TGGTCTCATCAAG	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"bromodomain-containing 7"			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.1642G>T	chr16.hg19:g.50354273C>A	ENSP00000378180:p.Glu548*	44.0	0.0		27.0	27.0	NM_001173984	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Nonsense_Mutation	SNP	ENST00000394688.3	hg19	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	C	42	9.334786	0.99140	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-18.4799	19.7507	0.96267	0.0:1.0:0.0:0.0	.	.	.	.	X	548;549	.	ENSP00000378180:E548X	E	-	1	0	BRD7	48911774	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.442000	0.80503	2.722000	0.93159	0.655000	0.94253	GAG	.	.		0.478	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		A	50354273	C	A	50354273	4	1	211	1	0	0	0	0	0	1	0	0	1507	835	29	3	325	3	BRD7	16	50354273	Nonsense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	20537984	50354273	40000480	76	30455										
TP53	7157	hgsc.bcm.edu	37	chr17	7578502	7578503	+	Frame_Shift_Ins	INS	-	-	CAGGG													0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ggaatcaacccacagctgcaINScagggcaggtcttggccagt					rs587782620		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr17:7578502_7578503insCAGGG	ENST00000269305.4	-	5	616_617	c.427_428insCCCTG	c.(427-429)gtgfs	p.V143fs	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Frame_Shift_Ins_p.V143fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.V143fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.V143fs|TP53_ENST00000455263.2_Frame_Shift_Ins_p.V143fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.V143fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	143	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> A (in sporadic cancers; somatic mutation; strong DNA binding ability at 32.5 degrees Celsius; strong reduction of transcriptional activity at 37.5 degrees Celsius; severely represses interaction with ZNF385A).|V -> E (in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> M (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V143M(19)|p.V143A(18)|p.0?(8)|p.V143E(5)|p.V143L(4)|p.V11A(2)|p.V50A(2)|p.V143fs*27(2)|p.V11M(1)|p.L137_W146del10(1)|p.V143fs*29(1)|p.P142_Q144delPVQ(1)|p.V50M(1)|p.K139fs*4(1)|p.A138_V143delAKTCPV(1)|p.V143G(1)|p.V143_S149del(1)|p.C141fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCACAGCTGCACAGGGCAGGTC	0.589		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.V143fs	Pancreas(47;798 1329 9957 10801)	Atlas-INDEL	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,-1,1	TP53	33396	.	70	Substitution - Missense(53)|Whole gene deletion(8)|Deletion - In frame(4)|Deletion - Frameshift(4)|Insertion - Frameshift(1)	large_intestine(12)|haematopoietic_and_lymphoid_tissue(8)|breast(8)|stomach(7)|lung(6)|upper_aerodigestive_tract(5)|urinary_tract(4)|oesophagus(4)|ovary(4)|bone(4)|central_nervous_system(3)|salivary_gland(2)|cervix(1)|vulva(1)|prostate(1)	c.428_429insCCCTG						.																																			SO:0001589	frameshift_variant	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.423_427dupCCCTG	chr17.hg19:g.7578503_7578507dupCAGGG	ENSP00000269305:p.Val143fs	82.0	0.0		51.0	34.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.589	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		CAGGG	7578503	-	CAGGG	7578502	7	5	211	1	0	1	1	0	0	0	0	0	16396	159	6	0	870	0	TP53	17	7578502	Frame_Shift_Ins	INS	-	TCGA-DD-AAE6-01A-11D-A40R-10		7578502	73616708	77	30456										
ANKFN1	162282	hgsc.bcm.edu	37	chr17	54543824	54543824	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gaggtggagatgctttattcAttttttaatggcaaatggat	11	3	1	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr17:54543824A>T	ENST00000318698.2	+	14	1709	c.1674A>T	c.(1672-1674)tcA>tcT	p.S558S	ANKFN1_ENST00000566473.2_Silent_p.S558S	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	558										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						TGCTTTATTCATTTTTTAATG	0.413																																					p.S558S		Atlas-SNP	.											.	ANKFN1	115	.	0			c.A1674T						.						105	94	98					17																	54543824		2203	4300	6503	SO:0001819	synonymous_variant	162282	exon14			TTATTCATTTTTT	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.1674A>T	chr17.hg19:g.54543824A>T		133.0	0.0		161.0	78.0	NM_153228		Silent	SNP	ENST00000318698.2	hg19	CCDS32686.1																																																																																			.	.		0.413	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		T	54543824	A	T	54543824	2	4	211	1	0	0	0	0	0	0	0	1	625	204	8	4		4	ANKFN1	17	54543824	Silent	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10	46965322	54543824	26651386	78	30457										
FBF1	85302	hgsc.bcm.edu	37	chr17	73910864	73910864	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	agggtgccctcccgctgggtGtccacctgcaatgcccgctc	12	17	0	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr17:73910864G>A	ENST00000586717.1	-	24	3009	c.2736C>T	c.(2734-2736)gaC>gaT	p.D912D	FBF1_ENST00000319129.5_Silent_p.D911D|RP11-552F3.12_ENST00000587556.1_5'Flank|FBF1_ENST00000389570.4_Silent_p.D912D			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	912					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						CCCGCTGGGTGTCCACCTGCA	0.706																																					p.D911D		Atlas-SNP	.											.	FBF1	48	.	0			c.C2733T						.						15	20	18					17																	73910864		2107	4203	6310	SO:0001819	synonymous_variant	85302	exon24			CTGGGTGTCCACC	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.2736C>T	chr17.hg19:g.73910864G>A		62.0	0.0		54.0	23.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	hg19																																																																																				.	.		0.706	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		A	73910864	G	A	73910864	2	1	211	1	0	0	0	0	0	0	0	1	5703	1368	48	3		3	FBF1	17	73910864	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	19367040	73910864	7284346	79	30458										
ANKLE1	126549	hgsc.bcm.edu	37	chr19	17393777	17393777	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	aggacccggacccggatcggGgcagagactcaggagcccga	16	13	1	1	rs368355885		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr19:17393777G>A	ENST00000394458.3	+	4	702	c.426G>A	c.(424-426)ggG>ggA	p.G142G	ANKLE1_ENST00000404085.1_Silent_p.G164G|ANKLE1_ENST00000594072.1_Silent_p.G131G|ANKLE1_ENST00000433424.2_Silent_p.G196G|ANKLE1_ENST00000598347.1_Silent_p.G142G	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	142										large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						CCCGGATCGGGGCAGAGACTC	0.682											OREG0025341	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G142G		Atlas-SNP	.											.	ANKLE1	27	.	0			c.G426A						.	G		0,4360		0,0,2180	10	14	13		426	0.8	0	19		13	2,8514		0,2,4256	no	coding-synonymous	ANKLE1	NM_152363.4		0,2,6436	AA,AG,GG		0.0235,0.0,0.0155		142/616	17393777	2,12874	2180	4258	6438	SO:0001819	synonymous_variant	126549	exon4			GATCGGGGCAGAG	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"Ankyrin repeat domain containing"	26812	protein-coding gene	gene with protein product	"LEM domain containing 6"		"ankyrin repeat domain 41"	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.426G>A	chr19.hg19:g.17393777G>A		55.0	0.0	717	91.0	12.0	NM_152363	A8VU82|Q8N8J8	Silent	SNP	ENST00000394458.3	hg19	CCDS12354.2																																																																																			.	.		0.682	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363		A	17393777	G	A	17393777	2	1	211	1	0	0	0	0	0	0	0	1	632	1219	43	3		3	ANKLE1	19	17393777	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10		17393777	41735206	80	30459										
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47425012	47425012	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tgggctgtctttcattatgaGcaattttgagagtaaactga	10	5	2	3			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr19:47425012G>A	ENST00000404338.3	+	1	3080	c.3080G>A	c.(3079-3081)aGc>aAc	p.S1027N		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	1027					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										TTCATTATGAGCAATTTTGAG	0.423																																					p.S1027N		Atlas-SNP	.											.	.	.	.	0			c.G3080A						.						60	57	58					19																	47425012		1866	4105	5971	SO:0001583	missense	2909	exon1			TTATGAGCAATTT	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.3080G>A	chr19.hg19:g.47425012G>A	ENSP00000385720:p.Ser1027Asn	67.0	0.0		58.0	26.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.584263	0.28268	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	T	0.07216	3.21	5.76	5.76	0.90799	.	0.270973	0.47455	D	0.000240	T	0.05044	0.0135	N	0.08118	0	0.41890	D	0.990361	B	0.06786	0.001	B	0.11329	0.006	T	0.47086	-0.9144	10	0.30854	T	0.27	-30.9876	12.1257	0.53915	0.0796:0.0:0.9204:0.0	.	1027	Q9NRY4-2	.	N	1027	ENSP00000385720:S1027N	ENSP00000324820:S1027N	S	+	2	0	ARHGAP35	52116852	0.992000	0.36948	1.000000	0.80357	0.984000	0.73092	1.557000	0.36299	2.726000	0.93360	0.655000	0.94253	AGC	.	.		0.423	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		A	47425012	G	A	47425012	3	1	211	1	0	0	0	0	1	0	0	0	6804	971	34	3	3082	3	ARHGAP35	19	47425012	Missense_Mutation	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	30031235	47425012	11703971	81	30460										
ZNF17	7565	hgsc.bcm.edu	37	chr19	57931108	57931108	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	agctttgtccacccagaaggCccagccctgtgagacatgta	10	13	0	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr19:57931108C>T	ENST00000601808.1	+	3	461	c.248C>T	c.(247-249)gCc>gTc	p.A83V	AC003002.6_ENST00000596400.1_Missense_Mutation_p.A95V|AC004076.7_ENST00000597410.1_Intron|ZNF17_ENST00000595206.1_3'UTR|ZNF17_ENST00000307658.7_Missense_Mutation_p.A85V	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	83	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		ACCCAGAAGGCCCAGCCCTGT	0.527																																					p.A83V	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.C248T						.						107	105	106					19																	57931108		2203	4300	6503	SO:0001583	missense	7565	exon3			AGAAGGCCCAGCC	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"Zinc fingers, C2H2-type", "-"	12958	protein-coding gene	gene with protein product			"zinc finger protein 17 (HPF3, KOX 10)"			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.248C>T	chr19.hg19:g.57931108C>T	ENSP00000471905:p.Ala83Val	125.0	0.0		136.0	24.0	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Missense_Mutation	SNP	ENST00000601808.1	hg19	CCDS42636.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.728487	0.30593	.	.	ENSG00000186272	ENST00000307658	.	.	.	1.85	0.78	0.18556	Krueppel-associated box (1);	.	.	.	.	T	0.26159	0.0638	L	0.28400	0.85	0.09310	N	1	B;B	0.25441	0.126;0.004	B;B	0.26416	0.069;0.0	T	0.21655	-1.0239	8	0.27082	T	0.32	.	4.3715	0.11249	0.0:0.7924:0.0:0.2076	.	85;83	P17021-2;P17021	.;ZNF17_HUMAN	V	83	.	ENSP00000302455:A83V	A	+	2	0	ZNF17	62622920	0.000000	0.05858	0.004000	0.12327	0.034000	0.12701	0.142000	0.16096	0.331000	0.23511	0.650000	0.86243	GCC	.	.		0.527	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959		T	57931108	C	T	57931108	3	4	211	1	0	0	0	0	1	0	0	0	17758	739	26	3	258	3	ZNF17	19	57931108	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	10506096	57931108	1197875	82	30461										
ZSCAN22	342945	hgsc.bcm.edu	37	chr19	58846306	58846306	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gaccacattgctcactctgaGgctgcacgcctgcgcttccg	10	16	2	1	rs138271492		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr19:58846306G>A	ENST00000329665.4	+	2	285	c.138G>A	c.(136-138)gaG>gaA	p.E46E		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	46					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|pancreas(1)|prostate(2)	16		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		CTCACTCTGAGGCTGCACGCC	0.627																																					p.E46E		Atlas-SNP	.											.	ZSCAN22	47	.	0			c.G138A						.						86	76	79					19																	58846306		2203	4300	6503	SO:0001819	synonymous_variant	342945	exon2			CTCTGAGGCTGCA	M20675	CCDS12975.1	19q13.43	2013-01-08	2006-09-20	2006-09-20				"-", "Zinc fingers, C2H2-type"	4929	protein-coding gene	gene with protein product	"oncogene HKR2"	165260	"zinc finger protein 50", "GLI-Kruppel family member HKR2"	ZNF50, HKR2		2850480, 1505991	Standard	NM_181846		Approved		uc002qsc.2	P10073		ENST00000329665.4:c.138G>A	chr19.hg19:g.58846306G>A		64.0	0.0		54.0	23.0	NM_181846	Q15922|Q7Z3L8	Silent	SNP	ENST00000329665.4	hg19	CCDS12975.1																																																																																			.	G|1.000;C|0.000		0.627	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846		A	58846306	G	A	58846306	2	1	211	1	0	0	0	0	0	0	0	1	18249	991	35	3		3	ZSCAN22	19	58846306	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	915198	58846306	282677	83	30462										
DLGAP4	22839	hgsc.bcm.edu	37	chr20	35068157	35068157	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tgctccccactccccaccagGagtctggaccgcctggattc	9	18	1	0	rs575582414		TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr20:35068157G>A	ENST00000373907.2	+	4	1441	c.1242G>A	c.(1240-1242)agG>agA	p.R414R	DLGAP4_ENST00000339266.5_Splice_Site_p.R414R|DLGAP4_ENST00000401952.2_Splice_Site_p.R414R|DLGAP4_ENST00000373913.3_Splice_Site_p.R414R			Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4	414					cell-cell signaling (GO:0007267)	membrane (GO:0016020)|synapse (GO:0045202)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				TCCCCACCAGGAGTCTGGACC	0.607											OREG0025903	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0	0.0014	5008	,	,		18941	0		0	False		,,,				2504	0				p.R414R		Atlas-SNP	.											.	DLGAP4	111	.	0			c.G1242A						.						67	54	59					20																	35068157		2203	4300	6503	SO:0001630	splice_region_variant	22839	exon4			CACCAGGAGTCTG	AF088030	CCDS13274.1, CCDS13275.1	20q11.23	2010-02-05			ENSG00000080845	ENSG00000080845			24476	protein-coding gene	gene with protein product						9115257	Standard	XM_005260329		Approved	DAP4, KIAA0964, SAPAP4	uc010zvp.2	Q9Y2H0	OTTHUMG00000032390	ENST00000373907.2:c.1242-1G>A	chr20.hg19:g.35068157G>A		42.0	0.0	852	63.0	11.0	NM_014902	E1P5T5|Q5QPG4|Q5T2Y4|Q5T2Y5|Q9H137|Q9H138|Q9H1L7	Silent	SNP	ENST00000373907.2	hg19																																																																																				.	.		0.607	DLGAP4-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000079025.2	NM_014902	Silent	A	35068157	G	A	35068157	5	1	211	1	0	0	0	0	0	0	1	0	4564	1188	41	3	1252	3	DLGAP4	20	35068157	Splice_Site	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10		35068157	27957363	84	30463										
GNAS	2778	hgsc.bcm.edu	37	chr20	57429421	57429421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	atggaaggagccgctgatgcCgcggagggaggaaaagtacc	17	8	0	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr20:57429421C>T	ENST00000306120.3	+	1	911	c.911C>T	c.(910-912)cCg>cTg	p.P304L	GNAS_ENST00000371102.4_Silent_p.A367A|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371100.4_Silent_p.A367A|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371099.2_Silent_p.A367A|GNAS_ENST00000464624.2_3'UTR			P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			CCGCTGATGCCGCGGAGGGAG	0.677			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.P305L	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	.	GNAS	867	.	0			c.C914T						.						14	24	20					20																	57429421		1960	4133	6093	SO:0001583	missense	2778	exon1			TGATGCCGCGGAG	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000306120.3:c.911C>T	chr20.hg19:g.57429421C>T	ENSP00000302237:p.Pro304Leu	80.0	0.0		156.0	50.0	NM_001077490	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000306120.3	hg19		.	.	.	.	.	.	.	.	.	.	C	3.923	-0.017659	0.07681	.	.	ENSG00000087460	ENST00000306120	.	.	.	4.52	-1.14	0.09741	.	.	.	.	.	T	0.37758	0.1015	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.40720	-0.9548	5	0.87932	D	0	.	5.6089	0.17394	0.0:0.5427:0.1537:0.3036	.	.	.	.	L	304	.	ENSP00000302237:P304L	P	+	2	0	GNAS	56862816	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.522000	0.06237	-0.298000	0.08921	0.462000	0.41574	CCG	.	.		0.677	GNAS-050	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000267987.1	NM_000516		T	57429421	C	T	57429421	3	4	211	1	0	0	0	0	1	0	0	0	6518	652	23	1	1845	1	GNAS	20	57429421	Missense_Mutation	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10	22361264	57429421	5596099	85	30464										
TPTE	7179	hgsc.bcm.edu	37	chr21	10933874	10933874	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gtgcctcctttacagtgaatCgctacgatgttttcaagatc	8	10	1	2			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr21:10933874C>T	ENST00000361285.4	-	17	1334	c.1005G>A	c.(1003-1005)gcG>gcA	p.A335A	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Silent_p.A297A|TPTE_ENST00000298232.7_Silent_p.A317A	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	335	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TACAGTGAATCGCTACGATGT	0.318																																					p.A335A		Atlas-SNP	.											TPTE_ENST00000361285,NS,carcinoma,-1,4	TPTE	513	.	0			c.G1005A						.						239	236	237					21																	10933874		2203	4300	6503	SO:0001819	synonymous_variant	7179	exon17			GTGAATCGCTACG	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1005G>A	chr21.hg19:g.10933874C>T		887.0	0.0		792.0	120.0	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Silent	SNP	ENST00000361285.4	hg19	CCDS13560.2																																																																																			.	.		0.318	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			T	10933874	C	T	10933874	2	4	211	1	0	0	0	0	0	0	0	1	16445	871	31	1		1	TPTE	21	10933874	Silent	SNP	C	TCGA-DD-AAE6-01A-11D-A40R-10		10933874	37196021	86	30465										
TMPRSS3	64699	hgsc.bcm.edu	37	chr21	43802304	43802304	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ggattgtccaacagggaaacTagacccacctggatggtcca	11	11	0	1			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr21:43802304T>G	ENST00000291532.3	-	9	1777	c.822A>C	c.(820-822)ctA>ctC	p.L274L	TMPRSS3_ENST00000398405.1_Silent_p.L272L|TMPRSS3_ENST00000398397.3_Silent_p.L274L|TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000433957.2_Silent_p.L274L|TMPRSS3_ENST00000380399.1_Silent_p.L358L	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	274	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						ACAGGGAAACTAGACCCACCT	0.507																																					p.L274L		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.A822C						.						102	76	85					21																	43802304		2203	4300	6503	SO:0001819	synonymous_variant	64699	exon9			GGAAACTAGACCC	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"Serine peptidases / Transmembrane"	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.822A>C	chr21.hg19:g.43802304T>G		67.0	0.0		91.0	39.0	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Silent	SNP	ENST00000291532.3	hg19	CCDS13686.1																																																																																			.	.		0.507	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1			G	43802304	T	G	43802304	2	3	211	1	0	0	0	0	0	0	0	1	16263	1509	53	5		5	TMPRSS3	21	43802304	Silent	SNP	T	TCGA-DD-AAE6-01A-11D-A40R-10	32868430	43802304	4327591	87	30466										
C21orf29	54084	hgsc.bcm.edu	37	chr21	45949775	45949775	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	accgccagcggggcgttcctGctgggacacagccttggggt	16	13	0	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr21:45949775G>A	ENST00000323084.4	-	5	761	c.696C>T	c.(694-696)agC>agT	p.S232S	TSPEAR_ENST00000397916.1_Silent_p.S164S	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	232	Laminin G-like.				sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						GGGCGTTCCTGCTGGGACACA	0.632																																					p.S232S		Atlas-SNP	.											.	TSPEAR	110	.	0			c.C696T						.						38	43	41					21																	45949775		2203	4300	6503	SO:0001819	synonymous_variant	54084	exon5			GTTCCTGCTGGGA	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"chromosome 21 open reading frame 29", "deafness, autosomal recessive 98"	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.696C>T	chr21.hg19:g.45949775G>A		48.0	0.0		45.0	14.0	NM_144991		Silent	SNP	ENST00000323084.4	hg19	CCDS13712.1																																																																																			.	.		0.632	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		A	45949775	G	A	45949775	2	1	211	1	0	0	0	0	0	0	0	1	2126	1310	46	3		3	C21orf29	21	45949775	Silent	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10	2147471	45949775	2180120	88	30467										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	39994193	39994193	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	gcatgctggtgatcctgctgAactgcgtgacacttggcatg	13	10	0	3			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chr22:39994193A>G	ENST00000402142.3	+	2	274	c.274A>G	c.(274-276)Aac>Gac	p.N92D	CACNA1I_ENST00000400164.3_Missense_Mutation_p.N92D|CACNA1I_ENST00000407673.1_Missense_Mutation_p.N92D|CACNA1I_ENST00000401624.1_Missense_Mutation_p.N92D|CACNA1I_ENST00000404898.1_Missense_Mutation_p.N92D|CACNA1I_ENST00000336649.4_Missense_Mutation_p.N92D	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	92					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	GATCCTGCTGAACTGCGTGAC	0.642																																					p.N92D		Atlas-SNP	.											.	CACNA1I	264	.	0			c.A274G						.						81	88	85					22																	39994193		2172	4261	6433	SO:0001583	missense	8911	exon2			CTGCTGAACTGCG	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.274A>G	chr22.hg19:g.39994193A>G	ENSP00000385019:p.Asn92Asp	38.0	0.0		25.0	17.0	NM_001003406	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	hg19	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.823344	0.90873	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.97976	-4.64;-4.64;-4.64;-4.64;-4.64;-4.64	4.03	4.03	0.46877	.	0.178102	0.47093	N	0.000256	D	0.98375	0.9460	M	0.78637	2.42	0.54753	D	0.999989	P;B;P;D	0.69078	0.694;0.265;0.911;0.997	B;B;P;D	0.75020	0.332;0.354;0.45;0.985	D	0.99218	1.0878	10	0.87932	D	0	.	13.1974	0.59746	1.0:0.0:0.0:0.0	.	92;92;92;92	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	D	92	ENSP00000385019:N92D;ENSP00000384093:N92D;ENSP00000383887:N92D;ENSP00000385680:N92D;ENSP00000337829:N92D;ENSP00000383028:N92D	ENSP00000337829:N92D	N	+	1	0	CACNA1I	38324139	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.020000	0.93667	1.703000	0.51240	0.449000	0.29647	AAC	.	.		0.642	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		G	39994193	A	G	39994193	3	3	211	1	0	0	0	0	1	0	0	0	2548	246	9	2	280	2	CACNA1I	22	39994193	Missense_Mutation	SNP	A	TCGA-DD-AAE6-01A-11D-A40R-10		39994193	11310373	89	30468										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382495	24382495	+	IGR	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	ctgctgctcctgctctagctGctgctgctgctcctgctcct	9	17	1	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chrX:24382495G>C								AC004552.1 (15472 upstream) : PDK3 (100842 downstream)																							tgctctagctgctgctgctgc	0.632																																					p.A540P		Atlas-SNP	.											.	.	.	.	0			c.G1618C						.						3	3	3					X																	24382495		1246	2954	4200	SO:0001628	intergenic_variant	100130302	exon1			CTAGCTGCTGCTG																													chrX.hg19:g.24382495G>C		106.0	0.0		108.0	8.0	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.632									C	24382495	G	C	24382495	1	2	211	0	1	0	0	0	0	0	0	0	5581	1319	46	4		4	FAM48B1	23	24382495	IGR	SNP	G	TCGA-DD-AAE6-01A-11D-A40R-10		24382495	130888065	90	30469										
TRPC5	7224	hgsc.bcm.edu	37	chrX	111195372	111195372	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	7	1	1.21248868778281	1.23723335488041	1.20846048616226	0.0497737556561086	0.431758392086709	0	tgcatcacccacatacacgcTgtggttcagcagtagctcca	8	14	2	0			TCGA-DD-AAE6-01A-11D-A40R-10	TCGA-DD-AAE6-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95b28a9a-7a85-4018-8418-c4381b9fc1a5	971f1297-9d76-49e3-9651-20e92dd3b3bc	g.chrX:111195372T>A	ENST00000262839.2	-	2	1195	c.277A>T	c.(277-279)Agc>Tgc	p.S93C		NM_012471.2	NP_036603.1	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel, subfamily C, member 5	93					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			biliary_tract(1)|breast(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(38)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						ACATACACGCTGTGGTTCAGC	0.552																																					p.S93C		Atlas-SNP	.											.	TRPC5	142	.	0			c.A277T						.						164	138	147					X																	111195372		2203	4300	6503	SO:0001583	missense	7224	exon2			ACACGCTGTGGTT	AF054568	CCDS14561.1	Xq23	2014-06-13			ENSG00000072315	ENSG00000072315		"Voltage-gated ion channels / Transient receptor potential cation channels"	12337	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 159"	300334				10493832, 16382100	Standard	NM_012471		Approved	PPP1R159	uc004epl.1	Q9UL62	OTTHUMG00000022212	ENST00000262839.2:c.277A>T	chrX.hg19:g.111195372T>A	ENSP00000262839:p.Ser93Cys	213.0	0.0		191.0	87.0	NM_012471	B2RP53|O75233|Q5JXY8|Q9Y514	Missense_Mutation	SNP	ENST00000262839.2	hg19	CCDS14561.1	.	.	.	.	.	.	.	.	.	.	T	13.87	2.365450	0.41902	.	.	ENSG00000072315	ENST00000262839	T	0.54071	0.59	5.51	5.51	0.81932	Ankyrin repeat-containing domain (3);	0.134289	0.64402	D	0.000002	T	0.42268	0.1195	L	0.45137	1.4	0.27262	N	0.958594	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.39057	-0.9632	10	0.54805	T	0.06	-13.9013	6.4141	0.21708	0.143:0.0785:0.0:0.7785	.	94;93	Q59G51;Q9UL62	.;TRPC5_HUMAN	C	93	ENSP00000262839:S93C	ENSP00000262839:S93C	S	-	1	0	TRPC5	111082028	1.000000	0.71417	0.995000	0.50966	0.927000	0.56198	2.831000	0.48144	1.840000	0.53500	0.417000	0.27973	AGC	.	.		0.552	TRPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057945.1	NM_012471		A	111195372	T	A	111195372	3	1	211	1	0	0	0	0	1	0	0	0	16597	1580	55	4	2684	4	TRPC5	23	111195372	Missense_Mutation	SNP	T	TCGA-DD-AAE6-01A-11D-A40R-10	86812877	111195372	44075188	91	30470										
SLC2A5	6518	hgsc.bcm.edu	37	chr1	9098489	9098489	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aggccagctttgggtacgtaCtgggcccgagggcatgtcct	15	11	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:9098489C>T	ENST00000377424.4	-	10	1354		c.e10+1		SLC2A5_ENST00000535586.1_Splice_Site|SLC2A5_ENST00000536305.1_Splice_Site	NM_003039.2	NP_003030.1	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated glucose/fructose transporter), member 5						carbohydrate metabolic process (GO:0005975)|cellular response to fructose stimulus (GO:0071332)|fructose transport (GO:0015755)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fructose transmembrane transporter activity (GO:0005353)|glucose transmembrane transporter activity (GO:0005355)			endometrium(6)|kidney(15)|large_intestine(6)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|urinary_tract(1)	36	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		TGGGTACGTACTGGGCCCGAG	0.577																																					.		Atlas-SNP	.											.	SLC2A5	77	.	0			c.1174+1G>A						.						111	99	103					1																	9098489		2203	4299	6502	SO:0001630	splice_region_variant	6518	exon11			TACGTACTGGGCC	BC001820	CCDS99.1, CCDS44054.1	1p36.2	2013-05-22			ENSG00000142583	ENSG00000142583		"Solute carriers"	11010	protein-coding gene	gene with protein product		138230		GLUT5		9691177	Standard	NM_003039		Approved		uc001apo.3	P22732	OTTHUMG00000001771	ENST00000377424.4:c.1174+1G>A	chr1.hg19:g.9098489C>T		70.0	0.0		65.0	20.0	NM_003039	Q14770|Q5T977|Q8IVB3	Splice_Site	SNP	ENST00000377424.4	hg19	CCDS99.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.258234	0.39896	.	.	ENSG00000142583	ENST00000377424;ENST00000456780;ENST00000536305;ENST00000535586	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1758	0.86841	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC2A5	9021076	1.000000	0.71417	0.999000	0.59377	0.088000	0.18126	7.410000	0.80065	2.396000	0.81511	0.655000	0.94253	.	.	.		0.577	SLC2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004932.1	NM_003039	Intron	T	9098489	C	T	9098489	5	4	212	1	0	0	0	0	0	0	1	0	14563	579	20	3	342	3	SLC2A5	1	9098489	Splice_Site	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10		9098489	240152132	1	30471										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27101213	27101213	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctcagcaaggcaccatgtggCaggggcgtaatgacatgacc	13	11	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:27101213C>T	ENST00000324856.7	+	18	4866	c.4495C>T	c.(4495-4497)Cag>Tag	p.Q1499*	ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q1116*|ARID1A_ENST00000457599.2_Intron	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1499					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CACCATGTGGCAGGGGCGTAA	0.577			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Q1499X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.C4495T						.						70	73	72					1																	27101213		2203	4300	6503	SO:0001587	stop_gained	8289	exon18			ATGTGGCAGGGGC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4495C>T	chr1.hg19:g.27101213C>T	ENSP00000320485:p.Gln1499*	68.0	0.0		97.0	5.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	44|44	10.678996|10.678996	0.99448|0.99448	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000430799|ENST00000324856;ENST00000374152	.|.	.|.	.|.	5.54|5.54	4.61|4.61	0.57282|0.57282	.|.	.|0.051740	.|0.85682	.|D	.|0.000000	T|.	0.65954|.	0.2741|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.61594|.	-0.7031|.	4|.	.|0.20519	.|T	.|0.43	-6.4368|-6.4368	16.3406|16.3406	0.83081|0.83081	0.0:0.8679:0.1321:0.0|0.0:0.8679:0.1321:0.0	.|.	.|.	.|.	.|.	V|X	395|1499;1116	.|.	.|ENSP00000320485:Q1499X	A|Q	+|+	2|1	0|0	ARID1A|ARID1A	26973800|26973800	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.228000|7.228000	0.78079|0.78079	1.541000|1.541000	0.49316|0.49316	0.650000|0.650000	0.86243|0.86243	GCA|CAG	.	.		0.577	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27101213	C	T	27101213	4	4	212	1	0	0	0	0	0	1	0	0	913	711	25	3	4565	3	ARID1A	1	27101213	Nonsense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	18002724	27101213	222149408	2	30472										
SNRNP40	9410	hgsc.bcm.edu	37	chr1	31766196	31766196	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gaggaacatcttggaggtccCtaaacaaaagagaagcacaa	10	8	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:31766196C>A	ENST00000263694.4	-	2	160		c.e2-1		SNRNP40_ENST00000446633.2_Splice_Site	NM_004814.2	NP_004805.2	Q96DI7	SNR40_HUMAN	small nuclear ribonucleoprotein 40kDa (U5)						gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	7						TTGGAGGTCCCTAAACAAAAG	0.488																																					.		Atlas-SNP	.											.	SNRNP40	18	.	0			c.142-1G>T						.						63	53	56					1																	31766196		2203	4300	6503	SO:0001630	splice_region_variant	9410	exon3			AGGTCCCTAAACA	AF090988	CCDS340.1	1p35.2	2013-01-09	2008-10-29	2008-10-29	ENSG00000060688	ENSG00000060688		"WD repeat domain containing"	30857	protein-coding gene	gene with protein product		607797	"WD repeat domain 57 (U5 snRNP specific)"	WDR57		9774689, 9731529, 10788320	Standard	NM_004814		Approved	PRP8BP, SPF38, PRPF8BP, HPRP8BP	uc009vtt.3	Q96DI7	OTTHUMG00000003790	ENST00000263694.4:c.142-1G>T	chr1.hg19:g.31766196C>A		81.0	0.0		102.0	22.0	NM_004814	B4DQJ1|O75938|O95320	Splice_Site	SNP	ENST00000263694.4	hg19	CCDS340.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.408012	0.83340	.	.	ENSG00000060688	ENST00000263694;ENST00000446633	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0483	0.93030	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SNRNP40	31538783	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.709000	0.84645	2.495000	0.84180	0.655000	0.94253	.	.	.		0.488	SNRNP40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010657.1	NM_004814	Intron	A	31766196	C	A	31766196	5	1	212	1	0	0	0	0	0	0	1	0	14871	695	24	3	968	3	SNRNP40	1	31766196	Splice_Site	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	4664983	31766196	217484425	3	30473										
FNDC5	252995	hgsc.bcm.edu	37	chr1	33330349	33330349	+	Frame_Shift_Del	DEL	T	T	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttttccttgttgttattgggTtcattgtccttgatgatgtc							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:33330349delT	ENST00000373471.3	-	5	615	c.549delA	c.(547-549)gaafs	p.E183fs	FNDC5_ENST00000609187.1_Frame_Shift_Del_p.E108fs|FNDC5_ENST00000481487.1_5'Flank|FNDC5_ENST00000496770.1_Frame_Shift_Del_p.E108fs	NM_001171940.1|NM_153756.2	NP_001165411.2|NP_715637.2	Q8NAU1	FNDC5_HUMAN	fibronectin type III domain containing 5	183					positive regulation of brown fat cell differentiation (GO:0090336)|response to muscle activity (GO:0014850)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(2)|ovary(1)	5		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				TGTTATTGGGTTCATTGTCCT	0.562																																					p.P109fs		Atlas-INDEL	.											.	FNDC5	16	.	0			c.325delC						.						167	140	149					1																	33330349		2203	4300	6503	SO:0001589	frameshift_variant	252995	exon5			.	AK092102	CCDS369.1, CCDS369.2, CCDS65483.1	1p34.3	2013-10-16			ENSG00000160097	ENSG00000160097		"Fibronectin type III domain containing"	20240	protein-coding gene	gene with protein product	"irisin"	611906				12384288, 22237023, 24120943	Standard	NM_153756		Approved	FRCP2	uc001bwg.3	Q8NAU1	OTTHUMG00000004015	ENST00000373471.3:c.549delA	chr1.hg19:g.33330349delT	ENSP00000362570:p.Glu183fs	60.0	0.0		73.0	22.0	NM_153756	A6NMC9|D3DPQ6|Q6P6D9|Q7Z676	Frame_Shift_Del	DEL	ENST00000373471.3	hg19																																																																																				.	.		0.562	FNDC5-001	KNOWN	non_ATG_start|basic	protein_coding	protein_coding	OTTHUMT00000011467.3	NM_153756		-	33330349	T	-	33330349	7	5	212	1	0	1	0	1	0	0	0	0	5980	1722	60	0	170	0	FNDC5	1	33330349	Frame_Shift_Del	DEL	T	TCGA-DD-AAE7-01A-11D-A40R-10	1564153	33330349	215920272	4	30474										
GNL2	29889	hgsc.bcm.edu	37	chr1	38061409	38061409	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atggtgctccgtcctttgtaCttgggcttcaccatcttggc	10	12	2	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:38061409C>T	ENST00000373062.3	-	1	113	c.15G>A	c.(13-15)aaG>aaA	p.K5K		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	5					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				GTCCTTTGTACTTGGGCTTCA	0.582																																					p.K5K		Atlas-SNP	.											.	GNL2	58	.	0			c.G15A						.						135	105	116					1																	38061409		2203	4300	6503	SO:0001819	synonymous_variant	29889	exon1			TTTGTACTTGGGC	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.15G>A	chr1.hg19:g.38061409C>T		73.0	0.0		61.0	13.0	NM_013285	Q9BWN7	Silent	SNP	ENST00000373062.3	hg19	CCDS421.1																																																																																			.	.		0.582	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285		T	38061409	C	T	38061409	2	4	212	1	0	0	0	0	0	0	0	1	6544	564	20	3		3	GNL2	1	38061409	Silent	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	4731060	38061409	211189212	5	30475										
TOE1	114034	hgsc.bcm.edu	37	chr1	45809148	45809148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	taacccagtgcctggggatgGattgcaccgggctggttttg	15	9	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:45809148G>A	ENST00000372090.5	+	8	1890	c.1307G>A	c.(1306-1308)gGa>gAa	p.G436E	TOE1_ENST00000539779.1_Missense_Mutation_p.G356E|TOE1_ENST00000495703.1_3'UTR|TESK2_ENST00000486676.1_5'Flank	NM_025077.3	NP_079353.3	Q96GM8	TOE1_HUMAN	target of EGR1, member 1 (nuclear)	436						nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	11	Acute lymphoblastic leukemia(166;0.155)					CCTGGGGATGGATTGCACCGG	0.557																																					p.G436E		Atlas-SNP	.											.	TOE1	27	.	0			c.G1307A						.						89	82	84					1																	45809148		2203	4300	6503	SO:0001583	missense	114034	exon8			GGGATGGATTGCA		CCDS521.1	1p33	2011-02-03			ENSG00000132773	ENSG00000132773			15954	protein-coding gene	gene with protein product		613931				12562764	Standard	NM_025077		Approved		uc009vxq.3	Q96GM8	OTTHUMG00000007678	ENST00000372090.5:c.1307G>A	chr1.hg19:g.45809148G>A	ENSP00000361162:p.Gly436Glu	59.0	0.0		88.0	28.0	NM_025077	B4DEM6|Q6IA35|Q8IWN5|Q9H846	Missense_Mutation	SNP	ENST00000372090.5	hg19	CCDS521.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.772275	0.90108	.	.	ENSG00000132773	ENST00000372090;ENST00000539779	T;T	0.22539	1.95;1.95	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.50377	0.1612	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.41484	-0.9506	10	0.87932	D	0	-13.2037	20.8794	0.99867	0.0:0.0:1.0:0.0	.	356;436	B4DEM6;Q96GM8	.;TOE1_HUMAN	E	436;356	ENSP00000361162:G436E;ENSP00000438900:G356E	ENSP00000361162:G436E	G	+	2	0	TOE1	45581735	0.984000	0.35163	0.968000	0.41197	0.981000	0.71138	2.009000	0.40903	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.557	TOE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020517.1	NM_025077		A	45809148	G	A	45809148	3	1	212	1	0	0	0	0	1	0	0	0	16364	1174	41	3	1337	3	TOE1	1	45809148	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	7747739	45809148	203441473	6	30476										
MAST2	23139	hgsc.bcm.edu	37	chr1	46497890	46497890	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttggccagccccatgtccccAcattctcagtcgtccaaccc	6	19	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:46497890A>T	ENST00000361297.2	+	25	3511	c.3228A>T	c.(3226-3228)ccA>ccT	p.P1076P	MAST2_ENST00000372009.2_Silent_p.P1006P	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CCATGTCCCCACATTCTCAGT	0.607																																					p.P1076P		Atlas-SNP	.											.	MAST2	136	.	0			c.A3228T						.						80	87	85					1																	46497890		2032	4191	6223	SO:0001819	synonymous_variant	23139	exon25			GTCCCCACATTCT	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.3228A>T	chr1.hg19:g.46497890A>T		58.0	0.0		77.0	25.0	NM_015112		Silent	SNP	ENST00000361297.2	hg19	CCDS41326.1																																																																																			.	.		0.607	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		T	46497890	A	T	46497890	2	4	212	1	0	0	0	0	0	0	0	1	9334	146	6	4		4	MAST2	1	46497890	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	688742	46497890	202752731	7	30477										
NRD1	4898	hgsc.bcm.edu	37	chr1	52281991	52281991	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	attgaatacttgctttttccTaaggaaagaaagaatgctgc	8	6	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:52281991T>G	ENST00000354831.7	-	13	1825	c.1636A>C	c.(1636-1638)Agg>Cgg	p.R546R	NRD1_ENST00000352171.7_Silent_p.R478R|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_Silent_p.R346R|NRD1_ENST00000539524.1_Silent_p.R414R	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	477					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						TGCTTTTTCCTAAGGAAAGAA	0.308																																					p.R546R		Atlas-SNP	.											.	NRD1	89	.	0			c.A1636C						.						57	62	60					1																	52281991		2203	4296	6499	SO:0001819	synonymous_variant	4898	exon13			TTTTCCTAAGGAA	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.1636A>C	chr1.hg19:g.52281991T>G		236.0	0.0		428.0	118.0	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Silent	SNP	ENST00000354831.7	hg19	CCDS559.1																																																																																			.	.		0.308	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		G	52281991	T	G	52281991	2	3	212	1	0	0	0	0	0	0	0	1	10654	1521	53	5		5	NRD1	1	52281991	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	5784101	52281991	196968630	8	30478										
MYSM1	114803	hgsc.bcm.edu	37	chr1	59158557	59158557	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cttccaacaacattttctcaAtaacagctctgttctcttca	2	13	4	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:59158557A>G	ENST00000472487.1	-	3	233	c.194T>C	c.(193-195)aTt>aCt	p.I65T		NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	65					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					CATTTTCTCAATAACAGCTCT	0.308																																					p.I65T		Atlas-SNP	.											.	MYSM1	50	.	0			c.T194C						.						201	200	200					1																	59158557		1826	4084	5910	SO:0001583	missense	114803	exon3			TTCTCAATAACAG	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.194T>C	chr1.hg19:g.59158557A>G	ENSP00000418734:p.Ile65Thr	35.0	0.0		66.0	18.0	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Missense_Mutation	SNP	ENST00000472487.1	hg19	CCDS41343.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.288396	0.80803	.	.	ENSG00000162601	ENST00000472487	T	0.36157	1.27	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.49115	0.1538	L	0.34521	1.04	0.58432	D	0.999995	D	0.76494	0.999	D	0.80764	0.994	T	0.51387	-0.8712	10	0.87932	D	0	-14.118	14.345	0.66654	1.0:0.0:0.0:0.0	.	65	Q5VVJ2	MYSM1_HUMAN	T	65	ENSP00000418734:I65T	ENSP00000418734:I65T	I	-	2	0	MYSM1	58931145	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.772000	0.85439	2.254000	0.74563	0.460000	0.39030	ATT	.	.		0.308	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481		G	59158557	A	G	59158557	3	3	212	1	0	0	0	0	1	0	0	0	10110	101	4	2	2364	2	MYSM1	1	59158557	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	6876566	59158557	190092064	9	30479										
DOCK7	85440	hgsc.bcm.edu	37	chr1	62941590	62941590	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atatgtgtcaaagtatggctCcacataggtaatctgaatat	8	6	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:62941590C>T	ENST00000340370.5	-	45	5673	c.5656G>A	c.(5656-5658)Gag>Aag	p.E1886K	DOCK7_ENST00000489185.1_5'UTR|DOCK7_ENST00000251157.5_Missense_Mutation_p.E1906K	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1917	DHR-2.				activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						AAGTATGGCTCCACATAGGTA	0.353																																					p.E1906K		Atlas-SNP	.											.	DOCK7	184	.	0			c.G5716A						.						139	139	139					1																	62941590		2203	4300	6503	SO:0001583	missense	85440	exon45			ATGGCTCCACATA		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.5656G>A	chr1.hg19:g.62941590C>T	ENSP00000340742:p.Glu1886Lys	27.0	0.0		64.0	16.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	hg19	CCDS30734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.712779|5.712779	0.96830|0.96830	.|.	.|.	ENSG00000116641|ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441|ENST00000454575	T;T|.	0.15718|.	2.41;2.4|.	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75722|0.75722	0.3888|0.3888	M|M	0.67397|0.67397	2.05|2.05	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	0.998;1.0;0.998;0.999;1.0;1.0|.	D;D;D;D;D;D|.	0.91635|.	0.996;0.999;0.997;0.996;0.999;0.997|.	T|T	0.72966|0.72966	-0.4131|-0.4131	10|5	0.72032|.	D|.	0.01|.	.|.	19.8965|19.8965	0.96963|0.96963	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1917;1906;1886;1875;1877;1908|.	Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6|.	DOCK7_HUMAN;.;.;.;.;.|.	K|E	1917;1906;1886;647|1079	ENSP00000251157:E1906K;ENSP00000340742:E1886K|.	ENSP00000251157:E1906K|.	E|G	-|-	1|2	0|0	DOCK7|DOCK7	62714178|62714178	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.818000|7.818000	0.86416|0.86416	2.717000|2.717000	0.92951|0.92951	0.655000|0.655000	0.94253|0.94253	GAG|GGA	.	.		0.353	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		T	62941590	C	T	62941590	3	4	212	1	0	0	0	0	1	0	0	0	4694	864	30	3	693	3	DOCK7	1	62941590	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	3783033	62941590	186309031	10	30480										
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77334301	77334301	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cagcagcagcagcagcagcaAcagcagcagcaggcgtcggc	14	14	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:77334301A>G	ENST00000477717.1	+	2	370	c.135A>G	c.(133-135)caA>caG	p.Q45Q	ST6GALNAC5_ENST00000496845.1_3'UTR	NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	45	Poly-Gln.				glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						agcagcagcaacagcagcagc	0.716																																					p.Q45Q		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.A135G						.						11	12	12					1																	77334301		2032	3963	5995	SO:0001819	synonymous_variant	81849	exon2			GCAGCAACAGCAG		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.135A>G	chr1.hg19:g.77334301A>G		131.0	0.0		98.0	4.0	NM_030965	B1AK82	Silent	SNP	ENST00000477717.1	hg19	CCDS673.1																																																																																			.	.		0.716	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		G	77334301	A	G	77334301	2	3	212	1	0	0	0	0	0	0	0	1	15242	40	2	2		2	ST6GALNAC5	1	77334301	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	14392711	77334301	171916320	11	30481										
WDR63	126820	hgsc.bcm.edu	37	chr1	85551546	85551546	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atttctcgaaaacgaagtgaAtttggtgcaccaattaagtt	8	6	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:85551546A>G	ENST00000294664.6	+	7	753	c.573A>G	c.(571-573)gaA>gaG	p.E191E	WDR63_ENST00000370596.1_Silent_p.E191E|WDR63_ENST00000326813.8_Silent_p.E191E	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	191										NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		AACGAAGTGAATTTGGTGCAC	0.358																																					p.E191E		Atlas-SNP	.											.	WDR63	91	.	0			c.A573G						.						109	100	103					1																	85551546		2203	4300	6503	SO:0001819	synonymous_variant	126820	exon7			AAGTGAATTTGGT		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"WD repeat domain containing"	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.573A>G	chr1.hg19:g.85551546A>G		147.0	0.0		265.0	82.0	NM_145172	A8K988|Q96L72|Q96NU4	Silent	SNP	ENST00000294664.6	hg19	CCDS702.1																																																																																			.	.		0.358	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172		G	85551546	A	G	85551546	2	3	212	1	0	0	0	0	0	0	0	1	17329	98	4	2		2	WDR63	1	85551546	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	8217245	85551546	163699075	12	30482										
CSF1	1435	hgsc.bcm.edu	37	chr1	110464543	110464543	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aatgtctttaatgaaacaaaGaatctccttgacaaggactg	7	7	2	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:110464543G>T	ENST00000329608.6	+	5	862	c.471G>T	c.(469-471)aaG>aaT	p.K157N	CSF1_ENST00000344188.5_Missense_Mutation_p.K157N|CSF1_ENST00000526001.1_3'UTR|CSF1_ENST00000369801.1_Missense_Mutation_p.K157N|CSF1_ENST00000369802.3_Missense_Mutation_p.K157N|CSF1_ENST00000420111.2_Missense_Mutation_p.K157N	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	157					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|developmental process involved in reproduction (GO:0003006)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary duct terminal end bud growth (GO:0060763)|mammary gland fat development (GO:0060611)|monocyte activation (GO:0042117)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of macrophage derived foam cell differentiation (GO:0010743)|regulation of ossification (GO:0030278)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|macrophage colony-stimulating factor receptor binding (GO:0005157)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		ATGAAACAAAGAATCTCCTTG	0.483																																					p.K157N		Atlas-SNP	.											.	CSF1	40	.	0			c.G471T						.						97	98	98					1																	110464543		2203	4300	6503	SO:0001583	missense	1435	exon5			AACAAAGAATCTC	BC021117	CCDS816.1, CCDS817.1, CCDS30797.1	1p13.3	2012-09-20			ENSG00000184371	ENSG00000184371			2432	protein-coding gene	gene with protein product		120420				1540160	Standard	NM_172210		Approved	M-CSF, MCSF, MGC31930	uc001dyw.4	P09603	OTTHUMG00000011646	ENST00000329608.6:c.471G>T	chr1.hg19:g.110464543G>T	ENSP00000327513:p.Lys157Asn	211.0	0.0		242.0	67.0	NM_172210	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Missense_Mutation	SNP	ENST00000329608.6	hg19	CCDS816.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.272149	0.40194	.	.	ENSG00000184371	ENST00000344188;ENST00000329608;ENST00000488198;ENST00000369802;ENST00000420111;ENST00000369801	T;T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38;2.38	5.03	3.17	0.36434	Four-helical cytokine-like, core (1);	0.341890	0.26304	N	0.025147	T	0.23727	0.0574	M	0.74258	2.255	0.33043	D	0.531732	P;D;D	0.89917	0.918;1.0;1.0	B;D;D	0.91635	0.294;0.999;0.999	T	0.06844	-1.0804	9	.	.	.	.	7.6321	0.28245	0.1962:0.0:0.8038:0.0	.	157;157;157	P09603-3;P09603;P09603-2	.;CSF1_HUMAN;.	N	157;157;116;157;157;157	ENSP00000342718:K157N;ENSP00000327513:K157N;ENSP00000433837:K116N;ENSP00000358817:K157N;ENSP00000407317:K157N;ENSP00000358816:K157N	.	K	+	3	2	CSF1	110266066	0.992000	0.36948	1.000000	0.80357	0.505000	0.33919	0.207000	0.17395	0.530000	0.28619	0.491000	0.48974	AAG	.	.		0.483	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757		T	110464543	G	T	110464543	3	4	212	1	0	0	0	0	1	0	0	0	3933	933	33	3	489	3	CSF1	1	110464543	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	24912997	110464543	138786078	13	30483										
C1orf103	55791	hgsc.bcm.edu	37	chr1	111492489	111492489	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctacctgttttctctctcctTccttcaccataaactctgtc	2	16	4	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:111492489T>G	ENST00000369763.4	-	3	2243	c.1853A>C	c.(1852-1854)gAa>gCa	p.E618A	LRIF1_ENST00000485275.2_Missense_Mutation_p.E82A|RP11-96K19.2_ENST00000440689.1_RNA|LRIF1_ENST00000494675.1_Missense_Mutation_p.E82A	NM_018372.3	NP_060842.3	Q5T3J3	LRIF1_HUMAN	ligand dependent nuclear receptor interacting factor 1	618					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(1)|urinary_tract(2)	28						TCTCTCTCCTTCCTTCACCAT	0.363																																					p.E618A		Atlas-SNP	.											.	LRIF1	65	.	0			c.A1853C						.						187	197	193					1																	111492489		2203	4300	6503	SO:0001583	missense	55791	exon3			TCTCCTTCCTTCA	AY190122	CCDS30800.1, CCDS41366.1	1p13.3	2011-04-15	2011-04-15	2011-04-15	ENSG00000121931	ENSG00000121931			30299	protein-coding gene	gene with protein product	"receptor interacting factor 1"	615354	"chromosome 1 open reading frame 103"	C1orf103		17455211	Standard	NM_018372		Approved	RIF1, FLJ11269	uc001eaa.3	Q5T3J3	OTTHUMG00000011913	ENST00000369763.4:c.1853A>C	chr1.hg19:g.111492489T>G	ENSP00000358778:p.Glu618Ala	47.0	0.0		79.0	21.0	NM_018372	Q86XS4|Q8N3B6|Q96HT4|Q9NUM5|Q9NV32	Missense_Mutation	SNP	ENST00000369763.4	hg19	CCDS30800.1	.	.	.	.	.	.	.	.	.	.	T	6.070	0.381285	0.11466	.	.	ENSG00000121931	ENST00000369763;ENST00000494675;ENST00000485275	T;T;T	0.34072	1.78;1.38;1.38	5.39	1.39	0.22231	.	0.299368	0.30781	N	0.008893	T	0.19604	0.0471	M	0.66939	2.045	0.09310	N	1	P;B	0.44139	0.827;0.004	B;B	0.41510	0.359;0.005	T	0.06058	-1.0848	10	0.51188	T	0.08	-2.3355	10.3971	0.44207	0.0:0.0:0.5072:0.4928	.	82;618	Q5T3J3-2;Q5T3J3	.;LRIF1_HUMAN	A	618;82;82	ENSP00000358778:E618A;ENSP00000435259:E82A;ENSP00000432290:E82A	ENSP00000358778:E618A	E	-	2	0	LRIF1	111294012	0.005000	0.15991	0.289000	0.24876	0.110000	0.19582	0.147000	0.16202	0.311000	0.23014	-0.461000	0.05368	GAA	.	.		0.363	LRIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032932.2	NM_018372		G	111492489	T	G	111492489	3	3	212	1	0	0	0	0	1	0	0	0	1979	1783	62	5	464	5	C1orf103	1	111492489	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	1027946	111492489	137758132	14	30484										
NRAS	4893	hgsc.bcm.edu	37	chr1	115256463	115256463	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atgacttgctattattgatgGcaaatacacagaggaagcct	9	7	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:115256463G>C	ENST00000369535.4	-	3	501	c.248C>G	c.(247-249)gCc>gGc	p.A83G		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	83					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)			NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATTATTGATGGCAAATACACA	0.418		50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																											p.A83G		Atlas-SNP	.		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	.	NRAS	3766	.	0			c.C248G						.						171	149	157					1																	115256463		2203	4300	6503	SO:0001583	missense	4893	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TTGATGGCAAATA	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.248C>G	chr1.hg19:g.115256463G>C	ENSP00000358548:p.Ala83Gly	64.0	0.0		84.0	28.0	NM_002524	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	hg19	CCDS877.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.609816	0.87258	.	.	ENSG00000213281	ENST00000369535	T	0.70516	-0.49	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000034	T	0.74199	0.3685	M	0.77712	2.385	0.80722	D	1	B	0.28820	0.224	B	0.41946	0.371	T	0.76940	-0.2773	10	0.87932	D	0	.	18.6626	0.91477	0.0:0.0:1.0:0.0	.	83	P01111	RASN_HUMAN	G	83	ENSP00000358548:A83G	ENSP00000358548:A83G	A	-	2	0	NRAS	115057986	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.554000	0.98121	2.624000	0.88883	0.655000	0.94253	GCC	.	.		0.418	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		C	115256463	G	C	115256463	3	2	212	1	0	0	0	0	1	0	0	0	10649	1203	42	4	333	4	NRAS	1	115256463	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	3763974	115256463	133994158	15	30485										
NBPF10	100132406	hgsc.bcm.edu	37	chr1	145304497	145304497	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccctgaggactcactggaggAatgtgccatcacttattcaa	9	11	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:145304497A>C	ENST00000369339.3	+	7	870	c.617A>C	c.(616-618)gAa>gCa	p.E206A	NBPF10_ENST00000369338.1_Missense_Mutation_p.E206A|NBPF10_ENST00000342960.5_Missense_Mutation_p.E477A|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	477	NBPF 1. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TCACTGGAGGAATGTGCCATC	0.458																																					p.E477A		Atlas-SNP	.											.	NBPF10	221	.	0			c.A1430C						.																																			SO:0001583	missense	100132406	exon10			TGGAGGAATGTGC	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"neuroblastoma breakpoint family"	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.617A>C	chr1.hg19:g.145304497A>C	ENSP00000358345:p.Glu206Ala	68.0	0.0		125.0	19.0	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	hg19		.	.	.	.	.	.	.	.	.	.	.	11.26	1.587733	0.28268	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.08984	3.03;3.03	0.811	0.811	0.18739	.	.	.	.	.	T	0.04634	0.0126	L	0.28192	0.835	0.09310	N	1	P;P;P;P	0.51240	0.892;0.747;0.943;0.876	P;P;P;B	0.59288	0.777;0.77;0.855;0.443	T	0.33548	-0.9864	9	0.66056	D	0.02	.	3.9352	0.09302	1.0:0.0:0.0:0.0	.	152;442;408;206	Q4VC10;Q3BBV7;Q5U227;A8MQ30	.;.;.;.	A	402;206;206;477	ENSP00000358344:E206A;ENSP00000345684:E477A	ENSP00000345684:E477A	E	+	2	0	NBPF10	144015854	0.003000	0.15002	0.002000	0.10522	0.085000	0.17905	0.337000	0.19841	0.607000	0.29982	0.234000	0.17832	GAA	.	.		0.458	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703		C	145304497	A	C	145304497	3	2	212	1	0	0	0	0	1	0	0	0	10202	246	9	5	1468	5	NBPF10	1	145304497	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	30048034	145304497	103946124	16	30486										
SLC27A3	11000	hgsc.bcm.edu	37	chr1	153747926	153747926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggaagggaggatcagggatgTttgcgagcggctggaaccag	19	6	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:153747926T>C	ENST00000368661.3	+	1	159	c.94T>C	c.(94-96)Ttt>Ctt	p.F32L	SLC27A3_ENST00000271857.2_Missense_Mutation_p.F113L|SLC27A3_ENST00000484014.1_Splice_Site	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	32					fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ATCAGGGATGTTTGCGAGCGG	0.642																																					p.F32L		Atlas-SNP	.											.	SLC27A3	42	.	0			c.T94C						.						71	77	75					1																	153747926		2203	4300	6503	SO:0001583	missense	11000	exon1			GGGATGTTTGCGA	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"Acyl-CoA synthetase family", "Solute carriers"	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.94T>C	chr1.hg19:g.153747926T>C	ENSP00000357650:p.Phe32Leu	51.0	0.0		42.0	13.0	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	hg19	CCDS1053.1	.	.	.	.	.	.	.	.	.	.	T	8.121	0.780939	0.16120	.	.	ENSG00000143554	ENST00000271857;ENST00000368661	T;T	0.59502	0.26;0.42	2.91	0.494	0.16884	.	.	.	.	.	T	0.12390	0.0301	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22800	-1.0206	9	0.35671	T	0.21	2.2899	3.2634	0.06856	0.0:0.1433:0.2938:0.5629	.	32	Q5K4L6	S27A3_HUMAN	L	113;32	ENSP00000271857:F113L;ENSP00000357650:F32L	ENSP00000271857:F113L	F	+	1	0	SLC27A3	152014550	0.140000	0.22579	0.002000	0.10522	0.004000	0.04260	0.354000	0.20146	0.082000	0.17018	0.379000	0.24179	TTT	.	.		0.642	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330		C	153747926	T	C	153747926	3	2	212	1	0	0	0	0	1	0	0	0	14542	1725	60	2	96	2	SLC27A3	1	153747926	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	8443429	153747926	95502695	17	30487										
FAM189B	10712	hgsc.bcm.edu	37	chr1	155220590	155220590	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tcaccaatggctgacagcacCagagacccgctgtccatgga	10	14	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:155220590C>T	ENST00000361361.2	-	9	1496	c.987G>A	c.(985-987)ctG>ctA	p.L329L	FAM189B_ENST00000472550.1_5'UTR|FAM189B_ENST00000368368.3_Silent_p.L311L|FAM189B_ENST00000350210.2_Silent_p.L233L	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	329						integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						CTGACAGCACCAGAGACCCGC	0.672											OREG0013858	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L329L		Atlas-SNP	.											.	FAM189B	51	.	0			c.G987A						.						10	12	11					1																	155220590		2178	4249	6427	SO:0001819	synonymous_variant	10712	exon9			CAGCACCAGAGAC	AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 2"	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.987G>A	chr1.hg19:g.155220590C>T		63.0	0.0	1769	75.0	30.0	NM_006589	B1AVS5|Q8IXL3|Q9BR66	Silent	SNP	ENST00000361361.2	hg19	CCDS1103.1																																																																																			.	.		0.672	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589		T	155220590	C	T	155220590	2	4	212	1	0	0	0	0	0	0	0	1	5522	581	21	3		3	FAM189B	1	155220590	Silent	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	1472664	155220590	94030031	18	30488										
PKLR	5313	hgsc.bcm.edu	37	chr1	155269945	155269945	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cgggctcggagtcaatgtccAgtaggcagaggtgttccagg	16	9	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:155269945A>C	ENST00000342741.4	-	2	265	c.227T>G	c.(226-228)cTg>cGg	p.L76R	PKLR_ENST00000392414.3_Missense_Mutation_p.L45R	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	76					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)	p.L76K(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	GTCAATGTCCAGTAGGCAGAG	0.602																																					p.L76R		Atlas-SNP	.											.,1	PKLR	70	.	1	Substitution - Missense(1)	lung(1)	c.T227G						.						63	63	63					1																	155269945		2203	4300	6503	SO:0001583	missense	5313	exon2			ATGTCCAGTAGGC	BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.227T>G	chr1.hg19:g.155269945A>C	ENSP00000339933:p.Leu76Arg	85.0	0.0		156.0	36.0	NM_000298	O75758|P11973	Missense_Mutation	SNP	ENST00000342741.4	hg19	CCDS1109.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.135307	0.77662	.	.	ENSG00000143627	ENST00000423816;ENST00000392414;ENST00000342741;ENST00000271946	D;D	0.99818	-6.92;-6.92	4.17	4.17	0.49024	Pyruvate/Phosphoenolpyruvate kinase (1);	0.000000	0.64402	D	0.000003	D	0.99622	0.9862	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97510	1.0066	10	0.87932	D	0	-16.18	11.1939	0.48700	1.0:0.0:0.0:0.0	.	76;67	P30613;B1AVT1	KPYR_HUMAN;.	R	101;45;76;12	ENSP00000376214:L45R;ENSP00000339933:L76R	ENSP00000271946:L12R	L	-	2	0	PKLR	153536569	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	8.980000	0.93460	1.737000	0.51674	0.472000	0.43445	CTG	.	.		0.602	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298		C	155269945	A	C	155269945	3	2	212	1	0	0	0	0	1	0	0	0	11985	188	7	5	1537	5	PKLR	1	155269945	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	49355	155269945	93980676	19	30489										
NIT1	4817	hgsc.bcm.edu	37	chr1	161089103	161089103	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggcatttgacttcattgcacGggaccctgcagagacgctac	11	12	1	2	rs149045755		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:161089103G>C	ENST00000368009.2	+	3	354	c.278G>C	c.(277-279)cGg>cCg	p.R93P	NIT1_ENST00000368008.1_Missense_Mutation_p.R93P|PFDN2_ENST00000368010.3_5'Flank|PFDN2_ENST00000468311.1_5'Flank|DEDD_ENST00000489249.1_5'Flank|NIT1_ENST00000496861.1_3'UTR|NIT1_ENST00000392190.5_Missense_Mutation_p.R57P|NIT1_ENST00000368007.4_Missense_Mutation_p.R78P	NM_005600.2	NP_005591.1	Q86X76	NIT1_HUMAN	nitrilase 1	93	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				nitrogen compound metabolic process (GO:0006807)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	nitrilase activity (GO:0000257)			NS(1)|breast(2)|endometrium(2)|large_intestine(3)|lung(3)|prostate(1)	12	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			TTCATTGCACGGGACCCTGCA	0.532											OREG0013937	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R93P		Atlas-SNP	.											.	NIT1	41	.	0			c.G278C						.						58	58	58					1																	161089103		2203	4300	6503	SO:0001583	missense	4817	exon3			TTGCACGGGACCC	AF069984	CCDS1218.1, CCDS53401.1, CCDS53402.1, CCDS53403.1	1q21-q22	2008-05-14			ENSG00000158793	ENSG00000158793			7828	protein-coding gene	gene with protein product		604618				9671749	Standard	NM_005600		Approved		uc001fxv.2	Q86X76	OTTHUMG00000031473	ENST00000368009.2:c.278G>C	chr1.hg19:g.161089103G>C	ENSP00000356988:p.Arg93Pro	98.0	0.0	1814	105.0	22.0	NM_001185092	B1AQP3|D3DVF4|O76091	Missense_Mutation	SNP	ENST00000368009.2	hg19	CCDS1218.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.474572	0.43942	.	.	ENSG00000158793	ENST00000368009;ENST00000368007;ENST00000368008;ENST00000392190	D;D;D;D	0.87966	-2.02;-2.02;-2.32;-2.02	5.01	4.1	0.47936	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.277370	0.35615	N	0.003094	T	0.69780	0.3149	N	0.04043	-0.29	0.09310	N	1	P;P;P	0.49090	0.919;0.81;0.888	P;P;P	0.54238	0.451;0.463;0.746	T	0.67409	-0.5678	10	0.30854	T	0.27	-9.1266	11.1228	0.48300	0.0897:0.0:0.9103:0.0	.	78;93;93	Q86X76-4;B1AQP4;Q86X76	.;.;NIT1_HUMAN	P	93;78;93;57	ENSP00000356988:R93P;ENSP00000356986:R78P;ENSP00000356987:R93P;ENSP00000376028:R57P	ENSP00000356986:R78P	R	+	2	0	NIT1	159355727	0.658000	0.27402	0.733000	0.30861	0.798000	0.45092	2.762000	0.47597	1.330000	0.45394	0.655000	0.94253	CGG	.	G|1.000;A|0.000		0.532	NIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077060.1			C	161089103	G	C	161089103	3	2	212	1	0	0	0	0	1	0	0	0	10442	1116	39	4	345	4	NIT1	1	161089103	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	5819158	161089103	88161518	20	30490										
TBX19	9095	hgsc.bcm.edu	37	chr1	168282157	168282157	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gcattgctgtgtccacctggAcagcagtggcctcgcatccc	11	15	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:168282157A>G	ENST00000367821.3	+	8	1315	c.1264A>G	c.(1264-1266)Aca>Gca	p.T422A	TBX19_ENST00000465440.1_3'UTR	NM_005149.2	NP_005140.1	O60806	TBX19_HUMAN	T-box 19	422					anatomical structure morphogenesis (GO:0009653)|cell fate commitment (GO:0045165)|pituitary gland development (GO:0021983)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(11)|prostate(2)|skin(2)|urinary_tract(1)	34	all_hematologic(923;0.215)					GTCCACCTGGACAGCAGTGGC	0.632																																					p.T422A		Atlas-SNP	.											.	TBX19	68	.	0			c.A1264G						.						51	49	49					1																	168282157		2203	4300	6503	SO:0001583	missense	9095	exon8			ACCTGGACAGCAG	AJ010277	CCDS1272.1	1q23-q24	2008-02-05			ENSG00000143178	ENSG00000143178		"T-boxes"	11596	protein-coding gene	gene with protein product	"TBS 19"	604614				9888994	Standard	NM_005149		Approved	dj747L4.1, TPIT	uc001gfl.3	O60806	OTTHUMG00000034648	ENST00000367821.3:c.1264A>G	chr1.hg19:g.168282157A>G	ENSP00000356795:p.Thr422Ala	94.0	0.0		86.0	4.0	NM_005149	Q52M53	Missense_Mutation	SNP	ENST00000367821.3	hg19	CCDS1272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.91|14.91	2.675689|2.675689	0.47781|0.47781	.|.	.|.	ENSG00000143178|ENSG00000143178	ENST00000431969;ENST00000441464|ENST00000367821;ENST00000367828	.|D	.|0.94330	.|-3.4	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	.|0.555807	.|0.18129	.|N	.|0.150795	T|T	0.76948|0.76948	0.4059|0.4059	L|L	0.31371|0.31371	0.925|0.925	.|0.31993	.|N	.|0.604346	.|B;B	.|0.24043	.|0.024;0.096	.|B;B	.|0.18263	.|0.012;0.021	T|T	0.64685|0.64685	-0.6349|-0.6349	4|9	.|0.08179	.|T	.|0.78	.|.	8.2793|8.2793	0.31892|0.31892	0.9117:0.0:0.0883:0.0|0.9117:0.0:0.0883:0.0	.|.	.|422;290	.|O60806;B3KRD9	.|TBX19_HUMAN;.	G|A	291;254|422;299	.|ENSP00000356795:T422A	.|ENSP00000356795:T422A	D|T	+|+	2|1	0|0	TBX19|TBX19	166548781|166548781	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	3.802000|3.802000	0.55553|0.55553	2.099000|2.099000	0.63709|0.63709	0.460000|0.460000	0.39030|0.39030	GAC|ACA	.	.		0.632	TBX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083825.1	NM_005149		G	168282157	A	G	168282157	3	3	212	1	0	0	0	0	1	0	0	0	15669	275	10	2	1294	2	TBX19	1	168282157	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	7193054	168282157	80968464	21	30491										
METTL13	51603	hgsc.bcm.edu	37	chr1	171751168	171751168	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttgactattgggagaagttcTtccagcagcgaggaaagaaa	12	6	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:171751168T>C	ENST00000361735.3	+	1	327	c.61T>C	c.(61-63)Ttc>Ctc	p.F21L	METTL13_ENST00000362019.3_Intron|METTL13_ENST00000458517.1_Missense_Mutation_p.F20L|METTL13_ENST00000367737.5_Missense_Mutation_p.F21L	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	21							methyltransferase activity (GO:0008168)			breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						GGAGAAGTTCTTCCAGCAGCG	0.483																																					p.F21L		Atlas-SNP	.											.	METTL13	67	.	0			c.T61C						.						95	95	95					1																	171751168		2203	4300	6503	SO:0001583	missense	51603	exon1			AAGTTCTTCCAGC	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"KIAA0859"	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.61T>C	chr1.hg19:g.171751168T>C	ENSP00000354920:p.Phe21Leu	100.0	0.0		118.0	28.0	NM_015935	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Missense_Mutation	SNP	ENST00000361735.3	hg19	CCDS1299.1	.	.	.	.	.	.	.	.	.	.	T	36	5.769585	0.96914	.	.	ENSG00000010165	ENST00000458517;ENST00000367737;ENST00000361735	T;T;T	0.67345	0.8;-0.26;0.8	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.77751	0.4177	M	0.74389	2.26	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.986	D;D;P	0.80764	0.957;0.994;0.726	T	0.81113	-0.1080	10	0.87932	D	0	-1.6906	15.4857	0.75564	0.0:0.0:0.0:1.0	.	20;21;21	B4E2X3;Q8N6R0-1;Q8N6R0	.;.;MTL13_HUMAN	L	20;21;21	ENSP00000401955:F20L;ENSP00000356711:F21L;ENSP00000354920:F21L	ENSP00000354920:F21L	F	+	1	0	METTL13	170017791	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.100000	0.76989	2.324000	0.78689	0.533000	0.62120	TTC	.	.		0.483	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955		C	171751168	T	C	171751168	3	2	212	1	0	0	0	0	1	0	0	0	9506	1609	56	2	63	2	METTL13	1	171751168	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	3469011	171751168	77499453	22	30492										
EDEM3	80267	hgsc.bcm.edu	37	chr1	184681698	184681698	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	agcaaataacaggtaaagatAtttaaacatttcagccaaga	6	6	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:184681698A>G	ENST00000318130.8	-	14	1671	c.1405T>C	c.(1405-1407)Tat>Cat	p.Y469H	EDEM3_ENST00000367512.3_Missense_Mutation_p.Y426H|EDEM3_ENST00000466392.1_5'Flank	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	469					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AGGTAAAGATATTTAAACATT	0.274																																					p.Y469H		Atlas-SNP	.											.	EDEM3	63	.	0			c.T1405C						.						44	45	44					1																	184681698		2202	4284	6486	SO:0001583	missense	80267	exon14			AAAGATATTTAAA	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"chromosome 1 open reading frame 22"	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.1405T>C	chr1.hg19:g.184681698A>G	ENSP00000318147:p.Tyr469His	59.0	0.0		186.0	67.0	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Missense_Mutation	SNP	ENST00000318130.8	hg19	CCDS1363.2	.	.	.	.	.	.	.	.	.	.	A	24.9	4.579843	0.86645	.	.	ENSG00000116406	ENST00000318130;ENST00000367512	T;T	0.71579	-0.58;-0.58	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.90270	0.6957	H	0.97874	4.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93785	0.7087	10	0.87932	D	0	.	16.1814	0.81903	1.0:0.0:0.0:0.0	.	469	Q9BZQ6	EDEM3_HUMAN	H	469;426	ENSP00000318147:Y469H;ENSP00000356482:Y426H	ENSP00000318147:Y469H	Y	-	1	0	EDEM3	182948321	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.135000	0.94478	2.234000	0.73211	0.533000	0.62120	TAT	.	.		0.274	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191		G	184681698	A	G	184681698	3	3	212	1	0	0	0	0	1	0	0	0	4915	449	16	2	1421	2	EDEM3	1	184681698	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	12930530	184681698	64568923	23	30493										
SYT14	255928	hgsc.bcm.edu	37	chr1	210187041	210187041	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tattatcttgatgctgctccTttttctctatattaataaga	4	7	2	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:210187041T>G	ENST00000472886.1	+	3	139	c.125T>G	c.(124-126)cTt>cGt	p.L42R	SYT14_ENST00000367019.1_Missense_Mutation_p.L42R|SYT14_ENST00000534859.1_Missense_Mutation_p.L42R|SYT14_ENST00000537238.1_Missense_Mutation_p.L4R|SYT14_ENST00000367015.1_Missense_Mutation_p.L4R|SYT14_ENST00000271745.7_3'UTR|SYT14_ENST00000422431.1_Missense_Mutation_p.L87R|SYT14_ENST00000399639.2_Missense_Mutation_p.L42R			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	42					cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)			endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		ATGCTGCTCCTTTTTCTCTAT	0.348																																					p.L87R		Atlas-SNP	.											.	SYT14	89	.	0			c.T260G						.						154	165	161					1																	210187041		2203	4300	6503	SO:0001583	missense	255928	exon4			TGCTCCTTTTTCT	AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"Synaptotagmins"	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.125T>G	chr1.hg19:g.210187041T>G	ENSP00000418901:p.Leu42Arg	40.0	0.0		97.0	19.0	NM_001146264	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Missense_Mutation	SNP	ENST00000472886.1	hg19	CCDS31014.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.973668	0.74246	.	.	ENSG00000143469	ENST00000422431;ENST00000534859;ENST00000399639;ENST00000537238;ENST00000367019;ENST00000472886;ENST00000367015	T;T;T;T;T;T;T	0.38401	2.24;2.11;1.14;2.66;2.11;2.39;2.66	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000001	T	0.57051	0.2027	M	0.61703	1.905	0.48632	D	0.999688	D;D;D;D	0.89917	1.0;0.999;0.999;1.0	D;D;D;D	0.83275	0.972;0.956;0.996;0.988	T	0.61128	-0.7125	10	0.87932	D	0	-7.901	13.9753	0.64268	0.0:0.0:0.0:1.0	.	70;42;42;87	A1L3Y1;Q8NB59;Q8NB59-6;F5H426	.;SYT14_HUMAN;.;.	R	87;42;42;4;42;42;4	ENSP00000389039:L87R;ENSP00000442891:L42R;ENSP00000445837:L42R;ENSP00000437423:L4R;ENSP00000355986:L42R;ENSP00000418901:L42R;ENSP00000355982:L4R	ENSP00000355982:L4R	L	+	2	0	SYT14	208253664	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.249000	0.72427	1.906000	0.55180	0.377000	0.23210	CTT	.	.		0.348	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262		G	210187041	T	G	210187041	3	3	212	1	0	0	0	0	1	0	0	0	15485	1609	56	5	274	5	SYT14	1	210187041	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	25505343	210187041	39063580	24	30494										
SLC30A1	7779	hgsc.bcm.edu	37	chr1	211748979	211748980	+	Frame_Shift_Ins	INS	-	-	CCTAC													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gaactacacttgatttagagINScctacactagcaaattcagg							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:211748979_211748980insCCTAC	ENST00000367001.4	-	2	1403_1404	c.1274_1275insGTAGG	c.(1273-1275)ggcfs	p.-425fs		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1						cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		TTGATTTAGAGCCTACACTAGC	0.446																																					p.G425_S426delinsGX		Atlas-INDEL	.											.	SLC30A1	27	.	0			c.1275_1276insGTAGG						.																																			SO:0001589	frameshift_variant	7779	exon2			.	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.1270_1274dupGTAGG	chr1.hg19:g.211748980_211748984dupCCTAC	ENSP00000355968:p.Gly425fs	71.0	0.0		84.0	19.0	NM_021194	Q0VAK9|Q9BZF6	Frame_Shift_Ins	INS	ENST00000367001.4	hg19	CCDS1499.1																																																																																			.	.		0.446	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			CCTAC	211748980	-	CCTAC	211748979	7	5	212	1	0	1	1	0	0	0	0	0	14568	958	34	0	252	0	SLC30A1	1	211748979	Frame_Shift_Ins	INS	-	TCGA-DD-AAE7-01A-11D-A40R-10	1561938	211748979	37501642	25	30495										
CENPF	1063	hgsc.bcm.edu	37	chr1	214811265	214811265	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tctgagcaaaaggccagagaAgtctgccacctggaggcaga	13	10	2	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:214811265A>C	ENST00000366955.3	+	11	1671	c.1503A>C	c.(1501-1503)gaA>gaC	p.E501D		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGGCCAGAGAAGTCTGCCACC	0.373																																					p.E501D	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A1503C						.						81	84	83					1																	214811265		2203	4300	6503	SO:0001583	missense	1063	exon11			CAGAGAAGTCTGC	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.1503A>C	chr1.hg19:g.214811265A>C	ENSP00000355922:p.Glu501Asp	309.0	0.0		575.0	27.0	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	17.18	3.324434	0.60634	.	.	ENSG00000117724	ENST00000366955	T	0.03745	3.82	5.9	2.41	0.29592	.	0.000000	0.39274	N	0.001404	T	0.02929	0.0087	.	.	.	0.31312	N	0.687088	P	0.44690	0.841	B	0.37888	0.26	T	0.38520	-0.9657	9	0.37606	T	0.19	.	5.8719	0.18809	0.6027:0.1272:0.2701:0.0	.	501	P49454	CENPF_HUMAN	D	501	ENSP00000355922:E501D	ENSP00000355922:E501D	E	+	3	2	CENPF	212877888	0.954000	0.32549	0.989000	0.46669	0.998000	0.95712	0.003000	0.13083	0.168000	0.19655	0.528000	0.53228	GAA	.	.		0.373	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		C	214811265	A	C	214811265	3	2	212	1	0	0	0	0	1	0	0	0	3233	69	3	5	1541	5	CENPF	1	214811265	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	3062286	214811265	34439356	26	30496										
EPRS	2058	hgsc.bcm.edu	37	chr1	220156627	220156627	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttttcaacaccaagtttcttGatctcagcatcaaaaaagtc	4	10	4	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:220156627G>T	ENST00000366923.3	-	22	3473	c.3204C>A	c.(3202-3204)atC>atA	p.I1068I		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1068	Proline--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	CAAGTTTCTTGATCTCAGCAT	0.423																																					p.I1068I		Atlas-SNP	.											.	EPRS	140	.	0			c.C3204A						.						85	88	87					1																	220156627		2203	4300	6503	SO:0001819	synonymous_variant	2058	exon22			TTTCTTGATCTCA	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3204C>A	chr1.hg19:g.220156627G>T		188.0	0.0		294.0	97.0	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Silent	SNP	ENST00000366923.3	hg19	CCDS31027.1																																																																																			.	.		0.423	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		T	220156627	G	T	220156627	2	4	212	1	0	0	0	0	0	0	0	1	5193	1280	45	3		3	EPRS	1	220156627	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	5345362	220156627	29093994	27	30497										
RYR2	6262	hgsc.bcm.edu	37	chr1	237948162	237948162	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cggacatctttggcctggatCtgaagagagaaggaggacag	15	7	2	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:237948162C>A	ENST00000366574.2	+	90	13467	c.13150C>A	c.(13150-13152)Ctg>Atg	p.L4384M	RYR2_ENST00000360064.6_Missense_Mutation_p.L4390M|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Missense_Mutation_p.L4368M	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4384					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGGCCTGGATCTGAAGAGAGA	0.537																																					p.L4384M		Atlas-SNP	.											RYR2,right_upper_lobe,carcinoma,0,1	RYR2	1273	.	0			c.C13150A						.						41	40	41					1																	237948162		1935	4130	6065	SO:0001583	missense	6262	exon90			CTGGATCTGAAGA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.13150C>A	chr1.hg19:g.237948162C>A	ENSP00000355533:p.Leu4384Met	51.0	0.0		92.0	28.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581562	0.28180	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.93547	-3.24;-3.24;-3.24	5.56	4.65	0.58169	Ryanodine Receptor TM 4-6 (1);	0.264471	0.24357	N	0.039229	D	0.92678	0.7673	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.984;0.999	D;D	0.87578	0.914;0.998	D	0.89923	0.4060	10	0.30078	T	0.28	-9.1367	6.783	0.23657	0.0:0.7022:0.0:0.2978	.	1358;4384	B4DGV4;Q92736	.;RYR2_HUMAN	M	4384;4390;4368;1358	ENSP00000355533:L4384M;ENSP00000353174:L4390M;ENSP00000443798:L4368M	ENSP00000353174:L4390M	L	+	1	2	RYR2	236014785	0.998000	0.40836	1.000000	0.80357	0.720000	0.41350	1.822000	0.39052	1.352000	0.45808	-0.140000	0.14226	CTG	.	.		0.537	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237948162	C	A	237948162	3	1	212	1	0	0	0	0	1	0	0	0	13784	912	32	3	13508	3	RYR2	1	237948162	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	17791535	237948162	11302459	28	30498										
AKT3	10000	hgsc.bcm.edu	37	chr1	243809237	243809237	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gaggcatccatctcttcctcTcctatattatcaatttgtga	5	11	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr1:243809237T>A	ENST00000366539.1	-	5	587	c.387A>T	c.(385-387)ggA>ggT	p.G129G	AKT3_ENST00000366540.1_Silent_p.G129G|AKT3_ENST00000263826.5_Silent_p.G129G|AKT3_ENST00000336199.5_Silent_p.G129G			Q9Y243	AKT3_HUMAN	v-akt murine thymoma viral oncogene homolog 3	129					mitochondrial genome maintenance (GO:0000002)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|skin(3)|stomach(1)	26	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			TCTCTTCCTCTCCTATATTAT	0.388																																					p.G129G		Atlas-SNP	.											.	AKT3	177	.	0			c.A387T						.						188	180	183					1																	243809237		2203	4300	6503	SO:0001819	synonymous_variant	10000	exon5			TTCCTCTCCTATA	AF124141	CCDS31076.1, CCDS31077.1	1q44	2013-07-09	2013-07-09		ENSG00000117020	ENSG00000117020	2.7.11.1	"Pleckstrin homology (PH) domain containing"	393	protein-coding gene	gene with protein product	"protein kinase B, gamma"	611223				10092583, 10208883	Standard	NM_005465		Approved	PKBG, RAC-gamma, PRKBG	uc001iab.2	Q9Y243	OTTHUMG00000039994	ENST00000366539.1:c.387A>T	chr1.hg19:g.243809237T>A		23.0	0.0		36.0	13.0	NM_001206729	Q0VAA6|Q5VTI1|Q5VTI2|Q96QV3|Q9UFP5	Silent	SNP	ENST00000366539.1	hg19	CCDS31077.1																																																																																			.	.		0.388	AKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096479.1	NM_181690		A	243809237	T	A	243809237	2	1	212	1	0	0	0	0	0	0	0	1	481	1538	54	4		4	AKT3	1	243809237	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	5861075	243809237	5441384	29	30499										
SH3YL1	26751	hgsc.bcm.edu	37	chr2	231165	231165	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tatctccaaataaaatgtcaTaagctcggatatcttgacaa	5	8	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:231165T>C	ENST00000405430.1	-	9	936	c.560A>G	c.(559-561)tAt>tGt	p.Y187C	SH3YL1_ENST00000468321.1_5'UTR|SH3YL1_ENST00000403712.2_Missense_Mutation_p.Y187C|SH3YL1_ENST00000415006.2_Missense_Mutation_p.Y91C|SH3YL1_ENST00000403658.1_Missense_Mutation_p.Y91C|SH3YL1_ENST00000403657.1_Missense_Mutation_p.Y91C|SH3YL1_ENST00000356150.5_Missense_Mutation_p.Y187C			Q96HL8	SH3Y1_HUMAN	SH3 and SYLF domain containing 1	187					phosphatidylinositol biosynthetic process (GO:0006661)|regulation of ruffle assembly (GO:1900027)	ruffle membrane (GO:0032587)	phosphatase binding (GO:0019902)|phosphatidylinositol binding (GO:0035091)			large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)		TAAAATGTCATAAGCTCGGAT	0.323																																					p.Y187C		Atlas-SNP	.											.	SH3YL1	49	.	0			c.A560G						.						53	47	49					2																	231165		1826	4068	5894	SO:0001583	missense	26751	exon7			ATGTCATAAGCTC		CCDS42646.1, CCDS42646.2, CCDS54332.1, CCDS62841.1	2p25.3	2013-10-18	2013-10-18		ENSG00000035115	ENSG00000035115			29546	protein-coding gene	gene with protein product			"SH3 domain containing, Ysc84-like 1 (S. cerevisiae)"			21624956	Standard	NM_001282687		Approved	Ray, DKFZP586F1318	uc002qvx.3	Q96HL8	OTTHUMG00000151359	ENST00000405430.1:c.560A>G	chr2.hg19:g.231165T>C	ENSP00000384269:p.Tyr187Cys	43.0	0.0		95.0	25.0	NM_001159597	A8K8E7|B7WNJ4|B7WPL6|Q8NEL2|Q9H5X4|Q9Y3V5	Missense_Mutation	SNP	ENST00000405430.1	hg19		.	.	.	.	.	.	.	.	.	.	T	7.923	0.738948	0.15642	.	.	ENSG00000035115	ENST00000415006;ENST00000403712;ENST00000403657;ENST00000405430;ENST00000356150;ENST00000403658;ENST00000451005;ENST00000431160	T;T;T;T;T;T;T	0.23147	2.15;2.14;2.15;1.97;1.97;2.15;1.92	5.0	1.26	0.21427	Ysc84 actin-binding domain (1);	0.627056	0.15721	N	0.247899	T	0.28699	0.0711	L	0.36672	1.1	0.09310	N	1	D;P;D;D	0.61697	0.99;0.929;0.972;0.971	P;P;P;P	0.58780	0.8;0.599;0.845;0.695	T	0.07966	-1.0745	10	0.62326	D	0.03	-37.892	4.0505	0.09793	0.0:0.2411:0.1841:0.5749	.	91;187;187;91	Q96HL8-4;Q96HL8-2;Q96HL8;Q96HL8-3	.;.;SH3Y1_HUMAN;.	C	91;187;91;187;187;91;119;143	ENSP00000404143:Y91C;ENSP00000384276:Y187C;ENSP00000385668:Y91C;ENSP00000384269:Y187C;ENSP00000348471:Y187C;ENSP00000383928:Y91C;ENSP00000416312:Y119C	ENSP00000348471:Y187C	Y	-	2	0	SH3YL1	221165	0.920000	0.31207	0.134000	0.22075	0.040000	0.13550	0.886000	0.28241	0.250000	0.21479	-0.429000	0.05907	TAT	.	.		0.323	SH3YL1-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322352.1	NM_015677		C	231165	T	C	231165	3	2	212	1	0	0	0	0	1	0	0	0	14278	1406	49	2	484	2	SH3YL1	2	231165	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10		231165	242968208	30	30500										
PPM1G	5496	hgsc.bcm.edu	37	chr2	27606940	27606940	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cctcctcactgctgtagccaTcctcttcctcgctgcattcc	5	19	2	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:27606940T>A	ENST00000344034.4	-	6	1109	c.845A>T	c.(844-846)gAt>gTt	p.D282V	PPM1G_ENST00000350803.4_Missense_Mutation_p.D282V	NM_177983.2	NP_817092.1	O15355	PPM1G_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1G	282	Asp/Glu-rich (acidic).				cell cycle arrest (GO:0007050)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					GCTGTAGCCATCCTCTTCCTC	0.547																																					p.D282V		Atlas-SNP	.											.	PPM1G	42	.	0			c.A845T						.						165	118	134					2																	27606940		2203	4300	6503	SO:0001583	missense	5496	exon6			TAGCCATCCTCTT	Y13936	CCDS1752.1	2p23.3	2012-04-17	2010-03-05		ENSG00000115241	ENSG00000115241	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9278	protein-coding gene	gene with protein product	"PP2C, gamma", "protein phosphatase 2C, gamma isoform"	605119	"protein phosphatase 1G (formerly 2C), magnesium-dependent, gamma isoform"			9276438	Standard	NM_177983		Approved	PP2CG, PP2Cgamma	uc002rkl.4	O15355	OTTHUMG00000097788	ENST00000344034.4:c.845A>T	chr2.hg19:g.27606940T>A	ENSP00000342778:p.Asp282Val	40.0	0.0		56.0	5.0	NM_177983		Missense_Mutation	SNP	ENST00000344034.4	hg19	CCDS1752.1	.	.	.	.	.	.	.	.	.	.	T	17.05	3.288849	0.59976	.	.	ENSG00000115241	ENST00000344034;ENST00000350803;ENST00000544412;ENST00000395543	T;T	0.50001	0.76;0.76	5.41	5.41	0.78517	Protein phosphatase 2C-like (3);	1.365020	0.04210	N	0.331601	T	0.68879	0.3049	L	0.56769	1.78	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.85130	0.983;0.997	T	0.45833	-0.9234	10	0.56958	D	0.05	-13.8511	11.8222	0.52245	0.0:0.0:0.0:1.0	.	83;282	Q59GB2;O15355	.;PPM1G_HUMAN	V	282;282;265;83	ENSP00000342778:D282V;ENSP00000264714:D282V	ENSP00000342778:D282V	D	-	2	0	PPM1G	27460444	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.361000	0.59461	2.037000	0.60232	0.528000	0.53228	GAT	.	.		0.547	PPM1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215032.1	NM_002707		A	27606940	T	A	27606940	3	1	212	1	0	0	0	0	1	0	0	0	12352	1435	50	4	815	4	PPM1G	2	27606940	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	27375775	27606940	215592433	31	30501										
IFT172	26160	hgsc.bcm.edu	37	chr2	27668656	27668656	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tggcacctcaaagggaatgtCtgtatcctgaaaatcagagt	10	8	3	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:27668656C>A	ENST00000260570.3	-	45	4973	c.4870G>T	c.(4870-4872)Gac>Tac	p.D1624Y	KRTCAP3_ENST00000543753.1_Intron	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	1624					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					AAGGGAATGTCTGTATCCTGA	0.547																																					p.D1624Y		Atlas-SNP	.											.	IFT172	119	.	0			c.G4870T						.						135	130	131					2																	27668656		2203	4300	6503	SO:0001583	missense	26160	exon45			GAATGTCTGTATC	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.4870G>T	chr2.hg19:g.27668656C>A	ENSP00000260570:p.Asp1624Tyr	96.0	0.0		109.0	31.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	hg19	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.004236	0.74932	.	.	ENSG00000138002	ENST00000260570	T	0.65364	-0.15	5.42	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.81418	0.4818	M	0.88310	2.945	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84921	0.0854	10	0.87932	D	0	-21.5043	13.3218	0.60436	0.0:0.8413:0.1587:0.0	.	1624	Q9UG01	IF172_HUMAN	Y	1624	ENSP00000260570:D1624Y	ENSP00000260570:D1624Y	D	-	1	0	IFT172	27522160	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.490000	0.81461	1.283000	0.44513	0.561000	0.74099	GAC	.	.		0.547	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		A	27668656	C	A	27668656	3	1	212	1	0	0	0	0	1	0	0	0	7566	913	32	3	395	3	IFT172	2	27668656	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	61716	27668656	215530717	32	30502										
FAM179A	165186	hgsc.bcm.edu	37	chr2	29237345	29237345	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tttttctcagtctgctcccaCgctgacagccttctcctttg	6	15	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:29237345C>T	ENST00000379558.4	+	8	1313	c.962C>T	c.(961-963)aCg>aTg	p.T321M	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Missense_Mutation_p.T321M	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	321										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TCTGCTCCCACGCTGACAGCC	0.592																																					p.T321M		Atlas-SNP	.											.	FAM179A	106	.	0			c.C962T						.						30	33	32					2																	29237345		2119	4249	6368	SO:0001583	missense	165186	exon8			CTCCCACGCTGAC	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.962C>T	chr2.hg19:g.29237345C>T	ENSP00000368876:p.Thr321Met	70.0	0.0		62.0	30.0	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	hg19	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	c	1.347	-0.592524	0.03799	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.10573	3.02;2.86	4.6	-4.84	0.03151	.	.	.	.	.	T	0.04363	0.0120	N	0.14661	0.345	0.09310	N	1	B;B	0.33694	0.421;0.017	B;B	0.24006	0.05;0.004	T	0.34477	-0.9827	9	0.33940	T	0.23	.	6.8807	0.24170	0.1318:0.2657:0.0:0.6026	.	321;321	F8W8E4;Q6ZUX3	.;F179A_HUMAN	M	321	ENSP00000368876:T321M;ENSP00000384699:T321M	ENSP00000368876:T321M	T	+	2	0	FAM179A	29090849	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.229000	0.02945	-1.293000	0.02362	-1.270000	0.01421	ACG	.	.		0.592	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		T	29237345	C	T	29237345	3	4	212	1	0	0	0	0	1	0	0	0	5510	536	19	1	988	1	FAM179A	2	29237345	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	1568689	29237345	213962028	33	30503										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54870184	54870184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gtcttacgatgaagccagaaAtctgcacagtaaatggttga	10	7	2	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:54870184A>G	ENST00000356805.4	+	19	4204	c.3923A>G	c.(3922-3924)aAt>aGt	p.N1308S	SPTBN1_ENST00000333896.5_Missense_Mutation_p.N1295S	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1308					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GAAGCCAGAAATCTGCACAGT	0.413																																					p.N1308S		Atlas-SNP	.											.	SPTBN1	378	.	0			c.A3923G						.						111	109	110					2																	54870184		2203	4300	6503	SO:0001583	missense	6711	exon19			CCAGAAATCTGCA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3923A>G	chr2.hg19:g.54870184A>G	ENSP00000349259:p.Asn1308Ser	118.0	0.0		157.0	29.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.447166	0.84101	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.32272	1.46;1.46	5.73	5.73	0.89815	.	0.044685	0.85682	D	0.000000	T	0.52435	0.1734	M	0.89214	3.015	0.58432	D	0.999995	B;B	0.33379	0.309;0.41	B;P	0.44422	0.202;0.449	T	0.55309	-0.8161	10	0.41790	T	0.15	.	16.0193	0.80468	1.0:0.0:0.0:0.0	.	1295;1308	Q01082-3;Q01082	.;SPTB2_HUMAN	S	1308;1295	ENSP00000349259:N1308S;ENSP00000334156:N1295S	ENSP00000334156:N1295S	N	+	2	0	SPTBN1	54723688	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.281000	0.95811	2.190000	0.69967	0.533000	0.62120	AAT	.	.		0.413	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			G	54870184	A	G	54870184	3	3	212	1	0	0	0	0	1	0	0	0	15134	101	4	2	4106	2	SPTBN1	2	54870184	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	25632839	54870184	188329189	34	30504										
UGP2	7360	hgsc.bcm.edu	37	chr2	64118290	64118290	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttgcaaatcatggtgacagaAttgatatcccacctggagca	9	9	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:64118290A>C	ENST00000337130.5	+	10	1932	c.1456A>C	c.(1456-1458)Att>Ctt	p.I486L	UGP2_ENST00000394417.2_Missense_Mutation_p.I475L|UGP2_ENST00000445915.2_Missense_Mutation_p.I495L|UGP2_ENST00000467648.2_Missense_Mutation_p.I475L	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	486	Oligomerization.				carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)			endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						TGGTGACAGAATTGATATCCC	0.378																																					p.I486L		Atlas-SNP	.											.	UGP2	38	.	0			c.A1456C						.						140	124	130					2																	64118290		2203	4300	6503	SO:0001583	missense	7360	exon10			GACAGAATTGATA		CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"UDP-glucose pyrophosphorylase 1"	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.1456A>C	chr2.hg19:g.64118290A>C	ENSP00000338703:p.Ile486Leu	69.0	0.0		108.0	33.0	NM_006759	Q07131|Q0P6K2|Q86Y81|Q9BU15	Missense_Mutation	SNP	ENST00000337130.5	hg19	CCDS1875.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.720084	0.89205	.	.	ENSG00000169764	ENST00000394417;ENST00000467648;ENST00000337130;ENST00000445915	T;T;T;T	0.47177	0.87;0.87;0.86;0.85	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.58366	0.2117	L	0.47190	1.495	0.80722	D	1	P;P	0.48589	0.912;0.912	P;P	0.60682	0.734;0.878	T	0.52373	-0.8584	10	0.23891	T	0.37	-16.8786	15.519	0.75851	1.0:0.0:0.0:0.0	.	495;486	E7EUC7;Q16851	.;UGPA_HUMAN	L	475;475;486;495	ENSP00000377939:I475L;ENSP00000420793:I475L;ENSP00000338703:I486L;ENSP00000411803:I495L	ENSP00000338703:I486L	I	+	1	0	UGP2	63971794	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.076000	0.62316	0.455000	0.32223	ATT	.	.		0.378	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759		C	64118290	A	C	64118290	3	2	212	1	0	0	0	0	1	0	0	0	16958	101	4	5	1494	5	UGP2	2	64118290	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	9248106	64118290	179081083	35	30505										
CEP68	23177	hgsc.bcm.edu	37	chr2	65299207	65299207	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgatagccgtgtgccagctgAccctgtcctgcaggactccg	12	14	0	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:65299207A>T	ENST00000377990.2	+	3	1180	c.977A>T	c.(976-978)gAc>gTc	p.D326V	RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000546106.1_Missense_Mutation_p.D326V|CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000260569.4_Missense_Mutation_p.D326V	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	326					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						GTGCCAGCTGACCCTGTCCTG	0.542																																					p.D326V		Atlas-SNP	.											.	CEP68	69	.	0			c.A977T						.						91	100	97					2																	65299207		2203	4300	6503	SO:0001583	missense	23177	exon3			CAGCTGACCCTGT	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"KIAA0582"	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.977A>T	chr2.hg19:g.65299207A>T	ENSP00000367229:p.Asp326Val	28.0	0.0		38.0	19.0	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	hg19	CCDS1880.2	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813394	0.50527	.	.	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.18810	2.19;2.19;2.2	5.32	5.32	0.75619	.	0.376195	0.28971	N	0.013544	T	0.45115	0.1326	M	0.66939	2.045	0.80722	D	1	P;P;P;D;P	0.76494	0.933;0.933;0.911;0.999;0.845	P;P;P;D;P	0.72075	0.629;0.629;0.593;0.976;0.535	T	0.42515	-0.9447	10	0.66056	D	0.02	-8.4248	15.2809	0.73784	1.0:0.0:0.0:0.0	.	314;326;326;326;326	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	V	326;326;326;314	ENSP00000367229:D326V;ENSP00000438306:D326V;ENSP00000260569:D326V	ENSP00000260569:D326V	D	+	2	0	CEP68	65152711	1.000000	0.71417	0.910000	0.35882	0.264000	0.26372	6.695000	0.74593	2.016000	0.59253	0.397000	0.26171	GAC	.	.		0.542	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		T	65299207	A	T	65299207	3	4	212	1	0	0	0	0	1	0	0	0	3260	275	10	4	983	4	CEP68	2	65299207	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	1180917	65299207	177900166	36	30506										
LOXL3	84695	hgsc.bcm.edu	37	chr2	74761507	74761507	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccctcagccaccttggtgccAtttggggtgaggatatcata	11	11	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:74761507A>G	ENST00000264094.3	-	11	1946	c.1875T>C	c.(1873-1875)aaT>aaC	p.N625N	LOXL3_ENST00000409249.1_Intron|LOXL3_ENST00000409549.1_Silent_p.N569N|LOXL3_ENST00000393937.2_Silent_p.N480N|LOXL3_ENST00000409986.1_Silent_p.N480N	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	625	Lysyl-oxidase like.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						CCTTGGTGCCATTTGGGGTGA	0.512																																					p.N625N		Atlas-SNP	.											.	LOXL3	73	.	0			c.T1875C						.						201	193	195					2																	74761507		2203	4300	6503	SO:0001819	synonymous_variant	84695	exon11			GGTGCCATTTGGG	AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.1875T>C	chr2.hg19:g.74761507A>G		68.0	0.0		111.0	34.0	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Silent	SNP	ENST00000264094.3	hg19	CCDS1953.1																																																																																			.	.		0.512	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		G	74761507	A	G	74761507	2	3	212	1	0	0	0	0	0	0	0	1	8910	214	8	2		2	LOXL3	2	74761507	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	9462300	74761507	168437866	37	30507										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84896476	84896476	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	acaccaaacggctggatcccTgggaacgaatcatacctact	8	13	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:84896476T>A	ENST00000237449.6	+	37	6156	c.6148T>A	c.(6148-6150)Tgg>Agg	p.W2050R	DNAH6_ENST00000389394.3_Missense_Mutation_p.W2050R|DNAH6_ENST00000398278.2_Missense_Mutation_p.W2050R|DNAH6_ENST00000602588.1_Missense_Mutation_p.W71R			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2050					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GCTGGATCCCTGGGAACGAAT	0.418																																					p.W2050R		Atlas-SNP	.											.	DNAH6	194	.	0			c.T6148A						.						148	122	130					2																	84896476		692	1591	2283	SO:0001583	missense	1768	exon38			GATCCCTGGGAAC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.6148T>A	chr2.hg19:g.84896476T>A	ENSP00000237449:p.Trp2050Arg	97.0	0.0		133.0	34.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.223136	0.79464	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.40225	1.05;1.04;1.05	5.25	5.25	0.73442	.	.	.	.	.	T	0.71204	0.3312	M	0.91300	3.195	0.54753	D	0.999989	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.78833	-0.2048	9	0.87932	D	0	.	14.4248	0.67207	0.0:0.0:0.0:1.0	.	2050;2050	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	R	2050	ENSP00000374045:W2050R;ENSP00000381326:W2050R;ENSP00000237449:W2050R	ENSP00000237449:W2050R	W	+	1	0	DNAH6	84749987	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.181000	0.71988	2.097000	0.63578	0.523000	0.50628	TGG	.	.		0.418	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84896476	T	A	84896476	3	1	212	1	0	0	0	0	1	0	0	0	4607	1580	55	4	6294	4	DNAH6	2	84896476	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	10134969	84896476	158302897	38	30508										
TMEM127	55654	hgsc.bcm.edu	37	chr2	96930988	96930988	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggctcggcgagggcagtgcaCagcgccgtgatagacagggc	18	11	0	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:96930988C>T	ENST00000258439.3	-	2	388	c.132G>A	c.(130-132)ctG>ctA	p.L44L	TMEM127_ENST00000432959.1_Silent_p.L44L|CIAO1_ENST00000488633.1_5'Flank	NM_001193304.2|NM_017849.3	NP_001180233.1|NP_060319.1	O75204	TM127_HUMAN	transmembrane protein 127	44					negative regulation of cell proliferation (GO:0008285)|negative regulation of TOR signaling (GO:0032007)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	5						GGGCAGTGCACAGCGCCGTGA	0.731																																					p.L44L		Atlas-SNP	.											.	TMEM127	13	.	0			c.G132A						.						11	11	11					2																	96930988		2184	4270	6454	SO:0001819	synonymous_variant	55654	exon2			AGTGCACAGCGCC	AK000514	CCDS2018.1	2q11.2	2014-09-17			ENSG00000135956	ENSG00000135956			26038	protein-coding gene	gene with protein product		613403				10493829	Standard	NM_017849		Approved	FLJ20507, FLJ22257	uc002svr.3	O75204	OTTHUMG00000130454	ENST00000258439.3:c.132G>A	chr2.hg19:g.96930988C>T		958.0	1.0		953.0	275.0	NM_001193304	D3DXH0	Silent	SNP	ENST00000258439.3	hg19	CCDS2018.1																																																																																			.	.		0.731	TMEM127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252845.3	NM_017849		T	96930988	C	T	96930988	2	4	212	1	0	0	0	0	0	0	0	1	16055	465	17	3		3	TMEM127	2	96930988	Silent	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	12034512	96930988	146268385	39	30509										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109383255	109383255	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	actaaaagtgtgtgctaatcAttggataacgactacgatga	9	6	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:109383255A>G	ENST00000283195.6	+	20	6386	c.6260A>G	c.(6259-6261)cAt>cGt	p.H2087R		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2087	RanBD1 2. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TGTGCTAATCATTGGATAACG	0.428																																					p.H2087R		Atlas-SNP	.											.	RANBP2	488	.	0			c.A6260G						.						228	239	235					2																	109383255		2203	4298	6501	SO:0001583	missense	5903	exon20			CTAATCATTGGAT	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.6260A>G	chr2.hg19:g.109383255A>G	ENSP00000283195:p.His2087Arg	34.0	0.0		53.0	12.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.403010	0.62288	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.47869	0.83	5.65	5.65	0.86999	Pleckstrin homology-type (1);Ran binding protein 1 (3);	.	.	.	.	T	0.72510	0.3469	M	0.85299	2.745	0.47308	D	0.999386	D	0.89917	1.0	D	0.97110	1.0	T	0.77832	-0.2441	9	0.87932	D	0	-26.0092	15.8694	0.79101	1.0:0.0:0.0:0.0	.	2087	P49792	RBP2_HUMAN	R	1111;2087	ENSP00000283195:H2087R	ENSP00000283195:H2087R	H	+	2	0	RANBP2	108749687	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	9.339000	0.96797	2.143000	0.66587	0.455000	0.32223	CAT	.	.		0.428	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109383255	A	G	109383255	3	3	212	1	0	0	0	0	1	0	0	0	13043	217	8	2	6338	2	RANBP2	2	109383255	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	12452267	109383255	133816118	40	30510										
ORC4L	5000	hgsc.bcm.edu	37	chr2	148715877	148715877	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgatacttacaaaaactttaTctccaactacattttccaga	2	10	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:148715877T>C	ENST00000392857.5	-	6	484	c.377A>G	c.(376-378)gAt>gGt	p.D126G	ORC4_ENST00000536575.1_Missense_Mutation_p.D42G|ORC4_ENST00000392858.1_Missense_Mutation_p.D126G|ORC4_ENST00000264169.2_Missense_Mutation_p.D126G|ORC4_ENST00000540442.1_Missense_Mutation_p.D52G|ORC4_ENST00000542387.1_5'UTR|ORC4_ENST00000535373.1_Missense_Mutation_p.D126G	NM_001190879.2|NM_001190882.2|NM_002552.4|NM_181741.3	NP_001177808.1|NP_001177811.1|NP_002543.2|NP_859525.1	O43929	ORC4_HUMAN	origin recognition complex, subunit 4	126					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	14						AAAAACTTTATCTCCAACTAC	0.299																																					p.D126G		Atlas-SNP	.											.	ORC4	40	.	0			c.A377G						.						63	64	64					2																	148715877		2202	4297	6499	SO:0001583	missense	5000	exon6			ACTTTATCTCCAA	AF022108	CCDS2187.1, CCDS54404.1, CCDS54405.1	2q22-q23	2010-10-12	2010-10-12	2010-10-12	ENSG00000115947	ENSG00000115947		"ATPases / AAA-type"	8490	protein-coding gene	gene with protein product		603056	"origin recognition complex, subunit 4 (yeast homolog)-like", "origin recognition complex, subunit 4-like (yeast)", "origin recognition complex, subunit 4-like (S. cerevisiae)", "origin recognition complex, subunit 4 homolog (S. cerevisiae)"	ORC4L		9353276, 9691185	Standard	NM_181742		Approved	HsORC4, Orc4p	uc002twk.3	O43929	OTTHUMG00000131849	ENST00000392857.5:c.377A>G	chr2.hg19:g.148715877T>C	ENSP00000376597:p.Asp126Gly	63.0	0.0		127.0	48.0	NM_002552	B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	hg19	CCDS2187.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.252658	0.59212	.	.	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000540442;ENST00000536575;ENST00000392857;ENST00000416719;ENST00000457954;ENST00000440042	T;T;T;D;D;T;T;T;T	0.92858	1.35;1.35;1.35;-3.12;-3.12;1.35;0.5;1.16;1.15	5.52	5.52	0.82312	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.045054	0.85682	D	0.000000	D	0.94311	0.8172	L	0.55213	1.73	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.73708	0.981;0.981;0.981	D	0.92970	0.6397	10	0.27082	T	0.32	-25.7992	15.2826	0.73797	0.0:0.0:0.0:1.0	.	126;126;126	B7Z2M4;A8K7H4;O43929	.;.;ORC4_HUMAN	G	126;126;126;52;42;126;126;126;126	ENSP00000264169:D126G;ENSP00000441953:D126G;ENSP00000376598:D126G;ENSP00000438326:D52G;ENSP00000441502:D42G;ENSP00000376597:D126G;ENSP00000413939:D126G;ENSP00000391484:D126G;ENSP00000403105:D126G	ENSP00000264169:D126G	D	-	2	0	ORC4	148432347	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.576000	0.82467	2.082000	0.62665	0.477000	0.44152	GAT	.	.		0.299	ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3	NM_181742		C	148715877	T	C	148715877	3	2	212	1	0	0	0	0	1	0	0	0	11273	1435	50	2	969	2	ORC4L	2	148715877	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	39332622	148715877	94483496	41	30511										
EPC2	26122	hgsc.bcm.edu	37	chr2	149528862	149528862	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	caggacagtgatagtgaagaAtgtacctcaagaaaaccagg	11	7	1	4			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:149528862A>T	ENST00000258484.6	+	10	1660	c.1626A>T	c.(1624-1626)gaA>gaT	p.E542D		NM_015630.3	NP_056445.3	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2 (Drosophila)	542					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0516)		ATAGTGAAGAATGTACCTCAA	0.393																																					p.E542D		Atlas-SNP	.											.	EPC2	57	.	0			c.A1626T						.						130	125	127					2																	149528862		1890	4100	5990	SO:0001583	missense	26122	exon10			TGAAGAATGTACC	AF286904	CCDS46422.1	2q23	2008-02-05			ENSG00000135999	ENSG00000135999			24543	protein-coding gene	gene with protein product		611000					Standard	NM_015630		Approved	DKFZP566F2124	uc010zbt.2	Q52LR7	OTTHUMG00000153739	ENST00000258484.6:c.1626A>T	chr2.hg19:g.149528862A>T	ENSP00000258484:p.Glu542Asp	156.0	0.0		241.0	52.0	NM_015630	B3KWT7|D3DP89|Q7L9J1|Q96RR7|Q9NUT8|Q9NVR1|Q9UFM9	Missense_Mutation	SNP	ENST00000258484.6	hg19	CCDS46422.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.370631	0.42003	.	.	ENSG00000135999	ENST00000258484	T	0.17370	2.28	5.36	2.81	0.32909	.	0.265507	0.39687	N	0.001298	T	0.11153	0.0272	L	0.27053	0.805	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.09207	-1.0685	10	0.45353	T	0.12	-4.4998	8.114	0.30930	0.7943:0.1347:0.071:0.0	.	542	Q52LR7	EPC2_HUMAN	D	542	ENSP00000258484:E542D	ENSP00000258484:E542D	E	+	3	2	EPC2	149245332	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.935000	0.40173	0.959000	0.37980	-0.400000	0.06385	GAA	.	.		0.393	EPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332278.1	NM_015630		T	149528862	A	T	149528862	3	4	212	1	0	0	0	0	1	0	0	0	5163	98	4	4	1664	4	EPC2	2	149528862	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	812985	149528862	93670511	42	30512										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167136943	167136943	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tagccataaataatgtgtttAaaactatgcaaatggtaatt	6	4	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:167136943A>C	ENST00000409435.1	-	13	2266	c.2267T>G	c.(2266-2268)tTa>tGa	p.L756*	SCN9A_ENST00000375387.4_Nonsense_Mutation_p.L757*|SCN9A_ENST00000303354.6_Nonsense_Mutation_p.L757*|SCN9A_ENST00000409672.1_Nonsense_Mutation_p.L745*|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	756					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TAATGTGTTTAAAACTATGCA	0.313																																					p.L745X		Atlas-SNP	.											.	SCN9A	296	.	0			c.T2234G						.						60	58	59					2																	167136943		1830	4087	5917	SO:0001587	stop_gained	6335	exon14			GTGTTTAAAACTA	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.2267T>G	chr2.hg19:g.167136943A>C	ENSP00000386330:p.Leu756*	73.0	0.0		123.0	32.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Nonsense_Mutation	SNP	ENST00000409435.1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	A	43	10.253693	0.99369	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	.	.	.	5.9	5.9	0.94986	.	0.000000	0.51477	D	0.000085	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.3736	0.49715	0.9302:0.0:0.0698:0.0	.	.	.	.	X	745;757;757;756	.	ENSP00000304748:L757X	L	-	2	0	SCN9A	166845189	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.489000	0.81451	2.251000	0.74343	0.528000	0.53228	TTA	.	.		0.313	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		C	167136943	A	C	167136943	4	2	212	1	0	0	0	0	0	1	0	0	13940	372	13	5	3755	5	SCN9A	2	167136943	Nonsense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	17608081	167136943	76062430	43	30513										
NOSTRIN	115677	hgsc.bcm.edu	37	chr2	169721359	169721359	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cacaggtgacattgtgattaTacacgagaaaaaagaaggag	11	5	0	4			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:169721359T>C	ENST00000317647.7	+	16	1629	c.1400T>C	c.(1399-1401)aTa>aCa	p.I467T	NOSTRIN_ENST00000421711.2_Missense_Mutation_p.I439T|NOSTRIN_ENST00000397206.2_Missense_Mutation_p.I389T|NOSTRIN_ENST00000445023.2_Missense_Mutation_p.I389T|NOSTRIN_ENST00000397209.2_Missense_Mutation_p.I439T|NOSTRIN_ENST00000444448.2_Missense_Mutation_p.I524T|NOSTRIN_ENST00000458381.2_Missense_Mutation_p.I524T	NM_001039724.3	NP_001034813.2	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficking	467	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoskeleton (GO:0005856)|endocytic vesicle membrane (GO:0030666)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						ATTGTGATTATACACGAGAAA	0.428																																					p.I524T		Atlas-SNP	.											.	NOSTRIN	68	.	0			c.T1571C						.						128	117	120					2																	169721359		1872	4105	5977	SO:0001583	missense	115677	exon21			TGATTATACACGA	AJ532842	CCDS42771.1, CCDS42772.1, CCDS54415.1, CCDS54416.1	2q31.1	2013-08-05	2013-08-05		ENSG00000163072	ENSG00000163072			20203	protein-coding gene	gene with protein product		607496	"nitric oxide synthase trafficker"			12446846	Standard	NM_001171631		Approved	MGC20702	uc002ueg.3	Q8IVI9	OTTHUMG00000153990	ENST00000317647.7:c.1400T>C	chr2.hg19:g.169721359T>C	ENSP00000318921:p.Ile467Thr	45.0	0.0		77.0	22.0	NM_001171631	A8K2I9|B3KSF5|E7EPT9|Q27HG3|Q53S62|Q96CJ9	Missense_Mutation	SNP	ENST00000317647.7	hg19	CCDS42771.1	.	.	.	.	.	.	.	.	.	.	T	19.30	3.800826	0.70567	.	.	ENSG00000163072	ENST00000458381;ENST00000444448;ENST00000317647;ENST00000445023;ENST00000397206;ENST00000397209;ENST00000421711	T;T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38;0.38	4.96	4.96	0.65561	Src homology-3 domain (5);	0.220288	0.43579	D	0.000543	T	0.73697	0.3620	M	0.88775	2.98	0.80722	D	1	D;D;D;D;D;D	0.65815	0.959;0.994;0.995;0.995;0.978;0.988	P;P;D;D;P;D	0.63957	0.564;0.818;0.92;0.913;0.828;0.909	T	0.79512	-0.1773	10	0.87932	D	0	-15.7456	12.4555	0.55702	0.0:0.0:0.0:1.0	.	439;389;524;361;467;524	Q8IVI9-2;Q8IVI9-3;B3KSF5;D3DPB9;Q8IVI9;E7EPT9	.;.;.;.;NOSTN_HUMAN;.	T	524;524;467;389;389;439;439	ENSP00000402140:I524T;ENSP00000394051:I524T;ENSP00000318921:I467T;ENSP00000404413:I389T;ENSP00000380390:I389T;ENSP00000380392:I439T;ENSP00000401316:I439T	ENSP00000318921:I467T	I	+	2	0	NOSTRIN	169429605	0.668000	0.27493	0.980000	0.43619	0.991000	0.79684	4.778000	0.62368	1.980000	0.57719	0.455000	0.32223	ATA	.	.		0.428	NOSTRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333356.4	NM_052946		C	169721359	T	C	169721359	3	2	212	1	0	0	0	0	1	0	0	0	10555	1406	49	2	1637	2	NOSTRIN	2	169721359	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	2584416	169721359	73478014	44	30514										
TLK1	9874	hgsc.bcm.edu	37	chr2	171974343	171974343	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	actcttgccttcttggatccAgactatgaagctcatccatt	6	12	3	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:171974343A>T	ENST00000431350.2	-	2	568	c.164T>A	c.(163-165)cTg>cAg	p.L55Q	TLK1_ENST00000360843.3_Missense_Mutation_p.L55Q|TLK1_ENST00000442919.2_Missense_Mutation_p.L7Q|TLK1_ENST00000521943.1_Missense_Mutation_p.L7Q			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	55					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TCTTGGATCCAGACTATGAAG	0.368																																					p.L55Q		Atlas-SNP	.											.	TLK1	134	.	0			c.T164A						.						118	110	113					2																	171974343		2203	4300	6503	SO:0001583	missense	9874	exon2			GGATCCAGACTAT	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.164T>A	chr2.hg19:g.171974343A>T	ENSP00000411099:p.Leu55Gln	24.0	0.0		43.0	11.0	NM_012290	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Missense_Mutation	SNP	ENST00000431350.2	hg19	CCDS2241.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.484091	0.84854	.	.	ENSG00000198586	ENST00000442919;ENST00000431350;ENST00000360843;ENST00000521943	D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15	5.18	5.18	0.71444	.	0.504521	0.20562	N	0.089900	D	0.96259	0.8780	M	0.74881	2.28	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.96596	0.9441	10	0.87932	D	0	.	14.0124	0.64505	1.0:0.0:0.0:0.0	.	55;55	Q9UKI8-2;Q9UKI8	.;TLK1_HUMAN	Q	7;55;55;7	ENSP00000402165:L7Q;ENSP00000411099:L55Q;ENSP00000354089:L55Q;ENSP00000428113:L7Q	ENSP00000352810:L55Q	L	-	2	0	TLK1	171682589	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.042000	0.89430	1.956000	0.56807	0.377000	0.23210	CTG	.	.		0.368	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		T	171974343	A	T	171974343	3	4	212	1	0	0	0	0	1	0	0	0	15958	188	7	4	2262	4	TLK1	2	171974343	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	2252984	171974343	71225030	45	30515										
TTN	7273	hgsc.bcm.edu	37	chr2	179583266	179583266	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccagtgtatgtggcctcgagAactatggggcttcctgtctc	12	11	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:179583266A>G	ENST00000591111.1	-	83	23840	c.23616T>C	c.(23614-23616)gtT>gtC	p.V7872V	TTN_ENST00000342992.6_Silent_p.V6945V|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.V8189V			Q8WZ42	TITIN_HUMAN	titin	12064	Ig-like 61.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGGCCTCGAGAACTATGGGGC	0.433																																					p.V8189V		Atlas-SNP	.											.	TTN	18412	.	0			c.T24567C						.						74	72	72					2																	179583266		1918	4154	6072	SO:0001819	synonymous_variant	7273	exon85			CTCGAGAACTATG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.23616T>C	chr2.hg19:g.179583266A>G		65.0	0.0		121.0	34.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179583266	A	G	179583266	2	3	212	1	0	0	0	0	0	0	0	1	16750	233	9	2		2	TTN	2	179583266	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	7608923	179583266	63616107	46	30516										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	203996708	203996708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gtgaccagattatggaacaaAtgttgaaatgcacgaacgtt	10	6	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:203996708A>G	ENST00000449802.1	+	25	3823	c.3490A>G	c.(3490-3492)Atg>Gtg	p.M1164V		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1164										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TATGGAACAAATGTTGAAATG	0.323																																					p.M1164V		Atlas-SNP	.											.	NBEAL1	266	.	0			c.A3490G						.						108	89	95					2																	203996708		692	1591	2283	SO:0001583	missense	65065	exon25			GAACAAATGTTGA	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.3490A>G	chr2.hg19:g.203996708A>G	ENSP00000399903:p.Met1164Val	93.0	0.0		218.0	64.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	A	14.48	2.548312	0.45383	.	.	ENSG00000144426	ENST00000449802;ENST00000340268	T	0.28255	1.62	5.09	5.09	0.68999	.	.	.	.	.	T	0.25531	0.0621	L	0.45581	1.43	0.48975	D	0.999735	P	0.39665	0.682	B	0.30316	0.114	T	0.06698	-1.0812	9	0.45353	T	0.12	.	14.8067	0.69962	1.0:0.0:0.0:0.0	.	1164	Q6ZS30	NBEL1_HUMAN	V	1164	ENSP00000399903:M1164V	ENSP00000344985:M1164V	M	+	1	0	NBEAL1	203704953	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.805000	0.86005	2.046000	0.60703	0.260000	0.18958	ATG	.	.		0.323	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			G	203996708	A	G	203996708	3	3	212	1	0	0	0	0	1	0	0	0	10197	101	4	2	3584	2	NBEAL1	2	203996708	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	24413442	203996708	39202665	47	30517										
MAP2	4133	hgsc.bcm.edu	37	chr2	210569340	210569340	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gccatactcaaaatcagggaAcaaggtaaggcggcaggtca	12	9	3	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:210569340A>G	ENST00000360351.4	+	11	5090				MAP2_ENST00000392194.1_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Intron|MAP2_ENST00000475600.1_Intron|MAP2_ENST00000199940.6_Missense_Mutation_p.N228S	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2						axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AAATCAGGGAACAAGGTAAGG	0.413																																					p.N228S	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.A683G						.						115	117	116					2																	210569340		2203	4299	6502	SO:0001627	intron_variant	4133	exon9			CAGGGAACAAGGT		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.4585-964A>G	chr2.hg19:g.210569340A>G		202.0	0.0		343.0	32.0	NM_001039538	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	hg19	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	A	3.241	-0.155344	0.06544	.	.	ENSG00000078018	ENST00000199940;ENST00000452717	T;T	0.41065	2.19;1.01	5.23	2.46	0.29980	.	.	.	.	.	T	0.21427	0.0516	N	0.22421	0.69	0.54753	D	0.999983	B	0.14012	0.009	B	0.12156	0.007	T	0.10019	-1.0648	9	0.02654	T	1	.	7.338	0.26621	0.6636:0.2166:0.0:0.1198	.	228	Q8IUX2	.	S	228;170	ENSP00000199940:N228S;ENSP00000388824:N170S	ENSP00000199940:N228S	N	+	2	0	MAP2	210277585	0.965000	0.33210	1.000000	0.80357	0.954000	0.61252	0.444000	0.21661	1.973000	0.57446	0.482000	0.46254	AAC	.	.		0.413	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		G	210569340	A	G	210569340	1	3	212	0	1	0	0	0	0	0	0	0	9244	43	2	2		2	MAP2	2	210569340	Intron	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	6572632	210569340	32630033	48	30518										
CHPF	79586	hgsc.bcm.edu	37	chr2	220406657	220406657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggaagaaccagtcaaagtcgTcgccgtgctgctccagcagg	13	12	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr2:220406657T>C	ENST00000243776.6	-	2	817	c.569A>G	c.(568-570)gAc>gGc	p.D190G	CHPF_ENST00000535926.1_Missense_Mutation_p.D28G|TMEM198_ENST00000344458.2_5'Flank|TMEM198_ENST00000373883.3_5'Flank|CHPF_ENST00000373891.2_Missense_Mutation_p.D190G	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	190					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		GTCAAAGTCGTCGCCGTGCTG	0.692											OREG0015229	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D190G		Atlas-SNP	.											.	CHPF	56	.	0			c.A569G						.						33	28	30					2																	220406657		2202	4300	6502	SO:0001583	missense	79586	exon2			AAGTCGTCGCCGT	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24291	protein-coding gene	gene with protein product	"chondroitin sulfate synthase 2"	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.569A>G	chr2.hg19:g.220406657T>C	ENSP00000243776:p.Asp190Gly	102.0	0.0	2266	103.0	32.0	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Missense_Mutation	SNP	ENST00000243776.6	hg19	CCDS2443.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.448412	0.43429	.	.	ENSG00000123989	ENST00000243776;ENST00000535926;ENST00000373891	T;T	0.15372	2.43;2.48	4.41	4.41	0.53225	.	0.373081	0.27298	N	0.020014	T	0.13841	0.0335	L	0.32530	0.975	0.42761	D	0.9938	B;B	0.17038	0.004;0.02	B;B	0.16289	0.015;0.014	T	0.04427	-1.0952	10	0.56958	D	0.05	-10.8017	10.8932	0.47008	0.0:0.0:0.1573:0.8427	.	190;190	F8W6H2;Q8IZ52	.;CHSS2_HUMAN	G	190;28;190	ENSP00000243776:D190G;ENSP00000445571:D28G	ENSP00000243776:D190G	D	-	2	0	CHPF	220114901	0.012000	0.17670	0.647000	0.29507	0.993000	0.82548	1.757000	0.38400	1.997000	0.58415	0.448000	0.29417	GAC	.	.		0.692	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536		C	220406657	T	C	220406657	3	2	212	1	0	0	0	0	1	0	0	0	3370	1667	58	2	1770	2	CHPF	2	220406657	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	9837317	220406657	22792716	49	30519										
FANCD2	2177	hgsc.bcm.edu	37	chr3	10084812	10084812	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tacaggcttcccaagtaaagTtgaaaagtaaaggacgagca	10	7	0	1	rs370641659		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:10084812T>C	ENST00000419585.1	+	12	1128	c.967T>C	c.(967-969)Ttg>Ctg	p.L323L	FANCD2_ENST00000383806.1_Silent_p.L323L|FANCD2_ENST00000287647.3_Silent_p.L323L|FANCD2_ENST00000383807.1_Silent_p.L323L			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	323	Interaction with BRCA2.				DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CCAAGTAAAGTTGAAAAGTAA	0.418			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.L323L		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.T967C						.						72	70	70					3																	10084812		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon12	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GTAAAGTTGAAAA	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.967T>C	chr3.hg19:g.10084812T>C		81.0	0.0		87.0	33.0	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	hg19	CCDS33696.1																																																																																			.	.		0.418	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			C	10084812	T	C	10084812	2	2	212	1	0	0	0	0	0	0	0	1	5673	1722	60	2		2	FANCD2	3	10084812	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10		10084812	187937618	50	30520										
EOMES	8320	hgsc.bcm.edu	37	chr3	27763601	27763601	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cgggctccccgctcaccgccTcgcaggagagactgccggaa	13	17	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:27763601T>A	ENST00000295743.4	-	1	388	c.185A>T	c.(184-186)gAg>gTg	p.E62V	EOMES_ENST00000449599.1_Missense_Mutation_p.E62V|EOMES_ENST00000461503.1_Intron|EOMES_ENST00000537516.1_Intron			O95936	EOMES_HUMAN	eomesodermin	62					brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						GCTCACCGCCTCGCAGGAGAG	0.697																																					p.E62V		Atlas-SNP	.											.	EOMES	65	.	0			c.A185T						.						2	2	2					3																	27763601		1420	3054	4474	SO:0001583	missense	8320	exon1			ACCGCCTCGCAGG	BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"T-boxes"	3372	protein-coding gene	gene with protein product	"T-box brain2"	604615	"eomesodermin (Xenopus laevis) homolog"			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.185A>T	chr3.hg19:g.27763601T>A	ENSP00000295743:p.Glu62Val	89.0	0.0		60.0	17.0	NM_005442	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Missense_Mutation	SNP	ENST00000295743.4	hg19	CCDS2646.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.642677	0.29246	.	.	ENSG00000163508	ENST00000295743;ENST00000449599	D;D	0.87334	-2.23;-2.24	4.09	4.09	0.47781	.	7.105440	0.00166	N	0.000001	D	0.84311	0.5444	N	0.22421	0.69	0.80722	D	1	B;B;B	0.24920	0.114;0.048;0.028	B;B;B	0.35688	0.208;0.014;0.006	T	0.65380	-0.6182	10	0.42905	T	0.14	.	9.4094	0.38482	0.0:0.0:0.0:1.0	.	62;62;62	F5H3K1;G3XAI5;O95936	.;.;EOMES_HUMAN	V	62	ENSP00000295743:E62V;ENSP00000388620:E62V	ENSP00000295743:E62V	E	-	2	0	EOMES	27738605	0.288000	0.24324	0.842000	0.33263	0.618000	0.37518	2.318000	0.43779	1.734000	0.51633	0.369000	0.22263	GAG	.	.		0.697	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442		A	27763601	T	A	27763601	3	1	212	1	0	0	0	0	1	0	0	0	5149	1551	54	4	1899	4	EOMES	3	27763601	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	17678789	27763601	170258829	51	30521										
VIPR1	7433	hgsc.bcm.edu	37	chr3	42576555	42576555	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttccggacaattttaagcctGaagtgaagatggtctttgag	11	6	1	4			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:42576555G>A	ENST00000325123.4	+	11	1212	c.1099G>A	c.(1099-1101)Gaa>Aaa	p.E367K	VIPR1_ENST00000433647.1_Missense_Mutation_p.E326K|VIPR1-AS1_ENST00000608869.1_RNA|VIPR1_ENST00000543411.1_Missense_Mutation_p.E319K|VIPR1-AS1_ENST00000610022.1_RNA|VIPR1_ENST00000438259.2_Missense_Mutation_p.E157K|VIPR1-AS1_ENST00000452639.3_RNA	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	367					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		TTTTAAGCCTGAAGTGAAGAT	0.507																																					p.E367K		Atlas-SNP	.											.	VIPR1	45	.	0			c.G1099A						.						193	175	181					3																	42576555		2203	4300	6503	SO:0001583	missense	7433	exon11			AAGCCTGAAGTGA	AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12694	protein-coding gene	gene with protein product	"VIP and PACAP receptor 1"	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.1099G>A	chr3.hg19:g.42576555G>A	ENSP00000327246:p.Glu367Lys	74.0	0.0		77.0	22.0	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Missense_Mutation	SNP	ENST00000325123.4	hg19	CCDS2698.1	.	.	.	.	.	.	.	.	.	.	G	10.25	1.299711	0.23650	.	.	ENSG00000114812	ENST00000433647;ENST00000543411;ENST00000438259;ENST00000325123	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	5.5	2.67	0.31697	GPCR, family 2-like (1);	0.057568	0.64402	D	0.000002	T	0.31949	0.0813	L	0.45422	1.42	0.51233	D	0.999917	B;B;P;B	0.40083	0.064;0.118;0.702;0.064	B;B;B;B	0.43990	0.137;0.101;0.438;0.226	T	0.02457	-1.1156	10	0.27082	T	0.32	.	8.5587	0.33498	0.1386:0.1266:0.7348:0.0	.	340;157;319;367	B4DNY6;B4DEB5;F5H1F5;P32241	.;.;.;VIPR1_HUMAN	K	326;319;157;367	ENSP00000394950:E326K;ENSP00000445701:E319K;ENSP00000415371:E157K;ENSP00000327246:E367K	ENSP00000327246:E367K	E	+	1	0	VIPR1	42551559	1.000000	0.71417	0.009000	0.14445	0.000000	0.00434	6.745000	0.74860	0.270000	0.21984	-0.251000	0.11542	GAA	.	.		0.507	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624		A	42576555	G	A	42576555	3	1	212	1	0	0	0	0	1	0	0	0	17184	1291	45	3	1141	3	VIPR1	3	42576555	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	14812954	42576555	155445875	52	30522										
CCDC71	64925	hgsc.bcm.edu	37	chr3	49200857	49200857	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gccggacactgggggacccaGtggctctgttggttttgctc	15	11	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:49200857G>C	ENST00000321895.6	-	2	891	c.785C>G	c.(784-786)aCt>aGt	p.T262S		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	262										endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGGGGACCCAGTGGCTCTGTT	0.622																																					p.T262S		Atlas-SNP	.											.	CCDC71	33	.	0			c.C785G						.						66	71	69					3																	49200857		2203	4300	6503	SO:0001583	missense	64925	exon2			GACCCAGTGGCTC	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.785C>G	chr3.hg19:g.49200857G>C	ENSP00000319006:p.Thr262Ser	42.0	0.0		55.0	9.0	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Missense_Mutation	SNP	ENST00000321895.6	hg19	CCDS2790.1	.	.	.	.	.	.	.	.	.	.	G	0.045	-1.267880	0.01433	.	.	ENSG00000177352	ENST00000321895	T	0.27557	1.66	4.9	1.01	0.19927	.	0.353710	0.26780	N	0.022540	T	0.19248	0.0462	L	0.47716	1.5	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.32161	-0.9917	10	0.08599	T	0.76	-5.7803	5.3015	0.15780	0.1512:0.0:0.5634:0.2854	.	262	Q8IV32	CCD71_HUMAN	S	262	ENSP00000319006:T262S	ENSP00000319006:T262S	T	-	2	0	CCDC71	49175861	0.393000	0.25237	0.000000	0.03702	0.114000	0.19823	2.159000	0.42339	0.001000	0.14605	0.491000	0.48974	ACT	.	.		0.622	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903		C	49200857	G	C	49200857	3	2	212	1	0	0	0	0	1	0	0	0	2846	1029	36	4	622	4	CCDC71	3	49200857	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	6624302	49200857	148821573	53	30523										
WDR82	80335	hgsc.bcm.edu	37	chr3	52304771	52304771	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	acaactgtgtttgctgcatgAgtgtatctgatgaggtccac	11	8	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:52304771A>T	ENST00000296490.3	-	2	497	c.216T>A	c.(214-216)acT>acA	p.T72T	MIRLET7G_ENST00000362280.1_RNA	NM_025222.3	NP_079498.2	Q6UXN9	WDR82_HUMAN	WD repeat domain 82	72					histone H3-K4 methylation (GO:0051568)	chromatin (GO:0000785)|histone methyltransferase complex (GO:0035097)|PTW/PP1 phosphatase complex (GO:0072357)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)								BRCA - Breast invasive adenocarcinoma(193;2.67e-05)|Kidney(197;0.00198)|KIRC - Kidney renal clear cell carcinoma(197;0.00223)|OV - Ovarian serous cystadenocarcinoma(275;0.246)		TTGCTGCATGAGTGTATCTGA	0.373																																					p.T72T		Atlas-SNP	.											.	WDR82	19	.	0			c.T216A						.						272	242	252					3																	52304771		1868	4107	5975	SO:0001819	synonymous_variant	80335	exon2			TGCATGAGTGTAT	AF132207	CCDS2851.2	3p21.2	2013-01-10	2007-07-04	2007-07-04	ENSG00000164091	ENSG00000164091		"WD repeat domain containing"	28826	protein-coding gene	gene with protein product		611059	"transmembrane protein 113"	TMEM113		17355966	Standard	NM_025222		Approved	PRO2730, MST107, MSTP107, PRO34047, WDR82A, SWD2	uc003ddl.2	Q6UXN9	OTTHUMG00000150391	ENST00000296490.3:c.216T>A	chr3.hg19:g.52304771A>T		46.0	0.0		91.0	24.0	NM_025222	A8K5R5|Q8TEB2	Silent	SNP	ENST00000296490.3	hg19	CCDS2851.2																																																																																			.	.		0.373	WDR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317919.1	NM_025222		T	52304771	A	T	52304771	2	4	212	1	0	0	0	0	0	0	0	1	17346	291	11	4		4	WDR82	3	52304771	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	3103914	52304771	145717659	54	30524										
LRIG1	26018	hgsc.bcm.edu	37	chr3	66431958	66431958	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tccatcgctttccacggctcTttgtgatacgcagacccagc	8	15	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:66431958T>C	ENST00000273261.3	-	17	3239	c.2715A>G	c.(2713-2715)aaA>aaG	p.K905K	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Silent_p.K882K	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	905					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TCCACGGCTCTTTGTGATACG	0.522																																					p.K905K		Atlas-SNP	.											.	LRIG1	138	.	0			c.A2715G						.						130	125	127					3																	66431958		2203	4300	6503	SO:0001819	synonymous_variant	26018	exon17			CGGCTCTTTGTGA	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.2715A>G	chr3.hg19:g.66431958T>C		56.0	0.0		68.0	25.0	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	hg19	CCDS33783.1																																																																																			.	.		0.522	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		C	66431958	T	C	66431958	2	2	212	1	0	0	0	0	0	0	0	1	8953	1606	56	2		2	LRIG1	3	66431958	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	14127187	66431958	131590472	55	30525										
PPP4R2	151987	hgsc.bcm.edu	37	chr3	73113262	73113262	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gagagcacagacagcaaagaGgcaaatttgcagcaaaatga	11	7	0	4			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:73113262G>A	ENST00000356692.5	+	7	856	c.603G>A	c.(601-603)gaG>gaA	p.E201E	PPP4R2_ENST00000394284.3_Silent_p.E144E|PPP4R2_ENST00000295862.9_Silent_p.E145E			Q9NY27	PP4R2_HUMAN	protein phosphatase 4, regulatory subunit 2	201					cellular protein modification process (GO:0006464)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA processing (GO:0006397)|regulation of catalytic activity (GO:0050790)|regulation of double-strand break repair via homologous recombination (GO:0010569)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)	protein binding, bridging (GO:0030674)|protein phosphatase type 4 regulator activity (GO:0030362)			breast(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|stomach(1)|urinary_tract(2)	12		Prostate(10;0.0187)|Lung SC(41;0.236)		Epithelial(33;1.76e-07)|BRCA - Breast invasive adenocarcinoma(55;9.42e-05)|LUSC - Lung squamous cell carcinoma(21;0.00211)|Lung(16;0.00643)|KIRC - Kidney renal clear cell carcinoma(39;0.0164)|Kidney(39;0.0193)|OV - Ovarian serous cystadenocarcinoma(275;0.031)		ACAGCAAAGAGGCAAATTTGC	0.378																																					p.E201E		Atlas-SNP	.											.	PPP4R2	30	.	0			c.G603A						.						29	33	32					3																	73113262		2189	4286	6475	SO:0001819	synonymous_variant	151987	exon7			CAAAGAGGCAAAT	AJ271448	CCDS2917.1	3q29	2010-06-18			ENSG00000163605	ENSG00000163605		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	18296	protein-coding gene	gene with protein product		613822				10769191	Standard	NM_174907		Approved		uc003dph.1	Q9NY27	OTTHUMG00000158816	ENST00000356692.5:c.603G>A	chr3.hg19:g.73113262G>A		136.0	0.0		233.0	61.0	NM_174907	A8K1I6|Q2TAJ9|Q498B8|Q8WXX6	Silent	SNP	ENST00000356692.5	hg19	CCDS2917.1	.	.	.	.	.	.	.	.	.	.	G	2.673	-0.277160	0.05679	.	.	ENSG00000163605	ENST00000460360	.	.	.	5.33	2.38	0.29361	.	.	.	.	.	T	0.54743	0.1877	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46247	-0.9205	4	.	.	.	.	6.7201	0.23325	0.1339:0.0:0.6032:0.2629	.	.	.	.	K	33	.	.	R	+	2	0	PPP4R2	73195952	0.102000	0.21896	0.983000	0.44433	0.351000	0.29236	-0.002000	0.12924	0.536000	0.28733	0.491000	0.48974	AGG	.	.		0.378	PPP4R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352321.1	NM_174907		A	73113262	G	A	73113262	2	1	212	1	0	0	0	0	0	0	0	1	12416	991	35	3		3	PPP4R2	3	73113262	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	6681304	73113262	124909168	56	30526										
FILIP1L	11259	hgsc.bcm.edu	37	chr3	99567920	99567920	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gaagatggccctccttggatTtcatccagggaatccatagc	10	11	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:99567920T>G	ENST00000354552.3	-	5	3070	c.2600A>C	c.(2599-2601)aAa>aCa	p.K867T	FILIP1L_ENST00000487087.1_Missense_Mutation_p.K443T|FILIP1L_ENST00000476723.1_Intron|FILIP1L_ENST00000331335.5_Missense_Mutation_p.K867T|FILIP1L_ENST00000383694.2_Missense_Mutation_p.K627T|FILIP1L_ENST00000471562.1_Missense_Mutation_p.K627T|CMSS1_ENST00000421999.2_Intron|CMSS1_ENST00000496116.1_Intron	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	867						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						CTCCTTGGATTTCATCCAGGG	0.478																																					p.K867T		Atlas-SNP	.											.	FILIP1L	154	.	0			c.A2600C						.						147	136	139					3																	99567920		1910	4133	6043	SO:0001583	missense	11259	exon5			TTGGATTTCATCC		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"downregulated in ovarian cancer 1", "GPBP-interacting protein of 130 kDa"	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.2600A>C	chr3.hg19:g.99567920T>G	ENSP00000346560:p.Lys867Thr	83.0	0.0		107.0	31.0	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Missense_Mutation	SNP	ENST00000354552.3	hg19	CCDS43117.1	.	.	.	.	.	.	.	.	.	.	T	15.62	2.886986	0.52014	.	.	ENSG00000168386	ENST00000354552;ENST00000487087;ENST00000471562;ENST00000331335;ENST00000383694;ENST00000441620;ENST00000495625	T;T;T;T;T;T	0.31510	1.8;1.49;1.49;1.8;1.49;1.5	5.99	5.99	0.97316	.	0.000000	0.56097	D	0.000031	T	0.51702	0.1690	L	0.55481	1.735	0.46564	D	0.999107	D;D	0.89917	1.0;1.0	D;D	0.71870	0.975;0.946	T	0.51810	-0.8658	10	0.72032	D	0.01	-14.9609	16.4943	0.84223	0.0:0.0:0.0:1.0	.	867;867	Q4L180-2;Q4L180	.;FIL1L_HUMAN	T	867;443;627;867;627;613;627	ENSP00000346560:K867T;ENSP00000417774:K443T;ENSP00000419642:K627T;ENSP00000327880:K867T;ENSP00000373192:K627T;ENSP00000419874:K627T	ENSP00000327880:K867T	K	-	2	0	FILIP1L	101050610	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.221000	0.58574	2.291000	0.77112	0.533000	0.62120	AAA	.	.		0.478	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890		G	99567920	T	G	99567920	3	3	212	1	0	0	0	0	1	0	0	0	5903	1841	64	5	836	5	FILIP1L	3	99567920	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	26454658	99567920	98454510	57	30527										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140401678	140401678	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctccgggcccatcctctgccAggtctgccgcaacaagcgca	10	18	2	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:140401678A>T	ENST00000286349.3	+	2	907	c.716A>T	c.(715-717)cAg>cTg	p.Q239L		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	239						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ATCCTCTGCCAGGTCTGCCGC	0.627																																					p.Q239L		Atlas-SNP	.											.	TRIM42	143	.	0			c.A716T						.						74	73	73					3																	140401678		2203	4300	6503	SO:0001583	missense	287015	exon2			TCTGCCAGGTCTG	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.716A>T	chr3.hg19:g.140401678A>T	ENSP00000286349:p.Gln239Leu	56.0	0.0		56.0	6.0	NM_152616	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	hg19	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.986536	0.74589	.	.	ENSG00000155890	ENST00000286349	T	0.39787	1.06	5.2	5.2	0.72013	.	0.223986	0.31612	N	0.007347	T	0.36717	0.0977	L	0.46157	1.445	0.36480	D	0.867818	P	0.49447	0.924	B	0.40741	0.339	T	0.52290	-0.8595	10	0.66056	D	0.02	-12.0434	11.4507	0.50151	1.0:0.0:0.0:0.0	.	239	Q8IWZ5	TRI42_HUMAN	L	239	ENSP00000286349:Q239L	ENSP00000286349:Q239L	Q	+	2	0	TRIM42	141884368	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.816000	0.69222	1.972000	0.57404	0.459000	0.35465	CAG	.	.		0.627	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		T	140401678	A	T	140401678	3	4	212	1	0	0	0	0	1	0	0	0	16532	188	7	4	722	4	TRIM42	3	140401678	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	40833758	140401678	57620752	58	30528										
TSC22D2	9819	hgsc.bcm.edu	37	chr3	150127758	150127758	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgcattagacacagcagtacTtttgaccagactgcggagcg	11	10	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:150127758T>G	ENST00000361875.3	+	1	1637	c.621T>G	c.(619-621)acT>acG	p.T207T	TSC22D2_ENST00000361136.2_Silent_p.T207T	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	207					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ACAGCAGTACTTTTGACCAGA	0.617																																					p.T207T		Atlas-SNP	.											.	TSC22D2	42	.	0			c.T621G						.						76	79	78					3																	150127758		2203	4300	6503	SO:0001819	synonymous_variant	9819	exon1			CAGTACTTTTGAC	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.621T>G	chr3.hg19:g.150127758T>G		60.0	0.0		84.0	17.0	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Silent	SNP	ENST00000361875.3	hg19	CCDS3149.1																																																																																			.	.		0.617	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779		G	150127758	T	G	150127758	2	3	212	1	0	0	0	0	0	0	0	1	16623	1596	56	5		5	TSC22D2	3	150127758	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	9726080	150127758	47894672	59	30529										
SERP1	27230	hgsc.bcm.edu	37	chr3	150262283	150262283	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	actttgaataatctggaaaaTtgctgtaaaaagaaagagca	8	4	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:150262283T>C	ENST00000479209.1	-	4	1435	c.163A>G	c.(163-165)Att>Gtt	p.I55V	SERP1_ENST00000487153.1_Silent_p.Q29Q|EIF2A_ENST00000273435.5_5'Flank|EIF2A_ENST00000460851.1_5'Flank|EIF2A_ENST00000406576.3_5'Flank|EIF2A_ENST00000487799.1_5'Flank|SERP1_ENST00000239944.2_Missense_Mutation_p.I55V			Q9Y6X1	SERP1_HUMAN	stress-associated endoplasmic reticulum protein 1	55					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucose metabolic process (GO:0006006)|multicellular organismal aging (GO:0010259)|muscle organ morphogenesis (GO:0048644)|plasma membrane organization (GO:0007009)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of organ growth (GO:0046622)|positive regulation of translation (GO:0045727)|post-embryonic development (GO:0009791)|protein glycosylation (GO:0006486)|protein transport (GO:0015031)|response to stress (GO:0006950)|skeletal system development (GO:0001501)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|ribosome (GO:0005840)				large_intestine(1)|lung(3)	4			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ATCTGGAAAATTGCTGTAAAA	0.328																																					p.I55V		Atlas-SNP	.											.	SERP1	9	.	0			c.A163G						.						83	87	85					3																	150262283		2203	4300	6503	SO:0001583	missense	27230	exon3			GGAAAATTGCTGT	AK125413	CCDS3150.1	3q25.1	2007-12-07	2007-12-07		ENSG00000120742	ENSG00000120742			10759	protein-coding gene	gene with protein product	"ribosome associated membrane protein 4"					10601334, 11230166	Standard	NM_014445		Approved	RAMP4, FLJ43424	uc003exy.3	Q9Y6X1	OTTHUMG00000159769	ENST00000479209.1:c.163A>G	chr3.hg19:g.150262283T>C	ENSP00000420076:p.Ile55Val	217.0	0.0		283.0	72.0	NM_014445	D3DNI6	Missense_Mutation	SNP	ENST00000479209.1	hg19	CCDS3150.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.529393	0.27387	.	.	ENSG00000120742	ENST00000239944;ENST00000479209	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.50292	0.1607	.	.	.	0.58432	D	0.999999	B	0.12013	0.005	B	0.14578	0.011	T	0.43327	-0.9398	8	0.20046	T	0.44	-1.4526	15.3236	0.74141	0.0:0.0:0.0:1.0	.	55	Q9Y6X1	SERP1_HUMAN	V	55	.	ENSP00000239944:I55V	I	-	1	0	SERP1	151744973	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.997000	0.76270	2.317000	0.78254	0.460000	0.39030	ATT	.	.		0.328	SERP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357239.1	NM_014445		C	150262283	T	C	150262283	3	2	212	1	0	0	0	0	1	0	0	0	14099	1493	52	2	41	2	SERP1	3	150262283	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	134525	150262283	47760147	60	30530										
DHX36	170506	hgsc.bcm.edu	37	chr3	154022720	154022720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctgactgcagatttctttcaTggatttcatcaagtacgata	7	8	4	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:154022720T>C	ENST00000496811.1	-	8	1090	c.1010A>G	c.(1009-1011)cAt>cGt	p.H337R	DHX36_ENST00000329463.5_Missense_Mutation_p.H337R|DHX36_ENST00000544526.1_Missense_Mutation_p.H337R|DHX36_ENST00000308361.6_Missense_Mutation_p.H337R	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	337	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			ATTTCTTTCATGGATTTCATC	0.313																																					p.H337R		Atlas-SNP	.											.	DHX36	98	.	0			c.A1010G						.						47	47	47					3																	154022720		2203	4298	6501	SO:0001583	missense	170506	exon8			CTTTCATGGATTT	AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.1010A>G	chr3.hg19:g.154022720T>C	ENSP00000417078:p.His337Arg	151.0	0.0		249.0	11.0	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Missense_Mutation	SNP	ENST00000496811.1	hg19	CCDS3171.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.556641	0.86231	.	.	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03	5.9	5.9	0.94986	DEAD-like helicase (2);DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.86251	0.5888	H	0.96889	3.9	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.76071	0.977;0.977;0.987	D	0.90858	0.4736	10	0.87932	D	0	.	16.3317	0.83023	0.0:0.0:0.0:1.0	.	337;337;337	Q9H2U1-2;Q9H2U1-3;Q9H2U1	.;.;DHX36_HUMAN	R	337;337;337;337;251	ENSP00000417078:H337R;ENSP00000309296:H337R;ENSP00000444247:H337R;ENSP00000330113:H337R;ENSP00000419862:H251R	ENSP00000309296:H337R	H	-	2	0	DHX36	155505414	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.672000	0.83956	2.264000	0.75181	0.533000	0.62120	CAT	.	.		0.313	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		C	154022720	T	C	154022720	3	2	212	1	0	0	0	0	1	0	0	0	4511	1464	51	2	2088	2	DHX36	3	154022720	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	3760437	154022720	43999710	61	30531										
IFT80	57560	hgsc.bcm.edu	37	chr3	160099508	160099508	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cccacacagcttactaattcTtgatgtgtcaccatgttaaa	5	11	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:160099508T>G	ENST00000326448.7	-	3	474	c.42A>C	c.(40-42)caA>caC	p.Q14H	IFT80_ENST00000483465.1_Splice_Site|IFT80_ENST00000477495.1_5'UTR|IFT80_ENST00000496589.1_Splice_Site|RP11-432B6.3_ENST00000483754.1_Intron	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	14				Q -> I (in Ref. 5; BAA92612). {ECO:0000305}.	bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TTACTAATTCTTGATGTGTCA	0.348																																					p.Q14H		Atlas-SNP	.											.	IFT80	68	.	0			c.A42C						.						95	92	93					3																	160099508		2203	4300	6503	SO:0001583	missense	57560	exon3			TAATTCTTGATGT	AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"Intraflagellar transport homologs", "WD repeat domain containing"	29262	protein-coding gene	gene with protein product		611177	"WD repeat domain 56", "intraflagellar transport 80 homolog (Chlamydomonas)"	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.42A>C	chr3.hg19:g.160099508T>G	ENSP00000312778:p.Gln14His	75.0	0.0		116.0	9.0	NM_020800	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Missense_Mutation	SNP	ENST00000326448.7	hg19	CCDS3188.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.398419	0.62177	.	.	ENSG00000068885	ENST00000326448;ENST00000498409;ENST00000489004;ENST00000478536	T;T;T;T	0.70869	1.56;-0.06;-0.52;-0.52	5.86	4.71	0.59529	.	0.235594	0.26023	U	0.026817	T	0.69504	0.3118	L	0.47716	1.5	0.80722	D	1	.	.	.	.	.	.	T	0.70714	-0.4796	8	0.54805	T	0.06	.	7.1202	0.25440	0.0:0.163:0.0:0.837	.	.	.	.	H	14	ENSP00000312778:Q14H;ENSP00000420001:Q14H;ENSP00000418455:Q14H;ENSP00000419468:Q14H	ENSP00000312778:Q14H	Q	-	3	2	IFT80	161582202	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.113000	0.31184	2.238000	0.73509	0.477000	0.44152	CAA	.	.		0.348	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800		G	160099508	T	G	160099508	3	3	212	1	0	0	0	0	1	0	0	0	7573	1623	56	5	2363	5	IFT80	3	160099508	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	6076788	160099508	37922922	62	30532										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173997093	173997094	+	In_Frame_Ins	INS	-	-	ACC													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gcaaagatgttttgagagaaINSaccattaagttcatgtatac							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:173997093_173997094insACC	ENST00000457714.1	+	6	1731_1732	c.1302_1303insACC	c.(1303-1305)acc>ACCacc	p.435_435T>TT	NLGN1_ENST00000361589.4_In_Frame_Ins_p.435_435T>TT|NLGN1_ENST00000401917.3_In_Frame_Ins_p.475_475T>TT|NLGN1_ENST00000545397.1_In_Frame_Ins_p.435_435T>TT|NLGN1_ENST00000466350.1_3'UTR	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	452					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TTTTGAGAGAAACCATTAAGTT	0.391																																					p.E434delinsET		Atlas-INDEL	.											.	NLGN1	209	.	0			c.1302_1303insACC						.																																			SO:0001652	inframe_insertion	22871	exon6			.	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.1303_1305dupACC	chr3.hg19:g.173997094_173997096dupACC	ENSP00000392500:p.Thr435dup	81.0	0.0		142.0	33.0	NM_014932	Q9UPT2	In_Frame_Ins	INS	ENST00000457714.1	hg19	CCDS3222.1																																																																																			.	.		0.391	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		ACC	173997094	-	ACC	173997093	7	5	212	1	0	1	1	0	0	0	0	0	10470	11	1	0	1316	0	NLGN1	3	173997093	In_Frame_Ins	INS	-	TCGA-DD-AAE7-01A-11D-A40R-10	13897585	173997093	24025337	63	30533										
DVL3	1857	hgsc.bcm.edu	37	chr3	183884260	183884260	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gagatcaactttgagaacatGagtaatgacgatgcagtccg	11	7	1	4			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:183884260G>C	ENST00000313143.3	+	9	1178	c.930G>C	c.(928-930)atG>atC	p.M310I	DVL3_ENST00000431765.1_Missense_Mutation_p.M310I|EIF2B5_ENST00000444495.1_Intron	NM_004423.3	NP_004414.3	Q92997	DVL3_HUMAN	dishevelled segment polarity protein 3	310	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|intracellular signal transduction (GO:0035556)|non-canonical Wnt signaling pathway (GO:0035567)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|outflow tract septum morphogenesis (GO:0003148)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	cell cortex (GO:0005938)	beta-catenin binding (GO:0008013)|frizzled binding (GO:0005109)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(6)|liver(1)|lung(13)|ovary(1)|prostate(1)	35	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)			TTGAGAACATGAGTAATGACG	0.532																																					p.M310I		Atlas-SNP	.											.	DVL3	68	.	0			c.G930C						.						164	164	164					3																	183884260		2203	4300	6503	SO:0001583	missense	1857	exon9			GAACATGAGTAAT	D86963	CCDS3253.1	3q27	2013-05-22	2013-05-22		ENSG00000161202	ENSG00000161202		"Dishevelled homologs"	3087	protein-coding gene	gene with protein product		601368	"dishevelled 3 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 3 (Drosophila)"			8817329	Standard	NM_004423		Approved	KIAA0208	uc003fms.3	Q92997	OTTHUMG00000156841	ENST00000313143.3:c.930G>C	chr3.hg19:g.183884260G>C	ENSP00000316054:p.Met310Ile	111.0	0.0		164.0	8.0	NM_004423	B4E3E5|D3DNT0|O14642|Q13531|Q8N5E9|Q92607	Missense_Mutation	SNP	ENST00000313143.3	hg19	CCDS3253.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.527403	0.85706	.	.	ENSG00000161202	ENST00000313143;ENST00000415612;ENST00000431765;ENST00000423300	T;T;T	0.27890	1.64;1.64;1.64	5.45	5.45	0.79879	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.44498	0.1296	L	0.27975	0.815	0.80722	D	1	B;P;D	0.56746	0.059;0.899;0.977	B;P;D	0.66602	0.387;0.771;0.945	T	0.43909	-0.9362	10	0.87932	D	0	-19.6695	19.2837	0.94061	0.0:0.0:1.0:0.0	.	310;142;310	B4E3E5;Q9UG07;Q92997	.;.;DVL3_HUMAN	I	310;310;310;208	ENSP00000316054:M310I;ENSP00000405885:M310I;ENSP00000393849:M208I	ENSP00000316054:M310I	M	+	3	0	DVL3	185366954	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.553000	0.86117	0.655000	0.94253	ATG	.	.		0.532	DVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346184.1	NM_004423		C	183884260	G	C	183884260	3	2	212	1	0	0	0	0	1	0	0	0	4839	1290	45	4	964	4	DVL3	3	183884260	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	9887167	183884260	14138170	64	30534										
VPS8	23355	hgsc.bcm.edu	37	chr3	184642719	184642719	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttaccttccttgctcggcagCttgcaaagcctgacaacacc	7	15	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:184642719C>T	ENST00000437079.3	+	30	2695	c.2524C>T	c.(2524-2526)Ctt>Ttt	p.L842F	VPS8_ENST00000446204.2_Missense_Mutation_p.L750F|VPS8_ENST00000436792.2_Missense_Mutation_p.L840F|VPS8_ENST00000287546.4_Missense_Mutation_p.L842F|VPS8_ENST00000463687.1_3'UTR	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	842							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TGCTCGGCAGCTTGCAAAGCC	0.413																																					p.L842F		Atlas-SNP	.											.	VPS8	109	.	0			c.C2524T						.						109	99	102					3																	184642719		1905	4122	6027	SO:0001583	missense	23355	exon29			CGGCAGCTTGCAA	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"KIAA0804"	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.2524C>T	chr3.hg19:g.184642719C>T	ENSP00000397879:p.Leu842Phe	43.0	0.0		66.0	10.0	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	hg19	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.521170	0.85600	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	6.06	6.06	0.98353	Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.48607	0.1509	L	0.55834	1.745	0.80722	D	1	D;P;D	0.76494	0.997;0.589;0.999	D;P;D	0.69142	0.916;0.573;0.962	T	0.16041	-1.0416	10	0.46703	T	0.11	-18.6441	20.2502	0.98404	0.0:1.0:0.0:0.0	.	842;750;840	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	F	842;842;840;750	ENSP00000287546:L842F;ENSP00000397879:L842F;ENSP00000404704:L840F;ENSP00000405483:L750F	ENSP00000287546:L842F	L	+	1	0	VPS8	186125413	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.225000	0.58600	2.880000	0.98712	0.650000	0.86243	CTT	.	.		0.413	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		T	184642719	C	T	184642719	3	4	212	1	0	0	0	0	1	0	0	0	17233	797	28	3	2634	3	VPS8	3	184642719	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	758459	184642719	13379711	65	30535										
ADIPOQ	9370	hgsc.bcm.edu	37	chr3	186572334	186572334	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tatgatcagtaccaggaaaaTaatgtggaccaggcctccgg	11	9	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:186572334T>A	ENST00000412955.2	+	3	717	c.576T>A	c.(574-576)aaT>aaA	p.N192K	ADIPOQ-AS1_ENST00000422718.1_RNA|ADIPOQ_ENST00000444204.2_Missense_Mutation_p.N192K|ADIPOQ_ENST00000320741.2_Missense_Mutation_p.N192K			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	192	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				adiponectin-activated signaling pathway (GO:0033211)|brown fat cell differentiation (GO:0050873)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to insulin stimulus (GO:0032869)|circadian rhythm (GO:0007623)|detection of oxidative stress (GO:0070994)|fatty acid beta-oxidation (GO:0006635)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|low-density lipoprotein particle clearance (GO:0034383)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of hormone secretion (GO:0046888)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular protein transport (GO:0090317)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metanephric mesenchymal cell migration (GO:2000590)|negative regulation of phagocytosis (GO:0050765)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of receptor binding (GO:1900121)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of synaptic transmission (GO:0050805)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|positive regulation of blood pressure (GO:0045777)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of metanephric glomerular visceral epithelial cell development (GO:2000478)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myeloid cell apoptotic process (GO:0033034)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal albumin absorption (GO:2000534)|positive regulation of signal transduction (GO:0009967)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|regulation of glucose metabolic process (GO:0010906)|response to activity (GO:0014823)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to linoleic acid (GO:0070543)|response to nutrient (GO:0007584)|response to sucrose (GO:0009744)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|sialic acid binding (GO:0033691)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(2)	16	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)		ACCAGGAAAATAATGTGGACC	0.512																																					p.N192K		Atlas-SNP	.											.	ADIPOQ	35	.	0			c.T576A						.						100	94	96					3																	186572334		2203	4300	6503	SO:0001583	missense	9370	exon4			GGAAAATAATGTG	D45371	CCDS3284.1	3q27	2013-02-26	2005-01-24	2005-01-27	ENSG00000181092	ENSG00000181092		"Endogenous ligands"	13633	protein-coding gene	gene with protein product	"adipose most abundant gene transcript 1", "adiponectin precursor"	605441	"adipocyte, C1Q and collagen domain containing"	ACDC		7592907, 8631877	Standard	NM_001177800		Approved	ACRP30, AdipoQ, apM1, GBP28, adiponectin	uc003fra.3	Q15848	OTTHUMG00000156521	ENST00000412955.2:c.576T>A	chr3.hg19:g.186572334T>A	ENSP00000405611:p.Asn192Lys	80.0	0.0		107.0	25.0	NM_001177800	Q58EX9	Missense_Mutation	SNP	ENST00000412955.2	hg19	CCDS3284.1	.	.	.	.	.	.	.	.	.	.	T	10.54	1.379643	0.24944	.	.	ENSG00000181092	ENST00000412955;ENST00000320741;ENST00000444204	T;T;T	0.38077	1.16;1.16;1.16	5.53	-1.02	0.10135	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.344714	0.29046	N	0.013310	T	0.13628	0.0330	N	0.17723	0.515	0.32858	D	0.507522	B	0.02656	0.0	B	0.10450	0.005	T	0.19582	-1.0301	10	0.06891	T	0.86	.	1.1676	0.01819	0.3199:0.217:0.3349:0.1282	.	192	Q15848	ADIPO_HUMAN	K	192	ENSP00000405611:N192K;ENSP00000320709:N192K;ENSP00000389814:N192K	ENSP00000320709:N192K	N	+	3	2	ADIPOQ	188055028	0.950000	0.32346	0.965000	0.40720	0.503000	0.33858	0.242000	0.18087	0.090000	0.17273	-0.168000	0.13345	AAT	.	.		0.512	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344490.2	NM_004797		A	186572334	T	A	186572334	3	1	212	1	0	0	0	0	1	0	0	0	317	1403	49	4	582	4	ADIPOQ	3	186572334	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	1929615	186572334	11450096	66	30536										
DLG1	1739	hgsc.bcm.edu	37	chr3	197009694	197009694	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tttggattatccagtaaggtCacttcataaaattcttgaat	6	6	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:197009694C>T	ENST00000419354.1	-	4	460	c.174G>A	c.(172-174)gtG>gtA	p.V58V	DLG1_ENST00000357674.4_Silent_p.V58V|DLG1_ENST00000314062.3_Silent_p.V58V|DLG1_ENST00000422288.1_Silent_p.V58V|DLG1_ENST00000392382.2_Silent_p.V58V|DLG1_ENST00000346964.2_Silent_p.V58V|DLG1_ENST00000450955.1_Silent_p.V58V|DLG1_ENST00000485409.1_5'UTR|DLG1_ENST00000448528.2_Silent_p.V58V			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	58	L27. {ECO:0000255|PROSITE- ProRule:PRU00365}.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		CCAGTAAGGTCACTTCATAAA	0.318																																					p.V58V		Atlas-SNP	.											.	DLG1	120	.	0			c.G174A						.						97	102	100					3																	197009694		2203	4300	6503	SO:0001819	synonymous_variant	1739	exon4			TAAGGTCACTTCA	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"discs large homolog 1", "presynaptic protein SAP97", "synapse-associated protein 97"	601014	"discs, large (Drosophila) homolog 1"			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.174G>A	chr3.hg19:g.197009694C>T		66.0	0.0		102.0	24.0	NM_001204386	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Silent	SNP	ENST00000419354.1	hg19	CCDS43194.1																																																																																			.	.		0.318	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087		T	197009694	C	T	197009694	2	4	212	1	0	0	0	0	0	0	0	1	4556	813	29	3		3	DLG1	3	197009694	Silent	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	10437360	197009694	1012736	67	30537										
DLG1	1739	hgsc.bcm.edu	37	chr3	197023325	197023325	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttttgaacgatattcctccaAaaggtgcaatgctctctggg	9	9	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr3:197023325A>C	ENST00000419354.1	-	3	329	c.43T>G	c.(43-45)Ttg>Gtg	p.L15V	DLG1_ENST00000357674.4_Missense_Mutation_p.L15V|DLG1_ENST00000314062.3_Missense_Mutation_p.L15V|DLG1-AS1_ENST00000430666.1_RNA|DLG1_ENST00000422288.1_Missense_Mutation_p.L15V|DLG1_ENST00000392382.2_Missense_Mutation_p.L15V|DLG1_ENST00000346964.2_Missense_Mutation_p.L15V|DLG1-AS1_ENST00000414529.1_RNA|DLG1_ENST00000450955.1_Missense_Mutation_p.L15V|DLG1_ENST00000485409.1_5'UTR|DLG1_ENST00000448528.2_Missense_Mutation_p.L15V|MIR4797_ENST00000577559.1_RNA			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	15	L27. {ECO:0000255|PROSITE- ProRule:PRU00365}.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		TATTCCTCCAAAAGGTGCAAT	0.378																																					p.L15V		Atlas-SNP	.											.	DLG1	120	.	0			c.T43G						.						141	141	141					3																	197023325		2203	4300	6503	SO:0001583	missense	1739	exon3			CCTCCAAAAGGTG	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"discs large homolog 1", "presynaptic protein SAP97", "synapse-associated protein 97"	601014	"discs, large (Drosophila) homolog 1"			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.43T>G	chr3.hg19:g.197023325A>C	ENSP00000407531:p.Leu15Val	62.0	0.0		79.0	22.0	NM_001204386	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	hg19	CCDS43194.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.287996	0.80803	.	.	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000422288;ENST00000448528;ENST00000392382;ENST00000450955;ENST00000456699;ENST00000392380;ENST00000419553;ENST00000436682;ENST00000412364;ENST00000434148	T;T;T;T;T;T;T;T;T;T;T	0.62498	1.74;1.64;1.65;1.77;1.65;1.77;1.69;1.64;0.04;0.03;0.02	5.09	3.95	0.45737	L27 (2);L27-1 (1);	0.000000	0.56097	D	0.000022	T	0.72771	0.3502	M	0.70842	2.15	0.58432	D	0.999995	D;D;D;P	0.71674	0.998;0.996;0.997;0.952	D;D;D;P	0.79108	0.99;0.986;0.992;0.606	T	0.74607	-0.3609	10	0.87932	D	0	.	5.5781	0.17235	0.8157:0.0:0.1842:0.0	.	15;15;15;15	Q12959-4;Q12959-3;Q12959;Q12959-2	.;.;DLG1_HUMAN;.	V	15	ENSP00000345731:L15V;ENSP00000350303:L15V;ENSP00000321087:L15V;ENSP00000407531:L15V;ENSP00000413238:L15V;ENSP00000391732:L15V;ENSP00000376187:L15V;ENSP00000411278:L15V;ENSP00000396474:L15V;ENSP00000376185:L15V;ENSP00000414189:L15V	ENSP00000321087:L15V	L	-	1	2	DLG1	198507722	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.303000	0.59098	2.213000	0.71641	0.528000	0.53228	TTG	.	.		0.378	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087		C	197023325	A	C	197023325	3	2	212	1	0	0	0	0	1	0	0	0	4556	11	1	5	2871	5	DLG1	3	197023325	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	13631	197023325	999105	68	30538										
WFS1	7466	hgsc.bcm.edu	37	chr4	6279336	6279336	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gaccccaggctggccctggcCctggtgttagagacgcagcg	15	14	0	1	rs111773340	byFrequency	TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:6279336C>T	ENST00000226760.1	+	2	324	c.154C>T	c.(154-156)Cct>Tct	p.P52S	WFS1_ENST00000503569.1_Missense_Mutation_p.P52S	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	52					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		TGGCCCTGGCCCTGGTGTTAG	0.692																																					p.P52S		Atlas-SNP	.											.	WFS1	71	.	0			c.C154T						.						12	13	13					4																	6279336		2165	4246	6411	SO:0001583	missense	7466	exon2			CCTGGCCCTGGTG	AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.154C>T	chr4.hg19:g.6279336C>T	ENSP00000226760:p.Pro52Ser	177.0	0.0		152.0	10.0	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Missense_Mutation	SNP	ENST00000226760.1	hg19	CCDS3386.1	.	.	.	.	.	.	.	.	.	.	C	10.27	1.305020	0.23736	.	.	ENSG00000109501	ENST00000503569;ENST00000226760	D;D	0.93076	-3.16;-3.16	4.08	1.26	0.21427	.	0.940554	0.08855	N	0.883838	D	0.87426	0.6174	L	0.38531	1.155	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.75499	-0.3296	10	0.44086	T	0.13	0.0966	3.6545	0.08215	0.0:0.5548:0.2108:0.2344	.	52	O76024	WFS1_HUMAN	S	52	ENSP00000423337:P52S;ENSP00000226760:P52S	ENSP00000226760:P52S	P	+	1	0	WFS1	6330237	0.014000	0.17966	0.009000	0.14445	0.154000	0.21943	0.201000	0.17276	0.417000	0.25871	0.462000	0.41574	CCT	.	C|0.999;A|0.001		0.692	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1			T	6279336	C	T	6279336	3	4	212	1	0	0	0	0	1	0	0	0	17375	623	22	3	156	3	WFS1	4	6279336	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10		6279336	184874940	69	30539										
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6596347	6596354	+	Frame_Shift_Del	DEL	GCTCGGTG	GCTCGGTG	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atcaacagccatgctgccgaGctcggtgtctcggtgcagta					rs368931196|rs201727705	byFrequency	TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	GCTCGGTG	GCTCGGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:6596347_6596354delGCTCGGTG	ENST00000285599.3	+	7	981_988	c.945_952delGCTCGGTG	c.(943-954)gagctcggtgtcfs	p.ELGV315fs	MAN2B2_ENST00000504248.1_Splice_Site_p.ELGV264fs	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	315					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						ATGCTGCCGAGCTCGGTGTCTCGGTGCA	0.601																																					p.315_317del		Atlas-INDEL	.											.	MAN2B2	80	.	0			c.944_951del						.																																			SO:0001589	frameshift_variant	23324	exon7			.	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"core-specific lysosomal alpha-1,6-Mannosidase"					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.945_952delGCTCGGTG	chr4.hg19:g.6596347_6596354delGCTCGGTG	ENSP00000285599:p.Glu315fs	46.0	0.0		51.0	14.0	NM_015274	Q66MP2|Q86T67	Frame_Shift_Del	DEL	ENST00000285599.3	hg19	CCDS33951.1																																																																																			.	.		0.601	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		-	6596354	GCTCGGTG	-	6596347	7	5	212	1	0	1	0	1	0	0	0	0	9226	962	34	0	971	0	MAN2B2	4	6596347	Frame_Shift_Del	DEL	GCTCGGTG	TCGA-DD-AAE7-01A-11D-A40R-10	317011	6596347	184557929	70	30540										
TLR6	10333	hgsc.bcm.edu	37	chr4	38828947	38828947	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	agattgtgatgggcaaaataGagttcgtaatggcaccactc	11	7	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:38828947G>T	ENST00000381950.1	-	1	2213	c.2148C>A	c.(2146-2148)ctC>ctA	p.L716L	TLR6_ENST00000436693.2_Silent_p.L716L			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	716	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGGCAAAATAGAGTTCGTAAT	0.403																																					p.L716L		Atlas-SNP	.											.	TLR6	67	.	0			c.C2148A						.						185	182	183					4																	38828947		2203	4300	6503	SO:0001819	synonymous_variant	10333	exon2			AAAATAGAGTTCG		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"CD molecules"	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.2148C>A	chr4.hg19:g.38828947G>T		75.0	0.0		137.0	6.0	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Silent	SNP	ENST00000381950.1	hg19	CCDS3446.1																																																																																			.	.		0.403	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			T	38828947	G	T	38828947	2	4	212	1	0	0	0	0	0	0	0	1	15970	929	33	3		3	TLR6	4	38828947	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	32232600	38828947	152325329	71	30541										
TXK	7294	hgsc.bcm.edu	37	chr4	48096195	48096195	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	agtcattcttttttatctgaTaatgttttatggcagcctcc	6	8	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:48096195T>C	ENST00000264316.4	-	8	693	c.608A>G	c.(607-609)tAt>tGt	p.Y203C	TXK_ENST00000510457.1_5'UTR	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	203	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						TTTTATCTGATAATGTTTTAT	0.383																																					p.Y203C		Atlas-SNP	.											.	TXK	58	.	0			c.A608G						.						125	117	120					4																	48096195		2203	4300	6503	SO:0001583	missense	7294	exon8			ATCTGATAATGTT	L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"SH2 domain containing"	12434	protein-coding gene	gene with protein product		600058	"PTK4 protein tyrosine kinase 4"	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.608A>G	chr4.hg19:g.48096195T>C	ENSP00000264316:p.Tyr203Cys	35.0	0.0		45.0	11.0	NM_003328	Q14220	Missense_Mutation	SNP	ENST00000264316.4	hg19	CCDS3480.1	.	.	.	.	.	.	.	.	.	.	T	17.54	3.414452	0.62511	.	.	ENSG00000074966	ENST00000264316	D	0.89810	-2.57	5.23	5.23	0.72850	SH2 motif (5);	0.000000	0.64402	D	0.000003	D	0.93344	0.7878	M	0.66297	2.02	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93983	0.7260	10	0.87932	D	0	.	14.0929	0.65002	0.0:0.0:0.0:1.0	.	203	P42681	TXK_HUMAN	C	203	ENSP00000264316:Y203C	ENSP00000264316:Y203C	Y	-	2	0	TXK	47790952	1.000000	0.71417	1.000000	0.80357	0.468000	0.32798	7.630000	0.83225	2.189000	0.69895	0.528000	0.53228	TAT	.	.		0.383	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328		C	48096195	T	C	48096195	3	2	212	1	0	0	0	0	1	0	0	0	16801	1406	49	2	1007	2	TXK	4	48096195	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	9267248	48096195	143058081	72	30542										
UGT2B4	7363	hgsc.bcm.edu	37	chr4	70361213	70361216	+	Frame_Shift_Del	DEL	GTAT	GTAT	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atccttacagaactttctaaGtatgtcattaaatgtccaca							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	GTAT	GTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:70361213_70361216delGTAT	ENST00000305107.6	-	1	410_413	c.364_367delATAC	c.(364-369)atacttfs	p.IL122fs	UGT2B4_ENST00000506580.1_5'UTR|UGT2B4_ENST00000381096.3_Intron|UGT2B4_ENST00000512583.1_Frame_Shift_Del_p.IL122fs	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	122					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	AACTTTCTAAGTATGTCATTAAAT	0.338																																					p.122_123del		Atlas-INDEL	.											.	UGT2B4	105	.	0			c.365_368del						.																																			SO:0001589	frameshift_variant	7363	exon1			.	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"UDP glucuronosyltransferases"	12553	protein-coding gene	gene with protein product		600067	"UDP glycosyltransferase 2 family, polypeptide B4"			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.364_367delATAC	chr4.hg19:g.70361213_70361216delGTAT	ENSP00000305221:p.Ile122fs	89.0	0.0		119.0	42.0	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Frame_Shift_Del	DEL	ENST00000305107.6	hg19	CCDS43234.1																																																																																			.	.		0.338	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139		-	70361216	GTAT	-	70361213	7	5	212	1	0	1	0	1	0	0	0	0	16976	1029	36	0	1243	0	UGT2B4	4	70361213	Frame_Shift_Del	DEL	GTAT	TCGA-DD-AAE7-01A-11D-A40R-10	22265018	70361213	120793063	73	30543										
SCARB2	950	hgsc.bcm.edu	37	chr4	77095407	77095407	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atatttctgcaggaactttaTaccgaaaggcaggcagtccc	9	10	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:77095407T>C	ENST00000264896.2	-	7	1233	c.884A>G	c.(883-885)tAt>tGt	p.Y295C	SCARB2_ENST00000452464.2_Missense_Mutation_p.Y152C	NM_005506.3	NP_005497.1	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2	295					cell adhesion (GO:0007155)|protein targeting to lysosome (GO:0006622)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(3)|prostate(2)|skin(1)	22			Lung(101;0.196)			AGGAACTTTATACCGAAAGGC	0.443																																					p.Y295C		Atlas-SNP	.											.	SCARB2	47	.	0			c.A884G						.						126	120	122					4																	77095407		2203	4300	6503	SO:0001583	missense	950	exon7			ACTTTATACCGAA	D12676	CCDS3577.1, CCDS56335.1	4q21.1	2014-07-11	2002-09-06	2002-09-06	ENSG00000138760	ENSG00000138760			1665	protein-coding gene	gene with protein product		602257	"CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2 (lysosomal integral membrane protein II)"	CD36L2		1374238	Standard	NM_005506		Approved	HLGP85, LIMPII, SR-BII, LIMP-2	uc003hju.2	Q14108	OTTHUMG00000130099	ENST00000264896.2:c.884A>G	chr4.hg19:g.77095407T>C	ENSP00000264896:p.Tyr295Cys	68.0	0.0		122.0	41.0	NM_005506	B4DKD8|E7EM68|Q53Y63	Missense_Mutation	SNP	ENST00000264896.2	hg19	CCDS3577.1	.	.	.	.	.	.	.	.	.	.	T	15.17	2.754917	0.49362	.	.	ENSG00000138760	ENST00000264896;ENST00000452464	T;T	0.80304	-1.36;-1.36	5.62	-2.9	0.05648	.	0.260386	0.45126	D	0.000399	D	0.88559	0.6469	M	0.88704	2.975	0.44380	D	0.997284	D;D	0.69078	0.997;0.985	D;P	0.68353	0.957;0.895	D	0.89186	0.3547	10	0.87932	D	0	.	13.5785	0.61888	0.7927:0.0:0.0:0.2073	.	152;295	E7EM68;Q14108	.;SCRB2_HUMAN	C	295;152	ENSP00000264896:Y295C;ENSP00000399154:Y152C	ENSP00000264896:Y295C	Y	-	2	0	SCARB2	77314431	1.000000	0.71417	0.080000	0.20451	0.179000	0.23085	2.831000	0.48144	-0.218000	0.10018	0.533000	0.62120	TAT	.	.		0.443	SCARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252403.1	NM_005506		C	77095407	T	C	77095407	3	2	212	1	0	0	0	0	1	0	0	0	13897	1406	49	2	576	2	SCARB2	4	77095407	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	6734194	77095407	114058869	74	30544										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85639621	85639621	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tatttccctggttgctgtcaTggtaaatccatcaatcacat	6	10	3	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:85639621T>A	ENST00000295888.4	-	48	8115	c.7708A>T	c.(7708-7710)Atg>Ttg	p.M2570L	WDFY3_ENST00000322366.6_Missense_Mutation_p.M2553L	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2570	Sufficient for translocalization to p62 bodies/ALIS.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GTTGCTGTCATGGTAAATCCA	0.403																																					p.M2570L		Atlas-SNP	.											.	WDFY3	314	.	0			c.A7708T						.						132	132	132					4																	85639621		2203	4300	6503	SO:0001583	missense	23001	exon48			CTGTCATGGTAAA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.7708A>T	chr4.hg19:g.85639621T>A	ENSP00000295888:p.Met2570Leu	64.0	0.0		102.0	24.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	T	9.271	1.045660	0.19748	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000514711	T;T;T	0.60797	0.19;0.19;0.16	5.68	5.68	0.88126	PH-BEACH domain (1);	0.000000	0.85682	D	0.000000	T	0.35566	0.0936	N	0.10945	0.07	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.31724	-0.9933	10	0.02654	T	1	.	15.9206	0.79562	0.0:0.0:0.0:1.0	.	2570	Q8IZQ1	WDFY3_HUMAN	L	2553;2570;173	ENSP00000318466:M2553L;ENSP00000295888:M2570L;ENSP00000424987:M173L	ENSP00000295888:M2570L	M	-	1	0	WDFY3	85858645	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.166000	0.68216	0.533000	0.62120	ATG	.	.		0.403	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85639621	T	A	85639621	3	1	212	1	0	0	0	0	1	0	0	0	17285	1464	51	4	2956	4	WDFY3	4	85639621	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	8544214	85639621	105514655	75	30545										
SLC39A8	64116	hgsc.bcm.edu	37	chr4	103236884	103236884	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cctcacatgggtgaaagttcAattgctgtaagactgctgga	11	8	2	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:103236884A>C	ENST00000394833.2	-	2	799	c.323T>G	c.(322-324)tTg>tGg	p.L108W	SLC39A8_ENST00000356736.4_Missense_Mutation_p.L108W|SLC39A8_ENST00000510255.1_5'UTR|SLC39A8_ENST00000424970.2_Missense_Mutation_p.L108W	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	108					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		GTGAAAGTTCAATTGCTGTAA	0.388																																					p.L108W		Atlas-SNP	.											.	SLC39A8	24	.	0			c.T323G						.						191	187	189					4																	103236884		2203	4300	6503	SO:0001583	missense	64116	exon2			AAGTTCAATTGCT		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"Solute carriers"	20862	protein-coding gene	gene with protein product		608732	"solute carrier family 39 (metal ion transporter), member 8"			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.323T>G	chr4.hg19:g.103236884A>C	ENSP00000378310:p.Leu108Trp	104.0	0.0		155.0	27.0	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Missense_Mutation	SNP	ENST00000394833.2	hg19	CCDS3656.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.114844	0.77210	.	.	ENSG00000138821	ENST00000424970;ENST00000356736;ENST00000394833	T;T;T	0.74947	-0.76;-0.89;-0.89	5.5	5.5	0.81552	.	0.289768	0.29152	N	0.012985	D	0.84678	0.5525	M	0.68952	2.095	0.27279	N	0.958141	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.994;0.997;0.998	T	0.79650	-0.1715	10	0.87932	D	0	-44.4349	14.7929	0.69857	1.0:0.0:0.0:0.0	.	108;108;41	B4E2H3;Q9C0K1;Q9C0K1-2	.;S39A8_HUMAN;.	W	108	ENSP00000394548:L108W;ENSP00000349174:L108W;ENSP00000378310:L108W	ENSP00000349174:L108W	L	-	2	0	SLC39A8	103455907	1.000000	0.71417	0.762000	0.31397	0.995000	0.86356	6.620000	0.74224	2.103000	0.63969	0.482000	0.46254	TTG	.	.		0.388	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154		C	103236884	A	C	103236884	3	2	212	1	0	0	0	0	1	0	0	0	14639	131	5	5	1164	5	SLC39A8	4	103236884	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	17597263	103236884	87917392	76	30546										
CFI	3426	hgsc.bcm.edu	37	chr4	110687778	110687778	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gacattccaaactcttttgtTgacagtatgttgggaagctt	9	7	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:110687778T>G	ENST00000394634.2	-	2	467	c.260A>C	c.(259-261)cAa>cCa	p.Q87P	CFI_ENST00000512148.1_Missense_Mutation_p.Q87P|CFI_ENST00000510800.1_Missense_Mutation_p.Q87P|CFI_ENST00000394635.3_Missense_Mutation_p.Q87P	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	87	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		ACTCTTTTGTTGACAGTATGT	0.428																																					p.Q87P		Atlas-SNP	.											.	CFI	59	.	0			c.A260C						.						120	114	116					4																	110687778		2203	4300	6503	SO:0001583	missense	3426	exon2			TTTTGTTGACAGT	J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"Complement system"	5394	protein-coding gene	gene with protein product	"Konglutinogen-activating factor", "C3b-inactivator"	217030	"I factor (complement)"	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.260A>C	chr4.hg19:g.110687778T>G	ENSP00000378130:p.Gln87Pro	87.0	0.0		100.0	24.0	NM_000204	O60442	Missense_Mutation	SNP	ENST00000394634.2	hg19	CCDS34049.1	.	.	.	.	.	.	.	.	.	.	T	15.80	2.940370	0.52972	.	.	ENSG00000205403	ENST00000394635;ENST00000394634;ENST00000540104;ENST00000512148;ENST00000536228;ENST00000510800	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.6	5.6	0.85130	Factor I / membrane attack complex (1);	0.248310	0.42053	D	0.000776	T	0.78616	0.4311	M	0.77820	2.39	0.43698	D	0.996152	D;D;D	0.71674	0.995;0.997;0.998	P;D;D	0.66602	0.873;0.945;0.914	T	0.81645	-0.0839	10	0.72032	D	0.01	-8.3276	15.7733	0.78190	0.0:0.0:0.0:1.0	.	87;87;87	E7ETH0;G3XAM2;P05156	.;.;CFAI_HUMAN	P	87;87;87;87;69;87	ENSP00000378131:Q87P;ENSP00000378130:Q87P;ENSP00000427438:Q87P;ENSP00000422009:Q87P	ENSP00000378130:Q87P	Q	-	2	0	CFI	110907227	1.000000	0.71417	0.877000	0.34402	0.038000	0.13279	5.861000	0.69553	2.122000	0.65172	0.533000	0.62120	CAA	.	.		0.428	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204		G	110687778	T	G	110687778	3	3	212	1	0	0	0	0	1	0	0	0	3291	1812	63	5	1539	5	CFI	4	110687778	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	7450894	110687778	80466498	77	30547										
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141543436	141543436	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttttttgcactggtaatcctGgccatcatgcacacgggctt	9	11	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:141543436G>A	ENST00000442267.2	-	21	3788	c.3714C>T	c.(3712-3714)gcC>gcT	p.A1238A		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	1238							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				TGGTAATCCTGGCCATCATGC	0.582																																					p.A1238A		Atlas-SNP	.											.	TBC1D9	198	.	0			c.C3714T						.						68	69	69					4																	141543436		2016	4179	6195	SO:0001819	synonymous_variant	23158	exon21			AATCCTGGCCATC	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.3714C>T	chr4.hg19:g.141543436G>A		138.0	0.0		127.0	15.0	NM_015130	A6H8U8|D3DNZ1|O94958	Silent	SNP	ENST00000442267.2	hg19	CCDS47136.1																																																																																			.	.		0.582	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		A	141543436	G	A	141543436	2	1	212	1	0	0	0	0	0	0	0	1	15642	1335	47	3		3	TBC1D9	4	141543436	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	30855658	141543436	49610840	78	30548										
PALLD	23022	hgsc.bcm.edu	37	chr4	169835138	169835138	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tcaaccaaagaggtcgaagtCcccggtctccctcaggccat	9	15	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:169835138C>G	ENST00000505667.1	+	16	2856	c.2683C>G	c.(2683-2685)Ccc>Gcc	p.P895A	PALLD_ENST00000507735.1_Missense_Mutation_p.P391A|CBR4_ENST00000509108.1_Intron|PALLD_ENST00000512127.1_Missense_Mutation_p.P496A|PALLD_ENST00000335742.7_Missense_Mutation_p.P720A|PALLD_ENST00000261509.6_Missense_Mutation_p.P878A			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	1102					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		AGGTCGAAGTCCCCGGTCTCC	0.393									Pancreatic Cancer, Familial Clustering of																												p.P895A	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C2683G						.						100	95	96					4																	169835138		2203	4300	6503	SO:0001583	missense	23022	exon16	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	CGAAGTCCCCGGT	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"Immunoglobulin superfamily / I-set domain containing"	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.2683C>G	chr4.hg19:g.169835138C>G	ENSP00000425556:p.Pro895Ala	64.0	0.0		109.0	8.0	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	hg19	CCDS54818.1	.	.	.	.	.	.	.	.	.	.	C	17.72	3.460053	0.63401	.	.	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000512127;ENST00000507735	T;T;T;T;T	0.65364	-0.15;-0.15;0.13;-0.11;0.19	5.46	5.46	0.80206	.	0.000000	0.31922	U	0.006845	T	0.44477	0.1295	N	0.16478	0.41	0.80722	D	1	B;B;B;B	0.25719	0.132;0.003;0.002;0.132	B;B;B;B	0.17098	0.017;0.003;0.003;0.01	T	0.35847	-0.9772	10	0.17832	T	0.49	.	14.8556	0.70335	0.0:0.8566:0.1433:0.0	.	895;1102;496;878	B7ZMM5;Q8WX93;B3KTG2;B2RTX2	.;PALLD_HUMAN;.;.	A	878;720;895;496;391	ENSP00000261509:P878A;ENSP00000336735:P720A;ENSP00000425556:P895A;ENSP00000426947:P496A;ENSP00000424016:P391A	ENSP00000261509:P878A	P	+	1	0	PALLD	170071713	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	2.345000	0.44018	2.560000	0.86352	0.655000	0.94253	CCC	.	.		0.393	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		G	169835138	C	G	169835138	3	3	212	1	0	0	0	0	1	0	0	0	11416	855	30	4	3248	4	PALLD	4	169835138	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	28291702	169835138	21319138	79	30549										
GLRA3	8001	hgsc.bcm.edu	37	chr4	175580328	175580328	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	catactgccatccaaatatcAatagctttgacatatgaaac	4	10	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:175580328A>G	ENST00000274093.3	-	8	1450	c.948T>C	c.(946-948)atT>atC	p.I316I	GLRA3_ENST00000340217.5_Silent_p.I316I	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	316					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)|Ivermectin(DB00602)|Lindane(DB00431)	TCCAAATATCAATAGCTTTGA	0.353																																					p.I316I		Atlas-SNP	.											.	GLRA3	76	.	0			c.T948C						.						81	77	78					4																	175580328		2203	4300	6503	SO:0001819	synonymous_variant	8001	exon8			AATATCAATAGCT	AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"Ligand-gated ion channels / Glycine receptors"	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.948T>C	chr4.hg19:g.175580328A>G		52.0	0.0		80.0	23.0	NM_001042543	D3DP44|O75816|Q5D0E3	Silent	SNP	ENST00000274093.3	hg19	CCDS3822.1																																																																																			.	.		0.353	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1			G	175580328	A	G	175580328	2	3	212	1	0	0	0	0	0	0	0	1	6464	126	5	2		2	GLRA3	4	175580328	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	5745190	175580328	15573948	80	30550										
TLR3	7098	hgsc.bcm.edu	37	chr4	186997921	186997921	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctcaggtacccgatgatctaCccacaaacataacagtgttg	7	12	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr4:186997921C>A	ENST00000296795.3	+	2	252	c.148C>A	c.(148-150)Ccc>Acc	p.P50T		NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	50	LRRNT.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		CGATGATCTACCCACAAACAT	0.483																																					p.P50T		Atlas-SNP	.											.	TLR3	83	.	0			c.C148A						.						130	118	122					4																	186997921		2203	4300	6503	SO:0001583	missense	7098	exon2			GATCTACCCACAA	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"CD molecules"	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.148C>A	chr4.hg19:g.186997921C>A	ENSP00000296795:p.Pro50Thr	81.0	0.0		87.0	30.0	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	hg19	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.158916	0.57368	.	.	ENSG00000164342	ENST00000296795;ENST00000513189;ENST00000542020	T;T	0.68479	-0.33;-0.33	5.47	5.47	0.80525	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87111	0.6096	M	0.93763	3.455	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.89884	0.4032	10	0.87932	D	0	.	19.6979	0.96034	0.0:1.0:0.0:0.0	.	50	O15455	TLR3_HUMAN	T	50	ENSP00000296795:P50T;ENSP00000423386:P50T	ENSP00000296795:P50T	P	+	1	0	TLR3	187234915	1.000000	0.71417	0.992000	0.48379	0.091000	0.18340	7.168000	0.77570	2.728000	0.93425	0.591000	0.81541	CCC	.	.		0.483	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			A	186997921	C	A	186997921	3	1	212	1	0	0	0	0	1	0	0	0	15967	507	18	3	150	3	TLR3	4	186997921	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	11417593	186997921	4156355	81	30551										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13718998	13718998	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tttctggactcaccactataTgttcttttcagtcctgcccg	6	13	4	0	rs141935657		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:13718998T>C	ENST00000265104.4	-	72	12596	c.12492A>G	c.(12490-12492)acA>acG	p.T4164T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4164	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CACCACTATATGTTCTTTTCA	0.403									Kartagener syndrome																												p.T4164T		Atlas-SNP	.											.	DNAH5	868	.	0			c.A12492G						.	T		1,4405	2.1+/-5.4	0,1,2202	100	102	101		12492	-9.5	0.3	5	dbSNP_134	101	0,8600		0,0,4300	no	coding-synonymous	DNAH5	NM_001369.2		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		4164/4625	13718998	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon72	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ACTATATGTTCTT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12492A>G	chr5.hg19:g.13718998T>C		65.0	0.0		85.0	30.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	hg19	CCDS3882.1																																																																																			.	T|1.000;C|0.000		0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13718998	T	C	13718998	2	2	212	1	0	0	0	0	0	0	0	1	4606	1451	51	2		2	DNAH5	5	13718998	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10		13718998	167196262	82	30552										
NPR3	4883	hgsc.bcm.edu	37	chr5	32739134	32739134	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aagggctcaatatggaggatTacgtaagtgcctgattatga	12	5	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:32739134T>A	ENST00000265074.8	+	3	1400	c.1057T>A	c.(1057-1059)Tac>Aac	p.Y353N	NPR3_ENST00000434067.2_Missense_Mutation_p.Y137N|NPR3_ENST00000415685.2_Missense_Mutation_p.Y137N|NPR3_ENST00000415167.2_Missense_Mutation_p.Y353N	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3	353					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	TATGGAGGATTACGTAAGTGC	0.418																																					p.Y353N		Atlas-SNP	.											.	NPR3	65	.	0			c.T1057A						.						107	105	105					5																	32739134		1895	4108	6003	SO:0001583	missense	4883	exon3			GAGGATTACGTAA		CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"guanylate cyclase C"	108962	"chromosome 5 open reading frame 23", "atrionatriuretic peptide receptor C", "natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)", "natriuretic peptide receptor C"	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.1057T>A	chr5.hg19:g.32739134T>A	ENSP00000265074:p.Tyr353Asn	43.0	0.0		58.0	16.0	NM_000908	A2RRD1|B4DT84|E7EPG9	Missense_Mutation	SNP	ENST00000265074.8	hg19	CCDS56357.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.345454	0.24426	.	.	ENSG00000113389	ENST00000509104;ENST00000434067;ENST00000415685;ENST00000265074;ENST00000415167	D;D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57	5.88	5.88	0.94601	Extracellular ligand-binding receptor (1);	0.157201	0.64402	D	0.000014	T	0.81108	0.4754	N	0.08118	0	0.52501	D	0.999953	B;B;B;D	0.89917	0.009;0.009;0.016;1.0	B;B;B;D	0.76575	0.01;0.01;0.007;0.988	T	0.78489	-0.2184	10	0.13108	T	0.6	-13.6443	16.2987	0.82793	0.0:0.0:0.0:1.0	.	137;137;353;353	E7EPG9;B4DT84;P17342;Q60I31	.;.;ANPRC_HUMAN;.	N	130;137;137;353;353	ENSP00000425325:Y130N;ENSP00000388408:Y137N;ENSP00000402490:Y137N;ENSP00000265074:Y353N;ENSP00000398028:Y353N	ENSP00000265074:Y353N	Y	+	1	0	NPR3	32774891	1.000000	0.71417	1.000000	0.80357	0.668000	0.39293	6.649000	0.74364	2.257000	0.74773	0.459000	0.35465	TAC	.	.		0.418	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908		A	32739134	T	A	32739134	3	1	212	1	0	0	0	0	1	0	0	0	10605	1754	61	4	1067	4	NPR3	5	32739134	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	19020136	32739134	148176126	83	30553										
RICTOR	253260	hgsc.bcm.edu	37	chr5	38945618	38945618	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgactacatattgcactcagTtggttgctgggctggaaacc	11	9	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:38945618T>A	ENST00000357387.3	-	34	4638	c.4608A>T	c.(4606-4608)caA>caT	p.Q1536H	RICTOR_ENST00000296782.5_Missense_Mutation_p.Q1560H	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					TTGCACTCAGTTGGTTGCTGG	0.388																																					p.Q1536H		Atlas-SNP	.											.	RICTOR	182	.	0			c.A4608T						.						130	119	123					5																	38945618		2203	4300	6503	SO:0001583	missense	253260	exon34			ACTCAGTTGGTTG		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.4608A>T	chr5.hg19:g.38945618T>A	ENSP00000349959:p.Gln1536His	64.0	0.0		89.0	27.0	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	T	14.53	2.562660	0.45694	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.48201	0.83;0.82	5.63	-0.663	0.11410	.	0.053669	0.85682	D	0.000000	T	0.31544	0.0800	N	0.11560	0.145	0.35712	D	0.816469	P;P	0.39624	0.545;0.681	P;P	0.45138	0.471;0.471	T	0.41980	-0.9478	10	0.87932	D	0	-14.4491	10.2569	0.43403	0.0:0.4372:0.0:0.5628	.	1536;1560	Q6R327;Q6R327-3	RICTR_HUMAN;.	H	1536;1560	ENSP00000349959:Q1536H;ENSP00000296782:Q1560H	ENSP00000296782:Q1560H	Q	-	3	2	RICTOR	38981375	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	0.626000	0.24492	-0.047000	0.13423	0.460000	0.39030	CAA	.	.		0.388	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		A	38945618	T	A	38945618	3	1	212	1	0	0	0	0	1	0	0	0	13373	1722	60	4	538	4	RICTOR	5	38945618	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	6206484	38945618	141969642	84	30554										
MAST4	375449	hgsc.bcm.edu	37	chr5	66396331	66396331	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	acaccagacgagttacacttCttatcaaaacatttctgtac	4	11	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:66396331C>A	ENST00000403625.2	+	8	1276	c.981C>A	c.(979-981)ttC>ttA	p.F327L	MAST4_ENST00000405643.1_Missense_Mutation_p.F148L|MAST4_ENST00000490016.2_Missense_Mutation_p.F138L|MAST4_ENST00000404260.3_Missense_Mutation_p.F330L|MAST4_ENST00000261569.7_Missense_Mutation_p.F133L|MAST4_ENST00000403666.1_Missense_Mutation_p.F138L	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	330						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AGTTACACTTCTTATCAAAAC	0.493																																					p.F327L		Atlas-SNP	.											.	MAST4	218	.	0			c.C981A						.						101	100	100					5																	66396331		2070	4212	6282	SO:0001583	missense	375449	exon8			ACACTTCTTATCA	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.981C>A	chr5.hg19:g.66396331C>A	ENSP00000385727:p.Phe327Leu	67.0	0.0		83.0	5.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.414818	0.62511	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000490016;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000436277;ENST00000432399	T;T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;1.61;1.61	6.07	3.78	0.43462	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.000000	0.64402	U	0.000003	T	0.53753	0.1816	M	0.85197	2.74	0.29344	N	0.865829	P;D;D;D;P	0.89917	0.592;1.0;0.999;0.971;0.685	P;D;D;P;B	0.79108	0.739;0.992;0.99;0.867;0.381	T	0.53528	-0.8426	10	0.56958	D	0.05	-13.8156	7.0967	0.25313	0.0:0.6378:0.0:0.3622	.	148;330;133;138;138	E7EWQ5;O15021;O15021-2;O15021-3;D6RAK1	.;MAST4_HUMAN;.;.;.	L	330;327;138;138;148;148;133;133;133	ENSP00000385048:F330L;ENSP00000385727:F327L;ENSP00000421739:F138L;ENSP00000384313:F138L;ENSP00000384099:F148L;ENSP00000261569:F133L;ENSP00000392478:F133L	ENSP00000261569:F133L	F	+	3	2	MAST4	66432087	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	1.530000	0.36007	1.415000	0.47037	0.655000	0.94253	TTC	.	.		0.493	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66396331	C	A	66396331	3	1	212	1	0	0	0	0	1	0	0	0	9336	912	32	3	1141	3	MAST4	5	66396331	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	27450713	66396331	114518929	85	30555										
HMGCR	3156	hgsc.bcm.edu	37	chr5	74650335	74650335	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tccatttctttagaaaggtgCaaaattccttagtgatgctg	8	7	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:74650335C>T	ENST00000287936.4	+	12	1532	c.1376C>T	c.(1375-1377)gCa>gTa	p.A459V	HMGCR_ENST00000343975.5_Missense_Mutation_p.A459V|HMGCR_ENST00000511206.1_Missense_Mutation_p.A459V	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	459	Catalytic.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	TAGAAAGGTGCAAAATTCCTT	0.373																																					p.A459V		Atlas-SNP	.											.	HMGCR	53	.	0			c.C1376T						.						72	65	67					5																	74650335		2203	4300	6503	SO:0001583	missense	3156	exon12			AAGGTGCAAAATT		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"hydroxymethylglutaryl-CoA reductase", "3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"	142910	"3-hydroxy-3-methylglutaryl-Coenzyme A reductase"				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.1376C>T	chr5.hg19:g.74650335C>T	ENSP00000287936:p.Ala459Val	46.0	0.0		77.0	10.0	NM_001130996	B7Z3Y9|Q8N190	Missense_Mutation	SNP	ENST00000287936.4	hg19	CCDS4027.1	.	.	.	.	.	.	.	.	.	.	C	31	5.088676	0.94100	.	.	ENSG00000113161	ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975	T;T;T	0.41758	0.99;0.99;0.99	5.14	5.14	0.70334	Hydroxymethylglutaryl-CoA reductase, N-terminal (1);Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding (1);	0.100150	0.64402	D	0.000002	T	0.53254	0.1785	L	0.42686	1.345	0.80722	D	1	B;D;B	0.58268	0.205;0.982;0.367	B;P;B	0.58970	0.034;0.849;0.034	T	0.41662	-0.9496	10	0.28530	T	0.3	-18.2885	18.978	0.92745	0.0:1.0:0.0:0.0	.	459;459;459	B2R649;P04035-2;P04035	.;.;HMDH_HUMAN	V	459;390;459;459	ENSP00000426745:A459V;ENSP00000287936:A459V;ENSP00000340816:A459V	ENSP00000287936:A459V	A	+	2	0	HMGCR	74686091	1.000000	0.71417	0.998000	0.56505	0.949000	0.60115	7.425000	0.80255	2.570000	0.86706	0.467000	0.42956	GCA	.	.		0.373	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			T	74650335	C	T	74650335	3	4	212	1	0	0	0	0	1	0	0	0	7240	710	25	3	1418	3	HMGCR	5	74650335	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	8254004	74650335	106264925	86	30556										
AP3B1	8546	hgsc.bcm.edu	37	chr5	77423969	77423969	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tatgagataaggtgccaagcTggaaatgatctctatctatt	9	6	2	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:77423969T>C	ENST00000255194.6	-	17	2028	c.1853A>G	c.(1852-1854)cAg>cGg	p.Q618R	AP3B1_ENST00000519295.1_Missense_Mutation_p.Q569R	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	618					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GGTGCCAAGCTGGAAATGATC	0.368									Hermansky-Pudlak syndrome																												p.Q618R		Atlas-SNP	.											.	AP3B1	94	.	0			c.A1853G						.						45	45	45					5																	77423969		2203	4300	6503	SO:0001583	missense	8546	exon17	Familial Cancer Database	HPS, HPS1-8	CCAAGCTGGAAAT	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1853A>G	chr5.hg19:g.77423969T>C	ENSP00000255194:p.Gln618Arg	33.0	0.0		76.0	29.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	T	12.78	2.039663	0.35989	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.57273	0.41;0.42	5.91	5.91	0.95273	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.60077	0.2241	M	0.82923	2.615	0.80722	D	1	B	0.24823	0.112	B	0.26864	0.074	T	0.60642	-0.7223	10	0.52906	T	0.07	-13.4045	16.3453	0.83126	0.0:0.0:0.0:1.0	.	618	O00203	AP3B1_HUMAN	R	618;569;618;522	ENSP00000255194:Q618R;ENSP00000430597:Q569R	ENSP00000255194:Q618R	Q	-	2	0	AP3B1	77459725	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.021000	0.88750	2.261000	0.74972	0.533000	0.62120	CAG	.	.		0.368	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			C	77423969	T	C	77423969	3	2	212	1	0	0	0	0	1	0	0	0	744	1580	55	2	1475	2	AP3B1	5	77423969	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	2773634	77423969	103491291	87	30557										
ERAP1	51752	hgsc.bcm.edu	37	chr5	96117490	96117490	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aaaactgatatttactataaAgaaaatcccagccttctgtg	5	8	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:96117490A>G	ENST00000443439.2	-	16	2420	c.2354T>C	c.(2353-2355)cTt>cCt	p.L785P	ERAP1_ENST00000296754.3_Missense_Mutation_p.L785P|ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000512856.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	785					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TTTACTATAAAGAAAATCCCA	0.453																																					p.L785P		Atlas-SNP	.											.	ERAP1	59	.	0			c.T2354C						.						80	86	84					5																	96117490		2203	4300	6503	SO:0001583	missense	51752	exon16			CTATAAAGAAAAT	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.2354T>C	chr5.hg19:g.96117490A>G	ENSP00000406304:p.Leu785Pro	47.0	0.0		65.0	14.0	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	hg19	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.703982	0.88924	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.09911	2.93;2.93	6.16	6.16	0.99307	.	0.063553	0.64402	D	0.000004	T	0.39462	0.1079	M	0.85542	2.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;1.0	T	0.32455	-0.9906	10	0.72032	D	0.01	.	16.4675	0.84087	1.0:0.0:0.0:0.0	.	785;785;785	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	P	785	ENSP00000296754:L785P;ENSP00000406304:L785P	ENSP00000296754:L785P	L	-	2	0	ERAP1	96143246	1.000000	0.71417	0.953000	0.39169	0.997000	0.91878	8.571000	0.90752	2.367000	0.80283	0.528000	0.53228	CTT	.	.		0.453	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		G	96117490	A	G	96117490	3	3	212	1	0	0	0	0	1	0	0	0	5205	72	3	2	520	2	ERAP1	5	96117490	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	18693521	96117490	84797770	88	30558										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140181280	140181280	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gcagatatcggaacaaattcGttgttgacttacagtcttga	9	7	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:140181280G>A	ENST00000522353.2	+	1	498	c.498G>A	c.(496-498)tcG>tcA	p.S166S	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000532566.2_Silent_p.S166S|PCDHA2_ENST00000520672.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	166	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAACAAATTCGTTGTTGACTT	0.398																																					p.S166S		Atlas-SNP	.											.	PCDHA3	396	.	0			c.G498A						.						76	81	79					5																	140181280		2203	4300	6503	SO:0001819	synonymous_variant	56145	exon1			AAATTCGTTGTTG	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.498G>A	chr5.hg19:g.140181280G>A		68.0	0.0		96.0	34.0	NM_031497	O75286	Silent	SNP	ENST00000522353.2	hg19	CCDS54915.1																																																																																			.	.		0.398	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		A	140181280	G	A	140181280	2	1	212	1	0	0	0	0	0	0	0	1	11534	1132	40	1		1	PCDHA3	5	140181280	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	44063790	140181280	40733980	89	30559										
MRPL22	29093	hgsc.bcm.edu	37	chr5	154330405	154330405	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttacctcaatcatatatccaCacaagtgcttctcttgacat	3	12	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:154330405C>G	ENST00000523037.1	+	3	143	c.102C>G	c.(100-102)caC>caG	p.H34Q	MRPL22_ENST00000522038.1_Missense_Mutation_p.H40Q|MRPL22_ENST00000265229.8_Intron|MRPL22_ENST00000439747.3_Missense_Mutation_p.H60Q	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	34					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CATATATCCACACAAGTGCTT	0.388																																					p.H34Q		Atlas-SNP	.											.	MRPL22	18	.	0			c.C102G						.						124	122	123					5																	154330405		2203	4300	6503	SO:0001583	missense	29093	exon3			TATCCACACAAGT	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"Mitochondrial ribosomal proteins / large subunits"	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.102C>G	chr5.hg19:g.154330405C>G	ENSP00000431040:p.His34Gln	44.0	0.0		67.0	5.0	NM_014180	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Missense_Mutation	SNP	ENST00000523037.1	hg19	CCDS4331.1	.	.	.	.	.	.	.	.	.	.	C	12.26	1.885539	0.33255	.	.	ENSG00000082515	ENST00000523037;ENST00000439747;ENST00000522038	T;T;T	0.55930	0.57;0.49;0.72	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.53948	0.1828	M	0.79693	2.465	0.58432	D	0.999994	B	0.28880	0.226	B	0.29524	0.103	T	0.60692	-0.7213	10	0.87932	D	0	-3.8561	9.6481	0.39881	0.0:0.9031:0.0:0.0969	.	34	Q9NWU5	RM22_HUMAN	Q	34;60;40	ENSP00000431040:H34Q;ENSP00000411177:H60Q;ENSP00000429039:H40Q	ENSP00000411177:H60Q	H	+	3	2	MRPL22	154310598	1.000000	0.71417	1.000000	0.80357	0.458000	0.32498	0.886000	0.28241	2.404000	0.81709	0.591000	0.81541	CAC	.	.		0.388	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2			G	154330405	C	G	154330405	3	3	212	1	0	0	0	0	1	0	0	0	9797	477	17	4	112	4	MRPL22	5	154330405	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	14149125	154330405	26584855	90	30560										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161128536	161128536	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aaatatcatctgaagaaaagGatcacttctctgtctttgcc	6	9	5	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:161128536G>T	ENST00000274545.5	+	9	1552	c.1119G>T	c.(1117-1119)agG>agT	p.R373S	GABRA6_ENST00000523217.1_Missense_Mutation_p.R363S			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	373					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TGAAGAAAAGGATCACTTCTC	0.398										TCGA Ovarian(5;0.080)																											p.R373S		Atlas-SNP	.											.	GABRA6	139	.	0			c.G1119T						.						107	112	110					5																	161128536		2203	4300	6503	SO:0001583	missense	2559	exon9			GAAAAGGATCACT		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.1119G>T	chr5.hg19:g.161128536G>T	ENSP00000274545:p.Arg373Ser	48.0	0.0		81.0	25.0	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	hg19	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.518012	0.44763	.	.	ENSG00000145863	ENST00000274545;ENST00000523217	D;D	0.83419	-1.72;-1.72	5.16	2.74	0.32292	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.377798	0.28057	N	0.016775	T	0.80984	0.4729	M	0.72894	2.215	0.36535	D	0.87093	P	0.38863	0.65	B	0.43155	0.41	T	0.76217	-0.3040	10	0.15499	T	0.54	.	9.2142	0.37337	0.8448:0.0:0.1552:0.0	.	373	Q16445	GBRA6_HUMAN	S	373;363	ENSP00000274545:R373S;ENSP00000430527:R363S	ENSP00000274545:R373S	R	+	3	2	GABRA6	161061114	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.021000	0.30040	0.363000	0.24346	-0.294000	0.09567	AGG	.	.		0.398	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			T	161128536	G	T	161128536	3	4	212	1	0	0	0	0	1	0	0	0	6173	1165	41	3	1153	3	GABRA6	5	161128536	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	6798131	161128536	19786724	91	30561										
CDHR2	54825	hgsc.bcm.edu	37	chr5	176018233	176018233	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	acaaccggaagcttcaagctAtgaaggctgccaaggaggcc	12	11	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:176018233A>G	ENST00000510636.1	+	29	3836	c.3562A>G	c.(3562-3564)Atg>Gtg	p.M1188V	CDHR2_ENST00000261944.5_Missense_Mutation_p.M1188V|CDHR2_ENST00000506348.1_Missense_Mutation_p.M1188V	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	1188					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						GCTTCAAGCTATGAAGGCTGC	0.602																																					p.M1188V		Atlas-SNP	.											.	CDHR2	152	.	0			c.A3562G						.						57	54	55					5																	176018233		2203	4300	6503	SO:0001583	missense	54825	exon29			CAAGCTATGAAGG	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.3562A>G	chr5.hg19:g.176018233A>G	ENSP00000424565:p.Met1188Val	97.0	0.0		91.0	22.0	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	hg19	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	a	0.022	-1.415332	0.01136	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.53423	0.62;0.62;0.62	4.24	0.564	0.17302	.	.	.	.	.	T	0.21509	0.0518	N	0.14661	0.345	0.23320	N	0.997911	B	0.02656	0.0	B	0.04013	0.001	T	0.28364	-1.0046	9	0.02654	T	1	-14.8133	4.6247	0.12472	0.5211:0.1673:0.3116:0.0	.	1188	Q9BYE9	CDHR2_HUMAN	V	1188	ENSP00000424565:M1188V;ENSP00000261944:M1188V;ENSP00000421078:M1188V	ENSP00000261944:M1188V	M	+	1	0	CDHR2	175950839	0.026000	0.19158	0.999000	0.59377	0.634000	0.38068	0.010000	0.13242	0.247000	0.21414	0.376000	0.23039	ATG	.	.		0.602	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		G	176018233	A	G	176018233	3	3	212	1	0	0	0	0	1	0	0	0	3121	449	16	2	3672	2	CDHR2	5	176018233	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	14889697	176018233	4897027	92	30562										
SLC34A1	6569	hgsc.bcm.edu	37	chr5	176813072	176813072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgagcacacctgcccctgtgGggaggtcctggagcgccatg	15	13	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr5:176813072G>A	ENST00000324417.5	+	3	285	c.194G>A	c.(193-195)gGg>gAg	p.G65E	SLC34A1_ENST00000512593.1_Missense_Mutation_p.G65E	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1	65					arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGCCCCTGTGGGGAGGTCCTG	0.687																																					p.G65E		Atlas-SNP	.											.	SLC34A1	73	.	0			c.G194A						.						34	37	36					5																	176813072		2203	4300	6503	SO:0001583	missense	6569	exon3			CCTGTGGGGAGGT	L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"Solute carriers"	11019	protein-coding gene	gene with protein product	"sodium/phosphate co-transporter", "solute carrier family 17 (sodium phosphate), member 2", "Na+-phosphate cotransporter type II"	182309	"solute carrier family 34 (sodium phosphate), member 1"	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.194G>A	chr5.hg19:g.176813072G>A	ENSP00000321424:p.Gly65Glu	107.0	0.0		100.0	8.0	NM_003052	B4DPE3	Missense_Mutation	SNP	ENST00000324417.5	hg19	CCDS4418.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.564823	0.27915	.	.	ENSG00000131183	ENST00000504577;ENST00000512593;ENST00000324417	T;T	0.56103	0.48;1.32	5.06	5.06	0.68205	.	0.159936	0.38217	N	0.001777	T	0.39809	0.1092	L	0.29908	0.895	0.20873	N	0.999839	D	0.53619	0.961	P	0.44597	0.454	T	0.28170	-1.0052	10	0.10111	T	0.7	-11.1428	12.541	0.56169	0.0:0.0:0.8342:0.1658	.	65	Q06495	NPT2A_HUMAN	E	65	ENSP00000423022:G65E;ENSP00000321424:G65E	ENSP00000321424:G65E	G	+	2	0	SLC34A1	176745678	1.000000	0.71417	0.995000	0.50966	0.246000	0.25737	3.316000	0.51960	2.642000	0.89623	0.561000	0.74099	GGG	.	.		0.687	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052		A	176813072	G	A	176813072	3	1	212	1	0	0	0	0	1	0	0	0	14582	1232	43	3	200	3	SLC34A1	5	176813072	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	794839	176813072	4102188	93	30563										
NUP153	9972	hgsc.bcm.edu	37	chr6	17675798	17675798	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	accactggtagttgagatgtTatcatcatcatgctgagagg	11	7	3	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:17675798T>G	ENST00000262077.2	-	3	537	c.538A>C	c.(538-540)Aac>Cac	p.N180H	NUP153_ENST00000537253.1_Missense_Mutation_p.N180H	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	180					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			GTTGAGATGTTATCATCATCA	0.383																																					p.N180H		Atlas-SNP	.											.	NUP153	116	.	0			c.A538C						.						79	76	77					6																	17675798		2203	4300	6503	SO:0001583	missense	9972	exon3			AGATGTTATCATC	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"nucleoporin 153kD"			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.538A>C	chr6.hg19:g.17675798T>G	ENSP00000262077:p.Asn180His	95.0	0.0		132.0	24.0	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	hg19	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.216511	0.79352	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.44881	0.91;0.91	5.37	5.37	0.77165	Nucleoporin, Nup153-like (1);	0.000000	0.56097	D	0.000021	T	0.56441	0.1985	M	0.72118	2.19	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.998	T	0.61950	-0.6957	10	0.62326	D	0.03	-14.39	15.3876	0.74714	0.0:0.0:0.0:1.0	.	180;202;180	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	H	180;202;180	ENSP00000262077:N180H;ENSP00000444029:N180H	ENSP00000262077:N180H	N	-	1	0	NUP153	17783777	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.622000	0.83099	2.041000	0.60428	0.528000	0.53228	AAC	.	.		0.383	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			G	17675798	T	G	17675798	3	3	212	1	0	0	0	0	1	0	0	0	10764	1754	61	5	3969	5	NUP153	6	17675798	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10		17675798	153439269	94	30564										
ETV7	51513	hgsc.bcm.edu	37	chr6	36334437	36334437	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gcccctcacggagagatttcTggcctcttgtccttgaactc	9	14	3	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:36334437T>A	ENST00000340181.4	-	8	1252	c.1011A>T	c.(1009-1011)ccA>ccT	p.P337P	ETV7_ENST00000339796.5_Intron|ETV7_ENST00000373738.1_Silent_p.P282P|ETV7_ENST00000373737.4_Silent_p.P260P|ETV7_ENST00000538992.1_Silent_p.P186P	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	337					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(4)	10						GAGAGATTTCTGGCCTCTTGT	0.597																																					p.P337P		Atlas-SNP	.											.	ETV7	31	.	0			c.A1011T						.						133	129	131					6																	36334437		2203	4300	6503	SO:0001819	synonymous_variant	51513	exon8			GATTTCTGGCCTC	AF116508	CCDS4819.1, CCDS56422.1, CCDS56423.1, CCDS56424.1, CCDS56425.1, CCDS75440.1, CCDS75441.1	6p21	2008-09-12	2008-09-12		ENSG00000010030	ENSG00000010030			18160	protein-coding gene	gene with protein product	"TEL2 oncogene"	605255	"ets variant gene 7 (TEL2 oncogene)"			10828014, 11108721	Standard	NM_016135		Approved	TEL2, TEL-2	uc003omb.3	Q9Y603	OTTHUMG00000014594	ENST00000340181.4:c.1011A>T	chr6.hg19:g.36334437T>A		61.0	0.0		76.0	20.0	NM_016135	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Silent	SNP	ENST00000340181.4	hg19	CCDS4819.1																																																																																			.	.		0.597	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135		A	36334437	T	A	36334437	2	1	212	1	0	0	0	0	0	0	0	1	5286	1567	55	4		4	ETV7	6	36334437	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	18658639	36334437	134780630	95	30565										
MEP1A	4224	hgsc.bcm.edu	37	chr6	46794122	46794122	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	actcttttggaccactgtacTtttgagaaggcaaacatctg	8	9	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:46794122T>C	ENST00000230588.4	+	9	819	c.810T>C	c.(808-810)acT>acC	p.T270T		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	270	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			ACCACTGTACTTTTGAGAAGG	0.423																																					p.T270T		Atlas-SNP	.											.	MEP1A	93	.	0			c.T810C						.						118	113	115					6																	46794122		2203	4300	6503	SO:0001819	synonymous_variant	4224	exon9			CTGTACTTTTGAG		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.810T>C	chr6.hg19:g.46794122T>C		50.0	0.0		92.0	33.0	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Silent	SNP	ENST00000230588.4	hg19	CCDS4918.1																																																																																			.	.		0.423	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		C	46794122	T	C	46794122	2	2	212	1	0	0	0	0	0	0	0	1	9484	1596	56	2		2	MEP1A	6	46794122	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	10459685	46794122	124320945	96	30566										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51889983	51889983	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	agtggggtcctggggccaagTctcttgtctggcacacaacg	14	11	2	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:51889983T>G	ENST00000371117.3	-	32	4900	c.4625A>C	c.(4624-4626)gAc>gCc	p.D1542A	PKHD1_ENST00000340994.4_Missense_Mutation_p.D1542A	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1542	IPT/TIG 10.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TGGGGCCAAGTCTCTTGTCTG	0.443																																					p.D1542A		Atlas-SNP	.											.	PKHD1	927	.	0			c.A4625C						.						60	61	60					6																	51889983		2203	4300	6503	SO:0001583	missense	5314	exon32			GCCAAGTCTCTTG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.4625A>C	chr6.hg19:g.51889983T>G	ENSP00000360158:p.Asp1542Ala	75.0	0.0		87.0	22.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	0.458	-0.890493	0.02491	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.74209	-0.82;-0.82	5.66	-2.59	0.06209	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.431689	0.25148	N	0.032762	T	0.51398	0.1672	M	0.64997	1.995	0.09310	N	1	B;P	0.44659	0.011;0.84	B;P	0.48334	0.041;0.574	T	0.62849	-0.6767	10	0.02654	T	1	.	12.8415	0.57805	0.0:0.4775:0.0:0.5225	.	1542;1542	P08F94-2;P08F94	.;PKHD1_HUMAN	A	1542	ENSP00000360158:D1542A;ENSP00000341097:D1542A	ENSP00000341097:D1542A	D	-	2	0	PKHD1	51997942	0.000000	0.05858	0.063000	0.19743	0.224000	0.24922	-0.035000	0.12205	-0.368000	0.08040	0.528000	0.53228	GAC	.	.		0.443	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51889983	T	G	51889983	3	3	212	1	0	0	0	0	1	0	0	0	11980	1667	58	5	7782	5	PKHD1	6	51889983	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	5095861	51889983	119225084	97	30567										
GSTA4	2941	hgsc.bcm.edu	37	chr6	52850272	52850272	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gttctctccttgaggttcttGccaaagagattgtgcttgtc	10	9	2	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:52850272G>T	ENST00000370959.1	-	4	366	c.249C>A	c.(247-249)ggC>ggA	p.G83G	GSTA4_ENST00000486559.1_5'UTR|GSTA4_ENST00000541324.1_Splice_Site|GSTA4_ENST00000370960.1_Intron			O15217	GSTA4_HUMAN	glutathione S-transferase alpha 4	83	GST N-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)|skin(2)|urinary_tract(1)	7	Lung NSC(77;0.103)				Glutathione(DB00143)	TGAGGTTCTTGCCAAAGAGAT	0.488																																					p.G83G		Atlas-SNP	.											.	GSTA4	20	.	0			c.C249A						.						190	152	165					6																	52850272		2203	4300	6503	SO:0001819	synonymous_variant	2941	exon4			GTTCTTGCCAAAG	AF020918	CCDS4948.1	6p12.2	2012-06-21	2008-11-26		ENSG00000170899	ENSG00000170899	2.5.1.18	"Glutathione S-transferases / Soluble"	4629	protein-coding gene	gene with protein product		605450	"glutathione S-transferase A4"			9480897	Standard	NM_001512		Approved		uc003pbf.3	O15217	OTTHUMG00000014868	ENST00000370959.1:c.249C>A	chr6.hg19:g.52850272G>T		97.0	0.0		118.0	28.0	NM_001512	B2RD15|Q5T7Q8|Q6P4G1|Q9BX18|Q9H414	Silent	SNP	ENST00000370959.1	hg19	CCDS4948.1																																																																																			.	.		0.488	GSTA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040946.1	NM_001512		T	52850272	G	T	52850272	2	4	212	1	0	0	0	0	0	0	0	1	6842	1306	46	3		3	GSTA4	6	52850272	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	960289	52850272	118264795	98	30568										
DST	667	hgsc.bcm.edu	37	chr6	56401645	56401645	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctccaagccctgagtgctagTgcttttggcagcactctgaa	10	12	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:56401645T>C	ENST00000361203.3	-	58	16076	c.16069A>G	c.(16069-16071)Act>Gct	p.T5357A	DST_ENST00000370769.4_Missense_Mutation_p.T5359A|DST_ENST00000312431.6_3'UTR|DST_ENST00000370754.5_Missense_Mutation_p.T5537A|DST_ENST00000244364.6_Missense_Mutation_p.T2945A|DST_ENST00000421834.2_Missense_Mutation_p.T3271A|DST_ENST00000370788.2_Missense_Mutation_p.T3271A|DST_ENST00000340834.4_5'UTR|DST_ENST00000446842.2_Missense_Mutation_p.T5033A			Q03001	DYST_HUMAN	dystonin	5357					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TGAGTGCTAGTGCTTTTGGCA	0.448																																					p.T2945A		Atlas-SNP	.											.	DST	1427	.	0			c.A8833G						.						150	149	149					6																	56401645		2022	4204	6226	SO:0001583	missense	667	exon43			TGCTAGTGCTTTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.16069A>G	chr6.hg19:g.56401645T>C	ENSP00000354508:p.Thr5357Ala	54.0	0.0		100.0	27.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	T	12.09	1.833360	0.32421	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.7	0.679	0.17975	.	0.390983	0.21571	N	0.072416	T	0.11580	0.0282	N	0.25201	0.72	0.25422	N	0.98827	B;B;B;B;B	0.19817	0.039;0.031;0.015;0.001;0.002	B;B;B;B;B	0.26969	0.036;0.075;0.02;0.009;0.008	T	0.22941	-1.0202	9	0.07813	T	0.8	.	9.827	0.40919	0.0:0.2452:0.0:0.7548	.	3271;5359;5537;5357;2945	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	A	2945;5537;5359;3271;5033;3271;5357	ENSP00000244364:T2945A;ENSP00000359790:T5537A;ENSP00000359805:T5359A;ENSP00000400883:T3271A;ENSP00000393645:T5033A;ENSP00000359824:T3271A;ENSP00000354508:T5357A	ENSP00000244364:T2945A	T	-	1	0	DST	56509604	0.814000	0.29104	0.513000	0.27749	0.972000	0.66771	0.270000	0.18607	0.133000	0.18654	0.477000	0.44152	ACT	.	.		0.448	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56401645	T	C	56401645	3	2	212	1	0	0	0	0	1	0	0	0	4785	1696	59	2	6850	2	DST	6	56401645	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	3551373	56401645	114713422	99	30569										
NT5E	4907	hgsc.bcm.edu	37	chr6	86194984	86194984	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tccaaagaggtgcctgctggGaagtacccattcatagtcac	10	11	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:86194984G>T	ENST00000257770.3	+	4	832	c.783G>T	c.(781-783)ggG>ggT	p.G261G	NT5E_ENST00000369651.3_Silent_p.G261G	NM_002526.3	NP_002517.1	P21589	5NTD_HUMAN	5'-nucleotidase, ecto (CD73)	261					adenosine biosynthetic process (GO:0046086)|AMP catabolic process (GO:0006196)|dephosphorylation (GO:0016311)|DNA metabolic process (GO:0006259)|negative regulation of inflammatory response (GO:0050728)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.G261G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Cytarabine(DB00987)|Pentoxifylline(DB00806)	TGCCTGCTGGGAAGTACCCAT	0.502																																					p.G261G	Melanoma(140;797 1765 2035 2752 18208)	Atlas-SNP	.											NT5E,rectum,carcinoma,0,1	NT5E	56	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G783T						.						102	87	92					6																	86194984		2203	4300	6503	SO:0001819	synonymous_variant	4907	exon4			TGCTGGGAAGTAC	X55740	CCDS5002.1, CCDS56439.1	6q14-q21	2013-08-28	2002-04-18	2002-04-19	ENSG00000135318	ENSG00000135318	3.1.3.5	"CD molecules"	8021	protein-coding gene	gene with protein product		129190	"5' nucleotidase (CD73)"	NT5			Standard	NM_002526		Approved	CD73, eN, eNT, CALJA	uc003pko.4	P21589	OTTHUMG00000015139	ENST00000257770.3:c.783G>T	chr6.hg19:g.86194984G>T		56.0	0.0		67.0	19.0	NM_001204813	B3KQI8|O75520|Q5W116	Silent	SNP	ENST00000257770.3	hg19	CCDS5002.1	.	.	.	.	.	.	.	.	.	.	G	9.172	1.021416	0.19433	.	.	ENSG00000135318	ENST00000416334	T	0.67523	-0.27	5.63	3.82	0.43975	.	0.000000	0.85682	D	0.000000	T	0.56441	0.1985	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67256	-0.5716	7	0.87932	D	0	-15.3447	2.3625	0.04310	0.1318:0.1432:0.4772:0.2478	.	.	.	.	V	26	ENSP00000414674:G26V	ENSP00000414674:G26V	G	+	2	0	NT5E	86251703	0.032000	0.19561	1.000000	0.80357	0.996000	0.88848	0.224000	0.17738	2.646000	0.89796	0.462000	0.41574	GGA	.	.		0.502	NT5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041388.1			T	86194984	G	T	86194984	2	4	212	1	0	0	0	0	0	0	0	1	10702	1161	41	3		3	NT5E	6	86194984	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	29793339	86194984	84920083	100	30570										
AKIRIN2	55122	hgsc.bcm.edu	37	chr6	88387595	88387595	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gaactttctcttcacgttctTtcaacaaacgttcacagatc	4	12	5	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:88387595T>G	ENST00000257787.5	-	3	994	c.470A>C	c.(469-471)aAa>aCa	p.K157T		NM_018064.3	NP_060534.1	Q53H80	AKIR2_HUMAN	akirin 2	157					embryo development (GO:0009790)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to lipopolysaccharide (GO:0032496)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)			large_intestine(4)	4						TTCACGTTCTTTCAACAAACG	0.388																																					p.K157T		Atlas-SNP	.											.	AKIRIN2	13	.	0			c.A470C						.						157	153	154					6																	88387595		2203	4300	6503	SO:0001583	missense	55122	exon3			CGTTCTTTCAACA	BC000764	CCDS5013.1	6q15	2009-04-17	2008-06-23	2008-06-23	ENSG00000135334	ENSG00000135334			21407	protein-coding gene	gene with protein product		615165	"chromosome 6 open reading frame 166"	C6orf166			Standard	NM_018064		Approved	FLJ10342, dJ486L4.2	uc003pmk.3	Q53H80	OTTHUMG00000015180	ENST00000257787.5:c.470A>C	chr6.hg19:g.88387595T>G	ENSP00000257787:p.Lys157Thr	52.0	0.0		86.0	29.0	NM_018064	Q9BQB1	Missense_Mutation	SNP	ENST00000257787.5	hg19	CCDS5013.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.439334	0.83885	.	.	ENSG00000135334	ENST00000257787	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.70605	0.3243	M	0.90425	3.115	0.80722	D	1	P	0.51537	0.946	P	0.48840	0.592	T	0.79172	-0.1913	9	0.87932	D	0	-17.9963	16.5764	0.84681	0.0:0.0:0.0:1.0	.	157	Q53H80	AKIR2_HUMAN	T	157	.	ENSP00000257787:K157T	K	-	2	0	AKIRIN2	88444314	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.926000	0.70070	2.371000	0.80710	0.533000	0.62120	AAA	.	.		0.388	AKIRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041455.1	NM_018064		G	88387595	T	G	88387595	3	3	212	1	0	0	0	0	1	0	0	0	462	1841	64	5	153	5	AKIRIN2	6	88387595	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	2192611	88387595	82727472	101	30571										
CCNC	892	hgsc.bcm.edu	37	chr6	100016396	100016396	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gggagctctgccaaaagttcCctgccatggaacacagcttg	11	12	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:100016396C>T	ENST00000520429.1	-	1	453	c.8G>A	c.(7-9)gGg>gAg	p.G3E	CCNC_ENST00000520371.1_Missense_Mutation_p.G3E|CCNC_ENST00000369220.4_Missense_Mutation_p.G3E|CCNC_ENST00000523985.1_5'UTR|RP1-199J3.7_ENST00000607332.1_RNA|CCNC_ENST00000521017.1_5'UTR|CCNC_ENST00000482541.2_Missense_Mutation_p.G3E|CCNC_ENST00000523799.1_Intron|CCNC_ENST00000518714.1_Missense_Mutation_p.G3E	NM_001013399.1|NM_005190.3	NP_001013417.1|NP_005181.2	P24863	CCNC_HUMAN	cyclin C	3					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|mediator complex (GO:0016592)|nucleoplasm (GO:0005654)							all_cancers(76;8.46e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.064)		CCAAAAGTTCCCTGCCATGGA	0.632																																					p.G3E	GBM(57;273 1020 40094 44454 49348)	Atlas-SNP	.											.	CCNC	23	.	0			c.G8A						.						55	54	54					6																	100016396		2203	4300	6503	SO:0001583	missense	892	exon1			AAGTTCCCTGCCA		CCDS34502.1, CCDS47461.1	6q21	2008-02-05			ENSG00000112237	ENSG00000112237			1581	protein-coding gene	gene with protein product		123838				1833066	Standard	XM_005267202		Approved	CycC	uc003pqe.3	P24863	OTTHUMG00000015268	ENST00000520429.1:c.8G>A	chr6.hg19:g.100016396C>T	ENSP00000428982:p.Gly3Glu	77.0	0.0		72.0	7.0	NM_005190	B4DPZ1|Q9H543	Missense_Mutation	SNP	ENST00000520429.1	hg19	CCDS34502.1	.	.	.	.	.	.	.	.	.	.	C	36	5.728326	0.96856	.	.	ENSG00000112237	ENST00000520429;ENST00000369220;ENST00000520371;ENST00000518714;ENST00000369217;ENST00000482541	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	5.25	5.25	0.73442	Cyclin-like (1);	0.000000	0.85682	D	0.000000	T	0.35335	0.0928	M	0.82630	2.6	0.80722	D	1	D;D;D	0.64830	0.988;0.994;0.988	P;P;P	0.54026	0.575;0.74;0.575	T	0.14172	-1.0482	9	.	.	.	-7.1502	18.3691	0.90401	0.0:1.0:0.0:0.0	.	3;36;3	Q7Z4L3;Q05CF7;P24863	.;.;CCNC_HUMAN	E	3	ENSP00000428982:G3E;ENSP00000358222:G3E;ENSP00000430381:G3E;ENSP00000430294:G3E	.	G	-	2	0	CCNC	100123117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.627000	0.74258	2.885000	0.99019	0.655000	0.94253	GGG	.	.		0.632	CCNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041613.2	NM_005190		T	100016396	C	T	100016396	3	4	212	1	0	0	0	0	1	0	0	0	2917	623	22	3	891	3	CCNC	6	100016396	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	11628801	100016396	71098671	102	30572										
AKD1	221264	hgsc.bcm.edu	37	chr6	109863371	109863371	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttctgtaagttgtacttctgGaagctaaaaacaaaaatcag	7	6	3	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:109863371G>T	ENST00000424296.2	-	27	3305	c.3229C>A	c.(3229-3231)Cca>Aca	p.P1077T	AK9_ENST00000355283.1_Missense_Mutation_p.P156T|AK9_ENST00000341338.6_Missense_Mutation_p.P156T	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1077	Adenylate kinase 2.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TGTACTTCTGGAAGCTAAAAA	0.333																																					p.P1077T		Atlas-SNP	.											.	AKD1	223	.	0			c.C3229A						.						67	61	63					6																	109863371		2202	4299	6501	SO:0001583	missense	221264	exon27			CTTCTGGAAGCTA	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"chromosome 6 open reading frame 224", "adenylate kinase domain containing 2", "chromosome 6 open reading frame 199", "adenylate kinase domain containing 1"	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.3229C>A	chr6.hg19:g.109863371G>T	ENSP00000410186:p.Pro1077Thr	50.0	0.0		98.0	29.0	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	hg19	CCDS55048.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.945|9.945	1.218611|1.218611	0.22373|0.22373	.|.	.|.	ENSG00000155085|ENSG00000155085	ENST00000491875|ENST00000424296;ENST00000355283;ENST00000341338	.|T;T;T	.|0.64085	.|0.0;-0.02;-0.08	5.3|5.3	1.01|1.01	0.19927|0.19927	.|ATPase, AAA+ type, core (1);	.|0.843243	.|0.10495	.|N	.|0.667922	T|T	0.22166|0.22166	0.0534|0.0534	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|B;B	.|0.31503	.|0.257;0.326	.|B;B	.|0.29077	.|0.098;0.096	T|T	0.12451|0.12451	-1.0547|-1.0547	5|9	.|.	.|.	.|.	.|.	4.6042|4.6042	0.12368|0.12368	0.078:0.2052:0.5163:0.2006|0.078:0.2052:0.5163:0.2006	.|.	.|156;1077	.|Q5TCS8-5;Q5TCS8	.|.;AKD1_HUMAN	L|T	11|1077;156;156	.|ENSP00000410186:P1077T;ENSP00000347431:P156T;ENSP00000344637:P156T	.|.	F|P	-|-	3|1	2|0	AKD1|AKD1	109970064|109970064	0.004000|0.004000	0.15560|0.15560	0.009000|0.009000	0.14445|0.14445	0.544000|0.544000	0.35116|0.35116	-0.091000|-0.091000	0.11146|0.11146	0.260000|0.260000	0.21731|0.21731	0.650000|0.650000	0.86243|0.86243	TTC|CCA	.	.		0.333	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		T	109863371	G	T	109863371	3	4	212	1	0	0	0	0	1	0	0	0	460	1174	41	3	2566	3	AKD1	6	109863371	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	9846975	109863371	61251696	103	30573										
TAAR2	9287	hgsc.bcm.edu	37	chr6	132938564	132938564	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cactattcctaaagttttggCagcttttttgtctttcttca	5	9	3	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:132938564C>A	ENST00000367931.1	-	2	780	c.781G>T	c.(781-783)Gcc>Tcc	p.A261S	TAAR2_ENST00000275191.2_Missense_Mutation_p.A216S|TAAR2_ENST00000537809.1_Missense_Mutation_p.A216S			Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2	261					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)	23	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		AAAGTTTTGGCAGCTTTTTTG	0.328																																					p.A261S		Atlas-SNP	.											.	TAAR2	45	.	0			c.G781T						.						58	47	51					6																	132938564		2203	4300	6503	SO:0001583	missense	9287	exon2			TTTTGGCAGCTTT	AF112460	CCDS34541.1, CCDS5157.1	6q24	2012-08-08	2005-02-23	2005-02-24	ENSG00000146378	ENSG00000146378		"GPCR / Class A : Trace amine associated receptors"	4514	protein-coding gene	gene with protein product		604849	"G protein-coupled receptor 58"	GPR58		10684976, 15718104	Standard	NM_014626		Approved		uc003qdl.1	Q9P1P5	OTTHUMG00000015585	ENST00000367931.1:c.781G>T	chr6.hg19:g.132938564C>A	ENSP00000356908:p.Ala261Ser	92.0	0.0		152.0	46.0	NM_001033080	Q5QD02|Q6NWS1|Q6NWS2|Q6NWS3	Missense_Mutation	SNP	ENST00000367931.1	hg19	CCDS34541.1	.	.	.	.	.	.	.	.	.	.	C	19.11	3.764113	0.69878	.	.	ENSG00000146378	ENST00000275191;ENST00000367931;ENST00000537809	T;T;T	0.74315	-0.83;-0.83;-0.83	6.1	6.1	0.99115	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.86045	0.5839	M	0.78637	2.42	0.47862	D	0.999539	D	0.89917	1.0	D	0.91635	0.999	D	0.85690	0.1306	10	0.72032	D	0.01	-31.153	20.7146	0.99709	0.0:1.0:0.0:0.0	.	261	Q9P1P5	TAAR2_HUMAN	S	216;261;216	ENSP00000275191:A216S;ENSP00000356908:A261S;ENSP00000441263:A216S	ENSP00000275191:A216S	A	-	1	0	TAAR2	132980257	0.956000	0.32656	1.000000	0.80357	0.949000	0.60115	2.128000	0.42045	2.902000	0.99343	0.650000	0.86243	GCC	.	.		0.328	TAAR2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390735.1	NM_014626		A	132938564	C	A	132938564	3	1	212	1	0	0	0	0	1	0	0	0	15505	710	25	3	278	3	TAAR2	6	132938564	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	23075193	132938564	38176503	104	30574										
HBS1L	10767	hgsc.bcm.edu	37	chr6	135357985	135357985	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tagtcagagagcctttgttgTttttcttattatccttagca	7	7	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:135357985T>G	ENST00000367837.5	-	4	637				HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.N537T|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000415177.2_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		GCCTTTGTTGTTTTTCTTATT	0.428																																					p.N537T		Atlas-SNP	.											.	HBS1L	75	.	0			c.A1610C						.						50	43	45					6																	135357985		692	1591	2283	SO:0001627	intron_variant	10767	exon5			TTGTTGTTTTTCT	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"eRF3 family member"	612450	"HBS1 (S. cerevisiae)-like", "HBS1-like (S. cerevisiae)"			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2725A>C	chr6.hg19:g.135357985T>G		53.0	0.0		99.0	26.0	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	hg19	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.685830	0.00738	.	.	ENSG00000112339	ENST00000367822	.	.	.	5.32	-5.91	0.02269	.	.	.	.	.	T	0.09335	0.0230	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.17228	-1.0376	7	0.08599	T	0.76	.	6.5883	0.22632	0.0889:0.2843:0.4983:0.1284	.	537	Q9Y450-2	.	T	537	.	ENSP00000356796:N537T	N	-	2	0	HBS1L	135399678	0.028000	0.19301	0.170000	0.22879	0.885000	0.51271	-1.150000	0.03178	-0.990000	0.03481	0.533000	0.62120	AAC	.	.		0.428	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			G	135357985	T	G	135357985	1	3	212	0	1	0	0	0	0	0	0	0	6996	1725	60	5		5	HBS1L	6	135357985	Intron	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	2419421	135357985	35757082	105	30575										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138584345	138584345	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gtcccttaccctgacataacTaacttcctgtcagtagactg	6	13	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:138584345T>C	ENST00000251691.4	+	12	1891	c.1725T>C	c.(1723-1725)acT>acC	p.T575T		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CTGACATAACTAACTTCCTGT	0.488																																					p.T575T		Atlas-SNP	.											.	KIAA1244	236	.	0			c.T1725C						.						112	103	106					6																	138584345		2203	4300	6503	SO:0001819	synonymous_variant	57221	exon12			CATAACTAACTTC	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.1725T>C	chr6.hg19:g.138584345T>C		84.0	0.0		75.0	30.0	NM_020340		Silent	SNP	ENST00000251691.4	hg19	CCDS5189.2																																																																																			.	.		0.488	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		C	138584345	T	C	138584345	2	2	212	1	0	0	0	0	0	0	0	1	8226	1509	53	2		2	KIAA1244	6	138584345	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	3226360	138584345	32530722	106	30576										
UTRN	7402	hgsc.bcm.edu	37	chr6	144869853	144869874	+	Frame_Shift_Del	DEL	ATTTCAATTCCTGCTGATCTTG	ATTTCAATTCCTGCTGATCTTG	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	agtctcatcgtacttcggaaAtttcaattcctgctgatctt					rs116515472	byFrequency	TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	ATTTCAATTCCTGCTGATCTTG	ATTTCAATTCCTGCTGATCTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:144869853_144869874delATTTCAATTCCTGCTGATCTTG	ENST00000367545.3	+	46	6673_6694	c.6673_6694delATTTCAATTCCTGCTGATCTTG	c.(6673-6696)atttcaattcctgctgatcttgatfs	p.ISIPADLD2225fs		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2225					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TACTTCGGAAATTTCAATTCCTGCTGATCTTGATAAAACTAT	0.401																																					p.2224_2231del		Atlas-INDEL	.											.	UTRN	327	.	0			c.6672_6693del						.																																			SO:0001589	frameshift_variant	7402	exon46			.	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.6673_6694delATTTCAATTCCTGCTGATCTTG	chr6.hg19:g.144869853_144869874delATTTCAATTCCTGCTGATCTTG	ENSP00000356515:p.Ile2225fs	73.0	0.0		102.0	12.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Frame_Shift_Del	DEL	ENST00000367545.3	hg19	CCDS34547.1																																																																																			.	.		0.401	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			-	144869874	ATTTCAATTCCTGCTGATCTTG	-	144869853	7	5	212	1	0	1	0	1	0	0	0	0	17118	101	4	0	6855	0	UTRN	6	144869853	Frame_Shift_Del	DEL	ATTTCAATTCCTGCTGATCTTG	TCGA-DD-AAE7-01A-11D-A40R-10	6285508	144869853	26245214	107	30577										
THBS2	7058	hgsc.bcm.edu	37	chr6	169650830	169650830	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggctctgaggacactcacctTgcgtgctgggccacacccac	11	16	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr6:169650830T>G	ENST00000366787.3	-	3	299	c.50A>C	c.(49-51)cAa>cCa	p.Q17P		NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	17					cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		ACACTCACCTTGCGTGCTGGG	0.547																																					p.Q17P	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.A50C						.						57	48	51					6																	169650830		2203	4300	6503	SO:0001583	missense	7058	exon3			TCACCTTGCGTGC		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.50A>C	chr6.hg19:g.169650830T>G	ENSP00000355751:p.Gln17Pro	77.0	0.0		125.0	38.0	NM_003247	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	hg19	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.557613	0.27827	.	.	ENSG00000186340	ENST00000366787;ENST00000435791	T	0.80994	-1.44	4.85	-0.542	0.11854	.	0.635159	0.12737	U	0.443334	T	0.51924	0.1703	L	0.53249	1.67	0.09310	N	1	B	0.29508	0.246	B	0.25405	0.06	T	0.48445	-0.9035	10	0.87932	D	0	-11.7346	2.2793	0.04110	0.1699:0.0923:0.1345:0.6032	.	17	P35442	TSP2_HUMAN	P	17	ENSP00000355751:Q17P	ENSP00000355751:Q17P	Q	-	2	0	THBS2	169392755	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-1.696000	0.01912	-0.241000	0.09681	0.533000	0.62120	CAA	.	.		0.547	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		G	169650830	T	G	169650830	3	3	212	1	0	0	0	0	1	0	0	0	15869	1812	63	5	3552	5	THBS2	6	169650830	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	24780977	169650830	1464237	108	30578										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18687484	18687484	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgttcctctgcctgggcagtAtggaggcagcatcccggcat	13	12	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr7:18687484A>G	ENST00000432645.2	+	9	1103	c.1103A>G	c.(1102-1104)tAt>tGt	p.Y368C	HDAC9_ENST00000406451.4_Missense_Mutation_p.Y368C|HDAC9_ENST00000524023.1_Missense_Mutation_p.Y291C|HDAC9_ENST00000456174.2_Missense_Mutation_p.Y340C|HDAC9_ENST00000441542.2_Missense_Mutation_p.Y371C|HDAC9_ENST00000417496.2_Missense_Mutation_p.Y366C|HDAC9_ENST00000406072.1_Missense_Mutation_p.Y355C|HDAC9_ENST00000428307.2_Missense_Mutation_p.Y324C|HDAC9_ENST00000401921.1_Missense_Mutation_p.Y327C|HDAC9_ENST00000405010.3_Missense_Mutation_p.Y368C	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	368					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	CCTGGGCAGTATGGAGGCAGC	0.502																																					p.Y371C		Atlas-SNP	.											.	HDAC9	560	.	0			c.A1112G						.						38	40	40					7																	18687484		2074	4219	6293	SO:0001583	missense	9734	exon9			GGCAGTATGGAGG	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1103A>G	chr7.hg19:g.18687484A>G	ENSP00000410337:p.Tyr368Cys	73.0	0.0		106.0	37.0	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	hg19	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	A	13.76	2.333428	0.41297	.	.	ENSG00000048052	ENST00000417496;ENST00000262069;ENST00000405010;ENST00000406451;ENST00000428307;ENST00000406072;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000456174;ENST00000524023;ENST00000341009	T;T;T;T;T;T;T;T;T;T	0.57907	0.92;0.94;0.37;0.93;0.93;0.37;0.37;0.37;0.94;0.93	5.64	5.64	0.86602	.	0.000000	0.51477	D	0.000097	T	0.67401	0.2889	L	0.51422	1.61	0.43211	D	0.995078	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.76494	0.997;0.975;0.999;0.985;0.999;0.998;0.986;0.999;0.998;0.979;0.975;0.998;0.985;0.999	P;P;D;P;P;D;P;D;D;P;P;D;P;P	0.81914	0.778;0.594;0.937;0.731;0.867;0.929;0.733;0.995;0.911;0.613;0.647;0.911;0.77;0.894	T	0.68085	-0.5502	10	0.51188	T	0.08	-21.3907	15.8344	0.78787	1.0:0.0:0.0:0.0	.	291;340;368;355;366;368;371;327;371;368;340;368;368;346	E7EX34;C9JS87;Q9UKV0-4;B5MCF1;B7Z917;Q9UKV0-2;Q68D71;Q9UKV0-6;Q9UKV0-7;Q9UKV0;B7Z928;Q9UKV0-5;Q9UKV0-3;Q8N879	.;.;.;.;.;.;.;.;.;HDAC9_HUMAN;.;.;.;.	C	366;369;368;368;324;355;327;368;371;340;291;368	ENSP00000401669:Y366C;ENSP00000384382:Y368C;ENSP00000384657:Y368C;ENSP00000395655:Y324C;ENSP00000384017:Y355C;ENSP00000383912:Y327C;ENSP00000410337:Y368C;ENSP00000408617:Y371C;ENSP00000388568:Y340C;ENSP00000430036:Y291C	ENSP00000262069:Y369C	Y	+	2	0	HDAC9	18654009	1.000000	0.71417	0.995000	0.50966	0.358000	0.29455	6.778000	0.75043	2.153000	0.67306	0.477000	0.44152	TAT	.	.		0.502	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			G	18687484	A	G	18687484	3	3	212	1	0	0	0	0	1	0	0	0	7023	449	16	2	1146	2	HDAC9	7	18687484	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10		18687484	140451179	109	30579										
STK31	56164	hgsc.bcm.edu	37	chr7	23776654	23776654	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cgctcttcttgaaagttataAggcgttagaattgaaagtag	10	5	2	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr7:23776654A>G	ENST00000355870.3	+	8	1093	c.974A>G	c.(973-975)aAg>aGg	p.K325R	STK31_ENST00000354639.3_Missense_Mutation_p.K302R|STK31_ENST00000428484.1_Missense_Mutation_p.K302R|STK31_ENST00000405627.3_3'UTR|STK31_ENST00000433467.2_Missense_Mutation_p.K325R	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	325						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GAAAGTTATAAGGCGTTAGAA	0.418																																					p.K325R		Atlas-SNP	.											.	STK31	175	.	0			c.A974G						.						64	67	66					7																	23776654		2203	4300	6503	SO:0001583	missense	56164	exon8			GTTATAAGGCGTT	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.974A>G	chr7.hg19:g.23776654A>G	ENSP00000348132:p.Lys325Arg	29.0	0.0		29.0	10.0	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	hg19	CCDS5386.1	.	.	.	.	.	.	.	.	.	.	a	8.921	0.960994	0.18583	.	.	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	5.7	4.54	0.55810	.	0.224235	0.45606	D	0.000346	T	0.26412	0.0645	M	0.62723	1.935	0.22639	N	0.998906	B;B	0.15473	0.013;0.013	B;B	0.12156	0.007;0.007	T	0.15206	-1.0445	10	0.33141	T	0.24	-9.8787	11.0951	0.48139	0.8447:0.1553:0.0:0.0	.	325;325	B4DZ06;Q9BXU1	.;STK31_HUMAN	R	325;325;302;302	ENSP00000348132:K325R;ENSP00000411852:K325R;ENSP00000346660:K302R;ENSP00000406146:K302R	ENSP00000346660:K302R	K	+	2	0	STK31	23743179	0.491000	0.26019	0.467000	0.27180	0.059000	0.15707	1.982000	0.40638	1.080000	0.41073	0.491000	0.48974	AAG	.	.		0.418	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		G	23776654	A	G	23776654	3	3	212	1	0	0	0	0	1	0	0	0	15311	72	3	2	1004	2	STK31	7	23776654	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	5089170	23776654	135362009	110	30580										
ZNF679	168417	hgsc.bcm.edu	37	chr7	63720639	63720639	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgtagtcatagaattctctcTggaggagtggcaatgcctgg	13	7	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr7:63720639T>A	ENST00000421025.1	+	3	349	c.80T>A	c.(79-81)cTg>cAg	p.L27Q	ZNF679_ENST00000255746.4_Missense_Mutation_p.L27Q	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	27	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						GAATTCTCTCTGGAGGAGTGG	0.408																																					p.L27Q		Atlas-SNP	.											.	ZNF679	80	.	0			c.T80A						.						60	53	55					7																	63720639		692	1591	2283	SO:0001583	missense	168417	exon3			TCTCTCTGGAGGA	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"Zinc fingers, C2H2-type", "-"	28650	protein-coding gene	gene with protein product	"hypothetical protein MGC42415"					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.80T>A	chr7.hg19:g.63720639T>A	ENSP00000416809:p.Leu27Gln	109.0	0.0		168.0	50.0	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	hg19	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	t	3.653	-0.071042	0.07228	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.01379	4.96;4.96	0.195	0.195	0.15151	Krueppel-associated box (4);	.	.	.	.	T	0.01254	0.0041	N	0.03930	-0.32	0.09310	N	0.999996	D	0.62365	0.991	P	0.62298	0.9	T	0.48479	-0.9032	9	0.12430	T	0.62	.	2.3209	0.04211	0.4746:1.0E-4:1.0E-4:0.5253	.	27	Q8IYX0	ZN679_HUMAN	Q	27	ENSP00000416809:L27Q;ENSP00000255746:L27Q	ENSP00000255746:L27Q	L	+	2	0	ZNF679	63358074	0.000000	0.05858	0.035000	0.18076	0.035000	0.12851	-2.012000	0.01451	0.257000	0.21650	0.254000	0.18369	CTG	.	.		0.408	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		A	63720639	T	A	63720639	3	1	212	1	0	0	0	0	1	0	0	0	18101	1580	55	4	86	4	ZNF679	7	63720639	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	39943985	63720639	95418024	111	30581										
HGF	3082	hgsc.bcm.edu	37	chr7	81350161	81350197	+	Splice_Site	DEL	AATCTAGACATAAAATATACAGAAATAAGTCCAATGA	AATCTAGACATAAAATATACAGAAATAAGTCCAATGA	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tttgccattcccacgataacAatctagacataaaatataca					rs151068465		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	AATCTAGACATAAAATATACAGAAATAAGTCCAATGA	AATCTAGACATAAAATATACAGAAATAAGTCCAATGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr7:81350161_81350197delAATCTAGACATAAAATATACAGAAATAAGTCCAATGA	ENST00000222390.5	-	10	1395_1397	c.1169_1171delTCATTGGACTTATTTCTGTATATTTTATGTCTAGATT	c.(1168-1173)gtcatt>gtt	p.I391fs	HGF_ENST00000457544.2_Splice_Site_p.I386fs	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	391	Kringle 4. {ECO:0000255|PROSITE- ProRule:PRU00121}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)	p.D390E(1)		NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						CCACGATAACAATCTAGACATAAAATATACAGAAATAAGTCCAATGAATATCAAGGC	0.35																																					p.390_391del		Atlas-INDEL	.											HGF,colon,carcinoma,0,1	HGF	171	.	1	Substitution - Missense(1)	endometrium(1)	c.1169_1172del						.																																			SO:0001630	splice_region_variant	3082	exon10			.		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.1169-1TCATTGGACTTATTTCTGTATATTTTATGTCTAGATT>-	chr7.hg19:g.81350161_81350197delAATCTAGACATAAAATATACAGAAATAAGTCCAATGA		44.0	0.0		76.0	18.0	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Frame_Shift_Del	DEL	ENST00000222390.5	hg19	CCDS5597.1																																																																																			.	.		0.35	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601	Frame_Shift_Del	-	81350197	AATCTAGACATAAAATATACAGAAATAAGTCCAATGA	-	81350161	8	5	212	1	0	1	0	1	0	0	1	0	7094	130	5	0	1051	0	HGF	7	81350161	Splice_Site	DEL	AATCTAGACATAAAATATACAGAAATAAGTCCAATGA	TCGA-DD-AAE7-01A-11D-A40R-10	17629522	81350161	77788502	112	30582										
ARPC1B	10095	hgsc.bcm.edu	37	chr7	98985732	98985732	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cgcaacgcctacgtgtggacGctgaagggccgcacatggaa	14	12	0	1	rs373569413		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr7:98985732G>A	ENST00000451682.1	+	6	549	c.240G>A	c.(238-240)acG>acA	p.T80T	ARPC1A_ENST00000432884.2_3'UTR|ARPC1B_ENST00000252725.5_Silent_p.T80T|ARPC1B_ENST00000474880.1_3'UTR			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	80					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			ACGTGTGGACGCTGAAGGGCC	0.652													G|||	1	0.000199681	0	0	5008	,	,		17516	0		0	False		,,,				2504	0.001				p.T80T		Atlas-SNP	.											.	ARPC1B	41	.	0			c.G240A						.	G		0,4406		0,0,2203	69	68	68		240	-9.2	0.7	7		68	1,8599		0,1,4299	no	coding-synonymous	ARPC1B	NM_005720.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		80/373	98985732	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10095	exon4			GTGGACGCTGAAG	AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"Actin related protein 2/3 complex subunits", "WD repeat domain containing"	704	protein-coding gene	gene with protein product	"ARP2/3 protein complex subunit p41", "actin related protein 2/3 complex, subunit 1A (41 kD)"	604223	"actin related protein 2/3 complex, subunit 1B (41 kD)"			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.240G>A	chr7.hg19:g.98985732G>A		161.0	0.0		146.0	44.0	NM_005720	Q9BU00	Silent	SNP	ENST00000451682.1	hg19	CCDS5661.1																																																																																			.	.		0.652	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720		A	98985732	G	A	98985732	2	1	212	1	0	0	0	0	0	0	0	1	970	1074	38	1		1	ARPC1B	7	98985732	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	17635571	98985732	60152931	113	30583										
AGFG2	3268	hgsc.bcm.edu	37	chr7	100148104	100148104	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tcctcagaaagtgaaggagtTtctccaggaaaaatatgaga	10	6	2	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr7:100148104T>C	ENST00000300176.4	+	3	523	c.401T>C	c.(400-402)tTt>tCt	p.F134S	AGFG2_ENST00000474713.1_3'UTR|AGFG2_ENST00000262935.4_Missense_Mutation_p.F134S	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	134	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GTGAAGGAGTTTCTCCAGGAA	0.423																																					p.F134S		Atlas-SNP	.											.	AGFG2	44	.	0			c.T401C						.						105	106	105					7																	100148104		2203	4300	6503	SO:0001583	missense	3268	exon3			AGGAGTTTCTCCA	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"ADP-ribosylation factor GTPase activating proteins"	5177	protein-coding gene	gene with protein product		604019	"HIV-1 Rev binding protein-like"	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.401T>C	chr7.hg19:g.100148104T>C	ENSP00000300176:p.Phe134Ser	57.0	0.0		70.0	19.0	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	hg19	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.038637	0.93630	.	.	ENSG00000106351	ENST00000300176;ENST00000262935	T;T	0.49432	0.78;0.78	6.14	6.14	0.99180	.	0.000000	0.85682	D	0.000000	T	0.74481	0.3722	M	0.89904	3.07	0.47214	D	0.99935	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.80070	-0.1536	10	0.87932	D	0	-20.6581	14.758	0.69583	0.0:0.0:0.0:1.0	.	134;134	O95081-2;O95081	.;AGFG2_HUMAN	S	134	ENSP00000300176:F134S;ENSP00000262935:F134S	ENSP00000262935:F134S	F	+	2	0	AGFG2	99986040	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.338000	0.79269	2.367000	0.80283	0.529000	0.55759	TTT	.	.		0.423	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076		C	100148104	T	C	100148104	3	2	212	1	0	0	0	0	1	0	0	0	381	1841	64	2	411	2	AGFG2	7	100148104	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	1162372	100148104	58990559	114	30584										
CALU	813	hgsc.bcm.edu	37	chr7	128394594	128394594	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gtcttgtagaatgattgtagAtaaaatagacgcggataaag	11	3	1	4			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr7:128394594A>G	ENST00000249364.4	+	3	517				CALU_ENST00000479257.1_Intron|CALU_ENST00000535623.1_3'UTR|CALU_ENST00000449187.2_Missense_Mutation_p.D78G|CALU_ENST00000538546.1_Intron|CALU_ENST00000542996.2_Missense_Mutation_p.D86G|CALU_ENST00000535011.2_Intron	NM_001219.4	NP_001210.1	O43852	CALU_HUMAN	calumenin						blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)			kidney(2)|large_intestine(3)|lung(5)	10						ATGATTGTAGATAAAATAGAC	0.438																																					p.D86G		Atlas-SNP	.											.	CALU	42	.	0			c.A257G						.						86	75	78					7																	128394594		692	1591	2283	SO:0001627	intron_variant	813	exon4			TTGTAGATAAAAT	AF013759	CCDS5805.1, CCDS47703.1, CCDS56506.1, CCDS56507.1, CCDS56508.1	7q32	2013-01-10			ENSG00000128595	ENSG00000128595		"EF-hand domain containing"	1458	protein-coding gene	gene with protein product		603420				9598325	Standard	NM_001219		Approved		uc003vnq.3	O43852	OTTHUMG00000158274	ENST00000249364.4:c.415+85A>G	chr7.hg19:g.128394594A>G		133.0	0.0		190.0	56.0	NM_001199672	B3KPG9|D6QS48|D6QS49|D6QS50|D6QS51|D6QS52|D6QS53|D6QS54|D6QS55|D6QS56|D6QS57|D6QS58|D6QS59|F5H1Q9|F5H879|O60456|Q6FHB9|Q96RL3|Q9NR43	Missense_Mutation	SNP	ENST00000249364.4	hg19	CCDS5805.1	.	.	.	.	.	.	.	.	.	.	A	14.98	2.697472	0.48202	.	.	ENSG00000128595	ENST00000542996;ENST00000537667;ENST00000537014;ENST00000449187	T;T	0.72725	-0.68;-0.68	5.96	5.96	0.96718	.	.	.	.	.	T	0.62183	0.2407	L	0.48260	1.515	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.58999	-0.7536	9	0.40728	T	0.16	.	8.8469	0.35174	0.9175:0.0:0.0825:0.0	.	86	D6QS48	.	G	86;78;78;78	ENSP00000438248:D86G;ENSP00000408838:D78G	ENSP00000408838:D78G	D	+	2	0	CALU	128181830	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.848000	0.55903	2.280000	0.76307	0.533000	0.62120	GAT	.	.		0.438	CALU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350533.1	NM_001219		G	128394594	A	G	128394594	1	3	212	0	1	0	0	0	0	0	0	0	2596	333	12	2		2	CALU	7	128394594	Intron	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	28246490	128394594	30744069	115	30585										
C8orf41	80185	hgsc.bcm.edu	37	chr8	33361357	33361357	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggtcaggatcagccgcaggaCctcatcacaatgggtggtgg	15	10	4	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr8:33361357C>A	ENST00000431156.2	-	5	1642	c.1024G>T	c.(1024-1026)Gtc>Ttc	p.V342F	TTI2_ENST00000360742.5_Missense_Mutation_p.V342F|TTI2_ENST00000519356.1_5'UTR|TTI2_ENST00000520636.1_Missense_Mutation_p.V311F	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	342																	AGCCGCAGGACCTCATCACAA	0.572																																					p.V342F		Atlas-SNP	.											.	.	.	.	0			c.G1024T						.						79	66	71					8																	33361357		2203	4300	6503	SO:0001583	missense	80185	exon5			GCAGGACCTCATC	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1024G>T	chr8.hg19:g.33361357C>A	ENSP00000411169:p.Val342Phe	58.0	0.0		45.0	17.0	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.654169	0.67472	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636	T;T;T	0.80123	-1.34;-1.34;-1.34	5.06	5.06	0.68205	.	0.000000	0.64402	D	0.000004	D	0.87474	0.6186	M	0.72894	2.215	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.70016	0.959;0.967	D	0.88060	0.2793	10	0.72032	D	0.01	-21.1261	11.6635	0.51361	0.0:0.9186:0.0:0.0814	.	342;311	Q6NXR4;E5RIH5	TTI2_HUMAN;.	F	342;342;342;311	ENSP00000353971:V342F;ENSP00000411169:V342F;ENSP00000428401:V311F	ENSP00000353971:V342F	V	-	1	0	C8orf41	33480899	1.000000	0.71417	0.960000	0.40013	0.763000	0.43281	3.565000	0.53798	2.629000	0.89072	0.650000	0.86243	GTC	.	.		0.572	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		A	33361357	C	A	33361357	3	1	212	1	0	0	0	0	1	0	0	0	2429	507	18	3	518	3	C8orf41	8	33361357	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10		33361357	113002665	116	30586										
UNC5D	137970	hgsc.bcm.edu	37	chr8	35579903	35579903	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cagaccttcaacttcaaaacAgtccgtcaaggtcagcggca	8	13	4	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr8:35579903A>T	ENST00000404895.2	+	9	1621	c.1293A>T	c.(1291-1293)acA>acT	p.T431T	UNC5D_ENST00000420357.1_Silent_p.T364T|UNC5D_ENST00000449677.1_5'Flank|UNC5D_ENST00000416672.1_Silent_p.T436T|UNC5D_ENST00000453357.2_Silent_p.T426T|UNC5D_ENST00000287272.2_Intron	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	431					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		ACTTCAAAACAGTCCGTCAAG	0.547																																					p.T431T		Atlas-SNP	.											.	UNC5D	393	.	0			c.A1293T						.						183	153	163					8																	35579903		2203	4300	6503	SO:0001819	synonymous_variant	137970	exon9			CAAAACAGTCCGT	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.1293A>T	chr8.hg19:g.35579903A>T		68.0	0.0		41.0	7.0	NM_080872	Q8WYP7	Silent	SNP	ENST00000404895.2	hg19	CCDS6093.2																																																																																			.	.		0.547	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			T	35579903	A	T	35579903	2	4	212	1	0	0	0	0	0	0	0	1	17010	175	7	4		4	UNC5D	8	35579903	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	2218546	35579903	110784119	117	30587										
IMPA1	3612	hgsc.bcm.edu	37	chr8	82598039	82598046	+	Intron	DEL	CTGTTTCT	CTGTTTCT	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aacacctgaactgtttcctgCtgtttctgtcctggtcacag							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	CTGTTTCT	CTGTTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr8:82598039_82598046delCTGTTTCT	ENST00000256108.5	-	1	442				IMPA1_ENST00000449740.2_Frame_Shift_Del_p.ETA36fs|IMPA1_ENST00000311489.4_Intron|IMPA1_ENST00000523710.1_Intron	NM_005536.3	NP_005527.1	P29218	IMPA1_HUMAN	inositol(myo)-1(or 4)-monophosphatase 1						inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|inositol monophosphate phosphatase activity (GO:0052834)|lithium ion binding (GO:0031403)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|stomach(1)	18					Lithium(DB01356)	CTGTTTCCTGCTGTTTCTGTCCTGGTCA	0.51																																					p.36_38del		Atlas-INDEL	.											.	IMPA1	46	.	0			c.106_113del						.																																			SO:0001627	intron_variant	3612	exon2			.		CCDS6231.1, CCDS47883.1, CCDS47884.1	8q21.1-q21.3	2008-01-28			ENSG00000133731	ENSG00000133731	3.1.3.25		6050	protein-coding gene	gene with protein product		602064		IMPA		1377913	Standard	NM_005536		Approved		uc011lfq.1	P29218	OTTHUMG00000164682	ENST00000256108.5:c.23+440AGAAACAG>-	chr8.hg19:g.82598039_82598046delCTGTTTCT		186.0	0.0		224.0	59.0	NM_001144878	B2R733|B4DLN3|B7Z6Q4|J3KQT7|Q9UK71	Frame_Shift_Del	DEL	ENST00000256108.5	hg19	CCDS6231.1																																																																																			.	.		0.51	IMPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379723.1			-	82598046	CTGTTTCT	-	82598039	6	5	212	0	1	1	0	1	0	0	0	0	7731	797	28	0		0	IMPA1	8	82598039	Intron	DEL	CTGTTTCT	TCGA-DD-AAE7-01A-11D-A40R-10	47018136	82598039	63765983	118	30588										
INTS8	55656	hgsc.bcm.edu	37	chr8	95884163	95884163	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atcacagtgaaagagctagtTcgatatacactcagtataaa	7	7	2	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr8:95884163T>G	ENST00000523731.1	+	21	2599	c.2466T>G	c.(2464-2466)gtT>gtG	p.V822V	INTS8_ENST00000447247.1_Silent_p.V822V	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	822					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					AAGAGCTAGTTCGATATACAC	0.348																																					p.V822V		Atlas-SNP	.											.	INTS8	92	.	0			c.T2466G						.						117	110	112					8																	95884163		2203	4300	6503	SO:0001819	synonymous_variant	55656	exon21			GCTAGTTCGATAT	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2466T>G	chr8.hg19:g.95884163T>G		42.0	0.0		75.0	25.0	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Silent	SNP	ENST00000523731.1	hg19	CCDS34925.1	.	.	.	.	.	.	.	.	.	.	T	9.708	1.156277	0.21454	.	.	ENSG00000164941	ENST00000520526	.	.	.	5.57	1.82	0.25136	.	.	.	.	.	T	0.51210	0.1661	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35251	-0.9796	4	.	.	.	-14.866	4.7485	0.13049	0.0:0.3583:0.1647:0.4771	.	.	.	.	C	644	.	.	F	+	2	0	INTS8	95953339	0.996000	0.38824	0.965000	0.40720	0.969000	0.65631	0.305000	0.19254	0.134000	0.18681	0.482000	0.46254	TTC	.	.		0.348	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		G	95884163	T	G	95884163	2	3	212	1	0	0	0	0	0	0	0	1	7793	1770	62	5		5	INTS8	8	95884163	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	13286124	95884163	50479859	119	30589										
ZNF706	51123	hgsc.bcm.edu	37	chr8	102213861	102213861	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gacagtgcaggtatatattaAggcagctttggcagcagcct	12	8	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr8:102213861A>C	ENST00000520347.1	-	2	3065	c.109T>G	c.(109-111)Tta>Gta	p.L37V	ZNF706_ENST00000521272.1_Missense_Mutation_p.L37V|ZNF706_ENST00000519744.1_Missense_Mutation_p.L37V|ZNF706_ENST00000519882.1_Missense_Mutation_p.L37V|ZNF706_ENST00000518336.1_Missense_Mutation_p.L37V|ZNF706_ENST00000517844.1_Missense_Mutation_p.L37V|ZNF706_ENST00000520984.1_Missense_Mutation_p.L37V|ZNF706_ENST00000311212.4_Missense_Mutation_p.L37V			Q9Y5V0	ZN706_HUMAN	zinc finger protein 706	37							metal ion binding (GO:0046872)			large_intestine(1)|ovary(2)	3	all_cancers(14;3.3e-07)|all_epithelial(15;3.47e-09)|Lung NSC(17;3.44e-05)|all_lung(17;0.000117)		Epithelial(11;8.57e-11)|all cancers(13;1.43e-08)|OV - Ovarian serous cystadenocarcinoma(57;1.43e-05)			GTATATATTAAGGCAGCTTTG	0.413																																					p.L37V		Atlas-SNP	.											.	ZNF706	12	.	0			c.T109G						.						138	130	133					8																	102213861		2203	4300	6503	SO:0001583	missense	51123	exon3			ATATTAAGGCAGC	AF125099	CCDS6291.1	8q22.3	2005-09-22				ENSG00000120963			24992	protein-coding gene	gene with protein product						11042152	Standard	NM_001042510		Approved	HSPC038	uc031tbv.1	Q9Y5V0		ENST00000520347.1:c.109T>G	chr8.hg19:g.102213861A>C	ENSP00000430823:p.Leu37Val	59.0	0.0		60.0	10.0	NM_001042510	A8K362	Missense_Mutation	SNP	ENST00000520347.1	hg19	CCDS6291.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.770884	0.49680	.	.	ENSG00000120963	ENST00000520984;ENST00000311212;ENST00000519744;ENST00000517844;ENST00000519103;ENST00000520347;ENST00000519882;ENST00000521272;ENST00000518336;ENST00000523922	.	.	.	5.14	3.99	0.46301	.	0.000000	0.85682	D	0.000000	T	0.69342	0.3100	.	.	.	0.58432	D	0.999995	P	0.51057	0.941	P	0.60415	0.874	T	0.70185	-0.4941	8	0.87932	D	0	.	8.0412	0.30523	0.8442:0.0:0.1558:0.0	.	37	Q9Y5V0	ZN706_HUMAN	V	37;37;37;37;9;37;37;37;37;37	.	ENSP00000311768:L37V	L	-	1	2	ZNF706	102283037	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.415000	0.44635	0.820000	0.34516	0.533000	0.62120	TTA	.	.		0.413	ZNF706-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380477.1	NM_016096		C	102213861	A	C	102213861	3	2	212	1	0	0	0	0	1	0	0	0	18125	69	3	5	129	5	ZNF706	8	102213861	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	6329698	102213861	44150161	120	30590										
ATP6V1C1	528	hgsc.bcm.edu	37	chr8	104065039	104065039	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggaaatcttcagaatttggaAcgaaagaatgcgtaagcaga	11	5	2	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr8:104065039A>G	ENST00000395862.3	+	6	621	c.462A>G	c.(460-462)gaA>gaG	p.E154E	ATP6V1C1_ENST00000518738.1_Silent_p.E154E|ATP6V1C1_ENST00000518857.1_Silent_p.E79E|ATP6V1C1_ENST00000521514.1_Silent_p.E79E	NM_001695.4	NP_001686.1	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1	154					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)			AGAATTTGGAACGAAAGAATG	0.368																																					p.E154E		Atlas-SNP	.											.	ATP6V1C1	33	.	0			c.A462G						.						85	88	87					8																	104065039		2203	4299	6502	SO:0001819	synonymous_variant	528	exon6			TTTGGAACGAAAG	X69151	CCDS6296.1	8p22.3	2011-05-24	2006-01-13	2002-05-10	ENSG00000155097	ENSG00000155097	3.6.3.14	"ATPases / V-type"	856	protein-coding gene	gene with protein product		603097	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) 42kD", "ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1"	ATP6D, ATP6C		8250920, 14580332	Standard	NM_001695		Approved	VATC, Vma5	uc003ykz.4	P21283	OTTHUMG00000164761	ENST00000395862.3:c.462A>G	chr8.hg19:g.104065039A>G		39.0	0.0		65.0	17.0	NM_001695		Silent	SNP	ENST00000395862.3	hg19	CCDS6296.1																																																																																			.	.		0.368	ATP6V1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380101.1	NM_001695		G	104065039	A	G	104065039	2	3	212	1	0	0	0	0	0	0	0	1	1180	40	2	2		2	ATP6V1C1	8	104065039	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	1851178	104065039	42298983	121	30591										
KLHL38	340359	hgsc.bcm.edu	37	chr8	124664885	124664885	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gtggcaatatgtgcctccccCgtatacacgtaggagacgat	11	11	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr8:124664885C>T	ENST00000325995.7	-	1	305	c.282G>A	c.(280-282)acG>acA	p.T94T	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	94	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						GTGCCTCCCCCGTATACACGT	0.567																																					p.T94T		Atlas-SNP	.											.	KLHL38	81	.	0			c.G282A						.						67	75	72					8																	124664885		2051	4184	6235	SO:0001819	synonymous_variant	340359	exon1			CTCCCCCGTATAC		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"Kelch-like", "BTB/POZ domain containing"	34435	protein-coding gene	gene with protein product			"kelch-like 38 (Drosophila)"				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.282G>A	chr8.hg19:g.124664885C>T		82.0	0.0		108.0	29.0	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	hg19	CCDS43766.1																																																																																			.	.		0.567	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1			T	124664885	C	T	124664885	2	4	212	1	0	0	0	0	0	0	0	1	8399	639	23	1		1	KLHL38	8	124664885	Silent	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	20599846	124664885	21699137	122	30592										
ZNF7	7553	hgsc.bcm.edu	37	chr8	146068016	146068016	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgtggaaaagccttcagtcaGagttccagccttatttacca	8	10	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr8:146068016G>C	ENST00000528372.1	+	5	1764	c.1524G>C	c.(1522-1524)caG>caC	p.Q508H	ZNF7_ENST00000325241.6_Missense_Mutation_p.Q508H|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Missense_Mutation_p.Q412H|ZNF7_ENST00000446747.2_Missense_Mutation_p.Q519H			P17097	ZNF7_HUMAN	zinc finger protein 7	508					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		CCTTCAGTCAGAGTTCCAGCC	0.463																																					p.Q508H		Atlas-SNP	.											.	ZNF7	62	.	0			c.G1524C						.						71	72	72					8																	146068016		2203	4300	6503	SO:0001583	missense	7553	exon5			CAGTCAGAGTTCC	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.1524G>C	chr8.hg19:g.146068016G>C	ENSP00000432724:p.Gln508His	49.0	0.0		127.0	63.0	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Missense_Mutation	SNP	ENST00000528372.1	hg19	CCDS6435.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.270072	0.40194	.	.	ENSG00000147789	ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	4.93	3.09	0.35607	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44688	D	0.000437	T	0.14700	0.0355	N	0.04805	-0.155	0.22127	N	0.999345	P;P	0.46784	0.884;0.884	B;B	0.39531	0.302;0.302	T	0.06954	-1.0798	9	.	.	.	-23.7472	6.5309	0.22326	0.1611:0.1542:0.6847:0.0	.	519;508	B4DT08;P17097	.;ZNF7_HUMAN	H	508;519;412;508	ENSP00000320627:Q508H;ENSP00000393260:Q519H;ENSP00000439424:Q412H;ENSP00000432724:Q508H	.	Q	+	3	2	ZNF7	146038820	0.000000	0.05858	0.998000	0.56505	0.880000	0.50808	-6.504000	0.00063	1.294000	0.44707	0.655000	0.94253	CAG	.	.		0.463	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		C	146068016	G	C	146068016	3	2	212	1	0	0	0	0	1	0	0	0	18117	933	33	4	1538	4	ZNF7	8	146068016	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	21403131	146068016	296006	123	30593										
JAK2	3717	hgsc.bcm.edu	37	chr9	5081813	5081813	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gcctttgaagaccgggatccTacacagtttgaagagagaca	11	9	0	5	rs112584696		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr9:5081813T>G	ENST00000381652.3	+	19	3017	c.2523T>G	c.(2521-2523)ccT>ccG	p.P841P	JAK2_ENST00000539801.1_Silent_p.P841P|JAK2_ENST00000544510.1_Silent_p.P692P|AL161450.1_ENST00000601793.1_Intron	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	841					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ACCGGGATCCTACACAGTTTG	0.348		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.P841P		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.T2523G						.						110	109	110					9																	5081813		2203	4300	6503	SO:0001819	synonymous_variant	3717	exon19	Familial Cancer Database		GGATCCTACACAG		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.2523T>G	chr9.hg19:g.5081813T>G		76.0	0.0		132.0	7.0	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	hg19	CCDS6457.1																																																																																			.	T|0.500;C|0.500		0.348	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			G	5081813	T	G	5081813	2	3	212	1	0	0	0	0	0	0	0	1	7947	1509	53	5		5	JAK2	9	5081813	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10		5081813	136131618	124	30594										
LOC645961	645961	hgsc.bcm.edu	37	chr9	90746809	90746809	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gcttgcactttattctgcgaCgcagggcaagctactccagt	10	12	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr9:90746809C>T								U6 (133559 upstream) : U3 (242374 downstream)																							TATTCTGCGACGCAGGGCAAG	0.512																																					p.A381A		Atlas-SNP	.											.	.	.	.	0			c.G1143A						.						8	8	8					9																	90746809		683	1579	2262	SO:0001628	intergenic_variant	645961	exon4			CTGCGACGCAGGG																													chr9.hg19:g.90746809C>T		67.0	0.0		75.0	20.0	NM_001166137		Silent	SNP		hg19																																																																																				.	.	0	0.512									T	90746809	C	T	90746809	1	4	212	0	1	0	0	0	0	0	0	0	8892	523	19	1		1	LOC645961	9	90746809	IGR	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	85664996	90746809	50466622	125	30595										
ZNF510	22869	hgsc.bcm.edu	37	chr9	99521444	99521447	+	Frame_Shift_Del	DEL	TTTT	TTTT	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgatgttgaatgagatgatcTtttcgccagaaggatttttc							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	TTTT	TTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr9:99521444_99521447delTTTT	ENST00000375231.1	-	6	2315_2318	c.1665_1668delAAAA	c.(1663-1668)cgaaaafs	p.RK555fs	ZNF510_ENST00000223428.4_Frame_Shift_Del_p.RK555fs			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	555					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				TGAGATGATCTTTTCGCCAGAAGG	0.417																																					p.556_557del		Atlas-INDEL	.											.	ZNF510	59	.	0			c.1666_1669del						.																																			SO:0001589	frameshift_variant	22869	exon6			.	AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"Zinc fingers, C2H2-type", "-"	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.1665_1668delAAAA	chr9.hg19:g.99521444_99521447delTTTT	ENSP00000364379:p.Arg555fs	78.0	0.0		88.0	19.0	NM_014930	Q5SZP5	Frame_Shift_Del	DEL	ENST00000375231.1	hg19	CCDS35074.1																																																																																			.	.		0.417	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930		-	99521447	TTTT	-	99521444	7	5	212	1	0	1	0	1	0	0	0	0	17969	1606	56	0	387	0	ZNF510	9	99521444	Frame_Shift_Del	DEL	TTTT	TCGA-DD-AAE7-01A-11D-A40R-10	8774635	99521444	41691987	126	30596										
FIBCD1	84929	hgsc.bcm.edu	37	chr9	133799206	133799206	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tagtgggtgggaaagacagaGtagacgccatcgtcctgctg	15	8	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr9:133799206G>A	ENST00000372338.4	-	4	1016	c.774C>T	c.(772-774)taC>taT	p.Y258Y	FIBCD1_ENST00000448616.1_Silent_p.Y258Y|FIBCD1_ENST00000372337.2_Silent_p.Y100Y|FIBCD1_ENST00000253018.4_Silent_p.Y100Y	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	258	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		GAAAGACAGAGTAGACGCCAT	0.687																																					p.Y258Y		Atlas-SNP	.											.	FIBCD1	34	.	0			c.C774T						.						90	77	81					9																	133799206		2203	4300	6503	SO:0001819	synonymous_variant	84929	exon5			GACAGAGTAGACG	AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"Fibrinogen C domain containing"	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.774C>T	chr9.hg19:g.133799206G>A		116.0	0.0		127.0	47.0	NM_001145106	A3KFK0|Q6UXK6|Q96SJ7	Silent	SNP	ENST00000372338.4	hg19	CCDS6937.1	.	.	.	.	.	.	.	.	.	.	G	1.723	-0.496026	0.04291	.	.	ENSG00000130720	ENST00000444139	.	.	.	5.54	3.36	0.38483	.	.	.	.	.	T	0.59729	0.2215	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57112	-0.7867	4	.	.	.	.	9.9519	0.41645	0.2416:0.0:0.7584:0.0	.	.	.	.	I	212	.	.	T	-	2	0	FIBCD1	132789027	1.000000	0.71417	0.982000	0.44146	0.051000	0.14879	3.382000	0.52463	1.334000	0.45468	0.462000	0.41574	ACT	.	.		0.687	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843		A	133799206	G	A	133799206	2	1	212	1	0	0	0	0	0	0	0	1	5892	1024	36	3		3	FIBCD1	9	133799206	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	34277762	133799206	7414225	127	30597										
COMMD3	23412	hgsc.bcm.edu	37	chr10	22605353	22605353	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	acggcgcgctcacaatggagCtctcggagtctgtgcagaaa	13	11	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr10:22605353C>T	ENST00000376836.3	+	1	451	c.7C>T	c.(7-9)Ctc>Ttc	p.L3F	COMMD3-BMI1_ENST00000602390.1_Missense_Mutation_p.L3F	NM_012071.3	NP_036203.1	Q9UBI1	COMD3_HUMAN	COMM domain containing 3	3										kidney(2)|lung(2)|ovary(1)	5						CACAATGGAGCTCTCGGAGTC	0.677																																					p.L3F		Atlas-SNP	.											.	.	.	.	0			c.C7T						.						56	36	43					10																	22605353		2099	4129	6228	SO:0001583	missense	0	exon1			ATGGAGCTCTCGG	AY542159	CCDS7137.1	10p12.2	2012-09-20	2004-02-13	2004-02-18	ENSG00000148444	ENSG00000148444			23332	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 8"	C10orf8		11042152, 15799966	Standard	NM_012071		Approved	BUP		Q9UBI1	OTTHUMG00000017806	ENST00000376836.3:c.7C>T	chr10.hg19:g.22605353C>T	ENSP00000366032:p.Leu3Phe	94.0	0.0		76.0	28.0	NM_001204062	D3DRU7|Q5T8Y9	Missense_Mutation	SNP	ENST00000376836.3	hg19	CCDS7137.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.99|17.99	3.522332|3.522332	0.64747|0.64747	.|.	.|.	ENSG00000148444|ENSG00000148444	ENST00000456711;ENST00000444869|ENST00000376836;ENST00000376776;ENST00000376787	.|T	.|0.64438	.|-0.1	4.78|4.78	2.92|2.92	0.33932|0.33932	.|.	.|0.083658	.|0.47852	.|N	.|0.000214	T|T	0.74688|0.74688	0.3749|0.3749	M|M	0.72118|0.72118	2.19|2.19	0.47245|0.47245	D|D	0.999361|0.999361	.|B;D	.|0.71674	.|0.037;0.998	.|B;D	.|0.78314	.|0.042;0.991	T|T	0.75323|0.75323	-0.3358|-0.3358	5|10	.|0.72032	.|D	.|0.01	-21.1052|-21.1052	10.1234|10.1234	0.42634|0.42634	0.0:0.8331:0.0:0.1669|0.0:0.8331:0.0:0.1669	.|.	.|3;3	.|Q9UBI1;E9PC68	.|COMD3_HUMAN;.	V|F	3;2|3	.|ENSP00000366032:L3F	.|ENSP00000365968:L3F	A|L	+|+	2|1	0|0	COMMD3|COMMD3	22645359|22645359	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	3.513000|3.513000	0.53414|0.53414	0.737000|0.737000	0.32582|0.32582	-0.140000|-0.140000	0.14226|0.14226	GCT|CTC	.	.		0.677	COMMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047159.1	NM_012071		T	22605353	C	T	22605353	3	4	212	1	0	0	0	0	1	0	0	0	3719	797	28	3	9	3	COMMD3	10	22605353	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10		22605353	112929394	128	30598										
AGAP6	414189	hgsc.bcm.edu	37	chr10	51768608	51768608	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cccactgccaacacacccacGcccgtttgcaagcggtccat	7	19	0	0	rs373725135	byFrequency	TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr10:51768608G>C	ENST00000374056.4	+	7	1052	c.654G>C	c.(652-654)acG>acC	p.T218T	AGAP6_ENST00000412531.3_Silent_p.T241T			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	218					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.T241T(2)		NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						ACACACCCACGCCCGTTTGCA	0.542													.|||	15	0.00299521	0.0061	0	5008	,	,		18332	0.002		0.001	False		,,,				2504	0.0041				p.T241T		Atlas-SNP	.											AGAP6,NS,carcinoma,0,2	AGAP6	53	.	2	Substitution - coding silent(2)	endometrium(2)	c.G723C						.																																			SO:0001819	synonymous_variant	414189	exon8			ACCCACGCCCGTT		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	23466	protein-coding gene	gene with protein product			"centaurin, gamma-like family, member 3"	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.654G>C	chr10.hg19:g.51768608G>C		48.0	1.0		45.0	3.0	NM_001077665		Silent	SNP	ENST00000374056.4	hg19																																																																																				.	G|0.500;C|0.500		0.542	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665		C	51768608	G	C	51768608	2	2	212	1	0	0	0	0	0	0	0	1	372	1074	38	4		4	AGAP6	10	51768608	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	29163255	51768608	83766139	129	30599										
PHYHIPL	84457	hgsc.bcm.edu	37	chr10	60996312	60996312	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tccgtggacactggtttttaAgcccaagaactgaatataca	8	9	0	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr10:60996312A>G	ENST00000373880.4	+	3	637	c.373A>G	c.(373-375)Agc>Ggc	p.S125G	PHYHIPL_ENST00000373878.3_Missense_Mutation_p.S99G|PHYHIPL_ENST00000472199.1_3'UTR	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	125	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(3)|skin(1)|urinary_tract(1)	18						CTGGTTTTTAAGCCCAAGAAC	0.418																																					p.S125G		Atlas-SNP	.											.	PHYHIPL	44	.	0			c.A373G						.						115	105	109					10																	60996312		2203	4300	6503	SO:0001583	missense	84457	exon3			TTTTTAAGCCCAA	AL834339	CCDS7254.1, CCDS44405.1	10q21.1	2013-02-11	2006-01-09		ENSG00000165443	ENSG00000165443		"Fibronectin type III domain containing"	29378	protein-coding gene	gene with protein product			"phytanoyl-CoA hydroxylase interacting protein-like"			11347906	Standard	NM_032439		Approved	KIAA1796, Em:AC025038.1	uc001jkk.4	Q96FC7	OTTHUMG00000018276	ENST00000373880.4:c.373A>G	chr10.hg19:g.60996312A>G	ENSP00000362987:p.Ser125Gly	61.0	0.0		84.0	30.0	NM_032439	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Missense_Mutation	SNP	ENST00000373880.4	hg19	CCDS7254.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.964011	0.92791	.	.	ENSG00000165443	ENST00000373880;ENST00000373878	T;T	0.57752	0.38;0.38	5.97	5.97	0.96955	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.63686	0.2532	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.72625	0.947;0.978	T	0.66484	-0.5912	10	0.72032	D	0.01	-8.5982	16.4461	0.83932	1.0:0.0:0.0:0.0	.	99;125	Q96FC7-2;Q96FC7	.;PHIPL_HUMAN	G	125;99	ENSP00000362987:S125G;ENSP00000362985:S99G	ENSP00000362985:S99G	S	+	1	0	PHYHIPL	60666318	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.310000	0.96267	2.285000	0.76669	0.528000	0.53228	AGC	.	.		0.418	PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439		G	60996312	A	G	60996312	3	3	212	1	0	0	0	0	1	0	0	0	11876	72	3	2	415	2	PHYHIPL	10	60996312	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	9227704	60996312	74538435	130	30600										
LGI1	9211	hgsc.bcm.edu	37	chr10	95557391	95557391	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttactcctttactcaagtgtAtaactgggatgcagagaaag	9	7	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr10:95557391A>G	ENST00000371418.4	+	8	1765	c.1505A>G	c.(1504-1506)tAt>tGt	p.Y502C	LGI1_ENST00000542308.1_Missense_Mutation_p.Y454C|LGI1_ENST00000371413.3_Intron	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	502					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|positive regulation of cell growth (GO:0030307)|positive regulation of synaptic transmission (GO:0050806)|protein homooligomerization (GO:0051260)	cell junction (GO:0030054)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|synapse (GO:0045202)	receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				ACTCAAGTGTATAACTGGGAT	0.378																																					p.Y502C		Atlas-SNP	.											.	LGI1	69	.	0			c.A1505G						.						71	72	72					10																	95557391		2203	4300	6503	SO:0001583	missense	9211	exon8			AAGTGTATAACTG	AF055636	CCDS7431.1	10q24	2008-08-01	2002-06-05		ENSG00000108231	ENSG00000108231			6572	protein-coding gene	gene with protein product		604619	"epilepsy, partial"	EPT		9879993, 11978770, 15079011	Standard	NM_005097		Approved	IB1099, ETL1, EPITEMPIN	uc001kjc.4	O95970	OTTHUMG00000018777	ENST00000371418.4:c.1505A>G	chr10.hg19:g.95557391A>G	ENSP00000360472:p.Tyr502Cys	1022.0	0.0		1673.0	310.0	NM_005097	A8K0Z1|B4E1S0|Q5W001|Q5W002|Q8NI23|Q96LF5	Missense_Mutation	SNP	ENST00000371418.4	hg19	CCDS7431.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.704147	0.48412	.	.	ENSG00000108231	ENST00000542308;ENST00000371418	D;D	0.86627	-2.15;-2.15	5.65	4.51	0.55191	.	0.000000	0.85682	D	0.000000	D	0.92453	0.7604	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;0.991	D;D	0.91635	0.999;0.969	D	0.92757	0.6221	10	0.87932	D	0	-12.0876	12.3183	0.54971	0.8733:0.0:0.0:0.1266	.	454;502	O95970-3;O95970	.;LGI1_HUMAN	C	454;502	ENSP00000440763:Y454C;ENSP00000360472:Y502C	ENSP00000360472:Y502C	Y	+	2	0	LGI1	95547381	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.964000	0.76061	1.141000	0.42275	-0.301000	0.09380	TAT	.	.		0.378	LGI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049445.1	NM_005097		G	95557391	A	G	95557391	3	3	212	1	0	0	0	0	1	0	0	0	8760	449	16	2	1535	2	LGI1	10	95557391	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	34561079	95557391	39977356	131	30601										
BLOC1S2	282991	hgsc.bcm.edu	37	chr10	102040753	102040753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	caatatctttcatttcaagaTacttcaagctggtgagttta	6	7	4	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr10:102040753T>C	ENST00000370372.2	-	3	282	c.230A>G	c.(229-231)tAt>tGt	p.Y77C	BLOC1S2_ENST00000441611.1_Missense_Mutation_p.Y34C|BLOC1S2_ENST00000361832.2_5'UTR	NM_173809.4	NP_776170.2	Q6QNY1	BL1S2_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 2	77					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|melanosome organization (GO:0032438)|microtubule nucleation (GO:0007020)|mitochondrial outer membrane permeabilization (GO:0097345)|neuron projection development (GO:0031175)|platelet dense granule organization (GO:0060155)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	BLOC-1 complex (GO:0031083)|centrosome (GO:0005813)|gamma-tubulin complex (GO:0000930)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	gamma-tubulin binding (GO:0043015)|protein C-terminus binding (GO:0008022)			large_intestine(1)|lung(2)|ovary(1)	4		Colorectal(252;0.117)		Epithelial(162;2.44e-10)|all cancers(201;1.97e-08)		CATTTCAAGATACTTCAAGCT	0.284																																					p.Y77C		Atlas-SNP	.											.	BLOC1S2	10	.	0			c.A230G						.						75	78	77					10																	102040753		2202	4299	6501	SO:0001583	missense	282991	exon3			TCAAGATACTTCA	AK054697	CCDS7490.1, CCDS73179.1	10q24.31	2012-08-01	2008-08-11		ENSG00000196072	ENSG00000196072		"Biogenesis of lysosomal organelles complex-1 subunits"	20984	protein-coding gene	gene with protein product	"centrosome protein oncogene", "Biogenesis of Lysosome-related Organelles complex-1 Subunit 2", "BLOC-1 subunit 2"	609768				11483580, 15102850	Standard	NM_173809		Approved	MGC10120, FLJ30135, BLOS2	uc001kqw.2	Q6QNY1	OTTHUMG00000018908	ENST00000370372.2:c.230A>G	chr10.hg19:g.102040753T>C	ENSP00000359398:p.Tyr77Cys	46.0	0.0		89.0	5.0	NM_173809	B4DQV2|Q5W040|Q8WUI8	Missense_Mutation	SNP	ENST00000370372.2	hg19	CCDS7490.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.276180	0.80580	.	.	ENSG00000196072	ENST00000361832;ENST00000358848;ENST00000441611;ENST00000370372	.	.	.	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.78253	0.4254	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.81315	-0.0988	9	0.87932	D	0	-4.2434	14.3247	0.66512	0.0:0.0:0.0:1.0	.	77	Q6QNY1	BL1S2_HUMAN	C	9;77;34;9	.	ENSP00000351716:Y77C	Y	-	2	0	BLOC1S2	102030743	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.435000	0.80391	1.979000	0.57680	0.533000	0.62120	TAT	.	.		0.284	BLOC1S2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049861.2	NM_173809		C	102040753	T	C	102040753	3	2	212	1	0	0	0	0	1	0	0	0	1449	1406	49	2	210	2	BLOC1S2	10	102040753	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	6483362	102040753	33493994	132	30602										
WDR11	55717	hgsc.bcm.edu	37	chr10	122626230	122626230	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgagtgatggcagggtcatgAtatgggaactcaagtctgca	14	6	3	3	rs543120664		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr10:122626230A>G	ENST00000263461.6	+	8	1390	c.1144A>G	c.(1144-1146)Ata>Gta	p.I382V		NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	493					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						CAGGGTCATGATATGGGAACT	0.443													A|||	1	0.000199681	0	0	5008	,	,		15774	0		0	False		,,,				2504	0.001				p.I382V		Atlas-SNP	.											.	WDR11	95	.	0			c.A1144G						.						168	160	162					10																	122626230		2203	4300	6503	SO:0001583	missense	55717	exon8			GTCATGATATGGG	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.1144A>G	chr10.hg19:g.122626230A>G	ENSP00000263461:p.Ile382Val	92.0	0.0		128.0	37.0	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	hg19	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	A	9.560	1.118139	0.20877	.	.	ENSG00000120008	ENST00000263461	T	0.27557	1.66	5.45	4.27	0.50696	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);	0.096661	0.64402	N	0.000001	T	0.26484	0.0647	L	0.47716	1.5	0.45662	D	0.99858	B	0.02656	0.0	B	0.04013	0.001	T	0.03706	-1.1011	10	0.37606	T	0.19	-15.4014	10.3059	0.43680	0.9158:0.0:0.0842:0.0	.	382	Q9BZH6	WDR11_HUMAN	V	382	ENSP00000263461:I382V	ENSP00000263461:I382V	I	+	1	0	WDR11	122616220	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.016000	0.49607	0.839000	0.34971	0.533000	0.62120	ATA	.	.		0.443	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			G	122626230	A	G	122626230	3	3	212	1	0	0	0	0	1	0	0	0	17288	333	12	2	1174	2	WDR11	10	122626230	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	20585477	122626230	12908517	133	30603										
IPO7	10527	hgsc.bcm.edu	37	chr11	9435885	9435885	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aaaggatcgttttatccagcTtctttctgaccagtctgatc	7	10	3	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:9435885T>G	ENST00000379719.3	+	5	705	c.563T>G	c.(562-564)cTt>cGt	p.L188R		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	188					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		TTTATCCAGCTTCTTTCTGAC	0.408																																					p.L188R		Atlas-SNP	.											.	IPO7	72	.	0			c.T563G						.						122	114	117					11																	9435885		2201	4296	6497	SO:0001583	missense	10527	exon5			TCCAGCTTCTTTC	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.563T>G	chr11.hg19:g.9435885T>G	ENSP00000369042:p.Leu188Arg	49.0	0.0		78.0	24.0	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	hg19	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.545203	0.86022	.	.	ENSG00000205339	ENST00000379719;ENST00000527431	T;T	0.70282	-0.47;-0.47	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.86826	0.6026	M	0.90145	3.09	0.80722	D	1	D	0.60160	0.987	D	0.76071	0.987	D	0.89664	0.3879	10	0.87932	D	0	.	15.6119	0.76727	0.0:0.0:0.0:1.0	.	188	O95373	IPO7_HUMAN	R	188;126	ENSP00000369042:L188R;ENSP00000435235:L126R	ENSP00000369042:L188R	L	+	2	0	IPO7	9392461	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.083000	0.62718	0.528000	0.53228	CTT	.	.		0.408	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		G	9435885	T	G	9435885	3	3	212	1	0	0	0	0	1	0	0	0	7806	1609	56	5	581	5	IPO7	11	9435885	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10		9435885	125570631	134	30604										
EIF4G2	1982	hgsc.bcm.edu	37	chr11	10823243	10823243	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctgtcctttcttagaaaaccGaggtggcatatccttcgact	8	11	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:10823243G>T	ENST00000526148.1	-	14	1888	c.1378C>A	c.(1378-1380)Cgg>Agg	p.R460R	EIF4G2_ENST00000396525.2_Intron|SNORD97_ENST00000459187.1_RNA|EIF4G2_ENST00000525681.1_Silent_p.R460R|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000339995.5_Silent_p.R460R	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TTAGAAAACCGAGGTGGCATA	0.423																																					p.R460R		Atlas-SNP	.											EIF4G2,NS,carcinoma,0,1	EIF4G2	89	.	0			c.C1378A						.						144	138	140					11																	10823243		2201	4294	6495	SO:0001819	synonymous_variant	1982	exon14			AAAACCGAGGTGG	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.1378C>A	chr11.hg19:g.10823243G>T		66.0	0.0		79.0	15.0	NM_001172705		Silent	SNP	ENST00000526148.1	hg19	CCDS31428.1																																																																																			.	.		0.423	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418		T	10823243	G	T	10823243	2	4	212	1	0	0	0	0	0	0	0	1	5039	1057	37	1		1	EIF4G2	11	10823243	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	1387358	10823243	124183273	135	30605										
EIF4G2	1982	hgsc.bcm.edu	37	chr11	10826502	10826502	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atgagtttagactctacaccCacattgaggagctcaaggca	9	10	2	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:10826502C>T	ENST00000526148.1	-	5	819	c.309G>A	c.(307-309)gtG>gtA	p.V103V	EIF4G2_ENST00000396525.2_Silent_p.V103V|EIF4G2_ENST00000525995.1_5'Flank|EIF4G2_ENST00000525681.1_Silent_p.V103V|EIF4G2_ENST00000339995.5_Silent_p.V103V	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		ACTCTACACCCACATTGAGGA	0.368																																					p.V103V		Atlas-SNP	.											.	EIF4G2	89	.	0			c.G309A						.						118	112	114					11																	10826502		2201	4294	6495	SO:0001819	synonymous_variant	1982	exon5			TACACCCACATTG	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.309G>A	chr11.hg19:g.10826502C>T		78.0	0.0		125.0	15.0	NM_001172705		Silent	SNP	ENST00000526148.1	hg19	CCDS31428.1																																																																																			.	.		0.368	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418		T	10826502	C	T	10826502	2	4	212	1	0	0	0	0	0	0	0	1	5039	581	21	3		3	EIF4G2	11	10826502	Silent	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	3259	10826502	124180014	136	30606										
HPS5	11234	hgsc.bcm.edu	37	chr11	18333536	18333536	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cctcctcctgaactgcccaaAgccaaccatttccgagacac	5	18	0	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:18333536A>T	ENST00000349215.3	-	3	421	c.144T>A	c.(142-144)gcT>gcA	p.A48A	HPS5_ENST00000531848.1_5'UTR|HPS5_ENST00000438420.2_5'UTR|HPS5_ENST00000396253.3_5'UTR	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	48					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						AACTGCCCAAAGCCAACCATT	0.448									Hermansky-Pudlak syndrome																												p.A48A		Atlas-SNP	.											.	HPS5	70	.	0			c.T144A						.						115	121	119					11																	18333536		2199	4293	6492	SO:0001819	synonymous_variant	11234	exon3	Familial Cancer Database	HPS, HPS1-8	GCCCAAAGCCAAC	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.144T>A	chr11.hg19:g.18333536A>T		58.0	0.0		80.0	22.0	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Silent	SNP	ENST00000349215.3	hg19	CCDS7836.1																																																																																			.	.		0.448	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507		T	18333536	A	T	18333536	2	4	212	1	0	0	0	0	0	0	0	1	7351	59	3	4		4	HPS5	11	18333536	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	7507034	18333536	116672980	137	30607										
ANO5	203859	hgsc.bcm.edu	37	chr11	22247597	22247597	+	Splice_Site	DEL	G	G	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gttggaaatagaagacaaaaGggtaaatgtagttgataatt							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:22247597delG	ENST00000324559.8	+	6	679	c.362delG	c.(361-363)agg>ag	p.R121fs		NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	121					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GAAGACAAAAGGGTAAATGTA	0.343																																					p.R121fs		Atlas-INDEL	.											.	ANO5	162	.	0			c.361delA						.						50	54	53					11																	22247597		2203	4300	6503	SO:0001630	splice_region_variant	203859	exon6			.	AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.363+1G>-	chr11.hg19:g.22247597delG		228.0	0.0		326.0	79.0	NM_213599		Frame_Shift_Del	DEL	ENST00000324559.8	hg19	CCDS31444.1																																																																																			.	.		0.343	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599	Frame_Shift_Del	-	22247597	G	-	22247597	8	5	212	1	0	1	0	1	0	0	1	0	700	1014	35	0	384	0	ANO5	11	22247597	Splice_Site	DEL	G	TCGA-DD-AAE7-01A-11D-A40R-10	3914061	22247597	112758919	138	30608										
PRR5L	79899	hgsc.bcm.edu	37	chr11	36472812	36472812	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tatttgcaactggaggagctGgtgaagcaagtggtttctcc	13	7	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:36472812G>A	ENST00000378867.3	+	9	994	c.639G>A	c.(637-639)ctG>ctA	p.L213L	PRR5L_ENST00000311599.5_Silent_p.L140L|PRR5L_ENST00000530639.1_Silent_p.L213L|PRR5L_ENST00000389693.3_3'UTR|PRR5L_ENST00000527487.1_Intron	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	213					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|regulation of fibroblast migration (GO:0010762)|TORC2 signaling (GO:0038203)	mitochondrion (GO:0005739)|TORC2 complex (GO:0031932)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						TGGAGGAGCTGGTGAAGCAAG	0.527																																					p.L213L		Atlas-SNP	.											.	PRR5L	35	.	0			c.G639A						.						188	158	168					11																	36472812		2202	4298	6500	SO:0001819	synonymous_variant	79899	exon9			GGAGCTGGTGAAG		CCDS31463.1, CCDS53617.1	11p13-p12	2009-07-09				ENSG00000135362			25878	protein-coding gene	gene with protein product	"protein observed with Rictor-2"	611728				17461779	Standard	NM_024841		Approved	FLJ14213, PROTOR-2	uc001mwp.3	Q6MZQ0		ENST00000378867.3:c.639G>A	chr11.hg19:g.36472812G>A		78.0	0.0		116.0	29.0	NM_024841	A4QN22|E9PKY1|Q96H46|Q9H7V4	Silent	SNP	ENST00000378867.3	hg19	CCDS31463.1																																																																																			.	.		0.527	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841		A	36472812	G	A	36472812	2	1	212	1	0	0	0	0	0	0	0	1	12614	1335	47	3		3	PRR5L	11	36472812	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	14225215	36472812	98533704	139	30609										
SYT13	57586	hgsc.bcm.edu	37	chr11	45307590	45307590	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gctcacctgttgtgcagaccCgagcaagctgggcttcgcct	12	14	1	1	rs139035860	byFrequency	TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:45307590C>A	ENST00000020926.3	-	1	280	c.169G>T	c.(169-171)Ggg>Tgg	p.G57W		NM_001247987.1|NM_020826.2	NP_001234916.1|NP_065877.1	Q7L8C5	SYT13_HUMAN	synaptotagmin XIII	57					vesicle-mediated transport (GO:0016192)	integral component of plasma membrane (GO:0005887)|transport vesicle (GO:0030133)				breast(1)|large_intestine(3)|lung(16)|ovary(1)|skin(2)	23						TGTGCAGACCCGAGCAAGCTG	0.721																																					p.G57W		Atlas-SNP	.											.	SYT13	45	.	0			c.G169T						.						17	21	19					11																	45307590		2202	4295	6497	SO:0001583	missense	57586	exon1			CAGACCCGAGCAA	AB037848	CCDS31470.1	11p12-p11	2013-01-21			ENSG00000019505	ENSG00000019505		"Synaptotagmins"	14962	protein-coding gene	gene with protein product		607716				11171101	Standard	NM_020826		Approved	KIAA1427	uc001myq.2	Q7L8C5	OTTHUMG00000166504	ENST00000020926.3:c.169G>T	chr11.hg19:g.45307590C>A	ENSP00000020926:p.Gly57Trp	66.0	0.0		66.0	19.0	NM_020826	A8K4P4|D3DQP1|Q9BQS3|Q9H041|Q9P2C0	Missense_Mutation	SNP	ENST00000020926.3	hg19	CCDS31470.1	.	.	.	.	.	.	.	.	.	.	C	7.314	0.615616	0.14129	.	.	ENSG00000019505	ENST00000020926	T	0.05717	3.4	3.82	-3.05	0.05396	.	0.680336	0.12091	N	0.500434	T	0.02727	0.0082	N	0.08118	0	0.09310	N	1	P	0.39759	0.687	B	0.34590	0.186	T	0.39078	-0.9631	10	0.87932	D	0	.	7.3907	0.26909	0.0:0.26:0.327:0.4131	.	57	Q7L8C5	SYT13_HUMAN	W	57	ENSP00000020926:G57W	ENSP00000020926:G57W	G	-	1	0	SYT13	45264166	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.163000	0.16520	-0.969000	0.03573	-0.458000	0.05436	GGG	.	C|0.999;G|0.001		0.721	SYT13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390110.1	NM_020826		A	45307590	C	A	45307590	3	1	212	1	0	0	0	0	1	0	0	0	15484	652	23	1	1135	1	SYT13	11	45307590	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	8834778	45307590	89698926	140	30610										
OR4D9	390199	hgsc.bcm.edu	37	chr11	59282778	59282778	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gccatctccaagcccctgcaCtatatgaccatcatgagtag	7	14	2	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:59282778C>T	ENST00000329328.3	+	1	393	c.393C>T	c.(391-393)caC>caT	p.H131H		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	131						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						AGCCCCTGCACTATATGACCA	0.527																																					p.H131H		Atlas-SNP	.											.	OR4D9	47	.	0			c.C393T						.						79	77	78					11																	59282778		2201	4295	6496	SO:0001819	synonymous_variant	390199	exon1			CCTGCACTATATG	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"GPCR / Class A : Olfactory receptors"	15178	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily D, member 9 pseudogene"				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.393C>T	chr11.hg19:g.59282778C>T		46.0	0.0		59.0	16.0	NM_001004711	Q6IFF3	Silent	SNP	ENST00000329328.3	hg19	CCDS31564.1																																																																																			.	.		0.527	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711		T	59282778	C	T	59282778	2	4	212	1	0	0	0	0	0	0	0	1	11068	564	20	3		3	OR4D9	11	59282778	Silent	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	13975188	59282778	75723738	141	30611										
CHRM1	1128	hgsc.bcm.edu	37	chr11	62678251	62678251	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	catgacggaggcattgctggCcacatagtccagggccagcc	13	13	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:62678251C>T	ENST00000306960.3	-	2	863	c.322G>A	c.(322-324)Gcc>Acc	p.A108T	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	108					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	GCATTGCTGGCCACATAGTCC	0.612																																					p.A108T		Atlas-SNP	.											.	CHRM1	29	.	0			c.G322A						.						69	60	63					11																	62678251		2201	4298	6499	SO:0001583	missense	1128	exon2			TGCTGGCCACATA	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1950	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 1"	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.322G>A	chr11.hg19:g.62678251C>T	ENSP00000306490:p.Ala108Thr	82.0	0.0		135.0	43.0	NM_000738	Q96RH1	Missense_Mutation	SNP	ENST00000306960.3	hg19	CCDS8040.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.176643	0.78564	.	.	ENSG00000168539	ENST00000306960;ENST00000543973;ENST00000536524	T;T;T	0.19806	2.12;2.12;2.12	4.57	4.57	0.56435	GPCR, rhodopsin-like superfamily (1);	0.093208	0.42053	D	0.000770	T	0.22513	0.0543	N	0.25426	0.745	0.53688	D	0.999972	P	0.41978	0.767	P	0.48334	0.574	T	0.01814	-1.1268	10	0.32370	T	0.25	-18.9112	14.8803	0.70528	0.0:1.0:0.0:0.0	.	108	P11229	ACM1_HUMAN	T	108	ENSP00000306490:A108T;ENSP00000441188:A108T;ENSP00000444482:A108T	ENSP00000306490:A108T	A	-	1	0	CHRM1	62434827	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.632000	0.83247	2.376000	0.81061	0.563000	0.77884	GCC	.	.		0.612	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738		T	62678251	C	T	62678251	3	4	212	1	0	0	0	0	1	0	0	0	3378	739	26	3	1064	3	CHRM1	11	62678251	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	3395473	62678251	72328265	142	30612										
CCS	9973	hgsc.bcm.edu	37	chr11	66367052	66367052	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctattgacggcctggagcctGggctgcatggactccacgtc	13	13	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:66367052G>T	ENST00000533244.1	+	4	814	c.373G>T	c.(373-375)Ggg>Tgg	p.G125W	CCS_ENST00000310190.4_Missense_Mutation_p.G106W	NM_005125.1	NP_005116.1	O14618	CCS_HUMAN	copper chaperone for superoxide dismutase	125	Superoxide dismutase-like.				copper ion transmembrane transport (GO:0035434)|intracellular copper ion transport (GO:0015680)|positive regulation of oxidoreductase activity (GO:0051353)|removal of superoxide radicals (GO:0019430)|superoxide metabolic process (GO:0006801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|protein disulfide oxidoreductase activity (GO:0015035)|superoxide dismutase activity (GO:0004784)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|large_intestine(2)|lung(3)|stomach(1)	9						CCTGGAGCCTGGGCTGCATGG	0.592																																					p.G125W		Atlas-SNP	.											.	CCS	22	.	0			c.G373T						.						39	38	38					11																	66367052		2200	4295	6495	SO:0001583	missense	9973	exon4			GAGCCTGGGCTGC	AF002210	CCDS8146.1	11q13.2	2012-09-20			ENSG00000173992	ENSG00000173992			1613	protein-coding gene	gene with protein product		603864				9295278	Standard	NM_005125		Approved		uc001oir.3	O14618	OTTHUMG00000167238	ENST00000533244.1:c.373G>T	chr11.hg19:g.66367052G>T	ENSP00000436318:p.Gly125Trp	207.0	0.0		196.0	54.0	NM_005125	Q2M366|Q8NEV0	Missense_Mutation	SNP	ENST00000533244.1	hg19	CCDS8146.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.667217	0.88251	.	.	ENSG00000173992	ENST00000533244;ENST00000310190	D;D	0.99818	-6.92;-6.92	5.23	5.23	0.72850	Superoxide dismutase, copper/zinc binding domain (3);	0.000000	0.85682	D	0.000000	D	0.99902	0.9953	H	0.99011	4.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96407	0.9301	10	0.87932	D	0	.	14.1637	0.65464	0.0:0.0:1.0:0.0	.	125	O14618	CCS_HUMAN	W	125;106	ENSP00000436318:G125W;ENSP00000307870:G106W	ENSP00000307870:G106W	G	+	1	0	CCS	66123628	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	9.008000	0.93601	2.732000	0.93576	0.655000	0.94253	GGG	.	.		0.592	CCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393826.1	NM_005125		T	66367052	G	T	66367052	3	4	212	1	0	0	0	0	1	0	0	0	2954	1348	47	3	387	3	CCS	11	66367052	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	3688801	66367052	68639464	143	30613										
MTNR1B	4544	hgsc.bcm.edu	37	chr11	92714649	92714649	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gagtctggcattggctgaccTggtggtggccttctacccct	13	12	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:92714649T>A	ENST00000257068.2	+	2	266	c.260T>A	c.(259-261)cTg>cAg	p.L87Q		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	87					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	TTGGCTGACCTGGTGGTGGCC	0.557																																					p.L87Q		Atlas-SNP	.											.	MTNR1B	75	.	0			c.T260A						.						280	272	275					11																	92714649		2201	4298	6499	SO:0001583	missense	4544	exon2			CTGACCTGGTGGT	AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"GPCR / Class A : Melatonin receptors"	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.260T>A	chr11.hg19:g.92714649T>A	ENSP00000257068:p.Leu87Gln	36.0	0.0		64.0	22.0	NM_005959		Missense_Mutation	SNP	ENST00000257068.2	hg19	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.175472	0.78564	.	.	ENSG00000134640	ENST00000257068	T	0.54071	0.59	3.97	3.97	0.46021	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000005	D	0.82614	0.5075	H	0.99042	4.41	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89232	0.3578	10	0.87932	D	0	-15.8101	13.3318	0.60492	0.0:0.0:0.0:1.0	.	87	P49286	MTR1B_HUMAN	Q	87	ENSP00000257068:L87Q	ENSP00000257068:L87Q	L	+	2	0	MTNR1B	92354297	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.082000	0.76851	1.803000	0.52742	0.402000	0.26972	CTG	.	.		0.557	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1			A	92714649	T	A	92714649	3	1	212	1	0	0	0	0	1	0	0	0	9961	1580	55	4	266	4	MTNR1B	11	92714649	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	26347597	92714649	42291867	144	30614										
CCDC67	159989	hgsc.bcm.edu	37	chr11	93104432	93104432	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgcaagaactgaaaatgtacCaaagacagtgccaggtgaag	11	7	0	4			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:93104432C>T	ENST00000298050.3	+	7	875	c.775C>T	c.(775-777)Caa>Taa	p.Q259*		NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	259					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				GAAAATGTACCAAAGACAGTG	0.308																																					p.Q259X		Atlas-SNP	.											.	CCDC67	57	.	0			c.C775T						.						49	47	47					11																	93104432		1818	4077	5895	SO:0001587	stop_gained	159989	exon7			ATGTACCAAAGAC	AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.775C>T	chr11.hg19:g.93104432C>T	ENSP00000298050:p.Gln259*	229.0	0.0		366.0	113.0	NM_181645	Q8NEF1|Q96LL7	Nonsense_Mutation	SNP	ENST00000298050.3	hg19	CCDS44707.1	.	.	.	.	.	.	.	.	.	.	C	38	6.860173	0.97893	.	.	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000532819	.	.	.	5.61	5.61	0.85477	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	18.6238	0.91330	0.0:1.0:0.0:0.0	.	.	.	.	X	259	.	ENSP00000298050:Q259X	Q	+	1	0	CCDC67	92744080	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.953000	0.63624	2.650000	0.89964	0.655000	0.94253	CAA	.	.		0.308	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645		T	93104432	C	T	93104432	4	4	212	1	0	0	0	0	0	1	0	0	2841	595	21	3	797	3	CCDC67	11	93104432	Nonsense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	389783	93104432	41902084	145	30615										
MAML2	84441	hgsc.bcm.edu	37	chr11	95724767	95724767	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tagagtctgcttctttcccaTcaattgctgattcaacagtg	7	10	4	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:95724767T>C	ENST00000524717.1	-	3	3544	c.2260A>G	c.(2260-2262)Atg>Gtg	p.M754V		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	754					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				TTCTTTCCCATCAATTGCTGA	0.483			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.M754V		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.A2260G						.						155	149	151					11																	95724767		1933	4150	6083	SO:0001583	missense	84441	exon3			TTCCCATCAATTG	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.2260A>G	chr11.hg19:g.95724767T>C	ENSP00000434552:p.Met754Val	63.0	0.0		97.0	6.0	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation	SNP	ENST00000524717.1	hg19	CCDS44714.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.419798	0.62622	.	.	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.42131	0.98;0.98	5.46	4.34	0.51931	.	0.339054	0.27327	N	0.019863	T	0.35770	0.0943	L	0.50333	1.59	0.38625	D	0.951245	B	0.11235	0.004	B	0.11329	0.006	T	0.17531	-1.0366	10	0.25106	T	0.35	-6.9862	10.8531	0.46782	0.0:0.0733:0.0:0.9267	.	754	Q8IZL2	MAML2_HUMAN	V	754	ENSP00000434552:M754V;ENSP00000412394:M754V	ENSP00000412394:M754V	M	-	1	0	MAML2	95364415	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.114000	0.41911	0.938000	0.37419	0.455000	0.32223	ATG	.	.		0.483	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			C	95724767	T	C	95724767	3	2	212	1	0	0	0	0	1	0	0	0	9215	1435	50	2	1222	2	MAML2	11	95724767	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	2620335	95724767	39281749	146	30616										
C11orf70	85016	hgsc.bcm.edu	37	chr11	101918604	101918604	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttgaccagacctttcagtccTatcggaaggatgatttcgtt	9	9	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:101918604T>A	ENST00000434758.2	+	2	197	c.169T>A	c.(169-171)Tat>Aat	p.Y57N	C11orf70_ENST00000526781.1_Missense_Mutation_p.Y57N|C11orf70_ENST00000534360.1_Missense_Mutation_p.Y57N	NM_032930.2	NP_116319.2	Q9BRQ4	CK070_HUMAN	chromosome 11 open reading frame 70	57										breast(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|skin(2)	12	all_epithelial(12;0.0137)	Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0335)		CTTTCAGTCCTATCGGAAGGA	0.522																																					p.Y57N		Atlas-SNP	.											.	C11orf70	33	.	0			c.T169A						.						75	67	70					11																	101918604		2203	4299	6502	SO:0001583	missense	85016	exon2			CAGTCCTATCGGA	AK094851	CCDS8313.1, CCDS8313.2, CCDS53698.1	11q22.1	2012-05-31			ENSG00000137691	ENSG00000137691			28188	protein-coding gene	gene with protein product							Standard	NM_032930		Approved	MGC13040	uc001pgp.3	Q9BRQ4	OTTHUMG00000167320	ENST00000434758.2:c.169T>A	chr11.hg19:g.101918604T>A	ENSP00000414390:p.Tyr57Asn	77.0	0.0		83.0	19.0	NM_032930	E9PJU1	Missense_Mutation	SNP	ENST00000434758.2	hg19	CCDS8313.2	.	.	.	.	.	.	.	.	.	.	T	16.37	3.104885	0.56291	.	.	ENSG00000137691	ENST00000434758;ENST00000526781;ENST00000534360;ENST00000393209;ENST00000423732	.	.	.	4.47	3.34	0.38264	.	0.000000	0.85682	D	0.000000	T	0.65616	0.2708	M	0.82923	2.615	0.26395	N	0.976518	D;D	0.76494	0.999;0.999	D;D	0.70016	0.952;0.967	T	0.58538	-0.7619	9	0.87932	D	0	-14.5655	7.3391	0.26627	0.0:0.1029:0.0:0.8971	.	57;57	Q9BRQ4;E9PJU1	CK070_HUMAN;.	N	57;57;57;19;19	.	ENSP00000376904:Y19N	Y	+	1	0	C11orf70	101423814	0.954000	0.32549	0.259000	0.24435	0.779000	0.44077	1.527000	0.35975	0.582000	0.29556	0.460000	0.39030	TAT	.	.		0.522	C11orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394144.1	NM_032930		A	101918604	T	A	101918604	3	1	212	1	0	0	0	0	1	0	0	0	1661	1522	53	4	57	4	C11orf70	11	101918604	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	6193837	101918604	33087912	147	30617										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105795386	105795386	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggcacacagaagagccagagGacggaaaggaaggacccagc	15	10	0	3	rs200205997		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:105795386G>T	ENST00000530497.1	+	11	1738	c.1738G>T	c.(1738-1740)Gac>Tac	p.D580Y	GRIA4_ENST00000282499.5_Missense_Mutation_p.D580Y|GRIA4_ENST00000525187.1_Missense_Mutation_p.D580Y|GRIA4_ENST00000393127.2_Missense_Mutation_p.D580Y			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	580					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		AGAGCCAGAGGACGGAAAGGA	0.478																																					p.D580Y		Atlas-SNP	.											.	GRIA4	380	.	0			c.G1738T						.						142	118	126					11																	105795386		2202	4299	6501	SO:0001583	missense	2893	exon12			CCAGAGGACGGAA	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1738G>T	chr11.hg19:g.105795386G>T	ENSP00000435775:p.Asp580Tyr	111.0	0.0		185.0	12.0	NM_001077243	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	G	31	5.086968	0.94100	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187	T;T;T;T	0.14144	2.69;2.53;2.69;2.53	6.05	6.05	0.98169	Ionotropic glutamate receptor (2);	0.000000	0.64402	D	0.000001	T	0.27419	0.0673	L	0.33339	1.005	0.80722	D	1	P;D	0.54397	0.845;0.966	P;P	0.60541	0.529;0.876	T	0.00089	-1.2089	10	0.44086	T	0.13	.	20.6013	0.99457	0.0:0.0:1.0:0.0	.	580;580	P48058;G3V164	GRIA4_HUMAN;.	Y	580	ENSP00000282499:D580Y;ENSP00000376835:D580Y;ENSP00000435775:D580Y;ENSP00000432180:D580Y	ENSP00000282499:D580Y	D	+	1	0	GRIA4	105300596	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.869000	0.99810	2.878000	0.98634	0.650000	0.86243	GAC	.	G|1.000;A|0.000		0.478	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			T	105795386	G	T	105795386	3	4	212	1	0	0	0	0	1	0	0	0	6779	1174	41	3	1817	3	GRIA4	11	105795386	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	3876782	105795386	29211130	148	30618										
FAM55B	120406	hgsc.bcm.edu	37	chr11	114550401	114550401	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tactcactttgtttccaaatGccatagctcgaaaattactg	5	10	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:114550401G>T	ENST00000389586.4	+	2	239	c.49G>T	c.(49-51)Gcc>Tcc	p.A17S	NXPE2_ENST00000375475.5_Missense_Mutation_p.A17S	NM_182495.5	NP_872301.2	Q96DL1	NXPE2_HUMAN	neurexophilin and PC-esterase domain family, member 2	17						integral component of membrane (GO:0016021)											GTTTCCAAATGCCATAGCTCG	0.353																																					p.A17S		Atlas-SNP	.											.	.	.	.	0			c.G49T						.						231	178	194					11																	114550401		692	1590	2282	SO:0001583	missense	120406	exon2			CCAAATGCCATAG	AK057953	CCDS44738.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000204361	ENSG00000204361			26331	protein-coding gene	gene with protein product			"family with sequence similarity 55, member B"	FAM55B			Standard	NM_182495		Approved	FLJ25224	uc009yyy.2	Q96DL1	OTTHUMG00000168293	ENST00000389586.4:c.49G>T	chr11.hg19:g.114550401G>T	ENSP00000374237:p.Ala17Ser	28.0	0.0		62.0	21.0	NM_182495	Q2NKI8	Missense_Mutation	SNP	ENST00000389586.4	hg19	CCDS44738.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.246085	0.22796	.	.	ENSG00000204361	ENST00000389586;ENST00000375475;ENST00000505358	T;T	0.17854	2.75;2.25	4.1	0.399	0.16325	.	0.831663	0.10288	N	0.692646	T	0.11836	0.0288	L	0.43152	1.355	0.09310	N	1	B	0.26318	0.146	B	0.22152	0.038	T	0.33137	-0.9880	10	0.34782	T	0.22	.	2.4915	0.04611	0.3393:0.0:0.4401:0.2206	.	17	Q96DL1	FA55B_HUMAN	S	17	ENSP00000374237:A17S;ENSP00000364624:A17S	ENSP00000364624:A17S	A	+	1	0	FAM55B	114055611	0.000000	0.05858	0.012000	0.15200	0.521000	0.34408	0.255000	0.18333	0.111000	0.17947	0.484000	0.47621	GCC	.	.		0.353	NXPE2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399181.1	NM_182495		T	114550401	G	T	114550401	3	4	212	1	0	0	0	0	1	0	0	0	5593	1319	46	3	55	3	FAM55B	11	114550401	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	8755015	114550401	20456115	149	30619										
OR8D2	283160	hgsc.bcm.edu	37	chr11	124190043	124190043	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgaagttctgggcgttgtgtCaagcctgccaggataaactc	12	9	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:124190043C>G	ENST00000357438.2	-	1	141	c.51G>C	c.(49-51)ttG>ttC	p.L17F		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		GGCGTTGTGTCAAGCCTGCCA	0.433																																					p.L17F		Atlas-SNP	.											.	OR8D2	65	.	0			c.G51C						.						67	67	67					11																	124190043		2200	4299	6499	SO:0001583	missense	283160	exon1			TTGTGTCAAGCCT	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"GPCR / Class A : Olfactory receptors"	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.51G>C	chr11.hg19:g.124190043C>G	ENSP00000350022:p.Leu17Phe	54.0	0.0		69.0	18.0	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	hg19	CCDS31707.1	.	.	.	.	.	.	.	.	.	.	c	9.749	1.167022	0.21621	.	.	ENSG00000197263	ENST00000357438	T	0.00009	9.5	3.42	2.21	0.28008	.	0.000000	0.32287	N	0.006309	T	0.00073	0.0002	L	0.39633	1.23	0.20307	N	0.999913	B	0.25390	0.125	B	0.20184	0.028	T	0.22730	-1.0208	10	0.59425	D	0.04	.	3.1741	0.06562	0.0:0.1629:0.2351:0.602	.	17	Q9GZM6	OR8D2_HUMAN	F	17	ENSP00000350022:L17F	ENSP00000350022:L17F	L	-	3	2	OR8D2	123695253	0.001000	0.12720	0.290000	0.24890	0.075000	0.17131	-0.456000	0.06754	0.590000	0.29694	0.395000	0.25975	TTG	.	.		0.433	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918		G	124190043	C	G	124190043	3	3	212	1	0	0	0	0	1	0	0	0	11241	825	29	4	887	4	OR8D2	11	124190043	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	9639642	124190043	10816473	150	30620										
VSIG2	23584	hgsc.bcm.edu	37	chr11	124618302	124618302	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tcaccgaaggtcactaccccCatatgtctccttgggcttct	7	15	4	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr11:124618302C>G	ENST00000326621.5	-	6	935	c.835G>C	c.(835-837)Ggg>Cgg	p.G279R	RP11-677M14.2_ENST00000531241.1_RNA|VSIG2_ENST00000403470.1_Missense_Mutation_p.G279R	NM_014312.3	NP_055127.2	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2	279						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(5)	19	all_hematologic(175;0.215)	Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0215)		TCACTACCCCCATATGTCTCC	0.592																																					p.G279R		Atlas-SNP	.											.	VSIG2	38	.	0			c.G835C						.						119	105	110					11																	124618302		2201	4299	6500	SO:0001583	missense	23584	exon6			TACCCCCATATGT	AF061022	CCDS8452.1	11q24	2013-01-11			ENSG00000019102	ENSG00000019102		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing"	17149	protein-coding gene	gene with protein product		606011				9862345	Standard	NM_014312		Approved	CTXL, CTH	uc001qas.3	Q96IQ7	OTTHUMG00000150357	ENST00000326621.5:c.835G>C	chr11.hg19:g.124618302C>G	ENSP00000318684:p.Gly279Arg	64.0	0.0		69.0	31.0	NM_014312	O95791|Q9NX42	Missense_Mutation	SNP	ENST00000326621.5	hg19	CCDS8452.1	.	.	.	.	.	.	.	.	.	.	C	19.83	3.900926	0.72754	.	.	ENSG00000019102	ENST00000326621;ENST00000403470	T;T	0.75938	-0.82;-0.98	5.53	4.6	0.57074	.	0.208205	0.34435	N	0.003967	T	0.69097	0.3073	M	0.68317	2.08	0.37115	D	0.900557	B	0.24882	0.113	B	0.23419	0.046	T	0.66760	-0.5842	10	0.13470	T	0.59	.	12.0522	0.53513	0.0:0.8271:0.1728:0.0	.	279	Q96IQ7	VSIG2_HUMAN	R	279	ENSP00000318684:G279R;ENSP00000385013:G279R	ENSP00000318684:G279R	G	-	1	0	VSIG2	124123512	0.128000	0.22383	0.994000	0.49952	0.959000	0.62525	0.228000	0.17814	1.525000	0.49052	0.655000	0.94253	GGG	.	.		0.592	VSIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317785.1	NM_014312		G	124618302	C	G	124618302	3	3	212	1	0	0	0	0	1	0	0	0	17239	594	21	4	156	4	VSIG2	11	124618302	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	428259	124618302	10388214	151	30621										
SLC6A13	6540	hgsc.bcm.edu	37	chr12	330614	330614	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atgcagaccatggaggacagAgccaggagccagcccagggc	15	12	0	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:330614A>G	ENST00000343164.4	-	14	1666	c.1614T>C	c.(1612-1614)gcT>gcC	p.A538A	SLC6A13_ENST00000539668.1_5'Flank|SLC6A13_ENST00000445055.2_Silent_p.A446A	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	538					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			TGGAGGACAGAGCCAGGAGCC	0.592																																					p.A538A		Atlas-SNP	.											.	SLC6A13	62	.	0			c.T1614C						.						57	60	59					12																	330614		2203	4300	6503	SO:0001819	synonymous_variant	6540	exon14			GGACAGAGCCAGG	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1614T>C	chr12.hg19:g.330614A>G		64.0	0.0		68.0	8.0	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Silent	SNP	ENST00000343164.4	hg19	CCDS8502.1																																																																																			.	.		0.592	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		G	330614	A	G	330614	2	3	212	1	0	0	0	0	0	0	0	1	14691	291	11	2		2	SLC6A13	12	330614	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10		330614	133521281	152	30622										
KCNA1	3736	hgsc.bcm.edu	37	chr12	5020868	5020868	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctgcggaggccggtcaacgtGcccctggacatgttctccga	13	14	2	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:5020868G>T	ENST00000382545.3	+	2	1431	c.324G>T	c.(322-324)gtG>gtT	p.V108V	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	108					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	CGGTCAACGTGCCCCTGGACA	0.617																																					p.V108V		Atlas-SNP	.											.	KCNA1	112	.	0			c.G324T						.						49	54	52					12																	5020868		2203	4300	6503	SO:0001819	synonymous_variant	3736	exon2			CAACGTGCCCCTG	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.324G>T	chr12.hg19:g.5020868G>T		97.0	0.0		65.0	14.0	NM_000217	A6NM83|Q3MIQ9	Silent	SNP	ENST00000382545.3	hg19	CCDS8535.1																																																																																			.	.		0.617	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217		T	5020868	G	T	5020868	2	4	212	1	0	0	0	0	0	0	0	1	8010	1306	46	3		3	KCNA1	12	5020868	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	4690254	5020868	128831027	153	30623										
A2M	2	hgsc.bcm.edu	37	chr12	9262919	9262919	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atgttgcttacctgaatgtaTactagtggaatctgaaagac	9	6	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:9262919T>C	ENST00000318602.7	-	5	802	c.495A>G	c.(493-495)gtA>gtG	p.V165V		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	165					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	CCTGAATGTATACTAGTGGAA	0.274																																					p.V165V		Atlas-SNP	.											.	A2M	180	.	0			c.A495G						.						74	63	66					12																	9262919		1725	3934	5659	SO:0001819	synonymous_variant	2	exon5			AATGTATACTAGT	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.495A>G	chr12.hg19:g.9262919T>C		27.0	0.0		37.0	14.0	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Silent	SNP	ENST00000318602.7	hg19	CCDS44827.1																																																																																			.	.		0.274	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		C	9262919	T	C	9262919	2	2	212	1	0	0	0	0	0	0	0	1	4	1393	49	2		2	A2M	12	9262919	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	4242051	9262919	124588976	154	30624										
CLEC12A	160364	hgsc.bcm.edu	37	chr12	10131563	10131563	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctgttaattttgctttccacAgcacctccagctccctctca	4	16	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:10131563A>T	ENST00000304361.4	+	2	273		c.e2-1		CLEC12A_ENST00000350667.4_Intron|CLEC12A_ENST00000434319.2_Splice_Site|CLEC12A_ENST00000355690.4_Splice_Site	NM_138337.5|NM_201623.3	NP_612210.4|NP_963917.2	Q5QGZ9	CL12A_HUMAN	C-type lectin domain family 12, member A							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	16						TGCTTTCCACAGCACCTCCAG	0.403																																					.	Melanoma(197;1487 2125 16611 22221 34855)	Atlas-SNP	.											.	CLEC12A	65	.	0			c.122-2A>T						.						182	169	173					12																	10131563		2203	4300	6503	SO:0001630	splice_region_variant	160364	exon3			TTCCACAGCACCT	AY498550	CCDS8608.1, CCDS8609.1, CCDS55803.1, CCDS73442.1	12p13.31	2010-08-17			ENSG00000172322	ENSG00000172322		"C-type lectin domain containing"	31713	protein-coding gene	gene with protein product		612088					Standard	NM_201623		Approved	CLL-1, MICL	uc001qwq.3	Q5QGZ9		ENST00000304361.4:c.92-1A>T	chr12.hg19:g.10131563A>T		50.0	0.0		73.0	15.0	NM_001207010	B2RA16|Q6P4H1|Q6RH77|Q6RH78|Q8TDQ6	Splice_Site	SNP	ENST00000304361.4	hg19	CCDS8608.1	.	.	.	.	.	.	.	.	.	.	A	6.103	0.387355	0.11581	.	.	ENSG00000172322	ENST00000355690;ENST00000396507;ENST00000304361;ENST00000434319	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9004	0.47049	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CLEC12A	10022830	0.783000	0.28701	0.086000	0.20670	0.033000	0.12548	3.560000	0.53763	2.005000	0.58758	0.528000	0.53228	.	.	.		0.403	CLEC12A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399545.1	NM_138337	Intron	T	10131563	A	T	10131563	5	4	212	1	0	0	0	0	0	0	1	0	3499	202	7	4	96	4	CLEC12A	12	10131563	Splice_Site	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	868644	10131563	123720332	155	30625										
LRP6	4040	hgsc.bcm.edu	37	chr12	12332891	12332891	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cgctcaattttcggaatttcTccccagtcagtccaatacat	5	13	3	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:12332891T>A	ENST00000261349.4	-	7	1474	c.1398A>T	c.(1396-1398)ggA>ggT	p.G466G	LRP6_ENST00000543091.1_Silent_p.G466G	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	466	Beta-propeller 2.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TCGGAATTTCTCCCCAGTCAG	0.378																																					p.G466G		Atlas-SNP	.											.	LRP6	170	.	0			c.A1398T						.						89	83	85					12																	12332891		2203	4300	6503	SO:0001819	synonymous_variant	4040	exon7			AATTTCTCCCCAG	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.1398A>T	chr12.hg19:g.12332891T>A		59.0	0.0		115.0	23.0	NM_002336	Q17RZ2	Silent	SNP	ENST00000261349.4	hg19	CCDS8647.1																																																																																			.	.		0.378	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			A	12332891	T	A	12332891	2	1	212	1	0	0	0	0	0	0	0	1	8971	1538	54	4		4	LRP6	12	12332891	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	2201328	12332891	121519004	156	30626										
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18576952	18576952	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccgctccttgcagagcatccAggttgcccatcgtctttact	8	15	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:18576952A>G	ENST00000266497.5	+	16	2398	c.2360A>G	c.(2359-2361)cAg>cGg	p.Q787R	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.Q787R|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.Q828R			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	787	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				CAGAGCATCCAGGTTGCCCAT	0.438																																					p.Q787R		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A2360G						.						70	66	67					12																	18576952		1883	4117	6000	SO:0001583	missense	5288	exon17			GCATCCAGGTTGC	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2360A>G	chr12.hg19:g.18576952A>G	ENSP00000266497:p.Gln787Arg	64.0	0.0		100.0	26.0	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	A	2.629	-0.286846	0.05605	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.61158	0.13;0.13;0.13	4.52	3.12	0.35913	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.077202	0.52532	N	0.000073	T	0.27933	0.0688	N	0.04746	-0.17	0.34095	D	0.661153	B;B;B	0.15719	0.014;0.011;0.014	B;B;B	0.22753	0.041;0.024;0.038	T	0.33828	-0.9853	10	0.02654	T	1	-7.2976	7.0123	0.24869	0.8484:0.0:0.1516:0.0	.	827;828;787	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	R	787;787;828	ENSP00000404845:Q787R;ENSP00000266497:Q787R;ENSP00000445381:Q828R	ENSP00000266497:Q787R	Q	+	2	0	PIK3C2G	18468219	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.096000	0.50243	0.861000	0.35504	0.377000	0.23210	CAG	.	.		0.438	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		G	18576952	A	G	18576952	3	3	212	1	0	0	0	0	1	0	0	0	11920	188	7	2	2422	2	PIK3C2G	12	18576952	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	6244061	18576952	115274943	157	30627										
ITGA5	3678	hgsc.bcm.edu	37	chr12	54798981	54798981	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tcctggtccaggtcccccagGggggtcaaggagctgccaaa	14	13	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:54798981G>T	ENST00000293379.4	-	12	1455	c.1194C>A	c.(1192-1194)ccC>ccA	p.P398P	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	398					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						GGTCCCCCAGGGGGGTCAAGG	0.602																																					p.P398P		Atlas-SNP	.											.	ITGA5	99	.	0			c.C1194A						.						62	67	65					12																	54798981		2203	4300	6503	SO:0001819	synonymous_variant	3678	exon12			CCCCAGGGGGGTC		CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"CD molecules", "Integrins"	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.1194C>A	chr12.hg19:g.54798981G>T		146.0	0.0		149.0	29.0	NM_002205	Q96HA5	Silent	SNP	ENST00000293379.4	hg19	CCDS8880.1																																																																																			.	.		0.602	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			T	54798981	G	T	54798981	2	4	212	1	0	0	0	0	0	0	0	1	7888	1219	43	3		3	ITGA5	12	54798981	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	36222029	54798981	79052914	158	30628										
ITGA5	3678	hgsc.bcm.edu	37	chr12	54799001	54799001	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gggggtcaaggagctgccaaAtcggccaaactcatcatggc	13	11	3	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:54799001A>C	ENST00000293379.4	-	12	1435	c.1174T>G	c.(1174-1176)Ttt>Gtt	p.F392V	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	392					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						GAGCTGCCAAATCGGCCAAAC	0.622																																					p.F392V		Atlas-SNP	.											.	ITGA5	99	.	0			c.T1174G						.						65	66	66					12																	54799001		2203	4300	6503	SO:0001583	missense	3678	exon12			TGCCAAATCGGCC		CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"CD molecules", "Integrins"	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.1174T>G	chr12.hg19:g.54799001A>C	ENSP00000293379:p.Phe392Val	142.0	0.0		153.0	26.0	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	hg19	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.463026	0.84425	.	.	ENSG00000161638	ENST00000293379	T	0.73258	-0.73	4.13	4.13	0.48395	.	0.000000	0.85682	D	0.000000	D	0.87358	0.6157	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.90171	0.4235	10	0.87932	D	0	.	11.4414	0.50099	1.0:0.0:0.0:0.0	.	392	P08648	ITA5_HUMAN	V	392	ENSP00000293379:F392V	ENSP00000293379:F392V	F	-	1	0	ITGA5	53085268	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.704000	0.91351	1.869000	0.54173	0.533000	0.62120	TTT	.	.		0.622	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			C	54799001	A	C	54799001	3	2	212	1	0	0	0	0	1	0	0	0	7888	101	4	5	2051	5	ITGA5	12	54799001	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	20	54799001	79052894	159	30629										
DGKA	1606	hgsc.bcm.edu	37	chr12	56346937	56346937	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tggccaagtgctctgagatcAccttccagtaaggaagactc	10	11	2	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:56346937A>G	ENST00000331886.5	+	22	2510	c.2056A>G	c.(2056-2058)Acc>Gcc	p.T686A	DGKA_ENST00000549079.2_3'UTR|DGKA_ENST00000394147.1_Missense_Mutation_p.T686A|DGKA_ENST00000551156.1_Missense_Mutation_p.T686A	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	686					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	CTCTGAGATCACCTTCCAGTA	0.567																																					p.T686A		Atlas-SNP	.											.	DGKA	70	.	0			c.A2056G						.						80	79	79					12																	56346937		2203	4300	6503	SO:0001583	missense	1606	exon22			GAGATCACCTTCC	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"EF-hand domain containing"	2849	protein-coding gene	gene with protein product		125855	"diacylglycerol kinase, alpha (80kD)"	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.2056A>G	chr12.hg19:g.56346937A>G	ENSP00000328405:p.Thr686Ala	57.0	0.0		72.0	24.0	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Missense_Mutation	SNP	ENST00000331886.5	hg19	CCDS8896.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.825075	0.71143	.	.	ENSG00000065357	ENST00000331886;ENST00000394147;ENST00000551156	T;T;T	0.29142	1.58;1.58;1.58	4.83	4.83	0.62350	Diacylglycerol kinase, accessory domain (2);	0.000000	0.85682	D	0.000000	T	0.47154	0.1430	M	0.74881	2.28	0.53005	D	0.999969	B	0.34290	0.447	P	0.47251	0.542	T	0.48811	-0.9002	10	0.49607	T	0.09	.	13.6807	0.62484	1.0:0.0:0.0:0.0	.	686	P23743	DGKA_HUMAN	A	686	ENSP00000328405:T686A;ENSP00000377703:T686A;ENSP00000450359:T686A	ENSP00000328405:T686A	T	+	1	0	DGKA	54633204	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.792000	0.91856	1.932000	0.55993	0.459000	0.35465	ACC	.	.		0.567	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1			G	56346937	A	G	56346937	3	3	212	1	0	0	0	0	1	0	0	0	4467	159	6	2	2138	2	DGKA	12	56346937	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	1547936	56346937	77504958	160	30630										
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56575848	56575848	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gcctcaatttcactcgctggGatccacgtgtcgtaactgcc	9	14	2	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:56575848G>T	ENST00000267064.4	-	8	734	c.648C>A	c.(646-648)atC>atA	p.I216I	RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000550164.1_Silent_p.I216I|SMARCC2_ENST00000394023.3_Silent_p.I216I|SMARCC2_ENST00000550859.1_5'UTR|SMARCC2_ENST00000347471.4_Silent_p.I216I	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	216					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			CACTCGCTGGGATCCACGTGT	0.443																																					p.I216I		Atlas-SNP	.											.	SMARCC2	212	.	0			c.C648A						.						81	74	77					12																	56575848		2203	4300	6503	SO:0001819	synonymous_variant	6601	exon8			CGCTGGGATCCAC	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.648C>A	chr12.hg19:g.56575848G>T		116.0	0.0		142.0	42.0	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Silent	SNP	ENST00000267064.4	hg19	CCDS8907.1																																																																																			.	.		0.443	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			T	56575848	G	T	56575848	2	4	212	1	0	0	0	0	0	0	0	1	14791	1164	41	3		3	SMARCC2	12	56575848	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	228911	56575848	77276047	161	30631										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70928714	70928714	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gagggaatcctggtccgctgGccagtaatgatcacacttta	11	10	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:70928714G>T	ENST00000261266.5	-	28	5478	c.5449C>A	c.(5449-5451)Cca>Aca	p.P1817T	PTPRB_ENST00000538708.1_Missense_Mutation_p.P1727T|RP11-588H23.3_ENST00000547656.1_RNA|RP11-588H23.3_ENST00000551438.1_RNA|PTPRB_ENST00000334414.6_Missense_Mutation_p.P2035T|PTPRB_ENST00000550857.1_Missense_Mutation_p.P1727T|RP11-588H23.3_ENST00000546836.1_RNA|RP11-588H23.3_ENST00000549460.1_RNA|PTPRB_ENST00000451516.2_Missense_Mutation_p.P1727T|PTPRB_ENST00000550358.1_Missense_Mutation_p.P1947T|RP11-588H23.3_ENST00000548687.1_RNA	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1817	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TGGTCCGCTGGCCAGTAATGA	0.512																																					p.P2035T		Atlas-SNP	.											.	PTPRB	676	.	0			c.C6103A						.						65	63	64					12																	70928714		1929	4131	6060	SO:0001583	missense	5787	exon30			CCGCTGGCCAGTA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.5449C>A	chr12.hg19:g.70928714G>T	ENSP00000261266:p.Pro1817Thr	88.0	0.0		97.0	25.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.772249	0.90108	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266	T;T;T;T;T;T	0.20200	2.09;2.09;2.09;2.09;2.09;2.09	5.5	5.5	0.81552	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.64068	0.2565	H	0.96720	3.87	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.76868	-0.2800	10	0.87932	D	0	.	19.7664	0.96346	0.0:0.0:1.0:0.0	.	1727;1727;2035;1817;1947	P23467-2;F5H3G6;P23467-3;P23467;F8VU56	.;.;.;PTPRB_HUMAN;.	T	2035;1727;1947;1727;1727;1817	ENSP00000334928:P2035T;ENSP00000393028:P1727T;ENSP00000448058:P1947T;ENSP00000438927:P1727T;ENSP00000447302:P1727T;ENSP00000261266:P1817T	ENSP00000261266:P1817T	P	-	1	0	PTPRB	69214981	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	9.420000	0.97426	2.735000	0.93741	0.655000	0.94253	CCA	.	.		0.512	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70928714	G	T	70928714	3	4	212	1	0	0	0	0	1	0	0	0	12811	1203	42	3	564	3	PTPRB	12	70928714	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	14352866	70928714	62923181	162	30632										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85279833	85279833	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cataagtagtattaaatatgGtaaaagatatgcacctaaag	7	4	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:85279833G>T	ENST00000266682.5	-	3	845	c.304C>A	c.(304-306)Cca>Aca	p.P102T	SLC6A15_ENST00000552192.1_5'UTR|SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000450363.3_Missense_Mutation_p.P102T	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	102					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						ATTAAATATGGTAAAAGATAT	0.308																																					p.P102T		Atlas-SNP	.											.	SLC6A15	159	.	0			c.C304A						.						47	53	51					12																	85279833		2202	4299	6501	SO:0001583	missense	55117	exon3			AATATGGTAAAAG	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.304C>A	chr12.hg19:g.85279833G>T	ENSP00000266682:p.Pro102Thr	102.0	0.0		174.0	58.0	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	hg19	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	G	18.20	3.570256	0.65765	.	.	ENSG00000072041	ENST00000266682;ENST00000450363	D;D	0.86769	-2.17;-2.17	5.18	4.29	0.51040	.	0.000000	0.85682	D	0.000000	D	0.94453	0.8215	M	0.91872	3.25	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.992	D	0.95393	0.8483	10	0.87932	D	0	.	13.996	0.64402	0.0738:0.0:0.9262:0.0	.	102;102	Q9H9F5;Q9H2J7	.;S6A15_HUMAN	T	102	ENSP00000266682:P102T;ENSP00000390706:P102T	ENSP00000266682:P102T	P	-	1	0	SLC6A15	83803964	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	7.537000	0.82033	1.318000	0.45170	0.585000	0.79938	CCA	.	.		0.308	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		T	85279833	G	T	85279833	3	4	212	1	0	0	0	0	1	0	0	0	14693	1261	44	3	2042	3	SLC6A15	12	85279833	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	14351119	85279833	48572062	163	30633										
HIP1R	9026	hgsc.bcm.edu	37	chr12	123340546	123340546	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggcccagcggtacatcgcgcAgctgaagagccaggtgaatg	15	11	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr12:123340546A>G	ENST00000253083.4	+	14	1273	c.1148A>G	c.(1147-1149)cAg>cGg	p.Q383R		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	383					receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		TACATCGCGCAGCTGAAGAGC	0.682																																					p.Q383R		Atlas-SNP	.											.	HIP1R	68	.	0			c.A1148G						.						39	39	39					12																	123340546		2195	4296	6491	SO:0001583	missense	9026	exon14			TCGCGCAGCTGAA	AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.1148A>G	chr12.hg19:g.123340546A>G	ENSP00000253083:p.Gln383Arg	142.0	0.0		133.0	21.0	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	hg19	CCDS31922.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.294675	0.60086	.	.	ENSG00000130787	ENST00000253083	T	0.17528	2.27	4.84	3.61	0.41365	.	0.055614	0.64402	D	0.000001	T	0.28632	0.0709	M	0.78637	2.42	0.52501	D	0.99995	P;P;P	0.49447	0.92;0.92;0.924	B;P;P	0.49829	0.439;0.623;0.512	T	0.04930	-1.0917	10	0.44086	T	0.13	-26.0226	10.3947	0.44194	0.8536:0.0:0.0:0.1464	.	383;383;371	O75146;Q6NXG8;B3KQW8	HIP1R_HUMAN;.;.	R	383	ENSP00000253083:Q383R	ENSP00000253083:Q383R	Q	+	2	0	HIP1R	121906499	1.000000	0.71417	0.989000	0.46669	0.562000	0.35680	7.337000	0.79256	1.816000	0.52996	0.459000	0.35465	CAG	.	.		0.682	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959		G	123340546	A	G	123340546	3	3	212	1	0	0	0	0	1	0	0	0	7124	188	7	2	1202	2	HIP1R	12	123340546	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	38060713	123340546	10511349	164	30634										
TPTE2	93492	hgsc.bcm.edu	37	chr13	20056675	20056675	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tcaacttcaaacttggaaagTcgttctaacatactttagcc	5	10	3	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr13:20056675T>C	ENST00000400230.2	-	4	176	c.132A>G	c.(130-132)cgA>cgG	p.R44R	TPTE2_ENST00000390680.2_Intron|TPTE2_ENST00000382977.4_Silent_p.R44R|TPTE2_ENST00000382978.1_Silent_p.R44R|TPTE2_ENST00000400103.2_Silent_p.R44R|TPTE2_ENST00000382975.4_Silent_p.R44R|TPTE2_ENST00000457266.2_Silent_p.R44R|TPTE2_ENST00000255310.6_Intron			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	44					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		ACTTGGAAAGTCGTTCTAACA	0.308																																					p.R44R		Atlas-SNP	.											.	TPTE2	225	.	0			c.A132G						.						53	52	53					13																	20056675		2201	4299	6500	SO:0001819	synonymous_variant	93492	exon5			GGAAAGTCGTTCT	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.132A>G	chr13.hg19:g.20056675T>C		279.0	0.0		495.0	138.0	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Silent	SNP	ENST00000400230.2	hg19	CCDS45014.1																																																																																			.	.		0.308	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		C	20056675	T	C	20056675	2	2	212	1	0	0	0	0	0	0	0	1	16446	1654	58	2		2	TPTE2	13	20056675	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10		20056675	95113203	165	30635										
TPTE2	93492	hgsc.bcm.edu	37	chr13	20067639	20067639	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctttaaattcgtttgtctgtGgactagcggatgataagaga	11	5	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr13:20067639G>A	ENST00000400230.2	-	2	58	c.14C>T	c.(13-15)cCa>cTa	p.P5L	TPTE2_ENST00000390680.2_Missense_Mutation_p.P5L|TPTE2_ENST00000382977.4_Missense_Mutation_p.P5L|TPTE2_ENST00000382978.1_Missense_Mutation_p.P5L|TPTE2_ENST00000400103.2_Missense_Mutation_p.P5L|TPTE2_ENST00000382975.4_Missense_Mutation_p.P5L|TPTE2_ENST00000457266.2_Missense_Mutation_p.P5L|TPTE2_ENST00000255310.6_Missense_Mutation_p.P5L			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	5					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		GTTTGTCTGTGGACTAGCGGA	0.358																																					p.P5L		Atlas-SNP	.											.	TPTE2	225	.	0			c.C14T						.						105	99	101					13																	20067639		2203	4300	6503	SO:0001583	missense	93492	exon3			GTCTGTGGACTAG	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.14C>T	chr13.hg19:g.20067639G>A	ENSP00000383089:p.Pro5Leu	26.0	0.0		35.0	11.0	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	hg19	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	G	6.425	0.446511	0.12223	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	D;D;D;D;D;D;D;D	0.97959	-4.06;-4.63;-3.57;-4.11;-4.11;-3.57;-4.06;-4.63	0.854	0.854	0.19007	.	.	.	.	.	D	0.93993	0.8076	L	0.36672	1.1	0.09310	N	1	B;B;B	0.25904	0.015;0.137;0.084	B;B;B	0.31614	0.005;0.133;0.063	D	0.87413	0.2377	8	.	.	.	.	5.0122	0.14319	0.0:0.0:1.0:0.0	.	5;5;5	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	L	5	ENSP00000372438:P5L;ENSP00000382974:P5L;ENSP00000383089:P5L;ENSP00000255310:P5L;ENSP00000375098:P5L;ENSP00000372437:P5L;ENSP00000372435:P5L;ENSP00000442218:P5L	.	P	-	2	0	TPTE2	18965639	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	-0.206000	0.09398	0.743000	0.32719	0.462000	0.41574	CCA	.	.		0.358	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		A	20067639	G	A	20067639	3	1	212	1	0	0	0	0	1	0	0	0	16446	1348	47	3	1630	3	TPTE2	13	20067639	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	10964	20067639	95102239	166	30636										
SACS	26278	hgsc.bcm.edu	37	chr13	23909684	23909684	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	acagatgcatgaaattgtttCcttttcaatctgtctccatc	5	10	3	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr13:23909684C>A	ENST00000382292.3	-	9	8604	c.8331G>T	c.(8329-8331)agG>agT	p.R2777S	SACS_ENST00000402364.1_Missense_Mutation_p.R2027S|SACS_ENST00000382298.3_Missense_Mutation_p.R2777S			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2777					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GAAATTGTTTCCTTTTCAATC	0.343																																					p.R2777S		Atlas-SNP	.											.	SACS	871	.	0			c.G8331T						.						104	96	99					13																	23909684		2203	4299	6502	SO:0001583	missense	26278	exon10			TTGTTTCCTTTTC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.8331G>T	chr13.hg19:g.23909684C>A	ENSP00000371729:p.Arg2777Ser	32.0	0.0		50.0	13.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	18.99	3.739123	0.69304	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.89415	-2.37;-2.51;-2.37	5.2	5.2	0.72013	.	0.051835	0.85682	D	0.000000	D	0.86623	0.5977	L	0.36672	1.1	0.40141	D	0.976831	D	0.59357	0.985	P	0.50314	0.637	D	0.86669	0.1909	10	0.49607	T	0.09	.	10.3663	0.44026	0.0:0.8773:0.0:0.1227	.	2777	Q9NZJ4	SACS_HUMAN	S	2777;2027;2777	ENSP00000371729:R2777S;ENSP00000385844:R2027S;ENSP00000371735:R2777S	ENSP00000371729:R2777S	R	-	3	2	SACS	22807684	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.769000	0.38522	2.584000	0.87258	0.462000	0.41574	AGG	.	.		0.343	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23909684	C	A	23909684	3	1	212	1	0	0	0	0	1	0	0	0	13819	854	30	3	5412	3	SACS	13	23909684	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	3842045	23909684	91260194	167	30637										
ENOX1	55068	hgsc.bcm.edu	37	chr13	43918692	43918692	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	acattgagtgagaatcccagTtaaggcatttttaaaattct	7	6	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr13:43918692T>C	ENST00000261488.6	-	9	1595	c.1018A>G	c.(1018-1020)Act>Gct	p.T340A	ENOX1_ENST00000540032.1_Missense_Mutation_p.T153A|ENOX1_ENST00000412891.1_Missense_Mutation_p.T340A	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	340					rhythmic process (GO:0048511)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(3)|large_intestine(7)|lung(18)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(1)	34		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		AGAATCCCAGTTAAGGCATTT	0.413																																					p.T340A		Atlas-SNP	.											.	ENOX1	158	.	0			c.A1018G						.						103	109	107					13																	43918692		2203	4300	6503	SO:0001583	missense	55068	exon9			TCCCAGTTAAGGC	EF432052	CCDS9389.1	13q14.11	2013-02-12			ENSG00000120658	ENSG00000120658		"RNA binding motif (RRM) containing"	25474	protein-coding gene	gene with protein product		610914				11360993	Standard	NM_001127615		Approved	FLJ10094, PIG38, CNOX, cCNOX	uc001uza.4	Q8TC92	OTTHUMG00000016818	ENST00000261488.6:c.1018A>G	chr13.hg19:g.43918692T>C	ENSP00000261488:p.Thr340Ala	126.0	0.0		137.0	43.0	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	hg19	CCDS9389.1	.	.	.	.	.	.	.	.	.	.	T	6.131	0.392382	0.11638	.	.	ENSG00000120658	ENST00000261488;ENST00000412891;ENST00000540032	T;T	0.40756	1.02;1.02	5.92	4.68	0.58851	.	0.381472	0.31519	N	0.007508	T	0.26666	0.0652	L	0.29908	0.895	0.32516	N	0.536881	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.23013	-1.0200	10	0.08837	T	0.75	-6.0281	10.1971	0.43060	0.2562:0.0:0.0:0.7438	.	153;340	B7Z5K1;Q8TC92	.;ENOX1_HUMAN	A	340;340;153	ENSP00000261488:T340A;ENSP00000415054:T340A	ENSP00000261488:T340A	T	-	1	0	ENOX1	42816692	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.476000	0.22180	2.263000	0.75096	0.533000	0.62120	ACT	.	.		0.413	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993		C	43918692	T	C	43918692	3	2	212	1	0	0	0	0	1	0	0	0	5128	1725	60	2	949	2	ENOX1	13	43918692	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	20009008	43918692	71251186	168	30638										
COG3	83548	hgsc.bcm.edu	37	chr13	46067517	46067517	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	actgtgtgtgtcattgtatgAtgtcttcaggccattgatca	10	7	4	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr13:46067517A>T	ENST00000349995.5	+	12	1335	c.1223A>T	c.(1222-1224)gAt>gTt	p.D408V	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	408					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		TCATTGTATGATGTCTTCAGG	0.333																																					p.D408V	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.A1223T						.						209	199	202					13																	46067517		2203	4300	6503	SO:0001583	missense	83548	exon12			TGTATGATGTCTT	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1223A>T	chr13.hg19:g.46067517A>T	ENSP00000258654:p.Asp408Val	82.0	0.0		127.0	44.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.516445	0.85495	.	.	ENSG00000136152	ENST00000349995	T	0.61392	0.11	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.80924	0.4717	M	0.91663	3.23	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.994;0.998;0.984	D	0.85326	0.1087	10	0.72032	D	0.01	-16.4288	15.0147	0.71576	1.0:0.0:0.0:0.0	.	245;408;408	B4E2F3;Q96JB2;Q96JB2-2	.;COG3_HUMAN;.	V	408	ENSP00000258654:D408V	ENSP00000258654:D408V	D	+	2	0	COG3	44965518	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.331000	0.96430	2.138000	0.66242	0.377000	0.23210	GAT	.	.		0.333	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			T	46067517	A	T	46067517	3	4	212	1	0	0	0	0	1	0	0	0	3661	333	12	4	1269	4	COG3	13	46067517	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	2148825	46067517	69102361	169	30639										
COG3	83548	hgsc.bcm.edu	37	chr13	46104830	46104830	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttctaagaataatattcagcAagtcttccagaagttccacg	6	9	3	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr13:46104830A>G	ENST00000349995.5	+	22	2484	c.2372A>G	c.(2371-2373)cAa>cGa	p.Q791R		NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	791					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AATATTCAGCAAGTCTTCCAG	0.398																																					p.Q791R	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.A2372G						.						107	105	106					13																	46104830		2203	4300	6503	SO:0001583	missense	83548	exon22			TTCAGCAAGTCTT	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.2372A>G	chr13.hg19:g.46104830A>G	ENSP00000258654:p.Gln791Arg	53.0	0.0		73.0	5.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	a	12.13	1.846113	0.32606	.	.	ENSG00000136152	ENST00000349995	T	0.48201	0.82	5.5	4.32	0.51571	.	0.148963	0.64402	D	0.000008	T	0.45657	0.1353	L	0.60455	1.87	0.80722	D	1	B;P	0.48230	0.176;0.907	B;B	0.44224	0.068;0.444	T	0.34625	-0.9821	10	0.34782	T	0.22	-10.2719	10.7764	0.46353	0.9255:0.0:0.0745:0.0	.	628;791	B4E2F3;Q96JB2	.;COG3_HUMAN	R	791	ENSP00000258654:Q791R	ENSP00000258654:Q791R	Q	+	2	0	COG3	45002831	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.166000	0.77553	0.921000	0.36994	-0.286000	0.09958	CAA	.	.		0.398	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			G	46104830	A	G	46104830	3	3	212	1	0	0	0	0	1	0	0	0	3661	130	5	2	2458	2	COG3	13	46104830	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	37313	46104830	69065048	170	30640										
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60348376	60348376	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	acattggactgagactctgcCgaacatctgttaaaaaaaaa	7	8	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr13:60348376C>A	ENST00000400324.4	-	27	3486	c.3266G>T	c.(3265-3267)cGg>cTg	p.R1089L	DIAPH3_ENST00000400319.1_Missense_Mutation_p.R1019L|DIAPH3_ENST00000400330.1_Missense_Mutation_p.R1089L|DIAPH3_ENST00000267215.4_Missense_Mutation_p.R1089L|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Missense_Mutation_p.R1043L|DIAPH3_ENST00000377908.2_Missense_Mutation_p.R1078L	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	1089					actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		GAGACTCTGCCGAACATCTGt	0.323																																					p.R1089L		Atlas-SNP	.											.	DIAPH3	139	.	0			c.G3266T						.						62	59	60					13																	60348376		1802	4071	5873	SO:0001583	missense	81624	exon27			CTCTGCCGAACAT	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.3266G>T	chr13.hg19:g.60348376C>A	ENSP00000383178:p.Arg1089Leu	195.0	0.0		301.0	18.0	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	hg19	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.068699	0.36470	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000267214	D;D;D;D;D;T	0.81739	-1.52;-1.52;-1.53;-1.51;-1.5;-1.49	5.59	2.93	0.34026	.	0.364730	0.25759	N	0.028489	T	0.64305	0.2586	L	0.29908	0.895	0.38703	D	0.953034	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.55192	-0.8179	10	0.41790	T	0.15	.	1.9514	0.03367	0.1232:0.468:0.1782:0.2305	.	826;1089	Q9NSV4-1;Q9NSV4	.;DIAP3_HUMAN	L	1089;1089;1078;1043;1019;1078;1019;1043;1089;826	ENSP00000383178:R1089L;ENSP00000383184:R1089L;ENSP00000367141:R1078L;ENSP00000383173:R1019L;ENSP00000383174:R1043L;ENSP00000267215:R1089L	ENSP00000267214:R826L	R	-	2	0	DIAPH3	59246377	0.342000	0.24809	0.986000	0.45419	0.995000	0.86356	0.643000	0.24750	0.316000	0.23135	0.655000	0.94253	CGG	.	.		0.323	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		A	60348376	C	A	60348376	3	1	212	1	0	0	0	0	1	0	0	0	4522	652	23	1	343	1	DIAPH3	13	60348376	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	14243546	60348376	54821502	171	30641										
RNF31	55072	hgsc.bcm.edu	37	chr14	24617276	24617276	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccctcagcggcctcggtactGgcgtggtgtcaagtttaata	12	11	2	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr14:24617276G>A	ENST00000324103.6	+	2	604	c.284G>A	c.(283-285)tGg>tAg	p.W95*	PSME2_ENST00000216802.5_5'Flank|RNF31_ENST00000382687.3_5'Flank|PSME2_ENST00000560410.1_5'Flank|PSME2_ENST00000471700.2_5'Flank|RNF31_ENST00000559275.1_5'UTR|RNF31_ENST00000557878.1_3'UTR	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	95	Polyubiquitin-binding.				CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		CCTCGGTACTGGCGTGGTGTC	0.587																																					p.W95X		Atlas-SNP	.											.	RNF31	95	.	0			c.G284A						.						103	105	104					14																	24617276		2026	4183	6209	SO:0001587	stop_gained	55072	exon2			GGTACTGGCGTGG	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"RING-type (C3HC4) zinc fingers"	16031	protein-coding gene	gene with protein product	"HOIL-1-interacting protein"	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.284G>A	chr14.hg19:g.24617276G>A	ENSP00000315112:p.Trp95*	44.0	0.0		47.0	15.0	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Nonsense_Mutation	SNP	ENST00000324103.6	hg19	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	G	36	5.800112	0.96960	.	.	ENSG00000092098	ENST00000324103	.	.	.	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.5194	17.9131	0.88940	0.0:0.0:1.0:0.0	.	.	.	.	X	95	.	.	W	+	2	0	RNF31	23687116	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	8.315000	0.89983	2.779000	0.95612	0.655000	0.94253	TGG	.	.		0.587	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		A	24617276	G	A	24617276	4	1	212	1	0	0	0	0	0	1	0	0	13502	1357	47	3	290	3	RNF31	14	24617276	Nonsense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10		24617276	82732264	172	30642										
GPHN	10243	hgsc.bcm.edu	37	chr14	67291253	67291253	+	Frame_Shift_Del	DEL	C	C	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gatattaacaactggaggaaCaggatttgcaccacgagatg							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr14:67291253delC	ENST00000315266.5	+	4	1384	c.263delC	c.(262-264)acafs	p.T88fs	GPHN_ENST00000459628.1_Intron|GPHN_ENST00000543237.1_Frame_Shift_Del_p.T88fs|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000478722.1_Frame_Shift_Del_p.T88fs|GPHN_ENST00000305960.9_Intron	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	88	MPT Mo-transferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		ACTGGAGGAACAGGATTTGCA	0.338			T	MLL	AL																																p.T88fs		Atlas-INDEL	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.262delA						.						102	95	97					14																	67291253		2203	4300	6503	SO:0001589	frameshift_variant	10243	exon4			.	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.263delC	chr14.hg19:g.67291253delC	ENSP00000312771:p.Thr88fs	77.0	0.0		103.0	25.0	NM_001024218	Q9H4E9|Q9P2G2	Frame_Shift_Del	DEL	ENST00000315266.5	hg19	CCDS32103.1																																																																																			.	.		0.338	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		-	67291253	C	-	67291253	7	5	212	1	0	1	0	1	0	0	0	0	6618	478	17	0	277	0	GPHN	14	67291253	Frame_Shift_Del	DEL	C	TCGA-DD-AAE7-01A-11D-A40R-10	42673977	67291253	40058287	173	30643										
PLEKHH1	57475	hgsc.bcm.edu	37	chr14	68046545	68046545	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggctttgccctcttcacggaCgatccctcgggcagggacct	12	15	2	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr14:68046545C>A	ENST00000329153.5	+	22	3267	c.3135C>A	c.(3133-3135)gaC>gaA	p.D1045E	PLEKHH1_ENST00000417684.2_5'UTR	NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	1045	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		TCTTCACGGACGATCCCTCGG	0.592																																					p.D1045E		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.C3135A						.						31	31	31					14																	68046545		1989	4162	6151	SO:0001583	missense	57475	exon22			CACGGACGATCCC	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"Pleckstrin homology (PH) domain containing"	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.3135C>A	chr14.hg19:g.68046545C>A	ENSP00000330278:p.Asp1045Glu	49.0	0.0		55.0	19.0	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	hg19	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.035093	0.54896	.	.	ENSG00000054690	ENST00000329153	T	0.60171	0.21	5.19	-6.3	0.02007	Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	T	0.52158	0.1717	M	0.67569	2.06	0.80722	D	1	P	0.34562	0.457	B	0.36186	0.219	T	0.49679	-0.8914	10	0.46703	T	0.11	.	17.0261	0.86447	0.0:0.1424:0.0:0.8576	.	1045	Q9ULM0	PKHH1_HUMAN	E	1045	ENSP00000330278:D1045E	ENSP00000330278:D1045E	D	+	3	2	PLEKHH1	67116298	0.046000	0.20272	0.333000	0.25482	0.575000	0.36095	-0.794000	0.04584	-1.415000	0.02022	-1.069000	0.02264	GAC	.	.		0.592	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		A	68046545	C	A	68046545	3	1	212	1	0	0	0	0	1	0	0	0	12085	535	19	1	3217	1	PLEKHH1	14	68046545	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	755292	68046545	39302995	174	30644										
SERPINA10	51156	hgsc.bcm.edu	37	chr14	94752462	94752462	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	taccctggatacttggagatTtcttccagtagctgagagtt	10	8	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr14:94752462T>G	ENST00000393096.1	-	4	1591	c.1126A>C	c.(1126-1128)Aat>Cat	p.N376H	SERPINA10_ENST00000261994.4_Missense_Mutation_p.N376H|SERPINA10_ENST00000554723.1_Missense_Mutation_p.N416H|SERPINA10_ENST00000554173.1_Missense_Mutation_p.N376H	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	376					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		ACTTGGAGATTTCTTCCAGTA	0.418																																					p.N376H		Atlas-SNP	.											.	SERPINA10	83	.	0			c.A1126C						.						94	84	87					14																	94752462		2203	4300	6503	SO:0001583	missense	51156	exon4			GGAGATTTCTTCC	AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"Serine (or cysteine) peptidase inhibitors"	15996	protein-coding gene	gene with protein product		605271	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.1126A>C	chr14.hg19:g.94752462T>G	ENSP00000376809:p.Asn376His	60.0	0.0		83.0	24.0	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Missense_Mutation	SNP	ENST00000393096.1	hg19	CCDS9923.1	.	.	.	.	.	.	.	.	.	.	T	4.702	0.130550	0.08981	.	.	ENSG00000140093	ENST00000554723;ENST00000393096;ENST00000261994;ENST00000554173	D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42	4.86	2.29	0.28610	Serpin domain (3);	0.561717	0.16103	N	0.229455	D	0.83672	0.5305	M	0.71296	2.17	0.09310	N	1	B	0.28900	0.227	B	0.27608	0.081	T	0.72364	-0.4316	10	0.36615	T	0.2	.	1.0894	0.01660	0.1459:0.215:0.1504:0.4887	.	376	Q9UK55	ZPI_HUMAN	H	416;376;376;376	ENSP00000450896:N416H;ENSP00000376809:N376H;ENSP00000261994:N376H;ENSP00000450971:N376H	ENSP00000261994:N376H	N	-	1	0	SERPINA10	93822215	0.055000	0.20627	0.012000	0.15200	0.237000	0.25408	1.379000	0.34340	0.593000	0.29745	0.260000	0.18958	AAT	.	.		0.418	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186		G	94752462	T	G	94752462	3	3	212	1	0	0	0	0	1	0	0	0	14102	1841	64	5	216	5	SERPINA10	14	94752462	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	26705917	94752462	12597078	175	30645										
INF2	64423	hgsc.bcm.edu	37	chr14	105180664	105180664	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cttgtagacgccgtgaccccCggccctcagcccaccctgga	10	19	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr14:105180664C>A	ENST00000392634.4	+	21	3277	c.3165C>A	c.(3163-3165)ccC>ccA	p.P1055P	INF2_ENST00000330634.7_Silent_p.P1055P	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	1055					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CCGTGACCCCCGGCCCTCAGC	0.667																																					p.P1055P		Atlas-SNP	.											.	INF2	148	.	0			c.C3165A						.						25	31	29					14																	105180664		1921	4101	6022	SO:0001819	synonymous_variant	64423	exon21			GACCCCCGGCCCT	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"inverted formin 2"	610982	"chromosome 14 open reading frame 151", "chromosome 14 open reading frame 173"	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.3165C>A	chr14.hg19:g.105180664C>A		46.0	0.0		59.0	26.0	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Silent	SNP	ENST00000392634.4	hg19	CCDS9989.2																																																																																			.	.		0.667	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		A	105180664	C	A	105180664	2	1	212	1	0	0	0	0	0	0	0	1	7743	639	23	1		1	INF2	14	105180664	Silent	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	10428202	105180664	2168876	176	30646										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24923532	24923532	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctgtcatcttgcagtctaccTttgtctccaggaaggaggag	11	10	4	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr15:24923532T>A	ENST00000329468.2	+	1	2992	c.2518T>A	c.(2518-2520)Ttt>Att	p.F840I		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	840					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											GCAGTCTACCTTTGTCTCCAG	0.507																																					p.F840I		Atlas-SNP	.											.	.	.	.	0			c.T2518A						.						116	105	109					15																	24923532		2203	4300	6503	SO:0001583	missense	23742	exon1			TCTACCTTTGTCT	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2518T>A	chr15.hg19:g.24923532T>A	ENSP00000333735:p.Phe840Ile	38.0	0.0		54.0	17.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	12.19	1.863291	0.32884	.	.	ENSG00000185823	ENST00000329468	T	0.06528	3.29	1.83	-0.557	0.11800	.	.	.	.	.	T	0.03651	0.0104	N	0.22421	0.69	0.09310	N	1	B	0.27823	0.19	B	0.17722	0.019	T	0.41998	-0.9477	9	0.38643	T	0.18	.	4.2576	0.10724	0.0:0.4931:0.0:0.5069	.	840	Q9NZP6	CO002_HUMAN	I	840	ENSP00000333735:F840I	ENSP00000333735:F840I	F	+	1	0	C15orf2	22474625	0.003000	0.15002	0.000000	0.03702	0.052000	0.14988	-0.192000	0.09587	-0.150000	0.11195	0.338000	0.21704	TTT	.	.		0.507	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24923532	T	A	24923532	3	1	212	1	0	0	0	0	1	0	0	0	1786	1609	56	4	2520	4	C15orf2	15	24923532	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10		24923532	77607860	177	30647										
SPINT1	6692	hgsc.bcm.edu	37	chr15	41136861	41136861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tccagggcacccaggccgggCcaccgcccgcgccccctggg	14	21	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr15:41136861C>T	ENST00000344051.4	+	2	343	c.109C>T	c.(109-111)Cca>Tca	p.P37S	SPINT1_ENST00000431806.1_Missense_Mutation_p.P37S|RP11-532F12.5_ENST00000565315.1_RNA|RP11-532F12.5_ENST00000564302.1_RNA|SPINT1_ENST00000562057.1_Missense_Mutation_p.P37S|RP11-532F12.5_ENST00000568419.1_RNA|RP11-532F12.5_ENST00000568525.1_RNA			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	37					branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		CCAGGCCGGGCCACCGCCCGC	0.751																																					p.P37S		Atlas-SNP	.											.	SPINT1	28	.	0			c.C109T						.						7	9	8					15																	41136861		2110	4128	6238	SO:0001583	missense	6692	exon2			GCCGGGCCACCGC		CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"serine protease inhibitor, Kunitz type 1"				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.109C>T	chr15.hg19:g.41136861C>T	ENSP00000342098:p.Pro37Ser	146.0	0.0		114.0	39.0	NM_181642	Q7Z7D2	Missense_Mutation	SNP	ENST00000344051.4	hg19	CCDS10067.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.790268	0.31685	.	.	ENSG00000166145	ENST00000344051;ENST00000431806	D;D	0.95238	-3.65;-3.65	4.04	3.12	0.35913	.	0.738856	0.12548	N	0.459326	D	0.84920	0.5579	N	0.08118	0	0.09310	N	1	B;B;B	0.22983	0.047;0.078;0.047	B;B;B	0.25291	0.027;0.059;0.027	T	0.73630	-0.3922	10	0.18710	T	0.47	-3.585	5.691	0.17829	0.0:0.6898:0.2:0.1101	.	37;37;37	B2RBU9;O43278-2;O43278	.;.;SPIT1_HUMAN	S	37	ENSP00000342098:P37S;ENSP00000409935:P37S	ENSP00000342098:P37S	P	+	1	0	SPINT1	38924153	0.883000	0.30277	0.346000	0.25655	0.003000	0.03518	1.434000	0.34958	1.030000	0.39839	0.563000	0.77884	CCA	.	.		0.751	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710		T	41136861	C	T	41136861	3	4	212	1	0	0	0	0	1	0	0	0	15083	739	26	3	111	3	SPINT1	15	41136861	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	16213329	41136861	61394531	178	30648										
PDIA3	2923	hgsc.bcm.edu	37	chr15	44060746	44060746	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctttgatggcaatctgaagaGatacctgaagtctgaaccta	9	8	2	5			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr15:44060746G>T	ENST00000300289.5	+	9	1236	c.1088G>T	c.(1087-1089)aGa>aTa	p.R363I	PDIA3_ENST00000538521.1_Missense_Mutation_p.R343I	NM_005313.4	NP_005304.3	P30101	PDIA3_HUMAN	protein disulfide isomerase family A, member 3	363	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein N-linked glycosylation via asparagine (GO:0018279)|protein retention in ER lumen (GO:0006621)|proteolysis (GO:0006508)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|phospholipase C activity (GO:0004629)|poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(2)|skin(1)	17		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)		AATCTGAAGAGATACCTGAAG	0.473																																					p.R363I		Atlas-SNP	.											.	PDIA3	40	.	0			c.G1088T						.						116	117	116					15																	44060746		2198	4296	6494	SO:0001583	missense	2923	exon9			TGAAGAGATACCT		CCDS10101.1	15q15	2009-11-20	2005-06-29	2005-03-03	ENSG00000167004	ENSG00000167004	5.3.4.1	"Protein disulfide isomerases"	4606	protein-coding gene	gene with protein product		602046	"glucose regulated protein, 58kDa", "protein disulfide isomerase-associated 3"	GRP58		8974399	Standard	NM_005313		Approved	P58, ERp61, ERp57, ERp60, GRP57, PI-PLC, HsT17083	uc001zsu.3	P30101	OTTHUMG00000044444	ENST00000300289.5:c.1088G>T	chr15.hg19:g.44060746G>T	ENSP00000300289:p.Arg363Ile	52.0	0.0		83.0	31.0	NM_005313	Q13453|Q14255|Q8IYF8|Q9UMU7	Missense_Mutation	SNP	ENST00000300289.5	hg19	CCDS10101.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.453777	0.63290	.	.	ENSG00000167004	ENST00000300289;ENST00000538826;ENST00000537673;ENST00000538521	T;T	0.22743	1.94;1.94	5.71	3.84	0.44239	Thioredoxin-like fold (3);	0.175943	0.64402	D	0.000016	T	0.21145	0.0509	L	0.50333	1.59	0.80722	D	1	P;P	0.38992	0.645;0.653	B;B	0.39299	0.296;0.255	T	0.03139	-1.1068	10	0.72032	D	0.01	.	9.8998	0.41340	0.222:0.0:0.778:0.0	.	343;363	G5EA52;P30101	.;PDIA3_HUMAN	I	363;338;137;343	ENSP00000300289:R363I;ENSP00000438260:R343I	ENSP00000300289:R363I	R	+	2	0	PDIA3	41848038	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.838000	0.55828	1.410000	0.46936	0.561000	0.74099	AGA	.	.		0.473	PDIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103532.3	NM_005313		T	44060746	G	T	44060746	3	4	212	1	0	0	0	0	1	0	0	0	11678	942	33	3	1122	3	PDIA3	15	44060746	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	2923885	44060746	58470646	179	30649										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48052603	48052603	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aattcgagacacactttataTtgctggcaggtaattttcct	7	8	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr15:48052603T>C	ENST00000316364.5	+	3	651	c.212T>C	c.(211-213)aTt>aCt	p.I71T	SEMA6D_ENST00000558014.1_Missense_Mutation_p.I71T|SEMA6D_ENST00000537942.1_Missense_Mutation_p.I71T|SEMA6D_ENST00000536845.2_Missense_Mutation_p.I71T|SEMA6D_ENST00000354744.4_Missense_Mutation_p.I71T|SEMA6D_ENST00000389428.3_Missense_Mutation_p.I71T|SEMA6D_ENST00000389433.2_Missense_Mutation_p.I71T|SEMA6D_ENST00000558816.1_Missense_Mutation_p.I71T|SEMA6D_ENST00000389432.2_Missense_Mutation_p.I71T|SEMA6D_ENST00000358066.4_Missense_Mutation_p.I71T|SEMA6D_ENST00000355997.3_Missense_Mutation_p.I71T|SEMA6D_ENST00000389425.3_Missense_Mutation_p.I71T	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	71	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		ACACTTTATATTGCTGGCAGG	0.388																																					p.I71T		Atlas-SNP	.											.	SEMA6D	322	.	0			c.T212C						.						82	81	82					15																	48052603		2198	4297	6495	SO:0001583	missense	80031	exon3			TTTATATTGCTGG	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.212T>C	chr15.hg19:g.48052603T>C	ENSP00000324857:p.Ile71Thr	54.0	0.0		95.0	4.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754694	0.69648	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.12879	2.64;2.64;2.64;2.64;2.64;2.64;2.64;2.64;2.64;2.64	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.046039	0.85682	D	0.000000	T	0.42675	0.1213	M	0.85197	2.74	0.80722	D	1	D;P;D;P;D	0.76494	0.999;0.881;0.974;0.78;0.999	D;P;P;P;D	0.71184	0.972;0.72;0.786;0.72;0.972	T	0.47328	-0.9126	10	0.87932	D	0	.	16.087	0.81065	0.0:0.0:0.0:1.0	.	71;71;71;71;71	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	T	71	ENSP00000442040:I71T;ENSP00000446152:I71T;ENSP00000324857:I71T;ENSP00000374084:I71T;ENSP00000374083:I71T;ENSP00000346786:I71T;ENSP00000350770:I71T;ENSP00000374079:I71T;ENSP00000348276:I71T;ENSP00000374076:I71T	ENSP00000324857:I71T	I	+	2	0	SEMA6D	45839895	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.202000	0.70862	0.533000	0.62120	ATT	.	.		0.388	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		C	48052603	T	C	48052603	3	2	212	1	0	0	0	0	1	0	0	0	14057	1493	52	2	218	2	SEMA6D	15	48052603	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	3991857	48052603	54478789	180	30650										
RORA	6095	hgsc.bcm.edu	37	chr15	60803529	60803529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cacatattggttctggtttgAttccattgatatcaagacct	7	8	2	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr15:60803529A>G	ENST00000335670.6	-	5	816	c.716T>C	c.(715-717)aTc>aCc	p.I239T	RP11-219B17.1_ENST00000501579.2_RNA|RP11-219B17.1_ENST00000558235.1_RNA|RP11-219B17.1_ENST00000559902.1_RNA|RORA_ENST00000309157.4_Missense_Mutation_p.I264T|RORA_ENST00000449337.2_Missense_Mutation_p.I184T|RP11-219B17.1_ENST00000558140.1_RNA|RP11-219B17.1_ENST00000559824.1_RNA|RORA_ENST00000560004.1_5'Flank|RORA_ENST00000261523.5_Missense_Mutation_p.I272T	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	239	Hinge.				angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						TTCTGGTTTGATTCCATTGAT	0.532																																					p.I272T		Atlas-SNP	.											.	RORA	114	.	0			c.T815C						.						213	158	176					15																	60803529		2203	4300	6503	SO:0001583	missense	6095	exon6			GGTTTGATTCCAT	U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"Nuclear hormone receptors"	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.716T>C	chr15.hg19:g.60803529A>G	ENSP00000335087:p.Ile239Thr	82.0	0.0		102.0	32.0	NM_134260	P35397|P35399|P45445|Q495X4|Q96H83	Missense_Mutation	SNP	ENST00000335670.6	hg19	CCDS10177.1	.	.	.	.	.	.	.	.	.	.	A	16.17	3.046933	0.55110	.	.	ENSG00000069667	ENST00000335670;ENST00000449337;ENST00000309157;ENST00000261523	D;D;D;D	0.94758	-3.45;-3.45;-3.51;-3.42	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.95708	0.8604	L	0.58925	1.835	0.80722	D	1	B;B;D;B	0.67145	0.094;0.126;0.996;0.364	B;B;D;B	0.67900	0.108;0.112;0.954;0.236	D	0.93838	0.7134	10	0.10111	T	0.7	.	16.3322	0.83039	1.0:0.0:0.0:0.0	.	239;264;272;184	P35398-2;P35398-3;P35398;P35398-4	.;.;RORA_HUMAN;.	T	239;184;264;272	ENSP00000335087:I239T;ENSP00000402971:I184T;ENSP00000309753:I264T;ENSP00000261523:I272T	ENSP00000261523:I272T	I	-	2	0	RORA	58590821	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	9.326000	0.96389	2.251000	0.74343	0.528000	0.53228	ATC	.	.		0.532	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2			G	60803529	A	G	60803529	3	3	212	1	0	0	0	0	1	0	0	0	13543	333	12	2	883	2	RORA	15	60803529	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	12750926	60803529	41727863	181	30651										
DENND4A	10260	hgsc.bcm.edu	37	chr15	65962168	65962168	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gagcagatgtgtcaagaccaGaggctgatgttgaaatgcaa	13	6	1	5			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr15:65962168G>A	ENST00000431932.2	-	26	4812	c.4604C>T	c.(4603-4605)tCt>tTt	p.S1535F	DENND4A_ENST00000443035.3_Missense_Mutation_p.S1578F	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1535					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						GTCAAGACCAGAGGCTGATGT	0.358																																					p.S1578F		Atlas-SNP	.											.	DENND4A	217	.	0			c.C4733T						.						116	109	112					15																	65962168		1884	4112	5996	SO:0001583	missense	10260	exon27			AGACCAGAGGCTG	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.4604C>T	chr15.hg19:g.65962168G>A	ENSP00000396830:p.Ser1535Phe	67.0	0.0		104.0	30.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	hg19	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	G	7.641	0.680932	0.14907	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.05996	3.37;3.36	5.64	5.64	0.86602	.	0.512841	0.19789	N	0.106040	T	0.05593	0.0147	L	0.27053	0.805	0.31650	N	0.646881	P;B	0.34462	0.454;0.207	B;B	0.23716	0.048;0.048	T	0.06881	-1.0802	10	0.62326	D	0.03	.	14.8629	0.70394	0.0707:0.0:0.9293:0.0	.	1578;1535	E7EPL3;Q7Z401	.;MYCPP_HUMAN	F	1578;1535	ENSP00000391167:S1578F;ENSP00000396830:S1535F	ENSP00000396830:S1535F	S	-	2	0	DENND4A	63749222	0.996000	0.38824	1.000000	0.80357	0.305000	0.27757	2.386000	0.44380	2.659000	0.90383	0.650000	0.86243	TCT	.	.		0.358	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		A	65962168	G	A	65962168	3	1	212	1	0	0	0	0	1	0	0	0	4435	942	33	3	1015	3	DENND4A	15	65962168	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	5158639	65962168	36569224	182	30652										
CCDC33	80125	hgsc.bcm.edu	37	chr15	74559069	74559069	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	agaaacaggagttgttgtccTacaaaatccccatcaagtac	7	10	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr15:74559069T>A	ENST00000398814.3	+	4	801	c.370T>A	c.(370-372)Tac>Aac	p.Y124N	CCDC33_ENST00000321288.5_Missense_Mutation_p.Y327N	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	327										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GTTGTTGTCCTACAAAATCCC	0.493																																					p.Y124N		Atlas-SNP	.											.	CCDC33	160	.	0			c.T370A						.						161	156	158					15																	74559069		1932	4142	6074	SO:0001583	missense	80125	exon4			TTGTCCTACAAAA	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"cancer/testis antigen 61"					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.370T>A	chr15.hg19:g.74559069T>A	ENSP00000381795:p.Tyr124Asn	64.0	0.0		95.0	26.0	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	hg19	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	T	17.99	3.522255	0.64747	.	.	ENSG00000140481	ENST00000321288;ENST00000398814	T;T	0.39787	1.06;1.06	4.45	4.45	0.53987	.	0.134612	0.32703	N	0.005750	T	0.50616	0.1626	L	0.56769	1.78	0.25473	N	0.987801	D	0.54207	0.965	P	0.54312	0.748	T	0.47535	-0.9110	10	0.87932	D	0	.	10.3962	0.44203	0.0:0.0:0.0:1.0	.	124	Q8N5R6-6	.	N	327;124	ENSP00000325012:Y327N;ENSP00000381795:Y124N	ENSP00000325012:Y327N	Y	+	1	0	CCDC33	72346122	0.874000	0.30092	0.691000	0.30163	0.979000	0.70002	3.910000	0.56371	1.781000	0.52344	0.379000	0.24179	TAC	.	.		0.493	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791		A	74559069	T	A	74559069	3	1	212	1	0	0	0	0	1	0	0	0	2808	1522	53	4	384	4	CCDC33	15	74559069	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	8596901	74559069	27972323	183	30653										
TMC3	342125	hgsc.bcm.edu	37	chr15	81635637	81635637	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	accaaatcattccttggttgTagactaaatgtagcacattc	6	9	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr15:81635637T>A	ENST00000359440.5	-	15	1832	c.1697A>T	c.(1696-1698)tAc>tTc	p.Y566F	RP11-761I4.3_ENST00000559277.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.Y567F|RP11-761I4.3_ENST00000560973.1_RNA|RP11-761I4.3_ENST00000560851.1_RNA|RP11-761I4.3_ENST00000559781.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						TCCTTGGTTGTAGACTAAATG	0.353																																					p.Y566F		Atlas-SNP	.											.	TMC3	112	.	0			c.A1697T						.						117	116	116					15																	81635637		1847	4097	5944	SO:0001583	missense	342125	exon15			TGGTTGTAGACTA	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.1697A>T	chr15.hg19:g.81635637T>A	ENSP00000352413:p.Tyr566Phe	51.0	0.0		112.0	37.0	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	hg19	CCDS45324.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.931068	0.52866	.	.	ENSG00000188869	ENST00000359440	T	0.68765	-0.35	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.68924	0.3054	N	0.25031	0.7	0.58432	D	0.999996	D;P	0.76494	0.999;0.943	D;P	0.72982	0.979;0.803	T	0.65569	-0.6136	10	0.22109	T	0.4	-22.9581	14.7994	0.69903	0.0:0.0:0.0:1.0	.	566;566	Q7Z5M5-2;Q7Z5M5	.;TMC3_HUMAN	F	566	ENSP00000352413:Y566F	ENSP00000352413:Y566F	Y	-	2	0	TMC3	79422692	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.539000	0.60657	2.136000	0.66102	0.533000	0.62120	TAC	.	.		0.353	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		A	81635637	T	A	81635637	3	1	212	1	0	0	0	0	1	0	0	0	16001	1638	57	4	1637	4	TMC3	15	81635637	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	7076568	81635637	20895755	184	30654										
CCNF	899	hgsc.bcm.edu	37	chr16	2483037	2483037	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccagcttccaggagctgtggCcgtctccagggaacctgaag	13	13	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:2483037C>A	ENST00000397066.4	+	3	335	c.247C>A	c.(247-249)Ccg>Acg	p.P83T		NM_001761.2	NP_001752.2	P41002	CCNF_HUMAN	cyclin F	83					mitotic nuclear division (GO:0007067)|negative regulation of centrosome duplication (GO:0010826)|placenta development (GO:0001890)|protein ubiquitination (GO:0016567)|re-entry into mitotic cell cycle (GO:0000320)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	centriole (GO:0005814)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(2)|lung(5)|prostate(4)|skin(1)	20		Ovarian(90;0.17)				GGAGCTGTGGCCGTCTCCAGG	0.592																																					p.P83T		Atlas-SNP	.											.	CCNF	110	.	0			c.C247A						.						75	68	70					16																	2483037		2198	4300	6498	SO:0001583	missense	899	exon3			CTGTGGCCGTCTC	Z36714	CCDS10467.1	16p13.3	2008-02-05			ENSG00000162063	ENSG00000162063		"F-boxes /  "other""	1591	protein-coding gene	gene with protein product		600227				7896286	Standard	NM_001761		Approved	FBX1, FBXO1	uc002cqd.1	P41002	OTTHUMG00000128858	ENST00000397066.4:c.247C>A	chr16.hg19:g.2483037C>A	ENSP00000380256:p.Pro83Thr	50.0	0.0		49.0	11.0	NM_001761	B2R8H3|Q96EG9	Missense_Mutation	SNP	ENST00000397066.4	hg19	CCDS10467.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.985295	0.93044	.	.	ENSG00000162063	ENST00000397066	T	0.21543	2.0	5.29	5.29	0.74685	F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	T	0.49029	0.1533	M	0.76002	2.32	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.50608	-0.8808	10	0.87932	D	0	-17.4443	17.872	0.88813	0.0:1.0:0.0:0.0	.	83	P41002	CCNF_HUMAN	T	83	ENSP00000380256:P83T	ENSP00000380256:P83T	P	+	1	0	CCNF	2423038	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.325000	0.79124	2.619000	0.88677	0.655000	0.94253	CCG	.	.		0.592	CCNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250801.1	NM_001761		A	2483037	C	A	2483037	3	1	212	1	0	0	0	0	1	0	0	0	2924	739	26	3	257	3	CCNF	16	2483037	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10		2483037	87871716	185	30655										
GDE1	51573	hgsc.bcm.edu	37	chr16	19514862	19514862	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aaccaagatgggattcgtagTaactcttttcatcaaaggta	8	7	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:19514862T>G	ENST00000353258.3	-	6	1106	c.926A>C	c.(925-927)tAc>tCc	p.Y309S	CTA-363E6.7_ENST00000569345.1_RNA	NM_016641.3	NP_057725.1	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1	309	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol glycerophosphodiesterase activity (GO:0047395)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	13						GGATTCGTAGTAACTCTTTTC	0.463											OREG0023659	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y309S		Atlas-SNP	.											.	GDE1	31	.	0			c.A926C						.						163	143	150					16																	19514862		2197	4300	6497	SO:0001583	missense	51573	exon6			TCGTAGTAACTCT		CCDS10578.1	16p12-p11.2	2011-01-25			ENSG00000006007	ENSG00000006007	3.1.4.46		29644	protein-coding gene	gene with protein product	"membrane interacting protein of RGS16"	605943				12576545, 16472945	Standard	NM_016641		Approved	MIR16	uc002dgh.3	Q9NZC3	OTTHUMG00000131454	ENST00000353258.3:c.926A>C	chr16.hg19:g.19514862T>G	ENSP00000261386:p.Tyr309Ser	55.0	0.0	733	94.0	13.0	NM_016641	O43334|Q6PKF7|Q7KYR4	Missense_Mutation	SNP	ENST00000353258.3	hg19	CCDS10578.1	.	.	.	.	.	.	.	.	.	.	T	19.29	3.799746	0.70567	.	.	ENSG00000006007	ENST00000353258	T	0.27720	1.65	6.08	3.63	0.41609	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.166743	0.56097	D	0.000038	T	0.51058	0.1652	M	0.80422	2.495	0.58432	D	0.999999	D	0.69078	0.997	D	0.67382	0.951	T	0.49808	-0.8900	10	0.34782	T	0.22	-20.1303	9.3852	0.38338	0.1172:0.0651:0.0:0.8176	.	309	Q9NZC3	GDE1_HUMAN	S	309	ENSP00000261386:Y309S	ENSP00000261386:Y309S	Y	-	2	0	GDE1	19422363	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	4.939000	0.63526	1.111000	0.41721	0.533000	0.62120	TAC	.	.		0.463	GDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254274.2	NM_016641		G	19514862	T	G	19514862	3	3	212	1	0	0	0	0	1	0	0	0	6318	1638	57	5	73	5	GDE1	16	19514862	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	17031825	19514862	70839891	186	30656										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48596122	48596122	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgactactgggtaggttctcTttattttcaaagagctttac	8	7	2	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:48596122T>G	ENST00000262384.3	-	2	668	c.432A>C	c.(430-432)aaA>aaC	p.K144N	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	144					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				GTAGGTTCTCTTTATTTTCAA	0.408																																					p.K144N		Atlas-SNP	.											.	N4BP1	121	.	0			c.A432C						.						85	84	85					16																	48596122		1865	4107	5972	SO:0001583	missense	9683	exon2			GTTCTCTTTATTT	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.432A>C	chr16.hg19:g.48596122T>G	ENSP00000262384:p.Lys144Asn	59.0	0.0		81.0	15.0	NM_153029	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	hg19	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	T	3.154	-0.173589	0.06421	.	.	ENSG00000102921	ENST00000262384	T	0.40756	1.02	5.45	-7.86	0.01187	.	0.189315	0.56097	N	0.000037	T	0.07007	0.0178	N	0.00788	-1.185	0.25293	N	0.989342	B	0.02656	0.0	B	0.01281	0.0	T	0.31194	-0.9952	10	0.02654	T	1	-6.9171	3.392	0.07293	0.3683:0.1854:0.3513:0.095	.	144	O75113	N4BP1_HUMAN	N	144	ENSP00000262384:K144N	ENSP00000262384:K144N	K	-	3	2	N4BP1	47153623	0.946000	0.32159	0.018000	0.16275	0.972000	0.66771	0.019000	0.13444	-1.614000	0.01575	-0.339000	0.08088	AAA	.	.		0.408	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		G	48596122	T	G	48596122	3	3	212	1	0	0	0	0	1	0	0	0	10118	1606	56	5	2282	5	N4BP1	16	48596122	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	29081260	48596122	41758631	187	30657										
HEATR3	55027	hgsc.bcm.edu	37	chr16	50100277	50100277	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccttttcgctctcatccgcaGctccagcacccgagcgccga	8	19	1	0	rs532568579		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:50100277G>T	ENST00000299192.7	+	2	329		c.e2-1		RP11-429P3.3_ENST00000568130.2_RNA|HEATR3_ENST00000285767.4_Intron	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3											cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						CTCATCCGCAGCTCCAGCACC	0.741																																					.		Atlas-SNP	.											.	HEATR3	59	.	0			c.139-1G>T						.						8	11	10					16																	50100277		2008	3991	5999	SO:0001630	splice_region_variant	55027	exon2			TCCGCAGCTCCAG	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.139-1G>T	chr16.hg19:g.50100277G>T		38.0	0.0		45.0	16.0	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Splice_Site	SNP	ENST00000299192.7	hg19	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.948180	0.73787	.	.	ENSG00000155393	ENST00000299192	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5296	0.84354	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HEATR3	48657778	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	8.261000	0.89860	2.298000	0.77334	0.462000	0.41574	.	.	.		0.741	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922	Intron	T	50100277	G	T	50100277	5	4	212	1	0	0	0	0	0	0	1	0	7038	985	34	3	144	3	HEATR3	16	50100277	Splice_Site	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	1504155	50100277	40254476	188	30658										
CHD9	80205	hgsc.bcm.edu	37	chr16	53340154	53340154	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aattgtttttagcagaaagtActactcacatgaaagcctat	6	7	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:53340154A>T	ENST00000398510.3	+	31	6712	c.6625A>T	c.(6625-6627)Act>Tct	p.T2209S	CHD9_ENST00000566029.1_Missense_Mutation_p.T2209S|CHD9_ENST00000564845.1_Missense_Mutation_p.T2209S|CHD9_ENST00000447540.1_Missense_Mutation_p.T2210S			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2209					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				AGCAGAAAGTACTACTCACAT	0.328																																					p.T2209S		Atlas-SNP	.											.	CHD9	203	.	0			c.A6625T						.						72	69	70					16																	53340154		1848	4095	5943	SO:0001583	missense	80205	exon32			GAAAGTACTACTC	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.6625A>T	chr16.hg19:g.53340154A>T	ENSP00000381522:p.Thr2209Ser	113.0	0.0		188.0	53.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	hg19		.	.	.	.	.	.	.	.	.	.	A	10.08	1.251232	0.22880	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	D;D	0.85629	-1.94;-2.01	5.88	2.27	0.28462	.	0.093544	0.46442	D	0.000286	T	0.72748	0.3499	N	0.12182	0.205	0.23366	N	0.997822	B;P;B;P;P	0.46220	0.384;0.801;0.03;0.836;0.874	B;B;B;P;P	0.50440	0.127;0.438;0.022;0.52;0.641	T	0.64279	-0.6445	10	0.09590	T	0.72	-2.211	5.3982	0.16281	0.5837:0.1379:0.2784:0.0	.	275;2209;2210;2209;2209	C9JR69;B7ZML1;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;.;CHD9_HUMAN;.	S	2210;2209;275	ENSP00000396345:T2210S;ENSP00000381522:T2209S	ENSP00000381522:T2209S	T	+	1	0	CHD9	51897655	0.057000	0.20700	0.987000	0.45799	0.459000	0.32528	0.253000	0.18296	0.487000	0.27698	0.528000	0.53228	ACT	.	.		0.328	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		T	53340154	A	T	53340154	3	4	212	1	0	0	0	0	1	0	0	0	3334	391	14	4	6747	4	CHD9	16	53340154	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	3239877	53340154	37014599	189	30659										
RPGRIP1L	23322	hgsc.bcm.edu	37	chr16	53639514	53639514	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tctggagggtcactgaccacGgtgaagcgaaggctggtaag	16	8	2	2	rs538306358		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:53639514G>C	ENST00000379925.3	-	26	3764	c.3714C>G	c.(3712-3714)acC>acG	p.T1238T	RPGRIP1L_ENST00000262135.4_Silent_p.T1158T|RPGRIP1L_ENST00000564374.1_Silent_p.T1192T|RPGRIP1L_ENST00000563746.1_Silent_p.T1204T	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1238					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)			endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CACTGACCACGGTGAAGCGAA	0.547																																					p.T1238T		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.C3714G						.						95	77	83					16																	53639514		2198	4300	6498	SO:0001819	synonymous_variant	23322	exon26			GACCACGGTGAAG		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"fantom homolog", "Meckel syndrome, type 5", "protein phosphatase 1, regulatory subunit 134"	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.3714C>G	chr16.hg19:g.53639514G>C		28.0	0.0		36.0	9.0	NM_015272	A0PJ88|Q9Y2K8	Silent	SNP	ENST00000379925.3	hg19	CCDS32447.1																																																																																			.	.		0.547	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		C	53639514	G	C	53639514	2	2	212	1	0	0	0	0	0	0	0	1	13565	1103	39	4		4	RPGRIP1L	16	53639514	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	299360	53639514	36715239	190	30660										
PSMB10	5699	hgsc.bcm.edu	37	chr16	67969964	67969964	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atcttggacgccaccatccgTgtggtcatctcggcgtccgc	11	15	3	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:67969964T>A	ENST00000358514.4	-	4	622	c.285A>T	c.(283-285)acA>acT	p.T95T	CTC-479C5.12_ENST00000573493.1_5'Flank	NM_002801.3	NP_002792.1	P40306	PSB10_HUMAN	proteasome (prosome, macropain) subunit, beta type, 10	95					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cell morphogenesis (GO:0000902)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|humoral immune response (GO:0006959)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			NS(2)|endometrium(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)	Carfilzomib(DB08889)	CCACCATCCGTGTGGTCATCT	0.672																																					p.T95T		Atlas-SNP	.											.	PSMB10	19	.	0			c.A285T						.						33	37	36					16																	67969964		2195	4285	6480	SO:0001819	synonymous_variant	5699	exon4			CATCCGTGTGGTC	Y13640	CCDS10853.1	16q22.1	2008-02-05			ENSG00000205220	ENSG00000205220		"Proteasome (prosome, macropain) subunits"	9538	protein-coding gene	gene with protein product		176847		MECL1		8268911	Standard	NM_002801		Approved	LMP10, MGC1665, beta2i	uc002eux.2	P40306	OTTHUMG00000137553	ENST00000358514.4:c.285A>T	chr16.hg19:g.67969964T>A		64.0	0.0		43.0	16.0	NM_002801	B2R5J4|Q5U098	Silent	SNP	ENST00000358514.4	hg19	CCDS10853.1																																																																																			.	.		0.672	PSMB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268887.1	NM_002801		A	67969964	T	A	67969964	2	1	212	1	0	0	0	0	0	0	0	1	12687	1683	59	4		4	PSMB10	16	67969964	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	14330450	67969964	22384789	191	30661										
SF3B3	23450	hgsc.bcm.edu	37	chr16	70597888	70597888	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	agagtaacaaccttattatcAttgaaacggaccacaatgcc	6	10	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:70597888A>T	ENST00000302516.5	+	18	2609	c.2398A>T	c.(2398-2400)Att>Ttt	p.I800F		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	800					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				CCTTATTATCATTGAAACGGA	0.458																																					p.I800F		Atlas-SNP	.											.	SF3B3	99	.	0			c.A2398T						.						157	136	143					16																	70597888		2198	4300	6498	SO:0001583	missense	23450	exon18			ATTATCATTGAAA	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.2398A>T	chr16.hg19:g.70597888A>T	ENSP00000305790:p.Ile800Phe	84.0	0.0		103.0	14.0	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	hg19	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.502342	0.85176	.	.	ENSG00000189091	ENST00000302516	T	0.17854	2.25	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.32285	0.0824	M	0.81942	2.565	0.80722	D	1	P	0.45176	0.852	P	0.47981	0.563	T	0.08472	-1.0720	10	0.33940	T	0.23	-16.5354	15.6284	0.76882	1.0:0.0:0.0:0.0	.	800	Q15393	SF3B3_HUMAN	F	800	ENSP00000305790:I800F	ENSP00000305790:I800F	I	+	1	0	SF3B3	69155389	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.229000	0.95273	2.155000	0.67459	0.533000	0.62120	ATT	.	.		0.458	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		T	70597888	A	T	70597888	3	4	212	1	0	0	0	0	1	0	0	0	14167	217	8	4	2464	4	SF3B3	16	70597888	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	2627924	70597888	19756865	192	30662										
ZNRF1	84937	hgsc.bcm.edu	37	chr16	75033939	75033939	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	acctgggctcccgagcctcgCtggcggatgctctacctctg	12	16	2	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:75033939C>A	ENST00000335325.4	+	1	1012	c.370C>A	c.(370-372)Ctg>Atg	p.L124M	WDR59_ENST00000562331.1_5'Flank|ZNRF1_ENST00000567962.1_Missense_Mutation_p.L124M|ZNRF1_ENST00000320619.6_Missense_Mutation_p.L124M|ZNRF1_ENST00000566250.1_Missense_Mutation_p.L124M	NM_032268.4	NP_115644.1	Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase	124					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)	1						CCGAGCCTCGCTGGCGGATGC	0.667																																					p.L124M		Atlas-SNP	.											.	ZNRF1	6	.	0			c.C370A						.						31	30	31					16																	75033939		2197	4299	6496	SO:0001583	missense	84937	exon1			GCCTCGCTGGCGG	AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187		"RING-type (C3HC4) zinc fingers"	18452	protein-coding gene	gene with protein product		612060	"zinc and ring finger 1"				Standard	NM_032268		Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606	ENST00000335325.4:c.370C>A	chr16.hg19:g.75033939C>A	ENSP00000335091:p.Leu124Met	72.0	0.0		61.0	24.0	NM_032268	D3DUJ9|Q9H083	Missense_Mutation	SNP	ENST00000335325.4	hg19	CCDS10912.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.953752	0.53293	.	.	ENSG00000186187	ENST00000320619;ENST00000335325	.	.	.	4.93	4.93	0.64822	.	0.000000	0.64402	D	0.000016	T	0.68155	0.2970	L	0.40543	1.245	0.48571	D	0.999671	D;P;D	0.62365	0.991;0.7;0.984	D;B;D	0.75484	0.986;0.368;0.969	T	0.64879	-0.6303	9	0.35671	T	0.21	-7.6933	17.2525	0.87046	0.0:1.0:0.0:0.0	.	124;124;124	B4DG67;Q8ND25-2;Q8ND25	.;.;ZNRF1_HUMAN	M	124	.	ENSP00000323362:L124M	L	+	1	2	ZNRF1	73591440	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.772000	0.55325	2.701000	0.92244	0.650000	0.86243	CTG	.	.		0.667	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2			A	75033939	C	A	75033939	3	1	212	1	0	0	0	0	1	0	0	0	18226	796	28	3	372	3	ZNRF1	16	75033939	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	4436051	75033939	15320814	193	30663										
KIAA0513	9764	hgsc.bcm.edu	37	chr16	85112566	85112566	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccgaggacgaaaagaaggggGagaagatctacctgtacacg	14	8	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:85112566G>T	ENST00000566428.1	+	8	1490	c.859G>T	c.(859-861)Gag>Tag	p.E287*	KIAA0513_ENST00000567328.1_Nonsense_Mutation_p.E287*|KIAA0513_ENST00000538274.1_Nonsense_Mutation_p.E287*|KIAA0513_ENST00000258180.3_Nonsense_Mutation_p.E287*			O60268	K0513_HUMAN	KIAA0513	287						cytoplasm (GO:0005737)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(9)|pancreas(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.234)		AAAGAAGGGGGAGAAGATCTA	0.607																																					p.E287X		Atlas-SNP	.											.	KIAA0513	43	.	0			c.G859T						.						117	100	106					16																	85112566		2198	4300	6498	SO:0001587	stop_gained	9764	exon8			AAGGGGGAGAAGA	AB011085	CCDS32499.1, CCDS67091.1, CCDS73919.1	16q24.1	2012-11-29			ENSG00000135709	ENSG00000135709			29058	protein-coding gene	gene with protein product		611675				9628581	Standard	XM_005256265		Approved		uc002fiu.3	O60268	OTTHUMG00000176597	ENST00000566428.1:c.859G>T	chr16.hg19:g.85112566G>T	ENSP00000457408:p.Glu287*	62.0	0.0		58.0	24.0	NM_014732	B4DSS5|D3DUM2|Q8N6G0	Nonsense_Mutation	SNP	ENST00000566428.1	hg19	CCDS32499.1	.	.	.	.	.	.	.	.	.	.	G	40	8.242504	0.98722	.	.	ENSG00000135709	ENST00000538274;ENST00000258180	.	.	.	5.62	5.62	0.85841	.	0.048418	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-7.6844	18.2538	0.90012	0.0:0.0:1.0:0.0	.	.	.	.	X	287	.	ENSP00000258180:E287X	E	+	1	0	KIAA0513	83670067	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.290000	0.78711	2.644000	0.89710	0.561000	0.74099	GAG	.	.		0.607	KIAA0513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432736.1	NM_014732		T	85112566	G	T	85112566	4	4	212	1	0	0	0	0	0	1	0	0	8190	1175	41	3	885	3	KIAA0513	16	85112566	Nonsense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	10078627	85112566	5242187	194	30664										
ZFPM1	161882	hgsc.bcm.edu	37	chr16	88555560	88555560	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggcagtccctggagcgggccAggtaaccacgcgggtggtgg	19	11	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:88555560A>G	ENST00000319555.3	+	3	589	c.267A>G	c.(265-267)ccA>ccG	p.P89P	ZFPM1_ENST00000569086.1_3'UTR	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	89					atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GGAGCGGGCCAGGTAACCACG	0.731																																					p.P89P	Pancreas(49;850 1106 29641 32847 38344)	Atlas-SNP	.											.	ZFPM1	32	.	0			c.A267G						.						38	31	33					16																	88555560		2172	4252	6424	SO:0001630	splice_region_variant	161882	exon3			CGGGCCAGGTAAC	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	19762	protein-coding gene	gene with protein product		601950	"zinc finger protein, multitype 1"				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.268+1A>G	chr16.hg19:g.88555560A>G		52.0	0.0		52.0	14.0	NM_153813		Silent	SNP	ENST00000319555.3	hg19	CCDS32502.1																																																																																			.	.		0.731	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		Silent	G	88555560	A	G	88555560	5	3	212	1	0	0	0	0	0	0	1	0	17672	202	7	2	277	2	ZFPM1	16	88555560	Splice_Site	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	3442994	88555560	1799193	195	30665										
MVD	4597	hgsc.bcm.edu	37	chr16	88723903	88723903	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cagccgtggggaagttgttcAccgatgccacgtgcaccttg	13	12	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:88723903A>G	ENST00000301012.3	-	4	373	c.344T>C	c.(343-345)gTg>gCg	p.V115A	MVD_ENST00000568709.1_5'UTR	NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	115					cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GAAGTTGTTCACCGATGCCAC	0.682																																					p.V115A		Atlas-SNP	.											.	MVD	27	.	0			c.T344C						.						39	33	35					16																	88723903		2198	4299	6497	SO:0001583	missense	4597	exon4			TTGTTCACCGATG	U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4.1.1.33		7529	protein-coding gene	gene with protein product	"mevalonate pyrophosphate decarboxylase"	603236				8626466	Standard	NM_002461		Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.344T>C	chr16.hg19:g.88723903A>G	ENSP00000301012:p.Val115Ala	170.0	0.0		173.0	8.0	NM_002461	Q53Y65	Missense_Mutation	SNP	ENST00000301012.3	hg19	CCDS10968.1	.	.	.	.	.	.	.	.	.	.	A	8.701	0.909655	0.17833	.	.	ENSG00000167508	ENST00000301012	D	0.85088	-1.94	5.18	-4.06	0.03986	Ribosomal protein S5 domain 2-type fold (1);GHMP kinase (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.667620	0.15084	N	0.281510	T	0.74152	0.3679	L	0.39514	1.22	0.42796	D	0.993917	B	0.15719	0.014	B	0.18871	0.023	T	0.50320	-0.8842	10	0.22109	T	0.4	-11.4073	10.1365	0.42710	0.2498:0.0:0.0636:0.6866	.	115	P53602	MVD1_HUMAN	A	115	ENSP00000301012:V115A	ENSP00000301012:V115A	V	-	2	0	MVD	87251404	0.067000	0.21026	0.086000	0.20670	0.118000	0.20060	0.451000	0.21779	-1.075000	0.03129	-1.546000	0.00904	GTG	.	.		0.682	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269547.2	NM_002461		G	88723903	A	G	88723903	3	3	212	1	0	0	0	0	1	0	0	0	10003	159	6	2	886	2	MVD	16	88723903	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	168343	88723903	1630850	196	30666										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89349878	89349878	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttctctttgtatctttctggTtttgtcttctccttcctttc	4	11	5	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr16:89349878T>C	ENST00000301030.4	-	9	3532	c.3072A>G	c.(3070-3072)aaA>aaG	p.K1024K	ANKRD11_ENST00000378330.2_Silent_p.K1024K	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1024	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		ATCTTTCTGGTTTTGTCTTCT	0.453																																					p.K1024K		Atlas-SNP	.											.	ANKRD11	195	.	0			c.A3072G						.						155	152	153					16																	89349878		2198	4300	6498	SO:0001819	synonymous_variant	29123	exon9			TTCTGGTTTTGTC	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.3072A>G	chr16.hg19:g.89349878T>C		33.0	0.0		55.0	15.0	NM_001256183	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	T	0.017	-1.487664	0.01018	.	.	ENSG00000167522	ENST00000330736	.	.	.	4.72	-7.07	0.01563	.	.	.	.	.	T	0.43166	0.1235	.	.	.	0.36447	D	0.865824	.	.	.	.	.	.	T	0.45145	-0.9281	5	0.14252	T	0.57	.	11.2506	0.49024	0.0:0.602:0.1003:0.2977	.	.	.	.	S	575	.	ENSP00000330815:N575S	N	-	2	0	ANKRD11	87877379	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	-0.058000	0.11750	-1.657000	0.01492	-0.912000	0.02778	AAC	.	.		0.453	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		C	89349878	T	C	89349878	2	2	212	1	0	0	0	0	0	0	0	1	639	1722	60	2		2	ANKRD11	16	89349878	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	625975	89349878	1004875	197	30667										
ASGR1	432	hgsc.bcm.edu	37	chr17	7077382	7077382	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggcctatgtggtgctggacaAatttctgaggagagagaagg	16	5	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:7077382A>C	ENST00000269299.3	-	8	998	c.599T>G	c.(598-600)tTt>tGt	p.F200C	ASGR1_ENST00000574388.1_Missense_Mutation_p.F161C|ASGR1_ENST00000380920.4_Missense_Mutation_p.F99C|ASGR1_ENST00000572879.1_Missense_Mutation_p.F60C	NM_001197216.2|NM_001671.4	NP_001184145.1|NP_001662.1	P07306	ASGR1_HUMAN	asialoglycoprotein receptor 1	200	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cellular response to extracellular stimulus (GO:0031668)|receptor-mediated endocytosis (GO:0006898)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	10						GTGCTGGACAAATTTCTGAGG	0.632																																					p.F200C		Atlas-SNP	.											.	ASGR1	20	.	0			c.T599G						.						111	113	112					17																	7077382		2203	4300	6503	SO:0001583	missense	432	exon8			TGGACAAATTTCT		CCDS11089.1, CCDS56017.1	17p13-p11	2011-08-30			ENSG00000141505	ENSG00000141505		"C-type lectin domain containing"	742	protein-coding gene	gene with protein product		108360					Standard	NM_001671		Approved	CLEC4H1	uc002ges.4	P07306	OTTHUMG00000102159	ENST00000269299.3:c.599T>G	chr17.hg19:g.7077382A>C	ENSP00000269299:p.Phe200Cys	80.0	0.0		86.0	30.0	NM_001671	I3L1X1	Missense_Mutation	SNP	ENST00000269299.3	hg19	CCDS11089.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.191804	0.38707	.	.	ENSG00000141505	ENST00000269299;ENST00000380920	T	0.26067	1.76	4.46	3.33	0.38152	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.125081	0.36854	N	0.002376	T	0.63593	0.2524	H	0.98612	4.28	0.21184	N	0.999765	D	0.89917	1.0	D	0.97110	1.0	T	0.61922	-0.6963	10	0.87932	D	0	.	8.6047	0.33767	0.828:0.0:0.0:0.172	.	200	P07306	ASGR1_HUMAN	C	200;161	ENSP00000269299:F200C	ENSP00000269299:F200C	F	-	2	0	ASGR1	7018106	0.419000	0.25449	0.230000	0.23976	0.441000	0.31987	1.535000	0.36061	0.805000	0.34159	0.165000	0.16767	TTT	.	.		0.632	ASGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220004.3	NM_001671		C	7077382	A	C	7077382	3	2	212	1	0	0	0	0	1	0	0	0	1039	14	1	5	284	5	ASGR1	17	7077382	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10		7077382	74117828	198	30668										
SLC2A4	6517	hgsc.bcm.edu	37	chr17	7187920	7187920	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgctccagctcctgggcagcCgtacccaccggcagcccctg	11	19	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:7187920C>G	ENST00000317370.8	+	7	1112	c.844C>G	c.(844-846)Cgt>Ggt	p.R282G	RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000571308.1_Missense_Mutation_p.R282G|SLC2A4_ENST00000424875.2_Missense_Mutation_p.R272G	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	282					amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						CCTGGGCAGCCGTACCCACCG	0.637																																					p.R282G		Atlas-SNP	.											SLC2A4,caecum,carcinoma,0,1	SLC2A4	44	.	0			c.C844G						.						37	42	40					17																	7187920		2200	4300	6500	SO:0001583	missense	6517	exon7			GGCAGCCGTACCC	M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"Solute carriers"	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.844C>G	chr17.hg19:g.7187920C>G	ENSP00000320935:p.Arg282Gly	78.0	0.0		86.0	23.0	NM_001042	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	hg19	CCDS11097.1	.	.	.	.	.	.	.	.	.	.	C	9.548	1.115161	0.20795	.	.	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.74947	-0.89;-0.89	4.82	3.84	0.44239	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.394340	0.26045	N	0.026668	T	0.63698	0.2533	L	0.38733	1.17	0.27305	N	0.95747	B;B	0.15473	0.0;0.013	B;B	0.18561	0.007;0.022	T	0.58405	-0.7642	10	0.51188	T	0.08	.	10.14	0.42730	0.3638:0.6362:0.0:0.0	.	282;272	P14672;F5H081	GTR4_HUMAN;.	G	282;272	ENSP00000320935:R282G;ENSP00000396887:R272G	ENSP00000320935:R282G	R	+	1	0	SLC2A4	7128644	0.005000	0.15991	0.662000	0.29724	0.538000	0.34931	0.865000	0.27940	1.239000	0.43787	-0.182000	0.12963	CGT	.	.		0.637	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3			G	7187920	C	G	7187920	3	3	212	1	0	0	0	0	1	0	0	0	14561	652	23	4	870	4	SLC2A4	17	7187920	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	110538	7187920	74007290	199	30669										
MYH10	4628	hgsc.bcm.edu	37	chr17	8416885	8416885	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cttccgctccatctcctccaGctctccttccaccttcgtct	3	21	3	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:8416885G>T	ENST00000269243.4	-	21	2761	c.2623C>A	c.(2623-2625)Ctg>Atg	p.L875M	MYH10_ENST00000396239.1_Missense_Mutation_p.L896M|RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000379980.4_Missense_Mutation_p.L891M|MYH10_ENST00000360416.3_Missense_Mutation_p.L906M	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	875					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						ATCTCCTCCAGCTCTCCTTCC	0.537																																					p.L906M		Atlas-SNP	.											.	MYH10	148	.	0			c.C2716A						.						185	137	153					17																	8416885		2203	4300	6503	SO:0001583	missense	4628	exon23			CCTCCAGCTCTCC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2623C>A	chr17.hg19:g.8416885G>T	ENSP00000269243:p.Leu875Met	21.0	0.0		44.0	5.0	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	hg19	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.685001	0.68157	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.76695	0.4023	M	0.68728	2.09	0.51233	D	0.999917	P;P;P	0.35600	0.499;0.511;0.499	B;B;B	0.38755	0.164;0.281;0.164	T	0.79006	-0.1979	10	0.62326	D	0.03	.	18.7586	0.91840	0.0:0.0:1.0:0.0	.	884;906;875	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	M	875;906;896;891	ENSP00000269243:L875M;ENSP00000353590:L906M;ENSP00000379539:L896M;ENSP00000369315:L891M	ENSP00000269243:L875M	L	-	1	2	MYH10	8357610	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	6.559000	0.73946	2.649000	0.89929	0.561000	0.74099	CTG	.	.		0.537	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			T	8416885	G	T	8416885	3	4	212	1	0	0	0	0	1	0	0	0	10039	962	34	3	3391	3	MYH10	17	8416885	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	1228965	8416885	72778325	200	30670										
MYH3	4621	hgsc.bcm.edu	37	chr17	10543714	10543714	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tctgcacacagcttgtgtccGggtgattagtttggccaggc	13	10	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:10543714G>T	ENST00000583535.1	-	21	2449	c.2362C>A	c.(2362-2364)Cgg>Agg	p.R788R	MYH3_ENST00000226209.7_Silent_p.R788R	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	788	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						GCTTGTGTCCGGGTGATTAGT	0.547																																					p.R788R		Atlas-SNP	.											.	MYH3	227	.	0			c.C2362A						.						112	109	110					17																	10543714		2203	4300	6503	SO:0001819	synonymous_variant	4621	exon21			GTGTCCGGGTGAT		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.2362C>A	chr17.hg19:g.10543714G>T		43.0	0.0		52.0	19.0	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	hg19	CCDS11157.1																																																																																			.	.		0.547	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		T	10543714	G	T	10543714	2	4	212	1	0	0	0	0	0	0	0	1	10045	1115	39	1		1	MYH3	17	10543714	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	2126829	10543714	70651496	201	30671										
NT5M	56953	hgsc.bcm.edu	37	chr17	17206959	17206959	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gggcgggctgggcctggcggGaggccgcgccctacgggtgc	22	13	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:17206959G>T	ENST00000389022.4	+	1	311	c.95G>T	c.(94-96)gGa>gTa	p.G32V		NM_020201.3	NP_064586.1	Q9NPB1	NT5M_HUMAN	5',3'-nucleotidase, mitochondrial	32					dephosphorylation (GO:0016311)|DNA replication (GO:0006260)|dUMP catabolic process (GO:0046079)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine deoxyribonucleotide catabolic process (GO:0009223)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotidase activity (GO:0008252)|nucleotide binding (GO:0000166)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						ggcctggcgggaggccgcgcc	0.766																																					p.G32V		Atlas-SNP	.											.	NT5M	17	.	0			c.G95T						.						6	6	6					17																	17206959		1947	3926	5873	SO:0001583	missense	56953	exon1			TGGCGGGAGGCCG	AF210652	CCDS32581.1	17p11.2	2007-08-01	2002-05-23		ENSG00000205309	ENSG00000205309	3.1.3.5		15769	protein-coding gene	gene with protein product		605292	"5' nucleotidase, mitochondrial"			10899995	Standard	XM_005256731		Approved	dNT-2, dNT2, mdN	uc002grf.3	Q9NPB1	OTTHUMG00000059277	ENST00000389022.4:c.95G>T	chr17.hg19:g.17206959G>T	ENSP00000373674:p.Gly32Val	56.0	0.0		60.0	21.0	NM_020201		Missense_Mutation	SNP	ENST00000389022.4	hg19	CCDS32581.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.490979	0.26774	.	.	ENSG00000205309	ENST00000446264;ENST00000389022	T	0.41758	0.99	3.05	0.898	0.19264	.	1.004140	0.08029	N	0.993176	T	0.20536	0.0494	N	0.08118	0	0.09310	N	0.999999	B;B;B	0.33171	0.278;0.278;0.4	B;B;B	0.34452	0.089;0.089;0.183	T	0.24799	-1.0150	10	0.15499	T	0.54	-1.9385	5.6994	0.17873	0.1224:0.4236:0.454:0.0	.	32;32;32	Q2I378;Q9NPB1;F6S3X3	.;NT5M_HUMAN;.	V	32	ENSP00000373674:G32V	ENSP00000373674:G32V	G	+	2	0	NT5M	17147684	1.000000	0.71417	0.046000	0.18839	0.376000	0.30014	2.221000	0.42917	0.126000	0.18424	0.313000	0.20887	GGA	.	.		0.766	NT5M-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446045.1			T	17206959	G	T	17206959	3	4	212	1	0	0	0	0	1	0	0	0	10703	1174	41	3	97	3	NT5M	17	17206959	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	6663245	17206959	63988251	202	30672										
MAP2K3	5606	hgsc.bcm.edu	37	chr17	21203863	21203863	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttccatccttcaagaactttGaggtggaggctgatgacttg	11	8	1	4			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:21203863G>T	ENST00000342679.4	+	4	421	c.172G>T	c.(172-174)Gag>Tag	p.E58*	MAP2K3_ENST00000361818.5_Nonsense_Mutation_p.E29*|MAP2K3_ENST00000316920.6_Nonsense_Mutation_p.E29*	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	58					activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CAAGAACTTTGAGGTGGAGGC	0.582																																					p.E58X		Atlas-SNP	.											.	MAP2K3	135	.	0			c.G172T						.						50	45	47					17																	21203863		2201	4299	6500	SO:0001587	stop_gained	5606	exon4			AACTTTGAGGTGG	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"Mitogen-activated protein kinase cascade / Kinase kinases"	6843	protein-coding gene	gene with protein product	"MAPK/ERK kinase 3", "MAP kinase kinase 3", "dual specificity mitogen activated protein kinase kinase 3"	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.172G>T	chr17.hg19:g.21203863G>T	ENSP00000345083:p.Glu58*	76.0	0.0		89.0	19.0	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Nonsense_Mutation	SNP	ENST00000342679.4	hg19	CCDS11217.1	.	.	.	.	.	.	.	.	.	.	G	35	5.516985	0.96416	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000526076;ENST00000316920	.	.	.	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-49.5232	19.3291	0.94278	0.0:0.0:1.0:0.0	.	.	.	.	X	58;29;29;29;62	.	ENSP00000319139:E62X	E	+	1	0	MAP2K3	21144456	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.760000	0.98935	2.582000	0.87167	0.655000	0.94253	GAG	.	.		0.582	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109		T	21203863	G	T	21203863	4	4	212	1	0	0	0	0	0	1	0	0	9247	1291	45	3	186	3	MAP2K3	17	21203863	Nonsense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	3996904	21203863	59991347	203	30673										
TADA2A	6871	hgsc.bcm.edu	37	chr17	35804827	35804827	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aattatgcagaatgggacttGagagacattgattttgttga	11	3	0	5			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:35804827G>A	ENST00000394395.2	+	8	734	c.561G>A	c.(559-561)ttG>ttA	p.L187L	TADA2A_ENST00000225396.6_Silent_p.L187L|TADA2A_ENST00000586023.1_Silent_p.L187L|TADA2A_ENST00000417170.1_Silent_p.L187L|TADA2A_ENST00000591992.1_3'UTR	NM_001166105.1	NP_001159577.1	O75478	TAD2A_HUMAN	transcriptional adaptor 2A	187					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)|skin(1)	13						AATGGGACTTGAGAGACATTG	0.403																																					p.L187L		Atlas-SNP	.											.	TADA2A	91	.	0			c.G561A						.						237	226	230					17																	35804827		2203	4300	6503	SO:0001819	synonymous_variant	6871	exon8			GGACTTGAGAGAC	AK022767	CCDS11319.1, CCDS45656.1	17q12-q21	2014-04-10	2009-10-02	2009-10-02	ENSG00000108264	ENSG00000276234			11531	protein-coding gene	gene with protein product		602276	"transcriptional adaptor 2 (ADA2 homolog, yeast)-like"	TADA2L		8552087	Standard	XM_006722043		Approved	ADA2, hADA2, ADA2A	uc002hnt.3	O75478	OTTHUMG00000188469	ENST00000394395.2:c.561G>A	chr17.hg19:g.35804827G>A		87.0	0.0		105.0	32.0	NM_001488	A8MVD0|B3KMU9|Q9BVJ0|Q9UCW2|Q9UP49	Silent	SNP	ENST00000394395.2	hg19	CCDS11319.1																																																																																			.	.		0.403	TADA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256677.3	NM_001488		A	35804827	G	A	35804827	2	1	212	1	0	0	0	0	0	0	0	1	15525	1281	45	3		3	TADA2A	17	35804827	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	14600964	35804827	45390383	204	30674										
HEXIM1	10614	hgsc.bcm.edu	37	chr17	43226702	43226702	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aggaggacagtaggtggcaaTcgagagcgttcccccagttg	15	9	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:43226702T>A	ENST00000332499.2	+	1	2019	c.145T>A	c.(145-147)Tcg>Acg	p.S49T	AC002117.1_ENST00000452741.1_RNA|AC002117.1_ENST00000589950.1_RNA	NM_006460.2	NP_006451.1	O94992	HEXI1_HUMAN	hexamethylene bis-acetamide inducible 1	49					heart development (GO:0007507)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|snRNA binding (GO:0017069)			breast(1)|kidney(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TAGGTGGCAATCGAGAGCGTT	0.662											OREG0024474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S49T		Atlas-SNP	.											.	HEXIM1	25	.	0			c.T145A						.						46	49	48					17																	43226702		2203	4300	6503	SO:0001583	missense	10614	exon1			TGGCAATCGAGAG	AB021179	CCDS11495.1	17q21.31	2006-03-28				ENSG00000186834			24953	protein-coding gene	gene with protein product		607328				12119119, 12832472	Standard	NM_006460		Approved	CLP-1, HIS1, MAQ1, EDG1	uc002iig.3	O94992		ENST00000332499.2:c.145T>A	chr17.hg19:g.43226702T>A	ENSP00000328773:p.Ser49Thr	197.0	0.0	914	193.0	54.0	NM_006460	B2R8Y5	Missense_Mutation	SNP	ENST00000332499.2	hg19	CCDS11495.1	.	.	.	.	.	.	.	.	.	.	T	14.40	2.523821	0.44866	.	.	ENSG00000186834	ENST00000332499	.	.	.	4.49	3.39	0.38822	.	0.701221	0.10831	U	0.629313	T	0.32971	0.0847	L	0.44542	1.39	0.27475	N	0.952763	B	0.30281	0.275	B	0.24701	0.055	T	0.19289	-1.0310	9	0.40728	T	0.16	-3.2714	7.9836	0.30198	0.0:0.0:0.2079:0.7921	.	49	O94992	HEXI1_HUMAN	T	49	.	ENSP00000328773:S49T	S	+	1	0	HEXIM1	40582485	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.364000	0.34171	0.737000	0.32582	0.533000	0.62120	TCG	.	.		0.662	HEXIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449821.2	NM_006460		A	43226702	T	A	43226702	3	1	212	1	0	0	0	0	1	0	0	0	7085	1435	50	4	147	4	HEXIM1	17	43226702	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	7421875	43226702	37968508	205	30675										
MED13	9969	hgsc.bcm.edu	37	chr17	60112898	60112898	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggtatacaggttgatgttggTtaatttccacactggtacaa	10	6	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:60112898T>C	ENST00000397786.2	-	4	618	c.542A>G	c.(541-543)aAc>aGc	p.N181S	Y_RNA_ENST00000363972.1_RNA	NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	181					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTGATGTTGGTTAATTTCCAC	0.358																																					p.N181S		Atlas-SNP	.											.	MED13	181	.	0			c.A542G						.						112	107	109					17																	60112898		1895	4141	6036	SO:0001583	missense	9969	exon4			TGTTGGTTAATTT	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.542A>G	chr17.hg19:g.60112898T>C	ENSP00000380888:p.Asn181Ser	41.0	0.0		84.0	6.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	9.127	1.010362	0.19277	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.75938	-0.98	5.28	5.28	0.74379	Mediator complex, subunit Med13, N-terminal, metazoa/fungi (1);	0.047299	0.85682	D	0.000000	T	0.66268	0.2772	L	0.60455	1.87	0.50632	D	0.99988	B	0.11235	0.004	B	0.14578	0.011	T	0.59144	-0.7509	10	0.09843	T	0.71	-19.484	10.2956	0.43623	0.0:0.0842:0.0:0.9158	.	181	Q9UHV7	MED13_HUMAN	S	181;180	ENSP00000380888:N181S	ENSP00000262436:N180S	N	-	2	0	MED13	57467680	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.498000	0.60373	2.119000	0.64992	0.455000	0.32223	AAC	.	.		0.358	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		C	60112898	T	C	60112898	3	2	212	1	0	0	0	0	1	0	0	0	9439	1725	60	2	6090	2	MED13	17	60112898	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	16886196	60112898	21082312	206	30676										
TACO1	51204	hgsc.bcm.edu	37	chr17	61678596	61678596	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctccgggcaggacgctgcacTttaccgcggctgtccccgcc	12	18	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:61678596T>C	ENST00000258975.6	+	1	366	c.154T>C	c.(154-156)Ttt>Ctt	p.F52L		NM_016360.3	NP_057444.2	Q9BSH4	TACO1_HUMAN	translational activator of mitochondrially encoded cytochrome c oxidase I	52					regulation of translation (GO:0006417)	mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|endometrium(1)|lung(1)	4						GACGCTGCACTTTACCGCGGC	0.701																																					p.F52L		Atlas-SNP	.											.	TACO1	13	.	0			c.T154C						.						14	12	13					17																	61678596		2183	4262	6445	SO:0001583	missense	51204	exon1			CTGCACTTTACCG	BC005049	CCDS11640.1	17q23.3	2009-06-26	2009-06-26	2009-06-26		ENSG00000136463			24316	protein-coding gene	gene with protein product		612958	"coiled-coil domain containing 44"	CCDC44		19503089	Standard	NM_016360		Approved		uc002jbd.3	Q9BSH4		ENST00000258975.6:c.154T>C	chr17.hg19:g.61678596T>C	ENSP00000258975:p.Phe52Leu	81.0	0.0		81.0	17.0	NM_016360	B2RD21|Q8N3N6|Q9UI60	Missense_Mutation	SNP	ENST00000258975.6	hg19	CCDS11640.1	.	.	.	.	.	.	.	.	.	.	T	0.813	-0.751410	0.03041	.	.	ENSG00000136463	ENST00000258975	T	0.38887	1.11	5.29	-0.2	0.13216	.	0.669509	0.15039	N	0.284001	T	0.10508	0.0257	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30679	-0.9970	10	0.02654	T	1	-4.1079	2.7245	0.05210	0.1222:0.3776:0.3218:0.1784	.	52	Q9BSH4	TACO1_HUMAN	L	52	ENSP00000258975:F52L	ENSP00000258975:F52L	F	+	1	0	TACO1	59032328	0.893000	0.30496	0.673000	0.29887	0.048000	0.14542	0.090000	0.15025	0.125000	0.18397	-0.252000	0.11476	TTT	.	.		0.701	TACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443862.1	NM_016360		C	61678596	T	C	61678596	3	2	212	1	0	0	0	0	1	0	0	0	15519	1609	56	2	156	2	TACO1	17	61678596	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	1565698	61678596	19516614	207	30677										
MRPS7	51081	hgsc.bcm.edu	37	chr17	73258604	73258604	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tcaggtgagatggagccgctAtagtcctgaattcaaggatc	12	8	2	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:73258604A>G	ENST00000245539.6	+	2	337	c.110A>G	c.(109-111)tAt>tGt	p.Y37C	GGA3_ENST00000582717.1_5'Flank|MRPS7_ENST00000579002.1_Missense_Mutation_p.Y66C|GGA3_ENST00000582486.1_5'Flank|GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000537686.1_5'Flank|GGA3_ENST00000538886.1_5'Flank|GGA3_ENST00000578348.1_5'Flank|MRPS7_ENST00000579761.1_Missense_Mutation_p.Y37C|GGA3_ENST00000351904.7_5'Flank|GGA3_ENST00000245541.6_5'Flank	NM_015971.3	NP_057055.2	Q9Y2R9	RT07_HUMAN	mitochondrial ribosomal protein S7	37					translation (GO:0006412)	cytosolic small ribosomal subunit (GO:0022627)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)	6	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)			TGGAGCCGCTATAGTCCTGAA	0.498																																					p.Y37C		Atlas-SNP	.											.	MRPS7	19	.	0			c.A110G						.						141	145	144					17																	73258604		2203	4300	6503	SO:0001583	missense	51081	exon2			GCCGCTATAGTCC	AB051348	CCDS11718.1	17q25.1	2012-09-13				ENSG00000125445		"Mitochondrial ribosomal proteins / small subunits"	14499	protein-coding gene	gene with protein product		611974					Standard	NM_015971		Approved	MRP-S, RP-S7, RPMS7	uc002jnm.4	Q9Y2R9		ENST00000245539.6:c.110A>G	chr17.hg19:g.73258604A>G	ENSP00000245539:p.Tyr37Cys	58.0	0.0		80.0	23.0	NM_015971	B2R9N5|Q53GD6	Missense_Mutation	SNP	ENST00000245539.6	hg19	CCDS11718.1	.	.	.	.	.	.	.	.	.	.	A	12.40	1.925564	0.34002	.	.	ENSG00000125445	ENST00000245539	T	0.52295	0.67	5.57	5.57	0.84162	Ribosomal protein S7 domain (2);	0.000000	0.85682	D	0.000000	T	0.67906	0.2943	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.71892	-0.4455	10	0.87932	D	0	-13.2234	15.7354	0.77839	1.0:0.0:0.0:0.0	.	37	Q9Y2R9	RT07_HUMAN	C	37	ENSP00000245539:Y37C	ENSP00000245539:Y37C	Y	+	2	0	MRPS7	70770199	1.000000	0.71417	0.936000	0.37596	0.308000	0.27856	9.099000	0.94207	2.122000	0.65172	0.528000	0.53228	TAT	.	.		0.498	MRPS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446666.1	NM_015971		G	73258604	A	G	73258604	3	3	212	1	0	0	0	0	1	0	0	0	9857	449	16	2	116	2	MRPS7	17	73258604	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	11580008	73258604	7936606	208	30678										
TRIM65	201292	hgsc.bcm.edu	37	chr17	73892831	73892831	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gcacgccgctgagggccacgTtgcggcgcagctcggcgccg	17	16	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr17:73892831T>G	ENST00000269383.3	-	1	253	c.188A>C	c.(187-189)aAc>aCc	p.N63T	RP11-552F3.10_ENST00000587267.1_RNA	NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	63						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			GAGGGCCACGTTGCGGCGCAG	0.786																																					p.N63T		Atlas-SNP	.											.	TRIM65	23	.	0			c.A188C						.						2	2	2					17																	73892831		1468	3073	4541	SO:0001583	missense	201292	exon1			GCCACGTTGCGGC	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	27316	protein-coding gene	gene with protein product			"tripartite motif-containing 65"			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.188A>C	chr17.hg19:g.73892831T>G	ENSP00000269383:p.Asn63Thr	36.0	0.0		57.0	21.0	NM_001256124	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	hg19	CCDS11732.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.49|16.49	3.137829|3.137829	0.56936|0.56936	.|.	.|.	ENSG00000141569|ENSG00000141569	ENST00000269383|ENST00000540128	T|.	0.22539|.	1.95|.	5.45|5.45	4.38|4.38	0.52667|0.52667	Zinc finger, RING/FYVE/PHD-type (1);|.	0.000000|.	0.53938|.	D|.	0.000048|.	T|T	0.27241|0.27241	0.0668|0.0668	N|N	0.08118|0.08118	0|0	0.34321|0.34321	D|D	0.686626|0.686626	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|T	0.34079|0.34079	-0.9843|-0.9843	10|5	0.51188|.	T|.	0.08|.	.|.	7.7749|7.7749	0.29030|0.29030	0.0:0.0725:0.1391:0.7884|0.0:0.0725:0.1391:0.7884	.|.	63|.	Q6PJ69|.	TRI65_HUMAN|.	T|H	63|54	ENSP00000269383:N63T|.	ENSP00000269383:N63T|.	N|Q	-|-	2|3	0|2	TRIM65|TRIM65	71404426|71404426	1.000000|1.000000	0.71417|0.71417	0.927000|0.927000	0.36925|0.36925	0.015000|0.015000	0.08874|0.08874	3.922000|3.922000	0.56462|0.56462	0.920000|0.920000	0.36970|0.36970	0.460000|0.460000	0.39030|0.39030	AAC|CAA	.	.		0.786	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547		G	73892831	T	G	73892831	3	3	212	1	0	0	0	0	1	0	0	0	16554	1725	60	5	1389	5	TRIM65	17	73892831	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	634227	73892831	7302379	209	30679										
SPIRE1	56907	hgsc.bcm.edu	37	chr18	12535487	12535487	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gtactcacctctttcgcactCttaattttggtcagaaatgt	6	10	4	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr18:12535487C>A	ENST00000409402.4	-	4	984	c.717G>T	c.(715-717)aaG>aaT	p.K239N	snoU13_ENST00000459256.1_RNA|SPIRE1_ENST00000410092.3_Missense_Mutation_p.K239N|SPIRE1_ENST00000309836.5_Missense_Mutation_p.K42N|SPIRE1_ENST00000383356.2_Missense_Mutation_p.K80N|SPIRE1_ENST00000453447.2_Missense_Mutation_p.K119N	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1											breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						CTTTCGCACTCTTAATTTTGG	0.368																																					p.K239N		Atlas-SNP	.											.	SPIRE1	120	.	0			c.G717T						.						154	137	143					18																	12535487		2203	4300	6503	SO:0001583	missense	56907	exon4			CGCACTCTTAATT	AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"spire homolog 1 (Drosophila)", "spire family actin nucleation factor 1"			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.717G>T	chr18.hg19:g.12535487C>A	ENSP00000387266:p.Lys239Asn	27.0	0.0		59.0	13.0	NM_020148		Missense_Mutation	SNP	ENST00000409402.4	hg19	CCDS45829.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.669560	0.67814	.	.	ENSG00000134278	ENST00000453447;ENST00000409402;ENST00000410092;ENST00000309836;ENST00000383356;ENST00000449797	T;T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26;1.26	5.83	2.1	0.27182	.	0.046511	0.85682	D	0.000000	T	0.48095	0.1481	L	0.60455	1.87	0.50813	D	0.999893	P;D;D	0.76494	0.93;0.993;0.999	P;D;D	0.68483	0.572;0.913;0.958	T	0.26849	-1.0091	10	0.28530	T	0.3	-12.5837	8.4823	0.33049	0.0:0.5413:0.0:0.4587	.	239;42;239	Q08AE8-2;B4DWX0;Q08AE8	.;.;SPIR1_HUMAN	N	119;239;239;42;80;119	ENSP00000407050:K119N;ENSP00000387266:K239N;ENSP00000387226:K239N;ENSP00000309661:K42N;ENSP00000372847:K80N;ENSP00000401392:K119N	ENSP00000309661:K42N	K	-	3	2	SPIRE1	12525487	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	0.710000	0.25748	0.103000	0.17682	0.557000	0.71058	AAG	.	.		0.368	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818		A	12535487	C	A	12535487	3	1	212	1	0	0	0	0	1	0	0	0	15086	912	32	3	1609	3	SPIRE1	18	12535487	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10		12535487	65541761	210	30680										
MIB1	57534	hgsc.bcm.edu	37	chr18	19437092	19437092	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctgtgttaccgttttccagaCtgtgctaacctgatgaaaaa	8	9	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr18:19437092C>T	ENST00000261537.6	+	19	2931	c.2667C>T	c.(2665-2667)aaC>aaT	p.N889N	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	889					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			GTTTTCCAGACTGTGCTAACC	0.398																																					p.N889N		Atlas-SNP	.											.	MIB1	87	.	0			c.C2667T						.						172	130	144					18																	19437092		2203	4300	6503	SO:0001630	splice_region_variant	57534	exon19			TCCAGACTGTGCT	AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.2666-1C>T	chr18.hg19:g.19437092C>T		55.0	0.0		65.0	22.0	NM_020774	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Silent	SNP	ENST00000261537.6	hg19	CCDS11871.1																																																																																			.	.		0.398	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774	Silent	T	19437092	C	T	19437092	5	4	212	1	0	0	0	0	0	0	1	0	9575	579	20	3	2741	3	MIB1	18	19437092	Splice_Site	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	6901605	19437092	58640156	211	30681										
MALT1	10892	hgsc.bcm.edu	37	chr18	56348515	56348515	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cacagtcacagaattgagtgAtttcctgcaggctatggaac	10	9	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr18:56348515A>G	ENST00000348428.3	+	2	581	c.323A>G	c.(322-324)gAt>gGt	p.D108G	MALT1_ENST00000345724.3_Missense_Mutation_p.D108G|RP11-126O1.4_ENST00000588835.1_RNA	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	108	Death.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						GAATTGAGTGATTTCCTGCAG	0.478			T	BIRC3	MALT																																p.D108G		Atlas-SNP	.		Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	.	MALT1	55	.	0			c.A323G						.						112	104	107					18																	56348515		2203	4300	6503	SO:0001583	missense	10892	exon2			TGAGTGATTTCCT		CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6819	protein-coding gene	gene with protein product	"paracaspase"	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.323A>G	chr18.hg19:g.56348515A>G	ENSP00000319279:p.Asp108Gly	79.0	0.0		100.0	26.0	NM_173844	Q9NTB7|Q9ULX4	Missense_Mutation	SNP	ENST00000348428.3	hg19	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	A	13.70	2.314949	0.40996	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.61274	0.12;0.12	6.03	6.03	0.97812	DEATH-like (2);	0.201056	0.52532	D	0.000078	T	0.42630	0.1211	N	0.12182	0.205	0.54753	D	0.999985	B;B	0.11235	0.004;0.003	B;B	0.10450	0.005;0.002	T	0.25641	-1.0126	10	0.41790	T	0.15	.	16.2338	0.82360	1.0:0.0:0.0:0.0	.	108;108	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	G	108	ENSP00000319279:D108G;ENSP00000304161:D108G	ENSP00000304161:D108G	D	+	2	0	MALT1	54499495	1.000000	0.71417	0.999000	0.59377	0.704000	0.40688	7.825000	0.86693	2.313000	0.78055	0.455000	0.32223	GAT	.	.		0.478	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2			G	56348515	A	G	56348515	3	3	212	1	0	0	0	0	1	0	0	0	9211	333	12	2	329	2	MALT1	18	56348515	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	36911423	56348515	21728733	212	30682										
MUC16	94025	hgsc.bcm.edu	37	chr19	9049646	9049646	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttgggaatgttgtactagtaTctgtccccgaaatagtgacc	10	8	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:9049646T>A	ENST00000397910.4	-	5	32188	c.31985A>T	c.(31984-31986)gAt>gTt	p.D10662V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10664	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGTACTAGTATCTGTCCCCGA	0.498																																					p.D10662V		Atlas-SNP	.											.	MUC16	4315	.	0			c.A31985T						.						150	135	140					19																	9049646		2033	4189	6222	SO:0001583	missense	94025	exon5			CTAGTATCTGTCC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31985A>T	chr19.hg19:g.9049646T>A	ENSP00000381008:p.Asp10662Val	79.0	0.0		107.0	36.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	4.267	0.048737	0.08243	.	.	ENSG00000181143	ENST00000397910	T	0.03065	4.06	2.5	0.0178	0.14113	.	.	.	.	.	T	0.04318	0.0119	L	0.29908	0.895	.	.	.	P	0.50710	0.938	P	0.50049	0.629	T	0.37056	-0.9722	8	0.87932	D	0	.	3.0434	0.06146	0.0:0.154:0.2514:0.5946	.	10662	B5ME49	.	V	10662	ENSP00000381008:D10662V	ENSP00000381008:D10662V	D	-	2	0	MUC16	8910646	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.144000	0.10280	-0.080000	0.12685	0.248000	0.18094	GAT	.	.		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9049646	T	A	9049646	3	1	212	1	0	0	0	0	1	0	0	0	9982	1435	50	4	11858	4	MUC16	19	9049646	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10		9049646	50079337	213	30683										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610240	10610240	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tctggtacatgacagcaccgTtcatgacgtggaggacacac	11	11	2	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:10610240T>C	ENST00000171111.5	-	2	1017	c.470A>G	c.(469-471)aAc>aGc	p.N157S	KEAP1_ENST00000393623.2_Missense_Mutation_p.N157S|KEAP1_ENST00000588024.1_5'Flank	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	157					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GACAGCACCGTTCATGACGTG	0.577																																					p.N157S		Atlas-SNP	.											.	KEAP1	182	.	0			c.A470G						.						183	144	157					19																	10610240		2203	4300	6503	SO:0001583	missense	9817	exon2			GCACCGTTCATGA	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.470A>G	chr19.hg19:g.10610240T>C	ENSP00000171111:p.Asn157Ser	99.0	0.0		82.0	12.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	T	9.822	1.186004	0.21870	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.65549	-0.16;-0.16	4.81	4.81	0.61882	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.132309	0.64402	D	0.000013	T	0.44746	0.1308	N	0.11364	0.135	0.53005	D	0.999962	P	0.39624	0.681	B	0.40741	0.339	T	0.46569	-0.9182	10	0.35671	T	0.21	.	12.3271	0.55018	0.0:0.0:0.0:1.0	.	157	Q14145	KEAP1_HUMAN	S	157	ENSP00000171111:N157S;ENSP00000377245:N157S	ENSP00000171111:N157S	N	-	2	0	KEAP1	10471240	0.990000	0.36364	0.992000	0.48379	0.484000	0.33280	2.136000	0.42121	1.811000	0.52892	0.459000	0.35465	AAC	.	.		0.577	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		C	10610240	T	C	10610240	3	2	212	1	0	0	0	0	1	0	0	0	8150	1725	60	2	1424	2	KEAP1	19	10610240	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	1560594	10610240	48518743	214	30684										
GADD45GIP1	90480	hgsc.bcm.edu	37	chr19	13065097	13065097	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gcagcagctcgcgcctccttCttccgtttctgtttttcctc	7	16	2	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:13065097C>A	ENST00000316939.1	-	2	617	c.594G>T	c.(592-594)aaG>aaT	p.K198N		NM_052850.3	NP_443082.2	Q8TAE8	G45IP_HUMAN	growth arrest and DNA-damage-inducible, gamma interacting protein 1	198					cell cycle (GO:0007049)|viral process (GO:0016032)	mitochondrion (GO:0005739)|nucleus (GO:0005634)				ovary(2)|prostate(1)|skin(1)	4						GCGCCTCCTTCTTCCGTTTCT	0.602																																					p.K198N		Atlas-SNP	.											.	GADD45GIP1	11	.	0			c.G594T						.						71	75	74					19																	13065097		2203	4300	6503	SO:0001583	missense	90480	exon2			CTCCTTCTTCCGT	AF479749	CCDS12290.1	19p13.2	2014-02-12				ENSG00000179271			29996	protein-coding gene	gene with protein product	"papillomavirus L2 interacting nuclear protein 1", "CKII beta binding protein 2", "CR6 interacting factor 1", "p53-responsive gene 6"	605162				10441517, 12482659	Standard	NM_052850		Approved	PLINP-1, MGC4667, MGC4758, CKBBP2, PRG6, Plinp1, CRIF1, CKbetaBP2	uc002mwb.4	Q8TAE8		ENST00000316939.1:c.594G>T	chr19.hg19:g.13065097C>A	ENSP00000323065:p.Lys198Asn	96.0	0.0		104.0	5.0	NM_052850	Q8IVM3|Q8TE51|Q969P9|Q9BSM6	Missense_Mutation	SNP	ENST00000316939.1	hg19	CCDS12290.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872594	0.51695	.	.	ENSG00000179271	ENST00000316939	.	.	.	5.04	3.99	0.46301	.	0.170944	0.48286	D	0.000189	T	0.68961	0.3058	M	0.75777	2.31	0.43885	D	0.996509	D	0.69078	0.997	D	0.68039	0.955	T	0.69822	-0.5041	9	0.72032	D	0.01	-0.2416	4.7827	0.13210	0.1817:0.6497:0.0:0.1686	.	198	Q8TAE8	G45IP_HUMAN	N	198	.	ENSP00000323065:K198N	K	-	3	2	GADD45GIP1	12926097	1.000000	0.71417	0.998000	0.56505	0.385000	0.30292	1.264000	0.33015	1.115000	0.41800	0.558000	0.71614	AAG	.	.		0.602	GADD45GIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452759.2	NM_052850		A	13065097	C	A	13065097	3	1	212	1	0	0	0	0	1	0	0	0	6192	912	32	3	78	3	GADD45GIP1	19	13065097	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	2454857	13065097	46063886	215	30685										
CILP2	148113	hgsc.bcm.edu	37	chr19	19655014	19655014	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgtaccacgaggtcaaggccAtgcggaagaaagccccggtc	13	12	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:19655014A>T	ENST00000291495.5	+	8	1745	c.1660A>T	c.(1660-1662)Atg>Ttg	p.M554L	CILP2_ENST00000586018.1_Missense_Mutation_p.M560L	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	554						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						GGTCAAGGCCATGCGGAAGAA	0.617																																					p.M554L		Atlas-SNP	.											.	CILP2	84	.	0			c.A1660T						.						76	82	80					19																	19655014		2203	4300	6503	SO:0001583	missense	148113	exon8			AAGGCCATGCGGA	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1660A>T	chr19.hg19:g.19655014A>T	ENSP00000291495:p.Met554Leu	63.0	0.0		50.0	15.0	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	hg19	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	A	0.319	-0.962991	0.02249	.	.	ENSG00000160161	ENST00000291495	T	0.38887	1.11	3.77	2.42	0.29668	.	0.153045	0.56097	N	0.000032	T	0.17365	0.0417	N	0.05534	-0.03	0.30559	N	0.76469	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.34304	-0.9834	10	0.02654	T	1	-10.23	8.978	0.35948	0.4523:0.5477:0.0:0.0	.	554;554	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	L	554	ENSP00000291495:M554L	ENSP00000291495:M554L	M	+	1	0	CILP2	19516014	0.907000	0.30839	0.988000	0.46212	0.959000	0.62525	0.920000	0.28705	0.144000	0.18951	0.352000	0.21897	ATG	.	.		0.617	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		T	19655014	A	T	19655014	3	4	212	1	0	0	0	0	1	0	0	0	3432	217	8	4	1690	4	CILP2	19	19655014	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	6589917	19655014	39473969	216	30686										
LSR	51599	hgsc.bcm.edu	37	chr19	35758146	35758146	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccaggggatgggaccaggagCccgccagggagcaggcaggc	19	12	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:35758146C>A	ENST00000361790.3	+	9	1582	c.1423C>A	c.(1423-1425)Ccc>Acc	p.P475T	LSR_ENST00000602122.1_Missense_Mutation_p.P455T|USF2_ENST00000222305.3_5'Flank|USF2_ENST00000595068.1_5'Flank|LSR_ENST00000360798.3_Missense_Mutation_p.P407T|LSR_ENST00000347609.4_Missense_Mutation_p.P417T|USF2_ENST00000594064.1_5'Flank|USF2_ENST00000343550.5_5'Flank|LSR_ENST00000354900.3_Missense_Mutation_p.P456T|AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000427250.1_Missense_Mutation_p.P319T|USF2_ENST00000379134.3_5'Flank	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	475					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GGACCAGGAGCCCGCCAGGGA	0.776																																					p.P475T		Atlas-SNP	.											.	LSR	60	.	0			c.C1423A						.						6	8	8					19																	35758146		1891	4016	5907	SO:0001583	missense	51599	exon9			CAGGAGCCCGCCA	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1423C>A	chr19.hg19:g.35758146C>A	ENSP00000354575:p.Pro475Thr	78.0	0.0		84.0	20.0	NM_205834	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Missense_Mutation	SNP	ENST00000361790.3	hg19	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	C	5.926	0.354977	0.11239	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000360798;ENST00000347609;ENST00000427250	T;T;T;T;T	0.63255	0.53;0.69;0.36;0.35;-0.03	4.45	-2.38	0.06622	.	0.803076	0.11011	N	0.609505	T	0.41719	0.1171	L	0.39898	1.24	0.09310	N	1	B;B;B;B;B;B	0.32467	0.094;0.0;0.152;0.372;0.094;0.361	B;B;B;B;B;B	0.21917	0.01;0.001;0.036;0.037;0.016;0.036	T	0.23547	-1.0185	10	0.48119	T	0.1	-7.9039	3.382	0.07257	0.2694:0.385:0.2633:0.0824	.	413;417;455;407;456;475	Q9BT33;Q86X29-2;Q86X29-3;A6NDW3;E9PHD4;Q86X29	.;.;.;.;.;LSR_HUMAN	T	475;456;407;417;319	ENSP00000354575:P475T;ENSP00000346976:P456T;ENSP00000354034:P407T;ENSP00000262627:P417T;ENSP00000394479:P319T	ENSP00000262627:P417T	P	+	1	0	LSR	40449986	0.000000	0.05858	0.099000	0.21106	0.005000	0.04900	-0.757000	0.04772	-0.245000	0.09625	-0.257000	0.10917	CCC	.	.		0.776	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		A	35758146	C	A	35758146	3	1	212	1	0	0	0	0	1	0	0	0	9073	739	26	3	1457	3	LSR	19	35758146	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	16103132	35758146	23370837	217	30687										
COX6B1	1340	hgsc.bcm.edu	37	chr19	36142180	36142180	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggagaccaaaatcaagaactAcaagaccgccccttttgaca	7	12	1	4			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:36142180A>G	ENST00000592141.1	+	2	300	c.35A>G	c.(34-36)tAc>tGc	p.Y12C	COX6B1_ENST00000246554.3_Missense_Mutation_p.Y12C|COX6B1_ENST00000392201.1_Missense_Mutation_p.Y12C			P14854	CX6B1_HUMAN	cytochrome c oxidase subunit VIb polypeptide 1 (ubiquitous)	12					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)			lung(6)|prostate(1)|stomach(1)	8	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ATCAAGAACTACAAGACCGCC	0.572																																					p.Y12C		Atlas-SNP	.											.	COX6B1	20	.	0			c.A35G						.						99	84	89					19																	36142180		2203	4300	6503	SO:0001583	missense	1340	exon2			AGAACTACAAGAC	BC001015	CCDS12469.1	19q13.1	2011-07-04	2010-01-07	2004-08-12	ENSG00000126267	ENSG00000126267	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2280	protein-coding gene	gene with protein product		124089	"cytochrome c oxidase subunit Vib", "cytochrome c oxidase subunit Vib polypeptide 1 (ubiquitous)"	COX6B		1650756	Standard	NM_001863		Approved	COXG	uc002oav.3	P14854	OTTHUMG00000048112	ENST00000592141.1:c.35A>G	chr19.hg19:g.36142180A>G	ENSP00000466818:p.Tyr12Cys	62.0	0.0		93.0	29.0	NM_001863	B2R5C9|Q6IBL4	Missense_Mutation	SNP	ENST00000592141.1	hg19	CCDS12469.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.217516	0.79352	.	.	ENSG00000126267	ENST00000246554;ENST00000392201	D	0.82893	-1.66	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.89577	0.6755	.	.	.	0.58432	D	0.999995	D	0.71674	0.998	D	0.65443	0.935	D	0.90473	0.4454	9	0.66056	D	0.02	-11.8536	11.6541	0.51306	1.0:0.0:0.0:0.0	.	12	P14854	CX6B1_HUMAN	C	12;29	ENSP00000246554:Y12C	ENSP00000246554:Y12C	Y	+	2	0	COX6B1	40834020	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.116000	0.89574	2.017000	0.59298	0.523000	0.50628	TAC	.	.		0.572	COX6B1-004	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459068.3	NM_001863		G	36142180	A	G	36142180	3	3	212	1	0	0	0	0	1	0	0	0	3778	391	14	2	37	2	COX6B1	19	36142180	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	384034	36142180	22986803	218	30688										
ZNF573	126231	hgsc.bcm.edu	37	chr19	38229948	38229948	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgttgaataaggtttgagccAgtactataggccttcccaca	9	9	0	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:38229948A>G	ENST00000590414.2	-	4	1464	c.1443T>C	c.(1441-1443)acT>acC	p.T481T	ZNF573_ENST00000357309.3_Silent_p.T393T|ZNF573_ENST00000339503.4_Silent_p.T423T|ZNF573_ENST00000392138.1_Silent_p.T394T|ZNF573_ENST00000536220.1_Silent_p.T393T			Q86YE8	ZN573_HUMAN	zinc finger protein 573	481					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			GGTTTGAGCCAGTACTATAGG	0.363																																					p.T481T		Atlas-SNP	.											.	ZNF573	63	.	0			c.T1443C						.						85	83	84					19																	38229948		2203	4300	6503	SO:0001819	synonymous_variant	126231	exon5			TGAGCCAGTACTA	AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"Zinc fingers, C2H2-type", "-"	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.1443T>C	chr19.hg19:g.38229948A>G		76.0	0.0		137.0	24.0	NM_001172690	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Silent	SNP	ENST00000590414.2	hg19	CCDS59381.1																																																																																			.	.		0.363	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360		G	38229948	A	G	38229948	2	3	212	1	0	0	0	0	0	0	0	1	18020	175	7	2		2	ZNF573	19	38229948	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	2087768	38229948	20899035	219	30689										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	40993612	40993612	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cctctcctccagatgagcggGaagccgtgcagaagaaaacc	11	13	1	4			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:40993612G>A	ENST00000352632.3	+	3	264	c.178G>A	c.(178-180)Gaa>Aaa	p.E60K	SPTBN4_ENST00000344104.3_Missense_Mutation_p.E60K|SPTBN4_ENST00000595535.1_Missense_Mutation_p.E60K|SPTBN4_ENST00000338932.3_Missense_Mutation_p.E60K|SPTBN4_ENST00000598249.1_Missense_Mutation_p.E60K			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	60	Actin-binding.				actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AGATGAGCGGGAAGCCGTGCA	0.647																																					p.E60K		Atlas-SNP	.											.	SPTBN4	213	.	0			c.G178A						.						44	45	45					19																	40993612		2203	4300	6503	SO:0001583	missense	57731	exon3			GAGCGGGAAGCCG	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.178G>A	chr19.hg19:g.40993612G>A	ENSP00000263373:p.Glu60Lys	47.0	0.0		60.0	22.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	G	34	5.329225	0.95733	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000344104	T;T;T	0.60672	0.17;0.17;0.17	4.28	4.28	0.50868	Calponin homology domain (2);	0.094520	0.41605	U	0.000851	T	0.68961	0.3058	M	0.68728	2.09	0.80722	D	1	D;D	0.63880	0.982;0.993	B;P	0.56916	0.446;0.809	T	0.72462	-0.4286	10	0.51188	T	0.08	.	15.6338	0.76933	0.0:0.0:1.0:0.0	.	60;60	Q9H254;Q71S06	SPTN4_HUMAN;.	K	60	ENSP00000263373:E60K;ENSP00000340345:E60K;ENSP00000340741:E60K	ENSP00000340345:E60K	E	+	1	0	SPTBN4	45685452	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.595000	0.98260	2.215000	0.71742	0.591000	0.81541	GAA	.	.		0.647	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			A	40993612	G	A	40993612	3	1	212	1	0	0	0	0	1	0	0	0	15136	1175	41	3	184	3	SPTBN4	19	40993612	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	2763664	40993612	18135371	220	30690										
CEACAM3	1084	hgsc.bcm.edu	37	chr19	42301605	42301605	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cagtgtcgcagaggggaaggAggtgcttctacttgtccaca	14	9	1	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:42301605A>T	ENST00000357396.3	+	2	390	c.149A>T	c.(148-150)gAg>gTg	p.E50V	CEACAM3_ENST00000344550.4_Missense_Mutation_p.E50V|CEACAM3_ENST00000221999.4_Missense_Mutation_p.E50V|CEACAM3_ENST00000595255.1_3'UTR	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	50	Ig-like V-type.					integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						GAGGGGAAGGAGGTGCTTCTA	0.507																																					p.E50V		Atlas-SNP	.											.	CEACAM3	37	.	0			c.A149T						.						172	158	163					19																	42301605		2203	4300	6503	SO:0001583	missense	1084	exon2			GGAAGGAGGTGCT	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.149A>T	chr19.hg19:g.42301605A>T	ENSP00000349971:p.Glu50Val	105.0	0.0		195.0	53.0	NM_001815	G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	hg19	CCDS12586.2	.	.	.	.	.	.	.	.	.	.	A	13.57	2.276239	0.40294	.	.	ENSG00000170956	ENST00000357396;ENST00000389667;ENST00000221999;ENST00000344550	T;T;T	0.65549	-0.16;-0.16;-0.16	3.44	1.13	0.20643	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.76241	0.3960	M	0.83852	2.665	0.09310	N	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.994	T	0.61865	-0.6975	9	0.87932	D	0	.	5.8708	0.18802	0.7344:0.0:0.2656:0.0	.	50;50	G5E978;P40198	.;CEAM3_HUMAN	V	50	ENSP00000349971:E50V;ENSP00000221999:E50V;ENSP00000341725:E50V	ENSP00000221999:E50V	E	+	2	0	CEACAM3	46993445	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.568000	0.23623	0.300000	0.22699	0.421000	0.28195	GAG	.	.		0.507	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815		T	42301605	A	T	42301605	3	4	212	1	0	0	0	0	1	0	0	0	3195	304	11	4	155	4	CEACAM3	19	42301605	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	1307993	42301605	16827378	221	30691										
C19orf61	56006	hgsc.bcm.edu	37	chr19	44249035	44249035	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	catcagtctgatccaacaggTactgtgggaaaatacataaa	8	8	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:44249035T>C	ENST00000270066.6	-	6	932	c.590A>G	c.(589-591)tAc>tGc	p.Y197C	SMG9_ENST00000601170.1_Splice_Site_p.Y197C	NM_019108.2	NP_061981.2	Q9H0W8	SMG9_HUMAN	SMG9 nonsense mediated mRNA decay factor	197					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|intracellular (GO:0005622)	identical protein binding (GO:0042802)			kidney(1)|large_intestine(5)|liver(1)|lung(7)|pancreas(1)|prostate(2)|urinary_tract(2)	19						ATCCAACAGGTACTGTGGGAA	0.547											OREG0025533	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y197C		Atlas-SNP	.											.	SMG9	39	.	0			c.A590G						.						154	111	126					19																	44249035		2203	4300	6503	SO:0001630	splice_region_variant	56006	exon6			AACAGGTACTGTG	BC008869	CCDS33043.2	19q13.31	2013-07-02	2013-07-02	2011-06-21	ENSG00000105771	ENSG00000105771			25763	protein-coding gene	gene with protein product		613176	"chromosome 19 open reading frame 61", "smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C19orf61		11230166, 19417104	Standard	NM_019108		Approved	FLJ12886	uc002oxj.2	Q9H0W8	OTTHUMG00000150337	ENST00000270066.6:c.589-1A>G	chr19.hg19:g.44249035T>C		72.0	0.0	922	121.0	26.0	NM_019108	O60429|Q9H9A9	Missense_Mutation	SNP	ENST00000270066.6	hg19	CCDS33043.2	.	.	.	.	.	.	.	.	.	.	T	16.54	3.150669	0.57151	.	.	ENSG00000105771	ENST00000270066	.	.	.	5.41	5.41	0.78517	.	0.074229	0.56097	D	0.000030	T	0.68421	0.2999	M	0.72894	2.215	0.58432	D	0.999994	D;D	0.63046	0.99;0.992	P;P	0.60345	0.799;0.873	T	0.70088	-0.4968	9	0.46703	T	0.11	-18.3183	8.814	0.34985	0.1676:0.0:0.0:0.8323	.	197;197	Q9H0W8-2;Q9H0W8	.;SMG9_HUMAN	C	197	.	ENSP00000270066:Y197C	Y	-	2	0	SMG9	48940875	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	5.162000	0.64942	2.059000	0.61396	0.374000	0.22700	TAC	.	.		0.547	SMG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317668.1	NM_019108	Missense_Mutation	C	44249035	T	C	44249035	5	2	212	1	0	0	0	0	0	0	1	0	1945	1652	57	2	1008	2	C19orf61	19	44249035	Splice_Site	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	1947430	44249035	14879948	222	30692										
ERCC2	2068	hgsc.bcm.edu	37	chr19	45860629	45860629	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gatgtccagcggggacagtgTctgtggcgggacagtgggag	20	7	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:45860629T>C	ENST00000391945.4	-	15	1455	c.1378A>G	c.(1378-1380)Aca>Gca	p.T460A	ERCC2_ENST00000391944.3_Splice_Site_p.T382A	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	460	Mediates interaction with MMS19.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		GGGGACAGTGTCTGTGGCGGG	0.637			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.T460A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"		E	.	ERCC2	78	.	0			c.A1378G						.						81	73	76					19																	45860629		2203	4300	6503	SO:0001630	splice_region_variant	2068	exon15	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ACAGTGTCTGTGG		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"General transcription factor IIH complex subunits"	3434	protein-coding gene	gene with protein product	"excision repair cross-complementing rodent repair deficiency, complementation group 2 protein", "TFIIH basal transcription factor complex helicase XPB subunit"	126340	"xeroderma pigmentosum complementary group D", "excision repair cross-complementing rodent repair deficiency, complementation group 2"	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.1378-1A>G	chr19.hg19:g.45860629T>C		91.0	0.0		147.0	42.0	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	hg19	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.544815	0.65198	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	D;D	0.91631	-2.88;-2.88	5.42	5.42	0.78866	.	0.107337	0.64402	D	0.000007	D	0.96071	0.8720	M	0.93197	3.39	0.80722	D	1	D;D;D	0.65815	0.995;0.987;0.969	P;P;P	0.57283	0.817;0.718;0.659	D	0.96709	0.9524	10	0.87932	D	0	-16.4385	11.8517	0.52415	0.0:0.0:0.0:1.0	.	382;460;153	E7EVE9;P18074;Q6ZNQ5	.;ERCC2_HUMAN;.	A	410;436;460;382	ENSP00000375809:T460A;ENSP00000375808:T382A	ENSP00000375805:T410A	T	-	1	0	ERCC2	50552469	1.000000	0.71417	0.955000	0.39395	0.244000	0.25665	6.731000	0.74785	2.052000	0.61016	0.533000	0.62120	ACA	.	.		0.637	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	Missense_Mutation	C	45860629	T	C	45860629	5	2	212	1	0	0	0	0	0	0	1	0	5215	1681	58	2	940	2	ERCC2	19	45860629	Splice_Site	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	1611594	45860629	13268354	223	30693										
PRR12	57479	hgsc.bcm.edu	37	chr19	50102580	50102580	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gtctgggaacctcatcgggtGatgccatatcaggcactgac	12	11	3	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:50102580G>C	ENST00000418929.2	+	5	3742	c.3730G>C	c.(3730-3732)Gat>Cat	p.D1244H		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CTCATCGGGTGATGCCATATC	0.612																																					p.D1244H		Atlas-SNP	.											.	PRR12	157	.	0			c.G3730C						.						31	32	32					19																	50102580		2068	4219	6287	SO:0001583	missense	57479	exon5			TCGGGTGATGCCA	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.3730G>C	chr19.hg19:g.50102580G>C	ENSP00000394510:p.Asp1244His	49.0	0.0		73.0	5.0	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	G	4.688	0.127918	0.08981	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	4.85	4.85	0.62838	.	0.128409	0.34879	N	0.003614	T	0.44787	0.1310	L	0.34521	1.04	0.21416	N	0.999691	P	0.47677	0.899	P	0.50378	0.639	T	0.38478	-0.9659	9	0.52906	T	0.07	-15.9338	16.889	0.86082	0.0:0.0:1.0:0.0	.	1244	Q9ULL5-3	.	H	1244;424;424	.	ENSP00000246798:D424H	D	+	1	0	PRR12	54794392	0.851000	0.29673	0.050000	0.19076	0.017000	0.09413	3.560000	0.53763	2.527000	0.85204	0.563000	0.77884	GAT	.	.		0.612	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		C	50102580	G	C	50102580	3	2	212	1	0	0	0	0	1	0	0	0	12596	1290	45	4	3748	4	PRR12	19	50102580	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	4241951	50102580	9026403	224	30694										
ZNF615	284370	hgsc.bcm.edu	37	chr19	52496613	52496613	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccagttaagcctttgccacaTtcactgcatacatagggttt	7	11	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:52496613T>C	ENST00000602063.1	-	6	2065	c.1716A>G	c.(1714-1716)gaA>gaG	p.E572E	ZNF615_ENST00000598071.1_Silent_p.E583E|ZNF615_ENST00000391795.3_Silent_p.E577E|ZNF615_ENST00000594083.1_Silent_p.E583E|ZNF615_ENST00000376716.5_Silent_p.E572E			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	572					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		CTTTGCCACATTCACTGCATA	0.433																																					p.E583E		Atlas-SNP	.											.	ZNF615	111	.	0			c.A1749G						.						119	102	108					19																	52496613		2203	4300	6503	SO:0001819	synonymous_variant	284370	exon7			GCCACATTCACTG	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.1716A>G	chr19.hg19:g.52496613T>C		47.0	0.0		75.0	18.0	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Silent	SNP	ENST00000602063.1	hg19	CCDS12846.1																																																																																			.	.		0.433	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		C	52496613	T	C	52496613	2	2	212	1	0	0	0	0	0	0	0	1	18055	1490	52	2		2	ZNF615	19	52496613	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	2394033	52496613	6632370	225	30695										
ZNF766	90321	hgsc.bcm.edu	37	chr19	52793977	52793977	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggcaaggtttatagtagcagTtcatacctagcacaacattg	9	8	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:52793977T>C	ENST00000439461.1	+	4	976	c.933T>C	c.(931-933)agT>agC	p.S311S	ZNF766_ENST00000359102.4_Silent_p.S326S|ZNF766_ENST00000593612.1_Silent_p.S326S|ZNF766_ENST00000599581.1_3'UTR|CTD-2525I3.5_ENST00000594865.1_RNA	NM_001010851.2	NP_001010851.1	Q5HY98	ZN766_HUMAN	zinc finger protein 766	311					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	17				GBM - Glioblastoma multiforme(134;0.00236)|OV - Ovarian serous cystadenocarcinoma(262;0.00871)		ATAGTAGCAGTTCATACCTAG	0.373																																					p.S311S		Atlas-SNP	.											.	ZNF766	45	.	0			c.T933C						.						34	37	36					19																	52793977		2140	4277	6417	SO:0001819	synonymous_variant	90321	exon4			TAGCAGTTCATAC	AK024074	CCDS46163.1	19q13.33	2013-01-08				ENSG00000196214		"Zinc fingers, C2H2-type", "-"	28063	protein-coding gene	gene with protein product							Standard	XM_006723458		Approved		uc002pyr.1	Q5HY98		ENST00000439461.1:c.933T>C	chr19.hg19:g.52793977T>C		90.0	0.0		167.0	33.0	NM_001010851	B2RNE0|Q7Z326	Silent	SNP	ENST00000439461.1	hg19	CCDS46163.1																																																																																			.	.		0.373	ZNF766-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462764.1	NM_001010851		C	52793977	T	C	52793977	2	2	212	1	0	0	0	0	0	0	0	1	18155	1722	60	2		2	ZNF766	19	52793977	Silent	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	297364	52793977	6335006	226	30696										
ZNF528	84436	hgsc.bcm.edu	37	chr19	52919622	52919622	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	caaggtcttcagtcgcagttCaaacctggtatgccatcaga	9	11	4	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:52919622C>A	ENST00000360465.3	+	7	1943	c.1517C>A	c.(1516-1518)tCa>tAa	p.S506*	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	506					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		AGTCGCAGTTCAAACCTGGTA	0.393																																					p.S506X		Atlas-SNP	.											.	ZNF528	95	.	0			c.C1517A						.						50	50	50					19																	52919622		2203	4300	6503	SO:0001587	stop_gained	84436	exon7			GCAGTTCAAACCT	AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"Zinc fingers, C2H2-type", "-"	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.1517C>A	chr19.hg19:g.52919622C>A	ENSP00000353652:p.Ser506*	72.0	0.0		153.0	43.0	NM_032423	B3KPN4|Q86T88|Q96JK0	Nonsense_Mutation	SNP	ENST00000360465.3	hg19	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	C	34	5.310654	0.95629	.	.	ENSG00000167555	ENST00000360465	.	.	.	1.83	-1.31	0.09230	.	.	.	.	.	.	.	.	.	.	.	0.53688	D	0.999976	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3109	0.32071	0.4038:0.5961:0.0:0.0	.	.	.	.	X	506	.	ENSP00000353652:S506X	S	+	2	0	ZNF528	57611434	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.583000	0.05807	0.070000	0.16634	-0.321000	0.08615	TCA	.	.		0.393	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423		A	52919622	C	A	52919622	4	1	212	1	0	0	0	0	0	1	0	0	17984	838	29	3	1531	3	ZNF528	19	52919622	Nonsense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	125645	52919622	6209361	227	30697										
ZNF415	55786	hgsc.bcm.edu	37	chr19	53613070	53613070	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tcttcaatgtcatgtttttcAtgttgttccaatgtcactgt	6	8	5	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:53613070A>T	ENST00000500065.4	-	4	561	c.228T>A	c.(226-228)caT>caA	p.H76Q	ZNF415_ENST00000421033.1_Missense_Mutation_p.H88Q|ZNF415_ENST00000601215.1_3'UTR|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000440291.1_Missense_Mutation_p.H63Q|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.H124Q|ZNF415_ENST00000455735.2_Missense_Mutation_p.H124Q|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000243643.4_Missense_Mutation_p.H76Q|ZNF415_ENST00000595813.1_3'UTR	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	124					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		CATGTTTTTCATGTTGTTCCA	0.383																																					p.H76Q		Atlas-SNP	.											.	ZNF415	68	.	0			c.T228A						.						161	140	147					19																	53613070		2203	4300	6503	SO:0001583	missense	55786	exon4			TTTTTCATGTTGT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.228T>A	chr19.hg19:g.53613070A>T	ENSP00000439435:p.His76Gln	72.0	0.0		122.0	30.0	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	hg19	CCDS54313.1	.	.	.	.	.	.	.	.	.	.	A	10.44	1.349984	0.24426	.	.	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.06933	3.4;3.4;3.24;3.24;3.24;3.29	2.5	1.44	0.22558	.	.	.	.	.	T	0.11367	0.0277	N	0.17631	0.505	0.09310	N	1	P;B;P;D;P;P	0.69078	0.879;0.138;0.895;0.997;0.879;0.936	B;B;B;D;B;P	0.75484	0.308;0.05;0.334;0.986;0.381;0.534	T	0.29088	-1.0023	9	0.27082	T	0.32	.	4.4153	0.11454	0.8286:0.0:0.1714:0.0	.	76;124;124;76;63;88	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	Q	76;76;124;88;124;63	ENSP00000243643:H76Q;ENSP00000439435:H76Q;ENSP00000396492:H124Q;ENSP00000395055:H88Q;ENSP00000388787:H124Q;ENSP00000414601:H63Q	ENSP00000243643:H76Q	H	-	3	2	ZNF415	58304882	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-0.534000	0.06150	0.196000	0.20367	0.260000	0.18958	CAT	.	.		0.383	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		T	53613070	A	T	53613070	3	4	212	1	0	0	0	0	1	0	0	0	17907	214	8	4	1443	4	ZNF415	19	53613070	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	693448	53613070	5515913	228	30698										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53643694	53643694	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aacagatactaaagggtttcCcacactcatatggtttctct	6	10	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:53643694C>A	ENST00000334197.7	-	5	2455	c.2387G>T	c.(2386-2388)gGg>gTg	p.G796V	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_Missense_Mutation_p.G797V|ZNF347_ENST00000452676.2_Missense_Mutation_p.G797V	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	796					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		AAAGGGTTTCCCACACTCATA	0.408																																					p.G797V	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.G2390T						.						184	182	182					19																	53643694		2203	4300	6503	SO:0001583	missense	84671	exon5			GGTTTCCCACACT	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2387G>T	chr19.hg19:g.53643694C>A	ENSP00000334146:p.Gly796Val	80.0	0.0		191.0	43.0	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	hg19	CCDS33097.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.97|11.97	1.798129|1.798129	0.31777|0.31777	.|.	.|.	ENSG00000197937|ENSG00000197937	ENST00000436933|ENST00000334197;ENST00000452676	.|T;T	.|0.17854	.|2.25;2.25	2.35|2.35	-1.87|-1.87	0.07737|0.07737	.|Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	.|T	.|0.32912	.|0.0845	M|M	0.74546|0.74546	2.27|2.27	0.19575|0.19575	N|N	0.999968|0.999968	.|D;D	.|0.89917	.|1.0;0.998	.|D;P	.|0.91635	.|0.999;0.786	.|T	.|0.17228	.|-1.0376	.|9	.|0.87932	.|D	.|0	.|.	2.8131|2.8131	0.05447|0.05447	0.182:0.5265:0.1775:0.114|0.182:0.5265:0.1775:0.114	.|.	.|797;796	.|G5E9N4;Q96SE7	.|.;ZN347_HUMAN	.|V	-1|796;797	.|ENSP00000334146:G796V;ENSP00000405218:G797V	.|ENSP00000334146:G796V	.|G	-|-	.|2	.|0	ZNF347|ZNF347	58335506|58335506	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-0.101000|-0.101000	0.10973|0.10973	-0.459000|-0.459000	0.07013|0.07013	-0.266000|-0.266000	0.10368|0.10368	.|GGG	.	.		0.408	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		A	53643694	C	A	53643694	3	1	212	1	0	0	0	0	1	0	0	0	17876	623	22	3	136	3	ZNF347	19	53643694	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	30624	53643694	5485289	229	30699										
ZNF761	388561	hgsc.bcm.edu	37	chr19	53959293	53959293	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tcggaagtcatacctcacatGccatcatagacttcatactg	6	12	4	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:53959293G>A	ENST00000454407.1	+	0	1985							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TACCTCACATGCCATCATAGA	0.418																																					p.C511Y		Atlas-SNP	.											.	ZNF761	104	.	0			c.G1532A						.						105	101	102					19																	53959293		2203	4300	6503			388561	exon7			TCACATGCCATCA	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		chr19.hg19:g.53959293G>A		78.0	0.0		142.0	7.0	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	hg19																																																																																				.	.		0.418	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		A	53959293	G	A	53959293	1	1	212	0	1	0	0	0	0	0	0	0	18151	1319	46	3		3	ZNF761	19	53959293	RNA	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	315599	53959293	5169690	230	30700										
MBOAT7	79143	hgsc.bcm.edu	37	chr19	54677808	54677808	+	Frame_Shift_Del	DEL	C	C	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccttccgccggctggggctgCccccacctaaagccagcccc							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:54677808delC	ENST00000245615.1	-	8	1829	c.1349delG	c.(1348-1350)ggcfs	p.G450fs	MBOAT7_ENST00000431666.2_Frame_Shift_Del_p.G377fs|TMC4_ENST00000476013.2_5'Flank|MBOAT7_ENST00000338624.6_Frame_Shift_Del_p.G377fs|TMC4_ENST00000376591.4_5'Flank|TMC4_ENST00000301187.4_5'Flank	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	450					glycerophospholipid biosynthetic process (GO:0046474)|layer formation in cerebral cortex (GO:0021819)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|ventricular system development (GO:0021591)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipid acyltransferase activity (GO:0071617)			endometrium(4)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	10	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GCTGGGGCTGCCCCCACCTAA	0.662																																					p.G450fs	NSCLC(97;826 2151 10470 22540)	Atlas-INDEL	.											.	MBOAT7	37	.	0			c.1350delC						.						29	30	30					19																	54677808		2203	4300	6503	SO:0001589	frameshift_variant	79143	exon8			.	AF211969	CCDS12883.1, CCDS54315.1, CCDS54316.1	19q13.4	2008-12-15	2008-01-17	2008-01-17	ENSG00000125505	ENSG00000125505			15505	protein-coding gene	gene with protein product	"lysophosphatidylinositol acyltransferase"	606048	"leukocyte receptor cluster (LRC) member 4"	LENG4		10941842, 8702217, 18094042	Standard	NM_024298		Approved	BB1, hMBOA-7, LPIAT	uc002qdr.3	Q96N66	OTTHUMG00000066516	ENST00000245615.1:c.1349delG	chr19.hg19:g.54677808delC	ENSP00000245615:p.Gly450fs	83.0	0.0		129.0	16.0	NM_024298	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Frame_Shift_Del	DEL	ENST00000245615.1	hg19	CCDS12883.1																																																																																			.	.		0.662	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298		-	54677808	C	-	54677808	7	5	212	1	0	1	0	1	0	0	0	0	9367	739	26	0	73	0	MBOAT7	19	54677808	Frame_Shift_Del	DEL	C	TCGA-DD-AAE7-01A-11D-A40R-10	718515	54677808	4451175	231	30701										
BRSK1	84446	hgsc.bcm.edu	37	chr19	55798667	55798667	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctacgagaacaagaaatattTgtaggtatttatagacaccc	7	7	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:55798667T>A	ENST00000309383.1	+	3	594	c.317T>A	c.(316-318)tTg>tAg	p.L106*	BRSK1_ENST00000590333.1_Splice_Site_p.L122*|BRSK1_ENST00000585418.1_Splice_Site_p.L106*	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	106	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		AAGAAATATTTGTAGGTATTT	0.557																																					p.L106X		Atlas-SNP	.											.	BRSK1	192	.	0			c.T317A						.						121	106	111					19																	55798667		2203	4300	6503	SO:0001630	splice_region_variant	84446	exon3			AATATTTGTAGGT	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.317+1T>A	chr19.hg19:g.55798667T>A		42.0	0.0		93.0	22.0	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Nonsense_Mutation	SNP	ENST00000309383.1	hg19	CCDS12921.1	.	.	.	.	.	.	.	.	.	.	.	40	8.174435	0.98691	.	.	ENSG00000160469	ENST00000309383	.	.	.	4.5	4.5	0.54988	.	0.000000	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4864	0.61369	0.0:0.0:0.0:1.0	.	.	.	.	X	106	.	ENSP00000310649:L106X	L	+	2	0	BRSK1	60490479	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.815000	0.69215	1.978000	0.57642	0.409000	0.27619	TTG	.	.		0.557	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	Nonsense_Mutation	A	55798667	T	A	55798667	5	1	212	1	0	0	0	0	0	0	1	0	1525	1826	63	4	327	4	BRSK1	19	55798667	Splice_Site	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	1120859	55798667	3330316	232	30702										
NLRP4	147945	hgsc.bcm.edu	37	chr19	56390306	56390306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctgtgaggccctgagacaccCagagtgtgccctgcaggtgc	14	13	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:56390306C>T	ENST00000301295.6	+	9	3265	c.2843C>T	c.(2842-2844)cCa>cTa	p.P948L	NLRP4_ENST00000346986.5_Missense_Mutation_p.P892L|NLRP4_ENST00000587891.1_Missense_Mutation_p.P873L	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	948					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CTGAGACACCCAGAGTGTGCC	0.582																																					p.P948L		Atlas-SNP	.											.	NLRP4	331	.	0			c.C2843T						.						66	60	62					19																	56390306		2203	4300	6503	SO:0001583	missense	147945	exon9			GACACCCAGAGTG	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.2843C>T	chr19.hg19:g.56390306C>T	ENSP00000301295:p.Pro948Leu	93.0	0.0		120.0	38.0	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	hg19	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	C	12.65	2.000550	0.35320	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.16324	2.35;2.35	4.01	0.488	0.16848	.	.	.	.	.	T	0.28134	0.0694	M	0.66939	2.045	0.09310	N	1	P;D;D	0.67145	0.663;0.996;0.994	B;P;P	0.59889	0.346;0.865;0.737	T	0.10474	-1.0628	9	0.51188	T	0.08	.	3.6292	0.08124	0.2003:0.5809:0.0:0.2188	.	892;873;948	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	L	948;892	ENSP00000301295:P948L;ENSP00000344787:P892L	ENSP00000301295:P948L	P	+	2	0	NLRP4	61082118	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	0.406000	0.21032	0.079000	0.16929	0.650000	0.86243	CCA	.	.		0.582	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56390306	C	T	56390306	3	4	212	1	0	0	0	0	1	0	0	0	10488	594	21	3	2873	3	NLRP4	19	56390306	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	591639	56390306	2738677	233	30703										
ZNF583	147949	hgsc.bcm.edu	37	chr19	56935118	56935153	+	In_Frame_Del	DEL	GTGGATACCTAATTGTACATCAGAGAATTCATACTG	GTGGATACCTAATTGTACATCAGAGAATTCATACTG	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgggaaagcctttagccatcGtggatacctaattgtacatc							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	GTGGATACCTAATTGTACATCAGAGAATTCATACTG	GTGGATACCTAATTGTACATCAGAGAATTCATACTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:56935118_56935153delGTGGATACCTAATTGTACATCAGAGAATTCATACTG	ENST00000333201.9	+	5	1301_1336	c.1091_1126delGTGGATACCTAATTGTACATCAGAGAATTCATACTG	c.(1090-1128)cgtggatacctaattgtacatcagagaattcatactgga>cga	p.GYLIVHQRIHTG365del	ZNF583_ENST00000585612.1_3'UTR|ZNF583_ENST00000291598.7_In_Frame_Del_p.GYLIVHQRIHTG365del	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	365					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q371*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		TTTAGCCATCGTGGATACCTAATTGTACATCAGAGAATTCATACTGGAGAGAGACC	0.415																																					p.364_375del		Atlas-INDEL	.											.	ZNF583	83	.	1	Substitution - Nonsense(1)	lung(1)	c.1090_1125del						.																																			SO:0001651	inframe_deletion	147949	exon5			.	AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"Zinc fingers, C2H2-type", "-"	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.1091_1126delGTGGATACCTAATTGTACATCAGAGAATTCATACTG	chr19.hg19:g.56935118_56935153delGTGGATACCTAATTGTACATCAGAGAATTCATACTG	ENSP00000388502:p.Gly365_Gly376del	55.0	0.0		126.0	18.0	NM_152478	O14850|Q2NKK3	In_Frame_Del	DEL	ENST00000333201.9	hg19	CCDS12943.1																																																																																			.	.		0.415	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478		-	56935153	GTGGATACCTAATTGTACATCAGAGAATTCATACTG	-	56935118	7	5	212	1	0	1	0	1	0	0	0	0	18030	1145	40	0	1105	0	ZNF583	19	56935118	In_Frame_Del	DEL	GTGGATACCTAATTGTACATCAGAGAATTCATACTG	TCGA-DD-AAE7-01A-11D-A40R-10	544812	56935118	2193865	234	30704										
ZNF329	79673	hgsc.bcm.edu	37	chr19	58639453	58639453	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ccttagtgtgaattctctggTgcttggtcagacaggagctg	13	8	2	2	rs201280634		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr19:58639453T>A	ENST00000598312.1	-	4	1651	c.1418A>T	c.(1417-1419)cAc>cTc	p.H473L	ZNF329_ENST00000358067.4_Missense_Mutation_p.H473L	NM_024620.3	NP_078896.3	Q86UD4	ZN329_HUMAN	zinc finger protein 329	473					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|large_intestine(10)|lung(5)|skin(3)|urinary_tract(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)		AATTCTCTGGTGCTTGGTCAG	0.512																																					p.H473L		Atlas-SNP	.											.	ZNF329	70	.	0			c.A1418T						.						97	92	94					19																	58639453		2203	4300	6503	SO:0001583	missense	79673	exon4			CTCTGGTGCTTGG	AK022648	CCDS12972.1	19q13.43	2013-01-08				ENSG00000181894		"Zinc fingers, C2H2-type"	14209	protein-coding gene	gene with protein product							Standard	XM_006723381		Approved	FLJ12586	uc002qrn.3	Q86UD4		ENST00000598312.1:c.1418A>T	chr19.hg19:g.58639453T>A	ENSP00000470008:p.His473Leu	50.0	0.0		127.0	28.0	NM_024620	B3KR32|Q9H9R7	Missense_Mutation	SNP	ENST00000598312.1	hg19	CCDS12972.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.447932	0.63178	.	.	ENSG00000181894	ENST00000358067;ENST00000500161	D;D	0.86865	-2.18;-2.18	4.31	4.31	0.51392	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43919	D	0.000510	D	0.95281	0.8469	H	0.98351	4.21	0.49051	D	0.999745	D	0.67145	0.996	P	0.60345	0.873	D	0.96722	0.9533	10	0.87932	D	0	-12.1513	13.3971	0.60861	0.0:0.0:0.0:1.0	.	473	Q86UD4	ZN329_HUMAN	L	473	ENSP00000350773:H473L;ENSP00000439527:H473L	ENSP00000350773:H473L	H	-	2	0	ZNF329	63331265	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.619000	0.83057	2.173000	0.68751	0.533000	0.62120	CAC	.	T|1.000;C|0.000		0.512	ZNF329-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466724.1	NM_024620		A	58639453	T	A	58639453	3	1	212	1	0	0	0	0	1	0	0	0	17862	1696	59	4	211	4	ZNF329	19	58639453	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	1704335	58639453	489530	235	30705										
FAM110A	83541	hgsc.bcm.edu	37	chr20	826010	826010	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gccgggtttgcaacgctccaAgtcggacttgagcgagcgct	14	12	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr20:826010A>T	ENST00000304189.2	+	3	944	c.563A>T	c.(562-564)aAg>aTg	p.K188M	FAM110A_ENST00000381939.1_Missense_Mutation_p.K188M|FAM110A_ENST00000381941.3_Missense_Mutation_p.K188M|FAM110A_ENST00000541082.1_Missense_Mutation_p.K188M|FAM110A_ENST00000246100.3_Missense_Mutation_p.K188M			Q9BQ89	F110A_HUMAN	family with sequence similarity 110, member A	188						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|lung(2)	3						CAACGCTCCAAGTCGGACTTG	0.701																																					p.K188M		Atlas-SNP	.											.	FAM110A	18	.	0			c.A563T						.						9	11	11					20																	826010		2145	4258	6403	SO:0001583	missense	83541	exon2			GCTCCAAGTCGGA	BC012800	CCDS13008.1	20p13	2007-06-21	2007-03-21	2007-03-21	ENSG00000125898	ENSG00000125898			16188	protein-coding gene	gene with protein product		611393	"chromosome 20 open reading frame 55"	C20orf55		17499476	Standard	NM_001042353		Approved	bA371L19.3	uc002wef.1	Q9BQ89	OTTHUMG00000031649	ENST00000304189.2:c.563A>T	chr20.hg19:g.826010A>T	ENSP00000354163:p.Lys188Met	172.0	0.0		135.0	47.0	NM_207121	D3DVW2|Q5R1M7	Missense_Mutation	SNP	ENST00000304189.2	hg19	CCDS13008.1	.	.	.	.	.	.	.	.	.	.	.	22.8	4.334585	0.81801	.	.	ENSG00000125898	ENST00000381941;ENST00000304189;ENST00000381939;ENST00000246100;ENST00000541082	T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52	4.73	4.73	0.59995	.	0.130221	0.48286	D	0.000194	T	0.71837	0.3387	M	0.79258	2.445	0.47547	D	0.999454	D	0.89917	1.0	D	0.91635	0.999	T	0.76258	-0.3025	10	0.87932	D	0	0.1606	13.181	0.59655	1.0:0.0:0.0:0.0	.	188	Q9BQ89	F110A_HUMAN	M	188	ENSP00000371367:K188M;ENSP00000354163:K188M;ENSP00000371365:K188M;ENSP00000246100:K188M;ENSP00000445228:K188M	ENSP00000246100:K188M	K	+	2	0	FAM110A	774010	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	9.090000	0.94144	1.997000	0.58415	0.254000	0.18369	AAG	.	.		0.701	FAM110A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077489.1	NM_031424		T	826010	A	T	826010	3	4	212	1	0	0	0	0	1	0	0	0	5401	72	3	4	565	4	FAM110A	20	826010	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10		826010	62199510	236	30706										
PLCB1	23236	hgsc.bcm.edu	37	chr20	8608966	8608966	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	caaattacgtgaacttttggAtgtggggaacatcgggcgcc	13	8	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr20:8608966A>G	ENST00000338037.6	+	4	299	c.272A>G	c.(271-273)gAt>gGt	p.D91G	PLCB1_ENST00000378641.3_Missense_Mutation_p.D91G|PLCB1_ENST00000378637.2_Missense_Mutation_p.D91G	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	91					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						GAACTTTTGGATGTGGGGAAC	0.438																																					p.L91R		Atlas-SNP	.											.	PLCB1	394	.	0			c.T272G						.						84	83	83					20																	8608966		2203	4300	6503	SO:0001583	missense	23236	exon4			TTTTGGATGTGGG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.272A>G	chr20.hg19:g.8608966A>G	ENSP00000338185:p.Asp91Gly	102.0	0.0		126.0	34.0	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	hg19	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.670535	0.29693	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000404098;ENST00000441163;ENST00000535719	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	6.17	6.17	0.99709	.	0.000000	0.39210	U	0.001434	T	0.26231	0.0640	N	0.05414	-0.055	0.48696	D	0.999694	B;B;P	0.42296	0.001;0.013;0.775	B;B;B	0.41412	0.002;0.008;0.356	T	0.11792	-1.0573	10	0.13470	T	0.59	.	15.8048	0.78491	1.0:0.0:0.0:0.0	.	91;91;90	Q9NQ66;Q9NQ66-2;B1AK73	PLCB1_HUMAN;.;.	G	91;91;91;90;11;11	ENSP00000367908:D91G;ENSP00000338185:D91G;ENSP00000367904:D91G;ENSP00000384001:D90G	ENSP00000338185:D91G	D	+	2	0	PLCB1	8556966	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	7.391000	0.79828	2.371000	0.80710	0.533000	0.62120	GAT	.	.		0.438	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			G	8608966	A	G	8608966	3	3	212	1	0	0	0	0	1	0	0	0	12036	333	12	2	286	2	PLCB1	20	8608966	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	7782956	8608966	54416554	237	30707										
C20orf72	92667	hgsc.bcm.edu	37	chr20	17968898	17968898	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	caacccactgcaagttgtggCatacatgggtgccatgaacc	10	12	0	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr20:17968898C>T	ENST00000377710.5	+	4	1109	c.821C>T	c.(820-822)gCa>gTa	p.A274V	MGME1_ENST00000467391.1_3'UTR|MGME1_ENST00000377709.1_Missense_Mutation_p.A194V|MGME1_ENST00000377704.4_Intron	NM_052865.2	NP_443097.1			mitochondrial genome maintenance exonuclease 1																		CAAGTTGTGGCATACATGGGT	0.408																																					p.A274V		Atlas-SNP	.											.	.	.	.	0			c.C821T						.						107	95	99					20																	17968898		2203	4300	6503	SO:0001583	missense	92667	exon4			TTGTGGCATACAT		CCDS13131.1	20p11.23	2013-08-29	2013-01-11	2013-01-11	ENSG00000125871	ENSG00000125871			16205	protein-coding gene	gene with protein product		615076	"chromosome 20 open reading frame 72"	C20orf72		23313956, 23358826, 23434322	Standard	NM_052865		Approved	bA504H3.4, DDK1	uc002wqh.3	Q9BQP7	OTTHUMG00000031955	ENST00000377710.5:c.821C>T	chr20.hg19:g.17968898C>T	ENSP00000366939:p.Ala274Val	93.0	0.0		95.0	23.0	NM_052865		Missense_Mutation	SNP	ENST00000377710.5	hg19	CCDS13131.1	.	.	.	.	.	.	.	.	.	.	C	35	5.453966	0.96223	.	.	ENSG00000125871	ENST00000377710;ENST00000377709	T;T	0.74106	-0.81;-0.45	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.89343	0.6688	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90977	0.4824	10	0.87932	D	0	-21.1275	19.2525	0.93930	0.0:1.0:0.0:0.0	.	274	Q9BQP7	CT072_HUMAN	V	274;194	ENSP00000366939:A274V;ENSP00000366938:A194V	ENSP00000366938:A194V	A	+	2	0	C20orf72	17916898	1.000000	0.71417	0.940000	0.37924	0.992000	0.81027	7.258000	0.78371	2.645000	0.89757	0.462000	0.41574	GCA	.	.		0.408	MGME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078139.1	NM_052865		T	17968898	C	T	17968898	3	4	212	1	0	0	0	0	1	0	0	0	2120	710	25	3	831	3	C20orf72	20	17968898	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	9359932	17968898	45056622	238	30708										
MATN4	8785	hgsc.bcm.edu	37	chr20	43922619	43922619	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cgaggctttcgcattcgcatGggctccgaagctctgtccct	11	14	1	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr20:43922619G>A	ENST00000372754.1	-	9	1747	c.1739C>T	c.(1738-1740)cCa>cTa	p.P580L	MATN4_ENST00000353917.5_Missense_Mutation_p.P457L|MATN4_ENST00000372756.1_Missense_Mutation_p.P539L|MATN4_ENST00000537548.1_Missense_Mutation_p.P539L|MATN4_ENST00000342716.4_Missense_Mutation_p.P539L|MATN4_ENST00000372751.4_Missense_Mutation_p.P390L|MATN4_ENST00000360607.6_Missense_Mutation_p.P498L			O95460	MATN4_HUMAN	matrilin 4	580					extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				GCATTCGCATGGGCTCCGAAG	0.632																																					p.P539L		Atlas-SNP	.											.	MATN4	57	.	0			c.C1616T						.						49	51	50					20																	43922619		2203	4300	6503	SO:0001583	missense	8785	exon9			TCGCATGGGCTCC	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.1739C>T	chr20.hg19:g.43922619G>A	ENSP00000361840:p.Pro580Leu	25.0	0.0		27.0	6.0	NM_003833	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Missense_Mutation	SNP	ENST00000372754.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.53	3.149166	0.57151	.	.	ENSG00000124159	ENST00000372753;ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132;ENST00000372751	T;T;T;T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04;0.04;0.04;0.04	4.76	2.82	0.32997	.	0.170176	0.28182	N	0.016285	T	0.57961	0.2089	L	0.52126	1.63	0.80722	D	1	B;B;B	0.23442	0.085;0.013;0.044	B;B;B	0.33960	0.173;0.021;0.056	T	0.57057	-0.7876	10	0.59425	D	0.04	.	10.213	0.43152	0.1619:0.0:0.8381:0.0	.	457;498;539	A6NNA4;O95460-4;O95460-2	.;.;.	L	390;580;539;457;498;539;539;580;390	ENSP00000361839:P390L;ENSP00000361840:P580L;ENSP00000361842:P539L;ENSP00000243983:P457L;ENSP00000353819:P498L;ENSP00000343164:P539L;ENSP00000440328:P539L;ENSP00000361837:P390L	ENSP00000255132:P580L	P	-	2	0	MATN4	43356033	1.000000	0.71417	0.532000	0.27989	0.934000	0.57294	5.539000	0.67199	0.619000	0.30197	-0.136000	0.14681	CCA	.	.		0.632	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1			A	43922619	G	A	43922619	3	1	212	1	0	0	0	0	1	0	0	0	9345	1348	47	3	137	3	MATN4	20	43922619	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	25953721	43922619	19102901	239	30709										
CSE1L	1434	hgsc.bcm.edu	37	chr20	47695153	47695153	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aaatatattatgatttttagAaatcaagtaagtagcttttt	5	2	1	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr20:47695153A>G	ENST00000262982.2	+	14	1599	c.1476A>G	c.(1474-1476)agA>agG	p.R492R	CSE1L_ENST00000542325.1_Silent_p.R275R|CSE1L_ENST00000396192.3_Silent_p.R436R	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	492					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			TGATTTTTAGAAATCAAGTAA	0.308																																					p.R492R		Atlas-SNP	.											.	CSE1L	83	.	0			c.A1476G						.						94	96	96					20																	47695153		2202	4284	6486	SO:0001819	synonymous_variant	1434	exon14			TTTTAGAAATCAA	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.1476A>G	chr20.hg19:g.47695153A>G		26.0	0.0		55.0	16.0	NM_001316	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Silent	SNP	ENST00000262982.2	hg19	CCDS13412.1																																																																																			.	.		0.308	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		G	47695153	A	G	47695153	2	3	212	1	0	0	0	0	0	0	0	1	3932	243	9	2		2	CSE1L	20	47695153	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	3772534	47695153	15330367	240	30710										
BCAS1	8537	hgsc.bcm.edu	37	chr20	52675210	52675210	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	taagtctctgcttctggttcAttctcttggtcttcaactct	6	11	7	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr20:52675210A>T	ENST00000395961.3	-	2	214	c.48T>A	c.(46-48)aaT>aaA	p.N16K	BCAS1_ENST00000371435.2_Missense_Mutation_p.N16K|BCAS1_ENST00000371440.3_Missense_Mutation_p.N16K|BCAS1_ENST00000411563.1_Intron	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	16						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			CTTCTGGTTCATTCTCTTGGT	0.383																																					p.N16K		Atlas-SNP	.											.	BCAS1	77	.	0			c.T48A						.						193	198	196					20																	52675210		2203	4300	6503	SO:0001583	missense	8537	exon2			TGGTTCATTCTCT	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.48T>A	chr20.hg19:g.52675210A>T	ENSP00000379290:p.Asn16Lys	35.0	0.0		49.0	17.0	NM_003657	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	hg19	CCDS13444.1	.	.	.	.	.	.	.	.	.	.	A	13.91	2.377355	0.42105	.	.	ENSG00000064787	ENST00000371440;ENST00000395961;ENST00000371435	T;T;T	0.14516	2.5;2.5;2.5	5.18	-7.66	0.01277	.	0.366486	0.23303	N	0.049656	T	0.10551	0.0258	L	0.54323	1.7	0.09310	N	0.999996	B;B;B	0.24368	0.102;0.102;0.102	B;B;B	0.24701	0.055;0.055;0.055	T	0.07616	-1.0763	10	0.62326	D	0.03	-3.5666	9.7481	0.40459	0.3474:0.0:0.5406:0.112	.	16;16;16	G3XAF7;A0AVG7;O75363	.;.;BCAS1_HUMAN	K	16	ENSP00000360495:N16K;ENSP00000379290:N16K;ENSP00000360490:N16K	ENSP00000360490:N16K	N	-	3	2	BCAS1	52108617	0.000000	0.05858	0.001000	0.08648	0.100000	0.18952	-2.087000	0.01360	-1.706000	0.01404	0.533000	0.62120	AAT	.	.		0.383	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657		T	52675210	A	T	52675210	3	4	212	1	0	0	0	0	1	0	0	0	1350	214	8	4	1750	4	BCAS1	20	52675210	Missense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	4980057	52675210	10350310	241	30711										
CASS4	57091	hgsc.bcm.edu	37	chr20	55027580	55027580	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cagtgatggctctgcagcacAaggtggtcagctctgtcgct	13	11	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr20:55027580A>T	ENST00000360314.3	+	6	1573	c.1348A>T	c.(1348-1350)Aag>Tag	p.K450*	CASS4_ENST00000434344.1_Intron|CASS4_ENST00000371336.3_Nonsense_Mutation_p.K450*	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	450					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						TCTGCAGCACAAGGTGGTCAG	0.562																																					p.K450X		Atlas-SNP	.											.	CASS4	121	.	0			c.A1348T						.						63	53	57					20																	55027580		2203	4300	6503	SO:0001587	stop_gained	57091	exon5			CAGCACAAGGTGG	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"Cas scaffolding proteins"	15878	protein-coding gene	gene with protein product	"HEF-like protein", "HEF1-Efs-p130Cas-like"		"chromosome 20 open reading frame 32"	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.1348A>T	chr20.hg19:g.55027580A>T	ENSP00000353462:p.Lys450*	55.0	0.0		66.0	18.0	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Nonsense_Mutation	SNP	ENST00000360314.3	hg19	CCDS33492.1	.	.	.	.	.	.	.	.	.	.	A	37	6.114249	0.97296	.	.	ENSG00000087589	ENST00000360314;ENST00000371336	.	.	.	5.6	-0.964	0.10326	.	0.570568	0.20583	N	0.089483	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06757	T	0.87	-9.9257	6.4888	0.22103	0.4805:0.3339:0.1856:0.0	.	.	.	.	X	450	.	ENSP00000353462:K450X	K	+	1	0	CASS4	54460987	0.230000	0.23740	0.961000	0.40146	0.739000	0.42172	0.172000	0.16704	-0.379000	0.07906	0.528000	0.53228	AAG	.	.		0.562	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		T	55027580	A	T	55027580	4	4	212	1	0	0	0	0	0	1	0	0	2685	131	5	4	1366	4	CASS4	20	55027580	Nonsense_Mutation	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	2352370	55027580	7997940	242	30712										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61526440	61526440	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttccacgtggaaagctctttAgatacaagttcttctggctt	8	9	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr20:61526440A>G	ENST00000266070.4	-	9	2617	c.2292T>C	c.(2290-2292)tcT>tcC	p.S764S	DIDO1_ENST00000395335.2_Silent_p.S764S|DIDO1_ENST00000395340.1_Silent_p.S764S|DIDO1_ENST00000395343.1_Silent_p.S764S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	764	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					AAAGCTCTTTAGATACAAGTT	0.453																																					p.S764S	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.T2292C						.						157	171	166					20																	61526440		2203	4300	6503	SO:0001819	synonymous_variant	11083	exon9			CTCTTTAGATACA	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.2292T>C	chr20.hg19:g.61526440A>G		60.0	0.0		84.0	26.0	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	hg19	CCDS33506.1																																																																																			.	.		0.453	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		G	61526440	A	G	61526440	2	3	212	1	0	0	0	0	0	0	0	1	4524	407	15	2		2	DIDO1	20	61526440	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10	6498860	61526440	1499080	243	30713										
GRIK1	2897	hgsc.bcm.edu	37	chr21	30927495	30927497	+	In_Frame_Del	DEL	CAC	CAC	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	aatattttccactcccagggCactggcttctttgttgtctt							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr21:30927495_30927497delCAC	ENST00000399907.1	-	16	2894_2896	c.2483_2485delGTG	c.(2482-2487)agtgcc>acc	p.828_829SA>T	GRIK1_ENST00000399909.1_In_Frame_Del_p.813_814SA>T|GRIK1_ENST00000535441.1_In_Frame_Del_p.830_831SA>T|GRIK1_ENST00000389124.2_In_Frame_Del_p.828_829SA>T|GRIK1_ENST00000389125.3_In_Frame_Del_p.813_814SA>T|GRIK1_ENST00000309434.7_In_Frame_Del_p.830_831SA>T|GRIK1_ENST00000399913.1_In_Frame_Del_p.828_829SA>T|GRIK1_ENST00000327783.4_In_Frame_Del_p.828_829SA>T|GRIK1_ENST00000399914.1_In_Frame_Del_p.813_814SA>T	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	828					adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	ACTCCCAGGGCACTGGCTTCTTT	0.463																																					p.828_829del		Atlas-INDEL	.											GRIK1_ENST00000399907,NS,carcinoma,0,2	GRIK1	293	.	0			c.2484_2486del						.																																			SO:0001651	inframe_deletion	2897	exon16			.		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.2483_2485delGTG	chr21.hg19:g.30927495_30927497delCAC	ENSP00000382791:p.Ser828_Ala829delinsThr	56.0	0.0		58.0	18.0	NM_000830	Q13001|Q86SU9	In_Frame_Del	DEL	ENST00000399907.1	hg19	CCDS42913.1																																																																																			.	.		0.463	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1			-	30927497	CAC	-	30927495	7	5	212	1	0	1	0	1	0	0	0	0	6782	710	25	0	439	0	GRIK1	21	30927495	In_Frame_Del	DEL	CAC	TCGA-DD-AAE7-01A-11D-A40R-10		30927495	17202400	244	30714										
BACE2	25825	hgsc.bcm.edu	37	chr21	42622773	42622773	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ttacttccctaaaatctccaTctacctgagagacgagaact	5	12	2	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr21:42622773T>C	ENST00000330333.6	+	7	1542	c.1079T>C	c.(1078-1080)aTc>aCc	p.I360T	BACE2_ENST00000466122.1_3'UTR|BACE2_ENST00000328735.6_Missense_Mutation_p.I360T|BACE2_ENST00000347667.5_Intron	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2	360					membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				AAAATCTCCATCTACCTGAGA	0.463																																					p.I360T		Atlas-SNP	.											.	BACE2	45	.	0			c.T1079C						.						119	101	107					21																	42622773		2203	4300	6503	SO:0001583	missense	25825	exon7			TCTCCATCTACCT	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.1079T>C	chr21.hg19:g.42622773T>C	ENSP00000332979:p.Ile360Thr	48.0	0.0		63.0	13.0	NM_138992	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	hg19	CCDS13668.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.536116	0.85812	.	.	ENSG00000182240	ENST00000330333;ENST00000328735;ENST00000544566	T;T	0.47177	0.85;0.85	5.48	5.48	0.80851	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.054482	0.64402	D	0.000001	T	0.68622	0.3021	M	0.74881	2.28	0.54753	D	0.999987	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.72679	-0.4220	10	0.72032	D	0.01	.	14.7744	0.69713	0.0:0.0:0.0:1.0	.	360;360	Q9Y5Z0-3;Q9Y5Z0	.;BACE2_HUMAN	T	360;360;265	ENSP00000332979:I360T;ENSP00000333854:I360T	ENSP00000333854:I360T	I	+	2	0	BACE2	41544643	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.338000	0.79269	2.082000	0.62665	0.528000	0.53228	ATC	.	.		0.463	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			C	42622773	T	C	42622773	3	2	212	1	0	0	0	0	1	0	0	0	1282	1435	50	2	1105	2	BACE2	21	42622773	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	11695278	42622773	5507122	245	30715										
COL6A2	1292	hgsc.bcm.edu	37	chr21	47549212	47549215	+	Intron	DEL	TAAA	TAAA	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tcccctgatccaacagttgcTaaacgccacggagctcacgc							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	TAAA	TAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr21:47549212_47549215delTAAA	ENST00000300527.4	+	28	2565				COL6A2_ENST00000409416.1_3'UTR|COL6A2_ENST00000357838.4_Frame_Shift_Del_p.LN855fs|COL6A2_ENST00000310645.5_3'UTR|COL6A2_ENST00000397763.1_Frame_Shift_Del_p.LN855fs	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CAACAGTTGCTAAACGCCACGGAG	0.701																																					p.855_856del		Atlas-INDEL	.											.	COL6A2	351	.	0			c.2563_2566del						.																																			SO:0001627	intron_variant	1292	exon28			.	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"Collagens"	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2462-2653TAAA>-	chr21.hg19:g.47549212_47549215delTAAA		147.0	0.0		134.0	41.0	NM_058174	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Frame_Shift_Del	DEL	ENST00000300527.4	hg19	CCDS13728.1																																																																																			.	.		0.701	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			-	47549215	TAAA	-	47549212	6	5	212	0	1	1	0	1	0	0	0	0	3702	1522	53	0		0	COL6A2	21	47549212	Intron	DEL	TAAA	TCGA-DD-AAE7-01A-11D-A40R-10	4926439	47549212	580683	246	30716										
CCDC116	164592	hgsc.bcm.edu	37	chr22	21988580	21988580	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cttgtggaggtgcaggacccAgtggaggtgccaagtggtgg	19	7	0	0			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr22:21988580A>G	ENST00000292779.3	+	3	503	c.342A>G	c.(340-342)ccA>ccG	p.P114P	CCDC116_ENST00000607942.1_Silent_p.P114P	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	114										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					TGCAGGACCCAGTGGAGGTGC	0.672																																					p.P114P		Atlas-SNP	.											.	CCDC116	56	.	0			c.A342G						.						89	82	84					22																	21988580		2203	4299	6502	SO:0001819	synonymous_variant	164592	exon3			GGACCCAGTGGAG	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.342A>G	chr22.hg19:g.21988580A>G		46.0	0.0		53.0	13.0	NM_152612	Q8N9Y9	Silent	SNP	ENST00000292779.3	hg19	CCDS13791.1																																																																																			.	.		0.672	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612		G	21988580	A	G	21988580	2	3	212	1	0	0	0	0	0	0	0	1	2755	175	7	2		2	CCDC116	22	21988580	Silent	SNP	A	TCGA-DD-AAE7-01A-11D-A40R-10		21988580	29315986	247	30717										
CYTSA	23384	hgsc.bcm.edu	37	chr22	24698203	24698203	+	Frame_Shift_Del	DEL	A	A	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	cgaagaggcagcccagaatgAagaaagcaagcaggagtgtt							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr22:24698203delA	ENST00000314328.9	+	3	289	c.4delA	c.(4-6)aagfs	p.K3fs	SPECC1L_ENST00000416735.1_3'UTR|SPECC1L_ENST00000437398.1_Frame_Shift_Del_p.K3fs|SPECC1L_ENST00000541492.1_Frame_Shift_Del_p.K3fs|SPECC1L-ADORA2A_ENST00000358654.2_Frame_Shift_Del_p.K3fs	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	3					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						GCCCAGAATGAAGAAAGCAAG	0.408																																					p.M1fs		Atlas-INDEL	.											.	SPECC1L	85	.	0			c.3delG						.						72	65	67					22																	24698203		2203	4300	6503	SO:0001589	frameshift_variant	23384	exon2			.	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"cytokinesis and spindle organization A", "cytospin A"	614140	"SPECC1-like"			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.4delA	chr22.hg19:g.24698203delA	ENSP00000325785:p.Lys3fs	147.0	0.0		215.0	66.0	NM_001145468	B7Z758|F5H1H6|O15081	Frame_Shift_Del	DEL	ENST00000314328.9	hg19	CCDS33619.1																																																																																			.	.		0.408	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		-	24698203	A	-	24698203	7	5	212	1	0	1	0	1	0	0	0	0	4211	247	9	0	6	0	CYTSA	22	24698203	Frame_Shift_Del	DEL	A	TCGA-DD-AAE7-01A-11D-A40R-10	2709623	24698203	26606363	248	30718										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38120263	38120263	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	agcctccagaacctcctctcCcaatagagccacacgagaca	6	17	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr22:38120263C>G	ENST00000406386.3	+	7	1955	c.1700C>G	c.(1699-1701)cCc>cGc	p.P567R		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	567					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					ACCTCCTCTCCCAATAGAGCC	0.577																																					p.P567R		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C1700G						.						32	53	46					22																	38120263		1830	4097	5927	SO:0001583	missense	11078	exon7			CCTCTCCCAATAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1700C>G	chr22.hg19:g.38120263C>G	ENSP00000384312:p.Pro567Arg	250.0	0.0		295.0	28.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	-	13.41	2.227411	0.39399	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.39229	1.09	3.08	2.02	0.26589	.	.	.	.	.	T	0.39937	0.1097	L	0.55481	1.735	0.21499	N	0.999663	P	0.42757	0.789	B	0.44278	0.445	T	0.28364	-1.0046	9	0.87932	D	0	.	5.493	0.16787	0.0:0.8236:0.0:0.1764	.	567	Q9H2D6	TARA_HUMAN	R	567	ENSP00000384312:P567R	ENSP00000384312:P567R	P	+	2	0	TRIOBP	36450209	0.318000	0.24598	0.281000	0.24762	0.446000	0.32137	1.709000	0.37909	0.266000	0.21894	0.289000	0.19496	CCC	.	.		0.577	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			G	38120263	C	G	38120263	3	3	212	1	0	0	0	0	1	0	0	0	16568	623	22	4	1718	4	TRIOBP	22	38120263	Missense_Mutation	SNP	C	TCGA-DD-AAE7-01A-11D-A40R-10	13422060	38120263	13184303	249	30719										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40059828	40059828	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atcgccctggagcggcctcaGatcgaggccggcagcaccgt	14	15	1	1	rs58500586	byFrequency	TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chr22:40059828G>A	ENST00000402142.3	+	19	3579	c.3579G>A	c.(3577-3579)caG>caA	p.Q1193Q	CACNA1I_ENST00000404898.1_Silent_p.Q1158Q|CACNA1I_ENST00000401624.1_Silent_p.Q1193Q|CACNA1I_ENST00000407673.1_Silent_p.Q1158Q|CACNA1I_ENST00000336649.4_Silent_p.Q1199Q|CACNA1I_ENST00000400164.3_Silent_p.Q1158Q	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1193					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	AGCGGCCTCAGATCGAGGCCG	0.622																																					p.Q1193Q		Atlas-SNP	.											.	CACNA1I	264	.	0			c.G3579A						.						98	108	105					22																	40059828		2034	4178	6212	SO:0001819	synonymous_variant	8911	exon19			GCCTCAGATCGAG	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.3579G>A	chr22.hg19:g.40059828G>A		66.0	0.0		51.0	15.0	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Silent	SNP	ENST00000402142.3	hg19	CCDS46710.1																																																																																			.	G|0.997;C|0.003		0.622	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		A	40059828	G	A	40059828	2	1	212	1	0	0	0	0	0	0	0	1	2548	933	33	3		3	CACNA1I	22	40059828	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	1939565	40059828	11244738	250	30720										
VCX3B	425054	hgsc.bcm.edu	37	chrX	8434394	8434395	+	Missense_Mutation	DNP	GA	GA	AT													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gaagaaccactgagtcaggaGagcgagatggaagaactacc							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chrX:8434394_8434395GA>AT	ENST00000381032.1	+	3	1018_1019	c.711_712GA>AT	c.(709-714)gaGAgc>gaATgc	p.S238C	VCX3B_ENST00000381029.4_Missense_Mutation_p.S206C|VCX3B_ENST00000444481.1_Missense_Mutation_p.S208C|VCX3B_ENST00000453306.1_Missense_Mutation_p.S178C|VCX3B_ENST00000440654.2_Missense_Mutation_p.S178C	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	238	14 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.					nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						TGAGTCAGGAGAGCGAGATGGA	0.559																																					p.E237E|p.S238C		Atlas-SNP	.											.	VCX3B	34	.	0			c.G711A|c.A712T						.																																			SO:0001583	missense	425054	exon3			TCAGGAGAGCGAG|CAGGAGAGCGAGA		CCDS48077.1, CCDS48077.2	Xp22.31	2009-01-14			ENSG00000205642	ENSG00000205642			31838	protein-coding gene	gene with protein product							Standard	NM_001001888		Approved	VCX-C	uc011mht.2	Q9H321	OTTHUMG00000021106	Exception_encountered	chrX.hg19:g.8434394_8434395delinsAT	ENSP00000370420:p.Ser238Cys	212.0	0.0		272.0	26.0	NM_001001888	C9JS46|Q4KN12	Silent|Missense_Mutation	SNP	ENST00000381032.1	hg19	CCDS48077.2																																																																																			.	.		0.559	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055691.1			AT	8434395	GA	AT	8434394	3	1	212	1	0	0	0	0	1	0	0	0	17160	933	33	3	631	3	VCX3B	23	8434394	Missense_Mutation	DNP	GA	TCGA-DD-AAE7-01A-11D-A40R-10		8434394	146836166	251	30721										
DMD	1756	hgsc.bcm.edu	37	chrX	31366711	31366711	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	atgctggaccaaagtccctgTgggcttcatgcagctgcctg	12	12	1	0	rs398124080		TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chrX:31366711T>G	ENST00000357033.4	-	61	9331	c.9125A>C	c.(9124-9126)cAc>cCc	p.H3042P	DMD_ENST00000541735.1_Missense_Mutation_p.H582P|DMD_ENST00000474231.1_Missense_Mutation_p.H582P|DMD_ENST00000343523.2_Missense_Mutation_p.H582P|DMD_ENST00000378677.2_Missense_Mutation_p.H3038P|DMD_ENST00000359836.1_Missense_Mutation_p.H582P|RNU6-894P_ENST00000517094.1_RNA|DMD_ENST00000378707.3_Missense_Mutation_p.H582P	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3042					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AAAGTCCCTGTGGGCTTCATG	0.408																																					p.H3042P		Atlas-SNP	.											.	DMD	2127	.	0			c.A9125C						.						67	58	61					X																	31366711		2202	4300	6502	SO:0001583	missense	1756	exon61			TCCCTGTGGGCTT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.9125A>C	chrX.hg19:g.31366711T>G	ENSP00000354923:p.His3042Pro	125.0	0.0		245.0	161.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.203333	0.79127	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231	T;T;T;T;T;T;T;T	0.64260	3.84;-0.09;-0.09;3.8;3.82;3.8;3.82;3.86	5.64	5.64	0.86602	.	0.000000	0.38663	U	0.001605	T	0.79209	0.4407	M	0.80028	2.48	0.46376	D	0.99901	P;D;D;D;D;D;D;D;D;D;D	0.71674	0.9;0.998;0.995;0.996;0.996;0.96;0.966;0.966;0.991;0.995;0.998	P;D;D;P;P;P;P;P;P;D;D	0.75484	0.699;0.915;0.986;0.896;0.896;0.782;0.703;0.703;0.823;0.914;0.964	T	0.79417	-0.1812	10	0.36615	T	0.2	.	14.8565	0.70341	0.0:0.0:0.0:1.0	.	3034;3042;3038;1701;1698;582;582;582;582;582;2919	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3	.;DMD_HUMAN;.;.;.;.;.;.;.;.;.	P	3034;1701;1698;738;3038;3042;582;582;3042;2919;582;582;582	ENSP00000350765:H738P;ENSP00000367948:H3038P;ENSP00000354923:H3042P;ENSP00000352894:H582P;ENSP00000340057:H582P;ENSP00000367979:H582P;ENSP00000444119:H582P;ENSP00000417123:H582P	ENSP00000340057:H582P	H	-	2	0	DMD	31276632	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.694000	0.74587	1.890000	0.54733	0.430000	0.28490	CAC	.	.		0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		G	31366711	T	G	31366711	3	3	212	1	0	0	0	0	1	0	0	0	4582	1696	59	5	2122	5	DMD	23	31366711	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	22932317	31366711	123903849	252	30722										
CXorf22	170063	hgsc.bcm.edu	37	chrX	35989801	35989801	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	agcggaaatagaagaggagcTgtcttcagcagcaaattcaa	11	7	3	2			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chrX:35989801T>A	ENST00000297866.5	+	12	2135	c.2069T>A	c.(2068-2070)cTg>cAg	p.L690Q		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	690										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						GAAGAGGAGCTGTCTTCAGCA	0.463																																					p.L690Q		Atlas-SNP	.											.	CXorf22	272	.	0			c.T2069A						.						42	36	38					X																	35989801		2202	4300	6502	SO:0001583	missense	170063	exon12			AGGAGCTGTCTTC	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.2069T>A	chrX.hg19:g.35989801T>A	ENSP00000297866:p.Leu690Gln	121.0	0.0		192.0	68.0	NM_152632	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	hg19	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	T	13.53	2.264398	0.39995	.	.	ENSG00000165164	ENST00000297866	T	0.17370	2.28	5.72	-9.28	0.00656	.	2.243790	0.01612	N	0.022591	T	0.13457	0.0326	M	0.69823	2.125	0.09310	N	1	P	0.37276	0.589	B	0.35971	0.215	T	0.30937	-0.9961	10	0.11794	T	0.64	.	2.4198	0.04445	0.2145:0.3968:0.2124:0.1763	.	690	Q6ZTR5	CX022_HUMAN	Q	690	ENSP00000297866:L690Q	ENSP00000297866:L690Q	L	+	2	0	CXorf22	35899722	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.767000	0.01795	-2.618000	0.00441	-0.391000	0.06502	CTG	.	.		0.463	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		A	35989801	T	A	35989801	3	1	212	1	0	0	0	0	1	0	0	0	4104	1580	55	4	2115	4	CXorf22	23	35989801	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	4623090	35989801	119280759	253	30723										
CXorf36	79742	hgsc.bcm.edu	37	chrX	45010995	45010995	+	Frame_Shift_Del	DEL	C	C	-													0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	gtctttcagctggctggcggCcccaaggacttctgggtctg							TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chrX:45010995delC	ENST00000398000.2	-	5	1278	c.1204delG	c.(1204-1206)gccfs	p.A403fs	CXorf36_ENST00000477281.1_5'UTR	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	403						extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						TGGCTGGCGGCCCCAAGGACT	0.537																																					p.A402fs		Atlas-INDEL	.											.	CXorf36	53	.	0			c.1205delC						.						74	67	69					X																	45010995		1568	3582	5150	SO:0001589	frameshift_variant	79742	exon5			.	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.1204delG	chrX.hg19:g.45010995delC	ENSP00000381086:p.Ala403fs	69.0	0.0		76.0	54.0	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Frame_Shift_Del	DEL	ENST00000398000.2	hg19	CCDS48096.1																																																																																			.	.		0.537	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689		-	45010995	C	-	45010995	7	5	212	1	0	1	0	1	0	0	0	0	4108	739	26	0	101	0	CXorf36	23	45010995	Frame_Shift_Del	DEL	C	TCGA-DD-AAE7-01A-11D-A40R-10	9021194	45010995	110259565	254	30724										
ARMCX2	9823	hgsc.bcm.edu	37	chrX	100912386	100912386	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ctgaatcctgacccaaggtcGattgtgaatccggctcttag	10	11	1	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chrX:100912386G>T	ENST00000328766.5	-	5	642	c.189C>A	c.(187-189)atC>atA	p.I63I	ARMCX2_ENST00000330154.2_Silent_p.I63I|ARMCX2_ENST00000356824.4_Silent_p.I63I|ARMCX2_ENST00000467416.1_5'UTR	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	63						integral component of membrane (GO:0016021)				NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(6)|prostate(1)|skin(1)	29						ACCCAAGGTCGATTGTGAATC	0.597																																					p.I63I		Atlas-SNP	.											.	ARMCX2	75	.	0			c.C189A						.						72	69	70					X																	100912386		2203	4300	6503	SO:0001819	synonymous_variant	9823	exon5			AAGGTCGATTGTG	AB011084	CCDS14490.1	Xq21.33-q22.2	2014-03-21			ENSG00000184867	ENSG00000184867		"Armadillo repeat containing"	16869	protein-coding gene	gene with protein product		300363				9628581, 11162520, 16221301, 22569362	Standard	XM_005278109		Approved	ALEX2, KIAA0512, GASP9	uc004eif.3	Q7L311	OTTHUMG00000022038	ENST00000328766.5:c.189C>A	chrX.hg19:g.100912386G>T		42.0	0.0		40.0	13.0	NM_014782	O60267|Q5H9D9	Silent	SNP	ENST00000328766.5	hg19	CCDS14490.1																																																																																			.	.		0.597	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057586.1	NM_014782		T	100912386	G	T	100912386	2	4	212	1	0	0	0	0	0	0	0	1	960	1048	37	1		1	ARMCX2	23	100912386	Silent	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	55901391	100912386	54358174	255	30725										
WDR44	54521	hgsc.bcm.edu	37	chrX	117570751	117570751	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	tgcctttgctgttttcaacaTatagattttgtcactgccat	6	9	2	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chrX:117570751T>A	ENST00000254029.3	+	14	2333	c.1938T>A	c.(1936-1938)caT>caA	p.H646Q	WDR44_ENST00000371825.3_Missense_Mutation_p.H646Q|WDR44_ENST00000371822.5_Missense_Mutation_p.H621Q	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	646						endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						GTTTTCAACATATAGATTTTG	0.348																																					p.H646Q		Atlas-SNP	.											.	WDR44	188	.	0			c.T1938A						.						111	97	102					X																	117570751		2202	4299	6501	SO:0001583	missense	54521	exon14			TCAACATATAGAT	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"WD repeat domain containing"	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.1938T>A	chrX.hg19:g.117570751T>A	ENSP00000254029:p.His646Gln	65.0	0.0		106.0	66.0	NM_001184965	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Missense_Mutation	SNP	ENST00000254029.3	hg19	CCDS14572.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.99|17.99	3.523682|3.523682	0.64747|0.64747	.|.	.|.	ENSG00000131725|ENSG00000131725	ENST00000371822;ENST00000254029;ENST00000371825;ENST00000318919|ENST00000371848	D;T;T|.	0.86865|.	-2.18;-1.49;-1.49|.	5.58|5.58	0.409|0.409	0.16382|0.16382	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75072|0.75072	0.3800|0.3800	M|M	0.88842|0.88842	2.985|2.985	0.45883|0.45883	D|D	0.99873|0.99873	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;0.999;0.999;1.0|.	T|T	0.74542|0.74542	-0.3631|-0.3631	10|5	0.87932|.	D|.	0|.	-7.626|-7.626	9.6514|9.6514	0.39899|0.39899	0.0:0.3823:0.0:0.6177|0.0:0.3823:0.0:0.6177	.|.	621;646;646;646|.	F8W913;E9PCI7;Q5JSH3-2;Q5JSH3|.	.;.;.;WDR44_HUMAN|.	Q|N	621;646;646;32|546	ENSP00000360887:H621Q;ENSP00000254029:H646Q;ENSP00000360890:H646Q|.	ENSP00000254029:H646Q|.	H|Y	+|+	3|1	2|0	WDR44|WDR44	117454779|117454779	0.997000|0.997000	0.39634|0.39634	0.999000|0.999000	0.59377|0.59377	0.996000|0.996000	0.88848|0.88848	0.381000|0.381000	0.20619|0.20619	0.015000|0.015000	0.14971|0.14971	0.478000|0.478000	0.44815|0.44815	CAT|TAT	.	.		0.348	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045		A	117570751	T	A	117570751	3	1	212	1	0	0	0	0	1	0	0	0	17311	1403	49	4	1992	4	WDR44	23	117570751	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	16658365	117570751	37699809	256	30726										
FAM70A	55026	hgsc.bcm.edu	37	chrX	119410802	119410802	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	caggaacaggccaacaatgtTgaggatggtggcagaccaga	14	8	0	3			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chrX:119410802T>A	ENST00000309720.5	-	8	808	c.685A>T	c.(685-687)Aac>Tac	p.N229Y	TMEM255A_ENST00000440464.1_Intron|TMEM255A_ENST00000371369.4_Missense_Mutation_p.N205Y|TMEM255A_ENST00000371352.1_Missense_Mutation_p.N65Y	NM_017938.3	NP_060408.3	Q5JRV8	T255A_HUMAN	transmembrane protein 255A	229						integral component of membrane (GO:0016021)											CCAACAATGTTGAGGATGGTG	0.517																																					p.N229Y		Atlas-SNP	.											.	.	.	.	0			c.A685T						.						234	169	191					X																	119410802		2203	4300	6503	SO:0001583	missense	55026	exon8			CAATGTTGAGGAT	BC047054	CCDS14597.1, CCDS43986.1, CCDS48157.1	Xq24	2012-11-30	2012-11-30	2012-11-30	ENSG00000125355	ENSG00000125355			26086	protein-coding gene	gene with protein product			"family with sequence similarity 70, member A"	FAM70A		12477932	Standard	NM_017938		Approved	FLJ20716	uc004eso.4	Q5JRV8	OTTHUMG00000022298	ENST00000309720.5:c.685A>T	chrX.hg19:g.119410802T>A	ENSP00000310110:p.Asn229Tyr	68.0	0.0		88.0	58.0	NM_017938	A8K0W9|B1APR4|B3KPI6|E9PAR3|Q86Y72|Q9NWN8	Missense_Mutation	SNP	ENST00000309720.5	hg19	CCDS14597.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.460942	0.84317	.	.	ENSG00000125355	ENST00000309720;ENST00000371369;ENST00000371352	T;T;T	0.57752	0.38;0.38;0.38	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.73830	0.3637	M	0.82716	2.605	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.997;0.999	T	0.78427	-0.2208	10	0.87932	D	0	-14.5795	13.3151	0.60403	0.0:0.0:0.0:1.0	.	205;229	B1APR4;Q5JRV8	.;FA70A_HUMAN	Y	229;205;65	ENSP00000310110:N229Y;ENSP00000360420:N205Y;ENSP00000360403:N65Y	ENSP00000310110:N229Y	N	-	1	0	FAM70A	119294830	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.698000	0.84413	1.737000	0.51674	0.481000	0.45027	AAC	.	.		0.517	TMEM255A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058091.1	NM_017938		A	119410802	T	A	119410802	3	1	212	1	0	0	0	0	1	0	0	0	5613	1812	63	4	376	4	FAM70A	23	119410802	Missense_Mutation	SNP	T	TCGA-DD-AAE7-01A-11D-A40R-10	1840051	119410802	35859758	257	30727										
ZNF75D	7626	hgsc.bcm.edu	37	chrX	134427746	134427746	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	9	1	1.12267225325885	1.92458100558659	0.842004189944134	1	1	0	ggatgatgcttctgcacccaGttctgggtctccttgggcag	13	11	3	1			TCGA-DD-AAE7-01A-11D-A40R-10	TCGA-DD-AAE7-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b7fc7c0-18c0-4c05-9a0a-5493e05b850c	b24da751-d43f-49c4-80e4-ac9d237e5bbe	g.chrX:134427746G>T	ENST00000370766.3	-	3	3030	c.321C>A	c.(319-321)aaC>aaA	p.N107K	ZNF75D_ENST00000370764.1_Missense_Mutation_p.N107K|ZNF75D_ENST00000494295.1_Intron	NM_007131.3	NP_009062.2	P51815	ZN75D_HUMAN	zinc finger protein 75D	107	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						TCTGCACCCAGTTCTGGGTCT	0.502																																					p.N107K		Atlas-SNP	.											.	ZNF75D	65	.	0			c.C321A						.						84	77	79					X																	134427746		2203	4300	6503	SO:0001583	missense	7626	exon2			CACCCAGTTCTGG	S43109	CCDS14648.1, CCDS55503.1	Xq26	2013-01-09	2008-06-11	2008-06-11	ENSG00000186376	ENSG00000186376		"Zinc fingers, C2H2-type", "-", "-", "-"	13145	protein-coding gene	gene with protein product		314997	"zinc finger protein 75 (D8C6)"	ZNF82, ZNF75		1505955	Standard	XM_005262469		Approved	ZKSCAN24, D8C6, ZSCAN28	uc004eyo.3	P51815	OTTHUMG00000022482	ENST00000370766.3:c.321C>A	chrX.hg19:g.134427746G>T	ENSP00000359802:p.Asn107Lys	38.0	0.0		77.0	14.0	NM_007131	A6NK62|B3KRI7|Q5JPG0|Q6LDE0	Missense_Mutation	SNP	ENST00000370766.3	hg19	CCDS14648.1	.	.	.	.	.	.	.	.	.	.	G	1.322	-0.599278	0.03744	.	.	ENSG00000186376	ENST00000370766;ENST00000370764	T;T	0.05319	3.46;3.46	2.98	2.09	0.27110	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.07234	0.0183	L	0.53249	1.67	0.09310	N	1	B;B	0.13145	0.004;0.007	B;B	0.14578	0.007;0.011	T	0.29150	-1.0021	9	0.54805	T	0.06	.	5.5968	0.17331	0.161:0.0:0.839:0.0	.	107;107	P51815;A6NK62	ZN75D_HUMAN;.	K	107	ENSP00000359802:N107K;ENSP00000359800:N107K	ENSP00000359800:N107K	N	-	3	2	ZNF75D	134255412	0.356000	0.24930	0.046000	0.18839	0.385000	0.30292	0.475000	0.22164	0.641000	0.30601	0.509000	0.49947	AAC	.	.		0.502	ZNF75D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058415.1	NM_007131		T	134427746	G	T	134427746	3	4	212	1	0	0	0	0	1	0	0	0	18149	1020	36	3	1231	3	ZNF75D	23	134427746	Missense_Mutation	SNP	G	TCGA-DD-AAE7-01A-11D-A40R-10	15016944	134427746	20842814	258	30728										
AIM1L	55057	hgsc.bcm.edu	37	chr1	26663754	26663754	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ctttgcttaccgtccggatgAcccggagggaggtcagcaac	13	12	1	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr1:26663754A>G	ENST00000308182.5	-	9	1055	c.626T>C	c.(625-627)gTc>gCc	p.V209A	AIM1L_ENST00000522993.1_5'UTR|AIM1L_ENST00000527815.1_Missense_Mutation_p.V380A			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	209	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.						carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		CGTCCGGATGACCCGGAGGGA	0.602																																					p.V1254A		Atlas-SNP	.											.	AIM1L	98	.	0			c.T3761C						.						93	85	87					1																	26663754		2203	4300	6503	SO:0001583	missense	55057	exon10			CGGATGACCCGGA			1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"beta-gamma crystallin domain containing 2"						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490	ENST00000308182.5:c.626T>C	chr1.hg19:g.26663754A>G	ENSP00000310435:p.Val209Ala	80.0	0.0		119.0	7.0	NM_001039775	B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	hg19		.	.	.	.	.	.	.	.	.	.	A	17.95	3.513747	0.64522	.	.	ENSG00000176092	ENST00000527815;ENST00000308182	T;T	0.76060	-0.99;-0.99	4.88	4.88	0.63580	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.831490	0.11239	N	0.584824	T	0.66528	0.2798	N	0.21545	0.675	0.80722	D	1	B;B	0.32051	0.089;0.354	B;B	0.39771	0.309;0.174	T	0.56257	-0.8009	10	0.13853	T	0.58	.	14.3291	0.66541	1.0:0.0:0.0:0.0	.	126;209	Q9NTH7;Q8N1P7	.;AIM1L_HUMAN	A	380;209	ENSP00000433931:V380A;ENSP00000310435:V209A	ENSP00000310435:V209A	V	-	2	0	AIM1L	26536341	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.675000	0.68123	2.055000	0.61198	0.533000	0.62120	GTC	.	.		0.602	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2		G	26663754	A	G	26663754	3	3	213	1	0	0	0	0	1	0	0	0	431	275	10	2	1268	2	AIM1L	1	26663754	Missense_Mutation	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10		26663754	222586867	1	30729										
SYCP1	6847	hgsc.bcm.edu	37	chr1	115400064	115400064	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tagaaacatctatctttttaGgttggtaattctgactgtca	7	6	4	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr1:115400064G>A	ENST00000369522.3	+	5	477		c.e5-1		SYCP1_ENST00000369518.1_Splice_Site	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1						chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TATCTTTTTAGGTTGGTAATT	0.289																																					.		Atlas-SNP	.											.	SYCP1	149	.	0			c.238-1G>A						.						32	32	32					1																	115400064		2203	4281	6484	SO:0001630	splice_region_variant	6847	exon5			TTTTTAGGTTGGT	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.238-1G>A	chr1.hg19:g.115400064G>A		265.0	0.0		261.0	65.0	NM_003176	O14963|Q5VXJ6	Splice_Site	SNP	ENST00000369522.3	hg19	CCDS879.1	.	.	.	.	.	.	.	.	.	.	G	5.062	0.197077	0.09599	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	.	.	.	4.57	2.53	0.30540	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.8399	0.18627	0.108:0.1964:0.6956:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SYCP1	115201587	1.000000	0.71417	0.998000	0.56505	0.149000	0.21700	2.745000	0.47459	1.043000	0.40175	-0.384000	0.06662	.	.	.		0.289	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176	Intron	A	115400064	G	A	115400064	5	1	213	1	0	0	0	0	0	0	1	0	15446	1014	35	3	251	3	SYCP1	1	115400064	Splice_Site	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	88736310	115400064	133850557	2	30730										
FCRL2	79368	hgsc.bcm.edu	37	chr1	157736740	157736740	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gaactccagctgtcatgaggTctcttctatagccatcaggt	9	11	4	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr1:157736740T>C	ENST00000361516.3	-	7	1232	c.1184A>G	c.(1183-1185)gAc>gGc	p.D395G	FCRL2_ENST00000469986.1_Missense_Mutation_p.D142G|FCRL2_ENST00000392274.3_Missense_Mutation_p.D395G|FCRL2_ENST00000368181.4_Missense_Mutation_p.D111G	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	395					cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TGTCATGAGGTCTCTTCTATA	0.458																																					p.D395G		Atlas-SNP	.											.	FCRL2	104	.	0			c.A1184G						.						114	114	114					1																	157736740		2203	4300	6503	SO:0001583	missense	79368	exon7			ATGAGGTCTCTTC	AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14875	protein-coding gene	gene with protein product		606509	"SH2 domain-containing phosphatase anchor protein 1"	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.1184A>G	chr1.hg19:g.157736740T>C	ENSP00000355157:p.Asp395Gly	326.0	0.0		440.0	90.0	NM_030764	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Missense_Mutation	SNP	ENST00000361516.3	hg19	CCDS1168.1	.	.	.	.	.	.	.	.	.	.	T	9.042	0.989950	0.18966	.	.	ENSG00000132704	ENST00000292389;ENST00000361516;ENST00000368181;ENST00000392274;ENST00000469986	T;T;T;T	0.21031	2.25;3.78;2.03;3.11	3.22	-2.7	0.06004	.	2.947670	0.02082	U	0.052465	T	0.02012	0.0063	N	0.11818	0.18	0.09310	N	1	B;B;B;B	0.29378	0.001;0.005;0.243;0.015	B;B;B;B	0.30716	0.007;0.005;0.119;0.026	T	0.10543	-1.0625	10	0.02654	T	1	.	2.342	0.04262	0.374:0.2398:0.0:0.3861	.	395;111;395;142	B4DVJ9;Q96LA5-5;Q96LA5;Q96LA5-2	.;.;FCRL2_HUMAN;.	G	111;395;111;395;142	ENSP00000355157:D395G;ENSP00000357163:D111G;ENSP00000376100:D395G;ENSP00000417393:D142G	ENSP00000292389:D111G	D	-	2	0	FCRL2	156003364	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	0.140000	0.16056	-0.724000	0.04908	0.533000	0.62120	GAC	.	.		0.458	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764		C	157736740	T	C	157736740	3	2	213	1	0	0	0	0	1	0	0	0	5803	1667	58	2	366	2	FCRL2	1	157736740	Missense_Mutation	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	42336676	157736740	91513881	3	30731										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186024715	186024715	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ggtcacatccttcagctgaaGaacattcatgtatctgacac	7	11	4	3			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr1:186024715G>T	ENST00000271588.4	+	45	7282	c.7053G>T	c.(7051-7053)aaG>aaT	p.K2351N	HMCN1_ENST00000367492.2_Missense_Mutation_p.K2351N	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2351	Ig-like C2-type 21.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TTCAGCTGAAGAACATTCATG	0.438																																					p.K2351N		Atlas-SNP	.											.	HMCN1	797	.	0			c.G7053T						.						154	133	140					1																	186024715		2203	4300	6503	SO:0001583	missense	83872	exon45			GCTGAAGAACATT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7053G>T	chr1.hg19:g.186024715G>T	ENSP00000271588:p.Lys2351Asn	156.0	0.0		231.0	12.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.789666	0.50102	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.67865	-0.29;-0.29	5.5	3.3	0.37823	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.308175	0.38272	N	0.001750	T	0.59074	0.2167	N	0.04959	-0.14	0.25310	N	0.989208	D	0.76494	0.999	D	0.85130	0.997	T	0.50684	-0.8799	10	0.22109	T	0.4	.	8.9041	0.35512	0.3339:0.0:0.6661:0.0	.	2351	Q96RW7	HMCN1_HUMAN	N	2351	ENSP00000271588:K2351N;ENSP00000356462:K2351N	ENSP00000271588:K2351N	K	+	3	2	HMCN1	184291338	0.997000	0.39634	0.974000	0.42286	0.816000	0.46133	0.569000	0.23638	1.316000	0.45131	0.650000	0.86243	AAG	.	.		0.438	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186024715	G	T	186024715	3	4	213	1	0	0	0	0	1	0	0	0	7229	933	33	3	7231	3	HMCN1	1	186024715	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	28287975	186024715	63225906	4	30732										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201009074	201009074	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ccatgccctctggggcctctCgtcctttcagtagctctgtt	9	15	4	0	rs368214163		TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr1:201009074C>G	ENST00000362061.3	-	44	5733	c.5507G>C	c.(5506-5508)cGa>cCa	p.R1836P	CACNA1S_ENST00000367338.3_Missense_Mutation_p.R1817P|RP11-168O16.2_ENST00000415359.1_RNA	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1836					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGGGCCTCTCGTCCTTTCAG	0.597																																					p.R1836P		Atlas-SNP	.											.	CACNA1S	249	.	0			c.G5507C						.	C	PRO/ARG	0,4406		0,0,2203	152	141	144		5507	1.2	0	1		144	1,8599		0,1,4299	no	missense	CACNA1S	NM_000069.2	103	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	possibly-damaging	1836/1874	201009074	1,13005	2203	4300	6503	SO:0001583	missense	779	exon44			GCCTCTCGTCCTT	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.5507G>C	chr1.hg19:g.201009074C>G	ENSP00000355192:p.Arg1836Pro	41.0	0.0		42.0	16.0	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	11.42	1.634961	0.29068	0.0	1.16E-4	ENSG00000081248	ENST00000362061;ENST00000367338	T;T	0.45668	0.89;0.89	4.36	1.22	0.21188	.	1.536250	0.04611	U	0.400231	T	0.39118	0.1066	L	0.50333	1.59	0.09310	N	1	P	0.35872	0.525	B	0.35510	0.204	T	0.33624	-0.9861	10	0.38643	T	0.18	.	8.8209	0.35025	0.0:0.7063:0.0:0.2937	.	1836	Q13698	CAC1S_HUMAN	P	1836;1817	ENSP00000355192:R1836P;ENSP00000356307:R1817P	ENSP00000355192:R1836P	R	-	2	0	CACNA1S	199275697	0.156000	0.22821	0.004000	0.12327	0.752000	0.42762	0.954000	0.29175	0.346000	0.23899	0.404000	0.27445	CGA	.	.		0.597	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		G	201009074	C	G	201009074	3	3	213	1	0	0	0	0	1	0	0	0	2549	884	31	4	118	4	CACNA1S	1	201009074	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10	14984359	201009074	48241547	5	30733										
LMOD1	25802	hgsc.bcm.edu	37	chr1	201869293	201869293	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ttttggtcttgctgtcatccTtggcttccttttcatgtaag	8	9	3	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr1:201869293T>C	ENST00000367288.4	-	2	1094	c.848A>G	c.(847-849)aAg>aGg	p.K283R	RP11-307B6.3_ENST00000458139.1_RNA|RP11-307B6.3_ENST00000414927.1_RNA	NM_012134.2	NP_036266.2	P29536	LMOD1_HUMAN	leiomodin 1 (smooth muscle)	283	8 X approximate tandem repeats.				muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GCTGTCATCCTTGGCTTCCTT	0.517																																					p.K283R		Atlas-SNP	.											.	LMOD1	59	.	0			c.A848G						.						102	103	102					1																	201869293		2007	4176	6183	SO:0001583	missense	25802	exon2			TCATCCTTGGCTT	X54162	CCDS53457.1	1q32.1	2008-05-22			ENSG00000163431	ENSG00000163431			6647	protein-coding gene	gene with protein product		602715					Standard	NM_012134		Approved	64kD, D1, 1D	uc021phl.1	P29536	OTTHUMG00000035802	ENST00000367288.4:c.848A>G	chr1.hg19:g.201869293T>C	ENSP00000356257:p.Lys283Arg	98.0	0.0		132.0	18.0	NM_012134	B1APV6|C4AMB1|Q68EN2	Missense_Mutation	SNP	ENST00000367288.4	hg19	CCDS53457.1	.	.	.	.	.	.	.	.	.	.	T	7.136	0.580896	0.13686	.	.	ENSG00000163431	ENST00000367288;ENST00000400965;ENST00000412469	D	0.94793	-3.52	5.32	-3.02	0.05446	.	0.665977	0.12390	N	0.473139	T	0.78616	0.4311	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.70802	-0.4773	10	0.08837	T	0.75	-2.743	6.3586	0.21414	0.0:0.3972:0.2589:0.3439	.	232;283	B4E3S9;P29536	.;LMOD1_HUMAN	R	283;283;232	ENSP00000356257:K283R	ENSP00000356257:K283R	K	-	2	0	LMOD1	200135916	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.352000	0.07701	-0.899000	0.03901	-0.322000	0.08575	AAG	.	.		0.517	LMOD1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087085.2			C	201869293	T	C	201869293	3	2	213	1	0	0	0	0	1	0	0	0	8865	1609	56	2	962	2	LMOD1	1	201869293	Missense_Mutation	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	860219	201869293	47381328	6	30734										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50318473	50318473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ttgcttacctgcagggtagcGctcgatcactggccagctgt	12	12	1	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr2:50318473G>A	ENST00000406316.2	-	19	5182	c.3706C>T	c.(3706-3708)Cgc>Tgc	p.R1236C	NRXN1_ENST00000402717.3_Missense_Mutation_p.R1228C|NRXN1_ENST00000405472.3_Missense_Mutation_p.R1228C|NRXN1_ENST00000401710.1_Missense_Mutation_p.R254C|NRXN1_ENST00000404971.1_Missense_Mutation_p.R1276C|NRXN1_ENST00000401669.2_Missense_Mutation_p.R1236C|NRXN1_ENST00000406859.3_Missense_Mutation_p.R1236C|NRXN1_ENST00000342183.5_Missense_Mutation_p.R201C	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1236	Laminin G-like 6. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GCAGGGTAGCGCTCGATCACT	0.448																																					p.R1276C		Atlas-SNP	.											.	NRXN1	1118	.	0			c.C3826T						.						216	199	205					2																	50318473		2203	4300	6503	SO:0001583	missense	9378	exon20			GGTAGCGCTCGAT	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3706C>T	chr2.hg19:g.50318473G>A	ENSP00000384311:p.Arg1236Cys	69.0	0.0		79.0	9.0	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.793215	0.90453	.	.	ENSG00000179915	ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.54	5.54	0.83059	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.56097	U	0.000034	D	0.88477	0.6447	M	0.79123	2.44	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.999;0.999	P;D;P;D	0.70487	0.701;0.969;0.853;0.913	D	0.88983	0.3409	10	0.62326	D	0.03	.	19.4609	0.94916	0.0:0.0:1.0:0.0	.	1276;201;1236;1228	Q9ULB1-3;P58400;F8WB18;A7E294	.;NRX1B_HUMAN;.;.	C	201;155;254;1276;1236;1228;1236;1277;1228;1236	ENSP00000341184:R201C;ENSP00000385580:R254C;ENSP00000385142:R1276C;ENSP00000384311:R1236C;ENSP00000434015:R1228C;ENSP00000385017:R1236C;ENSP00000385434:R1228C;ENSP00000385681:R1236C	ENSP00000341184:R201C	R	-	1	0	NRXN1	50171977	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.600000	0.87896	0.563000	0.77884	CGC	.	.		0.448	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	50318473	G	A	50318473	3	1	213	1	0	0	0	0	1	0	0	0	10674	1087	38	1	837	1	NRXN1	2	50318473	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10		50318473	192880900	7	30735										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50765499	50765499	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gcaagggttgctaaggcacgGttttgctgtttcctttgagc	13	8	0	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr2:50765499G>T	ENST00000406316.2	-	10	3511	c.2035C>A	c.(2035-2037)Ccg>Acg	p.P679T	NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000402717.3_Missense_Mutation_p.P671T|NRXN1_ENST00000405472.3_Missense_Mutation_p.P671T|NRXN1_ENST00000404971.1_Missense_Mutation_p.P719T|NRXN1_ENST00000401669.2_Missense_Mutation_p.P679T|NRXN1_ENST00000406859.3_Missense_Mutation_p.P679T	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	679	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CTAAGGCACGGTTTTGCTGTT	0.483																																					p.P719T		Atlas-SNP	.											.	NRXN1	1118	.	0			c.C2155A						.						322	323	323					2																	50765499		2137	4271	6408	SO:0001583	missense	9378	exon11			GGCACGGTTTTGC	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.2035C>A	chr2.hg19:g.50765499G>T	ENSP00000384311:p.Pro679Thr	160.0	0.0		152.0	41.0	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870957	0.72065	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78;-0.78;-0.78	5.16	5.16	0.70880	.	0.056804	0.64402	D	0.000001	T	0.67636	0.2914	L	0.37466	1.105	0.43203	D	0.995058	B;P;B	0.40638	0.352;0.725;0.354	B;B;B	0.37198	0.236;0.243;0.129	T	0.71984	-0.4427	10	0.56958	D	0.05	.	18.8479	0.92215	0.0:0.0:1.0:0.0	.	719;679;671	Q9ULB1-3;F8WB18;A7E294	.;.;.	T	719;679;671;679;720;671;679	ENSP00000385142:P719T;ENSP00000384311:P679T;ENSP00000434015:P671T;ENSP00000385017:P679T;ENSP00000385434:P671T;ENSP00000385681:P679T	ENSP00000385017:P679T	P	-	1	0	NRXN1	50619003	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.657000	0.98554	2.682000	0.91365	0.585000	0.79938	CCG	.	.		0.483	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50765499	G	T	50765499	3	4	213	1	0	0	0	0	1	0	0	0	10674	1261	44	3	2807	3	NRXN1	2	50765499	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	447026	50765499	192433874	8	30736										
CD8B	926	hgsc.bcm.edu	37	chr2	87085479	87085479	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	cgcaggacagcatcaccatcTtgttggtttgcacctttatg	9	11	2	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr2:87085479T>A	ENST00000390655.6	-	2	162	c.104A>T	c.(103-105)aAg>aTg	p.K35M	CD8B_ENST00000393759.2_Missense_Mutation_p.K35M|CD8B_ENST00000431506.2_Intron|CD8B_ENST00000349455.3_Missense_Mutation_p.K35M|CD8B_ENST00000393761.2_Missense_Mutation_p.K35M|CD8B_ENST00000331469.2_Missense_Mutation_p.K35M	NM_004931.4	NP_004922.1	P10966	CD8B_HUMAN	CD8b molecule	35	Ig-like V-type.				immune response (GO:0006955)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|MHC class I protein binding (GO:0042288)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	13						CATCACCATCTTGTTGGTTTG	0.512																																					p.K35M		Atlas-SNP	.											.	CD8B	37	.	0			c.A104T						.						77	68	71					2																	87085479		2203	4298	6501	SO:0001583	missense	926	exon2			ACCATCTTGTTGG		CCDS1994.1, CCDS1995.1, CCDS42708.1, CCDS1997.1, CCDS54376.1	2p12	2013-01-11	2006-03-28	2006-03-09	ENSG00000172116	ENSG00000172116		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1707	protein-coding gene	gene with protein product		186730	"CD8 antigen, beta polypeptide 1 (p37)"	CD8B1		1541829	Standard	NM_172213		Approved		uc002srw.3	P10966	OTTHUMG00000130264	ENST00000390655.6:c.104A>T	chr2.hg19:g.87085479T>A	ENSP00000375070:p.Lys35Met	235.0	0.0		289.0	92.0	NM_004931	P14860|P14861|Q15980|Q496E0|Q496E1|Q496E2|Q9UDB4|Q9UDB5|Q9UDB6|Q9UDB7|Q9UDB8|Q9UDB9|Q9UDC0|Q9UQ55	Missense_Mutation	SNP	ENST00000390655.6	hg19	CCDS1997.1	.	.	.	.	.	.	.	.	.	.	T	9.560	1.118239	0.20877	.	.	ENSG00000172116	ENST00000393761;ENST00000393759;ENST00000349455;ENST00000331469;ENST00000390655;ENST00000445248	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	4.49	0.375	0.16188	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.042940	0.07459	N	0.900284	T	0.42877	0.1222	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B	0.31893	0.345;0.22;0.22;0.131;0.161;0.184	B;B;B;B;B;B	0.27076	0.055;0.076;0.055;0.015;0.034;0.045	T	0.39683	-0.9602	10	0.87932	D	0	3.5803	1.1103	0.01703	0.1874:0.1069:0.1942:0.5116	.	35;35;35;35;35;35	Q496E2;Q53QL8;P10966;P10966-3;P10966-2;P10966-6	.;.;CD8B_HUMAN;.;.;.	M	35	ENSP00000377358:K35M;ENSP00000377356:K35M;ENSP00000340592:K35M;ENSP00000331172:K35M;ENSP00000375070:K35M	ENSP00000331172:K35M	K	-	2	0	CD8B	86938990	0.000000	0.05858	0.004000	0.12327	0.013000	0.08279	-0.260000	0.08708	0.132000	0.18615	0.533000	0.62120	AAG	.	.		0.512	CD8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330402.1	NM_172099		A	87085479	T	A	87085479	3	1	213	1	0	0	0	0	1	0	0	0	3047	1609	56	4	822	4	CD8B	2	87085479	Missense_Mutation	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	36319980	87085479	156113894	9	30737										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99012463	99012463	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	cccagaagtgaggttcaaccGcctactgaagttttcccggc	10	13	1	3			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr2:99012463G>A	ENST00000272602.2	+	7	869	c.830G>A	c.(829-831)cGc>cAc	p.R277H	CNGA3_ENST00000393504.1_Missense_Mutation_p.R277H|CNGA3_ENST00000409937.1_Missense_Mutation_p.R281H|CNGA3_ENST00000436404.2_Missense_Mutation_p.R259H			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	277			R -> C (in ACHM2; also found in patients with cone-rod dystrophy). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:15712225, ECO:0000269|PubMed:18521937, ECO:0000269|PubMed:24903488}.|R -> H (in ACHM2; also found in patients with cone-rod dystrophy; does not form functional homomeric or heteromeric channels). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:24903488}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AGGTTCAACCGCCTACTGAAG	0.498																																					p.R277H		Atlas-SNP	.											.	CNGA3	118	.	0			c.G830A	GRCh37	CM014539	CNGA3	M		.						89	81	84					2																	99012463		2203	4300	6503	SO:0001583	missense	1261	exon8			TCAACCGCCTACT	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.830G>A	chr2.hg19:g.99012463G>A	ENSP00000272602:p.Arg277His	182.0	0.0		176.0	12.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577406	0.86645	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.99353	-5.77;-5.77;-5.77;-5.77	5.15	5.15	0.70609	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99645	0.9869	H	0.96777	3.88	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.97631	1.0142	10	0.87932	D	0	.	17.5731	0.87940	0.0:0.0:1.0:0.0	.	281;259;277	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	H	277;259;277;281	ENSP00000377140:R277H;ENSP00000410070:R259H;ENSP00000272602:R277H;ENSP00000386761:R281H	ENSP00000272602:R277H	R	+	2	0	CNGA3	98378895	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.487000	0.81328	2.677000	0.91161	0.563000	0.77884	CGC	.	.		0.498	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		A	99012463	G	A	99012463	3	1	213	1	0	0	0	0	1	0	0	0	3600	1087	38	1	856	1	CNGA3	2	99012463	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	11926984	99012463	144186910	10	30738										
MAP4K4	9448	hgsc.bcm.edu	37	chr2	102501674	102501674	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tatgaaagaatcaaatttctGgtgattgctttgaagagttc	9	4	2	5			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr2:102501674G>A	ENST00000347699.4	+	26	3111	c.3111G>A	c.(3109-3111)ctG>ctA	p.L1037L	MAP4K4_ENST00000302217.5_Silent_p.L840L|MAP4K4_ENST00000324219.4_Silent_p.L1118L|MAP4K4_ENST00000350198.4_Silent_p.L956L|MAP4K4_ENST00000456652.1_Silent_p.L836L|MAP4K4_ENST00000413150.2_Silent_p.L952L|MAP4K4_ENST00000425019.1_Silent_p.L1070L|MAP4K4_ENST00000350878.4_Silent_p.L1077L	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	1037	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.|Mediates interaction with RAP2A.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCAAATTTCTGGTGATTGCTT	0.353																																					p.L1071L		Atlas-SNP	.											.	MAP4K4	111	.	0			c.G3213A						.						68	64	65					2																	102501674		1828	4082	5910	SO:0001819	synonymous_variant	9448	exon27			ATTTCTGGTGATT	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.3111G>A	chr2.hg19:g.102501674G>A		104.0	0.0		84.0	19.0	NM_145686	O75172|Q9NST7	Silent	SNP	ENST00000347699.4	hg19	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	G	9.283	1.048565	0.19827	.	.	ENSG00000071054	ENST00000421882	.	.	.	6.02	3.08	0.35506	.	.	.	.	.	T	0.54727	0.1876	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44832	-0.9302	4	.	.	.	.	6.4263	0.21772	0.1423:0.0:0.6076:0.25	.	.	.	.	S	854	.	.	G	+	1	0	MAP4K4	101868106	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.900000	0.48687	0.341000	0.23771	0.650000	0.86243	GGT	.	.		0.353	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		A	102501674	G	A	102501674	2	1	213	1	0	0	0	0	0	0	0	1	9271	1335	47	3		3	MAP4K4	2	102501674	Silent	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	3489211	102501674	140697699	11	30739										
ANAPC1	64682	hgsc.bcm.edu	37	chr2	112560035	112560035	+	Frame_Shift_Del	DEL	G	G	-													0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	agaaattctggcttcacaaaGtccaacaaatacatggtgtc							TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr2:112560035delG	ENST00000341068.3	-	33	4963	c.4191delC	c.(4189-4191)gacfs	p.D1397fs		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	1397					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						GCTTCACAAAGTCCAACAAAT	0.433																																					p.F1398fs		Atlas-INDEL	.											.	ANAPC1	116	.	0			c.4192delT						.						14	13	13					2																	112560035		2194	4269	6463	SO:0001589	frameshift_variant	64682	exon33			.	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"Anaphase promoting complex subunits"	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.4191delC	chr2.hg19:g.112560035delG	ENSP00000339109:p.Asp1397fs	919.0	0.0		951.0	145.0	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Frame_Shift_Del	DEL	ENST00000341068.3	hg19	CCDS2093.1																																																																																			.	.		0.433	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662		-	112560035	G	-	112560035	7	5	213	1	0	1	0	1	0	0	0	0	598	1020	36	0	1707	0	ANAPC1	2	112560035	Frame_Shift_Del	DEL	G	TCGA-DD-AAE8-01A-11D-A40R-10	10058361	112560035	130639338	12	30740										
STK39	27347	hgsc.bcm.edu	37	chr2	168986082	168986082	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tttgggctatgtctggtgttCttgtaagcagcttctcaatc	10	8	3	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr2:168986082C>A	ENST00000355999.4	-	10	1763	c.1058G>T	c.(1057-1059)aGa>aTa	p.R353I		NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	353					cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						GTCTGGTGTTCTTGTAAGCAG	0.388																																					p.R353I		Atlas-SNP	.											.	STK39	95	.	0			c.G1058T						.						316	287	296					2																	168986082		1898	4115	6013	SO:0001583	missense	27347	exon10			GGTGTTCTTGTAA	AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648			17717	protein-coding gene	gene with protein product	"STE20/SPS1 homolog (yeast)"	607648				10980603	Standard	NM_013233		Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.1058G>T	chr2.hg19:g.168986082C>A	ENSP00000348278:p.Arg353Ile	194.0	0.0		194.0	52.0	NM_013233	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	Missense_Mutation	SNP	ENST00000355999.4	hg19	CCDS42770.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.249524	0.59212	.	.	ENSG00000198648	ENST00000355999	T	0.21191	2.02	5.8	5.8	0.92144	Protein kinase-like domain (1);	0.173414	0.56097	D	0.000023	T	0.12774	0.0310	N	0.14661	0.345	0.54753	D	0.999983	B	0.09022	0.002	B	0.14023	0.01	T	0.10683	-1.0619	10	0.34782	T	0.22	-20.6608	10.4529	0.44533	0.0:0.8559:0.0:0.1441	.	353	Q9UEW8	STK39_HUMAN	I	353	ENSP00000348278:R353I	ENSP00000348278:R353I	R	-	2	0	STK39	168694328	0.994000	0.37717	0.998000	0.56505	0.997000	0.91878	2.329000	0.43876	2.746000	0.94184	0.563000	0.77884	AGA	.	.		0.388	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258112.2	NM_013233		A	168986082	C	A	168986082	3	1	213	1	0	0	0	0	1	0	0	0	15320	913	32	3	615	3	STK39	2	168986082	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10	56426047	168986082	74213291	13	30741										
SMARCAL1	50485	hgsc.bcm.edu	37	chr2	217293425	217293425	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	acatctctcagtctcacgccAgatgtcccagaggcagacct	8	15	3	3			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr2:217293425A>C	ENST00000357276.4	+	7	1584	c.1254A>C	c.(1252-1254)ccA>ccC	p.P418P	SMARCAL1_ENST00000479008.1_3'UTR|SMARCAL1_ENST00000358207.5_Silent_p.P418P	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	418					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		GTCTCACGCCAGATGTCCCAG	0.547									Schimke Immuno-Osseous Dysplasia																												p.P418P		Atlas-SNP	.											.	SMARCAL1	93	.	0			c.A1254C						.						158	142	148					2																	217293425		2203	4300	6503	SO:0001819	synonymous_variant	50485	exon7	Familial Cancer Database	SIOD	CACGCCAGATGTC	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"HepA-related protein", "ATP-driven annealing helicase"	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.1254A>C	chr2.hg19:g.217293425A>C		74.0	0.0		78.0	18.0	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Silent	SNP	ENST00000357276.4	hg19	CCDS2403.1																																																																																			.	.		0.547	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			C	217293425	A	C	217293425	2	2	213	1	0	0	0	0	0	0	0	1	14788	175	7	5		5	SMARCAL1	2	217293425	Silent	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10	48307343	217293425	25905948	14	30742										
C3orf23	285343	hgsc.bcm.edu	37	chr3	44442703	44442703	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	attttattgcagtgacagatAtgctccaagcttgcatgaac	8	8	0	3			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr3:44442703A>T	ENST00000342649.4	+	10	1554	c.1127A>T	c.(1126-1128)tAt>tTt	p.Y376F	TCAIM_ENST00000417237.1_Missense_Mutation_p.Y376F	NM_001282913.1|NM_173826.3	NP_001269842.1|NP_776187.2	Q8N3R3	TCAIM_HUMAN	T cell activation inhibitor, mitochondrial	376						mitochondrion (GO:0005739)											AGTGACAGATATGCTCCAAGC	0.393																																					p.Y376F		Atlas-SNP	.											.	.	.	.	0			c.A1127T						.						140	133	135					3																	44442703		2203	4300	6503	SO:0001583	missense	285343	exon10			ACAGATATGCTCC		CCDS2712.1, CCDS43076.1	3p21.33-p21.32	2012-08-22	2012-08-22	2012-08-22	ENSG00000179152	ENSG00000179152			25241	protein-coding gene	gene with protein product	"tolerance associated gene-1"		"chromosome 3 open reading frame 23"	C3orf23		12477932	Standard	NM_001029840		Approved	DKFZp313N0621, TOAG-1	uc003cnd.4	Q8N3R3	OTTHUMG00000133049	ENST00000342649.4:c.1127A>T	chr3.hg19:g.44442703A>T	ENSP00000341539:p.Tyr376Phe	95.0	0.0		74.0	18.0	NM_173826	A8K9P1|Q0P5T9|Q495R1|Q495R3|Q4G0M4|Q6GMU8	Missense_Mutation	SNP	ENST00000342649.4	hg19	CCDS2712.1	.	.	.	.	.	.	.	.	.	.	A	5.609	0.297042	0.10622	.	.	ENSG00000179152	ENST00000417237;ENST00000342649	T;T	0.42900	0.96;0.96	5.61	5.61	0.85477	.	0.114845	0.64402	D	0.000008	T	0.26846	0.0657	L	0.31294	0.92	0.32416	N	0.550034	B	0.18461	0.028	B	0.14578	0.011	T	0.24977	-1.0145	10	0.06099	T	0.92	.	10.963	0.47395	0.8605:0.0:0.0:0.1394	.	376	Q8N3R3	CC023_HUMAN	F	376	ENSP00000402581:Y376F;ENSP00000341539:Y376F	ENSP00000341539:Y376F	Y	+	2	0	C3orf23	44417707	0.892000	0.30473	0.956000	0.39512	0.983000	0.72400	1.947000	0.40293	2.138000	0.66242	0.459000	0.35465	TAT	.	.		0.393	TCAIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256655.2	NM_173826		T	44442703	A	T	44442703	3	4	213	1	0	0	0	0	1	0	0	0	2218	449	16	4	1213	4	C3orf23	3	44442703	Missense_Mutation	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10		44442703	153579727	15	30743										
ARGFX	503582	hgsc.bcm.edu	37	chr3	121305241	121305241	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	agatatccagctcttctttcCactgtctgtatcagtatctc	5	12	5	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr3:121305241C>T	ENST00000334384.3	+	4	752	c.742C>T	c.(742-744)Cac>Tac	p.H248Y		NM_001012659.1	NP_001012677.1	A6NJG6	ARGFX_HUMAN	arginine-fifty homeobox	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(114;0.152)		CTCTTCTTTCCACTGTCTGTA	0.473																																					p.H248Y		Atlas-SNP	.											.	ARGFX	36	.	0			c.C742T						.						104	102	102					3																	121305241		2203	4300	6503	SO:0001583	missense	503582	exon5			TCTTTCCACTGTC		CCDS33834.1	3q13.33	2011-06-20			ENSG00000186103	ENSG00000186103		"Homeoboxes / PRD class"	30146	protein-coding gene	gene with protein product		611164					Standard	XM_005247505		Approved		uc003eef.3	A6NJG6	OTTHUMG00000159395	ENST00000334384.3:c.742C>T	chr3.hg19:g.121305241C>T	ENSP00000335578:p.His248Tyr	90.0	0.0		85.0	22.0	NM_001012659		Missense_Mutation	SNP	ENST00000334384.3	hg19	CCDS33834.1	.	.	.	.	.	.	.	.	.	.	C	0.031	-1.332787	0.01298	.	.	ENSG00000186103	ENST00000334384	D	0.88664	-2.41	2.97	-3.08	0.05347	.	1.692040	0.03378	N	0.199968	T	0.75488	0.3856	N	0.12182	0.205	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.60047	-0.7339	10	0.56958	D	0.05	0.8731	0.4001	0.00424	0.2049:0.2543:0.1657:0.3751	.	248	A6NJG6	ARGFX_HUMAN	Y	248	ENSP00000335578:H248Y	ENSP00000335578:H248Y	H	+	1	0	ARGFX	122787931	0.000000	0.05858	0.000000	0.03702	0.401000	0.30781	-0.619000	0.05572	-0.771000	0.04608	0.561000	0.74099	CAC	.	.		0.473	ARGFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355096.2	NM_001012659		T	121305241	C	T	121305241	3	4	213	1	0	0	0	0	1	0	0	0	859	594	21	3	756	3	ARGFX	3	121305241	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10	76862538	121305241	76717189	16	30744										
ACAP2	23527	hgsc.bcm.edu	37	chr3	195102681	195102681	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gagccaggtctcgaatcccaTtcatgaactgtttatttgca	8	10	2	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr3:195102681T>C	ENST00000326793.6	-	3	412	c.182A>G	c.(181-183)aAt>aGt	p.N61S		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	61	BAR.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						TCGAATCCCATTCATGAACTG	0.318																																					p.N61S		Atlas-SNP	.											.	ACAP2	72	.	0			c.A182G						.						83	86	85					3																	195102681		2203	4300	6503	SO:0001583	missense	23527	exon3			ATCCCATTCATGA		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.182A>G	chr3.hg19:g.195102681T>C	ENSP00000324287:p.Asn61Ser	254.0	0.0		262.0	90.0	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	hg19	CCDS33924.1	.	.	.	.	.	.	.	.	.	.	T	5.957	0.360627	0.11296	.	.	ENSG00000114331	ENST00000326793;ENST00000439666	T;T	0.03951	3.75;3.75	5.39	5.39	0.77823	.	0.087672	0.85682	D	0.000000	T	0.03695	0.0105	N	0.21240	0.645	0.42291	D	0.992139	B;B	0.21753	0.06;0.003	B;B	0.20184	0.028;0.006	T	0.28267	-1.0049	10	0.06494	T	0.89	.	13.3588	0.60644	0.0:0.0:0.0:1.0	.	17;61	C9J8L1;Q15057	.;ACAP2_HUMAN	S	61;17	ENSP00000324287:N61S;ENSP00000411336:N17S	ENSP00000324287:N61S	N	-	2	0	ACAP2	196583970	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.093000	0.41710	2.029000	0.59856	0.460000	0.39030	AAT	.	.		0.318	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287		C	195102681	T	C	195102681	3	2	213	1	0	0	0	0	1	0	0	0	119	1493	52	2	2238	2	ACAP2	3	195102681	Missense_Mutation	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	73797440	195102681	2919749	17	30745										
MUC4	4585	hgsc.bcm.edu	37	chr3	195474197	195474197	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	aagaacgcgtcgagtttcatGctcaggtgctcacagtgctc	11	11	3	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr3:195474197G>A	ENST00000346145.4	-	24	3420	c.3381C>T	c.(3379-3381)agC>agT	p.S1127S	MUC4_ENST00000475231.1_Silent_p.S5311S|MUC4_ENST00000463781.3_Silent_p.S5363S|MUC4_ENST00000349607.4_Silent_p.S1076S	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2120					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CGAGTTTCATGCTCAGGTGCT	0.627																																					p.S5363S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C16089T						.						74	62	66					3																	195474197		2203	4300	6503	SO:0001819	synonymous_variant	4585	exon25			TTTCATGCTCAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.3381C>T	chr3.hg19:g.195474197G>A		241.0	0.0		286.0	18.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	hg19	CCDS3310.1																																																																																			.	.		0.627	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		A	195474197	G	A	195474197	2	1	213	1	0	0	0	0	0	0	0	1	9987	1310	46	3		3	MUC4	3	195474197	Silent	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	371516	195474197	2548233	18	30746										
RGS12	6002	hgsc.bcm.edu	37	chr4	3318452	3318452	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tttgatgttggacatgaaagTataaataatccaaatcccaa	6	6	0	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr4:3318452T>A	ENST00000344733.5	+	2	1459	c.555T>A	c.(553-555)agT>agA	p.S185R	RGS12_ENST00000382788.3_Missense_Mutation_p.S185R|RGS12_ENST00000336727.3_Missense_Mutation_p.S185R|RGS12_ENST00000543385.1_Missense_Mutation_p.S185R	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	185					positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GACATGAAAGTATAAATAATC	0.393																																					p.S185R		Atlas-SNP	.											.	RGS12	128	.	0			c.T555A						.						61	64	63					4																	3318452		2203	4300	6503	SO:0001583	missense	6002	exon2			TGAAAGTATAAAT	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"Regulators of G-protein signaling"	9994	protein-coding gene	gene with protein product		602512	"regulator of G-protein signalling 12"			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.555T>A	chr4.hg19:g.3318452T>A	ENSP00000339381:p.Ser185Arg	93.0	0.0		87.0	16.0	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	hg19	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	T	7.811	0.715629	0.15306	.	.	ENSG00000159788	ENST00000543385;ENST00000344733;ENST00000336727;ENST00000382788	T;T;T;T	0.32272	1.46;1.58;1.58;1.58	3.86	-1.72	0.08107	.	0.885835	0.09810	U	0.752875	T	0.24198	0.0586	M	0.63428	1.95	0.09310	N	1	B;B;B	0.28584	0.026;0.138;0.216	B;B;B	0.32864	0.005;0.074;0.154	T	0.35126	-0.9801	10	0.21540	T	0.41	2.0E-4	0.9439	0.01361	0.1541:0.2791:0.1586:0.4082	.	185;185;185	Q8WX97;O14924;O14924-4	.;RGS12_HUMAN;.	R	185	ENSP00000440566:S185R;ENSP00000339381:S185R;ENSP00000338509:S185R;ENSP00000372238:S185R	ENSP00000338509:S185R	S	+	3	2	RGS12	3288250	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	0.330000	0.19715	-0.345000	0.08325	0.402000	0.26972	AGT	.	.		0.393	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926		A	3318452	T	A	3318452	3	1	213	1	0	0	0	0	1	0	0	0	13310	1635	57	4	557	4	RGS12	4	3318452	Missense_Mutation	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10		3318452	187835824	19	30747										
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69179827	69179827	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	caaaagcccattatcttctaTatcgacctctctcccctcgg	4	16	3	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr4:69179827T>G	ENST00000344157.4	-	17	2509	c.2174A>C	c.(2173-2175)tAt>tCt	p.Y725S	YTHDC1_ENST00000579690.1_Missense_Mutation_p.Y733S|YTHDC1_ENST00000355665.3_Missense_Mutation_p.Y707S	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	725	Arg-rich.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						TTATCTTCTATATCGACCTCT	0.373																																					p.Y725S		Atlas-SNP	.											.	YTHDC1	81	.	0			c.A2174C						.						63	65	65					4																	69179827		2203	4300	6503	SO:0001583	missense	91746	exon17			CTTCTATATCGAC	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.2174A>C	chr4.hg19:g.69179827T>G	ENSP00000339245:p.Tyr725Ser	104.0	0.0		62.0	21.0	NM_001031732	Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	hg19	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	T	15.58	2.874690	0.51695	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.33216	1.42;1.44	5.69	5.69	0.88448	.	0.057323	0.64402	D	0.000001	T	0.42810	0.1219	N	0.24115	0.695	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.75484	0.986;0.969	T	0.44034	-0.9354	10	0.87932	D	0	.	15.6236	0.76829	0.0:0.0:0.0:1.0	.	707;725	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	S	725;707	ENSP00000339245:Y725S;ENSP00000347888:Y707S	ENSP00000339245:Y725S	Y	-	2	0	YTHDC1	68862422	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.512000	0.73737	2.167000	0.68274	0.460000	0.39030	TAT	.	.		0.373	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		G	69179827	T	G	69179827	3	3	213	1	0	0	0	0	1	0	0	0	17511	1406	49	5	13	5	YTHDC1	4	69179827	Missense_Mutation	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	65861375	69179827	121974449	20	30748										
ALB	213	hgsc.bcm.edu	37	chr4	74272394	74272394	+	De_novo_Start_InFrame	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	cagcagtgtccatttgaagaTcatgtaaaattagtgaatga	9	5	1	4			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr4:74272394T>G	ENST00000503124.1	+	0	155				ALB_ENST00000295897.4_Missense_Mutation_p.D62E|ALB_ENST00000401494.3_Intron|ALB_ENST00000415165.2_Intron|ALB_ENST00000509063.1_Missense_Mutation_p.D62E			Q8TES7	FBF1_HUMAN	albumin						apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CATTTGAAGATCATGTAAAAT	0.318																																					p.D62E		Atlas-SNP	.											.	ALB	132	.	0			c.T186G						.						127	121	123					4																	74272394		2203	4300	6503			213	exon3			TGAAGATCATGTA	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919		chr4.hg19:g.74272394T>G		70.0	0.0		45.0	12.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0	-2.813415	0.00073	.	.	ENSG00000163631	ENST00000441319;ENST00000295897;ENST00000329326;ENST00000509063;ENST00000430202	T;T;T	0.69306	-0.39;-0.39;-0.39	5.39	-10.8	0.00216	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.549222	0.17976	N	0.155712	T	0.17152	0.0412	N	0.00801	-1.175	0.38421	D	0.946194	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.67868	-0.5559	10	0.02654	T	1	-4.162	0.7623	0.01009	0.2903:0.2133:0.1284:0.3681	.	62;62	A6NBZ8;P02768	.;ALBU_HUMAN	E	64;62;62;62;71	ENSP00000392541:D64E;ENSP00000295897:D62E;ENSP00000422784:D62E	ENSP00000295897:D62E	D	+	3	2	ALB	74491258	0.000000	0.05858	0.000000	0.03702	0.151000	0.21798	-7.643000	0.00032	-5.202000	0.00019	-1.280000	0.01385	GAT	.	.		0.318	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		G	74272394	T	G	74272394	1	3	213	1	0	1	0	0	0	0	0	0	486	1432	50	5		5	ALB	4	74272394	De_novo_Start_InFrame	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	5092567	74272394	116881882	21	30749										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155157584	155157584	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ttttctgcatctgaagcttgGacagttaaggtgaattttgt	10	5	2	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr4:155157584G>T	ENST00000357232.4	-	25	6854	c.6855C>A	c.(6853-6855)gtC>gtA	p.V2285V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2285	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CTGAAGCTTGGACAGTTAAGG	0.353																																					p.V2285V		Atlas-SNP	.											.	DCHS2	594	.	0			c.C6855A						.						79	80	80					4																	155157584		2203	4300	6503	SO:0001819	synonymous_variant	54798	exon25			AGCTTGGACAGTT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6855C>A	chr4.hg19:g.155157584G>T		196.0	0.0		159.0	71.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	hg19	CCDS3785.1																																																																																			.	.		0.353	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		T	155157584	G	T	155157584	2	4	213	1	0	0	0	0	0	0	0	1	4290	1161	41	3		3	DCHS2	4	155157584	Silent	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	80885190	155157584	35996692	22	30750										
IRX1	79192	hgsc.bcm.edu	37	chr5	3599701	3599701	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ggcagcgacaccgagggcgaCccggagaaggccgaggacga	18	12	0	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr5:3599701C>G	ENST00000302006.3	+	2	691	c.639C>G	c.(637-639)gaC>gaG	p.D213E	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	213					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CCGAGGGCGACCCGGAGAAGG	0.627																																					p.D213E		Atlas-SNP	.											.	IRX1	106	.	0			c.C639G						.						66	59	61					5																	3599701		2203	4300	6503	SO:0001583	missense	79192	exon2			GGGCGACCCGGAG	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.639C>G	chr5.hg19:g.3599701C>G	ENSP00000305244:p.Asp213Glu	179.0	0.0		225.0	61.0	NM_024337	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	hg19	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	C	9.464	1.093783	0.20471	.	.	ENSG00000170549	ENST00000302006	T	0.58940	0.3	4.65	3.76	0.43208	.	0.098933	0.64402	D	0.000002	T	0.43010	0.1228	L	0.31065	0.9	0.51767	D	0.999939	B	0.17667	0.023	B	0.17098	0.017	T	0.28202	-1.0051	10	0.17832	T	0.49	.	13.0819	0.59119	0.0:0.9198:0.0:0.0802	.	213	P78414	IRX1_HUMAN	E	213	ENSP00000305244:D213E	ENSP00000305244:D213E	D	+	3	2	IRX1	3652701	0.891000	0.30450	1.000000	0.80357	0.802000	0.45316	0.981000	0.29526	2.089000	0.63090	0.609000	0.83330	GAC	.	.		0.627	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		G	3599701	C	G	3599701	3	3	213	1	0	0	0	0	1	0	0	0	7852	506	18	4	645	4	IRX1	5	3599701	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10		3599701	177315559	23	30751										
FAM174A	345757	hgsc.bcm.edu	37	chr5	99871534	99871534	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gacgatcacggagggaaggcCggggaaggctcggtgggtgg	22	7	1	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr5:99871534C>T	ENST00000312637.4	+	1	526	c.300C>T	c.(298-300)gcC>gcT	p.A100A	CTD-2001C12.1_ENST00000499025.1_lincRNA	NM_198507.1	NP_940909.1	Q8TBP5	F174A_HUMAN	family with sequence similarity 174, member A	100						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						GAGGGAAGGCCGGGGAAGGCT	0.706																																					p.A100A		Atlas-SNP	.											.	FAM174A	13	.	0			c.C300T						.						20	22	21					5																	99871534		2201	4296	6497	SO:0001819	synonymous_variant	345757	exon1			GAAGGCCGGGGAA	AY359108	CCDS4090.1	5q21.1	2008-06-19	2008-06-19	2008-06-19	ENSG00000174132	ENSG00000174132			24943	protein-coding gene	gene with protein product			"transmembrane protein 157"	TMEM157		12975309	Standard	NM_198507		Approved	UNQ1912	uc003knj.1	Q8TBP5	OTTHUMG00000128726	ENST00000312637.4:c.300C>T	chr5.hg19:g.99871534C>T		81.0	0.0		116.0	39.0	NM_198507	A8K0H4	Silent	SNP	ENST00000312637.4	hg19	CCDS4090.1																																																																																			.	.		0.706	FAM174A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250631.2	NM_198507		T	99871534	C	T	99871534	2	4	213	1	0	0	0	0	0	0	0	1	5500	639	23	1		1	FAM174A	5	99871534	Silent	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10	96271833	99871534	81043726	24	30752										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135551937	135551937	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	acctgggctttcaggacgtaTctttttatgagccgtttcat	9	9	3	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr5:135551937T>C	ENST00000513104.1	-	11	2652	c.2370A>G	c.(2368-2370)agA>agG	p.R790R	TRPC7-AS1_ENST00000514459.1_RNA|TRPC7_ENST00000355180.3_Silent_p.R729R|TRPC7_ENST00000426057.2_Silent_p.R674R	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	790					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TCAGGACGTATCTTTTTATGA	0.473																																					p.R790R		Atlas-SNP	.											.	TRPC7	126	.	0			c.A2370G						.						104	103	103					5																	135551937		1912	4134	6046	SO:0001819	synonymous_variant	57113	exon11			GACGTATCTTTTT	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.2370A>G	chr5.hg19:g.135551937T>C		53.0	0.0		75.0	17.0	NM_020389	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Silent	SNP	ENST00000513104.1	hg19	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	T	9.056	0.993367	0.19043	.	.	ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753	.	.	.	4.92	2.46	0.29980	.	.	.	.	.	T	0.54175	0.1842	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44034	-0.9354	4	.	.	.	-15.8113	6.0593	0.19828	0.0:0.2146:0.1278:0.6575	.	.	.	.	V	674;729;735	.	.	I	-	1	0	TRPC7	135579836	0.909000	0.30893	1.000000	0.80357	0.899000	0.52679	-0.057000	0.11768	0.424000	0.26061	0.459000	0.35465	ATA	.	.		0.473	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		C	135551937	T	C	135551937	2	2	213	1	0	0	0	0	0	0	0	1	16599	1432	50	2		2	TRPC7	5	135551937	Silent	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	35680403	135551937	45363323	25	30753										
C6orf47	57827	hgsc.bcm.edu	37	chr6	31627256	31627256	+	Missense_Mutation	SNP	A	A	G													0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tcctggttccccccgcagccAgcccaacagcttctcacgcc							TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr6:31627256A>G	ENST00000375911.1	-	1	1293	c.469T>C	c.(469-471)Tgg>Cgg	p.W157R	C6orf47-AS1_ENST00000422049.1_RNA	NM_021184.3	NP_067007.3	O95873	CF047_HUMAN	chromosome 6 open reading frame 47	157						cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9						CCCCGCAGCCAGCCCAACAGC	0.642																																					p.W157R		Atlas-SNP	.											.	C6orf47	15	.	0			c.T469C						.						62	73	69					6																	31627256		1508	2708	4216	SO:0001583	missense	57827	exon1			GCAGCCAGCCCAA	AF129756	CCDS34399.1	6p21.3	2011-12-13			ENSG00000204439	ENSG00000204439			19076	protein-coding gene	gene with protein product						2477242	Standard	NM_021184		Approved	D6S53E, G4	uc003nvm.1	O95873	OTTHUMG00000031172	ENST00000375911.1:c.469T>C	chr6.hg19:g.31627256A>G	ENSP00000365076:p.Trp157Arg	85.0	0.0		91.0	7.0	NM_021184	B0UXA1|B0UZ50|Q5SSS6|Q95IG0	Missense_Mutation	SNP	ENST00000375911.1	hg19	CCDS34399.1	.	.	.	.	.	.	.	.	.	.	A	19.10	3.761382	0.69763	.	.	ENSG00000204439	ENST00000375911;ENST00000538106	T	0.52983	0.64	5.79	5.79	0.91817	.	0.000000	0.46758	D	0.000276	T	0.56485	0.1988	M	0.62723	1.935	0.34156	D	0.668055	D	0.89917	1.0	D	0.91635	0.999	T	0.65709	-0.6102	10	0.87932	D	0	-11.1174	12.5142	0.56024	1.0:0.0:0.0:0.0	.	157	O95873	CF047_HUMAN	R	157	ENSP00000365076:W157R	ENSP00000365076:W157R	W	-	1	0	C6orf47	31735235	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	4.241000	0.58707	2.208000	0.71279	0.533000	0.62120	TGG	.	.		0.642	C6orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076324.1	NM_021184		G	31627256	A	G	31627256	3	3	213	1	0	0	0	0	1	0	0	0	2366	188	7	2	419	2	C6orf47	6	31627256	Missense_Mutation	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10		31627256	139487811	26	30754	160	2								
C6orf47	57827	hgsc.bcm.edu	37	chr6	31627264	31627264	+	Missense_Mutation	SNP	A	A	G													0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ccccccgcagccagcccaacAgcttctcacgcctaccaggt							TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr6:31627264A>G	ENST00000375911.1	-	1	1285	c.461T>C	c.(460-462)cTg>cCg	p.L154P	C6orf47-AS1_ENST00000422049.1_RNA	NM_021184.3	NP_067007.3	O95873	CF047_HUMAN	chromosome 6 open reading frame 47	154						cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9						CCAGCCCAACAGCTTCTCACG	0.637																																					p.L154P		Atlas-SNP	.											.	C6orf47	15	.	0			c.T461C						.						62	74	70					6																	31627264		1508	2708	4216	SO:0001583	missense	57827	exon1			CCCAACAGCTTCT	AF129756	CCDS34399.1	6p21.3	2011-12-13			ENSG00000204439	ENSG00000204439			19076	protein-coding gene	gene with protein product						2477242	Standard	NM_021184		Approved	D6S53E, G4	uc003nvm.1	O95873	OTTHUMG00000031172	ENST00000375911.1:c.461T>C	chr6.hg19:g.31627264A>G	ENSP00000365076:p.Leu154Pro	78.0	0.0		83.0	6.0	NM_021184	B0UXA1|B0UZ50|Q5SSS6|Q95IG0	Missense_Mutation	SNP	ENST00000375911.1	hg19	CCDS34399.1	.	.	.	.	.	.	.	.	.	.	A	18.79	3.699565	0.68501	.	.	ENSG00000204439	ENST00000375911;ENST00000538106	T	0.51817	0.69	5.79	5.79	0.91817	.	0.000000	0.47093	D	0.000245	T	0.57388	0.2050	M	0.62723	1.935	0.53688	D	0.999979	D	0.89917	1.0	D	0.91635	0.999	T	0.63567	-0.6608	10	0.87932	D	0	-6.3093	12.5142	0.56024	1.0:0.0:0.0:0.0	.	154	O95873	CF047_HUMAN	P	154	ENSP00000365076:L154P	ENSP00000365076:L154P	L	-	2	0	C6orf47	31735243	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	4.485000	0.60279	2.208000	0.71279	0.533000	0.62120	CTG	.	.		0.637	C6orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076324.1	NM_021184		G	31627264	A	G	31627264	3	3	213	1	0	0	0	0	1	0	0	0	2366	188	7	2	427	2	C6orf47	6	31627264	Missense_Mutation	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10	8	31627264	139487803	27	30755	160	2								
GPR115	221393	hgsc.bcm.edu	37	chr6	47681900	47681900	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ctatcctgagagaagcccacTtgcaaaatgtgagtcttccc	8	12	1	3			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr6:47681900T>C	ENST00000283303.2	+	6	1177	c.919T>C	c.(919-921)Ttg>Ctg	p.L307L	RN7SKP116_ENST00000516902.1_RNA|GPR115_ENST00000371220.1_Silent_p.L364L|GPR115_ENST00000327753.3_Silent_p.L307L	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	307					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						AGAAGCCCACTTGCAAAATGT	0.468																																					p.L307L	GBM(22;431 510 9010 26644 32828)	Atlas-SNP	.											.	GPR115	140	.	0			c.T919C						.						61	65	64					6																	47681900		2203	4300	6503	SO:0001819	synonymous_variant	221393	exon6			GCCCACTTGCAAA	AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.919T>C	chr6.hg19:g.47681900T>C		110.0	0.0		109.0	9.0	NM_153838	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Silent	SNP	ENST00000283303.2	hg19	CCDS4922.2																																																																																			.	.		0.468	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		C	47681900	T	C	47681900	2	2	213	1	0	0	0	0	0	0	0	1	6640	1606	56	2		2	GPR115	6	47681900	Silent	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	16054636	47681900	123433167	28	30756										
IBTK	25998	hgsc.bcm.edu	37	chr6	82941527	82941527	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	atgacccagggtaaaatttgTattatcgccccaagtataaa	7	8	0	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr6:82941527T>C	ENST00000306270.7	-	4	1000	c.451A>G	c.(451-453)Aca>Gca	p.T151A	IBTK_ENST00000503631.1_Missense_Mutation_p.T151A|IBTK_ENST00000510291.1_Missense_Mutation_p.T151A	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	151					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		GTAAAATTTGTATTATCGCCC	0.313																																					p.T151A		Atlas-SNP	.											.	IBTK	128	.	0			c.A451G						.						96	93	94					6																	82941527		2203	4300	6503	SO:0001583	missense	25998	exon4			AATTTGTATTATC	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.451A>G	chr6.hg19:g.82941527T>C	ENSP00000305721:p.Thr151Ala	94.0	0.0		82.0	26.0	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	hg19	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	T	15.39	2.819758	0.50633	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	D;D;D	0.85013	-1.93;-1.93;-1.93	5.92	3.6	0.41247	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.263184	0.43579	D	0.000555	T	0.71316	0.3325	L	0.59436	1.845	0.39687	D	0.970992	B;B;P;P	0.38729	0.309;0.097;0.644;0.549	B;B;B;B	0.40134	0.197;0.056;0.307;0.32	T	0.68750	-0.5326	10	0.14656	T	0.56	-18.7484	8.7601	0.34669	0.0:0.188:0.0:0.812	.	151;151;151;151	E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0	.;.;.;IBTK_HUMAN	A	151	ENSP00000305721:T151A;ENSP00000422762:T151A;ENSP00000426405:T151A	ENSP00000305721:T151A	T	-	1	0	IBTK	82998246	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.580000	0.46068	2.260000	0.74910	0.528000	0.53228	ACA	.	.		0.313	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		C	82941527	T	C	82941527	3	2	213	1	0	0	0	0	1	0	0	0	7485	1638	57	2	3714	2	IBTK	6	82941527	Missense_Mutation	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	35259627	82941527	88173540	29	30757										
PNRC1	10957	hgsc.bcm.edu	37	chr6	89793582	89793582	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ataaacagacagaaaagcaaAtataacttgccactaaccaa	4	9	0	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr6:89793582A>C	ENST00000336032.3	+	2	768	c.651A>C	c.(649-651)aaA>aaC	p.K217N	PNRC1_ENST00000354922.3_Missense_Mutation_p.K32N|PNRC1_ENST00000369472.1_Missense_Mutation_p.K32N	NM_006813.2	NP_006804.1	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1	217					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		AGAAAAGCAAATATAACTTGC	0.388										Multiple Myeloma(7;0.094)																											p.K217N		Atlas-SNP	.											.	PNRC1	17	.	0			c.A651C						.						68	69	69					6																	89793582		2203	4300	6503	SO:0001583	missense	10957	exon2			AAGCAAATATAAC	U03105	CCDS5018.1	6q16.1	2008-02-05	2003-09-25	2003-09-26	ENSG00000146278	ENSG00000146278			17278	protein-coding gene	gene with protein product		606714	"proline rich 2"	PROL2		7578250	Standard	NM_006813		Approved	B4-2, PRR2	uc003pmv.3	Q12796	OTTHUMG00000015191	ENST00000336032.3:c.651A>C	chr6.hg19:g.89793582A>C	ENSP00000336931:p.Lys217Asn	363.0	0.0		343.0	25.0	NM_006813	B2R6Q0|E1P515|Q5T7J6|Q7Z5N0	Missense_Mutation	SNP	ENST00000336032.3	hg19	CCDS5018.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.924607	0.52653	.	.	ENSG00000146278	ENST00000369472;ENST00000336032;ENST00000354922	T;T;T	0.67865	0.07;-0.29;0.07	5.73	3.39	0.38822	.	0.343196	0.32120	N	0.006558	T	0.62344	0.2420	M	0.71581	2.175	0.29316	N	0.867716	D	0.55800	0.973	P	0.59546	0.859	T	0.60234	-0.7303	10	0.66056	D	0.02	-3.3194	4.7301	0.12961	0.6592:0.0:0.2088:0.132	.	217	Q12796	PNRC1_HUMAN	N	32;217;32	ENSP00000358484:K32N;ENSP00000336931:K217N;ENSP00000347000:K32N	ENSP00000336931:K217N	K	+	3	2	PNRC1	89850301	1.000000	0.71417	0.930000	0.37139	0.980000	0.70556	2.630000	0.46494	0.995000	0.38917	0.533000	0.62120	AAA	.	.		0.388	PNRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041471.1	NM_006813		C	89793582	A	C	89793582	3	2	213	1	0	0	0	0	1	0	0	0	12183	98	4	5	657	5	PNRC1	6	89793582	Missense_Mutation	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10	6852055	89793582	81321485	30	30758										
C6orf182	285753	hgsc.bcm.edu	37	chr6	109484145	109484145	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	taatcttcaaatgaaattgaGaagagatgatatcatgtggg	10	3	3	4			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr6:109484145G>A	ENST00000517392.1	+	11	1781	c.1355G>A	c.(1354-1356)aGa>aAa	p.R452K	CEP57L1_ENST00000359793.3_Missense_Mutation_p.R452K|CEP57L1_ENST00000523787.1_Missense_Mutation_p.R455K|CEP57L1_ENST00000368968.2_3'UTR|CEP57L1_ENST00000368970.2_Missense_Mutation_p.R469K|CEP57L1_ENST00000521522.1_Missense_Mutation_p.R399K|CEP57L1_ENST00000336977.4_Missense_Mutation_p.R352K|C6orf183_ENST00000417143.3_RNA|CEP57L1_ENST00000407272.1_Missense_Mutation_p.R452K|CEP57L1_ENST00000520883.1_Missense_Mutation_p.R352K	NM_001271852.1|NM_001271853.1	NP_001258781.1|NP_001258782.1	Q8IYX8	CE57L_HUMAN	centrosomal protein 57kDa-like 1	452					microtubule anchoring (GO:0034453)	cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.R452I(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)	11						ATGAAATTGAGAAGAGATGAT	0.333																																					p.R452K		Atlas-SNP	.											CEP57L1,NS,carcinoma,0,1	CEP57L1	24	.	1	Substitution - Missense(1)	kidney(1)	c.G1355A						.						56	57	57					6																	109484145		2203	4300	6503	SO:0001583	missense	285753	exon11			AATTGAGAAGAGA	AK092723	CCDS5071.1, CCDS64491.1	6q21	2014-01-28	2010-09-30	2010-09-30	ENSG00000183137	ENSG00000183137			21561	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 182"	C6orf182			Standard	NM_001083535		Approved	bA487F23.2, MGC21731	uc003psy.4	Q8IYX8	OTTHUMG00000015336	ENST00000517392.1:c.1355G>A	chr6.hg19:g.109484145G>A	ENSP00000427844:p.Arg452Lys	321.0	0.0		331.0	92.0	NM_173830	G5E992	Missense_Mutation	SNP	ENST00000517392.1	hg19	CCDS5071.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.275551	0.40294	.	.	ENSG00000183137	ENST00000517392;ENST00000407272;ENST00000336977;ENST00000521522;ENST00000368970;ENST00000520883;ENST00000523787;ENST00000359793	T;T;T;T;T;T;T;T	0.44482	1.0;1.0;0.97;0.92;1.03;0.97;1.0;1.0	5.68	5.68	0.88126	.	0.273372	0.36482	N	0.002568	T	0.21801	0.0525	L	0.49350	1.555	0.36381	D	0.861913	B	0.15930	0.015	B	0.11329	0.006	T	0.04796	-1.0926	10	0.28530	T	0.3	-8.2543	11.0829	0.48070	0.0848:0.0:0.9152:0.0	.	452	Q8IYX8	CE57L_HUMAN	K	452;452;352;399;469;352;455;452	ENSP00000427844:R452K;ENSP00000383936:R452K;ENSP00000337392:R352K;ENSP00000428344:R399K;ENSP00000357966:R469K;ENSP00000430011:R352K;ENSP00000430529:R455K;ENSP00000352841:R452K	ENSP00000337392:R352K	R	+	2	0	CEP57L1	109590838	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.884000	0.56175	2.838000	0.97847	0.591000	0.81541	AGA	.	.		0.333	CEP57L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041734.4	NM_173830		A	109484145	G	A	109484145	3	1	213	1	0	0	0	0	1	0	0	0	2348	942	33	3	1393	3	C6orf182	6	109484145	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	19690563	109484145	61630922	31	30759										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121563446	121563446	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	cctttgggggtggcagcaaaAtgtagtaaatcatctaacaa	10	7	2	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr6:121563446A>G	ENST00000398212.2	-	18	2107	c.2058T>C	c.(2056-2058)caT>caC	p.H686H	TBC1D32_ENST00000275159.6_Silent_p.H686H	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	686					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TGGCAGCAAAATGTAGTAAAT	0.328																																					p.H686H		Atlas-SNP	.											.,1	C6orf170	146	.	0			c.T2058C						.						91	87	88					6																	121563446		1834	4088	5922	SO:0001819	synonymous_variant	221322	exon18			AGCAAAATGTAGT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.2058T>C	chr6.hg19:g.121563446A>G		154.0	0.0		125.0	10.0	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	hg19	CCDS43501.1																																																																																			.	.		0.328	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		G	121563446	A	G	121563446	2	3	213	1	0	0	0	0	0	0	0	1	2346	98	4	2		2	C6orf170	6	121563446	Silent	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10	12079301	121563446	49551621	32	30760										
PRKAR2B	5577	hgsc.bcm.edu	37	chr7	106799922	106799922	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gtgcaagcatttgaaaggctTctgggaccttgcatggaaat	12	7	1	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr7:106799922T>C	ENST00000265717.4	+	11	1411	c.1152T>C	c.(1150-1152)ctT>ctC	p.L384L		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	384					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TTGAAAGGCTTCTGGGACCTT	0.363																																					p.L384L		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.T1152C						.						102	93	96					7																	106799922		2203	4300	6503	SO:0001819	synonymous_variant	5577	exon11			AAGGCTTCTGGGA		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.1152T>C	chr7.hg19:g.106799922T>C		92.0	0.0		97.0	9.0	NM_002736	A4D0R9	Silent	SNP	ENST00000265717.4	hg19	CCDS5740.1																																																																																			.	.		0.363	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			C	106799922	T	C	106799922	2	2	213	1	0	0	0	0	0	0	0	1	12518	1770	62	2		2	PRKAR2B	7	106799922	Silent	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10		106799922	52338741	33	30761										
TEX15	56154	hgsc.bcm.edu	37	chr8	30695229	30695229	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	agaaatttctgcaaaagcgtCccatggtctggtgaaaatgt	10	7	2	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr8:30695229C>A	ENST00000256246.2	-	3	7496	c.7422G>T	c.(7420-7422)ggG>ggT	p.G2474G		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	2474					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		GCAAAAGCGTCCCATGGTCTG	0.398																																					p.G2474G		Atlas-SNP	.											.	TEX15	350	.	0			c.G7422T						.						101	104	103					8																	30695229		2203	4300	6503	SO:0001819	synonymous_variant	56154	exon3			AAGCGTCCCATGG	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.7422G>T	chr8.hg19:g.30695229C>A		129.0	0.0		90.0	34.0	NM_031271		Silent	SNP	ENST00000256246.2	hg19	CCDS6080.1																																																																																			.	.		0.398	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30695229	C	A	30695229	2	1	213	1	0	0	0	0	0	0	0	1	15794	842	30	3		3	TEX15	8	30695229	Silent	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10		30695229	115668793	34	30762										
PRDM14	63978	hgsc.bcm.edu	37	chr8	70971011	70971011	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	agggggtgtacttgaggtgcTtatctctgtaatatttgtag	13	4	1	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr8:70971011T>G	ENST00000276594.2	-	6	1451	c.1250A>C	c.(1249-1251)aAg>aCg	p.K417T		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	417					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			CTTGAGGTGCTTATCTCTGTA	0.468																																					p.K417T	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											.	PRDM14	102	.	0			c.A1250C						.						114	101	105					8																	70971011		2203	4300	6503	SO:0001583	missense	63978	exon6			AGGTGCTTATCTC	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1250A>C	chr8.hg19:g.70971011T>G	ENSP00000276594:p.Lys417Thr	111.0	0.0		112.0	21.0	NM_024504	Q86UX9	Missense_Mutation	SNP	ENST00000276594.2	hg19	CCDS6206.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.688167	0.88639	.	.	ENSG00000147596	ENST00000276594	T	0.41758	0.99	5.73	5.73	0.89815	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.49592	0.1566	N	0.17278	0.47	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53535	-0.8425	10	0.48119	T	0.1	-31.1781	16.0233	0.80516	0.0:0.0:0.0:1.0	.	417	Q9GZV8	PRD14_HUMAN	T	417	ENSP00000276594:K417T	ENSP00000276594:K417T	K	-	2	0	PRDM14	71133565	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.550000	0.82173	2.186000	0.69663	0.533000	0.62120	AAG	.	.		0.468	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			G	70971011	T	G	70971011	3	3	213	1	0	0	0	0	1	0	0	0	12467	1609	56	5	477	5	PRDM14	8	70971011	Missense_Mutation	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	40275782	70971011	75393011	35	30763										
LOC645961	645961	hgsc.bcm.edu	37	chr9	90747470	90747470	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gatgcttggttcgaggatccGgggaagctaacggggagaca	17	7	0	1	rs200958103		TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr9:90747470G>T								U6 (134220 upstream) : U3 (241713 downstream)																							TCGAGGATCCGGGGAAGCTAA	0.612																																					p.P161Q		Atlas-SNP	.											.	.	.	.	0			c.C482A						.	G	GLN/PRO	1,1383		0,1,691	51	63	59		482	0.4	0	9		59	2,3180		0,2,1589	no	missense	FAM75C2	NM_001166137.1	76	0,3,2280	TT,TG,GG		0.0629,0.0723,0.0657	possibly-damaging	161/1135	90747470	3,4563	692	1591	2283	SO:0001628	intergenic_variant	645961	exon4			GGATCCGGGGAAG																													chr9.hg19:g.90747470G>T		122.0	0.0		99.0	47.0	NM_001166137		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.612									T	90747470	G	T	90747470	1	4	213	0	1	0	0	0	0	0	0	0	8892	1116	39	1		1	LOC645961	9	90747470	IGR	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10		90747470	50465961	36	30764										
WNK2	65268	hgsc.bcm.edu	37	chr9	96054796	96054796	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gtacctgcttttgtgagaccTgcacgtgtggagcccacaga	12	11	0	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr9:96054796T>A	ENST00000297954.4	+	23	5160	c.5160T>A	c.(5158-5160)ccT>ccA	p.P1720P	WNK2_ENST00000395477.2_Silent_p.P1683P|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000349097.3_Silent_p.P1332P|WNK2_ENST00000356055.3_Silent_p.P47P|WNK2_ENST00000427277.2_Silent_p.P1295P	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1720					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TTGTGAGACCTGCACGTGTGG	0.592																																					p.P1683P		Atlas-SNP	.											.	WNK2	277	.	0			c.T5049A						.						62	55	57					9																	96054796		2203	4298	6501	SO:0001819	synonymous_variant	65268	exon22			GAGACCTGCACGT	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.5160T>A	chr9.hg19:g.96054796T>A		104.0	0.0		80.0	8.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	5.043|5.043	0.193652|0.193652	0.09599|0.09599	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730;ENST00000448251;ENST00000453718	.|.	.|.	.|.	4.39|4.39	0.576|0.576	0.17380|0.17380	.|.	.|.	.|.	.|.	.|.	T|T	0.21631|0.21631	0.0521|0.0521	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999996|0.999996	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.22487|0.22487	-1.0215|-1.0215	4|4	.|.	.|.	.|.	.|.	2.5405|2.5405	0.04724|0.04724	0.289:0.2622:0.0:0.4488|0.289:0.2622:0.0:0.4488	.|.	.|.	.|.	.|.	S|Q	1287|1679;480;205	.|.	.|.	C|L	+|+	1|2	0|0	WNK2|WNK2	95094617|95094617	0.000000|0.000000	0.05858|0.05858	0.092000|0.092000	0.20876|0.20876	0.006000|0.006000	0.05464|0.05464	0.028000|0.028000	0.13644|0.13644	0.341000|0.341000	0.23771|0.23771	0.459000|0.459000	0.35465|0.35465	TGC|CTG	.	.		0.592	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		A	96054796	T	A	96054796	2	1	213	1	0	0	0	0	0	0	0	1	17393	1567	55	4		4	WNK2	9	96054796	Silent	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	5307326	96054796	45158635	37	30765										
ZNF248	57209	hgsc.bcm.edu	37	chr10	38121809	38121809	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ggcttctttctggaacagttCtttttactaataattaagcc	6	8	3	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr10:38121809C>G	ENST00000395867.3	-	6	1024	c.474G>C	c.(472-474)aaG>aaC	p.K158N	ZNF248_ENST00000357328.4_Missense_Mutation_p.K158N|ZNF248_ENST00000494133.1_Intron|ZNF248_ENST00000374648.3_Intron|AL135791.1_ENST00000583461.1_RNA	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TGGAACAGTTCTTTTTACTAA	0.323																																					p.K158N		Atlas-SNP	.											.	ZNF248	61	.	0			c.G474C						.						47	50	49					10																	38121809		2200	4296	6496	SO:0001583	missense	57209	exon6			ACAGTTCTTTTTA	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"Zinc fingers, C2H2-type", "-"	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.474G>C	chr10.hg19:g.38121809C>G	ENSP00000379208:p.Lys158Asn	206.0	0.0		298.0	27.0	NM_001267597	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	hg19	CCDS7194.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.256033	0.39896	.	.	ENSG00000198105	ENST00000395867;ENST00000357328	T;T	0.05139	3.49;3.49	4.86	-0.193	0.13244	.	0.000000	0.49916	D	0.000135	T	0.05914	0.0154	L	0.60455	1.87	0.32198	N	0.578258	B	0.15930	0.015	B	0.17433	0.018	T	0.09840	-1.0656	10	0.37606	T	0.19	.	3.3566	0.07171	0.1787:0.4351:0.0:0.3862	.	158	Q8NDW4	ZN248_HUMAN	N	158	ENSP00000379208:K158N;ENSP00000349882:K158N	ENSP00000349882:K158N	K	-	3	2	ZNF248	38161815	0.778000	0.28640	0.989000	0.46669	0.974000	0.67602	0.814000	0.27239	0.076000	0.16826	-0.311000	0.09066	AAG	.	.		0.323	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		G	38121809	C	G	38121809	3	3	213	1	0	0	0	0	1	0	0	0	17808	912	32	4	1269	4	ZNF248	10	38121809	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10		38121809	97412938	38	30766										
DUSP8	1850	hgsc.bcm.edu	37	chr11	1578679	1578679	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gactgggcggaggctccggcGtccctgagggggtgcccggg	21	12	0	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr11:1578679G>A	ENST00000397374.3	-	7	1074	c.947C>T	c.(946-948)aCg>aTg	p.T316M	DUSP8_ENST00000528778.1_5'Flank|DUSP8_ENST00000331588.4_Missense_Mutation_p.T316M	NM_004420.2	NP_004411.2	Q13202	DUS8_HUMAN	dual specificity phosphatase 8	316	Pro-rich.|Tyrosine-protein phosphatase.				inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|lung(2)|prostate(1)|urinary_tract(1)	5		all_epithelial(84;0.000134)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000621)|Lung(200;0.0687)|LUSC - Lung squamous cell carcinoma(625;0.0825)		AGGCTCCGGCGTCCCTGAGGG	0.716																																					p.T316M		Atlas-SNP	.											.	DUSP8	22	.	0			c.C947T						.						5	7	6					11																	1578679		1833	3744	5577	SO:0001583	missense	1850	exon7			TCCGGCGTCCCTG		CCDS7724.1	11p15.5	2011-06-09			ENSG00000184545	ENSG00000184545		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3074	protein-coding gene	gene with protein product	"serine/threonine specific protein phosphatase", "H1 phosphatase, vaccinia virus homolog"	602038	"chromosome 11 open reading frame 81"	C11orf81		7561881, 9192849	Standard	NM_004420		Approved	HVH-5, HB5, FLJ42958	uc001lts.2	Q13202	OTTHUMG00000133348	ENST00000397374.3:c.947C>T	chr11.hg19:g.1578679G>A	ENSP00000380530:p.Thr316Met	26.0	0.0		29.0	11.0	NM_004420	Q86SS8	Missense_Mutation	SNP	ENST00000397374.3	hg19	CCDS7724.1	.	.	.	.	.	.	.	.	.	.	G	5.970	0.362915	0.11296	.	.	ENSG00000184545	ENST00000397374;ENST00000331588	T;T	0.02258	4.37;4.37	3.03	2.1	0.27182	.	1.007410	0.08009	U	0.989974	T	0.01124	0.0037	N	0.03608	-0.345	0.09310	N	1	B	0.31435	0.323	B	0.18871	0.023	T	0.48139	-0.9061	10	0.33940	T	0.23	.	4.9888	0.14203	0.1111:0.0:0.5524:0.3365	.	316	Q13202	DUS8_HUMAN	M	316	ENSP00000380530:T316M;ENSP00000329539:T316M	ENSP00000329539:T316M	T	-	2	0	DUSP8	1535255	0.000000	0.05858	0.336000	0.25522	0.521000	0.34408	0.586000	0.23894	0.474000	0.27392	0.306000	0.20318	ACG	.	.		0.716	DUSP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257178.3	NM_004420		A	1578679	G	A	1578679	3	1	213	1	0	0	0	0	1	0	0	0	4833	1145	40	1	934	1	DUSP8	11	1578679	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10		1578679	133427837	39	30767										
RRM1	6240	hgsc.bcm.edu	37	chr11	4159583	4159583	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	atggtgtgctctttggagaaTagagatgaatgtctgatgtg	14	3	2	4			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr11:4159583T>C	ENST00000300738.5	+	19	2553	c.2349T>C	c.(2347-2349)aaT>aaC	p.N783N	RRM1_ENST00000537197.1_Silent_p.N445N|RRM1_ENST00000534285.1_Silent_p.N561N|RRM1-AS1_ENST00000529323.1_RNA|RRM1_ENST00000423050.2_Silent_p.N686N	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	783					cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	CTTTGGAGAATAGAGATGAAT	0.413																																					p.N783N	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.T2349C						.						74	74	74					11																	4159583		2201	4298	6499	SO:0001819	synonymous_variant	6240	exon19			GGAGAATAGAGAT	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"ribonucleotide reductase M1 polypeptide"			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.2349T>C	chr11.hg19:g.4159583T>C		95.0	0.0		70.0	14.0	NM_001033	Q9UNN2	Silent	SNP	ENST00000300738.5	hg19	CCDS7750.1																																																																																			.	.		0.413	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		C	4159583	T	C	4159583	2	2	213	1	0	0	0	0	0	0	0	1	13696	1403	49	2		2	RRM1	11	4159583	Silent	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	2580904	4159583	130846933	40	30768										
MRGPRF	116535	hgsc.bcm.edu	37	chr11	68772956	68772956	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	cagatgcacaggtcagtgacGtactcggggaagggggccgg	18	9	1	2	rs144312357		TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr11:68772956G>A	ENST00000309099.6	-	3	1204	c.822C>T	c.(820-822)taC>taT	p.Y274Y	RP11-554A11.5_ENST00000562506.1_RNA|MRGPRF_ENST00000441623.1_Silent_p.Y274Y	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	274						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GGTCAGTGACGTACTCGGGGA	0.617																																					p.Y274Y		Atlas-SNP	.											MRGPRF,NS,carcinoma,0,2	MRGPRF	22	.	0			c.C822T						.	G	,	0,4392		0,0,2196	38	28	31		822,822	0	1	11	dbSNP_134	31	1,8579		0,1,4289	no	coding-synonymous,coding-synonymous	MRGPRF	NM_001098515.1,NM_145015.4	,	0,1,6485	AA,AG,GG		0.0117,0.0,0.0077	,	274/344,274/344	68772956	1,12971	2196	4290	6486	SO:0001819	synonymous_variant	116535	exon3			AGTGACGTACTCG	AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"GPCR / Class A : Orphans"	24828	protein-coding gene	gene with protein product		607233	"G protein-coupled receptor 168", "G protein-coupled receptor 140"	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.822C>T	chr11.hg19:g.68772956G>A		104.0	0.0		116.0	28.0	NM_001098515	B3KV43|Q8NBK8	Silent	SNP	ENST00000309099.6	hg19	CCDS8188.1																																																																																			.	G|1.000;A|0.000		0.617	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015		A	68772956	G	A	68772956	2	1	213	1	0	0	0	0	0	0	0	1	9774	1140	40	1		1	MRGPRF	11	68772956	Silent	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	64613373	68772956	66233560	41	30769										
ZBTB16	7704	hgsc.bcm.edu	37	chr11	113934393	113934393	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gtgcctgaagatgctggagaCcatccaggcctcagacgaca	12	12	1	4			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr11:113934393C>A	ENST00000335953.4	+	2	751	c.371C>A	c.(370-372)aCc>aAc	p.T124N	ZBTB16_ENST00000392996.2_Missense_Mutation_p.T124N	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	124					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		ATGCTGGAGACCATCCAGGCC	0.602																																					p.T124N		Atlas-SNP	.											.	ZBTB16	101	.	0			c.C371A						.						45	45	45					11																	113934393		2201	4296	6497	SO:0001583	missense	7704	exon2			TGGAGACCATCCA	Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12930	protein-coding gene	gene with protein product	"promyelocytic leukaemia zinc finger"	176797	"zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.371C>A	chr11.hg19:g.113934393C>A	ENSP00000338157:p.Thr124Asn	76.0	0.0		109.0	20.0	NM_006006	Q8TAL4	Missense_Mutation	SNP	ENST00000335953.4	hg19	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052114	0.75960	.	.	ENSG00000109906	ENST00000335953;ENST00000535700;ENST00000392996;ENST00000310883	T;T;T	0.67345	-0.26;-0.26;-0.26	5.53	5.53	0.82687	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (1);	0.000000	0.85682	D	0.000000	T	0.72803	0.3506	N	0.20445	0.575	0.80722	D	1	D;D	0.64830	0.994;0.992	D;P	0.77004	0.989;0.86	T	0.74876	-0.3515	10	0.52906	T	0.07	-16.029	19.827	0.96621	0.0:1.0:0.0:0.0	.	124;129	Q05516;Q59H43	ZBT16_HUMAN;.	N	124	ENSP00000338157:T124N;ENSP00000443013:T124N;ENSP00000376721:T124N	ENSP00000309507:T124N	T	+	2	0	ZBTB16	113439603	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.939000	0.70179	2.759000	0.94783	0.561000	0.74099	ACC	.	.		0.602	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		A	113934393	C	A	113934393	3	1	213	1	0	0	0	0	1	0	0	0	17541	507	18	3	373	3	ZBTB16	11	113934393	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10	45161437	113934393	21072123	42	30770										
TPI1	7167	hgsc.bcm.edu	37	chr12	6978268	6978268	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	catctcttcctttagccctgGcatgatcaaagactgcggag	9	12	2	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr12:6978268G>C	ENST00000229270.4	+	3	693	c.356G>C	c.(355-357)gGc>gCc	p.G119A	TPI1_ENST00000488464.2_5'UTR|TPI1_ENST00000535434.1_5'UTR|TPI1_ENST00000396705.5_Missense_Mutation_p.G82A	NM_001159287.1	NP_001152759.1	P60174	TPIS_HUMAN	triosephosphate isomerase 1	119					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glyceraldehyde-3-phosphate metabolic process (GO:0019682)|glycolytic process (GO:0006096)|multicellular organismal development (GO:0007275)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	triose-phosphate isomerase activity (GO:0004807)			endometrium(2)|kidney(2)|large_intestine(1)|lung(11)|prostate(1)|skin(2)	19						TTTAGCCCTGGCATGATCAAA	0.567											OREG0021638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G119A		Atlas-SNP	.											.	TPI1	64	.	0			c.G356C						.						107	110	109					12																	6978268		2203	4300	6503	SO:0001583	missense	7167	exon3			GCCCTGGCATGAT		CCDS8566.1, CCDS53740.1, CCDS58206.1	12p13.31	2012-10-02			ENSG00000111669	ENSG00000111669	5.3.1.1		12009	protein-coding gene	gene with protein product		190450					Standard	NM_000365		Approved		uc001qrk.4	P60174	OTTHUMG00000133767	ENST00000229270.4:c.356G>C	chr12.hg19:g.6978268G>C	ENSP00000229270:p.Gly119Ala	75.0	0.0	638	78.0	6.0	NM_001159287	B7Z5D8|D3DUS9|P00938|Q6FHP9|Q6IS07|Q8WWD0|Q96AG5	Missense_Mutation	SNP	ENST00000229270.4	hg19	CCDS53740.1	.	.	.	.	.	.	.	.	.	.	G	9.129	1.010965	0.19277	.	.	ENSG00000111669	ENST00000229270;ENST00000396705	D;D	0.93604	-3.25;-3.25	4.77	3.86	0.44501	Aldolase-type TIM barrel (1);	0.065597	0.64402	U	0.000012	T	0.69269	0.3092	N	0.00057	-2.355	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	T	0.71768	-0.4493	10	0.10636	T	0.68	.	11.4754	0.50295	0.0:0.4588:0.5412:0.0	.	119	P60174	TPIS_HUMAN	A	119;82	ENSP00000229270:G119A;ENSP00000379933:G82A	ENSP00000229270:G119A	G	+	2	0	TPI1	6848529	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.564000	0.73969	2.187000	0.69744	0.462000	0.41574	GGC	.	.		0.567	TPI1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258252.1	NM_000365		C	6978268	G	C	6978268	3	2	213	1	0	0	0	0	1	0	0	0	16418	1203	42	4	366	4	TPI1	12	6978268	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10		6978268	126873627	43	30771										
SLC2A13	114134	hgsc.bcm.edu	37	chr12	40153944	40153944	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gccacatgtacatagcctgtTgtcaaagagtgattcaattt	8	8	2	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr12:40153944T>C	ENST00000280871.4	-	10	1881	c.1831A>G	c.(1831-1833)Aac>Gac	p.N611D		NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	611					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				CATAGCCTGTTGTCAAAGAGT	0.403										HNSCC(50;0.14)																											p.N611D		Atlas-SNP	.											.	SLC2A13	91	.	0			c.A1831G						.						114	108	110					12																	40153944		2203	4300	6503	SO:0001583	missense	114134	exon10			GCCTGTTGTCAAA	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.1831A>G	chr12.hg19:g.40153944T>C	ENSP00000280871:p.Asn611Asp	76.0	0.0		88.0	14.0	NM_052885	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	hg19	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	T	13.16	2.155546	0.38021	.	.	ENSG00000151229	ENST00000280871	D	0.81499	-1.5	5.33	1.43	0.22495	.	0.353469	0.31949	N	0.006806	T	0.64283	0.2584	N	0.19112	0.55	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.49881	-0.8892	10	0.13470	T	0.59	-5.5145	12.7848	0.57498	0.0:0.0:0.4091:0.5908	.	611	Q96QE2	MYCT_HUMAN	D	611	ENSP00000280871:N611D	ENSP00000280871:N611D	N	-	1	0	SLC2A13	38440211	0.968000	0.33430	0.999000	0.59377	0.987000	0.75469	0.979000	0.29500	-0.000000	0.14550	-0.429000	0.05907	AAC	.	.		0.403	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			C	40153944	T	C	40153944	3	2	213	1	0	0	0	0	1	0	0	0	14557	1812	63	2	119	2	SLC2A13	12	40153944	Missense_Mutation	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	33175676	40153944	93697951	44	30772										
NFYB	4801	hgsc.bcm.edu	37	chr12	104519915	104519915	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tcccgtttgaggtatggcatTtttcattatcctagccacgt	8	10	1	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr12:104519915T>G	ENST00000240055.3	-	4	435	c.208A>C	c.(208-210)Aat>Cat	p.N70H	RNA5SP370_ENST00000362545.1_RNA|NFYB_ENST00000551727.1_Missense_Mutation_p.N70H	NM_006166.3	NP_006157.1	P25208	NFYB_HUMAN	nuclear transcription factor Y, beta	70	B domain.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	6						GGTATGGCATTTTTCATTATC	0.368																																					p.N70H		Atlas-SNP	.											.	NFYB	11	.	0			c.A208C						.						200	180	187					12																	104519915		2203	4300	6503	SO:0001583	missense	4801	exon4			TGGCATTTTTCAT		CCDS9098.1	12q22-q23	2008-11-11				ENSG00000120837			7805	protein-coding gene	gene with protein product		189904				1774067, 9612081	Standard	NM_006166		Approved	CBF-A, HAP3, NF-YB	uc001tkl.1	P25208	OTTHUMG00000170176	ENST00000240055.3:c.208A>C	chr12.hg19:g.104519915T>G	ENSP00000240055:p.Asn70His	65.0	0.0		55.0	14.0	NM_006166	A8K7B9|Q96IY8	Missense_Mutation	SNP	ENST00000240055.3	hg19	CCDS9098.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628087	0.66901	.	.	ENSG00000120837	ENST00000240055;ENST00000551727;ENST00000551446	T;T;T	0.44482	1.91;1.91;0.92	5.63	5.63	0.86233	Histone-fold (2);Transcription factor CBF/NF-Y/archaeal histone (1);	0.000000	0.85682	D	0.000000	T	0.44030	0.1274	M	0.78637	2.42	0.80722	D	1	P	0.39940	0.696	B	0.32090	0.14	T	0.51601	-0.8685	10	0.49607	T	0.09	3.4802	15.87	0.79108	0.0:0.0:0.0:1.0	.	70	P25208	NFYB_HUMAN	H	70;70;71	ENSP00000240055:N70H;ENSP00000447486:N70H;ENSP00000448250:N71H	ENSP00000240055:N70H	N	-	1	0	NFYB	103044045	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.145000	0.66743	0.533000	0.62120	AAT	.	.		0.368	NFYB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407786.1			G	104519915	T	G	104519915	3	3	213	1	0	0	0	0	1	0	0	0	10399	1841	64	5	435	5	NFYB	12	104519915	Missense_Mutation	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	64365971	104519915	29331980	45	30773										
LPAR6	10161	hgsc.bcm.edu	37	chr13	48986448	48986448	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gcagatgaaaatgtatatggCaacacaattggatattaacc	8	6	0	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr13:48986448C>A	ENST00000378434.4	-	7	1736	c.112G>T	c.(112-114)Gcc>Tcc	p.A38S	RB1_ENST00000267163.4_Intron|LPAR6_ENST00000345941.2_Missense_Mutation_p.A38S	NM_005767.5	NP_005758.2	P43657	LPAR6_HUMAN	lysophosphatidic acid receptor 6	38						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.0?(15)|p.?(4)		NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	14						ATGTATATGGCAACACAATTG	0.378																																					p.A38S		Atlas-SNP	.											.	LPAR6	38	.	19	Whole gene deletion(15)|Unknown(4)	bone(10)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.G112T						.						94	90	92					13																	48986448		2203	4300	6503	SO:0001583	missense	10161	exon5			ATATGGCAACACA	AF000546	CCDS9410.1	13q14	2012-08-08	2009-06-23	2009-06-23	ENSG00000139679	ENSG00000139679		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	15520	protein-coding gene	gene with protein product		609239	"purinergic receptor P2Y, G-protein coupled, 5"	P2RY5		11004484, 9755289, 19386608	Standard	NM_005767		Approved	P2Y5	uc010acu.3	P43657	OTTHUMG00000016895	ENST00000378434.4:c.112G>T	chr13.hg19:g.48986448C>A	ENSP00000367691:p.Ala38Ser	107.0	0.0		64.0	5.0	NM_001162497	A4FTW9|B3KVF2|F2YGU4|O15133|Q3KPF5|Q53FA0|Q5VW44|Q7Z3S0|Q7Z3S6	Missense_Mutation	SNP	ENST00000378434.4	hg19	CCDS9410.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.969835	0.74246	.	.	ENSG00000139679	ENST00000378434;ENST00000345941	T;T	0.72835	-0.69;-0.69	6.17	6.17	0.99709	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	L	0.37466	1.105	0.80722	D	1	P	0.47191	0.891	P	0.49276	0.605	T	0.69371	-0.5163	10	0.41790	T	0.15	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	38	P43657	LPAR6_HUMAN	S	38	ENSP00000367691:A38S;ENSP00000344353:A38S	ENSP00000344353:A38S	A	-	1	0	LPAR6	47884449	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.378	LPAR6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276280.2	NM_005767		A	48986448	C	A	48986448	3	1	213	1	0	0	0	0	1	0	0	0	8918	710	25	3	926	3	LPAR6	13	48986448	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10		48986448	66183430	46	30774										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88328839	88328839	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ctgccaggagcgaaagatcgAgagcatcgctgaactgcagc	13	11	0	3			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr13:88328839A>T	ENST00000325089.6	+	2	1415	c.1196A>T	c.(1195-1197)gAg>gTg	p.E399V	SLITRK5_ENST00000400028.3_Missense_Mutation_p.E158V	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	399	LRRNT.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					CGAAAGATCGAGAGCATCGCT	0.552																																					p.E399V		Atlas-SNP	.											.	SLITRK5	192	.	0			c.A1196T						.						89	74	79					13																	88328839		2203	4300	6503	SO:0001583	missense	26050	exon2			AGATCGAGAGCAT	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.1196A>T	chr13.hg19:g.88328839A>T	ENSP00000366283:p.Glu399Val	44.0	0.0		47.0	11.0	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	hg19	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	A	12.06	1.825140	0.32237	.	.	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.50813	0.73;0.73	5.75	5.75	0.90469	Leucine-rich repeat-containing N-terminal (1);	0.057183	0.64402	D	0.000002	T	0.41236	0.1150	L	0.39898	1.24	0.44579	D	0.997543	B;B	0.26081	0.141;0.054	B;B	0.29862	0.108;0.044	T	0.22977	-1.0201	9	.	.	.	-18.4966	14.007	0.64470	1.0:0.0:0.0:0.0	.	158;399	B4DSH5;O94991	.;SLIK5_HUMAN	V	399;158	ENSP00000366283:E399V;ENSP00000442244:E158V	.	E	+	2	0	SLITRK5	87126840	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.327000	0.79147	2.192000	0.70111	0.459000	0.35465	GAG	.	.		0.552	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			T	88328839	A	T	88328839	3	4	213	1	0	0	0	0	1	0	0	0	14761	304	11	4	1198	4	SLITRK5	13	88328839	Missense_Mutation	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10	39342391	88328839	26841039	47	30775										
EFNB2	1948	hgsc.bcm.edu	37	chr13	107164955	107164955	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ttcttgaaacttgatggtgaAtttgatatcttggtctggtt	10	4	3	4			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr13:107164955A>T	ENST00000245323.4	-	2	477	c.328T>A	c.(328-330)Ttc>Atc	p.F110I		NM_004093.3	NP_004084.1	P52799	EFNB2_HUMAN	ephrin-B2	110	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				anatomical structure morphogenesis (GO:0009653)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|lymph vessel development (GO:0001945)|negative regulation of keratinocyte proliferation (GO:0010839)|organ morphogenesis (GO:0009887)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|regulation of chemotaxis (GO:0050920)|viral process (GO:0016032)	focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					TTGATGGTGAATTTGATATCT	0.338																																					p.F110I		Atlas-SNP	.											.	EFNB2	39	.	0			c.T328A						.						142	141	142					13																	107164955		2203	4300	6503	SO:0001583	missense	1948	exon2			TGGTGAATTTGAT	L38734	CCDS9507.1	13q33	2011-03-09			ENSG00000125266	ENSG00000125266		"Ephrins"	3227	protein-coding gene	gene with protein product	"HTK ligand", "ligand of eph-related kinase 5", "eph-related receptor tyrosine kinase ligand 5"	600527		EPLG5		7833926	Standard	NM_004093		Approved	LERK5, Htk-L, HTKL, MGC126226, MGC126227, MGC126228	uc001vqi.3	P52799	OTTHUMG00000017324	ENST00000245323.4:c.328T>A	chr13.hg19:g.107164955A>T	ENSP00000245323:p.Phe110Ile	167.0	0.0		207.0	16.0	NM_004093	Q5JV56	Missense_Mutation	SNP	ENST00000245323.4	hg19	CCDS9507.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.347526	0.82022	.	.	ENSG00000125266	ENST00000245323	D	0.94537	-3.45	5.41	5.41	0.78517	Ephrin, conserved site (1);Cupredoxin (2);	0.045114	0.85682	D	0.000000	D	0.96713	0.8927	M	0.70903	2.155	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	D	0.96638	0.9472	10	0.48119	T	0.1	.	15.7499	0.77976	1.0:0.0:0.0:0.0	.	110	P52799	EFNB2_HUMAN	I	110	ENSP00000245323:F110I	ENSP00000245323:F110I	F	-	1	0	EFNB2	105962956	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.910000	0.92685	2.188000	0.69820	0.533000	0.62120	TTC	.	.		0.338	EFNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045733.4	NM_004093		T	107164955	A	T	107164955	3	4	213	1	0	0	0	0	1	0	0	0	4958	101	4	4	689	4	EFNB2	13	107164955	Missense_Mutation	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10	18836116	107164955	8004923	48	30776										
NID2	22795	hgsc.bcm.edu	37	chr14	52534630	52534630	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tcgtaagcgcctacctgctcCcaggtggccaggaaggcgtg	14	13	0	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr14:52534630C>A	ENST00000216286.5	-	2	479	c.480G>T	c.(478-480)tgG>tgT	p.W160C	NID2_ENST00000541773.1_Missense_Mutation_p.W107C	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	160	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					CTACCTGCTCCCAGGTGGCCA	0.662																																					p.W160C		Atlas-SNP	.											.	NID2	201	.	0			c.G480T						.						62	76	71					14																	52534630		2167	4268	6435	SO:0001583	missense	22795	exon2			CTGCTCCCAGGTG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.480G>T	chr14.hg19:g.52534630C>A	ENSP00000216286:p.Trp160Cys	103.0	0.0		126.0	42.0	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	C	34	5.306368	0.95629	.	.	ENSG00000087303	ENST00000216286;ENST00000541773;ENST00000395707	T;T	0.23552	1.9;1.9	5.58	5.58	0.84498	Nidogen, extracellular domain (2);	0.000000	0.85682	D	0.000000	T	0.62780	0.2456	M	0.93507	3.425	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.993	P;D;P	0.66351	0.891;0.943;0.72	T	0.73310	-0.4023	10	0.87932	D	0	.	19.579	0.95458	0.0:1.0:0.0:0.0	.	107;162;160	Q14112-2;Q5CZI2;Q14112	.;.;NID2_HUMAN	C	160;107;162	ENSP00000216286:W160C;ENSP00000443730:W107C	ENSP00000216286:W160C	W	-	3	0	NID2	51604380	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.199000	0.77831	2.626000	0.88956	0.563000	0.77884	TGG	.	.		0.662	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			A	52534630	C	A	52534630	3	1	213	1	0	0	0	0	1	0	0	0	10424	624	22	3	3731	3	NID2	14	52534630	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10		52534630	54814910	49	30777										
PLD4	122618	hgsc.bcm.edu	37	chr14	105395137	105395137	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ctgccatctgcagccggcagCccctctgcccagcctctggg	11	19	3	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr14:105395137C>A	ENST00000392593.4	+	4	504	c.336C>A	c.(334-336)agC>agA	p.S112R	PLD4_ENST00000540372.1_Missense_Mutation_p.S119R	NM_138790.2	NP_620145.2	Q96BZ4	PLD4_HUMAN	phospholipase D family, member 4	112					glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phagocytosis (GO:0006909)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|trans-Golgi network membrane (GO:0032588)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase D activity (GO:0004630)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	13		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00067)|OV - Ovarian serous cystadenocarcinoma(23;0.00976)|Epithelial(46;0.0201)|GBM - Glioblastoma multiforme(11;0.116)			CAGCCGGCAGCCCCTCTGCCC	0.667																																					p.S112R		Atlas-SNP	.											.	PLD4	46	.	0			c.C336A						.						30	33	32					14																	105395137		1941	4142	6083	SO:0001583	missense	122618	exon4			CGGCAGCCCCTCT		CCDS9995.2	14q32.33	2014-01-28	2005-05-20	2005-05-20	ENSG00000166428	ENSG00000166428			23792	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 175"	C14orf175			Standard	XM_006720024		Approved		uc001ypu.1	Q96BZ4	OTTHUMG00000144167	ENST00000392593.4:c.336C>A	chr14.hg19:g.105395137C>A	ENSP00000376372:p.Ser112Arg	104.0	0.0		94.0	31.0	NM_138790	Q6UWD2	Missense_Mutation	SNP	ENST00000392593.4	hg19	CCDS9995.2	.	.	.	.	.	.	.	.	.	.	C	8.806	0.934056	0.18206	.	.	ENSG00000166428	ENST00000540372;ENST00000392593;ENST00000557573	T;T;T	0.24538	1.89;1.89;1.85	4.23	1.02	0.19986	.	0.421043	0.26428	N	0.024422	T	0.22627	0.0546	M	0.67397	2.05	0.09310	N	1	B;B	0.18013	0.025;0.015	B;B	0.23574	0.047;0.021	T	0.17961	-1.0352	10	0.40728	T	0.16	-1.0E-4	4.1871	0.10404	0.1578:0.5939:0.1539:0.0944	.	119;112	F5H2B5;Q96BZ4	.;PLD4_HUMAN	R	119;112;110	ENSP00000438677:S119R;ENSP00000376372:S112R;ENSP00000451278:S110R	ENSP00000376372:S112R	S	+	3	2	PLD4	104466182	0.000000	0.05858	0.277000	0.24703	0.599000	0.36880	-0.055000	0.11807	0.340000	0.23745	0.645000	0.84053	AGC	.	.		0.667	PLD4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000291348.2	NM_138790		A	105395137	C	A	105395137	3	1	213	1	0	0	0	0	1	0	0	0	12057	738	26	3	346	3	PLD4	14	105395137	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10	52860507	105395137	1954403	50	30778										
BRF1	2972	hgsc.bcm.edu	37	chr14	105766805	105766805	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tccagggacacgaactggccCacggccgaggagccgccgcc	14	17	0	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr14:105766805C>T	ENST00000546474.1	-	1	15121	c.162G>A	c.(160-162)gtG>gtA	p.V54V	BRF1_ENST00000440513.3_Intron|BRF1_ENST00000379937.2_Silent_p.V54V|PACS2_ENST00000430725.2_5'Flank|BRF1_ENST00000548421.1_Silent_p.V54V|BRF1_ENST00000327359.3_Intron	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	54					gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		CGAACTGGCCCACGGCCGAGG	0.721																																					p.V54V		Atlas-SNP	.											.	BRF1	102	.	0			c.G162A						.						14	14	14					14																	105766805		1857	3518	5375	SO:0001819	synonymous_variant	2972	exon1			CTGGCCCACGGCC	U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"General transcription factors"	11551	protein-coding gene	gene with protein product		604902	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2", "BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.162G>A	chr14.hg19:g.105766805C>T		63.0	0.0		46.0	18.0	NM_001519	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Silent	SNP	ENST00000546474.1	hg19	CCDS10001.1	.	.	.	.	.	.	.	.	.	.	C	10.52	1.373683	0.24857	.	.	ENSG00000185024	ENST00000546417	.	.	.	3.18	0.917	0.19380	.	.	.	.	.	T	0.51787	0.1695	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38993	-0.9635	4	.	.	.	.	5.6411	0.17565	0.2007:0.3686:0.4307:0.0	.	.	.	.	R	1	.	.	G	-	1	0	BRF1	104837850	0.861000	0.29849	0.993000	0.49108	0.612000	0.37316	-0.224000	0.09164	0.267000	0.21916	0.455000	0.32223	GGG	.	.		0.721	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519		T	105766805	C	T	105766805	2	4	213	1	0	0	0	0	0	0	0	1	1512	581	21	3		3	BRF1	14	105766805	Silent	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10	371668	105766805	1582735	51	30779										
MTMR15	22909	hgsc.bcm.edu	37	chr15	31203039	31203039	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gttttgttggctattgttacAgtaaaaacatttaaaatgtt	7	3	0	0	rs373034831		TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr15:31203039A>G	ENST00000362065.4	+	4	1868				FAN1_ENST00000561607.1_Missense_Mutation_p.Q533R|FAN1_ENST00000561594.1_Missense_Mutation_p.Q533R|FAN1_ENST00000565466.1_Missense_Mutation_p.Q533R	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1						DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						CTATTGTTACAGTAAAAACAT	0.328								Direct reversal of damage																													p.Q533R		Atlas-SNP	.											.	FAN1	77	.	0			c.A1598G						.						47	47	47					15																	31203039		2202	4300	6502	SO:0001627	intron_variant	22909	exon4			TGTTACAGTAAAA		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"KIAA1018", "myotubularin related protein 15"	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.1577+21A>G	chr15.hg19:g.31203039A>G		104.0	0.0		123.0	35.0	NM_001146095	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	hg19	CCDS32186.1																																																																																			.	.		0.328	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967		G	31203039	A	G	31203039	1	3	213	0	1	0	0	0	0	0	0	0	9952	188	7	2		2	MTMR15	15	31203039	Intron	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10		31203039	71328353	52	30780										
NDUFAF1	51103	hgsc.bcm.edu	37	chr15	41688875	41688875	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tatccaaatcttctttccccCggaattgccagacaaccttg	5	14	2	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr15:41688875C>G	ENST00000260361.4	-	2	764	c.383G>C	c.(382-384)cGg>cCg	p.R128P		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	128					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		TTCTTTCCCCCGGAATTGCCA	0.463																																					p.R128P		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.G383C						.						95	91	92					15																	41688875		2203	4300	6503	SO:0001583	missense	51103	exon2			TTCCCCCGGAATT	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"Mitochondrial respiratory chain complex assembly factors"	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.383G>C	chr15.hg19:g.41688875C>G	ENSP00000260361:p.Arg128Pro	123.0	0.0		140.0	29.0	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	hg19	CCDS10075.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.748483	0.69533	.	.	ENSG00000137806	ENST00000260361	T	0.76968	-1.06	4.7	4.7	0.59300	NADH:ubiquinone oxidoreductase intermediate-associated protein 30 (1);Galactose-binding domain-like (1);	0.098554	0.64402	D	0.000003	D	0.87830	0.6276	M	0.74881	2.28	0.54753	D	0.99998	D	0.89917	1.0	D	0.80764	0.994	D	0.89298	0.3624	10	0.66056	D	0.02	-24.0484	18.0656	0.89389	0.0:1.0:0.0:0.0	.	128	Q9Y375	CIA30_HUMAN	P	128	ENSP00000260361:R128P	ENSP00000260361:R128P	R	-	2	0	NDUFAF1	39476167	1.000000	0.71417	0.988000	0.46212	0.754000	0.42855	4.491000	0.60326	2.334000	0.79466	0.449000	0.29647	CGG	.	.		0.463	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013		G	41688875	C	G	41688875	3	3	213	1	0	0	0	0	1	0	0	0	10283	652	23	4	616	4	NDUFAF1	15	41688875	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10	10485836	41688875	60842517	53	30781										
EEF2K	29904	hgsc.bcm.edu	37	chr16	22291589	22291589	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tgacggactgtgatgagggcGgtgagtacgacggaatgcag	18	6	0	4			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr16:22291589G>A	ENST00000263026.5	+	17	2434	c.1960G>A	c.(1960-1962)Ggt>Agt	p.G654S		NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	654					insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		TGATGAGGGCGGTGAGTACGA	0.607																																					p.G654S	NSCLC(195;1411 2157 20319 27471 51856)	Atlas-SNP	.											.	EEF2K	142	.	0			c.G1960A						.						107	83	91					16																	22291589		2197	4300	6497	SO:0001583	missense	29904	exon17			GAGGGCGGTGAGT	U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.1960G>A	chr16.hg19:g.22291589G>A	ENSP00000263026:p.Gly654Ser	108.0	0.0		56.0	21.0	NM_013302	Q8N588	Missense_Mutation	SNP	ENST00000263026.5	hg19	CCDS10604.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.931551	0.73442	.	.	ENSG00000103319	ENST00000263026	T	0.09630	2.96	5.58	5.58	0.84498	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.31670	0.0804	M	0.79475	2.455	0.80722	D	1	D	0.69078	0.997	P	0.56398	0.797	T	0.03354	-1.1045	10	0.72032	D	0.01	-16.8331	19.563	0.95380	0.0:0.0:1.0:0.0	.	654	O00418	EF2K_HUMAN	S	654	ENSP00000263026:G654S	ENSP00000263026:G654S	G	+	1	0	EEF2K	22199090	1.000000	0.71417	0.197000	0.23402	0.018000	0.09664	9.439000	0.97543	2.630000	0.89119	0.561000	0.74099	GGT	.	.		0.607	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302		A	22291589	G	A	22291589	3	1	213	1	0	0	0	0	1	0	0	0	4932	1116	39	1	2022	1	EEF2K	16	22291589	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10		22291589	68063164	54	30782										
VAC14	55697	hgsc.bcm.edu	37	chr16	70731096	70731096	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tctgggtgaggaagcagaggGacaccgtggtgactgggttg	19	6	1	3			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr16:70731096G>C	ENST00000261776.5	-	16	2161	c.1901C>G	c.(1900-1902)tCc>tGc	p.S634C	VAC14_ENST00000536184.2_Missense_Mutation_p.S66C	NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)	634					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				GAAGCAGAGGGACACCGTGGT	0.602																																					p.S634C		Atlas-SNP	.											.	VAC14	65	.	0			c.C1901G						.						197	133	155					16																	70731096		2198	4300	6498	SO:0001583	missense	55697	exon16			CAGAGGGACACCG	AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"Tax1 (human T-cell leukemia virus type I) binding protein 2"	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583	ENST00000261776.5:c.1901C>G	chr16.hg19:g.70731096G>C	ENSP00000261776:p.Ser634Cys	151.0	0.0		135.0	8.0	NM_018052	B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Missense_Mutation	SNP	ENST00000261776.5	hg19	CCDS10896.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.983283	0.93044	.	.	ENSG00000103043	ENST00000261776;ENST00000536184	T	0.66995	-0.24	5.51	5.51	0.81932	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80752	0.4683	M	0.64080	1.96	0.80722	D	1	D;P	0.89917	1.0;0.848	D;P	0.75020	0.985;0.549	T	0.81409	-0.0946	10	0.62326	D	0.03	-30.2626	19.4185	0.94710	0.0:0.0:1.0:0.0	.	564;634	B4DMP4;Q08AM6	.;VAC14_HUMAN	C	634;66	ENSP00000261776:S634C	ENSP00000261776:S634C	S	-	2	0	VAC14	69288597	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.396000	0.97270	2.601000	0.87937	0.555000	0.69702	TCC	.	.		0.602	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3	NM_018052		C	70731096	G	C	70731096	3	2	213	1	0	0	0	0	1	0	0	0	17126	1174	41	4	463	4	VAC14	16	70731096	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	48439507	70731096	19623657	55	30783										
FTSJD1	55783	hgsc.bcm.edu	37	chr16	71317949	71317949	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tgtagaaggcagtccaaaaaTaaacgctggtaagttggatc	11	6	0	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr16:71317949T>C	ENST00000338099.5	-	3	2211	c.1875A>G	c.(1873-1875)ttA>ttG	p.L625L	CMTR2_ENST00000434935.2_Silent_p.L625L			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	625					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										AGTCCAAAAATAAACGCTGGT	0.403																																					p.L625L		Atlas-SNP	.											.	FTSJD1	70	.	0			c.A1875G						.						63	64	63					16																	71317949		2198	4300	6498	SO:0001819	synonymous_variant	55783	exon3			CAAAAATAAACGC	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"adrift homolog (Drosophila)"		"FtsJ methyltransferase domain containing 1"	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.1875A>G	chr16.hg19:g.71317949T>C		101.0	0.0		73.0	36.0	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Silent	SNP	ENST00000338099.5	hg19	CCDS10898.1																																																																																			.	.		0.403	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		C	71317949	T	C	71317949	2	2	213	1	0	0	0	0	0	0	0	1	6098	1403	49	2		2	FTSJD1	16	71317949	Silent	SNP	T	TCGA-DD-AAE8-01A-11D-A40R-10	586853	71317949	19036804	56	30784										
TP53	7157	hgsc.bcm.edu	37	chr17	7577023	7577033	+	Frame_Shift_Del	DEL	CTTAGTGCTCC	CTTAGTGCTCC	-													0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tgtcctgcttgcttacctcgCttagtgctccctgggggcag					rs587782654|rs587782391		TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	CTTAGTGCTCC	CTTAGTGCTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr17:7577023_7577033delCTTAGTGCTCC	ENST00000269305.4	-	8	1094_1104	c.905_915delGGAGCACTAAG	c.(904-915)gggagcactaagfs	p.GSTK302fs	TP53_ENST00000455263.2_Frame_Shift_Del_p.GSTK302fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.GSTK302fs|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Frame_Shift_Del_p.GSTK302fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.GSTK302fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	302	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		G -> A (in a sporadic cancer; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in a sporadic cancer; somatic mutation).|G -> V (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.K305*(19)|p.0?(8)|p.K305N(3)|p.G302E(3)|p.G302G(3)|p.?(3)|p.S303N(3)|p.S303T(3)|p.K305R(2)|p.T304I(2)|p.T304A(2)|p.S303C(2)|p.T304fs*41(2)|p.K305K(1)|p.K305E(1)|p.G293fs*1(1)|p.K305T(1)|p.T304N(1)|p.T304T(1)|p.H296_S303delHHELPPGS(1)|p.P301_S303delPGS(1)|p.L299fs*2(1)|p.L265_K305del41(1)|p.S303fs*42(1)|p.G302fs*2(1)|p.K305fs*32(1)|p.K305fs*1(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCTTACCTCGCTTAGTGCTCCCTGGGGGCAG	0.555		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.302_306del	Pancreas(47;798 1329 9957 10801)	Atlas-INDEL	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,adenocarcinoma,0,166	TP53	33396	.	69	Substitution - Missense(23)|Substitution - Nonsense(19)|Whole gene deletion(8)|Deletion - Frameshift(6)|Substitution - coding silent(5)|Deletion - In frame(3)|Unknown(3)|Insertion - Frameshift(2)	upper_aerodigestive_tract(14)|urinary_tract(7)|lung(7)|breast(7)|oesophagus(7)|large_intestine(6)|haematopoietic_and_lymphoid_tissue(6)|bone(5)|central_nervous_system(3)|stomach(2)|soft_tissue(1)|skin(1)|pancreas(1)|prostate(1)|liver(1)	c.906_916del	GRCh37	CM942123	TP53	M		.																																			SO:0001589	frameshift_variant	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.905_915delGGAGCACTAAG	chr17.hg19:g.7577023_7577033delCTTAGTGCTCC	ENSP00000269305:p.Gly302fs	71.0	0.0		73.0	22.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.555	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7577033	CTTAGTGCTCC	-	7577023	7	5	213	1	0	1	0	1	0	0	0	0	16396	796	28	0	371	0	TP53	17	7577023	Frame_Shift_Del	DEL	CTTAGTGCTCC	TCGA-DD-AAE8-01A-11D-A40R-10		7577023	73618187	57	30785										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11539972	11539972	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tgctagacatagcaggaaacCtccttgaaagaccgctggta	10	10	0	3			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr17:11539972C>T	ENST00000262442.4	+	9	1725	c.1657C>T	c.(1657-1659)Ctc>Ttc	p.L553F	DNAH9_ENST00000454412.2_Missense_Mutation_p.L553F	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	553	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGCAGGAAACCTCCTTGAAAG	0.433																																					p.L553F		Atlas-SNP	.											.	DNAH9	695	.	0			c.C1657T						.						96	93	94					17																	11539972		2203	4300	6503	SO:0001583	missense	1770	exon9			GGAAACCTCCTTG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.1657C>T	chr17.hg19:g.11539972C>T	ENSP00000262442:p.Leu553Phe	87.0	0.0		125.0	8.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.410967	0.62399	.	.	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.66460	-0.21;-0.21	5.69	5.69	0.88448	Dynein heavy chain, domain-1 (1);	0.161907	0.41097	D	0.000959	T	0.68540	0.3012	M	0.66506	2.035	0.80722	D	1	B	0.31730	0.337	B	0.41036	0.346	T	0.64993	-0.6276	10	0.32370	T	0.25	.	11.1031	0.48186	0.0:0.9154:0.0:0.0846	.	553	Q9NYC9	DYH9_HUMAN	F	553	ENSP00000262442:L553F;ENSP00000414874:L553F	ENSP00000262442:L553F	L	+	1	0	DNAH9	11480697	0.993000	0.37304	0.943000	0.38184	0.978000	0.69477	2.266000	0.43320	2.844000	0.97970	0.650000	0.86243	CTC	.	.		0.433	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11539972	C	T	11539972	3	4	213	1	0	0	0	0	1	0	0	0	4610	681	24	3	1691	3	DNAH9	17	11539972	Missense_Mutation	SNP	C	TCGA-DD-AAE8-01A-11D-A40R-10	3962949	11539972	69655238	58	30786										
SPHK1	8877	hgsc.bcm.edu	37	chr17	74383560	74383560	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	aattgatggttagcgaggccGtgcagggccaggtgcaccca	15	10	0	1	rs55648239		TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr17:74383560G>A	ENST00000545180.1	+	8	1857	c.1048G>A	c.(1048-1050)Gtg>Atg	p.V350M	SPHK1_ENST00000323374.4_Missense_Mutation_p.V436M|SPHK1_ENST00000392496.3_Missense_Mutation_p.V350M|SPHK1_ENST00000590959.1_Missense_Mutation_p.V364M|SPHK1_ENST00000592299.1_Missense_Mutation_p.V350M			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	350					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	TAGCGAGGCCGTGCAGGGCCA	0.617													G|||	1	0.000199681	0	0	5008	,	,		18780	0		0	False		,,,				2504	0.001				p.V436M	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.G1306A						.						62	65	64					17																	74383560		2203	4300	6503	SO:0001583	missense	8877	exon6			GAGGCCGTGCAGG	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.1048G>A	chr17.hg19:g.74383560G>A	ENSP00000440970:p.Val350Met	63.0	0.0		67.0	19.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	hg19	CCDS45785.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.751713	0.69533	.	.	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.16743	2.32;2.32;2.32	5.08	5.08	0.68730	.	0.284658	0.33199	N	0.005162	T	0.25865	0.0630	L	0.58428	1.81	0.38261	D	0.941897	D;P;D	0.61697	0.988;0.956;0.99	P;P;P	0.48400	0.576;0.475;0.556	T	0.09207	-1.0685	10	0.72032	D	0.01	-34.4439	14.1781	0.65557	0.0:0.1498:0.8502:0.0	rs55648239	436;364;350	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	M	350;436;350;349	ENSP00000440970:V350M;ENSP00000313681:V436M;ENSP00000376285:V350M	ENSP00000313681:V436M	V	+	1	0	SPHK1	71895155	0.999000	0.42202	0.982000	0.44146	0.863000	0.49368	2.875000	0.48491	2.355000	0.79922	0.456000	0.33151	GTG	.	.		0.617	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		A	74383560	G	A	74383560	3	1	213	1	0	0	0	0	1	0	0	0	15061	1145	40	1	1370	1	SPHK1	17	74383560	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	62843588	74383560	6811650	59	30787										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41073990	41073990	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gcggcggcctgagcggcaagAgtcagtcgatcaatccgagg	16	11	2	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr19:41073990A>T	ENST00000352632.3	+	31	6844	c.6758A>T	c.(6757-6759)gAg>gTg	p.E2253V	SPTBN4_ENST00000392025.1_Missense_Mutation_p.E996V|SPTBN4_ENST00000598249.1_Missense_Mutation_p.E2253V			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	2253					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GAGCGGCAAGAGTCAGTCGAT	0.731																																					p.E2253V		Atlas-SNP	.											.	SPTBN4	213	.	0			c.A6758T						.						13	12	13					19																	41073990		2116	4152	6268	SO:0001583	missense	57731	exon31			GGCAAGAGTCAGT	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.6758A>T	chr19.hg19:g.41073990A>T	ENSP00000263373:p.Glu2253Val	149.0	0.0		137.0	7.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	A	11.88	1.769493	0.31320	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000392025	T;T	0.76839	-1.05;0.28	3.53	2.4	0.29515	.	0.115012	0.35040	U	0.003483	T	0.57607	0.2065	N	0.14661	0.345	0.36186	D	0.849761	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.59752	-0.7395	10	0.45353	T	0.12	.	7.2997	0.26413	0.8031:0.0:0.0:0.1969	.	996;2253	C9JY79;Q9H254	.;SPTN4_HUMAN	V	2253;2253;996	ENSP00000263373:E2253V;ENSP00000375879:E996V	ENSP00000263373:E2253V	E	+	2	0	SPTBN4	45765830	1.000000	0.71417	0.973000	0.42090	0.037000	0.13140	2.288000	0.43514	1.592000	0.50018	0.459000	0.35465	GAG	.	.		0.731	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			T	41073990	A	T	41073990	3	4	213	1	0	0	0	0	1	0	0	0	15136	304	11	4	6970	4	SPTBN4	19	41073990	Missense_Mutation	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10		41073990	18054993	60	30788										
TRAPPC6A	79090	hgsc.bcm.edu	37	chr19	45668161	45668161	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	cttctggaacaccgccacccAcaggtctttgcacaagaact	7	15	2	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr19:45668161A>G	ENST00000585934.1	-	3	238	c.220T>C	c.(220-222)Tgg>Cgg	p.W74R	TRAPPC6A_ENST00000592647.1_Missense_Mutation_p.V65A|TRAPPC6A_ENST00000588062.1_Missense_Mutation_p.V51A|TRAPPC6A_ENST00000006275.4_Missense_Mutation_p.W88R	NM_001270891.1	NP_001257820.1	O75865	TPC6A_HUMAN	trafficking protein particle complex 6A	74					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	8		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00872)|GBM - Glioblastoma multiforme(486;0.233)		ACCGCCACCCACAGGTCTTTG	0.647																																					p.W88R		Atlas-SNP	.											.	TRAPPC6A	16	.	0			c.T262C						.						85	84	84					19																	45668161		2203	4300	6503	SO:0001583	missense	79090	exon3			CCACCCACAGGTC	AF161407	CCDS12655.1, CCDS59395.1, CCDS59396.1, CCDS59397.1	19q13.32	2012-10-02				ENSG00000007255		"Trafficking protein particle complex"	23069	protein-coding gene	gene with protein product		610396					Standard	NM_024108		Approved	TRS33, MGC2650, HSPC289	uc002pav.4	O75865		ENST00000585934.1:c.220T>C	chr19.hg19:g.45668161A>G	ENSP00000468612:p.Trp74Arg	69.0	0.0		82.0	27.0	NM_024108	K7ERB1|K7ERQ4|Q9BQ45|Q9P092	Missense_Mutation	SNP	ENST00000585934.1	hg19	CCDS59397.1	.	.	.	.	.	.	.	.	.	.	a	18.85	3.711218	0.68730	.	.	ENSG00000007255	ENST00000006275	T	0.68624	-0.34	4.51	4.51	0.55191	NO signalling/Golgi transport  ligand-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.83986	0.5373	M	0.92367	3.3	0.25430	N	0.988195	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77474	-0.2574	10	0.87932	D	0	-7.9562	10.2163	0.43170	1.0:0.0:0.0:0.0	.	74;88	O75865;O75865-2	TPC6A_HUMAN;.	R	88	ENSP00000006275:W88R	ENSP00000006275:W88R	W	-	1	0	TRAPPC6A	50360001	1.000000	0.71417	0.902000	0.35471	0.910000	0.53928	7.344000	0.79328	1.671000	0.50874	0.460000	0.39030	TGG	.	.		0.647	TRAPPC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457556.1	NM_024108		G	45668161	A	G	45668161	3	3	213	1	0	0	0	0	1	0	0	0	16478	159	6	2	275	2	TRAPPC6A	19	45668161	Missense_Mutation	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10	4594171	45668161	13460822	61	30789										
GGTLC1	92086	hgsc.bcm.edu	37	chr20	23965975	23965975	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gatctgggtgtgatggtgccGggtctccagggctgcagtca	17	9	3	1			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr20:23965975G>T	ENST00000335694.4	-	6	760	c.556C>A	c.(556-558)Cgg>Agg	p.R186R	GGTLC1_ENST00000278765.4_Silent_p.R186R|GGTLC1_ENST00000286890.4_Silent_p.R186R	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	186					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						TGATGGTGCCGGGTCTCCAGG	0.637																																					p.R186R		Atlas-SNP	.											.	GGTLC1	37	.	0			c.C556A						.						75	78	77					20																	23965975		2203	4300	6503	SO:0001819	synonymous_variant	92086	exon6			GGTGCCGGGTCTC	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"Gamma-glutamyltransferases"	16437	protein-coding gene	gene with protein product		612338	"gamma-glutamyltransferase-like activity 4", "gamma-glutamyltransferase-like activity 3"	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.556C>A	chr20.hg19:g.23965975G>T		143.0	0.0		135.0	7.0	NM_178311	D3DW43|Q08246	Silent	SNP	ENST00000335694.4	hg19	CCDS13163.1																																																																																			.	.		0.637	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2		T	23965975	G	T	23965975	2	4	213	1	0	0	0	0	0	0	0	1	6373	1115	39	1		1	GGTLC1	20	23965975	Silent	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10		23965975	39059545	62	30790										
ELMO2	63916	hgsc.bcm.edu	37	chr20	45002045	45002045	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	cggagacactgaccttgttgAagtcctctgctgttgccctc	10	13	1	3			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr20:45002045A>T	ENST00000290246.6	-	16	1603	c.1409T>A	c.(1408-1410)tTc>tAc	p.F470Y	ELMO2_ENST00000488853.1_5'Flank|ELMO2_ENST00000352077.2_Missense_Mutation_p.F468Y|ELMO2_ENST00000454865.2_Missense_Mutation_p.F202Y|ELMO2_ENST00000396391.1_Missense_Mutation_p.F470Y|ELMO2_ENST00000445496.2_Missense_Mutation_p.F287Y|ELMO2_ENST00000372176.1_Missense_Mutation_p.F382Y|ELMO2_ENST00000439931.2_Missense_Mutation_p.F482Y	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	470	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				GACCTTGTTGAAGTCCTCTGC	0.547																																					p.F470Y		Atlas-SNP	.											.	ELMO2	51	.	0			c.T1409A						.						145	111	123					20																	45002045		2203	4300	6503	SO:0001583	missense	63916	exon15			TTGTTGAAGTCCT	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"Engulfment and cell motility proteins"	17233	protein-coding gene	gene with protein product		606421	"engulfment and cell motility 2 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.1409T>A	chr20.hg19:g.45002045A>T	ENSP00000290246:p.Phe470Tyr	56.0	0.0		65.0	13.0	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Missense_Mutation	SNP	ENST00000290246.6	hg19	CCDS13398.1	.	.	.	.	.	.	.	.	.	.	A	31	5.100124	0.94197	.	.	ENSG00000062598	ENST00000290246;ENST00000372176;ENST00000452857;ENST00000396391;ENST00000439931;ENST00000445496;ENST00000454865;ENST00000352077;ENST00000425546	T;T;T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99	4.91	4.91	0.64330	Engulfment/cell motility, ELMO (2);	0.000000	0.85682	D	0.000000	T	0.60676	0.2287	M	0.61703	1.905	0.80722	D	1	B;D;P;D;P	0.89917	0.097;1.0;0.635;0.988;0.494	B;D;P;D;P	0.77557	0.14;0.99;0.612;0.934;0.457	T	0.63161	-0.6699	10	0.56958	D	0.05	-25.6017	13.8983	0.63787	1.0:0.0:0.0:0.0	.	482;202;470;287;470	B4DRL5;B4DZ20;E9PBG2;B7Z1S8;Q96JJ3	.;.;.;.;ELMO2_HUMAN	Y	470;382;37;470;482;287;202;468;258	ENSP00000290246:F470Y;ENSP00000361249:F382Y;ENSP00000414329:F37Y;ENSP00000379673:F470Y;ENSP00000396519:F482Y;ENSP00000409920:F287Y;ENSP00000415641:F202Y;ENSP00000326172:F468Y;ENSP00000388962:F258Y	ENSP00000290246:F470Y	F	-	2	0	ELMO2	44435452	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.139000	0.94554	2.056000	0.61249	0.459000	0.35465	TTC	.	.		0.547	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086		T	45002045	A	T	45002045	3	4	213	1	0	0	0	0	1	0	0	0	5068	246	9	4	781	4	ELMO2	20	45002045	Missense_Mutation	SNP	A	TCGA-DD-AAE8-01A-11D-A40R-10	21036070	45002045	18023475	63	30791										
ITGB2	3689	hgsc.bcm.edu	37	chr21	46314957	46314957	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	ctcccccacggctgacttggGgatgatctcggtgagtttct	12	12	2	3			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr21:46314957G>T	ENST00000397850.2	-	10	1464	c.1012C>A	c.(1012-1014)Ccc>Acc	p.P338T	ITGB2_ENST00000397852.1_Missense_Mutation_p.P338T|ITGB2_ENST00000397857.1_Missense_Mutation_p.P338T|ITGB2_ENST00000397854.3_Missense_Mutation_p.P281T|ITGB2_ENST00000355153.4_Missense_Mutation_p.P338T|ITGB2_ENST00000302347.5_Missense_Mutation_p.P338T			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	338	VWFA.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	GCTGACTTGGGGATGATCTCG	0.577																																					p.P338T		Atlas-SNP	.											.	ITGB2	107	.	0			c.C1012A						.						113	93	100					21																	46314957		2203	4300	6503	SO:0001583	missense	3689	exon9			ACTTGGGGATGAT	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.1012C>A	chr21.hg19:g.46314957G>T	ENSP00000380948:p.Pro338Thr	64.0	0.0		48.0	8.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	hg19	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055104	0.75960	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347;ENST00000545414	T;T;T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51;-0.51;-0.51	5.28	5.28	0.74379	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	.	.	.	.	D	0.86569	0.5964	M	0.89353	3.025	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.89087	0.3480	9	0.87932	D	0	.	16.4453	0.83925	0.0:0.0:1.0:0.0	.	281;338	A8MYE6;P05107	.;ITB2_HUMAN	T	338;338;281;338;338;338;281	ENSP00000380950:P338T;ENSP00000380955:P338T;ENSP00000380952:P281T;ENSP00000347279:P338T;ENSP00000380948:P338T;ENSP00000303242:P338T	ENSP00000303242:P338T	P	-	1	0	ITGB2	45139385	1.000000	0.71417	1.000000	0.80357	0.655000	0.38815	8.978000	0.93450	2.482000	0.83794	0.585000	0.79938	CCC	.	.		0.577	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		T	46314957	G	T	46314957	3	4	213	1	0	0	0	0	1	0	0	0	7903	1232	43	3	1329	3	ITGB2	21	46314957	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10		46314957	1814938	64	30792										
PMM1	5372	hgsc.bcm.edu	37	chr22	41973917	41973917	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	tcggggaagacgtcaaagctGatcatgcctcctgtgggcag	14	10	2	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chr22:41973917G>A	ENST00000216259.7	-	7	645	c.561C>T	c.(559-561)atC>atT	p.I187I		NM_002676.2	NP_002667.2	Q92871	PMM1_HUMAN	phosphomannomutase 1	187					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|mannose biosynthetic process (GO:0019307)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	metal ion binding (GO:0046872)|phosphomannomutase activity (GO:0004615)			NS(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(2)	11						CGTCAAAGCTGATCATGCCTC	0.552																																					p.I187I		Atlas-SNP	.											.	PMM1	21	.	0			c.C561T						.						102	79	87					22																	41973917		2203	4300	6503	SO:0001819	synonymous_variant	5372	exon7			AAAGCTGATCATG		CCDS14020.1	22q13	2008-12-01			ENSG00000100417	ENSG00000100417	5.4.2.8		9114	protein-coding gene	gene with protein product	"brain glucose-1,6-bisphosphatase"	601786				9070917, 9271215	Standard	NM_002676		Approved	Sec53	uc003bal.2	Q92871	OTTHUMG00000150972	ENST00000216259.7:c.561C>T	chr22.hg19:g.41973917G>A		68.0	0.0		104.0	18.0	NM_002676	A8K003|Q92586	Silent	SNP	ENST00000216259.7	hg19	CCDS14020.1																																																																																			.	.		0.552	PMM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320711.3	NM_002676		A	41973917	G	A	41973917	2	1	213	1	0	0	0	0	0	0	0	1	12145	1280	45	3		3	PMM1	22	41973917	Silent	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10		41973917	9330649	65	30793										
RPS6KA6	27330	hgsc.bcm.edu	37	chrX	83419338	83419338	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	attaacataaatacttacatGacaagaatctgcttctccct	3	10	2	2			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chrX:83419338G>T	ENST00000262752.2	-	2	146	c.139C>A	c.(139-141)Cat>Aat	p.H47N	RPS6KA6_ENST00000543399.1_Missense_Mutation_p.H47N	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	47					axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						ATACTTACATGACAAGAATCT	0.303																																					p.H47N		Atlas-SNP	.											.	RPS6KA6	116	.	0			c.C139A						.						95	86	89					X																	83419338		2203	4296	6499	SO:0001583	missense	27330	exon2			TTACATGACAAGA	AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.139C>A	chrX.hg19:g.83419338G>T	ENSP00000262752:p.His47Asn	327.0	0.0		288.0	34.0	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	hg19	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	G	7.384	0.629350	0.14257	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.68765	-0.35;-0.34	4.22	3.34	0.38264	.	0.978140	0.08447	N	0.944571	T	0.48874	0.1524	N	0.14661	0.345	0.22666	N	0.99888	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32188	-0.9916	10	0.24483	T	0.36	.	9.651	0.39897	0.0:0.0:0.6253:0.3747	.	47;47	B7ZL90;Q9UK32	.;KS6A6_HUMAN	N	47	ENSP00000262752:H47N;ENSP00000440830:H47N	ENSP00000262752:H47N	H	-	1	0	RPS6KA6	83305994	1.000000	0.71417	0.053000	0.19242	0.980000	0.70556	1.583000	0.36579	0.757000	0.33036	0.429000	0.28392	CAT	.	.		0.303	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		T	83419338	G	T	83419338	3	4	213	1	0	0	0	0	1	0	0	0	13670	1290	45	3	2182	3	RPS6KA6	23	83419338	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10		83419338	71851222	66	30794										
ARMCX1	51309	hgsc.bcm.edu	37	chrX	100808335	100808335	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0454545454545455	3	1	0.869742198100407	0.911158493248046	0.850414593698176	1	1	0	gaacaggacccttgcaccgaGtttaccctgcccaggaggca	11	14	0	0			TCGA-DD-AAE8-01A-11D-A40R-10	TCGA-DD-AAE8-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0b6c61a-a389-4f78-a06a-a7cb308657de	bce559c8-f5e9-41a2-8339-05113ef1a254	g.chrX:100808335G>C	ENST00000372829.3	+	4	793	c.422G>C	c.(421-423)aGt>aCt	p.S141T		NM_016608.1	NP_057692.1	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1	141						integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(2)|ovary(3)|pancreas(1)|urinary_tract(1)	19						CTTGCACCGAGTTTACCCTGC	0.617																																					p.S141T		Atlas-SNP	.											.	ARMCX1	67	.	0			c.G422C						.						64	61	62					X																	100808335		2203	4300	6503	SO:0001583	missense	51309	exon4			CACCGAGTTTACC	AB039670	CCDS14487.1	Xq21.33-q22.2	2014-03-21			ENSG00000126947	ENSG00000126947		"Armadillo repeat containing"	18073	protein-coding gene	gene with protein product		300362				11162520, 16221301, 22569362	Standard	NM_016608		Approved	ALEX1, GASP7	uc004ehv.3	Q9P291	OTTHUMG00000022033	ENST00000372829.3:c.422G>C	chrX.hg19:g.100808335G>C	ENSP00000361917:p.Ser141Thr	76.0	0.0		94.0	60.0	NM_016608	Q53HK2|Q9H2Q0	Missense_Mutation	SNP	ENST00000372829.3	hg19	CCDS14487.1	.	.	.	.	.	.	.	.	.	.	g	8.347	0.829975	0.16749	.	.	ENSG00000126947	ENST00000372829	T	0.28069	1.63	3.86	3.86	0.44501	.	0.364574	0.24786	N	0.035612	T	0.14056	0.0340	N	0.19112	0.55	0.27632	N	0.948019	P	0.35155	0.487	B	0.27380	0.079	T	0.12993	-1.0526	10	0.07030	T	0.85	-3.9483	10.1908	0.43026	0.0:0.0:1.0:0.0	.	141	Q9P291	ARMX1_HUMAN	T	141	ENSP00000361917:S141T	ENSP00000361917:S141T	S	+	2	0	ARMCX1	100694991	0.999000	0.42202	0.988000	0.46212	0.876000	0.50452	3.785000	0.55424	2.160000	0.67779	0.556000	0.70494	AGT	.	.		0.617	ARMCX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057561.1	NM_016608		C	100808335	G	C	100808335	3	2	213	1	0	0	0	0	1	0	0	0	959	1029	36	4	424	4	ARMCX1	23	100808335	Missense_Mutation	SNP	G	TCGA-DD-AAE8-01A-11D-A40R-10	17388997	100808335	54462225	67	30795										
ARHGEF10L	55160	hgsc.bcm.edu	37	chr1	17981137	17981137	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctctgtctctgcagcttgggGccctggtccacagtcctgtc	11	15	2	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr1:17981137G>T	ENST00000361221.3	+	23	2560	c.2401G>T	c.(2401-2403)Gcc>Tcc	p.A801S	ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.A762S|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.A762S|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.A574S|ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.A796S|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.A504S	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	801						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GCAGCTTGGGGCCCTGGTCCA	0.582																																					p.A801S		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.G2401T						.						232	227	229					1																	17981137		2203	4300	6503	SO:0001583	missense	55160	exon23			CTTGGGGCCCTGG	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.2401G>T	chr1.hg19:g.17981137G>T	ENSP00000355060:p.Ala801Ser	35.0	0.0		33.0	24.0	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	hg19	CCDS182.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.223476	0.39300	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415;ENST00000375408;ENST00000457829;ENST00000167825	T;T;T;T;T;T	0.06294	3.32;3.32;3.32;3.32;3.32;3.32	4.49	3.46	0.39613	.	0.254366	0.38164	N	0.001799	T	0.06462	0.0166	L	0.41236	1.265	0.29015	N	0.886666	B;B;B;B;B;B;B	0.13594	0.005;0.008;0.002;0.001;0.004;0.008;0.001	B;B;B;B;B;B;B	0.15052	0.005;0.012;0.006;0.003;0.007;0.006;0.002	T	0.11842	-1.0571	10	0.29301	T	0.29	-15.8421	12.6564	0.56790	0.0:0.0:0.8227:0.1773	.	574;796;504;562;757;762;801	Q5VXI4;Q9HCE6-5;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;.;ARGAL_HUMAN	S	801;762;796;762;574;574;504	ENSP00000355060:A801S;ENSP00000399401:A762S;ENSP00000394621:A796S;ENSP00000364564:A762S;ENSP00000364557:A574S;ENSP00000167825:A504S	ENSP00000167825:A504S	A	+	1	0	ARHGEF10L	17853724	0.995000	0.38212	1.000000	0.80357	0.970000	0.65996	3.186000	0.50942	2.048000	0.60808	0.561000	0.74099	GCC	.	.		0.582	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		T	17981137	G	T	17981137	3	4	214	1	0	0	0	0	1	0	0	0	895	1203	42	3	2487	3	ARHGEF10L	1	17981137	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10		17981137	231269484	1	30796										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22158249	22158249	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	atggcccagggccagtggtgTgggatggcggatggtggcca	20	8	0	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr1:22158249T>C	ENST00000374695.3	-	82	11327	c.11248A>G	c.(11248-11250)Aca>Gca	p.T3750A	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3750	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCCAGTGGTGTGGGATGGCGG	0.652																																					p.T3750A		Atlas-SNP	.											.	HSPG2	311	.	0			c.A11248G						.						60	64	63					1																	22158249		2203	4299	6502	SO:0001583	missense	3339	exon82			GTGGTGTGGGATG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.11248A>G	chr1.hg19:g.22158249T>C	ENSP00000363827:p.Thr3750Ala	301.0	1.0		224.0	171.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	t	17.64	3.440208	0.63067	.	.	ENSG00000142798	ENST00000374695	T	0.77098	-1.07	5.31	4.18	0.49190	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.182919	0.26387	N	0.024666	T	0.79736	0.4497	L	0.44542	1.39	0.36946	D	0.892625	P;D	0.71674	0.587;0.998	P;D	0.71414	0.479;0.973	T	0.76440	-0.2958	10	0.11485	T	0.65	.	10.0121	0.41992	0.0:0.0807:0.0:0.9193	.	1690;3750	Q59EG0;P98160	.;PGBM_HUMAN	A	3750	ENSP00000363827:T3750A	ENSP00000363827:T3750A	T	-	1	0	HSPG2	22030836	0.998000	0.40836	0.656000	0.29637	0.704000	0.40688	3.053000	0.49901	0.855000	0.35359	0.454000	0.30748	ACA	.	.		0.652	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		C	22158249	T	C	22158249	3	2	214	1	0	0	0	0	1	0	0	0	7439	1696	59	2	1991	2	HSPG2	1	22158249	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	4177112	22158249	227092372	2	30797										
PCSK9	255738	hgsc.bcm.edu	37	chr1	55527047	55527047	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gctggctttcctctgccccaGgctgcagctcccactgggag	12	16	1	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr1:55527047G>T	ENST00000302118.5	+	11	1971		c.e11-1		PCSK9_ENST00000490692.1_Splice_Site|PCSK9_ENST00000543384.1_Splice_Site	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9						apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						CTCTGCCCCAGGCTGCAGCTC	0.627																																					.	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.1682-1G>T						.						18	19	18					1																	55527047		2200	4299	6499	SO:0001630	splice_region_variant	255738	exon11			GCCCCAGGCTGCA	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"hypercholesterolemia, autosomal dominant 3"	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1682-1G>T	chr1.hg19:g.55527047G>T		285.0	0.0		199.0	99.0	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Splice_Site	SNP	ENST00000302118.5	hg19	CCDS603.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.568138	0.45798	.	.	ENSG00000169174	ENST00000302118	.	.	.	3.68	2.65	0.31530	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6166	0.51094	0.0:0.0:0.8212:0.1788	.	.	.	.	.	-1	.	.	.	+	.	.	PCSK9	55299635	1.000000	0.71417	0.996000	0.52242	0.764000	0.43329	3.586000	0.53950	1.741000	0.51731	0.456000	0.33151	.	.	.		0.627	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	Intron	T	55527047	G	T	55527047	5	4	214	1	0	0	0	0	0	0	1	0	11615	1014	35	3	1723	3	PCSK9	1	55527047	Splice_Site	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	33368798	55527047	193723574	3	30798										
TNNI3K	100526835	hgsc.bcm.edu	37	chr1	74833646	74833646	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gaagattaaaagcatgacaaAaggtacctataatctgggac	9	6	1	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr1:74833646A>T	ENST00000370899.3	+	15	1659	c.1622A>T	c.(1621-1623)aAa>aTa	p.K541I	TNNI3K_ENST00000370891.2_Missense_Mutation_p.K541I|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.K554I|TNNI3K_ENST00000326637.3_Missense_Mutation_p.K440I|RP11-439H8.4_ENST00000415549.2_RNA|FPGT-TNNI3K_ENST00000370895.1_Missense_Mutation_p.K541I	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		AGCATGACAAAAGGTACCTAT	0.289																																					p.K541I		Atlas-SNP	.											.	.	.	.	0			c.A1622T						.						60	62	62					1																	74833646		2203	4297	6500	SO:0001583	missense	100526835	exon15			TGACAAAAGGTAC			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.1622A>T	chr1.hg19:g.74833646A>T	ENSP00000359936:p.Lys541Ile	358.0	0.0		289.0	94.0	NM_001112808		Missense_Mutation	SNP	ENST00000370899.3	hg19		.	.	.	.	.	.	.	.	.	.	A	31	5.092087	0.94149	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000534632;ENST00000557284;ENST00000370891;ENST00000326637	T;T;T;T;T	0.75938	-0.98;-0.69;-0.98;-0.98;-0.96	5.9	5.9	0.94986	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.73567	0.3603	L	0.27053	0.805	0.58432	D	0.999999	D;D;D;D	0.76494	0.998;0.999;0.999;0.999	P;D;D;D	0.71656	0.878;0.974;0.974;0.952	T	0.78056	-0.2353	10	0.56958	D	0.05	.	16.3155	0.82918	1.0:0.0:0.0:0.0	.	440;541;541;541	Q59H18;Q59H18-1;Q59H18-4;Q59H18-3	TNI3K_HUMAN;.;.;.	I	541;541;162;541;541;440	ENSP00000359936:K541I;ENSP00000359932:K541I;ENSP00000450895:K541I;ENSP00000359928:K541I;ENSP00000322251:K440I	ENSP00000322251:K440I	K	+	2	0	RP11-653A5.2;AC093158.1	74606234	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.558000	0.90704	2.260000	0.74910	0.528000	0.53228	AAA	.	.		0.289	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			T	74833646	A	T	74833646	3	4	214	1	0	0	0	0	1	0	0	0	16344	14	1	4	1724	4	TNNI3K	1	74833646	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	19306599	74833646	174416975	4	30799										
INTS3	65123	hgsc.bcm.edu	37	chr1	153743174	153743174	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctcacagagcacccagaggcCctgtcctgcctactgcttca	8	17	2	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr1:153743174C>T	ENST00000318967.2	+	25	3085	c.2517C>T	c.(2515-2517)gcC>gcT	p.A839A	INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000435409.2_Silent_p.A839A|INTS3_ENST00000456435.1_Silent_p.A633A|INTS3_ENST00000512605.1_Silent_p.A633A	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	840					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ACCCAGAGGCCCTGTCCTGCC	0.537																																					p.A839A		Atlas-SNP	.											.	INTS3	83	.	0			c.C2517T						.						56	53	54					1																	153743174		2203	4300	6503	SO:0001819	synonymous_variant	65123	exon25			AGAGGCCCTGTCC	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"sensor of single-strand DNA complex subunit A"	611347	"chromosome 1 open reading frame 60"	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.2517C>T	chr1.hg19:g.153743174C>T		54.0	0.0		69.0	26.0	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Silent	SNP	ENST00000318967.2	hg19	CCDS1052.1																																																																																			.	.		0.537	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		T	153743174	C	T	153743174	2	4	214	1	0	0	0	0	0	0	0	1	7788	610	22	3		3	INTS3	1	153743174	Silent	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	78909528	153743174	95507447	5	30800										
C1orf92	149499	hgsc.bcm.edu	37	chr1	156899104	156899104	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cgacacggggactccaaaacGgaccgtgagaagagtcagat	13	10	1	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr1:156899104G>C	ENST00000337428.7	+	10	1183	c.1029G>C	c.(1027-1029)acG>acC	p.T343T	LRRC71_ENST00000490146.1_3'UTR	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	343										endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						ACTCCAAAACGGACCGTGAGA	0.557																																					p.T343T		Atlas-SNP	.											.	LRRC71	33	.	0			c.G1029C						.						57	57	57					1																	156899104		1977	4165	6142	SO:0001819	synonymous_variant	149499	exon10			CAAAACGGACCGT	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 92"	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.1029G>C	chr1.hg19:g.156899104G>C		125.0	0.0		167.0	20.0	NM_144702	Q96M24	Silent	SNP	ENST00000337428.7	hg19	CCDS44249.1																																																																																			.	.		0.557	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702		C	156899104	G	C	156899104	2	2	214	1	0	0	0	0	0	0	0	1	2071	1103	39	4		4	C1orf92	1	156899104	Silent	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	3155930	156899104	92351517	6	30801										
TMEM81	388730	hgsc.bcm.edu	37	chr1	205052921	205052921	+	Frame_Shift_Del	DEL	A	A	-													0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ggaggaaggaccctcaacccAaaatagagcctcttgacgag							TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr1:205052921delA	ENST00000367167.3	-	1	724	c.528delT	c.(526-528)tttfs	p.F176fs		NM_203376.1	NP_976310.1	Q6P7N7	TMM81_HUMAN	transmembrane protein 81	176						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9	all_cancers(21;0.144)|Breast(84;0.0437)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			CCCTCAACCCAAAATAGAGCC	0.418																																					p.G177fs		Atlas-INDEL	.											.	TMEM81	23	.	0			c.529delG						.						78	80	79					1																	205052921		2203	4300	6503	SO:0001589	frameshift_variant	388730	exon1			.	BC061592	CCDS1450.1	1q32.1	2013-01-11			ENSG00000174529	ENSG00000174529		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	32349	protein-coding gene	gene with protein product							Standard	NM_203376		Approved	UNQ2788, MGC75217, HC3107, KVLA2788	uc001hbt.3	Q6P7N7	OTTHUMG00000037103	ENST00000367167.3:c.528delT	chr1.hg19:g.205052921delA	ENSP00000356135:p.Phe176fs	148.0	0.0		253.0	104.0	NM_203376	Q6UVZ4	Frame_Shift_Del	DEL	ENST00000367167.3	hg19	CCDS1450.1																																																																																			.	.		0.418	TMEM81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090076.1	NM_203376		-	205052921	A	-	205052921	7	5	214	1	0	1	0	1	0	0	0	0	16220	127	5	0	243	0	TMEM81	1	205052921	Frame_Shift_Del	DEL	A	TCGA-DD-AAE9-01A-11D-A40R-10	48153817	205052921	44197700	7	30802										
CTSE	1510	hgsc.bcm.edu	37	chr1	206319173	206319173	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tcatcttcgacactggctccTccaacctctgggtcccctct	6	18	4	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr1:206319173T>C	ENST00000358184.2	+	3	416	c.298T>C	c.(298-300)Tcc>Ccc	p.S100P	CTSE_ENST00000361052.3_Missense_Mutation_p.S100P|CTSE_ENST00000432969.2_Missense_Mutation_p.S25P|CTSE_ENST00000360218.2_Missense_Mutation_p.S100P	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E	100					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|digestion (GO:0007586)|protein autoprocessing (GO:0016540)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(3)	16			BRCA - Breast invasive adenocarcinoma(75;0.0754)			CACTGGCTCCTCCAACCTCTG	0.567																																					p.S100P		Atlas-SNP	.											.	CTSE	72	.	0			c.T298C						.						120	107	111					1																	206319173		2203	4300	6503	SO:0001583	missense	1510	exon3			GGCTCCTCCAACC	BC042537	CCDS73012.1, CCDS73013.1	1q32.1	2008-02-05			ENSG00000196188	ENSG00000196188	3.4.23.5	"Cathepsins"	2530	protein-coding gene	gene with protein product		116890				2369841, 2674141	Standard	NM_001910		Approved		uc001hdu.3	P14091	OTTHUMG00000036121	ENST00000358184.2:c.298T>C	chr1.hg19:g.206319173T>C	ENSP00000350911:p.Ser100Pro	57.0	0.0		109.0	44.0	NM_001910	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Missense_Mutation	SNP	ENST00000358184.2	hg19	CCDS1462.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846146	0.71603	.	.	ENSG00000196188	ENST00000358184;ENST00000361052;ENST00000360218;ENST00000432969	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	4.78	3.65	0.41850	.	0.175329	0.40385	N	0.001108	D	0.82907	0.5139	M	0.90309	3.105	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.997;0.999	D	0.84679	0.0716	10	0.87932	D	0	.	10.3393	0.43868	0.0:0.0786:0.0:0.9214	.	25;100;100	B4DNU8;P14091-2;P14091-1	.;.;.	P	100;100;100;25	ENSP00000350911:S100P;ENSP00000354337:S100P;ENSP00000353350:S100P;ENSP00000394607:S25P	ENSP00000350911:S100P	S	+	1	0	CTSE	204485796	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	5.556000	0.67307	0.970000	0.38263	-0.256000	0.11100	TCC	.	.		0.567	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087998.1	NM_001910		C	206319173	T	C	206319173	3	2	214	1	0	0	0	0	1	0	0	0	4035	1551	54	2	308	2	CTSE	1	206319173	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	1266252	206319173	42931448	8	30803										
C1orf107	27042	hgsc.bcm.edu	37	chr1	210010380	210010380	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	accgggacctgttctacccgGaaaggactgctctgaagaac	11	12	2	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr1:210010380G>A	ENST00000491415.2	+	6	943	c.886G>A	c.(886-888)Gaa>Aaa	p.E296K		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	296					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						GTTCTACCCGGAAAGGACTGC	0.488																																					p.E296K		Atlas-SNP	.											.	DIEXF	97	.	0			c.G886A						.						69	71	71					1																	210010380		2203	4300	6503	SO:0001583	missense	27042	exon6			TACCCGGAAAGGA	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.886G>A	chr1.hg19:g.210010380G>A	ENSP00000419005:p.Glu296Lys	130.0	0.0		213.0	104.0	NM_014388	O75992|Q4VY00|Q63HL9	Missense_Mutation	SNP	ENST00000491415.2	hg19	CCDS1493.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.206911	0.39003	.	.	ENSG00000117597	ENST00000491415	T	0.44881	0.91	5.81	4.9	0.64082	.	0.236438	0.50627	N	0.000118	T	0.34135	0.0887	L	0.55743	1.74	0.41738	D	0.989593	P	0.35411	0.5	B	0.29267	0.1	T	0.15867	-1.0422	10	0.08837	T	0.75	-23.1277	15.1781	0.72931	0.0674:0.0:0.9326:0.0	.	296	Q68CQ4	DIEXF_HUMAN	K	296	ENSP00000419005:E296K	ENSP00000419005:E296K	E	+	1	0	DIEXF	208077003	1.000000	0.71417	0.995000	0.50966	0.310000	0.27922	6.373000	0.73128	1.465000	0.48006	-0.126000	0.14955	GAA	.	.		0.488	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		A	210010380	G	A	210010380	3	1	214	1	0	0	0	0	1	0	0	0	1983	1175	41	3	908	3	C1orf107	1	210010380	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	3691207	210010380	39240241	9	30804										
ALLC	55821	hgsc.bcm.edu	37	chr2	3729266	3729266	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	aagaggaaccaggacaggagCtgcagccactcctgaggagt	14	10	0	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr2:3729266C>T	ENST00000252505.3	+	6	503	c.341C>T	c.(340-342)gCt>gTt	p.A114V		NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	133					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		AGGACAGGAGCTGCAGCCACT	0.443										HNSCC(21;0.051)																											p.A114V		Atlas-SNP	.											.	ALLC	61	.	0			c.C341T						.						52	57	55					2																	3729266		1915	4126	6041	SO:0001583	missense	55821	exon6			CAGGAGCTGCAGC	AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.341C>T	chr2.hg19:g.3729266C>T	ENSP00000252505:p.Ala114Val	110.0	0.0		83.0	35.0	NM_018436	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	hg19	CCDS46223.1	.	.	.	.	.	.	.	.	.	.	C	4.162	0.028568	0.08054	.	.	ENSG00000151360	ENST00000252505	.	.	.	4.98	2.02	0.26589	Allantoicase domain (1);Galactose-binding domain-like (1);	0.630810	0.17333	N	0.178051	T	0.25269	0.0614	L	0.28115	0.83	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.12477	-1.0546	9	0.39692	T	0.17	-13.8322	4.6385	0.12536	0.0:0.6238:0.1812:0.195	.	133	Q8N6M5	ALLC_HUMAN	V	114	.	ENSP00000252505:A114V	A	+	2	0	ALLC	3707141	0.001000	0.12720	0.001000	0.08648	0.017000	0.09413	0.275000	0.18698	0.800000	0.34041	0.650000	0.86243	GCT	.	.		0.443	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1			T	3729266	C	T	3729266	3	4	214	1	0	0	0	0	1	0	0	0	534	797	28	3	359	3	ALLC	2	3729266	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10		3729266	239470107	10	30805										
APOB	338	hgsc.bcm.edu	37	chr2	21234820	21234821	+	Frame_Shift_Ins	INS	-	-	G													0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tccttagtgtcgccttgtgaINSgcaccactattaattttgtc							TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr2:21234820_21234821insG	ENST00000233242.1	-	26	5046_5047	c.4919_4920insC	c.(4918-4920)gctfs	p.A1640fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1640					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCGCCTTGTGAGCACCACTATT	0.45																																					p.A1640fs		Atlas-INDEL	.											.	APOB	761	.	0			c.4920_4921insC						.																																			SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.4920dupC	chr2.hg19:g.21234821_21234821dupG	ENSP00000233242:p.Ala1640fs	56.0	0.0		62.0	26.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.45	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21234821	-	G	21234820	7	5	214	1	0	1	1	0	0	0	0	0	785	291	11	0	8787	0	APOB	2	21234820	Frame_Shift_Ins	INS	-	TCGA-DD-AAE9-01A-11D-A40R-10	17505554	21234820	221964553	11	30806										
TUBA3E	112714	hgsc.bcm.edu	37	chr2	130951585	130951585	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cgtggtaggccttctcagctGagatgactggggcgtaggtg	17	8	1	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr2:130951585G>T	ENST00000312988.7	-	4	930	c.830C>A	c.(829-831)tCa>tAa	p.S277*		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	277					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					CTTCTCAGCTGAGATGACTGG	0.597																																					p.S277X		Atlas-SNP	.											.	TUBA3E	73	.	0			c.C830A						.						118	103	108					2																	130951585		2203	4300	6503	SO:0001587	stop_gained	112714	exon4			TCAGCTGAGATGA	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"Tubulins"	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.830C>A	chr2.hg19:g.130951585G>T	ENSP00000318197:p.Ser277*	113.0	0.0		77.0	4.0	NM_207312		Nonsense_Mutation	SNP	ENST00000312988.7	hg19	CCDS2158.1	.	.	.	.	.	.	.	.	.	.	g	36	5.775866	0.96922	.	.	ENSG00000152086	ENST00000312988	.	.	.	2.92	2.92	0.33932	.	0.000000	0.45606	U	0.000359	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.6717	0.51406	0.0:0.0:1.0:0.0	.	.	.	.	X	277	.	ENSP00000318197:S277X	S	-	2	0	TUBA3E	130668055	1.000000	0.71417	0.933000	0.37362	0.944000	0.59088	8.339000	0.90041	1.664000	0.50801	0.449000	0.29647	TCA	.	.		0.597	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312		T	130951585	G	T	130951585	4	4	214	1	0	0	0	0	0	1	0	0	16763	1294	45	3	530	3	TUBA3E	2	130951585	Nonsense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	109716765	130951585	112247788	12	30807										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185802939	185802939	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cctgcttgaacacaaagaaaGaagtgagaatataaatctta	7	6	1	4			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr2:185802939G>A	ENST00000302277.6	+	4	3410	c.2816G>A	c.(2815-2817)aGa>aAa	p.R939K		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	939							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						CACAAAGAAAGAAGTGAGAAT	0.378																																					p.R939K		Atlas-SNP	.											ZNF804A,mucosal,malignant_melanoma,0,1	ZNF804A	322	.	0			c.G2816A						.						79	77	78					2																	185802939		2203	4300	6503	SO:0001583	missense	91752	exon4			AAGAAAGAAGTGA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.2816G>A	chr2.hg19:g.185802939G>A	ENSP00000303252:p.Arg939Lys	151.0	0.0		119.0	49.0	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	G	5.678	0.309723	0.10733	.	.	ENSG00000170396	ENST00000302277	T	0.04809	3.55	5.57	0.948	0.19561	.	0.765320	0.12203	N	0.490060	T	0.02727	0.0082	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.47649	-0.9101	10	0.05436	T	0.98	-1.8297	6.4963	0.22144	0.2835:0.1379:0.5786:0.0	.	939	Q7Z570	Z804A_HUMAN	K	939	ENSP00000303252:R939K	ENSP00000303252:R939K	R	+	2	0	ZNF804A	185511184	1.000000	0.71417	0.215000	0.23724	0.747000	0.42532	0.713000	0.25794	0.243000	0.21327	-0.218000	0.12543	AGA	.	.		0.378	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		A	185802939	G	A	185802939	3	1	214	1	0	0	0	0	1	0	0	0	18185	942	33	3	2830	3	ZNF804A	2	185802939	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	54851354	185802939	57396434	13	30808										
GPR55	9290	hgsc.bcm.edu	37	chr2	231775507	231775507	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	atcatgtagatggaggtggcAgcataatcgggccacctgtt	13	8	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr2:231775507A>T	ENST00000392040.1	-	2	363	c.171T>A	c.(169-171)gcT>gcA	p.A57A	AC012507.4_ENST00000454890.1_RNA|GPR55_ENST00000392039.2_Silent_p.A57A	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	57					activation of phospholipase C activity (GO:0007202)|bone resorption (GO:0045453)|cannabinoid signaling pathway (GO:0038171)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho protein signal transduction (GO:0035025)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|G-protein coupled receptor activity (GO:0004930)			endometrium(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)		TGGAGGTGGCAGCATAATCGG	0.572																																					p.A57A		Atlas-SNP	.											.	GPR55	46	.	0			c.T171A						.						84	73	76					2																	231775507		2203	4300	6503	SO:0001819	synonymous_variant	9290	exon2			GGTGGCAGCATAA	AF096786	CCDS2480.1	2q37	2012-08-21			ENSG00000135898	ENSG00000135898		"GPCR / Class A : Orphans"	4511	protein-coding gene	gene with protein product		604107				9931487	Standard	NM_005683		Approved		uc002vrg.3	Q9Y2T6	OTTHUMG00000133224	ENST00000392040.1:c.171T>A	chr2.hg19:g.231775507A>T		229.0	0.0		171.0	61.0	NM_005683	Q8N580	Silent	SNP	ENST00000392040.1	hg19	CCDS2480.1																																																																																			.	.		0.572	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683		T	231775507	A	T	231775507	2	4	214	1	0	0	0	0	0	0	0	1	6707	175	7	4		4	GPR55	2	231775507	Silent	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	45972568	231775507	11423866	14	30809										
NMUR1	10316	hgsc.bcm.edu	37	chr2	232393719	232393719	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gaggacagagcaattgaggcAgagaggagtctgtggaacag	17	5	1	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr2:232393719A>C	ENST00000305141.4	-	2	146	c.13T>G	c.(13-15)Tgc>Ggc	p.C5G		NM_006056.4	NP_006047.3	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	5					activation of phospholipase C activity (GO:0007202)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|chloride transport (GO:0006821)|G-protein coupled receptor signaling pathway (GO:0007186)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|smooth muscle contraction (GO:0006939)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuromedin U receptor activity (GO:0001607)|neuropeptide receptor activity (GO:0008188)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(12)|pancreas(1)|skin(1)	24		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;8.37e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		CAATTGAGGCAGAGAGGAGTC	0.567																																					p.C5G		Atlas-SNP	.											.	NMUR1	46	.	0			c.T13G						.						29	31	31					2																	232393719		2203	4299	6502	SO:0001583	missense	10316	exon2			TGAGGCAGAGAGG	AF044600	CCDS2486.1	2q37.1	2012-08-08	2004-05-27	2004-05-28	ENSG00000171596	ENSG00000171596		"GPCR / Class A : Neuromedin U receptors"	4518	protein-coding gene	gene with protein product		604153	"G protein-coupled receptor 66"	GPR66		9782091	Standard	NM_006056		Approved	GPC-R, FM-3, NMU1R	uc002vry.4	Q9HB89	OTTHUMG00000133225	ENST00000305141.4:c.13T>G	chr2.hg19:g.232393719A>C	ENSP00000305877:p.Cys5Gly	39.0	0.0		26.0	11.0	NM_006056	O43664|Q7LDP6|Q8NE20	Missense_Mutation	SNP	ENST00000305141.4	hg19	CCDS2486.1	.	.	.	.	.	.	.	.	.	.	a	15.97	2.989963	0.54041	.	.	ENSG00000171596	ENST00000305141	T	0.67698	-0.28	5.2	-2.08	0.07254	.	1.424610	0.04518	N	0.384082	T	0.55641	0.1933	L	0.51422	1.61	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.49890	-0.8891	10	0.87932	D	0	-13.7255	1.6405	0.02751	0.4389:0.2584:0.0844:0.2183	.	5	Q9HB89	NMUR1_HUMAN	G	5	ENSP00000305877:C5G	ENSP00000305877:C5G	C	-	1	0	NMUR1	232101963	0.083000	0.21467	0.338000	0.25549	0.832000	0.47134	1.743000	0.38258	0.258000	0.21686	0.449000	0.29647	TGC	.	.		0.567	NMUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256961.1	NM_006056		C	232393719	A	C	232393719	3	2	214	1	0	0	0	0	1	0	0	0	10515	188	7	5	1275	5	NMUR1	2	232393719	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	618212	232393719	10805654	15	30810										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234863846	234863846	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cttctgctggagtggaaccaGctggacttagccaatgatga	12	9	1	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr2:234863846G>T	ENST00000324695.4	+	11	1354	c.1314G>T	c.(1312-1314)caG>caT	p.Q438H	AC005538.5_ENST00000455991.1_RNA|TRPM8_ENST00000433712.2_Missense_Mutation_p.Q126H	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	438					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	AGTGGAACCAGCTGGACTTAG	0.522																																					p.Q438H		Atlas-SNP	.											.	TRPM8	146	.	0			c.G1314T						.						109	101	104					2																	234863846		2203	4300	6503	SO:0001583	missense	79054	exon11			GAACCAGCTGGAC	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.1314G>T	chr2.hg19:g.234863846G>T	ENSP00000323926:p.Gln438His	127.0	0.0		107.0	40.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	hg19	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.599666	0.66332	.	.	ENSG00000144481	ENST00000324695;ENST00000433712	T;T	0.35973	1.28;1.28	5.99	5.1	0.69264	.	0.000000	0.64402	D	0.000002	T	0.55800	0.1943	M	0.68317	2.08	0.39158	D	0.96234	D;D	0.71674	0.989;0.998	P;D	0.79784	0.804;0.993	T	0.62039	-0.6938	10	0.87932	D	0	-32.155	10.536	0.45004	0.1495:0.0:0.8505:0.0	.	126;438	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	H	438;126	ENSP00000323926:Q438H;ENSP00000404423:Q126H	ENSP00000323926:Q438H	Q	+	3	2	TRPM8	234528585	0.997000	0.39634	1.000000	0.80357	0.978000	0.69477	0.491000	0.22419	1.512000	0.48834	0.655000	0.94253	CAG	.	.		0.522	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		T	234863846	G	T	234863846	3	4	214	1	0	0	0	0	1	0	0	0	16607	962	34	3	1352	3	TRPM8	2	234863846	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	2470127	234863846	8335527	16	30811										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9094837	9094837	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cgactgtgttggaaggcatcGgagacatcaaagtcctccac	11	11	1	1	rs369059791		TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr3:9094837G>C	ENST00000383836.3	-	9	1624	c.1197C>G	c.(1195-1197)tcC>tcG	p.S399S	SRGAP3_ENST00000360413.3_Silent_p.S399S|SRGAP3_ENST00000433332.3_5'UTR	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	399	F-BAR domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GGAAGGCATCGGAGACATCAA	0.507			T	RAF1	pilocytic astrocytoma																																p.S399S		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.C1197G						.						146	119	128					3																	9094837		2203	4300	6503	SO:0001819	synonymous_variant	9901	exon9			GGCATCGGAGACA	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.1197C>G	chr3.hg19:g.9094837G>C		104.0	0.0		104.0	9.0	NM_014850	Q8IX13|Q8IZV8	Silent	SNP	ENST00000383836.3	hg19	CCDS2572.1																																																																																			.	.		0.507	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			C	9094837	G	C	9094837	2	2	214	1	0	0	0	0	0	0	0	1	15162	1103	39	4		4	SRGAP3	3	9094837	Silent	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10		9094837	188927593	17	30812										
EOMES	8320	hgsc.bcm.edu	37	chr3	27763181	27763181	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cgaactgcgccctcccgggtGggcacacagccgcggggaag	16	15	0	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr3:27763181G>T	ENST00000295743.4	-	1	808	c.605C>A	c.(604-606)cCa>cAa	p.P202Q	EOMES_ENST00000461503.1_Intron|EOMES_ENST00000449599.1_Missense_Mutation_p.P202Q|EOMES_ENST00000537516.1_Intron			O95936	EOMES_HUMAN	eomesodermin	202	Gly-rich.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						CCTCCCGGGTGGGCACACAGC	0.771																																					p.P202Q		Atlas-SNP	.											.	EOMES	65	.	0			c.C605A						.						2	3	3					3																	27763181		1395	3181	4576	SO:0001583	missense	8320	exon1			CCGGGTGGGCACA	BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"T-boxes"	3372	protein-coding gene	gene with protein product	"T-box brain2"	604615	"eomesodermin (Xenopus laevis) homolog"			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.605C>A	chr3.hg19:g.27763181G>T	ENSP00000295743:p.Pro202Gln	60.0	0.0		80.0	35.0	NM_005442	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Missense_Mutation	SNP	ENST00000295743.4	hg19	CCDS2646.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.608472	0.28623	.	.	ENSG00000163508	ENST00000295743;ENST00000449599;ENST00000535713	D;D	0.85411	-1.98;-1.98	4.39	3.49	0.39957	.	0.654196	0.15813	N	0.243379	D	0.83908	0.5356	L	0.47716	1.5	0.80722	D	1	P;P;P	0.47677	0.899;0.799;0.697	P;B;B	0.48227	0.571;0.282;0.146	T	0.81113	-0.1080	10	0.40728	T	0.16	.	12.4311	0.55575	0.0:0.1705:0.8295:0.0	.	202;202;202	F5H3K1;G3XAI5;O95936	.;.;EOMES_HUMAN	Q	202;202;67	ENSP00000295743:P202Q;ENSP00000388620:P202Q	ENSP00000295743:P202Q	P	-	2	0	EOMES	27738185	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	4.048000	0.57390	0.913000	0.36797	0.462000	0.41574	CCA	.	.		0.771	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442		T	27763181	G	T	27763181	3	4	214	1	0	0	0	0	1	0	0	0	5149	1348	47	3	1479	3	EOMES	3	27763181	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	18668344	27763181	170259249	18	30813										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266124	41266124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gaatccattctggtgccactAccacagctccttctctgagt	7	14	2	1	rs121913412		TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr3:41266124A>G	ENST00000349496.5	+	3	401	c.121A>G	c.(121-123)Acc>Gcc	p.T41A	CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41A|CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41A|CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	41			T -> A (in hepatoblastoma and hepatocellular carcinoma; also in a desmoid tumor; strongly reduces phosphorylation and degradation; abolishes phosphorylation on Ser-33 and Ser-37 and enhances transactivation of target genes). {ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10398436, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10655994, ECO:0000269|PubMed:9927029}.|T -> I (in PTR, hepatocellular carcinoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T41A(550)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41P(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.A39_T42del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGTGCCACTACCACAGCTCC	0.507	T41A(CCK81_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.T41A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	681	Substitution - Missense(559)|Deletion - In frame(96)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)	soft_tissue(387)|liver(158)|large_intestine(61)|endometrium(17)|kidney(11)|stomach(8)|biliary_tract(7)|ovary(6)|small_intestine(4)|lung(4)|prostate(4)|adrenal_gland(3)|haematopoietic_and_lymphoid_tissue(3)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|salivary_gland(1)|pituitary(1)|pancreas(1)	c.A121G						.						89	77	81					3																	41266124		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCCACTACCACAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.121A>G	chr3.hg19:g.41266124A>G	ENSP00000344456:p.Thr41Ala	151.0	0.0		153.0	93.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449381	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.63117	0.2484	M	0.79258	2.445	0.80722	D	1	P	0.50943	0.94	P	0.52267	0.694	T	0.68561	-0.5376	10	0.87932	D	0	-8.9189	16.3453	0.83126	1.0:0.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	A	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34A;ENSP00000385604:T41A;ENSP00000412219:T41A;ENSP00000379486:T41A;ENSP00000344456:T41A;ENSP00000411226:T34A;ENSP00000379488:T41A;ENSP00000409302:T41A;ENSP00000401599:T41A	ENSP00000344456:T41A	T	+	1	0	CTNNB1	41241128	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	ACC	.	.		0.507	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266124	A	G	41266124	3	3	214	1	0	0	0	0	1	0	0	0	4018	391	14	2	127	2	CTNNB1	3	41266124	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	13502943	41266124	156756306	19	30814										
SENP7	57337	hgsc.bcm.edu	37	chr3	101059023	101059023	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cattagttactcctaatcccCccttagtaggtggtggagga	10	10	0	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr3:101059023C>A	ENST00000394095.2	-	16	2326	c.2273G>T	c.(2272-2274)gGg>gTg	p.G758V	SENP7_ENST00000394094.2_Missense_Mutation_p.G693V|SENP7_ENST00000314261.7_Missense_Mutation_p.G692V|SENP7_ENST00000358203.3_Missense_Mutation_p.G594V|SENP7_ENST00000394091.1_Missense_Mutation_p.G594V|SENP7_ENST00000348610.3_Missense_Mutation_p.G725V	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	758						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TCCTAATCCCCCCTTAGTAGG	0.294																																					p.G758V		Atlas-SNP	.											.	SENP7	170	.	0			c.G2273T						.						53	49	51					3																	101059023		2201	4285	6486	SO:0001583	missense	57337	exon16			AATCCCCCCTTAG		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.2273G>T	chr3.hg19:g.101059023C>A	ENSP00000377655:p.Gly758Val	437.0	0.0		567.0	152.0	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	hg19	CCDS2941.2	.	.	.	.	.	.	.	.	.	.	C	23.0	4.357131	0.82243	.	.	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42;1.42	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.58495	0.2126	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.958	D;D;D;D	0.97110	1.0;1.0;1.0;0.953	T	0.62105	-0.6924	10	0.87932	D	0	-11.5671	18.8056	0.92035	0.0:1.0:0.0:0.0	.	594;692;725;758	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	V	758;693;692;594;594;725	ENSP00000377655:G758V;ENSP00000377654:G693V;ENSP00000313624:G692V;ENSP00000377651:G594V;ENSP00000350936:G594V;ENSP00000342159:G725V	ENSP00000313624:G692V	G	-	2	0	SENP7	102541713	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.875000	0.75551	2.606000	0.88127	0.563000	0.77884	GGG	.	.		0.294	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		A	101059023	C	A	101059023	3	1	214	1	0	0	0	0	1	0	0	0	14066	623	22	3	915	3	SENP7	3	101059023	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	59792899	101059023	96963407	20	30815										
N4BP2	55728	hgsc.bcm.edu	37	chr4	40122514	40122514	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	atccttatctacagcacatgAggcctgttggggcacaagct	10	11	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr4:40122514A>T	ENST00000261435.6	+	9	3199	c.2783A>T	c.(2782-2784)gAg>gTg	p.E928V		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	928					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						ACAGCACATGAGGCCTGTTGG	0.418																																					p.E928V		Atlas-SNP	.											.	N4BP2	166	.	0			c.A2783T						.						59	57	58					4																	40122514		2203	4300	6503	SO:0001583	missense	55728	exon9			CACATGAGGCCTG	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.2783A>T	chr4.hg19:g.40122514A>T	ENSP00000261435:p.Glu928Val	215.0	0.0		187.0	71.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.069|9.069	0.996371|0.996371	0.19043|0.19043	.|.	.|.	ENSG00000078177|ENSG00000078177	ENST00000261435;ENST00000381804|ENST00000513269	T|.	0.19532|.	2.14|.	5.38|5.38	4.13|4.13	0.48395|0.48395	.|.	0.508000|.	0.21425|.	N|.	0.074754|.	T|.	0.43033|.	0.1229|.	L|L	0.59436|0.59436	1.845|1.845	0.09310|0.09310	N|N	1|1	D;P|.	0.76494|.	0.999;0.956|.	D;B|.	0.66351|.	0.943;0.444|.	T|.	0.36480|.	-0.9746|.	10|.	0.87932|.	D|.	0|.	-9.8925|-9.8925	5.1273|5.1273	0.14892|0.14892	0.7515:0.0:0.0881:0.1604|0.7515:0.0:0.0881:0.1604	.|.	928;928|.	Q86UW6-2;Q86UW6|.	.;N4BP2_HUMAN|.	V|C	928;848|574	ENSP00000261435:E928V|.	ENSP00000261435:E928V|.	E|X	+|+	2|3	0|0	N4BP2|N4BP2	39798909|39798909	0.880000|0.880000	0.30214|0.30214	0.739000|0.739000	0.30968|0.30968	0.068000|0.068000	0.16541|0.16541	1.291000|1.291000	0.33330|0.33330	2.175000|2.175000	0.68902|0.68902	0.533000|0.533000	0.62120|0.62120	GAG|TGA	.	.		0.418	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		T	40122514	A	T	40122514	3	4	214	1	0	0	0	0	1	0	0	0	10119	304	11	4	2809	4	N4BP2	4	40122514	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10		40122514	151031762	21	30816										
MRPL1	65008	hgsc.bcm.edu	37	chr4	78830432	78830432	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctaactagattccattggccGtgacatccccaaaatgcttg	7	12	0	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr4:78830432G>T	ENST00000315567.8	+	7	1012	c.683G>T	c.(682-684)cGt>cTt	p.R228L	MRPL1_ENST00000506674.1_3'UTR	NM_020236.3	NP_064621.3	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1	228					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)	17						TCCATTGGCCGTGACATCCCC	0.313																																					p.R228L		Atlas-SNP	.											.	MRPL1	37	.	0			c.G683T						.						91	99	96					4																	78830432		2203	4295	6498	SO:0001583	missense	65008	exon7			TTGGCCGTGACAT	AB049474	CCDS3583.2	4q21.1	2012-09-13			ENSG00000169288	ENSG00000169288		"Mitochondrial ribosomal proteins / large subunits"	14275	protein-coding gene	gene with protein product		611821					Standard	NM_020236		Approved	BM022	uc003hku.2	Q9BYD6	OTTHUMG00000130200	ENST00000315567.8:c.683G>T	chr4.hg19:g.78830432G>T	ENSP00000315017:p.Arg228Leu	550.0	0.0		447.0	162.0	NM_020236	A6NG03|Q4W5B8|Q6IAG4|Q96BW3|Q9H793|Q9NRL5	Missense_Mutation	SNP	ENST00000315567.8	hg19	CCDS3583.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.618|7.618	0.676134|0.676134	0.14841|0.14841	.|.	.|.	ENSG00000169288|ENSG00000169288	ENST00000315567;ENST00000538314|ENST00000504901	T|.	0.40476|.	1.03|.	5.56|5.56	0.877|0.877	0.19145|0.19145	Ribosomal protein L1, 3-layer alpha/beta-sandwich (1);Ribosomal protein L1, superfamily (1);|.	0.628304|.	0.17011|.	N|.	0.190514|.	T|T	0.47857|0.47857	0.1468|0.1468	L|L	0.57536|0.57536	1.79|1.79	0.31798|0.31798	N|N	0.628815|0.628815	B;B|.	0.18461|.	0.015;0.028|.	B;B|.	0.17433|.	0.007;0.018|.	T|T	0.53251|0.53251	-0.8465|-0.8465	10|5	0.11485|.	T|.	0.65|.	-2.0923|-2.0923	8.2309|8.2309	0.31597|0.31597	0.4168:0.0:0.5832:0.0|0.4168:0.0:0.5832:0.0	.|.	206;228|.	A0PJ79;Q9BYD6|.	.;RM01_HUMAN|.	L|L	228;206|22	ENSP00000315017:R228L|.	ENSP00000315017:R228L|.	R|V	+|+	2|1	0|0	MRPL1|MRPL1	79049456|79049456	1.000000|1.000000	0.71417|0.71417	0.945000|0.945000	0.38365|0.38365	0.988000|0.988000	0.76386|0.76386	1.255000|1.255000	0.32909|0.32909	0.062000|0.062000	0.16340|0.16340	-0.150000|-0.150000	0.13652|0.13652	CGT|GTG	.	.		0.313	MRPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252518.3	NM_020236		T	78830432	G	T	78830432	3	4	214	1	0	0	0	0	1	0	0	0	9783	1145	40	1	709	1	MRPL1	4	78830432	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	38707918	78830432	112323844	22	30817										
VEGFC	7424	hgsc.bcm.edu	37	chr4	177650707	177650707	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ttttcaagatctctgtattaTaatgtgctgcagcaaatttt	6	6	2	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr4:177650707T>A	ENST00000280193.2	-	2	756	c.341A>T	c.(340-342)tAt>tTt	p.Y114F	VEGFC_ENST00000507638.1_5'UTR	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	114					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)			biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		CTCTGTATTATAATGTGCTGC	0.378																																					p.Y114F		Atlas-SNP	.											.	VEGFC	94	.	0			c.A341T						.						133	121	125					4																	177650707		1858	4089	5947	SO:0001583	missense	7424	exon2			GTATTATAATGTG	BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"vascular endothelial growth factor-related protein"	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.341A>T	chr4.hg19:g.177650707T>A	ENSP00000280193:p.Tyr114Phe	75.0	0.0		50.0	19.0	NM_005429	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	hg19	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	T	9.920	1.211881	0.22289	.	.	ENSG00000150630	ENST00000280193	.	.	.	5.06	5.06	0.68205	.	0.137149	0.51477	D	0.000085	T	0.57917	0.2086	L	0.54323	1.7	0.40619	D	0.981748	B	0.12013	0.005	B	0.06405	0.002	T	0.56390	-0.7987	9	0.36615	T	0.2	-24.3868	15.1017	0.72284	0.0:0.0:0.0:1.0	.	114	P49767	VEGFC_HUMAN	F	114	.	ENSP00000280193:Y114F	Y	-	2	0	VEGFC	177887701	1.000000	0.71417	1.000000	0.80357	0.144000	0.21451	4.010000	0.57117	2.049000	0.60858	0.397000	0.26171	TAT	.	.		0.378	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		A	177650707	T	A	177650707	3	1	214	1	0	0	0	0	1	0	0	0	17167	1406	49	4	945	4	VEGFC	4	177650707	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	98820275	177650707	13503569	23	30818										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13692162	13692162	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ggggtctgggctgtcctgagAtccacagcggcaatgtagtt	15	9	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr5:13692162A>T	ENST00000265104.4	-	79	13910	c.13806T>A	c.(13804-13806)gaT>gaA	p.D4602E		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4602					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTGTCCTGAGATCCACAGCGG	0.502									Kartagener syndrome																												p.D4602E		Atlas-SNP	.											.	DNAH5	868	.	0			c.T13806A						.						122	111	115					5																	13692162		2203	4300	6503	SO:0001583	missense	1767	exon79	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCTGAGATCCACA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.13806T>A	chr5.hg19:g.13692162A>T	ENSP00000265104:p.Asp4602Glu	158.0	0.0		124.0	48.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.291839	0.40594	.	.	ENSG00000039139	ENST00000265104	T	0.07908	3.15	5.76	1.97	0.26223	Dynein heavy chain (1);	0.104831	0.64402	N	0.000005	T	0.04724	0.0128	N	0.26162	0.8	0.54753	D	0.999987	B	0.06786	0.001	B	0.13407	0.009	T	0.44174	-0.9345	10	0.31617	T	0.26	.	1.7257	0.02921	0.3348:0.1467:0.3938:0.1247	.	4602	Q8TE73	DYH5_HUMAN	E	4602	ENSP00000265104:D4602E	ENSP00000265104:D4602E	D	-	3	2	DNAH5	13745162	0.854000	0.29725	0.998000	0.56505	0.831000	0.47069	-0.076000	0.11412	0.082000	0.17018	-0.128000	0.14901	GAT	.	.		0.502	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13692162	A	T	13692162	3	4	214	1	0	0	0	0	1	0	0	0	4606	330	12	4	72	4	DNAH5	5	13692162	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10		13692162	167223098	24	30819										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130938979	130938979	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cttaccaaaagagaacctgaTtgccactgtatctctcatag	6	11	2	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr5:130938979T>C	ENST00000509018.1	-	3	387	c.182A>G	c.(181-183)aAt>aGt	p.N61S	RAPGEF6_ENST00000510071.1_Missense_Mutation_p.N61S|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.N61S|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.N61S|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.N111S|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.N61S|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.N61S	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	61					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		GAGAACCTGATTGCCACTGTA	0.259																																					p.N61S	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.A182G						.						78	84	82					5																	130938979		2203	4292	6495	SO:0001583	missense	51735	exon3			ACCTGATTGCCAC	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.182A>G	chr5.hg19:g.130938979T>C	ENSP00000421684:p.Asn61Ser	458.0	0.0		384.0	113.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.423872	0.43020	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000308008;ENST00000510071;ENST00000514667	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	4.67	4.67	0.58626	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.000000	0.64402	D	0.000001	T	0.63698	0.2533	M	0.77103	2.36	0.80722	D	1	B;B;D;B;B;B	0.76494	0.02;0.011;0.999;0.011;0.034;0.004	B;B;D;B;B;B	0.85130	0.016;0.009;0.997;0.027;0.035;0.004	T	0.68224	-0.5465	10	0.72032	D	0.01	.	11.9104	0.52735	0.0:0.0:0.0:1.0	.	61;61;61;111;61;61	A3KN82;B7ZML2;Q8TEU7-2;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;.;RPGF6_HUMAN	S	61;61;61;61;61;61;61;111	ENSP00000421684:N61S;ENSP00000309298:N61S;ENSP00000426081:N61S;ENSP00000296859:N61S;ENSP00000311419:N61S;ENSP00000425389:N61S;ENSP00000426948:N111S	ENSP00000426948:N111S	N	-	2	0	RAPGEF6;FNIP1	130966878	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.030000	0.70903	1.858000	0.53909	0.454000	0.30748	AAT	.	.		0.259	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		C	130938979	T	C	130938979	3	2	214	1	0	0	0	0	1	0	0	0	13063	1493	52	2	5213	2	RAPGEF6	5	130938979	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	117246817	130938979	49976281	25	30820										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140432978	140432978	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gaccccatgatgcagaaattGatcattcttgttcaggatca	8	9	4	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr5:140432978G>A	ENST00000306549.3	+	1	2000	c.1923G>A	c.(1921-1923)ttG>ttA	p.L641L		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	641	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGCAGAAATTGATCATTCTTG	0.448																																					p.L641L		Atlas-SNP	.											.	PCDHB1	148	.	0			c.G1923A						.						134	130	131					5																	140432978		2203	4300	6503	SO:0001819	synonymous_variant	29930	exon1			GAAATTGATCATT	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1923G>A	chr5.hg19:g.140432978G>A		86.0	0.0		91.0	37.0	NM_013340	Q2M257	Silent	SNP	ENST00000306549.3	hg19	CCDS4243.1																																																																																			.	.		0.448	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		A	140432978	G	A	140432978	2	1	214	1	0	0	0	0	0	0	0	1	11543	1281	45	3		3	PCDHB1	5	140432978	Silent	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	9493999	140432978	40482282	26	30821										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168727521	168727521	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gggcaggggtactcacaggcGctcagcgttgcgggggatgc	19	10	2	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr5:168727521G>T	ENST00000519560.1	-	1	612	c.193C>A	c.(193-195)Cgc>Agc	p.R65S	SLIT3_ENST00000332966.8_Missense_Mutation_p.R65S|SLIT3_ENST00000404867.3_Missense_Mutation_p.R65S|SLIT3_ENST00000521130.1_5'UTR	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	65					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACTCACAGGCGCTCAGCGTTG	0.741																																					p.R65S	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C193A						.						5	6	6					5																	168727521		1834	3651	5485	SO:0001583	missense	6586	exon1			ACAGGCGCTCAGC	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.193C>A	chr5.hg19:g.168727521G>T	ENSP00000430333:p.Arg65Ser	120.0	0.0		90.0	35.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	hg19	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.518591	0.64634	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.22743	1.94;1.94;1.94	3.85	3.85	0.44370	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.46758	D	0.000270	T	0.28665	0.0710	N	0.17764	0.52	0.44677	D	0.997661	D;D	0.89917	0.992;1.0	D;D	0.81914	0.969;0.995	T	0.06643	-1.0815	10	0.66056	D	0.02	.	11.2153	0.48823	0.0:0.0:1.0:0.0	.	65;65	O75094-2;O75094	.;SLIT3_HUMAN	S	65	ENSP00000430333:R65S;ENSP00000332164:R65S;ENSP00000384890:R65S	ENSP00000332164:R65S	R	-	1	0	SLIT3	168660099	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.109000	0.41863	1.995000	0.58328	0.555000	0.69702	CGC	.	.		0.741	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		T	168727521	G	T	168727521	3	4	214	1	0	0	0	0	1	0	0	0	14756	1087	38	1	4522	1	SLIT3	5	168727521	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	28294543	168727521	12187739	27	30822										
HK3	3101	hgsc.bcm.edu	37	chr5	176318414	176318414	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ccatgtggggtggaccccacGtatgtaggcagcatccggac	14	12	0	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr5:176318414G>A	ENST00000292432.5	-	3	325	c.234C>T	c.(232-234)taC>taT	p.Y78Y		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	78	Hexokinase type-1 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGGACCCCACGTATGTAGGCA	0.602																																					p.Y78Y		Atlas-SNP	.											.	HK3	210	.	0			c.C234T						.						116	117	117					5																	176318414		2203	4300	6503	SO:0001819	synonymous_variant	3101	exon3			CCCCACGTATGTA		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.234C>T	chr5.hg19:g.176318414G>A		51.0	0.0		32.0	16.0	NM_002115	Q8N1E7	Silent	SNP	ENST00000292432.5	hg19	CCDS4407.1																																																																																			.	.		0.602	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			A	176318414	G	A	176318414	2	1	214	1	0	0	0	0	0	0	0	1	7201	1140	40	1		1	HK3	5	176318414	Silent	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	7590893	176318414	4596846	28	30823										
DOK3	79930	hgsc.bcm.edu	37	chr5	176930063	176930063	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ggttcaggatgtgccaagggTgtgtgcagctgaggtggagt	19	5	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr5:176930063T>A	ENST00000357198.4	-	0	1729				DOK3_ENST00000377112.4_Missense_Mutation_p.T224S|RP11-1334A24.6_ENST00000506025.1_RNA|DOK3_ENST00000312943.6_Missense_Mutation_p.T326S	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3						Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|lung(7)	13	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			gtgccaagggtgtgtgcagct	0.602																																					p.T326S		Atlas-SNP	.											.	DOK3	41	.	0			c.A976T						.						11	12	11					5																	176930063		692	1591	2283	SO:0001628	intergenic_variant	79930	exon6			CAAGGGTGTGTGC	AK026223	CCDS4426.1, CCDS47349.1, CCDS47350.1	5q35	2008-02-05			ENSG00000146094	ENSG00000146094			24583	protein-coding gene	gene with protein product		611435				10733577, 12595900	Standard	NM_024872		Approved	FLJ22570	uc003mhk.3	Q7L591	OTTHUMG00000130850		chr5.hg19:g.176930063T>A		62.0	0.0		49.0	22.0	NM_001144875	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	Missense_Mutation	SNP	ENST00000357198.4	hg19	CCDS4426.1	.	.	.	.	.	.	.	.	.	.	T	12.65	2.001866	0.35320	.	.	ENSG00000146094	ENST00000312943;ENST00000377112	T;T	0.51071	0.77;0.72	1.7	-1.14	0.09741	.	.	.	.	.	T	0.21921	0.0528	N	0.08118	0	0.09310	N	0.999999	B;B;B	0.14805	0.006;0.001;0.011	B;B;B	0.09377	0.002;0.001;0.004	T	0.17471	-1.0368	9	0.87932	D	0	.	1.6896	0.02849	0.2866:0.193:0.0:0.5203	.	224;326;212	E9PAT0;Q7L591-3;Q7L591-2	.;.;.	S	326;224	ENSP00000325174:T326S;ENSP00000366316:T224S	ENSP00000325174:T326S	T	-	1	0	DOK3	176862669	0.001000	0.12720	0.001000	0.08648	0.015000	0.08874	-0.207000	0.09384	-0.273000	0.09246	0.260000	0.18958	ACC	.	.		0.602	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872		A	176930063	T	A	176930063	1	1	214	0	1	0	0	0	0	0	0	0	4700	1696	59	4		4	DOK3	5	176930063	IGR	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	611649	176930063	3985197	29	30824										
BTN3A1	11119	hgsc.bcm.edu	37	chr6	26413486	26413486	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	agcgtgccaaggagccccagGatctgccagacaaccctgag	12	14	1	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr6:26413486G>T	ENST00000289361.6	+	10	1476	c.1108G>T	c.(1108-1110)Gat>Tat	p.D370Y	BTN3A1_ENST00000414912.2_Missense_Mutation_p.D318Y	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	370	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						GGAGCCCCAGGATCTGCCAGA	0.517																																					p.D370Y		Atlas-SNP	.											.	BTN3A1	80	.	0			c.G1108T						.						142	156	151					6																	26413486		2203	4300	6503	SO:0001583	missense	11119	exon10			CCCCAGGATCTGC	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.1108G>T	chr6.hg19:g.26413486G>T	ENSP00000289361:p.Asp370Tyr	204.0	0.0		288.0	52.0	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Missense_Mutation	SNP	ENST00000289361.6	hg19	CCDS4608.1	.	.	.	.	.	.	.	.	.	.	.	12.40	1.927284	0.34002	.	.	ENSG00000026950	ENST00000289361;ENST00000414912	T;T	0.11495	2.77;2.77	2.96	-3.92	0.04155	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.04182	0.0116	L	0.51914	1.62	0.09310	N	1	P;P	0.52577	0.924;0.954	P;P	0.48952	0.478;0.596	T	0.10520	-1.0626	9	0.59425	D	0.04	.	1.8679	0.03202	0.5231:0.1471:0.1815:0.1482	.	318;370	E9PGB4;O00481	.;BT3A1_HUMAN	Y	370;318	ENSP00000289361:D370Y;ENSP00000406667:D318Y	ENSP00000289361:D370Y	D	+	1	0	BTN3A1	26521465	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.719000	0.01873	-0.938000	0.03714	0.609000	0.83330	GAT	.	.		0.517	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3			T	26413486	G	T	26413486	3	4	214	1	0	0	0	0	1	0	0	0	1564	1174	41	3	1310	3	BTN3A1	6	26413486	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10		26413486	144701581	30	30825										
HLA-A	3105	hgsc.bcm.edu	37	chr6	29910588	29910588	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gtcccggcccggccgcggggAgccccgcttcatcgccgtgg	16	18	1	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr6:29910588A>T	ENST00000396634.1	+	4	469	c.128A>T	c.(127-129)gAg>gTg	p.E43V	HLA-A_ENST00000376809.5_Missense_Mutation_p.E43V|HLA-A_ENST00000376802.2_Missense_Mutation_p.E43V|HLA-A_ENST00000376806.5_Missense_Mutation_p.E43V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	43	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.R41fs*31(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GGCCGCGGGGAGCCCCGCTTC	0.701									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.E43V		Atlas-SNP	.											.	HLA-A	89	.	1	Deletion - Frameshift(1)	ovary(1)	c.A128T						.						24	22	23					6																	29910588		2198	4295	6493	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCGGGGAGCCCCG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.128A>T	chr6.hg19:g.29910588A>T	ENSP00000379873:p.Glu43Val	129.0	0.0		195.0	63.0	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	hg19	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	14.89	2.670518	0.47781	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00009	9.48;9.48;9.48;9.48	3.57	0.876	0.19138	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	2.237780	0.03383	N	0.200671	T	0.00210	0.0006	H	0.96398	3.815	0.09310	N	1	D;B;D;D;D	0.76494	0.999;0.172;0.995;0.959;0.995	D;B;D;D;D	0.87578	0.998;0.362;0.995;0.986;0.995	T	0.48725	-0.9010	10	0.87932	D	0	.	7.8239	0.29303	0.5813:0.4187:0.0:0.0	.	43;43;43;43;43	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	V	43	ENSP00000379873:E43V;ENSP00000366002:E43V;ENSP00000366005:E43V;ENSP00000365998:E43V	ENSP00000348012:E43V	E	+	2	0	HLA-A	30018567	0.002000	0.14202	0.000000	0.03702	0.426000	0.31534	0.278000	0.18753	0.084000	0.17077	-0.689000	0.03729	GAG	.	.		0.701	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		T	29910588	A	T	29910588	3	4	214	1	0	0	0	0	1	0	0	0	7204	304	11	4	134	4	HLA-A	6	29910588	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	3497102	29910588	141204479	31	30826										
CCHCR1	54535	hgsc.bcm.edu	37	chr6	31122472	31122472	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tctgctgcagcgaggtctccCgcaggagccggacctcctcc	12	17	2	0	rs576214578	byFrequency	TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr6:31122472C>A	ENST00000376266.5	-	4	457	c.335G>T	c.(334-336)cGg>cTg	p.R112L	CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000396263.2_Missense_Mutation_p.R112L|CCHCR1_ENST00000451521.2_Missense_Mutation_p.R165L|CCHCR1_ENST00000396268.3_Missense_Mutation_p.R201L	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	112					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R112Q(1)|p.R201Q(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CGAGGTCTCCCGCAGGAGCCG	0.692																																					p.R201L		Atlas-SNP	.											CCHCR1_ENST00000396268,NS,carcinoma,0,3	CCHCR1	68	.	2	Substitution - Missense(2)	kidney(2)	c.G602T						.						41	50	47					6																	31122472		1507	2709	4216	SO:0001583	missense	54535	exon4			GTCTCCCGCAGGA	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"chromosome 6 open reading frame 18"	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.335G>T	chr6.hg19:g.31122472C>A	ENSP00000365442:p.Arg112Leu	55.0	0.0		97.0	72.0	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	hg19	CCDS4695.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.023133	0.54683	.	.	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521;ENST00000448141;ENST00000508683;ENST00000448162;ENST00000513222;ENST00000503420;ENST00000515274;ENST00000507751;ENST00000455279;ENST00000412245;ENST00000503934;ENST00000426967;ENST00000502557;ENST00000507829	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.05199	3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48	4.8	3.03	0.35002	.	0.325746	0.22679	N	0.056980	T	0.09291	0.0229	M	0.70595	2.14	0.28550	N	0.911641	D;D;D;D;D	0.76494	0.998;0.998;0.998;0.999;0.998	D;D;D;D;D	0.75484	0.97;0.959;0.959;0.986;0.963	T	0.08249	-1.0731	10	0.42905	T	0.14	-22.6889	6.9406	0.24490	0.0:0.7948:0.0:0.2052	.	112;112;112;165;201	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	L	201;112;112;112;165;76;76;112;86;76;112;112;112;138;112;210;112;112	ENSP00000379566:R201L;ENSP00000365442:R112L;ENSP00000379561:R112L;ENSP00000401039:R165L;ENSP00000414323:R76L;ENSP00000421393:R76L;ENSP00000390027:R112L;ENSP00000425682:R86L;ENSP00000421992:R76L;ENSP00000420941:R112L;ENSP00000398715:R112L;ENSP00000425595:R112L;ENSP00000402432:R210L;ENSP00000425377:R112L;ENSP00000420911:R112L	ENSP00000365442:R112L	R	-	2	0	CCHCR1	31230451	0.977000	0.34250	0.949000	0.38748	0.511000	0.34104	0.523000	0.22925	0.646000	0.30693	-0.158000	0.13435	CGG	.	.		0.692	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052		A	31122472	C	A	31122472	3	1	214	1	0	0	0	0	1	0	0	0	2879	652	23	1	2073	1	CCHCR1	6	31122472	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	1211884	31122472	139992595	32	30827										
LHFPL5	222662	hgsc.bcm.edu	37	chr6	35773575	35773575	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctccgtactggtcatggcccTcttcatccagccctactgga	8	16	3	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr6:35773575T>A	ENST00000373853.1	+	1	506	c.128T>A	c.(127-129)cTc>cAc	p.L43H	LHFPL5_ENST00000360215.1_Missense_Mutation_p.L43H			Q8TAF8	TMHS_HUMAN	lipoma HMGIC fusion partner-like 5	43					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transport (GO:0006811)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)				endometrium(4)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|urinary_tract(1)	20						GTCATGGCCCTCTTCATCCAG	0.592																																					p.L43H		Atlas-SNP	.											.	LHFPL5	44	.	0			c.T128A						.						238	206	216					6																	35773575		2203	4300	6503	SO:0001583	missense	222662	exon1			TGGCCCTCTTCAT	BC028630	CCDS4812.1	6p21.31	2014-01-28				ENSG00000197753			21253	protein-coding gene	gene with protein product		609427	"deafness, autosomal recessive 67"	DFNB67		16459341	Standard	NM_182548		Approved	MGC33835, dJ510O8.8, Tmhs	uc003olg.1	Q8TAF8		ENST00000373853.1:c.128T>A	chr6.hg19:g.35773575T>A	ENSP00000362960:p.Leu43His	128.0	0.0		149.0	55.0	NM_182548	B3KX66	Missense_Mutation	SNP	ENST00000373853.1	hg19	CCDS4812.1	.	.	.	.	.	.	.	.	.	.	t	24.4	4.531413	0.85706	.	.	ENSG00000197753	ENST00000373853;ENST00000360215	T;T	0.72615	-0.67;-0.67	5.57	5.57	0.84162	.	0.192828	0.45606	D	0.000357	T	0.57902	0.2085	N	0.22421	0.69	0.26232	N	0.979002	D	0.63880	0.993	P	0.60173	0.87	T	0.59198	-0.7499	10	0.87932	D	0	-27.9671	8.4085	0.32629	0.0:0.116:0.0:0.884	.	43	Q8TAF8	TMHS_HUMAN	H	43	ENSP00000362960:L43H;ENSP00000353346:L43H	ENSP00000353346:L43H	L	+	2	0	LHFPL5	35881553	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	1.617000	0.36943	2.133000	0.65898	0.439000	0.28862	CTC	.	.		0.592	LHFPL5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040323.1	NM_182548		A	35773575	T	A	35773575	3	1	214	1	0	0	0	0	1	0	0	0	8777	1551	54	4	130	4	LHFPL5	6	35773575	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	4651103	35773575	135341492	33	30828										
DAAM2	23500	hgsc.bcm.edu	37	chr6	39851783	39851783	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	atgagattgatgacatgcagGtatttcggatcctggaccta	11	7	0	3	rs376832339		TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr6:39851783G>C	ENST00000398904.2	+	15	2073	c.1891G>C	c.(1891-1893)Gta>Cta	p.V631L	RP11-61I13.3_ENST00000607675.1_RNA|DAAM2_ENST00000538976.1_Missense_Mutation_p.V631L|DAAM2_ENST00000274867.4_Missense_Mutation_p.V631L|RP11-61I13.3_ENST00000607215.1_RNA			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	631	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					TGACATGCAGGTATTTCGGAT	0.498																																					p.V631L		Atlas-SNP	.											.	DAAM2	101	.	0			c.G1891C						.						106	101	103					6																	39851783		1937	4133	6070	SO:0001583	missense	23500	exon15			ATGCAGGTATTTC	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.1891G>C	chr6.hg19:g.39851783G>C	ENSP00000381876:p.Val631Leu	58.0	0.0		137.0	19.0	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.629634	0.67015	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.16743	2.32;2.32;2.32	5.93	3.22	0.36961	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.188417	0.45126	D	0.000385	T	0.12008	0.0292	L	0.52011	1.625	0.80722	D	1	B;P	0.49185	0.026;0.92	B;P	0.54889	0.032;0.763	T	0.07328	-1.0778	10	0.12103	T	0.63	.	11.0471	0.47865	0.2011:0.0:0.7989:0.0	.	631;631	G5EA45;Q86T65	.;DAAM2_HUMAN	L	631	ENSP00000274867:V631L;ENSP00000381876:V631L;ENSP00000437808:V631L	ENSP00000274867:V631L	V	+	1	0	DAAM2	39959761	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	5.729000	0.68538	0.423000	0.26033	0.561000	0.74099	GTA	.	.		0.498	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			C	39851783	G	C	39851783	3	2	214	1	0	0	0	0	1	0	0	0	4218	1261	44	4	1945	4	DAAM2	6	39851783	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	4078208	39851783	131263284	34	30829										
DLK2	65989	hgsc.bcm.edu	37	chr6	43419007	43419007	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	actgcccgccattgcggcatGgggagctgtggtaggggtga	18	9	0	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr6:43419007G>A	ENST00000357338.3	-	6	1122	c.422C>T	c.(421-423)cCa>cTa	p.P141L	DLK2_ENST00000372488.3_Missense_Mutation_p.P141L|DLK2_ENST00000372485.1_Missense_Mutation_p.P135L|DLK2_ENST00000414245.1_Missense_Mutation_p.P135L	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	141	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			ATTGCGGCATGGGGAGCTGTG	0.587																																					p.P141L		Atlas-SNP	.											.	DLK2	22	.	0			c.C422T						.						46	33	37					6																	43419007		2203	4300	6503	SO:0001583	missense	65989	exon6			CGGCATGGGGAGC	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"EGF-like-domain, multiple 9"	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.422C>T	chr6.hg19:g.43419007G>A	ENSP00000349893:p.Pro141Leu	99.0	0.0		181.0	53.0	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Missense_Mutation	SNP	ENST00000357338.3	hg19	CCDS4897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.8|21.8	4.201332|4.201332	0.79015|0.79015	.|.	.|.	ENSG00000171462|ENSG00000171462	ENST00000430324|ENST00000372485;ENST00000372488;ENST00000357338;ENST00000414245	.|D;D;D;D	.|0.96104	.|-3.91;-3.91;-3.91;-3.91	4.51|4.51	4.51|4.51	0.55191|0.55191	.|Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97420|0.97420	0.9156|0.9156	M|M	0.79614|0.79614	2.46|2.46	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.83275	.|0.996	D|D	0.98016|0.98016	1.0368|1.0368	5|10	.|0.87932	.|D	.|0	.|.	17.7506|17.7506	0.88432|0.88432	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|141	.|Q6UY11	.|DLK2_HUMAN	Y|L	47|135;141;141;135	.|ENSP00000361563:P135L;ENSP00000361566:P141L;ENSP00000349893:P141L;ENSP00000398906:P135L	.|ENSP00000349893:P141L	H|P	-|-	1|2	0|0	DLK2|DLK2	43526985|43526985	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.665000|0.665000	0.39181|0.39181	7.209000|7.209000	0.77916|0.77916	2.507000|2.507000	0.84556|0.84556	0.455000|0.455000	0.32223|0.32223	CAT|CCA	.	.		0.587	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932		A	43419007	G	A	43419007	3	1	214	1	0	0	0	0	1	0	0	0	4567	1348	47	3	733	3	DLK2	6	43419007	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	3567224	43419007	127696060	35	30830										
YIPF3	25844	hgsc.bcm.edu	37	chr6	43480851	43480851	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ggtgatctgggcgttgcacaGgtaggcaaggaagtaaatga	16	5	1	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr6:43480851G>A	ENST00000372422.2	-	6	804	c.622C>T	c.(622-624)Ctg>Ttg	p.L208L	LRRC73_ENST00000372441.1_5'Flank|YIPF3_ENST00000506469.1_Silent_p.L214L	NM_015388.3	NP_056203.2	Q9GZM5	YIPF3_HUMAN	Yip1 domain family, member 3	208					cell differentiation (GO:0030154)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			GCGTTGCACAGGTAGGCAAGG	0.567																																					p.L208L		Atlas-SNP	.											.	YIPF3	20	.	0			c.C622T						.						135	135	135					6																	43480851		2203	4300	6503	SO:0001819	synonymous_variant	25844	exon6			TGCACAGGTAGGC	AK000946	CCDS4899.1	6p21.1	2009-10-06	2005-07-04	2005-07-04	ENSG00000137207	ENSG00000137207		"Yip1 domain family"	21023	protein-coding gene	gene with protein product		609775	"chromosome 6 open reading frame 109"	C6orf109			Standard	NM_015388		Approved	DKFZp566C243, KLIP1, dJ337H4.3, FinGER3	uc003ovl.2	Q9GZM5	OTTHUMG00000014738	ENST00000372422.2:c.622C>T	chr6.hg19:g.43480851G>A		83.0	0.0		158.0	34.0	NM_015388	Q5JTD2|Q6FI85|Q8NI57|Q9NWE3|Q9Y3U9	Silent	SNP	ENST00000372422.2	hg19	CCDS4899.1																																																																																			.	.		0.567	YIPF3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040639.2	NM_015388		A	43480851	G	A	43480851	2	1	214	1	0	0	0	0	0	0	0	1	17494	991	35	3		3	YIPF3	6	43480851	Silent	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	61844	43480851	127634216	36	30831										
HCRTR2	3062	hgsc.bcm.edu	37	chr6	55145187	55145187	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gcctggtttaccttttcacaCtggcttgtatatgccaatag	8	10	1	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr6:55145187C>G	ENST00000370862.3	+	6	1386	c.1050C>G	c.(1048-1050)caC>caG	p.H350Q		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	350					circadian sleep/wake cycle process (GO:0022410)|feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|orexin receptor activity (GO:0016499)			breast(3)|endometrium(2)|kidney(1)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	46	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			CCTTTTCACACTGGCTTGTAT	0.388																																					p.H350Q		Atlas-SNP	.											.	HCRTR2	112	.	0			c.C1050G						.						206	197	200					6																	55145187		2203	4300	6503	SO:0001583	missense	3062	exon6			TTCACACTGGCTT	AF041245	CCDS4956.1	6p12.1	2012-09-20			ENSG00000137252	ENSG00000137252		"GPCR / Class A : Hypocretin (orexin) receptors"	4849	protein-coding gene	gene with protein product		602393				9491897	Standard	NM_001526		Approved	OX2R	uc003pcl.3	O43614	OTTHUMG00000016150	ENST00000370862.3:c.1050C>G	chr6.hg19:g.55145187C>G	ENSP00000359899:p.His350Gln	119.0	0.0		186.0	44.0	NM_001526	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	hg19	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.484514	0.63962	.	.	ENSG00000137252	ENST00000370862	T	0.36878	1.23	5.62	1.77	0.24775	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.38268	0.1034	M	0.67569	2.06	0.54753	D	0.999983	D	0.56035	0.974	D	0.67548	0.952	T	0.17561	-1.0365	10	0.40728	T	0.16	.	8.7828	0.34802	0.0:0.6341:0.0:0.3659	.	350	O43614	OX2R_HUMAN	Q	350	ENSP00000359899:H350Q	ENSP00000359899:H350Q	H	+	3	2	HCRTR2	55253146	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	1.161000	0.31773	0.039000	0.15632	0.585000	0.79938	CAC	.	.		0.388	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			G	55145187	C	G	55145187	3	3	214	1	0	0	0	0	1	0	0	0	7011	564	20	4	1072	4	HCRTR2	6	55145187	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	11664336	55145187	115969880	37	30832										
NPSR1	387129	hgsc.bcm.edu	37	chr7	34867102	34867102	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tcatatttgggaagaggacaCtgtccaacggtgaagtgcag	13	7	1	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr7:34867102C>G	ENST00000360581.1	+	5	696	c.568C>G	c.(568-570)Ctg>Gtg	p.L190V	NPSR1_ENST00000359791.1_Missense_Mutation_p.L190V|NPSR1_ENST00000381539.3_Missense_Mutation_p.L190V|NPSR1_ENST00000531252.1_Missense_Mutation_p.L179V|NPSR1_ENST00000381542.1_Missense_Mutation_p.L124V	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	190						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	GAAGAGGACACTGTCCAACGG	0.542																																					p.L190V		Atlas-SNP	.											.	NPSR1	134	.	0			c.C568G						.						149	128	135					7																	34867102		2203	4300	6503	SO:0001583	missense	387129	exon5			AGGACACTGTCCA	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"GPCR / Class A : Neuropeptide receptors : S"	23631	protein-coding gene	gene with protein product		608595	"G protein-coupled receptor 154"	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.568C>G	chr7.hg19:g.34867102C>G	ENSP00000353788:p.Leu190Val	120.0	0.0		108.0	61.0	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	hg19	CCDS5444.1	.	.	.	.	.	.	.	.	.	.	C	3.992	-0.004284	0.07773	.	.	ENSG00000187258	ENST00000360581;ENST00000381542;ENST00000359791;ENST00000531252;ENST00000381539;ENST00000334481	T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19	5.44	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.36026	0.0952	N	0.17248	0.465	0.45427	D	0.998401	D;D;D;B;D;B	0.76494	0.999;0.999;0.998;0.207;0.999;0.246	D;D;P;B;D;B	0.69307	0.944;0.963;0.875;0.219;0.96;0.326	T	0.14587	-1.0467	9	0.02654	T	1	-30.3633	13.0884	0.59154	0.0:0.9231:0.0:0.0769	.	124;179;124;190;190;190	B7ZMA2;Q6W5P4-5;Q6W5P4-2;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;.;.;NPSR1_HUMAN	V	190;124;190;179;190;53	ENSP00000353788:L190V;ENSP00000370953:L124V;ENSP00000352839:L190V;ENSP00000433258:L179V;ENSP00000370950:L190V	ENSP00000334093:L53V	L	+	1	2	NPSR1	34833627	0.997000	0.39634	0.224000	0.23877	0.485000	0.33311	3.919000	0.56439	1.298000	0.44778	0.655000	0.94253	CTG	.	.		0.542	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173		G	34867102	C	G	34867102	3	3	214	1	0	0	0	0	1	0	0	0	10609	564	20	4	586	4	NPSR1	7	34867102	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10		34867102	124271561	38	30833										
TNS3	64759	hgsc.bcm.edu	37	chr7	47440024	47440024	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ggcgtggcagagaagactaaTtcaaccttcccatagtcagg	11	10	2	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr7:47440024T>C	ENST00000398879.1	-	15	1251	c.885A>G	c.(883-885)gaA>gaG	p.E295E	TNS3_ENST00000311160.9_Silent_p.E295E|TNS3_ENST00000355730.3_Intron			Q68CZ2	TENS3_HUMAN	tensin 3	295	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						AGAAGACTAATTCAACCTTCC	0.438																																					p.E295E		Atlas-SNP	.											.	TNS3	140	.	0			c.A885G						.						76	75	76					7																	47440024		1985	4155	6140	SO:0001819	synonymous_variant	64759	exon15			GACTAATTCAACC	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.885A>G	chr7.hg19:g.47440024T>C		230.0	0.0		216.0	56.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Silent	SNP	ENST00000398879.1	hg19	CCDS5506.2																																																																																			.	.		0.438	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		C	47440024	T	C	47440024	2	2	214	1	0	0	0	0	0	0	0	1	16359	1490	52	2		2	TNS3	7	47440024	Silent	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	12572922	47440024	111698639	39	30834										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48413971	48413971	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tttcgacaaccgcctttggaCaaggggtattttttattaca	8	8	0	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr7:48413971C>A	ENST00000435803.1	+	34	11185	c.11161C>A	c.(11161-11163)Caa>Aaa	p.Q3721K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3721					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CGCCTTTGGACAAGGGGTATT	0.408																																					p.Q3721K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C11161A						.						84	78	80					7																	48413971		1893	4113	6006	SO:0001583	missense	154664	exon34			TTTGGACAAGGGG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11161C>A	chr7.hg19:g.48413971C>A	ENSP00000411096:p.Gln3721Lys	121.0	0.0		137.0	30.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.699398	0.68501	.	.	ENSG00000179869	ENST00000435803	D	0.81499	-1.5	5.51	5.51	0.81932	.	0.000000	0.48767	D	0.000170	D	0.86772	0.6013	L	0.55481	1.735	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.69824	0.922;0.966	D	0.84576	0.0658	10	0.33940	T	0.23	.	16.9365	0.86204	0.0:1.0:0.0:0.0	.	1423;3721	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	K	3721	ENSP00000411096:Q3721K	ENSP00000411096:Q3721K	Q	+	1	0	ABCA13	48384517	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	4.841000	0.62824	2.736000	0.93811	0.655000	0.94253	CAA	.	.		0.408	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48413971	C	A	48413971	3	1	214	1	0	0	0	0	1	0	0	0	31	479	17	3	11124	3	ABCA13	7	48413971	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	973947	48413971	110724692	40	30835										
CHCHD3	54927	hgsc.bcm.edu	37	chr7	132659975	132659975	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cctcgctacatatcctctccCgaaggatggctctggttaac	8	14	2	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr7:132659975C>T	ENST00000262570.5	-	4	467	c.323G>A	c.(322-324)cGg>cAg	p.R108Q	CHCHD3_ENST00000542753.1_Missense_Mutation_p.R108Q|CHCHD3_ENST00000476546.1_5'UTR|CHCHD3_ENST00000448878.1_Missense_Mutation_p.R108Q	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	108					inner mitochondrial membrane organization (GO:0007007)|mitochondrial fusion (GO:0008053)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein complex scaffold (GO:0032947)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	7						TATCCTCTCCCGAAGGATGGC	0.453																																					p.R108Q		Atlas-SNP	.											.	CHCHD3	21	.	0			c.G323A						.						91	83	86					7																	132659975		2203	4300	6503	SO:0001583	missense	54927	exon4			CTCTCCCGAAGGA	BC011596	CCDS5828.1	7q33	2012-10-02			ENSG00000106554	ENSG00000106554		"Coiled-coil-helix-coiled-coil-helix domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21906	protein-coding gene	gene with protein product	"mitochondrial inner membrane organizing system 3", "protein phosphatase 1, regulatory subunit 22"	613748				22252321, 23019327, 21081504, 17624330	Standard	NM_017812		Approved	FLJ20420, MINOS3, PPP1R22	uc003vre.3	Q9NX63	OTTHUMG00000155231	ENST00000262570.5:c.323G>A	chr7.hg19:g.132659975C>T	ENSP00000262570:p.Arg108Gln	85.0	0.0		101.0	11.0	NM_017812		Missense_Mutation	SNP	ENST00000262570.5	hg19	CCDS5828.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.471212	0.43942	.	.	ENSG00000106554	ENST00000262570;ENST00000448878;ENST00000542753	T;T;T	0.55760	0.5;0.5;0.5	5.77	-2.07	0.07276	.	0.307287	0.34676	N	0.003777	T	0.39963	0.1098	M	0.78637	2.42	0.19775	N	0.999951	P;B;B	0.35456	0.502;0.017;0.061	B;B;B	0.29267	0.1;0.008;0.036	T	0.29610	-1.0006	10	0.21014	T	0.42	1.7276	4.7098	0.12867	0.2211:0.4754:0.0:0.3036	.	108;108;108	G3V1K1;C9JRZ6;Q9NX63	.;.;CHCH3_HUMAN	Q	108	ENSP00000262570:R108Q;ENSP00000389297:R108Q;ENSP00000440267:R108Q	ENSP00000262570:R108Q	R	-	2	0	CHCHD3	132310515	0.474000	0.25886	0.008000	0.14137	0.745000	0.42441	1.238000	0.32707	-0.369000	0.08028	-0.140000	0.14226	CGG	.	.		0.453	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812		T	132659975	C	T	132659975	3	4	214	1	0	0	0	0	1	0	0	0	3319	652	23	1	380	1	CHCHD3	7	132659975	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	84246004	132659975	26478688	41	30836										
TEX15	56154	hgsc.bcm.edu	37	chr8	30706087	30706087	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gaaaaattaccttggtccttAcattgccctgccatggtaac	7	11	0	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr8:30706087A>G	ENST00000256246.2	-	1	521	c.447T>C	c.(445-447)tgT>tgC	p.C149C	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	149					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.C149*(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		CTTGGTCCTTACATTGCCCTG	0.433																																					p.C149C		Atlas-SNP	.											TEX15,NS,carcinoma,0,1	TEX15	350	.	1	Substitution - Nonsense(1)	lung(1)	c.T447C						.						102	98	100					8																	30706087		2203	4300	6503	SO:0001819	synonymous_variant	56154	exon1			GTCCTTACATTGC	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.447T>C	chr8.hg19:g.30706087A>G		113.0	0.0		56.0	28.0	NM_031271		Silent	SNP	ENST00000256246.2	hg19	CCDS6080.1																																																																																			.	.		0.433	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			G	30706087	A	G	30706087	2	3	214	1	0	0	0	0	0	0	0	1	15794	389	14	2		2	TEX15	8	30706087	Silent	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10		30706087	115657935	42	30837										
POTEA	340441	hgsc.bcm.edu	37	chr8	43173614	43173614	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tcaaggttgaagaagaaatgCagaagcatggaagtaataat	11	3	1	4	rs547056757	byFrequency	TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr8:43173614C>T	ENST00000522175.2	+	0	900							Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A											breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(27)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						AGAAGAAATGCAGAAGCATGG	0.353													c|||	11	0.00219649	0	0	5008	,	,		18067	0		0	False		,,,				2504	0.0112				p.Q346X		Atlas-SNP	.											.	POTEA	87	.	0			c.C1036T						.						142	136	138					8																	43173614		2198	4297	6495			340441	exon9			GAAATGCAGAAGC	AY462869		8p11.1	2013-01-11	2008-11-26	2008-11-26	ENSG00000188877	ENSG00000188877		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33893	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 3"	608915	"ANKRD26-like family A, member 1"	A26A1			Standard	NM_001002920		Approved	POTE8, POTE-8, CT104.3	uc003xpz.1	Q6S8J7	OTTHUMG00000164111		chr8.hg19:g.43173614C>T		268.0	1.0		129.0	94.0	NM_001005365	A6ND17|A6ND71|Q6S8J6	Nonsense_Mutation	SNP	ENST00000522175.2	hg19																																																																																				.	.		0.353	POTEA-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000383492.1	NM_001002920		T	43173614	C	T	43173614	1	4	214	0	1	0	0	0	0	0	0	0	12270	711	25	3		3	POTEA	8	43173614	RNA	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	12467527	43173614	103190408	43	30838										
TPD52	7163	hgsc.bcm.edu	37	chr8	80954863	80954863	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctctctacttgcctttaagtTttcgaccttttcttcaaatg	4	11	3	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr8:80954863T>A	ENST00000379097.3	-	5	909	c.547A>T	c.(547-549)Aac>Tac	p.N183Y	TPD52_ENST00000379096.5_Missense_Mutation_p.N143Y|TPD52_ENST00000448733.2_Missense_Mutation_p.N197Y|TPD52_ENST00000518937.1_Missense_Mutation_p.N166Y|TPD52_ENST00000523395.1_5'UTR|TPD52_ENST00000520527.1_Missense_Mutation_p.N206Y|TPD52_ENST00000519303.2_Missense_Mutation_p.N19Y|TPD52_ENST00000517427.1_Missense_Mutation_p.N192Y|TPD52_ENST00000537855.1_Missense_Mutation_p.N183Y	NM_001025252.1	NP_001020423.1	P55327	TPD52_HUMAN	tumor protein D52	183					anatomical structure morphogenesis (GO:0009653)|B cell differentiation (GO:0030183)|positive regulation of cell proliferation (GO:0008284)|secretion (GO:0046903)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)			GCCTTTAAGTTTTCGACCTTT	0.308																																					p.N183Y		Atlas-SNP	.											.	TPD52	40	.	0			c.A547T						.						119	123	121					8																	80954863		2202	4299	6501	SO:0001583	missense	7163	exon5			TTAAGTTTTCGAC	U18914	CCDS34912.1, CCDS47879.1, CCDS55249.1, CCDS75757.1, CCDS75758.1, CCDS75759.1	8q21.13	2014-06-24			ENSG00000076554	ENSG00000076554			12005	protein-coding gene	gene with protein product		604068				7796418	Standard	NM_001287144		Approved	D52, hD52, N8L	uc003ybr.1	P55327	OTTHUMG00000164565	ENST00000379097.3:c.547A>T	chr8.hg19:g.80954863T>A	ENSP00000368391:p.Asn183Tyr	52.0	0.0		107.0	20.0	NM_001025252	B7Z414|C9J502|D0UFD1|D0UFD2|D0UFD3|D0UFD4|D0UFD5|E5RKB4|Q13056|Q53EK8|Q6FGP3|Q6FGS3|Q86YZ2|Q9UCX8	Missense_Mutation	SNP	ENST00000379097.3	hg19	CCDS34912.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.246044	0.80024	.	.	ENSG00000076554	ENST00000537855;ENST00000379096;ENST00000518937;ENST00000520527;ENST00000517427;ENST00000448733;ENST00000379097;ENST00000425513;ENST00000519303	T;T;T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88	5.11	5.11	0.69529	.	0.260772	0.41938	D	0.000786	T	0.47619	0.1455	M	0.68952	2.095	0.80722	D	1	D;D;D	0.67145	0.983;0.958;0.996	P;P;D	0.65874	0.862;0.905;0.939	T	0.49688	-0.8913	10	0.87932	D	0	-32.0978	14.5302	0.67920	0.0:0.0:0.0:1.0	.	143;166;183	P55327-2;E5RKB4;P55327	.;.;TPD52_HUMAN	Y	183;143;166;206;192;197;183;143;19	ENSP00000438113:N183Y;ENSP00000368390:N143Y;ENSP00000429915:N166Y;ENSP00000429309:N206Y;ENSP00000429351:N192Y;ENSP00000410222:N197Y;ENSP00000368391:N183Y;ENSP00000428951:N19Y	ENSP00000368390:N143Y	N	-	1	0	TPD52	81117418	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.448000	0.60027	2.265000	0.75225	0.482000	0.46254	AAC	.	.		0.308	TPD52-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379539.2	NM_005079		A	80954863	T	A	80954863	3	1	214	1	0	0	0	0	1	0	0	0	16412	1841	64	4	135	4	TPD52	8	80954863	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	37781249	80954863	65409159	44	30839										
NECAB1	64168	hgsc.bcm.edu	37	chr8	91836943	91836943	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctctttgttcttgccatttcAgatgatggaaaattatcctt	6	8	3	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr8:91836943A>T	ENST00000417640.2	+	3	461		c.e3-1		NECAB1_ENST00000521954.1_Splice_Site|RP11-662G23.1_ENST00000517884.1_RNA	NM_022351.4	NP_071746.1	Q8N987	NECA1_HUMAN	N-terminal EF-hand calcium binding protein 1							cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)	12			BRCA - Breast invasive adenocarcinoma(11;0.0499)			TTGCCATTTCAGATGATGGAA	0.338																																					.		Atlas-SNP	.											.	NECAB1	31	.	0			c.125-2A>T						.						39	37	38					8																	91836943		1799	4035	5834	SO:0001630	splice_region_variant	64168	exon3			CATTTCAGATGAT	AF414126	CCDS47889.1	8q21.3	2013-01-10	2007-12-06	2007-12-06	ENSG00000123119	ENSG00000123119		"N-terminal EF-hand calcium binding proteins", "EF-hand domain containing"	20983	protein-coding gene	gene with protein product			"EF-hand calcium binding protein 1"	EFCBP1			Standard	NM_022351		Approved		uc011lgg.2	Q8N987	OTTHUMG00000164009	ENST00000417640.2:c.125-1A>T	chr8.hg19:g.91836943A>T		179.0	0.0		328.0	44.0	NM_022351	Q6NUS7|Q96AZ7|Q9HBW8	Splice_Site	SNP	ENST00000417640.2	hg19	CCDS47889.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.124726	0.77436	.	.	ENSG00000123119	ENST00000417640	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1072	0.65099	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NECAB1	91906119	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	8.187000	0.89708	1.981000	0.57761	0.533000	0.62120	.	.	.		0.338	NECAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376728.1	NM_022351	Intron	T	91836943	A	T	91836943	5	4	214	1	0	0	0	0	0	0	1	0	10313	202	7	4	133	4	NECAB1	8	91836943	Splice_Site	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	10882080	91836943	54527079	45	30840										
TOP1MT	116447	hgsc.bcm.edu	37	chr8	144416922	144416922	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	caccttacctggctccactgCccttctgcgtcctgcgcgag	9	18	1	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr8:144416922C>T	ENST00000329245.4	-	1	144	c.110G>A	c.(109-111)gGc>gAc	p.G37D	TOP1MT_ENST00000521193.1_Intron|TOP1MT_ENST00000519148.1_Intron|TOP1MT_ENST00000523676.1_5'UTR	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	37					DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	GGCTCCACTGCCCTTCTGCGT	0.741																																					p.G37D		Atlas-SNP	.											.	TOP1MT	63	.	0			c.G110A						.						15	20	19					8																	144416922		2200	4297	6497	SO:0001583	missense	116447	exon1			CCACTGCCCTTCT	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.110G>A	chr8.hg19:g.144416922C>T	ENSP00000328835:p.Gly37Asp	150.0	0.0		256.0	85.0	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Missense_Mutation	SNP	ENST00000329245.4	hg19	CCDS6400.1	.	.	.	.	.	.	.	.	.	.	c	12.08	1.830877	0.32329	.	.	ENSG00000184428	ENST00000329245;ENST00000522043	T;T	0.62364	1.97;0.03	1.14	-2.28	0.06826	DNA topoisomerase I, DNA binding, eukaryotic-type (1);	.	.	.	.	T	0.33731	0.0873	N	0.14661	0.345	0.21220	N	0.99975	B	0.26002	0.139	B	0.19666	0.026	T	0.12400	-1.0549	9	0.18710	T	0.47	.	2.2928	0.04143	0.4091:0.3479:0.0:0.243	.	37	Q969P6	TOP1M_HUMAN	D	37	ENSP00000328835:G37D;ENSP00000428931:G37D	ENSP00000328835:G37D	G	-	2	0	TOP1MT	144488297	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	-1.413000	0.02473	-1.510000	0.01796	-0.476000	0.04901	GGC	.	.		0.741	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963		T	144416922	C	T	144416922	3	4	214	1	0	0	0	0	1	0	0	0	16379	739	26	3	1751	3	TOP1MT	8	144416922	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	52579979	144416922	1947100	46	30841										
ZNF7	7553	hgsc.bcm.edu	37	chr8	146068419	146068419	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gtgaagactgtgagaagataTttaggtggcgttcacaccta	12	6	1	4			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr8:146068419T>G	ENST00000528372.1	+	5	2167	c.1927T>G	c.(1927-1929)Ttt>Gtt	p.F643V	ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Missense_Mutation_p.F547V|ZNF7_ENST00000446747.2_Missense_Mutation_p.F654V|ZNF7_ENST00000325241.6_Missense_Mutation_p.F643V			P17097	ZNF7_HUMAN	zinc finger protein 7	643					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		TGAGAAGATATTTAGGTGGCG	0.418																																					p.F643V		Atlas-SNP	.											.	ZNF7	62	.	0			c.T1927G						.						75	79	78					8																	146068419		2203	4300	6503	SO:0001583	missense	7553	exon5			AAGATATTTAGGT	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.1927T>G	chr8.hg19:g.146068419T>G	ENSP00000432724:p.Phe643Val	126.0	0.0		205.0	38.0	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Missense_Mutation	SNP	ENST00000528372.1	hg19	CCDS6435.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.303009	0.81136	.	.	ENSG00000147789	ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	4.75	4.75	0.60458	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46758	D	0.000269	T	0.15696	0.0378	N	0.08118	0	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.64042	0.921;0.921	T	0.26121	-1.0112	9	.	.	.	-13.9987	13.363	0.60667	0.0:0.0:0.0:1.0	.	654;643	B4DT08;P17097	.;ZNF7_HUMAN	V	643;654;547;643	ENSP00000320627:F643V;ENSP00000393260:F654V;ENSP00000439424:F547V;ENSP00000432724:F643V	.	F	+	1	0	ZNF7	146039223	1.000000	0.71417	0.956000	0.39512	0.833000	0.47200	6.988000	0.76212	1.992000	0.58205	0.533000	0.62120	TTT	.	.		0.418	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		G	146068419	T	G	146068419	3	3	214	1	0	0	0	0	1	0	0	0	18117	1493	52	5	1941	5	ZNF7	8	146068419	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	1651497	146068419	295603	47	30842			1	45		2	2	20	T		6.873877e-05
ZNF7	7553	hgsc.bcm.edu	37	chr8	146068438	146068438	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	atttaggtggcgttcacaccTaattatacaccagagaattc	7	9	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr8:146068438T>C	ENST00000528372.1	+	5	2186	c.1946T>C	c.(1945-1947)cTa>cCa	p.L649P	ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Missense_Mutation_p.L553P|ZNF7_ENST00000446747.2_Missense_Mutation_p.L660P|ZNF7_ENST00000325241.6_Missense_Mutation_p.L649P			P17097	ZNF7_HUMAN	zinc finger protein 7	649					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		CGTTCACACCTAATTATACAC	0.418																																					p.L649P		Atlas-SNP	.											.	ZNF7	62	.	0			c.T1946C						.						82	88	86					8																	146068438		2203	4300	6503	SO:0001583	missense	7553	exon5			CACACCTAATTAT	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.1946T>C	chr8.hg19:g.146068438T>C	ENSP00000432724:p.Leu649Pro	139.0	0.0		215.0	34.0	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Missense_Mutation	SNP	ENST00000528372.1	hg19	CCDS6435.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.138063	0.56936	.	.	ENSG00000147789	ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	4.47	4.47	0.54385	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33772	N	0.004573	T	0.74951	0.3784	M	0.88031	2.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.79801	-0.1650	9	.	.	.	-9.9351	12.8614	0.57915	0.0:0.0:0.0:1.0	.	660;649	B4DT08;P17097	.;ZNF7_HUMAN	P	649;660;553;649	ENSP00000320627:L649P;ENSP00000393260:L660P;ENSP00000439424:L553P;ENSP00000432724:L649P	.	L	+	2	0	ZNF7	146039242	0.105000	0.21958	0.011000	0.14972	0.897000	0.52465	2.872000	0.48467	1.879000	0.54435	0.533000	0.62120	CTA	.	.		0.418	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		C	146068438	T	C	146068438	3	2	214	1	0	0	0	0	1	0	0	0	18117	1522	53	2	1960	2	ZNF7	8	146068438	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	19	146068438	295584	48	30843			1	45		2	2	20	T		6.873877e-05
C9orf64	84267	hgsc.bcm.edu	37	chr9	86559849	86559849	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctccttttccttccaatacaCtccacgtatctgctacaagg	4	15	1	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr9:86559849C>T	ENST00000376344.3	-	3	869	c.653G>A	c.(652-654)aGt>aAt	p.S218N	C9orf64_ENST00000314700.1_Missense_Mutation_p.S77N	NM_032307.3	NP_115683.3	Q5T6V5	CI064_HUMAN	chromosome 9 open reading frame 64	218										central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						TTCCAATACACTCCACGTATC	0.408																																					p.S218N		Atlas-SNP	.											.	C9orf64	28	.	0			c.G653A						.						111	93	99					9																	86559849		2203	4300	6503	SO:0001583	missense	84267	exon3			AATACACTCCACG	AK090882	CCDS6666.2	9q22.1	2014-06-11			ENSG00000165118	ENSG00000165118			28144	protein-coding gene	gene with protein product		611342				24911101	Standard	NM_032307		Approved	MGC10999	uc004anb.3	Q5T6V5	OTTHUMG00000020111	ENST00000376344.3:c.653G>A	chr9.hg19:g.86559849C>T	ENSP00000365522:p.Ser218Asn	101.0	0.0		80.0	35.0	NM_032307	B2RPI6|Q8N2B1|Q9BT18	Missense_Mutation	SNP	ENST00000376344.3	hg19	CCDS6666.2	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374287	0.61735	.	.	ENSG00000165118	ENST00000376344;ENST00000314700	.	.	.	5.24	5.24	0.73138	.	0.166402	0.53938	D	0.000046	T	0.75774	0.3895	M	0.79926	2.475	0.80722	D	1	D	0.53312	0.959	P	0.53313	0.723	T	0.77819	-0.2446	9	0.48119	T	0.1	-8.3718	19.2094	0.93748	0.0:1.0:0.0:0.0	.	218	Q5T6V5	CI064_HUMAN	N	218;77	.	ENSP00000318375:S77N	S	-	2	0	C9orf64	85749669	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.759000	0.68785	2.614000	0.88457	0.655000	0.94253	AGT	.	.		0.408	C9orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052865.1	NM_032307		T	86559849	C	T	86559849	3	4	214	1	0	0	0	0	1	0	0	0	2491	565	20	3	380	3	C9orf64	9	86559849	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10		86559849	54653582	49	30844										
ABCA1	19	hgsc.bcm.edu	37	chr9	107571793	107571793	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ggtcccgaagccagggtcttTggtgagggcgtttaagagtt	16	7	1	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr9:107571793T>C	ENST00000374736.3	-	30	4622	c.4228A>G	c.(4228-4230)Aaa>Gaa	p.K1410E		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1410					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CCAGGGTCTTTGGTGAGGGCG	0.512																																					p.K1410E		Atlas-SNP	.											.	ABCA1	244	.	0			c.A4228G						.						110	106	107					9																	107571793		2203	4300	6503	SO:0001583	missense	19	exon30			GGTCTTTGGTGAG	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.4228A>G	chr9.hg19:g.107571793T>C	ENSP00000363868:p.Lys1410Glu	144.0	0.0		114.0	37.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	T	3.114	-0.181970	0.06340	.	.	ENSG00000165029	ENST00000374736	D	0.93712	-3.27	5.68	3.18	0.36537	.	0.380726	0.34362	N	0.004021	T	0.75243	0.3823	N	0.01668	-0.77	0.33931	D	0.642116	B	0.02656	0.0	B	0.04013	0.001	T	0.68522	-0.5386	10	0.05351	T	0.99	.	5.7057	0.17907	0.0:0.2163:0.1315:0.6522	.	1410	O95477	ABCA1_HUMAN	E	1410	ENSP00000363868:K1410E	ENSP00000363868:K1410E	K	-	1	0	ABCA1	106611614	0.004000	0.15560	0.993000	0.49108	0.722000	0.41435	1.206000	0.32321	0.366000	0.24427	0.529000	0.55759	AAA	.	.		0.512	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		C	107571793	T	C	107571793	3	2	214	1	0	0	0	0	1	0	0	0	28	1821	63	2	2641	2	ABCA1	9	107571793	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	21011944	107571793	33641638	50	30845										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114187765	114187765	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gacctaatggcttaatcttgAtttctggacagctttaaata	7	7	2	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr9:114187765A>G	ENST00000338205.5	-	11	1367	c.1148T>C	c.(1147-1149)aTc>aCc	p.I383T	KIAA0368_ENST00000259335.4_Missense_Mutation_p.I561T			Q5VYK3	ECM29_HUMAN	KIAA0368	389					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						CTTAATCTTGATTTCTGGACA	0.318																																					p.I561T		Atlas-SNP	.											.	KIAA0368	144	.	0			c.T1682C						.						50	47	48					9																	114187765		1824	4067	5891	SO:0001583	missense	23392	exon13			ATCTTGATTTCTG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1148T>C	chr9.hg19:g.114187765A>G	ENSP00000339889:p.Ile383Thr	214.0	0.0		169.0	50.0	NM_001080398	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	hg19		.	.	.	.	.	.	.	.	.	.	A	7.022	0.558863	0.13436	.	.	ENSG00000136813	ENST00000338205;ENST00000259335	T	0.39997	1.05	5.42	5.42	0.78866	Armadillo-like helical (1);Armadillo-type fold (1);	0.226060	0.45126	D	0.000391	T	0.13927	0.0337	N	0.01352	-0.895	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19128	-1.0315	10	0.14252	T	0.57	-7.5133	6.723	0.23340	0.7131:0.2052:0.0818:0.0	.	389	Q5VYK3	ECM29_HUMAN	T	383;561	ENSP00000259335:I561T	ENSP00000259335:I561T	I	-	2	0	KIAA0368	113227586	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	2.651000	0.46674	2.186000	0.69663	0.459000	0.35465	ATC	.	.		0.318	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		G	114187765	A	G	114187765	3	3	214	1	0	0	0	0	1	0	0	0	8180	333	12	2	4527	2	KIAA0368	9	114187765	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	6615972	114187765	27025666	51	30846										
OR1L4	254973	hgsc.bcm.edu	37	chr9	125486747	125486747	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ccacctacattccctgttccGcgtgctacttatgtctcgct	6	16	1	0	rs370090548		TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr9:125486747G>A	ENST00000259466.1	+	1	479	c.479G>A	c.(478-480)cGc>cAc	p.R160H		NM_001005235.1	NP_001005235.1	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L, member 4	160						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(3)|lung(13)|prostate(1)|skin(1)	20						TCCCTGTTCCGCGTGCTACTT	0.478																																					p.R160H		Atlas-SNP	.											.	OR1L4	38	.	0			c.G479A						.	G	HIS/ARG	0,4406		0,0,2203	184	158	166		479	3.1	0	9		166	1,8593		0,1,4296	no	missense	OR1L4	NM_001005235.1	29	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	160/312	125486747	1,12999	2203	4297	6500	SO:0001583	missense	254973	exon1			TGTTCCGCGTGCT		CCDS35129.1	9q33.2	2013-09-20			ENSG00000136939	ENSG00000136939		"GPCR / Class A : Olfactory receptors"	8216	protein-coding gene	gene with protein product				OR1L5			Standard	NM_001005235		Approved	OR9-E	uc004bmu.1	Q8NGR5	OTTHUMG00000020620	ENST00000259466.1:c.479G>A	chr9.hg19:g.125486747G>A	ENSP00000259466:p.Arg160His	130.0	0.0		89.0	24.0	NM_001005235	Q6IFN0|Q96R81	Missense_Mutation	SNP	ENST00000259466.1	hg19	CCDS35129.1	.	.	.	.	.	.	.	.	.	.	.	0.004	-2.305906	0.00240	0.0	1.16E-4	ENSG00000136939	ENST00000259466	T	0.00017	9.1	4.01	3.11	0.35812	GPCR, rhodopsin-like superfamily (1);	0.352654	0.24645	N	0.036780	T	0.00039	0.0001	N	0.00055	-2.37	0.09310	N	1	B	0.18166	0.026	B	0.17098	0.017	T	0.43523	-0.9386	10	0.02654	T	1	-0.0046	3.5503	0.07844	0.2092:0.0:0.591:0.1998	.	160	Q8NGR5	OR1L4_HUMAN	H	160	ENSP00000259466:R160H	ENSP00000259466:R160H	R	+	2	0	OR1L4	124526568	0.000000	0.05858	0.015000	0.15790	0.384000	0.30261	0.187000	0.16998	0.914000	0.36822	0.298000	0.19748	CGC	.	.		0.478	OR1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053951.1			A	125486747	G	A	125486747	3	1	214	1	0	0	0	0	1	0	0	0	10974	1087	38	1	481	1	OR1L4	9	125486747	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	11298982	125486747	15726684	52	30847										
SLC25A25	114789	hgsc.bcm.edu	37	chr9	130866085	130866085	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gccgtatccagaacctgcacGgcccccctggacaggctcaa	10	17	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr9:130866085G>T	ENST00000373064.5	+	5	875	c.612G>T	c.(610-612)acG>acT	p.T204T	SLC25A25_ENST00000432073.2_Silent_p.T224T|SLC25A25_ENST00000373068.2_Silent_p.T238T|SLC25A25_ENST00000433501.1_Silent_p.T101T|SLC25A25_ENST00000373069.5_Silent_p.T250T|SLC25A25_ENST00000373066.5_Silent_p.T236T	NM_052901.4	NP_443133.2	Q6KCM7	SCMC2_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 25	204					adipose tissue development (GO:0060612)|ATP metabolic process (GO:0046034)|calcium ion transmembrane transport (GO:0070588)|camera-type eye development (GO:0043010)|cellular respiration (GO:0045333)|multicellular organism growth (GO:0035264)|response to activity (GO:0014823)|response to dietary excess (GO:0002021)|response to food (GO:0032094)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)	10						GAACCTGCACGGCCCCCCTGG	0.647																																					p.T238T		Atlas-SNP	.											.	SLC25A25	119	.	0			c.G714T						.						40	44	43					9																	130866085		2203	4300	6503	SO:0001819	synonymous_variant	114789	exon5			CTGCACGGCCCCC	AJ619963	CCDS6890.1, CCDS35151.1, CCDS48031.1, CCDS59146.1	9q34	2013-05-22			ENSG00000148339	ENSG00000148339		"Solute carriers", "EF-hand domain containing"	20663	protein-coding gene	gene with protein product		608745				15123600	Standard	NM_052901		Approved	KIAA1896, PCSCL, MCSC	uc004btb.4	Q6KCM7	OTTHUMG00000020736	ENST00000373064.5:c.612G>T	chr9.hg19:g.130866085G>T		87.0	0.0		60.0	23.0	NM_001006641	Q5SYW7|Q5SYW8|Q5SYX3|Q5VWU2|Q5VWU3|Q5VWU4|Q6KCM4|Q6KCM6|Q6UX48|Q705K2|Q96PZ1|Q9BSA6	Silent	SNP	ENST00000373064.5	hg19	CCDS6890.1	.	.	.	.	.	.	.	.	.	.	G	9.007	0.981594	0.18812	.	.	ENSG00000148339	ENST00000466983	.	.	.	5.52	-11.0	0.00169	.	.	.	.	.	T	0.30885	0.0779	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39333	-0.9619	4	.	.	.	-8.6159	1.2678	0.02015	0.1992:0.1865:0.3288:0.2855	.	.	.	.	C	29	.	.	G	+	1	0	SLC25A25	129905906	0.000000	0.05858	0.412000	0.26496	0.954000	0.61252	-3.386000	0.00489	-2.558000	0.00475	-1.148000	0.01847	GGC	.	.		0.647	SLC25A25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054407.1	NM_052901		T	130866085	G	T	130866085	2	4	214	1	0	0	0	0	0	0	0	1	14503	1103	39	1		1	SLC25A25	9	130866085	Silent	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	5379338	130866085	10347346	53	30848										
ANAPC2	29882	hgsc.bcm.edu	37	chr9	140075299	140075299	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gccagcagcgagcggtactcAttgatgaagaggtccttgct	13	10	1	3	rs371943537		TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr9:140075299A>G	ENST00000323927.2	-	8	1555	c.1551T>C	c.(1549-1551)aaT>aaC	p.N517N		NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	517					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		AGCGGTACTCATTGATGAAGA	0.647																																					p.N517N		Atlas-SNP	.											.	ANAPC2	57	.	0			c.T1551C						.			2,4404	4.2+/-10.8	0,2,2201	98	84	88		1551	-4.8	0.8	9		88	0,8600		0,0,4300	no	coding-synonymous	ANAPC2	NM_013366.3		0,2,6501	GG,GA,AA		0.0,0.0454,0.0154		517/823	140075299	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	29882	exon8			GTACTCATTGATG	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"Anaphase promoting complex subunits"	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.1551T>C	chr9.hg19:g.140075299A>G		59.0	0.0		39.0	13.0	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Silent	SNP	ENST00000323927.2	hg19	CCDS7033.1																																																																																			.	.		0.647	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366		G	140075299	A	G	140075299	2	3	214	1	0	0	0	0	0	0	0	1	603	214	8	2		2	ANAPC2	9	140075299	Silent	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	9209214	140075299	1138132	54	30849										
ANAPC2	29882	hgsc.bcm.edu	37	chr9	140075345	140075345	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	agatgctgaccagcaggctgAtgatgtccgatgaacgccgc	13	11	0	5			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr9:140075345A>C	ENST00000323927.2	-	8	1509	c.1505T>G	c.(1504-1506)aTc>aGc	p.I502S		NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	502					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		CAGCAGGCTGATGATGTCCGA	0.637																																					p.I502S		Atlas-SNP	.											.	ANAPC2	57	.	0			c.T1505G						.						122	107	112					9																	140075345		2203	4300	6503	SO:0001583	missense	29882	exon8			AGGCTGATGATGT	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"Anaphase promoting complex subunits"	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.1505T>G	chr9.hg19:g.140075345A>C	ENSP00000314004:p.Ile502Ser	61.0	0.0		47.0	22.0	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Missense_Mutation	SNP	ENST00000323927.2	hg19	CCDS7033.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.190008	0.78789	.	.	ENSG00000176248	ENST00000323927	T	0.76839	-1.05	5.41	5.41	0.78517	Cullin, N-terminal (1);Cullin homology (2);	0.046866	0.85682	D	0.000000	D	0.89301	0.6676	M	0.89287	3.02	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.992	D	0.91188	0.4981	10	0.87932	D	0	-36.7872	13.3824	0.60775	1.0:0.0:0.0:0.0	.	502;499	Q9UJX6;Q9UJX6-2	ANC2_HUMAN;.	S	502	ENSP00000314004:I502S	ENSP00000314004:I502S	I	-	2	0	ANAPC2	139195166	1.000000	0.71417	1.000000	0.80357	0.594000	0.36715	8.635000	0.91006	2.053000	0.61076	0.459000	0.35465	ATC	.	.		0.637	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366		C	140075345	A	C	140075345	3	2	214	1	0	0	0	0	1	0	0	0	603	333	12	5	987	5	ANAPC2	9	140075345	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	46	140075345	1138086	55	30850										
GDI2	2665	hgsc.bcm.edu	37	chr10	5836921	5836921	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ttatagacaaagctcccttcAgtcactttaaaatccagata	4	10	2	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr10:5836921A>T	ENST00000380191.4	-	4	605	c.315T>A	c.(313-315)acT>acA	p.T105T	GDI2_ENST00000380132.4_Silent_p.T109T|GDI2_ENST00000380181.3_Intron	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2	105					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|Rab GDP-dissociation inhibitor activity (GO:0005093)|Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|large_intestine(1)|lung(6)|urinary_tract(1)	10						AGCTCCCTTCAGTCACTTTAA	0.378																																					p.T105T		Atlas-SNP	.											.	GDI2	26	.	0			c.T315A						.						85	82	83					10																	5836921		2203	4300	6503	SO:0001819	synonymous_variant	2665	exon4			CCCTTCAGTCACT	D13988	CCDS7071.1, CCDS44352.1	10p15	2010-03-16			ENSG00000057608	ENSG00000057608			4227	protein-coding gene	gene with protein product	"rab GDP-dissociation"	600767				9434952	Standard	NM_001494		Approved	RABGDIB	uc001iil.4	P50395	OTTHUMG00000017607	ENST00000380191.4:c.315T>A	chr10.hg19:g.5836921A>T		143.0	0.0		166.0	83.0	NM_001494	O43928|Q5SX88|Q9UQM6	Silent	SNP	ENST00000380191.4	hg19	CCDS7071.1																																																																																			.	.		0.378	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	NM_001494		T	5836921	A	T	5836921	2	4	214	1	0	0	0	0	0	0	0	1	6329	175	7	4		4	GDI2	10	5836921	Silent	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10		5836921	129697826	56	30851										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7217971	7217971	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctgtatttggttttggtatgAatggagcagttctctgggca	13	5	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr10:7217971A>G	ENST00000361972.4	-	17	2055	c.1965T>C	c.(1963-1965)atT>atC	p.I655I	SFMBT2_ENST00000397167.1_Silent_p.I655I	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	655					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						TTTTGGTATGAATGGAGCAGT	0.403																																					p.I655I		Atlas-SNP	.											.	SFMBT2	209	.	0			c.T1965C						.						183	181	182					10																	7217971		2203	4300	6503	SO:0001819	synonymous_variant	57713	exon17			GGTATGAATGGAG	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.1965T>C	chr10.hg19:g.7217971A>G		77.0	0.0		92.0	49.0	NM_001029880	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	hg19	CCDS31138.1																																																																																			.	.		0.403	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		G	7217971	A	G	7217971	2	3	214	1	0	0	0	0	0	0	0	1	14173	242	9	2		2	SFMBT2	10	7217971	Silent	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	1381050	7217971	128316776	57	30852										
RTKN2	219790	hgsc.bcm.edu	37	chr10	63958086	63958086	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gttaccatcaaagagtgtggCccaaggaggtggtaaggatt	14	6	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr10:63958086C>G	ENST00000373789.3	-	12	1507	c.1411G>C	c.(1411-1413)Gcc>Ccc	p.A471P	RTKN2_ENST00000395265.1_Missense_Mutation_p.A492P|RTKN2_ENST00000315289.2_Missense_Mutation_p.A273P	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	471					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					AAGAGTGTGGCCCAAGGAGGT	0.388																																					p.A471P		Atlas-SNP	.											.	RTKN2	68	.	0			c.G1411C						.						117	118	118					10																	63958086		2203	4300	6503	SO:0001583	missense	219790	exon12			GTGTGGCCCAAGG	BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"Pleckstrin homology (PH) domain containing"	19364	protein-coding gene	gene with protein product			"pleckstrin homology domain containing, family K member 1"	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.1411G>C	chr10.hg19:g.63958086C>G	ENSP00000362894:p.Ala471Pro	98.0	0.0		106.0	58.0	NM_145307	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	Missense_Mutation	SNP	ENST00000373789.3	hg19	CCDS7263.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.913051	0.52439	.	.	ENSG00000182010	ENST00000315289;ENST00000395265;ENST00000373789	T;T;T	0.50277	0.75;1.35;1.38	5.61	4.7	0.59300	.	0.109202	0.64402	D	0.000010	T	0.64692	0.2621	L	0.61218	1.895	0.58432	D	0.999994	D;D	0.89917	1.0;0.999	D;D	0.70227	0.968;0.95	T	0.67745	-0.5591	10	0.62326	D	0.03	-3.5932	14.2352	0.65922	0.0:0.9286:0.0:0.0713	.	273;471	Q5SVY4;Q8IZC4	.;RTKN2_HUMAN	P	273;492;471	ENSP00000325379:A273P;ENSP00000378682:A492P;ENSP00000362894:A471P	ENSP00000325379:A273P	A	-	1	0	RTKN2	63628092	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	2.675000	0.46875	1.377000	0.46286	0.655000	0.94253	GCC	.	.		0.388	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307		G	63958086	C	G	63958086	3	3	214	1	0	0	0	0	1	0	0	0	13738	739	26	4	422	4	RTKN2	10	63958086	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	56740115	63958086	71576661	58	30853										
P4HA1	5033	hgsc.bcm.edu	37	chr10	74810812	74810812	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	attggcttttccactttaccAttttgataccctccccacgg	5	14	0	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr10:74810812A>G	ENST00000307116.2	-	7	1015	c.899T>C	c.(898-900)aTg>aCg	p.M300T	P4HA1_ENST00000412021.2_Splice_Site_p.M300T|P4HA1_ENST00000373008.2_Splice_Site_p.M300T|P4HA1_ENST00000263556.3_Splice_Site_p.M300T|P4HA1_ENST00000394890.2_Splice_Site_p.M300T|P4HA1_ENST00000440381.1_Splice_Site_p.M300T			P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha polypeptide I	300					collagen fibril organization (GO:0030199)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|procollagen-proline 4-dioxygenase complex (GO:0016222)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	CCACTTTACCATTTTGATACC	0.403																																					p.M300T	Colon(147;367 2405 2662 52127)	Atlas-SNP	.											.	P4HA1	86	.	0			c.T899C						.						254	236	242					10																	74810812		2203	4300	6503	SO:0001630	splice_region_variant	5033	exon7			TTTACCATTTTGA		CCDS7320.1, CCDS41537.1, CCDS44432.1	10q21.3-q23.1	2008-12-09	2008-12-09		ENSG00000122884	ENSG00000122884	1.14.11.2		8546	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(I)"	176710	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I"	P4HA		2556027	Standard	NM_001017962		Approved	C-P4Halpha(I)	uc001jtg.3	P13674	OTTHUMG00000018449	ENST00000307116.2:c.900+1T>C	chr10.hg19:g.74810812A>G		88.0	0.0		102.0	59.0	NM_001142596	C9JL12|Q15082|Q15083|Q5VSQ5	Missense_Mutation	SNP	ENST00000307116.2	hg19		.	.	.	.	.	.	.	.	.	.	A	17.89	3.500824	0.64298	.	.	ENSG00000122884	ENST00000307116;ENST00000373008;ENST00000412021;ENST00000394890;ENST00000263556;ENST00000440381	T;T;T;T;T;T	0.42900	0.97;0.97;0.97;0.97;0.97;0.96	5.67	5.67	0.87782	.	0.036451	0.85682	D	0.000000	T	0.53384	0.1793	M	0.79926	2.475	0.80722	D	1	B;P;P	0.34892	0.161;0.474;0.474	B;B;B	0.40199	0.184;0.322;0.322	T	0.59037	-0.7529	10	0.66056	D	0.02	-1.2853	15.9045	0.79412	1.0:0.0:0.0:0.0	.	300;300;300	C9JL12;Q5VSQ6;P13674	.;.;P4HA1_HUMAN	T	300	ENSP00000307318:M300T;ENSP00000362099:M300T;ENSP00000411688:M300T;ENSP00000378353:M300T;ENSP00000263556:M300T;ENSP00000414464:M300T	ENSP00000263556:M300T	M	-	2	0	P4HA1	74480818	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.933000	0.92911	2.157000	0.67596	0.455000	0.32223	ATG	.	.		0.403	P4HA1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000048601.1	NM_000917	Missense_Mutation	G	74810812	A	G	74810812	5	3	214	1	0	0	0	0	0	0	1	0	11365	231	8	2	816	2	P4HA1	10	74810812	Splice_Site	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	10852726	74810812	60723935	59	30854										
LOXL4	84171	hgsc.bcm.edu	37	chr10	100013487	100013487	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gggcacaatacagctggctgAgcgggcggtcctccaagtag	15	11	0	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr10:100013487A>T	ENST00000260702.3	-	11	1808	c.1658T>A	c.(1657-1659)cTc>cAc	p.L553H	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	553	Lysyl-oxidase like.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		CAGCTGGCTGAGCGGGCGGTC	0.622																																					p.L553H		Atlas-SNP	.											.	LOXL4	60	.	0			c.T1658A						.						80	76	77					10																	100013487		2203	4300	6503	SO:0001583	missense	84171	exon11			TGGCTGAGCGGGC	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.1658T>A	chr10.hg19:g.100013487A>T	ENSP00000260702:p.Leu553His	82.0	0.0		76.0	14.0	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Missense_Mutation	SNP	ENST00000260702.3	hg19	CCDS7473.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.601602	0.87055	.	.	ENSG00000138131	ENST00000260702	T	0.42513	0.97	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.67344	0.2883	M	0.85945	2.785	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.73714	-0.3896	10	0.87932	D	0	.	13.6238	0.62153	1.0:0.0:0.0:0.0	.	553	Q96JB6	LOXL4_HUMAN	H	553	ENSP00000260702:L553H	ENSP00000260702:L553H	L	-	2	0	LOXL4	100003477	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.139000	0.94554	2.052000	0.61016	0.402000	0.26972	CTC	.	.		0.622	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211		T	100013487	A	T	100013487	3	4	214	1	0	0	0	0	1	0	0	0	8911	304	11	4	632	4	LOXL4	10	100013487	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	25202675	100013487	35521260	60	30855										
MGEA5	10724	hgsc.bcm.edu	37	chr10	103557782	103557782	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	catagacattatactcttgaTatcccaaacataggagtaca	5	9	1	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr10:103557782T>A	ENST00000361464.3	-	10	2334	c.1939A>T	c.(1939-1941)Atc>Ttc	p.I647F	MGEA5_ENST00000357797.5_Missense_Mutation_p.I594F|MGEA5_ENST00000370094.3_Missense_Mutation_p.I647F|MGEA5_ENST00000482611.1_5'UTR|MGEA5_ENST00000439817.1_Missense_Mutation_p.I594F	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	647					aging (GO:0007568)|dATP metabolic process (GO:0046060)|glycoprotein catabolic process (GO:0006516)|N-acetylglucosamine metabolic process (GO:0006044)|necrotic cell death (GO:0070265)|negative regulation of cardiac muscle adaptation (GO:0010616)|negative regulation of protein glycosylation (GO:0060051)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cell killing (GO:0031343)|positive regulation of DNA metabolic process (GO:0051054)|positive regulation of glucose import (GO:0046326)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of proteolysis (GO:0045862)|protein targeting to membrane (GO:0006612)|response to steroid hormone (GO:0048545)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	23		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		ATACTCTTGATATCCCAAACA	0.388																																					p.I647F		Atlas-SNP	.											.	MGEA5	53	.	0			c.A1939T						.						131	118	122					10																	103557782		2203	4300	6503	SO:0001583	missense	10724	exon10			TCTTGATATCCCA	AF036144	CCDS7520.1, CCDS44471.1	10q24.1-q24.3	2008-08-01			ENSG00000198408	ENSG00000198408			7056	protein-coding gene	gene with protein product	"nuclear cytoplasmic O-GlcNAcase and acetyltransferase"	604039				9811929, 16356930	Standard	NM_012215		Approved	MEA5, NCOAT, OGA	uc001ktv.2	O60502	OTTHUMG00000018939	ENST00000361464.3:c.1939A>T	chr10.hg19:g.103557782T>A	ENSP00000354850:p.Ile647Phe	90.0	0.0		70.0	37.0	NM_012215	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Missense_Mutation	SNP	ENST00000361464.3	hg19	CCDS7520.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.776037	0.90195	.	.	ENSG00000198408	ENST00000439817;ENST00000361464;ENST00000357797;ENST00000370094	T;T;T;T	0.36878	1.29;1.27;1.27;1.23	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.57562	0.2062	M	0.70595	2.14	0.80722	D	1	D;D;D;D	0.60160	0.972;0.987;0.981;0.982	P;P;P;P	0.62382	0.549;0.81;0.901;0.741	T	0.61811	-0.6986	10	0.72032	D	0.01	-11.181	15.8033	0.78473	0.0:0.0:0.0:1.0	.	594;594;647;647	E9PGF9;O60502-2;O60502-3;O60502	.;.;.;NCOAT_HUMAN	F	594;647;594;647	ENSP00000409973:I594F;ENSP00000354850:I647F;ENSP00000350445:I594F;ENSP00000359112:I647F	ENSP00000350445:I594F	I	-	1	0	MGEA5	103547772	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.036000	0.88901	2.133000	0.65898	0.533000	0.62120	ATC	.	.		0.388	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215		A	103557782	T	A	103557782	3	1	214	1	0	0	0	0	1	0	0	0	9564	1406	49	4	839	4	MGEA5	10	103557782	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	3544295	103557782	31976965	61	30856										
ADAM12	8038	hgsc.bcm.edu	37	chr10	127753435	127753435	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gcagatgccattgtagcagtAgccgtccacatcctgacatg	10	12	0	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr10:127753435A>G	ENST00000368679.4	-	14	1867	c.1558T>C	c.(1558-1560)Tac>Cac	p.Y520H	ADAM12_ENST00000368676.4_Missense_Mutation_p.Y520H|ADAM12_ENST00000467145.1_5'UTR	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	520	Cys-rich.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		TTGTAGCAGTAGCCGTCCACA	0.612																																					p.Y520H		Atlas-SNP	.											.	ADAM12	388	.	0			c.T1558C						.						128	92	104					10																	127753435		2203	4300	6503	SO:0001583	missense	8038	exon14			AGCAGTAGCCGTC	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1558T>C	chr10.hg19:g.127753435A>G	ENSP00000357668:p.Tyr520His	63.0	0.0		51.0	13.0	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	hg19	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.757140	0.89843	.	.	ENSG00000148848	ENST00000368679;ENST00000368676	T;T	0.26067	1.76;1.76	5.11	5.11	0.69529	ADAM, cysteine-rich (2);	0.000000	0.64402	D	0.000001	T	0.54078	0.1836	M	0.86740	2.835	0.80722	D	1	P;P;P;P;D	0.60575	0.875;0.849;0.849;0.849;0.988	P;P;P;P;D	0.63381	0.615;0.48;0.48;0.48;0.914	T	0.63620	-0.6596	10	0.87932	D	0	.	15.0789	0.72099	1.0:0.0:0.0:0.0	.	517;517;520;517;520	A8K6G4;O43184-3;O43184-2;O43184-4;O43184	.;.;.;.;ADA12_HUMAN	H	520	ENSP00000357668:Y520H;ENSP00000357665:Y520H	ENSP00000357665:Y520H	Y	-	1	0	ADAM12	127743425	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	6.015000	0.70791	2.145000	0.66743	0.528000	0.53228	TAC	.	.		0.612	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			G	127753435	A	G	127753435	3	3	214	1	0	0	0	0	1	0	0	0	236	420	15	2	1319	2	ADAM12	10	127753435	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	24195653	127753435	7781312	62	30857										
WT1	7490	hgsc.bcm.edu	37	chr11	32456885	32456885	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gacacacgtggaagccgggtCctgcagcaagaggaagtcca	14	11	0	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr11:32456885C>T	ENST00000332351.3	-	1	291	c.7G>A	c.(7-9)Gac>Aac	p.D3N	WT1-AS_ENST00000395900.1_RNA|WT1-AS_ENST00000459866.1_RNA|WT1-AS_ENST00000478367.1_RNA|WT1_ENST00000448076.3_Missense_Mutation_p.D3N|WT1-AS_ENST00000426618.2_RNA|WT1-AS_ENST00000494911.1_RNA|WT1-AS_ENST00000525436.1_RNA	NM_024424.3|NM_024426.4	NP_077742.2|NP_077744	P19544	WT1_HUMAN	Wilms tumor 1	0					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)		EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			GAAGCCGGGTCCTGCAGCAAG	0.716			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																												p.D3N		Atlas-SNP	.	yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	.	WT1	744	.	0			c.G7A						.						1	1	1					11																	32456885		1027	2203	3230	SO:0001583	missense	7490	exon1	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	CCGGGTCCTGCAG		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000332351.3:c.7G>A	chr11.hg19:g.32456885C>T	ENSP00000331327:p.Asp3Asn	203.0	0.0		148.0	50.0	NM_024424	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000332351.3	hg19	CCDS7878.2	.	.	.	.	.	.	.	.	.	.	C	10.48	1.363313	0.24684	.	.	ENSG00000184937	ENST00000332351;ENST00000452863;ENST00000448076	T;T;T	0.13538	3.2;2.99;2.58	2.96	2.02	0.26589	.	.	.	.	.	T	0.07324	0.0185	N	0.08118	0	0.58432	D	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19353	-1.0308	9	0.72032	D	0.01	.	10.0525	0.42225	0.0:0.4563:0.5437:0.0	.	8;8	P19544-8;P19544-7	.;.	N	3	ENSP00000331327:D3N;ENSP00000415516:D3N;ENSP00000413452:D3N	ENSP00000331327:D3N	D	-	1	0	WT1	32413461	0.938000	0.31826	0.651000	0.29564	0.253000	0.25986	1.304000	0.33482	0.430000	0.26230	-0.556000	0.04195	GAC	.	.		0.716	WT1-001	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000095436.2	NM_000378		T	32456885	C	T	32456885	3	4	214	1	0	0	0	0	1	0	0	0	17423	855	30	3	1586	3	WT1	11	32456885	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10		32456885	102549631	63	30858										
CAT	847	hgsc.bcm.edu	37	chr11	34478274	34478274	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctggtcttaaaccggaatccAgttaattactttgctgaggt	9	8	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr11:34478274A>G	ENST00000241052.4	+	8	1055	c.966A>G	c.(964-966)ccA>ccG	p.P322P		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	322					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	ACCGGAATCCAGTTAATTACT	0.468																																					p.P322P		Atlas-SNP	.											.	CAT	42	.	0			c.A966G						.						132	119	123					11																	34478274		2202	4298	6500	SO:0001819	synonymous_variant	847	exon8			GAATCCAGTTAAT	AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.966A>G	chr11.hg19:g.34478274A>G		166.0	0.0		119.0	48.0	NM_001752	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Silent	SNP	ENST00000241052.4	hg19	CCDS7891.1																																																																																			.	.		0.468	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752		G	34478274	A	G	34478274	2	3	214	1	0	0	0	0	0	0	0	1	2688	175	7	2		2	CAT	11	34478274	Silent	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	2021389	34478274	100528242	64	30859										
SLC22A9	114571	hgsc.bcm.edu	37	chr11	63176251	63176251	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctccacccctgccctggatcAtctatggagtcttccccttc	6	18	3	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr11:63176251A>G	ENST00000279178.3	+	9	1750	c.1501A>G	c.(1501-1503)Atc>Gtc	p.I501V	SLC22A9_ENST00000310969.4_3'UTR	NM_080866.2	NP_543142.2	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion transporter), member 9	501					hormone transport (GO:0009914)|short-chain fatty acid import (GO:0015913)|sodium-independent organic anion transport (GO:0043252)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	anion:anion antiporter activity (GO:0015301)|short-chain fatty acid uptake transporter activity (GO:0015636)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	18						GCCCTGGATCATCTATGGAGT	0.488																																					p.I501V		Atlas-SNP	.											.	SLC22A9	77	.	0			c.A1501G						.						149	135	140					11																	63176251		2201	4298	6499	SO:0001583	missense	114571	exon9			TGGATCATCTATG	AP001880	CCDS8043.1	11q12.3	2014-05-20	2008-01-11		ENSG00000149742	ENSG00000149742		"Solute carriers"	16261	protein-coding gene	gene with protein product		607579				11327718, 17393504	Standard	NM_080866		Approved	OAT4, FLJ23666, UST3, OAT7	uc001nww.3	Q8IVM8	OTTHUMG00000167805	ENST00000279178.3:c.1501A>G	chr11.hg19:g.63176251A>G	ENSP00000279178:p.Ile501Val	147.0	0.0		111.0	38.0	NM_080866	A0AVB7|A4PB24|Q8TCC8|Q8TEC0|Q8WYN7	Missense_Mutation	SNP	ENST00000279178.3	hg19	CCDS8043.1	.	.	.	.	.	.	.	.	.	.	A	9.008	0.981879	0.18812	.	.	ENSG00000149742	ENST00000279178	T	0.58506	0.33	2.63	0.0447	0.14227	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.368800	0.28403	N	0.015478	T	0.39682	0.1087	L	0.52266	1.64	0.80722	D	1	P	0.38167	0.621	B	0.33295	0.161	T	0.07770	-1.0755	10	0.27785	T	0.31	.	3.8701	0.09033	0.65:0.2174:0.1326:0.0	.	501	Q8IVM8	S22A9_HUMAN	V	501	ENSP00000279178:I501V	ENSP00000279178:I501V	I	+	1	0	SLC22A9	62932827	1.000000	0.71417	0.923000	0.36655	0.721000	0.41392	1.522000	0.35921	-0.107000	0.12088	0.172000	0.16884	ATC	.	.		0.488	SLC22A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396371.1	NM_080866		G	63176251	A	G	63176251	3	3	214	1	0	0	0	0	1	0	0	0	14476	217	8	2	1535	2	SLC22A9	11	63176251	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	28697977	63176251	71830265	65	30860										
RAB30	27314	hgsc.bcm.edu	37	chr11	82693383	82693383	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tgaggtctccagataatacaTgtcctgagcttctgagaatt	9	8	2	4			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr11:82693383T>C	ENST00000533486.1	-	6	720	c.436A>G	c.(436-438)Atg>Gtg	p.M146V	RAB30_ENST00000534141.1_Silent_p.T144T|RAB30_ENST00000527633.1_Missense_Mutation_p.M146V|RAB30_ENST00000260056.2_Missense_Mutation_p.M146V|RP11-659G9.3_ENST00000527550.1_RNA	NM_014488.3	NP_055303.2	Q15771	RAB30_HUMAN	RAB30, member RAS oncogene family	146					Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cis-Golgi network (GO:0005801)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13						AGATAATACATGTCCTGAGCT	0.438																																					p.M146V		Atlas-SNP	.											.	RAB30	28	.	0			c.A436G						.						119	108	112					11																	82693383		2203	4300	6503	SO:0001583	missense	27314	exon6			AATACATGTCCTG	U57092	CCDS8264.1	11q12-q14	2008-07-21				ENSG00000137502		"RAB, member RAS oncogene"	9770	protein-coding gene	gene with protein product		605693				8863739, 9792283	Standard	NM_014488		Approved		uc001ozu.3	Q15771		ENST00000533486.1:c.436A>G	chr11.hg19:g.82693383T>C	ENSP00000435189:p.Met146Val	82.0	0.0		77.0	30.0	NM_014488	Q6FGK1|Q6MZH2|Q96CI8	Missense_Mutation	SNP	ENST00000533486.1	hg19	CCDS8264.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.991444	0.54041	.	.	ENSG00000137502	ENST00000533486;ENST00000260056;ENST00000533014;ENST00000527633;ENST00000531021	T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19	5.96	5.96	0.96718	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.74658	0.3745	N	0.25825	0.765	0.80722	D	1	D	0.57257	0.979	P	0.50590	0.645	T	0.73805	-0.3867	9	.	.	.	.	16.4277	0.83824	0.0:0.0:0.0:1.0	.	146	Q15771	RAB30_HUMAN	V	146;146;110;146;146	ENSP00000435189:M146V;ENSP00000260056:M146V;ENSP00000433832:M110V;ENSP00000435089:M146V;ENSP00000434953:M146V	.	M	-	1	0	RAB30	82371031	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.186000	0.72026	2.279000	0.76181	0.533000	0.62120	ATG	.	.		0.438	RAB30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392141.1	NM_014488		C	82693383	T	C	82693383	3	2	214	1	0	0	0	0	1	0	0	0	12934	1464	51	2	179	2	RAB30	11	82693383	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	19517132	82693383	52313133	66	30861										
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120350697	120350697	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ttgaagcagttgctggtgcaAcagctaggtttgactgagaa	13	6	0	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr11:120350697A>T	ENST00000397843.2	+	38	3961	c.3795A>T	c.(3793-3795)caA>caT	p.Q1265H	ARHGEF12_ENST00000356641.3_Missense_Mutation_p.Q1246H|ARHGEF12_ENST00000532993.1_Missense_Mutation_p.Q1162H	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	1265					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		TGCTGGTGCAACAGCTAGGTT	0.453			T	MLL	AML																																p.Q1265H		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.A3795T						.						130	119	123					11																	120350697		1867	4099	5966	SO:0001583	missense	23365	exon38			GGTGCAACAGCTA	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.3795A>T	chr11.hg19:g.120350697A>T	ENSP00000380942:p.Gln1265His	114.0	0.0		108.0	40.0	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	hg19	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	A	10.97	1.502624	0.26949	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	T;T;T	0.70045	-0.35;-0.45;-0.33	5.5	-10.2	0.00374	.	0.295030	0.24343	N	0.039342	T	0.40473	0.1118	N	0.19112	0.55	0.22378	N	0.999159	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.03684	-1.1013	10	0.37606	T	0.19	-1.0513	11.5917	0.50949	0.2577:0.224:0.5183:0.0	.	1246;1265	Q9NZN5-2;Q9NZN5	.;ARHGC_HUMAN	H	1265;1246;1162	ENSP00000380942:Q1265H;ENSP00000349056:Q1246H;ENSP00000432984:Q1162H	ENSP00000349056:Q1246H	Q	+	3	2	ARHGEF12	119855907	0.216000	0.23585	0.028000	0.17463	0.555000	0.35460	-0.819000	0.04462	-2.528000	0.00493	-1.162000	0.01777	CAA	.	.		0.453	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		T	120350697	A	T	120350697	3	4	214	1	0	0	0	0	1	0	0	0	897	40	2	4	3945	4	ARHGEF12	11	120350697	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	37657314	120350697	14655819	67	30862										
CLEC6A	93978	hgsc.bcm.edu	37	chr12	8612284	8612284	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	acctgcttcagtgaagggacAaaggtgccaggtaaatcttt	11	8	2	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr12:8612284A>G	ENST00000382073.3	+	3	399	c.213A>G	c.(211-213)acA>acG	p.T71T		NM_001007033.1	NP_001007034.1	Q6EIG7	CLC6A_HUMAN	C-type lectin domain family 6, member A	71					defense response to fungus (GO:0050832)|innate immune response (GO:0045087)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|large_intestine(2)|lung(7)	10	Lung SC(5;0.184)					GTGAAGGGACAAAGGTGCCAG	0.383																																					p.T71T		Atlas-SNP	.											.	CLEC6A	19	.	0			c.A213G						.						120	116	117					12																	8612284		2203	4300	6503	SO:0001819	synonymous_variant	93978	exon3			AGGGACAAAGGTG	AY321309	CCDS31739.1	12p13	2005-09-21	2005-02-09	2005-02-11	ENSG00000205846	ENSG00000205846		"C-type lectin domain containing"	14556	protein-coding gene	gene with protein product		613579	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 10"	CLECSF10			Standard	NM_001007033		Approved	dectin-2	uc001qum.1	Q6EIG7	OTTHUMG00000168672	ENST00000382073.3:c.213A>G	chr12.hg19:g.8612284A>G		82.0	0.0		63.0	18.0	NM_001007033	A2RUK3	Silent	SNP	ENST00000382073.3	hg19	CCDS31739.1																																																																																			.	.		0.383	CLEC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400562.1	NM_001007033		G	8612284	A	G	8612284	2	3	214	1	0	0	0	0	0	0	0	1	3522	117	5	2		2	CLEC6A	12	8612284	Silent	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10		8612284	125239611	68	30863										
DNM1L	10059	hgsc.bcm.edu	37	chr12	32883956	32883977	+	Frame_Shift_Del	DEL	GTGCTAGAATTTGTTATATTTT	GTGCTAGAATTTGTTATATTTT	-													0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	attgcctttcagatgcggtgGtgctagaatttgttatattt							TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	GTGCTAGAATTTGTTATATTTT	GTGCTAGAATTTGTTATATTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr12:32883956_32883977delGTGCTAGAATTTGTTATATTTT	ENST00000549701.1	+	10	1162_1183	c.1088_1109delGTGCTAGAATTTGTTATATTTT	c.(1087-1110)ggtgctagaatttgttatattttcfs	p.GARICYIF363fs	DNM1L_ENST00000547312.1_Frame_Shift_Del_p.GARICYIF363fs|DNM1L_ENST00000414834.2_Frame_Shift_Del_p.GARICYIF160fs|DNM1L_ENST00000358214.5_Frame_Shift_Del_p.GARICYIF376fs|DNM1L_ENST00000266481.6_Frame_Shift_Del_p.GARICYIF363fs|DNM1L_ENST00000381000.4_Frame_Shift_Del_p.GARICYIF376fs|YARS2_ENST00000551673.1_Intron|DNM1L_ENST00000553257.1_Frame_Shift_Del_p.GARICYIF376fs|DNM1L_ENST00000452533.2_Frame_Shift_Del_p.GARICYIF363fs			O00429	DNM1L_HUMAN	dynamin 1-like	363	Middle domain.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					AGATGCGGTGGTGCTAGAATTTGTTATATTTTCCATGAGACT	0.383																																					p.363_370del		Atlas-INDEL	.											.	DNM1L	52	.	0			c.1087_1108del						.																																			SO:0001589	frameshift_variant	10059	exon10			.	AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.1088_1109delGTGCTAGAATTTGTTATATTTT	chr12.hg19:g.32883956_32883977delGTGCTAGAATTTGTTATATTTT	ENSP00000450399:p.Gly363fs	120.0	0.0		87.0	13.0	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Frame_Shift_Del	DEL	ENST00000549701.1	hg19	CCDS8729.1																																																																																			.	.		0.383	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062		-	32883977	GTGCTAGAATTTGTTATATTTT	-	32883956	7	5	214	1	0	1	0	1	0	0	0	0	4673	1261	44	0	1126	0	DNM1L	12	32883956	Frame_Shift_Del	DEL	GTGCTAGAATTTGTTATATTTT	TCGA-DD-AAE9-01A-11D-A40R-10	24271672	32883956	100967939	69	30864										
ABCD2	225	hgsc.bcm.edu	37	chr12	40012907	40012907	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	agttctgaaggccaaagccaAtttgcattccaggtacctta	8	10	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr12:40012907A>G	ENST00000308666.3	-	1	646	c.511T>C	c.(511-513)Ttg>Ctg	p.L171L		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	171	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.|Interaction with PEX19.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						GCCAAAGCCAATTTGCATTCC	0.423																																					p.L171L		Atlas-SNP	.											.	ABCD2	127	.	0			c.T511C						.						110	108	109					12																	40012907		2203	4300	6503	SO:0001819	synonymous_variant	225	exon1			AAGCCAATTTGCA	U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.511T>C	chr12.hg19:g.40012907A>G		263.0	0.0		223.0	96.0	NM_005164	B2RAM3|Q13210|Q2M3H9	Silent	SNP	ENST00000308666.3	hg19	CCDS8734.1																																																																																			.	.		0.423	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164		G	40012907	A	G	40012907	2	3	214	1	0	0	0	0	0	0	0	1	61	98	4	2		2	ABCD2	12	40012907	Silent	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	7128951	40012907	93838988	70	30865										
HDAC7	51564	hgsc.bcm.edu	37	chr12	48179583	48179583	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gcctcagaggcgtcacagatGgctgtgaggtcatggccacc	14	12	3	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr12:48179583G>T	ENST00000427332.2	-	23	2697	c.2541C>A	c.(2539-2541)gcC>gcA	p.A847A	HDAC7_ENST00000354334.3_Silent_p.A849A|HDAC7_ENST00000080059.7_Silent_p.A886A|AC004466.1_ENST00000599515.1_3'UTR|HDAC7_ENST00000552960.1_Silent_p.A869A|HDAC7_ENST00000380610.4_Silent_p.A903A			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	847	Histone deacetylase.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		CGTCACAGATGGCTGTGAGGT	0.607																																					p.A886A		Atlas-SNP	.											.	HDAC7	71	.	0			c.C2658A						.						48	35	40					12																	48179583		2203	4300	6503	SO:0001819	synonymous_variant	51564	exon23			ACAGATGGCTGTG	AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"histone deacetylase 7A"	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.2541C>A	chr12.hg19:g.48179583G>T		189.0	0.0		135.0	53.0	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Silent	SNP	ENST00000427332.2	hg19		.	.	.	.	.	.	.	.	.	.	G	9.595	1.127083	0.20959	.	.	ENSG00000061273	ENST00000548080	.	.	.	4.25	3.36	0.38483	.	.	.	.	.	T	0.56688	0.2002	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52548	-0.8561	4	.	.	.	.	7.9374	0.29937	0.1906:0.0:0.8094:0.0	.	.	.	.	Q	279	.	.	P	-	2	0	HDAC7	46465850	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.513000	0.35823	1.179000	0.42884	-0.284000	0.09977	CCA	.	.		0.607	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2			T	48179583	G	T	48179583	2	4	214	1	0	0	0	0	0	0	0	1	7021	1335	47	3		3	HDAC7	12	48179583	Silent	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	8166676	48179583	85672312	71	30866										
SYT1	6857	hgsc.bcm.edu	37	chr12	79837902	79837902	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	aatggtaagaggctgaagaaGaaaaagacaacaattaaaaa	9	3	0	5			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr12:79837902G>T	ENST00000261205.4	+	10	1635	c.978G>T	c.(976-978)aaG>aaT	p.K326N	SYT1_ENST00000393240.3_Missense_Mutation_p.K326N|SYT1_ENST00000552744.1_Missense_Mutation_p.K326N|RP1-78O14.1_ENST00000550268.1_lincRNA|SYT1_ENST00000457153.2_Missense_Mutation_p.K323N	NM_005639.2	NP_005630.1	P21579	SYT1_HUMAN	synaptotagmin I	326	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000305}.				calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|detection of calcium ion (GO:0005513)|glutamate secretion (GO:0014047)|neurotransmitter secretion (GO:0007269)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of vesicle fusion (GO:0031340)|protein homooligomerization (GO:0051260)|regulation of exocytosis (GO:0017157)|regulation of regulated secretory pathway (GO:1903305)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|vesicle docking (GO:0048278)	cell junction (GO:0030054)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|endocytic vesicle membrane (GO:0030666)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol binding (GO:0005545)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|pancreas(2)|skin(6)	25						GGCTGAAGAAGAAAAAGACAA	0.338																																					p.K326N		Atlas-SNP	.											.	SYT1	70	.	0			c.G978T						.						148	134	139					12																	79837902		2203	4300	6503	SO:0001583	missense	6857	exon11			GAAGAAGAAAAAG		CCDS9017.1	12q21.2	2013-09-20			ENSG00000067715	ENSG00000067715		"Synaptotagmins"	11509	protein-coding gene	gene with protein product		185605		SYT, SVP65		1840599	Standard	NM_001135805		Approved	P65	uc001syv.3	P21579	OTTHUMG00000134326	ENST00000261205.4:c.978G>T	chr12.hg19:g.79837902G>T	ENSP00000261205:p.Lys326Asn	142.0	0.0		93.0	31.0	NM_001135805	Q6AI31	Missense_Mutation	SNP	ENST00000261205.4	hg19	CCDS9017.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221238	0.79464	.	.	ENSG00000067715	ENST00000393240;ENST00000261205;ENST00000457153;ENST00000552744	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	5.45	5.45	0.79879	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.85128	0.5626	M	0.87827	2.91	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.87233	0.2261	10	0.87932	D	0	.	12.6052	0.56519	0.0756:0.0:0.9244:0.0	.	326;326	Q6AI31;P21579	.;SYT1_HUMAN	N	326;326;323;326	ENSP00000376932:K326N;ENSP00000261205:K326N;ENSP00000391056:K323N;ENSP00000447575:K326N	ENSP00000261205:K326N	K	+	3	2	SYT1	78362033	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.863000	0.69568	2.567000	0.86603	0.655000	0.94253	AAG	.	.		0.338	SYT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259415.1	NM_005639		T	79837902	G	T	79837902	3	4	214	1	0	0	0	0	1	0	0	0	15480	933	33	3	1004	3	SYT1	12	79837902	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	31658319	79837902	54013993	72	30867										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80707277	80707277	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ttgacgttacttcttttgccAaaaattgtcatgaagataca	6	7	2	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr12:80707277A>G	ENST00000547103.1	+	30	3451	c.3445A>G	c.(3445-3447)Aaa>Gaa	p.K1149E	OTOGL_ENST00000458043.2_Missense_Mutation_p.K1149E			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1149					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TTCTTTTGCCAAAAATTGTCA	0.348																																					p.K1149E		Atlas-SNP	.											.	OTOGL	235	.	0			c.A3445G						.						127	128	128					12																	80707277		2146	4277	6423	SO:0001583	missense	283310	exon30			TTTGCCAAAAATT	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.3445A>G	chr12.hg19:g.80707277A>G	ENSP00000447211:p.Lys1149Glu	115.0	0.0		98.0	34.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.	.	.	.	.	.	.	.	.	.	A	26.0	4.695995	0.88830	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.75704	-0.96;-0.96	5.64	5.64	0.86602	.	.	.	.	.	T	0.62636	0.2444	N	0.17838	0.53	0.53005	D	0.999965	.	.	.	.	.	.	T	0.59621	-0.7420	7	0.05833	T	0.94	.	15.8614	0.79026	1.0:0.0:0.0:0.0	.	.	.	.	E	1149	ENSP00000447211:K1149E;ENSP00000400895:K1149E	ENSP00000400895:K1149E	K	+	1	0	OTOGL	79231408	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.856000	0.92245	2.137000	0.66172	0.528000	0.53228	AAA	.	.		0.348	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		G	80707277	A	G	80707277	3	3	214	1	0	0	0	0	1	0	0	0	1709	131	5	2	3563	2	C12orf64	12	80707277	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	869375	80707277	53144618	73	30868										
AMDHD1	144193	hgsc.bcm.edu	37	chr12	96360166	96360166	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctgtgtaaacatgagaatgtCcatgcctgaggccttggccg	12	10	0	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr12:96360166C>G	ENST00000266736.2	+	8	1179	c.1073C>G	c.(1072-1074)tCc>tGc	p.S358C		NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	358					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						ATGAGAATGTCCATGCCTGAG	0.488																																					p.S358C		Atlas-SNP	.											.	AMDHD1	56	.	0			c.C1073G						.						147	128	135					12																	96360166		2203	4300	6503	SO:0001583	missense	144193	exon8			GAATGTCCATGCC	AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.1073C>G	chr12.hg19:g.96360166C>G	ENSP00000266736:p.Ser358Cys	78.0	0.0		75.0	24.0	NM_152435	A8K463|Q68CI8	Missense_Mutation	SNP	ENST00000266736.2	hg19	CCDS9057.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.346021	0.82022	.	.	ENSG00000139344	ENST00000266736	T	0.72394	-0.65	5.62	5.62	0.85841	Amidohydrolase 3 (1);Metal-dependent hydrolase, composite domain (1);	0.105169	0.64402	D	0.000002	D	0.88621	0.6486	M	0.94063	3.49	0.58432	D	0.999998	D	0.76494	0.999	D	0.71656	0.974	D	0.91059	0.4884	10	0.87932	D	0	-1.1515	19.6523	0.95822	0.0:1.0:0.0:0.0	.	358	Q96NU7	HUTI_HUMAN	C	358	ENSP00000266736:S358C	ENSP00000266736:S358C	S	+	2	0	AMDHD1	94884297	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.733000	0.68571	2.650000	0.89964	0.561000	0.74099	TCC	.	.		0.488	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435		G	96360166	C	G	96360166	3	3	214	1	0	0	0	0	1	0	0	0	567	855	30	4	1103	4	AMDHD1	12	96360166	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	15652889	96360166	37491729	74	30869										
FAM71C	196472	hgsc.bcm.edu	37	chr12	100043076	100043076	+	Frame_Shift_Del	DEL	T	T	-													0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctctccctagggatatgccaTgaagttttgtgaagagaagg					rs35488750		TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr12:100043076delT	ENST00000324341.1	+	2	1048	c.626delT	c.(625-627)atgfs	p.M209fs	ANKS1B_ENST00000547776.2_Intron|ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	209										breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		GGATATGCCATGAAGTTTTGT	0.373																																					p.M209X		Atlas-INDEL	.											.	FAM71C	48	.	0			c.625delA						.						171	167	169					12																	100043076		2203	4300	6503	SO:0001589	frameshift_variant	196472	exon2			.		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.626delT	chr12.hg19:g.100043076delT	ENSP00000315247:p.Met209fs	93.0	0.0		65.0	19.0	NM_153364	B2R6Y6	Frame_Shift_Del	DEL	ENST00000324341.1	hg19	CCDS9072.1																																																																																			.	.		0.373	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364		-	100043076	T	-	100043076	7	5	214	1	0	1	0	1	0	0	0	0	5617	1464	51	0	632	0	FAM71C	12	100043076	Frame_Shift_Del	DEL	T	TCGA-DD-AAE9-01A-11D-A40R-10	3682910	100043076	33808819	75	30870										
GPR109A	338442	hgsc.bcm.edu	37	chr12	123187347	123187347	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cggcatcttcttcttcaggaGgtggactgtcaggccaatag	12	10	5	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr12:123187347G>T	ENST00000328880.5	-	1	543	c.484C>A	c.(484-486)Ctc>Atc	p.L162I	HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	162					negative regulation of lipid catabolic process (GO:0050995)|neutrophil apoptotic process (GO:0001781)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of neutrophil apoptotic process (GO:0033031)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nicotinic acid receptor activity (GO:0070553)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	15					Niacin(DB00627)	TTCTTCAGGAGGTGGACTGTC	0.547																																					p.L162I		Atlas-SNP	.											.	HCAR2	36	.	0			c.C484A						.						111	97	102					12																	123187347		2203	4300	6503	SO:0001583	missense	338442	exon1			TCAGGAGGTGGAC	AY148884	CCDS9235.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000182782	ENSG00000182782		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	24827	protein-coding gene	gene with protein product	"niacin receptor 1"	609163	"G protein-coupled receptor 109A"	GPR109A		21167710, 12522134, 12646212, 19141678, 18983141, 21454438	Standard	NM_177551		Approved	HCA2, HM74A, PUMAG, Puma-g, NIACR1	uc001ucx.1	Q8TDS4	OTTHUMG00000162722	ENST00000328880.5:c.484C>A	chr12.hg19:g.123187347G>T	ENSP00000375066:p.Leu162Ile	109.0	0.0		145.0	27.0	NM_177551	A0PJL5|A7LGG3	Missense_Mutation	SNP	ENST00000328880.5	hg19	CCDS9235.1	.	.	.	.	.	.	.	.	.	.	G	14.06	2.421627	0.43020	.	.	ENSG00000182782	ENST00000328880;ENST00000536970	T	0.38077	1.16	5.25	4.36	0.52297	GPCR, rhodopsin-like superfamily (1);	0.099186	0.41001	D	0.000970	T	0.39410	0.1077	L	0.40543	1.245	0.32175	N	0.581159	D	0.56746	0.977	D	0.63877	0.919	T	0.32322	-0.9911	10	0.12766	T	0.61	-41.3881	6.2038	0.20591	0.0911:0.0:0.7228:0.1861	.	162	Q8TDS4	HCAR2_HUMAN	I	162	ENSP00000375066:L162I	ENSP00000375066:L162I	L	-	1	0	HCAR2	121753300	1.000000	0.71417	0.996000	0.52242	0.349000	0.29174	1.434000	0.34958	2.894000	0.99253	0.655000	0.94253	CTC	.	.		0.547	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551		T	123187347	G	T	123187347	3	4	214	1	0	0	0	0	1	0	0	0	6633	1000	35	3	611	3	GPR109A	12	123187347	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	23144271	123187347	10664548	76	30871										
WASF3	10810	hgsc.bcm.edu	37	chr13	27255212	27255212	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tcacatgcatcggacgttacGgattactcttacccggctac	8	13	2	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr13:27255212G>A	ENST00000335327.5	+	8	916	c.738G>A	c.(736-738)acG>acA	p.T246T	WASF3_ENST00000361042.4_Silent_p.T243T	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	246					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		CGGACGTTACGGATTACTCTT	0.498																																					p.T246T		Atlas-SNP	.											.	WASF3	68	.	0			c.G738A						.						87	97	94					13																	27255212		2203	4300	6503	SO:0001819	synonymous_variant	10810	exon8			CGTTACGGATTAC	AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.738G>A	chr13.hg19:g.27255212G>A		169.0	0.0		159.0	61.0	NM_006646	O94974|Q86VQ2	Silent	SNP	ENST00000335327.5	hg19	CCDS9318.1																																																																																			.	.		0.498	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1			A	27255212	G	A	27255212	2	1	214	1	0	0	0	0	0	0	0	1	17269	1103	39	1		1	WASF3	13	27255212	Silent	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10		27255212	87914666	77	30872										
FREM2	341640	hgsc.bcm.edu	37	chr13	39265017	39265018	+	Frame_Shift_Ins	INS	-	-	C													0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ttttcagagagacagttcttINSccccattgtaatcattccca							TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr13:39265017_39265018insC	ENST00000280481.7	+	1	3752_3753	c.3536_3537insC	c.(3535-3540)ttccccfs	p.FP1179fs		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1179					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AGACAGTTCTTCCCCATTGTAA	0.416																																					p.F1179fs		Atlas-INDEL	.											.	FREM2	385	.	0			c.3536_3537insC						.																																			SO:0001589	frameshift_variant	341640	exon1			.	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.3540dupC	chr13.hg19:g.39265021_39265021dupC	ENSP00000280481:p.Phe1179fs	142.0	0.0		101.0	40.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Frame_Shift_Ins	INS	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.416	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39265018	-	C	39265017	7	5	214	1	0	1	1	0	0	0	0	0	6053	1783	62	0	3538	0	FREM2	13	39265017	Frame_Shift_Ins	INS	-	TCGA-DD-AAE9-01A-11D-A40R-10	12009805	39265017	75904861	78	30873										
ANG	283	hgsc.bcm.edu	37	chr14	21162046	21162046	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ggtcaccacttgcaagctacAtggaggttccccctggcctc	10	15	1	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr14:21162046A>T	ENST00000336811.6	+	2	923	c.323A>T	c.(322-324)cAt>cTt	p.H108L	RNASE4_ENST00000555597.1_Intron|AL163636.6_ENST00000553909.1_Intron|ANG_ENST00000554073.1_Intron|ANG_ENST00000397990.4_Missense_Mutation_p.H108L|RP11-903H12.3_ENST00000554286.1_RNA|RNASE4_ENST00000304704.4_Intron|RNASE4_ENST00000555835.1_Intron|RNASE4_ENST00000397995.2_Intron	NM_001145.4	NP_001136.1	P03950	ANGI_HUMAN	angiogenin, ribonuclease, RNase A family, 5	108					actin filament polymerization (GO:0030041)|activation of phospholipase A2 activity (GO:0032431)|activation of phospholipase C activity (GO:0007202)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|cell communication (GO:0007154)|cell death (GO:0008219)|cell migration (GO:0016477)|diacylglycerol biosynthetic process (GO:0006651)|homeostatic process (GO:0042592)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of translation (GO:0017148)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oocyte maturation (GO:0001556)|ovarian follicle development (GO:0001541)|placenta development (GO:0001890)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein secretion (GO:0050714)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|RNA phosphodiester bond hydrolysis (GO:0090501)|rRNA transcription (GO:0009303)	angiogenin-PRI complex (GO:0032311)|basal lamina (GO:0005605)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)	actin binding (GO:0003779)|copper ion binding (GO:0005507)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|heparin binding (GO:0008201)|peptide binding (GO:0042277)|receptor binding (GO:0005102)|ribonuclease activity (GO:0004540)|rRNA binding (GO:0019843)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)|prostate(1)	5	all_cancers(95;0.00387)	all_cancers(140;0.196)|all_epithelial(140;0.156)	Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	OV - Ovarian serous cystadenocarcinoma(311;3.25e-17)|GBM - Glioblastoma multiforme(265;5.56e-07)		TGCAAGCTACATGGAGGTTCC	0.498																																					p.H108L		Atlas-SNP	.											.	ANG	8	.	0			c.A323T						.						108	102	104					14																	21162046		2203	4300	6503	SO:0001583	missense	283	exon2			AGCTACATGGAGG		CCDS9554.1	14q11.1-q11.2	2014-09-17			ENSG00000214274	ENSG00000214274	3.1.27.-	"Ribonucleases, RNase A"	483	protein-coding gene	gene with protein product		105850				1978563	Standard	NM_001145		Approved	RNASE5	uc001vxw.4	P03950	OTTHUMG00000029576	ENST00000336811.6:c.323A>T	chr14.hg19:g.21162046A>T	ENSP00000336762:p.His108Leu	216.0	0.0		202.0	55.0	NM_001097577	Q05CV1|Q53X86|Q6P5T2|Q8WXE7	Missense_Mutation	SNP	ENST00000336811.6	hg19	CCDS9554.1	.	.	.	.	.	.	.	.	.	.	A	6.505	0.461358	0.12342	.	.	ENSG00000214274	ENST00000336811;ENST00000397990	T;T	0.72282	-0.64;-0.64	4.83	-9.65	0.00537	Ribonuclease A, domain (4);	3.935250	0.01972	U	0.044187	T	0.43433	0.1247	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.45366	-0.9266	10	0.45353	T	0.12	.	2.4464	0.04507	0.3474:0.2088:0.3407:0.1031	.	108	P03950	ANGI_HUMAN	L	108	ENSP00000336762:H108L;ENSP00000381077:H108L	ENSP00000336762:H108L	H	+	2	0	ANG	20231886	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.300000	0.00071	-4.334000	0.00056	-2.863000	0.00101	CAT	.	.		0.498	ANG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073731.3	NM_001097577		T	21162046	A	T	21162046	3	4	214	1	0	0	0	0	1	0	0	0	607	217	8	4	325	4	ANG	14	21162046	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10		21162046	86187494	79	30874										
RPGRIP1	57096	hgsc.bcm.edu	37	chr14	21790033	21790034	+	Missense_Mutation	DNP	GA	GA	AT													0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gaggaactggaggcaatgatGacaaaagctgacaatgataa							TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr14:21790033_21790034GA>AT	ENST00000400017.2	+	13	1632_1633	c.1632_1633GA>AT	c.(1630-1635)atGAca>atATca	p.544_545MT>IS	RPGRIP1_ENST00000307974.4_5'Flank|RPGRIP1_ENST00000382933.4_Missense_Mutation_p.186_187MT>IS|RPGRIP1_ENST00000553500.1_3'UTR|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.544_545MT>IS|RPGRIP1_ENST00000556336.1_Missense_Mutation_p.517_518MT>IS|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.517_518MT>IS	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	544					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		AGGCAATGATGACAAAAGCTGA	0.406																																					p.M544I|p.T545S		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.G1632A|c.A1633T						.																																			SO:0001583	missense	57096	exon13			AATGATGACAAAA|ATGATGACAAAAG	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	Exception_encountered	chr14.hg19:g.21790033_21790034delinsAT	ENSP00000382895:p.M544_T545delinsIS	159.0|161.0	0.0		159.0|156.0	48.0|46.0	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	hg19	CCDS45080.1																																																																																			.	.		0.406	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		AT	21790034	GA	AT	21790033	3	1	214	1	0	0	0	0	1	0	0	0	13564	1290	45	3	1682	3	RPGRIP1	14	21790033	Missense_Mutation	DNP	GA	TCGA-DD-AAE9-01A-11D-A40R-10	627987	21790033	85559507	80	30875										
STXBP6	29091	hgsc.bcm.edu	37	chr14	25325147	25325147	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	caaatgtccactcacctcccAtaattttggattggcagtta	6	11	1	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr14:25325147A>G	ENST00000323944.5	-	4	897	c.446T>C	c.(445-447)aTg>aCg	p.M149T	STXBP6_ENST00000546511.1_Missense_Mutation_p.M149T|STXBP6_ENST00000548724.1_Missense_Mutation_p.M149T|STXBP6_ENST00000550887.1_Missense_Mutation_p.M149T|STXBP6_ENST00000396700.1_Missense_Mutation_p.M149T|STXBP6_ENST00000358326.2_Missense_Mutation_p.M149T|STXBP6_ENST00000419632.2_Missense_Mutation_p.M149T			Q8NFX7	STXB6_HUMAN	syntaxin binding protein 6 (amisyn)	149					negative regulation of exocytosis (GO:0045920)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|large_intestine(3)	7				GBM - Glioblastoma multiforme(265;0.0296)		CTCACCTCCCATAATTTTGGA	0.418																																					p.M149T		Atlas-SNP	.											.	STXBP6	22	.	0			c.T446C						.						121	109	113					14																	25325147		2203	4299	6502	SO:0001583	missense	29091	exon4			CCTCCCATAATTT	AF161505	CCDS9634.1	14q11.2	2002-12-18			ENSG00000168952	ENSG00000168952			19666	protein-coding gene	gene with protein product		607958				12145319	Standard	NM_014178		Approved	amisyn, HSPC156	uc001wpu.3	Q8NFX7	OTTHUMG00000140186	ENST00000323944.5:c.446T>C	chr14.hg19:g.25325147A>G	ENSP00000324302:p.Met149Thr	93.0	0.0		101.0	25.0	NM_014178	D3DS78|Q8N3H1|Q8N8D5|Q96GF3|Q9P008	Missense_Mutation	SNP	ENST00000323944.5	hg19	CCDS9634.1	.	.	.	.	.	.	.	.	.	.	A	13.32	2.201879	0.38905	.	.	ENSG00000168952	ENST00000396700;ENST00000548724;ENST00000323944;ENST00000419632;ENST00000546511;ENST00000550887;ENST00000358326	.	.	.	5.18	5.18	0.71444	.	0.219917	0.52532	D	0.000080	T	0.40297	0.1111	N	0.16478	0.41	0.43793	D	0.99633	B	0.02656	0.0	B	0.01281	0.0	T	0.23404	-1.0189	9	0.22706	T	0.39	-18.6291	12.9799	0.58557	1.0:0.0:0.0:0.0	.	149	Q8NFX7	STXB6_HUMAN	T	149	.	ENSP00000324302:M149T	M	-	2	0	STXBP6	24394987	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.330000	0.96422	1.961000	0.56991	0.477000	0.44152	ATG	.	.		0.418	STXBP6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409166.1			G	25325147	A	G	25325147	3	3	214	1	0	0	0	0	1	0	0	0	15373	217	8	2	198	2	STXBP6	14	25325147	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	3535114	25325147	82024393	81	30876										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68257468	68257468	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cccctgaactgggtgaggacTtcaggttgaacgtgaacagc	13	10	1	4			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr14:68257468T>A	ENST00000347230.4	-	15	2714	c.2576A>T	c.(2575-2577)aAg>aTg	p.K859M	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.K859M	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	859					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		GGGTGAGGACTTCAGGTTGAA	0.512																																					p.K859M		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A2576T						.						145	128	134					14																	68257468		2203	4300	6503	SO:0001583	missense	23503	exon15			GAGGACTTCAGGT	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.2576A>T	chr14.hg19:g.68257468T>A	ENSP00000251119:p.Lys859Met	154.0	0.0		121.0	53.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.386366	0.82902	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.31247	1.65;1.5	5.33	5.33	0.75918	.	0.350334	0.30714	N	0.009036	T	0.47857	0.1468	M	0.63428	1.95	0.43435	D	0.995601	D;D	0.62365	0.989;0.991	P;P	0.56474	0.799;0.747	T	0.51052	-0.8754	10	0.87932	D	0	-17.5849	15.6241	0.76840	0.0:0.0:0.0:1.0	.	859;859	G3V2D8;Q68DK2	.;ZFY26_HUMAN	M	859;838;859	ENSP00000251119:K859M;ENSP00000450603:K859M	ENSP00000251119:K859M	K	-	2	0	ZFYVE26	67327221	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	5.658000	0.68003	2.145000	0.66743	0.533000	0.62120	AAG	.	.		0.512	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68257468	T	A	68257468	3	1	214	1	0	0	0	0	1	0	0	0	17683	1609	56	4	5155	4	ZFYVE26	14	68257468	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	42932321	68257468	39092072	82	30877										
PTPN21	11099	hgsc.bcm.edu	37	chr14	88945839	88945839	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gagccgcaggccctccaggcCgtggctgagcccggccacct	14	18	0	1	rs576261282	byFrequency	TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr14:88945839C>A	ENST00000556564.1	-	13	2220	c.1936G>T	c.(1936-1938)Ggc>Tgc	p.G646C	PTPN21_ENST00000328736.3_Missense_Mutation_p.G646C	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	646					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CCCTCCAGGCCGTGGCTGAGC	0.726																																					p.G646C		Atlas-SNP	.											.	PTPN21	113	.	0			c.G1936T						.						17	20	19					14																	88945839		2178	4257	6435	SO:0001583	missense	11099	exon13			CCAGGCCGTGGCT	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.1936G>T	chr14.hg19:g.88945839C>A	ENSP00000452414:p.Gly646Cys	33.0	0.0		33.0	12.0	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	hg19	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.732608	0.48939	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	T;T	0.75477	-0.94;-0.94	5.17	-1.32	0.09201	.	0.194142	0.56097	N	0.000035	T	0.72708	0.3494	L	0.49126	1.545	0.09310	N	0.999998	D	0.61080	0.989	P	0.58077	0.832	T	0.65994	-0.6033	10	0.66056	D	0.02	.	4.5001	0.11860	0.24:0.4213:0.0:0.3387	.	646	Q16825	PTN21_HUMAN	C	646	ENSP00000330276:G646C;ENSP00000452414:G646C	ENSP00000330276:G646C	G	-	1	0	PTPN21	88015592	0.972000	0.33761	0.000000	0.03702	0.002000	0.02628	0.417000	0.21214	-0.953000	0.03645	-2.838000	0.00105	GGC	.	.		0.726	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			A	88945839	C	A	88945839	3	1	214	1	0	0	0	0	1	0	0	0	12801	652	23	1	1616	1	PTPN21	14	88945839	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	20688371	88945839	18403701	83	30878										
TTC8	123016	hgsc.bcm.edu	37	chr14	89336480	89336480	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	aatactcatgtggaagccatCgcatgcattggaagcaacca	9	10	1	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr14:89336480C>G	ENST00000345383.5	+	10	1041	c.957C>G	c.(955-957)atC>atG	p.I319M	TTC8_ENST00000354441.6_Missense_Mutation_p.I64M|TTC8_ENST00000338104.6_Missense_Mutation_p.I345M|TTC8_ENST00000358622.5_Missense_Mutation_p.I131M|TTC8_ENST00000380656.2_Missense_Mutation_p.I329M|TTC8_ENST00000346301.4_Missense_Mutation_p.I289M|TTC8_ENST00000536576.1_Missense_Mutation_p.I90M	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	355					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						TGGAAGCCATCGCATGCATTG	0.398																																					p.I329M		Atlas-SNP	.											.	TTC8	42	.	0			c.C987G						.						160	147	151					14																	89336480		2203	4300	6503	SO:0001583	missense	123016	exon11			AGCCATCGCATGC	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"Tetratricopeptide (TTC) repeat domain containing"	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.957C>G	chr14.hg19:g.89336480C>G	ENSP00000339486:p.Ile319Met	142.0	0.0		110.0	44.0	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Missense_Mutation	SNP	ENST00000345383.5	hg19	CCDS9885.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	17.73|17.73|17.73	3.460692|3.460692|3.460692	0.63513|0.63513|0.63513	.|.|.	.|.|.	ENSG00000165533|ENSG00000165533|ENSG00000165533	ENST00000345383;ENST00000536576;ENST00000346301;ENST00000338104;ENST00000354441;ENST00000380656;ENST00000358622|ENST00000557580|ENST00000554686	T;T;T;T;T;T;T|.|.	0.53423|.|.	0.62;0.67;0.62;0.62;0.67;0.62;0.62|.|.	5.62|5.62|5.62	-6.01|-6.01|-6.01	0.02199|0.02199|0.02199	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.71341|0.71341|0.71341	0.3328|0.3328|0.3328	M|M|M	0.83223|0.83223|0.83223	2.63|2.63|2.63	0.58432|0.58432|0.58432	D|D|D	0.999994|0.999994|0.999994	D;D;D;D;D|.|.	0.89917|.|.	1.0;1.0;0.999;1.0;1.0|.|.	D;D;D;D;D|.|.	0.97110|.|.	1.0;0.992;0.995;0.997;0.997|.|.	T|T|T	0.75491|0.75491|0.75491	-0.3299|-0.3299|-0.3299	10|5|5	0.72032|.|.	D|.|.	0.01|.|.	-18.3264|-18.3264|-18.3264	13.3315|13.3315|13.3315	0.60490|0.60490|0.60490	0.0:0.476:0.0:0.524|0.0:0.476:0.0:0.524|0.0:0.476:0.0:0.524	.|.|.	64;90;355;299;329|.|.	Q8TAM2-2;B3KSL8;Q8TAM2;Q8TAM2-3;Q8TAM2-4|.|.	.;.;TTC8_HUMAN;.;.|.|.	M|G|W	319;90;289;345;64;329;131|118|279	ENSP00000339486:I319M;ENSP00000445067:I90M;ENSP00000298324:I289M;ENSP00000337653:I345M;ENSP00000346427:I64M;ENSP00000370031:I329M;ENSP00000351439:I131M|.|.	ENSP00000337653:I345M|.|.	I|R|S	+|+|+	3|1|2	3|0|0	TTC8|TTC8|TTC8	88406233|88406233|88406233	0.030000|0.030000|0.030000	0.19436|0.19436|0.19436	0.850000|0.850000|0.850000	0.33497|0.33497|0.33497	0.979000|0.979000|0.979000	0.70002|0.70002|0.70002	-0.899000|-0.899000|-0.899000	0.04101|0.04101|0.04101	-1.382000|-1.382000|-1.382000	0.02109|0.02109|0.02109	-1.090000|-1.090000|-1.090000	0.02178|0.02178|0.02178	ATC|CGC|TCG	.	.		0.398	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596		G	89336480	C	G	89336480	3	3	214	1	0	0	0	0	1	0	0	0	16729	874	31	4	1029	4	TTC8	14	89336480	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	390641	89336480	18013060	84	30879										
TBC1D2B	23102	hgsc.bcm.edu	37	chr15	78305207	78305207	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cgatatctggattccgccagGagaaggcgaggaggacattg	15	8	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr15:78305207G>T	ENST00000300584.3	-	9	2227	c.2228C>A	c.(2227-2229)tCc>tAc	p.S743Y	TBC1D2B_ENST00000409931.3_Missense_Mutation_p.S743Y	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	743	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						ATTCCGCCAGGAGAAGGCGAG	0.517																																					p.S743Y		Atlas-SNP	.											.	TBC1D2B	104	.	0			c.C2228A						.						115	95	102					15																	78305207		2196	4293	6489	SO:0001583	missense	23102	exon9			CGCCAGGAGAAGG	AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.2228C>A	chr15.hg19:g.78305207G>T	ENSP00000300584:p.Ser743Tyr	122.0	0.0		98.0	78.0	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Missense_Mutation	SNP	ENST00000300584.3	hg19	CCDS45314.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.6|23.6	4.438236|4.438236	0.83885|0.83885	.|.	.|.	ENSG00000167202|ENSG00000167202	ENST00000418039|ENST00000409931;ENST00000300584	.|T;T	.|0.05513	.|3.43;3.43	5.47|5.47	5.47|5.47	0.80525|0.80525	.|Rab-GAP/TBC domain (4);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.41373|0.41373	0.1156|0.1156	H|H	0.96916|0.96916	3.905|3.905	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.993;0.999	T|T	0.60125|0.60125	-0.7324|-0.7324	5|10	.|0.87932	.|D	.|0	.|.	18.6826|18.6826	0.91551|0.91551	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|743;195;743	.|Q9UPU7-2;Q9UPU7-3;Q9UPU7	.|.;.;TBD2B_HUMAN	T|Y	625|743	.|ENSP00000387165:S743Y;ENSP00000300584:S743Y	.|ENSP00000300584:S743Y	P|S	-|-	1|2	0|0	TBC1D2B|TBC1D2B	76092262|76092262	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.755000|0.755000	0.42902|0.42902	7.676000|7.676000	0.84012|0.84012	2.723000|2.723000	0.93209|0.93209	0.655000|0.655000	0.94253|0.94253	CCT|TCC	.	.		0.517	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079		T	78305207	G	T	78305207	3	4	214	1	0	0	0	0	1	0	0	0	15634	1174	41	3	683	3	TBC1D2B	15	78305207	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10		78305207	24226185	85	30880										
PRSS21	10942	hgsc.bcm.edu	37	chr16	2867809	2867809	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctgaccatccgaggaccatgCggccgacgggtcatcacgtc	12	15	2	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr16:2867809C>A	ENST00000005995.3	+	3	141	c.99C>A	c.(97-99)tgC>tgA	p.C33*	PRSS21_ENST00000455114.1_Nonsense_Mutation_p.C33*|PRSS21_ENST00000450020.3_Nonsense_Mutation_p.C33*			Q9Y6M0	TEST_HUMAN	protease, serine, 21 (testisin)	33					spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	15						GAGGACCATGCGGCCGACGGG	0.677																																					p.C33X		Atlas-SNP	.											.	PRSS21	32	.	0			c.C99A						.						13	14	14					16																	2867809		2092	4107	6199	SO:0001587	stop_gained	10942	exon3			ACCATGCGGCCGA	AF058300	CCDS10478.1, CCDS45388.1	16p13.3	2010-05-07			ENSG00000007038	ENSG00000007038		"Serine peptidases / Serine peptidases"	9485	protein-coding gene	gene with protein product		608159				10397266, 9826525	Standard	NM_006799		Approved	ESP-1, TEST1, TESTISIN	uc002crt.4	Q9Y6M0	OTTHUMG00000128931	ENST00000005995.3:c.99C>A	chr16.hg19:g.2867809C>A	ENSP00000005995:p.Cys33*	95.0	0.0		60.0	8.0	NM_144957	Q9NS34|Q9P2V6	Nonsense_Mutation	SNP	ENST00000005995.3	hg19	CCDS10478.1	.	.	.	.	.	.	.	.	.	.	c	13.56	2.274441	0.40194	.	.	ENSG00000007038	ENST00000455114;ENST00000450020;ENST00000005995	.	.	.	2.86	-5.72	0.02406	.	0.000000	0.34932	U	0.003570	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.136	0.59409	0.0:0.1957:0.0:0.8043	.	.	.	.	X	33	.	ENSP00000005995:C33X	C	+	3	2	PRSS21	2807810	0.001000	0.12720	0.000000	0.03702	0.081000	0.17604	-2.524000	0.00948	-2.370000	0.00602	-1.073000	0.02249	TGC	.	.		0.677	PRSS21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250910.1	NM_006799		A	2867809	C	A	2867809	4	1	214	1	0	0	0	0	0	1	0	0	12630	776	27	1	109	1	PRSS21	16	2867809	Nonsense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10		2867809	87486944	86	30881										
A2BP1	54715	hgsc.bcm.edu	37	chr16	7726804	7726804	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tgctgcataccgctacgcccAgcctacccctgccactgccg	8	20	0	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr16:7726804A>T	ENST00000550418.1	+	14	1947	c.959A>T	c.(958-960)cAg>cTg	p.Q320L	RBFOX1_ENST00000547372.1_Missense_Mutation_p.Q363L|RBFOX1_ENST00000311745.5_Missense_Mutation_p.Q341L|RBFOX1_ENST00000547338.1_Missense_Mutation_p.Q320L|RBFOX1_ENST00000553186.1_Missense_Mutation_p.Q293L|RBFOX1_ENST00000340209.4_Missense_Mutation_p.Q325L|RBFOX1_ENST00000535565.2_Missense_Mutation_p.Q277L|RBFOX1_ENST00000355637.4_Missense_Mutation_p.Q341L|RBFOX1_ENST00000552089.1_Missense_Mutation_p.Q337L|RBFOX1_ENST00000436368.2_Missense_Mutation_p.Q341L|RBFOX1_ENST00000422070.4_Missense_Mutation_p.Q363L	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	320					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						CGCTACGCCCAGCCTACCCCT	0.517																																					p.Q341L	Ovarian(157;934 2567 15163 39509)	Atlas-SNP	.											.	RBFOX1	341	.	0			c.A1022T						.						175	125	142					16																	7726804		2197	4300	6497	SO:0001583	missense	54715	exon11			ACGCCCAGCCTAC	AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"RNA binding motif (RRM) containing"	18222	protein-coding gene	gene with protein product	"ataxin 2-binding protein 1", "hexaribonucleotide binding protein 1"	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.959A>T	chr16.hg19:g.7726804A>T	ENSP00000450031:p.Gln320Leu	64.0	0.0		39.0	20.0	NM_145891	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	hg19	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082226	0.76528	.	.	ENSG00000078328	ENST00000550418;ENST00000553186;ENST00000547372;ENST00000422070;ENST00000535565;ENST00000552089;ENST00000547338;ENST00000436368;ENST00000311745;ENST00000355637;ENST00000352951;ENST00000340209	T;T;T;T;T;T;T;T;T	0.47528	1.1;1.33;0.84;1.35;1.1;1.3;1.49;1.27;1.11	5.43	4.35	0.52113	.	0.056469	0.64402	D	0.000001	T	0.62356	0.2421	M	0.68952	2.095	0.46798	D	0.999203	D;P;D;D;D;P;D;D	0.76494	0.998;0.949;0.999;0.994;0.998;0.859;0.969;0.998	D;P;D;D;D;B;P;D	0.85130	0.995;0.542;0.997;0.986;0.948;0.351;0.856;0.969	T	0.58891	-0.7556	10	0.22706	T	0.39	-7.511	10.8121	0.46553	0.9252:0.0:0.0748:0.0	.	314;277;363;341;341;341;293;320	F8WAC5;F5H0M1;B7Z1U7;Q9NWB1-2;Q9NWB1-4;Q9NWB1-5;Q9NWB1-3;Q9NWB1	.;.;.;.;.;.;.;RFOX1_HUMAN	L	320;293;363;363;277;337;320;341;341;341;314;325	ENSP00000450031:Q320L;ENSP00000447753:Q293L;ENSP00000446842:Q363L;ENSP00000391269:Q363L;ENSP00000447717:Q320L;ENSP00000402745:Q341L;ENSP00000309117:Q341L;ENSP00000347855:Q341L;ENSP00000344196:Q325L	ENSP00000309117:Q341L	Q	+	2	0	RBFOX1	7666805	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.945000	0.75947	1.018000	0.39521	0.528000	0.53228	CAG	.	.		0.517	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		T	7726804	A	T	7726804	3	4	214	1	0	0	0	0	1	0	0	0	3	188	7	4	1139	4	A2BP1	16	7726804	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	4858995	7726804	82627949	87	30882										
ORAI3	93129	hgsc.bcm.edu	37	chr16	30964577	30964577	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctgctggtggccttcagtgcCtgcaccaccgtgctggtggc	14	14	1	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr16:30964577C>T	ENST00000318663.4	+	2	524	c.300C>T	c.(298-300)gcC>gcT	p.A100A	ORAI3_ENST00000566237.1_Silent_p.A100A|AC135048.13_ENST00000566056.1_RNA|ORAI3_ENST00000562699.1_Intron	NM_152288.2	NP_689501.1	Q9BRQ5	ORAI3_HUMAN	ORAI calcium release-activated calcium modulator 3	100					store-operated calcium entry (GO:0002115)	integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6						CCTTCAGTGCCTGCACCACCG	0.592											OREG0023742	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A100A		Atlas-SNP	.											.	ORAI3	19	.	0			c.C300T						.						109	93	98					16																	30964577		2197	4300	6497	SO:0001819	synonymous_variant	93129	exon2			CAGTGCCTGCACC	BC006126	CCDS10697.1	16p11.2	2007-08-14	2007-08-14	2007-08-14	ENSG00000175938	ENSG00000175938		"ORAI calcium release-activated calcium modulators"	28185	protein-coding gene	gene with protein product		610930	"transmembrane protein 142C"	TMEM142C		16582901	Standard	NM_152288		Approved	MGC13024	uc002eac.3	Q9BRQ5	OTTHUMG00000132409	ENST00000318663.4:c.300C>T	chr16.hg19:g.30964577C>T		62.0	0.0	821	43.0	5.0	NM_152288	Q96BI8	Silent	SNP	ENST00000318663.4	hg19	CCDS10697.1																																																																																			.	.		0.592	ORAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255545.20	NM_152288		T	30964577	C	T	30964577	2	4	214	1	0	0	0	0	0	0	0	1	11268	668	24	3		3	ORAI3	16	30964577	Silent	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	23237773	30964577	59390176	88	30883										
YBX2	51087	hgsc.bcm.edu	37	chr17	7193784	7193784	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tgaatcggcgggacttacgtCggttgggggcataacggctg	17	8	0	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr17:7193784C>T	ENST00000007699.5	-	5	593	c.530G>A	c.(529-531)cGa>cAa	p.R177Q	YBX2_ENST00000570627.1_5'UTR	NM_015982.3	NP_057066.2	Q9Y2T7	YBOX2_HUMAN	Y box binding protein 2	177					mRNA stabilization (GO:0048255)|negative regulation of binding (GO:0051100)|negative regulation of translation (GO:0017148)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|translational attenuation (GO:0009386)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lipid binding (GO:0008289)|mRNA 3'-UTR binding (GO:0003730)|ribonucleoprotein complex binding (GO:0043021)|translation regulator activity (GO:0045182)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|skin(3)	12						GGACTTACGTCGGTTGGGGGC	0.627																																					p.R177Q		Atlas-SNP	.											.	YBX2	28	.	0			c.G530A						.						32	36	35					17																	7193784		2199	4291	6490	SO:0001583	missense	51087	exon5			TTACGTCGGTTGG	AF096834	CCDS11098.1	17p13.1	2013-12-20			ENSG00000006047	ENSG00000006047			17948	protein-coding gene	gene with protein product		611447				10100484, 9780336	Standard	NM_015982		Approved	MSY2, CSDA3	uc002gfq.2	Q9Y2T7	OTTHUMG00000177992	ENST00000007699.5:c.530G>A	chr17.hg19:g.7193784C>T	ENSP00000007699:p.Arg177Gln	95.0	0.0		74.0	20.0	NM_015982	D3DTP1|Q8N4P0	Missense_Mutation	SNP	ENST00000007699.5	hg19	CCDS11098.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.912445	0.92178	.	.	ENSG00000006047	ENST00000007699	T	0.29397	1.57	4.67	4.67	0.58626	.	0.151312	0.44097	D	0.000495	T	0.57344	0.2047	M	0.80508	2.5	0.43761	D	0.99627	D	0.76494	0.999	D	0.72625	0.978	T	0.63111	-0.6710	10	0.87932	D	0	-7.0809	15.478	0.75501	0.0:1.0:0.0:0.0	.	177	Q9Y2T7	YBOX2_HUMAN	Q	177	ENSP00000007699:R177Q	ENSP00000007699:R177Q	R	-	2	0	YBX2	7134508	0.999000	0.42202	0.999000	0.59377	0.943000	0.58893	3.256000	0.51492	2.613000	0.88420	0.561000	0.74099	CGA	.	.		0.627	YBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440172.2	NM_015982		T	7193784	C	T	7193784	3	4	214	1	0	0	0	0	1	0	0	0	17485	884	31	1	580	1	YBX2	17	7193784	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10		7193784	74001426	89	30884										
ZBTB4	57659	hgsc.bcm.edu	37	chr17	7366504	7366504	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	acagtgatctgacacagtggAggtggagcctgcagctgaga	15	8	1	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr17:7366504A>C	ENST00000311403.4	-	4	2136	c.1797T>G	c.(1795-1797)ccT>ccG	p.P599P	ZBTB4_ENST00000380599.4_Silent_p.P599P	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	599					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		GACACAGTGGAGGTGGAGCCT	0.652																																					p.P599P		Atlas-SNP	.											.	ZBTB4	163	.	0			c.T1797G						.						23	20	21					17																	7366504		2203	4299	6502	SO:0001819	synonymous_variant	57659	exon4			CAGTGGAGGTGGA	AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.1797T>G	chr17.hg19:g.7366504A>C		22.0	0.0		26.0	9.0	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Silent	SNP	ENST00000311403.4	hg19	CCDS11107.1																																																																																			.	.		0.652	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899		C	7366504	A	C	7366504	2	2	214	1	0	0	0	0	0	0	0	1	17556	291	11	5		5	ZBTB4	17	7366504	Silent	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	172720	7366504	73828706	90	30885										
NF1	4763	hgsc.bcm.edu	37	chr17	29586118	29586118	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	atgcggcctttcaatgatttTgtgaaaagcaactttgatgc	9	7	1	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr17:29586118T>A	ENST00000358273.4	+	33	4784	c.4401T>A	c.(4399-4401)ttT>ttA	p.F1467L	NF1_ENST00000356175.3_Missense_Mutation_p.F1446L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1467					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(5)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TCAATGATTTTGTGAAAAGCA	0.348			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.F1467L		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	13	Whole gene deletion(8)|Unknown(5)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)|lung(1)	c.T4401A						.						53	48	49					17																	29586118		2201	4298	6499	SO:0001583	missense	4763	exon33	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	TGATTTTGTGAAA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4401T>A	chr17.hg19:g.29586118T>A	ENSP00000351015:p.Phe1467Leu	132.0	0.0		114.0	5.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.671608	0.88348	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;D;D	0.84944	-1.92;-1.92;-1.92	5.78	4.71	0.59529	Rho GTPase activation protein (1);Armadillo-type fold (1);Ras GTPase-activating protein (2);	0.000000	0.85682	D	0.000000	D	0.87402	0.6168	L	0.42487	1.325	0.80722	D	1	P;P;B	0.52577	0.717;0.954;0.209	B;D;B	0.66351	0.263;0.943;0.134	D	0.85716	0.1322	10	0.44086	T	0.13	.	9.3926	0.38383	0.0:0.1545:0.0:0.8455	.	496;1446;1467	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	L	1467;1446;1112	ENSP00000351015:F1467L;ENSP00000348498:F1446L;ENSP00000389907:F1112L	ENSP00000348498:F1446L	F	+	3	2	NF1	26610244	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.010000	0.49559	1.021000	0.39600	0.454000	0.30748	TTT	.	.		0.348	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		A	29586118	T	A	29586118	3	1	214	1	0	0	0	0	1	0	0	0	10365	1809	63	4	4592	4	NF1	17	29586118	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	22219614	29586118	51609092	91	30886										
G6PC	2538	hgsc.bcm.edu	37	chr17	41063257	41063257	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	aagtggctcccattccgcctCagctctattgtagcctccct	7	16	2	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr17:41063257C>G	ENST00000253801.2	+	5	967	c.888C>G	c.(886-888)ctC>ctG	p.L296L	G6PC_ENST00000592383.1_3'UTR|G6PC_ENST00000585489.1_3'UTR	NM_000151.3	NP_000142.2	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit	296					carbohydrate metabolic process (GO:0005975)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|hexose transport (GO:0008645)|multicellular organism growth (GO:0035264)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)|urate metabolic process (GO:0046415)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)|phosphate ion binding (GO:0042301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		CATTCCGCCTCAGCTCTATTG	0.567																																					p.L296L		Atlas-SNP	.											.	G6PC	48	.	0			c.C888G						.						124	117	119					17																	41063257		2203	4300	6503	SO:0001819	synonymous_variant	2538	exon5			CCGCCTCAGCTCT	U01120	CCDS11446.1, CCDS59291.1	17q21	2014-09-17	2006-06-28			ENSG00000131482	3.1.3.9		4056	protein-coding gene	gene with protein product	"glycogen storage disease type I, von Gierke disease"	613742	"glucose-6-phosphatase, catalytic (glycogen storage disease type I, von Gierke disease)"	G6PT		7774924	Standard	NM_000151		Approved	GSD1a	uc002icb.2	P35575		ENST00000253801.2:c.888C>G	chr17.hg19:g.41063257C>G		140.0	0.0		104.0	30.0	NM_000151	A1L4C0|B4E1C3|K7EL82	Silent	SNP	ENST00000253801.2	hg19	CCDS11446.1																																																																																			.	.		0.567	G6PC-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452451.1	NM_000151		G	41063257	C	G	41063257	2	3	214	1	0	0	0	0	0	0	0	1	6151	813	29	4		4	G6PC	17	41063257	Silent	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	11477139	41063257	40131953	92	30887										
MRC2	9902	hgsc.bcm.edu	37	chr17	60742244	60742244	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gcacccttgagcgtggtgacCagacccgcagtggccagtgg	15	13	0	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr17:60742244C>T	ENST00000303375.5	+	2	856	c.454C>T	c.(454-456)Cag>Tag	p.Q152*		NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	152	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						GCGTGGTGACCAGACCCGCAG	0.652																																					p.Q152X		Atlas-SNP	.											.	MRC2	126	.	0			c.C454T						.						52	52	52					17																	60742244		2203	4300	6503	SO:0001587	stop_gained	9902	exon2			GGTGACCAGACCC	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.454C>T	chr17.hg19:g.60742244C>T	ENSP00000307513:p.Gln152*	86.0	0.0		59.0	22.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Nonsense_Mutation	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	C	40	8.139523	0.98672	.	.	ENSG00000011028	ENST00000303375	.	.	.	5.23	5.23	0.72850	.	0.414724	0.25881	N	0.027682	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-15.947	18.8087	0.92048	0.0:1.0:0.0:0.0	.	.	.	.	X	152	.	ENSP00000307513:Q152X	Q	+	1	0	MRC2	58095976	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.718000	0.54919	2.450000	0.82876	0.561000	0.74099	CAG	.	.		0.652	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			T	60742244	C	T	60742244	4	4	214	1	0	0	0	0	0	1	0	0	9767	595	21	3	460	3	MRC2	17	60742244	Nonsense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	19678987	60742244	20452966	93	30888										
OSBPL1A	114876	hgsc.bcm.edu	37	chr18	21948322	21948322	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tagaggtgtccagcccaagtTagacttacttcttcctaaaa	7	10	1	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr18:21948322T>C	ENST00000319481.3	-	3	342	c.136A>G	c.(136-138)Aac>Gac	p.N46D	RP11-621L6.2_ENST00000579347.1_RNA|OSBPL1A_ENST00000582618.1_5'UTR|OSBPL1A_ENST00000399441.4_Missense_Mutation_p.N46D	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	46	Interaction with RAB7A.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					CAGCCCAAGTTAGACTTACTT	0.343																																					p.N46D		Atlas-SNP	.											.	OSBPL1A	94	.	0			c.A136G						.						95	92	93					18																	21948322		2203	4300	6503	SO:0001583	missense	114876	exon3			CCAAGTTAGACTT	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"Oxysterol binding proteins", "Ankyrin repeat domain containing"	16398	protein-coding gene	gene with protein product		606730	"oxysterol binding protein-like 1B"	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.136A>G	chr18.hg19:g.21948322T>C	ENSP00000320291:p.Asn46Asp	476.0	0.0		426.0	151.0	NM_080597	B7Z7D3|Q9BZF5|Q9NW87	Missense_Mutation	SNP	ENST00000319481.3	hg19	CCDS11884.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.214442	0.79352	.	.	ENSG00000141447	ENST00000319481;ENST00000399441	T;T	0.57595	0.63;0.39	4.42	4.42	0.53409	Ankyrin repeat-containing domain (3);	0.000000	0.85682	U	0.000000	T	0.49372	0.1553	N	0.05031	-0.125	0.53688	D	0.999975	D	0.69078	0.997	D	0.79108	0.992	T	0.52837	-0.8522	10	0.30078	T	0.28	-26.6142	12.924	0.58249	0.0:0.0:0.0:1.0	.	46	Q9BXW6	OSBL1_HUMAN	D	46	ENSP00000320291:N46D;ENSP00000382370:N46D	ENSP00000320291:N46D	N	-	1	0	OSBPL1A	20202320	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.440000	0.73435	1.757000	0.51966	0.482000	0.46254	AAC	.	.		0.343	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		C	21948322	T	C	21948322	3	2	214	1	0	0	0	0	1	0	0	0	11286	1754	61	2	2820	2	OSBPL1A	18	21948322	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10		21948322	56128926	94	30889										
CNN1	1264	hgsc.bcm.edu	37	chr19	11660435	11660435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gggcatggagcactgcgacaCgctcaatgtcagcctgcaga	13	12	2	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr19:11660435C>T	ENST00000252456.2	+	7	930	c.719C>T	c.(718-720)aCg>aTg	p.T240M	CNN1_ENST00000544952.1_Missense_Mutation_p.T220M|CNN1_ENST00000535659.2_Missense_Mutation_p.T190M|CNN1_ENST00000592923.1_Missense_Mutation_p.T190M	NM_001299.4	NP_001290.2	P51911	CNN1_HUMAN	calponin 1, basic, smooth muscle	240					actomyosin structure organization (GO:0031032)|regulation of smooth muscle contraction (GO:0006940)	cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9						CACTGCGACACGCTCAATGTC	0.657																																					p.T240M		Atlas-SNP	.											.	CNN1	34	.	0			c.C719T						.						45	44	44					19																	11660435		2203	4300	6503	SO:0001583	missense	1264	exon7			GCGACACGCTCAA	U37019	CCDS12263.1	19p13.2-p13.1	2008-07-16				ENSG00000130176			2155	protein-coding gene	gene with protein product		600806				8526917, 9332369	Standard	XM_005259741		Approved	SMCC, Sm-Calp	uc002msc.1	P51911		ENST00000252456.2:c.719C>T	chr19.hg19:g.11660435C>T	ENSP00000252456:p.Thr240Met	134.0	0.0		103.0	35.0	NM_001299	B2R868|B4DUX6|O00638|Q15416|Q8IY93|Q99438	Missense_Mutation	SNP	ENST00000252456.2	hg19	CCDS12263.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.961669	0.34659	.	.	ENSG00000130176	ENST00000252456;ENST00000535659;ENST00000544952	T;T;T	0.31247	1.5;1.5;1.5	4.78	0.18	0.15068	.	0.238555	0.40908	N	0.000991	T	0.22513	0.0543	L	0.47716	1.5	0.32339	N	0.559965	B	0.15930	0.015	B	0.08055	0.003	T	0.10200	-1.0640	10	0.72032	D	0.01	-20.5818	6.2798	0.21001	0.0:0.6384:0.1339:0.2277	.	240	P51911	CNN1_HUMAN	M	240;190;220	ENSP00000252456:T240M;ENSP00000442031:T190M;ENSP00000437470:T220M	ENSP00000252456:T240M	T	+	2	0	CNN1	11521435	0.001000	0.12720	0.314000	0.25224	0.986000	0.74619	-0.056000	0.11787	-0.008000	0.14320	0.542000	0.68232	ACG	.	.		0.657	CNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458854.1	NM_001299		T	11660435	C	T	11660435	3	4	214	1	0	0	0	0	1	0	0	0	3611	536	19	1	745	1	CNN1	19	11660435	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10		11660435	47468548	95	30890										
RYR1	6261	hgsc.bcm.edu	37	chr19	39055621	39055621	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gaaggagtccaagcgccagtTcatcttcgacgtggtgaacg	13	10	2	1	rs118192165|rs118192128		TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr19:39055621T>A	ENST00000359596.3	+	91	12647	c.12647T>A	c.(12646-12648)tTc>tAc	p.F4216Y	RYR1_ENST00000355481.4_Missense_Mutation_p.F4211Y|RYR1_ENST00000360985.3_Missense_Mutation_p.F4211Y			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4216			Missing (in CCD).		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	AAGCGCCAGTTCATCTTCGAC	0.632																																					p.F4216Y		Atlas-SNP	.											.	RYR1	708	.	0			c.T12647A						.						28	22	24					19																	39055621		2200	4296	6496	SO:0001583	missense	6261	exon91			GCCAGTTCATCTT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.12647T>A	chr19.hg19:g.39055621T>A	ENSP00000352608:p.Phe4216Tyr	984.0	0.0		706.0	277.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812665	0.50527	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98150	-4.75;-4.75;-4.75	3.07	3.07	0.35406	.	0.000000	0.64402	U	0.000001	D	0.98435	0.9479	M	0.85777	2.775	0.48571	D	0.999676	D;D;D	0.61080	0.989;0.989;0.981	D;D;D	0.70487	0.953;0.969;0.931	D	0.98626	1.0669	10	0.62326	D	0.03	.	11.4175	0.49960	0.0:0.0:0.0:1.0	.	4211;4211;4216	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	Y	4216;4211;4211	ENSP00000352608:F4216Y;ENSP00000347667:F4211Y;ENSP00000354254:F4211Y	ENSP00000347667:F4211Y	F	+	2	0	RYR1	43747461	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.741000	0.84997	1.424000	0.47217	0.414000	0.27820	TTC	.	.		0.632	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	39055621	T	A	39055621	3	1	214	1	0	0	0	0	1	0	0	0	13783	1783	62	4	13009	4	RYR1	19	39055621	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	27395186	39055621	20073362	96	30891										
PSG8	440533	hgsc.bcm.edu	37	chr19	43268178	43268178	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gggtgacattctggatcagcAgggatgcattggaatatatt	13	5	2	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr19:43268178A>G	ENST00000306511.4	-	2	417	c.320T>C	c.(319-321)cTg>cCg	p.L107P	PSG8_ENST00000406636.3_Intron|PSG8_ENST00000401467.2_Missense_Mutation_p.L107P|PSG8_ENST00000404209.4_Missense_Mutation_p.L107P	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	107	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				CTGGATCAGCAGGGATGCATT	0.423																																					p.L107P		Atlas-SNP	.											.	PSG8	101	.	0			c.T320C						.						378	381	380					19																	43268178		2203	4299	6502	SO:0001583	missense	440533	exon2			ATCAGCAGGGATG	M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.320T>C	chr19.hg19:g.43268178A>G	ENSP00000305005:p.Leu107Pro	113.0	0.0		69.0	23.0	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	hg19	CCDS33037.1	.	.	.	.	.	.	.	.	.	.	a	12.24	1.879831	0.33162	.	.	ENSG00000124467	ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.09723	2.95;2.95;2.95	1.35	1.35	0.21983	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.42787	0.1218	H	0.97940	4.11	0.26424	N	0.976049	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;1.0	T	0.23261	-1.0193	9	0.87932	D	0	.	4.8841	0.13694	1.0:0.0:0.0:0.0	.	107;107;107;107;107	B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.;.	P	107	ENSP00000385869:L107P;ENSP00000386090:L107P;ENSP00000305005:L107P	ENSP00000305005:L107P	L	-	2	0	PSG8	47960018	0.705000	0.27846	0.189000	0.23252	0.141000	0.21300	2.096000	0.41738	0.879000	0.35944	0.155000	0.16302	CTG	.	.		0.423	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1			G	43268178	A	G	43268178	3	3	214	1	0	0	0	0	1	0	0	0	12673	188	7	2	997	2	PSG8	19	43268178	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	4212557	43268178	15860805	97	30892										
ZNF45	7596	hgsc.bcm.edu	37	chr19	44419099	44419099	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	acacaatgttctcctttgtaGggtttttcaccagtgtggac	9	9	2	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr19:44419099G>A	ENST00000269973.5	-	10	1579	c.489C>T	c.(487-489)ccC>ccT	p.P163P	ZNF45_ENST00000589703.1_Silent_p.P163P|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	163					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						CTCCTTTGTAGGGTTTTTCAC	0.413																																					p.P163P		Atlas-SNP	.											.	ZNF45	51	.	0			c.C489T						.						132	127	128					19																	44419099		2203	4300	6503	SO:0001819	synonymous_variant	7596	exon10			TTTGTAGGGTTTT	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"Zinc fingers, C2H2-type", "-"	13111	protein-coding gene	gene with protein product		194554	"zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)", "zinc finger protein 13"	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.489C>T	chr19.hg19:g.44419099G>A		71.0	0.0		76.0	28.0	NM_003425	P17016|P78472|Q9P1U9	Silent	SNP	ENST00000269973.5	hg19	CCDS12632.1																																																																																			.	.		0.413	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425		A	44419099	G	A	44419099	2	1	214	1	0	0	0	0	0	0	0	1	17936	987	35	3		3	ZNF45	19	44419099	Silent	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	1150921	44419099	14709884	98	30893										
EHD2	30846	hgsc.bcm.edu	37	chr19	48221838	48221838	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gacaccccgggtatcctgtcGggtgccaagcagagagtgag	15	11	0	2	rs369297316		TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr19:48221838G>A	ENST00000263277.3	+	3	728	c.477G>A	c.(475-477)tcG>tcA	p.S159S	CTD-2571L23.8_ENST00000599924.1_lincRNA|EHD2_ENST00000538399.1_Silent_p.S23S	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	159	Dynamin-type G.				blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		GTATCCTGTCGGGTGCCAAGC	0.657																																					p.S159S		Atlas-SNP	.											.	EHD2	59	.	0			c.G477A						.						47	37	40					19																	48221838		2197	4293	6490	SO:0001819	synonymous_variant	30846	exon3			CCTGTCGGGTGCC	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"EF-hand domain containing"	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.477G>A	chr19.hg19:g.48221838G>A		56.0	0.0		55.0	21.0	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	hg19	CCDS12704.1																																																																																			.	.		0.657	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1			A	48221838	G	A	48221838	2	1	214	1	0	0	0	0	0	0	0	1	4980	1103	39	1		1	EHD2	19	48221838	Silent	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	3802739	48221838	10907145	99	30894										
POLD1	5424	hgsc.bcm.edu	37	chr19	50902183	50902183	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	cgtgggggcctctgggatgaTgatgatgcacctcggccatc	15	11	1	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr19:50902183T>C	ENST00000440232.2	+	2	128	c.75T>C	c.(73-75)gaT>gaC	p.D25D	RN7SL324P_ENST00000577945.1_RNA|POLD1_ENST00000599857.1_Silent_p.D25D|POLD1_ENST00000595904.1_Silent_p.D25D	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	25					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		TCTGGGATGATGATGATGCAC	0.662								DNA polymerases (catalytic subunits)																													p.D25D		Atlas-SNP	.											.	POLD1	174	.	0			c.T75C						.						40	30	33					19																	50902183		2201	4299	6500	SO:0001819	synonymous_variant	5424	exon2			GGATGATGATGAT		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.75T>C	chr19.hg19:g.50902183T>C		117.0	0.0		78.0	20.0	NM_002691	Q8NER3|Q96H98	Silent	SNP	ENST00000440232.2	hg19	CCDS12795.1																																																																																			.	.		0.662	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			C	50902183	T	C	50902183	2	2	214	1	0	0	0	0	0	0	0	1	12199	1461	51	2		2	POLD1	19	50902183	Silent	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	2680345	50902183	8226800	100	30895										
ZNF841	284371	hgsc.bcm.edu	37	chr19	52569046	52569046	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	aggatttctgtgatatcttgCaagttttgaactttggataa	9	4	2	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr19:52569046C>A	ENST00000426391.2	-	5	2292	c.1741G>T	c.(1741-1743)Gca>Tca	p.A581S	ZNF841_ENST00000594295.1_Missense_Mutation_p.A697S|ZNF841_ENST00000389534.4_Missense_Mutation_p.A697S|ZNF432_ENST00000598446.1_Intron|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000359973.2_Intron			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	581					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						TGATATCTTGCAAGTTTTGAA	0.393																																					p.A697S		Atlas-SNP	.											.	ZNF841	183	.	0			c.G2089T						.						93	80	84					19																	52569046		692	1591	2283	SO:0001583	missense	284371	exon7			ATCTTGCAAGTTT	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"Zinc fingers, C2H2-type", "-"	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.1741G>T	chr19.hg19:g.52569046C>A	ENSP00000415453:p.Ala581Ser	139.0	0.0		125.0	6.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	hg19		.	.	.	.	.	.	.	.	.	.	C	10.40	1.339452	0.24339	.	.	ENSG00000197608	ENST00000389534;ENST00000426391	T;T	0.15017	2.46;2.46	2.14	-0.208	0.13185	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07279	0.0184	N	0.20328	0.56	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.41627	-0.9498	9	0.07175	T	0.84	.	2.7349	0.05237	0.1995:0.2884:0.0:0.5121	.	697;581	Q6ZN19-3;Q6ZN19	.;ZN841_HUMAN	S	697;581	ENSP00000374185:A697S;ENSP00000415453:A581S	ENSP00000374185:A697S	A	-	1	0	ZNF841	57260858	0.000000	0.05858	0.000000	0.03702	0.130000	0.20726	-4.245000	0.00267	-0.277000	0.09193	0.313000	0.20887	GCA	.	.		0.393	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		A	52569046	C	A	52569046	3	1	214	1	0	0	0	0	1	0	0	0	18204	710	25	3	689	3	ZNF841	19	52569046	Missense_Mutation	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	1666863	52569046	6559937	101	30896										
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55592156	55592156	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	gcaggcggagctgatccgagAggacatccagggggctctgc	17	11	1	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr19:55592156A>T	ENST00000201647.6	+	7	502	c.446A>T	c.(445-447)gAg>gTg	p.E149V	EPS8L1_ENST00000588359.1_Intron|EPS8L1_ENST00000540810.1_Missense_Mutation_p.E85V|EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000586329.1_Missense_Mutation_p.E131V|EPS8L1_ENST00000245618.5_Missense_Mutation_p.E22V	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	149					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CTGATCCGAGAGGACATCCAG	0.677																																					p.E149V	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.A446T						.						18	24	22					19																	55592156		2193	4297	6490	SO:0001583	missense	54869	exon7			TCCGAGAGGACAT	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.446A>T	chr19.hg19:g.55592156A>T	ENSP00000201647:p.Glu149Val	210.0	0.0		179.0	73.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	hg19	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.031882	0.75504	.	.	ENSG00000131037	ENST00000310075;ENST00000201647;ENST00000540810;ENST00000245618	T;T;T	0.32753	1.44;1.44;3.2	3.91	3.91	0.45181	Tensin phosphotyrosine-binding domain (1);	0.385142	0.24901	N	0.034699	T	0.43255	0.1239	L	0.50333	1.59	0.80722	D	1	B;D;B;B	0.64830	0.261;0.994;0.22;0.091	B;P;B;B	0.62014	0.078;0.897;0.07;0.043	T	0.34925	-0.9809	10	0.66056	D	0.02	-25.1616	9.4431	0.38681	1.0:0.0:0.0:0.0	.	85;131;22;149	B4DKV7;Q8TE68-3;Q8TE68-2;Q8TE68	.;.;.;ES8L1_HUMAN	V	131;149;85;22	ENSP00000201647:E149V;ENSP00000437541:E85V;ENSP00000245618:E22V	ENSP00000201647:E149V	E	+	2	0	EPS8L1	60283968	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.915000	0.39976	1.542000	0.49330	0.402000	0.26972	GAG	.	.		0.677	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		T	55592156	A	T	55592156	3	4	214	1	0	0	0	0	1	0	0	0	5197	304	11	4	520	4	EPS8L1	19	55592156	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	3023110	55592156	3536827	102	30897										
WISP2	8839	hgsc.bcm.edu	37	chr20	43353453	43353453	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	agaccttccagccccactgcAgcatccgctgccgctgcgag	10	18	0	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr20:43353453A>T	ENST00000372868.2	+	4	695	c.352A>T	c.(352-354)Agc>Tgc	p.S118C	RP11-445H22.4_ENST00000445420.1_RNA|WISP2_ENST00000372865.4_Intron|WISP2_ENST00000190983.4_Missense_Mutation_p.S118C|RP11-445H22.4_ENST00000427303.1_RNA|RP11-445H22.4_ENST00000427598.1_RNA|WISP2_ENST00000471629.1_3'UTR			O76076	WISP2_HUMAN	WNT1 inducible signaling pathway protein 2	118	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				skin(1)	1		Myeloproliferative disorder(115;0.0122)				GCCCCACTGCAGCATCCGCTG	0.682																																					p.S118C		Atlas-SNP	.											.	WISP2	28	.	0			c.A352T						.						30	24	26					20																	43353453		2198	4296	6494	SO:0001583	missense	8839	exon3			CACTGCAGCATCC	AF100780	CCDS13336.1	20q13.12	2007-05-14			ENSG00000064205	ENSG00000064205			12770	protein-coding gene	gene with protein product		603399				9843955	Standard	NM_003881		Approved	CT58, CTGF-L, CCN5	uc002xmp.3	O76076	OTTHUMG00000033071	ENST00000372868.2:c.352A>T	chr20.hg19:g.43353453A>T	ENSP00000361959:p.Ser118Cys	155.0	0.0		150.0	37.0	NM_003881	B2R9N4|E1P612|Q6PEG3	Missense_Mutation	SNP	ENST00000372868.2	hg19	CCDS13336.1	.	.	.	.	.	.	.	.	.	.	A	15.86	2.956816	0.53293	.	.	ENSG00000064205	ENST00000372868;ENST00000190983	T;T	0.72615	-0.67;-0.67	4.66	2.27	0.28462	von Willebrand factor, type C (4);	0.388539	0.30723	N	0.009010	T	0.52901	0.1763	N	0.01705	-0.755	0.27939	N	0.937592	D	0.63046	0.992	P	0.52758	0.708	T	0.56798	-0.7919	10	0.54805	T	0.06	-13.8678	11.1912	0.48685	0.7064:0.2936:0.0:0.0	.	118	O76076	WISP2_HUMAN	C	118	ENSP00000361959:S118C;ENSP00000190983:S118C	ENSP00000190983:S118C	S	+	1	0	WISP2	42786867	0.998000	0.40836	0.803000	0.32268	0.312000	0.27988	0.974000	0.29436	0.141000	0.18875	0.374000	0.22700	AGC	.	.		0.682	WISP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127824.1	NM_003881		T	43353453	A	T	43353453	3	4	214	1	0	0	0	0	1	0	0	0	17388	188	7	4	362	4	WISP2	20	43353453	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10		43353453	19672067	103	30898										
BAGE2	85319	hgsc.bcm.edu	37	chr21	11058299	11058299	+	RNA	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	acagcatttgatagtggctcCaaagtgcttacaaaatgcac	8	9	0	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr21:11058299C>G	ENST00000470054.1	-	0	348							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ATAGTGGCTCCAAAGTGCTTA	0.398																																					p.L47F		Atlas-SNP	.											.	.	.	.	0			c.G141C						.						139	103	114					21																	11058299		692	1591	2283			85318	exon3			TGGCTCCAAAGTG	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"cancer/testis antigen family 2, member 2"					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		chr21.hg19:g.11058299C>G		346.0	0.0		225.0	12.0	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	hg19																																																																																				.	.		0.398	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		G	11058299	C	G	11058299	1	3	214	0	1	0	0	0	0	0	0	0	1292	593	21	4		4	BAGE2	21	11058299	RNA	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10		11058299	37071596	104	30899										
GRIK1	2897	hgsc.bcm.edu	37	chr21	31062249	31062249	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	agactgcacagcactgacggAggagctatgggaagggccaa	15	9	0	2			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr21:31062249A>T	ENST00000399907.1	-	3	754	c.343T>A	c.(343-345)Tcc>Acc	p.S115T	GRIK1_ENST00000399913.1_Missense_Mutation_p.S115T|GRIK1_ENST00000389125.3_Missense_Mutation_p.S115T|GRIK1_ENST00000535441.1_Missense_Mutation_p.S115T|GRIK1_ENST00000399909.1_Missense_Mutation_p.S115T|GRIK1_ENST00000472429.1_5'UTR|GRIK1_ENST00000399914.1_Missense_Mutation_p.S115T|GRIK1_ENST00000389124.2_Missense_Mutation_p.S115T|GRIK1_ENST00000309434.7_Missense_Mutation_p.S115T|GRIK1_ENST00000327783.4_Missense_Mutation_p.S115T	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	115					adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	GCACTGACGGAGGAGCTATGG	0.542																																					p.S115T		Atlas-SNP	.											.	GRIK1	293	.	0			c.T343A						.						86	80	82					21																	31062249		2203	4300	6503	SO:0001583	missense	2897	exon3			TGACGGAGGAGCT		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.343T>A	chr21.hg19:g.31062249A>T	ENSP00000382791:p.Ser115Thr	130.0	0.0		93.0	43.0	NM_175611	Q13001|Q86SU9	Missense_Mutation	SNP	ENST00000399907.1	hg19	CCDS42913.1	.	.	.	.	.	.	.	.	.	.	A	12.66	2.005892	0.35415	.	.	ENSG00000171189	ENST00000327783;ENST00000389125;ENST00000399913;ENST00000399914;ENST00000535441;ENST00000541508;ENST00000389124;ENST00000399907;ENST00000399909;ENST00000309434	D;D;D;D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	5.17	5.17	0.71159	Extracellular ligand-binding receptor (1);	0.058916	0.64402	D	0.000001	T	0.77731	0.4174	N	0.25144	0.715	0.80722	D	1	B;P;P;P;P	0.37441	0.413;0.595;0.595;0.595;0.54	B;B;B;B;B	0.40901	0.343;0.343;0.343;0.343;0.232	T	0.74665	-0.3589	10	0.15499	T	0.54	.	14.8479	0.70272	1.0:0.0:0.0:0.0	.	115;115;115;115;115	E7EPY9;E9PD61;B7Z3V7;P39086;P39086-2	.;.;.;GRIK1_HUMAN;.	T	115;115;115;115;115;59;115;115;115;115	ENSP00000327687:S115T;ENSP00000373777:S115T;ENSP00000382797:S115T;ENSP00000382798:S115T;ENSP00000446326:S115T;ENSP00000373776:S115T;ENSP00000382791:S115T;ENSP00000382793:S115T;ENSP00000311646:S115T	ENSP00000311646:S115T	S	-	1	0	GRIK1	29984120	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	8.660000	0.91121	2.158000	0.67659	0.533000	0.62120	TCC	.	.		0.542	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1			T	31062249	A	T	31062249	3	4	214	1	0	0	0	0	1	0	0	0	6782	304	11	4	2633	4	GRIK1	21	31062249	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	20003950	31062249	17067646	105	30900										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37617730	37617730	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctgtgcacccatccccatggGgggcagggcgtaccccaagc	13	16	0	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr21:37617730G>A	ENST00000399151.3	+	19	3537	c.3452G>A	c.(3451-3453)gGg>gAg	p.G1151E		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1151					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						ATCCCCATGGGGGGCAGGGCG	0.642																																					p.G1151E		Atlas-SNP	.											.	DOPEY2	184	.	0			c.G3452A						.						73	60	65					21																	37617730		2203	4300	6503	SO:0001583	missense	9980	exon19			CCATGGGGGGCAG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.3452G>A	chr21.hg19:g.37617730G>A	ENSP00000382104:p.Gly1151Glu	80.0	0.0		70.0	25.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	G	0.064	-1.216088	0.01542	.	.	ENSG00000142197	ENST00000399151	T	0.26223	1.75	4.53	-2.48	0.06423	.	0.665291	0.15603	N	0.253787	T	0.13200	0.0320	L	0.46157	1.445	0.09310	N	1	B;P	0.43477	0.328;0.808	B;B	0.37267	0.079;0.245	T	0.37911	-0.9685	10	0.02654	T	1	.	6.6582	0.22998	0.1074:0.6127:0.1453:0.1346	.	1151;1151	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	E	1151	ENSP00000382104:G1151E	ENSP00000382104:G1151E	G	+	2	0	DOPEY2	36539600	0.001000	0.12720	0.000000	0.03702	0.186000	0.23388	-0.034000	0.12225	-0.329000	0.08527	0.650000	0.86243	GGG	.	.		0.642	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		A	37617730	G	A	37617730	3	1	214	1	0	0	0	0	1	0	0	0	4710	1232	43	3	3522	3	DOPEY2	21	37617730	Missense_Mutation	SNP	G	TCGA-DD-AAE9-01A-11D-A40R-10	6555481	37617730	10512165	106	30901										
PRMT2	3275	hgsc.bcm.edu	37	chr21	48064248	48064248	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tgagaggagaaaaaattcttAtcctgagacaaaccactgca	8	8	1	3			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr21:48064248A>T	ENST00000397637.1	+	4	1129	c.175A>T	c.(175-177)Atc>Ttc	p.I59F	PRMT2_ENST00000458387.2_Missense_Mutation_p.I59F|PRMT2_ENST00000355680.3_Missense_Mutation_p.I59F|PRMT2_ENST00000334494.4_Missense_Mutation_p.I59F|PRMT2_ENST00000397638.2_Missense_Mutation_p.I59F|PRMT2_ENST00000291705.6_Missense_Mutation_p.I59F|PRMT2_ENST00000397628.1_Missense_Mutation_p.I59F|PRMT2_ENST00000440086.1_Missense_Mutation_p.I59F|PRMT2_ENST00000451211.2_Missense_Mutation_p.I59F			P55345	ANM2_HUMAN	protein arginine methyltransferase 2	59	Interaction with ESR1.|SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				developmental cell growth (GO:0048588)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|protein methylation (GO:0006479)|regulation of androgen receptor signaling pathway (GO:0060765)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (GO:0042054)|histone-arginine N-methyltransferase activity (GO:0008469)|peroxisome proliferator activated receptor binding (GO:0042975)|progesterone receptor binding (GO:0033142)|protein homodimerization activity (GO:0042803)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|retinoic acid receptor binding (GO:0042974)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)		AAAAATTCTTATCCTGAGACA	0.433																																					p.I59F		Atlas-SNP	.											.	PRMT2	48	.	0			c.A175T						.						60	64	63					21																	48064248		2203	4300	6503	SO:0001583	missense	3275	exon4			ATTCTTATCCTGA	U80213	CCDS13737.1, CCDS56219.1, CCDS56220.1, CCDS68230.1, CCDS68231.1, CCDS74806.1	21q22.3	2014-06-12	2006-02-16	2006-02-16	ENSG00000160310	ENSG00000160310	2.1.1.125	"Protein arginine methyltransferases"	5186	protein-coding gene	gene with protein product		601961	"HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 1", "HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae)"	HRMT1L1		9545638	Standard	XM_005261111		Approved	MGC111373	uc002zjy.3	P55345	OTTHUMG00000048806	ENST00000397637.1:c.175A>T	chr21.hg19:g.48064248A>T	ENSP00000380759:p.Ile59Phe	105.0	0.0		78.0	33.0	NM_001242864	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Missense_Mutation	SNP	ENST00000397637.1	hg19	CCDS13737.1	.	.	.	.	.	.	.	.	.	.	A	16.72	3.201670	0.58234	.	.	ENSG00000160310	ENST00000355680;ENST00000397638;ENST00000458387;ENST00000451211;ENST00000291705;ENST00000397637;ENST00000334494;ENST00000397628;ENST00000440086	T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.4	0.326	0.15908	Src homology-3 domain (5);	0.246452	0.41097	D	0.000954	T	0.60143	0.2246	M	0.78916	2.43	0.39738	D	0.971718	B;D;B;D;P	0.67145	0.04;0.996;0.4;0.987;0.555	B;D;B;D;B	0.72982	0.034;0.919;0.113;0.979;0.178	T	0.57207	-0.7851	10	0.39692	T	0.17	-12.5495	5.5589	0.17131	0.5308:0.1432:0.3261:0.0	.	59;59;59;59;59	B7U632;B7U630;B7U631;Q498Y5;P55345	.;.;.;.;ANM2_HUMAN	F	59	ENSP00000347906:I59F;ENSP00000380760:I59F;ENSP00000407463:I59F;ENSP00000411984:I59F;ENSP00000291705:I59F;ENSP00000380759:I59F;ENSP00000335490:I59F;ENSP00000380752:I59F;ENSP00000397266:I59F	ENSP00000291705:I59F	I	+	1	0	PRMT2	46888676	0.836000	0.29430	0.962000	0.40283	0.998000	0.95712	0.956000	0.29202	0.114000	0.18032	0.482000	0.46254	ATC	.	.		0.433	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535		T	48064248	A	T	48064248	3	4	214	1	0	0	0	0	1	0	0	0	12549	449	16	4	185	4	PRMT2	21	48064248	Missense_Mutation	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	10446518	48064248	65647	107	30902										
NCF4	4689	hgsc.bcm.edu	37	chr22	37271978	37271978	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tgtaacaagccatcaacgtcCagggtggcctggccagcctc	11	14	1	0			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chr22:37271978C>T	ENST00000248899.6	+	9	942				NCF4_ENST00000397147.4_Missense_Mutation_p.P304L	NM_000631.4	NP_000622.2	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4, 40kDa						antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of catalytic activity (GO:0043085)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|membrane (GO:0016020)|NADPH oxidase complex (GO:0043020)|phagolysosome (GO:0032010)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein dimerization activity (GO:0046983)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16					Dextromethorphan(DB00514)	CATCAACGTCCAGGGTGGCCT	0.612																																					p.P304L		Atlas-SNP	.											.	NCF4	66	.	0			c.C911T						.						59	52	55					22																	37271978		2203	4300	6503	SO:0001627	intron_variant	4689	exon8			AACGTCCAGGGTG	X77094	CCDS13934.1, CCDS13935.1	22q13.1	2014-09-17	2002-08-29		ENSG00000100365	ENSG00000100365			7662	protein-coding gene	gene with protein product	"neutrophil NADPH oxidase factor 4"	601488	"neutrophil cytosolic factor 4 (40kD)"			8839867	Standard	NM_013416		Approved	p40phox, SH3PXD4	uc003apy.4	Q15080	OTTHUMG00000150548	ENST00000248899.6:c.759-93C>T	chr22.hg19:g.37271978C>T		178.0	0.0		112.0	35.0	NM_013416	A8K4F9|O60808|Q86U56|Q9BU98|Q9NP45	Missense_Mutation	SNP	ENST00000248899.6	hg19	CCDS13934.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.320697	0.41096	.	.	ENSG00000100365	ENST00000397147	T	0.58652	0.32	2.95	1.91	0.25777	.	3.522020	0.01253	N	0.008929	T	0.42471	0.1204	.	.	.	0.09310	N	1	P	0.36065	0.535	B	0.31614	0.133	T	0.33266	-0.9875	8	.	.	.	1.9134	6.7144	0.23294	0.0:0.8552:0.0:0.1448	.	304	A8K4F9	.	L	304	ENSP00000380334:P304L	.	P	+	2	0	NCF4	35601924	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	1.185000	0.32065	0.551000	0.29008	-0.126000	0.14955	CCA	.	.		0.612	NCF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318863.1	NM_000631		T	37271978	C	T	37271978	1	4	214	0	1	0	0	0	0	0	0	0	10227	594	21	3		3	NCF4	22	37271978	Intron	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10		37271978	14032588	108	30903										
HDX	139324	hgsc.bcm.edu	37	chrX	83588776	83588777	+	Nonsense_Mutation	DNP	CA	CA	TC													0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	aaattacctaccttataatcCaagaaagagtttacttgttc							TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chrX:83588776_83588777CA>TC	ENST00000297977.5	-	8	1925_1926	c.1814_1815TG>GA	c.(1813-1815)tTG>tGA	p.L605*	HDX_ENST00000373177.2_Nonsense_Mutation_p.L605*|HDX_ENST00000506585.2_Nonsense_Mutation_p.L547*	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	605						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						CCTTATAATCCAAGAAAGAGTT	0.252																																					p.L605L|p.L605W	Pancreas(53;231 1169 36156 43751 51139)	Atlas-SNP	.											.	HDX	124	.	0			c.G1815A|c.T1814G						.																																			SO:0001587	stop_gained	139324	exon8			ATAATCCAAGAAA|TAATCCAAGAAAG	BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"Homeoboxes / POU class"	26411	protein-coding gene	gene with protein product			"chromosome X open reading frame 43"	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.1814_1815delinsTC	chrX.hg19:g.83588776_83588777delinsTC	ENSP00000297977:p.Leu605*	199.0	0.0		270.0|271.0	220.0|223.0	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Silent|Missense_Mutation	SNP	ENST00000297977.5	hg19	CCDS35342.1																																																																																			.	.		0.252	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		TC	83588777	CA	TC	83588776	4	4	214	1	0	0	0	0	0	1	0	0	7035	593	21	3	269	3	HDX	23	83588776	Nonsense_Mutation	DNP	CA	TCGA-DD-AAE9-01A-11D-A40R-10		83588776	71681784	109	30904										
ARMCX2	9823	hgsc.bcm.edu	37	chrX	100911840	100911840	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ccaggaaccaccgctgttctAggggaaccagaagttccagg	12	12	1	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chrX:100911840A>G	ENST00000328766.5	-	5	1188	c.735T>C	c.(733-735)ccT>ccC	p.P245P	ARMCX2_ENST00000356824.4_Silent_p.P245P|ARMCX2_ENST00000330154.2_Silent_p.P245P|ARMCX2_ENST00000467416.1_5'Flank	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	245	Ala-rich.					integral component of membrane (GO:0016021)				NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(6)|prostate(1)|skin(1)	29						CCGCTGTTCTAGGGGAACCAG	0.612																																					p.P245P		Atlas-SNP	.											.	ARMCX2	75	.	0			c.T735C						.						46	45	45					X																	100911840		2203	4300	6503	SO:0001819	synonymous_variant	9823	exon5			TGTTCTAGGGGAA	AB011084	CCDS14490.1	Xq21.33-q22.2	2014-03-21			ENSG00000184867	ENSG00000184867		"Armadillo repeat containing"	16869	protein-coding gene	gene with protein product		300363				9628581, 11162520, 16221301, 22569362	Standard	XM_005278109		Approved	ALEX2, KIAA0512, GASP9	uc004eif.3	Q7L311	OTTHUMG00000022038	ENST00000328766.5:c.735T>C	chrX.hg19:g.100911840A>G		52.0	0.0		75.0	4.0	NM_014782	O60267|Q5H9D9	Silent	SNP	ENST00000328766.5	hg19	CCDS14490.1																																																																																			.	.		0.612	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057586.1	NM_014782		G	100911840	A	G	100911840	2	3	214	1	0	0	0	0	0	0	0	1	960	407	15	2		2	ARMCX2	23	100911840	Silent	SNP	A	TCGA-DD-AAE9-01A-11D-A40R-10	17323064	100911840	54358720	110	30905										
AIFM1	9131	hgsc.bcm.edu	37	chrX	129265689	129265689	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	tttggggttgtcttgtgcagTtgcttttgcaaaaacaccaa	10	7	1	0	rs369259253		TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chrX:129265689T>C	ENST00000287295.3	-	14	1764	c.1534A>G	c.(1534-1536)Act>Gct	p.T512A	AIFM1_ENST00000319908.3_Missense_Mutation_p.T508A|AIFM1_ENST00000460436.2_Missense_Mutation_p.T173A|AIFM1_ENST00000535724.1_3'UTR|AIFM1_ENST00000440263.1_Missense_Mutation_p.T160A|AIFM1_ENST00000346424.2_Missense_Mutation_p.T225A	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	512					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	TCTTGTGCAGTTGCTTTTGCA	0.483													T|||	1	0.000264901	0	0	3775	,	,		15048	0		0	False		,,,				2504	0.001				p.T512A		Atlas-SNP	.											.	AIFM1	75	.	0			c.A1534G						.	T	ALA/THR,,ALA/THR,ALA/THR,ALA/THR	1,3834		0,1,1631,571	210	184	193		478,,1534,1522,673	4.6	1	X		193	0,6728		0,0,2428,1872	no	missense,utr-3,missense,missense,missense	AIFM1	NM_001130846.2,NM_001130847.3,NM_004208.3,NM_145812.2,NM_145813.2	58,,58,58,58	0,1,4059,2443	CC,CT,TT,T		0.0,0.0261,0.0095	benign,,benign,benign,benign	160/262,,512/614,508/610,225/327	129265689	1,10562	2203	4300	6503	SO:0001583	missense	9131	exon14			GTGCAGTTGCTTT	AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"programmed cell death 8 (apoptosis-inducing factor)", "neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.1534A>G	chrX.hg19:g.129265689T>C	ENSP00000287295:p.Thr512Ala	94.0	0.0		115.0	97.0	NM_004208	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Missense_Mutation	SNP	ENST00000287295.3	hg19	CCDS14618.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.979971	0.53827	2.61E-4	0.0	ENSG00000156709	ENST00000460436;ENST00000346424;ENST00000319908;ENST00000440263;ENST00000287295	T;T;D;T;T	0.83250	0.93;0.93;-1.7;0.94;-0.7	5.8	4.62	0.57501	FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (1);	0.045678	0.85682	D	0.000000	T	0.80154	0.4571	M	0.64170	1.965	0.80722	D	1	B;B;B	0.13594	0.001;0.008;0.002	B;B;B	0.11329	0.004;0.006;0.002	T	0.74172	-0.3751	10	0.48119	T	0.1	-13.2794	11.4314	0.50043	0.1372:0.0:0.0:0.8628	.	225;508;512	O95831-2;O95831-3;O95831	.;.;AIFM1_HUMAN	A	173;225;508;160;512	ENSP00000431222:T173A;ENSP00000316320:T225A;ENSP00000315122:T508A;ENSP00000405879:T160A;ENSP00000287295:T512A	ENSP00000287295:T512A	T	-	1	0	AIFM1	129093370	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.760000	0.62235	0.787000	0.33731	0.486000	0.48141	ACT	.	.		0.483	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2			C	129265689	T	C	129265689	3	2	214	1	0	0	0	0	1	0	0	0	426	1725	60	2	319	2	AIFM1	23	129265689	Missense_Mutation	SNP	T	TCGA-DD-AAE9-01A-11D-A40R-10	28353849	129265689	26004871	111	30906										
ABCD1	215	hgsc.bcm.edu	37	chrX	153005587	153005587	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0267857142857143	3	1	0.75181758096497	0.774599931903303	0.740921673994463	1	1	0	ctcatcacaggccccaatggCtgcggcaagagctccctgtt	10	15	2	1			TCGA-DD-AAE9-01A-11D-A40R-10	TCGA-DD-AAE9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	870e02bb-395f-439a-99fd-00d1054e69d9	864a2672-99b0-4252-9953-5feb85ff19d6	g.chrX:153005587C>G	ENST00000218104.3	+	6	1929	c.1530C>G	c.(1528-1530)ggC>ggG	p.G510G	U52111.14_ENST00000434284.1_RNA	NM_000033.3	NP_000024.2	P33897	ABCD1_HUMAN	ATP-binding cassette, sub-family D (ALD), member 1	510	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				alpha-linolenic acid metabolic process (GO:0036109)|ATP catabolic process (GO:0006200)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|linoleic acid metabolic process (GO:0043651)|long-chain fatty acid catabolic process (GO:0042758)|peroxisomal long-chain fatty acid import (GO:0015910)|peroxisomal membrane transport (GO:0015919)|peroxisome organization (GO:0007031)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid catabolic process (GO:0042760)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|peroxisomal fatty-acyl-CoA transporter activity (GO:0005325)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(2)	18	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCCCCAATGGCTGCGGCAAGA	0.652																																					p.G510G		Atlas-SNP	.											.	ABCD1	59	.	0			c.C1530G						.						109	94	99					X																	153005587		2203	4300	6503	SO:0001819	synonymous_variant	215	exon6			CAATGGCTGCGGC	Z21876	CCDS14728.1	Xq28	2012-03-14			ENSG00000101986	ENSG00000101986		"ATP binding cassette transporters / subfamily D"	61	protein-coding gene	gene with protein product		300371		ALD		8441467, 6795626	Standard	NM_000033		Approved	AMN, ALDP, adrenoleukodystrophy	uc004fif.2	P33897	OTTHUMG00000024215	ENST00000218104.3:c.1530C>G	chrX.hg19:g.153005587C>G		52.0	0.0		85.0	41.0	NM_000033	Q6GTZ2	Silent	SNP	ENST00000218104.3	hg19	CCDS14728.1	.	.	.	.	.	.	.	.	.	.	C	6.282	0.420108	0.11928	.	.	ENSG00000101986	ENST00000443684	.	.	.	4.93	3.13	0.36017	.	.	.	.	.	T	0.58337	0.2115	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54221	-0.8326	4	.	.	.	-32.6616	8.6945	0.34287	0.0:0.8023:0.0:0.1977	.	.	.	.	G	178	.	.	A	+	2	0	ABCD1	152658781	0.996000	0.38824	1.000000	0.80357	0.616000	0.37450	0.494000	0.22467	1.074000	0.40909	0.429000	0.28392	GCT	.	.		0.652	ABCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061041.1	NM_000033		G	153005587	C	G	153005587	2	3	214	1	0	0	0	0	0	0	0	1	60	784	28	4		4	ABCD1	23	153005587	Silent	SNP	C	TCGA-DD-AAE9-01A-11D-A40R-10	23739898	153005587	2264973	112	30907										
RERE	473	hgsc.bcm.edu	37	chr1	8418319	8418319	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aatgtgagagtgctggtgatGgtgcggagtcacgttgaaca	16	5	1	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:8418319G>A	ENST00000337907.3	-	21	4910	c.4276C>T	c.(4276-4278)Cat>Tat	p.H1426Y	RERE_ENST00000377464.1_Missense_Mutation_p.H1158Y|RERE_ENST00000400907.2_Intron|RERE_ENST00000476556.1_Missense_Mutation_p.H872Y|RERE_ENST00000400908.2_Missense_Mutation_p.H1426Y	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1426	His-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		tgctggtgatggtgCGGAGTC	0.647																																					p.H1426Y		Atlas-SNP	.											.	RERE	129	.	0			c.C4276T						.						132	106	115					1																	8418319		2203	4300	6503	SO:0001583	missense	473	exon21			GGTGATGGTGCGG	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.4276C>T	chr1.hg19:g.8418319G>A	ENSP00000338629:p.His1426Tyr	66.0	0.0		38.0	7.0	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	hg19	CCDS95.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112835	0.77210	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908	T;T;T	0.52057	0.68;0.71;0.68	5.61	5.61	0.85477	.	.	.	.	.	T	0.68879	0.3049	M	0.70275	2.135	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	T	0.65022	-0.6269	9	0.36615	T	0.2	-17.8192	18.9896	0.92786	0.0:0.0:1.0:0.0	.	1426	Q9P2R6	RERE_HUMAN	Y	1426;1158;872;1426	ENSP00000338629:H1426Y;ENSP00000366684:H1158Y;ENSP00000383700:H1426Y	ENSP00000338629:H1426Y	H	-	1	0	RERE	8340906	1.000000	0.71417	0.993000	0.49108	0.846000	0.48090	9.723000	0.98772	2.793000	0.96121	0.655000	0.94253	CAT	.	.		0.647	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			A	8418319	G	A	8418319	3	1	215	1	0	0	0	0	1	0	0	0	13246	1348	47	3	440	3	RERE	1	8418319	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10		8418319	240832302	1	30908										
SH2D5	400745	hgsc.bcm.edu	37	chr1	21048322	21048322	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gctctgcctcggacttggcaTggctgaggggccggagagtc	17	11	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:21048322T>A	ENST00000444387.2	-	10	1632	c.1235A>T	c.(1234-1236)cAt>cTt	p.H412L	SH2D5_ENST00000460804.1_5'UTR|SH2D5_ENST00000375031.1_Missense_Mutation_p.H328L	NM_001103161.1	NP_001096631.1	Q6ZV89	SH2D5_HUMAN	SH2 domain containing 5	412										lung(4)|prostate(1)|upper_aerodigestive_tract(1)	6		Colorectal(325;3.46e-05)|all_lung(284;5.32e-05)|Lung NSC(340;5.51e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|GBM - Glioblastoma multiforme(114;0.000465)|Kidney(64;0.000476)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(64;0.00634)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGACTTGGCATGGCTGAGGGG	0.716																																					p.H412L		Atlas-SNP	.											.	SH2D5	26	.	0			c.A1235T						.						10	13	12					1																	21048322		1835	4061	5896	SO:0001583	missense	400745	exon10			TTGGCATGGCTGA	AK124869, AK123236	CCDS41280.1, CCDS44080.1	1p36.12	2008-02-05			ENSG00000189410	ENSG00000189410			28819	protein-coding gene	gene with protein product							Standard	NM_001103161		Approved		uc009vpy.1	Q6ZV89	OTTHUMG00000002620	ENST00000444387.2:c.1235A>T	chr1.hg19:g.21048322T>A	ENSP00000406026:p.His412Leu	129.0	0.0		116.0	34.0	NM_001103161	B7Z3W3|Q5SSJ2	Missense_Mutation	SNP	ENST00000444387.2	hg19	CCDS44080.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.316354	0.81469	.	.	ENSG00000189410	ENST00000375031;ENST00000444387	.	.	.	5.01	5.01	0.66863	.	0.000000	0.46145	D	0.000317	T	0.43523	0.1251	N	0.24115	0.695	0.33567	D	0.598058	D	0.56968	0.978	P	0.53649	0.731	T	0.58323	-0.7656	9	0.52906	T	0.07	.	8.9444	0.35749	0.0:0.0887:0.0:0.9113	.	412	Q6ZV89	SH2D5_HUMAN	L	328;412	.	ENSP00000364171:H328L	H	-	2	0	SH2D5	20920909	0.997000	0.39634	0.997000	0.53966	0.982000	0.71751	2.889000	0.48601	1.888000	0.54679	0.460000	0.39030	CAT	.	.		0.716	SH2D5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007455.2	XM_375698		A	21048322	T	A	21048322	3	1	215	1	0	0	0	0	1	0	0	0	14252	1464	51	4	40	4	SH2D5	1	21048322	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	12630003	21048322	228202299	2	30909										
GPR3	2827	hgsc.bcm.edu	37	chr1	27721062	27721062	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ccacactggccgtggtgcttGgagcctttgccgcctgctgg	14	14	0	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:27721062G>C	ENST00000374024.3	+	2	859	c.760G>C	c.(760-762)Gga>Cga	p.G254R		NM_005281.3	NP_005272.1	P46089	GPR3_HUMAN	G protein-coupled receptor 3	254					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|regulation of meiosis (GO:0040020)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(3)|ovary(1)|skin(1)	8		Breast(348;1.53e-05)|Ovarian(437;0.0606)|all_lung(284;0.157)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;2.81e-26)|Colorectal(126;1.24e-08)|KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;4.45e-06)|Lung(427;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|LUSC - Lung squamous cell carcinoma(448;0.008)|READ - Rectum adenocarcinoma(331;0.0419)		CGTGGTGCTTGGAGCCTTTGC	0.627																																					p.G254R		Atlas-SNP	.											.	GPR3	23	.	0			c.G760C						.						175	138	150					1																	27721062		2203	4300	6503	SO:0001583	missense	2827	exon2			GTGCTTGGAGCCT	BC032702	CCDS303.1	1p36.1-p35	2012-08-21			ENSG00000181773	ENSG00000181773		"GPCR / Class A : Orphans"	4484	protein-coding gene	gene with protein product		600241				7851889	Standard	NM_005281		Approved	ACCA	uc001bod.4	P46089	OTTHUMG00000003397	ENST00000374024.3:c.760G>C	chr1.hg19:g.27721062G>C	ENSP00000363136:p.Gly254Arg	48.0	0.0		56.0	15.0	NM_005281	A8K570	Missense_Mutation	SNP	ENST00000374024.3	hg19	CCDS303.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.591157	0.66219	.	.	ENSG00000181773	ENST00000374024	T	0.38401	1.14	5.64	5.64	0.86602	GPCR, rhodopsin-like superfamily (1);	0.205916	0.42821	D	0.000645	T	0.74038	0.3664	H	0.96547	3.84	0.50039	D	0.999848	D	0.89917	1.0	D	0.97110	1.0	T	0.82643	-0.0356	10	0.87932	D	0	.	19.3241	0.94254	0.0:0.0:1.0:0.0	.	254	P46089	GPR3_HUMAN	R	254	ENSP00000363136:G254R	ENSP00000363136:G254R	G	+	1	0	GPR3	27593649	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.541000	0.82084	2.655000	0.90218	0.462000	0.41574	GGA	.	.		0.627	GPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009522.1	NM_005281		C	27721062	G	C	27721062	3	2	215	1	0	0	0	0	1	0	0	0	6694	1349	47	4	762	4	GPR3	1	27721062	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	6672740	27721062	221529559	3	30910										
ZMYM1	79830	hgsc.bcm.edu	37	chr1	35580361	35580361	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aggattagatactatattacAaaatttaaagttatgttttt	5	2	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:35580361A>G	ENST00000373330.1	+	11	3104	c.2930A>G	c.(2929-2931)cAa>cGa	p.Q977R	ZMYM1_ENST00000373329.1_3'UTR|ZMYM1_ENST00000359858.4_Missense_Mutation_p.Q977R			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	977						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ACTATATTACAAAATTTAAAG	0.254																																					p.Q977R		Atlas-SNP	.											.	ZMYM1	86	.	0			c.A2930G						.						15	15	15					1																	35580361		1762	3974	5736	SO:0001583	missense	79830	exon10			TATTACAAAATTT	AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"Zinc fingers, MYM type"	26253	protein-coding gene	gene with protein product			"zinc finger, MYM domain containing 1"			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.2930A>G	chr1.hg19:g.35580361A>G	ENSP00000362427:p.Gln977Arg	241.0	0.0		275.0	78.0	NM_024772	D3DPR7|Q7Z3Q4	Missense_Mutation	SNP	ENST00000373330.1	hg19	CCDS41302.1	.	.	.	.	.	.	.	.	.	.	A	0.941	-0.709646	0.03230	.	.	ENSG00000197056	ENST00000359858;ENST00000373329;ENST00000373330	T;T;T	0.18016	2.5;2.24;2.5	4.1	2.98	0.34508	Ribonuclease H-like (1);	0.541346	0.15579	N	0.255008	T	0.08088	0.0202	N	0.14661	0.345	0.09310	N	0.999998	B;B	0.23442	0.085;0.035	B;B	0.19666	0.026;0.018	T	0.33394	-0.9870	9	.	.	.	-0.2559	4.3683	0.11235	0.6936:0.2023:0.1041:0.0	.	958;977	B4DSJ9;Q5SVZ6	.;ZMYM1_HUMAN	R	977;902;977	ENSP00000352920:Q977R;ENSP00000362426:Q902R;ENSP00000362427:Q977R	.	Q	+	2	0	ZMYM1	35352948	0.981000	0.34729	0.761000	0.31378	0.004000	0.04260	2.192000	0.42649	0.925000	0.37094	-0.385000	0.06624	CAA	.	.		0.254	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772		G	35580361	A	G	35580361	3	3	215	1	0	0	0	0	1	0	0	0	17714	130	5	2	2964	2	ZMYM1	1	35580361	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	7859299	35580361	213670260	4	30911										
ZNF642	339559	hgsc.bcm.edu	37	chr1	40955271	40955271	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gagccatggatggcagagaaAgaaggcccaggagatcccag	15	9	0	3	rs148845197	byFrequency	TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:40955271A>T	ENST00000372706.1	+	5	1423	c.417A>T	c.(415-417)aaA>aaT	p.K139N	ZFP69_ENST00000482712.1_3'UTR|ZFP69_ENST00000372705.3_Missense_Mutation_p.K139N			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	139	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TGGCAGAGAAAGAAGGCCCAG	0.383																																					p.K139N		Atlas-SNP	.											.	.	.	.	0			c.A417T						.						146	161	156					1																	40955271		2203	4300	6503	SO:0001583	missense	339559	exon5			AGAGAAAGAAGGC	AK122618	CCDS30686.1	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187815	ENSG00000187815		"Zinc fingers, C2H2-type", "-", "-", "-"	24708	protein-coding gene	gene with protein product	"ZFP69 zinc finger protein A"		"zinc finger protein 642"	ZNF642			Standard	XM_005270808		Approved	ZKSCAN23A, FLJ16030, ZFP69A, ZSCAN54A	uc001cfo.3	Q49AA0	OTTHUMG00000007303	ENST00000372706.1:c.417A>T	chr1.hg19:g.40955271A>T	ENSP00000361791:p.Lys139Asn	109.0	0.0		155.0	48.0	NM_198494	Q5SWM5|Q6ZWK8	Missense_Mutation	SNP	ENST00000372706.1	hg19	CCDS30686.1	.	.	.	.	.	.	.	.	.	.	A	13.69	2.311804	0.40895	.	.	ENSG00000187815	ENST00000372706;ENST00000372705	T;T	0.04970	3.52;3.52	4.13	1.5	0.22942	Krueppel-associated box (1);	0.779497	0.10939	N	0.617447	T	0.04272	0.0118	N	0.25031	0.7	0.23277	N	0.997996	B	0.02656	0.0	B	0.04013	0.001	T	0.41945	-0.9480	10	0.51188	T	0.08	-4.1434	3.1102	0.06356	0.5946:0.0:0.1124:0.293	.	139	Q49AA0	ZN642_HUMAN	N	139	ENSP00000361791:K139N;ENSP00000361790:K139N	ENSP00000361790:K139N	K	+	3	2	ZNF642	40727858	0.325000	0.24660	0.996000	0.52242	0.997000	0.91878	1.156000	0.31712	0.267000	0.21916	0.533000	0.62120	AAA	.	A|0.997;G|0.003		0.383	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494		T	40955271	A	T	40955271	3	4	215	1	0	0	0	0	1	0	0	0	18073	69	3	4	431	4	ZNF642	1	40955271	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	5374910	40955271	208295350	5	30912										
TIE1	7075	hgsc.bcm.edu	37	chr1	43774798	43774798	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	caagccagacggcactgtgcTcctggtcagcccccaatcac	9	17	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:43774798T>C	ENST00000372476.3	+	8	1263	c.1184T>C	c.(1183-1185)cTc>cCc	p.L395P	TIE1_ENST00000441333.2_Intron|TIE1_ENST00000433781.2_Missense_Mutation_p.L40P	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	395	Ig-like C2-type 2.				angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GGCACTGTGCTCCTGGTCAGC	0.617																																					p.L395P		Atlas-SNP	.											.	TIE1	132	.	0			c.T1184C						.						41	44	43					1																	43774798		2203	4300	6503	SO:0001583	missense	7075	exon8			CTGTGCTCCTGGT	BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11809	protein-coding gene	gene with protein product		600222	"tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.1184T>C	chr1.hg19:g.43774798T>C	ENSP00000361554:p.Leu395Pro	143.0	0.0		167.0	48.0	NM_005424	B5A949|B5A950	Missense_Mutation	SNP	ENST00000372476.3	hg19	CCDS482.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.465736	0.84425	.	.	ENSG00000066056	ENST00000372476;ENST00000433781	T;T	0.40756	2.25;1.02	5.13	5.13	0.70059	Immunoglobulin-like fold (1);	0.215542	0.23409	N	0.048481	T	0.63546	0.2520	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D	0.89917	0.993;0.994;0.975;0.988;1.0	D;D;D;P;D	0.72075	0.912;0.947;0.916;0.819;0.976	T	0.67917	-0.5546	10	0.87932	D	0	.	14.9642	0.71179	0.0:0.0:0.0:1.0	.	40;350;395;40;395	E9PG63;B4DTW8;B5A952;B4DKW0;P35590	.;.;.;.;TIE1_HUMAN	P	395;40	ENSP00000361554:L395P;ENSP00000411728:L40P	ENSP00000361554:L395P	L	+	2	0	TIE1	43547385	1.000000	0.71417	0.614000	0.29051	0.984000	0.73092	7.662000	0.83803	1.941000	0.56285	0.460000	0.39030	CTC	.	.		0.617	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424		C	43774798	T	C	43774798	3	2	215	1	0	0	0	0	1	0	0	0	15908	1551	54	2	1214	2	TIE1	1	43774798	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	2819527	43774798	205475823	6	30913										
TNNI3K	100526835	hgsc.bcm.edu	37	chr1	74716453	74716453	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttgcatttagcagtttacaaGgtaggacactttaattccca	7	8	0	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:74716453G>A	ENST00000370899.3	+	6	673	c.636G>A	c.(634-636)aaG>aaA	p.K212K	TNNI3K_ENST00000370891.2_Splice_Site_p.K212K|FPGT-TNNI3K_ENST00000370895.1_Splice_Site_p.K212K|FPGT-TNNI3K_ENST00000557284.2_Splice_Site_p.K225K|TNNI3K_ENST00000326637.3_Splice_Site_p.K111K	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		CAGTTTACAAGGTAGGACACT	0.353																																					p.K212K		Atlas-SNP	.											.	.	.	.	0			c.G636A						.						83	77	79					1																	74716453		2203	4300	6503	SO:0001630	splice_region_variant	100526835	exon6			TTACAAGGTAGGA			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.636+1G>A	chr1.hg19:g.74716453G>A		61.0	0.0		60.0	19.0	NM_001199327		Silent	SNP	ENST00000370899.3	hg19																																																																																				.	.		0.353	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3		Silent	A	74716453	G	A	74716453	5	1	215	1	0	0	0	0	0	0	1	0	16344	1014	35	3	702	3	TNNI3K	1	74716453	Splice_Site	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	30941655	74716453	174534168	7	30914										
ZNF644	84146	hgsc.bcm.edu	37	chr1	91406719	91406719	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gtattatttttctgaaatgaTgtttgacaatcttttggctt	7	4	2	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:91406719T>C	ENST00000370440.1	-	3	409	c.192A>G	c.(190-192)acA>acG	p.T64T	ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000337393.5_Silent_p.T64T|ZNF644_ENST00000347275.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	64					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TCTGAAATGATGTTTGACAAT	0.373																																					p.T64T		Atlas-SNP	.											.	ZNF644	120	.	0			c.A192G						.						167	163	164					1																	91406719		2203	4300	6503	SO:0001819	synonymous_variant	84146	exon3			AAATGATGTTTGA	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.192A>G	chr1.hg19:g.91406719T>C		123.0	0.0		125.0	38.0	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Silent	SNP	ENST00000370440.1	hg19	CCDS731.1																																																																																			.	.		0.373	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		C	91406719	T	C	91406719	2	2	215	1	0	0	0	0	0	0	0	1	18075	1451	51	2		2	ZNF644	1	91406719	Silent	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	16690266	91406719	157843902	8	30915										
FNDC7	163479	hgsc.bcm.edu	37	chr1	109265059	109265059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	agctttcaattatactgtgaTggctttgagcgactcttcag	9	8	3	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:109265059T>C	ENST00000370017.3	+	5	978	c.701T>C	c.(700-702)aTg>aCg	p.M234T	FNDC7_ENST00000271311.2_Missense_Mutation_p.M235T	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	234	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		TATACTGTGATGGCTTTGAGC	0.483																																					p.M234T		Atlas-SNP	.											.	FNDC7	113	.	0			c.T701C						.						95	88	91					1																	109265059		2203	4300	6503	SO:0001583	missense	163479	exon5			CTGTGATGGCTTT		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"Fibronectin type III domain containing"	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.701T>C	chr1.hg19:g.109265059T>C	ENSP00000359034:p.Met234Thr	95.0	0.0		139.0	7.0	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	hg19	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	T	7.155	0.584613	0.13749	.	.	ENSG00000143107	ENST00000370017;ENST00000271311	T;T	0.52295	0.67;0.67	5.78	0.599	0.17519	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.755938	0.13995	N	0.348530	T	0.05686	0.0149	N	0.08118	0	0.09310	N	0.999994	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.35895	-0.9770	10	0.08837	T	0.75	-0.9092	1.9873	0.03439	0.1227:0.226:0.1261:0.5252	.	235;234	Q5VTL7;E9PAZ5	FNDC7_HUMAN;.	T	234;235	ENSP00000359034:M234T;ENSP00000271311:M235T	ENSP00000271311:M235T	M	+	2	0	FNDC7	109066582	0.856000	0.29760	0.219000	0.23793	0.936000	0.57629	1.205000	0.32308	0.091000	0.17302	0.374000	0.22700	ATG	.	.		0.483	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532		C	109265059	T	C	109265059	3	2	215	1	0	0	0	0	1	0	0	0	5981	1464	51	2	719	2	FNDC7	1	109265059	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	17858340	109265059	139985562	9	30916										
VANGL1	81839	hgsc.bcm.edu	37	chr1	116206555	116206555	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttatctccatggcattcaaaCtcctcattctgctcataggg	6	12	5	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:116206555C>T	ENST00000355485.2	+	4	749	c.478C>T	c.(478-480)Ctc>Ttc	p.L160F	VANGL1_ENST00000369510.4_Missense_Mutation_p.L158F|VANGL1_ENST00000310260.3_Missense_Mutation_p.L160F|VANGL1_ENST00000369509.1_Missense_Mutation_p.L160F	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	160					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		GGCATTCAAACTCCTCATTCT	0.512																																					p.L160F		Atlas-SNP	.											.	VANGL1	65	.	0			c.C478T						.						121	124	123					1																	116206555		2203	4300	6503	SO:0001583	missense	81839	exon4			TTCAAACTCCTCA	AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)", "vang-like 1 (van gogh, Drosophila)"			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.478C>T	chr1.hg19:g.116206555C>T	ENSP00000347672:p.Leu160Phe	87.0	0.0		105.0	38.0	NM_001172412	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	hg19	CCDS883.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.815675	0.90790	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.94308	0.8171	M	0.88241	2.94	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94530	0.7735	10	0.66056	D	0.02	-0.168	19.4118	0.94677	0.0:1.0:0.0:0.0	.	158;160	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	F	160;158;160;160	ENSP00000347672:L160F;ENSP00000358523:L158F;ENSP00000310800:L160F;ENSP00000358522:L160F	ENSP00000310800:L160F	L	+	1	0	VANGL1	116008078	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.487000	0.81328	2.662000	0.90505	0.650000	0.86243	CTC	.	.		0.512	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			T	116206555	C	T	116206555	3	4	215	1	0	0	0	0	1	0	0	0	17134	565	20	3	488	3	VANGL1	1	116206555	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	6941496	116206555	133044066	10	30917										
RPRD2	23248	hgsc.bcm.edu	37	chr1	150437119	150437119	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctcacaaccctctggcaaatAtcctctccaaggtggagatc	7	14	3	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:150437119A>G	ENST00000369068.4	+	10	1532	c.1528A>G	c.(1528-1530)Atc>Gtc	p.I510V	RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.I484V|RPRD2_ENST00000539519.1_Missense_Mutation_p.I484V	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	510	Ser-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TCTGGCAAATATCCTCTCCAA	0.547											OREG0013786	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I510V		Atlas-SNP	.											.	RPRD2	189	.	0			c.A1528G						.						90	102	98					1																	150437119		2044	4189	6233	SO:0001583	missense	23248	exon10			GCAAATATCCTCT	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.1528A>G	chr1.hg19:g.150437119A>G	ENSP00000358064:p.Ile510Val	62.0	0.0	1732	108.0	37.0	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	hg19	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	A	18.93	3.728496	0.69074	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.56941	0.54;0.51;0.43	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.52885	0.1762	M	0.61703	1.905	0.41573	D	0.988691	P;P;P	0.50528	0.766;0.894;0.936	B;P;P	0.52424	0.33;0.502;0.698	T	0.55755	-0.8091	10	0.46703	T	0.11	-13.1513	15.4877	0.75578	1.0:0.0:0.0:0.0	.	484;510;484	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	V	484;484;510	ENSP00000383785:I484V;ENSP00000445482:I484V;ENSP00000358064:I510V	ENSP00000358064:I510V	I	+	1	0	RPRD2	148703743	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.347000	0.65998	2.248000	0.74166	0.533000	0.62120	ATC	.	.		0.547	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		G	150437119	A	G	150437119	3	3	215	1	0	0	0	0	1	0	0	0	13632	449	16	2	1566	2	RPRD2	1	150437119	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	34230564	150437119	98813502	11	30918										
PRG4	10216	hgsc.bcm.edu	37	chr1	186282008	186282008	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gaaaacctgacggctatgatTactatgccttttctaaaggt	8	8	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:186282008T>A	ENST00000445192.2	+	12	4144	c.4099T>A	c.(4099-4101)Tac>Aac	p.Y1367N	RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367486.3_Missense_Mutation_p.Y1324N|PRG4_ENST00000367483.4_Missense_Mutation_p.Y1326N|TPR_ENST00000367478.4_3'UTR|PRG4_ENST00000367484.3_Missense_Mutation_p.Y896N|PRG4_ENST00000367485.4_Missense_Mutation_p.Y1274N	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1367					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CGGCTATGATTACTATGCCTT	0.373																																					p.Y1367N		Atlas-SNP	.											.	PRG4	259	.	0			c.T4099A						.						107	101	103					1																	186282008		2203	4300	6503	SO:0001583	missense	10216	exon12			TATGATTACTATG	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.4099T>A	chr1.hg19:g.186282008T>A	ENSP00000399679:p.Tyr1367Asn	85.0	0.0		172.0	78.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	hg19	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.390499	0.62066	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64	5.78	5.78	0.91487	Hemopexin/matrixin (2);	0.000000	0.41500	D	0.000863	T	0.68522	0.3010	M	0.70275	2.135	0.48830	D	0.999713	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.997;0.999	T	0.72070	-0.4401	10	0.87932	D	0	-6.1025	15.7842	0.78289	0.0:0.0:0.0:1.0	.	1233;1274;1367;1326	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	N	1324;896;1326;1274;1367	ENSP00000356456:Y1324N;ENSP00000356454:Y896N;ENSP00000356453:Y1326N;ENSP00000356455:Y1274N;ENSP00000399679:Y1367N	ENSP00000356453:Y1326N	Y	+	1	0	PRG4	184548631	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.109000	0.64615	2.206000	0.71126	0.477000	0.44152	TAC	.	.		0.373	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		A	186282008	T	A	186282008	3	1	215	1	0	0	0	0	1	0	0	0	12493	1754	61	4	4141	4	PRG4	1	186282008	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	35844889	186282008	62968613	12	30919										
CFH	3075	hgsc.bcm.edu	37	chr1	196648796	196648796	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gttataaatggatctcctatAtctcagaagattatttataa	5	5	2	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:196648796A>G	ENST00000359637.2	+	5	533	c.471A>G	c.(469-471)atA>atG	p.I157M	CFH_ENST00000439155.2_Missense_Mutation_p.I221M|CFH_ENST00000367429.4_Missense_Mutation_p.I221M			P08603	CFAH_HUMAN	complement factor H	221	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						GATCTCCTATATCTCAGAAGA	0.313																																					p.I221M		Atlas-SNP	.											.	CFH	251	.	0			c.A663G						.						54	58	57					1																	196648796		2203	4297	6500	SO:0001583	missense	3075	exon6			TCCTATATCTCAG	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000359637.2:c.471A>G	chr1.hg19:g.196648796A>G	ENSP00000352658:p.Ile157Met	165.0	0.0		300.0	77.0	NM_001014975	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000359637.2	hg19		.	.	.	.	.	.	.	.	.	.	A	14.23	2.474628	0.43942	.	.	ENSG00000000971	ENST00000367429;ENST00000439155;ENST00000391986;ENST00000359637	T;T;T	0.67698	-0.28;-0.28;-0.28	5.99	-2.77	0.05877	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.66197	0.2765	M	0.71581	2.175	0.09310	N	1	P;P;D;P	0.55605	0.837;0.852;0.972;0.86	P;P;P;B	0.52424	0.698;0.579;0.698;0.331	T	0.57493	-0.7802	9	0.27785	T	0.31	.	4.6656	0.12664	0.2978:0.0:0.1543:0.5479	.	157;221;221;221	Q5TFM2;P08603-2;P08603;F8WDX4	.;.;CFAH_HUMAN;.	M	221;221;221;157	ENSP00000356399:I221M;ENSP00000402656:I221M;ENSP00000352658:I157M	ENSP00000352658:I157M	I	+	3	3	CFH	194915419	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.081000	0.03403	-0.387000	0.07809	0.533000	0.62120	ATA	.	.		0.313	CFH-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000087502.1	NM_000186		G	196648796	A	G	196648796	3	3	215	1	0	0	0	0	1	0	0	0	3285	439	16	2	685	2	CFH	1	196648796	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	10366788	196648796	52601825	13	30920										
NR5A2	2494	hgsc.bcm.edu	37	chr1	200017315	200017315	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aacagctgtaagggccgaccGaatgcgtggaggaaggaata	15	7	0	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:200017315G>A	ENST00000367362.3	+	5	725	c.479G>A	c.(478-480)cGa>cAa	p.R160Q	NR5A2_ENST00000544748.1_Missense_Mutation_p.R88Q|NR5A2_ENST00000236914.3_Missense_Mutation_p.R114Q	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	160					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					AGGGCCGACCGAATGCGTGGA	0.463																																					p.R160K	Melanoma(179;1138 2773 15678 26136)	Atlas-SNP	.											.	NR5A2	83	.	0			c.G479A						.						68	70	69					1																	200017315		2203	4300	6503	SO:0001583	missense	2494	exon5			CCGACCGAATGCG	U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"Nuclear hormone receptors"	7984	protein-coding gene	gene with protein product	"liver receptor homolog-1"	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.479G>A	chr1.hg19:g.200017315G>A	ENSP00000356331:p.Arg160Gln	91.0	0.0		153.0	36.0	NM_205860	B4E2P3|O95642|Q147U3	Missense_Mutation	SNP	ENST00000367362.3	hg19	CCDS1401.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.430947|5.430947	0.96150|0.96150	.|.	.|.	ENSG00000116833|ENSG00000116833	ENST00000367357|ENST00000367362;ENST00000236914;ENST00000544748;ENST00000235480	.|T;T;T	.|0.78707	.|-1.2;-1.2;-1.2	5.75|5.75	5.75|5.75	0.90469|0.90469	.|Zinc finger, NHR/GATA-type (1);Nuclear hormone receptor, ligand-binding (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88855|0.88855	0.6550|0.6550	M|M	0.78916|0.78916	2.43|2.43	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	D|D	0.87633|0.87633	0.2517|0.2517	5|9	.|.	.|.	.|.	.|.	20.312|20.312	0.98644|0.98644	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|114;160	.|F1D8R9;O00482	.|.;NR5A2_HUMAN	K|Q	81|160;114;88;80	.|ENSP00000356331:R160Q;ENSP00000236914:R114Q;ENSP00000439116:R88Q	.|.	E|R	+|+	1|2	0|0	NR5A2|NR5A2	198283938|198283938	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.747000|9.747000	0.98863|0.98863	2.866000|2.866000	0.98385|0.98385	0.650000|0.650000	0.86243|0.86243	GAA|CGA	.	.		0.463	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2			A	200017315	G	A	200017315	3	1	215	1	0	0	0	0	1	0	0	0	10645	1058	37	1	497	1	NR5A2	1	200017315	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	3368519	200017315	49233306	14	30921										
IL10	3586	hgsc.bcm.edu	37	chr1	206941984	206941984	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gtcgccaccctgatgtctcaGtttcgtatcttcattgtcat	7	12	4	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:206941984G>A	ENST00000423557.1	-	5	592	c.534C>T	c.(532-534)aaC>aaT	p.N178N	IL10_ENST00000471071.1_5'Flank	NM_000572.2	NP_000563.1	P22301	IL10_HUMAN	interleukin 10	178					B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to lipopolysaccharide (GO:0071222)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|defense response to bacterium (GO:0042742)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|leukocyte chemotaxis (GO:0030595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of chronic inflammatory response to antigenic stimulus (GO:0002875)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interferon-alpha biosynthetic process (GO:0045355)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of myeloid dendritic cell activation (GO:0030886)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor biosynthetic process (GO:0032800)|regulation of gene expression (GO:0010468)|regulation of isotype switching (GO:0045191)|regulation of sensory perception of pain (GO:0051930)|response to activity (GO:0014823)|response to carbon monoxide (GO:0034465)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to inactivity (GO:0014854)|response to insulin (GO:0032868)|response to molecule of bacterial origin (GO:0002237)|type 2 immune response (GO:0042092)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-10 receptor binding (GO:0005141)			endometrium(1)|large_intestine(6)|lung(4)|prostate(1)	12	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			TGATGTCTCAGTTTCGTATCT	0.463																																					p.N178N		Atlas-SNP	.											.	IL10	22	.	0			c.C534T						.						139	118	125					1																	206941984		2203	4300	6503	SO:0001819	synonymous_variant	3586	exon5			GTCTCAGTTTCGT	M57627	CCDS1467.1	1q31-q32	2011-07-14			ENSG00000136634	ENSG00000136634		"Interleukins and interleukin receptors"	5962	protein-coding gene	gene with protein product	"cytokine synthesis inhibitory factor", "T-cell growth inhibitory factor"	124092				9162098	Standard	NM_000572		Approved	CSIF, TGIF, IL10A, IL-10	uc001hen.1	P22301	OTTHUMG00000036386	ENST00000423557.1:c.534C>T	chr1.hg19:g.206941984G>A		61.0	0.0		78.0	37.0	NM_000572		Silent	SNP	ENST00000423557.1	hg19	CCDS1467.1																																																																																			.	.		0.463	IL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088564.3	NM_000572		A	206941984	G	A	206941984	2	1	215	1	0	0	0	0	0	0	0	1	7628	1020	36	3		3	IL10	1	206941984	Silent	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	6924669	206941984	42308637	15	30922										
C4BPA	722	hgsc.bcm.edu	37	chr1	207288805	207288805	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	agttacgtaatgggcaagtaGagattaagacagatttatct	10	4	1	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr1:207288805G>A	ENST00000367070.3	+	4	567	c.373G>A	c.(373-375)Gag>Aag	p.E125K		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	125	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						TGGGCAAGTAGAGATTAAGAC	0.348																																					p.E125K		Atlas-SNP	.											.	C4BPA	70	.	0			c.G373A						.						103	102	102					1																	207288805		2203	4300	6503	SO:0001583	missense	722	exon4			CAAGTAGAGATTA	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"complement component 4-binding protein, alpha"	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.373G>A	chr1.hg19:g.207288805G>A	ENSP00000356037:p.Glu125Lys	107.0	0.0		172.0	51.0	NM_000715	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	hg19	CCDS1477.1	.	.	.	.	.	.	.	.	.	.	G	9.410	1.080358	0.20309	.	.	ENSG00000123838	ENST00000367070;ENST00000421786	T;T	0.63255	-0.03;-0.03	5.36	2.14	0.27477	Complement control module (2);Sushi/SCR/CCP (3);	1.727610	0.02959	N	0.142827	T	0.55130	0.1901	L	0.27944	0.81	0.09310	N	1	B	0.32031	0.352	P	0.44394	0.448	T	0.48885	-0.8995	10	0.06236	T	0.91	.	6.0865	0.19970	0.4824:0.0:0.5176:0.0	.	125	P04003	C4BPA_HUMAN	K	125	ENSP00000356037:E125K;ENSP00000403386:E125K	ENSP00000356037:E125K	E	+	1	0	C4BPA	205355428	0.047000	0.20315	0.003000	0.11579	0.022000	0.10575	0.318000	0.19504	0.588000	0.29660	0.585000	0.79938	GAG	.	.		0.348	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			A	207288805	G	A	207288805	3	1	215	1	0	0	0	0	1	0	0	0	2251	943	33	3	383	3	C4BPA	1	207288805	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	346821	207288805	41961816	16	30923										
RASGRP3	25780	hgsc.bcm.edu	37	chr2	33749508	33749508	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttttattgcagaagctccttCagctcaaaaattttaacacc	4	10	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:33749508C>A	ENST00000403687.3	+	9	1440	c.700C>A	c.(700-702)Cag>Aag	p.Q234K	RASGRP3_ENST00000402538.3_Missense_Mutation_p.Q234K|RASGRP3_ENST00000407811.1_Missense_Mutation_p.Q234K	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	234	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)			large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					GAAGCTCCTTCAGCTCAAAAA	0.348																																					p.Q234K		Atlas-SNP	.											.	RASGRP3	87	.	0			c.C700A						.						50	47	48					2																	33749508		1821	4084	5905	SO:0001583	missense	25780	exon10			CTCCTTCAGCTCA	AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"EF-hand domain containing"	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.700C>A	chr2.hg19:g.33749508C>A	ENSP00000384192:p.Gln234Lys	125.0	0.0		149.0	53.0	NM_170672	D6W583|O94931|Q53SD7	Missense_Mutation	SNP	ENST00000403687.3	hg19	CCDS46256.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.810636	0.50421	.	.	ENSG00000152689	ENST00000402538;ENST00000403687;ENST00000407811	T;T;T	0.26957	1.7;1.7;1.7	5.34	5.34	0.76211	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.064270	0.64402	D	0.000007	T	0.20659	0.0497	N	0.21282	0.65	0.31990	N	0.604737	B;B	0.31859	0.343;0.343	B;B	0.36092	0.217;0.217	T	0.18967	-1.0320	10	0.38643	T	0.18	-13.3663	13.3651	0.60678	0.0:0.9248:0.0:0.0752	.	234;234	D6W583;Q8IV61	.;GRP3_HUMAN	K	234	ENSP00000385886:Q234K;ENSP00000384192:Q234K;ENSP00000383917:Q234K	ENSP00000385886:Q234K	Q	+	1	0	RASGRP3	33603012	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.723000	0.54955	2.496000	0.84212	0.655000	0.94253	CAG	.	.		0.348	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376		A	33749508	C	A	33749508	3	1	215	1	0	0	0	0	1	0	0	0	13091	827	29	3	726	3	RASGRP3	2	33749508	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10		33749508	209449865	17	30924										
USP34	9736	hgsc.bcm.edu	37	chr2	61441503	61441503	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tttattgtgatttgtagctaTtgctggctcagaaagtttag	10	4	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:61441503T>C	ENST00000398571.2	-	68	8450	c.8374A>G	c.(8374-8376)Ata>Gta	p.I2792V	USP34_ENST00000472689.1_Intron	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2792					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TTTGTAGCTATTGCTGGCTCA	0.388																																					p.I2792V		Atlas-SNP	.											.	USP34	334	.	0			c.A8374G						.						114	108	110					2																	61441503		1881	4112	5993	SO:0001583	missense	9736	exon68			TAGCTATTGCTGG	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.8374A>G	chr2.hg19:g.61441503T>C	ENSP00000381577:p.Ile2792Val	125.0	0.0		151.0	53.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.38|14.38	2.519649|2.519649	0.44866|0.44866	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571|ENST00000411912	T|.	0.39406|.	1.08|.	5.78|5.78	5.78|5.78	0.91487|0.91487	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.57902|0.57902	0.2085|0.2085	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	P|.	0.35745|.	0.518|.	P|.	0.47827|.	0.558|.	T|T	0.54241|0.54241	-0.8323|-0.8323	10|5	0.25106|.	T|.	0.35|.	.|.	16.1095|16.1095	0.81250|0.81250	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2792|.	Q70CQ2|.	UBP34_HUMAN|.	V|S	2640;2640;2792|551	ENSP00000381577:I2792V|.	ENSP00000263989:I2640V|.	I|N	-|-	1|2	0|0	USP34|USP34	61295007|61295007	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	8.013000|8.013000	0.88655|0.88655	2.210000|2.210000	0.71456|0.71456	0.482000|0.482000	0.46254|0.46254	ATA|AAT	.	.		0.388	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			C	61441503	T	C	61441503	3	2	215	1	0	0	0	0	1	0	0	0	17080	1493	52	2	2318	2	USP34	2	61441503	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	27691995	61441503	181757870	18	30925										
TET3	200424	hgsc.bcm.edu	37	chr2	74274165	74274165	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctctgccctcccgcagccttCtcattccaccccccaggctt	5	22	2	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:74274165C>G	ENST00000409262.3	+	1	716	c.716C>G	c.(715-717)tCt>tGt	p.S239C		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	239					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCGCAGCCTTCTCATTCCACC	0.597																																					p.S239C		Atlas-SNP	.											.	TET3	101	.	0			c.C716G						.						45	49	48					2																	74274165		2048	4196	6244	SO:0001583	missense	200424	exon1			AGCCTTCTCATTC		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.716C>G	chr2.hg19:g.74274165C>G	ENSP00000386869:p.Ser239Cys	52.0	0.0		69.0	26.0	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	ENST00000409262.3	hg19	CCDS46339.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.901326	0.52227	.	.	ENSG00000187605	ENST00000305799;ENST00000409262;ENST00000233310	T;T	0.25912	1.77;2.6	5.84	5.84	0.93424	.	.	.	.	.	T	0.24699	0.0599	N	0.14661	0.345	0.25373	N	0.988682	D	0.63880	0.993	P	0.49999	0.628	T	0.13548	-1.0505	9	0.72032	D	0.01	.	13.8201	0.63315	0.1533:0.8467:0.0:0.0	.	239	O43151	TET3_HUMAN	C	281;239;239	ENSP00000307803:S281C;ENSP00000386869:S239C	ENSP00000233310:S239C	S	+	2	0	TET3	74127673	0.012000	0.17670	1.000000	0.80357	0.990000	0.78478	2.360000	0.44151	2.768000	0.95171	0.561000	0.74099	TCT	.	.		0.597	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			G	74274165	C	G	74274165	3	3	215	1	0	0	0	0	1	0	0	0	15786	913	32	4	718	4	TET3	2	74274165	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	12832662	74274165	168925208	19	30926										
C2orf3	6936	hgsc.bcm.edu	37	chr2	75937765	75937765	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tttggtggcacgccgggagcTcgcccagacccggccccggc	15	17	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:75937765T>A	ENST00000321027.3	-	1	350	c.217A>T	c.(217-219)Agc>Tgc	p.S73C	GCFC2_ENST00000409857.3_Missense_Mutation_p.S73C|GCFC2_ENST00000470503.1_Missense_Mutation_p.S73C|GCFC2_ENST00000541687.1_Missense_Mutation_p.S73C	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	73					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)										CGCCGGGAGCTCGCCCAGACC	0.756																																					p.S73C		Atlas-SNP	.											.	.	.	.	0			c.A217T						.						2	2	2					2																	75937765		1340	2997	4337	SO:0001583	missense	6936	exon1			GGGAGCTCGCCCA	AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"GC binding factor"	189901	"transcription factor 9 (binds GC-rich sequences)", "chromosome 2 open reading frame 3"	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.217A>T	chr2.hg19:g.75937765T>A	ENSP00000318690:p.Ser73Cys	47.0	0.0		35.0	16.0	NM_001201335	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	hg19	CCDS1961.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.466362	0.43839	.	.	ENSG00000005436	ENST00000321027;ENST00000541687;ENST00000409857;ENST00000442309	T;T;T;T	0.52057	1.94;0.88;1.34;0.68	3.76	2.59	0.31030	.	1.482010	0.03709	N	0.249902	T	0.61098	0.2320	L	0.60455	1.87	0.27845	N	0.94097	D;D	0.76494	0.999;0.992	P;P	0.60345	0.873;0.615	T	0.33574	-0.9863	10	0.62326	D	0.03	-3.2265	6.0083	0.19559	0.0:0.1192:0.0:0.8808	.	73;73	A4UHQ8;P16383	.;GCF_HUMAN	C	73	ENSP00000318690:S73C;ENSP00000437767:S73C;ENSP00000386552:S73C;ENSP00000415831:S73C	ENSP00000318690:S73C	S	-	1	0	C2orf3	75791273	0.696000	0.27757	0.880000	0.34516	0.062000	0.15995	1.811000	0.38942	0.793000	0.33875	-0.451000	0.05528	AGC	.	.		0.756	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203		A	75937765	T	A	75937765	3	1	215	1	0	0	0	0	1	0	0	0	2164	1551	54	4	2196	4	C2orf3	2	75937765	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	1663600	75937765	167261608	20	30927										
CHST10	9486	hgsc.bcm.edu	37	chr2	101014387	101014387	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	caccatttagaacaatcagcActttcttccactgggtgttg	7	11	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:101014387A>G	ENST00000264249.3	-	5	795	c.410T>C	c.(409-411)gTg>gCg	p.V137A	CHST10_ENST00000542617.1_Missense_Mutation_p.V185A|CHST10_ENST00000409701.1_Missense_Mutation_p.V137A	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	137					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						AACAATCAGCACTTTCTTCCA	0.522																																					p.V137A		Atlas-SNP	.											.	CHST10	42	.	0			c.T410C						.						149	135	140					2																	101014387		2203	4300	6503	SO:0001583	missense	9486	exon5			ATCAGCACTTTCT	BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"Sulfotransferases, membrane-bound"	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.410T>C	chr2.hg19:g.101014387A>G	ENSP00000264249:p.Val137Ala	83.0	0.0		103.0	30.0	NM_004854	Q53T18	Missense_Mutation	SNP	ENST00000264249.3	hg19	CCDS2047.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.135354	0.77662	.	.	ENSG00000115526	ENST00000264249;ENST00000542617;ENST00000409701;ENST00000409046	T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.85274	0.5659	M	0.78344	2.41	0.80722	D	1	D	0.56968	0.978	D	0.64410	0.925	D	0.86263	0.1656	10	0.51188	T	0.08	-28.2325	15.7533	0.78005	1.0:0.0:0.0:0.0	.	137	O43529	CHSTA_HUMAN	A	137;185;137;137	ENSP00000264249:V137A;ENSP00000438869:V185A;ENSP00000387309:V137A;ENSP00000387121:V137A	ENSP00000264249:V137A	V	-	2	0	CHST10	100380819	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	9.339000	0.96797	2.123000	0.65237	0.533000	0.62120	GTG	.	.		0.522	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854		G	101014387	A	G	101014387	3	3	215	1	0	0	0	0	1	0	0	0	3400	159	6	2	672	2	CHST10	2	101014387	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	25076622	101014387	142184986	21	30928										
MAP3K2	10746	hgsc.bcm.edu	37	chr2	128065257	128065257	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aaatctcgagtatagtctgaGacatgaggtggcagctttgg	13	6	2	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:128065257G>C	ENST00000409947.1	-	17	2040	c.1758C>G	c.(1756-1758)gtC>gtG	p.V586V	MAP3K2_ENST00000344908.5_Silent_p.V586V			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	586	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	TATAGTCTGAGACATGAGGTG	0.443																																					p.V586V		Atlas-SNP	.											.	MAP3K2	78	.	0			c.C1758G						.						71	75	74					2																	128065257		2081	4222	6303	SO:0001819	synonymous_variant	10746	exon16			GTCTGAGACATGA	AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6854	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 2"	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.1758C>G	chr2.hg19:g.128065257G>C		114.0	0.0		131.0	36.0	NM_006609	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Silent	SNP	ENST00000409947.1	hg19	CCDS46404.1																																																																																			.	.		0.443	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609		C	128065257	G	C	128065257	2	2	215	1	0	0	0	0	0	0	0	1	9259	929	33	4		4	MAP3K2	2	128065257	Silent	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	27050870	128065257	115134116	22	30929										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141812829	141812829	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttcacatgcatggcttctgaCtacaacaaataaaaaacagc	5	10	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:141812829C>A	ENST00000389484.3	-	10	2380		c.e10-1			NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B						protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGGCTTCTGACTACAACAAAT	0.398										TSP Lung(27;0.18)																											.	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.1409-1G>T						.						74	67	70					2																	141812829		2203	4300	6503	SO:0001630	splice_region_variant	53353	exon11			TTCTGACTACAAC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1409-1G>T	chr2.hg19:g.141812829C>A		78.0	0.0		75.0	19.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Splice_Site	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.572186	0.86542	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2912	0.94100	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRP1B	141529299	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	7.396000	0.79891	2.569000	0.86673	0.557000	0.71058	.	.	.		0.398	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Intron	A	141812829	C	A	141812829	5	1	215	1	0	0	0	0	0	0	1	0	8964	579	20	3	12719	3	LRP1B	2	141812829	Splice_Site	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	13747572	141812829	101386544	23	30930										
NEB	4703	hgsc.bcm.edu	37	chr2	152350375	152350375	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tttccccaggttctctttgtAtaacacctgtgagatacaaa	6	10	1	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:152350375A>G	ENST00000172853.10	-	142	19165	c.19018T>C	c.(19018-19020)Tac>Cac	p.Y6340H	NEB_ENST00000498015.2_Intron|RIF1_ENST00000457745.1_Intron|NEB_ENST00000397336.2_Missense_Mutation_p.Y171H|NEB_ENST00000604864.1_Missense_Mutation_p.Y8196H|NEB_ENST00000509223.2_Intron|NEB_ENST00000397345.3_Missense_Mutation_p.Y8196H|NEB_ENST00000603639.1_Missense_Mutation_p.Y8196H|NEB_ENST00000427231.2_Missense_Mutation_p.Y8196H|NEB_ENST00000409198.1_Missense_Mutation_p.Y6340H			P20929	NEBU_HUMAN	nebulin	6340					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTCTCTTTGTATAACACCTGT	0.393																																					p.Y8231H		Atlas-SNP	.											.	NEB	1697	.	0			c.T24691C						.						58	54	55					2																	152350375		1823	4078	5901	SO:0001583	missense	4703	exon176			CTTTGTATAACAC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.19018T>C	chr2.hg19:g.152350375A>G	ENSP00000172853:p.Tyr6340His	83.0	0.0		97.0	31.0	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.67|19.67	3.871833|3.871833	0.72180|0.72180	.|.	.|.	ENSG00000183091|ENSG00000183091	ENST00000421461|ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853;ENST00000397336	.|D;D;D;D;D	.|0.99958	.|-9.03;-9.03;-9.03;-9.03;-9.03	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	.|0.229361	.|0.46145	.|D	.|0.000314	D|D	0.99963|0.99963	0.9985|0.9985	H|H	0.95611|0.95611	3.695|3.695	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.999;0.999	D|D	0.96009|0.96009	0.9000|0.9000	5|10	.|0.87932	.|D	.|0	.|.	16.0454|16.0454	0.80717|0.80717	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|171;6340;8196	.|B7Z6P9;P20929;F8WCL5	.|.;NEBU_HUMAN;.	T|H	341|6340;8196;8196;6340;171	.|ENSP00000386259:Y6340H;ENSP00000380505:Y8196H;ENSP00000416578:Y8196H;ENSP00000172853:Y6340H;ENSP00000380497:Y171H	.|ENSP00000172853:Y6340H	I|Y	-|-	2|1	0|0	NEB|NEB	152058621|152058621	1.000000|1.000000	0.71417|0.71417	0.933000|0.933000	0.37362|0.37362	0.931000|0.931000	0.56810|0.56810	7.003000|7.003000	0.76310|0.76310	2.258000|2.258000	0.74832|0.74832	0.533000|0.533000	0.62120|0.62120	ATA|TAC	.	.		0.393	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152350375	A	G	152350375	3	3	215	1	0	0	0	0	1	0	0	0	10311	449	16	2	1023	2	NEB	2	152350375	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	10537546	152350375	90848998	24	30931										
FAP	2191	hgsc.bcm.edu	37	chr2	163059608	163059608	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tccttgtcactaaatattttGtagtacgaaatggcatcata	6	7	2	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:163059608G>T	ENST00000188790.4	-	13	1302	c.1095C>A	c.(1093-1095)taC>taA	p.Y365*	FAP_ENST00000443424.1_Nonsense_Mutation_p.Y340*	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						TAAATATTTTGTAGTACGAAA	0.338																																					p.Y365X		Atlas-SNP	.											FAP,NS,carcinoma,0,1	FAP	122	.	0			c.C1095A						.						82	78	79					2																	163059608		2203	4299	6502	SO:0001587	stop_gained	2191	exon13			TATTTTGTAGTAC	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.1095C>A	chr2.hg19:g.163059608G>T	ENSP00000188790:p.Tyr365*	89.0	0.0		94.0	19.0	NM_004460		Nonsense_Mutation	SNP	ENST00000188790.4	hg19	CCDS33311.1	.	.	.	.	.	.	.	.	.	.	G	39	7.431903	0.98279	.	.	ENSG00000078098	ENST00000188790;ENST00000443424	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.3153	20.3011	0.98612	0.0:0.0:1.0:0.0	.	.	.	.	X	365;340	.	ENSP00000188790:Y365X	Y	-	3	2	FAP	162767854	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.250000	0.78287	2.804000	0.96469	0.650000	0.86243	TAC	.	.		0.338	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			T	163059608	G	T	163059608	4	4	215	1	0	0	0	0	0	1	0	0	5681	1372	48	3	1243	3	FAP	2	163059608	Nonsense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	10709233	163059608	80139765	25	30932										
AOX1	316	hgsc.bcm.edu	37	chr2	201462122	201462122	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttcttttgcattctgaaggcAtcacccagccaatgcctgtc	7	13	3	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:201462122A>G	ENST00000374700.2	+	4	444	c.203A>G	c.(202-204)cAt>cGt	p.H68R		NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	68	2Fe-2S ferredoxin-type. {ECO:0000255|PROSITE-ProRule:PRU00465}.				inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TTCTGAAGGCATCACCCAGCC	0.483																																					p.H68R		Atlas-SNP	.											.	AOX1	152	.	0			c.A203G						.						116	98	105					2																	201462122		2203	4300	6503	SO:0001583	missense	316	exon4			GAAGGCATCACCC	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.203A>G	chr2.hg19:g.201462122A>G	ENSP00000363832:p.His68Arg	37.0	0.0		41.0	14.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	hg19	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	A	17.55	3.417876	0.62622	.	.	ENSG00000138356	ENST00000374700;ENST00000454629	T;T	0.55052	1.75;0.54	5.29	5.29	0.74685	Beta-grasp fold, ferredoxin-type (1);Ferredoxin (3);	0.000000	0.85682	D	0.000000	T	0.60766	0.2294	M	0.67625	2.065	0.80722	D	1	B	0.33904	0.431	B	0.43225	0.412	T	0.65038	-0.6265	10	0.72032	D	0.01	-47.6721	15.0474	0.71838	1.0:0.0:0.0:0.0	.	68	Q06278	ADO_HUMAN	R	68;43	ENSP00000363832:H68R;ENSP00000392485:H43R	ENSP00000363832:H68R	H	+	2	0	AOX1	201170367	1.000000	0.71417	0.917000	0.36280	0.292000	0.27327	8.034000	0.88864	2.211000	0.71520	0.533000	0.62120	CAT	.	.		0.483	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		G	201462122	A	G	201462122	3	3	215	1	0	0	0	0	1	0	0	0	729	217	8	2	217	2	AOX1	2	201462122	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	38402514	201462122	41737251	26	30933										
AOX1	316	hgsc.bcm.edu	37	chr2	201515713	201515713	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ataggtgcgaatcataaacaTgtacaaggaaattgatcaaa	8	5	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:201515713T>C	ENST00000374700.2	+	26	3105	c.2864T>C	c.(2863-2865)aTg>aCg	p.M955T	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	955					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	ATCATAAACATGTACAAGGAA	0.433																																					p.M955T		Atlas-SNP	.											.	AOX1	152	.	0			c.T2864C						.						95	87	90					2																	201515713		2203	4300	6503	SO:0001583	missense	316	exon26			TAAACATGTACAA	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.2864T>C	chr2.hg19:g.201515713T>C	ENSP00000363832:p.Met955Thr	113.0	0.0		131.0	35.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	hg19	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.880323	0.72294	.	.	ENSG00000138356	ENST00000374700	T	0.38560	1.13	5.41	5.41	0.78517	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.130792	0.64402	D	0.000002	T	0.68403	0.2997	M	0.91663	3.23	0.80722	D	1	P	0.45957	0.869	P	0.57009	0.811	T	0.76225	-0.3037	10	0.87932	D	0	-51.9765	15.612	0.76733	0.0:0.0:0.0:1.0	.	955	Q06278	ADO_HUMAN	T	955	ENSP00000363832:M955T	ENSP00000363832:M955T	M	+	2	0	AOX1	201223958	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.161000	0.77505	2.281000	0.76405	0.533000	0.62120	ATG	.	.		0.433	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		C	201515713	T	C	201515713	3	2	215	1	0	0	0	0	1	0	0	0	729	1464	51	2	2966	2	AOX1	2	201515713	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	53591	201515713	41683660	27	30934										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204066340	204066340	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gctatttgtagtatcacatgAtgcaaagttgctcttcagtg	9	7	3	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr2:204066340A>G	ENST00000449802.1	+	49	7559	c.7226A>G	c.(7225-7227)gAt>gGt	p.D2409G		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2409										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						GTATCACATGATGCAAAGTTG	0.393																																					p.D2409G		Atlas-SNP	.											.	NBEAL1	266	.	0			c.A7226G						.						155	135	141					2																	204066340		1876	4120	5996	SO:0001583	missense	65065	exon49			CACATGATGCAAA	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.7226A>G	chr2.hg19:g.204066340A>G	ENSP00000399903:p.Asp2409Gly	173.0	0.0		213.0	56.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.729527	0.89390	.	.	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	T;T	0.38887	4.62;1.11	5.87	5.87	0.94306	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.67040	0.2851	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.67166	-0.5739	10	0.32370	T	0.25	.	15.9289	0.79644	1.0:0.0:0.0:0.0	.	2409;2398	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	G	2409;2340;424	ENSP00000399903:D2409G;ENSP00000388466:D424G	ENSP00000344985:D2340G	D	+	2	0	NBEAL1	203774585	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.797000	0.91882	2.242000	0.73789	0.533000	0.62120	GAT	.	.		0.393	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			G	204066340	A	G	204066340	3	3	215	1	0	0	0	0	1	0	0	0	10197	333	12	2	7416	2	NBEAL1	2	204066340	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	2550627	204066340	39133033	28	30935										
ANKRD28	23243	hgsc.bcm.edu	37	chr3	15736711	15736711	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttacaacatctagaggagttTcacttgcaatctgaaataaa	6	7	3	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:15736711T>C	ENST00000399451.2	-	16	1947	c.1580A>G	c.(1579-1581)gAa>gGa	p.E527G	MIR3134_ENST00000579433.1_RNA|ANKRD28_ENST00000383777.1_Missense_Mutation_p.E560G|ANKRD28_ENST00000497037.1_5'UTR	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	527						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						TAGAGGAGTTTCACTTGCAAT	0.333																																					p.E527G		Atlas-SNP	.											.	ANKRD28	121	.	0			c.A1580G						.						63	58	60					3																	15736711		1836	4085	5921	SO:0001583	missense	23243	exon16			GGAGTTTCACTTG	AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	29024	protein-coding gene	gene with protein product	"phosphatase interactor targeting K protein", "protein phosphatase 6 ankyrin repeat subunit A", "protein phosphatase 1, regulatory subunit 65"	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.1580A>G	chr3.hg19:g.15736711T>C	ENSP00000382379:p.Glu527Gly	281.0	0.0		359.0	109.0	NM_015199	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Missense_Mutation	SNP	ENST00000399451.2	hg19	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.141605	0.57044	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	T;T;T	0.65364	1.34;-0.15;1.34	6.07	6.07	0.98685	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.53997	0.1831	L	0.34521	1.04	0.80722	D	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.12156	0.007;0.007;0.003	T	0.46871	-0.9160	10	0.38643	T	0.18	.	16.6288	0.85011	0.0:0.0:0.0:1.0	.	560;557;527	O15084-1;O15084-4;O15084	.;.;ANR28_HUMAN	G	527;560;527	ENSP00000382379:E527G;ENSP00000373287:E560G;ENSP00000397341:E527G	ENSP00000373287:E560G	E	-	2	0	ANKRD28	15711715	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.326000	0.78906	0.533000	0.62120	GAA	.	.		0.333	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		C	15736711	T	C	15736711	3	2	215	1	0	0	0	0	1	0	0	0	656	1783	62	2	1633	2	ANKRD28	3	15736711	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10		15736711	182285719	29	30936										
LRRC2	79442	hgsc.bcm.edu	37	chr3	46586621	46586621	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gtgaactctgccttgtgagaGtgttcctttcaatcttgtcc	9	10	3	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:46586621G>C	ENST00000395905.3	-	3	640	c.248C>G	c.(247-249)aCt>aGt	p.T83S	LRRC2_ENST00000496388.1_5'Flank|LRRC2_ENST00000296144.3_Missense_Mutation_p.T83S	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	83			T -> A (in dbSNP:rs17286758).							breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		CCTTGTGAGAGTGTTCCTTTC	0.542																																					p.T83S		Atlas-SNP	.											.	LRRC2	37	.	0			c.C248G						.						238	214	222					3																	46586621		2203	4300	6503	SO:0001583	missense	79442	exon3			GTGAGAGTGTTCC	AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"leucine-rich repeat-containing 2"			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.248C>G	chr3.hg19:g.46586621G>C	ENSP00000379241:p.Thr83Ser	82.0	0.0		130.0	50.0	NM_024512	B2RDQ7|Q96LT5	Missense_Mutation	SNP	ENST00000395905.3	hg19	CCDS2741.1	.	.	.	.	.	.	.	.	.	.	G	0.433	-0.902292	0.02453	.	.	ENSG00000163827	ENST00000395905;ENST00000296144	T;T	0.15952	2.38;2.38	5.23	3.18	0.36537	.	1.238380	0.05597	N	0.575640	T	0.07234	0.0183	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29058	-1.0024	10	0.06236	T	0.91	.	8.5735	0.33583	0.2209:0.0:0.7791:0.0	.	83	Q9BYS8	LRRC2_HUMAN	S	83	ENSP00000379241:T83S;ENSP00000296144:T83S	ENSP00000296144:T83S	T	-	2	0	LRRC2	46561625	0.027000	0.19231	0.000000	0.03702	0.001000	0.01503	2.186000	0.42593	0.540000	0.28808	-0.145000	0.13849	ACT	.	.		0.542	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2			C	46586621	G	C	46586621	3	2	215	1	0	0	0	0	1	0	0	0	8985	1029	36	4	895	4	LRRC2	3	46586621	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	30849910	46586621	151435809	30	30937										
GMPPB	29925	hgsc.bcm.edu	37	chr3	49759883	49759883	+	Frame_Shift_Del	DEL	A	A	-													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	accctgtaactccatggcatAtagctgcccctccttggcca							TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:49759883delA	ENST00000480687.1	-	7	738	c.622delT	c.(622-624)tatfs	p.Y208fs	GMPPB_ENST00000308375.6_Frame_Shift_Del_p.Y208fs|AMIGO3_ENST00000320431.7_5'Flank|AMIGO3_ENST00000535833.1_5'UTR|GMPPB_ENST00000308388.6_Frame_Shift_Del_p.Y208fs			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B	208					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TCCATGGCATATAGCTGCCCC	0.617																																					p.Y208fs		Atlas-INDEL	.											.	GMPPB	14	.	0			c.623delA						.						95	94	94					3																	49759883		2203	4300	6503	SO:0001589	frameshift_variant	29925	exon6			.	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.622delT	chr3.hg19:g.49759883delA	ENSP00000418565:p.Tyr208fs	73.0	0.0		65.0	25.0	NM_013334	A8K6N5|Q9H7U3	Frame_Shift_Del	DEL	ENST00000480687.1	hg19	CCDS2803.1																																																																																			.	.		0.617	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334		-	49759883	A	-	49759883	7	5	215	1	0	1	0	1	0	0	0	0	6503	449	16	0	553	0	GMPPB	3	49759883	Frame_Shift_Del	DEL	A	TCGA-DD-AAEA-01A-11D-A40R-10	3173262	49759883	148262547	31	30938										
KCTD6	200845	hgsc.bcm.edu	37	chr3	58487150	58487158	+	In_Frame_Del	DEL	GACACCAGA	GACACCAGA	-													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	agtggaataagcacatgatgGacaccagagactgccaggtt							TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	GACACCAGA	GACACCAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:58487150_58487158delGACACCAGA	ENST00000355076.6	+	2	1488_1496	c.505_513delGACACCAGA	c.(505-513)gacaccagadel	p.DTR169del	KCTD6_ENST00000404589.3_In_Frame_Del_p.DTR169del|KCTD6_ENST00000490264.1_In_Frame_Del_p.DTR169del	NM_153331.3	NP_699162.3	Q8NC69	KCTD6_HUMAN	potassium channel tetramerization domain containing 6	169					protein homooligomerization (GO:0051260)		ankyrin binding (GO:0030506)			endometrium(1)|large_intestine(2)|lung(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(55;0.000177)|Kidney(10;0.00229)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.148)		GCACATGATGGACACCAGAGACTGCCAGG	0.421																																					p.168_171del		Atlas-INDEL	.											.	KCTD6	14	.	0			c.504_512del						.																																			SO:0001651	inframe_deletion	200845	exon3			.	AK074934	CCDS2891.1	3p21.2	2013-06-20	2013-06-20		ENSG00000168301	ENSG00000168301			22235	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 6"			21472142	Standard	NM_153331		Approved	MGC27385, KCASH3	uc003dkj.4	Q8NC69	OTTHUMG00000159161	ENST00000355076.6:c.505_513delGACACCAGA	chr3.hg19:g.58487150_58487158delGACACCAGA	ENSP00000347188:p.Asp169_Arg171del	172.0	0.0		169.0	36.0	NM_001128214	B3KNI5|Q8NBS6|Q8TCA6	In_Frame_Del	DEL	ENST00000355076.6	hg19	CCDS2891.1																																																																																			.	.		0.421	KCTD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353591.1	NM_153331		-	58487158	GACACCAGA	-	58487150	7	5	215	1	0	1	0	1	0	0	0	0	8122	1174	41	0	511	0	KCTD6	3	58487150	In_Frame_Del	DEL	GACACCAGA	TCGA-DD-AAEA-01A-11D-A40R-10	8727267	58487150	139535280	32	30939										
ARL6IP5	10550	hgsc.bcm.edu	37	chr3	69134210	69134210	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gctgagaacatggacgttaaTatcgccccactccgcgcctg	10	14	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:69134210T>A	ENST00000273258.3	+	1	116	c.12T>A	c.(10-12)aaT>aaA	p.N4K	ARL6IP5_ENST00000478935.1_Missense_Mutation_p.N4K	NM_006407.3	NP_006398.1	O75915	PRAF3_HUMAN	ADP-ribosylation factor-like 6 interacting protein 5	4					intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|L-glutamate transport (GO:0015813)|negative regulation of mitochondrial membrane potential (GO:0010917)|negative regulation of transport (GO:0051051)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of stress-activated MAPK cascade (GO:0032874)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				biliary_tract(1)|endometrium(1)|large_intestine(2)|ovary(1)|prostate(1)|urinary_tract(1)	7		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.78e-05)|Epithelial(33;0.000818)|LUSC - Lung squamous cell carcinoma(21;0.0118)|Lung(16;0.0189)|KIRC - Kidney renal clear cell carcinoma(39;0.203)|Kidney(39;0.238)		TGGACGTTAATATCGCCCCAC	0.592																																					p.N4K		Atlas-SNP	.											.	ARL6IP5	19	.	0			c.T12A						.						53	59	57					3																	69134210		2203	4300	6503	SO:0001583	missense	10550	exon1			CGTTAATATCGCC	AF070523	CCDS2912.1	3p14	2014-05-12	2014-05-12		ENSG00000144746	ENSG00000144746			16937	protein-coding gene	gene with protein product	"PRA1 domain family 3"	605709				11242046, 11042152	Standard	NM_006407		Approved	PRAF3, JWA, GTRAP3-18, DERP11, HSPC127	uc003dnr.3	O75915	OTTHUMG00000158773	ENST00000273258.3:c.12T>A	chr3.hg19:g.69134210T>A	ENSP00000273258:p.Asn4Lys	68.0	0.0		66.0	25.0	NM_006407	B2R6V5|Q53ES3|Q5KU08	Missense_Mutation	SNP	ENST00000273258.3	hg19	CCDS2912.1	.	.	.	.	.	.	.	.	.	.	T	14.59	2.581596	0.46006	.	.	ENSG00000144746	ENST00000273258;ENST00000412089;ENST00000478935	T;T	0.39997	1.05;1.05	5.69	-6.35	0.01975	.	0.822034	0.11613	N	0.546584	T	0.15912	0.0383	N	0.08118	0	0.09310	N	0.999997	B	0.06786	0.001	B	0.10450	0.005	T	0.11275	-1.0594	10	0.44086	T	0.13	-0.5963	3.6533	0.08212	0.2171:0.406:0.2639:0.1131	.	4	O75915	PRAF3_HUMAN	K	4	ENSP00000273258:N4K;ENSP00000420138:N4K	ENSP00000273258:N4K	N	+	3	2	ARL6IP5	69216900	0.110000	0.22057	0.000000	0.03702	0.545000	0.35147	-0.114000	0.10757	-0.947000	0.03673	-0.297000	0.09499	AAT	.	.		0.592	ARL6IP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352132.1	NM_006407		A	69134210	T	A	69134210	3	1	215	1	0	0	0	0	1	0	0	0	944	1403	49	4	14	4	ARL6IP5	3	69134210	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	10647060	69134210	128888220	33	30940										
CNTN3	5067	hgsc.bcm.edu	37	chr3	74414775	74414776	+	Frame_Shift_Ins	INS	-	-	T													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggaaggcttgggcttgccgcINSttgccctgcattcccaataa							TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:74414775_74414776insT	ENST00000263665.6	-	8	1051_1052	c.1024_1025insA	c.(1024-1026)agcfs	p.S342fs		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	342	Ig-like C2-type 4.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		GGGCTTGCCGCTTGCCCTGCAT	0.475																																					p.S342fs		Atlas-INDEL	.											.	CNTN3	174	.	0			c.1025_1026insA						.																																			SO:0001589	frameshift_variant	5067	exon8			.	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1025dupA	chr3.hg19:g.74414777_74414777dupT	ENSP00000263665:p.Ser342fs	83.0	0.0		121.0	39.0	NM_020872	B9EK50|Q9H039	Frame_Shift_Ins	INS	ENST00000263665.6	hg19	CCDS33790.1																																																																																			.	.		0.475	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		T	74414776	-	T	74414775	7	5	215	1	0	1	1	0	0	0	0	0	3644	797	28	0	2121	0	CNTN3	3	74414775	Frame_Shift_Ins	INS	-	TCGA-DD-AAEA-01A-11D-A40R-10	5280565	74414775	123607655	34	30941										
CHMP2B	25978	hgsc.bcm.edu	37	chr3	87276703	87276703	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tcttcaagaagaaaaccgtgGatggtgagttccaggccggg	14	8	2	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:87276703G>T	ENST00000263780.4	+	1	269	c.31G>T	c.(31-33)Gat>Tat	p.D11Y	CHMP2B_ENST00000494980.1_Missense_Mutation_p.D11Y|MIR4795_ENST00000584182.1_RNA|CHMP2B_ENST00000472024.1_3'UTR|CHMP2B_ENST00000471660.1_5'UTR	NM_014043.3	NP_054762.2	Q9UQN3	CHM2B_HUMAN	charged multivesicular body protein 2B	11					cell death (GO:0008219)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	12	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		GAAAACCGTGGATGGTGAGTT	0.652																																					p.D11Y		Atlas-SNP	.											.	CHMP2B	28	.	0			c.G31T						.						62	73	69					3																	87276703		2203	4300	6503	SO:0001583	missense	25978	exon1			ACCGTGGATGGTG	BC001553	CCDS2918.1, CCDS58840.1	3p12.1	2011-09-21	2011-09-21		ENSG00000083937	ENSG00000083937		"Charged multivesicular body proteins"	24537	protein-coding gene	gene with protein product	"VPS2 homolog B (S. cerevisiae)"	609512	"chromatin modifying protein 2B"			11559748	Standard	NM_014043		Approved	DKFZP564O123, CHMP2.5, VPS2B	uc003dqp.4	Q9UQN3	OTTHUMG00000158982	ENST00000263780.4:c.31G>T	chr3.hg19:g.87276703G>T	ENSP00000263780:p.Asp11Tyr	153.0	0.0		123.0	49.0	NM_014043	B4DJG8|Q53HC7|Q9Y4U6	Missense_Mutation	SNP	ENST00000263780.4	hg19	CCDS2918.1	.	.	.	.	.	.	.	.	.	.	G	16.27	3.076568	0.55753	.	.	ENSG00000083937	ENST00000263780;ENST00000494980	D;D	0.89050	-2.42;-2.46	4.2	4.2	0.49525	.	0.097447	0.64402	D	0.000002	D	0.87529	0.6200	M	0.65498	2.005	0.58432	D	0.999999	B	0.22480	0.07	B	0.26614	0.071	D	0.86740	0.1954	10	0.87932	D	0	-40.5373	12.2244	0.54451	0.0:0.0:1.0:0.0	.	11	Q9UQN3	CHM2B_HUMAN	Y	11	ENSP00000263780:D11Y;ENSP00000418920:D11Y	ENSP00000263780:D11Y	D	+	1	0	CHMP2B	87359393	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	4.140000	0.58031	2.330000	0.79161	0.455000	0.32223	GAT	.	.		0.652	CHMP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352779.2	NM_014043		T	87276703	G	T	87276703	3	4	215	1	0	0	0	0	1	0	0	0	3357	1174	41	3	33	3	CHMP2B	3	87276703	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	12861928	87276703	110745727	35	30942										
KTELC1	56983	hgsc.bcm.edu	37	chr3	119209506	119209506	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gagtggctagaattcttctaTccacagctgaagccatgggt	11	9	2	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:119209506T>C	ENST00000295588.4	+	9	990	c.906T>C	c.(904-906)taT>taC	p.Y302Y		NM_152305.2	NP_689518.1	Q8NBL1	PGLT1_HUMAN	protein O-glucosyltransferase 1	302					cardiovascular system development (GO:0072358)|Notch signaling pathway (GO:0007219)|protein O-linked glycosylation (GO:0006493)|regulation of Notch signaling pathway (GO:0008593)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	glucosyltransferase activity (GO:0046527)|protein xylosyltransferase activity (GO:0030158)|UDP-glucosyltransferase activity (GO:0035251)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(1)	16						AATTCTTCTATCCACAGCTGA	0.443																																					p.Y302Y		Atlas-SNP	.											.	POGLUT1	32	.	0			c.T906C						.						142	131	135					3																	119209506		2203	4300	6503	SO:0001819	synonymous_variant	56983	exon9			CTTCTATCCACAG	BC030614	CCDS2988.1	3q13.33	2010-09-29	2010-09-29	2010-09-29	ENSG00000163389	ENSG00000163389			22954	protein-coding gene	gene with protein product	"KDELC family like 1"	615618	"chromosome 3 open reading frame 9", "KTEL (Lys-Tyr-Glu-Leu) containing 1"	C3orf9, KTELC1		16524674	Standard	NM_152305		Approved	MDS010, MGC32995, 9630046K23Rik, MDSRP, hCLP46, KDELCL1, Rumi	uc003ecm.3	Q8NBL1	OTTHUMG00000159379	ENST00000295588.4:c.906T>C	chr3.hg19:g.119209506T>C		97.0	0.0		88.0	26.0	NM_152305	B2RD13|Q53GJ4|Q8N2T1	Silent	SNP	ENST00000295588.4	hg19	CCDS2988.1																																																																																			.	.		0.443	POGLUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355034.2	NM_152305		C	119209506	T	C	119209506	2	2	215	1	0	0	0	0	0	0	0	1	8592	1442	50	2		2	KTELC1	3	119209506	Silent	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	31932803	119209506	78812924	36	30943										
MBNL1	4154	hgsc.bcm.edu	37	chr3	152174105	152174105	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	actgtgtccgcagcaacaacAtctgccacaagtgttccctt	7	14	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:152174105A>G	ENST00000463374.1	+	7	1576	c.1065A>G	c.(1063-1065)acA>acG	p.T355T	MBNL1_ENST00000355460.2_Silent_p.T337T|MBNL1_ENST00000485910.1_Silent_p.T269T|MBNL1_ENST00000282488.7_Silent_p.T269T|MBNL1_ENST00000545754.1_Silent_p.T281T|MBNL1_ENST00000357472.3_Intron|MBNL1_ENST00000324210.5_Silent_p.T349T|MBNL1_ENST00000498502.1_Intron|MBNL1_ENST00000282486.6_Silent_p.T355T|MBNL1_ENST00000492948.1_Intron|MBNL1_ENST00000324196.5_Missense_Mutation_p.H286R|MBNL1_ENST00000493459.1_Silent_p.T310T|MBNL1_ENST00000485509.1_Missense_Mutation_p.H286R|RP11-362A9.3_ENST00000463255.1_RNA	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	355					alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			CAGCAACAACATCTGCCACAA	0.463																																					p.H286R		Atlas-SNP	.											.	MBNL1	100	.	0			c.A857G						.						212	219	217					3																	152174105		2203	4300	6503	SO:0001819	synonymous_variant	4154	exon5			AACAACATCTGCC	Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"Zinc fingers, CCCH-type domain containing"	6923	protein-coding gene	gene with protein product		606516	"muscleblind (Drosophila)-like", "muscleblind-like (Drosophila)"	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.1065A>G	chr3.hg19:g.152174105A>G		232.0	0.0		295.0	98.0	NM_207296	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Missense_Mutation	SNP	ENST00000463374.1	hg19	CCDS3165.1	.	.	.	.	.	.	.	.	.	.	A	10.05	1.243492	0.22796	.	.	ENSG00000152601	ENST00000324196;ENST00000485509	T;T	0.42513	0.97;0.97	5.51	4.33	0.51752	.	.	.	.	.	T	0.57154	0.2034	.	.	.	0.80722	D	1	P	0.50156	0.932	P	0.58520	0.84	T	0.56329	-0.7997	8	0.44086	T	0.13	.	11.7765	0.51989	0.8682:0.0:0.0:0.1318	.	286	E9PBW7	.	R	286	ENSP00000319374:H286R;ENSP00000418876:H286R	ENSP00000319374:H286R	H	+	2	0	MBNL1	153656795	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.834000	0.62774	0.881000	0.35993	0.460000	0.39030	CAT	.	.		0.463	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038		G	152174105	A	G	152174105	2	3	215	1	0	0	0	0	0	0	0	1	9362	217	8	2		2	MBNL1	3	152174105	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	32964599	152174105	45848325	37	30944										
SGEF	26084	hgsc.bcm.edu	37	chr3	153909105	153909105	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aatccatcctttaaggaagtAttgtcaaggattgagtccca	8	8	1	1	rs370646022		TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:153909105A>G	ENST00000356448.4	+	8	1952	c.1668A>G	c.(1666-1668)gtA>gtG	p.V556V	ARHGEF26_ENST00000465093.1_Silent_p.V556V|ARHGEF26_ENST00000465817.1_Intron	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	556	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V556V(3)		endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						TTAAGGAAGTATTGTCAAGGA	0.418																																					p.V556V	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											SGEF,NS,carcinoma,0,2	ARHGEF26	158	.	3	Substitution - coding silent(3)	lung(3)	c.A1668G						.	A		0,3752		0,0,1876	106	96	99		1668	-7.2	0.3	3		99	1,8223		0,1,4111	no	coding-synonymous	ARHGEF26	NM_015595.3		0,1,5987	GG,GA,AA		0.0122,0.0,0.0084		556/872	153909105	1,11975	1876	4112	5988	SO:0001819	synonymous_variant	26084	exon8			GGAAGTATTGTCA	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.1668A>G	chr3.hg19:g.153909105A>G		52.0	0.0		48.0	14.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Silent	SNP	ENST00000356448.4	hg19	CCDS46938.1																																																																																			.	.		0.418	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		G	153909105	A	G	153909105	2	3	215	1	0	0	0	0	0	0	0	1	14220	436	16	2		2	SGEF	3	153909105	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	1735000	153909105	44113325	38	30945										
RARRES1	5918	hgsc.bcm.edu	37	chr3	158415600	158415600	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggtaccagaccaagtgaatgCgacagggaattatttcctag	11	8	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:158415600C>T	ENST00000237696.5	-	6	1032	c.752G>A	c.(751-753)cGc>cAc	p.R251H	RP11-379F4.6_ENST00000606185.1_lincRNA	NM_206963.1	NP_996846.1	P49788	TIG1_HUMAN	retinoic acid receptor responder (tazarotene induced) 1	251					negative regulation of cell proliferation (GO:0008285)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R251H(1)		NS(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)	CAAGTGAATGCGACAGGGAAT	0.373																																					p.R251H		Atlas-SNP	.											RARRES1,colon,carcinoma,0,1	RARRES1	22	.	1	Substitution - Missense(1)	large_intestine(1)	c.G752A						.						87	88	88					3																	158415600		2203	4300	6503	SO:0001583	missense	5918	exon6			TGAATGCGACAGG	U27185	CCDS3184.1, CCDS54665.1	3q25.32	2013-07-29			ENSG00000118849	ENSG00000118849			9867	protein-coding gene	gene with protein product	"latexin-like"	605090				8601727, 9270552	Standard	NM_002888		Approved	TIG1, LXNL	uc003fci.3	P49788	OTTHUMG00000158834	ENST00000237696.5:c.752G>A	chr3.hg19:g.158415600C>T	ENSP00000237696:p.Arg251His	244.0	0.0		252.0	63.0	NM_206963	Q8N1D7	Missense_Mutation	SNP	ENST00000237696.5	hg19	CCDS3184.1	.	.	.	.	.	.	.	.	.	.	C	6.639	0.486441	0.12641	.	.	ENSG00000118849	ENST00000237696	T	0.24723	1.84	5.73	-2.85	0.05734	.	0.653776	0.17141	N	0.185445	T	0.17577	0.0422	L	0.50333	1.59	0.09310	N	0.999999	B	0.20550	0.046	B	0.17979	0.02	T	0.27502	-1.0072	10	0.20519	T	0.43	-31.8035	7.8898	0.29672	0.1033:0.405:0.0:0.4917	.	251	P49788	TIG1_HUMAN	H	251	ENSP00000237696:R251H	ENSP00000237696:R251H	R	-	2	0	RARRES1	159898294	0.000000	0.05858	0.000000	0.03702	0.718000	0.41266	-1.052000	0.03503	-0.709000	0.05008	-0.813000	0.03139	CGC	.	.		0.373	RARRES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352358.1			T	158415600	C	T	158415600	3	4	215	1	0	0	0	0	1	0	0	0	13070	768	27	1	136	1	RARRES1	3	158415600	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	4506495	158415600	39606830	39	30946										
CLCN2	1181	hgsc.bcm.edu	37	chr3	184071906	184071907	+	Frame_Shift_Ins	INS	-	-	A													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	actggtggcggccccagccgINSagctcaggcaggtagggcag					rs372735937		TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr3:184071906_184071907insA	ENST00000265593.4	-	15	1874_1875	c.1703_1704insT	c.(1702-1704)ctcfs	p.L568fs	CLCN2_ENST00000434054.2_Frame_Shift_Ins_p.L524fs|CLCN2_ENST00000475279.1_5'Flank|CLCN2_ENST00000423355.2_3'UTR|CLCN2_ENST00000457512.1_Frame_Shift_Ins_p.L568fs|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000344937.7_Frame_Shift_Ins_p.L551fs	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	568					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	GGCCCCAGCCGAGCTCAGGCAG	0.624											OREG0015949	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L568fs		Atlas-INDEL	.											.	CLCN2	74	.	0			c.1704_1705insT						.																																			SO:0001589	frameshift_variant	1181	exon15			.	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"Ion channels / Chloride channels : Voltage-sensitive"	2020	protein-coding gene	gene with protein product		600570	"chloride channel 2"			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.1704dupT	chr3.hg19:g.184071907_184071907dupA	ENSP00000265593:p.Leu568fs	62.0	0.0	1989	101.0	28.0	NM_004366	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Frame_Shift_Ins	INS	ENST00000265593.4	hg19	CCDS3263.1																																																																																			.	.		0.624	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			A	184071907	-	A	184071906	7	5	215	1	0	1	1	0	0	0	0	0	3465	1045	37	0	1032	0	CLCN2	3	184071906	Frame_Shift_Ins	INS	-	TCGA-DD-AAEA-01A-11D-A40R-10	25656306	184071906	13950524	40	30947										
PROM1	8842	hgsc.bcm.edu	37	chr4	16077376	16077376	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tagttcaaagagaatgccaaTgggtccagctttatgggagt	12	6	1	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr4:16077376T>C	ENST00000510224.1	-	2	402	c.154A>G	c.(154-156)Att>Gtt	p.I52V	PROM1_ENST00000505450.1_Missense_Mutation_p.I52V|PROM1_ENST00000543373.1_Missense_Mutation_p.I52V|PROM1_ENST00000540805.1_Missense_Mutation_p.I52V|PROM1_ENST00000508167.1_Missense_Mutation_p.I52V|PROM1_ENST00000447510.2_Missense_Mutation_p.I52V|PROM1_ENST00000539194.1_Missense_Mutation_p.I52V			O43490	PROM1_HUMAN	prominin 1	52					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						AGAATGCCAATGGGTCCAGCT	0.453																																					p.I52V		Atlas-SNP	.											.	PROM1	91	.	0			c.A154G						.						76	75	75					4																	16077376		1918	4141	6059	SO:0001583	missense	8842	exon2			TGCCAATGGGTCC	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.154A>G	chr4.hg19:g.16077376T>C	ENSP00000426809:p.Ile52Val	117.0	0.0		151.0	57.0	NM_001145847	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	hg19	CCDS47029.1	.	.	.	.	.	.	.	.	.	.	T	10.64	1.406307	0.25378	.	.	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373;ENST00000508322	T;T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.1	5.62	0.401	0.16338	.	0.363933	0.26571	N	0.023621	T	0.30885	0.0779	L	0.45051	1.395	0.09310	N	1	B;B;B;B;B;P	0.35107	0.429;0.429;0.429;0.429;0.319;0.484	B;B;B;B;B;B	0.38225	0.175;0.175;0.175;0.175;0.069;0.268	T	0.24083	-1.0170	10	0.15952	T	0.53	-6.5814	8.4625	0.32936	0.0:0.3014:0.0:0.6986	.	52;52;52;52;52;52	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490	.;.;.;.;.;PROM1_HUMAN	V	52	ENSP00000415481:I52V;ENSP00000438045:I52V;ENSP00000443620:I52V;ENSP00000426090:I52V;ENSP00000427346:I52V;ENSP00000426809:I52V;ENSP00000445526:I52V;ENSP00000425927:I52V	ENSP00000415481:I52V	I	-	1	0	PROM1	15686474	0.210000	0.23517	0.000000	0.03702	0.376000	0.30014	0.672000	0.25187	-0.125000	0.11703	0.528000	0.53228	ATT	.	.		0.453	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		C	16077376	T	C	16077376	3	2	215	1	0	0	0	0	1	0	0	0	12567	1464	51	2	2547	2	PROM1	4	16077376	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10		16077376	175076900	41	30948										
PRDM5	11107	hgsc.bcm.edu	37	chr4	121720828	121720828	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tagtttacctgagtgggtgaTcatatgacgttttagctgat	11	5	1	4			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr4:121720828T>A	ENST00000264808.3	-	9	1258	c.1018A>T	c.(1018-1020)Atc>Ttc	p.I340F	PRDM5_ENST00000428209.2_Missense_Mutation_p.I309F|PRDM5_ENST00000515109.1_Missense_Mutation_p.I309F	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	340					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GAGTGGGTGATCATATGACGT	0.274																																					p.I340F		Atlas-SNP	.											.	PRDM5	76	.	0			c.A1018T						.						61	62	62					4																	121720828		2201	4297	6498	SO:0001583	missense	11107	exon9			GGGTGATCATATG	AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"Zinc fingers, C2H2-type"	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.1018A>T	chr4.hg19:g.121720828T>A	ENSP00000264808:p.Ile340Phe	252.0	0.0		162.0	79.0	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Missense_Mutation	SNP	ENST00000264808.3	hg19	CCDS3716.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.161376	0.78226	.	.	ENSG00000138738	ENST00000264808;ENST00000515109;ENST00000428209	T;T;T	0.18502	2.21;2.21;2.21	5.77	5.77	0.91146	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.26340	0.0643	N	0.11927	0.2	0.80722	D	1	D;D;D	0.76494	0.999;0.995;0.999	D;P;D	0.83275	0.996;0.885;0.996	T	0.20207	-1.0282	10	0.72032	D	0.01	-20.759	16.3948	0.83586	0.0:0.0:0.0:1.0	.	309;309;340	Q0VAI9;Q9NQX1-2;Q9NQX1	.;.;PRDM5_HUMAN	F	340;309;309	ENSP00000264808:I340F;ENSP00000422309:I309F;ENSP00000404832:I309F	ENSP00000264808:I340F	I	-	1	0	PRDM5	121940278	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.793000	0.85851	2.326000	0.78906	0.533000	0.62120	ATC	.	.		0.274	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2			A	121720828	T	A	121720828	3	1	215	1	0	0	0	0	1	0	0	0	12472	1435	50	4	906	4	PRDM5	4	121720828	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	105643452	121720828	69433448	42	30949										
TMEM184C	55751	hgsc.bcm.edu	37	chr4	148555393	148555393	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	caaaatgaacatacaagtttAttatcatcatcatcacaaga	3	8	4	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr4:148555393A>G	ENST00000296582.3	+	10	1699	c.1125A>G	c.(1123-1125)ttA>ttG	p.L375L	TMEM184C_ENST00000508208.1_Intron	NM_018241.2	NP_060711.2	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	375						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(2)|prostate(1)	16						ATACAAGTTTATTATCATCAT	0.413																																					p.L375L		Atlas-SNP	.											.	TMEM184C	25	.	0			c.A1125G						.						84	76	79					4																	148555393		2203	4300	6503	SO:0001819	synonymous_variant	55751	exon10			AAGTTTATTATCA	AF305823	CCDS3770.1	4q31.22	2008-06-05	2008-06-05	2008-06-05		ENSG00000164168			25587	protein-coding gene	gene with protein product		613937	"transmembrane protein 34"	TMEM34			Standard	NM_018241		Approved	FLJ10846	uc003ila.4	Q9NVA4		ENST00000296582.3:c.1125A>G	chr4.hg19:g.148555393A>G		121.0	0.0		199.0	67.0	NM_018241	D3DP04|Q86X84|Q969I7|Q9NXM2	Silent	SNP	ENST00000296582.3	hg19	CCDS3770.1																																																																																			.	.		0.413	TMEM184C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364644.1	NM_018241		G	148555393	A	G	148555393	2	3	215	1	0	0	0	0	0	0	0	1	16121	446	16	2		2	TMEM184C	4	148555393	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	26834565	148555393	42598883	43	30950										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155155901	155155901	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tgtttcggaggcacctgcccCaggtttactgccggcattct	11	13	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr4:155155901C>A	ENST00000357232.4	-	25	8537	c.8538G>T	c.(8536-8538)ctG>ctT	p.L2846L		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2846					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GCACCTGCCCCAGGTTTACTG	0.502																																					p.L2846L		Atlas-SNP	.											.	DCHS2	594	.	0			c.G8538T						.						118	119	119					4																	155155901		2203	4300	6503	SO:0001819	synonymous_variant	54798	exon25			CTGCCCCAGGTTT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.8538G>T	chr4.hg19:g.155155901C>A		104.0	0.0		114.0	25.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	hg19	CCDS3785.1																																																																																			.	.		0.502	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155155901	C	A	155155901	2	1	215	1	0	0	0	0	0	0	0	1	4290	581	21	3		3	DCHS2	4	155155901	Silent	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	6600508	155155901	35998375	44	30951										
TLR3	7098	hgsc.bcm.edu	37	chr4	187004611	187004611	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	atttatttgaactaaagatcAtcgatttaggattgaataat	6	3	1	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr4:187004611A>G	ENST00000296795.3	+	4	1875	c.1771A>G	c.(1771-1773)Atc>Gtc	p.I591V	TLR3_ENST00000504367.1_Missense_Mutation_p.I314V	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	591					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		ACTAAAGATCATCGATTTAGG	0.388																																					p.I591V		Atlas-SNP	.											.	TLR3	83	.	0			c.A1771G						.						76	77	77					4																	187004611		2203	4300	6503	SO:0001583	missense	7098	exon4			AAGATCATCGATT	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"CD molecules"	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.1771A>G	chr4.hg19:g.187004611A>G	ENSP00000296795:p.Ile591Val	147.0	0.0		190.0	54.0	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	hg19	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	A	4.851	0.158145	0.09236	.	.	ENSG00000164342	ENST00000296795;ENST00000542020;ENST00000504367	T;T	0.59906	0.23;0.23	5.88	1.79	0.24919	.	0.259965	0.39544	N	0.001326	T	0.41627	0.1167	N	0.10707	0.03	0.09310	N	0.999994	B	0.30482	0.281	B	0.43783	0.431	T	0.39396	-0.9616	10	0.51188	T	0.08	.	6.1583	0.20350	0.3947:0.3435:0.0:0.2617	.	591	O15455	TLR3_HUMAN	V	591;591;314	ENSP00000296795:I591V;ENSP00000423684:I314V	ENSP00000296795:I591V	I	+	1	0	TLR3	187241605	0.058000	0.20735	0.210000	0.23637	0.023000	0.10783	0.577000	0.23758	0.450000	0.26774	0.455000	0.32223	ATC	.	.		0.388	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			G	187004611	A	G	187004611	3	3	215	1	0	0	0	0	1	0	0	0	15967	217	8	2	1781	2	TLR3	4	187004611	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	31848710	187004611	4149665	45	30952										
FAT1	2195	hgsc.bcm.edu	37	chr4	187534378	187534378	+	Frame_Shift_Del	DEL	T	T	-													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggggcgttatcgttcacatcTtctagcgtgagcacaatact					rs375792265	byFrequency	TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr4:187534378delT	ENST00000441802.2	-	13	9557	c.9348delA	c.(9346-9348)gaafs	p.E3116fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3116	Cadherin 28. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CGTTCACATCTTCTAGCGTGA	0.532										HNSCC(5;0.00058)																											p.D3117fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.9349delG						.						97	103	101					4																	187534378		2043	4194	6237	SO:0001589	frameshift_variant	2195	exon13			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.9348delA	chr4.hg19:g.187534378delT	ENSP00000406229:p.Glu3116fs	70.0	0.0		69.0	28.0	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.532	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187534378	T	-	187534378	7	5	215	1	0	1	0	1	0	0	0	0	5697	1606	56	0	4478	0	FAT1	4	187534378	Frame_Shift_Del	DEL	T	TCGA-DD-AAEA-01A-11D-A40R-10	529767	187534378	3619898	46	30953										
TTC33	23548	hgsc.bcm.edu	37	chr5	40716422	40716422	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	caatctcatcactttcaaagTcatagtctggaattgacttt	5	9	5	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:40716422T>A	ENST00000337702.4	-	5	766	c.614A>T	c.(613-615)gAc>gTc	p.D205V	TTC33_ENST00000503936.2_5'UTR	NM_012382.2	NP_036514.1	Q6PID6	TTC33_HUMAN	tetratricopeptide repeat domain 33	205										NS(1)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)|urinary_tract(1)	11						ACTTTCAAAGTCATAGTCTGG	0.413																																					p.D205V		Atlas-SNP	.											.	TTC33	29	.	0			c.A614T						.						120	107	112					5																	40716422		2203	4300	6503	SO:0001583	missense	23548	exon5			TCAAAGTCATAGT	BC015701	CCDS3931.1	5p13.1	2013-01-11			ENSG00000113638	ENSG00000113638		"Tetratricopeptide (TTC) repeat domain containing"	29959	protein-coding gene	gene with protein product	"osmosis responsive factor"					12477932	Standard	NM_012382		Approved	OSRF	uc003jma.3	Q6PID6	OTTHUMG00000131142	ENST00000337702.4:c.614A>T	chr5.hg19:g.40716422T>A	ENSP00000338533:p.Asp205Val	85.0	0.0		153.0	25.0	NM_012382	B2R6G0|O95105	Missense_Mutation	SNP	ENST00000337702.4	hg19	CCDS3931.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.131045	0.77549	.	.	ENSG00000113638	ENST00000337702	T	0.46451	0.87	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.62183	0.2407	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64067	-0.6494	10	0.54805	T	0.06	-24.377	15.4334	0.75121	0.0:0.0:0.0:1.0	.	205	Q6PID6	TTC33_HUMAN	V	205	ENSP00000338533:D205V	ENSP00000338533:D205V	D	-	2	0	TTC33	40752179	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.470000	0.73558	2.051000	0.60960	0.528000	0.53228	GAC	.	.		0.413	TTC33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253831.1	NM_012382		A	40716422	T	A	40716422	3	1	215	1	0	0	0	0	1	0	0	0	16717	1667	58	4	178	4	TTC33	5	40716422	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10		40716422	140198838	47	30954										
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41018447	41018447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctaggggattacttacctcaAtatcatttgtcagcactttc	6	10	3	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:41018447A>G	ENST00000399564.4	-	27	3209	c.2759T>C	c.(2758-2760)aTt>aCt	p.I920T	MROH2B_ENST00000506092.2_Missense_Mutation_p.I475T	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	920																	ACTTACCTCAATATCATTTGT	0.423																																					p.I920T		Atlas-SNP	.											.	.	.	.	0			c.T2759C						.						92	84	86					5																	41018447		1874	4106	5980	SO:0001583	missense	133558	exon27			ACCTCAATATCAT		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.2759T>C	chr5.hg19:g.41018447A>G	ENSP00000382476:p.Ile920Thr	37.0	0.0		96.0	15.0	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	hg19	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	A	10.58	1.389784	0.25118	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.07021	3.23;3.23	5.64	-1.21	0.09524	Armadillo-type fold (1);	1.142800	0.06568	N	0.747965	T	0.05777	0.0151	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.45498	-0.9257	10	0.19590	T	0.45	.	5.1104	0.14806	0.5992:0.0:0.2726:0.1282	.	920	Q7Z745	HTRB2_HUMAN	T	475;625;920	ENSP00000441504:I475T;ENSP00000382476:I920T	ENSP00000296803:I625T	I	-	2	0	HEATR7B2	41054204	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	0.186000	0.16978	-0.045000	0.13468	-0.274000	0.10170	ATT	.	.		0.423	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		G	41018447	A	G	41018447	3	3	215	1	0	0	0	0	1	0	0	0	7044	101	4	2	2062	2	HEATR7B2	5	41018447	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	302025	41018447	139896813	48	30955										
PPWD1	23398	hgsc.bcm.edu	37	chr5	64868010	64868010	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tccaaccagcgtatgtttttCaccagatgggaagaaaatag	9	8	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:64868010C>G	ENST00000261308.5	+	5	938	c.866C>G	c.(865-867)tCa>tGa	p.S289*	PPWD1_ENST00000535264.1_Nonsense_Mutation_p.S259*|PPWD1_ENST00000538977.1_Nonsense_Mutation_p.S133*	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	289					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		GTATGTTTTTCACCAGATGGG	0.333																																					p.S289X		Atlas-SNP	.											.	PPWD1	47	.	0			c.C866G						.						61	67	65					5																	64868010		2203	4299	6502	SO:0001587	stop_gained	23398	exon5			GTTTTTCACCAGA	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"WD repeat domain containing"	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.866C>G	chr5.hg19:g.64868010C>G	ENSP00000261308:p.Ser289*	108.0	0.0		160.0	14.0	NM_015342	B4DWR9|Q15002|Q7KZ89	Nonsense_Mutation	SNP	ENST00000261308.5	hg19	CCDS3985.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.453113	0.84209	.	.	ENSG00000113593	ENST00000261308;ENST00000535264;ENST00000538977;ENST00000505380	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.5825	0.95473	0.0:1.0:0.0:0.0	.	.	.	.	X	289;259;133;208	.	ENSP00000261308:S289X	S	+	2	0	PPWD1	64903766	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.669000	0.83911	2.630000	0.89119	0.561000	0.74099	TCA	.	.		0.333	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342		G	64868010	C	G	64868010	4	3	215	1	0	0	0	0	0	1	0	0	12426	838	29	4	884	4	PPWD1	5	64868010	Nonsense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	23849563	64868010	116047250	49	30956										
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79747408	79747408	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cacctacttttcagaaacttGatgatctctcattaccaagt	4	11	3	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:79747408G>T	ENST00000338008.5	+	10	3667	c.3487G>T	c.(3487-3489)Gat>Tat	p.D1163Y	ZFYVE16_ENST00000510158.1_Missense_Mutation_p.D1163Y|ZFYVE16_ENST00000505560.1_Missense_Mutation_p.D1163Y	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1163					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		TCAGAAACTTGATGATCTCTC	0.368																																					p.D1163Y	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.G3487T						.						119	120	119					5																	79747408		2203	4300	6503	SO:0001583	missense	9765	exon11			AAACTTGATGATC	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"Zinc fingers, FYVE domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20756	protein-coding gene	gene with protein product	"endofin", "protein phosphatase 1, regulatory subunit 69"	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.3487G>T	chr5.hg19:g.79747408G>T	ENSP00000337159:p.Asp1163Tyr	109.0	0.0		150.0	32.0	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Missense_Mutation	SNP	ENST00000338008.5	hg19	CCDS4050.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692785	0.68271	.	.	ENSG00000039319	ENST00000338008;ENST00000510158;ENST00000505560	T;T;T	0.41758	0.99;0.99;0.99	5.7	5.7	0.88788	.	0.000000	0.56097	D	0.000023	T	0.58192	0.2105	L	0.54323	1.7	0.38527	D	0.948876	D	0.89917	1.0	D	0.77004	0.989	T	0.62760	-0.6786	10	0.87932	D	0	-23.7142	12.0057	0.53257	0.0801:0.0:0.9199:0.0	.	1163	Q7Z3T8	ZFY16_HUMAN	Y	1163	ENSP00000337159:D1163Y;ENSP00000423663:D1163Y;ENSP00000426848:D1163Y	ENSP00000337159:D1163Y	D	+	1	0	ZFYVE16	79783164	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.837000	0.55820	2.684000	0.91462	0.650000	0.86243	GAT	.	.		0.368	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		T	79747408	G	T	79747408	3	4	215	1	0	0	0	0	1	0	0	0	17679	1290	45	3	3521	3	ZFYVE16	5	79747408	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	14879398	79747408	101167852	50	30957										
ANKRD34B	340120	hgsc.bcm.edu	37	chr5	79854721	79854721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	taaggccagctgagagctggGaatcagagctgtagtgattt	14	6	1	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:79854721G>A	ENST00000338682.3	-	5	1790	c.1118C>T	c.(1117-1119)tCc>tTc	p.S373F		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	373						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	28		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		TGAGAGCTGGGAATCAGAGCT	0.448																																					p.S373F		Atlas-SNP	.											.	ANKRD34B	61	.	0			c.C1118T						.						51	56	54					5																	79854721		2200	4299	6499	SO:0001583	missense	340120	exon5			AGCTGGGAATCAG		CCDS34194.1	5q14.1	2014-08-12			ENSG00000189127	ENSG00000189127		"Ankyrin repeat domain containing"	33736	protein-coding gene	gene with protein product							Standard	NM_001004441		Approved	DP58	uc003kgw.3	A5PLL1	OTTHUMG00000162541	ENST00000338682.3:c.1118C>T	chr5.hg19:g.79854721G>A	ENSP00000339802:p.Ser373Phe	35.0	0.0		73.0	23.0	NM_001004441	B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	hg19	CCDS34194.1	.	.	.	.	.	.	.	.	.	.	G	19.49	3.837810	0.71373	.	.	ENSG00000189127	ENST00000338682	T	0.19669	2.13	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000002	T	0.46541	0.1398	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.03750	-1.1007	10	0.25106	T	0.35	-15.6207	19.4575	0.94900	0.0:0.0:1.0:0.0	.	373	A5PLL1	AN34B_HUMAN	F	373	ENSP00000339802:S373F	ENSP00000339802:S373F	S	-	2	0	ANKRD34B	79890477	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.754000	0.98908	2.941000	0.99782	0.655000	0.94253	TCC	.	.		0.448	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441		A	79854721	G	A	79854721	3	1	215	1	0	0	0	0	1	0	0	0	663	1174	41	3	430	3	ANKRD34B	5	79854721	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	107313	79854721	101060539	51	30958										
CHD1	1105	hgsc.bcm.edu	37	chr5	98234033	98234033	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	caatgcatgcttgaaactttTtggaaatgagagctccatct	8	8	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:98234033T>G	ENST00000284049.3	-	9	1441	c.1292A>C	c.(1291-1293)aAa>aCa	p.K431T		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	431	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.				chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TTGAAACTTTTTGGAAATGAG	0.383																																					p.K431T		Atlas-SNP	.											.	CHD1	137	.	0			c.A1292C						.						84	86	86					5																	98234033		2203	4300	6503	SO:0001583	missense	1105	exon9			AACTTTTTGGAAA	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.1292A>C	chr5.hg19:g.98234033T>G	ENSP00000284049:p.Lys431Thr	75.0	0.0		98.0	24.0	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	19.63	3.863992	0.71949	.	.	ENSG00000153922	ENST00000284049	T	0.74209	-0.82	5.61	5.61	0.85477	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (2);	0.000000	0.35646	U	0.003062	T	0.81226	0.4778	M	0.77820	2.39	0.58432	D	0.999998	P	0.34662	0.462	B	0.43916	0.436	T	0.82880	-0.0238	10	0.72032	D	0.01	.	15.7959	0.78409	0.0:0.0:0.0:1.0	.	431	O14646	CHD1_HUMAN	T	431	ENSP00000284049:K431T	ENSP00000284049:K431T	K	-	2	0	CHD1	98261933	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.171000	0.50824	2.136000	0.66102	0.482000	0.46254	AAA	.	.		0.383	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		G	98234033	T	G	98234033	3	3	215	1	0	0	0	0	1	0	0	0	3325	1841	64	5	3948	5	CHD1	5	98234033	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	18379312	98234033	82681227	52	30959										
SLCO4C1	353189	hgsc.bcm.edu	37	chr5	101627231	101627231	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tcgtagcttgatgaaatcagGccagtcagggaactcttcat	10	9	4	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:101627231G>T	ENST00000310954.6	-	2	721	c.435C>A	c.(433-435)ggC>ggA	p.G145G		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		ATGAAATCAGGCCAGTCAGGG	0.363																																					p.G145G		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.C435A						.						64	62	63					5																	101627231		2203	4300	6503	SO:0001819	synonymous_variant	353189	exon2			AATCAGGCCAGTC	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"Solute carriers"	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.435C>A	chr5.hg19:g.101627231G>T		239.0	0.0		331.0	90.0	NM_180991		Silent	SNP	ENST00000310954.6	hg19	CCDS34205.1																																																																																			.	.		0.363	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991		T	101627231	G	T	101627231	2	4	215	1	0	0	0	0	0	0	0	1	14745	1190	42	3		3	SLCO4C1	5	101627231	Silent	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	3393198	101627231	79288029	53	30960										
SNX2	6643	hgsc.bcm.edu	37	chr5	122137803	122137803	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	catgaatgcctatatggcatAtagagtaacaacaaaggtga	9	6	0	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:122137803A>G	ENST00000379516.2	+	5	593	c.485A>G	c.(484-486)tAt>tGt	p.Y162C	SNX2_ENST00000510372.1_3'UTR|SNX2_ENST00000514949.1_Missense_Mutation_p.Y45C	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	162	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		TATATGGCATATAGAGTAACA	0.318																																					p.Y162C		Atlas-SNP	.											.	SNX2	42	.	0			c.A485G						.						126	138	134					5																	122137803		2203	4300	6503	SO:0001583	missense	6643	exon5			TGGCATATAGAGT	AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"Sorting nexins"	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.485A>G	chr5.hg19:g.122137803A>G	ENSP00000368831:p.Tyr162Cys	167.0	0.0		222.0	56.0	NM_003100	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Missense_Mutation	SNP	ENST00000379516.2	hg19	CCDS34217.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.144254	0.77888	.	.	ENSG00000205302	ENST00000379516;ENST00000505934;ENST00000514949	T;T;T	0.66099	-0.19;-0.19;-0.19	5.51	5.51	0.81932	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	D	0.87834	0.6277	H	0.99211	4.47	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92617	0.6104	10	0.87932	D	0	-17.1257	14.4899	0.67645	1.0:0.0:0.0:0.0	.	162	O60749	SNX2_HUMAN	C	162;161;45	ENSP00000368831:Y162C;ENSP00000422413:Y161C;ENSP00000421663:Y45C	ENSP00000368831:Y162C	Y	+	2	0	SNX2	122165702	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	8.895000	0.92512	2.230000	0.72887	0.528000	0.53228	TAT	.	.		0.318	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100		G	122137803	A	G	122137803	3	3	215	1	0	0	0	0	1	0	0	0	14906	449	16	2	503	2	SNX2	5	122137803	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	20510572	122137803	58777457	54	30961										
FBN2	2201	hgsc.bcm.edu	37	chr5	127685084	127685084	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	caacgtaaggccttcagggcActcgcaatgaaaagatccct	9	12	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:127685084A>G	ENST00000508053.1	-	29	3918	c.2944T>C	c.(2944-2946)Tgc>Cgc	p.C982R	FBN2_ENST00000508989.1_Missense_Mutation_p.C949R|FBN2_ENST00000262464.4_Missense_Mutation_p.C982R			P35556	FBN2_HUMAN	fibrillin 2	982	EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CCTTCAGGGCACTCGCAATGA	0.463																																					p.C982R		Atlas-SNP	.											.	FBN2	858	.	0			c.T2944C						.						118	97	104					5																	127685084		2203	4300	6503	SO:0001583	missense	2201	exon23			CAGGGCACTCGCA	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.2944T>C	chr5.hg19:g.127685084A>G	ENSP00000424571:p.Cys982Arg	159.0	0.0		188.0	32.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.116430	0.77323	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.99445	-5.91;-5.91;-5.91	4.04	4.04	0.47022	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000005	D	0.99782	0.9909	H	0.99650	4.68	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.991;0.999	D	0.96586	0.9434	10	0.87932	D	0	.	14.0381	0.64658	1.0:0.0:0.0:0.0	.	949;982	D6RJI3;P35556	.;FBN2_HUMAN	R	982;982;949	ENSP00000262464:C982R;ENSP00000424571:C982R;ENSP00000425596:C949R	ENSP00000262464:C982R	C	-	1	0	FBN2	127712983	1.000000	0.71417	0.991000	0.47740	0.993000	0.82548	9.013000	0.93629	2.070000	0.61991	0.533000	0.62120	TGC	.	.		0.463	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		G	127685084	A	G	127685084	3	3	215	1	0	0	0	0	1	0	0	0	5711	159	6	2	5966	2	FBN2	5	127685084	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	5547281	127685084	53230176	55	30962										
AFF4	27125	hgsc.bcm.edu	37	chr5	132219082	132219082	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggtcccaaatttcggtggcaTagaggaagttggatgtgacc	14	7	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:132219082T>C	ENST00000265343.5	-	20	3693	c.3314A>G	c.(3313-3315)tAt>tGt	p.Y1105C		NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	1105					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTCGGTGGCATAGAGGAAGTT	0.473																																					p.Y1105C	Ovarian(126;889 1733 2942 10745 11605)	Atlas-SNP	.											.	AFF4	120	.	0			c.A3314G						.						129	121	124					5																	132219082		2203	4300	6503	SO:0001583	missense	27125	exon20			GTGGCATAGAGGA	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.3314A>G	chr5.hg19:g.132219082T>C	ENSP00000265343:p.Tyr1105Cys	92.0	0.0		131.0	26.0	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	hg19	CCDS4164.1	.	.	.	.	.	.	.	.	.	.	T	17.15	3.317210	0.60524	.	.	ENSG00000072364	ENST00000265343	T	0.64438	-0.1	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.77671	0.4165	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.76971	-0.2761	10	0.41790	T	0.15	-11.458	16.4075	0.83691	0.0:0.0:0.0:1.0	.	1105	Q9UHB7	AFF4_HUMAN	C	1105	ENSP00000265343:Y1105C	ENSP00000265343:Y1105C	Y	-	2	0	AFF4	132246981	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.143000	0.71756	2.275000	0.75901	0.528000	0.53228	TAT	.	.		0.473	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		C	132219082	T	C	132219082	3	2	215	1	0	0	0	0	1	0	0	0	359	1406	49	2	185	2	AFF4	5	132219082	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	4533998	132219082	48696178	56	30963										
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140736599	140736599	+	Frame_Shift_Del	DEL	C	C	-													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gtcctacagcctactcaagtCcagcgagccgggactatttg							TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:140736599delC	ENST00000571252.1	+	1	1832	c.1832delC	c.(1831-1833)tccfs	p.S612fs	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	612	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTACTCAAGTCCAGCGAGCCG	0.627																																					p.S611fs		Atlas-INDEL	.											.	PCDHGA4	150	.	0			c.1831delT						.						45	53	50					5																	140736599		2194	4300	6494	SO:0001589	frameshift_variant	56111	exon1			.	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1832delC	chr5.hg19:g.140736599delC	ENSP00000458570:p.Ser612fs	143.0	0.0		126.0	14.0	NM_018917	Q9Y5D3	Frame_Shift_Del	DEL	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.		0.627	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		-	140736599	C	-	140736599	7	5	215	1	0	1	0	1	0	0	0	0	11565	855	30	0	1834	0	PCDHGA4	5	140736599	Frame_Shift_Del	DEL	C	TCGA-DD-AAEA-01A-11D-A40R-10	8517517	140736599	40178661	57	30964										
PCDHGA9	56102	hgsc.bcm.edu	37	chr5	140784951	140784951	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ccctttggttccggtgagttCattttttttctttctttctt	6	9	4	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:140784951C>A	ENST00000576222.1	+	1	2546				PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB6_ENST00000520790.1_5'Flank|PCDHGA7_ENST00000518325.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGGTGAGTTCATTTTTTTTC	0.398																																					p.S811X		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.C2432A						.						30	32	32					5																	140784951		2020	4194	6214	SO:0001627	intron_variant	56107	exon1			TGAGTTCATTTTT	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+32575C>A	chr5.hg19:g.140784951C>A		73.0	0.0		82.0	14.0	NM_032089	A7E229|Q9Y5C7	Nonsense_Mutation	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.		0.398	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140784951	C	A	140784951	1	1	215	0	1	0	0	0	0	0	0	0	11570	838	29	3		3	PCDHGA9	5	140784951	Intron	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	48352	140784951	40130309	58	30965										
SLU7	10569	hgsc.bcm.edu	37	chr5	159833579	159833579	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tgagtactccacatagtcttCagtctgggctaaaagcaatt	8	9	3	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:159833579C>G	ENST00000297151.4	-	12	1570	c.1183G>C	c.(1183-1185)Gaa>Caa	p.E395Q		NM_006425.4	NP_006416.3	O95391	SLU7_HUMAN	SLU7 splicing factor homolog (S. cerevisiae)	395					alternative mRNA splicing, via spliceosome (GO:0000380)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	pre-mRNA 3'-splice site binding (GO:0030628)|second spliceosomal transesterification activity (GO:0000386)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(4)|lung(6)|ovary(1)	20	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACATAGTCTTCAGTCTGGGCT	0.448																																					p.E395Q		Atlas-SNP	.											.	SLU7	35	.	0			c.G1183C						.						126	111	116					5																	159833579		2203	4300	6503	SO:0001583	missense	10569	exon12			AGTCTTCAGTCTG	AF101074	CCDS4352.1	5q33.3	2010-04-13			ENSG00000164609	ENSG00000164609			16939	protein-coding gene	gene with protein product	zinc knuckle motif containing	605974				10197984, 15728250	Standard	NM_006425		Approved	9G8	uc003lyg.3	O95391	OTTHUMG00000130324	ENST00000297151.4:c.1183G>C	chr5.hg19:g.159833579C>G	ENSP00000297151:p.Glu395Gln	92.0	0.0		102.0	31.0	NM_006425	D3DQK2|Q3LUJ0|Q3LUJ1|Q6RXQ5|Q96FM9	Missense_Mutation	SNP	ENST00000297151.4	hg19	CCDS4352.1	.	.	.	.	.	.	.	.	.	.	C	35	5.501439	0.96371	.	.	ENSG00000164609	ENST00000297151	T	0.52983	0.64	6.07	6.07	0.98685	Pre-mRNA splicing Prp18-interacting factor (1);	0.000000	0.85682	D	0.000000	T	0.76983	0.4064	M	0.90019	3.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80030	-0.1553	10	0.87932	D	0	-18.8173	20.6593	0.99626	0.0:1.0:0.0:0.0	.	395	O95391	SLU7_HUMAN	Q	395	ENSP00000297151:E395Q	ENSP00000297151:E395Q	E	-	1	0	SLU7	159766157	1.000000	0.71417	0.970000	0.41538	0.995000	0.86356	7.328000	0.79160	2.885000	0.99019	0.655000	0.94253	GAA	.	.		0.448	SLU7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252673.1	NM_006425		G	159833579	C	G	159833579	3	3	215	1	0	0	0	0	1	0	0	0	14770	835	29	4	597	4	SLU7	5	159833579	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	19048628	159833579	21081681	59	30966										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161116701	161116701	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aaggaccactttactcagtaGaagtcccagaagaatcttca	7	10	3	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:161116701G>T	ENST00000274545.5	+	6	1022	c.589G>T	c.(589-591)Gaa>Taa	p.E197*	GABRA6_ENST00000523217.1_Nonsense_Mutation_p.E187*|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	197					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TTACTCAGTAGAAGTCCCAGA	0.333										TCGA Ovarian(5;0.080)																											p.E197X		Atlas-SNP	.											.	GABRA6	139	.	0			c.G589T						.						65	71	69					5																	161116701		2202	4300	6502	SO:0001587	stop_gained	2559	exon6			TCAGTAGAAGTCC		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.589G>T	chr5.hg19:g.161116701G>T	ENSP00000274545:p.Glu197*	231.0	0.0		271.0	36.0	NM_000811	A8K096|Q4VAV2	Nonsense_Mutation	SNP	ENST00000274545.5	hg19	CCDS4356.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.557183|7.557183	0.98358|0.98358	.|.	.|.	ENSG00000145863|ENSG00000145863	ENST00000274545;ENST00000523217;ENST00000517823;ENST00000523691|ENST00000520000	.|.	.|.	.|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.097406|.	0.64402|.	D|.	0.000001|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.48119|.	T|.	0.1|.	.|.	19.1903|19.1903	0.93663|0.93663	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|Y	197;187;144;117|136	.|.	ENSP00000274545:E197X|.	E|X	+|+	1|3	0|2	GABRA6|GABRA6	161049279|161049279	1.000000|1.000000	0.71417|0.71417	0.955000|0.955000	0.39395|0.39395	0.988000|0.988000	0.76386|0.76386	9.671000|9.671000	0.98627|0.98627	2.526000|2.526000	0.85167|0.85167	0.655000|0.655000	0.94253|0.94253	GAA|TAG	.	.		0.333	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			T	161116701	G	T	161116701	4	4	215	1	0	0	0	0	0	1	0	0	6173	943	33	3	611	3	GABRA6	5	161116701	Nonsense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	1283122	161116701	19798559	60	30967										
KCNMB1	3779	hgsc.bcm.edu	37	chr5	169805835	169805835	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gggcctggggcccgtagaggCgctggaataggacgctggtt	19	9	0	1	rs200287944		TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr5:169805835C>A	ENST00000274629.4	-	4	891	c.449G>T	c.(448-450)cGc>cTc	p.R150L	KCNIP1_ENST00000518527.1_Intron|KCNIP1_ENST00000377360.4_Intron	NM_004137.3	NP_004128.1	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 1	150					blood coagulation (GO:0007596)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to calcium ion (GO:0051592)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			endometrium(1)|large_intestine(1)|lung(7)|ovary(2)	11	Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.175)	Miconazole(DB01110)|Procaine(DB00721)	CCCGTAGAGGCGCTGGAATAG	0.607																																					p.P150L		Atlas-SNP	.											.	KCNMB1	38	.	0			c.C449T						.						86	84	85					5																	169805835		2203	4300	6503	SO:0001583	missense	3779	exon4			TAGAGGCGCTGGA	AF035046	CCDS4373.1	5q34	2012-02-23			ENSG00000145936	ENSG00000145936		"Potassium channels"	6285	protein-coding gene	gene with protein product	"BK channel beta subunit"	603951				8799178, 9888999	Standard	NM_004137		Approved	hslo-beta	uc003maq.2	Q16558	OTTHUMG00000130439	ENST00000274629.4:c.449G>T	chr5.hg19:g.169805835C>A	ENSP00000274629:p.Arg150Leu	103.0	0.0		126.0	36.0	NM_004137	O00707|O00708|P78475|Q53YR0|Q8TAX3|Q93005	Missense_Mutation	SNP	ENST00000274629.4	hg19	CCDS4373.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.074008	0.55646	.	.	ENSG00000145936	ENST00000274629	T	0.15834	2.39	5.3	4.43	0.53597	.	0.310182	0.30177	N	0.010223	T	0.33469	0.0864	M	0.63843	1.955	0.52501	D	0.999951	D	0.89917	1.0	D	0.70935	0.971	T	0.01692	-1.1294	9	.	.	.	.	8.5798	0.33621	0.0:0.8236:0.0:0.1764	.	150	Q16558	KCMB1_HUMAN	L	150	ENSP00000274629:R150L	.	R	-	2	0	KCNMB1	169738413	0.996000	0.38824	0.998000	0.56505	0.328000	0.28507	1.749000	0.38319	2.457000	0.83068	0.585000	0.79938	CGC	.	C|1.000;T|0.000		0.607	KCNMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252830.3			A	169805835	C	A	169805835	3	1	215	1	0	0	0	0	1	0	0	0	8083	768	27	1	130	1	KCNMB1	5	169805835	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	8689134	169805835	11109425	61	30968										
NOL7	51406	hgsc.bcm.edu	37	chr6	13621055	13621062	+	Stop_Codon_Del	DEL	AGTAAATC	AGTAAATC	-													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cagaaagatgaaaactaagaAgtaaatcaatgctaaatgaa							TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	AGTAAATC	AGTAAATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:13621055_13621062delAGTAAATC	ENST00000451315.2	+	0	802_809				RANBP9_ENST00000469916.1_5'Flank|AL441883.1_ENST00000600057.1_Frame_Shift_Del_p.LIY20fs|NOL7_ENST00000474485.1_3'UTR	NM_016167.3	NP_057251.2	Q9UMY1	NOL7_HUMAN	nucleolar protein 7, 27kDa							nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(3)|lung(1)	5	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.135)	Epithelial(50;0.176)			AAAACTAAGAAGTAAATCAATGCTAAAT	0.264																																					p.257_258del		Atlas-INDEL	.											.	NOL7	18	.	0			c.769_806del						.																																			SO:0001567	stop_retained_variant	51406	exon8			.	AF172066	CCDS4528.1	6p23	2008-05-23	2004-02-10		ENSG00000225921	ENSG00000225921			21040	protein-coding gene	gene with protein product		611533	"chromosome 6 open reading frame 90", "polyglutamine binding protein 3"	C6orf90, PQBP3		16205646	Standard	NM_016167		Approved	NOP27, RARG-1, dJ223E5.2	uc003naz.3	Q9UMY1	OTTHUMG00000014277	Exception_encountered	chr6.hg19:g.13621055_13621062delAGTAAATC	ENSP00000405674:p.*258Tyrext*1	353.0	0.0		354.0	58.0	NM_016167	Q5T297|Q9Y3U7	Frame_Shift_Del	DEL	ENST00000451315.2	hg19	CCDS4528.1																																																																																			.	.		0.264	NOL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039904.1	NM_016167		-	13621062	AGTAAATC	-	13621055	7	5	215	1	0	1	0	1	0	0	0	0	10535	72	3	0	800	0	NOL7	6	13621055	Stop_Codon_Del	DEL	AGTAAATC	TCGA-DD-AAEA-01A-11D-A40R-10		13621055	157494012	62	30969										
HIST1H4H	8365	hgsc.bcm.edu	37	chr6	26285638	26285638	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cgccggatagctggcttagtGatgccctggatgttatcgcg	14	10	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:26285638G>A	ENST00000377727.1	-	1	99	c.90C>T	c.(88-90)atC>atT	p.I30I	HIST1H4H_ENST00000289352.1_Silent_p.I30I	NM_003543.3	NP_003534.1	P62805	H4_HUMAN	histone cluster 1, H4h	30					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(2)|ovary(2)|upper_aerodigestive_tract(3)	7						CTGGCTTAGTGATGCCCTGGA	0.537										HNSCC(76;0.23)																											p.I30I		Atlas-SNP	.											.	HIST1H4H	16	.	0			c.C90T						.						116	109	112					6																	26285638		2203	4300	6503	SO:0001819	synonymous_variant	8365	exon1			CTTAGTGATGCCC	X60487	CCDS4604.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158406	ENSG00000158406		"Histones / Replication-dependent"	4788	protein-coding gene	gene with protein product		602828	"H4 histone family, member H", "histone 1, H4h"	H4FH		9119399, 12408966	Standard	NM_003543		Approved	H4/h	uc003nhm.2	P62805	OTTHUMG00000014454	ENST00000377727.1:c.90C>T	chr6.hg19:g.26285638G>A		99.0	0.0		105.0	40.0	NM_003543	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377727.1	hg19	CCDS4604.1																																																																																			.	.		0.537	HIST1H4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040119.1	NM_003543		A	26285638	G	A	26285638	2	1	215	1	0	0	0	0	0	0	0	1	7181	1280	45	3		3	HIST1H4H	6	26285638	Silent	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	12664583	26285638	144829429	63	30970										
GSTA5	221357	hgsc.bcm.edu	37	chr6	52697726	52697726	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tagtagaaaagttccaccagGtgaatgtcagcccagctcag	10	10	2	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:52697726G>C	ENST00000370989.2	-	5	506	c.477C>G	c.(475-477)caC>caG	p.H159Q	GSTA5_ENST00000284562.2_Missense_Mutation_p.H159Q|GSTA5_ENST00000475052.1_5'UTR			Q7RTV2	GSTA5_HUMAN	glutathione S-transferase alpha 5	159	GST C-terminal.				glutathione metabolic process (GO:0006749)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Lung NSC(77;0.0912)				Glutathione(DB00143)	GTTCCACCAGGTGAATGTCAG	0.502																																					p.H159Q		Atlas-SNP	.											.	GSTA5	42	.	0			c.C477G						.						147	130	136					6																	52697726		2203	4300	6503	SO:0001583	missense	221357	exon6			CACCAGGTGAATG	BK000212	CCDS4946.1	6p12.2	2012-06-21	2008-11-26		ENSG00000182793	ENSG00000182793	2.5.1.18	"Glutathione S-transferases / Soluble"	19662	protein-coding gene	gene with protein product		607605	"glutathione S-transferase A5"			12042665	Standard	NM_153699		Approved		uc003pba.1	Q7RTV2	OTTHUMG00000014857	ENST00000370989.2:c.477C>G	chr6.hg19:g.52697726G>C	ENSP00000360028:p.His159Gln	87.0	0.0		89.0	28.0	NM_153699	Q5SZC2	Missense_Mutation	SNP	ENST00000370989.2	hg19	CCDS4946.1	.	.	.	.	.	.	.	.	.	.	G	0.713	-0.786423	0.02907	.	.	ENSG00000182793	ENST00000370989;ENST00000284562	T;T	0.02067	4.47;4.47	2.66	-0.805	0.10879	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.652466	0.15473	N	0.260507	T	0.00328	0.0010	N	0.11313	0.125	0.26018	N	0.981903	B	0.11235	0.004	B	0.12837	0.008	T	0.39375	-0.9617	10	0.09338	T	0.73	.	3.021	0.06076	0.1231:0.4625:0.2705:0.1438	.	159	Q7RTV2	GSTA5_HUMAN	Q	159	ENSP00000360028:H159Q;ENSP00000284562:H159Q	ENSP00000284562:H159Q	H	-	3	2	GSTA5	52805685	0.010000	0.17322	0.983000	0.44433	0.509000	0.34042	-1.419000	0.02460	0.030000	0.15379	-0.840000	0.03056	CAC	.	.		0.502	GSTA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040917.1	NM_153699		C	52697726	G	C	52697726	3	2	215	1	0	0	0	0	1	0	0	0	6843	1252	44	4	199	4	GSTA5	6	52697726	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	26412088	52697726	118417341	64	30971										
AIM1	202	hgsc.bcm.edu	37	chr6	106968297	106968297	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	atcacttagccactcctcaaAggccagatcagactgttaca	6	13	3	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:106968297A>G	ENST00000369066.3	+	2	2477	c.1990A>G	c.(1990-1992)Agg>Ggg	p.R664G		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		CACTCCTCAAAGGCCAGATCA	0.488																																					p.R664G		Atlas-SNP	.											.	AIM1	161	.	0			c.A1990G						.						49	49	49					6																	106968297		2203	4300	6503	SO:0001583	missense	202	exon2			CCTCAAAGGCCAG	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1990A>G	chr6.hg19:g.106968297A>G	ENSP00000358062:p.Arg664Gly	132.0	0.0		194.0	51.0	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	A	11.73	1.726188	0.30593	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.72725	-0.68	6.17	0.986	0.19784	.	0.693359	0.13286	N	0.399408	T	0.34832	0.0911	L	0.40543	1.245	0.09310	N	0.999997	B	0.02656	0.0	B	0.04013	0.001	T	0.23583	-1.0184	10	0.32370	T	0.25	.	5.6056	0.17377	0.6459:0.1352:0.2189:0.0	.	664	Q9Y4K1	AIM1_HUMAN	G	1072;664	ENSP00000358062:R664G	ENSP00000285105:R1072G	R	+	1	2	AIM1	107074990	0.002000	0.14202	0.000000	0.03702	0.020000	0.10135	1.214000	0.32419	0.155000	0.19261	0.533000	0.62120	AGG	.	.		0.488	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			G	106968297	A	G	106968297	3	3	215	1	0	0	0	0	1	0	0	0	430	63	3	2	1996	2	AIM1	6	106968297	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	54270571	106968297	64146770	65	30972										
AKD1	221264	hgsc.bcm.edu	37	chr6	109935589	109935589	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cagcaatatatttctttaccTtcttcatcaattgatgagtg	5	8	4	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:109935589T>A	ENST00000424296.2	-	14	1570	c.1494A>T	c.(1492-1494)gaA>gaT	p.E498D	AK9_ENST00000341338.6_De_novo_Start_OutOfFrame|AK9_ENST00000368948.2_Splice_Site_p.E498D	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	498					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TTTCTTTACCTTCTTCATCAA	0.318																																					p.E498D		Atlas-SNP	.											.	AKD1	223	.	0			c.A1494T						.						153	127	135					6																	109935589		692	1591	2283	SO:0001630	splice_region_variant	221264	exon14			TTTACCTTCTTCA	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"chromosome 6 open reading frame 224", "adenylate kinase domain containing 2", "chromosome 6 open reading frame 199", "adenylate kinase domain containing 1"	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.1495+1A>T	chr6.hg19:g.109935589T>A		113.0	0.0		107.0	31.0	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	hg19	CCDS55048.1	.	.	.	.	.	.	.	.	.	.	T	2.497	-0.316091	0.05422	.	.	ENSG00000155085	ENST00000424296;ENST00000368948	T;T	0.64438	-0.1;-0.09	3.24	-0.843	0.10744	.	1.071710	0.07370	N	0.885533	T	0.09379	0.0231	N	0.01576	-0.805	0.22127	N	0.99935	B	0.02656	0.0	B	0.01281	0.0	T	0.13737	-1.0498	9	.	.	.	3.3528	2.8848	0.05658	0.3661:0.0:0.3127:0.3212	.	498	Q5TCS8	AKD1_HUMAN	D	498	ENSP00000410186:E498D;ENSP00000357944:E498D	.	E	-	3	2	AKD1	110042282	0.032000	0.19561	0.001000	0.08648	0.115000	0.19883	-0.124000	0.10595	-0.139000	0.11414	-0.811000	0.03165	GAA	.	.		0.318	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	Missense_Mutation	A	109935589	T	A	109935589	5	1	215	1	0	0	0	0	0	0	1	0	460	1623	56	4	4353	4	AKD1	6	109935589	Splice_Site	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	2967292	109935589	61179478	66	30973										
ZUFSP	221302	hgsc.bcm.edu	37	chr6	116977888	116977888	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cgtcaaaaccaagagctaatGattccatcatatcagctttt	5	10	3	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:116977888G>C	ENST00000368576.3	-	5	1163	c.920C>G	c.(919-921)tCa>tGa	p.S307*	ZUFSP_ENST00000471919.1_5'UTR|ZUFSP_ENST00000368573.1_Intron	NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	307							metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		AAGAGCTAATGATTCCATCAT	0.338																																					p.S307X		Atlas-SNP	.											.	ZUFSP	46	.	0			c.C920G						.						111	102	105					6																	116977888		2203	4299	6502	SO:0001587	stop_gained	221302	exon5			GCTAATGATTCCA	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"Zinc fingers, C2H2-type"	21224	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 113"	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.920C>G	chr6.hg19:g.116977888G>C	ENSP00000357565:p.Ser307*	87.0	0.0		113.0	6.0	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Nonsense_Mutation	SNP	ENST00000368576.3	hg19	CCDS5110.1	.	.	.	.	.	.	.	.	.	.	G	38	6.929586	0.97944	.	.	ENSG00000153975	ENST00000368576	.	.	.	5.78	5.78	0.91487	.	0.120439	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-12.3699	16.4878	0.84189	0.0:0.1395:0.8605:0.0	.	.	.	.	X	307	.	ENSP00000357565:S307X	S	-	2	0	ZUFSP	117084581	1.000000	0.71417	0.963000	0.40424	0.890000	0.51754	5.656000	0.67988	2.726000	0.93360	0.561000	0.74099	TCA	.	.		0.338	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062		C	116977888	G	C	116977888	4	2	215	1	0	0	0	0	0	1	0	0	18261	1294	45	4	840	4	ZUFSP	6	116977888	Nonsense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	7042299	116977888	54137179	67	30974										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146264427	146264427	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggcagtaaaaaggcttgatcTtcagatttttctcatcataa	7	7	4	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:146264427T>C	ENST00000367505.2	-	9	2354	c.2090A>G	c.(2089-2091)aAg>aGg	p.K697R	SHPRH_ENST00000275233.7_Missense_Mutation_p.K697R|SHPRH_ENST00000367503.3_Missense_Mutation_p.K697R|SHPRH_ENST00000438092.2_Missense_Mutation_p.K697R			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	697					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		AGGCTTGATCTTCAGATTTTT	0.453																																					p.K697R		Atlas-SNP	.											.	SHPRH	169	.	0			c.A2090G						.						71	74	73					6																	146264427		1960	4157	6117	SO:0001583	missense	257218	exon9			TTGATCTTCAGAT	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.2090A>G	chr6.hg19:g.146264427T>C	ENSP00000356475:p.Lys697Arg	120.0	0.0		150.0	51.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	hg19	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	T	17.30	3.354220	0.61293	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233;ENST00000444767	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.36	4.2	0.49525	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);DEAD-like helicase (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.134339	0.49916	D	0.000133	T	0.51736	0.1692	L	0.43152	1.355	0.35465	D	0.796818	B;D;D;D	0.62365	0.007;0.97;0.962;0.991	B;P;P;P	0.59424	0.007;0.725;0.604;0.857	T	0.53049	-0.8493	10	0.27785	T	0.31	-21.4122	8.7142	0.34401	0.0:0.1477:0.0:0.8523	.	586;697;697;586	Q149N8-2;Q149N8;Q149N8-4;F8WEL0	.;SHPRH_HUMAN;.;.	R	697;697;697;697;586	ENSP00000356475:K697R;ENSP00000356473:K697R;ENSP00000412797:K697R;ENSP00000275233:K697R	ENSP00000275233:K697R	K	-	2	0	SHPRH	146306120	0.986000	0.35501	0.977000	0.42913	0.991000	0.79684	1.993000	0.40747	0.980000	0.38523	0.528000	0.53228	AAG	.	.		0.453	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		C	146264427	T	C	146264427	3	2	215	1	0	0	0	0	1	0	0	0	14306	1609	56	2	3093	2	SHPRH	6	146264427	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	29286539	146264427	24850640	68	30975										
RAET1G	353091	hgsc.bcm.edu	37	chr6	150240446	150240446	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctcacaagacatcctggcctGcagggtgaggggttctgccc	13	13	2	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:150240446G>T	ENST00000367360.2	-	3	431	c.364C>A	c.(364-366)Cag>Aag	p.Q122K	RAET1E-AS1_ENST00000605899.1_RNA|RP11-244K5.8_ENST00000606915.1_RNA|RAET1G_ENST00000479265.1_Missense_Mutation_p.Q122K|RAET1E-AS1_ENST00000446954.2_RNA	NM_001001788.2	NP_001001788.2			retinoic acid early transcript 1G											NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|urinary_tract(1)	13		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		ATCCTGGCCTGCAGGGTGAGG	0.517																																					p.Q122K		Atlas-SNP	.											.	RAET1G	31	.	0			c.C364A						.						122	117	119					6																	150240446		2203	4300	6503	SO:0001583	missense	353091	exon3			TGGCCTGCAGGGT	AY172579	CCDS43514.1	6q24.1-25.1	2009-04-29	2004-11-22		ENSG00000203722	ENSG00000203722			16795	protein-coding gene	gene with protein product		609244	"retinoic acid early transcript 1G pseudogene"			11827464, 15240696	Standard	NM_001001788		Approved	ULBP5	uc010kii.1	Q6H3X3	OTTHUMG00000015802	ENST00000367360.2:c.364C>A	chr6.hg19:g.150240446G>T	ENSP00000356329:p.Gln122Lys	61.0	0.0		90.0	39.0	NM_001001788		Missense_Mutation	SNP	ENST00000367360.2	hg19	CCDS43514.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.958374	0.34565	.	.	ENSG00000203722	ENST00000367360;ENST00000479265	T;T	0.14640	2.49;2.49	2.67	-1.99	0.07457	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.18800	0.0451	M	0.79926	2.475	0.09310	N	1	D	0.89917	1.0	D	0.81914	0.995	T	0.04178	-1.0971	9	0.87932	D	0	.	7.2321	0.26049	0.0:0.5323:0.2876:0.1801	.	122	Q6H3X3	RET1G_HUMAN	K	122	ENSP00000356329:Q122K;ENSP00000417503:Q122K	ENSP00000356329:Q122K	Q	-	1	0	RAET1G	150282139	0.195000	0.23338	0.001000	0.08648	0.001000	0.01503	0.720000	0.25896	-0.469000	0.06911	-0.458000	0.05436	CAG	.	.		0.517	RAET1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042668.2			T	150240446	G	T	150240446	3	4	215	1	0	0	0	0	1	0	0	0	13015	1328	46	3	652	3	RAET1G	6	150240446	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	3976019	150240446	20874621	69	30976										
WTAP	9589	hgsc.bcm.edu	37	chr6	160176075	160176075	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cacagaactgaatgacttcaTcatccagcttgatgaagaag	8	9	2	6			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:160176075T>C	ENST00000358372.4	+	8	2380	c.623T>C	c.(622-624)aTc>aCc	p.I208T	SOD2_ENST00000546087.1_Intron	NM_001270531.1|NM_004906.4	NP_001257460.1|NP_004897.2	Q15007	FL2D_HUMAN	Wilms tumor 1 associated protein	208					cell cycle (GO:0007049)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	MIS complex (GO:0036396)|nuclear membrane (GO:0031965)|nuclear speck (GO:0016607)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	18		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)		AATGACTTCATCATCCAGCTT	0.448																																					p.I208T		Atlas-SNP	.											.	WTAP	44	.	0			c.T623C						.						50	49	49					6																	160176075		2203	4300	6503	SO:0001583	missense	9589	exon8			ACTTCATCATCCA	AJ276706	CCDS5266.1, CCDS5267.1, CCDS75542.1	6q25-q27	2008-02-05			ENSG00000146457	ENSG00000146457			16846	protein-coding gene	gene with protein product		605442				7788527, 11001926	Standard	NM_004906		Approved	KIAA0105, MGC3925	uc003qsl.4	Q15007	OTTHUMG00000015933	ENST00000358372.4:c.623T>C	chr6.hg19:g.160176075T>C	ENSP00000351141:p.Ile208Thr	115.0	0.0		148.0	57.0	NM_001270531	Q5TCL8|Q5TCL9|Q96T28|Q9BYJ7|Q9H4E2	Missense_Mutation	SNP	ENST00000358372.4	hg19	CCDS5266.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.992383	0.74703	.	.	ENSG00000146457	ENST00000358372	T	0.46063	0.88	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.39436	0.1078	N	0.14661	0.345	0.80722	D	1	D;D	0.89917	1.0;0.989	D;D	0.85130	0.997;0.985	T	0.47209	-0.9135	10	0.46703	T	0.11	-3.2925	16.8222	0.85835	0.0:0.0:0.0:1.0	.	208;208	A8K489;Q15007	.;FL2D_HUMAN	T	208	ENSP00000351141:I208T	ENSP00000351141:I208T	I	+	2	0	WTAP	160096065	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.018000	0.88722	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.448	WTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042905.1	NM_152857		C	160176075	T	C	160176075	3	2	215	1	0	0	0	0	1	0	0	0	17424	1435	50	2	653	2	WTAP	6	160176075	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	9935629	160176075	10938992	70	30977										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160448307	160448307	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	acaccaggcgtttgatgttgGccagccccgggacggactga	14	12	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:160448307G>C	ENST00000356956.1	+	6	885	c.737G>C	c.(736-738)gGc>gCc	p.G246A		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	246					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TTTGATGTTGGCCAGCCCCGG	0.592																																					p.G246A		Atlas-SNP	.											.	IGF2R	251	.	0			c.G737C						.						34	34	34					6																	160448307		2203	4300	6503	SO:0001583	missense	3482	exon6			ATGTTGGCCAGCC	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.737G>C	chr6.hg19:g.160448307G>C	ENSP00000349437:p.Gly246Ala	274.0	0.0		252.0	91.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.733813	0.69189	.	.	ENSG00000197081	ENST00000356956	T	0.74209	-0.82	5.22	5.22	0.72569	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	D	0.88749	0.6521	M	0.92923	3.36	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90731	0.4642	10	0.66056	D	0.02	-10.141	19.1446	0.93459	0.0:0.0:1.0:0.0	.	246	P11717	MPRI_HUMAN	A	246	ENSP00000349437:G246A	ENSP00000349437:G246A	G	+	2	0	IGF2R	160368297	1.000000	0.71417	0.987000	0.45799	0.266000	0.26442	7.299000	0.78831	2.577000	0.86979	0.655000	0.94253	GGC	.	.		0.592	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160448307	G	C	160448307	3	2	215	1	0	0	0	0	1	0	0	0	7585	1203	42	4	759	4	IGF2R	6	160448307	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	272232	160448307	10666760	71	30978										
THBS2	7058	hgsc.bcm.edu	37	chr6	169632798	169632798	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gcttccaggccgaccccgacGggctggttccctctgtatcg	12	16	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr6:169632798G>A	ENST00000366787.3	-	13	2142	c.1893C>T	c.(1891-1893)ccC>ccT	p.P631P	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	631					cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CGACCCCGACGGGCTGGTTCC	0.607																																					p.P631P	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.C1893T						.						63	68	67					6																	169632798		2203	4299	6502	SO:0001819	synonymous_variant	7058	exon13			CCCGACGGGCTGG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.1893C>T	chr6.hg19:g.169632798G>A		106.0	0.0		92.0	35.0	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	hg19	CCDS34574.1																																																																																			.	.		0.607	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		A	169632798	G	A	169632798	2	1	215	1	0	0	0	0	0	0	0	1	15869	1103	39	1		1	THBS2	6	169632798	Silent	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	9184491	169632798	1482269	72	30979										
SDK1	221935	hgsc.bcm.edu	37	chr7	4249794	4249794	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	agcccttggcccctgtacaaGgtaagacccggggttgggga	15	11	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr7:4249794G>C	ENST00000404826.2	+	38	5678	c.5539G>C	c.(5539-5541)Ggg>Cgg	p.G1847R	SDK1_ENST00000389531.3_Splice_Site_p.G1827R	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1847	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CCCTGTACAAGGTAAGACCCG	0.667																																					p.G1847R		Atlas-SNP	.											.	SDK1	361	.	0			c.G5539C						.						25	25	25					7																	4249794		2203	4300	6503	SO:0001630	splice_region_variant	221935	exon38			GTACAAGGTAAGA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.5539+1G>C	chr7.hg19:g.4249794G>C		24.0	0.0		32.0	9.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.295840	0.40594	.	.	ENSG00000146555	ENST00000404826;ENST00000446104;ENST00000389531	T;T	0.58652	0.32;0.32	4.98	4.98	0.66077	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.73583	0.3605	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	0.979;0.969;1.0	P;P;D	0.78314	0.74;0.77;0.991	T	0.69423	-0.5149	10	0.16420	T	0.52	.	18.2677	0.90057	0.0:0.0:1.0:0.0	.	1827;334;1847	F8W6X9;F2Z3E9;Q7Z5N4	.;.;SDK1_HUMAN	R	1847;95;1827	ENSP00000385899:G1847R;ENSP00000374182:G1827R	ENSP00000374182:G1827R	G	+	1	0	SDK1	4216320	1.000000	0.71417	0.999000	0.59377	0.049000	0.14656	9.363000	0.97131	2.318000	0.78349	0.563000	0.77884	GGG	.	.		0.667	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	Missense_Mutation	C	4249794	G	C	4249794	5	2	215	1	0	0	0	0	0	0	1	0	13983	1014	35	4	5689	4	SDK1	7	4249794	Splice_Site	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10		4249794	154888869	73	30980										
SCIN	85477	hgsc.bcm.edu	37	chr7	12666228	12666228	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gattcaagttcttccagaagGaggtgaaacaccaatcttca	8	9	4	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr7:12666228G>C	ENST00000297029.5	+	8	1102	c.1001G>C	c.(1000-1002)gGa>gCa	p.G334A	SCIN_ENST00000519209.1_Missense_Mutation_p.G87A|SCIN_ENST00000445618.2_Missense_Mutation_p.G87A|SCIN_ENST00000473722.1_3'UTR	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	334	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		CTTCCAGAAGGAGGTGAAACA	0.343																																					p.G334A		Atlas-SNP	.											.	SCIN	105	.	0			c.G1001C						.						30	26	27					7																	12666228		1683	3798	5481	SO:0001583	missense	85477	exon8			CAGAAGGAGGTGA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.1001G>C	chr7.hg19:g.12666228G>C	ENSP00000297029:p.Gly334Ala	88.0	0.0		120.0	25.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	hg19	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.183428	0.57800	.	.	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.63255	-0.03;-0.03;-0.03	5.94	5.94	0.96194	Gelsolin domain (1);	0.106853	0.64402	D	0.000006	T	0.79149	0.4397	H	0.96861	3.895	0.47905	D	0.999549	P	0.50443	0.935	P	0.47864	0.559	D	0.85644	0.1278	10	0.87932	D	0	-20.8521	13.5436	0.61690	0.0708:0.0:0.9292:0.0	.	334	Q9Y6U3	ADSV_HUMAN	A	334;87;87	ENSP00000297029:G334A;ENSP00000430997:G87A;ENSP00000390189:G87A	ENSP00000297029:G334A	G	+	2	0	SCIN	12632753	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.007000	0.49536	2.816000	0.96949	0.563000	0.77884	GGA	.	.		0.343	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		C	12666228	G	C	12666228	3	2	215	1	0	0	0	0	1	0	0	0	13920	1174	41	4	1031	4	SCIN	7	12666228	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	8416434	12666228	146472435	74	30981										
TRA2A	29896	hgsc.bcm.edu	37	chr7	23545772	23545772	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	attacctgtatcggtaatcaTagtcttcatatctgtcatac	5	9	5	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr7:23545772T>C	ENST00000297071.4	-	6	971	c.755A>G	c.(754-756)tAt>tGt	p.Y252C	TRA2A_ENST00000392502.4_Missense_Mutation_p.Y151C|TRA2A_ENST00000538367.1_Missense_Mutation_p.Y151C|TRA2A_ENST00000474586.1_5'Flank	NM_013293.3	NP_037425.1	Q13595	TRA2A_HUMAN	transformer 2 alpha homolog (Drosophila)	252	Arg/Ser-rich (RS2 domain).				mRNA splicing, via spliceosome (GO:0000398)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	10						TCGGTAATCATAGTCTTCATA	0.418																																					p.Y252C	Pancreas(121;2137 2973 46590)	Atlas-SNP	.											.	TRA2A	29	.	0			c.A755G						.						109	114	112					7																	23545772		2203	4300	6503	SO:0001583	missense	29896	exon6			TAATCATAGTCTT	U53209	CCDS5383.1, CCDS64609.1, CCDS75569.1	7p15.3	2014-02-12			ENSG00000164548	ENSG00000164548		"RNA binding motif (RRM) containing"	16645	protein-coding gene	gene with protein product		602718				8799144, 9546399	Standard	XM_005249725		Approved	htra-2-alpha, tra2a, AWMS1	uc003swi.3	Q13595	OTTHUMG00000128459	ENST00000297071.4:c.755A>G	chr7.hg19:g.23545772T>C	ENSP00000297071:p.Tyr252Cys	69.0	0.0		126.0	15.0	NM_013293	B4DUA9	Missense_Mutation	SNP	ENST00000297071.4	hg19	CCDS5383.1	.	.	.	.	.	.	.	.	.	.	T	14.84	2.655917	0.47467	.	.	ENSG00000164548	ENST00000297071;ENST00000392502;ENST00000538367	T;T;T	0.27256	1.68;1.85;1.82	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.32734	0.0839	L	0.54323	1.7	0.49130	D	0.999758	P	0.52463	0.953	P	0.47075	0.536	T	0.04481	-1.0948	10	0.41790	T	0.15	-9.1505	15.2005	0.73132	0.0:0.0:0.0:1.0	.	252	Q13595	TRA2A_HUMAN	C	252;151;151	ENSP00000297071:Y252C;ENSP00000376290:Y151C;ENSP00000441116:Y151C	ENSP00000297071:Y252C	Y	-	2	0	TRA2A	23512297	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.503000	0.60407	2.060000	0.61445	0.529000	0.55759	TAT	.	.		0.418	TRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250257.1	NM_013293		C	23545772	T	C	23545772	3	2	215	1	0	0	0	0	1	0	0	0	16448	1406	49	2	105	2	TRA2A	7	23545772	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	10879544	23545772	135592891	75	30982										
FZD9	8326	hgsc.bcm.edu	37	chr7	72848989	72848989	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gcgcaccgcgctgcgggcccGgcgtcgaggtgttctggtcc	17	15	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr7:72848989G>A	ENST00000344575.3	+	1	881	c.652G>A	c.(652-654)Ggc>Agc	p.G218S		NM_003508.2	NP_003499.1	O00144	FZD9_HUMAN	frizzled class receptor 9	218					B cell differentiation (GO:0030183)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|learning or memory (GO:0007611)|nervous system development (GO:0007399)|neuroblast proliferation (GO:0007405)|vasculature development (GO:0001944)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|skin(1)	14		Lung NSC(55;0.0659)|all_lung(88;0.152)				CTGCGGGCCCGGCGTCGAGGT	0.692																																					p.G218S	Pancreas(144;909 1878 36867 38226 39554)	Atlas-SNP	.											.	FZD9	51	.	0			c.G652A						.						28	31	30					7																	72848989		2201	4299	6500	SO:0001583	missense	8326	exon1			GGGCCCGGCGTCG	U82169	CCDS5548.1	7q11.23	2014-01-29	2014-01-29		ENSG00000188763	ENSG00000188763		"GPCR / Class F : Frizzled receptors", "CD molecules"	4047	protein-coding gene	gene with protein product		601766	"frizzled (Drosophila) homolog 9", "frizzled homolog 9 (Drosophila)", "frizzled 9, seven transmembrane spanning receptor", "frizzled family receptor 9"			9147651, 10198163	Standard	NM_003508		Approved	FZD3, CD349	uc003tyb.3	O00144	OTTHUMG00000023051	ENST00000344575.3:c.652G>A	chr7.hg19:g.72848989G>A	ENSP00000345785:p.Gly218Ser	26.0	0.0		32.0	10.0	NM_003508		Missense_Mutation	SNP	ENST00000344575.3	hg19	CCDS5548.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.479658	0.26511	.	.	ENSG00000188763	ENST00000344575	T	0.77098	-1.07	3.4	3.4	0.38934	.	0.066273	0.64402	U	0.000017	T	0.57286	0.2043	N	0.12746	0.255	0.43130	D	0.994862	B	0.24675	0.109	B	0.17098	0.017	T	0.54275	-0.8318	10	0.09084	T	0.74	.	14.2073	0.65741	0.0:0.0:1.0:0.0	.	218	O00144	FZD9_HUMAN	S	218	ENSP00000345785:G218S	ENSP00000345785:G218S	G	+	1	0	FZD9	72486925	1.000000	0.71417	0.953000	0.39169	0.820000	0.46376	7.935000	0.87658	1.633000	0.50488	0.196000	0.17591	GGC	.	.		0.692	FZD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252120.1			A	72848989	G	A	72848989	3	1	215	1	0	0	0	0	1	0	0	0	6145	1116	39	1	654	1	FZD9	7	72848989	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	49303217	72848989	86289674	76	30983										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117424330	117424330	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tgtccattcttagcagcagaAtacaaggcagaatggccatc	9	10	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr7:117424330A>G	ENST00000160373.3	-	5	2338	c.2247T>C	c.(2245-2247)taT>taC	p.Y749Y		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	749					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TAGCAGCAGAATACAAGGCAG	0.403																																					p.Y749Y		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.T2247C						.						131	136	134					7																	117424330		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon5			AGCAGAATACAAG		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.2247T>C	chr7.hg19:g.117424330A>G		123.0	0.0		212.0	50.0	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	A	9.048	0.991407	0.18966	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	T	0.71771	0.3379	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71130	-0.4682	4	.	.	.	-0.8195	15.8142	0.78586	1.0:0.0:0.0:0.0	.	.	.	.	L	237	.	.	F	-	1	0	CTTNBP2	117211566	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.572000	0.74005	2.184000	0.69523	0.533000	0.62120	TTC	.	.		0.403	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		G	117424330	A	G	117424330	2	3	215	1	0	0	0	0	0	0	0	1	4047	108	4	2		2	CTTNBP2	7	117424330	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	44575341	117424330	41714333	77	30984										
ATP6V0A4	50617	hgsc.bcm.edu	37	chr7	138400553	138400553	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	agagccgcaggtaggaggctGtgtttgaaatgcagcccagg	16	8	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr7:138400553G>T	ENST00000310018.2	-	20	2495	c.2213C>A	c.(2212-2214)aCa>aAa	p.T738K	ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.T738K|ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.T738K	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	738					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						GTAGGAGGCTGTGTTTGAAAT	0.542																																					p.T738K		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.C2213A						.						162	153	156					7																	138400553		2203	4300	6503	SO:0001583	missense	50617	exon19			GAGGCTGTGTTTG	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"ATPases / V-type"	866	protein-coding gene	gene with protein product		605239	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 4", "ATPase, H+ transporting, lysosomal V0 subunit A4"	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.2213C>A	chr7.hg19:g.138400553G>T	ENSP00000308122:p.Thr738Lys	88.0	0.0		160.0	45.0	NM_130841	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	hg19	CCDS5849.1	.	.	.	.	.	.	.	.	.	.	G	32	5.120548	0.94385	.	.	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.88586	-2.4;-2.4;-2.4	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.96842	0.8969	H	0.97491	4.015	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97994	1.0356	10	0.87932	D	0	-17.115	19.3838	0.94548	0.0:0.0:1.0:0.0	.	738	Q9HBG4	VPP4_HUMAN	K	738	ENSP00000308122:T738K;ENSP00000376774:T738K;ENSP00000253856:T738K	ENSP00000308122:T738K	T	-	2	0	ATP6V0A4	138051093	1.000000	0.71417	0.962000	0.40283	0.909000	0.53808	9.813000	0.99286	2.670000	0.90874	0.655000	0.94253	ACA	.	.		0.542	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632		T	138400553	G	T	138400553	3	4	215	1	0	0	0	0	1	0	0	0	1170	1377	48	3	321	3	ATP6V0A4	7	138400553	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	20976223	138400553	20738110	78	30985										
UBE3C	9690	hgsc.bcm.edu	37	chr7	157013403	157013403	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gtcactcagctctatgtgccAgcatccagacatgtgtggag	11	11	3	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr7:157013403A>T	ENST00000348165.5	+	15	2295	c.1935A>T	c.(1933-1935)ccA>ccT	p.P645P		NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	645					protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		TCTATGTGCCAGCATCCAGAC	0.557																																					p.P645P		Atlas-SNP	.											.	UBE3C	124	.	0			c.A1935T						.						116	93	100					7																	157013403		2203	4300	6503	SO:0001819	synonymous_variant	9690	exon15			TGTGCCAGCATCC	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.1935A>T	chr7.hg19:g.157013403A>T		50.0	0.0		90.0	19.0	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Silent	SNP	ENST00000348165.5	hg19	CCDS34789.1																																																																																			.	.		0.557	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		T	157013403	A	T	157013403	2	4	215	1	0	0	0	0	0	0	0	1	16896	175	7	4		4	UBE3C	7	157013403	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	18612850	157013403	2125260	79	30986										
KIF13B	23303	hgsc.bcm.edu	37	chr8	29035027	29035027	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	agcctgtcccctgcagcgccTgtcttcgttgctcgttcact	9	16	2	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr8:29035027T>C	ENST00000524189.1	-	9	827	c.789A>G	c.(787-789)acA>acG	p.T263T	KIF13B_ENST00000521515.1_Silent_p.T263T	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	263	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		CTGCAGCGCCTGTCTTCGTTG	0.428											OREG0018684	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T263T		Atlas-SNP	.											.	KIF13B	192	.	0			c.A789G						.						134	136	135					8																	29035027		1932	4155	6087	SO:0001819	synonymous_variant	23303	exon9			AGCGCCTGTCTTC	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.789A>G	chr8.hg19:g.29035027T>C		60.0	0.0	806	74.0	30.0	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Silent	SNP	ENST00000524189.1	hg19	CCDS55217.1																																																																																			.	.		0.428	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			C	29035027	T	C	29035027	2	2	215	1	0	0	0	0	0	0	0	1	8284	1567	55	2		2	KIF13B	8	29035027	Silent	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10		29035027	117328995	80	30987										
POLB	5423	hgsc.bcm.edu	37	chr8	42218871	42218871	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	catcccagcttcacttcagaAtcaaccaaacaggtgcctca	5	15	4	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr8:42218871A>G	ENST00000265421.4	+	10	779	c.609A>G	c.(607-609)gaA>gaG	p.E203E	POLB_ENST00000538005.1_Silent_p.E49E	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	203					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	TCACTTCAGAATCAACCAAAC	0.403								DNA polymerases (catalytic subunits)																													p.E203E		Atlas-SNP	.											.	POLB	60	.	0			c.A609G						.						139	120	126					8																	42218871		2203	4300	6503	SO:0001819	synonymous_variant	5423	exon10			TTCAGAATCAACC		CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	2.7.7.7	"DNA polymerases"	9174	protein-coding gene	gene with protein product		174760					Standard	NM_002690		Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.609A>G	chr8.hg19:g.42218871A>G		80.0	0.0		92.0	29.0	NM_002690	B2RC78|Q3KP48|Q6FI34	Silent	SNP	ENST00000265421.4	hg19	CCDS6129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.541|1.541	-0.541860|-0.541860	0.04053|0.04053	.|.	.|.	ENSG00000070501|ENSG00000070501	ENST00000521290|ENST00000518579;ENST00000517393	.|.	.|.	.|.	5.58|5.58	-2.33|-2.33	0.06724|0.06724	.|.	.|.	.|.	.|.	.|.	T|T	0.65407|0.65407	0.2688|0.2688	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.61836|0.61836	-0.6981|-0.6981	4|4	.|.	.|.	.|.	-7.2388|-7.2388	14.644|14.644	0.68745|0.68745	0.29:0.0:0.71:0.0|0.29:0.0:0.71:0.0	.|.	.|.	.|.	.|.	V|S	134|61;19	.|.	.|.	I|N	+|+	1|2	0|0	POLB|POLB	42338028|42338028	0.213000|0.213000	0.23551|0.23551	0.757000|0.757000	0.31301|0.31301	0.124000|0.124000	0.20399|0.20399	-0.388000|-0.388000	0.07352|0.07352	-0.867000|-0.867000	0.04063|0.04063	0.460000|0.460000	0.39030|0.39030	ATC|AAT	.	.		0.403	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377242.1	NM_002690		G	42218871	A	G	42218871	2	3	215	1	0	0	0	0	0	0	0	1	12198	98	4	2		2	POLB	8	42218871	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	13183844	42218871	104145151	81	30988										
SLC10A5	347051	hgsc.bcm.edu	37	chr8	82606702	82606702	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gcaaaggtctcttccatactGtttgaaacagctgtaattca	7	9	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr8:82606702G>C	ENST00000518568.1	-	1	1707	c.506C>G	c.(505-507)aCa>aGa	p.T169R		NM_001010893.2	NP_001010893.1	Q5PT55	NTCP5_HUMAN	solute carrier family 10, member 5	169						integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)	15						CTTCCATACTGTTTGAAACAG	0.363																																					p.T169R		Atlas-SNP	.											.	SLC10A5	35	.	0			c.C506G						.						61	63	62					8																	82606702		2203	4300	6503	SO:0001583	missense	347051	exon1			CATACTGTTTGAA		CCDS34915.1	8q21.13	2013-07-18	2013-07-18		ENSG00000253598	ENSG00000253598		"Solute carriers"	22981	protein-coding gene	gene with protein product							Standard	NM_001010893		Approved		uc011lfs.2	Q5PT55	OTTHUMG00000164683	ENST00000518568.1:c.506C>G	chr8.hg19:g.82606702G>C	ENSP00000428612:p.Thr169Arg	83.0	0.0		138.0	49.0	NM_001010893	B2RN26	Missense_Mutation	SNP	ENST00000518568.1	hg19	CCDS34915.1	.	.	.	.	.	.	.	.	.	.	G	8.457	0.854370	0.17106	.	.	ENSG00000253598	ENST00000518568	T	0.10960	2.82	5.98	0.541	0.17168	.	0.700302	0.12884	N	0.431205	T	0.04679	0.0127	N	0.11154	0.105	0.09310	N	1	B	0.12630	0.006	B	0.12156	0.007	T	0.45614	-0.9249	10	0.17832	T	0.49	-0.9866	5.6459	0.17588	0.3109:0.2475:0.4416:0.0	.	169	Q5PT55	NTCP5_HUMAN	R	169	ENSP00000428612:T169R	ENSP00000428612:T169R	T	-	2	0	SLC10A5	82769257	0.000000	0.05858	0.008000	0.14137	0.985000	0.73830	0.066000	0.14489	0.138000	0.18790	0.563000	0.77884	ACA	.	.		0.363	SLC10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379736.1	XM_294493		C	82606702	G	C	82606702	3	2	215	1	0	0	0	0	1	0	0	0	14392	1377	48	4	812	4	SLC10A5	8	82606702	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	40387831	82606702	63757320	82	30989										
SAMD12	401474	hgsc.bcm.edu	37	chr8	119391939	119391939	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	taagtctcagcagggctcgcCctgcagggttttaagaaata	11	9	1	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr8:119391939C>T	ENST00000314727.4	-	4	459	c.323G>A	c.(322-324)gGg>gAg	p.G108E	AC023590.1_ENST00000430457.1_Intron|SAMD12_ENST00000409003.4_Splice_Site_p.G108E|SAMD12_ENST00000527515.1_5'Flank	NM_207506.2	NP_997389.2	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12	108	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)	9	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			CAGGGCTCGCCCTGCAGGGTT	0.473																																					p.G108E		Atlas-SNP	.											.	SAMD12	24	.	0			c.G323A						.						71	68	69					8																	119391939		2203	4300	6503	SO:0001630	splice_region_variant	401474	exon4			GCTCGCCCTGCAG	AK096777	CCDS6325.1, CCDS47913.1	8q24.12	2013-01-10			ENSG00000177570	ENSG00000177570		"Sterile alpha motif (SAM) domain containing"	31750	protein-coding gene	gene with protein product							Standard	NM_207506		Approved	FLJ39458	uc003yom.2	Q8N8I0	OTTHUMG00000059817	ENST00000314727.4:c.323-1G>A	chr8.hg19:g.119391939C>T		60.0	0.0		94.0	31.0	NM_207506	Q0P502	Missense_Mutation	SNP	ENST00000314727.4	hg19	CCDS6325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.267520|5.267520	0.95399|0.95399	.|.	.|.	ENSG00000177570|ENSG00000177570	ENST00000409003;ENST00000524796;ENST00000314727;ENST00000526328|ENST00000526765	D;D;D;D|D	0.85629|0.85556	-2.01;-2.01;-2.01;-2.01|-2.0	6.17|6.17	6.17|6.17	0.99709|0.99709	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.94571|0.94571	0.8251|0.8251	M|M	0.92026|0.92026	3.265|3.265	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.992|.	D|D	0.94416|0.94416	0.7636|0.7636	9|7	.|.	.|.	.|.	.|.	20.8794|20.8794	0.99867|0.99867	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	108;108|.	B8ZZB7;Q8N8I0|.	.;SAM12_HUMAN|.	E|S	108;100;108;108|123	ENSP00000387133:G108E;ENSP00000435927:G100E;ENSP00000314173:G108E;ENSP00000431360:G108E|ENSP00000434079:G123S	.|.	G|G	-|-	2|1	0|0	SAMD12|SAMD12	119461120|119461120	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.928000|0.928000	0.56348|0.56348	7.487000|7.487000	0.81328|0.81328	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GGG|GGC	.	.		0.473	SAMD12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132989.3	NM_207506	Missense_Mutation	T	119391939	C	T	119391939	5	4	215	1	0	0	0	0	0	0	1	0	13832	637	22	3	313	3	SAMD12	8	119391939	Splice_Site	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	36785237	119391939	26972083	83	30990										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2182157	2182157	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tcaggaaaggattcgtaatcAtaagtaccggagcctaggcg	12	8	2	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr9:2182157A>G	ENST00000382203.1	+	31	4585	c.4376A>G	c.(4375-4377)cAt>cGt	p.H1459R	SMARCA2_ENST00000324954.5_Missense_Mutation_p.H105R|SMARCA2_ENST00000382186.1_Missense_Mutation_p.H123R|SMARCA2_ENST00000382194.1_Missense_Mutation_p.H1441R|SMARCA2_ENST00000357248.2_Missense_Mutation_p.H1441R|SMARCA2_ENST00000349721.2_Missense_Mutation_p.H1459R|SMARCA2_ENST00000302401.3_Missense_Mutation_p.H147R|SMARCA2_ENST00000382185.1_Missense_Mutation_p.H105R			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	1459	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		ATTCGTAATCATAAGTACCGG	0.438																																					p.H1459R		Atlas-SNP	.											.	SMARCA2	313	.	0			c.A4376G						.						139	137	138					9																	2182157		2203	4300	6503	SO:0001583	missense	6595	exon31			GTAATCATAAGTA	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.4376A>G	chr9.hg19:g.2182157A>G	ENSP00000371638:p.His1459Arg	65.0	0.0		71.0	25.0	NM_003070	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.848563	0.32699	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000382203;ENST00000382194;ENST00000452193;ENST00000302401;ENST00000324954;ENST00000423555;ENST00000382186;ENST00000417599;ENST00000382185;ENST00000382183;ENST00000416751	T;T;T;T;T;T;T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62	5.84	5.84	0.93424	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.44265	0.1285	L	0.33293	1	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.959;0.967	D;D;D;D	0.77557	0.99;0.99;0.972;0.983	T	0.17653	-1.0362	10	0.25751	T	0.34	-30.5819	16.2322	0.82352	1.0:0.0:0.0:0.0	.	145;147;1441;1459	B4DNT1;B1ALF6;P51531-2;P51531	.;.;.;SMCA2_HUMAN	R	1459;1441;1459;1441;123;147;105;145;123;145;105;105;105	ENSP00000265773:H1459R;ENSP00000349788:H1441R;ENSP00000371638:H1459R;ENSP00000371629:H1441R;ENSP00000401096:H123R;ENSP00000305411:H147R;ENSP00000324770:H105R;ENSP00000413057:H145R;ENSP00000371621:H123R;ENSP00000387486:H145R;ENSP00000371620:H105R;ENSP00000371618:H105R;ENSP00000412242:H105R	ENSP00000305411:H147R	H	+	2	0	SMARCA2	2172157	1.000000	0.71417	0.992000	0.48379	0.239000	0.25481	9.317000	0.96327	2.233000	0.73108	0.454000	0.30748	CAT	.	.		0.438	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		G	2182157	A	G	2182157	3	3	215	1	0	0	0	0	1	0	0	0	14784	217	8	2	4494	2	SMARCA2	9	2182157	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10		2182157	139031274	84	30991										
SNAPC3	6619	hgsc.bcm.edu	37	chr9	15423939	15423939	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gaaatgccttgaggacggtgAggatccagaagtcattccgg	14	8	1	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr9:15423939A>T	ENST00000380821.3	+	2	523	c.347A>T	c.(346-348)gAg>gTg	p.E116V	SNAPC3_ENST00000461041.1_3'UTR	NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	116					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		GAGGACGGTGAGGATCCAGAA	0.398																																					p.E116V		Atlas-SNP	.											.	SNAPC3	28	.	0			c.A347T						.						200	180	187					9																	15423939		2203	4300	6503	SO:0001583	missense	6619	exon2			ACGGTGAGGATCC	U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"small nuclear RNA activating complex, polypeptide 3, 50kD"			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.347A>T	chr9.hg19:g.15423939A>T	ENSP00000370200:p.Glu116Val	115.0	0.0		145.0	11.0	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	hg19	CCDS6478.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.304125	0.23736	.	.	ENSG00000164975	ENST00000380821;ENST00000380807;ENST00000447670;ENST00000421710	T	0.51817	0.69	5.79	4.64	0.57946	.	0.331668	0.33253	N	0.005112	T	0.58779	0.2146	M	0.62723	1.935	0.25786	N	0.984671	D;P	0.61080	0.989;0.704	P;B	0.58266	0.836;0.145	T	0.55341	-0.8156	10	0.87932	D	0	-7.6058	10.0758	0.42360	0.8313:0.1687:0.0:0.0	.	87;116	B4DDR9;Q92966	.;SNPC3_HUMAN	V	116;116;87;116	ENSP00000370200:E116V	ENSP00000370185:E116V	E	+	2	0	SNAPC3	15413939	1.000000	0.71417	0.078000	0.20375	0.007000	0.05969	3.188000	0.50958	1.001000	0.39076	0.533000	0.62120	GAG	.	.		0.398	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697		T	15423939	A	T	15423939	3	4	215	1	0	0	0	0	1	0	0	0	14851	304	11	4	353	4	SNAPC3	9	15423939	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	13241782	15423939	125789492	85	30992										
HAUS6	54801	hgsc.bcm.edu	37	chr9	19076617	19076617	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aacctggaagtgaagcaggaTactgacaaagaatactcttt	9	7	1	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr9:19076617T>C	ENST00000380502.3	-	11	1744	c.1277A>G	c.(1276-1278)tAt>tGt	p.Y426C	HAUS6_ENST00000380496.1_Missense_Mutation_p.Y290C|RNU6-264P_ENST00000517134.1_RNA	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	426					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TGAAGCAGGATACTGACAAAG	0.333																																					p.Y426C		Atlas-SNP	.											.	HAUS6	66	.	0			c.A1277G						.						78	75	76					9																	19076617		2203	4300	6503	SO:0001583	missense	54801	exon11			GCAGGATACTGAC	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"HAUS augmin-like complex subunits"	25948	protein-coding gene	gene with protein product		613433	"family with sequence similarity 29, member A"	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.1277A>G	chr9.hg19:g.19076617T>C	ENSP00000369871:p.Tyr426Cys	353.0	0.0		446.0	153.0	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	hg19	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	T	16.25	3.070931	0.55646	.	.	ENSG00000147874	ENST00000380502;ENST00000380496	T;T	0.39229	1.09;1.13	5.46	5.46	0.80206	.	0.119049	0.64402	D	0.000017	T	0.65004	0.2650	M	0.77616	2.38	0.48901	D	0.999729	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.988;0.98;0.999;0.988	T	0.68526	-0.5385	10	0.59425	D	0.04	-14.1711	13.7502	0.62904	0.0:0.0:0.0:1.0	.	391;426;290;426	Q7Z4H7-3;Q7Z4H7-2;Q5VY60;Q7Z4H7	.;.;.;HAUS6_HUMAN	C	426;290	ENSP00000369871:Y426C;ENSP00000369865:Y290C	ENSP00000369865:Y290C	Y	-	2	0	HAUS6	19066617	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	3.185000	0.50934	2.186000	0.69663	0.482000	0.46254	TAT	.	.		0.333	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645		C	19076617	T	C	19076617	3	2	215	1	0	0	0	0	1	0	0	0	6979	1406	49	2	1618	2	HAUS6	9	19076617	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	3652678	19076617	122136814	86	30993										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79862174	79862174	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aaaagatttacatttttccaGgtctactgtatattattgaa	5	5	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr9:79862174G>T	ENST00000360280.3	+	20	2160		c.e20-1		VPS13A_ENST00000376634.4_Splice_Site|VPS13A_ENST00000357409.5_Splice_Site|VPS13A_ENST00000376636.3_Splice_Site	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)						cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CATTTTTCCAGGTCTACTGTA	0.269																																					.		Atlas-SNP	.											VPS13A_ENST00000376634,NS,carcinoma,0,2	VPS13A	735	.	0			c.1901-1G>T						.						59	67	65					9																	79862174		2201	4282	6483	SO:0001630	splice_region_variant	23230	exon20			TTTCCAGGTCTAC	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.1901-1G>T	chr9.hg19:g.79862174G>T		264.0	0.0		228.0	108.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Splice_Site	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.428053	0.62844	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0429	0.93008	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	VPS13A	79051994	1.000000	0.71417	0.996000	0.52242	0.584000	0.36387	8.994000	0.93529	2.571000	0.86741	0.563000	0.77884	.	.	.		0.269	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	Intron	T	79862174	G	T	79862174	5	4	215	1	0	0	0	0	0	0	1	0	17204	1014	35	3	1978	3	VPS13A	9	79862174	Splice_Site	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	60785557	79862174	61351257	87	30994										
NCBP1	4686	hgsc.bcm.edu	37	chr9	100431136	100431136	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tgccttctatagcgaagtgaTgatgacgacagaagcagtga	12	7	1	5			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr9:100431136T>C	ENST00000375147.3	+	21	2281	c.2025T>C	c.(2023-2025)gaT>gaC	p.D675D		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	675					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				AGCGAAGTGATGATGACGACA	0.418																																					p.D675D	Ovarian(36;879 898 2893 44212 50307)	Atlas-SNP	.											.	NCBP1	64	.	0			c.T2025C						.						85	83	84					9																	100431136		2203	4300	6503	SO:0001819	synonymous_variant	4686	exon21			AAGTGATGATGAC	BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.2025T>C	chr9.hg19:g.100431136T>C		135.0	0.0		90.0	43.0	NM_002486	B2R718|Q59G76|Q5T1V0|Q5T7X2	Silent	SNP	ENST00000375147.3	hg19	CCDS6728.1																																																																																			.	.		0.418	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		C	100431136	T	C	100431136	2	2	215	1	0	0	0	0	0	0	0	1	10220	1461	51	2		2	NCBP1	9	100431136	Silent	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	20568962	100431136	40782295	88	30995										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55698674	55698674	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctcataatccagaggtccatTcacatagataacacctgtga	6	11	2	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr10:55698674T>C	ENST00000320301.6	-	25	3668	c.3274A>G	c.(3274-3276)Aat>Gat	p.N1092D	PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395445.1_Missense_Mutation_p.N1099D|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Missense_Mutation_p.N1097D|PCDH15_ENST00000437009.1_Missense_Mutation_p.N1021D|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000373965.2_Missense_Mutation_p.N1099D|PCDH15_ENST00000395430.1_Missense_Mutation_p.N1092D|PCDH15_ENST00000395433.1_Missense_Mutation_p.N1070D|PCDH15_ENST00000409834.1_Missense_Mutation_p.N703D|PCDH15_ENST00000395438.1_Missense_Mutation_p.N1092D|PCDH15_ENST00000395432.2_Missense_Mutation_p.N1055D|PCDH15_ENST00000361849.3_Missense_Mutation_p.N1092D|PCDH15_ENST00000373957.3_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1092	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				AGAGGTCCATTCACATAGATA	0.383										HNSCC(58;0.16)																											p.N1097D		Atlas-SNP	.											.	PCDH15	1715	.	0			c.A3289G						.						106	99	102					10																	55698674		2203	4299	6502	SO:0001583	missense	65217	exon26			GTCCATTCACATA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3274A>G	chr10.hg19:g.55698674T>C	ENSP00000322604:p.Asn1092Asp	55.0	0.0		77.0	13.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.053068	0.36181	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.71	4.59	0.56863	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.46852	0.1414	M	0.66439	2.03	0.24965	N	0.99171	B;B;B;B;B;B;B;B;B;B;B;B;B	0.29188	0.024;0.1;0.061;0.061;0.236;0.1;0.024;0.006;0.027;0.027;0.002;0.004;0.061	B;B;B;B;B;B;B;B;B;B;B;B;B	0.33960	0.06;0.038;0.038;0.038;0.173;0.038;0.06;0.042;0.038;0.038;0.012;0.012;0.038	T	0.43491	-0.9388	9	0.44086	T	0.13	.	7.6258	0.28212	0.0:0.1592:0.0:0.8408	.	1070;1092;1092;1097;1021;1055;1092;1092;1099;1099;1092;1097;1092	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	D	1099;1097;1092;1092;703;1099;1055;1092;1070;1092;1092;1097;1021	ENSP00000363076:N1099D;ENSP00000410304:N1097D;ENSP00000378826:N1092D;ENSP00000386693:N703D;ENSP00000378832:N1099D;ENSP00000378820:N1055D;ENSP00000354950:N1092D;ENSP00000378821:N1070D;ENSP00000322604:N1092D;ENSP00000378818:N1092D;ENSP00000412628:N1021D	ENSP00000322604:N1092D	N	-	1	0	PCDH15	55368680	0.945000	0.32115	0.993000	0.49108	0.472000	0.32918	2.210000	0.42816	2.175000	0.68902	0.533000	0.62120	AAT	.	.		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		C	55698674	T	C	55698674	3	2	215	1	0	0	0	0	1	0	0	0	11520	1783	62	2	4248	2	PCDH15	10	55698674	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10		55698674	79836073	89	30996										
CTNNA3	29119	hgsc.bcm.edu	37	chr10	67726454	67726454	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	agttggtgggagtagaacttAatctgttccaggtaggccaa	13	6	1	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr10:67726454A>T	ENST00000433211.2	-	17	2490	c.2316T>A	c.(2314-2316)atT>atA	p.I772I	CTNNA3_ENST00000373735.1_5'UTR|CTNNA3_ENST00000373744.4_Silent_p.I772I	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						AGTAGAACTTAATCTGTTCCA	0.408																																					p.I772I		Atlas-SNP	.											.	CTNNA3	401	.	0			c.T2316A						.						100	95	97					10																	67726454		2203	4300	6503	SO:0001819	synonymous_variant	29119	exon17			GAACTTAATCTGT	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.2316T>A	chr10.hg19:g.67726454A>T		69.0	0.0		105.0	28.0	NM_013266		Silent	SNP	ENST00000433211.2	hg19	CCDS7269.1																																																																																			.	.		0.408	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		T	67726454	A	T	67726454	2	4	215	1	0	0	0	0	0	0	0	1	4016	358	13	4		4	CTNNA3	10	67726454	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	12027780	67726454	67808293	90	30997										
CTNNA3	29119	hgsc.bcm.edu	37	chr10	67862920	67862920	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gttgaagtgacataccctatCagttttcccttcggtctgaa	8	10	2	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr10:67862920C>T	ENST00000433211.2	-	14	2146	c.1972G>A	c.(1972-1974)Gat>Aat	p.D658N	CTNNA3_ENST00000373744.4_Missense_Mutation_p.D658N|RP11-210G22.1_ENST00000608793.1_RNA	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						CATACCCTATCAGTTTTCCCT	0.498																																					p.D658N		Atlas-SNP	.											.	CTNNA3	401	.	0			c.G1972A						.						230	173	192					10																	67862920		2203	4300	6503	SO:0001583	missense	29119	exon14			CCCTATCAGTTTT	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.1972G>A	chr10.hg19:g.67862920C>T	ENSP00000389714:p.Asp658Asn	76.0	0.0		97.0	30.0	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	hg19	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.854417	0.51270	.	.	ENSG00000183230	ENST00000433211;ENST00000373744	T;T	0.42900	0.96;0.96	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000016	T	0.57373	0.2049	L	0.47716	1.5	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.54417	-0.8297	10	0.48119	T	0.1	-19.0597	15.1792	0.72941	0.0:1.0:0.0:0.0	.	658	Q9UI47	CTNA3_HUMAN	N	658	ENSP00000389714:D658N;ENSP00000362849:D658N	ENSP00000362849:D658N	D	-	1	0	CTNNA3	67532926	1.000000	0.71417	1.000000	0.80357	0.324000	0.28378	4.818000	0.62657	2.715000	0.92844	0.655000	0.94253	GAT	.	.		0.498	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		T	67862920	C	T	67862920	3	4	215	1	0	0	0	0	1	0	0	0	4016	826	29	3	735	3	CTNNA3	10	67862920	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	136466	67862920	67671827	91	30998										
PBLD	64081	hgsc.bcm.edu	37	chr10	70045070	70045073	+	Intron	DEL	CAAA	CAAA	-													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aacactagcttcgaattaggCaaataaaaaagaaattggta							TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	CAAA	CAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr10:70045070_70045073delCAAA	ENST00000358769.2	-	9	957				PBLD_ENST00000309049.4_Intron|PBLD_ENST00000336578.1_Intron|PBLD_ENST00000432941.1_Frame_Shift_Del_p.YL262fs|PBLD_ENST00000495025.2_Frame_Shift_Del_p.YL262fs	NM_022129.3	NP_071412.2	P30039	PBLD_HUMAN	phenazine biosynthesis-like protein domain containing						biosynthetic process (GO:0009058)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein import into nucleus (GO:0060392)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	isomerase activity (GO:0016853)			endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21						TCGAATTAGGCAAATAAAAAAGAA	0.392																																					p.263_264del		Atlas-INDEL	.											.	PBLD	53	.	0			c.787_790del						.																																			SO:0001627	intron_variant	64081	exon9			.	AK027673	CCDS7277.2, CCDS44413.1	10q21.3	2006-11-27			ENSG00000108187	ENSG00000108187			23301	protein-coding gene	gene with protein product	MAWD binding protein	612189				11355021	Standard	XM_005270028		Approved	MAWBP, MAWDBP, FLJ14767	uc001jns.1	P30039	OTTHUMG00000073949	ENST00000358769.2:c.754+31TTTG>-	chr10.hg19:g.70045070_70045073delCAAA		57.0	0.0		58.0	13.0	NM_001033083	A8MZJ3|C9JIM0|Q9HCC2	Frame_Shift_Del	DEL	ENST00000358769.2	hg19	CCDS7277.2																																																																																			.	.		0.392	PBLD-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048314.1	NM_022129		-	70045073	CAAA	-	70045070	6	5	215	0	1	1	0	1	0	0	0	0	11498	709	25	0		0	PBLD	10	70045070	Intron	DEL	CAAA	TCGA-DD-AAEA-01A-11D-A40R-10	2182150	70045070	65489677	92	30999										
GLUD1	2746	hgsc.bcm.edu	37	chr10	88827833	88827833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tactcacatagtgccctatgGtgctggcataggtatcagcg	11	10	2	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr10:88827833G>A	ENST00000277865.4	-	5	824	c.728C>T	c.(727-729)aCc>aTc	p.T243I	GLUD1_ENST00000537649.1_Missense_Mutation_p.T76I|GLUD1_ENST00000544149.1_Missense_Mutation_p.T110I	NM_005271.3	NP_005262.1	P00367	DHE3_HUMAN	glutamate dehydrogenase 1	243					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamine metabolic process (GO:0006541)|positive regulation of insulin secretion (GO:0032024)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|tricarboxylic acid metabolic process (GO:0072350)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|leucine binding (GO:0070728)|NAD+ binding (GO:0070403)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(11)|prostate(1)	22					Hexachlorophene(DB00756)	GTGCCCTATGGTGCTGGCATA	0.507																																					p.T243I		Atlas-SNP	.											.	GLUD1	30	.	0			c.C728T						.						75	66	69					10																	88827833		2203	4300	6503	SO:0001583	missense	2746	exon5			CCTATGGTGCTGG	M20867	CCDS7382.1	10q23.2	2010-03-17			ENSG00000148672	ENSG00000148672	1.4.1.3		4335	protein-coding gene	gene with protein product		138130		GLUD		2757358	Standard	NM_005271		Approved	GDH	uc001keh.3	P00367	OTTHUMG00000018666	ENST00000277865.4:c.728C>T	chr10.hg19:g.88827833G>A	ENSP00000277865:p.Thr243Ile	40.0	0.0		68.0	21.0	NM_005271	B3KV55|B4DGN5|Q5TBU3	Missense_Mutation	SNP	ENST00000277865.4	hg19	CCDS7382.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.927186	0.92389	.	.	ENSG00000148672	ENST00000277865;ENST00000394415;ENST00000537649;ENST00000513510;ENST00000544149	D;D;D	0.96365	-3.99;-3.9;-3.92	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.97383	0.9144	L	0.58583	1.82	0.80722	D	1	D;D	0.64830	0.972;0.994	P;D	0.66847	0.877;0.947	D	0.96848	0.9623	10	0.36615	T	0.2	.	18.8695	0.92308	0.0:0.0:1.0:0.0	.	110;243	B4DGN5;P00367	.;DHE3_HUMAN	I	243;200;76;175;110	ENSP00000277865:T243I;ENSP00000439291:T76I;ENSP00000444732:T110I	ENSP00000277865:T243I	T	-	2	0	GLUD1	88817813	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.009000	0.88606	2.479000	0.83701	0.655000	0.94253	ACC	.	.		0.507	GLUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049188.1	NM_005271		A	88827833	G	A	88827833	3	1	215	1	0	0	0	0	1	0	0	0	6484	1261	44	3	984	3	GLUD1	10	88827833	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	18782763	88827833	46706914	93	31000										
C10orf96	374355	hgsc.bcm.edu	37	chr10	118084838	118084838	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggtcggaaataaccagatgtCgtgaaaaaattaagaaagca	10	5	0	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr10:118084838C>G	ENST00000333254.3	+	3	354	c.103C>G	c.(103-105)Cgt>Ggt	p.R35G	CCDC172_ENST00000497093.1_3'UTR	NM_198515.2	NP_940917.1	P0C7W6	CC172_HUMAN	coiled-coil domain containing 172	35																	AACCAGATGTCGTGAAAAAAT	0.333																																					p.R35G		Atlas-SNP	.											.	.	.	.	0			c.C103G						.						64	70	68					10																	118084838		2203	4300	6503	SO:0001583	missense	374355	exon3			AGATGTCGTGAAA	BC044830	CCDS31291.1	10q26.11-q26.12	2012-05-31	2012-05-31	2012-05-31	ENSG00000182645	ENSG00000182645			30524	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 96"	C10orf96		12477932	Standard	NM_198515		Approved	MGC35062	uc001lck.3	P0C7W6	OTTHUMG00000019098	ENST00000333254.3:c.103C>G	chr10.hg19:g.118084838C>G	ENSP00000329860:p.Arg35Gly	227.0	0.0		292.0	100.0	NM_198515		Missense_Mutation	SNP	ENST00000333254.3	hg19	CCDS31291.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.665128	0.67700	.	.	ENSG00000182645	ENST00000333254;ENST00000423072	.	.	.	5.49	5.49	0.81192	.	0.284478	0.35067	N	0.003469	T	0.67674	0.2918	M	0.68317	2.08	0.33284	D	0.562679	D	0.63046	0.992	P	0.61003	0.882	T	0.76719	-0.2856	9	0.62326	D	0.03	-20.681	15.2337	0.73411	0.0:1.0:0.0:0.0	.	35	P0C7W6	CJ096_HUMAN	G	35	.	ENSP00000329860:R35G	R	+	1	0	C10orf96	118074828	1.000000	0.71417	0.993000	0.49108	0.833000	0.47200	2.485000	0.45250	2.733000	0.93635	0.655000	0.94253	CGT	.	.		0.333	CCDC172-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050516.2	NM_198515		G	118084838	C	G	118084838	3	3	215	1	0	0	0	0	1	0	0	0	1629	884	31	4	109	4	C10orf96	10	118084838	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	29257005	118084838	17449909	94	31001										
JAKMIP3	282973	hgsc.bcm.edu	37	chr10	133955475	133955475	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tccggcagctgaccatggagTaccaggccctgcagcgtgcc	13	15	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr10:133955475T>C	ENST00000298622.4	+	10	1663	c.1525T>C	c.(1525-1527)Tac>Cac	p.Y509H		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	509						Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		GACCATGGAGTACCAGGCCCT	0.612																																					p.Y509H		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.T1525C						.						103	66	79					10																	133955475		2201	4295	6496	SO:0001583	missense	282973	exon10			ATGGAGTACCAGG	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"neuroendocrine long coiled-coil 2"	611198	"chromosome 10 open reading frame 39", "chromosome 10 open reading frame 14"	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.1525T>C	chr10.hg19:g.133955475T>C	ENSP00000298622:p.Tyr509His	57.0	0.0		43.0	11.0	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	hg19	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.330270	0.81690	.	.	ENSG00000188385	ENST00000298622	T	0.33216	1.42	3.87	3.87	0.44632	.	0.070244	0.64402	D	0.000015	T	0.45094	0.1325	L	0.50333	1.59	0.51482	D	0.99992	D	0.76494	0.999	D	0.85130	0.997	T	0.24870	-1.0148	10	0.15499	T	0.54	-13.3685	13.151	0.59490	0.0:0.0:0.0:1.0	.	509	Q5VZ66	JKIP3_HUMAN	H	509	ENSP00000298622:Y509H	ENSP00000298622:Y509H	Y	+	1	0	JAKMIP3	133805465	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.430000	0.80321	1.772000	0.52199	0.459000	0.35465	TAC	.	.		0.612	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303		C	133955475	T	C	133955475	3	2	215	1	0	0	0	0	1	0	0	0	7951	1638	57	2	1563	2	JAKMIP3	10	133955475	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	15870637	133955475	1579272	95	31002										
TSPAN4	7106	hgsc.bcm.edu	37	chr11	862548	862548	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctctcctgttgctgtgccccAgctgggaggctgtggcgtgc	15	13	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:862548A>G	ENST00000397404.1	+	4	322		c.e4-1		TSPAN4_ENST00000525201.1_Splice_Site|TSPAN4_ENST00000397408.1_Splice_Site|TSPAN4_ENST00000397397.2_Splice_Site|TSPAN4_ENST00000397396.1_Splice_Site|TSPAN4_ENST00000409543.2_Splice_Site|TSPAN4_ENST00000346501.4_Splice_Site|TSPAN4_ENST00000409531.1_Splice_Site|TSPAN4_ENST00000397411.2_Splice_Site|TSPAN4_ENST00000397406.1_Splice_Site|RP11-1391J7.1_ENST00000506172.2_RNA	NM_001025237.1	NP_001020408.1	O14817	TSN4_HUMAN	tetraspanin 4						protein complex assembly (GO:0006461)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	antigen binding (GO:0003823)|integrin binding (GO:0005178)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)	3		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCTGTGCCCCAGCTGGGAGGC	0.677																																					.		Atlas-SNP	.											.	TSPAN4	14	.	0			c.64-2A>G						.						48	46	46					11																	862548		2201	4299	6500	SO:0001630	splice_region_variant	7106	exon3			TGCCCCAGCTGGG	AF022813	CCDS7721.1, CCDS41589.1	11p15.5	2013-02-14	2005-03-21	2005-03-21	ENSG00000214063	ENSG00000214063		"Tetraspanins"	11859	protein-coding gene	gene with protein product		602644	"transmembrane 4 superfamily member 7"	TM4SF7		9360996	Standard	XM_005253102		Approved	NAG-2, TSPAN-4, TETRASPAN	uc001lsf.1	O14817	OTTHUMG00000133305	ENST00000397404.1:c.64-1A>G	chr11.hg19:g.862548A>G		36.0	0.0		36.0	12.0	NM_001025238	Q6IAP6	Splice_Site	SNP	ENST00000397404.1	hg19	CCDS7721.1	.	.	.	.	.	.	.	.	.	.	A	15.32	2.798074	0.50208	.	.	ENSG00000214063	ENST00000397397;ENST00000397411;ENST00000397408;ENST00000530404;ENST00000397406;ENST00000409543;ENST00000397404;ENST00000346501;ENST00000409531;ENST00000527644	.	.	.	3.67	2.45	0.29901	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0231	0.42055	0.8309:0.1691:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TSPAN4	852548	1.000000	0.71417	0.999000	0.59377	0.817000	0.46193	7.213000	0.77950	1.551000	0.49450	0.459000	0.35465	.	.	.		0.677	TSPAN4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257102.2		Intron	G	862548	A	G	862548	5	3	215	1	0	0	0	0	0	0	1	0	16664	202	7	2	68	2	TSPAN4	11	862548	Splice_Site	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10		862548	134143968	96	31003										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6651061	6651061	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gcgtggccgagcgcggcgggGagccgtggtctgaggccacc	20	13	1	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:6651061G>T	ENST00000299441.3	-	11	5288	c.4877C>A	c.(4876-4878)tCc>tAc	p.S1626Y	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1626	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCGCGGCGGGGAGCCGTGGTC	0.652																																					p.S1626Y		Atlas-SNP	.											.	DCHS1	277	.	0			c.C4877A						.						43	44	44					11																	6651061		2201	4296	6497	SO:0001583	missense	8642	exon11			GGCGGGGAGCCGT	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.4877C>A	chr11.hg19:g.6651061G>T	ENSP00000299441:p.Ser1626Tyr	39.0	0.0		57.0	19.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	G	1.321	-0.599438	0.03744	.	.	ENSG00000166341	ENST00000299441	T	0.03607	3.87	5.1	5.1	0.69264	Cadherin (4);Cadherin-like (1);	0.000000	0.47455	D	0.000226	T	0.07279	0.0184	M	0.85197	2.74	0.37836	D	0.928884	P	0.44578	0.838	B	0.40329	0.326	T	0.02202	-1.1196	10	0.51188	T	0.08	.	5.9413	0.19194	0.0969:0.0:0.7112:0.1919	.	1626	Q96JQ0	PCD16_HUMAN	Y	1626	ENSP00000299441:S1626Y	ENSP00000299441:S1626Y	S	-	2	0	DCHS1	6607637	0.995000	0.38212	0.999000	0.59377	0.021000	0.10359	1.422000	0.34826	2.668000	0.90789	0.563000	0.77884	TCC	.	.		0.652	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		T	6651061	G	T	6651061	3	4	215	1	0	0	0	0	1	0	0	0	4289	1174	41	3	5063	3	DCHS1	11	6651061	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	5788513	6651061	128355455	97	31004										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6662053	6662053	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ccaggggccaggctctcagaCaccacagcatggtagcggct	13	14	1	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:6662053C>A	ENST00000299441.3	-	2	1203	c.792G>T	c.(790-792)gtG>gtT	p.V264V		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	264	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCTCTCAGACACCACAGCAT	0.612																																					p.V264V		Atlas-SNP	.											.	DCHS1	277	.	0			c.G792T						.						78	81	80					11																	6662053		2201	4296	6497	SO:0001819	synonymous_variant	8642	exon2			CTCAGACACCACA	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.792G>T	chr11.hg19:g.6662053C>A		70.0	0.0		97.0	39.0	NM_003737	O15098	Silent	SNP	ENST00000299441.3	hg19	CCDS7771.1																																																																																			.	.		0.612	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6662053	C	A	6662053	2	1	215	1	0	0	0	0	0	0	0	1	4289	465	17	3		3	DCHS1	11	6662053	Silent	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	10992	6662053	128344463	98	31005										
LUZP2	338645	hgsc.bcm.edu	37	chr11	25004794	25004794	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	actcggatgttactcccaccCaggaatattgcctctaagct	7	13	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:25004794C>A	ENST00000336930.6	+	9	786	c.720C>A	c.(718-720)ccC>ccA	p.P240P	LUZP2_ENST00000533227.1_Silent_p.P154P			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	240						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						TACTCCCACCCAGGAATATTG	0.448																																					p.P240P		Atlas-SNP	.											.	LUZP2	90	.	0			c.C720A						.						142	124	130					11																	25004794		2203	4300	6503	SO:0001819	synonymous_variant	338645	exon9			CCCACCCAGGAAT	AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.720C>A	chr11.hg19:g.25004794C>A		75.0	0.0		85.0	30.0	NM_001009909	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Silent	SNP	ENST00000336930.6	hg19	CCDS31446.1																																																																																			.	.		0.448	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909		A	25004794	C	A	25004794	2	1	215	1	0	0	0	0	0	0	0	1	9096	581	21	3		3	LUZP2	11	25004794	Silent	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	18342741	25004794	110001722	99	31006										
PRDM11	56981	hgsc.bcm.edu	37	chr11	45246226	45246226	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ccgaggcctcccttgcatctGaccctcatgaacttcccacc	6	19	2	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:45246226G>A	ENST00000530656.1	+	7	1303	c.1303G>A	c.(1303-1305)Gac>Aac	p.D435N	PRDM11_ENST00000263765.4_Missense_Mutation_p.D435N|CTD-2560E9.3_ENST00000527450.1_RNA|PRDM11_ENST00000424263.2_Missense_Mutation_p.D401N|PRDM11_ENST00000528980.1_Intron			Q9NQV5	PRD11_HUMAN	PR domain containing 11	435							methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						CCTTGCATCTGACCCTCATGA	0.542																																					p.D401N	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											.	PRDM11	53	.	0			c.G1201A						.						206	212	210					11																	45246226		2203	4299	6502	SO:0001583	missense	56981	exon7			GCATCTGACCCTC	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"PR-domain containing protein 11"						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.1303G>A	chr11.hg19:g.45246226G>A	ENSP00000435976:p.Asp435Asn	117.0	0.0		147.0	53.0	NM_001256695	Q8N9F1	Missense_Mutation	SNP	ENST00000530656.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.32	1.901876	0.33535	.	.	ENSG00000019485	ENST00000263765;ENST00000530656;ENST00000424263	T;T;T	0.25579	1.79;1.79;1.79	5.68	5.68	0.88126	.	0.091877	0.47852	D	0.000215	T	0.13884	0.0336	N	0.12182	0.205	0.09310	N	0.999996	B	0.32653	0.379	B	0.30029	0.11	T	0.17745	-1.0359	10	0.36615	T	0.2	-38.1012	10.2455	0.43339	0.1461:0.0:0.8539:0.0	.	435	Q9NQV5	PRD11_HUMAN	N	435;435;401	ENSP00000263765:D435N;ENSP00000435976:D435N;ENSP00000394314:D401N	ENSP00000263765:D435N	D	+	1	0	PRDM11	45202802	0.974000	0.33945	0.758000	0.31321	0.861000	0.49209	3.774000	0.55341	2.689000	0.91719	0.655000	0.94253	GAC	.	.		0.542	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229		A	45246226	G	A	45246226	3	1	215	1	0	0	0	0	1	0	0	0	12464	1290	45	3	1329	3	PRDM11	11	45246226	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	20241432	45246226	89760290	100	31007										
LRP4	4038	hgsc.bcm.edu	37	chr11	46897190	46897190	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gtgctgcaccggtgacaccaAtgtatgccgattggcaccat	11	12	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:46897190A>T	ENST00000378623.1	-	27	3984	c.3742T>A	c.(3742-3744)Ttg>Atg	p.L1248M	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1248					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GGTGACACCAATGTATGCCGA	0.572																																					p.L1248M		Atlas-SNP	.											.	LRP4	160	.	0			c.T3742A						.						73	55	61					11																	46897190		2201	4299	6500	SO:0001583	missense	4038	exon27			ACACCAATGTATG	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.3742T>A	chr11.hg19:g.46897190A>T	ENSP00000367888:p.Leu1248Met	70.0	0.0		75.0	22.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	A	17.37	3.372682	0.61624	.	.	ENSG00000134569	ENST00000378623	D	0.92048	-2.96	5.61	-1.59	0.08453	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000001	D	0.92993	0.7770	L	0.60957	1.885	0.46298	D	0.998974	D	0.58620	0.983	D	0.64237	0.923	D	0.90827	0.4713	10	0.72032	D	0.01	.	11.0797	0.48053	0.4069:0.0:0.5931:0.0	.	1248	O75096	LRP4_HUMAN	M	1248	ENSP00000367888:L1248M	ENSP00000367888:L1248M	L	-	1	2	LRP4	46853766	0.893000	0.30496	0.080000	0.20451	0.913000	0.54294	1.340000	0.33896	-0.327000	0.08551	0.454000	0.30748	TTG	.	.		0.572	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		T	46897190	A	T	46897190	3	4	215	1	0	0	0	0	1	0	0	0	8968	98	4	4	2023	4	LRP4	11	46897190	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	1650964	46897190	88109326	101	31008										
OR9I1	219954	hgsc.bcm.edu	37	chr11	57886845	57886845	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aacaccagaaagaggggaatCtccaatttggggtggtccat	12	8	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:57886845C>T	ENST00000302610.1	-	1	71	c.72G>A	c.(70-72)gaG>gaA	p.E24E	OR9Q1_ENST00000335397.3_Intron	NM_001005211.1	NP_001005211.1	Q8NGQ6	OR9I1_HUMAN	olfactory receptor, family 9, subfamily I, member 1	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|liver(1)|lung(15)|pancreas(1)|skin(1)|urinary_tract(1)	23		Breast(21;0.0589)				AGAGGGGAATCTCCAATTTGG	0.448																																					p.E24E		Atlas-SNP	.											.	OR9I1	53	.	0			c.G72A						.						93	85	88					11																	57886845		2201	4296	6497	SO:0001819	synonymous_variant	219954	exon1			GGGAATCTCCAAT	AB065733	CCDS31542.1	11q12.1	2012-08-09			ENSG00000172377	ENSG00000172377		"GPCR / Class A : Olfactory receptors"	14718	protein-coding gene	gene with protein product							Standard	NM_001005211		Approved		uc021qjl.1	Q8NGQ6	OTTHUMG00000167404	ENST00000302610.1:c.72G>A	chr11.hg19:g.57886845C>T		125.0	0.0		149.0	39.0	NM_001005211	Q6IFH0|Q96RA8	Silent	SNP	ENST00000302610.1	hg19	CCDS31542.1																																																																																			.	.		0.448	OR9I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394539.1	NM_001005211		T	57886845	C	T	57886845	2	4	215	1	0	0	0	0	0	0	0	1	11262	912	32	3		3	OR9I1	11	57886845	Silent	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	10989655	57886845	77119671	102	31009										
C11orf20	25858	hgsc.bcm.edu	37	chr11	64070969	64070969	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cccagaaaagtcttcctcaaTgtcatcactcaatattgcga	5	12	5	1	rs372953044		TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:64070969T>C	ENST00000328404.6	+	3	388	c.368T>C	c.(367-369)aTg>aCg	p.M123T	ESRRA_ENST00000405666.1_5'Flank|TEX40_ENST00000539943.1_Missense_Mutation_p.M81T|RP11-783K16.10_ENST00000539086.1_RNA|ESRRA_ENST00000000442.6_5'Flank|ESRRA_ENST00000406310.1_5'Flank	NM_001039496.1	NP_001034585.1	Q9NTU4	TEX40_HUMAN	testis expressed 40	123					cell differentiation (GO:0030154)|male meiosis (GO:0007140)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)											TCTTCCTCAATGTCATCACTC	0.562																																					p.M123T		Atlas-SNP	.											.	.	.	.	0			c.T368C						.	T	THR/MET	1,4059		0,1,2029	71	72	71		368	-5.6	0	11		71	0,8370		0,0,4185	no	missense	C11orf20	NM_001039496.1	81	0,1,6214	CC,CT,TT		0.0,0.0246,0.0080	benign	123/201	64070969	1,12429	2030	4185	6215	SO:0001583	missense	25858	exon3			CCTCAATGTCATC			11q13.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000219435	ENSG00000219435			19231	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 20"	C11orf20			Standard	NM_001039496		Approved	DKFZP566E164	uc009ypm.3	Q9NTU4	OTTHUMG00000167820	ENST00000328404.6:c.368T>C	chr11.hg19:g.64070969T>C	ENSP00000330877:p.Met123Thr	60.0	0.0		58.0	16.0	NM_001039496		Missense_Mutation	SNP	ENST00000328404.6	hg19		.	.	.	.	.	.	.	.	.	.	T	2.719	-0.266993	0.05754	2.46E-4	0.0	ENSG00000219435	ENST00000328404;ENST00000539943	T;T	0.41758	0.99;0.99	3.76	-5.56	0.02529	.	.	.	.	.	T	0.14743	0.0356	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.18713	-1.0328	9	0.26408	T	0.33	-0.0472	4.7875	0.13232	0.5056:0.3005:0.0:0.1939	.	123	Q9NTU4	CK020_HUMAN	T	123;81	ENSP00000330877:M123T;ENSP00000443917:M81T	ENSP00000330877:M123T	M	+	2	0	C11orf20	63827545	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.740000	0.04861	-1.151000	0.02836	-0.411000	0.06167	ATG	.	.		0.562	TEX40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039496		C	64070969	T	C	64070969	3	2	215	1	0	0	0	0	1	0	0	0	1636	1464	51	2	378	2	C11orf20	11	64070969	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	6184124	64070969	70935547	103	31010										
PGM2L1	283209	hgsc.bcm.edu	37	chr11	74049640	74049640	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttggctgtttttactcacagGcagcacctatgcaaaatggc	9	10	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:74049640G>T	ENST00000298198.4	-	13	1950	c.1639C>A	c.(1639-1641)Cct>Act	p.P547T		NM_173582.3	NP_775853.2	Q6PCE3	PGM2L_HUMAN	phosphoglucomutase 2-like 1	547					glucose metabolic process (GO:0006006)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	glucose-1,6-bisphosphate synthase activity (GO:0047933)|intramolecular transferase activity, phosphotransferases (GO:0016868)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(11;3.32e-06)					TTACTCACAGGCAGCACCTAT	0.338																																					p.P547T		Atlas-SNP	.											.	PGM2L1	59	.	0			c.C1639A						.						105	94	97					11																	74049640		2200	4293	6493	SO:0001583	missense	283209	exon13			TCACAGGCAGCAC	AB019210	CCDS8231.1	11q13.3	2008-12-01			ENSG00000165434	ENSG00000165434			20898	protein-coding gene	gene with protein product	"glucose-1,6-bisphosphate synthase"	611610				17804405	Standard	NM_173582		Approved	FLJ32029, BM32A	uc001ovb.1	Q6PCE3	OTTHUMG00000168132	ENST00000298198.4:c.1639C>A	chr11.hg19:g.74049640G>T	ENSP00000298198:p.Pro547Thr	63.0	0.0		100.0	8.0	NM_173582	Q96MQ7|Q9UIK3	Missense_Mutation	SNP	ENST00000298198.4	hg19	CCDS8231.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.531379	0.85706	.	.	ENSG00000165434	ENST00000298198	T	0.28895	1.59	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.65270	0.2675	H	0.95780	3.72	0.80722	D	1	D	0.60575	0.988	P	0.62014	0.897	T	0.72561	-0.4256	10	0.38643	T	0.18	-13.2641	17.2446	0.87023	0.0:0.0:1.0:0.0	.	547	Q6PCE3	PGM2L_HUMAN	T	547	ENSP00000298198:P547T	ENSP00000298198:P547T	P	-	1	0	PGM2L1	73727288	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.435000	0.97529	2.737000	0.93849	0.563000	0.77884	CCT	.	.		0.338	PGM2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398324.1	NM_173582		T	74049640	G	T	74049640	3	4	215	1	0	0	0	0	1	0	0	0	11808	1203	42	3	237	3	PGM2L1	11	74049640	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	9978671	74049640	60956876	104	31011										
UBE4A	9354	hgsc.bcm.edu	37	chr11	118243850	118243850	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gaggtcattgaagccttgatAttggatgaggaagttagaac	13	4	1	4			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:118243850A>G	ENST00000431736.2	+	7	864	c.792A>G	c.(790-792)atA>atG	p.I264M	UBE4A_ENST00000252108.3_Missense_Mutation_p.I257M					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		AAGCCTTGATATTGGATGAGG	0.368																																					p.I264M		Atlas-SNP	.											.	UBE4A	97	.	0			c.A792G						.						125	120	122					11																	118243850		2200	4296	6496	SO:0001583	missense	9354	exon7			CTTGATATTGGAT	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"U-box domain containing"	12499	protein-coding gene	gene with protein product		603753	"ubiquitination factor E4A (homologous to yeast UFD2)", "ubiquitination factor E4A (UFD2 homolog, yeast)"			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.792A>G	chr11.hg19:g.118243850A>G	ENSP00000387362:p.Ile264Met	96.0	0.0		101.0	35.0	NM_004788		Missense_Mutation	SNP	ENST00000431736.2	hg19	CCDS8396.1	.	.	.	.	.	.	.	.	.	.	A	11.58	1.682336	0.29872	.	.	ENSG00000110344	ENST00000252108;ENST00000431736	T;T	0.51325	0.71;0.71	6.04	1.18	0.20946	.	0.505173	0.22526	N	0.058917	T	0.24890	0.0604	N	0.14661	0.345	0.24368	N	0.994847	B;B	0.21381	0.055;0.014	B;B	0.20384	0.013;0.029	T	0.11203	-1.0597	10	0.34782	T	0.22	0.0129	5.2164	0.15344	0.4196:0.0:0.4326:0.1478	.	257;264	Q14139;Q14139-2	UBE4A_HUMAN;.	M	257;264	ENSP00000252108:I257M;ENSP00000387362:I264M	ENSP00000252108:I257M	I	+	3	3	UBE4A	117749060	0.077000	0.21312	0.048000	0.18961	0.983000	0.72400	0.398000	0.20899	0.167000	0.19631	0.460000	0.39030	ATA	.	.		0.368	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		G	118243850	A	G	118243850	3	3	215	1	0	0	0	0	1	0	0	0	16897	439	16	2	814	2	UBE4A	11	118243850	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	44194210	118243850	16762666	105	31012										
TECTA	7007	hgsc.bcm.edu	37	chr11	120996462	120996462	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttttgtgcacagctgcgtgtAtgacctgtgcagtgtgaggg	15	7	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr11:120996462A>G	ENST00000392793.1	+	8	1926	c.1655A>G	c.(1654-1656)tAt>tGt	p.Y552C	TECTA_ENST00000264037.2_Missense_Mutation_p.Y552C			O75443	TECTA_HUMAN	tectorin alpha	552					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AGCTGCGTGTATGACCTGTGC	0.572																																					p.Y552C		Atlas-SNP	.											.	TECTA	329	.	0			c.A1655G						.						117	111	113					11																	120996462		2203	4299	6502	SO:0001583	missense	7007	exon7			GCGTGTATGACCT	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1655A>G	chr11.hg19:g.120996462A>G	ENSP00000376543:p.Tyr552Cys	27.0	0.0		35.0	13.0	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	A	17.36	3.370069	0.61624	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.77620	-1.11;-1.11	4.91	3.7	0.42460	Uncharacterised domain, cysteine-rich (2);	0.069187	0.64402	D	0.000012	D	0.88829	0.6543	M	0.91972	3.26	0.41971	D	0.990752	D	0.89917	1.0	D	0.79108	0.992	D	0.90293	0.4324	10	0.62326	D	0.03	.	10.7621	0.46270	0.8579:0.0:0.0:0.1421	.	552	O75443	TECTA_HUMAN	C	552	ENSP00000376543:Y552C;ENSP00000264037:Y552C	ENSP00000264037:Y552C	Y	+	2	0	TECTA	120501672	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.948000	0.70249	1.985000	0.57927	0.460000	0.39030	TAT	.	.		0.572	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		G	120996462	A	G	120996462	3	3	215	1	0	0	0	0	1	0	0	0	15762	449	16	2	1681	2	TECTA	11	120996462	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	2752612	120996462	14010054	106	31013										
A2M	2	hgsc.bcm.edu	37	chr12	9265122	9265122	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttacctcctcattggatgaaGactttgggacctgaaataca	8	9	1	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr12:9265122G>A	ENST00000318602.7	-	3	588	c.281C>T	c.(280-282)tCt>tTt	p.S94F		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	94					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	ATTGGATGAAGACTTTGGGAC	0.498																																					p.S94F		Atlas-SNP	.											.	A2M	180	.	0			c.C281T						.						75	71	72					12																	9265122		1934	4122	6056	SO:0001583	missense	2	exon3			GATGAAGACTTTG	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.281C>T	chr12.hg19:g.9265122G>A	ENSP00000323929:p.Ser94Phe	58.0	0.0		54.0	18.0	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	hg19	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	1.778	-0.482539	0.04383	.	.	ENSG00000175899	ENST00000318602;ENST00000540099;ENST00000404455	T;T	0.08193	3.12;3.12	5.77	1.41	0.22369	.	1.202260	0.05790	N	0.610215	T	0.11623	0.0283	M	0.75264	2.295	0.09310	N	1	B	0.11235	0.004	B	0.15484	0.013	T	0.51020	-0.8758	10	0.10111	T	0.7	.	8.3819	0.32477	0.3669:0.0:0.6331:0.0	.	94	P01023	A2MG_HUMAN	F	94;109;94	ENSP00000323929:S94F;ENSP00000385710:S94F	ENSP00000323929:S94F	S	-	2	0	A2M	9156389	0.004000	0.15560	0.000000	0.03702	0.002000	0.02628	1.422000	0.34826	0.369000	0.24510	-0.137000	0.14449	TCT	.	.		0.498	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		A	9265122	G	A	9265122	3	1	215	1	0	0	0	0	1	0	0	0	4	942	33	3	4279	3	A2M	12	9265122	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10		9265122	124586773	107	31014										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41331460	41331460	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tgaaaacacatatggagccaTttatgcaaatgctgagttga	9	6	0	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr12:41331460T>C	ENST00000551295.2	+	11	1316	c.1199T>C	c.(1198-1200)aTt>aCt	p.I400T	CNTN1_ENST00000360099.3_Missense_Mutation_p.I400T|CNTN1_ENST00000348761.2_Missense_Mutation_p.I389T|CNTN1_ENST00000547702.1_Missense_Mutation_p.I400T|CNTN1_ENST00000547849.1_Missense_Mutation_p.I400T|CNTN1_ENST00000347616.1_Missense_Mutation_p.I400T	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	400	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TATGGAGCCATTTATGCAAAT	0.323																																					p.I400T		Atlas-SNP	.											.	CNTN1	207	.	0			c.T1199C						.						125	121	122					12																	41331460		2203	4300	6503	SO:0001583	missense	1272	exon11			GAGCCATTTATGC	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1199T>C	chr12.hg19:g.41331460T>C	ENSP00000447006:p.Ile400Thr	92.0	0.0		151.0	45.0	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.446066	0.63178	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;-0.19	5.26	5.26	0.73747	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.106747	0.64402	D	0.000015	T	0.70868	0.3273	L	0.41710	1.295	0.47341	D	0.999396	D;P;P	0.59767	0.986;0.851;0.877	D;B;P	0.65874	0.939;0.395;0.53	T	0.73285	-0.4031	10	0.59425	D	0.04	.	15.4901	0.75600	0.0:0.0:0.0:1.0	.	400;389;400	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	T	400;400;400;400;400;389	ENSP00000448004:I400T;ENSP00000447006:I400T;ENSP00000448653:I400T;ENSP00000325660:I400T;ENSP00000353213:I400T;ENSP00000261160:I389T	ENSP00000325660:I400T	I	+	2	0	CNTN1	39617727	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.728000	0.68531	2.132000	0.65825	0.533000	0.62120	ATT	.	.		0.323	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		C	41331460	T	C	41331460	3	2	215	1	0	0	0	0	1	0	0	0	3642	1493	52	2	1237	2	CNTN1	12	41331460	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	32066338	41331460	92520435	108	31015										
ZNF740	283337	hgsc.bcm.edu	37	chr12	53578697	53578697	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aagtctcctggcttgtgaagGcctagcaggtgtgagtttgg	15	7	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr12:53578697G>A	ENST00000416904.3	+	3	477	c.32G>A	c.(31-33)gGc>gAc	p.G11D		NM_001004304.3	NP_001004304.1	Q8NDX6	ZN740_HUMAN	zinc finger protein 740	11					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)	3						GCTTGTGAAGGCCTAGCAGGT	0.552																																					p.G11D		Atlas-SNP	.											.	ZNF740	15	.	0			c.G32A						.						43	43	43					12																	53578697		2101	4238	6339	SO:0001583	missense	283337	exon3			GTGAAGGCCTAGC	BC053557	CCDS44896.1	12q13.13	2013-01-08				ENSG00000139651		"Zinc fingers, C2H2-type"	27465	protein-coding gene	gene with protein product							Standard	NM_001004304		Approved	Zfp740	uc001scb.4	Q8NDX6		ENST00000416904.3:c.32G>A	chr12.hg19:g.53578697G>A	ENSP00000409463:p.Gly11Asp	76.0	0.0		109.0	13.0	NM_001004304	A8K9M9	Missense_Mutation	SNP	ENST00000416904.3	hg19	CCDS44896.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.347809	0.82022	.	.	ENSG00000139651	ENST00000416904	T	0.08008	3.14	4.95	4.95	0.65309	.	0.128966	0.32918	N	0.005493	T	0.05364	0.0142	N	0.08118	0	0.35686	D	0.814451	D	0.58620	0.983	B	0.40101	0.319	T	0.35895	-0.9770	10	0.87932	D	0	-7.9496	15.5834	0.76462	0.0:0.0:1.0:0.0	.	11	Q8NDX6	ZN740_HUMAN	D	11	ENSP00000409463:G11D	ENSP00000409463:G11D	G	+	2	0	ZNF740	51864964	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.237000	0.65360	2.753000	0.94483	0.455000	0.32223	GGC	.	.		0.552	ZNF740-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406890.2	NM_001004304		A	53578697	G	A	53578697	3	1	215	1	0	0	0	0	1	0	0	0	18143	1203	42	3	38	3	ZNF740	12	53578697	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	12247237	53578697	80273198	109	31016										
OR6C2	341416	hgsc.bcm.edu	37	chr12	55846217	55846217	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tagaagtctcatttactacaGtctgcattcccagattcttg	6	10	3	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr12:55846217G>T	ENST00000322678.1	+	1	220	c.220G>T	c.(220-222)Gtc>Ttc	p.V74F	RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_054105.1	NP_473446.1	Q9NZP2	OR6C2_HUMAN	olfactory receptor, family 6, subfamily C, member 2	74					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(5)|lung(8)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	23						ATTTACTACAGTCTGCATTCC	0.383																																					p.V74F		Atlas-SNP	.											.	OR6C2	39	.	0			c.G220T						.						114	117	116					12																	55846217		2203	4300	6503	SO:0001583	missense	341416	exon1			ACTACAGTCTGCA	AF179766	CCDS31824.1	12q13.2	2012-08-09				ENSG00000179695		"GPCR / Class A : Olfactory receptors"	15436	protein-coding gene	gene with protein product							Standard	NM_054105		Approved	OR6C67	uc001sgz.1	Q9NZP2	OTTHUMG00000169957	ENST00000322678.1:c.220G>T	chr12.hg19:g.55846217G>T	ENSP00000323606:p.Val74Phe	66.0	0.0		94.0	6.0	NM_054105		Missense_Mutation	SNP	ENST00000322678.1	hg19	CCDS31824.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.623632	0.28889	.	.	ENSG00000179695	ENST00000322678	T	0.01240	5.12	5.42	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.120271	0.37437	N	0.002098	T	0.02727	0.0082	M	0.84219	2.685	0.09310	N	1	B	0.19817	0.039	B	0.25506	0.061	T	0.34129	-0.9841	10	0.72032	D	0.01	.	3.9661	0.09433	0.2398:0.0:0.5878:0.1724	.	74	Q9NZP2	OR6C2_HUMAN	F	74	ENSP00000323606:V74F	ENSP00000323606:V74F	V	+	1	0	OR6C2	54132484	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.421000	0.21280	1.527000	0.49086	0.609000	0.83330	GTC	.	.		0.383	OR6C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406676.1	NM_054105		T	55846217	G	T	55846217	3	4	215	1	0	0	0	0	1	0	0	0	11200	1029	36	3	222	3	OR6C2	12	55846217	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	2267520	55846217	78005678	110	31017										
OR6C70	390327	hgsc.bcm.edu	37	chr12	55863831	55863831	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tcatgctcaacacacaatttAgaagtagaaataagaaaatt	5	6	2	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr12:55863831A>G	ENST00000327335.4	-	1	91	c.92T>C	c.(91-93)cTa>cCa	p.L31P	RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_001005499.1	NP_001005499.1	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C, member 70	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	18						CACACAATTTAGAAGTAGAAA	0.368																																					p.L31P		Atlas-SNP	.											.	OR6C70	35	.	0			c.T92C						.						48	50	49					12																	55863831		2203	4298	6501	SO:0001583	missense	390327	exon1			CAATTTAGAAGTA		CCDS31825.1	12q13.2	2013-09-23			ENSG00000184954	ENSG00000184954		"GPCR / Class A : Olfactory receptors"	31299	protein-coding gene	gene with protein product							Standard	NM_001005499		Approved		uc010spn.2	A6NIJ9	OTTHUMG00000171127	ENST00000327335.4:c.92T>C	chr12.hg19:g.55863831A>G	ENSP00000329153:p.Leu31Pro	130.0	0.0		125.0	32.0	NM_001005499		Missense_Mutation	SNP	ENST00000327335.4	hg19	CCDS31825.1	.	.	.	.	.	.	.	.	.	.	A	12.01	1.808874	0.31961	.	.	ENSG00000184954	ENST00000327335	T	0.00441	7.41	3.89	3.89	0.44902	.	0.000000	0.38492	N	0.001679	T	0.00845	0.0028	M	0.80847	2.515	0.20563	N	0.999882	P	0.52692	0.955	P	0.55871	0.786	T	0.35500	-0.9786	10	0.72032	D	0.01	.	10.0492	0.42205	0.8314:0.1686:0.0:0.0	.	31	A6NIJ9	O6C70_HUMAN	P	31	ENSP00000329153:L31P	ENSP00000329153:L31P	L	-	2	0	OR6C70	54150098	0.090000	0.21635	0.950000	0.38849	0.168000	0.22595	3.556000	0.53734	1.771000	0.52183	0.451000	0.29950	CTA	.	.		0.368	OR6C70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411820.1			G	55863831	A	G	55863831	3	3	215	1	0	0	0	0	1	0	0	0	11206	420	15	2	848	2	OR6C70	12	55863831	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	17614	55863831	77988064	111	31018										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85255460	85255460	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	taatatctgccatcaagtacCctattccataccgtccattg	4	13	2	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr12:85255460C>T	ENST00000266682.5	-	12	2685	c.2144G>A	c.(2143-2145)gGg>gAg	p.G715E	SLC6A15_ENST00000552192.1_Missense_Mutation_p.G608E|SLC6A15_ENST00000309283.7_3'UTR	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	715					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						CATCAAGTACCCTATTCCATA	0.413																																					p.G715E		Atlas-SNP	.											.	SLC6A15	159	.	0			c.G2144A						.						133	127	129					12																	85255460		2203	4300	6503	SO:0001583	missense	55117	exon12			AAGTACCCTATTC	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.2144G>A	chr12.hg19:g.85255460C>T	ENSP00000266682:p.Gly715Glu	119.0	0.0		129.0	40.0	NM_182767	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	hg19	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.175434	0.78564	.	.	ENSG00000072041	ENST00000266682;ENST00000552192;ENST00000548267	T;T	0.76578	-0.85;-1.03	5.6	5.6	0.85130	.	0.221574	0.46145	D	0.000311	D	0.85318	0.5669	L	0.48642	1.525	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.86037	0.1517	10	0.72032	D	0.01	.	19.6223	0.95663	0.0:1.0:0.0:0.0	.	715	Q9H2J7	S6A15_HUMAN	E	715;608;193	ENSP00000266682:G715E;ENSP00000450145:G608E	ENSP00000266682:G715E	G	-	2	0	SLC6A15	83779591	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.274000	0.78538	2.616000	0.88540	0.655000	0.94253	GGG	.	.		0.413	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		T	85255460	C	T	85255460	3	4	215	1	0	0	0	0	1	0	0	0	14693	623	22	3	52	3	SLC6A15	12	85255460	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	29391629	85255460	48596435	112	31019										
UTP20	27340	hgsc.bcm.edu	37	chr12	101736269	101736269	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cagtacaaaacttgttaaagCattgtgtggaccctacaagc	8	9	0	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr12:101736269C>A	ENST00000261637.4	+	33	4321	c.4147C>A	c.(4147-4149)Cat>Aat	p.H1383N		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1383					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CTTGTTAAAGCATTGTGTGGA	0.343																																					p.H1383N		Atlas-SNP	.											.	UTP20	222	.	0			c.C4147A						.						78	80	79					12																	101736269		2203	4300	6503	SO:0001583	missense	27340	exon33			TTAAAGCATTGTG	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.4147C>A	chr12.hg19:g.101736269C>A	ENSP00000261637:p.His1383Asn	82.0	0.0		80.0	4.0	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	hg19	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	C	1.247	-0.619766	0.03636	.	.	ENSG00000120800	ENST00000261637	T	0.63913	-0.07	4.89	2.79	0.32731	Armadillo-type fold (1);	0.311028	0.35615	N	0.003090	T	0.47469	0.1447	L	0.28115	0.83	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.29518	-1.0009	10	0.25106	T	0.35	-15.6791	14.857	0.70344	0.2733:0.7267:0.0:0.0	.	1383	O75691	UTP20_HUMAN	N	1383	ENSP00000261637:H1383N	ENSP00000261637:H1383N	H	+	1	0	UTP20	100260400	0.989000	0.36119	0.003000	0.11579	0.937000	0.57800	2.997000	0.49457	1.029000	0.39812	0.650000	0.86243	CAT	.	.		0.343	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		A	101736269	C	A	101736269	3	1	215	1	0	0	0	0	1	0	0	0	17114	710	25	3	4277	3	UTP20	12	101736269	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	16480809	101736269	32115626	113	31020										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112638561	112638561	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cagtatcgcaccagcacaccTtcactgcggaggtacgtttc	9	14	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr12:112638561T>A	ENST00000430131.2	-	54	8327	c.7182A>T	c.(7180-7182)gaA>gaT	p.E2394D	HECTD4_ENST00000550722.1_Missense_Mutation_p.E2670D|HECTD4_ENST00000377560.5_Missense_Mutation_p.E2644D			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2394					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CCAGCACACCTTCACTGCGGA	0.488																																					p.E2682D		Atlas-SNP	.											.	.	.	.	0			c.A8046T						.						130	127	128					12																	112638561		2078	4229	6307	SO:0001583	missense	283450	exon55			CACACCTTCACTG	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.7182A>T	chr12.hg19:g.112638561T>A	ENSP00000404379:p.Glu2394Asp	168.0	0.0		157.0	59.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.98	3.272532	0.59649	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722;ENST00000548896	T;T;T	0.23348	1.91;1.91;1.91	5.86	3.53	0.40419	.	.	.	.	.	T	0.33847	0.0877	L	0.29908	0.895	0.41902	D	0.990429	P	0.52842	0.956	D	0.65010	0.931	T	0.07083	-1.0791	9	0.87932	D	0	.	9.3388	0.38067	0.0:0.2177:0.0:0.7823	.	2394	Q9Y4D8	K0614_HUMAN	D	2644;2394;2670;25	ENSP00000366783:E2644D;ENSP00000404379:E2394D;ENSP00000449784:E2670D	ENSP00000366783:E2644D	E	-	3	2	C12orf51	111122944	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	0.738000	0.26158	0.577000	0.29470	0.528000	0.53228	GAA	.	.		0.488	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		A	112638561	T	A	112638561	3	1	215	1	0	0	0	0	1	0	0	0	1698	1606	56	4	4896	4	C12orf51	12	112638561	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	10902292	112638561	21213334	114	31021										
COQ5	84274	hgsc.bcm.edu	37	chr12	120954429	120954429	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cctttagcatctccttgttgAtgtcacacaccacgacacga	6	14	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr12:120954429A>C	ENST00000288532.6	-	3	555	c.515T>G	c.(514-516)aTc>aGc	p.I172S	COQ5_ENST00000445328.2_Intron	NM_032314.3	NP_115690.3	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase (S. cerevisiae)	172					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	methyltransferase activity (GO:0008168)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(3)	20	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTCCTTGTTGATGTCACACAC	0.473																																					p.I172S		Atlas-SNP	.											.	COQ5	26	.	0			c.T515G						.						290	283	285					12																	120954429		2203	4300	6503	SO:0001583	missense	84274	exon3			TTGTTGATGTCAC	AK057777	CCDS31912.1	12q24.31	2011-09-16	2006-04-04		ENSG00000110871	ENSG00000110871	2.1.1.201		28722	protein-coding gene	gene with protein product	"2-methoxy-6-polyprenyl-1,4-benzoquinol methylase"		"coenzyme Q5 homolog, methyltransferase (yeast)"				Standard	NM_032314		Approved	MGC4767	uc001tyn.3	Q5HYK3	OTTHUMG00000169375	ENST00000288532.6:c.515T>G	chr12.hg19:g.120954429A>C	ENSP00000288532:p.Ile172Ser	85.0	0.0		108.0	29.0	NM_032314	B4DEJ4|Q32Q28|Q53HH0|Q96LV1|Q9BSP8	Missense_Mutation	SNP	ENST00000288532.6	hg19	CCDS31912.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.725950	0.89298	.	.	ENSG00000110871	ENST00000288532;ENST00000302223;ENST00000552443;ENST00000547943;ENST00000551769	T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4	5.41	5.41	0.78517	.	0.045311	0.85682	D	0.000000	D	0.84170	0.5413	M	0.88310	2.945	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	D	0.87505	0.2436	10	0.87932	D	0	.	15.112	0.72365	1.0:0.0:0.0:0.0	.	172	Q5HYK3	COQ5_HUMAN	S	172;120;91;122;91	ENSP00000288532:I172S;ENSP00000449863:I91S;ENSP00000449874:I122S;ENSP00000450001:I91S	ENSP00000288532:I172S	I	-	2	0	COQ5	119438812	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.983000	0.93477	2.051000	0.60960	0.455000	0.32223	ATC	.	.		0.473	COQ5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403767.2	NM_032314		C	120954429	A	C	120954429	3	2	215	1	0	0	0	0	1	0	0	0	3750	333	12	5	488	5	COQ5	12	120954429	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	8315868	120954429	12897466	115	31022										
ZMYM5	9205	hgsc.bcm.edu	37	chr13	20425899	20425899	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttttagttccaggaagtcccCattcgataaaacaggaagac	8	9	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr13:20425899C>A	ENST00000337963.4	-	3	686	c.422G>T	c.(421-423)tGg>tTg	p.W141L	ZMYM5_ENST00000382907.4_Missense_Mutation_p.W141L|ZMYM5_ENST00000382905.4_Missense_Mutation_p.W141L	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	141						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		AGGAAGTCCCCATTCGATAAA	0.373																																					p.W141L		Atlas-SNP	.											.	ZMYM5	73	.	0			c.G422T						.						82	87	85					13																	20425899		2203	4300	6503	SO:0001583	missense	9205	exon3			AGTCCCCATTCGA	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.422G>T	chr13.hg19:g.20425899C>A	ENSP00000337034:p.Trp141Leu	134.0	0.0		156.0	49.0	NM_001039650	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	hg19		.	.	.	.	.	.	.	.	.	.	C	15.10	2.733197	0.48939	.	.	ENSG00000132950	ENST00000337963;ENST00000502168;ENST00000382907;ENST00000382905	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	4.41	4.41	0.53225	.	.	.	.	.	T	0.40956	0.1138	M	0.62723	1.935	0.33357	D	0.571851	P;P;D	0.57571	0.948;0.944;0.98	P;P;P	0.52957	0.666;0.714;0.714	T	0.54296	-0.8315	9	0.45353	T	0.12	-2.8604	17.5374	0.87835	0.0:1.0:0.0:0.0	.	141;141;141	Q9UJ78;Q9UJ78-2;Q9UJ78-1	ZMYM5_HUMAN;.;.	L	141;131;141;141	ENSP00000337034:W141L;ENSP00000445779:W131L;ENSP00000372364:W141L;ENSP00000372361:W141L	ENSP00000337034:W141L	W	-	2	0	ZMYM5	19323899	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	5.131000	0.64751	2.468000	0.83385	0.491000	0.48974	TGG	.	.		0.373	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		A	20425899	C	A	20425899	3	1	215	1	0	0	0	0	1	0	0	0	17718	595	21	3	1722	3	ZMYM5	13	20425899	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10		20425899	94743979	116	31023										
MRPS31	10240	hgsc.bcm.edu	37	chr13	41345190	41345190	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tgagtagcataatcgcagccGctgatgtctccgggcttcca	11	12	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr13:41345190G>A	ENST00000323563.6	-	1	119	c.83C>T	c.(82-84)gCg>gTg	p.A28V		NM_005830.3	NP_005821.2	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31	28						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)		AATCGCAGCCGCTGATGTCTC	0.602																																					p.A28V		Atlas-SNP	.											.	MRPS31	30	.	0			c.C83T						.						80	76	77					13																	41345190		2203	4300	6503	SO:0001583	missense	10240	exon1			GCAGCCGCTGATG	Z68747	CCDS9372.1	13q14.11	2012-09-13			ENSG00000102738	ENSG00000102738		"Mitochondrial ribosomal proteins / small subunits"	16632	protein-coding gene	gene with protein product		611992				11279123, 8567980	Standard	NM_005830		Approved	IMOGN38	uc001uxm.4	Q92665	OTTHUMG00000016777	ENST00000323563.6:c.83C>T	chr13.hg19:g.41345190G>A	ENSP00000315397:p.Ala28Val	125.0	0.0		68.0	39.0	NM_005830	B2RCS3|Q5VYC8|Q8WTV8	Missense_Mutation	SNP	ENST00000323563.6	hg19	CCDS9372.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.494276	0.26774	.	.	ENSG00000102738	ENST00000323563	T	0.29142	1.58	4.24	1.24	0.21308	.	2.088160	0.02261	N	0.067555	T	0.18635	0.0447	N	0.20986	0.625	0.09310	N	1	B	0.27117	0.168	B	0.16722	0.016	T	0.12734	-1.0536	10	0.19590	T	0.45	.	3.0438	0.06147	0.2311:0.0:0.5576:0.2113	.	28	Q92665	RT31_HUMAN	V	28	ENSP00000315397:A28V	ENSP00000315397:A28V	A	-	2	0	MRPS31	40243190	0.000000	0.05858	0.001000	0.08648	0.100000	0.18952	-0.127000	0.10547	0.524000	0.28502	0.563000	0.77884	GCG	.	.		0.602	MRPS31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044640.2			A	41345190	G	A	41345190	3	1	215	1	0	0	0	0	1	0	0	0	9850	1087	38	1	1132	1	MRPS31	13	41345190	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	20919291	41345190	73824688	117	31024										
GPR183	1880	hgsc.bcm.edu	37	chr13	99948232	99948232	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	atttttttcctgttttgaacAatgacgaccaaggctagtaa	7	7	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr13:99948232A>T	ENST00000376414.4	-	2	251	c.168T>A	c.(166-168)atT>atA	p.I56I	UBAC2_ENST00000403766.3_Intron|UBAC2_ENST00000376440.2_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	56					G-protein coupled receptor signaling pathway (GO:0007186)|humoral immune response (GO:0006959)|immune response (GO:0006955)|mature B cell differentiation involved in immune response (GO:0002313)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|oxysterol binding (GO:0008142)			cervix(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	23						TGTTTTGAACAATGACGACCA	0.433																																					p.I56I		Atlas-SNP	.											.	GPR183	38	.	0			c.T168A						.						96	94	95					13																	99948232		2203	4300	6503	SO:0001819	synonymous_variant	1880	exon2			TTGAACAATGACG	L08177	CCDS9492.1	13q32.3	2012-08-21	2008-07-21	2008-07-21	ENSG00000169508	ENSG00000169508		"GPCR / Class A : Orphans"	3128	protein-coding gene	gene with protein product	"EBV-induced G-protein coupled receptor 2"	605741	"Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor)"	EBI2		8383238	Standard	NM_004951		Approved		uc001vog.3	P32249	OTTHUMG00000017263	ENST00000376414.4:c.168T>A	chr13.hg19:g.99948232A>T		189.0	0.0		191.0	54.0	NM_004951	B2R8N5|Q53F99|Q5JUH7	Silent	SNP	ENST00000376414.4	hg19	CCDS9492.1																																																																																			.	.		0.433	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045582.2	NM_004951		T	99948232	A	T	99948232	2	4	215	1	0	0	0	0	0	0	0	1	6686	126	5	4		4	GPR183	13	99948232	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	58603042	99948232	15221646	118	31025										
NPAS3	64067	hgsc.bcm.edu	37	chr14	34269098	34269098	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	acccggacagccgcgacagcGacgacagcttcgagcactcg	12	16	0	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr14:34269098G>A	ENST00000356141.4	+	12	1585	c.1585G>A	c.(1585-1587)Gac>Aac	p.D529N	NPAS3_ENST00000551492.1_Missense_Mutation_p.D534N|NPAS3_ENST00000346562.2_Missense_Mutation_p.D497N|NPAS3_ENST00000548645.1_Missense_Mutation_p.D499N|NPAS3_ENST00000357798.5_Missense_Mutation_p.D516N			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	529					locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		CCGCGACAGCGACGACAGCTT	0.642																																					p.D529N		Atlas-SNP	.											.	NPAS3	266	.	0			c.G1585A						.						55	57	56					14																	34269098		2203	4300	6503	SO:0001583	missense	64067	exon12			GACAGCGACGACA	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.1585G>A	chr14.hg19:g.34269098G>A	ENSP00000348460:p.Asp529Asn	67.0	0.0		83.0	28.0	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.916481	0.73098	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.71222	-0.55;3.11;3.12;3.12;3.11;2.98	5.17	4.27	0.50696	.	0.103202	0.64402	D	0.000005	T	0.53690	0.1812	N	0.14661	0.345	0.80722	D	1	P;P;P;P	0.47106	0.89;0.824;0.89;0.89	B;B;B;B	0.39217	0.294;0.154;0.294;0.294	T	0.56968	-0.7891	10	0.39692	T	0.17	.	15.6653	0.77225	0.0:0.1379:0.8621:0.0	.	499;529;497;516	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	N	503;534;497;499;529;516	ENSP00000448373:D503N;ENSP00000450392:D534N;ENSP00000319610:D497N;ENSP00000448916:D499N;ENSP00000348460:D529N;ENSP00000350446:D516N	ENSP00000319610:D497N	D	+	1	0	NPAS3	33338849	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.413000	0.97351	1.148000	0.42385	0.555000	0.69702	GAC	.	.		0.642	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			A	34269098	G	A	34269098	3	1	215	1	0	0	0	0	1	0	0	0	10573	1058	37	1	1686	1	NPAS3	14	34269098	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10		34269098	73080442	119	31026										
DAAM1	23002	hgsc.bcm.edu	37	chr14	59819293	59819293	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cattgacctattggaggaacAtaaacacgaactggatcgga	10	8	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr14:59819293A>G	ENST00000395125.1	+	18	2263	c.2240A>G	c.(2239-2241)cAt>cGt	p.H747R	DAAM1_ENST00000360909.3_Missense_Mutation_p.H737R|DAAM1_ENST00000553966.1_3'UTR|DAAM1_ENST00000351081.1_Missense_Mutation_p.H747R	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	747	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		TTGGAGGAACATAAACACGAA	0.398																																					p.H747R		Atlas-SNP	.											.	DAAM1	95	.	0			c.A2240G						.						131	119	123					14																	59819293		2203	4300	6503	SO:0001583	missense	23002	exon18			AGGAACATAAACA	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.2240A>G	chr14.hg19:g.59819293A>G	ENSP00000378557:p.His747Arg	113.0	0.0		146.0	47.0	NM_014992	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	hg19	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	A	14.91	2.677026	0.47886	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000358498;ENST00000395125	T;T;T	0.17213	2.29;2.29;2.29	6.04	6.04	0.98038	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.45377	0.1339	M	0.84219	2.685	0.80722	D	1	D;P	0.76494	0.999;0.885	D;P	0.70487	0.969;0.833	T	0.37842	-0.9688	10	0.35671	T	0.21	.	16.5885	0.84745	1.0:0.0:0.0:0.0	.	737;747	Q9Y4D1-2;Q9Y4D1	.;DAAM1_HUMAN	R	737;747;747;747	ENSP00000354162:H737R;ENSP00000247170:H747R;ENSP00000378557:H747R	ENSP00000247170:H747R	H	+	2	0	DAAM1	58889046	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	9.317000	0.96327	2.317000	0.78254	0.460000	0.39030	CAT	.	.		0.398	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		G	59819293	A	G	59819293	3	3	215	1	0	0	0	0	1	0	0	0	4217	217	8	2	2310	2	DAAM1	14	59819293	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	25550195	59819293	47530247	120	31027										
C14orf148	122945	hgsc.bcm.edu	37	chr14	77861072	77861072	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggtaaggtggtcttggagaaCaggactacttgagagatgct	15	5	1	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr14:77861072C>G	ENST00000380835.2	-	6	1148	c.982G>C	c.(982-984)Gtt>Ctt	p.V328L		NM_001113475.2	NP_001106946.1	Q6NXP6	NXRD1_HUMAN	NADP-dependent oxidoreductase domain containing 1	328					proline biosynthetic process (GO:0006561)		pyrroline-5-carboxylate reductase activity (GO:0004735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9						TCTTGGAGAACAGGACTACTT	0.453																																					p.V328L		Atlas-SNP	.											.	NOXRED1	23	.	0			c.G982C						.						137	123	127					14																	77861072		1568	3582	5150	SO:0001583	missense	122945	exon6			GGAGAACAGGACT	AK057371	CCDS45142.1	14q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000165555	ENSG00000165555			20487	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 148"	C14orf148			Standard	NM_001113475		Approved	FLJ32809	uc001xtr.3	Q6NXP6	OTTHUMG00000171554	ENST00000380835.2:c.982G>C	chr14.hg19:g.77861072C>G	ENSP00000370215:p.Val328Leu	151.0	0.0		186.0	59.0	NM_001113475	B3KQ47|O95435	Missense_Mutation	SNP	ENST00000380835.2	hg19	CCDS45142.1	.	.	.	.	.	.	.	.	.	.	C	4.173	0.030630	0.08101	.	.	ENSG00000165555	ENST00000380835	T	0.53423	0.62	5.14	-2.29	0.06805	.	1.143370	0.06369	N	0.713148	T	0.19327	0.0464	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16719	-1.0393	10	0.10377	T	0.69	0.1743	0.9	0.01272	0.3249:0.3176:0.1111:0.2464	.	328	Q6NXP6	NXRD1_HUMAN	L	328	ENSP00000370215:V328L	ENSP00000370215:V328L	V	-	1	0	C14orf148	76930825	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	-1.667000	0.01961	-0.136000	0.11475	-0.257000	0.10917	GTT	.	.		0.453	NOXRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414103.1	NM_138791		G	77861072	C	G	77861072	3	3	215	1	0	0	0	0	1	0	0	0	1753	478	17	4	101	4	C14orf148	14	77861072	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	18041779	77861072	29488468	121	31028										
GALC	2581	hgsc.bcm.edu	37	chr14	88431941	88431941	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tcccataaggcaactgttcaTagtaactagccactaaattc	5	11	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr14:88431941T>C	ENST00000261304.2	-	9	1047	c.941A>G	c.(940-942)tAt>tGt	p.Y314C	GALC_ENST00000393569.2_Missense_Mutation_p.Y288C|GALC_ENST00000393568.4_Missense_Mutation_p.Y291C|GALC_ENST00000544807.2_Missense_Mutation_p.Y258C	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	314			Y -> C (in GLD). {ECO:0000269|PubMed:8940268}.		carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CAACTGTTCATAGTAACTAGC	0.423																																					p.Y314C		Atlas-SNP	.											.	GALC	48	.	0			c.A941G	GRCh37	CM960684	GALC	M		.						54	60	58					14																	88431941		1891	4125	6016	SO:0001583	missense	2581	exon9			TGTTCATAGTAAC	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"Krabbe disease"	606890	"galactosylceramidase (Krabbe disease)"				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.941A>G	chr14.hg19:g.88431941T>C	ENSP00000261304:p.Tyr314Cys	138.0	0.0		145.0	39.0	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Missense_Mutation	SNP	ENST00000261304.2	hg19	CCDS9878.2	.	.	.	.	.	.	.	.	.	.	T	24.9	4.585800	0.86748	.	.	ENSG00000054983	ENST00000261304;ENST00000544807;ENST00000393569;ENST00000539620;ENST00000393568;ENST00000445021	D;D;D;D	0.95103	-3.61;-3.61;-3.61;-3.61	5.77	5.77	0.91146	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.97748	0.9261	M	0.91406	3.205	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;1.0;0.999;1.0	D	0.98440	1.0586	10	0.62326	D	0.03	-22.0506	15.3757	0.74602	0.0:0.0:0.0:1.0	.	258;291;288;314;314	P54803-5;E7EPA4;P54803-4;G3XAI6;P54803	.;.;.;.;GALC_HUMAN	C	314;258;288;103;291;314	ENSP00000261304:Y314C;ENSP00000437513:Y258C;ENSP00000377199:Y288C;ENSP00000377198:Y291C	ENSP00000261304:Y314C	Y	-	2	0	GALC	87501694	1.000000	0.71417	0.983000	0.44433	0.995000	0.86356	7.658000	0.83755	2.326000	0.78906	0.533000	0.62120	TAT	.	.		0.423	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2			C	88431941	T	C	88431941	3	2	215	1	0	0	0	0	1	0	0	0	6209	1406	49	2	1215	2	GALC	14	88431941	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	10570869	88431941	18917599	122	31029										
MARK3	4140	hgsc.bcm.edu	37	chr14	103969371	103969371	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggacgccaataactgcgactAtgagcagagggagcgcttct	13	10	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr14:103969371A>G	ENST00000429436.2	+	18	2579	c.2069A>G	c.(2068-2070)tAt>tGt	p.Y690C	MARK3_ENST00000561071.1_3'UTR|MARK3_ENST00000416682.2_Missense_Mutation_p.Y689C|MARK3_ENST00000440884.3_Missense_Mutation_p.Y596C|MARK3_ENST00000553942.1_Missense_Mutation_p.Y681C|MARK3_ENST00000335102.5_Missense_Mutation_p.Y713C|MARK3_ENST00000303622.9_Missense_Mutation_p.Y666C|MARK3_ENST00000216288.7_Missense_Mutation_p.Y650C	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	690						plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			AACTGCGACTATGAGCAGAGG	0.552																																					p.Y690C		Atlas-SNP	.											.	MARK3	86	.	0			c.A2069G						.						71	72	72					14																	103969371		2059	4215	6274	SO:0001583	missense	4140	exon18			GCGACTATGAGCA	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.2069A>G	chr14.hg19:g.103969371A>G	ENSP00000411397:p.Tyr690Cys	113.0	0.0		138.0	45.0	NM_001128918	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	hg19	CCDS45165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.78|15.78	2.934998|2.934998	0.52866|0.52866	.|.	.|.	ENSG00000075413|ENSG00000075413	ENST00000554627|ENST00000335102;ENST00000411530;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942;ENST00000556744	.|T;T;T;T;T;T;T;T	.|0.60299	.|0.2;0.2;0.2;0.2;0.2;0.2;0.2;0.2	6.17|6.17	5.03|5.03	0.67393|0.67393	.|Kinase-associated KA1 (2);	.|0.104403	.|0.64402	.|D	.|0.000002	T|T	0.73345|0.73345	0.3575|0.3575	M|M	0.72479|0.72479	2.2|2.2	0.80722|0.80722	D|D	1|1	.|B;D;P;D;B;B;P;B;B	.|0.89917	.|0.377;1.0;0.519;0.996;0.077;0.097;0.948;0.175;0.377	.|B;D;B;P;B;B;B;B;B	.|0.91635	.|0.289;0.999;0.432;0.9;0.099;0.317;0.41;0.16;0.289	T|T	0.73920|0.73920	-0.3830|-0.3830	5|10	.|0.48119	.|T	.|0.1	.|.	12.4531|12.4531	0.55688|0.55688	0.935:0.0:0.065:0.0|0.935:0.0:0.065:0.0	.|.	.|697;268;689;399;650;690;596;681;666	.|P27448-7;A2SY06;P27448-2;B4DKN1;P27448-6;P27448;Q86TT8;P27448-4;P27448-3	.|.;.;.;.;.;MARK3_HUMAN;.;.;.	V|C	442|713;382;596;689;690;666;650;681;268	.|ENSP00000335347:Y713C;ENSP00000402104:Y596C;ENSP00000408092:Y689C;ENSP00000411397:Y690C;ENSP00000303698:Y666C;ENSP00000216288:Y650C;ENSP00000450772:Y681C;ENSP00000451623:Y268C	.|ENSP00000216288:Y681C	M|Y	+|+	1|2	0|0	MARK3|MARK3	103039124|103039124	1.000000|1.000000	0.71417|0.71417	0.783000|0.783000	0.31826|0.31826	0.574000|0.574000	0.36063|0.36063	9.220000|9.220000	0.95180|0.95180	1.147000|1.147000	0.42369|0.42369	-0.290000|-0.290000	0.09829|0.09829	ATG|TAT	.	.		0.552	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		G	103969371	A	G	103969371	3	3	215	1	0	0	0	0	1	0	0	0	9323	449	16	2	2139	2	MARK3	14	103969371	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	15537430	103969371	3380169	123	31030										
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23889515	23889515	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	atcagatcctccctgacacaGttgcctttcataaagatgag	7	11	2	4			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr15:23889515G>T	ENST00000532292.1	-	1	1660	c.1566C>A	c.(1564-1566)aaC>aaA	p.N522K		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	405					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		CCCTGACACAGTTGCCTTTCA	0.463																																					p.N1125K		Atlas-SNP	.											.	MAGEL2	108	.	0			c.C3375A						.						70	66	67					15																	23889515		1898	4123	6021	SO:0001583	missense	54551	exon1			GACACAGTTGCCT	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.1566C>A	chr15.hg19:g.23889515G>T	ENSP00000433433:p.Asn522Lys	79.0	0.0		139.0	37.0	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.67	1.414862	0.25465	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.57	-1.54	0.08584	.	.	.	.	.	T	0.59676	0.2211	M	0.86573	2.825	0.09310	N	1	.	.	.	.	.	.	T	0.57051	-0.7877	5	.	.	.	.	8.8628	0.35267	0.4645:0.0:0.5355:0.0	.	.	.	.	N	554	.	.	T	-	2	0	MAGEL2	21440608	0.035000	0.19736	0.368000	0.25939	0.259000	0.26198	-0.805000	0.04530	-0.156000	0.11079	-0.600000	0.04104	ACT	.	.		0.463	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		T	23889515	G	T	23889515	3	4	215	1	0	0	0	0	1	0	0	0	9198	1020	36	3	378	3	MAGEL2	15	23889515	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10		23889515	78641877	124	31031										
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42106909	42106909	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	caaggtgtactcggctctgtAtcattcttcctgcgtctgga	10	11	4	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr15:42106909A>G	ENST00000456763.2	+	11	1356	c.1160A>G	c.(1159-1161)tAt>tGt	p.Y387C	MAPKBP1_ENST00000514566.1_Missense_Mutation_p.Y381C|MAPKBP1_ENST00000457542.2_Missense_Mutation_p.Y381C|MAPKBP1_ENST00000221214.6_Intron|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.Y269C	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	387										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		TCGGCTCTGTATCATTCTTCC	0.512																																					p.Y387C		Atlas-SNP	.											.	MAPKBP1	120	.	0			c.A1160G						.						252	225	234					15																	42106909		2203	4300	6503	SO:0001583	missense	23005	exon11			CTCTGTATCATTC	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.1160A>G	chr15.hg19:g.42106909A>G	ENSP00000393099:p.Tyr387Cys	113.0	0.0		165.0	24.0	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	hg19	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	a	27.8	4.863431	0.91511	.	.	ENSG00000137802	ENST00000457542;ENST00000260357;ENST00000456763;ENST00000514566	T;T;T;T	0.54675	5.04;0.56;5.03;5.03	6.06	6.06	0.98353	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.74512	0.3726	M	0.79926	2.475	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;D	0.91635	0.999;0.994;0.997;0.992	T	0.76143	-0.3067	10	0.49607	T	0.09	-11.8615	16.6165	0.84917	1.0:0.0:0.0:0.0	.	269;381;387;381	F8WC21;O60336-2;O60336;O60336-6	.;.;MABP1_HUMAN;.	C	381;269;387;381	ENSP00000397570:Y381C;ENSP00000260357:Y269C;ENSP00000393099:Y387C;ENSP00000426154:Y381C	ENSP00000260357:Y269C	Y	+	2	0	MAPKBP1	39894201	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.501000	0.81600	2.323000	0.78572	0.529000	0.55759	TAT	.	.		0.512	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		G	42106909	A	G	42106909	3	3	215	1	0	0	0	0	1	0	0	0	9301	449	16	2	1198	2	MAPKBP1	15	42106909	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	18217394	42106909	60424483	125	31032										
USP8	9101	hgsc.bcm.edu	37	chr15	50757317	50757317	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ttgattataatggatgctcgAagaatgcaggattatcagga	11	4	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr15:50757317A>T	ENST00000396444.3	+	7	953	c.615A>T	c.(613-615)cgA>cgT	p.R205R	USP8_ENST00000425032.3_Silent_p.R128R|USP8_ENST00000307179.4_Silent_p.R205R|USP8_ENST00000433963.1_Silent_p.R205R|RNA5SP395_ENST00000516567.1_RNA	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	205	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		TGGATGCTCGAAGAATGCAGG	0.393																																					p.R205R		Atlas-SNP	.											.	USP8	90	.	0			c.A615T						.						116	93	101					15																	50757317		2196	4294	6490	SO:0001819	synonymous_variant	9101	exon7			TGCTCGAAGAATG	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"Ubiquitin-specific peptidases"	12631	protein-coding gene	gene with protein product		603158	"ubiquitin specific protease 8"			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.615A>T	chr15.hg19:g.50757317A>T		151.0	0.0		199.0	17.0	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Silent	SNP	ENST00000396444.3	hg19	CCDS10137.1																																																																																			.	.		0.393	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		T	50757317	A	T	50757317	2	4	215	1	0	0	0	0	0	0	0	1	17104	233	9	4		4	USP8	15	50757317	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	8650408	50757317	51774075	126	31033										
TRPM7	54822	hgsc.bcm.edu	37	chr15	50901794	50901794	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ataccgtgttaaaccagaatTttacaattggtgcatgataa	7	6	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr15:50901794T>A	ENST00000313478.7	-	19	2845	c.2564A>T	c.(2563-2565)aAa>aTa	p.K855I	TRPM7_ENST00000560955.1_Missense_Mutation_p.K855I	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	855					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		AAACCAGAATTTTACAATTGG	0.333																																					p.K855I		Atlas-SNP	.											.	TRPM7	145	.	0			c.A2564T						.						161	147	152					15																	50901794		1825	4070	5895	SO:0001583	missense	54822	exon19			CAGAATTTTACAA	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.2564A>T	chr15.hg19:g.50901794T>A	ENSP00000320239:p.Lys855Ile	228.0	0.0		337.0	89.0	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	hg19	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.716401	0.89205	.	.	ENSG00000092439	ENST00000313478	T	0.80653	-1.4	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.87819	0.6273	L	0.58510	1.815	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.89060	0.3462	10	0.87932	D	0	-22.1064	15.4966	0.75658	0.0:0.0:0.0:1.0	.	855	Q96QT4	TRPM7_HUMAN	I	855	ENSP00000320239:K855I	ENSP00000320239:K855I	K	-	2	0	TRPM7	48689086	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.073000	0.62155	0.383000	0.25322	AAA	.	.		0.333	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		A	50901794	T	A	50901794	3	1	215	1	0	0	0	0	1	0	0	0	16606	1841	64	4	3117	4	TRPM7	15	50901794	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	144477	50901794	51629598	127	31034										
SNUPN	10073	hgsc.bcm.edu	37	chr15	75890985	75890985	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	agggagtgcttccggggctgTagtgggtctgtttgtggtag	19	5	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr15:75890985T>C	ENST00000564644.1	-	10	1375	c.797A>G	c.(796-798)tAc>tGc	p.Y266C	CTD-2323K18.1_ENST00000568707.1_RNA|SNUPN_ENST00000567134.1_Missense_Mutation_p.Y266C|SNUPN_ENST00000564675.1_Missense_Mutation_p.Y266C|SNUPN_ENST00000371091.5_Missense_Mutation_p.Y308C|SNUPN_ENST00000308588.5_Missense_Mutation_p.Y266C			O95149	SPN1_HUMAN	snurportin 1	266	Necessary for binding to the m3G-cap structure.				gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein import into nucleus (GO:0006606)|RNA metabolic process (GO:0016070)|snRNA import into nucleus (GO:0061015)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear pore (GO:0005643)	protein transporter activity (GO:0008565)|RNA cap binding (GO:0000339)			endometrium(2)|large_intestine(3)|lung(2)|pancreas(1)	8						TCCGGGGCTGTAGTGGGTCTG	0.562																																					p.Y266C		Atlas-SNP	.											.	SNUPN	26	.	0			c.A797G						.						97	110	106					15																	75890985		2197	4292	6489	SO:0001583	missense	10073	exon9			GGGCTGTAGTGGG	AF039029	CCDS10281.1	15q24.2	2008-02-05	2006-07-14	2006-07-14	ENSG00000169371	ENSG00000169371			14245	protein-coding gene	gene with protein product		607902	"RNA, U transporter 1"	RNUT1		9670026	Standard	NM_005701		Approved	SNURPORTIN-1, Snurportin1	uc002bas.3	O95149	OTTHUMG00000142833	ENST00000564644.1:c.797A>G	chr15.hg19:g.75890985T>C	ENSP00000454852:p.Tyr266Cys	68.0	0.0		70.0	15.0	NM_001042581	A6NE34|A8K0B0|D3DW76	Missense_Mutation	SNP	ENST00000564644.1	hg19	CCDS10281.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.567615	0.86439	.	.	ENSG00000169371	ENST00000308588;ENST00000371091	D;D	0.89746	-2.56;-2.56	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.94905	0.8353	M	0.85630	2.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95502	0.8578	10	0.87932	D	0	-21.612	15.5478	0.76123	0.0:0.0:0.0:1.0	.	308;266	C9K0X5;O95149	.;SPN1_HUMAN	C	266;308	ENSP00000309831:Y266C;ENSP00000360132:Y308C	ENSP00000309831:Y266C	Y	-	2	0	SNUPN	73678040	1.000000	0.71417	0.985000	0.45067	0.991000	0.79684	7.501000	0.81600	2.268000	0.75426	0.454000	0.30748	TAC	.	.		0.562	SNUPN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420332.1	NM_005701		C	75890985	T	C	75890985	3	2	215	1	0	0	0	0	1	0	0	0	14892	1638	57	2	289	2	SNUPN	15	75890985	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	24989191	75890985	26640407	128	31035										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88678352	88678352	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctggaaagggctccttgaggAagtggccattgatggtctgg	16	7	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr15:88678352A>T	ENST00000360948.2	-	9	1345	c.1184T>A	c.(1183-1185)tTc>tAc	p.F395Y	NTRK3_ENST00000355254.2_Missense_Mutation_p.F395Y|NTRK3_ENST00000394480.2_Missense_Mutation_p.F395Y|NTRK3_ENST00000317501.3_Missense_Mutation_p.F395Y|NTRK3_ENST00000357724.2_Missense_Mutation_p.F395Y|NTRK3_ENST00000558676.1_Missense_Mutation_p.F395Y|NTRK3_ENST00000557856.1_Missense_Mutation_p.F395Y|NTRK3_ENST00000542733.2_Missense_Mutation_p.F297Y|NTRK3_ENST00000540489.2_Missense_Mutation_p.F395Y	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	395					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CTCCTTGAGGAAGTGGCCATT	0.532			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.F395Y		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.T1184A						.						208	190	196					15																	88678352		2201	4299	6500	SO:0001583	missense	4916	exon10			TTGAGGAAGTGGC	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1184T>A	chr15.hg19:g.88678352A>T	ENSP00000354207:p.Phe395Tyr	146.0	0.0		159.0	42.0	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.960831	0.92791	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.75260	-0.92;-0.87;-0.88;-0.92;-0.8;-0.13;-0.13	5.28	5.28	0.74379	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.84511	0.5488	M	0.65677	2.01	0.58432	D	0.999994	D;D;D;D;D;D	0.89917	0.999;0.994;1.0;1.0;0.997;1.0	D;D;D;D;D;D	0.91635	0.993;0.965;0.999;0.995;0.986;0.998	D	0.86353	0.1712	10	0.87932	D	0	.	14.4111	0.67115	1.0:0.0:0.0:0.0	.	297;395;395;395;395;395	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	Y	395;395;395;395;297;395;395	ENSP00000377990:F395Y;ENSP00000354207:F395Y;ENSP00000350356:F395Y;ENSP00000347397:F395Y;ENSP00000437773:F297Y;ENSP00000444673:F395Y;ENSP00000318328:F395Y	ENSP00000318328:F395Y	F	-	2	0	NTRK3	86479356	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.907000	0.92634	1.997000	0.58415	0.460000	0.39030	TTC	.	.		0.532	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				T	88678352	A	T	88678352	3	4	215	1	0	0	0	0	1	0	0	0	10717	246	9	4	1641	4	NTRK3	15	88678352	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	12787367	88678352	13853040	129	31036										
RCCD1	91433	hgsc.bcm.edu	37	chr15	91500546	91500546	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ccgaggccgaaggggaagacGatccggccggtgaggcccag	18	12	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr15:91500546G>C	ENST00000394258.2	+	3	572	c.370G>C	c.(370-372)Gat>Cat	p.D124H	RCCD1_ENST00000555155.1_Missense_Mutation_p.D124H|RCCD1_ENST00000556774.1_Intron|AC068831.6_ENST00000553321.1_RNA|RCCD1_ENST00000556618.1_Missense_Mutation_p.D124H	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	124						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			AGGGGAAGACGATCCGGCCGG	0.726																																					p.D124H		Atlas-SNP	.											.	RCCD1	9	.	0			c.G370C						.						10	10	10					15																	91500546		2007	3968	5975	SO:0001583	missense	91433	exon3			GAAGACGATCCGG		CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.370G>C	chr15.hg19:g.91500546G>C	ENSP00000377801:p.Asp124His	79.0	0.0		63.0	21.0	NM_001017919	B2RTP9|Q29RX6	Missense_Mutation	SNP	ENST00000394258.2	hg19	CCDS32333.1	.	.	.	.	.	.	.	.	.	.	G	10.11	1.260445	0.23051	.	.	ENSG00000166965	ENST00000394258;ENST00000555155;ENST00000556618	T;T;T	0.38401	1.14;1.14;1.14	3.54	1.57	0.23409	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (1);	3.285740	0.01446	N	0.015310	T	0.22044	0.0531	N	0.08118	0	0.09310	N	1	P;P	0.44816	0.844;0.759	B;B	0.39805	0.31;0.164	T	0.18618	-1.0331	10	0.56958	D	0.05	.	6.0224	0.19636	0.1106:0.1926:0.6968:0.0	.	124;124	G3V2I3;A6NED2	.;RCCD1_HUMAN	H	124	ENSP00000377801:D124H;ENSP00000450678:D124H;ENSP00000451963:D124H	ENSP00000377801:D124H	D	+	1	0	RCCD1	89301550	0.004000	0.15560	0.000000	0.03702	0.004000	0.04260	0.665000	0.25083	0.294000	0.22547	-0.266000	0.10368	GAT	.	.		0.726	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544		C	91500546	G	C	91500546	3	2	215	1	0	0	0	0	1	0	0	0	13190	1058	37	4	376	4	RCCD1	15	91500546	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	2822194	91500546	11030846	130	31037										
AXIN1	8312	hgsc.bcm.edu	37	chr16	396667	396667	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gcttcctgaagccagtgcagGcaaaccagaagtccagcaag	11	12	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr16:396667G>T	ENST00000262320.3	-	2	730	c.359C>A	c.(358-360)gCc>gAc	p.A120D	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Missense_Mutation_p.A120D	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	120	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GCCAGTGCAGGCAAACCAGAA	0.532											OREG0003698	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.A120D		Atlas-SNP	.											.	AXIN1	290	.	0			c.C359A						.						56	53	54					16																	396667		2203	4300	6503	SO:0001583	missense	8312	exon2			GTGCAGGCAAACC	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.359C>A	chr16.hg19:g.396667G>T	ENSP00000262320:p.Ala120Asp	62.0	0.0	588	37.0	15.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	G	19.77	3.889594	0.72524	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	T;T	0.02015	4.5;4.5	5.75	5.75	0.90469	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.23054	0.0557	H	0.95611	3.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.17289	-1.0374	10	0.87932	D	0	-22.6722	19.9396	0.97154	0.0:0.0:1.0:0.0	.	120;120	O15169-2;O15169	.;AXIN1_HUMAN	D	120	ENSP00000262320:A120D;ENSP00000346935:A120D	ENSP00000262320:A120D	A	-	2	0	AXIN1	336668	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.892000	0.87324	2.720000	0.93068	0.655000	0.94253	GCC	.	.		0.532	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			T	396667	G	T	396667	3	4	215	1	0	0	0	0	1	0	0	0	1236	1203	42	3	2269	3	AXIN1	16	396667	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10		396667	89958086	131	31038										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24818081	24818081	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aaaaagggccatcaccaataAatgctttcagcaacttccct	5	12	2	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr16:24818081A>G	ENST00000395799.3	+	17	4645	c.4516A>G	c.(4516-4518)Aat>Gat	p.N1506D	CTD-2515A14.1_ENST00000568895.1_RNA|TNRC6A_ENST00000432286.2_5'Flank|TNRC6A_ENST00000315183.7_Missense_Mutation_p.N1457D	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1506					cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ATCACCAATAAATGCTTTCAG	0.502																																					p.N1506D		Atlas-SNP	.											.	TNRC6A	171	.	0			c.A4516G						.						137	117	123					16																	24818081		2197	4300	6497	SO:0001583	missense	27327	exon17			CCAATAAATGCTT	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.4516A>G	chr16.hg19:g.24818081A>G	ENSP00000379144:p.Asn1506Asp	139.0	0.0		129.0	35.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.96|15.96	2.985928|2.985928	0.53934|0.53934	.|.	.|.	ENSG00000090905|ENSG00000090905	ENST00000450465|ENST00000315183;ENST00000395799	.|T;T	.|0.12984	.|2.67;2.63	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	.|0.166777	.|0.56097	.|D	.|0.000029	T|T	0.16257|0.16257	0.0391|0.0391	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	.|B;B;B;P	.|0.39782	.|0.277;0.227;0.13;0.688	.|B;B;B;B	.|0.33750	.|0.049;0.138;0.055;0.169	T|T	0.01444|0.01444	-1.1353|-1.1353	5|10	.|0.39692	.|T	.|0.17	-5.2564|-5.2564	16.8222|16.8222	0.85835|0.85835	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|173;645;1457;1506	.|B3KSX2;C9JA83;Q8NDV7-6;Q8NDV7	.|.;.;.;TNR6A_HUMAN	R|D	396|1457;1506	.|ENSP00000326900:N1457D;ENSP00000379144:N1506D	.|ENSP00000326900:N1457D	K|N	+|+	2|1	0|0	TNRC6A|TNRC6A	24725582|24725582	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.647000|5.647000	0.67923|0.67923	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	AAA|AAT	.	.		0.502	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24818081	A	G	24818081	3	3	215	1	0	0	0	0	1	0	0	0	16355	14	1	2	4582	2	TNRC6A	16	24818081	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	24421414	24818081	65536672	132	31039										
ZNF668	79759	hgsc.bcm.edu	37	chr16	31072498	31072498	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	catgcttgcgcaagtcgctgGcactcaagaaggccttggga	13	11	1	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr16:31072498G>C	ENST00000538906.1	-	3	2535	c.1751C>G	c.(1750-1752)gCc>gGc	p.A584G	ZNF668_ENST00000535577.1_Missense_Mutation_p.A584G|ZNF668_ENST00000539836.3_Missense_Mutation_p.A607G|ZNF668_ENST00000394983.2_Missense_Mutation_p.A584G|ZNF668_ENST00000426488.2_Missense_Mutation_p.A607G|ZNF668_ENST00000300849.4_Missense_Mutation_p.A584G|ZNF668_ENST00000417110.2_5'Flank	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	584					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CAAGTCGCTGGCACTCAAGAA	0.637																																					p.A607G	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C1820G						.						62	64	64					16																	31072498		2197	4300	6497	SO:0001583	missense	79759	exon4			TCGCTGGCACTCA		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"Zinc fingers, C2H2-type"	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.1751C>G	chr16.hg19:g.31072498G>C	ENSP00000440149:p.Ala584Gly	100.0	0.0		95.0	21.0	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Missense_Mutation	SNP	ENST00000538906.1	hg19	CCDS10701.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023194	0.54683	.	.	ENSG00000167394	ENST00000539836;ENST00000535577;ENST00000538906;ENST00000394983;ENST00000300849	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	4.93	4.93	0.64822	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000001	T	0.25754	0.0627	N	0.14661	0.345	0.46954	D	0.999264	D	0.56968	0.978	P	0.50617	0.646	T	0.01621	-1.1310	10	0.28530	T	0.3	-22.282	12.8872	0.58051	0.0:0.164:0.836:0.0	.	584	Q96K58	ZN668_HUMAN	G	607;584;584;584;584	ENSP00000442573:A607G;ENSP00000441349:A584G;ENSP00000440149:A584G;ENSP00000378434:A584G;ENSP00000300849:A584G	ENSP00000300849:A584G	A	-	2	0	ZNF668	30979999	0.877000	0.30153	1.000000	0.80357	0.985000	0.73830	3.882000	0.56160	2.581000	0.87130	0.561000	0.74099	GCC	.	.		0.637	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706		C	31072498	G	C	31072498	3	2	215	1	0	0	0	0	1	0	0	0	18090	1203	42	4	112	4	ZNF668	16	31072498	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	6254417	31072498	59282255	133	31040										
GPT2	84706	hgsc.bcm.edu	37	chr16	46960942	46960942	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggcagagggaaggcacttacCacttcaggtatgacttcctc	11	11	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr16:46960942C>T	ENST00000340124.4	+	11	1586	c.1474C>T	c.(1474-1476)Cac>Tac	p.H492Y	GPT2_ENST00000440783.2_Missense_Mutation_p.H392Y	NM_133443.2	NP_597700.1	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase (alanine aminotransferase) 2	492					2-oxoglutarate metabolic process (GO:0006103)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|L-alanine metabolic process (GO:0042851)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)	p.H492N(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|Phenelzine(DB00780)	AGGCACTTACCACTTCAGGTA	0.542																																					p.H492Y		Atlas-SNP	.											GPT2,colon,carcinoma,0,1	GPT2	40	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1474T						.						100	88	92					16																	46960942		2203	4300	6503	SO:0001583	missense	84706	exon11			ACTTACCACTTCA		CCDS10725.1, CCDS45478.1	16q12.1	2008-02-05			ENSG00000166123	ENSG00000166123	2.6.1.2		18062	protein-coding gene	gene with protein product		138210					Standard	NM_133443		Approved	ALT2	uc002eel.3	Q8TD30	OTTHUMG00000132541	ENST00000340124.4:c.1474C>T	chr16.hg19:g.46960942C>T	ENSP00000345282:p.His492Tyr	54.0	0.0		76.0	18.0	NM_133443	Q8N9E2	Missense_Mutation	SNP	ENST00000340124.4	hg19	CCDS10725.1	.	.	.	.	.	.	.	.	.	.	C	31	5.059648	0.93846	.	.	ENSG00000166123	ENST00000340124;ENST00000440783	D;T	0.90444	-2.67;2.06	4.94	4.94	0.65067	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.96673	0.8914	M	0.93420	3.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.97619	1.0134	10	0.72032	D	0.01	.	18.5083	0.90905	0.0:1.0:0.0:0.0	.	392;492	Q8TD30-2;Q8TD30	.;ALAT2_HUMAN	Y	492;392	ENSP00000345282:H492Y;ENSP00000413804:H392Y	ENSP00000345282:H492Y	H	+	1	0	GPT2	45518443	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.759000	0.85235	2.456000	0.83038	0.655000	0.94253	CAC	.	.		0.542	GPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255741.2			T	46960942	C	T	46960942	3	4	215	1	0	0	0	0	1	0	0	0	6747	594	21	3	1512	3	GPT2	16	46960942	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	15888444	46960942	43393811	134	31041										
CHD9	80205	hgsc.bcm.edu	37	chr16	53265378	53265378	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tacgttgaagtagacagagtAttagaagtctctttttgtga	10	4	1	5			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr16:53265378A>G	ENST00000398510.3	+	8	2421	c.2334A>G	c.(2332-2334)gtA>gtG	p.V778V	CHD9_ENST00000564845.1_Silent_p.V778V|CHD9_ENST00000566029.1_Silent_p.V778V|CHD9_ENST00000447540.1_Silent_p.V778V			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	778	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TAGACAGAGTATTAGAAGTCT	0.299																																					p.V778V		Atlas-SNP	.											CHD9,NS,carcinoma,0,1	CHD9	203	.	0			c.A2334G						.						70	70	70					16																	53265378		1794	4066	5860	SO:0001819	synonymous_variant	80205	exon9			CAGAGTATTAGAA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.2334A>G	chr16.hg19:g.53265378A>G		257.0	0.0		300.0	98.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	hg19																																																																																				.	.		0.299	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		G	53265378	A	G	53265378	2	3	215	1	0	0	0	0	0	0	0	1	3334	436	16	2		2	CHD9	16	53265378	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	6304436	53265378	37089375	135	31042										
SLC38A8	146167	hgsc.bcm.edu	37	chr16	84075664	84075664	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gctcccagcgcggacttcatGaggatgaagacagcgcccat	12	13	1	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr16:84075664G>A	ENST00000299709.3	-	1	98	c.99C>T	c.(97-99)ctC>ctT	p.L33L	RNA5SP432_ENST00000362480.1_RNA	NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	33					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						CGGACTTCATGAGGATGAAGA	0.642																																					p.L33L		Atlas-SNP	.											.	SLC38A8	60	.	0			c.C99T						.						92	102	99					16																	84075664		2200	4300	6500	SO:0001819	synonymous_variant	146167	exon1			CTTCATGAGGATG		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"Solute carriers"	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.99C>T	chr16.hg19:g.84075664G>A		60.0	0.0		53.0	6.0	NM_001080442		Silent	SNP	ENST00000299709.3	hg19	CCDS32495.1																																																																																			.	.		0.642	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442		A	84075664	G	A	84075664	2	1	215	1	0	0	0	0	0	0	0	1	14625	1277	45	3		3	SLC38A8	16	84075664	Silent	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	30810286	84075664	6279089	136	31043										
ZCCHC14	23174	hgsc.bcm.edu	37	chr16	87445967	87445967	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aggaagtttgcccagaaatgGcagaatcagcaggaacagat	12	7	1	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr16:87445967G>A	ENST00000268616.4	-	12	2166	c.1949C>T	c.(1948-1950)gCc>gTc	p.A650V		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	650							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		CCCAGAAATGGCAGAATCAGC	0.562																																					p.A650V		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.C1949T						.						98	112	107					16																	87445967		2198	4300	6498	SO:0001583	missense	23174	exon12			GAAATGGCAGAAT	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"Zinc fingers, CCHC domain containing", "Sterile alpha motif (SAM) domain containing"	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.1949C>T	chr16.hg19:g.87445967G>A	ENSP00000268616:p.Ala650Val	105.0	0.0		89.0	21.0	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Missense_Mutation	SNP	ENST00000268616.4	hg19	CCDS10961.1	.	.	.	.	.	.	.	.	.	.	G	6.699	0.497709	0.12762	.	.	ENSG00000140948	ENST00000268616	T	0.21543	2.0	5.83	4.88	0.63580	.	0.142961	0.47093	N	0.000254	T	0.15219	0.0367	L	0.29908	0.895	0.09310	N	0.999999	B;B	0.31318	0.319;0.087	B;B	0.23419	0.046;0.02	T	0.12656	-1.0539	10	0.38643	T	0.18	-21.7537	13.1254	0.59351	0.0738:0.0:0.9262:0.0	.	650;650	Q8WYQ9-2;Q8WYQ9	.;ZCH14_HUMAN	V	650	ENSP00000268616:A650V	ENSP00000268616:A650V	A	-	2	0	ZCCHC14	86003468	0.970000	0.33590	0.052000	0.19188	0.096000	0.18686	4.847000	0.62867	1.464000	0.47987	0.563000	0.77884	GCC	.	.		0.562	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144		A	87445967	G	A	87445967	3	1	215	1	0	0	0	0	1	0	0	0	17598	1203	42	3	908	3	ZCCHC14	16	87445967	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	3370303	87445967	2908786	137	31044										
TP53	7157	hgsc.bcm.edu	37	chr17	7578265	7578265	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gcaaatttccttccactcggAtaagatgctgaggaggggcc	12	10	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:7578265A>C	ENST00000269305.4	-	6	773	c.584T>G	c.(583-585)aTc>aGc	p.I195S	TP53_ENST00000359597.4_Missense_Mutation_p.I195S|TP53_ENST00000413465.2_Missense_Mutation_p.I195S|TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.I195S|TP53_ENST00000455263.2_Missense_Mutation_p.I195S|TP53_ENST00000420246.2_Missense_Mutation_p.I195S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	195	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		I -> F (in sporadic cancers; somatic mutation).|I -> L (in a sporadic cancer; somatic mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation).|I -> T (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:9450901}.|I -> V (in a sporadic cancer; somatic mutation).|I -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I195T(69)|p.I195N(12)|p.I195S(10)|p.0?(8)|p.I195fs*14(5)|p.?(5)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.I102S(2)|p.I102T(2)|p.I63T(2)|p.I63S(2)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.I102fs*14(1)|p.I195fs*12(1)|p.I195fs*50(1)|p.I195_G199delIRVEG(1)|p.P98_E105>Q(1)|p.I63fs*14(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTCCACTCGGATAAGATGCTG	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.I195S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,5	TP53	33396	.	134	Substitution - Missense(99)|Whole gene deletion(8)|Insertion - Frameshift(7)|Deletion - In frame(6)|Complex - deletion inframe(6)|Unknown(5)|Deletion - Frameshift(2)|Complex - frameshift(1)	ovary(37)|breast(21)|large_intestine(18)|lung(10)|central_nervous_system(8)|biliary_tract(6)|haematopoietic_and_lymphoid_tissue(5)|skin(5)|stomach(4)|oesophagus(4)|bone(4)|endometrium(3)|urinary_tract(3)|upper_aerodigestive_tract(2)|liver(2)|pancreas(2)	c.T584G						.						100	89	93					17																	7578265		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ACTCGGATAAGAT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.584T>G	chr17.hg19:g.7578265A>C	ENSP00000269305:p.Ile195Ser	144.0	0.0		118.0	59.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.439821	0.43326	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99825	-6.97;-6.97;-6.97;-6.97;-6.97;-6.97;-6.97;-6.97	5.41	3.21	0.36854	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.103171	0.64402	D	0.000004	D	0.99743	0.9898	M	0.85099	2.735	0.54753	D	0.999986	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;0.999;0.999;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.996;0.979;0.991;0.996;0.997;0.996	D	0.98579	1.0649	10	0.87932	D	0	-18.4587	8.2743	0.31864	0.8356:0.0:0.1644:0.0	.	156;195;195;102;195;195;195	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	S	195;195;195;195;195;195;184;102;63;102;63	ENSP00000410739:I195S;ENSP00000352610:I195S;ENSP00000269305:I195S;ENSP00000398846:I195S;ENSP00000391127:I195S;ENSP00000391478:I195S;ENSP00000425104:I63S;ENSP00000423862:I102S	ENSP00000269305:I195S	I	-	2	0	TP53	7518990	1.000000	0.71417	0.946000	0.38457	0.026000	0.11368	9.287000	0.95975	0.456000	0.26937	-0.256000	0.11100	ATC	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578265	A	C	7578265	3	2	215	1	0	0	0	0	1	0	0	0	16396	333	12	5	710	5	TP53	17	7578265	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10		7578265	73616945	138	31045										
ALOX12B	242	hgsc.bcm.edu	37	chr17	7984083	7984083	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	atgagaattgggaatcccggAatatagccattccacctgtg	10	9	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:7984083A>C	ENST00000319144.4	-	5	803	c.543T>G	c.(541-543)atT>atG	p.I181M	AC129492.6_ENST00000399413.3_3'UTR|ALOX12B_ENST00000577351.1_5'Flank	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	181	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						GGAATCCCGGAATATAGCCAT	0.597										Multiple Myeloma(8;0.094)	OREG0024153	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I181M		Atlas-SNP	.											.	ALOX12B	61	.	0			c.T543G						.						101	109	106					17																	7984083		2203	4300	6503	SO:0001583	missense	242	exon5			TCCCGGAATATAG	AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"Arachidonate lipoxygenases"	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.543T>G	chr17.hg19:g.7984083A>C	ENSP00000315167:p.Ile181Met	64.0	0.0	645	62.0	32.0	NM_001139		Missense_Mutation	SNP	ENST00000319144.4	hg19	CCDS11129.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.720914	0.30503	.	.	ENSG00000179477	ENST00000319144	D	0.90133	-2.62	4.34	0.926	0.19430	Lipoxygenase, C-terminal (2);	0.437153	0.25208	N	0.032339	D	0.83064	0.5173	L	0.44542	1.39	0.19575	N	0.999968	B	0.32010	0.351	B	0.33042	0.157	T	0.71269	-0.4643	10	0.37606	T	0.19	-10.3684	3.866	0.09016	0.3923:0.1977:0.41:0.0	.	181	O75342	LX12B_HUMAN	M	181	ENSP00000315167:I181M	ENSP00000315167:I181M	I	-	3	3	ALOX12B	7924808	0.292000	0.24362	0.965000	0.40720	0.902000	0.53008	0.007000	0.13174	0.071000	0.16664	0.454000	0.30748	ATT	.	.		0.597	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3			C	7984083	A	C	7984083	3	2	215	1	0	0	0	0	1	0	0	0	537	242	9	5	1606	5	ALOX12B	17	7984083	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	405818	7984083	73211127	139	31046										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11778398	11778398	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	atgccaccattctcatcaacTgtgagcgctggccactcatg	8	14	3	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:11778398T>A	ENST00000262442.4	+	53	10443	c.10375T>A	c.(10375-10377)Tgt>Agt	p.C3459S	RP11-628O18.1_ENST00000579621.1_RNA|DNAH9_ENST00000454412.2_Missense_Mutation_p.C3459S	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3459	AAA 5. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TCTCATCAACTGTGAGCGCTG	0.542																																					p.C3459S		Atlas-SNP	.											.	DNAH9	695	.	0			c.T10375A						.						94	83	87					17																	11778398		2203	4300	6503	SO:0001583	missense	1770	exon53			ATCAACTGTGAGC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10375T>A	chr17.hg19:g.11778398T>A	ENSP00000262442:p.Cys3459Ser	83.0	0.0		53.0	23.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.973915	0.53720	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.44083	0.93;0.93	4.66	3.52	0.40303	.	0.172266	0.52532	D	0.000072	T	0.15782	0.0380	N	0.02379	-0.575	0.80722	D	1	B	0.16396	0.017	B	0.19148	0.024	T	0.11717	-1.0576	10	0.07325	T	0.83	.	10.7101	0.45977	0.1422:0.0:0.0:0.8578	.	3459	Q9NYC9	DYH9_HUMAN	S	3459;3459;2041	ENSP00000262442:C3459S;ENSP00000414874:C3459S	ENSP00000262442:C3459S	C	+	1	0	DNAH9	11719123	1.000000	0.71417	0.981000	0.43875	0.945000	0.59286	3.920000	0.56446	1.965000	0.57142	0.533000	0.62120	TGT	.	.		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11778398	T	A	11778398	3	1	215	1	0	0	0	0	1	0	0	0	4610	1580	55	4	10585	4	DNAH9	17	11778398	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	3794315	11778398	69416812	140	31047										
SSH2	85464	hgsc.bcm.edu	37	chr17	27958047	27958047	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	agaactagtcaattcaagtcCtgccctggggagcaaatact	9	10	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:27958047C>T	ENST00000269033.3	-	15	4235	c.4084G>A	c.(4084-4086)Gga>Aga	p.G1362R	SSH2_ENST00000540801.1_Missense_Mutation_p.G1389R|RP11-68I3.2_ENST00000581474.1_RNA	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	1362					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AATTCAAGTCCTGCCCTGGGG	0.557																																					p.G1362R		Atlas-SNP	.											.	SSH2	107	.	0			c.G4084A						.						94	83	87					17																	27958047		2203	4300	6503	SO:0001583	missense	85464	exon15			CAAGTCCTGCCCT	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.4084G>A	chr17.hg19:g.27958047C>T	ENSP00000269033:p.Gly1362Arg	83.0	0.0		112.0	41.0	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	hg19	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.232523	0.39498	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.08720	3.06;3.06	6.17	5.2	0.72013	.	0.731959	0.13508	N	0.382719	T	0.08758	0.0217	L	0.38531	1.155	0.80722	D	1	B;B	0.12630	0.006;0.004	B;B	0.13407	0.009;0.004	T	0.20405	-1.0276	10	0.16420	T	0.52	-5.1077	14.6875	0.69059	0.0:0.9302:0.0:0.0698	.	1389;1362	F5H527;Q76I76	.;SSH2_HUMAN	R	1362;1389	ENSP00000269033:G1362R;ENSP00000444743:G1389R	ENSP00000269033:G1362R	G	-	1	0	SSH2	24982173	0.098000	0.21812	0.919000	0.36401	0.962000	0.63368	2.589000	0.46145	1.598000	0.50083	0.655000	0.94253	GGA	.	.		0.557	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		T	27958047	C	T	27958047	3	4	215	1	0	0	0	0	1	0	0	0	15200	690	24	3	191	3	SSH2	17	27958047	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	16179649	27958047	53237163	141	31048										
SLFN11	91607	hgsc.bcm.edu	37	chr17	33679955	33679955	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggaggccactgcaatccaagTggctggtctgaaagtaatcc	12	10	1	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:33679955T>C	ENST00000394566.1	-	7	2398	c.2126A>G	c.(2125-2127)cAc>cGc	p.H709R	SLFN11_ENST00000308377.4_Missense_Mutation_p.H709R	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	709					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GCAATCCAAGTGGCTGGTCTG	0.488																																					p.H709R		Atlas-SNP	.											.	SLFN11	112	.	0			c.A2126G						.						115	120	118					17																	33679955		2203	4300	6503	SO:0001583	missense	91607	exon5			TCCAAGTGGCTGG	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.2126A>G	chr17.hg19:g.33679955T>C	ENSP00000378067:p.His709Arg	96.0	0.0		107.0	34.0	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	hg19	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	t	17.15	3.315021	0.60524	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	D;D	0.86497	-2.13;-2.13	4.0	4.0	0.46444	.	0.000000	0.50627	D	0.000103	D	0.92358	0.7575	M	0.88377	2.95	0.29677	N	0.841994	D	0.59357	0.985	P	0.60415	0.874	D	0.88843	0.3314	10	0.62326	D	0.03	.	9.4902	0.38955	0.0:0.0:0.0:1.0	.	709	Q7Z7L1	SLN11_HUMAN	R	709	ENSP00000312402:H709R;ENSP00000378067:H709R	ENSP00000312402:H709R	H	-	2	0	SLFN11	30704068	1.000000	0.71417	0.936000	0.37596	0.930000	0.56654	4.974000	0.63771	1.799000	0.52666	0.533000	0.62120	CAC	.	.		0.488	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		C	33679955	T	C	33679955	3	2	215	1	0	0	0	0	1	0	0	0	14748	1696	59	2	583	2	SLFN11	17	33679955	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	5721908	33679955	47515255	142	31049										
CCL16	6360	hgsc.bcm.edu	37	chr17	34304751	34304751	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gttggtgcagacttctcggtTcctcttggtgacgaagctgc	13	10	2	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:34304751T>G	ENST00000293275.3	-	3	289	c.214A>C	c.(214-216)Aac>Cac	p.N72H		NM_004590.2	NP_004581.1	O15467	CCL16_HUMAN	chemokine (C-C motif) ligand 16	72					cell chemotaxis (GO:0060326)|cell communication (GO:0007154)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive chemotaxis (GO:0050918)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)			endometrium(1)|lung(2)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACTTCTCGGTTCCTCTTGGTG	0.567																																					p.N72H		Atlas-SNP	.											.	CCL16	7	.	0			c.A214C						.						168	154	159					17																	34304751		2203	4300	6503	SO:0001583	missense	6360	exon3			CTCGGTTCCTCTT	AB007454	CCDS11303.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000161573	ENSG00000275152		"Chemokine ligands", "Endogenous ligands"	10614	protein-coding gene	gene with protein product		601394	"small inducible cytokine subfamily A (Cys-Cys), member 16"	SCYA16		8661057	Standard	NM_004590		Approved	NCC-4, SCYL4, LEC, HCC-4, LMC, LCC-1, CKb12, Mtn-1	uc002hkl.3	O15467	OTTHUMG00000188402	ENST00000293275.3:c.214A>C	chr17.hg19:g.34304751T>G	ENSP00000293275:p.Asn72His	125.0	0.0		147.0	67.0	NM_004590	Q4KKU0	Missense_Mutation	SNP	ENST00000293275.3	hg19	CCDS11303.1	.	.	.	.	.	.	.	.	.	.	T	13.79	2.342817	0.41498	.	.	ENSG00000161573	ENST00000293275	T	0.04119	3.7	5.14	2.78	0.32641	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.846463	0.10107	N	0.715244	T	0.05914	0.0154	L	0.55481	1.735	0.09310	N	1	B	0.17038	0.02	B	0.17979	0.02	T	0.38265	-0.9669	10	0.66056	D	0.02	.	3.218	0.06705	0.2064:0.1117:0.0:0.682	.	72	O15467	CCL16_HUMAN	H	72	ENSP00000293275:N72H	ENSP00000293275:N72H	N	-	1	0	CCL16	31328864	0.001000	0.12720	0.004000	0.12327	0.737000	0.42083	0.909000	0.28558	0.920000	0.36970	0.379000	0.24179	AAC	.	.		0.567	CCL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256579.1	NM_004590		G	34304751	T	G	34304751	3	3	215	1	0	0	0	0	1	0	0	0	2889	1783	62	5	152	5	CCL16	17	34304751	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	624796	34304751	46890459	143	31050										
G6PC	2538	hgsc.bcm.edu	37	chr17	41059553	41059553	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cctttagggagcccctctggCcatgccatgggcacagcagg	13	14	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:41059553C>G	ENST00000253801.2	+	3	433	c.354C>G	c.(352-354)ggC>ggG	p.G118G	G6PC_ENST00000585489.1_Silent_p.G118G|G6PC_ENST00000592383.1_Intron	NM_000151.3	NP_000142.2	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit	118					carbohydrate metabolic process (GO:0005975)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|hexose transport (GO:0008645)|multicellular organism growth (GO:0035264)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)|urate metabolic process (GO:0046415)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)|phosphate ion binding (GO:0042301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCCCCTCTGGCCATGCCATGG	0.507																																					p.G118G		Atlas-SNP	.											.	G6PC	48	.	0			c.C354G						.						58	49	52					17																	41059553		2203	4300	6503	SO:0001819	synonymous_variant	2538	exon3			CTCTGGCCATGCC	U01120	CCDS11446.1, CCDS59291.1	17q21	2014-09-17	2006-06-28			ENSG00000131482	3.1.3.9		4056	protein-coding gene	gene with protein product	"glycogen storage disease type I, von Gierke disease"	613742	"glucose-6-phosphatase, catalytic (glycogen storage disease type I, von Gierke disease)"	G6PT		7774924	Standard	NM_000151		Approved	GSD1a	uc002icb.2	P35575		ENST00000253801.2:c.354C>G	chr17.hg19:g.41059553C>G		67.0	0.0		83.0	31.0	NM_000151	A1L4C0|B4E1C3|K7EL82	Silent	SNP	ENST00000253801.2	hg19	CCDS11446.1																																																																																			.	.		0.507	G6PC-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452451.1	NM_000151		G	41059553	C	G	41059553	2	3	215	1	0	0	0	0	0	0	0	1	6151	726	26	4		4	G6PC	17	41059553	Silent	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	6754802	41059553	40135657	144	31051										
FMNL1	752	hgsc.bcm.edu	37	chr17	43318781	43318781	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gaatcgaccgccatggggccCtccaggcgtcccccagagcc	12	18	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:43318781C>A	ENST00000331495.3	+	14	1701	c.1365C>A	c.(1363-1365)ccC>ccA	p.P455P	FMNL1_ENST00000587489.1_Silent_p.P33P|CTD-2020K17.3_ENST00000393507.2_RNA|CTD-2020K17.3_ENST00000587534.1_RNA|FMNL1_ENST00000328118.3_Silent_p.P455P	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	455	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.			P -> A (in Ref. 1; AAP32476, 3; AAL99920 and 4; AAH73988). {ECO:0000305}.	actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						CCATGGGGCCCTCCAGGCGTC	0.672																																					p.P455P	GBM(164;1247 1997 8702 11086 51972)	Atlas-SNP	.											.	FMNL1	78	.	0			c.C1365A						.						7	6	6					17																	43318781		2121	4180	6301	SO:0001819	synonymous_variant	752	exon14			GGGGCCCTCCAGG	AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"formin-like"	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.1365C>A	chr17.hg19:g.43318781C>A		58.0	0.0		89.0	29.0	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Silent	SNP	ENST00000331495.3	hg19	CCDS11497.1																																																																																			.	.		0.672	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892		A	43318781	C	A	43318781	2	1	215	1	0	0	0	0	0	0	0	1	5959	668	24	3		3	FMNL1	17	43318781	Silent	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	2259228	43318781	37876429	145	31052										
TRIM37	4591	hgsc.bcm.edu	37	chr17	57089748	57089748	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gctgtaactctccagtttcaGaattattttccaaatcagtc	5	10	3	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:57089748G>T	ENST00000262294.7	-	22	2895	c.2636C>A	c.(2635-2637)tCt>tAt	p.S879Y	TRIM37_ENST00000393066.3_Missense_Mutation_p.S879Y|TRIM37_ENST00000393065.2_Missense_Mutation_p.S845Y|TRIM37_ENST00000376149.3_Missense_Mutation_p.S757Y	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	879					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					TCCAGTTTCAGAATTATTTTC	0.393									Mulibrey Nanism																												p.S879Y		Atlas-SNP	.											.	TRIM37	105	.	0			c.C2636A						.						91	89	89					17																	57089748		2203	4300	6503	SO:0001583	missense	4591	exon22	Familial Cancer Database	Perheentupa syndrome	GTTTCAGAATTAT	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.2636C>A	chr17.hg19:g.57089748G>T	ENSP00000262294:p.Ser879Tyr	42.0	0.0		42.0	14.0	NM_015294	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000262294.7	hg19	CCDS32694.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.898786	0.33535	.	.	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065	T;T;T;T	0.66280	1.57;1.57;-0.2;1.18	6.07	5.11	0.69529	.	0.295020	0.35708	N	0.003031	T	0.51295	0.1666	N	0.24115	0.695	0.36434	D	0.865063	P;P;P	0.40107	0.573;0.703;0.664	B;B;B	0.42798	0.165;0.398;0.125	T	0.63310	-0.6666	10	0.72032	D	0.01	-5.6968	10.1512	0.42794	0.0689:0.0:0.7961:0.135	.	845;757;879	F8WEE6;O94972-2;O94972	.;.;TRI37_HUMAN	Y	879;879;757;845	ENSP00000376785:S879Y;ENSP00000262294:S879Y;ENSP00000365319:S757Y;ENSP00000376784:S845Y	ENSP00000262294:S879Y	S	-	2	0	TRIM37	54444530	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.772000	0.47678	1.578000	0.49821	0.655000	0.94253	TCT	.	.		0.393	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		T	57089748	G	T	57089748	3	4	215	1	0	0	0	0	1	0	0	0	16526	942	33	3	278	3	TRIM37	17	57089748	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	13770967	57089748	24105462	146	31053										
HEATR6	63897	hgsc.bcm.edu	37	chr17	58134607	58134613	+	Frame_Shift_Del	DEL	CCACCAA	CCACCAA	-													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggtcctgcaggggctttcttCcaccaatcaggagggctgag					rs139897992		TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	CCACCAA	CCACCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:58134607_58134613delCCACCAA	ENST00000184956.6	-	12	1891_1897	c.1875_1881delTTGGTGG	c.(1873-1881)gattggtggfs	p.DWW625fs	HEATR6_ENST00000585976.1_Frame_Shift_Del_p.DWW625fs	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	625							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			GGGCTTTCTTCCACCAATCAGGAGGGC	0.527																																					p.626_628del		Atlas-INDEL	.											.	HEATR6	98	.	0			c.1876_1882del						.																																			SO:0001589	frameshift_variant	63897	exon12			.	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"amplified in breast cancer 1"					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.1875_1881delTTGGTGG	chr17.hg19:g.58134607_58134613delCCACCAA	ENSP00000184956:p.Asp625fs	102.0	0.0		122.0	49.0	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Frame_Shift_Del	DEL	ENST00000184956.6	hg19	CCDS11623.1																																																																																			.	.		0.527	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070		-	58134613	CCACCAA	-	58134607	7	5	215	1	0	1	0	1	0	0	0	0	7042	856	30	0	1700	0	HEATR6	17	58134607	Frame_Shift_Del	DEL	CCACCAA	TCGA-DD-AAEA-01A-11D-A40R-10	1044859	58134607	23060603	147	31054										
TANC2	26115	hgsc.bcm.edu	37	chr17	61476200	61476200	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	agattgtctcctacctacttGatcttccagaaaaagatgaa	6	9	2	5			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:61476200G>C	ENST00000424789.2	+	17	3038	c.3034G>C	c.(3034-3036)Gat>Cat	p.D1012H	AC015923.1_ENST00000431604.1_RNA|TANC2_ENST00000389520.4_Missense_Mutation_p.D1012H|RP11-269G24.3_ENST00000583552.1_RNA	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	1012					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						CTACCTACTTGATCTTCCAGA	0.463																																					p.D1012H		Atlas-SNP	.											.	TANC2	266	.	0			c.G3034C						.						103	100	101					17																	61476200		1935	4145	6080	SO:0001583	missense	26115	exon17			CTACTTGATCTTC	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.3034G>C	chr17.hg19:g.61476200G>C	ENSP00000387593:p.Asp1012His	115.0	0.0		134.0	59.0	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Missense_Mutation	SNP	ENST00000424789.2	hg19	CCDS45754.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700073	0.88924	.	.	ENSG00000170921	ENST00000389520;ENST00000424789	T;T	0.65916	-0.18;-0.18	5.92	5.92	0.95590	Ankyrin repeat-containing domain (3);	0.046228	0.85682	D	0.000000	T	0.78168	0.4241	M	0.65677	2.01	0.58432	D	0.999999	D;P	0.63880	0.993;0.953	D;P	0.63877	0.919;0.863	T	0.78388	-0.2223	10	0.72032	D	0.01	.	20.3206	0.98668	0.0:0.0:1.0:0.0	.	1012;1012	Q9HCD6-2;Q9HCD6	.;TANC2_HUMAN	H	1012	ENSP00000374171:D1012H;ENSP00000387593:D1012H	ENSP00000374171:D1012H	D	+	1	0	TANC2	58829932	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.892000	0.87324	2.813000	0.96785	0.561000	0.74099	GAT	.	.		0.463	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			C	61476200	G	C	61476200	3	2	215	1	0	0	0	0	1	0	0	0	15560	1290	45	4	3100	4	TANC2	17	61476200	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	3341593	61476200	19719010	148	31055										
BPTF	2186	hgsc.bcm.edu	37	chr17	65871691	65871691	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gagccaacagaagttggggaTaaaggtaactctgtgtcagc	13	7	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:65871691T>G	ENST00000321892.4	+	5	1945	c.1884T>G	c.(1882-1884)gaT>gaG	p.D628E	BPTF_ENST00000306378.6_Intron|BPTF_ENST00000424123.3_Missense_Mutation_p.D489E|BPTF_ENST00000335221.5_Missense_Mutation_p.D628E			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	628					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAGTTGGGGATAAAGGTAACT	0.438																																					p.D628E		Atlas-SNP	.											.	BPTF	415	.	0			c.T1884G						.						97	94	95					17																	65871691		2203	4300	6503	SO:0001583	missense	2186	exon5			TGGGGATAAAGGT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.1884T>G	chr17.hg19:g.65871691T>G	ENSP00000315454:p.Asp628Glu	63.0	0.0		92.0	44.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	T	13.26	2.183632	0.38609	.	.	ENSG00000171634	ENST00000544491;ENST00000335221;ENST00000321892;ENST00000544778	T;T	0.64085	-0.08;-0.06	5.47	3.25	0.37280	.	.	.	.	.	T	0.65512	0.2698	L	0.36672	1.1	0.33766	D	0.622484	D;D	0.64830	0.994;0.994	D;P	0.72625	0.978;0.876	T	0.66732	-0.5849	9	0.23302	T	0.38	.	8.7076	0.34365	0.0:0.1497:0.0:0.8503	.	628;628	Q12830;Q12830-4	BPTF_HUMAN;.	E	533;628;628;489	ENSP00000334351:D628E;ENSP00000315454:D628E	ENSP00000315454:D628E	D	+	3	2	BPTF	63302153	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.580000	0.53907	0.461000	0.27071	-0.456000	0.05471	GAT	.	.		0.438	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65871691	T	G	65871691	3	3	215	1	0	0	0	0	1	0	0	0	1497	1403	49	5	1902	5	BPTF	17	65871691	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	4395491	65871691	15323519	149	31056										
LGALS3BP	3959	hgsc.bcm.edu	37	chr17	76968304	76968304	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gagtcttcttctggaacaggGcctcgtggctccagtacagg	13	11	3	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:76968304G>A	ENST00000262776.3	-	6	1420	c.1112C>T	c.(1111-1113)gCc>gTc	p.A371V	LGALS3BP_ENST00000591778.1_3'UTR	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	371					cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(5)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			CTGGAACAGGGCCTCGTGGCT	0.582											OREG0024787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A371V	GBM(89;1105 1755 18102 21513)	Atlas-SNP	.											.	LGALS3BP	47	.	0			c.C1112T						.						64	67	66					17																	76968304		2203	4300	6503	SO:0001583	missense	3959	exon6			AACAGGGCCTCGT	L13210	CCDS11759.1	17q25	2014-07-09				ENSG00000108679		"BTB/POZ domain containing", "Endogenous ligands"	6564	protein-coding gene	gene with protein product	"L3 antigen", "Mac-2-binding protein", "serum protein 90K", "transport and golgi organization 10 homolog B (Drosophila)"	600626				7698018, 8034587, 8390986	Standard	NM_005567		Approved	MAC-2-BP, 90K, BTBD17B, TANGO10B, M2BP, gp90, CyCAP	uc002jwh.3	Q08380		ENST00000262776.3:c.1112C>T	chr17.hg19:g.76968304G>A	ENSP00000262776:p.Ala371Val	73.0	0.0	1172	104.0	25.0	NM_005567	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Missense_Mutation	SNP	ENST00000262776.3	hg19	CCDS11759.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.640612	0.29157	.	.	ENSG00000108679	ENST00000262776;ENST00000536190	T	0.01438	4.89	3.41	1.39	0.22231	.	0.000000	0.38959	N	0.001505	T	0.01870	0.0059	M	0.62723	1.935	0.09310	N	0.999997	B	0.28636	0.218	B	0.28638	0.092	T	0.40627	-0.9553	10	0.49607	T	0.09	-30.3837	5.5361	0.17011	0.2597:0.0:0.7403:0.0	.	371	Q08380	LG3BP_HUMAN	V	371;359	ENSP00000262776:A371V	ENSP00000262776:A371V	A	-	2	0	LGALS3BP	74479899	0.000000	0.05858	0.082000	0.20525	0.353000	0.29299	0.600000	0.24104	0.445000	0.26639	0.561000	0.74099	GCC	.	.		0.582	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567		A	76968304	G	A	76968304	3	1	215	1	0	0	0	0	1	0	0	0	8753	1203	42	3	649	3	LGALS3BP	17	76968304	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	11096613	76968304	4226906	150	31057										
SGSH	6448	hgsc.bcm.edu	37	chr17	78184755	78184755	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tggatggtcttcgagccaaaGatggcgtagctggggtacgg	17	7	1	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr17:78184755G>T	ENST00000326317.6	-	8	1091	c.1005C>A	c.(1003-1005)atC>atA	p.I335I	SGSH_ENST00000572208.1_5'Flank|SGSH_ENST00000534910.1_Silent_p.I132I	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase	335					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|metal ion binding (GO:0046872)|N-sulfoglucosamine sulfohydrolase activity (GO:0016250)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TCGAGCCAAAGATGGCGTAGC	0.652																																					p.I335I		Atlas-SNP	.											.	SGSH	27	.	0			c.C1005A						.						72	55	61					17																	78184755		2203	4300	6503	SO:0001819	synonymous_variant	6448	exon8			GCCAAAGATGGCG	BC047318	CCDS11770.1	17q25.3	2011-11-08	2008-07-31			ENSG00000181523	3.10.1.1		10818	protein-coding gene	gene with protein product	"sulfamidase", "mucopolysaccharidosis type IIIA"	605270				7493035	Standard	NM_000199		Approved	HSS, MPS3A, SFMD	uc002jxz.4	P51688		ENST00000326317.6:c.1005C>A	chr17.hg19:g.78184755G>T		890.0	0.0		1031.0	278.0	NM_000199	A8K5E2	Silent	SNP	ENST00000326317.6	hg19	CCDS11770.1																																																																																			.	.		0.652	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199		T	78184755	G	T	78184755	2	4	215	1	0	0	0	0	0	0	0	1	14236	932	33	3		3	SGSH	17	78184755	Silent	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	1216451	78184755	3010455	151	31058										
LPIN2	9663	hgsc.bcm.edu	37	chr18	2926805	2926805	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cctccttggattctggcagcTgtaacagcaagatgataatg	10	9	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr18:2926805T>A	ENST00000261596.4	-	13	1949		c.e13-2			NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2						cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		TTCTGGCAGCTGTAACAGCAA	0.532																																					.		Atlas-SNP	.											.	LPIN2	75	.	0			c.1711-2A>T						.						61	56	57					18																	2926805		2203	4300	6503	SO:0001630	splice_region_variant	9663	exon14			GGCAGCTGTAACA	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.1711-2A>T	chr18.hg19:g.2926805T>A		28.0	0.0		33.0	8.0	NM_014646	A7MD25|D3DUH3	Splice_Site	SNP	ENST00000261596.4	hg19	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.192696	0.38707	.	.	ENSG00000101577	ENST00000261596	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.1441	0.42753	0.0:0.075:0.0:0.925	.	.	.	.	.	-1	.	.	.	-	.	.	LPIN2	2916805	1.000000	0.71417	0.982000	0.44146	0.796000	0.44982	3.250000	0.51445	2.185000	0.69588	0.460000	0.39030	.	.	.		0.532	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646	Intron	A	2926805	T	A	2926805	5	1	215	1	0	0	0	0	0	0	1	0	8928	1594	55	4	1013	4	LPIN2	18	2926805	Splice_Site	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10		2926805	75150443	152	31059										
FAM38B	63895	hgsc.bcm.edu	37	chr18	10691266	10691266	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gtaattgtagctcttggtgaGgaagttccccaggactcgcg	13	9	1	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr18:10691266G>A	ENST00000503781.3	-	44	6966	c.6967C>T	c.(6967-6969)Ctc>Ttc	p.L2323F	PIEZO2_ENST00000285141.4_Missense_Mutation_p.L178F|PIEZO2_ENST00000538948.1_Missense_Mutation_p.L280F|PIEZO2_ENST00000580640.1_Missense_Mutation_p.L2348F|PIEZO2_ENST00000302079.6_Missense_Mutation_p.L2323F	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2323					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										CTCTTGGTGAGGAAGTTCCCC	0.507																																					p.L2323F		Atlas-SNP	.											.	.	.	.	0			c.C6967T						.						124	108	113					18																	10691266		2203	4300	6503	SO:0001583	missense	63895	exon44			TGGTGAGGAAGTT	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"chromosome 18 open reading frame 30", "chromosome 18 open reading frame 58", "family with sequence similarity 38, member B"	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.6967C>T	chr18.hg19:g.10691266G>A	ENSP00000421377:p.Leu2323Phe	115.0	0.0		160.0	59.0	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Missense_Mutation	SNP	ENST00000503781.3	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.304284	0.95601	.	.	ENSG00000154864	ENST00000503781;ENST00000302079;ENST00000538948;ENST00000285141	T;T;T	0.79749	-1.3;-1.13;-1.04	5.62	5.62	0.85841	.	0.089656	0.47852	D	0.000209	D	0.87732	0.6251	L	0.58583	1.82	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.83127	-0.0115	10	0.20519	T	0.43	.	20.0247	0.97519	0.0:0.0:1.0:0.0	.	280	D6RFZ0	.	F	280;2323;280;178	ENSP00000303316:L2323F;ENSP00000443129:L280F;ENSP00000285141:L178F	ENSP00000285141:L178F	L	-	1	0	FAM38B	10681266	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.824000	0.99380	2.804000	0.96469	0.655000	0.94253	CTC	.	.		0.507	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		A	10691266	G	A	10691266	3	1	215	1	0	0	0	0	1	0	0	0	5563	1000	35	3	1327	3	FAM38B	18	10691266	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	7764461	10691266	67385982	153	31060										
CHMP1B	57132	hgsc.bcm.edu	37	chr18	11852040	11852040	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gggccagaccggctccgtggGcacgagcgtggcttcggcgg	19	13	0	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr18:11852040G>C	ENST00000526991.2	+	1	646	c.530G>C	c.(529-531)gGc>gCc	p.G177A	GNAL_ENST00000423027.3_Intron|GNAL_ENST00000334049.6_Intron|GNAL_ENST00000535121.1_Intron|GNAL_ENST00000269162.5_Intron|RP11-78A19.3_ENST00000586474.1_RNA	NM_020412.4	NP_065145.2	Q7LBR1	CHM1B_HUMAN	charged multivesicular body protein 1B	177	Interaction with SPAST.				cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|protein transport (GO:0015031)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)			endometrium(1)|lung(1)|urinary_tract(1)	3						GGCTCCGTGGGCACGAGCGTG	0.632																																					p.G177A		Atlas-SNP	.											.	CHMP1B	16	.	0			c.G530C						.						20	25	23					18																	11852040		2005	4151	6156	SO:0001583	missense	57132	exon1			CCGTGGGCACGAG	AF306520	CCDS54180.1	18p11.21	2011-09-21	2011-09-21		ENSG00000255112	ENSG00000255112		"Charged multivesicular body proteins"	24287	protein-coding gene	gene with protein product		606486	"chromatin modifying protein 1B"			15537668	Standard	NM_020412		Approved	CHMP1.5, C18orf2, Vps46B	uc002kqe.3	Q7LBR1	OTTHUMG00000165820	ENST00000526991.2:c.530G>C	chr18.hg19:g.11852040G>C	ENSP00000432279:p.Gly177Ala	60.0	0.0		55.0	15.0	NM_020412	Q96E89|Q9HD41	Missense_Mutation	SNP	ENST00000526991.2	hg19	CCDS54180.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.371131	0.24771	.	.	ENSG00000255112	ENST00000526991	D	0.85556	-2.0	5.21	1.15	0.20763	.	.	.	.	.	T	0.73297	0.3569	L	0.28608	0.87	0.51482	D	0.999928	B	0.02656	0.0	B	0.01281	0.0	T	0.60172	-0.7315	9	0.16896	T	0.51	.	9.9412	0.41580	0.077:0.3882:0.5348:0.0	.	177	Q7LBR1	CHM1B_HUMAN	A	177	ENSP00000432279:G177A	ENSP00000432279:G177A	G	+	2	0	CHMP1B	11842040	1.000000	0.71417	0.537000	0.28052	0.992000	0.81027	1.943000	0.40253	0.435000	0.26365	0.655000	0.94253	GGC	.	.		0.632	CHMP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386375.2	NM_020412		C	11852040	G	C	11852040	3	2	215	1	0	0	0	0	1	0	0	0	3355	1203	42	4	532	4	CHMP1B	18	11852040	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	1160774	11852040	66225208	154	31061										
TCF4	6925	hgsc.bcm.edu	37	chr18	53128331	53128331	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggtcatgtggtcatagggagTcccatctccatagttctgta	11	9	4	0	rs567398278		TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr18:53128331T>C	ENST00000356073.4	-	5	834	c.223A>G	c.(223-225)Act>Gct	p.T75A	TCF4_ENST00000398339.1_Missense_Mutation_p.T177A|TCF4_ENST00000543082.1_Missense_Mutation_p.T33A|TCF4_ENST00000567880.1_Missense_Mutation_p.T75A|TCF4_ENST00000566286.1_Missense_Mutation_p.T73A|TCF4_ENST00000568740.1_Missense_Mutation_p.T51A|TCF4_ENST00000564999.1_Missense_Mutation_p.T75A|TCF4_ENST00000540999.1_Missense_Mutation_p.T51A|TCF4_ENST00000566279.1_Missense_Mutation_p.T75A|TCF4_ENST00000354452.3_Missense_Mutation_p.T75A|TCF4_ENST00000565018.2_Missense_Mutation_p.T75A|TCF4_ENST00000568673.1_Missense_Mutation_p.T51A|TCF4_ENST00000564403.2_Missense_Mutation_p.T75A|TCF4_ENST00000537578.1_Missense_Mutation_p.T51A|RP11-619L19.1_ENST00000587660.1_RNA	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	75	Essential for MYOD1 inhibition. {ECO:0000250}.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		TCATAGGGAGTCCCATCTCCA	0.363													T|||	1	0.000199681	0	0	5008	,	,		18115	0		0	False		,,,				2504	0.001				p.T177A		Atlas-SNP	.											.	TCF4	178	.	0			c.A529G						.						93	91	92					18																	53128331		2203	4300	6503	SO:0001583	missense	6925	exon6			AGGGAGTCCCATC	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.223A>G	chr18.hg19:g.53128331T>C	ENSP00000348374:p.Thr75Ala	87.0	0.0		96.0	33.0	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	T	8.258	0.810504	0.16537	.	.	ENSG00000196628	ENST00000354452;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000398339	T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83	5.95	5.95	0.96441	.	0.109014	0.42172	D	0.000758	T	0.22589	0.0545	N	0.02247	-0.625	0.37238	D	0.905995	B;B;B;B;B	0.23540	0.001;0.026;0.087;0.001;0.002	B;B;B;B;B	0.21151	0.003;0.033;0.024;0.001;0.003	T	0.27571	-1.0070	10	0.10377	T	0.69	-19.8964	14.6535	0.68814	0.0:0.0:0.0:1.0	.	51;75;177;75;33	B7Z5M6;G0LNT9;E9PH57;P15884;B3KUC0	.;.;.;ITF2_HUMAN;.	A	75;75;33;51;51;177	ENSP00000346440:T75A;ENSP00000348374:T75A;ENSP00000439656:T33A;ENSP00000445202:T51A;ENSP00000440731:T51A;ENSP00000381382:T177A	ENSP00000346440:T75A	T	-	1	0	TCF4	51279329	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.624000	0.46444	2.279000	0.76181	0.533000	0.62120	ACT	.	.		0.363	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		C	53128331	T	C	53128331	3	2	215	1	0	0	0	0	1	0	0	0	15710	1667	58	2	1852	2	TCF4	18	53128331	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	41276291	53128331	24948917	155	31062										
NETO1	81832	hgsc.bcm.edu	37	chr18	70532098	70532098	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tacttgctgggatagttgggAgaggtaaagatacctccctc	12	8	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr18:70532098A>G	ENST00000327305.6	-	3	822	c.165T>C	c.(163-165)tcT>tcC	p.S55S	NETO1_ENST00000583169.1_Silent_p.S55S|NETO1_ENST00000580049.1_5'UTR|NETO1_ENST00000299430.2_Silent_p.S54S|NETO1_ENST00000397929.1_Silent_p.S54S	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	55	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		GATAGTTGGGAGAGGTAAAGA	0.438																																					p.S55S		Atlas-SNP	.											.	NETO1	178	.	0			c.T165C						.						119	108	112					18																	70532098		2203	4300	6503	SO:0001819	synonymous_variant	81832	exon3			GTTGGGAGAGGTA	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.165T>C	chr18.hg19:g.70532098A>G		99.0	0.0		106.0	28.0	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Silent	SNP	ENST00000327305.6	hg19	CCDS12000.1																																																																																			.	.		0.438	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		G	70532098	A	G	70532098	2	3	215	1	0	0	0	0	0	0	0	1	10348	291	11	2		2	NETO1	18	70532098	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	17403767	70532098	7545150	156	31063										
CNDP2	55748	hgsc.bcm.edu	37	chr18	72186270	72186270	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aggccacgggcaagaacgtcAtgctgctgcctgtggggtca	15	11	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr18:72186270A>G	ENST00000324262.4	+	11	1613	c.1297A>G	c.(1297-1299)Atg>Gtg	p.M433V	CNDP2_ENST00000579847.1_Missense_Mutation_p.M433V|CNDP2_ENST00000324301.8_Missense_Mutation_p.M349V	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	433					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.M433V(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		CAAGAACGTCATGCTGCTGCC	0.592																																					p.M433V		Atlas-SNP	.											CNDP2,NS,carcinoma,0,1	CNDP2	55	.	1	Substitution - Missense(1)	endometrium(1)	c.A1297G						.						82	81	81					18																	72186270		2203	4300	6503	SO:0001583	missense	55748	exon11			AACGTCATGCTGC	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.1297A>G	chr18.hg19:g.72186270A>G	ENSP00000325548:p.Met433Val	99.0	0.0		106.0	41.0	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	hg19	CCDS12006.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.023295	0.35701	.	.	ENSG00000133313	ENST00000324262;ENST00000324301	T;T	0.41065	1.01;1.01	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.25644	0.0624	N	0.17922	0.545	0.80722	D	1	B;B	0.34290	0.447;0.104	B;B	0.25884	0.064;0.053	T	0.08207	-1.0733	10	0.15952	T	0.53	-25.2161	15.4304	0.75092	1.0:0.0:0.0:0.0	.	349;433	Q96KP4-2;Q96KP4	.;CNDP2_HUMAN	V	433;349	ENSP00000325548:M433V;ENSP00000325756:M349V	ENSP00000325548:M433V	M	+	1	0	CNDP2	70337250	1.000000	0.71417	0.994000	0.49952	0.462000	0.32619	7.205000	0.77881	2.054000	0.61138	0.528000	0.53228	ATG	.	.		0.592	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		G	72186270	A	G	72186270	3	3	215	1	0	0	0	0	1	0	0	0	3596	217	8	2	1335	2	CNDP2	18	72186270	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	1654172	72186270	5890978	157	31064										
DUS3L	56931	hgsc.bcm.edu	37	chr19	5789493	5789493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctgcagggctttgtccaggcCgttgcggatggacgggggct	18	10	0	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:5789493C>T	ENST00000309061.7	-	3	721	c.625G>A	c.(625-627)Ggc>Agc	p.G209S	DUS3L_ENST00000590681.1_5'UTR|DUS3L_ENST00000320699.8_Intron	NM_020175.2	NP_064560.2	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like (S. cerevisiae)	209							flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA dihydrouridine synthase activity (GO:0017150)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(2)	14						TTGTCCAGGCCGTTGCGGATG	0.726																																					p.G209S		Atlas-SNP	.											.	DUS3L	42	.	0			c.G625A						.						9	13	12					19																	5789493		2150	4224	6374	SO:0001583	missense	56931	exon3			CCAGGCCGTTGCG		CCDS32880.1, CCDS54202.1	19p13.3	2014-02-12			ENSG00000141994	ENSG00000141994			26920	protein-coding gene	gene with protein product						12477932	Standard	NM_020175		Approved	DUS3, FLJ13896	uc002mdc.3	Q96G46	OTTHUMG00000162311	ENST00000309061.7:c.625G>A	chr19.hg19:g.5789493C>T	ENSP00000311977:p.Gly209Ser	66.0	0.0		63.0	23.0	NM_020175	Q96HM5|Q9BSU4|Q9H877|Q9NPR1	Missense_Mutation	SNP	ENST00000309061.7	hg19	CCDS32880.1	.	.	.	.	.	.	.	.	.	.	C	5.854	0.341799	0.11069	.	.	ENSG00000141994	ENST00000309061	T	0.16743	2.32	4.51	1.15	0.20763	.	0.170564	0.49305	N	0.000146	T	0.08846	0.0219	N	0.25201	0.72	0.28585	N	0.909914	B	0.06786	0.001	B	0.08055	0.003	T	0.28235	-1.0050	10	0.20519	T	0.43	-53.1615	6.1525	0.20320	0.0:0.5804:0.0:0.4196	.	209	Q96G46	DUS3L_HUMAN	S	209	ENSP00000311977:G209S	ENSP00000311977:G209S	G	-	1	0	DUS3L	5740493	0.909000	0.30893	0.456000	0.27044	0.331000	0.28603	0.464000	0.21988	0.346000	0.23899	0.491000	0.48974	GGC	.	.		0.726	DUS3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451870.2	NM_020175		T	5789493	C	T	5789493	3	4	215	1	0	0	0	0	1	0	0	0	4809	652	23	1	1371	1	DUS3L	19	5789493	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10		5789493	53339490	158	31065										
C19orf59	199675	hgsc.bcm.edu	37	chr19	7743056	7743056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctggttgtacagagccatccTgagcctgtacatcctcctgg	10	13	0	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:7743056T>C	ENST00000333598.3	+	3	705	c.251T>C	c.(250-252)cTg>cCg	p.L84P	CTD-3214H19.16_ENST00000597959.1_5'Flank|TRAPPC5_ENST00000596148.1_5'Flank|C19orf59_ENST00000597445.1_Missense_Mutation_p.L41P|TRAPPC5_ENST00000317378.5_5'Flank|TRAPPC5_ENST00000426877.2_5'Flank	NM_174918.2	NP_777578.2	Q8IX19	MCEM1_HUMAN		84						integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|skin(1)|stomach(1)	5						AGAGCCATCCTGAGCCTGTAC	0.592											OREG0025208	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L84P		Atlas-SNP	.											.	C19orf59	15	.	0			c.T251C						.						128	118	121					19																	7743056		2203	4300	6503	SO:0001583	missense	199675	exon3			CCATCCTGAGCCT																												ENST00000333598.3:c.251T>C	chr19.hg19:g.7743056T>C	ENSP00000329920:p.Leu84Pro	60.0	0.0	644	65.0	22.0	NM_174918	Q8IX20	Missense_Mutation	SNP	ENST00000333598.3	hg19	CCDS12183.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.209276	0.39003	.	.	ENSG00000183019	ENST00000333598	T	0.34072	1.38	3.94	3.94	0.45596	.	0.436137	0.19540	N	0.111839	T	0.35799	0.0944	N	0.14661	0.345	0.52501	D	0.99995	D	0.64830	0.994	P	0.59889	0.865	T	0.25710	-1.0124	10	0.72032	D	0.01	-16.2768	9.7525	0.40483	0.0:0.0:0.0:1.0	.	84	Q8IX19	MCEM1_HUMAN	P	84	ENSP00000329920:L84P	ENSP00000329920:L84P	L	+	2	0	C19orf59	7649056	0.483000	0.25956	0.833000	0.33012	0.167000	0.22549	0.691000	0.25467	1.731000	0.51592	0.459000	0.35465	CTG	.	.		0.592	C19orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461248.1			C	7743056	T	C	7743056	3	2	215	1	0	0	0	0	1	0	0	0	1942	1580	55	2	261	2	C19orf59	19	7743056	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	1953563	7743056	51385927	159	31066										
MUC16	94025	hgsc.bcm.edu	37	chr19	8959675	8959675	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	actgttgctggacgttgtatTctccttccttcttccgccgg	9	13	2	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:8959675T>G	ENST00000397910.4	-	84	43660	c.43457A>C	c.(43456-43458)gAa>gCa	p.E14486A	MUC16_ENST00000380951.5_Missense_Mutation_p.E1127A	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	22131	SEA 16. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GACGTTGTATTCTCCTTCCTT	0.602																																					p.E14486A		Atlas-SNP	.											.	MUC16	4315	.	0			c.A43457C						.						96	98	97					19																	8959675		2012	4186	6198	SO:0001583	missense	94025	exon84			TTGTATTCTCCTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.43457A>C	chr19.hg19:g.8959675T>G	ENSP00000381008:p.Glu14486Ala	72.0	0.0		77.0	23.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.23|11.23	1.576779|1.576779	0.28092|0.28092	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T|.	0.01963|.	4.53|.	3.47|3.47	1.29|1.29	0.21616|0.21616	.|.	.|.	.|.	.|.	.|.	T|T	0.34077|0.34077	0.0885|0.0885	L|L	0.44542|0.44542	1.39|1.39	.|.	.|.	.|.	B;B|.	0.20988|.	0.005;0.05|.	B;B|.	0.20767|.	0.003;0.031|.	T|T	0.37572|0.37572	-0.9700|-0.9700	8|4	0.41790|.	T|.	0.15|.	.|.	3.6684|3.6684	0.08265|0.08265	0.0:0.1225:0.2252:0.6523|0.0:0.1225:0.2252:0.6523	.|.	22131;14486|.	Q8WXI7;B5ME49|.	MUC16_HUMAN;.|.	A|H	14486;1127|1309	ENSP00000381008:E14486A|.	ENSP00000370338:E1127A|.	E|N	-|-	2|1	0|0	MUC16|MUC16	8820675|8820675	0.003000|0.003000	0.15002|0.15002	0.002000|0.002000	0.10522|0.10522	0.007000|0.007000	0.05969|0.05969	1.155000|1.155000	0.31700|0.31700	0.202000|0.202000	0.20498|0.20498	0.402000|0.402000	0.26972|0.26972	GAA|AAT	.	.		0.602	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	8959675	T	G	8959675	3	3	215	1	0	0	0	0	1	0	0	0	9982	1783	62	5	70	5	MUC16	19	8959675	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	1216619	8959675	50169308	160	31067										
MUC16	94025	hgsc.bcm.edu	37	chr19	8993436	8993436	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctcagtgatgctgtgggtcaGctggctcagctccaaataca	11	11	3	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:8993436G>T	ENST00000397910.4	-	66	41856	c.41653C>A	c.(41653-41655)Ctg>Atg	p.L13885M	MUC16_ENST00000380951.5_Missense_Mutation_p.L526M	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13888	SEA 12. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGTGGGTCAGCTGGCTCAGC	0.592																																					p.L13885M		Atlas-SNP	.											.	MUC16	4315	.	0			c.C41653A						.						137	128	130					19																	8993436		2034	4172	6206	SO:0001583	missense	94025	exon66			GGGTCAGCTGGCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.41653C>A	chr19.hg19:g.8993436G>T	ENSP00000381008:p.Leu13885Met	66.0	0.0		82.0	5.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	14.86|14.86	2.662276|2.662276	0.47572|0.47572	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T;T|.	0.51071|.	0.72;0.72|.	3.61|3.61	-2.7|-2.7	0.06004|0.06004	SEA (1);|.	1.919400|.	0.03817|.	U|.	0.266884|.	T|T	0.52693|0.52693	0.1750|0.1750	M|M	0.62266|0.62266	1.93|1.93	.|.	.|.	.|.	P;D|.	0.57899|.	0.938;0.981|.	P;D|.	0.79784|.	0.69;0.993|.	T|T	0.60576|0.60576	-0.7236|-0.7236	9|4	0.36615|.	T|.	0.2|.	.|.	9.0969|9.0969	0.36645|0.36645	0.122:0.2454:0.6326:0.0|0.122:0.2454:0.6326:0.0	.|.	21530;13885|.	Q8WXI7;B5ME49|.	MUC16_HUMAN;.|.	M|R	13885;526|724	ENSP00000381008:L13885M;ENSP00000370338:L526M|.	ENSP00000370338:L526M|.	L|S	-|-	1|3	2|2	MUC16|MUC16	8854436|8854436	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.806000|0.806000	0.45545|0.45545	-1.156000|-1.156000	0.03160|0.03160	-0.271000|-0.271000	0.09272|0.09272	0.557000|0.557000	0.71058|0.71058	CTG|AGC	.	.		0.592	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	8993436	G	T	8993436	3	4	215	1	0	0	0	0	1	0	0	0	9982	962	34	3	1946	3	MUC16	19	8993436	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	33761	8993436	50135547	161	31068										
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19766404	19766404	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aagaggatgaagatgaaggtCtccaggttgttcgcagtcac	13	7	2	4			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:19766404C>G	ENST00000357324.6	-	10	1355	c.1329G>C	c.(1327-1329)gaG>gaC	p.E443D	ATP13A1_ENST00000496082.1_5'Flank|ATP13A1_ENST00000291503.5_Missense_Mutation_p.E325D	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	443						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						AGATGAAGGTCTCCAGGTTGT	0.582																																					p.E443D	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.G1329C						.						78	68	71					19																	19766404		2203	4300	6503	SO:0001583	missense	57130	exon10			GAAGGTCTCCAGG	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"ATPases / P-type"	24215	protein-coding gene	gene with protein product	"cation transporting ATPase"		"ATPase type 13A"	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.1329G>C	chr19.hg19:g.19766404C>G	ENSP00000349877:p.Glu443Asp	82.0	0.0		92.0	42.0	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Missense_Mutation	SNP	ENST00000357324.6	hg19	CCDS32970.2	.	.	.	.	.	.	.	.	.	.	C	19.02	3.746203	0.69418	.	.	ENSG00000105726	ENST00000291503;ENST00000357324	D;D	0.88586	-2.4;-2.4	4.25	0.871	0.19107	ATPase, P-type, ATPase-associated domain (1);	0.106634	0.64402	D	0.000005	D	0.86531	0.5955	L	0.46614	1.455	0.54753	D	0.999981	P;P	0.45634	0.863;0.723	P;B	0.54312	0.748;0.018	T	0.80077	-0.1533	10	0.13108	T	0.6	-30.16	6.6069	0.22729	0.0:0.588:0.0:0.412	.	443;325	Q9HD20;Q9HD20-2	AT131_HUMAN;.	D	325;443	ENSP00000291503:E325D;ENSP00000349877:E443D	ENSP00000291503:E325D	E	-	3	2	ATP13A1	19627404	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.784000	0.26816	0.465000	0.27167	0.561000	0.74099	GAG	.	.		0.582	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		G	19766404	C	G	19766404	3	3	215	1	0	0	0	0	1	0	0	0	1123	912	32	4	2353	4	ATP13A1	19	19766404	Missense_Mutation	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	10772968	19766404	39362579	162	31069										
HPN	3249	hgsc.bcm.edu	37	chr19	35551277	35551277	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gccgcaggaagctgcccgtgGaccgcatcgtgggaggccgg	18	13	0	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:35551277G>T	ENST00000262626.2	+	8	1306	c.481G>T	c.(481-483)Gac>Tac	p.D161Y	HPN_ENST00000392226.1_Missense_Mutation_p.D161Y|HPN_ENST00000597419.1_Intron|HPN-AS1_ENST00000392227.2_RNA	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin	161					basement membrane disassembly (GO:0034769)|cholesterol homeostasis (GO:0042632)|cochlea morphogenesis (GO:0090103)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|epithelium development (GO:0060429)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pilomotor reflex (GO:0097195)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|positive regulation of gene expression (GO:0010628)|positive regulation of hepatocyte proliferation (GO:2000347)|positive regulation of plasminogen activation (GO:0010756)|positive regulation of thyroid hormone generation (GO:2000611)|potassium ion transmembrane transport (GO:0071805)|proteolysis (GO:0006508)|regulation of cell shape (GO:0008360)|response to thyroid hormone (GO:0097066)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	GCTGCCCGTGGACCGCATCGT	0.687																																					p.D161Y		Atlas-SNP	.											.	HPN	45	.	0			c.G481T						.						40	46	44					19																	35551277		2203	4298	6501	SO:0001583	missense	3249	exon8			CCCGTGGACCGCA		CCDS32993.1	19q13.12	2013-04-25	2008-12-08		ENSG00000105707	ENSG00000105707		"Serine peptidases / Transmembrane"	5155	protein-coding gene	gene with protein product	"transmembrane protease, serine 1"	142440				2835076	Standard	NM_182983		Approved	TMPRSS1	uc002nxq.2	P05981	OTTHUMG00000182474	ENST00000262626.2:c.481G>T	chr19.hg19:g.35551277G>T	ENSP00000262626:p.Asp161Tyr	63.0	0.0		98.0	54.0	NM_182983	B2RDS4	Missense_Mutation	SNP	ENST00000262626.2	hg19	CCDS32993.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025858	0.75390	.	.	ENSG00000105707	ENST00000262626;ENST00000392226;ENST00000541345	D;D	0.89050	-2.46;-2.46	4.92	4.92	0.64577	Peptidase cysteine/serine, trypsin-like (1);	0.051226	0.85682	D	0.000000	D	0.91764	0.7395	L	0.43554	1.36	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.998	D;D;P	0.70227	0.942;0.968;0.898	D	0.92439	0.5960	10	0.72032	D	0.01	.	15.6684	0.77252	0.0:0.0:1.0:0.0	.	133;161;161	B7Z1L4;B2ZDQ2;P05981	.;.;HEPS_HUMAN	Y	161;161;133	ENSP00000262626:D161Y;ENSP00000376060:D161Y	ENSP00000262626:D161Y	D	+	1	0	HPN	40243117	1.000000	0.71417	0.362000	0.25862	0.948000	0.59901	7.097000	0.76967	2.561000	0.86390	0.555000	0.69702	GAC	.	.		0.687	HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1	NM_002151		T	35551277	G	T	35551277	3	4	215	1	0	0	0	0	1	0	0	0	7345	1174	41	3	507	3	HPN	19	35551277	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	15784873	35551277	23577706	163	31070										
ZNF229	7772	hgsc.bcm.edu	37	chr19	44933829	44933829	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cacactcctcacatttatagGgtctccttcctgtgtgcacc	6	15	2	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:44933829G>T	ENST00000588931.1	-	6	1560	c.1127C>A	c.(1126-1128)cCc>cAc	p.P376H	CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000291187.4_Missense_Mutation_p.P370H|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	376					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				ACATTTATAGGGTCTCCTTCC	0.478																																					p.P376H		Atlas-SNP	.											.	ZNF229	123	.	0			c.C1127A						.						100	108	106					19																	44933829		2165	4294	6459	SO:0001583	missense	7772	exon6			TTATAGGGTCTCC	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"Zinc fingers, C2H2-type", "-"	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1127C>A	chr19.hg19:g.44933829G>T	ENSP00000466519:p.Pro376His	77.0	0.0		153.0	36.0	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	hg19	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.297676	0.81025	.	.	ENSG00000167383	ENST00000291187	.	.	.	4.07	1.38	0.22167	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.67562	0.2906	M	0.83223	2.63	0.26784	N	0.969543	D	0.76494	0.999	D	0.64410	0.925	T	0.62067	-0.6932	8	0.87932	D	0	.	12.869	0.57955	0.0:0.44:0.56:0.0	.	376	Q9UJW7	ZN229_HUMAN	H	376	.	ENSP00000291187:P376H	P	-	2	0	ZNF229	49625669	0.994000	0.37717	0.000000	0.03702	0.498000	0.33706	2.911000	0.48774	0.015000	0.14971	0.609000	0.83330	CCC	.	.		0.478	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		T	44933829	G	T	44933829	3	4	215	1	0	0	0	0	1	0	0	0	17797	1232	43	3	1354	3	ZNF229	19	44933829	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	9382552	44933829	14195154	164	31071										
C19orf63	284361	hgsc.bcm.edu	37	chr19	50984147	50984147	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tccccttgccccagccctgaGacggcggccttcattgagcg	11	17	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:50984147G>T	ENST00000334976.6	+	6	637	c.591G>T	c.(589-591)gaG>gaT	p.E197D	CTD-2545M3.2_ENST00000598194.1_RNA|EMC10_ENST00000598585.1_Missense_Mutation_p.E197D|EMC10_ENST00000376918.3_Missense_Mutation_p.E197D	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	197						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											CCAGCCCTGAGACGGCGGCCT	0.657																																					p.E197D		Atlas-SNP	.											.	.	.	.	0			c.G591T						.						42	53	50					19																	50984147		2203	4300	6503	SO:0001583	missense	284361	exon6			CCCTGAGACGGCG	BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"hematopoietic signal peptide-containing secreted 1", "hematopoietic signal peptide-containing membrane domain-containing 1"	614545	"chromosome 19 open reading frame 63"	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.591G>T	chr19.hg19:g.50984147G>T	ENSP00000334037:p.Glu197Asp	83.0	0.0		119.0	63.0	NM_175063	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Missense_Mutation	SNP	ENST00000334976.6	hg19	CCDS12796.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.733873	0.30684	.	.	ENSG00000161671	ENST00000334976;ENST00000376918;ENST00000376920	.	.	.	4.47	3.43	0.39272	.	0.111617	0.64402	D	0.000016	T	0.49098	0.1537	N	0.21142	0.635	0.58432	D	0.999996	P;D;P	0.71674	0.791;0.998;0.569	B;D;B	0.64042	0.281;0.921;0.182	T	0.43940	-0.9360	9	0.05620	T	0.96	-16.9198	12.0572	0.53542	0.0888:0.0:0.9112:0.0	.	197;197;197	Q5UCC4;Q5UCC4-2;Q5UCC4-3	INM02_HUMAN;.;.	D	197	.	ENSP00000334037:E197D	E	+	3	2	C19orf63	55675959	1.000000	0.71417	0.369000	0.25952	0.011000	0.07611	3.677000	0.54619	1.194000	0.43101	0.491000	0.48974	GAG	.	.		0.657	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063		T	50984147	G	T	50984147	3	4	215	1	0	0	0	0	1	0	0	0	1947	933	33	3	613	3	C19orf63	19	50984147	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	6050318	50984147	8144836	165	31072										
LILRB3	11025	hgsc.bcm.edu	37	chr19	54724954	54724954	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tgaacccgctgggctcctcaCctgccatcaggatgttcagg	11	14	3	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:54724954C>A	ENST00000391750.1	-	6	1092		c.e6+1		LILRB3_ENST00000424807.1_Splice_Site|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Splice_Site|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Splice_Site|LILRB3_ENST00000469273.1_5'Flank|LILRB3_ENST00000346401.6_Splice_Site|LILRB3_ENST00000407860.2_Splice_Site|LILRA6_ENST00000391735.3_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3						cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGGCTCCTCACCTGCCATCAG	0.682																																					.		Atlas-SNP	.											.	LILRB3	67	.	0			c.955+1G>T						.						8	8	8					19																	54724954		1528	1746	3274	SO:0001630	splice_region_variant	11025	exon6			TCCTCACCTGCCA	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.955+1G>T	chr19.hg19:g.54724954C>A		50.0	0.0		66.0	33.0	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Splice_Site	SNP	ENST00000391750.1	hg19	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	.	1.661	-0.511463	0.04231	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000270464	.	.	.	2.52	1.47	0.22746	.	.	.	.	.	.	.	.	.	.	.	0.29538	N	0.852298	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.0204	0.14358	0.0:0.829:0.0:0.171	.	.	.	.	.	-1	.	.	.	-	.	.	LILRB3;LILRA6	59416766	0.027000	0.19231	0.430000	0.26722	0.105000	0.19272	0.893000	0.28336	0.628000	0.30357	0.573000	0.79308	.	.	.		0.682	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	Intron	A	54724954	C	A	54724954	5	1	215	1	0	0	0	0	0	0	1	0	8801	521	18	3	978	3	LILRB3	19	54724954	Splice_Site	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	3740807	54724954	4404029	166	31073										
ZIM3	114026	hgsc.bcm.edu	37	chr19	57648312	57648312	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cttgttccaacctcaagatcAcatcgggtttggtggtttcc	9	11	2	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:57648312A>G	ENST00000269834.1	-	4	555	c.170T>C	c.(169-171)gTg>gCg	p.V57A	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	57	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CCTCAAGATCACATCGGGTTT	0.512																																					p.V57A		Atlas-SNP	.											.	ZIM3	107	.	0			c.T170C						.						280	195	224					19																	57648312		2203	4300	6503	SO:0001583	missense	114026	exon4			AAGATCACATCGG	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.170T>C	chr19.hg19:g.57648312A>G	ENSP00000269834:p.Val57Ala	126.0	0.0		203.0	89.0	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	hg19	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.762688	0.31228	.	.	ENSG00000141946	ENST00000269834	T	0.00864	5.6	2.58	2.58	0.30949	Krueppel-associated box (3);	.	.	.	.	T	0.01523	0.0049	L	0.58354	1.805	0.21878	N	0.999494	B	0.31837	0.342	B	0.34138	0.176	T	0.40887	-0.9539	9	0.62326	D	0.03	.	7.9963	0.30269	1.0:0.0:0.0:0.0	.	57	Q96PE6	ZIM3_HUMAN	A	57	ENSP00000269834:V57A	ENSP00000269834:V57A	V	-	2	0	ZIM3	62340124	0.026000	0.19158	0.225000	0.23894	0.052000	0.14988	2.220000	0.42908	1.049000	0.40321	0.260000	0.18958	GTG	.	.		0.512	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			G	57648312	A	G	57648312	3	3	215	1	0	0	0	0	1	0	0	0	17700	159	6	2	1256	2	ZIM3	19	57648312	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	2923358	57648312	1480671	167	31074										
ZNF587	84914	hgsc.bcm.edu	37	chr19	58370623	58370623	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aaatcttatagtcgaaagagCagccttattcaacatcagcg	7	9	3	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr19:58370623C>T	ENST00000339656.5	+	3	1025	c.843C>T	c.(841-843)agC>agT	p.S281S	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF587_ENST00000423137.1_Silent_p.S280S|ZNF587_ENST00000419854.1_Silent_p.S238S|ZNF814_ENST00000597652.1_5'Flank|ZNF814_ENST00000597342.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	281					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		GTCGAAAGAGCAGCCTTATTC	0.458																																					p.S281S	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.C843T						.						70	71	70					19																	58370623		2198	4290	6488	SO:0001819	synonymous_variant	84914	exon3			AAAGAGCAGCCTT	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"Zinc fingers, C2H2-type", "-"	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.843C>T	chr19.hg19:g.58370623C>T		211.0	0.0		296.0	154.0	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	hg19	CCDS12964.1																																																																																			.	.		0.458	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828		T	58370623	C	T	58370623	2	4	215	1	0	0	0	0	0	0	0	1	18035	709	25	3		3	ZNF587	19	58370623	Silent	SNP	C	TCGA-DD-AAEA-01A-11D-A40R-10	722311	58370623	758360	168	31075										
CDC25B	994	hgsc.bcm.edu	37	chr20	3783772	3783772	+	Frame_Shift_Del	DEL	G	G	-													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cagatggtggccctattgacGggcaagttcagcaacatcgt					rs146556613	byFrequency	TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr20:3783772delG	ENST00000245960.5	+	13	1972	c.1275delG	c.(1273-1275)acgfs	p.T425fs	CDC25B_ENST00000344256.6_Frame_Shift_Del_p.T361fs|CDC25B_ENST00000379598.5_Frame_Shift_Del_p.T334fs|CDC25B_ENST00000467519.1_3'UTR|CDC25B_ENST00000340833.4_Frame_Shift_Del_p.T384fs|CDC25B_ENST00000439880.2_Frame_Shift_Del_p.T411fs	NM_004358.3|NM_021872.2|NM_021873.2	NP_004349.1|NP_068658.1|NP_068659.1	P30305	MPIP2_HUMAN	cell division cycle 25B	425					female meiosis I (GO:0007144)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|oocyte maturation (GO:0001556)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein kinase activity (GO:0045860)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(1)	18						CCCTATTGACGGGCAAGTTCA	0.557																																					p.T425fs		Atlas-INDEL	.											.	CDC25B	76	.	0			c.1274delC						.						86	75	79					20																	3783772		2203	4300	6503	SO:0001589	frameshift_variant	994	exon13			.		CCDS13065.1, CCDS13066.1, CCDS13067.1, CCDS74700.1, CCDS74701.1	20p13	2013-01-17	2013-01-17		ENSG00000101224	ENSG00000101224		"Protein tyrosine phosphatases / Class III Cys-based PTPs"	1726	protein-coding gene	gene with protein product		116949	"cell division cycle 25B", "cell division cycle 25 homolog B (S. cerevisiae)", "cell division cycle 25 homolog B (S. pombe)"			1836978	Standard	NM_021873		Approved		uc002wjn.3	P30305	OTTHUMG00000031764	ENST00000245960.5:c.1275delG	chr20.hg19:g.3783772delG	ENSP00000245960:p.Thr425fs	116.0	0.0		121.0	34.0	NM_021873	D3DVY1|D3DVY2|D3DVY3|D3DVY4|O43551|Q13971|Q5JX77|Q6RSS1|Q9BRA6	Frame_Shift_Del	DEL	ENST00000245960.5	hg19	CCDS13067.1																																																																																			.	.		0.557	CDC25B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077779.2	NM_021874		-	3783772	G	-	3783772	7	5	215	1	0	1	0	1	0	0	0	0	3065	1103	39	0	1325	0	CDC25B	20	3783772	Frame_Shift_Del	DEL	G	TCGA-DD-AAEA-01A-11D-A40R-10		3783772	59241748	169	31076										
ITCH	83737	hgsc.bcm.edu	37	chr20	33059320	33059320	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tttgaggattcctttcaacaGgtactgtttcattctctcaa	6	9	4	1			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr20:33059320G>C	ENST00000262650.6	+	17	1828	c.1692G>C	c.(1690-1692)caG>caC	p.Q564H	ITCH_ENST00000483727.1_3'UTR|ITCH_ENST00000374864.4_Splice_Site_p.Q523H|ITCH_ENST00000535650.1_Splice_Site_p.Q413H			Q96J02	ITCH_HUMAN	itchy E3 ubiquitin protein ligase	564					apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of defense response to virus (GO:0050687)|negative regulation of JNK cascade (GO:0046329)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cell growth (GO:0001558)|regulation of protein deubiquitination (GO:0090085)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	CXCR chemokine receptor binding (GO:0045236)|ligase activity (GO:0016874)|ribonucleoprotein complex binding (GO:0043021)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(9)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(13)|skin(1)|upper_aerodigestive_tract(1)	36						CCTTTCAACAGGTACTGTTTC	0.408																																					p.Q564H		Atlas-SNP	.											.	ITCH	73	.	0			c.G1692C						.						111	110	110					20																	33059320		2203	4300	6503	SO:0001630	splice_region_variant	83737	exon17			TCAACAGGTACTG	AF095745	CCDS13234.1, CCDS58768.1, CCDS58769.1	20q11.22	2014-09-17	2012-02-23		ENSG00000078747	ENSG00000078747			13890	protein-coding gene	gene with protein product		606409	"itchy (mouse homolog) E3 ubiquitin protein ligase", "itchy E3 ubiquitin protein ligase homolog (mouse)"			11318614	Standard	NM_001257137		Approved	AIP4	uc010geu.2	Q96J02	OTTHUMG00000032300	ENST00000262650.6:c.1692+1G>C	chr20.hg19:g.33059320G>C		69.0	0.0		112.0	54.0	NM_001257137	A6NEW4|B4E234|E1P5P3|F5H217|O43584|Q5QP37|Q5TEL0|Q96F66|Q9BY75|Q9H451|Q9H4U5	Missense_Mutation	SNP	ENST00000262650.6	hg19	CCDS58768.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.223968	0.79576	.	.	ENSG00000078747	ENST00000374864;ENST00000535650;ENST00000262650	T;T;T	0.76578	-1.03;-1.03;-1.03	5.62	5.62	0.85841	HECT (1);	0.000000	0.85682	D	0.000000	D	0.84647	0.5518	L	0.60904	1.88	0.80722	D	1	D;D;D	0.76494	0.981;0.998;0.999	D;P;D	0.66602	0.935;0.891;0.945	D	0.85501	0.1191	10	0.87932	D	0	.	13.9095	0.63857	0.0739:0.0:0.9261:0.0	.	475;564;523	B4DN85;Q96J02;Q5QP37	.;ITCH_HUMAN;.	H	523;413;564	ENSP00000363998:Q523H;ENSP00000445608:Q413H;ENSP00000262650:Q564H	ENSP00000262650:Q564H	Q	+	3	2	ITCH	32522981	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	6.381000	0.73163	2.802000	0.96397	0.655000	0.94253	CAG	.	.		0.408	ITCH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078783.2		Missense_Mutation	C	33059320	G	C	33059320	5	2	215	1	0	0	0	0	0	0	1	0	7877	1014	35	4	1623	4	ITCH	20	33059320	Splice_Site	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	29275548	33059320	29966200	170	31077										
ITCH	83737	hgsc.bcm.edu	37	chr20	33095536	33095536	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ctgccaccatacaagagctaTgagcaactgaaggaaaagct	9	10	0	3			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr20:33095536T>C	ENST00000262650.6	+	26	2785	c.2649T>C	c.(2647-2649)taT>taC	p.Y883Y	ITCH_ENST00000374864.4_Silent_p.Y842Y|ITCH_ENST00000535650.1_Silent_p.Y732Y			Q96J02	ITCH_HUMAN	itchy E3 ubiquitin protein ligase	883	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of defense response to virus (GO:0050687)|negative regulation of JNK cascade (GO:0046329)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cell growth (GO:0001558)|regulation of protein deubiquitination (GO:0090085)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	CXCR chemokine receptor binding (GO:0045236)|ligase activity (GO:0016874)|ribonucleoprotein complex binding (GO:0043021)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(9)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(13)|skin(1)|upper_aerodigestive_tract(1)	36						ACAAGAGCTATGAGCAACTGA	0.383																																					p.Y883Y		Atlas-SNP	.											.	ITCH	73	.	0			c.T2649C						.						113	105	108					20																	33095536		2203	4300	6503	SO:0001819	synonymous_variant	83737	exon26			GAGCTATGAGCAA	AF095745	CCDS13234.1, CCDS58768.1, CCDS58769.1	20q11.22	2014-09-17	2012-02-23		ENSG00000078747	ENSG00000078747			13890	protein-coding gene	gene with protein product		606409	"itchy (mouse homolog) E3 ubiquitin protein ligase", "itchy E3 ubiquitin protein ligase homolog (mouse)"			11318614	Standard	NM_001257137		Approved	AIP4	uc010geu.2	Q96J02	OTTHUMG00000032300	ENST00000262650.6:c.2649T>C	chr20.hg19:g.33095536T>C		64.0	0.0		106.0	22.0	NM_001257137	A6NEW4|B4E234|E1P5P3|F5H217|O43584|Q5QP37|Q5TEL0|Q96F66|Q9BY75|Q9H451|Q9H4U5	Silent	SNP	ENST00000262650.6	hg19	CCDS58768.1																																																																																			.	.		0.383	ITCH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078783.2			C	33095536	T	C	33095536	2	2	215	1	0	0	0	0	0	0	0	1	7877	1471	51	2		2	ITCH	20	33095536	Silent	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	36216	33095536	29929984	171	31078										
CEP250	11190	hgsc.bcm.edu	37	chr20	34063355	34063355	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tgctgatgggcctggaagccAaacagtcagaatcactcagt	11	10	3	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr20:34063355A>G	ENST00000397527.1	+	15	2320	c.1600A>G	c.(1600-1602)Aaa>Gaa	p.K534E	RP3-477O4.14_ENST00000453914.1_RNA|RP3-477O4.14_ENST00000416260.1_RNA|CEP250_ENST00000342580.4_Missense_Mutation_p.K534E|RP3-477O4.14_ENST00000444933.1_RNA	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	534	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			CCTGGAAGCCAAACAGTCAGA	0.507																																					p.K534E		Atlas-SNP	.											.	CEP250	141	.	0			c.A1600G						.						131	116	121					20																	34063355		2203	4300	6503	SO:0001583	missense	11190	exon15			GAAGCCAAACAGT	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.1600A>G	chr20.hg19:g.34063355A>G	ENSP00000380661:p.Lys534Glu	75.0	0.0		105.0	31.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.17|17.17	3.322447|3.322447	0.60634|0.60634	.|.	.|.	ENSG00000126001|ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000425934|ENST00000425096	T;T;T|.	0.31247|.	2.4;2.43;1.5|.	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	0.369047|.	0.22832|.	N|.	0.055096|.	T|T	0.57695|0.57695	0.2071|0.2071	M|M	0.65975|0.65975	2.015|2.015	0.30555|0.30555	N|N	0.765114|0.765114	P|.	0.47350|.	0.894|.	B|.	0.43990|.	0.438|.	T|T	0.60875|0.60875	-0.7176|-0.7176	10|5	0.19147|.	T|.	0.46|.	.|.	13.2082|13.2082	0.59809|0.59809	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	534|.	Q9BV73|.	CP250_HUMAN|.	E|R	534;534;533|47	ENSP00000380661:K534E;ENSP00000341541:K534E;ENSP00000413827:K533E|.	ENSP00000341541:K534E|.	K|Q	+|+	1|2	0|0	CEP250|CEP250	33526769|33526769	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.720000|0.720000	0.41350|0.41350	5.472000|5.472000	0.66768|0.66768	2.246000|2.246000	0.74042|0.74042	0.533000|0.533000	0.62120|0.62120	AAA|CAA	.	.		0.507	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		G	34063355	A	G	34063355	3	3	215	1	0	0	0	0	1	0	0	0	3254	131	5	2	1646	2	CEP250	20	34063355	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	967819	34063355	28962165	172	31079										
SAMHD1	25939	hgsc.bcm.edu	37	chr20	35533779	35533780	+	Frame_Shift_Ins	INS	-	-	A													0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aactcacccttttaatctttINSatttgtcctgttggctgcgt							TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr20:35533779_35533780insA	ENST00000262878.4	-	12	1596_1597	c.1397_1398insT	c.(1396-1398)atafs	p.I466fs		NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	466					dATP catabolic process (GO:0046061)|defense response to virus (GO:0051607)|dGTP catabolic process (GO:0006203)|immune response (GO:0006955)|innate immune response (GO:0045087)|protein homotetramerization (GO:0051289)|regulation of innate immune response (GO:0045088)	intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dGTP binding (GO:0032567)|dGTPase activity (GO:0008832)|nucleic acid binding (GO:0003676)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	20		Myeloproliferative disorder(115;0.00878)				TTTTAATCTTTATTTGTCCTGT	0.396																																					p.I466fs		Atlas-INDEL	.											.	SAMHD1	62	.	0			c.1398_1399insT						.																																			SO:0001589	frameshift_variant	25939	exon12			.	AF228421	CCDS13288.1	20q11.23	2014-09-17			ENSG00000101347	ENSG00000101347		"Sterile alpha motif (SAM) domain containing"	15925	protein-coding gene	gene with protein product	"HD domain containing 1", "monocyte protein 5", "Aicardi-Goutieres syndrome 5"	606754				11064105, 11230166	Standard	NM_015474		Approved	SBBI88, Mg11, HDDC1, MOP-5, AGS5	uc002xgh.2	Q9Y3Z3	OTTHUMG00000032402	ENST00000262878.4:c.1398dupT	chr20.hg19:g.35533780_35533780dupA	ENSP00000262878:p.Ile466fs	107.0	0.0		238.0	40.0	NM_015474	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Frame_Shift_Ins	INS	ENST00000262878.4	hg19	CCDS13288.1																																																																																			.	.		0.396	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474		A	35533780	-	A	35533779	7	5	215	1	0	1	1	0	0	0	0	0	13843	1744	61	0	502	0	SAMHD1	20	35533779	Frame_Shift_Ins	INS	-	TCGA-DD-AAEA-01A-11D-A40R-10	1470424	35533779	27491741	173	31080										
KIAA0406	9675	hgsc.bcm.edu	37	chr20	36641091	36641091	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	gtggcaagggaatgcaggctTtctgacaagatgtcagcgag	15	7	2	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr20:36641091T>G	ENST00000373448.2	-	3	1366	c.1128A>C	c.(1126-1128)gaA>gaC	p.E376D	TTI1_ENST00000373447.3_Missense_Mutation_p.E376D|TTI1_ENST00000449821.1_Missense_Mutation_p.E376D|TTI1_ENST00000487362.1_Intron	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	376					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						AATGCAGGCTTTCTGACAAGA	0.453																																					p.E376D		Atlas-SNP	.											.	TTI1	104	.	0			c.A1128C						.						153	155	155					20																	36641091		2203	4300	6503	SO:0001583	missense	9675	exon3			CAGGCTTTCTGAC	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"	614425	"KIAA0406", "Tel2 interacting protein 1 homolog (S. pombe)"	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.1128A>C	chr20.hg19:g.36641091T>G	ENSP00000362547:p.Glu376Asp	97.0	0.0		183.0	73.0	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	hg19	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.459123	0.63401	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.17528	2.27;2.27;2.27	5.5	-0.494	0.12034	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.36110	0.0955	M	0.78049	2.395	0.52501	D	0.999951	D	0.76494	0.999	D	0.74348	0.983	T	0.04737	-1.0930	10	0.34782	T	0.22	-12.1816	11.4134	0.49939	0.0:0.5725:0.0:0.4275	.	376	O43156	TTI1_HUMAN	D	376	ENSP00000362547:E376D;ENSP00000362546:E376D;ENSP00000407270:E376D	ENSP00000362546:E376D	E	-	3	2	TTI1	36074505	1.000000	0.71417	0.989000	0.46669	0.915000	0.54546	1.143000	0.31553	-0.260000	0.09418	0.533000	0.62120	GAA	.	.		0.453	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657		G	36641091	T	G	36641091	3	3	215	1	0	0	0	0	1	0	0	0	8182	1838	64	5	2169	5	KIAA0406	20	36641091	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	1107312	36641091	26384429	174	31081										
MC3R	4159	hgsc.bcm.edu	37	chr20	54823965	54823965	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	aatggctcggagcacctccaAgcccctttcttcagcaacca	7	16	2	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr20:54823965A>G	ENST00000243911.2	+	1	178	c.66A>G	c.(64-66)caA>caG	p.Q22Q		NM_019888.3	NP_063941.3	P41968	MC3R_HUMAN	melanocortin 3 receptor	22					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|homoiothermy (GO:0042309)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of blood pressure (GO:0008217)|regulation of heart rate (GO:0002027)|sodium ion homeostasis (GO:0055078)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(3)|skin(1)	26			Colorectal(105;0.202)			AGCACCTCCAAGCCCCTTTCT	0.572																																					p.Q22Q		Atlas-SNP	.											.	MC3R	83	.	0			c.A66G						.						115	113	113					20																	54823965		2203	4300	6503	SO:0001819	synonymous_variant	4159	exon1			CCTCCAAGCCCCT		CCDS13449.2	20q13.2-q13.3	2012-08-10			ENSG00000124089	ENSG00000124089		"GPCR / Class A : Melanocortin receptors"	6931	protein-coding gene	gene with protein product		155540				8463333	Standard	NM_019888		Approved	MC3	uc002xxb.2	P41968	OTTHUMG00000032785	ENST00000243911.2:c.66A>G	chr20.hg19:g.54823965A>G		40.0	0.0		75.0	13.0	NM_019888	Q4KN27|Q9H517	Silent	SNP	ENST00000243911.2	hg19	CCDS13449.2																																																																																			.	.		0.572	MC3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079786.2			G	54823965	A	G	54823965	2	3	215	1	0	0	0	0	0	0	0	1	9374	69	3	2		2	MC3R	20	54823965	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	18182874	54823965	8201555	175	31082										
MC3R	4159	hgsc.bcm.edu	37	chr20	54823996	54823996	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	tcagcaaccagagcagcagcGccttctgtgagcaggtcttc	11	13	3	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr20:54823996G>A	ENST00000243911.2	+	1	209	c.97G>A	c.(97-99)Gcc>Acc	p.A33T		NM_019888.3	NP_063941.3	P41968	MC3R_HUMAN	melanocortin 3 receptor	33					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|homoiothermy (GO:0042309)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of blood pressure (GO:0008217)|regulation of heart rate (GO:0002027)|sodium ion homeostasis (GO:0055078)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(3)|skin(1)	26			Colorectal(105;0.202)			GAGCAGCAGCGCCTTCTGTGA	0.557																																					p.A33T		Atlas-SNP	.											.	MC3R	83	.	0			c.G97A	GRCh37	CM074934	MC3R	M		.						122	113	116					20																	54823996		2203	4300	6503	SO:0001583	missense	4159	exon1			AGCAGCGCCTTCT		CCDS13449.2	20q13.2-q13.3	2012-08-10			ENSG00000124089	ENSG00000124089		"GPCR / Class A : Melanocortin receptors"	6931	protein-coding gene	gene with protein product		155540				8463333	Standard	NM_019888		Approved	MC3	uc002xxb.2	P41968	OTTHUMG00000032785	ENST00000243911.2:c.97G>A	chr20.hg19:g.54823996G>A	ENSP00000243911:p.Ala33Thr	41.0	0.0		80.0	22.0	NM_019888	Q4KN27|Q9H517	Missense_Mutation	SNP	ENST00000243911.2	hg19	CCDS13449.2	.	.	.	.	.	.	.	.	.	.	G	2.886	-0.230838	0.05983	.	.	ENSG00000124089	ENST00000243911	T	0.36878	1.23	5.01	-1.94	0.07571	.	0.488989	0.19418	N	0.114767	T	0.15912	0.0383	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.08953	-1.0697	10	0.40728	T	0.16	.	8.5843	0.33649	0.1886:0.3029:0.5085:0.0	.	70	P41968	MC3R_HUMAN	T	33	ENSP00000243911:A33T	ENSP00000243911:A33T	A	+	1	0	MC3R	54257403	0.053000	0.20554	0.000000	0.03702	0.240000	0.25518	2.055000	0.41345	-1.096000	0.03046	-0.810000	0.03169	GCC	.	.		0.557	MC3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079786.2			A	54823996	G	A	54823996	3	1	215	1	0	0	0	0	1	0	0	0	9374	1087	38	1	99	1	MC3R	20	54823996	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	31	54823996	8201524	176	31083										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32241108	32241108	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	ggaggcccactgcgacatctAtggggacaggccccgtgcag	15	13	1	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr22:32241108A>G	ENST00000382112.3	+	29	2949	c.2879A>G	c.(2878-2880)tAt>tGt	p.Y960C	DEPDC5_ENST00000400248.2_Missense_Mutation_p.Y960C|DEPDC5_ENST00000400246.1_Missense_Mutation_p.Y969C|DEPDC5_ENST00000535622.1_Missense_Mutation_p.Y891C|DEPDC5_ENST00000400249.2_Missense_Mutation_p.Y960C|DEPDC5_ENST00000382105.2_Missense_Mutation_p.Y891C|DEPDC5_ENST00000266091.3_Missense_Mutation_p.Y969C|DEPDC5_ENST00000382111.2_Missense_Mutation_p.Y969C	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	969					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						TGCGACATCTATGGGGACAGG	0.622																																					p.Y969C		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A2906G						.						74	80	78					22																	32241108		2135	4244	6379	SO:0001583	missense	9681	exon30			ACATCTATGGGGA	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.2879A>G	chr22.hg19:g.32241108A>G	ENSP00000371546:p.Tyr960Cys	38.0	0.0		64.0	20.0	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.532144	0.85812	.	.	ENSG00000100150	ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	T;T;T;T;T;T;T;T	0.36157	1.3;1.7;1.7;1.67;1.27;1.69;1.67;1.7	5.3	5.3	0.74995	.	0.139654	0.49916	D	0.000131	T	0.57315	0.2045	M	0.64404	1.975	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.997;0.997;0.998;0.998;0.988;0.996	T	0.60110	-0.7327	10	0.62326	D	0.03	.	14.4368	0.67287	1.0:0.0:0.0:0.0	.	290;969;891;969;960;960	B4DSS1;B9EGN9;B4DH93;O75140-4;A8MPX9;O75140	.;.;.;.;.;DEPD5_HUMAN	C	891;969;960;891;969;891;960;969;960	ENSP00000440210:Y891C;ENSP00000266091:Y969C;ENSP00000383108:Y960C;ENSP00000383105:Y969C;ENSP00000371539:Y891C;ENSP00000371546:Y960C;ENSP00000371545:Y969C;ENSP00000383107:Y960C	ENSP00000266091:Y969C	Y	+	2	0	DEPDC5	30571108	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	6.739000	0.74827	2.016000	0.59253	0.460000	0.39030	TAT	.	.		0.622	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		G	32241108	A	G	32241108	3	3	215	1	0	0	0	0	1	0	0	0	4444	449	16	2	3011	2	DEPDC5	22	32241108	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10		32241108	19063458	177	31084										
ACO2	50	hgsc.bcm.edu	37	chr22	41903896	41903896	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	caagtcgtacctgcggctgcGgccggaccgtgtggccatgc	15	14	0	0	rs147763800		TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chr22:41903896G>A	ENST00000216254.4	+	3	297	c.275G>A	c.(274-276)cGg>cAg	p.R92Q	ACO2_ENST00000396512.3_Missense_Mutation_p.R92Q	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	92					cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						CTGCGGCTGCGGCCGGACCGT	0.627																																					p.R92Q		Atlas-SNP	.											.	ACO2	58	.	0			c.G275A						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	36	36	36		275	4.7	1	22	dbSNP_134	36	0,8600		0,0,4300	no	missense	ACO2	NM_001098.2	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	92/781	41903896	1,13005	2203	4300	6503	SO:0001583	missense	50	exon3			GGCTGCGGCCGGA	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"aconitate hydratase, mitochondrial"	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.275G>A	chr22.hg19:g.41903896G>A	ENSP00000216254:p.Arg92Gln	112.0	0.0		129.0	42.0	NM_001098	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Missense_Mutation	SNP	ENST00000216254.4	hg19	CCDS14017.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.644129	0.67244	2.27E-4	0.0	ENSG00000100412	ENST00000544234;ENST00000216254;ENST00000396512	T;T	0.53206	0.63;0.63	4.66	4.66	0.58398	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 (1);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);	0.053969	0.85682	D	0.000000	T	0.47544	0.1451	M	0.78285	2.405	0.58432	D	0.999999	P;P	0.46395	0.588;0.877	B;B	0.32583	0.148;0.138	T	0.63501	-0.6623	10	0.66056	D	0.02	.	17.9056	0.88917	0.0:0.0:1.0:0.0	.	92;92	A2A274;Q99798	.;ACON_HUMAN	Q	92	ENSP00000216254:R92Q;ENSP00000379769:R92Q	ENSP00000216254:R92Q	R	+	2	0	ACO2	40233842	1.000000	0.71417	0.999000	0.59377	0.744000	0.42396	6.325000	0.72901	2.290000	0.77057	0.491000	0.48974	CGG	.	G|1.000;A|0.000		0.627	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098		A	41903896	G	A	41903896	3	1	215	1	0	0	0	0	1	0	0	0	147	1116	39	1	285	1	ACO2	22	41903896	Missense_Mutation	SNP	G	TCGA-DD-AAEA-01A-11D-A40R-10	9662788	41903896	9400670	178	31085										
GPR64	10149	hgsc.bcm.edu	37	chrX	19051754	19051754	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	atgcattgaaggtttttactAtagtgattttagttttttct	7	3	1	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chrX:19051754A>G	ENST00000379869.3	-	8	444	c.281T>C	c.(280-282)aTa>aCa	p.I94T	GPR64_ENST00000340581.3_Intron|GPR64_ENST00000356606.4_Intron|GPR64_ENST00000357544.3_Intron|GPR64_ENST00000379876.1_Missense_Mutation_p.I70T|GPR64_ENST00000354791.3_Missense_Mutation_p.I78T|GPR64_ENST00000379878.3_Missense_Mutation_p.I78T|GPR64_ENST00000379873.2_Missense_Mutation_p.I94T|GPR64_ENST00000357991.3_Missense_Mutation_p.I91T|GPR64_ENST00000360279.4_Intron	NM_001079858.2|NM_005756.3	NP_001073327.1|NP_005747.2	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64	94					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)|spermatogenesis (GO:0007283)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(18)|stomach(1)|urinary_tract(1)	42	Hepatocellular(33;0.183)					GGTTTTTACTATAGTGATTTT	0.249																																					p.I94T		Atlas-SNP	.											.	GPR64	102	.	0			c.T281C						.						36	37	36					X																	19051754		2191	4284	6475	SO:0001583	missense	10149	exon8			TTTACTATAGTGA	X81892	CCDS14191.1, CCDS43921.1, CCDS43922.1, CCDS43923.1, CCDS55376.1, CCDS55377.1, CCDS55378.1, CCDS55379.1	Xp22.13	2014-08-08			ENSG00000173698	ENSG00000173698		"-", "GPCR / Class B : Orphans"	4516	protein-coding gene	gene with protein product	"epididymal protein 6"	300572				9739419, 9150425	Standard	NM_005756		Approved	HE6, TM7LN2, EDDM6	uc004cyx.3	Q8IZP9	OTTHUMG00000021223	ENST00000379869.3:c.281T>C	chrX.hg19:g.19051754A>G	ENSP00000369198:p.Ile94Thr	345.0	0.0		415.0	263.0	NM_001184834	B1AWB3|B1AWB4|B1AWB6|B1AWB7|O00406|Q14CE0|Q8IWT2|Q8IZE4|Q8IZE5|Q8IZE6|Q8IZE7|Q8IZP3|Q8IZP4	Missense_Mutation	SNP	ENST00000379869.3	hg19	CCDS43923.1	.	.	.	.	.	.	.	.	.	.	A	15.95	2.985247	0.53934	.	.	ENSG00000173698	ENST00000379873;ENST00000379878;ENST00000354791;ENST00000379876;ENST00000379869;ENST00000357991	T;T;T;T;T;T	0.35421	1.31;1.41;1.42;1.41;1.47;1.47	4.83	4.83	0.62350	.	0.000000	0.42821	D	0.000656	T	0.43986	0.1272	L	0.27053	0.805	0.29783	N	0.833842	D;D;D;D;D;D	0.71674	0.998;0.998;0.998;0.991;0.985;0.997	D;D;D;P;P;D	0.81914	0.995;0.995;0.995;0.763;0.585;0.989	T	0.41645	-0.9497	10	0.87932	D	0	.	9.699	0.40175	1.0:0.0:0.0:0.0	.	70;78;94;91;94;78	Q8IZP9-5;Q8IZP9-3;Q8IZP9-9;Q8IZP9-2;Q8IZP9;Q14CE1	.;.;.;.;GPR64_HUMAN;.	T	94;78;78;70;94;91	ENSP00000369202:I94T;ENSP00000369207:I78T;ENSP00000346845:I78T;ENSP00000369205:I70T;ENSP00000369198:I94T;ENSP00000350680:I91T	ENSP00000346845:I78T	I	-	2	0	GPR64	18961675	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.953000	0.56699	1.892000	0.54788	0.412000	0.27726	ATA	.	.		0.249	GPR64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055970.2			G	19051754	A	G	19051754	3	3	215	1	0	0	0	0	1	0	0	0	6713	449	16	2	2860	2	GPR64	23	19051754	Missense_Mutation	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10		19051754	136218806	179	31086										
MAOA	4128	hgsc.bcm.edu	37	chrX	43571157	43571157	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	cggggcgcctttccaccagtAtggaatcccattgcatattt	9	12	0	0			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chrX:43571157A>G	ENST00000338702.3	+	4	468	c.345A>G	c.(343-345)gtA>gtG	p.V115V	MAOA_ENST00000497485.1_3'UTR|MAOA_ENST00000542639.1_5'UTR	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	115					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	TTCCACCAGTATGGAATCCCA	0.373																																					p.V115V		Atlas-SNP	.											.	MAOA	48	.	0			c.A345G						.						149	138	142					X																	43571157		2203	4300	6503	SO:0001819	synonymous_variant	4128	exon4			ACCAGTATGGAAT		CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.345A>G	chrX.hg19:g.43571157A>G		53.0	0.0		73.0	41.0	NM_000240	B4DF46|Q16426	Silent	SNP	ENST00000338702.3	hg19	CCDS14260.1																																																																																			.	.		0.373	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240		G	43571157	A	G	43571157	2	3	215	1	0	0	0	0	0	0	0	1	9234	436	16	2		2	MAOA	23	43571157	Silent	SNP	A	TCGA-DD-AAEA-01A-11D-A40R-10	24519403	43571157	111699403	180	31087										
SMC1A	8243	hgsc.bcm.edu	37	chrX	53421753	53421753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0773480662983425	14	1	1.7585265022885	2.17722328854766	1.47489319546777	1	1	0	caatgagggcctctcgtgcaTagatactggaaattctctgt	10	9	2	2			TCGA-DD-AAEA-01A-11D-A40R-10	TCGA-DD-AAEA-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9570a286-fdf7-4d2c-ad57-ed9e9d7f29ef	7ea301e0-14bb-4e22-8891-42db5e0556e7	g.chrX:53421753T>C	ENST00000322213.4	-	19	3045	c.2918A>G	c.(2917-2919)tAt>tGt	p.Y973C		NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	973					DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						CTCTCGTGCATAGATACTGGA	0.557																																					p.Y973C		Atlas-SNP	.											.	SMC1A	112	.	0			c.A2918G						.						130	91	104					X																	53421753		2203	4300	6503	SO:0001583	missense	8243	exon19			CGTGCATAGATAC	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"Structural maintenance of chromosomes proteins"	11111	protein-coding gene	gene with protein product		300040	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.2918A>G	chrX.hg19:g.53421753T>C	ENSP00000323421:p.Tyr973Cys	19.0	0.0		17.0	8.0	NM_006306	O14995|Q16351|Q2M228	Missense_Mutation	SNP	ENST00000322213.4	hg19	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	-	19.18	3.777367	0.70107	.	.	ENSG00000072501	ENST00000322213	T	0.77877	-1.13	5.06	5.06	0.68205	RecF/RecN/SMC (1);	0.165870	0.39615	N	0.001306	D	0.86318	0.5904	M	0.83012	2.62	0.80722	D	1	D	0.58970	0.984	P	0.59288	0.855	D	0.87997	0.2753	10	0.59425	D	0.04	.	13.1602	0.59540	0.0:0.0:0.0:1.0	.	973	Q14683	SMC1A_HUMAN	C	973	ENSP00000323421:Y973C	ENSP00000323421:Y973C	Y	-	2	0	SMC1A	53438478	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	4.130000	0.57964	1.817000	0.53016	0.427000	0.28365	TAT	.	.		0.557	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		C	53421753	T	C	53421753	3	2	215	1	0	0	0	0	1	0	0	0	14796	1406	49	2	811	2	SMC1A	23	53421753	Missense_Mutation	SNP	T	TCGA-DD-AAEA-01A-11D-A40R-10	9850596	53421753	101848807	181	31088										
AKR7A2	8574	hgsc.bcm.edu	37	chr1	19630804	19630805	+	Frame_Shift_Ins	INS	-	-	C													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agccggctccaggggcccttINScctctgttgctgccaagttc							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr1:19630804_19630805insC	ENST00000235835.3	-	7	1015_1016	c.994_995insG	c.(994-996)gaafs	p.E332fs	RNU6-1099P_ENST00000363533.1_RNA	NM_003689.3	NP_003680.2	O43488	ARK72_HUMAN	aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)	332					carbohydrate metabolic process (GO:0005975)|cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|phenanthrene-9,10-epoxide hydrolase activity (GO:0019119)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CAGGGGCCCTTCCTCTGTTGCT	0.604																																					p.E332fs		Atlas-INDEL	.											.	AKR7A2	19	.	0			c.995_996insG						.																																			SO:0001589	frameshift_variant	8574	exon7			.	AF026947	CCDS194.1	1p36.13	2010-09-30			ENSG00000053371	ENSG00000053371		"Aldo-keto reductases"	389	protein-coding gene	gene with protein product		603418				9576847	Standard	NM_003689		Approved	AFAR	uc001bbw.3	O43488	OTTHUMG00000002522	ENST00000235835.3:c.995dupG	chr1.hg19:g.19630806_19630806dupC	ENSP00000235835:p.Glu332fs	206.0	0.0		205.0	37.0	NM_003689	O75749|Q5TG63	Frame_Shift_Ins	INS	ENST00000235835.3	hg19	CCDS194.1																																																																																			.	.		0.604	AKR7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007165.2	NM_003689		C	19630805	-	C	19630804	7	5	216	1	0	1	1	0	0	0	0	0	475	1783	62	0	88	0	AKR7A2	1	19630804	Frame_Shift_Ins	INS	-	TCGA-DD-AAEB-01A-11D-A40R-10		19630804	229619817	1	31089	161	2								
AKR7A2	8574	hgsc.bcm.edu	37	chr1	19630807	19630807	+	Missense_Mutation	SNP	T	T	G													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ccggctccaggggcccttccTctgttgctgccaagttctgc							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr1:19630807T>G	ENST00000235835.3	-	7	1013	c.992A>C	c.(991-993)gAg>gCg	p.E331A	RNU6-1099P_ENST00000363533.1_RNA	NM_003689.3	NP_003680.2	O43488	ARK72_HUMAN	aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)	331					carbohydrate metabolic process (GO:0005975)|cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|phenanthrene-9,10-epoxide hydrolase activity (GO:0019119)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GGGCCCTTCCTCTGTTGCTGC	0.607																																					p.E331A		Atlas-SNP	.											.	AKR7A2	19	.	0			c.A992C						.						69	72	71					1																	19630807		2203	4300	6503	SO:0001583	missense	8574	exon7			CCTTCCTCTGTTG	AF026947	CCDS194.1	1p36.13	2010-09-30			ENSG00000053371	ENSG00000053371		"Aldo-keto reductases"	389	protein-coding gene	gene with protein product		603418				9576847	Standard	NM_003689		Approved	AFAR	uc001bbw.3	O43488	OTTHUMG00000002522	ENST00000235835.3:c.992A>C	chr1.hg19:g.19630807T>G	ENSP00000235835:p.Glu331Ala	202.0	0.0		203.0	20.0	NM_003689	O75749|Q5TG63	Missense_Mutation	SNP	ENST00000235835.3	hg19	CCDS194.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223387	0.39300	.	.	ENSG00000053371	ENST00000235835;ENST00000330072;ENST00000489286	T;T	0.04551	3.6;3.6	4.63	4.63	0.57726	NADP-dependent oxidoreductase domain (3);	0.119152	0.56097	D	0.000022	T	0.05227	0.0139	L	0.35341	1.055	0.40110	D	0.976475	B	0.11235	0.004	B	0.14578	0.011	T	0.31833	-0.9929	10	0.49607	T	0.09	.	12.3172	0.54964	0.0:0.0:0.0:1.0	.	331	O43488	ARK72_HUMAN	A	331;286;193	ENSP00000235835:E331A;ENSP00000339084:E286A	ENSP00000235835:E331A	E	-	2	0	AKR7A2	19503394	1.000000	0.71417	0.986000	0.45419	0.702000	0.40608	5.094000	0.64523	2.056000	0.61249	0.533000	0.62120	GAG	.	.		0.607	AKR7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007165.2	NM_003689		G	19630807	T	G	19630807	3	3	216	1	0	0	0	0	1	0	0	0	475	1551	54	5	91	5	AKR7A2	1	19630807	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	3	19630807	229619814	2	31090	161	2								
IQCC	55721	hgsc.bcm.edu	37	chr1	32672166	32672166	+	Frame_Shift_Del	DEL	G	G	-													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agggtagcaaatccagagcaGgggctgtggaaccacttccc							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr1:32672166delG	ENST00000291358.6	+	3	264	c.243delG	c.(241-243)cagfs	p.Q81fs	DCDC2B_ENST00000409358.1_5'Flank|IQCC_ENST00000537469.1_Frame_Shift_Del_p.Q161fs|RP4-622L5.7_ENST00000373604.4_RNA|RP4-622L5.7_ENST00000421616.1_RNA	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	81										endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ATCCAGAGCAGGGGCTGTGGA	0.532																																					p.Q161fs		Atlas-INDEL	.											.	IQCC	46	.	0			c.482delA						.						97	105	102					1																	32672166		2203	4300	6503	SO:0001589	frameshift_variant	55721	exon3			.	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.243delG	chr1.hg19:g.32672166delG	ENSP00000291358:p.Gln81fs	253.0	0.0		302.0	131.0	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Frame_Shift_Del	DEL	ENST00000291358.6	hg19	CCDS355.1																																																																																			.	.		0.532	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134		-	32672166	G	-	32672166	7	5	216	1	0	1	0	1	0	0	0	0	7813	991	35	0	493	0	IQCC	1	32672166	Frame_Shift_Del	DEL	G	TCGA-DD-AAEB-01A-11D-A40R-10	13041359	32672166	216578455	3	31091										
C1orf94	84970	hgsc.bcm.edu	37	chr1	34643459	34643459	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttccagaaagagaggaggagGatggccagcgggaatgggct	18	6	0	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr1:34643459G>C	ENST00000488417.1	+	1	189	c.69G>C	c.(67-69)agG>agC	p.R23S	C1orf94_ENST00000373374.3_Intron|AC115286.1_ENST00000408126.1_RNA	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	23										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				AGAGGAGGAGGATGGCCAGCG	0.617																																					p.R23S		Atlas-SNP	.											.	C1orf94	156	.	0			c.G69C						.						25	28	27					1																	34643459		692	1591	2283	SO:0001583	missense	84970	exon1			GAGGAGGATGGCC	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.69G>C	chr1.hg19:g.34643459G>C	ENSP00000435634:p.Arg23Ser	49.0	0.0		80.0	29.0	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	hg19	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	G	11.32	1.604682	0.28623	.	.	ENSG00000142698	ENST00000488417	T	0.47528	0.84	5.07	4.16	0.48862	.	.	.	.	.	T	0.40909	0.1136	L	0.44542	1.39	0.30511	N	0.7694	B	0.16396	0.017	B	0.12156	0.007	T	0.45249	-0.9274	9	0.62326	D	0.03	-3.9473	10.9488	0.47317	0.0:0.22:0.78:0.0	.	23	Q6P1W5	CA094_HUMAN	S	23	ENSP00000435634:R23S	ENSP00000435634:R23S	R	+	3	2	C1orf94	34416046	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	3.866000	0.56040	1.349000	0.45751	0.561000	0.74099	AGG	.	.		0.617	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884		C	34643459	G	C	34643459	3	2	216	1	0	0	0	0	1	0	0	0	2073	1165	41	4	71	4	C1orf94	1	34643459	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	1971293	34643459	214607162	4	31092										
STIL	6491	hgsc.bcm.edu	37	chr1	47717255	47717255	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tctgcattgtcgggaggttcCtcttcatcttcactattgtc	8	11	5	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr1:47717255C>T	ENST00000360380.3	-	18	3780	c.3417G>A	c.(3415-3417)gaG>gaA	p.E1139E	STIL_ENST00000396221.2_Silent_p.E1122E|STIL_ENST00000337817.5_Silent_p.E1139E|STIL_ENST00000371877.3_Silent_p.E1140E|STIL_ENST00000243182.6_Silent_p.E1139E	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	1139					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				CGGGAGGTTCCTCTTCATCTT	0.388																																					p.E1140E		Atlas-SNP	.											.	STIL	91	.	0			c.G3420A						.						168	168	168					1																	47717255		2203	4300	6503	SO:0001819	synonymous_variant	6491	exon17			AGGTTCCTCTTCA	M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"TAL1 (SCL) interrupting locus"	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.3417G>A	chr1.hg19:g.47717255C>T		110.0	0.0		118.0	51.0	NM_001048166	Q5T0C5|Q68CN9	Silent	SNP	ENST00000360380.3	hg19	CCDS548.1																																																																																			.	.		0.388	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035		T	47717255	C	T	47717255	2	4	216	1	0	0	0	0	0	0	0	1	15297	680	24	3		3	STIL	1	47717255	Silent	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	13073796	47717255	201533366	5	31093										
VAV3	10451	hgsc.bcm.edu	37	chr1	108247593	108247593	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	caggcttacctcaggagcatCtggcagactttgcaggatgt	12	10	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr1:108247593C>G	ENST00000370056.4	-	16	1867	c.1593G>C	c.(1591-1593)caG>caC	p.Q531H	VAV3_ENST00000527011.1_Missense_Mutation_p.Q531H|VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000371846.4_Missense_Mutation_p.Q466H	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	531					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TCAGGAGCATCTGGCAGACTT	0.418																																					p.Q531H		Atlas-SNP	.											.	VAV3	176	.	0			c.G1593C						.						96	85	89					1																	108247593		2203	4300	6503	SO:0001583	missense	10451	exon16			GAGCATCTGGCAG	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1593G>C	chr1.hg19:g.108247593C>G	ENSP00000359073:p.Gln531His	91.0	0.0		103.0	51.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.69|12.69	2.013166|2.013166	0.35511|0.35511	.|.	.|.	ENSG00000134215|ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000371846|ENST00000529809;ENST00000490388	D;D;D|.	0.87650|.	-2.28;-2.28;-2.28|.	6.16|6.16	5.24|5.24	0.73138|0.73138	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);|.	0.055211|.	0.85682|.	D|.	0.000000|.	T|T	0.31295|0.31295	0.0792|0.0792	N|N	0.16098|0.16098	0.37|0.37	0.48632|0.48632	D|D	0.999682|0.999682	B;B;B;B|.	0.06786|.	0.0;0.0;0.001;0.001|.	B;B;B;B|.	0.10450|.	0.001;0.0;0.005;0.005|.	T|T	0.27739|0.27739	-1.0065|-1.0065	10|5	0.37606|.	T|.	0.19|.	.|.	13.7877|13.7877	0.63119|0.63119	0.0:0.8718:0.0:0.1282|0.0:0.8718:0.0:0.1282	.|.	531;531;466;531|.	B7ZLR1;E9PQ97;B4DHL6;Q9UKW4|.	.;.;.;VAV3_HUMAN|.	H|T	531;531;466|83;526	ENSP00000359073:Q531H;ENSP00000432540:Q531H;ENSP00000360912:Q466H|.	ENSP00000359073:Q531H|.	Q|R	-|-	3|2	2|0	VAV3|VAV3	108049116|108049116	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.794000|1.794000	0.38774|0.38774	1.595000|1.595000	0.50050|0.50050	0.650000|0.650000	0.86243|0.86243	CAG|AGA	.	.		0.418	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		G	108247593	C	G	108247593	3	3	216	1	0	0	0	0	1	0	0	0	17148	912	32	4	1023	4	VAV3	1	108247593	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	60530338	108247593	141003028	6	31094										
HSD17B7	51478	hgsc.bcm.edu	37	chr1	162769552	162769570	+	Frame_Shift_Del	DEL	TCCTCTGTCACAGTGACAA	TCCTCTGTCACAGTGACAA	-													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gattcgggaactggagcctcTcctctgtcacagtgacaatc					rs528471207	byFrequency	TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	TCCTCTGTCACAGTGACAA	TCCTCTGTCACAGTGACAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr1:162769552_162769570delTCCTCTGTCACAGTGACAA	ENST00000254521.3	+	5	522_540	c.467_485delTCCTCTGTCACAGTGACAA	c.(466-486)ctcctctgtcacagtgacaatfs	p.LLCHSDN156fs	HSD17B7_ENST00000485405.1_3'UTR|HSD17B7_ENST00000367917.3_Frame_Shift_Del_p.LLCHSDN156fs	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	156					cholesterol biosynthetic process (GO:0006695)|estrogen biosynthetic process (GO:0006703)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	3-keto sterol reductase activity (GO:0000253)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)					CTGGAGCCTCTCCTCTGTCACAGTGACAATCCATCTCAG	0.42																																					p.156_162del		Atlas-INDEL	.											.	HSD17B7	25	.	0			c.466_484del						.																																			SO:0001589	frameshift_variant	51478	exon5			.	AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	1.1.1.270	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	5215	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 37C, member 1"	606756				10544267, 10419022, 19027726	Standard	NM_016371		Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.467_485delTCCTCTGTCACAGTGACAA	chr1.hg19:g.162769552_162769570delTCCTCTGTCACAGTGACAA	ENSP00000254521:p.Leu156fs	324.0	0.0		492.0	85.0	NM_016371	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	Frame_Shift_Del	DEL	ENST00000254521.3	hg19	CCDS1242.1																																																																																			.	.		0.42	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1	NM_016371		-	162769570	TCCTCTGTCACAGTGACAA	-	162769552	7	5	216	1	0	1	0	1	0	0	0	0	7397	1551	54	0	485	0	HSD17B7	1	162769552	Frame_Shift_Del	DEL	TCCTCTGTCACAGTGACAA	TCGA-DD-AAEB-01A-11D-A40R-10	54521959	162769552	86481069	7	31095										
LRRN2	10446	hgsc.bcm.edu	37	chr1	204588798	204588798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	catggaaatcacagtctcggGcatccgaaaagctgttctgg	11	10	3	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr1:204588798G>A	ENST00000367175.1	-	1	2535	c.323C>T	c.(322-324)gCc>gTc	p.A108V	LRRN2_ENST00000367177.3_Missense_Mutation_p.A108V|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367176.3_Missense_Mutation_p.A108V			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	108					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			ACAGTCTCGGGCATCCGAAAA	0.607																																					p.A108V		Atlas-SNP	.											.	LRRN2	81	.	0			c.C323T						.						104	103	103					1																	204588798		2203	4300	6503	SO:0001583	missense	10446	exon3			TCTCGGGCATCCG	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"Immunoglobulin superfamily / I-set domain containing"	16914	protein-coding gene	gene with protein product	"leucine rich and ankyrin repeats 1", "fibronectin type III, immunoglobulin and leucine rich repeat domain 7"	605492	"leucine rich repeat neuronal 5"	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.323C>T	chr1.hg19:g.204588798G>A	ENSP00000356143:p.Ala108Val	164.0	0.0		286.0	79.0	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	hg19	CCDS1448.1	.	.	.	.	.	.	.	.	.	.	G	0.820	-0.749002	0.03065	.	.	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.22336	1.96;1.96;1.96	5.67	5.67	0.87782	.	0.169234	0.27956	N	0.017166	T	0.07863	0.0197	N	0.03304	-0.355	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.37753	-0.9692	10	0.08381	T	0.77	.	7.8425	0.29406	0.195:0.0:0.805:0.0	.	108	O75325	LRRN2_HUMAN	V	108	ENSP00000356144:A108V;ENSP00000356145:A108V;ENSP00000356143:A108V	ENSP00000356143:A108V	A	-	2	0	LRRN2	202855421	0.245000	0.23899	0.644000	0.29465	0.745000	0.42441	3.593000	0.54001	2.684000	0.91462	0.650000	0.86243	GCC	.	.		0.607	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338		A	204588798	G	A	204588798	3	1	216	1	0	0	0	0	1	0	0	0	9044	1203	42	3	1822	3	LRRN2	1	204588798	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	41819246	204588798	44661823	8	31096										
MTR	4548	hgsc.bcm.edu	37	chr1	236973846	236973846	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gctctgggtccgactaataaGacactctctgtgtccccatc	8	14	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr1:236973846G>T	ENST00000366577.5	+	5	847	c.453G>T	c.(451-453)aaG>aaT	p.K151N	MTR_ENST00000418145.2_Missense_Mutation_p.K207N|MTR_ENST00000535889.1_Missense_Mutation_p.K151N	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	151	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	CGACTAATAAGACACTCTCTG	0.438																																					p.K151N		Atlas-SNP	.											.	MTR	127	.	0			c.G453T						.						139	148	145					1																	236973846		2203	4300	6503	SO:0001583	missense	4548	exon5			TAATAAGACACTC	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.453G>T	chr1.hg19:g.236973846G>T	ENSP00000355536:p.Lys151Asn	155.0	1.0		205.0	133.0	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Missense_Mutation	SNP	ENST00000366577.5	hg19	CCDS1614.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.069063	0.76301	.	.	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000418145;ENST00000535889	T;T;T	0.12361	2.69;2.69;2.69	5.95	5.04	0.67666	Homocysteine S-methyltransferase (4);	0.048709	0.85682	D	0.000000	T	0.42698	0.1214	M	0.91920	3.255	0.42328	D	0.992289	D;D;D	0.53619	0.961;0.961;0.961	P;P;P	0.62298	0.9;0.9;0.9	T	0.54437	-0.8294	10	0.87932	D	0	-24.5432	12.8382	0.57786	0.1344:0.0:0.8656:0.0	.	151;151;151	B7ZLW8;B7ZLW7;Q99707	.;.;METH_HUMAN	N	151;151;207;151	ENSP00000355536:K151N;ENSP00000402255:K207N;ENSP00000441845:K151N	ENSP00000355536:K151N	K	+	3	2	MTR	235040469	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.281000	0.43452	1.530000	0.49136	0.655000	0.94253	AAG	.	.		0.438	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254		T	236973846	G	T	236973846	3	4	216	1	0	0	0	0	1	0	0	0	9967	933	33	3	471	3	MTR	1	236973846	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	32385048	236973846	12276775	9	31097										
OR2G2	81470	hgsc.bcm.edu	37	chr1	247752346	247752346	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gctacattgcccacgcagtgTtgaggattaagtcagctacc	10	11	1	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr1:247752346T>A	ENST00000320065.1	+	1	685	c.685T>A	c.(685-687)Ttg>Atg	p.L229M	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	229						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			CCACGCAGTGTTGAGGATTAA	0.478																																					p.L229M		Atlas-SNP	.											.	OR2G2	88	.	0			c.T685A						.						155	147	150					1																	247752346		2203	4300	6503	SO:0001583	missense	81470	exon1			GCAGTGTTGAGGA	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"GPCR / Class A : Olfactory receptors"	15007	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily G, member 2", "olfactory receptor, family 2, subfamily G, member 2 pseudogene"				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.685T>A	chr1.hg19:g.247752346T>A	ENSP00000326349:p.Leu229Met	127.0	0.0		227.0	65.0	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	hg19	CCDS31092.1	.	.	.	.	.	.	.	.	.	.	T	9.317	1.057110	0.19907	.	.	ENSG00000177489	ENST00000320065	T	0.00309	8.16	4.29	-6.15	0.02105	GPCR, rhodopsin-like superfamily (1);	0.000000	0.29884	U	0.010954	T	0.00384	0.0012	M	0.68728	2.09	0.09310	N	1	P	0.51791	0.948	P	0.57057	0.812	T	0.02683	-1.1124	10	0.48119	T	0.1	.	16.7803	0.85562	0.0:0.7499:0.0:0.2501	.	229	Q8NGZ5	OR2G2_HUMAN	M	229	ENSP00000326349:L229M	ENSP00000326349:L229M	L	+	1	2	OR2G2	245818969	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-2.132000	0.01309	-1.267000	0.02443	-0.391000	0.06502	TTG	.	.		0.478	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1			A	247752346	T	A	247752346	3	1	216	1	0	0	0	0	1	0	0	0	11007	1722	60	4	687	4	OR2G2	1	247752346	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	10778500	247752346	1498275	10	31098										
CAPN13	92291	hgsc.bcm.edu	37	chr2	30993238	30993238	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tggttttggtggcgaggacgCacaaagaggcatttatctcc	13	8	1	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr2:30993238C>T	ENST00000295055.8	-	5	641	c.465G>A	c.(463-465)gtG>gtA	p.V155V	CAPN13_ENST00000534090.2_Silent_p.V155V|CAPN13_ENST00000465960.2_5'UTR	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	155	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					GGCGAGGACGCACAAAGAGGC	0.552																																					p.V155V		Atlas-SNP	.											.	CAPN13	70	.	0			c.G465A						.						186	195	192					2																	30993238		2135	4250	6385	SO:0001819	synonymous_variant	92291	exon5			AGGACGCACAAAG		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.465G>A	chr2.hg19:g.30993238C>T		109.0	0.0		135.0	49.0	NM_144575	Q17RF0|Q580X1|Q8TE80	Silent	SNP	ENST00000295055.8	hg19	CCDS46252.1																																																																																			.	.		0.552	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		T	30993238	C	T	30993238	2	4	216	1	0	0	0	0	0	0	0	1	2628	697	25	3		3	CAPN13	2	30993238	Silent	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10		30993238	212206135	11	31099										
GMCL1	64395	hgsc.bcm.edu	37	chr2	70106092	70106092	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttctgatcttccctttatatAtctgctgtaacttcttgtat	4	9	4	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr2:70106092A>G	ENST00000282570.3	+	14	1755	c.1504A>G	c.(1504-1506)Atc>Gtc	p.I502V		NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	502					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)				endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						CCCTTTATATATCTGCTGTAA	0.328																																					p.I502V		Atlas-SNP	.											.	GMCL1	50	.	0			c.A1504G						.						123	128	126					2																	70106092		2203	4300	6503	SO:0001583	missense	64395	exon14			TTATATATCTGCT	AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"BTB/POZ domain containing"	23843	protein-coding gene	gene with protein product	"spermatogenesis associated 29"		"germ cell-less homolog 1 (Drosophila)"				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.1504A>G	chr2.hg19:g.70106092A>G	ENSP00000282570:p.Ile502Val	217.0	0.0		230.0	90.0	NM_178439	Q9H826|Q9H8V7|Q9H927	Missense_Mutation	SNP	ENST00000282570.3	hg19	CCDS1895.1	.	.	.	.	.	.	.	.	.	.	A	10.35	1.325326	0.24080	.	.	ENSG00000087338	ENST00000282570	T	0.55413	0.52	4.77	4.77	0.60923	.	0.118444	0.64402	N	0.000018	T	0.26774	0.0655	N	0.04669	-0.19	0.42308	D	0.992204	B	0.19073	0.033	B	0.17098	0.017	T	0.15723	-1.0427	10	0.06757	T	0.87	-21.456	12.5551	0.56248	1.0:0.0:0.0:0.0	.	502	Q96IK5	GMCL1_HUMAN	V	502	ENSP00000282570:I502V	ENSP00000282570:I502V	I	+	1	0	GMCL1	69959596	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.279000	0.65597	2.117000	0.64856	0.455000	0.32223	ATC	.	.		0.328	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439		G	70106092	A	G	70106092	3	3	216	1	0	0	0	0	1	0	0	0	6493	449	16	2	1558	2	GMCL1	2	70106092	Missense_Mutation	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	39112854	70106092	173093281	12	31100										
ITGB6	3694	hgsc.bcm.edu	37	chr2	161052880	161052880	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttgacatcctttagctaaaaGgtttgctggggtatcacacc	9	9	1	1	rs369726068		TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr2:161052880G>A	ENST00000283249.2	-	3	430	c.193C>T	c.(193-195)Ctt>Ttt	p.L65F	ITGB6_ENST00000428609.2_Missense_Mutation_p.L23F|ITGB6_ENST00000485635.1_5'UTR|ITGB6_ENST00000409872.1_Missense_Mutation_p.L65F|ITGB6_ENST00000409967.2_Missense_Mutation_p.L65F	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	65					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						TTAGCTAAAAGGTTTGCTGGG	0.348													G|||	1	0.000199681	0	0	5008	,	,		19276	0.001		0	False		,,,				2504	0				p.L65F		Atlas-SNP	.											.	ITGB6	68	.	0			c.C193T						.						147	160	156					2																	161052880		2203	4300	6503	SO:0001583	missense	3694	exon3			CTAAAAGGTTTGC		CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"Integrins"	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.193C>T	chr2.hg19:g.161052880G>A	ENSP00000283249:p.Leu65Phe	99.0	0.0		117.0	39.0	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Missense_Mutation	SNP	ENST00000283249.2	hg19	CCDS2212.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.875122	0.72180	.	.	ENSG00000115221	ENST00000283249;ENST00000428609;ENST00000409967;ENST00000409872	D;D;D;D	0.94931	-3.56;-3.56;-3.56;-3.56	5.67	4.78	0.61160	Integrin beta subunit, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.97539	0.9194	M	0.90309	3.105	0.54753	D	0.999986	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97804	1.0246	10	0.62326	D	0.03	.	14.8945	0.70633	0.0697:0.0:0.9303:0.0	.	23;65	E9PEE8;P18564	.;ITB6_HUMAN	F	65;23;65;65	ENSP00000283249:L65F;ENSP00000408024:L23F;ENSP00000386828:L65F;ENSP00000386367:L65F	ENSP00000283249:L65F	L	-	1	0	ITGB6	160761126	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	5.600000	0.67599	2.670000	0.90874	0.655000	0.94253	CTT	.	.		0.348	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888		A	161052880	G	A	161052880	3	1	216	1	0	0	0	0	1	0	0	0	7908	1000	35	3	2225	3	ITGB6	2	161052880	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	90946788	161052880	82146493	13	31101										
TTN	7273	hgsc.bcm.edu	37	chr2	179456870	179456870	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gagaggtgaccactgggcgcTggcaacatctctcctctcaa	11	13	2	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr2:179456870T>C	ENST00000591111.1	-	252	55062	c.54838A>G	c.(54838-54840)Agc>Ggc	p.S18280G	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S19921G|TTN_ENST00000342992.6_Missense_Mutation_p.S17353G|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S11048G|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S10981G|TTN_ENST00000460472.2_Missense_Mutation_p.S10856G			Q8WZ42	TITIN_HUMAN	titin	18280	Fibronectin type-III 32. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACTGGGCGCTGGCAACATCT	0.448																																					p.S19921G		Atlas-SNP	.											.	TTN	18412	.	0			c.A59761G						.						75	72	73					2																	179456870		1929	4158	6087	SO:0001583	missense	7273	exon302			GGGCGCTGGCAAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.54838A>G	chr2.hg19:g.179456870T>C	ENSP00000465570:p.Ser18280Gly	87.0	0.0		97.0	37.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	8.776	0.927045	0.18056	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	6.03	4.88	0.63580	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.45895	0.1365	L	0.52011	1.625	0.21220	N	0.999752	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.004;0.004;0.004;0.004	T	0.45041	-0.9288	9	0.87932	D	0	.	7.1235	0.25458	0.1603:0.0721:0.0:0.7677	.	10856;10981;11048;18280	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	17353;10856;11048;10981;10854	ENSP00000343764:S17353G;ENSP00000434586:S10856G;ENSP00000340554:S11048G;ENSP00000352154:S10981G	ENSP00000340554:S11048G	S	-	1	0	TTN	179165116	0.965000	0.33210	0.973000	0.42090	0.952000	0.60782	1.748000	0.38308	1.107000	0.41642	0.455000	0.32223	AGC	.	.		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179456870	T	C	179456870	3	2	216	1	0	0	0	0	1	0	0	0	16750	1580	55	2	48462	2	TTN	2	179456870	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	18403990	179456870	63742503	14	31102										
NDUFS1	4719	hgsc.bcm.edu	37	chr2	206991519	206991519	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	taggagagacttcttccaatCtgttccttacttgatccaga	7	10	2	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr2:206991519C>A	ENST00000233190.6	-	17	2200	c.1934G>T	c.(1933-1935)aGa>aTa	p.R645I	NDUFS1_ENST00000455934.2_Missense_Mutation_p.R659I|NDUFS1_ENST00000457011.1_Missense_Mutation_p.R529I|NDUFS1_ENST00000440274.1_Missense_Mutation_p.R609I|NDUFS1_ENST00000449699.1_Missense_Mutation_p.R645I|NDUFS1_ENST00000423725.1_Missense_Mutation_p.R588I|NDUFS1_ENST00000432169.1_Missense_Mutation_p.R534I	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	645					apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTCTTCCAATCTGTTCCTTAC	0.383																																					p.R659I		Atlas-SNP	.											.	NDUFS1	82	.	0			c.G1976T						.						143	144	144					2																	206991519		2203	4300	6503	SO:0001583	missense	4719	exon17			TCCAATCTGTTCC		CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7707	protein-coding gene	gene with protein product	"complex I 75kDa subunit", "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"	157655	"NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.1934G>T	chr2.hg19:g.206991519C>A	ENSP00000233190:p.Arg645Ile	164.0	0.0		177.0	68.0	NM_001199984	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Missense_Mutation	SNP	ENST00000233190.6	hg19	CCDS2366.1	.	.	.	.	.	.	.	.	.	.	C	32	5.173952	0.94807	.	.	ENSG00000023228	ENST00000233190;ENST00000423725;ENST00000457011;ENST00000440274;ENST00000455934;ENST00000449699;ENST00000432169	D;D;D;D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84;-1.84;-1.84;-1.84	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.94574	0.8252	M	0.92691	3.335	0.80722	D	1	P;D;D;D	0.89917	0.913;1.0;1.0;1.0	P;D;D;D	0.97110	0.788;0.999;1.0;0.999	D	0.95170	0.8289	10	0.72032	D	0.01	-17.9482	19.7635	0.96333	0.0:1.0:0.0:0.0	.	534;609;659;645	B4DPG1;E7ENF3;B4DJA0;P28331	.;.;.;NDUS1_HUMAN	I	645;588;529;609;659;645;534	ENSP00000233190:R645I;ENSP00000397760:R588I;ENSP00000400976:R529I;ENSP00000409766:R609I;ENSP00000392709:R659I;ENSP00000399912:R645I;ENSP00000409689:R534I	ENSP00000233190:R645I	R	-	2	0	NDUFS1	206699764	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.487000	0.81328	2.682000	0.91365	0.555000	0.69702	AGA	.	.		0.383	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006		A	206991519	C	A	206991519	3	1	216	1	0	0	0	0	1	0	0	0	10300	913	32	3	261	3	NDUFS1	2	206991519	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	27534649	206991519	36207854	15	31103										
WDR69	164781	hgsc.bcm.edu	37	chr2	228767773	228767773	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ggcgactggaagtatggacaCaacagccaaattgtgggaca	13	8	0	0	rs145956341	byFrequency	TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr2:228767773C>A	ENST00000309931.2	+	7	679	c.596C>A	c.(595-597)aCa>aAa	p.T199K	DAW1_ENST00000373666.2_Missense_Mutation_p.T199K|DAW1_ENST00000545118.1_Missense_Mutation_p.T184K	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	199						cilium (GO:0005929)											AGTATGGACACAACAGCCAAA	0.358													C|||	21	0.00419329	0	0	5008	,	,		20239	0.001		0	False		,,,				2504	0.0204				p.T199K		Atlas-SNP	.											.	.	.	.	0			c.C596A						.						144	134	137					2																	228767773		2203	4300	6503	SO:0001583	missense	164781	exon7			TGGACACAACAGC		CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"WD repeat domain containing"	26383	protein-coding gene	gene with protein product	"outer row dynein assembly 16 homolog (Chlamydomonas)"		"WD repeat domain 69"	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.596C>A	chr2.hg19:g.228767773C>A	ENSP00000311899:p.Thr199Lys	222.0	0.0		246.0	15.0	NM_178821	Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	hg19	CCDS2470.1	.	.	.	.	.	.	.	.	.	.	C	9.969	1.224947	0.22457	.	.	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000545118	T;T;T	0.57273	0.41;1.7;1.7	4.54	2.68	0.31781	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.277673	0.34879	N	0.003605	T	0.21468	0.0517	N	0.00823	-1.155	0.41910	D	0.990467	B	0.30211	0.273	B	0.39068	0.289	T	0.29941	-0.9995	10	0.02654	T	1	.	9.8463	0.41028	0.158:0.6897:0.1522:0.0	.	199	Q8N136	WDR69_HUMAN	K	199;199;184	ENSP00000362770:T199K;ENSP00000311899:T199K;ENSP00000437887:T184K	ENSP00000311899:T199K	T	+	2	0	WDR69	228476017	1.000000	0.71417	0.900000	0.35374	0.823000	0.46562	5.010000	0.64004	0.337000	0.23665	0.306000	0.20318	ACA	.	.		0.358	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821		A	228767773	C	A	228767773	3	1	216	1	0	0	0	0	1	0	0	0	17334	478	17	3	622	3	WDR69	2	228767773	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	21776254	228767773	14431600	16	31104										
ILKAP	80895	hgsc.bcm.edu	37	chr2	239092696	239092697	+	Frame_Shift_Ins	INS	-	-	T													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	taaggaactcttcatcagtaINStgcttgaaagtgtccaaaag							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr2:239092696_239092697insT	ENST00000254654.3	-	7	765_766	c.590_591insA	c.(589-591)catfs	p.H197fs		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	197	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)		CTTCATCAGTATGCTTGAAAGT	0.401																																					p.H197fs		Atlas-INDEL	.											.	ILKAP	42	.	0			c.591_592insA						.																																			SO:0001589	frameshift_variant	80895	exon7			.	AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	15566	protein-coding gene	gene with protein product			"integrin-linked kinase-associated serine/threonine phosphatase 2C"				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.591dupA	chr2.hg19:g.239092697_239092697dupT	ENSP00000254654:p.His197fs	82.0	0.0		101.0	27.0	NM_030768	B3KM39	Frame_Shift_Ins	INS	ENST00000254654.3	hg19	CCDS2526.1																																																																																			.	.		0.401	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768		T	239092697	-	T	239092696	7	5	216	1	0	1	1	0	0	0	0	0	7723	446	16	0	611	0	ILKAP	2	239092696	Frame_Shift_Ins	INS	-	TCGA-DD-AAEB-01A-11D-A40R-10	10324923	239092696	4106677	17	31105										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10384457	10384457	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aacaaagagcagggtgaagaTgagggcaagctggtagacag	16	5	0	5			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:10384457T>C	ENST00000352432.4	-	18	2965	c.2896A>G	c.(2896-2898)Atc>Gtc	p.I966V	ATP2B2_ENST00000383800.4_Missense_Mutation_p.I921V|ATP2B2_ENST00000360273.2_Missense_Mutation_p.I966V|ATP2B2_ENST00000343816.4_Missense_Mutation_p.I952V|ATP2B2_ENST00000397077.1_Missense_Mutation_p.I921V			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	966					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						AGGGTGAAGATGAGGGCAAGC	0.612																																					p.I966V	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A2896G						.						149	118	128					3																	10384457		2203	4300	6503	SO:0001583	missense	491	exon19			TGAAGATGAGGGC	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.2896A>G	chr3.hg19:g.10384457T>C	ENSP00000324172:p.Ile966Val	66.0	0.0		62.0	29.0	NM_001001331	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	t	15.63	2.891071	0.52014	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000429937;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.88509	-2.39;-2.39;-2.39;-2.39;-2.39;-2.39	4.0	4.0	0.46444	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.89241	0.6659	L	0.37850	1.14	0.80722	D	1	P;B;B	0.44090	0.826;0.002;0.003	P;B;B	0.57009	0.811;0.006;0.015	D	0.87201	0.2241	10	0.30078	T	0.28	-28.4506	13.1955	0.59736	0.0:0.0:0.0:1.0	.	901;933;966	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	V	966;921;921;966;952;901;155;822;966	ENSP00000324172:I966V;ENSP00000373311:I921V;ENSP00000380267:I921V;ENSP00000353414:I966V;ENSP00000344677:I952V;ENSP00000414854:I822V	ENSP00000342954:I966V	I	-	1	0	ATP2B2	10359457	1.000000	0.71417	1.000000	0.80357	0.631000	0.37964	6.016000	0.70798	1.575000	0.49775	0.255000	0.18592	ATC	.	.		0.612	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		C	10384457	T	C	10384457	3	2	216	1	0	0	0	0	1	0	0	0	1140	1464	51	2	855	2	ATP2B2	3	10384457	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10		10384457	187637973	18	31106										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19554546	19554546	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aggaggaggagggggaggaaGaggaggcagtctccctctct	19	7	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:19554546G>T	ENST00000328405.2	+	13	2430	c.2164G>T	c.(2164-2166)Gag>Tag	p.E722*		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	722	Poly-Glu.				potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						gggggaggaagaggaggCAGT	0.507																																					p.E722X	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.G2164T						.						60	50	53					3																	19554546		2203	4300	6503	SO:0001587	stop_gained	131096	exon13			GAGGAAGAGGAGG	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2164G>T	chr3.hg19:g.19554546G>T	ENSP00000328813:p.Glu722*	167.0	0.0		240.0	96.0	NM_144633	B7Z2I7|Q59GQ6	Nonsense_Mutation	SNP	ENST00000328405.2	hg19	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	G	41	8.787511	0.98954	.	.	ENSG00000183960	ENST00000328405	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4503	0.87590	0.0:0.0:1.0:0.0	.	.	.	.	X	722	.	.	E	+	1	0	KCNH8	19529550	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	5.057000	0.64294	2.559000	0.86315	0.585000	0.79938	GAG	.	.		0.507	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		T	19554546	G	T	19554546	4	4	216	1	0	0	0	0	0	1	0	0	8047	943	33	3	2214	3	KCNH8	3	19554546	Nonsense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	9170089	19554546	178467884	19	31107										
ITGA9	3680	hgsc.bcm.edu	37	chr3	37583948	37583948	+	Frame_Shift_Del	DEL	A	A	-													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttctgatggctgacgtggccAaaaaggagaagggccagatg					rs146867977		TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:37583948delA	ENST00000264741.5	+	15	1817	c.1561delA	c.(1561-1563)aaafs	p.K522fs	ITGA9_ENST00000422441.1_Frame_Shift_Del_p.K522fs	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	522					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		TGACGTGGCCAAAAAGGAGAA	0.517																																					p.A520fs		Atlas-INDEL	.											.	ITGA9	98	.	0			c.1560delC						.						143	133	136					3																	37583948		2203	4300	6503	SO:0001589	frameshift_variant	3680	exon15			.	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.1561delA	chr3.hg19:g.37583948delA	ENSP00000264741:p.Lys522fs	179.0	0.0		212.0	86.0	NM_002207	Q14638	Frame_Shift_Del	DEL	ENST00000264741.5	hg19	CCDS2669.1																																																																																			.	.		0.517	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		-	37583948	A	-	37583948	7	5	216	1	0	1	0	1	0	0	0	0	7892	131	5	0	1619	0	ITGA9	3	37583948	Frame_Shift_Del	DEL	A	TCGA-DD-AAEB-01A-11D-A40R-10	18029402	37583948	160438482	20	31108										
C3orf23	285343	hgsc.bcm.edu	37	chr3	44449133	44449133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttatgcaagatggagaccttTgtattccttggaattggaag	11	5	0	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:44449133T>C	ENST00000342649.4	+	11	1877	c.1450T>C	c.(1450-1452)Tgt>Cgt	p.C484R	TCAIM_ENST00000417237.1_Missense_Mutation_p.C484R	NM_001282913.1|NM_173826.3	NP_001269842.1|NP_776187.2	Q8N3R3	TCAIM_HUMAN	T cell activation inhibitor, mitochondrial	484						mitochondrion (GO:0005739)											TGGAGACCTTTGTATTCCTTG	0.333																																					p.C484R		Atlas-SNP	.											.	.	.	.	0			c.T1450C						.						82	87	85					3																	44449133		2203	4300	6503	SO:0001583	missense	285343	exon11			GACCTTTGTATTC		CCDS2712.1, CCDS43076.1	3p21.33-p21.32	2012-08-22	2012-08-22	2012-08-22	ENSG00000179152	ENSG00000179152			25241	protein-coding gene	gene with protein product	"tolerance associated gene-1"		"chromosome 3 open reading frame 23"	C3orf23		12477932	Standard	NM_001029840		Approved	DKFZp313N0621, TOAG-1	uc003cnd.4	Q8N3R3	OTTHUMG00000133049	ENST00000342649.4:c.1450T>C	chr3.hg19:g.44449133T>C	ENSP00000341539:p.Cys484Arg	248.0	0.0		268.0	96.0	NM_173826	A8K9P1|Q0P5T9|Q495R1|Q495R3|Q4G0M4|Q6GMU8	Missense_Mutation	SNP	ENST00000342649.4	hg19	CCDS2712.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.850371	0.91277	.	.	ENSG00000179152	ENST00000417237;ENST00000342649	T;T	0.53423	0.62;0.62	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.71517	0.3349	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75428	-0.3321	10	0.87932	D	0	.	16.6288	0.85011	0.0:0.0:0.0:1.0	.	484	Q8N3R3	CC023_HUMAN	R	484	ENSP00000402581:C484R;ENSP00000341539:C484R	ENSP00000341539:C484R	C	+	1	0	C3orf23	44424137	1.000000	0.71417	0.993000	0.49108	0.999000	0.98932	7.282000	0.78630	2.326000	0.78906	0.533000	0.62120	TGT	.	.		0.333	TCAIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256655.2	NM_173826		C	44449133	T	C	44449133	3	2	216	1	0	0	0	0	1	0	0	0	2218	1812	63	2	1540	2	C3orf23	3	44449133	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	6865185	44449133	153573297	21	31109										
SETD2	29072	hgsc.bcm.edu	37	chr3	47084191	47084191	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tttgtcacaaccatttcagaCtacaaagaaaacacacacat	3	11	2	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:47084191C>A	ENST00000409792.3	-	17	7141		c.e17-1			NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2						angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CCATTTCAGACTACAAAGAAA	0.413			"N, F, S, Mis"		clear cell renal carcinoma																																.		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.7099-1G>T						.						99	99	99					3																	47084191		2203	4300	6503	SO:0001630	splice_region_variant	29072	exon18			TTCAGACTACAAA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7099-1G>T	chr3.hg19:g.47084191C>A		108.0	0.0		104.0	37.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Splice_Site	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	21.5	4.154189	0.78114	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7322	0.91739	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SETD2	47059195	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.386000	0.52492	2.650000	0.89964	0.655000	0.94253	.	.	.		0.413	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	Intron	A	47084191	C	A	47084191	5	1	216	1	0	0	0	0	0	0	1	0	14146	579	20	3	616	3	SETD2	3	47084191	Splice_Site	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	2635058	47084191	150938239	22	31110										
MGLL	11343	hgsc.bcm.edu	37	chr3	127441310	127441310	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ggaagacaggaagcccagggTagtctttctgcatggaatcc	13	9	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:127441310T>C	ENST00000434178.2	-	4	1228	c.332A>G	c.(331-333)tAc>tGc	p.Y111C	MGLL_ENST00000398104.1_Missense_Mutation_p.Y111C|MGLL_ENST00000398101.3_Missense_Mutation_p.Y85C|MGLL_ENST00000265052.5_Missense_Mutation_p.Y121C|MGLL_ENST00000453507.2_Missense_Mutation_p.Y121C			Q99685	MGLL_HUMAN	monoglyceride lipase	111					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						AAGCCCAGGGTAGTCTTTCTG	0.557																																					p.Y121C		Atlas-SNP	.											.	MGLL	19	.	0			c.A362G						.						97	103	101					3																	127441310		1992	4184	6176	SO:0001583	missense	11343	exon4			CCAGGGTAGTCTT	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.332A>G	chr3.hg19:g.127441310T>C	ENSP00000402798:p.Tyr111Cys	110.0	0.0		105.0	42.0	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Missense_Mutation	SNP	ENST00000434178.2	hg19	CCDS43148.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.143032	0.77888	.	.	ENSG00000074416	ENST00000434178;ENST00000265052;ENST00000398104;ENST00000398101;ENST00000487473;ENST00000536024;ENST00000453507;ENST00000484451;ENST00000493611	T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08	4.69	4.69	0.59074	.	0.345575	0.31427	N	0.007667	D	0.87838	0.6278	M	0.85777	2.775	0.58432	D	0.999991	D;D;D;D;D	0.65815	0.992;0.98;0.979;0.992;0.995	P;P;D;D;D	0.70716	0.797;0.705;0.935;0.97;0.963	D	0.88382	0.3002	10	0.44086	T	0.13	-24.7539	13.1775	0.59635	0.0:0.0:0.0:1.0	.	121;111;111;121;85	B7Z9D1;B2ZGL7;Q99685;B3KRC2;E7EWX8	.;.;MGLL_HUMAN;.;.	C	111;121;111;85;35;121;121;35;48	ENSP00000402798:Y111C;ENSP00000265052:Y121C;ENSP00000381176:Y111C;ENSP00000381173:Y85C	ENSP00000265052:Y121C	Y	-	2	0	MGLL	128924000	1.000000	0.71417	0.966000	0.40874	0.966000	0.64601	7.241000	0.78201	1.762000	0.52044	0.254000	0.18369	TAC	.	.		0.557	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283		C	127441310	T	C	127441310	3	2	216	1	0	0	0	0	1	0	0	0	9565	1638	57	2	599	2	MGLL	3	127441310	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	80357119	127441310	70581120	23	31111										
MGLL	11343	hgsc.bcm.edu	37	chr3	127540591	127540591	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agaggtactgtccgtctgcaTtgaccaggtgagggaggtcc	15	9	1	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:127540591T>G	ENST00000434178.2	-	2	967	c.71A>C	c.(70-72)aAt>aCt	p.N24T	MGLL_ENST00000398104.1_Missense_Mutation_p.N24T|MGLL_ENST00000265052.5_Missense_Mutation_p.N34T|MGLL_ENST00000453507.2_Missense_Mutation_p.N34T			Q99685	MGLL_HUMAN	monoglyceride lipase	24					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						TCCGTCTGCATTGACCAGGTG	0.582																																					p.N34T		Atlas-SNP	.											.	MGLL	19	.	0			c.A101C						.						119	124	122					3																	127540591		1905	4112	6017	SO:0001583	missense	11343	exon2			TCTGCATTGACCA	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.71A>C	chr3.hg19:g.127540591T>G	ENSP00000402798:p.Asn24Thr	95.0	0.0		90.0	32.0	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Missense_Mutation	SNP	ENST00000434178.2	hg19	CCDS43148.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.762030	0.69763	.	.	ENSG00000074416	ENST00000434178;ENST00000265052;ENST00000398104;ENST00000536024;ENST00000453507;ENST00000494830	T;T;T	0.74526	-0.85;-0.85;-0.85	5.12	5.12	0.69794	.	0.100765	0.64402	D	0.000005	T	0.81772	0.4893	L	0.60455	1.87	0.47584	D	0.999466	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79108	0.992;0.992;0.992;0.992	T	0.78529	-0.2169	10	0.19590	T	0.45	0.2073	13.5166	0.61543	0.0:0.0:0.0:1.0	.	34;24;24;34	B7Z9D1;B2ZGL7;Q99685;B3KRC2	.;.;MGLL_HUMAN;.	T	24;34;24;34;34;24	ENSP00000402798:N24T;ENSP00000265052:N34T;ENSP00000381176:N24T	ENSP00000265052:N34T	N	-	2	0	MGLL	129023281	1.000000	0.71417	0.897000	0.35233	0.725000	0.41563	6.184000	0.72008	1.934000	0.56057	0.482000	0.46254	AAT	.	.		0.582	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283		G	127540591	T	G	127540591	3	3	216	1	0	0	0	0	1	0	0	0	9565	1493	52	5	868	5	MGLL	3	127540591	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	99281	127540591	70481839	24	31112										
ASTE1	28990	hgsc.bcm.edu	37	chr3	130743203	130743232	+	In_Frame_Del	DEL	GACATAAGTACCACACTGGAAGAAGTCCTG	GACATAAGTACCACACTGGAAGAAGTCCTG	-													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agattcaaggcatctggacaGacataagtaccacactggaa					rs149777056		TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	GACATAAGTACCACACTGGAAGAAGTCCTG	GACATAAGTACCACACTGGAAGAAGTCCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:130743203_130743232delGACATAAGTACCACACTGGAAGAAGTCCTG	ENST00000264992.3	-	3	1360_1389	c.919_948delCAGGACTTCTTCCAGTGTGGTACTTATGTC	c.(919-948)caggacttcttccagtgtggtacttatgtcdel	p.QDFFQCGTYV307del	NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000429253.2_5'Flank|NEK11_ENST00000412440.2_5'Flank|NEK11_ENST00000511262.1_5'Flank|ASTE1_ENST00000514044.1_In_Frame_Del_p.QDFFQCGTYV307del|NEK11_ENST00000383366.4_5'Flank|NEK11_ENST00000356918.4_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	307					DNA repair (GO:0006281)		nuclease activity (GO:0004518)	p.F310fs*25(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						CATCTGGACAGACATAAGTACCACACTGGAAGAAGTCCTGTAGCTTCACC	0.426																																					p.307_317del		Atlas-INDEL	.											.	ASTE1	67	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.920_949del						.																																			SO:0001651	inframe_deletion	28990	exon3			.	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.919_948delCAGGACTTCTTCCAGTGTGGTACTTATGTC	chr3.hg19:g.130743203_130743232delGACATAAGTACCACACTGGAAGAAGTCCTG	ENSP00000264992:p.Gln307_Val316del	130.0	0.0		107.0	29.0	NM_014065	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	In_Frame_Del	DEL	ENST00000264992.3	hg19	CCDS3068.1																																																																																			.	.		0.426	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		-	130743232	GACATAAGTACCACACTGGAAGAAGTCCTG	-	130743203	7	5	216	1	0	1	0	1	0	0	0	0	1062	929	33	0	1107	0	ASTE1	3	130743203	In_Frame_Del	DEL	GACATAAGTACCACACTGGAAGAAGTCCTG	TCGA-DD-AAEB-01A-11D-A40R-10	3202612	130743203	67279227	25	31113										
NPHP3	27031	hgsc.bcm.edu	37	chr3	132413781	132413781	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ctggaaacactgatgaaggaTtttatctaaattgcctgctc	8	8	1	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:132413781T>C	ENST00000337331.5	-	16	2286	c.2200A>G	c.(2200-2202)Atc>Gtc	p.I734V	NPHP3_ENST00000326682.8_3'UTR	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	734					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TGATGAAGGATTTTATCTAAA	0.378																																					p.I734V		Atlas-SNP	.											.	NPHP3	110	.	0			c.A2200G						.						120	120	120					3																	132413781		2203	4300	6503	SO:0001583	missense	27031	exon16			GAAGGATTTTATC	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"Tetratricopeptide (TTC) repeat domain containing"	7907	protein-coding gene	gene with protein product	"nephrocystin-3", "Meckel syndrome, type 7", "cilia and flagella associated protein 31"	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.2200A>G	chr3.hg19:g.132413781T>C	ENSP00000338766:p.Ile734Val	93.0	0.0		95.0	34.0	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	hg19	CCDS3078.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.335983	0.24253	.	.	ENSG00000113971	ENST00000393144;ENST00000337331	T	0.65916	-0.18	5.56	1.96	0.26148	.	0.432765	0.28125	N	0.016520	T	0.31327	0.0793	N	0.03115	-0.41	0.21020	N	0.999802	B	0.02656	0.0	B	0.01281	0.0	T	0.18304	-1.0341	10	0.13470	T	0.59	-1.2643	7.8324	0.29351	0.0:0.2319:0.0:0.7681	.	734	Q7Z494	NPHP3_HUMAN	V	14;734	ENSP00000338766:I734V	ENSP00000338766:I734V	I	-	1	0	NPHP3	133896471	0.995000	0.38212	0.066000	0.19879	0.992000	0.81027	1.870000	0.39529	0.403000	0.25479	0.460000	0.39030	ATC	.	.		0.378	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		C	132413781	T	C	132413781	3	2	216	1	0	0	0	0	1	0	0	0	10589	1493	52	2	1840	2	NPHP3	3	132413781	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	1670578	132413781	65608649	26	31114										
MED12L	116931	hgsc.bcm.edu	37	chr3	151105931	151105931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agaaaacaaaaggaaggaagCgcaagacgaaatctagctca	10	7	2	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:151105931C>T	ENST00000474524.1	+	35	5355	c.5317C>T	c.(5317-5319)Cgc>Tgc	p.R1773C	MED12L_ENST00000273432.4_Missense_Mutation_p.R1633C	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1773						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGGAAGGAAGCGCAAGACGAA	0.433																																					p.R1773C		Atlas-SNP	.											.	MED12L	271	.	0			c.C5317T						.						55	52	53					3																	151105931		2203	4300	6503	SO:0001583	missense	116931	exon35			AGGAAGCGCAAGA	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5317C>T	chr3.hg19:g.151105931C>T	ENSP00000417235:p.Arg1773Cys	19.0	0.0		21.0	9.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891221	0.72524	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.62364	0.22;0.03	5.81	5.81	0.92471	.	0.171350	0.51477	D	0.000084	T	0.66268	0.2772	N	0.19112	0.55	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;P;P	0.83275	0.996;0.649;0.799	T	0.69632	-0.5093	10	0.87932	D	0	-17.84	12.6448	0.56728	0.2059:0.7941:0.0:0.0	.	1633;1772;1773	F8WAE6;Q86YW9-4;Q86YW9	.;.;MD12L_HUMAN	C	1773;1633	ENSP00000417235:R1773C;ENSP00000273432:R1633C	ENSP00000273432:R1633C	R	+	1	0	MED12L	152588621	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	1.329000	0.33770	2.746000	0.94184	0.655000	0.94253	CGC	.	.		0.433	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		T	151105931	C	T	151105931	3	4	216	1	0	0	0	0	1	0	0	0	9438	768	27	1	5455	1	MED12L	3	151105931	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	18692150	151105931	46916499	27	31115										
DGKG	1608	hgsc.bcm.edu	37	chr3	185970881	185970883	+	Splice_Site	DEL	CCT	CCT	-													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	accattagcatgcaaactcaCctcctccccagcggagacaa							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:185970881_185970883delCCT	ENST00000265022.3	-	18	2138_2140	c.1599_1601delAGG	c.(1597-1602)ggaggt>ggt	p.533_534GG>G	DGKG_ENST00000544847.1_Splice_Site_p.474_475GG>G|DGKG_ENST00000344484.4_Splice_Site_p.508_509GG>G|DGKG_ENST00000382164.4_Splice_Site_p.494_495GG>G	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	533	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	TGCAAACTCACCTCCTCCCCAGC	0.502																																					p.534_534del		Atlas-INDEL	.											.	DGKG	98	.	0			c.1600_1600del						.																																			SO:0001630	splice_region_variant	1608	exon18			.	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.1600+1AGG>-	chr3.hg19:g.185970884_185970886delCCT		53.0	0.0		48.0	14.0	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Frame_Shift_Del	DEL	ENST00000265022.3	hg19	CCDS3274.1																																																																																			.	.		0.502	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3		In_Frame_Del	-	185970883	CCT	-	185970881	8	5	216	1	0	1	0	1	0	0	1	0	4471	521	18	0	806	0	DGKG	3	185970881	Splice_Site	DEL	CCT	TCGA-DD-AAEB-01A-11D-A40R-10	34864950	185970881	12051549	28	31116										
KNG1	3827	hgsc.bcm.edu	37	chr3	186459957	186459957	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tgacgattggatccctgataTccagatagacccaaatggcc	9	11	0	4			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:186459957T>A	ENST00000265023.4	+	10	1984	c.1772T>A	c.(1771-1773)aTc>aAc	p.I591N	KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000596329.1_RNA|RP11-573D15.8_ENST00000609726.1_RNA|KNG1_ENST00000287611.2_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	591					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		ATCCCTGATATCCAGATAGAC	0.453																																					p.I591N		Atlas-SNP	.											.	KNG1	129	.	0			c.T1772A						.						144	135	138					3																	186459957		1932	4127	6059	SO:0001583	missense	3827	exon10			CTGATATCCAGAT		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"Endogenous ligands"	6383	protein-coding gene	gene with protein product	"alpha-2-thiol proteinase inhibitor", "bradykinin"	612358	"kininogen"	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.1772T>A	chr3.hg19:g.186459957T>A	ENSP00000265023:p.Ile591Asn	133.0	0.0		150.0	63.0	NM_001102416	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	hg19	CCDS43183.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.692278	0.30052	.	.	ENSG00000113889	ENST00000265023	T	0.30448	1.53	5.4	5.4	0.78164	.	0.330322	0.22608	N	0.057874	T	0.45418	0.1341	L	0.54323	1.7	0.80722	D	1	D	0.71674	0.998	P	0.60789	0.879	T	0.29243	-1.0018	9	.	.	.	-6.5395	12.1266	0.53920	0.0:0.0:0.0:1.0	.	591	P01042	KNG1_HUMAN	N	591	ENSP00000265023:I591N	.	I	+	2	0	KNG1	187942651	0.171000	0.23029	0.710000	0.30468	0.135000	0.20990	4.195000	0.58400	2.190000	0.69967	0.533000	0.62120	ATC	.	.		0.453	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416		A	186459957	T	A	186459957	3	1	216	1	0	0	0	0	1	0	0	0	8436	1435	50	4	1810	4	KNG1	3	186459957	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	489076	186459957	11562473	29	31117										
RNF168	165918	hgsc.bcm.edu	37	chr3	196199524	196199524	+	Missense_Mutation	SNP	T	T	C													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aaccatggcataggggactcTattgaagaatctgcaccttg							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:196199524T>C	ENST00000318037.3	-	6	1476	c.882A>G	c.(880-882)atA>atG	p.I294M	CTD-2002J20.1_ENST00000610042.1_RNA	NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	294					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		TAGGGGACTCTATTGAAGAAT	0.458																																					p.I294M		Atlas-SNP	.											.	RNF168	49	.	0			c.A882G						.						130	124	126					3																	196199524		2203	4300	6503	SO:0001583	missense	165918	exon6			GGACTCTATTGAA	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.882A>G	chr3.hg19:g.196199524T>C	ENSP00000320898:p.Ile294Met	115.0	0.0		148.0	51.0	NM_152617	Q8NA67|Q96NS4	Missense_Mutation	SNP	ENST00000318037.3	hg19	CCDS3317.1	.	.	.	.	.	.	.	.	.	.	T	5.880	0.346572	0.11126	.	.	ENSG00000163961	ENST00000318037	T	0.07567	3.18	5.86	-2.49	0.06403	.	2.505920	0.01098	N	0.005301	T	0.05318	0.0141	N	0.12182	0.205	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.36841	-0.9731	10	0.34782	T	0.22	1.2268	6.5101	0.22216	0.0:0.3888:0.134:0.4772	.	294	Q8IYW5	RN168_HUMAN	M	294	ENSP00000320898:I294M	ENSP00000320898:I294M	I	-	3	3	RNF168	197683921	0.231000	0.23751	0.001000	0.08648	0.001000	0.01503	0.101000	0.15251	-0.687000	0.05162	-1.039000	0.02377	ATA	.	.		0.458	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		C	196199524	T	C	196199524	3	2	216	1	0	0	0	0	1	0	0	0	13474	1512	53	2	837	2	RNF168	3	196199524	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	9739567	196199524	1822906	30	31118	162	2								
RNF168	165918	hgsc.bcm.edu	37	chr3	196199527	196199527	+	Silent	SNP	T	T	G													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	catggcataggggactctatTgaagaatctgcaccttgttc							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr3:196199527T>G	ENST00000318037.3	-	6	1473	c.879A>C	c.(877-879)tcA>tcC	p.S293S	CTD-2002J20.1_ENST00000610042.1_RNA	NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	293					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		GGGACTCTATTGAAGAATCTG	0.453																																					p.S293S		Atlas-SNP	.											.	RNF168	49	.	0			c.A879C						.						124	119	120					3																	196199527		2203	4300	6503	SO:0001819	synonymous_variant	165918	exon6			CTCTATTGAAGAA	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.879A>C	chr3.hg19:g.196199527T>G		117.0	0.0		145.0	51.0	NM_152617	Q8NA67|Q96NS4	Silent	SNP	ENST00000318037.3	hg19	CCDS3317.1																																																																																			.	.		0.453	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		G	196199527	T	G	196199527	2	3	216	1	0	0	0	0	0	0	0	1	13474	1799	63	5		5	RNF168	3	196199527	Silent	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	3	196199527	1822903	31	31119	162	2								
ZAR1	326340	hgsc.bcm.edu	37	chr4	48496259	48496259	+	Nonstop_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tcagcttcaaatacatcattTaggtgaaagtcagtgttgct	8	7	4	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr4:48496259T>G	ENST00000327939.4	+	4	1313	c.1273T>G	c.(1273-1275)Tag>Gag	p.*425E		NM_175619.1	NP_783318.1	Q86SH2	ZAR1_HUMAN	zygote arrest 1	0					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(4)	5						ATACATCATTTAGGTGAAAGT	0.498																																					p.X425E		Atlas-SNP	.											.	ZAR1	15	.	0			c.T1273G						.						87	90	89					4																	48496259		2203	4300	6503	SO:0001578	stop_lost	326340	exon4			ATCATTTAGGTGA	AY193890	CCDS3483.1	4p11	2014-02-20			ENSG00000182223	ENSG00000182223			20436	protein-coding gene	gene with protein product	"zinc finger, 3CxxC-type 6"	607520				12539046	Standard	NM_175619		Approved	Z3CXXC6	uc003gyd.3	Q86SH2	OTTHUMG00000102093	ENST00000327939.4:c.1273T>G	chr4.hg19:g.48496259T>G	ENSP00000329803:p.*425Gluext*13	65.0	0.0		49.0	16.0	NM_175619		Missense_Mutation	SNP	ENST00000327939.4	hg19	CCDS3483.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.454401	0.26161	.	.	ENSG00000182223	ENST00000327939	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1659	0.81754	0.0:0.0:0.0:1.0	.	.	.	.	E	425	.	.	X	+	1	0	ZAR1	48191016	1.000000	0.71417	0.969000	0.41365	0.076000	0.17211	7.671000	0.83941	2.221000	0.72209	0.383000	0.25322	TAG	.	.		0.498	ZAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219927.3			G	48496259	T	G	48496259	4	3	216	1	0	0	0	0	0	0	0	0	17530	1767	61	5	1287	5	ZAR1	4	48496259	Nonstop_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10		48496259	142658017	32	31120										
PPAT	5471	hgsc.bcm.edu	37	chr4	57261620	57261620	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ccattttcttggatcataatAtcgtgctttttctctttctg	5	9	4	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr4:57261620A>G	ENST00000264220.2	-	11	1589	c.1452T>C	c.(1450-1452)gaT>gaC	p.D484D	RP11-646I6.6_ENST00000602749.1_lincRNA	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	484					'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	GGATCATAATATCGTGCTTTT	0.358																																					p.D484D		Atlas-SNP	.											.	PPAT	41	.	0			c.T1452C						.						107	101	103					4																	57261620		2203	4300	6503	SO:0001819	synonymous_variant	5471	exon11			CATAATATCGTGC		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.1452T>C	chr4.hg19:g.57261620A>G		298.0	1.0		322.0	116.0	NM_002703		Silent	SNP	ENST00000264220.2	hg19	CCDS3505.1																																																																																			.	.		0.358	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		G	57261620	A	G	57261620	2	3	216	1	0	0	0	0	0	0	0	1	12311	446	16	2		2	PPAT	4	57261620	Silent	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	8765361	57261620	133892656	33	31121										
PAICS	10606	hgsc.bcm.edu	37	chr4	57312971	57312971	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gaatagcaactggttcttttCtcaaaagaaatcctggtgtc	8	8	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr4:57312971C>T	ENST00000512576.1	+	3	486	c.325C>T	c.(325-327)Ctc>Ttc	p.L109F	PAICS_ENST00000399688.3_Missense_Mutation_p.L116F|PAICS_ENST00000264221.2_Missense_Mutation_p.L109F|PAICS_ENST00000514888.1_Missense_Mutation_p.L17F	NM_001079524.1	NP_001072992.1	P22234	PUR6_HUMAN	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase	109	SAICAR synthetase.				'de novo' IMP biosynthetic process (GO:0006189)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|phosphoribosylaminoimidazole carboxylase activity (GO:0004638)|phosphoribosylaminoimidazolesuccinocarboxamide synthase activity (GO:0004639)			endometrium(1)|kidney(2)|large_intestine(1)|urinary_tract(1)	5	Glioma(25;0.08)|all_neural(26;0.101)				L-Aspartic Acid(DB00128)	TGGTTCTTTTCTCAAAAGAAA	0.388																																					p.L116F	GBM(53;429 1144 8755 40726)	Atlas-SNP	.											.	PAICS	21	.	0			c.C346T						.						44	43	44					4																	57312971		1840	4082	5922	SO:0001583	missense	10606	exon4			TCTTTTCTCAAAA	X53793	CCDS47060.1, CCDS47061.1	4q12	2012-07-13			ENSG00000128050	ENSG00000128050	4.1.1.21, 6.3.2.6		8587	protein-coding gene	gene with protein product		172439		PAIS		2253271, 8106516	Standard	NM_006452		Approved	ADE2H1, AIRC	uc003hbt.1	P22234	OTTHUMG00000160957	ENST00000512576.1:c.325C>T	chr4.hg19:g.57312971C>T	ENSP00000421096:p.Leu109Phe	244.0	0.0		264.0	114.0	NM_001079525	E9PDH9|Q68CQ5	Missense_Mutation	SNP	ENST00000512576.1	hg19	CCDS47061.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.468674	0.84533	.	.	ENSG00000128050	ENST00000514888;ENST00000264221;ENST00000505164;ENST00000399688;ENST00000512576	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.43	5.43	0.79202	ATP-grasp fold, subdomain 2 (1);	0.000000	0.85682	D	0.000000	T	0.71247	0.3317	M	0.86805	2.84	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.994;0.995	T	0.75634	-0.3250	10	0.72032	D	0.01	-10.9649	12.9038	0.58141	0.0:0.9254:0.0:0.0746	.	109;116;109	E9PBS1;P22234-2;P22234	.;.;PUR6_HUMAN	F	17;109;109;116;109	ENSP00000424907:L17F;ENSP00000264221:L109F;ENSP00000424053:L109F;ENSP00000382595:L116F;ENSP00000421096:L109F	ENSP00000264221:L109F	L	+	1	0	PAICS	57007728	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.064000	0.57506	2.718000	0.92993	0.585000	0.79938	CTC	.	.		0.388	PAICS-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363136.2	NM_006452		T	57312971	C	T	57312971	3	4	216	1	0	0	0	0	1	0	0	0	11404	913	32	3	360	3	PAICS	4	57312971	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	51351	57312971	133841305	34	31122										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87643469	87643469	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	acaagccaaaatggcccttaGacagtctcggttgagcctat	9	11	1	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr4:87643469G>T	ENST00000411767.2	+	10	1553	c.1490G>T	c.(1489-1491)aGa>aTa	p.R497I	PTPN13_ENST00000316707.6_Missense_Mutation_p.R497I|PTPN13_ENST00000511467.1_Missense_Mutation_p.R497I|PTPN13_ENST00000427191.2_Missense_Mutation_p.R497I|PTPN13_ENST00000436978.1_Missense_Mutation_p.R497I			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	497					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		ATGGCCCTTAGACAGTCTCGG	0.443																																					p.R497I		Atlas-SNP	.											.	PTPN13	203	.	0			c.G1490T						.						125	118	120					4																	87643469		1929	4135	6064	SO:0001583	missense	5783	exon10			CCCTTAGACAGTC		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.1490G>T	chr4.hg19:g.87643469G>T	ENSP00000407249:p.Arg497Ile	382.0	0.0		408.0	163.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.141864	0.57044	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39	4.92	4.92	0.64577	.	0.000000	0.49916	D	0.000129	T	0.60534	0.2276	M	0.67953	2.075	0.54753	D	0.999989	D;D;D;D	0.89917	0.994;1.0;1.0;1.0	D;D;D;D	0.97110	0.963;1.0;0.999;0.999	T	0.64672	-0.6352	10	0.87932	D	0	.	18.4798	0.90807	0.0:0.0:1.0:0.0	.	497;497;497;497	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	I	497;497;497;497;497;465	ENSP00000408368:R497I;ENSP00000394794:R497I;ENSP00000322675:R497I;ENSP00000407249:R497I;ENSP00000426626:R497I	ENSP00000322675:R497I	R	+	2	0	PTPN13	87862493	1.000000	0.71417	0.365000	0.25901	0.144000	0.21451	7.103000	0.77014	2.444000	0.82710	0.655000	0.94253	AGA	.	.		0.443	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			T	87643469	G	T	87643469	3	4	216	1	0	0	0	0	1	0	0	0	12795	942	33	3	1524	3	PTPN13	4	87643469	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	30330498	87643469	103510807	35	31123										
SLC25A31	83447	hgsc.bcm.edu	37	chr4	128689945	128689945	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aagaaaactccatttcttgtCtcctttttcattgctcaagt	4	10	4	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr4:128689945C>T	ENST00000281154.4	+	5	840	c.672C>T	c.(670-672)gtC>gtT	p.V224V		NM_031291.2	NP_112581.1	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	224					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|nucleus (GO:0005634)	transporter activity (GO:0005215)			NS(1)|breast(1)|large_intestine(10)|lung(8)|skin(2)	22						CATTTCTTGTCTCCTTTTTCA	0.323																																					p.V224V		Atlas-SNP	.											.	SLC25A31	42	.	0			c.C672T						.						118	109	112					4																	128689945		2203	4299	6502	SO:0001819	synonymous_variant	83447	exon5			TCTTGTCTCCTTT	AL136857	CCDS3733.1	4q28	2013-05-22			ENSG00000151475	ENSG00000151475		"Solute carriers"	25319	protein-coding gene	gene with protein product		610796				15670820	Standard	NM_031291		Approved	DKFZP434N1235, ANT4	uc003ifl.3	Q9H0C2	OTTHUMG00000133300	ENST00000281154.4:c.672C>T	chr4.hg19:g.128689945C>T		85.0	0.0		99.0	32.0	NM_031291		Silent	SNP	ENST00000281154.4	hg19	CCDS3733.1																																																																																			.	.		0.323	SLC25A31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257094.2	NM_031291		T	128689945	C	T	128689945	2	4	216	1	0	0	0	0	0	0	0	1	14510	900	32	3		3	SLC25A31	4	128689945	Silent	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	41046476	128689945	62464331	36	31124										
SNX25	83891	hgsc.bcm.edu	37	chr4	186244738	186244738	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aatttctttgtggagagcaaAgaaatatctgtggaaaaatc	9	4	2	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr4:186244738A>G	ENST00000504273.1	+	9	1335	c.1041A>G	c.(1039-1041)aaA>aaG	p.K347K	SNX25_ENST00000512853.1_3'UTR|SNX25_ENST00000264694.8_Silent_p.K347K			Q9H3E2	SNX25_HUMAN	sorting nexin 25	347	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		TGGAGAGCAAAGAAATATCTG	0.313																																					p.K347K		Atlas-SNP	.											.	SNX25	100	.	0			c.A1041G						.						49	55	53					4																	186244738		2202	4295	6497	SO:0001819	synonymous_variant	83891	exon9			GAGCAAAGAAATA	AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"Sorting nexins"	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.1041A>G	chr4.hg19:g.186244738A>G		202.0	0.0		106.0	5.0	NM_031953	Q3ZT30|Q8N6K3	Silent	SNP	ENST00000504273.1	hg19	CCDS34116.1																																																																																			.	.		0.313	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953		G	186244738	A	G	186244738	2	3	216	1	0	0	0	0	0	0	0	1	14911	69	3	2		2	SNX25	4	186244738	Silent	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	57554793	186244738	4909538	37	31125										
TERT	7015	hgsc.bcm.edu	37	chr5	1294122	1294122	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	cccacggatgggtgggagtgGcgcgtgccagagagcgcacc	18	12	0	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr5:1294122G>T	ENST00000310581.5	-	2	936	c.879C>A	c.(877-879)cgC>cgA	p.R293R	TERT_ENST00000296820.5_Silent_p.R293R|TERT_ENST00000334602.6_Silent_p.R293R|TERT_ENST00000522877.1_5'Flank|TERT_ENST00000508104.2_Silent_p.R293R	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	293	Linker.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	GGTGGGAGTGGCGCGTGCCAG	0.697									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.R293R		Atlas-SNP	.											.	TERT	2594	.	0			c.C879A						.						21	20	20					5																	1294122		2171	4268	6439	SO:0001819	synonymous_variant	7015	exon2	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	GGAGTGGCGCGTG	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.879C>A	chr5.hg19:g.1294122G>T		91.0	0.0		102.0	47.0	NM_001193376	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	hg19	CCDS3861.2																																																																																			.	.		0.697	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			T	1294122	G	T	1294122	2	4	216	1	0	0	0	0	0	0	0	1	15779	1190	42	3		3	TERT	5	1294122	Silent	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10		1294122	179621138	38	31126										
NNT	23530	hgsc.bcm.edu	37	chr5	43650682	43650682	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gcattcatatcctctgtcaaCattgcaggtatgatgtcagt	8	9	4	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr5:43650682C>T	ENST00000264663.5	+	12	1931	c.1710C>T	c.(1708-1710)aaC>aaT	p.N570N	NNT_ENST00000344920.4_Silent_p.N570N|NNT_ENST00000512996.2_Silent_p.N439N	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	570					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					CCTCTGTCAACATTGCAGGTA	0.413																																					p.N570N		Atlas-SNP	.											.	NNT	92	.	0			c.C1710T						.						164	143	150					5																	43650682		2203	4300	6503	SO:0001819	synonymous_variant	23530	exon12			TGTCAACATTGCA	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.1710C>T	chr5.hg19:g.43650682C>T		72.0	0.0		77.0	30.0	NM_182977	Q16796|Q2TB60|Q8N3V4	Silent	SNP	ENST00000264663.5	hg19	CCDS3949.1																																																																																			.	.		0.413	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		T	43650682	C	T	43650682	2	4	216	1	0	0	0	0	0	0	0	1	10519	477	17	3		3	NNT	5	43650682	Silent	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	42356560	43650682	137264578	39	31127										
HEXB	3074	hgsc.bcm.edu	37	chr5	74009421	74009421	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gaggaattcgagtcctgccaGaatttgatacccctgggcat	11	10	0	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr5:74009421G>T	ENST00000261416.7	+	7	979	c.862G>T	c.(862-864)Gaa>Taa	p.E288*	HEXB_ENST00000511181.1_Nonsense_Mutation_p.E63*	NM_000521.3	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B (beta polypeptide)	288					astrocyte cell migration (GO:0043615)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|ganglioside catabolic process (GO:0006689)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|lipid storage (GO:0019915)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|male courtship behavior (GO:0008049)|myelination (GO:0042552)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|oogenesis (GO:0048477)|penetration of zona pellucida (GO:0007341)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(3)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		AGTCCTGCCAGAATTTGATAC	0.363																																					p.E288X	Melanoma(66;841 1270 13391 18706 27225)	Atlas-SNP	.											.	HEXB	34	.	0			c.G862T						.						137	135	135					5																	74009421		2203	4300	6503	SO:0001587	stop_gained	3074	exon7			CTGCCAGAATTTG	M13519	CCDS4022.1	5q13.3	2012-10-02			ENSG00000049860	ENSG00000049860	3.2.1.52		4879	protein-coding gene	gene with protein product		606873				2579389, 3013851	Standard	NM_000521		Approved		uc003kdf.4	P07686	OTTHUMG00000102057	ENST00000261416.7:c.862G>T	chr5.hg19:g.74009421G>T	ENSP00000261416:p.Glu288*	121.0	0.0		160.0	57.0	NM_000521		Nonsense_Mutation	SNP	ENST00000261416.7	hg19	CCDS4022.1	.	.	.	.	.	.	.	.	.	.	G	46	12.895377	0.99704	.	.	ENSG00000049860	ENST00000511181;ENST00000261416	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-31.8421	19.5902	0.95508	0.0:0.0:1.0:0.0	.	.	.	.	X	63;288	.	ENSP00000261416:E288X	E	+	1	0	HEXB	74045177	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	9.869000	0.99810	2.629000	0.89072	0.555000	0.69702	GAA	.	.		0.363	HEXB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219859.6	NM_000521		T	74009421	G	T	74009421	4	4	216	1	0	0	0	0	0	1	0	0	7083	943	33	3	888	3	HEXB	5	74009421	Nonsense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	30358739	74009421	106905839	40	31128										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140264085	140264085	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	actctagtgtgctccagcgcGgcagggagttggtcgtactc	14	11	1	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr5:140264085G>T	ENST00000289272.2	+	1	2232	c.2232G>T	c.(2230-2232)gcG>gcT	p.A744A	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000409494.1_Silent_p.A744A|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA12_ENST00000398631.2_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	744	6 X 4 AA repeats of P-X-X-P.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTCCAGCGCGGCAGGGAGTT	0.682																																					p.A744A	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.G2232T						.						50	55	53					5																	140264085		2203	4299	6502	SO:0001819	synonymous_variant	56136	exon1			CAGCGCGGCAGGG	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.2232G>T	chr5.hg19:g.140264085G>T		166.0	0.0		188.0	76.0	NM_031865	O75277	Silent	SNP	ENST00000289272.2	hg19	CCDS4240.1																																																																																			.	.		0.682	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		T	140264085	G	T	140264085	2	4	216	1	0	0	0	0	0	0	0	1	11532	1103	39	1		1	PCDHA13	5	140264085	Silent	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	66254664	140264085	40651175	41	31129										
GPLD1	2822	hgsc.bcm.edu	37	chr6	24466935	24466935	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	cattctccaacatgaagcttGttagatggtaaatattagtg	8	6	1	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr6:24466935G>T	ENST00000230036.1	-	10	904	c.794C>A	c.(793-795)aCa>aAa	p.T265K	GPLD1_ENST00000474784.1_5'UTR	NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	265					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						CATGAAGCTTGTTAGATGGTA	0.408																																					p.T265K		Atlas-SNP	.											.	GPLD1	91	.	0			c.C794A						.						58	54	55					6																	24466935		2203	4300	6503	SO:0001583	missense	2822	exon10			AAGCTTGTTAGAT	L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.794C>A	chr6.hg19:g.24466935G>T	ENSP00000230036:p.Thr265Lys	141.0	0.0		137.0	51.0	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	hg19	CCDS4553.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.251025	0.39797	.	.	ENSG00000112293	ENST00000230036	T	0.66638	-0.22	5.65	2.92	0.33932	.	0.476791	0.22098	N	0.064656	T	0.46678	0.1405	M	0.67953	2.075	0.42996	D	0.994506	B	0.33583	0.418	B	0.35607	0.206	T	0.41161	-0.9524	10	0.25106	T	0.35	-3.7026	9.7057	0.40214	0.2289:0.0:0.7711:0.0	.	265	P80108	PHLD_HUMAN	K	265	ENSP00000230036:T265K	ENSP00000230036:T265K	T	-	2	0	GPLD1	24574914	0.067000	0.21026	0.060000	0.19600	0.962000	0.63368	0.732000	0.26072	0.756000	0.33013	0.638000	0.83543	ACA	.	.		0.408	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503		T	24466935	G	T	24466935	3	4	216	1	0	0	0	0	1	0	0	0	6622	1377	48	3	1792	3	GPLD1	6	24466935	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10		24466935	146648132	42	31130										
TRIM39	56658	hgsc.bcm.edu	37	chr6	30303626	30303626	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ctttcacgactggaagaagaGgaacaggacattctgcagcg	12	9	2	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr6:30303626G>A	ENST00000396547.1	+	4	814	c.654G>A	c.(652-654)gaG>gaA	p.E218E	TRIM39_ENST00000376659.5_Silent_p.E218E|TRIM39-RPP21_ENST00000513556.1_Silent_p.E130E|TRIM39_ENST00000396551.3_Silent_p.E218E|TRIM39_ENST00000396548.1_Silent_p.E218E|TRIM39_ENST00000540416.1_Silent_p.E218E|TRIM39_ENST00000376656.4_Silent_p.E218E			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	218					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						TGGAAGAAGAGGAACAGGACA	0.567																																					p.E218E		Atlas-SNP	.											.	TRIM39	56	.	0			c.G654A						.						64	62	62					6																	30303626		1511	2709	4220	SO:0001819	synonymous_variant	56658	exon5			AGAAGAGGAACAG	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10065	protein-coding gene	gene with protein product		605700	"ring finger protein 23", "tripartite motif-containing 39"	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.654G>A	chr6.hg19:g.30303626G>A		109.0	0.0		149.0	66.0	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Silent	SNP	ENST00000396547.1	hg19	CCDS34377.1	.	.	.	.	.	.	.	.	.	.	G	8.069	0.769844	0.15983	.	.	ENSG00000204599	ENST00000420746	.	.	.	5.33	-0.575	0.11734	.	.	.	.	.	T	0.40423	0.1116	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35301	-0.9794	4	.	.	.	.	9.3148	0.37928	0.487:0.0:0.513:0.0	.	.	.	.	K	148	.	.	R	+	2	0	TRIM39	30411605	0.960000	0.32886	0.983000	0.44433	0.825000	0.46686	0.011000	0.13264	-0.329000	0.08527	-0.827000	0.03088	AGG	.	.		0.567	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016		A	30303626	G	A	30303626	2	1	216	1	0	0	0	0	0	0	0	1	16528	991	35	3		3	TRIM39	6	30303626	Silent	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	5836691	30303626	140811441	43	31131										
TRAM2	9697	hgsc.bcm.edu	37	chr6	52369497	52369497	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gtgccgcagctgggagtggaTgaagcgccacatgagccagg	17	10	0	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr6:52369497T>A	ENST00000182527.3	-	10	930	c.931A>T	c.(931-933)Atc>Ttc	p.I311F	EFHC1_ENST00000433625.2_Intron	NM_012288.3	NP_036420.1	Q15035	TRAM2_HUMAN	translocation associated membrane protein 2	311	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				collagen biosynthetic process (GO:0032964)|protein transport (GO:0015031)	integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(1)|lung(7)|prostate(1)|skin(1)	13	Lung NSC(77;0.109)					TGGGAGTGGATGAAGCGCCAC	0.637																																					p.I311F		Atlas-SNP	.											.	TRAM2	27	.	0			c.A931T						.						34	31	32					6																	52369497		2203	4300	6503	SO:0001583	missense	9697	exon10			AGTGGATGAAGCG	D31762	CCDS34477.1	6p21.1-p12	2008-02-05			ENSG00000065308	ENSG00000065308			16855	protein-coding gene	gene with protein product		608485				7584044, 10594243	Standard	NM_012288		Approved	KIAA0057	uc003paq.3	Q15035	OTTHUMG00000014850	ENST00000182527.3:c.931A>T	chr6.hg19:g.52369497T>A	ENSP00000182527:p.Ile311Phe	39.0	0.0		47.0	24.0	NM_012288	A8K6T6	Missense_Mutation	SNP	ENST00000182527.3	hg19	CCDS34477.1	.	.	.	.	.	.	.	.	.	.	T	17.71	3.457253	0.63401	.	.	ENSG00000065308	ENST00000182527	D	0.86164	-2.08	5.15	5.15	0.70609	TRAM/LAG1/CLN8 homology domain (3);	0.045343	0.85682	D	0.000000	T	0.78136	0.4236	L	0.55743	1.74	0.80722	D	1	B	0.25235	0.121	B	0.26094	0.066	T	0.76255	-0.3026	10	0.29301	T	0.29	.	15.274	0.73728	0.0:0.0:0.0:1.0	.	311	Q15035	TRAM2_HUMAN	F	311	ENSP00000182527:I311F	ENSP00000182527:I311F	I	-	1	0	TRAM2	52477456	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.585000	0.67497	2.074000	0.62210	0.459000	0.35465	ATC	.	.		0.637	TRAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040910.1	NM_012288		A	52369497	T	A	52369497	3	1	216	1	0	0	0	0	1	0	0	0	16468	1464	51	4	189	4	TRAM2	6	52369497	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	22065871	52369497	118745570	44	31132										
EYS	346007	hgsc.bcm.edu	37	chr6	65612046	65612046	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tgttccattatttttgcaagGttcagaggaacattcattaa	7	6	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr6:65612046G>A	ENST00000370621.3	-	18	3332	c.2806C>T	c.(2806-2808)Cct>Tct	p.P936S	EYS_ENST00000503581.1_Missense_Mutation_p.P936S|EYS_ENST00000370616.2_Missense_Mutation_p.P936S			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	936	EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TTTTTGCAAGGTTCAGAGGAA	0.313																																					p.P936S		Atlas-SNP	.											.	EYS	527	.	0			c.C2806T						.						122	109	113					6																	65612046		692	1591	2283	SO:0001583	missense	346007	exon18			TGCAAGGTTCAGA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2806C>T	chr6.hg19:g.65612046G>A	ENSP00000359655:p.Pro936Ser	311.0	0.0		367.0	15.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.31	2.796491	0.50208	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.95238	-3.65;-3.65;-3.65	4.51	2.71	0.32032	.	.	.	.	.	D	0.95335	0.8486	M	0.90595	3.13	0.80722	D	1	P	0.50943	0.94	P	0.56434	0.798	D	0.94057	0.7323	9	0.56958	D	0.05	.	8.331	0.32187	0.1857:0.0:0.8143:0.0	.	936	Q5T1H1-1	.	S	936	ENSP00000424243:P936S;ENSP00000359655:P936S;ENSP00000359650:P936S	ENSP00000359650:P936S	P	-	1	0	EYS	65668767	0.983000	0.35010	0.596000	0.28811	0.844000	0.47949	1.804000	0.38873	0.457000	0.26962	0.591000	0.81541	CCT	.	.		0.313	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	65612046	G	A	65612046	3	1	216	1	0	0	0	0	1	0	0	0	5334	1261	44	3	6577	3	EYS	6	65612046	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	13242549	65612046	105503021	45	31133										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75860905	75860905	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aatggtgagatcatccactaTcctggagagtgactcaaaat	9	8	2	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr6:75860905T>C	ENST00000322507.8	-	21	4408	c.4099A>G	c.(4099-4101)Ata>Gta	p.I1367V	COL12A1_ENST00000416123.2_Missense_Mutation_p.I1367V|COL12A1_ENST00000345356.6_Missense_Mutation_p.I203V|COL12A1_ENST00000483888.2_Missense_Mutation_p.I1367V	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1367	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TCATCCACTATCCTGGAGAGT	0.413																																					p.I1367V		Atlas-SNP	.											.	COL12A1	385	.	0			c.A4099G						.						166	163	164					6																	75860905		1904	4129	6033	SO:0001583	missense	1303	exon21			CCACTATCCTGGA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4099A>G	chr6.hg19:g.75860905T>C	ENSP00000325146:p.Ile1367Val	75.0	0.0		94.0	33.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.2|23.2	4.389657|4.389657	0.82902|0.82902	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000419671|ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	.|D;D;D;D	.|0.84223	.|-1.82;-1.82;-1.82;-1.82	5.6|5.6	5.6|5.6	0.85130|0.85130	.|von Willebrand factor, type A (3);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.87148|0.87148	0.6105|0.6105	L|L	0.51422|0.51422	1.61|1.61	0.49915|0.49915	D|D	0.99983|0.99983	.|P;D	.|0.59767	.|0.742;0.986	.|P;D	.|0.68943	.|0.784;0.961	D|D	0.86577|0.86577	0.1851|0.1851	5|10	.|0.37606	.|T	.|0.19	.|.	15.7728|15.7728	0.78184|0.78184	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|203;1367	.|Q99715-2;Q99715	.|.;COCA1_HUMAN	G|V	108|1367;1367;203;1367;1367	.|ENSP00000325146:I1367V;ENSP00000305147:I203V;ENSP00000412864:I1367V;ENSP00000421216:I1367V	.|ENSP00000325146:I1367V	D|I	-|-	2|1	0|0	COL12A1|COL12A1	75917625|75917625	1.000000|1.000000	0.71417|0.71417	0.811000|0.811000	0.32455|0.32455	0.957000|0.957000	0.61999|0.61999	7.698000|7.698000	0.84413|0.84413	2.125000|2.125000	0.65367|0.65367	0.533000|0.533000	0.62120|0.62120	GAT|ATA	.	.		0.413	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75860905	T	C	75860905	3	2	216	1	0	0	0	0	1	0	0	0	3671	1435	50	2	5276	2	COL12A1	6	75860905	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	10248859	75860905	95254162	46	31134										
SENP6	26054	hgsc.bcm.edu	37	chr6	76419283	76419283	+	Frame_Shift_Del	DEL	A	A	-													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ctaaactatagcgatgaatcAcctgaagctggtaaaatgct							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr6:76419283delA	ENST00000447266.2	+	20	3235	c.2757delA	c.(2755-2757)tcafs	p.S919fs	SENP6_ENST00000370010.2_Frame_Shift_Del_p.S912fs|SENP6_ENST00000370014.3_Frame_Shift_Del_p.S919fs|SENP6_ENST00000541192.1_3'UTR	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	919	Protease.				protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				GCGATGAATCACCTGAAGCTG	0.343																																					p.S919fs		Atlas-INDEL	.											.	SENP6	189	.	0			c.2756delC						.						103	95	97					6																	76419283		1838	4080	5918	SO:0001589	frameshift_variant	26054	exon20			.		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.2757delA	chr6.hg19:g.76419283delA	ENSP00000402527:p.Ser919fs	114.0	0.0		103.0	41.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Frame_Shift_Del	DEL	ENST00000447266.2	hg19	CCDS47454.1																																																																																			.	.		0.343	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		-	76419283	A	-	76419283	7	5	216	1	0	1	0	1	0	0	0	0	14065	146	6	0	2835	0	SENP6	6	76419283	Frame_Shift_Del	DEL	A	TCGA-DD-AAEB-01A-11D-A40R-10	558378	76419283	94695784	47	31135										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160468364	160468364	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gggagtgggcttccctgaatAtcaggtaggaatgtttgttc	14	6	1	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr6:160468364A>G	ENST00000356956.1	+	16	2373	c.2225A>G	c.(2224-2226)tAt>tGt	p.Y742C		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	742					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TTCCCTGAATATCAGGTAGGA	0.512																																					p.Y742C		Atlas-SNP	.											.	IGF2R	251	.	0			c.A2225G						.						63	61	62					6																	160468364		2203	4300	6503	SO:0001583	missense	3482	exon16			CTGAATATCAGGT	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.2225A>G	chr6.hg19:g.160468364A>G	ENSP00000349437:p.Tyr742Cys	25.0	0.0		39.0	11.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	A	17.13	3.310131	0.60414	.	.	ENSG00000197081	ENST00000356956	T	0.02258	4.37	5.6	5.6	0.85130	Mannose-6-phosphate receptor, binding (1);	0.112785	0.64402	D	0.000007	T	0.08935	0.0221	M	0.85859	2.78	0.48571	D	0.999675	D	0.89917	1.0	D	0.65773	0.938	T	0.00998	-1.1486	10	0.72032	D	0.01	-10.5289	16.0863	0.81056	1.0:0.0:0.0:0.0	.	742	P11717	MPRI_HUMAN	C	742	ENSP00000349437:Y742C	ENSP00000349437:Y742C	Y	+	2	0	IGF2R	160388354	1.000000	0.71417	0.261000	0.24466	0.502000	0.33828	5.255000	0.65462	2.251000	0.74343	0.528000	0.53228	TAT	.	.		0.512	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		G	160468364	A	G	160468364	3	3	216	1	0	0	0	0	1	0	0	0	7585	449	16	2	2287	2	IGF2R	6	160468364	Missense_Mutation	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	84049081	160468364	10646703	48	31136										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5352635	5352635	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gaggaggaggaagaggaggaTgaggaggaggaggaggagga	25	0	0	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr7:5352635T>G	ENST00000430969.1	-	27	8235	c.7887A>C	c.(7885-7887)tcA>tcC	p.S2629S	TNRC18_ENST00000399537.4_Silent_p.S2629S	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2629	Ser-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		aagaggaggatgaggaggagg	0.642																																					p.S2629S		Atlas-SNP	.											.	TNRC18	311	.	0			c.A7887C						.						5	8	7					7																	5352635		1423	3213	4636	SO:0001819	synonymous_variant	84629	exon27			GGAGGATGAGGAG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7887A>C	chr7.hg19:g.5352635T>G		2.0	0.0		5.0	4.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	N	0.020	-1.445364	0.01089	.	.	ENSG00000182095	ENST00000399544	.	.	.	3.4	-6.8	0.01709	.	1.000120	0.08080	N	1.000000	T	0.52853	0.1760	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60979	-0.7155	6	0.87932	D	0	.	3.168	0.06542	0.3128:0.3903:0.1985:0.0984	.	.	.	.	P	1142	.	ENSP00000382459:H1142P	H	-	2	0	TNRC18	5319161	0.989000	0.36119	0.000000	0.03702	0.001000	0.01503	-1.429000	0.02437	-4.431000	0.00049	-3.452000	0.00036	CAT	.	.		0.642	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	5352635	T	G	5352635	2	3	216	1	0	0	0	0	0	0	0	1	16354	1451	51	5		5	TNRC18	7	5352635	Silent	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10		5352635	153786028	49	31137										
LIMK1	3984	hgsc.bcm.edu	37	chr7	73520215	73520215	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttacccacagagtggatccgGgctgcatgagcccagatgtg	13	11	0	3	rs406970		TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr7:73520215G>T	ENST00000336180.2	+	6	670	c.619G>T	c.(619-621)Ggc>Tgc	p.G207C	LIMK1_ENST00000491052.1_3'UTR|LIMK1_ENST00000538333.3_Missense_Mutation_p.G173C|LIMK1_ENST00000418310.1_Missense_Mutation_p.G237C	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	207	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	AGTGGATCCGGGCTGCATGAG	0.597																																					p.G207C		Atlas-SNP	.											.	LIMK1	55	.	0			c.G619T						.						59	53	55					7																	73520215		2202	4300	6502	SO:0001583	missense	3984	exon6			GATCCGGGCTGCA	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.619G>T	chr7.hg19:g.73520215G>T	ENSP00000336740:p.Gly207Cys	61.0	0.0		93.0	24.0	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	ENST00000336180.2	hg19	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399386	0.62177	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000423685;ENST00000538333	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.35	4.35	0.52113	PDZ/DHR/GLGF (4);	0.105138	0.64402	D	0.000006	T	0.37812	0.1017	N	0.08118	0	0.35415	D	0.792771	P;P	0.52170	0.951;0.917	P;P	0.56343	0.796;0.796	T	0.53294	-0.8459	10	0.44086	T	0.13	-37.2885	14.4796	0.67573	0.0:0.0:1.0:0.0	.	173;207	B7Z6I8;P53667	.;LIMK1_HUMAN	C	237;207;207;173;173	ENSP00000409717:G237C;ENSP00000336740:G207C;ENSP00000396480:G173C;ENSP00000444452:G173C	ENSP00000336740:G207C	G	+	1	0	LIMK1	73158151	1.000000	0.71417	0.975000	0.42487	0.788000	0.44548	5.137000	0.64789	2.283000	0.76528	0.644000	0.83932	GGC	.	G|1.000;|0.000		0.597	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		T	73520215	G	T	73520215	3	4	216	1	0	0	0	0	1	0	0	0	8810	1232	43	3	641	3	LIMK1	7	73520215	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	68167580	73520215	85618448	50	31138										
STYXL1	51657	hgsc.bcm.edu	37	chr7	75659739	75659739	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gcttttttccaagtacttacCcaataaacagagatagttgg	7	8	0	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr7:75659739C>T	ENST00000248600.1	-	2	445	c.103G>A	c.(103-105)Gat>Aat	p.D35N	STYXL1_ENST00000340062.5_Splice_Site_p.D35N|STYXL1_ENST00000460184.2_5'UTR|STYXL1_ENST00000360591.3_Splice_Site_p.D35N|STYXL1_ENST00000451157.1_Splice_Site_p.D35N|STYXL1_ENST00000359697.3_Splice_Site_p.D35N|STYXL1_ENST00000431581.1_Splice_Site_p.D35N	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	35	Rhodanese.				intracellular signal transduction (GO:0035556)|protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10						AAGTACTTACCCAATAAACAG	0.428																																					p.D35N		Atlas-SNP	.											.	STYXL1	35	.	0			c.G103A						.						115	100	105					7																	75659739		2203	4300	6503	SO:0001630	splice_region_variant	51657	exon2			ACTTACCCAATAA	AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	18165	protein-coding gene	gene with protein product			"dual specificity phosphatase 24 (putative)"	DUSP24		9757831	Standard	NM_016086		Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.103+1G>A	chr7.hg19:g.75659739C>T		90.0	0.0		162.0	57.0	NM_016086	Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	Missense_Mutation	SNP	ENST00000248600.1	hg19	CCDS5580.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.490331	0.84962	.	.	ENSG00000127952	ENST00000248600;ENST00000359697;ENST00000340062;ENST00000404050;ENST00000360591;ENST00000431581;ENST00000451157	T;T;D;D;T;T	0.82081	-1.0;-1.0;-1.57;-1.57;-1.0;-1.0	5.5	5.5	0.81552	Rhodanese-like (4);	0.111999	0.64402	D	0.000014	D	0.90645	0.7066	M	0.74881	2.28	0.50039	D	0.999845	D;D;D;D	0.89917	0.999;0.987;1.0;0.999	D;P;D;D	0.83275	0.981;0.843;0.996;0.978	D	0.90290	0.4322	9	.	.	.	-14.8446	16.8745	0.86048	0.0:1.0:0.0:0.0	.	35;35;35;35	C9J4H0;Q9Y6J8-2;Q9Y6J8-4;Q9Y6J8	.;.;.;STYL1_HUMAN	N	35	ENSP00000248600:D35N;ENSP00000352726:D35N;ENSP00000343383:D35N;ENSP00000353798:D35N;ENSP00000392221:D35N;ENSP00000411812:D35N	.	D	-	1	0	STYXL1	75497675	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	4.972000	0.63756	2.586000	0.87340	0.637000	0.83480	GAT	.	.		0.428	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	NM_016086	Missense_Mutation	T	75659739	C	T	75659739	5	4	216	1	0	0	0	0	0	0	1	0	15376	637	22	3	870	3	STYXL1	7	75659739	Splice_Site	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	2139524	75659739	83478924	51	31139										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83610698	83610698	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ccaagcacagtaagggtctcGggcgaggcaacactcagcac	12	13	2	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr7:83610698G>T	ENST00000265362.4	-	14	1905	c.1591C>A	c.(1591-1593)Cga>Aga	p.R531R	SEMA3A_ENST00000436949.1_Silent_p.R531R	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	531					apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						TAAGGGTCTCGGGCGAGGCAA	0.458																																					p.R531R		Atlas-SNP	.											.	SEMA3A	121	.	0			c.C1591A						.						77	71	73					7																	83610698		2203	4300	6503	SO:0001819	synonymous_variant	10371	exon14			GGTCTCGGGCGAG	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1591C>A	chr7.hg19:g.83610698G>T		147.0	0.0		261.0	73.0	NM_006080		Silent	SNP	ENST00000265362.4	hg19	CCDS5599.1																																																																																			.	.		0.458	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		T	83610698	G	T	83610698	2	4	216	1	0	0	0	0	0	0	0	1	14039	1124	39	1		1	SEMA3A	7	83610698	Silent	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	7950959	83610698	75527965	52	31140										
TRPV5	56302	hgsc.bcm.edu	37	chr7	142605860	142605860	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gctagagtcccactctcagcCccagagggctgtttctcaga	10	14	2	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr7:142605860C>T	ENST00000265310.1	-	15	2358	c.2010G>A	c.(2008-2010)ggG>ggA	p.G670G		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	670					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					CACTCTCAGCCCCAGAGGGCT	0.567																																					p.G670G		Atlas-SNP	.											.	TRPV5	164	.	0			c.G2010A						.						63	61	62					7																	142605860		2203	4300	6503	SO:0001819	synonymous_variant	56302	exon15			CTCAGCCCCAGAG	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.2010G>A	chr7.hg19:g.142605860C>T		68.0	0.0		104.0	65.0	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Silent	SNP	ENST00000265310.1	hg19	CCDS5875.1																																																																																			.	.		0.567	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		T	142605860	C	T	142605860	2	4	216	1	0	0	0	0	0	0	0	1	16614	610	22	3		3	TRPV5	7	142605860	Silent	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	58995162	142605860	16532803	53	31141										
EZH2	2146	hgsc.bcm.edu	37	chr7	148506446	148506446	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ccgaatgatttgcaaaacgaAttttgttacccttgcgggtt	9	8	0	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr7:148506446A>C	ENST00000460911.1	-	18	2139	c.2051T>G	c.(2050-2052)aTt>aGt	p.I684S	EZH2_ENST00000350995.2_Missense_Mutation_p.I645S|EZH2_ENST00000476773.1_Missense_Mutation_p.I633S|EZH2_ENST00000478654.1_Missense_Mutation_p.I633S|EZH2_ENST00000483967.1_Missense_Mutation_p.I675S|EZH2_ENST00000320356.2_Missense_Mutation_p.I689S|EZH2_ENST00000541220.1_Missense_Mutation_p.I633S			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	684	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			TGCAAAACGAATTTTGTTACC	0.378			Mis		DLBCL																																p.I689S		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	.	EZH2	823	.	0			c.T2066G						.						117	116	116					7																	148506446		2203	4300	6503	SO:0001583	missense	2146	exon18			AAACGAATTTTGT		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"Chromatin-modifying enzymes / K-methyltransferases"	3527	protein-coding gene	gene with protein product		601573	"enhancer of zeste (Drosophila) homolog 2", "enhancer of zeste homolog 2 (Drosophila)"			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.2051T>G	chr7.hg19:g.148506446A>C	ENSP00000419711:p.Ile684Ser	86.0	0.0		137.0	45.0	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	hg19	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	a	24.9	4.579903	0.86645	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967	T;D;D;D;T;T;D	0.84298	-1.45;-1.83;-1.83;-1.83;-1.45;-1.45;-1.83	5.13	5.13	0.70059	SET domain (3);	0.000000	0.85682	D	0.000000	T	0.78104	0.4231	N	0.00754	-1.215	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.997;0.999	D;D;D;D;D	0.97110	0.996;0.997;1.0;0.967;0.996	T	0.82478	-0.0437	10	0.25106	T	0.35	.	14.9541	0.71098	1.0:0.0:0.0:0.0	.	675;633;684;645;689	Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;EZH2_HUMAN;.;.	S	633;689;684;645;633;633;675	ENSP00000417062:I633S;ENSP00000320147:I689S;ENSP00000419711:I684S;ENSP00000223193:I645S;ENSP00000443219:I633S;ENSP00000419050:I633S;ENSP00000419856:I675S	ENSP00000320147:I689S	I	-	2	0	EZH2	148137379	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.042000	0.93793	1.925000	0.55765	0.533000	0.62120	ATT	.	.		0.378	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		C	148506446	A	C	148506446	3	2	216	1	0	0	0	0	1	0	0	0	5336	101	4	5	201	5	EZH2	7	148506446	Missense_Mutation	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	5900586	148506446	10632217	54	31142										
ABCB8	11194	hgsc.bcm.edu	37	chr7	150731818	150731818	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tgtcccatgccagacaagacAtcaccttctttgacgccaat	6	14	2	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr7:150731818A>G	ENST00000297504.6	+	6	784	c.718A>G	c.(718-720)Atc>Gtc	p.I240V	ABCB8_ENST00000477092.1_Missense_Mutation_p.I223V|ABCB8_ENST00000356058.4_Missense_Mutation_p.I260V|ABCB8_ENST00000542328.1_Missense_Mutation_p.I135V|ABCB8_ENST00000477719.1_Missense_Mutation_p.I223V|ABCB8_ENST00000498578.1_Missense_Mutation_p.I223V|ABCB8_ENST00000358849.4_Missense_Mutation_p.I223V			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	240	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	CAGACAAGACATCACCTTCTT	0.517																																					p.I223V		Atlas-SNP	.											.	ABCB8	65	.	0			c.A667G						.						126	105	112					7																	150731818		2203	4300	6503	SO:0001583	missense	11194	exon5			CAAGACATCACCT	AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"ATP binding cassette transporters / subfamily B"	49	protein-coding gene	gene with protein product	"mitochondrial ABC protein"	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.718A>G	chr7.hg19:g.150731818A>G	ENSP00000297504:p.Ile240Val	56.0	0.0		114.0	30.0	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	hg19		.	.	.	.	.	.	.	.	.	.	A	10.63	1.403478	0.25291	.	.	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092	D;D;D;D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51;-2.51;-2.51	5.06	5.06	0.68205	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.131141	0.52532	D	0.000068	T	0.79695	0.4490	N	0.11673	0.155	0.48135	D	0.999597	B;B;B;B;B;P;P	0.36683	0.042;0.106;0.072;0.173;0.042;0.565;0.565	B;B;B;B;B;B;B	0.42882	0.075;0.163;0.047;0.208;0.075;0.401;0.401	T	0.76806	-0.2823	10	0.29301	T	0.29	-0.4999	7.55	0.27790	0.905:0.0:0.095:0.0	.	135;223;53;240;223;223;260	G3XAP3;A5D8W3;B3KND2;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8	.;.;.;ABCB8_HUMAN;.;.;.	V	223;206;240;135;223;260;223;223	ENSP00000351717:I223V;ENSP00000297504:I240V;ENSP00000438776:I135V;ENSP00000418271:I223V;ENSP00000348353:I260V;ENSP00000419891:I223V;ENSP00000419558:I223V	ENSP00000297504:I240V	I	+	1	0	ABCB8	150362751	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	4.210000	0.58500	1.919000	0.55581	0.533000	0.62120	ATC	.	.		0.517	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188		G	150731818	A	G	150731818	3	3	216	1	0	0	0	0	1	0	0	0	47	217	8	2	685	2	ABCB8	7	150731818	Missense_Mutation	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	2225372	150731818	8406845	55	31143										
TOX	9760	hgsc.bcm.edu	37	chr8	59750854	59750854	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ccatatcagaggcaggccgcTtctctccaccattgatctga	8	14	3	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr8:59750854T>C	ENST00000361421.1	-	5	930	c.710A>G	c.(709-711)aAg>aGg	p.K237R		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	237						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				GGCAGGCCGCTTCTCTCCACC	0.433																																					p.K237R	Pancreas(161;610 1969 17913 21374 22725)	Atlas-SNP	.											.	TOX	83	.	0			c.A710G						.						51	60	57					8																	59750854		2199	4296	6495	SO:0001583	missense	9760	exon5			GGCCGCTTCTCTC		CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.710A>G	chr8.hg19:g.59750854T>C	ENSP00000354842:p.Lys237Arg	46.0	0.0		74.0	23.0	NM_014729	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	hg19	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	T	19.11	3.764642	0.69878	.	.	ENSG00000198846	ENST00000361421	T	0.18810	2.19	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.38639	0.1048	M	0.80422	2.495	0.80722	D	1	P	0.51057	0.941	P	0.49332	0.607	T	0.30504	-0.9976	9	.	.	.	.	16.1304	0.81428	0.0:0.0:0.0:1.0	.	237	O94900	TOX_HUMAN	R	237	ENSP00000354842:K237R	.	K	-	2	0	TOX	59913408	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.040000	0.89188	2.202000	0.70862	0.482000	0.46254	AAG	.	.		0.433	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		C	59750854	T	C	59750854	3	2	216	1	0	0	0	0	1	0	0	0	16392	1609	56	2	890	2	TOX	8	59750854	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10		59750854	86613168	56	31144										
C8orf34	116328	hgsc.bcm.edu	37	chr8	69728153	69728153	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttcttctttgcgttccatgcTcttcttgtcctacgctggtc	7	13	4	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr8:69728153T>A	ENST00000539993.1	+	13	1873	c.1324T>A	c.(1324-1326)Tct>Act	p.S442T	C8orf34_ENST00000518698.1_Missense_Mutation_p.S528T|C8orf34_ENST00000337103.4_Missense_Mutation_p.S417T			Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	442										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(12)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	36			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			CGTTCCATGCTCTTCTTGTCC	0.443																																					p.S528T		Atlas-SNP	.											.	C8orf34	170	.	0			c.T1582A						.						367	317	334					8																	69728153		2203	4300	6503	SO:0001583	missense	116328	exon13			CCATGCTCTTCTT	AB056652	CCDS6203.1, CCDS6203.2	8q13	2009-10-01			ENSG00000165084	ENSG00000165084			30905	protein-coding gene	gene with protein product	"vestibule 1"						Standard	NM_052958		Approved	vest-1, VEST1	uc010lyz.3	Q49A92	OTTHUMG00000164438	ENST00000539993.1:c.1324T>A	chr8.hg19:g.69728153T>A	ENSP00000438159:p.Ser442Thr	85.0	0.0		133.0	77.0	NM_052958	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	Missense_Mutation	SNP	ENST00000539993.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.63	2.891728	0.52014	.	.	ENSG00000165084	ENST00000518698;ENST00000539993;ENST00000337103	T;T;T	0.52295	0.67;0.79;0.78	4.2	4.2	0.49525	.	0.471455	0.20720	N	0.086937	T	0.45736	0.1357	N	0.14661	0.345	0.25942	N	0.982865	P	0.52577	0.954	D	0.63597	0.916	T	0.25398	-1.0133	9	.	.	.	-1.1301	10.0033	0.41942	0.0:0.0:0.0:1.0	.	442	Q49A92	CH034_HUMAN	T	528;442;417	ENSP00000427820:S528T;ENSP00000438159:S442T;ENSP00000337174:S417T	.	S	+	1	0	C8orf34	69890707	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.683000	0.37638	2.132000	0.65825	0.529000	0.55759	TCT	.	.		0.443	C8orf34-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_052958		A	69728153	T	A	69728153	3	1	216	1	0	0	0	0	1	0	0	0	2424	1551	54	4	1295	4	C8orf34	8	69728153	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	9977299	69728153	76635869	57	31145										
CRISPLD1	83690	hgsc.bcm.edu	37	chr8	75926334	75926334	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	cctggtgtgcaattactcccCaaagtgagtagacaaaacac	8	11	0	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr8:75926334C>T	ENST00000262207.4	+	5	1091	c.623C>T	c.(622-624)cCa>cTa	p.P208L	CRISPLD1_ENST00000523524.1_Missense_Mutation_p.P20L|CRISPLD1_ENST00000517786.1_Intron	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	208					face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			AATTACTCCCCAAAGTGAGTA	0.393																																					p.P208L		Atlas-SNP	.											.	CRISPLD1	94	.	0			c.C623T						.						109	91	97					8																	75926334		2203	4300	6503	SO:0001583	missense	83690	exon5			ACTCCCCAAAGTG	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.623C>T	chr8.hg19:g.75926334C>T	ENSP00000262207:p.Pro208Leu	67.0	0.0		112.0	65.0	NM_031461	B2RA60|B7Z929	Missense_Mutation	SNP	ENST00000262207.4	hg19	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.955841	0.92726	.	.	ENSG00000121005	ENST00000262207;ENST00000523524	T;T	0.81415	2.26;-1.49	4.85	4.85	0.62838	Allergen V5/Tpx-1-related, conserved site (1);CAP domain (2);	0.000000	0.85682	D	0.000000	D	0.88104	0.6347	M	0.64404	1.975	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	D	0.89229	0.3576	10	0.72032	D	0.01	.	18.164	0.89719	0.0:1.0:0.0:0.0	.	208	Q9H336	CRLD1_HUMAN	L	208;20	ENSP00000262207:P208L;ENSP00000430105:P20L	ENSP00000262207:P208L	P	+	2	0	CRISPLD1	76088889	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.551000	0.82182	2.505000	0.84491	0.650000	0.86243	CCA	.	.		0.393	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		T	75926334	C	T	75926334	3	4	216	1	0	0	0	0	1	0	0	0	3884	594	21	3	637	3	CRISPLD1	8	75926334	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	6198181	75926334	70437688	58	31146										
SLC26A7	115111	hgsc.bcm.edu	37	chr8	92346676	92346676	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttcctgtagatttagttttgGtaagtataaaatcaacattt	6	4	1	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr8:92346676G>T	ENST00000276609.3	+	6	1034		c.e6+1		SLC26A7_ENST00000309536.2_Splice_Site|SLC26A7_ENST00000523719.1_Splice_Site	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			TTTAGTTTTGGTAAGTATAAA	0.358																																					.		Atlas-SNP	.											.	SLC26A7	207	.	0			c.795+1G>T						.						81	78	79					8																	92346676		2202	4298	6500	SO:0001630	splice_region_variant	115111	exon6			GTTTTGGTAAGTA	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"Solute carriers"	14467	protein-coding gene	gene with protein product		608479	"solute carrier family 26, member 7"			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.795+1G>T	chr8.hg19:g.92346676G>T		56.0	0.0		76.0	48.0	NM_134266		Splice_Site	SNP	ENST00000276609.3	hg19	CCDS6254.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.151745	0.78001	.	.	ENSG00000147606	ENST00000523719;ENST00000276609;ENST00000309536;ENST00000520818	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2699	0.98469	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC26A7	92415852	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.417000	0.73337	2.854000	0.98071	0.655000	0.94253	.	.	.		0.358	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1		Intron	T	92346676	G	T	92346676	5	4	216	1	0	0	0	0	0	0	1	0	14537	1275	44	3	814	3	SLC26A7	8	92346676	Splice_Site	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	16420342	92346676	54017346	59	31147										
INTS8	55656	hgsc.bcm.edu	37	chr8	95861725	95861725	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gtaaatttagaaaaagcttcAgagtctttgaaaggaaacat	8	4	2	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr8:95861725A>T	ENST00000523731.1	+	11	1429	c.1296A>T	c.(1294-1296)tcA>tcT	p.S432S	INTS8_ENST00000447247.1_Silent_p.S432S	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	432					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					AAAAAGCTTCAGAGTCTTTGA	0.259																																					p.S432S		Atlas-SNP	.											.	INTS8	92	.	0			c.A1296T						.						58	67	64					8																	95861725		2198	4287	6485	SO:0001819	synonymous_variant	55656	exon11			AGCTTCAGAGTCT	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.1296A>T	chr8.hg19:g.95861725A>T		490.0	1.0		792.0	190.0	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Silent	SNP	ENST00000523731.1	hg19	CCDS34925.1	.	.	.	.	.	.	.	.	.	.	A	9.929	1.214251	0.22289	.	.	ENSG00000164941	ENST00000520526	.	.	.	5.55	1.86	0.25419	.	.	.	.	.	T	0.43986	0.1272	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25363	-1.0134	4	.	.	.	-25.0914	2.564	0.04778	0.6105:0.1273:0.1396:0.1226	.	.	.	.	L	254	.	.	Q	+	2	0	INTS8	95930901	0.942000	0.31987	1.000000	0.80357	0.991000	0.79684	0.036000	0.13819	0.462000	0.27095	-0.250000	0.11733	CAG	.	.		0.259	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		T	95861725	A	T	95861725	2	4	216	1	0	0	0	0	0	0	0	1	7793	175	7	4		4	INTS8	8	95861725	Silent	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	3515049	95861725	50502297	60	31148										
CSMD3	114788	hgsc.bcm.edu	37	chr8	114186141	114186141	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tttccacaagagctactctgCaattctattaaaaaggagga	7	8	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr8:114186141C>A	ENST00000297405.5	-	4	763	c.519G>T	c.(517-519)ttG>ttT	p.L173F	CSMD3_ENST00000519485.1_5'Flank|CSMD3_ENST00000455883.2_Missense_Mutation_p.L173F|CSMD3_ENST00000352409.3_Missense_Mutation_p.L173F|CSMD3_ENST00000343508.3_Missense_Mutation_p.L133F	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	173	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AGCTACTCTGCAATTCTATTA	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.L173F		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G519T						.						58	57	57					8																	114186141		2203	4300	6503	SO:0001583	missense	114788	exon4			ACTCTGCAATTCT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.519G>T	chr8.hg19:g.114186141C>A	ENSP00000297405:p.Leu173Phe	63.0	0.0		112.0	24.0	NM_052900	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951014	0.53186	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.26957	2.02;2.0;1.7;2.0	5.1	-0.126	0.13515	CUB (3);	0.000000	0.42294	U	0.000738	T	0.27134	0.0665	N	0.21373	0.66	0.27105	N	0.962523	D;D;B;P	0.76494	0.999;0.999;0.0;0.954	D;D;B;P	0.87578	0.996;0.998;0.001;0.812	T	0.22591	-1.0212	10	0.15952	T	0.53	.	8.1197	0.30963	0.0:0.2861:0.0:0.7139	.	173;173;173;133	Q7Z407-3;Q7Z407-4;Q7Z407;Q7Z407-2	.;.;CSMD3_HUMAN;.	F	133;173;173;173	ENSP00000345799:L133F;ENSP00000297405:L173F;ENSP00000412263:L173F;ENSP00000343124:L173F	ENSP00000297405:L173F	L	-	3	2	CSMD3	114255317	1.000000	0.71417	0.999000	0.59377	0.916000	0.54674	0.942000	0.29017	0.102000	0.17638	0.655000	0.94253	TTG	.	.		0.363	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	114186141	C	A	114186141	3	1	216	1	0	0	0	0	1	0	0	0	3948	709	25	3	10876	3	CSMD3	8	114186141	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	18324416	114186141	32177881	61	31149										
DEPDC6	64798	hgsc.bcm.edu	37	chr8	120940716	120940716	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	acccaaactgttttgtcgcaAaagaactgattgactggctg	9	9	0	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr8:120940716A>G	ENST00000286234.5	+	2	329	c.199A>G	c.(199-201)Aaa>Gaa	p.K67E	DEPTOR_ENST00000523492.1_Intron	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	67	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						TTTTGTCGCAAAAGAACTGAT	0.413																																					p.K67E		Atlas-SNP	.											.	DEPTOR	41	.	0			c.A199G						.						124	119	121					8																	120940716		2203	4300	6503	SO:0001583	missense	64798	exon2			GTCGCAAAAGAAC		CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792			22953	protein-coding gene	gene with protein product		612974	"DEP domain containing 6"	DEPDC6		19446321	Standard	NM_022783		Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.199A>G	chr8.hg19:g.120940716A>G	ENSP00000286234:p.Lys67Glu	102.0	0.0		175.0	46.0	NM_022783	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	Missense_Mutation	SNP	ENST00000286234.5	hg19	CCDS6331.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.426830	0.83667	.	.	ENSG00000155792	ENST00000286234	T	0.24350	1.86	5.95	5.95	0.96441	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.36690	0.0976	L	0.47190	1.495	0.58432	D	0.999999	P	0.51791	0.948	P	0.53102	0.718	T	0.02307	-1.1179	10	0.32370	T	0.25	-28.3344	16.397	0.83610	1.0:0.0:0.0:0.0	.	67	Q8TB45	DPTOR_HUMAN	E	67	ENSP00000286234:K67E	ENSP00000286234:K67E	K	+	1	0	DEPTOR	121009897	1.000000	0.71417	0.940000	0.37924	0.997000	0.91878	8.679000	0.91220	2.275000	0.75901	0.459000	0.35465	AAA	.	.		0.413	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381601.1	NM_022783		G	120940716	A	G	120940716	3	3	216	1	0	0	0	0	1	0	0	0	4445	15	1	2	205	2	DEPDC6	8	120940716	Missense_Mutation	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	6754575	120940716	25423306	62	31150										
SLA	6503	hgsc.bcm.edu	37	chr8	134052339	134052339	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ccgtgctttgtgtcaggcagGgcgtggtgagcacacagcac	15	11	1	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr8:134052339G>A	ENST00000338087.5	-	8	1340	c.521C>T	c.(520-522)cCc>cTc	p.P174L	SLA_ENST00000517648.1_Missense_Mutation_p.P147L|SLA_ENST00000524345.1_Missense_Mutation_p.P66L|TG_ENST00000220616.4_Intron|TG_ENST00000377869.1_Intron|SLA_ENST00000395352.3_Missense_Mutation_p.P191L|TG_ENST00000542445.1_Intron|TG_ENST00000519543.1_Intron|SLA_ENST00000427060.2_Missense_Mutation_p.P214L	NM_001045556.2	NP_001039021.1	Q13239	SLAP1_HUMAN	Src-like-adaptor	174	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				positive regulation of signal transduction (GO:0009967)	endosome (GO:0005768)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(6)|prostate(1)|skin(1)	17	all_epithelial(106;3.51e-21)|Lung NSC(106;4.24e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0279)|Breast(495;0.037)	BRCA - Breast invasive adenocarcinoma(115;0.000701)			TGTCAGGCAGGGCGTGGTGAG	0.637																																					p.P214L		Atlas-SNP	.											SLA_ENST00000427060,right_upper_lobe,carcinoma,0,2	SLA	63	.	0			c.C641T						.						66	41	50					8																	134052339		2189	4280	6469	SO:0001583	missense	6503	exon6			AGGCAGGGCGTGG		CCDS6370.1, CCDS47922.1, CCDS47923.1, CCDS64977.1, CCDS64978.1	8q24.22	2013-09-19	2001-11-28		ENSG00000155926	ENSG00000155926		"SH2 domain containing"	10902	protein-coding gene	gene with protein product		601099	"Src-like-adapter"			8825655, 11179692	Standard	NM_001045556		Approved	SLA1	uc011ljd.2	Q13239	OTTHUMG00000164439	ENST00000338087.5:c.521C>T	chr8.hg19:g.134052339G>A	ENSP00000337548:p.Pro174Leu	62.0	0.0		121.0	35.0	NM_006748	B7Z4J2|B7Z4L6|Q6FI01|Q9UMQ8	Missense_Mutation	SNP	ENST00000338087.5	hg19	CCDS6370.1	.	.	.	.	.	.	.	.	.	.	G	33	5.285789	0.95517	.	.	ENSG00000155926	ENST00000338087;ENST00000427060;ENST00000395352;ENST00000524345;ENST00000517648	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.38	5.77	5.77	0.91146	SH2 motif (2);	0.000000	0.85682	D	0.000000	T	0.77725	0.4173	H	0.96777	3.88	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;1.0	D	0.84993	0.0895	10	0.87932	D	0	-37.8829	18.5671	0.91120	0.0:0.0:1.0:0.0	.	147;174;174;174	B7Z4J2;Q6FI01;Q5TZW1;Q13239	.;.;.;SLAP1_HUMAN	L	174;214;191;66;147	ENSP00000337548:P174L;ENSP00000394049:P214L;ENSP00000378759:P191L;ENSP00000427928:P66L;ENSP00000428559:P147L	ENSP00000337548:P174L	P	-	2	0	SLA	134121521	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	8.541000	0.90644	2.727000	0.93392	0.650000	0.86243	CCC	.	.		0.637	SLA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378771.1			A	134052339	G	A	134052339	3	1	216	1	0	0	0	0	1	0	0	0	14378	1232	43	3	317	3	SLA	8	134052339	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	13111623	134052339	12311683	63	31151										
ABCA1	19	hgsc.bcm.edu	37	chr9	107562206	107562206	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttgcaggttggcccggagaaTggcattgttgatgacattca	13	7	1	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr9:107562206T>C	ENST00000374736.3	-	36	5231	c.4837A>G	c.(4837-4839)Att>Gtt	p.I1613V		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1613					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	GCCCGGAGAATGGCATTGTTG	0.478																																					p.I1613V		Atlas-SNP	.											.	ABCA1	244	.	0			c.A4837G						.						139	126	131					9																	107562206		2203	4300	6503	SO:0001583	missense	19	exon36			GGAGAATGGCATT	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.4837A>G	chr9.hg19:g.107562206T>C	ENSP00000363868:p.Ile1613Val	67.0	0.0		108.0	39.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.731046	0.48939	.	.	ENSG00000165029	ENST00000374736	D	0.87571	-2.27	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.85097	0.5619	L	0.46614	1.455	0.80722	D	1	B	0.20368	0.044	B	0.26693	0.072	T	0.81583	-0.0866	10	0.52906	T	0.07	.	16.3979	0.83621	0.0:0.0:0.0:1.0	.	1613	O95477	ABCA1_HUMAN	V	1613	ENSP00000363868:I1613V	ENSP00000363868:I1613V	I	-	1	0	ABCA1	106602027	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.203000	0.58453	2.333000	0.79357	0.533000	0.62120	ATT	.	.		0.478	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		C	107562206	T	C	107562206	3	2	216	1	0	0	0	0	1	0	0	0	28	1464	51	2	2008	2	ABCA1	9	107562206	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10		107562206	33651225	64	31152										
IKBKAP	8518	hgsc.bcm.edu	37	chr9	111653509	111653510	+	Frame_Shift_Ins	INS	-	-	GC													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agttctgccgaggcccaccaINSgctggtctttggtaaagtta							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr9:111653509_111653510insGC	ENST00000374647.5	-	28	3440_3441	c.3133_3134insGC	c.(3133-3135)ctgfs	p.L1045fs	IKBKAP_ENST00000537196.1_Frame_Shift_Ins_p.L696fs|IKBKAP_ENST00000467959.1_5'Flank	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	1045					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						GAGGCCCACCAGCTGGTCTTTG	0.441																																					p.L1045fs		Atlas-INDEL	.											.	IKBKAP	122	.	0			c.3134_3135insGC						.																																			SO:0001589	frameshift_variant	8518	exon28			.	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"Elongator acetyltransferase complex subunits"	5959	protein-coding gene	gene with protein product	"elongator acetyltransferase complex subunit 1"	603722	"dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.3132_3133dupGC	chr9.hg19:g.111653510_111653511dupGC	ENSP00000363779:p.Leu1045fs	119.0	0.0		125.0	55.0	NM_003640	Q5JSV2|Q9H327|Q9UG87	Frame_Shift_Ins	INS	ENST00000374647.5	hg19	CCDS6773.1																																																																																			.	.		0.441	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1			GC	111653510	-	GC	111653509	7	5	216	1	0	1	1	0	0	0	0	0	7619	188	7	0	904	0	IKBKAP	9	111653509	Frame_Shift_Ins	INS	-	TCGA-DD-AAEB-01A-11D-A40R-10	4091303	111653509	29559922	65	31153										
CEL	1056	hgsc.bcm.edu	37	chr9	135947089	135947089	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ccacgggtgactctgaggctGcccctgtgccccccacagat	11	17	1	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr9:135947089G>C	ENST00000372080.4	+	11	2225	c.2209G>C	c.(2209-2211)Gcc>Ccc	p.A737P	CEL_ENST00000351304.7_Missense_Mutation_p.A668P	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	734	17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CTCTGAGGCTGCCCCTGTGCC	0.667																																					p.A737P		Atlas-SNP	.											.	CEL	71	.	0			c.G2209C						.						17	20	19					9																	135947089		1846	4080	5926	SO:0001583	missense	1056	exon11			GAGGCTGCCCCTG	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"bile salt-stimulated lipase"	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.2209G>C	chr9.hg19:g.135947089G>C	ENSP00000361151:p.Ala737Pro	463.0	0.0		506.0	183.0	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	hg19	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	g	6.623	0.483286	0.12581	.	.	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.71817	-0.39;-0.6	2.5	-1.98	0.07480	.	.	.	.	.	T	0.45316	0.1336	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.30297	-0.9983	9	0.07030	T	0.85	.	4.1192	0.10098	0.3445:0.3354:0.3201:0.0	.	734	P19835	CEL_HUMAN	P	737;668;703	ENSP00000361151:A737P;ENSP00000342217:A668P	ENSP00000304021:A703P	A	+	1	0	CEL	134936910	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.508000	0.06344	-0.476000	0.06842	-0.360000	0.07572	GCC	.	.		0.667	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1			C	135947089	G	C	135947089	3	2	216	1	0	0	0	0	1	0	0	0	3211	1319	46	4	2251	4	CEL	9	135947089	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	24293580	135947089	5266342	66	31154										
ADAMTS13	11093	hgsc.bcm.edu	37	chr9	136310099	136310099	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aggctccagtgactgaggggCctggctccgtagatgagaag	16	9	0	4			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr9:136310099C>T	ENST00000371929.3	+	20	2980	c.2536C>T	c.(2536-2538)Cct>Tct	p.P846S	ADAMTS13_ENST00000356589.2_Missense_Mutation_p.P815S|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.P846S|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000536611.1_3'UTR|ADAMTS13_ENST00000485925.1_3'UTR	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	846	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GACTGAGGGGCCTGGCTCCGT	0.652																																					p.P846S		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C2536T						.						73	58	63					9																	136310099		2203	4300	6503	SO:0001583	missense	11093	exon20			GAGGGGCCTGGCT	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"ADAM metallopeptidases with thrombospondin type 1 motif"	1366	protein-coding gene	gene with protein product		604134	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.2536C>T	chr9.hg19:g.136310099C>T	ENSP00000360997:p.Pro846Ser	41.0	0.0		49.0	21.0	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	hg19	CCDS6970.1	.	.	.	.	.	.	.	.	.	.	C	8.176	0.792842	0.16327	.	.	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589	T;T;T	0.67171	-0.23;-0.25;-0.23	5.55	3.68	0.42216	.	.	.	.	.	T	0.51652	0.1687	M	0.62723	1.935	0.09310	N	0.999999	P;P;P	0.42010	0.768;0.529;0.762	B;B;B	0.33454	0.164;0.164;0.164	T	0.41448	-0.9508	9	0.15066	T	0.55	.	3.3496	0.07147	0.1457:0.5739:0.1414:0.1391	.	846;815;846	Q76LX8;Q76LX8-3;Q76LX8-2	ATS13_HUMAN;.;.	S	846;846;815	ENSP00000360997:P846S;ENSP00000347927:P846S;ENSP00000348997:P815S	ENSP00000347927:P846S	P	+	1	0	ADAMTS13	135299920	0.001000	0.12720	0.059000	0.19551	0.009000	0.06853	0.571000	0.23669	1.326000	0.45319	0.561000	0.74099	CCT	.	.		0.652	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025		T	136310099	C	T	136310099	3	4	216	1	0	0	0	0	1	0	0	0	258	739	26	3	2614	3	ADAMTS13	9	136310099	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	363010	136310099	4903332	67	31155										
DNAJB12	54788	hgsc.bcm.edu	37	chr10	74100799	74100799	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ggtcttcaggggagatgtcgGcctcaaagccacggtggaaa	15	9	3	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr10:74100799G>A	ENST00000444643.2	-	4	919	c.587C>T	c.(586-588)gCc>gTc	p.A196V	DNAJB12_ENST00000394903.2_Missense_Mutation_p.A230V|DNAJB12_ENST00000461919.1_5'UTR|DNAJB12_ENST00000338820.3_Missense_Mutation_p.A230V			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	196						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						GGAGATGTCGGCCTCAAAGCC	0.597																																					p.A230V		Atlas-SNP	.											.	DNAJB12	22	.	0			c.C689T						.						61	55	57					10																	74100799		2203	4300	6503	SO:0001583	missense	54788	exon4			ATGTCGGCCTCAA	AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"Heat shock proteins / DNAJ (HSP40)"	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000444643.2:c.587C>T	chr10.hg19:g.74100799G>A	ENSP00000403313:p.Ala196Val	68.0	0.0		81.0	31.0	NM_017626	B7Z7I3|Q9H6H0	Missense_Mutation	SNP	ENST00000444643.2	hg19		.	.	.	.	.	.	.	.	.	.	G	24.9	4.586388	0.86851	.	.	ENSG00000148719	ENST00000338820;ENST00000394903;ENST00000444643	T;T;T	0.72942	-0.7;-0.7;-0.7	5.66	5.66	0.87406	Heat shock protein DnaJ, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.72894	2.215	0.80722	D	1	D;D	0.76494	0.999;0.998	D;P	0.72338	0.977;0.906	D	0.85152	0.0987	10	0.87932	D	0	-11.5344	19.8154	0.96566	0.0:0.0:1.0:0.0	.	196;196	Q9NXW2-2;Q9NXW2	.;DJB12_HUMAN	V	230;230;196	ENSP00000345575:A230V;ENSP00000378363:A230V;ENSP00000403313:A196V	ENSP00000345575:A230V	A	-	2	0	DNAJB12	73770805	1.000000	0.71417	0.969000	0.41365	0.964000	0.63967	9.869000	0.99810	2.683000	0.91414	0.650000	0.86243	GCC	.	.		0.597	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2			A	74100799	G	A	74100799	3	1	216	1	0	0	0	0	1	0	0	0	4619	1203	42	3	560	3	DNAJB12	10	74100799	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10		74100799	61433948	68	31156										
CYP2C8	1558	hgsc.bcm.edu	37	chr10	96798766	96798766	+	Frame_Shift_Del	DEL	G	G	-													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tctttgtcatcatgtagcacGgaagtcagtaatgccattat					rs181052138		TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr10:96798766delG	ENST00000371270.3	-	8	1273	c.1179delC	c.(1177-1179)tccfs	p.S393fs	CYP2C8_ENST00000535898.1_Frame_Shift_Del_p.S291fs	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	393				GTTIMALLTS -> SFDNKIMLAA (in Ref. 1; AAA35740). {ECO:0000305}.	arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	CATGTAGCACGGAAGTCAGTA	0.388																																					p.V394fs		Atlas-INDEL	.											.	CYP2C8	73	.	0			c.1180delG						.						128	119	122					10																	96798766		2203	4300	6503	SO:0001589	frameshift_variant	1558	exon8			.	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"Cytochrome P450s"	2622	protein-coding gene	gene with protein product		601129	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.1179delC	chr10.hg19:g.96798766delG	ENSP00000360317:p.Ser393fs	102.0	0.0		121.0	36.0	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Frame_Shift_Del	DEL	ENST00000371270.3	hg19	CCDS7438.1																																																																																			.	.		0.388	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770		-	96798766	G	-	96798766	7	5	216	1	0	1	0	1	0	0	0	0	4169	1103	39	0	301	0	CYP2C8	10	96798766	Frame_Shift_Del	DEL	G	TCGA-DD-AAEB-01A-11D-A40R-10	22697967	96798766	38735981	69	31157										
SCD	6319	hgsc.bcm.edu	37	chr10	102114194	102114194	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ctctccccagaatgatgtctAtgaatgggctcgtgaccacc	9	13	2	4			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr10:102114194A>G	ENST00000370355.2	+	4	833	c.452A>G	c.(451-453)tAt>tGt	p.Y151C		NM_005063.4	NP_005054.3	O00767	ACOD_HUMAN	stearoyl-CoA desaturase (delta-9-desaturase)	151					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|large_intestine(3)|lung(5)	9		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)		AATGATGTCTATGAATGGGCT	0.498																																					p.Y151C	Colon(67;260 1459 9574 11663)	Atlas-SNP	.											.	SCD	25	.	0			c.A452G						.						104	94	97					10																	102114194		2203	4300	6503	SO:0001583	missense	6319	exon4			ATGTCTATGAATG	AF097514	CCDS7493.1	10q23-q24	2013-01-25			ENSG00000099194	ENSG00000099194	1.14.19.1	"Fatty acid desaturases"	10571	protein-coding gene	gene with protein product	"acyl-CoA desaturase", "fatty acid desaturase", "delta-9-desaturase"	604031	"stearoyl-CoA desaturase opposite strand"	SCDOS		7909540, 10229681	Standard	NM_005063		Approved	FADS5	uc001kqy.3	O00767	OTTHUMG00000018906	ENST00000370355.2:c.452A>G	chr10.hg19:g.102114194A>G	ENSP00000359380:p.Tyr151Cys	45.0	0.0		42.0	15.0	NM_005063	B2R5U0|D3DR68|Q16150|Q53GR9|Q5W037|Q5W038|Q6GSS4|Q96KF6|Q9BS07|Q9Y695	Missense_Mutation	SNP	ENST00000370355.2	hg19	CCDS7493.1	.	.	.	.	.	.	.	.	.	.	A	16.67	3.187639	0.57909	.	.	ENSG00000099194	ENST00000423840;ENST00000370355	T	0.13538	2.58	5.31	-10.6	0.00265	Fatty acid desaturase, type 1 (1);	0.539943	0.18230	N	0.147605	T	0.35595	0.0937	M	0.91090	3.175	0.27497	N	0.952095	D	0.63880	0.993	D	0.64410	0.925	T	0.60622	-0.7227	10	0.87932	D	0	-3.7665	17.4691	0.87641	0.2111:0.0:0.0:0.7889	.	151	O00767	ACOD_HUMAN	C	151	ENSP00000359380:Y151C	ENSP00000359380:Y151C	Y	+	2	0	SCD	102104184	0.000000	0.05858	0.010000	0.14722	0.891000	0.51852	-0.188000	0.09642	-1.909000	0.01085	-0.728000	0.03583	TAT	.	.		0.498	SCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049857.2	NM_005063		G	102114194	A	G	102114194	3	3	216	1	0	0	0	0	1	0	0	0	13901	449	16	2	466	2	SCD	10	102114194	Missense_Mutation	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	5315428	102114194	33420553	70	31158										
C10orf32	100528007	hgsc.bcm.edu	37	chr10	104620107	104620107	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agctgctaggtcaggcagctCgaaacatggtactccaggaa	12	10	1	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr10:104620107C>A	ENST00000299353.6	+	2	175	c.160C>A	c.(160-162)Cga>Aga	p.R54R	C10orf32_ENST00000369883.3_Silent_p.R54R|C10orf32_ENST00000339834.5_Silent_p.R54R					C10orf32-ASMT readthrough (NMD candidate)																		TCAGGCAGCTCGAAACATGGT	0.383																																					p.R54R		Atlas-SNP	.											.	C10orf32	3	.	0			c.C160A						.						131	133	132					10																	104620107		2203	4300	6503	SO:0001819	synonymous_variant	119032	exon2			GCAGCTCGAAACA			10q24.32	2013-09-25			ENSG00000270316	ENSG00000270316			49183	other	readthrough							Standard	NR_037644		Approved				OTTHUMG00000184175	ENST00000299353.6:c.160C>A	chr10.hg19:g.104620107C>A		74.0	0.0		79.0	37.0	NM_001136200		Silent	SNP	ENST00000299353.6	hg19	CCDS7542.2																																																																																			.	.		0.383	C10orf32-ASMT-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000468206.2			A	104620107	C	A	104620107	2	1	216	1	0	0	0	0	0	0	0	1	1604	876	31	1		1	C10orf32	10	104620107	Silent	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	2505913	104620107	30914640	71	31159										
GSTO1	9446	hgsc.bcm.edu	37	chr10	106019401	106019401	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttaagaaaaatccctttggtCtggtgccagttctggaaaac	9	8	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr10:106019401C>G	ENST00000369713.5	+	3	405	c.211C>G	c.(211-213)Ctg>Gtg	p.L71V	GSTO1_ENST00000539281.1_Missense_Mutation_p.L43V|GSTO1_ENST00000493946.1_3'UTR|GSTO1_ENST00000369710.4_Missense_Mutation_p.L71V	NM_004832.2	NP_004823.1	P78417	GSTO1_HUMAN	glutathione S-transferase omega 1	71	GST N-terminal.				cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014810)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)			large_intestine(1)|lung(1)|stomach(1)	3		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)|Vitamin E(DB00163)	TCCCTTTGGTCTGGTGCCAGT	0.458																																					p.L71V		Atlas-SNP	.											.	GSTO1	14	.	0			c.C211G						.						87	87	87					10																	106019401		2203	4300	6503	SO:0001583	missense	9446	exon3			TTTGGTCTGGTGC	AF212303	CCDS7555.1, CCDS53572.1, CCDS53573.1	10q25.1	2012-06-21			ENSG00000148834	ENSG00000148834	2.5.1.18, 1.8.5.1, 1.20.4.2	"Glutathione S-transferases / Soluble"	13312	protein-coding gene	gene with protein product		605482				10783391, 12618591	Standard	NM_004832		Approved	GSTTLp28, P28	uc001kya.3	P78417	OTTHUMG00000019001	ENST00000369713.5:c.211C>G	chr10.hg19:g.106019401C>G	ENSP00000358727:p.Leu71Val	72.0	0.0		96.0	41.0	NM_001191002	D3DRA3|F5H7H0|Q5TA03|Q7Z3T2	Missense_Mutation	SNP	ENST00000369713.5	hg19	CCDS7555.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.446825	0.43429	.	.	ENSG00000148834	ENST00000539281;ENST00000369710;ENST00000369713;ENST00000445155;ENST00000432659	T;T;T;T;T	0.27557	1.66;1.66;1.66;1.66;1.66	5.53	3.67	0.42095	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.213069	0.40469	N	0.001091	T	0.34803	0.0910	L	0.56199	1.76	0.53688	D	0.999979	P	0.36171	0.541	B	0.42555	0.391	T	0.14008	-1.0488	10	0.59425	D	0.04	-12.4927	11.4764	0.50300	0.0:0.8059:0.1261:0.068	.	71	P78417	GSTO1_HUMAN	V	43;71;71;43;43	ENSP00000441488:L43V;ENSP00000358724:L71V;ENSP00000358727:L71V;ENSP00000406708:L43V;ENSP00000405325:L43V	ENSP00000358724:L71V	L	+	1	2	GSTO1	106009391	0.305000	0.24481	0.723000	0.30687	0.926000	0.56050	0.717000	0.25851	0.806000	0.34183	-0.300000	0.09419	CTG	.	.		0.458	GSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050193.1	NM_004832		G	106019401	C	G	106019401	3	3	216	1	0	0	0	0	1	0	0	0	6851	912	32	4	221	4	GSTO1	10	106019401	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	1399294	106019401	29515346	72	31160										
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411971	6411972	+	In_Frame_Ins	INS	-	-	GCTGGC													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gcgctggcgctggcgctggcINStctgtctgactctcgggttc					rs281860676		TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr11:6411971_6411972insGCTGGC	ENST00000342245.4	+	1	311_312	c.143_144insGCTGGC	c.(142-147)gctctg>gcGCTGGCtctg	p.48_49AL>ALAL	SMPD1_ENST00000527275.1_In_Frame_Ins_p.48_49AL>ALAL|SMPD1_ENST00000356761.2_In_Frame_Ins_p.48_49AL>ALAL|SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000299397.3_In_Frame_Ins_p.48_49AL>ALAL	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	47			D -> V (in NPDB). {ECO:0000269|PubMed:12369017}.		cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	ctggcgctggcTCTGTCTGACT	0.693																																					p.A48delinsALA		Atlas-INDEL	.											SMPD1_ENST00000342245,colon,carcinoma,0,2	SMPD1	108	.	0			c.143_144insGCTGGC						.																																			SO:0001652	inframe_insertion	6609	exon1			.	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.138_143dupGCTGGC	chr11.hg19:g.6411966_6411971dupGCTGGC	ENSP00000340409:p.Leu47_Ala48dup	84.0	0.0		91.0	16.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	In_Frame_Ins	INS	ENST00000342245.4	hg19	CCDS44531.1																																																																																			.	GCTGGCGCTGGC|1.000;|0.000		0.693	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		GCTGGC	6411972	-	GCTGGC	6411971	7	5	216	1	0	1	1	0	0	0	0	0	14819	797	28	0	145	0	SMPD1	11	6411971	In_Frame_Ins	INS	-	TCGA-DD-AAEB-01A-11D-A40R-10		6411971	128594545	73	31161										
OR5R1	219479	hgsc.bcm.edu	37	chr11	56185036	56185036	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agtagagcggatccttaggaTagcggcaataataaagatgt	12	5	0	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr11:56185036T>C	ENST00000312253.1	-	1	672	c.673A>G	c.(673-675)Atc>Gtc	p.I225V		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					ATCCTTAGGATAGCGGCAATA	0.438																																					p.I225V		Atlas-SNP	.											.	OR5R1	83	.	0			c.A673G						.						125	112	116					11																	56185036		2201	4296	6497	SO:0001583	missense	219479	exon1			TTAGGATAGCGGC	AB065504	CCDS31530.1	11q11	2012-08-09		2004-03-10	ENSG00000174942	ENSG00000174942		"GPCR / Class A : Olfactory receptors"	14841	protein-coding gene	gene with protein product				OR5R1P			Standard	NM_001004744		Approved		uc010rji.2	Q8NH85	OTTHUMG00000154219	ENST00000312253.1:c.673A>G	chr11.hg19:g.56185036T>C	ENSP00000308595:p.Ile225Val	147.0	0.0		168.0	69.0	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	hg19	CCDS31530.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.469564	0.43839	.	.	ENSG00000174942	ENST00000312253	T	0.00024	8.98	5.53	4.4	0.53042	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33327	U	0.005038	T	0.00178	0.0005	L	0.38531	1.155	0.09310	N	0.999999	P	0.40578	0.722	P	0.48400	0.576	T	0.38672	-0.9650	10	0.56958	D	0.05	-12.1393	9.3702	0.38250	0.0:0.1498:0.0:0.8502	.	225	Q8NH85	OR5R1_HUMAN	V	225	ENSP00000308595:I225V	ENSP00000308595:I225V	I	-	1	0	OR5R1	55941612	0.093000	0.21703	0.543000	0.28128	0.763000	0.43281	0.314000	0.19432	0.927000	0.37143	0.472000	0.43445	ATC	.	.		0.438	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744		C	56185036	T	C	56185036	3	2	216	1	0	0	0	0	1	0	0	0	11189	1406	49	2	303	2	OR5R1	11	56185036	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	49773065	56185036	78821480	74	31162										
ANO1	55107	hgsc.bcm.edu	37	chr11	70033927	70033927	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agccagcagatccacaaggaGaaggtgctcatggtggagct	14	9	1	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr11:70033927G>T	ENST00000355303.5	+	26	3083	c.2778G>T	c.(2776-2778)gaG>gaT	p.E926D	ANO1_ENST00000525494.1_3'UTR|ANO1_ENST00000538023.1_Missense_Mutation_p.E926D|ANO1_ENST00000530676.1_Missense_Mutation_p.E780D|ANO1_ENST00000398543.2_Missense_Mutation_p.E780D|ANO1-AS1_ENST00000524987.1_RNA|ANO1_ENST00000531349.1_Missense_Mutation_p.E635D	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	926					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	TCCACAAGGAGAAGGTGCTCA	0.577																																					p.E926D		Atlas-SNP	.											.	ANO1	156	.	0			c.G2778T						.						40	48	45					11																	70033927		2126	4235	6361	SO:0001583	missense	55107	exon26			CAAGGAGAAGGTG	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	21625	protein-coding gene	gene with protein product		610108	"oral cancer overexpressed 2", "transmembrane protein 16A"	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.2778G>T	chr11.hg19:g.70033927G>T	ENSP00000347454:p.Glu926Asp	96.0	0.0		78.0	32.0	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Missense_Mutation	SNP	ENST00000355303.5	hg19	CCDS44663.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.977738	0.92982	.	.	ENSG00000131620	ENST00000355303;ENST00000538023;ENST00000398543;ENST00000546327;ENST00000530676;ENST00000531349;ENST00000539321	T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.75117	0.3806	M	0.77616	2.38	0.80722	D	1	P;P	0.51057	0.941;0.941	P;P	0.55011	0.651;0.766	T	0.77892	-0.2418	9	.	.	.	.	17.3129	0.87214	0.0:0.0:1.0:0.0	.	635;926	E9PNA7;Q5XXA6	.;ANO1_HUMAN	D	926;926;780;684;780;635;253	ENSP00000347454:E926D;ENSP00000444689:E926D;ENSP00000381551:E780D;ENSP00000435797:E780D;ENSP00000432843:E635D	.	E	+	3	2	ANO1	69711575	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.263000	0.65507	2.099000	0.63709	0.462000	0.41574	GAG	.	.		0.577	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043		T	70033927	G	T	70033927	3	4	216	1	0	0	0	0	1	0	0	0	695	933	33	3	2880	3	ANO1	11	70033927	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	13848891	70033927	64972589	75	31163										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76867076	76867076	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tgcccccccacatctttgccAttgctgacaactgctacttc	5	17	1	1	rs376016858		TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr11:76867076A>T	ENST00000409709.3	+	5	681	c.409A>T	c.(409-411)Att>Ttt	p.I137F	MYO7A_ENST00000458637.2_Missense_Mutation_p.I137F|MYO7A_ENST00000409893.1_Missense_Mutation_p.I137F|MYO7A_ENST00000409619.2_Missense_Mutation_p.I126F	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	137	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CATCTTTGCCATTGCTGACAA	0.567																																					p.I137F		Atlas-SNP	.											.	MYO7A	164	.	0			c.A409T						.						55	57	56					11																	76867076		2069	4206	6275	SO:0001583	missense	4647	exon5			TTTGCCATTGCTG	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.409A>T	chr11.hg19:g.76867076A>T	ENSP00000386331:p.Ile137Phe	67.0	0.0		74.0	41.0	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	a	17.89	3.500552	0.64298	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.64	5.1	5.1	0.69264	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.96725	0.8931	H	0.96489	3.83	0.80722	D	1	D;P;P	0.58620	0.983;0.692;0.848	D;P;P	0.71184	0.972;0.795;0.875	D	0.97900	1.0302	10	0.72032	D	0.01	.	15.05	0.71862	1.0:0.0:0.0:0.0	.	137;137;137	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	F	137;137;137;126;136;136;136;136	ENSP00000386331:I137F;ENSP00000386689:I137F;ENSP00000392185:I137F;ENSP00000386635:I126F	ENSP00000345075:I136F	I	+	1	0	MYO7A	76544724	1.000000	0.71417	0.980000	0.43619	0.397000	0.30659	6.163000	0.71880	2.149000	0.67028	0.478000	0.44815	ATT	.	.		0.567	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		T	76867076	A	T	76867076	3	4	216	1	0	0	0	0	1	0	0	0	10091	217	8	4	423	4	MYO7A	11	76867076	Missense_Mutation	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	6833149	76867076	58139440	76	31164										
PRCP	5547	hgsc.bcm.edu	37	chr11	82536148	82536148	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tactccacctcctgaccaggGgtctagttcaccattgctgc	8	15	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr11:82536148G>T	ENST00000313010.3	-	9	1485	c.1291C>A	c.(1291-1293)Ccc>Acc	p.P431T	PRCP_ENST00000525772.1_5'UTR|PRCP_ENST00000393399.2_Missense_Mutation_p.P452T|PRCP_ENST00000535099.1_Missense_Mutation_p.P326T	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	431					angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						CCTGACCAGGGGTCTAGTTCA	0.428																																					p.P452T		Atlas-SNP	.											.	PRCP	69	.	0			c.C1354A						.						65	60	62					11																	82536148		2203	4300	6503	SO:0001583	missense	5547	exon10			ACCAGGGGTCTAG	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.1291C>A	chr11.hg19:g.82536148G>T	ENSP00000317362:p.Pro431Thr	87.0	0.0		90.0	32.0	NM_199418	A8MU24|B2R7B7|B3KRK5|B5BU34	Missense_Mutation	SNP	ENST00000313010.3	hg19	CCDS8262.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.531771	0.85706	.	.	ENSG00000137509	ENST00000313010;ENST00000393399;ENST00000535099	T;T;T	0.35789	1.29;1.29;1.29	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.73976	0.3656	H	0.96460	3.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82721	-0.0317	9	.	.	.	-15.0747	19.2129	0.93765	0.0:0.0:1.0:0.0	.	431;452	P42785;A8MU24	PCP_HUMAN;.	T	431;452;326	ENSP00000317362:P431T;ENSP00000377055:P452T;ENSP00000442077:P326T	.	P	-	1	0	PRCP	82213796	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.190000	0.89714	2.629000	0.89072	0.467000	0.42956	CCC	.	.		0.428	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040		T	82536148	G	T	82536148	3	4	216	1	0	0	0	0	1	0	0	0	12461	1232	43	3	203	3	PRCP	11	82536148	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	5669072	82536148	52470368	77	31165										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117375715	117375715	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agcacaccagctttgccgtaGatgccatcctggttgttggg	12	11	0	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr11:117375715G>A	ENST00000321322.6	-	10	2287	c.2286C>T	c.(2284-2286)atC>atT	p.I762I	DSCAML1_ENST00000527706.1_Silent_p.I492I	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	702	Ig-like C2-type 8.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CTTTGCCGTAGATGCCATCCT	0.562																																					p.I762I		Atlas-SNP	.											.	DSCAML1	286	.	0			c.C2286T						.						106	90	95					11																	117375715		2201	4296	6497	SO:0001819	synonymous_variant	57453	exon10			GCCGTAGATGCCA		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2286C>T	chr11.hg19:g.117375715G>A		64.0	0.0		65.0	25.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	hg19	CCDS8384.1																																																																																			.	.		0.562	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		A	117375715	G	A	117375715	2	1	216	1	0	0	0	0	0	0	0	1	4771	932	33	3		3	DSCAML1	11	117375715	Silent	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	34839567	117375715	17630801	78	31166										
SLC6A12	6539	hgsc.bcm.edu	37	chr12	301686	301686	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttcaggagggtgatgacgacGaagagtgggacacagaccat	15	7	1	4	rs138858909		TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr12:301686G>T	ENST00000428720.1	-	15	2402	c.1659C>A	c.(1657-1659)ttC>ttA	p.F553L	RP11-283I3.1_ENST00000544067.1_RNA|SLC6A12_ENST00000536824.1_Missense_Mutation_p.F553L|SLC6A12_ENST00000424061.2_Missense_Mutation_p.F553L|SLC6A12_ENST00000397296.2_Missense_Mutation_p.F553L|SLC6A12_ENST00000359674.4_Missense_Mutation_p.F553L	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	553					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			TGATGACGACGAAGAGTGGGA	0.562																																					p.F553L		Atlas-SNP	.											.	SLC6A12	60	.	0			c.C1659A						.						109	110	110					12																	301686		2203	4300	6503	SO:0001583	missense	6539	exon15			GACGACGAAGAGT	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"Solute carriers"	11045	protein-coding gene	gene with protein product	"betaine/GABA transporter-1"	603080	"solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.1659C>A	chr12.hg19:g.301686G>T	ENSP00000388184:p.Phe553Leu	103.0	0.0		123.0	57.0	NM_001122848	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	hg19	CCDS8501.1	.	.	.	.	.	.	.	.	.	.	G	4.047	0.006307	0.07866	.	.	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824	T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75	4.49	1.05	0.20165	.	0.277462	0.35936	N	0.002881	T	0.60090	0.2242	L	0.42008	1.315	0.09310	N	1	B	0.11235	0.004	B	0.16722	0.016	T	0.47407	-0.9120	10	0.37606	T	0.19	.	4.5752	0.12230	0.3054:0.1556:0.5389:0.0	.	553	P48065	S6A12_HUMAN	L	553	ENSP00000352702:F553L;ENSP00000380464:F553L;ENSP00000388184:F553L;ENSP00000399136:F553L;ENSP00000444268:F553L	ENSP00000352702:F553L	F	-	3	2	SLC6A12	171947	0.001000	0.12720	0.045000	0.18777	0.006000	0.05464	-0.012000	0.12699	0.085000	0.17107	-0.175000	0.13238	TTC	.	G|1.000;A|0.000		0.562	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044		T	301686	G	T	301686	3	4	216	1	0	0	0	0	1	0	0	0	14690	1049	37	1	193	1	SLC6A12	12	301686	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10		301686	133550209	79	31167										
GPR162	27239	hgsc.bcm.edu	37	chr12	6933886	6933886	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	caggtcaccaacttggtcagCgccatcgtctttctctatga	8	13	4	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr12:6933886C>T	ENST00000311268.3	+	2	1609	c.822C>T	c.(820-822)agC>agT	p.S274S	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	274						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						ACTTGGTCAGCGCCATCGTCT	0.597																																					p.S274S		Atlas-SNP	.											GPR162,NS,carcinoma,0,1	GPR162	55	.	0			c.C822T						.						63	63	63					12																	6933886		2203	4300	6503	SO:0001819	synonymous_variant	27239	exon2			GGTCAGCGCCATC	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"GPCR / Class A : Orphans"	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.822C>T	chr12.hg19:g.6933886C>T		46.0	1.0		49.0	20.0	NM_019858	Q16664|Q59EH5|Q66K56	Silent	SNP	ENST00000311268.3	hg19	CCDS8563.1																																																																																			.	.		0.597	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		T	6933886	C	T	6933886	2	4	216	1	0	0	0	0	0	0	0	1	6674	767	27	1		1	GPR162	12	6933886	Silent	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	6632200	6933886	126918009	80	31168										
PAN2	9924	hgsc.bcm.edu	37	chr12	56713218	56713225	+	Frame_Shift_Del	DEL	GGCATCGA	GGCATCGA	-													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aggtgcttggaggaaattttGgcatcgaggtcaccaggctt							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	GGCATCGA	GGCATCGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr12:56713218_56713225delGGCATCGA	ENST00000425394.2	-	23	3525_3532	c.3149_3156delTCGATGCC	c.(3148-3156)ctcgatgccfs	p.LDA1050fs	PAN2_ENST00000257931.5_Frame_Shift_Del_p.LDA1049fs|PAN2_ENST00000440411.3_Frame_Shift_Del_p.LDA1046fs|PAN2_ENST00000549090.1_5'UTR|PAN2_ENST00000548043.1_Frame_Shift_Del_p.LDA1050fs	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	205					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	AGGAAATTTTGGCATCGAGGTCACCAGG	0.447																																					p.1050_1053del		Atlas-INDEL	.											.	PAN2	107	.	0			c.3150_3157del						.																																			SO:0001589	frameshift_variant	9924	exon23			.	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.3149_3156delTCGATGCC	chr12.hg19:g.56713218_56713225delGGCATCGA	ENSP00000401721:p.Leu1050fs	68.0	0.0		75.0	20.0	NM_001127460		Frame_Shift_Del	DEL	ENST00000425394.2	hg19	CCDS44922.1																																																																																			.	.		0.447	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		-	56713225	GGCATCGA	-	56713218	7	5	216	1	0	1	0	1	0	0	0	0	11423	1335	47	0	468	0	PAN2	12	56713218	Frame_Shift_Del	DEL	GGCATCGA	TCGA-DD-AAEB-01A-11D-A40R-10	49779332	56713218	77138677	81	31169										
NACA	4666	hgsc.bcm.edu	37	chr12	57107416	57107416	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gatattcttagatttccggaTagtgactctagtaactcctg	8	8	2	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr12:57107416T>C	ENST00000454682.1	-	6	6156	c.5875A>G	c.(5875-5877)Atc>Gtc	p.I1959V	NACA_ENST00000546392.1_Missense_Mutation_p.I96V|NACA_ENST00000552540.1_Missense_Mutation_p.I96V|NACA_ENST00000393891.4_Missense_Mutation_p.I96V|NACA_ENST00000550952.1_Missense_Mutation_p.I806V|NACA_ENST00000551793.1_5'Flank|NACA_ENST00000548563.1_Missense_Mutation_p.I17V|NACA_ENST00000356769.3_Missense_Mutation_p.I96V	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1959	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GATTTCCGGATAGTGACTCTA	0.423			T	BCL6	NHL																																p.I806V		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.A2416G						.						156	160	159					12																	57107416		2203	4300	6503	SO:0001583	missense	4666	exon8			TCCGGATAGTGAC	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.5875A>G	chr12.hg19:g.57107416T>C	ENSP00000403817:p.Ile1959Val	71.0	0.0		100.0	37.0	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	hg19		.	.	.	.	.	.	.	.	.	.	T	20.4	3.976022	0.74360	.	.	ENSG00000196531	ENST00000550920;ENST00000454682;ENST00000550952;ENST00000356769;ENST00000552540;ENST00000393891;ENST00000548563;ENST00000546392;ENST00000549259;ENST00000552055;ENST00000546862;ENST00000549855	T;T;T;T;T;T;T;T;T;T	0.55930	0.75;0.57;0.49;0.74;0.74;0.74;0.74;0.75;0.63;0.6	5.15	5.15	0.70609	Nascent polypeptide-associated complex NAC (2);	0.000000	0.85682	D	0.000000	T	0.70701	0.3254	M	0.77103	2.36	0.54753	D	0.999986	P;D;P	0.64830	0.949;0.994;0.76	D;D;P	0.66084	0.94;0.941;0.484	T	0.73496	-0.3964	10	0.49607	T	0.09	.	13.9523	0.64126	0.0:0.0:0.0:1.0	.	1959;806;96	E9PAV3;F8VU71;Q13765	.;.;NACA_HUMAN	V	94;1959;806;96;96;96;17;96;96;92;17;96	ENSP00000448039:I94V;ENSP00000403817:I1959V;ENSP00000448035:I806V;ENSP00000349212:I96V;ENSP00000447821:I96V;ENSP00000377469:I96V;ENSP00000446801:I96V;ENSP00000447133:I96V;ENSP00000450383:I92V;ENSP00000447764:I96V	ENSP00000349212:I96V	I	-	1	0	NACA	55393683	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.972000	0.88022	1.950000	0.56595	0.455000	0.32223	ATC	.	.		0.423	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		C	57107416	T	C	57107416	3	2	216	1	0	0	0	0	1	0	0	0	10142	1406	49	2	377	2	NACA	12	57107416	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	394198	57107416	76744479	82	31170										
SYT1	6857	hgsc.bcm.edu	37	chr12	79611325	79611325	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gagcgagagtcaccatgaggCcctggcagccccgcctgtca	13	15	2	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr12:79611325C>G	ENST00000261205.4	+	4	683	c.26C>G	c.(25-27)gCc>gGc	p.A9G	SYT1_ENST00000393240.3_Missense_Mutation_p.A9G|SYT1_ENST00000552744.1_Missense_Mutation_p.A9G|SYT1_ENST00000457153.2_Missense_Mutation_p.A9G	NM_005639.2	NP_005630.1	P21579	SYT1_HUMAN	synaptotagmin I	9					calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|detection of calcium ion (GO:0005513)|glutamate secretion (GO:0014047)|neurotransmitter secretion (GO:0007269)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of vesicle fusion (GO:0031340)|protein homooligomerization (GO:0051260)|regulation of exocytosis (GO:0017157)|regulation of regulated secretory pathway (GO:1903305)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|vesicle docking (GO:0048278)	cell junction (GO:0030054)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|endocytic vesicle membrane (GO:0030666)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol binding (GO:0005545)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|pancreas(2)|skin(6)	25						CACCATGAGGCCCTGGCAGCC	0.532																																					p.A9G		Atlas-SNP	.											.	SYT1	70	.	0			c.C26G						.						43	44	44					12																	79611325		2203	4300	6503	SO:0001583	missense	6857	exon5			ATGAGGCCCTGGC		CCDS9017.1	12q21.2	2013-09-20			ENSG00000067715	ENSG00000067715		"Synaptotagmins"	11509	protein-coding gene	gene with protein product		185605		SYT, SVP65		1840599	Standard	NM_001135805		Approved	P65	uc001syv.3	P21579	OTTHUMG00000134326	ENST00000261205.4:c.26C>G	chr12.hg19:g.79611325C>G	ENSP00000261205:p.Ala9Gly	43.0	0.0		27.0	8.0	NM_001135805	Q6AI31	Missense_Mutation	SNP	ENST00000261205.4	hg19	CCDS9017.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.207659	0.58343	.	.	ENSG00000067715	ENST00000393240;ENST00000261205;ENST00000457153;ENST00000552074;ENST00000547046;ENST00000549671;ENST00000551304;ENST00000552744;ENST00000552624;ENST00000446242	T;T;T;T;T;T	0.61040	0.16;0.16;0.14;0.16;1.74;2.34	5.51	5.51	0.81932	.	0.119371	0.56097	D	0.000029	T	0.51483	0.1677	L	0.55990	1.75	0.58432	D	0.999994	B;B	0.30193	0.272;0.272	B;B	0.26770	0.073;0.073	T	0.51140	-0.8743	10	0.41790	T	0.15	.	12.7221	0.57147	0.0:0.9246:0.0:0.0754	.	9;9	Q6AI31;P21579	.;SYT1_HUMAN	G	9	ENSP00000376932:A9G;ENSP00000261205:A9G;ENSP00000391056:A9G;ENSP00000447575:A9G;ENSP00000448861:A9G;ENSP00000401559:A9G	ENSP00000261205:A9G	A	+	2	0	SYT1	78135456	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.299000	0.59073	2.583000	0.87209	0.643000	0.83706	GCC	.	.		0.532	SYT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259415.1	NM_005639		G	79611325	C	G	79611325	3	3	216	1	0	0	0	0	1	0	0	0	15480	739	26	4	28	4	SYT1	12	79611325	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	22503909	79611325	54240570	83	31171										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85518023	85518023	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	caaacagtgacagcactctgCaaaatggagtcttctactct	7	11	4	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr12:85518023C>T	ENST00000393217.2	+	17	3794	c.3733C>T	c.(3733-3735)Caa>Taa	p.Q1245*		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1245										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		CAGCACTCTGCAAAATGGAGT	0.478																																					p.Q1245X		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.C3733T						.						100	103	102					12																	85518023		2203	4300	6503	SO:0001587	stop_gained	84125	exon17			ACTCTGCAAAATG	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.3733C>T	chr12.hg19:g.85518023C>T	ENSP00000376910:p.Gln1245*	80.0	0.0		97.0	39.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Nonsense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	C	37	6.591134	0.97688	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	.	.	.	5.61	4.7	0.59300	.	0.983063	0.08264	N	0.972481	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	9.7991	0.40753	0.1392:0.5589:0.3019:0.0	.	.	.	.	X	1245;1220;1245	.	ENSP00000256007:Q1245X	Q	+	1	0	LRRIQ1	84042154	1.000000	0.71417	0.017000	0.16124	0.004000	0.04260	1.420000	0.34804	1.320000	0.45209	0.585000	0.79938	CAA	.	.		0.478	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85518023	C	T	85518023	4	4	216	1	0	0	0	0	0	1	0	0	9038	711	25	3	3795	3	LRRIQ1	12	85518023	Nonsense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	5906698	85518023	48333872	84	31172										
ATP2B1	490	hgsc.bcm.edu	37	chr12	90035972	90035972	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ggaggctgataaaaagaaagGcccaatgatactatggctgc	12	7	0	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr12:90035972G>C	ENST00000428670.3	-	3	825	c.369C>G	c.(367-369)ggC>ggG	p.G123G	ATP2B1_ENST00000261173.2_Silent_p.G123G|ATP2B1_ENST00000359142.3_Silent_p.G123G|ATP2B1_ENST00000348959.3_Silent_p.G123G			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	123					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						AAAAAGAAAGGCCCAATGATA	0.358																																					p.G123G		Atlas-SNP	.											.	ATP2B1	191	.	0			c.C369G						.						139	155	149					12																	90035972		2203	4299	6502	SO:0001819	synonymous_variant	490	exon2			AGAAAGGCCCAAT	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.369C>G	chr12.hg19:g.90035972G>C		83.0	0.0		92.0	33.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Silent	SNP	ENST00000428670.3	hg19	CCDS9035.1																																																																																			.	.		0.358	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		C	90035972	G	C	90035972	2	2	216	1	0	0	0	0	0	0	0	1	1139	1190	42	4		4	ATP2B1	12	90035972	Silent	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	4517949	90035972	43815923	85	31173										
CORO1C	23603	hgsc.bcm.edu	37	chr12	109051082	109051083	+	Missense_Mutation	DNP	GA	GA	TT													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agcctggggagggcgtaccgGattccagagagccagctgcc							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr12:109051082_109051083GA>TT	ENST00000261401.3	-	6	919_920	c.747_748TC>AA	c.(745-750)aaTCcg>aaAAcg	p.249_250NP>KT	CORO1C_ENST00000549772.1_Missense_Mutation_p.255_256NP>KT|CORO1C_ENST00000549384.1_Intron|CORO1C_ENST00000421578.2_Missense_Mutation_p.144_145NP>KT|CORO1C_ENST00000420959.2_Missense_Mutation_p.302_303NP>KT|CORO1C_ENST00000541050.1_Missense_Mutation_p.249_250NP>KT	NM_001105237.2|NM_001276471.1|NM_014325.2	NP_001098707.1|NP_001263400.1|NP_055140.1	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C	249					actin cytoskeleton organization (GO:0030036)|phagocytosis (GO:0006909)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|skin(4)	24						GGGCGTACCGGATTCCAGAGAG	0.535																																					p.M250M|p.F249L		Atlas-SNP	.											.	CORO1C	53	.	0			c.A748A|c.C747A						.																																			SO:0001583	missense	23603	exon6			GTACCGGATTCCA|TACCGGATTCCAG	BC002342	CCDS9120.1, CCDS61236.1	12q24.1	2013-01-10	2001-11-28			ENSG00000110880		"Coronins", "WD repeat domain containing"	2254	protein-coding gene	gene with protein product		605269	"coronin, actin-binding protein, 1C"			9778037, 10461187	Standard	NM_014325		Approved	coronin-3, HCRNN4	uc009zva.4	Q9ULV4		ENST00000261401.3:c.747_748delinsTT	chr12.hg19:g.109051082_109051083delinsTT	ENSP00000261401:p.N249_P250delinsKT	67.0	0.0		42.0	12.0	NM_014325	A7MAP0|A7MAP1|B3KU12|Q9NSK5	Silent|Missense_Mutation	SNP	ENST00000261401.3	hg19	CCDS9120.1																																																																																			.	.		0.535	CORO1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403802.1	NM_014325		TT	109051083	GA	TT	109051082	3	4	216	1	0	0	0	0	1	0	0	0	3757	1174	41	3	700	3	CORO1C	12	109051082	Missense_Mutation	DNP	GA	TCGA-DD-AAEB-01A-11D-A40R-10	19015110	109051082	24800813	86	31174										
NHLRC3	387921	hgsc.bcm.edu	37	chr13	39613820	39613820	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gccagtactctatatgaacaAtccgtctggatcacggatgt	9	10	3	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr13:39613820A>G	ENST00000379600.3	+	3	679	c.357A>G	c.(355-357)caA>caG	p.Q119Q	PROSER1_ENST00000352251.3_5'Flank|PROSER1_ENST00000350125.3_5'Flank|NHLRC3_ENST00000470258.1_5'UTR|NHLRC3_ENST00000379599.2_Silent_p.Q119Q	NM_001012754.3	NP_001012772.1	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3	119						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|skin(2)	11		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		TATATGAACAATCCGTCTGGA	0.368																																					p.Q119Q		Atlas-SNP	.											.	NHLRC3	35	.	0			c.A357G						.						89	88	88					13																	39613820		2203	4300	6503	SO:0001819	synonymous_variant	387921	exon3			TGAACAATCCGTC		CCDS31961.1, CCDS31962.1	13q13.3	2007-12-18			ENSG00000188811	ENSG00000188811			33751	protein-coding gene	gene with protein product							Standard	NM_001017370		Approved		uc001uxc.4	Q5JS37	OTTHUMG00000016765	ENST00000379600.3:c.357A>G	chr13.hg19:g.39613820A>G		87.0	0.0		124.0	43.0	NM_001012754	B2RTZ2|B4DTL0|Q69YI9	Silent	SNP	ENST00000379600.3	hg19	CCDS31961.1																																																																																			.	.		0.368	NHLRC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044616.2	NM_001012754		G	39613820	A	G	39613820	2	3	216	1	0	0	0	0	0	0	0	1	10416	98	4	2		2	NHLRC3	13	39613820	Silent	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10		39613820	75556058	87	31175										
RASA3	22821	hgsc.bcm.edu	37	chr13	114778624	114778624	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agccggtcactcaccgtgtgGtgcggcgtgagctggaagag	17	10	2	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr13:114778624G>T	ENST00000334062.7	-	15	1627	c.1506C>A	c.(1504-1506)caC>caA	p.H502Q	RASA3_ENST00000389544.4_Missense_Mutation_p.H470Q	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	502	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			TCACCGTGTGGTGCGGCGTGA	0.642																																					p.H502Q		Atlas-SNP	.											.	RASA3	83	.	0			c.C1506A						.						91	71	78					13																	114778624		2203	4300	6503	SO:0001583	missense	22821	exon15			CGTGTGGTGCGGC		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"Pleckstrin homology (PH) domain containing"	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.1506C>A	chr13.hg19:g.114778624G>T	ENSP00000335029:p.His502Gln	55.0	0.0		61.0	20.0	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	hg19	CCDS32016.1	.	.	.	.	.	.	.	.	.	.	G	11.46	1.643944	0.29246	.	.	ENSG00000185989	ENST00000334062;ENST00000389544	T;T	0.79033	-1.23;-1.23	5.0	1.83	0.25207	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.000000	0.85682	D	0.000000	T	0.76026	0.3930	L	0.50847	1.595	0.80722	D	1	B	0.30686	0.29	P	0.46975	0.533	T	0.66893	-0.5808	9	.	.	.	.	5.4691	0.16660	0.5661:0.0:0.4339:0.0	.	502	Q14644	RASA3_HUMAN	Q	502;470	ENSP00000335029:H502Q;ENSP00000374195:H470Q	.	H	-	3	2	RASA3	113796726	1.000000	0.71417	0.998000	0.56505	0.380000	0.30137	0.536000	0.23129	0.516000	0.28340	0.491000	0.48974	CAC	.	.		0.642	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368		T	114778624	G	T	114778624	3	4	216	1	0	0	0	0	1	0	0	0	13077	1252	44	3	1038	3	RASA3	13	114778624	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	75164804	114778624	391254	88	31176										
CRIP2	1397	hgsc.bcm.edu	37	chr14	105945139	105945139	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aggggccgcaggtcaccggcCccatcgaggtccccgcggcc	15	18	1	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr14:105945139C>T	ENST00000329146.4	+	4	981	c.268C>T	c.(268-270)Ccc>Tcc	p.P90S	CRIP2_ENST00000548989.1_3'UTR|CRIP2_ENST00000483017.3_Missense_Mutation_p.P164S	NM_001312.3	NP_001303.1	P52943	CRIP2_HUMAN	cysteine-rich protein 2	90					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	cell cortex (GO:0005938)	zinc ion binding (GO:0008270)			lung(2)	2		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.235)		GGTCACCGGCCCCATCGAGGT	0.761																																					p.P164S		Atlas-SNP	.											.	CRIP2	7	.	0			c.C490T						.						1	1	1					14																	105945139		732	1540	2272	SO:0001583	missense	1397	exon4			ACCGGCCCCATCG		CCDS10003.1, CCDS59246.1	14q32.3	2008-08-11			ENSG00000182809	ENSG00000182809			2361	protein-coding gene	gene with protein product		601183				8843343, 10681529	Standard	NM_001312		Approved	CRP2, ESP1	uc031qqr.1	P52943	OTTHUMG00000029906	ENST00000329146.4:c.268C>T	chr14.hg19:g.105945139C>T	ENSP00000328521:p.Pro90Ser	23.0	0.0		40.0	10.0	NM_001270837	A1A4U1|B7Z6C0|E9PD13	Missense_Mutation	SNP	ENST00000329146.4	hg19	CCDS10003.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	11.18|11.18	1.562887|1.562887	0.27915|0.27915	.|.	.|.	ENSG00000182809|ENSG00000182809	ENST00000538259|ENST00000483017;ENST00000329146	.|T;T	.|0.71341	.|-0.56;-0.23	3.46|3.46	3.46|3.46	0.39613|0.39613	.|.	51.284300|51.284300	0.00783|0.00783	U|U	0.001289|0.001289	T|T	0.56426|0.56426	0.1984|0.1984	N|N	0.14661|0.14661	0.345|0.345	0.43351|0.43351	D|D	0.995413|0.995413	.|B;B;B	.|0.26081	.|0.141;0.141;0.002	.|B;B;B	.|0.20767	.|0.012;0.031;0.001	T|T	0.24728|0.24728	-1.0152|-1.0152	6|10	.|0.07990	.|T	.|0.79	-0.1639|-0.1639	13.6859|13.6859	0.62515|0.62515	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|164;90;90	.|B7Z6C0;Q53FN1;P52943	.|.;.;CRIP2_HUMAN	L|S	73|164;90	.|ENSP00000426119:P164S;ENSP00000328521:P90S	.|ENSP00000328521:P90S	P|P	+|+	2|1	0|0	CRIP2|CRIP2	105016184|105016184	0.512000|0.512000	0.26186|0.26186	1.000000|1.000000	0.80357|0.80357	0.880000|0.880000	0.50808|0.50808	1.502000|1.502000	0.35704|0.35704	1.787000|1.787000	0.52448|0.52448	0.282000|0.282000	0.19409|0.19409	CCC|CCC	.	.		0.761	CRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074597.3	NM_001312		T	105945139	C	T	105945139	3	4	216	1	0	0	0	0	1	0	0	0	3877	623	22	3	282	3	CRIP2	14	105945139	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10		105945139	1404401	89	31177										
NDN	4692	hgsc.bcm.edu	37	chr15	23931788	23931788	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gtagatgaggctcaggatcaTgagcaggaggcctgtcatgg	16	7	3	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr15:23931788T>G	ENST00000331837.4	-	1	662	c.577A>C	c.(577-579)Atg>Ctg	p.M193L		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	193	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		CTCAGGATCATGAGCAGGAGG	0.652									Prader-Willi syndrome																												p.M193L		Atlas-SNP	.											.	NDN	79	.	0			c.A577C						.						26	25	25					15																	23931788		2202	4292	6494	SO:0001583	missense	4692	exon1	Familial Cancer Database	Prader-Labhart-Willi syndrome	GGATCATGAGCAG	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"Prader-Willi syndrome chromosome region"	602117	"necdin (mouse) homolog", "necdin homolog (mouse)"			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.577A>C	chr15.hg19:g.23931788T>G	ENSP00000332643:p.Met193Leu	61.0	0.0		98.0	44.0	NM_002487	B2R6Z5	Missense_Mutation	SNP	ENST00000331837.4	hg19	CCDS10014.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.686539	0.47991	.	.	ENSG00000182636	ENST00000331837	T	0.03860	3.78	3.22	3.22	0.36961	.	0.059288	0.64402	D	0.000003	T	0.01695	0.0054	N	0.00885	-1.115	0.29880	N	0.826124	B	0.20988	0.05	B	0.31290	0.127	T	0.42982	-0.9419	10	0.12766	T	0.61	.	8.2254	0.31566	0.0:0.0:0.0:1.0	.	193	Q99608	NECD_HUMAN	L	193	ENSP00000332643:M193L	ENSP00000332643:M193L	M	-	1	0	NDN	21482881	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.268000	0.33062	1.720000	0.51447	0.459000	0.35465	ATG	.	.		0.652	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487		G	23931788	T	G	23931788	3	3	216	1	0	0	0	0	1	0	0	0	10256	1464	51	5	392	5	NDN	15	23931788	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10		23931788	78599604	90	31178										
USP3	9960	hgsc.bcm.edu	37	chr15	63881201	63881201	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	cgccgctgtggtggtgcaccAtggttccgggtgagtacaac	15	11	0	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr15:63881201A>G	ENST00000380324.3	+	14	1517	c.1388A>G	c.(1387-1389)cAt>cGt	p.H463R	USP3-AS1_ENST00000559737.1_RNA|USP3-AS1_ENST00000560962.1_RNA|USP3-AS1_ENST00000559357.1_RNA|USP3-AS1_ENST00000561191.1_RNA|USP3-AS1_ENST00000559861.1_RNA|USP3_ENST00000268049.7_Missense_Mutation_p.H441R|USP3_ENST00000558285.1_Missense_Mutation_p.H446R|USP3_ENST00000559711.1_Missense_Mutation_p.H374R|USP3-AS1_ENST00000560350.1_RNA|USP3-AS1_ENST00000560622.1_RNA|USP3-AS1_ENST00000558831.1_RNA|USP3-AS1_ENST00000561256.1_RNA|USP3_ENST00000539772.1_Missense_Mutation_p.H214R|USP3_ENST00000540797.1_Missense_Mutation_p.H419R|USP3_ENST00000558218.1_3'UTR	NM_006537.3	NP_006528.2	Q9Y6I4	UBP3_HUMAN	ubiquitin specific peptidase 3	463	USP.				DNA repair (GO:0006281)|histone deubiquitination (GO:0016578)|mitotic cell cycle (GO:0000278)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear chromatin (GO:0000790)	histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(7)|lung(4)	14				GBM - Glioblastoma multiforme(80;0.0187)		GTGGTGCACCATGGTTCCGGG	0.552																																					p.H463R		Atlas-SNP	.											.	USP3	37	.	0			c.A1388G						.						170	165	167					15																	63881201		2203	4300	6503	SO:0001583	missense	9960	exon14			TGCACCATGGTTC	AF073344	CCDS32265.1, CCDS58370.1	15q22.3	2008-04-11	2005-08-08			ENSG00000140455		"Ubiquitin-specific peptidases"	12626	protein-coding gene	gene with protein product		604728	"ubiquitin specific protease 3"			12838346	Standard	NM_006537		Approved		uc002amf.4	Q9Y6I4		ENST00000380324.3:c.1388A>G	chr15.hg19:g.63881201A>G	ENSP00000369681:p.His463Arg	103.0	0.0		94.0	36.0	NM_006537	B4DVU5|F5H1A6|Q8WVD0	Missense_Mutation	SNP	ENST00000380324.3	hg19	CCDS32265.1	.	.	.	.	.	.	.	.	.	.	A	19.40	3.821312	0.71028	.	.	ENSG00000140455	ENST00000540797;ENST00000380324;ENST00000268049;ENST00000539772;ENST00000538686	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	5.28	5.28	0.74379	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.34919	0.0914	L	0.61036	1.89	0.58432	D	0.999999	B;B;B;B	0.26708	0.064;0.157;0.157;0.157	B;B;B;B	0.31245	0.056;0.126;0.126;0.126	T	0.10405	-1.0631	10	0.27785	T	0.31	.	15.493	0.75624	1.0:0.0:0.0:0.0	.	419;419;441;463	F5H1A6;B4DVU5;Q6JHV3;Q9Y6I4	.;.;.;UBP3_HUMAN	R	419;463;441;214;294	ENSP00000445828:H419R;ENSP00000369681:H463R;ENSP00000268049:H441R;ENSP00000445642:H214R	ENSP00000268049:H441R	H	+	2	0	USP3	61668254	1.000000	0.71417	0.928000	0.36995	0.992000	0.81027	7.469000	0.80959	2.129000	0.65627	0.533000	0.62120	CAT	.	.		0.552	USP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417773.1			G	63881201	A	G	63881201	3	3	216	1	0	0	0	0	1	0	0	0	17075	217	8	2	1442	2	USP3	15	63881201	Missense_Mutation	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10	39949413	63881201	38650191	91	31179										
SEMA7A	8482	hgsc.bcm.edu	37	chr15	74703257	74703257	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	atgagtaggtggcgtggcggGattccatggggcagctcagg	19	7	1	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr15:74703257G>A	ENST00000261918.4	-	14	2257	c.1709C>T	c.(1708-1710)tCc>tTc	p.S570F	SEMA7A_ENST00000542748.1_Missense_Mutation_p.S405F|SEMA7A_ENST00000543145.2_Missense_Mutation_p.S556F	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	570	Ig-like C2-type.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						GGCGTGGCGGGATTCCATGGG	0.617																																					p.S570F		Atlas-SNP	.											.	SEMA7A	58	.	0			c.C1709T						.						100	102	101					15																	74703257		2197	4296	6493	SO:0001583	missense	8482	exon14			TGGCGGGATTCCA	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"Semaphorins", "CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10741	protein-coding gene	gene with protein product	"John Milton Hagen blood group", "H-Sema K1"	607961	"sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A", "sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1709C>T	chr15.hg19:g.74703257G>A	ENSP00000261918:p.Ser570Phe	59.0	0.0		60.0	27.0	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	hg19	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.056403	0.76074	.	.	ENSG00000138623	ENST00000261918;ENST00000543145;ENST00000542748	T;T;T	0.14516	2.5;2.5;2.5	4.55	4.55	0.56014	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.33789	0.0875	L	0.59436	1.845	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.07290	-1.0780	10	0.72032	D	0.01	-29.3795	15.1021	0.72288	0.0:0.0:1.0:0.0	.	556;570	F5H1S0;O75326	.;SEM7A_HUMAN	F	570;556;405	ENSP00000261918:S570F;ENSP00000438966:S556F;ENSP00000441493:S405F	ENSP00000261918:S570F	S	-	2	0	SEMA7A	72490310	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.133000	0.71682	2.094000	0.63399	0.555000	0.69702	TCC	.	.		0.617	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		A	74703257	G	A	74703257	3	1	216	1	0	0	0	0	1	0	0	0	14058	1174	41	3	295	3	SEMA7A	15	74703257	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	10822056	74703257	27828135	92	31180										
VPS33B	26276	hgsc.bcm.edu	37	chr15	91548981	91548981	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gagctcctgggacacgaaatTcttcatctgcttaatgtcca	8	11	3	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr15:91548981T>C	ENST00000333371.3	-	13	1326	c.973A>G	c.(973-975)Aat>Gat	p.N325D	VPS33B_ENST00000535843.1_Missense_Mutation_p.N234D|VPS33B_ENST00000535906.1_Missense_Mutation_p.N298D	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	325					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|membrane fusion (GO:0061025)|platelet alpha granule organization (GO:0070889)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule (GO:0031091)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|stomach(2)	16	Lung NSC(78;0.0987)|all_lung(78;0.175)					GACACGAAATTCTTCATCTGC	0.567																																					p.N325D		Atlas-SNP	.											.	VPS33B	42	.	0			c.A973G						.						100	88	92					15																	91548981		2198	4298	6496	SO:0001583	missense	26276	exon13			CGAAATTCTTCAT	AF201694	CCDS10369.1, CCDS73783.1	15q26.1	2006-12-19	2006-12-19		ENSG00000184056	ENSG00000184056			12712	protein-coding gene	gene with protein product		608552	"vacuolar protein sorting 33B (yeast homolog)"			8996080	Standard	XM_005254887		Approved	FLJ14848	uc002bqp.1	Q9H267	OTTHUMG00000149835	ENST00000333371.3:c.973A>G	chr15.hg19:g.91548981T>C	ENSP00000327650:p.Asn325Asp	69.0	0.0		98.0	37.0	NM_018668	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Missense_Mutation	SNP	ENST00000333371.3	hg19	CCDS10369.1	.	.	.	.	.	.	.	.	.	.	T	2.975	-0.211555	0.06140	.	.	ENSG00000184056	ENST00000333371;ENST00000535906;ENST00000535843;ENST00000537510	T;T;T	0.79454	-1.27;-1.27;-1.27	5.65	3.36	0.38483	.	0.206931	0.48767	N	0.000162	T	0.49745	0.1575	N	0.04018	-0.295	0.36927	D	0.89168	B;B	0.18610	0.023;0.029	B;B	0.18561	0.013;0.022	T	0.48670	-0.9015	10	0.02654	T	1	-15.5283	8.9629	0.35858	0.0:0.2121:0.0:0.7879	.	298;325	F5H008;Q9H267	.;VP33B_HUMAN	D	325;298;234;280	ENSP00000327650:N325D;ENSP00000444053:N298D;ENSP00000446267:N234D	ENSP00000327650:N325D	N	-	1	0	VPS33B	89349985	1.000000	0.71417	1.000000	0.80357	0.450000	0.32258	1.109000	0.31135	0.567000	0.29293	-0.256000	0.11100	AAT	.	.		0.567	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668		C	91548981	T	C	91548981	3	2	216	1	0	0	0	0	1	0	0	0	17217	1783	62	2	924	2	VPS33B	15	91548981	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	16845724	91548981	10982411	93	31181										
NDUFB10	4716	hgsc.bcm.edu	37	chr16	2011585	2011586	+	Nonsense_Mutation	DNP	TA	TA	AT													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	cagaactaccagcagaactgTatcaaggaagtggagcagtt							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T|A	T|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr16:2011585_2011586TA>AT	ENST00000268668.6	+	3	474_475	c.357_358TA>AT	c.(355-360)tgTAtc>tgATtc	p.119_120CI>*F	NDUFB10_ENST00000543683.2_Nonsense_Mutation_p.119_120CI>*F|SNORA10_ENST00000384084.1_RNA|SNORA64_ENST00000384674.1_RNA|NDUFB10_ENST00000569148.1_Nonsense_Mutation_p.108_109CI>*F	NM_004548.2	NP_004539.1	O96000	NDUBA_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa	119					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			lung(1)|urinary_tract(1)	2						AGCAGAACTGTATCAAGGAAGT	0.564																																					p.C119X|p.I120F		Atlas-SNP	.											.	NDUFB10	17	.	0			c.T357A|c.A358T						.																																			SO:0001587	stop_gained	4716	exon3			GAACTGTATCAAG|AACTGTATCAAGG	AF044954	CCDS10451.1	16p13.3	2011-07-04	2002-08-29		ENSG00000140990	ENSG00000140990		"Mitochondrial respiratory chain complex / Complex I"	7696	protein-coding gene	gene with protein product	"complex I PDSW subunit"	603843	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10 (22kD, PDSW)"			9763677, 9878551	Standard	NM_004548		Approved	PDSW	uc002cni.2	O96000	OTTHUMG00000128709	Exception_encountered	chr16.hg19:g.2011585_2011586delinsAT	ENSP00000268668:p.C119_I120delins*F	98.0	0.0		101.0	44.0	NM_004548	Q96II6	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000268668.6	hg19	CCDS10451.1																																																																																			.	.		0.564	NDUFB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250614.2	NM_004548		AT	2011586	TA	AT	2011585	4	1	216	1	0	0	0	0	0	1	0	0	10288	1644	57	4	367	4	NDUFB10	16	2011585	Nonsense_Mutation	DNP	TA	TCGA-DD-AAEB-01A-11D-A40R-10		2011585	88343168	94	31182										
OTOA	146183	hgsc.bcm.edu	37	chr16	21698947	21698947	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	agcggctccctcgggacctgCgcgaggatgcctttaagaac	13	13	0	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr16:21698947C>T	ENST00000286149.4	+	7	614	c.613C>T	c.(613-615)Cgc>Tgc	p.R205C	OTOA_ENST00000388956.4_Missense_Mutation_p.R126C|OTOA_ENST00000388958.3_Missense_Mutation_p.R205C			Q7RTW8	OTOAN_HUMAN	otoancorin	205					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)		p.R205G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		TCGGGACCTGCGCGAGGATGC	0.542																																					p.R205C		Atlas-SNP	.											OTOA,NS,carcinoma,0,1	OTOA	144	.	1	Substitution - Missense(1)	lung(1)	c.C613T						.						33	31	32					16																	21698947		2199	4300	6499	SO:0001583	missense	146183	exon7			GACCTGCGCGAGG	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"cancer/testis antigen 108"	607038	"deafness, autosomal recessive 22"	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.613C>T	chr16.hg19:g.21698947C>T	ENSP00000286149:p.Arg205Cys	78.0	0.0		98.0	39.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	hg19		.	.	.	.	.	.	.	.	.	.	C	4.169	0.029956	0.08101	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956	T;T;T	0.13196	2.61;2.61;2.61	4.36	1.24	0.21308	.	0.331976	0.25192	N	0.032444	T	0.09992	0.0245	L	0.40543	1.245	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.23154	-1.0196	10	0.45353	T	0.12	-0.245	6.0997	0.20041	0.0:0.6637:0.1542:0.1821	.	126;205	B3KWU3;E9PF51	.;.	C	205;205;126	ENSP00000373610:R205C;ENSP00000286149:R205C;ENSP00000373608:R126C	ENSP00000286149:R205C	R	+	1	0	OTOA	21606448	0.033000	0.19621	0.033000	0.17914	0.134000	0.20937	0.725000	0.25970	-0.001000	0.14495	-0.262000	0.10625	CGC	.	.		0.542	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1			T	21698947	C	T	21698947	3	4	216	1	0	0	0	0	1	0	0	0	11311	768	27	1	673	1	OTOA	16	21698947	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	19687362	21698947	68655806	95	31183										
IRX3	79191	hgsc.bcm.edu	37	chr16	54318534	54318534	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gggagagcgggtgcaggcggGggccgggcggtgggcctgga	26	8	0	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr16:54318534G>C	ENST00000329734.3	-	2	1971	c.1259C>G	c.(1258-1260)cCc>cGc	p.P420R		NM_024336.2	NP_077312.2	P78415	IRX3_HUMAN	iroquois homeobox 3	420	Pro-rich.				mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of neuron differentiation (GO:0045666)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	14						GTGCAGGCGGGGGCCGGGCGG	0.781																																					p.P420R	GBM(143;1830 1866 4487 4646 37383)	Atlas-SNP	.											.	IRX3	25	.	0			c.C1259G						.						2	2	2					16																	54318534		898	2112	3010	SO:0001583	missense	79191	exon2			AGGCGGGGGCCGG	U90308	CCDS10750.1	16q12.2	2011-06-20	2007-07-13		ENSG00000177508	ENSG00000177508		"Homeoboxes / TALE class"	14360	protein-coding gene	gene with protein product		612985					Standard	NM_024336		Approved	IRX-1	uc002eht.1	P78415	OTTHUMG00000133200	ENST00000329734.3:c.1259C>G	chr16.hg19:g.54318534G>C	ENSP00000331608:p.Pro420Arg	21.0	0.0		18.0	13.0	NM_024336	Q7Z4A4|Q7Z4A5|Q8IVC6	Missense_Mutation	SNP	ENST00000329734.3	hg19	CCDS10750.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.427863	0.25726	.	.	ENSG00000177508	ENST00000329734	T	0.54071	0.59	4.4	3.45	0.39498	.	0.509375	0.19782	N	0.106198	T	0.43590	0.1254	L	0.36672	1.1	0.24597	N	0.993794	D	0.61080	0.989	P	0.47573	0.55	T	0.20371	-1.0277	10	0.24483	T	0.36	-4.5461	8.096	0.30829	0.1104:0.0:0.8896:0.0	.	420	P78415	IRX3_HUMAN	R	420	ENSP00000331608:P420R	ENSP00000331608:P420R	P	-	2	0	IRX3	52876035	0.180000	0.23148	0.965000	0.40720	0.001000	0.01503	0.461000	0.21940	1.060000	0.40578	-0.136000	0.14681	CCC	.	.		0.781	IRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256910.2			C	54318534	G	C	54318534	3	2	216	1	0	0	0	0	1	0	0	0	7854	1232	43	4	258	4	IRX3	16	54318534	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	32619587	54318534	36036219	96	31184										
DPEP2	64174	hgsc.bcm.edu	37	chr16	68023228	68023228	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	cacagggaaggcactcacttGccggccccatcataatctcc	8	16	3	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr16:68023228G>T	ENST00000572888.1	-	8	1718	c.1068C>A	c.(1066-1068)ggC>ggA	p.G356G	DPEP2_ENST00000412757.2_Silent_p.G356G|DPEP2_ENST00000393847.1_Silent_p.G356G			Q9H4A9	DPEP2_HUMAN	dipeptidase 2	356					arachidonic acid metabolic process (GO:0019369)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		GCACTCACTTGCCGGCCCCAT	0.557																																					p.G356G		Atlas-SNP	.											.	DPEP2	43	.	0			c.C1068A						.						123	90	101					16																	68023228		2198	4300	6498	SO:0001819	synonymous_variant	64174	exon9			TCACTTGCCGGCC	AJ295149	CCDS10857.1	16q22.1	2011-07-22			ENSG00000167261	ENSG00000167261	3.4.13.19		23028	protein-coding gene	gene with protein product		609925					Standard	NM_022355		Approved		uc002eve.4	Q9H4A9	OTTHUMG00000137542	ENST00000572888.1:c.1068C>A	chr16.hg19:g.68023228G>T		62.0	0.0		62.0	31.0	NM_022355	B2RCF8|Q6UX92|Q8TC95	Silent	SNP	ENST00000572888.1	hg19	CCDS10857.1																																																																																			.	.		0.557	DPEP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437026.1	NM_022355		T	68023228	G	T	68023228	2	4	216	1	0	0	0	0	0	0	0	1	4716	1306	46	3		3	DPEP2	16	68023228	Silent	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	13704694	68023228	22331525	97	31185										
ZNF276	92822	hgsc.bcm.edu	37	chr16	89799791	89799791	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aagaagccgggacccaagccCggatggaagaagaagcttcg	14	10	0	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr16:89799791C>T	ENST00000443381.2	+	7	1348	c.1251C>T	c.(1249-1251)ccC>ccT	p.P417P	ZNF276_ENST00000446326.2_Silent_p.P203P|ZNF276_ENST00000289816.5_Silent_p.P342P|ZNF276_ENST00000568064.1_Silent_p.P325P	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	417					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)	14		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		GACCCAAGCCCGGATGGAAGA	0.547																																					p.P417P		Atlas-SNP	.											.	ZNF276	70	.	0			c.C1251T						.						120	138	132					16																	89799791		2198	4300	6498	SO:0001819	synonymous_variant	92822	exon7			CAAGCCCGGATGG	AK026482	CCDS10986.1, CCDS45554.1	16q24.3	2014-02-17	2006-02-10	2006-02-10	ENSG00000158805	ENSG00000158805		"Zinc fingers, C2H2-type"	23330	protein-coding gene	gene with protein product	"centromere protein Z", "zinc finger, AD-type"	608460	"zinc finger protein 276 homolog (mouse)"	ZFP276		10936049, 20813266	Standard	NM_152287		Approved	MGC45417, ZNF477, CENPZ, CENP-Z, ZADT	uc002fos.4	Q8N554	OTTHUMG00000138050	ENST00000443381.2:c.1251C>T	chr16.hg19:g.89799791C>T		142.0	0.0		155.0	71.0	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Silent	SNP	ENST00000443381.2	hg19	CCDS45554.1																																																																																			.	.		0.547	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287		T	89799791	C	T	89799791	2	4	216	1	0	0	0	0	0	0	0	1	17826	639	23	1		1	ZNF276	16	89799791	Silent	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	21776563	89799791	554962	98	31186										
CLTC	1213	hgsc.bcm.edu	37	chr17	57743863	57743863	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tgcagatgctattctaggcaAtcagatgttcacacattatg	8	8	3	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr17:57743863A>G	ENST00000269122.3	+	12	2079	c.1805A>G	c.(1804-1806)aAt>aGt	p.N602S	CLTC_ENST00000393043.1_Missense_Mutation_p.N602S|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	602	Distal segment.|Heavy chain arm.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					ATTCTAGGCAATCAGATGTTC	0.393			T	"ALK, TFE3"	"ALCL, renal "																																p.N602S		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.A1805G						.						106	103	104					17																	57743863		2203	4300	6503	SO:0001583	missense	1213	exon12			TAGGCAATCAGAT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.1805A>G	chr17.hg19:g.57743863A>G	ENSP00000269122:p.Asn602Ser	110.0	0.0		113.0	44.0	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.904339	0.92035	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.22743	1.94;1.94	5.84	5.84	0.93424	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.50956	0.1646	M	0.82630	2.6	0.80722	D	1	D;B	0.69078	0.997;0.283	D;B	0.80764	0.994;0.349	T	0.55617	-0.8113	10	0.59425	D	0.04	.	16.226	0.82293	1.0:0.0:0.0:0.0	.	602;602	Q00610;Q00610-2	CLH1_HUMAN;.	S	602	ENSP00000269122:N602S;ENSP00000376763:N602S	ENSP00000269122:N602S	N	+	2	0	CLTC	55098645	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.339000	0.96797	2.230000	0.72887	0.528000	0.53228	AAT	.	.		0.393	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		G	57743863	A	G	57743863	3	3	216	1	0	0	0	0	1	0	0	0	3568	101	4	2	1851	2	CLTC	17	57743863	Missense_Mutation	SNP	A	TCGA-DD-AAEB-01A-11D-A40R-10		57743863	23451347	99	31187										
SETBP1	26040	hgsc.bcm.edu	37	chr18	42643462	42643463	+	In_Frame_Ins	INS	-	-	CCC													0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	cgccaccgccgccgcccctgINSccgccaccgccgccaccacc							TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr18:42643462_42643463insCCC	ENST00000282030.5	+	6	4886_4887	c.4590_4591insCCC	c.(4591-4593)ccg>CCCccg	p.1531_1531P>PP		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1531	3 X 8 AA tandem repeats of P-P-L-P-P-P-P- P.					nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		cgccgcccctgccgccaccgcc	0.752									Schinzel-Giedion syndrome																												p.L1530delinsLP		Atlas-INDEL	.											.	SETBP1	577	.	0			c.4590_4591insCCC						.																																			SO:0001652	inframe_insertion	26040	exon6	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	.	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	Exception_encountered	chr18.hg19:g.42643462_42643463insCCC	ENSP00000282030:p.Pro1537dup	116.0	0.0		156.0	11.0	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	In_Frame_Ins	INS	ENST00000282030.5	hg19	CCDS11923.2																																																																																			.	.		0.752	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		CCC	42643463	-	CCC	42643462	7	5	216	1	0	1	1	0	0	0	0	0	14144	1306	46	0	4801	0	SETBP1	18	42643462	In_Frame_Ins	INS	-	TCGA-DD-AAEB-01A-11D-A40R-10		42643462	35433786	100	31188										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43490657	43490657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	tttctttcaacaaattgataTgagcaggactttgaaaaaac	6	6	2	3	rs200456950		TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr18:43490657T>C	ENST00000282041.5	-	23	4068	c.4034A>G	c.(4033-4035)cAt>cGt	p.H1345R	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1345					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CAAATTGATATGAGCAGGACT	0.428											OREG0024952	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H1345R		Atlas-SNP	.											.	EPG5	199	.	0			c.A4034G						.	T	ARG/HIS	0,3754		0,0,1877	80	77	78		4034	5.2	1	18		78	1,8227		0,1,4113	no	missense	EPG5	NM_020964.2	29	0,1,5990	CC,CT,TT		0.0122,0.0,0.0083	benign	1345/2580	43490657	1,11981	1877	4114	5991	SO:0001583	missense	57724	exon23			TTGATATGAGCAG	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.4034A>G	chr18.hg19:g.43490657T>C	ENSP00000282041:p.His1345Arg	93.0	0.0	916	95.0	34.0	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	T	20.4	3.986623	0.74589	0.0	1.22E-4	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.09911	2.93	5.22	5.22	0.72569	.	0.092864	0.40908	D	0.001000	T	0.19604	0.0471	L	0.59436	1.845	0.49582	D	0.9998	P;P	0.51933	0.949;0.949	P;P	0.51550	0.673;0.673	T	0.00458	-1.1727	10	0.62326	D	0.03	-16.202	11.4923	0.50387	0.1342:0.0:0.0:0.8658	.	1345;1345	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	R	1345;220	ENSP00000282041:H1345R	ENSP00000282041:H1345R	H	-	2	0	EPG5	41744655	1.000000	0.71417	0.996000	0.52242	0.958000	0.62258	5.907000	0.69908	1.977000	0.57605	0.533000	0.62120	CAT	.	T|0.999;C|0.001		0.428	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43490657	T	C	43490657	3	2	216	1	0	0	0	0	1	0	0	0	8258	1464	51	2	3793	2	KIAA1632	18	43490657	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10	847195	43490657	34586591	101	31189										
C19orf42	79086	hgsc.bcm.edu	37	chr19	16764845	16764845	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gaaagggcaggctggactcaCacaatcatgcagaacatcat	10	10	3	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr19:16764845C>T	ENST00000487416.2	-	4	259		c.e4+1		CTC-429P9.4_ENST00000593962.1_Splice_Site|SMIM7_ENST00000597711.1_Intron|SMIM7_ENST00000358726.6_Splice_Site|CTC-429P9.4_ENST00000600705.1_Intron|SMIM7_ENST00000397349.2_Splice_Site	NM_024104.3	NP_077009.2	Q9BQ49	SMIM7_HUMAN	small integral membrane protein 7							integral component of membrane (GO:0016021)											GCTGGACTCACACAATCATGC	0.478																																					.		Atlas-SNP	.											.	.	.	.	0			c.212+1G>A						.						91	93	92					19																	16764845		2029	4185	6214	SO:0001630	splice_region_variant	79086	exon5			GACTCACACAATC	AK025602	CCDS12348.2, CCDS74307.1	19p13.11	2012-10-26	2012-10-26	2012-10-26	ENSG00000214046	ENSG00000214046			28419	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 42"	C19orf42		12477932	Standard	NM_024104		Approved	MGC2747	uc002ner.3	Q9BQ49	OTTHUMG00000149895	ENST00000487416.2:c.212+1G>A	chr19.hg19:g.16764845C>T		57.0	0.0		56.0	22.0	NM_024104	A8MX44	Splice_Site	SNP	ENST00000487416.2	hg19	CCDS12348.2	.	.	.	.	.	.	.	.	.	.	C	19.71	3.878536	0.72294	.	.	ENSG00000214046	ENST00000487416;ENST00000358726	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0574	0.80816	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C19orf42	16625845	1.000000	0.71417	1.000000	0.80357	0.704000	0.40688	7.025000	0.76449	2.655000	0.90218	0.650000	0.86243	.	.	.		0.478	SMIM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313801.2	NM_024104	Intron	T	16764845	C	T	16764845	5	4	216	1	0	0	0	0	0	0	1	0	1927	492	17	3	22	3	C19orf42	19	16764845	Splice_Site	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10		16764845	42364138	102	31190										
MLL4	9757	hgsc.bcm.edu	37	chr19	36216413	36216413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	aagtctgctgtgacccattcCacccattctgcctggaggag	10	13	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr19:36216413C>T	ENST00000222270.7	+	12	3676	c.3676C>T	c.(3676-3678)Cac>Tac	p.H1226Y	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.H1226Y	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1226					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TGACCCATTCCACCCATTCTG	0.607																																					p.H1226Y		Atlas-SNP	.											.	MLL4	229	.	0			c.C3676T						.						199	215	210					19																	36216413		2097	4225	6322	SO:0001583	missense	8085	exon12			CCATTCCACCCAT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.3676C>T	chr19.hg19:g.36216413C>T	ENSP00000222270:p.His1226Tyr	26.0	0.0		27.0	11.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.764356	0.49574	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.99849	-7.15;-7.15	5.54	5.54	0.83059	Zinc finger, PHD-finger (1);Zinc finger, PHD-type (1);	0.000000	0.47455	D	0.000238	D	0.99809	0.9917	M	0.79926	2.475	0.80722	D	1	D	0.69078	0.997	D	0.75484	0.986	D	0.97234	0.9886	10	0.87932	D	0	.	18.4191	0.90582	0.0:1.0:0.0:0.0	.	1226	Q9UMN6	MLL4_HUMAN	Y	1226	ENSP00000222270:H1226Y;ENSP00000398837:H1226Y	ENSP00000222270:H1226Y	H	+	1	0	AD000671.1	40908253	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.178000	0.77657	2.884000	0.98904	0.655000	0.94253	CAC	.	.		0.607	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		T	36216413	C	T	36216413	3	4	216	1	0	0	0	0	1	0	0	0	9632	594	21	3	3722	3	MLL4	19	36216413	Missense_Mutation	SNP	C	TCGA-DD-AAEB-01A-11D-A40R-10	19451568	36216413	22912570	103	31191										
ZFP30	22835	hgsc.bcm.edu	37	chr19	38126047	38126047	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ccacattccttacagtcataGggcttttcaccagtatgaat	6	11	2	1	rs575517303		TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr19:38126047G>A	ENST00000351218.2	-	6	1952	c.1395C>T	c.(1393-1395)ccC>ccT	p.P465P	ZFP30_ENST00000589018.1_Intron|ZFP30_ENST00000392144.1_Silent_p.P465P|ZFP30_ENST00000514101.2_Silent_p.P465P	NM_014898.2	NP_055713.1	Q9Y2G7	ZFP30_HUMAN	ZFP30 zinc finger protein	465					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	21			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TACAGTCATAGGGCTTTTCAC	0.368													G|||	1	0.000199681	0	0	5008	,	,		20515	0		0	False		,,,				2504	0.001				p.P465P		Atlas-SNP	.											.	ZFP30	68	.	0			c.C1395T						.						86	81	83					19																	38126047		2203	4300	6503	SO:0001819	synonymous_variant	22835	exon6			GTCATAGGGCTTT	AB023178	CCDS33005.1	19q13.13	2013-01-08	2012-11-27		ENSG00000120784	ENSG00000120784		"Zinc fingers, C2H2-type", "-"	29555	protein-coding gene	gene with protein product			"zinc finger protein 30 homolog (mouse)"			10231032	Standard	NM_014898		Approved	ZNF745, KIAA0961	uc002ogx.1	Q9Y2G7	OTTHUMG00000048177	ENST00000351218.2:c.1395C>T	chr19.hg19:g.38126047G>A		107.0	0.0		117.0	56.0	NM_014898	Q58EY8	Silent	SNP	ENST00000351218.2	hg19	CCDS33005.1																																																																																			.	.		0.368	ZFP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109601.2	NM_014898		A	38126047	G	A	38126047	2	1	216	1	0	0	0	0	0	0	0	1	17659	987	35	3		3	ZFP30	19	38126047	Silent	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	1909634	38126047	21002936	104	31192										
ZNF83	55769	hgsc.bcm.edu	37	chr19	53116801	53116801	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttgtaaggtttctctccagtGtggattctccagtgatttac	9	8	2	1			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr19:53116801G>A	ENST00000597597.1	-	2	3270	c.1017C>T	c.(1015-1017)caC>caT	p.H339H	ZNF83_ENST00000541777.2_Silent_p.H339H|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000301096.3_Silent_p.H339H|ZNF83_ENST00000545872.1_Silent_p.H339H|ZNF83_ENST00000391789.4_Silent_p.H311H|ZNF83_ENST00000536937.1_Silent_p.H339H|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000544146.1_Silent_p.H339H			P51522	ZNF83_HUMAN	zinc finger protein 83	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		TCTCTCCAGTGTGGATTCTCC	0.418																																					p.H339H		Atlas-SNP	.											ZNF83,NS,carcinoma,0,2	ZNF83	73	.	0			c.C1017T						.						118	120	120					19																	53116801		2203	4300	6503	SO:0001819	synonymous_variant	55769	exon3			TCCAGTGTGGATT	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"Zinc fingers, C2H2-type"	13158	protein-coding gene	gene with protein product		194558	"zinc finger protein 83 (HPF1)", "zinc finger protein 816B"	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.1017C>T	chr19.hg19:g.53116801G>A		110.0	2.0		136.0	8.0	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Silent	SNP	ENST00000597597.1	hg19	CCDS12854.1																																																																																			.	.		0.418	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300		A	53116801	G	A	53116801	2	1	216	1	0	0	0	0	0	0	0	1	18198	1368	48	3		3	ZNF83	19	53116801	Silent	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	14990754	53116801	6012182	105	31193										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54313913	54313913	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gatgagcaaagatagctcagGgagcagcttcttccgaatta	11	8	2	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr19:54313913G>A	ENST00000324134.6	-	3	1168	c.1000C>T	c.(1000-1002)Cct>Tct	p.P334S	NLRP12_ENST00000391775.3_Missense_Mutation_p.P334S|NLRP12_ENST00000535162.1_Missense_Mutation_p.P334S|NLRP12_ENST00000345770.5_Missense_Mutation_p.P334S|NLRP12_ENST00000391772.1_Missense_Mutation_p.P334S|NLRP12_ENST00000354278.3_Missense_Mutation_p.P334S|NLRP12_ENST00000351894.4_Missense_Mutation_p.P334S|NLRP12_ENST00000391773.1_Missense_Mutation_p.P334S	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	334	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		GATAGCTCAGGGAGCAGCTTC	0.582																																					p.S334S		Atlas-SNP	.											.	NLRP12	236	.	0			c.T1000T						.						64	68	66					19																	54313913		2203	4300	6503	SO:0001583	missense	91662	exon3			GCTCAGGGAGCAG	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.1000C>T	chr19.hg19:g.54313913G>A	ENSP00000319377:p.Pro334Ser	44.0	0.0		78.0	29.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	hg19	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.036571	0.54896	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4;-1.4;-1.4;-1.4	4.64	4.64	0.57946	NACHT nucleoside triphosphatase (1);	0.000000	0.42682	D	0.000662	D	0.89012	0.6594	M	0.79123	2.44	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.998	D;D;D;D	0.71656	0.947;0.947;0.947;0.974	D	0.90599	0.4543	10	0.87932	D	0	.	15.4217	0.75018	0.0:0.0:1.0:0.0	.	334;334;334;334	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	S	334	ENSP00000319377:P334S;ENSP00000438030:P334S;ENSP00000340473:P334S;ENSP00000346231:P334S;ENSP00000375655:P334S;ENSP00000375653:P334S;ENSP00000375652:P334S	ENSP00000319377:P334S	P	-	1	0	NLRP12	59005725	1.000000	0.71417	0.945000	0.38365	0.405000	0.30901	3.118000	0.50414	2.315000	0.78130	0.485000	0.47835	CCT	.	.		0.582	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		A	54313913	G	A	54313913	3	1	216	1	0	0	0	0	1	0	0	0	10483	1232	43	3	2313	3	NLRP12	19	54313913	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	1197112	54313913	4815070	106	31194										
SAMHD1	25939	hgsc.bcm.edu	37	chr20	35563535	35563535	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ttgaaattgaggtgtatcaaTgattcggacgaggagagggt	15	3	1	4			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr20:35563535T>A	ENST00000262878.4	-	4	605	c.406A>T	c.(406-408)Att>Ttt	p.I136F	SAMHD1_ENST00000373694.5_5'UTR	NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	136					dATP catabolic process (GO:0046061)|defense response to virus (GO:0051607)|dGTP catabolic process (GO:0006203)|immune response (GO:0006955)|innate immune response (GO:0045087)|protein homotetramerization (GO:0051289)|regulation of innate immune response (GO:0045088)	intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dGTP binding (GO:0032567)|dGTPase activity (GO:0008832)|nucleic acid binding (GO:0003676)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	20		Myeloproliferative disorder(115;0.00878)				GGTGTATCAATGATTCGGACG	0.388																																					p.I136F		Atlas-SNP	.											.	SAMHD1	62	.	0			c.A406T						.						139	130	133					20																	35563535		2203	4300	6503	SO:0001583	missense	25939	exon4			TATCAATGATTCG	AF228421	CCDS13288.1	20q11.23	2014-09-17			ENSG00000101347	ENSG00000101347		"Sterile alpha motif (SAM) domain containing"	15925	protein-coding gene	gene with protein product	"HD domain containing 1", "monocyte protein 5", "Aicardi-Goutieres syndrome 5"	606754				11064105, 11230166	Standard	NM_015474		Approved	SBBI88, Mg11, HDDC1, MOP-5, AGS5	uc002xgh.2	Q9Y3Z3	OTTHUMG00000032402	ENST00000262878.4:c.406A>T	chr20.hg19:g.35563535T>A	ENSP00000262878:p.Ile136Phe	147.0	0.0		178.0	77.0	NM_015474	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Missense_Mutation	SNP	ENST00000262878.4	hg19	CCDS13288.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.039053	0.93630	.	.	ENSG00000101347	ENST00000262878	D	0.97620	-4.46	6.05	6.05	0.98169	HD domain (1);	0.000000	0.85682	D	0.000000	D	0.98689	0.9560	M	0.94021	3.485	0.80722	D	1	P	0.49862	0.929	P	0.59595	0.86	D	0.99402	1.0928	10	0.72032	D	0.01	-22.8833	16.5932	0.84781	0.0:0.0:0.0:1.0	.	136	Q9Y3Z3	SAMH1_HUMAN	F	136	ENSP00000262878:I136F	ENSP00000262878:I136F	I	-	1	0	SAMHD1	34996949	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	7.991000	0.88244	2.320000	0.78422	0.528000	0.53228	ATT	.	.		0.388	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474		A	35563535	T	A	35563535	3	1	216	1	0	0	0	0	1	0	0	0	13843	1464	51	4	1526	4	SAMHD1	20	35563535	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10		35563535	27461985	107	31195										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32638770	32638770	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ctgtcctcccgccagatgtcTgcagatttggagcgtttctt	10	12	2	2			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr21:32638770T>A	ENST00000286827.3	-	5	990	c.519A>T	c.(517-519)gcA>gcT	p.A173A	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Silent_p.A173A	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	173					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						GCCAGATGTCTGCAGATTTGG	0.502																																					p.A173A		Atlas-SNP	.											.	TIAM1	522	.	0			c.A519T						.						101	99	100					21																	32638770		2203	4300	6503	SO:0001819	synonymous_variant	7074	exon5			GATGTCTGCAGAT		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.519A>T	chr21.hg19:g.32638770T>A		64.0	0.0		65.0	26.0	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	hg19	CCDS13609.1																																																																																			.	.		0.502	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		A	32638770	T	A	32638770	2	1	216	1	0	0	0	0	0	0	0	1	15905	1567	55	4		4	TIAM1	21	32638770	Silent	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10		32638770	15491125	108	31196										
ZMAT5	55954	hgsc.bcm.edu	37	chr22	30144469	30144469	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	gcagcccgttcaggtgcttcTtgcggttgtggaggttgtcc	15	10	2	0			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr22:30144469T>C	ENST00000344318.3	-	2	181	c.65A>G	c.(64-66)aAg>aGg	p.K22R	ZMAT5_ENST00000397781.3_Missense_Mutation_p.K22R	NM_001003692.1	NP_001003692.1	Q9UDW3	ZMAT5_HUMAN	zinc finger, matrin-type 5	22					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(5;0.000597)|all cancers(5;0.0534)|Epithelial(10;0.0574)			CAGGTGCTTCTTGCGGTTGTG	0.622																																					p.K22R		Atlas-SNP	.											.	ZMAT5	12	.	0			c.A65G						.						146	121	129					22																	30144469		2203	4300	6503	SO:0001583	missense	55954	exon2			TGCTTCTTGCGGT		CCDS13868.1	22q12.2	2013-09-20	2010-09-15		ENSG00000100319	ENSG00000100319		"Zinc fingers, matrin-type"	28046	protein-coding gene	gene with protein product	"U11/U12 snRNP 20K"					9847074	Standard	NM_019103		Approved	SNRNP20	uc003agn.3	Q9UDW3	OTTHUMG00000151292	ENST00000344318.3:c.65A>G	chr22.hg19:g.30144469T>C	ENSP00000344241:p.Lys22Arg	85.0	0.0		104.0	41.0	NM_001003692	A8K9F6	Missense_Mutation	SNP	ENST00000344318.3	hg19	CCDS13868.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.645414	0.87859	.	.	ENSG00000100319	ENST00000344318;ENST00000397781	.	.	.	5.36	5.36	0.76844	Zinc finger, U1-C type (1);	0.000000	0.85682	D	0.000000	T	0.70413	0.3221	L	0.53561	1.675	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70901	-0.4746	9	0.46703	T	0.11	-41.5185	13.0873	0.59149	0.0:0.0:0.0:1.0	.	22	Q9UDW3	ZMAT5_HUMAN	R	22	.	ENSP00000344241:K22R	K	-	2	0	ZMAT5	28474469	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.574000	0.82434	2.036000	0.60181	0.418000	0.28097	AAG	.	.		0.622	ZMAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322114.1	NM_019103		C	30144469	T	C	30144469	3	2	216	1	0	0	0	0	1	0	0	0	17710	1609	56	2	467	2	ZMAT5	22	30144469	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10		30144469	21160097	109	31197										
ARFGAP3	26286	hgsc.bcm.edu	37	chr22	43227599	43227599	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ccacaggccttgatgttaaaGaagatggttctgctattgct	10	8	1	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chr22:43227599G>C	ENST00000263245.5	-	6	740	c.521C>G	c.(520-522)tCt>tGt	p.S174C	ARFGAP3_ENST00000437119.2_Missense_Mutation_p.S130C|ARFGAP3_ENST00000429508.2_Missense_Mutation_p.S102C	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	174					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						TGATGTTAAAGAAGATGGTTC	0.413																																					p.S174C	GBM(58;544 1030 21460 27159 48838)	Atlas-SNP	.											.	ARFGAP3	48	.	0			c.C521G						.						142	129	133					22																	43227599		2203	4300	6503	SO:0001583	missense	26286	exon6			GTTAAAGAAGATG	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"ADP-ribosylation factor GTPase activating proteins"	661	protein-coding gene	gene with protein product		612439	"ADP-ribosylation factor GTPase activating protein 1"	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.521C>G	chr22.hg19:g.43227599G>C	ENSP00000263245:p.Ser174Cys	91.0	0.0		85.0	40.0	NM_014570	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Missense_Mutation	SNP	ENST00000263245.5	hg19	CCDS14042.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.15|19.15	3.770901|3.770901	0.69992|0.69992	.|.	.|.	ENSG00000242247|ENSG00000242247	ENST00000453516|ENST00000263245;ENST00000429508;ENST00000437119;ENST00000454099	.|T;T;T;T	.|0.48201	.|3.4;3.3;3.37;0.82	4.77|4.77	3.75|3.75	0.43078|0.43078	.|.	.|0.944481	.|0.08868	.|N	.|0.881991	T|T	0.62950|0.62950	0.2470|0.2470	L|L	0.56769|0.56769	1.78|1.78	0.09310|0.09310	N|N	1|1	.|D;D;D	.|0.76494	.|0.999;0.965;0.996	.|D;P;P	.|0.65987	.|0.94;0.571;0.789	T|T	0.47898|0.47898	-0.9081|-0.9081	5|10	.|0.66056	.|D	.|0.02	0.635|0.635	9.7865|9.7865	0.40679|0.40679	0.0983:0.0:0.9017:0.0|0.0983:0.0:0.9017:0.0	.|.	.|102;130;174	.|C9JZR4;E9PB03;Q9NP61	.|.;.;ARFG3_HUMAN	L|C	20|174;102;130;102	.|ENSP00000263245:S174C;ENSP00000393959:S102C;ENSP00000388791:S130C;ENSP00000403520:S102C	.|ENSP00000263245:S174C	F|S	-|-	3|2	2|0	ARFGAP3|ARFGAP3	41557543|41557543	0.002000|0.002000	0.14202|0.14202	0.001000|0.001000	0.08648|0.08648	0.585000|0.585000	0.36419|0.36419	1.236000|1.236000	0.32683|0.32683	1.000000|1.000000	0.39049|0.39049	0.561000|0.561000	0.74099|0.74099	TTC|TCT	.	.		0.413	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570		C	43227599	G	C	43227599	3	2	216	1	0	0	0	0	1	0	0	0	851	942	33	4	1073	4	ARFGAP3	22	43227599	Missense_Mutation	SNP	G	TCGA-DD-AAEB-01A-11D-A40R-10	13083130	43227599	8076967	110	31198										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12735950	12735950	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.055045871559633	6	1	1.04550438596491	2.35238486842105	0.672109962406015	1	1	0	ggagatggagcctgaaactaTggagactaagtcggtcactg	14	7	1	3			TCGA-DD-AAEB-01A-11D-A40R-10	TCGA-DD-AAEB-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ba6d6e9d-643f-400c-b52e-e08fb1d79709	a6b0ad70-8f87-4734-8dc2-6b9203d461d0	g.chrX:12735950T>C	ENST00000380682.1	+	16	3511	c.3005T>C	c.(3004-3006)aTg>aCg	p.M1002T		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	1002					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						CCTGAAACTATGGAGACTAAG	0.537																																					p.M1002T		Atlas-SNP	.											.	FRMPD4	214	.	0			c.T3005C						.						88	79	82					X																	12735950		2203	4300	6503	SO:0001583	missense	9758	exon16			AAACTATGGAGAC	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.3005T>C	chrX.hg19:g.12735950T>C	ENSP00000370057:p.Met1002Thr	126.0	0.0		155.0	126.0	NM_014728	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	hg19	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	T	13.31	2.197762	0.38806	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.08102	3.13	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.13372	0.0324	M	0.72118	2.19	0.42803	D	0.993935	P;P	0.44946	0.846;0.846	B;B	0.39339	0.297;0.297	T	0.01706	-1.1291	10	0.72032	D	0.01	-7.6628	14.6319	0.68663	0.0:0.0:0.0:1.0	.	994;1002	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	T	1002;993;991	ENSP00000370057:M1002T	ENSP00000304583:M991T	M	+	2	0	FRMPD4	12645871	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.607000	0.82883	1.835000	0.53391	0.417000	0.27973	ATG	.	.		0.537	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		C	12735950	T	C	12735950	3	2	216	1	0	0	0	0	1	0	0	0	6067	1464	51	2	3067	2	FRMPD4	23	12735950	Missense_Mutation	SNP	T	TCGA-DD-AAEB-01A-11D-A40R-10		12735950	142534610	111	31199										
MMACHC	25974	hgsc.bcm.edu	37	chr1	45974808	45974808	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tccctttaccacacccgcccCcaagaagcctgggaatccca	6	19	0	1	rs201601241		TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:45974808C>T	ENST00000401061.4	+	4	1050	c.770C>T	c.(769-771)cCc>cTc	p.P257L		NM_015506.2	NP_056321.2	Q9Y4U1	MMAC_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblC type, with homocystinuria	257					cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8	Acute lymphoblastic leukemia(166;0.155)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACACCCGCCCCCAAGAAGCCT	0.627																																					p.P257L		Atlas-SNP	.											.	MMACHC	22	.	0			c.C770T						.	C	LEU/PRO	0,3692		0,0,1846	89	100	96		770	2.5	0	1		96	1,8173		0,1,4086	yes	missense	MMACHC	NM_015506.2	98	0,1,5932	TT,TC,CC		0.0122,0.0,0.0084	benign	257/283	45974808	1,11865	1846	4087	5933	SO:0001583	missense	25974	exon4			CCGCCCCCAAGAA		CCDS41324.1	1p34.1	2011-05-12			ENSG00000132763	ENSG00000132763			24525	protein-coding gene	gene with protein product		609831				16311595	Standard	NM_015506		Approved	DKFZP564I122, cblC	uc009vxv.3	Q9Y4U1	OTTHUMG00000007742	ENST00000401061.4:c.770C>T	chr1.hg19:g.45974808C>T	ENSP00000383840:p.Pro257Leu	80.0	0.0		87.0	45.0	NM_015506	Q5T157|Q9BRQ7	Missense_Mutation	SNP	ENST00000401061.4	hg19	CCDS41324.1	.	.	.	.	.	.	.	.	.	.	C	9.169	1.020625	0.19433	0.0	1.22E-4	ENSG00000132763	ENST00000401061	D	0.94793	-3.52	3.43	2.48	0.30137	.	0.891026	0.09188	N	0.836537	D	0.90086	0.6903	L	0.29908	0.895	0.09310	N	1	B	0.22414	0.069	B	0.23419	0.046	T	0.82186	-0.0582	10	0.62326	D	0.03	-0.5441	8.8392	0.35131	0.0:0.7705:0.2295:0.0	.	257	Q9Y4U1	MMAC_HUMAN	L	257	ENSP00000383840:P257L	ENSP00000383840:P257L	P	+	2	0	MMACHC	45747395	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.560000	0.23500	0.753000	0.32945	0.563000	0.77884	CCC	.	.		0.627	MMACHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020864.2	NM_015506		T	45974808	C	T	45974808	3	4	217	1	0	0	0	0	1	0	0	0	9650	623	22	3	784	3	MMACHC	1	45974808	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10		45974808	203275813	1	31200										
TTC24	164118	hgsc.bcm.edu	37	chr1	156551636	156551636	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ggagaagcctgggcaaaaatGggagcctgctaccaggctct	14	10	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:156551636G>A	ENST00000368237.3	+	1	480	c.480G>A	c.(478-480)atG>atA	p.M160I	TTC24_ENST00000368236.3_Missense_Mutation_p.M160I			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	160										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGCAAAAATGGGAGCCTGCT	0.642																																					p.M160I		Atlas-SNP	.											.	TTC24	46	.	0			c.G480A						.						10	12	11					1																	156551636		692	1589	2281	SO:0001583	missense	164118	exon2			AAAAATGGGAGCC		CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"Tetratricopeptide (TTC) repeat domain containing"	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.480G>A	chr1.hg19:g.156551636G>A	ENSP00000357220:p.Met160Ile	94.0	0.0		145.0	93.0	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	hg19	CCDS53379.1	.	.	.	.	.	.	.	.	.	.	G	3.502	-0.101525	0.06967	.	.	ENSG00000187862	ENST00000368236;ENST00000368237	T;T	0.61392	0.11;0.11	4.83	3.9	0.45041	.	0.000000	0.52532	D	0.000063	T	0.18676	0.0448	N	0.08118	0	0.26334	N	0.977478	.	.	.	.	.	.	T	0.14337	-1.0476	8	0.25106	T	0.35	-11.7295	11.0461	0.47859	0.093:0.0:0.907:0.0	.	.	.	.	I	160	ENSP00000357219:M160I;ENSP00000357220:M160I	ENSP00000357219:M160I	M	+	3	0	TTC24	154818260	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.548000	0.60718	1.230000	0.43646	0.462000	0.41574	ATG	.	.		0.642	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		A	156551636	G	A	156551636	3	1	217	1	0	0	0	0	1	0	0	0	16707	1348	47	3	482	3	TTC24	1	156551636	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	110576828	156551636	92698985	2	31201										
ATP1A2	477	hgsc.bcm.edu	37	chr1	160094210	160094210	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	cctccggatcatctcttctcAtggctgtaaggtgaggaggt	12	10	3	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:160094210A>G	ENST00000361216.3	+	6	709	c.620A>G	c.(619-621)cAt>cGt	p.H207R	ATP1A2_ENST00000392233.3_Missense_Mutation_p.H207R	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	207					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			ATCTCTTCTCATGGCTGTAAG	0.562																																					p.H207R		Atlas-SNP	.											.	ATP1A2	167	.	0			c.A620G						.						87	68	75					1																	160094210		2203	4300	6503	SO:0001583	missense	477	exon6			CTTCTCATGGCTG	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.620A>G	chr1.hg19:g.160094210A>G	ENSP00000354490:p.His207Arg	79.0	0.0		124.0	37.0	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	hg19	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.039126	0.35989	.	.	ENSG00000018625	ENST00000538123;ENST00000361216;ENST00000392233	D;D	0.90324	-2.65;-2.65	5.27	5.27	0.74061	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.201617	0.51477	D	0.000097	T	0.72195	0.3430	N	0.16862	0.45	0.40150	D	0.976937	B;B	0.14012	0.0;0.009	B;B	0.13407	0.003;0.009	T	0.68903	-0.5286	10	0.13470	T	0.59	.	14.1697	0.65500	1.0:0.0:0.0:0.0	.	52;207	B4DHD7;P50993	.;AT1A2_HUMAN	R	52;207;207	ENSP00000354490:H207R;ENSP00000376066:H207R	ENSP00000354490:H207R	H	+	2	0	ATP1A2	158360834	0.996000	0.38824	0.981000	0.43875	0.986000	0.74619	5.342000	0.65970	1.997000	0.58415	0.533000	0.62120	CAT	.	.		0.562	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		G	160094210	A	G	160094210	3	3	217	1	0	0	0	0	1	0	0	0	1129	217	8	2	642	2	ATP1A2	1	160094210	Missense_Mutation	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	3542574	160094210	89156411	3	31202										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181693620	181693620	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ccccagacacgctactgaatGtgttcttggctatcgctgtg	10	12	1	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:181693620G>T	ENST00000367573.2	+	17	2089	c.2089G>T	c.(2089-2091)Gtg>Ttg	p.V697L	CACNA1E_ENST00000526775.1_Missense_Mutation_p.V697L|CACNA1E_ENST00000367567.4_Missense_Mutation_p.V304L|CACNA1E_ENST00000360108.3_Missense_Mutation_p.V697L|CACNA1E_ENST00000358338.5_Missense_Mutation_p.V648L|CACNA1E_ENST00000367570.1_Missense_Mutation_p.V697L|CACNA1E_ENST00000357570.5_Missense_Mutation_p.V648L	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	697					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GCTACTGAATGTGTTCTTGGC	0.473																																					p.V697L		Atlas-SNP	.											.	CACNA1E	778	.	0			c.G2089T						.						142	131	134					1																	181693620		1980	4164	6144	SO:0001583	missense	777	exon17			CTGAATGTGTTCT	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2089G>T	chr1.hg19:g.181693620G>T	ENSP00000356545:p.Val697Leu	50.0	0.0		99.0	51.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.844899	0.51164	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.97041	-4.22;-4.22;-4.22;-4.22;-4.22;-4.22;-4.22	4.86	3.95	0.45737	.	0.241030	0.41823	D	0.000805	D	0.92922	0.7748	N	0.21583	0.68	0.51012	D	0.999904	B;B	0.20261	0.043;0.043	B;B	0.20384	0.029;0.029	D	0.89313	0.3634	10	0.35671	T	0.21	.	12.7227	0.57152	0.0809:0.0:0.9191:0.0	.	697;697	Q15878-2;Q15878-3	.;.	L	697;697;648;648;304;697;697	ENSP00000356542:V697L;ENSP00000434814:V697L;ENSP00000350183:V648L;ENSP00000351101:V648L;ENSP00000356539:V304L;ENSP00000353222:V697L;ENSP00000356545:V697L	ENSP00000350183:V648L	V	+	1	0	CACNA1E	179960243	1.000000	0.71417	0.995000	0.50966	0.802000	0.45316	9.675000	0.98638	1.162000	0.42619	0.462000	0.41574	GTG	.	.		0.473	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181693620	G	T	181693620	3	4	217	1	0	0	0	0	1	0	0	0	2544	1377	48	3	2155	3	CACNA1E	1	181693620	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	21599410	181693620	67557001	4	31203										
USH2A	7399	hgsc.bcm.edu	37	chr1	216011440	216011440	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	caggcatatattgtgcagacTtcaacctgcaaacattagtt	7	9	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:216011440T>C	ENST00000307340.3	-	47	9650	c.9264A>G	c.(9262-9264)gaA>gaG	p.E3088E	USH2A_ENST00000366943.2_Silent_p.E3088E	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3088	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> K (in dbSNP:rs56056328). {ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTGTGCAGACTTCAACCTGCA	0.383										HNSCC(13;0.011)																											p.E3088E		Atlas-SNP	.											.	USH2A	1168	.	0			c.A9264G						.						179	165	170					1																	216011440		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon47			GCAGACTTCAACC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9264A>G	chr1.hg19:g.216011440T>C		138.0	0.0		211.0	63.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.383	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	216011440	T	C	216011440	2	2	217	1	0	0	0	0	0	0	0	1	17051	1606	56	2		2	USH2A	1	216011440	Silent	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10	34317820	216011440	33239181	5	31204										
GPR137B	7107	hgsc.bcm.edu	37	chr1	236306038	236306038	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gctgaccccggccgtgccccCctacgtgaagcttggcctca	11	18	1	2	rs199613305		TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:236306038C>A	ENST00000366592.3	+	1	207	c.116C>A	c.(115-117)cCc>cAc	p.P39H	GPR137B_ENST00000366591.4_Missense_Mutation_p.P39H	NM_003272.3	NP_003263.1	O60478	G137B_HUMAN	G protein-coupled receptor 137B	39						integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			GCCGTGCCCCCCTACGTGAAG	0.711																																					p.P39H		Atlas-SNP	.											.	GPR137B	57	.	0			c.C116A						.						61	44	50					1																	236306038		2203	4300	6503	SO:0001583	missense	7107	exon1			TGCCCCCCTACGT	AF027826	CCDS1609.1	1q42-q43	2012-08-10	2006-01-26	2006-01-26	ENSG00000077585	ENSG00000077585			11862	protein-coding gene	gene with protein product		604658	"transmembrane 7 superfamily member 1 (upregulated in kidney)"	TM7SF1		9521871	Standard	NM_003272		Approved		uc001hxq.3	O60478	OTTHUMG00000037994	ENST00000366592.3:c.116C>A	chr1.hg19:g.236306038C>A	ENSP00000355551:p.Pro39His	54.0	0.0		100.0	60.0	NM_003272	Q53EK7|Q5TAE6|Q6FHI3	Missense_Mutation	SNP	ENST00000366592.3	hg19	CCDS1609.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.086274	0.76642	.	.	ENSG00000077585	ENST00000366592;ENST00000366591;ENST00000391852	T;T	0.14266	2.52;2.52	4.8	2.89	0.33648	.	0.053259	0.85682	D	0.000000	T	0.32071	0.0817	M	0.77103	2.36	0.53005	D	0.999969	D	0.69078	0.997	D	0.63192	0.912	T	0.02477	-1.1153	10	0.56958	D	0.05	-14.0193	10.022	0.42048	0.0:0.7855:0.1385:0.0761	.	39	O60478	G137B_HUMAN	H	39;39;38	ENSP00000355551:P39H;ENSP00000355550:P39H	ENSP00000355550:P39H	P	+	2	0	GPR137B	234372661	1.000000	0.71417	0.967000	0.41034	0.893000	0.52053	5.645000	0.67909	0.437000	0.26423	-0.510000	0.04470	CCC	.	C|0.999;T|0.001		0.711	GPR137B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092761.1	NM_003272		A	236306038	C	A	236306038	3	1	217	1	0	0	0	0	1	0	0	0	6654	623	22	3	118	3	GPR137B	1	236306038	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	20294598	236306038	12944583	6	31205										
PXDN	7837	hgsc.bcm.edu	37	chr2	1667507	1667507	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gttcccgatgacaggaccagGtgccgccggtccacggagag	15	13	0	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr2:1667507G>T	ENST00000252804.4	-	12	1487	c.1437C>A	c.(1435-1437)caC>caA	p.H479Q	PXDN_ENST00000483018.1_5'Flank	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	479	Ig-like C2-type 3.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		ACAGGACCAGGTGCCGCCGGT	0.602																																					p.H479Q		Atlas-SNP	.											.	PXDN	255	.	0			c.C1437A						.						59	67	65					2																	1667507		2037	4177	6214	SO:0001583	missense	7837	exon12			GACCAGGTGCCGC	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1437C>A	chr2.hg19:g.1667507G>T	ENSP00000252804:p.His479Gln	23.0	0.0		52.0	19.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	hg19	CCDS46221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.34|17.34	3.364925|3.364925	0.61513|0.61513	.|.	.|.	ENSG00000130508|ENSG00000130508	ENST00000252804|ENST00000433670	T|.	0.67698|.	-0.28|.	5.79|5.79	1.52|1.52	0.23074|0.23074	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.49338|0.49338	0.1551|0.1551	L|L	0.31157|0.31157	0.91|0.91	0.45580|0.45580	D|D	0.998529|0.998529	D;D|.	0.76494|.	0.998;0.999|.	D;D|.	0.77557|.	0.935;0.99|.	T|T	0.30966|0.30966	-0.9960|-0.9960	10|5	0.27785|.	T|.	0.31|.	-66.3747|-66.3747	11.3772|11.3772	0.49735|0.49735	0.3991:0.0:0.6009:0.0|0.3991:0.0:0.6009:0.0	.|.	479;479|.	Q92626-2;Q92626|.	.;PXDN_HUMAN|.	Q|N	479|475	ENSP00000252804:H479Q|.	ENSP00000252804:H479Q|.	H|T	-|-	3|2	2|0	PXDN|PXDN	1646514|1646514	0.946000|0.946000	0.32159|0.32159	1.000000|1.000000	0.80357|0.80357	0.930000|0.930000	0.56654|0.56654	0.119000|0.119000	0.15626|0.15626	0.387000|0.387000	0.25024|0.25024	-0.137000|-0.137000	0.14449|0.14449	CAC|ACC	.	.		0.602	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1667507	G	T	1667507	3	4	217	1	0	0	0	0	1	0	0	0	12862	1252	44	3	3050	3	PXDN	2	1667507	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10		1667507	241531866	7	31206										
MFSD9	84804	hgsc.bcm.edu	37	chr2	103340215	103340215	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ctgtgagataaaacccatccTctaattcagtgagatagcca	7	10	2	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr2:103340215T>C	ENST00000258436.5	-	5	624	c.581A>G	c.(580-582)gAg>gGg	p.E194G		NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	194					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						AAACCCATCCTCTAATTCAGT	0.473																																					p.E194G		Atlas-SNP	.											.	MFSD9	56	.	0			c.A581G						.						82	81	81					2																	103340215		2203	4300	6503	SO:0001583	missense	84804	exon5			CCATCCTCTAATT		CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.581A>G	chr2.hg19:g.103340215T>C	ENSP00000258436:p.Glu194Gly	99.0	0.0		101.0	41.0	NM_032718	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Missense_Mutation	SNP	ENST00000258436.5	hg19	CCDS2063.1	.	.	.	.	.	.	.	.	.	.	T	13.28	2.188942	0.38707	.	.	ENSG00000135953	ENST00000258436	T	0.59224	0.28	4.99	4.99	0.66335	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.118515	0.56097	D	0.000037	T	0.40247	0.1109	N	0.19112	0.55	0.41948	D	0.990644	B	0.27068	0.167	B	0.30716	0.119	T	0.30446	-0.9978	10	0.02654	T	1	-29.2361	14.664	0.68893	0.0:0.0:0.0:1.0	.	194	Q8NBP5	MFSD9_HUMAN	G	194	ENSP00000258436:E194G	ENSP00000258436:E194G	E	-	2	0	MFSD9	102706647	0.999000	0.42202	0.028000	0.17463	0.087000	0.18053	7.543000	0.82106	1.856000	0.53863	0.383000	0.25322	GAG	.	.		0.473	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718		C	103340215	T	C	103340215	3	2	217	1	0	0	0	0	1	0	0	0	9548	1551	54	2	851	2	MFSD9	2	103340215	Missense_Mutation	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10	101672708	103340215	139859158	8	31207										
GPR148	344561	hgsc.bcm.edu	37	chr2	131486815	131486815	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	agacaccctgcatgccccaaGcagccagcaacacttccttg	7	17	0	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr2:131486815G>A	ENST00000309926.4	+	1	173	c.91G>A	c.(91-93)Gca>Aca	p.A31T		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	31				CMPQAASNTSLGLGDLRVPSSMLYWLFLPSSLLAAA -> S S (in Ref. 2; AAP34196). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					CATGCCCCAAGCAGCCAGCAA	0.627																																					p.A31T		Atlas-SNP	.											.	GPR148	54	.	0			c.G91A						.						87	83	85					2																	131486815		2203	4300	6503	SO:0001583	missense	344561	exon1			CCCCAAGCAGCCA	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"GPCR / Class A : Orphans"	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.91G>A	chr2.hg19:g.131486815G>A	ENSP00000308908:p.Ala31Thr	91.0	0.0		114.0	34.0	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	hg19	CCDS2163.1	.	.	.	.	.	.	.	.	.	.	.	4.650	0.120777	0.08881	.	.	ENSG00000173302	ENST00000309926	T	0.08282	3.11	2.41	-2.11	0.07187	.	1.636260	0.04504	U	0.381712	T	0.03520	0.0101	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.39683	-0.9602	10	0.13108	T	0.6	-0.6633	2.5715	0.04796	0.2756:0.0:0.2989:0.4255	.	31	Q8TDV2	GP148_HUMAN	T	31	ENSP00000308908:A31T	ENSP00000308908:A31T	A	+	1	0	GPR148	131203285	0.011000	0.17503	0.000000	0.03702	0.574000	0.36063	0.601000	0.24119	-0.581000	0.05937	0.462000	0.41574	GCA	.	.		0.627	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092		A	131486815	G	A	131486815	3	1	217	1	0	0	0	0	1	0	0	0	6661	971	34	3	93	3	GPR148	2	131486815	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	28146600	131486815	111712558	9	31208										
FMNL2	114793	hgsc.bcm.edu	37	chr2	153476054	153476054	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ccagtaacaccacctatgccAccgccgccgccgccccctcc	6	24	0	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr2:153476054A>G	ENST00000288670.9	+	15	2026	c.1659A>G	c.(1657-1659)ccA>ccG	p.P553P	FMNL2_ENST00000475377.2_5'Flank	NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	553	Pro-rich.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						CACCTATGCCACCGCCGCCGC	0.582																																					p.P553P		Atlas-SNP	.											.	FMNL2	75	.	0			c.A1659G						.						14	13	14					2																	153476054		1424	3286	4710	SO:0001819	synonymous_variant	114793	exon15			TATGCCACCGCCG	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1659A>G	chr2.hg19:g.153476054A>G		20.0	0.0		50.0	10.0	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	hg19	CCDS46429.1																																																																																			.	.		0.582	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		G	153476054	A	G	153476054	2	3	217	1	0	0	0	0	0	0	0	1	5960	146	6	2		2	FMNL2	2	153476054	Silent	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	21989239	153476054	89723319	10	31209										
ALPP	250	hgsc.bcm.edu	37	chr2	233243546	233243546	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gcatgctgctgctgctgctgCtgctgggcctgaggctacag	15	12	0	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr2:233243546C>T	ENST00000392027.2	+	1	303	c.34C>T	c.(34-36)Ctg>Ttg	p.L12L	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	12					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		gctgctgctgctgctgGGCCT	0.642																																					p.L12L		Atlas-SNP	.											.	ALPP	53	.	0			c.C34T						.						48	53	51					2																	233243546		2203	4300	6503	SO:0001819	synonymous_variant	250	exon1			CTGCTGCTGCTGG	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"Regan isozyme"	171800	"alkaline phosphatase, placental (Regan isozyme)"			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.34C>T	chr2.hg19:g.233243546C>T		71.0	0.0		81.0	33.0	NM_001632	P05188|P06861|Q53S78|Q96DB7	Silent	SNP	ENST00000392027.2	hg19	CCDS2490.1																																																																																			.	.		0.642	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632		T	233243546	C	T	233243546	2	4	217	1	0	0	0	0	0	0	0	1	548	796	28	3		3	ALPP	2	233243546	Silent	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	79767492	233243546	9955827	11	31210										
ACOX2	8309	hgsc.bcm.edu	37	chr3	58510285	58510285	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gagagagagatctctgtggcGtggagccaggggacatctga	17	7	2	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr3:58510285G>A	ENST00000302819.5	-	11	1685	c.1394C>T	c.(1393-1395)aCg>aTg	p.T465M	ACOX2_ENST00000481527.1_5'Flank|ACOX2_ENST00000459701.2_Missense_Mutation_p.T451M	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	465					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		TCTCTGTGGCGTGGAGCCAGG	0.617																																					p.T465M		Atlas-SNP	.											.	ACOX2	53	.	0			c.C1394T						.						88	79	82					3																	58510285		2203	4300	6503	SO:0001583	missense	8309	exon11			TGTGGCGTGGAGC	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"trihydroxycoprostanoyl-CoA oxidase", "3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"	601641	"acyl-Coenzyme A oxidase 2, branched chain"			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.1394C>T	chr3.hg19:g.58510285G>A	ENSP00000307697:p.Thr465Met	72.0	0.0		79.0	26.0	NM_003500	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	hg19	CCDS33775.1	.	.	.	.	.	.	.	.	.	.	G	9.495	1.101656	0.20632	.	.	ENSG00000168306	ENST00000459701;ENST00000302819	T;T	0.15139	2.46;2.45	4.85	2.97	0.34412	Acyl-CoA dehydrogenase/oxidase C-terminal (1);	1.283950	0.05299	N	0.522624	T	0.09158	0.0226	N	0.08118	0	0.09310	N	1	P	0.42296	0.775	B	0.36666	0.23	T	0.24012	-1.0172	10	0.37606	T	0.19	-44.5598	6.526	0.22301	0.0957:0.0:0.7274:0.1769	.	465	Q99424	ACOX2_HUMAN	M	451;465	ENSP00000418562:T451M;ENSP00000307697:T465M	ENSP00000307697:T465M	T	-	2	0	ACOX2	58485325	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.264000	0.18497	0.519000	0.28406	0.484000	0.47621	ACG	.	.		0.617	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			A	58510285	G	A	58510285	3	1	217	1	0	0	0	0	1	0	0	0	159	1145	40	1	671	1	ACOX2	3	58510285	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10		58510285	139512145	12	31211										
PLCH1	23007	hgsc.bcm.edu	37	chr3	155311807	155311807	+	Frame_Shift_Del	DEL	C	C	-													0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	aggtacttgaggcctgtgatCcaggtgcgggcctcctcggg							TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr3:155311807delC	ENST00000340059.7	-	3	356	c.357delG	c.(355-357)tggfs	p.W119fs	PLCH1_ENST00000460012.1_Frame_Shift_Del_p.W101fs|PLCH1_ENST00000447496.2_Frame_Shift_Del_p.W119fs|PLCH1_ENST00000414191.1_Frame_Shift_Del_p.W101fs|PLCH1_ENST00000334686.6_Frame_Shift_Del_p.W101fs|PLCH1_ENST00000494598.1_Frame_Shift_Del_p.W119fs	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	119	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GGCCTGTGATCCAGGTGCGGG	0.542																																					p.I120fs		Atlas-INDEL	.											.	PLCH1	406	.	0			c.358delA						.						80	75	77					3																	155311807		2203	4300	6503	SO:0001589	frameshift_variant	23007	exon3			.	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.357delG	chr3.hg19:g.155311807delC	ENSP00000345988:p.Trp119fs	104.0	0.0		138.0	63.0	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Frame_Shift_Del	DEL	ENST00000340059.7	hg19	CCDS46939.1																																																																																			.	.		0.542	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		-	155311807	C	-	155311807	7	5	217	1	0	1	0	1	0	0	0	0	12046	856	30	0	4823	0	PLCH1	3	155311807	Frame_Shift_Del	DEL	C	TCGA-DD-AAED-01A-12D-A40R-10	96801522	155311807	42710623	13	31212										
VEPH1	79674	hgsc.bcm.edu	37	chr3	156983419	156983419	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ttgcttctctttaagttttcCttctatgagaggctggccat	8	9	2	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr3:156983419C>A	ENST00000362010.2	-	13	2468	c.2161G>T	c.(2161-2163)Gga>Tga	p.G721*	VEPH1_ENST00000392833.2_Nonsense_Mutation_p.G676*|RP11-550I24.2_ENST00000487238.1_RNA|RP11-550I24.2_ENST00000488040.1_RNA|VEPH1_ENST00000543418.1_Nonsense_Mutation_p.G676*|VEPH1_ENST00000392832.2_Nonsense_Mutation_p.G721*|RP11-550I24.2_ENST00000475102.1_RNA	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	721	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			TTAAGTTTTCCTTCTATGAGA	0.368																																					p.G721X		Atlas-SNP	.											.	VEPH1	129	.	0			c.G2161T						.						144	133	137					3																	156983419		2203	4300	6503	SO:0001587	stop_gained	79674	exon13			GTTTTCCTTCTAT	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"Pleckstrin homology (PH) domain containing"	25735	protein-coding gene	gene with protein product		609594	"ventricular zone expressed PH domain homolog 1 (zebrafish)"			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.2161G>T	chr3.hg19:g.156983419C>A	ENSP00000354919:p.Gly721*	93.0	0.0		134.0	53.0	NM_001167912	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Nonsense_Mutation	SNP	ENST00000362010.2	hg19	CCDS3179.1	.	.	.	.	.	.	.	.	.	.	C	42	9.820790	0.99272	.	.	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-11.2672	19.5283	0.95215	0.0:1.0:0.0:0.0	.	.	.	.	X	676;721;676;721	.	ENSP00000354919:G721X	G	-	1	0	VEPH1	158466113	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.672000	0.83956	2.596000	0.87737	0.655000	0.94253	GGA	.	.		0.368	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621		A	156983419	C	A	156983419	4	1	217	1	0	0	0	0	0	1	0	0	17169	690	24	3	348	3	VEPH1	3	156983419	Nonsense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	1671612	156983419	41039011	14	31213										
ATP11B	23200	hgsc.bcm.edu	37	chr3	182597383	182597383	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	aaactatttatggaagtttgCagaaattgttcagctgtatt	8	4	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr3:182597383C>T	ENST00000323116.5	+	20	2612	c.2352C>T	c.(2350-2352)tgC>tgT	p.C784C		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	784					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TGGAAGTTTGCAGAAATTGTT	0.388																																					p.C784C		Atlas-SNP	.											.	ATP11B	115	.	0			c.C2352T						.						111	110	111					3																	182597383		2203	4300	6503	SO:0001819	synonymous_variant	23200	exon20			AGTTTGCAGAAAT	AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"ATPases / P-type"	13553	protein-coding gene	gene with protein product		605869	"ATPase, Class VI, type 11B"			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.2352C>T	chr3.hg19:g.182597383C>T		281.0	1.0		360.0	147.0	NM_014616	Q96FN1|Q9UKK7	Silent	SNP	ENST00000323116.5	hg19	CCDS33896.1	.	.	.	.	.	.	.	.	.	.	C	4.653	0.121436	0.08881	.	.	ENSG00000058063	ENST00000498086	.	.	.	4.78	1.57	0.23409	.	.	.	.	.	T	0.55114	0.1900	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47736	-0.9094	4	.	.	.	.	7.7193	0.28723	0.0:0.5112:0.0:0.4888	.	.	.	.	V	585	.	.	A	+	2	0	ATP11B	184080077	1.000000	0.71417	1.000000	0.80357	0.467000	0.32768	0.736000	0.26130	0.533000	0.28675	0.585000	0.79938	GCA	.	.		0.388	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616		T	182597383	C	T	182597383	2	4	217	1	0	0	0	0	0	0	0	1	1120	718	25	3		3	ATP11B	3	182597383	Silent	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	25613964	182597383	15425047	15	31214										
KIT	3815	hgsc.bcm.edu	37	chr4	55602719	55602719	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	cattttcaactgtgtatacaCgtttgaaagtgacgtctggt	9	7	2	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr4:55602719C>T	ENST00000288135.5	+	18	2637	c.2540C>T	c.(2539-2541)aCg>aTg	p.T847M		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	847	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		T -> P (in PBT). {ECO:0000269|PubMed:9699740}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGTGTATACACGTTTGAAAGT	0.408		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.T847M		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	KIT,colon,carcinoma,0,1	KIT	7396	.	0			c.C2540T						.						172	168	169					4																	55602719		2203	4300	6503	SO:0001583	missense	3815	exon18	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	TATACACGTTTGA	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2540C>T	chr4.hg19:g.55602719C>T	ENSP00000288135:p.Thr847Met	119.0	0.0		65.0	46.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.724516	0.68959	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.90900	-2.75;-2.75	5.7	5.7	0.88788	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000012	D	0.95360	0.8494	M	0.73753	2.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.994	D	0.95354	0.8449	10	0.87932	D	0	.	19.8411	0.96685	0.0:1.0:0.0:0.0	.	843;847	P10721-2;P10721	.;KIT_HUMAN	M	847;843	ENSP00000288135:T847M;ENSP00000390987:T843M	ENSP00000288135:T847M	T	+	2	0	KIT	55297476	1.000000	0.71417	0.990000	0.47175	0.158000	0.22134	7.695000	0.84257	2.683000	0.91414	0.655000	0.94253	ACG	.	.		0.408	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55602719	C	T	55602719	3	4	217	1	0	0	0	0	1	0	0	0	8338	536	19	1	2610	1	KIT	4	55602719	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10		55602719	135551557	16	31215										
COQ2	27235	hgsc.bcm.edu	37	chr4	84191021	84191021	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	taatttctttacctgatgggCataaatagtatcatatatta	5	5	2	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr4:84191021C>A	ENST00000311469.4	-	5	903	c.904G>T	c.(904-906)Gcc>Tcc	p.A302S	COQ2_ENST00000311461.7_Missense_Mutation_p.A252S|COQ2_ENST00000439031.2_Missense_Mutation_p.A265S	NM_015697.7	NP_056512.5	Q96H96	COQ2_HUMAN	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	252					cell death (GO:0008219)|glycerol metabolic process (GO:0006071)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	4-hydroxybenzoate decaprenyltransferase activity (GO:0002083)|4-hydroxybenzoate nonaprenyltransferase activity (GO:0047293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)	8		Hepatocellular(203;0.114)				ACCTGATGGGCATAAATAGTA	0.328																																					p.A302S		Atlas-SNP	.											.	COQ2	22	.	0			c.G904T						.						56	51	52					4																	84191021		1819	4089	5908	SO:0001583	missense	27235	exon5			GATGGGCATAAAT		CCDS47090.1, CCDS47090.2	4q21.23	2013-05-23	2013-05-23				2.5.1.39		25223	protein-coding gene	gene with protein product	"4-hydroxybenzoate polyprenyltransferase"	609825	"coenzyme Q2 homolog, prenyltransferase (yeast)"			15153069, 17332895	Standard	NM_015697		Approved	CL640, FLJ26072	uc003hog.3	Q96H96		ENST00000311469.4:c.904G>T	chr4.hg19:g.84191021C>A	ENSP00000310873:p.Ala302Ser	441.0	2.0		214.0	159.0	NM_015697	O95331|Q1JQ78|Q684R2	Missense_Mutation	SNP	ENST00000311469.4	hg19	CCDS47090.2	.	.	.	.	.	.	.	.	.	.	C	19.31	3.802644	0.70682	.	.	ENSG00000173085	ENST00000311469;ENST00000439031;ENST00000311461	D;D;D	0.92099	-2.97;-2.97;-2.97	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.97081	0.9046	M	0.92412	3.305	0.80722	D	1	D;D	0.56746	0.971;0.977	D;P	0.67382	0.951;0.794	D	0.96789	0.9581	10	0.56958	D	0.05	0.1232	19.6509	0.95805	0.0:1.0:0.0:0.0	.	252;252	E2QRG7;Q96H96	.;COQ2_HUMAN	S	302;265;252	ENSP00000310873:A302S;ENSP00000409275:A265S;ENSP00000311835:A252S	ENSP00000311835:A252S	A	-	1	0	COQ2	84410045	1.000000	0.71417	1.000000	0.80357	0.215000	0.24574	7.587000	0.82613	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.328	COQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363027.3	NM_015697		A	84191021	C	A	84191021	3	1	217	1	0	0	0	0	1	0	0	0	3747	710	25	3	373	3	COQ2	4	84191021	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	28588302	84191021	106963255	17	31216										
AFF1	4299	hgsc.bcm.edu	37	chr4	88035865	88035865	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ccgggcaggttcacggaccaGcctgcagggggaaagggagc	18	11	1	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr4:88035865G>T	ENST00000307808.6	+	11	2279	c.1859G>T	c.(1858-1860)aGc>aTc	p.S620I	AFF1_ENST00000544085.1_Missense_Mutation_p.S258I|AFF1_ENST00000395146.4_Missense_Mutation_p.S627I	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	620					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TCACGGACCAGCCTGCAGGGG	0.607																																					p.S627I		Atlas-SNP	.											.	AFF1	102	.	0			c.G1880T						.						35	42	40					4																	88035865		2201	4298	6499	SO:0001583	missense	4299	exon12			GGACCAGCCTGCA	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.1859G>T	chr4.hg19:g.88035865G>T	ENSP00000305689:p.Ser620Ile	215.0	0.0		163.0	124.0	NM_001166693	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	hg19	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.705590	0.48412	.	.	ENSG00000172493	ENST00000395146;ENST00000541943;ENST00000307808;ENST00000544085	T;T;T	0.64803	-0.12;-0.12;-0.12	5.93	3.89	0.44902	.	2.212320	0.01226	N	0.008224	T	0.59998	0.2235	N	0.25647	0.755	0.09310	N	1	P;P;P	0.42161	0.772;0.772;0.772	B;B;B	0.44224	0.444;0.444;0.444	T	0.55509	-0.8130	10	0.35671	T	0.21	2.0044	12.8761	0.57991	0.071:0.119:0.81:0.0	.	627;620;620	E9PBM3;Q14C88;P51825	.;.;AFF1_HUMAN	I	627;279;620;258	ENSP00000378578:S627I;ENSP00000305689:S620I;ENSP00000440843:S258I	ENSP00000305689:S620I	S	+	2	0	AFF1	88254889	0.972000	0.33761	0.033000	0.17914	0.036000	0.12997	4.358000	0.59442	1.509000	0.48786	0.561000	0.74099	AGC	.	.		0.607	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		T	88035865	G	T	88035865	3	4	217	1	0	0	0	0	1	0	0	0	356	971	34	3	1943	3	AFF1	4	88035865	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	3844844	88035865	103118411	18	31217										
TLL1	7092	hgsc.bcm.edu	37	chr4	166986934	166986934	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	aagtgcctgaagtgatcacaTcccagttcaacaatatgaga	8	9	2	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr4:166986934T>C	ENST00000061240.2	+	16	2754	c.2107T>C	c.(2107-2109)Tcc>Ccc	p.S703P	TLL1_ENST00000507499.1_Missense_Mutation_p.S726P	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	703	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		AGTGATCACATCCCAGTTCAA	0.398																																					p.S703P		Atlas-SNP	.											.	TLL1	194	.	0			c.T2107C						.						149	145	146					4																	166986934		2203	4299	6502	SO:0001583	missense	7092	exon16			ATCACATCCCAGT	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2107T>C	chr4.hg19:g.166986934T>C	ENSP00000061240:p.Ser703Pro	173.0	0.0		100.0	80.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	hg19	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	T	18.96	3.733051	0.69189	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	T;T	0.41400	1.0;1.0	5.97	5.97	0.96955	CUB (5);	0.000000	0.85682	U	0.000000	T	0.74846	0.3770	H	0.94808	3.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82575	-0.0389	10	0.87932	D	0	.	16.4608	0.84044	0.0:0.0:0.0:1.0	.	726;703	E9PD25;O43897	.;TLL1_HUMAN	P	703;726	ENSP00000061240:S703P;ENSP00000426082:S726P	ENSP00000061240:S703P	S	+	1	0	TLL1	167206384	1.000000	0.71417	0.449000	0.26957	0.174000	0.22865	7.997000	0.88414	2.288000	0.76882	0.533000	0.62120	TCC	.	.		0.398	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			C	166986934	T	C	166986934	3	2	217	1	0	0	0	0	1	0	0	0	15960	1435	50	2	2169	2	TLL1	4	166986934	Missense_Mutation	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10	78951069	166986934	24167342	19	31218										
TRIP13	9319	hgsc.bcm.edu	37	chr5	908114	908114	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gggttccagagtggcaagctGgtaaccaagatgtttcagaa	13	7	1	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:908114G>A	ENST00000166345.3	+	8	1040	c.684G>A	c.(682-684)ctG>ctA	p.L228L		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	228					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			GTGGCAAGCTGGTAACCAAGA	0.502																																					p.L228L		Atlas-SNP	.											.	TRIP13	41	.	0			c.G684A						.						161	141	148					5																	908114		2203	4300	6503	SO:0001819	synonymous_variant	9319	exon8			CAAGCTGGTAACC	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"ATPases / AAA-type"	12307	protein-coding gene	gene with protein product	"thyroid receptor interacting protein 13"	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.684G>A	chr5.hg19:g.908114G>A		93.0	0.0		146.0	29.0	NM_004237	C9K0T3|D3DTC0|O15324	Silent	SNP	ENST00000166345.3	hg19	CCDS3858.1	.	.	.	.	.	.	.	.	.	.	.	10.07	1.250794	0.22880	.	.	ENSG00000071539	ENST00000513435	.	.	.	5.62	2.74	0.32292	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-9.828	6.6383	0.22895	0.1613:0.0:0.6395:0.1992	.	.	.	.	X	224	.	.	W	+	2	0	TRIP13	961114	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.625000	0.24477	1.521000	0.48983	0.655000	0.94253	TGG	.	.		0.502	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237		A	908114	G	A	908114	2	1	217	1	0	0	0	0	0	0	0	1	16572	1335	47	3		3	TRIP13	5	908114	Silent	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10		908114	180007146	20	31219										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5462390	5462390	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gctgcagtgcagggagatggGcagaagcaaaggcagcctca	16	9	1	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:5462390G>A	ENST00000296564.7	+	13	3165	c.2943G>A	c.(2941-2943)ggG>ggA	p.G981G		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		981					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AGGGAGATGGGCAGAAGCAAA	0.483																																					p.G981G		Atlas-SNP	.											.	KIAA0947	301	.	0			c.G2943A						.						34	36	35					5																	5462390		2049	4232	6281	SO:0001819	synonymous_variant	23379	exon13			AGATGGGCAGAAG																												ENST00000296564.7:c.2943G>A	chr5.hg19:g.5462390G>A		104.0	0.0		103.0	52.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	hg19	CCDS47187.1																																																																																			.	.		0.483	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			A	5462390	G	A	5462390	2	1	217	1	0	0	0	0	0	0	0	1	8211	1190	42	3		3	KIAA0947	5	5462390	Silent	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	4554276	5462390	175452870	21	31220										
ZFR	51663	hgsc.bcm.edu	37	chr5	32417841	32417841	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gctgttggttgttggtagtaTtgcttactatcataagctac	10	6	1	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:32417841T>C	ENST00000265069.8	-	4	579	c.477A>G	c.(475-477)caA>caG	p.Q159Q		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	159	Ala-rich.				multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		GTTGGTAGTATTGCTTACTAT	0.438																																					p.Q159Q		Atlas-SNP	.											.	ZFR	98	.	0			c.A477G						.						124	123	124					5																	32417841		2203	4300	6503	SO:0001819	synonymous_variant	51663	exon4			GTAGTATTGCTTA	AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.477A>G	chr5.hg19:g.32417841T>C		68.0	0.0		68.0	23.0	NM_016107	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Silent	SNP	ENST00000265069.8	hg19	CCDS34139.1																																																																																			.	.		0.438	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			C	32417841	T	C	32417841	2	2	217	1	0	0	0	0	0	0	0	1	17674	1490	52	2		2	ZFR	5	32417841	Silent	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10	26955451	32417841	148497419	22	31221										
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64521991	64521991	+	IGR	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	atcaccgcaggagcacgttcAgtgtagaaattataaccttc	8	10	2	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:64521991A>C								ADAMTS6 (27399 upstream) : ADAMTS6 (71043 downstream)																							GAGCACGTTCAGTGTAGAAAT	0.443																																					p.T663T		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.T1989G						.						103	96	98					5																	64521991		2203	4300	6503	SO:0001628	intergenic_variant	11174	exon16			ACGTTCAGTGTAG																													chr5.hg19:g.64521991A>C		175.0	0.0		192.0	87.0	NM_197941		Silent	SNP		hg19																																																																																				.	.	0	0.443									C	64521991	A	C	64521991	1	2	217	0	1	0	0	0	0	0	0	0	270	175	7	5		5	ADAMTS6	5	64521991	IGR	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	32104150	64521991	116393269	23	31222										
OCLN	100506658	hgsc.bcm.edu	37	chr5	68849479	68849479	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	caagaagatggttggagactAtgatagacagaaaacataga	11	4	0	7			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:68849479A>G	ENST00000355237.2	+	9	1986	c.1550A>G	c.(1549-1551)tAt>tGt	p.Y517C	OCLN_ENST00000380766.2_Missense_Mutation_p.Y463C|OCLN_ENST00000542132.1_Missense_Mutation_p.Y195C|OCLN_ENST00000538151.1_Missense_Mutation_p.Y266C|OCLN_ENST00000396442.2_Missense_Mutation_p.Y517C|OCLN_ENST00000514370.1_3'UTR	NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN	occludin	517					apoptotic process (GO:0006915)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|protein complex assembly (GO:0006461)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethionine metabolic process (GO:0046500)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|structural molecule activity (GO:0005198)|thiopurine S-methyltransferase activity (GO:0008119)			endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		GTTGGAGACTATGATAGACAG	0.368																																					p.Y517C		Atlas-SNP	.											.	OCLN	22	.	0			c.A1550G						.						83	89	87					5																	68849479		2203	4299	6502	SO:0001583	missense	100506658	exon9			GAGACTATGATAG	U49184	CCDS4006.1, CCDS54864.1	5q13.1	2014-06-13			ENSG00000197822	ENSG00000197822			8104	protein-coding gene	gene with protein product	"tight junction protein occludin TM4 minus", "phosphatase 1, regulatory subunit 115"	602876				8601611	Standard	NM_002538		Approved	PPP1R115	uc003jwu.3	Q16625	OTTHUMG00000099356	ENST00000355237.2:c.1550A>G	chr5.hg19:g.68849479A>G	ENSP00000347379:p.Tyr517Cys	1057.0	0.0		1059.0	387.0	NM_001205254	B5BU70|D2DU64|D2DU65|D2IGC0|D2IGC1|E2CYV9|Q5U1V4|Q8N6K1	Missense_Mutation	SNP	ENST00000355237.2	hg19	CCDS4006.1	.	.	.	.	.	.	.	.	.	.	A	17.91	3.504575	0.64410	.	.	ENSG00000197822	ENST00000355237;ENST00000396442;ENST00000380766;ENST00000538151;ENST00000542132	T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17	5.6	5.6	0.85130	Occludin/RNA polymerase II elongation factor, ELL domain (1);	0.117665	0.64402	D	0.000013	T	0.65512	0.2698	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72424	-0.4298	10	0.87932	D	0	-22.6701	14.837	0.70192	1.0:0.0:0.0:0.0	.	517	Q16625	OCLN_HUMAN	C	517;517;463;266;195	ENSP00000347379:Y517C;ENSP00000379719:Y517C;ENSP00000370143:Y463C;ENSP00000445940:Y266C;ENSP00000440000:Y195C	ENSP00000347379:Y517C	Y	+	2	0	OCLN	68885235	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.483000	0.73617	2.144000	0.66660	0.451000	0.29950	TAT	.	.		0.368	OCLN-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216794.1	NM_002538		G	68849479	A	G	68849479	3	3	217	1	0	0	0	0	1	0	0	0	10829	449	16	2	1580	2	OCLN	5	68849479	Missense_Mutation	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	4327488	68849479	112065781	24	31223										
PAPD4	167153	hgsc.bcm.edu	37	chr5	78938692	78938692	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tcagaagactgaagcacggcAtatactcaccttagtccata	7	11	2	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:78938692A>G	ENST00000296783.3	+	8	1009	c.710A>G	c.(709-711)cAt>cGt	p.H237R	PAPD4_ENST00000504233.1_Missense_Mutation_p.H237R|PAPD4_ENST00000453514.1_Missense_Mutation_p.H237R|PAPD4_ENST00000423041.2_Missense_Mutation_p.H233R|PAPD4_ENST00000428308.2_Missense_Mutation_p.H237R			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	237					hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)			biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		GAAGCACGGCATATACTCACC	0.323																																					p.H237R		Atlas-SNP	.											.	PAPD4	51	.	0			c.A710G						.						104	92	96					5																	78938692		2203	4300	6503	SO:0001583	missense	167153	exon8			CACGGCATATACT	AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"TUTase2"	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.710A>G	chr5.hg19:g.78938692A>G	ENSP00000296783:p.His237Arg	92.0	0.0		86.0	28.0	NM_173797	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	hg19	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.281545	0.40394	.	.	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000504233;ENST00000428308;ENST00000296783	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	5.88	5.88	0.94601	.	0.241752	0.49305	D	0.000143	T	0.24353	0.0590	N	0.12920	0.275	0.41035	D	0.985189	B;B;B	0.12630	0.0;0.002;0.006	B;B;B	0.12837	0.0;0.008;0.002	T	0.12993	-1.0526	10	0.09338	T	0.73	-15.6384	12.0969	0.53761	0.9314:0.0:0.0686:0.0	.	237;233;237	Q6PIY7;Q6PIY7-2;D6RAF2	GLD2_HUMAN;.;.	R	237;233;237;237;237	ENSP00000397563:H237R;ENSP00000393412:H233R;ENSP00000421966:H237R;ENSP00000396861:H237R;ENSP00000296783:H237R	ENSP00000296783:H237R	H	+	2	0	PAPD4	78974448	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.724000	0.61972	2.248000	0.74166	0.477000	0.44152	CAT	.	.		0.323	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		G	78938692	A	G	78938692	3	3	217	1	0	0	0	0	1	0	0	0	11433	217	8	2	732	2	PAPD4	5	78938692	Missense_Mutation	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	10089213	78938692	101976568	25	31224										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79031059	79031059	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gtgacacaaaatccacctacAcaaccaaaggtggctaagcc	7	13	0	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:79031059A>G	ENST00000446378.2	+	2	6502	c.6471A>G	c.(6469-6471)acA>acG	p.T2157T		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2157					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		ATCCACCTACACAACCAAAGG	0.453																																					p.T2157T		Atlas-SNP	.											.	CMYA5	643	.	0			c.A6471G						.						76	73	74					5																	79031059		1877	4107	5984	SO:0001819	synonymous_variant	202333	exon2			ACCTACACAACCA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6471A>G	chr5.hg19:g.79031059A>G		266.0	1.0		305.0	119.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.		0.453	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		G	79031059	A	G	79031059	2	3	217	1	0	0	0	0	0	0	0	1	3592	146	6	2		2	CMYA5	5	79031059	Silent	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	92367	79031059	101884201	26	31225										
RASA1	5921	hgsc.bcm.edu	37	chr5	86659193	86659193	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	aaacgttggaaaaatttataTtttatcttagagggtagtga	9	2	1	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:86659193T>G	ENST00000274376.6	+	11	2046	c.1482T>G	c.(1480-1482)taT>taG	p.Y494*	RASA1_ENST00000456692.2_Nonsense_Mutation_p.Y317*|RASA1_ENST00000512763.1_Nonsense_Mutation_p.Y327*|RASA1_ENST00000506290.1_Nonsense_Mutation_p.Y328*	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	494	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		AAAATTTATATTTTATCTTAG	0.294																																					p.Y494X		Atlas-SNP	.											.	RASA1	213	.	0			c.T1482G						.						51	55	54					5																	86659193		2203	4297	6500	SO:0001587	stop_gained	5921	exon11			TTTATATTTTATC		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.1482T>G	chr5.hg19:g.86659193T>G	ENSP00000274376:p.Tyr494*	88.0	0.0		101.0	35.0	NM_002890	B2R6W3|Q9UDI1	Nonsense_Mutation	SNP	ENST00000274376.6	hg19	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	T	41	8.944730	0.99012	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	.	.	.	5.58	3.23	0.37069	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6399	0.33970	0.0:0.2207:0.0:0.7793	.	.	.	.	X	494;527;317;327;328	.	ENSP00000274376:Y494X	Y	+	3	2	RASA1	86694949	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	1.653000	0.37323	0.941000	0.37499	-0.605000	0.04089	TAT	.	.		0.294	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		G	86659193	T	G	86659193	4	3	217	1	0	0	0	0	0	1	0	0	13075	1500	52	5	1536	5	RASA1	5	86659193	Nonsense_Mutation	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10	7628134	86659193	94256067	27	31226										
GALNT10	55568	hgsc.bcm.edu	37	chr5	153709146	153709146	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ctctagctgcaacagcaagcGctacctggagacacttccca	8	15	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:153709146G>A	ENST00000297107.6	+	4	553	c.416G>A	c.(415-417)cGc>cAc	p.R139H	SAP30L-AS1_ENST00000519727.1_RNA|GALNT10_ENST00000425427.2_Missense_Mutation_p.R139H|GALNT10_ENST00000377661.2_Missense_Mutation_p.R139H	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	139					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.R139H(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			AACAGCAAGCGCTACCTGGAG	0.577																																					p.R139H		Atlas-SNP	.											GALNT10,NS,carcinoma,+1,2	GALNT10	70	.	1	Substitution - Missense(1)	large_intestine(1)	c.G416A						.						163	123	137					5																	153709146		2203	4300	6503	SO:0001583	missense	55568	exon4			GCAAGCGCTACCT	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19873	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 10"	608043	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.416G>A	chr5.hg19:g.153709146G>A	ENSP00000297107:p.Arg139His	70.0	0.0		88.0	20.0	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Missense_Mutation	SNP	ENST00000297107.6	hg19	CCDS4325.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.963195	0.53507	.	.	ENSG00000164574	ENST00000425427;ENST00000297107;ENST00000377661	T;T;T	0.59364	0.27;0.27;0.27	5.28	2.08	0.27032	.	2.769860	0.00906	N	0.002404	T	0.38692	0.1050	N	0.11845	0.185	0.80722	D	1	P;P;P	0.50369	0.572;0.763;0.934	B;B;B	0.36959	0.231;0.076;0.237	T	0.31779	-0.9931	10	0.46703	T	0.11	.	7.1293	0.25490	0.0943:0.0:0.3079:0.5979	.	139;139;139	Q86SR1-2;Q86SR1;Q86SR1-3	.;GLT10_HUMAN;.	H	139	ENSP00000415210:R139H;ENSP00000297107:R139H;ENSP00000366889:R139H	ENSP00000297107:R139H	R	+	2	0	GALNT10	153689339	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.988000	0.40697	0.566000	0.29273	0.655000	0.94253	CGC	.	.		0.577	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321		A	153709146	G	A	153709146	3	1	217	1	0	0	0	0	1	0	0	0	6216	1087	38	1	430	1	GALNT10	5	153709146	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	67049953	153709146	27206114	28	31227										
CDYL	9425	hgsc.bcm.edu	37	chr6	4892318	4892318	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tctctctccagccggaagaaCatggacctagcgaagtcagg	11	12	3	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr6:4892318C>A	ENST00000328908.5	+	4	689	c.558C>A	c.(556-558)aaC>aaA	p.N186K	CDYL_ENST00000397588.3_Missense_Mutation_p.N132K|CDYL_ENST00000449732.2_De_novo_Start_InFrame|CDYL_ENST00000343762.5_De_novo_Start_InFrame|CDYL_ENST00000472453.1_Intron			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	186	Interaction with EZH2.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		GCCGGAAGAACATGGACCTAG	0.532																																					p.N132K		Atlas-SNP	.											.	CDYL	74	.	0			c.C396A						.						87	88	87					6																	4892318		2203	4300	6503	SO:0001583	missense	9425	exon2			GAAGAACATGGAC	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"CDY-like, autosomal", "testis-specific chromodomain Y-like protein"	603778	"chromodomain protein, Y chromosome-like"			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.558C>A	chr6.hg19:g.4892318C>A	ENSP00000330512:p.Asn186Lys	122.0	0.0		157.0	68.0	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	hg19		.	.	.	.	.	.	.	.	.	.	C	5.083	0.200884	0.09652	.	.	ENSG00000153046	ENST00000328908;ENST00000397588	T;T	0.54279	0.97;0.58	5.79	-5.41	0.02648	.	0.225483	0.44688	D	0.000439	T	0.18299	0.0439	L	0.33485	1.01	0.80722	D	1	B;B	0.11235	0.001;0.004	B;B	0.12837	0.008;0.005	T	0.17410	-1.0370	10	0.17369	T	0.5	.	15.693	0.77469	0.0:0.1478:0.0:0.8522	.	132;186	Q9Y232-2;Q9Y232	.;CDYL1_HUMAN	K	186;132	ENSP00000330512:N186K;ENSP00000380718:N132K	ENSP00000330512:N186K	N	+	3	2	CDYL	4837317	0.845000	0.29573	0.679000	0.29978	0.972000	0.66771	0.044000	0.13992	-1.004000	0.03421	-0.312000	0.09012	AAC	.	.		0.532	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		A	4892318	C	A	4892318	3	1	217	1	0	0	0	0	1	0	0	0	3187	477	17	3	402	3	CDYL	6	4892318	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10		4892318	166222749	29	31228										
RGL2	5863	hgsc.bcm.edu	37	chr6	33266246	33266246	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tctcacctcttcttcttcctCctcctcttcctcctgccccc	1	23	5	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr6:33266246C>T	ENST00000497454.1	-	2	637	c.142G>A	c.(142-144)Gag>Aag	p.E48K	RGL2_ENST00000437840.2_Intron|RGL2_ENST00000444031.2_Intron	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2	48					positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						tcttcttcctcctcctcttcc	0.632																																					p.E48K		Atlas-SNP	.											.	RGL2	58	.	0			c.G142A						.						3	4	4					6																	33266246		1981	3928	5909	SO:0001583	missense	5863	exon2			CTTCCTCCTCCTC		CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"RAB2, member RAS oncogene family-like"	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.142G>A	chr6.hg19:g.33266246C>T	ENSP00000420211:p.Glu48Lys	445.0	1.0		430.0	200.0	NM_004761	B4DG72|Q5STK0|Q9Y3F3	Missense_Mutation	SNP	ENST00000497454.1	hg19	CCDS4774.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.976718	0.53720	.	.	ENSG00000237441	ENST00000497454;ENST00000425946	T	0.11277	2.79	4.83	4.83	0.62350	.	0.771349	0.11255	N	0.583161	T	0.01730	0.0055	N	0.05078	-0.115	0.80722	D	1	B	0.29531	0.247	B	0.25759	0.063	T	0.29610	-1.0006	10	0.06365	T	0.9	.	13.2872	0.60249	0.0:1.0:0.0:0.0	.	48	O15211	RGL2_HUMAN	K	48	ENSP00000420211:E48K	ENSP00000392918:E48K	E	-	1	0	RGL2	33374224	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.023000	0.49666	2.516000	0.84829	0.579000	0.79373	GAG	.	.		0.632	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2			T	33266246	C	T	33266246	3	4	217	1	0	0	0	0	1	0	0	0	13292	864	30	3	2259	3	RGL2	6	33266246	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	28373928	33266246	137848821	30	31229										
KLHL7	55975	hgsc.bcm.edu	37	chr7	23212604	23212604	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	caatgattgaagccaggaagAatcatgggctggtatttgta	12	5	1	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:23212604A>C	ENST00000339077.5	+	10	1660	c.1417A>C	c.(1417-1419)Aat>Cat	p.N473H	KLHL7_ENST00000322231.7_Missense_Mutation_p.N451H|KLHL7_ENST00000539124.1_Missense_Mutation_p.N397H|KLHL7_ENST00000545443.1_Missense_Mutation_p.N451H|KLHL7_ENST00000542558.1_Missense_Mutation_p.N248H|KLHL7_ENST00000409689.1_Missense_Mutation_p.N425H|AC005082.1_ENST00000366347.4_Intron	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	473					protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AGCCAGGAAGAATCATGGGCT	0.373																																					p.N473H		Atlas-SNP	.											.	KLHL7	102	.	0			c.A1417C						.						284	265	272					7																	23212604		2203	4300	6503	SO:0001583	missense	55975	exon10			AGGAAGAATCATG		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"Kelch-like", "BTB/POZ domain containing"	15646	protein-coding gene	gene with protein product	"retinitis pigmentosa 42"	611119	"kelch-like 7 (Drosophila)"			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.1417A>C	chr7.hg19:g.23212604A>C	ENSP00000343273:p.Asn473His	202.0	0.0		209.0	89.0	NM_001031710	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Missense_Mutation	SNP	ENST00000339077.5	hg19	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	A	7.699	0.692648	0.15039	.	.	ENSG00000122550	ENST00000538858;ENST00000322231;ENST00000339077;ENST00000539124;ENST00000542558;ENST00000409689;ENST00000545443	T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	5.68	4.53	0.55603	Kelch-type beta propeller (1);	0.042337	0.85682	D	0.000000	T	0.75087	0.3802	N	0.16368	0.405	0.53005	D	0.999963	B;P;D	0.76494	0.422;0.856;0.999	B;P;P	0.61070	0.397;0.525;0.883	T	0.74309	-0.3707	10	0.38643	T	0.18	.	11.543	0.50677	0.9302:0.0:0.0698:0.0	.	248;473;451	B7Z3P9;Q8IXQ5;Q8IXQ5-2	.;KLHL7_HUMAN;.	H	314;451;473;397;248;425;451	ENSP00000322958:N451H;ENSP00000343273:N473H;ENSP00000441136:N397H;ENSP00000442367:N248H;ENSP00000386263:N425H;ENSP00000442366:N451H	ENSP00000322958:N451H	N	+	1	0	KLHL7	23179129	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.938000	0.92943	0.991000	0.38814	0.477000	0.44152	AAT	.	.		0.373	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846		C	23212604	A	C	23212604	3	2	217	1	0	0	0	0	1	0	0	0	8403	246	9	5	1518	5	KLHL7	7	23212604	Missense_Mutation	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10		23212604	135926059	31	31230										
RFC2	5982	hgsc.bcm.edu	37	chr7	73654297	73654297	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gtctccctgggccgtgaagaTgatggcttctaggccgtcat	13	11	3	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:73654297T>C	ENST00000055077.3	-	7	724	c.664A>G	c.(664-666)Atc>Gtc	p.I222V	RFC2_ENST00000352131.3_Missense_Mutation_p.I188V	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	222					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						GCCGTGAAGATGATGGCTTCT	0.587																																					p.I222V		Atlas-SNP	.											.	RFC2	27	.	0			c.A664G						.						135	87	103					7																	73654297		2203	4300	6503	SO:0001583	missense	5982	exon7			TGAAGATGATGGC		CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"ATPases / AAA-type"	9970	protein-coding gene	gene with protein product	"activator 1"	600404	"replication factor C (activator 1) 2 (40kD)"			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.664A>G	chr7.hg19:g.73654297T>C	ENSP00000055077:p.Ile222Val	121.0	0.0		112.0	38.0	NM_181471	B5BU07|D3DXG3|P32846|Q9BU93	Missense_Mutation	SNP	ENST00000055077.3	hg19	CCDS5568.1	.	.	.	.	.	.	.	.	.	.	T	8.748	0.920590	0.17982	.	.	ENSG00000049541	ENST00000352131;ENST00000055077	T;T	0.38887	1.11;1.11	5.19	0.151	0.14888	.	0.198965	0.53938	N	0.000054	T	0.16599	0.0399	N	0.13327	0.33	0.50467	D	0.999874	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.28808	-1.0032	10	0.02654	T	1	.	5.1254	0.14882	0.0:0.3123:0.1492:0.5384	.	188;188;222	P35250-2;Q75MT5;P35250	.;.;RFC2_HUMAN	V	188;222	ENSP00000275627:I188V;ENSP00000055077:I222V	ENSP00000055077:I222V	I	-	1	0	RFC2	73292233	1.000000	0.71417	0.854000	0.33618	0.955000	0.61496	2.210000	0.42816	0.066000	0.16515	0.459000	0.35465	ATC	.	.		0.587	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471		C	73654297	T	C	73654297	3	2	217	1	0	0	0	0	1	0	0	0	13260	1464	51	2	420	2	RFC2	7	73654297	Missense_Mutation	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10	50441693	73654297	85484366	32	31231										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81642821	81642821	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	aatggaaggaatttcataatAataacctgaaatatacatat	5	4	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:81642821A>G	ENST00000356253.5	-	14	1483	c.1228T>C	c.(1228-1230)Tat>Cat	p.Y410H	CACNA2D1_ENST00000464354.1_5'UTR|MIR1255B1_ENST00000439234.1_RNA|MIR1255B1_ENST00000454066.1_RNA|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.Y410H			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	410	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	ATTTCATAATAATAACCTGAA	0.189																																					p.Y410H		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.T1228C						.						8	8	8					7																	81642821		1827	3719	5546	SO:0001583	missense	781	exon14			CATAATAATAACC	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.1228T>C	chr7.hg19:g.81642821A>G	ENSP00000348589:p.Tyr410His	650.0	0.0		748.0	319.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	hg19		.	.	.	.	.	.	.	.	.	.	A	23.6	4.434542	0.83776	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253	T;T	0.14516	2.5;2.5	5.72	5.72	0.89469	.	0.052077	0.85682	D	0.000000	T	0.40247	0.1109	M	0.80616	2.505	0.80722	D	1	D	0.69078	0.997	D	0.72075	0.976	T	0.34900	-0.9810	10	0.87932	D	0	-19.3369	14.9805	0.71309	1.0:0.0:0.0:0.0	.	410	P54289-2	.	H	410	ENSP00000349320:Y410H;ENSP00000348589:Y410H	ENSP00000284088:Y410H	Y	-	1	0	CACNA2D1	81480757	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.811000	0.75221	2.183000	0.69458	0.383000	0.25322	TAT	.	.		0.189	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				G	81642821	A	G	81642821	3	3	217	1	0	0	0	0	1	0	0	0	2550	362	13	2	2151	2	CACNA2D1	7	81642821	Missense_Mutation	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	7988524	81642821	77495842	33	31232										
PCLO	27445	hgsc.bcm.edu	37	chr7	82784467	82784467	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gctgttgagatgggggctttGctgagccaggctgttgaggt	18	6	0	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:82784467G>A	ENST00000333891.9	-	2	1827	c.1490C>T	c.(1489-1491)gCa>gTa	p.A497V	PCLO_ENST00000423517.2_Missense_Mutation_p.A497V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGGGGGCTTTGCTGAGCCAGG	0.607																																					p.A497V		Atlas-SNP	.											.	PCLO	1506	.	0			c.C1490T						.						93	102	99					7																	82784467		1946	4134	6080	SO:0001583	missense	27445	exon2			GGCTTTGCTGAGC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.1490C>T	chr7.hg19:g.82784467G>A	ENSP00000334319:p.Ala497Val	23.0	0.0		32.0	9.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.487|4.487	0.090288|0.090288	0.08632|0.08632	.|.	.|.	ENSG00000186472|ENSG00000186472	ENST00000333891;ENST00000423517|ENST00000431819	T;T|.	0.16597|.	2.33;2.33|.	4.64|4.64	3.73|3.73	0.42828|0.42828	.|.	.|.	.|.	.|.	.|.	T|T	0.30262|0.30262	0.0759|0.0759	L|L	0.32530|0.32530	0.975|0.975	0.19775|0.19775	N|N	0.99996|0.99996	B;B|.	0.28850|.	0.225;0.225|.	B;B|.	0.30316|.	0.114;0.114|.	T|T	0.26780|0.26780	-1.0093|-1.0093	9|6	0.87932|0.72032	D|D	0|0.01	.|.	4.7611|4.7611	0.13108|0.13108	0.0841:0.1631:0.6057:0.1471|0.0841:0.1631:0.6057:0.1471	.|.	497;497|.	Q9Y6V0-5;Q9Y6V0-6|.	.;.|.	V|L	497|443	ENSP00000334319:A497V;ENSP00000388393:A497V|.	ENSP00000334319:A497V|ENSP00000403939:P443L	A|P	-|-	2|2	0|0	PCLO|PCLO	82622403|82622403	0.001000|0.001000	0.12720|0.12720	0.028000|0.028000	0.17463|0.17463	0.090000|0.090000	0.18270|0.18270	0.529000|0.529000	0.23019|0.23019	1.036000|1.036000	0.39998|0.39998	0.561000|0.561000	0.74099|0.74099	GCA|CCA	.	.		0.607	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82784467	G	A	82784467	3	1	217	1	0	0	0	0	1	0	0	0	11592	1319	46	3	14051	3	PCLO	7	82784467	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	1141646	82784467	76354196	34	31233										
DOCK4	9732	hgsc.bcm.edu	37	chr7	111555875	111555875	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	atcccagcttccttgttatgGatactccatgagaaaatact	6	10	0	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:111555875G>T	ENST00000437633.1	-	13	1407	c.1151C>A	c.(1150-1152)tCc>tAc	p.S384Y	DOCK4_ENST00000428084.1_Missense_Mutation_p.S384Y|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	384					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)	p.S372F(1)|p.S384F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				CCTTGTTATGGATACTCCATG	0.373																																					p.S384Y		Atlas-SNP	.											DOCK4_ENST00000437633,NS,carcinoma,0,2	DOCK4	365	.	2	Substitution - Missense(2)	lung(2)	c.C1151A						.						58	53	55					7																	111555875		1820	4080	5900	SO:0001583	missense	9732	exon13			GTTATGGATACTC		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.1151C>A	chr7.hg19:g.111555875G>T	ENSP00000404179:p.Ser384Tyr	110.0	0.0		119.0	49.0	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.2|26.2	4.710821|4.710821	0.89112|0.89112	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000445943|ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	.|T;T	.|0.03152	.|4.04;4.03	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.14614|0.14614	0.0353|0.0353	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	D|D	1|1	.|D;D	.|0.54047	.|0.964;0.964	.|P;P	.|0.59056	.|0.851;0.714	T|T	0.00002|0.00002	-1.2647|-1.2647	5|10	.|0.87932	.|D	.|0	.|.	19.3311|19.3311	0.94288|0.94288	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|384;384	.|Q149N5;Q8N1I0	.|.;DOCK4_HUMAN	T|Y	372|372;384;384;372;383	.|ENSP00000410746:S384Y;ENSP00000404179:S384Y	.|ENSP00000345432:S372Y	P|S	-|-	1|2	0|0	DOCK4|DOCK4	111343111|111343111	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	8.322000|8.322000	0.90000|0.90000	2.868000|2.868000	0.98415|0.98415	0.555000|0.555000	0.69702|0.69702	CCA|TCC	.	.		0.373	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		T	111555875	G	T	111555875	3	4	217	1	0	0	0	0	1	0	0	0	4691	1174	41	3	4909	3	DOCK4	7	111555875	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	28771408	111555875	47582788	35	31234										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117431229	117431229	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	aggcacctggtctacaggatGaggcactaacggggtttatg	14	8	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:117431229G>A	ENST00000160373.3	-	4	2112	c.2021C>T	c.(2020-2022)tCa>tTa	p.S674L	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	674					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TCTACAGGATGAGGCACTAAC	0.483																																					p.S674L		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.C2021T						.						118	110	113					7																	117431229		2203	4300	6503	SO:0001583	missense	83992	exon4			CAGGATGAGGCAC		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.2021C>T	chr7.hg19:g.117431229G>A	ENSP00000160373:p.Ser674Leu	145.0	0.0		196.0	85.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163486	0.78226	.	.	ENSG00000077063	ENST00000160373	T	0.68025	-0.3	5.68	5.68	0.88126	.	0.113271	0.64402	D	0.000007	T	0.77068	0.4076	M	0.76574	2.34	0.51767	D	0.999932	D	0.58620	0.983	P	0.51016	0.656	T	0.79472	-0.1789	10	0.72032	D	0.01	-0.725	20.153	0.98091	0.0:0.0:1.0:0.0	.	674	Q8WZ74	CTTB2_HUMAN	L	674	ENSP00000160373:S674L	ENSP00000160373:S674L	S	-	2	0	CTTNBP2	117218465	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.011000	0.93618	2.838000	0.97847	0.563000	0.77884	TCA	.	.		0.483	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		A	117431229	G	A	117431229	3	1	217	1	0	0	0	0	1	0	0	0	4047	1294	45	3	3050	3	CTTNBP2	7	117431229	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	5875354	117431229	41707434	36	31235										
GPR124	25960	hgsc.bcm.edu	37	chr8	37699537	37699537	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	agtctgcacaacagccccacCgacagctacctgggcagcag	10	16	1	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr8:37699537C>T	ENST00000412232.2	+	19	3694	c.3681C>T	c.(3679-3681)acC>acT	p.T1227T	GPR124_ENST00000315215.7_Silent_p.T1010T	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	1227					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			ACAGCCCCACCGACAGCTACC	0.741																																					p.T1227T		Atlas-SNP	.											.	GPR124	85	.	0			c.C3681T						.						2	3	2					8																	37699537		1211	2420	3631	SO:0001819	synonymous_variant	25960	exon19			CCCCACCGACAGC	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.3681C>T	chr8.hg19:g.37699537C>T		15.0	0.0		20.0	18.0	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Silent	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	C	8.908	0.958046	0.18507	.	.	ENSG00000020181	ENST00000416514	.	.	.	3.95	-2.01	0.07410	.	.	.	.	.	.	.	.	.	.	.	0.30433	N	0.776948	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-11.071	2.1908	0.03898	0.1036:0.3087:0.301:0.2867	.	.	.	.	X	1220	.	ENSP00000405145:R1220X	R	+	1	2	GPR124	37818695	0.000000	0.05858	0.743000	0.31040	0.816000	0.46133	-2.794000	0.00765	-0.266000	0.09339	0.313000	0.20887	CGA	.	.		0.741	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			T	37699537	C	T	37699537	2	4	217	1	0	0	0	0	0	0	0	1	6646	639	23	1		1	GPR124	8	37699537	Silent	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10		37699537	108664485	37	31236										
PGCP	10404	hgsc.bcm.edu	37	chr8	97797377	97797377	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ctgagtggctccaagaacctAgaaaaagccatccaaattat	7	10	0	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr8:97797377A>G	ENST00000220763.5	+	2	462	c.252A>G	c.(250-252)ctA>ctG	p.L84L		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	84					peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)										CCAAGAACCTAGAAAAAGCCA	0.488																																					p.L84L		Atlas-SNP	.											.	.	.	.	0			c.A252G						.						91	85	87					8																	97797377		2203	4300	6503	SO:0001819	synonymous_variant	10404	exon2			GAACCTAGAAAAA	AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"lysosomal dipeptidase", "Ser-Met dipeptidase", "plasma glutamate carboxypeptidase"					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.252A>G	chr8.hg19:g.97797377A>G		192.0	0.0		316.0	98.0	NM_016134	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Silent	SNP	ENST00000220763.5	hg19	CCDS6273.1																																																																																			.	.		0.488	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134		G	97797377	A	G	97797377	2	3	217	1	0	0	0	0	0	0	0	1	11795	407	15	2		2	PGCP	8	97797377	Silent	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	60097840	97797377	48566645	38	31237										
ZHX2	22882	hgsc.bcm.edu	37	chr8	123964558	123964558	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	atactaccaaatacaactctGccctggatacaaatgccacg	5	13	1	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr8:123964558G>A	ENST00000314393.4	+	3	1643	c.808G>A	c.(808-810)Gcc>Acc	p.A270T		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	270	Required for homodimerization.|Required for interaction with NFYA.|Required for repressor activity.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			ATACAACTCTGCCCTGGATAC	0.493																																					p.A270T	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G808A						.						153	157	156					8																	123964558		2203	4300	6503	SO:0001583	missense	22882	exon3			AACTCTGCCCTGG	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.808G>A	chr8.hg19:g.123964558G>A	ENSP00000314709:p.Ala270Thr	103.0	0.0		196.0	48.0	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	hg19	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	G	17.98	3.521675	0.64747	.	.	ENSG00000178764	ENST00000314393	T	0.20738	2.05	5.93	5.93	0.95920	Homeobox (1);Homeodomain-like (1);	0.116646	0.64402	D	0.000017	T	0.31295	0.0792	M	0.76838	2.35	0.50813	D	0.999895	P	0.48503	0.911	B	0.39840	0.311	T	0.14896	-1.0456	10	0.45353	T	0.12	-25.4178	20.3437	0.98782	0.0:0.0:1.0:0.0	.	270	Q9Y6X8	ZHX2_HUMAN	T	270	ENSP00000314709:A270T	ENSP00000314709:A270T	A	+	1	0	ZHX2	124033739	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.802000	0.62539	2.821000	0.97095	0.555000	0.69702	GCC	.	.		0.493	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		A	123964558	G	A	123964558	3	1	217	1	0	0	0	0	1	0	0	0	17691	1319	46	3	810	3	ZHX2	8	123964558	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	26167181	123964558	22399464	39	31238										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139824123	139824124	+	Frame_Shift_Ins	INS	-	-	G													0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gggtgggaggccgctggggtINSgggggtggaggtggaggctc					rs377477852	byFrequency	TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr8:139824123_139824124insG	ENST00000303045.6	-	9	1813_1814	c.1367_1368insC	c.(1366-1368)ccafs	p.P456fs	COL22A1_ENST00000435777.1_Frame_Shift_Ins_p.P456fs	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	456	Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GCCGCTGGGGTGGGGGTGGAGG	0.604										HNSCC(7;0.00092)																											p.P456fs		Atlas-INDEL	.											.	COL22A1	390	.	0			c.1368_1369insC						.																																			SO:0001589	frameshift_variant	169044	exon9			.	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1368dupC	chr8.hg19:g.139824128_139824128dupG	ENSP00000303153:p.Pro456fs	114.0	0.0		211.0	13.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Frame_Shift_Ins	INS	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.604	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		G	139824124	-	G	139824123	7	5	217	1	0	1	1	0	0	0	0	0	3683	1683	59	0	3740	0	COL22A1	8	139824123	Frame_Shift_Ins	INS	-	TCGA-DD-AAED-01A-12D-A40R-10	15859565	139824123	6539899	40	31239										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77454953	77454953	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gctttacctgtattgatgccTtcagttattatccacgctcc	6	12	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr9:77454953T>G	ENST00000360774.1	-	5	768	c.531A>C	c.(529-531)gaA>gaC	p.E177D	TRPM6_ENST00000451710.3_Missense_Mutation_p.E177D|TRPM6_ENST00000361255.3_Missense_Mutation_p.E172D|TRPM6_ENST00000376864.4_Missense_Mutation_p.E177D|TRPM6_ENST00000359047.2_Missense_Mutation_p.E177D|TRPM6_ENST00000376872.3_Missense_Mutation_p.E177D|TRPM6_ENST00000376871.3_Missense_Mutation_p.E177D|TRPM6_ENST00000449912.2_Missense_Mutation_p.E172D	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	177					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TATTGATGCCTTCAGTTATTA	0.463																																					p.E177D		Atlas-SNP	.											.	TRPM6	377	.	0			c.A531C						.						133	120	124					9																	77454953		2203	4300	6503	SO:0001583	missense	140803	exon5			GATGCCTTCAGTT	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.531A>C	chr9.hg19:g.77454953T>G	ENSP00000354006:p.Glu177Asp	98.0	0.0		67.0	49.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	T	12.01	1.808872	0.31961	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376870;ENST00000376864;ENST00000359047	T;T;T;T;T;T;T;T	0.02974	4.09;4.09;4.09;4.09;4.09;4.09;4.09;4.09	5.86	5.86	0.93980	.	0.043658	0.85682	D	0.000000	T	0.03136	0.0092	L	0.33189	0.99	0.46927	D	0.999259	B;B;B;B;B;B	0.25007	0.003;0.003;0.023;0.002;0.021;0.116	B;B;B;B;B;B	0.19391	0.004;0.011;0.011;0.007;0.025;0.025	T	0.51172	-0.8739	10	0.48119	T	0.1	.	10.5821	0.45261	0.0:0.0715:0.0:0.9285	.	177;177;177;177;177;172	Q9BX84-7;Q9BX84-6;Q9BX84-5;Q96LV9;Q9BX84;Q9BX84-3	.;.;.;.;TRPM6_HUMAN;.	D	177;177;177;177;172;172;176;177;177	ENSP00000354006:E177D;ENSP00000407341:E177D;ENSP00000366068:E177D;ENSP00000366067:E177D;ENSP00000396672:E172D;ENSP00000354962:E172D;ENSP00000366060:E177D;ENSP00000351942:E177D	ENSP00000351942:E177D	E	-	3	2	TRPM6	76644773	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.098000	0.41757	2.240000	0.73641	0.533000	0.62120	GAA	.	.		0.463	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		G	77454953	T	G	77454953	3	3	217	1	0	0	0	0	1	0	0	0	16605	1606	56	5	5677	5	TRPM6	9	77454953	Missense_Mutation	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10		77454953	63758478	41	31240										
EPB41L4B	54566	hgsc.bcm.edu	37	chr9	111962537	111962537	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	aactatactgtcttgttaacTtcctcactcggggaggcttg	9	10	2	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr9:111962537T>A	ENST00000374566.3	-	20	2541	c.2024A>T	c.(2023-2025)aAg>aTg	p.K675M		NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	675					actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCTTGTTAACTTCCTCACTCG	0.408																																					p.K675M		Atlas-SNP	.											.	EPB41L4B	111	.	0			c.A2024T						.						83	81	82					9																	111962537		1867	4108	5975	SO:0001583	missense	54566	exon20			GTTAACTTCCTCA	AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.2024A>T	chr9.hg19:g.111962537T>A	ENSP00000363694:p.Lys675Met	116.0	0.0		84.0	70.0	NM_019114	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Missense_Mutation	SNP	ENST00000374566.3	hg19	CCDS43859.1	.	.	.	.	.	.	.	.	.	.	T	19.39	3.818518	0.71028	.	.	ENSG00000095203	ENST00000262536;ENST00000374566	D	0.86497	-2.13	5.61	4.48	0.54585	.	0.224284	0.22947	N	0.053711	D	0.83954	0.5366	L	0.47716	1.5	0.80722	D	1	D	0.56287	0.975	P	0.46629	0.522	T	0.82975	-0.0190	10	0.72032	D	0.01	.	7.6322	0.28247	0.0:0.0975:0.0:0.9025	.	675	Q9H329	E41LB_HUMAN	M	360;675	ENSP00000363694:K675M	ENSP00000262536:K360M	K	-	2	0	EPB41L4B	111002358	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.811000	0.47986	0.967000	0.38186	0.533000	0.62120	AAG	.	.		0.408	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424		A	111962537	T	A	111962537	3	1	217	1	0	0	0	0	1	0	0	0	5158	1609	56	4	706	4	EPB41L4B	9	111962537	Missense_Mutation	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10	34507584	111962537	29250894	42	31241										
GDF2	2658	hgsc.bcm.edu	37	chr10	48413997	48413997	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ctcacctgcctctgtggagcCgtccttggacagcttcttga	10	14	3	1	rs201711410	byFrequency	TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr10:48413997C>A	ENST00000249598.1	-	2	1030	c.871G>T	c.(871-873)Ggc>Tgc	p.G291C		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	291					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						TCTGTGGAGCCGTCCTTGGAC	0.617																																					p.G291C		Atlas-SNP	.											.	GDF2	77	.	0			c.G871T						.						85	72	76					10																	48413997		2203	4300	6503	SO:0001583	missense	2658	exon2			TGGAGCCGTCCTT	AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"Endogenous ligands"	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.871G>T	chr10.hg19:g.48413997C>A	ENSP00000249598:p.Gly291Cys	75.0	0.0		85.0	29.0	NM_016204	Q5VSQ9|Q9Y571	Missense_Mutation	SNP	ENST00000249598.1	hg19	CCDS7219.1	.	.	.	.	.	.	.	.	.	.	C	9.640	1.138643	0.21123	.	.	ENSG00000128802	ENST00000249598	T	0.79033	-1.23	5.46	-7.65	0.01281	.	1.295450	0.04583	N	0.395367	T	0.70815	0.3267	L	0.43152	1.355	0.09310	N	1	D	0.54772	0.968	P	0.45610	0.487	T	0.72097	-0.4393	10	0.87932	D	0	.	10.4445	0.44486	0.0:0.4232:0.0881:0.4888	.	291	Q9UK05	GDF2_HUMAN	C	291	ENSP00000249598:G291C	ENSP00000249598:G291C	G	-	1	0	GDF2	48034003	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.437000	0.06914	-1.226000	0.02574	-0.373000	0.07131	GGC	.	C|1.000;T|0.000		0.617	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204		A	48413997	C	A	48413997	3	1	217	1	0	0	0	0	1	0	0	0	6322	652	23	1	422	1	GDF2	10	48413997	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10		48413997	87120750	43	31242										
CC2D2B	387707	hgsc.bcm.edu	37	chr10	97787105	97787105	+	Intron	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	taggaagctttgtttcatctGaaggagataatgaatttgaa	10	3	2	4			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr10:97787105G>A	ENST00000344386.3	+	9	944				ENTPD1-AS1_ENST00000458228.1_RNA|ENTPD1-AS1_ENST00000449197.1_RNA|CC2D2B_ENST00000371198.2_3'UTR|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA|RP11-690P14.4_ENST00000475252.2_3'UTR|ENTPD1-AS1_ENST00000452728.1_RNA|ENTPD1-AS1_ENST00000416301.1_RNA|CC2D2B_ENST00000410012.2_Missense_Mutation_p.E326K	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B											large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		TGTTTCATCTGAAGGAGATAA	0.318																																					p.E326K		Atlas-SNP	.											.	CC2D2B	46	.	0			c.G976A						.						189	153	164					10																	97787105		692	1591	2283	SO:0001627	intron_variant	387707	exon11			TCATCTGAAGGAG	BC075861	CCDS41555.1, CCDS53560.1	10q23.33	2008-11-06	2007-10-19	2007-10-19	ENSG00000188649	ENSG00000188649			31666	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 130"	C10orf130			Standard	NM_001001732		Approved	bA248J23.4	uc010qop.2	Q6DHV5	OTTHUMG00000018820	ENST00000344386.3:c.781-4472G>A	chr10.hg19:g.97787105G>A		134.0	0.0		179.0	81.0	NM_001159747	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Missense_Mutation	SNP	ENST00000344386.3	hg19	CCDS41555.1	.	.	.	.	.	.	.	.	.	.	G	8.009	0.757107	0.15846	.	.	ENSG00000188649	ENST00000451649;ENST00000410012	T	0.71579	-0.58	5.8	5.8	0.92144	.	.	.	.	.	T	0.54775	0.1879	N	0.20986	0.625	0.23144	N	0.998228	B	0.14012	0.009	B	0.12156	0.007	T	0.35450	-0.9788	9	0.13853	T	0.58	.	10.9752	0.47461	0.0844:0.0:0.9156:0.0	.	326	E9PCC3	.	K	326	ENSP00000386988:E326K	ENSP00000386988:E326K	E	+	1	0	CC2D2B	97777095	0.958000	0.32768	0.998000	0.56505	0.033000	0.12548	1.366000	0.34193	2.741000	0.93983	0.650000	0.86243	GAA	.	.		0.318	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732		A	97787105	G	A	97787105	1	1	217	0	1	0	0	0	0	0	0	0	2731	1291	45	3		3	CC2D2B	10	97787105	Intron	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	49373108	97787105	37747642	44	31243										
PNLIPRP3	119548	hgsc.bcm.edu	37	chr10	118225668	118225668	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tatccttgtagatcctacacAtcttttaaagcagtaagtaa	5	8	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr10:118225668A>G	ENST00000369230.3	+	8	1061	c.915A>G	c.(913-915)acA>acG	p.T305T		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	305					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		GATCCTACACATCTTTTAAAG	0.323																																					p.T305T		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.A915G						.						96	92	93					10																	118225668		2202	4299	6501	SO:0001819	synonymous_variant	119548	exon8			CTACACATCTTTT	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.915A>G	chr10.hg19:g.118225668A>G		81.0	0.0		92.0	44.0	NM_001011709		Silent	SNP	ENST00000369230.3	hg19	CCDS31292.1																																																																																			.	.		0.323	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		G	118225668	A	G	118225668	2	3	217	1	0	0	0	0	0	0	0	1	12161	204	8	2		2	PNLIPRP3	10	118225668	Silent	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	20438563	118225668	17309079	45	31244										
UBQLNL	143630	hgsc.bcm.edu	37	chr11	5537631	5537631	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gcagacctgatggacatccaCtctgggacatcctggatgtt	11	11	1	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr11:5537631C>G	ENST00000380184.1	-	1	304	c.41G>C	c.(40-42)aGt>aCt	p.S14T	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	14										endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		TGGACATCCACTCTGGGACAT	0.532																																					p.S14T		Atlas-SNP	.											.	UBQLNL	74	.	0			c.G41C						.						80	78	79					11																	5537631		2201	4297	6498	SO:0001583	missense	143630	exon1			CATCCACTCTGGG	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"Ubiquilin family"	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.41G>C	chr11.hg19:g.5537631C>G	ENSP00000369531:p.Ser14Thr	61.0	0.0		75.0	30.0	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Missense_Mutation	SNP	ENST00000380184.1	hg19	CCDS31385.1	.	.	.	.	.	.	.	.	.	.	C	6.287	0.421012	0.11928	.	.	ENSG00000175518	ENST00000380184;ENST00000538889	T	0.45668	0.89	4.94	-2.31	0.06765	.	0.608853	0.15582	N	0.254825	T	0.29190	0.0726	L	0.53249	1.67	0.09310	N	1	B	0.33694	0.421	B	0.32864	0.154	T	0.20538	-1.0272	10	0.62326	D	0.03	.	2.462	0.04544	0.1469:0.2338:0.4326:0.1867	.	14	Q8IYU4	UBQLN_HUMAN	T	14	ENSP00000369531:S14T	ENSP00000369531:S14T	S	-	2	0	UBQLNL	5494207	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-1.132000	0.03235	-0.257000	0.09459	0.650000	0.86243	AGT	.	.		0.532	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053		G	5537631	C	G	5537631	3	3	217	1	0	0	0	0	1	0	0	0	16915	565	20	4	1390	4	UBQLNL	11	5537631	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10		5537631	129468885	46	31245										
MMP20	9313	hgsc.bcm.edu	37	chr11	102477304	102477304	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	agctccttccccagcattgtCacagcgtcaaaggatgagct	9	13	2	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr11:102477304C>T	ENST00000260228.2	-	6	927	c.915G>A	c.(913-915)gtG>gtA	p.V305V	RP11-817J15.2_ENST00000544115.1_RNA|MMP20_ENST00000544938.1_5'UTR|RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	324					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	CCAGCATTGTCACAGCGTCAA	0.582																																					p.V305V		Atlas-SNP	.											.	MMP20	52	.	0			c.G915A						.						128	111	117					11																	102477304		2203	4299	6502	SO:0001819	synonymous_variant	9313	exon6			CATTGTCACAGCG	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"enamelysin"	604629	"matrix metalloproteinase 20 (enamelysin)"			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.915G>A	chr11.hg19:g.102477304C>T		167.0	0.0		165.0	31.0	NM_004771	D3DUA8|Q9H3Q0	Silent	SNP	ENST00000260228.2	hg19	CCDS8318.1																																																																																			.	.		0.582	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1			T	102477304	C	T	102477304	2	4	217	1	0	0	0	0	0	0	0	1	9668	813	29	3		3	MMP20	11	102477304	Silent	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	96939673	102477304	32529212	47	31246										
ROBO4	54538	hgsc.bcm.edu	37	chr11	124766129	124766129	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gggctgcgcggctctccctaTgtcctgcgctgttggtggcc	15	14	1	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr11:124766129T>C	ENST00000306534.3	-	4	1129	c.644A>G	c.(643-645)cAt>cGt	p.H215R	ROBO4_ENST00000526899.1_5'UTR|ROBO4_ENST00000533054.1_Missense_Mutation_p.H70R	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	215	Ig-like C2-type 2.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GCTCTCCCTATGTCCTGCGCT	0.622																																					p.H215R		Atlas-SNP	.											.	ROBO4	130	.	0			c.A644G						.						86	84	85					11																	124766129		2201	4299	6500	SO:0001583	missense	54538	exon4			TCCCTATGTCCTG	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.644A>G	chr11.hg19:g.124766129T>C	ENSP00000304945:p.His215Arg	49.0	0.0		47.0	4.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	hg19	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	T	3.912	-0.019822	0.07634	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.65732	-0.17;-0.17	5.04	-3.63	0.04529	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.453940	0.04684	N	0.412847	T	0.26846	0.0657	N	0.01277	-0.915	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.15896	-1.0421	10	0.11182	T	0.66	.	5.3946	0.16263	0.0:0.2943:0.2597:0.4461	.	105;215	Q8WZ75-3;Q8WZ75	.;ROBO4_HUMAN	R	215;105;70	ENSP00000304945:H215R;ENSP00000437129:H70R	ENSP00000304945:H215R	H	-	2	0	ROBO4	124271339	0.000000	0.05858	0.004000	0.12327	0.057000	0.15508	-0.431000	0.06965	-0.760000	0.04677	0.528000	0.53228	CAT	.	.		0.622	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		C	124766129	T	C	124766129	3	2	217	1	0	0	0	0	1	0	0	0	13531	1464	51	2	2439	2	ROBO4	11	124766129	Missense_Mutation	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10	22288825	124766129	10240387	48	31247										
KCNC2	3747	hgsc.bcm.edu	37	chr12	75601377	75601377	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tcctcgaagagcggcccgcaCacgtctgcggggcagtgcag	15	14	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr12:75601377C>A	ENST00000549446.1	-	2	1067	c.387G>T	c.(385-387)gtG>gtT	p.V129V	KCNC2_ENST00000350228.2_Silent_p.V129V|KCNC2_ENST00000341669.3_Silent_p.V129V|KCNC2_ENST00000540018.1_Silent_p.V129V|KCNC2_ENST00000393288.2_Silent_p.V129V|KCNC2_ENST00000550433.1_Silent_p.V129V|KCNC2_ENST00000548513.1_Silent_p.V129V|KCNC2_ENST00000298972.1_Silent_p.V129V	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	129					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	GCGGCCCGCACACGTCTGCGG	0.682																																					p.V129V		Atlas-SNP	.											.	KCNC2	239	.	0			c.G387T						.						31	35	34					12																	75601377		2202	4299	6501	SO:0001819	synonymous_variant	3747	exon2			CCCGCACACGTCT	AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.387G>T	chr12.hg19:g.75601377C>A		435.0	1.0		526.0	229.0	NM_139137	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Silent	SNP	ENST00000549446.1	hg19	CCDS9007.1																																																																																			.	.		0.682	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		A	75601377	C	A	75601377	2	1	217	1	0	0	0	0	0	0	0	1	8024	465	17	3		3	KCNC2	12	75601377	Silent	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10		75601377	58250518	49	31248										
MED13L	23389	hgsc.bcm.edu	37	chr12	116675396	116675396	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	aagcaggttagcttgcagacAgcggatgaaacttaacagaa	11	7	0	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr12:116675396A>T	ENST00000281928.3	-	2	393	c.187T>A	c.(187-189)Tgt>Agt	p.C63S	MED13L_ENST00000551197.1_5'UTR	NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	63						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		GCTTGCAGACAGCGGATGAAA	0.473																																					p.C63S		Atlas-SNP	.											.	MED13L	193	.	0			c.T187A						.						176	157	164					12																	116675396		2203	4300	6503	SO:0001583	missense	23389	exon2			GCAGACAGCGGAT	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.187T>A	chr12.hg19:g.116675396A>T	ENSP00000281928:p.Cys63Ser	224.0	0.0		216.0	87.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.079561	0.76528	.	.	ENSG00000123066	ENST00000281928;ENST00000548743	T;T	0.80304	-1.36;-1.36	5.57	5.57	0.84162	Mediator complex, subunit Med13, N-terminal, metazoa/fungi (1);	0.000000	0.64402	D	0.000001	D	0.89815	0.6824	M	0.84683	2.71	0.54753	D	0.999985	P	0.37594	0.601	P	0.54965	0.765	D	0.90760	0.4664	10	0.72032	D	0.01	.	15.7209	0.77710	1.0:0.0:0.0:0.0	.	63	Q71F56	MD13L_HUMAN	S	63;53	ENSP00000281928:C63S;ENSP00000448553:C53S	ENSP00000281928:C63S	C	-	1	0	MED13L	115159779	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.279000	0.95777	2.123000	0.65237	0.459000	0.35465	TGT	.	.		0.473	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			T	116675396	A	T	116675396	3	4	217	1	0	0	0	0	1	0	0	0	9440	188	7	4	6565	4	MED13L	12	116675396	Missense_Mutation	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	41074019	116675396	17176499	50	31249										
C15orf57	90416	hgsc.bcm.edu	37	chr15	40849416	40849416	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tagacggggaatcgattaccTctcatcagaatcaagtccat	8	10	3	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr15:40849416T>A	ENST00000358005.3	-	3	673	c.400A>T	c.(400-402)Agc>Tgc	p.S134C	C15orf57_ENST00000416810.2_Splice_Site_p.S134C|C15orf57_ENST00000561011.1_Splice_Site_p.R134W|C15orf57_ENST00000558750.1_Splice_Site_p.S143C|C15orf57_ENST00000559911.1_Splice_Site_p.R134W|C15orf57_ENST00000560305.1_Splice_Site_p.S134C|C15orf57_ENST00000558113.1_Splice_Site_p.R134W|C15orf57_ENST00000558871.1_Missense_Mutation_p.R134W|RP11-111A22.1_ENST00000561460.1_RNA	NM_001080791.1|NM_052849.2	NP_001074260.1|NP_443081.1	Q9BV29	CO057_HUMAN	chromosome 15 open reading frame 57	134										endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	9						ATCGATTACCTCTCATCAGAA	0.428																																					p.S143C		Atlas-SNP	.											.	C15orf57	20	.	0			c.A427T						.						113	101	105					15																	40849416		2203	4300	6503	SO:0001630	splice_region_variant	90416	exon3			ATTACCTCTCATC	BC012189	CCDS10060.1, CCDS42022.1, CCDS73706.1	15q15.1	2008-05-30	2008-05-30	2008-05-30	ENSG00000128891	ENSG00000128891			28295	protein-coding gene	gene with protein product			"coiled-coil domain containing 32"	CCDC32		12477932	Standard	NM_001080791		Approved	MGC20481	uc001zma.1	Q9BV29	OTTHUMG00000129993	ENST00000358005.3:c.401+1A>T	chr15.hg19:g.40849416T>A		112.0	0.0		131.0	56.0	NM_001080791	A8KAL4|Q86TC4|Q8N788|Q8NAR7	Missense_Mutation	SNP	ENST00000358005.3	hg19	CCDS10060.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.936732	0.92458	.	.	ENSG00000128891	ENST00000358005;ENST00000416810	T	0.54866	0.55	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.70518	0.3233	M	0.62723	1.935	0.36270	D	0.855147	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.78119	-0.2328	10	0.72032	D	0.01	-14.7446	15.9681	0.79991	0.0:0.0:0.0:1.0	.	134;143	Q9BV29;Q9BV29-2	CO057_HUMAN;.	C	134;143	ENSP00000350695:S134C	ENSP00000350695:S134C	S	-	1	0	C15orf57	38636708	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.502000	0.66956	2.170000	0.68504	0.454000	0.30748	AGC	.	.		0.428	C15orf57-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252259.2	NM_052849	Missense_Mutation	A	40849416	T	A	40849416	5	1	217	1	0	0	0	0	0	0	1	0	1807	1565	54	4	165	4	C15orf57	15	40849416	Splice_Site	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10		40849416	61681976	51	31250										
GOLGA6A	342096	hgsc.bcm.edu	37	chr15	74364639	74364639	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ctcctcactgtccagatgttGtcctccatctcctgtaggga	8	14	2	1	rs200350318		TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr15:74364639G>C	ENST00000290438.3	-	14	1553	c.1513C>G	c.(1513-1515)Caa>Gaa	p.Q505E	RN7SL429P_ENST00000479090.2_RNA	NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	505						Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						TCCAGATGTTGTCCTCCATCT	0.632																																					p.Q505E		Atlas-SNP	.											GOLGA6A,NS,carcinoma,0,1	GOLGA6A	28	.	0			c.C1513G						.	C	GLU/GLN	13,2839		0,13,1413	43	76	64		1513	-1.8	0	15		64	41,5189		0,41,2574	no	missense	GOLGA6A	NM_001038640.2	29	0,54,3987	CC,CG,GG		0.7839,0.4558,0.6682	benign	505/694	74364639	54,8028	1426	2615	4041	SO:0001583	missense	342096	exon14			GATGTTGTCCTCC	AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289			13567	protein-coding gene	gene with protein product		610288	"golgi autoantigen, golgin subfamily a, member 6", "golgi autoantigen, golgin subfamily a, 6", "golgi autoantigen, golgin subfamily a, 6A"	GOLGA6		11161787	Standard	NM_001038640		Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1513C>G	chr15.hg19:g.74364639G>C	ENSP00000290438:p.Gln505Glu	31.0	2.0		32.0	7.0	NM_001038640	A8K959|Q9NYA7	Missense_Mutation	SNP	ENST00000290438.3	hg19	CCDS32290.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.871708	0.00062	0.004558	0.007839	ENSG00000159289	ENST00000290438	T	0.17213	2.29	0.887	-1.77	0.07982	.	.	.	.	.	T	0.02193	0.0068	N	0.00677	-1.265	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22068	-1.0227	9	0.02654	T	1	.	5.0871	0.14689	0.1703:0.3999:0.4298:0.0	.	505	Q9NYA3	GOG6A_HUMAN	E	505	ENSP00000290438:Q505E	ENSP00000290438:Q505E	Q	-	1	0	GOLGA6A	72151692	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.799000	0.00762	-2.200000	0.00747	-2.001000	0.00444	CAA	.	G|0.999;C|0.001		0.632	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421835.1	XM_292357		C	74364639	G	C	74364639	3	2	217	1	0	0	0	0	1	0	0	0	6565	1386	48	4	588	4	GOLGA6A	15	74364639	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	33515223	74364639	28166753	52	31251										
FURIN	5045	hgsc.bcm.edu	37	chr15	91423324	91423324	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	catggtgctctcctgcacagAgacatcgggaaacggctcga	12	12	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr15:91423324A>T	ENST00000268171.3	+	13	1656	c.1377A>T	c.(1375-1377)aaA>aaT	p.K459N		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	459					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TCCTGCACAGAGACATCGGGA	0.692																																					p.K459N		Atlas-SNP	.											.	FURIN	85	.	0			c.A1377T						.						38	38	38					15																	91423324		2198	4298	6496	SO:0001630	splice_region_variant	5045	exon13			GCACAGAGACATC	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1377-1A>T	chr15.hg19:g.91423324A>T		76.0	0.0		110.0	45.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	hg19	CCDS10364.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.27|14.27	2.484282|2.484282	0.44147|0.44147	.|.	.|.	ENSG00000140564|ENSG00000140564	ENST00000535252|ENST00000268171	.|T	.|0.62941	.|-0.01	4.65|4.65	2.76|2.76	0.32466|0.32466	.|Galactose-binding domain-like (1);	0.200094|0.200094	0.52532|0.52532	D|D	0.000066|0.000066	T|T	0.49745|0.49745	0.1575|0.1575	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	D|D	1|1	.|B	.|0.19817	.|0.039	.|B	.|0.18263	.|0.021	T|T	0.34875|0.34875	-0.9811|-0.9811	6|9	.|.	.|.	.|.	.|.	10.0037|10.0037	0.41944|0.41944	0.1667:0.0:0.8333:0.0|0.1667:0.0:0.8333:0.0	.|.	.|459	.|P09958	.|FURIN_HUMAN	M|N	58|459	.|ENSP00000268171:K459N	.|.	K|K	+|+	2|3	0|2	FURIN|FURIN	89224328|89224328	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.475000|0.475000	0.33008|0.33008	2.481000|2.481000	0.45215|0.45215	0.558000|0.558000	0.29135|0.29135	-0.425000|-0.425000	0.05940|0.05940	AAG|AAA	.	.		0.692	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	Missense_Mutation	T	91423324	A	T	91423324	5	4	217	1	0	0	0	0	0	0	1	0	6107	318	11	4	1423	4	FURIN	15	91423324	Splice_Site	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	17058685	91423324	11108068	53	31252										
PRMT7	54496	hgsc.bcm.edu	37	chr16	68358647	68358647	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ggtgaaggacagaggacagaAggccttggttctcgacattg	15	7	1	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr16:68358647A>G	ENST00000339507.5	+	5	1024	c.194A>G	c.(193-195)aAg>aGg	p.K65R	PRMT7_ENST00000449359.3_Intron|PRMT7_ENST00000348497.4_Missense_Mutation_p.K65R|PRMT7_ENST00000564441.1_3'UTR|PRMT7_ENST00000441236.1_Intron			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	65	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		AGAGGACAGAAGGCCTTGGTT	0.517																																					p.K65R		Atlas-SNP	.											.	PRMT7	51	.	0			c.A194G						.						144	117	126					16																	68358647		2198	4300	6498	SO:0001583	missense	54496	exon5			GACAGAAGGCCTT	AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"Protein arginine methyltransferases"	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.194A>G	chr16.hg19:g.68358647A>G	ENSP00000343103:p.Lys65Arg	173.0	0.0		108.0	78.0	NM_019023	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Missense_Mutation	SNP	ENST00000339507.5	hg19	CCDS10866.1	.	.	.	.	.	.	.	.	.	.	A	12.34	1.908869	0.33721	.	.	ENSG00000132600	ENST00000348497;ENST00000339507	T;T	0.77229	-1.08;-1.04	5.46	4.3	0.51218	.	0.217571	0.47852	D	0.000212	T	0.58047	0.2095	N	0.11560	0.145	0.20403	N	0.999906	B;B	0.15141	0.009;0.012	B;B	0.20384	0.029;0.013	T	0.40021	-0.9585	10	0.16896	T	0.51	-32.3451	11.7641	0.51920	0.8432:0.1568:0.0:0.0	.	65;65	Q9NVM4;Q9NVM4-4	ANM7_HUMAN;.	R	65	ENSP00000345775:K65R;ENSP00000343103:K65R	ENSP00000343103:K65R	K	+	2	0	PRMT7	66916148	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	1.443000	0.35057	2.062000	0.61559	0.482000	0.46254	AAG	.	.		0.517	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023		G	68358647	A	G	68358647	3	3	217	1	0	0	0	0	1	0	0	0	12553	72	3	2	204	2	PRMT7	16	68358647	Missense_Mutation	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10		68358647	21996106	54	31253										
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84476156	84476156	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tgcggtcatcagaaagaacgCcgtgatggggcagcccaccg	14	12	2	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr16:84476156C>T	ENST00000262429.4	+	15	1441	c.1352C>T	c.(1351-1353)gCc>gTc	p.A451V	ATP2C2_ENST00000416219.2_Missense_Mutation_p.A451V|ATP2C2_ENST00000420010.2_3'UTR	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	451					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						AGAAAGAACGCCGTGATGGGG	0.562																																					p.A451V		Atlas-SNP	.											.	ATP2C2	75	.	0			c.C1352T						.						163	168	166					16																	84476156		1882	4108	5990	SO:0001583	missense	9914	exon15			AGAACGCCGTGAT	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"ATPases / P-type"	29103	protein-coding gene	gene with protein product	"secretory pathway calcium ATPase 2"	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.1352C>T	chr16.hg19:g.84476156C>T	ENSP00000262429:p.Ala451Val	92.0	0.0		56.0	38.0	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Missense_Mutation	SNP	ENST00000262429.4	hg19	CCDS42207.1	.	.	.	.	.	.	.	.	.	.	C	8.505	0.865107	0.17250	.	.	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	T;T	0.70631	-0.5;-0.5	4.92	4.92	0.64577	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.710792	0.13564	N	0.378527	T	0.46347	0.1388	N	0.01789	-0.72	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.004;0.002;0.003;0.002	T	0.32666	-0.9898	10	0.34782	T	0.22	.	13.9502	0.64111	0.0:0.8354:0.1646:0.0	.	451;300;468;451	E7ES94;F8WAA5;O75185-2;O75185	.;.;.;AT2C2_HUMAN	V	451;451;300	ENSP00000397925:A451V;ENSP00000262429:A451V	ENSP00000262429:A451V	A	+	2	0	ATP2C2	83033657	0.002000	0.14202	0.007000	0.13788	0.268000	0.26511	1.748000	0.38308	2.436000	0.82500	0.491000	0.48974	GCC	.	.		0.562	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		T	84476156	C	T	84476156	3	4	217	1	0	0	0	0	1	0	0	0	1144	739	26	3	1410	3	ATP2C2	16	84476156	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	16117509	84476156	5878597	55	31254										
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88688677	88688677	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	aagagagcagatgagtggaaGgacccttggcgccgatccaa	14	9	0	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr16:88688677G>T	ENST00000301011.5	+	9	1748	c.1548G>T	c.(1546-1548)aaG>aaT	p.K516N	ZC3H18_ENST00000452588.2_Missense_Mutation_p.K540N	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	516						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		ATGAGTGGAAGGACCCTTGGC	0.597																																					p.K516N	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.G1548T						.						56	58	57					16																	88688677		2198	4300	6498	SO:0001583	missense	124245	exon9			GTGGAAGGACCCT	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.1548G>T	chr16.hg19:g.88688677G>T	ENSP00000301011:p.Lys516Asn	210.0	1.0		131.0	108.0	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	hg19	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123933	0.56613	.	.	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588	T;T	0.54279	0.58;0.58	5.83	3.88	0.44766	.	0.148768	0.64402	D	0.000013	T	0.41351	0.1155	L	0.45581	1.43	0.41213	D	0.986456	P;P	0.45474	0.859;0.859	B;B	0.39503	0.301;0.301	T	0.27706	-1.0066	10	0.14252	T	0.57	-41.2211	11.719	0.51670	0.1429:0.0:0.8571:0.0	.	540;516	E7ERS3;Q86VM9	.;ZCH18_HUMAN	N	516;484;540	ENSP00000301011:K516N;ENSP00000416951:K540N	ENSP00000289509:K484N	K	+	3	2	ZC3H18	87216178	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.147000	0.31602	1.480000	0.48289	0.655000	0.94253	AAG	.	.		0.597	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		T	88688677	G	T	88688677	3	4	217	1	0	0	0	0	1	0	0	0	17583	991	35	3	1578	3	ZC3H18	16	88688677	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	4212521	88688677	1666076	56	31255										
TP53	7157	hgsc.bcm.edu	37	chr17	7578555	7578555	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ttgttgagggcaggggagtaCtgtaggaagaggaaggagac	19	3	0	3			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr17:7578555C>T	ENST00000269305.4	-	5	565		c.e5-1		TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000445888.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(39)|p.0?(8)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGGGGAGTACTGTAGGAAGA	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,58	TP53	33396	.	51	Unknown(39)|Whole gene deletion(8)|Deletion - Frameshift(3)|Insertion - In frame(1)	ovary(9)|pancreas(6)|bone(5)|upper_aerodigestive_tract(4)|liver(4)|lung(4)|breast(4)|large_intestine(3)|central_nervous_system(3)|oesophagus(3)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|endometrium(1)|urinary_tract(1)|autonomic_ganglia(1)	c.376-1G>A						.						42	42	42					17																	7578555		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGAGTACTGTAGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.376-1G>A	chr17.hg19:g.7578555C>T		72.0	0.0		45.0	36.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.431133	0.62844	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	.	.	.	4.87	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4246	0.50003	0.0:0.9094:0.0:0.0906	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519280	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	7.639000	0.83342	1.359000	0.45940	0.655000	0.94253	.	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	T	7578555	C	T	7578555	5	4	217	1	0	0	0	0	0	0	1	0	16396	579	20	3	923	3	TP53	17	7578555	Splice_Site	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10		7578555	73616655	57	31256										
SREBF1	6720	hgsc.bcm.edu	37	chr17	17719813	17719813	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	cttatggtagaccagggctgCgtctcgggcgctggcgctag	16	11	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr17:17719813C>T	ENST00000261646.5	-	10	2189	c.2005G>A	c.(2005-2007)Gca>Aca	p.A669T	SREBF1_ENST00000583732.1_5'Flank|SREBF1_ENST00000355815.4_Missense_Mutation_p.A699T|MIR33B_ENST00000385104.1_RNA|SREBF1_ENST00000395757.1_Missense_Mutation_p.A415T|SREBF1_ENST00000338854.5_Missense_Mutation_p.A669T	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	669					aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						ACCAGGGCTGCGTCTCGGGCG	0.697																																					p.A699T		Atlas-SNP	.											.	SREBF1	47	.	0			c.G2095A						.						11	11	11					17																	17719813		2174	4272	6446	SO:0001583	missense	6720	exon11			GGGCTGCGTCTCG	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"Basic helix-loop-helix proteins"	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.2005G>A	chr17.hg19:g.17719813C>T	ENSP00000261646:p.Ala669Thr	56.0	0.0		72.0	39.0	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Missense_Mutation	SNP	ENST00000261646.5	hg19	CCDS11189.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.73|18.73	3.687461|3.687461	0.68157|0.68157	.|.	.|.	ENSG00000072310|ENSG00000072310	ENST00000338854;ENST00000355815;ENST00000261646;ENST00000395757;ENST00000395756;ENST00000418712;ENST00000423161|ENST00000395751	T;T;T;T|.	0.12984|.	2.63;2.63;2.63;2.63|.	5.4|5.4	3.35|3.35	0.38373|0.38373	.|.	0.060400|.	0.64402|.	D|.	0.000004|.	T|T	0.69079|0.69079	0.3071|0.3071	L|L	0.61036|0.61036	1.89|1.89	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.988;0.995;0.999|.	T|T	0.66775|0.66775	-0.5838|-0.5838	10|5	0.51188|.	T|.	0.08|.	-18.258|-18.258	14.2833|14.2833	0.66228|0.66228	0.2707:0.7293:0.0:0.0|0.2707:0.7293:0.0:0.0	.|.	669;699;288|.	P36956;P36956-4;A8MTU8|.	SRBP1_HUMAN;.;.|.	T|H	669;699;669;415;288;506;595|676	ENSP00000345822:A669T;ENSP00000348069:A699T;ENSP00000261646:A669T;ENSP00000379106:A415T|.	ENSP00000261646:A669T|.	A|R	-|-	1|2	0|0	SREBF1|SREBF1	17660538|17660538	1.000000|1.000000	0.71417|0.71417	0.008000|0.008000	0.14137|0.14137	0.161000|0.161000	0.22273|0.22273	5.975000|5.975000	0.70475|0.70475	0.609000|0.609000	0.30018|0.30018	0.561000|0.561000	0.74099|0.74099	GCA|CGC	.	.		0.697	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		T	17719813	C	T	17719813	3	4	217	1	0	0	0	0	1	0	0	0	15156	768	27	1	1478	1	SREBF1	17	17719813	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	10141258	17719813	63475397	58	31257										
ATAD5	79915	hgsc.bcm.edu	37	chr17	29219640	29219640	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tgtaggtggaaatagcagaaAtgtacaactagtttgctctg	11	5	1	1	rs77256126	byFrequency	TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr17:29219640A>T	ENST00000321990.4	+	20	4652	c.4274A>T	c.(4273-4275)aAt>aTt	p.N1425I		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1425					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AATAGCAGAAATGTACAACTA	0.313																																					p.N1425I		Atlas-SNP	.											.	ATAD5	150	.	0			c.A4274T						.						79	80	80					17																	29219640		2203	4300	6503	SO:0001583	missense	79915	exon20			GCAGAAATGTACA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.4274A>T	chr17.hg19:g.29219640A>T	ENSP00000313171:p.Asn1425Ile	245.0	0.0		296.0	126.0	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.558722	0.86231	.	.	ENSG00000176208	ENST00000321990	T	0.17054	2.3	4.84	4.84	0.62591	.	1.035660	0.07725	U	0.944257	T	0.40145	0.1105	M	0.64997	1.995	0.36743	D	0.882342	D	0.69078	0.997	D	0.65773	0.938	T	0.10268	-1.0637	10	0.72032	D	0.01	.	12.1036	0.53798	1.0:0.0:0.0:0.0	.	1425	Q96QE3	ATAD5_HUMAN	I	1425	ENSP00000313171:N1425I	ENSP00000313171:N1425I	N	+	2	0	ATAD5	26243766	0.107000	0.21998	0.686000	0.30086	0.776000	0.43924	1.855000	0.39378	1.939000	0.56221	0.260000	0.18958	AAT	.	.		0.313	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		T	29219640	A	T	29219640	3	4	217	1	0	0	0	0	1	0	0	0	1076	101	4	4	4352	4	ATAD5	17	29219640	Missense_Mutation	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	11499827	29219640	51975570	59	31258										
TBX2	6909	hgsc.bcm.edu	37	chr17	59485703	59485703	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	acagccgggagcctagccccCtgcccgagctggctctccgc	12	19	1	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr17:59485703C>G	ENST00000240328.3	+	7	2256	c.1975C>G	c.(1975-1977)Ctg>Gtg	p.L659V	RP11-332H18.4_ENST00000592009.1_RNA	NM_005994.3	NP_005985.3	Q13207	TBX2_HUMAN	T-box 2	659					aorta morphogenesis (GO:0035909)|atrioventricular canal development (GO:0036302)|cardiac muscle tissue development (GO:0048738)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|developmental growth involved in morphogenesis (GO:0060560)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|endocardial cushion morphogenesis (GO:0003203)|mammary placode formation (GO:0060596)|muscle cell fate determination (GO:0007521)|negative regulation of cardiac chamber formation (GO:1901211)|negative regulation of heart looping (GO:1901208)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|palate development (GO:0060021)|pharynx development (GO:0060465)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(7)|ovary(1)	9						GCCTAGCCCCCTGCCCGAGCT	0.687																																					p.L659V	GBM(3;187 253 11467 14965 23079)	Atlas-SNP	.											.	TBX2	30	.	0			c.C1975G						.						12	10	11					17																	59485703		2190	4280	6470	SO:0001583	missense	6909	exon7			AGCCCCCTGCCCG	AB209378	CCDS11627.2	17q23.2	2012-01-23			ENSG00000121068	ENSG00000121068		"T-boxes"	11597	protein-coding gene	gene with protein product		600747				8530034	Standard	NM_005994		Approved		uc010wox.2	Q13207	OTTHUMG00000156986	ENST00000240328.3:c.1975C>G	chr17.hg19:g.59485703C>G	ENSP00000240328:p.Leu659Val	123.0	0.0		171.0	60.0	NM_005994	Q16424|Q7Z647	Missense_Mutation	SNP	ENST00000240328.3	hg19	CCDS11627.2	.	.	.	.	.	.	.	.	.	.	C	1.958	-0.439654	0.04636	.	.	ENSG00000121068	ENST00000240328	D	0.85556	-2.0	4.99	4.99	0.66335	.	1.082090	0.07085	N	0.837652	T	0.70272	0.3205	N	0.08118	0	0.37207	D	0.904656	B	0.12013	0.005	B	0.08055	0.003	T	0.54735	-0.8249	10	0.02654	T	1	.	12.144	0.54014	0.1713:0.8287:0.0:0.0	.	659	Q13207	TBX2_HUMAN	V	659	ENSP00000240328:L659V	ENSP00000240328:L659V	L	+	1	2	TBX2	56840485	0.974000	0.33945	0.960000	0.40013	0.811000	0.45836	2.241000	0.43097	2.610000	0.88304	0.561000	0.74099	CTG	.	.		0.687	TBX2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346977.2	NM_005994		G	59485703	C	G	59485703	3	3	217	1	0	0	0	0	1	0	0	0	15670	680	24	4	2001	4	TBX2	17	59485703	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	30266063	59485703	21709507	60	31259										
ABHD3	171586	hgsc.bcm.edu	37	chr18	19263881	19263881	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tgtcatttaaatttacttacCaagagattctcccccgccac	4	13	2	1	rs562863991		TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr18:19263881C>T	ENST00000289119.2	-	4	694	c.555G>A	c.(553-555)ttG>ttA	p.L185L	RP11-13N13.6_ENST00000578583.1_RNA|ABHD3_ENST00000579875.1_Intron|ABHD3_ENST00000580981.1_Intron|ABHD3_ENST00000578270.1_5'UTR|MIR320C1_ENST00000408566.1_RNA	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	185						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						ATTTACTTACCAAGAGATTCT	0.284													C|||	1	0.000199681	0	0	5008	,	,		10951	0.001		0	False		,,,				2504	0				p.L185L		Atlas-SNP	.											.	ABHD3	32	.	0			c.G555A						.						58	64	62					18																	19263881		2203	4295	6498	SO:0001630	splice_region_variant	171586	exon4			ACTTACCAAGAGA	AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201		"Abhydrolase domain containing"	18718	protein-coding gene	gene with protein product		612197					Standard	NM_138340		Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.555+1G>A	chr18.hg19:g.19263881C>T		443.0	1.0		430.0	161.0	NM_138340	B0YIV0|B7Z5C2|O43411	Silent	SNP	ENST00000289119.2	hg19	CCDS32802.1																																																																																			.	.		0.284	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1		Silent	T	19263881	C	T	19263881	5	4	217	1	0	0	0	0	0	0	1	0	83	608	21	3	698	3	ABHD3	18	19263881	Splice_Site	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10		19263881	58813367	61	31260										
SLC39A6	25800	hgsc.bcm.edu	37	chr18	33703524	33703524	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gccagtgccacaaggaaactCaggagaaatttgaaaaacac	9	9	1	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr18:33703524C>A	ENST00000590986.1	-	4	1363	c.1074G>T	c.(1072-1074)ctG>ctT	p.L358L	SLC39A6_ENST00000269187.5_Silent_p.L358L|SLC39A6_ENST00000440549.2_Silent_p.L83L			Q13433	S39A6_HUMAN	solute carrier family 39 (zinc transporter), member 6	358					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|lamellipodium membrane (GO:0031258)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	41						CAAGGAAACTCAGGAGAAATT	0.428																																					p.L358L		Atlas-SNP	.											.	SLC39A6	81	.	0			c.G1074T						.						185	185	185					18																	33703524		1873	4114	5987	SO:0001819	synonymous_variant	25800	exon4			GAAACTCAGGAGA	U41060	CCDS42428.1, CCDS45854.1	18q12.2	2013-05-22				ENSG00000141424		"Solute carriers"	18607	protein-coding gene	gene with protein product		608731	"solute carrier family 39 (metal ion transporter), member 6"			12659941, 12839489	Standard	NM_012319		Approved	LIV-1	uc010dmy.3	Q13433		ENST00000590986.1:c.1074G>T	chr18.hg19:g.33703524C>A		148.0	0.0		208.0	106.0	NM_012319	B4DR49|B4E224|Q8IXR3|Q96HP5	Silent	SNP	ENST00000590986.1	hg19	CCDS42428.1																																																																																			.	.		0.428	SLC39A6-004	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000444136.1			A	33703524	C	A	33703524	2	1	217	1	0	0	0	0	0	0	0	1	14637	813	29	3		3	SLC39A6	18	33703524	Silent	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	14439643	33703524	44373724	62	31261										
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13919681	13919681	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	cccaccgccggcgcaggaatCgaggacgccaactgctggca	13	16	0	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr19:13919681C>A	ENST00000254323.2	+	4	933	c.744C>A	c.(742-744)atC>atA	p.I248I	ZSWIM4_ENST00000440752.2_5'UTR	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	248							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			GCGCAGGAATCGAGGACGCCA	0.662																																					p.I248I		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.C744A						.						18	19	19					19																	13919681		2193	4295	6488	SO:0001819	synonymous_variant	65249	exon4			AGGAATCGAGGAC	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.744C>A	chr19.hg19:g.13919681C>A		136.0	0.0		145.0	65.0	NM_023072		Silent	SNP	ENST00000254323.2	hg19	CCDS32924.1																																																																																			.	.		0.662	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		A	13919681	C	A	13919681	2	1	217	1	0	0	0	0	0	0	0	1	18258	874	31	1		1	ZSWIM4	19	13919681	Silent	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10		13919681	45209302	63	31262										
MAP1S	55201	hgsc.bcm.edu	37	chr19	17837678	17837678	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gccacccaccctagacctggCcaggagcgccctggggtggc	14	17	0	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr19:17837678C>T	ENST00000324096.4	+	5	1636	c.1485C>T	c.(1483-1485)ggC>ggT	p.G495G	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000597681.1_Intron|MAP1S_ENST00000544059.2_Silent_p.G469G	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	495	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CTAGACCTGGCCAGGAGCGCC	0.682																																					p.G495G		Atlas-SNP	.											.	MAP1S	74	.	0			c.C1485T						.						3	4	4					19																	17837678		1936	3852	5788	SO:0001819	synonymous_variant	55201	exon5			ACCTGGCCAGGAG	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.1485C>T	chr19.hg19:g.17837678C>T		110.0	0.0		150.0	69.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Silent	SNP	ENST00000324096.4	hg19	CCDS32954.1																																																																																			.	.		0.682	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		T	17837678	C	T	17837678	2	4	217	1	0	0	0	0	0	0	0	1	9243	726	26	3		3	MAP1S	19	17837678	Silent	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	3917997	17837678	41291305	64	31263										
MLL4	9757	hgsc.bcm.edu	37	chr19	36214101	36214101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tcggggctgcctacgtgtgcAggactgtgggtcctgtgtca	16	10	1	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr19:36214101A>G	ENST00000222270.7	+	6	2927	c.2927A>G	c.(2926-2928)cAg>cGg	p.Q976R	KMT2B_ENST00000420124.1_Missense_Mutation_p.Q976R|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	976					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CTACGTGTGCAGGACTGTGGG	0.617																																					p.Q976R		Atlas-SNP	.											.	MLL4	229	.	0			c.A2927G						.						46	53	51					19																	36214101		2148	4251	6399	SO:0001583	missense	8085	exon6			GTGTGCAGGACTG	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.2927A>G	chr19.hg19:g.36214101A>G	ENSP00000222270:p.Gln976Arg	64.0	0.0		71.0	29.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	A	11.93	1.786108	0.31593	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.83250	-1.7;-1.7	5.3	5.3	0.74995	Zinc finger, CXXC-type (2);	0.000000	0.42548	D	0.000690	T	0.82047	0.4952	N	0.19112	0.55	0.33580	D	0.599713	D	0.59357	0.985	P	0.57468	0.821	D	0.87656	0.2531	10	0.66056	D	0.02	.	14.3572	0.66745	1.0:0.0:0.0:0.0	.	976	Q9UMN6	MLL4_HUMAN	R	976	ENSP00000222270:Q976R;ENSP00000398837:Q976R	ENSP00000222270:Q976R	Q	+	2	0	AD000671.1	40905941	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.873000	0.75541	2.225000	0.72522	0.533000	0.62120	CAG	.	.		0.617	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		G	36214101	A	G	36214101	3	3	217	1	0	0	0	0	1	0	0	0	9632	188	7	2	2949	2	MLL4	19	36214101	Missense_Mutation	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10	18376423	36214101	22914882	65	31264										
ZNF813	126017	hgsc.bcm.edu	37	chr19	53994274	53994274	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	aaacctagtgtgccatcgtaGatgtcacactggggagaaac	11	9	1	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr19:53994274G>T	ENST00000396403.4	+	4	916	c.788G>T	c.(787-789)aGa>aTa	p.R263I	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	263					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		TGCCATCGTAGATGTCACACT	0.413																																					p.R263I		Atlas-SNP	.											.	ZNF813	81	.	0			c.G788T						.						76	78	78					19																	53994274		2201	4298	6499	SO:0001583	missense	126017	exon4			ATCGTAGATGTCA	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"Zinc fingers, C2H2-type", "-"	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.788G>T	chr19.hg19:g.53994274G>T	ENSP00000379684:p.Arg263Ile	143.0	0.0		181.0	80.0	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	hg19	CCDS46172.1	.	.	.	.	.	.	.	.	.	.	g	12.28	1.890420	0.33348	.	.	ENSG00000198346	ENST00000396403	T	0.02446	4.29	1.15	1.15	0.20763	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11067	0.0270	M	0.74467	2.265	0.19575	N	0.999967	D	0.76494	0.999	D	0.66084	0.941	T	0.08371	-1.0725	9	0.51188	T	0.08	.	8.7303	0.34494	0.0:0.0:1.0:0.0	.	263	Q6ZN06	ZN813_HUMAN	I	263	ENSP00000379684:R263I	ENSP00000379684:R263I	R	+	2	0	ZNF813	58686086	0.000000	0.05858	0.080000	0.20451	0.109000	0.19521	-3.818000	0.00358	0.194000	0.20326	0.197000	0.17608	AGA	.	.		0.413	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301		T	53994274	G	T	53994274	3	4	217	1	0	0	0	0	1	0	0	0	18190	942	33	3	798	3	ZNF813	19	53994274	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	17780173	53994274	5134709	66	31265										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44669254	44669254	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ttcgacccacccaacttcccGtgagtgctgctgctctgagc	9	16	1	2	rs142641765		TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr20:44669254G>C	ENST00000454036.2	+	7	972		c.e7+1		SLC12A5_ENST00000372315.1_Silent_p.P285P|SLC12A5_ENST00000243964.3_Splice_Site	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5						cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCAACTTCCCGTGAGTGCTGC	0.567																																					.		Atlas-SNP	.											SLC12A5,NS,lymphoid_neoplasm,0,1	SLC12A5	181	.	0			c.923+1G>C						.						183	151	162					20																	44669254		2203	4300	6503	SO:0001630	splice_region_variant	57468	exon7			CTTCCCGTGAGTG	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.923+1G>C	chr20.hg19:g.44669254G>C		52.0	0.0		76.0	31.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Splice_Site	SNP	ENST00000454036.2	hg19	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573137	0.86542	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3986	0.87453	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A5	44102661	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.657000	0.98554	2.572000	0.86782	0.655000	0.94253	.	.	G|1.000;A|0.000		0.567	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		Intron	C	44669254	G	C	44669254	5	2	217	1	0	0	0	0	0	0	1	0	14401	1159	40	4	1006	4	SLC12A5	20	44669254	Splice_Site	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10		44669254	18356266	67	31266										
NHP2L1	4809	hgsc.bcm.edu	37	chr22	42071125	42071125	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	acacagcagcggcaggtgcaGaatgatctccagtggctcgg	14	11	1	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr22:42071125G>A	ENST00000401959.1	-	4	515	c.199C>T	c.(199-201)Ctg>Ttg	p.L67L	NHP2L1_ENST00000355257.3_Silent_p.L67L|NHP2L1_ENST00000215956.5_Silent_p.L67L|NHP2L1_ENST00000402458.1_Silent_p.L71L|NHP2L1_ENST00000463675.1_5'UTR	NM_005008.3	NP_004999.1	P55769	NH2L1_HUMAN	NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae)	67					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ribosome biogenesis (GO:0042254)|RNA splicing (GO:0008380)	box C/D snoRNP complex (GO:0031428)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|lung(1)|prostate(1)	4						GGCAGGTGCAGAATGATCTCC	0.582																																					p.L67L		Atlas-SNP	.											.	NHP2L1	13	.	0			c.C199T						.						64	62	62					22																	42071125		2203	4300	6503	SO:0001819	synonymous_variant	4809	exon3			GGTGCAGAATGAT		CCDS14022.1, CCDS33653.1	22q13	2009-01-06	2001-11-28		ENSG00000100138	ENSG00000100138			7819	protein-coding gene	gene with protein product	"small nuclear ribonucleoprotein 15.5kDa (U4/U6.U5)"	601304	"non-histone chromosome protein 2 (S. cerevisiae)-like 1", "sperm specific antigen 1"	SSFA1		8978773	Standard	NM_005008		Approved	SNU13, FA-1, SPAG12, SNRNP15-5, 15.5K	uc003bav.3	P55769	OTTHUMG00000151189	ENST00000401959.1:c.199C>T	chr22.hg19:g.42071125G>A		69.0	0.0		108.0	69.0	NM_001003796		Silent	SNP	ENST00000401959.1	hg19	CCDS14022.1																																																																																			.	.		0.582	NHP2L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321682.1	NM_001003796		A	42071125	G	A	42071125	2	1	217	1	0	0	0	0	0	0	0	1	10419	933	33	3		3	NHP2L1	22	42071125	Silent	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10		42071125	9233441	68	31267										
TLR8	51311	hgsc.bcm.edu	37	chrX	12939763	12939763	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	gtgtgtttagctaaggtaaaAggctacaggtctctttccac	10	8	1	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:12939763A>G	ENST00000218032.6	+	2	2691	c.2604A>G	c.(2602-2604)aaA>aaG	p.K868K	TLR8_ENST00000311912.5_Silent_p.K886K	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	868					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CTAAGGTAAAAGGCTACAGGT	0.408																																					p.K868K		Atlas-SNP	.											.	TLR8	134	.	0			c.A2604G						.						152	144	146					X																	12939763		2203	4300	6503	SO:0001819	synonymous_variant	51311	exon2			GGTAAAAGGCTAC	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2604A>G	chrX.hg19:g.12939763A>G		65.0	0.0		98.0	5.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	hg19	CCDS14152.1																																																																																			.	.		0.408	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		G	12939763	A	G	12939763	2	3	217	1	0	0	0	0	0	0	0	1	15972	69	3	2		2	TLR8	23	12939763	Silent	SNP	A	TCGA-DD-AAED-01A-12D-A40R-10		12939763	142330797	69	31268										
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53263732	53263732	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tagggccctgtttgtgggctGgagggtgctggggggcagga	22	6	0	0			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:53263732G>A	ENST00000375368.5	-	14	4306	c.4106C>T	c.(4105-4107)cCa>cTa	p.P1369L	IQSEC2_ENST00000396435.3_Missense_Mutation_p.P1379L|IQSEC2_ENST00000375365.2_3'UTR			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1369	Pro-rich.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						TTTGTGGGCTGGAGGGTGCTG	0.677																																					p.P1379L		Atlas-SNP	.											.	IQSEC2	195	.	0			c.C4136T						.						8	7	8					X																	53263732		687	1576	2263	SO:0001583	missense	23096	exon15			TGGGCTGGAGGGT	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.4106C>T	chrX.hg19:g.53263732G>A	ENSP00000364517:p.Pro1369Leu	70.0	0.0		65.0	52.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	g	15.13	2.741957	0.49151	.	.	ENSG00000124313	ENST00000396435;ENST00000375368	T;T	0.11063	2.81;2.81	2.69	2.69	0.31865	.	0.701726	0.11901	U	0.518576	T	0.06234	0.0161	N	0.08118	0	0.46356	D	0.999009	B	0.14012	0.009	B	0.16289	0.015	T	0.27673	-1.0067	10	0.42905	T	0.14	.	10.6206	0.45478	0.0:0.0:1.0:0.0	.	1379	Q5JU85-2	.	L	1379;1369	ENSP00000379712:P1379L;ENSP00000364517:P1369L	ENSP00000364517:P1369L	P	-	2	0	IQSEC2	53280457	0.874000	0.30092	1.000000	0.80357	0.906000	0.53458	1.273000	0.33121	1.619000	0.50296	0.411000	0.27672	CCA	.	.		0.677	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		A	53263732	G	A	53263732	3	1	217	1	0	0	0	0	1	0	0	0	7827	1348	47	3	334	3	IQSEC2	23	53263732	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	40323969	53263732	102006828	70	31269										
AWAT2	158835	hgsc.bcm.edu	37	chrX	69264286	69264286	+	Frame_Shift_Del	DEL	A	A	-													0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tggtgtgaacaccaccaggtAgaggttgacagcaatcacag							TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:69264286delA	ENST00000276101.3	-	2	117	c.112delT	c.(112-114)tacfs	p.Y38fs		NM_001002254.1	NP_001002254.1	Q6E213	AWAT2_HUMAN	acyl-CoA wax alcohol acyltransferase 2	38					wax biosynthetic process (GO:0010025)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(3)|lung(2)|ovary(1)	9						ACCACCAGGTAGAGGTTGACA	0.522																																					p.Y38fs	NSCLC(80;1334 1436 9350 24214 26427)	Atlas-INDEL	.											.	AWAT2	36	.	0			c.113delA						.						126	93	104					X																	69264286		2203	4300	6503	SO:0001589	frameshift_variant	158835	exon2			.	BC063698	CCDS35320.1	Xq13.1	2009-02-23	2009-02-23	2009-02-23	ENSG00000147160	ENSG00000147160			23251	protein-coding gene	gene with protein product	"multifunctional O-acyltransferase"	300925	"diacylglycerol O-acyltransferase 2-like 4"	DGAT2L4		14970677, 16106050, 15671038	Standard	NM_001002254		Approved	MFAT	uc004dxt.1	Q6E213	OTTHUMG00000021763	ENST00000276101.3:c.112delT	chrX.hg19:g.69264286delA	ENSP00000421172:p.Tyr38fs	221.0	0.0		256.0	211.0	NM_001002254	Q6IEE3|Q6P437	Frame_Shift_Del	DEL	ENST00000276101.3	hg19	CCDS35320.1																																																																																			.	.		0.522	AWAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358738.1	NM_001002254		-	69264286	A	-	69264286	7	5	217	1	0	1	0	1	0	0	0	0	1235	420	15	0	913	0	AWAT2	23	69264286	Frame_Shift_Del	DEL	A	TCGA-DD-AAED-01A-12D-A40R-10	16000554	69264286	86006274	71	31270										
P2RY10	27334	hgsc.bcm.edu	37	chrX	78216621	78216621	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tggtcgggatgattacagttGctgagcttgcaggatttgtg	15	5	0	2			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:78216621G>T	ENST00000171757.2	+	4	884	c.604G>T	c.(604-606)Gct>Tct	p.A202S	P2RY10_ENST00000544091.1_Missense_Mutation_p.A202S	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2)	42						GATTACAGTTGCTGAGCTTGC	0.453																																					p.A202S		Atlas-SNP	.											.	P2RY10	99	.	0			c.G604T						.						177	130	146					X																	78216621		2203	4300	6503	SO:0001583	missense	27334	exon2			ACAGTTGCTGAGC	AF000545	CCDS14442.1	Xq21.1	2012-08-23			ENSG00000078589	ENSG00000078589		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	19906	protein-coding gene	gene with protein product		300529				11004484, 9755289	Standard	NM_014499		Approved	P2Y10	uc004edf.3	O00398	OTTHUMG00000021896	ENST00000171757.2:c.604G>T	chrX.hg19:g.78216621G>T	ENSP00000171757:p.Ala202Ser	50.0	0.0		69.0	60.0	NM_198333	D3DTE5|Q4VBN7|Q86V16	Missense_Mutation	SNP	ENST00000171757.2	hg19	CCDS14442.1	.	.	.	.	.	.	.	.	.	.	G	17.37	3.371981	0.61624	.	.	ENSG00000078589	ENST00000544091;ENST00000171757	T;T	0.69806	-0.43;-0.43	4.82	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.71467	0.3343	L	0.45352	1.415	0.45607	D	0.998542	P	0.50943	0.94	P	0.62014	0.897	T	0.65401	-0.6177	10	0.11182	T	0.66	.	15.5411	0.76048	0.0:0.0:1.0:0.0	.	202	O00398	P2Y10_HUMAN	S	202	ENSP00000443138:A202S;ENSP00000171757:A202S	ENSP00000171757:A202S	A	+	1	0	P2RY10	78103277	0.994000	0.37717	0.998000	0.56505	0.988000	0.76386	3.523000	0.53488	2.231000	0.72958	0.540000	0.68198	GCT	.	.		0.453	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1			T	78216621	G	T	78216621	3	4	217	1	0	0	0	0	1	0	0	0	11356	1319	46	3	606	3	P2RY10	23	78216621	Missense_Mutation	SNP	G	TCGA-DD-AAED-01A-12D-A40R-10	8952335	78216621	77053939	72	31271										
GPR112	139378	hgsc.bcm.edu	37	chrX	135428111	135428111	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	ttctggaaccacatccataaCcaatatgcctgaatttaaac	4	11	1	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:135428111C>A	ENST00000394143.1	+	6	2537	c.2246C>A	c.(2245-2247)aCc>aAc	p.T749N	GPR112_ENST00000394141.1_Missense_Mutation_p.T544N|GPR112_ENST00000370652.1_Missense_Mutation_p.T749N|GPR112_ENST00000287534.4_Missense_Mutation_p.T686N|GPR112_ENST00000412101.1_Missense_Mutation_p.T544N	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	749					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					ACATCCATAACCAATATGCCT	0.378																																					p.T749N		Atlas-SNP	.											.	GPR112	459	.	0			c.C2246A						.						78	64	69					X																	135428111		2203	4300	6503	SO:0001583	missense	139378	exon6			CCATAACCAATAT	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.2246C>A	chrX.hg19:g.135428111C>A	ENSP00000377699:p.Thr749Asn	234.0	0.0		252.0	231.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	c	11.55	1.673419	0.29693	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.33865	1.43;1.43;1.39;1.52;1.39	2.86	0.923	0.19413	.	.	.	.	.	T	0.30603	0.0770	L	0.27053	0.805	0.09310	N	1	B;B;D	0.64830	0.087;0.045;0.994	B;B;P	0.53266	0.047;0.015;0.722	T	0.12941	-1.0528	9	0.62326	D	0.03	.	2.4185	0.04442	0.3023:0.5201:0.0:0.1776	.	686;544;749	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	N	749;749;544;686;544	ENSP00000377699:T749N;ENSP00000359686:T749N;ENSP00000416526:T544N;ENSP00000287534:T686N;ENSP00000377697:T544N	ENSP00000287534:T686N	T	+	2	0	GPR112	135255777	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	0.638000	0.24674	0.362000	0.24319	0.279000	0.19357	ACC	.	.		0.378	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			A	135428111	C	A	135428111	3	1	217	1	0	0	0	0	1	0	0	0	6637	507	18	3	2256	3	GPR112	23	135428111	Missense_Mutation	SNP	C	TCGA-DD-AAED-01A-12D-A40R-10	57211490	135428111	19842449	73	31272										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144905309	144905309	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	4	1	1.12406015037594	0	1.31140350877193	0.0606060606060606	0.491436100131752	0	tgcaatatctctatttagagTataatgtcattaaggaaatt	6	4	2	1			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:144905309T>A	ENST00000370490.1	+	1	5621	c.1366T>A	c.(1366-1368)Tat>Aat	p.Y456N	SLITRK2_ENST00000413937.2_Missense_Mutation_p.Y456N|SLITRK2_ENST00000434188.2_Missense_Mutation_p.Y456N|SLITRK2_ENST00000447897.2_Missense_Mutation_p.Y456N|SLITRK2_ENST00000428560.2_Missense_Mutation_p.Y456N			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	456					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CTATTTAGAGTATAATGTCAT	0.388																																					p.Y456N		Atlas-SNP	.											.	SLITRK2	221	.	0			c.T1366A						.						133	140	138					X																	144905309		2203	4300	6503	SO:0001583	missense	84631	exon5			TTAGAGTATAATG	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.1366T>A	chrX.hg19:g.144905309T>A	ENSP00000359521:p.Tyr456Asn	80.0	0.0		95.0	84.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	hg19	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.618482	0.46736	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49;0.49	5.69	4.52	0.55395	.	0.000000	0.85682	D	0.000000	T	0.35682	0.0940	N	0.02721	-0.515	0.52501	D	0.999957	P	0.45827	0.867	P	0.51701	0.677	T	0.18116	-1.0347	10	0.23302	T	0.38	-6.5822	8.8304	0.35080	0.0:0.0897:0.0:0.9103	.	456	Q9H156	SLIK2_HUMAN	N	456	ENSP00000334374:Y456N;ENSP00000411681:Y456N;ENSP00000359521:Y456N;ENSP00000397015:Y456N;ENSP00000407347:Y456N;ENSP00000412010:Y456N	ENSP00000334374:Y456N	Y	+	1	0	SLITRK2	144713001	1.000000	0.71417	0.998000	0.56505	0.502000	0.33828	8.040000	0.89188	0.770000	0.33336	-0.314000	0.08810	TAT	.	.		0.388	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144905309	T	A	144905309	3	1	217	1	0	0	0	0	1	0	0	0	14758	1638	57	4	1368	4	SLITRK2	23	144905309	Missense_Mutation	SNP	T	TCGA-DD-AAED-01A-12D-A40R-10	9477198	144905309	10365251	74	31273										
PADI4	23569	hgsc.bcm.edu	37	chr1	17668580	17668580	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	accgacttcccggggctcatTaccctcaccatctccctgct	6	19	3	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr1:17668580T>G	ENST00000375448.4	+	7	821	c.795T>G	c.(793-795)atT>atG	p.I265M	AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	265					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	CGGGGCTCATTACCCTCACCA	0.632																																					p.I265M		Atlas-SNP	.											.	PADI4	70	.	0			c.T795G						.						79	76	77					1																	17668580		2203	4300	6503	SO:0001583	missense	23569	exon7			GCTCATTACCCTC	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"Peptidyl arginine deiminases"	18368	protein-coding gene	gene with protein product		605347	"peptidyl arginine deiminase, type V"	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.795T>G	chr1.hg19:g.17668580T>G	ENSP00000364597:p.Ile265Met	113.0	0.0		143.0	24.0	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	hg19	CCDS180.1	.	.	.	.	.	.	.	.	.	.	t	13.54	2.268358	0.40095	.	.	ENSG00000159339	ENST00000375448	T	0.23147	1.92	4.63	-3.6	0.04570	Protein-arginine deiminase (PAD), central domain (2);	0.362581	0.29676	N	0.011491	T	0.37489	0.1005	M	0.73598	2.24	0.27846	N	0.940928	D;D	0.53462	0.96;0.96	P;P	0.55455	0.776;0.776	T	0.39461	-0.9613	10	0.72032	D	0.01	-6.0275	11.4194	0.49971	0.0:0.6282:0.0:0.3718	.	265;265	A8K392;Q9UM07	.;PADI4_HUMAN	M	265	ENSP00000364597:I265M	ENSP00000364597:I265M	I	+	3	3	PADI4	17541167	0.000000	0.05858	0.198000	0.23420	0.207000	0.24258	-2.933000	0.00687	-0.657000	0.05373	-0.375000	0.07067	ATT	.	.		0.632	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387		G	17668580	T	G	17668580	3	3	218	1	0	0	0	0	1	0	0	0	11389	1742	61	5	821	5	PADI4	1	17668580	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10		17668580	231582041	1	31274										
LRRC8D	55144	hgsc.bcm.edu	37	chr1	90400553	90400553	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	aatgtcgctgagctggaactCcagaactgtgagctagagag	13	8	0	4			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr1:90400553C>A	ENST00000337338.5	+	3	2333	c.1926C>A	c.(1924-1926)ctC>ctA	p.L642L	LRRC8D_ENST00000394593.3_Silent_p.L642L	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	642					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		AGCTGGAACTCCAGAACTGTG	0.403																																					p.L642L		Atlas-SNP	.											.	LRRC8D	78	.	0			c.C1926A						.						67	67	67					1																	90400553		2203	4300	6503	SO:0001819	synonymous_variant	55144	exon3			GGAACTCCAGAAC	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.1926C>A	chr1.hg19:g.90400553C>A		106.0	0.0		101.0	5.0	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Silent	SNP	ENST00000337338.5	hg19	CCDS726.1																																																																																			.	.		0.403	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		A	90400553	C	A	90400553	2	1	218	1	0	0	0	0	0	0	0	1	9033	842	30	3		3	LRRC8D	1	90400553	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	72731973	90400553	158850068	2	31275										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179631411	179631411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gtattcatcatgtaaagaaaTgccacagaaggttagatcct	8	7	2	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr1:179631411T>C	ENST00000367614.1	+	14	2692	c.2333T>C	c.(2332-2334)aTg>aCg	p.M778T	TDRD5_ENST00000444136.1_Missense_Mutation_p.M832T|TDRD5_ENST00000294848.8_Missense_Mutation_p.M778T	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	778					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						TGTAAAGAAATGCCACAGAAG	0.473																																					p.M832T		Atlas-SNP	.											.	TDRD5	149	.	0			c.T2495C						.						71	67	69					1																	179631411		2203	4300	6503	SO:0001583	missense	163589	exon15			AAGAAATGCCACA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2333T>C	chr1.hg19:g.179631411T>C	ENSP00000356586:p.Met778Thr	46.0	0.0		75.0	22.0	NM_001199085	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	T	0.964	-0.702250	0.03255	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.30448	2.72;2.72;2.93;1.53	5.15	1.3	0.21679	.	1.559390	0.03460	N	0.212089	T	0.24812	0.0602	L	0.40543	1.245	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.15578	-1.0432	10	0.30078	T	0.28	-20.7514	3.9519	0.09372	0.1581:0.1827:0.0:0.6592	.	832;778	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	T	778;778;832;288	ENSP00000356586:M778T;ENSP00000294848:M778T;ENSP00000406052:M832T;ENSP00000410744:M288T	ENSP00000294848:M778T	M	+	2	0	TDRD5	177898034	0.096000	0.21769	0.162000	0.22713	0.781000	0.44180	0.431000	0.21444	0.308000	0.22923	0.528000	0.53228	ATG	.	.		0.473	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		C	179631411	T	C	179631411	3	2	218	1	0	0	0	0	1	0	0	0	15748	1464	51	2	2383	2	TDRD5	1	179631411	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	89230858	179631411	69619210	3	31276										
TARBP1	6894	hgsc.bcm.edu	37	chr1	234541734	234541734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ttcttcaacacttaacacttTacacacagtccagagtttct	3	12	3	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr1:234541734T>C	ENST00000040877.1	-	24	3903	c.3904A>G	c.(3904-3906)Aaa>Gaa	p.K1302E	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1302					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			CTTAACACTTTACACACAGTC	0.448																																					p.K1302E		Atlas-SNP	.											.	TARBP1	111	.	0			c.A3904G						.						142	129	133					1																	234541734		2203	4300	6503	SO:0001583	missense	6894	exon24			ACACTTTACACAC		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"tRNA methyltransferase 3 homolog (S. cerevisiae)"	605052	"Tar (HIV-1) RNA binding protein 1"			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.3904A>G	chr1.hg19:g.234541734T>C	ENSP00000040877:p.Lys1302Glu	210.0	0.0		343.0	158.0	NM_005646	Q9H581	Missense_Mutation	SNP	ENST00000040877.1	hg19	CCDS1601.1	.	.	.	.	.	.	.	.	.	.	T	8.133	0.783430	0.16189	.	.	ENSG00000059588	ENST00000040877	T	0.31510	1.49	4.46	4.46	0.54185	Armadillo-type fold (1);	0.181870	0.46758	D	0.000277	T	0.29817	0.0745	L	0.57536	1.79	0.42529	D	0.993038	B	0.27656	0.184	B	0.22152	0.038	T	0.08330	-1.0727	10	0.30854	T	0.27	-25.421	13.7029	0.62620	0.0:0.0:0.0:1.0	.	1302	Q13395	TARB1_HUMAN	E	1302	ENSP00000040877:K1302E	ENSP00000040877:K1302E	K	-	1	0	TARBP1	232608357	1.000000	0.71417	0.677000	0.29947	0.029000	0.11900	3.619000	0.54196	1.645000	0.50612	0.379000	0.24179	AAA	.	.		0.448	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646		C	234541734	T	C	234541734	3	2	218	1	0	0	0	0	1	0	0	0	15570	1763	61	2	989	2	TARBP1	1	234541734	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	54910323	234541734	14708887	4	31277										
FMN2	56776	hgsc.bcm.edu	37	chr1	240374413	240374413	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	actccagtacttcacttattTgggaaaaaattgaagagcca	7	8	1	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr1:240374413T>C	ENST00000319653.9	+	6	4173	c.3943T>C	c.(3943-3945)Tgg>Cgg	p.W1315R		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1315	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.I1457fs(2)|p.W1458fs*5(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TTCACTTATTTGGGAAAAAAT	0.323																																					p.W1315R		Atlas-SNP	.											FMN2,extremity,malignant_melanoma,-2,1	FMN2	451	.	3	Complex(2)|Insertion - Frameshift(1)	central_nervous_system(3)	c.T3943C						.						82	85	84					1																	240374413		2203	4300	6503	SO:0001583	missense	56776	exon6			CTTATTTGGGAAA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3943T>C	chr1.hg19:g.240374413T>C	ENSP00000318884:p.Trp1315Arg	37.0	0.0		73.0	37.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	T	14.76	2.632864	0.47049	.	.	ENSG00000155816	ENST00000319653	T	0.44881	0.91	4.49	4.49	0.54785	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.56097	D	0.000028	T	0.68137	0.2968	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75297	-0.3367	10	0.87932	D	0	.	13.8153	0.63287	0.0:0.0:0.0:1.0	.	1315	Q9NZ56	FMN2_HUMAN	R	1315	ENSP00000318884:W1315R	ENSP00000318884:W1315R	W	+	1	0	FMN2	238441036	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.709000	0.84645	1.669000	0.50854	0.533000	0.62120	TGG	.	.		0.323	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		C	240374413	T	C	240374413	3	2	218	1	0	0	0	0	1	0	0	0	5958	1812	63	2	3965	2	FMN2	1	240374413	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	5832679	240374413	8876208	5	31278										
APOB	338	hgsc.bcm.edu	37	chr2	21227156	21227156	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tttacctgagggctgtagtaGaagttccatttagaaaagtc	10	6	0	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr2:21227156G>T	ENST00000233242.1	-	28	12199	c.12072C>A	c.(12070-12072)ttC>ttA	p.F4024L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4024					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCTGTAGTAGAAGTTCCATT	0.483																																					p.F4024L		Atlas-SNP	.											.	APOB	761	.	0			c.C12072A						.						96	94	94					2																	21227156		2203	4300	6503	SO:0001583	missense	338	exon28			GTAGTAGAAGTTC	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.12072C>A	chr2.hg19:g.21227156G>T	ENSP00000233242:p.Phe4024Leu	47.0	0.0		57.0	23.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	0.058	-1.230949	0.01518	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.26067	1.76	5.99	0.562	0.17290	.	1.374180	0.04574	N	0.393733	T	0.08935	0.0221	N	0.02315	-0.6	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.50171	-0.8859	10	0.02654	T	1	.	6.0254	0.19652	0.1332:0.3837:0.3918:0.0913	.	4024	P04114	APOB_HUMAN	L	4024	ENSP00000233242:F4024L	ENSP00000233242:F4024L	F	-	3	2	APOB	21080661	0.181000	0.23161	0.612000	0.29024	0.205000	0.24178	-0.540000	0.06106	0.411000	0.25702	-0.211000	0.12701	TTC	.	.		0.483	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21227156	G	T	21227156	3	4	218	1	0	0	0	0	1	0	0	0	785	933	33	3	1627	3	APOB	2	21227156	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10		21227156	221972217	6	31279										
UGP2	7360	hgsc.bcm.edu	37	chr2	64109686	64109686	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ctagtggtggtgaaactcaaTggtggtttgggaaccagcat	14	6	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr2:64109686T>C	ENST00000337130.5	+	4	818	c.342T>C	c.(340-342)aaT>aaC	p.N114N	UGP2_ENST00000487469.1_3'UTR|UGP2_ENST00000394417.2_Silent_p.N103N|ACA59_ENST00000515966.1_RNA|UGP2_ENST00000445915.2_Silent_p.N123N|UGP2_ENST00000467648.2_Silent_p.N103N	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	114					carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)			endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						TGAAACTCAATGGTGGTTTGG	0.423																																					p.N114N		Atlas-SNP	.											.	UGP2	38	.	0			c.T342C						.						123	129	127					2																	64109686		2203	4300	6503	SO:0001819	synonymous_variant	7360	exon4			ACTCAATGGTGGT		CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"UDP-glucose pyrophosphorylase 1"	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.342T>C	chr2.hg19:g.64109686T>C		98.0	0.0		156.0	67.0	NM_006759	Q07131|Q0P6K2|Q86Y81|Q9BU15	Silent	SNP	ENST00000337130.5	hg19	CCDS1875.1																																																																																			.	.		0.423	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759		C	64109686	T	C	64109686	2	2	218	1	0	0	0	0	0	0	0	1	16958	1461	51	2		2	UGP2	2	64109686	Silent	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	42882530	64109686	179089687	7	31280										
POLR1B	84172	hgsc.bcm.edu	37	chr2	113300078	113300078	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gtgcaggtggccacatggatCctggcagccggtggcggaac	17	11	0	0	rs114489202	byFrequency	TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr2:113300078C>A	ENST00000263331.5	+	1	587	c.7C>A	c.(7-9)Cct>Act	p.P3T	POLR1B_ENST00000409894.3_Missense_Mutation_p.P3T|POLR1B_ENST00000537335.1_De_novo_Start_OutOfFrame|POLR1B_ENST00000417433.2_Missense_Mutation_p.P3T|POLR1B_ENST00000541869.1_Missense_Mutation_p.P41T	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	3					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						CCACATGGATCCTGGCAGCCG	0.637																																					p.P3T	Ovarian(16;256 576 9537 23969 41147)	Atlas-SNP	.											.	POLR1B	95	.	0			c.C7A						.						40	43	42					2																	113300078		2203	4300	6503	SO:0001583	missense	84172	exon1			ATGGATCCTGGCA	AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"RNA polymerase subunits"	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.7C>A	chr2.hg19:g.113300078C>A	ENSP00000263331:p.Pro3Thr	135.0	0.0		204.0	63.0	NM_019014	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Missense_Mutation	SNP	ENST00000263331.5	hg19	CCDS2097.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.036971	0.35893	.	.	ENSG00000125630	ENST00000263331;ENST00000438748;ENST00000430769;ENST00000541869;ENST00000409894;ENST00000417433	T;T;T;T	0.75704	-0.95;-0.96;-0.36;-0.94	5.55	0.504	0.16946	.	0.539199	0.21181	N	0.078811	T	0.43765	0.1262	N	0.08118	0	0.28848	N	0.896231	B;B;B;B	0.18166	0.001;0.026;0.0;0.0	B;B;B;B	0.17979	0.002;0.02;0.001;0.0	T	0.33137	-0.9880	10	0.06494	T	0.89	-4.2535	4.8076	0.13328	0.1175:0.2556:0.4823:0.1447	.	41;3;3;3	F5GZX4;F8W898;Q9H9Y6-2;Q9H9Y6	.;.;.;RPA2_HUMAN	T	3;3;3;41;3;3	ENSP00000263331:P3T;ENSP00000444136:P41T;ENSP00000387143:P3T;ENSP00000405358:P3T	ENSP00000263331:P3T	P	+	1	0	POLR1B	113016549	0.000000	0.05858	0.265000	0.24526	0.092000	0.18411	-0.756000	0.04777	-0.078000	0.12730	0.655000	0.94253	CCT	.	C|0.987;T|0.013		0.637	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014		A	113300078	C	A	113300078	3	1	218	1	0	0	0	0	1	0	0	0	12219	855	30	3	9	3	POLR1B	2	113300078	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	49190392	113300078	129899295	8	31281										
TUBA3E	112714	hgsc.bcm.edu	37	chr2	130951946	130951946	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cttgctgtaatccactgagaGccgctccatgagcagagatg	11	11	0	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr2:130951946G>T	ENST00000312988.7	-	4	569	c.469C>A	c.(469-471)Ctc>Atc	p.L157I		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	157					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					TCCACTGAGAGCCGCTCCATG	0.582																																					p.L157I		Atlas-SNP	.											.	TUBA3E	73	.	0			c.C469A						.						78	82	81					2																	130951946		2202	4299	6501	SO:0001583	missense	112714	exon4			CTGAGAGCCGCTC	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"Tubulins"	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.469C>A	chr2.hg19:g.130951946G>T	ENSP00000318197:p.Leu157Ile	154.0	0.0		262.0	128.0	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	hg19	CCDS2158.1	.	.	.	.	.	.	.	.	.	.	g	11.68	1.710455	0.30322	.	.	ENSG00000152086	ENST00000312988	T	0.74106	-0.81	2.71	2.71	0.32032	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.39274	U	0.001407	T	0.73225	0.3560	L	0.53617	1.68	0.44469	D	0.997407	B	0.09022	0.002	B	0.36464	0.225	T	0.74842	-0.3527	10	0.72032	D	0.01	.	11.1953	0.48709	0.0:0.0:1.0:0.0	.	157	Q6PEY2	TBA3E_HUMAN	I	157	ENSP00000318197:L157I	ENSP00000318197:L157I	L	-	1	0	TUBA3E	130668416	1.000000	0.71417	0.999000	0.59377	0.869000	0.49853	8.207000	0.89746	1.540000	0.49301	0.449000	0.29647	CTC	.	.		0.582	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312		T	130951946	G	T	130951946	3	4	218	1	0	0	0	0	1	0	0	0	16763	971	34	3	891	3	TUBA3E	2	130951946	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	17651868	130951946	112247427	9	31282										
POTEE	445582	hgsc.bcm.edu	37	chr2	132021637	132021637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gcccatctatgaggggaatgCcctcccccatgccaccctgc	9	18	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr2:132021637C>T	ENST00000356920.5	+	15	2703	c.2609C>T	c.(2608-2610)gCc>gTc	p.A870V	POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	870	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.A870V(1)									GAGGGGAATGCCCTCCCCCAT	0.617																																					p.A870V		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	endometrium(1)	c.C2609T						.						29	30	29					2																	132021637		2170	4227	6397	SO:0001583	missense	445582	exon15			GGAATGCCCTCCC	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33895	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 2"	608914	"ANKRD26-like family C, member 1A"	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.2609C>T	chr2.hg19:g.132021637C>T	ENSP00000439189:p.Ala870Val	121.0	0.0		135.0	45.0	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	hg19	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	16.25	3.070481	0.55539	.	.	ENSG00000188219	ENST00000356920	T	0.06687	3.27	.	.	.	.	.	.	.	.	T	0.15392	0.0371	L	0.48218	1.51	0.80722	D	1	D	0.76494	0.999	D	0.63877	0.919	T	0.03335	-1.1047	8	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	.	870	Q6S8J3	POTEE_HUMAN	V	870	ENSP00000439189:A870V	ENSP00000439189:A870V	A	+	2	0	AC131180.1	131738107	1.000000	0.71417	0.113000	0.21522	0.114000	0.19823	5.240000	0.65378	0.119000	0.18210	0.121000	0.15741	GCC	.	.		0.617	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		T	132021637	C	T	132021637	3	4	218	1	0	0	0	0	1	0	0	0	12273	739	26	3	2667	3	POTEE	2	132021637	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	1069691	132021637	111177736	10	31283										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10370571	10370571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ctgatttgcttgtgtcggtcGtcaggttgatcccactgtcg	12	10	1	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr3:10370571G>A	ENST00000352432.4	-	22	3728	c.3659C>T	c.(3658-3660)aCg>aTg	p.T1220M	ATP2B2_ENST00000383800.4_Missense_Mutation_p.T1175M|ATP2B2_ENST00000360273.2_Missense_Mutation_p.T1220M|ATP2B2_ENST00000467702.2_5'UTR|ATP2B2_ENST00000343816.4_Missense_Mutation_p.T1206M|ATP2B2_ENST00000397077.1_Missense_Mutation_p.T1175M|MIR378B_ENST00000578876.1_RNA			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	1220					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						TGTGTCGGTCGTCAGGTTGAT	0.602																																					p.T1220M	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											ATP2B2_ENST00000360273,NS,carcinoma,0,4	ATP2B2	304	.	0			c.C3659T						.						123	106	112					3																	10370571		2203	4300	6503	SO:0001583	missense	491	exon23			TCGGTCGTCAGGT	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.3659C>T	chr3.hg19:g.10370571G>A	ENSP00000324172:p.Thr1220Met	82.0	0.0		115.0	5.0	NM_001001331	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.781780	0.70222	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000429937;ENST00000452124	D;D;D;D;D;D	0.92299	-3.01;-3.0;-3.0;-3.01;-3.01;-3.0	5.97	5.09	0.68999	.	0.211192	0.48767	D	0.000168	D	0.95201	0.8444	L	0.60455	1.87	0.80722	D	1	D;P;P	0.89917	1.0;0.791;0.871	D;B;B	0.85130	0.997;0.301;0.301	D	0.95603	0.8665	10	0.72032	D	0.01	-21.7517	17.28	0.87126	0.0:0.1255:0.8745:0.0	.	1155;1187;1220	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	M	1220;1175;1175;1220;1206;1155;409;1076	ENSP00000324172:T1220M;ENSP00000373311:T1175M;ENSP00000380267:T1175M;ENSP00000353414:T1220M;ENSP00000344677:T1206M;ENSP00000414854:T1076M	ENSP00000344677:T1206M	T	-	2	0	ATP2B2	10345571	1.000000	0.71417	0.994000	0.49952	0.996000	0.88848	7.923000	0.87546	1.518000	0.48934	0.585000	0.79938	ACG	.	.		0.602	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10370571	G	A	10370571	3	1	218	1	0	0	0	0	1	0	0	0	1140	1145	40	1	76	1	ATP2B2	3	10370571	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10		10370571	187651859	11	31284										
PLCL2	23228	hgsc.bcm.edu	37	chr3	17052798	17052798	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cctttaatgaagtgcttgccAgcaagtacgccaatgaaaat	8	9	0	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr3:17052798A>T	ENST00000418129.2	+	2	2047	c.1582A>T	c.(1582-1584)Agc>Tgc	p.S528C	PLCL2_ENST00000396755.2_Missense_Mutation_p.S528C|PLCL2_ENST00000432376.1_Missense_Mutation_p.S528C	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	654	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						AGTGCTTGCCAGCAAGTACGC	0.408																																					p.S528C		Atlas-SNP	.											.	PLCL2	145	.	0			c.A1582T						.						102	106	104					3																	17052798		2203	4300	6503	SO:0001583	missense	23228	exon2			CTTGCCAGCAAGT	AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"phospholipase C, epsilon 2"	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.1582A>T	chr3.hg19:g.17052798A>T	ENSP00000409637:p.Ser528Cys	79.0	0.0		151.0	56.0	NM_015184	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Missense_Mutation	SNP	ENST00000418129.2	hg19	CCDS33713.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.597983	0.46318	.	.	ENSG00000154822	ENST00000418129;ENST00000285094;ENST00000396755;ENST00000432376	T;T;T	0.68331	-0.32;-0.32;-0.32	5.63	5.63	0.86233	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.221688	0.53938	D	0.000047	T	0.75759	0.3893	.	.	.	0.47094	D	0.999311	D	0.59767	0.986	P	0.61874	0.895	T	0.75499	-0.3296	9	0.38643	T	0.18	.	10.2319	0.43260	0.9263:0.0:0.0737:0.0	.	654	Q9UPR0	PLCL2_HUMAN	C	528;655;528;528	ENSP00000409637:S528C;ENSP00000379979:S528C;ENSP00000412836:S528C	ENSP00000285094:S655C	S	+	1	0	PLCL2	17027802	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.295000	0.72744	2.149000	0.67028	0.528000	0.53228	AGC	.	.		0.408	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3			T	17052798	A	T	17052798	3	4	218	1	0	0	0	0	1	0	0	0	12049	188	7	4	1960	4	PLCL2	3	17052798	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	6682227	17052798	180969632	12	31285										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	88.0	0.0		143.0	83.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	218	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	24213338	41266136	156756294	13	31286										
SI	6476	hgsc.bcm.edu	37	chr3	164755792	164755792	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tacatatcaacccgttgtttCctccatggcctttttgcacc	5	14	1	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr3:164755792C>T	ENST00000264382.3	-	21	2384	c.2322G>A	c.(2320-2322)agG>agA	p.R774R		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	774	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	CCCGTTGTTTCCTCCATGGCC	0.333										HNSCC(35;0.089)																											p.R774R		Atlas-SNP	.											.	SI	500	.	0			c.G2322A						.						125	122	123					3																	164755792		2203	4300	6503	SO:0001819	synonymous_variant	6476	exon21			TTGTTTCCTCCAT	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.2322G>A	chr3.hg19:g.164755792C>T		45.0	0.0		65.0	29.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	hg19	CCDS3196.1																																																																																			.	.		0.333	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		T	164755792	C	T	164755792	2	4	218	1	0	0	0	0	0	0	0	1	14312	854	30	3		3	SI	3	164755792	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	123489656	164755792	33266638	14	31287										
SAMD7	344658	hgsc.bcm.edu	37	chr3	169639109	169639109	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	aaatatggcaaatgtgttgtCcagtcggatctacccaggta	10	8	1	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr3:169639109C>T	ENST00000428432.2	+	4	583	c.194C>T	c.(193-195)tCc>tTc	p.S65F	SAMD7_ENST00000335556.3_Missense_Mutation_p.S65F	NM_182610.2	NP_872416.1	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	65										NS(1)|biliary_tract(1)|breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			AATGTGTTGTCCAGTCGGATC	0.443																																					p.S65F		Atlas-SNP	.											.	SAMD7	69	.	0			c.C194T						.						135	114	121					3																	169639109		2203	4300	6503	SO:0001583	missense	344658	exon4			TGTTGTCCAGTCG	BX537903	CCDS3209.1	3q26.31	2013-01-10			ENSG00000187033	ENSG00000187033		"Sterile alpha motif (SAM) domain containing"	25394	protein-coding gene	gene with protein product							Standard	NM_182610		Approved	DKFZp686E1583	uc003fgd.3	Q7Z3H4	OTTHUMG00000158730	ENST00000428432.2:c.194C>T	chr3.hg19:g.169639109C>T	ENSP00000391299:p.Ser65Phe	69.0	0.0		95.0	35.0	NM_182610		Missense_Mutation	SNP	ENST00000428432.2	hg19	CCDS3209.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.031937	0.54790	.	.	ENSG00000187033	ENST00000428432;ENST00000335556	T;T	0.55588	0.51;0.51	5.52	4.64	0.57946	.	0.258640	0.39544	N	0.001329	T	0.49643	0.1569	L	0.59436	1.845	0.09310	N	0.999999	B	0.20368	0.044	B	0.20384	0.029	T	0.50668	-0.8801	10	0.66056	D	0.02	-3.9081	12.2418	0.54546	0.0:0.9213:0.0:0.0787	.	65	Q7Z3H4	SAMD7_HUMAN	F	65	ENSP00000391299:S65F;ENSP00000334668:S65F	ENSP00000334668:S65F	S	+	2	0	SAMD7	171121803	0.955000	0.32602	0.007000	0.13788	0.010000	0.07245	4.408000	0.59761	1.471000	0.48121	0.655000	0.94253	TCC	.	.		0.443	SAMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351959.1	NM_182610		T	169639109	C	T	169639109	3	4	218	1	0	0	0	0	1	0	0	0	13839	855	30	3	200	3	SAMD7	3	169639109	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	4883317	169639109	28383321	15	31288										
C4orf44	345222	hgsc.bcm.edu	37	chr4	3255044	3255044	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gtcctgtgatggcaaactgcCggacagccagccgccggggc	15	14	0	1	rs541435320		TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr4:3255044C>T	ENST00000438480.2	+	2	2178	c.431C>T	c.(430-432)cCg>cTg	p.P144L	MSANTD1_ENST00000510580.1_Missense_Mutation_p.P144L|MSANTD1_ENST00000507492.1_Missense_Mutation_p.P131L	NM_001042690.1	NP_001036155.1	Q6ZTZ1	MSD1_HUMAN	Myb/SANT-like DNA-binding domain containing 1	144								p.P144Q(2)		endometrium(1)|lung(2)	3						GGCAAACTGCCGGACAGCCAG	0.642													C|||	1	0.000199681	0	0.0014	5008	,	,		15148	0		0	False		,,,				2504	0				p.P144L		Atlas-SNP	.											MSANTD1,NS,carcinoma,0,2	MSANTD1	14	.	2	Substitution - Missense(2)	endometrium(2)	c.C431T						.						56	68	64					4																	3255044		2203	4300	6503	SO:0001583	missense	345222	exon2			AACTGCCGGACAG		CCDS47003.1	4p16.2	2012-03-02	2012-03-02	2012-03-02	ENSG00000188981	ENSG00000188981			33741	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 44"	C4orf44			Standard	NM_001042690		Approved	LOC345222	uc003ggs.3	Q6ZTZ1	OTTHUMG00000159977	ENST00000438480.2:c.431C>T	chr4.hg19:g.3255044C>T	ENSP00000411584:p.Pro144Leu	53.0	0.0		74.0	39.0	NM_001042690	C9J6V0	Missense_Mutation	SNP	ENST00000438480.2	hg19	CCDS47003.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.904968	0.52333	.	.	ENSG00000188981	ENST00000507492;ENST00000438480;ENST00000510580	.	.	.	5.52	4.6	0.57074	.	0.312527	0.31747	N	0.007122	T	0.44808	0.1311	L	0.40543	1.245	0.38007	D	0.934424	B;B	0.18166	0.026;0.026	B;B	0.11329	0.006;0.002	T	0.39981	-0.9587	9	0.21540	T	0.41	.	10.2959	0.43625	0.2952:0.7048:0.0:0.0	.	144;144	D6RD98;Q6ZTZ1	.;CD044_HUMAN	L	131;144;144	.	ENSP00000411584:P144L	P	+	2	0	C4orf44	3224842	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.098000	0.50259	2.615000	0.88500	0.591000	0.81541	CCG	.	.		0.642	MSANTD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370924.1	NM_001012982		T	3255044	C	T	3255044	3	4	218	1	0	0	0	0	1	0	0	0	2274	652	23	1	437	1	C4orf44	4	3255044	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10		3255044	187899232	16	31289										
ADH4	127	hgsc.bcm.edu	37	chr4	100060242	100060242	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cacacaaatttgtgagtggaCtcagacaaaacttgcatttt	7	8	1	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr4:100060242C>G	ENST00000265512.7	-	4	394	c.320G>C	c.(319-321)aGt>aCt	p.S107T	ADH4_ENST00000505590.1_Missense_Mutation_p.S126T|ADH4_ENST00000504581.1_5'Flank|ADH4_ENST00000423445.1_Missense_Mutation_p.S126T|ADH4_ENST00000508393.1_Missense_Mutation_p.S126T|RP11-696N14.1_ENST00000500358.2_RNA	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	107					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		TGTGAGTGGACTCAGACAAAA	0.358																																					p.S107T		Atlas-SNP	.											.	ADH4	35	.	0			c.G320C						.						94	87	89					4																	100060242		2203	4300	6503	SO:0001583	missense	127	exon4			AGTGGACTCAGAC	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"Alcohol dehydrogenases"	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.320G>C	chr4.hg19:g.100060242C>G	ENSP00000265512:p.Ser107Thr	64.0	0.0		146.0	50.0	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Missense_Mutation	SNP	ENST00000265512.7	hg19	CCDS34032.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.888840	0.33348	.	.	ENSG00000198099	ENST00000508393;ENST00000265512;ENST00000423445;ENST00000505590;ENST00000512499;ENST00000504125	T;T;T;T;T;T	0.04917	3.53;3.53;3.53;3.53;3.53;3.53	4.0	2.26	0.28386	GroES-like (1);Alcohol dehydrogenase GroES-like (1);	0.128751	0.49305	D	0.000152	T	0.13157	0.0319	M	0.71871	2.18	0.39617	D	0.969975	P;B	0.34522	0.455;0.0	P;B	0.46110	0.504;0.071	T	0.01914	-1.1248	10	0.87932	D	0	-11.6196	7.2803	0.26308	0.0:0.634:0.0:0.366	.	126;107	P08319-2;P08319	.;ADH4_HUMAN	T	126;107;126;126;126;107	ENSP00000424630:S126T;ENSP00000265512:S107T;ENSP00000397939:S126T;ENSP00000425416:S126T;ENSP00000423571:S126T;ENSP00000427525:S107T	ENSP00000265512:S107T	S	-	2	0	ADH4	100279265	0.049000	0.20398	0.949000	0.38748	0.963000	0.63663	-0.140000	0.10342	0.474000	0.27392	0.555000	0.69702	AGT	.	.		0.358	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670		G	100060242	C	G	100060242	3	3	218	1	0	0	0	0	1	0	0	0	310	565	20	4	846	4	ADH4	4	100060242	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	96805198	100060242	91094034	17	31290										
INTS12	57117	hgsc.bcm.edu	37	chr4	106604433	106604433	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ccactagttactgacgaggaAacgctggcactagaagaatt	10	9	0	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr4:106604433A>T	ENST00000451321.2	-	7	1325	c.846T>A	c.(844-846)gtT>gtA	p.V282V	INTS12_ENST00000340139.5_Silent_p.V282V|INTS12_ENST00000394735.1_Silent_p.V282V	NM_001142471.1	NP_001135943.1	Q96CB8	INT12_HUMAN	integrator complex subunit 12	282	Ser-rich.				snRNA processing (GO:0016180)	integrator complex (GO:0032039)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(123;5.12e-07)		CTGACGAGGAAACGCTGGCAC	0.378																																					p.V282V		Atlas-SNP	.											.	INTS12	35	.	0			c.T846A						.						38	40	40					4																	106604433		2202	4298	6500	SO:0001819	synonymous_variant	57117	exon8			CGAGGAAACGCTG		CCDS3671.1	4q24	2013-01-28	2006-03-15	2006-03-15	ENSG00000138785	ENSG00000138785		"Zinc fingers, PHD-type"	25067	protein-coding gene	gene with protein product	"hypothetical nuclear factor SBBI22"	611355	"PHD finger protein 22"	PHF22		16239144	Standard	NM_020395		Approved	SBBI22, INT12	uc010ilr.3	Q96CB8	OTTHUMG00000131215	ENST00000451321.2:c.846T>A	chr4.hg19:g.106604433A>T		61.0	0.0		100.0	53.0	NM_020395	B2RC48|Q3B6Z3|Q9HD71	Silent	SNP	ENST00000451321.2	hg19	CCDS3671.1																																																																																			.	.		0.378	INTS12-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318624.1	NM_020395		T	106604433	A	T	106604433	2	4	218	1	0	0	0	0	0	0	0	1	7786	1	1	4		4	INTS12	4	106604433	Silent	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	6544191	106604433	84549843	18	31291										
IRX4	50805	hgsc.bcm.edu	37	chr5	1878323	1878323	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	atggggtcgtggaagaccccGtccacccagtttctgagact	12	12	1	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr5:1878323G>T	ENST00000505790.1	-	6	1776	c.1320C>A	c.(1318-1320)gaC>gaA	p.D440E	IRX4_ENST00000505938.1_5'Flank|IRX4_ENST00000231357.2_Missense_Mutation_p.D440E|IRX4_ENST00000513692.1_Missense_Mutation_p.D440E	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	440					establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		GGAAGACCCCGTCCACCCAGT	0.701																																					p.D440E		Atlas-SNP	.											.	IRX4	45	.	0			c.C1320A						.						9	11	10					5																	1878323		2177	4275	6452	SO:0001583	missense	50805	exon5			GACCCCGTCCACC	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"Homeoboxes / TALE class"	6129	protein-coding gene	gene with protein product		606199	"iroquois homeobox protein 4"			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.1320C>A	chr5.hg19:g.1878323G>T	ENSP00000423161:p.Asp440Glu	60.0	0.0		83.0	49.0	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Missense_Mutation	SNP	ENST00000505790.1	hg19	CCDS3867.1	.	.	.	.	.	.	.	.	.	.	g	15.10	2.733280	0.48939	.	.	ENSG00000113430	ENST00000231357;ENST00000505790;ENST00000513692	T;T;T	0.74421	-0.84;-0.84;-0.84	3.42	0.0782	0.14411	.	0.177118	0.47093	D	0.000247	T	0.80363	0.4609	M	0.66939	2.045	0.44871	D	0.99788	D	0.76494	0.999	D	0.79784	0.993	T	0.76534	-0.2924	10	0.62326	D	0.03	-33.678	6.9326	0.24449	0.464:0.0:0.536:0.0	.	440	P78413	IRX4_HUMAN	E	440	ENSP00000231357:D440E;ENSP00000423161:D440E;ENSP00000424235:D440E	ENSP00000231357:D440E	D	-	3	2	IRX4	1931323	0.883000	0.30277	0.997000	0.53966	0.992000	0.81027	-0.078000	0.11375	-0.094000	0.12374	0.552000	0.68991	GAC	.	.		0.701	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358		T	1878323	G	T	1878323	3	4	218	1	0	0	0	0	1	0	0	0	7855	1136	40	1	243	1	IRX4	5	1878323	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10		1878323	179036937	19	31292										
ADCY2	108	hgsc.bcm.edu	37	chr5	7727323	7727323	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	caagtattatgtgacttgtgCctgtctcatattcttctgca	7	9	3	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr5:7727323C>A	ENST00000338316.4	+	14	1909	c.1820C>A	c.(1819-1821)gCc>gAc	p.A607D	RP11-711G10.1_ENST00000514105.2_RNA|ADCY2_ENST00000537121.1_Missense_Mutation_p.A427D	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	607					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						GTGACTTGTGCCTGTCTCATA	0.507																																					p.A607D		Atlas-SNP	.											.	ADCY2	337	.	0			c.C1820A						.						226	198	207					5																	7727323		2203	4300	6503	SO:0001583	missense	108	exon14			CTTGTGCCTGTCT	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1820C>A	chr5.hg19:g.7727323C>A	ENSP00000342952:p.Ala607Asp	33.0	0.0		49.0	27.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667702	0.88348	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	T;D	0.83335	-1.23;-1.71	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.89949	0.6863	M	0.76328	2.33	0.80722	D	1	D;D	0.63046	0.992;0.991	D;D	0.66497	0.944;0.944	D	0.91224	0.5009	10	0.87932	D	0	.	15.3084	0.74011	0.0:1.0:0.0:0.0	.	427;607	B7Z2C1;Q08462	.;ADCY2_HUMAN	D	607;440;427	ENSP00000342952:A607D;ENSP00000444803:A427D	ENSP00000342952:A607D	A	+	2	0	ADCY2	7780323	1.000000	0.71417	0.512000	0.27736	0.905000	0.53344	6.984000	0.76186	2.329000	0.79093	0.650000	0.86243	GCC	.	.		0.507	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7727323	C	A	7727323	3	1	218	1	0	0	0	0	1	0	0	0	294	739	26	3	1874	3	ADCY2	5	7727323	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	5849000	7727323	173187937	20	31293										
PRDM9	56979	hgsc.bcm.edu	37	chr5	23527109	23527109	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	caggggagaagccctatgtcTgcagggagtgtgggcggggc	20	8	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr5:23527109T>G	ENST00000296682.3	+	11	2094	c.1912T>G	c.(1912-1914)Tgc>Ggc	p.C638G		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	638					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GCCCTATGTCTGCAGGGAGTG	0.622										HNSCC(3;0.000094)																											p.C638G		Atlas-SNP	.											.	PRDM9	344	.	0			c.T1912G						.						21	22	22					5																	23527109		1390	3096	4486	SO:0001583	missense	56979	exon11			TATGTCTGCAGGG	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1912T>G	chr5.hg19:g.23527109T>G	ENSP00000296682:p.Cys638Gly	221.0	0.0		338.0	95.0	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	hg19	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.676972	0.29783	.	.	ENSG00000164256	ENST00000296682	D	0.85258	-1.96	2.47	2.47	0.30058	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39687	N	0.001284	D	0.94420	0.8205	H	0.98525	4.255	0.49582	D	0.999803	D	0.89917	1.0	D	0.97110	1.0	D	0.93924	0.7208	10	0.87932	D	0	-7.045	8.7536	0.34633	0.0:0.0:0.0:1.0	.	638	Q9NQV7	PRDM9_HUMAN	G	638	ENSP00000296682:C638G	ENSP00000296682:C638G	C	+	1	0	PRDM9	23562866	1.000000	0.71417	0.963000	0.40424	0.026000	0.11368	6.072000	0.71238	1.370000	0.46153	0.454000	0.30748	TGC	.	.		0.622	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		G	23527109	T	G	23527109	3	3	218	1	0	0	0	0	1	0	0	0	12475	1580	55	5	1950	5	PRDM9	5	23527109	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	15799786	23527109	157388151	21	31294										
KDM3B	51780	hgsc.bcm.edu	37	chr5	137762974	137762974	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ctacctagctactttgtaagGcctgatctgggccccaagat	9	12	1	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr5:137762974G>T	ENST00000314358.5	+	19	4799	c.4599G>T	c.(4597-4599)agG>agT	p.R1533S	KDM3B_ENST00000394866.1_Missense_Mutation_p.R1189S|KDM3B_ENST00000542866.1_Missense_Mutation_p.R565S	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1533	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						ACTTTGTAAGGCCTGATCTGG	0.458																																					p.R1533S		Atlas-SNP	.											.	KDM3B	177	.	0			c.G4599T						.						97	94	95					5																	137762974		2203	4300	6503	SO:0001583	missense	51780	exon19			TGTAAGGCCTGAT	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.4599G>T	chr5.hg19:g.137762974G>T	ENSP00000326563:p.Arg1533Ser	56.0	0.0		128.0	88.0	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.627529	0.66901	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	D;D;D	0.84516	-1.86;-1.86;-1.86	5.48	1.66	0.24008	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.055875	0.64402	D	0.000002	D	0.90359	0.6983	M	0.86805	2.84	0.58432	D	0.999993	P;D	0.62365	0.827;0.991	B;D	0.70016	0.429;0.967	D	0.86889	0.2047	10	0.62326	D	0.03	-13.5503	3.9957	0.09558	0.345:0.0:0.3879:0.2671	.	1189;1533	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	S	1533;1323;1189;565	ENSP00000326563:R1533S;ENSP00000378335:R1189S;ENSP00000439462:R565S	ENSP00000326563:R1533S	R	+	3	2	KDM3B	137790873	0.982000	0.34865	0.994000	0.49952	0.968000	0.65278	0.180000	0.16860	0.279000	0.22186	-0.126000	0.14955	AGG	.	.		0.458	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		T	137762974	G	T	137762974	3	4	218	1	0	0	0	0	1	0	0	0	8136	1194	42	3	4673	3	KDM3B	5	137762974	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	114235865	137762974	43152286	22	31295										
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140773210	140773210	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tgagggaatcaacggaaaagTggcatacaaattccggaaaa	11	6	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr5:140773210T>C	ENST00000398604.2	+	1	830	c.830T>C	c.(829-831)gTg>gCg	p.V277A	PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	277	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACGGAAAAGTGGCATACAAA	0.433																																					p.V277A		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.T830C						.						71	76	74					5																	140773210		1849	4096	5945	SO:0001583	missense	9708	exon1			GAAAAGTGGCATA	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.830T>C	chr5.hg19:g.140773210T>C	ENSP00000381605:p.Val277Ala	188.0	0.0		369.0	144.0	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	hg19	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	18.12	3.553915	0.65425	.	.	ENSG00000253767	ENST00000398604	T	0.52295	0.67	5.41	5.41	0.78517	Cadherin (4);Cadherin-like (1);	0.000000	0.28624	U	0.014683	T	0.79981	0.4540	H	0.98388	4.22	0.35978	D	0.835798	D;D	0.67145	0.996;0.995	D;P	0.65773	0.938;0.897	D	0.90748	0.4655	10	0.87932	D	0	.	15.117	0.72410	0.0:0.0:0.0:1.0	.	277;277	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	A	277	ENSP00000381605:V277A	ENSP00000381605:V277A	V	+	2	0	PCDHGA8	140753394	0.864000	0.29904	0.709000	0.30452	0.707000	0.40811	5.066000	0.64351	2.064000	0.61679	0.533000	0.62120	GTG	.	.		0.433	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		C	140773210	T	C	140773210	3	2	218	1	0	0	0	0	1	0	0	0	11569	1696	59	2	832	2	PCDHGA8	5	140773210	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	3010236	140773210	40142050	23	31296										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140792981	140792981	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	aggtaggacgcagcttttctCtctgaacccgcgcagcggca	12	13	2	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr5:140792981C>A	ENST00000398610.2	+	1	239	c.239C>A	c.(238-240)tCt>tAt	p.S80Y	PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	80	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCTTTTCTCTCTGAACCCG	0.622																																					p.S80Y		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.C239A						.						61	76	71					5																	140792981		2121	4267	6388	SO:0001583	missense	56106	exon1			TTTTCTCTCTGAA		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.239C>A	chr5.hg19:g.140792981C>A	ENSP00000381611:p.Ser80Tyr	84.0	0.0		242.0	58.0	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	hg19	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	c	15.62	2.887538	0.52014	.	.	ENSG00000253846	ENST00000398610	T	0.29655	1.56	5.89	5.89	0.94794	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.59459	0.2195	M	0.88310	2.945	0.24546	N	0.994044	P;P	0.51791	0.936;0.948	P;P	0.59761	0.771;0.863	T	0.59048	-0.7527	9	0.72032	D	0.01	.	14.6802	0.69012	0.1453:0.8547:0.0:0.0	.	80;80	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	Y	80	ENSP00000381611:S80Y	ENSP00000381611:S80Y	S	+	2	0	PCDHGA10	140773165	0.000000	0.05858	0.977000	0.42913	0.377000	0.30045	0.391000	0.20784	2.788000	0.95919	0.557000	0.71058	TCT	.	.		0.622	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		A	140792981	C	A	140792981	3	1	218	1	0	0	0	0	1	0	0	0	11560	913	32	3	241	3	PCDHGA10	5	140792981	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	19771	140792981	40122279	24	31297										
SH3RF2	153769	hgsc.bcm.edu	37	chr5	145439465	145439465	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	acccctccagtccgggatccCcactctcgtggtaggctccc	9	19	1	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr5:145439465C>T	ENST00000511217.1	+	8	1644	c.1592C>T	c.(1591-1593)cCc>cTc	p.P531L	SH3RF2_ENST00000511705.1_3'UTR|SH3RF2_ENST00000359120.4_Missense_Mutation_p.P531L			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	531					negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCGGGATCCCCACTCTCGTG	0.627																																					p.P531L		Atlas-SNP	.											.	SH3RF2	58	.	0			c.C1592T						.						48	46	47					5																	145439465		2203	4300	6503	SO:0001583	missense	153769	exon9			GGATCCCCACTCT	AL833297	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	26299	protein-coding gene	gene with protein product	"heart protein phosphatase 1-binding protein", "POSH-eliminating RING protein"	613377	"protein phosphatase 1, regulatory subunit 39"	PPP1R39		22128169	Standard	NM_152550		Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	Q8TEC5	OTTHUMG00000129685	ENST00000511217.1:c.1592C>T	chr5.hg19:g.145439465C>T	ENSP00000424497:p.Pro531Leu	69.0	0.0		174.0	41.0	NM_152550	A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Missense_Mutation	SNP	ENST00000511217.1	hg19	CCDS4280.1	.	.	.	.	.	.	.	.	.	.	C	11.81	1.750162	0.30955	.	.	ENSG00000156463	ENST00000359120;ENST00000511217	T;T	0.21734	1.99;1.99	4.89	3.09	0.35607	.	0.199556	0.34725	N	0.003725	T	0.34542	0.0901	L	0.54323	1.7	0.22940	N	0.998535	D;B	0.89917	1.0;0.007	D;B	0.87578	0.998;0.006	T	0.05084	-1.0907	10	0.59425	D	0.04	-14.8596	5.2118	0.15320	0.1749:0.6623:0.0:0.1628	.	22;531	Q8TEC5-2;Q8TEC5	.;SH3R2_HUMAN	L	531	ENSP00000352028:P531L;ENSP00000424497:P531L	ENSP00000352028:P531L	P	+	2	0	SH3RF2	145419658	0.292000	0.24362	0.918000	0.36340	0.685000	0.39939	1.139000	0.31504	1.037000	0.40024	0.536000	0.68110	CCC	.	.		0.627	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550		T	145439465	C	T	145439465	3	4	218	1	0	0	0	0	1	0	0	0	14274	623	22	3	1622	3	SH3RF2	5	145439465	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	4646484	145439465	35475795	25	31298										
TCERG1	10915	hgsc.bcm.edu	37	chr5	145858215	145858215	+	Splice_Site	DEL	A	A	-													0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	atggaggaattgaagaaactAagtaagttttaaattaggaa							TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr5:145858215delA	ENST00000296702.5	+	10	1799	c.1761delA	c.(1759-1761)cta>ct	p.L587fs	TCERG1_ENST00000394421.2_Splice_Site_p.L566fs	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	587					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGAAGAAACTAAGTAAGTTTT	0.343																																					p.L587fs		Atlas-INDEL	.											.	TCERG1	148	.	0			c.1760delT						.						36	38	38					5																	145858215		2201	4298	6499	SO:0001630	splice_region_variant	10915	exon10			.	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.1762+1A>-	chr5.hg19:g.145858215delA		62.0	0.0		176.0	34.0	NM_006706	Q2NKN2|Q59EA1	Frame_Shift_Del	DEL	ENST00000296702.5	hg19	CCDS4282.1																																																																																			.	.		0.343	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006	Frame_Shift_Del	-	145858215	A	-	145858215	8	5	218	1	0	1	0	1	0	0	1	0	15700	376	13	0	1799	0	TCERG1	5	145858215	Splice_Site	DEL	A	TCGA-DD-AAEE-01A-11D-A40R-10	418750	145858215	35057045	26	31299										
EBF1	1879	hgsc.bcm.edu	37	chr5	158139179	158139179	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tactggcatagggggagttgGcagctgagccgttgaggaag	18	6	0	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr5:158139179G>T	ENST00000313708.6	-	14	1814	c.1532C>A	c.(1531-1533)gCc>gAc	p.A511D	EBF1_ENST00000517373.1_Intron|EBF1_ENST00000380654.4_Missense_Mutation_p.A480D|EBF1_ENST00000518836.1_5'UTR	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	511	Pro/Ser/Thr-rich.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGGGGAGTTGGCAGCTGAGCC	0.567			T	HMGA2	lipoma																																p.A511D		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	.	EBF1	110	.	0			c.C1532A						.						63	50	54					5																	158139179		2203	4300	6503	SO:0001583	missense	1879	exon14			GAGTTGGCAGCTG	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"early B-cell factor"	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1532C>A	chr5.hg19:g.158139179G>T	ENSP00000322898:p.Ala511Asp	74.0	0.0		209.0	40.0	NM_024007	Q8IW11	Missense_Mutation	SNP	ENST00000313708.6	hg19	CCDS4343.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.146980	0.57151	.	.	ENSG00000164330	ENST00000318060;ENST00000313708;ENST00000380654	T;T	0.52526	0.66;0.66	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.58104	0.2099	M	0.76328	2.33	0.80722	D	1	B;P;P;B	0.38250	0.0;0.624;0.554;0.214	B;B;B;B	0.43478	0.001;0.307;0.421;0.326	T	0.64322	-0.6435	10	0.62326	D	0.03	-7.8475	18.4976	0.90870	0.0:0.0:1.0:0.0	.	511;498;511;480	A8K0Z7;B4E2U8;Q9UH73;Q9UH73-2	.;.;COE1_HUMAN;.	D	511;511;480	ENSP00000322898:A511D;ENSP00000370029:A480D	ENSP00000322898:A511D	A	-	2	0	EBF1	158071757	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.366000	0.59492	2.428000	0.82296	0.650000	0.86243	GCC	.	.		0.567	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		T	158139179	G	T	158139179	3	4	218	1	0	0	0	0	1	0	0	0	4882	1203	42	3	255	3	EBF1	5	158139179	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	12280964	158139179	22776081	27	31300										
PRELID1	27166	hgsc.bcm.edu	37	chr5	176733526	176733534	+	In_Frame_Del	DEL	CAAGGCGGC	CAAGGCGGC	-													0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	aaggccaaggacctcgccagCaaggcggccaccaagaagca					rs201616411		TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	CAAGGCGGC	CAAGGCGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr5:176733526_176733534delCAAGGCGGC	ENST00000303204.4	+	5	827_835	c.615_623delCAAGGCGGC	c.(613-624)agcaaggcggcc>agc	p.KAA206del	MXD3_ENST00000427908.2_3'UTR|PRELID1_ENST00000503216.1_In_Frame_Del_p.KAA195del|RAB24_ENST00000303251.6_5'Flank|RAB24_ENST00000393611.2_5'Flank|RAB24_ENST00000303270.6_5'Flank			Q9Y255	PRLD1_HUMAN	PRELI domain containing 1	206					apoptotic process (GO:0006915)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitochondrial membrane potential (GO:0010917)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of cellular respiration (GO:1901857)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of T cell apoptotic process (GO:0070234)|regulation of membrane lipid distribution (GO:0097035)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of T cell differentiation (GO:0045580)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(1)|kidney(2)|lung(2)|prostate(1)|stomach(1)	7	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACCTCGCCAGCAAGGCGGCCACCAAGAAG	0.574																																					p.205_208del		Atlas-INDEL	.											.	PRELID1	10	.	0			c.614_622del						.																																			SO:0001651	inframe_deletion	27166	exon5			.	BC013748	CCDS4415.1, CCDS64328.1	5q35.3	2010-01-18			ENSG00000169230	ENSG00000169230			30255	protein-coding gene	gene with protein product	"protein of relevant evolutionary and lymphoid interest", "px19-like protein"	605733				10784606, 14640972	Standard	NM_013237		Approved	CGI-106, PX19, PRELI	uc003mfx.4	Q9Y255	OTTHUMG00000130847	ENST00000303204.4:c.615_623delCAAGGCGGC	chr5.hg19:g.176733526_176733534delCAAGGCGGC	ENSP00000302114:p.Lys206_Ala208del	85.0	0.0		131.0	21.0	NM_013237	B2R5F7|D6RD25|Q549N2|Q9UI13|Q9UJS9	In_Frame_Del	DEL	ENST00000303204.4	hg19	CCDS4415.1																																																																																			.	.		0.574	PRELID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253414.1	NM_013237		-	176733534	CAAGGCGGC	-	176733526	7	5	218	1	0	1	0	1	0	0	0	0	12483	709	25	0	633	0	PRELID1	5	176733526	In_Frame_Del	DEL	CAAGGCGGC	TCGA-DD-AAEE-01A-11D-A40R-10	18594347	176733526	4181734	28	31301										
OR10C1	442194	hgsc.bcm.edu	37	chr6	29408581	29408581	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	atctatattcgccctaaggcCagctacgatccggccactga	8	14	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr6:29408581C>T	ENST00000444197.2	+	1	1499	c.789C>T	c.(787-789)gcC>gcT	p.A263A	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	263						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GCCCTAAGGCCAGCTACGATC	0.582																																					p.A263A		Atlas-SNP	.											.	OR10C1	58	.	0			c.C789T						.						236	260	251					6																	29408581		1511	2709	4220	SO:0001819	synonymous_variant	442194	exon1			TAAGGCCAGCTAC		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"GPCR / Class A : Olfactory receptors"	8165	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily C, member 2", "olfactory receptor, family 10, subfamily C, member 1"	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.789C>T	chr6.hg19:g.29408581C>T		39.0	0.0		71.0	28.0	NM_013941	Q5SUN7|Q96R18	Silent	SNP	ENST00000444197.2	hg19	CCDS34364.1																																																																																			.	.		0.582	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			T	29408581	C	T	29408581	2	4	218	1	0	0	0	0	0	0	0	1	10907	581	21	3		3	OR10C1	6	29408581	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10		29408581	141706486	29	31302										
GPSM3	63940	hgsc.bcm.edu	37	chr6	32160269	32160269	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ctgctcaccatcctcttcttCctggggtctctcagcctcca	6	18	5	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr6:32160269C>A	ENST00000375040.3	-	1	414	c.22G>T	c.(22-24)Gaa>Taa	p.E8*	GPSM3_ENST00000375043.3_Nonsense_Mutation_p.E8*|GPSM3_ENST00000487761.1_5'UTR|PBX2_ENST00000375050.4_5'Flank	NM_001276501.1	NP_001263430.1	Q9Y4H4	GPSM3_HUMAN	G-protein signaling modulator 3	8					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cytoplasm (GO:0005737)	GDP-dissociation inhibitor activity (GO:0005092)			large_intestine(1)	1						TCCTCTTCTTCCTGGGGTCTC	0.617																																					p.E8X		Atlas-SNP	.											.	GPSM3	9	.	0			c.G22T						.						35	24	28					6																	32160269		1510	2708	4218	SO:0001587	stop_gained	63940	exon5			CTTCTTCCTGGGG	AF155657	CCDS34419.1	6p21.3	2010-06-24	2010-06-24	2004-02-04	ENSG00000213654	ENSG00000213654			13945	protein-coding gene	gene with protein product	"activator of G-protein signaling 4"		"chromosome 6 open reading frame 9", "G-protein signalling modulator 3 (AGS3-like, C. elegans)"	C6orf9		2259622, 15096500	Standard	NM_022107		Approved	NG1, G18, G18.1a, G18.1b, G18.2, AGS4	uc003oaz.3	Q9Y4H4	OTTHUMG00000031244	ENST00000375040.3:c.22G>T	chr6.hg19:g.32160269C>A	ENSP00000364180:p.Glu8*	48.0	0.0		46.0	23.0	NM_022107	A2BFJ3	Nonsense_Mutation	SNP	ENST00000375040.3	hg19	CCDS34419.1	.	.	.	.	.	.	.	.	.	.	C	38	6.696739	0.97772	.	.	ENSG00000213654	ENST00000375040;ENST00000375043	.	.	.	3.33	2.45	0.29901	.	0.000000	0.53938	U	0.000042	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-18.7475	6.5847	0.22614	0.0:0.8635:0.0:0.1365	.	.	.	.	X	8	.	ENSP00000364180:E8X	E	-	1	0	GPSM3	32268247	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	0.902000	0.28459	0.748000	0.32831	0.467000	0.42956	GAA	.	.		0.617	GPSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076509.1	NM_022107		A	32160269	C	A	32160269	4	1	218	1	0	0	0	0	0	1	0	0	6745	864	30	3	476	3	GPSM3	6	32160269	Nonsense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	2751688	32160269	138954798	30	31303										
RXRB	6257	hgsc.bcm.edu	37	chr6	33165574	33165574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cagtggccaggcacttctgaTagcggcagtactgacagcgg	14	11	1	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr6:33165574T>C	ENST00000374680.3	-	4	996	c.785A>G	c.(784-786)tAt>tGt	p.Y262C	RXRB_ENST00000413614.2_Missense_Mutation_p.Y166C|RXRB_ENST00000544186.1_Missense_Mutation_p.Y72C|RXRB_ENST00000374685.4_Missense_Mutation_p.Y262C|RNY4P10_ENST00000365571.1_RNA	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	262					cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	GCACTTCTGATAGCGGCAGTA	0.572																																					p.Y262C		Atlas-SNP	.											.	RXRB	34	.	0			c.A785G						.						69	61	64					6																	33165574		1511	2709	4220	SO:0001583	missense	6257	exon4			TTCTGATAGCGGC	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"Nuclear hormone receptors"	10478	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 2"	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.785A>G	chr6.hg19:g.33165574T>C	ENSP00000363812:p.Tyr262Cys	37.0	0.0		92.0	31.0	NM_021976	P28703|Q59G65|Q5JP92|Q5STQ1	Missense_Mutation	SNP	ENST00000374680.3	hg19	CCDS4768.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.459626	0.84317	.	.	ENSG00000204231	ENST00000374685;ENST00000374680;ENST00000544186;ENST00000413614	D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4	4.52	4.52	0.55395	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.000000	0.85682	D	0.000000	D	0.98773	0.9587	H	0.95917	3.74	0.58432	D	0.999997	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;1.0;0.999;0.999;0.998;0.999;0.999;0.999	D	0.99537	1.0962	10	0.87932	D	0	.	12.1371	0.53977	0.0:0.0:0.0:1.0	.	166;262;145;72;262;262;302;262	B7Z3E4;B7Z6J2;B7Z6X3;E9PK95;Q5STQ1;Q5STP9;Q59G65;P28702	.;.;.;.;.;.;.;RXRB_HUMAN	C	262;262;72;166	ENSP00000363817:Y262C;ENSP00000363812:Y262C;ENSP00000439222:Y72C;ENSP00000415561:Y166C	ENSP00000363812:Y262C	Y	-	2	0	RXRB	33273552	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	4.817000	0.62650	2.028000	0.59812	0.368000	0.22195	TAT	.	.		0.572	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		C	33165574	T	C	33165574	3	2	218	1	0	0	0	0	1	0	0	0	13779	1406	49	2	844	2	RXRB	6	33165574	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	1005305	33165574	137949493	31	31304										
UNC5CL	222643	hgsc.bcm.edu	37	chr6	41002766	41002766	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cttgccactgggacccccacCagcagtaggaactgggaggg	14	13	0	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr6:41002766C>T	ENST00000373164.1	-	1	108	c.48G>A	c.(46-48)ctG>ctA	p.L16L	UNC5CL_ENST00000470102.1_5'Flank|UNC5CL_ENST00000244565.3_Silent_p.L16L			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	16					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					GGACCCCCACCAGCAGTAGGA	0.602																																					p.L16L		Atlas-SNP	.											.	UNC5CL	52	.	0			c.G48A						.						57	52	54					6																	41002766		2203	4300	6503	SO:0001819	synonymous_variant	222643	exon2			CCCCACCAGCAGT	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"ZU5 and death domain containing"					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.48G>A	chr6.hg19:g.41002766C>T		37.0	0.0		65.0	21.0	NM_173561	Q5TGU1	Silent	SNP	ENST00000373164.1	hg19	CCDS4847.1																																																																																			.	.		0.602	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561		T	41002766	C	T	41002766	2	4	218	1	0	0	0	0	0	0	0	1	17009	581	21	3		3	UNC5CL	6	41002766	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	7837192	41002766	130112301	32	31305										
PRPH2	5961	hgsc.bcm.edu	37	chr6	42689887	42689887	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	acccccatccctatcaatgaGttgggcacaaaatggctctc	7	14	2	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr6:42689887G>T	ENST00000230381.5	-	1	425	c.186C>A	c.(184-186)aaC>aaA	p.N62K		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	62					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			CTATCAATGAGTTGGGCACAA	0.512																																					p.N62K		Atlas-SNP	.											.	PRPH2	47	.	0			c.C186A						.						128	101	110					6																	42689887		2203	4300	6503	SO:0001583	missense	5961	exon1			CAATGAGTTGGGC		CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"Tetraspanins"	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"retinal degeneration, slow (retinitis pigmentosa 7)", "retinal degeneration, slow"	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.186C>A	chr6.hg19:g.42689887G>T	ENSP00000230381:p.Asn62Lys	75.0	0.0		96.0	47.0	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	hg19	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.631371	0.67015	.	.	ENSG00000112619	ENST00000230381	T	0.79033	-1.23	5.81	1.96	0.26148	.	0.000000	0.85682	D	0.000000	T	0.71091	0.3299	M	0.77820	2.39	0.52501	D	0.999951	P	0.38677	0.642	P	0.48334	0.574	T	0.68588	-0.5369	10	0.30854	T	0.27	.	7.0159	0.24887	0.5358:0.0:0.4642:0.0	.	62	P23942	PRPH2_HUMAN	K	62	ENSP00000230381:N62K	ENSP00000230381:N62K	N	-	3	2	PRPH2	42797865	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.180000	0.50895	0.766000	0.33244	0.655000	0.94253	AAC	.	.		0.512	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322		T	42689887	G	T	42689887	3	4	218	1	0	0	0	0	1	0	0	0	12589	1020	36	3	866	3	PRPH2	6	42689887	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	1687121	42689887	128425180	33	31306										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76023019	76023019	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gatctttccacgggtttcttCaatcccacctgccgaagatt	7	13	3	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr6:76023019C>G	ENST00000237172.7	-	5	2859	c.2529G>C	c.(2527-2529)ttG>ttC	p.L843F	FILIP1_ENST00000393004.2_Missense_Mutation_p.L843F|FILIP1_ENST00000370020.1_Missense_Mutation_p.L744F|FILIP1_ENST00000498523.1_5'UTR	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	843										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						CGGGTTTCTTCAATCCCACCT	0.453																																					p.L843F		Atlas-SNP	.											.	FILIP1	173	.	0			c.G2529C						.						125	138	133					6																	76023019		2203	4300	6503	SO:0001583	missense	27145	exon5			TTTCTTCAATCCC	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.2529G>C	chr6.hg19:g.76023019C>G	ENSP00000237172:p.Leu843Phe	114.0	0.0		137.0	47.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	hg19	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	C	6.050	0.377539	0.11466	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.20200	2.09;2.09;2.09	5.66	4.6	0.57074	.	0.071794	0.56097	D	0.000036	T	0.05731	0.0150	L	0.47716	1.5	0.48571	D	0.999674	P;B;B	0.35050	0.482;0.07;0.044	B;B;B	0.26202	0.066;0.03;0.067	T	0.08432	-1.0722	10	0.09843	T	0.71	-13.0594	7.7235	0.28746	0.1456:0.7108:0.0:0.1437	.	843;843;843	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	F	843;843;744	ENSP00000376728:L843F;ENSP00000237172:L843F;ENSP00000359037:L744F	ENSP00000237172:L843F	L	-	3	2	FILIP1	76079739	1.000000	0.71417	0.820000	0.32676	0.710000	0.40934	0.852000	0.27764	2.678000	0.91216	0.563000	0.77884	TTG	.	.		0.453	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		G	76023019	C	G	76023019	3	3	218	1	0	0	0	0	1	0	0	0	5902	825	29	4	1120	4	FILIP1	6	76023019	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	33333132	76023019	95092048	34	31307										
FBXL4	26235	hgsc.bcm.edu	37	chr6	99323549	99323549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tctccacagatccagggtccGgagttttttacacttggctc	9	12	1	1	rs398123061		TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr6:99323549G>A	ENST00000369244.2	-	9	1872	c.1444C>T	c.(1444-1446)Cgg>Tgg	p.R482W	FBXL4_ENST00000229971.1_Missense_Mutation_p.R482W	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	482			R -> W (in MTDPS13). {ECO:0000269|PubMed:23993194}.		ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		TCCAGGGTCCGGAGTTTTTTA	0.423																																					p.R482W		Atlas-SNP	.											.	FBXL4	54	.	0			c.C1444T						.						75	77	76					6																	99323549		2202	4300	6502	SO:0001583	missense	26235	exon8			GGGTCCGGAGTTT	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"F-boxes / Leucine-rich repeats"	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.1444C>T	chr6.hg19:g.99323549G>A	ENSP00000358247:p.Arg482Trp	62.0	0.0		92.0	11.0	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	hg19	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002275	0.74932	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.03717	3.83;3.83	6.02	5.13	0.70059	.	0.150727	0.64402	D	0.000009	T	0.12390	0.0301	M	0.84683	2.71	0.58432	D	0.999998	D;D	0.76494	0.999;0.997	D;P	0.63033	0.91;0.723	T	0.01621	-1.1310	10	0.72032	D	0.01	.	16.4802	0.84156	0.0:0.0:0.8678:0.1322	.	482;482	B2R7Q5;Q9UKA2	.;FBXL4_HUMAN	W	482	ENSP00000358247:R482W;ENSP00000229971:R482W	ENSP00000229971:R482W	R	-	1	2	FBXL4	99430270	0.995000	0.38212	0.790000	0.31976	0.998000	0.95712	3.342000	0.52159	1.513000	0.48852	0.591000	0.81541	CGG	.	.		0.423	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			A	99323549	G	A	99323549	3	1	218	1	0	0	0	0	1	0	0	0	5729	1115	39	1	429	1	FBXL4	6	99323549	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	23300530	99323549	71791518	35	31308										
SASH1	23328	hgsc.bcm.edu	37	chr6	148855918	148855918	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cactttcctgttcaatggatAtgaagatttggacaccttta	7	8	1	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr6:148855918A>G	ENST00000367467.3	+	16	2451	c.1976A>G	c.(1975-1977)tAt>tGt	p.Y659C		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	659	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		TTCAATGGATATGAAGATTTG	0.498																																					p.Y659C		Atlas-SNP	.											.	SASH1	123	.	0			c.A1976G						.						132	126	128					6																	148855918		2203	4300	6503	SO:0001583	missense	23328	exon16			ATGGATATGAAGA	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1976A>G	chr6.hg19:g.148855918A>G	ENSP00000356437:p.Tyr659Cys	60.0	0.0		43.0	36.0	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	hg19	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.394954	0.83011	.	.	ENSG00000111961	ENST00000367467;ENST00000535767;ENST00000537769	D	0.84589	-1.87	5.15	5.15	0.70609	Src homology-3 domain (1);Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.92811	0.7714	M	0.91663	3.23	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94493	0.7703	10	0.87932	D	0	-12.6465	15.0027	0.71486	1.0:0.0:0.0:0.0	.	640;659	Q6P4R9;O94885	.;SASH1_HUMAN	C	659;420;69	ENSP00000356437:Y659C	ENSP00000356437:Y659C	Y	+	2	0	SASH1	148897611	1.000000	0.71417	0.985000	0.45067	0.989000	0.77384	7.306000	0.78905	1.953000	0.56701	0.459000	0.35465	TAT	.	.		0.498	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		G	148855918	A	G	148855918	3	3	218	1	0	0	0	0	1	0	0	0	13863	449	16	2	2038	2	SASH1	6	148855918	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	49532369	148855918	22259149	36	31309										
LATS1	9113	hgsc.bcm.edu	37	chr6	150001298	150001298	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ccttatcttggaatgaataaTatagacgaactacccattca	5	9	2	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr6:150001298T>C	ENST00000543571.1	-	5	2853	c.2306A>G	c.(2305-2307)tAt>tGt	p.Y769C	LATS1_ENST00000253339.5_Missense_Mutation_p.Y769C|LATS1_ENST00000542747.1_5'UTR	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		GAATGAATAATATAGACGAAC	0.383																																					p.Y769C		Atlas-SNP	.											.	LATS1	241	.	0			c.A2306G						.						123	122	122					6																	150001298		2203	4300	6503	SO:0001583	missense	9113	exon5			GAATAATATAGAC	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2306A>G	chr6.hg19:g.150001298T>C	ENSP00000437550:p.Tyr769Cys	88.0	0.0		82.0	61.0	NM_004690		Missense_Mutation	SNP	ENST00000543571.1	hg19	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	T	19.73	3.882206	0.72294	.	.	ENSG00000131023	ENST00000543571;ENST00000253339	T;T	0.09723	2.95;2.95	5.5	5.5	0.81552	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.51477	D	0.000091	T	0.21186	0.0510	M	0.64404	1.975	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	T	0.00662	-1.1621	9	.	.	.	.	15.9043	0.79412	0.0:0.0:0.0:1.0	.	769	O95835	LATS1_HUMAN	C	769	ENSP00000437550:Y769C;ENSP00000253339:Y769C	.	Y	-	2	0	LATS1	150042991	1.000000	0.71417	0.993000	0.49108	0.970000	0.65996	7.655000	0.83696	2.203000	0.70933	0.460000	0.39030	TAT	.	.		0.383	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		C	150001298	T	C	150001298	3	2	218	1	0	0	0	0	1	0	0	0	8655	1406	49	2	1102	2	LATS1	6	150001298	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	1145380	150001298	21113769	37	31310										
CREB5	9586	hgsc.bcm.edu	37	chr7	28843947	28843947	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	catcacatgcactcgcacccGcatcagcaccagacactgcc	6	19	2	1	rs139638068		TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr7:28843947G>T	ENST00000357727.2	+	8	1224	c.834G>T	c.(832-834)ccG>ccT	p.P278P	CREB5_ENST00000396299.2_Silent_p.P245P|CREB5_ENST00000396298.2_Silent_p.P139P|CREB5_ENST00000409603.1_Silent_p.P245P|CREB5_ENST00000396300.2_Silent_p.P271P	NM_182898.2	NP_878901.2	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	278					adipose tissue development (GO:0060612)|fat cell differentiation (GO:0045444)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(13)|prostate(1)|skin(3)	32						actcgcacccgcatcagcacc	0.587																																					p.P278P		Atlas-SNP	.											.	CREB5	115	.	0			c.G834T						.						565	342	417					7																	28843947		2203	4300	6503	SO:0001819	synonymous_variant	9586	exon8			GCACCCGCATCAG	L05515	CCDS5417.1, CCDS5418.1, CCDS43562.1, CCDS43563.1	7p15	2013-01-10			ENSG00000146592	ENSG00000146592		"basic leucine zipper proteins"	16844	protein-coding gene	gene with protein product	"cAMP response element binding protein CRE-Bpa"					8378084, 8440710	Standard	XM_005249906		Approved	H_GS165L15.1, CRE-BPA	uc003szr.3	Q02930	OTTHUMG00000097081	ENST00000357727.2:c.834G>T	chr7.hg19:g.28843947G>T		77.0	0.0		143.0	59.0	NM_182898	A8KA51|B4DU13|B5BUH3|C9JK47|Q05886|Q06246|Q75N02|Q86UJ9	Silent	SNP	ENST00000357727.2	hg19	CCDS5417.1																																																																																			.	G|1.000;A|0.000		0.587	CREB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214204.4	NM_004904		T	28843947	G	T	28843947	2	4	218	1	0	0	0	0	0	0	0	1	3862	1074	38	1		1	CREB5	7	28843947	Silent	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10		28843947	130294716	38	31311										
CUX1	1523	hgsc.bcm.edu	37	chr7	101845470	101845470	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	agaacggcatctgccagagaAtcttcggggagaaggtaagg	15	7	2	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr7:101845470A>G	ENST00000292535.7	+	18	2931	c.2893A>G	c.(2893-2895)Atc>Gtc	p.I965V	CUX1_ENST00000550008.2_Missense_Mutation_p.I909V|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Missense_Mutation_p.I863V|CUX1_ENST00000360264.3_Missense_Mutation_p.I976V|CUX1_ENST00000549414.2_Missense_Mutation_p.I943V|CUX1_ENST00000556210.1_Missense_Mutation_p.I807V|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	965					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						CTGCCAGAGAATCTTCGGGGA	0.567																																					p.I976V		Atlas-SNP	.											.	CUX1	253	.	0			c.A2926G						.						72	79	76					7																	101845470		2203	4300	6503	SO:0001583	missense	1523	exon18			CAGAGAATCTTCG	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.2893A>G	chr7.hg19:g.101845470A>G	ENSP00000292535:p.Ile965Val	85.0	0.0		97.0	46.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494025	0.64186	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.61859	0.08;0.09;0.07;0.07;0.07;0.08	5.14	5.14	0.70334	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	T	0.62307	0.2417	N	0.25825	0.765	0.80722	D	1	P;P	0.45348	0.856;0.826	P;P	0.60949	0.881;0.811	T	0.61836	-0.6981	10	0.37606	T	0.19	-22.5499	14.9669	0.71201	1.0:0.0:0.0:0.0	.	965;976	P39880;P39880-3	CUX1_HUMAN;.	V	976;965;943;909;863;807	ENSP00000353401:I976V;ENSP00000292535:I965V;ENSP00000446630:I943V;ENSP00000447373:I909V;ENSP00000450125:I863V;ENSP00000451558:I807V	ENSP00000292535:I965V	I	+	1	0	CUX1	101632190	1.000000	0.71417	0.987000	0.45799	0.956000	0.61745	7.000000	0.76290	1.953000	0.56701	0.533000	0.62120	ATC	.	.		0.567	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		G	101845470	A	G	101845470	3	3	218	1	0	0	0	0	1	0	0	0	4066	101	4	2	3030	2	CUX1	7	101845470	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	73001523	101845470	57293193	39	31312										
TTC26	79989	hgsc.bcm.edu	37	chr7	138849981	138849981	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gatttactaccttcgtcaagGtaagaaaaatttgtcctggt	8	7	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr7:138849981G>T	ENST00000464848.1	+	9	975		c.e9+1		TTC26_ENST00000495038.1_Splice_Site|TTC26_ENST00000343187.4_Splice_Site|TTC26_ENST00000430935.1_Splice_Site|TTC26_ENST00000478836.2_Splice_Site|TTC26_ENST00000481482.1_Splice_Site			A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26						cilium assembly (GO:0042384)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle B (GO:0030992)|primary cilium (GO:0072372)				breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	24						CTTCGTCAAGGTAAGAAAAAT	0.378																																					.		Atlas-SNP	.											.	TTC26	50	.	0			c.895+1G>T						.						106	94	98					7																	138849981		2203	4300	6503	SO:0001630	splice_region_variant	79989	exon9			GTCAAGGTAAGAA	AK022633	CCDS5852.1, CCDS55172.1, CCDS55173.1, CCDS75665.1	7q34	2013-01-11			ENSG00000105948	ENSG00000105948		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	21882	protein-coding gene	gene with protein product							Standard	NM_001144920		Approved	FLJ12571, dyf-13, DYF13	uc003vus.2	A0AVF1	OTTHUMG00000157472	ENST00000464848.1:c.895+1G>T	chr7.hg19:g.138849981G>T		50.0	0.0		95.0	40.0	NM_001144920	A4D1S3|B7Z5M0|C9J2N7|F8W724|Q9H9S8|Q9NTC0	Splice_Site	SNP	ENST00000464848.1	hg19	CCDS5852.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.169242	0.78339	.	.	ENSG00000105948	ENST00000430935;ENST00000495038;ENST00000478836;ENST00000464848;ENST00000343187	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0069	0.86395	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TTC26	138500521	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	8.740000	0.91579	2.384000	0.81235	0.655000	0.94253	.	.	.		0.378	TTC26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348919.2	NM_024926	Intron	T	138849981	G	T	138849981	5	4	218	1	0	0	0	0	0	0	1	0	16709	1275	44	3	930	3	TTC26	7	138849981	Splice_Site	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	37004511	138849981	20288682	40	31313										
CLCN1	1180	hgsc.bcm.edu	37	chr7	143018842	143018842	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gaaatgaagacaatacttcgTggggttgtcctgaaggaata	12	5	0	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr7:143018842T>A	ENST00000343257.2	+	5	684	c.597T>A	c.(595-597)cgT>cgA	p.R199R	CLCN1_ENST00000495612.1_3'UTR	NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	199					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					CAATACTTCGTGGGGTTGTCC	0.517																																					p.R199R		Atlas-SNP	.											.	CLCN1	141	.	0			c.T597A						.						90	77	81					7																	143018842		2203	4300	6503	SO:0001819	synonymous_variant	1180	exon5			ACTTCGTGGGGTT	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.597T>A	chr7.hg19:g.143018842T>A		82.0	0.0		99.0	10.0	NM_000083	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	hg19	CCDS5881.1																																																																																			.	.		0.517	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		A	143018842	T	A	143018842	2	1	218	1	0	0	0	0	0	0	0	1	3464	1683	59	4		4	CLCN1	7	143018842	Silent	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	4168861	143018842	16119821	41	31314										
GIMAP7	168537	hgsc.bcm.edu	37	chr7	150217878	150217878	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gaagaagctgagagaaatatAtttaaagatgtttttaatag	9	1	0	4			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr7:150217878A>G	ENST00000313543.4	+	2	973	c.816A>G	c.(814-816)atA>atG	p.I272M		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	272					GTP catabolic process (GO:0006184)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGAGAAATATATTTAAAGATG	0.249																																					p.I272M		Atlas-SNP	.											.	GIMAP7	47	.	0			c.A816G						.						31	34	33					7																	150217878		2191	4264	6455	SO:0001583	missense	168537	exon2			AAATATATTTAAA	BC027613	CCDS5903.1	7q36.1	2014-04-04			ENSG00000179144	ENSG00000179144		"GTPases, IMAP"	22404	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 7"					15474311	Standard	NM_153236		Approved	MGC27027, IAN7	uc003whk.3	Q8NHV1	OTTHUMG00000157626	ENST00000313543.4:c.816A>G	chr7.hg19:g.150217878A>G	ENSP00000315474:p.Ile272Met	67.0	0.0		139.0	54.0	NM_153236		Missense_Mutation	SNP	ENST00000313543.4	hg19	CCDS5903.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.262019	0.39995	.	.	ENSG00000179144	ENST00000313543	T	0.05855	3.38	4.94	1.07	0.20283	.	0.514735	0.19268	N	0.118497	T	0.09992	0.0245	M	0.71581	2.175	0.09310	N	1	D	0.56521	0.976	P	0.49853	0.624	T	0.15178	-1.0446	10	0.38643	T	0.18	.	3.2226	0.06721	0.6342:0.0:0.1926:0.1731	.	272	Q8NHV1	GIMA7_HUMAN	M	272	ENSP00000315474:I272M	ENSP00000315474:I272M	I	+	3	3	GIMAP7	149848811	0.002000	0.14202	0.002000	0.10522	0.004000	0.04260	0.676000	0.25247	0.393000	0.25203	0.528000	0.53228	ATA	.	.		0.249	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236		G	150217878	A	G	150217878	3	3	218	1	0	0	0	0	1	0	0	0	6392	439	16	2	818	2	GIMAP7	7	150217878	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	7199036	150217878	8920785	42	31315										
JPH1	56704	hgsc.bcm.edu	37	chr8	75157174	75157174	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ctgctcatcagccacactccTtttgtcttggttgagtctcg	8	13	4	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr8:75157174T>C	ENST00000342232.4	-	4	1535	c.1495A>G	c.(1495-1497)Agg>Ggg	p.R499G	JPH1_ENST00000518195.1_5'Flank	NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	499					calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			GCCACACTCCTTTTGTCTTGG	0.562																																					p.R499G		Atlas-SNP	.											.	JPH1	77	.	0			c.A1495G						.						130	109	116					8																	75157174		2203	4300	6503	SO:0001583	missense	56704	exon4			CACTCCTTTTGTC	AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.1495A>G	chr8.hg19:g.75157174T>C	ENSP00000344488:p.Arg499Gly	61.0	0.0		136.0	39.0	NM_020647	B2RTZ0	Missense_Mutation	SNP	ENST00000342232.4	hg19	CCDS6217.1	.	.	.	.	.	.	.	.	.	.	T	10.59	1.393460	0.25205	.	.	ENSG00000104369	ENST00000342232	T	0.56941	0.43	5.16	-0.266	0.12942	.	0.522889	0.20754	N	0.086299	T	0.32645	0.0836	N	0.14661	0.345	0.18873	N	0.999985	B	0.17667	0.023	B	0.16289	0.015	T	0.13818	-1.0495	10	0.23302	T	0.38	.	14.6527	0.68808	0.0:0.0:0.503:0.497	.	499	Q9HDC5	JPH1_HUMAN	G	499	ENSP00000344488:R499G	ENSP00000344488:R499G	R	-	1	2	JPH1	75319728	1.000000	0.71417	0.565000	0.28409	0.996000	0.88848	1.364000	0.34171	-0.172000	0.10779	0.528000	0.53228	AGG	.	.		0.562	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1			C	75157174	T	C	75157174	3	2	218	1	0	0	0	0	1	0	0	0	7969	1608	56	2	498	2	JPH1	8	75157174	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10		75157174	71206848	43	31316										
DGAT1	8694	hgsc.bcm.edu	37	chr8	145541100	145541100	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	aagatgagccagatgaggtgAttggggacctggcagggagg	19	5	0	5			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr8:145541100A>C	ENST00000332324.4	-	13	1263	c.990T>G	c.(988-990)aaT>aaG	p.N330K	GS1-393G12.12_ENST00000525023.1_RNA|DGAT1_ENST00000527438.1_5'Flank	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1	330					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	diacylglycerol O-acyltransferase activity (GO:0004144)|retinol O-fatty-acyltransferase activity (GO:0050252)|transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			AGATGAGGTGATTGGGGACCT	0.602																																					p.N330K		Atlas-SNP	.											.	DGAT1	26	.	0			c.T990G						.						102	116	111					8																	145541100		2203	4296	6499	SO:0001583	missense	8694	exon13			GAGGTGATTGGGG	AF059202	CCDS6420.1	8q24.3	2014-05-06	2010-06-24	2001-11-09	ENSG00000185000	ENSG00000185000	2.3.1.20		2843	protein-coding gene	gene with protein product		604900	"diacylglycerol O-acyltransferase homolog 1 (mouse)"			9756920	Standard	NM_012079		Approved	ARGP1, DGAT	uc003zbv.3	O75907	OTTHUMG00000174606	ENST00000332324.4:c.990T>G	chr8.hg19:g.145541100A>C	ENSP00000332258:p.Asn330Lys	25.0	0.0		63.0	31.0	NM_012079	B2RWQ2|D3DWL6|Q96BB8	Missense_Mutation	SNP	ENST00000332324.4	hg19	CCDS6420.1	.	.	.	.	.	.	.	.	.	.	A	15.96	2.986902	0.53934	.	.	ENSG00000185000	ENST00000332324	T	0.72725	-0.68	5.12	-1.06	0.10002	.	0.094443	0.64402	D	0.000001	D	0.83972	0.5370	M	0.91354	3.2	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83392	0.0018	10	0.87932	D	0	-15.1327	10.1934	0.43041	0.551:0.0:0.449:0.0	.	330	O75907	DGAT1_HUMAN	K	330	ENSP00000332258:N330K	ENSP00000332258:N330K	N	-	3	2	DGAT1	145511908	0.994000	0.37717	0.993000	0.49108	0.611000	0.37282	0.249000	0.18216	-0.273000	0.09246	-1.070000	0.02257	AAT	.	.		0.602	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	NM_012079		C	145541100	A	C	145541100	3	2	218	1	0	0	0	0	1	0	0	0	4459	330	12	5	496	5	DGAT1	8	145541100	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	70383926	145541100	822922	44	31317										
ZNF462	58499	hgsc.bcm.edu	37	chr9	109691842	109691842	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gacttcatcattctgggcaaCggcccccgcttgcagaactc	9	15	3	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr9:109691842C>T	ENST00000277225.5	+	3	5938	c.5649C>T	c.(5647-5649)aaC>aaT	p.N1883N	ZNF462_ENST00000457913.1_Silent_p.N1883N|ZNF462_ENST00000441147.2_Silent_p.N728N			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1883					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						TTCTGGGCAACGGCCCCCGCT	0.517																																					p.N1883N		Atlas-SNP	.											.	ZNF462	322	.	0			c.C5649T						.						91	77	82					9																	109691842		2203	4300	6503	SO:0001819	synonymous_variant	58499	exon3			GGGCAACGGCCCC	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.5649C>T	chr9.hg19:g.109691842C>T		58.0	0.0		99.0	5.0	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	hg19	CCDS35096.1																																																																																			.	.		0.517	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		T	109691842	C	T	109691842	2	4	218	1	0	0	0	0	0	0	0	1	17941	535	19	1		1	ZNF462	9	109691842	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10		109691842	31521589	45	31318										
CTNNAL1	8727	hgsc.bcm.edu	37	chr9	111761413	111761413	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	atcccagttttcattggctaTagcttctcctactttaacaa	4	11	2	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr9:111761413T>C	ENST00000325551.4	-	2	351	c.265A>G	c.(265-267)Ata>Gta	p.I89V	CTNNAL1_ENST00000325580.6_Missense_Mutation_p.I89V|CTNNAL1_ENST00000374593.4_Missense_Mutation_p.I89V|CTNNAL1_ENST00000374595.4_Missense_Mutation_p.I89V	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	89					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		TCATTGGCTATAGCTTCTCCT	0.353																																					p.I89V		Atlas-SNP	.											.	CTNNAL1	51	.	0			c.A265G						.						165	163	164					9																	111761413		2203	4300	6503	SO:0001583	missense	8727	exon2			TGGCTATAGCTTC	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.265A>G	chr9.hg19:g.111761413T>C	ENSP00000320434:p.Ile89Val	86.0	0.0		165.0	72.0	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	hg19	CCDS6775.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.601433	0.87055	.	.	ENSG00000119326	ENST00000374595;ENST00000325551;ENST00000325580;ENST00000374593	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.69024	0.3065	M	0.86864	2.845	0.80722	D	1	D;D;D	0.76494	0.993;0.999;0.993	D;D;D	0.87578	0.987;0.998;0.987	T	0.73525	-0.3955	10	0.54805	T	0.06	-22.9378	14.5927	0.68378	0.0:0.0:0.0:1.0	.	89;89;89	B2RBI4;Q9UBT7-2;Q9UBT7	.;.;CTNL1_HUMAN	V	89	ENSP00000363723:I89V;ENSP00000320434:I89V;ENSP00000323351:I89V;ENSP00000363721:I89V	ENSP00000320434:I89V	I	-	1	0	CTNNAL1	110801234	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.005000	0.88553	2.326000	0.78906	0.533000	0.62120	ATA	.	.		0.353	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		C	111761413	T	C	111761413	3	2	218	1	0	0	0	0	1	0	0	0	4017	1406	49	2	2011	2	CTNNAL1	9	111761413	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	2069571	111761413	29452018	46	31319										
SETX	23064	hgsc.bcm.edu	37	chr9	135156934	135156934	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gcgatggatgagtggagtaaGagtctcaatttcacaagact	12	6	2	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr9:135156934G>C	ENST00000224140.5	-	20	6756	c.6574C>G	c.(6574-6576)Ctt>Gtt	p.L2192V	SETX_ENST00000393220.1_Missense_Mutation_p.L2192V|SETX_ENST00000372169.2_Missense_Mutation_p.L2192V	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2192					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		AGTGGAGTAAGAGTCTCAATT	0.398																																					p.L2192V		Atlas-SNP	.											.	SETX	234	.	0			c.C6574G						.						114	105	108					9																	135156934		2203	4300	6503	SO:0001583	missense	23064	exon20			GAGTAAGAGTCTC	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.6574C>G	chr9.hg19:g.135156934G>C	ENSP00000224140:p.Leu2192Val	110.0	0.0		149.0	58.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.006883	0.74932	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.90197	-2.63;-2.63;-2.63;-2.63	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000002	D	0.95595	0.8568	M	0.81942	2.565	0.49389	D	0.999789	D;D;D	0.76494	0.993;0.996;0.999	D;D;D	0.83275	0.983;0.97;0.996	D	0.95822	0.8850	10	0.87932	D	0	.	18.5257	0.90971	0.0:0.0:1.0:0.0	.	2192;2192;2192	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	V	2192;434;2192;2192	ENSP00000224140:L2192V;ENSP00000409143:L434V;ENSP00000361242:L2192V;ENSP00000376913:L2192V	ENSP00000224140:L2192V	L	-	1	0	SETX	134146755	1.000000	0.71417	0.076000	0.20297	0.929000	0.56500	3.989000	0.56958	2.626000	0.88956	0.650000	0.86243	CTT	.	.		0.398	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		C	135156934	G	C	135156934	3	2	218	1	0	0	0	0	1	0	0	0	14156	942	33	4	1487	4	SETX	9	135156934	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	23395521	135156934	6056497	47	31320										
GTF3C4	9329	hgsc.bcm.edu	37	chr9	135554698	135554698	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	caagaagctttggaaaaaaaGattgaaagcagtggagtcac	11	5	1	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr9:135554698G>T	ENST00000372146.4	+	2	2256	c.1692G>T	c.(1690-1692)aaG>aaT	p.K564N		NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	564					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		TGGAAAAAAAGATTGAAAGCA	0.353																																					p.K564N	Pancreas(142;417 1875 11086 31973 47667)	Atlas-SNP	.											.	GTF3C4	53	.	0			c.G1692T						.						89	101	97					9																	135554698		2203	4298	6501	SO:0001583	missense	9329	exon2			AAAAAAGATTGAA	AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"Chromatin-modifying enzymes / K-acetyltransferases", "General transcription factors"	4667	protein-coding gene	gene with protein product		604892	"general transcription factor IIIC, polypeptide 4 (90kD)"			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.1692G>T	chr9.hg19:g.135554698G>T	ENSP00000361219:p.Lys564Asn	66.0	0.0		107.0	39.0	NM_012204	Q5VZJ7	Missense_Mutation	SNP	ENST00000372146.4	hg19	CCDS6953.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.805767	0.50421	.	.	ENSG00000125484	ENST00000372146	T	0.53206	0.63	5.69	4.78	0.61160	.	0.044883	0.85682	D	0.000000	T	0.51126	0.1656	N	0.24115	0.695	0.52501	D	0.999959	D	0.76494	0.999	D	0.64144	0.922	T	0.48969	-0.8987	10	0.44086	T	0.13	-42.4157	13.8581	0.63542	0.0757:0.0:0.9243:0.0	.	564	Q9UKN8	TF3C4_HUMAN	N	564	ENSP00000361219:K564N	ENSP00000361219:K564N	K	+	3	2	GTF3C4	134544519	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.928000	0.63447	2.696000	0.92011	0.655000	0.94253	AAG	.	.		0.353	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1			T	135554698	G	T	135554698	3	4	218	1	0	0	0	0	1	0	0	0	6884	933	33	3	1698	3	GTF3C4	9	135554698	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	397764	135554698	5658733	48	31321										
ARMC4	55130	hgsc.bcm.edu	37	chr10	28276331	28276331	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tcaccttcaacacatgcttgGgcttccttcaacttcccagt	5	15	3	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr10:28276331G>T	ENST00000305242.5	-	3	458	c.366C>A	c.(364-366)gcC>gcA	p.A122A	ARMC4_ENST00000239715.3_5'UTR	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	122					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						CACATGCTTGGGCTTCCTTCA	0.428																																					p.A122A		Atlas-SNP	.											.	ARMC4	177	.	0			c.C366A						.						85	79	81					10																	28276331		2203	4300	6503	SO:0001819	synonymous_variant	55130	exon3			TGCTTGGGCTTCC	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"Armadillo repeat containing"	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.366C>A	chr10.hg19:g.28276331G>T		66.0	0.0		96.0	36.0	NM_018076	A8K906|B7Z7I1|Q9H0C0	Silent	SNP	ENST00000305242.5	hg19	CCDS7157.1																																																																																			.	.		0.428	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076		T	28276331	G	T	28276331	2	4	218	1	0	0	0	0	0	0	0	1	953	1219	43	3		3	ARMC4	10	28276331	Silent	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10		28276331	107258416	49	31322										
ANK3	288	hgsc.bcm.edu	37	chr10	61831548	61831548	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	aggtgggcataaacctacatAactctggtgtttggaaactt	10	7	1	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr10:61831548A>G	ENST00000280772.2	-	37	9282	c.9091T>C	c.(9091-9093)Tat>Cat	p.Y3031H	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3031					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						AAACCTACATAACTCTGGTGT	0.413																																					p.Y3031H		Atlas-SNP	.											.	ANK3	703	.	0			c.T9091C						.						73	80	78					10																	61831548		2203	4300	6503	SO:0001583	missense	288	exon37			CTACATAACTCTG	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.9091T>C	chr10.hg19:g.61831548A>G	ENSP00000280772:p.Tyr3031His	40.0	0.0		73.0	32.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.608454	0.46527	.	.	ENSG00000151150	ENST00000280772	T	0.63744	-0.06	5.36	5.36	0.76844	.	0.201611	0.24678	N	0.036481	T	0.38026	0.1025	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27806	-1.0063	10	0.15499	T	0.54	.	9.8113	0.40824	0.923:0.0:0.077:0.0	.	3031	Q12955	ANK3_HUMAN	H	3031	ENSP00000280772:Y3031H	ENSP00000280772:Y3031H	Y	-	1	0	ANK3	61501554	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	2.745000	0.47459	2.034000	0.60081	0.379000	0.24179	TAT	.	.		0.413	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		G	61831548	A	G	61831548	3	3	218	1	0	0	0	0	1	0	0	0	622	362	13	2	4383	2	ANK3	10	61831548	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	33555217	61831548	73703199	50	31323										
CPEB3	22849	hgsc.bcm.edu	37	chr10	93999597	93999597	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ctgtgccggctgcggcgcggGcgcaggcggcggcggctgct	21	14	0	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr10:93999597G>A	ENST00000265997.4	-	2	683	c.511C>T	c.(511-513)Ccc>Tcc	p.P171S	CPEB3_ENST00000412050.4_Missense_Mutation_p.P171S	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	171	Ala-rich.|Pro-rich.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				tgcggcgcgggcgcaggcggc	0.741																																					p.P171S		Atlas-SNP	.											.	CPEB3	43	.	0			c.C511T						.						4	6	5					10																	93999597		1859	3716	5575	SO:0001583	missense	22849	exon2			GCGCGGGCGCAGG	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.511C>T	chr10.hg19:g.93999597G>A	ENSP00000265997:p.Pro171Ser	35.0	0.0		36.0	18.0	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	hg19	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	G	2.709	-0.269251	0.05716	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.44881	0.91;0.92	0.926	0.926	0.19430	.	0.410133	0.19134	N	0.121880	T	0.28764	0.0713	N	0.08118	0	0.23210	N	0.998117	B;P;P	0.51449	0.002;0.909;0.945	B;P;P	0.56648	0.001;0.641;0.803	T	0.12553	-1.0543	10	0.20046	T	0.44	-6.0617	5.1721	0.15116	0.0:0.0:1.0:0.0	.	171;171;171	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	S	171	ENSP00000398310:P171S;ENSP00000265997:P171S	ENSP00000265997:P171S	P	-	1	0	CPEB3	93989577	0.987000	0.35691	0.984000	0.44739	0.484000	0.33280	-0.229000	0.09098	0.770000	0.33336	0.313000	0.20887	CCC	.	.		0.741	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		A	93999597	G	A	93999597	3	1	218	1	0	0	0	0	1	0	0	0	3804	1203	42	3	1648	3	CPEB3	10	93999597	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	32168049	93999597	41535150	51	31324										
DOCK1	1793	hgsc.bcm.edu	37	chr10	129179616	129179616	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ggcttacaccttgcttctccAtgcaaagcttcttaaggtaa	7	11	2	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr10:129179616A>G	ENST00000280333.6	+	37	3837	c.3728A>G	c.(3727-3729)cAt>cGt	p.H1243R		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1243	DHR-2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TTGCTTCTCCATGCAAAGCTT	0.368																																					p.H1243R		Atlas-SNP	.											.	DOCK1	188	.	0			c.A3728G						.						149	139	142					10																	129179616		1860	4112	5972	SO:0001583	missense	1793	exon37			TTCTCCATGCAAA	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.3728A>G	chr10.hg19:g.129179616A>G	ENSP00000280333:p.His1243Arg	45.0	0.0		66.0	28.0	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	hg19		.	.	.	.	.	.	.	.	.	.	A	21.3	4.125409	0.77436	.	.	ENSG00000150760	ENST00000280333	T	0.26223	1.75	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.61388	0.2343	M	0.93763	3.455	0.80722	D	1	D;D;D	0.89917	1.0;0.994;1.0	D;P;D	0.97110	0.992;0.781;1.0	T	0.73212	-0.4054	10	0.87932	D	0	.	14.7436	0.69474	1.0:0.0:0.0:0.0	.	1243;1309;1243	B2RUU3;A8MU08;Q14185	.;.;DOCK1_HUMAN	R	1243	ENSP00000280333:H1243R	ENSP00000280333:H1243R	H	+	2	0	DOCK1	129069606	1.000000	0.71417	0.986000	0.45419	0.943000	0.58893	8.924000	0.92827	2.072000	0.62099	0.533000	0.62120	CAT	.	.		0.368	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		G	129179616	A	G	129179616	3	3	218	1	0	0	0	0	1	0	0	0	4686	217	8	2	3874	2	DOCK1	10	129179616	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	35180019	129179616	6355131	52	31325										
MUC2	4583	hgsc.bcm.edu	37	chr11	1084794	1084794	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	catggcacctgctccatttaCgggagtggccactacatcac	9	14	1	0	rs559546110		TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr11:1084794C>T	ENST00000441003.2	+	20	2616	c.2589C>T	c.(2587-2589)taC>taT	p.Y863Y	MUC2_ENST00000359061.5_Silent_p.Y863Y	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	863	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCTCCATTTACGGGAGTGGCC	0.597													C|||	1	0.000199681	0	0.0014	5008	,	,		19253	0		0	False		,,,				2504	0				p.Y863Y		Atlas-SNP	.											.	MUC2	614	.	0			c.C2589T						.						68	69	69					11																	1084794		2153	4247	6400	SO:0001819	synonymous_variant	4583	exon20			CATTTACGGGAGT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.2589C>T	chr11.hg19:g.1084794C>T		61.0	0.0		111.0	47.0	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.		0.597	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1084794	C	T	1084794	2	4	218	1	0	0	0	0	0	0	0	1	9984	547	19	1		1	MUC2	11	1084794	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10		1084794	133921722	53	31326										
MUC2	4583	hgsc.bcm.edu	37	chr11	1091476	1091476	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tcctgctttattgcagttttAtcaacaactccgagtaagtg	7	9	1	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr11:1091476A>C	ENST00000441003.2	+	29	3912	c.3885A>C	c.(3883-3885)ttA>ttC	p.L1295F	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.L1296F	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1295					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TTGCAGTTTTATCAACAACTC	0.368																																					p.L1295F		Atlas-SNP	.											.	MUC2	614	.	0			c.A3885C						.						69	67	68					11																	1091476		1892	4115	6007	SO:0001583	missense	4583	exon29			AGTTTTATCAACA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3885A>C	chr11.hg19:g.1091476A>C	ENSP00000415183:p.Leu1295Phe	185.0	0.0		255.0	15.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.162	-1.080045	0.01888	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13307	2.64;2.6	2.14	-4.28	0.03732	.	5.854200	0.01814	U	0.033653	T	0.06050	0.0157	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28996	-1.0026	10	0.15952	T	0.53	.	3.8845	0.09093	0.3308:0.2769:0.0:0.3923	.	1295	E7EUV1	.	F	1295;1296	ENSP00000415183:L1295F;ENSP00000351956:L1296F	ENSP00000351956:L1296F	L	+	3	2	MUC2	1081476	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.429000	0.06982	-2.496000	0.00513	-0.712000	0.03635	TTA	.	.		0.368	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1091476	A	C	1091476	3	2	218	1	0	0	0	0	1	0	0	0	9984	446	16	5	3999	5	MUC2	11	1091476	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	6682	1091476	133915040	54	31327										
OR4D10	390197	hgsc.bcm.edu	37	chr11	59245374	59245374	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ggggctttgtccactccatcGtgcagatttccctgttgctc	10	13	0	1	rs200781301		TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr11:59245374G>A	ENST00000530162.1	+	1	529	c.472G>A	c.(472-474)Gtg>Atg	p.V158M		NM_001004705.1	NP_001004705.1	Q8NGI6	OR4DA_HUMAN	olfactory receptor, family 4, subfamily D, member 10	158						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V158M(1)|p.V156M(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCACTCCATCGTGCAGATTTC	0.547																																					p.V158M		Atlas-SNP	.											OR4D10_ENST00000530162,colon,carcinoma,0,4	OR4D10	120	.	2	Substitution - Missense(2)	endometrium(2)	c.G472A						.	G	MET/VAL	0,4402		0,0,2201	102	103	103		472	0.7	0.7	11		103	1,8589	1.2+/-3.3	0,1,4294	no	missense	OR4D10	NM_001004705.1	21	0,1,6495	AA,AG,GG		0.0116,0.0,0.0077	benign	158/312	59245374	1,12991	2201	4295	6496	SO:0001583	missense	390197	exon1			TCCATCGTGCAGA	AB065808	CCDS53636.1	11q12.1	2012-10-03		2004-03-10	ENSG00000254466	ENSG00000254466		"GPCR / Class A : Olfactory receptors"	15173	protein-coding gene	gene with protein product				OR4D10P			Standard	NM_001004705		Approved	OST711	uc001nnz.1	Q8NGI6	OTTHUMG00000167341	ENST00000530162.1:c.472G>A	chr11.hg19:g.59245374G>A	ENSP00000436424:p.Val158Met	64.0	0.0		108.0	15.0	NM_001004705	B2RNH6	Missense_Mutation	SNP	ENST00000530162.1	hg19	CCDS53636.1	.	.	.	.	.	.	.	.	.	.	G	10.07	1.249495	0.22880	0.0	1.16E-4	ENSG00000254466	ENST00000530162	T	0.38560	1.13	4.71	0.745	0.18359	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.36635	0.0974	L	0.56124	1.755	0.09310	N	1	B	0.19817	0.039	B	0.27380	0.079	T	0.40590	-0.9555	9	0.72032	D	0.01	.	5.5604	0.17140	0.3238:0.134:0.5422:0.0	.	158	Q8NGI6	OR4DA_HUMAN	M	158	ENSP00000436424:V158M	ENSP00000436424:V158M	V	+	1	0	OR4D10	59001950	0.000000	0.05858	0.704000	0.30370	0.724000	0.41520	-0.097000	0.11042	-0.053000	0.13289	-0.126000	0.14955	GTG	.	.		0.547	OR4D10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394235.1	NM_001004705		A	59245374	G	A	59245374	3	1	218	1	0	0	0	0	1	0	0	0	11063	1145	40	1	474	1	OR4D10	11	59245374	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	58153898	59245374	75761142	55	31328										
MTA2	9219	hgsc.bcm.edu	37	chr11	62367685	62367685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ggctactagaaatgtccctgCgccggaaaagacagacaacc	10	12	0	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr11:62367685C>T	ENST00000278823.2	-	3	532	c.143G>A	c.(142-144)cGc>cAc	p.R48H	MTA2_ENST00000527204.1_5'UTR|MTA2_ENST00000524902.1_5'Flank	NM_004739.3	NP_004730.2	O94776	MTA2_HUMAN	metastasis associated 1 family, member 2	48	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin assembly or disassembly (GO:0006333)|DNA methylation (GO:0006306)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	histone deacetylase complex (GO:0000118)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|histone deacetylase activity (GO:0004407)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	26						aatgtccctgcgccggaaaag	0.458																																					p.R48H		Atlas-SNP	.											.	MTA2	54	.	0			c.G143A						.						124	124	124					11																	62367685		2202	4299	6501	SO:0001583	missense	9219	exon3			TCCCTGCGCCGGA	AB016591	CCDS8022.1	11q12-q13.1	2013-01-25	2004-12-15	2003-12-17	ENSG00000149480	ENSG00000149480		"GATA zinc finger domain containing"	7411	protein-coding gene	gene with protein product		603947	"metastasis associated gene family, member 2"	MTA1L1		9929979	Standard	NM_004739		Approved	MTA1-L1	uc001ntq.2	O94776	OTTHUMG00000167684	ENST00000278823.2:c.143G>A	chr11.hg19:g.62367685C>T	ENSP00000278823:p.Arg48His	146.0	0.0		176.0	64.0	NM_004739	Q68DB1|Q9UQB5	Missense_Mutation	SNP	ENST00000278823.2	hg19	CCDS8022.1	.	.	.	.	.	.	.	.	.	.	C	32	5.182981	0.94885	.	.	ENSG00000149480	ENST00000278823	T	0.37752	1.18	5.56	5.56	0.83823	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	D	0.000000	T	0.64283	0.2584	M	0.84846	2.72	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.69499	-0.5129	10	0.87932	D	0	-0.3396	15.0452	0.71822	0.0:1.0:0.0:0.0	.	48	O94776	MTA2_HUMAN	H	48	ENSP00000278823:R48H	ENSP00000278823:R48H	R	-	2	0	MTA2	62124261	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.628000	0.61282	2.629000	0.89072	0.655000	0.94253	CGC	.	.		0.458	MTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395578.1	NM_004739		T	62367685	C	T	62367685	3	4	218	1	0	0	0	0	1	0	0	0	9918	768	27	1	1927	1	MTA2	11	62367685	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	3122311	62367685	72638831	56	31329										
TM7SF2	7108	hgsc.bcm.edu	37	chr11	64880095	64880095	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	acccgcgtccctgccggggcTggaggtgctgtggagcccac	16	15	0	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr11:64880095T>A	ENST00000279263.7	+	2	323	c.161T>A	c.(160-162)cTg>cAg	p.L54Q	AP003068.9_ENST00000528887.1_RNA|TM7SF2_ENST00000345348.5_Missense_Mutation_p.L54Q|TM7SF2_ENST00000540748.1_5'UTR	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	54					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	delta14-sterol reductase activity (GO:0050613)			lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CTGCCGGGGCTGGAGGTGCTG	0.756																																					p.L54Q		Atlas-SNP	.											.	TM7SF2	30	.	0			c.T161A						.						2	2	2					11																	64880095		1470	3237	4707	SO:0001583	missense	7108	exon2			CGGGGCTGGAGGT	BC012857	CCDS41669.1, CCDS60846.1	11q13.1	2013-05-23			ENSG00000149809	ENSG00000149809	1.3.1.70		11863	protein-coding gene	gene with protein product	"delta(14)-sterol reductase"	603414				9615229, 9286704	Standard	NM_003273		Approved	ANG1, DHCR14A, NET47	uc001oct.4	O76062	OTTHUMG00000165603	ENST00000279263.7:c.161T>A	chr11.hg19:g.64880095T>A	ENSP00000279263:p.Leu54Gln	71.0	0.0		77.0	24.0	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Missense_Mutation	SNP	ENST00000279263.7	hg19	CCDS41669.1	.	.	.	.	.	.	.	.	.	.	t	12.88	2.071119	0.36566	.	.	ENSG00000149809	ENST00000526809;ENST00000279263;ENST00000524986;ENST00000534371;ENST00000525385;ENST00000345348;ENST00000531321;ENST00000529414;ENST00000530750	D;D;D;D;D;D;D;D;T	0.99167	-4.89;-5.08;-4.39;-5.45;-4.57;-5.26;-5.51;-4.64;-1.45	4.91	-0.0421	0.13865	.	2.067490	0.01756	N	0.030251	D	0.99174	0.9714	M	0.86651	2.83	0.20563	N	0.999885	P;P	0.48764	0.915;0.881	P;P	0.59948	0.739;0.866	D	0.93365	0.6730	10	0.33141	T	0.24	1.5301	8.5502	0.33447	0.0:0.3023:0.0:0.6977	.	54;54	O76062-2;O76062	.;ERG24_HUMAN	Q	54;54;25;54;25;54;25;54;54	ENSP00000432171:L54Q;ENSP00000279263:L54Q;ENSP00000435972:L25Q;ENSP00000432187:L54Q;ENSP00000433325:L25Q;ENSP00000329520:L54Q;ENSP00000431300:L25Q;ENSP00000433275:L54Q;ENSP00000432413:L54Q	ENSP00000279263:L54Q	L	+	2	0	TM7SF2	64636671	0.000000	0.05858	0.001000	0.08648	0.063000	0.16089	-0.512000	0.06313	-0.160000	0.11002	-0.386000	0.06593	CTG	.	.		0.756	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273		A	64880095	T	A	64880095	3	1	218	1	0	0	0	0	1	0	0	0	15989	1580	55	4	167	4	TM7SF2	11	64880095	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	2512410	64880095	70126421	57	31330										
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101834056	101834056	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ttagaaaaccaggatctgcaAaagtccaatcaggctttata	7	8	2	1	rs138416296		TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr11:101834056A>G	ENST00000263468.8	+	6	2560	c.2290A>G	c.(2290-2292)Aaa>Gaa	p.K764E	KIAA1377_ENST00000537689.1_Missense_Mutation_p.K565E	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	764										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AGGATCTGCAAAAGTCCAATC	0.363																																					p.K764E		Atlas-SNP	.											.	KIAA1377	111	.	0			c.A2290G						.	A	GLU/LYS	0,4406		0,0,2203	68	75	73		2290	4.4	1	11	dbSNP_134	73	1,8597	1.2+/-3.3	0,1,4298	no	missense	KIAA1377	NM_020802.2	56	0,1,6501	GG,GA,AA		0.0116,0.0,0.0077	possibly-damaging	764/1118	101834056	1,13003	2203	4299	6502	SO:0001583	missense	57562	exon6			TCTGCAAAAGTCC	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.2290A>G	chr11.hg19:g.101834056A>G	ENSP00000263468:p.Lys764Glu	104.0	0.0		145.0	7.0	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	hg19	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	A	12.43	1.934845	0.34189	0.0	1.16E-4	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.13420	2.59;2.59	5.52	4.39	0.52855	.	0.161033	0.43919	D	0.000506	T	0.25827	0.0629	M	0.64997	1.995	0.28370	N	0.92005	D	0.58620	0.983	P	0.53146	0.719	T	0.07046	-1.0793	10	0.72032	D	0.01	-15.6109	12.8491	0.57848	0.8557:0.1442:0.0:0.0	.	764	Q9P2H0	K1377_HUMAN	E	764;565	ENSP00000263468:K764E;ENSP00000443184:K565E	ENSP00000263468:K764E	K	+	1	0	KIAA1377	101339266	0.070000	0.21116	0.956000	0.39512	0.067000	0.16453	2.100000	0.41777	1.037000	0.40024	0.533000	0.62120	AAA	.	A|1.000;G|0.000		0.363	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		G	101834056	A	G	101834056	3	3	218	1	0	0	0	0	1	0	0	0	8236	15	1	2	2312	2	KIAA1377	11	101834056	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	36953961	101834056	33172460	58	31331										
MMP10	4319	hgsc.bcm.edu	37	chr11	102641594	102641594	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cattggggtcaaactcaaacTgtgatgatccactgaagaag	10	8	2	4			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr11:102641594T>A	ENST00000279441.4	-	10	1397	c.1361A>T	c.(1360-1362)cAg>cTg	p.Q454L		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	454					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	AAACTCAAACTGTGATGATCC	0.378																																					p.Q454L		Atlas-SNP	.											.	MMP10	44	.	0			c.A1361T						.						117	101	107					11																	102641594		2203	4299	6502	SO:0001583	missense	4319	exon10			TCAAACTGTGATG	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"matrix metalloproteinase 10 (stromelysin 2)"	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.1361A>T	chr11.hg19:g.102641594T>A	ENSP00000279441:p.Gln454Leu	92.0	0.0		115.0	39.0	NM_002425	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	hg19	CCDS8321.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.865767	0.51588	.	.	ENSG00000166670	ENST00000279441	T	0.02552	4.25	3.96	3.96	0.45880	Hemopexin/matrixin (2);	0.410152	0.18526	N	0.138631	T	0.15349	0.0370	M	0.82923	2.615	0.49483	D	0.99979	D	0.89917	1.0	D	0.97110	1.0	T	0.01238	-1.1409	10	0.39692	T	0.17	.	13.3079	0.60363	0.0:0.0:0.0:1.0	.	454	P09238	MMP10_HUMAN	L	454	ENSP00000279441:Q454L	ENSP00000279441:Q454L	Q	-	2	0	MMP10	102146804	0.996000	0.38824	0.988000	0.46212	0.476000	0.33039	2.027000	0.41078	1.766000	0.52107	0.533000	0.62120	CAG	.	.		0.378	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1			A	102641594	T	A	102641594	3	1	218	1	0	0	0	0	1	0	0	0	9658	1580	55	4	73	4	MMP10	11	102641594	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	807538	102641594	32364922	59	31332										
MMP10	4319	hgsc.bcm.edu	37	chr11	102650306	102650306	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	aagtgaccaacgtcaggaacTccacacctgggcttgcgcat	10	13	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr11:102650306T>G	ENST00000279441.4	-	2	312	c.276A>C	c.(274-276)ggA>ggC	p.G92G		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	92					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	CGTCAGGAACTCCACACCTGG	0.473																																					p.G92G		Atlas-SNP	.											.	MMP10	44	.	0			c.A276C						.						112	90	98					11																	102650306		2203	4299	6502	SO:0001819	synonymous_variant	4319	exon2			AGGAACTCCACAC	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"matrix metalloproteinase 10 (stromelysin 2)"	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.276A>C	chr11.hg19:g.102650306T>G		79.0	0.0		135.0	56.0	NM_002425	B2R9X9|Q53HH9	Silent	SNP	ENST00000279441.4	hg19	CCDS8321.1																																																																																			.	.		0.473	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1			G	102650306	T	G	102650306	2	3	218	1	0	0	0	0	0	0	0	1	9658	1538	54	5		5	MMP10	11	102650306	Silent	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	8712	102650306	32356210	60	31333										
TECTA	7007	hgsc.bcm.edu	37	chr11	121016728	121016728	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gactcttgcatcgatgggggCgcggtgcagaccgcctgcag	16	12	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr11:121016728C>A	ENST00000392793.1	+	12	4279	c.4008C>A	c.(4006-4008)ggC>ggA	p.G1336G	TECTA_ENST00000264037.2_Silent_p.G1336G|TECTA_ENST00000478058.1_3'UTR			O75443	TECTA_HUMAN	tectorin alpha	1336					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TCGATGGGGGCGCGGTGCAGA	0.562																																					p.G1336G		Atlas-SNP	.											.	TECTA	329	.	0			c.C4008A						.						99	96	97					11																	121016728		2203	4299	6502	SO:0001819	synonymous_variant	7007	exon11			TGGGGGCGCGGTG	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.4008C>A	chr11.hg19:g.121016728C>A		1014.0	2.0		1428.0	572.0	NM_005422		Silent	SNP	ENST00000392793.1	hg19	CCDS8434.1																																																																																			.	.		0.562	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	121016728	C	A	121016728	2	1	218	1	0	0	0	0	0	0	0	1	15762	755	27	1		1	TECTA	11	121016728	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	18366422	121016728	13989788	61	31334										
TFCP2	7024	hgsc.bcm.edu	37	chr12	51566149	51566149	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	aggctagcatcaaagtcctgCaccaacccggattcaatcac	7	14	3	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr12:51566149C>T	ENST00000257915.5	-	1	515	c.57G>A	c.(55-57)gtG>gtA	p.V19V	TFCP2_ENST00000549867.1_Silent_p.V19V|TFCP2_ENST00000548115.1_Silent_p.V19V|TFCP2_ENST00000307660.4_Silent_p.V19V	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	19					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						CAAAGTCCTGCACCAACCCGG	0.567																																					p.V19V		Atlas-SNP	.											.	TFCP2	49	.	0			c.G57A						.						125	118	120					12																	51566149		2203	4300	6503	SO:0001819	synonymous_variant	7024	exon1			GTCCTGCACCAAC	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.57G>A	chr12.hg19:g.51566149C>T		43.0	0.0		74.0	24.0	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Silent	SNP	ENST00000257915.5	hg19	CCDS8808.1																																																																																			.	.		0.567	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653		T	51566149	C	T	51566149	2	4	218	1	0	0	0	0	0	0	0	1	15810	697	25	3		3	TFCP2	12	51566149	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10		51566149	82285746	62	31335										
HOXC4	3221	hgsc.bcm.edu	37	chr12	54447994	54447994	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	caccccgagaaatcacagtcGctctgcgagccggcgcctct	10	17	3	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr12:54447994G>T	ENST00000430889.2	+	1	334	c.288G>T	c.(286-288)tcG>tcT	p.S96S	HOXC4_ENST00000609810.1_Silent_p.S96S|HOXC4_ENST00000303406.4_Silent_p.S96S	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	96					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						AATCACAGTCGCTCTGCGAGC	0.736																																					p.S96S		Atlas-SNP	.											.	HOXC4	29	.	0			c.G288T						.						14	19	17					12																	54447994		2189	4278	6467	SO:0001819	synonymous_variant	3221	exon3			ACAGTCGCTCTGC		CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"Homeoboxes / ANTP class : HOXL subclass"	5126	protein-coding gene	gene with protein product		142974	"homeo box C4"	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.288G>T	chr12.hg19:g.54447994G>T		62.0	0.0		100.0	49.0	NM_014620		Silent	SNP	ENST00000430889.2	hg19	CCDS8873.1																																																																																			.	.		0.736	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1			T	54447994	G	T	54447994	2	4	218	1	0	0	0	0	0	0	0	1	7322	1074	38	1		1	HOXC4	12	54447994	Silent	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	2881845	54447994	79403901	63	31336										
NR1H4	9971	hgsc.bcm.edu	37	chr12	100957256	100957256	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cacttctctgtgaaatctggGacgtgcagtgatggggatta	13	7	2	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr12:100957256G>A	ENST00000551379.1	+	9	1478	c.1450G>A	c.(1450-1452)Gac>Aac	p.D484N	NR1H4_ENST00000549996.1_Missense_Mutation_p.D423N|NR1H4_ENST00000392986.3_Missense_Mutation_p.D474N|NR1H4_ENST00000188403.7_Missense_Mutation_p.D480N|NR1H4_ENST00000548884.1_Missense_Mutation_p.D470N			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	484					bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	TGAAATCTGGGACGTGCAGTG	0.438																																					p.D484N		Atlas-SNP	.											.	NR1H4	145	.	0			c.G1450A						.						105	103	103					12																	100957256		2203	4300	6503	SO:0001583	missense	9971	exon9			ATCTGGGACGTGC	U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"Nuclear hormone receptors"	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.1450G>A	chr12.hg19:g.100957256G>A	ENSP00000447149:p.Asp484Asn	66.0	0.0		100.0	37.0	NM_001206993	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Missense_Mutation	SNP	ENST00000551379.1	hg19	CCDS55876.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250484	0.59212	.	.	ENSG00000012504	ENST00000548884;ENST00000392986;ENST00000549996;ENST00000551379;ENST00000188403	D;D;D;D;D	0.96073	-3.9;-3.9;-3.9;-3.9;-3.9	5.59	5.59	0.84812	Nuclear hormone receptor, ligand-binding (2);	0.042114	0.85682	D	0.000000	D	0.97114	0.9057	L	0.55481	1.735	0.80722	D	1	D;B;D;D;P	0.89917	1.0;0.394;1.0;1.0;0.725	D;B;D;D;P	0.87578	0.998;0.311;0.998;0.995;0.721	D	0.96802	0.9590	10	0.51188	T	0.08	.	19.96	0.97242	0.0:0.0:1.0:0.0	.	423;484;480;474;470	F8VYG8;Q96RI1;Q96RI1-4;F1DAL1;B6ZGS9	.;NR1H4_HUMAN;.;.;.	N	470;474;423;484;480	ENSP00000448506:D470N;ENSP00000376712:D474N;ENSP00000448978:D423N;ENSP00000447149:D484N;ENSP00000188403:D480N	ENSP00000188403:D480N	D	+	1	0	NR1H4	99481387	1.000000	0.71417	1.000000	0.80357	0.227000	0.25037	9.772000	0.98984	2.793000	0.96121	0.561000	0.74099	GAC	.	.		0.438	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123		A	100957256	G	A	100957256	3	1	218	1	0	0	0	0	1	0	0	0	10628	1174	41	3	1442	3	NR1H4	12	100957256	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	46509262	100957256	32894639	64	31337										
RCBTB2	1102	hgsc.bcm.edu	37	chr13	49086978	49086978	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cactaaaccatgattagttgTcccattgcccagctggctat	7	12	0	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr13:49086978T>C	ENST00000344532.3	-	7	826	c.403A>G	c.(403-405)Aca>Gca	p.T135A	RCBTB2_ENST00000481144.1_5'UTR|RCBTB2_ENST00000430805.2_Missense_Mutation_p.T140A|RCBTB2_ENST00000544904.1_Missense_Mutation_p.T111A|RCBTB2_ENST00000544492.1_Intron	NM_001268.2	NP_001259.1	O95199	RCBT2_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	135					positive regulation of Ran GTPase activity (GO:0032853)	acrosomal vesicle (GO:0001669)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			breast(5)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(3)	31		all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116)		TGATTAGTTGTCCCATTGCCC	0.388																																					p.T135A		Atlas-SNP	.											.	RCBTB2	62	.	0			c.A403G						.						132	124	127					13																	49086978		2203	4300	6503	SO:0001583	missense	1102	exon7			TAGTTGTCCCATT	AF060219	CCDS9411.1, CCDS73570.1, CCDS73571.1, CCDS73572.1	13q14.3	2013-01-08	2005-05-09	2005-05-09	ENSG00000136161	ENSG00000136161		"BTB/POZ domain containing"	1914	protein-coding gene	gene with protein product		603524	"chromosome condensation 1-like"	CHC1L		9806834	Standard	XM_005266242		Approved		uc001vch.3	O95199	OTTHUMG00000016902	ENST00000344532.3:c.403A>G	chr13.hg19:g.49086978T>C	ENSP00000345144:p.Thr135Ala	65.0	0.0		57.0	33.0	NM_001268	B2RDW8	Missense_Mutation	SNP	ENST00000344532.3	hg19	CCDS9411.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.255571	0.59321	.	.	ENSG00000136161	ENST00000344532;ENST00000450343;ENST00000452987;ENST00000430805;ENST00000544904	D;D;D	0.85629	-2.01;-2.01;-2.01	5.63	4.44	0.53790	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.089095	0.85682	N	0.000000	T	0.79364	0.4433	L	0.50847	1.595	0.52099	D	0.999949	B;B;B;B	0.14012	0.008;0.009;0.001;0.009	B;B;B;B	0.24701	0.015;0.034;0.007;0.055	T	0.71052	-0.4704	10	0.28530	T	0.3	.	6.8414	0.23965	0.1341:0.0711:0.0:0.7948	.	111;140;139;135	B4DPP7;B4DWG0;B3KVB1;O95199	.;.;.;RCBT2_HUMAN	A	135;139;140;140;111	ENSP00000345144:T135A;ENSP00000389910:T140A;ENSP00000443904:T111A	ENSP00000345144:T135A	T	-	1	0	RCBTB2	47984979	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.661000	0.61518	1.058000	0.40530	0.477000	0.44152	ACA	.	.		0.388	RCBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044888.2	NM_001268		C	49086978	T	C	49086978	3	2	218	1	0	0	0	0	1	0	0	0	13187	1667	58	2	1288	2	RCBTB2	13	49086978	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10		49086978	66082900	65	31338										
MYH6	4624	hgsc.bcm.edu	37	chr14	23868178	23868178	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tggttgtcgtacagcttggcCttgaaggtcatgtcagtggc	14	8	2	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr14:23868178C>T	ENST00000356287.3	-	14	1679	c.1650G>A	c.(1648-1650)aaG>aaA	p.K550K	MYH6_ENST00000405093.3_Silent_p.K550K			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	550	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		ACAGCTTGGCCTTGAAGGTCA	0.552																																					p.K550K		Atlas-SNP	.											.	MYH6	274	.	0			c.G1650A						.						222	161	182					14																	23868178		2203	4300	6503	SO:0001819	synonymous_variant	4624	exon15			CTTGGCCTTGAAG	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.1650G>A	chr14.hg19:g.23868178C>T		78.0	0.0		104.0	52.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	hg19	CCDS9600.1																																																																																			.	.		0.552	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23868178	C	T	23868178	2	4	218	1	0	0	0	0	0	0	0	1	10047	680	24	3		3	MYH6	14	23868178	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10		23868178	83481362	66	31339										
PCNX	22990	hgsc.bcm.edu	37	chr14	71575423	71575423	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ctactgctatagcagccggcAttcatccctccggatgtcca	8	15	1	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr14:71575423A>G	ENST00000304743.2	+	34	6850	c.6404A>G	c.(6403-6405)cAt>cGt	p.H2135R	PCNX_ENST00000439984.3_Missense_Mutation_p.H2024R|PCNX_ENST00000556272.1_3'UTR|PCNX_ENST00000238570.5_Missense_Mutation_p.H2063R	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	2135	Ser-rich.					integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		AGCAGCCGGCATTCATCCCTC	0.567																																					p.H2135R		Atlas-SNP	.											.	PCNX	198	.	0			c.A6404G						.						69	65	66					14																	71575423		2203	4300	6503	SO:0001583	missense	22990	exon34			GCCGGCATTCATC	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.6404A>G	chr14.hg19:g.71575423A>G	ENSP00000304192:p.His2135Arg	78.0	0.0		64.0	49.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.961|4.961	0.178500|0.178500	0.09443|0.09443	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984|ENST00000554691	T;T;T|.	0.09163|.	3.42;3.46;3.01|.	5.94|5.94	4.73|4.73	0.59995|0.59995	.|.	0.046608|.	0.85682|.	D|.	0.000000|.	T|T	0.53753|0.53753	0.1816|0.1816	L|L	0.56769|0.56769	1.78|1.78	0.27291|0.27291	N|N	0.957848|0.957848	B;P;P|.	0.40731|.	0.386;0.651;0.728|.	B;B;B|.	0.31946|.	0.124;0.084;0.138|.	T|T	0.48801|0.48801	-0.9003|-0.9003	10|5	0.10111|.	T|.	0.7|.	.|.	12.8894|12.8894	0.58064|0.58064	0.8645:0.1355:0.0:0.0|0.8645:0.1355:0.0:0.0	.|.	2063;2024;2135|.	Q96RV3-3;B2RTR6;Q96RV3|.	.;.;PCX1_HUMAN|.	R|V	2135;2063;2024|1122	ENSP00000304192:H2135R;ENSP00000238570:H2063R;ENSP00000396617:H2024R|.	ENSP00000238570:H2063R|.	H|I	+|+	2|1	0|0	PCNX|PCNX	70645176|70645176	1.000000|1.000000	0.71417|0.71417	0.951000|0.951000	0.38953|0.38953	0.135000|0.135000	0.20990|0.20990	6.866000|6.866000	0.75506|0.75506	2.276000|2.276000	0.75962|0.75962	0.455000|0.455000	0.32223|0.32223	CAT|ATT	.	.		0.567	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		G	71575423	A	G	71575423	3	3	218	1	0	0	0	0	1	0	0	0	11600	217	8	2	6538	2	PCNX	14	71575423	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	47707245	71575423	35774117	67	31340										
C14orf73	91828	hgsc.bcm.edu	37	chr14	103570678	103570678	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gcggccgccgaggtccccgaGgtgctgcagggcctctacca	15	16	1	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr14:103570678G>A	ENST00000380069.3	+	4	1312	c.1236G>A	c.(1234-1236)gaG>gaA	p.E412E		NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	412					exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						AGGTCCCCGAGGTGCTGCAGG	0.672																																					p.E412E		Atlas-SNP	.											.	EXOC3L4	35	.	0			c.G1236A						.						11	12	12					14																	103570678		2192	4289	6481	SO:0001819	synonymous_variant	91828	exon4			CCCCGAGGTGCTG	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 73"	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.1236G>A	chr14.hg19:g.103570678G>A		82.0	0.0		58.0	40.0	NM_001077594	Q14CR2	Silent	SNP	ENST00000380069.3	hg19	CCDS32163.1																																																																																			.	.		0.672	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093		A	103570678	G	A	103570678	2	1	218	1	0	0	0	0	0	0	0	1	1781	991	35	3		3	C14orf73	14	103570678	Silent	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	31995255	103570678	3778862	68	31341										
CKB	1152	hgsc.bcm.edu	37	chr14	103988750	103988750	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	agcaccttggccatgtggttGttgtgggcgctcaggtcggg	17	9	1	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr14:103988750G>A	ENST00000348956.2	-	2	438	c.81C>T	c.(79-81)aaC>aaT	p.N27N	RP11-600F24.7_ENST00000568177.1_RNA	NM_001823.4	NP_001814.2	P12277	KCRB_HUMAN	creatine kinase, brain	27	Phosphagen kinase N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00842}.				cellular chloride ion homeostasis (GO:0030644)|cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			lung(2)|prostate(1)	3		Melanoma(154;0.155)	Epithelial(46;0.14)		Creatine(DB00148)	CCATGTGGTTGTTGTGGGCGC	0.687																																					p.N27N	Esophageal Squamous(186;2492 2823 49929 50127)	Atlas-SNP	.											.	CKB	9	.	0			c.C81T						.						66	60	62					14																	103988750		2203	4300	6503	SO:0001819	synonymous_variant	1152	exon2			GTGGTTGTTGTGG		CCDS9981.1	14q32.32	2012-10-02			ENSG00000166165	ENSG00000166165	2.7.3.2		1991	protein-coding gene	gene with protein product		123280		CKBB			Standard	NM_001823		Approved		uc001ynf.2	P12277	OTTHUMG00000171786	ENST00000348956.2:c.81C>T	chr14.hg19:g.103988750G>A		52.0	0.0		39.0	32.0	NM_001823	A8K236|B2R5R4|Q2LE07|Q6FG40|Q9UC66	Silent	SNP	ENST00000348956.2	hg19	CCDS9981.1																																																																																			.	.		0.687	CKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415111.1			A	103988750	G	A	103988750	2	1	218	1	0	0	0	0	0	0	0	1	3448	1368	48	3		3	CKB	14	103988750	Silent	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	418072	103988750	3360790	69	31342										
TGM5	9333	hgsc.bcm.edu	37	chr15	43527750	43527750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cgtgcagcagagactgggcaCtcaggttcactttgaggtcc	13	11	2	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr15:43527750C>T	ENST00000220420.5	-	10	1638	c.1631G>A	c.(1630-1632)aGt>aAt	p.S544N	TGM5_ENST00000349114.4_Missense_Mutation_p.S462N	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	544					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	AGACTGGGCACTCAGGTTCAC	0.557																																					p.S544N		Atlas-SNP	.											.	TGM5	88	.	0			c.G1631A						.						82	61	68					15																	43527750		2203	4299	6502	SO:0001583	missense	9333	exon10			TGGGCACTCAGGT	AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"Transglutaminases"	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.1631G>A	chr15.hg19:g.43527750C>T	ENSP00000220420:p.Ser544Asn	68.0	0.0		96.0	41.0	NM_201631	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	hg19	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.082888	0.76642	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	T;T	0.70164	-0.46;-0.46	5.05	5.05	0.67936	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.047776	0.85682	D	0.000000	T	0.79076	0.4385	M	0.61703	1.905	0.35154	D	0.77001	B;D	0.89917	0.207;1.0	B;D	0.79784	0.219;0.993	T	0.83095	-0.0131	10	0.44086	T	0.13	-17.4727	15.9436	0.79776	0.0:1.0:0.0:0.0	.	462;544	O43548-2;O43548	.;TGM5_HUMAN	N	544;462;543	ENSP00000220420:S544N;ENSP00000220419:S462N	ENSP00000220420:S544N	S	-	2	0	TGM5	41315042	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.056000	0.30480	2.631000	0.89168	0.655000	0.94253	AGT	.	.		0.557	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		T	43527750	C	T	43527750	3	4	218	1	0	0	0	0	1	0	0	0	15848	565	20	3	547	3	TGM5	15	43527750	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10		43527750	59003642	70	31343										
PYGO1	26108	hgsc.bcm.edu	37	chr15	55881035	55881035	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tttgtaagcgggagctggagAgttctcggcgggcatgtggg	19	6	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr15:55881035A>T	ENST00000302000.6	-	1	110	c.16T>A	c.(16-18)Tct>Act	p.S6T	PYGO1_ENST00000563719.1_5'Flank	NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	6					hematopoietic progenitor cell differentiation (GO:0002244)|kidney development (GO:0001822)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|spermatid nucleus differentiation (GO:0007289)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(6)|lung(6)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	27				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		GGAGCTGGAGAGTTCTCGGCG	0.582																																					p.S6T		Atlas-SNP	.											.	PYGO1	56	.	0			c.T16A						.						107	102	104					15																	55881035		2193	4292	6485	SO:0001583	missense	26108	exon1			CTGGAGAGTTCTC	AF457207	CCDS10155.1	15q21.1	2013-10-09	2013-10-09		ENSG00000171016	ENSG00000171016		"Zinc fingers, PHD-type"	30256	protein-coding gene	gene with protein product		606902	"pygopus homolog 1 (Drosophila)"			11988739	Standard	NM_015617		Approved		uc002adf.1	Q9Y3Y4	OTTHUMG00000132009	ENST00000302000.6:c.16T>A	chr15.hg19:g.55881035A>T	ENSP00000302327:p.Ser6Thr	46.0	0.0		54.0	26.0	NM_015617	A7Y2D6	Missense_Mutation	SNP	ENST00000302000.6	hg19	CCDS10155.1	.	.	.	.	.	.	.	.	.	.	a	13.90	2.374917	0.42105	.	.	ENSG00000171016	ENST00000302000	T	0.43688	0.94	1.9	1.9	0.25705	.	0.960325	0.08383	U	0.954185	T	0.21307	0.0513	N	0.08118	0	0.21861	N	0.999504	B	0.18310	0.027	B	0.09377	0.004	T	0.16600	-1.0397	10	0.33141	T	0.24	.	5.8343	0.18599	1.0:0.0:0.0:0.0	.	6	Q9Y3Y4	PYGO1_HUMAN	T	6	ENSP00000302327:S6T	ENSP00000302327:S6T	S	-	1	0	PYGO1	53668327	0.036000	0.19791	0.053000	0.19242	0.406000	0.30931	0.792000	0.26929	1.150000	0.42419	0.241000	0.17934	TCT	.	.		0.582	PYGO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254977.2	NM_015617		T	55881035	A	T	55881035	3	4	218	1	0	0	0	0	1	0	0	0	12878	304	11	4	1255	4	PYGO1	15	55881035	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	12353285	55881035	46650357	71	31344										
BTBD12	84464	hgsc.bcm.edu	37	chr16	3633142	3633142	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ctgccatccacagaggtggcCacggattcttgagaggctgg	14	11	1	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr16:3633142C>T	ENST00000294008.3	-	14	5749	c.5109G>A	c.(5107-5109)gtG>gtA	p.V1703V	RP11-461A8.1_ENST00000573982.1_lincRNA	NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1703	Interaction with PLK1 and TERF2-TERF2IP.|Interaction with SLX1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CAGAGGTGGCCACGGATTCTT	0.597								Direct reversal of damage																													p.V1703V		Atlas-SNP	.											.	SLX4	173	.	0			c.G5109A						.						124	114	117					16																	3633142		2197	4300	6497	SO:0001819	synonymous_variant	84464	exon14			GGTGGCCACGGAT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.5109G>A	chr16.hg19:g.3633142C>T		75.0	0.0		86.0	30.0	NM_032444	Q69YT8|Q8TF15|Q96JP1	Silent	SNP	ENST00000294008.3	hg19	CCDS10506.2																																																																																			.	.		0.597	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		T	3633142	C	T	3633142	2	4	218	1	0	0	0	0	0	0	0	1	1542	581	21	3		3	BTBD12	16	3633142	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10		3633142	86721611	72	31345										
FOXC2	2303	hgsc.bcm.edu	37	chr16	86602407	86602407	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	atccacgccgcctctctatcGccacgcagccccctactcct	5	22	1	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr16:86602407G>T	ENST00000320354.4	+	1	1551	c.1466G>T	c.(1465-1467)cGc>cTc	p.R489L	RP11-463O9.5_ENST00000563280.1_RNA	NM_005251.2	NP_005242.1	Q99958	FOXC2_HUMAN	forkhead box C2 (MFH-1, mesenchyme forkhead 1)	489					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|embryonic viscerocranium morphogenesis (GO:0048703)|glomerular endothelium development (GO:0072011)|glomerular mesangial cell development (GO:0072144)|glomerular visceral epithelial cell differentiation (GO:0072112)|heart development (GO:0007507)|insulin receptor signaling pathway (GO:0008286)|lymphangiogenesis (GO:0001946)|mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|ossification (GO:0001503)|paraxial mesodermal cell fate commitment (GO:0048343)|patterning of blood vessels (GO:0001569)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular wound healing (GO:0035470)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|response to hormone (GO:0009725)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	15						CCTCTCTATCGCCACGCAGCC	0.667									Late-onset Hereditary Lymphedema																												p.R489L		Atlas-SNP	.											.	FOXC2	46	.	0			c.G1466T						.						29	28	28					16																	86602407		2089	4144	6233	SO:0001583	missense	2303	exon1	Familial Cancer Database	Hereditary Lymphedema type II, Meige Lymphedema	TCTATCGCCACGC	Y08223	CCDS10958.1	16q24.1	2008-04-10			ENSG00000176692	ENSG00000176692		"Forkhead boxes"	3801	protein-coding gene	gene with protein product		602402		FKHL14		9169153, 8674414	Standard	NM_005251		Approved	MFH-1	uc002fjq.3	Q99958	OTTHUMG00000137652	ENST00000320354.4:c.1466G>T	chr16.hg19:g.86602407G>T	ENSP00000326371:p.Arg489Leu	239.0	0.0		393.0	160.0	NM_005251	C6KMR9|Q14DA6	Missense_Mutation	SNP	ENST00000320354.4	hg19	CCDS10958.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.083091	0.55861	.	.	ENSG00000176692	ENST00000320354	D	0.83075	-1.68	4.35	4.35	0.52113	.	3.799080	0.01714	U	0.027918	D	0.89873	0.6841	L	0.39245	1.2	0.58432	D	0.999998	D	0.76494	0.999	D	0.79784	0.993	T	0.77824	-0.2444	10	0.87932	D	0	.	15.5954	0.76574	0.0:0.0:1.0:0.0	.	489	Q99958	FOXC2_HUMAN	L	489	ENSP00000326371:R489L	ENSP00000326371:R489L	R	+	2	0	FOXC2	85159908	1.000000	0.71417	1.000000	0.80357	0.122000	0.20287	8.870000	0.92336	2.223000	0.72356	0.462000	0.41574	CGC	.	.		0.667	FOXC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269104.2	NM_005251		T	86602407	G	T	86602407	3	4	218	1	0	0	0	0	1	0	0	0	6003	1087	38	1	1468	1	FOXC2	16	86602407	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	82969265	86602407	3752346	73	31346										
SLFN11	91607	hgsc.bcm.edu	37	chr17	33680410	33680410	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gtagagaattctgtgtgcctCacagtgaaacacattcctga	9	9	2	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr17:33680410C>A	ENST00000394566.1	-	6	2139	c.1867G>T	c.(1867-1869)Gag>Tag	p.E623*	SLFN11_ENST00000308377.4_Nonsense_Mutation_p.E623*	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	623					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.E623K(1)		autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTGTGTGCCTCACAGTGAAAC	0.448																																					p.E623X		Atlas-SNP	.											SLFN11,NS,carcinoma,0,1	SLFN11	112	.	1	Substitution - Missense(1)	lung(1)	c.G1867T						.						50	48	48					17																	33680410		2202	4279	6481	SO:0001587	stop_gained	91607	exon4			GTGCCTCACAGTG	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.1867G>T	chr17.hg19:g.33680410C>A	ENSP00000378067:p.Glu623*	328.0	0.0		598.0	276.0	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Nonsense_Mutation	SNP	ENST00000394566.1	hg19	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	c	38	6.917570	0.97932	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	.	.	.	3.84	0.484	0.16825	.	0.641420	0.13615	N	0.374871	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	5.8179	0.18506	0.0:0.507:0.3822:0.1108	.	.	.	.	X	623	.	ENSP00000312402:E623X	E	-	1	0	SLFN11	30704523	0.000000	0.05858	0.021000	0.16686	0.540000	0.34992	-2.185000	0.01252	0.039000	0.15632	0.650000	0.86243	GAG	.	.		0.448	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		A	33680410	C	A	33680410	4	1	218	1	0	0	0	0	0	1	0	0	14748	835	29	3	846	3	SLFN11	17	33680410	Nonsense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10		33680410	47514800	74	31347										
KRT10	3858	hgsc.bcm.edu	37	chr17	38975315	38975317	+	Missense_Mutation	TNP	TGG	TGG	GAA													0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cgccgccggaactgccgccgTggccgccgccgtggccgccg							TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T|G|G	T|G|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr17:38975315_38975317TGG>GAA	ENST00000269576.5	-	7	1479_1481	c.1470_1472CCA>TTC	c.(1468-1473)ggCCAc>ggTTCc	p.H491S	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	491	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 1; AAA60544). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				actgccgccgtggccgccgccgt	0.798																																					p.H491P|p.H491Y|p.G490G		Atlas-SNP	.											.	KRT10	56	.	0			c.A1472C|c.C1471T|c.C1470T						.																																			SO:0001583	missense	3858	exon7			CCGCCGTGGCCGC|CGCCGTGGCCGCC|GCCGTGGCCGCCG	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1470_1472CCA>TTC	chr17.hg19:g.38975315TGG>GAA	ENSP00000269576:p.His491Ser	17.0|16.0|16.0	0.0		85.0|85.0|88.0	18.0|18.0|20.0	NM_000421	Q14664|Q8N175	Missense_Mutation|Missense_Mutation|Silent	SNP	ENST00000269576.5	hg19	CCDS11377.1																																																																																			.	.		0.798	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		GAA	38975317	TGG	GAA	38975315	3	3	218	1	0	0	0	0	1	0	0	0	8457	1696	59	5	290	5	KRT10	17	38975315	Missense_Mutation	TNP	TGG	TCGA-DD-AAEE-01A-11D-A40R-10	5294905	38975315	42219895	75	31348	163	2								
KRT10	3858	hgsc.bcm.edu	37	chr17	38975319	38975319	+	Missense_Mutation	SNP	C	C	T													0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gccggaactgccgccgtggcCgccgccgtggccgccgccgg							TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr17:38975319C>T	ENST00000269576.5	-	7	1477	c.1468G>A	c.(1468-1470)Ggc>Agc	p.G490S	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ccgccgtggccgccgccgtgg	0.791																																					p.G490S		Atlas-SNP	.											.	KRT10	56	.	0			c.G1468A						.																																			SO:0001583	missense	3858	exon7			CGTGGCCGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1468G>A	chr17.hg19:g.38975319C>T	ENSP00000269576:p.Gly490Ser	14.0	0.0		90.0	19.0	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546565	0.86022	.	.	ENSG00000186395	ENST00000269576	D	0.96587	-4.06	4.38	4.38	0.52667	.	0.845686	0.09879	N	0.743932	D	0.94778	0.8314	N	0.08118	0	0.27860	N	0.940431	D	0.89917	1.0	D	0.76071	0.987	D	0.87790	0.2618	10	0.18710	T	0.47	.	12.7512	0.57310	0.0:1.0:0.0:0.0	.	490	P13645	K1C10_HUMAN	S	490	ENSP00000269576:G490S	ENSP00000269576:G490S	G	-	1	0	KRT10	36228845	0.019000	0.18553	0.876000	0.34364	0.184000	0.23303	0.448000	0.21726	2.739000	0.93911	0.603000	0.83216	GGC	.	.		0.791	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		T	38975319	C	T	38975319	3	4	218	1	0	0	0	0	1	0	0	0	8457	652	23	1	294	1	KRT10	17	38975319	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	4	38975319	42219891	76	31349	163	2								
FZD2	2535	hgsc.bcm.edu	37	chr17	42636226	42636226	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	accatcaccatcctggccatGggccagatcgacggcgacct	10	16	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr17:42636226G>T	ENST00000315323.3	+	1	1302	c.1170G>T	c.(1168-1170)atG>atT	p.M390I		NM_001466.3	NP_001457.1	Q14332	FZD2_HUMAN	frizzled class receptor 2	390					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cell-cell signaling (GO:0007267)|cochlea morphogenesis (GO:0090103)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|inner ear receptor cell development (GO:0060119)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|sensory perception of smell (GO:0007608)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(8)	33		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		TCCTGGCCATGGGCCAGATCG	0.667																																					p.M390I		Atlas-SNP	.											.	FZD2	81	.	0			c.G1170T						.						69	69	69					17																	42636226		2203	4299	6502	SO:0001583	missense	2535	exon1			GGCCATGGGCCAG	L37882	CCDS11484.1	17q21.1	2014-01-29	2014-01-29			ENSG00000180340		"GPCR / Class F : Frizzled receptors"	4040	protein-coding gene	gene with protein product		600667	"frizzled (Drosophila) homolog 2", "frizzled homolog 2 (Drosophila)", "frizzled 2, seven transmembrane spanning receptor", "frizzled family receptor 2"			7558010, 9813155	Standard	NM_001466		Approved		uc002igx.2	Q14332		ENST00000315323.3:c.1170G>T	chr17.hg19:g.42636226G>T	ENSP00000323901:p.Met390Ile	25.0	0.0		67.0	16.0	NM_001466	Q0VG82	Missense_Mutation	SNP	ENST00000315323.3	hg19	CCDS11484.1	.	.	.	.	.	.	.	.	.	.	g	15.15	2.747560	0.49257	.	.	ENSG00000180340	ENST00000541149;ENST00000315323	D	0.81659	-1.52	5.14	5.14	0.70334	GPCR, family 2-like (1);	0.123655	0.64402	D	0.000001	D	0.85860	0.5795	M	0.91717	3.235	0.58432	D	0.999998	B	0.12013	0.005	B	0.21151	0.033	D	0.85132	0.0975	10	0.72032	D	0.01	.	18.213	0.89877	0.0:0.0:1.0:0.0	.	390	Q14332	FZD2_HUMAN	I	466;390	ENSP00000323901:M390I	ENSP00000323901:M390I	M	+	3	0	FZD2	39991752	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.733000	0.62036	2.379000	0.81126	0.561000	0.74099	ATG	.	.		0.667	FZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457806.1	NM_001466		T	42636226	G	T	42636226	3	4	218	1	0	0	0	0	1	0	0	0	6138	1348	47	3	1172	3	FZD2	17	42636226	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	3660907	42636226	38558984	77	31350										
QRICH2	84074	hgsc.bcm.edu	37	chr17	74288391	74288392	+	Missense_Mutation	DNP	GC	GC	AT													0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gcaccaaaccacgctgaactGcaccaggttgcaccaaacca					rs530614567|rs550406051	byFrequency	TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr17:74288391_74288392GC>AT	ENST00000262765.5	-	4	2097_2098	c.1918_1919GC>AT	c.(1918-1920)GCa>ATa	p.A640I		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	640	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						acgctgaactgcaccaggttgc	0.54																																					p.A640V|p.A640T		Atlas-SNP	.											.	QRICH2	143	.	0			c.C1919T|c.G1918A						.																																			SO:0001583	missense	84074	exon4			TGAACTGCACCAG|GAACTGCACCAGG	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.1918_1919delinsAT	chr17.hg19:g.74288391_74288392delinsAT	ENSP00000262765:p.Ala640Ile	89.0|87.0	0.0		113.0|115.0	30.0	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	hg19	CCDS32741.1																																																																																			.	.		0.54	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		AT	74288392	GC	AT	74288391	3	1	218	1	0	0	0	0	1	0	0	0	12895	1319	46	3	3136	3	QRICH2	17	74288391	Missense_Mutation	DNP	GC	TCGA-DD-AAEE-01A-11D-A40R-10	31652165	74288391	6906819	78	31351										
COLEC12	81035	hgsc.bcm.edu	37	chr18	347058	347058	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tggttctgcagattgccctgGagcacgctggtatcttgctg	13	10	2	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr18:347058G>T	ENST00000400256.3	-	5	771	c.564C>A	c.(562-564)ctC>ctA	p.L188L		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	188					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				GATTGCCCTGGAGCACGCTGG	0.463																																					p.L188L		Atlas-SNP	.											COLEC12,right_upper_lobe,carcinoma,0,1	COLEC12	121	.	0			c.C564A						.						155	153	154					18																	347058		2203	4300	6503	SO:0001819	synonymous_variant	81035	exon5			GCCCTGGAGCACG	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"Collectins"	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.564C>A	chr18.hg19:g.347058G>T		42.0	0.0		57.0	25.0	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Silent	SNP	ENST00000400256.3	hg19	CCDS32782.1																																																																																			.	.		0.463	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			T	347058	G	T	347058	2	4	218	1	0	0	0	0	0	0	0	1	3714	1161	41	3		3	COLEC12	18	347058	Silent	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10		347058	77730190	79	31352										
MAPK4	5596	hgsc.bcm.edu	37	chr18	48190380	48190380	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tctatgggtatgacctcggtGggcgctttgttgacttccaa	12	9	1	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr18:48190380G>C	ENST00000400384.2	+	2	1088	c.52G>C	c.(52-54)Ggg>Cgg	p.G18R	MAPK4_ENST00000592595.1_Missense_Mutation_p.G18R|MAPK4_ENST00000540640.1_Intron|MAPK4_ENST00000588540.1_Missense_Mutation_p.G18R	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	18					cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			lung(4)|skin(3)|upper_aerodigestive_tract(1)	8		Colorectal(6;0.0297)		Colorectal(21;0.156)		TGACCTCGGTGGGCGCTTTGT	0.597																																					p.G18R		Atlas-SNP	.											.	MAPK4	75	.	0			c.G52C						.						102	106	105					18																	48190380		2058	4201	6259	SO:0001583	missense	5596	exon2			CTCGGTGGGCGCT	X59727	CCDS42437.1	18q21.1	2012-10-02			ENSG00000141639	ENSG00000141639		"Mitogen-activated protein kinase cascade / Kinases"	6878	protein-coding gene	gene with protein product		176949		PRKM4		8290275	Standard	XM_005258299		Approved	Erk3-related, Erk4	uc002lev.3	P31152	OTTHUMG00000179853	ENST00000400384.2:c.52G>C	chr18.hg19:g.48190380G>C	ENSP00000383234:p.Gly18Arg	47.0	0.0		71.0	28.0	NM_002747	A1A4C4|Q0VG04	Missense_Mutation	SNP	ENST00000400384.2	hg19	CCDS42437.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.429401	0.43122	.	.	ENSG00000141639	ENST00000400384	T	0.45668	0.89	5.67	2.7	0.31948	Protein kinase-like domain (1);	0.122950	0.37857	N	0.001917	T	0.35451	0.0932	N	0.20445	0.575	0.24868	N	0.992305	P;P	0.37663	0.604;0.604	P;P	0.46543	0.52;0.52	T	0.23940	-1.0174	10	0.26408	T	0.33	-4.9077	13.0808	0.59114	0.0:0.0:0.3809:0.6191	.	18;18	Q0VG04;P31152	.;MK04_HUMAN	R	18	ENSP00000383234:G18R	ENSP00000383234:G18R	G	+	1	0	MAPK4	46444378	0.998000	0.40836	0.040000	0.18447	0.988000	0.76386	3.043000	0.49823	0.719000	0.32188	0.561000	0.74099	GGG	.	.		0.597	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448631.2	NM_002747		C	48190380	G	C	48190380	3	2	218	1	0	0	0	0	1	0	0	0	9289	1348	47	4	54	4	MAPK4	18	48190380	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	47843322	48190380	29886868	80	31353										
FZR1	51343	hgsc.bcm.edu	37	chr19	3534791	3534791	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tgccatccccatgtgtctgcAggagtctgtgtctgtgctca	11	12	4	0			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr19:3534791A>G	ENST00000395095.3	+	13	1449		c.e13-1		FZR1_ENST00000441788.2_Splice_Site|FZR1_ENST00000313639.8_Splice_Site	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)						activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGTGTCTGCAGGAGTCTGTG	0.652																																					.		Atlas-SNP	.											.	FZR1	42	.	0			c.1441-2A>G						.						112	88	96					19																	3534791		2203	4300	6503	SO:0001630	splice_region_variant	51343	exon14			GTCTGCAGGAGTC	AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"WD repeat domain containing"	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.1450-1A>G	chr19.hg19:g.3534791A>G		36.0	0.0		30.0	20.0	NM_016263	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Splice_Site	SNP	ENST00000395095.3	hg19	CCDS45916.1	.	.	.	.	.	.	.	.	.	.	A	18.53	3.644761	0.67358	.	.	ENSG00000105325	ENST00000441788;ENST00000395095;ENST00000313639	.	.	.	4.41	4.41	0.53225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.317	0.49399	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FZR1	3485791	1.000000	0.71417	0.997000	0.53966	0.757000	0.42996	8.437000	0.90302	1.753000	0.51906	0.459000	0.35465	.	.	.		0.652	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263	Intron	G	3534791	A	G	3534791	5	3	218	1	0	0	0	0	0	0	1	0	6146	202	7	2	1498	2	FZR1	19	3534791	Splice_Site	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10		3534791	55594192	81	31354										
NFIX	4784	hgsc.bcm.edu	37	chr19	13192654	13192654	+	Frame_Shift_Del	DEL	C	C	-													0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gtgtgctcggatggctcgggCcaggccaccggacaggtgag							TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr19:13192654delC	ENST00000592199.1	+	8	1239	c.1239delC	c.(1237-1239)ggcfs	p.G413fs	NFIX_ENST00000397661.2_Frame_Shift_Del_p.G413fs|NFIX_ENST00000588228.1_Frame_Shift_Del_p.G366fs|NFIX_ENST00000587260.1_Frame_Shift_Del_p.G412fs|NFIX_ENST00000360105.4_Frame_Shift_Del_p.G375fs|NFIX_ENST00000587760.1_Frame_Shift_Del_p.G405fs|NFIX_ENST00000585575.1_Frame_Shift_Del_p.G405fs|NFIX_ENST00000358552.3_Frame_Shift_Del_p.G371fs			Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription factor)	413					astrocyte differentiation (GO:0048708)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell layer development (GO:0021680)|DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			ATGGCTCGGGCCAGGCCACCG	0.632											OREG0025286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G421fs		Atlas-INDEL	.											.	NFIX	61	.	0			c.1262delG						.						42	45	44					19																	13192654		2010	4158	6168	SO:0001589	frameshift_variant	4784	exon8			.	U18761	CCDS45996.1, CCDS59359.1	19p13.3	2008-02-05				ENSG00000008441			7788	protein-coding gene	gene with protein product		164005				8340106, 7590749	Standard	NM_001271043		Approved	NF1A	uc010xmx.2	Q14938		ENST00000592199.1:c.1239delC	chr19.hg19:g.13192654delC	ENSP00000467512:p.Gly413fs	60.0	0.0	685	58.0	31.0	NM_001271043	B4DM25|O60413|Q0VG09|Q12859|Q13050|Q13052|Q5U094|Q9UPH1|Q9Y6R8	Frame_Shift_Del	DEL	ENST00000592199.1	hg19																																																																																				.	.		0.632	NFIX-013	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000452763.1	NM_002501		-	13192654	C	-	13192654	7	5	218	1	0	1	0	1	0	0	0	0	10383	726	26	0	1269	0	NFIX	19	13192654	Frame_Shift_Del	DEL	C	TCGA-DD-AAEE-01A-11D-A40R-10	9657863	13192654	45936329	82	31355										
ZNF101	94039	hgsc.bcm.edu	37	chr19	19790278	19790278	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	agtagtggtgcacggcgcacAgtaacaccaactcgaaagag	12	10	0	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr19:19790278A>G	ENST00000592502.1	+	4	590	c.480A>G	c.(478-480)acA>acG	p.T160T	ZNF101_ENST00000444249.2_3'UTR|ZNF101_ENST00000415784.2_Silent_p.T40T			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	160					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						CACGGCGCACAGTAACACCAA	0.473																																					p.T160T		Atlas-SNP	.											.	ZNF101	43	.	0			c.A480G						.						96	98	97					19																	19790278		2203	4300	6503	SO:0001819	synonymous_variant	94039	exon4			GCGCACAGTAACA	AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"Zinc fingers, C2H2-type", "-"	12881	protein-coding gene	gene with protein product		603983	"zinc finger protein 101 (Y2)"			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.480A>G	chr19.hg19:g.19790278A>G		76.0	0.0		105.0	49.0	NM_033204	C9JU83|Q0VDG9	Silent	SNP	ENST00000592502.1	hg19	CCDS32971.1																																																																																			.	.		0.473	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		G	19790278	A	G	19790278	2	3	218	1	0	0	0	0	0	0	0	1	17729	175	7	2		2	ZNF101	19	19790278	Silent	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	6597624	19790278	39338705	83	31356										
ZFP112	7771	hgsc.bcm.edu	37	chr19	44833582	44833582	+	Frame_Shift_Del	DEL	T	T	-													0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tctcctctgtttgaattgacTcctgattaagtaatgatacc							TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr19:44833582delT	ENST00000337401.4	-	5	834	c.746delA	c.(745-747)gagfs	p.E249fs	ZNF112_ENST00000536500.1_Frame_Shift_Del_p.E266fs|ZNF112_ENST00000354340.4_Frame_Shift_Del_p.E243fs	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TTGAATTGACTCCTGATTAAG	0.413																																					p.E249fs		Atlas-INDEL	.											.	ZFP112	219	.	0			c.747delG						.						128	123	125					19																	44833582		2203	4300	6503	SO:0001589	frameshift_variant	7771	exon5			.	AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.746delA	chr19.hg19:g.44833582delT	ENSP00000337081:p.Glu249fs	70.0	0.0		101.0	40.0	NM_001083335	A4FU53|Q9HCA7	Frame_Shift_Del	DEL	ENST00000337401.4	hg19	CCDS54276.1																																																																																			.	.		0.413	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		-	44833582	T	-	44833582	7	5	218	1	0	1	0	1	0	0	0	0	17653	1551	54	0	1999	0	ZFP112	19	44833582	Frame_Shift_Del	DEL	T	TCGA-DD-AAEE-01A-11D-A40R-10	25043304	44833582	14295401	84	31357										
FOSB	2354	hgsc.bcm.edu	37	chr19	45974560	45974560	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	tgaccgaccgactccaggcgGtgaggacaggccctggggtg	17	12	0	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr19:45974560G>T	ENST00000353609.3	+	3	1147		c.e3+1		FOSB_ENST00000586615.1_Splice_Site|FOSB_ENST00000417353.2_Intron|ERCC1_ENST00000423698.2_Intron|FOSB_ENST00000592436.1_Splice_Site|FOSB_ENST00000592811.1_Splice_Site|FOSB_ENST00000590335.1_3'UTR|FOSB_ENST00000585836.1_Intron|FOSB_ENST00000591858.1_Splice_Site|FOSB_ENST00000443841.2_Intron	NM_006732.2	NP_006723.2	P53539	FOSB_HUMAN	FBJ murine osteosarcoma viral oncogene homolog B						cellular response to calcium ion (GO:0071277)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	13		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00814)|Epithelial(262;0.18)|GBM - Glioblastoma multiforme(486;0.242)		ACTCCAGGCGGTGAGGACAGG	0.602																																					.		Atlas-SNP	.											.	FOSB	29	.	0			c.555+1G>T						.						30	22	25					19																	45974560		2164	4231	6395	SO:0001630	splice_region_variant	2354	exon3			CAGGCGGTGAGGA		CCDS12664.1, CCDS46113.1	19q13.3	2013-01-10						"basic leucine zipper proteins"	3797	protein-coding gene	gene with protein product	"oncogene FOS-B", "activator protein 1"	164772				1301997	Standard	NM_006732		Approved	G0S3, GOSB, GOS3, AP-1, MGC42291, DKFZp686C0818	uc002pbx.4	P53539		ENST00000353609.3:c.555+1G>T	chr19.hg19:g.45974560G>T		33.0	0.0		70.0	23.0	NM_006732	A8K9K5|A8VJE1|A8VJE6|A8VJF0|A8VJF3|A8VJF7|A8VJG1|A8VJG5|A8VJG9|E7EPR6|E9PHJ3|K7EMJ6|Q49AD7	Splice_Site	SNP	ENST00000353609.3	hg19	CCDS12664.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.420662	0.83559	.	.	ENSG00000125740	ENST00000353609;ENST00000455928	.	.	.	4.51	4.51	0.55191	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7514	0.69528	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FOSB	50666400	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.214000	0.95140	2.349000	0.79799	0.561000	0.74099	.	.	.		0.602	FOSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459561.1	NM_006732	Intron	T	45974560	G	T	45974560	5	4	218	1	0	0	0	0	0	0	1	0	5994	1275	44	3	566	3	FOSB	19	45974560	Splice_Site	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	1140978	45974560	13154423	85	31358										
PIH1D1	55011	hgsc.bcm.edu	37	chr19	49951314	49951314	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gtcgtaggcggtacatccctGgccttctgcggggagaaaaa	14	10	1	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr19:49951314G>C	ENST00000262265.5	-	4	578	c.343C>G	c.(343-345)Cag>Gag	p.Q115E	PIH1D1_ENST00000602226.1_5'Flank|PIH1D1_ENST00000596049.1_Missense_Mutation_p.Q115E	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	115					box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		GTACATCCCTGGCCTTCTGCG	0.642																																					p.Q115E		Atlas-SNP	.											.	PIH1D1	23	.	0			c.C343G						.						47	41	43					19																	49951314		2203	4300	6503	SO:0001583	missense	55011	exon4			ATCCCTGGCCTTC	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.343C>G	chr19.hg19:g.49951314G>C	ENSP00000262265:p.Gln115Glu	73.0	0.0		92.0	31.0	NM_017916	B4DGN7|B4E2X7|Q9BVL0	Missense_Mutation	SNP	ENST00000262265.5	hg19	CCDS12765.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.652592	0.47362	.	.	ENSG00000104872	ENST00000262265	T	0.16324	2.35	4.68	3.59	0.41128	.	0.260464	0.38492	N	0.001667	T	0.15609	0.0376	N	0.21282	0.65	0.41384	D	0.987575	P	0.38280	0.625	P	0.46110	0.504	T	0.02345	-1.1173	10	0.52906	T	0.07	-27.8553	9.1202	0.36782	0.0:0.0:0.7657:0.2343	.	115	Q9NWS0	PIHD1_HUMAN	E	115	ENSP00000262265:Q115E	ENSP00000262265:Q115E	Q	-	1	0	PIH1D1	54643126	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.867000	0.39499	2.423000	0.82170	0.655000	0.94253	CAG	.	.		0.642	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916		C	49951314	G	C	49951314	3	2	218	1	0	0	0	0	1	0	0	0	11915	1357	47	4	553	4	PIH1D1	19	49951314	Missense_Mutation	SNP	G	TCGA-DD-AAEE-01A-11D-A40R-10	3976754	49951314	9177669	86	31359										
ZNF83	55769	hgsc.bcm.edu	37	chr19	53116865	53116865	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ccttgccacactcattacatTtgtaaggtttctctccagta	5	12	2	0	rs141749555		TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr19:53116865T>C	ENST00000597597.1	-	2	3206	c.953A>G	c.(952-954)aAa>aGa	p.K318R	ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Missense_Mutation_p.K318R|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_Missense_Mutation_p.K318R|ZNF83_ENST00000301096.3_Missense_Mutation_p.K318R|ZNF83_ENST00000544146.1_Missense_Mutation_p.K318R|ZNF83_ENST00000391789.4_Missense_Mutation_p.K290R|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000545872.1_Missense_Mutation_p.K318R			P51522	ZNF83_HUMAN	zinc finger protein 83	318					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		CTCATTACATTTGTAAGGTTT	0.413																																					p.K318R		Atlas-SNP	.											.	ZNF83	73	.	0			c.A953G						.						98	104	102					19																	53116865		2203	4300	6503	SO:0001583	missense	55769	exon3			TTACATTTGTAAG	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"Zinc fingers, C2H2-type"	13158	protein-coding gene	gene with protein product		194558	"zinc finger protein 83 (HPF1)", "zinc finger protein 816B"	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.953A>G	chr19.hg19:g.53116865T>C	ENSP00000472619:p.Lys318Arg	68.0	0.0		108.0	10.0	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Missense_Mutation	SNP	ENST00000597597.1	hg19	CCDS12854.1	.	.	.	.	.	.	.	.	.	.	N	8.722	0.914503	0.17907	.	.	ENSG00000167766	ENST00000536937;ENST00000301096;ENST00000544146;ENST00000434535;ENST00000545872;ENST00000541777;ENST00000391789	T;T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11;2.11	2.16	1.09	0.20402	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22551	0.0544	N	0.16201	0.385	0.09310	N	1	B;D	0.69078	0.017;0.997	B;D	0.81914	0.01;0.995	T	0.10706	-1.0618	9	0.54805	T	0.06	.	3.4318	0.07432	0.0:0.144:0.2323:0.6237	.	290;318	P51522-2;P51522	.;ZNF83_HUMAN	R	318;318;318;290;318;318;290	ENSP00000445993:K318R;ENSP00000301096:K318R;ENSP00000445470:K318R;ENSP00000440713:K318R;ENSP00000439681:K318R;ENSP00000375666:K290R	ENSP00000301096:K318R	K	-	2	0	ZNF83	57808677	0.000000	0.05858	0.706000	0.30403	0.082000	0.17680	-0.250000	0.08830	0.101000	0.17610	-0.540000	0.04249	AAA	.	.		0.413	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300		C	53116865	T	C	53116865	3	2	218	1	0	0	0	0	1	0	0	0	18198	1841	64	2	601	2	ZNF83	19	53116865	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	3165551	53116865	6012118	87	31360										
TPTE	7179	hgsc.bcm.edu	37	chr21	10906970	10906970	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	aaaaagtatctccacggcaaAatctgatggataaattctcc	6	9	3	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chr21:10906970A>T	ENST00000361285.4	-	24	1920	c.1591T>A	c.(1591-1593)Ttt>Att	p.F531I	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Missense_Mutation_p.F493I|TPTE_ENST00000298232.7_Missense_Mutation_p.F513I	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	531	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCCACGGCAAAATCTGATGGA	0.348																																					p.F531I		Atlas-SNP	.											.	TPTE	513	.	0			c.T1591A						.						135	121	126					21																	10906970		2203	4300	6503	SO:0001583	missense	7179	exon24			CGGCAAAATCTGA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1591T>A	chr21.hg19:g.10906970A>T	ENSP00000355208:p.Phe531Ile	154.0	0.0		204.0	12.0	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	16.06	3.015489	0.54468	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.88664	-2.41;-2.41;-2.41	2.39	2.39	0.29439	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	U	0.000000	D	0.93726	0.7995	M	0.87180	2.865	0.48632	D	0.99968	D;D;D	0.89917	1.0;1.0;0.967	D;D;D	0.87578	0.998;0.998;0.928	D	0.93203	0.6593	10	0.72032	D	0.01	-27.5535	8.6793	0.34198	1.0:0.0:0.0:0.0	.	493;513;531	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	I	513;531;493	ENSP00000298232:F513I;ENSP00000355208:F531I;ENSP00000344441:F493I	ENSP00000298232:F513I	F	-	1	0	TPTE	9928841	0.998000	0.40836	0.082000	0.20525	0.005000	0.04900	5.171000	0.64996	1.339000	0.45563	0.155000	0.16302	TTT	.	.		0.348	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			T	10906970	A	T	10906970	3	4	218	1	0	0	0	0	1	0	0	0	16445	14	1	4	68	4	TPTE	21	10906970	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10		10906970	37222925	88	31361										
PDHA1	5160	hgsc.bcm.edu	37	chrX	19369497	19369497	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	actttcacccggggcctttcCgtccgagaaattctcgcaga	9	14	2	2			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chrX:19369497C>T	ENST00000422285.2	+	4	495	c.390C>T	c.(388-390)tcC>tcT	p.S130S	PDHA1_ENST00000379806.5_Silent_p.S168S|PDHA1_ENST00000379805.3_Silent_p.S130S|PDHA1_ENST00000540249.1_Silent_p.S130S|PDHA1_ENST00000545074.1_Silent_p.S137S			P08559	ODPA_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 1	130					acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)	18	Hepatocellular(33;0.183)					GGGGCCTTTCCGTCCGAGAAA	0.488																																					p.S168S		Atlas-SNP	.											.	PDHA1	85	.	0			c.C504T						.						96	92	93					X																	19369497		2203	4300	6503	SO:0001819	synonymous_variant	5160	exon5			CCTTTCCGTCCGA		CCDS14192.1, CCDS55380.1, CCDS55381.1, CCDS55382.1	Xp22.1	2008-02-05			ENSG00000131828	ENSG00000131828	1.2.4.1		8806	protein-coding gene	gene with protein product		300502		PDHA			Standard	NM_001173454		Approved		uc004czh.4	P08559	OTTHUMG00000021224	ENST00000422285.2:c.390C>T	chrX.hg19:g.19369497C>T		174.0	0.0		266.0	88.0	NM_001173454	A5YVE9|B2R5P7|B7Z3T7|B7Z3X5|Q53H41|Q5JPT8|Q9NP12|Q9UBJ8|Q9UBU0|Q9UNG4|Q9UNG5	Silent	SNP	ENST00000422285.2	hg19	CCDS14192.1																																																																																			.	.		0.488	PDHA1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055977.1			T	19369497	C	T	19369497	2	4	218	1	0	0	0	0	0	0	0	1	11673	639	23	1		1	PDHA1	23	19369497	Silent	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10		19369497	135901063	89	31362										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34149803	34149803	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	cgggaggctctgggaggagaTgggacaccggagtctcggga	20	8	2	1			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chrX:34149803T>G	ENST00000346193.3	-	1	644	c.593A>C	c.(592-594)cAt>cCt	p.H198P		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	198	Pro-rich.									NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						TGGGAGGAGATGGGACACCGG	0.607																																					p.H198P		Atlas-SNP	.											.	FAM47A	249	.	0			c.A593C						.						52	55	54					X																	34149803		2200	4296	6496	SO:0001583	missense	158724	exon1			AGGAGATGGGACA	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.593A>C	chrX.hg19:g.34149803T>G	ENSP00000345029:p.His198Pro	42.0	0.0		80.0	4.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	T	7.208	0.594785	0.13875	.	.	ENSG00000185448	ENST00000346193	T	0.13420	2.59	0.603	0.603	0.17541	.	.	.	.	.	T	0.11239	0.0274	L	0.48642	1.525	0.09310	N	1	B	0.17667	0.023	B	0.17722	0.019	T	0.34304	-0.9834	8	0.25106	T	0.35	.	.	.	.	.	198	Q5JRC9	FA47A_HUMAN	P	198	ENSP00000345029:H198P	ENSP00000345029:H198P	H	-	2	0	FAM47A	34059724	0.014000	0.17966	0.045000	0.18777	0.044000	0.14063	-0.226000	0.09139	0.451000	0.26802	0.441000	0.28932	CAT	.	.		0.607	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		G	34149803	T	G	34149803	3	3	218	1	0	0	0	0	1	0	0	0	5577	1464	51	5	1786	5	FAM47A	23	34149803	Missense_Mutation	SNP	T	TCGA-DD-AAEE-01A-11D-A40R-10	14780306	34149803	121120757	90	31363										
TBX22	50945	hgsc.bcm.edu	37	chrX	79277884	79277884	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	gcctgagctgcgggagaaaaAgggcggagaggaagaggagg	21	5	0	4			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chrX:79277884A>G	ENST00000373294.5	+	1	144	c.116A>G	c.(115-117)aAg>aGg	p.K39R	TBX22_ENST00000373291.1_5'Flank|TBX22_ENST00000476373.1_3'UTR|TBX22_ENST00000373296.3_Missense_Mutation_p.K39R|TBX22_ENST00000442340.1_5'UTR	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	39					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						CGGGAGAAAAAGGGCGGAGAG	0.607																																					p.K39R		Atlas-SNP	.											.	TBX22	118	.	0			c.A116G						.						59	48	52					X																	79277884		2203	4297	6500	SO:0001583	missense	50945	exon1			AGAAAAAGGGCGG	AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"T-boxes"	11600	protein-coding gene	gene with protein product		300307	"cleft palate and/or ankyloglossia"	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.116A>G	chrX.hg19:g.79277884A>G	ENSP00000362390:p.Lys39Arg	71.0	0.0		114.0	5.0	NM_016954	Q5JZ06|Q96LC0|Q9HBF1	Missense_Mutation	SNP	ENST00000373294.5	hg19	CCDS14445.1	.	.	.	.	.	.	.	.	.	.	A	1.426	-0.571531	0.03882	.	.	ENSG00000122145	ENST00000373296;ENST00000373294	D;D	0.86769	-2.17;-2.17	4.62	1.95	0.26073	.	0.810458	0.11000	N	0.610618	T	0.66479	0.2793	N	0.03608	-0.345	0.09310	N	0.99999	B	0.02656	0.0	B	0.04013	0.001	T	0.55211	-0.8176	10	0.14656	T	0.56	.	4.4557	0.11642	0.643:0.1764:0.1805:0.0	.	39	Q9Y458	TBX22_HUMAN	R	39	ENSP00000362393:K39R;ENSP00000362390:K39R	ENSP00000362390:K39R	K	+	2	0	TBX22	79164540	0.001000	0.12720	0.017000	0.16124	0.070000	0.16714	1.155000	0.31700	1.512000	0.48834	0.486000	0.48141	AAG	.	.		0.607	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954		G	79277884	A	G	79277884	3	3	218	1	0	0	0	0	1	0	0	0	15673	72	3	2	118	2	TBX22	23	79277884	Missense_Mutation	SNP	A	TCGA-DD-AAEE-01A-11D-A40R-10	45128081	79277884	75992676	91	31364										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128630827	128630827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.570496894409938	3.19478260869565	0	0.454545454545454	1	0	ccagcaagcgagtcatctggCtgaaaatgagaacccttgaa	10	10	2	3			TCGA-DD-AAEE-01A-11D-A40R-10	TCGA-DD-AAEE-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80030570-7419-492e-92fc-246a27b5b673	bf19b000-ebe1-4b9b-9827-d946d815d0b4	g.chrX:128630827C>T	ENST00000371122.4	-	12	1655	c.1526G>A	c.(1525-1527)aGc>aAc	p.S509N	SMARCA1_ENST00000371121.3_Missense_Mutation_p.S509N|SMARCA1_ENST00000371123.1_Missense_Mutation_p.S509N	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	509	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						AGTCATCTGGCTGAAAATGAG	0.388																																					p.S509N		Atlas-SNP	.											.	SMARCA1	126	.	0			c.G1526A						.						115	105	108					X																	128630827		2203	4300	6503	SO:0001583	missense	6594	exon12			ATCTGGCTGAAAA	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.1526G>A	chrX.hg19:g.128630827C>T	ENSP00000360163:p.Ser509Asn	118.0	0.0		152.0	118.0	NM_139035	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	hg19	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.874123	0.91664	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	5.3	5.3	0.74995	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93792	0.8015	H	0.99764	4.76	0.80722	D	1	D;D;D;D	0.71674	0.998;0.996;0.997;0.996	D;D;D;D	0.69142	0.947;0.917;0.962;0.917	D	0.96997	0.9726	10	0.87932	D	0	-9.5525	18.0774	0.89432	0.0:1.0:0.0:0.0	.	488;509;509;509	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	N	509;509;509;488	ENSP00000360162:S509N;ENSP00000360164:S509N;ENSP00000360163:S509N;ENSP00000404275:S488N	ENSP00000360162:S509N	S	-	2	0	SMARCA1	128458508	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.742000	0.85008	2.205000	0.71048	0.422000	0.28245	AGC	.	.		0.388	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		T	128630827	C	T	128630827	3	4	218	1	0	0	0	0	1	0	0	0	14783	797	28	3	1690	3	SMARCA1	23	128630827	Missense_Mutation	SNP	C	TCGA-DD-AAEE-01A-11D-A40R-10	49352943	128630827	26639733	92	31365										
RHCE	6006	hgsc.bcm.edu	37	chr1	25735269	25735269	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ccaagcgccagcatgaagagGttgaaggccacactgctcca	11	13	0	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:25735269G>T	ENST00000294413.7	-	2	298	c.240C>A	c.(238-240)aaC>aaA	p.N80K	RHCE_ENST00000349320.3_Missense_Mutation_p.N64K|RHCE_ENST00000425135.1_Missense_Mutation_p.N80K|RHCE_ENST00000340849.4_Missense_Mutation_p.N80K|RHCE_ENST00000346452.4_Missense_Mutation_p.N80K|AL031284.1_ENST00000577655.1_RNA|RHCE_ENST00000243186.6_Missense_Mutation_p.N80K|RHCE_ENST00000455194.1_Missense_Mutation_p.N80K|RHCE_ENST00000374352.2_Missense_Mutation_p.N64K|RHCE_ENST00000413854.1_Missense_Mutation_p.N80K|RHCE_ENST00000349438.4_Missense_Mutation_p.N80K|RHCE_ENST00000495048.1_5'UTR	NM_020485.4	NP_065231	P18577	RHCE_HUMAN	Rh blood group, CcEe antigens	80						integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			endometrium(8)|large_intestine(6)|lung(3)	17		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)		GCATGAAGAGGTTGAAGGCCA	0.582																																					p.N80K		Atlas-SNP	.											.	RHCE	36	.	0			c.C240A						.						82	50	62					1																	25735269		2169	3642	5811	SO:0001583	missense	6006	exon2			GAAGAGGTTGAAG	BC075081	CCDS30634.1, CCDS30635.1, CCDS30636.1, CCDS30637.1	1p36.11	2014-09-17	2006-02-23		ENSG00000188672	ENSG00000188672		"CD molecules", "Blood group antigens"	10008	protein-coding gene	gene with protein product		111700	"Rhesus blood group, CcEe antigens"	RH		8220426	Standard	NM_138618		Approved	CD240CE	uc001bkf.3	P18577	OTTHUMG00000007650	ENST00000294413.7:c.240C>A	chr1.hg19:g.25735269G>T	ENSP00000294413:p.Asn80Lys	232.0	1.0		217.0	157.0	NM_138617	A7DW68|B7UDF3|B7UDF4|B7UDF5|B7UDF6|B7UDF7|B7UDF8|B7UDF9|B7UDG0|B7UDG1|B7UDG2|B7UDG3|Q02163|Q02164|Q02165|Q16160|Q2MJW0|Q2VC86|Q3LTM6|Q6AZX5|Q6J2U3|Q7RU06|Q8IZT2|Q8IZT3|Q8IZT4|Q8IZT5|Q9UD13|Q9UD14|Q9UD15|Q9UD16|Q9UD73|Q9UD74|Q9UEC2|Q9UEC3|Q9UPN0	Missense_Mutation	SNP	ENST00000294413.7	hg19	CCDS30635.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212941	0.39102	.	.	ENSG00000188672	ENST00000413854;ENST00000539650;ENST00000455194;ENST00000374352;ENST00000243186;ENST00000425135;ENST00000340849;ENST00000349320;ENST00000346452;ENST00000294413;ENST00000447203;ENST00000349438	T;T;T;T;T;T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83	4.34	2.43	0.29744	Ammonium transporter AmtB-like (3);	0.266849	0.40818	N	0.001016	T	0.54806	0.1881	M	0.93462	3.42	0.50039	D	0.999846	D;D;D;D;D	0.67145	0.984;0.986;0.996;0.992;0.996	D;D;D;D;D	0.85130	0.939;0.934;0.969;0.911;0.997	T	0.55528	-0.8127	10	0.87932	D	0	-7.6805	6.2622	0.20907	0.2275:0.0:0.7725:0.0	.	64;80;80;80;80	Q5VSJ9;E7EQ47;Q5VSJ7;Q5VSJ8;P18577	.;.;.;.;RHCE_HUMAN	K	80;80;80;64;80;80;80;64;80;80;80;80	ENSP00000415417:N80K;ENSP00000416275:N80K;ENSP00000363472:N64K;ENSP00000243186:N80K;ENSP00000392809:N80K;ENSP00000345084:N80K;ENSP00000311185:N64K;ENSP00000344485:N80K;ENSP00000294413:N80K;ENSP00000334570:N80K	ENSP00000243186:N80K	N	-	3	2	RHCE	25607856	1.000000	0.71417	0.995000	0.50966	0.145000	0.21501	0.921000	0.28718	0.449000	0.26747	0.561000	0.74099	AAC	.	.		0.582	RHCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020312.2	NM_020485		T	25735269	G	T	25735269	3	4	219	1	0	0	0	0	1	0	0	0	13340	1252	44	3	1049	3	RHCE	1	25735269	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10		25735269	223515352	1	31366										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27023300	27023300	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gcgatggggtgggggcgcctCctcactcagccgcggccgcc	17	16	2	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:27023300C>A	ENST00000324856.7	+	1	777	c.406C>A	c.(406-408)Cct>Act	p.P136T	ARID1A_ENST00000457599.2_Missense_Mutation_p.P136T|RP5-968P14.2_ENST00000569378.1_RNA	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	136					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		gggggcgCCTCCTCACTCAGC	0.766			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.P136T		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.C406A						.						1	1	1					1																	27023300		633	1495	2128	SO:0001583	missense	8289	exon1			GCGCCTCCTCACT	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.406C>A	chr1.hg19:g.27023300C>A	ENSP00000320485:p.Pro136Thr	22.0	0.0		20.0	5.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.015745	0.35606	.	.	ENSG00000117713	ENST00000324856;ENST00000457599	T;T	0.02301	4.56;4.35	3.07	3.07	0.35406	.	0.342163	0.22384	U	0.060780	T	0.01353	0.0044	N	0.08118	0	0.80722	D	1	P;P	0.40302	0.588;0.712	B;B	0.39660	0.161;0.306	T	0.66767	-0.5840	10	0.10377	T	0.69	-2.9899	9.7357	0.40386	0.0:1.0:0.0:0.0	.	136;136	O14497;O14497-2	ARI1A_HUMAN;.	T	136	ENSP00000320485:P136T;ENSP00000387636:P136T	ENSP00000320485:P136T	P	+	1	0	ARID1A	26895887	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	0.551000	0.23361	1.715000	0.51383	0.385000	0.25706	CCT	.	.		0.766	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27023300	C	A	27023300	3	1	219	1	0	0	0	0	1	0	0	0	913	855	30	3	408	3	ARID1A	1	27023300	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	1288031	27023300	222227321	2	31367										
C1orf175	374977	hgsc.bcm.edu	37	chr1	55118887	55118887	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gctccagcctccctccagatCaccagttcttgttctggtga	8	15	3	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:55118887C>A	ENST00000421030.2	+	3	573	c.288C>A	c.(286-288)atC>atA	p.I96I	MROH7-TTC4_ENST00000414150.2_Silent_p.I96I|MROH7_ENST00000454855.2_Intron|MROH7_ENST00000339553.5_Silent_p.I96I|MROH7_ENST00000409996.1_Intron|MROH7_ENST00000545244.1_Intron|MROH7_ENST00000395690.2_Silent_p.I96I|MROH7_ENST00000472987.1_3'UTR	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	96						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CCCTCCAGATCACCAGTTCTT	0.567																																					p.I96I		Atlas-SNP	.											.	.	.	.	0			c.C288A						.						84	83	83					1																	55118887		1965	4144	6109	SO:0001819	synonymous_variant	374977	exon3			CCAGATCACCAGT	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.288C>A	chr1.hg19:g.55118887C>A		70.0	0.0		66.0	9.0	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	hg19	CCDS41342.2																																																																																			.	.		0.567	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		A	55118887	C	A	55118887	2	1	219	1	0	0	0	0	0	0	0	1	2018	816	29	3		3	C1orf175	1	55118887	Silent	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	28095587	55118887	194131734	3	31368										
HRNR	388697	hgsc.bcm.edu	37	chr1	152193174	152193174	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ccccgaaccggacccatgtcGgacgtggctaggagactggc	14	14	0	1	rs139907915	byFrequency	TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:152193174G>A	ENST00000368801.2	-	3	1006	c.931C>T	c.(931-933)Cga>Tga	p.R311*	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	311					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACCCATGTCGGACGTGGCTA	0.607																																					p.R311X		Atlas-SNP	.											.	HRNR	403	.	0			c.C931T						.						97	105	102					1																	152193174		2203	4300	6503	SO:0001587	stop_gained	388697	exon3			CATGTCGGACGTG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.931C>T	chr1.hg19:g.152193174G>A	ENSP00000357791:p.Arg311*	97.0	0.0		189.0	8.0	NM_001009931	Q5DT20|Q5U1F4	Nonsense_Mutation	SNP	ENST00000368801.2	hg19	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.417316	0.62622	.	.	ENSG00000197915	ENST00000368801	.	.	.	3.6	-7.2	0.01495	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	.	3.1173	0.06379	0.0847:0.1998:0.2514:0.4641	.	.	.	.	X	311	.	ENSP00000357791:R311X	R	-	1	2	HRNR	150459798	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.145000	0.10265	-1.739000	0.01347	-0.282000	0.10007	CGA	.	G|0.999;T|0.001		0.607	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		A	152193174	G	A	152193174	4	1	219	1	0	0	0	0	0	1	0	0	7368	1124	39	1	7625	1	HRNR	1	152193174	Nonsense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	97074287	152193174	97057447	4	31369										
FLG2	388698	hgsc.bcm.edu	37	chr1	152325270	152325270	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cctgtatgtgtgtgtgagacCcctgagtgcacttcactgtc	11	11	1	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:152325270C>A	ENST00000388718.5	-	3	5064	c.4992G>T	c.(4990-4992)ggG>ggT	p.G1664G	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1664					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTGTGAGACCCCTGAGTGCA	0.512																																					p.G1664G		Atlas-SNP	.											.	FLG2	431	.	0			c.G4992T						.						462	406	425					1																	152325270		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			TGAGACCCCTGAG	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.4992G>T	chr1.hg19:g.152325270C>A		64.0	0.0		138.0	9.0	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	hg19	CCDS30861.1																																																																																			.	.		0.512	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152325270	C	A	152325270	2	1	219	1	0	0	0	0	0	0	0	1	5931	610	22	3		3	FLG2	1	152325270	Silent	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	132096	152325270	96925351	5	31370										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842253	154842253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gctgctgctgaagctgcggaGgctgaggctgcagcgagggt	19	9	0	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:154842253G>T	ENST00000271915.4	-	1	503	c.188C>A	c.(187-189)cCt>cAt	p.P63H	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	63	Gln-rich.|Pro-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	aagctgcggaggctgaggctg	0.697																																					p.P63H		Atlas-SNP	.											.	KCNN3	141	.	0			c.C188A						.						6	4	5					1																	154842253		1984	3925	5909	SO:0001583	missense	3782	exon1			TGCGGAGGCTGAG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.188C>A	chr1.hg19:g.154842253G>T	ENSP00000271915:p.Pro63His	64.0	0.0		176.0	19.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	g	11.14	1.552427	0.27739	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.56275	0.47	5.07	3.18	0.36537	.	1.727610	0.03258	N	0.182822	T	0.18551	0.0445	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.11372	-1.0590	8	0.33141	T	0.24	-4.1487	6.4327	0.21807	0.0918:0.0:0.7284:0.1798	.	.	.	.	H	63;158	ENSP00000271915:P63H	ENSP00000271915:P63H	P	-	2	0	KCNN3	153108877	0.863000	0.29885	1.000000	0.80357	0.998000	0.95712	1.873000	0.39558	0.823000	0.34589	0.563000	0.77884	CCT	.	.		0.697	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154842253	G	T	154842253	3	4	219	1	0	0	0	0	1	0	0	0	8089	1000	35	3	2061	3	KCNN3	1	154842253	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	2516983	154842253	94408368	6	31371										
PEAR1	375033	hgsc.bcm.edu	37	chr1	156878621	156878621	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cagtgcgcgccgggttacacGgtgaggcgcgcccggctgca	17	14	0	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:156878621G>A	ENST00000338302.3	+	11	1515	c.1290G>A	c.(1288-1290)acG>acA	p.T430T	PEAR1_ENST00000292357.7_Splice_Site_p.T430T			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	430	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CGGGTTACACGGTGAGGCGCG	0.687																																					p.T430T		Atlas-SNP	.											.	PEAR1	118	.	0			c.G1290A						.						37	31	33					1																	156878621		2202	4300	6502	SO:0001630	splice_region_variant	375033	exon10			TTACACGGTGAGG	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"multiple EGF-like-domains 12"	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.1290+1G>A	chr1.hg19:g.156878621G>A		39.0	0.0		79.0	12.0	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	hg19	CCDS30892.1																																																																																			.	.		0.687	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	Silent	A	156878621	G	A	156878621	5	1	219	1	0	0	0	0	0	0	1	0	11721	1130	39	1	1324	1	PEAR1	1	156878621	Splice_Site	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	2036368	156878621	92372000	7	31372										
QSOX1	5768	hgsc.bcm.edu	37	chr1	180144477	180144477	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tcttcaaggcctttaccaagAacggctcgggagcagtattt	10	10	2	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:180144477A>G	ENST00000367602.3	+	3	462	c.388A>G	c.(388-390)Aac>Gac	p.N130D	QSOX1_ENST00000367600.5_Missense_Mutation_p.N130D			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	130	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						CTTTACCAAGAACGGCTCGGG	0.537																																					p.N130D		Atlas-SNP	.											.	QSOX1	79	.	0			c.A388G						.						146	128	134					1																	180144477		2203	4300	6503	SO:0001583	missense	5768	exon3			ACCAAGAACGGCT	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"quiescin Q6"	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.388A>G	chr1.hg19:g.180144477A>G	ENSP00000356574:p.Asn130Asp	123.0	0.0		345.0	18.0	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Missense_Mutation	SNP	ENST00000367602.3	hg19	CCDS1337.1	.	.	.	.	.	.	.	.	.	.	A	0.119	-1.127801	0.01770	.	.	ENSG00000116260	ENST00000367602;ENST00000367600	T;T	0.16597	2.33;2.33	3.87	0.263	0.15602	Thioredoxin-like fold (3);	0.938103	0.09142	N	0.842812	T	0.08891	0.0220	N	0.16478	0.41	0.24208	N	0.995481	B;B;B	0.13145	0.007;0.004;0.005	B;B;B	0.15052	0.009;0.012;0.005	T	0.43491	-0.9388	10	0.12766	T	0.61	-0.2332	6.6242	0.22820	0.6589:0.0:0.3411:0.0	.	130;130;130	A8K477;O00391;O00391-2	.;QSOX1_HUMAN;.	D	130	ENSP00000356574:N130D;ENSP00000356572:N130D	ENSP00000356572:N130D	N	+	1	0	QSOX1	178411100	0.048000	0.20356	0.160000	0.22671	0.040000	0.13550	0.171000	0.16685	0.030000	0.15379	-0.899000	0.02877	AAC	.	.		0.537	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826		G	180144477	A	G	180144477	3	3	219	1	0	0	0	0	1	0	0	0	12898	246	9	2	398	2	QSOX1	1	180144477	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	23265856	180144477	69106144	8	31373										
DHX9	1660	hgsc.bcm.edu	37	chr1	182828232	182828232	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aattgatgtaccagttggaaCaggatcatgatttgcaagca	10	6	1	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:182828232C>T	ENST00000367549.3	+	11	1230	c.1120C>T	c.(1120-1122)Cag>Tag	p.Q374*		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	374	MTAD.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						CCAGTTGGAACAGGATCATGA	0.378																																					p.Q374X	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.C1120T						.						117	105	108					1																	182828232		1868	4116	5984	SO:0001587	stop_gained	1660	exon11			TTGGAACAGGATC	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.1120C>T	chr1.hg19:g.182828232C>T	ENSP00000356520:p.Gln374*	80.0	0.0		194.0	18.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Nonsense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	C	38	7.269519	0.98175	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	.	.	.	5.9	5.9	0.94986	.	0.120124	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	15.5092	0.75766	0.139:0.861:0.0:0.0	.	.	.	.	X	374	.	ENSP00000356520:Q374X	Q	+	1	0	DHX9	181094855	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.123000	0.64703	2.786000	0.95864	0.563000	0.77884	CAG	.	.		0.378	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		T	182828232	C	T	182828232	4	4	219	1	0	0	0	0	0	1	0	0	4518	479	17	3	1158	3	DHX9	1	182828232	Nonsense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	2683755	182828232	66422389	9	31374										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186136049	186136049	+	Frame_Shift_Del	DEL	A	A	-													0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tgtggaagtggctttcgaagAacctctgatgggctgagttg							TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:186136049delA	ENST00000271588.4	+	100	15778	c.15549delA	c.(15547-15549)agafs	p.R5183fs	HMCN1_ENST00000367492.2_Frame_Shift_Del_p.R5183fs	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5183	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GCTTTCGAAGAACCTCTGATG	0.453																																					p.R5183fs		Atlas-INDEL	.											.	HMCN1	797	.	0			c.15548delG						.						195	172	180					1																	186136049		2203	4300	6503	SO:0001589	frameshift_variant	83872	exon100			.	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15549delA	chr1.hg19:g.186136049delA	ENSP00000271588:p.Arg5183fs	98.0	0.0		214.0	142.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Frame_Shift_Del	DEL	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.453	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		-	186136049	A	-	186136049	7	5	219	1	0	1	0	1	0	0	0	0	7229	243	9	0	15947	0	HMCN1	1	186136049	Frame_Shift_Del	DEL	A	TCGA-DD-AAEG-01A-11D-A38X-10	3307817	186136049	63114572	10	31375										
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186908281	186908281	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aaaagatatgttgagtctttAtggaagaagaaaagctctgg	11	3	2	4			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:186908281A>T	ENST00000367466.3	+	9	989	c.837A>T	c.(835-837)ttA>ttT	p.L279F	PLA2G4A_ENST00000442353.2_Missense_Mutation_p.L219F|PLA2G4A_ENST00000466600.1_3'UTR	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	279	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	TTGAGTCTTTATGGAAGAAGA	0.353																																					p.L279F		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.A837T						.						80	81	81					1																	186908281		2203	4300	6503	SO:0001583	missense	5321	exon9			GTCTTTATGGAAG	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.837A>T	chr1.hg19:g.186908281A>T	ENSP00000356436:p.Leu279Phe	155.0	0.0		331.0	21.0	NM_024420	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	hg19	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.949421	0.73787	.	.	ENSG00000116711	ENST00000367466;ENST00000442353	T;T	0.14144	2.53;2.53	5.93	-3.22	0.05125	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.000000	0.85682	D	0.000000	T	0.39733	0.1089	M	0.89353	3.025	0.47341	D	0.99939	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.48269	-0.9050	10	0.87932	D	0	-16.2632	16.02	0.80473	0.3428:0.0:0.6572:0.0	.	219;279	E7EU42;P47712	.;PA24A_HUMAN	F	279;219	ENSP00000356436:L279F;ENSP00000406892:L219F	ENSP00000356436:L279F	L	+	3	2	PLA2G4A	185174904	0.778000	0.28640	0.927000	0.36925	0.996000	0.88848	-0.050000	0.11904	-0.917000	0.03813	0.533000	0.62120	TTA	.	.		0.353	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		T	186908281	A	T	186908281	3	4	219	1	0	0	0	0	1	0	0	0	12010	446	16	4	867	4	PLA2G4A	1	186908281	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	772232	186908281	62342340	11	31376										
CD46	4179	hgsc.bcm.edu	37	chr1	207934753	207934753	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gagcacgatttattgtggtgAcaattcagtgtggagtcgtg	14	5	1	1	rs147837939		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:207934753A>G	ENST00000358170.2	+	5	791	c.635A>G	c.(634-636)gAc>gGc	p.D212G	CD46_ENST00000361067.1_Missense_Mutation_p.D212G|CD46_ENST00000322875.4_Missense_Mutation_p.D212G|CD46_ENST00000322918.5_Missense_Mutation_p.D212G|CD46_ENST00000367042.1_Missense_Mutation_p.D212G|CD46_ENST00000367047.1_Missense_Mutation_p.D149G|CD46_ENST00000354848.1_Missense_Mutation_p.D212G|CD46_ENST00000360212.2_Missense_Mutation_p.D212G|CD46_ENST00000469535.1_3'UTR|CD46_ENST00000441839.2_Missense_Mutation_p.D212G|CD46_ENST00000367041.1_Missense_Mutation_p.D212G|CD46_ENST00000357714.1_Missense_Mutation_p.D212G|CD46_ENST00000480003.1_Missense_Mutation_p.D212G	NM_002389.4	NP_002380.3	P15529	MCP_HUMAN	CD46 molecule, complement regulatory protein	212	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adaptive immune response (GO:0002250)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|interleukin-10 production (GO:0032613)|negative regulation of complement activation (GO:0045916)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transforming growth factor beta production (GO:0071636)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)|regulation of Notch signaling pathway (GO:0008593)|sequestering of extracellular ligand from receptor (GO:0035581)|single fertilization (GO:0007338)|T cell mediated immunity (GO:0002456)|viral process (GO:0016032)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|inner acrosomal membrane (GO:0002079)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cadherin binding (GO:0045296)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	19						TATTGTGGTGACAATTCAGTG	0.368																																					p.D212G		Atlas-SNP	.											.	CD46	34	.	0			c.A635G						.						177	149	158					1																	207934753		2203	4300	6503	SO:0001583	missense	4179	exon5			GTGGTGACAATTC	BC030594	CCDS1479.1, CCDS1480.1, CCDS1481.1, CCDS1482.1, CCDS1484.1, CCDS1485.1, CCDS31008.1, CCDS31009.1	1q32	2014-09-17	2006-03-28	2006-02-09	ENSG00000117335	ENSG00000117335		"CD molecules", "Complement system"	6953	protein-coding gene	gene with protein product		120920	"antigen identified by monoclonal antibody TRA-2-10", "membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)", "CD46 antigen, complement regulatory protein"	MIC10, MCP		7929741	Standard	NM_002389		Approved	TRA2.10, MGC26544, TLX	uc001hgj.3	P15529	OTTHUMG00000036397	ENST00000358170.2:c.635A>G	chr1.hg19:g.207934753A>G	ENSP00000350893:p.Asp212Gly	79.0	0.0		165.0	19.0	NM_172352	A0T1T0|A0T1T1|A0T1T2|Q15429|Q53GV9|Q5HY94|Q5VWS6|Q5VWS7|Q5VWS8|Q5VWS9|Q5VWT0|Q5VWT1|Q5VWT2|Q6N0A1|Q7Z3R5|Q9NNW2|Q9NNW3|Q9NNW4|Q9UCJ4	Missense_Mutation	SNP	ENST00000358170.2	hg19	CCDS1485.1	.	.	.	.	.	.	.	.	.	.	A	0.501	-0.870770	0.02570	.	.	ENSG00000117335	ENST00000358170;ENST00000354848;ENST00000322918;ENST00000367042;ENST00000367041;ENST00000357714;ENST00000322875;ENST00000367047;ENST00000441839;ENST00000361067;ENST00000360212;ENST00000480003	T;T;T;T;T;T;T;T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15	4.85	-5.27	0.02763	Complement control module (2);Sushi/SCR/CCP (3);	2.089050	0.02063	N	0.050905	T	0.34658	0.0905	N	0.02202	-0.64	0.09310	N	1	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.33448	0.0;0.0;0.0;0.0;0.076;0.213;0.0;0.0;0.0;0.001;0.0;0.175;0.412;0.252	B;B;B;B;B;B;B;B;B;B;B;B;B;P	0.44422	0.001;0.0;0.002;0.001;0.173;0.321;0.001;0.002;0.001;0.003;0.001;0.237;0.314;0.449	T	0.38156	-0.9674	10	0.02654	T	1	.	2.4359	0.04483	0.31:0.3888:0.191:0.1102	.	212;212;212;212;212;212;212;212;212;212;212;212;212;212	P15529-4;P15529-5;P15529-14;P15529-3;P15529-12;P15529-13;P15529-2;P15529-11;P15529-7;P15529-9;P15529-15;P15529-6;P15529-8;P15529	.;.;.;.;.;.;.;.;.;.;.;.;.;MCP_HUMAN	G	212;212;212;212;212;212;212;149;212;212;212;212	ENSP00000350893:D212G;ENSP00000346912:D212G;ENSP00000314664:D212G;ENSP00000356009:D212G;ENSP00000356008:D212G;ENSP00000350346:D212G;ENSP00000313875:D212G;ENSP00000356014:D149G;ENSP00000413543:D212G;ENSP00000354358:D212G;ENSP00000353342:D212G;ENSP00000418471:D212G	ENSP00000313875:D212G	D	+	2	0	CD46	206001376	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.024000	0.03603	-0.936000	0.03723	0.477000	0.44152	GAC	.	A|1.000;T|0.000		0.368	CD46-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088588.3	NM_172361		G	207934753	A	G	207934753	3	3	219	1	0	0	0	0	1	0	0	0	3020	275	10	2	653	2	CD46	1	207934753	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	21026472	207934753	41315868	12	31377										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214542922	214542922	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tcaagcccgtggttgcatagCaaacagaatccgttcgaaac	9	11	1	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:214542922C>A	ENST00000366956.5	-	17	3343	c.3149G>T	c.(3148-3150)tGc>tTc	p.C1050F	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	1050	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GGTTGCATAGCAAACAGAATC	0.502																																					p.C1050F	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											.	PTPN14	168	.	0			c.G3149T						.						255	232	240					1																	214542922		2203	4300	6503	SO:0001583	missense	5784	exon17			GCATAGCAAACAG	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.3149G>T	chr1.hg19:g.214542922C>A	ENSP00000355923:p.Cys1050Phe	159.0	0.0		308.0	13.0	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.526823	0.64860	.	.	ENSG00000152104	ENST00000366956	T	0.13420	2.59	5.51	5.51	0.81932	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.096235	0.64402	D	0.000001	T	0.12220	0.0297	L	0.48218	1.51	0.80722	D	1	P	0.41848	0.763	B	0.32342	0.144	T	0.15521	-1.0434	10	0.10902	T	0.67	.	19.4235	0.94732	0.0:1.0:0.0:0.0	.	1050	Q15678	PTN14_HUMAN	F	1050	ENSP00000355923:C1050F	ENSP00000355923:C1050F	C	-	2	0	PTPN14	212609545	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.840000	0.62817	2.564000	0.86499	0.650000	0.86243	TGC	.	.		0.502	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		A	214542922	C	A	214542922	3	1	219	1	0	0	0	0	1	0	0	0	12796	710	25	3	426	3	PTPN14	1	214542922	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	6608169	214542922	34707699	13	31378										
USH2A	7399	hgsc.bcm.edu	37	chr1	216405413	216405413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gctattacagatgtgattaaCtgcaccagttgtatggcatg	10	7	0	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:216405413C>T	ENST00000307340.3	-	14	3261	c.2875G>A	c.(2875-2877)Gtt>Att	p.V959I	USH2A_ENST00000366942.3_Missense_Mutation_p.V959I|USH2A_ENST00000366943.2_Missense_Mutation_p.V959I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	959	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATGTGATTAACTGCACCAGTT	0.403										HNSCC(13;0.011)																											p.V959I		Atlas-SNP	.											.	USH2A	1168	.	0			c.G2875A						.						126	113	117					1																	216405413		2203	4300	6503	SO:0001583	missense	7399	exon14			GATTAACTGCACC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.2875G>A	chr1.hg19:g.216405413C>T	ENSP00000305941:p.Val959Ile	290.0	0.0		618.0	27.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	5.481	0.273755	0.10403	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.54866	0.55;0.55;0.55	5.93	4.01	0.46588	EGF-like, laminin (3);	0.000000	0.40554	N	0.001066	T	0.42810	0.1219	L	0.46885	1.475	0.09310	N	1	B;P	0.39352	0.036;0.669	B;B	0.38156	0.059;0.266	T	0.22661	-1.0210	10	0.30078	T	0.28	.	8.7254	0.34467	0.2696:0.662:0.0:0.0684	.	959;959	O75445-2;O75445	.;USH2A_HUMAN	I	959	ENSP00000305941:V959I;ENSP00000355910:V959I;ENSP00000355909:V959I	ENSP00000305941:V959I	V	-	1	0	USH2A	214472036	0.697000	0.27767	0.002000	0.10522	0.003000	0.03518	1.409000	0.34680	0.786000	0.33708	0.650000	0.86243	GTT	.	.		0.403	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216405413	C	T	216405413	3	4	219	1	0	0	0	0	1	0	0	0	17051	565	20	3	12983	3	USH2A	1	216405413	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	1862491	216405413	32845208	14	31379										
OR2B11	127623	hgsc.bcm.edu	37	chr1	247614647	247614647	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gaaggatgagagccaggggcAccaacacgaagaaggccacc	14	11	0	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr1:247614647A>T	ENST00000318749.6	-	1	661	c.638T>A	c.(637-639)gTg>gAg	p.V213E		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			AGCCAGGGGCACCAACACGAA	0.567																																					p.V213E		Atlas-SNP	.											.	OR2B11	102	.	0			c.T638A						.						72	73	73					1																	247614647		2203	4300	6503	SO:0001583	missense	127623	exon1			AGGGGCACCAACA		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"GPCR / Class A : Olfactory receptors"	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.638T>A	chr1.hg19:g.247614647A>T	ENSP00000325682:p.Val213Glu	131.0	0.0		221.0	156.0	NM_001004492	B2RP03	Missense_Mutation	SNP	ENST00000318749.6	hg19	CCDS31090.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.669343	0.47677	.	.	ENSG00000177535	ENST00000318749	T	0.40756	1.02	5.09	5.09	0.68999	GPCR, rhodopsin-like superfamily (1);	0.312268	0.23201	N	0.050793	T	0.59088	0.2168	M	0.81942	2.565	0.31642	N	0.647853	P	0.51933	0.949	P	0.57846	0.828	T	0.69383	-0.5160	10	0.87932	D	0	.	9.2717	0.37675	0.8184:0.1816:0.0:0.0	.	213	Q5JQS5	OR2BB_HUMAN	E	213	ENSP00000325682:V213E	ENSP00000325682:V213E	V	-	2	0	OR2B11	245681270	0.000000	0.05858	0.706000	0.30403	0.250000	0.25880	0.034000	0.13776	2.273000	0.75805	0.523000	0.50628	GTG	.	.		0.567	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492		T	247614647	A	T	247614647	3	4	219	1	0	0	0	0	1	0	0	0	10997	159	6	4	318	4	OR2B11	1	247614647	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	31209234	247614647	1635974	15	31380										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	catggccgggcgagctggagGaggaggaggaggaggaggag	24	5	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						.						3	4	4					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	184.0	0.0		227.0	10.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73613036	G	C	73613036	3	2	219	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10		73613036	169586337	16	31381										
IL1R1	3554	hgsc.bcm.edu	37	chr2	102791045	102791045	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tttttttttctttttgctatAgtcactaatttccagaagca	4	7	2	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr2:102791045A>G	ENST00000410023.1	+	10	1309		c.e10-1		AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000409329.1_Splice_Site|IL1R1_ENST00000424272.1_Splice_Site|IL1R1_ENST00000409929.1_Splice_Site|IL1R1_ENST00000233946.3_Splice_Site|IL1R1_ENST00000409288.1_Splice_Site|IL1R1_ENST00000409589.1_Intron			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I						cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	TTTTTGCTATAGTCACTAATT	0.308																																					.		Atlas-SNP	.											.	IL1R1	52	.	0			c.992-2A>G						.						104	94	97					2																	102791045		2203	4299	6502	SO:0001630	splice_region_variant	3554	exon9			TGCTATAGTCACT	M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.992-1A>G	chr2.hg19:g.102791045A>G		30.0	0.0		33.0	8.0	NM_000877	Q587I7	Splice_Site	SNP	ENST00000410023.1	hg19	CCDS2055.1	.	.	.	.	.	.	.	.	.	.	A	5.793	0.330726	0.10956	.	.	ENSG00000115594	ENST00000409929;ENST00000424272;ENST00000409329;ENST00000428279;ENST00000409288;ENST00000410023;ENST00000233946	.	.	.	5.38	4.2	0.49525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8295	0.52285	0.8685:0.0:0.0:0.1315	.	.	.	.	.	-1	.	.	.	+	.	.	IL1R1	102157477	1.000000	0.71417	0.059000	0.19551	0.005000	0.04900	6.693000	0.74582	0.954000	0.37851	0.533000	0.62120	.	.	.		0.308	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1		Intron	G	102791045	A	G	102791045	5	3	219	1	0	0	0	0	0	0	1	0	7667	434	15	2	1020	2	IL1R1	2	102791045	Splice_Site	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	29178009	102791045	140408328	17	31382										
EPB41L5	57669	hgsc.bcm.edu	37	chr2	120848050	120848050	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ccccgtccaaaagagttctcAtcgatcaggatttattcgac	7	12	2	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr2:120848050A>G	ENST00000263713.5	+	12	1215	c.1001A>G	c.(1000-1002)cAt>cGt	p.H334R	EPB41L5_ENST00000452780.1_Missense_Mutation_p.H334R|EPB41L5_ENST00000443124.1_Missense_Mutation_p.H334R|EPB41L5_ENST00000331393.4_Missense_Mutation_p.H334R|EPB41L5_ENST00000443902.2_Missense_Mutation_p.H334R	NM_020909.3	NP_065960.2	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	334			H -> Y (in dbSNP:rs28930677).		actomyosin structure organization (GO:0031032)|apical constriction (GO:0003383)|axial mesoderm morphogenesis (GO:0048319)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ectoderm development (GO:0007398)|embryonic foregut morphogenesis (GO:0048617)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|in utero embryonic development (GO:0001701)|left/right axis specification (GO:0070986)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of protein binding (GO:0032091)|neural plate morphogenesis (GO:0001839)|paraxial mesoderm development (GO:0048339)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein binding (GO:0032092)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of establishment of protein localization (GO:0070201)|somite rostral/caudal axis specification (GO:0032525)|substrate-dependent cell migration, cell attachment to substrate (GO:0006931)|unidimensional cell growth (GO:0009826)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(12)|ovary(1)	26						AAGAGTTCTCATCGATCAGGA	0.388																																					p.H334R		Atlas-SNP	.											.	EPB41L5	98	.	0			c.A1001G						.						148	139	142					2																	120848050		2203	4300	6503	SO:0001583	missense	57669	exon12			GTTCTCATCGATC	AK023019	CCDS2130.1, CCDS54392.1, CCDS54393.1	2q14.2	2009-07-28			ENSG00000115109	ENSG00000115109			19819	protein-coding gene	gene with protein product		611730					Standard	NM_001184937		Approved	KIAA1548, FLJ12957, BE37, YMO1	uc002tmg.3	Q9HCM4	OTTHUMG00000131433	ENST00000263713.5:c.1001A>G	chr2.hg19:g.120848050A>G	ENSP00000263713:p.His334Arg	129.0	0.0		109.0	19.0	NM_020909	Q7Z5S1|Q8IZ12|Q9H975	Missense_Mutation	SNP	ENST00000263713.5	hg19	CCDS2130.1	.	.	.	.	.	.	.	.	.	.	A	8.423	0.846841	0.17034	.	.	ENSG00000115109	ENST00000263713;ENST00000443902;ENST00000331393;ENST00000443124;ENST00000452780	T;T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49;-1.49	5.41	4.25	0.50352	.	0.529047	0.19160	N	0.121216	T	0.53786	0.1818	N	0.02391	-0.57	0.33400	D	0.577252	B;B;B;B	0.12630	0.001;0.006;0.0;0.004	B;B;B;B	0.10450	0.001;0.005;0.0;0.002	T	0.57051	-0.7877	10	0.38643	T	0.18	.	4.6039	0.12366	0.7257:0.0:0.2743:0.0	.	334;334;334;334	Q9HCM4-3;Q9HCM4-4;Q9HCM4-2;Q9HCM4	.;.;.;E41L5_HUMAN	R	334	ENSP00000263713:H334R;ENSP00000393856:H334R;ENSP00000329687:H334R;ENSP00000393722:H334R;ENSP00000390439:H334R	ENSP00000263713:H334R	H	+	2	0	EPB41L5	120564520	0.844000	0.29557	0.944000	0.38274	0.954000	0.61252	2.641000	0.46587	2.184000	0.69523	0.477000	0.44152	CAT	.	.		0.388	EPB41L5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254230.2	NM_020909		G	120848050	A	G	120848050	3	3	219	1	0	0	0	0	1	0	0	0	5159	217	8	2	1043	2	EPB41L5	2	120848050	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	18057005	120848050	122351323	18	31383										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	203987055	203987055	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	caggaaacaaagtagtgaacTgggacattaaggtaaattaa	10	4	0	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr2:203987055T>A	ENST00000449802.1	+	18	2917	c.2584T>A	c.(2584-2586)Tgg>Agg	p.W862R		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	862										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AGTAGTGAACTGGGACATTAA	0.299																																					p.W862R		Atlas-SNP	.											.	NBEAL1	266	.	0			c.T2584A						.						141	115	123					2																	203987055		692	1587	2279	SO:0001583	missense	65065	exon18			GTGAACTGGGACA	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.2584T>A	chr2.hg19:g.203987055T>A	ENSP00000399903:p.Trp862Arg	80.0	0.0		78.0	20.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	T	19.44	3.828514	0.71258	.	.	ENSG00000144426	ENST00000449802;ENST00000340268	T	0.30448	1.53	5.0	5.0	0.66597	.	.	.	.	.	T	0.51466	0.1676	M	0.68317	2.08	0.58432	D	0.999991	D	0.89917	1.0	D	0.91635	0.999	T	0.45760	-0.9239	9	0.22109	T	0.4	.	14.6419	0.68732	0.0:0.0:0.0:1.0	.	862	Q6ZS30	NBEL1_HUMAN	R	862	ENSP00000399903:W862R	ENSP00000344985:W862R	W	+	1	0	NBEAL1	203695300	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.538000	0.82048	1.998000	0.58463	0.383000	0.25322	TGG	.	.		0.299	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			A	203987055	T	A	203987055	3	1	219	1	0	0	0	0	1	0	0	0	10197	1580	55	4	2650	4	NBEAL1	2	203987055	Missense_Mutation	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10	83139005	203987055	39212318	19	31384										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215813385	215813385	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	atacaaatgttcttccacagTtaccaggtcatctaaggcat	6	10	3	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr2:215813385T>C	ENST00000272895.7	-	47	7258	c.7039A>G	c.(7039-7041)Act>Gct	p.T2347A	ABCA12_ENST00000389661.4_Missense_Mutation_p.T2029A|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2347	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCTTCCACAGTTACCAGGTCA	0.378																																					p.T2347A	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.A7039G						.						105	97	100					2																	215813385		2203	4300	6503	SO:0001583	missense	26154	exon47			CCACAGTTACCAG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.7039A>G	chr2.hg19:g.215813385T>C	ENSP00000272895:p.Thr2347Ala	183.0	0.0		167.0	16.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.033652	0.75504	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.83419	-1.72;-1.72	5.48	-4.44	0.03557	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.400939	0.23746	N	0.044969	D	0.88800	0.6535	H	0.94808	3.585	0.80722	D	1	P;P	0.39696	0.683;0.471	P;B	0.48089	0.566;0.355	D	0.87897	0.2688	10	0.87932	D	0	.	13.6615	0.62370	0.659:0.0:0.0:0.341	.	2347;2029	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	A	2347;2029	ENSP00000272895:T2347A;ENSP00000374312:T2029A	ENSP00000272895:T2347A	T	-	1	0	ABCA12	215521630	0.992000	0.36948	0.045000	0.18777	0.997000	0.91878	2.200000	0.42724	-1.130000	0.02914	0.533000	0.62120	ACT	.	.		0.378	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		C	215813385	T	C	215813385	3	2	219	1	0	0	0	0	1	0	0	0	30	1725	60	2	776	2	ABCA12	2	215813385	Missense_Mutation	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10	11826330	215813385	27385988	20	31385										
TOP2B	7155	hgsc.bcm.edu	37	chr3	25670387	25670387	+	Frame_Shift_Del	DEL	C	C	-													0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tggttttctatatgttttttCcattcgtcaaattcaggaat							TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:25670387delC	ENST00000264331.4	-	15	1856	c.1857delG	c.(1855-1857)tggfs	p.W619fs	TOP2B_ENST00000435706.2_Frame_Shift_Del_p.W614fs	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	619					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	TATGTTTTTTCCATTCGTCAA	0.259																																					p.K615fs		Atlas-INDEL	.											.	TOP2B	98	.	0			c.1843delA						.						52	49	50					3																	25670387		1787	4047	5834	SO:0001589	frameshift_variant	7155	exon15			.	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.1857delG	chr3.hg19:g.25670387delC	ENSP00000264331:p.Trp619fs	344.0	0.0		306.0	41.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Frame_Shift_Del	DEL	ENST00000264331.4	hg19																																																																																				.	.		0.259	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				-	25670387	C	-	25670387	7	5	219	1	0	1	0	1	0	0	0	0	16381	856	30	0	3111	0	TOP2B	3	25670387	Frame_Shift_Del	DEL	C	TCGA-DD-AAEG-01A-11D-A38X-10		25670387	172352043	21	31386										
FYCO1	79443	hgsc.bcm.edu	37	chr3	46010096	46010096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ccgtagctgcttctcccgcaCctccaactggtccagctcta	7	18	2	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:46010096C>T	ENST00000296137.2	-	8	935	c.730G>A	c.(730-732)Gtg>Atg	p.V244M	FYCO1_ENST00000535325.1_Missense_Mutation_p.V244M	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	244					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TTCTCCCGCACCTCCAACTGG	0.572																																					p.V244M		Atlas-SNP	.											.	FYCO1	115	.	0			c.G730A						.						73	69	70					3																	46010096		2203	4300	6503	SO:0001583	missense	79443	exon8			CCCGCACCTCCAA	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.730G>A	chr3.hg19:g.46010096C>T	ENSP00000296137:p.Val244Met	24.0	0.0		23.0	10.0	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.469752	0.43839	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.22539	1.95;1.98	5.45	-0.532	0.11890	.	0.528594	0.19544	N	0.111724	T	0.12475	0.0303	L	0.50919	1.6	0.29384	N	0.863079	B;B	0.33883	0.38;0.43	B;B	0.27608	0.081;0.045	T	0.12192	-1.0557	10	0.46703	T	0.11	-11.6461	0.8898	0.01252	0.251:0.1957:0.3493:0.2041	.	244;244	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	M	244	ENSP00000296137:V244M;ENSP00000441178:V244M	ENSP00000296137:V244M	V	-	1	0	FYCO1	45985100	0.526000	0.26298	0.997000	0.53966	0.983000	0.72400	0.248000	0.18198	-0.016000	0.14127	0.563000	0.77884	GTG	.	.		0.572	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		T	46010096	C	T	46010096	3	4	219	1	0	0	0	0	1	0	0	0	6133	507	18	3	3750	3	FYCO1	3	46010096	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	20339709	46010096	152012334	22	31387										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52387648	52387648	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	caaggagtacgccatcgagcAggtgggtagccaccagcggg	16	11	0	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:52387648A>T	ENST00000420323.2	+	20	3740	c.3479A>T	c.(3478-3480)cAg>cTg	p.Q1160L		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1160	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GCCATCGAGCAGGTGGGTAGC	0.622																																					p.Q1160L		Atlas-SNP	.											.	DNAH1	534	.	0			c.A3479T						.						12	14	14					3																	52387648		2059	4192	6251	SO:0001630	splice_region_variant	25981	exon20			TCGAGCAGGTGGG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.3480+1A>T	chr3.hg19:g.52387648A>T		46.0	0.0		46.0	21.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.694377	0.88830	.	.	ENSG00000114841	ENST00000420323	T	0.61742	0.08	5.74	5.74	0.90152	.	0.264926	0.27076	N	0.021054	T	0.68174	0.2972	M	0.62088	1.915	0.80722	D	1	B;P	0.49961	0.372;0.93	B;P	0.53954	0.216;0.738	T	0.69617	-0.5097	10	0.51188	T	0.08	.	16.0214	0.80499	1.0:0.0:0.0:0.0	.	1160;1160	C9JXH6;Q9P2D7-3	.;.	L	1160	ENSP00000401514:Q1160L	ENSP00000401514:Q1160L	Q	+	2	0	DNAH1	52362688	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.617000	0.74210	2.198000	0.70561	0.496000	0.49642	CAG	.	.		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	Missense_Mutation	T	52387648	A	T	52387648	5	4	219	1	0	0	0	0	0	0	1	0	4599	202	7	4	3553	4	DNAH1	3	52387648	Splice_Site	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	6377552	52387648	145634782	23	31388										
SPATA12	353324	hgsc.bcm.edu	37	chr3	57107930	57107930	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cagcctctgccctcccagagCtgacatttcagggggatgtg	12	13	2	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:57107930C>G	ENST00000334325.1	+	2	883	c.208C>G	c.(208-210)Ctg>Gtg	p.L70V	ARHGEF3_ENST00000338458.4_Intron	NM_181727.1	NP_859078.1	Q7Z6I5	SPT12_HUMAN	spermatogenesis associated 12	70										large_intestine(2)|lung(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0111)|Kidney(284;0.0129)		CCTCCCAGAGCTGACATTTCA	0.537																																					p.L70V		Atlas-SNP	.											.	SPATA12	9	.	0			c.C208G						.						71	72	71					3																	57107930		2203	4300	6503	SO:0001583	missense	353324	exon2			CCAGAGCTGACAT	AY221117	CCDS2879.1	3p21.2	2012-09-19			ENSG00000186451	ENSG00000186451			23221	protein-coding gene	gene with protein product		609869				22981541, 17251597	Standard	NM_181727		Approved		uc003dij.1	Q7Z6I5	OTTHUMG00000158862	ENST00000334325.1:c.208C>G	chr3.hg19:g.57107930C>G	ENSP00000335392:p.Leu70Val	116.0	0.0		105.0	40.0	NM_181727	A0AVA8|B2RMW1	Missense_Mutation	SNP	ENST00000334325.1	hg19	CCDS2879.1	.	.	.	.	.	.	.	.	.	.	C	8.975	0.973899	0.18736	.	.	ENSG00000186451	ENST00000334325	.	.	.	2.33	-0.97	0.10306	.	.	.	.	.	T	0.16599	0.0399	N	0.08118	0	0.09310	N	1	P	0.50156	0.932	P	0.47470	0.548	T	0.10706	-1.0618	8	0.87932	D	0	.	2.3512	0.04284	0.2354:0.4505:0.0:0.3141	.	70	Q7Z6I5	SPT12_HUMAN	V	70	.	ENSP00000335392:L70V	L	+	1	2	SPATA12	57082970	0.000000	0.05858	0.001000	0.08648	0.235000	0.25334	-1.260000	0.02858	-0.271000	0.09272	0.563000	0.77884	CTG	.	.		0.537	SPATA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352457.2	NM_181727		G	57107930	C	G	57107930	3	3	219	1	0	0	0	0	1	0	0	0	15014	796	28	4	210	4	SPATA12	3	57107930	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	4720282	57107930	140914500	24	31389										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108366815	108366815	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gaaatagaagagttacagaaTgaggaagaagaactaagtcc	11	4	0	6			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:108366815T>A	ENST00000361582.3	+	16	2048	c.1818T>A	c.(1816-1818)aaT>aaA	p.N606K	DZIP3_ENST00000463306.1_Missense_Mutation_p.N606K	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	606					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						AGTTACAGAATGAGGAAGAAG	0.323																																					p.N606K		Atlas-SNP	.											.	DZIP3	111	.	0			c.T1818A						.						93	98	96					3																	108366815		2203	4299	6502	SO:0001583	missense	9666	exon16			ACAGAATGAGGAA	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.1818T>A	chr3.hg19:g.108366815T>A	ENSP00000355028:p.Asn606Lys	238.0	0.0		280.0	23.0	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	hg19	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.091301	0.36855	.	.	ENSG00000198919	ENST00000361582;ENST00000479138;ENST00000463306	T;T	0.22743	1.94;1.94	5.25	2.87	0.33458	.	0.200590	0.35708	N	0.003039	T	0.23014	0.0556	N	0.16478	0.41	0.27343	N	0.956466	D;D;B	0.64830	0.97;0.994;0.043	P;D;B	0.63488	0.681;0.915;0.016	T	0.03587	-1.1022	10	0.56958	D	0.05	-15.2579	6.8142	0.23820	0.0:0.1828:0.0:0.8172	.	224;606;606	D3DN61;C9J9M8;Q86Y13	.;.;DZIP3_HUMAN	K	606	ENSP00000355028:N606K;ENSP00000419981:N606K	ENSP00000355028:N606K	N	+	3	2	DZIP3	109849505	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	-0.003000	0.12901	0.452000	0.26830	-0.287000	0.09952	AAT	.	.		0.323	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		A	108366815	T	A	108366815	3	1	219	1	0	0	0	0	1	0	0	0	4867	1461	51	4	1876	4	DZIP3	3	108366815	Missense_Mutation	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10	51258885	108366815	89655615	25	31390										
CCDC52	152185	hgsc.bcm.edu	37	chr3	113176014	113176014	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ggagagaattttaagttgctCttctgcctgggtggtgttaa	13	5	2	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:113176014C>T	ENST00000295872.4	-	13	1885	c.1626G>A	c.(1624-1626)aaG>aaA	p.K542K		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	542					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						TTAAGTTGCTCTTCTGCCTGG	0.393																																					p.K542K		Atlas-SNP	.											.	SPICE1	130	.	0			c.G1626A						.						74	73	73					3																	113176014		2203	4300	6503	SO:0001819	synonymous_variant	152185	exon13			GTTGCTCTTCTGC	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.1626G>A	chr3.hg19:g.113176014C>T		69.0	0.0		55.0	12.0	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	hg19	CCDS2973.1																																																																																			.	.		0.393	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		T	113176014	C	T	113176014	2	4	219	1	0	0	0	0	0	0	0	1	2824	912	32	3		3	CCDC52	3	113176014	Silent	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	4809199	113176014	84846416	26	31391										
COPB2	9276	hgsc.bcm.edu	37	chr3	139077908	139077908	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cttcacccattcttcaacaaCaaaggcttcttttaatccag	3	13	4	0	rs201811724		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:139077908C>T	ENST00000333188.5	-	19	2597	c.2416G>A	c.(2416-2418)Gtt>Att	p.V806I	COPB2_ENST00000507777.1_Missense_Mutation_p.V777I	NM_004766.2	NP_004757.1	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta prime)	806					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	24						TCTTCAACAACAAAGGCTTCT	0.448																																					p.V806I		Atlas-SNP	.											.	COPB2	80	.	0			c.G2416A						.						157	160	159					3																	139077908		2203	4300	6503	SO:0001583	missense	9276	exon19			CAACAACAAAGGC	BC000326	CCDS3108.1	3q23	2013-01-10			ENSG00000184432	ENSG00000184432		"WD repeat domain containing"	2232	protein-coding gene	gene with protein product		606990				9858824	Standard	NM_004766		Approved	beta'-COP, betaprime-COP	uc003etf.4	P35606	OTTHUMG00000159959	ENST00000333188.5:c.2416G>A	chr3.hg19:g.139077908C>T	ENSP00000329419:p.Val806Ile	101.0	0.0		86.0	25.0	NM_004766	B4DZI8	Missense_Mutation	SNP	ENST00000333188.5	hg19	CCDS3108.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.96|13.96	2.393085|2.393085	0.42410|0.42410	.|.	.|.	ENSG00000184432|ENSG00000184432	ENST00000503326|ENST00000333188;ENST00000507777	.|T;T	.|0.62232	.|0.04;0.14	5.04|5.04	2.88|2.88	0.33553|0.33553	.|.	.|0.372503	.|0.29522	.|N	.|0.011920	T|T	0.52645|0.52645	0.1747|0.1747	L|L	0.43152|0.43152	1.355|1.355	0.35461|0.35461	D|D	0.796494|0.796494	.|B	.|0.14012	.|0.009	.|B	.|0.10450	.|0.005	T|T	0.59936|0.59936	-0.7360|-0.7360	5|10	.|0.45353	.|T	.|0.12	-11.1033|-11.1033	12.3636|12.3636	0.55217|0.55217	0.0:0.836:0.0:0.164|0.0:0.836:0.0:0.164	.|.	.|806	.|P35606	.|COPB2_HUMAN	Y|I	19|806;777	.|ENSP00000329419:V806I;ENSP00000422295:V777I	.|ENSP00000329419:V806I	C|V	-|-	2|1	0|0	COPB2|COPB2	140560598|140560598	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	1.241000|1.241000	0.32743|0.32743	1.123000|1.123000	0.41961|0.41961	0.655000|0.655000	0.94253|0.94253	TGT|GTT	.	.		0.448	COPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358495.2	NM_004766		T	139077908	C	T	139077908	3	4	219	1	0	0	0	0	1	0	0	0	3731	478	17	3	320	3	COPB2	3	139077908	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	25901894	139077908	58944522	27	31392										
PLOD2	5352	hgsc.bcm.edu	37	chr3	145878772	145878772	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gaggcttcaccgtgcatcccCccatattcggccctcgaggg	11	16	1	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:145878772C>T	ENST00000360060.3	-	1	182	c.5G>A	c.(4-6)gGg>gAg	p.G2E	PLOD2_ENST00000282903.5_Missense_Mutation_p.G2E|PLOD2_ENST00000494950.1_5'UTR	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	2					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	CGTGCATCCCCCCATATTCGG	0.721																																					p.G2E		Atlas-SNP	.											.	PLOD2	81	.	0			c.G5A						.						28	29	28					3																	145878772		2181	4271	6452	SO:0001583	missense	5352	exon1			CATCCCCCCATAT	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"lysyl hydroxlase 2"	601865	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.5G>A	chr3.hg19:g.145878772C>T	ENSP00000353170:p.Gly2Glu	153.0	0.0		160.0	55.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	hg19	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.504891	0.26949	.	.	ENSG00000152952	ENST00000282903;ENST00000360060	T;T	0.65732	-0.16;-0.17	4.52	1.4	0.22301	.	1.527540	0.04108	N	0.314073	T	0.40932	0.1137	N	0.08118	0	0.22435	N	0.999107	B;B	0.22414	0.041;0.069	B;B	0.18871	0.01;0.023	T	0.33137	-0.9880	10	0.52906	T	0.07	-5.9246	3.839	0.08906	0.1545:0.5696:0.1727:0.1032	.	2;2	O00469;O00469-2	PLOD2_HUMAN;.	E	2	ENSP00000282903:G2E;ENSP00000353170:G2E	ENSP00000282903:G2E	G	-	2	0	PLOD2	147361462	0.026000	0.19158	0.094000	0.20943	0.002000	0.02628	0.246000	0.18160	0.350000	0.24002	-0.268000	0.10319	GGG	.	.		0.721	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		T	145878772	C	T	145878772	3	4	219	1	0	0	0	0	1	0	0	0	12111	623	22	3	2351	3	PLOD2	3	145878772	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	6800864	145878772	52143658	28	31393										
MBNL1	4154	hgsc.bcm.edu	37	chr3	152132752	152132752	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ccgttgctccagggagaactGcaaatatcttcatccacccc	7	15	2	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:152132752G>A	ENST00000463374.1	+	2	708	c.197G>A	c.(196-198)tGc>tAc	p.C66Y	MBNL1_ENST00000485910.1_Missense_Mutation_p.C66Y|MBNL1_ENST00000545754.1_Missense_Mutation_p.C66Y|MBNL1_ENST00000324196.5_Missense_Mutation_p.C66Y|MBNL1_ENST00000282488.7_Missense_Mutation_p.C66Y|MBNL1_ENST00000493459.1_Missense_Mutation_p.C9Y|MBNL1_ENST00000324210.5_Missense_Mutation_p.C66Y|MBNL1_ENST00000282486.6_Missense_Mutation_p.C66Y|MBNL1_ENST00000485509.1_Missense_Mutation_p.C66Y|MBNL1_ENST00000355460.2_Missense_Mutation_p.C66Y|MBNL1_ENST00000357472.3_Missense_Mutation_p.C66Y|MBNL1_ENST00000492948.1_Missense_Mutation_p.C66Y|MBNL1_ENST00000498502.1_Missense_Mutation_p.C66Y	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	66					alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			AGGGAGAACTGCAAATATCTT	0.393																																					p.C66Y		Atlas-SNP	.											.	MBNL1	100	.	0			c.G197A						.						111	106	108					3																	152132752		2203	4300	6503	SO:0001583	missense	4154	exon3			AGAACTGCAAATA	Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"Zinc fingers, CCCH-type domain containing"	6923	protein-coding gene	gene with protein product		606516	"muscleblind (Drosophila)-like", "muscleblind-like (Drosophila)"	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.197G>A	chr3.hg19:g.152132752G>A	ENSP00000418108:p.Cys66Tyr	118.0	0.0		125.0	5.0	NM_207292	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Missense_Mutation	SNP	ENST00000463374.1	hg19	CCDS3165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.3|20.3	3.972532|3.972532	0.74246|0.74246	.|.	.|.	ENSG00000152601|ENSG00000152601	ENST00000464596|ENST00000282486;ENST00000282488;ENST00000355460;ENST00000493459;ENST00000324210;ENST00000459747;ENST00000498502;ENST00000324196;ENST00000545754;ENST00000357472;ENST00000485910;ENST00000463374;ENST00000465907;ENST00000492948;ENST00000485509	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.52754	.|0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65	5.8|5.8	5.8|5.8	0.92144|0.92144	.|Zinc finger, CCCH-type (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.79299|0.79299	0.4422|0.4422	H|H	0.94264|0.94264	3.515|3.515	0.80722|0.80722	D|D	1|1	.|D;B;B;B;D;B;D;D	.|0.89917	.|1.0;0.001;0.001;0.095;1.0;0.057;1.0;1.0	.|D;B;B;B;D;B;D;D	.|0.97110	.|0.99;0.005;0.005;0.159;0.999;0.102;1.0;1.0	D|D	0.84359|0.84359	0.0537|0.0537	5|10	.|0.87932	.|D	.|0	.|.	20.0693|20.0693	0.97712|0.97712	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|66;66;66;66;66;9;66;66	.|E9PBW7;Q9NR56-3;Q96RE3;Q9NR56;Q86UV8;Q86VM6;Q9NR56-2;Q96P92	.|.;.;.;MBNL1_HUMAN;.;.;.;.	T|Y	65|66;66;66;9;66;10;66;66;66;66;66;66;66;66;66	.|ENSP00000282486:C66Y;ENSP00000282488:C66Y;ENSP00000347637:C66Y;ENSP00000419347:C9Y;ENSP00000319429:C66Y;ENSP00000417169:C10Y;ENSP00000420327:C66Y;ENSP00000319374:C66Y;ENSP00000437491:C66Y;ENSP00000350064:C66Y;ENSP00000418427:C66Y;ENSP00000418108:C66Y;ENSP00000417630:C66Y;ENSP00000420103:C66Y;ENSP00000418876:C66Y	.|ENSP00000282486:C66Y	A|C	+|+	1|2	0|0	MBNL1|MBNL1	153615442|153615442	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	9.731000|9.731000	0.98807|0.98807	2.758000|2.758000	0.94735|0.94735	0.563000|0.563000	0.77884|0.77884	GCA|TGC	.	.		0.393	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038		A	152132752	G	A	152132752	3	1	219	1	0	0	0	0	1	0	0	0	9362	1319	46	3	203	3	MBNL1	3	152132752	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	6253980	152132752	45889678	29	31394										
PLCH1	23007	hgsc.bcm.edu	37	chr3	155199724	155199724	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ctctcctatattcacaggttGttagagaaagattttctgat	7	7	3	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:155199724G>T	ENST00000340059.7	-	23	4114	c.4115C>A	c.(4114-4116)aCa>aAa	p.T1372K	PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000334686.6_Missense_Mutation_p.T1334K|PLCH1_ENST00000460012.1_Missense_Mutation_p.T1334K|PLCH1_ENST00000414191.1_Missense_Mutation_p.T1334K	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1372					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TTCACAGGTTGTTAGAGAAAG	0.423																																					p.T1372K		Atlas-SNP	.											.	PLCH1	406	.	0			c.C4115A						.						46	50	49					3																	155199724		2203	4300	6503	SO:0001583	missense	23007	exon23			CAGGTTGTTAGAG	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.4115C>A	chr3.hg19:g.155199724G>T	ENSP00000345988:p.Thr1372Lys	91.0	0.0		78.0	14.0	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	hg19	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.674648	0.47781	.	.	ENSG00000114805	ENST00000460012;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.47	4.5	0.54988	.	1.432160	0.04132	N	0.318083	T	0.72748	0.3499	L	0.34521	1.04	0.18873	N	0.999987	P;P	0.39480	0.675;0.546	B;B	0.35413	0.202;0.1	T	0.64141	-0.6477	10	0.87932	D	0	.	13.8156	0.63290	0.0791:0.0:0.9209:0.0	.	1334;1372	Q4KWH8-2;Q4KWH8	.;PLCH1_HUMAN	K	1334;1372;1334;1334	ENSP00000417502:T1334K;ENSP00000345988:T1372K;ENSP00000335469:T1334K;ENSP00000412977:T1334K	ENSP00000335469:T1334K	T	-	2	0	PLCH1	156682418	0.753000	0.28349	0.001000	0.08648	0.141000	0.21300	2.995000	0.49441	1.141000	0.42275	0.585000	0.79938	ACA	.	.		0.423	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		T	155199724	G	T	155199724	3	4	219	1	0	0	0	0	1	0	0	0	12046	1377	48	3	970	3	PLCH1	3	155199724	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	3066972	155199724	42822706	30	31395										
MASP1	5648	hgsc.bcm.edu	37	chr3	186980347	186980347	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ttacccacagccatgtagtgGgcatcaaagcctgtgaaacg	10	11	1	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr3:186980347G>C	ENST00000337774.5	-	3	788	c.399C>G	c.(397-399)gcC>gcG	p.A133A	MASP1_ENST00000495249.1_Intron|MASP1_ENST00000296280.6_Silent_p.A133A|MASP1_ENST00000392470.2_Silent_p.A107A|MASP1_ENST00000392472.2_Silent_p.A20A|MASP1_ENST00000169293.6_Silent_p.A133A	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	133	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.|Homodimerization. {ECO:0000250}.|Interaction with FCN2.|Interaction with MBL2.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		CCATGTAGTGGGCATCAAAGC	0.527																																					p.A133A		Atlas-SNP	.											.	MASP1	240	.	0			c.C399G						.						72	75	74					3																	186980347		2203	4300	6503	SO:0001819	synonymous_variant	5648	exon3			GTAGTGGGCATCA	D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"Serine peptidases / Serine peptidases"	6901	protein-coding gene	gene with protein product		600521	"mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.399C>G	chr3.hg19:g.186980347G>C		272.0	1.0		304.0	130.0	NM_139125	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Silent	SNP	ENST00000337774.5	hg19	CCDS33907.1																																																																																			.	.		0.527	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879		C	186980347	G	C	186980347	2	2	219	1	0	0	0	0	0	0	0	1	9331	1219	43	4		4	MASP1	3	186980347	Silent	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	31780623	186980347	11042083	31	31396										
ZNF721	170960	hgsc.bcm.edu	37	chr4	435883	435883	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ttagcaaagcttgaggatgaCgtaatgactttgccacattc	9	8	0	3	rs371250652		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr4:435883C>T	ENST00000338977.5	-	2	2385	c.2337G>A	c.(2335-2337)acG>acA	p.T779T	ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000511833.2_Silent_p.T791T			Q8TF20	ZN721_HUMAN	zinc finger protein 721	779					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						TTGAGGATGACGTAATGACTT	0.378																																					p.N791K		Atlas-SNP	.											ZNF721_ENST00000511833,NS,carcinoma,0,2	ZNF721	205	.	0			c.C2373A						.	G		0,4214		0,0,2107	67	71	70		2373	0.1	0	4		70	1,8475		0,1,4237	no	coding-synonymous	ZNF721	NM_133474.2		0,1,6344	TT,TC,CC		0.0118,0.0,0.0079		791/924	435883	1,12689	2107	4238	6345	SO:0001819	synonymous_variant	170960	exon3			GGATGACGTAATG	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.2337G>A	chr4.hg19:g.435883C>T		95.0	0.0		96.0	12.0	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	hg19																																																																																				.	.		0.378	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		T	435883	C	T	435883	2	4	219	1	0	0	0	0	0	0	0	1	18137	523	19	1		1	ZNF721	4	435883	Silent	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10		435883	190718393	32	31397										
WHSC1	7468	hgsc.bcm.edu	37	chr4	1920344	1920344	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gtcttctgtcaaaaacacagGgatgaggtcagtactaagtt	10	7	4	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr4:1920344G>T	ENST00000382895.3	+	7	1835	c.1404G>T	c.(1402-1404)agG>agT	p.R468S	WHSC1_ENST00000503128.1_Missense_Mutation_p.R468S|WHSC1_ENST00000514045.1_Missense_Mutation_p.R468S|WHSC1_ENST00000382892.2_Missense_Mutation_p.R468S|WHSC1_ENST00000398261.1_Missense_Mutation_p.R468S|WHSC1_ENST00000508803.1_Missense_Mutation_p.R468S|WHSC1_ENST00000420906.2_Missense_Mutation_p.R468S|WHSC1_ENST00000382891.5_Missense_Mutation_p.R468S	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	468					anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		AAAAACACAGGGATGAGGTCA	0.468			T	IGH@	MM																																p.R468S		Atlas-SNP	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.G1404T						.						31	35	33					4																	1920344		2199	4299	6498	SO:0001583	missense	7468	exon5			ACACAGGGATGAG	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"Zinc fingers, PHD-type"	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.1404G>T	chr4.hg19:g.1920344G>T	ENSP00000372351:p.Arg468Ser	126.0	0.0		136.0	45.0	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	hg19	CCDS33940.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.530446	0.45073	.	.	ENSG00000109685	ENST00000508803;ENST00000514045;ENST00000382891;ENST00000382892;ENST00000420906;ENST00000382895;ENST00000503128;ENST00000398261	D;D;D;D;D;D;D;D	0.98617	-5.03;-5.03;-5.03;-5.03;-5.03;-5.03;-5.03;-5.03	5.23	1.99	0.26369	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.56097	D	0.000037	D	0.98526	0.9508	M	0.89968	3.075	0.80722	D	1	D;B;D;D	0.57899	0.96;0.167;0.981;0.981	P;B;P;P	0.56278	0.737;0.049;0.795;0.795	D	0.96998	0.9727	10	0.32370	T	0.25	.	5.6673	0.17702	0.5355:0.0:0.4645:0.0	.	468;468;468;468	O96028-3;O96028;O96028-5;O96028-6	.;NSD2_HUMAN;.;.	S	468	ENSP00000423972:R468S;ENSP00000421681:R468S;ENSP00000372347:R468S;ENSP00000372348:R468S;ENSP00000399251:R468S;ENSP00000372351:R468S;ENSP00000425761:R468S;ENSP00000381311:R468S	ENSP00000308780:R468S	R	+	3	2	WHSC1	1890142	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.955000	0.49121	0.677000	0.31305	-0.291000	0.09656	AGG	.	.		0.468	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		T	1920344	G	T	1920344	3	4	219	1	0	0	0	0	1	0	0	0	17377	1223	43	3	1418	3	WHSC1	4	1920344	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	1484461	1920344	189233932	33	31398										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30724132	30724132	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gctgctgcgccttgacgagaCgtccggctggctcagcgtcc	14	15	1	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr4:30724132C>T	ENST00000361762.2	+	1	2096	c.1088C>T	c.(1087-1089)aCg>aTg	p.T363M	PCDH7_ENST00000543491.1_Missense_Mutation_p.T363M	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	363	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						CTTGACGAGACGTCCGGCTGG	0.701																																					p.T363M		Atlas-SNP	.											.	PCDH7	215	.	0			c.C1088T						.						28	31	30					4																	30724132		2190	4267	6457	SO:0001583	missense	5099	exon1			ACGAGACGTCCGG	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1088C>T	chr4.hg19:g.30724132C>T	ENSP00000355243:p.Thr363Met	135.0	0.0		122.0	20.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.476533	0.26511	.	.	ENSG00000169851	ENST00000361762;ENST00000543491;ENST00000333135	T;T	0.52983	0.64;0.64	5.69	3.96	0.45880	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.42539	0.1207	L	0.28054	0.825	0.35362	D	0.788299	P;P;P	0.51791	0.948;0.948;0.928	P;P;P	0.52189	0.565;0.565;0.692	T	0.54139	-0.8338	9	0.87932	D	0	.	6.4268	0.21773	0.1368:0.662:0.1318:0.0694	.	363;316;363	F5GWJ1;O60245-3;O60245	.;.;PCDH7_HUMAN	M	363;363;316	ENSP00000355243:T363M;ENSP00000441802:T363M	ENSP00000330302:T316M	T	+	2	0	PCDH7	30333230	1.000000	0.71417	0.761000	0.31378	0.002000	0.02628	3.272000	0.51616	0.749000	0.32854	-0.175000	0.13238	ACG	.	.		0.701	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		T	30724132	C	T	30724132	3	4	219	1	0	0	0	0	1	0	0	0	11525	536	19	1	1090	1	PCDH7	4	30724132	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	28803788	30724132	160430144	34	31399										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	73943153	73943153	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gttacaattcctgtactatcTcgctccattgcttgatgttg	7	10	1	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr4:73943153T>A	ENST00000358602.4	-	32	7622	c.7506A>T	c.(7504-7506)cgA>cgT	p.R2502R	ANKRD17_ENST00000509867.2_Silent_p.R2389R|ANKRD17_ENST00000330838.6_Silent_p.R2251R	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2502					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTGTACTATCTCGCTCCATTG	0.448																																					p.R2502R		Atlas-SNP	.											.	ANKRD17	214	.	0			c.A7506T						.						194	175	181					4																	73943153		2203	4300	6503	SO:0001819	synonymous_variant	26057	exon32			ACTATCTCGCTCC	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.7506A>T	chr4.hg19:g.73943153T>A		68.0	0.0		97.0	11.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.448	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		A	73943153	T	A	73943153	2	1	219	1	0	0	0	0	0	0	0	1	646	1538	54	4		4	ANKRD17	4	73943153	Silent	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10	43219021	73943153	117211123	35	31400										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113352274	113352274	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aatatcttcctccctaatggGtaagaatgttcagagggaac	9	8	2	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr4:113352274G>C	ENST00000458497.1	+	11	1850	c.1571G>C	c.(1570-1572)gGt>gCt	p.G524A	ALPK1_ENST00000504176.2_Missense_Mutation_p.G446A|ALPK1_ENST00000177648.9_Missense_Mutation_p.G524A	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	524							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		TCCCTAATGGGTAAGAATGTT	0.418																																					p.G524A		Atlas-SNP	.											.	ALPK1	125	.	0			c.G1571C						.						54	54	54					4																	113352274		2203	4300	6503	SO:0001583	missense	80216	exon11			TAATGGGTAAGAA	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.1571G>C	chr4.hg19:g.113352274G>C	ENSP00000398048:p.Gly524Ala	95.0	0.0		119.0	27.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	hg19	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.649556	0.00785	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.02301	4.42;4.42;4.35	4.29	1.63	0.23807	.	0.724858	0.12495	N	0.463889	T	0.00608	0.0020	N	0.00289	-1.7	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45731	-0.9241	10	0.02654	T	1	-0.0733	7.0544	0.25091	0.0:0.6546:0.1256:0.2198	.	446;446;524	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	A	524;524;446	ENSP00000398048:G524A;ENSP00000177648:G524A;ENSP00000426044:G446A	ENSP00000177648:G524A	G	+	2	0	ALPK1	113571723	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.656000	0.05342	0.201000	0.20466	-0.769000	0.03391	GGT	.	.		0.418	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		C	113352274	G	C	113352274	3	2	219	1	0	0	0	0	1	0	0	0	544	1261	44	4	1605	4	ALPK1	4	113352274	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	39409121	113352274	77802002	36	31401										
ANK2	287	hgsc.bcm.edu	37	chr4	114153356	114153356	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	acatggctgcccaagagaatCacattgatgttgtaaaatat	8	7	1	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr4:114153356C>T	ENST00000357077.4	+	5	477	c.424C>T	c.(424-426)Cac>Tac	p.H142Y	ANK2_ENST00000264366.6_Missense_Mutation_p.H142Y|ANK2_ENST00000506722.1_Missense_Mutation_p.H121Y|ANK2_ENST00000394537.3_Missense_Mutation_p.H142Y	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	142					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CCAAGAGAATCACATTGATGT	0.378																																					p.H142Y		Atlas-SNP	.											.	ANK2	576	.	0			c.C424T						.						145	137	139					4																	114153356		2203	4300	6503	SO:0001583	missense	287	exon5			GAGAATCACATTG	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.424C>T	chr4.hg19:g.114153356C>T	ENSP00000349588:p.His142Tyr	85.0	0.0		76.0	16.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.016884	0.93404	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000508613;ENST00000343056;ENST00000515034	T;T;T;T;T;T;T;T;T	0.68025	-0.28;-0.3;-0.28;-0.28;-0.28;-0.28;-0.28;-0.24;-0.28	5.35	5.35	0.76521	Ankyrin repeat-containing domain (4);	0.000000	0.46758	D	0.000278	T	0.76716	0.4026	L	0.38649	1.16	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.999;0.997;0.975	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.995;0.974	T	0.78656	-0.2119	10	0.87932	D	0	.	19.4355	0.94792	0.0:1.0:0.0:0.0	.	142;142;142;121;121	Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	ANK2_HUMAN;.;.;.;.	Y	121;121;121;157;142;142;142;157;121;7	ENSP00000423799:H121Y;ENSP00000421011:H121Y;ENSP00000421067:H121Y;ENSP00000424722:H157Y;ENSP00000378044:H142Y;ENSP00000349588:H142Y;ENSP00000264366:H142Y;ENSP00000422900:H157Y;ENSP00000421059:H7Y	ENSP00000264366:H142Y	H	+	1	0	ANK2	114372805	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.776000	0.85560	2.668000	0.90789	0.655000	0.94253	CAC	.	.		0.378	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		T	114153356	C	T	114153356	3	4	219	1	0	0	0	0	1	0	0	0	621	826	29	3	467	3	ANK2	4	114153356	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	801082	114153356	77000920	37	31402										
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125593424	125593424	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	acaaaaagtctttggcacagCcagagatataaaccatttag	7	8	1	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr4:125593424C>G	ENST00000504087.1	-	4	2045	c.1008G>C	c.(1006-1008)tgG>tgC	p.W336C	ANKRD50_ENST00000515641.1_Missense_Mutation_p.W157C	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	336										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TTTGGCACAGCCAGAGATATA	0.358																																					p.W336C		Atlas-SNP	.											.	ANKRD50	136	.	0			c.G1008C						.						64	67	66					4																	125593424		2203	4299	6502	SO:0001583	missense	57182	exon4			GCACAGCCAGAGA	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1008G>C	chr4.hg19:g.125593424C>G	ENSP00000425658:p.Trp336Cys	152.0	0.0		177.0	72.0	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	hg19	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.234146	0.58886	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.69040	-0.37;-0.35	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.80358	0.4608	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.80879	-0.1185	10	0.72032	D	0.01	.	19.4269	0.94746	0.0:1.0:0.0:0.0	.	336	Q9ULJ7	ANR50_HUMAN	C	336;157	ENSP00000425658:W336C;ENSP00000425355:W157C	ENSP00000425658:W336C	W	-	3	0	ANKRD50	125812874	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.164000	0.77533	2.822000	0.97130	0.650000	0.86243	TGG	.	.		0.358	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		G	125593424	C	G	125593424	3	3	219	1	0	0	0	0	1	0	0	0	677	740	26	4	3285	4	ANKRD50	4	125593424	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	11440068	125593424	65560852	38	31403										
PDGFC	56034	hgsc.bcm.edu	37	chr4	157732066	157732066	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	agatacaaatcttatcctaaTttgatttcctttagaaatct	3	7	2	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr4:157732066T>C	ENST00000502773.1	-	3	908	c.418A>G	c.(418-420)Att>Gtt	p.I140V	PDGFC_ENST00000541126.1_5'UTR|PDGFC_ENST00000542208.1_Intron|PDGFC_ENST00000422544.2_Missense_Mutation_p.I140V	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	140	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		CTTATCCTAATTTGATTTCCT	0.403																																					p.I140V		Atlas-SNP	.											.	PDGFC	46	.	0			c.A418G						.						88	89	89					4																	157732066		2203	4300	6503	SO:0001583	missense	56034	exon3			TCCTAATTTGATT	AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.418A>G	chr4.hg19:g.157732066T>C	ENSP00000422464:p.Ile140Val	332.0	0.0		313.0	22.0	NM_016205	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Missense_Mutation	SNP	ENST00000502773.1	hg19	CCDS3795.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.263165	0.80358	.	.	ENSG00000145431	ENST00000502773;ENST00000422544;ENST00000543489	T;T	0.16196	2.36;2.36	5.08	5.08	0.68730	CUB (5);	0.000000	0.85682	D	0.000000	T	0.26011	0.0634	N	0.17872	0.535	0.80722	D	1	D	0.61697	0.99	D	0.65573	0.936	T	0.04522	-1.0945	10	0.49607	T	0.09	-25.5924	15.1364	0.72569	0.0:0.0:0.0:1.0	.	140	Q9NRA1	PDGFC_HUMAN	V	140	ENSP00000422464:I140V;ENSP00000410048:I140V	ENSP00000410048:I140V	I	-	1	0	PDGFC	157951516	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	4.797000	0.62503	2.041000	0.60428	0.460000	0.39030	ATT	.	.		0.403	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1			C	157732066	T	C	157732066	3	2	219	1	0	0	0	0	1	0	0	0	11668	1493	52	2	635	2	PDGFC	4	157732066	Missense_Mutation	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10	32138642	157732066	33422210	39	31404										
WDR36	134430	hgsc.bcm.edu	37	chr5	110432780	110432780	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tttgtattttctgctaggtaAttctgttccacaggatatct	7	7	3	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr5:110432780A>G	ENST00000513710.2	+	3	366	c.362A>G	c.(361-363)aAt>aGt	p.N121S	WDR36_ENST00000506538.2_Missense_Mutation_p.N121S|WDR36_ENST00000505303.1_Missense_Mutation_p.N65S			Q8NI36	WDR36_HUMAN	WD repeat domain 36	121					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		CTGCTAGGTAATTCTGTTCCA	0.338																																					p.N121S		Atlas-SNP	.											.	WDR36	111	.	0			c.A362G						.						125	122	123					5																	110432780		2202	4300	6502	SO:0001583	missense	134430	exon3			TAGGTAATTCTGT	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.362A>G	chr5.hg19:g.110432780A>G	ENSP00000424628:p.Asn121Ser	46.0	0.0		75.0	7.0	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	SNP	ENST00000513710.2	hg19	CCDS4102.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.803060	0.70682	.	.	ENSG00000134987	ENST00000506538;ENST00000513710;ENST00000505303	T;T;T	0.27720	1.65;1.65;3.35	5.56	5.56	0.83823	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.44685	0.1305	L	0.43152	1.355	0.80722	D	1	D	0.63880	0.993	P	0.58970	0.849	T	0.40869	-0.9540	10	0.87932	D	0	-18.3439	15.6895	0.77439	1.0:0.0:0.0:0.0	.	121	Q8NI36	WDR36_HUMAN	S	121;121;65	ENSP00000423067:N121S;ENSP00000424628:N121S;ENSP00000422158:N65S	ENSP00000422158:N65S	N	+	2	0	WDR36	110460679	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.120000	0.94369	2.099000	0.63709	0.533000	0.62120	AAT	.	.		0.338	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		G	110432780	A	G	110432780	3	3	219	1	0	0	0	0	1	0	0	0	17305	101	4	2	372	2	WDR36	5	110432780	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10		110432780	70482480	40	31405										
FAM193B	54540	hgsc.bcm.edu	37	chr5	176952090	176952090	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aggaagctgttgacccgatcCagttcccggtcgggccactc	12	14	0	1	rs371452748		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr5:176952090C>T	ENST00000514747.1	-	6	1440	c.1392G>A	c.(1390-1392)ctG>ctA	p.L464L	FAM193B_ENST00000443375.2_Silent_p.L431L|FAM193B_ENST00000329540.5_Silent_p.L90L|FAM193B_ENST00000508298.1_5'Flank	NM_001190946.1	NP_001177875.1	Q96PV7	F193B_HUMAN	family with sequence similarity 193, member B	544						cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)	4						TGACCCGATCCAGTTCCCGGT	0.572																																					p.L464L		Atlas-SNP	.											.	FAM193B	28	.	0			c.G1392A						.	C		1,3907		0,1,1953	62	64	63		1392	5	1	5		63	0,8280		0,0,4140	no	coding-synonymous	FAM193B	NM_001190946.1		0,1,6093	TT,TC,CC		0.0,0.0256,0.0082		464/823	176952090	1,12187	1954	4140	6094	SO:0001819	synonymous_variant	54540	exon6			CCGATCCAGTTCC		CCDS54954.1	5q35	2010-02-17			ENSG00000146067	ENSG00000146067			25524	protein-coding gene	gene with protein product		615813				11572484	Standard	NR_024019		Approved	KIAA1931, FLJ10404	uc003mhu.3	Q96PV7	OTTHUMG00000163396	ENST00000514747.1:c.1392G>A	chr5.hg19:g.176952090C>T		145.0	0.0		147.0	25.0	NM_001190946	E9PET5|Q9NW00	Silent	SNP	ENST00000514747.1	hg19	CCDS54954.1	.	.	.	.	.	.	.	.	.	.	C	9.087	1.000865	0.19121	2.56E-4	0.0	ENSG00000146067	ENST00000524677	.	.	.	5.86	4.96	0.65561	.	.	.	.	.	T	0.71871	0.3391	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69953	-0.5005	4	.	.	.	-10.1237	16.3864	0.83505	0.1323:0.8677:0.0:0.0	.	.	.	.	R	150	.	.	G	-	1	0	FAM193B	176884696	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	2.377000	0.44300	2.771000	0.95319	0.563000	0.77884	GGA	.	.		0.572	FAM193B-003	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373121.1	NM_019057		T	176952090	C	T	176952090	2	4	219	1	0	0	0	0	0	0	0	1	5530	581	21	3		3	FAM193B	5	176952090	Silent	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	66519310	176952090	3963170	41	31406										
DST	667	hgsc.bcm.edu	37	chr6	56481396	56481397	+	Frame_Shift_Ins	INS	-	-	T													0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	attgggattagggaaaactcINSttgtgttgctggatggctca					rs112473525	byFrequency	TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr6:56481396_56481397insT	ENST00000370765.6	-	24	6975_6976	c.6868_6869insA	c.(6868-6870)agafs	p.R2290fs	DST_ENST00000370788.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000244364.6_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1628					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AGGGAAAACTCTTGTGTTGCTG	0.421																																					p.R2290fs		Atlas-INDEL	.											.	DST	1427	.	0			c.6869_6870insA						.																																			SO:0001589	frameshift_variant	667	exon24			.	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.6869dupA	chr6.hg19:g.56481398_56481398dupT	ENSP00000359801:p.Arg2290fs	80.0	0.0		57.0	17.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Frame_Shift_Ins	INS	ENST00000370765.6	hg19	CCDS4959.1																																																																																			.	.		0.421	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		T	56481397	-	T	56481396	7	5	219	1	0	1	1	0	0	0	0	0	4785	913	32	0	13530	0	DST	6	56481396	Frame_Shift_Ins	INS	-	TCGA-DD-AAEG-01A-11D-A38X-10		56481396	114633671	42	31407										
LATS1	9113	hgsc.bcm.edu	37	chr6	149997738	149997738	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tataattgggagtcccaaccAaagaatgtgctagacatcgc	9	9	0	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr6:149997738A>G	ENST00000543571.1	-	6	3276	c.2729T>C	c.(2728-2730)tTg>tCg	p.L910S	LATS1_ENST00000253339.5_Missense_Mutation_p.L910S|LATS1_ENST00000542747.1_5'UTR	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		AGTCCCAACCAAAGAATGTGC	0.473																																					p.L910S		Atlas-SNP	.											.	LATS1	241	.	0			c.T2729C						.						74	73	73					6																	149997738		2203	4300	6503	SO:0001583	missense	9113	exon6			CCAACCAAAGAAT	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2729T>C	chr6.hg19:g.149997738A>G	ENSP00000437550:p.Leu910Ser	61.0	0.0		51.0	28.0	NM_004690		Missense_Mutation	SNP	ENST00000543571.1	hg19	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.695017	0.88830	.	.	ENSG00000131023	ENST00000543571;ENST00000253339	T;T	0.08720	3.06;3.06	5.81	5.81	0.92471	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.44285	D	0.000462	T	0.10551	0.0258	L	0.27944	0.81	0.80722	D	1	D	0.69078	0.997	D	0.75484	0.986	T	0.32666	-0.9898	9	.	.	.	.	16.1708	0.81812	1.0:0.0:0.0:0.0	.	910	O95835	LATS1_HUMAN	S	910	ENSP00000437550:L910S;ENSP00000253339:L910S	.	L	-	2	0	LATS1	150039431	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.225000	0.72522	0.533000	0.62120	TTG	.	.		0.473	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		G	149997738	A	G	149997738	3	3	219	1	0	0	0	0	1	0	0	0	8655	131	5	2	675	2	LATS1	6	149997738	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	93516342	149997738	21117329	43	31408										
LANCL2	55915	hgsc.bcm.edu	37	chr7	55466207	55466207	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tacgtaaaaagaacacttcgGaatctgaatggccgcagggt	11	8	1	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr7:55466207G>T	ENST00000254770.2	+	3	992	c.414G>T	c.(412-414)cgG>cgT	p.R138R	LANCL2_ENST00000486376.1_3'UTR	NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	138					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			GAACACTTCGGAATCTGAATG	0.517																																					p.R138R		Atlas-SNP	.											LANCL2,NS,carcinoma,0,1	LANCL2	54	.	0			c.G414T						.						87	85	85					7																	55466207		2203	4300	6503	SO:0001819	synonymous_variant	55915	exon3			ACTTCGGAATCTG	AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434			6509	protein-coding gene	gene with protein product	"testis-specific adriamycin sensitivity protein", "G protein-coupled receptor 69B"	612919	"LanC (bacterial lantibiotic synthetase component C)-like 2"	GPR69B		11762191	Standard	NM_018697		Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.414G>T	chr7.hg19:g.55466207G>T		109.0	0.0		98.0	43.0	NM_018697	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Silent	SNP	ENST00000254770.2	hg19	CCDS5517.1																																																																																			.	.		0.517	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697		T	55466207	G	T	55466207	2	4	219	1	0	0	0	0	0	0	0	1	8630	1161	41	3		3	LANCL2	7	55466207	Silent	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10		55466207	103672456	44	31409										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83643585	83643585	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gagtgttctccatctattgcAttttcacggaagaaaaagta	8	7	3	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr7:83643585A>G	ENST00000265362.4	-	7	1064	c.750T>C	c.(748-750)aaT>aaC	p.N250N	SEMA3A_ENST00000436949.1_Silent_p.N250N	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	250	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CATCTATTGCATTTTCACGGA	0.383																																					p.N250N		Atlas-SNP	.											.	SEMA3A	121	.	0			c.T750C						.						112	108	109					7																	83643585		2203	4300	6503	SO:0001819	synonymous_variant	10371	exon7			TATTGCATTTTCA	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.750T>C	chr7.hg19:g.83643585A>G		69.0	0.0		55.0	6.0	NM_006080		Silent	SNP	ENST00000265362.4	hg19	CCDS5599.1																																																																																			.	.		0.383	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		G	83643585	A	G	83643585	2	3	219	1	0	0	0	0	0	0	0	1	14039	214	8	2		2	SEMA3A	7	83643585	Silent	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	28177378	83643585	75495078	45	31410										
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106508205	106508205	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	acgtggccggccacggcaacGtggagcagatgaaggcccag	16	12	0	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr7:106508205G>A	ENST00000359195.3	+	2	509	c.199G>A	c.(199-201)Gtg>Atg	p.V67M	PIK3CG_ENST00000440650.2_Missense_Mutation_p.V67M|PIK3CG_ENST00000496166.1_Missense_Mutation_p.V67M	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	67	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						CCACGGCAACGTGGAGCAGAT	0.657																																					p.V67M		Atlas-SNP	.											PIK3CG,NS,carcinoma,0,1	PIK3CG	279	.	0			c.G199A						.						26	31	29					7																	106508205		2200	4295	6495	SO:0001583	missense	5294	exon2			GGCAACGTGGAGC		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.199G>A	chr7.hg19:g.106508205G>A	ENSP00000352121:p.Val67Met	81.0	0.0		67.0	4.0	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	hg19	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.082979	0.76642	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.74315	-0.83;-0.83;-0.83	5.64	5.64	0.86602	.	0.107094	0.64402	D	0.000006	D	0.85212	0.5645	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	D	0.85484	0.1181	10	0.72032	D	0.01	-23.9341	20.0585	0.97663	0.0:0.0:1.0:0.0	.	67	P48736	PK3CG_HUMAN	M	67	ENSP00000392258:V67M;ENSP00000419260:V67M;ENSP00000352121:V67M	ENSP00000352121:V67M	V	+	1	0	PIK3CG	106295441	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.464000	0.97655	2.812000	0.96745	0.557000	0.71058	GTG	.	.		0.657	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			A	106508205	G	A	106508205	3	1	219	1	0	0	0	0	1	0	0	0	11925	1145	40	1	201	1	PIK3CG	7	106508205	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	22864620	106508205	52630458	46	31411										
GCC1	79571	hgsc.bcm.edu	37	chr7	127222196	127222196	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ctggcggcccagggagtcagGtaaggtcaggaagcggtaga	18	8	2	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr7:127222196G>A	ENST00000321407.2	-	2	2624	c.2200C>T	c.(2200-2202)Cct>Tct	p.P734S	GCC1_ENST00000497650.1_5'Flank	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	734	GRIP. {ECO:0000255|PROSITE- ProRule:PRU00250}.				protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						AGGGAGTCAGGTAAGGTCAGG	0.532																																					p.P734S		Atlas-SNP	.											.	GCC1	83	.	0			c.C2200T						.						257	248	251					7																	127222196		2203	4300	6503	SO:0001583	missense	79571	exon2			AGTCAGGTAAGGT	AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"golgi coiled-coil 1"			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.2200C>T	chr7.hg19:g.127222196G>A	ENSP00000318821:p.Pro734Ser	221.0	0.0		245.0	26.0	NM_024523	Q9H6N7	Missense_Mutation	SNP	ENST00000321407.2	hg19	CCDS5796.1	.	.	.	.	.	.	.	.	.	.	G	9.137	1.012937	0.19277	.	.	ENSG00000179562	ENST00000321407	T	0.10573	2.86	5.87	4.05	0.47172	GRIP (4);	0.207402	0.51477	N	0.000091	T	0.05731	0.0150	N	0.12182	0.205	0.58432	D	0.99999	B	0.22800	0.075	B	0.23018	0.043	T	0.28138	-1.0053	10	0.09338	T	0.73	-9.6801	11.4873	0.50361	0.1551:0.0:0.8449:0.0	.	734	Q96CN9	GCC1_HUMAN	S	734	ENSP00000318821:P734S	ENSP00000318821:P734S	P	-	1	0	GCC1	127009432	1.000000	0.71417	0.952000	0.39060	0.954000	0.61252	6.024000	0.70857	1.632000	0.50472	-0.140000	0.14226	CCT	.	.		0.532	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523		A	127222196	G	A	127222196	3	1	219	1	0	0	0	0	1	0	0	0	6293	1261	44	3	131	3	GCC1	7	127222196	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	20713991	127222196	31916467	47	31412										
ASH2L	9070	hgsc.bcm.edu	37	chr8	37986410	37986410	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gagacgtcctgggattttatAttaatcttcctgaagacaca	8	8	1	3	rs539322046		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr8:37986410A>G	ENST00000343823.6	+	12	1777	c.1468A>G	c.(1468-1470)Att>Gtt	p.I490V	ASH2L_ENST00000545394.1_Missense_Mutation_p.I351V|ASH2L_ENST00000521652.1_Missense_Mutation_p.I396V|ASH2L_ENST00000250635.7_Missense_Mutation_p.I396V|ASH2L_ENST00000428278.2_Missense_Mutation_p.I396V	NM_004674.4	NP_004665.2	Q9UBL3	ASH2L_HUMAN	ash2 (absent, small, or homeotic)-like (Drosophila)	490	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				cellular response to DNA damage stimulus (GO:0006974)|hemopoiesis (GO:0030097)|histone H3-K4 methylation (GO:0051568)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)	19	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)				GGGATTTTATATTAATCTTCC	0.473																																					p.I490V		Atlas-SNP	.											.	ASH2L	62	.	0			c.A1468G						.						214	222	219					8																	37986410		2203	4300	6503	SO:0001583	missense	9070	exon12			TTTTATATTAATC	AF056717	CCDS6101.1, CCDS47840.1, CCDS59100.1, CCDS64872.1	8p11.2	2013-01-28	2001-11-28		ENSG00000129691	ENSG00000129691		"Zinc fingers, PHD-type"	744	protein-coding gene	gene with protein product		604782	"ash2 (absent, small, or homeotic, Drosophila, homolog)-like"	ASH2L1		10393421	Standard	NM_004674		Approved	ASH2L2, ASH2, Bre2	uc003xkt.5	Q9UBL3	OTTHUMG00000164016	ENST00000343823.6:c.1468A>G	chr8.hg19:g.37986410A>G	ENSP00000340896:p.Ile490Val	75.0	0.0		75.0	27.0	NM_004674	A8K7C3|D3DSW9|O60659|O60660|Q96B62	Missense_Mutation	SNP	ENST00000343823.6	hg19	CCDS6101.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.90|16.90	3.249822|3.249822	0.59212|0.59212	.|.	.|.	ENSG00000129691|ENSG00000129691	ENST00000343823;ENST00000250635;ENST00000545394;ENST00000428278;ENST00000521652|ENST00000524247	T;T;T;T;T|T	0.73363|0.69175	-0.74;-0.74;-0.74;-0.74;-0.74|-0.38	5.42|5.42	5.42|5.42	0.78866|0.78866	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);|.	0.042432|.	0.85682|.	N|.	0.000000|.	T|T	0.80989|0.80989	0.4730|0.4730	M|M	0.83483|0.83483	2.645|2.645	0.80722|0.80722	D|D	1|1	B;B|.	0.24721|.	0.11;0.002|.	B;B|.	0.35931|.	0.214;0.012|.	D|D	0.83452|0.83452	0.0049|0.0049	10|7	0.87932|0.56958	D|D	0|0.05	0.2925|0.2925	15.5087|15.5087	0.75764|0.75764	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	396;490|.	Q9UBL3-2;Q9UBL3|.	.;ASH2L_HUMAN|.	V|C	490;396;351;396;396|85	ENSP00000340896:I490V;ENSP00000250635:I396V;ENSP00000443606:I351V;ENSP00000395310:I396V;ENSP00000430259:I396V|ENSP00000429387:Y85C	ENSP00000250635:I396V|ENSP00000429387:Y85C	I|Y	+|+	1|2	0|0	ASH2L|ASH2L	38105567|38105567	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.921000|0.921000	0.55340|0.55340	7.488000|7.488000	0.81441|0.81441	2.072000|2.072000	0.62099|0.62099	0.397000|0.397000	0.26171|0.26171	ATT|TAT	.	.		0.473	ASH2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376749.4	NM_004674		G	37986410	A	G	37986410	3	3	219	1	0	0	0	0	1	0	0	0	1042	449	16	2	1514	2	ASH2L	8	37986410	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10		37986410	108377612	48	31413										
NOV	4856	hgsc.bcm.edu	37	chr8	120430340	120430340	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gttcgatggggtcatctaccGcagtggagagaaatttcagc	13	8	3	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr8:120430340G>A	ENST00000259526.3	+	3	580	c.353G>A	c.(352-354)cGc>cAc	p.R118H	RP11-775B15.2_ENST00000519786.1_RNA	NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	0	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			GTCATCTACCGCAGTGGAGAG	0.498																																					p.R118H		Atlas-SNP	.											NOV,NS,carcinoma,0,2	NOV	51	.	0			c.G353A						.						101	105	104					8																	120430340		2203	4300	6503	SO:0001583	missense	4856	exon3			TCTACCGCAGTGG	X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"nephroblastoma overexpressed gene"			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.353G>A	chr8.hg19:g.120430340G>A	ENSP00000259526:p.Arg118His	119.0	0.0		282.0	27.0	NM_002514		Missense_Mutation	SNP	ENST00000259526.3	hg19	CCDS6328.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260726	0.80246	.	.	ENSG00000136999	ENST00000259526	T	0.72505	-0.66	5.51	2.63	0.31362	von Willebrand factor, type C (3);	0.251742	0.42821	N	0.000660	T	0.61776	0.2374	L	0.50333	1.59	0.40710	D	0.982568	B	0.24368	0.102	B	0.23419	0.046	T	0.56498	-0.7969	10	0.44086	T	0.13	-19.3073	9.239	0.37484	0.219:0.0:0.781:0.0	.	118	P48745	NOV_HUMAN	H	118	ENSP00000259526:R118H	ENSP00000259526:R118H	R	+	2	0	NOV	120499521	0.974000	0.33945	0.988000	0.46212	0.993000	0.82548	0.960000	0.29253	0.373000	0.24621	0.561000	0.74099	CGC	.	.		0.498	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514		A	120430340	G	A	120430340	3	1	219	1	0	0	0	0	1	0	0	0	10562	1087	38	1	363	1	NOV	8	120430340	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	82443930	120430340	25933682	49	31414										
FBXO10	26267	hgsc.bcm.edu	37	chr9	37541364	37541364	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tacacacctgggaagagcacAattcggtcatacaggctggc	11	11	1	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr9:37541364A>G	ENST00000432825.2	-	2	450	c.402T>C	c.(400-402)atT>atC	p.I134I	FBXO10_ENST00000541829.1_Intron|RP11-613M10.8_ENST00000544475.1_5'UTR|RP11-613M10.8_ENST00000537239.2_3'UTR	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	134					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		GGAAGAGCACAATTCGGTCAT	0.587																																					p.I134I		Atlas-SNP	.											.	FBXO10	75	.	0			c.T402C						.						151	152	151					9																	37541364		2060	4200	6260	SO:0001819	synonymous_variant	26267	exon2			GAGCACAATTCGG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"F-boxes /  "other""	13589	protein-coding gene	gene with protein product		609092	"F-box only protein 10"			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.402T>C	chr9.hg19:g.37541364A>G		91.0	0.0		81.0	34.0	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Silent	SNP	ENST00000432825.2	hg19	CCDS47966.1																																																																																			.	.		0.587	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3			G	37541364	A	G	37541364	2	3	219	1	0	0	0	0	0	0	0	1	5734	126	5	2		2	FBXO10	9	37541364	Silent	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10		37541364	103672067	50	31415										
FGD3	89846	hgsc.bcm.edu	37	chr9	95780470	95780470	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tacattcatcataacaggaaGaaaaaggtccctggagctgc	9	9	2	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr9:95780470G>T	ENST00000375482.3	+	11	1824	c.1328G>T	c.(1327-1329)aGa>aTa	p.R443I	FGD3_ENST00000416701.2_Missense_Mutation_p.R443I|FGD3_ENST00000538555.1_Missense_Mutation_p.R46I|FGD3_ENST00000337352.6_Missense_Mutation_p.R443I	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	443	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						ATAACAGGAAGAAAAAGGTCC	0.438																																					p.R443I		Atlas-SNP	.											.	FGD3	116	.	0			c.G1328T						.						119	122	121					9																	95780470		1959	4149	6108	SO:0001583	missense	89846	exon11			CAGGAAGAAAAAG	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16027	protein-coding gene	gene with protein product			"FGD1 family, member 3"			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.1328G>T	chr9.hg19:g.95780470G>T	ENSP00000364631:p.Arg443Ile	65.0	0.0		76.0	24.0	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Missense_Mutation	SNP	ENST00000375482.3	hg19	CCDS43849.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184723	0.38609	.	.	ENSG00000127084	ENST00000375482;ENST00000416701;ENST00000337352;ENST00000538555	T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0	4.7	-7.27	0.01461	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.596324	0.13937	N	0.352500	T	0.76884	0.4050	L	0.55481	1.735	0.32090	N	0.591956	P;P;P	0.43542	0.702;0.81;0.703	B;P;P	0.53988	0.419;0.452;0.739	T	0.80113	-0.1518	10	0.87932	D	0	-20.2911	17.5283	0.87807	0.8647:0.0:0.1353:0.0	.	443;443;443	Q5JSP0-2;F8W7P2;Q5JSP0	.;.;FGD3_HUMAN	I	443;443;443;46	ENSP00000364631:R443I;ENSP00000413833:R443I;ENSP00000336914:R443I;ENSP00000442560:R46I	ENSP00000336914:R443I	R	+	2	0	FGD3	94820291	0.992000	0.36948	0.000000	0.03702	0.094000	0.18550	1.266000	0.33039	-1.551000	0.01706	-1.073000	0.02249	AGA	.	.		0.438	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086		T	95780470	G	T	95780470	3	4	219	1	0	0	0	0	1	0	0	0	5842	942	33	3	1362	3	FGD3	9	95780470	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	58239106	95780470	45432961	51	31416										
NINJ1	4814	hgsc.bcm.edu	37	chr9	95888799	95888799	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tggggccctgttccacgacgGccttcagctgggacgcgttg	15	13	1	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr9:95888799G>A	ENST00000375446.4	-	2	267	c.197C>T	c.(196-198)gCc>gTc	p.A66V	NINJ1_ENST00000489274.1_5'Flank	NM_004148.3	NP_004139.2	Q92982	NINJ1_HUMAN	ninjurin 1	66					cell adhesion (GO:0007155)|hyaloid vascular plexus regression (GO:1990384)|nervous system development (GO:0007399)|positive regulation of cell-matrix adhesion (GO:0001954)|tissue regeneration (GO:0042246)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|upper_aerodigestive_tract(1)	4						TTCCACGACGGCCTTCAGCTG	0.627																																					p.A66V		Atlas-SNP	.											.	NINJ1	7	.	0			c.C197T						.						115	93	101					9																	95888799		2203	4300	6503	SO:0001583	missense	4814	exon2			ACGACGGCCTTCA	U91512	CCDS6703.1	9q22	2008-07-21			ENSG00000131669	ENSG00000131669			7824	protein-coding gene	gene with protein product	"nerve injury-induced protein-1"	602062				8780658	Standard	NM_004148		Approved	NIN1	uc004atg.4	Q92982	OTTHUMG00000020242	ENST00000375446.4:c.197C>T	chr9.hg19:g.95888799G>A	ENSP00000364595:p.Ala66Val	116.0	0.0		112.0	10.0	NM_004148	Q6GU89|Q8WUV5|Q9BT07	Missense_Mutation	SNP	ENST00000375446.4	hg19	CCDS6703.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700247	0.88924	.	.	ENSG00000131669	ENST00000375446	T	0.41758	0.99	4.49	4.49	0.54785	.	0.049158	0.85682	D	0.000000	T	0.58935	0.2157	M	0.71581	2.175	0.58432	D	0.999996	D	0.69078	0.997	D	0.64321	0.924	T	0.54569	-0.8274	10	0.17832	T	0.49	-18.758	16.2853	0.82717	0.0:0.0:1.0:0.0	.	66	Q92982	NINJ1_HUMAN	V	66	ENSP00000364595:A66V	ENSP00000364595:A66V	A	-	2	0	NINJ1	94928620	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	9.320000	0.96346	2.502000	0.84385	0.462000	0.41574	GCC	.	.		0.627	NINJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053123.2	NM_004148		A	95888799	G	A	95888799	3	1	219	1	0	0	0	0	1	0	0	0	10427	1203	42	3	269	3	NINJ1	9	95888799	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	108329	95888799	45324632	52	31417										
DDX50	79009	hgsc.bcm.edu	37	chr10	70673836	70673836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ttctgaagacaatcctcagaCtttacttttttctgcaactt	4	10	3	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr10:70673836C>T	ENST00000373585.3	+	7	1072	c.965C>T	c.(964-966)aCt>aTt	p.T322I	RNU6-571P_ENST00000384128.1_RNA	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	322	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						AATCCTCAGACTTTACTTTTT	0.353																																					p.T322I		Atlas-SNP	.											.	DDX50	65	.	0			c.C965T						.						45	45	45					10																	70673836		2203	4300	6503	SO:0001583	missense	79009	exon7			CTCAGACTTTACT	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.965C>T	chr10.hg19:g.70673836C>T	ENSP00000362687:p.Thr322Ile	157.0	0.0		142.0	57.0	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	hg19	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.280225	0.80692	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.14022	2.54	5.49	5.49	0.81192	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.31638	0.0803	L	0.55481	1.735	0.80722	D	1	P;P	0.51240	0.943;0.94	P;P	0.58391	0.775;0.838	T	0.00242	-1.1885	10	0.51188	T	0.08	-12.286	19.7394	0.96219	0.0:1.0:0.0:0.0	.	322;322	Q9BQ39;B4DED6	DDX50_HUMAN;.	I	322	ENSP00000362687:T322I	ENSP00000362687:T322I	T	+	2	0	DDX50	70343842	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.745000	0.94114	0.462000	0.41574	ACT	.	.		0.353	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		T	70673836	C	T	70673836	3	4	219	1	0	0	0	0	1	0	0	0	4370	565	20	3	991	3	DDX50	10	70673836	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10		70673836	64860911	53	31418										
CARS	833	hgsc.bcm.edu	37	chr11	3039725	3039725	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cacgagtgcatgaggaaggcCagccgcaactgccgtgctgt	14	12	0	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr11:3039725C>A	ENST00000397111.5	-	13	1538	c.1293G>T	c.(1291-1293)ctG>ctT	p.L431L	CARS_ENST00000278224.9_Silent_p.L431L|CARS_ENST00000380525.4_Silent_p.L514L|CARS_ENST00000401769.3_Silent_p.L444L|CARS_ENST00000397114.3_Silent_p.L421L			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	431					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)		CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	TGAGGAAGGCCAGCCGCAACT	0.557			T	ALK	ALCL																																p.L514L	Ovarian(61;932 1157 5961 20446 52152)	Atlas-SNP	.		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	.	CARS	114	.	0			c.G1542T						.						64	61	62					11																	3039725		2202	4298	6500	SO:0001819	synonymous_variant	833	exon14			GAAGGCCAGCCGC	AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"Aminoacyl tRNA synthetases / Class I"	1493	protein-coding gene	gene with protein product	"cysteine tRNA ligase 1, cytoplasmic"	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.1293G>T	chr11.hg19:g.3039725C>A		65.0	0.0		75.0	22.0	NM_001014437	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Silent	SNP	ENST00000397111.5	hg19	CCDS7742.1																																																																																			.	.		0.557	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751		A	3039725	C	A	3039725	2	1	219	1	0	0	0	0	0	0	0	1	2659	581	21	3		3	CARS	11	3039725	Silent	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10		3039725	131966791	54	31419										
CTNND1	1500	hgsc.bcm.edu	37	chr11	57559030	57559030	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ggcccagtttgagaagctgaCccgggcgctggaggaggaac	17	10	0	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr11:57559030C>T	ENST00000399050.4	+	3	616	c.80C>T	c.(79-81)aCc>aTc	p.T27I	CTNND1_ENST00000361796.4_Missense_Mutation_p.T27I|CTNND1_ENST00000428599.2_Missense_Mutation_p.T27I|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000528621.1_5'UTR|CTNND1_ENST00000361391.6_Missense_Mutation_p.T27I|CTNND1_ENST00000529919.1_Missense_Mutation_p.T27I|CTNND1_ENST00000531014.1_Intron|CTNND1_ENST00000426142.2_Intron|CTNND1_ENST00000532463.1_Intron|CTNND1_ENST00000530094.1_Intron|RP11-691N7.6_ENST00000531074.1_3'UTR|CTNND1_ENST00000527467.1_Intron|CTNND1_ENST00000415361.2_Intron|CTNND1_ENST00000360682.6_Missense_Mutation_p.T27I|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000526357.1_5'UTR|CTNND1_ENST00000532649.1_5'UTR|CTNND1_ENST00000526938.1_Missense_Mutation_p.T27I|CTNND1_ENST00000528232.1_Intron|CTNND1_ENST00000532787.1_Intron|CTNND1_ENST00000530748.1_5'UTR|CTNND1_ENST00000529873.1_5'UTR|CTNND1_ENST00000529986.1_Intron|CTNND1_ENST00000524630.1_Missense_Mutation_p.T27I|CTNND1_ENST00000534579.1_5'UTR|CTNND1_ENST00000532245.1_Intron|CTNND1_ENST00000399039.4_Missense_Mutation_p.T27I|CTNND1_ENST00000358694.6_Missense_Mutation_p.T27I|CTNND1_ENST00000361332.4_Missense_Mutation_p.T27I|CTNND1_ENST00000529526.1_5'UTR|TMX2-CTNND1_ENST00000528395.1_3'UTR|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000532844.1_5'UTR	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	27					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				GAGAAGCTGACCCGGGCGCTG	0.637																																					p.T27I		Atlas-SNP	.											.	CTNND1	203	.	0			c.C80T						.						20	23	22					11																	57559030		1998	4152	6150	SO:0001583	missense	1500	exon3			AGCTGACCCGGGC	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"Armadillo repeat containing"	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.80C>T	chr11.hg19:g.57559030C>T	ENSP00000382004:p.Thr27Ile	133.0	0.0		139.0	17.0	NM_001085461	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Missense_Mutation	SNP	ENST00000399050.4	hg19	CCDS44604.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.949231	0.92660	.	.	ENSG00000198561	ENST00000524630;ENST00000529919;ENST00000399039;ENST00000360682;ENST00000361796;ENST00000399050;ENST00000361391;ENST00000361332;ENST00000358694;ENST00000428599;ENST00000526938	T;T;T;T;T;T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51	5.62	5.62	0.85841	.	0.110655	0.64402	D	0.000010	T	0.55033	0.1895	M	0.62723	1.935	0.49798	D	0.999823	D;D;D;D;D;D	0.76494	0.993;0.993;0.988;0.999;0.993;0.988	P;P;P;D;P;P	0.72982	0.857;0.857;0.723;0.979;0.857;0.723	T	0.54556	-0.8276	10	0.87932	D	0	-21.8398	18.7943	0.91988	0.0:1.0:0.0:0.0	.	27;27;27;27;27;27	O60716-3;O60716-2;O60716;O60716-5;F8WA43;C9JZR2	.;.;CTND1_HUMAN;.;.;.	I	27	ENSP00000436543:T27I;ENSP00000434808:T27I;ENSP00000381996:T27I;ENSP00000353902:T27I;ENSP00000354907:T27I;ENSP00000382004:T27I;ENSP00000354785:T27I;ENSP00000354823:T27I;ENSP00000351527:T27I;ENSP00000413586:T27I;ENSP00000432041:T27I	ENSP00000351527:T27I	T	+	2	0	CTNND1	57315606	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	4.568000	0.60857	2.809000	0.96659	0.655000	0.94253	ACC	.	.		0.637	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331		T	57559030	C	T	57559030	3	4	219	1	0	0	0	0	1	0	0	0	4021	507	18	3	82	3	CTNND1	11	57559030	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	54519305	57559030	77447486	55	31420										
MS4A2	2206	hgsc.bcm.edu	37	chr11	59857213	59857213	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tctccccaggaagtatcttcAggcagactattgaagtcggc	10	11	3	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr11:59857213A>G	ENST00000278888.3	+	2	207	c.105A>G	c.(103-105)tcA>tcG	p.S35S		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	35					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	AAGTATCTTCAGGCAGACTAT	0.463																																					p.S35S		Atlas-SNP	.											.	MS4A2	41	.	0			c.A105G						.						130	125	127					11																	59857213		2201	4295	6496	SO:0001819	synonymous_variant	2206	exon2			ATCTTCAGGCAGA	M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"	147138	"IgE responsiveness (atopic)", "membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	ENST00000278888.3:c.105A>G	chr11.hg19:g.59857213A>G		63.0	0.0		43.0	8.0	NM_000139	Q54A81	Silent	SNP	ENST00000278888.3	hg19	CCDS7980.1																																																																																			.	.		0.463	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1			G	59857213	A	G	59857213	2	3	219	1	0	0	0	0	0	0	0	1	9869	175	7	2		2	MS4A2	11	59857213	Silent	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	2298183	59857213	75149303	56	31421										
SIK2	23235	hgsc.bcm.edu	37	chr11	111574147	111574147	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gatcagcagaaaaccattgaGgtaaagtgatcagagatttc	10	6	2	4			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr11:111574147G>A	ENST00000304987.3	+	7	1121	c.948G>A	c.(946-948)gaG>gaA	p.E316E		NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	316	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						AAACCATTGAGGTAAAGTGAT	0.453																																					p.E316E		Atlas-SNP	.											.	SIK2	89	.	0			c.G948A						.						62	59	60					11																	111574147		2201	4297	6498	SO:0001630	splice_region_variant	23235	exon7			CATTGAGGTAAAG	AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"SNF1-like kinase 2"	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.948+1G>A	chr11.hg19:g.111574147G>A		56.0	0.0		44.0	13.0	NM_015191	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Silent	SNP	ENST00000304987.3	hg19	CCDS8347.1																																																																																			.	.		0.453	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191	Silent	A	111574147	G	A	111574147	5	1	219	1	0	0	0	0	0	0	1	0	14333	1014	35	3	974	3	SIK2	11	111574147	Splice_Site	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	51716934	111574147	23432369	57	31422										
FLI1	2313	hgsc.bcm.edu	37	chr11	128628065	128628065	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ctttgactcagcgtacggagCggcagcccatctccccaagg	11	15	2	1	rs200865469	byFrequency	TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr11:128628065C>G	ENST00000527786.2	+	2	563	c.74C>G	c.(73-75)gCg>gGg	p.A25G	FLI1_ENST00000525560.1_5'UTR|FLI1_ENST00000344954.6_5'UTR|FLI1_ENST00000534087.2_5'UTR	NM_001271010.1|NM_002017.4	NP_001257939.1|NP_002008.2	Q01543	FLI1_HUMAN	Fli-1 proto-oncogene, ETS transcription factor	25					blood circulation (GO:0008015)|cell differentiation (GO:0030154)|hemostasis (GO:0007599)|megakaryocyte development (GO:0035855)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/FLI1(2569)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(2)	31	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		GCGTACGGAGCGGCAGCCCAT	0.622			T	EWSR1	Ewing sarcoma																																p.A25G		Atlas-SNP	.		Dom	yes		11	11q24	2313	Friend leukemia virus integration 1		M	.	FLI1	72	.	0			c.C74G						.						32	39	37					11																	128628065		2158	4256	6414	SO:0001583	missense	2313	exon2			ACGGAGCGGCAGC	M98833	CCDS44768.1, CCDS53725.1, CCDS59230.1, CCDS59231.1	11q24.1-q24.3	2014-09-17	2013-08-07		ENSG00000151702	ENSG00000151702			3749	protein-coding gene	gene with protein product		193067	"Friend leukemia virus integration 1"			1765382	Standard	NM_001167681		Approved	SIC-1, EWSR2	uc010sbu.2	Q01543	OTTHUMG00000165792	ENST00000527786.2:c.74C>G	chr11.hg19:g.128628065C>G	ENSP00000433488:p.Ala25Gly	70.0	0.0		68.0	17.0	NM_002017	B2R8H2|B4DFV4|B4DTC6|G3V183|Q14319|Q92480|Q9UE07	Missense_Mutation	SNP	ENST00000527786.2	hg19	CCDS44768.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072160	0.76415	.	.	ENSG00000151702	ENST00000429175	T	0.15256	2.44	4.54	4.54	0.55810	.	0.155915	0.56097	N	0.000025	T	0.25419	0.0618	L	0.29908	0.895	0.80722	D	1	D	0.69078	0.997	P	0.57244	0.816	T	0.01786	-1.1274	10	0.29301	T	0.29	.	18.1645	0.89721	0.0:1.0:0.0:0.0	.	25	Q01543	FLI1_HUMAN	G	25	ENSP00000399985:A25G	ENSP00000399985:A25G	A	+	2	0	FLI1	128133275	1.000000	0.71417	0.820000	0.32676	0.504000	0.33889	7.100000	0.76989	2.428000	0.82296	0.561000	0.74099	GCG	.	C|1.000;T|0.000		0.622	FLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386226.2	NM_002017		G	128628065	C	G	128628065	3	3	219	1	0	0	0	0	1	0	0	0	5932	768	27	4	80	4	FLI1	11	128628065	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	17053918	128628065	6378451	58	31423										
DDX11	1663	hgsc.bcm.edu	37	chr12	31238054	31238054	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tgatgaggagaaaaaggtggCgagcaggtgagacagaggcg	19	4	0	5			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr12:31238054C>T	ENST00000407793.2	+	5	883	c.632C>T	c.(631-633)gCg>gTg	p.A211V	DDX11_ENST00000228264.6_Missense_Mutation_p.A185V|DDX11_ENST00000545668.1_Missense_Mutation_p.A211V|DDX11_ENST00000251758.5_Missense_Mutation_p.A211V|DDX11_ENST00000350437.4_Missense_Mutation_p.A211V|DDX11_ENST00000542838.1_Missense_Mutation_p.A211V	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	211	Glu-rich.|Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					AAAAAGGTGGCGAGCAGGTGA	0.612										Multiple Myeloma(12;0.14)																											p.A211V		Atlas-SNP	.											.	DDX11	188	.	0			c.C632T						.						32	32	32					12																	31238054		2190	4278	6468	SO:0001583	missense	1663	exon5			AGGTGGCGAGCAG	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.632C>T	chr12.hg19:g.31238054C>T	ENSP00000384703:p.Ala211Val	206.0	0.0		194.0	57.0	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	hg19	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	C	8.208	0.799606	0.16397	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000251758;ENST00000228264;ENST00000438391;ENST00000415475;ENST00000545668;ENST00000350437	D;T;T;T;T;T;T;T	0.81499	-1.5;-0.65;3.98;-1.41;0.31;4.05;-0.65;-1.2	3.7	1.78	0.24846	Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	2.500470	0.01725	N	0.028554	T	0.72220	0.3433	L	0.36672	1.1	0.09310	N	1	B;B;B;B	0.11235	0.001;0.002;0.004;0.002	B;B;B;B	0.08055	0.001;0.001;0.003;0.003	T	0.52064	-0.8625	10	0.23302	T	0.38	.	6.0476	0.19768	0.0:0.7467:0.0:0.2533	.	211;211;211;211	B4DZY1;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	V	211;211;211;185;182;185;211;211	ENSP00000443426:A211V;ENSP00000384703:A211V;ENSP00000251758:A211V;ENSP00000228264:A185V;ENSP00000407646:A182V;ENSP00000406457:A185V;ENSP00000440402:A211V;ENSP00000309965:A211V	ENSP00000228264:A185V	A	+	2	0	DDX11	31129321	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.009000	0.13219	0.762000	0.33152	0.505000	0.49811	GCG	.	.		0.612	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		T	31238054	C	T	31238054	3	4	219	1	0	0	0	0	1	0	0	0	4345	768	27	1	646	1	DDX11	12	31238054	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10		31238054	102613841	59	31424										
NELL2	4753	hgsc.bcm.edu	37	chr12	45001007	45001007	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	caggcacacacattagcggcAatacaggctcctccattcct	7	15	0	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr12:45001007A>C	ENST00000429094.2	-	15	2112	c.1608T>G	c.(1606-1608)atT>atG	p.I536M	NELL2_ENST00000333837.4_Missense_Mutation_p.I559M|NELL2_ENST00000551601.1_Missense_Mutation_p.I535M|NELL2_ENST00000452445.2_Missense_Mutation_p.I536M|NELL2_ENST00000549027.1_Missense_Mutation_p.I535M|NELL2_ENST00000395487.2_Missense_Mutation_p.I535M|NELL2_ENST00000437801.2_Missense_Mutation_p.I586M	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	536	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		CATTAGCGGCAATACAGGCTC	0.383																																					p.I586M		Atlas-SNP	.											.	NELL2	286	.	0			c.T1758G						.						86	82	83					12																	45001007		2203	4299	6502	SO:0001583	missense	4753	exon16			AGCGGCAATACAG	D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.1608T>G	chr12.hg19:g.45001007A>C	ENSP00000390680:p.Ile536Met	248.0	0.0		235.0	23.0	NM_001145107	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	hg19	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.196812	0.58126	.	.	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801;ENST00000543684	D;D;D;D;D;D;D	0.92099	-2.31;-2.31;-2.97;-2.31;-2.31;-2.49;-2.31	5.68	2.03	0.26663	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.050997	0.85682	D	0.000000	D	0.90631	0.7062	L	0.58969	1.84	0.43287	D	0.995269	D;P;P;P;P	0.56035	0.974;0.552;0.919;0.868;0.552	P;B;P;B;B	0.52267	0.694;0.248;0.507;0.38;0.168	D	0.87299	0.2304	10	0.56958	D	0.05	-21.2665	4.349	0.11146	0.6322:0.0:0.2324:0.1354	.	559;586;535;536;535	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2	.;.;.;NELL2_HUMAN;.	M	535;536;535;536;535;559;586;535	ENSP00000378866:I535M;ENSP00000390680:I536M;ENSP00000449332:I535M;ENSP00000394612:I536M;ENSP00000447927:I535M;ENSP00000327988:I559M;ENSP00000416341:I586M	ENSP00000327988:I559M	I	-	3	3	NELL2	43287274	0.987000	0.35691	1.000000	0.80357	0.982000	0.71751	0.375000	0.20518	0.498000	0.27948	-0.290000	0.09829	ATT	.	.		0.383	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		C	45001007	A	C	45001007	3	2	219	1	0	0	0	0	1	0	0	0	10343	126	5	5	866	5	NELL2	12	45001007	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	13762953	45001007	88850888	60	31425										
BCDIN3D	144233	hgsc.bcm.edu	37	chr12	50236859	50236859	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ctccctccatccagttccgtGggcaccgccattagcctcaa	7	18	1	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr12:50236859G>A	ENST00000333924.4	-	1	53	c.12C>T	c.(10-12)ccC>ccT	p.P4P	BCDIN3D-AS1_ENST00000548872.1_RNA|BCDIN3D-AS1_ENST00000549124.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	4					miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						CCAGTTCCGTGGGCACCGCCA	0.647																																					p.P4P		Atlas-SNP	.											.	BCDIN3D	20	.	0			c.C12T						.						37	35	36					12																	50236859		2201	4296	6497	SO:0001819	synonymous_variant	144233	exon1			TTCCGTGGGCACC		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.12C>T	chr12.hg19:g.50236859G>A		87.0	0.0		101.0	10.0	NM_181708	A8K829	Silent	SNP	ENST00000333924.4	hg19	CCDS8790.1																																																																																			.	.		0.647	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708		A	50236859	G	A	50236859	2	1	219	1	0	0	0	0	0	0	0	1	1357	1335	47	3		3	BCDIN3D	12	50236859	Silent	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	5235852	50236859	83615036	61	31426										
AVPR1A	552	hgsc.bcm.edu	37	chr12	63544382	63544382	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gcgggacgtcttgcgcggcgTccggtgcagagccagcagta	17	12	1	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr12:63544382T>C	ENST00000299178.2	-	1	340	c.235A>G	c.(235-237)Acg>Gcg	p.T79A		NM_000706.4	NP_000697.1	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	79					activation of phospholipase C activity (GO:0007202)|blood circulation (GO:0008015)|calcium-mediated signaling (GO:0019722)|cellular response to water deprivation (GO:0042631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|grooming behavior (GO:0007625)|maternal aggressive behavior (GO:0002125)|maternal behavior (GO:0042711)|myotube differentiation (GO:0014902)|negative regulation of female receptivity (GO:0007621)|negative regulation of transmission of nerve impulse (GO:0051970)|penile erection (GO:0043084)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glutamate secretion (GO:0014049)|positive regulation of heart rate (GO:0010460)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of vasoconstriction (GO:0045907)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to corticosterone (GO:0051412)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|telencephalon development (GO:0021537)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|prostate(2)|skin(1)	26			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	TTGCGCGGCGTCCGGTGCAGA	0.657																																					p.T79A		Atlas-SNP	.											.	AVPR1A	85	.	0			c.A235G						.						24	26	25					12																	63544382		2203	4299	6502	SO:0001583	missense	552	exon1			GCGGCGTCCGGTG	L25615	CCDS8965.1	12q14-q15	2012-08-08				ENSG00000166148		"GPCR / Class A : Vasopressin and oxytocin receptors"	895	protein-coding gene	gene with protein product		600821		AVPR1		8106369	Standard	NM_000706		Approved		uc001sro.2	P37288		ENST00000299178.2:c.235A>G	chr12.hg19:g.63544382T>C	ENSP00000299178:p.Thr79Ala	59.0	0.0		54.0	13.0	NM_000706		Missense_Mutation	SNP	ENST00000299178.2	hg19	CCDS8965.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.868504	0.51588	.	.	ENSG00000166148	ENST00000299178	T	0.19250	2.16	5.33	5.33	0.75918	GPCR, rhodopsin-like superfamily (1);	0.051955	0.85682	D	0.000000	T	0.24314	0.0589	L	0.56280	1.765	0.52099	D	0.999947	B	0.24576	0.106	B	0.36378	0.223	T	0.06734	-1.0810	9	.	.	.	-26.4506	9.5386	0.39237	0.1571:0.0:0.0:0.8429	.	79	P37288	V1AR_HUMAN	A	79	ENSP00000299178:T79A	.	T	-	1	0	AVPR1A	61830649	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.718000	0.38001	2.015000	0.59207	0.459000	0.35465	ACG	.	.		0.657	AVPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406734.1			C	63544382	T	C	63544382	3	2	219	1	0	0	0	0	1	0	0	0	1231	1667	58	2	1029	2	AVPR1A	12	63544382	Missense_Mutation	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10	13307523	63544382	70307513	62	31427										
LEMD3	23592	hgsc.bcm.edu	37	chr12	65564347	65564347	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gatgaatgacagggcggcggCtgccgggagtctagacagga	18	8	1	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr12:65564347C>T	ENST00000308330.2	+	1	997	c.971C>T	c.(970-972)gCt>gTt	p.A324V	LEMD3_ENST00000541171.1_Intron	NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	324	Poly-Ala.				negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of cell cycle (GO:0051726)|skeletal muscle cell differentiation (GO:0035914)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	36			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		AGGGCGGCGGCTGCCGGGAGT	0.647																																					p.A324V		Atlas-SNP	.											.	LEMD3	68	.	0			c.C971T						.						22	26	25					12																	65564347		2203	4300	6503	SO:0001583	missense	23592	exon1			CGGCGGCTGCCGG	AF263918	CCDS8972.1	12q14	2008-02-05			ENSG00000174106	ENSG00000174106			28887	protein-coding gene	gene with protein product		607844				10671519, 15489854	Standard	NM_014319		Approved	MAN1	uc001ssl.2	Q9Y2U8	OTTHUMG00000168840	ENST00000308330.2:c.971C>T	chr12.hg19:g.65564347C>T	ENSP00000308369:p.Ala324Val	77.0	0.0		82.0	27.0	NM_001167614	Q9NT47|Q9NYA5	Missense_Mutation	SNP	ENST00000308330.2	hg19	CCDS8972.1	.	.	.	.	.	.	.	.	.	.	C	18.80	3.701117	0.68501	.	.	ENSG00000174106	ENST00000308330	T	0.56776	0.44	3.54	0.671	0.17929	.	0.464547	0.20195	N	0.097240	T	0.29061	0.0722	N	0.19112	0.55	0.34428	D	0.698205	B	0.02656	0.0	B	0.06405	0.002	T	0.14671	-1.0464	9	.	.	.	-2.9735	4.8775	0.13664	0.0:0.6152:0.1777:0.2071	.	324	Q9Y2U8	MAN1_HUMAN	V	324	ENSP00000308369:A324V	.	A	+	2	0	LEMD3	63850614	0.001000	0.12720	0.945000	0.38365	0.993000	0.82548	1.351000	0.34022	0.134000	0.18681	0.462000	0.41574	GCT	.	.		0.647	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401312.2			T	65564347	C	T	65564347	3	4	219	1	0	0	0	0	1	0	0	0	8730	797	28	3	973	3	LEMD3	12	65564347	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	2019965	65564347	68287548	63	31428										
PLEKHG7	440107	hgsc.bcm.edu	37	chr12	93139255	93139255	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tgctcttcctttcttgcagtAtttccgagggagtctctgtc	9	11	3	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr12:93139255A>G	ENST00000344636.3	+	5	387	c.203A>G	c.(202-204)tAt>tGt	p.Y68C	PLEKHG7_ENST00000549856.1_Splice_Site_p.Y68C	NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	68	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						TTCTTGCAGTATTTCCGAGGG	0.448																																					p.Y68C		Atlas-SNP	.											.	PLEKHG7	38	.	0			c.A203G						.						98	91	93					12																	93139255		2203	4300	6503	SO:0001630	splice_region_variant	440107	exon5			TGCAGTATTTCCG	AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"Pleckstrin homology (PH) domain containing"	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.202-1A>G	chr12.hg19:g.93139255A>G		88.0	0.0		71.0	5.0	NM_001004330	B2RNR7	Missense_Mutation	SNP	ENST00000344636.3	hg19	CCDS31873.1	.	.	.	.	.	.	.	.	.	.	A	12.96	2.093496	0.36952	.	.	ENSG00000187510	ENST00000344636	T	0.69040	-0.37	4.94	-0.438	0.12268	Dbl homology (DH) domain (4);	0.637939	0.16705	N	0.202957	T	0.46288	0.1385	L	0.27053	0.805	0.24705	N	0.993236	P	0.40834	0.73	B	0.41619	0.361	T	0.35201	-0.9798	10	0.38643	T	0.18	-10.971	1.8646	0.03195	0.538:0.1248:0.2164:0.1207	.	68	Q6ZR37	PKHG7_HUMAN	C	68	ENSP00000344961:Y68C	ENSP00000344961:Y68C	Y	+	2	0	PLEKHG7	91663386	0.869000	0.29996	0.846000	0.33378	0.216000	0.24613	0.011000	0.13264	-0.248000	0.09583	-0.256000	0.11100	TAT	.	.		0.448	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330	Missense_Mutation	G	93139255	A	G	93139255	5	3	219	1	0	0	0	0	0	0	1	0	12084	463	16	2	217	2	PLEKHG7	12	93139255	Splice_Site	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	27574908	93139255	40712640	64	31429										
USPL1	10208	hgsc.bcm.edu	37	chr13	31195968	31195968	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tagagagaagggaaagttaaAagccttaaagacttaccgaa	10	5	0	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr13:31195968A>G	ENST00000255304.4	+	3	509	c.167A>G	c.(166-168)aAa>aGa	p.K56R	USPL1_ENST00000465952.1_3'UTR	NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	56					Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		GGAAAGTTAAAAGCCTTAAAG	0.294																																					p.K56R	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.A167G						.						99	106	104					13																	31195968		2203	4295	6498	SO:0001583	missense	10208	exon3			AGTTAAAAGCCTT	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 22"	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.167A>G	chr13.hg19:g.31195968A>G	ENSP00000255304:p.Lys56Arg	284.0	0.0		202.0	24.0	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	hg19	CCDS9336.1	.	.	.	.	.	.	.	.	.	.	A	14.49	2.550772	0.45383	.	.	ENSG00000132952	ENST00000255304	T	0.07021	3.23	6.06	4.84	0.62591	.	0.481828	0.24848	N	0.035107	T	0.15176	0.0366	M	0.62723	1.935	0.09310	N	1	D	0.53462	0.96	P	0.50537	0.643	T	0.08638	-1.0712	10	0.48119	T	0.1	-10.1764	9.135	0.36868	0.8571:0.0:0.1429:0.0	.	56	Q5W0Q7	USPL1_HUMAN	R	56	ENSP00000255304:K56R	ENSP00000255304:K56R	K	+	2	0	USPL1	30093968	0.999000	0.42202	0.912000	0.35992	0.946000	0.59487	3.064000	0.49986	1.068000	0.40764	0.533000	0.62120	AAA	.	.		0.294	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		G	31195968	A	G	31195968	3	3	219	1	0	0	0	0	1	0	0	0	17107	14	1	2	173	2	USPL1	13	31195968	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10		31195968	83973910	65	31430										
LMO7	4008	hgsc.bcm.edu	37	chr13	76397850	76397850	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gtagcagcaacagaagaagaTgtgacaaggctgccctctcc	11	11	1	4	rs374411902		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr13:76397850T>A	ENST00000321797.8	+	13	2812	c.2091T>A	c.(2089-2091)gaT>gaA	p.D697E	LMO7_ENST00000357063.3_Missense_Mutation_p.D982E|LMO7_ENST00000341547.4_Missense_Mutation_p.D648E|LMO7_ENST00000465261.2_Missense_Mutation_p.D697E|LMO7_ENST00000526202.1_Missense_Mutation_p.D547E|LMO7_ENST00000377534.3_Missense_Mutation_p.D982E			Q8WWI1	LMO7_HUMAN	LIM domain 7	982					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		CAGAAGAAGATGTGACAAGGC	0.517																																					p.D697E		Atlas-SNP	.											.	LMO7	334	.	0			c.T2091A						.						134	111	119					13																	76397850		2203	4300	6503	SO:0001583	missense	4008	exon12			AGAAGATGTGACA	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"F-box only protein 20"	604362	"LIM domain only 7"	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.2091T>A	chr13.hg19:g.76397850T>A	ENSP00000317802:p.Asp697Glu	140.0	0.0		124.0	66.0	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	12.18|12.18|12.18	1.861813|1.861813|1.861813	0.32884|0.32884|0.32884	.|.|.	.|.|.	ENSG00000136153|ENSG00000136153|ENSG00000136153	ENST00000447038|ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261|ENST00000524651	.|T;T;T;T;T;T;T|.	.|0.42900|.	.|1.56;1.54;1.55;0.98;0.98;0.97;0.96|.	5.98|5.98|5.98	-5.86|-5.86|-5.86	0.02304|0.02304|0.02304	.|.|.	.|2.049870|.	.|0.01754|.	.|N|.	.|0.030112|.	T|T|T	0.24470|0.24470|0.24470	0.0593|0.0593|0.0593	L|L|L	0.46157|0.46157|0.46157	1.445|1.445|1.445	0.09310|0.09310|0.09310	N|N|N	1|1|1	.|B;B;B;B;B|.	.|0.10296|.	.|0.0;0.002;0.001;0.0;0.003|.	.|B;B;B;B;B|.	.|0.11329|.	.|0.001;0.003;0.0;0.001;0.006|.	T|T|T	0.36432|0.36432|0.36432	-0.9748|-0.9748|-0.9748	5|10|5	.|0.19147|.	.|T|.	.|0.46|.	4.1222|4.1222|4.1222	0.4658|0.4658|0.4658	0.00523|0.00523|0.00523	0.204:0.2116:0.2703:0.3142|0.204:0.2116:0.2703:0.3142|0.204:0.2116:0.2703:0.3142	.|.|.	.|547;648;982;697;930|.	.|E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5|.	.|.;.;LMO7_HUMAN;.;.|.	S|E|K	606|648;982;982;596;697;547;697|2	.|ENSP00000342112:D648E;ENSP00000349571:D982E;ENSP00000366757:D982E;ENSP00000366719:D596E;ENSP00000317802:D697E;ENSP00000431129:D547E;ENSP00000433352:D697E|.	.|ENSP00000317802:D697E|.	C|D|M	+|+|+	1|3|2	0|2|0	LMO7|LMO7|LMO7	75295851|75295851|75295851	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.002000|0.002000|0.002000	0.02628|0.02628|0.02628	-0.068000|-0.068000|-0.068000	0.11561|0.11561|0.11561	-0.643000|-0.643000|-0.643000	0.05473|0.05473|0.05473	-0.408000|-0.408000|-0.408000	0.06270|0.06270|0.06270	TGT|GAT|ATG	.	.		0.517	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		A	76397850	T	A	76397850	3	1	219	1	0	0	0	0	1	0	0	0	8864	1461	51	4	3008	4	LMO7	13	76397850	Missense_Mutation	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10	45201882	76397850	38772028	66	31431										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111132579	111132579	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cctgacaggtctgcctggtgAtagaggggaccctggggaca	16	10	1	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr13:111132579A>G	ENST00000360467.5	+	31	2906	c.2600A>G	c.(2599-2601)gAt>gGt	p.D867G		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	867	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			CTGCCTGGTGATAGAGGGGAC	0.547																																					p.D867G		Atlas-SNP	.											.	COL4A2	178	.	0			c.A2600G						.						106	106	106					13																	111132579		1910	4128	6038	SO:0001583	missense	1284	exon31			CTGGTGATAGAGG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.2600A>G	chr13.hg19:g.111132579A>G	ENSP00000353654:p.Asp867Gly	67.0	0.0		40.0	8.0	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	hg19	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.719894	0.30503	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.93189	-3.18	4.93	4.93	0.64822	.	0.754074	0.11828	N	0.525490	D	0.91955	0.7452	L	0.27975	0.815	0.29886	N	0.825601	P	0.46621	0.881	P	0.53988	0.739	D	0.86229	0.1636	10	0.24483	T	0.36	.	12.1281	0.53928	1.0:0.0:0.0:0.0	.	867	P08572	CO4A2_HUMAN	G	867	ENSP00000353654:D867G	ENSP00000257309:D867G	D	+	2	0	COL4A2	109930580	0.986000	0.35501	0.962000	0.40283	0.151000	0.21798	4.178000	0.58284	1.844000	0.53588	0.379000	0.24179	GAT	.	.		0.547	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		G	111132579	A	G	111132579	3	3	219	1	0	0	0	0	1	0	0	0	3692	333	12	2	2718	2	COL4A2	13	111132579	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	34734729	111132579	4037299	67	31432										
HNRNPC	3183	hgsc.bcm.edu	37	chr14	21702344	21702344	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tctgtcttgttggtaacgttGctggccatcgtgtttgatgg	13	7	2	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr14:21702344G>A	ENST00000320084.7	-	2	248	c.9C>T	c.(7-9)agC>agT	p.S3S	HNRNPC_ENST00000336053.6_Silent_p.S3S|HNRNPC_ENST00000555914.1_Silent_p.S3S|HNRNPC_ENST00000449098.1_Silent_p.S3S|HNRNPC_ENST00000555309.1_Silent_p.S3S|HNRNPC_ENST00000555883.1_Silent_p.S3S|HNRNPC_ENST00000430246.2_Silent_p.S3S|HNRNPC_ENST00000554455.1_Silent_p.S3S|HNRNPC_ENST00000556142.1_Silent_p.S3S|HNRNPC_ENST00000420743.2_Silent_p.S3S|HNRNPC_ENST00000556897.1_Silent_p.S3S|HNRNPC_ENST00000556513.1_Silent_p.S3S|HNRNPC_ENST00000556628.1_Silent_p.S3S|HNRNPC_ENST00000554969.1_Silent_p.S3S|HNRNPC_ENST00000553753.1_Silent_p.S3S|HNRNPC_ENST00000553300.1_Silent_p.S3S|HNRNPC_ENST00000557201.1_Silent_p.S3S	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	3					3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		TGGTAACGTTGCTGGCCATCG	0.413																																					p.S3S	NSCLC(108;607 2244 12726 38757)	Atlas-SNP	.											.	HNRNPC	31	.	0			c.C9T						.						107	103	104					14																	21702344		2137	4267	6404	SO:0001819	synonymous_variant	3183	exon2			AACGTTGCTGGCC		CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"RNA binding motif (RRM) containing"	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.9C>T	chr14.hg19:g.21702344G>A		69.0	0.0		69.0	9.0	NM_001077443	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Silent	SNP	ENST00000320084.7	hg19	CCDS41915.1																																																																																			.	.		0.413	HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1			A	21702344	G	A	21702344	2	1	219	1	0	0	0	0	0	0	0	1	7271	1310	46	3		3	HNRNPC	14	21702344	Silent	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10		21702344	85647196	68	31433										
PNN	5411	hgsc.bcm.edu	37	chr14	39648641	39648641	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ccagctacccaaaaactaatAgaagagtcacagagaaaaat	6	9	1	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr14:39648641A>G	ENST00000216832.4	+	8	835	c.768A>G	c.(766-768)atA>atG	p.I256M	PNN_ENST00000557680.1_3'UTR	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	256	Glu-rich.|Necessary for interaction with RNPS1.|Sufficient for PSAP complex assembly.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		AAAAACTAATAGAAGAGTCAC	0.338																																					p.I256M		Atlas-SNP	.											.	PNN	67	.	0			c.A768G						.						60	63	62					14																	39648641		2203	4300	6503	SO:0001583	missense	5411	exon8			ACTAATAGAAGAG	U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.768A>G	chr14.hg19:g.39648641A>G	ENSP00000216832:p.Ile256Met	401.0	0.0		381.0	37.0	NM_002687	B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	Missense_Mutation	SNP	ENST00000216832.4	hg19	CCDS9671.1	.	.	.	.	.	.	.	.	.	.	A	12.49	1.953107	0.34471	.	.	ENSG00000100941	ENST00000216832	T	0.33438	1.41	5.96	3.48	0.39840	Pinin/SDK/MemA protein (1);	0.262936	0.44483	D	0.000460	T	0.18759	0.0450	L	0.31926	0.97	0.80722	D	1	B	0.26258	0.145	B	0.30105	0.111	T	0.09400	-1.0676	10	0.24483	T	0.36	-5.0253	2.1393	0.03771	0.4276:0.1301:0.0738:0.3685	.	256	Q9H307	PININ_HUMAN	M	256	ENSP00000216832:I256M	ENSP00000216832:I256M	I	+	3	3	PNN	38718392	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.070000	0.30653	1.046000	0.40249	0.533000	0.62120	ATA	.	.		0.338	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687		G	39648641	A	G	39648641	3	3	219	1	0	0	0	0	1	0	0	0	12169	410	15	2	798	2	PNN	14	39648641	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	17946297	39648641	67700899	69	31434										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64492109	64492109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aattcatccgaaggcaaaatGccacttgaggaaagaatcca	8	9	1	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr14:64492109G>A	ENST00000344113.4	+	41	6434	c.6222G>A	c.(6220-6222)atG>atA	p.M2074I	SYNE2_ENST00000358025.3_Missense_Mutation_p.M2074I|SYNE2_ENST00000554584.1_Missense_Mutation_p.M2074I|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2074					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAGGCAAAATGCCACTTGAGG	0.343																																					p.M2074I		Atlas-SNP	.											.	SYNE2	577	.	0			c.G6222A						.						57	53	54					14																	64492109		1809	4077	5886	SO:0001583	missense	23224	exon41			CAAAATGCCACTT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.6222G>A	chr14.hg19:g.64492109G>A	ENSP00000341781:p.Met2074Ile	43.0	0.0		32.0	17.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.494248	0.44352	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.57107	0.77;0.77;0.42	5.9	5.9	0.94986	.	0.079494	0.56097	D	0.000035	T	0.38904	0.1058	L	0.27053	0.805	0.80722	D	1	P;P	0.47962	0.844;0.903	B;B	0.43052	0.23;0.406	T	0.12192	-1.0557	10	0.14252	T	0.57	.	11.2884	0.49234	0.1231:0.0:0.8769:0.0	.	2074;2074	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	I	2074	ENSP00000350719:M2074I;ENSP00000341781:M2074I;ENSP00000452570:M2074I	ENSP00000261678:M2074I	M	+	3	0	SYNE2	63561862	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.408000	0.52651	2.800000	0.96347	0.455000	0.32223	ATG	.	.		0.343	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64492109	G	A	64492109	3	1	219	1	0	0	0	0	1	0	0	0	15461	1319	46	3	6380	3	SYNE2	14	64492109	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	24843468	64492109	42857431	70	31435										
AKAP5	9495	hgsc.bcm.edu	37	chr14	64935781	64935781	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gataatgggcattctgctatTcaaacgggaactctaatcct	8	9	3	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr14:64935781T>G	ENST00000394718.4	+	2	1047	c.669T>G	c.(667-669)atT>atG	p.I223M	ZBTB25_ENST00000555424.1_Intron|ZBTB25_ENST00000555220.1_Intron|AKAP5_ENST00000320636.5_Missense_Mutation_p.I223M	NM_004857.3	NP_004848.3	P24588	AKAP5_HUMAN	A kinase (PRKA) anchor protein 5	223					energy reserve metabolic process (GO:0006112)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|stomach(1)	13				all cancers(60;0.00749)|OV - Ovarian serous cystadenocarcinoma(108;0.0095)|BRCA - Breast invasive adenocarcinoma(234;0.0449)		ATTCTGCTATTCAAACGGGAA	0.403																																					p.I223M		Atlas-SNP	.											.	AKAP5	23	.	0			c.T669G						.						96	103	101					14																	64935781		2203	4300	6503	SO:0001583	missense	9495	exon2			TGCTATTCAAACG	M90359	CCDS9764.1	14q23.3	2012-05-16			ENSG00000179841	ENSG00000179841		"A-kinase anchor proteins"	375	protein-coding gene	gene with protein product		604688				1512224, 1618839	Standard	NM_004857		Approved	AKAP75, AKAP79	uc001xhd.4	P24588	OTTHUMG00000029634	ENST00000394718.4:c.669T>G	chr14.hg19:g.64935781T>G	ENSP00000378207:p.Ile223Met	103.0	0.0		72.0	16.0	NM_004857	A2RRB8	Missense_Mutation	SNP	ENST00000394718.4	hg19	CCDS9764.1	.	.	.	.	.	.	.	.	.	.	T	9.444	1.088938	0.20390	.	.	ENSG00000179841	ENST00000394718;ENST00000320636	T;T	0.30981	1.51;1.51	6.02	3.64	0.41730	.	0.437167	0.21244	N	0.077773	T	0.34366	0.0895	L	0.50333	1.59	0.09310	N	1	P	0.50272	0.933	P	0.51945	0.685	T	0.16571	-1.0398	10	0.52906	T	0.07	-18.6918	4.7835	0.13213	0.0:0.166:0.1613:0.6727	.	223	P24588	AKAP5_HUMAN	M	223	ENSP00000378207:I223M;ENSP00000315615:I223M	ENSP00000315615:I223M	I	+	3	3	AKAP5	64005534	0.021000	0.18746	0.105000	0.21289	0.588000	0.36517	0.595000	0.24029	0.503000	0.28060	0.528000	0.53228	ATT	.	.		0.403	AKAP5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268070.3			G	64935781	T	G	64935781	3	3	219	1	0	0	0	0	1	0	0	0	454	1771	62	5	671	5	AKAP5	14	64935781	Missense_Mutation	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10	443672	64935781	42413759	71	31436										
SMEK1	55671	hgsc.bcm.edu	37	chr14	91927808	91927808	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tcctggggatccaggtgatcCcggagaaccaggcagatttg	14	10	0	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr14:91927808C>A	ENST00000554943.1	-	14	2423	c.2308G>T	c.(2308-2310)Gga>Tga	p.G770*	SMEK1_ENST00000555462.1_Nonsense_Mutation_p.G531*|SMEK1_ENST00000337238.4_Nonsense_Mutation_p.G757*|SMEK1_ENST00000554684.1_Nonsense_Mutation_p.G757*|SMEK1_ENST00000428424.2_Nonsense_Mutation_p.G531*|SMEK1_ENST00000555718.1_5'UTR			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	770					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		CCAGGTGATCCCGGAGAACCA	0.507																																					p.G757X		Atlas-SNP	.											.	SMEK1	94	.	0			c.G2269T						.						160	168	165					14																	91927808		2203	4300	6503	SO:0001587	stop_gained	55671	exon15			GTGATCCCGGAGA	AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"KIAA2010"	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.2308G>T	chr14.hg19:g.91927808C>A	ENSP00000450883:p.Gly770*	147.0	0.0		104.0	14.0	NM_032560	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Nonsense_Mutation	SNP	ENST00000554943.1	hg19		.	.	.	.	.	.	.	.	.	.	C	44	10.775905	0.99465	.	.	ENSG00000100796	ENST00000554684;ENST00000337238;ENST00000428424;ENST00000554943;ENST00000555462	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-11.3977	19.7503	0.96265	0.0:1.0:0.0:0.0	.	.	.	.	X	757;757;531;770;531	.	ENSP00000337125:G757X	G	-	1	0	SMEK1	90997561	1.000000	0.71417	0.983000	0.44433	0.893000	0.52053	7.380000	0.79704	2.675000	0.91044	0.557000	0.71058	GGA	.	.		0.507	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560		A	91927808	C	A	91927808	4	1	219	1	0	0	0	0	0	1	0	0	14808	632	22	3	201	3	SMEK1	14	91927808	Nonsense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	26992027	91927808	15421732	72	31437										
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40268649	40268649	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ggacggctgctgctacgcagTgaagcgcatccccatcaacc	11	15	1	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr15:40268649T>C	ENST00000263791.5	+	12	1896	c.1853T>C	c.(1852-1854)gTg>gCg	p.V618A	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.V618A	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	618	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		TGCTACGCAGTGAAGCGCATC	0.617																																					p.V618A		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.T1853C						.						32	34	34					15																	40268649		2094	4218	6312	SO:0001583	missense	440275	exon12			ACGCAGTGAAGCG	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.1853T>C	chr15.hg19:g.40268649T>C	ENSP00000263791:p.Val618Ala	136.0	0.0		143.0	13.0	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	hg19	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.773129	0.90108	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.29917	1.55;1.55	5.07	5.07	0.68467	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.53997	0.1831	M	0.72624	2.21	0.58432	D	0.999997	D	0.71674	0.998	D	0.69479	0.964	T	0.59263	-0.7487	10	0.87932	D	0	-17.8179	15.1173	0.72413	0.0:0.0:0.0:1.0	.	618	Q9P2K8	E2AK4_HUMAN	A	618	ENSP00000263791:V618A;ENSP00000372174:V618A	ENSP00000263791:V618A	V	+	2	0	EIF2AK4	38055941	1.000000	0.71417	0.998000	0.56505	0.682000	0.39822	8.013000	0.88655	2.025000	0.59659	0.377000	0.23210	GTG	.	.		0.617	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			C	40268649	T	C	40268649	3	2	219	1	0	0	0	0	1	0	0	0	5001	1696	59	2	1899	2	EIF2AK4	15	40268649	Missense_Mutation	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10		40268649	62262743	73	31438										
MGA	23269	hgsc.bcm.edu	37	chr15	42059132	42059132	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tattgatggagggaagaataCttctggcctccctgcagagc	12	9	1	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr15:42059132C>G	ENST00000570161.1	+	23	8852	c.8852C>G	c.(8851-8853)aCt>aGt	p.T2951S	MGA_ENST00000219905.7_Missense_Mutation_p.T2951S|MGA_ENST00000566586.1_Missense_Mutation_p.T2742S|MGA_ENST00000389936.4_Missense_Mutation_p.T2912S|MGA_ENST00000545763.1_Missense_Mutation_p.T2742S			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GGGAAGAATACTTCTGGCCTC	0.493																																					p.T2951S		Atlas-SNP	.											.	MGA	264	.	0			c.C8852G						.						54	55	55					15																	42059132		1925	4118	6043	SO:0001583	missense	23269	exon24			AGAATACTTCTGG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.8852C>G	chr15.hg19:g.42059132C>G	ENSP00000457035:p.Thr2951Ser	93.0	0.0		94.0	40.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	C	10.74	1.434840	0.25813	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.85556	-1.97;-1.95;-2.0	5.5	3.59	0.41128	.	0.250675	0.27478	N	0.019199	T	0.73666	0.3616	N	0.24115	0.695	0.20764	N	0.99986	B;B	0.12630	0.006;0.003	B;B	0.13407	0.009;0.004	T	0.62567	-0.6827	10	0.44086	T	0.13	.	8.4454	0.32838	0.1539:0.7656:0.0:0.0804	.	2742;2951	F5H7K2;E7ENI0	.;.	S	2951;2912;2742	ENSP00000219905:T2951S;ENSP00000374586:T2912S;ENSP00000442467:T2742S	ENSP00000219905:T2951S	T	+	2	0	MGA	39846424	0.926000	0.31397	1.000000	0.80357	0.948000	0.59901	2.132000	0.42083	0.845000	0.35118	0.655000	0.94253	ACT	.	.		0.493	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	42059132	C	G	42059132	3	3	219	1	0	0	0	0	1	0	0	0	9549	565	20	4	8942	4	MGA	15	42059132	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	1790483	42059132	60472260	74	31439										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48063719	48063719	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	acttaaactcaccaaatggtGttttgttatccagacagcct	6	10	1	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr15:48063719G>A	ENST00000316364.5	+	19	3398	c.2959G>A	c.(2959-2961)Gtt>Att	p.V987I	SEMA6D_ENST00000537942.1_Missense_Mutation_p.V925I|SEMA6D_ENST00000389432.2_Missense_Mutation_p.V944I|SEMA6D_ENST00000354744.4_Missense_Mutation_p.V931I|SEMA6D_ENST00000358066.4_Missense_Mutation_p.V925I|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000558014.1_Missense_Mutation_p.V925I|SEMA6D_ENST00000389433.2_Missense_Mutation_p.V968I|SEMA6D_ENST00000536845.2_Missense_Mutation_p.V987I|SEMA6D_ENST00000389428.3_Missense_Mutation_p.V912I	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	987					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		ACCAAATGGTGTTTTGTTATC	0.453																																					p.V987I		Atlas-SNP	.											.	SEMA6D	322	.	0			c.G2959A						.						105	106	106					15																	48063719		2198	4297	6495	SO:0001583	missense	80031	exon19			AATGGTGTTTTGT	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.2959G>A	chr15.hg19:g.48063719G>A	ENSP00000324857:p.Val987Ile	150.0	0.0		132.0	48.0	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.151092	0.57151	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428	T;T;T;T;T;T;T;T	0.17854	2.25;2.29;2.29;2.28;2.25;2.25;2.25;2.25	5.8	5.8	0.92144	.	0.123074	0.53938	D	0.000042	T	0.21801	0.0525	L	0.36672	1.1	0.80722	D	1	P;P;P;P	0.38195	0.622;0.481;0.552;0.622	B;B;B;B	0.41691	0.275;0.275;0.248;0.364	T	0.00706	-1.1601	10	0.56958	D	0.05	.	20.0693	0.97712	0.0:0.0:1.0:0.0	.	912;931;987;925	Q8NFY4-3;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;SEM6D_HUMAN;.	I	925;987;987;968;944;931;925;912	ENSP00000442040:V925I;ENSP00000446152:V987I;ENSP00000324857:V987I;ENSP00000374084:V968I;ENSP00000374083:V944I;ENSP00000346786:V931I;ENSP00000350770:V925I;ENSP00000374079:V912I	ENSP00000324857:V987I	V	+	1	0	SEMA6D	45851011	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	6.227000	0.72282	2.758000	0.94735	0.563000	0.77884	GTT	.	.		0.453	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48063719	G	A	48063719	3	1	219	1	0	0	0	0	1	0	0	0	14057	1377	48	3	3072	3	SEMA6D	15	48063719	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	6004587	48063719	54467673	75	31440										
RNF111	54778	hgsc.bcm.edu	37	chr15	59381902	59381902	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gctatcctcacatccgttacAtttcatcaggattggatgga	8	10	3	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr15:59381902A>G	ENST00000557998.1	+	11	2874	c.2587A>G	c.(2587-2589)Att>Gtt	p.I863V	RNF111_ENST00000434298.1_Missense_Mutation_p.I872V|RNF111_ENST00000559209.1_Missense_Mutation_p.I872V|RNF111_ENST00000348370.4_Missense_Mutation_p.I863V|RNF111_ENST00000561186.1_Missense_Mutation_p.I872V	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	863					gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		CATCCGTTACATTTCATCAGG	0.343																																					p.I872V	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.A2614G						.						156	164	161					15																	59381902		2192	4291	6483	SO:0001583	missense	54778	exon11			CGTTACATTTCAT	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.2587A>G	chr15.hg19:g.59381902A>G	ENSP00000452732:p.Ile863Val	43.0	0.0		39.0	12.0	NM_001270528	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Missense_Mutation	SNP	ENST00000557998.1	hg19	CCDS58366.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.120754	0.77436	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	T;T	0.15017	2.48;2.46	5.44	5.44	0.79542	.	0.111510	0.64402	D	0.000014	T	0.18718	0.0449	L	0.44542	1.39	0.58432	D	0.999998	P;P;P	0.42556	0.783;0.622;0.629	B;B;B	0.42062	0.374;0.158;0.36	T	0.02075	-1.1218	10	0.28530	T	0.3	-19.1918	15.5053	0.75735	1.0:0.0:0.0:0.0	.	872;863;863	Q6ZNA4-3;Q6ZNA4;Q6ZNA4-2	.;RN111_HUMAN;.	V	863;872	ENSP00000288199:I863V;ENSP00000393641:I872V	ENSP00000288199:I863V	I	+	1	0	RNF111	57169194	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	6.936000	0.75892	2.065000	0.61736	0.460000	0.39030	ATT	.	.		0.343	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		G	59381902	A	G	59381902	3	3	219	1	0	0	0	0	1	0	0	0	13440	217	8	2	2625	2	RNF111	15	59381902	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	11318183	59381902	43149490	76	31441										
GLCE	26035	hgsc.bcm.edu	37	chr15	69561008	69561008	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gtggctggccaattatggtgAcccgtaagttaggggaaggg	17	6	0	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr15:69561008A>C	ENST00000261858.2	+	5	1507	c.1279A>C	c.(1279-1281)Acc>Ccc	p.T427P	GLCE_ENST00000559420.2_Missense_Mutation_p.T363P|GLCE_ENST00000559500.1_3'UTR	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	427					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						AATTATGGTGACCCGTAAGTT	0.488																																					p.T427P		Atlas-SNP	.											.	GLCE	48	.	0			c.A1279C						.						78	70	73					15																	69561008		2200	4298	6498	SO:0001583	missense	26035	exon5			ATGGTGACCCGTA	AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"heparan sulfate epimerase"	612134	"D-glucuronyl C5-epimerase", "UDP-glucuronic acid epimerase"			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.1279A>C	chr15.hg19:g.69561008A>C	ENSP00000261858:p.Thr427Pro	76.0	0.0		93.0	11.0	NM_015554	Q6GUQ2	Missense_Mutation	SNP	ENST00000261858.2	hg19	CCDS32277.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.626414	0.66901	.	.	ENSG00000138604	ENST00000261858	T	0.45668	0.89	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.58235	0.2108	M	0.63428	1.95	0.80722	D	1	D	0.71674	0.998	D	0.66351	0.943	T	0.55817	-0.8081	10	0.30854	T	0.27	-11.7991	14.0134	0.64511	1.0:0.0:0.0:0.0	.	427	O94923	GLCE_HUMAN	P	427	ENSP00000261858:T427P	ENSP00000261858:T427P	T	+	1	0	GLCE	67348062	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.342000	0.79310	1.999000	0.58509	0.455000	0.32223	ACC	.	.		0.488	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		C	69561008	A	C	69561008	3	2	219	1	0	0	0	0	1	0	0	0	6440	275	10	5	1289	5	GLCE	15	69561008	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	10179106	69561008	32970384	77	31442										
ZNF774	342132	hgsc.bcm.edu	37	chr15	90904318	90904318	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tcaatcagagctcccactttAttacccatcagcgaatccac	4	15	3	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr15:90904318A>G	ENST00000354377.3	+	4	1441	c.1255A>G	c.(1255-1257)Att>Gtt	p.I419V	ZNF774_ENST00000379090.5_Intron	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	419					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			CTCCCACTTTATTACCCATCA	0.512																																					p.I419V		Atlas-SNP	.											.	ZNF774	35	.	0			c.A1255G						.						75	70	71					15																	90904318		2199	4298	6497	SO:0001583	missense	342132	exon4			CACTTTATTACCC	BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"Zinc fingers, C2H2-type"	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.1255A>G	chr15.hg19:g.90904318A>G	ENSP00000346348:p.Ile419Val	114.0	0.0		126.0	31.0	NM_001004309	A8K020	Missense_Mutation	SNP	ENST00000354377.3	hg19	CCDS32330.1	.	.	.	.	.	.	.	.	.	.	A	9.634	1.137221	0.21123	.	.	ENSG00000196391	ENST00000354377	T	0.21191	2.02	5.73	2.13	0.27403	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.214383	0.23102	N	0.051918	T	0.09247	0.0228	N	0.05012	-0.13	0.09310	N	1	B	0.09022	0.002	B	0.21360	0.034	T	0.25363	-1.0134	10	0.45353	T	0.12	.	5.5269	0.16962	0.6964:0.1467:0.1568:0.0	.	419	Q6NX45	ZN774_HUMAN	V	419	ENSP00000346348:I419V	ENSP00000346348:I419V	I	+	1	0	ZNF774	88705322	0.024000	0.19004	0.116000	0.21606	0.662000	0.39071	2.869000	0.48444	0.107000	0.17824	0.533000	0.62120	ATT	.	.		0.512	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309		G	90904318	A	G	90904318	3	3	219	1	0	0	0	0	1	0	0	0	18162	449	16	2	1265	2	ZNF774	15	90904318	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	21343310	90904318	11627074	78	31443										
MAN2A2	4122	hgsc.bcm.edu	37	chr15	91454130	91454130	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	catcattcatgcagcccactAtctggtgctgggggacaagg	12	11	3	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr15:91454130A>G	ENST00000559717.1	+	12	2273	c.1814A>G	c.(1813-1815)tAt>tGt	p.Y605C	MAN2A2_ENST00000360468.3_Missense_Mutation_p.Y605C|MAN2A2_ENST00000431652.2_Missense_Mutation_p.Y113C|MAN2A2_ENST00000430376.2_5'Flank			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	605					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GCAGCCCACTATCTGGTGCTG	0.592																																					p.Y605C		Atlas-SNP	.											.	MAN2A2	99	.	0			c.A1814G						.						68	64	65					15																	91454130		2198	4298	6496	SO:0001583	missense	4122	exon11			CCCACTATCTGGT	L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.1814A>G	chr15.hg19:g.91454130A>G	ENSP00000452948:p.Tyr605Cys	53.0	0.0		47.0	12.0	NM_006122	A6NH12|A8K1E8|Q13754	Missense_Mutation	SNP	ENST00000559717.1	hg19	CCDS32332.1	.	.	.	.	.	.	.	.	.	.	A	14.01	2.409198	0.42715	.	.	ENSG00000196547	ENST00000360468;ENST00000431652	T;T	0.74947	-0.89;-0.89	5.08	3.91	0.45181	.	0.103647	0.64402	D	0.000002	T	0.80768	0.4686	M	0.63428	1.95	0.80722	D	1	B;D;D;P	0.61080	0.07;0.989;0.988;0.89	B;P;P;P	0.61328	0.067;0.775;0.887;0.662	T	0.79181	-0.1909	10	0.42905	T	0.14	-16.9224	11.2727	0.49148	0.863:0.0:0.0:0.137	.	113;233;605;605	B4DEU9;B4DIK4;P49641-1;P49641	.;.;.;MA2A2_HUMAN	C	605;113	ENSP00000353655:Y605C;ENSP00000388221:Y113C	ENSP00000353655:Y605C	Y	+	2	0	MAN2A2	89255134	1.000000	0.71417	0.979000	0.43373	0.949000	0.60115	3.898000	0.56281	0.843000	0.35070	0.254000	0.18369	TAT	.	.		0.592	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122		G	91454130	A	G	91454130	3	3	219	1	0	0	0	0	1	0	0	0	9224	449	16	2	1856	2	MAN2A2	15	91454130	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	549812	91454130	11077262	79	31444										
KIF22	3835	hgsc.bcm.edu	37	chr16	29816222	29816222	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cggagctactggctcatgggCgccaaaaaatactggatctg	12	10	2	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr16:29816222C>A	ENST00000160827.4	+	12	1805	c.1765C>A	c.(1765-1767)Cgc>Agc	p.R589S	KIF22_ENST00000561482.1_Missense_Mutation_p.R521S|KIF22_ENST00000569382.2_Missense_Mutation_p.R535S|MAZ_ENST00000322945.6_5'Flank|MAZ_ENST00000563402.1_5'Flank|AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000219782.6_5'Flank|MAZ_ENST00000545521.1_5'Flank|KIF22_ENST00000400751.5_Missense_Mutation_p.R521S|MAZ_ENST00000562337.1_5'Flank|MAZ_ENST00000566906.2_5'Flank	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22	589					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA repair (GO:0006281)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)			endometrium(1)|large_intestine(1)|lung(11)|skin(1)	14						GGCTCATGGGCGCCAAAAAAT	0.602																																					p.R589S		Atlas-SNP	.											.	KIF22	29	.	0			c.C1765A						.						40	39	39					16																	29816222		2197	4296	6493	SO:0001583	missense	3835	exon12			CATGGGCGCCAAA	D38751	CCDS10653.1, CCDS58444.1	16p11.2	2008-03-03	2003-01-09	2003-01-10	ENSG00000079616	ENSG00000079616		"Kinesins"	6391	protein-coding gene	gene with protein product		603213	"kinesin-like 4"	KNSL4		8599929, 11416179	Standard	NM_007317		Approved	Kid, OBP-1, OBP-2	uc002dts.4	Q14807	OTTHUMG00000097771	ENST00000160827.4:c.1765C>A	chr16.hg19:g.29816222C>A	ENSP00000160827:p.Arg589Ser	51.0	0.0		73.0	21.0	NM_007317	B2R5M0|B7Z265|O60845|O94814|Q53F58|Q9BT46	Missense_Mutation	SNP	ENST00000160827.4	hg19	CCDS10653.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.154945	0.78114	.	.	ENSG00000079616	ENST00000160827;ENST00000400751	T;T	0.74421	-0.74;-0.84	5.64	2.65	0.31530	.	.	.	.	.	T	0.60051	0.2239	L	0.27053	0.805	0.80722	D	1	P;P	0.51449	0.838;0.945	B;B	0.44278	0.182;0.445	T	0.57585	-0.7786	9	0.72032	D	0.01	.	4.5168	0.11939	0.1545:0.5983:0.0:0.2472	.	521;589	B7Z265;Q14807	.;KIF22_HUMAN	S	589;521	ENSP00000160827:R589S;ENSP00000383562:R521S	ENSP00000160827:R589S	R	+	1	0	KIF22	29723723	1.000000	0.71417	0.756000	0.31282	0.844000	0.47949	4.135000	0.57997	0.331000	0.23511	0.561000	0.74099	CGC	.	.		0.602	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2			A	29816222	C	A	29816222	3	1	219	1	0	0	0	0	1	0	0	0	8299	768	27	1	1811	1	KIF22	16	29816222	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10		29816222	60538531	80	31445										
CETP	1071	hgsc.bcm.edu	37	chr16	56996939	56996939	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tagtgaaccacgagactgccAaggtgatccagaccgccttc	10	13	0	4			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr16:56996939A>G	ENST00000200676.3	+	2	266	c.136A>G	c.(136-138)Aag>Gag	p.K46E	CETP_ENST00000379780.2_Missense_Mutation_p.K46E|CETP_ENST00000566128.1_5'UTR|CETP_ENST00000569082.1_3'UTR	NM_000078.2	NP_000069.2			cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						CGAGACTGCCAAGGTGATCCA	0.612																																					p.K46E		Atlas-SNP	.											.	CETP	50	.	0			c.A136G						.						86	64	72					16																	56996939		2198	4300	6498	SO:0001583	missense	1071	exon2			ACTGCCAAGGTGA	M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"BPI fold containing"	1869	protein-coding gene	gene with protein product	"BPI fold containing family F"	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000200676.3:c.136A>G	chr16.hg19:g.56996939A>G	ENSP00000200676:p.Lys46Glu	58.0	0.0		45.0	17.0	NM_000078		Missense_Mutation	SNP	ENST00000200676.3	hg19	CCDS10772.1	.	.	.	.	.	.	.	.	.	.	A	9.237	1.037372	0.19669	.	.	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.06768	3.26;3.26	4.77	3.66	0.41972	Lipid-binding serum glycoprotein, conserved site (1);Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.224693	0.36893	U	0.002354	T	0.07052	0.0179	N	0.19112	0.55	0.80722	D	1	D;B	0.60160	0.987;0.107	P;B	0.50136	0.632;0.16	T	0.39563	-0.9608	10	0.08599	T	0.76	-2.8921	9.0636	0.36449	0.6385:0.3615:0.0:0.0	.	46;46	P11597-2;P11597	.;CETP_HUMAN	E	46	ENSP00000200676:K46E;ENSP00000369106:K46E	ENSP00000200676:K46E	K	+	1	0	CETP	55554440	0.476000	0.25901	0.987000	0.45799	0.159000	0.22180	0.777000	0.26718	0.646000	0.30693	0.482000	0.46254	AAG	.	.		0.612	CETP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257059.1	NM_000078		G	56996939	A	G	56996939	3	3	219	1	0	0	0	0	1	0	0	0	3279	131	5	2	142	2	CETP	16	56996939	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	27180717	56996939	33357814	81	31446										
RPA1	6117	hgsc.bcm.edu	37	chr17	1780506	1780506	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	atgatcgatttggtttgtagGtggaccatttgtgctcgtgt	13	5	0	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr17:1780506G>A	ENST00000254719.5	+	8	698	c.588G>A	c.(586-588)aaG>aaA	p.K196K	RPA1_ENST00000573924.1_3'UTR	NM_002945.3	NP_002936.1	P27694	RFA1_HUMAN	replication protein A1, 70kDa	196					base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of cell proliferation (GO:0008284)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|DNA replication factor A complex (GO:0005662)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|single-stranded DNA binding (GO:0003697)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)	10						TGGTTTGTAGGTGGACCATTT	0.448								Nucleotide excision repair (NER)																													p.K196K		Atlas-SNP	.											.	RPA1	48	.	0			c.G588A						.						122	96	105					17																	1780506		2203	4300	6503	SO:0001630	splice_region_variant	6117	exon8			TTGTAGGTGGACC	M63488	CCDS11014.1	17p13.3	2008-02-05	2002-08-29		ENSG00000132383	ENSG00000132383			10289	protein-coding gene	gene with protein product		179835	"replication protein A1 (70kD)"			8454588	Standard	NM_002945		Approved	REPA1, RPA70, HSSB, RF-A, RP-A	uc002fto.2	P27694	OTTHUMG00000090579	ENST00000254719.5:c.588-1G>A	chr17.hg19:g.1780506G>A		170.0	0.0		180.0	46.0	NM_002945	A8K0Y9|Q59ES9	Silent	SNP	ENST00000254719.5	hg19	CCDS11014.1																																																																																			.	.		0.448	RPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207118.2	NM_002945	Silent	A	1780506	G	A	1780506	5	1	219	1	0	0	0	0	0	0	1	0	13551	1275	44	3	618	3	RPA1	17	1780506	Splice_Site	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10		1780506	79414704	82	31447										
ALOX12B	242	hgsc.bcm.edu	37	chr17	7980038	7980038	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	atgctgttgatctggacggtGtatcgggtatgggggatgag	18	4	1	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr17:7980038G>A	ENST00000319144.4	-	10	1559	c.1299C>T	c.(1297-1299)taC>taT	p.Y433Y	ALOX12B_ENST00000577351.1_5'UTR|AC129492.6_ENST00000399413.3_5'Flank	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	433	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						TCTGGACGGTGTATCGGGTAT	0.577										Multiple Myeloma(8;0.094)																											p.Y433Y		Atlas-SNP	.											.	ALOX12B	61	.	0			c.C1299T						.						43	37	39					17																	7980038		2117	4124	6241	SO:0001819	synonymous_variant	242	exon10			GACGGTGTATCGG	AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"Arachidonate lipoxygenases"	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.1299C>T	chr17.hg19:g.7980038G>A		82.0	0.0		93.0	14.0	NM_001139		Silent	SNP	ENST00000319144.4	hg19	CCDS11129.1																																																																																			.	.		0.577	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3			A	7980038	G	A	7980038	2	1	219	1	0	0	0	0	0	0	0	1	537	1372	48	3		3	ALOX12B	17	7980038	Silent	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	6199532	7980038	73215172	83	31448										
RICH2	9912	hgsc.bcm.edu	37	chr17	12877579	12877579	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ggacagccccgcggcccccgCgctctctccatccggcctgg	12	21	1	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr17:12877579C>T	ENST00000379672.5	+	18	2015	c.1715C>T	c.(1714-1716)gCg>gTg	p.A572V	ARHGAP44_ENST00000578087.1_3'UTR|ARHGAP44_ENST00000340825.3_Missense_Mutation_p.A566V|ARHGAP44_ENST00000262444.9_Missense_Mutation_p.A572V|RN7SL550P_ENST00000583299.1_RNA	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	572					exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						GCGGCCCCCGCGCTCTCTCCA	0.796																																					p.A572V		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.C1715T						.						2	2	2					17																	12877579		1100	2362	3462	SO:0001583	missense	9912	exon18			CCCCCGCGCTCTC		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"Rho GTPase activating proteins"	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.1715C>T	chr17.hg19:g.12877579C>T	ENSP00000368994:p.Ala572Val	65.0	0.0		37.0	9.0	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Missense_Mutation	SNP	ENST00000379672.5	hg19	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	C	16.47	3.131126	0.56828	.	.	ENSG00000006740	ENST00000379672;ENST00000544416;ENST00000340825;ENST00000262444	T;T	0.16897	2.32;2.31	5.42	2.35	0.29111	.	0.934688	0.09044	N	0.856895	T	0.09468	0.0233	N	0.08118	0	0.28948	N	0.890573	B;B;B;B	0.13145	0.0;0.003;0.007;0.002	B;B;B;B	0.08055	0.0;0.003;0.002;0.001	T	0.31586	-0.9938	10	0.40728	T	0.16	.	8.9446	0.35751	0.0:0.7534:0.0:0.2466	.	566;30;228;572	A6NCP5;E7ERK8;F5H6L3;Q17R89	.;.;.;RHG44_HUMAN	V	572;228;566;30	ENSP00000368994:A572V;ENSP00000342566:A566V	ENSP00000262444:A30V	A	+	2	0	ARHGAP44	12818304	0.884000	0.30299	0.302000	0.25058	0.114000	0.19823	1.883000	0.39658	0.266000	0.21894	0.557000	0.71058	GCG	.	.		0.796	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859		T	12877579	C	T	12877579	3	4	219	1	0	0	0	0	1	0	0	0	13372	768	27	1	1785	1	RICH2	17	12877579	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	4897541	12877579	68317631	84	31449										
BLMH	642	hgsc.bcm.edu	37	chr17	28599605	28599605	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	atgtcactgaggcccagcttGctattgaagtgttttccaac	9	10	1	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr17:28599605G>C	ENST00000261714.6	-	9	1176	c.1002C>G	c.(1000-1002)agC>agG	p.S334R	BLMH_ENST00000394819.3_Missense_Mutation_p.S247R|BLMH_ENST00000582669.1_5'Flank	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	334					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	GGCCCAGCTTGCTATTGAAGT	0.413																																					p.S334R	Pancreas(127;628 1772 12912 33293 36203)	Atlas-SNP	.											.	BLMH	42	.	0			c.C1002G						.						218	217	217					17																	28599605		2203	4300	6503	SO:0001583	missense	642	exon9			CAGCTTGCTATTG	X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.1002C>G	chr17.hg19:g.28599605G>C	ENSP00000261714:p.Ser334Arg	68.0	0.0		89.0	6.0	NM_000386	B2R796|Q53F86|Q9UER9	Missense_Mutation	SNP	ENST00000261714.6	hg19	CCDS32604.1	.	.	.	.	.	.	.	.	.	.	G	5.430	0.264433	0.10294	.	.	ENSG00000108578	ENST00000261714;ENST00000394819	T;T	0.40225	1.04;1.04	5.91	4.91	0.64330	.	0.136793	0.64402	D	0.000002	T	0.14141	0.0342	N	0.00869	-1.13	0.46564	D	0.999104	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.002	T	0.26780	-1.0093	10	0.02654	T	1	-7.0305	15.6277	0.76874	0.0:0.0:0.8625:0.1375	.	247;334	E7EMN3;Q13867	.;BLMH_HUMAN	R	334;247	ENSP00000261714:S334R;ENSP00000378296:S247R	ENSP00000261714:S334R	S	-	3	2	BLMH	25623731	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.451000	0.60047	2.793000	0.96121	0.655000	0.94253	AGC	.	.		0.413	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386		C	28599605	G	C	28599605	3	2	219	1	0	0	0	0	1	0	0	0	1446	1310	46	4	381	4	BLMH	17	28599605	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	15722026	28599605	52595605	85	31450										
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305774	39305775	+	In_Frame_Ins	INS	-	-	TGGCAGCAGCTGGGG													0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tggtcctgcagcaggtggtcINStggcagcagcaggggcggca					rs137947981|rs535144703|rs141265645|rs58117746	byFrequency	TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr17:39305774_39305775insTGGCAGCAGCTGGGG	ENST00000343246.4	-	1	279_280	c.245_246insCCCCAGCTGCTGCCA	c.(244-246)cag>caCCCCAGCTGCTGCCAg	p.81_82insHPSCC		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	81	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.Q82H(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			agcaggtggtctggcagcagca	0.653																																					p.Q82delinsHPSCCQ		Atlas-INDEL	.											KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	.	1	Substitution - Missense(1)	lung(1)	c.246_247insCCCCAGCTGCTGCCA						.																																			SO:0001652	inframe_insertion	85289	exon1			.	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.245_246insCCCCAGCTGCTGCCA	chr17.hg19:g.39305774_39305775insTGGCAGCAGCTGGGG	ENSP00000340546:p.Cys81_Gln82insHisProSerCysCys	54.0	0.0		48.0	12.0	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	hg19	CCDS32650.1																																																																																			.	.		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			TGGCAGCAGCTGGGG	39305775	-	TGGCAGCAGCTGGGG	39305774	7	5	219	1	0	1	1	0	0	0	0	0	8563	912	32	0	303	0	KRTAP4-5	17	39305774	In_Frame_Ins	INS	-	TCGA-DD-AAEG-01A-11D-A38X-10	10706169	39305774	41889436	86	31451										
NGFR	4804	hgsc.bcm.edu	37	chr17	47590068	47590068	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ctctcctctggtttctctgcAgccctcaagggtgacggagg	12	13	4	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr17:47590068A>T	ENST00000172229.3	+	6	1107		c.e6-1		NGFR_ENST00000504201.1_Splice_Site|RP5-1029K10.2_ENST00000514506.1_RNA	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor						apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					GTTTCTCTGCAGCCCTCAAGG	0.647																																					.		Atlas-SNP	.											.	NGFR	46	.	0			c.983-2A>T						.						50	54	53					17																	47590068		2185	4272	6457	SO:0001630	splice_region_variant	4804	exon6			CTCTGCAGCCCTC	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"Tumor necrosis factor receptor superfamily", "CD molecules"	7809	protein-coding gene	gene with protein product	"low affinity nerve growth factor receptor", "TNFR superfamily, member 16"	162010	"nerve growth factor receptor (TNFR superfamily, member 16)"			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.983-1A>T	chr17.hg19:g.47590068A>T		133.0	0.0		140.0	21.0	NM_002507	B2R961|B4E096	Splice_Site	SNP	ENST00000172229.3	hg19	CCDS11549.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.623689	0.66901	.	.	ENSG00000064300	ENST00000172229;ENST00000504201	.	.	.	4.88	4.88	0.63580	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.0256	0.53368	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NGFR	44945067	1.000000	0.71417	0.998000	0.56505	0.761000	0.43186	5.812000	0.69194	1.819000	0.53055	0.459000	0.35465	.	.	.		0.647	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1		Intron	T	47590068	A	T	47590068	5	4	219	1	0	0	0	0	0	0	1	0	10405	202	7	4	1003	4	NGFR	17	47590068	Splice_Site	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	8284294	47590068	33605142	87	31452										
UNC13D	201294	hgsc.bcm.edu	37	chr17	73831746	73831746	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	acctctctgaggagctcatgCgcagctggcagagctccttg	12	13	2	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr17:73831746C>T	ENST00000207549.4	-	19	2088	c.1709G>A	c.(1708-1710)cGc>cAc	p.R570H	UNC13D_ENST00000412096.2_Missense_Mutation_p.R570H	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	570	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGAGCTCATGCGCAGCTGGCA	0.647									Familial Hemophagocytic Lymphohistiocytosis																												p.R570H		Atlas-SNP	.											.	UNC13D	68	.	0			c.G1709A						.						34	33	33					17																	73831746		2203	4300	6503	SO:0001583	missense	201294	exon19	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CTCATGCGCAGCT	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.1709G>A	chr17.hg19:g.73831746C>T	ENSP00000207549:p.Arg570His	53.0	0.0		62.0	6.0	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	C	0.583	-0.836338	0.02692	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.70869	-0.51;-0.52	4.88	2.64	0.31445	Munc13 homology 1 (1);	0.768652	0.12175	N	0.492658	T	0.50120	0.1597	N	0.15975	0.35	0.27558	N	0.950271	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.31833	-0.9929	10	0.15499	T	0.54	-6.1973	10.095	0.42469	0.1458:0.7719:0.0:0.0823	.	570;570	Q70J99-3;Q70J99	.;UN13D_HUMAN	H	570	ENSP00000207549:R570H;ENSP00000388093:R570H	ENSP00000207549:R570H	R	-	2	0	UNC13D	71343341	0.998000	0.40836	0.926000	0.36857	0.056000	0.15407	1.006000	0.29847	1.039000	0.40074	-0.339000	0.08088	CGC	.	.		0.647	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		T	73831746	C	T	73831746	3	4	219	1	0	0	0	0	1	0	0	0	17002	768	27	1	1619	1	UNC13D	17	73831746	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	26241678	73831746	7363464	88	31453										
RPTOR	57521	hgsc.bcm.edu	37	chr17	78919549	78919549	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aaattccaccccttcacgccGtgcatcgccgtagccgacaa	7	17	1	0	rs149016810	byFrequency	TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr17:78919549G>C	ENST00000306801.3	+	26	3470	c.3108G>C	c.(3106-3108)ccG>ccC	p.P1036P	RPTOR_ENST00000544334.2_Silent_p.P878P|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1036					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CCTTCACGCCGTGCATCGCCG	0.587																																					p.P1036P		Atlas-SNP	.											.	RPTOR	122	.	0			c.G3108C						.						83	73	77					17																	78919549		2203	4300	6503	SO:0001819	synonymous_variant	57521	exon26			CACGCCGTGCATC		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.3108G>C	chr17.hg19:g.78919549G>C		64.0	0.0		82.0	29.0	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	hg19	CCDS11773.1																																																																																			.	G|0.999;A|0.001		0.587	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		C	78919549	G	C	78919549	2	2	219	1	0	0	0	0	0	0	0	1	13680	1132	40	4		4	RPTOR	17	78919549	Silent	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	5087803	78919549	2275661	89	31454										
RTTN	25914	hgsc.bcm.edu	37	chr18	67715231	67715231	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aggattacatcactaagttgTtctagagatttctgattttc	7	6	3	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr18:67715231T>C	ENST00000255674.6	-	40	5803	c.5517A>G	c.(5515-5517)gaA>gaG	p.E1839E	RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1839					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CACTAAGTTGTTCTAGAGATT	0.358																																					p.E1839E		Atlas-SNP	.											.	RTTN	184	.	0			c.A5517G						.						106	102	103					18																	67715231		1868	4105	5973	SO:0001819	synonymous_variant	25914	exon40			AAGTTGTTCTAGA	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.5517A>G	chr18.hg19:g.67715231T>C		37.0	0.0		45.0	9.0	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Silent	SNP	ENST00000255674.6	hg19	CCDS42443.1																																																																																			.	.		0.358	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		C	67715231	T	C	67715231	2	2	219	1	0	0	0	0	0	0	0	1	13752	1722	60	2		2	RTTN	18	67715231	Silent	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10		67715231	10362017	90	31455										
SBNO2	22904	hgsc.bcm.edu	37	chr19	1108560	1108560	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ggtgaggtccagcacctctcCggggccgcaaggcagcgcca	15	15	1	1	rs576784181		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr19:1108560C>T	ENST00000361757.3	-	32	3997	c.3760G>A	c.(3760-3762)Gga>Aga	p.G1254R	SBNO2_ENST00000438103.2_Missense_Mutation_p.G1197R|SBNO2_ENST00000587024.1_Missense_Mutation_p.G1244R	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	1254	Pro-rich.				bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCACCTCTCCGGGGCCGCAA	0.791													c|||	1	0.000199681	0	0	5008	,	,		3823	0.001		0	False		,,,				2504	0				p.G1254R		Atlas-SNP	.											.	SBNO2	112	.	0			c.G3760A						.						1	1	1					19																	1108560		328	656	984	SO:0001583	missense	22904	exon32			CCTCTCCGGGGCC	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.3760G>A	chr19.hg19:g.1108560C>T	ENSP00000354733:p.Gly1254Arg	3.0	0.0		8.0	7.0	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Missense_Mutation	SNP	ENST00000361757.3	hg19	CCDS45894.1	.	.	.	.	.	.	.	.	.	.	c	19.89	3.910643	0.72983	.	.	ENSG00000064932	ENST00000361757;ENST00000438103;ENST00000250872	.	.	.	3.74	2.7	0.31948	.	1.585890	0.04110	U	0.314449	T	0.33644	0.0870	N	0.19112	0.55	0.09310	N	0.999999	D;D	0.57899	0.968;0.981	B;P	0.50405	0.436;0.64	T	0.33007	-0.9885	9	0.54805	T	0.06	-29.2617	6.379	0.21523	0.1986:0.6951:0.0:0.1063	.	1254;1197	Q9Y2G9;Q9Y2G9-3	SBNO2_HUMAN;.	R	1254;1197;1272	.	ENSP00000250872:G1272R	G	-	1	0	SBNO2	1059560	0.000000	0.05858	0.646000	0.29493	0.304000	0.27724	0.137000	0.15995	2.101000	0.63845	0.394000	0.25966	GGA	.	.		0.791	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		T	1108560	C	T	1108560	3	4	219	1	0	0	0	0	1	0	0	0	13878	661	23	1	344	1	SBNO2	19	1108560	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10		1108560	58020423	91	31456										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10084600	10084600	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cccaagagttctcacctctgAtccagtggggccttggggac	12	13	2	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr19:10084600A>G	ENST00000264828.3	-	48	3638	c.3553T>C	c.(3553-3555)Tca>Cca	p.S1185P		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1185	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CTCACCTCTGATCCAGTGGGG	0.582																																					p.S1185P		Atlas-SNP	.											.	COL5A3	243	.	0			c.T3553C						.						54	65	61					19																	10084600		2203	4300	6503	SO:0001583	missense	50509	exon48			CCTCTGATCCAGT	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3553T>C	chr19.hg19:g.10084600A>G	ENSP00000264828:p.Ser1185Pro	61.0	0.0		41.0	22.0	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	A	9.965	1.223864	0.22457	.	.	ENSG00000080573	ENST00000264828	D	0.90069	-2.61	4.84	-6.17	0.02091	.	1.014930	0.07900	N	0.972546	T	0.68604	0.3019	N	0.03948	-0.315	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.56980	-0.7889	10	0.24483	T	0.36	.	5.3394	0.15974	0.1779:0.5554:0.1562:0.1105	.	1185	P25940	CO5A3_HUMAN	P	1185	ENSP00000264828:S1185P	ENSP00000264828:S1185P	S	-	1	0	COL5A3	9945600	0.001000	0.12720	0.513000	0.27749	0.136000	0.21042	0.580000	0.23803	-1.397000	0.02068	0.397000	0.26171	TCA	.	.		0.582	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		G	10084600	A	G	10084600	3	3	219	1	0	0	0	0	1	0	0	0	3700	333	12	2	1764	2	COL5A3	19	10084600	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	8976040	10084600	49044383	92	31457										
ZNF44	51710	hgsc.bcm.edu	37	chr19	12386801	12386801	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	caggttcctaatggtttctcGcatcacatctctgtagagat	8	10	3	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr19:12386801G>C	ENST00000356109.5	-	3	362	c.244C>G	c.(244-246)Cga>Gga	p.R82G	ZNF44_ENST00000355684.5_Missense_Mutation_p.R34G	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	82	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		ATGGTTTCTCGCATCACATCT	0.448																																					p.R82G		Atlas-SNP	.											.	ZNF44	55	.	0			c.C244G						.						189	200	196					19																	12386801		2203	4300	6503	SO:0001583	missense	51710	exon3			TTTCTCGCATCAC	X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"Zinc fingers, C2H2-type", "-"	13110	protein-coding gene	gene with protein product		194542	"zinc finger protein 58", "zinc finger protein 44 (KOX 7)", "zinc finger protein 55"	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.244C>G	chr19.hg19:g.12386801G>C	ENSP00000348419:p.Arg82Gly	67.0	0.0		89.0	5.0	NM_001164276	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Missense_Mutation	SNP	ENST00000356109.5	hg19	CCDS54223.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.595890	0.28445	.	.	ENSG00000197857	ENST00000393337;ENST00000356109;ENST00000457673;ENST00000355684	T;T;T	0.01871	4.59;4.59;4.59	1.33	-1.35	0.09114	Krueppel-associated box (4);	.	.	.	.	T	0.02688	0.0081	L	0.60067	1.865	.	.	.	B;B	0.32753	0.383;0.0	B;B	0.34301	0.179;0.001	T	0.38824	-0.9643	8	0.72032	D	0.01	.	2.0677	0.03606	0.3627:0.0:0.3864:0.2509	.	82;34	P15621;F8W7T7	ZNF44_HUMAN;.	G	82;82;34;34	ENSP00000377008:R82G;ENSP00000348419:R82G;ENSP00000347910:R34G	ENSP00000347910:R34G	R	-	1	2	ZNF44	12247801	0.253000	0.23982	0.777000	0.31699	0.551000	0.35334	-0.227000	0.09126	-0.246000	0.09611	0.313000	0.20887	CGA	.	.		0.448	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264		C	12386801	G	C	12386801	3	2	219	1	0	0	0	0	1	0	0	0	17927	1095	38	4	1759	4	ZNF44	19	12386801	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	2302201	12386801	46742182	93	31458										
ZNF222	7673	hgsc.bcm.edu	37	chr19	44531618	44531618	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	agttttgggtgatggggacaAcaagccaaagagaagggaat	15	4	0	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr19:44531618A>G	ENST00000187879.8	+	3	304				AC067968.3_ENST00000592583.1_lincRNA|ZNF222_ENST00000590160.1_3'UTR|ZNF222_ENST00000391960.3_Missense_Mutation_p.T80A|ZNF223_ENST00000591793.1_Missense_Mutation_p.T80A|ZNF222_ENST00000587846.1_Missense_Mutation_p.T80A	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				GATGGGGACAACAAGCCAAAG	0.458																																					p.T80A		Atlas-SNP	.											.	ZNF222	90	.	0			c.A238G						.						221	194	202					19																	44531618		692	1591	2283	SO:0001627	intron_variant	7673	exon3			GGGACAACAAGCC	AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.142+317A>G	chr19.hg19:g.44531618A>G		133.0	0.0		144.0	12.0	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Missense_Mutation	SNP	ENST00000187879.8	hg19	CCDS33045.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.142294	0.00332	.	.	ENSG00000159885	ENST00000391960	T	0.05319	3.46	1.61	-1.08	0.09936	.	.	.	.	.	T	0.01765	0.0056	N	0.02111	-0.68	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.46978	-0.9152	9	0.08837	T	0.75	.	2.6321	0.04947	0.226:0.3129:0.4612:0.0	.	80	G5E9B9	.	A	80	ENSP00000375822:T80A	ENSP00000375822:T80A	T	+	1	0	ZNF222	49223458	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.255000	0.08769	-0.198000	0.10333	-0.483000	0.04790	ACA	.	.		0.458	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			G	44531618	A	G	44531618	1	3	219	0	1	0	0	0	0	0	0	0	17791	43	2	2		2	ZNF222	19	44531618	Intron	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	32144817	44531618	14597365	94	31459										
BCL2L12	83596	hgsc.bcm.edu	37	chr19	50169299	50169299	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	agaccgcaagttgagtggagGaggcggcggtggggccccgg	21	9	0	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr19:50169299G>A	ENST00000246785.3	+	1	477	c.219G>A	c.(217-219)agG>agA	p.R73R	IRF3_ENST00000596822.1_5'Flank|IRF3_ENST00000309877.7_5'Flank|BCL2L12_ENST00000246784.3_Silent_p.R73R|IRF3_ENST00000599144.1_5'Flank|IRF3_ENST00000600022.1_5'Flank|IRF3_ENST00000596765.1_5'Flank|IRF3_ENST00000598808.1_5'Flank|IRF3_ENST00000377135.4_5'Flank|IRF3_ENST00000593922.1_5'Flank|BCL2L12_ENST00000441864.2_Silent_p.R73R|IRF3_ENST00000377139.3_5'Flank|IRF3_ENST00000600911.1_5'Flank|IRF3_ENST00000599223.1_5'Flank|IRF3_ENST00000601291.1_5'Flank|IRF3_ENST00000442265.2_5'Flank|IRF3_ENST00000597198.1_5'Flank	NM_001040668.1|NM_138639.1	NP_001035758.1|NP_619580.1	Q9HB09	B2L12_HUMAN	BCL2-like 12 (proline rich)	73					inhibition of cysteine-type endopeptidase activity involved in apoptotic process (GO:1990001)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	8		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.000681)|GBM - Glioblastoma multiforme(134;0.0214)		TTGAGTGGAGGAGGCGGCGGT	0.657																																					p.R73R		Atlas-SNP	.											.	BCL2L12	22	.	0			c.G219A						.						9	10	10					19																	50169299		2160	4229	6389	SO:0001819	synonymous_variant	83596	exon1			GTGGAGGAGGCGG	AF289220	CCDS12776.1, CCDS46144.1, CCDS74424.1, CCDS74423.1	19q13.3	2014-03-07				ENSG00000126453			13787	protein-coding gene	gene with protein product		610837					Standard	NM_001040668		Approved		uc002ppa.3	Q9HB09		ENST00000246785.3:c.219G>A	chr19.hg19:g.50169299G>A		134.0	0.0		115.0	17.0	NM_001040668	Q3SY11|Q3SY13|Q96I96|Q9HB08	Silent	SNP	ENST00000246785.3	hg19	CCDS12776.1																																																																																			.	.		0.657	BCL2L12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465770.1	NM_052842		A	50169299	G	A	50169299	2	1	219	1	0	0	0	0	0	0	0	1	1370	1165	41	3		3	BCL2L12	19	50169299	Silent	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	5637681	50169299	8959684	95	31460										
NKX2-2	4821	hgsc.bcm.edu	37	chr20	21494192	21494192	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cggccctcttggctggctcgGgcccctcgttctcttcctcc	10	19	2	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr20:21494192G>T	ENST00000377142.4	-	1	472	c.116C>A	c.(115-117)cCc>cAc	p.P39H	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2	39					astrocyte differentiation (GO:0048708)|brain development (GO:0007420)|digestive tract development (GO:0048565)|endocrine pancreas development (GO:0031018)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|oligodendrocyte development (GO:0014003)|optic nerve development (GO:0021554)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell fate commitment (GO:0003327)|ventral spinal cord interneuron fate determination (GO:0060580)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|core promoter proximal region DNA binding (GO:0001159)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						GGCTGGCTCGGGCCCCTCGTT	0.657																																					p.P39H		Atlas-SNP	.											.	NKX2-2	49	.	0			c.C116A						.						28	28	28					20																	21494192		2203	4300	6503	SO:0001583	missense	4821	exon1			GGCTCGGGCCCCT	AF019415	CCDS13145.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125820	ENSG00000125820		"Homeoboxes / ANTP class : NKL subclass"	7835	protein-coding gene	gene with protein product		604612	"NK-2 (Drosophila) homolog B", "NK2 transcription factor related, locus 2 (Drosophila)"	NKX2B		9703340, 1346742	Standard	NM_002509		Approved	NKX2.2	uc002wsi.3	O95096	OTTHUMG00000170524	ENST00000377142.4:c.116C>A	chr20.hg19:g.21494192G>T	ENSP00000366347:p.Pro39His	65.0	0.0		84.0	9.0	NM_002509		Missense_Mutation	SNP	ENST00000377142.4	hg19	CCDS13145.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.770931	0.49680	.	.	ENSG00000125820	ENST00000377142	D	0.90324	-2.65	5.02	5.02	0.67125	.	0.398025	0.22467	N	0.059676	D	0.83880	0.5350	N	0.14661	0.345	0.38250	D	0.941585	B	0.26809	0.16	B	0.25405	0.06	T	0.82404	-0.0474	10	0.42905	T	0.14	.	17.9439	0.89034	0.0:0.0:1.0:0.0	.	39	O95096	NKX22_HUMAN	H	39	ENSP00000366347:P39H	ENSP00000366347:P39H	P	-	2	0	NKX2-2	21442192	1.000000	0.71417	0.870000	0.34147	0.942000	0.58702	7.458000	0.80787	2.323000	0.78572	0.557000	0.71058	CCC	.	.		0.657	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078278.9			T	21494192	G	T	21494192	3	4	219	1	0	0	0	0	1	0	0	0	10459	1232	43	3	713	3	NKX2-2	20	21494192	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10		21494192	41531328	96	31461										
DNMT3B	1789	hgsc.bcm.edu	37	chr20	31375142	31375142	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cacagaggacacacatgggaCgccccagagcagcagtaccc	11	15	0	2	rs537913125		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr20:31375142C>T	ENST00000328111.2	+	6	860	c.539C>T	c.(538-540)aCg>aTg	p.T180M	DNMT3B_ENST00000201963.3_Missense_Mutation_p.T192M|DNMT3B_ENST00000348286.2_Missense_Mutation_p.T180M|DNMT3B_ENST00000443239.3_Missense_Mutation_p.T138M|DNMT3B_ENST00000456297.2_Missense_Mutation_p.T104M|DNMT3B_ENST00000375623.4_Missense_Mutation_p.T138M|DNMT3B_ENST00000344505.4_Missense_Mutation_p.T180M|DNMT3B_ENST00000353855.2_Missense_Mutation_p.T180M	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	180	Interaction with DNMT1 and DNMT3A.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ACACATGGGACGCCCCAGAGC	0.652																																					p.T192M		Atlas-SNP	.											.	DNMT3B	196	.	0			c.C575T						.						109	96	101					20																	31375142		2203	4300	6503	SO:0001583	missense	1789	exon6			ATGGGACGCCCCA		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.539C>T	chr20.hg19:g.31375142C>T	ENSP00000328547:p.Thr180Met	147.0	0.0		124.0	54.0	NM_175850	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	hg19	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	C	8.450	0.852967	0.17106	.	.	ENSG00000088305	ENST00000328111;ENST00000537219;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000375623;ENST00000201963	D;D;D;D;D;D;T;D	0.97328	-4.31;-4.34;-4.28;-4.29;-4.32;-4.16;-0.16;-4.34	3.79	0.559	0.17272	.	1.045820	0.07448	N	0.898573	D	0.90981	0.7164	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B	0.32031	0.352;0.057;0.172;0.104;0.054;0.009	B;B;B;B;B;B	0.18561	0.022;0.015;0.013;0.021;0.021;0.005	D	0.83917	0.0299	10	0.36615	T	0.2	3.2048	5.5643	0.17163	0.0:0.4774:0.0:0.5226	.	104;138;192;180;180;180	E9PBF2;E7EN63;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;.;DNM3B_HUMAN	M	180;266;180;180;138;104;180;138;192	ENSP00000328547:T180M;ENSP00000313397:T180M;ENSP00000337764:T180M;ENSP00000403169:T138M;ENSP00000412305:T104M;ENSP00000345105:T180M;ENSP00000364774:T138M;ENSP00000201963:T192M	ENSP00000201963:T192M	T	+	2	0	DNMT3B	30838803	0.003000	0.15002	0.011000	0.14972	0.201000	0.24016	0.264000	0.18497	0.114000	0.18032	-0.252000	0.11476	ACG	.	.		0.652	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		T	31375142	C	T	31375142	3	4	219	1	0	0	0	0	1	0	0	0	4679	536	19	1	597	1	DNMT3B	20	31375142	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	9880950	31375142	31650378	97	31462										
RBM39	9584	hgsc.bcm.edu	37	chr20	34326925	34326925	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tcatggccgttggcactgctCaacttgttctcatcctaagc	8	13	3	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr20:34326925C>T	ENST00000253363.6	-	3	89	c.66G>A	c.(64-66)ttG>ttA	p.L22L	RBM39_ENST00000407261.4_5'UTR|RBM39_ENST00000361162.6_Silent_p.L22L|RBM39_ENST00000397370.3_Silent_p.L22L|RBM39_ENST00000463098.1_5'Flank|RBM39_ENST00000528062.3_Silent_p.L22L			Q14498	RBM39_HUMAN	RNA binding motif protein 39	22					mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					TGGCACTGCTCAACTTGTTCT	0.433																																					p.L22L		Atlas-SNP	.											.	RBM39	68	.	0			c.G66A						.						132	110	117					20																	34326925		2203	4300	6503	SO:0001819	synonymous_variant	9584	exon3			ACTGCTCAACTTG	L10910	CCDS13265.1, CCDS13266.1, CCDS56186.1	20q11.22	2014-07-03	2006-07-11	2006-07-11	ENSG00000131051	ENSG00000131051		"RNA binding motif (RRM) containing"	15923	protein-coding gene	gene with protein product	"coactivator of activating protein-1 and estrogen receptors", "functional spliceosome-associated protein 59"	604739	"RNA-binding region (RNP1, RRM) containing 2"	RNPC2		8227358, 15694343, 21551269	Standard	NM_184234		Approved	CC1.3, HCC1, CAPER, fSAP59, CAPERalpha	uc002xeb.3	Q14498	OTTHUMG00000032358	ENST00000253363.6:c.66G>A	chr20.hg19:g.34326925C>T		132.0	0.0		112.0	7.0	NM_184234	A2RRD3|A5D8W2|B0BLV3|E1P5S0|E1P5S1|Q14499	Silent	SNP	ENST00000253363.6	hg19	CCDS13266.1																																																																																			.	.		0.433	RBM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078931.2	NM_184237		T	34326925	C	T	34326925	2	4	219	1	0	0	0	0	0	0	0	1	13148	825	29	3		3	RBM39	20	34326925	Silent	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	2951783	34326925	28698595	98	31463										
CHD6	84181	hgsc.bcm.edu	37	chr20	40162110	40162110	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aacatcttcaattttctcttCttgatcagtgctgcagtcaa	5	10	6	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr20:40162110C>G	ENST00000373233.3	-	3	310	c.133G>C	c.(133-135)Gaa>Caa	p.E45Q	CHD6_ENST00000309279.7_Missense_Mutation_p.E45Q|CHD6_ENST00000373222.3_Missense_Mutation_p.E80Q	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	45	Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.E45K(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				ATTTTCTCTTCTTGATCAGTG	0.413																																					p.E45Q		Atlas-SNP	.											CHD6,NS,carcinoma,0,1	CHD6	312	.	1	Substitution - Missense(1)	breast(1)	c.G133C						.						80	76	77					20																	40162110		2203	4300	6503	SO:0001583	missense	84181	exon3			TCTCTTCTTGATC	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.133G>C	chr20.hg19:g.40162110C>G	ENSP00000362330:p.Glu45Gln	69.0	0.0		106.0	7.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.877168	0.33162	.	.	ENSG00000124177	ENST00000373233;ENST00000309279;ENST00000373222;ENST00000440647	D;D;T	0.95069	-2.11;-3.6;-1.43	5.9	4.96	0.65561	.	0.291010	0.29760	N	0.011267	D	0.88994	0.6589	L	0.27053	0.805	0.26260	N	0.978588	B;B	0.24823	0.112;0.001	B;B	0.17722	0.019;0.002	T	0.79553	-0.1756	10	0.32370	T	0.25	-6.8857	11.7797	0.52006	0.0:0.8091:0.1237:0.0672	.	80;45	Q8TD26-2;Q8TD26	.;CHD6_HUMAN	Q	45;45;80;45	ENSP00000362330:E45Q;ENSP00000308684:E45Q;ENSP00000362319:E80Q	ENSP00000308684:E45Q	E	-	1	0	CHD6	39595524	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.368000	0.44222	1.503000	0.48686	0.655000	0.94253	GAA	.	.		0.413	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			G	40162110	C	G	40162110	3	3	219	1	0	0	0	0	1	0	0	0	3331	922	32	4	8154	4	CHD6	20	40162110	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	5835185	40162110	22863410	99	31464										
KCNS1	3787	hgsc.bcm.edu	37	chr20	43726446	43726446	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ctggtcgcccagtgccacacCagccagcagcgtgagataga	12	14	0	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr20:43726446C>T	ENST00000306117.1	-	4	1363	c.967G>A	c.(967-969)Ggt>Agt	p.G323S	KCNS1_ENST00000537075.1_Missense_Mutation_p.G323S	NM_002251.3	NP_002242.2	Q96KK3	KCNS1_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1	323					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(1)|lung(3)|ovary(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				AGTGCCACACCAGCCAGCAGC	0.632																																					p.G323S		Atlas-SNP	.											.	KCNS1	30	.	0			c.G967A						.						67	52	57					20																	43726446		2203	4300	6503	SO:0001583	missense	3787	exon4			CCACACCAGCCAG	AF043473	CCDS13342.1	20q12	2011-07-05			ENSG00000124134	ENSG00000124134		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6300	protein-coding gene	gene with protein product		602905				9305895, 16382104	Standard	NM_002251		Approved	Kv9.1	uc002xnc.3	Q96KK3	OTTHUMG00000033079	ENST00000306117.1:c.967G>A	chr20.hg19:g.43726446C>T	ENSP00000307694:p.Gly323Ser	65.0	0.0		47.0	7.0	NM_002251	A2RUL9|B7ZM31|O43652|Q6DJU6	Missense_Mutation	SNP	ENST00000306117.1	hg19	CCDS13342.1	.	.	.	.	.	.	.	.	.	.	C	9.708	1.156353	0.21454	.	.	ENSG00000124134	ENST00000306117;ENST00000537075	D;D	0.98249	-4.82;-4.82	5.31	3.01	0.34805	Ion transport (1);	0.155438	0.56097	N	0.000025	D	0.93374	0.7887	N	0.12887	0.27	0.34504	D	0.706423	B	0.02656	0.0	B	0.09377	0.004	D	0.91493	0.5213	10	0.16420	T	0.52	.	12.9091	0.58171	0.0:0.844:0.0:0.156	.	323	Q96KK3	KCNS1_HUMAN	S	323	ENSP00000307694:G323S;ENSP00000445595:G323S	ENSP00000307694:G323S	G	-	1	0	KCNS1	43159860	0.796000	0.28864	0.217000	0.23759	0.442000	0.32017	1.666000	0.37460	1.245000	0.43885	-0.291000	0.09656	GGT	.	.		0.632	KCNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080507.3	NM_002251		T	43726446	C	T	43726446	3	4	219	1	0	0	0	0	1	0	0	0	8097	594	21	3	621	3	KCNS1	20	43726446	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	3564336	43726446	19299074	100	31465										
SEMG2	6407	hgsc.bcm.edu	37	chr20	43851311	43851313	+	In_Frame_Del	DEL	ATC	ATC	-													0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ggccataaggaaaataaaatAtcataccaatcttcaagtac					rs191175081		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr20:43851311_43851313delATC	ENST00000372769.3	+	2	1128_1130	c.1038_1040delATC	c.(1036-1041)atatca>ata	p.S347del		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	347	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				AAAATAAAATATCATACCAATCT	0.379																																					p.346_347del		Atlas-INDEL	.											.	SEMG2	92	.	0			c.1037_1039del						.																																			SO:0001651	inframe_deletion	6407	exon2			.		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"Semenogelin 2"	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.1038_1040delATC	chr20.hg19:g.43851311_43851313delATC	ENSP00000361855:p.Ser347del	197.0	0.0		182.0	41.0	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	In_Frame_Del	DEL	ENST00000372769.3	hg19	CCDS13346.1																																																																																			.	.		0.379	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		-	43851313	ATC	-	43851311	7	5	219	1	0	1	0	1	0	0	0	0	14060	439	16	0	1044	0	SEMG2	20	43851311	In_Frame_Del	DEL	ATC	TCGA-DD-AAEG-01A-11D-A38X-10	124865	43851311	19174209	101	31466										
TFAP2C	7022	hgsc.bcm.edu	37	chr20	55206890	55206890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gaccagcacctgttgctgcaCgatcagacagtcattcgcaa	9	13	2	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr20:55206890C>T	ENST00000201031.2	+	3	807	c.564C>T	c.(562-564)caC>caT	p.H188H	TFAP2C_ENST00000544508.1_Silent_p.H19H	NM_003222.3	NP_003213.1	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma)	188					cell-cell signaling (GO:0007267)|cerebral cortex development (GO:0021987)|dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis (GO:0060598)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|forebrain neuron fate commitment (GO:0021877)|germ-line stem cell maintenance (GO:0030718)|hair follicle development (GO:0001942)|keratinocyte development (GO:0003334)|male gonad development (GO:0008584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermis development (GO:0045682)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sebaceous gland development (GO:0048733)|somatic stem cell maintenance (GO:0035019)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			Colorectal(105;0.229)			TGTTGCTGCACGATCAGACAG	0.547																																					p.H188H		Atlas-SNP	.											.	TFAP2C	51	.	0			c.C564T						.						117	101	107					20																	55206890		2203	4300	6503	SO:0001819	synonymous_variant	7022	exon3			GCTGCACGATCAG		CCDS13454.1	20q13.2	2008-07-17	2001-11-28		ENSG00000087510	ENSG00000087510			11744	protein-coding gene	gene with protein product	"estrogen receptor factor 1"	601602	"transcription factor AP-2 gamma (activating enhancer-binding protein 2 gamma)"			8661133	Standard	NM_003222		Approved	AP2-GAMMA, ERF1, TFAP2G, hAP-2g	uc002xya.3	Q92754	OTTHUMG00000032805	ENST00000201031.2:c.564C>T	chr20.hg19:g.55206890C>T		90.0	0.0		74.0	9.0	NM_003222	B4DWK3|O00685|O00730|Q86V30|Q8IVB6|Q9P1X2	Silent	SNP	ENST00000201031.2	hg19	CCDS13454.1																																																																																			.	.		0.547	TFAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079823.2	NM_003222		T	55206890	C	T	55206890	2	4	219	1	0	0	0	0	0	0	0	1	15804	535	19	1		1	TFAP2C	20	55206890	Silent	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	11355579	55206890	7818630	102	31467										
KRTAP19-4	337971	hgsc.bcm.edu	37	chr21	31869331	31869331	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cacagccataacccagtctgCggaagctgccacatccacag	8	16	1	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr21:31869331C>T	ENST00000334058.2	-	1	120	c.98G>A	c.(97-99)cGc>cAc	p.R33H		NM_181610.1	NP_853641.1	Q3LI73	KR194_HUMAN	keratin associated protein 19-4	33						intermediate filament (GO:0005882)				central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						ACCCAGTCTGCGGAAGCTGCC	0.532																																					p.R33H		Atlas-SNP	.											KRTAP19-4,NS,carcinoma,-1,1	KRTAP19-4	22	.	0			c.G98A						.						123	128	126					21																	31869331		2203	4300	6503	SO:0001583	missense	337971	exon1			AGTCTGCGGAAGC	AP001708	CCDS33534.1	21q22.1	2011-02-10			ENSG00000186967	ENSG00000186967		"Keratin associated proteins"	18939	protein-coding gene	gene with protein product						12359730	Standard	NM_181610		Approved	KAP19.4	uc011acz.2	Q3LI73	OTTHUMG00000057767	ENST00000334058.2:c.98G>A	chr21.hg19:g.31869331C>T	ENSP00000335567:p.Arg33His	100.0	0.0		99.0	31.0	NM_181610	Q17RT4|Q17RT6	Missense_Mutation	SNP	ENST00000334058.2	hg19	CCDS33534.1	.	.	.	.	.	.	.	.	.	.	C	6.844	0.524883	0.13066	.	.	ENSG00000186967	ENST00000334058	T	0.10668	2.85	4.54	-5.25	0.02781	.	.	.	.	.	T	0.07234	0.0183	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39742	-0.9599	8	0.87932	D	0	.	6.1988	0.20565	0.0:0.2126:0.2572:0.5301	.	33	Q3LI73	KR194_HUMAN	H	33	ENSP00000335567:R33H	ENSP00000335567:R33H	R	-	2	0	KRTAP19-4	30791202	0.000000	0.05858	0.000000	0.03702	0.425000	0.31504	-2.714000	0.00815	-1.056000	0.03205	-0.203000	0.12734	CGC	.	.		0.532	KRTAP19-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128219.2			T	31869331	C	T	31869331	3	4	219	1	0	0	0	0	1	0	0	0	8540	768	27	1	159	1	KRTAP19-4	21	31869331	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10		31869331	16260564	103	31468										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37581073	37581073	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aaagaggtgttttacaccgcCctctgggggagcgtcctggc	14	11	1	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr21:37581073C>A	ENST00000399151.3	+	5	637	c.552C>A	c.(550-552)gcC>gcA	p.A184A	DOPEY2_ENST00000492760.1_3'UTR	NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	184					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TTTACACCGCCCTCTGGGGGA	0.622																																					p.A184A		Atlas-SNP	.											.	DOPEY2	184	.	0			c.C552A						.						72	58	63					21																	37581073		2203	4300	6503	SO:0001819	synonymous_variant	9980	exon5			CACCGCCCTCTGG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.552C>A	chr21.hg19:g.37581073C>A		56.0	0.0		74.0	23.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	hg19	CCDS13643.1																																																																																			.	.		0.622	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		A	37581073	C	A	37581073	2	1	219	1	0	0	0	0	0	0	0	1	4710	610	22	3		3	DOPEY2	21	37581073	Silent	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	5711742	37581073	10548822	104	31469										
PRODH	8214	hgsc.bcm.edu	37	chr22	18900834	18900834	+	IGR	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gggcagcacctccatcacggGgccatagggcacgtacttgt	13	13	1	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr22:18900834G>C	ENST00000331444.6	+	0	1214				PRODH_ENST00000357068.6_Missense_Mutation_p.P553A|PRODH_ENST00000334029.2_Missense_Mutation_p.P445A|PRODH_ENST00000420436.1_Missense_Mutation_p.P445A	NM_005675.4	NP_005666.2	Q14129	DGCR6_HUMAN	DiGeorge syndrome critical region gene 6						cell adhesion (GO:0007155)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|upper_aerodigestive_tract(1)	3						TCCATCACGGGGCCATAGGGC	0.662																																					p.P553A		Atlas-SNP	.											.	PRODH	42	.	0			c.C1657G						.						34	34	34					22																	18900834		2187	4267	6454	SO:0001628	intergenic_variant	5625	exon15			TCACGGGGCCATA	X96484	CCDS13753.1	22q11.21	2008-06-12			ENSG00000183628	ENSG00000183628			2846	protein-coding gene	gene with protein product		601279				8733130	Standard	NM_005675		Approved		uc002zoh.4	Q14129	OTTHUMG00000150162		chr22.hg19:g.18900834G>C		173.0	0.0		127.0	34.0	NM_016335	B2RCH5|D3DX15|G5E9J8|Q9BY28	Missense_Mutation	SNP	ENST00000331444.6	hg19	CCDS13753.1	.	.	.	.	.	.	.	.	.	.	N	25.0	4.588119	0.86851	.	.	ENSG00000100033	ENST00000357068;ENST00000313755	T	0.35236	1.32	4.43	4.43	0.53597	Proline dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.62841	0.2461	M	0.82433	2.59	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.69610	-0.5099	10	0.72032	D	0.01	-16.931	14.911	0.70758	0.0:0.0:1.0:0.0	.	469;553;445	O43272-1;O43272;E7EQL6	.;PROD_HUMAN;.	A	553;198	ENSP00000349577:P553A	ENSP00000318329:P198A	P	-	1	0	PRODH	17280834	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	5.262000	0.65501	2.196000	0.70406	0.505000	0.49811	CCC	.	.		0.662	DGCR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316631.2	NM_005675		C	18900834	G	C	18900834	1	2	219	0	1	0	0	0	0	0	0	0	12560	1232	43	4		4	PRODH	22	18900834	IGR	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10		18900834	32403732	105	31470										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26423225	26423225	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	acccattcagctggaaactcCcaagcctcgactacgaacgc	7	16	1	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr22:26423225C>A	ENST00000407587.2	+	43	7457	c.7288C>A	c.(7288-7290)Cca>Aca	p.P2430T	MYO18B_ENST00000335473.7_Missense_Mutation_p.P2429T|MYO18B_ENST00000536101.1_Missense_Mutation_p.P2429T			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2429						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CTGGAAACTCCCAAGCCTCGA	0.557																																					p.P2429T		Atlas-SNP	.											.	MYO18B	322	.	0			c.C7285A						.						106	109	108					22																	26423225		1998	4163	6161	SO:0001583	missense	84700	exon43			AAACTCCCAAGCC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7288C>A	chr22.hg19:g.26423225C>A	ENSP00000386096:p.Pro2430Thr	118.0	0.0		147.0	51.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	14.20	2.465344	0.43839	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.89617	-2.52;-2.52;-2.54	4.79	4.79	0.61399	.	0.117222	0.34700	N	0.003754	D	0.93363	0.7884	M	0.62723	1.935	0.40212	D	0.977631	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.997;0.997;0.999;0.999	D	0.94498	0.7707	10	0.87932	D	0	.	16.398	0.83630	0.0:1.0:0.0:0.0	.	1942;2431;2429;2430;2429	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	T	2429;2429;2430	ENSP00000441229:P2429T;ENSP00000334563:P2429T;ENSP00000386096:P2430T	ENSP00000334563:P2429T	P	+	1	0	MYO18B	24753225	0.989000	0.36119	0.664000	0.29753	0.054000	0.15201	3.717000	0.54911	2.206000	0.71126	0.561000	0.74099	CCA	.	.		0.557	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26423225	C	A	26423225	3	1	219	1	0	0	0	0	1	0	0	0	10075	623	22	3	7451	3	MYO18B	22	26423225	Missense_Mutation	SNP	C	TCGA-DD-AAEG-01A-11D-A38X-10	7522391	26423225	24881341	106	31471										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885651	29885651	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tccccagtgaaggcagaagcAaagtcccctgagaaggccaa	11	12	0	3	rs267607535		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr22:29885651A>C	ENST00000310624.6	+	4	2055	c.2022A>C	c.(2020-2022)gcA>gcC	p.A674A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	680	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGCAGAAGCAAAGTCCCCTG	0.567																																					p.A674A		Atlas-SNP	.											.	NEFH	178	.	0			c.A2022C						.						92	98	96					22																	29885651		2203	4297	6500	SO:0001819	synonymous_variant	4744	exon4			AGAAGCAAAGTCC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2022A>C	chr22.hg19:g.29885651A>C		291.0	0.0		304.0	17.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.567	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		C	29885651	A	C	29885651	2	2	219	1	0	0	0	0	0	0	0	1	10323	117	5	5		5	NEFH	22	29885651	Silent	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	3462426	29885651	21418915	107	31472										
KDELR3	11015	hgsc.bcm.edu	37	chr22	38878529	38878540	+	Stop_Codon_Del	DEL	AATGCCAATCTG	AATGCCAATCTG	-													0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	ggaaagaagttaagtcttccAatgccaatctgaggaccttc					rs546524854		TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	AATGCCAATCTG	AATGCCAATCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chr22:38878529_38878540delAATGCCAATCTG	ENST00000216014.4	+	0	805_816				KDELR3_ENST00000471268.1_3'UTR	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					TAAGTCTTCCAATGCCAATCTGAGGACCTTCA	0.358																																					p.211_215del	Ovarian(11;103 529 24120 28493 32980)	Atlas-INDEL	.											.	KDELR3	39	.	0			c.632_643del						.																																			SO:0001567	stop_retained_variant	11015	exon5			.	AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520	Exception_encountered	chr22.hg19:g.38878529_38878540delAATGCCAATCTG	ENSP00000216014:p.*215Trpext*9	88.0	0.0		57.0	19.0	NM_006855	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	In_Frame_Del	DEL	ENST00000216014.4	hg19	CCDS13972.1																																																																																			.	.		0.358	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1			-	38878540	AATGCCAATCTG	-	38878529	7	5	219	1	0	1	0	1	0	0	0	0	8130	117	5	0	710	0	KDELR3	22	38878529	Stop_Codon_Del	DEL	AATGCCAATCTG	TCGA-DD-AAEG-01A-11D-A38X-10	8992878	38878529	12426037	108	31473										
BMX	660	hgsc.bcm.edu	37	chrX	15555298	15555298	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aagagattaccttgttgaagGagctgggaagtggccagttt	14	5	0	2			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chrX:15555298G>C	ENST00000357607.2	+	14	1452	c.1264G>C	c.(1264-1266)Gag>Cag	p.E422Q	BMX_ENST00000348343.6_Missense_Mutation_p.E422Q|BMX_ENST00000342014.6_Missense_Mutation_p.E422Q			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	422	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					CTTGTTGAAGGAGCTGGGAAG	0.488																																					p.E422Q		Atlas-SNP	.											.	BMX	73	.	0			c.G1264C						.						186	173	178					X																	15555298		2203	4300	6503	SO:0001583	missense	660	exon14			TTGAAGGAGCTGG	AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1079	protein-coding gene	gene with protein product	"BTK-like on X chromosome"	300101				7970727	Standard	NM_203281		Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.1264G>C	chrX.hg19:g.15555298G>C	ENSP00000350224:p.Glu422Gln	207.0	0.0		214.0	25.0	NM_001721	A6NIH9|O60564|Q12871	Missense_Mutation	SNP	ENST00000357607.2	hg19	CCDS14168.1	.	.	.	.	.	.	.	.	.	.	g	24.7	4.564856	0.86439	.	.	ENSG00000102010	ENST00000357607;ENST00000348343;ENST00000342014	T;T;T	0.26660	1.72;1.72;1.72	5.56	4.67	0.58626	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.088102	0.48767	N	0.000175	T	0.40886	0.1135	L	0.37561	1.115	0.44976	D	0.99799	D	0.76494	0.999	D	0.80764	0.994	T	0.27971	-1.0058	10	0.87932	D	0	.	13.8528	0.63508	0.0:0.1503:0.8497:0.0	.	422	P51813	BMX_HUMAN	Q	422	ENSP00000350224:E422Q;ENSP00000308774:E422Q;ENSP00000340082:E422Q	ENSP00000340082:E422Q	E	+	1	0	BMX	15465219	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	7.714000	0.84703	1.055000	0.40461	0.525000	0.51046	GAG	.	.		0.488	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	NM_001721		C	15555298	G	C	15555298	3	2	219	1	0	0	0	0	1	0	0	0	1473	1175	41	4	1314	4	BMX	23	15555298	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10		15555298	139715262	109	31474										
DMD	1756	hgsc.bcm.edu	37	chrX	32382769	32382769	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	aaagtgtgtcagcctgaatgAtccactttgtgatgtggtcc	11	8	1	3			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chrX:32382769A>T	ENST00000357033.4	-	36	5290	c.5084T>A	c.(5083-5085)aTc>aAc	p.I1695N	DMD_ENST00000378677.2_Missense_Mutation_p.I1691N	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1695	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AGCCTGAATGATCCACTTTGT	0.378																																					p.I1695N		Atlas-SNP	.											.	DMD	2127	.	0			c.T5084A						.						248	196	214					X																	32382769		2202	4300	6502	SO:0001583	missense	1756	exon36			TGAATGATCCACT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.5084T>A	chrX.hg19:g.32382769A>T	ENSP00000354923:p.Ile1695Asn	110.0	0.0		91.0	4.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.675765	0.88445	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.43688	0.94;0.94	5.38	5.38	0.77491	.	0.000000	0.35235	U	0.003356	T	0.50514	0.1620	L	0.50333	1.59	0.80722	D	1	P;P;P;P;P	0.49696	0.899;0.927;0.918;0.918;0.918	P;P;P;P;P	0.52109	0.466;0.69;0.601;0.505;0.505	T	0.54309	-0.8313	10	0.87932	D	0	.	14.5942	0.68392	1.0:0.0:0.0:0.0	.	1687;1695;1691;354;351	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	N	1687;354;351;1691;1695;1695;1572	ENSP00000367948:I1691N;ENSP00000354923:I1695N	ENSP00000354923:I1695N	I	-	2	0	DMD	32292690	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.701000	0.84566	1.895000	0.54865	0.437000	0.28790	ATC	.	.		0.378	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32382769	A	T	32382769	3	4	219	1	0	0	0	0	1	0	0	0	4582	333	12	4	6297	4	DMD	23	32382769	Missense_Mutation	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	16827471	32382769	122887791	110	31475										
ZNF674	641339	hgsc.bcm.edu	37	chrX	46359734	46359734	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cctgtatgagttctatgatgGacagagaggtgtgactttcc	12	7	1	4			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chrX:46359734G>A	ENST00000523374.1	-	6	1500	c.1290C>T	c.(1288-1290)gtC>gtT	p.V430V	ZNF674_ENST00000518795.1_5'Flank|ZNF674_ENST00000414387.2_Silent_p.V424V	NM_001039891.2|NM_001146291.1|NM_001190417.1	NP_001034980.1|NP_001139763.1|NP_001177346.1	Q2M3X9	ZN674_HUMAN	zinc finger protein 674	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)	2						TTCTATGATGGACAGAGAGGT	0.418																																					p.V430V		Atlas-SNP	.											.	ZNF674	3	.	0			c.C1290T						.						91	92	92					X																	46359734		2187	4287	6474	SO:0001819	synonymous_variant	641339	exon6			ATGATGGACAGAG	AY971607	CCDS48099.1, CCDS55406.1	Xp11.3	2013-01-08	2010-09-15		ENSG00000251192	ENSG00000251192		"Zinc fingers, C2H2-type", "-"	17625	protein-coding gene	gene with protein product		300573		MRX92		16385466	Standard	NM_001039891		Approved	ZNF673B	uc004dgr.3	Q2M3X9	OTTHUMG00000021420	ENST00000523374.1:c.1290C>T	chrX.hg19:g.46359734G>A		72.0	0.0		99.0	8.0	NM_001039891	B4DHE2|E9PHQ4	Silent	SNP	ENST00000523374.1	hg19	CCDS48099.1																																																																																			.	.		0.418	ZNF674-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056357.2	NM_001039891		A	46359734	G	A	46359734	2	1	219	1	0	0	0	0	0	0	0	1	18096	1161	41	3		3	ZNF674	23	46359734	Silent	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	13976965	46359734	108910826	111	31476										
SYN1	6853	hgsc.bcm.edu	37	chrX	47434654	47434654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	cctggtggtcaccaatgagcGgcatggaggaacccaccacc	12	14	1	1			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chrX:47434654G>A	ENST00000295987.7	-	10	1302	c.1178C>T	c.(1177-1179)cCg>cTg	p.P393L	SYN1_ENST00000340666.4_Missense_Mutation_p.P393L	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	393	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						ACCAATGAGCGGCATGGAGGA	0.617																																					p.P393L		Atlas-SNP	.											.	SYN1	84	.	0			c.C1178T						.						53	34	41					X																	47434654		2199	4300	6499	SO:0001583	missense	6853	exon10			ATGAGCGGCATGG		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.1178C>T	chrX.hg19:g.47434654G>A	ENSP00000295987:p.Pro393Leu	275.0	0.0		286.0	30.0	NM_006950	B1AJQ1|O75825|Q5H9A9	Missense_Mutation	SNP	ENST00000295987.7	hg19	CCDS14280.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868324	0.72065	.	.	ENSG00000008056	ENST00000295987;ENST00000340666	T;T	0.35973	1.71;1.28	5.17	5.17	0.71159	ATP-grasp fold, subdomain 2 (1);Synapsin, ATP-binding domain (1);	0.000000	0.64402	D	0.000002	T	0.67031	0.2850	M	0.89715	3.055	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.989;0.999	T	0.75294	-0.3368	10	0.87932	D	0	-7.9147	15.0484	0.71844	0.0:0.0:1.0:0.0	.	393;393	P17600;P17600-2	SYN1_HUMAN;.	L	393	ENSP00000295987:P393L;ENSP00000343206:P393L	ENSP00000295987:P393L	P	-	2	0	SYN1	47319598	1.000000	0.71417	0.990000	0.47175	0.544000	0.35116	6.014000	0.70784	2.141000	0.66446	0.600000	0.82982	CCG	.	.		0.617	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950		A	47434654	G	A	47434654	3	1	219	1	0	0	0	0	1	0	0	0	15455	1116	39	1	955	1	SYN1	23	47434654	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	1074920	47434654	107835906	112	31477										
MUM1L1	139221	hgsc.bcm.edu	37	chrX	105450458	105450458	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gaaattttcagagactggatTttgaagaacttgaggaagaa	11	3	1	5			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chrX:105450458T>A	ENST00000357175.2	+	4	1682	c.1033T>A	c.(1033-1035)Ttt>Att	p.F345I	MUM1L1_ENST00000372552.1_Missense_Mutation_p.F345I|MUM1L1_ENST00000337685.2_Missense_Mutation_p.F345I	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	345						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						GAGACTGGATTTTGAAGAACT	0.398																																					p.F345I		Atlas-SNP	.											.	MUM1L1	166	.	0			c.T1033A						.						22	20	21					X																	105450458		1844	4073	5917	SO:0001583	missense	139221	exon5			CTGGATTTTGAAG	AK090835	CCDS55469.1	Xq22.3	2008-02-05			ENSG00000157502	ENSG00000157502			26583	protein-coding gene	gene with protein product							Standard	NM_152423		Approved	FLJ33516	uc004emf.2	Q5H9M0	OTTHUMG00000022146	ENST00000357175.2:c.1033T>A	chrX.hg19:g.105450458T>A	ENSP00000349699:p.Phe345Ile	173.0	0.0		145.0	30.0	NM_152423	D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Missense_Mutation	SNP	ENST00000357175.2	hg19	CCDS55469.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.643528	0.29246	.	.	ENSG00000157502	ENST00000357175;ENST00000337685;ENST00000372552	T;T;T	0.22134	1.97;1.97;1.97	5.1	-0.803	0.10886	.	0.521928	0.17623	N	0.167669	T	0.15089	0.0364	M	0.62723	1.935	0.21697	N	0.999584	B	0.10296	0.003	B	0.12156	0.007	T	0.27123	-1.0083	10	0.23302	T	0.38	.	1.2619	0.02003	0.3021:0.0908:0.1534:0.4537	.	345	Q5H9M0	MUML1_HUMAN	I	345	ENSP00000349699:F345I;ENSP00000338641:F345I;ENSP00000361632:F345I	ENSP00000338641:F345I	F	+	1	0	MUM1L1	105337114	0.449000	0.25689	0.174000	0.22961	0.147000	0.21601	-0.068000	0.11561	-0.332000	0.08489	0.481000	0.45027	TTT	.	.		0.398	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423		A	105450458	T	A	105450458	3	1	219	1	0	0	0	0	1	0	0	0	9995	1841	64	4	1035	4	MUM1L1	23	105450458	Missense_Mutation	SNP	T	TCGA-DD-AAEG-01A-11D-A38X-10	58015804	105450458	49820102	113	31478										
LUZP4	51213	hgsc.bcm.edu	37	chrX	114536617	114536617	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	tgaagaagaaaagaataaaaGacagaaccatagtaaaaagg	9	3	0	6			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chrX:114536617G>T	ENST00000371920.3	+	2	159	c.152G>T	c.(151-153)aGa>aTa	p.R51I	LUZP4_ENST00000451986.2_Missense_Mutation_p.D9Y	NM_016383.3	NP_057467.1	Q9P127	LUZP4_HUMAN	leucine zipper protein 4	51						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	14						AAGAATAAAAGACAGAACCAT	0.338																																					p.R51I		Atlas-SNP	.											.	LUZP4	51	.	0			c.G152T						.						136	128	131					X																	114536617		2203	4300	6503	SO:0001583	missense	51213	exon2			ATAAAAGACAGAA	AF124430	CCDS14567.1	Xq24	2009-03-25			ENSG00000102021	ENSG00000102021			24971	protein-coding gene	gene with protein product	"cancer/testis antigen 28"	300616				12032826, 11051238	Standard	XM_005268343		Approved	HOM-TES-85, CT-8, CT28	uc004eqa.3	Q9P127	OTTHUMG00000022234	ENST00000371920.3:c.152G>T	chrX.hg19:g.114536617G>T	ENSP00000360988:p.Arg51Ile	603.0	0.0		636.0	232.0	NM_016383	B3KSD6	Missense_Mutation	SNP	ENST00000371920.3	hg19	CCDS14567.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.635|1.635	-0.518095|-0.518095	0.04171|0.04171	.|.	.|.	ENSG00000102021|ENSG00000102021	ENST00000451986|ENST00000371921;ENST00000371920	T|T;T	0.57436|0.45276	0.4|0.9;1.5	2.64|2.64	-2.2|-2.2	0.06994|0.06994	.|.	.|.	.|.	.|.	.|.	T|T	0.20455|0.20455	0.0492|0.0492	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	P|P	0.38020|0.41848	0.615|0.763	B|B	0.28232|0.35114	0.087|0.196	T|T	0.09840|0.09840	-1.0656|-1.0656	9|9	0.87932|0.45353	D|T	0|0.12	.|.	4.4287|4.4287	0.11517|0.11517	0.4713:0.2323:0.2964:0.0|0.4713:0.2323:0.2964:0.0	.|.	9|51	B3KSD6|Q9P127	.|LUZP4_HUMAN	Y|I	9|51	ENSP00000411212:D9Y|ENSP00000360989:R51I;ENSP00000360988:R51I	ENSP00000411212:D9Y|ENSP00000360988:R51I	D|R	+|+	1|2	0|0	LUZP4|LUZP4	114442873|114442873	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-2.383000|-2.383000	0.01063|0.01063	-0.720000|-0.720000	0.04935|0.04935	-0.422000|-0.422000	0.05995|0.05995	GAC|AGA	.	.		0.338	LUZP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057972.1	NM_016383		T	114536617	G	T	114536617	3	4	219	1	0	0	0	0	1	0	0	0	9097	942	33	3	158	3	LUZP4	23	114536617	Missense_Mutation	SNP	G	TCGA-DD-AAEG-01A-11D-A38X-10	9086159	114536617	40733943	114	31479										
ZIC3	7547	hgsc.bcm.edu	37	chrX	136649300	136649300	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0347826086956522	4	1	0.565154088813395	0.565154088813395	0.565154088813395	0.559440559440559	1	0	gcgagcagcctgcatgctccAgctggcatccccgagccccc	11	19	0	0			TCGA-DD-AAEG-01A-11D-A38X-10	TCGA-DD-AAEG-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	60545315-ae1b-4ac7-bf17-6dff14fcc159	69827eac-d9d6-41e2-8db4-5e5482ff1418	g.chrX:136649300A>T	ENST00000287538.5	+	1	1000	c.450A>T	c.(448-450)ccA>ccT	p.P150P	RP1-137H15.2_ENST00000442841.1_RNA|ZIC3_ENST00000370606.3_Silent_p.P150P	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	150					anterior/posterior pattern specification (GO:0009952)|cell differentiation (GO:0030154)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of left/right asymmetry in nervous system (GO:0035545)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|heart looping (GO:0001947)|lung development (GO:0030324)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					TGCATGCTCCAGCTGGCATCC	0.697																																					p.P150P		Atlas-SNP	.											.	ZIC3	93	.	0			c.A450T						.						11	13	12					X																	136649300		2149	4188	6337	SO:0001819	synonymous_variant	7547	exon1			TGCTCCAGCTGGC	AF028706	CCDS14663.1	Xq24-q27.1	2013-01-08	2011-05-19		ENSG00000156925	ENSG00000156925		"Zinc fingers, C2H2-type"	12874	protein-coding gene	gene with protein product		300265	"heterotaxy 1", "Zic family member 3 (odd-paired homolog, Drosophila)"	HTX1		8298651, 7747776	Standard	NM_003413		Approved	HTX, ZNF203	uc004fak.3	O60481	OTTHUMG00000022525	ENST00000287538.5:c.450A>T	chrX.hg19:g.136649300A>T		114.0	0.0		112.0	14.0	NM_003413	B2CNW4|Q14DE5|Q5JY75	Silent	SNP	ENST00000287538.5	hg19	CCDS14663.1																																																																																			.	.		0.697	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1			T	136649300	A	T	136649300	2	4	219	1	0	0	0	0	0	0	0	1	17695	175	7	4		4	ZIC3	23	136649300	Silent	SNP	A	TCGA-DD-AAEG-01A-11D-A38X-10	22112683	136649300	18621260	115	31480										
C1orf158	93190	hgsc.bcm.edu	37	chr1	12820816	12820816	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	accccagaccaccgttgtgcGctatgtcctggagggagcat	12	13	0	1	rs140110943		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:12820816G>A	ENST00000288048.5	+	4	733	c.517G>A	c.(517-519)Gct>Act	p.A173T	C1orf158_ENST00000376210.3_Missense_Mutation_p.A135T	NM_152290.2	NP_689503.2	Q8N1D5	CA158_HUMAN	chromosome 1 open reading frame 158	173										central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|ovary(1)|skin(2)|urinary_tract(3)	10	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		ACCGTTGTGCGCTATGTCCTG	0.577																																					p.A173T		Atlas-SNP	.											.	C1orf158	28	.	0			c.G517A						.	G	THR/ALA	2,4404		0,2,2201	142	118	126		517	2.8	0	1	dbSNP_134	126	0,8600		0,0,4300	no	missense	C1orf158	NM_152290.2	58	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	173/195	12820816	2,13004	2203	4300	6503	SO:0001583	missense	93190	exon4			TTGTGCGCTATGT	BX647383	CCDS147.1	1p36.21	2008-02-05			ENSG00000157330	ENSG00000157330			28567	protein-coding gene	gene with protein product						12477932	Standard	NM_152290		Approved	MGC35194	uc001auh.3	Q8N1D5	OTTHUMG00000001888	ENST00000288048.5:c.517G>A	chr1.hg19:g.12820816G>A	ENSP00000288048:p.Ala173Thr	57.0	0.0		74.0	8.0	NM_152290	Q5VUY4	Missense_Mutation	SNP	ENST00000288048.5	hg19	CCDS147.1	.	.	.	.	.	.	.	.	.	.	.	11.80	1.746198	0.30955	4.54E-4	0.0	ENSG00000157330	ENST00000288048;ENST00000376210	T;T	0.51071	0.76;0.72	4.75	2.78	0.32641	.	0.396303	0.24580	N	0.037313	T	0.41190	0.1148	M	0.65975	2.015	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.32666	-0.9898	10	0.41790	T	0.15	-12.3831	6.4952	0.22138	0.101:0.1843:0.7147:0.0	.	173	Q8N1D5	CA158_HUMAN	T	173;135	ENSP00000288048:A173T;ENSP00000365383:A135T	ENSP00000288048:A173T	A	+	1	0	C1orf158	12743403	0.000000	0.05858	0.024000	0.17045	0.005000	0.04900	-0.036000	0.12185	1.183000	0.42943	0.563000	0.77884	GCT	.	G|1.000;A|0.000		0.577	C1orf158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005325.1	NM_152290		A	12820816	G	A	12820816	3	1	220	1	0	0	0	0	1	0	0	0	2009	1087	38	1	531	1	C1orf158	1	12820816	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10		12820816	236429805	1	31481										
NSUN4	387338	hgsc.bcm.edu	37	chr1	46827352	46827352	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tgccattgagctcctggccaAtcaatacagcatccaggtac	8	13	1	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:46827352A>G	ENST00000474844.1	+	6	1639	c.989A>G	c.(988-990)aAt>aGt	p.N330S	NSUN4_ENST00000498008.1_3'UTR|NSUN4_ENST00000537428.1_Missense_Mutation_p.N281S|NSUN4_ENST00000536062.1_Missense_Mutation_p.N281S	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	330					rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)			endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					CTCCTGGCCAATCAATACAGC	0.493																																					p.N330S		Atlas-SNP	.											.	NSUN4	26	.	0			c.A989G						.						296	270	279					1																	46827352		2203	4300	6503	SO:0001583	missense	387338	exon6			TGGCCAATCAATA	AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"NOP2/Sun domain containing"	31802	protein-coding gene	gene with protein product	"sperm head and tail associated protein"	615394	"NOL1/NOP2/Sun domain family 4", "NOL1/NOP2/Sun domain family, member 4"				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	ENST00000474844.1:c.989A>G	chr1.hg19:g.46827352A>G	ENSP00000419740:p.Asn330Ser	121.0	0.0		103.0	28.0	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Missense_Mutation	SNP	ENST00000474844.1	hg19	CCDS534.1	.	.	.	.	.	.	.	.	.	.	A	8.892	0.954117	0.18431	.	.	ENSG00000117481	ENST00000474844;ENST00000536062;ENST00000537428	T;T;T	0.09445	2.98;2.98;2.98	5.43	4.3	0.51218	.	0.151534	0.64402	D	0.000012	T	0.06416	0.0165	L	0.31120	0.905	0.30225	N	0.796439	B;B	0.22683	0.021;0.073	B;B	0.25987	0.009;0.065	T	0.29150	-1.0021	10	0.11182	T	0.66	-12.1768	2.8814	0.05648	0.5529:0.2452:0.0786:0.1233	.	197;330	B3KUM0;Q96CB9	.;NSUN4_HUMAN	S	330;281;281	ENSP00000419740:N330S;ENSP00000438912:N281S;ENSP00000437758:N281S	ENSP00000419740:N330S	N	+	2	0	NSUN4	46599939	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	1.461000	0.35255	1.068000	0.40764	0.533000	0.62120	AAT	.	.		0.493	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044		G	46827352	A	G	46827352	3	3	220	1	0	0	0	0	1	0	0	0	10689	101	4	2	1011	2	NSUN4	1	46827352	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	34006536	46827352	202423269	2	31482										
MRPL37	51253	hgsc.bcm.edu	37	chr1	54666136	54666136	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tgccctggctggcgcggccgAtctttccgccctgggaccgc	14	17	1	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:54666136A>G	ENST00000360840.5	+	1	297	c.220A>G	c.(220-222)Atc>Gtc	p.I74V	CYB5RL_ENST00000542737.1_5'Flank|RP11-446E24.4_ENST00000311841.7_5'Flank|MRPL37_ENST00000336230.6_Silent_p.R43R|MRPL37_ENST00000487096.1_Intron|CYB5RL_ENST00000537208.1_5'Flank|MRPL37_ENST00000605337.1_Missense_Mutation_p.I74V	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	74					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						GGCGCGGCCGATCTTTCCGCC	0.622																																					p.I74V		Atlas-SNP	.											.	MRPL37	36	.	0			c.A220G						.						59	56	57					1																	54666136		2203	4300	6503	SO:0001583	missense	51253	exon1			CGGCCGATCTTTC	AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221		"Mitochondrial ribosomal proteins / large subunits"	14034	protein-coding gene	gene with protein product		611843				10600119	Standard	NM_016491		Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.220A>G	chr1.hg19:g.54666136A>G	ENSP00000354086:p.Ile74Val	124.0	0.0		164.0	51.0	NM_016491	Q96Q67|Q9BWR1|Q9P0P3	Missense_Mutation	SNP	ENST00000360840.5	hg19	CCDS589.1	.	.	.	.	.	.	.	.	.	.	A	3.218	-0.160140	0.06502	.	.	ENSG00000116221	ENST00000360840;ENST00000329505	T	0.27720	1.65	4.81	-0.913	0.10500	.	0.586833	0.17152	N	0.185013	T	0.09024	0.0223	N	0.02539	-0.55	0.09310	N	0.99999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.37150	-0.9718	10	0.07644	T	0.81	-4.0557	7.8303	0.29338	0.2013:0.119:0.6797:0.0	.	11;74	E9PB99;Q9BZE1	.;RM37_HUMAN	V	74;11	ENSP00000354086:I74V	ENSP00000328799:I11V	I	+	1	0	MRPL37	54438724	0.619000	0.27059	0.712000	0.30502	0.908000	0.53690	1.409000	0.34680	-0.243000	0.09653	-0.270000	0.10280	ATC	.	.		0.622	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022224.1	NM_016491		G	54666136	A	G	54666136	3	3	220	1	0	0	0	0	1	0	0	0	9809	333	12	2	222	2	MRPL37	1	54666136	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	7838784	54666136	194584485	3	31483										
KPRP	448834	hgsc.bcm.edu	37	chr1	152732150	152732150	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	cttctgctcctctcaatcccCctttgcccagagccaagtgg	7	17	2	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:152732150C>A	ENST00000606109.1	+	1	114	c.86C>A	c.(85-87)cCc>cAc	p.P29H	KPRP_ENST00000368773.1_Missense_Mutation_p.P29H			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	29	Gln-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTCAATCCCCCTTTGCCCAG	0.582																																					p.P29H		Atlas-SNP	.											.	KPRP	152	.	0			c.C86A						.						122	120	121					1																	152732150		2203	4300	6503	SO:0001583	missense	448834	exon2			AATCCCCCTTTGC	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.86C>A	chr1.hg19:g.152732150C>A	ENSP00000475216:p.Pro29His	87.0	0.0		141.0	34.0	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	hg19	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	C	10.61	1.398900	0.25291	.	.	ENSG00000203786	ENST00000368773	T	0.14144	2.53	5.26	2.4	0.29515	.	0.451045	0.19115	N	0.122331	T	0.13798	0.0334	L	0.60455	1.87	0.09310	N	1	D	0.71674	0.998	P	0.62740	0.906	T	0.03193	-1.1062	10	0.87932	D	0	-2.7757	6.6995	0.23217	0.0:0.7193:0.0:0.2807	.	29	Q5T749	KPRP_HUMAN	H	29	ENSP00000357762:P29H	ENSP00000357762:P29H	P	+	2	0	KPRP	150998774	0.000000	0.05858	0.001000	0.08648	0.067000	0.16453	0.186000	0.16978	0.923000	0.37045	0.655000	0.94253	CCC	.	.		0.582	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		A	152732150	C	A	152732150	3	1	220	1	0	0	0	0	1	0	0	0	8445	623	22	3	88	3	KPRP	1	152732150	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	98066014	152732150	96518471	4	31484										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153907290	153907290	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	cacctgctcctgctgctgctGctgctgctgctgctgttgct	11	15	0	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:153907290G>C	ENST00000361217.4	-	18	3137	c.2719C>G	c.(2719-2721)Cag>Gag	p.Q907E	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	907	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tgctgctgctgctgctgctgc	0.637																																					p.Q907E		Atlas-SNP	.											.	DENND4B	210	.	0			c.C2719G						.						26	34	31					1																	153907290		2187	4278	6465	SO:0001583	missense	9909	exon18			GCTGCTGCTGCTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2719C>G	chr1.hg19:g.153907290G>C	ENSP00000354597:p.Gln907Glu	40.0	0.0		50.0	4.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	g	2.536	-0.307398	0.05458	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06142	3.34;3.34	2.18	2.18	0.27775	.	2.965800	0.00748	N	0.001049	T	0.00906	0.0030	N	0.08118	0	0.27538	N	0.95088	B	0.10296	0.003	B	0.06405	0.002	T	0.28427	-1.0044	10	0.02654	T	1	-2.8917	8.0948	0.30822	0.0:0.0:1.0:0.0	.	907	O75064	DEN4B_HUMAN	E	907;918	ENSP00000354597:Q907E;ENSP00000357635:Q918E	ENSP00000354597:Q907E	Q	-	1	0	DENND4B	152173914	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	1.183000	0.32041	1.576000	0.49790	0.271000	0.19318	CAG	.	.		0.637	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153907290	G	C	153907290	3	2	220	1	0	0	0	0	1	0	0	0	4436	1328	46	4	1815	4	DENND4B	1	153907290	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	1175140	153907290	95343331	5	31485										
ATP8B2	57198	hgsc.bcm.edu	37	chr1	154321379	154321379	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	accgctgcatgcggcgggttGgccgcactggctcccggcgc	16	16	0	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:154321379G>C	ENST00000368489.3	+	28	3457	c.3457G>C	c.(3457-3459)Ggc>Cgc	p.G1153R		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	1139					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GCGGCGGGTTGGCCGCACTGG	0.647																																					p.G1153R		Atlas-SNP	.											.	ATP8B2	158	.	0			c.G3457C						.						22	26	25					1																	154321379		2203	4299	6502	SO:0001583	missense	57198	exon28			CGGGTTGGCCGCA	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.3457G>C	chr1.hg19:g.154321379G>C	ENSP00000357475:p.Gly1153Arg	126.0	0.0		179.0	38.0	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	hg19	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	G	6.586	0.476436	0.12521	.	.	ENSG00000143515	ENST00000368489	T	0.38240	1.15	4.23	4.23	0.50019	.	0.085282	0.48767	D	0.000171	T	0.02418	0.0074	N	0.00197	-1.87	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47086	-0.9144	10	0.02654	T	1	.	11.3881	0.49798	0.0:0.1838:0.8162:0.0	.	1153	P98198-3	.	R	1153	ENSP00000357475:G1153R	ENSP00000357475:G1153R	G	+	1	0	ATP8B2	152588003	0.758000	0.28405	0.917000	0.36280	0.852000	0.48524	0.924000	0.28777	2.173000	0.68751	0.561000	0.74099	GGC	.	.		0.647	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		C	154321379	G	C	154321379	3	2	220	1	0	0	0	0	1	0	0	0	1195	1348	47	4	3697	4	ATP8B2	1	154321379	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	414089	154321379	94929242	6	31486										
CCT3	7203	hgsc.bcm.edu	37	chr1	156290762	156290762	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctgatggctttggtagtaatAgagctgttgatgatgttcag	13	4	1	4			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:156290762A>G	ENST00000295688.3	-	7	757	c.477T>C	c.(475-477)tcT>tcC	p.S159S	CCT3_ENST00000368261.3_Silent_p.S114S|CCT3_ENST00000472765.2_Silent_p.S114S|CCT3_ENST00000368259.2_Silent_p.S121S	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	159					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					TGGTAGTAATAGAGCTGTTGA	0.438																																					p.S159S		Atlas-SNP	.											.	CCT3	61	.	0			c.T477C						.						195	171	179					1																	156290762		2203	4300	6503	SO:0001819	synonymous_variant	7203	exon7			AGTAATAGAGCTG	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"Heat Shock Proteins / Chaperonins"	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.477T>C	chr1.hg19:g.156290762A>G		71.0	0.0		131.0	43.0	NM_005998	A6NE14|Q5SZY1|Q9BR64	Silent	SNP	ENST00000295688.3	hg19	CCDS1140.2																																																																																			.	.		0.438	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		G	156290762	A	G	156290762	2	3	220	1	0	0	0	0	0	0	0	1	2956	407	15	2		2	CCT3	1	156290762	Silent	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	1969383	156290762	92959859	7	31487										
CADM3	57863	hgsc.bcm.edu	37	chr1	159166162	159166162	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ccttctccacagacacaccaActgcgatgattaggccagac	7	15	1	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:159166162A>C	ENST00000368125.4	+	6	857	c.700A>C	c.(700-702)Act>Cct	p.T234P	CTA-134P22.2_ENST00000415675.2_RNA|CADM3_ENST00000368124.4_Missense_Mutation_p.T268P	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	234	Ig-like C2-type 2.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					AGACACACCAACTGCGATGAT	0.507											OREG0013913	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T268P		Atlas-SNP	.											.	CADM3	118	.	0			c.A802C						.						206	143	164					1																	159166162		2203	4300	6503	SO:0001583	missense	57863	exon7			ACACCAACTGCGA	AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17601	protein-coding gene	gene with protein product	"nectin-like 1"	609743	"immunoglobulin superfamily, member 4B"	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.700A>C	chr1.hg19:g.159166162A>C	ENSP00000357107:p.Thr234Pro	98.0	0.0	1799	149.0	45.0	NM_021189	Q8IZQ9|Q9NVJ5|Q9UJP1	Missense_Mutation	SNP	ENST00000368125.4	hg19	CCDS44251.1	.	.	.	.	.	.	.	.	.	.	A	12.97	2.096991	0.37048	.	.	ENSG00000162706	ENST00000368124;ENST00000368125;ENST00000416746	T;T;T	0.15718	2.4;2.4;2.45	4.78	4.78	0.61160	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.328508	0.29838	N	0.011076	T	0.14787	0.0357	M	0.64997	1.995	0.21861	N	0.999501	P;P;D	0.61080	0.927;0.947;0.989	P;P;P	0.52454	0.477;0.699;0.656	T	0.05115	-1.0905	10	0.37606	T	0.19	.	10.6186	0.45465	1.0:0.0:0.0:0.0	.	188;234;268	Q8N126-3;Q8N126;Q8N126-2	.;CADM3_HUMAN;.	P	268;234;188	ENSP00000357106:T268P;ENSP00000357107:T234P;ENSP00000387802:T188P	ENSP00000357106:T268P	T	+	1	0	CADM3	157432786	0.482000	0.25948	0.070000	0.20053	0.275000	0.26752	4.681000	0.61663	1.999000	0.58509	0.533000	0.62120	ACT	.	.		0.507	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189		C	159166162	A	C	159166162	3	2	220	1	0	0	0	0	1	0	0	0	2570	43	2	5	828	5	CADM3	1	159166162	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	2875400	159166162	90084459	8	31488										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172547511	172547511	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	atcactcagaacgccaggaaCtatttgatgaggactatggt	10	8	2	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:172547511C>T	ENST00000263688.3	+	14	1633	c.1414C>T	c.(1414-1416)Cta>Tta	p.L472L	SUCO_ENST00000610051.1_Silent_p.L435L|SUCO_ENST00000608151.1_Silent_p.L624L|SUCO_ENST00000367723.4_Silent_p.L623L	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	472					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											ACGCCAGGAACTATTTGATGA	0.348																																					p.L472L		Atlas-SNP	.											.	.	.	.	0			c.C1414T						.						124	115	118					1																	172547511		2203	4300	6503	SO:0001819	synonymous_variant	51430	exon14			CAGGAACTATTTG	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1414C>T	chr1.hg19:g.172547511C>T		59.0	0.0		120.0	7.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Silent	SNP	ENST00000263688.3	hg19	CCDS1303.1																																																																																			.	.		0.348	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		T	172547511	C	T	172547511	2	4	220	1	0	0	0	0	0	0	0	1	2069	564	20	3		3	C1orf9	1	172547511	Silent	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	13381349	172547511	76703110	9	31489										
LAMC2	3918	hgsc.bcm.edu	37	chr1	183201974	183201974	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctgagcctggcagaaagtgaAgcttccttgggaaacactgt	12	9	0	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:183201974A>G	ENST00000264144.4	+	14	2267	c.2202A>G	c.(2200-2202)gaA>gaG	p.E734E	LAMC2_ENST00000493293.1_Silent_p.E734E	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	734	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						CAGAAAGTGAAGCTTCCTTGG	0.488																																					p.E734E		Atlas-SNP	.											.	LAMC2	113	.	0			c.A2202G						.						68	69	69					1																	183201974		2203	4300	6503	SO:0001819	synonymous_variant	3918	exon14			AAGTGAAGCTTCC	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.2202A>G	chr1.hg19:g.183201974A>G		61.0	0.0		99.0	25.0	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Silent	SNP	ENST00000264144.4	hg19	CCDS1352.1																																																																																			.	.		0.488	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		G	183201974	A	G	183201974	2	3	220	1	0	0	0	0	0	0	0	1	8624	69	3	2		2	LAMC2	1	183201974	Silent	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	10654463	183201974	66048647	10	31490										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185704070	185704070	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gatgtgactggttctatgtaTgatgatttagttcaggtgat	12	3	2	4			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:185704070T>A	ENST00000271588.4	+	1	388	c.159T>A	c.(157-159)taT>taA	p.Y53*	HMCN1_ENST00000367492.2_Nonsense_Mutation_p.Y53*	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	53	VWFA.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GTTCTATGTATGATGATTTAG	0.463																																					p.Y53X		Atlas-SNP	.											.	HMCN1	797	.	0			c.T159A						.						138	145	143					1																	185704070		2203	4300	6503	SO:0001587	stop_gained	83872	exon1			TATGTATGATGAT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.159T>A	chr1.hg19:g.185704070T>A	ENSP00000271588:p.Tyr53*	130.0	0.0		240.0	63.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Nonsense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	40	8.197602	0.98701	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	.	.	.	5.7	-2.16	0.07080	.	0.000000	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8529	0.63508	0.0:0.7676:0.0:0.2324	.	.	.	.	X	53	.	ENSP00000271588:Y53X	Y	+	3	2	HMCN1	183970693	0.896000	0.30565	0.992000	0.48379	0.997000	0.91878	0.012000	0.13287	-0.332000	0.08489	0.528000	0.53228	TAT	.	.		0.463	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	185704070	T	A	185704070	4	1	220	1	0	0	0	0	0	1	0	0	7229	1471	51	4	161	4	HMCN1	1	185704070	Nonsense_Mutation	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10	2502096	185704070	63546551	11	31491										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186082011	186082011	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	caacaatgctgacctaggtgAtacagccaattatacctgtg	8	10	0	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:186082011A>G	ENST00000271588.4	+	72	11286	c.11057A>G	c.(11056-11058)gAt>gGt	p.D3686G	HMCN1_ENST00000367492.2_Missense_Mutation_p.D3686G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3686	Ig-like C2-type 35.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GACCTAGGTGATACAGCCAAT	0.408																																					p.D3686G		Atlas-SNP	.											.	HMCN1	797	.	0			c.A11057G						.						125	119	121					1																	186082011		2203	4300	6503	SO:0001583	missense	83872	exon72			TAGGTGATACAGC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11057A>G	chr1.hg19:g.186082011A>G	ENSP00000271588:p.Asp3686Gly	95.0	0.0		127.0	40.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	18.42	3.620691	0.66787	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.81739	-1.53;-1.53	4.91	4.91	0.64330	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94321	0.8175	H	0.99415	4.555	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96719	0.9531	10	0.87932	D	0	.	14.8338	0.70166	1.0:0.0:0.0:0.0	.	3686	Q96RW7	HMCN1_HUMAN	G	3686	ENSP00000271588:D3686G;ENSP00000356462:D3686G	ENSP00000271588:D3686G	D	+	2	0	HMCN1	184348634	1.000000	0.71417	0.618000	0.29105	0.309000	0.27889	9.080000	0.94040	1.957000	0.56846	0.533000	0.62120	GAT	.	.		0.408	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186082011	A	G	186082011	3	3	220	1	0	0	0	0	1	0	0	0	7229	333	12	2	11343	2	HMCN1	1	186082011	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	377941	186082011	63168610	12	31492										
EPHX1	2052	hgsc.bcm.edu	37	chr1	226033008	226033008	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ggagccggagctgctcgcccAggacatccgcaagttcctgt	13	14	0	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:226033008A>C	ENST00000366837.4	+	9	1524	c.1328A>C	c.(1327-1329)cAg>cCg	p.Q443P	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Missense_Mutation_p.Q443P	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	443					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					CTGCTCGCCCAGGACATCCGC	0.612																																					p.Q443P		Atlas-SNP	.											.	EPHX1	57	.	0			c.A1328C						.						40	41	41					1																	226033008		2203	4300	6503	SO:0001583	missense	2052	exon9			TCGCCCAGGACAT	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.1328A>C	chr1.hg19:g.226033008A>C	ENSP00000355802:p.Gln443Pro	39.0	0.0		63.0	7.0	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Missense_Mutation	SNP	ENST00000366837.4	hg19	CCDS1547.1	.	.	.	.	.	.	.	.	.	.	A	9.738	1.164177	0.21538	.	.	ENSG00000143819	ENST00000272167;ENST00000366837	T;T	0.37752	1.18;1.18	4.94	-7.46	0.01369	.	1.345280	0.04747	N	0.423936	T	0.47002	0.1422	M	0.81341	2.54	0.18873	N	0.999986	P	0.37663	0.604	B	0.43386	0.418	T	0.58549	-0.7617	10	0.52906	T	0.07	-16.3533	14.7709	0.69679	0.4284:0.0:0.5716:0.0	.	443	P07099	HYEP_HUMAN	P	443	ENSP00000272167:Q443P;ENSP00000355802:Q443P	ENSP00000272167:Q443P	Q	+	2	0	EPHX1	224099631	0.191000	0.23288	0.011000	0.14972	0.067000	0.16453	0.935000	0.28924	-1.800000	0.01247	-1.467000	0.01014	CAG	.	.		0.612	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120		C	226033008	A	C	226033008	3	2	220	1	0	0	0	0	1	0	0	0	5181	188	7	5	1358	5	EPHX1	1	226033008	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	39950997	226033008	23217613	13	31493										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228525730	228525730	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gctgcgggaaggccagtatgTggaggtcctggatgcagccc	17	10	0	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:228525730T>A	ENST00000422127.1	+	67	16930	c.16886T>A	c.(16885-16887)gTg>gAg	p.V5629E	OBSCN_ENST00000366709.4_Missense_Mutation_p.V2748E|OBSCN_ENST00000570156.2_Missense_Mutation_p.V6586E|OBSCN_ENST00000366707.4_Missense_Mutation_p.V3263E|OBSCN_ENST00000284548.11_Missense_Mutation_p.V5629E	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5629	SH3.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGCCAGTATGTGGAGGTCCTG	0.632																																					p.V6586E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T19757A						.						39	40	39					1																	228525730		2188	4289	6477	SO:0001583	missense	84033	exon78			AGTATGTGGAGGT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.16886T>A	chr1.hg19:g.228525730T>A	ENSP00000409493:p.Val5629Glu	64.0	0.0		88.0	43.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.7|25.7	4.663213|4.663213	0.88251|0.88251	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.|T;T;T;T	.|0.32753	.|1.44;1.44;1.44;1.44	4.35|4.35	4.35|4.35	0.52113|0.52113	.|Src homology-3 domain (2);	.|0.000000	.|0.64402	.|D	.|0.000007	.|T	.|0.51787	.|0.1695	M|M	0.63843|0.63843	1.955|1.955	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.997;0.999	.|T	.|0.55121	.|-0.8190	.|10	.|0.62326	.|D	.|0.03	.|.	13.9922|13.9922	0.64374|0.64374	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|5629;5629	.|Q5VST9;Q5VST9-3	.|OBSCN_HUMAN;.	X|E	244|5629;5629;3263;2748	.|ENSP00000284548:V5629E;ENSP00000409493:V5629E;ENSP00000355668:V3263E;ENSP00000355670:V2748E	.|ENSP00000284548:V5629E	C|V	+|+	3|2	2|0	OBSCN|OBSCN	226592353|226592353	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.669000|0.669000	0.39330|0.39330	7.764000|7.764000	0.85297|0.85297	1.968000|1.968000	0.57251|0.57251	0.402000|0.402000	0.26972|0.26972	TGT|GTG	.	.		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228525730	T	A	228525730	3	1	220	1	0	0	0	0	1	0	0	0	10821	1696	59	4	17148	4	OBSCN	1	228525730	Missense_Mutation	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10	2492722	228525730	20724891	14	31494										
FMN2	56776	hgsc.bcm.edu	37	chr1	240601508	240601508	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	aacaaacttcttctacaagaGaggtaggtattttcatttgc	7	7	3	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr1:240601508G>T	ENST00000319653.9	+	16	5288	c.5058G>T	c.(5056-5058)gaG>gaT	p.E1686D	FMN2_ENST00000545751.1_Missense_Mutation_p.E282D	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1686	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TTCTACAAGAGAGGTAGGTAT	0.388																																					p.E1686D		Atlas-SNP	.											FMN2,right_upper_lobe,carcinoma,0,1	FMN2	451	.	0			c.G5058T						.						97	97	97					1																	240601508		2203	4300	6503	SO:0001583	missense	56776	exon16			ACAAGAGAGGTAG	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.5058G>T	chr1.hg19:g.240601508G>T	ENSP00000318884:p.Glu1686Asp	50.0	0.0		81.0	18.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730557	0.48939	.	.	ENSG00000155816	ENST00000319653;ENST00000545751;ENST00000537355;ENST00000406993	T;T	0.53640	0.61;0.61	5.91	0.0799	0.14418	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (2);	0.000000	0.64402	D	0.000009	T	0.62183	0.2407	M	0.73598	2.24	0.80722	D	1	P;D;D	0.76494	0.7;0.999;0.964	B;D;P	0.78314	0.136;0.991;0.766	T	0.61686	-0.7012	10	0.66056	D	0.02	.	8.9729	0.35917	0.5826:0.0:0.4174:0.0	.	282;315;1686	B4DP05;B4DN09;Q9NZ56	.;.;FMN2_HUMAN	D	1686;282;313;162	ENSP00000318884:E1686D;ENSP00000437918:E282D	ENSP00000318884:E1686D	E	+	3	2	FMN2	238668131	0.998000	0.40836	0.999000	0.59377	0.989000	0.77384	0.465000	0.22004	0.103000	0.17682	0.579000	0.79373	GAG	.	.		0.388	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240601508	G	T	240601508	3	4	220	1	0	0	0	0	1	0	0	0	5958	933	33	3	5120	3	FMN2	1	240601508	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	12075778	240601508	8649113	15	31495										
STON1	11037	hgsc.bcm.edu	37	chr2	48822410	48822410	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	taaaatcgatggagaagaccCagataaaattggtgactgca	10	6	0	4			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:48822410C>T	ENST00000406226.1	+	5	2372	c.2177C>T	c.(2176-2178)cCa>cTa	p.P726L	STON1-GTF2A1L_ENST00000405008.1_Intron|STON1_ENST00000309835.3_Missense_Mutation_p.P726L|STON1_ENST00000404752.1_Missense_Mutation_p.P726L|STON1-GTF2A1L_ENST00000394754.1_Intron|STON1-GTF2A1L_ENST00000309827.2_Intron|STON1-GTF2A1L_ENST00000402114.2_Intron|STON1-GTF2A1L_ENST00000394751.3_Intron	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	726					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GGAGAAGACCCAGATAAAATT	0.398																																					p.P726L		Atlas-SNP	.											.	STON1	100	.	0			c.C2177T						.						125	113	117					2																	48822410		2203	4300	6503	SO:0001583	missense	11037	exon5			AAGACCCAGATAA	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.2177C>T	chr2.hg19:g.48822410C>T	ENSP00000384615:p.Pro726Leu	99.0	0.0		100.0	34.0	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Missense_Mutation	SNP	ENST00000406226.1	hg19	CCDS1841.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.508112	0.64410	.	.	ENSG00000243244	ENST00000404752;ENST00000406226;ENST00000309835	T;T;T	0.09255	3.0;3.0;3.0	4.9	4.9	0.64082	.	.	.	.	.	T	0.13114	0.0318	L	0.44542	1.39	0.80722	D	1	P	0.37423	0.594	B	0.38562	0.276	T	0.09952	-1.0651	9	0.25751	T	0.34	.	18.2553	0.90017	0.0:1.0:0.0:0.0	.	726	Q9Y6Q2	STON1_HUMAN	L	726	ENSP00000385273:P726L;ENSP00000384615:P726L;ENSP00000310969:P726L	ENSP00000310969:P726L	P	+	2	0	STON1	48675914	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.932000	0.70121	2.551000	0.86045	0.455000	0.32223	CCA	.	.		0.398	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		T	48822410	C	T	48822410	3	4	220	1	0	0	0	0	1	0	0	0	15331	594	21	3	2187	3	STON1	2	48822410	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10		48822410	194376963	16	31496										
AFTPH	54812	hgsc.bcm.edu	37	chr2	64808325	64808325	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	acggtcactgaatttcaagcTagtggaggttccactcttct	9	10	4	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:64808325T>G	ENST00000422803.1	+	8	2771	c.2457T>G	c.(2455-2457)gcT>gcG	p.A819A	AFTPH_ENST00000487769.1_Intron|AFTPH_ENST00000238856.4_Intron|RNU6-100P_ENST00000516605.1_RNA|AFTPH_ENST00000238855.7_Splice_Site_p.A819A|AFTPH_ENST00000409183.1_Splice_Site_p.A450A|AFTPH_ENST00000409933.1_Splice_Site_p.A819A			Q6ULP2	AFTIN_HUMAN	aftiphilin	819					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						AATTTCAAGCTAGTGGAGGTT	0.488																																					p.A819A		Atlas-SNP	.											.	AFTPH	117	.	0			c.T2457G						.						73	74	73					2																	64808325		1938	4149	6087	SO:0001630	splice_region_variant	54812	exon8			TCAAGCTAGTGGA	AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.2456-1T>G	chr2.hg19:g.64808325T>G		59.0	0.0		71.0	18.0	NM_203437	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Silent	SNP	ENST00000422803.1	hg19																																																																																				.	.		0.488	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657	Silent	G	64808325	T	G	64808325	5	3	220	1	0	0	0	0	0	0	1	0	364	1536	53	5	2483	5	AFTPH	2	64808325	Splice_Site	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10	15985915	64808325	178391048	17	31497										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80835353	80835353	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gatttattagcctaccttcaAcgaattgccttgtattgcca	6	10	1	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:80835353A>T	ENST00000402739.4	+	16	2345	c.2340A>T	c.(2338-2340)caA>caT	p.Q780H	AC008067.2_ENST00000430876.1_RNA|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000361291.4_Missense_Mutation_p.Q814H|AC008067.2_ENST00000609950.1_RNA|CTNNA2_ENST00000343114.3_Missense_Mutation_p.Q459H|AC008067.2_ENST00000595478.1_RNA|CTNNA2_ENST00000466387.1_Missense_Mutation_p.Q780H|AC008067.2_ENST00000599412.2_RNA|AC008067.2_ENST00000596783.1_RNA|CTNNA2_ENST00000541047.1_Missense_Mutation_p.Q780H|AC008067.2_ENST00000596887.1_RNA|CTNNA2_ENST00000496558.1_Missense_Mutation_p.Q780H	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	780					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CCTACCTTCAACGAATTGCCT	0.408																																					p.Q780H		Atlas-SNP	.											.	CTNNA2	462	.	0			c.A2340T						.						150	137	141					2																	80835353		1905	4152	6057	SO:0001583	missense	1496	exon17			CCTTCAACGAATT		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.2340A>T	chr2.hg19:g.80835353A>T	ENSP00000384638:p.Gln780His	52.0	0.0		65.0	32.0	NM_004389	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	A	15.75	2.927006	0.52759	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000343114	T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1	5.91	1.79	0.24919	.	0.000000	0.85682	D	0.000000	T	0.63153	0.2487	M	0.85630	2.765	0.80722	D	1	P;D;D	0.76494	0.941;0.999;0.991	P;D;D	0.77004	0.881;0.989;0.952	T	0.62015	-0.6943	9	.	.	.	.	9.5992	0.39593	0.4804:0.0:0.5196:0.0	.	412;780;780	F6KRI5;P26232;P26232-2	.;CTNA2_HUMAN;.	H	780;780;814;780;780;459	ENSP00000418191:Q780H;ENSP00000419295:Q780H;ENSP00000355398:Q814H;ENSP00000384638:Q780H;ENSP00000444675:Q780H;ENSP00000341500:Q459H	.	Q	+	3	2	CTNNA2	80688864	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.799000	0.38824	0.059000	0.16252	-0.261000	0.10672	CAA	.	.		0.408	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		T	80835353	A	T	80835353	3	4	220	1	0	0	0	0	1	0	0	0	4015	40	2	4	2194	4	CTNNA2	2	80835353	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	16027028	80835353	162364020	18	31498										
DPP10	57628	hgsc.bcm.edu	37	chr2	116525977	116525977	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	cacgtagctatgttcctcatCcaggtaagtgctggcttttt	9	10	1	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:116525977C>T	ENST00000410059.1	+	13	1698	c.1218C>T	c.(1216-1218)atC>atT	p.I406I	DPP10_ENST00000393147.2_Silent_p.I410I|DPP10_ENST00000310323.8_Silent_p.I399I|DPP10_ENST00000409163.1_Silent_p.I356I	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	406						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						TGTTCCTCATCCAGGTAAGTG	0.473																																					p.I410I		Atlas-SNP	.											.	DPP10	415	.	0			c.C1230T						.						128	123	125					2																	116525977		2203	4300	6503	SO:0001819	synonymous_variant	57628	exon13			CCTCATCCAGGTA	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1218C>T	chr2.hg19:g.116525977C>T		59.0	0.0		81.0	25.0	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Silent	SNP	ENST00000410059.1	hg19	CCDS46400.1																																																																																			.	.		0.473	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		T	116525977	C	T	116525977	2	4	220	1	0	0	0	0	0	0	0	1	4729	845	30	3		3	DPP10	2	116525977	Silent	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	35690624	116525977	126673396	19	31499										
MAP3K2	10746	hgsc.bcm.edu	37	chr2	128096589	128096589	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctggccttatgaaggacagcCaaatcttgcatgattgagtt	10	8	1	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:128096589C>A	ENST00000409947.1	-	3	324	c.42G>T	c.(40-42)ttG>ttT	p.L14F	MAP3K2_ENST00000344908.5_Missense_Mutation_p.L14F			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	14					activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	GAAGGACAGCCAAATCTTGCA	0.338																																					p.L14F		Atlas-SNP	.											.	MAP3K2	78	.	0			c.G42T						.						104	97	99					2																	128096589		1854	4092	5946	SO:0001583	missense	10746	exon2			GACAGCCAAATCT	AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6854	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 2"	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.42G>T	chr2.hg19:g.128096589C>A	ENSP00000387246:p.Leu14Phe	239.0	0.0		296.0	91.0	NM_006609	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Missense_Mutation	SNP	ENST00000409947.1	hg19	CCDS46404.1	.	.	.	.	.	.	.	.	.	.	C	34	5.343348	0.95783	.	.	ENSG00000169967	ENST00000409947;ENST00000344908;ENST00000409179	T;T	0.77229	-1.08;-1.08	6.11	6.11	0.99139	.	0.000000	0.85682	D	0.000000	D	0.88459	0.6442	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88123	0.2833	10	0.87932	D	0	.	20.3293	0.98710	0.0:1.0:0.0:0.0	.	14	Q9Y2U5	M3K2_HUMAN	F	14	ENSP00000387246:L14F;ENSP00000343463:L14F	ENSP00000343463:L14F	L	-	3	2	MAP3K2	127813059	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.318000	0.65829	2.906000	0.99361	0.655000	0.94253	TTG	.	.		0.338	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609		A	128096589	C	A	128096589	3	1	220	1	0	0	0	0	1	0	0	0	9259	593	21	3	1877	3	MAP3K2	2	128096589	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	11570612	128096589	115102784	20	31500										
TANC1	85461	hgsc.bcm.edu	37	chr2	160050974	160050974	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gctgctggccacatgaagctGgtgtgtctgctgaccaagaa	13	10	1	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:160050974G>A	ENST00000263635.6	+	17	3186	c.2949G>A	c.(2947-2949)ctG>ctA	p.L983L	TANC1_ENST00000454300.1_Silent_p.L877L	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	983					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						ACATGAAGCTGGTGTGTCTGC	0.542																																					p.L983L		Atlas-SNP	.											.	TANC1	157	.	0			c.G2949A						.						63	68	66					2																	160050974		2117	4230	6347	SO:0001819	synonymous_variant	85461	exon17			GAAGCTGGTGTGT	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29364	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.2949G>A	chr2.hg19:g.160050974G>A		61.0	0.0		91.0	25.0	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	hg19	CCDS42766.1																																																																																			.	.		0.542	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			A	160050974	G	A	160050974	2	1	220	1	0	0	0	0	0	0	0	1	15559	1335	47	3		3	TANC1	2	160050974	Silent	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	31954385	160050974	83148399	21	31501										
KIAA1715	80856	hgsc.bcm.edu	37	chr2	176802102	176802102	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctggttgtctgatgaaagcaCacttcctgatggcaagggac	12	9	1	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:176802102C>A	ENST00000272748.4	-	12	1271	c.1024G>T	c.(1024-1026)Gtg>Ttg	p.V342L	KIAA1715_ENST00000544803.1_Missense_Mutation_p.V373L|KIAA1715_ENST00000535310.1_Missense_Mutation_p.V267L	NM_030650.1	NP_085153.1	Q9C0E8	LNP_HUMAN	KIAA1715	342					blood coagulation (GO:0007596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|limb development (GO:0060173)|regulation of chondrocyte differentiation (GO:0032330)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)	20			OV - Ovarian serous cystadenocarcinoma(117;0.0793)			GATGAAAGCACACTTCCTGAT	0.393																																					p.V342L		Atlas-SNP	.											.	KIAA1715	61	.	0			c.G1024T						.						116	110	112					2																	176802102		2203	4300	6503	SO:0001583	missense	80856	exon12			AAAGCACACTTCC	AB051502	CCDS33332.1	2q31	2014-06-27			ENSG00000144320	ENSG00000144320			21610	protein-coding gene	gene with protein product	"lunapark", "limb and neural patterns"	610236				11214970, 22729086	Standard	NM_030650		Approved	ulnaless, Ul, LNP1, LNP	uc002ukc.1	Q9C0E8	OTTHUMG00000154112	ENST00000272748.4:c.1024G>T	chr2.hg19:g.176802102C>A	ENSP00000272748:p.Val342Leu	116.0	0.0		137.0	55.0	NM_030650	B7ZLA8|Q2M2V8|Q2YD99|Q658W8|Q8N5V9|Q96MS5	Missense_Mutation	SNP	ENST00000272748.4	hg19	CCDS33332.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.514965	0.27123	.	.	ENSG00000144320	ENST00000272748;ENST00000536291;ENST00000409660;ENST00000544803;ENST00000535310	.	.	.	5.31	-6.55	0.01854	.	1.488990	0.03628	N	0.237413	T	0.28962	0.0719	L	0.41236	1.265	0.09310	N	1	B;B;B;B	0.28850	0.225;0.001;0.144;0.0	B;B;B;B	0.23574	0.047;0.001;0.021;0.0	T	0.39461	-0.9613	9	0.87932	D	0	1.542	5.2422	0.15477	0.2154:0.3475:0.0:0.4371	.	344;373;339;342	F5H2Y7;B7ZLA8;B7ZLA9;Q9C0E8	.;.;.;LNP_HUMAN	L	342;344;219;373;267	.	ENSP00000272748:V342L	V	-	1	0	KIAA1715	176510348	.	.	0.903000	0.35520	0.791000	0.44710	.	.	-0.688000	0.05155	-0.469000	0.05056	GTG	.	.		0.393	KIAA1715-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333949.3	XM_042834		A	176802102	C	A	176802102	3	1	220	1	0	0	0	0	1	0	0	0	8263	478	17	3	270	3	KIAA1715	2	176802102	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	16751128	176802102	66397271	22	31502										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098966	178098966	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	acttactccaagatctatatCttgcctccaaagtatgtcaa	4	11	3	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:178098966C>A	ENST00000397062.3	-	2	633	c.79G>T	c.(79-81)Gat>Tat	p.D27Y	NFE2L2_ENST00000397063.4_Missense_Mutation_p.D11Y|NFE2L2_ENST00000423513.1_Missense_Mutation_p.D11Y|NFE2L2_ENST00000446151.2_Missense_Mutation_p.D11Y|NFE2L2_ENST00000464747.1_Missense_Mutation_p.D11Y	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	27					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D27Y(1)|p.D27H(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AGATCTATATCTTGCCTCCAA	0.353			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.D27Y		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,0,2	NFE2L2	225	.	2	Substitution - Missense(2)	lung(1)|oesophagus(1)	c.G79T						.						62	55	57					2																	178098966		1843	4100	5943	SO:0001583	missense	4780	exon2			CTATATCTTGCCT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.79G>T	chr2.hg19:g.178098966C>A	ENSP00000380252:p.Asp27Tyr	39.0	0.0		39.0	18.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.042196	0.75732	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.64327	0.2588	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.999;0.999	T	0.69087	-0.5238	10	0.87932	D	0	.	19.9976	0.97389	0.0:1.0:0.0:0.0	.	11;11;11;27	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	Y	11;27;11;11;11;11;11	ENSP00000380253:D11Y;ENSP00000380252:D27Y;ENSP00000411575:D11Y;ENSP00000391590:D11Y;ENSP00000400073:D11Y;ENSP00000412191:D11Y;ENSP00000410015:D11Y	ENSP00000380252:D27Y	D	-	1	0	NFE2L2	177807212	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.487000	0.81328	2.737000	0.93849	0.563000	0.77884	GAT	.	.		0.353	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		A	178098966	C	A	178098966	3	1	220	1	0	0	0	0	1	0	0	0	10377	913	32	3	1754	3	NFE2L2	2	178098966	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	1296864	178098966	65100407	23	31503										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198260907	198260907	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ttgaacattcagttcaggaaCtctgtattcattcattaagg	7	7	5	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:198260907C>G	ENST00000335508.6	-	23	3503	c.3412G>C	c.(3412-3414)Gtt>Ctt	p.V1138L		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	1138					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AGTTCAGGAACTCTGTATTCA	0.378			Mis		myelodysplastic syndrome																																p.V1138L		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.G3412C						.						171	163	166					2																	198260907		2203	4300	6503	SO:0001583	missense	23451	exon23			CAGGAACTCTGTA	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.3412G>C	chr2.hg19:g.198260907C>G	ENSP00000335321:p.Val1138Leu	231.0	0.0		267.0	98.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.65|19.65	3.867363|3.867363	0.72065|0.72065	.|.	.|.	ENSG00000115524|ENSG00000115524	ENST00000424674|ENST00000335508	.|.	.|.	.|.	5.93|5.93	5.93|5.93	0.95920|0.95920	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.71719|0.71719	0.3373|0.3373	M|M	0.70842|0.70842	2.15|2.15	0.80722|0.80722	D|D	1|1	.|B	.|0.24317	.|0.101	.|B	.|0.30646	.|0.118	T|T	0.68288|0.68288	-0.5448|-0.5448	5|9	.|0.56958	.|D	.|0.05	.|.	20.3539|20.3539	0.98825|0.98825	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1138	.|O75533	.|SF3B1_HUMAN	D|L	153|1138	.|.	.|ENSP00000335321:V1138L	E|V	-|-	3|1	2|0	SF3B1|SF3B1	197969152|197969152	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.743000|7.743000	0.85020|0.85020	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GAG|GTT	.	.		0.378	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			G	198260907	C	G	198260907	3	3	220	1	0	0	0	0	1	0	0	0	14164	565	20	4	514	4	SF3B1	2	198260907	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	20161941	198260907	44938466	24	31504										
SP140	11262	hgsc.bcm.edu	37	chr2	231109774	231109774	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gagatgctgaagatgcacccAgcctactaccaggtggggga	14	10	0	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:231109774A>T	ENST00000392045.3	+	6	757	c.643A>T	c.(643-645)Agc>Tgc	p.S215C	SP140_ENST00000420434.3_Missense_Mutation_p.S215C|SP140_ENST00000417495.3_Missense_Mutation_p.S215C|SP140_ENST00000350136.5_Missense_Mutation_p.S195C|SP140_ENST00000343805.6_Missense_Mutation_p.S215C|SP140_ENST00000486687.2_Missense_Mutation_p.S215C	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	215					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		AGATGCACCCAGCCTACTACC	0.443																																					p.S215C		Atlas-SNP	.											.	SP140	121	.	0			c.A643T						.						116	108	111					2																	231109774		1933	4144	6077	SO:0001583	missense	11262	exon6			GCACCCAGCCTAC	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.643A>T	chr2.hg19:g.231109774A>T	ENSP00000375899:p.Ser215Cys	41.0	0.0		59.0	21.0	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	hg19	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	A	12.10	1.837542	0.32513	.	.	ENSG00000079263	ENST00000486687;ENST00000392044;ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434	T;T;T;T;T	0.58797	0.55;0.75;0.61;0.31;0.54	2.59	0.15	0.14883	.	.	.	.	.	T	0.52821	0.1758	L	0.27053	0.805	0.09310	N	1	D;D;D;D;D	0.69078	0.989;0.987;0.992;0.997;0.987	P;B;P;P;P	0.61328	0.712;0.334;0.668;0.887;0.468	T	0.41088	-0.9528	9	0.30078	T	0.28	-0.4504	4.578	0.12243	0.6921:0.0:0.3079:0.0	.	215;215;215;215;215	E7EUR5;E7ESH9;E9PFJ6;Q13342;E7EX75	.;.;.;LY10_HUMAN;.	C	215;215;195;215;215;215;215	ENSP00000440107:S215C;ENSP00000345846:S195C;ENSP00000375899:S215C;ENSP00000342096:S215C;ENSP00000398210:S215C	ENSP00000342096:S215C	S	+	1	0	SP140	230818018	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.064000	0.14437	0.026000	0.15269	0.523000	0.50628	AGC	.	.		0.443	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		T	231109774	A	T	231109774	3	4	220	1	0	0	0	0	1	0	0	0	14977	188	7	4	782	4	SP140	2	231109774	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	32848867	231109774	12089599	25	31505										
CHRND	1144	hgsc.bcm.edu	37	chr2	233393032	233393032	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ttggaaacatcagtgtcctgCgcctccccccggacatggtg	11	14	1	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr2:233393032C>G	ENST00000258385.3	+	4	336	c.304C>G	c.(304-306)Cgc>Ggc	p.R102G	CHRND_ENST00000457943.2_Missense_Mutation_p.C11W|CHRND_ENST00000543200.1_Missense_Mutation_p.R87G|CHRND_ENST00000536614.1_Missense_Mutation_p.R102G	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)	102					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	CAGTGTCCTGCGCCTCCCCCC	0.577																																					p.R102G		Atlas-SNP	.											.	CHRND	67	.	0			c.C304G						.						118	115	116					2																	233393032		2203	4300	6503	SO:0001583	missense	1144	exon4			GTCCTGCGCCTCC	X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1965	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, delta (muscle)"	100720	"cholinergic receptor, nicotinic, delta"	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.304C>G	chr2.hg19:g.233393032C>G	ENSP00000258385:p.Arg102Gly	64.0	0.0		65.0	24.0	NM_000751	A8K661|B4DT92|Q52LH4	Missense_Mutation	SNP	ENST00000258385.3	hg19	CCDS2494.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.25|13.25	2.181467|2.181467	0.38511|0.38511	.|.	.|.	ENSG00000135902|ENSG00000135902	ENST00000457943|ENST00000449596;ENST00000543200;ENST00000258385;ENST00000536614	D|T;T;T;T	0.87809|0.80738	-2.3|-1.41;-1.41;-1.41;-1.41	4.4|4.4	3.52|3.52	0.40303|0.40303	.|Neurotransmitter-gated ion-channel ligand-binding (3);	.|0.225845	.|0.44902	.|D	.|0.000415	D|D	0.89550|0.89550	0.6747|0.6747	M|M	0.90198|0.90198	3.095|3.095	0.42608|0.42608	D|D	0.993302|0.993302	P|D;D	0.52463|0.89917	0.953|1.0;1.0	P|D;D	0.44990|0.97110	0.466|0.999;1.0	D|D	0.89562|0.89562	0.3807|0.3807	9|10	0.38643|0.87932	T|D	0.18|0	.|.	7.6629|7.6629	0.28413|0.28413	0.1622:0.7547:0.0:0.0831|0.1622:0.7547:0.0:0.0831	.|.	11|87;102	B4E3W4|B4DT92;Q07001	.|.;ACHD_HUMAN	W|G	11|87;87;102;102	ENSP00000391055:C11W|ENSP00000404950:R87G;ENSP00000438380:R87G;ENSP00000258385:R102G;ENSP00000437740:R102G	ENSP00000391055:C11W|ENSP00000258385:R102G	C|R	+|+	3|1	2|0	CHRND|CHRND	233101276|233101276	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.923000|0.923000	0.55619|0.55619	5.491000|5.491000	0.66887|0.66887	1.216000|1.216000	0.43427|0.43427	0.561000|0.561000	0.74099|0.74099	TGC|CGC	.	.		0.577	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2			G	233393032	C	G	233393032	3	3	220	1	0	0	0	0	1	0	0	0	3396	768	27	4	318	4	CHRND	2	233393032	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	2283258	233393032	9806341	26	31506										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	93.0	1.0		121.0	48.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	220	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10		41266136	156756294	27	31507										
ERC2	26059	hgsc.bcm.edu	37	chr3	55768826	55768826	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tttaattgatgtactagtcgGtctttttcccgcttgagggc	10	8	1	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr3:55768826G>C	ENST00000288221.6	-	15	2940	c.2685C>G	c.(2683-2685)gaC>gaG	p.D895E		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	895						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		GTACTAGTCGGTCTTTTTCCC	0.483																																					p.D893E		Atlas-SNP	.											.	ERC2	221	.	0			c.C2679G						.						107	101	103					3																	55768826		1872	4113	5985	SO:0001583	missense	26059	exon14			TAGTCGGTCTTTT	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2685C>G	chr3.hg19:g.55768826G>C	ENSP00000288221:p.Asp895Glu	79.0	0.0		126.0	44.0	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	hg19	CCDS46851.1	.	.	.	.	.	.	.	.	.	.	G	18.36	3.607851	0.66558	.	.	ENSG00000187672	ENST00000288221	T	0.46063	0.88	5.67	1.64	0.23874	.	0.000000	0.85682	D	0.000000	T	0.48169	0.1485	L	0.39245	1.2	0.42923	D	0.99429	D	0.63046	0.992	D	0.74348	0.983	T	0.28586	-1.0039	10	0.35671	T	0.21	-18.2625	7.9495	0.30006	0.3723:0.0:0.6277:0.0	.	895	O15083	ERC2_HUMAN	E	895	ENSP00000288221:D895E	ENSP00000288221:D895E	D	-	3	2	ERC2	55743866	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	3.536000	0.53582	-0.005000	0.14395	-0.140000	0.14226	GAC	.	.		0.483	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		C	55768826	G	C	55768826	3	2	220	1	0	0	0	0	1	0	0	0	5213	1252	44	4	200	4	ERC2	3	55768826	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	14502690	55768826	142253604	28	31508										
TOMM70A	9868	hgsc.bcm.edu	37	chr3	100105787	100105787	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gctttaaaatatttattgccTttattcttggctgcttgggc	8	7	1	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr3:100105787T>C	ENST00000284320.5	-	2	808	c.360A>G	c.(358-360)aaA>aaG	p.K120K		NM_014820.4	NP_055635.3	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70 homolog A (S. cerevisiae)	120					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			endometrium(11)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	32						ATTTATTGCCTTTATTCTTGG	0.363																																					p.K120K		Atlas-SNP	.											.	TOMM70A	65	.	0			c.A360G						.						109	103	105					3																	100105787		2203	4300	6503	SO:0001819	synonymous_variant	9868	exon2			ATTGCCTTTATTC	AB018262	CCDS33807.1	3q12.2	2013-01-10	2006-04-04		ENSG00000154174	ENSG00000154174		"Tetratricopeptide (TTC) repeat domain containing"	11985	protein-coding gene	gene with protein product		606081	"translocase of outer mitochondrial membrane 70 (yeast) homolog A", "translocase of outer mitochondrial membrane 70 homolog A (yeast)"			10582581	Standard	NM_014820		Approved	KIAA0719	uc003dtw.3	O94826	OTTHUMG00000159065	ENST00000284320.5:c.360A>G	chr3.hg19:g.100105787T>C		107.0	0.0		124.0	38.0	NM_014820	D3DN48	Silent	SNP	ENST00000284320.5	hg19	CCDS33807.1																																																																																			.	.		0.363	TOMM70A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353141.2			C	100105787	T	C	100105787	2	2	220	1	0	0	0	0	0	0	0	1	16377	1606	56	2		2	TOMM70A	3	100105787	Silent	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10	44336961	100105787	97916643	29	31509										
ARHGAP31	57514	hgsc.bcm.edu	37	chr3	119133155	119133155	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	cctccaactcctctggaggaGtcaactccagtcctgctttc	7	16	2	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr3:119133155G>C	ENST00000264245.4	+	12	2911	c.2379G>C	c.(2377-2379)gaG>gaC	p.E793D		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	793					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						CTCTGGAGGAGTCAACTCCAG	0.542																																					p.E793D	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.G2379C						.						53	56	55					3																	119133155		1902	4115	6017	SO:0001583	missense	57514	exon12			GGAGGAGTCAACT		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.2379G>C	chr3.hg19:g.119133155G>C	ENSP00000264245:p.Glu793Asp	82.0	0.0		103.0	43.0	NM_020754	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	hg19	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.101087	0.37048	.	.	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.07114	3.22	4.97	4.09	0.47781	.	0.466255	0.20808	N	0.085310	T	0.08846	0.0219	L	0.32530	0.975	0.41159	D	0.986081	D	0.56521	0.976	P	0.47206	0.541	T	0.01643	-1.1305	10	0.66056	D	0.02	.	7.9834	0.30196	0.0861:0.0:0.752:0.1619	.	793	Q2M1Z3	RHG31_HUMAN	D	793	ENSP00000264245:E793D	ENSP00000264245:E793D	E	+	3	2	ARHGAP31	120615845	0.254000	0.23992	0.971000	0.41717	0.160000	0.22226	0.435000	0.21510	2.757000	0.94681	0.655000	0.94253	GAG	.	.		0.542	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			C	119133155	G	C	119133155	3	2	220	1	0	0	0	0	1	0	0	0	880	1020	36	4	2425	4	ARHGAP31	3	119133155	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	19027368	119133155	78889275	30	31510										
ATR	545	hgsc.bcm.edu	37	chr3	142278092	142278092	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctgttgctaatttgtactcaCcttgcatataaatcaaagca	5	9	2	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr3:142278092C>A	ENST00000350721.4	-	7	1854		c.e7+1		ATR_ENST00000383101.3_Splice_Site	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase						cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TTTGTACTCACCTTGCATATA	0.353								Other conserved DNA damage response genes																													.		Atlas-SNP	.											.	ATR	285	.	0			c.1732+1G>T						.						79	79	79					3																	142278092		2203	4300	6503	SO:0001630	splice_region_variant	545	exon8			TACTCACCTTGCA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.1732+1G>T	chr3.hg19:g.142278092C>A		144.0	0.0		177.0	59.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Splice_Site	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.860451	0.71834	.	.	ENSG00000175054	ENST00000350721;ENST00000383101;ENST00000515149	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5553	0.91081	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATR	143760782	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.038000	0.64177	2.817000	0.96982	0.563000	0.77884	.	.	.		0.353	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	Intron	A	142278092	C	A	142278092	5	1	220	1	0	0	0	0	0	0	1	0	1204	521	18	3	6365	3	ATR	3	142278092	Splice_Site	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	23144937	142278092	55744338	31	31511										
DHX15	1665	hgsc.bcm.edu	37	chr4	24531339	24531339	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	agtagagggatgcaactgaaCcacctggttatctttcacag	10	9	2	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr4:24531339C>T	ENST00000336812.4	-	13	2311	c.2155G>A	c.(2155-2157)Gtt>Att	p.V719I	DHX15_ENST00000508032.1_5'UTR	NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	719					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	30		Breast(46;0.0503)				TGCAACTGAACCACCTGGTTA	0.388																																					p.V719I		Atlas-SNP	.											.	DHX15	69	.	0			c.G2155A						.						158	145	149					4																	24531339		2203	4300	6503	SO:0001583	missense	1665	exon13			ACTGAACCACCTG	AB001636	CCDS33966.1	4p15.3	2013-05-13	2013-05-13	2003-06-20	ENSG00000109606	ENSG00000109606		"DEAH-boxes"	2738	protein-coding gene	gene with protein product		603403	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15", "DEAH (Asp-Glu-Ala-His) box polypeptide 15"	DDX15		9388478	Standard	NM_001358		Approved	HRH2, DBP1, PRP43, PrPp43p, PRPF43	uc003gqx.3	O43143	OTTHUMG00000160304	ENST00000336812.4:c.2155G>A	chr4.hg19:g.24531339C>T	ENSP00000336741:p.Val719Ile	147.0	0.0		141.0	40.0	NM_001358	Q9NQT7	Missense_Mutation	SNP	ENST00000336812.4	hg19	CCDS33966.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.963405	0.92791	.	.	ENSG00000109606	ENST00000336812;ENST00000535946	T	0.03772	3.81	5.83	4.96	0.65561	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.29652	0.0740	M	0.91249	3.19	0.80722	D	1	D;D;D	0.58268	0.982;0.982;0.977	D;D;D	0.91635	0.999;0.999;0.998	T	0.13845	-1.0494	10	0.87932	D	0	-19.199	17.0234	0.86440	0.0:0.8733:0.1267:0.0	.	719;708;708	O43143;B4E0S6;F5H6K0	DHX15_HUMAN;.;.	I	719;708	ENSP00000336741:V719I	ENSP00000336741:V719I	V	-	1	0	DHX15	24140437	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.426000	0.80270	2.749000	0.94314	0.650000	0.86243	GTT	.	.		0.388	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1	NM_001358		T	24531339	C	T	24531339	3	4	220	1	0	0	0	0	1	0	0	0	4503	507	18	3	240	3	DHX15	4	24531339	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10		24531339	166622937	32	31512										
TBCK	93627	hgsc.bcm.edu	37	chr4	107133975	107133975	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	atgaaatgcaatcatctgagAgaagacagtcagatactctg	9	7	4	5			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr4:107133975A>T	ENST00000273980.5	-	21	2239	c.1792T>A	c.(1792-1794)Tct>Act	p.S598T	TBCK_ENST00000514689.1_5'UTR|TBCK_ENST00000394708.2_Missense_Mutation_p.S598T|TBCK_ENST00000394706.3_Missense_Mutation_p.S559T|TBCK_ENST00000361687.4_Missense_Mutation_p.S535T|TBCK_ENST00000432496.2_Missense_Mutation_p.S598T					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						ATCATCTGAGAGAAGACAGTC	0.323																																					p.S598T		Atlas-SNP	.											.	TBCK	89	.	0			c.T1792A						.						135	142	139					4																	107133975		2203	4299	6502	SO:0001583	missense	93627	exon20			TCTGAGAGAAGAC		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1792T>A	chr4.hg19:g.107133975A>T	ENSP00000273980:p.Ser598Thr	344.0	0.0		406.0	126.0	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	hg19	CCDS54788.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.228967	0.79688	.	.	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394706;ENST00000394708	T;T;T;T;T	0.11385	2.78;2.78;2.78;2.78;2.78	5.25	5.25	0.73442	Rab-GAP/TBC domain (5);	0.000000	0.85682	D	0.000000	T	0.33847	0.0877	M	0.78637	2.42	0.80722	D	1	D;D;D	0.76494	0.987;0.999;0.995	D;D;D	0.85130	0.926;0.997;0.966	T	0.04811	-1.0925	10	0.35671	T	0.21	.	15.4434	0.75208	1.0:0.0:0.0:0.0	.	598;559;535	Q8TEA7;Q8TEA7-2;Q8TEA7-3	TBCK_HUMAN;.;.	T	598;598;535;559;598	ENSP00000273980:S598T;ENSP00000405847:S598T;ENSP00000355338:S535T;ENSP00000378196:S559T;ENSP00000378198:S598T	ENSP00000273980:S598T	S	-	1	0	TBCK	107353424	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.798000	0.91888	2.105000	0.64084	0.402000	0.26972	TCT	.	.		0.323	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		T	107133975	A	T	107133975	3	4	220	1	0	0	0	0	1	0	0	0	15651	304	11	4	917	4	TBCK	4	107133975	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	82602636	107133975	84020301	33	31513										
ANK2	287	hgsc.bcm.edu	37	chr4	114276434	114276434	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ccgtgtggcagcctgatggaGgggacccctcagattagttc	14	11	1	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr4:114276434G>A	ENST00000357077.4	+	38	6713	c.6660G>A	c.(6658-6660)gaG>gaA	p.E2220E	ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Silent_p.E2187E	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2220					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GCCTGATGGAGGGGACCCCTC	0.507																																					p.E2220E		Atlas-SNP	.											.	ANK2	576	.	0			c.G6660A						.						63	67	66					4																	114276434		2203	4299	6502	SO:0001819	synonymous_variant	287	exon38			GATGGAGGGGACC	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.6660G>A	chr4.hg19:g.114276434G>A		103.0	0.0		121.0	56.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.		0.507	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114276434	G	A	114276434	2	1	220	1	0	0	0	0	0	0	0	1	621	991	35	3		3	ANK2	4	114276434	Silent	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	7142459	114276434	76877842	34	31514										
MAP9	79884	hgsc.bcm.edu	37	chr4	156294546	156294546	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	atcatctgatatatgaaagtCattcatttttttattaactg	4	5	4	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr4:156294546C>T	ENST00000311277.4	-	4	486	c.223G>A	c.(223-225)Gac>Aac	p.D75N	MAP9_ENST00000379248.2_Missense_Mutation_p.D3N|MAP9_ENST00000515654.1_Missense_Mutation_p.D75N|AC097467.2_ENST00000596165.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	75					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		ATATGAAAGTCATTCATTTTT	0.284																																					p.D75N		Atlas-SNP	.											.	MAP9	79	.	0			c.G223A						.						42	44	43					4																	156294546		2201	4299	6500	SO:0001583	missense	79884	exon4			GAAAGTCATTCAT	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"aster-associated protein"	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.223G>A	chr4.hg19:g.156294546C>T	ENSP00000310593:p.Asp75Asn	69.0	0.0		67.0	29.0	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	hg19	CCDS35493.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.908378	0.33721	.	.	ENSG00000164114	ENST00000311277;ENST00000515654;ENST00000433024;ENST00000393836;ENST00000379248	T;T;T;T	0.09163	3.01;3.01;3.01;3.01	5.96	4.24	0.50183	.	0.302802	0.29900	N	0.010904	T	0.07098	0.0180	L	0.29908	0.895	0.39412	D	0.966767	B;P;B;B	0.45474	0.36;0.859;0.197;0.197	B;B;B;B	0.38458	0.139;0.274;0.062;0.062	T	0.40496	-0.9560	10	0.25751	T	0.34	-19.153	8.2369	0.31631	0.0:0.8262:0.0:0.1738	.	75;3;75;75	B4DVG9;A8MSM7;B9EJB6;Q49MG5	.;.;.;MAP9_HUMAN	N	75;75;75;75;3	ENSP00000310593:D75N;ENSP00000427402:D75N;ENSP00000394048:D75N;ENSP00000368550:D3N	ENSP00000310593:D75N	D	-	1	0	MAP9	156513996	1.000000	0.71417	1.000000	0.80357	0.637000	0.38172	1.397000	0.34543	1.540000	0.49301	0.650000	0.86243	GAC	.	.		0.284	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580		T	156294546	C	T	156294546	3	4	220	1	0	0	0	0	1	0	0	0	9279	826	29	3	1764	3	MAP9	4	156294546	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	42018112	156294546	34859730	35	31515										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33546183	33546183	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ccaggtcccagttcccagtgGcccagtgacagcacaggtgc	12	15	0	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr5:33546183G>T	ENST00000504830.1	-	22	4762	c.4427C>A	c.(4426-4428)gCc>gAc	p.A1476D	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.A1391D	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1476	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GTTCCCAGTGGCCCAGTGACA	0.438										HNSCC(64;0.19)																											p.A1476D		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.C4427A						.						118	104	108					5																	33546183		2203	4300	6503	SO:0001583	missense	81792	exon22			CCAGTGGCCCAGT	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.4427C>A	chr5.hg19:g.33546183G>T	ENSP00000422554:p.Ala1476Asp	254.0	0.0		292.0	87.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.971821	0.34754	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.60797	0.16;0.16	5.36	1.05	0.20165	.	0.678921	0.15277	N	0.270899	T	0.53594	0.1806	L	0.47016	1.485	0.58432	D	0.999999	P;P	0.44429	0.835;0.78	P;P	0.49387	0.474;0.609	T	0.46693	-0.9173	10	0.38643	T	0.18	.	6.0968	0.20025	0.4981:0.0:0.5019:0.0	.	1391;1476	P58397-3;P58397	.;ATS12_HUMAN	D	1476;1391	ENSP00000422554:A1476D;ENSP00000344847:A1391D	ENSP00000344847:A1391D	A	-	2	0	ADAMTS12	33581940	0.001000	0.12720	0.995000	0.50966	0.794000	0.44872	0.333000	0.19768	0.277000	0.22141	-0.136000	0.14681	GCC	.	.		0.438	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		T	33546183	G	T	33546183	3	4	220	1	0	0	0	0	1	0	0	0	257	1203	42	3	369	3	ADAMTS12	5	33546183	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10		33546183	147369077	36	31516										
CATSPER3	347732	hgsc.bcm.edu	37	chr5	134332010	134332010	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tgcacatctgagttgtccatGaaggtctatgtggaccccat	10	10	2	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr5:134332010G>T	ENST00000282611.6	+	3	386	c.300G>T	c.(298-300)atG>atT	p.M100I		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	100					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGTTGTCCATGAAGGTCTATG	0.498																																					p.M100I		Atlas-SNP	.											.	CATSPER3	38	.	0			c.G300T						.						250	202	218					5																	134332010		2203	4300	6503	SO:0001583	missense	347732	exon3			GTCCATGAAGGTC	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"Voltage-gated ion channels / Cation channels, sperm associated"	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.300G>T	chr5.hg19:g.134332010G>T	ENSP00000282611:p.Met100Ile	50.0	0.0		45.0	12.0	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	hg19	CCDS4181.1	.	.	.	.	.	.	.	.	.	.	G	3.571	-0.087564	0.07097	.	.	ENSG00000152705	ENST00000282611	D	0.98105	-4.72	4.14	1.2	0.21068	Ion transport (1);	0.319638	0.27912	N	0.017350	D	0.92763	0.7699	N	0.22421	0.69	0.28707	N	0.903763	B	0.21520	0.057	B	0.20955	0.032	D	0.86640	0.1891	10	0.39692	T	0.17	-21.4185	7.3255	0.26553	0.0:0.356:0.4605:0.1834	.	100	Q86XQ3	CTSR3_HUMAN	I	100	ENSP00000282611:M100I	ENSP00000282611:M100I	M	+	3	0	CATSPER3	134359909	0.999000	0.42202	0.742000	0.31022	0.008000	0.06430	0.525000	0.22956	0.241000	0.21283	0.561000	0.74099	ATG	.	.		0.498	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019		T	134332010	G	T	134332010	3	4	220	1	0	0	0	0	1	0	0	0	2691	1290	45	3	310	3	CATSPER3	5	134332010	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	100785827	134332010	46583250	37	31517										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33145004	33145004	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	cctggggcccgggaagacccTacatacagggaaagagaagt	14	10	0	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr6:33145004T>C	ENST00000374708.4	-	22	1972		c.e22-2		COL11A2_ENST00000374713.1_Splice_Site|COL11A2_ENST00000374712.1_Splice_Site|COL11A2_ENST00000395197.1_Splice_Site|COL11A2_ENST00000357486.1_Splice_Site|COL11A2_ENST00000374714.1_Splice_Site|COL11A2_ENST00000477772.1_Splice_Site|COL11A2_ENST00000341947.2_Splice_Site|COL11A2_ENST00000361917.1_Splice_Site	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2						cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						GGGAAGACCCTACATACAGGG	0.547																																					.	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.1714-2A>G						.						42	50	47					6																	33145004		1507	2706	4213	SO:0001630	splice_region_variant	1302	exon23			AGACCCTACATAC	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.1714-2A>G	chr6.hg19:g.33145004T>C		69.0	0.0		132.0	72.0	NM_080681	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Splice_Site	SNP	ENST00000374708.4	hg19	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	T	11.73	1.726066	0.30593	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917;ENST00000395196	.	.	.	4.16	4.16	0.48862	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.5266	0.39169	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL11A2	33252982	1.000000	0.71417	0.953000	0.39169	0.287000	0.27160	6.195000	0.72088	1.755000	0.51935	0.523000	0.50628	.	.	.		0.547	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		Intron	C	33145004	T	C	33145004	5	2	220	1	0	0	0	0	0	0	1	0	3670	1536	53	2	3412	2	COL11A2	6	33145004	Splice_Site	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10		33145004	137970063	38	31518										
CRIP3	401262	hgsc.bcm.edu	37	chr6	43274045	43274046	+	Missense_Mutation	DNP	TT	TT	AC													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ttctgcctaatgacatcaccTtctcagctggtggtggaaag							TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr6:43274045_43274046TT>AC	ENST00000274990.4	-	6	410_411	c.406_407AA>GT	c.(406-408)AAg>GTg	p.K136V	ZNF318_ENST00000607252.1_5'Flank|CRIP3_ENST00000372569.3_Missense_Mutation_p.K136V			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	136	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			TGACATCACCTTCTCAGCTGGT	0.569																																					p.K136M|p.K136E		Atlas-SNP	.											.	CRIP3	30	.	0			c.A407T|c.A406G						.																																			SO:0001583	missense	401262	exon6			ATCACCTTCTCAG|TCACCTTCTCAGC	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.406_407delinsAC	chr6.hg19:g.43274045_43274046delinsAC	ENSP00000274990:p.Lys136Val	51.0|50.0	0.0		133.0	17.0|16.0	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	hg19																																																																																				.	.		0.569	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			AC	43274046	TT	AC	43274045	3	1	220	1	0	0	0	0	1	0	0	0	3878	1609	56	4	219	4	CRIP3	6	43274045	Missense_Mutation	DNP	TT	TCGA-DD-AAEH-01A-11D-A40R-10	10129041	43274045	127841022	39	31519										
GTPBP2	54676	hgsc.bcm.edu	37	chr6	43592642	43592642	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	taccaatcccagtgttggcaCtgacgaggagcagggcgcag	14	11	0	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr6:43592642C>A	ENST00000307126.5	-	6	862	c.863G>T	c.(862-864)aGt>aTt	p.S288I	GTPBP2_ENST00000307114.7_Missense_Mutation_p.S200I|GTPBP2_ENST00000476510.1_5'UTR	NM_019096.3	NP_061969.3			GTP binding protein 2											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			AGTGTTGGCACTGACGAGGAG	0.572																																					p.S288I	GBM(116;405 1620 28302 32150 44768)	Atlas-SNP	.											.	GTPBP2	39	.	0			c.G863T						.						160	129	140					6																	43592642		2203	4300	6503	SO:0001583	missense	54676	exon6			TTGGCACTGACGA	AB024574	CCDS4903.1, CCDS69124.1	6p21	2008-07-28			ENSG00000172432	ENSG00000172432			4670	protein-coding gene	gene with protein product		607434				10833435, 11054535	Standard	NM_019096		Approved		uc003ovs.3	Q9BX10	OTTHUMG00000014744	ENST00000307126.5:c.863G>T	chr6.hg19:g.43592642C>A	ENSP00000303997:p.Ser288Ile	69.0	0.0		140.0	30.0	NM_019096		Missense_Mutation	SNP	ENST00000307126.5	hg19	CCDS4903.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.3|24.3	4.514749|4.514749	0.85389|0.85389	.|.	.|.	ENSG00000172432|ENSG00000172432	ENST00000307126;ENST00000307114|ENST00000442748	T;T|.	0.48201|.	0.82;0.82|.	5.41|5.41	5.41|5.41	0.78517|0.78517	Protein synthesis factor, GTP-binding (1);|.	0.044177|.	0.85682|.	D|.	0.000000|.	D|D	0.85531|0.85531	0.5718|0.5718	M|M	0.93241|0.93241	3.395|3.395	0.80722|0.80722	D|D	1|1	D;P|.	0.63880|.	0.993;0.918|.	P;P|.	0.59889|.	0.865;0.522|.	D|D	0.89075|0.89075	0.3472|0.3472	10|5	0.87932|.	D|.	0|.	-9.4257|-9.4257	19.1891|19.1891	0.93656|0.93656	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	280;288|.	Q9BX10-4;Q9BX10|.	.;GTPB2_HUMAN|.	I|L	288;200|254	ENSP00000303997:S288I;ENSP00000304893:S200I|.	ENSP00000304893:S200I|.	S|V	-|-	2|1	0|0	GTPBP2|GTPBP2	43700620|43700620	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.042000|6.042000	0.70996|0.70996	2.521000|2.521000	0.84997|0.84997	0.555000|0.555000	0.69702|0.69702	AGT|GTG	.	.		0.572	GTPBP2-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040679.1			A	43592642	C	A	43592642	3	1	220	1	0	0	0	0	1	0	0	0	6889	565	20	3	973	3	GTPBP2	6	43592642	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	318597	43592642	127522425	40	31520										
CARD11	84433	hgsc.bcm.edu	37	chr7	2978336	2978336	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gtctcgcagctcctctgcctGgcgggcctcctcctgcaggt	12	17	2	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr7:2978336G>A	ENST00000396946.4	-	7	1397	c.994C>T	c.(994-996)Cag>Tag	p.Q332*		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	332					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TCCTCTGCCTGGCGGGCCTCC	0.667			Mis		DLBCL																																p.Q332X		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.C994T						.						59	46	50					7																	2978336		2203	4300	6503	SO:0001587	stop_gained	84433	exon7			CTGCCTGGCGGGC	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.994C>T	chr7.hg19:g.2978336G>A	ENSP00000380150:p.Gln332*	29.0	0.0		35.0	12.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Nonsense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	43	9.848978	0.99279	.	.	ENSG00000198286	ENST00000396946	.	.	.	5.72	5.72	0.89469	.	0.116020	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-57.327	18.8612	0.92273	0.0:0.0:1.0:0.0	.	.	.	.	X	332	.	ENSP00000380150:Q332X	Q	-	1	0	CARD11	2944862	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	9.644000	0.98468	2.690000	0.91761	0.591000	0.81541	CAG	.	.		0.667	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2978336	G	A	2978336	4	1	220	1	0	0	0	0	0	1	0	0	2647	1357	47	3	2546	3	CARD11	7	2978336	Nonsense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10		2978336	156160327	41	31521										
HNRNPA2B1	3181	hgsc.bcm.edu	37	chr7	26232938	26232940	+	In_Frame_Del	DEL	AGA	AGA	-													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctcttcattggaccgtagttAgaaggttgctggttataatt							TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr7:26232938_26232940delAGA	ENST00000354667.4	-	10	1099_1101	c.931_933delTCT	c.(931-933)tctdel	p.S311del	HNRNPA2B1_ENST00000356674.7_In_Frame_Del_p.S299del|HNRNPA2B1_ENST00000476233.1_5'Flank	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	311	Gly-rich.|Nuclear targeting sequence. {ECO:0000250}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|RNA binding (GO:0003723)|single-stranded telomeric DNA binding (GO:0043047)		HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22						GACCGTAGTTAGAAGGTTGCTGG	0.34			T	ETV1	prostate																																p.311_312del		Atlas-INDEL	.		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	.	HNRNPA2B1	70	.	0			c.932_934del						.																																			SO:0001651	inframe_deletion	3181	exon10			.	D28877	CCDS5397.1, CCDS43557.1	7p15	2013-02-12		2007-08-16	ENSG00000122566	ENSG00000122566		"RNA binding motif (RRM) containing"	5033	protein-coding gene	gene with protein product		600124		HNRPA2B1		8029005	Standard	NM_002137		Approved		uc003sxr.4	P22626	OTTHUMG00000023471	ENST00000354667.4:c.931_933delTCT	chr7.hg19:g.26232938_26232940delAGA	ENSP00000346694:p.Ser311del	89.0	0.0		93.0	33.0	NM_031243	A8K064|P22627|Q9UC98|Q9UDJ2	In_Frame_Del	DEL	ENST00000354667.4	hg19	CCDS43557.1																																																																																			.	.		0.34	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137		-	26232940	AGA	-	26232938	7	5	220	1	0	1	0	1	0	0	0	0	7268	407	15	0	136	0	HNRNPA2B1	7	26232938	In_Frame_Del	DEL	AGA	TCGA-DD-AAEH-01A-11D-A40R-10	23254602	26232938	132905725	42	31522										
PCLO	27445	hgsc.bcm.edu	37	chr7	82582023	82582023	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ttttcacatccattgtagaaGcagaaagatcaatacattta	5	7	2	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr7:82582023G>T	ENST00000333891.9	-	5	8583	c.8246C>A	c.(8245-8247)gCt>gAt	p.A2749D	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Missense_Mutation_p.A2749D	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CATTGTAGAAGCAGAAAGATC	0.343																																					p.A2749D		Atlas-SNP	.											.	PCLO	1506	.	0			c.C8246A						.						76	74	74					7																	82582023		1883	4115	5998	SO:0001583	missense	27445	exon5			GTAGAAGCAGAAA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.8246C>A	chr7.hg19:g.82582023G>T	ENSP00000334319:p.Ala2749Asp	87.0	0.0		132.0	49.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	8.910	0.958378	0.18507	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19669	2.13;2.15	5.54	3.68	0.42216	.	.	.	.	.	T	0.21761	0.0524	L	0.54323	1.7	0.80722	D	1	B;B	0.17667	0.023;0.023	B;B	0.16722	0.016;0.016	T	0.05886	-1.0858	9	0.87932	D	0	.	10.836	0.46688	0.069:0.0:0.8019:0.1291	.	2749;2749	Q9Y6V0-5;Q9Y6V0-6	.;.	D	2680;2749;2749	ENSP00000334319:A2749D;ENSP00000388393:A2749D	ENSP00000334319:A2749D	A	-	2	0	PCLO	82419959	1.000000	0.71417	0.862000	0.33874	0.729000	0.41735	7.605000	0.82844	1.289000	0.44618	0.655000	0.94253	GCT	.	.		0.343	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82582023	G	T	82582023	3	4	220	1	0	0	0	0	1	0	0	0	11592	971	34	3	7283	3	PCLO	7	82582023	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	56349085	82582023	76556640	43	31523										
ZNF746	155061	hgsc.bcm.edu	37	chr7	149172236	149172236	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctcgggccccgtcctcgggtTcaggcccactggcggtttac	13	16	1	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr7:149172236T>A	ENST00000340622.3	-	7	1454	c.1174A>T	c.(1174-1176)Aac>Tac	p.N392Y	ZNF746_ENST00000458143.2_Missense_Mutation_p.N393Y			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	392					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			GTCCTCGGGTTCAGGCCCACT	0.667																																					p.N393Y		Atlas-SNP	.											.	ZNF746	68	.	0			c.A1177T						.						13	16	15					7																	149172236		2194	4294	6488	SO:0001583	missense	155061	exon7			TCGGGTTCAGGCC	AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"Zinc fingers, C2H2-type", "-"	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.1174A>T	chr7.hg19:g.149172236T>A	ENSP00000345140:p.Asn392Tyr	61.0	0.0		69.0	22.0	NM_001163474	A8K6Z9|Q6ZRF9	Missense_Mutation	SNP	ENST00000340622.3	hg19	CCDS5897.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.526436	0.44969	.	.	ENSG00000181220	ENST00000340622;ENST00000458143	T;T	0.08546	3.12;3.08	4.29	3.04	0.35103	.	0.505055	0.16524	N	0.210677	T	0.09158	0.0226	N	0.19112	0.55	0.24917	N	0.992001	P;P	0.49447	0.924;0.875	P;P	0.51135	0.66;0.459	T	0.12016	-1.0564	10	0.87932	D	0	-24.0345	8.3079	0.32053	0.0:0.0:0.2162:0.7838	.	393;392	Q6NUN9-2;Q6NUN9	.;ZN746_HUMAN	Y	392;393	ENSP00000345140:N392Y;ENSP00000395007:N393Y	ENSP00000345140:N392Y	N	-	1	0	ZNF746	148803169	0.045000	0.20229	1.000000	0.80357	0.707000	0.40811	0.701000	0.25616	1.561000	0.49584	0.460000	0.39030	AAC	.	.		0.667	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557		A	149172236	T	A	149172236	3	1	220	1	0	0	0	0	1	0	0	0	18144	1783	62	4	764	4	ZNF746	7	149172236	Missense_Mutation	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10	66590213	149172236	9966427	44	31524										
CPSF1	29894	hgsc.bcm.edu	37	chr8	145625402	145625402	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	atctcgccgcccttgagggaGatgaccatcttgtcgtagga	12	11	2	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr8:145625402G>C	ENST00000349769.3	-	10	1105	c.1011C>G	c.(1009-1011)atC>atG	p.I337M	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	337					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CCTTGAGGGAGATGACCATCT	0.662																																					p.I337M	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.C1011G						.						29	25	26					8																	145625402		2202	4299	6501	SO:0001583	missense	29894	exon10			GAGGGAGATGACC	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1011C>G	chr8.hg19:g.145625402G>C	ENSP00000339353:p.Ile337Met	100.0	0.0		147.0	26.0	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	hg19	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803477	0.70682	.	.	ENSG00000071894	ENST00000349769	T	0.54479	0.57	5.67	4.79	0.61399	.	0.050507	0.85682	D	0.000000	T	0.64427	0.2597	L	0.61218	1.895	0.58432	D	0.999995	D;P	0.67145	0.996;0.933	D;P	0.66602	0.945;0.739	T	0.64972	-0.6281	10	0.49607	T	0.09	-6.1594	8.5164	0.33248	0.1743:0.0:0.8257:0.0	.	259;337	D3DWL9;Q10570	.;CPSF1_HUMAN	M	337	ENSP00000339353:I337M	ENSP00000339353:I337M	I	-	3	3	CPSF1	145596210	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.349000	0.52217	1.392000	0.46585	0.555000	0.69702	ATC	.	.		0.662	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		C	145625402	G	C	145625402	3	2	220	1	0	0	0	0	1	0	0	0	3826	932	33	4	3436	4	CPSF1	8	145625402	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10		145625402	738620	45	31525										
MAPKAP1	79109	hgsc.bcm.edu	37	chr9	128305415	128305415	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tggtaacctttgtgttgtccAcctgaataagggagaatcca	10	8	0	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr9:128305415A>G	ENST00000373498.1	-	6	949	c.881T>C	c.(880-882)gTg>gCg	p.V294A	MAPKAP1_ENST00000373511.2_Missense_Mutation_p.V294A|MAPKAP1_ENST00000394060.3_Missense_Mutation_p.V294A|MAPKAP1_ENST00000394063.1_Missense_Mutation_p.V102A|MAPKAP1_ENST00000265960.3_Missense_Mutation_p.V294A|MAPKAP1_ENST00000350766.3_Missense_Mutation_p.V294A|MAPKAP1_ENST00000373497.5_Missense_Mutation_p.V43A|MAPKAP1_ENST00000373503.3_Missense_Mutation_p.V102A			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	294					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						TGTGTTGTCCACCTGAATAAG	0.388																																					p.V294A		Atlas-SNP	.											.	MAPKAP1	68	.	0			c.T881C						.						164	155	158					9																	128305415		2203	4300	6503	SO:0001583	missense	79109	exon7			TTGTCCACCTGAA	M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487			18752	protein-coding gene	gene with protein product	"stress-activated protein kinase-interacting 1"	610558				15363842	Standard	NM_001006620		Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000373498.1:c.881T>C	chr9.hg19:g.128305415A>G	ENSP00000362597:p.Val294Ala	96.0	0.0		116.0	26.0	NM_001006618	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Missense_Mutation	SNP	ENST00000373498.1	hg19	CCDS35140.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824362	0.50739	.	.	ENSG00000119487	ENST00000373511;ENST00000350766;ENST00000373503;ENST00000373498;ENST00000265960;ENST00000394063;ENST00000373497;ENST00000420643;ENST00000394060;ENST00000427078	.	.	.	5.8	5.8	0.92144	.	0.053174	0.85682	D	0.000000	T	0.54191	0.1843	L	0.58428	1.81	0.80722	D	1	P;P;P;P;P	0.48503	0.679;0.739;0.911;0.66;0.583	B;B;B;B;B	0.42593	0.335;0.164;0.392;0.214;0.345	T	0.52888	-0.8515	9	0.16420	T	0.52	-1.7411	14.7322	0.69391	1.0:0.0:0.0:0.0	.	43;294;294;294;294	B7Z5E5;Q9BPZ7-5;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7	.;.;.;.;SIN1_HUMAN	A	294;294;102;294;294;102;43;102;294;102	.	ENSP00000265960:V294A	V	-	2	0	MAPKAP1	127345236	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.406000	0.90216	2.213000	0.71641	0.477000	0.44152	GTG	.	.		0.388	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1			G	128305415	A	G	128305415	3	3	220	1	0	0	0	0	1	0	0	0	9297	159	6	2	729	2	MAPKAP1	9	128305415	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10		128305415	12908016	46	31526										
ADAMTS13	11093	hgsc.bcm.edu	37	chr9	136308565	136308565	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	cctgcgggagcggccagtgcGctgcgtggaggcccagggca	19	13	0	0	rs369510827		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr9:136308565G>T	ENST00000371929.3	+	19	2747	c.2303G>T	c.(2302-2304)cGc>cTc	p.R768L	ADAMTS13_ENST00000356589.2_Missense_Mutation_p.R737L|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.R768L|ADAMTS13_ENST00000536611.1_Intron|ADAMTS13_ENST00000485925.1_Intron|ADAMTS13_ENST00000371916.1_3'UTR	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	768	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CGGCCAGTGCGCTGCGTGGAG	0.716																																					p.R768L		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.G2303T						.						9	10	9					9																	136308565		2175	4261	6436	SO:0001583	missense	11093	exon19			CAGTGCGCTGCGT	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"ADAM metallopeptidases with thrombospondin type 1 motif"	1366	protein-coding gene	gene with protein product		604134	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.2303G>T	chr9.hg19:g.136308565G>T	ENSP00000360997:p.Arg768Leu	101.0	0.0		129.0	32.0	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	hg19	CCDS6970.1	.	.	.	.	.	.	.	.	.	.	g	2.138	-0.397487	0.04899	.	.	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589	T;T;T	0.59772	0.66;0.24;0.24	4.74	-0.549	0.11829	.	.	.	.	.	T	0.46698	0.1406	L	0.34521	1.04	0.09310	N	0.999997	D;B;P	0.54397	0.966;0.333;0.851	P;B;P	0.56343	0.796;0.184;0.619	T	0.38757	-0.9646	9	0.06625	T	0.88	.	1.259	0.01997	0.2445:0.1155:0.4045:0.2355	.	768;737;768	Q76LX8;Q76LX8-3;Q76LX8-2	ATS13_HUMAN;.;.	L	768;768;737	ENSP00000360997:R768L;ENSP00000347927:R768L;ENSP00000348997:R737L	ENSP00000347927:R768L	R	+	2	0	ADAMTS13	135298386	0.000000	0.05858	0.001000	0.08648	0.501000	0.33797	-0.698000	0.05092	-0.770000	0.04614	-1.326000	0.01283	CGC	.	.		0.716	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025		T	136308565	G	T	136308565	3	4	220	1	0	0	0	0	1	0	0	0	258	1087	38	1	2377	1	ADAMTS13	9	136308565	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	8003150	136308565	4904866	47	31527										
ABCA2	20	hgsc.bcm.edu	37	chr9	139906760	139906760	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctcttgggcaggttggcacgCaggatggcgttgttgaggct	17	8	1	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr9:139906760C>T	ENST00000371605.3	-	32	5400	c.5253G>A	c.(5251-5253)ctG>ctA	p.L1751L	ABCA2_ENST00000341511.6_Silent_p.L1752L|ABCA2_ENST00000265662.5_Silent_p.L1752L			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1751					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GGTTGGCACGCAGGATGGCGT	0.637																																					p.L1782L		Atlas-SNP	.											.	ABCA2	113	.	0			c.G5346A						.						63	66	65					9																	139906760		2081	4224	6305	SO:0001819	synonymous_variant	20	exon33			GGCACGCAGGATG	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.5253G>A	chr9.hg19:g.139906760C>T		61.0	0.0		65.0	28.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	hg19		.	.	.	.	.	.	.	.	.	.	C	4.654	0.121675	0.08931	.	.	ENSG00000107331	ENST00000477420	.	.	.	4.32	1.19	0.21007	.	.	.	.	.	T	0.58807	0.2148	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54323	-0.8311	4	.	.	.	.	10.7015	0.45931	0.0:0.5833:0.3338:0.0829	.	.	.	.	T	164	.	.	A	-	1	0	ABCA2	139026581	0.996000	0.38824	1.000000	0.80357	0.492000	0.33523	0.455000	0.21843	0.443000	0.26582	0.313000	0.20887	GCG	.	.		0.637	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		T	139906760	C	T	139906760	2	4	220	1	0	0	0	0	0	0	0	1	32	697	25	3		3	ABCA2	9	139906760	Silent	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	3598195	139906760	1306671	48	31528										
DPP7	29952	hgsc.bcm.edu	37	chr9	140008389	140008402	+	Frame_Shift_Del	DEL	AAGTCGGCCAGGGC	AAGTCGGCCAGGGC	-													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gcgcgcggagcagctctgcgAagtcggccagggcctgctcc					rs375634482		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	AAGTCGGCCAGGGC	AAGTCGGCCAGGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr9:140008389_140008402delAAGTCGGCCAGGGC	ENST00000371579.2	-	4	404_417	c.400_413delGCCCTGGCCGACTT	c.(400-414)gccctggccgacttcfs	p.ALADF134fs		NM_013379.2	NP_037511.2	Q9UHL4	DPP2_HUMAN	dipeptidyl-peptidase 7	134						cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;4.25e-05)|Epithelial(140;0.000633)		CAGCTCTGCGAAGTCGGCCAGGGCCTGCTCCACC	0.724																																					p.134_138del		Atlas-INDEL	.											.	DPP7	22	.	0			c.401_414del						.																																			SO:0001589	frameshift_variant	29952	exon4			.	AF154502	CCDS7030.1	9q34.3	2008-02-05	2006-01-12		ENSG00000176978	ENSG00000176978			14892	protein-coding gene	gene with protein product		610537	"dipeptidylpeptidase 7"			10477574, 11139392	Standard	XM_005266075		Approved	DPPII	uc004clh.3	Q9UHL4	OTTHUMG00000020977	ENST00000371579.2:c.400_413delGCCCTGGCCGACTT	chr9.hg19:g.140008389_140008402delAAGTCGGCCAGGGC	ENSP00000360635:p.Ala134fs	54.0	0.0		40.0	11.0	NM_013379	A8K7U7|Q5VSF1|Q969X4	Frame_Shift_Del	DEL	ENST00000371579.2	hg19	CCDS7030.1																																																																																			.	.		0.724	DPP7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055279.1	NM_013379		-	140008402	AAGTCGGCCAGGGC	-	140008389	7	5	220	1	0	1	0	1	0	0	0	0	4733	246	9	0	1105	0	DPP7	9	140008389	Frame_Shift_Del	DEL	AAGTCGGCCAGGGC	TCGA-DD-AAEH-01A-11D-A40R-10	101629	140008389	1205042	49	31529										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26312983	26312983	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	aaaactaaggcagcctgagcTatggtcagcagaattcaatg	10	8	2	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr10:26312983T>C	ENST00000265944.5	+	9	930	c.764T>C	c.(763-765)cTa>cCa	p.L255P	MYO3A_ENST00000543632.1_Missense_Mutation_p.L255P	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	255	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CAGCCTGAGCTATGGTCAGCA	0.383																																					p.L255P		Atlas-SNP	.											.	MYO3A	371	.	0			c.T764C						.						135	136	136					10																	26312983		2203	4300	6503	SO:0001583	missense	53904	exon9			CTGAGCTATGGTC	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.764T>C	chr10.hg19:g.26312983T>C	ENSP00000265944:p.Leu255Pro	102.0	0.0		136.0	46.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	T	17.74	3.464776	0.63513	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	T;T	0.63913	-0.07;-0.07	5.86	5.86	0.93980	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.239623	0.44097	D	0.000495	T	0.72260	0.3438	L	0.48935	1.535	0.80722	D	1	D;D;P	0.63046	0.99;0.992;0.949	D;D;P	0.67103	0.914;0.949;0.718	T	0.69105	-0.5233	10	0.30078	T	0.28	.	16.2644	0.82568	0.0:0.0:0.0:1.0	.	255;255;255	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	P	255	ENSP00000265944:L255P;ENSP00000445909:L255P	ENSP00000265944:L255P	L	+	2	0	MYO3A	26352989	1.000000	0.71417	0.897000	0.35233	0.989000	0.77384	5.425000	0.66470	2.244000	0.73946	0.528000	0.53228	CTA	.	.		0.383	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		C	26312983	T	C	26312983	3	2	220	1	0	0	0	0	1	0	0	0	10085	1522	53	2	790	2	MYO3A	10	26312983	Missense_Mutation	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10		26312983	109221764	50	31530										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27356167	27356167	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tagtggagcactttcaataaTatcaataccattttcttttt	4	7	3	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr10:27356167T>C	ENST00000376087.4	-	10	1291	c.1126A>G	c.(1126-1128)Att>Gtt	p.I376V	ANKRD26_ENST00000436985.2_Missense_Mutation_p.I425V	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	376					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CTTTCAATAATATCAATACCA	0.299																																					p.I376V		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A1126G						.						176	155	162					10																	27356167		1828	4077	5905	SO:0001583	missense	22852	exon10			CAATAATATCAAT	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.1126A>G	chr10.hg19:g.27356167T>C	ENSP00000365255:p.Ile376Val	49.0	0.0		77.0	32.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	hg19	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	T	0.029	-1.348904	0.01266	.	.	ENSG00000107890	ENST00000376087;ENST00000436985	T;T	0.29142	1.61;1.58	3.59	-3.95	0.04118	.	1.041750	0.07723	N	0.943979	T	0.17577	0.0422	L	0.31926	0.97	0.09310	N	1	B;B;B	0.17038	0.02;0.012;0.012	B;B;B	0.09377	0.004;0.002;0.002	T	0.28681	-1.0036	10	0.26408	T	0.33	.	4.2393	0.10640	0.1741:0.4381:0.0:0.3877	.	376;376;425	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	V	376;425	ENSP00000365255:I376V;ENSP00000405112:I425V	ENSP00000365255:I376V	I	-	1	0	ANKRD26	27396173	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.331000	0.07914	-0.497000	0.06641	-0.376000	0.06991	ATT	.	.		0.299	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			C	27356167	T	C	27356167	3	2	220	1	0	0	0	0	1	0	0	0	654	1406	49	2	4106	2	ANKRD26	10	27356167	Missense_Mutation	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10	1043184	27356167	108178580	51	31531										
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72324178	72324178	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gcagctgcggagcctgcagtActtggagcgctatgtctgcc	14	12	1	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr10:72324178A>G	ENST00000263563.6	+	19	2589	c.2321A>G	c.(2320-2322)tAc>tGc	p.Y774C		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	774						cytosol (GO:0005829)											AGCCTGCAGTACTTGGAGCGC	0.622																																					p.Y774C		Atlas-SNP	.											.	.	.	.	0			c.A2321G						.						113	110	111					10																	72324178		2203	4300	6503	SO:0001583	missense	27143	exon19			TGCAGTACTTGGA	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"paladin", "KIAA1274"	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.2321A>G	chr10.hg19:g.72324178A>G	ENSP00000263563:p.Tyr774Cys	85.0	0.0		121.0	33.0	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	hg19	CCDS31215.1	.	.	.	.	.	.	.	.	.	.	A	16.54	3.152304	0.57259	.	.	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.29655	1.56	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.58977	0.2160	M	0.84683	2.71	0.58432	D	0.999998	D	0.89917	1.0	D	0.71414	0.973	T	0.66960	-0.5791	10	0.87932	D	0	-24.844	14.4366	0.67284	1.0:0.0:0.0:0.0	.	774	Q9ULE6	PALD_HUMAN	C	774;750	ENSP00000263563:Y774C	ENSP00000263563:Y774C	Y	+	2	0	KIAA1274	71994184	1.000000	0.71417	1.000000	0.80357	0.449000	0.32228	5.120000	0.64685	1.903000	0.55091	0.454000	0.30748	TAC	.	.		0.622	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		G	72324178	A	G	72324178	3	3	220	1	0	0	0	0	1	0	0	0	8229	391	14	2	2391	2	KIAA1274	10	72324178	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	44968011	72324178	63210569	52	31532										
PHRF1	57661	hgsc.bcm.edu	37	chr11	597422	597422	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tcccgtgagtgaggaggaggTctccctgctcttggctgatg	15	10	2	3	rs377428073		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr11:597422T>G	ENST00000264555.5	+	8	874	c.746T>G	c.(745-747)gTc>gGc	p.V249G	PHRF1_ENST00000416188.2_Missense_Mutation_p.V249G|PHRF1_ENST00000413872.2_Missense_Mutation_p.V248G|PHRF1_ENST00000533464.1_Missense_Mutation_p.V245G	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	249					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GAGGAGGAGGTCTCCCTGCTC	0.657																																					p.V249G		Atlas-SNP	.											.	PHRF1	188	.	0			c.T746G						.						58	69	65					11																	597422		2096	4211	6307	SO:0001583	missense	57661	exon8			AGGAGGTCTCCCT	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.746T>G	chr11.hg19:g.597422T>G	ENSP00000264555:p.Val249Gly	67.0	0.0		72.0	23.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	T	17.12	3.308010	0.60305	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	D;D;D;D	0.81739	-1.52;-1.53;-1.52;-1.53	4.5	4.5	0.54988	.	0.249515	0.21812	N	0.068750	D	0.87172	0.6111	M	0.64997	1.995	0.58432	D	0.999997	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.69479	0.922;0.964;0.964;0.922	D	0.88412	0.3022	10	0.72032	D	0.01	-38.6757	14.0339	0.64634	0.0:0.0:0.0:1.0	.	245;248;249;249	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	G	249;248;249;245	ENSP00000264555:V249G;ENSP00000388589:V248G;ENSP00000410626:V249G;ENSP00000431870:V245G	ENSP00000264555:V249G	V	+	2	0	PHRF1	587422	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	4.202000	0.58446	1.912000	0.55364	0.454000	0.30748	GTC	.	.		0.657	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		G	597422	T	G	597422	3	3	220	1	0	0	0	0	1	0	0	0	11870	1667	58	5	772	5	PHRF1	11	597422	Missense_Mutation	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10		597422	134409094	53	31533										
OR52A5	390054	hgsc.bcm.edu	37	chr11	5153167	5153167	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	attaaaggccttgaatcgtgCctccttctggggcagctgaa	11	10	1	2	rs376219001		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr11:5153167C>T	ENST00000307388.1	-	1	705	c.706G>A	c.(706-708)Gca>Aca	p.A236T		NM_001005160.2	NP_001005160.1	Q9H2C5	O52A5_HUMAN	olfactory receptor, family 52, subfamily A, member 5	236					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(18)|skin(3)	35		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		TTGAATCGTGCCTCCTTCTGG	0.413																																					p.A236T		Atlas-SNP	.											.	OR52A5	80	.	0			c.G706A						.						105	95	99					11																	5153167		2201	4298	6499	SO:0001583	missense	390054	exon1			ATCGTGCCTCCTT	BK004433	CCDS31373.1	11p15.4	2012-08-09			ENSG00000171944	ENSG00000171944		"GPCR / Class A : Olfactory receptors"	19580	protein-coding gene	gene with protein product							Standard	NM_001005160		Approved		uc010qyx.2	Q9H2C5	OTTHUMG00000066616	ENST00000307388.1:c.706G>A	chr11.hg19:g.5153167C>T	ENSP00000303469:p.Ala236Thr	115.0	0.0		123.0	54.0	NM_001005160		Missense_Mutation	SNP	ENST00000307388.1	hg19	CCDS31373.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563633	0.45694	.	.	ENSG00000171944	ENST00000307388	T	0.00130	8.69	4.89	4.89	0.63831	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000204	T	0.00440	0.0014	M	0.89163	3.01	0.30966	N	0.723055	P	0.35944	0.529	P	0.48524	0.58	T	0.01930	-1.1245	10	0.72032	D	0.01	.	15.9656	0.79968	0.0:1.0:0.0:0.0	.	236	Q9H2C5	O52A5_HUMAN	T	236	ENSP00000303469:A236T	ENSP00000303469:A236T	A	-	1	0	OR52A5	5109743	0.000000	0.05858	0.995000	0.50966	0.070000	0.16714	0.197000	0.17197	2.707000	0.92482	0.655000	0.94253	GCA	.	.		0.413	OR52A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142823.1	NM_001005160		T	5153167	C	T	5153167	3	4	220	1	0	0	0	0	1	0	0	0	11119	739	26	3	247	3	OR52A5	11	5153167	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	4555745	5153167	129853349	54	31534										
HBG2	3048	hgsc.bcm.edu	37	chr11	5275588	5275588	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctcagctgggcaaaggtgccCttgagatcatccaggtgctt	12	11	2	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr11:5275588C>A	ENST00000380259.2	-	7	1489	c.249G>T	c.(247-249)aaG>aaT	p.K83N	HBG2_ENST00000336906.4_Missense_Mutation_p.K83N|HBG2_ENST00000380252.1_Missense_Mutation_p.K73N			P69892	HBG2_HUMAN	hemoglobin, gamma G	83					blood coagulation (GO:0007596)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	13		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAAAGGTGCCCTTGAGATCAT	0.527																																					p.K83N		Atlas-SNP	.											.	HBG2	20	.	0			c.G249T						.						289	224	246					11																	5275588		2201	4298	6499	SO:0001583	missense	3048	exon2			GGTGCCCTTGAGA	BC029387	CCDS7755.1	11p15.5	2014-05-19			ENSG00000196565	ENSG00000196565			4832	protein-coding gene	gene with protein product		142250				2649166	Standard	NM_000184		Approved	HBG-T1		P69892	OTTHUMG00000066673	ENST00000380259.2:c.249G>T	chr11.hg19:g.5275588C>A	ENSP00000369609:p.Lys83Asn	254.0	0.0		258.0	50.0	NM_000184	A8MZE0|P02096|P62027|Q14491|Q68NH9|Q96FH6|Q96FH7	Missense_Mutation	SNP	ENST00000380259.2	hg19	CCDS7755.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.560718	0.27827	.	.	ENSG00000196565	ENST00000380252;ENST00000380259;ENST00000336906;ENST00000380247	D;D;D	0.93307	-3.2;-3.2;-3.2	4.08	-0.26	0.12967	Globin-like (2);Globin, structural domain (2);	.	.	.	.	D	0.95245	0.8458	M	0.81497	2.545	0.50039	D	0.999844	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.994	D	0.92148	0.5726	9	0.87932	D	0	.	5.1575	0.15042	0.0:0.5668:0.1482:0.285	.	83;83	P69892;P69891	HBG2_HUMAN;HBG1_HUMAN	N	73;83;83;83	ENSP00000369602:K73N;ENSP00000369609:K83N;ENSP00000338082:K83N	ENSP00000338082:K83N	K	-	3	2	HBG2	5232164	0.140000	0.22579	0.004000	0.12327	0.029000	0.11900	1.016000	0.29976	-0.154000	0.11118	-0.142000	0.14014	AAG	.	.		0.527	HBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142967.2	NM_000184		A	5275588	C	A	5275588	3	1	220	1	0	0	0	0	1	0	0	0	6992	680	24	3	202	3	HBG2	11	5275588	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	122421	5275588	129730928	55	31535										
PSMA1	5682	hgsc.bcm.edu	37	chr11	14539222	14539222	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	atcagcagtaagccccgcaaTtgagataccaatatggttgt	9	9	1	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr11:14539222T>C	ENST00000396394.2	-	4	616	c.220A>G	c.(220-222)Att>Gtt	p.I74V	PSMA1_ENST00000530457.1_Missense_Mutation_p.I49V|PSMA1_ENST00000419365.2_Missense_Mutation_p.I74V|PSMA1_ENST00000418988.2_Missense_Mutation_p.I80V|PSMA1_ENST00000555531.1_Missense_Mutation_p.I74V|PSMA1_ENST00000396393.1_Missense_Mutation_p.I74V	NM_002786.3	NP_002777.1	P25786	PSA1_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 1	74					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysome (GO:0005844)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	RNA binding (GO:0003723)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	3						AGCCCCGCAATTGAGATACCA	0.328																																					p.I80V		Atlas-SNP	.											.	PSMA1	22	.	0			c.A238G						.						116	115	115					11																	14539222		2200	4294	6494	SO:0001583	missense	5682	exon5			CCGCAATTGAGAT	X61969	CCDS7816.1, CCDS31431.1	11p15.1	2005-10-10			ENSG00000129084	ENSG00000129084		"Proteasome (prosome, macropain) subunits"	9530	protein-coding gene	gene with protein product		602854				1398136, 2025653	Standard	NM_148976		Approved	HC2, NU, PROS30, MGC14542, MGC14575, MGC14751, MGC1667, MGC21459, MGC22853, MGC23915	uc001mlk.3	P25786	OTTHUMG00000165825	ENST00000396394.2:c.220A>G	chr11.hg19:g.14539222T>C	ENSP00000379676:p.Ile74Val	242.0	0.0		282.0	101.0	NM_148976	A8K400|Q53YE8|Q9BRV9	Missense_Mutation	SNP	ENST00000396394.2	hg19	CCDS7816.1	.	.	.	.	.	.	.	.	.	.	T	17.58	3.424181	0.62733	.	.	ENSG00000129084	ENST00000419365;ENST00000396394;ENST00000396393;ENST00000530457;ENST00000418988	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	5.64	5.64	0.86602	.	0.096845	0.64402	D	0.000001	T	0.20210	0.0486	L	0.37800	1.135	0.80722	D	1	B;B;B	0.17465	0.022;0.006;0.004	B;B;B	0.24155	0.024;0.023;0.051	T	0.02385	-1.1167	10	0.44086	T	0.13	-10.282	14.4348	0.67274	0.0:0.0:0.0:1.0	.	74;80;74	B4E0X6;P25786-2;P25786	.;.;PSA1_HUMAN	V	74;74;74;49;80	ENSP00000392242:I74V;ENSP00000379676:I74V;ENSP00000379675:I74V;ENSP00000441166:I49V;ENSP00000414359:I80V	ENSP00000379675:I74V	I	-	1	0	PSMA1	14495798	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.329000	0.79170	2.136000	0.66102	0.533000	0.62120	ATT	.	.		0.328	PSMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386421.3	NM_002786		C	14539222	T	C	14539222	3	2	220	1	0	0	0	0	1	0	0	0	12678	1493	52	2	649	2	PSMA1	11	14539222	Missense_Mutation	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10	9263634	14539222	120467294	56	31536										
SMTNL1	219537	hgsc.bcm.edu	37	chr11	57310839	57310841	+	Intron	DEL	GAG	GAG	-													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	aagaggaggcggaggatgcaGaggaggcagtgagtgaggca					rs370650341		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr11:57310839_57310841delGAG	ENST00000399154.2	+	2	621				SMTNL1_ENST00000457912.1_In_Frame_Del_p.E261del|SMTNL1_ENST00000527972.1_In_Frame_Del_p.E243del			A8MU46	SMTL1_HUMAN	smoothelin-like 1						negative regulation of vasodilation (GO:0045908)|positive regulation of vasoconstriction (GO:0045907)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	8						GGAGGATGCAGAGGAGGCAGTGA	0.562																																					p.241_242del		Atlas-INDEL	.											.	SMTNL1	68	.	0			c.723_725del						.																																			SO:0001627	intron_variant	219537	exon1			.	BX116227		11q12.1	2006-02-02				ENSG00000214872			32394	protein-coding gene	gene with protein product	"calponin homology-associated smooth muscle protein"	613664				15327999	Standard	NM_001105565		Approved	CHASM	uc021qjh.1	A8MU46		ENST00000399154.2:c.621+25GAG>-	chr11.hg19:g.57310842_57310844delGAG		187.0	0.0		235.0	36.0	NM_001105565		In_Frame_Del	DEL	ENST00000399154.2	hg19																																																																																				.	.		0.562	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203		-	57310841	GAG	-	57310839	6	5	220	0	1	1	0	1	0	0	0	0	14830	943	33	0		0	SMTNL1	11	57310839	Intron	DEL	GAG	TCGA-DD-AAEH-01A-11D-A40R-10	42771617	57310839	77695677	57	31537										
P2RY6	5031	hgsc.bcm.edu	37	chr11	73008130	73008130	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	cctgccctggccacccactaTatgccctatggcatggctct	8	17	1	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr11:73008130T>C	ENST00000393590.2	+	2	866	c.567T>C	c.(565-567)taT>taC	p.Y189Y	P2RY6_ENST00000540124.1_Silent_p.Y189Y|P2RY6_ENST00000542092.1_Silent_p.Y189Y|P2RY6_ENST00000538328.1_Silent_p.Y189Y|P2RY6_ENST00000349767.2_Silent_p.Y189Y|P2RY6_ENST00000393592.2_Silent_p.Y189Y|P2RY6_ENST00000540342.1_Silent_p.Y189Y|P2RY6_ENST00000393591.1_Silent_p.Y189Y	NM_001277207.1|NM_001277208.1	NP_001264136.1|NP_001264137.1	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 6	189					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)	14						CCACCCACTATATGCCCTATG	0.642																																					p.Y189Y		Atlas-SNP	.											.	P2RY6	45	.	0			c.T567C						.						106	94	98					11																	73008130		2178	4263	6441	SO:0001819	synonymous_variant	5031	exon4			CCACTATATGCCC		CCDS8220.1	11q13.5	2012-08-08				ENSG00000171631		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8543	protein-coding gene	gene with protein product		602451				8670200	Standard	NM_176797		Approved	P2Y6	uc001otr.4	Q15077		ENST00000393590.2:c.567T>C	chr11.hg19:g.73008130T>C		20.0	0.0		17.0	9.0	NM_176796	Q15754	Silent	SNP	ENST00000393590.2	hg19	CCDS8220.1																																																																																			.	.		0.642	P2RY6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397349.1			C	73008130	T	C	73008130	2	2	220	1	0	0	0	0	0	0	0	1	11363	1413	49	2		2	P2RY6	11	73008130	Silent	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10	15697291	73008130	61998386	58	31538										
RPS3	6188	hgsc.bcm.edu	37	chr11	75115747	75115747	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	atcaaggtgaagatcatgctGccctgggacccaactggtaa	11	10	2	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr11:75115747G>T	ENST00000531188.1	+	6	632	c.570G>T	c.(568-570)ctG>ctT	p.L190L	RPS3_ENST00000278572.6_Silent_p.L206L|RPS3_ENST00000526608.1_Silent_p.L178L|RPS3_ENST00000529285.1_3'UTR|SNORD15B_ENST00000384714.1_RNA|RPS3_ENST00000534440.1_Silent_p.L105L|RPS3_ENST00000527446.1_Silent_p.L190L|RPS3_ENST00000524851.1_Silent_p.L190L	NM_001005.4|NM_001260506.1|NM_001260507.1	NP_000996.2|NP_001247435.1|NP_001247436.1	P23396	RS3_HUMAN	ribosomal protein S3	190					cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic translation (GO:0002181)|DNA catabolic process, endonucleolytic (GO:0000737)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of DNA repair (GO:0045738)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of DNA N-glycosylase activity (GO:1902546)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ruffle membrane (GO:0032587)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|enzyme binding (GO:0019899)|iron-sulfur cluster binding (GO:0051536)|mRNA binding (GO:0003729)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						AGATCATGCTGCCCTGGGACC	0.552																																					p.L206L		Atlas-SNP	.											.	RPS3	20	.	0			c.G618T						.						73	66	68					11																	75115747		2200	4293	6493	SO:0001819	synonymous_variant	6188	exon6			CATGCTGCCCTGG		CCDS8236.1, CCDS58161.1	11q13.3-q13.5	2011-04-05				ENSG00000149273		"S ribosomal proteins"	10420	protein-coding gene	gene with protein product	"IMR-90 ribosomal protein S3", "40S ribosomal protein S3"	600454				1712897, 7789996	Standard	NM_001005		Approved	FLJ26283, FLJ27450, MGC87870, S3	uc031qcs.1	P23396		ENST00000531188.1:c.570G>T	chr11.hg19:g.75115747G>T		144.0	0.0		138.0	38.0	NM_001260506	B2R7N5|J3KN86|Q498B5|Q8NI95	Silent	SNP	ENST00000531188.1	hg19	CCDS8236.1	.	.	.	.	.	.	.	.	.	.	g	11.05	1.524912	0.27299	.	.	ENSG00000149273	ENST00000525933	.	.	.	5.24	2.27	0.28462	.	.	.	.	.	T	0.54886	0.1886	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44605	-0.9317	4	.	.	.	-15.4598	6.9338	0.24455	0.083:0.0:0.4403:0.4768	.	.	.	.	F	118	.	.	C	+	2	0	RPS3	74793395	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.988000	0.49386	0.303000	0.22785	0.558000	0.71614	TGC	.	.		0.552	RPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384158.2	NM_001005		T	75115747	G	T	75115747	2	4	220	1	0	0	0	0	0	0	0	1	13658	1306	46	3		3	RPS3	11	75115747	Silent	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	2107617	75115747	59890769	59	31539										
ZCRB1	85437	hgsc.bcm.edu	37	chr12	42707501	42707502	+	Frame_Shift_Del	DEL	TA	TA	-													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	caatttaatacctggaatgcTatggcctgactgaggctgtc							TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr12:42707501_42707502delTA	ENST00000266529.3	-	7	695_696	c.512_513delTA	c.(511-513)atafs	p.I171fs	ZCRB1_ENST00000552673.1_Frame_Shift_Del_p.I130fs|PPHLN1_ENST00000549190.1_Intron	NM_033114.3	NP_149105.3	Q8TBF4	ZCRB1_HUMAN	zinc finger CCHC-type and RNA binding motif 1	171					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)	8	all_cancers(12;0.000348)|Breast(8;0.221)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0689)		CCTGGAATGCTATGGCCTGACT	0.381																																					p.171_172del		Atlas-INDEL	.											.	ZCRB1	20	.	0			c.513_514del						.																																			SO:0001589	frameshift_variant	85437	exon7			.	BC022543	CCDS8740.1	12q12	2013-02-12				ENSG00000139168		"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	29620	protein-coding gene	gene with protein product	"U11/U12 snRNP 31K"	610750				15146077, 16959469	Standard	NM_033114		Approved	MADP-1, MADP1, RBM36, ZCCHC19, SNRNP31	uc001rmz.3	Q8TBF4	OTTHUMG00000169382	ENST00000266529.3:c.512_513delTA	chr12.hg19:g.42707501_42707502delTA	ENSP00000266529:p.Ile171fs	84.0	0.0		116.0	43.0	NM_033114	Q6PJX0|Q96TA6	Frame_Shift_Del	DEL	ENST00000266529.3	hg19	CCDS8740.1																																																																																			.	.		0.381	ZCRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403813.1	NM_033114		-	42707502	TA	-	42707501	7	5	220	1	0	1	0	1	0	0	0	0	17611	1512	53	0	148	0	ZCRB1	12	42707501	Frame_Shift_Del	DEL	TA	TCGA-DD-AAEH-01A-11D-A40R-10		42707501	91144394	60	31540										
ARID2	196528	hgsc.bcm.edu	37	chr12	46244346	46244347	+	Frame_Shift_Del	DEL	AC	AC	-													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	acataccagcatgtacttctAcagtttcacagggtcaacag					rs148307427		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr12:46244346_46244347delAC	ENST00000334344.6	+	15	2612_2613	c.2440_2441delAC	c.(2440-2442)acafs	p.T814fs	ARID2_ENST00000422737.1_Frame_Shift_Del_p.T665fs|ARID2_ENST00000444670.1_Frame_Shift_Del_p.T424fs|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	814	Gln-rich.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		ATGTACTTCTACAGTTTCACAG	0.45			"N, S, F"		hepatocellular carcinoma																																p.813_814del		Atlas-INDEL	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.2439_2440del						.																																			SO:0001589	frameshift_variant	196528	exon15			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2440_2441delAC	chr12.hg19:g.46244346_46244347delAC	ENSP00000335044:p.Thr814fs	90.0	0.0		110.0	35.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.45	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		-	46244347	AC	-	46244346	7	5	220	1	0	1	0	1	0	0	0	0	915	391	14	0	2498	0	ARID2	12	46244346	Frame_Shift_Del	DEL	AC	TCGA-DD-AAEH-01A-11D-A40R-10	3536845	46244346	87607549	61	31541										
WNT1	7471	hgsc.bcm.edu	37	chr12	49375114	49375114	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ggcagcaaccgcgcttcgcgGgcggagctgctgcgcctgga	17	14	0	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr12:49375114G>T	ENST00000293549.3	+	4	840	c.804G>T	c.(802-804)cgG>cgT	p.R268R		NM_005430.3	NP_005421.1	P04628	WNT1_HUMAN	wingless-type MMTV integration site family, member 1	268					bone development (GO:0060348)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to peptide hormone stimulus (GO:0071375)|central nervous system morphogenesis (GO:0021551)|cerebellum formation (GO:0021588)|diencephalon development (GO:0021536)|embryonic axis specification (GO:0000578)|forebrain anterior/posterior pattern specification (GO:0021797)|hematopoietic stem cell proliferation (GO:0071425)|hepatocyte differentiation (GO:0070365)|inner ear morphogenesis (GO:0042472)|midbrain development (GO:0030901)|midbrain-hindbrain boundary maturation during brain development (GO:0022004)|myoblast fusion (GO:0007520)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell aging (GO:0090344)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|neuron fate determination (GO:0048664)|organ regeneration (GO:0031100)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dermatome development (GO:0061184)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to wounding (GO:0009611)|signal transduction in response to DNA damage (GO:0042770)|Spemann organizer formation (GO:0060061)|spinal cord association neuron differentiation (GO:0021527)|T cell differentiation in thymus (GO:0033077)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(357;0.244)		GCGCTTCGCGGGCGGAGCTGC	0.706																																					p.R268R		Atlas-SNP	.											.	WNT1	13	.	0			c.G804T						.						8	10	9					12																	49375114		2129	4127	6256	SO:0001819	synonymous_variant	7471	exon4			TTCGCGGGCGGAG	X03072	CCDS8776.1	12q13	2013-02-28				ENSG00000125084		"Wingless-type MMTV integration sites", "Endogenous ligands"	12774	protein-coding gene	gene with protein product		164820		INT1		2998762, 3281802	Standard	NM_005430		Approved		uc001rsu.3	P04628	OTTHUMG00000170403	ENST00000293549.3:c.804G>T	chr12.hg19:g.49375114G>T		86.0	0.0		95.0	29.0	NM_005430	Q5U0N2	Silent	SNP	ENST00000293549.3	hg19	CCDS8776.1																																																																																			.	.		0.706	WNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408937.1			T	49375114	G	T	49375114	2	4	220	1	0	0	0	0	0	0	0	1	17396	1219	43	3		3	WNT1	12	49375114	Silent	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	3130768	49375114	84476781	62	31542										
PRIM1	5557	hgsc.bcm.edu	37	chr12	57132217	57132217	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	agcttcaaaatattaccttaCctctggttctatgtttgaca	5	9	3	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr12:57132217C>T	ENST00000338193.6	-	11	1181		c.e11+1			NM_000946.2	NP_000937.1	P49642	PRI1_HUMAN	primase, DNA, polypeptide 1 (49kDa)						DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			kidney(1)|lung(6)|prostate(1)	8						TATTACCTTACCTCTGGTTCT	0.363																																					.		Atlas-SNP	.											.	PRIM1	22	.	0			c.1144+1G>A						.						115	103	107					12																	57132217		1849	4082	5931	SO:0001630	splice_region_variant	5557	exon12			ACCTTACCTCTGG	BC005266	CCDS44926.1	12q13.3	2007-06-19	2007-06-19			ENSG00000198056			9369	protein-coding gene	gene with protein product		176635				8530050	Standard	NM_000946		Approved		uc001smd.3	P49642	OTTHUMG00000170034	ENST00000338193.6:c.1144+1G>A	chr12.hg19:g.57132217C>T		57.0	0.0		70.0	26.0	NM_000946		Splice_Site	SNP	ENST00000338193.6	hg19	CCDS44926.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.061366	0.36373	.	.	ENSG00000198056	ENST00000537418;ENST00000338193	.	.	.	4.29	3.39	0.38822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2042	0.43103	0.0:0.7976:0.2024:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRIM1	55418484	1.000000	0.71417	0.980000	0.43619	0.516000	0.34256	4.839000	0.62810	1.137000	0.42214	0.467000	0.42956	.	.	.		0.363	PRIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406956.1	NM_000946	Intron	T	57132217	C	T	57132217	5	4	220	1	0	0	0	0	0	0	1	0	12502	521	18	3	129	3	PRIM1	12	57132217	Splice_Site	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	7757103	57132217	76719678	63	31543										
MGAT4C	25834	hgsc.bcm.edu	37	chr12	86373973	86373973	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ccatctaggattgggtaataCtcctctggagcatgtataac	9	9	2	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr12:86373973C>T	ENST00000604798.1	-	8	1735	c.531G>A	c.(529-531)gaG>gaA	p.E177E	MGAT4C_ENST00000549405.2_Silent_p.E177E|MGAT4C_ENST00000552808.2_Silent_p.E177E|MGAT4C_ENST00000548651.1_Silent_p.E177E|MGAT4C_ENST00000393205.2_Silent_p.E206E|MGAT4C_ENST00000552435.2_Intron|MGAT4C_ENST00000332156.1_Silent_p.E177E			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	177					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TTGGGTAATACTCCTCTGGAG	0.373																																					p.E177E		Atlas-SNP	.											.	MGAT4C	110	.	0			c.G531A						.						111	111	111					12																	86373973		2203	4300	6503	SO:0001819	synonymous_variant	25834	exon7			GTAATACTCCTCT		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	30871	protein-coding gene	gene with protein product		607385	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.531G>A	chr12.hg19:g.86373973C>T		90.0	0.0		109.0	25.0	NM_013244	B4DRH2|Q4G199|Q9UIU5	Silent	SNP	ENST00000604798.1	hg19	CCDS9030.1																																																																																			.	.		0.373	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		T	86373973	C	T	86373973	2	4	220	1	0	0	0	0	0	0	0	1	9556	564	20	3		3	MGAT4C	12	86373973	Silent	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	29241756	86373973	47477922	64	31544										
PDS5B	23047	hgsc.bcm.edu	37	chr13	33241913	33241913	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tttttcagaatttaaacaagCaagcatatgatttggcaaag	7	5	1	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr13:33241913C>G	ENST00000315596.10	+	7	823	c.637C>G	c.(637-639)Caa>Gaa	p.Q213E		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	213					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		TTTAAACAAGCAAGCATATGA	0.303																																					p.Q213E		Atlas-SNP	.											.	PDS5B	141	.	0			c.C637G						.						53	49	50					13																	33241913		1808	4061	5869	SO:0001583	missense	23047	exon7			AACAAGCAAGCAT	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"androgen-induced proliferation inhibitor"	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.637C>G	chr13.hg19:g.33241913C>G	ENSP00000313851:p.Gln213Glu	277.0	0.0		411.0	143.0	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	hg19	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.201579	0.58234	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	4.67	4.67	0.58626	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.44705	0.1306	N	0.20401	0.57	0.80722	D	1	P;B	0.36768	0.569;0.028	B;B	0.38264	0.269;0.023	T	0.34030	-0.9845	9	0.15952	T	0.53	-13.6391	17.9602	0.89083	0.0:1.0:0.0:0.0	.	213;213	Q9NTI5;Q9NTI5-3	PDS5B_HUMAN;.	E	213	.	ENSP00000313851:Q213E	Q	+	1	0	PDS5B	32139913	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.689000	0.84165	2.290000	0.77057	0.655000	0.94253	CAA	.	.		0.303	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		G	33241913	C	G	33241913	3	3	220	1	0	0	0	0	1	0	0	0	11701	711	25	4	659	4	PDS5B	13	33241913	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10		33241913	81927965	65	31545										
SUGT1	10910	hgsc.bcm.edu	37	chr13	53232539	53232539	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tctttttctacacagttgctGttgctgatgcaaagaagtct	8	8	3	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr13:53232539G>T	ENST00000343788.6	+	4	275	c.193G>T	c.(193-195)Gtt>Ttt	p.V65F	SUGT1_ENST00000310528.8_Missense_Mutation_p.V65F|SUGT1_ENST00000535397.1_Missense_Mutation_p.V9F|SUGT1_ENST00000483074.1_3'UTR	NM_001130912.1	NP_001124384.1	Q9Y2Z0	SUGT1_HUMAN	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	65					innate immune response (GO:0045087)|mitotic nuclear division (GO:0007067)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				kidney(3)|large_intestine(3)|lung(2)	8		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		CACAGTTGCTGTTGCTGATGC	0.358																																					p.V65F		Atlas-SNP	.											.	SUGT1	37	.	0			c.G193T						.						116	114	115					13																	53232539		2203	4300	6503	SO:0001583	missense	10910	exon4			GTTGCTGTTGCTG	AF068289	CCDS9436.1, CCDS45050.1	13q14.3	2014-03-20			ENSG00000165416	ENSG00000165416			16987	protein-coding gene	gene with protein product		604098				10445024	Standard	NM_006704		Approved	SGT1	uc001vhc.2	Q9Y2Z0	OTTHUMG00000016977	ENST00000343788.6:c.193G>T	chr13.hg19:g.53232539G>T	ENSP00000367208:p.Val65Phe	74.0	0.0		64.0	14.0	NM_001130912	A2A303|Q5JAK5|Q5TAM6|Q6VXY6	Missense_Mutation	SNP	ENST00000343788.6	hg19	CCDS45050.1	.	.	.	.	.	.	.	.	.	.	G	9.341	1.062925	0.19987	.	.	ENSG00000165416	ENST00000343788;ENST00000535397;ENST00000310528	T;T;T	0.74842	0.18;-0.88;0.18	4.42	1.3	0.21679	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.175795	0.50627	D	0.000115	T	0.76716	0.4026	L	0.58510	1.815	0.42241	D	0.991936	B;P;P	0.45986	0.11;0.87;0.789	B;P;B	0.56434	0.067;0.798;0.391	T	0.71666	-0.4524	10	0.42905	T	0.14	-11.0625	7.5282	0.27668	0.4504:0.0:0.5496:0.0	.	9;65;65	F5H5A9;Q9Y2Z0;Q9Y2Z0-2	.;SUGT1_HUMAN;.	F	65;9;65	ENSP00000367208:V65F;ENSP00000443521:V9F;ENSP00000308067:V65F	ENSP00000308067:V65F	V	+	1	0	SUGT1	52130540	1.000000	0.71417	0.995000	0.50966	0.127000	0.20565	0.704000	0.25661	-0.004000	0.14419	0.563000	0.77884	GTT	.	.		0.358	SUGT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045104.2			T	53232539	G	T	53232539	3	4	220	1	0	0	0	0	1	0	0	0	15384	1377	48	3	207	3	SUGT1	13	53232539	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	19990626	53232539	61937339	66	31546										
CASC5	57082	hgsc.bcm.edu	37	chr15	40943693	40943693	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctcttagaactggaggtacaAaaagagcagacccttgctca	9	10	2	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr15:40943693A>G	ENST00000346991.5	+	21	6705	c.6315A>G	c.(6313-6315)caA>caG	p.Q2105Q	CASC5_ENST00000399668.2_Silent_p.Q2079Q			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	2105	Necessary for kinetochore localization and for interaction with NSL1 and DSN1.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TGGAGGTACAAAAAGAGCAGA	0.348																																					p.Q2105Q		Atlas-SNP	.											.	CASC5	269	.	0			c.A6315G						.						76	68	71					15																	40943693		1810	4081	5891	SO:0001819	synonymous_variant	57082	exon21			GGTACAAAAAGAG	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.6315A>G	chr15.hg19:g.40943693A>G		117.0	0.0		196.0	100.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Silent	SNP	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.		0.348	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		G	40943693	A	G	40943693	2	3	220	1	0	0	0	0	0	0	0	1	2665	11	1	2		2	CASC5	15	40943693	Silent	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10		40943693	61587699	67	31547										
FBN1	2200	hgsc.bcm.edu	37	chr15	48760684	48760684	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	atagctgcctggagtgttgaCacagttcccactgatgcacg	11	11	0	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr15:48760684C>T	ENST00000316623.5	-	37	4962	c.4507G>A	c.(4507-4509)Gtc>Atc	p.V1503I		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1503	EGF-like 26; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GGAGTGTTGACACAGTTCCCA	0.473																																					p.V1503I		Atlas-SNP	.											.	FBN1	310	.	0			c.G4507A						.						125	101	109					15																	48760684		2198	4296	6494	SO:0001583	missense	2200	exon37			TGTTGACACAGTT	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.4507G>A	chr15.hg19:g.48760684C>T	ENSP00000325527:p.Val1503Ile	67.0	0.0		76.0	18.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.472515	0.26423	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.93247	-3.19	5.64	-1.36	0.09085	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.742875	0.13432	N	0.388353	T	0.81206	0.4774	N	0.12471	0.22	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.64914	-0.6295	10	0.08837	T	0.75	.	6.6163	0.22778	0.0:0.4517:0.1931:0.3552	.	1503	P35555	FBN1_HUMAN	I	1503;71;393	ENSP00000325527:V1503I	ENSP00000325527:V1503I	V	-	1	0	FBN1	46547976	0.001000	0.12720	0.846000	0.33378	0.886000	0.51366	-1.148000	0.03185	-0.252000	0.09528	-0.300000	0.09419	GTC	.	.		0.473	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48760684	C	T	48760684	3	4	220	1	0	0	0	0	1	0	0	0	5710	478	17	3	4228	3	FBN1	15	48760684	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	7816991	48760684	53770708	68	31548										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52611468	52611468	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctcatcggcgatactggaggTtcgctttctcaaccctgtgg	11	12	2	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr15:52611468T>A	ENST00000399231.3	-	38	5191	c.4948A>T	c.(4948-4950)Acc>Tcc	p.T1650S	MYO5A_ENST00000358212.6_Missense_Mutation_p.T1675S|MYO5A_ENST00000356338.6_Missense_Mutation_p.T1623S|MYO5A_ENST00000553916.1_Missense_Mutation_p.T1648S|MYO5A_ENST00000399233.2_Missense_Mutation_p.T1647S	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1650	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ATACTGGAGGTTCGCTTTCTC	0.547																																					p.T1650S		Atlas-SNP	.											.	MYO5A	145	.	0			c.A4948T						.						120	127	125					15																	52611468		2173	4266	6439	SO:0001583	missense	4644	exon38			TGGAGGTTCGCTT		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.4948A>T	chr15.hg19:g.52611468T>A	ENSP00000382177:p.Thr1650Ser	72.0	0.0		104.0	37.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	hg19	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	T	1.696	-0.502894	0.04261	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	D;D;D;D;D	0.85171	-1.9;-1.9;-1.93;-1.95;-1.9	5.7	5.7	0.88788	Dilute (1);	0.000000	0.85682	D	0.000000	T	0.63616	0.2526	N	0.01640	-0.785	0.58432	D	0.999992	B;B;B	0.24258	0.018;0.003;0.1	B;B;B	0.24006	0.039;0.003;0.05	T	0.66364	-0.5942	10	0.02654	T	1	.	15.9672	0.79984	0.0:0.0:0.0:1.0	.	380;1650;1623	B5LY56;Q9Y4I1;Q9Y4I1-2	.;MYO5A_HUMAN;.	S	1650;1157;1647;1623;1675;1253;1648	ENSP00000382177:T1650S;ENSP00000382179:T1647S;ENSP00000348693:T1623S;ENSP00000350945:T1675S;ENSP00000451109:T1648S	ENSP00000348693:T1623S	T	-	1	0	MYO5A	50398760	1.000000	0.71417	0.969000	0.41365	0.041000	0.13682	5.006000	0.63978	2.181000	0.69327	0.460000	0.39030	ACC	.	.		0.547	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		A	52611468	T	A	52611468	3	1	220	1	0	0	0	0	1	0	0	0	10087	1725	60	4	635	4	MYO5A	15	52611468	Missense_Mutation	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10	3850784	52611468	49919924	69	31549										
TUFM	25970	hgsc.bcm.edu	37	chr16	28857319	28857319	+	5'Flank	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	catgtggcttgtcgcgcacgTaagtcttcttggcctccacg	11	13	2	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr16:28857319T>A	ENST00000322610.8	+	0	0				TUFM_ENST00000313511.3_Missense_Mutation_p.Y54F|MIR4721_ENST00000577590.1_RNA			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1						blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						GTCGCGCACGTAAGTCTTCTT	0.632																																					p.Y54F		Atlas-SNP	.											.	TUFM	33	.	0			c.A161T						.						72	61	64					16																	28857319		2197	4300	6497	SO:0001631	upstream_gene_variant	7284	exon2			CGCACGTAAGTCT	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	30417	protein-coding gene	gene with protein product	"SH2-B homolog"	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2			chr16.hg19:g.28857319T>A	Exception_encountered	71.0	0.0		88.0	36.0	NM_003321	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	ENST00000322610.8	hg19	CCDS53996.1	.	.	.	.	.	.	.	.	.	.	T	10.56	1.385631	0.25031	.	.	ENSG00000178952	ENST00000313511	T	0.70516	-0.49	6.0	6.0	0.97389	.	0.129752	0.53938	D	0.000049	T	0.47116	0.1428	N	0.08118	0	0.48135	D	0.999594	B	0.21753	0.06	B	0.17433	0.018	T	0.49360	-0.8948	10	0.02654	T	1	-25.7142	14.0279	0.64597	0.0:0.0:0.0:1.0	.	51	P49411	EFTU_HUMAN	F	54	ENSP00000322439:Y54F	ENSP00000322439:Y54F	Y	-	2	0	TUFM	28764820	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	3.545000	0.53648	2.297000	0.77311	0.533000	0.62120	TAC	.	.		0.632	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503		A	28857319	T	A	28857319	1	1	220	0	1	0	0	0	0	0	0	0	16786	1638	57	4		4	TUFM	16	28857319	5'Flank	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10		28857319	61497434	70	31550										
ITGAM	3684	hgsc.bcm.edu	37	chr16	31289337	31289337	+	Frame_Shift_Del	DEL	G	G	-													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	cgggtgcaaagcctggttctGggggcacctcgatatcagca							TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr16:31289337delG	ENST00000287497.8	+	12	1338	c.1263delG	c.(1261-1263)ctgfs	p.L421fs	ITGAM_ENST00000544665.3_Frame_Shift_Del_p.L421fs			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	421					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						GCCTGGTTCTGGGGGCACCTC	0.587																																					p.L421fs		Atlas-INDEL	.											.	ITGAM	137	.	0			c.1262delT						.						46	47	47					16																	31289337		2047	4191	6238	SO:0001589	frameshift_variant	3684	exon12			.	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.1263delG	chr16.hg19:g.31289337delG	ENSP00000287497:p.Leu421fs	76.0	0.0		126.0	41.0	NM_000632	Q4VAK0|Q4VAK1|Q4VAK2	Frame_Shift_Del	DEL	ENST00000287497.8	hg19	CCDS45470.1																																																																																			.	.		0.587	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		-	31289337	G	-	31289337	7	5	220	1	0	1	0	1	0	0	0	0	7896	1335	47	0	1309	0	ITGAM	16	31289337	Frame_Shift_Del	DEL	G	TCGA-DD-AAEH-01A-11D-A40R-10	2432018	31289337	59065416	71	31551										
BRD7	29117	hgsc.bcm.edu	37	chr16	50388735	50388736	+	Frame_Shift_Ins	INS	-	-	T													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ctaaagagcttgtgagaggcINSttctcaggaggcaagtctaa							TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr16:50388735_50388736insT	ENST00000394688.3	-	3	515_516	c.356_357insA	c.(355-357)aagfs	p.K119fs	snoU13_ENST00000459559.1_RNA|BRD7_ENST00000401491.3_5'UTR|BRD7_ENST00000394689.2_Frame_Shift_Ins_p.K119fs			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	119					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				TTGTGAGAGGCTTCTCAGGAGG	0.45																																					p.K119fs		Atlas-INDEL	.											.	BRD7	61	.	0			c.357_358insA						.																																			SO:0001589	frameshift_variant	29117	exon3			.	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"bromodomain-containing 7"			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.357dupA	chr16.hg19:g.50388737_50388737dupT	ENSP00000378180:p.Lys119fs	175.0	0.0		161.0	70.0	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Frame_Shift_Ins	INS	ENST00000394688.3	hg19	CCDS10742.1																																																																																			.	.		0.45	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		T	50388736	-	T	50388735	7	5	220	1	0	1	1	0	0	0	0	0	1507	796	28	0	1661	0	BRD7	16	50388735	Frame_Shift_Ins	INS	-	TCGA-DD-AAEH-01A-11D-A40R-10	19099398	50388735	39966018	72	31552										
PLEKHG4	25894	hgsc.bcm.edu	37	chr16	67316522	67316522	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gttggtccaaacactggaggCccgggaaagcggactgcacc	14	12	0	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr16:67316522C>A	ENST00000360461.5	+	9	3905	c.1370C>A	c.(1369-1371)gCc>gAc	p.A457D	PLEKHG4_ENST00000450733.1_Missense_Mutation_p.A376D|PLEKHG4_ENST00000379344.3_Missense_Mutation_p.A457D|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.A457D	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	457							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		ACACTGGAGGCCCGGGAAAGC	0.592																																					p.A457D		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.C1370A						.						72	67	69					16																	67316522		2198	4300	6498	SO:0001583	missense	25894	exon10			TGGAGGCCCGGGA	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24501	protein-coding gene	gene with protein product	"puratrophin-1"	609526	"spinocerebellar ataxia 4"	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.1370C>A	chr16.hg19:g.67316522C>A	ENSP00000353646:p.Ala457Asp	57.0	0.0		48.0	29.0	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	hg19	CCDS32466.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.490816	0.26774	.	.	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.09911	2.93;2.93;2.93;2.96	5.93	4.93	0.64822	.	0.253279	0.20765	N	0.086094	T	0.12433	0.0302	M	0.65975	2.015	0.25683	N	0.98578	P;P	0.44478	0.836;0.747	B;B	0.40101	0.319;0.17	T	0.20538	-1.0272	10	0.13470	T	0.59	.	11.5993	0.50993	0.1773:0.8227:0.0:0.0	.	376;457	Q58EX7-2;Q58EX7	.;PKHG4_HUMAN	D	457;457;457;376	ENSP00000353646:A457D;ENSP00000401118:A457D;ENSP00000368649:A457D;ENSP00000398030:A376D	ENSP00000353646:A457D	A	+	2	0	PLEKHG4	65874023	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	1.944000	0.40263	2.826000	0.97356	0.655000	0.94253	GCC	.	.		0.592	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432		A	67316522	C	A	67316522	3	1	220	1	0	0	0	0	1	0	0	0	12080	739	26	3	1404	3	PLEKHG4	16	67316522	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	16927787	67316522	23038231	73	31553										
WDR16	146845	hgsc.bcm.edu	37	chr17	9497562	9497562	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ccatctgtggcagccctgcaGccggcctcaatgttggcaat	11	14	2	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr17:9497562G>A	ENST00000352665.5	+	4	529	c.460G>A	c.(460-462)Gcc>Acc	p.A154T	WDR16_ENST00000299764.5_Missense_Mutation_p.A164T|WDR16_ENST00000396219.3_Missense_Mutation_p.A86T|WDR16_ENST00000576499.1_3'UTR	NM_145054.4	NP_659491.4			WD repeat domain 16											NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						CAGCCCTGCAGCCGGCCTCAA	0.488																																					p.A154T		Atlas-SNP	.											.	WDR16	67	.	0			c.G460A						.						107	110	109					17																	9497562		2203	4300	6503	SO:0001583	missense	146845	exon4			CCTGCAGCCGGCC	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"WD repeat domain containing"	16053	protein-coding gene	gene with protein product	"WD40-repeat protein upregulated in HCC"	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000352665.5:c.460G>A	chr17.hg19:g.9497562G>A	ENSP00000339449:p.Ala154Thr	51.0	0.0		75.0	22.0	NM_145054		Missense_Mutation	SNP	ENST00000352665.5	hg19	CCDS11149.2	.	.	.	.	.	.	.	.	.	.	G	16.25	3.071241	0.55646	.	.	ENSG00000166596	ENST00000352665;ENST00000396219;ENST00000299764	T;D;T	0.89939	1.5;-2.59;1.51	5.3	5.3	0.74995	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.112104	0.64402	D	0.000007	D	0.89100	0.6619	L	0.52266	1.64	0.39203	D	0.963182	P;P;P	0.51449	0.906;0.945;0.696	P;P;B	0.52909	0.713;0.713;0.338	D	0.87777	0.2609	10	0.32370	T	0.25	-23.0586	11.7588	0.51890	0.0:0.0:0.7191:0.2809	.	164;86;154	Q8N1V2-2;Q8N1V2-3;Q8N1V2	.;.;WDR16_HUMAN	T	154;86;164	ENSP00000339449:A154T;ENSP00000379521:A86T;ENSP00000299764:A164T	ENSP00000299764:A164T	A	+	1	0	WDR16	9438287	1.000000	0.71417	0.126000	0.21872	0.307000	0.27823	4.753000	0.62183	2.645000	0.89757	0.591000	0.81541	GCC	.	.		0.488	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054		A	9497562	G	A	9497562	3	1	220	1	0	0	0	0	1	0	0	0	17291	971	34	3	474	3	WDR16	17	9497562	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10		9497562	71697648	74	31554										
TANC2	26115	hgsc.bcm.edu	37	chr17	61497385	61497385	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tcgcagcagccttagaggacCtgaacgaggccatcaagctg	12	12	1	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr17:61497385C>A	ENST00000424789.2	+	25	4046	c.4042C>A	c.(4042-4044)Ctg>Atg	p.L1348M	RP11-269G24.3_ENST00000583552.1_RNA|TANC2_ENST00000389520.4_Missense_Mutation_p.L1358M	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	1348					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						CTTAGAGGACCTGAACGAGGC	0.502																																					p.L1348M		Atlas-SNP	.											.	TANC2	266	.	0			c.C4042A						.						25	28	27					17																	61497385		1870	3631	5501	SO:0001583	missense	26115	exon25			GAGGACCTGAACG	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.4042C>A	chr17.hg19:g.61497385C>A	ENSP00000387593:p.Leu1348Met	50.0	0.0		81.0	47.0	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Missense_Mutation	SNP	ENST00000424789.2	hg19	CCDS45754.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.851912	0.91355	.	.	ENSG00000170921	ENST00000389520;ENST00000424789	T;T	0.62105	0.05;0.05	5.95	5.95	0.96441	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.81273	0.4788	M	0.78223	2.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81326	-0.0983	10	0.62326	D	0.03	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	1348	Q9HCD6	TANC2_HUMAN	M	1358;1348	ENSP00000374171:L1358M;ENSP00000387593:L1348M	ENSP00000374171:L1358M	L	+	1	2	TANC2	58851117	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	CTG	.	.		0.502	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			A	61497385	C	A	61497385	3	1	220	1	0	0	0	0	1	0	0	0	15560	680	24	3	4140	3	TANC2	17	61497385	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	51999823	61497385	19697825	75	31555										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21422363	21422363	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tcttttttcctcttagaatcAagtgaccctgagaggacgtg	9	9	3	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr18:21422363A>T	ENST00000313654.9	+	28	3582	c.3341A>T	c.(3340-3342)cAa>cTa	p.Q1114L	LAMA3_ENST00000399516.3_Missense_Mutation_p.Q1114L	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1114	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TCTTAGAATCAAGTGACCCTG	0.443																																					p.Q1114L		Atlas-SNP	.											.	LAMA3	397	.	0			c.A3341T						.						97	94	95					18																	21422363		1875	4104	5979	SO:0001583	missense	3909	exon28			AGAATCAAGTGAC	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3341A>T	chr18.hg19:g.21422363A>T	ENSP00000324532:p.Gln1114Leu	194.0	0.0		273.0	98.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	A	18.99	3.740652	0.69304	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.18657	2.22;2.2	5.46	5.46	0.80206	.	.	.	.	.	T	0.47173	0.1431	M	0.77820	2.39	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.78314	0.91;0.991	T	0.41106	-0.9527	9	0.32370	T	0.25	.	15.5466	0.76108	1.0:0.0:0.0:0.0	.	1114;1114	Q6VU67;Q16787	.;LAMA3_HUMAN	L	1114;1114;1112	ENSP00000324532:Q1114L;ENSP00000382432:Q1114L	ENSP00000324532:Q1114L	Q	+	2	0	LAMA3	19676361	1.000000	0.71417	0.991000	0.47740	0.542000	0.35054	4.191000	0.58372	2.088000	0.63022	0.533000	0.62120	CAA	.	.		0.443	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21422363	A	T	21422363	3	4	220	1	0	0	0	0	1	0	0	0	8616	130	5	4	3451	4	LAMA3	18	21422363	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10		21422363	56654885	76	31556										
HMHA1	23526	hgsc.bcm.edu	37	chr19	1068487	1068487	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ccgcccgctgggtcctccggCgtcaaggccacagggaccct	13	18	1	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr19:1068487C>T	ENST00000313093.2	+	2	396	c.165C>T	c.(163-165)ggC>ggT	p.G55G	HMHA1_ENST00000586866.1_Silent_p.G59G|HMHA1_ENST00000543365.1_5'Flank|HMHA1_ENST00000539243.2_Silent_p.G71G|HMHA1_ENST00000536472.1_Intron|HMHA1_ENST00000590214.1_Silent_p.G82G	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	55					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTCCTCCGGCGTCAAGGCCA	0.726																																					p.G71G		Atlas-SNP	.											.	HMHA1	78	.	0			c.C213T						.						5	5	5					19																	1068487		1985	3953	5938	SO:0001819	synonymous_variant	23526	exon2			CTCCGGCGTCAAG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"Rho GTPase activating proteins"	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.165C>T	chr19.hg19:g.1068487C>T		119.0	0.0		118.0	41.0	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	hg19	CCDS32863.1																																																																																			.	.		0.726	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1			T	1068487	C	T	1068487	2	4	220	1	0	0	0	0	0	0	0	1	7249	755	27	1		1	HMHA1	19	1068487	Silent	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10		1068487	58060496	77	31557										
RYR1	6261	hgsc.bcm.edu	37	chr19	38976259	38976259	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	catcctggagctgtcggagcGcctggacctgcagcgcttcc	13	15	0	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr19:38976259G>T	ENST00000359596.3	+	34	4964	c.4964G>T	c.(4963-4965)cGc>cTc	p.R1655L	RYR1_ENST00000355481.4_Missense_Mutation_p.R1655L|RYR1_ENST00000360985.3_Missense_Mutation_p.R1655L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1655	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTGTCGGAGCGCCTGGACCTG	0.622																																					p.R1655L		Atlas-SNP	.											.	RYR1	708	.	0			c.G4964T						.						42	41	41					19																	38976259		2201	4295	6496	SO:0001583	missense	6261	exon34			CGGAGCGCCTGGA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.4964G>T	chr19.hg19:g.38976259G>T	ENSP00000352608:p.Arg1655Leu	27.0	0.0		36.0	7.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.992313	0.54041	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96651	-4.08;-4.08;-4.08	3.98	3.98	0.46160	.	0.078316	0.48767	U	0.000169	D	0.95896	0.8664	L	0.41236	1.265	0.42017	D	0.990968	D;B	0.69078	0.997;0.146	D;B	0.63877	0.919;0.199	D	0.94590	0.7787	10	0.35671	T	0.21	.	10.9611	0.47385	0.0952:0.0:0.9048:0.0	.	1655;1655	P21817-2;P21817	.;RYR1_HUMAN	L	1655	ENSP00000352608:R1655L;ENSP00000347667:R1655L;ENSP00000354254:R1655L	ENSP00000347667:R1655L	R	+	2	0	RYR1	43668099	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.189000	0.50965	2.043000	0.60533	0.650000	0.86243	CGC	.	.		0.622	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38976259	G	T	38976259	3	4	220	1	0	0	0	0	1	0	0	0	13783	1087	38	1	5098	1	RYR1	19	38976259	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	37907772	38976259	20152724	78	31558										
DYRK1B	9149	hgsc.bcm.edu	37	chr19	40319067	40319067	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gctcaggcgtggccagaaagAgcagtgccgtgcagagctgc	16	11	1	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr19:40319067A>G	ENST00000593685.1	-	6	1145	c.677T>C	c.(676-678)cTc>cCc	p.L226P	DYRK1B_ENST00000323039.5_Missense_Mutation_p.L226P|DYRK1B_ENST00000430012.2_Missense_Mutation_p.L226P|DYRK1B_ENST00000348817.3_Missense_Mutation_p.L226P|DYRK1B_ENST00000597639.1_Missense_Mutation_p.L226P			Q9Y463	DYR1B_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1B	226	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adipose tissue development (GO:0060612)|myoblast fusion (GO:0007520)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(7)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	24	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)		Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)			GGCCAGAAAGAGCAGTGCCGT	0.602																																					p.L226P		Atlas-SNP	.											.	DYRK1B	114	.	0			c.T677C						.						73	65	68					19																	40319067		2203	4300	6503	SO:0001583	missense	9149	exon6			AGAAAGAGCAGTG	Y17999	CCDS12543.1, CCDS12544.1, CCDS46075.1	19q13.2	2012-10-02			ENSG00000105204	ENSG00000105204	2.7.12.1		3092	protein-coding gene	gene with protein product	"minibrain-related kinase"	604556				9918863	Standard	XM_005259395		Approved	MIRK	uc002omj.3	Q9Y463		ENST00000593685.1:c.677T>C	chr19.hg19:g.40319067A>G	ENSP00000469863:p.Leu226Pro	79.0	0.0		99.0	32.0	NM_006483	O75258|O75788|O75789	Missense_Mutation	SNP	ENST00000593685.1	hg19	CCDS12543.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.357820	0.61403	.	.	ENSG00000105204	ENST00000323039;ENST00000348817;ENST00000430012	T;T;T	0.65549	-0.16;-0.16;-0.16	5.95	5.95	0.96441	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	T	0.76097	0.3940	M	0.71871	2.18	0.80722	D	1	D;D;D	0.76494	0.993;0.999;0.993	D;D;D	0.68765	0.921;0.96;0.921	T	0.74429	-0.3668	10	0.30854	T	0.27	.	14.3573	0.66745	1.0:0.0:0.0:0.0	.	226;226;226	Q9Y463-2;Q9Y463;Q9Y463-3	.;DYR1B_HUMAN;.	P	226	ENSP00000312789:L226P;ENSP00000221803:L226P;ENSP00000403182:L226P	ENSP00000312789:L226P	L	-	2	0	DYRK1B	45010907	1.000000	0.71417	1.000000	0.80357	0.518000	0.34316	9.313000	0.96297	2.279000	0.76181	0.402000	0.26972	CTC	.	.		0.602	DYRK1B-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462874.2	NM_004714		G	40319067	A	G	40319067	3	3	220	1	0	0	0	0	1	0	0	0	4857	304	11	2	1236	2	DYRK1B	19	40319067	Missense_Mutation	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	1342808	40319067	18809916	79	31559										
FBL	2091	hgsc.bcm.edu	37	chr19	40331279	40331279	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	cctcttcctcctcctccaccGccgccgccgcctccacctcc	4	27	1	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr19:40331279G>A	ENST00000221801.3	-	2	272	c.159C>T	c.(157-159)ggC>ggT	p.G53G	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	53	DMA/Gly-rich.				histone glutamine methylation (GO:1990258)|osteoblast differentiation (GO:0001649)|rRNA processing (GO:0006364)|snoRNA metabolic process (GO:0016074)|tRNA processing (GO:0008033)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone-glutamine methyltransferase activity (GO:1990259)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)	9	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		ctcctccaccgccgccgccgc	0.657																																					p.G53G		Atlas-SNP	.											.	FBL	37	.	0			c.C159T						.						18	21	20					19																	40331279		2201	4299	6500	SO:0001819	synonymous_variant	2091	exon2			TCCACCGCCGCCG	AC005393	CCDS12545.1	19q13.1	2010-02-17			ENSG00000105202	ENSG00000105202			3599	protein-coding gene	gene with protein product		134795				1846968, 2026646	Standard	NM_001436		Approved	RNU3IP1, FLRN, FIB	uc002omn.3	P22087		ENST00000221801.3:c.159C>T	chr19.hg19:g.40331279G>A		86.0	0.0		121.0	5.0	NM_001436	B5BUE8|O75259|Q6IAT5|Q9UPI6	Silent	SNP	ENST00000221801.3	hg19	CCDS12545.1																																																																																			.	.		0.657	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436		A	40331279	G	A	40331279	2	1	220	1	0	0	0	0	0	0	0	1	5704	1074	38	1		1	FBL	19	40331279	Silent	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	12212	40331279	18797704	80	31560										
GPR4	2828	hgsc.bcm.edu	37	chr19	46094941	46094941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gcagatgtacagcaggtcggCgatgctgaggttcatcaggt	15	8	2	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr19:46094941C>T	ENST00000323040.4	-	2	1128	c.184G>A	c.(184-186)Gcc>Acc	p.A62T	OPA3_ENST00000544371.1_Intron|GPR4_ENST00000591614.1_5'Flank	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	62					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		AGCAGGTCGGCGATGCTGAGG	0.647																																					p.A62T	Esophageal Squamous(117;181 1612 1673 14956 42937)	Atlas-SNP	.											.	GPR4	54	.	0			c.G184A						.						110	91	97					19																	46094941		2203	4300	6503	SO:0001583	missense	2828	exon2			GGTCGGCGATGCT	BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464		"GPCR / Class A : Orphans"	4497	protein-coding gene	gene with protein product		600551				8595909	Standard	NM_005282		Approved		uc002pcm.3	P46093		ENST00000323040.4:c.184G>A	chr19.hg19:g.46094941C>T	ENSP00000319744:p.Ala62Thr	72.0	0.0		91.0	38.0	NM_005282	A8K3T3|B0M0K1|Q6NWM4	Missense_Mutation	SNP	ENST00000323040.4	hg19	CCDS12669.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.009988	0.75046	.	.	ENSG00000177464	ENST00000323040	T	0.78003	-1.14	5.09	5.09	0.68999	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000009	D	0.85221	0.5647	M	0.66297	2.02	0.43673	D	0.996105	D	0.89917	1.0	D	0.74023	0.982	D	0.86398	0.1740	10	0.87932	D	0	.	11.133	0.48358	0.1845:0.8155:0.0:0.0	.	62	P46093	GPR4_HUMAN	T	62	ENSP00000319744:A62T	ENSP00000319744:A62T	A	-	1	0	GPR4	50786781	0.988000	0.35896	0.997000	0.53966	0.934000	0.57294	2.457000	0.45005	2.355000	0.79922	0.297000	0.19635	GCC	.	.		0.647	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459603.1	NM_005282		T	46094941	C	T	46094941	3	4	220	1	0	0	0	0	1	0	0	0	6702	768	27	1	908	1	GPR4	19	46094941	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	5763662	46094941	13034042	81	31561										
SIGLEC10	89790	hgsc.bcm.edu	37	chr19	51920112	51920112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	gaaagaagggggtggacattCctcaaaggcccagttaaaca	12	8	1	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr19:51920112C>T	ENST00000339313.5	-	3	630	c.514G>A	c.(514-516)Gaa>Aaa	p.E172K	SIGLEC10_ENST00000353836.5_Missense_Mutation_p.E172K|CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000525998.1_Missense_Mutation_p.E172K|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000432469.2_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Intron|SIGLEC10_ENST00000436984.2_Intron|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.E172K|SIGLEC10_ENST00000439889.2_Intron			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	172	Ig-like C2-type 1.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		GGTGGACATTCCTCAAAGGCC	0.602																																					p.E172K		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.G514A						.						101	100	100					19																	51920112		2203	4300	6503	SO:0001583	missense	89790	exon3			GACATTCCTCAAA	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15620	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 10 Ig-like lectin 7", "siglec-like gene 2"	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.514G>A	chr19.hg19:g.51920112C>T	ENSP00000345243:p.Glu172Lys	122.0	0.0		185.0	12.0	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	hg19	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	11.48	1.650199	0.29336	.	.	ENSG00000142512	ENST00000353836;ENST00000356298;ENST00000525998;ENST00000339313;ENST00000530476	T;T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94;-0.94	4.69	-3.05	0.05396	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.077330	0.07177	N	0.853380	T	0.58977	0.2160	L	0.40543	1.245	0.09310	N	1	B;B;B	0.32862	0.387;0.045;0.058	B;B;B	0.35039	0.194;0.026;0.021	T	0.45659	-0.9246	10	0.10636	T	0.68	.	5.8825	0.18864	0.0:0.256:0.357:0.387	.	172;172;172	E9PL79;Q96LC7-2;Q96LC7	.;.;SIG10_HUMAN	K	172;172;172;172;139	ENSP00000342389:E172K;ENSP00000348646:E172K;ENSP00000431444:E172K;ENSP00000345243:E172K;ENSP00000433838:E139K	ENSP00000345243:E172K	E	-	1	0	SIGLEC10	56611924	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.461000	0.06712	-0.176000	0.10707	-0.657000	0.03884	GAA	.	.		0.602	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		T	51920112	C	T	51920112	3	4	220	1	0	0	0	0	1	0	0	0	14321	864	30	3	1615	3	SIGLEC10	19	51920112	Missense_Mutation	SNP	C	TCGA-DD-AAEH-01A-11D-A40R-10	5825171	51920112	7208871	82	31562										
FPR3	2359	hgsc.bcm.edu	37	chr19	52327369	52327369	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	caccatcattgctctggaccGctgtatttgtgtcctgcatc	8	13	2	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr19:52327369G>A	ENST00000339223.4	+	2	547	c.368G>A	c.(367-369)cGc>cAc	p.R123H	FPR3_ENST00000595991.1_Missense_Mutation_p.R123H	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	123					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)			NS(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)	35						GCTCTGGACCGCTGTATTTGT	0.478																																					p.R123H		Atlas-SNP	.											.	FPR3	66	.	0			c.G368A						.						92	77	82					19																	52327369		2203	4300	6503	SO:0001583	missense	2359	exon2			TGGACCGCTGTAT		CCDS12841.1	19q13.3-q13.4	2012-08-08	2008-04-17	2008-04-17		ENSG00000187474		"GPCR / Class A : Formyl peptide receptors"	3828	protein-coding gene	gene with protein product		136539	"formyl peptide receptor-like 2"	FPRL2		1612600, 8198572	Standard	NM_002030		Approved	FPRH1, FMLPY, RMLP-R-I	uc002pxt.1	P25089		ENST00000339223.4:c.368G>A	chr19.hg19:g.52327369G>A	ENSP00000341821:p.Arg123His	109.0	0.0		99.0	26.0	NM_002030		Missense_Mutation	SNP	ENST00000339223.4	hg19	CCDS12841.1	.	.	.	.	.	.	.	.	.	.	.	12.15	1.850699	0.32699	.	.	ENSG00000187474	ENST00000339223	D	0.97161	-4.27	2.34	2.34	0.29019	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	D	0.97297	0.9116	M	0.91406	3.205	0.32098	N	0.590994	B	0.30605	0.287	B	0.40228	0.323	D	0.99869	1.1094	10	0.56958	D	0.05	.	10.3497	0.43927	0.0:0.0:1.0:0.0	.	123	P25089	FPR3_HUMAN	H	123	ENSP00000341821:R123H	ENSP00000341821:R123H	R	+	2	0	FPR3	57019181	1.000000	0.71417	0.967000	0.41034	0.071000	0.16799	4.369000	0.59511	1.323000	0.45263	0.467000	0.42956	CGC	.	.		0.478	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030		A	52327369	G	A	52327369	3	1	220	1	0	0	0	0	1	0	0	0	6048	1087	38	1	370	1	FPR3	19	52327369	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	407257	52327369	6801614	83	31563										
PDYN	5173	hgsc.bcm.edu	37	chr20	1961381	1961381	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tcttgctcagagtgttctccTttgttgagatacttgggaga	11	7	3	3			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr20:1961381T>C	ENST00000217305.2	-	4	578	c.353A>G	c.(352-354)aAg>aGg	p.K118R	RP4-684O24.5_ENST00000446562.1_RNA|PDYN_ENST00000539905.1_Missense_Mutation_p.K118R|PDYN_ENST00000540134.1_Missense_Mutation_p.K118R	NM_001190892.1|NM_001190898.2|NM_024411.4	NP_001177821.1|NP_001177827.1|NP_077722.1	P01213	PDYN_HUMAN	prodynorphin	118					cell death (GO:0008219)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						AGTGTTCTCCTTTGTTGAGAT	0.552																																					p.K118R		Atlas-SNP	.											.	PDYN	74	.	0			c.A353G						.						109	106	107					20																	1961381		2203	4300	6503	SO:0001583	missense	5173	exon4			TTCTCCTTTGTTG		CCDS13023.1	20p13	2014-09-17			ENSG00000101327	ENSG00000101327		"Endogenous ligands"	8820	protein-coding gene	gene with protein product	"preproenkephalin B", "rimorphin", "beta-neoendorphin", "dynorphin", "leu-enkephalin", "leumorphin", "neoendorphin-dynorphin-enkephalin prepropeptide"	131340	"spinocerebellar ataxia 23"	SCA23		21035104	Standard	NM_001190892		Approved	PENKB, ADCA	uc021vzs.1	P01213	OTTHUMG00000031683	ENST00000217305.2:c.353A>G	chr20.hg19:g.1961381T>C	ENSP00000217305:p.Lys118Arg	82.0	0.0		148.0	41.0	NM_001190898	A8K0Q3	Missense_Mutation	SNP	ENST00000217305.2	hg19	CCDS13023.1	.	.	.	.	.	.	.	.	.	.	T	2.026	-0.423654	0.04734	.	.	ENSG00000101327	ENST00000539905;ENST00000540134;ENST00000217305	T;T;T	0.80824	-1.42;-1.42;-1.42	3.96	2.86	0.33363	.	0.811582	0.11477	N	0.560117	T	0.57446	0.2054	N	0.03608	-0.345	0.25176	N	0.990246	B	0.09022	0.002	B	0.04013	0.001	T	0.45026	-0.9289	10	0.23891	T	0.37	-8.7273	7.4029	0.26975	0.0:0.1072:0.0:0.8928	.	118	P01213	PDYN_HUMAN	R	118	ENSP00000440185:K118R;ENSP00000442259:K118R;ENSP00000217305:K118R	ENSP00000217305:K118R	K	-	2	0	PDYN	1909381	0.149000	0.22717	0.263000	0.24496	0.098000	0.18820	0.978000	0.29488	0.625000	0.30304	0.391000	0.25812	AAG	.	.		0.552	PDYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077569.2			C	1961381	T	C	1961381	3	2	220	1	0	0	0	0	1	0	0	0	11708	1609	56	2	415	2	PDYN	20	1961381	Missense_Mutation	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10		1961381	61064139	84	31564										
C20orf94	128710	hgsc.bcm.edu	37	chr20	10602024	10602024	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tgtgcagagagttcacttccTcccagtgcaaagctccggag	11	12	1	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr20:10602024T>C	ENST00000334534.5	+	7	648	c.468T>C	c.(466-468)ccT>ccC	p.P156P		NM_001009608.1	NP_001009608.1	Q5VYV7	SLX4I_HUMAN	SLX4 interacting protein	156																	GTTCACTTCCTCCCAGTGCAA	0.403																																					p.P156P		Atlas-SNP	.											.	.	.	.	0			c.T468C						.						142	124	130					20																	10602024		2203	4300	6503	SO:0001819	synonymous_variant	128710	exon7			ACTTCCTCCCAGT	AL035456	CCDS33439.1	20p12	2012-10-30	2012-10-30	2012-10-30	ENSG00000149346	ENSG00000149346			16225	protein-coding gene	gene with protein product		615958	"chromosome 20 open reading frame 94"	C20orf94		19596235	Standard	XM_005260664		Approved	dJ1099D15.3	uc010zre.2	Q5VYV7	OTTHUMG00000031873	ENST00000334534.5:c.468T>C	chr20.hg19:g.10602024T>C		83.0	0.0		179.0	86.0	NM_001009608	Q05CG2|Q05CT9	Silent	SNP	ENST00000334534.5	hg19	CCDS33439.1																																																																																			.	.		0.403	SLX4IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078000.3	NM_001009608		C	10602024	T	C	10602024	2	2	220	1	0	0	0	0	0	0	0	1	2123	1538	54	2		2	C20orf94	20	10602024	Silent	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10	8640643	10602024	52423496	85	31565										
NANP	140838	hgsc.bcm.edu	37	chr20	25596729	25596729	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ttgaggcctccttggatgtcGgtttctaatgtgtcaccgac	11	10	2	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr20:25596729G>C	ENST00000304788.3	-	2	805	c.579C>G	c.(577-579)acC>acG	p.T193T		NM_152667.2	NP_689880.1	Q8TBE9	NANP_HUMAN	N-acetylneuraminic acid phosphatase	193					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate biosynthetic process (GO:0046380)		N-acylneuraminate-9-phosphatase activity (GO:0050124)			endometrium(2)|lung(2)|prostate(1)	5						CTTGGATGTCGGTTTCTAATG	0.473																																					p.T193T		Atlas-SNP	.											.	NANP	10	.	0			c.C579G						.						120	109	112					20																	25596729		2203	4300	6503	SO:0001819	synonymous_variant	140838	exon2			GATGTCGGTTTCT	AL031673	CCDS13173.1	20p11.1	2006-10-24	2006-01-24	2006-01-24	ENSG00000170191	ENSG00000170191			16140	protein-coding gene	gene with protein product		610763	"chromosome 20 open reading frame 147", "haloacid dehalogenase-like hydrolase domain containing 4"	C20orf147, HDHD4		16237198	Standard	NM_152667		Approved	dJ694B14.3, MGC26833	uc002wuy.3	Q8TBE9	OTTHUMG00000032132	ENST00000304788.3:c.579C>G	chr20.hg19:g.25596729G>C		65.0	0.0		122.0	24.0	NM_152667	B3KP12|Q5JYN8|Q8TE97|Q9Y3N0	Silent	SNP	ENST00000304788.3	hg19	CCDS13173.1																																																																																			.	.		0.473	NANP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078457.2	NM_152667		C	25596729	G	C	25596729	2	2	220	1	0	0	0	0	0	0	0	1	10163	1103	39	4		4	NANP	20	25596729	Silent	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	14994705	25596729	37428791	86	31566										
WFDC3	140686	hgsc.bcm.edu	37	chr20	44417610	44417610	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	atccgaccacagcctgtggtGcagcacttctgttcagccgg	11	14	2	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr20:44417610G>A	ENST00000243938.4	-	3	254	c.171C>T	c.(169-171)tgC>tgT	p.C57C	DNTTIP1_ENST00000372622.3_5'Flank|WFDC3_ENST00000372632.2_Silent_p.C57C|WFDC3_ENST00000372630.2_Intron|WFDC3_ENST00000481847.1_Intron	NM_080614.1	NP_542181.1	Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3	57	WAP 1. {ECO:0000255|PROSITE- ProRule:PRU00722}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				AGCCTGTGGTGCAGCACTTCT	0.512																																					p.C57C		Atlas-SNP	.											.	WFDC3	18	.	0			c.C171T						.						231	210	217					20																	44417610		2203	4300	6503	SO:0001819	synonymous_variant	140686	exon3			TGTGGTGCAGCAC	AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116		"WAP four-disulfide core domain containing"	15957	protein-coding gene	gene with protein product						12206714, 10680116	Standard	NM_080614		Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000243938.4:c.171C>T	chr20.hg19:g.44417610G>A		57.0	0.0		95.0	18.0	NM_080614	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	Silent	SNP	ENST00000243938.4	hg19	CCDS33478.1	.	.	.	.	.	.	.	.	.	.	G	3.992	-0.004255	0.07773	.	.	ENSG00000124116	ENST00000337205	.	.	.	3.57	0.403	0.16350	.	.	.	.	.	T	0.51975	0.1706	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38351	-0.9665	4	.	.	.	-6.9051	6.3144	0.21182	0.3578:0.0:0.6422:0.0	.	.	.	.	V	51	.	.	A	-	2	0	WFDC3	43851017	0.880000	0.30214	0.512000	0.27736	0.443000	0.32047	0.500000	0.22562	-0.003000	0.14444	0.655000	0.94253	GCA	.	.		0.512	WFDC3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316858.1			A	44417610	G	A	44417610	2	1	220	1	0	0	0	0	0	0	0	1	17368	1311	46	3		3	WFDC3	20	44417610	Silent	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	18820881	44417610	18607910	87	31567										
RTEL1	51750	hgsc.bcm.edu	37	chr20	62316913	62316928	+	Frame_Shift_Del	DEL	GTTCCCCAGCAGGGCT	GTTCCCCAGCAGGGCT	-													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	cccctccgagggcagccctgGttccccagcagggctggggg							TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	GTTCCCCAGCAGGGCT	GTTCCCCAGCAGGGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr20:62316913_62316928delGTTCCCCAGCAGGGCT	ENST00000360203.5	+	15	1554_1569	c.1229_1244delGTTCCCCAGCAGGGCT	c.(1228-1245)ggttccccagcagggctgfs	p.GSPAGL410fs	RTEL1_ENST00000318100.4_Frame_Shift_Del_p.GSPAGL410fs|RTEL1_ENST00000370018.3_Frame_Shift_Del_p.GSPAGL410fs|RTEL1_ENST00000508582.2_Frame_Shift_Del_p.GSPAGL434fs|RTEL1-TNFRSF6B_ENST00000482936.1_Frame_Shift_Del_p.GSPAGL410fs					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			GGCAGCCCTGGTTCCCCAGCAGGGCTGGGGGCCTTA	0.634																																					p.434_439del		Atlas-INDEL	.											.	RTEL1	114	.	0			c.1300_1315del						.																																			SO:0001589	frameshift_variant	51750	exon15			.	AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"chromosome 20 open reading frame 41"	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.1229_1244delGTTCCCCAGCAGGGCT	chr20.hg19:g.62316913_62316928delGTTCCCCAGCAGGGCT	ENSP00000353332:p.Gly410fs	61.0	0.0		102.0	15.0	NM_032957		Frame_Shift_Del	DEL	ENST00000360203.5	hg19																																																																																				.	.		0.634	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957		-	62316928	GTTCCCCAGCAGGGCT	-	62316913	7	5	220	1	0	1	0	1	0	0	0	0	13735	1261	44	0	1283	0	RTEL1	20	62316913	Frame_Shift_Del	DEL	GTTCCCCAGCAGGGCT	TCGA-DD-AAEH-01A-11D-A40R-10	17899303	62316913	708607	88	31568										
CRYAA	1409	hgsc.bcm.edu	37	chr21	44589306	44589306	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ttttcggcgagggcctttttGagtatgacctgctgcccttc	11	11	0	2			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr21:44589306G>A	ENST00000291554.2	+	1	189	c.97G>A	c.(97-99)Gag>Aag	p.E33K	CRYAA_ENST00000398133.1_5'Flank|CRYAA_ENST00000398132.1_5'Flank|CRYAA_ENST00000482775.1_3'UTR	NM_000394.2	NP_000385.1	P02489	CRYAA_HUMAN	crystallin, alpha A	33					negative regulation of apoptotic process (GO:0043066)|negative regulation of intracellular transport (GO:0032387)|protein homooligomerization (GO:0051260)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural constituent of eye lens (GO:0005212)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	11						GGGCCTTTTTGAGTATGACCT	0.612																																					p.E33K		Atlas-SNP	.											.	CRYAA	23	.	0			c.G97A						.						167	164	165					21																	44589306		2203	4300	6503	SO:0001583	missense	1409	exon1			CTTTTTGAGTATG		CCDS13695.1	21q22.3	2011-09-05			ENSG00000160202	ENSG00000160202		"Heat shock proteins / HSPB"	2388	protein-coding gene	gene with protein product		123580		CRYA1			Standard	XM_005261093		Approved	HSPB4	uc002zdd.1	P02489	OTTHUMG00000086842	ENST00000291554.2:c.97G>A	chr21.hg19:g.44589306G>A	ENSP00000291554:p.Glu33Lys	44.0	0.0		58.0	13.0	NM_000394	Q53X53	Missense_Mutation	SNP	ENST00000291554.2	hg19	CCDS13695.1	.	.	.	.	.	.	.	.	.	.	G	35	5.486293	0.96323	.	.	ENSG00000160202	ENST00000291554	D	0.86956	-2.19	4.88	4.88	0.63580	Alpha-crystallin, N-terminal (1);	0.051800	0.85682	D	0.000000	D	0.92407	0.7590	L	0.61036	1.89	0.80722	D	1	D	0.53745	0.962	D	0.69824	0.966	D	0.93127	0.6530	10	0.66056	D	0.02	-33.302	18.0021	0.89200	0.0:0.0:1.0:0.0	.	33	P02489	CRYAA_HUMAN	K	33	ENSP00000291554:E33K	ENSP00000291554:E33K	E	+	1	0	CRYAA	43462375	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.858000	0.92256	2.256000	0.74724	0.609000	0.83330	GAG	.	.		0.612	CRYAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195562.1			A	44589306	G	A	44589306	3	1	220	1	0	0	0	0	1	0	0	0	3907	1291	45	3	99	3	CRYAA	21	44589306	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10		44589306	3540589	89	31569										
KRTAP10-7	386675	hgsc.bcm.edu	37	chr21	46020873	46020874	+	Frame_Shift_Del	DEL	GT	GT	-													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	agcaggcctgctgcatgcccGtctgctgcaagactgtctgc					rs369241670		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr21:46020873_46020874delGT	ENST00000380102.2	+	1	377_378	c.352_353delGT	c.(352-354)gtcfs	p.V118fs	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	118	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						CTGCATGCCCGTCTGCTGCAAG	0.629																																					p.112_113del		Atlas-INDEL	.											.	KRTAP10-7	41	.	0			c.336_337del						.																																			SO:0001589	frameshift_variant	386675	exon2			.	AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"Keratin associated proteins"	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.352_353delGT	chr21.hg19:g.46020873_46020874delGT	ENSP00000369445:p.Val118fs	42.0	0.0		52.0	11.0	NM_198689	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	hg19																																																																																				.	.		0.629	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689		-	46020874	GT	-	46020873	7	5	220	1	0	1	0	1	0	0	0	0	8523	1145	40	0	343	0	KRTAP10-7	21	46020873	Frame_Shift_Del	DEL	GT	TCGA-DD-AAEH-01A-11D-A40R-10	1431567	46020873	2109022	90	31570										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885648	29885648	+	Silent	SNP	A	A	G													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	aagtccccagtgaaggcagaAgcaaagtcccctgagaaggc					rs267607535		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr22:29885648A>G	ENST00000310624.6	+	4	2052	c.2019A>G	c.(2017-2019)gaA>gaG	p.E673E		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	679	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						TGAAGGCAGAAGCAAAGTCCC	0.567																																					p.E673E		Atlas-SNP	.											.	NEFH	178	.	0			c.A2019G						.						93	99	97					22																	29885648		2203	4299	6502	SO:0001819	synonymous_variant	4744	exon4			GGCAGAAGCAAAG		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2019A>G	chr22.hg19:g.29885648A>G		255.0	0.0		353.0	18.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.567	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		G	29885648	A	G	29885648	2	3	220	1	0	0	0	0	0	0	0	1	10323	69	3	2		2	NEFH	22	29885648	Silent	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10		29885648	21418918	91	31571	164	2								
NEFH	4744	hgsc.bcm.edu	37	chr22	29885651	29885651	+	Silent	SNP	A	A	C													0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	tccccagtgaaggcagaagcAaagtcccctgagaaggccaa					rs267607535		TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chr22:29885651A>C	ENST00000310624.6	+	4	2055	c.2022A>C	c.(2020-2022)gcA>gcC	p.A674A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	680	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGCAGAAGCAAAGTCCCCTG	0.567																																					p.A674A		Atlas-SNP	.											.	NEFH	178	.	0			c.A2022C						.						92	98	96					22																	29885651		2203	4297	6500	SO:0001819	synonymous_variant	4744	exon4			AGAAGCAAAGTCC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2022A>C	chr22.hg19:g.29885651A>C		264.0	0.0		358.0	19.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.567	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		C	29885651	A	C	29885651	2	2	220	1	0	0	0	0	0	0	0	1	10323	117	5	5		5	NEFH	22	29885651	Silent	SNP	A	TCGA-DD-AAEH-01A-11D-A40R-10	3	29885651	21418915	92	31572	164	2								
TRO	7216	hgsc.bcm.edu	37	chrX	54957051	54957051	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ggactgggcaccaatgctagTttcggcagcacacttggcac	12	12	0	0			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chrX:54957051T>C	ENST00000173898.7	+	12	4006	c.3894T>C	c.(3892-3894)agT>agC	p.S1298S	TRO_ENST00000375022.4_Intron|TRO_ENST00000420798.2_Silent_p.S829S|TRO_ENST00000319167.8_Intron|TRO_ENST00000399736.1_Intron|TRO_ENST00000375041.2_Silent_p.S901S	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	1298	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						CCAATGCTAGTTTCGGCAGCA	0.587																																					p.S1298S		Atlas-SNP	.											.	TRO	246	.	0			c.T3894C						.						81	76	77					X																	54957051		2133	4231	6364	SO:0001819	synonymous_variant	7216	exon12			TGCTAGTTTCGGC	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.3894T>C	chrX.hg19:g.54957051T>C		32.0	0.0		50.0	35.0	NM_001039705	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Silent	SNP	ENST00000173898.7	hg19	CCDS43959.1																																																																																			.	.		0.587	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		C	54957051	T	C	54957051	2	2	220	1	0	0	0	0	0	0	0	1	16589	1722	60	2		2	TRO	23	54957051	Silent	SNP	T	TCGA-DD-AAEH-01A-11D-A40R-10		54957051	100313509	93	31573										
CXCR3	2833	hgsc.bcm.edu	37	chrX	70836725	70836725	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ttgtattggcagtgggtggcGttgaggcgctcgtcgtggtg	19	6	0	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chrX:70836725G>T	ENST00000373693.3	-	2	664	c.597C>A	c.(595-597)aaC>aaA	p.N199K	CXCR3_ENST00000373691.4_Missense_Mutation_p.N246K	NM_001504.1	NP_001495.1	P49682	CXCR3_HUMAN	chemokine (C-X-C motif) receptor 3	199					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|calcium-mediated signaling (GO:0019722)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|chemokine (C-C motif) ligand 11 production (GO:0071954)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of leukocyte migration (GO:0002685)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|chemokine binding (GO:0019956)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(2)|lung(3)|ovary(2)	10	Renal(35;0.156)					AGTGGGTGGCGTTGAGGCGCT	0.662																																					p.N246K		Atlas-SNP	.											.	CXCR3	57	.	0			c.C738A						.						35	30	32					X																	70836725		2202	4295	6497	SO:0001583	missense	2833	exon2			GGTGGCGTTGAGG	U32674	CCDS14416.1, CCDS48135.1	Xq13	2012-08-08	2002-08-22	2002-08-23	ENSG00000186810	ENSG00000186810		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	4540	protein-coding gene	gene with protein product		300574	"G protein-coupled receptor 9"	GPR9		8666380, 9064356	Standard	NM_001142797		Approved	CKR-L2, CMKAR3, IP10-R, MigR, CD183	uc011mpx.2	P49682	OTTHUMG00000033326	ENST00000373693.3:c.597C>A	chrX.hg19:g.70836725G>T	ENSP00000362797:p.Asn199Lys	81.0	0.0		80.0	59.0	NM_001142797	B2R982|O15185|Q7Z710|Q9P2T4|Q9P2T5	Missense_Mutation	SNP	ENST00000373693.3	hg19	CCDS14416.1	.	.	.	.	.	.	.	.	.	.	G	3.738	-0.054130	0.07362	.	.	ENSG00000186810	ENST00000373691;ENST00000373693;ENST00000373687	T;T	0.40476	1.03;1.03	5.15	-10.2	0.00374	GPCR, rhodopsin-like superfamily (1);	0.669254	0.13737	N	0.366245	T	0.20292	0.0488	L	0.37750	1.13	0.09310	N	1	B;B	0.14438	0.01;0.007	B;B	0.19391	0.013;0.025	T	0.05750	-1.0866	10	0.30854	T	0.27	.	2.9748	0.05934	0.183:0.2001:0.4175:0.1993	.	246;199	P49682-2;P49682	.;CXCR3_HUMAN	K	246;199;199	ENSP00000362795:N246K;ENSP00000362797:N199K	ENSP00000362791:N199K	N	-	3	2	CXCR3	70753450	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-3.524000	0.00442	-2.177000	0.00769	-2.583000	0.00167	AAC	.	.		0.662	CXCR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144141.1			T	70836725	G	T	70836725	3	4	220	1	0	0	0	0	1	0	0	0	4094	1136	40	1	513	1	CXCR3	23	70836725	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	15879674	70836725	84433835	94	31574										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73963704	73963704	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0319148936170213	3	1	0.766057664858693	0.879547689282203	0.719629927594529	1	1	0	ataatagcttttctgagccgGatcctccaagtcaatgtcag	8	10	3	1			TCGA-DD-AAEH-01A-11D-A40R-10	TCGA-DD-AAEH-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa21884c-96c0-4146-a5fe-65cade5f3658	3c6c79fc-5876-4247-8e0c-edba801ceb16	g.chrX:73963704G>T	ENST00000055682.6	-	3	1299	c.688C>A	c.(688-690)Ccg>Acg	p.P230T		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	230					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						TTCTGAGCCGGATCCTCCAAG	0.478																																					p.P230T		Atlas-SNP	.											.	KIAA2022	262	.	0			c.C688A						.						162	147	152					X																	73963704		2203	4298	6501	SO:0001583	missense	340533	exon3			GAGCCGGATCCTC		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.688C>A	chrX.hg19:g.73963704G>T	ENSP00000055682:p.Pro230Thr	96.0	0.0		104.0	66.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.863192	0.51482	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.39229	1.09;1.09	5.97	5.97	0.96955	.	0.052061	0.85682	D	0.000000	T	0.56202	0.1969	L	0.50333	1.59	0.54753	D	0.999981	D	0.56746	0.977	P	0.55923	0.787	T	0.57177	-0.7856	10	0.87932	D	0	-4.6567	19.3296	0.94280	0.0:0.0:1.0:0.0	.	230	Q5QGS0	K2022_HUMAN	T	230	ENSP00000362567:P230T;ENSP00000055682:P230T	ENSP00000055682:P230T	P	-	1	0	KIAA2022	73880429	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.145000	0.58065	2.517000	0.84864	0.600000	0.82982	CCG	.	.		0.478	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		T	73963704	G	T	73963704	3	4	220	1	0	0	0	0	1	0	0	0	8278	1174	41	3	3870	3	KIAA2022	23	73963704	Missense_Mutation	SNP	G	TCGA-DD-AAEH-01A-11D-A40R-10	3126979	73963704	81306856	95	31575										
KAZ	23254	hgsc.bcm.edu	37	chr1	15382644	15382644	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ccaagcggcattccctcgccAtgccgggcgagacggtgctc	13	16	0	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr1:15382644A>T	ENST00000376030.2	+	5	1078	c.784A>T	c.(784-786)Atg>Ttg	p.M262L	KAZN_ENST00000361144.5_Missense_Mutation_p.M256L|KAZN_ENST00000400798.2_Missense_Mutation_p.M168L|KAZN_ENST00000400797.3_Missense_Mutation_p.M168L|KAZN_ENST00000503743.1_Missense_Mutation_p.M262L|KAZN_ENST00000422387.2_Missense_Mutation_p.M262L	NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	262	Interaction with PPL.				keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						TTCCCTCGCCATGCCGGGCGA	0.597																																					p.M262L		Atlas-SNP	.											.	KAZN	57	.	0			c.A784T						.						76	73	74					1																	15382644		2203	4300	6503	SO:0001583	missense	23254	exon5			CTCGCCATGCCGG	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.784A>T	chr1.hg19:g.15382644A>T	ENSP00000365198:p.Met262Leu	189.0	0.0		169.0	61.0	NM_015209	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	hg19	CCDS152.2	.	.	.	.	.	.	.	.	.	.	A	20.2	3.946075	0.73672	.	.	ENSG00000189337	ENST00000376030;ENST00000503743;ENST00000422387;ENST00000361144;ENST00000400798;ENST00000400797	T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81	5.68	5.68	0.88126	.	0.073974	0.85682	D	0.000000	T	0.35740	0.0942	L	0.27053	0.805	0.45183	D	0.998197	B;B;B;B	0.16396	0.003;0.017;0.01;0.003	B;B;B;B	0.08055	0.003;0.003;0.003;0.001	T	0.11767	-1.0574	10	0.23891	T	0.37	-31.2401	15.1533	0.72720	1.0:0.0:0.0:0.0	.	262;168;256;262	Q674X7-2;Q674X7-4;Q674X7-3;Q674X7	.;.;.;KAZRN_HUMAN	L	262;262;262;256;168;168	ENSP00000365198:M262L;ENSP00000426015:M262L;ENSP00000391728:M262L;ENSP00000354727:M256L;ENSP00000383602:M168L;ENSP00000383601:M168L	ENSP00000354727:M256L	M	+	1	0	KAZN	15255231	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.836000	0.75349	2.176000	0.68965	0.454000	0.30748	ATG	.	.		0.597	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		T	15382644	A	T	15382644	3	4	221	1	0	0	0	0	1	0	0	0	7997	217	8	4	1014	4	KAZ	1	15382644	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10		15382644	233867977	1	31576										
AHDC1	27245	hgsc.bcm.edu	37	chr1	27876698	27876698	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggggcctggtgcaccgactcCggctcactgggtgtccagca	15	14	1	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr1:27876698C>T	ENST00000247087.5	-	5	2525	c.1929G>A	c.(1927-1929)ccG>ccA	p.P643P	AHDC1_ENST00000374011.2_Silent_p.P643P			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	643							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GCACCGACTCCGGCTCACTGG	0.677																																					p.P643P		Atlas-SNP	.											.	AHDC1	98	.	0			c.G1929A						.						54	57	56					1																	27876698		2203	4298	6501	SO:0001819	synonymous_variant	27245	exon6			CGACTCCGGCTCA	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.1929G>A	chr1.hg19:g.27876698C>T		70.0	0.0		77.0	30.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Silent	SNP	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.		0.677	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			T	27876698	C	T	27876698	2	4	221	1	0	0	0	0	0	0	0	1	412	639	23	1		1	AHDC1	1	27876698	Silent	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	12494054	27876698	221373923	2	31577										
PPT1	5538	hgsc.bcm.edu	37	chr1	40562825	40562825	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ccaacggcagcggcgccggcGggtccagatgctgcagcgcc	16	16	0	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr1:40562825G>T	ENST00000433473.3	-	1	550	c.86C>A	c.(85-87)cCg>cAg	p.P29Q	PPT1_ENST00000449045.2_Missense_Mutation_p.P29Q	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1	29					adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CGGCGCCGGCGGGTCCAGATG	0.612																																					p.P29Q		Atlas-SNP	.											.	PPT1	18	.	0			c.C86A						.						77	92	87					1																	40562825		2203	4300	6503	SO:0001583	missense	5538	exon1			GCCGGCGGGTCCA	U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"ceroid-lipofuscinosis, neuronal 1, infantile"	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495	ENST00000433473.3:c.86C>A	chr1.hg19:g.40562825G>T	ENSP00000394863:p.Pro29Gln	411.0	1.0		436.0	138.0	NM_000310	B4DY24|Q6FGQ4	Missense_Mutation	SNP	ENST00000433473.3	hg19	CCDS447.1	.	.	.	.	.	.	.	.	.	.	G	10.82	1.458532	0.26248	.	.	ENSG00000131238	ENST00000433473;ENST00000449045;ENST00000372779	D;D;D	0.97772	-4.53;-3.67;-3.34	4.44	1.4	0.22301	.	1.031490	0.07620	N	0.926940	D	0.95433	0.8517	N	0.12182	0.205	0.58432	D	0.999998	D;B	0.76494	0.999;0.001	D;B	0.64776	0.929;0.002	D	0.89117	0.3500	10	0.18276	T	0.48	-9.0386	3.8965	0.09141	0.0908:0.1622:0.5793:0.1677	.	29;29	P50897-2;P50897	.;PPT1_HUMAN	Q	29	ENSP00000394863:P29Q;ENSP00000392293:P29Q;ENSP00000361865:P29Q	ENSP00000361865:P29Q	P	-	2	0	PPT1	40335412	0.150000	0.22732	0.053000	0.19242	0.036000	0.12997	0.171000	0.16685	0.194000	0.20326	-0.188000	0.12872	CCG	.	.		0.612	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310		T	40562825	G	T	40562825	3	4	221	1	0	0	0	0	1	0	0	0	12423	1116	39	1	870	1	PPT1	1	40562825	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	12686127	40562825	208687796	3	31578										
LRP8	7804	hgsc.bcm.edu	37	chr1	53716470	53716470	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ttgtcaaaattcatgcttttGgtgttcttccgcttccagtt	7	9	3	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr1:53716470G>T	ENST00000306052.6	-	17	2669	c.2568C>A	c.(2566-2568)acC>acA	p.T856T	LRP8_ENST00000347547.2_Silent_p.T686T|LRP8_ENST00000354412.3_Silent_p.T652T|LRP8_ENST00000465675.1_Silent_p.T409T|LRP8_ENST00000371454.2_Silent_p.T856T	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	856					ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						TCATGCTTTTGGTGTTCTTCC	0.488																																					p.T856T		Atlas-SNP	.											.	LRP8	58	.	0			c.C2568A						.						302	255	271					1																	53716470		2203	4300	6503	SO:0001819	synonymous_variant	7804	exon17			GCTTTTGGTGTTC	D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"Low density lipoprotein receptors"	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.2568C>A	chr1.hg19:g.53716470G>T		59.0	0.0		65.0	22.0	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Silent	SNP	ENST00000306052.6	hg19	CCDS578.1																																																																																			.	.		0.488	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		T	53716470	G	T	53716470	2	4	221	1	0	0	0	0	0	0	0	1	8972	1335	47	3		3	LRP8	1	53716470	Silent	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	13153645	53716470	195534151	4	31579										
ASB17	127247	hgsc.bcm.edu	37	chr1	76397715	76397715	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cacacatatttcagtgaagtCgaggttaaaacttacttcaa	6	8	2	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr1:76397715C>A	ENST00000284142.6	-	1	401	c.262G>T	c.(262-264)Gac>Tac	p.D88Y		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	88					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	21						TCAGTGAAGTCGAGGTTAAAA	0.378																																					p.D88Y		Atlas-SNP	.											ASB17,colon,carcinoma,0,1	ASB17	53	.	0			c.G262T						.						105	99	101					1																	76397715		2203	4300	6503	SO:0001583	missense	127247	exon1			TGAAGTCGAGGTT	AF403035	CCDS671.1	1p22.3	2013-01-11	2011-01-25		ENSG00000154007	ENSG00000154007		"Ankyrin repeat domain containing"	19769	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 17"			12076535	Standard	NM_080868		Approved		uc001dhe.2	Q8WXJ9	OTTHUMG00000009787	ENST00000284142.6:c.262G>T	chr1.hg19:g.76397715C>A	ENSP00000284142:p.Asp88Tyr	184.0	0.0		192.0	65.0	NM_080868	B1APB8|Q8N0X5	Missense_Mutation	SNP	ENST00000284142.6	hg19	CCDS671.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.027149	0.54683	.	.	ENSG00000154007	ENST00000284142	T	0.34072	1.38	5.97	5.97	0.96955	.	0.103499	0.42172	D	0.000741	T	0.16041	0.0386	N	0.08118	0	0.32374	N	0.555447	P	0.49447	0.924	P	0.45660	0.489	T	0.07009	-1.0795	10	0.87932	D	0	.	15.9063	0.79433	0.0:1.0:0.0:0.0	.	88	Q8WXJ9	ASB17_HUMAN	Y	88	ENSP00000284142:D88Y	ENSP00000284142:D88Y	D	-	1	0	ASB17	76170303	0.999000	0.42202	1.000000	0.80357	0.458000	0.32498	4.054000	0.57434	2.831000	0.97527	0.655000	0.94253	GAC	.	.		0.378	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868		A	76397715	C	A	76397715	3	1	221	1	0	0	0	0	1	0	0	0	1021	884	31	1	637	1	ASB17	1	76397715	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	22681245	76397715	172852906	5	31580										
MCOLN2	255231	hgsc.bcm.edu	37	chr1	85406668	85406668	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ccaggacatactgagcatttTtctgagctgaggaataaaac	9	8	1	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr1:85406668T>A	ENST00000370608.3	-	8	921	c.854A>T	c.(853-855)aAa>aTa	p.K285I	MCOLN2_ENST00000531325.1_5'UTR|MCOLN2_ENST00000284027.5_Missense_Mutation_p.K257I	NM_153259.2	NP_694991.2	Q8IZK6	MCLN2_HUMAN	mucolipin 2	285					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	18				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		CTGAGCATTTTTCTGAGCTGA	0.353																																					p.K285I		Atlas-SNP	.											.	MCOLN2	60	.	0			c.A854T						.						111	95	101					1																	85406668		2203	4300	6503	SO:0001583	missense	255231	exon8			GCATTTTTCTGAG	AK094010	CCDS30762.1	1p22	2011-12-16			ENSG00000153898	ENSG00000153898		"Voltage-gated ion channels / Transient receptor potential cation channels"	13357	protein-coding gene	gene with protein product		607399				16382100	Standard	XM_005270719		Approved	TRPML2, FLJ36691, TRP-ML2	uc001dkm.3	Q8IZK6	OTTHUMG00000009954	ENST00000370608.3:c.854A>T	chr1.hg19:g.85406668T>A	ENSP00000359640:p.Lys285Ile	122.0	0.0		93.0	31.0	NM_153259	A6NI99|Q2M3I6|Q5TAG5|Q8N9R3	Missense_Mutation	SNP	ENST00000370608.3	hg19	CCDS30762.1	.	.	.	.	.	.	.	.	.	.	T	12.19	1.864426	0.32977	.	.	ENSG00000153898	ENST00000370608;ENST00000284027	T;T	0.80304	-1.36;-1.36	5.69	4.57	0.56435	.	0.043144	0.85682	D	0.000000	T	0.76097	0.3940	M	0.65975	2.015	0.48696	D	0.999699	P	0.50710	0.938	P	0.52267	0.694	T	0.74639	-0.3598	10	0.29301	T	0.29	-37.61	10.8523	0.46777	0.0:0.0746:0.0:0.9254	.	285	Q8IZK6	MCLN2_HUMAN	I	285;257	ENSP00000359640:K285I;ENSP00000284027:K257I	ENSP00000284027:K257I	K	-	2	0	MCOLN2	85179256	1.000000	0.71417	0.961000	0.40146	0.480000	0.33159	3.081000	0.50120	1.006000	0.39211	0.533000	0.62120	AAA	.	.		0.353	MCOLN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027567.2	NM_153259		A	85406668	T	A	85406668	3	1	221	1	0	0	0	0	1	0	0	0	9405	1841	64	4	874	4	MCOLN2	1	85406668	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	9008953	85406668	163843953	6	31581										
MCOLN2	255231	hgsc.bcm.edu	37	chr1	85422189	85422189	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tttcttgtaatgctgcttacAgacttttaagccaattctat	5	8	2	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr1:85422189A>T	ENST00000370608.3	-	4	557	c.490T>A	c.(490-492)Tgt>Agt	p.C164S	MCOLN2_ENST00000531325.1_5'UTR|MCOLN2_ENST00000284027.5_Missense_Mutation_p.C136S	NM_153259.2	NP_694991.2	Q8IZK6	MCLN2_HUMAN	mucolipin 2	164					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	18				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		TGCTGCTTACAGACTTTTAAG	0.373																																					p.C164S		Atlas-SNP	.											.	MCOLN2	60	.	0			c.T490A						.						222	211	215					1																	85422189		2203	4300	6503	SO:0001583	missense	255231	exon4			GCTTACAGACTTT	AK094010	CCDS30762.1	1p22	2011-12-16			ENSG00000153898	ENSG00000153898		"Voltage-gated ion channels / Transient receptor potential cation channels"	13357	protein-coding gene	gene with protein product		607399				16382100	Standard	XM_005270719		Approved	TRPML2, FLJ36691, TRP-ML2	uc001dkm.3	Q8IZK6	OTTHUMG00000009954	ENST00000370608.3:c.490T>A	chr1.hg19:g.85422189A>T	ENSP00000359640:p.Cys164Ser	133.0	0.0		144.0	6.0	NM_153259	A6NI99|Q2M3I6|Q5TAG5|Q8N9R3	Missense_Mutation	SNP	ENST00000370608.3	hg19	CCDS30762.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.651683	0.88056	.	.	ENSG00000153898	ENST00000370608;ENST00000284027	T;T	0.57107	0.42;0.42	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.69904	0.3163	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.76165	-0.3059	10	0.66056	D	0.02	-43.9047	14.9755	0.71267	1.0:0.0:0.0:0.0	.	164	Q8IZK6	MCLN2_HUMAN	S	164;136	ENSP00000359640:C164S;ENSP00000284027:C136S	ENSP00000284027:C136S	C	-	1	0	MCOLN2	85194777	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.557000	0.90700	2.073000	0.62155	0.528000	0.53228	TGT	.	.		0.373	MCOLN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027567.2	NM_153259		T	85422189	A	T	85422189	3	4	221	1	0	0	0	0	1	0	0	0	9405	188	7	4	1254	4	MCOLN2	1	85422189	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	15521	85422189	163828432	7	31582										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171484941	171484941	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cagctggggatcaggaaaaaAaagaaaaggaaacaaatgat	11	4	1	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr1:171484941A>G	ENST00000338920.4	+	5	700	c.463A>G	c.(463-465)Aaa>Gaa	p.K155E	PRRC2C_ENST00000367742.3_Missense_Mutation_p.K157E|PRRC2C_ENST00000476522.1_3'UTR|PRRC2C_ENST00000426496.2_Missense_Mutation_p.K155E|PRRC2C_ENST00000392078.3_Missense_Mutation_p.K157E	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	155					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TCAGGAAAAAAAAGAAAAGGA	0.358																																					p.K155E		Atlas-SNP	.											.	.	.	.	0			c.A463G						.						73	73	73					1																	171484941		2203	4300	6503	SO:0001583	missense	23215	exon5			GAAAAAAAAGAAA	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.463A>G	chr1.hg19:g.171484941A>G	ENSP00000343629:p.Lys155Glu	559.0	0.0		587.0	218.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	A	14.81	2.645066	0.47258	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	5.62	5.62	0.85841	BAT2, N-terminal (1);	0.000000	0.47852	D	0.000217	T	0.16428	0.0395	N	0.08118	0	0.37848	D	0.929294	D;D;B	0.69078	0.996;0.997;0.224	P;P;B	0.62885	0.851;0.908;0.171	T	0.28650	-1.0037	10	0.72032	D	0.01	.	16.1189	0.81329	1.0:0.0:0.0:0.0	.	155;157;155	Q9Y520-4;E7EPN9;Q9Y520	.;.;PRC2C_HUMAN	E	157;155;155;157;155	ENSP00000375928:K157E;ENSP00000410219:K155E;ENSP00000356716:K157E;ENSP00000343629:K155E	ENSP00000343629:K155E	K	+	1	0	PRRC2C	169751565	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.667000	0.91153	2.263000	0.75096	0.533000	0.62120	AAA	.	.		0.358	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		G	171484941	A	G	171484941	3	3	221	1	0	0	0	0	1	0	0	0	1321	15	1	2	477	2	BAT2L2	1	171484941	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	86062752	171484941	77765680	8	31583										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186088326	186088326	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ttttttttcatttttaggagCaattgaaatacttgccaccc	5	8	1	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr1:186088326C>A	ENST00000271588.4	+	78	12081	c.11852C>A	c.(11851-11853)gCa>gAa	p.A3951E	HMCN1_ENST00000367492.2_Missense_Mutation_p.A3951E	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3951	Ig-like C2-type 38.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.A3951V(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TTTTTAGGAGCAATTGAAATA	0.363																																					p.A3951E		Atlas-SNP	.											HMCN1,NS,carcinoma,+1,1	HMCN1	797	.	1	Substitution - Missense(1)	large_intestine(1)	c.C11852A						.						76	75	76					1																	186088326		2203	4300	6503	SO:0001583	missense	83872	exon78			TAGGAGCAATTGA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11852C>A	chr1.hg19:g.186088326C>A	ENSP00000271588:p.Ala3951Glu	140.0	0.0		161.0	57.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.836205	0.71373	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.66099	-0.19;-0.19	5.44	5.44	0.79542	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.350254	0.33496	N	0.004859	T	0.52125	0.1715	L	0.31476	0.935	0.09310	N	0.999997	P	0.48834	0.916	P	0.50405	0.64	T	0.45977	-0.9224	10	0.06757	T	0.87	.	9.2806	0.37727	0.0:0.7773:0.1464:0.0763	.	3951	Q96RW7	HMCN1_HUMAN	E	3951	ENSP00000271588:A3951E;ENSP00000356462:A3951E	ENSP00000271588:A3951E	A	+	2	0	HMCN1	184354949	0.027000	0.19231	0.982000	0.44146	0.978000	0.69477	2.525000	0.45598	2.563000	0.86464	0.585000	0.79938	GCA	.	.		0.363	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186088326	C	A	186088326	3	1	221	1	0	0	0	0	1	0	0	0	7229	710	25	3	12162	3	HMCN1	1	186088326	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	14603385	186088326	63162295	9	31584										
APOB	338	hgsc.bcm.edu	37	chr2	21231201	21231202	+	Frame_Shift_Ins	INS	-	-	A													0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tttccctcaatagcatttccINSaaaaaacagcatttcactcc							TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:21231201_21231202insA	ENST00000233242.1	-	26	8665_8666	c.8538_8539insT	c.(8536-8541)tttggafs	p.G2847fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2847					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATAGCATTTCCAAAAAACAGCA	0.406																																					p.G2847fs		Atlas-INDEL	.											APOB,NS,carcinoma,0,1	APOB	761	.	0			c.8539_8540insT						.																																			SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8539dupT	chr2.hg19:g.21231207_21231207dupA	ENSP00000233242:p.Gly2847fs	84.0	0.0		105.0	38.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.406	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21231202	-	A	21231201	7	5	221	1	0	1	1	0	0	0	0	0	785	603	21	0	5168	0	APOB	2	21231201	Frame_Shift_Ins	INS	-	TCGA-DD-AAEI-01A-11D-A40R-10		21231201	221968172	10	31585										
USP34	9736	hgsc.bcm.edu	37	chr2	61632843	61632843	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	acaccacctattttacatacCtcaatagtagggtgagtatt	6	9	1	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:61632843C>T	ENST00000398571.2	-	3	628	c.552G>A	c.(550-552)gaG>gaA	p.E184E		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	184					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TTTTACATACCTCAATAGTAG	0.343																																					p.E184E		Atlas-SNP	.											.	USP34	334	.	0			c.G552A						.						53	50	51					2																	61632843		1821	4070	5891	SO:0001630	splice_region_variant	9736	exon3			ACATACCTCAATA	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.552+1G>A	chr2.hg19:g.61632843C>T		316.0	1.0		300.0	106.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.		0.343	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		Silent	T	61632843	C	T	61632843	5	4	221	1	0	0	0	0	0	0	1	0	17080	695	24	3	10400	3	USP34	2	61632843	Splice_Site	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	40401642	61632843	181566530	11	31586										
ARHGAP25	9938	hgsc.bcm.edu	37	chr2	69014971	69014971	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	aagtgctaattcttcctccaGcctcatgggaccagaatcgc	8	13	2	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:69014971G>A	ENST00000295381.3	+	4	768		c.e4-1		ARHGAP25_ENST00000467265.1_Intron|ARHGAP25_ENST00000497079.1_Splice_Site|ARHGAP25_ENST00000409202.3_Splice_Site|ARHGAP25_ENST00000409030.3_Splice_Site|ARHGAP25_ENST00000409220.1_Splice_Site|ARHGAP25_ENST00000544262.1_Splice_Site|ARHGAP25_ENST00000456116.2_Intron	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25						regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						TCTTCCTCCAGCCTCATGGGA	0.493																																					.		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.350-1G>A						.						133	126	129					2																	69014971		2203	4300	6503	SO:0001630	splice_region_variant	9938	exon4			CCTCCAGCCTCAT	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.350-1G>A	chr2.hg19:g.69014971G>A		84.0	0.0		77.0	24.0	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Splice_Site	SNP	ENST00000295381.3	hg19		.	.	.	.	.	.	.	.	.	.	G	19.32	3.805391	0.70682	.	.	ENSG00000163219	ENST00000544262;ENST00000295381;ENST00000409202;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000497079;ENST00000543533	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5025	0.75709	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGAP25	68868475	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	5.337000	0.65941	2.722000	0.93159	0.467000	0.42956	.	.	.		0.493	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	Intron	A	69014971	G	A	69014971	5	1	221	1	0	0	0	0	0	0	1	0	874	985	34	3	403	3	ARHGAP25	2	69014971	Splice_Site	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	7382128	69014971	174184402	12	31587										
LRRTM1	347730	hgsc.bcm.edu	37	chr2	80529433	80529433	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gtacacgagccatactcgttGatgatcaccagggctccctc	9	14	1	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:80529433G>C	ENST00000295057.3	-	2	2168	c.1512C>G	c.(1510-1512)atC>atG	p.I504M	CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000466387.1_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.I504M|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000540488.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	504					exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						CATACTCGTTGATGATCACCA	0.537										HNSCC(69;0.2)																											p.I504M		Atlas-SNP	.											.	LRRTM1	251	.	0			c.C1512G						.						122	100	108					2																	80529433		2203	4300	6503	SO:0001583	missense	347730	exon2			CTCGTTGATGATC	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.1512C>G	chr2.hg19:g.80529433G>C	ENSP00000295057:p.Ile504Met	65.0	0.0		75.0	28.0	NM_178839	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	hg19	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534723	0.64972	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.45276	0.9;0.9	4.99	2.89	0.33648	.	0.000000	0.64402	U	0.000001	T	0.44685	0.1305	L	0.34521	1.04	0.53688	D	0.999972	D	0.76494	0.999	D	0.80764	0.994	T	0.36407	-0.9749	9	.	.	.	.	4.1559	0.10260	0.5312:0.0:0.4688:0.0	.	504	Q86UE6	LRRT1_HUMAN	M	504	ENSP00000295057:I504M;ENSP00000386646:I504M	.	I	-	3	3	LRRTM1	80382944	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.463000	0.60128	1.069000	0.40788	0.561000	0.74099	ATC	.	.		0.537	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		C	80529433	G	C	80529433	3	2	221	1	0	0	0	0	1	0	0	0	9048	1280	45	4	60	4	LRRTM1	2	80529433	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	11514462	80529433	162669940	13	31588										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84838966	84838966	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tgcctaatgctcttcgagccGctactcagccaggtatgaaa	9	12	2	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:84838966G>A	ENST00000237449.6	+	21	3471	c.3463G>A	c.(3463-3465)Gct>Act	p.A1155T	DNAH6_ENST00000389394.3_Missense_Mutation_p.A1155T|DNAH6_ENST00000398278.2_Missense_Mutation_p.A1155T			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1155	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TCTTCGAGCCGCTACTCAGCC	0.438																																					p.A1155T		Atlas-SNP	.											.	DNAH6	194	.	0			c.G3463A						.						10	17	15					2																	84838966		691	1590	2281	SO:0001583	missense	1768	exon22			CGAGCCGCTACTC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.3463G>A	chr2.hg19:g.84838966G>A	ENSP00000237449:p.Ala1155Thr	459.0	0.0		506.0	166.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.019585	0.75275	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.60672	0.17;0.17;0.17	5.6	4.72	0.59763	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.30135	0.0755	N	0.02960	-0.455	0.37171	D	0.903055	P	0.39831	0.69	B	0.33690	0.168	T	0.32771	-0.9894	9	0.19147	T	0.46	.	14.7236	0.69326	0.0:0.0:0.8537:0.1463	.	1155	Q9C0G6	DYH6_HUMAN	T	1155	ENSP00000374045:A1155T;ENSP00000381326:A1155T;ENSP00000237449:A1155T	ENSP00000237449:A1155T	A	+	1	0	DNAH6	84692477	1.000000	0.71417	0.936000	0.37596	0.929000	0.56500	6.457000	0.73505	1.336000	0.45506	0.655000	0.94253	GCT	.	.		0.438	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84838966	G	A	84838966	3	1	221	1	0	0	0	0	1	0	0	0	4607	1087	38	1	3545	1	DNAH6	2	84838966	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	4309533	84838966	158360407	14	31589										
CHST10	9486	hgsc.bcm.edu	37	chr2	101023123	101023123	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	aagcatgcggccagcagaagCcactggtggtgcatgttgtc	14	10	0	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:101023123C>A	ENST00000264249.3	-	3	400	c.15G>T	c.(13-15)tgG>tgT	p.W5C	CHST10_ENST00000485085.1_5'Flank|CHST10_ENST00000542617.1_Missense_Mutation_p.W53C|CHST10_ENST00000409701.1_Missense_Mutation_p.W5C	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	5					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						CCAGCAGAAGCCACTGGTGGT	0.478																																					p.W5C		Atlas-SNP	.											.	CHST10	42	.	0			c.G15T						.						164	162	163					2																	101023123		2203	4300	6503	SO:0001583	missense	9486	exon3			CAGAAGCCACTGG	BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"Sulfotransferases, membrane-bound"	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.15G>T	chr2.hg19:g.101023123C>A	ENSP00000264249:p.Trp5Cys	112.0	0.0		119.0	30.0	NM_004854	Q53T18	Missense_Mutation	SNP	ENST00000264249.3	hg19	CCDS2047.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.445829	0.84101	.	.	ENSG00000115526	ENST00000264249;ENST00000542617;ENST00000409701;ENST00000409046;ENST00000420858;ENST00000448989;ENST00000421474;ENST00000418201;ENST00000435960	T;T;T;T;T;T;T;T;T	0.80480	-0.69;-0.83;-0.69;0.54;0.44;-0.92;-0.4;-0.78;-1.38	5.18	5.18	0.71444	.	0.126578	0.64402	D	0.000020	D	0.85669	0.5750	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.87273	0.2287	10	0.87932	D	0	-14.9306	19.0742	0.93154	0.0:1.0:0.0:0.0	.	5	O43529	CHSTA_HUMAN	C	5;53;5;5;5;53;5;5;5	ENSP00000264249:W5C;ENSP00000438869:W53C;ENSP00000387309:W5C;ENSP00000387121:W5C;ENSP00000405922:W5C;ENSP00000387977:W53C;ENSP00000407525:W5C;ENSP00000416831:W5C;ENSP00000395643:W5C	ENSP00000264249:W5C	W	-	3	0	CHST10	100389555	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.596000	0.74113	2.576000	0.86940	0.655000	0.94253	TGG	.	.		0.478	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854		A	101023123	C	A	101023123	3	1	221	1	0	0	0	0	1	0	0	0	3400	740	26	3	1075	3	CHST10	2	101023123	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	16184157	101023123	142176250	15	31590										
GCC2	9648	hgsc.bcm.edu	37	chr2	109087121	109087121	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	aactaaatgagacatttttgTcagattcagaaaaagaaaaa	6	4	2	4			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:109087121T>A	ENST00000309863.6	+	6	2050	c.1336T>A	c.(1336-1338)Tca>Aca	p.S446T		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	446					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						GACATTTTTGTCAGATTCAGA	0.303																																					p.S446T		Atlas-SNP	.											.	GCC2	129	.	0			c.T1336A						.						29	33	31					2																	109087121		2198	4280	6478	SO:0001583	missense	9648	exon6			TTTTTGTCAGATT	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.1336T>A	chr2.hg19:g.109087121T>A	ENSP00000307939:p.Ser446Thr	472.0	1.0		446.0	158.0	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	hg19	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.494343	0.44352	.	.	ENSG00000135968	ENST00000435553;ENST00000309863;ENST00000409896;ENST00000393318	T	0.34275	1.37	5.82	5.82	0.92795	.	0.509240	0.18819	N	0.130285	T	0.42921	0.1224	M	0.67953	2.075	0.09310	N	0.999997	D	0.53151	0.958	P	0.45276	0.475	T	0.43310	-0.9399	10	0.27082	T	0.32	.	16.1832	0.81925	0.0:0.0:0.0:1.0	.	446	Q8IWJ2	GCC2_HUMAN	T	446;446;409;191	ENSP00000307939:S446T	ENSP00000307939:S446T	S	+	1	0	GCC2	108453553	0.699000	0.27786	0.993000	0.49108	0.708000	0.40852	2.938000	0.48987	2.218000	0.71995	0.533000	0.62120	TCA	.	.		0.303	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		A	109087121	T	A	109087121	3	1	221	1	0	0	0	0	1	0	0	0	6294	1667	58	4	1358	4	GCC2	2	109087121	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	8063998	109087121	134112252	16	31591										
NEB	4703	hgsc.bcm.edu	37	chr2	152581406	152581406	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cgacactttctttgcatgttCaatatcctttgctttttcat	4	10	3	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:152581406C>T	ENST00000172853.10	-	7	619	c.472G>A	c.(472-474)Gaa>Aaa	p.E158K	NEB_ENST00000409198.1_Missense_Mutation_p.E158K|NEB_ENST00000427231.2_Missense_Mutation_p.E158K|NEB_ENST00000604864.1_Missense_Mutation_p.E158K|NEB_ENST00000603639.1_Missense_Mutation_p.E158K|NEB_ENST00000397345.3_Missense_Mutation_p.E158K			P20929	NEBU_HUMAN	nebulin	158					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTTGCATGTTCAATATCCTTT	0.413																																					p.E158K		Atlas-SNP	.											.	NEB	1697	.	0			c.G472A						.						250	225	233					2																	152581406		2041	4202	6243	SO:0001583	missense	4703	exon7			CATGTTCAATATC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.472G>A	chr2.hg19:g.152581406C>T	ENSP00000172853:p.Glu158Lys	68.0	0.0		57.0	20.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	C	18.14	3.556751	0.65425	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853;ENST00000439291	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.71	5.71	0.89125	.	0.060071	0.64402	D	0.000003	T	0.48003	0.1476	N	0.19112	0.55	0.80722	D	1	D	0.64830	0.994	D	0.67231	0.95	T	0.24728	-1.0152	10	0.10902	T	0.67	.	19.8546	0.96752	0.0:1.0:0.0:0.0	.	158	P20929	NEBU_HUMAN	K	158	ENSP00000386259:E158K;ENSP00000380505:E158K;ENSP00000416578:E158K;ENSP00000172853:E158K	ENSP00000172853:E158K	E	-	1	0	NEB	152289652	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.660000	0.74417	2.697000	0.92050	0.655000	0.94253	GAA	.	.		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152581406	C	T	152581406	3	4	221	1	0	0	0	0	1	0	0	0	10311	835	29	3	25918	3	NEB	2	152581406	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	43494285	152581406	90617967	17	31592										
SLC4A10	57282	hgsc.bcm.edu	37	chr2	162738921	162738921	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggtcaacagtaccatgagatTggcagatcaattgcaaccct	9	10	2	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:162738921T>A	ENST00000446997.1	+	10	1254	c.1161T>A	c.(1159-1161)atT>atA	p.I387I	SLC4A10_ENST00000272716.5_Silent_p.I357I|SLC4A10_ENST00000375514.5_Silent_p.I368I|SLC4A10_ENST00000535165.1_Intron|SLC4A10_ENST00000421911.1_Silent_p.I387I|SLC4A10_ENST00000493021.1_3'UTR|SLC4A10_ENST00000415876.2_Silent_p.I357I	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	387					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	ACCATGAGATTGGCAGATCAA	0.358																																					p.I387I		Atlas-SNP	.											.	SLC4A10	309	.	0			c.T1161A						.						53	55	54					2																	162738921		1981	4222	6203	SO:0001819	synonymous_variant	57282	exon10			TGAGATTGGCAGA		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.1161T>A	chr2.hg19:g.162738921T>A		347.0	0.0		316.0	109.0	NM_001178015	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Silent	SNP	ENST00000446997.1	hg19	CCDS54411.1																																																																																			.	.		0.358	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		A	162738921	T	A	162738921	2	1	221	1	0	0	0	0	0	0	0	1	14666	1800	63	4		4	SLC4A10	2	162738921	Silent	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	10157515	162738921	80460452	18	31593										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220497642	220497642	+	Frame_Shift_Del	DEL	A	A	-													0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	accaccctgccaggcattgcAcacctcgtggtggagaccat							TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:220497642delA	ENST00000358055.3	+	9	1700	c.1188delA	c.(1186-1188)gcafs	p.A396fs	SLC4A3_ENST00000373760.2_Frame_Shift_Del_p.A396fs|SLC4A3_ENST00000373762.3_Frame_Shift_Del_p.A423fs|SLC4A3_ENST00000273063.6_Frame_Shift_Del_p.A423fs|SLC4A3_ENST00000317151.3_Frame_Shift_Del_p.A396fs			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	396					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGGCATTGCACACCTCGTGG	0.612																																					p.A423fs		Atlas-INDEL	.											.	SLC4A3	144	.	0			c.1268delC						.						85	70	75					2																	220497642		2203	4300	6503	SO:0001589	frameshift_variant	6508	exon9			.		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1188delA	chr2.hg19:g.220497642delA	ENSP00000350756:p.Ala396fs	149.0	0.0		144.0	49.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Frame_Shift_Del	DEL	ENST00000358055.3	hg19	CCDS2445.1																																																																																			.	.		0.612	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		-	220497642	A	-	220497642	7	5	221	1	0	1	0	1	0	0	0	0	14670	146	6	0	1299	0	SLC4A3	2	220497642	Frame_Shift_Del	DEL	A	TCGA-DD-AAEI-01A-11D-A40R-10	57758721	220497642	22701731	19	31594										
NEU4	129807	hgsc.bcm.edu	37	chr2	242758032	242758032	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cccatgccctttgctgccccGccccagagccccacgtggct	9	21	0	1	rs570038056	byFrequency	TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr2:242758032G>A	ENST00000391969.2	+	5	1824	c.1113G>A	c.(1111-1113)ccG>ccA	p.P371P	NEU4_ENST00000405370.1_Silent_p.P371P|NEU4_ENST00000404257.1_Silent_p.P383P|NEU4_ENST00000407683.1_Silent_p.P371P|NEU4_ENST00000325935.6_Silent_p.P384P	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	371	Pro-rich.				ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		TTGCTGCCCCGCCCCAGAGCC	0.721													g|||	3	0.000599042	0	0	5008	,	,		13245	0		0	False		,,,				2504	0.0031				p.P384P		Atlas-SNP	.											.	NEU4	39	.	0			c.G1152A						.						7	9	8					2																	242758032		2139	4212	6351	SO:0001819	synonymous_variant	129807	exon4			TGCCCCGCCCCAG	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.1113G>A	chr2.hg19:g.242758032G>A		72.0	0.0		78.0	26.0	NM_001167599	A8K056|J3KNJ5|Q96D64	Silent	SNP	ENST00000391969.2	hg19	CCDS54442.1																																																																																			.	.		0.721	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741		A	242758032	G	A	242758032	2	1	221	1	0	0	0	0	0	0	0	1	10353	1074	38	1		1	NEU4	2	242758032	Silent	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	22260390	242758032	441341	20	31595										
ZNF589	51385	hgsc.bcm.edu	37	chr3	48310031	48310032	+	Missense_Mutation	DNP	GG	GG	TT													0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tctgcggagagtgtgggcgaGgctttatagttgagtcagtc							TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr3:48310031_48310032GG>TT	ENST00000354698.3	+	4	922_923	c.850_851GG>TT	c.(850-852)GGc>TTc	p.G284F	ZNF589_ENST00000440261.2_Intron|ZNF589_ENST00000427617.2_Intron|ZNF589_ENST00000412564.1_Intron	NM_016089.2	NP_057173.2	Q86UQ0	ZN589_HUMAN	zinc finger protein 589	284					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)|ovary(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GTGTGGGCGAGGCTTTATAGTT	0.545																																					p.G284C|p.G284V	Colon(9;319 328 25374 27611 50948)	Atlas-SNP	.											.	ZNF589	20	.	0			c.G850T|c.G851T						.																																			SO:0001583	missense	51385	exon4			GGGCGAGGCTTTA|GGCGAGGCTTTAT	AF114816	CCDS43085.1	3p21	2013-01-08			ENSG00000164048	ENSG00000164048		"Zinc fingers, C2H2-type", "-"	16747	protein-coding gene	gene with protein product						10029171	Standard	NM_016089		Approved	SZF1	uc003csl.4	Q86UQ0	OTTHUMG00000156833	Exception_encountered	chr3.hg19:g.48310031_48310032delinsTT	ENSP00000346729:p.Gly284Phe	151.0|148.0	0.0		151.0	57.0|56.0	NM_016089	Q86UC9|Q9BRI6|Q9BRY3|Q9Y611|Q9Y612	Missense_Mutation	SNP	ENST00000354698.3	hg19	CCDS43085.1																																																																																			.	.		0.545	ZNF589-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346124.1	NM_016089		TT	48310032	GG	TT	48310031	3	4	221	1	0	0	0	0	1	0	0	0	18036	1000	35	3	864	3	ZNF589	3	48310031	Missense_Mutation	DNP	GG	TCGA-DD-AAEI-01A-11D-A40R-10		48310031	149712399	21	31596										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57493370	57493370	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tatatataaagtgtatgtacCtgatttgacataagtgtgga	9	3	0	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr3:57493370C>T	ENST00000351747.2	-	8	1077	c.897G>A	c.(895-897)caG>caA	p.Q299Q	DNAH12_ENST00000311202.6_Splice_Site_p.Q299Q|DNAH12_ENST00000389536.4_Splice_Site_p.Q299Q	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	299	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						GTGTATGTACCTGATTTGACA	0.269																																					p.Q299Q		Atlas-SNP	.											.	DNAH12	182	.	0			c.G897A						.						72	67	69					3																	57493370		2203	4300	6503	SO:0001630	splice_region_variant	201625	exon8			ATGTACCTGATTT	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.897+1G>A	chr3.hg19:g.57493370C>T		59.0	0.0		62.0	25.0	NM_198564	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Silent	SNP	ENST00000351747.2	hg19																																																																																				.	.		0.269	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	Silent	T	57493370	C	T	57493370	5	4	221	1	0	0	0	0	0	0	1	0	4602	695	24	3	8632	3	DNAH12	3	57493370	Splice_Site	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	9183339	57493370	140529060	22	31597										
BOC	91653	hgsc.bcm.edu	37	chr3	112997029	112997029	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tcaccagacttgaccccgggAgcttgtatgaagtggagatg	13	9	1	4			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr3:112997029A>T	ENST00000495514.1	+	10	2331	c.1627A>T	c.(1627-1629)Agc>Tgc	p.S543C	BOC_ENST00000497495.1_3'UTR|BOC_ENST00000273395.4_Missense_Mutation_p.S544C|BOC_ENST00000355385.3_Missense_Mutation_p.S543C			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	543	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGACCCCGGGAGCTTGTATGA	0.562																																					p.S543C		Atlas-SNP	.											.	BOC	139	.	0			c.A1627T						.						138	126	130					3																	112997029		2203	4300	6503	SO:0001583	missense	91653	exon10			CCCGGGAGCTTGT	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1627A>T	chr3.hg19:g.112997029A>T	ENSP00000418663:p.Ser543Cys	123.0	0.0		136.0	55.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	hg19	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.919317	0.92249	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.58652	0.32;0.32;0.32	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.088381	0.85682	D	0.000000	T	0.74831	0.3768	M	0.68317	2.08	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77120	-0.2705	10	0.66056	D	0.02	.	16.1384	0.81506	1.0:0.0:0.0:0.0	.	544;543	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	C	543;544;543	ENSP00000418663:S543C;ENSP00000273395:S544C;ENSP00000347546:S543C	ENSP00000273395:S544C	S	+	1	0	BOC	114479719	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	8.954000	0.93051	2.203000	0.70933	0.460000	0.39030	AGC	.	.		0.562	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		T	112997029	A	T	112997029	3	4	221	1	0	0	0	0	1	0	0	0	1481	304	11	4	1657	4	BOC	3	112997029	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	55503659	112997029	85025401	23	31598										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113380094	113380094	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ttggaataaacaataattttTttttgaacctggtcactagg	7	5	1	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr3:113380094T>A	ENST00000478658.1	-	5	452	c.435A>T	c.(433-435)aaA>aaT	p.K145N	KIAA2018_ENST00000316407.4_Missense_Mutation_p.K145N|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	145						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						CAATAATTTTTTTTTGAACCT	0.368																																					p.K145N		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A435T						.						89	85	86					3																	113380094		1810	4072	5882	SO:0001583	missense	205717	exon7			AATTTTTTTTTGA	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.435A>T	chr3.hg19:g.113380094T>A	ENSP00000420721:p.Lys145Asn	186.0	0.0		215.0	70.0	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	hg19	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.126316	0.56721	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.20738	2.05;2.05	5.95	3.57	0.40892	.	0.000000	0.85682	D	0.000000	T	0.29061	0.0722	L	0.32530	0.975	0.54753	D	0.999981	D	0.89917	1.0	D	0.85130	0.997	T	0.07770	-1.0755	10	0.87932	D	0	-17.0997	4.5277	0.11990	0.0:0.3439:0.0:0.6561	.	145	Q68DE3	K2018_HUMAN	N	145	ENSP00000320794:K145N;ENSP00000420721:K145N	ENSP00000320794:K145N	K	-	3	2	KIAA2018	114862784	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	2.926000	0.48892	1.054000	0.40438	0.533000	0.62120	AAA	.	.		0.368	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		A	113380094	T	A	113380094	3	1	221	1	0	0	0	0	1	0	0	0	8277	1838	64	4	6306	4	KIAA2018	3	113380094	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	383065	113380094	84642336	24	31599										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140123468	140123468	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cttcaaagagccagcctacaAggctgttgtgacggagggca	13	10	1	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr3:140123468A>T	ENST00000458420.3	+	4	687	c.497A>T	c.(496-498)aAg>aTg	p.K166M	AC092988.1_ENST00000580582.1_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	166	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						CCAGCCTACAAGGCTGTTGTG	0.537										HNSCC(16;0.037)																											p.K166M	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.A497T						.						129	104	112					3																	140123468		2203	4300	6503	SO:0001583	missense	64084	exon4			CCTACAAGGCTGT	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.497A>T	chr3.hg19:g.140123468A>T	ENSP00000402460:p.Lys166Met	199.0	0.0		181.0	72.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.464565	0.63513	.	.	ENSG00000158258	ENST00000458420	T	0.52754	0.65	5.66	3.31	0.37934	Cadherin (4);Cadherin-like (1);	0.268084	0.35903	N	0.002914	T	0.58949	0.2158	M	0.69248	2.105	0.37010	D	0.895677	D	0.67145	0.996	D	0.64042	0.921	T	0.61888	-0.6970	10	0.51188	T	0.08	-14.8873	6.9825	0.24711	0.7451:0.0:0.2549:0.0	.	166	Q9H4D0	CSTN2_HUMAN	M	166	ENSP00000402460:K166M	ENSP00000402460:K166M	K	+	2	0	CLSTN2	141606158	0.969000	0.33509	0.908000	0.35775	0.941000	0.58515	1.429000	0.34903	0.444000	0.26612	0.460000	0.39030	AAG	.	.		0.537	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		T	140123468	A	T	140123468	3	4	221	1	0	0	0	0	1	0	0	0	3564	72	3	4	511	4	CLSTN2	3	140123468	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	26743374	140123468	57898962	25	31600										
ATR	545	hgsc.bcm.edu	37	chr3	142215316	142215316	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	accagcctttctagctacccTggcactctgcagccagcatt	7	16	2	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr3:142215316T>A	ENST00000350721.4	-	34	5906	c.5785A>T	c.(5785-5787)Agg>Tgg	p.R1929W	ATR_ENST00000383101.3_Missense_Mutation_p.R1865W	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1929	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CTAGCTACCCTGGCACTCTGC	0.483								Other conserved DNA damage response genes																													p.R1929W		Atlas-SNP	.											.	ATR	285	.	0			c.A5785T						.						156	130	139					3																	142215316		2203	4300	6503	SO:0001583	missense	545	exon34			CTACCCTGGCACT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5785A>T	chr3.hg19:g.142215316T>A	ENSP00000343741:p.Arg1929Trp	70.0	0.0		57.0	24.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.548996	0.86127	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.70399	-0.48;-0.48	5.78	3.24	0.37175	PIK-related kinase (1);Tetratricopeptide-like helical (1);PIK-related kinase, FAT (1);	0.000000	0.85682	D	0.000000	T	0.81945	0.4930	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83907	0.0293	10	0.87932	D	0	-18.9969	13.3687	0.60701	0.0:0.0:0.474:0.526	.	1929	Q13535	ATR_HUMAN	W	1929;1865	ENSP00000343741:R1929W;ENSP00000372581:R1865W	ENSP00000343741:R1929W	R	-	1	2	ATR	143698006	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.144000	0.64832	0.997000	0.38969	-0.313000	0.08912	AGG	.	.		0.483	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142215316	T	A	142215316	3	1	221	1	0	0	0	0	1	0	0	0	1204	1579	55	4	2205	4	ATR	3	142215316	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	2091848	142215316	55807114	26	31601										
SLC2A2	6514	hgsc.bcm.edu	37	chr3	170732355	170732355	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggaccagagcatggtgattaGttgagcagctgccacagtct	13	9	1	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr3:170732355G>C	ENST00000314251.3	-	3	353	c.274C>G	c.(274-276)Cta>Gta	p.L92V	SLC2A2_ENST00000382808.4_Intron	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	92					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	ATGGTGATTAGTTGAGCAGCT	0.488																																					p.L92V		Atlas-SNP	.											.	SLC2A2	71	.	0			c.C274G						.						218	200	206					3																	170732355		2203	4300	6503	SO:0001583	missense	6514	exon3			TGATTAGTTGAGC	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.274C>G	chr3.hg19:g.170732355G>C	ENSP00000323568:p.Leu92Val	145.0	0.0		144.0	49.0	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	hg19	CCDS3215.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.579973	0.28180	.	.	ENSG00000163581	ENST00000314251	D	0.83506	-1.73	6.08	2.85	0.33270	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.791364	0.12021	N	0.506963	T	0.76758	0.4032	L	0.42245	1.32	0.09310	N	1	B	0.13145	0.007	B	0.16722	0.016	T	0.58572	-0.7613	10	0.15952	T	0.53	.	13.9806	0.64301	0.0:0.0:0.5885:0.4115	.	92	P11168	GTR2_HUMAN	V	92	ENSP00000323568:L92V	ENSP00000323568:L92V	L	-	1	2	SLC2A2	172215049	0.000000	0.05858	0.008000	0.14137	0.106000	0.19336	-0.161000	0.10026	0.803000	0.34113	0.655000	0.94253	CTA	.	.		0.488	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		C	170732355	G	C	170732355	3	2	221	1	0	0	0	0	1	0	0	0	14559	1020	36	4	1336	4	SLC2A2	3	170732355	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	28517039	170732355	27290075	27	31602										
TAPT1	202018	hgsc.bcm.edu	37	chr4	16168391	16168391	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tttccccaacagcacgatgcTattaagtactttcagggata	7	10	1	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr4:16168391T>A	ENST00000405303.2	-	13	1422	c.1339A>T	c.(1339-1341)Agc>Tgc	p.S447C	TAPT1_ENST00000304584.8_3'UTR|TAPT1_ENST00000399920.3_Missense_Mutation_p.S336C	NM_153365.2	NP_699196.2	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation 1	447					embryonic skeletal system development (GO:0048706)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|post-embryonic development (GO:0009791)	integral component of membrane (GO:0016021)	growth hormone-releasing hormone receptor activity (GO:0016520)			NS(1)|breast(2)|cervix(1)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)	10						AGCACGATGCTATTAAGTACT	0.458																																					p.S447C		Atlas-SNP	.											.	TAPT1	31	.	0			c.A1339T						.						127	127	127					4																	16168391		1958	4137	6095	SO:0001583	missense	202018	exon13			CGATGCTATTAAG	AK074494	CCDS47030.1	4p15.32	2014-01-28			ENSG00000169762	ENSG00000169762			26887	protein-coding gene	gene with protein product		612758				12477932	Standard	NM_153365		Approved	FLJ90013	uc010ied.1	Q6NXT6	OTTHUMG00000160177	ENST00000405303.2:c.1339A>T	chr4.hg19:g.16168391T>A	ENSP00000385347:p.Ser447Cys	99.0	0.0		95.0	53.0	NM_153365	Q8N2S3|Q9NZK9	Missense_Mutation	SNP	ENST00000405303.2	hg19	CCDS47030.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.768750	0.90020	.	.	ENSG00000169762	ENST00000405303;ENST00000542770;ENST00000399920	T;T	0.36699	1.24;1.28	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.60766	0.2294	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65602	-0.6128	10	0.72032	D	0.01	-10.5153	15.2568	0.73591	0.0:0.0:0.0:1.0	.	447	Q6NXT6	TAPT1_HUMAN	C	447;447;336	ENSP00000385347:S447C;ENSP00000382803:S336C	ENSP00000382803:S336C	S	-	1	0	TAPT1	15777489	1.000000	0.71417	0.956000	0.39512	0.927000	0.56198	7.534000	0.82004	2.074000	0.62210	0.528000	0.53228	AGC	.	.		0.458	TAPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359568.1	NM_153365		A	16168391	T	A	16168391	3	1	221	1	0	0	0	0	1	0	0	0	15569	1522	53	4	372	4	TAPT1	4	16168391	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10		16168391	174985885	28	31603										
PIGY	100996939	hgsc.bcm.edu	37	chr4	89444729	89444729	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cggggcggctcctcagtcttCttgccccggtcggccaaagg	14	15	3	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr4:89444729C>T	ENST00000273968.4	-	1	235	c.123G>A	c.(121-123)aaG>aaA	p.K41K	HERC3_ENST00000601319.1_3'UTR|PIGY_ENST00000527353.1_5'Flank	NM_001042616.2|NM_032906.4	NP_001036081.1|NP_116295.1	Q96I23	PREY_HUMAN	PIGY upstream reading frame	41					GPI anchor biosynthetic process (GO:0006506)|positive regulation of metabolic process (GO:0009893)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|mitochondrion (GO:0005739)											CCTCAGTCTTCTTGCCCCGGT	0.726																																					p.K41K		Atlas-SNP	.											.	.	.	.	0			c.G123A						.						9	12	11					4																	89444729		690	1586	2276	SO:0001819	synonymous_variant	100996939	exon1			AGTCTTCTTGCCC			4q22.1	2012-08-14			ENSG00000145337	ENSG00000145337			44317	protein-coding gene	gene with protein product						16162815	Standard	NM_032906		Approved	PreY	uc003hru.2	Q96I23	OTTHUMG00000130949	ENST00000273968.4:c.123G>A	chr4.hg19:g.89444729C>T		182.0	0.0		153.0	29.0	NM_032906	B2R571	Silent	SNP	ENST00000273968.4	hg19	CCDS3631.1																																																																																			.	.		0.726	PYURF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253550.1	NM_032906.4		T	89444729	C	T	89444729	2	4	221	1	0	0	0	0	0	0	0	1	11913	912	32	3		3	PIGY	4	89444729	Silent	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	73276338	89444729	101709547	29	31604										
INTU	27152	hgsc.bcm.edu	37	chr4	128564999	128564999	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	aggagtcattgtccaacagcGatacaaagatgtgaatgttt	10	6	1	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr4:128564999G>A	ENST00000335251.6	+	2	573	c.470G>A	c.(469-471)cGa>cAa	p.R157Q	INTU_ENST00000296461.5_Missense_Mutation_p.R157Q	NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	157					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)		p.R157L(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						GTCCAACAGCGATACAAAGAT	0.393																																					p.R157Q		Atlas-SNP	.											INTU,NS,carcinoma,0,1	INTU	92	.	1	Substitution - Missense(1)	lung(1)	c.G470A						.						95	94	94					4																	128564999		2203	4300	6503	SO:0001583	missense	27152	exon2			AACAGCGATACAA	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.470G>A	chr4.hg19:g.128564999G>A	ENSP00000334003:p.Arg157Gln	494.0	0.0		464.0	172.0	NM_015693	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	hg19	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.423726	0.25639	.	.	ENSG00000164066	ENST00000504491;ENST00000335251;ENST00000296461	T	0.41065	1.01	5.1	1.44	0.22558	.	0.357608	0.29417	N	0.012203	T	0.22551	0.0544	L	0.27053	0.805	0.32999	D	0.525964	B	0.20780	0.048	B	0.15052	0.012	T	0.20240	-1.0281	10	0.16896	T	0.51	-1.8835	5.0901	0.14704	0.417:0.0:0.4477:0.1353	.	157	Q9ULD6	PDZD6_HUMAN	Q	138;157;157	ENSP00000296461:R157Q	ENSP00000296461:R157Q	R	+	2	0	INTU	128784449	0.486000	0.25980	0.206000	0.23566	0.445000	0.32107	0.062000	0.14389	0.053000	0.16036	-0.136000	0.14681	CGA	.	.		0.393	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		A	128564999	G	A	128564999	3	1	221	1	0	0	0	0	1	0	0	0	7795	1058	37	1	476	1	INTU	4	128564999	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	39120270	128564999	62589277	30	31605										
HELT	391723	hgsc.bcm.edu	37	chr4	185940790	185940790	+	Intron	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gagcgcagggcgaacctcagGaggctctggcgcagatccgc	16	13	2	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr4:185940790G>A	ENST00000515777.1	+	3	220				HELT_ENST00000338875.4_Missense_Mutation_p.E93K|HELT_ENST00000505610.1_Intron			A6NFD8	HELT_HUMAN	helt bHLH transcription factor						central nervous system development (GO:0007417)|GABAergic neuron differentiation in basal ganglia (GO:0021858)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	14		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;8.92e-26)|Epithelial(43;3.02e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-11)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		CGAACCTCAGGAGGCTCTGGC	0.741																																					p.E93K		Atlas-SNP	.											.	HELT	34	.	0			c.G277A						.						7	10	9					4																	185940790		2146	4240	6386	SO:0001627	intron_variant	391723	exon3			CCTCAGGAGGCTC	BC144567	CCDS75214.1, CCDS75215.1	4q35.1	2014-07-17	2011-09-12		ENSG00000187821	ENSG00000187821		"Basic helix-loop-helix proteins"	33783	protein-coding gene	gene with protein product	"megane bHLH factor", "HES-like"		"Hey-like transcription factor (zebrafish)", "HES/HEY-like transcription factor"			14764602, 17611227	Standard	XM_005262989		Approved	HESL, HCM1228, Mgn, bHLHb44, MEGANE	uc011ckq.2	A6NFD8	OTTHUMG00000160484	ENST00000515777.1:c.133-111G>A	chr4.hg19:g.185940790G>A		149.0	0.0		158.0	51.0	NM_001029887	B2RTS5|B7ZMI7|B7ZMI8	Missense_Mutation	SNP	ENST00000515777.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.725	1.160601	0.21454	.	.	ENSG00000187821	ENST00000338875	T	0.21191	2.02	2.78	0.716	0.18191	Helix-loop-helix DNA-binding (4);	.	.	.	.	T	0.09113	0.0225	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.38802	-0.9644	9	0.21014	T	0.42	.	6.5549	0.22454	0.0:0.2792:0.5271:0.1937	.	93	A6NFD8	HELT_HUMAN	K	93	ENSP00000343464:E93K	ENSP00000343464:E93K	E	+	1	0	HELT	186177784	0.255000	0.24002	0.000000	0.03702	0.003000	0.03518	1.726000	0.38085	0.095000	0.17434	0.561000	0.74099	GAG	.	.		0.741	HELT-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000360792.1	NM_001300781		A	185940790	G	A	185940790	1	1	221	0	1	0	0	0	0	0	0	0	7057	1175	41	3		3	HELT	4	185940790	Intron	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	57375791	185940790	5213486	31	31606										
PJA2	9867	hgsc.bcm.edu	37	chr5	108679977	108679977	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	atcatccttaatatactcacTgcaacagattggacagcatt	5	10	2	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr5:108679977T>A	ENST00000361189.2	-	9	2154	c.1915A>T	c.(1915-1917)Agt>Tgt	p.S639C	PJA2_ENST00000361557.3_Missense_Mutation_p.S639C	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	639	Interaction with PRKAR1A, PRKAR2A and PRKAR2B.				long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		ATATACTCACTGCAACAGATT	0.368																																					p.S639C		Atlas-SNP	.											.	PJA2	53	.	0			c.A1915T						.						99	92	94					5																	108679977		2202	4300	6502	SO:0001583	missense	9867	exon9			ACTCACTGCAACA	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"RING-type (C3HC4) zinc fingers"	17481	protein-coding gene	gene with protein product			"ring finger protein 131", "praja ring finger 2"	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.1915A>T	chr5.hg19:g.108679977T>A	ENSP00000354775:p.Ser639Cys	408.0	1.0		431.0	156.0	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	hg19	CCDS4099.1	.	.	.	.	.	.	.	.	.	.	T	19.25	3.790668	0.70452	.	.	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.44083	0.93;0.93	6.03	4.8	0.61643	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	T	0.42966	0.1226	N	0.12502	0.225	0.45662	D	0.99858	D	0.60575	0.988	D	0.64687	0.928	T	0.43081	-0.9413	10	0.45353	T	0.12	-20.5468	13.0322	0.58848	0.0:0.0:0.1341:0.8659	.	639	O43164	PJA2_HUMAN	C	639	ENSP00000354775:S639C;ENSP00000355284:S639C	ENSP00000354775:S639C	S	-	1	0	PJA2	108707876	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.995000	0.29706	2.308000	0.77769	0.533000	0.62120	AGT	.	.		0.368	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819		A	108679977	T	A	108679977	3	1	221	1	0	0	0	0	1	0	0	0	11971	1580	55	4	219	4	PJA2	5	108679977	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10		108679977	72235283	32	31607										
PCDHB13	56123	hgsc.bcm.edu	37	chr5	140595753	140595753	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	caggcccaggccgacttgctCaccgtctacctggtggtggc	13	15	2	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr5:140595753C>T	ENST00000341948.4	+	1	2245	c.2058C>T	c.(2056-2058)ctC>ctT	p.L686L		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	686					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCGACTTGCTCACCGTCTACC	0.692																																					p.L686L		Atlas-SNP	.											.	PCDHB13	142	.	0			c.C2058T						.						80	85	83					5																	140595753		2182	4270	6452	SO:0001819	synonymous_variant	56123	exon1			CTTGCTCACCGTC	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"Cadherins / Protocadherins : Clustered"	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.2058C>T	chr5.hg19:g.140595753C>T		112.0	0.0		96.0	31.0	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	hg19	CCDS4255.1																																																																																			.	.		0.692	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		T	140595753	C	T	140595753	2	4	221	1	0	0	0	0	0	0	0	1	11547	813	29	3		3	PCDHB13	5	140595753	Silent	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	31915776	140595753	40319507	33	31608										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161495110	161495110	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ctcctgctgtcgctctacccTgggtaagatgtgcccttttt	9	13	1	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr5:161495110T>C	ENST00000361925.4	+	1	325	c.105T>C	c.(103-105)ccT>ccC	p.P35P	GABRG2_ENST00000393933.4_5'UTR|GABRG2_ENST00000356592.3_Silent_p.P35P|GABRG2_ENST00000414552.2_Silent_p.P35P			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	35					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CGCTCTACCCTGGGTAAGATG	0.507																																					p.P35P		Atlas-SNP	.											.	GABRG2	142	.	0			c.T105C						.						80	71	74					5																	161495110		2203	4300	6503	SO:0001819	synonymous_variant	2566	exon1			CTACCCTGGGTAA		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.105T>C	chr5.hg19:g.161495110T>C		84.0	0.0		98.0	41.0	NM_198904	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Silent	SNP	ENST00000361925.4	hg19	CCDS4358.1																																																																																			.	.		0.507	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			C	161495110	T	C	161495110	2	2	221	1	0	0	0	0	0	0	0	1	6180	1567	55	2		2	GABRG2	5	161495110	Silent	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	20899357	161495110	19420150	34	31609										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169138990	169138990	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tccatctgcgattcatgtttCgacatcggtcatctctggaa	8	11	4	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr5:169138990C>T	ENST00000256935.8	+	16	1614	c.1534C>T	c.(1534-1536)Cga>Tga	p.R512*	DOCK2_ENST00000520908.1_Silent_p.F38F|DOCK2_ENST00000540750.1_5'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	512	DHR-1.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATTCATGTTTCGACATCGGTC	0.502																																					p.R512X		Atlas-SNP	.											DOCK2,NS,carcinoma,0,2	DOCK2	389	.	0			c.C1534T						.						203	171	182					5																	169138990		2203	4300	6503	SO:0001587	stop_gained	1794	exon16			ATGTTTCGACATC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.1534C>T	chr5.hg19:g.169138990C>T	ENSP00000256935:p.Arg512*	89.0	0.0		96.0	33.0	NM_004946	Q2M3I0|Q96AK7	Nonsense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	40	8.082213	0.98646	.	.	ENSG00000134516	ENST00000256935;ENST00000343291	.	.	.	5.49	4.61	0.57282	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.7037	0.57049	0.4536:0.5464:0.0:0.0	.	.	.	.	X	512;30	.	ENSP00000256935:R512X	R	+	1	2	DOCK2	169071568	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.172000	0.50832	1.292000	0.44672	0.655000	0.94253	CGA	.	.		0.502	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169138990	C	T	169138990	4	4	221	1	0	0	0	0	0	1	0	0	4689	876	31	1	1596	1	DOCK2	5	169138990	Nonsense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	7643880	169138990	11776270	35	31610										
PHACTR1	221692	hgsc.bcm.edu	37	chr6	13286433	13286433	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cactgagatggaagttcatgAattgagtagacacttaacaa	9	6	1	4			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr6:13286433A>T	ENST00000379335.3	+	4	503	c.398A>T	c.(397-399)gAa>gTa	p.E133V	PHACTR1_ENST00000457702.2_Missense_Mutation_p.E424V|RP1-257A7.4_ENST00000399446.2_RNA|RP1-257A7.4_ENST00000606150.1_RNA|PHACTR1_ENST00000332995.7_Missense_Mutation_p.E569V			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	569					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			GAAGTTCATGAATTGAGTAGA	0.393																																					p.E569V		Atlas-SNP	.											.	PHACTR1	94	.	0			c.A1706T						.						78	84	82					6																	13286433		1851	4094	5945	SO:0001583	missense	221692	exon14			TTCATGAATTGAG	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"Phosphatase and actin regulators"	20990	protein-coding gene	gene with protein product		608723	"RPEL repeat containing 1"	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379335.3:c.398A>T	chr6.hg19:g.13286433A>T	ENSP00000368639:p.Glu133Val	114.0	0.0		143.0	32.0	NM_030948	A8K1V2|Q3MJ93|Q5JSJ2	Missense_Mutation	SNP	ENST00000379335.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	29.8|29.8	5.036595|5.036595	0.93630|0.93630	.|.	.|.	ENSG00000112137|ENSG00000112137	ENST00000332995;ENST00000457702;ENST00000379335|ENST00000415087	T;T|.	0.38887|.	1.12;1.11|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59662|0.59662	0.2210|0.2210	L|L	0.49640|0.49640	1.575|1.575	0.80722|0.80722	D|D	1|1	B|.	0.25955|.	0.138|.	B|.	0.30716|.	0.119|.	T|T	0.58719|0.58719	-0.7587|-0.7587	10|5	0.62326|.	D|.	0.03|.	-17.1197|-17.1197	16.0034|16.0034	0.80327|0.80327	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	569|.	Q9C0D0|.	PHAR1_HUMAN|.	V|Y	569;424;133|404	ENSP00000329880:E569V;ENSP00000397669:E424V|.	ENSP00000329880:E569V|.	E|N	+|+	2|1	0|0	PHACTR1|PHACTR1	13394412|13394412	1.000000|1.000000	0.71417|0.71417	0.955000|0.955000	0.39395|0.39395	0.997000|0.997000	0.91878|0.91878	7.359000|7.359000	0.79477|0.79477	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	GAA|AAT	.	.		0.393	PHACTR1-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000039878.1	XM_166420		T	13286433	A	T	13286433	3	4	221	1	0	0	0	0	1	0	0	0	11818	246	9	4	1752	4	PHACTR1	6	13286433	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10		13286433	157828634	36	31611										
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33410881	33410881	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggacttacagggtgatgggcCtggtggccgcctcaacagca	15	11	1	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr6:33410881C>T	ENST00000418600.2	+	15	2653	c.2552C>T	c.(2551-2553)cCt>cTt	p.P851L	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.P851L|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.P792L	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	851					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GGTGATGGGCCTGGTGGCCGC	0.607																																					p.P851L		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.C2552T						.						89	73	79					6																	33410881		2203	4300	6503	SO:0001583	missense	8831	exon15			ATGGGCCTGGTGG	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.2552C>T	chr6.hg19:g.33410881C>T	ENSP00000403636:p.Pro851Leu	123.0	0.0		97.0	44.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	hg19	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	C	14.89	2.670994	0.47781	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.15487	2.42;2.51;2.5	4.52	4.52	0.55395	.	0.653596	0.15967	N	0.235966	T	0.16257	0.0391	L	0.36672	1.1	0.43708	D	0.996175	D;D;D	0.76494	0.999;0.997;0.999	D;D;D	0.81914	0.995;0.958;0.991	T	0.04029	-1.0983	10	0.10636	T	0.68	.	12.5968	0.56474	0.0:1.0:0.0:0.0	.	851;851;851	Q96PV0;Q96PV0-2;Q96PV0-4	SYGP1_HUMAN;.;.	L	851;851;837;792	ENSP00000293748:P851L;ENSP00000403636:P851L;ENSP00000412475:P792L	ENSP00000293748:P851L	P	+	2	0	SYNGAP1	33518859	1.000000	0.71417	0.963000	0.40424	0.994000	0.84299	4.828000	0.62730	2.343000	0.79666	0.591000	0.81541	CCT	.	.		0.607	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		T	33410881	C	T	33410881	3	4	221	1	0	0	0	0	1	0	0	0	15462	681	24	3	2610	3	SYNGAP1	6	33410881	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	20124448	33410881	137704186	37	31612										
FGD2	221472	hgsc.bcm.edu	37	chr6	36993582	36993582	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cctcaggtggtgtgtgccagGtgctccgactaccgggccga	15	13	1	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr6:36993582G>T	ENST00000274963.8	+	14	1644	c.1473G>T	c.(1471-1473)agG>agT	p.R491S		NM_173558.3	NP_775829.2	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	491					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	25						TGTGTGCCAGGTGCTCCGACT	0.627																																					p.R491S		Atlas-SNP	.											.	FGD2	65	.	0			c.G1473T						.						116	94	102					6																	36993582		2203	4300	6503	SO:0001583	missense	221472	exon14			TGCCAGGTGCTCC	AK097230	CCDS4829.1	6p21.2	2013-01-10	2004-08-24		ENSG00000146192	ENSG00000146192		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	3664	protein-coding gene	gene with protein product		605091	"FGD1 family, member 2"			10458911	Standard	NM_173558		Approved	ZFYVE4	uc010jwp.1	Q7Z6J4	OTTHUMG00000014616	ENST00000274963.8:c.1473G>T	chr6.hg19:g.36993582G>T	ENSP00000274963:p.Arg491Ser	109.0	0.0		90.0	32.0	NM_173558	Q5T8I1|Q6P6A8|Q6ZNL5|Q8IZ32|Q8N868|Q9H7M2	Missense_Mutation	SNP	ENST00000274963.8	hg19	CCDS4829.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756112	0.49362	.	.	ENSG00000146192	ENST00000274963;ENST00000394459	T	0.75938	-0.98	5.2	3.35	0.38373	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.473710	0.17885	N	0.158710	T	0.33990	0.0882	N	0.05199	-0.095	0.30384	N	0.781656	P;B	0.36683	0.565;0.332	B;B	0.37015	0.239;0.138	T	0.20174	-1.0283	10	0.87932	D	0	-4.2643	6.2324	0.20742	0.1585:0.3989:0.4426:0.0	.	491;68	Q7Z6J4;Q7Z6J4-2	FGD2_HUMAN;.	S	491;119	ENSP00000274963:R491S	ENSP00000274963:R491S	R	+	3	2	FGD2	37101560	0.998000	0.40836	0.999000	0.59377	0.882000	0.50991	0.615000	0.24329	1.292000	0.44672	0.563000	0.77884	AGG	.	.		0.627	FGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040398.2	NM_173558		T	36993582	G	T	36993582	3	4	221	1	0	0	0	0	1	0	0	0	5841	1252	44	3	1527	3	FGD2	6	36993582	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	3582701	36993582	134121485	38	31613										
C6orf223	221416	hgsc.bcm.edu	37	chr6	43970601	43970617	+	Frame_Shift_Del	DEL	CGGGACAGGTGACTCCT	CGGGACAGGTGACTCCT	-													0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggcgcgcgcgccgaggagccCgggacaggtgactcctagag					rs117880737	byFrequency	TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	CGGGACAGGTGACTCCT	CGGGACAGGTGACTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr6:43970601_43970617delCGGGACAGGTGACTCCT	ENST00000336600.5	+	4	487_503	c.467_483delCGGGACAGGTGACTCCT	c.(466-483)ccgggacaggtgactcctfs	p.PGQVTP156fs	C6orf223_ENST00000448947.2_3'UTR|C6orf223_ENST00000439969.2_3'UTR|C6orf223_ENST00000442114.2_Frame_Shift_Del_p.PGQVTP136fs|RP5-1120P11.1_ENST00000422059.1_RNA|RP5-1120P11.1_ENST00000607590.1_RNA	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	156										central_nervous_system(1)|lung(2)|pancreas(1)|prostate(1)|urinary_tract(1)	6	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)			CCGAGGAGCCCGGGACAGGTGACTCCTAGAGGACTGC	0.774																																					p.156_161del		Atlas-INDEL	.											.	C6orf223	14	.	0			c.466_482del						.																																			SO:0001589	frameshift_variant	221416	exon4			.	BC032706	CCDS34459.1, CCDS55016.1	6p21.1	2012-09-05			ENSG00000181577	ENSG00000181577			28692	protein-coding gene	gene with protein product						12477932	Standard	NM_153246		Approved	MGC45491	uc003own.3	Q8N319	OTTHUMG00000014753	ENST00000336600.5:c.467_483delCGGGACAGGTGACTCCT	chr6.hg19:g.43970601_43970617delCGGGACAGGTGACTCCT	ENSP00000426159:p.Pro156fs	40.0	0.0		42.0	12.0	NM_153246	E9PB59|Q8N575	Frame_Shift_Del	DEL	ENST00000336600.5	hg19	CCDS34459.1																																																																																			.	.		0.774	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246		-	43970617	CGGGACAGGTGACTCCT	-	43970601	7	5	221	1	0	1	0	1	0	0	0	0	2359	652	23	0	524	0	C6orf223	6	43970601	Frame_Shift_Del	DEL	CGGGACAGGTGACTCCT	TCGA-DD-AAEI-01A-11D-A40R-10	6977019	43970601	127144466	39	31614										
EYS	346007	hgsc.bcm.edu	37	chr6	66063431	66063431	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	catggaaggtgactccacagTagcagaggtgttgatgaatt	13	6	0	4			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr6:66063431T>G	ENST00000370621.3	-	9	1905	c.1379A>C	c.(1378-1380)tAc>tCc	p.Y460S	EYS_ENST00000393380.2_Missense_Mutation_p.Y460S|EYS_ENST00000370618.3_Missense_Mutation_p.Y460S|EYS_ENST00000342421.5_Missense_Mutation_p.Y460S|EYS_ENST00000503581.1_Missense_Mutation_p.Y460S|EYS_ENST00000370616.2_Missense_Mutation_p.Y460S			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	460					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GACTCCACAGTAGCAGAGGTG	0.373																																					p.Y460S		Atlas-SNP	.											.	EYS	527	.	0			c.A1379C						.						119	108	112					6																	66063431		2203	4300	6503	SO:0001583	missense	346007	exon9			CCACAGTAGCAGA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1379A>C	chr6.hg19:g.66063431T>G	ENSP00000359655:p.Tyr460Ser	324.0	0.0		328.0	41.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	t	11.26	1.585927	0.28268	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39	4.05	1.27	0.21489	.	.	.	.	.	T	0.05686	0.0149	N	0.24115	0.695	0.09310	N	1	B;B;B	0.21309	0.013;0.054;0.032	B;B;B	0.17722	0.006;0.019;0.014	T	0.41592	-0.9500	9	0.07325	T	0.83	.	4.7147	0.12889	0.1857:0.0:0.3817:0.4327	.	460;460;460	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	S	460	ENSP00000424243:Y460S;ENSP00000359655:Y460S;ENSP00000359650:Y460S;ENSP00000377042:Y460S;ENSP00000341818:Y460S;ENSP00000359652:Y460S	ENSP00000341818:Y460S	Y	-	2	0	EYS	66120152	0.000000	0.05858	0.010000	0.14722	0.004000	0.04260	-0.350000	0.07721	0.405000	0.25532	0.482000	0.46254	TAC	.	.		0.373	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	66063431	T	G	66063431	3	3	221	1	0	0	0	0	1	0	0	0	5334	1638	57	5	8157	5	EYS	6	66063431	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	22092830	66063431	105051636	40	31615										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47976458	47976458	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	catacctatcagcactgttaTcacaatccagaggcgcctgt	7	13	2	1	rs145116707		TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr7:47976458T>A	ENST00000289672.2	-	4	433	c.383A>T	c.(382-384)gAt>gTt	p.D128V		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	128					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						AGCACTGTTATCACAATCCAG	0.378																																					p.D128V		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A383T						.						132	132	132					7																	47976458		2202	4300	6502	SO:0001583	missense	168507	exon4			CTGTTATCACAAT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.383A>T	chr7.hg19:g.47976458T>A	ENSP00000289672:p.Asp128Val	87.0	0.0		90.0	37.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	7.765	0.706294	0.15239	.	.	ENSG00000158683	ENST00000289672	T	0.25579	1.79	3.01	-4.79	0.03200	.	.	.	.	.	T	0.08891	0.0220	N	0.08118	0	0.09310	N	1	P	0.39480	0.675	B	0.31101	0.124	T	0.20638	-1.0269	9	0.87932	D	0	-0.0969	5.3878	0.16227	0.0:0.5184:0.1634:0.3181	.	128	Q8TDX9	PK1L1_HUMAN	V	128	ENSP00000289672:D128V	ENSP00000289672:D128V	D	-	2	0	PKD1L1	47942983	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.599000	0.05700	-1.142000	0.02869	0.456000	0.33151	GAT	.	T|1.000;C|0.000		0.378	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47976458	T	A	47976458	3	1	221	1	0	0	0	0	1	0	0	0	11973	1435	50	4	8382	4	PKD1L1	7	47976458	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10		47976458	111162205	41	31616										
ZNF282	8427	hgsc.bcm.edu	37	chr7	148895458	148895458	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	acatggacgcccggcggccaAtgccttttcagttcccaccc	9	17	1	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr7:148895458A>C	ENST00000262085.3	+	2	304	c.199A>C	c.(199-201)Atg>Ctg	p.M67L	ZNF282_ENST00000479907.1_Missense_Mutation_p.M67L	NM_003575.2	NP_003566.1	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	67					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	17	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)		CCGGCGGCCAATGCCTTTTCA	0.592																																					p.M67L		Atlas-SNP	.											.	ZNF282	42	.	0			c.A199C						.						65	63	64					7																	148895458		2203	4300	6503	SO:0001583	missense	8427	exon2			CGGCCAATGCCTT	D30612	CCDS5895.1	7q36.1	2013-01-08			ENSG00000170265	ENSG00000170265		"Zinc fingers, C2H2-type", "-"	13076	protein-coding gene	gene with protein product		603397				9396811	Standard	NM_003575		Approved	HUB1	uc003wfm.3	Q9UDV7	OTTHUMG00000158974	ENST00000262085.3:c.199A>C	chr7.hg19:g.148895458A>C	ENSP00000262085:p.Met67Leu	99.0	0.0		162.0	44.0	NM_003575	B4DRI5|O43691|Q6DKK0	Missense_Mutation	SNP	ENST00000262085.3	hg19	CCDS5895.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.905543	0.33628	.	.	ENSG00000170265	ENST00000262085;ENST00000479907	T;T	0.05447	3.44;5.18	4.56	1.99	0.26369	.	0.000000	0.51477	D	0.000085	T	0.03136	0.0092	N	0.24115	0.695	0.21105	N	0.999783	B;B;B;B	0.26081	0.012;0.141;0.141;0.141	B;B;B;B	0.20767	0.01;0.031;0.031;0.031	T	0.44982	-0.9292	10	0.06099	T	0.92	-23.6365	6.3333	0.21282	0.7796:0.0:0.2204:0.0	.	67;18;39;67	B4DRI5;Q86YG2;Q7Z2V4;Q9UDV7	.;.;.;ZN282_HUMAN	L	67	ENSP00000262085:M67L;ENSP00000418840:M67L	ENSP00000262085:M67L	M	+	1	0	ZNF282	148526391	0.000000	0.05858	0.872000	0.34217	0.958000	0.62258	-0.016000	0.12613	0.619000	0.30197	0.260000	0.18958	ATG	.	.		0.592	ZNF282-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352746.1	NM_003575		C	148895458	A	C	148895458	3	2	221	1	0	0	0	0	1	0	0	0	17834	101	4	5	205	5	ZNF282	7	148895458	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	100919000	148895458	10243205	42	31617										
SLCO5A1	81796	hgsc.bcm.edu	37	chr8	70594495	70594495	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	taattccatctgatccacagActggctcatactcgtgtatt	6	11	2	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr8:70594495A>G	ENST00000260126.4	-	7	2412	c.1706T>C	c.(1705-1707)gTc>gCc	p.V569A	SLCO5A1_ENST00000524945.1_Missense_Mutation_p.V569A|SLCO5A1_ENST00000530307.1_Missense_Mutation_p.V514A	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	569	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			TGATCCACAGACTGGCTCATA	0.433																																					p.V569A		Atlas-SNP	.											.	SLCO5A1	142	.	0			c.T1706C						.						186	159	168					8																	70594495		2203	4300	6503	SO:0001583	missense	81796	exon7			CCACAGACTGGCT	AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"Solute carriers"	19046	protein-coding gene	gene with protein product		613543	"solute carrier family 21 (organic anion transporter), member 15"	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.1706T>C	chr8.hg19:g.70594495A>G	ENSP00000260126:p.Val569Ala	138.0	0.0		281.0	13.0	NM_030958	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Missense_Mutation	SNP	ENST00000260126.4	hg19	CCDS6205.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.935904	0.92458	.	.	ENSG00000137571	ENST00000260126;ENST00000524945;ENST00000530307	T;T;T	0.15952	2.38;2.38;2.38	5.77	5.77	0.91146	Proteinase inhibitor I1, Kazal (1);Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Protease inhibitor, Kazal-type (1);	0.000000	0.85682	D	0.000000	T	0.54615	0.1869	H	0.94385	3.53	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.79108	0.992;0.978;0.982	T	0.68629	-0.5358	10	0.87932	D	0	.	16.1024	0.81184	1.0:0.0:0.0:0.0	.	514;569;569	E9PKK5;Q9H2Y9;G3V1C0	.;SO5A1_HUMAN;.	A	569;569;514	ENSP00000260126:V569A;ENSP00000434422:V569A;ENSP00000431611:V514A	ENSP00000260126:V569A	V	-	2	0	SLCO5A1	70757049	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.273000	0.95719	2.200000	0.70718	0.459000	0.35465	GTC	.	.		0.433	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958		G	70594495	A	G	70594495	3	3	221	1	0	0	0	0	1	0	0	0	14746	275	10	2	856	2	SLCO5A1	8	70594495	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10		70594495	75769527	43	31618										
MTSS1	9788	hgsc.bcm.edu	37	chr8	125565918	125565918	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggtcaccacttacagagaaaTaatcataatctgaaactgat	6	8	3	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr8:125565918T>C	ENST00000518547.1	-	14	2056	c.1583A>G	c.(1582-1584)tAt>tGt	p.Y528C	MTSS1_ENST00000524090.1_Missense_Mutation_p.Y418C|MTSS1_ENST00000325064.5_Missense_Mutation_p.Y532C|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000431961.2_Missense_Mutation_p.Y246C|MTSS1_ENST00000395508.2_Missense_Mutation_p.Y302C|MTSS1_ENST00000378017.3_Missense_Mutation_p.Y503C|MTSS1_ENST00000354184.4_Missense_Mutation_p.Y246C|MTSS1_ENST00000523587.1_5'UTR	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	528					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TACAGAGAAATAATCATAATC	0.458																																					p.Y528C	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.A1583G						.						39	37	37					8																	125565918		2203	4300	6503	SO:0001583	missense	9788	exon14			GAGAAATAATCAT	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1583A>G	chr8.hg19:g.125565918T>C	ENSP00000429064:p.Tyr528Cys	87.0	0.0		190.0	44.0	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Missense_Mutation	SNP	ENST00000518547.1	hg19	CCDS6353.1	.	.	.	.	.	.	.	.	.	.	T	8.096	0.775656	0.16051	.	.	ENSG00000170873	ENST00000378017;ENST00000518547;ENST00000354184;ENST00000395508;ENST00000325064;ENST00000431961;ENST00000524090	T;T;T;T;T;T;T	0.30714	1.52;1.59;1.57;1.56;1.59;1.57;1.56	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.41926	0.1180	N	0.24115	0.695	0.52099	D	0.999947	B;D;B;B;B;D;D	0.89917	0.114;1.0;0.016;0.013;0.013;1.0;1.0	B;D;B;B;B;D;D	0.76071	0.034;0.987;0.006;0.007;0.009;0.947;0.956	T	0.27640	-1.0068	10	0.38643	T	0.18	-9.4794	15.9478	0.79806	0.0:0.0:0.0:1.0	.	418;302;503;528;503;246;177	E7EWW5;B7Z3B6;A5YM41;O43312;O43312-4;O43312-2;Q6ZTG0	.;.;.;MTSS1_HUMAN;.;.;.	C	503;528;246;302;532;246;418	ENSP00000367256:Y503C;ENSP00000429064:Y528C;ENSP00000346119:Y246C;ENSP00000378884:Y302C;ENSP00000322804:Y532C;ENSP00000393606:Y246C;ENSP00000428319:Y418C	ENSP00000322804:Y532C	Y	-	2	0	MTSS1	125635099	1.000000	0.71417	1.000000	0.80357	0.526000	0.34562	3.470000	0.53100	2.171000	0.68590	0.402000	0.26972	TAT	.	.		0.458	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		C	125565918	T	C	125565918	3	2	221	1	0	0	0	0	1	0	0	0	9971	1406	49	2	688	2	MTSS1	8	125565918	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	54971423	125565918	20798104	44	31619										
PLIN2	123	hgsc.bcm.edu	37	chr9	19119797	19119797	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ataacttggcttctgaaccaGatcaaatccttcaacttttt	4	10	3	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr9:19119797G>T	ENST00000276914.2	-	6	807	c.628C>A	c.(628-630)Ctg>Atg	p.L210M	PLIN2_ENST00000411567.1_Silent_p.I166I	NM_001122.3	NP_001113.2	Q99541	PLIN2_HUMAN	perilipin 2	210					cellular lipid metabolic process (GO:0044255)|lipid storage (GO:0019915)|long-chain fatty acid transport (GO:0015909)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	19						TTCTGAACCAGATCAAATCCT	0.418																																					p.L210M		Atlas-SNP	.											.	PLIN2	41	.	0			c.C628A						.						151	157	155					9																	19119797		2203	4300	6503	SO:0001583	missense	123	exon6			GAACCAGATCAAA	X97324	CCDS6490.1	9p22.1	2009-08-12	2009-08-12	2009-08-12	ENSG00000147872	ENSG00000147872		"Perilipins"	248	protein-coding gene	gene with protein product	"adipophilin"	103195	"adipose differentiation-related protein"	ADFP		9003395, 19638644	Standard	NM_001122		Approved	ADRP	uc003zno.3	Q99541	OTTHUMG00000019624	ENST00000276914.2:c.628C>A	chr9.hg19:g.19119797G>T	ENSP00000276914:p.Leu210Met	105.0	0.0		91.0	30.0	NM_001122	Q9BSC3	Missense_Mutation	SNP	ENST00000276914.2	hg19	CCDS6490.1	.	.	.	.	.	.	.	.	.	.	G	5.435	0.265445	0.10294	.	.	ENSG00000147872	ENST00000276914	T	0.17370	2.28	5.98	-11.7	0.00046	.	1.923010	0.02306	N	0.071673	T	0.02970	0.0088	N	0.00289	-1.7	0.09310	N	1	B	0.06786	0.001	B	0.15052	0.012	T	0.45629	-0.9248	10	0.35671	T	0.21	.	4.3327	0.11071	0.1725:0.4453:0.2662:0.1159	.	210	Q99541	PLIN2_HUMAN	M	210	ENSP00000276914:L210M	ENSP00000276914:L210M	L	-	1	2	PLIN2	19109797	0.000000	0.05858	0.000000	0.03702	0.713000	0.41058	-1.233000	0.02934	-2.131000	0.00815	-0.860000	0.03012	CTG	.	.		0.418	PLIN2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051835.1	NM_001122		T	19119797	G	T	19119797	3	4	221	1	0	0	0	0	1	0	0	0	12099	933	33	3	697	3	PLIN2	9	19119797	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10		19119797	122093634	45	31620										
IFNA16	3449	hgsc.bcm.edu	37	chr9	21217149	21217149	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	aaatcatatctgtccttcagGcaggagaaatgagagattct	9	7	4	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr9:21217149G>A	ENST00000380216.1	-	1	161	c.156C>T	c.(154-156)tgC>tgT	p.C52C		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	52					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		TGTCCTTCAGGCAGGAGAAAT	0.512																																					p.C52C		Atlas-SNP	.											.	IFNA16	27	.	0			c.C156T						.						106	107	106					9																	21217149		2203	4300	6503	SO:0001819	synonymous_variant	3449	exon1			CTTCAGGCAGGAG		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"Interferons"	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.156C>T	chr9.hg19:g.21217149G>A		194.0	0.0		205.0	78.0	NM_002173	Q5VV12	Silent	SNP	ENST00000380216.1	hg19	CCDS34996.1																																																																																			.	.		0.512	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173		A	21217149	G	A	21217149	2	1	221	1	0	0	0	0	0	0	0	1	7544	1195	42	3		3	IFNA16	9	21217149	Silent	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	2097352	21217149	119996282	46	31621										
IFNA2	3440	hgsc.bcm.edu	37	chr9	21385205	21385205	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	agagattctcctcatctgtgCcaggagcatcaaggtcctcc	9	13	4	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr9:21385205C>A	ENST00000380206.2	-	1	191	c.124G>T	c.(124-126)Gca>Tca	p.A42S		NM_000605.3	NP_000596.2	P01563	IFNA2_HUMAN	interferon, alpha 2	42					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of gene expression (GO:0010629)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	type I interferon receptor binding (GO:0005132)			breast(2)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	13				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		CTCATCTGTGCCAGGAGCATC	0.542																																					p.A42S		Atlas-SNP	.											.	IFNA2	32	.	0			c.G124T						.						114	112	113					9																	21385205		2203	4300	6503	SO:0001583	missense	3440	exon1			TCTGTGCCAGGAG		CCDS6506.1	9p22	2010-08-24			ENSG00000188379	ENSG00000188379		"Interferons"	5423	protein-coding gene	gene with protein product	"alpha-2a interferon", "interferon alpha 2b", "interferon alpha A"	147562				1385305	Standard	NM_000605		Approved	IFNA, IFN-alphaA	uc003zpb.3	P01563	OTTHUMG00000019674	ENST00000380206.2:c.124G>T	chr9.hg19:g.21385205C>A	ENSP00000369554:p.Ala42Ser	122.0	0.0		103.0	40.0	NM_000605	H2DF54|H2DF55|P01564|Q14606|Q6DJX8|Q96KI6	Missense_Mutation	SNP	ENST00000380206.2	hg19	CCDS6506.1	.	.	.	.	.	.	.	.	.	.	C	8.650	0.897930	0.17686	.	.	ENSG00000188379	ENST00000380206	T	0.40225	1.04	3.24	-0.168	0.13343	.	0.761996	0.12212	N	0.489217	T	0.28499	0.0705	L	0.41124	1.26	0.09310	N	1	B	0.11235	0.004	B	0.23150	0.044	T	0.24657	-1.0154	10	0.39692	T	0.17	.	2.7784	0.05354	0.0:0.4258:0.2516:0.3226	.	42	Q6DJX8	.	S	42	ENSP00000369554:A42S	ENSP00000369554:A42S	A	-	1	0	IFNA2	21375205	0.000000	0.05858	0.066000	0.19879	0.085000	0.17905	-0.686000	0.05161	0.103000	0.17682	0.484000	0.47621	GCA	.	.		0.542	IFNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051903.1	NM_000605		A	21385205	C	A	21385205	3	1	221	1	0	0	0	0	1	0	0	0	7546	739	26	3	446	3	IFNA2	9	21385205	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	168056	21385205	119828226	47	31622										
CDC14B	8555	hgsc.bcm.edu	37	chr9	99296248	99296248	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggcaccctcagcattttcacAgatatctaggaattctttga	7	10	4	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr9:99296248A>G	ENST00000375241.1	-	9	1358	c.907T>C	c.(907-909)Tgt>Cgt	p.C303R	CDC14B_ENST00000463569.1_Missense_Mutation_p.C303R|CDC14B_ENST00000375242.3_Missense_Mutation_p.C266R|CDC14B_ENST00000375236.1_Missense_Mutation_p.C303R|CDC14B_ENST00000375240.3_Missense_Mutation_p.C303R|CDC14B_ENST00000265659.2_Missense_Mutation_p.C303R	NM_003671.3|NM_033331.2	NP_003662.1|NP_201588.1	O60729	CC14B_HUMAN	cell division cycle 14B	303	B.				activation of anaphase-promoting complex activity (GO:0051488)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	15		Acute lymphoblastic leukemia(62;0.0559)				GCATTTTCACAGATATCTAGG	0.418																																					p.C303R		Atlas-SNP	.											.	CDC14B	64	.	0			c.T907C						.						66	57	60					9																	99296248		2203	4300	6503	SO:0001583	missense	8555	exon9			TTTCACAGATATC	AF023158	CCDS6721.1, CCDS6722.1, CCDS43853.1	9q22.3	2013-01-17	2013-01-17		ENSG00000081377	ENSG00000081377		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1719	protein-coding gene	gene with protein product		603505	"CDC14 (cell division cycle 14, S. cerevisiae) homolog B", "CDC14 cell division cycle 14 homolog B (S. cerevisiae)"			9367992	Standard	NM_003671		Approved	Cdc14B1, Cdc14B2, CDC14B3, hCDC14B	uc004awj.3	O60729	OTTHUMG00000020300	ENST00000375241.1:c.907T>C	chr9.hg19:g.99296248A>G	ENSP00000364389:p.Cys303Arg	265.0	0.0		236.0	77.0	NM_033331	A6N5X8|A8MQ20|B1AL31|B1AL32|O43183|O60730|Q5JU08	Missense_Mutation	SNP	ENST00000375241.1	hg19	CCDS6722.1	.	.	.	.	.	.	.	.	.	.	A	19.28	3.797218	0.70567	.	.	ENSG00000081377	ENST00000265659;ENST00000375241;ENST00000375240;ENST00000375242;ENST00000463569;ENST00000375236	T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94	5.42	4.27	0.50696	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (1);	0.043904	0.85682	D	0.000000	T	0.44138	0.1279	M	0.73319	2.225	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.72075	0.959;0.976;0.976	T	0.42515	-0.9447	10	0.87932	D	0	-6.0934	12.7445	0.57273	0.8628:0.1372:0.0:0.0	.	303;303;266	O60729-2;O60729;A8MQ20	.;CC14B_HUMAN;.	R	303;303;303;266;303;303	ENSP00000265659:C303R;ENSP00000364389:C303R;ENSP00000364388:C303R;ENSP00000364390:C266R;ENSP00000420572:C303R;ENSP00000364384:C303R	ENSP00000265659:C303R	C	-	1	0	CDC14B	98336069	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	9.139000	0.94554	1.057000	0.40506	-0.321000	0.08615	TGT	.	.		0.418	CDC14B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053278.2	NM_033331		G	99296248	A	G	99296248	3	3	221	1	0	0	0	0	1	0	0	0	3059	188	7	2	613	2	CDC14B	9	99296248	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	77911043	99296248	41917183	48	31623										
AKNA	80709	hgsc.bcm.edu	37	chr9	117120428	117120428	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	acctggtggcttcatagataCcatcttctccgtggcctccc	8	15	3	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr9:117120428C>G	ENST00000307564.4	-	12	2673	c.2512G>C	c.(2512-2514)Gta>Cta	p.V838L	AKNA_ENST00000374075.5_Missense_Mutation_p.V757L|AKNA_ENST00000374088.3_Missense_Mutation_p.V838L|AKNA_ENST00000223791.3_Missense_Mutation_p.V298L	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	838					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TTCATAGATACCATCTTCTCC	0.632																																					p.V838L		Atlas-SNP	.											.	AKNA	119	.	0			c.G2512C						.						77	65	69					9																	117120428		2203	4300	6503	SO:0001583	missense	80709	exon12			TAGATACCATCTT	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.2512G>C	chr9.hg19:g.117120428C>G	ENSP00000303769:p.Val838Leu	82.0	0.0		76.0	32.0	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	hg19	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	C	2.519	-0.311230	0.05458	.	.	ENSG00000106948	ENST00000307564;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T	0.15487	2.64;2.64;2.42;2.64	3.67	2.78	0.32641	.	1.536310	0.03947	N	0.287797	T	0.13072	0.0317	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.33214	-0.9877	10	0.10636	T	0.68	0.0302	11.9937	0.53189	0.0:0.8226:0.1774:0.0	.	838;757	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	L	838;838;298;757	ENSP00000303769:V838L;ENSP00000363201:V838L;ENSP00000223791:V298L;ENSP00000363188:V757L	ENSP00000223791:V298L	V	-	1	0	AKNA	116160249	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	1.025000	0.30090	0.545000	0.28902	-2.315000	0.00254	GTA	.	.		0.632	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		G	117120428	C	G	117120428	3	3	221	1	0	0	0	0	1	0	0	0	463	507	18	4	1851	4	AKNA	9	117120428	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	17824180	117120428	24093003	49	31624										
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139393656	139393656	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gggcagccaggatcagtggcGtcgtgccatcatgcatgcgg	16	11	2	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr9:139393656G>A	ENST00000277541.6	-	32	6065	c.5990C>T	c.(5989-5991)aCg>aTg	p.T1997M		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1997					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GATCAGTGGCGTCGTGCCATC	0.647			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.T1997M		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.C5990T						.						61	66	64					9																	139393656		2202	4300	6502	SO:0001583	missense	4851	exon32			AGTGGCGTCGTGC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5990C>T	chr9.hg19:g.139393656G>A	ENSP00000277541:p.Thr1997Met	67.0	0.0		78.0	31.0	NM_017617	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	hg19	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.706161	0.68615	.	.	ENSG00000148400	ENST00000277541	T	0.59906	0.23	5.07	5.07	0.68467	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	D	0.82527	0.5056	M	0.93328	3.405	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87381	0.2357	10	0.87932	D	0	.	17.7871	0.88541	0.0:0.0:1.0:0.0	.	1997	P46531	NOTC1_HUMAN	M	1997	ENSP00000277541:T1997M	ENSP00000277541:T1997M	T	-	2	0	NOTCH1	138513477	1.000000	0.71417	0.082000	0.20525	0.241000	0.25554	9.154000	0.94694	2.512000	0.84698	0.561000	0.74099	ACG	.	.		0.647	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139393656	G	A	139393656	3	1	221	1	0	0	0	0	1	0	0	0	10556	1145	40	1	1689	1	NOTCH1	9	139393656	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	22273228	139393656	1819775	50	31625										
LARP4B	23185	hgsc.bcm.edu	37	chr10	875345	875345	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	caagggtgggtcaagatagcTgtgcgttgctgaccacgtct	14	9	2	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr10:875345T>A	ENST00000316157.3	-	10	1145	c.1105A>T	c.(1105-1107)Agc>Tgc	p.S369C		NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	369					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						TCAAGATAGCTGTGCGTTGCT	0.483																																					p.S369C		Atlas-SNP	.											.	LARP4B	110	.	0			c.A1105T						.						40	40	40					10																	875345		2203	4300	6503	SO:0001583	missense	23185	exon11			GATAGCTGTGCGT	D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"La ribonucleoprotein domain containing"	28987	protein-coding gene	gene with protein product			"KIAA0217", "La ribonucleoprotein domain family, member 5"	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.1105A>T	chr10.hg19:g.875345T>A	ENSP00000326128:p.Ser369Cys	122.0	0.0		106.0	51.0	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Missense_Mutation	SNP	ENST00000316157.3	hg19	CCDS31131.1	.	.	.	.	.	.	.	.	.	.	T	16.93	3.257550	0.59321	.	.	ENSG00000107929	ENST00000316157	T	0.33865	1.39	5.4	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.44329	0.1288	N	0.22421	0.69	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.42849	-0.9427	10	0.72032	D	0.01	-7.668	11.4767	0.50302	0.0:0.0709:0.0:0.9291	.	369	Q92615	LAR4B_HUMAN	C	369	ENSP00000326128:S369C	ENSP00000326128:S369C	S	-	1	0	LARP4B	865345	1.000000	0.71417	0.976000	0.42696	0.485000	0.33311	4.082000	0.57635	0.984000	0.38629	0.533000	0.62120	AGC	.	.		0.483	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		A	875345	T	A	875345	3	1	221	1	0	0	0	0	1	0	0	0	8640	1580	55	4	1143	4	LARP4B	10	875345	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10		875345	134659402	51	31626										
ANK3	288	hgsc.bcm.edu	37	chr10	61832432	61832432	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggccatctgactttctgtctTcttgagacatgtccttactt	7	11	4	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr10:61832432T>A	ENST00000280772.2	-	37	8398	c.8207A>T	c.(8206-8208)gAa>gTa	p.E2736V	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2736					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CTTTCTGTCTTCTTGAGACAT	0.423																																					p.E2736V		Atlas-SNP	.											.	ANK3	703	.	0			c.A8207T						.						126	126	126					10																	61832432		2203	4300	6503	SO:0001583	missense	288	exon37			CTGTCTTCTTGAG	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.8207A>T	chr10.hg19:g.61832432T>A	ENSP00000280772:p.Glu2736Val	107.0	0.0		135.0	33.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384963	0.82792	.	.	ENSG00000151150	ENST00000280772	T	0.66280	-0.2	5.82	5.82	0.92795	.	0.161017	0.28883	N	0.013840	T	0.52041	0.1710	N	0.24115	0.695	0.80722	D	1	P	0.42123	0.771	B	0.40410	0.328	T	0.56312	-0.8000	10	0.49607	T	0.09	.	16.1852	0.81946	0.0:0.0:0.0:1.0	.	2736	Q12955	ANK3_HUMAN	V	2736	ENSP00000280772:E2736V	ENSP00000280772:E2736V	E	-	2	0	ANK3	61502438	1.000000	0.71417	0.998000	0.56505	0.890000	0.51754	5.792000	0.69052	2.223000	0.72356	0.454000	0.30748	GAA	.	.		0.423	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61832432	T	A	61832432	3	1	221	1	0	0	0	0	1	0	0	0	622	1783	62	4	5267	4	ANK3	10	61832432	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	60957087	61832432	73702315	52	31627										
TECTB	6975	hgsc.bcm.edu	37	chr10	114046125	114046125	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	agcatgggcacatttgagagCcaactgtctctcaacttcta	8	11	3	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr10:114046125C>T	ENST00000369422.3	+	4	459	c.459C>T	c.(457-459)agC>agT	p.S153S		NM_058222.1	NP_478129.1	Q96PL2	TECTB_HUMAN	tectorin beta	153	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.198)		Epithelial(162;0.0143)|all cancers(201;0.0242)		CATTTGAGAGCCAACTGTCTC	0.493																																					p.S153S		Atlas-SNP	.											.	TECTB	35	.	0			c.C459T						.						143	113	123					10																	114046125		2203	4300	6503	SO:0001819	synonymous_variant	6975	exon4			TGAGAGCCAACTG	AF312827	CCDS7571.1	10q25-q26	2005-06-09			ENSG00000119913	ENSG00000119913			11721	protein-coding gene	gene with protein product		602653				9079715	Standard	NM_058222		Approved		uc001kzr.1	Q96PL2	OTTHUMG00000019056	ENST00000369422.3:c.459C>T	chr10.hg19:g.114046125C>T		129.0	0.0		81.0	39.0	NM_058222	Q5VW53	Silent	SNP	ENST00000369422.3	hg19	CCDS7571.1																																																																																			.	.		0.493	TECTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050381.1	NM_058222		T	114046125	C	T	114046125	2	4	221	1	0	0	0	0	0	0	0	1	15763	738	26	3		3	TECTB	10	114046125	Silent	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	52213693	114046125	21488622	53	31628										
MKI67	4288	hgsc.bcm.edu	37	chr10	129905646	129905646	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gctattttggtagttttctcGtgagtcgtgggcttgtcagt	13	6	2	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr10:129905646G>C	ENST00000368654.3	-	13	4833	c.4458C>G	c.(4456-4458)caC>caG	p.H1486Q	MKI67_ENST00000368653.3_Missense_Mutation_p.H1126Q	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1486	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TAGTTTTCTCGTGAGTCGTGG	0.517																																					p.H1486Q		Atlas-SNP	.											.	MKI67	363	.	0			c.C4458G						.						295	276	283					10																	129905646		2203	4300	6503	SO:0001583	missense	4288	exon13			TTTCTCGTGAGTC	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.4458C>G	chr10.hg19:g.129905646G>C	ENSP00000357643:p.His1486Gln	159.0	0.0		138.0	46.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	G	1.872	-0.459998	0.04508	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01246	5.16;5.11	3.46	-0.678	0.11353	.	4.389550	0.00682	N	0.000691	T	0.01320	0.0043	L	0.29908	0.895	0.09310	N	1	B;P;B	0.36483	0.079;0.555;0.206	B;B;B	0.36567	0.043;0.228;0.056	T	0.44159	-0.9346	10	0.13853	T	0.58	.	1.8183	0.03105	0.5718:0.1694:0.0957:0.1631	.	1485;1126;1486	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	Q	1486;1126;1485	ENSP00000357643:H1486Q;ENSP00000357642:H1126Q	ENSP00000357642:H1126Q	H	-	3	2	MKI67	129795636	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.921000	0.04008	-0.233000	0.09797	-1.762000	0.00668	CAC	.	.		0.517	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		C	129905646	G	C	129905646	3	2	221	1	0	0	0	0	1	0	0	0	9607	1136	40	4	5324	4	MKI67	10	129905646	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	15859521	129905646	5629101	54	31629										
TUBGCP2	10844	hgsc.bcm.edu	37	chr10	135098648	135098648	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ttgctgatccagacgctgcaGagctgccgctccacgtgctt	11	14	0	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr10:135098648G>A	ENST00000252936.3	-	12	2004	c.1965C>T	c.(1963-1965)ctC>ctT	p.L655L	TUBGCP2_ENST00000368562.1_Silent_p.L248L|TUBGCP2_ENST00000417178.2_Silent_p.L525L|TUBGCP2_ENST00000543663.1_Silent_p.L683L|TUBGCP2_ENST00000368563.2_Silent_p.L655L			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	655					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		AGACGCTGCAGAGCTGCCGCT	0.617																																					p.L683L		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.C2049T						.						92	70	77					10																	135098648		2203	4300	6503	SO:0001819	synonymous_variant	10844	exon14			GCTGCAGAGCTGC	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.1965C>T	chr10.hg19:g.135098648G>A		64.0	0.0		56.0	14.0	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	hg19	CCDS7676.1																																																																																			.	.		0.617	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1			A	135098648	G	A	135098648	2	1	221	1	0	0	0	0	0	0	0	1	16781	929	33	3		3	TUBGCP2	10	135098648	Silent	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	5193002	135098648	436099	55	31630										
SYT8	90019	hgsc.bcm.edu	37	chr11	1857147	1857147	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tgtggatggcctggagtccaGcccgggggatgctcagcaat	16	10	1	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr11:1857147G>A	ENST00000381968.3	+	4	460	c.332G>A	c.(331-333)aGc>aAc	p.S111N	SYT8_ENST00000436964.2_Missense_Mutation_p.S97N|SYT8_ENST00000341958.3_Missense_Mutation_p.S97N|SYT8_ENST00000483280.1_3'UTR|SYT8_ENST00000535046.1_Missense_Mutation_p.S249N	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	111					acrosome reaction (GO:0007340)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CTGGAGTCCAGCCCGGGGGAT	0.647																																					p.S111N		Atlas-SNP	.											.	SYT8	29	.	0			c.G332A						.						46	47	47					11																	1857147		2201	4299	6500	SO:0001583	missense	90019	exon4			AGTCCAGCCCGGG	AL137708	CCDS7726.2	11p15.5	2013-01-21			ENSG00000149043	ENSG00000149043		"Synaptotagmins"	19264	protein-coding gene	gene with protein product		607719				7791877	Standard	XM_005253216		Approved	DKFZp434K0322	uc001lue.1	Q8NBV8	OTTHUMG00000009026	ENST00000381968.3:c.332G>A	chr11.hg19:g.1857147G>A	ENSP00000371394:p.Ser111Asn	130.0	0.0		108.0	39.0	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	hg19	CCDS7726.2	.	.	.	.	.	.	.	.	.	.	g	7.507	0.653884	0.14580	.	.	ENSG00000149043	ENST00000436964;ENST00000430303;ENST00000417052;ENST00000535046;ENST00000381968;ENST00000341958	T;T;T;T;T;T	0.47177	2.22;0.85;0.86;2.19;3.11;3.11	2.75	1.81	0.25067	C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.31389	0.0795	L	0.45137	1.4	0.09310	N	1	B;B;B	0.14012	0.009;0.003;0.003	B;B;B	0.08055	0.003;0.002;0.002	T	0.32903	-0.9889	9	0.02654	T	1	.	7.0146	0.24881	0.2365:0.0:0.7635:0.0	.	97;111;97	C9JSK3;Q8NBV8;A6NCR4	.;SYT8_HUMAN;.	N	97;97;97;249;111;97	ENSP00000414626:S97N;ENSP00000392469:S97N;ENSP00000387678:S97N;ENSP00000443325:S249N;ENSP00000371394:S111N;ENSP00000343691:S97N	ENSP00000343691:S97N	S	+	2	0	SYT8	1813723	0.023000	0.18921	0.000000	0.03702	0.006000	0.05464	1.528000	0.35985	0.491000	0.27793	0.305000	0.20034	AGC	.	.		0.647	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4			A	1857147	G	A	1857147	3	1	221	1	0	0	0	0	1	0	0	0	15495	971	34	3	346	3	SYT8	11	1857147	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10		1857147	133149369	56	31631										
RRM1	6240	hgsc.bcm.edu	37	chr11	4141136	4141136	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	atataacaacacagctcgatAtgtggatcaaggtgggaaca	10	7	1	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr11:4141136A>G	ENST00000300738.5	+	9	1058	c.854A>G	c.(853-855)tAt>tGt	p.Y285C	RRM1_ENST00000537197.1_5'UTR|RRM1_ENST00000534285.1_Missense_Mutation_p.Y63C|RRM1_ENST00000528470.1_3'UTR|RRM1_ENST00000423050.2_Missense_Mutation_p.Y188C	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	285	Allosteric effector binding, determines substrate specificity.				cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	ACAGCTCGATATGTGGATCAA	0.393																																					p.Y285C	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.A854G						.						150	136	140					11																	4141136		2201	4298	6499	SO:0001583	missense	6240	exon9			CTCGATATGTGGA	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"ribonucleotide reductase M1 polypeptide"			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.854A>G	chr11.hg19:g.4141136A>G	ENSP00000300738:p.Tyr285Cys	121.0	0.0		95.0	22.0	NM_001033	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	hg19	CCDS7750.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.797877	0.90538	.	.	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838	T;T;T	0.47869	0.83;0.83;0.83	5.65	5.65	0.86999	Ribonucleoside-diphosphate reductase, alpha subunit (1);Ribonucleotide reductase large subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.72011	0.3408	M	0.89353	3.025	0.80722	D	1	D	0.76494	0.999	D	0.64595	0.927	T	0.78532	-0.2168	10	0.87932	D	0	-12.9793	15.0275	0.71680	1.0:0.0:0.0:0.0	.	285	P23921	RIR1_HUMAN	C	285;188;198;63;63	ENSP00000300738:Y285C;ENSP00000390539:Y188C;ENSP00000431464:Y63C	ENSP00000300738:Y285C	Y	+	2	0	RRM1	4097712	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.933000	0.92911	2.146000	0.66826	0.482000	0.46254	TAT	.	.		0.393	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		G	4141136	A	G	4141136	3	3	221	1	0	0	0	0	1	0	0	0	13696	449	16	2	888	2	RRM1	11	4141136	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	2283989	4141136	130865380	57	31632										
OR56A3	390083	hgsc.bcm.edu	37	chr11	5968733	5968733	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	acaccaccctcctgatgaccAtctggctggaggcctctctg	9	16	2	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr11:5968733A>G	ENST00000329564.6	+	1	164	c.157A>G	c.(157-159)Atc>Gtc	p.I53V	AC025016.1_ENST00000528915.1_lincRNA	NM_001003443.2	NP_001003443.2	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A, member 3	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(27)|stomach(1)|upper_aerodigestive_tract(1)	41		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCTGATGACCATCTGGCTGGA	0.612																																					p.I53V		Atlas-SNP	.											.	OR56A3	81	.	0			c.A157G						.						122	123	123					11																	5968733		2201	4296	6497	SO:0001583	missense	390083	exon1			ATGACCATCTGGC		CCDS41614.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184478	ENSG00000184478		"GPCR / Class A : Olfactory receptors"	14786	protein-coding gene	gene with protein product				OR56A6, OR56A3P			Standard	NM_001003443		Approved		uc010qzt.2	Q8NH54	OTTHUMG00000165373	ENST00000329564.6:c.157A>G	chr11.hg19:g.5968733A>G	ENSP00000331572:p.Ile53Val	145.0	0.0		123.0	39.0	NM_001003443	A6NN77|Q6IFF7	Missense_Mutation	SNP	ENST00000329564.6	hg19	CCDS41614.1	.	.	.	.	.	.	.	.	.	.	A	7.864	0.726771	0.15439	.	.	ENSG00000184478	ENST00000329564	T	0.06687	3.27	5.12	4.0	0.46444	GPCR, rhodopsin-like superfamily (1);	0.100375	0.43919	D	0.000502	T	0.08891	0.0220	L	0.46947	1.48	0.31915	N	0.614133	B	0.30824	0.296	B	0.33454	0.164	T	0.06826	-1.0805	10	0.35671	T	0.21	-32.9041	9.0774	0.36531	0.9133:0.0:0.0867:0.0	.	53	Q8NH54	O56A3_HUMAN	V	53	ENSP00000331572:I53V	ENSP00000331572:I53V	I	+	1	0	OR56A3	5925309	0.022000	0.18835	0.985000	0.45067	0.014000	0.08584	0.800000	0.27042	0.988000	0.38734	-0.268000	0.10319	ATC	.	.		0.612	OR56A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383753.1	NM_001003443		G	5968733	A	G	5968733	3	3	221	1	0	0	0	0	1	0	0	0	11143	217	8	2	159	2	OR56A3	11	5968733	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	1827597	5968733	129037783	58	31633										
CTNND1	1500	hgsc.bcm.edu	37	chr11	57575697	57575697	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	catctcacttcttaaggagaGcaagactcctgccatcctag	7	13	2	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr11:57575697G>A	ENST00000399050.4	+	13	2560	c.2024G>A	c.(2023-2025)aGc>aAc	p.S675N	CTNND1_ENST00000361332.4_Missense_Mutation_p.S669N|CTNND1_ENST00000532649.1_Missense_Mutation_p.S615N|CTNND1_ENST00000529526.1_Missense_Mutation_p.S615N|CTNND1_ENST00000399039.4_Missense_Mutation_p.S675N|CTNND1_ENST00000524630.1_Missense_Mutation_p.S669N|CTNND1_ENST00000529986.1_Missense_Mutation_p.S568N|CTNND1_ENST00000532245.1_Missense_Mutation_p.S568N|CTNND1_ENST00000426142.2_Missense_Mutation_p.S568N|CTNND1_ENST00000529873.1_Missense_Mutation_p.S615N|CTNND1_ENST00000428599.2_Missense_Mutation_p.S669N|CTNND1_ENST00000358694.6_Missense_Mutation_p.S669N|CTNND1_ENST00000526357.1_Missense_Mutation_p.S615N|CTNND1_ENST00000532463.1_Missense_Mutation_p.S568N|CTNND1_ENST00000531014.1_Missense_Mutation_p.S346N|CTNND1_ENST00000534579.1_Missense_Mutation_p.S615N|CTNND1_ENST00000532844.1_Missense_Mutation_p.S621N|CTNND1_ENST00000415361.2_Missense_Mutation_p.S574N|CTNND1_ENST00000360682.6_Missense_Mutation_p.S675N|CTNND1_ENST00000527467.1_Missense_Mutation_p.S352N|CTNND1_ENST00000530748.1_Missense_Mutation_p.S621N|CTNND1_ENST00000361391.6_Missense_Mutation_p.S669N|CTNND1_ENST00000525902.1_Missense_Mutation_p.S352N|CTNND1_ENST00000528232.1_Missense_Mutation_p.S574N|CTNND1_ENST00000528621.1_Missense_Mutation_p.S615N|CTNND1_ENST00000533667.1_Missense_Mutation_p.S346N|CTNND1_ENST00000532787.1_Missense_Mutation_p.S568N|CTNND1_ENST00000529919.1_Missense_Mutation_p.S675N|CTNND1_ENST00000361796.4_Missense_Mutation_p.S669N|CTNND1_ENST00000526772.1_Missense_Mutation_p.S346N|CTNND1_ENST00000526938.1_Missense_Mutation_p.S675N|CTNND1_ENST00000530094.1_Missense_Mutation_p.S568N	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	675					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				CTTAAGGAGAGCAAGACTCCT	0.478																																					p.S675N		Atlas-SNP	.											CTNND1_ENST00000399050,NS,carcinoma,0,2	CTNND1	203	.	0			c.G2024A						.						83	74	76					11																	57575697		1894	4112	6006	SO:0001583	missense	1500	exon13			AGGAGAGCAAGAC	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"Armadillo repeat containing"	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.2024G>A	chr11.hg19:g.57575697G>A	ENSP00000382004:p.Ser675Asn	89.0	0.0		92.0	40.0	NM_001085458	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Missense_Mutation	SNP	ENST00000399050.4	hg19	CCDS44604.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650490	0.87958	.	.	ENSG00000198561	ENST00000524630;ENST00000529919;ENST00000399039;ENST00000360682;ENST00000361796;ENST00000529526;ENST00000426142;ENST00000399050;ENST00000361391;ENST00000361332;ENST00000532463;ENST00000529986;ENST00000358694;ENST00000532787;ENST00000533667;ENST00000532649;ENST00000528621;ENST00000530748;ENST00000428599;ENST00000527467;ENST00000528232;ENST00000531014;ENST00000526772;ENST00000529873;ENST00000525902;ENST00000532844;ENST00000526357;ENST00000530094;ENST00000415361;ENST00000532245;ENST00000534579;ENST00000526938	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	5.13	5.13	0.70059	Armadillo-like helical (1);Armadillo-type fold (1);	0.227898	0.44902	D	0.000401	D	0.90253	0.6952	M	0.90082	3.085	0.54753	D	0.999983	P;P;P;P;P;P;D;P;P	0.65815	0.882;0.882;0.813;0.867;0.882;0.933;0.995;0.882;0.813	P;P;B;B;P;P;D;P;B	0.63957	0.503;0.503;0.307;0.445;0.503;0.503;0.92;0.503;0.307	D	0.91570	0.5271	10	0.59425	D	0.04	-6.8317	14.2087	0.65750	0.0:0.1497:0.8503:0.0	.	675;669;675;568;615;615;669;675;675	O60716-3;O60716-2;O60716;O60716-18;O60716-14;O60716-10;O60716-5;F8WA43;C9JZR2	.;.;CTND1_HUMAN;.;.;.;.;.;.	N	669;675;675;675;669;615;568;675;669;669;568;568;669;568;346;615;615;621;669;352;574;346;346;615;352;621;615;568;574;568;615;675	ENSP00000436543:S669N;ENSP00000434808:S675N;ENSP00000381996:S675N;ENSP00000353902:S675N;ENSP00000354907:S669N;ENSP00000436323:S615N;ENSP00000409930:S568N;ENSP00000382004:S675N;ENSP00000354785:S669N;ENSP00000354823:S669N;ENSP00000432075:S568N;ENSP00000437156:S568N;ENSP00000351527:S669N;ENSP00000434949:S568N;ENSP00000437051:S346N;ENSP00000435379:S615N;ENSP00000432243:S615N;ENSP00000436744:S621N;ENSP00000413586:S669N;ENSP00000434900:S352N;ENSP00000435266:S574N;ENSP00000432623:S346N;ENSP00000433158:S346N;ENSP00000435494:S615N;ENSP00000434672:S352N;ENSP00000433276:S621N;ENSP00000433334:S615N;ENSP00000437327:S568N;ENSP00000403518:S574N;ENSP00000434017:S568N;ENSP00000435789:S615N;ENSP00000432041:S675N	ENSP00000351527:S669N	S	+	2	0	CTNND1	57332273	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.257000	0.65473	2.566000	0.86566	0.460000	0.39030	AGC	.	.		0.478	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331		A	57575697	G	A	57575697	3	1	221	1	0	0	0	0	1	0	0	0	4021	971	34	3	2066	3	CTNND1	11	57575697	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	51606964	57575697	77430819	59	31634										
CTSW	1521	hgsc.bcm.edu	37	chr11	65650839	65650839	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	agtctcagcctcagcctccaCaccccaccccatactggatc	5	20	2	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr11:65650839C>T	ENST00000307886.3	+	9	1010	c.964C>T	c.(964-966)Cac>Tac	p.H322Y	FIBP_ENST00000426652.2_5'Flank|CTSW_ENST00000528419.1_Missense_Mutation_p.H322Y	NM_001335.3	NP_001326	P56202	CATW_HUMAN	cathepsin W	322					immune response (GO:0006955)	membrane (GO:0016020)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)	9				READ - Rectum adenocarcinoma(159;0.168)		TCAGCCTCCACACCCCACCCC	0.592																																					p.H322Y		Atlas-SNP	.											.	CTSW	18	.	0			c.C964T						.						91	90	90					11																	65650839		2201	4296	6497	SO:0001583	missense	1521	exon9			CCTCCACACCCCA	AF055903	CCDS8117.1	11q13.1	2008-02-01	2006-12-05		ENSG00000172543	ENSG00000172543		"Cathepsins"	2546	protein-coding gene	gene with protein product		602364	"cathepsin W (lymphopain)"			9108299, 9675123	Standard	NM_001335		Approved		uc001ogc.1	P56202	OTTHUMG00000166663	ENST00000307886.3:c.964C>T	chr11.hg19:g.65650839C>T	ENSP00000311300:p.His322Tyr	106.0	0.0		88.0	25.0	NM_001335	Q86VT4	Missense_Mutation	SNP	ENST00000307886.3	hg19	CCDS8117.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.862066	0.32884	.	.	ENSG00000172543	ENST00000307886;ENST00000528419	T;T	0.29142	1.58;1.58	4.99	3.96	0.45880	Peptidase C1A, papain C-terminal (2);	7.976250	0.00166	N	0.000010	T	0.30070	0.0753	L	0.43152	1.355	0.09310	N	1	P;P	0.40398	0.68;0.716	B;B	0.38880	0.273;0.284	T	0.27468	-1.0073	10	0.56958	D	0.05	.	5.486	0.16749	0.0:0.8184:0.0:0.1816	.	322;322	P56202;E9PI30	CATW_HUMAN;.	Y	322	ENSP00000311300:H322Y;ENSP00000436568:H322Y	ENSP00000311300:H322Y	H	+	1	0	CTSW	65407415	0.000000	0.05858	0.013000	0.15412	0.079000	0.17450	0.352000	0.20113	2.317000	0.78254	0.491000	0.48974	CAC	.	.		0.592	CTSW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391042.1	NM_001335		T	65650839	C	T	65650839	3	4	221	1	0	0	0	0	1	0	0	0	4044	478	17	3	998	3	CTSW	11	65650839	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	8075142	65650839	69355677	60	31635										
ATM	472	hgsc.bcm.edu	37	chr11	108206607	108206607	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	agacaagatgctgtcatgcaAcaggtcttccagatgtgtaa	10	8	2	3	rs587781946		TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr11:108206607A>T	ENST00000452508.2	+	57	8376	c.8187A>T	c.(8185-8187)caA>caT	p.Q2729H	ATM_ENST00000278616.4_Missense_Mutation_p.Q2729H|C11orf65_ENST00000525729.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2729	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CTGTCATGCAACAGGTCTTCC	0.353			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.Q2729H		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.A8187T						.						112	104	107					11																	108206607		2201	4298	6499	SO:0001583	missense	472	exon56	Familial Cancer Database	AT, Louis-Bar syndrome	CATGCAACAGGTC	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.8187A>T	chr11.hg19:g.108206607A>T	ENSP00000388058:p.Gln2729His	106.0	0.0		91.0	51.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.533279	0.85812	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	D;D	0.88896	-2.44;-2.44	5.56	4.64	0.57946	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.95095	0.8411	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95458	0.8540	10	0.87932	D	0	.	11.7253	0.51706	0.1494:0.0:0.8505:0.0	.	2729	Q13315	ATM_HUMAN	H	2729	ENSP00000278616:Q2729H;ENSP00000388058:Q2729H	ENSP00000278616:Q2729H	Q	+	3	2	ATM	107711817	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.725000	0.47294	1.335000	0.45486	-0.242000	0.12053	CAA	.	.		0.353	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108206607	A	T	108206607	3	4	221	1	0	0	0	0	1	0	0	0	1109	40	2	4	8405	4	ATM	11	108206607	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	42555768	108206607	26799909	61	31636										
USP28	57646	hgsc.bcm.edu	37	chr11	113683133	113683133	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gatgtcattgtacttgagccAgctctgtcggggttgattat	12	7	2	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr11:113683133A>T	ENST00000003302.4	-	16	1905	c.1837T>A	c.(1837-1839)Tgg>Agg	p.W613R	USP28_ENST00000544967.1_Missense_Mutation_p.W321R|USP28_ENST00000545540.1_Missense_Mutation_p.W488R|USP28_ENST00000260188.5_Missense_Mutation_p.W613R	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	613	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		TACTTGAGCCAGCTCTGTCGG	0.438																																					p.W613R	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	Atlas-SNP	.											.	USP28	135	.	0			c.T1837A						.						152	154	153					11																	113683133		2201	4296	6497	SO:0001583	missense	57646	exon16			TGAGCCAGCTCTG	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.1837T>A	chr11.hg19:g.113683133A>T	ENSP00000003302:p.Trp613Arg	79.0	0.0		81.0	21.0	NM_020886	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	hg19	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990150	0.74589	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540;ENST00000538475	T;T;T;T;T	0.61274	0.12;0.12;0.12;0.12;0.12	5.43	5.43	0.79202	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	D	0.83018	0.5163	H	0.95151	3.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88415	0.3024	10	0.87932	D	0	-8.4685	15.4805	0.75521	1.0:0.0:0.0:0.0	.	488;613;321	B4E3L3;Q96RU2;G3V1N5	.;UBP28_HUMAN;.	R	613;613;321;488;317	ENSP00000003302:W613R;ENSP00000260188:W613R;ENSP00000442431:W321R;ENSP00000444991:W488R;ENSP00000442257:W317R	ENSP00000003302:W613R	W	-	1	0	USP28	113188343	1.000000	0.71417	0.996000	0.52242	0.634000	0.38068	8.962000	0.93254	2.053000	0.61076	0.533000	0.62120	TGG	.	.		0.438	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			T	113683133	A	T	113683133	3	4	221	1	0	0	0	0	1	0	0	0	17073	188	7	4	1436	4	USP28	11	113683133	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	5476526	113683133	21323383	62	31637										
CDON	50937	hgsc.bcm.edu	37	chr11	125848206	125848206	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	attattaacatacctattgtTgtttcgacaatttcggcagt	6	7	0	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr11:125848206T>A	ENST00000392693.3	-	18	3476	c.3349A>T	c.(3349-3351)Aac>Tac	p.N1117Y	CDON_ENST00000531738.1_Missense_Mutation_p.N494Y|CDON_ENST00000263577.7_Missense_Mutation_p.N1117Y	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1117					anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		TACCTATTGTTGTTTCGACAA	0.418																																					p.N1117Y		Atlas-SNP	.											.	CDON	137	.	0			c.A3349T						.						96	78	84					11																	125848206		2201	4299	6500	SO:0001583	missense	50937	exon18			TATTGTTGTTTCG	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17104	protein-coding gene	gene with protein product	"cell adhesion molecule-related/down-regulated by oncogenes"	608707	"Cdon homolog (mouse)"			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.3349A>T	chr11.hg19:g.125848206T>A	ENSP00000376458:p.Asn1117Tyr	96.0	0.0		92.0	23.0	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	hg19	CCDS58192.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.365146	0.82463	.	.	ENSG00000064309	ENST00000392693;ENST00000531738;ENST00000263577	T;T;T	0.79141	-1.22;-0.63;-1.24	5.68	5.68	0.88126	.	0.000000	0.52532	D	0.000067	D	0.87406	0.6169	M	0.72894	2.215	0.53688	D	0.999978	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.88761	0.3257	10	0.87932	D	0	-30.9435	15.9253	0.79611	0.0:0.0:0.0:1.0	.	1117;1117;494	Q4KMG0;Q4KMG0-2;E9PN78	CDON_HUMAN;.;.	Y	1117;494;1117	ENSP00000376458:N1117Y;ENSP00000432901:N494Y;ENSP00000263577:N1117Y	ENSP00000263577:N1117Y	N	-	1	0	CDON	125353416	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	7.620000	0.83070	2.165000	0.68154	0.366000	0.22137	AAC	.	.		0.418	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		A	125848206	T	A	125848206	3	1	221	1	0	0	0	0	1	0	0	0	3172	1812	63	4	457	4	CDON	11	125848206	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	12165073	125848206	9158310	63	31638										
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128843038	128843038	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggtgcattattctggaggtgGaactgctctgctggtcgatc	14	8	2	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr11:128843038G>T	ENST00000310343.9	-	21	3320	c.3321C>A	c.(3319-3321)ttC>ttA	p.F1107L	ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000527272.1_Missense_Mutation_p.F758L|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.F758L	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1107					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						TCTGGAGGTGGAACTGCTCTG	0.488																																					p.F1107L		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.C3321A						.						205	191	196					11																	128843038		2201	4297	6498	SO:0001583	missense	9743	exon21			GAGGTGGAACTGC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.3321C>A	chr11.hg19:g.128843038G>T	ENSP00000310561:p.Phe1107Leu	152.0	0.0		134.0	52.0	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.439577	0.00180	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.05925	3.37;3.38;3.38	5.61	-1.75	0.08031	.	0.938757	0.09089	N	0.850175	T	0.04003	0.0112	L	0.39898	1.24	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48445	-0.9035	10	0.10377	T	0.69	.	1.4424	0.02357	0.2772:0.2783:0.304:0.1405	.	1107	A7KAX9	RHG32_HUMAN	L	1107;758;758	ENSP00000310561:F1107L;ENSP00000376425:F758L;ENSP00000432862:F758L	ENSP00000310561:F1107L	F	-	3	2	ARHGAP32	128348248	0.003000	0.15002	0.001000	0.08648	0.237000	0.25408	-0.178000	0.09782	-0.166000	0.10890	-1.845000	0.00574	TTC	.	.		0.488	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		T	128843038	G	T	128843038	3	4	221	1	0	0	0	0	1	0	0	0	881	1165	41	3	2950	3	ARHGAP32	11	128843038	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	2994832	128843038	6163478	64	31639										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20806880	20806880	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tcacttgtattttatttctaGggtgatgaagaggccagcct	10	7	2	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr12:20806880G>A	ENST00000359062.3	+	15	2965		c.e15-1		PDE3A_ENST00000544307.1_Splice_Site	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited						blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)	p.?(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	TTTATTTCTAGGGTGATGAAG	0.428																																					.		Atlas-SNP	.											PDE3A,NS,carcinoma,0,1	PDE3A	184	.	1	Unknown(1)	lung(1)	c.2926-1G>A						.						57	58	58					12																	20806880		2203	4299	6502	SO:0001630	splice_region_variant	5139	exon15			TTTCTAGGGTGAT		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.2926-1G>A	chr12.hg19:g.20806880G>A		95.0	0.0		63.0	30.0	NM_000921	O60865|Q13348|Q17RD1	Splice_Site	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.092705	0.56075	.	.	ENSG00000172572	ENST00000359062	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3412	0.94342	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PDE3A	20698147	1.000000	0.71417	0.997000	0.53966	0.433000	0.31745	9.358000	0.97109	2.657000	0.90304	0.655000	0.94253	.	.	.		0.428	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		Intron	A	20806880	G	A	20806880	5	1	221	1	0	0	0	0	0	0	1	0	11646	1014	35	3	2983	3	PDE3A	12	20806880	Splice_Site	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10		20806880	113045015	65	31640										
FGD4	121512	hgsc.bcm.edu	37	chr12	32777980	32777980	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	aaatgcaattgcaaaggataAtgacattcactcagaggttt	8	6	2	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr12:32777980A>G	ENST00000427716.2	+	13	2037	c.1613A>G	c.(1612-1614)aAt>aGt	p.N538S	FGD4_ENST00000266482.3_Missense_Mutation_p.N290S|FGD4_ENST00000525053.1_Missense_Mutation_p.N650S|FGD4_ENST00000534526.2_Missense_Mutation_p.N675S|FGD4_ENST00000531134.1_Missense_Mutation_p.N623S|FGD4_ENST00000546442.1_Missense_Mutation_p.N445S	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	538					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					GCAAAGGATAATGACATTCAC	0.348																																					p.N538S		Atlas-SNP	.											.	FGD4	86	.	0			c.A1613G						.						118	125	122					12																	32777980		2203	4300	6503	SO:0001583	missense	121512	exon13			AGGATAATGACAT	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.1613A>G	chr12.hg19:g.32777980A>G	ENSP00000394487:p.Asn538Ser	263.0	1.0		245.0	98.0	NM_139241	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	hg19	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	A	11.70	1.717920	0.30413	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000427716;ENST00000266482;ENST00000546442;ENST00000525053	D;D;D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27;-2.27;-2.27	5.81	4.67	0.58626	.	0.225111	0.31246	N	0.007994	T	0.75982	0.3924	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.18863	0.014;0.014;0.031;0.004	B;B;B;B	0.14023	0.01;0.01;0.006;0.003	T	0.68484	-0.5396	10	0.31617	T	0.26	-19.2165	11.4675	0.50248	0.9304:0.0:0.0696:0.0	.	650;623;538;290	E9PJX4;B7Z493;Q96M96;G3XA97	.;.;FGD4_HUMAN;.	S	675;623;538;290;445;650	ENSP00000449273:N675S;ENSP00000431323:N623S;ENSP00000394487:N538S;ENSP00000266482:N290S;ENSP00000446695:N445S;ENSP00000433666:N650S	ENSP00000266482:N290S	N	+	2	0	FGD4	32669247	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.530000	0.53539	1.037000	0.40024	0.533000	0.62120	AAT	.	.		0.348	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		G	32777980	A	G	32777980	3	3	221	1	0	0	0	0	1	0	0	0	5843	101	4	2	1655	2	FGD4	12	32777980	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	11971100	32777980	101073915	66	31641										
ARID2	196528	hgsc.bcm.edu	37	chr12	46230722	46230722	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	actttctgcacatagtcattTtatttctttaaggcaattag	5	7	3	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr12:46230722T>G	ENST00000334344.6	+	8	1143	c.971T>G	c.(970-972)tTt>tGt	p.F324C	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Missense_Mutation_p.F175C|ARID2_ENST00000444670.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	324					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CATAGTCATTTTATTTCTTTA	0.368			"N, S, F"		hepatocellular carcinoma																																p.F324C		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.T971G						.						150	143	145					12																	46230722		2203	4300	6503	SO:0001583	missense	196528	exon8			GTCATTTTATTTC		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.971T>G	chr12.hg19:g.46230722T>G	ENSP00000335044:p.Phe324Cys	121.0	0.0		117.0	8.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.193908	0.78902	.	.	ENSG00000189079	ENST00000334344;ENST00000422737	T;T	0.48522	0.81;0.81	5.87	5.87	0.94306	.	0.051051	0.85682	D	0.000000	T	0.60470	0.2271	L	0.44542	1.39	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	T	0.63189	-0.6693	10	0.87932	D	0	-12.9744	16.2628	0.82557	0.0:0.0:0.0:1.0	.	324	Q68CP9	ARID2_HUMAN	C	324;175	ENSP00000335044:F324C;ENSP00000415650:F175C	ENSP00000335044:F324C	F	+	2	0	ARID2	44516989	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.004000	0.88535	2.233000	0.73108	0.482000	0.46254	TTT	.	.		0.368	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		G	46230722	T	G	46230722	3	3	221	1	0	0	0	0	1	0	0	0	915	1841	64	5	1001	5	ARID2	12	46230722	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	13452742	46230722	87621173	67	31642										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48378844	48378844	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cgagccccctgaggacctggAggtccaggacgaccatcttc	12	15	1	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr12:48378844A>T	ENST00000380518.3	-	27	1931	c.1767T>A	c.(1765-1767)ccT>ccA	p.P589P	COL2A1_ENST00000337299.6_Silent_p.P520P|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	589	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	GAGGACCTGGAGGTCCAGGAC	0.527																																					p.P589P		Atlas-SNP	.											.	COL2A1	368	.	0			c.T1767A						.						47	42	44					12																	48378844		2202	4300	6502	SO:0001819	synonymous_variant	1280	exon27			ACCTGGAGGTCCA	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.1767T>A	chr12.hg19:g.48378844A>T		174.0	0.0		182.0	44.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	hg19	CCDS41778.1																																																																																			.	.		0.527	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		T	48378844	A	T	48378844	2	4	221	1	0	0	0	0	0	0	0	1	3689	291	11	4		4	COL2A1	12	48378844	Silent	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	2148122	48378844	85473051	68	31643										
MLL2	8085	hgsc.bcm.edu	37	chr12	49446022	49446022	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cggccgggacaggtgcaatgCctcaggaagtggggatgcgg	19	9	1	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr12:49446022C>T	ENST00000301067.7	-	10	1443	c.1444G>A	c.(1444-1446)Gca>Aca	p.A482T		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	482	15 X 5 AA repeats of S/P-P-P-E/P-E/A.|Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										AGGTGCAATGCCTCAGGAAGT	0.622																																					p.A482T		Atlas-SNP	.											.	MLL2	1173	.	0			c.G1444A						.						89	100	96					12																	49446022		2119	4217	6336	SO:0001583	missense	8085	exon10			GCAATGCCTCAGG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.1444G>A	chr12.hg19:g.49446022C>T	ENSP00000301067:p.Ala482Thr	139.0	0.0		154.0	51.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	5.570	0.290008	0.10567	.	.	ENSG00000167548	ENST00000301067	T	0.79940	-1.32	2.28	2.28	0.28536	.	.	.	.	.	T	0.63046	0.2478	N	0.08118	0	0.09310	N	1	B	0.18461	0.028	B	0.06405	0.002	T	0.58194	-0.7679	9	0.87932	D	0	.	10.167	0.42886	0.0:1.0:0.0:0.0	.	482	O14686	MLL2_HUMAN	T	482	ENSP00000301067:A482T	ENSP00000301067:A482T	A	-	1	0	MLL2	47732289	0.000000	0.05858	0.099000	0.21106	0.359000	0.29487	-0.107000	0.10873	1.257000	0.44085	0.313000	0.20887	GCA	.	.		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49446022	C	T	49446022	3	4	221	1	0	0	0	0	1	0	0	0	9630	739	26	3	15349	3	MLL2	12	49446022	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	1067178	49446022	84405873	69	31644										
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72050734	72050734	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	atctttaacttttttcaaacGgttcttatctcctggtaaag	5	8	4	0	rs561382640		TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr12:72050734G>A	ENST00000378743.3	-	2	1304	c.946C>T	c.(946-948)Cgt>Tgt	p.R316C	ZFC3H1_ENST00000548100.1_Missense_Mutation_p.R316C|ZFC3H1_ENST00000549407.1_5'UTR|ZFC3H1_ENST00000552037.1_Missense_Mutation_p.R316C	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	316					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TTTTTCAAACGGTTCTTATCT	0.348																																					p.R316C		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.C946T						.						129	124	125					12																	72050734		1817	4071	5888	SO:0001583	missense	196441	exon2			TCAAACGGTTCTT	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.946C>T	chr12.hg19:g.72050734G>A	ENSP00000368017:p.Arg316Cys	116.0	0.0		127.0	61.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	hg19	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477836	0.63849	.	.	ENSG00000133858	ENST00000378743;ENST00000548100;ENST00000552037	T	0.39056	1.1	5.72	3.66	0.41972	.	0.163980	0.40222	N	0.001160	T	0.48943	0.1528	N	0.24115	0.695	0.47621	D	0.999477	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.83275	0.996;0.992;0.719	T	0.53837	-0.8382	10	0.72032	D	0.01	.	12.8853	0.58040	0.0:0.0:0.6131:0.3869	.	316;316;316	G3V1X1;O60293-4;O60293	.;.;ZC3H1_HUMAN	C	316	ENSP00000368017:R316C	ENSP00000368017:R316C	R	-	1	0	ZFC3H1	70337001	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.614000	0.46359	1.380000	0.46344	0.563000	0.77884	CGT	.	.		0.348	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		A	72050734	G	A	72050734	3	1	221	1	0	0	0	0	1	0	0	0	17648	1116	39	1	5159	1	ZFC3H1	12	72050734	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	22604712	72050734	61801161	70	31645										
CUX2	23316	hgsc.bcm.edu	37	chr12	111729223	111729223	+	Splice_Site	DEL	C	C	-													0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tctttctctccctgcacagaCcccgtgcctgtgtttgaggc							TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr12:111729223delC	ENST00000261726.6	+	5	457	c.303delC	c.(301-303)gac>ga	p.D101fs		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	101					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						CCTGCACAGACCCCGTGCCTG	0.647																																					p.D101fs		Atlas-INDEL	.											.	CUX2	145	.	0			c.302delA						.						61	67	65					12																	111729223		2034	4171	6205	SO:0001630	splice_region_variant	23316	exon5			.	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.302-1C>-	chr12.hg19:g.111729223delC		74.0	0.0		100.0	33.0	NM_015267	A7E2Y4	Frame_Shift_Del	DEL	ENST00000261726.6	hg19	CCDS41837.1																																																																																			.	.		0.647	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	Frame_Shift_Del	-	111729223	C	-	111729223	8	5	221	1	0	1	0	1	0	0	1	0	4067	521	18	0	321	0	CUX2	12	111729223	Splice_Site	DEL	C	TCGA-DD-AAEI-01A-11D-A40R-10	39678489	111729223	22122672	71	31646										
SOHLH2	54937	hgsc.bcm.edu	37	chr13	36747903	36747903	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	agcacgtattagtcaggaatTggagccctctctcaggggag	13	9	3	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr13:36747903T>A	ENST00000379881.3	-	9	1014	c.926A>T	c.(925-927)cAa>cTa	p.Q309L	CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.Q386L|SOHLH2_ENST00000554962.1_Missense_Mutation_p.Q386L	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	309					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		AGTCAGGAATTGGAGCCCTCT	0.468																																					p.Q386L		Atlas-SNP	.											.	.	.	.	0			c.A1157T						.						123	113	117					13																	36747903		2203	4300	6503	SO:0001583	missense	100526761	exon14			AGGAATTGGAGCC	AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"Basic helix-loop-helix proteins"	26026	protein-coding gene	gene with protein product	"spermatogenesis associated 28"					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.926A>T	chr13.hg19:g.36747903T>A	ENSP00000369210:p.Gln309Leu	96.0	0.0		88.0	32.0	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Missense_Mutation	SNP	ENST00000379881.3	hg19	CCDS9355.1	.	.	.	.	.	.	.	.	.	.	T	8.096	0.775680	0.16051	.	.	ENSG00000120669;ENSG00000120669;ENSG00000250709	ENST00000379881;ENST00000554962;ENST00000511166	T;T;T	0.34859	1.34;1.34;1.34	5.6	4.67	0.58626	.	0.480573	0.19554	N	0.111482	T	0.24044	0.0582	L	0.38175	1.15	0.09310	N	1	P;P	0.34462	0.454;0.454	B;B	0.30401	0.053;0.115	T	0.28459	-1.0043	10	0.62326	D	0.03	-0.7942	3.7495	0.08561	0.0:0.7176:0.0:0.2824	.	386;309	B4DX90;Q9NX45	.;SOLH2_HUMAN	L	309;386;386	ENSP00000369210:Q309L;ENSP00000451542:Q386L;ENSP00000421868:Q386L	ENSP00000421868:Q386L	Q	-	2	0	CCDC169-SOHLH2;SOHLH2	35645903	0.445000	0.25657	0.003000	0.11579	0.008000	0.06430	1.882000	0.39648	1.188000	0.43014	0.460000	0.39030	CAA	.	.		0.468	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826		A	36747903	T	A	36747903	3	1	221	1	0	0	0	0	1	0	0	0	14939	1812	63	4	363	4	SOHLH2	13	36747903	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10		36747903	78421975	72	31647										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42876689	42876689	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ctggcagcagaagtcattacAgaagctgagaaaatagcaaa	10	7	1	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr13:42876689A>T	ENST00000025301.2	+	8	3982	c.3807A>T	c.(3805-3807)acA>acT	p.T1269T		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1269					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		AAGTCATTACAGAAGCTGAGA	0.368																																					p.T1269T		Atlas-SNP	.											.	AKAP11	146	.	0			c.A3807T						.						72	74	73					13																	42876689		2203	4300	6503	SO:0001819	synonymous_variant	11215	exon8			CATTACAGAAGCT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.3807A>T	chr13.hg19:g.42876689A>T		155.0	0.0		162.0	51.0	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	hg19	CCDS9383.1																																																																																			.	.		0.368	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		T	42876689	A	T	42876689	2	4	221	1	0	0	0	0	0	0	0	1	447	175	7	4		4	AKAP11	13	42876689	Silent	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	6128786	42876689	72293189	73	31648										
EFNB2	1948	hgsc.bcm.edu	37	chr13	107147231	107147231	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cagatcatgctgttatacctGgatttggttttacaaaggga	10	6	1	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr13:107147231G>A	ENST00000245323.4	-	4	760	c.611C>T	c.(610-612)cCa>cTa	p.P204L		NM_004093.3	NP_004084.1	P52799	EFNB2_HUMAN	ephrin-B2	204					anatomical structure morphogenesis (GO:0009653)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|lymph vessel development (GO:0001945)|negative regulation of keratinocyte proliferation (GO:0010839)|organ morphogenesis (GO:0009887)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|regulation of chemotaxis (GO:0050920)|viral process (GO:0016032)	focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					TGTTATACCTGGATTTGGTTT	0.418																																					p.P204L		Atlas-SNP	.											.	EFNB2	39	.	0			c.C611T						.						262	232	242					13																	107147231		2203	4300	6503	SO:0001583	missense	1948	exon4			ATACCTGGATTTG	L38734	CCDS9507.1	13q33	2011-03-09			ENSG00000125266	ENSG00000125266		"Ephrins"	3227	protein-coding gene	gene with protein product	"HTK ligand", "ligand of eph-related kinase 5", "eph-related receptor tyrosine kinase ligand 5"	600527		EPLG5		7833926	Standard	NM_004093		Approved	LERK5, Htk-L, HTKL, MGC126226, MGC126227, MGC126228	uc001vqi.3	P52799	OTTHUMG00000017324	ENST00000245323.4:c.611C>T	chr13.hg19:g.107147231G>A	ENSP00000245323:p.Pro204Leu	68.0	0.0		80.0	8.0	NM_004093	Q5JV56	Missense_Mutation	SNP	ENST00000245323.4	hg19	CCDS9507.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.663830	0.47572	.	.	ENSG00000125266	ENST00000245323	D	0.90620	-2.7	6.07	6.07	0.98685	.	0.636389	0.17852	N	0.159813	D	0.86306	0.5901	L	0.27053	0.805	0.58432	D	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.79127	-0.1931	10	0.38643	T	0.18	.	18.8244	0.92111	0.0:0.0:1.0:0.0	.	204	P52799	EFNB2_HUMAN	L	204	ENSP00000245323:P204L	ENSP00000245323:P204L	P	-	2	0	EFNB2	105945232	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.394000	0.73223	2.890000	0.99128	0.650000	0.86243	CCA	.	.		0.418	EFNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045733.4	NM_004093		A	107147231	G	A	107147231	3	1	221	1	0	0	0	0	1	0	0	0	4958	1348	47	3	398	3	EFNB2	13	107147231	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	64270542	107147231	8022647	74	31649										
MYH6	4624	hgsc.bcm.edu	37	chr14	23858666	23858666	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gggtataagagagcttccccCgggtcagctgcgagattagc	14	10	1	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr14:23858666C>A	ENST00000356287.3	-	27	3943	c.3914G>T	c.(3913-3915)cGg>cTg	p.R1305L	MIR208A_ENST00000362287.1_RNA|MYH6_ENST00000405093.3_Missense_Mutation_p.R1305L			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1305					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		GAGCTTCCCCCGGGTCAGCTG	0.592																																					p.R1305L		Atlas-SNP	.											.	MYH6	274	.	0			c.G3914T						.						71	70	71					14																	23858666		2203	4300	6503	SO:0001583	missense	4624	exon28			TTCCCCCGGGTCA	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.3914G>T	chr14.hg19:g.23858666C>A	ENSP00000348634:p.Arg1305Leu	136.0	0.0		110.0	40.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	c	31	5.088037	0.94100	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.79749	-1.3;-1.3	4.63	4.63	0.57726	Myosin tail (1);	.	.	.	.	D	0.92368	0.7578	M	0.93197	3.39	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.94450	0.7666	9	0.72032	D	0.01	.	17.8701	0.88808	0.0:1.0:0.0:0.0	.	1305	P13533	MYH6_HUMAN	L	1305	ENSP00000386041:R1305L;ENSP00000348634:R1305L	ENSP00000348634:R1305L	R	-	2	0	MYH6	22928506	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.634000	0.83273	2.280000	0.76307	0.655000	0.94253	CGG	.	.		0.592	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23858666	C	A	23858666	3	1	221	1	0	0	0	0	1	0	0	0	10047	652	23	1	1953	1	MYH6	14	23858666	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10		23858666	83490874	75	31650										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64676274	64676274	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggtgttgtacacgagtgccaAagaggaactgaagaggtttg	15	5	0	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr14:64676274A>G	ENST00000344113.4	+	102	18730	c.18518A>G	c.(18517-18519)aAa>aGa	p.K6173R	SYNE2_ENST00000554584.1_Missense_Mutation_p.K6135R|SYNE2_ENST00000555002.1_Missense_Mutation_p.K2807R|SYNE2_ENST00000554805.1_5'UTR|SYNE2_ENST00000555022.1_Missense_Mutation_p.K51R|SYNE2_ENST00000358025.3_Missense_Mutation_p.K6173R|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000357395.3_Missense_Mutation_p.K2558R|SYNE2_ENST00000394768.2_Missense_Mutation_p.K2558R	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6173					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ACGAGTGCCAAAGAGGAACTG	0.517																																					p.K6173R		Atlas-SNP	.											.	SYNE2	577	.	0			c.A18518G						.						63	58	60					14																	64676274		2203	4300	6503	SO:0001583	missense	23224	exon102			GTGCCAAAGAGGA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.18518A>G	chr14.hg19:g.64676274A>G	ENSP00000341781:p.Lys6173Arg	75.0	0.0		76.0	28.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.840012	0.51057	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768;ENST00000556906;ENST00000555022	T;T;T;T;T;T;T;T	0.60299	0.67;0.67;0.67;0.2;0.67;0.67;0.71;0.67	5.54	5.54	0.83059	.	0.000000	0.52532	D	0.000072	T	0.70979	0.3286	M	0.72894	2.215	0.80722	D	1	P;D;D;P;D	0.56521	0.755;0.96;0.976;0.614;0.957	P;P;D;P;P	0.62955	0.823;0.872;0.909;0.889;0.841	T	0.67803	-0.5576	10	0.15952	T	0.53	.	15.6693	0.77262	1.0:0.0:0.0:0.0	.	2558;561;6135;6173;6173	Q8WXH0-7;Q7Z362;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;.;SYNE2_HUMAN;.	R	6173;2558;6173;6135;6141;2807;2558;143;51	ENSP00000350719:K6173R;ENSP00000349969:K2558R;ENSP00000341781:K6173R;ENSP00000452570:K6135R;ENSP00000450831:K2807R;ENSP00000378249:K2558R;ENSP00000452298:K143R;ENSP00000451009:K51R	ENSP00000261678:K6141R	K	+	2	0	SYNE2	63746027	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.520000	0.81821	2.087000	0.62958	0.496000	0.49642	AAA	.	.		0.517	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64676274	A	G	64676274	3	3	221	1	0	0	0	0	1	0	0	0	15461	14	1	2	18920	2	SYNE2	14	64676274	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	40817608	64676274	42673266	76	31651										
HSP90AA1	91833	hgsc.bcm.edu	37	chr14	102605737	102605737	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cgtccccgcccgaacacgggGgcatccgcgctccccgtagg	13	19	0	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr14:102605737G>A	ENST00000342702.3	+	0	0				HSP90AA1_ENST00000558600.1_5'UTR|HSP90AA1_ENST00000334701.7_Missense_Mutation_p.P2L|WDR20_ENST00000558567.1_5'Flank|WDR20_ENST00000299135.6_5'Flank|WDR20_ENST00000556807.1_5'Flank|WDR20_ENST00000556511.2_5'Flank|WDR20_ENST00000335263.5_5'Flank|WDR20_ENST00000424963.2_5'Flank|WDR20_ENST00000499851.2_5'Flank|WDR20_ENST00000322340.5_5'Flank|WDR20_ENST00000454394.2_5'Flank	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20											breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						CGAACACGGGGGCATCCGCGC	0.726																																					p.P2L		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.C5T						.						7	9	8					14																	102605737		2163	4242	6405	SO:0001631	upstream_gene_variant	3320	exon1			CACGGGGGCATCC	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3			chr14.hg19:g.102605737G>A	Exception_encountered	156.0	0.0		142.0	50.0	NM_001017963	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Missense_Mutation	SNP	ENST00000342702.3	hg19	CCDS9969.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.308775	0.40895	.	.	ENSG00000080824	ENST00000334701	T	0.10288	2.89	2.79	1.85	0.25348	.	.	.	.	.	T	0.12944	0.0314	N	0.08118	0	0.18873	N	0.999982	D	0.69078	0.997	D	0.78314	0.991	T	0.19877	-1.0292	9	0.87932	D	0	.	6.8707	0.24119	0.0:0.0:0.7253:0.2747	.	2	P07900-2	.	L	2	ENSP00000335153:P2L	ENSP00000335153:P2L	P	-	2	0	HSP90AA1	101675490	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-0.728000	0.04925	0.702000	0.31825	0.511000	0.50034	CCC	.	.		0.726	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		A	102605737	G	A	102605737	1	1	221	0	1	0	0	0	0	0	0	0	7410	1232	43	3		3	HSP90AA1	14	102605737	5'Flank	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	37929463	102605737	4743803	77	31652										
NIPA1	123606	hgsc.bcm.edu	37	chr15	23086286	23086286	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tgtagcacgaacgtggacccGttcaccaggctcgacacgac	11	14	1	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr15:23086286G>T	ENST00000337435.4	-	1	150	c.126C>A	c.(124-126)aaC>aaA	p.N42K	NIPA1_ENST00000561183.1_Intron|NIPA1_ENST00000437912.2_Intron|NIPA1_ENST00000538684.1_5'UTR	NM_001142275.1|NM_144599.4	NP_001135747.1|NP_653200.2	Q7RTP0	NIPA1_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 1	42					cell death (GO:0008219)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)		ACGTGGACCCGTTCACCAGGC	0.791																																					p.N42K		Atlas-SNP	.											.	NIPA1	26	.	0			c.C126A						.						12	10	11					15																	23086286		2166	4233	6399	SO:0001583	missense	123606	exon1			GGACCCGTTCACC	BK001020	CCDS73691.1, CCDS73692.1	15q11.2	2006-10-06			ENSG00000170113	ENSG00000170113			17043	protein-coding gene	gene with protein product		608145	"spastic paraplegia 6 (autosomal dominant)"	SPG6		14508710	Standard	NM_144599		Approved	MGC35570	uc001yvc.3	Q7RTP0	OTTHUMG00000129099	ENST00000337435.4:c.126C>A	chr15.hg19:g.23086286G>T	ENSP00000337452:p.Asn42Lys	526.0	1.0		579.0	208.0	NM_144599	B2RA76|Q5HYA9|Q7KZB0|Q86XW4	Missense_Mutation	SNP	ENST00000337435.4	hg19	CCDS10011.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.046780	0.75846	.	.	ENSG00000170113	ENST00000337435	D	0.89875	-2.58	3.81	2.89	0.33648	.	0.000000	0.85682	D	0.000000	D	0.82508	0.5052	L	0.44542	1.39	0.80722	D	1	P	0.47677	0.899	B	0.40602	0.334	T	0.79995	-0.1568	10	0.87932	D	0	-15.3246	7.2383	0.26082	0.1305:0.0:0.8695:0.0	.	42	Q7RTP0	NIPA1_HUMAN	K	42	ENSP00000337452:N42K	ENSP00000337452:N42K	N	-	3	2	NIPA1	20637727	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	0.506000	0.22658	0.588000	0.29660	0.305000	0.20034	AAC	.	.		0.791	NIPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251135.2	NM_144599		T	23086286	G	T	23086286	3	4	221	1	0	0	0	0	1	0	0	0	10431	1136	40	1	883	1	NIPA1	15	23086286	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10		23086286	79445106	78	31653										
FGF7	2252	hgsc.bcm.edu	37	chr15	49716642	49716642	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	atgtgaactgttccagccctGagcgacacacaagaagttat	9	10	0	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr15:49716642G>T	ENST00000267843.4	+	2	759	c.148G>T	c.(148-150)Gag>Tag	p.E50*	FGF7_ENST00000560270.1_Nonsense_Mutation_p.E50*|FAM227B_ENST00000561064.1_Intron|FAM227B_ENST00000299338.6_Intron	NM_002009.3	NP_002000.1	P21781	FGF7_HUMAN	fibroblast growth factor 7	50					actin cytoskeleton reorganization (GO:0031532)|branching involved in salivary gland morphogenesis (GO:0060445)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle morphogenesis (GO:0031069)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mesenchymal cell proliferation (GO:0010463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization to cell surface (GO:0034394)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|response to wounding (GO:0009611)|secretion by lung epithelial cell involved in lung growth (GO:0061033)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		all_lung(180;0.00391)		all cancers(107;3.61e-08)|GBM - Glioblastoma multiforme(94;4.06e-05)		TTCCAGCCCTGAGCGACACAC	0.428																																					p.E50X		Atlas-SNP	.											.	FGF7	21	.	0			c.G148T						.						137	127	130					15																	49716642		2196	4295	6491	SO:0001587	stop_gained	2252	exon2			AGCCCTGAGCGAC	M60828	CCDS10131.1	15q21.2	2014-01-30	2010-08-18		ENSG00000140285	ENSG00000140285		"Endogenous ligands"	3685	protein-coding gene	gene with protein product	"keratinocyte growth factor"	148180	"fibroblast growth factor 7 (keratinocyte growth factor)"			7749227, 1409637	Standard	NM_002009		Approved	KGF	uc001zxn.3	P21781	OTTHUMG00000131517	ENST00000267843.4:c.148G>T	chr15.hg19:g.49716642G>T	ENSP00000267843:p.Glu50*	150.0	0.0		159.0	47.0	NM_002009	H0YNY5|Q6FGV5|Q96FG5	Nonsense_Mutation	SNP	ENST00000267843.4	hg19	CCDS10131.1	.	.	.	.	.	.	.	.	.	.	G	39	7.531707	0.98342	.	.	ENSG00000140285	ENST00000267843	.	.	.	5.7	5.7	0.88788	.	0.078136	0.49916	D	0.000127	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	19.8389	0.96675	0.0:0.0:1.0:0.0	.	.	.	.	X	50	.	ENSP00000267843:E50X	E	+	1	0	FGF7	47503934	1.000000	0.71417	0.985000	0.45067	0.999000	0.98932	9.229000	0.95273	2.703000	0.92315	0.655000	0.94253	GAG	.	.		0.428	FGF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254374.3	NM_002009		T	49716642	G	T	49716642	4	4	221	1	0	0	0	0	0	1	0	0	5865	1291	45	3	150	3	FGF7	15	49716642	Nonsense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	26630356	49716642	52814750	79	31654										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1269083	1269083	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ccctccacgccctgtcccctCggggcacagcccgctccccc	8	25	0	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr16:1269083C>T	ENST00000348261.5	+	34	6249	c.6001C>T	c.(6001-6003)Cgg>Tgg	p.R2001W	CACNA1H_ENST00000358590.4_Missense_Mutation_p.R1995W|CACNA1H_ENST00000565831.1_Missense_Mutation_p.R1995W	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	2001					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCTGTCCCCTCGGGGCACAGC	0.697																																					p.R2001W		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C6001T						.						6	7	6					16																	1269083		1697	3633	5330	SO:0001583	missense	8912	exon34			TCCCCTCGGGGCA	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.6001C>T	chr16.hg19:g.1269083C>T	ENSP00000334198:p.Arg2001Trp	120.0	0.0		135.0	41.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	c	20.3	3.959798	0.74016	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.97089	-4.24;-4.19	4.04	4.04	0.47022	.	2.135640	0.03389	U	0.201639	D	0.97046	0.9035	L	0.42245	1.32	0.09310	N	1	D;D;D;D;D	0.69078	0.978;0.995;0.995;0.997;0.978	B;P;P;P;B	0.52856	0.353;0.586;0.586;0.711;0.353	D	0.90652	0.4583	10	0.66056	D	0.02	.	13.4982	0.61438	0.0:1.0:0.0:0.0	.	747;725;731;1995;2001	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	W	2001;1995	ENSP00000334198:R2001W;ENSP00000351401:R1995W	ENSP00000334198:R2001W	R	+	1	2	CACNA1H	1209084	0.002000	0.14202	0.004000	0.12327	0.080000	0.17528	1.677000	0.37576	2.103000	0.63969	0.461000	0.40582	CGG	.	.		0.697	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1269083	C	T	1269083	3	4	221	1	0	0	0	0	1	0	0	0	2547	875	31	1	6131	1	CACNA1H	16	1269083	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10		1269083	89085670	80	31655										
RNF151	146310	hgsc.bcm.edu	37	chr16	2018778	2018778	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ccaagccaccagtgtcgttcGtagagagctggcggagctca	13	12	1	1	rs376750121		TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr16:2018778G>T	ENST00000569714.1	+	4	598	c.590G>T	c.(589-591)cGt>cTt	p.R197L	RNF151_ENST00000321392.3_Missense_Mutation_p.R196L|RNF151_ENST00000569210.2_3'UTR	NM_174903.4	NP_777563.2	Q2KHN1	RN151_HUMAN	ring finger protein 151	197					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)	2						AGTGTCGTTCGTAGAGAGCTG	0.677																																					p.R197L		Atlas-SNP	.											.	RNF151	12	.	0			c.G590T						.						8	10	10					16																	2018778		2096	4203	6299	SO:0001583	missense	146310	exon4			TCGTTCGTAGAGA	BC029501	CCDS58405.1	16p13.3	2013-01-09			ENSG00000179580	ENSG00000179580		"RING-type (C3HC4) zinc fingers"	23235	protein-coding gene	gene with protein product						12477932	Standard	NM_174903		Approved		uc002cnt.1	Q2KHN1	OTTHUMG00000176852	ENST00000569714.1:c.590G>T	chr16.hg19:g.2018778G>T	ENSP00000456566:p.Arg197Leu	131.0	0.0		155.0	59.0	NM_174903	Q8NHS5	Missense_Mutation	SNP	ENST00000569714.1	hg19	CCDS58405.1	.	.	.	.	.	.	.	.	.	.	g	8.767	0.924948	0.18056	.	.	ENSG00000179580	ENST00000321392	T	0.27720	1.65	5.25	1.03	0.20045	TRAF-like (1);	0.712898	0.12687	N	0.447488	T	0.19765	0.0475	L	0.32530	0.975	0.09310	N	0.999993	P	0.44090	0.826	B	0.37346	0.247	T	0.09574	-1.0668	10	0.59425	D	0.04	-19.2332	7.0882	0.25270	0.3697:0.0:0.6303:0.0	.	197	Q2KHN1	RN151_HUMAN	L	196	ENSP00000325794:R196L	ENSP00000325794:R196L	R	+	2	0	RNF151	1958779	0.086000	0.21541	0.003000	0.11579	0.002000	0.02628	1.203000	0.32284	0.212000	0.20703	0.655000	0.94253	CGT	.	.		0.677	RNF151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434030.1	NM_174903		T	2018778	G	T	2018778	3	4	221	1	0	0	0	0	1	0	0	0	13467	1145	40	1	604	1	RNF151	16	2018778	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	749695	2018778	88335975	81	31656										
SCNN1G	6340	hgsc.bcm.edu	37	chr16	23203678	23203678	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tcctcttattcacagtgctcAaatgacacctccgactgtgc	6	14	3	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr16:23203678A>C	ENST00000300061.2	+	4	767	c.624A>C	c.(622-624)tcA>tcC	p.S208S	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	208					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	CACAGTGCTCAAATGACACCT	0.502																																					p.S208S		Atlas-SNP	.											.	SCNN1G	82	.	0			c.A624C						.						138	118	125					16																	23203678		2197	4300	6497	SO:0001819	synonymous_variant	6340	exon4			GTGCTCAAATGAC	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.624A>C	chr16.hg19:g.23203678A>C		76.0	0.0		74.0	29.0	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Silent	SNP	ENST00000300061.2	hg19	CCDS10608.1																																																																																			.	.		0.502	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		C	23203678	A	C	23203678	2	2	221	1	0	0	0	0	0	0	0	1	13945	117	5	5		5	SCNN1G	16	23203678	Silent	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	21184900	23203678	67151075	82	31657										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24834981	24834981	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	actaactgtggagaccttcaCggcacttcactctgggggac	11	12	3	1	rs373265827	byFrequency	TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr16:24834981C>T	ENST00000395799.3	+	25	5871	c.5742C>T	c.(5740-5742)caC>caT	p.H1914H	TNRC6A_ENST00000432286.2_Silent_p.H392H|TNRC6A_ENST00000315183.7_Silent_p.H1865H	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1914	Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		GAGACCTTCACGGCACTTCAC	0.597													c|||	2	0.000399361	0	0	5008	,	,		15912	0		0.001	False		,,,				2504	0.001				p.H1914H		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C5742T						.	C		1,4393	2.1+/-5.4	0,1,2196	105	105	105		5742	-0.4	1	16		105	0,8600		0,0,4300	no	coding-synonymous	TNRC6A	NM_014494.2		0,1,6496	TT,TC,CC		0.0,0.0228,0.0077		1914/1963	24834981	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	27327	exon25			CCTTCACGGCACT	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.5742C>T	chr16.hg19:g.24834981C>T		141.0	0.0		128.0	42.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	c	1.778	-0.482756	0.04383	2.28E-4	0.0	ENSG00000090905	ENST00000450465	.	.	.	5.64	-0.428	0.12306	.	.	.	.	.	T	0.51702	0.1690	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41448	-0.9508	4	.	.	.	-5.0747	6.5391	0.22370	0.0:0.2026:0.1509:0.6465	.	.	.	.	W	805	.	.	R	+	1	2	TNRC6A	24742482	0.999000	0.42202	0.998000	0.56505	0.998000	0.95712	0.579000	0.23788	0.027000	0.15297	0.651000	0.88453	CGG	.	.		0.597	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		T	24834981	C	T	24834981	2	4	221	1	0	0	0	0	0	0	0	1	16355	535	19	1		1	TNRC6A	16	24834981	Silent	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	1631303	24834981	65519772	83	31658										
SALL1	6299	hgsc.bcm.edu	37	chr16	51172810	51172810	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	aagacagaggcccagacgggAcgtgactggtgggggtgtcc	18	9	0	4			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr16:51172810A>T	ENST00000251020.4	-	2	3356	c.3323T>A	c.(3322-3324)gTc>gAc	p.V1108D	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.V1011D|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1108					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			CCCAGACGGGACGTGACTGGT	0.562																																					p.V1108D	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.T3323A						.						101	87	92					16																	51172810		2198	4300	6498	SO:0001583	missense	6299	exon2			GACGGGACGTGAC	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3323T>A	chr16.hg19:g.51172810A>T	ENSP00000251020:p.Val1108Asp	139.0	0.0		116.0	36.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.393479	0.62066	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.08282	3.11;3.12	5.42	4.34	0.51931	.	0.354056	0.32106	N	0.006575	T	0.07007	0.0178	L	0.39898	1.24	0.54753	D	0.999983	B	0.33448	0.412	B	0.29267	0.1	T	0.33879	-0.9851	10	0.30854	T	0.27	.	9.7213	0.40304	0.8622:0.0:0.1378:0.0	.	1108	Q9NSC2	SALL1_HUMAN	D	1108;1011;1072	ENSP00000251020:V1108D;ENSP00000407914:V1011D	ENSP00000251020:V1108D	V	-	2	0	SALL1	49730311	1.000000	0.71417	0.954000	0.39281	0.803000	0.45373	6.128000	0.71650	2.046000	0.60703	0.460000	0.39030	GTC	.	.		0.562	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		T	51172810	A	T	51172810	3	4	221	1	0	0	0	0	1	0	0	0	13825	275	10	4	659	4	SALL1	16	51172810	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	26337829	51172810	39181943	84	31659										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81208430	81208430	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	agctggaggagctgctcgggGccaccctcgccttgcagagc	15	14	0	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr16:81208430G>A	ENST00000527937.1	-	0	554				PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000533478.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GCTGCTCGGGGCCACCCTCGC	0.572																																					p.G891G		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2673T						.						57	57	57					16																	81208430		2064	4218	6282			114780	exon16			CTCGGGGCCACCC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		chr16.hg19:g.81208430G>A		67.0	0.0		57.0	19.0	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000527937.1	hg19		.	.	.	.	.	.	.	.	.	.	G	6.385	0.439214	0.12104	.	.	ENSG00000166473	ENST00000526632	.	.	.	4.7	3.72	0.42706	.	.	.	.	.	T	0.46908	0.1417	.	.	.	0.29299	N	0.868815	.	.	.	.	.	.	T	0.41805	-0.9488	4	.	.	.	-12.4898	12.2557	0.54623	0.0:0.172:0.828:0.0	.	.	.	.	S	419	.	.	P	-	1	0	PKD1L2	79765931	0.370000	0.25047	0.134000	0.22075	0.134000	0.20937	2.181000	0.42547	1.067000	0.40740	0.555000	0.69702	CCC	.	.		0.572	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1			A	81208430	G	A	81208430	1	1	221	0	1	0	0	0	0	0	0	0	11974	1190	42	3		3	PKD1L2	16	81208430	RNA	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	30035620	81208430	9146323	85	31660										
FOXL1	2300	hgsc.bcm.edu	37	chr16	86612573	86612573	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tctaccagttcatcatggacCgcttccccttctaccacgac	5	17	4	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr16:86612573C>A	ENST00000320241.3	+	1	459	c.244C>A	c.(244-246)Cgc>Agc	p.R82S		NM_005250.2	NP_005241.1	Q12952	FOXL1_HUMAN	forkhead box L1	82					heart development (GO:0007507)|multicellular organismal development (GO:0007275)|organ morphogenesis (GO:0009887)|Peyer's patch morphogenesis (GO:0061146)|proteoglycan biosynthetic process (GO:0030166)|regulation of Wnt signaling pathway (GO:0030111)|transcription, DNA-templated (GO:0006351)|visceral mesoderm-endoderm interaction involved in midgut development (GO:0007495)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(2)|prostate(3)|skin(1)|urinary_tract(1)	15						CATCATGGACCGCTTCCCCTT	0.617																																					p.R82S	NSCLC(163;308 2020 10889 11476 18208)	Atlas-SNP	.											.	FOXL1	39	.	0			c.C244A						.						111	112	112					16																	86612573		2198	4300	6498	SO:0001583	missense	2300	exon1			ATGGACCGCTTCC	AF315075	CCDS10959.1	16q24	2014-07-15			ENSG00000176678	ENSG00000176678		"Forkhead boxes"	3817	protein-coding gene	gene with protein product		603252		FKHL11		7957066	Standard	NM_005250		Approved	FREAC7, FKH6	uc002fjr.3	Q12952	OTTHUMG00000137653	ENST00000320241.3:c.244C>A	chr16.hg19:g.86612573C>A	ENSP00000326272:p.Arg82Ser	265.0	0.0		249.0	104.0	NM_005250	Q17RR1|Q9H242	Missense_Mutation	SNP	ENST00000320241.3	hg19	CCDS10959.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.350185	0.82132	.	.	ENSG00000176678	ENST00000320241	D	0.95518	-3.73	3.78	3.78	0.43462	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	U	0.000000	D	0.97139	0.9065	M	0.78223	2.4	0.58432	D	0.999993	D	0.57899	0.981	D	0.66084	0.941	D	0.97355	0.9966	10	0.54805	T	0.06	.	14.7693	0.69662	0.0:1.0:0.0:0.0	.	82	Q12952	FOXL1_HUMAN	S	82	ENSP00000326272:R82S	ENSP00000326272:R82S	R	+	1	0	FOXL1	85170074	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.436000	0.59948	1.951000	0.56629	0.491000	0.48974	CGC	.	.		0.617	FOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269105.2	NM_005250		A	86612573	C	A	86612573	3	1	221	1	0	0	0	0	1	0	0	0	6024	652	23	1	246	1	FOXL1	16	86612573	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	5404143	86612573	3742180	86	31661										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89350828	89350828	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	atctttaaagagccattcttTttcttctaatttcattttgc	3	8	5	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr16:89350828T>C	ENST00000301030.4	-	9	2582	c.2122A>G	c.(2122-2124)Aaa>Gaa	p.K708E	ANKRD11_ENST00000378330.2_Missense_Mutation_p.K708E	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	708	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		AGCCATTCTTTTTCTTCTAAT	0.348																																					p.K708E		Atlas-SNP	.											.	ANKRD11	195	.	0			c.A2122G						.						69	68	69					16																	89350828		2198	4300	6498	SO:0001583	missense	29123	exon9			ATTCTTTTTCTTC	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.2122A>G	chr16.hg19:g.89350828T>C	ENSP00000301030:p.Lys708Glu	103.0	0.0		118.0	51.0	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	T	18.51	3.640725	0.67244	.	.	ENSG00000167522	ENST00000301030;ENST00000378330;ENST00000330736	T;T	0.39787	1.06;1.06	5.82	5.82	0.92795	.	0.125578	0.52532	D	0.000077	T	0.62048	0.2396	M	0.63843	1.955	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.69654	0.965;0.923	T	0.65055	-0.6261	10	0.87932	D	0	.	16.1778	0.81874	0.0:0.0:0.0:1.0	.	327;708	Q7Z5E5;Q6UB99	.;ANR11_HUMAN	E	708;708;327	ENSP00000301030:K708E;ENSP00000367581:K708E	ENSP00000301030:K708E	K	-	1	0	ANKRD11	87878329	1.000000	0.71417	0.017000	0.16124	0.930000	0.56654	7.789000	0.85783	2.225000	0.72522	0.459000	0.35465	AAA	.	.		0.348	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		C	89350828	T	C	89350828	3	2	221	1	0	0	0	0	1	0	0	0	639	1850	64	2	5889	2	ANKRD11	16	89350828	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	2738255	89350828	1003925	87	31662										
TP53	7157	hgsc.bcm.edu	37	chr17	7579521	7579521	+	Frame_Shift_Del	DEL	C	C	-													0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ttcatctggacctgggtcttCagtgaaccattgttcaatat							TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr17:7579521delC	ENST00000269305.4	-	4	355	c.166delG	c.(166-168)gaafs	p.E56fs	TP53_ENST00000413465.2_Frame_Shift_Del_p.E56fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.E56fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Frame_Shift_Del_p.E56fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.E56fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.E56fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	56	Interaction with HRMT1L2.		E -> K (in sporadic cancers; somatic mutation).|E -> V (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.E56*(7)|p.E56K(3)|p.E56fs*73(3)|p.E51fs*59(1)|p.Q52fs*67(1)|p.D48fs*55(1)|p.E56fs*67(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCTGGGTCTTCAGTGAACCAT	0.597		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E56fs	Pancreas(47;798 1329 9957 10801)	Atlas-INDEL	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000413465,NS,carcinoma,-1,3	TP53	33396	.	27	Whole gene deletion(8)|Substitution - Nonsense(7)|Deletion - Frameshift(6)|Insertion - Frameshift(3)|Substitution - Missense(3)	upper_aerodigestive_tract(4)|bone(4)|liver(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|breast(2)|pancreas(2)|large_intestine(1)|stomach(1)|endometrium(1)|lung(1)|skin(1)|prostate(1)	c.167delA						.						158	159	159					17																	7579521		2203	4300	6503	SO:0001589	frameshift_variant	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.166delG	chr17.hg19:g.7579521delC	ENSP00000269305:p.Glu56fs	137.0	0.0		66.0	45.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.597	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7579521	C	-	7579521	7	5	221	1	0	1	0	1	0	0	0	0	16396	835	29	0	1136	0	TP53	17	7579521	Frame_Shift_Del	DEL	C	TCGA-DD-AAEI-01A-11D-A40R-10		7579521	73615689	88	31663										
MYH4	4622	hgsc.bcm.edu	37	chr17	10358067	10358067	+	Frame_Shift_Del	DEL	G	G	-													0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ttgaaatacagcttcatccaGggccagtgcttcacattcat							TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr17:10358067delG	ENST00000255381.2	-	22	2606	c.2496delC	c.(2494-2496)cccfs	p.P832fs	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	832					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						GCTTCATCCAGGGCCAGTGCT	0.423																																					p.W833fs		Atlas-INDEL	.											.	MYH4	349	.	0			c.2497delT						.						137	124	128					17																	10358067		2203	4300	6503	SO:0001589	frameshift_variant	4622	exon22			.		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.2496delC	chr17.hg19:g.10358067delG	ENSP00000255381:p.Pro832fs	122.0	0.0		77.0	43.0	NM_017533		Frame_Shift_Del	DEL	ENST00000255381.2	hg19	CCDS11154.1																																																																																			.	.		0.423	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		-	10358067	G	-	10358067	7	5	221	1	0	1	0	1	0	0	0	0	10046	987	35	0	3399	0	MYH4	17	10358067	Frame_Shift_Del	DEL	G	TCGA-DD-AAEI-01A-11D-A40R-10	2778546	10358067	70837143	89	31664										
KRT39	390792	hgsc.bcm.edu	37	chr17	39118496	39118496	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tctccttttggcagcattgcTgctgttgagagctggtcacc	11	11	2	1			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr17:39118496T>A	ENST00000355612.2	-	5	949	c.914A>T	c.(913-915)cAg>cTg	p.Q305L	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	305	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	17		Breast(137;0.00043)|Ovarian(249;0.15)				GCAGCATTGCTGCTGTTGAGA	0.473																																					p.Q305L		Atlas-SNP	.											.	KRT39	53	.	0			c.A914T						.						223	205	211					17																	39118496		2203	4296	6499	SO:0001583	missense	390792	exon5			CATTGCTGCTGTT	AJ786657	CCDS11382.1	17q21.2	2013-01-16			ENSG00000196859	ENSG00000196859		"-", "Intermediate filaments type I, keratins (acidic)"	32971	protein-coding gene	gene with protein product						16831889	Standard	NM_213656		Approved	KA35	uc002hvo.1	Q6A163	OTTHUMG00000133424	ENST00000355612.2:c.914A>T	chr17.hg19:g.39118496T>A	ENSP00000347823:p.Gln305Leu	73.0	0.0		38.0	19.0	NM_213656	B2RXK6|Q6IFU6	Missense_Mutation	SNP	ENST00000355612.2	hg19	CCDS11382.1	.	.	.	.	.	.	.	.	.	.	T	7.157	0.584845	0.13749	.	.	ENSG00000196859	ENST00000355612	T	0.71461	-0.57	5.7	4.56	0.56223	Filament (1);	0.000000	0.42548	D	0.000683	T	0.23649	0.0572	N	0.00068	-2.285	0.37853	D	0.929459	B	0.11235	0.004	B	0.11329	0.006	T	0.50491	-0.8822	10	0.02654	T	1	.	8.8091	0.34956	0.3221:0.0:0.0:0.6779	.	305	Q6A163	K1C39_HUMAN	L	305	ENSP00000347823:Q305L	ENSP00000347823:Q305L	Q	-	2	0	KRT39	36372022	0.698000	0.27777	1.000000	0.80357	0.982000	0.71751	5.166000	0.64965	2.173000	0.68751	0.533000	0.62120	CAG	.	.		0.473	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656		A	39118496	T	A	39118496	3	1	221	1	0	0	0	0	1	0	0	0	8485	1580	55	4	573	4	KRT39	17	39118496	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	28760429	39118496	42076714	90	31665										
CRHR1	1394	hgsc.bcm.edu	37	chr17	43893892	43893892	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gccccgcagccctgcggggcAgctagtggttcggccctgcc	15	17	0	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr17:43893892A>T	ENST00000398285.3	+	3	185	c.185A>T	c.(184-186)cAg>cTg	p.Q62L	CRHR1_ENST00000577353.1_Missense_Mutation_p.Q62L|CRHR1_ENST00000352855.5_Intron|CRHR1_ENST00000339069.5_5'UTR|RP11-105N13.4_ENST00000587305.1_RNA|CRHR1_ENST00000314537.5_Missense_Mutation_p.Q62L|CRHR1_ENST00000293493.7_5'UTR	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	62					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CCTGCGGGGCAGCTAGTGGTT	0.607																																					p.Q62L	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.A185T						.						41	45	43					17																	43893892		1934	4113	6047	SO:0001583	missense	1394	exon3			CGGGGCAGCTAGT	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"GPCR / Class B : Corticotropin-releasing factor receptors"	2357	protein-coding gene	gene with protein product	"corticotropin-releasing factor receptor"	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.185A>T	chr17.hg19:g.43893892A>T	ENSP00000381333:p.Gln62Leu	77.0	0.0		49.0	35.0	NM_001145148	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Missense_Mutation	SNP	ENST00000398285.3	hg19	CCDS45712.1	.	.	.	.	.	.	.	.	.	.	A	16.05	3.012995	0.54468	.	.	ENSG00000120088	ENST00000398285;ENST00000314537;ENST00000347197	T;T;T	0.64618	-0.11;-0.11;-0.11	5.04	5.04	0.67666	GPCR, family 2, secretin-like, conserved site (1);GPCR, family 2, extracellular hormone receptor domain (3);	0.120686	0.56097	D	0.000022	T	0.45915	0.1366	N	0.17800	0.525	0.80722	D	1	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.19666	0.005;0.026;0.002	T	0.37220	-0.9715	10	0.28530	T	0.3	.	11.109	0.48221	1.0:0.0:0.0:0.0	.	62;62;62	P34998-4;P34998;P34998-2	.;CRFR1_HUMAN;.	L	62	ENSP00000381333:Q62L;ENSP00000326060:Q62L;ENSP00000239167:Q62L	ENSP00000326060:Q62L	Q	+	2	0	CRHR1	41249673	0.999000	0.42202	1.000000	0.80357	0.958000	0.62258	5.230000	0.65321	2.126000	0.65437	0.533000	0.62120	CAG	.	.		0.607	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3			T	43893892	A	T	43893892	3	4	221	1	0	0	0	0	1	0	0	0	3873	188	7	4	195	4	CRHR1	17	43893892	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	4775396	43893892	37301318	91	31666										
CCDC45	90799	hgsc.bcm.edu	37	chr17	62532722	62532722	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cgattaaataactgacagatAtttaagaaactgtttgaaga	7	4	0	5			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr17:62532722A>G	ENST00000556440.2	+	18	2583	c.2073A>G	c.(2071-2073)atA>atG	p.I691M	CEP95_ENST00000553412.1_Missense_Mutation_p.I527M	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	691						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						ACTGACAGATATTTAAGAAAC	0.318																																					p.I691M		Atlas-SNP	.											.	CEP95	103	.	0			c.A2073G						.						56	57	57					17																	62532722		1833	4087	5920	SO:0001583	missense	90799	exon18			ACAGATATTTAAG	AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.2073A>G	chr17.hg19:g.62532722A>G	ENSP00000450461:p.Ile691Met	452.0	0.0		458.0	165.0	NM_138363	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	hg19	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.456659	0.26161	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	T;T	0.37752	1.29;1.18	5.48	1.65	0.23941	.	0.108254	0.64402	D	0.000005	T	0.31167	0.0788	L	0.46157	1.445	0.36224	D	0.852201	P	0.36199	0.543	B	0.34489	0.184	T	0.46233	-0.9206	10	0.72032	D	0.01	-9.3789	13.7593	0.62956	0.4621:0.5379:0.0:0.0	.	691	Q96GE4	CEP95_HUMAN	M	626;691;527	ENSP00000450461:I691M;ENSP00000450906:I527M	ENSP00000438458:I626M	I	+	3	3	CEP95	59963184	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.988000	0.40697	0.414000	0.25790	0.528000	0.53228	ATA	.	.		0.318	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		G	62532722	A	G	62532722	3	3	221	1	0	0	0	0	1	0	0	0	2818	439	16	2	2143	2	CCDC45	17	62532722	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	18638830	62532722	18662488	92	31667										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2772286	2772286	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cttctgaaaagaaagctatcAgaacaagaagaactgaagaa	8	6	2	7			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr18:2772286A>T	ENST00000320876.6	+	41	5429	c.5091A>T	c.(5089-5091)tcA>tcT	p.S1697S	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Silent_p.S1697S|snoU13_ENST00000459147.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1697					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GAAAGCTATCAGAACAAGAAG	0.353																																					p.S1697S		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A5091T						.						86	76	79					18																	2772286		1813	4076	5889	SO:0001819	synonymous_variant	23347	exon41			GCTATCAGAACAA	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.5091A>T	chr18.hg19:g.2772286A>T		109.0	0.0		97.0	35.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.		0.353	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2772286	A	T	2772286	2	4	221	1	0	0	0	0	0	0	0	1	14803	175	7	4		4	SMCHD1	18	2772286	Silent	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10		2772286	75304962	93	31668										
ZNF519	162655	hgsc.bcm.edu	37	chr18	14105451	14105454	+	Frame_Shift_Del	DEL	AGGT	AGGT	-													0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ggattctctggtgttgagtaAggtatgaccccctgttaaag							TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	AGGT	AGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr18:14105451_14105454delAGGT	ENST00000590202.1	-	3	1237_1240	c.1085_1088delACCT	c.(1084-1089)taccttfs	p.YL362fs	RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589498.1_Intron|ZNF519_ENST00000589203.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	362					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						GTGTTGAGTAAGGTATGACCCCCT	0.422																																					p.362_363del		Atlas-INDEL	.											.	ZNF519	53	.	0			c.1086_1089del						.																																			SO:0001589	frameshift_variant	162655	exon3			.	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"Zinc fingers, C2H2-type", "-"	30574	protein-coding gene	gene with protein product	"similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.1085_1088delACCT	chr18.hg19:g.14105451_14105454delAGGT	ENSP00000464872:p.Tyr362fs	67.0	0.0		61.0	17.0	NM_145287		Frame_Shift_Del	DEL	ENST00000590202.1	hg19	CCDS32797.1																																																																																			.	.		0.422	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		-	14105454	AGGT	-	14105451	7	5	221	1	0	1	0	1	0	0	0	0	17979	72	3	0	538	0	ZNF519	18	14105451	Frame_Shift_Del	DEL	AGGT	TCGA-DD-AAEI-01A-11D-A40R-10	11333165	14105451	63971797	94	31669										
EEF2	1938	hgsc.bcm.edu	37	chr19	3981359	3981359	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tcagcaggggtttgccttctTtgtccttgtcctcgctgtcc	10	13	2	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr19:3981359T>G	ENST00000309311.6	-	7	1077	c.989A>C	c.(988-990)aAa>aCa	p.K330T	EEF2_ENST00000600720.1_5'Flank|SNORD37_ENST00000384048.1_RNA	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	330	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)			endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		TTTGCCTTCTTTGTCCTTGTC	0.547																																					p.K330T	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											.	EEF2	57	.	0			c.A989C						.						311	256	275					19																	3981359		2203	4300	6503	SO:0001583	missense	1938	exon7			CCTTCTTTGTCCT	Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"polypeptidyl-tRNA translocase"	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.989A>C	chr19.hg19:g.3981359T>G	ENSP00000307940:p.Lys330Thr	80.0	0.0		92.0	34.0	NM_001961	B2RMP5|D6W618|Q58J86	Missense_Mutation	SNP	ENST00000309311.6	hg19	CCDS12117.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.858141	0.51376	.	.	ENSG00000167658	ENST00000543343;ENST00000309311	T	0.29397	1.57	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.41743	0.1172	L	0.55213	1.73	0.80722	D	1	P	0.51537	0.946	P	0.51550	0.673	T	0.34875	-0.9811	10	0.66056	D	0.02	-32.1649	14.5906	0.68362	0.0:0.0:0.0:1.0	.	330	P13639	EF2_HUMAN	T	330	ENSP00000307940:K330T	ENSP00000307940:K330T	K	-	2	0	EEF2	3932359	1.000000	0.71417	0.907000	0.35723	0.631000	0.37964	7.985000	0.88162	2.042000	0.60477	0.459000	0.35465	AAA	.	.		0.547	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961		G	3981359	T	G	3981359	3	3	221	1	0	0	0	0	1	0	0	0	4931	1841	64	5	1623	5	EEF2	19	3981359	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10		3981359	55147624	95	31670										
DUS3L	56931	hgsc.bcm.edu	37	chr19	5790068	5790068	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ccgcacttgcctggattaggGagggacacagcctgttcttg	13	11	1	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr19:5790068G>C	ENST00000309061.7	-	2	473	c.377C>G	c.(376-378)tCc>tGc	p.S126C	DUS3L_ENST00000590681.1_5'UTR|DUS3L_ENST00000320699.8_Intron	NM_020175.2	NP_064560.2	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like (S. cerevisiae)	126							flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA dihydrouridine synthase activity (GO:0017150)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(2)	14						CTGGATTAGGGAGGGACACAG	0.617																																					p.S126C		Atlas-SNP	.											.	DUS3L	42	.	0			c.C377G						.						77	76	77					19																	5790068		2203	4300	6503	SO:0001583	missense	56931	exon2			ATTAGGGAGGGAC		CCDS32880.1, CCDS54202.1	19p13.3	2014-02-12			ENSG00000141994	ENSG00000141994			26920	protein-coding gene	gene with protein product						12477932	Standard	NM_020175		Approved	DUS3, FLJ13896	uc002mdc.3	Q96G46	OTTHUMG00000162311	ENST00000309061.7:c.377C>G	chr19.hg19:g.5790068G>C	ENSP00000311977:p.Ser126Cys	159.0	0.0		165.0	46.0	NM_020175	Q96HM5|Q9BSU4|Q9H877|Q9NPR1	Missense_Mutation	SNP	ENST00000309061.7	hg19	CCDS32880.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.941754	0.53079	.	.	ENSG00000141994	ENST00000309061	T	0.21361	2.01	4.74	3.61	0.41365	Zinc finger, CCCH-type (1);	0.222750	0.39687	N	0.001285	T	0.28599	0.0708	M	0.79614	2.46	0.39487	D	0.967973	P	0.36125	0.538	B	0.38106	0.265	T	0.32955	-0.9887	10	0.72032	D	0.01	0.0328	12.3594	0.55194	0.0:0.1718:0.8282:0.0	.	126	Q96G46	DUS3L_HUMAN	C	126	ENSP00000311977:S126C	ENSP00000311977:S126C	S	-	2	0	DUS3L	5741068	1.000000	0.71417	0.100000	0.21137	0.876000	0.50452	7.213000	0.77950	2.332000	0.79248	0.655000	0.94253	TCC	.	.		0.617	DUS3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451870.2	NM_020175		C	5790068	G	C	5790068	3	2	221	1	0	0	0	0	1	0	0	0	4809	1174	41	4	1623	4	DUS3L	19	5790068	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	1808709	5790068	53338915	96	31671										
SH2D3A	10045	hgsc.bcm.edu	37	chr19	6752638	6752638	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ccaggcgctgcgacaggacgCcgaggacgcgctggaacttc	15	14	0	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr19:6752638C>T	ENST00000245908.6	-	10	1966	c.1697G>A	c.(1696-1698)gGc>gAc	p.G566D	SH2D3A_ENST00000437152.3_Missense_Mutation_p.G473D|CTD-3128G10.6_ENST00000594056.1_RNA|SH2D3A_ENST00000599563.1_5'Flank	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	566					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						CGACAGGACGCCGAGGACGCG	0.672																																					p.G566D		Atlas-SNP	.											.	SH2D3A	53	.	0			c.G1697A						.						16	21	20					19																	6752638		2190	4286	6476	SO:0001583	missense	10045	exon10			AGGACGCCGAGGA	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"SH2 domain containing"	16885	protein-coding gene	gene with protein product		604721	"SH2 domain-containing 3A"			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.1697G>A	chr19.hg19:g.6752638C>T	ENSP00000245908:p.Gly566Asp	87.0	0.0		87.0	9.0	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Missense_Mutation	SNP	ENST00000245908.6	hg19	CCDS12173.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.197357	0.38806	.	.	ENSG00000125731	ENST00000245908;ENST00000437152	T;T	0.28895	2.63;1.59	4.77	1.28	0.21552	.	0.376200	0.22710	N	0.056591	T	0.12220	0.0297	N	0.03608	-0.345	0.09310	N	1	B;B	0.22800	0.075;0.013	B;B	0.18871	0.023;0.01	T	0.23013	-1.0200	10	0.36615	T	0.2	-5.6676	8.6964	0.34298	0.0:0.6314:0.2847:0.084	.	473;566	B4DRS7;Q9BRG2	.;SH23A_HUMAN	D	566;473	ENSP00000245908:G566D;ENSP00000393303:G473D	ENSP00000245908:G566D	G	-	2	0	SH2D3A	6703638	0.000000	0.05858	0.192000	0.23308	0.757000	0.42996	0.162000	0.16501	0.591000	0.29711	0.563000	0.77884	GGC	.	.		0.672	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490		T	6752638	C	T	6752638	3	4	221	1	0	0	0	0	1	0	0	0	14248	739	26	3	37	3	SH2D3A	19	6752638	Missense_Mutation	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	962570	6752638	52376345	97	31672										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10087234	10087234	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gaaaagatgggggcactcacCgggggacctgggtgtcctgc	17	10	1	1	rs146470482	byFrequency	TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr19:10087234C>T	ENST00000264828.3	-	45	3427	c.3342G>A	c.(3340-3342)ccG>ccA	p.P1114P		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1114	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			GGGCACTCACCGGGGGACCTG	0.532																																					p.P1114P		Atlas-SNP	.											COL5A3,NS,carcinoma,0,1	COL5A3	243	.	0			c.G3342A						.						22	25	24					19																	10087234		2202	4300	6502	SO:0001630	splice_region_variant	50509	exon45			ACTCACCGGGGGA	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3342+1G>A	chr19.hg19:g.10087234C>T		30.0	0.0		58.0	17.0	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	hg19	CCDS12222.1																																																																																			.	C|0.999;G|0.001		0.532	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	Silent	T	10087234	C	T	10087234	5	4	221	1	0	0	0	0	0	0	1	0	3700	666	23	1	1987	1	COL5A3	19	10087234	Splice_Site	SNP	C	TCGA-DD-AAEI-01A-11D-A40R-10	3334596	10087234	49041749	98	31673										
ZNF285	26974	hgsc.bcm.edu	37	chr19	44891428	44891428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gttgtgaagggaagagctgcGcctgaagcccttgccacatt	13	10	0	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr19:44891428G>A	ENST00000330997.4	-	4	1043	c.979C>T	c.(979-981)Cgc>Tgc	p.R327C	ZNF285_ENST00000544719.2_Missense_Mutation_p.R327C|ZNF285_ENST00000591679.1_Missense_Mutation_p.R334C|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						GAAGAGCTGCGCCTGAAGCCC	0.493																																					p.R327C		Atlas-SNP	.											.	ZNF285	86	.	0			c.C979T						.						93	93	93					19																	44891428		2203	4300	6503	SO:0001583	missense	26974	exon4			AGCTGCGCCTGAA	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.979C>T	chr19.hg19:g.44891428G>A	ENSP00000333595:p.Arg327Cys	135.0	0.0		111.0	37.0	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	hg19	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.084260	0.36758	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.16196	2.36	3.5	-1.58	0.08479	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10380	0.0254	L	0.35793	1.09	0.09310	N	1	B;B	0.12630	0.006;0.002	B;B	0.08055	0.001;0.003	T	0.34650	-0.9820	9	0.30078	T	0.28	.	3.018	0.06066	0.3928:0.0:0.2628:0.3444	.	351;327	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	C	350;327	ENSP00000333595:R327C	ENSP00000333595:R327C	R	-	1	0	ZNF285	49583268	0.000000	0.05858	0.000000	0.03702	0.666000	0.39218	-2.537000	0.00939	-0.177000	0.10690	0.454000	0.30748	CGC	.	.		0.493	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		A	44891428	G	A	44891428	3	1	221	1	0	0	0	0	1	0	0	0	17837	1087	38	1	797	1	ZNF285	19	44891428	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	34804194	44891428	14237555	99	31674										
MYBPC2	4606	hgsc.bcm.edu	37	chr19	50961957	50961957	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tagttggggtcaacatcgcgGggcgcagcgagccggccacc	16	13	1	0			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr19:50961957G>T	ENST00000357701.5	+	21	2503	c.2452G>T	c.(2452-2454)Ggg>Tgg	p.G818W		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	818	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		CAACATCGCGGGGCGCAGCGA	0.672																																					p.G818W		Atlas-SNP	.											.	MYBPC2	103	.	0			c.G2452T						.						28	36	33					19																	50961957		2042	4181	6223	SO:0001583	missense	4606	exon21			ATCGCGGGGCGCA		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7550	protein-coding gene	gene with protein product	"fast-type muscle myosin-binding-protein C"	160793	"myosin-binding protein C, fast-type"			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.2452G>T	chr19.hg19:g.50961957G>T	ENSP00000350332:p.Gly818Trp	60.0	0.0		79.0	25.0	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	hg19	CCDS46152.1	.	.	.	.	.	.	.	.	.	.	g	23.6	4.435950	0.83885	.	.	ENSG00000086967	ENST00000357701	T	0.69306	-0.39	4.05	4.05	0.47172	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.35407	U	0.003229	D	0.88551	0.6467	H	0.98629	4.285	0.52099	D	0.999946	D	0.89917	1.0	D	0.97110	1.0	D	0.93192	0.6584	10	0.87932	D	0	.	15.339	0.74282	0.0:0.0:1.0:0.0	.	818	Q14324	MYPC2_HUMAN	W	818	ENSP00000350332:G818W	ENSP00000350332:G818W	G	+	1	0	MYBPC2	55653769	1.000000	0.71417	0.979000	0.43373	0.955000	0.61496	8.532000	0.90613	1.992000	0.58205	0.457000	0.33378	GGG	.	.		0.672	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533		T	50961957	G	T	50961957	3	4	221	1	0	0	0	0	1	0	0	0	10021	1232	43	3	2534	3	MYBPC2	19	50961957	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	6070529	50961957	8167026	100	31675										
ZNF784	147808	hgsc.bcm.edu	37	chr19	56133523	56133524	+	In_Frame_Ins	INS	-	-	CCG													0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	aggcttccccaccgctgcgcINSccgccgccgccgccgccatc							TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr19:56133523_56133524insCCG	ENST00000325351.4	-	2	604_605	c.565_566insCGG	c.(565-567)ggc>gCGGgc	p.188_189insA	ZNF784_ENST00000591479.1_3'UTR	NM_203374.1	NP_976308.1	Q8NCA9	ZN784_HUMAN	zinc finger protein 784	188					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			upper_aerodigestive_tract(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		caccgctgcgcccgccgccgcc	0.728																																					p.G189delinsAG		Atlas-INDEL	.											.	ZNF784	9	.	0			c.566_567insCGG						.																																			SO:0001652	inframe_insertion	147808	exon2			.	AK074859	CCDS12930.1	19q13.42	2013-01-08			ENSG00000179922	ENSG00000179922		"Zinc fingers, C2H2-type"	33111	protein-coding gene	gene with protein product							Standard	NM_203374		Approved	MGC75238	uc002qll.1	Q8NCA9	OTTHUMG00000180860	ENST00000325351.4:c.563_565dupCGG	chr19.hg19:g.56133530_56133532dupCCG	ENSP00000320096:p.Ala190_Ala191dup	40.0	0.0		39.0	14.0	NM_203374		In_Frame_Ins	INS	ENST00000325351.4	hg19	CCDS12930.1																																																																																			.	.		0.728	ZNF784-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453355.2	NM_203374		CCG	56133524	-	CCG	56133523	7	5	221	1	0	1	1	0	0	0	0	0	18171	739	26	0	409	0	ZNF784	19	56133523	In_Frame_Ins	INS	-	TCGA-DD-AAEI-01A-11D-A40R-10	5171566	56133523	2995460	101	31676										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9424869	9424869	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	cagcagaaggagctaaattcTttaaagaagaaacatgcaaa	8	6	1	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr20:9424869T>A	ENST00000378493.1	+	28	2838	c.2823T>A	c.(2821-2823)tcT>tcA	p.S941S	PLCB4_ENST00000278655.4_Silent_p.S941S|PLCB4_ENST00000414679.2_Silent_p.S953S|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378473.3_Silent_p.S953S|PLCB4_ENST00000334005.3_Silent_p.S941S|PLCB4_ENST00000378501.2_Silent_p.S941S			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	941					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						AGCTAAATTCTTTAAAGAAGA	0.313																																					p.S953S		Atlas-SNP	.											.	PLCB4	204	.	0			c.T2859A						.						72	73	72					20																	9424869		2203	4299	6502	SO:0001819	synonymous_variant	5332	exon31			AAATTCTTTAAAG		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.2823T>A	chr20.hg19:g.9424869T>A		101.0	0.0		120.0	48.0	NM_001172646	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Silent	SNP	ENST00000378493.1	hg19	CCDS13105.1																																																																																			.	.		0.313	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			A	9424869	T	A	9424869	2	1	221	1	0	0	0	0	0	0	0	1	12039	1596	56	4		4	PLCB4	20	9424869	Silent	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10		9424869	53600651	102	31677										
SEC23B	10483	hgsc.bcm.edu	37	chr20	18506573	18506573	+	Frame_Shift_Del	DEL	G	G	-													0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tccattgctgttggcttgctGgaggtaatttaaaatttacc							TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr20:18506573delG	ENST00000336714.3	+	7	1263	c.831delG	c.(829-831)ctgfs	p.L277fs	SEC23B_ENST00000377465.1_Frame_Shift_Del_p.L277fs|SEC23B_ENST00000262544.2_Frame_Shift_Del_p.L277fs|SEC23B_ENST00000377475.3_Frame_Shift_Del_p.L277fs	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	277					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						TTGGCTTGCTGGAGGTAATTT	0.433																																					p.L277fs		Atlas-INDEL	.											.	SEC23B	70	.	0			c.830delT						.						101	100	100					20																	18506573		2203	4300	6503	SO:0001589	frameshift_variant	10483	exon7			.	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"Sec23 (S. cerevisiae) homolog B", "congenital dyserythropoietic anemia, type II"	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.831delG	chr20.hg19:g.18506573delG	ENSP00000338844:p.Leu277fs	124.0	0.0		120.0	38.0	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Frame_Shift_Del	DEL	ENST00000336714.3	hg19	CCDS13137.1																																																																																			.	.		0.433	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			-	18506573	G	-	18506573	7	5	221	1	0	1	0	1	0	0	0	0	14007	1335	47	0	853	0	SEC23B	20	18506573	Frame_Shift_Del	DEL	G	TCGA-DD-AAEI-01A-11D-A40R-10	9081704	18506573	44518947	103	31678										
MORC3	23515	hgsc.bcm.edu	37	chr21	37742093	37742093	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	aatgagagtaaaagtgaaatGgatgagatggctgtgcagct	14	3	0	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chr21:37742093G>A	ENST00000400485.1	+	15	2503	c.2427G>A	c.(2425-2427)atG>atA	p.M809I	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	809					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						AAAGTGAAATGGATGAGATGG	0.398																																					p.M809I		Atlas-SNP	.											.	MORC3	78	.	0			c.G2427A						.						134	126	129					21																	37742093		2012	4187	6199	SO:0001583	missense	23515	exon15			TGAAATGGATGAG	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"zinc finger, CW-type with coiled-coil domain 3", "zinc finger, CW type with coiled-coil domain 3"	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.2427G>A	chr21.hg19:g.37742093G>A	ENSP00000383333:p.Met809Ile	103.0	0.0		115.0	40.0	NM_015358	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	hg19	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	G	11.31	1.600701	0.28534	.	.	ENSG00000159256	ENST00000400485	T	0.13089	2.62	5.56	5.56	0.83823	.	0.498441	0.23565	N	0.046805	T	0.10852	0.0265	L	0.38175	1.15	0.25884	N	0.983555	B	0.11235	0.004	B	0.13407	0.009	T	0.26430	-1.0103	10	0.13470	T	0.59	-7.7086	11.0861	0.48089	0.0716:0.1302:0.7983:0.0	.	809	Q14149	MORC3_HUMAN	I	809	ENSP00000383333:M809I	ENSP00000383333:M809I	M	+	3	0	MORC3	36663963	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.789000	0.26886	2.600000	0.87896	0.655000	0.94253	ATG	.	.		0.398	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		A	37742093	G	A	37742093	3	1	221	1	0	0	0	0	1	0	0	0	9712	1348	47	3	2485	3	MORC3	21	37742093	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10		37742093	10387802	104	31679										
TCEANC	170082	hgsc.bcm.edu	37	chrX	13681525	13681525	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	ataaaataaaatgcagacgcTgtgagaaatacaattgcaaa	7	5	0	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chrX:13681525T>C	ENST00000380600.1	+	2	985	c.898T>C	c.(898-900)Tgt>Cgt	p.C300R	TCEANC_ENST00000544987.1_Missense_Mutation_p.C300R|TCEANC_ENST00000314720.4_Missense_Mutation_p.C330R|TCEANC_ENST00000545566.1_Missense_Mutation_p.C300R|TCEANC_ENST00000490617.1_3'UTR			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	300					regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						ATGCAGACGCTGTGAGAAATA	0.418																																					p.C330R		Atlas-SNP	.											.	TCEANC	29	.	0			c.T988C						.						32	27	28					X																	13681525		1887	4078	5965	SO:0001583	missense	170082	exon4			AGACGCTGTGAGA		CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.898T>C	chrX.hg19:g.13681525T>C	ENSP00000369974:p.Cys300Arg	147.0	1.0		143.0	101.0	NM_152634	A6NI06|B2RDM3	Missense_Mutation	SNP	ENST00000380600.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.41	3.822509	0.71028	.	.	ENSG00000176896	ENST00000545566;ENST00000544987;ENST00000314720;ENST00000380600	T;T;T;T	0.74526	-0.85;-0.85;-0.72;-0.85	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.88032	0.6328	M	0.89478	3.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.90326	0.4348	10	0.87932	D	0	.	14.5594	0.68126	0.0:0.0:0.0:1.0	.	330;300	Q8N8B7-2;Q8N8B7	.;TEANC_HUMAN	R	300;300;330;300	ENSP00000438952:C300R;ENSP00000440038:C300R;ENSP00000313886:C330R;ENSP00000369974:C300R	ENSP00000313886:C330R	C	+	1	0	TCEANC	13591446	1.000000	0.71417	0.994000	0.49952	0.940000	0.58332	7.601000	0.82783	1.819000	0.53055	0.486000	0.48141	TGT	.	.		0.418	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055796.1	NM_152634		C	13681525	T	C	13681525	3	2	221	1	0	0	0	0	1	0	0	0	15693	1580	55	2	994	2	TCEANC	23	13681525	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10		13681525	141589035	105	31680										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20185787	20185787	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	tcgttcagagaaaaatttttGtctaagaattttatccagca	6	6	2	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chrX:20185787G>C	ENST00000379565.3	-	17	1729	c.1522C>G	c.(1522-1524)Caa>Gaa	p.Q508E	RPS6KA3_ENST00000379548.4_Missense_Mutation_p.Q478E|RPS6KA3_ENST00000540702.1_Missense_Mutation_p.Q479E|RPS6KA3_ENST00000479809.1_5'UTR|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.Q480E	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	508	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.Q508K(1)		breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	AAAAATTTTTGTCTAAGAATT	0.348																																					p.Q508E		Atlas-SNP	.											.	RPS6KA3	110	.	1	Substitution - Missense(1)	kidney(1)	c.C1522G						.						164	172	169					X																	20185787		2203	4300	6503	SO:0001583	missense	6197	exon17			ATTTTTGTCTAAG	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1522C>G	chrX.hg19:g.20185787G>C	ENSP00000368884:p.Gln508Glu	195.0	0.0		202.0	135.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.916446	0.52546	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.8	4.94	0.65067	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.43211	0.1237	N	0.05330	-0.07	0.58432	D	0.999998	B;B;B;B	0.17465	0.022;0.018;0.005;0.022	B;B;B;B	0.22152	0.026;0.015;0.011;0.038	T	0.22977	-1.0201	10	0.29301	T	0.29	.	14.1151	0.65149	0.074:0.0:0.926:0.0	.	479;478;480;508	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	E	508;480;478;479	ENSP00000368884:Q508E;ENSP00000440220:Q480E;ENSP00000368865:Q478E;ENSP00000444837:Q479E	ENSP00000368865:Q478E	Q	-	1	0	RPS6KA3	20095708	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	9.869000	0.99810	1.198000	0.43158	0.513000	0.50165	CAA	.	.		0.348	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		C	20185787	G	C	20185787	3	2	221	1	0	0	0	0	1	0	0	0	13667	1386	48	4	724	4	RPS6KA3	23	20185787	Missense_Mutation	SNP	G	TCGA-DD-AAEI-01A-11D-A40R-10	6504262	20185787	135084773	106	31681										
AR	367	hgsc.bcm.edu	37	chrX	66765176	66765176	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gctgcagcagcagcagcagcAgcagcagcagcagcagcagc	14	14	0	0	rs62636527		TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chrX:66765176A>T	ENST00000374690.3	+	1	712	c.188A>T	c.(187-189)cAg>cTg	p.Q63L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q63L|AR_ENST00000504326.1_Missense_Mutation_p.Q63L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	63	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.672									Androgen Insensitivity Syndrome																												p.Q63L		Atlas-SNP	.											.	AR	249	.	0			c.A188T						.						5	8	7					X																	66765176		1640	3236	4876	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.188A>T	chrX.hg19:g.66765176A>T	ENSP00000363822:p.Gln63Leu	76.0	0.0		96.0	22.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.08	1.532203	0.27387	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.78246	-1.16;-1.16;-1.16	.	.	.	.	0.479323	0.15343	U	0.267412	T	0.62624	0.2443	N	0.19112	0.55	0.09310	N	0.999992	P;D;.	0.58268	0.755;0.982;.	B;P;.	0.48627	0.089;0.584;.	T	0.56408	-0.7984	8	0.17832	T	0.49	.	.	.	.	rs62636527	63;63;61	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	63	ENSP00000363822:Q63L;ENSP00000421155:Q63L;ENSP00000379359:Q63L	ENSP00000363822:Q63L	Q	+	2	0	AR	66681901	0.810000	0.29049	0.871000	0.34182	0.555000	0.35460	1.078000	0.30754	0.000000	0.14550	0.000000	0.15137	CAG	.	A|0.982;T|0.018		0.672	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765176	A	T	66765176	3	4	221	1	0	0	0	0	1	0	0	0	836	188	7	4	190	4	AR	23	66765176	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	46579389	66765176	88505384	107	31682										
PCDH19	57526	hgsc.bcm.edu	37	chrX	99596912	99596912	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	agtccttaccatgatcaggcAtctgagatcccatggaggtc	10	11	2	2			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chrX:99596912A>C	ENST00000373034.4	-	5	4512	c.2837T>G	c.(2836-2838)aTg>aGg	p.M946R	PCDH19_ENST00000420881.2_Missense_Mutation_p.M898R|PCDH19_ENST00000255531.7_Missense_Mutation_p.M899R	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	946					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						ATGATCAGGCATCTGAGATCC	0.463																																					p.M946R		Atlas-SNP	.											.	PCDH19	269	.	0			c.T2837G						.						137	121	126					X																	99596912		2084	4199	6283	SO:0001583	missense	57526	exon5			TCAGGCATCTGAG	AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.2837T>G	chrX.hg19:g.99596912A>C	ENSP00000362125:p.Met946Arg	54.0	0.0		66.0	11.0	NM_001184880	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	hg19	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	A	9.856	1.195046	0.22037	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.52295	0.67;0.78;0.72	5.99	5.99	0.97316	.	0.251960	0.45606	D	0.000351	T	0.26085	0.0636	N	0.08118	0	0.35538	D	0.802837	B;B;B	0.27498	0.18;0.004;0.002	B;B;B	0.23018	0.043;0.004;0.002	T	0.36768	-0.9734	10	0.16896	T	0.51	.	12.0859	0.53698	0.8489:0.1511:0.0:0.0	.	946;899;898	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	R	898;946;899	ENSP00000400327:M898R;ENSP00000362125:M946R;ENSP00000255531:M899R	ENSP00000255531:M899R	M	-	2	0	PCDH19	99483568	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.745000	0.68672	2.025000	0.59659	0.486000	0.48141	ATG	.	.		0.463	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		C	99596912	A	C	99596912	3	2	221	1	0	0	0	0	1	0	0	0	11523	217	8	5	617	5	PCDH19	23	99596912	Missense_Mutation	SNP	A	TCGA-DD-AAEI-01A-11D-A40R-10	32831736	99596912	55673648	108	31683										
ARMCX3	51566	hgsc.bcm.edu	37	chrX	100880947	100880947	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0458715596330275	5	1	0.909939544807966	1.15259009009009	0.864442567567568	0.265734265734266	0.917767417767419	0	gaaaatgaacctactcagaaTcaattcggtgaaggttcact	8	8	3	3			TCGA-DD-AAEI-01A-11D-A40R-10	TCGA-DD-AAEI-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	076dd458-720e-4989-8ec2-6d49897b1479	233f19ee-f0d2-4fa9-ae52-fa3da11b3489	g.chrX:100880947T>G	ENST00000341189.4	+	5	1844	c.978T>G	c.(976-978)aaT>aaG	p.N326K	ARMCX3_ENST00000537169.1_Missense_Mutation_p.N326K|ARMCX3-AS1_ENST00000454228.1_RNA|ARMCX3_ENST00000471229.2_Missense_Mutation_p.N326K|RP4-545K15.5_ENST00000564612.1_RNA	NM_016607.3	NP_057691.1	Q9UH62	ARMX3_HUMAN	armadillo repeat containing, X-linked 3	326					cellular protein localization (GO:0034613)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of mitochondrial outer membrane (GO:0031307)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11						CTACTCAGAATCAATTCGGTG	0.308																																					p.N326K		Atlas-SNP	.											.	ARMCX3	33	.	0			c.T978G						.						49	54	52					X																	100880947		2190	4289	6479	SO:0001583	missense	51566	exon5			TCAGAATCAATTC	AY359079	CCDS14489.1	Xq22.1	2014-03-21			ENSG00000102401	ENSG00000102401		"Armadillo repeat containing"	24065	protein-coding gene	gene with protein product		300364				11162520, 11042152, 19304657, 16221301, 22569362	Standard	NM_016607		Approved	ALEX3, GASP6	uc004eia.1	Q9UH62	OTTHUMG00000022035	ENST00000341189.4:c.978T>G	chrX.hg19:g.100880947T>G	ENSP00000340672:p.Asn326Lys	186.0	0.0		195.0	138.0	NM_016607	Q53HC6|Q7LCF5|Q9NPE4	Missense_Mutation	SNP	ENST00000341189.4	hg19	CCDS14489.1	.	.	.	.	.	.	.	.	.	.	T	0.048	-1.260541	0.01445	.	.	ENSG00000102401	ENST00000341189;ENST00000537169	T;T	0.27890	1.64;1.64	4.44	0.168	0.15012	Armadillo-type fold (1);	0.477766	0.25711	N	0.028803	T	0.08935	0.0221	N	0.02011	-0.69	0.28502	N	0.913949	B	0.17852	0.024	B	0.24701	0.055	T	0.26155	-1.0111	9	.	.	.	-7.3172	3.5266	0.07761	0.0:0.2416:0.1961:0.5624	.	326	Q9UH62	ARMX3_HUMAN	K	326	ENSP00000340672:N326K;ENSP00000439032:N326K	.	N	+	3	2	ARMCX3	100767603	1.000000	0.71417	0.965000	0.40720	0.972000	0.66771	1.606000	0.36826	-0.066000	0.12998	0.486000	0.48141	AAT	.	.		0.308	ARMCX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057568.2	NM_016607		G	100880947	T	G	100880947	3	3	221	1	0	0	0	0	1	0	0	0	961	1432	50	5	980	5	ARMCX3	23	100880947	Missense_Mutation	SNP	T	TCGA-DD-AAEI-01A-11D-A40R-10	1284035	100880947	54389613	109	31684										
CCNL2	81669	hgsc.bcm.edu	37	chr1	1326223	1326223	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ccgcacgaagacgtcggtgcGaaggctgtcgttcatgtaat	13	10	1	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr1:1326223G>A	ENST00000400809.3	-	6	687	c.682C>T	c.(682-684)Cgc>Tgc	p.R228C	CCNL2_ENST00000408952.5_Missense_Mutation_p.R6C|CCNL2_ENST00000505849.1_5'UTR	NM_030937.4	NP_112199.2	Q96S94	CCNL2_HUMAN	cyclin L2	228	Cyclin-like 2.				regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		ACGTCGGTGCGAAGGCTGTCG	0.547																																					p.R228C		Atlas-SNP	.											.	CCNL2	54	.	0			c.C682T						.						79	79	79					1																	1326223		2203	4296	6499	SO:0001583	missense	81669	exon6			CGGTGCGAAGGCT	AF251294	CCDS30557.1, CCDS30558.1	1p36.33	2014-07-03			ENSG00000221978	ENSG00000221978			20570	protein-coding gene	gene with protein product	"cyclin S"	613482	"cyclin M"	CCNM		14725631	Standard	NM_030937		Approved	ania-6b, PCEE, SB138, HLA-ISO, CCNS	uc001afi.2	Q96S94	OTTHUMG00000002917	ENST00000400809.3:c.682C>T	chr1.hg19:g.1326223G>A	ENSP00000383611:p.Arg228Cys	408.0	0.0		302.0	30.0	NM_030937	A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00	Missense_Mutation	SNP	ENST00000400809.3	hg19	CCDS30557.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.542993	0.65198	.	.	ENSG00000221978	ENST00000400809;ENST00000408952	T;T	0.21734	1.99;1.99	5.84	5.84	0.93424	Cyclin, C-terminal (1);Cyclin-like (3);	0.000000	0.64402	D	0.000001	T	0.48333	0.1494	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.41052	-0.9530	10	0.45353	T	0.12	.	14.5921	0.68373	0.0:0.0:0.8451:0.1549	.	228	Q96S94	CCNL2_HUMAN	C	228;6	ENSP00000383611:R228C;ENSP00000386132:R6C	ENSP00000383611:R228C	R	-	1	0	CCNL2	1316086	1.000000	0.71417	0.995000	0.50966	0.502000	0.33828	4.806000	0.62569	2.779000	0.95612	0.655000	0.94253	CGC	.	.		0.547	CCNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008146.2	NM_030937		A	1326223	G	A	1326223	3	1	222	1	0	0	0	0	1	0	0	0	2934	1058	37	1	904	1	CCNL2	1	1326223	Missense_Mutation	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10		1326223	247924398	1	31685										
AADACL3	126767	hgsc.bcm.edu	37	chr1	12785194	12785194	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ttgattcctttttagttaccGcaagttacctaagcataagt	6	8	0	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr1:12785194G>T	ENST00000359318.5	+	4	489	c.284G>T	c.(283-285)cGc>cTc	p.R95L	AADACL3_ENST00000332530.3_Missense_Mutation_p.R25L	NM_001103170.1	NP_001096640.1	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3	95							hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	15	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TTTAGTTACCGCAAGTTACCT	0.463																																					p.R95L		Atlas-SNP	.											AADACL3_ENST00000359318,colon,carcinoma,0,2	AADACL3	84	.	0			c.G284T						.						109	113	112					1																	12785194		1966	4154	6120	SO:0001583	missense	126767	exon4			GTTACCGCAAGTT		CCDS41253.1	1p36.21	2014-07-17			ENSG00000188984	ENSG00000188984			32037	protein-coding gene	gene with protein product							Standard	XM_006710337		Approved	OTTHUMG00000001887	uc009vnn.1	Q5VUY0	OTTHUMG00000001887	ENST00000359318.5:c.284G>T	chr1.hg19:g.12785194G>T	ENSP00000352268:p.Arg95Leu	90.0	0.0		68.0	31.0	NM_001103170	B3KXR9|Q5VUY1	Missense_Mutation	SNP	ENST00000359318.5	hg19	CCDS41253.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.585885	0.66105	.	.	ENSG00000188984	ENST00000332530;ENST00000359318	T;T	0.21191	2.02;2.02	5.31	2.36	0.29203	Alpha/beta hydrolase fold-3 (1);	0.053408	0.64402	D	0.000001	T	0.60715	0.2290	H	0.99130	4.44	0.50467	D	0.999873	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.66019	-0.6027	10	0.87932	D	0	-15.1905	8.3834	0.32486	0.1432:0.1274:0.7294:0.0	.	95;25	Q5VUY0;Q5VUY0-2	ADCL3_HUMAN;.	L	25;95	ENSP00000333352:R25L;ENSP00000352268:R95L	ENSP00000333352:R25L	R	+	2	0	AADACL3	12707781	0.999000	0.42202	0.003000	0.11579	0.021000	0.10359	3.128000	0.50492	0.225000	0.20959	0.484000	0.47621	CGC	.	.		0.463	AADACL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005324.2	NM_001103170		T	12785194	G	T	12785194	3	4	222	1	0	0	0	0	1	0	0	0	12	1087	38	1	302	1	AADACL3	1	12785194	Missense_Mutation	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10	11458971	12785194	236465427	2	31686										
CCDC17	149483	hgsc.bcm.edu	37	chr1	46088424	46088429	+	Splice_Site	DEL	GGATTT	GGATTT	-													0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ctccggccccggctctcaccGgatttcggcagccagagttc					rs143656439		TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	GGATTT	GGATTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr1:46088424_46088429delGGATTT	ENST00000528266.1	-	5	881_886	c.734_739delAAATCC	c.(733-741)gaaatccgg>ggg	p.245_247EIR>G	CCDC17_ENST00000343901.2_Splice_Site_p.213_215EIR>G|CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000464739.1_5'UTR|CCDC17_ENST00000421127.2_Splice_Site_p.236_238EIR>G			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	245										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					GGCTCTCACCGGATTTCGGCAGCCAG	0.655																																					p.245_247del		Atlas-INDEL	.											.	CCDC17	54	.	0			c.735_740del						.																																			SO:0001630	splice_region_variant	149483	exon5			.		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.740+1AAATCC>-	chr1.hg19:g.46088424_46088429delGGATTT		187.0	0.0		127.0	14.0	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	In_Frame_Del	DEL	ENST00000528266.1	hg19	CCDS44131.2																																																																																			.	.		0.655	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	In_Frame_Del	-	46088429	GGATTT	-	46088424	8	5	222	1	0	1	0	1	0	0	1	0	2795	1130	39	0	1165	0	CCDC17	1	46088424	Splice_Site	DEL	GGATTT	TCGA-DD-AAEK-01A-11D-A40R-10	33303230	46088424	203162197	3	31687										
OVGP1	5016	hgsc.bcm.edu	37	chr1	111957295	111957295	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	agcttccatctgaagacccaAgttacccatcctggggtgag	10	12	1	3			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr1:111957295A>C	ENST00000369732.3	-	11	1883	c.1828T>G	c.(1828-1830)Ttg>Gtg	p.L610V		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	610					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		TGAAGACCCAAGTTACCCATC	0.522																																					p.L610V		Atlas-SNP	.											.	OVGP1	177	.	0			c.T1828G						.						84	82	83					1																	111957295		2203	4300	6503	SO:0001583	missense	5016	exon11			GACCCAAGTTACC	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"Mucins"	8524	protein-coding gene	gene with protein product	"oviductin"	603578	"mucin 9"	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1828T>G	chr1.hg19:g.111957295A>C	ENSP00000358747:p.Leu610Val	139.0	0.0		105.0	21.0	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	hg19	CCDS834.1	.	.	.	.	.	.	.	.	.	.	A	10.91	1.483418	0.26598	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.05447	3.44	4.16	1.76	0.24704	.	47.035900	0.00166	N	0.000000	T	0.01489	0.0048	N	0.22421	0.69	0.09310	N	0.999999	B;B	0.15930	0.005;0.015	B;B	0.09377	0.003;0.004	T	0.42481	-0.9449	10	0.46703	T	0.11	3.0E-4	3.4746	0.07579	0.4949:0.1683:0.0:0.3368	.	610;674	Q12889;Q59HH5	OVGP1_HUMAN;.	V	610;674;418	ENSP00000358747:L610V	ENSP00000358743:L674V	L	-	1	2	OVGP1	111758818	0.000000	0.05858	0.054000	0.19295	0.129000	0.20672	0.733000	0.26087	0.365000	0.24400	0.477000	0.44152	TTG	.	.		0.522	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		C	111957295	A	C	111957295	3	2	222	1	0	0	0	0	1	0	0	0	11334	69	3	5	212	5	OVGP1	1	111957295	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	65868871	111957295	137293326	4	31688										
PLEKHO1	51177	hgsc.bcm.edu	37	chr1	150129195	150129195	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ccatcacccgagccaagaacCgtatcttggatgaggtcagg	11	12	3	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr1:150129195C>A	ENST00000369124.4	+	4	687	c.409C>A	c.(409-411)Cgt>Agt	p.R137S	PLEKHO1_ENST00000025469.6_Missense_Mutation_p.R137S|PLEKHO1_ENST00000479194.1_3'UTR|PLEKHO1_ENST00000369126.1_5'UTR	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	137	Interaction with ATM, CKIP, IFP35 and NMI.|Interaction with capping proteins (CPs).					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCCAAGAACCGTATCTTGGA	0.597																																					p.R137S		Atlas-SNP	.											.	PLEKHO1	37	.	0			c.C409A						.						83	80	81					1																	150129195		2203	4300	6503	SO:0001583	missense	51177	exon4			AAGAACCGTATCT	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.409C>A	chr1.hg19:g.150129195C>A	ENSP00000358120:p.Arg137Ser	94.0	0.0		123.0	43.0	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Missense_Mutation	SNP	ENST00000369124.4	hg19	CCDS945.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.839396	0.91117	.	.	ENSG00000023902	ENST00000025469;ENST00000369124	T;T	0.16897	2.31;2.31	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.32645	0.0836	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.02437	-1.1159	10	0.49607	T	0.09	-15.5364	17.1577	0.86795	0.0:1.0:0.0:0.0	.	137	Q53GL0	PKHO1_HUMAN	S	137	ENSP00000025469:R137S;ENSP00000358120:R137S	ENSP00000025469:R137S	R	+	1	0	PLEKHO1	148395819	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.363000	0.52321	2.599000	0.87857	0.561000	0.74099	CGT	.	.		0.597	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		A	150129195	C	A	150129195	3	1	222	1	0	0	0	0	1	0	0	0	12093	652	23	1	423	1	PLEKHO1	1	150129195	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	38171900	150129195	99121426	5	31689										
PSMD4	5710	hgsc.bcm.edu	37	chr1	151239737	151239737	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tgtggatcccaacaatgaagCcattcgaaatgctatgggct	10	9	0	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr1:151239737C>G	ENST00000368884.3	+	10	1132	c.1052C>G	c.(1051-1053)gCc>gGc	p.A351G	PSMD4_ENST00000368881.4_Missense_Mutation_p.A354G	NM_002810.2	NP_002801.1	P55036	PSMD4_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	351					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle, base subcomplex (GO:0008540)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(7)	11	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			AACAATGAAGCCATTCGAAAT	0.547																																					p.A351G		Atlas-SNP	.											.	PSMD4	27	.	0			c.C1052G						.						113	104	107					1																	151239737		2203	4300	6503	SO:0001583	missense	5710	exon10			ATGAAGCCATTCG	U51007	CCDS991.1	1q21.2	2008-05-22			ENSG00000159352	ENSG00000159352		"Proteasome (prosome, macropain) subunits"	9561	protein-coding gene	gene with protein product		601648				8641424	Standard	XM_005245354		Approved	S5A, AF-1, AF, Rpn10	uc001exl.3	P55036	OTTHUMG00000012349	ENST00000368884.3:c.1052C>G	chr1.hg19:g.151239737C>G	ENSP00000357879:p.Ala351Gly	136.0	0.0		153.0	13.0	NM_002810	D3DV16|Q5VWC5|Q9NS92	Missense_Mutation	SNP	ENST00000368884.3	hg19	CCDS991.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	30|30|30	5.054734|5.054734|5.054734	0.93793|0.93793|0.93793	.|.|.	.|.|.	ENSG00000159352|ENSG00000159352|ENSG00000159352	ENST00000368884;ENST00000368881|ENST00000453615|ENST00000445776	.|.|.	.|.|.	.|.|.	5.64|5.64|5.64	4.72|4.72|4.72	0.59763|0.59763|0.59763	.|.|.	0.059639|.|.	0.64402|.|.	D|.|.	0.000004|.|.	T|T|T	0.69851|0.69851|0.69851	0.3157|0.3157|0.3157	M|M|M	0.80616|0.80616|0.80616	2.505|2.505|2.505	0.58432|0.58432|0.58432	D|D|D	0.999998|0.999998|0.999998	D;P|.|.	0.54964|.|.	0.969;0.945|.|.	P;P|.|.	0.48425|.|.	0.577;0.577|.|.	T|T|T	0.73509|0.73509|0.73509	-0.3960|-0.3960|-0.3960	9|5|5	0.35671|.|.	T|.|.	0.21|.|.	-19.4623|-19.4623|-19.4623	15.4089|15.4089|15.4089	0.74902|0.74902|0.74902	0.0:0.8603:0.1397:0.0|0.0:0.8603:0.1397:0.0|0.0:0.8603:0.1397:0.0	.|.|.	354;351|.|.	Q5VWC4;P55036|.|.	.;PSMD4_HUMAN|.|.	G|A|R	351;354|58|166	.|.|.	ENSP00000357876:A354G|.|.	A|P|S	+|+|+	2|1|3	0|0|2	PSMD4|PSMD4|PSMD4	149506361|149506361|149506361	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	7.061000|7.061000|7.061000	0.76699|0.76699|0.76699	1.600000|1.600000|1.600000	0.50102|0.50102|0.50102	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	GCC|CCA|AGC	.	.		0.547	PSMD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034409.3	NM_002810		G	151239737	C	G	151239737	3	3	222	1	0	0	0	0	1	0	0	0	12712	739	26	4	1090	4	PSMD4	1	151239737	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	1110542	151239737	98010884	6	31690										
THBS3	7059	hgsc.bcm.edu	37	chr1	155171290	155171290	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gggctgggctgtggcaggtcCgggctgggaggcagccctgg	22	10	0	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr1:155171290C>T	ENST00000368378.3	-	11	1267	c.1247G>A	c.(1246-1248)cGg>cAg	p.R416Q	RP11-263K19.4_ENST00000454348.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|THBS3_ENST00000541990.1_5'UTR|THBS3_ENST00000541576.1_5'UTR|RP11-263K19.4_ENST00000422665.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000430312.1_RNA|THBS3_ENST00000457183.2_Missense_Mutation_p.R296Q	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	416	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GTGGCAGGTCCGGGCTGGGAG	0.617																																					p.R416Q		Atlas-SNP	.											THBS3,NS,carcinoma,0,1	THBS3	70	.	0			c.G1247A						.						49	55	53					1																	155171290		2203	4300	6503	SO:0001583	missense	7059	exon11			CAGGTCCGGGCTG	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.1247G>A	chr1.hg19:g.155171290C>T	ENSP00000357362:p.Arg416Gln	295.0	0.0		361.0	116.0	NM_007112	B1AVR8|B4DQ20|Q8WV34	Missense_Mutation	SNP	ENST00000368378.3	hg19	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	C	15.96	2.987796	0.53934	.	.	ENSG00000169231	ENST00000368378;ENST00000457183;ENST00000428962	T;T;T	0.81415	-1.43;-1.49;-1.03	4.71	4.71	0.59529	Epidermal growth factor-like, type 3 (1);	0.207707	0.42294	D	0.000737	T	0.66723	0.2818	L	0.54908	1.71	0.36440	D	0.865448	B;B;B;B	0.31859	0.343;0.184;0.184;0.343	B;B;B;B	0.30943	0.122;0.026;0.043;0.043	T	0.69939	-0.5009	10	0.40728	T	0.16	-22.7002	13.3465	0.60575	0.0:1.0:0.0:0.0	.	296;416;416;416	B4DQ20;Q53FK6;Q2HIZ0;P49746	.;.;.;TSP3_HUMAN	Q	416;296;266	ENSP00000357362:R416Q;ENSP00000392207:R296Q;ENSP00000404040:R266Q	ENSP00000357362:R416Q	R	-	2	0	THBS3	153437914	0.001000	0.12720	0.968000	0.41197	0.995000	0.86356	-0.094000	0.11094	2.618000	0.88619	0.591000	0.81541	CGG	.	.		0.617	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		T	155171290	C	T	155171290	3	4	222	1	0	0	0	0	1	0	0	0	15870	652	23	1	1675	1	THBS3	1	155171290	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	3931553	155171290	94079331	7	31691										
PPOX	5498	hgsc.bcm.edu	37	chr1	161140408	161140408	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cagtgctatattccctccttAggtgatgctgggaggttcct	11	10	0	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr1:161140408A>C	ENST00000367999.4	+	11	1364		c.e11-1		PPOX_ENST00000535223.1_Splice_Site|PPOX_ENST00000352210.5_Splice_Site|PPOX_ENST00000495483.1_Splice_Site|B4GALT3_ENST00000470882.1_5'Flank|PPOX_ENST00000432542.2_Splice_Site|PPOX_ENST00000544598.1_Splice_Site	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase						heme biosynthetic process (GO:0006783)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound biosynthetic process (GO:0006779)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of mitochondrial inner membrane (GO:0031304)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)	flavin adenine dinucleotide binding (GO:0050660)|oxygen-dependent protoporphyrinogen oxidase activity (GO:0004729)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			TTCCCTCCTTAGGTGATGCTG	0.537																																					.		Atlas-SNP	.											.	PPOX	34	.	0			c.1099-2A>C						.						118	121	120					1																	161140408		2203	4300	6503	SO:0001630	splice_region_variant	5498	exon11			CTCCTTAGGTGAT	BC002357	CCDS1221.1	1q22	2008-02-05			ENSG00000143224	ENSG00000143224	1.3.3.4		9280	protein-coding gene	gene with protein product		600923	"variegate porphyria"	VP		8575762, 10457135	Standard	NM_000309		Approved	PPO	uc001fyg.2	P50336	OTTHUMG00000034342	ENST00000367999.4:c.1099-1A>C	chr1.hg19:g.161140408A>C		69.0	0.0		110.0	13.0	NM_000309	D3DVG0|Q5VTW8	Splice_Site	SNP	ENST00000367999.4	hg19	CCDS1221.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.178404	0.57692	.	.	ENSG00000143224	ENST00000352210;ENST00000367999;ENST00000544598;ENST00000435935;ENST00000535223;ENST00000432542;ENST00000537523;ENST00000537829	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3518	0.66708	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PPOX	159407032	0.998000	0.40836	0.935000	0.37517	0.910000	0.53928	3.973000	0.56845	2.275000	0.75901	0.528000	0.53228	.	.	.		0.537	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309	Intron	C	161140408	A	C	161140408	5	2	222	1	0	0	0	0	0	0	1	0	12360	434	15	5	1135	5	PPOX	1	161140408	Splice_Site	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	5969118	161140408	88110213	8	31692										
LBR	3930	hgsc.bcm.edu	37	chr1	225600294	225600294	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cacgtaatgaaactctacgcCctggaagagagatgttccga	10	10	1	3			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr1:225600294C>A	ENST00000338179.2	-	8	1071	c.946G>T	c.(946-948)Ggc>Tgc	p.G316C	AC092811.1_ENST00000366845.2_5'Flank|LBR_ENST00000272163.4_Missense_Mutation_p.G316C	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	316					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		AACTCTACGCCCTGGAAGAGA	0.378																																					p.G316C		Atlas-SNP	.											.	LBR	54	.	0			c.G946T						.						73	73	73					1																	225600294		2203	4300	6503	SO:0001583	missense	3930	exon8			CTACGCCCTGGAA	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"Tudor domain containing"	6518	protein-coding gene	gene with protein product	"tudor domain containing 18"	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.946G>T	chr1.hg19:g.225600294C>A	ENSP00000339883:p.Gly316Cys	469.0	0.0		481.0	70.0	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	hg19	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.795265	0.50208	.	.	ENSG00000143815	ENST00000272163;ENST00000338179	D;D	0.97976	-4.64;-4.64	6.07	5.17	0.71159	.	0.435805	0.27323	N	0.019894	D	0.98566	0.9521	H	0.95574	3.69	0.38739	D	0.953832	D	0.59767	0.986	P	0.54856	0.762	D	0.99838	1.1059	10	0.45353	T	0.12	-7.9541	10.4419	0.44471	0.0:0.7844:0.1428:0.0727	.	316	Q14739	LBR_HUMAN	C	316	ENSP00000272163:G316C;ENSP00000339883:G316C	ENSP00000272163:G316C	G	-	1	0	LBR	223666917	0.995000	0.38212	0.921000	0.36526	0.021000	0.10359	2.124000	0.42006	1.586000	0.49944	0.655000	0.94253	GGC	.	.		0.378	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		A	225600294	C	A	225600294	3	1	222	1	0	0	0	0	1	0	0	0	8661	623	22	3	929	3	LBR	1	225600294	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	64459886	225600294	23650327	9	31693										
STRN	6801	hgsc.bcm.edu	37	chr2	37129895	37129895	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	aacccacctcctgtagatacCtgtgtgaagagaatccttag	8	11	0	3			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr2:37129895C>A	ENST00000263918.4	-	5	500		c.e5-1		STRN_ENST00000379213.2_Splice_Site	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein						dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				CTGTAGATACCTGTGTGAAGA	0.358																																					.		Atlas-SNP	.											.	STRN	71	.	0			c.492-1G>T						.						122	122	122					2																	37129895		2203	4300	6503	SO:0001630	splice_region_variant	6801	exon6			AGATACCTGTGTG	AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"WD repeat domain containing"	11424	protein-coding gene	gene with protein product		614765	"striatin, calmodulin-binding protein"			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.492-1G>T	chr2.hg19:g.37129895C>A		48.0	0.0		41.0	12.0	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Splice_Site	SNP	ENST00000263918.4	hg19	CCDS1784.1	.	.	.	.	.	.	.	.	.	.	C	17.87	3.496070	0.64186	.	.	ENSG00000115808	ENST00000263918;ENST00000538092;ENST00000379213	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5752	0.91153	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	STRN	36983399	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	6.870000	0.75526	2.446000	0.82766	0.655000	0.94253	.	.	.		0.358	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1		Intron	A	37129895	C	A	37129895	5	1	222	1	0	0	0	0	0	0	1	0	15344	695	24	3	1907	3	STRN	2	37129895	Splice_Site	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10		37129895	206069478	10	31694										
NRXN1	9378	hgsc.bcm.edu	37	chr2	51255005	51255005	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tggacttgacctccacccacTtggcctccacctggtcgatg	9	16	0	1	rs202118977		TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr2:51255005T>C	ENST00000406316.2	-	2	1883	c.407A>G	c.(406-408)aAg>aGg	p.K136R	NRXN1_ENST00000401669.2_Missense_Mutation_p.K136R|NRXN1_ENST00000402717.3_Missense_Mutation_p.K136R|NRXN1_ENST00000406859.3_Missense_Mutation_p.K136R|NRXN1_ENST00000405472.3_Missense_Mutation_p.K136R|NRXN1_ENST00000405581.1_Missense_Mutation_p.K136R|NRXN1_ENST00000404971.1_Missense_Mutation_p.K136R	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	136	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CTCCACCCACTTGGCCTCCAC	0.682																																					p.K136R		Atlas-SNP	.											.	NRXN1	1118	.	0			c.A407G						.						29	34	32					2																	51255005		2138	4244	6382	SO:0001583	missense	9378	exon2			ACCCACTTGGCCT	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.407A>G	chr2.hg19:g.51255005T>C	ENSP00000384311:p.Lys136Arg	101.0	0.0		83.0	27.0	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	T	8.865	0.947848	0.18356	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859;ENST00000405581	T;T;T;T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17	4.97	2.59	0.31030	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.942673	0.08464	U	0.941992	T	0.69513	0.3119	L	0.46614	1.455	0.23607	N	0.997301	B;B;B	0.26195	0.0;0.007;0.144	B;B;B	0.23716	0.001;0.008;0.048	T	0.51364	-0.8715	10	0.19590	T	0.45	.	8.9498	0.35781	0.0:0.1523:0.0:0.8477	.	136;136;136	Q9ULB1-3;F8WB18;Q9ULB1	.;.;NRX1A_HUMAN	R	136	ENSP00000385142:K136R;ENSP00000384311:K136R;ENSP00000434015:K136R;ENSP00000385017:K136R;ENSP00000385434:K136R;ENSP00000385681:K136R;ENSP00000385310:K136R	ENSP00000385017:K136R	K	-	2	0	NRXN1	51108509	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.278000	0.51662	0.257000	0.21650	-0.371000	0.07208	AAG	.	.		0.682	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			C	51255005	T	C	51255005	3	2	222	1	0	0	0	0	1	0	0	0	10674	1609	56	2	4591	2	NRXN1	2	51255005	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	14125110	51255005	191944368	11	31695										
CHST10	9486	hgsc.bcm.edu	37	chr2	101019079	101019080	+	Frame_Shift_Ins	INS	-	-	GG													0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	aacttcctcacttccggcatINSggttgtcaggaacagaaact							TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr2:101019079_101019080insGG	ENST00000264249.3	-	4	523_524	c.138_139insCC	c.(136-141)accatgfs	p.M47fs	CHST10_ENST00000409701.1_Frame_Shift_Ins_p.M47fs|CHST10_ENST00000542617.1_Frame_Shift_Ins_p.M95fs	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	47					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						ACTTCCGGCATGGTTGTCAGGA	0.525																																					p.M47fs		Atlas-INDEL	.											.	CHST10	42	.	0			c.139_140insCC						.																																			SO:0001589	frameshift_variant	9486	exon4			.	BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"Sulfotransferases, membrane-bound"	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.137_138dupCC	chr2.hg19:g.101019080_101019081dupGG	ENSP00000264249:p.Met47fs	50.0	0.0		52.0	12.0	NM_004854	Q53T18	Frame_Shift_Ins	INS	ENST00000264249.3	hg19	CCDS2047.1																																																																																			.	.		0.525	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854		GG	101019080	-	GG	101019079	7	5	222	1	0	1	1	0	0	0	0	0	3400	1464	51	0	947	0	CHST10	2	101019079	Frame_Shift_Ins	INS	-	TCGA-DD-AAEK-01A-11D-A40R-10	49764074	101019079	142180294	12	31696										
MAP3K2	10746	hgsc.bcm.edu	37	chr2	128065249	128065249	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gtttgaggaaatctcgagtaTagtctgagacatgaggtggc	14	5	2	3	rs370911611		TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr2:128065249T>C	ENST00000409947.1	-	17	2048	c.1766A>G	c.(1765-1767)tAt>tGt	p.Y589C	MAP3K2_ENST00000344908.5_Missense_Mutation_p.Y589C			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	589	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	ATCTCGAGTATAGTCTGAGAC	0.458																																					p.Y589C		Atlas-SNP	.											.	MAP3K2	78	.	0			c.A1766G						.	T	CYS/TYR	0,4140		0,0,2070	69	73	72		1766	5.7	1	2		72	1,8445		0,1,4222	no	missense	MAP3K2	NM_006609.4	194	0,1,6292	CC,CT,TT		0.0118,0.0,0.0079	benign	589/620	128065249	1,12585	2070	4223	6293	SO:0001583	missense	10746	exon16			CGAGTATAGTCTG	AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6854	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 2"	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.1766A>G	chr2.hg19:g.128065249T>C	ENSP00000387246:p.Tyr589Cys	139.0	0.0		99.0	32.0	NM_006609	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Missense_Mutation	SNP	ENST00000409947.1	hg19	CCDS46404.1	.	.	.	.	.	.	.	.	.	.	T	15.02	2.709679	0.48517	0.0	1.18E-4	ENSG00000169967	ENST00000409947;ENST00000344908	T;T	0.65364	-0.15;-0.15	5.7	5.7	0.88788	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.141127	0.64402	D	0.000005	T	0.55081	0.1898	L	0.38175	1.15	0.53688	D	0.99997	B	0.02656	0.0	B	0.01281	0.0	T	0.52132	-0.8616	10	0.59425	D	0.04	.	16.2585	0.82528	0.0:0.0:0.0:1.0	.	589	Q9Y2U5	M3K2_HUMAN	C	589	ENSP00000387246:Y589C;ENSP00000343463:Y589C	ENSP00000343463:Y589C	Y	-	2	0	MAP3K2	127781719	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.256000	0.72473	2.295000	0.77249	0.528000	0.53228	TAT	.	.		0.458	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609		C	128065249	T	C	128065249	3	2	222	1	0	0	0	0	1	0	0	0	9259	1406	49	2	97	2	MAP3K2	2	128065249	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	27046170	128065249	115134124	13	31697										
RAPGEF4	11069	hgsc.bcm.edu	37	chr2	173879264	173879264	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ctcaacaataagaggcgagtCatccgcctggttctacagtg	10	11	3	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr2:173879264C>T	ENST00000397081.3	+	18	1874	c.1731C>T	c.(1729-1731)gtC>gtT	p.V577V	RAPGEF4_ENST00000397087.3_Silent_p.V433V|RAPGEF4_ENST00000540783.1_Silent_p.V424V|RAPGEF4_ENST00000264111.6_Silent_p.V576V|RAPGEF4_ENST00000409036.1_Silent_p.V577V|RAPGEF4_ENST00000535187.1_Silent_p.V357V|RAPGEF4_ENST00000539331.1_Silent_p.V424V|RAPGEF4_ENST00000538974.1_Silent_p.V406V	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	577	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			AGAGGCGAGTCATCCGCCTGG	0.527																																					p.V577V		Atlas-SNP	.											.	RAPGEF4	103	.	0			c.C1731T						.						90	92	92					2																	173879264		2035	4191	6226	SO:0001819	synonymous_variant	11069	exon18			GCGAGTCATCCGC	U78516	CCDS42775.1, CCDS42776.1, CCDS63060.1, CCDS63061.1, CCDS74604.1	2q31-q32	2008-02-05	2004-03-26		ENSG00000091428	ENSG00000091428			16626	protein-coding gene	gene with protein product	"cAMP-regulated guanine nucleotide exchange factor II", " exchange protein directly activated by cAMP 2"	606058	"RAP guanine-nucleotide-exchange factor (GEF) 4"			10777494, 9856955	Standard	NM_007023		Approved	cAMP-GEFII, CGEF2	uc002uhv.4	Q8WZA2	OTTHUMG00000133677	ENST00000397081.3:c.1731C>T	chr2.hg19:g.173879264C>T		174.0	0.0		168.0	61.0	NM_007023	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Silent	SNP	ENST00000397081.3	hg19	CCDS42775.1																																																																																			.	.		0.527	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023		T	173879264	C	T	173879264	2	4	222	1	0	0	0	0	0	0	0	1	13061	813	29	3		3	RAPGEF4	2	173879264	Silent	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	45814015	173879264	69320109	14	31698										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234916713	234916713	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ttttcattaacttctttgcaGaatgaggcatcgatttagac	7	7	2	3			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr2:234916713G>T	ENST00000324695.4	+	24	3270		c.e24-1		TRPM8_ENST00000433712.2_Splice_Site	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8						calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	CTTCTTTGCAGAATGAGGCAT	0.323																																					.		Atlas-SNP	.											.	TRPM8	146	.	0			c.3231-1G>T						.						224	216	219					2																	234916713		2203	4300	6503	SO:0001630	splice_region_variant	79054	exon24			TTTGCAGAATGAG	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.3231-1G>T	chr2.hg19:g.234916713G>T		69.0	0.0		51.0	8.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Splice_Site	SNP	ENST00000324695.4	hg19	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.553955	0.65425	.	.	ENSG00000144481	ENST00000324695;ENST00000433712;ENST00000456930	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7965	0.69881	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TRPM8	234581452	1.000000	0.71417	0.990000	0.47175	0.900000	0.52787	5.546000	0.67243	2.580000	0.87095	0.655000	0.94253	.	.	.		0.323	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	Intron	T	234916713	G	T	234916713	5	4	222	1	0	0	0	0	0	0	1	0	16607	956	33	3	3320	3	TRPM8	2	234916713	Splice_Site	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10	61037449	234916713	8282660	15	31699										
GPR35	2859	hgsc.bcm.edu	37	chr2	241569491	241569491	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cctgctgctcaacagcctggCgctctgggtgttctgctgcc	12	15	3	0	rs148595408		TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr2:241569491C>A	ENST00000319838.5	+	6	1064	c.122C>A	c.(121-123)gCg>gAg	p.A41E	GPR35_ENST00000403859.1_Missense_Mutation_p.A41E|GPR35_ENST00000407714.1_Missense_Mutation_p.A41E|GPR35_ENST00000438013.2_Missense_Mutation_p.A72E|GPR35_ENST00000430267.1_Missense_Mutation_p.A41E	NM_001195381.1	NP_001182310.1	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35	41					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|cervix(1)|endometrium(1)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	17		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;5.29e-32)|all cancers(36;1.38e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.02e-06)|Lung(119;0.00163)|Colorectal(34;0.00463)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.031)		AACAGCCTGGCGCTCTGGGTG	0.652																																					p.A72E		Atlas-SNP	.											.	GPR35	43	.	0			c.C215A						.						75	69	71					2																	241569491		2203	4300	6503	SO:0001583	missense	2859	exon6			GCCTGGCGCTCTG		CCDS2541.1, CCDS56174.1	2q37.3	2012-08-21			ENSG00000178623	ENSG00000178623		"GPCR / Class A : Orphans"	4492	protein-coding gene	gene with protein product		602646				9479505	Standard	NM_005301		Approved		uc021vze.1	Q9HC97	OTTHUMG00000133356	ENST00000319838.5:c.122C>A	chr2.hg19:g.241569491C>A	ENSP00000322731:p.Ala41Glu	42.0	0.0		49.0	16.0	NM_001195382	J3KR30|O43495|Q17R58|Q4VBN5|Q4ZFV2|Q6FHI8|Q86UH4	Missense_Mutation	SNP	ENST00000319838.5	hg19	CCDS2541.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.612214	0.66672	.	.	ENSG00000178623	ENST00000319838;ENST00000403859;ENST00000438013;ENST00000407714;ENST00000430267	T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7	3.81	2.9	0.33743	GPCR, rhodopsin-like superfamily (1);	0.063722	0.64402	U	0.000009	D	0.85474	0.5705	M	0.92026	3.265	0.37917	D	0.931563	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.997;0.997	D	0.88585	0.3139	10	0.87932	D	0	-20.192	11.1666	0.48547	0.0:0.8108:0.1892:0.0	.	126;72;41	Q6ZMP9;A8K2J1;Q9HC97	.;.;GPR35_HUMAN	E	41;41;72;41;41	ENSP00000322731:A41E;ENSP00000385140:A41E;ENSP00000415890:A72E;ENSP00000384263:A41E;ENSP00000411788:A41E	ENSP00000322731:A41E	A	+	2	0	GPR35	241218164	0.003000	0.15002	0.995000	0.50966	0.863000	0.49368	0.026000	0.13599	0.908000	0.36671	0.462000	0.41574	GCG	.	C|1.000;T|0.000		0.652	GPR35-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325631.1	NM_001195382		A	241569491	C	A	241569491	3	1	222	1	0	0	0	0	1	0	0	0	6698	768	27	1	124	1	GPR35	2	241569491	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	6652778	241569491	1629882	16	31700										
ING5	84289	hgsc.bcm.edu	37	chr2	242662681	242662681	+	Frame_Shift_Del	DEL	A	A	-													0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cttaccacgaaacccaaaggAaaatggtgagtgtggggacg							TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr2:242662681delA	ENST00000313552.6	+	7	701	c.675delA	c.(673-675)ggafs	p.G225fs	AC114730.11_ENST00000435195.1_RNA|ING5_ENST00000406941.1_Frame_Shift_Del_p.G225fs	NM_032329.4	NP_115705.2	Q8WYH8	ING5_HUMAN	inhibitor of growth family, member 5	225					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|skin(1)	3		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.16e-33)|all cancers(36;4.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		AACCCAAAGGAAAATGGTGAG	0.542																																					p.G225fs		Atlas-INDEL	.											.	ING5	14	.	0			c.674delG						.						208	216	213					2																	242662681		2203	4300	6503	SO:0001589	frameshift_variant	84289	exon7			.	AF189286	CCDS33425.1	2q37.3	2013-01-28			ENSG00000168395	ENSG00000168395		"Zinc fingers, PHD-type"	19421	protein-coding gene	gene with protein product		608525				12750254	Standard	NM_032329		Approved	FLJ23842, p28ING5	uc002wcd.3	Q8WYH8	OTTHUMG00000151501	ENST00000313552.6:c.675delA	chr2.hg19:g.242662681delA	ENSP00000322142:p.Gly225fs	134.0	0.0		126.0	38.0	NM_032329	A8K1P3|Q53NU6|Q57Z54|Q9BS30	Frame_Shift_Del	DEL	ENST00000313552.6	hg19	CCDS33425.1																																																																																			.	.		0.542	ING5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322901.3	NM_032329		-	242662681	A	-	242662681	7	5	222	1	0	1	0	1	0	0	0	0	7748	233	9	0	701	0	ING5	2	242662681	Frame_Shift_Del	DEL	A	TCGA-DD-AAEK-01A-11D-A40R-10	1093190	242662681	536692	17	31701										
TRNT1	51095	hgsc.bcm.edu	37	chr3	3182289	3182289	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tttacaactgactggcagaaAgatgcggaacgcagagatct	11	8	1	4			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr3:3182289A>C	ENST00000251607.6	+	4	540	c.438A>C	c.(436-438)aaA>aaC	p.K146N	TRNT1_ENST00000280591.6_Missense_Mutation_p.K146N	NM_182916.2	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	146					protein targeting to mitochondrion (GO:0006626)|tRNA 3'-end processing (GO:0042780)|tRNA 3'-terminal CCA addition (GO:0001680)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity (GO:0052929)|CTP:3'-cytidine-tRNA cytidylyltransferase activity (GO:0052928)|CTP:tRNA cytidylyltransferase activity (GO:0052927)|tRNA adenylyltransferase activity (GO:0004810)|tRNA binding (GO:0000049)			breast(2)|endometrium(3)|large_intestine(4)|lung(2)|urinary_tract(1)	12				Epithelial(13;0.00226)|OV - Ovarian serous cystadenocarcinoma(96;0.00592)|all cancers(10;0.011)		ACTGGCAGAAAGATGCGGAAC	0.368																																					p.K146N		Atlas-SNP	.											.	TRNT1	34	.	0			c.A438C						.						96	97	96					3																	3182289		2203	4300	6503	SO:0001583	missense	51095	exon4			GCAGAAAGATGCG	AF151805	CCDS2561.2	3p25.1	2002-05-30			ENSG00000072756	ENSG00000072756	2.7.7.25		17341	protein-coding gene	gene with protein product		612907				10810093, 11504732	Standard	NM_182916		Approved	MtCCA, CGI-47, CCA1	uc003bpp.4	Q96Q11	OTTHUMG00000090259	ENST00000251607.6:c.438A>C	chr3.hg19:g.3182289A>C	ENSP00000251607:p.Lys146Asn	279.0	0.0		179.0	51.0	NM_182916	A8K2Z6|B7WP13|C9JKA2|Q8ND57|Q9BS97|Q9Y362	Missense_Mutation	SNP	ENST00000251607.6	hg19	CCDS2561.2	.	.	.	.	.	.	.	.	.	.	A	19.62	3.862317	0.71949	.	.	ENSG00000072756	ENST00000251607;ENST00000280591	T;T	0.44083	0.93;0.93	5.71	-2.49	0.06403	Poly A polymerase, head domain (1);	0.084915	0.85682	D	0.000000	T	0.28134	0.0694	L	0.28694	0.88	0.80722	D	1	B;P	0.37548	0.024;0.599	B;B	0.37239	0.061;0.244	T	0.02683	-1.1124	10	0.46703	T	0.11	-18.9096	12.9605	0.58455	0.53:0.0:0.47:0.0	.	146;146	Q96Q11-2;Q96Q11	.;TRNT1_HUMAN	N	146	ENSP00000251607:K146N;ENSP00000280591:K146N	ENSP00000251607:K146N	K	+	3	2	TRNT1	3157289	0.994000	0.37717	0.976000	0.42696	0.997000	0.91878	0.591000	0.23969	-0.720000	0.04935	0.533000	0.62120	AAA	.	.		0.368	TRNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337616.1			C	3182289	A	C	3182289	3	2	222	1	0	0	0	0	1	0	0	0	16588	69	3	5	448	5	TRNT1	3	3182289	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10		3182289	194840141	18	31702										
GRM7	2917	hgsc.bcm.edu	37	chr3	7620197	7620197	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gccaggacagagaaagaagaCacagaaaggaactccttgct	11	9	0	4			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr3:7620197C>A	ENST00000357716.4	+	8	1878	c.1604C>A	c.(1603-1605)aCa>aAa	p.T535K	GRM7_ENST00000403881.1_Missense_Mutation_p.T535K|GRM7_ENST00000389336.4_Missense_Mutation_p.T535K|GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000486284.1_Missense_Mutation_p.T535K|GRM7_ENST00000402647.2_Missense_Mutation_p.T535K	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	535					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						AGAAAGAAGACACAGAAAGGA	0.498																																					p.T535K		Atlas-SNP	.											.	GRM7	223	.	0			c.C1604A						.						132	126	128					3																	7620197		2203	4300	6503	SO:0001583	missense	2917	exon8			AGAAGACACAGAA	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1604C>A	chr3.hg19:g.7620197C>A	ENSP00000350348:p.Thr535Lys	237.0	0.0		199.0	34.0	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	hg19	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.465968	0.26335	.	.	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647;ENST00000413492	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	5.93	4.12	0.48240	GPCR, family 3, nine cysteines domain (1);	0.305792	0.36200	N	0.002739	T	0.74207	0.3686	L	0.31294	0.92	0.21325	N	0.999721	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.08055	0.002;0.0;0.001;0.001;0.003	T	0.63743	-0.6568	10	0.54805	T	0.06	.	5.4616	0.16619	0.0:0.6279:0.1505:0.2216	.	535;535;290;535;535	B7ZKK0;Q14831-5;Q59G95;Q14831;Q14831-2	.;.;.;GRM7_HUMAN;.	K	535	ENSP00000350348:T535K;ENSP00000417536:T535K;ENSP00000373987:T535K;ENSP00000385664:T535K;ENSP00000384585:T535K	ENSP00000350348:T535K	T	+	2	0	GRM7	7595197	0.417000	0.25432	0.562000	0.28370	0.884000	0.51177	0.819000	0.27308	0.820000	0.34516	0.655000	0.94253	ACA	.	.		0.498	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		A	7620197	C	A	7620197	3	1	222	1	0	0	0	0	1	0	0	0	6811	478	17	3	1634	3	GRM7	3	7620197	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	4437908	7620197	190402233	19	31703										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266112	41266112	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	acctggactctggaatccatTctggtgccactaccacagct	8	14	2	0	rs121913416|rs121913228		TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr3:41266112T>G	ENST00000349496.5	+	3	389	c.109T>G	c.(109-111)Tct>Gct	p.S37A	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S37A|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S37A|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S37A|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S30A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S37A(62)|p.A5_A80del(53)|p.S37P(21)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.I35_S37>T(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.S37T(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGAATCCATTCTGGTGCCAC	0.498	S37P(HEC108_ENDOMETRIUM)|S37P(SNGM_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S37A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	214	Deletion - In frame(102)|Substitution - Missense(84)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(108)|large_intestine(33)|stomach(21)|endometrium(13)|small_intestine(10)|parathyroid(9)|central_nervous_system(8)|skin(3)|ovary(3)|pancreas(2)|adrenal_gland(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|pituitary(1)	c.T109G						.						94	79	84					3																	41266112		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ATCCATTCTGGTG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.109T>G	chr3.hg19:g.41266112T>G	ENSP00000344456:p.Ser37Ala	143.0	0.0		118.0	14.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.591559	0.86953	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.67468	0.2896	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72357	-0.4318	10	0.87932	D	0	-15.9763	16.0677	0.80897	0.0:0.0:0.0:1.0	.	37	P35222	CTNB1_HUMAN	A	30;37;37;37;37;30;37;37;37	ENSP00000400508:S30A;ENSP00000385604:S37A;ENSP00000412219:S37A;ENSP00000379486:S37A;ENSP00000344456:S37A;ENSP00000411226:S30A;ENSP00000379488:S37A;ENSP00000409302:S37A;ENSP00000401599:S37A	ENSP00000344456:S37A	S	+	1	0	CTNNB1	41241116	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266112	T	G	41266112	3	3	222	1	0	0	0	0	1	0	0	0	4018	1783	62	5	115	5	CTNNB1	3	41266112	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	33645915	41266112	156756318	20	31704										
ZNF502	91392	hgsc.bcm.edu	37	chr3	44763338	44763338	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	aacctctctcagcatcagagAattcatagtggagagaaacc	8	10	4	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr3:44763338A>G	ENST00000296091.4	+	4	1285	c.1029A>G	c.(1027-1029)agA>agG	p.R343R	ZNF502_ENST00000436624.2_Silent_p.R343R|ZNF502_ENST00000449836.1_Silent_p.R343R	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		AGCATCAGAGAATTCATAGTG	0.403																																					p.R343R		Atlas-SNP	.											.	ZNF502	58	.	0			c.A1029G						.						50	54	53					3																	44763338		2203	4300	6503	SO:0001819	synonymous_variant	91392	exon4			TCAGAGAATTCAT	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"Zinc fingers, C2H2-type"	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.1029A>G	chr3.hg19:g.44763338A>G		138.0	0.0		120.0	18.0	NM_001134440		Silent	SNP	ENST00000296091.4	hg19	CCDS2719.1	.	.	.	.	.	.	.	.	.	.	A	8.139	0.784706	0.16189	.	.	ENSG00000196653	ENST00000427783	.	.	.	4.27	3.1	0.35709	.	.	.	.	.	T	0.64527	0.2606	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65154	-0.6237	5	0.72032	D	0.01	-21.4789	8.9095	0.35543	0.908:0.0:0.092:0.0	.	.	.	.	G	343	.	ENSP00000397812:E343G	E	+	2	0	ZNF502	44738342	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-0.231000	0.09069	0.792000	0.33850	0.533000	0.62120	GAA	.	.		0.403	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		G	44763338	A	G	44763338	2	3	222	1	0	0	0	0	0	0	0	1	17965	243	9	2		2	ZNF502	3	44763338	Silent	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	3497226	44763338	153259092	21	31705										
KNG1	3827	hgsc.bcm.edu	37	chr3	186459974	186459974	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	atatccagatagacccaaatGgcctttcatttaacccaata	4	11	1	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr3:186459974G>A	ENST00000265023.4	+	10	2001	c.1789G>A	c.(1789-1791)Ggc>Agc	p.G597S	KNG1_ENST00000287611.2_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000609726.1_RNA|RP11-573D15.8_ENST00000596329.1_RNA|RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000447445.1_Intron	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	597					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)	p.G597C(1)		endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		AGACCCAAATGGCCTTTCATT	0.453																																					p.G597S		Atlas-SNP	.											KNG1_ENST00000265023,NS,carcinoma,0,1	KNG1	129	.	1	Substitution - Missense(1)	endometrium(1)	c.G1789A						.						139	130	133					3																	186459974		1901	4115	6016	SO:0001583	missense	3827	exon10			CCAAATGGCCTTT		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"Endogenous ligands"	6383	protein-coding gene	gene with protein product	"alpha-2-thiol proteinase inhibitor", "bradykinin"	612358	"kininogen"	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.1789G>A	chr3.hg19:g.186459974G>A	ENSP00000265023:p.Gly597Ser	126.0	0.0		148.0	21.0	NM_001102416	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	hg19	CCDS43183.1	.	.	.	.	.	.	.	.	.	.	G	1.384	-0.582660	0.03827	.	.	ENSG00000113889	ENST00000265023	T	0.05580	3.42	5.18	-0.451	0.12214	.	0.381500	0.22838	N	0.055003	T	0.02455	0.0075	N	0.10874	0.06	0.09310	N	0.999997	B	0.06786	0.001	B	0.04013	0.001	T	0.43845	-0.9366	9	.	.	.	-1.7458	3.2892	0.06943	0.4402:0.0:0.3704:0.1895	.	597	P01042	KNG1_HUMAN	S	597	ENSP00000265023:G597S	.	G	+	1	0	KNG1	187942668	0.989000	0.36119	0.096000	0.21009	0.045000	0.14185	1.208000	0.32345	0.056000	0.16144	-0.471000	0.05019	GGC	.	.		0.453	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416		A	186459974	G	A	186459974	3	1	222	1	0	0	0	0	1	0	0	0	8436	1348	47	3	1827	3	KNG1	3	186459974	Missense_Mutation	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10	141696636	186459974	11562456	22	31706										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11385065	11385065	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cgactgcttgggcgaggagcCgcgcggcgcggcgtaggtgg	21	11	0	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr5:11385065C>T	ENST00000304623.8	-	7	1078	c.889G>A	c.(889-891)Ggc>Agc	p.G297S	CTNND2_ENST00000495388.2_5'Flank|CTNND2_ENST00000503622.1_Intron|CTNND2_ENST00000458100.2_Intron|CTNND2_ENST00000359640.2_Missense_Mutation_p.G297S|CTNND2_ENST00000511377.1_Missense_Mutation_p.G206S	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	297					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						ggcgaggagccgcgcggcgcg	0.771																																					p.G297S		Atlas-SNP	.											.	CTNND2	289	.	0			c.G889A						.						28	35	33					5																	11385065		2173	4252	6425	SO:0001583	missense	1501	exon7			AGGAGCCGCGCGG	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.889G>A	chr5.hg19:g.11385065C>T	ENSP00000307134:p.Gly297Ser	45.0	0.0		35.0	8.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	10.24	1.295971	0.23650	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377	T;T;T	0.75477	-0.86;-0.94;-0.83	3.5	3.5	0.40072	.	0.748719	0.10145	U	0.710384	T	0.47801	0.1465	N	0.03608	-0.345	0.80722	D	1	B	0.31274	0.317	B	0.21151	0.033	T	0.35895	-0.9770	10	0.11794	T	0.64	-9.688	11.7937	0.52084	0.0:0.8206:0.1794:0.0	.	297	Q9UQB3	CTND2_HUMAN	S	297;297;206	ENSP00000307134:G297S;ENSP00000352661:G297S;ENSP00000426510:G206S	ENSP00000307134:G297S	G	-	1	0	CTNND2	11438065	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	1.447000	0.35101	1.466000	0.48025	0.462000	0.41574	GGC	.	.		0.771	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		T	11385065	C	T	11385065	3	4	222	1	0	0	0	0	1	0	0	0	4022	652	23	1	2852	1	CTNND2	5	11385065	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10		11385065	169530195	23	31707										
VARS	7407	hgsc.bcm.edu	37	chr6	31750583	31750583	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cgtgccgctgcccaacttcaTagtcattttggtcatgtgcg	10	12	3	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr6:31750583T>C	ENST00000375663.3	-	15	2242	c.1802A>G	c.(1801-1803)tAt>tGt	p.Y601C	VARS_ENST00000482996.1_5'Flank|VARS_ENST00000444930.2_Intron	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	601					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	CCCAACTTCATAGTCATTTTG	0.592																																					p.Y601C		Atlas-SNP	.											.	VARS	76	.	0			c.A1802G						.						52	50	51					6																	31750583		1509	2708	4217	SO:0001583	missense	7407	exon15			ACTTCATAGTCAT	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	12651	protein-coding gene	gene with protein product	"valine tRNA ligase 1, cytoplasmic"	192150	"valyl-tRNA synthetase 2"	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.1802A>G	chr6.hg19:g.31750583T>C	ENSP00000364815:p.Tyr601Cys	83.0	0.0		120.0	19.0	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Missense_Mutation	SNP	ENST00000375663.3	hg19	CCDS34412.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.949568	0.73787	.	.	ENSG00000204394	ENST00000375663	T	0.55413	0.52	5.09	5.09	0.68999	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.85682	D	0.000000	T	0.76948	0.4059	H	0.97131	3.945	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.84942	0.0866	10	0.87932	D	0	-18.8418	12.8172	0.57671	0.0:0.0:0.0:1.0	.	601	P26640	SYVC_HUMAN	C	601	ENSP00000364815:Y601C	ENSP00000364815:Y601C	Y	-	2	0	VARS	31858562	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	4.284000	0.58983	1.919000	0.55581	0.460000	0.39030	TAT	.	.		0.592	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295		C	31750583	T	C	31750583	3	2	222	1	0	0	0	0	1	0	0	0	17138	1406	49	2	2056	2	VARS	6	31750583	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10		31750583	139364484	24	31708										
CD109	135228	hgsc.bcm.edu	37	chr6	74481156	74481156	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tttctctcttttttagataaAgctatattggagtaaagtga	7	4	2	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr6:74481156A>C	ENST00000287097.5	+	15	1791	c.1679A>C	c.(1678-1680)aAg>aCg	p.K560T	CD109_ENST00000422508.2_Missense_Mutation_p.K483T|CD109_ENST00000437994.2_Missense_Mutation_p.K560T			Q6YHK3	CD109_HUMAN	CD109 molecule	560					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTTTAGATAAAGCTATATTGG	0.378																																					p.K560T		Atlas-SNP	.											.	CD109	170	.	0			c.A1679C						.						68	68	68					6																	74481156		2203	4300	6503	SO:0001583	missense	135228	exon15			AGATAAAGCTATA	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.1679A>C	chr6.hg19:g.74481156A>C	ENSP00000287097:p.Lys560Thr	42.0	0.0		37.0	12.0	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	hg19	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	A	7.146	0.582795	0.13749	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.63255	-0.03;-0.03;-0.03	5.5	3.12	0.35913	Alpha-2-macroglobulin, N-terminal 2 (1);	0.821791	0.11492	N	0.558636	T	0.34832	0.0911	L	0.42245	1.32	0.23628	N	0.997251	B;B;B;B	0.24368	0.027;0.102;0.041;0.019	B;B;B;B	0.31016	0.02;0.086;0.123;0.044	T	0.32824	-0.9892	10	0.34782	T	0.22	.	8.3501	0.32297	0.7792:0.1424:0.0784:0.0	.	483;560;560;560	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	T	560;483;560	ENSP00000388062:K560T;ENSP00000404475:K483T;ENSP00000287097:K560T	ENSP00000287097:K560T	K	+	2	0	CD109	74537877	0.311000	0.24536	0.728000	0.30774	0.637000	0.38172	1.009000	0.29886	1.113000	0.41760	0.533000	0.62120	AAG	.	.		0.378	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		C	74481156	A	C	74481156	3	2	222	1	0	0	0	0	1	0	0	0	2965	72	3	5	1737	5	CD109	6	74481156	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	42730573	74481156	96633911	25	31709										
TAB2	23118	hgsc.bcm.edu	37	chr6	149699603	149699604	+	Frame_Shift_Ins	INS	-	-	A													0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tggtaactttagccccaaatINSatccagactggtcgtaatac							TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr6:149699603_149699604insA	ENST00000367456.1	+	4	1129_1130	c.552_553insA	c.(553-555)atcfs	p.I185fs	TAB2_ENST00000392282.1_Frame_Shift_Ins_p.I185fs|TAB2_ENST00000538427.1_Frame_Shift_Ins_p.I185fs|TAB2_ENST00000536230.1_Frame_Shift_Ins_p.I153fs|TAB2_ENST00000286332.5_Frame_Shift_Ins_p.I185fs			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	185					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase activity (GO:0045860)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						TAGCCCCAAATATCCAGACTGG	0.416																																					p.N184fs		Atlas-INDEL	.											.	TAB2	55	.	0			c.552_553insA						.																																			SO:0001589	frameshift_variant	23118	exon5			.	AF241230	CCDS5214.1	6q25.1	2010-08-05	2010-02-05	2010-02-05	ENSG00000055208	ENSG00000055208			17075	protein-coding gene	gene with protein product		605101	"mitogen-activated protein kinase kinase kinase 7 interacting protein 2"	MAP3K7IP2		9872452, 10882101	Standard	XR_250046		Approved	KIAA0733	uc010kib.2	Q9NYJ8	OTTHUMG00000015783	ENST00000367456.1:c.553dupA	chr6.hg19:g.149699604_149699604dupA	ENSP00000356426:p.Ile185fs	85.0	0.0		56.0	18.0	NM_015093	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Frame_Shift_Ins	INS	ENST00000367456.1	hg19	CCDS5214.1																																																																																			.	.		0.416	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3			A	149699604	-	A	149699603	7	5	222	1	0	1	1	0	0	0	0	0	15511	1403	49	0	558	0	TAB2	6	149699603	Frame_Shift_Ins	INS	-	TCGA-DD-AAEK-01A-11D-A40R-10	75218447	149699603	21415464	26	31710										
C6orf118	168090	hgsc.bcm.edu	37	chr6	165713968	165713968	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ggctgcacgtgcaaattttcTggagctcctggaggaaaaac	12	9	1	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr6:165713968T>G	ENST00000230301.8	-	3	781	c.761A>C	c.(760-762)cAg>cCg	p.Q254P	C6orf118_ENST00000543069.1_Missense_Mutation_p.Q150P	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	254										breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		GCAAATTTTCTGGAGCTCCTG	0.458																																					p.Q254P		Atlas-SNP	.											.	C6orf118	116	.	0			c.A761C						.						117	135	129					6																	165713968		2203	4300	6503	SO:0001583	missense	168090	exon3			ATTTTCTGGAGCT		CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.761A>C	chr6.hg19:g.165713968T>G	ENSP00000230301:p.Gln254Pro	45.0	0.0		29.0	5.0	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	hg19	CCDS5288.1	.	.	.	.	.	.	.	.	.	.	T	13.19	2.164586	0.38217	.	.	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.17054	2.52;2.3	5.02	5.02	0.67125	.	0.106984	0.39759	N	0.001261	T	0.26882	0.0658	M	0.65975	2.015	0.38655	D	0.951949	D	0.76494	0.999	D	0.67548	0.952	T	0.03684	-1.1013	10	0.54805	T	0.06	.	12.2852	0.54788	0.0:0.0:0.0:1.0	.	254	Q5T5N4	CF118_HUMAN	P	254;150	ENSP00000230301:Q254P;ENSP00000439288:Q150P	ENSP00000230301:Q254P	Q	-	2	0	C6orf118	165633958	1.000000	0.71417	1.000000	0.80357	0.079000	0.17450	1.787000	0.38704	1.876000	0.54355	0.533000	0.62120	CAG	.	.		0.458	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980		G	165713968	T	G	165713968	3	3	222	1	0	0	0	0	1	0	0	0	2325	1580	55	5	676	5	C6orf118	6	165713968	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	16014365	165713968	5401099	27	31711										
TTYH3	80727	hgsc.bcm.edu	37	chr7	2687142	2687142	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ccgggcggcccgagcccctgCgagccgtacagaggctgcag	16	16	0	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr7:2687142C>A	ENST00000258796.7	+	4	701	c.496C>A	c.(496-498)Cga>Aga	p.R166R	TTYH3_ENST00000403167.1_5'Flank|TTYH3_ENST00000407643.1_Silent_p.R166R	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3	166					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|intracellular calcium activated chloride channel activity (GO:0005229)			kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		CGAGCCCCTGCGAGCCGTACA	0.726																																					p.R166R		Atlas-SNP	.											.	TTYH3	36	.	0			c.C496A						.						5	6	5					7																	2687142		1952	3869	5821	SO:0001819	synonymous_variant	80727	exon4			CCCCTGCGAGCCG		CCDS34588.1	7p22	2013-09-02	2013-09-02		ENSG00000136295	ENSG00000136295			22222	protein-coding gene	gene with protein product		608919	"tweety homolog 3 (Drosophila)"				Standard	NM_025250		Approved	KIAA1691	uc003smp.3	Q9C0H2	OTTHUMG00000152050	ENST00000258796.7:c.496C>A	chr7.hg19:g.2687142C>A		50.0	0.0		54.0	8.0	NM_025250	A4D201|B7WP98|Q6L749|Q6ZVG3|Q8TEG6	Silent	SNP	ENST00000258796.7	hg19	CCDS34588.1																																																																																			.	.		0.726	TTYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325082.2	XM_166523		A	2687142	C	A	2687142	2	1	222	1	0	0	0	0	0	0	0	1	16756	760	27	1		1	TTYH3	7	2687142	Silent	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10		2687142	156451521	28	31712										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11514132	11514132	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tttgccagtggtacactgtgCaaggatgctcattacagctt	10	9	1	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr7:11514132C>A	ENST00000423059.4	-	8	2332	c.2081G>T	c.(2080-2082)tGc>tTc	p.C694F	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	694	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		GTACACTGTGCAAGGATGCTC	0.483										HNSCC(18;0.044)																											p.C694F		Atlas-SNP	.											.	THSD7A	219	.	0			c.G2081T						.						76	75	75					7																	11514132		2011	4178	6189	SO:0001583	missense	221981	exon8			ACTGTGCAAGGAT		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.2081G>T	chr7.hg19:g.11514132C>A	ENSP00000406482:p.Cys694Phe	101.0	0.0		93.0	21.0	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	hg19	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.713699	0.68730	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	D	0.98762	-5.12	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.99566	0.9844	H	0.98407	4.225	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97833	1.0264	10	0.87932	D	0	.	19.8575	0.96767	0.0:1.0:0.0:0.0	.	694	Q9UPZ6	THS7A_HUMAN	F	694	ENSP00000406482:C694F	ENSP00000262042:C694F	C	-	2	0	THSD7A	11480657	1.000000	0.71417	0.997000	0.53966	0.404000	0.30871	7.776000	0.85560	2.767000	0.95098	0.563000	0.77884	TGC	.	.		0.483	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		A	11514132	C	A	11514132	3	1	222	1	0	0	0	0	1	0	0	0	15894	710	25	3	2972	3	THSD7A	7	11514132	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	8826990	11514132	147624531	29	31713										
SLC13A1	6561	hgsc.bcm.edu	37	chr7	122774580	122774580	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	aggcaacgacagtcaggataGcgtctgtgtgaaaacatgga	13	7	2	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr7:122774580G>A	ENST00000194130.2	-	8	855	c.816C>T	c.(814-816)cgC>cgT	p.R272R	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	272					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	AGTCAGGATAGCGTCTGTGTG	0.488																																					p.R272R		Atlas-SNP	.											.	SLC13A1	110	.	0			c.C816T						.						162	132	142					7																	122774580		2203	4300	6503	SO:0001819	synonymous_variant	6561	exon8			AGGATAGCGTCTG		CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"Solute carriers"	10916	protein-coding gene	gene with protein product		606193	"solute carrier family 13 (sodium/sulphate symporters), member 1"			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.816C>T	chr7.hg19:g.122774580G>A		92.0	0.0		81.0	22.0	NM_022444	Q9H5Z0	Silent	SNP	ENST00000194130.2	hg19	CCDS5786.1																																																																																			.	.		0.488	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		A	122774580	G	A	122774580	2	1	222	1	0	0	0	0	0	0	0	1	14406	958	34	3		3	SLC13A1	7	122774580	Silent	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10	111260448	122774580	36364083	30	31714										
TMUB1	83590	hgsc.bcm.edu	37	chr7	150779558	150779558	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tccccgccctcagcggtgtgCgttgagacccaggcaagggc	14	15	1	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr7:150779558C>T	ENST00000392818.3	-	2	450	c.93G>A	c.(91-93)acG>acA	p.T31T	FASTK_ENST00000482571.1_5'Flank|TMUB1_ENST00000482202.1_Silent_p.T31T|FASTK_ENST00000540185.1_5'Flank|TMUB1_ENST00000462940.1_Silent_p.T31T|FASTK_ENST00000353841.2_5'Flank|FASTK_ENST00000297532.6_5'Flank|TMUB1_ENST00000476627.1_Silent_p.T31T|TMUB1_ENST00000297533.4_Silent_p.T31T|FASTK_ENST00000489884.1_5'Flank	NM_031434.3	NP_113622.1	Q9BVT8	TMUB1_HUMAN	transmembrane and ubiquitin-like domain containing 1	31						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGCGGTGTGCGTTGAGACCC	0.662																																					p.T31T		Atlas-SNP	.											.	TMUB1	7	.	0			c.G93A						.						62	64	63					7																	150779558		2203	4300	6503	SO:0001819	synonymous_variant	83590	exon2			GGTGTGCGTTGAG	BC000936	CCDS5920.1	7q36.1	2006-06-27	2006-06-27	2006-06-27	ENSG00000164897	ENSG00000164897			21709	protein-coding gene	gene with protein product		614792	"chromosome 7 open reading frame 21"	C7orf21			Standard	NM_001136044		Approved	SB144	uc003wjd.3	Q9BVT8	OTTHUMG00000158621	ENST00000392818.3:c.93G>A	chr7.hg19:g.150779558C>T		135.0	0.0		136.0	37.0	NM_031434	D3DX06|Q53AQ2	Silent	SNP	ENST00000392818.3	hg19	CCDS5920.1																																																																																			.	.		0.662	TMUB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351485.1	NM_031434		T	150779558	C	T	150779558	2	4	222	1	0	0	0	0	0	0	0	1	16279	755	27	1		1	TMUB1	7	150779558	Silent	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	28004978	150779558	8359105	31	31715										
C8orf76	84933	hgsc.bcm.edu	37	chr8	124243859	124243859	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ctctgccaatttgccccagtTccaaggattaaaaggatgca	8	11	1	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr8:124243859T>A	ENST00000276704.4	-	4	547	c.496A>T	c.(496-498)Aac>Tac	p.N166Y	ZHX1-C8ORF76_ENST00000357082.4_Missense_Mutation_p.N134Y|C8orf76_ENST00000521310.1_5'UTR	NM_032847.2	NP_116236.1	Q96K31	CH076_HUMAN	chromosome 8 open reading frame 76	166										NS(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(4)	17	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			TTGCCCCAGTTCCAAGGATTA	0.448																																					p.N166Y		Atlas-SNP	.											.	C8orf76	26	.	0			c.A496T						.						112	120	117					8																	124243859		2203	4300	6503	SO:0001583	missense	84933	exon4			CCCAGTTCCAAGG	AK027731	CCDS6341.1	8q24.13	2012-06-27			ENSG00000189376	ENSG00000189376			25924	protein-coding gene	gene with protein product							Standard	NM_032847		Approved	FLJ14825	uc003yqc.2	Q96K31	OTTHUMG00000172562	ENST00000276704.4:c.496A>T	chr8.hg19:g.124243859T>A	ENSP00000276704:p.Asn166Tyr	79.0	0.0		98.0	47.0	NM_032847	Q53HC1	Missense_Mutation	SNP	ENST00000276704.4	hg19	CCDS6341.1	.	.	.	.	.	.	.	.	.	.	T	8.777	0.927336	0.18056	.	.	ENSG00000189376	ENST00000276704;ENST00000357082	T;T	0.75704	-0.96;-0.96	5.74	5.74	0.90152	Tetratricopeptide-like helical (1);	0.340781	0.37483	N	0.002068	T	0.62551	0.2437	L	0.41236	1.265	0.29225	N	0.873654	P;P	0.49090	0.919;0.919	B;P	0.45506	0.406;0.483	T	0.60224	-0.7305	10	0.02654	T	1	-1.2328	8.2152	0.31507	0.1305:0.0:0.1358:0.7337	.	134;166	Q96EF9;Q96K31	.;CH076_HUMAN	Y	166;134	ENSP00000276704:N166Y;ENSP00000349593:N134Y	ENSP00000276704:N166Y	N	-	1	0	C8orf76	124313040	0.672000	0.27530	1.000000	0.80357	0.946000	0.59487	0.234000	0.17930	2.193000	0.70182	0.533000	0.62120	AAC	.	.		0.448	C8orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381748.1	NM_032847		A	124243859	T	A	124243859	3	1	222	1	0	0	0	0	1	0	0	0	2439	1783	62	4	658	4	C8orf76	8	124243859	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10		124243859	22120163	32	31716										
KIFC2	90990	hgsc.bcm.edu	37	chr8	145693163	145693163	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gtcgactgcgcctgggcgtgGtgaggctgcagggagacctg	19	10	0	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr8:145693163G>A	ENST00000301332.2	+	6	1058		c.e6+1		CYHR1_ENST00000424149.2_5'Flank|CYHR1_ENST00000306145.5_5'Flank|CTD-2517M22.16_ENST00000525461.1_RNA|KIFC2_ENST00000301331.5_Splice_Site|CYHR1_ENST00000403000.2_5'Flank|CYHR1_ENST00000438911.2_5'Flank	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2						ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			CCTGGGCGTGGTGAGGCTGCA	0.642											OREG0019057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	KIFC2	53	.	0			c.681+1G>A						.						43	48	46					8																	145693163		2203	4300	6503	SO:0001630	splice_region_variant	90990	exon6			GGCGTGGTGAGGC	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"Kinesins"	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.681+1G>A	chr8.hg19:g.145693163G>A		155.0	0.0	1696	204.0	26.0	NM_145754	E9PHB2|Q96NN6	Splice_Site	SNP	ENST00000301332.2	hg19	CCDS6427.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.233639	0.58886	.	.	ENSG00000167702	ENST00000301332;ENST00000528415	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5804	0.84713	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIFC2	145663971	1.000000	0.71417	1.000000	0.80357	0.618000	0.37518	6.996000	0.76263	2.521000	0.84997	0.655000	0.94253	.	.	.		0.642	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754	Intron	A	145693163	G	A	145693163	5	1	222	1	0	0	0	0	0	0	1	0	8322	1275	44	3	704	3	KIFC2	8	145693163	Splice_Site	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10	21449304	145693163	670859	33	31717										
FAM188A	80013	hgsc.bcm.edu	37	chr10	15875655	15875655	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ctgagcactctctatcaccaTcccatacattagaaacagca	4	14	2	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr10:15875655T>C	ENST00000277632.3	-	8	924	c.704A>G	c.(703-705)gAt>gGt	p.D235G	FAM188A_ENST00000477891.1_5'UTR	NM_024948.2	NP_079224.1	Q9H8M7	F188A_HUMAN	family with sequence similarity 188, member A	235					apoptotic process (GO:0006915)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	22						TCTATCACCATCCCATACATT	0.313																																					p.D235G	Pancreas(159;946 1953 2111 4475 22008)	Atlas-SNP	.											.	FAM188A	44	.	0			c.A704G						.						115	107	110					10																	15875655		2203	4298	6501	SO:0001583	missense	80013	exon8			TCACCATCCCATA	AK023459	CCDS7110.1	10p13	2009-07-14	2009-07-14	2009-07-14	ENSG00000148481	ENSG00000148481			23578	protein-coding gene	gene with protein product	"caspase recruitment domain containing pro-apoptotic protein", "CARD-containing protein"	611649	"chromosome 10 open reading frame 97"	C10orf97		12054670, 17652099	Standard	XM_005252600		Approved	FLJ13397, CARP, my042, DERP5	uc001iod.1	Q9H8M7	OTTHUMG00000017734	ENST00000277632.3:c.704A>G	chr10.hg19:g.15875655T>C	ENSP00000277632:p.Asp235Gly	310.0	0.0		237.0	38.0	NM_024948	Q5SZ68|Q5SZ69|Q5SZ70|Q6IA40|Q6P7P0|Q7Z2S1|Q8WUF1|Q9H3I4	Missense_Mutation	SNP	ENST00000277632.3	hg19	CCDS7110.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.470713	0.84533	.	.	ENSG00000148481	ENST00000277632;ENST00000418767;ENST00000436829	T;T;T	0.37235	1.21;1.21;1.21	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.66025	0.2748	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72711	-0.4211	10	0.72032	D	0.01	-16.662	15.8509	0.78930	0.0:0.0:0.0:1.0	.	235	Q9H8M7	F188A_HUMAN	G	235;75;88	ENSP00000277632:D235G;ENSP00000388661:D75G;ENSP00000389883:D88G	ENSP00000277632:D235G	D	-	2	0	FAM188A	15915661	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.361000	0.79497	2.148000	0.66965	0.455000	0.32223	GAT	.	.		0.313	FAM188A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046990.2	NM_024948		C	15875655	T	C	15875655	3	2	222	1	0	0	0	0	1	0	0	0	5519	1435	50	2	665	2	FAM188A	10	15875655	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10		15875655	119659092	34	31718										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55663063	55663063	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gatacacctccgatgtagaaTtttttctgaaacactggggg	10	8	1	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr10:55663063T>G	ENST00000320301.6	-	26	3835	c.3441A>C	c.(3439-3441)aaA>aaC	p.K1147N	PCDH15_ENST00000395433.1_Missense_Mutation_p.K1125N|PCDH15_ENST00000414778.1_Missense_Mutation_p.K1152N|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395445.1_Missense_Mutation_p.K1154N|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.K1110N|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373965.2_Missense_Mutation_p.K1154N|PCDH15_ENST00000395430.1_Missense_Mutation_p.K1147N|PCDH15_ENST00000409834.1_Missense_Mutation_p.K758N|PCDH15_ENST00000395438.1_Missense_Mutation_p.K1147N|PCDH15_ENST00000437009.1_Missense_Mutation_p.K1076N|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.K1147N	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1147	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CGATGTAGAATTTTTTCTGAA	0.353										HNSCC(58;0.16)																											p.K1152N		Atlas-SNP	.											.,4	PCDH15	1715	.	0			c.A3456C						.						87	88	88					10																	55663063		2203	4300	6503	SO:0001583	missense	65217	exon27			GTAGAATTTTTTC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3441A>C	chr10.hg19:g.55663063T>G	ENSP00000322604:p.Lys1147Asn	49.0	0.0		58.0	8.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	t	16.76	3.213223	0.58452	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T;T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15	5.01	2.47	0.30058	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.56673	0.2001	L	0.34521	1.04	0.45837	D	0.998705	D;P;P;P;P;P;D;P;P;P;P;P;P	0.76494	0.999;0.945;0.945;0.885;0.944;0.573;0.999;0.82;0.902;0.902;0.67;0.895;0.945	D;P;P;P;P;B;D;B;P;P;P;P;P	0.85130	0.997;0.696;0.621;0.521;0.696;0.244;0.997;0.392;0.621;0.621;0.468;0.468;0.621	T	0.58171	-0.7683	9	0.34782	T	0.22	.	1.7411	0.02952	0.2554:0.2451:0.0:0.4995	.	1125;1147;1147;1152;1076;1110;1147;1147;1154;1154;1147;1152;1147	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	N	1154;1152;1147;1147;758;1154;1110;1147;1125;1147;1147;1152;1076	ENSP00000363076:K1154N;ENSP00000410304:K1152N;ENSP00000378826:K1147N;ENSP00000386693:K758N;ENSP00000378832:K1154N;ENSP00000378820:K1110N;ENSP00000354950:K1147N;ENSP00000378821:K1125N;ENSP00000322604:K1147N;ENSP00000378818:K1147N;ENSP00000412628:K1076N	ENSP00000322604:K1147N	K	-	3	2	PCDH15	55333069	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.750000	0.26334	1.878000	0.54408	0.352000	0.21897	AAA	.	.		0.353	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		G	55663063	T	G	55663063	3	3	222	1	0	0	0	0	1	0	0	0	11520	1490	52	5	4077	5	PCDH15	10	55663063	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	39787408	55663063	79871684	35	31719										
TET1	80312	hgsc.bcm.edu	37	chr10	70426952	70426952	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	accggctatacacagagctcAcagagaatctaaagtcatac	7	11	3	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr10:70426952A>C	ENST00000373644.4	+	7	4821	c.4612A>C	c.(4612-4614)Aca>Cca	p.T1538P		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1538					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CACAGAGCTCACAGAGAATCT	0.483																																					p.T1538P		Atlas-SNP	.											.	TET1	255	.	0			c.A4612C						.						90	73	79					10																	70426952		2203	4300	6503	SO:0001583	missense	80312	exon7			GAGCTCACAGAGA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.4612A>C	chr10.hg19:g.70426952A>C	ENSP00000362748:p.Thr1538Pro	100.0	0.0		116.0	15.0	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	A	16.77	3.214600	0.58452	.	.	ENSG00000138336	ENST00000373644;ENST00000545846	T	0.37584	1.19	5.21	4.08	0.47627	TET cysteine-rich domain (1);	0.186444	0.46145	D	0.000320	T	0.56863	0.2014	M	0.71036	2.16	0.42146	D	0.991533	D	0.89917	1.0	D	0.85130	0.997	T	0.60063	-0.7336	10	0.87932	D	0	.	11.0615	0.47950	0.9267:0.0:0.0733:0.0	.	1538	Q8NFU7	TET1_HUMAN	P	1538;10	ENSP00000362748:T1538P	ENSP00000362748:T1538P	T	+	1	0	TET1	70096958	1.000000	0.71417	0.031000	0.17742	0.399000	0.30720	7.455000	0.80726	0.927000	0.37143	0.477000	0.44152	ACA	.	.		0.483	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		C	70426952	A	C	70426952	3	2	222	1	0	0	0	0	1	0	0	0	15784	159	6	5	4634	5	TET1	10	70426952	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	14763889	70426952	65107795	36	31720										
VCL	7414	hgsc.bcm.edu	37	chr10	75842271	75842271	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tccaaactgaaccaggccaaAggttggctccgtgaccctag	10	13	0	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr10:75842271A>T	ENST00000211998.4	+	7	937	c.843A>T	c.(841-843)aaA>aaT	p.K281N	VCL_ENST00000478896.2_Intron|VCL_ENST00000417648.2_Intron|VCL_ENST00000372755.3_Missense_Mutation_p.K281N	NM_014000.2	NP_054706.1	P18206	VINC_HUMAN	vinculin	281	3 X 112 AA tandem repeats.|N-terminal globular head.				adherens junction assembly (GO:0034333)|apical junction assembly (GO:0043297)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|epithelial cell-cell adhesion (GO:0090136)|lamellipodium assembly (GO:0030032)|morphogenesis of an epithelium (GO:0002009)|muscle contraction (GO:0006936)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|protein localization to cell surface (GO:0034394)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cell-substrate junction (GO:0030055)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	actin binding (GO:0003779)|alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)		VCL/ALK(4)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Prostate(51;0.0112)					ACCAGGCCAAAGGTTGGCTCC	0.448																																					p.K281N		Atlas-SNP	.											.	VCL	77	.	0			c.A843T						.						86	79	81					10																	75842271		2203	4300	6503	SO:0001583	missense	7414	exon7			GGCCAAAGGTTGG	M33308	CCDS7340.1, CCDS7341.1	10q22.1-q23	2014-09-17			ENSG00000035403	ENSG00000035403			12665	protein-coding gene	gene with protein product	"metavinculin"	193065				1339348	Standard	NM_014000		Approved		uc001jwd.3	P18206	OTTHUMG00000018498	ENST00000211998.4:c.843A>T	chr10.hg19:g.75842271A>T	ENSP00000211998:p.Lys281Asn	78.0	0.0		82.0	9.0	NM_003373	Q16450|Q5SWX2|Q7Z3B8|Q8IXU7	Missense_Mutation	SNP	ENST00000211998.4	hg19	CCDS7341.1	.	.	.	.	.	.	.	.	.	.	A	16.05	3.011523	0.54468	.	.	ENSG00000035403	ENST00000372755;ENST00000211998;ENST00000415462;ENST00000537043	T;T	0.38401	1.14;1.14	5.52	3.2	0.36748	Vinculin, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	L	0.42245	1.32	0.80722	D	1	D;D;D	0.63880	0.993;0.993;0.991	D;D;D	0.78314	0.974;0.974;0.991	T	0.23940	-1.0174	10	0.41790	T	0.15	.	8.2026	0.31434	0.7826:0.0:0.2174:0.0	.	208;281;281	F5H7T3;P18206-2;P18206	.;.;VINC_HUMAN	N	281;281;188;208	ENSP00000361841:K281N;ENSP00000211998:K281N	ENSP00000211998:K281N	K	+	3	2	VCL	75512277	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.218000	0.32467	0.402000	0.25451	0.524000	0.50904	AAA	.	.		0.448	VCL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003373, NM_014000		T	75842271	A	T	75842271	3	4	222	1	0	0	0	0	1	0	0	0	17154	69	3	4	869	4	VCL	10	75842271	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	5415319	75842271	59692476	37	31721										
C10orf58	84293	hgsc.bcm.edu	37	chr10	82187098	82187098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cactccatagaaaaagttctAtggtccacaaaggcggaaga	9	9	1	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr10:82187098A>G	ENST00000372181.1	+	4	892	c.422A>G	c.(421-423)tAt>tGt	p.Y141C	FAM213A_ENST00000372185.1_Missense_Mutation_p.Y130C|FAM213A_ENST00000372188.1_Missense_Mutation_p.Y141C|FAM213A_ENST00000372187.5_Missense_Mutation_p.Y141C	NM_001243778.1|NM_001243782.1	NP_001230707.1|NP_001230711.1	Q9BRX8	F213A_HUMAN	family with sequence similarity 213, member A	141					oxidation-reduction process (GO:0055114)|regulation of osteoclast differentiation (GO:0045670)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)										AAAAAGTTCTATGGTCCACAA	0.493																																					p.Y141C		Atlas-SNP	.											.	.	.	.	0			c.A422G						.						115	111	112					10																	82187098		2203	4300	6503	SO:0001583	missense	84293	exon5			AGTTCTATGGTCC	AF086462	CCDS7368.1, CCDS58089.1	10q23.1	2011-12-08	2011-12-08	2011-12-08	ENSG00000122378	ENSG00000122378			28651	protein-coding gene	gene with protein product	"peroxiredoxin-like 2 activated in M-CSF stimulated monocytes"		"chromosome 10 open reading frame 58"	C10orf58		11483580, 19951071	Standard	NM_032333		Approved	MGC4248, PAMM	uc001kce.4	Q9BRX8	OTTHUMG00000018614	ENST00000372181.1:c.422A>G	chr10.hg19:g.82187098A>G	ENSP00000361254:p.Tyr141Cys	73.0	0.0		74.0	11.0	NM_032333	B2RD81|Q6UW08|Q8N2K3|Q8NBK9|Q96JR0	Missense_Mutation	SNP	ENST00000372181.1	hg19	CCDS7368.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.526674	0.64860	.	.	ENSG00000122378	ENST00000372188;ENST00000372187;ENST00000372185;ENST00000372181	T;T;T;T	0.59772	0.24;0.24;0.24;0.24	5.97	4.81	0.61882	.	0.053430	0.85682	D	0.000000	T	0.79257	0.4415	M	0.91612	3.225	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82080	-0.0634	10	0.87932	D	0	-4.2926	10.5986	0.45354	0.8558:0.0:0.0:0.1442	.	141	Q9BRX8	PAMM_HUMAN	C	141;141;130;141	ENSP00000361262:Y141C;ENSP00000361261:Y141C;ENSP00000361259:Y130C;ENSP00000361254:Y141C	ENSP00000361254:Y141C	Y	+	2	0	C10orf58	82177078	1.000000	0.71417	0.841000	0.33234	0.722000	0.41435	7.084000	0.76866	1.023000	0.39654	0.533000	0.62120	TAT	.	.		0.493	FAM213A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049077.2			G	82187098	A	G	82187098	3	3	222	1	0	0	0	0	1	0	0	0	1612	449	16	2	436	2	C10orf58	10	82187098	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	6344827	82187098	53347649	38	31722										
C10orf28	27291	hgsc.bcm.edu	37	chr10	99991445	99991445	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cgggttttctgcagttatcaGtgagtatgcaaatgattgtg	12	5	2	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr10:99991445G>A	ENST00000298999.3	+	6	2264		c.e6+1		R3HCC1L_ENST00000314594.5_Splice_Site|R3HCC1L_ENST00000370586.2_Splice_Site|R3HCC1L_ENST00000370584.3_Splice_Site	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like								nucleotide binding (GO:0000166)										GCAGTTATCAGTGAGTATGCA	0.358																																					.		Atlas-SNP	.											C10orf28,NS,carcinoma,0,1	R3HCC1L	3	.	0			c.2003+1G>A						.						92	92	92					10																	99991445		2203	4300	6503	SO:0001630	splice_region_variant	27291	exon7			TTATCAGTGAGTA	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 28"	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1961+1G>A	chr10.hg19:g.99991445G>A		102.0	1.0		68.0	13.0	NM_001256619	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Splice_Site	SNP	ENST00000298999.3	hg19	CCDS31267.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.424351	0.83667	.	.	ENSG00000166024	ENST00000370584;ENST00000298999;ENST00000370586;ENST00000314594;ENST00000544834	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6448	0.91407	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C10orf28	99981435	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	7.744000	0.85034	2.687000	0.91594	0.655000	0.94253	.	.	.		0.358	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	Intron	A	99991445	G	A	99991445	5	1	222	1	0	0	0	0	0	0	1	0	1603	1043	36	3	1968	3	C10orf28	10	99991445	Splice_Site	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10	17804347	99991445	35543302	39	31723										
FGF8	2253	hgsc.bcm.edu	37	chr10	103530257	103530257	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cgcgtcttggagcccttgcgGggccggcccttgcgggtgaa	17	13	1	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr10:103530257G>A	ENST00000344255.3	-	6	530	c.531C>T	c.(529-531)ccC>ccT	p.P177P	FGF8_ENST00000485728.1_5'UTR|FGF8_ENST00000320185.2_Silent_p.P188P|FGF8_ENST00000346714.3_Silent_p.P148P|FGF8_ENST00000347978.2_Silent_p.P159P			P55075	FGF8_HUMAN	fibroblast growth factor 8 (androgen-induced)	177					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in mesendoderm migration (GO:0090134)|cell proliferation in forebrain (GO:0021846)|corticotropin hormone secreting cell differentiation (GO:0060128)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral axon guidance (GO:0033563)|embryonic hindlimb morphogenesis (GO:0035116)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain morphogenesis (GO:0048853)|forebrain neuron development (GO:0021884)|gastrulation (GO:0007369)|gonad development (GO:0008406)|heart looping (GO:0001947)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lung morphogenesis (GO:0060425)|male genitalia development (GO:0030539)|MAPK cascade (GO:0000165)|mesodermal cell migration (GO:0008078)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|midbrain-hindbrain boundary development (GO:0030917)|motor neuron axon guidance (GO:0008045)|negative regulation of cardiac muscle tissue development (GO:0055026)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate morphogenesis (GO:0001839)|neuroepithelial cell differentiation (GO:0060563)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|pallium development (GO:0021543)|patterning of blood vessels (GO:0001569)|pharyngeal system development (GO:0060037)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitosis (GO:0045840)|positive regulation of organ growth (GO:0046622)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)|signal transduction involved in regulation of gene expression (GO:0023019)|subpallium development (GO:0021544)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(2)	5		Colorectal(252;0.122)		Epithelial(162;3.94e-09)|all cancers(201;2.13e-07)		AGCCCTTGCGGGGCCGGCCCT	0.637																																					p.P188P		Atlas-SNP	.											.	FGF8	23	.	0			c.C564T						.						50	46	47					10																	103530257		2203	4300	6503	SO:0001819	synonymous_variant	2253	exon6			CTTGCGGGGCCGG	D38752	CCDS7515.1, CCDS7516.1, CCDS7517.1, CCDS7518.1, CCDS73185.1	10q25-q26	2014-01-30			ENSG00000107831	ENSG00000107831		"Endogenous ligands"	3686	protein-coding gene	gene with protein product		600483				8595889	Standard	NM_033164		Approved	AIGF	uc001ktq.2	P55075	OTTHUMG00000018940	ENST00000344255.3:c.531C>T	chr10.hg19:g.103530257G>A		94.0	0.0		88.0	15.0	NM_033163	A1A514|Q14915|Q15766	Silent	SNP	ENST00000344255.3	hg19	CCDS7517.1																																																																																			.	.		0.637	FGF8-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049999.1	NM_006119, NM_033165		A	103530257	G	A	103530257	2	1	222	1	0	0	0	0	0	0	0	1	5866	1219	43	3		3	FGF8	10	103530257	Silent	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10	3538812	103530257	32004490	40	31724										
DOCK1	1793	hgsc.bcm.edu	37	chr10	128860039	128860039	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	agaccagaccgtccgggtgaAggtgagtgccggccactgcc	15	13	0	4			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr10:128860039A>C	ENST00000280333.6	+	23	2490	c.2381A>C	c.(2380-2382)aAg>aCg	p.K794T		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	794					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GTCCGGGTGAAGGTGAGTGCC	0.468																																					p.K794T		Atlas-SNP	.											.	DOCK1	188	.	0			c.A2381C						.						36	37	37					10																	128860039		1919	4127	6046	SO:0001630	splice_region_variant	1793	exon23			GGGTGAAGGTGAG	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.2382+1A>C	chr10.hg19:g.128860039A>C		56.0	0.0		58.0	5.0	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	hg19		.	.	.	.	.	.	.	.	.	.	A	19.49	3.837498	0.71373	.	.	ENSG00000150760	ENST00000280333	T	0.68331	-0.32	4.99	4.99	0.66335	.	0.000000	0.64402	U	0.000005	T	0.74512	0.3726	M	0.76574	2.34	0.58432	D	0.999998	P;P	0.42556	0.783;0.783	P;P	0.49226	0.603;0.603	T	0.78727	-0.2091	10	0.87932	D	0	.	13.9995	0.64424	1.0:0.0:0.0:0.0	.	794;794	B2RUU3;Q14185	.;DOCK1_HUMAN	T	794	ENSP00000280333:K794T	ENSP00000280333:K794T	K	+	2	0	DOCK1	128750029	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	8.452000	0.90346	2.003000	0.58678	0.533000	0.62120	AAG	.	.		0.468	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	Missense_Mutation	C	128860039	A	C	128860039	5	2	222	1	0	0	0	0	0	0	1	0	4686	86	3	5	2471	5	DOCK1	10	128860039	Splice_Site	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	25329782	128860039	6674708	41	31725										
NUP98	4928	hgsc.bcm.edu	37	chr11	3744592	3744592	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ggggtttgaggaataggtttGgcaatagggttagtataaaa	15	1	0	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr11:3744592G>T	ENST00000324932.7	-	16	2361	c.1941C>A	c.(1939-1941)gcC>gcA	p.A647A	NUP98_ENST00000397007.4_Silent_p.A664A|NUP98_ENST00000397004.4_Silent_p.A647A|NUP98_ENST00000355260.3_Silent_p.A647A|NUP98_ENST00000359171.4_Silent_p.A647A	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	664					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		GAATAGGTTTGGCAATAGGGT	0.408			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																p.A664A		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.C1992A						.						131	114	119					11																	3744592		2201	4298	6499	SO:0001819	synonymous_variant	4928	exon16			AGGTTTGGCAATA	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.1941C>A	chr11.hg19:g.3744592G>T		147.0	0.0		81.0	4.0	NM_005387	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Silent	SNP	ENST00000324932.7	hg19	CCDS7746.1																																																																																			.	.		0.408	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		T	3744592	G	T	3744592	2	4	222	1	0	0	0	0	0	0	0	1	10782	1335	47	3		3	NUP98	11	3744592	Silent	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10		3744592	131261924	42	31726										
OR52E6	390078	hgsc.bcm.edu	37	chr11	5862416	5862416	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	agagccacaggtgttgagagCtttgagtcgagcttcccagg	14	9	0	3	rs61735020	byFrequency	TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr11:5862416C>A	ENST00000329322.5	-	1	711	c.712G>T	c.(712-714)Gct>Tct	p.A238S	OR52E6_ENST00000379946.2_Missense_Mutation_p.A242S|TRIM5_ENST00000380027.1_Intron	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTGTTGAGAGCTTTGAGTCGA	0.443																																					p.A238S		Atlas-SNP	.											.	OR52E6	70	.	0			c.G712T						.						64	65	65					11																	5862416		2197	4294	6491	SO:0001583	missense	390078	exon1			TGAGAGCTTTGAG	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"GPCR / Class A : Olfactory receptors"	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.712G>T	chr11.hg19:g.5862416C>A	ENSP00000328878:p.Ala238Ser	129.0	0.0		109.0	20.0	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	hg19	CCDS53597.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.414454	0.42817	.	.	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.00359	7.87;7.87	3.23	3.23	0.37069	GPCR, rhodopsin-like superfamily (1);	0.110508	0.40144	N	0.001174	T	0.00724	0.0024	M	0.80028	2.48	0.38300	D	0.942944	D	0.64830	0.994	D	0.68039	0.955	T	0.74438	-0.3665	10	0.51188	T	0.08	.	13.1659	0.59571	0.0:1.0:0.0:0.0	.	238	Q96RD3	O52E6_HUMAN	S	238;242	ENSP00000328878:A238S;ENSP00000369279:A242S	ENSP00000328878:A238S	A	-	1	0	OR52E6	5818992	0.998000	0.40836	0.504000	0.27639	0.080000	0.17528	3.007000	0.49536	1.631000	0.50456	0.551000	0.68910	GCT	.	C|0.984;T|0.016		0.443	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167		A	5862416	C	A	5862416	3	1	222	1	0	0	0	0	1	0	0	0	11126	797	28	3	231	3	OR52E6	11	5862416	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	2117824	5862416	129144100	43	31727										
MS4A4A	51338	hgsc.bcm.edu	37	chr11	60059725	60059725	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tctgctgccatgacaaccatGcaaggaatggaacaggccat	10	11	1	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr11:60059725G>A	ENST00000337908.4	+	2	159	c.69G>A	c.(67-69)atG>atA	p.M23I	MS4A4A_ENST00000395016.3_Missense_Mutation_p.M4I|MS4A4A_ENST00000532114.1_Missense_Mutation_p.M23I|MS4A4A_ENST00000355131.3_Missense_Mutation_p.M4I	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	23						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						TGACAACCATGCAAGGAATGG	0.483																																					p.M23I		Atlas-SNP	.											.	MS4A4A	76	.	0			c.G69A						.						77	77	77					11																	60059725		2203	4300	6503	SO:0001583	missense	51338	exon2			AACCATGCAAGGA	AB013102	CCDS7982.1, CCDS58135.1	11q12	2012-02-28	2012-02-28		ENSG00000110079	ENSG00000110079			13371	protein-coding gene	gene with protein product		606547	"membrane-spanning 4-domains, subfamily A, member 4"	MS4A4		11245982, 11401424	Standard	NM_148975		Approved	CD20L1, MS4A7	uc001noz.3	Q96JQ5	OTTHUMG00000154949	ENST00000337908.4:c.69G>A	chr11.hg19:g.60059725G>A	ENSP00000338648:p.Met23Ile	137.0	0.0		89.0	21.0	NM_148975	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Missense_Mutation	SNP	ENST00000337908.4	hg19	CCDS7982.1	.	.	.	.	.	.	.	.	.	.	g	10.13	1.266577	0.23136	.	.	ENSG00000110079	ENST00000532114;ENST00000337908;ENST00000355131;ENST00000395016	T;T;T;T	0.18960	2.18;3.02;3.06;3.06	2.94	-0.975	0.10289	.	5.503770	0.01045	U	0.004372	T	0.12135	0.0295	N	0.20685	0.6	0.09310	N	1	B;B	0.13594	0.008;0.004	B;B	0.11329	0.006;0.002	T	0.18366	-1.0339	10	0.07030	T	0.85	-0.287	5.8453	0.18663	0.609:0.0:0.391:0.0	.	23;23	Q96JQ5-2;Q96JQ5	.;M4A4A_HUMAN	I	23;23;4;4	ENSP00000434506:M23I;ENSP00000338648:M23I;ENSP00000347252:M4I;ENSP00000378462:M4I	ENSP00000338648:M23I	M	+	3	0	MS4A4A	59816301	0.000000	0.05858	0.008000	0.14137	0.914000	0.54420	-1.416000	0.02467	-0.193000	0.10415	0.460000	0.39030	ATG	.	.		0.483	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2			A	60059725	G	A	60059725	3	1	222	1	0	0	0	0	1	0	0	0	9871	1319	46	3	75	3	MS4A4A	11	60059725	Missense_Mutation	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10	54197309	60059725	74946791	44	31728										
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101793445	101793445	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tgcagcaacaaaaaatatgtCgaaatcgagcacgtaaatat	7	7	0	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr11:101793445C>T	ENST00000263468.8	+	2	472	c.202C>T	c.(202-204)Cga>Tga	p.R68*		NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	68								p.R68*(1)		breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AAAAATATGTCGAAATCGAGC	0.303																																					p.R68X		Atlas-SNP	.											KIAA1377,NS,carcinoma,-1,3	KIAA1377	111	.	1	Substitution - Nonsense(1)	breast(1)	c.C202T						.						65	68	67					11																	101793445		2203	4299	6502	SO:0001587	stop_gained	57562	exon2			ATATGTCGAAATC	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.202C>T	chr11.hg19:g.101793445C>T	ENSP00000263468:p.Arg68*	228.0	0.0		139.0	28.0	NM_020802	Q4G0U6	Nonsense_Mutation	SNP	ENST00000263468.8	hg19	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	C	39	7.577581	0.98368	.	.	ENSG00000110318	ENST00000263468	.	.	.	5.84	4.91	0.64330	.	0.000000	0.53938	D	0.000056	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.1498	13.8959	0.63770	0.1536:0.8464:0.0:0.0	.	.	.	.	X	68	.	ENSP00000263468:R68X	R	+	1	2	KIAA1377	101298655	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	0.963000	0.29293	1.426000	0.47256	0.591000	0.81541	CGA	.	.		0.303	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		T	101793445	C	T	101793445	4	4	222	1	0	0	0	0	0	1	0	0	8236	876	31	1	208	1	KIAA1377	11	101793445	Nonsense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	41733720	101793445	33213071	45	31729										
SORL1	6653	hgsc.bcm.edu	37	chr11	121360805	121360805	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	atcatgattcaggaacatgtCaagtccttttcttggtaagt	8	7	4	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr11:121360805C>G	ENST00000260197.7	+	5	873	c.744C>G	c.(742-744)gtC>gtG	p.V248V	SORL1_ENST00000532451.1_3'UTR	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	248					cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		AGGAACATGTCAAGTCCTTTT	0.438																																					p.V248V		Atlas-SNP	.											.	SORL1	218	.	0			c.C744G						.						220	182	195					11																	121360805		2203	4299	6502	SO:0001819	synonymous_variant	6653	exon5			ACATGTCAAGTCC	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.744C>G	chr11.hg19:g.121360805C>G		88.0	0.0		82.0	19.0	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	hg19	CCDS8436.1																																																																																			.	.		0.438	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		G	121360805	C	G	121360805	2	3	222	1	0	0	0	0	0	0	0	1	14949	813	29	4		4	SORL1	11	121360805	Silent	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	19567360	121360805	13645711	46	31730										
FOXRED1	55572	hgsc.bcm.edu	37	chr11	126143301	126143301	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ctcgggctacctcttgctggCttcagaaaaggatgctgcag	12	11	2	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr11:126143301C>G	ENST00000263578.5	+	4	562	c.488C>G	c.(487-489)gCt>gGt	p.A163G	FOXRED1_ENST00000442061.2_5'UTR|FOXRED1_ENST00000532125.1_Missense_Mutation_p.A149G|FOXRED1_ENST00000534011.1_3'UTR	NM_017547.3	NP_060017.1	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing 1	163						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		CTCTTGCTGGCTTCAGAAAAG	0.577																																					p.A163G		Atlas-SNP	.											.	FOXRED1	38	.	0			c.C488G						.						74	79	77					11																	126143301		2201	4298	6499	SO:0001583	missense	55572	exon4			TGCTGGCTTCAGA		CCDS8471.1	11q24.2	2006-02-03			ENSG00000110074	ENSG00000110074			26927	protein-coding gene	gene with protein product		613622				10497265	Standard	NM_017547		Approved	H17	uc001qdi.3	Q96CU9	OTTHUMG00000165827	ENST00000263578.5:c.488C>G	chr11.hg19:g.126143301C>G	ENSP00000263578:p.Ala163Gly	56.0	0.0		61.0	9.0	NM_017547	B3KN84|B4DHU2|Q71MG0|Q9BU39|Q9UKY9	Missense_Mutation	SNP	ENST00000263578.5	hg19	CCDS8471.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.071451	0.76301	.	.	ENSG00000110074	ENST00000263578;ENST00000532125	D;D	0.85339	-1.97;-1.97	5.45	5.45	0.79879	FAD dependent oxidoreductase (1);	0.065505	0.64402	D	0.000011	D	0.93423	0.7902	M	0.85462	2.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	D	0.94097	0.7358	10	0.87932	D	0	-7.9586	19.2849	0.94067	0.0:1.0:0.0:0.0	.	149;163	Q96CU9-3;Q96CU9	.;FXRD1_HUMAN	G	163;149	ENSP00000263578:A163G;ENSP00000434178:A149G	ENSP00000263578:A163G	A	+	2	0	FOXRED1	125648511	1.000000	0.71417	0.991000	0.47740	0.180000	0.23129	6.833000	0.75334	2.547000	0.85894	0.650000	0.86243	GCT	.	.		0.577	FOXRED1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386434.1	NM_017547		G	126143301	C	G	126143301	3	3	222	1	0	0	0	0	1	0	0	0	6041	797	28	4	502	4	FOXRED1	11	126143301	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	4782496	126143301	8863215	47	31731										
ANO2	57101	hgsc.bcm.edu	37	chr12	5853336	5853336	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cacataccccacagagccatGaagatagagaagaagacggt	10	10	0	6			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr12:5853336G>A	ENST00000356134.5	-	13	1400	c.1329C>T	c.(1327-1329)ttC>ttT	p.F443F	ANO2_ENST00000327087.8_Silent_p.F442F|ANO2_ENST00000546188.1_Silent_p.F443F	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	447					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						ACAGAGCCATGAAGATAGAGA	0.542																																					p.F442F		Atlas-SNP	.											ANO2_ENST00000327087,left_upper_lobe,carcinoma,0,2	ANO2	309	.	0			c.C1326T						.						91	97	95					12																	5853336		2062	4213	6275	SO:0001819	synonymous_variant	57101	exon12			AGCCATGAAGATA	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	1183	protein-coding gene	gene with protein product	"transmembrane protein 16B (eight membrane-spanning domains)"	610109	"chromosome 12 open reading frame 3", "transmembrane protein 16B", "anoctamin 2"	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.1329C>T	chr12.hg19:g.5853336G>A		84.0	0.0		85.0	19.0	NM_020373	C4N787|Q9H847	Silent	SNP	ENST00000356134.5	hg19																																																																																				.	.		0.542	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		A	5853336	G	A	5853336	2	1	222	1	0	0	0	0	0	0	0	1	697	1281	45	3		3	ANO2	12	5853336	Silent	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10		5853336	127998559	48	31732										
ARID2	196528	hgsc.bcm.edu	37	chr12	46233237	46233237	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ctgaaattaggccacaagctAtagagcaagtccaaacccag	8	11	0	2	rs370535448		TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr12:46233237A>G	ENST00000334344.6	+	11	1628	c.1456A>G	c.(1456-1458)Ata>Gta	p.I486V	ARID2_ENST00000422737.1_Missense_Mutation_p.I337V|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Missense_Mutation_p.I96V	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	486					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GCCACAAGCTATAGAGCAAGT	0.418			"N, S, F"		hepatocellular carcinoma																																p.I486V		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.A1456G						.	A	VAL/ILE	2,4404	4.2+/-10.8	0,2,2201	200	181	187		1456	-3.5	0.9	12		187	0,8600		0,0,4300	no	missense	ARID2	NM_152641.2	29	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	benign	486/1836	46233237	2,13004	2203	4300	6503	SO:0001583	missense	196528	exon11			CAAGCTATAGAGC		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1456A>G	chr12.hg19:g.46233237A>G	ENSP00000335044:p.Ile486Val	127.0	0.0		93.0	15.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	2.500	-0.315388	0.05422	4.54E-4	0.0	ENSG00000189079	ENST00000334344;ENST00000422737;ENST00000444670	T	0.26223	1.75	5.19	-3.55	0.04639	.	0.514032	0.20612	N	0.088952	T	0.05273	0.0140	N	0.00538	-1.39	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.46816	-0.9164	10	0.02654	T	1	0.0722	13.1195	0.59318	0.5292:0.0:0.4708:0.0	.	486;337;486	Q68CP9-3;F8WCU9;Q68CP9	.;.;ARID2_HUMAN	V	486;337;96	ENSP00000335044:I486V	ENSP00000335044:I486V	I	+	1	0	ARID2	44519504	1.000000	0.71417	0.875000	0.34327	0.973000	0.67179	0.937000	0.28951	-1.016000	0.03371	-0.899000	0.02877	ATA	.	.		0.418	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		G	46233237	A	G	46233237	3	3	222	1	0	0	0	0	1	0	0	0	915	449	16	2	1498	2	ARID2	12	46233237	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	40379901	46233237	87618658	49	31733										
KRT2	3849	hgsc.bcm.edu	37	chr12	53045630	53045631	+	In_Frame_Ins	INS	-	-	CCGCCTCCAAAGCCGCTG													0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tgccacctccaaagctgctgINSccgcctccaaaaccacctcc							TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr12:53045630_53045631insCCGCCTCCAAAGCCGCTG	ENST00000309680.3	-	1	317_318	c.296_297insCAGCGGCTTTGGAGGCGG	c.(295-297)ggc>ggCAGCGGCTTTGGAGGCGGc	p.99_99G>GSGFGGG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	99	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		caaagctgctgccgcctccaaa	0.619																																					p.G99delinsGSGFGGG		Atlas-INDEL	.											.	KRT2	94	.	0			c.297_298insCAGCGGCTTTGGAGGCGG						.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.296_297insCAGCGGCTTTGGAGGCGG	chr12.hg19:g.53045630_53045631insCCGCCTCCAAAGCCGCTG	Exception_encountered	210.0	0.0		181.0	23.0	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.619	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		CCGCCTCCAAAGCCGCTG	53045631	-	CCGCCTCCAAAGCCGCTG	53045630	7	5	222	1	0	1	1	0	0	0	0	0	8466	1306	46	0	1658	0	KRT2	12	53045630	In_Frame_Ins	INS	-	TCGA-DD-AAEK-01A-11D-A40R-10	6812393	53045630	80806265	50	31734										
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100453094	100453094	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	catgtctctggaaaattggaTgtagaagattaaaattgtca	9	4	2	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr12:100453094T>C	ENST00000279907.7	-	14	2173	c.1961A>G	c.(1960-1962)cAt>cGt	p.H654R	UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.H304R	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	654										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						GAAAATTGGATGTAGAAGATT	0.303																																					p.H654R		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.A1961G						.						54	62	59					12																	100453094		2203	4300	6503	SO:0001583	missense	23074	exon14			ATTGGATGTAGAA		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.1961A>G	chr12.hg19:g.100453094T>C	ENSP00000279907:p.His654Arg	97.0	0.0		74.0	25.0	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	hg19	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	T	15.10	2.733725	0.48939	.	.	ENSG00000111647	ENST00000279907;ENST00000545232	T;T	0.12147	2.77;2.71	5.56	4.39	0.52855	.	0.050342	0.85682	D	0.000000	T	0.35856	0.0946	M	0.74258	2.255	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.10222	-1.0639	10	0.87932	D	0	-14.7995	11.8246	0.52259	0.1315:0.0:0.0:0.8685	.	654	A0JNW5	UH1BL_HUMAN	R	654;304	ENSP00000279907:H654R;ENSP00000444824:H304R	ENSP00000279907:H654R	H	-	2	0	UHRF1BP1L	98977225	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	6.102000	0.71486	0.914000	0.36822	0.528000	0.53228	CAT	.	.		0.303	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		C	100453094	T	C	100453094	3	2	222	1	0	0	0	0	1	0	0	0	16984	1464	51	2	2465	2	UHRF1BP1L	12	100453094	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	47407464	100453094	33398801	51	31735										
DCLK1	9201	hgsc.bcm.edu	37	chr13	36410249	36410249	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	atatcgttctgttattgtagCtggaatctggaagccttcct	9	8	2	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr13:36410249C>G	ENST00000360631.3	-	8	1361	c.1150G>C	c.(1150-1152)Gct>Cct	p.A384P	DCLK1_ENST00000379893.1_Missense_Mutation_p.A77P|DCLK1_ENST00000255448.4_Missense_Mutation_p.A384P			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	384					axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		GTTATTGTAGCTGGAATCTGG	0.363																																					p.A384P		Atlas-SNP	.											.	DCLK1	350	.	0			c.G1150C						.						238	223	228					13																	36410249		2203	4300	6503	SO:0001583	missense	9201	exon8			TTGTAGCTGGAAT	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1150G>C	chr13.hg19:g.36410249C>G	ENSP00000353846:p.Ala384Pro	113.0	0.0		65.0	15.0	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	hg19		.	.	.	.	.	.	.	.	.	.	C	15.52	2.858765	0.51376	.	.	ENSG00000133083	ENST00000399319;ENST00000255448;ENST00000360631;ENST00000379893;ENST00000539451	T;T;T	0.39056	1.1;1.1;1.1	6.04	6.04	0.98038	.	0.166820	0.53938	D	0.000051	T	0.33933	0.0880	N	0.19112	0.55	0.80722	D	1	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.15052	0.008;0.012;0.005	T	0.04752	-1.0929	10	0.33141	T	0.24	.	20.5948	0.99439	0.0:1.0:0.0:0.0	.	77;384;77	O15075-4;O15075-2;O15075-3	.;.;.	P	76;384;384;77;384	ENSP00000255448:A384P;ENSP00000353846:A384P;ENSP00000369223:A77P	ENSP00000255448:A384P	A	-	1	0	DCLK1	35308249	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.310000	0.59141	2.873000	0.98535	0.563000	0.77884	GCT	.	.		0.363	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		G	36410249	C	G	36410249	3	3	222	1	0	0	0	0	1	0	0	0	4293	797	28	4	1083	4	DCLK1	13	36410249	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10		36410249	78759629	52	31736										
CYSLTR2	57105	hgsc.bcm.edu	37	chr13	49281602	49281602	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gcctgctgccatttttcacaCtcagcatctgttatctgctg	7	13	4	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr13:49281602C>G	ENST00000282018.3	+	1	652	c.649C>G	c.(649-651)Ctc>Gtc	p.L217V		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	217					immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell death (GO:0010942)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteinyl leukotriene receptor activity (GO:0001631)|leukotriene receptor activity (GO:0004974)			endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)	ATTTTTCACACTCAGCATCTG	0.478																																					p.L217V		Atlas-SNP	.											.	CYSLTR2	55	.	0			c.C649G						.						103	103	103					13																	49281602		2203	4300	6503	SO:0001583	missense	57105	exon1			TTCACACTCAGCA	AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207		"GPCR / Class A : Leukotriene receptors"	18274	protein-coding gene	gene with protein product		605666				10913337, 1085123	Standard	NM_020377		Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.649C>G	chr13.hg19:g.49281602C>G	ENSP00000282018:p.Leu217Val	35.0	0.0		52.0	14.0	NM_020377	Q9HCQ2	Missense_Mutation	SNP	ENST00000282018.3	hg19	CCDS9412.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.459401	0.43736	.	.	ENSG00000152207	ENST00000282018	T	0.26518	1.73	5.89	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.105827	0.36972	N	0.002310	T	0.31136	0.0787	L	0.48362	1.52	0.32195	N	0.578609	P	0.51791	0.948	P	0.54499	0.754	T	0.19943	-1.0290	10	0.26408	T	0.33	.	8.3036	0.32029	0.2335:0.6894:0.0:0.0771	.	217	Q9NS75	CLTR2_HUMAN	V	217	ENSP00000282018:L217V	ENSP00000282018:L217V	L	+	1	0	CYSLTR2	48179603	0.999000	0.42202	0.964000	0.40570	0.678000	0.39670	4.634000	0.61325	2.793000	0.96121	0.655000	0.94253	CTC	.	.		0.478	CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1			G	49281602	C	G	49281602	3	3	222	1	0	0	0	0	1	0	0	0	4204	565	20	4	651	4	CYSLTR2	13	49281602	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	12871353	49281602	65888276	53	31737										
OLFM4	10562	hgsc.bcm.edu	37	chr13	53624695	53624695	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	catggtatgtggggttctgtAtgccacccgtactatgaaca	11	9	1	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr13:53624695A>C	ENST00000219022.2	+	5	1400	c.1322A>C	c.(1321-1323)tAt>tCt	p.Y441S		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	441	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		GGGGTTCTGTATGCCACCCGT	0.408																																					p.Y441S		Atlas-SNP	.											.	OLFM4	94	.	0			c.A1322C						.						145	129	135					13																	53624695		2203	4300	6503	SO:0001583	missense	10562	exon5			TTCTGTATGCCAC	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.1322A>C	chr13.hg19:g.53624695A>C	ENSP00000219022:p.Tyr441Ser	95.0	0.0		73.0	22.0	NM_006418	O95362|Q5VWG0|Q86T22	Missense_Mutation	SNP	ENST00000219022.2	hg19	CCDS9440.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.738931	0.89573	.	.	ENSG00000102837	ENST00000219022	D	0.95885	-3.84	5.92	5.92	0.95590	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.98403	0.9469	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99593	1.0976	10	0.87932	D	0	.	16.3604	0.83263	1.0:0.0:0.0:0.0	.	441	Q6UX06	OLFM4_HUMAN	S	441	ENSP00000219022:Y441S	ENSP00000219022:Y441S	Y	+	2	0	OLFM4	52522696	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.339000	0.96797	2.260000	0.74910	0.528000	0.53228	TAT	.	.		0.408	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418		C	53624695	A	C	53624695	3	2	222	1	0	0	0	0	1	0	0	0	10864	449	16	5	1340	5	OLFM4	13	53624695	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	4343093	53624695	61545183	54	31738										
TGDS	23483	hgsc.bcm.edu	37	chr13	95235445	95235445	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ttaccaaaacgtgagtgccaTaaacattaacataggtaaac	6	8	0	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr13:95235445T>C	ENST00000261296.5	-	5	479	c.359A>G	c.(358-360)tAt>tGt	p.Y120C	TGDS_ENST00000498294.1_5'UTR	NM_014305.2	NP_055120.1	O95455	TGDS_HUMAN	TDP-glucose 4,6-dehydratase	120					nucleotide-sugar metabolic process (GO:0009225)		coenzyme binding (GO:0050662)|dTDP-glucose 4,6-dehydratase activity (GO:0008460)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					GTGAGTGCCATAAACATTAAC	0.383																																					p.Y120C		Atlas-SNP	.											.	TGDS	24	.	0			c.A359G						.						128	107	114					13																	95235445		2203	4300	6503	SO:0001583	missense	23483	exon5			GTGCCATAAACAT	AF048686	CCDS9471.1	13q32.1	2012-02-22			ENSG00000088451	ENSG00000088451	4.2.1.46	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	20324	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 2E, member 1"					19027726	Standard	NM_014305		Approved	TDPGD, SDR2E1	uc001vlw.3	O95455	OTTHUMG00000046308	ENST00000261296.5:c.359A>G	chr13.hg19:g.95235445T>C	ENSP00000261296:p.Tyr120Cys	66.0	0.0		78.0	29.0	NM_014305	Q05DQ3|Q2TU31|Q5T3Z2|Q9H1T9	Missense_Mutation	SNP	ENST00000261296.5	hg19	CCDS9471.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.040741	0.75732	.	.	ENSG00000088451	ENST00000261296	D	0.93189	-3.18	5.61	5.61	0.85477	NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1);	0.114581	0.64402	D	0.000014	D	0.96160	0.8748	M	0.70275	2.135	0.58432	D	0.999994	D	0.76494	0.999	D	0.70716	0.97	D	0.96623	0.9461	10	0.87932	D	0	.	16.0994	0.81158	0.0:0.0:0.0:1.0	.	120	O95455	TGDS_HUMAN	C	120	ENSP00000261296:Y120C	ENSP00000261296:Y120C	Y	-	2	0	TGDS	94033446	1.000000	0.71417	0.992000	0.48379	0.990000	0.78478	6.112000	0.71547	2.261000	0.74972	0.533000	0.62120	TAT	.	.		0.383	TGDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106904.2	NM_014305		C	95235445	T	C	95235445	3	2	222	1	0	0	0	0	1	0	0	0	15829	1406	49	2	725	2	TGDS	13	95235445	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	41610750	95235445	19934433	55	31739										
TOX4	9878	hgsc.bcm.edu	37	chr14	21964732	21964732	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tcttggcctgggtagcctctAgaaattcaaacacagtggtg	11	9	3	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr14:21964732A>G	ENST00000405508.1	+	10	2110	c.1834A>G	c.(1834-1836)Aga>Gga	p.R612G	TOX4_ENST00000448790.2_Missense_Mutation_p.R589G|TOX4_ENST00000262709.3_Missense_Mutation_p.R612G			O94842	TOX4_HUMAN	TOX high mobility group box family member 4	612						chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)			large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		GGTAGCCTCTAGAAATTCAAA	0.388																																					p.R612G		Atlas-SNP	.											.	TOX4	50	.	0			c.A1834G						.						145	134	138					14																	21964732		2203	4300	6503	SO:0001583	missense	9878	exon9			GCCTCTAGAAATT	AB018280	CCDS32043.1	14q11.2	2007-03-20	2007-03-20	2007-03-20	ENSG00000092203	ENSG00000092203			20161	protein-coding gene	gene with protein product		614032	"chromosome 14 open reading frame 92", "KIAA0737"	C14orf92, KIAA0737			Standard	NM_014828		Approved	LCP1	uc001waz.3	O94842	OTTHUMG00000150278	ENST00000405508.1:c.1834A>G	chr14.hg19:g.21964732A>G	ENSP00000385102:p.Arg612Gly	78.0	0.0		74.0	13.0	NM_014828	B4DPY8|B4DSM0|E7EV69	Missense_Mutation	SNP	ENST00000405508.1	hg19	CCDS32043.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.401772	0.62288	.	.	ENSG00000092203	ENST00000405508;ENST00000262709;ENST00000448790;ENST00000545559	T;T;T	0.15952	2.38;2.38;2.39	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.26702	0.0653	L	0.35854	1.095	0.46874	D	0.999239	P;P	0.48350	0.909;0.909	P;P	0.60789	0.879;0.879	T	0.01294	-1.1393	10	0.87932	D	0	.	9.1536	0.36978	0.8163:0.1836:0.0:0.0	.	589;612	B4DPY8;O94842	.;TOX4_HUMAN	G	612;612;589;540	ENSP00000385102:R612G;ENSP00000262709:R612G;ENSP00000393080:R589G	ENSP00000262709:R612G	R	+	1	2	TOX4	21034572	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.616000	0.46376	2.234000	0.73211	0.528000	0.53228	AGA	.	.		0.388	TOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317287.2	NM_014828		G	21964732	A	G	21964732	3	3	222	1	0	0	0	0	1	0	0	0	16395	412	15	2	1868	2	TOX4	14	21964732	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10		21964732	85384808	56	31740										
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102552400	102552400	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gtataaggttaatatgcagcTctttcccagagtctaattta	7	7	2	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr14:102552400T>A	ENST00000216281.8	-	3	429	c.224A>T	c.(223-225)gAg>gTg	p.E75V	HSP90AA1_ENST00000441629.2_Intron|HSP90AA1_ENST00000334701.7_Missense_Mutation_p.E197V	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	75					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	AATATGCAGCTCTTTCCCAGA	0.388																																					p.E197V		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.A590T						.						70	71	71					14																	102552400		2203	4300	6503	SO:0001583	missense	3320	exon4			TGCAGCTCTTTCC	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.224A>T	chr14.hg19:g.102552400T>A	ENSP00000216281:p.Glu75Val	77.0	0.0		66.0	9.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Missense_Mutation	SNP	ENST00000216281.8	hg19	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	T	18.40	3.616046	0.66672	.	.	ENSG00000080824	ENST00000216281;ENST00000334701;ENST00000553585	T;T;T	0.56941	2.04;2.04;0.43	3.79	3.79	0.43588	ATPase-like, ATP-binding domain (4);	0.213930	0.38548	U	0.001642	T	0.65354	0.2683	H	0.94964	3.605	0.80722	D	1	P;B	0.35208	0.49;0.083	B;B	0.37144	0.242;0.182	T	0.74743	-0.3562	10	0.87932	D	0	.	12.8341	0.57763	0.0:0.0:0.0:1.0	.	197;75	P07900-2;P07900	.;HS90A_HUMAN	V	75;197;75	ENSP00000216281:E75V;ENSP00000335153:E197V;ENSP00000450712:E75V	ENSP00000216281:E75V	E	-	2	0	HSP90AA1	101622153	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	5.935000	0.70145	1.500000	0.48636	0.467000	0.42956	GAG	.	.		0.388	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		A	102552400	T	A	102552400	3	1	222	1	0	0	0	0	1	0	0	0	7410	1551	54	4	2010	4	HSP90AA1	14	102552400	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	80587668	102552400	4797140	57	31741										
HERC1	8925	hgsc.bcm.edu	37	chr15	63920927	63920927	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ccatgcagcactgtggcagcGgccagccgagatctgccgaa	13	14	1	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr15:63920927G>A	ENST00000443617.2	-	70	13141	c.13054C>T	c.(13054-13056)Cgc>Tgc	p.R4352C		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4352					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CTGTGGCAGCGGCCAGCCGAG	0.517																																					p.R4352C		Atlas-SNP	.											HERC1_ENST00000443617,colon,carcinoma,0,2	HERC1	624	.	0			c.C13054T						.						83	88	87					15																	63920927		1960	4170	6130	SO:0001583	missense	8925	exon70			GGCAGCGGCCAGC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13054C>T	chr15.hg19:g.63920927G>A	ENSP00000390158:p.Arg4352Cys	66.0	0.0		71.0	3.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.735138	0.89482	.	.	ENSG00000103657	ENST00000443617	D	0.84944	-1.92	5.89	5.89	0.94794	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.64402	D	0.000001	D	0.87281	0.6138	N	0.21282	0.65	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88359	0.2986	10	0.72032	D	0.01	.	15.0168	0.71591	0.0:0.0:0.8577:0.1423	.	4352	Q15751	HERC1_HUMAN	C	4352	ENSP00000390158:R4352C	ENSP00000390158:R4352C	R	-	1	0	HERC1	61707980	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	7.795000	0.85887	2.781000	0.95711	0.555000	0.69702	CGC	.	.		0.517	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63920927	G	A	63920927	3	1	222	1	0	0	0	0	1	0	0	0	7066	1116	39	1	1567	1	HERC1	15	63920927	Missense_Mutation	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10		63920927	38610465	58	31742										
PTPN9	5780	hgsc.bcm.edu	37	chr15	75798259	75798283	+	Frame_Shift_Del	DEL	TCAATTTTGACGTACCCACCCAGGT	TCAATTTTGACGTACCCACCCAGGT	-													0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ggaaattccaagtggcgagaTcaattttgacgtacccaccc					rs371087693|rs551948447|rs530559093	byFrequency	TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	TCAATTTTGACGTACCCACCCAGGT	TCAATTTTGACGTACCCACCCAGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr15:75798259_75798283delTCAATTTTGACGTACCCACCCAGGT	ENST00000306726.2	-	7	1213_1237	c.701_725delACCTGGGTGGGTACGTCAAAATTGA	c.(700-726)aacctgggtgggtacgtcaaaattgatfs	p.NLGGYVKID234fs	PTPN9_ENST00000564970.1_5'Flank	NM_002833.2	NP_002824.1	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type 9	234	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGTGGCGAGATCAATTTTGACGTACCCACCCAGGTTTTCTGGAAG	0.502																																					p.234_242del		Atlas-INDEL	.											.	PTPN9	53	.	0			c.702_726del						.																																			SO:0001589	frameshift_variant	5780	exon7			.		CCDS10280.1	15q23	2011-06-09			ENSG00000169410	ENSG00000169410		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9661	protein-coding gene	gene with protein product		600768				1557404	Standard	NM_002833		Approved	MEG2	uc002bal.3	P43378	OTTHUMG00000142838	ENST00000306726.2:c.701_725delACCTGGGTGGGTACGTCAAAATTGA	chr15.hg19:g.75798259_75798283delTCAATTTTGACGTACCCACCCAGGT	ENSP00000303554:p.Asn234fs	163.0	0.0		175.0	12.0	NM_002833	Q53XR9	Frame_Shift_Del	DEL	ENST00000306726.2	hg19	CCDS10280.1																																																																																			.	.		0.502	PTPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286474.1			-	75798283	TCAATTTTGACGTACCCACCCAGGT	-	75798259	7	5	222	1	0	1	0	1	0	0	0	0	12809	1435	50	0	1084	0	PTPN9	15	75798259	Frame_Shift_Del	DEL	TCAATTTTGACGTACCCACCCAGGT	TCGA-DD-AAEK-01A-11D-A40R-10	11877332	75798259	26733133	59	31743										
MEF2A	4205	hgsc.bcm.edu	37	chr15	100252747	100252747	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gcagcagcagcagcagccgcCgccaccaccgcagccccagc	11	21	0	0	rs369815961		TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr15:100252747C>A	ENST00000557785.1	+	11	1614	c.1265C>A	c.(1264-1266)cCg>cAg	p.P422Q	MEF2A_ENST00000449277.2_Missense_Mutation_p.P354Q|MEF2A_ENST00000558812.1_Missense_Mutation_p.P362Q|MEF2A_ENST00000338042.6_Missense_Mutation_p.P431Q|MEF2A_ENST00000453228.2_Missense_Mutation_p.P422Q|MEF2A_ENST00000557942.1_Missense_Mutation_p.P430Q|MEF2A_ENST00000354410.5_Missense_Mutation_p.P424Q	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	432	Gln/Pro-rich.				apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)	p.P432Q(1)|p.P422Q(1)|p.P424Q(1)		endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			cagcagcCGCCGCCACCACCG	0.637																																					p.P424Q		Atlas-SNP	.											MEF2A_ENST00000453228,NS,carcinoma,-1,3	MEF2A	138	.	3	Substitution - Missense(3)	lung(3)	c.C1271A						.						5	8	7					15																	100252747		1639	3328	4967	SO:0001583	missense	4205	exon11			AGCCGCCGCCACC		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"Myocyte enhancer factors"	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.1265C>A	chr15.hg19:g.100252747C>A	ENSP00000453441:p.Pro422Gln	67.0	0.0		58.0	6.0	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Missense_Mutation	SNP	ENST00000557785.1	hg19	CCDS53978.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.687083	0.00738	.	.	ENSG00000068305	ENST00000453228;ENST00000354410;ENST00000338042;ENST00000449277	T;T;T	0.59224	0.29;0.28;0.29	5.55	-1.61	0.08399	.	0.480375	0.14766	N	0.299691	T	0.49541	0.1563	N	0.22421	0.69	0.09310	N	1	P;B;B;B;P;B	0.46512	0.808;0.001;0.001;0.003;0.879;0.003	P;B;B;B;P;B	0.50934	0.452;0.002;0.002;0.012;0.654;0.012	T	0.50709	-0.8796	10	0.15952	T	0.53	.	16.1596	0.81693	0.653:0.347:0.0:0.0	.	432;362;343;422;424;430	Q02078;B4DFQ7;Q7Z6C9;Q02078-6;Q02078-5;Q02078-2	MEF2A_HUMAN;.;.;.;.;.	Q	422;424;431;362	ENSP00000404110:P422Q;ENSP00000346389:P424Q;ENSP00000337202:P431Q	ENSP00000337202:P431Q	P	+	2	0	MEF2A	98070270	0.993000	0.37304	0.000000	0.03702	0.015000	0.08874	0.872000	0.28037	-0.125000	0.11703	-0.516000	0.04426	CCG	.	.		0.637	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1			A	100252747	C	A	100252747	3	1	222	1	0	0	0	0	1	0	0	0	9464	652	23	1	1469	1	MEF2A	15	100252747	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	24454488	100252747	2278645	60	31744										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2814150	2814150	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gtattcaaagacacacttagAaccccgccaagggaaagaag	9	10	1	3			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr16:2814150A>C	ENST00000301740.8	+	11	4170	c.3621A>C	c.(3619-3621)agA>agC	p.R1207S		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1207	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						ACACACTTAGAACCCCGCCAA	0.458																																					p.R1207S		Atlas-SNP	.											.	SRRM2	263	.	0			c.A3621C						.						104	108	107					16																	2814150		2198	4300	6498	SO:0001583	missense	23524	exon11			ACTTAGAACCCCG	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.3621A>C	chr16.hg19:g.2814150A>C	ENSP00000301740:p.Arg1207Ser	127.0	0.0		110.0	16.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	A	0.782	-0.762063	0.02996	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	D	0.92647	-3.08	5.82	4.71	0.59529	.	0.530522	0.19876	N	0.104093	D	0.86965	0.6060	L	0.40543	1.245	0.09310	N	1	B	0.13594	0.008	B	0.16722	0.016	T	0.78130	-0.2324	10	0.62326	D	0.03	-0.28	7.3106	0.26473	0.8734:0.0:0.1266:0.0	.	1207	Q9UQ35	SRRM2_HUMAN	S	1207;1207;459	ENSP00000301740:R1207S	ENSP00000301740:R1207S	R	+	3	2	SRRM2	2754151	0.000000	0.05858	0.018000	0.16275	0.010000	0.07245	0.332000	0.19751	2.228000	0.72767	0.533000	0.62120	AGA	.	.		0.458	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			C	2814150	A	C	2814150	3	2	222	1	0	0	0	0	1	0	0	0	15184	243	9	5	3659	5	SRRM2	16	2814150	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10		2814150	87540603	61	31745										
SF3B3	23450	hgsc.bcm.edu	37	chr16	70562901	70562901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tcggtgttatccggtcactcAtggcctttaggctgacaggt	12	10	2	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr16:70562901A>G	ENST00000302516.5	+	3	407	c.196A>G	c.(196-198)Atg>Gtg	p.M66V	SNORD111B_ENST00000408587.1_RNA	NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	66					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				CCGGTCACTCATGGCCTTTAG	0.478																																					p.M66V		Atlas-SNP	.											.	SF3B3	99	.	0			c.A196G						.						134	118	123					16																	70562901		2198	4300	6498	SO:0001583	missense	23450	exon3			TCACTCATGGCCT	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.196A>G	chr16.hg19:g.70562901A>G	ENSP00000305790:p.Met66Val	191.0	0.0		137.0	25.0	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	hg19	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	A	13.51	2.260243	0.39995	.	.	ENSG00000189091	ENST00000302516;ENST00000310750	T	0.05081	3.5	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.10937	0.0267	M	0.68317	2.08	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.02385	-1.1167	10	0.44086	T	0.13	.	15.7649	0.78117	1.0:0.0:0.0:0.0	.	66	Q15393	SF3B3_HUMAN	V	66	ENSP00000305790:M66V	ENSP00000305790:M66V	M	+	1	0	SF3B3	69120402	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	9.339000	0.96797	2.120000	0.65058	0.459000	0.35465	ATG	.	.		0.478	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		G	70562901	A	G	70562901	3	3	222	1	0	0	0	0	1	0	0	0	14167	217	8	2	202	2	SF3B3	16	70562901	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10	67748751	70562901	19791852	62	31746										
PLCG2	5336	hgsc.bcm.edu	37	chr16	81922861	81922861	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tgcgtgaaactgctgagcctTtcttgtttgtggatgaggtg	14	6	1	3			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr16:81922861T>A	ENST00000359376.3	+	10	1064	c.850T>A	c.(850-852)Ttc>Atc	p.F284I		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	284					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						TGCTGAGCCTTTCTTGTTTGT	0.448																																					p.F284I		Atlas-SNP	.											.	PLCG2	276	.	0			c.T850A						.						180	174	176					16																	81922861		2037	4196	6233	SO:0001583	missense	5336	exon10			GAGCCTTTCTTGT		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.850T>A	chr16.hg19:g.81922861T>A	ENSP00000352336:p.Phe284Ile	119.0	0.0		102.0	22.0	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	hg19	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.328517	0.60743	.	.	ENSG00000197943	ENST00000359376	T	0.29142	1.58	5.09	5.09	0.68999	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);	0.173944	0.52532	D	0.000068	T	0.24160	0.0585	L	0.27053	0.805	0.46631	D	0.999131	B;P	0.35656	0.079;0.514	B;B	0.35182	0.065;0.197	T	0.05084	-1.0907	10	0.42905	T	0.14	.	14.8381	0.70201	0.0:0.0:0.0:1.0	.	151;284	B4E3H3;P16885	.;PLCG2_HUMAN	I	284	ENSP00000352336:F284I	ENSP00000352336:F284I	F	+	1	0	PLCG2	80480362	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	5.440000	0.66563	2.046000	0.60703	0.460000	0.39030	TTC	.	.		0.448	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			A	81922861	T	A	81922861	3	1	222	1	0	0	0	0	1	0	0	0	12045	1841	64	4	884	4	PLCG2	16	81922861	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	11359960	81922861	8431892	63	31747										
NLGN2	57555	hgsc.bcm.edu	37	chr17	7318376	7318376	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ggctgctggcagccaaggtgGgctgtgaccgagaggacagc	18	10	0	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr17:7318376G>T	ENST00000302926.2	+	5	1019	c.946G>T	c.(946-948)Ggc>Tgc	p.G316C	NLGN2_ENST00000575301.1_Missense_Mutation_p.G316C	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	316					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				AGCCAAGGTGGGCTGTGACCG	0.652																																					p.G316C		Atlas-SNP	.											.	NLGN2	61	.	0			c.G946T						.						42	41	41					17																	7318376		2203	4300	6503	SO:0001583	missense	57555	exon5			AAGGTGGGCTGTG	AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.946G>T	chr17.hg19:g.7318376G>T	ENSP00000305288:p.Gly316Cys	98.0	0.0		94.0	39.0	NM_020795	Q9P2I1	Missense_Mutation	SNP	ENST00000302926.2	hg19	CCDS11103.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.625597	0.66901	.	.	ENSG00000169992	ENST00000302926	T	0.69306	-0.39	5.17	5.17	0.71159	Carboxylesterase, type B (1);	0.000000	0.85682	D	0.000000	D	0.87478	0.6187	H	0.96365	3.81	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.91035	0.4867	10	0.87932	D	0	.	16.2209	0.82257	0.0:0.0:1.0:0.0	.	316	Q8NFZ4	NLGN2_HUMAN	C	316	ENSP00000305288:G316C	ENSP00000305288:G316C	G	+	1	0	NLGN2	7259100	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.612000	0.74187	2.711000	0.92665	0.561000	0.74099	GGC	.	.		0.652	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795		T	7318376	G	T	7318376	3	4	222	1	0	0	0	0	1	0	0	0	10471	1232	43	3	964	3	NLGN2	17	7318376	Missense_Mutation	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10		7318376	73876834	64	31748										
TRIM16	10626	hgsc.bcm.edu	37	chr17	15539431	15539431	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tccatctcggcactcctgtaCtccaggtgggccttgatacc	9	15	1	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr17:15539431C>T	ENST00000578237.1	-	8	1623	c.768G>A	c.(766-768)gaG>gaA	p.E256E	TRIM16_ENST00000581224.1_5'Flank|RP11-385D13.1_ENST00000455584.2_Silent_p.E256E|TRIM16_ENST00000577886.1_Silent_p.E40E|TRIM16_ENST00000416464.2_Silent_p.E126E|TRIM16_ENST00000336708.7_Silent_p.E256E|TRIM16_ENST00000579219.1_Silent_p.E40E			O95361	TRI16_HUMAN	tripartite motif containing 16	256					histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		CACTCCTGTACTCCAGGTGGG	0.592																																					p.E256E		Atlas-SNP	.											.	TRIM16	45	.	0			c.G768A						.						119	98	106					17																	15539431		2189	4298	6487	SO:0001819	synonymous_variant	10626	exon6			CCTGTACTCCAGG	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"Tripartite motif containing / Tripartite motif containing"	17241	protein-coding gene	gene with protein product	"estrogen-responsive B box protein"	609505	"tripartite motif-containing 16"			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.768G>A	chr17.hg19:g.15539431C>T		112.0	0.0		115.0	32.0	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Silent	SNP	ENST00000578237.1	hg19	CCDS11171.1	.	.	.	.	.	.	.	.	.	.	c	8.498	0.863660	0.17250	.	.	ENSG00000251537	ENST00000455584	.	.	.	3.97	3.0	0.34707	.	.	.	.	.	T	0.58921	0.2156	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54957	-0.8215	4	.	.	.	.	9.4618	0.38789	0.0:0.8942:0.0:0.1058	.	.	.	.	N	271	.	.	S	-	2	0	RP11-385D13.1	15480156	1.000000	0.71417	0.991000	0.47740	0.878000	0.50629	2.227000	0.42972	1.034000	0.39945	0.555000	0.69702	AGT	.	.		0.592	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470		T	15539431	C	T	15539431	2	4	222	1	0	0	0	0	0	0	0	1	16506	564	20	3		3	TRIM16	17	15539431	Silent	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	8221055	15539431	65655779	65	31749										
HOXB2	3212	hgsc.bcm.edu	37	chr17	46620510	46620510	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ggaaaaagggaccgggctgtCgagagaaccctgtaggctag	16	8	0	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr17:46620510C>A	ENST00000330070.4	-	2	2158	c.991G>T	c.(991-993)Gac>Tac	p.D331Y	HOXB2_ENST00000504772.3_5'Flank|HOXB-AS1_ENST00000508688.1_RNA|HOXB-AS1_ENST00000504972.3_RNA|HOXB-AS1_ENST00000435312.1_RNA	NM_002145.3	NP_002136.1	P14652	HXB2_HUMAN	homeobox B2	331					anterior/posterior pattern specification (GO:0009952)|blood circulation (GO:0008015)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|neural nucleus development (GO:0048857)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	11						ACCGGGCTGTCGAGAGAACCC	0.582																																					p.D331Y		Atlas-SNP	.											.	HOXB2	23	.	0			c.G991T						.						75	79	78					17																	46620510		2203	4300	6503	SO:0001583	missense	3212	exon2			GGCTGTCGAGAGA		CCDS11527.1	17q21.32	2012-02-22	2005-12-22		ENSG00000173917	ENSG00000173917		"Homeoboxes / ANTP class : HOXL subclass"	5113	protein-coding gene	gene with protein product		142967	"homeo box B2"	HOX2, HOX2H		1973146, 1358459	Standard	XM_005257276		Approved		uc002inm.3	P14652	OTTHUMG00000159930	ENST00000330070.4:c.991G>T	chr17.hg19:g.46620510C>A	ENSP00000331741:p.Asp331Tyr	79.0	0.0		83.0	13.0	NM_002145	P10913|P17485	Missense_Mutation	SNP	ENST00000330070.4	hg19	CCDS11527.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.715097	0.48622	.	.	ENSG00000173917	ENST00000330070	T	0.11930	2.73	5.49	2.39	0.29439	.	0.107197	0.64402	D	0.000009	T	0.13628	0.0330	L	0.42245	1.32	0.48185	D	0.999601	P	0.44776	0.843	P	0.44673	0.457	T	0.02320	-1.1177	10	0.87932	D	0	.	7.0379	0.25002	0.0:0.5886:0.2665:0.1449	.	331	P14652	HXB2_HUMAN	Y	331	ENSP00000331741:D331Y	ENSP00000331741:D331Y	D	-	1	0	HOXB2	43975509	0.938000	0.31826	0.125000	0.21846	0.659000	0.38960	1.988000	0.40697	0.279000	0.22186	0.655000	0.94253	GAC	.	.		0.582	HOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358384.2			A	46620510	C	A	46620510	3	1	222	1	0	0	0	0	1	0	0	0	7310	884	31	1	83	1	HOXB2	17	46620510	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	31081079	46620510	34574700	66	31750										
CASKIN2	57513	hgsc.bcm.edu	37	chr17	73501979	73501979	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tgtccagcgccgtctggttaTacgtattccggatgttcacg	11	11	2	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr17:73501979T>C	ENST00000321617.3	-	9	1344	c.758A>G	c.(757-759)tAt>tGt	p.Y253C	CASKIN2_ENST00000433559.2_Missense_Mutation_p.Y171C|CASKIN2_ENST00000581870.1_Missense_Mutation_p.Y253C	NM_020753.3	NP_065804.2	Q8WXE0	CSKI2_HUMAN	CASK interacting protein 2	253						cytoplasm (GO:0005737)				endometrium(1)|kidney(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGTCTGGTTATACGTATTCCG	0.572																																					p.P253R		Atlas-SNP	.											.	CASKIN2	66	.	0			c.C758G						.						132	105	114					17																	73501979		2202	4299	6501	SO:0001583	missense	57513	exon9			TGGTTATACGTAT	AB032965	CCDS11723.1, CCDS45775.1	17q25.1	2014-09-04			ENSG00000177303	ENSG00000177303		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	18200	protein-coding gene	gene with protein product		612185				12040031	Standard	NM_020753		Approved	KIAA1139, FLJ21609, ANKS5B	uc002joc.4	Q8WXE0	OTTHUMG00000179683	ENST00000321617.3:c.758A>G	chr17.hg19:g.73501979T>C	ENSP00000325355:p.Tyr253Cys	39.0	0.0		59.0	16.0	NM_020753	B4DTT3|B7Z9H1|Q7LG69|Q9ULT1	Missense_Mutation	SNP	ENST00000321617.3	hg19	CCDS11723.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.449017	0.84101	.	.	ENSG00000177303	ENST00000321617;ENST00000433559	T;T	0.53857	0.6;0.6	5.53	5.53	0.82687	Ankyrin repeat-containing domain (3);	0.000000	0.42294	D	0.000730	T	0.63260	0.2496	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	T	0.65335	-0.6193	10	0.54805	T	0.06	.	15.6478	0.77068	0.0:0.0:0.0:1.0	.	171;253	Q8WXE0-2;Q8WXE0	.;CSKI2_HUMAN	C	253;171	ENSP00000325355:Y253C;ENSP00000406963:Y171C	ENSP00000325355:Y253C	Y	-	2	0	CASKIN2	71013574	1.000000	0.71417	0.130000	0.21974	0.592000	0.36648	7.945000	0.87732	2.100000	0.63781	0.533000	0.62120	TAT	.	.		0.572	CASKIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447609.1	NM_020753		C	73501979	T	C	73501979	3	2	222	1	0	0	0	0	1	0	0	0	2669	1406	49	2	2898	2	CASKIN2	17	73501979	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	26881469	73501979	7693231	67	31751										
FBF1	85302	hgsc.bcm.edu	37	chr17	73922395	73922395	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	cctatctgcctcttctctgcTttggggctgtctccaaaccc	7	16	4	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr17:73922395T>C	ENST00000586717.1	-	10	939	c.666A>G	c.(664-666)aaA>aaG	p.K222K	FBF1_ENST00000319129.5_Silent_p.K222K|FBF1_ENST00000389570.4_Silent_p.K222K			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	222					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TCTTCTCTGCTTTGGGGCTGT	0.532																																					p.K222K		Atlas-SNP	.											.	FBF1	48	.	0			c.A666G						.						33	35	35					17																	73922395		1931	4133	6064	SO:0001819	synonymous_variant	85302	exon10			CTCTGCTTTGGGG	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.666A>G	chr17.hg19:g.73922395T>C		31.0	0.0		49.0	6.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	hg19																																																																																				.	.		0.532	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		C	73922395	T	C	73922395	2	2	222	1	0	0	0	0	0	0	0	1	5703	1606	56	2		2	FBF1	17	73922395	Silent	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10	420416	73922395	7272815	68	31752										
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56001068	56001068	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	agcaaagagaaccctcctcaAggttgaggtcatgcagtgtc	11	10	2	2			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr18:56001068A>C	ENST00000400345.3	+	12	1292	c.1009A>C	c.(1009-1011)Agg>Cgg	p.R337R	NEDD4L_ENST00000256832.7_Silent_p.R216R|NEDD4L_ENST00000356462.6_Silent_p.R337R|NEDD4L_ENST00000382850.4_Silent_p.R337R|NEDD4L_ENST00000456986.1_Silent_p.R216R|NEDD4L_ENST00000357895.5_Silent_p.R329R|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000586263.1_Silent_p.R329R|NEDD4L_ENST00000435432.2_Silent_p.R216R|NEDD4L_ENST00000256830.9_Silent_p.R337R|NEDD4L_ENST00000431212.2_Silent_p.R216R|NEDD4L_ENST00000456173.2_Silent_p.R216R	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	337					cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						ACCCTCCTCAAGGTTGAGGTC	0.438																																					p.R337R		Atlas-SNP	.											.	NEDD4L	126	.	0			c.A1009C						.						100	97	98					18																	56001068		1947	4144	6091	SO:0001819	synonymous_variant	23327	exon12			TCCTCAAGGTTGA	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1009A>C	chr18.hg19:g.56001068A>C		97.0	0.0		91.0	15.0	NM_015277	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	hg19	CCDS45872.1																																																																																			.	.		0.438	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			C	56001068	A	C	56001068	2	2	222	1	0	0	0	0	0	0	0	1	10320	63	3	5		5	NEDD4L	18	56001068	Silent	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10		56001068	22076180	69	31753										
FBN3	84467	hgsc.bcm.edu	37	chr19	8196669	8196669	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	ggagccctcggtgttggtacAgtggccgttcacgcagatgc	15	11	1	1			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr19:8196669A>G	ENST00000600128.1	-	15	2173	c.1759T>C	c.(1759-1761)Tgt>Cgt	p.C587R	FBN3_ENST00000601739.1_Missense_Mutation_p.C587R|FBN3_ENST00000270509.2_Missense_Mutation_p.C587R			Q75N90	FBN3_HUMAN	fibrillin 3	587	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GTGTTGGTACAGTGGCCGTTC	0.677																																					p.C587R		Atlas-SNP	.											.	FBN3	300	.	0			c.T1759C						.						24	25	25					19																	8196669		2202	4300	6502	SO:0001583	missense	84467	exon14			TGGTACAGTGGCC		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.1759T>C	chr19.hg19:g.8196669A>G	ENSP00000470498:p.Cys587Arg	57.0	0.0		76.0	14.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	a	12.93	2.085061	0.36758	.	.	ENSG00000142449	ENST00000270509	D	0.99445	-5.91	2.92	2.92	0.33932	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.99764	0.9904	H	0.99777	4.77	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.97189	0.9856	10	0.87932	D	0	.	10.9744	0.47456	1.0:0.0:0.0:0.0	.	587	Q75N90	FBN3_HUMAN	R	587	ENSP00000270509:C587R	ENSP00000270509:C587R	C	-	1	0	FBN3	8102669	1.000000	0.71417	0.306000	0.25113	0.030000	0.12068	7.956000	0.87863	0.961000	0.38030	0.155000	0.16302	TGT	.	.		0.677	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		G	8196669	A	G	8196669	3	3	222	1	0	0	0	0	1	0	0	0	5712	188	7	2	6870	2	FBN3	19	8196669	Missense_Mutation	SNP	A	TCGA-DD-AAEK-01A-11D-A40R-10		8196669	50932314	70	31754										
HAPLN4	404037	hgsc.bcm.edu	37	chr19	19369378	19369378	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gcgtcgtagcgttcctcggcGttatggcgatacccgtagtt	13	11	0	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr19:19369378G>A	ENST00000291481.7	-	4	834	c.771C>T	c.(769-771)aaC>aaT	p.N257N	AC138430.4_ENST00000586064.2_RNA	NM_023002.2	NP_075378.1	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4	257	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)	16			Epithelial(12;0.00575)		Hyaluronan(DB08818)	GTTCCTCGGCGTTATGGCGAT	0.701																																					p.N257N		Atlas-SNP	.											.	HAPLN4	44	.	0			c.C771T						.						76	62	67					19																	19369378		2203	4300	6503	SO:0001819	synonymous_variant	404037	exon4			CTCGGCGTTATGG	AB107883	CCDS12398.1	19p13.1	2013-01-11						"Immunoglobulin superfamily / V-set domain containing"	31357	protein-coding gene	gene with protein product	"brain link protein 2"					12663660	Standard	NM_023002		Approved	BRAL2, KIAA1926	uc002nmb.3	Q86UW8		ENST00000291481.7:c.771C>T	chr19.hg19:g.19369378G>A		89.0	0.0		85.0	33.0	NM_023002	A5PKW5|Q96PW2	Silent	SNP	ENST00000291481.7	hg19	CCDS12398.1																																																																																			.	.		0.701	HAPLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460117.2	NM_023002		A	19369378	G	A	19369378	2	1	222	1	0	0	0	0	0	0	0	1	6966	1136	40	1		1	HAPLN4	19	19369378	Silent	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10	11172709	19369378	39759605	71	31755										
PNMAL1	55228	hgsc.bcm.edu	37	chr19	46974172	46974172	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gaggaccccattcaaggtctCctcaatttctgcctgcccac	7	16	4	0			TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr19:46974172C>T	ENST00000313683.10	-	2	426	c.121G>A	c.(121-123)Gag>Aag	p.E41K	PNMAL1_ENST00000602246.1_Missense_Mutation_p.E41K|PNMAL1_ENST00000438932.2_Missense_Mutation_p.E41K	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	41										cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		ttcaaggtctcctcaatttct	0.542																																					p.E41K		Atlas-SNP	.											PNMAL1_ENST00000438932,caecum,carcinoma,+2,2	PNMAL1	87	.	0			c.G121A						.						81	68	72					19																	46974172		2203	4300	6503	SO:0001583	missense	55228	exon2			AGGTCTCCTCAAT	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"Paraneoplastic Ma antigens"	25578	protein-coding gene	gene with protein product			"PNMA-like 1"			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.121G>A	chr19.hg19:g.46974172C>T	ENSP00000318131:p.Glu41Lys	48.0	0.0		61.0	14.0	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Missense_Mutation	SNP	ENST00000313683.10	hg19	CCDS33059.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611023	0.87258	.	.	ENSG00000182013	ENST00000438932;ENST00000313683;ENST00000417103	T;T	0.14516	2.5;2.5	3.94	3.94	0.45596	.	0.000000	0.41396	D	0.000895	T	0.33818	0.0876	M	0.72353	2.195	0.35297	D	0.782704	D;P	0.89917	1.0;0.746	D;B	0.83275	0.996;0.385	T	0.41752	-0.9491	10	0.56958	D	0.05	-20.0036	11.7787	0.52001	0.0:1.0:0.0:0.0	.	41;41	Q86V59-2;Q86V59	.;PNML1_HUMAN	K	41	ENSP00000410273:E41K;ENSP00000318131:E41K	ENSP00000318131:E41K	E	-	1	0	PNMAL1	51666012	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.004000	0.40854	2.491000	0.84063	0.655000	0.94253	GAG	.	.		0.542	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215		T	46974172	C	T	46974172	3	4	222	1	0	0	0	0	1	0	0	0	12166	864	30	3	1228	3	PNMAL1	19	46974172	Missense_Mutation	SNP	C	TCGA-DD-AAEK-01A-11D-A40R-10	27604794	46974172	12154811	72	31756										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58470629	58470631	+	In_Frame_Del	DEL	TTC	TTC	-													0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	catttgcagtggtggtttaaTtcttcttcttcgtggtggta							TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr20:58470629_58470631delTTC	ENST00000357552.3	-	20	1751_1753	c.1526_1528delGAA	c.(1525-1530)agaatt>att	p.R509del	SYCP2_ENST00000371001.2_In_Frame_Del_p.R509del			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	509					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)	p.R509K(1)		NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			GGTGGTTTAATTCTTCTTCTTCG	0.374																																					p.509_510del		Atlas-INDEL	.											.	SYCP2	204	.	1	Substitution - Missense(1)	NS(1)	c.1527_1529del						.			1,4263		0,1,2131						-3.3	0.5			191	2,8252		0,2,4125	no	coding	SYCP2	NM_014258.2		0,3,6256	A1A1,A1R,RR		0.0242,0.0235,0.024				3,12515				SO:0001651	inframe_deletion	10388	exon19			.	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1526_1528delGAA	chr20.hg19:g.58470638_58470640delTTC	ENSP00000350162:p.Arg509del	129.0	0.0		118.0	12.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	In_Frame_Del	DEL	ENST00000357552.3	hg19	CCDS13482.1																																																																																			.	.		0.374	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		-	58470631	TTC	-	58470629	7	5	222	1	0	1	0	1	0	0	0	0	15447	1493	52	0	3168	0	SYCP2	20	58470629	In_Frame_Del	DEL	TTC	TCGA-DD-AAEK-01A-11D-A40R-10		58470629	4554891	73	31757										
GRIK1	2897	hgsc.bcm.edu	37	chr21	30968882	30968882	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	tacaagtgtttagacacttcGccagcagccttggttttcag	9	10	1	1	rs374777692		TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr21:30968882G>T	ENST00000399907.1	-	9	1626	c.1215C>A	c.(1213-1215)ggC>ggA	p.G405G	GRIK1_ENST00000327783.4_Silent_p.G405G|GRIK1-AS2_ENST00000333765.4_3'UTR|GRIK1_ENST00000535441.1_Silent_p.G407G|GRIK1_ENST00000472429.1_5'Flank|GRIK1_ENST00000389125.3_Intron|GRIK1_ENST00000399909.1_Intron|GRIK1_ENST00000399914.1_Intron|GRIK1_ENST00000399913.1_Silent_p.G405G|BACH1_ENST00000462262.1_3'UTR|GRIK1_ENST00000389124.2_Silent_p.G405G|GRIK1_ENST00000309434.7_Silent_p.G407G	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	405					adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	TAGACACTTCGCCAGCAGCCT	0.428																																					p.G405G		Atlas-SNP	.											.	GRIK1	293	.	0			c.C1215A						.						125	124	124					21																	30968882		1858	4097	5955	SO:0001819	synonymous_variant	2897	exon9			CACTTCGCCAGCA		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.1215C>A	chr21.hg19:g.30968882G>T		68.0	0.0		63.0	10.0	NM_000830	Q13001|Q86SU9	Silent	SNP	ENST00000399907.1	hg19	CCDS42913.1																																																																																			.	.		0.428	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1			T	30968882	G	T	30968882	2	4	222	1	0	0	0	0	0	0	0	1	6782	1074	38	1		1	GRIK1	21	30968882	Silent	SNP	G	TCGA-DD-AAEK-01A-11D-A40R-10		30968882	17161013	74	31758										
CSNK1E	1454	hgsc.bcm.edu	37	chr22	38694819	38694819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	3	1	1.05645161290323	1.5494623655914	0.911448450347881	1	1	0	gcatgttccagtcaaagacgTagtcataggagaagccctgc	11	10	2	2	rs11548926		TCGA-DD-AAEK-01A-11D-A40R-10	TCGA-DD-AAEK-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0714057-ac5a-402f-b552-a914b5564c0c	4037ad92-fc4e-4737-8fb7-e3c276624c39	g.chr22:38694819T>C	ENST00000396832.1	-	7	1117	c.857A>G	c.(856-858)tAc>tGc	p.Y286C	CSNK1E_ENST00000359867.3_Missense_Mutation_p.Y286C|CSNK1E_ENST00000413574.2_Missense_Mutation_p.Y286C|CSNK1E_ENST00000405675.3_Missense_Mutation_p.Y286C|CSNK1E_ENST00000403904.1_Missense_Mutation_p.Y286C|CSNK1E_ENST00000498529.1_5'UTR|CSNK1E_ENST00000400206.2_Missense_Mutation_p.Y286C	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	286					cellular protein localization (GO:0034613)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Melanoma(58;0.045)					GTCAAAGACGTAGTCATAGGA	0.582											OREG0026559	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y286C	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)	Atlas-SNP	.											.	CSNK1E	143	.	0			c.A857G						.						140	135	137					22																	38694819		2203	4300	6503	SO:0001583	missense	1454	exon7			AAGACGTAGTCAT		CCDS13970.1	22q13.1	2013-01-17			ENSG00000213923	ENSG00000213923			2453	protein-coding gene	gene with protein product		600863				7797465, 10535959	Standard	NM_001894		Approved	HCKIE, CKIE, CKIepsilon	uc003avk.3	P49674	OTTHUMG00000151135	ENST00000396832.1:c.857A>G	chr22.hg19:g.38694819T>C	ENSP00000380044:p.Tyr286Cys	85.0	0.0	880	105.0	14.0	NM_001894		Missense_Mutation	SNP	ENST00000396832.1	hg19	CCDS13970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.38|16.38	3.106279|3.106279	0.56291|0.56291	.|.	.|.	ENSG00000213923|ENSG00000213923	ENST00000451964|ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904;ENST00000413574;ENST00000405675	.|T;T;T;T;T;T	.|0.10477	.|2.87;2.87;2.87;2.87;2.87;2.87	5.14|5.14	4.09|4.09	0.47781|0.47781	.|Protein kinase-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.25568|0.25568	0.0622|0.0622	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|0.997;1.0;1.0	.|P;D;D	.|0.64877	.|0.739;0.93;0.922	T|T	0.00536|0.00536	-1.1683|-1.1683	5|10	.|0.87932	.|D	.|0	.|.	11.3274|11.3274	0.49456|0.49456	0.1362:0.0:0.0:0.8638|0.1362:0.0:0.0:0.8638	rs11548926;rs11548926|rs11548926;rs11548926	.|286;286;286	.|B0QY35;B0QY34;P49674	.|.;.;KC1E_HUMAN	A|C	224|286	.|ENSP00000352929:Y286C;ENSP00000380044:Y286C;ENSP00000383067:Y286C;ENSP00000384074:Y286C;ENSP00000407235:Y286C;ENSP00000384426:Y286C	.|ENSP00000352929:Y286C	T|Y	-|-	1|2	0|0	CSNK1E|CSNK1E	37024765|37024765	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.977000|0.977000	0.68977|0.68977	8.028000|8.028000	0.88798|0.88798	0.785000|0.785000	0.33685|0.33685	0.533000|0.533000	0.62120|0.62120	ACG|TAC	.	T|1.000;|0.000		0.582	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894		C	38694819	T	C	38694819	3	2	222	1	0	0	0	0	1	0	0	0	3955	1638	57	2	409	2	CSNK1E	22	38694819	Missense_Mutation	SNP	T	TCGA-DD-AAEK-01A-11D-A40R-10		38694819	12609747	75	31759										
CSF3R	1441	hgsc.bcm.edu	37	chr1	36937988	36937988	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gggcctccaaggggagggggCccacctggtgaggggtggac	21	10	0	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr1:36937988C>T	ENST00000373106.1	-	8	1395	c.848G>A	c.(847-849)gGc>gAc	p.G283D	CSF3R_ENST00000331941.5_Missense_Mutation_p.G283D|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000361632.4_Missense_Mutation_p.G283D|CSF3R_ENST00000373104.1_Missense_Mutation_p.G283D|CSF3R_ENST00000373103.1_Missense_Mutation_p.G283D|CSF3R_ENST00000338937.5_Missense_Mutation_p.G283D|CSF3R_ENST00000418048.2_Missense_Mutation_p.G283D|CSF3R_ENST00000440588.2_Missense_Mutation_p.G283D	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	283	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GGGGAGGGGGCCCACCTGGTG	0.682																																					p.G283D		Atlas-SNP	.											.	CSF3R	157	.	0			c.G848A						.						25	29	28					1																	36937988		2201	4294	6495	SO:0001583	missense	1441	exon8			AGGGGGCCCACCT	M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"CD molecules", "Fibronectin type III domain containing"	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.848G>A	chr1.hg19:g.36937988C>T	ENSP00000362198:p.Gly283Asp	53.0	0.0		46.0	9.0	NM_156039		Missense_Mutation	SNP	ENST00000373106.1	hg19	CCDS413.1	.	.	.	.	.	.	.	.	.	.	C	4.946	0.175825	0.09443	.	.	ENSG00000119535	ENST00000373106;ENST00000373104;ENST00000373103;ENST00000361632;ENST00000331941;ENST00000418048;ENST00000338937;ENST00000440588	T;T;T;T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57	4.02	-3.66	0.04489	Fibronectin, type III (3);Immunoglobulin-like fold (1);	2.017800	0.01587	N	0.021342	T	0.33760	0.0874	L	0.40543	1.245	0.09310	N	1	P;P;P;B	0.41947	0.766;0.664;0.534;0.379	B;B;B;B	0.32211	0.142;0.095;0.047;0.082	T	0.26189	-1.0110	10	0.13108	T	0.6	-0.0929	5.3844	0.16211	0.1783:0.2865:0.4562:0.0789	.	283;283;283;283	E1B6W6;Q99062-3;Q99062;Q99062-4	.;.;CSF3R_HUMAN;.	D	283	ENSP00000362198:G283D;ENSP00000362196:G283D;ENSP00000362195:G283D;ENSP00000355406:G283D;ENSP00000332180:G283D;ENSP00000401588:G283D;ENSP00000345013:G283D;ENSP00000397568:G283D	ENSP00000332180:G283D	G	-	2	0	CSF3R	36710575	0.000000	0.05858	0.017000	0.16124	0.034000	0.12701	-0.100000	0.10990	-0.709000	0.05008	0.655000	0.94253	GGC	.	.		0.682	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039		T	36937988	C	T	36937988	3	4	223	1	0	0	0	0	1	0	0	0	3939	739	26	3	1892	3	CSF3R	1	36937988	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10		36937988	212312633	1	31760										
PTCH2	8643	hgsc.bcm.edu	37	chr1	45288095	45288095	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tcagctgctctttcacccagTggctggacctggtcccctgg	11	15	3	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr1:45288095T>C	ENST00000372192.3	-	22	3734	c.3604A>G	c.(3604-3606)Act>Gct	p.T1202A	PTCH2_ENST00000447098.2_Intron|RNU5E-6P_ENST00000365574.1_RNA	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	1202					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					TTTCACCCAGTGGCTGGACCT	0.622									Basal Cell Nevus syndrome																												p.T1202A		Atlas-SNP	.											.	PTCH2	96	.	0			c.A3604G						.						44	48	47					1																	45288095		2203	4300	6503	SO:0001583	missense	8643	exon22	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	ACCCAGTGGCTGG	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"patched (Drosophila) homolog 2", "patched homolog 2 (Drosophila)"			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.3604A>G	chr1.hg19:g.45288095T>C	ENSP00000361266:p.Thr1202Ala	49.0	0.0		32.0	10.0	NM_003738	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	hg19	CCDS516.1	.	.	.	.	.	.	.	.	.	.	t	17.42	3.383974	0.61845	.	.	ENSG00000117425	ENST00000372192	D	0.92199	-2.99	4.96	0.975	0.19721	.	1.395140	0.05215	N	0.507480	D	0.82995	0.5158	N	0.08118	0	0.09310	N	1	B	0.18461	0.028	B	0.16722	0.016	T	0.72697	-0.4215	10	0.87932	D	0	-0.5648	5.8512	0.18694	0.1591:0.0:0.3301:0.5108	.	1202	Q9Y6C5	PTC2_HUMAN	A	1202	ENSP00000361266:T1202A	ENSP00000361266:T1202A	T	-	1	0	PTCH2	45060682	0.111000	0.22076	0.006000	0.13384	0.400000	0.30750	0.415000	0.21181	0.338000	0.23692	0.451000	0.29950	ACT	.	.		0.622	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738		C	45288095	T	C	45288095	3	2	223	1	0	0	0	0	1	0	0	0	12743	1696	59	2	31	2	PTCH2	1	45288095	Missense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	8350107	45288095	203962526	2	31761										
WDR63	126820	hgsc.bcm.edu	37	chr1	85598554	85598555	+	Frame_Shift_Ins	INS	-	-	A													0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	cagaaaacatatcagaagtcINSaaaagaacaaatgcaggctg					rs371944443		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr1:85598554_85598555insA	ENST00000294664.6	+	23	2729_2730	c.2549_2550insA	c.(2548-2553)tcaaaafs	p.SK850fs	MIR4423_ENST00000580922.1_RNA|WDR63_ENST00000326813.8_Frame_Shift_Ins_p.SK811fs|WDR63_ENST00000370596.1_Frame_Shift_Ins_p.SK811fs	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	850										NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		TATCAGAAGTCAAAAGAACAAA	0.376																																					p.S850fs		Atlas-INDEL	.											.	WDR63	91	.	0			c.2549_2550insA						.																																			SO:0001589	frameshift_variant	126820	exon23			.		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"WD repeat domain containing"	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.2553dupA	chr1.hg19:g.85598558_85598558dupA	ENSP00000294664:p.Ser850fs	76.0	0.0		66.0	26.0	NM_145172	A8K988|Q96L72|Q96NU4	Frame_Shift_Ins	INS	ENST00000294664.6	hg19	CCDS702.1																																																																																			.	.		0.376	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172		A	85598555	-	A	85598554	7	5	223	1	0	1	1	0	0	0	0	0	17329	838	29	0	2635	0	WDR63	1	85598554	Frame_Shift_Ins	INS	-	TCGA-DD-AAVP-01A-11D-A40R-10	40310459	85598554	163652067	3	31762										
SIKE1	80143	hgsc.bcm.edu	37	chr1	115318966	115318966	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ctaaattagctacaatcttaCctctaattgggctaattttt	4	8	2	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr1:115318966C>G	ENST00000060969.5	-	4	592		c.e4+1		SIKE1_ENST00000506320.1_5'Flank|SIKE1_ENST00000369528.5_Splice_Site			Q9BRV8	SIKE1_HUMAN	suppressor of IKBKE 1						innate immune response (GO:0045087)	cytosol (GO:0005829)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6						TACAATCTTACCTCTAATTGG	0.373																																					.		Atlas-SNP	.											SIKE1,bladder,carcinoma,0,1	SIKE1	12	.	0			c.534+1G>C						.						150	146	147					1																	115318966		2203	4300	6503	SO:0001630	splice_region_variant	80143	exon5			ATCTTACCTCTAA	AK024821	CCDS878.1, CCDS41371.1	1p13.1	2009-08-13			ENSG00000052723	ENSG00000052723			26119	protein-coding gene	gene with protein product	"suppressor of IKK epsilon"	611656				16281057	Standard	NM_025073		Approved	FLJ21168, SIKE	uc001efp.4	Q9BRV8	OTTHUMG00000012061	ENST00000060969.5:c.522+1G>C	chr1.hg19:g.115318966C>G		76.0	0.0		69.0	8.0	NM_001102396	Q5TEZ7|Q5TEZ9|Q68DZ4|Q9H778	Splice_Site	SNP	ENST00000060969.5	hg19	CCDS878.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.628525	0.87560	.	.	ENSG00000052723	ENST00000369528;ENST00000060969	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6101	0.95602	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SIKE1	115120489	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.217000	0.77982	2.717000	0.92951	0.585000	0.79938	.	.	.		0.373	SIKE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033401.1	NM_025073	Intron	G	115318966	C	G	115318966	5	3	223	1	0	0	0	0	0	0	1	0	14335	521	18	4	108	4	SIKE1	1	115318966	Splice_Site	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	29720412	115318966	133931655	4	31763										
HCN3	57657	hgsc.bcm.edu	37	chr1	155247573	155247573	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	aacaagttctcccttcgggtGttcggcagccacaaagcagt	10	12	1	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr1:155247573G>T	ENST00000368358.3	+	1	200	c.192G>T	c.(190-192)gtG>gtT	p.V64V	HCN3_ENST00000496230.1_3'UTR|CLK2_ENST00000536801.1_5'Flank	NM_020897.2	NP_065948.1	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 3	64	Involved in subunit assembly. {ECO:0000250}.				potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CCCTTCGGGTGTTCGGCAGCC	0.622																																					p.V64V		Atlas-SNP	.											.	HCN3	74	.	0			c.G192T						.						23	25	24					1																	155247573		2202	4299	6501	SO:0001819	synonymous_variant	57657	exon1			TCGGGTGTTCGGC	AB040968	CCDS1108.1	1q21.2	2011-07-05			ENSG00000143630	ENSG00000143630		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	19183	protein-coding gene	gene with protein product		609973				16382102	Standard	NM_020897		Approved	KIAA1535	uc001fjz.2	Q9P1Z3	OTTHUMG00000035872	ENST00000368358.3:c.192G>T	chr1.hg19:g.155247573G>T		258.0	1.0		317.0	205.0	NM_020897	D3DV90|Q4VX12|Q8N6W6|Q9BWQ2	Silent	SNP	ENST00000368358.3	hg19	CCDS1108.1																																																																																			.	.		0.622	HCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087388.1	NM_020897		T	155247573	G	T	155247573	2	4	223	1	0	0	0	0	0	0	0	1	7007	1364	48	3		3	HCN3	1	155247573	Silent	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	39928607	155247573	94003048	5	31764										
KIRREL	55243	hgsc.bcm.edu	37	chr1	158054346	158054346	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ggttccgggacgggacgcagCaggagggcgctgtggccagc	20	11	0	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr1:158054346C>G	ENST00000359209.6	+	4	554	c.487C>G	c.(487-489)Cag>Gag	p.Q163E	KIRREL_ENST00000368173.3_Missense_Mutation_p.Q163E|KIRREL_ENST00000392272.2_Intron|KIRREL_ENST00000368172.1_5'Flank|KIRREL_ENST00000360089.4_Intron|KIRREL_ENST00000416935.2_Missense_Mutation_p.Q63E			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	163	Ig-like C2-type 2.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					CGGGACGCAGCAGGAGGGCGC	0.647																																					p.Q163E		Atlas-SNP	.											.	KIRREL	346	.	0			c.C487G						.						46	51	50					1																	158054346		692	1591	2283	SO:0001583	missense	55243	exon4			ACGCAGCAGGAGG	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15734	protein-coding gene	gene with protein product	"nephrin-like protein 1"	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.487C>G	chr1.hg19:g.158054346C>G	ENSP00000352138:p.Gln163Glu	164.0	0.0		183.0	9.0	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Missense_Mutation	SNP	ENST00000359209.6	hg19	CCDS1172.2	.	.	.	.	.	.	.	.	.	.	C	18.65	3.669125	0.67814	.	.	ENSG00000183853	ENST00000368173;ENST00000359209;ENST00000416935	T;T;T	0.75367	-0.93;-0.93;-0.93	5.77	5.77	0.91146	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.41001	D	0.000980	T	0.53029	0.1771	N	0.24115	0.695	0.41596	D	0.988823	B;P	0.43578	0.293;0.811	B;B	0.43575	0.275;0.424	T	0.54649	-0.8262	10	0.15066	T	0.55	-25.9084	17.4764	0.87660	0.0:1.0:0.0:0.0	.	63;163	B4DN67;Q96J84	.;KIRR1_HUMAN	E	163;163;63	ENSP00000357155:Q163E;ENSP00000352138:Q163E;ENSP00000389674:Q63E	ENSP00000352138:Q163E	Q	+	1	0	KIRREL	156320970	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	2.569000	0.45973	2.734000	0.93682	0.650000	0.86243	CAG	.	.		0.647	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240		G	158054346	C	G	158054346	3	3	223	1	0	0	0	0	1	0	0	0	8333	711	25	4	501	4	KIRREL	1	158054346	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	2806773	158054346	91196275	6	31765										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186056407	186056407	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gatggtggtgaatacacttgTatagctatcaatcaagctgg	11	6	2	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr1:186056407T>G	ENST00000271588.4	+	59	9334	c.9105T>G	c.(9103-9105)tgT>tgG	p.C3035W	HMCN1_ENST00000367492.2_Missense_Mutation_p.C3035W	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3035	Ig-like C2-type 28.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AATACACTTGTATAGCTATCA	0.368																																					p.C3035W		Atlas-SNP	.											.	HMCN1	797	.	0			c.T9105G						.						146	141	143					1																	186056407		2203	4300	6503	SO:0001583	missense	83872	exon59			CACTTGTATAGCT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.9105T>G	chr1.hg19:g.186056407T>G	ENSP00000271588:p.Cys3035Trp	191.0	0.0		242.0	54.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	18.37	3.609223	0.66558	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.58358	0.34;0.34	5.84	0.748	0.18376	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.81498	0.4835	H	0.99435	4.565	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82450	-0.0451	10	0.87932	D	0	.	9.4068	0.38466	0.0:0.2709:0.0:0.7291	.	3035	Q96RW7	HMCN1_HUMAN	W	3035	ENSP00000271588:C3035W;ENSP00000356462:C3035W	ENSP00000271588:C3035W	C	+	3	2	HMCN1	184323030	1.000000	0.71417	0.969000	0.41365	0.998000	0.95712	1.260000	0.32968	0.093000	0.17368	0.533000	0.62120	TGT	.	.		0.368	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186056407	T	G	186056407	3	3	223	1	0	0	0	0	1	0	0	0	7229	1644	57	5	9339	5	HMCN1	1	186056407	Missense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	28002061	186056407	63194214	7	31766										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190068054	190068054	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ccctggctgagcatgtagccGgtgttgcaggtgccgcagcg	16	12	0	1	rs370368224		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr1:190068054G>T	ENST00000367462.3	-	8	1626	c.1395C>A	c.(1393-1395)acC>acA	p.T465T	BRINP3_ENST00000534846.1_Silent_p.T363T	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	465					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)		p.T465T(1)									GCATGTAGCCGGTGTTGCAGG	0.597																																					p.T465T		Atlas-SNP	.											FAM5C,NS,carcinoma,-2,1	FAM5C	343	.	1	Substitution - coding silent(1)	lung(1)	c.C1395A						.						88	89	89					1																	190068054		2203	4300	6503	SO:0001819	synonymous_variant	339479	exon8			GTAGCCGGTGTTG	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1395C>A	chr1.hg19:g.190068054G>T		102.0	0.0		140.0	30.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Silent	SNP	ENST00000367462.3	hg19	CCDS1373.1																																																																																			.	.		0.597	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190068054	G	T	190068054	2	4	223	1	0	0	0	0	0	0	0	1	5602	1103	39	1		1	FAM5C	1	190068054	Silent	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	4011647	190068054	59182567	8	31767										
SYT14	255928	hgsc.bcm.edu	37	chr1	210332796	210332796	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ctgttgtctaaaacacttgaTaggtggacaggtttatataa	9	5	1	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr1:210332796T>A	ENST00000472886.1	+	8	1368				SYT14_ENST00000422431.1_Missense_Mutation_p.I507K|SYT14_ENST00000537238.1_Intron|SYT14_ENST00000367019.1_Missense_Mutation_p.I462K|SYT14_ENST00000534859.1_Missense_Mutation_p.I469K|SYT14_ENST00000399639.2_3'UTR|SYT14_ENST00000367015.1_Intron|SYT14_ENST00000271745.7_Intron			Q8NB59	SYT14_HUMAN	synaptotagmin XIV						cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)			endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		AAACACTTGATAGGTGGACAG	0.418																																					p.I507K		Atlas-SNP	.											.	SYT14	89	.	0			c.T1520A						.						211	173	184					1																	210332796		692	1591	2283	SO:0001627	intron_variant	255928	exon9			ACTTGATAGGTGG	AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"Synaptotagmins"	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.1355-1278T>A	chr1.hg19:g.210332796T>A		183.0	0.0		221.0	56.0	NM_001146261	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Missense_Mutation	SNP	ENST00000472886.1	hg19	CCDS31014.1	.	.	.	.	.	.	.	.	.	.	T	18.90	3.722460	0.68959	.	.	ENSG00000143469	ENST00000422431;ENST00000534859;ENST00000367019	T;T;T	0.07327	3.4;3.2;3.28	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.17746	0.0426	L	0.27053	0.805	0.80722	D	1	D;D	0.76494	0.997;0.999	P;D	0.66351	0.881;0.943	T	0.01208	-1.1418	10	0.87932	D	0	-19.5701	16.226	0.82293	0.0:0.0:0.0:1.0	.	462;507	Q8NB59-6;F5H426	.;.	K	507;469;462	ENSP00000389039:I507K;ENSP00000442891:I469K;ENSP00000355986:I462K	ENSP00000355986:I462K	I	+	2	0	SYT14	208399419	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.590000	0.82653	2.292000	0.77174	0.482000	0.46254	ATA	.	.		0.418	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262		A	210332796	T	A	210332796	1	1	223	0	1	0	0	0	0	0	0	0	15485	1406	49	4		4	SYT14	1	210332796	Intron	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	20264742	210332796	38917825	9	31768										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228496077	228496077	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gcttcctctgcccagctcacCgtcagaggtagccacaggcg	11	16	3	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr1:228496077C>A	ENST00000422127.1	+	47	12776	c.12732C>A	c.(12730-12732)acC>acA	p.T4244T	OBSCN_ENST00000366707.4_Silent_p.T1878T|OBSCN_ENST00000284548.11_Silent_p.T4244T|OBSCN_ENST00000366709.4_Silent_p.T1363T|OBSCN_ENST00000570156.2_Silent_p.T5201T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4244					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCCAGCTCACCGTCAGAGGTA	0.617																																					p.T5201T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C15603A						.																																			SO:0001819	synonymous_variant	84033	exon58			GCTCACCGTCAGA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.12732C>A	chr1.hg19:g.228496077C>A		60.0	0.0		73.0	18.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.617	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228496077	C	A	228496077	2	1	223	1	0	0	0	0	0	0	0	1	10821	639	23	1		1	OBSCN	1	228496077	Silent	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	18163281	228496077	20754544	10	31769										
DPYSL5	56896	hgsc.bcm.edu	37	chr2	27121441	27121441	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gaacgatgactgcacccacgAggctgacgtctacatcgaga	11	12	1	3			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr2:27121441A>G	ENST00000288699.6	+	2	232	c.74A>G	c.(73-75)gAg>gGg	p.E25G	DPYSL5_ENST00000401478.1_Missense_Mutation_p.E25G	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	25					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)|signal transduction (GO:0007165)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			breast(1)|endometrium(5)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCACCCACGAGGCTGACGTC	0.567																																					p.E25G		Atlas-SNP	.											.	DPYSL5	69	.	0			c.A74G						.						167	140	149					2																	27121441		2203	4300	6503	SO:0001583	missense	56896	exon2			CCCACGAGGCTGA	AF264015	CCDS1730.1	2p23.3	2008-02-05			ENSG00000157851	ENSG00000157851			20637	protein-coding gene	gene with protein product		608383				10851247, 11034345	Standard	NM_020134		Approved	CRMP5, Ulip6, CRMP-5, CRAM	uc002rhu.4	Q9BPU6	OTTHUMG00000097071	ENST00000288699.6:c.74A>G	chr2.hg19:g.27121441A>G	ENSP00000288699:p.Glu25Gly	181.0	0.0		166.0	68.0	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Missense_Mutation	SNP	ENST00000288699.6	hg19	CCDS1730.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.956193	0.53293	.	.	ENSG00000157851	ENST00000450961;ENST00000288699;ENST00000401478;ENST00000431402;ENST00000434719	T;D;D;T;T	0.86030	-1.15;-2.06;-2.06;-1.14;-1.15	4.61	4.61	0.57282	Metal-dependent hydrolase, composite domain (1);	0.048925	0.85682	D	0.000000	T	0.79118	0.4392	L	0.43598	1.365	0.50467	D	0.999877	B	0.33940	0.433	B	0.31495	0.131	T	0.77718	-0.2483	10	0.34782	T	0.22	-30.9847	13.2923	0.60278	1.0:0.0:0.0:0.0	.	25	Q9BPU6	DPYL5_HUMAN	G	25	ENSP00000407174:E25G;ENSP00000288699:E25G;ENSP00000385549:E25G;ENSP00000399581:E25G;ENSP00000413075:E25G	ENSP00000288699:E25G	E	+	2	0	DPYSL5	26974945	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.624000	0.67764	1.854000	0.53819	0.459000	0.35465	GAG	.	.		0.567	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134		G	27121441	A	G	27121441	3	3	223	1	0	0	0	0	1	0	0	0	4752	304	11	2	76	2	DPYSL5	2	27121441	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10		27121441	216077932	11	31770										
SLC30A3	7781	hgsc.bcm.edu	37	chr2	27481124	27481124	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tcatgctgcccacatccgccAgcaagtgggctgcatcggtc	11	15	1	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr2:27481124A>T	ENST00000233535.4	-	3	681	c.329T>A	c.(328-330)cTg>cAg	p.L110Q	SLC30A3_ENST00000447008.2_Missense_Mutation_p.L105Q	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	110					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACATCCGCCAGCAAGTGGGC	0.577																																					p.L110Q		Atlas-SNP	.											.	SLC30A3	39	.	0			c.T329A						.						46	47	46					2																	27481124		2203	4300	6503	SO:0001583	missense	7781	exon3			TCCGCCAGCAAGT	U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"Solute carriers"	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.329T>A	chr2.hg19:g.27481124A>T	ENSP00000233535:p.Leu110Gln	117.0	0.0		79.0	27.0	NM_003459	Q8TC03	Missense_Mutation	SNP	ENST00000233535.4	hg19	CCDS1743.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.757108	0.89843	.	.	ENSG00000115194	ENST00000233535;ENST00000447008;ENST00000432351;ENST00000426924;ENST00000424577;ENST00000450118;ENST00000426569	T;T;T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.89431	0.6713	H	0.97365	3.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.92754	0.6218	10	0.87932	D	0	-11.5116	13.8767	0.63657	1.0:0.0:0.0:0.0	.	105;110	F5H3B7;Q99726	.;ZNT3_HUMAN	Q	110;105;61;97;88;61;61	ENSP00000233535:L110Q;ENSP00000415226:L105Q;ENSP00000414320:L61Q;ENSP00000393545:L97Q;ENSP00000403959:L88Q;ENSP00000403912:L61Q;ENSP00000392673:L61Q	ENSP00000233535:L110Q	L	-	2	0	SLC30A3	27334628	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	9.251000	0.95483	2.234000	0.73211	0.459000	0.35465	CTG	.	.		0.577	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2			T	27481124	A	T	27481124	3	4	223	1	0	0	0	0	1	0	0	0	14571	188	7	4	861	4	SLC30A3	2	27481124	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10	359683	27481124	215718249	12	31771										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186671383	186671383	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gtaaacctggaatttttcccGctaagtttttagaagatgtt	8	6	0	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr2:186671383G>A	ENST00000424728.1	+	17	17350	c.17350G>A	c.(17350-17352)Gct>Act	p.A5784T	FSIP2_ENST00000343098.5_Missense_Mutation_p.A5873T			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5784										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						AATTTTTCCCGCTAAGTTTTT	0.333																																					p.A5873T		Atlas-SNP	.											.	FSIP2	251	.	0			c.G17617A						.						72	68	69					2																	186671383		1804	4072	5876	SO:0001583	missense	401024	exon17			TTTCCCGCTAAGT	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.17350G>A	chr2.hg19:g.186671383G>A	ENSP00000401306:p.Ala5784Thr	254.0	0.0		243.0	102.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.81	1.748834	0.30955	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.62364	0.03;0.04	5.06	2.27	0.28462	.	.	.	.	.	T	0.50667	0.1629	L	0.34521	1.04	0.09310	N	1	.	.	.	.	.	.	T	0.44817	-0.9303	7	0.51188	T	0.08	.	4.4373	0.11557	0.1844:0.0:0.6388:0.1768	.	.	.	.	T	5873;5784	ENSP00000344403:A5873T;ENSP00000401306:A5784T	ENSP00000344403:A5873T	A	+	1	0	FSIP2	186379628	0.151000	0.22747	0.096000	0.21009	0.298000	0.27526	0.723000	0.25939	0.299000	0.22661	-0.194000	0.12790	GCT	.	.		0.333	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		A	186671383	G	A	186671383	3	1	223	1	0	0	0	0	1	0	0	0	6083	1087	38	1	17683	1	FSIP2	2	186671383	Missense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	159190259	186671383	56527990	13	31772										
SPEG	10290	hgsc.bcm.edu	37	chr2	220344828	220344828	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ttgtagcacccgagattgtcAatcagagccccgtgtctgga	11	11	3	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr2:220344828A>C	ENST00000312358.7	+	25	5440	c.5308A>C	c.(5308-5310)Aat>Cat	p.N1770H	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1770	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CGAGATTGTCAATCAGAGCCC	0.617																																					p.N1770H		Atlas-SNP	.											.	SPEG	272	.	0			c.A5308C						.						80	84	83					2																	220344828		2089	4221	6310	SO:0001583	missense	10290	exon25			ATTGTCAATCAGA	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.5308A>C	chr2.hg19:g.220344828A>C	ENSP00000311684:p.Asn1770His	40.0	0.0		29.0	12.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	a	14.57	2.574323	0.45902	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.66638	-0.22	4.55	3.38	0.38709	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.45361	D	0.000361	T	0.61627	0.2362	L	0.41632	1.29	0.80722	D	1	P	0.40602	0.723	P	0.44990	0.466	T	0.63278	-0.6673	10	0.72032	D	0.01	.	10.2244	0.43216	0.921:0.0:0.079:0.0	.	1770	Q15772	SPEG_HUMAN	H	1770	ENSP00000311684:N1770H	ENSP00000265327:N1770H	N	+	1	0	SPEG	220053072	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.791000	0.69045	0.880000	0.35969	0.492000	0.49549	AAT	.	.		0.617	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		C	220344828	A	C	220344828	3	2	223	1	0	0	0	0	1	0	0	0	15051	130	5	5	5418	5	SPEG	2	220344828	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10	33673445	220344828	22854545	14	31773										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266107	41266107	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gtcttacctggactctggaaTccattctggtgccactacca	8	13	3	0	rs121913416		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr3:41266107T>G	ENST00000349496.5	+	3	384	c.104T>G	c.(103-105)aTc>aGc	p.I35S	CTNNB1_ENST00000396185.3_Missense_Mutation_p.I35S|CTNNB1_ENST00000396183.3_Missense_Mutation_p.I35S|CTNNB1_ENST00000405570.1_Missense_Mutation_p.I35S|CTNNB1_ENST00000453024.1_Missense_Mutation_p.I28S	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	35			I -> S (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.I35S(20)|p.I35T(13)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.I35_S37>T(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.S29_H36del(1)|p.I35_T41del(1)|p.I35N(1)|p.I35_G38del(1)|p.I35K(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GACTCTGGAATCCATTCTGGT	0.493		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.I35S	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	169	Deletion - In frame(107)|Substitution - Missense(35)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(3)	liver(118)|large_intestine(19)|salivary_gland(12)|stomach(7)|soft_tissue(2)|small_intestine(2)|endometrium(2)|skin(2)|adrenal_gland(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|pituitary(1)|kidney(1)	c.T104G						.						95	80	85					3																	41266107		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTGGAATCCATTC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.104T>G	chr3.hg19:g.41266107T>G	ENSP00000344456:p.Ile35Ser	107.0	0.0		97.0	34.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.188620	0.78789	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	M	0.79614	2.46	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.73949	-0.3821	10	0.87932	D	0	-3.5499	16.0677	0.80897	0.0:0.0:0.0:1.0	.	35	P35222	CTNB1_HUMAN	S	28;35;35;35;35;28;35;35;35	ENSP00000400508:I28S;ENSP00000385604:I35S;ENSP00000412219:I35S;ENSP00000379486:I35S;ENSP00000344456:I35S;ENSP00000411226:I28S;ENSP00000379488:I35S;ENSP00000409302:I35S;ENSP00000401599:I35S	ENSP00000344456:I35S	I	+	2	0	CTNNB1	41241111	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	ATC	.	.		0.493	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266107	T	G	41266107	3	3	223	1	0	0	0	0	1	0	0	0	4018	1435	50	5	110	5	CTNNB1	3	41266107	Missense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10		41266107	156756323	15	31774										
SPATA16	83893	hgsc.bcm.edu	37	chr3	172834939	172834940	+	Missense_Mutation	DNP	CC	CC	AA													0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tgttctgaactgtcctgctgCcaaggcgtatttcttttgtc							TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr3:172834939_172834940CC>AA	ENST00000351008.3	-	2	765_766	c.582_583GG>TT	c.(580-585)ttGGca>ttTTca	p.194_195LA>FS		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	194					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			TGTCCTGCTGCCAAGGCGTATT	0.406																																					p.A195S|p.L194F		Atlas-SNP	.											.	SPATA16	111	.	0			c.G583T|c.G582T						.																																			SO:0001583	missense	83893	exon2			CTGCTGCCAAGGC|TGCTGCCAAGGCG	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.582_583delinsAA	chr3.hg19:g.172834939_172834940delinsAA	ENSP00000341765:p.L194_A195delinsFS	91.0|92.0	0.0		70.0	22.0|21.0	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	hg19	CCDS3221.1																																																																																			.	.		0.406	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955		AA	172834940	CC	AA	172834939	3	1	223	1	0	0	0	0	1	0	0	0	15016	739	26	3	1166	3	SPATA16	3	172834939	Missense_Mutation	DNP	CC	TCGA-DD-AAVP-01A-11D-A40R-10	131568832	172834939	25187491	16	31775										
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25836840	25836840	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ctgggtaatccatcctctggCgtcgagtggcctccagctct	11	14	2	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr4:25836840C>T	ENST00000399878.3	-	3	961	c.839G>A	c.(838-840)cGc>cAc	p.R280H	SEL1L3_ENST00000502949.1_Missense_Mutation_p.R127H|SEL1L3_ENST00000513364.1_5'UTR|SEL1L3_ENST00000264868.5_Missense_Mutation_p.R245H	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	280						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						CATCCTCTGGCGTCGAGTGGC	0.532																																					p.R280H		Atlas-SNP	.											.	SEL1L3	62	.	0			c.G839A						.						124	125	125					4																	25836840		1969	4148	6117	SO:0001583	missense	23231	exon3			CTCTGGCGTCGAG	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.839G>A	chr4.hg19:g.25836840C>T	ENSP00000382767:p.Arg280His	65.0	0.0		61.0	17.0	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.994514	0.54041	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.16457	2.34;2.34;2.34	6.02	5.18	0.71444	.	0.782834	0.13011	N	0.420833	T	0.14657	0.0354	L	0.47716	1.5	0.27456	N	0.953299	P	0.51147	0.942	B	0.37346	0.247	T	0.13098	-1.0522	10	0.42905	T	0.14	-0.3889	9.2909	0.37786	0.0:0.8388:0.0:0.1612	.	280	Q68CR1	SE1L3_HUMAN	H	280;245;127	ENSP00000382767:R280H;ENSP00000264868:R245H;ENSP00000425438:R127H	ENSP00000264868:R245H	R	-	2	0	SEL1L3	25445938	0.992000	0.36948	0.997000	0.53966	0.966000	0.64601	0.551000	0.23361	1.569000	0.49696	0.655000	0.94253	CGC	.	.		0.532	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		T	25836840	C	T	25836840	3	4	223	1	0	0	0	0	1	0	0	0	14027	768	27	1	2647	1	SEL1L3	4	25836840	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10		25836840	165317436	17	31776										
KIT	3815	hgsc.bcm.edu	37	chr4	55564702	55564702	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ggagggcaagtcagtgctgtCggaaaaattcatcctgaaag	13	7	2	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr4:55564702C>T	ENST00000288135.5	+	3	687	c.590C>T	c.(589-591)tCg>tTg	p.S197L		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	197	Ig-like C2-type 2.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCAGTGCTGTCGGAAAAATTC	0.498		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.S197L		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	KIT,NS,haematopoietic_neoplasm,0,1	KIT	7396	.	0			c.C590T						.						104	94	98					4																	55564702		2203	4300	6503	SO:0001583	missense	3815	exon3	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	TGCTGTCGGAAAA	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.590C>T	chr4.hg19:g.55564702C>T	ENSP00000288135:p.Ser197Leu	59.0	0.0		41.0	16.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.836686	0.50951	.	.	ENSG00000157404	ENST00000288135;ENST00000412167;ENST00000536403	D;D	0.81659	-1.52;-1.51	5.75	4.91	0.64330	Immunoglobulin-like fold (1);	0.113900	0.39834	N	0.001251	D	0.86548	0.5959	M	0.78637	2.42	0.53005	D	0.999969	D;D	0.71674	0.982;0.998	P;P	0.56216	0.674;0.794	D	0.88178	0.2869	10	0.87932	D	0	.	12.9428	0.58354	0.0:0.9253:0.0:0.0747	.	197;197	P10721-2;P10721	.;KIT_HUMAN	L	197	ENSP00000288135:S197L;ENSP00000390987:S197L	ENSP00000288135:S197L	S	+	2	0	KIT	55259459	0.999000	0.42202	0.062000	0.19696	0.022000	0.10575	5.295000	0.65692	1.440000	0.47531	0.643000	0.83706	TCG	.	.		0.498	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55564702	C	T	55564702	3	4	223	1	0	0	0	0	1	0	0	0	8338	893	31	1	600	1	KIT	4	55564702	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	29727862	55564702	135589574	18	31777										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85719181	85719181	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gttcataactcagtgaacttGgtttgtggaccctatattgt	9	7	2	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr4:85719181G>A	ENST00000295888.4	-	18	3310	c.2903C>T	c.(2902-2904)cCa>cTa	p.P968L	WDFY3_ENST00000322366.6_Missense_Mutation_p.P968L	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	968					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CAGTGAACTTGGTTTGTGGAC	0.333																																					p.P968L		Atlas-SNP	.											.	WDFY3	314	.	0			c.C2903T						.						133	133	133					4																	85719181		2203	4300	6503	SO:0001583	missense	23001	exon18			GAACTTGGTTTGT	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.2903C>T	chr4.hg19:g.85719181G>A	ENSP00000295888:p.Pro968Leu	88.0	0.0		60.0	18.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	33	5.221059	0.95139	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.62941	-0.01;-0.01	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.62380	0.2423	N	0.08118	0	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.60505	-0.7250	10	0.15952	T	0.53	.	19.7348	0.96198	0.0:0.0:1.0:0.0	.	968	Q8IZQ1	WDFY3_HUMAN	L	968	ENSP00000318466:P968L;ENSP00000295888:P968L	ENSP00000295888:P968L	P	-	2	0	WDFY3	85938205	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.416000	0.97383	2.716000	0.92895	0.655000	0.94253	CCA	.	.		0.333	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85719181	G	A	85719181	3	1	223	1	0	0	0	0	1	0	0	0	17285	1348	47	3	7881	3	WDFY3	4	85719181	Missense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	30154479	85719181	105435095	19	31778										
AQPEP	206338	hgsc.bcm.edu	37	chr5	115318983	115318983	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tttccccaaaatgtatttcaGggccctgttagcgtcccagc	8	13	1	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr5:115318983G>T	ENST00000357872.4	+	2	819		c.e2-1		AQPEP_ENST00000395528.2_Splice_Site	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN								integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										ATGTATTTCAGGGCCCTGTTA	0.373																																					.		Atlas-SNP	.											.	.	.	.	0			c.696-1G>T						.						43	40	41					5																	115318983		2200	4296	6496	SO:0001630	splice_region_variant	0	exon2			ATTTCAGGGCCCT																												ENST00000357872.4:c.696-1G>T	chr5.hg19:g.115318983G>T		442.0	0.0		353.0	130.0	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Splice_Site	SNP	ENST00000357872.4	hg19	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.943841	0.73672	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3048	0.90176	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AC010282.1	115346882	1.000000	0.71417	0.986000	0.45419	0.836000	0.47400	8.536000	0.90627	2.681000	0.91329	0.650000	0.86243	.	.	.		0.373	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		Intron	T	115318983	G	T	115318983	5	4	223	1	0	0	0	0	0	0	1	0	834	1014	35	3	701	3	AQPEP	5	115318983	Splice_Site	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10		115318983	65596277	20	31779										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168189636	168189636	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ccctcacagcgacacttctcGgggcacacgaggtccatgaa	10	15	2	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr5:168189636G>A	ENST00000519560.1	-	15	1937	c.1518C>T	c.(1516-1518)ccC>ccT	p.P506P	SLIT3_ENST00000404867.3_Silent_p.P506P|SLIT3_ENST00000332966.8_Silent_p.P506P	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	506	LRRNT 3.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GACACTTCTCGGGGCACACGA	0.607																																					p.P506P	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C1518T						.						151	144	146					5																	168189636		2203	4300	6503	SO:0001819	synonymous_variant	6586	exon15			CTTCTCGGGGCAC	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.1518C>T	chr5.hg19:g.168189636G>A		80.0	0.0		56.0	18.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.607	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		A	168189636	G	A	168189636	2	1	223	1	0	0	0	0	0	0	0	1	14756	1103	39	1		1	SLIT3	5	168189636	Silent	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	52870653	168189636	12725624	21	31780										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327918	16327919	+	In_Frame_Ins	INS	-	-	TGCTGA													0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gctgctgctgatgctgatgcINStgctgctgctgctgctgctg					rs28555263	byFrequency	TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr6:16327918_16327919insTGCTGA	ENST00000244769.4	-	8	1559_1560	c.623_624insTCAGCA	c.(622-624)cag>caTCAGCAg	p.207_208insHQ	ATXN1_ENST00000436367.1_In_Frame_Ins_p.207_208insHQ	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	207	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gatgctgatgctgctgctgctg	0.663																																					p.Q208delinsHQQ		Atlas-INDEL	.											ATXN1,rectum,carcinoma,0,1	ATXN1	117	.	0			c.624_625insTCAGCA						.																																			SO:0001652	inframe_insertion	6310	exon8			.	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.623_624insTCAGCA	chr6.hg19:g.16327918_16327919insTGCTGA	ENSP00000244769:p.Gln207_Gln208insHisGln	35.0	0.0		25.0	12.0	NM_000332	Q17S02|Q9UJG2|Q9Y4J1	In_Frame_Ins	INS	ENST00000244769.4	hg19	CCDS34342.1																																																																																			.	.		0.663	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		TGCTGA	16327919	-	TGCTGA	16327918	7	5	223	1	0	1	1	0	0	0	0	0	1209	796	28	0	1831	0	ATXN1	6	16327918	In_Frame_Ins	INS	-	TCGA-DD-AAVP-01A-11D-A40R-10		16327918	154787149	22	31781										
MDFI	4188	hgsc.bcm.edu	37	chr6	41613971	41613972	+	Intron	DNP	CC	CC	AA													0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	aggaggcggcaacccccatgCcccaaggcaatggccctggc							TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr6:41613971_41613972CC>AA	ENST00000373050.4	+	3	263							Q99750	MDFI_HUMAN	MyoD family inhibitor						activation of JUN kinase activity (GO:0007257)|cytoplasmic sequestering of transcription factor (GO:0042994)|dorsal/ventral axis specification (GO:0009950)|embryo development (GO:0009790)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|prostate(2)|skin(1)|urinary_tract(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.121)		Colorectal(64;0.0123)|COAD - Colon adenocarcinoma(64;0.0264)|KIRC - Kidney renal clear cell carcinoma(1;0.138)			AACCCCCATGCCCCAAGGCAAT	0.649																																					p.P62T|p.P62H		Atlas-SNP	.											MDFI,NS,malignant_melanoma,0,1|.	MDFI	19	.	0			c.C184A|c.C185A						.																																			SO:0001627	intron_variant	4188	exon3			CCCATGCCCCAAG|CCATGCCCCAAGG	U78313	CCDS4857.1, CCDS75451.1	6p21	2008-08-29			ENSG00000112559	ENSG00000112559			6967	protein-coding gene	gene with protein product	"inhibitor of MyoD family a"	604971				9250874, 17289077	Standard	NM_005586		Approved	I-mfa	uc003oqq.4	Q99750	OTTHUMG00000014681	Exception_encountered	chr6.hg19:g.41613971_41613972delinsAA		225.0|223.0	0.0		140.0|142.0	62.0|61.0	NM_005586		Missense_Mutation	SNP	ENST00000373050.4	hg19																																																																																				.	.		0.649	MDFI-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000040519.2	NM_005586		AA	41613972	CC	AA	41613971	1	1	223	0	1	0	0	0	0	0	0	0	9413	739	26	3		3	MDFI	6	41613971	Intron	DNP	CC	TCGA-DD-AAVP-01A-11D-A40R-10	25286053	41613971	129501096	23	31782										
CRIP3	401262	hgsc.bcm.edu	37	chr6	43274226	43274226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gccagggcacagcgaggtctCcccagtgaatgtcttcatat	11	12	3	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr6:43274226C>T	ENST00000274990.4	-	5	362	c.358G>A	c.(358-360)Gag>Aag	p.E120K	CRIP3_ENST00000372569.3_Missense_Mutation_p.E120K|ZNF318_ENST00000607252.1_5'Flank			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	120					T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			AGCGAGGTCTCCCCAGTGAAT	0.587																																					p.E120K		Atlas-SNP	.											.	CRIP3	30	.	0			c.G358A						.						59	58	59					6																	43274226		2203	4300	6503	SO:0001583	missense	401262	exon5			AGGTCTCCCCAGT	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.358G>A	chr6.hg19:g.43274226C>T	ENSP00000274990:p.Glu120Lys	81.0	0.0		51.0	21.0	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	hg19		.	.	.	.	.	.	.	.	.	.	C	25.2	4.616203	0.87359	.	.	ENSG00000146215	ENST00000372569;ENST00000274990	T;T	0.44482	0.92;0.92	4.75	4.75	0.60458	.	0.481258	0.19617	N	0.109984	T	0.39708	0.1088	N	0.19112	0.55	0.54753	D	0.999987	P;D	0.67145	0.698;0.996	B;D	0.77557	0.14;0.99	T	0.36383	-0.9750	10	0.44086	T	0.13	-23.322	15.6048	0.76658	0.0:1.0:0.0:0.0	.	120;120	Q6Q6R5;Q6Q6R5-3	CRIP3_HUMAN;.	K	120	ENSP00000361650:E120K;ENSP00000274990:E120K	ENSP00000274990:E120K	E	-	1	0	CRIP3	43382204	1.000000	0.71417	0.995000	0.50966	0.901000	0.52897	6.082000	0.71318	2.343000	0.79666	0.561000	0.74099	GAG	.	.		0.587	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			T	43274226	C	T	43274226	3	4	223	1	0	0	0	0	1	0	0	0	3878	864	30	3	272	3	CRIP3	6	43274226	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	1660255	43274226	127840841	24	31783										
GPR110	266977	hgsc.bcm.edu	37	chr6	46976900	46976900	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	agcagcaccacaacgaagttCacagccacaatagccagtgc	8	14	1	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr6:46976900C>A	ENST00000371253.2	-	11	2486	c.2271G>T	c.(2269-2271)gtG>gtT	p.V757V	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Silent_p.V560V	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	757					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						CAACGAAGTTCACAGCCACAA	0.517																																					p.V757V		Atlas-SNP	.											.	GPR110	102	.	0			c.G2271T						.						80	85	83					6																	46976900		2203	4300	6503	SO:0001819	synonymous_variant	266977	exon11			GAAGTTCACAGCC	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.2271G>T	chr6.hg19:g.46976900C>A		191.0	0.0		163.0	58.0	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	hg19	CCDS34471.1																																																																																			.	.		0.517	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		A	46976900	C	A	46976900	2	1	223	1	0	0	0	0	0	0	0	1	6635	813	29	3		3	GPR110	6	46976900	Silent	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	3702674	46976900	124138167	25	31784										
TNFRSF21	27242	hgsc.bcm.edu	37	chr6	47251829	47251829	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tactgcacaccacaatcaccAcaagcaccagcagcaggaaa	6	15	1	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr6:47251829A>T	ENST00000296861.2	-	3	1481	c.1088T>A	c.(1087-1089)gTg>gAg	p.V363E		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	363					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			CACAATCACCACAAGCACCAG	0.522																																					p.V363E		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.T1088A						.						157	148	152					6																	47251829		2203	4300	6503	SO:0001583	missense	27242	exon3			ATCACCACAAGCA	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"Tumor necrosis factor receptor superfamily", "CD molecules"	13469	protein-coding gene	gene with protein product	"death receptor 6"	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1088T>A	chr6.hg19:g.47251829A>T	ENSP00000296861:p.Val363Glu	89.0	0.0		79.0	34.0	NM_014452	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	hg19	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.773108	0.90108	.	.	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.74737	-0.87	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.82250	0.4996	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.84347	0.0530	10	0.87932	D	0	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	363	O75509	TNR21_HUMAN	E	363;52	ENSP00000296861:V363E	ENSP00000296861:V363E	V	-	2	0	TNFRSF21	47359788	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.659000	0.91116	2.371000	0.80710	0.533000	0.62120	GTG	.	.		0.522	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		T	47251829	A	T	47251829	3	4	223	1	0	0	0	0	1	0	0	0	16310	159	6	4	895	4	TNFRSF21	6	47251829	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10	274929	47251829	123863238	26	31785										
HDAC2	3066	hgsc.bcm.edu	37	chr6	114277278	114277278	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	cctccagcccaattaacagcCatatcagtctgttgtcggtt	7	13	2	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr6:114277278C>A	ENST00000519065.1	-	5	772	c.396G>T	c.(394-396)atG>atT	p.M132I	HDAC2_ENST00000398283.2_Missense_Mutation_p.M226I|HDAC2_ENST00000368632.2_Missense_Mutation_p.M102I|HDAC2_ENST00000519108.1_Missense_Mutation_p.M102I			Q92769	HDAC2_HUMAN	histone deacetylase 2	132	Histone deacetylase.				ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	AATTAACAGCCATATCAGTCT	0.358																																					p.M132I		Atlas-SNP	.											.	HDAC2	102	.	0			c.G396T						.						106	102	103					6																	114277278		1857	4101	5958	SO:0001583	missense	3066	exon5			AACAGCCATATCA	U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.396G>T	chr6.hg19:g.114277278C>A	ENSP00000430432:p.Met132Ile	91.0	0.0		56.0	37.0	NM_001527	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Missense_Mutation	SNP	ENST00000519065.1	hg19	CCDS43493.2	.	.	.	.	.	.	.	.	.	.	C	5.579	0.291725	0.10567	.	.	ENSG00000196591	ENST00000519065;ENST00000398283;ENST00000519108;ENST00000368632;ENST00000425835;ENST00000523628	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.56	5.56	0.83823	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	T	0.06325	0.0163	N	0.00006	-3.24	0.51482	D	0.999924	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.54741	-0.8248	10	0.02654	T	1	-11.9209	14.6977	0.69134	0.1451:0.8549:0.0:0.0	.	102;132	B3KRS5;Q92769	.;HDAC2_HUMAN	I	132;226;102;102;122;102	ENSP00000430432:M132I;ENSP00000381331:M226I;ENSP00000430008:M102I;ENSP00000357621:M102I;ENSP00000417026:M122I	ENSP00000357621:M102I	M	-	3	0	HDAC2	114383971	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.075000	0.41538	2.763000	0.94921	0.585000	0.79938	ATG	.	.		0.358	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2			A	114277278	C	A	114277278	3	1	223	1	0	0	0	0	1	0	0	0	7016	594	21	3	1110	3	HDAC2	6	114277278	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	67025449	114277278	56837789	27	31786										
MTRF1L	54516	hgsc.bcm.edu	37	chr6	153316354	153316354	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gatacatatcaaatatctctGatgtaaacaacattgcctcc	4	10	2	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr6:153316354G>A	ENST00000367233.5	-	3	439	c.440C>T	c.(439-441)tCa>tTa	p.S147L	MTRF1L_ENST00000367231.5_Missense_Mutation_p.S147L|MTRF1L_ENST00000367230.1_Intron|MTRF1L_ENST00000464135.1_5'UTR	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	147						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		AAATATCTCTGATGTAAACAA	0.358																																					p.S147L		Atlas-SNP	.											.	MTRF1L	21	.	0			c.C440T						.						38	36	36					6																	153316354		2201	4277	6478	SO:0001583	missense	54516	exon3			ATCTCTGATGTAA	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.440C>T	chr6.hg19:g.153316354G>A	ENSP00000356202:p.Ser147Leu	211.0	0.0		194.0	71.0	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Missense_Mutation	SNP	ENST00000367233.5	hg19	CCDS5243.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.467480	0.43839	.	.	ENSG00000112031	ENST00000367233;ENST00000367231	T;T	0.12361	2.69;2.69	5.43	4.56	0.56223	Peptide chain release factor (2);	0.397901	0.25327	N	0.031474	T	0.11580	0.0282	M	0.80332	2.49	0.80722	D	1	B;B	0.13594	0.003;0.008	B;B	0.16289	0.007;0.015	T	0.03184	-1.1063	10	0.87932	D	0	-0.1384	14.4477	0.67364	0.0715:0.0:0.9285:0.0	.	147;147	Q9UGC7-2;Q9UGC7	.;RF1ML_HUMAN	L	147	ENSP00000356202:S147L;ENSP00000356200:S147L	ENSP00000356200:S147L	S	-	2	0	MTRF1L	153358047	1.000000	0.71417	0.995000	0.50966	0.976000	0.68499	6.227000	0.72282	1.293000	0.44690	0.585000	0.79938	TCA	.	.		0.358	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041		A	153316354	G	A	153316354	3	1	223	1	0	0	0	0	1	0	0	0	9969	1294	45	3	722	3	MTRF1L	6	153316354	Missense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	39039076	153316354	17798713	28	31787										
THBS2	7058	hgsc.bcm.edu	37	chr6	169620434	169620434	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tccttcatgcactaagactcTaaaaatggtgtttaaaaaga	6	7	2	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr6:169620434T>G	ENST00000366787.3	-	22	3621		c.e22-2		XXyac-YX65C7_A.2_ENST00000444188.1_RNA|THBS2_ENST00000488355.1_Splice_Site	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2						cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		ACTAAGACTCTAAAAATGGTG	0.463																																					.	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.3372-2A>C						.						109	116	114					6																	169620434		2203	4300	6503	SO:0001630	splice_region_variant	7058	exon23			AGACTCTAAAAAT		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.3372-2A>C	chr6.hg19:g.169620434T>G		113.0	0.0		83.0	32.0	NM_003247	A6H8N1|A7E232|Q5RI52	Splice_Site	SNP	ENST00000366787.3	hg19	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	T	15.25	2.776717	0.49786	.	.	ENSG00000186340	ENST00000366787;ENST00000392099	.	.	.	4.64	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.078	0.64903	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	THBS2	169362359	1.000000	0.71417	0.689000	0.30133	0.553000	0.35397	7.474000	0.81024	1.719000	0.51432	0.391000	0.25812	.	.	.		0.463	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	Intron	G	169620434	T	G	169620434	5	3	223	1	0	0	0	0	0	0	1	0	15869	1536	53	5	156	5	THBS2	6	169620434	Splice_Site	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	16304080	169620434	1494633	29	31788										
THBS2	7058	hgsc.bcm.edu	37	chr6	169646339	169646339	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tgcttagaatatcttccacaGagttttcaaacactaggtgg	8	8	2	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr6:169646339G>T	ENST00000366787.3	-	5	896	c.647C>A	c.(646-648)tCt>tAt	p.S216Y		NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	216	Heparin-binding. {ECO:0000255}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		ATCTTCCACAGAGTTTTCAAA	0.408																																					p.S216Y	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.C647A						.						117	112	114					6																	169646339		2203	4300	6503	SO:0001583	missense	7058	exon5			TCCACAGAGTTTT		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.647C>A	chr6.hg19:g.169646339G>T	ENSP00000355751:p.Ser216Tyr	88.0	0.0		66.0	25.0	NM_003247	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	hg19	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.177219	0.57692	.	.	ENSG00000186340	ENST00000366787	T	0.02177	4.41	5.13	5.13	0.70059	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.39687	U	0.001289	T	0.05502	0.0145	M	0.67953	2.075	0.37885	D	0.930523	D	0.63880	0.993	P	0.59056	0.851	T	0.13602	-1.0503	10	0.72032	D	0.01	-28.4404	16.1088	0.81244	0.0:0.0:1.0:0.0	.	216	P35442	TSP2_HUMAN	Y	216	ENSP00000355751:S216Y	ENSP00000355751:S216Y	S	-	2	0	THBS2	169388264	0.997000	0.39634	0.046000	0.18839	0.006000	0.05464	8.596000	0.90844	2.381000	0.81170	0.655000	0.94253	TCT	.	.		0.408	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		T	169646339	G	T	169646339	3	4	223	1	0	0	0	0	1	0	0	0	15869	942	33	3	2947	3	THBS2	6	169646339	Missense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	25905	169646339	1468728	30	31789										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5352833	5352833	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ctgctactgctgccactactGctgctgctgctgctctcgga	10	15	1	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr7:5352833G>A	ENST00000430969.1	-	27	8037	c.7689C>T	c.(7687-7689)agC>agT	p.S2563S	TNRC18_ENST00000399537.4_Silent_p.S2563S	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2563	Ser-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		tgccactactgctgctgctgc	0.672																																					p.S2563S		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7689T						.						3	5	4					7																	5352833		1128	2739	3867	SO:0001819	synonymous_variant	84629	exon27			ACTACTGCTGCTG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7689C>T	chr7.hg19:g.5352833G>A		47.0	0.0		78.0	5.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	g	0.008	-1.904535	0.00512	.	.	ENSG00000182095	ENST00000328270	.	.	.	4.38	1.45	0.22620	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.8385	0.08905	0.1403:0.149:0.519:0.1916	.	.	.	.	X	377	.	.	Q	-	1	0	TNRC18	5319359	0.004000	0.15560	0.014000	0.15608	0.007000	0.05969	-0.229000	0.09098	-0.173000	0.10761	-1.164000	0.01763	CAG	.	.		0.672	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5352833	G	A	5352833	2	1	223	1	0	0	0	0	0	0	0	1	16354	1310	46	3		3	TNRC18	7	5352833	Silent	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10		5352833	153785830	31	31790										
CUX1	1523	hgsc.bcm.edu	37	chr7	101844891	101844891	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	agaagccctccgcagctcctGaggccggtgcctctgctctg	12	16	2	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr7:101844891G>C	ENST00000292535.7	+	18	2352	c.2314G>C	c.(2314-2316)Gag>Cag	p.E772Q	CUX1_ENST00000549414.2_Missense_Mutation_p.E750Q|CUX1_ENST00000550008.2_Missense_Mutation_p.E716Q|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Missense_Mutation_p.E614Q|CUX1_ENST00000546411.2_Missense_Mutation_p.E670Q|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.E783Q	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	772					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						CGCAGCTCCTGAGGCCGGTGC	0.677																																					p.E783Q		Atlas-SNP	.											.	CUX1	253	.	0			c.G2347C						.						91	101	97					7																	101844891		2203	4300	6503	SO:0001583	missense	1523	exon18			GCTCCTGAGGCCG	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.2314G>C	chr7.hg19:g.101844891G>C	ENSP00000292535:p.Glu772Gln	59.0	0.0		55.0	16.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	G	7.010	0.556633	0.13436	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.60548	0.19;0.2;0.19;0.18;0.2;0.2	5.44	5.44	0.79542	.	0.275088	0.35407	N	0.003235	T	0.50786	0.1636	L	0.36672	1.1	0.80722	D	1	B;B	0.30361	0.181;0.277	B;B	0.32289	0.042;0.143	T	0.42865	-0.9426	10	0.20046	T	0.44	-2.9602	19.279	0.94044	0.0:0.0:1.0:0.0	.	772;783	P39880;P39880-3	CUX1_HUMAN;.	Q	783;772;750;716;670;614	ENSP00000353401:E783Q;ENSP00000292535:E772Q;ENSP00000446630:E750Q;ENSP00000447373:E716Q;ENSP00000450125:E670Q;ENSP00000451558:E614Q	ENSP00000292535:E772Q	E	+	1	0	CUX1	101631611	1.000000	0.71417	0.388000	0.26195	0.057000	0.15508	5.272000	0.65559	2.560000	0.86352	0.655000	0.94253	GAG	.	.		0.677	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		C	101844891	G	C	101844891	3	2	223	1	0	0	0	0	1	0	0	0	4066	1291	45	4	2451	4	CUX1	7	101844891	Missense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	96492058	101844891	57293772	32	31791										
PODXL	5420	hgsc.bcm.edu	37	chr7	131241049	131241050	+	In_Frame_Ins	INS	-	-	CGACGC													0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ggcgacggcgacggcgacggINScgacgacggcagcagcggcg					rs201847316		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr7:131241049_131241050insCGACGC	ENST00000378555.3	-	1	316_317	c.69_70insGCGTCG	c.(67-72)tcgccg>tcgGCGTCGccg	p.22_23insSA	PODXL_ENST00000322985.9_In_Frame_Ins_p.22_23insSA|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000541194.1_In_Frame_Ins_p.22_23insSA|PODXL_ENST00000537928.1_In_Frame_Ins_p.22_23insSA			O00592	PODXL_HUMAN	podocalyxin-like	22					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					gacggcgacggcgacgacggca	0.738																																					p.P24delinsASP		Atlas-INDEL	.											.	PODXL	53	.	0			c.70_71insGCGTCG						.																																			SO:0001652	inframe_insertion	5420	exon1			.		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.69_70insGCGTCG	chr7.hg19:g.131241049_131241050insCGACGC	ENSP00000367817:p.Ser22_Ser23insSerAla	75.0	0.0		65.0	27.0	NM_005397	A6NHX8|Q52LZ7|Q53ER6	In_Frame_Ins	INS	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.738	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		CGACGC	131241050	-	CGACGC	131241049	7	5	223	1	0	1	1	0	0	0	0	0	12189	1203	42	0	1642	0	PODXL	7	131241049	In_Frame_Ins	INS	-	TCGA-DD-AAVP-01A-11D-A40R-10	29396158	131241049	27897614	33	31792										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	132192829	132192829	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gcgaacatgccatccgcctcAgagttcttggtcagtttccg	10	13	3	1	rs142932361		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr7:132192829A>C	ENST00000359827.3	-	2	1586	c.624T>G	c.(622-624)tcT>tcG	p.S208S	PLXNA4_ENST00000321063.4_Silent_p.S208S|PLXNA4_ENST00000378539.5_Silent_p.S208S|PLXNA4_ENST00000423507.2_Silent_p.S208S			Q9HCM2	PLXA4_HUMAN	plexin A4	208	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CATCCGCCTCAGAGTTCTTGG	0.522																																					p.S208S		Atlas-SNP	.											.	PLXNA4	873	.	0			c.T624G						.						144	138	140					7																	132192829		2203	4300	6503	SO:0001819	synonymous_variant	91584	exon2			CGCCTCAGAGTTC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.624T>G	chr7.hg19:g.132192829A>C		57.0	0.0		52.0	22.0	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	hg19	CCDS43646.1																																																																																			.	A|1.000;G|0.000		0.522	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		C	132192829	A	C	132192829	2	2	223	1	0	0	0	0	0	0	0	1	12131	175	7	5		5	PLXNA4	7	132192829	Silent	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10	951780	132192829	26945834	34	31793										
GPR124	25960	hgsc.bcm.edu	37	chr8	37699548	37699548	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	cagccccaccgacagctaccTgggcagcagccgcaacagcc	10	19	0	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr8:37699548T>A	ENST00000412232.2	+	19	3705	c.3692T>A	c.(3691-3693)cTg>cAg	p.L1231Q	GPR124_ENST00000315215.7_Missense_Mutation_p.L1014Q	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	1231					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			GACAGCTACCTGGGCAGCAGC	0.731																																					p.L1231Q		Atlas-SNP	.											.	GPR124	85	.	0			c.T3692A						.						2	3	2					8																	37699548		1145	2256	3401	SO:0001583	missense	25960	exon19			GCTACCTGGGCAG	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.3692T>A	chr8.hg19:g.37699548T>A	ENSP00000406367:p.Leu1231Gln	9.0	0.0		26.0	11.0	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	T	2.846	-0.239458	0.05944	.	.	ENSG00000020181	ENST00000315215;ENST00000412232	T;T	0.56776	0.44;0.56	3.52	0.358	0.16084	.	0.680781	0.13068	U	0.416315	T	0.27241	0.0668	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.20773	-1.0265	10	0.11794	T	0.64	-6.7977	5.1621	0.15066	0.43:0.3919:0.0:0.1781	.	1014;1231	Q96PE1-2;Q96PE1	.;GP124_HUMAN	Q	1014;1231	ENSP00000323508:L1014Q;ENSP00000406367:L1231Q	ENSP00000323508:L1014Q	L	+	2	0	GPR124	37818706	0.000000	0.05858	0.365000	0.25901	0.420000	0.31355	-0.519000	0.06260	-0.089000	0.12484	-0.736000	0.03550	CTG	.	.		0.731	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			A	37699548	T	A	37699548	3	1	223	1	0	0	0	0	1	0	0	0	6646	1580	55	4	3745	4	GPR124	8	37699548	Missense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10		37699548	108664474	35	31794										
PAG1	55824	hgsc.bcm.edu	37	chr8	81888943	81888943	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	aggctctggctcctcgctggGcctccctgctggtggaagtg	15	13	1	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr8:81888943G>A	ENST00000220597.4	-	9	1845	c.1135C>T	c.(1135-1137)Ccc>Tcc	p.P379S	PAG1_ENST00000523463.1_5'Flank	NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	379					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			TCCTCGCTGGGCCTCCCTGCT	0.542																																					p.P379S		Atlas-SNP	.											.	PAG1	39	.	0			c.C1135T						.						83	78	80					8																	81888943		2203	4300	6503	SO:0001583	missense	55824	exon9			CGCTGGGCCTCCC	AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"Csk-binding protein", "transmembrane adaptor protein PAG"	605767	"phosphoprotein associated with glycosphingolipid microdomains 1"			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.1135C>T	chr8.hg19:g.81888943G>A	ENSP00000220597:p.Pro379Ser	123.0	0.0		92.0	30.0	NM_018440	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Missense_Mutation	SNP	ENST00000220597.4	hg19	CCDS6227.1	.	.	.	.	.	.	.	.	.	.	G	2.287	-0.363324	0.05103	.	.	ENSG00000076641	ENST00000220597	.	.	.	4.52	1.65	0.23941	.	0.268289	0.36234	N	0.002720	T	0.26448	0.0646	L	0.36672	1.1	0.09310	N	1	B	0.14805	0.011	B	0.17098	0.017	T	0.17167	-1.0378	9	0.14656	T	0.56	-15.8353	6.8149	0.23824	0.1608:0.2739:0.5654:0.0	.	379	Q9NWQ8	PAG1_HUMAN	S	379	.	ENSP00000220597:P379S	P	-	1	0	PAG1	82051498	0.241000	0.23857	0.021000	0.16686	0.038000	0.13279	0.508000	0.22692	0.604000	0.29930	0.655000	0.94253	CCC	.	.		0.542	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440		A	81888943	G	A	81888943	3	1	223	1	0	0	0	0	1	0	0	0	11397	1203	42	3	167	3	PAG1	8	81888943	Missense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	44189395	81888943	64475079	36	31795										
CDH17	1015	hgsc.bcm.edu	37	chr8	95188826	95188826	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tgactggagaaacgtgggtcGattgtcgttgatgtccttca	13	7	1	3			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr8:95188826G>T	ENST00000027335.3	-	5	491	c.367C>A	c.(367-369)Cga>Aga	p.R123R	CDH17_ENST00000441892.2_Silent_p.R123R|CDH17_ENST00000450165.2_Silent_p.R123R	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	123	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)	p.R123*(1)		NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			AACGTGGGTCGATTGTCGTTG	0.493																																					p.R123R		Atlas-SNP	.											CDH17,NS,malignant_melanoma,+1,1	CDH17	119	.	1	Substitution - Nonsense(1)	ovary(1)	c.C367A						.						255	214	228					8																	95188826		2203	4300	6503	SO:0001819	synonymous_variant	1015	exon5			TGGGTCGATTGTC	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.367C>A	chr8.hg19:g.95188826G>T		176.0	0.0		149.0	54.0	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	hg19	CCDS6260.1																																																																																			.	.		0.493	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		T	95188826	G	T	95188826	2	4	223	1	0	0	0	0	0	0	0	1	3104	1066	37	1		1	CDH17	8	95188826	Silent	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	13299883	95188826	51175196	37	31796										
RECQL4	113655	hgsc.bcm.edu	37	chr8	145738712	145738712	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	agccccagatgcagcacagcCcgcacatctggccggtccag	11	17	1	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr8:145738712C>T	ENST00000301327.4	+	0	1548				RECQL4_ENST00000428558.2_Silent_p.R784R|RECQL4_ENST00000532237.1_5'UTR|CTD-2517M22.17_ENST00000580385.1_RNA	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GCAGCACAGCCCGCACATCTG	0.711																																					p.R784R		Atlas-SNP	.											.	RECQL4	75	.	0			c.G2352A						.						13	18	16					8																	145738712		2052	4173	6225	SO:0001628	intergenic_variant	9401	exon15			CACAGCCCGCACA		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		chr8.hg19:g.145738712C>T		61.0	0.0		52.0	18.0	NM_004260		Silent	SNP	ENST00000301327.4	hg19	CCDS6431.1																																																																																			.	.		0.711	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		T	145738712	C	T	145738712	1	4	223	0	1	0	0	0	0	0	0	0	13217	623	22	3		3	RECQL4	8	145738712	IGR	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	50549886	145738712	625310	38	31797										
MLANA	2315	hgsc.bcm.edu	37	chr9	5906982	5906982	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	caaagtgtctcttcaagagaAaaactgtgaacctgtggtag	10	7	2	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr9:5906982A>C	ENST00000381477.3	+	4	432	c.272A>C	c.(271-273)aAa>aCa	p.K91T	MLANA_ENST00000490518.1_3'UTR|MLANA_ENST00000381471.1_Missense_Mutation_p.K91T|MLANA_ENST00000381476.1_Missense_Mutation_p.K91T|KIAA2026_ENST00000443149.2_Intron	NM_005511.1	NP_005502.1	Q16655	MAR1_HUMAN	melan-A	91						endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|melanosome (GO:0042470)|trans-Golgi network (GO:0005802)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	8		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(1;1.15e-06)|Lung(218;0.103)		CTTCAAGAGAAAAACTGTGAA	0.378																																					p.K91T		Atlas-SNP	.											.	MLANA	16	.	0			c.A272C						.						90	88	89					9																	5906982		2203	4300	6503	SO:0001583	missense	2315	exon4			AAGAGAAAAACTG		CCDS6466.1	9p24.1	2008-02-05			ENSG00000120215	ENSG00000120215			7124	protein-coding gene	gene with protein product		605513					Standard	NM_005511		Approved	MART1	uc003zjo.1	Q16655	OTTHUMG00000019510	ENST00000381477.3:c.272A>C	chr9.hg19:g.5906982A>C	ENSP00000370886:p.Lys91Thr	120.0	0.0		80.0	24.0	NM_005511	Q6ICU4	Missense_Mutation	SNP	ENST00000381477.3	hg19	CCDS6466.1	.	.	.	.	.	.	.	.	.	.	A	4.134	0.023132	0.08006	.	.	ENSG00000120215	ENST00000381477;ENST00000381476;ENST00000381471	.	.	.	6.07	2.35	0.29111	.	0.545956	0.21417	N	0.074892	T	0.29817	0.0745	L	0.44542	1.39	0.27103	N	0.962564	B	0.28636	0.218	B	0.31101	0.124	T	0.17379	-1.0371	9	0.28530	T	0.3	-2.2595	4.2637	0.10752	0.6935:0.0:0.1596:0.1469	.	91	Q16655	MAR1_HUMAN	T	91	.	ENSP00000370880:K91T	K	+	2	0	MLANA	5896982	0.036000	0.19791	0.674000	0.29902	0.339000	0.28857	0.333000	0.19768	0.150000	0.19136	-0.263000	0.10527	AAA	.	.		0.378	MLANA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051643.1			C	5906982	A	C	5906982	3	2	223	1	0	0	0	0	1	0	0	0	9620	14	1	5	282	5	MLANA	9	5906982	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10		5906982	135306449	39	31798										
OR1J1	347168	hgsc.bcm.edu	37	chr9	125239744	125239744	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	agggtatgcaaaagagcacaCgcacaagcgatgacccagga	12	10	0	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr9:125239744C>A	ENST00000259357.2	-	1	491	c.462G>T	c.(460-462)gcG>gcT	p.A154A	RP11-542K23.9_ENST00000412262.2_RNA	NM_001004451.1	NP_001004451.1	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J, member 1	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	16						AAAGAGCACACGCACAAGCGA	0.537																																					p.A154A		Atlas-SNP	.											.	OR1J1	46	.	0			c.G462T						.						91	79	83					9																	125239744		2203	4300	6503	SO:0001819	synonymous_variant	347168	exon1			AGCACACGCACAA	AL353767	CCDS35120.1	9q33.2	2013-09-20			ENSG00000136834	ENSG00000136834		"GPCR / Class A : Olfactory receptors"	8208	protein-coding gene	gene with protein product							Standard	NM_001004451		Approved	hg32	uc011lyu.2	Q8NGS3	OTTHUMG00000020603	ENST00000259357.2:c.462G>T	chr9.hg19:g.125239744C>A		96.0	0.0		82.0	31.0	NM_001004451	A3KFL8|Q6IF10|Q96R88	Silent	SNP	ENST00000259357.2	hg19	CCDS35120.1																																																																																			.	.		0.537	OR1J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053931.1			A	125239744	C	A	125239744	2	1	223	1	0	0	0	0	0	0	0	1	10968	523	19	1		1	OR1J1	9	125239744	Silent	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	119332762	125239744	15973687	40	31799										
GATA3	2625	hgsc.bcm.edu	37	chr10	8106026	8106026	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	cgagatggcacgggacactaCctgtgcaacgcctgcgggct	14	13	0	1	rs138698611		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr10:8106026C>T	ENST00000346208.3	+	4	1301	c.846C>T	c.(844-846)taC>taT	p.Y282Y	GATA3_ENST00000379328.3_Silent_p.Y283Y|GATA3_ENST00000461472.1_Intron			P23771	GATA3_HUMAN	GATA binding protein 3	282					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						CGGGACACTACCTGTGCAACG	0.557			"F, N, S"		breast		"HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"																														p.Y283Y		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.C849T						.	C	,	0,4406		0,0,2203	143	113	123		849,846	5.6	1	10	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	GATA3	NM_001002295.1,NM_002051.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	283/445,282/444	8106026	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2625	exon4			ACACTACCTGTGC	X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"GATA zinc finger domain containing"	4172	protein-coding gene	gene with protein product		131320	"GATA-binding protein 3"			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.846C>T	chr10.hg19:g.8106026C>T		159.0	0.0		107.0	35.0	NM_001002295	Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	hg19	CCDS7083.1																																																																																			.	C|1.000;T|0.000		0.557	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		T	8106026	C	T	8106026	2	4	223	1	0	0	0	0	0	0	0	1	6263	518	18	3		3	GATA3	10	8106026	Silent	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10		8106026	127428721	41	31800										
CUBN	8029	hgsc.bcm.edu	37	chr10	17147494	17147494	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	acaggggtgacttaggcaaaTattactgagctgcacacatc	10	9	0	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr10:17147494T>G	ENST00000377833.4	-	11	1257	c.1192A>C	c.(1192-1194)Att>Ctt	p.I398L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	398	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CTTAGGCAAATATTACTGAGC	0.428																																					p.I398L		Atlas-SNP	.											.	CUBN	515	.	0			c.A1192C						.						165	144	151					10																	17147494		2203	4300	6503	SO:0001583	missense	8029	exon11			GGCAAATATTACT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1192A>C	chr10.hg19:g.17147494T>G	ENSP00000367064:p.Ile398Leu	92.0	0.0		60.0	29.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	7.847	0.723232	0.15439	.	.	ENSG00000107611	ENST00000377833	D	0.94862	-3.54	5.65	0.386	0.16254	Growth factor, receptor (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.659509	0.13242	N	0.402767	D	0.86180	0.5871	N	0.17474	0.49	0.09310	N	0.999998	B	0.15719	0.014	B	0.12837	0.008	T	0.73251	-0.4042	10	0.28530	T	0.3	.	6.3365	0.21298	0.0:0.132:0.2485:0.6194	.	398	O60494	CUBN_HUMAN	L	398	ENSP00000367064:I398L	ENSP00000367064:I398L	I	-	1	0	CUBN	17187500	0.047000	0.20315	0.002000	0.10522	0.116000	0.19942	1.078000	0.30754	-0.165000	0.10908	-0.353000	0.07706	ATT	.	.		0.428	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17147494	T	G	17147494	3	3	223	1	0	0	0	0	1	0	0	0	4053	1406	49	5	9907	5	CUBN	10	17147494	Missense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	9041468	17147494	118387253	42	31801										
HERC4	26091	hgsc.bcm.edu	37	chr10	69750905	69750906	+	Frame_Shift_Ins	INS	-	-	A													0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ttgccacttacctaacagctINSaaaaaacttccatttaggca					rs370234029		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr10:69750905_69750906insA	ENST00000395198.3	-	12	1569_1570	c.1322_1323insT	c.(1321-1323)ttafs	p.L441fs	HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000373700.4_Frame_Shift_Ins_p.L441fs|HERC4_ENST00000277817.6_Frame_Shift_Ins_p.L331fs|HERC4_ENST00000412272.2_Frame_Shift_Ins_p.L441fs	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	441					cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.L441fs*4(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						ACCTAACAGCTAAAAAACTTCC	0.223																																					p.L441fs		Atlas-INDEL	.											.,1	HERC4	78	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1323_1324insT						.																																			SO:0001589	frameshift_variant	26091	exon12			.	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"hect domain and RLD 4"			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.1323dupT	chr10.hg19:g.69750911_69750911dupA	ENSP00000378624:p.Leu441fs	645.0	0.0		501.0	158.0	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Frame_Shift_Ins	INS	ENST00000395198.3	hg19	CCDS41533.1																																																																																			.	.		0.223	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601		A	69750906	-	A	69750905	7	5	223	1	0	1	1	0	0	0	0	0	7069	1519	53	0	1910	0	HERC4	10	69750905	Frame_Shift_Ins	INS	-	TCGA-DD-AAVP-01A-11D-A40R-10	52603411	69750905	65783842	43	31802										
ZMIZ1	57178	hgsc.bcm.edu	37	chr10	81064989	81064989	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tggaggtgtcctgtgtgcaaGtgagtgatgcccaccccggt	15	10	0	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr10:81064989G>C	ENST00000334512.5	+	20	2926		c.e20+1		ZMIZ1_ENST00000446377.2_5'Flank	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1						artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CTGTGTGCAAGTGAGTGATGC	0.597																																					.		Atlas-SNP	.											.	ZMIZ1	101	.	0			c.2354+1G>C						.						121	101	108					10																	81064989		2203	4300	6503	SO:0001630	splice_region_variant	57178	exon20			GTGCAAGTGAGTG	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"Zinc fingers, MIZ-type"	16493	protein-coding gene	gene with protein product		607159	"retinoic acid induced 17"	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.2354+1G>C	chr10.hg19:g.81064989G>C		80.0	0.0		40.0	6.0	NM_020338	Q5JSH9|Q7Z7E6	Splice_Site	SNP	ENST00000334512.5	hg19	CCDS7357.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.264298	0.80358	.	.	ENSG00000108175	ENST00000334512;ENST00000360331;ENST00000372347	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9192	0.92518	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZMIZ1	80734995	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.476000	0.97823	2.475000	0.83589	0.591000	0.81541	.	.	.		0.597	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338	Intron	C	81064989	G	C	81064989	5	2	223	1	0	0	0	0	0	0	1	0	17711	1043	36	4	2417	4	ZMIZ1	10	81064989	Splice_Site	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	11314084	81064989	54469758	44	31803										
MAT1A	4143	hgsc.bcm.edu	37	chr10	82034403	82034403	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ctcggccacaccaatggcatAggaaaccttccagcaaggtg	10	13	0	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr10:82034403A>T	ENST00000372213.3	-	8	1218	c.958T>A	c.(958-960)Tat>Aat	p.Y320N	MAT1A_ENST00000485270.1_5'UTR	NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	320					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	CCAATGGCATAGGAAACCTTC	0.557																																					p.Y320N		Atlas-SNP	.											.	MAT1A	52	.	0			c.T958A						.						108	96	100					10																	82034403		2203	4300	6503	SO:0001583	missense	4143	exon8			TGGCATAGGAAAC		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"S-adenosylmethionine synthetase"	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.958T>A	chr10.hg19:g.82034403A>T	ENSP00000361287:p.Tyr320Asn	71.0	0.0		45.0	17.0	NM_000429	D3DWD5|Q5QP09	Missense_Mutation	SNP	ENST00000372213.3	hg19	CCDS7365.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.214920	0.79352	.	.	ENSG00000151224	ENST00000372213;ENST00000372206	D	0.98792	-5.14	5.16	5.16	0.70880	S-adenosylmethionine synthetase, C-terminal (1);S-adenosylmethionine synthetase superfamily (1);	0.000000	0.85682	D	0.000000	D	0.99504	0.9823	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97962	1.0338	10	0.87932	D	0	-21.5107	13.249	0.60041	1.0:0.0:0.0:0.0	.	320	Q00266	METK1_HUMAN	N	320	ENSP00000361287:Y320N	ENSP00000361280:Y320N	Y	-	1	0	MAT1A	82024383	1.000000	0.71417	0.999000	0.59377	0.715000	0.41141	8.962000	0.93254	2.081000	0.62600	0.533000	0.62120	TAT	.	.		0.557	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429		T	82034403	A	T	82034403	3	4	223	1	0	0	0	0	1	0	0	0	9338	420	15	4	237	4	MAT1A	10	82034403	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10	969414	82034403	53500344	45	31804										
ARFIP2	23647	hgsc.bcm.edu	37	chr11	6500162	6500162	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	agtccgtgagcctcgaccaaAtcgttctgataacagttgct	9	11	1	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr11:6500162A>G	ENST00000254584.2	-	5	426	c.343T>C	c.(343-345)Ttt>Ctt	p.F115L	ARFIP2_ENST00000396777.3_Missense_Mutation_p.F115L|ARFIP2_ENST00000445086.2_Missense_Mutation_p.F30L|ARFIP2_ENST00000423813.2_Missense_Mutation_p.F77L|TIMM10B_ENST00000472836.1_5'Flank|ARFIP2_ENST00000525235.1_Missense_Mutation_p.F115L|TIMM10B_ENST00000530751.1_5'Flank|TIMM10B_ENST00000254616.6_5'Flank	NM_012402.3	NP_036534.1	P53365	ARFP2_HUMAN	ADP-ribosylation factor interacting protein 2	115					actin cytoskeleton organization (GO:0030036)|cellular component movement (GO:0006928)|lamellipodium assembly (GO:0030032)|ruffle organization (GO:0031529)|small GTPase mediated signal transduction (GO:0007264)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|Rac GTPase binding (GO:0048365)			endometrium(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(2)	15		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCTCGACCAAATCGTTCTGAT	0.537																																					p.F148L	Melanoma(119;796 1674 9049 20480 24794)	Atlas-SNP	.											.	ARFIP2	23	.	0			c.T442C						.						73	55	61					11																	6500162		2201	4296	6497	SO:0001583	missense	23647	exon5			GACCAAATCGTTC	BC000392	CCDS7765.1, CCDS55739.1, CCDS55740.1, CCDS73250.1	11p15	2008-08-01	2008-08-01		ENSG00000132254	ENSG00000132254			17160	protein-coding gene	gene with protein product	"arfaptin 2"	601638				8670882, 9038142	Standard	NM_012402		Approved	POR1	uc010ran.2	P53365	OTTHUMG00000133406	ENST00000254584.2:c.343T>C	chr11.hg19:g.6500162A>G	ENSP00000254584:p.Phe115Leu	69.0	0.0		46.0	19.0	NM_001242854	B4DX86|B4E306|D3DQT5	Missense_Mutation	SNP	ENST00000254584.2	hg19	CCDS7765.1	.	.	.	.	.	.	.	.	.	.	A	11.57	1.678795	0.29783	.	.	ENSG00000132254	ENST00000254584;ENST00000396777;ENST00000445086;ENST00000423813;ENST00000525235	T;T;T;T;T	0.73363	-0.74;-0.74;-0.74;-0.74;-0.74	5.68	5.68	0.88126	Arfaptin-like (1);	0.000000	0.85682	D	0.000000	T	0.73505	0.3595	N	0.19112	0.55	0.80722	D	1	D;B;D	0.69078	0.997;0.004;0.992	D;B;D	0.80764	0.994;0.004;0.987	T	0.68273	-0.5452	10	0.02654	T	1	.	15.5881	0.76502	1.0:0.0:0.0:0.0	.	148;30;115	B4DUZ3;B4E306;P53365	.;.;ARFP2_HUMAN	L	115;115;30;77;115	ENSP00000254584:F115L;ENSP00000379998:F115L;ENSP00000391427:F30L;ENSP00000398375:F77L;ENSP00000434124:F115L	ENSP00000254584:F115L	F	-	1	0	ARFIP2	6456738	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.156000	0.71840	2.177000	0.69029	0.402000	0.26972	TTT	.	.		0.537	ARFIP2-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387044.1	NM_012402		G	6500162	A	G	6500162	3	3	223	1	0	0	0	0	1	0	0	0	855	101	4	2	698	2	ARFIP2	11	6500162	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10		6500162	128506354	46	31805										
ZDHHC13	54503	hgsc.bcm.edu	37	chr11	19173800	19173800	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	acttcactgggcagttgcagCaggaaatgttaatgcagttg	12	7	1	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr11:19173800C>T	ENST00000446113.2	+	7	801	c.680C>T	c.(679-681)gCa>gTa	p.A227V	ZDHHC13_ENST00000532812.1_3'UTR|ZDHHC13_ENST00000399351.3_Missense_Mutation_p.A97V	NM_019028.2	NP_061901.2	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC-type containing 13	227					metabolic process (GO:0008152)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	magnesium ion transmembrane transporter activity (GO:0015095)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6						GCAGTTGCAGCAGGAAATGTT	0.393																																					p.A227V		Atlas-SNP	.											.	ZDHHC13	40	.	0			c.C680T						.						132	121	125					11																	19173800		1858	4092	5950	SO:0001583	missense	54503	exon7			TTGCAGCAGGAAA	AB024495	CCDS44550.1, CCDS44551.1	11p15.1	2013-01-10			ENSG00000177054	ENSG00000177054		"Zinc fingers, DHHC-type", "Ankyrin repeat domain containing"	18413	protein-coding gene	gene with protein product		612815				18794299	Standard	NM_001001483		Approved	FLJ10852, FLJ10941, HIP14L	uc001mpi.3	Q8IUH4	OTTHUMG00000166099	ENST00000446113.2:c.680C>T	chr11.hg19:g.19173800C>T	ENSP00000400113:p.Ala227Val	154.0	0.0		104.0	38.0	NM_019028	Q7Z2D3|Q86VK2|Q9NV30|Q9NV99	Missense_Mutation	SNP	ENST00000446113.2	hg19	CCDS44550.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434257	0.83776	.	.	ENSG00000177054	ENST00000446113;ENST00000399351	T;T	0.53206	0.63;0.63	5.47	5.47	0.80525	Ankyrin repeat-containing domain (4);	0.000000	0.56097	D	0.000036	T	0.47911	0.1471	L	0.28740	0.885	0.80722	D	1	P	0.52577	0.954	P	0.48952	0.596	T	0.43718	-0.9374	10	0.45353	T	0.12	0.1598	18.9329	0.92574	0.0:1.0:0.0:0.0	.	227	Q8IUH4	ZDH13_HUMAN	V	227;97	ENSP00000400113:A227V;ENSP00000382288:A97V	ENSP00000382288:A97V	A	+	2	0	ZDHHC13	19130376	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	5.913000	0.69957	2.582000	0.87167	0.591000	0.81541	GCA	.	.		0.393	ZDHHC13-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387821.1	NM_019028		T	19173800	C	T	19173800	3	4	223	1	0	0	0	0	1	0	0	0	17618	710	25	3	706	3	ZDHHC13	11	19173800	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	12673638	19173800	115832716	47	31806										
OR8K3	219473	hgsc.bcm.edu	37	chr11	56086232	56086232	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ctggtagcaatcccttacctCtattgcacattcatttctct	4	13	3	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr11:56086232C>T	ENST00000312711.1	+	1	450	c.450C>T	c.(448-450)ctC>ctT	p.L150L		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					TCCCTTACCTCTATTGCACAT	0.428																																					p.L150L		Atlas-SNP	.											.	OR8K3	92	.	0			c.C450T						.						119	117	118					11																	56086232		2201	4296	6497	SO:0001819	synonymous_variant	219473	exon1			TTACCTCTATTGC	AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"GPCR / Class A : Olfactory receptors"	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.450C>T	chr11.hg19:g.56086232C>T		115.0	0.0		86.0	28.0	NM_001005202	Q6IFC4	Silent	SNP	ENST00000312711.1	hg19	CCDS31527.1																																																																																			.	.		0.428	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	NM_001005202		T	56086232	C	T	56086232	2	4	223	1	0	0	0	0	0	0	0	1	11253	900	32	3		3	OR8K3	11	56086232	Silent	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	36912432	56086232	78920284	48	31807										
FAM111A	63901	hgsc.bcm.edu	37	chr11	58919496	58919496	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	aggctgtcagaaaagagataGaaactcaccaaggccaagaa	10	8	2	4			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr11:58919496G>T	ENST00000528737.1	+	5	3173	c.355G>T	c.(355-357)Gaa>Taa	p.E119*	FAM111A_ENST00000531147.1_Nonsense_Mutation_p.E119*|FAM111A_ENST00000361723.3_Nonsense_Mutation_p.E119*|FAM111A_ENST00000420244.1_Nonsense_Mutation_p.E119*|FAM111A_ENST00000533703.1_Nonsense_Mutation_p.E119*			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	119					defense response to virus (GO:0051607)|DNA replication (GO:0006260)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				AAAAGAGATAGAAACTCACCA	0.443																																					p.E119X		Atlas-SNP	.											.	FAM111A	57	.	0			c.G355T						.						77	74	75					11																	58919496		2201	4295	6496	SO:0001587	stop_gained	63901	exon5			GAGATAGAAACTC	AK092953	CCDS7973.1	11q12.1	2014-03-13				ENSG00000166801			24725	protein-coding gene	gene with protein product		615292				11572484, 23996431, 23684011	Standard	NM_022074		Approved	FLJ22794, KIAA1895	uc001nnq.3	Q96PZ2		ENST00000528737.1:c.355G>T	chr11.hg19:g.58919496G>T	ENSP00000434435:p.Glu119*	150.0	0.0		123.0	43.0	NM_001142520	A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Nonsense_Mutation	SNP	ENST00000528737.1	hg19	CCDS7973.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.215064	0.79352	.	.	ENSG00000166801	ENST00000528737;ENST00000420244;ENST00000361723;ENST00000527629;ENST00000533703;ENST00000531147	.	.	.	5.49	-2.03	0.07365	.	0.921525	0.09200	N	0.834797	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-5.4258	10.0867	0.42423	0.5176:0.0:0.4824:0.0	.	.	.	.	X	119	.	ENSP00000355264:E119X	E	+	1	0	FAM111A	58676072	0.000000	0.05858	0.000000	0.03702	0.333000	0.28666	-0.513000	0.06305	-0.607000	0.05738	0.650000	0.86243	GAA	.	.		0.443	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074		T	58919496	G	T	58919496	4	4	223	1	0	0	0	0	0	1	0	0	5404	943	33	3	361	3	FAM111A	11	58919496	Nonsense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	2833264	58919496	76087020	49	31808										
PLCB3	5331	hgsc.bcm.edu	37	chr11	64023939	64023939	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	cgagactcaacgaagtgctgTacccgcccctgcggccctcc	10	18	1	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr11:64023939T>A	ENST00000540288.1	+	9	893	c.790T>A	c.(790-792)Tac>Aac	p.Y264N	PLCB3_ENST00000279230.6_Missense_Mutation_p.Y264N|PLCB3_ENST00000325234.5_Missense_Mutation_p.Y197N	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	264					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						CGAAGTGCTGTACCCGCCCCT	0.632																																					p.Y264N		Atlas-SNP	.											.	PLCB3	103	.	0			c.T790A						.						77	95	89					11																	64023939		2200	4295	6495	SO:0001583	missense	5331	exon9			GTGCTGTACCCGC	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.790T>A	chr11.hg19:g.64023939T>A	ENSP00000443631:p.Tyr264Asn	120.0	0.0		123.0	44.0	NM_000932	A5PKZ6|G5E960|Q8N1A4	Missense_Mutation	SNP	ENST00000540288.1	hg19	CCDS8064.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.833406	0.91036	.	.	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	T;T;T	0.48201	0.82;0.82;0.82	5.32	5.32	0.75619	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);EF-hand-like domain (1);	0.060377	0.64402	D	0.000002	T	0.71324	0.3326	M	0.85197	2.74	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.78314	0.977;0.991	T	0.77008	-0.2747	10	0.87932	D	0	.	14.2567	0.66058	0.0:0.0:0.0:1.0	.	197;264	G5E960;Q01970	.;PLCB3_HUMAN	N	264;264;197	ENSP00000279230:Y264N;ENSP00000443631:Y264N;ENSP00000324660:Y197N	ENSP00000279230:Y264N	Y	+	1	0	PLCB3	63780515	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.924000	0.87555	2.019000	0.59389	0.459000	0.35465	TAC	.	.		0.632	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1			A	64023939	T	A	64023939	3	1	223	1	0	0	0	0	1	0	0	0	12038	1638	57	4	824	4	PLCB3	11	64023939	Missense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	5104443	64023939	70982577	50	31809										
PRSS23	11098	hgsc.bcm.edu	37	chr11	86518742	86518742	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tttctgctctgtgctgttggGcaagtgagcccttacagtgc	12	10	2	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr11:86518742G>C	ENST00000280258.5	+	2	482	c.57G>C	c.(55-57)ggG>ggC	p.G19G	PRSS23_ENST00000441050.1_Silent_p.G19G|PRSS23_ENST00000533902.2_Intron	NM_007173.4	NP_009104.1	O95084	PRS23_HUMAN	protease, serine, 23	19						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(9)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GTGCTGTTGGGCAAGTGAGCC	0.557																																					p.G19G		Atlas-SNP	.											.	PRSS23	49	.	0			c.G57C						.						135	138	137					11																	86518742		2201	4299	6500	SO:0001819	synonymous_variant	11098	exon2			TGTTGGGCAAGTG	AF015287	CCDS8278.1	11q14.2	2010-05-12			ENSG00000150687	ENSG00000150687		"Serine peptidases / Serine peptidases"	14370	protein-coding gene	gene with protein product							Standard	XM_005273727		Approved	SPUVE, SIG13	uc001pcb.3	O95084		ENST00000280258.5:c.57G>C	chr11.hg19:g.86518742G>C		99.0	0.0		68.0	28.0	NM_007173	B2RDJ1|B4E2J3|Q6IBI0	Silent	SNP	ENST00000280258.5	hg19	CCDS8278.1																																																																																			.	.		0.557	PRSS23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393805.2	NM_007173		C	86518742	G	C	86518742	2	2	223	1	0	0	0	0	0	0	0	1	12632	1190	42	4		4	PRSS23	11	86518742	Silent	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	22494803	86518742	48487774	51	31810										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41387040	41387040	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ggtagaggagagcccagtatAccatctaacagaattaaaac	9	8	1	3			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr12:41387040A>G	ENST00000551295.2	+	17	2199	c.2082A>G	c.(2080-2082)atA>atG	p.I694M	CNTN1_ENST00000348761.2_Missense_Mutation_p.I683M|CNTN1_ENST00000347616.1_Missense_Mutation_p.I694M	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	694	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				AGCCCAGTATACCATCTAACA	0.398																																					p.I694M		Atlas-SNP	.											.	CNTN1	207	.	0			c.A2082G						.						81	81	81					12																	41387040		2203	4300	6503	SO:0001583	missense	1272	exon17			CAGTATACCATCT	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.2082A>G	chr12.hg19:g.41387040A>G	ENSP00000447006:p.Ile694Met	136.0	0.0		112.0	38.0	NM_001843	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	A	10.79	1.448564	0.26074	.	.	ENSG00000018236	ENST00000551295;ENST00000347616;ENST00000348761	T;T;T	0.53857	0.6;0.6;0.6	5.2	5.2	0.72013	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.544953	0.22402	N	0.060529	T	0.25865	0.0630	N	0.02802	-0.49	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.12156	0.007;0.003	T	0.11012	-1.0605	10	0.46703	T	0.11	.	5.8337	0.18594	0.7886:0.0:0.2114:0.0	.	683;694	Q12860-2;Q12860	.;CNTN1_HUMAN	M	694;694;683	ENSP00000447006:I694M;ENSP00000325660:I694M;ENSP00000261160:I683M	ENSP00000325660:I694M	I	+	3	3	CNTN1	39673307	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	1.302000	0.33459	2.083000	0.62718	0.454000	0.30748	ATA	.	.		0.398	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		G	41387040	A	G	41387040	3	3	223	1	0	0	0	0	1	0	0	0	3642	381	14	2	2144	2	CNTN1	12	41387040	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10		41387040	92464855	52	31811										
NBEA	26960	hgsc.bcm.edu	37	chr13	35624441	35624441	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	aggagttggttactctgctcAttttgttggcaactgtttaa	10	6	2	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr13:35624441A>G	ENST00000400445.3	+	6	1415	c.881A>G	c.(880-882)cAt>cGt	p.H294R	NBEA_ENST00000379939.2_Missense_Mutation_p.H294R|NBEA_ENST00000540320.1_Missense_Mutation_p.H294R|NBEA_ENST00000310336.4_Missense_Mutation_p.H294R	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	294					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TACTCTGCTCATTTTGTTGGC	0.353																																					p.H294R		Atlas-SNP	.											.	NBEA	340	.	0			c.A881G						.						73	63	66					13																	35624441		1828	4082	5910	SO:0001583	missense	26960	exon6			CTGCTCATTTTGT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.881A>G	chr13.hg19:g.35624441A>G	ENSP00000383295:p.His294Arg	131.0	0.0		78.0	33.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.500365	0.85176	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.84009	0.5378	M	0.77616	2.38	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.85642	0.1277	10	0.56958	D	0.05	.	15.5853	0.76475	1.0:0.0:0.0:0.0	.	294	Q5T321	.	R	294	ENSP00000440951:H294R;ENSP00000383295:H294R;ENSP00000369271:H294R;ENSP00000308534:H294R	ENSP00000308534:H294R	H	+	2	0	NBEA	34522441	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.287000	0.95975	2.146000	0.66826	0.477000	0.44152	CAT	.	.		0.353	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35624441	A	G	35624441	3	3	223	1	0	0	0	0	1	0	0	0	10196	217	8	2	903	2	NBEA	13	35624441	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10		35624441	79545437	53	31812										
OR11H12	440153	hgsc.bcm.edu	37	chr14	19378063	19378063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	catgactgggcatctctgtgCcaaactggtcatactgtgct	10	11	2	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr14:19378063C>T	ENST00000550708.1	+	1	542	c.470C>T	c.(469-471)gCc>gTc	p.A157V		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	157						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A157D(1)		NS(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CATCTCTGTGCCAAACTGGTC	0.468																																					p.A157V		Atlas-SNP	.											OR11H12,NS,carcinoma,0,1	OR11H12	58	.	1	Substitution - Missense(1)	lung(1)	c.C470T						.						168	179	175					14																	19378063		2201	4294	6495	SO:0001583	missense	440153	exon1			TCTGTGCCAAACT		CCDS32017.1	14q11.2	2013-01-25			ENSG00000257115	ENSG00000257115		"GPCR / Class A : Olfactory receptors"	30738	protein-coding gene	gene with protein product							Standard	NM_001013354		Approved		uc010tkp.2	B2RN74	OTTHUMG00000170298	ENST00000550708.1:c.470C>T	chr14.hg19:g.19378063C>T	ENSP00000449002:p.Ala157Val	530.0	0.0		395.0	35.0	NM_001013354		Missense_Mutation	SNP	ENST00000550708.1	hg19	CCDS32017.1	.	.	.	.	.	.	.	.	.	.	c	0.025	-1.382542	0.01204	.	.	ENSG00000257115	ENST00000550708	T	0.36157	1.27	0.585	0.585	0.17428	GPCR, rhodopsin-like superfamily (1);	1.418070	0.05301	N	0.523033	T	0.16938	0.0407	N	0.11818	0.18	0.23823	N	0.996741	B	0.10296	0.003	B	0.15484	0.013	T	0.24440	-1.0160	9	0.07813	T	0.8	.	3.0137	0.06052	0.0:0.6523:0.0:0.3477	.	157	B2RN74	O11HC_HUMAN	V	157	ENSP00000449002:A157V	ENSP00000449002:A157V	A	+	2	0	CR383656.1	18448063	0.000000	0.05858	0.869000	0.34112	0.213000	0.24496	-2.442000	0.01014	0.619000	0.30197	0.064000	0.15345	GCC	.	.		0.468	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354		T	19378063	C	T	19378063	3	4	223	1	0	0	0	0	1	0	0	0	10936	739	26	3	472	3	OR11H12	14	19378063	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10		19378063	87971477	54	31813										
MIPOL1	145282	hgsc.bcm.edu	37	chr14	37754588	37754588	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ctgttatgtctagactgcaaTtagccattgaggagagagat	11	6	1	4			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr14:37754588T>G	ENST00000327441.7	+	8	1025	c.559T>G	c.(559-561)Tta>Gta	p.L187V	MIPOL1_ENST00000556451.1_Missense_Mutation_p.L156V|MIPOL1_ENST00000537471.1_Missense_Mutation_p.L187V|MIPOL1_ENST00000545536.1_Missense_Mutation_p.L156V|MIPOL1_ENST00000536774.1_Missense_Mutation_p.L6V|MIPOL1_ENST00000539062.2_Missense_Mutation_p.L156V|MIPOL1_ENST00000396294.2_Missense_Mutation_p.L187V	NM_001195296.1|NM_001195297.1|NM_138731.6	NP_001182225.1|NP_001182226.1|NP_620059.1	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1	187						nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)		TAGACTGCAATTAGCCATTGA	0.378																																					p.L187V		Atlas-SNP	.											.	MIPOL1	50	.	0			c.T559G						.						216	198	204					14																	37754588		2203	4300	6503	SO:0001583	missense	145282	exon9			CTGCAATTAGCCA	AY059470	CCDS9664.1	14q13.3	2010-05-25			ENSG00000151338	ENSG00000151338			21460	protein-coding gene	gene with protein product		606850				11954550, 19667180	Standard	NM_001195296		Approved		uc001wuc.3	Q8TD10	OTTHUMG00000140252	ENST00000327441.7:c.559T>G	chr14.hg19:g.37754588T>G	ENSP00000333539:p.Leu187Val	86.0	0.0		81.0	32.0	NM_001195296	D3DSA4|Q7Z3J0|Q8IV14	Missense_Mutation	SNP	ENST00000327441.7	hg19	CCDS9664.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.374018	0.61735	.	.	ENSG00000151338	ENST00000327441;ENST00000536774;ENST00000539062;ENST00000556451;ENST00000396294;ENST00000537471;ENST00000545536	T;T;T;T;T;T	0.58060	0.39;0.4;0.36;0.39;0.39;0.36	5.4	3.0	0.34707	.	0.073027	0.56097	D	0.000027	T	0.65101	0.2659	M	0.75777	2.31	0.33826	D	0.629676	D;D	0.76494	0.992;0.999	P;D	0.68353	0.857;0.957	T	0.69339	-0.5171	10	0.31617	T	0.26	-0.5021	7.2328	0.26053	0.13:0.0708:0.0:0.7992	.	187;156	Q8TD10;Q49AL5	MIPO1_HUMAN;.	V	187;6;156;156;187;187;156	ENSP00000333539:L187V;ENSP00000438319:L156V;ENSP00000450479:L156V;ENSP00000379589:L187V;ENSP00000444254:L187V;ENSP00000442529:L156V	ENSP00000333539:L187V	L	+	1	2	MIPOL1	36824339	1.000000	0.71417	0.448000	0.26945	0.990000	0.78478	2.679000	0.46909	0.344000	0.23847	0.459000	0.35465	TTA	.	.		0.378	MIPOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276734.1	NM_138731		G	37754588	T	G	37754588	3	3	223	1	0	0	0	0	1	0	0	0	9602	1490	52	5	577	5	MIPOL1	14	37754588	Missense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	18376525	37754588	69594952	55	31814										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42360572	42360572	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ttccctcactgccacaagagTcgtgggttgcatccagttta	9	12	1	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr14:42360572T>C	ENST00000298119.4	+	4	2694	c.1505T>C	c.(1504-1506)gTc>gCc	p.V502A	LRFN5_ENST00000554171.1_Intron|LRFN5_ENST00000554120.1_Intron	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	502	Fibronectin type-III.					integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		GCCACAAGAGTCGTGGGTTGC	0.433										HNSCC(30;0.082)																											p.V502A		Atlas-SNP	.											.	LRFN5	269	.	0			c.T1505C						.						224	198	207					14																	42360572		2203	4300	6503	SO:0001583	missense	145581	exon4			CAAGAGTCGTGGG	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.1505T>C	chr14.hg19:g.42360572T>C	ENSP00000298119:p.Val502Ala	71.0	0.0		54.0	20.0	NM_152447	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	hg19	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.147527	0.57151	.	.	ENSG00000165379	ENST00000298119	T	0.52526	0.66	5.68	5.68	0.88126	Fibronectin, type III (1);	0.000000	0.49305	D	0.000154	T	0.43853	0.1266	L	0.55481	1.735	0.80722	D	1	B	0.33826	0.427	B	0.33799	0.17	T	0.32771	-0.9894	10	0.26408	T	0.33	.	13.8872	0.63714	0.0:0.0:0.0:1.0	.	502	Q96NI6	LRFN5_HUMAN	A	502	ENSP00000298119:V502A	ENSP00000298119:V502A	V	+	2	0	LRFN5	41430322	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.040000	0.89188	2.159000	0.67721	0.528000	0.53228	GTC	.	.		0.433	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		C	42360572	T	C	42360572	3	2	223	1	0	0	0	0	1	0	0	0	8950	1667	58	2	1511	2	LRFN5	14	42360572	Missense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	4605984	42360572	64988968	56	31815										
VPS39	23339	hgsc.bcm.edu	37	chr15	42458377	42458377	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	cttcaggccatcttctgggaAgtctctcagcacccacactg	8	15	5	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr15:42458377A>T	ENST00000348544.4	-	17	1692	c.1693T>A	c.(1693-1695)Ttc>Atc	p.F565I	VPS39_ENST00000318006.5_Missense_Mutation_p.F554I			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	565					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		TCTTCTGGGAAGTCTCTCAGC	0.493																																					p.F554I		Atlas-SNP	.											.	VPS39	53	.	0			c.T1660A						.						119	118	118					15																	42458377		2203	4299	6502	SO:0001583	missense	23339	exon16			CTGGGAAGTCTCT	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.1693T>A	chr15.hg19:g.42458377A>T	ENSP00000335193:p.Phe565Ile	127.0	0.0		82.0	27.0	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Missense_Mutation	SNP	ENST00000348544.4	hg19	CCDS10083.1	.	.	.	.	.	.	.	.	.	.	A	13.90	2.374423	0.42105	.	.	ENSG00000166887	ENST00000318006;ENST00000348544	T;T	0.42513	0.97;0.97	5.89	5.89	0.94794	.	0.207418	0.52532	D	0.000076	T	0.29556	0.0737	N	0.22421	0.69	0.39583	D	0.969463	B;B	0.18610	0.009;0.029	B;B	0.23574	0.021;0.047	T	0.15235	-1.0444	10	0.28530	T	0.3	-22.2276	10.6236	0.45495	0.9288:0.0:0.0712:0.0	.	565;554	Q96JC1;Q96JC1-2	VPS39_HUMAN;.	I	554;565	ENSP00000326534:F554I;ENSP00000335193:F565I	ENSP00000326534:F554I	F	-	1	0	VPS39	40245669	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.843000	0.69424	2.254000	0.74563	0.533000	0.62120	TTC	.	.		0.493	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		T	42458377	A	T	42458377	3	4	223	1	0	0	0	0	1	0	0	0	17224	72	3	4	1007	4	VPS39	15	42458377	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10		42458377	60073015	57	31816										
HCN4	10021	hgsc.bcm.edu	37	chr15	73615463	73615463	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gggtgtctctggcgtgctcaGtgggccagtggccagaccta	16	11	2	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr15:73615463G>T	ENST00000261917.3	-	8	3964	c.2971C>A	c.(2971-2973)Ctg>Atg	p.L991M		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	991	Pro-rich.				blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GGCGTGCTCAGTGGGCCAGTG	0.697																																					p.L991M		Atlas-SNP	.											HCN4,NS,carcinoma,0,1	HCN4	150	.	0			c.C2971A						.						6	8	7					15																	73615463		1978	4069	6047	SO:0001583	missense	10021	exon8			TGCTCAGTGGGCC	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.2971C>A	chr15.hg19:g.73615463G>T	ENSP00000261917:p.Leu991Met	104.0	0.0		57.0	22.0	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	hg19	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	G	0.261	-0.999387	0.02128	.	.	ENSG00000138622	ENST00000261917	D	0.97575	-4.44	2.76	-0.591	0.11675	.	.	.	.	.	D	0.90086	0.6903	N	0.14661	0.345	0.09310	N	1	B	0.25105	0.118	B	0.17722	0.019	T	0.81217	-0.1033	9	0.30078	T	0.28	.	4.6093	0.12395	0.2179:0.1794:0.6027:0.0	.	991	Q9Y3Q4	HCN4_HUMAN	M	991	ENSP00000261917:L991M	ENSP00000261917:L991M	L	-	1	2	HCN4	71402516	0.039000	0.19947	0.001000	0.08648	0.002000	0.02628	2.080000	0.41586	-0.433000	0.07286	-0.537000	0.04273	CTG	.	.		0.697	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		T	73615463	G	T	73615463	3	4	223	1	0	0	0	0	1	0	0	0	7008	1020	36	3	644	3	HCN4	15	73615463	Missense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	31157086	73615463	28915929	58	31817										
IL16	3603	hgsc.bcm.edu	37	chr15	81598392	81598392	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ctccgccaagctcgagagccCaggcaagctgtgattgtcac	11	14	1	2	rs145310121		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr15:81598392C>G	ENST00000302987.4	+	16	3564	c.3564C>G	c.(3562-3564)ccC>ccG	p.P1188P	IL16_ENST00000394660.2_Silent_p.P1188P|RP11-761I4.4_ENST00000607019.1_RNA|IL16_ENST00000394652.2_Silent_p.P487P			Q14005	IL16_HUMAN	interleukin 16	1188	Interaction with PPP1R12A, PPP1R12B and PPP1R12C.|PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						CTCGAGAGCCCAGGCAAGCTG	0.572																																					p.P1188P		Atlas-SNP	.											.	IL16	254	.	0			c.C3564G						.						128	129	129					15																	81598392		2203	4300	6503	SO:0001819	synonymous_variant	3603	exon17			AGAGCCCAGGCAA	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.3564C>G	chr15.hg19:g.81598392C>G		31.0	0.0		50.0	19.0	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	hg19	CCDS42069.1																																																																																			.	C|1.000;T|0.000		0.572	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		G	81598392	C	G	81598392	2	3	223	1	0	0	0	0	0	0	0	1	7642	581	21	4		4	IL16	15	81598392	Silent	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	7982929	81598392	20933000	59	31818										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99465501	99465501	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	aagagctggagacagagtacCctttctttgagagcagagtg	13	7	1	5			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr15:99465501C>A	ENST00000268035.6	+	11	2937	c.2326C>A	c.(2326-2328)Cct>Act	p.P776T	IGF1R_ENST00000558762.1_Missense_Mutation_p.P776T	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	776	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GACAGAGTACCCTTTCTTTGA	0.527																																					p.P776T		Atlas-SNP	.											.	IGF1R	147	.	0			c.C2326A						.						107	105	106					15																	99465501		2197	4297	6494	SO:0001583	missense	3480	exon11			GAGTACCCTTTCT	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2326C>A	chr15.hg19:g.99465501C>A	ENSP00000268035:p.Pro776Thr	93.0	0.0		82.0	26.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.523365	0.64747	.	.	ENSG00000140443	ENST00000268035	T	0.73897	-0.79	5.49	5.49	0.81192	Fibronectin, type III (2);	0.000000	0.56097	D	0.000021	T	0.75737	0.3890	M	0.76574	2.34	0.80722	D	1	P;B	0.42010	0.768;0.017	B;B	0.37692	0.256;0.008	T	0.78600	-0.2141	10	0.48119	T	0.1	.	19.3821	0.94542	0.0:1.0:0.0:0.0	.	776;776	C9J5X1;P08069	.;IGF1R_HUMAN	T	776	ENSP00000268035:P776T	ENSP00000268035:P776T	P	+	1	0	IGF1R	97283024	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	3.880000	0.56145	2.562000	0.86427	0.650000	0.86243	CCT	.	.		0.527	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99465501	C	A	99465501	3	1	223	1	0	0	0	0	1	0	0	0	7580	623	22	3	2368	3	IGF1R	15	99465501	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	17867109	99465501	3065891	60	31819										
PDIA2	64714	hgsc.bcm.edu	37	chr16	335428	335428	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ggggaggcagctccccgcttCcgggggcaggtactgggggg	21	11	0	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr16:335428C>A	ENST00000219406.6	+	6	930	c.912C>A	c.(910-912)ttC>ttA	p.F304L	PDIA2_ENST00000404312.1_Missense_Mutation_p.F301L|PDIA2_ENST00000462950.1_3'UTR	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	304					cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				CTCCCCGCTTCCGGGGGCAGG	0.682																																					p.F304L		Atlas-SNP	.											.	PDIA2	51	.	0			c.C912A						.						16	18	18					16																	335428		1842	4083	5925	SO:0001583	missense	64714	exon6			CCGCTTCCGGGGG	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"Protein disulfide isomerases"	14180	protein-coding gene	gene with protein product		608012	"protein disulfide isomerase, pancreatic", "protein disulfide isomerase-associated 2"	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.912C>A	chr16.hg19:g.335428C>A	ENSP00000219406:p.Phe304Leu	33.0	0.0		45.0	13.0	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	hg19	CCDS42089.1	.	.	.	.	.	.	.	.	.	.	c	13.73	2.325259	0.41197	.	.	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312	T;T	0.11385	2.78;2.78	4.03	4.03	0.46877	Thioredoxin-like fold (1);	0.055174	0.64402	D	0.000001	T	0.29817	0.0745	M	0.83223	2.63	0.51767	D	0.99993	P	0.49961	0.93	P	0.61722	0.893	T	0.02868	-1.1100	10	0.87932	D	0	.	8.9865	0.35997	0.0:0.8943:0.0:0.1057	.	304	Q13087	PDIA2_HUMAN	L	304;273;301	ENSP00000219406:F304L;ENSP00000384410:F301L	ENSP00000219406:F304L	F	+	3	2	PDIA2	275429	0.950000	0.32346	0.941000	0.38009	0.207000	0.24258	0.162000	0.16501	2.092000	0.63282	0.486000	0.48141	TTC	.	.		0.682	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849		A	335428	C	A	335428	3	1	223	1	0	0	0	0	1	0	0	0	11677	854	30	3	934	3	PDIA2	16	335428	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10		335428	90019325	61	31820										
ZNF768	79724	hgsc.bcm.edu	37	chr16	30536540	30536540	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tcgccagtgtgggtgcgctgGtgtttgatgaggtcagagct	17	7	1	3			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr16:30536540G>T	ENST00000380412.5	-	2	1096	c.921C>A	c.(919-921)caC>caA	p.H307Q	ZNF768_ENST00000562803.1_Missense_Mutation_p.H276Q	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	307					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	DNA-directed RNA polymerase II, core complex (GO:0005665)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						GGGTGCGCTGGTGTTTGATGA	0.612																																					p.H307Q		Atlas-SNP	.											.	ZNF768	28	.	0			c.C921A						.						82	81	81					16																	30536540		2197	4300	6497	SO:0001583	missense	79724	exon2			GCGCTGGTGTTTG	BC013760	CCDS10681.2	16p11.2	2013-01-08			ENSG00000169957	ENSG00000169957		"Zinc fingers, C2H2-type"	26273	protein-coding gene	gene with protein product						12477932	Standard	NM_024671		Approved	FLJ23436	uc002dyk.4	Q9H5H4	OTTHUMG00000132392	ENST00000380412.5:c.921C>A	chr16.hg19:g.30536540G>T	ENSP00000369777:p.His307Gln	64.0	0.0		61.0	21.0	NM_024671	Q569L7|Q96CX4	Missense_Mutation	SNP	ENST00000380412.5	hg19	CCDS10681.2	.	.	.	.	.	.	.	.	.	.	G	18.29	3.592346	0.66219	.	.	ENSG00000169957	ENST00000380412	D	0.86865	-2.18	4.7	3.67	0.42095	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46758	D	0.000272	D	0.93249	0.7849	M	0.91818	3.245	0.34117	D	0.663656	D	0.69078	0.997	D	0.71870	0.975	D	0.94734	0.7912	10	0.87932	D	0	-16.102	8.1632	0.31211	0.1661:0.0:0.8339:0.0	.	307	Q9H5H4	ZN768_HUMAN	Q	307	ENSP00000369777:H307Q	ENSP00000369777:H307Q	H	-	3	2	ZNF768	30444041	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.034000	0.49751	2.448000	0.82819	0.407000	0.27541	CAC	.	.		0.612	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671		T	30536540	G	T	30536540	3	4	223	1	0	0	0	0	1	0	0	0	18156	1252	44	3	705	3	ZNF768	16	30536540	Missense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	30201112	30536540	59818213	62	31821										
LCAT	3931	hgsc.bcm.edu	37	chr16	67977971	67977971	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	cagcagccccagcagcagcgTcacccactgccatggggagc	12	17	1	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr16:67977971T>G	ENST00000264005.5	-	1	63	c.34A>C	c.(34-36)Acg>Ccg	p.T12P	CTC-479C5.17_ENST00000590594.1_lincRNA|SLC12A4_ENST00000422611.2_3'UTR	NM_000229.1	NP_000220.1	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase	12					cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of high-density lipoprotein particle assembly (GO:0090107)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	apolipoprotein A-I binding (GO:0034186)|phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607)			cervix(4)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)		AGCAGCAGCGTCACCCACTGC	0.662																																					p.T12P		Atlas-SNP	.											.	LCAT	31	.	0			c.A34C						.						13	13	13					16																	67977971		1958	3860	5818	SO:0001583	missense	3931	exon1			GCAGCGTCACCCA		CCDS10854.1	16q22.1	2012-10-02			ENSG00000213398	ENSG00000213398	2.3.1.43		6522	protein-coding gene	gene with protein product		606967					Standard	NM_000229		Approved		uc002euy.1	P04180	OTTHUMG00000137551	ENST00000264005.5:c.34A>C	chr16.hg19:g.67977971T>G	ENSP00000264005:p.Thr12Pro	143.0	0.0		101.0	39.0	NM_000229	Q53XQ3	Missense_Mutation	SNP	ENST00000264005.5	hg19	CCDS10854.1	.	.	.	.	.	.	.	.	.	.	T	7.861	0.726005	0.15439	.	.	ENSG00000213398	ENST00000264005	D	0.96491	-4.03	4.55	3.6	0.41247	.	1.493400	0.04986	N	0.466591	D	0.91379	0.7280	N	0.08118	0	0.40066	D	0.97595	B	0.02656	0.0	B	0.01281	0.0	T	0.77864	-0.2429	10	0.48119	T	0.1	.	10.4368	0.44441	0.0:0.0:0.8041:0.1959	.	12	P04180	LCAT_HUMAN	P	12	ENSP00000264005:T12P	ENSP00000264005:T12P	T	-	1	0	LCAT	66535472	0.737000	0.28175	0.985000	0.45067	0.752000	0.42762	0.712000	0.25779	1.067000	0.40740	-0.708000	0.03648	ACG	.	.		0.662	LCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268885.3			G	67977971	T	G	67977971	3	3	223	1	0	0	0	0	1	0	0	0	8667	1667	58	5	1312	5	LCAT	16	67977971	Missense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	37441431	67977971	22376782	63	31822										
PLEKHM1	9842	hgsc.bcm.edu	37	chr17	43531021	43531021	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gctggtgtctggcaggatgtCccggatggtctccacgccgt	15	12	2	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr17:43531021C>A	ENST00000430334.3	-	7	2330	c.2197G>T	c.(2197-2199)Gac>Tac	p.D733Y	PLEKHM1_ENST00000421073.2_Missense_Mutation_p.D644Y|AC091132.1_ENST00000433601.1_RNA	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	733	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					GGCAGGATGTCCCGGATGGTC	0.562																																					p.D733Y		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.G2197T						.						9	8	8					17																	43531021		2079	4103	6182	SO:0001583	missense	9842	exon7			GGATGTCCCGGAT	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"Pleckstrin homology (PH) domain containing"	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.2197G>T	chr17.hg19:g.43531021C>A	ENSP00000389913:p.Asp733Tyr	162.0	0.0		139.0	52.0	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Missense_Mutation	SNP	ENST00000430334.3	hg19	CCDS32671.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.000014	0.54147	.	.	ENSG00000225190	ENST00000430334;ENST00000446609;ENST00000421073	T;T	0.62788	0.0;0.0	4.91	4.91	0.64330	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.71117	0.3302	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.994	T	0.74244	-0.3728	10	0.72032	D	0.01	.	16.8908	0.86087	0.0:1.0:0.0:0.0	.	644;682;733	F8W648;B4DRX1;Q9Y4G2	.;.;PKHM1_HUMAN	Y	733;682;644	ENSP00000389913:D733Y;ENSP00000414352:D644Y	ENSP00000414352:D644Y	D	-	1	0	PLEKHM1	40886804	1.000000	0.71417	0.997000	0.53966	0.233000	0.25261	7.279000	0.78599	2.572000	0.86782	0.586000	0.80456	GAC	.	.		0.562	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798		A	43531021	C	A	43531021	3	1	223	1	0	0	0	0	1	0	0	0	12089	855	30	3	997	3	PLEKHM1	17	43531021	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10		43531021	37664189	64	31823										
NOTUM	147111	hgsc.bcm.edu	37	chr17	79914895	79914895	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gatggctgggtagcccagctTctccagctgctcagccacac	11	15	2	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr17:79914895T>A	ENST00000409678.3	-	7	1134	c.751A>T	c.(751-753)Aag>Tag	p.K251*		NM_178493.5	NP_848588.3	Q6P988	NOTUM_HUMAN	notum pectinacetylesterase homolog (Drosophila)	251						extracellular region (GO:0005576)	hydrolase activity (GO:0016787)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	15	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			TAGCCCAGCTTCTCCAGCTGC	0.652																																					p.K251X		Atlas-SNP	.											.	NOTUM	50	.	0			c.A751T						.						71	58	62					17																	79914895		2203	4300	6503	SO:0001587	stop_gained	147111	exon7			CCAGCTTCTCCAG	BC060882	CCDS32771.2	17q25.3	2008-02-05			ENSG00000185269	ENSG00000185269			27106	protein-coding gene	gene with protein product		609847					Standard	NM_178493		Approved		uc010wvg.2	Q6P988	OTTHUMG00000154416	ENST00000409678.3:c.751A>T	chr17.hg19:g.79914895T>A	ENSP00000387310:p.Lys251*	41.0	0.0		39.0	11.0	NM_178493	Q8N410|Q8NI82	Nonsense_Mutation	SNP	ENST00000409678.3	hg19	CCDS32771.2	.	.	.	.	.	.	.	.	.	.	C	29.2	4.982752	0.93044	.	.	ENSG00000185269	ENST00000409678;ENST00000425009	.	.	.	4.54	3.54	0.40534	.	0.297193	0.37053	N	0.002272	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	9.0322	0.36264	0.0:0.643:0.2784:0.0786	.	.	.	.	X	251	.	ENSP00000387310:K251X	K	-	1	0	NOTUM	77508185	1.000000	0.71417	0.998000	0.56505	0.697000	0.40408	2.238000	0.43070	0.330000	0.23485	-0.642000	0.03964	AAG	.	.		0.652	NOTUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335123.2	NM_178493		A	79914895	T	A	79914895	4	1	223	1	0	0	0	0	0	1	0	0	10561	1792	62	4	759	4	NOTUM	17	79914895	Nonsense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	36383874	79914895	1280315	65	31824										
HMHA1	23526	hgsc.bcm.edu	37	chr19	1084297	1084297	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tgccgtacctggaggcgggcGaggcggtggtctacccgctg	18	12	1	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr19:1084297G>A	ENST00000313093.2	+	22	3247	c.3016G>A	c.(3016-3018)Gag>Aag	p.E1006K	HMHA1_ENST00000591169.1_3'UTR|HMHA1_ENST00000590577.1_Missense_Mutation_p.E641K|HMHA1_ENST00000590214.1_Missense_Mutation_p.E1033K|HMHA1_ENST00000586866.1_Missense_Mutation_p.E1010K|HMHA1_ENST00000543365.1_Missense_Mutation_p.E889K|HMHA1_ENST00000536472.1_Missense_Mutation_p.E874K|HMHA1_ENST00000539243.2_Missense_Mutation_p.E1022K	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	1006					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAGGCGGGCGAGGCGGTGGT	0.687																																					p.E1022K		Atlas-SNP	.											.	HMHA1	78	.	0			c.G3064A						.						52	54	53					19																	1084297		2203	4294	6497	SO:0001583	missense	23526	exon22			GCGGGCGAGGCGG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"Rho GTPase activating proteins"	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.3016G>A	chr19.hg19:g.1084297G>A	ENSP00000316772:p.Glu1006Lys	146.0	0.0		109.0	10.0	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	hg19	CCDS32863.1	.	.	.	.	.	.	.	.	.	.	G	6.135	0.393087	0.11638	.	.	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000536472;ENST00000412039;ENST00000543365	T;T;T;T	0.21932	2.02;2.04;2.02;1.98	3.85	1.6	0.23607	.	1.281560	0.05837	N	0.618602	T	0.15609	0.0376	L	0.40543	1.245	0.09310	N	1	B;B;B;B;B;B	0.21381	0.055;0.055;0.033;0.001;0.055;0.019	B;B;B;B;B;B	0.10450	0.005;0.005;0.002;0.002;0.005;0.002	T	0.34179	-0.9839	10	0.08381	T	0.77	-3.2296	6.8237	0.23870	0.2324:0.0:0.7676:0.0	.	874;1022;888;641;889;1006	F5H4A3;F6QP70;B3KXW7;B3KVA9;F5H1R4;Q92619	.;.;.;.;.;HMHA1_HUMAN	K	1022;1006;874;1000;889	ENSP00000439601:E1022K;ENSP00000316772:E1006K;ENSP00000445109:E874K;ENSP00000438979:E889K	ENSP00000316772:E1006K	E	+	1	0	HMHA1	1035297	0.590000	0.26815	0.000000	0.03702	0.010000	0.07245	1.452000	0.35156	0.227000	0.20999	-0.258000	0.10820	GAG	.	.		0.687	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1			A	1084297	G	A	1084297	3	1	223	1	0	0	0	0	1	0	0	0	7249	1059	37	1	3102	1	HMHA1	19	1084297	Missense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10		1084297	58044686	66	31825										
ZNF560	147741	hgsc.bcm.edu	37	chr19	9583900	9583900	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tctcaactcttcttcttccaAccaagagatgacactgggtt	6	12	4	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr19:9583900A>G	ENST00000301480.4	-	5	406	c.193T>C	c.(193-195)Ttg>Ctg	p.L65L		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	65	KRAB 1. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						TCTTCTTCCAACCAAGAGATG	0.433																																					p.L65L		Atlas-SNP	.											.	ZNF560	162	.	0			c.T193C						.						188	189	188					19																	9583900		2203	4300	6503	SO:0001819	synonymous_variant	147741	exon5			CTTCCAACCAAGA	AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"Zinc fingers, C2H2-type", "-"	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.193T>C	chr19.hg19:g.9583900A>G		51.0	0.0		28.0	9.0	NM_152476	Q495S9|Q495T1	Silent	SNP	ENST00000301480.4	hg19	CCDS12214.1																																																																																			.	.		0.433	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476		G	9583900	A	G	9583900	2	3	223	1	0	0	0	0	0	0	0	1	18006	40	2	2		2	ZNF560	19	9583900	Silent	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10	8499603	9583900	49545083	67	31826										
KCTD15	79047	hgsc.bcm.edu	37	chr19	34291425	34291425	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	cacggcagcaccggcaccgcGgtgagcctgcagggtgggct	17	14	0	1	rs142074601		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr19:34291425G>T	ENST00000430256.3	+	2	474	c.66G>T	c.(64-66)gcG>gcT	p.A22A	KCTD15_ENST00000589786.1_Splice_Site_p.A22A|KCTD15_ENST00000284006.6_Splice_Site_p.A22A|KCTD15_ENST00000588881.1_Splice_Site_p.A22A			Q96SI1	KCD15_HUMAN	potassium channel tetramerization domain containing 15	22					multicellular organismal development (GO:0007275)|protein homooligomerization (GO:0051260)					endometrium(1)|lung(2)|pancreas(1)|urinary_tract(1)	5	Esophageal squamous(110;0.162)					CCGGCACCGCGGTGAGCCTGC	0.642																																					p.A22A	Melanoma(36;646 1094 5145 14504 45302)|GBM(25;193 541 1518 14388 52178)	Atlas-SNP	.											.	KCTD15	18	.	0			c.G66T						.						15	17	17					19																	34291425		2199	4288	6487	SO:0001630	splice_region_variant	79047	exon3			CACCGCGGTGAGC	AK025590	CCDS12434.1, CCDS46039.1	19q13.12	2013-06-20	2013-06-20			ENSG00000153885			23297	protein-coding gene	gene with protein product		615240	"potassium channel tetramerisation domain containing 15"			12477932	Standard	NM_024076		Approved	MGC25497	uc002nuw.4	Q96SI1		ENST00000430256.3:c.66+1G>T	chr19.hg19:g.34291425G>T		153.0	0.0		136.0	59.0	NM_001129995	A8K600|Q9BVI6	Silent	SNP	ENST00000430256.3	hg19	CCDS46039.1																																																																																			.	G|1.000;A|0.000		0.642	KCTD15-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451462.2	NM_024076	Silent	T	34291425	G	T	34291425	5	4	223	1	0	0	0	0	0	0	1	0	8111	1130	39	1	68	1	KCTD15	19	34291425	Splice_Site	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	24707525	34291425	24837558	68	31827										
UBA2	10054	hgsc.bcm.edu	37	chr19	34925843	34925843	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	attgaaagtggaacagctggGtatcttggacaagtaactac	11	6	1	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr19:34925843G>A	ENST00000246548.4	+	5	499	c.429G>A	c.(427-429)ggG>ggA	p.G143G	UBA2_ENST00000439527.2_Silent_p.G47G	NM_005499.2	NP_005490.1	Q9UBT2	SAE2_HUMAN	ubiquitin-like modifier activating enzyme 2	143					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|SUMO activating enzyme complex (GO:0031510)	ATP binding (GO:0005524)|enzyme activator activity (GO:0008047)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SUMO activating enzyme activity (GO:0019948)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	20	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			GAACAGCTGGGTATCTTGGAC	0.358																																					p.G143G		Atlas-SNP	.											.	UBA2	53	.	0			c.G429A						.						40	39	39					19																	34925843		2202	4300	6502	SO:0001819	synonymous_variant	10054	exon5			AGCTGGGTATCTT	BC003153	CCDS12439.1	19q13.11	2008-02-05	2007-11-30	2007-11-30		ENSG00000126261		"Ubiquitin-like modifier activating enzymes"	30661	protein-coding gene	gene with protein product	"UBA2, ubiquitin-activating enzyme E1 homolog (yeast)"	613295	"SUMO1 activating enzyme subunit 2"	SAE2		10187858, 9920803	Standard	NM_005499		Approved	FLJ13058, HRIHFB2115, ARX	uc002nvk.3	Q9UBT2		ENST00000246548.4:c.429G>A	chr19.hg19:g.34925843G>A		421.0	0.0		338.0	129.0	NM_005499	B3KWB9|O95605|Q59H87|Q6IBP6|Q9NTJ1|Q9UED2	Silent	SNP	ENST00000246548.4	hg19	CCDS12439.1																																																																																			.	.		0.358	UBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459257.3	NM_005499		A	34925843	G	A	34925843	2	1	223	1	0	0	0	0	0	0	0	1	16843	1248	44	3		3	UBA2	19	34925843	Silent	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10	634418	34925843	24203140	69	31828										
ZNF30	90075	hgsc.bcm.edu	37	chr19	35435358	35435358	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ggaaagacttttagtcgagcCtcgtaccttgtacaacatag	9	9	0	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr19:35435358C>T	ENST00000601142.1	+	5	1725	c.1488C>T	c.(1486-1488)gcC>gcT	p.A496A	ZNF30_ENST00000439785.1_Silent_p.A497A|ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000426813.2_Silent_p.A415A|ZNF30_ENST00000303586.7_Silent_p.A497A			P17039	ZNF30_HUMAN	zinc finger protein 30	496					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		TTAGTCGAGCCTCGTACCTTG	0.453																																					p.A497A		Atlas-SNP	.											.	ZNF30	44	.	0			c.C1491T						.						87	94	91					19																	35435358		2196	4299	6495	SO:0001819	synonymous_variant	90075	exon5			TCGAGCCTCGTAC	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"Zinc fingers, C2H2-type", "-"	13090	protein-coding gene	gene with protein product			"zinc finger protein 30 (KOX 28)"				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.1488C>T	chr19.hg19:g.35435358C>T		73.0	0.0		71.0	23.0	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Silent	SNP	ENST00000601142.1	hg19	CCDS46045.1																																																																																			.	.		0.453	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325		T	35435358	C	T	35435358	2	4	223	1	0	0	0	0	0	0	0	1	17845	668	24	3		3	ZNF30	19	35435358	Silent	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	509515	35435358	23693625	70	31829										
ZNF114	163071	hgsc.bcm.edu	37	chr19	48789079	48789079	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ccggatattcttcctaaaagAacatttcctgaagccaacag	6	11	1	2			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr19:48789079A>G	ENST00000595607.1	+	6	692	c.198A>G	c.(196-198)agA>agG	p.R66R	ZNF114_ENST00000315849.1_Silent_p.R66R|ZNF114_ENST00000597695.1_Silent_p.R32R|ZNF114_ENST00000600687.1_Silent_p.R66R			Q8NC26	ZN114_HUMAN	zinc finger protein 114	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(6)|lung(11)	18		all_epithelial(76;8.01e-05)|all_lung(116;0.000112)|Lung NSC(112;0.000192)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;7.56e-05)|all cancers(93;0.000113)|Epithelial(262;0.00962)|GBM - Glioblastoma multiforme(486;0.0153)		TTCCTAAAAGAACATTTCCTG	0.443																																					p.R66R		Atlas-SNP	.											.	ZNF114	46	.	0			c.A198G						.						91	84	86					19																	48789079		2203	4300	6503	SO:0001819	synonymous_variant	163071	exon5			TAAAAGAACATTT	BC014935	CCDS12713.1, CCDS74412.1	19q13.32	2013-01-08			ENSG00000178150	ENSG00000178150		"Zinc fingers, C2H2-type", "-"	12894	protein-coding gene	gene with protein product		603996					Standard	XM_005258580		Approved	MGC17986	uc002pim.1	Q8NC26		ENST00000595607.1:c.198A>G	chr19.hg19:g.48789079A>G		139.0	0.0		88.0	37.0	NM_153608	A8K6B0|Q08AQ6	Silent	SNP	ENST00000595607.1	hg19	CCDS12713.1																																																																																			.	.		0.443	ZNF114-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465601.1	NM_153608		G	48789079	A	G	48789079	2	3	223	1	0	0	0	0	0	0	0	1	17731	243	9	2		2	ZNF114	19	48789079	Silent	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10	13353721	48789079	10339904	71	31830										
SAPS1	22870	hgsc.bcm.edu	37	chr19	55751023	55751023	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gccggtcgtcctcatcgtcaCtggaggagtgtaggtggtgg	17	9	2	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr19:55751023C>T	ENST00000412770.2	-	14	2158	c.1592G>A	c.(1591-1593)aGt>aAt	p.S531N	PPP6R1_ENST00000587283.1_Missense_Mutation_p.S531N	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	531					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						CTCATCGTCACTGGAGGAGTG	0.657																																					p.S531N		Atlas-SNP	.											.	PPP6R1	63	.	0			c.G1592A						.						58	63	61					19																	55751023		2104	4197	6301	SO:0001583	missense	22870	exon14			TCGTCACTGGAGG	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	29195	protein-coding gene	gene with protein product		610875	"KIAA1115", "SAPS domain family, member 1"	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.1592G>A	chr19.hg19:g.55751023C>T	ENSP00000414202:p.Ser531Asn	62.0	0.0		61.0	18.0	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	hg19	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.411497	0.62399	.	.	ENSG00000105063	ENST00000412770	T	0.53857	0.6	5.04	4.01	0.46588	.	0.071856	0.56097	N	0.000037	T	0.65471	0.2694	L	0.55213	1.73	0.35795	D	0.82266	D	0.89917	1.0	D	0.73380	0.98	T	0.73275	-0.4034	10	0.46703	T	0.11	-18.0612	12.9362	0.58316	0.0:0.9197:0.0:0.0803	.	531	Q9UPN7	PP6R1_HUMAN	N	531	ENSP00000414202:S531N	ENSP00000414202:S531N	S	-	2	0	PPP6R1	60442835	1.000000	0.71417	0.988000	0.46212	0.392000	0.30506	5.298000	0.65710	1.497000	0.48584	0.650000	0.86243	AGT	.	.		0.657	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931		T	55751023	C	T	55751023	3	4	223	1	0	0	0	0	1	0	0	0	13851	565	20	3	1097	3	SAPS1	19	55751023	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10	6961944	55751023	3377960	72	31831										
ZNF335	63925	hgsc.bcm.edu	37	chr20	44590731	44590731	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	gtcccggctgtgcacagcggCgtgccgaatgacgtccttcc	13	15	0	1	rs140842666		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr20:44590731C>A	ENST00000322927.2	-	10	1724	c.1624G>T	c.(1624-1626)Gcc>Tcc	p.A542S	ZNF335_ENST00000426788.1_Missense_Mutation_p.A387S	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	542					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				TGCACAGCGGCGTGCCGAATG	0.627																																					p.A542S		Atlas-SNP	.											.	ZNF335	115	.	0			c.G1624T						.						143	114	124					20																	44590731		2203	4300	6503	SO:0001583	missense	63925	exon10			CAGCGGCGTGCCG	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.1624G>T	chr20.hg19:g.44590731C>A	ENSP00000325326:p.Ala542Ser	25.0	0.0		33.0	13.0	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	hg19	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	C	6.876	0.531010	0.13127	.	.	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	T;T	0.28255	1.62;1.62	4.87	3.86	0.44501	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.302185	0.31989	N	0.006749	T	0.09818	0.0241	N	0.01576	-0.805	0.37479	D	0.915939	B;B	0.19073	0.008;0.033	B;B	0.15052	0.009;0.012	T	0.22034	-1.0228	10	0.09084	T	0.74	-21.3424	10.2106	0.43138	0.347:0.653:0.0:0.0	.	387;542	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	S	542;319;387	ENSP00000325326:A542S;ENSP00000397098:A387S	ENSP00000243961:A319S	A	-	1	0	ZNF335	44024138	1.000000	0.71417	0.468000	0.27192	0.198000	0.23893	5.009000	0.63998	2.526000	0.85167	0.491000	0.48974	GCC	.	C|1.000;T|0.000		0.627	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		A	44590731	C	A	44590731	3	1	223	1	0	0	0	0	1	0	0	0	17867	768	27	1	2480	1	ZNF335	20	44590731	Missense_Mutation	SNP	C	TCGA-DD-AAVP-01A-11D-A40R-10		44590731	18434789	73	31832										
LCA5L	150082	hgsc.bcm.edu	37	chr21	40778273	40778273	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tgtcttctttgtctgaggggGcctttcgtgtagggagcagt	15	7	3	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr21:40778273G>T	ENST00000358268.2	-	10	2076	c.1548C>A	c.(1546-1548)ggC>ggA	p.G516G	LCA5L_ENST00000288350.3_Silent_p.G516G|LCA5L_ENST00000380671.2_Silent_p.G516G|WRB_ENST00000541890.1_Intron|LCA5L_ENST00000495240.1_5'UTR			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	516										breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				GTCTGAGGGGGCCTTTCGTGT	0.473																																					p.G516G		Atlas-SNP	.											.	LCA5L	57	.	0			c.C1548A						.						111	92	98					21																	40778273		2203	4300	6503	SO:0001819	synonymous_variant	150082	exon10			GAGGGGGCCTTTC	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 13"	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.1548C>A	chr21.hg19:g.40778273G>T		90.0	0.0		99.0	4.0	NM_152505	D3DSI0|Q3ZCT0	Silent	SNP	ENST00000358268.2	hg19	CCDS13665.1																																																																																			.	.		0.473	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		T	40778273	G	T	40778273	2	4	223	1	0	0	0	0	0	0	0	1	8666	1190	42	3		3	LCA5L	21	40778273	Silent	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10		40778273	7351622	74	31833										
C22orf39	128977	hgsc.bcm.edu	37	chr22	19435059	19435059	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ggcgcggtaggcctcgcaggGgcgcggcggctgcggcgaga	22	12	0	1			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr22:19435059G>A	ENST00000399562.4	-	2	577	c.145C>T	c.(145-147)Ccc>Tcc	p.P49S	C22orf39_ENST00000542103.1_Missense_Mutation_p.P49S|AC000068.5_ENST00000431090.1_RNA|HIRA_ENST00000546308.1_5'UTR|C22orf39_ENST00000399568.1_Missense_Mutation_p.P12S|C22orf39_ENST00000333059.5_Missense_Mutation_p.P12S|HIRA_ENST00000541063.1_Intron	NM_173793.4	NP_776154.3	Q6P5X5	CV039_HUMAN	chromosome 22 open reading frame 39	49												Colorectal(54;0.0993)					GCCTCGCAGGGGCGCGGCGGC	0.756																																					p.P49S		Atlas-SNP	.											.	C22orf39	11	.	0			c.C145T						.						2	3	3					22																	19435059		1722	3580	5302	SO:0001583	missense	128977	exon2			CGCAGGGGCGCGG		CCDS33599.1, CCDS33599.2, CCDS54498.1	22q11.21	2008-10-31			ENSG00000242259	ENSG00000242259			27012	protein-coding gene	gene with protein product							Standard	NM_173793		Approved	MGC74441	uc002zpk.2	Q6P5X5	OTTHUMG00000150137	ENST00000399562.4:c.145C>T	chr22.hg19:g.19435059G>A	ENSP00000382474:p.Pro49Ser	13.0	0.0		33.0	14.0	NM_173793	A8MTW6|D3DX18|F5H3A8|J3KNP9	Missense_Mutation	SNP	ENST00000399562.4	hg19	CCDS33599.2	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250273	0.59212	.	.	ENSG00000242259	ENST00000399568;ENST00000542103;ENST00000399562;ENST00000333059	.	.	.	5.91	2.57	0.30868	.	0.567884	0.17718	N	0.164343	T	0.37625	0.1010	M	0.64260	1.97	0.28944	N	0.890821	B;B	0.20887	0.018;0.049	B;B	0.21151	0.011;0.033	T	0.27606	-1.0069	8	.	.	.	-33.0879	2.2481	0.04036	0.2197:0.1825:0.4621:0.1357	.	12;49	Q6P5X5;F5H3A8	CV039_HUMAN;.	S	12;49;12;49	.	.	P	-	1	0	C22orf39	17815059	0.053000	0.20554	0.999000	0.59377	0.973000	0.67179	0.315000	0.19451	0.839000	0.34971	-0.152000	0.13540	CCC	.	.		0.756	C22orf39-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316494.3	NM_173793		A	19435059	G	A	19435059	3	1	223	1	0	0	0	0	1	0	0	0	2149	1232	43	3	346	3	C22orf39	22	19435059	Missense_Mutation	SNP	G	TCGA-DD-AAVP-01A-11D-A40R-10		19435059	31869507	75	31834										
ARVCF	421	hgsc.bcm.edu	37	chr22	19960689	19960692	+	Frame_Shift_Del	DEL	GAGC	GAGC	-													0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ggcaccccgcgtgcctgcagGagcgagcgcgcgttatccag					rs538460279		TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	GAGC	GAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chr22:19960689_19960692delGAGC	ENST00000263207.3	-	14	2679_2682	c.2388_2391delGCTC	c.(2386-2391)tcgctcfs	p.SL796fs	ARVCF_ENST00000406259.1_Frame_Shift_Del_p.SL790fs|ARVCF_ENST00000401994.1_Frame_Shift_Del_p.SL733fs|ARVCF_ENST00000344269.3_Frame_Shift_Del_p.SL733fs|ARVCF_ENST00000406522.1_Frame_Shift_Del_p.SL727fs	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	796					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					GTGCCTGCAGGAGCGAGCGCGCGT	0.716																																					p.797_798del		Atlas-INDEL	.											.	ARVCF	54	.	0			c.2389_2392del						.																																			SO:0001589	frameshift_variant	421	exon14			.		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"Armadillo repeat containing"	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.2388_2391delGCTC	chr22.hg19:g.19960693_19960696delGAGC	ENSP00000263207:p.Ser796fs	51.0	0.0		49.0	23.0	NM_001670	B7WNV2	Frame_Shift_Del	DEL	ENST00000263207.3	hg19	CCDS13771.1																																																																																			.	.		0.716	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		-	19960692	GAGC	-	19960689	7	5	223	1	0	1	0	1	0	0	0	0	1003	1161	41	0	521	0	ARVCF	22	19960689	Frame_Shift_Del	DEL	GAGC	TCGA-DD-AAVP-01A-11D-A40R-10	525630	19960689	31343877	76	31835										
XG	7499	hgsc.bcm.edu	37	chrX	2712585	2712585	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	ctgccccacaggttacttcaAtgatgtggaccgtgatgacg	11	11	1	3			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chrX:2712585A>G	ENST00000381174.5	+	6	488	c.263A>G	c.(262-264)aAt>aGt	p.N88S	XG_ENST00000419513.2_Missense_Mutation_p.N88S|XG_ENST00000426774.1_Missense_Mutation_p.N89S			P55808	XG_HUMAN	Xg blood group	88						integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	8		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				GGTTACTTCAATGATGTGGAC	0.617																																					p.N89S		Atlas-SNP	.											.	XG	22	.	0			c.A266G						.						60	48	52					X																	2712585		2203	4298	6501	SO:0001583	missense	7499	exon6			ACTTCAATGATGT	AF380356	CCDS14120.1, CCDS48073.1	Xp22.32	2014-07-19	2006-01-12		ENSG00000124343	ENSG00000124343		"Blood group antigens", "Pseudoautosomal regions / PAR1"	12806	protein-coding gene	gene with protein product		300879	"Xg blood group (pseudoautosomal boundary-divided on the X chromosome)"	PBDX		8054981	Standard	NM_175569		Approved		uc004cqp.3	P55808	OTTHUMG00000021075	ENST00000381174.5:c.263A>G	chrX.hg19:g.2712585A>G	ENSP00000370566:p.Asn88Ser	57.0	0.0		71.0	62.0	NM_001141920	E9PCH1|Q496N8|Q496N9|Q496P0|Q71BZ5	Missense_Mutation	SNP	ENST00000381174.5	hg19	CCDS14120.1	.	.	.	.	.	.	.	.	.	.	a	6.207	0.406353	0.11754	.	.	ENSG00000124343	ENST00000381174;ENST00000419513;ENST00000426774;ENST00000509484	T;T;T;T	0.15372	2.43;2.43;2.43;2.43	1.95	-0.83	0.10792	.	0.909679	0.09269	U	0.825452	T	0.05135	0.0137	N	0.03324	-0.35	0.09310	N	1	B;B	0.10296	0.001;0.003	B;B	0.14023	0.01;0.006	T	0.40572	-0.9556	10	0.02654	T	1	.	4.5196	0.11952	0.5027:0.0:0.4973:0.0	.	88;88	P55808;P55808-3	XG_HUMAN;.	S	88;88;89;66	ENSP00000370566:N88S;ENSP00000411004:N88S;ENSP00000398503:N89S;ENSP00000430005:N66S	ENSP00000370566:N88S	N	+	2	0	XG	2722585	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.086000	0.14935	-0.240000	0.09696	0.478000	0.44815	AAT	.	.		0.617	XG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055633.2	NM_175569		G	2712585	A	G	2712585	3	3	223	1	0	0	0	0	1	0	0	0	17442	101	4	2	288	2	XG	23	2712585	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10		2712585	152557975	77	31836										
STAG2	10735	hgsc.bcm.edu	37	chrX	123182871	123182871	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	acagcttcaggaaaatcaagAtgaaatagaaaatatgatga	8	4	2	5			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chrX:123182871A>G	ENST00000371160.1	+	10	1126	c.836A>G	c.(835-837)gAt>gGt	p.D279G	STAG2_ENST00000354548.5_Missense_Mutation_p.D210G|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.D279G|STAG2_ENST00000371157.3_Missense_Mutation_p.D279G|STAG2_ENST00000371144.3_Missense_Mutation_p.D279G|STAG2_ENST00000371145.3_Missense_Mutation_p.D279G	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	279					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GAAAATCAAGATGAAATAGAA	0.284																																					p.D279G		Atlas-SNP	.											.	STAG2	309	.	0			c.A836G						.						95	88	90					X																	123182871		2203	4297	6500	SO:0001583	missense	10735	exon10			ATCAAGATGAAAT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.836A>G	chrX.hg19:g.123182871A>G	ENSP00000360202:p.Asp279Gly	337.0	0.0		627.0	192.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.542588	0.85917	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42;1.42;1.42	5.61	5.61	0.85477	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.49287	0.1548	M	0.80422	2.495	0.80722	D	1	P;P	0.41008	0.735;0.616	P;B	0.49853	0.624;0.418	T	0.51293	-0.8724	10	0.48119	T	0.1	-1.4563	14.3807	0.66908	1.0:0.0:0.0:0.0	.	279;279	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	G	279;279;210;279;279;279;279	ENSP00000218089:D279G;ENSP00000397265:D279G;ENSP00000346555:D210G;ENSP00000360202:D279G;ENSP00000360199:D279G;ENSP00000360187:D279G;ENSP00000360186:D279G	ENSP00000218089:D279G	D	+	2	0	STAG2	123010552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.228000	0.95250	1.860000	0.53959	0.486000	0.48141	GAT	.	.		0.284	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		G	123182871	A	G	123182871	3	3	223	1	0	0	0	0	1	0	0	0	15258	333	12	2	866	2	STAG2	23	123182871	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10	120470286	123182871	32087689	78	31837										
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128645791	128645791	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	tctcacttactctggcatccTtgtctccgacaaaacaaatg	5	13	3	0			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chrX:128645791T>C	ENST00000371122.4	-	6	929	c.800A>G	c.(799-801)aAg>aGg	p.K267R	SMARCA1_ENST00000371121.3_Missense_Mutation_p.K267R|SMARCA1_ENST00000371123.1_Missense_Mutation_p.K267R|SMARCA1_ENST00000478420.1_5'UTR	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	267	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						TCTGGCATCCTTGTCTCCGAC	0.363																																					p.K267R		Atlas-SNP	.											.	SMARCA1	126	.	0			c.A800G						.						123	119	120					X																	128645791		2203	4300	6503	SO:0001583	missense	6594	exon6			GCATCCTTGTCTC	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.800A>G	chrX.hg19:g.128645791T>C	ENSP00000360163:p.Lys267Arg	156.0	0.0		434.0	406.0	NM_139035	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	hg19	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.015612	0.54468	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23	5.5	5.5	0.81552	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.64402	D	0.000002	D	0.89924	0.6856	L	0.37697	1.125	0.50467	D	0.999873	B;B;B;B	0.14012	0.009;0.009;0.007;0.009	B;B;B;B	0.17979	0.013;0.02;0.011;0.02	D	0.86433	0.1762	10	0.54805	T	0.06	-15.7599	14.5783	0.68265	0.0:0.0:0.0:1.0	.	246;267;267;267	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	R	267;267;267;246	ENSP00000360162:K267R;ENSP00000360164:K267R;ENSP00000360163:K267R;ENSP00000404275:K246R	ENSP00000360162:K267R	K	-	2	0	SMARCA1	128473472	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.953000	0.63624	1.823000	0.53134	0.486000	0.48141	AAG	.	.		0.363	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		C	128645791	T	C	128645791	3	2	223	1	0	0	0	0	1	0	0	0	14783	1609	56	2	2440	2	SMARCA1	23	128645791	Missense_Mutation	SNP	T	TCGA-DD-AAVP-01A-11D-A40R-10	5462920	128645791	26624769	79	31838										
SAGE1	55511	hgsc.bcm.edu	37	chrX	134990278	134990278	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0375	3	1	0.975360576923077	1.40885416666667	0.8453125	1	1	0	cattcacaatctgcgtgaagAgaagaaagataacagccaac	8	9	2	4			TCGA-DD-AAVP-01A-11D-A40R-10	TCGA-DD-AAVP-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ee32767-8d4e-47ab-bbf6-9f623159f16b	c86ff390-e3fe-44f9-8f26-e7c7dd6c5536	g.chrX:134990278A>T	ENST00000370709.3	+	10	1190	c.1190A>T	c.(1189-1191)gAg>gTg	p.E397V	SAGE1_ENST00000324447.3_Missense_Mutation_p.E397V|SAGE1_ENST00000537770.1_Intron|SAGE1_ENST00000535938.1_Missense_Mutation_p.E397V			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	397						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					CTGCGTGAAGAGAAGAAAGAT	0.463																																					p.E397V		Atlas-SNP	.											.	SAGE1	160	.	0			c.A1190T						.						159	135	143					X																	134990278		2203	4300	6503	SO:0001583	missense	55511	exon11			GTGAAGAGAAGAA	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.1190A>T	chrX.hg19:g.134990278A>T	ENSP00000359743:p.Glu397Val	101.0	0.0		193.0	172.0	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	hg19	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.917113	0.33815	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000370709	T;T;T	0.49720	0.77;0.77;0.77	1.17	1.17	0.20885	.	.	.	.	.	T	0.47266	0.1436	L	0.29908	0.895	0.09310	N	0.999994	D	0.69078	0.997	D	0.66497	0.944	T	0.25950	-1.0117	9	0.36615	T	0.2	.	4.2197	0.10552	1.0:0.0:0.0:0.0	.	397	Q9NXZ1	SAGE1_HUMAN	V	397	ENSP00000323191:E397V;ENSP00000445959:E397V;ENSP00000359743:E397V	ENSP00000323191:E397V	E	+	2	0	SAGE1	134817944	0.985000	0.35326	0.130000	0.21974	0.208000	0.24298	2.468000	0.45102	0.724000	0.32296	0.046000	0.15203	GAG	.	.		0.463	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		T	134990278	A	T	134990278	3	4	223	1	0	0	0	0	1	0	0	0	13824	304	11	4	1228	4	SAGE1	23	134990278	Missense_Mutation	SNP	A	TCGA-DD-AAVP-01A-11D-A40R-10	6344487	134990278	20280282	80	31839										
CLCN6	1185	hgsc.bcm.edu	37	chr1	11886262	11886262	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtttaacttcccctatttccGaagcgacaggtatggaaagg	10	9	0	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr1:11886262G>T	ENST00000346436.6	+	9	750	c.698G>T	c.(697-699)cGa>cTa	p.R233L	CLCN6_ENST00000376487.3_Missense_Mutation_p.R211L|CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000312413.6_Missense_Mutation_p.R233L|CLCN6_ENST00000376496.3_Missense_Mutation_p.R233L	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	233					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CCCTATTTCCGAAGCGACAGG	0.433																																					p.R233L		Atlas-SNP	.											.	CLCN6	77	.	0			c.G698T						.						132	130	131					1																	11886262		2203	4300	6503	SO:0001583	missense	1185	exon9			ATTTCCGAAGCGA	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"Ion channels / Chloride channels : Voltage-sensitive"	2024	protein-coding gene	gene with protein product		602726	"chloride channel 6"			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.698G>T	chr1.hg19:g.11886262G>T	ENSP00000234488:p.Arg233Leu	74.0	0.0		62.0	8.0	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	hg19	CCDS138.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.789898	0.90367	.	.	ENSG00000011021	ENST00000312413;ENST00000346436;ENST00000376487;ENST00000376496;ENST00000376490;ENST00000376491;ENST00000376492	D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24	5.76	4.85	0.62838	Chloride channel, core (2);	0.052716	0.85682	D	0.000000	D	0.96116	0.8734	M	0.84773	2.715	0.80722	D	1	P;D;D;D;D	0.59357	0.947;0.982;0.985;0.985;0.957	P;P;P;P;P	0.58780	0.702;0.683;0.793;0.845;0.803	D	0.96405	0.9300	10	0.72032	D	0.01	-4.9429	14.0578	0.64781	0.0721:0.0:0.9279:0.0	.	211;233;233;233;233	F8W9R3;P51797-3;P51797-4;P51797-2;P51797	.;.;.;.;CLCN6_HUMAN	L	233;233;211;233;233;233;233	ENSP00000308367:R233L;ENSP00000234488:R233L;ENSP00000365670:R211L;ENSP00000365679:R233L	ENSP00000308367:R233L	R	+	2	0	CLCN6	11808849	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.284000	0.95882	1.433000	0.47394	-0.150000	0.13652	CGA	.	.		0.433	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		T	11886262	G	T	11886262	3	4	224	1	0	0	0	0	1	0	0	0	3469	1058	37	1	732	1	CLCN6	1	11886262	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10		11886262	237364359	1	31840										
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94655494	94655494	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	attctcacccatcaacttttTcttcttcagttgaatttgtg	4	10	5	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr1:94655494T>G	ENST00000260526.6	-	13	1609	c.1427A>C	c.(1426-1428)gAa>gCa	p.E476A	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	476					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		ATCAACTTTTTCTTCTTCAGT	0.353																																					p.E476A		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.A1427C						.						75	75	75					1																	94655494		2203	4300	6503	SO:0001583	missense	9411	exon13			ACTTTTTCTTCTT		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.1427A>C	chr1.hg19:g.94655494T>G	ENSP00000260526:p.Glu476Ala	65.0	0.0		59.0	5.0	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	hg19	CCDS748.1	.	.	.	.	.	.	.	.	.	.	T	12.59	1.983358	0.35036	.	.	ENSG00000137962	ENST00000260526	T	0.22945	1.93	6.16	5.04	0.67666	.	0.188580	0.25801	N	0.028213	T	0.09291	0.0229	L	0.43152	1.355	0.80722	D	1	B;B	0.27068	0.167;0.005	B;B	0.24394	0.053;0.011	T	0.07028	-1.0794	10	0.37606	T	0.19	-14.0541	7.4134	0.27029	0.0:0.1286:0.1216:0.7499	.	476;476	F8VWZ8;Q52LW3	.;RHG29_HUMAN	A	476	ENSP00000260526:E476A	ENSP00000260526:E476A	E	-	2	0	ARHGAP29	94428082	.	.	0.994000	0.49952	0.900000	0.52787	.	.	1.139000	0.42245	0.528000	0.53228	GAA	.	.		0.353	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		G	94655494	T	G	94655494	3	3	224	1	0	0	0	0	1	0	0	0	878	1783	62	5	2402	5	ARHGAP29	1	94655494	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10	82769232	94655494	154595127	2	31841										
NUP133	55746	hgsc.bcm.edu	37	chr1	229623290	229623290	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agcacacatagacagcacttTcgttatacagataggcagtc	8	10	0	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr1:229623290T>C	ENST00000261396.3	-	10	1356	c.1265A>G	c.(1264-1266)gAa>gGa	p.E422G	NUP133_ENST00000537506.1_Missense_Mutation_p.E406G	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	422					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GACAGCACTTTCGTTATACAG	0.388																																					p.E422G		Atlas-SNP	.											.	NUP133	111	.	0			c.A1265G						.						110	111	111					1																	229623290		2203	4300	6503	SO:0001583	missense	55746	exon10			GCACTTTCGTTAT		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1265A>G	chr1.hg19:g.229623290T>C	ENSP00000261396:p.Glu422Gly	52.0	0.0		112.0	6.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	hg19	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	T	19.27	3.795557	0.70452	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.22743	1.94;1.94;1.94	5.07	5.07	0.68467	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.090399	0.85682	D	0.000000	T	0.32704	0.0838	M	0.63428	1.95	0.58432	D	0.999995	D	0.53312	0.959	P	0.50860	0.652	T	0.04029	-1.0983	10	0.33940	T	0.23	-16.2575	15.1233	0.72463	0.0:0.0:0.0:1.0	.	422	Q8WUM0	NU133_HUMAN	G	422;422;422;406	ENSP00000261396:E422G;ENSP00000355640:E422G;ENSP00000443496:E406G	ENSP00000261396:E422G	E	-	2	0	NUP133	227689913	1.000000	0.71417	0.166000	0.22797	0.484000	0.33280	6.913000	0.75759	2.042000	0.60477	0.477000	0.44152	GAA	.	.		0.388	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		C	229623290	T	C	229623290	3	2	224	1	0	0	0	0	1	0	0	0	10763	1783	62	2	2273	2	NUP133	1	229623290	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10	134967796	229623290	19627331	3	31842										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245772752	245772752	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aacctgcgggacctgctgtcGgaggtggccacgggcagcct	16	13	0	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr1:245772752G>A	ENST00000407071.2	+	8	2276	c.1836G>A	c.(1834-1836)tcG>tcA	p.S612S	KIF26B_ENST00000366518.4_Silent_p.S231S	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	612	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			ACCTGCTGTCGGAGGTGGCCA	0.642																																					p.S612S		Atlas-SNP	.											.	KIF26B	343	.	0			c.G1836A						.						15	20	19					1																	245772752		1976	4135	6111	SO:0001819	synonymous_variant	55083	exon8			GCTGTCGGAGGTG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.1836G>A	chr1.hg19:g.245772752G>A		229.0	0.0		314.0	55.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	.		0.642	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245772752	G	A	245772752	2	1	224	1	0	0	0	0	0	0	0	1	8304	1103	39	1		1	KIF26B	1	245772752	Silent	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	16149462	245772752	3477869	4	31843										
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458151	248458151	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ataaaagagtcccaccacagCcacatgtgaagagcaggtgg	11	10	0	3	rs369908991		TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr1:248458151C>A	ENST00000317996.1	-	1	729	c.730G>T	c.(730-732)Gct>Tct	p.A244S		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			CCCACCACAGCCACATGTGAA	0.512													N|||	1	0.000199681	8e-04	0	5008	,	,		20472	0		0	False		,,,				2504	0				p.A244S		Atlas-SNP	.											.	OR2T12	113	.	0			c.G730T						.	C	SER/ALA	1,4405	2.1+/-5.4	0,1,2202	78	78	78		730	-1.2	0.2	1		78	0,8594		0,0,4297	no	missense	OR2T12	NM_001004692.1	99	0,1,6499	AA,AC,CC		0.0,0.0227,0.0077	benign	244/321	248458151	1,12999	2203	4297	6500	SO:0001583	missense	127064	exon1			CCACAGCCACATG	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.730G>T	chr1.hg19:g.248458151C>A	ENSP00000324583:p.Ala244Ser	269.0	0.0		449.0	219.0	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	hg19	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	c	10.45	1.354309	0.24512	2.27E-4	0.0	ENSG00000177201	ENST00000317996	T	0.37915	1.17	1.55	-1.22	0.09494	GPCR, rhodopsin-like superfamily (1);	0.744958	0.10900	N	0.621742	T	0.18215	0.0437	N	0.13198	0.31	0.09310	N	1	B	0.26672	0.156	B	0.29267	0.1	T	0.26052	-1.0114	10	0.51188	T	0.08	.	3.4517	0.07501	0.0:0.3847:0.2115:0.4038	.	244	Q8NG77	O2T12_HUMAN	S	244	ENSP00000324583:A244S	ENSP00000324583:A244S	A	-	1	0	OR2T12	246524774	0.000000	0.05858	0.246000	0.24233	0.701000	0.40568	-1.292000	0.02772	0.645000	0.30675	0.175000	0.17021	GCT	.	.		0.512	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		A	248458151	C	A	248458151	3	1	224	1	0	0	0	0	1	0	0	0	11028	739	26	3	235	3	OR2T12	1	248458151	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	2685399	248458151	792470	5	31844										
SH3BP5L	80851	hgsc.bcm.edu	37	chr1	249106244	249106244	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctccacggagtcgcacttcTgcaggtctgaagccaccgtg	12	14	2	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr1:249106244T>C	ENST00000366472.5	-	7	2266	c.1037A>G	c.(1036-1038)cAg>cGg	p.Q346R	SH3BP5L_ENST00000475978.1_5'UTR|SH3BP5L_ENST00000411742.2_Missense_Mutation_p.Q314R	NM_030645.1	NP_085148.1	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	346										endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			GTCGCACTTCTGCAGGTCTGA	0.711																																					p.Q346R		Atlas-SNP	.											.	SH3BP5L	47	.	0			c.A1037G						.						19	24	23					1																	249106244		2201	4297	6498	SO:0001583	missense	80851	exon7			CACTTCTGCAGGT	AB051507	CCDS31126.1	1q44	2008-02-05			ENSG00000175137	ENSG00000175137			29360	protein-coding gene	gene with protein product							Standard	NM_030645		Approved	KIAA1720	uc001iew.1	Q7L8J4	OTTHUMG00000040389	ENST00000366472.5:c.1037A>G	chr1.hg19:g.249106244T>C	ENSP00000355428:p.Gln346Arg	99.0	0.0		140.0	27.0	NM_030645	B4DQ94|Q96FI5|Q9BQH8|Q9C0E3	Missense_Mutation	SNP	ENST00000366472.5	hg19	CCDS31126.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.137725	0.37728	.	.	ENSG00000175137	ENST00000366472;ENST00000411742	.	.	.	4.27	4.27	0.50696	.	0.059109	0.64402	D	0.000002	T	0.28499	0.0705	N	0.24115	0.695	0.37437	D	0.91426	P;P;B;P	0.39480	0.675;0.675;0.276;0.675	B;B;B;B	0.28553	0.091;0.066;0.084;0.066	T	0.36456	-0.9747	9	0.46703	T	0.11	-43.7652	11.6585	0.51332	0.0:0.0:0.0:1.0	.	314;239;346;204	B4DQ94;B4DSF1;Q7L8J4;Q96MW4	.;.;3BP5L_HUMAN;.	R	346;314	.	ENSP00000355428:Q346R	Q	-	2	0	SH3BP5L	247072867	1.000000	0.71417	1.000000	0.80357	0.559000	0.35586	6.929000	0.75852	1.922000	0.55676	0.260000	0.18958	CAG	.	.		0.711	SH3BP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097140.1	NM_030645		C	249106244	T	C	249106244	3	2	224	1	0	0	0	0	1	0	0	0	14263	1580	55	2	148	2	SH3BP5L	1	249106244	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10	648093	249106244	144377	6	31845										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	24033262	24033262	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctagtctatgcacagagaatCtttctagagtgtgcaaaagt	9	7	3	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr2:24033262C>A	ENST00000238789.5	-	18	2721	c.2378G>T	c.(2377-2379)aGa>aTa	p.R793I	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	793						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACAGAGAATCTTTCTAGAGT	0.478																																					p.R793I		Atlas-SNP	.											.	ATAD2B	110	.	0			c.G2378T						.						92	95	94					2																	24033262		1927	4136	6063	SO:0001583	missense	54454	exon18			GAGAATCTTTCTA	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.2378G>T	chr2.hg19:g.24033262C>A	ENSP00000238789:p.Arg793Ile	106.0	0.0		119.0	17.0	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	hg19	CCDS46227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.19|17.19	3.325488|3.325488	0.60743|0.60743	.|.	.|.	ENSG00000119778|ENSG00000119778	ENST00000381024|ENST00000238789	.|D	.|0.95001	.|-3.58	5.51|5.51	2.27|2.27	0.28462|0.28462	.|.	.|1.760050	.|0.03101	.|N	.|0.161139	D|D	0.90703|0.90703	0.7083|0.7083	N|N	0.24115|0.24115	0.695|0.695	0.51767|0.51767	D|D	0.999934|0.999934	.|B;B	.|0.27140	.|0.105;0.169	.|B;B	.|0.32211	.|0.067;0.142	T|T	0.76542|0.76542	-0.2921|-0.2921	5|10	.|0.46703	.|T	.|0.11	.|.	7.1434|7.1434	0.25568|0.25568	0.0:0.2551:0.0:0.7449|0.0:0.2551:0.0:0.7449	.|.	.|793;793	.|Q9ULI0;Q9ULI0-2	.|ATD2B_HUMAN;.	Y|I	74|793	.|ENSP00000238789:R793I	.|ENSP00000238789:R793I	D|R	-|-	1|2	0|0	ATAD2B|ATAD2B	23886766|23886766	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.969000|0.969000	0.65631|0.65631	3.501000|3.501000	0.53325|0.53325	0.257000|0.257000	0.21650|0.21650	0.655000|0.655000	0.94253|0.94253	GAT|AGA	.	.		0.478	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		A	24033262	C	A	24033262	3	1	224	1	0	0	0	0	1	0	0	0	1072	913	32	3	2042	3	ATAD2B	2	24033262	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10		24033262	219166111	7	31846										
SDPR	8436	hgsc.bcm.edu	37	chr2	192700699	192700699	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	gggctgcacggggtccccatCggagcgctccgcctcctcgg	15	17	0	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr2:192700699C>T	ENST00000304141.4	-	2	1557	c.1228G>A	c.(1228-1230)Gat>Aat	p.D410N		NM_004657.5	NP_004648.1			serum deprivation response											NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			GGGTCCCCATCGGAGCGCTCC	0.637																																					p.D410N		Atlas-SNP	.											.	SDPR	67	.	0			c.G1228A						.						49	50	50					2																	192700699		2203	4300	6503	SO:0001583	missense	8436	exon2			CCCCATCGGAGCG	AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"phosphatidylserine binding protein"	606728	"serum deprivation response (phosphatidylserine-binding protein)", "serum deprivation response (phosphatidylserine binding protein)"			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.1228G>A	chr2.hg19:g.192700699C>T	ENSP00000305675:p.Asp410Asn	21.0	0.0		40.0	20.0	NM_004657		Missense_Mutation	SNP	ENST00000304141.4	hg19	CCDS2313.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.741892	0.49151	.	.	ENSG00000168497	ENST00000304141	T	0.66815	-0.23	4.79	2.97	0.34412	.	1.359500	0.04585	N	0.395729	T	0.63721	0.2535	L	0.50333	1.59	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.52305	-0.8593	10	0.66056	D	0.02	-0.5275	9.3715	0.38256	0.0:0.8554:0.0:0.1446	.	410	O95810	SDPR_HUMAN	N	410	ENSP00000305675:D410N	ENSP00000305675:D410N	D	-	1	0	SDPR	192408944	0.061000	0.20836	0.000000	0.03702	0.004000	0.04260	1.242000	0.32755	0.626000	0.30322	0.563000	0.77884	GAT	.	.		0.637	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657		T	192700699	C	T	192700699	3	4	224	1	0	0	0	0	1	0	0	0	13985	884	31	1	53	1	SDPR	2	192700699	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	168667437	192700699	50498674	8	31847										
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226447236	226447236	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaagcttcccgtgctggaaaAcgtgtcttacatgaaacagc	10	10	1	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr2:226447236A>G	ENST00000272907.6	+	4	1516	c.1103A>G	c.(1102-1104)aAc>aGc	p.N368S	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	368	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GTGCTGGAAAACGTGTCTTAC	0.662																																					p.N368S		Atlas-SNP	.											.	.	.	.	0			c.A1103G						.						16	20	19					2																	226447236		1976	4142	6118	SO:0001583	missense	57624	exon4			TGGAAAACGTGTC	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1103A>G	chr2.hg19:g.226447236A>G	ENSP00000272907:p.Asn368Ser	184.0	0.0		269.0	55.0	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	hg19	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	A	15.73	2.918800	0.52546	.	.	ENSG00000144460	ENST00000272907	T	0.47528	0.84	5.16	4.0	0.46444	.	0.048846	0.85682	N	0.000000	T	0.48995	0.1531	M	0.79258	2.445	0.80722	D	1	B	0.15930	0.015	B	0.19148	0.024	T	0.48658	-0.9016	10	0.59425	D	0.04	-37.2006	10.6399	0.45586	0.9248:0.0:0.0752:0.0	.	368	Q9P242	K1486_HUMAN	S	368	ENSP00000272907:N368S	ENSP00000272907:N368S	N	+	2	0	KIAA1486	226155480	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	7.174000	0.77620	0.811000	0.34303	0.528000	0.53228	AAC	.	.		0.662	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		G	226447236	A	G	226447236	3	3	224	1	0	0	0	0	1	0	0	0	8246	43	2	2	1113	2	KIAA1486	2	226447236	Missense_Mutation	SNP	A	TCGA-DD-AAVQ-01A-11D-A40R-10	33746537	226447236	16752137	9	31848										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	113.0	0.0		118.0	18.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	224	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10		41266136	156756294	10	31849										
KLHL18	23276	hgsc.bcm.edu	37	chr3	47371504	47371504	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acaatgatgtgtgctgtgctGtacgacgctgccaacagctt	11	10	0	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr3:47371504G>C	ENST00000232766.5	+	4	485	c.465G>C	c.(463-465)ctG>ctC	p.L155L	KLHL18_ENST00000455924.2_Silent_p.L43L	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	155	BACK.									endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	21		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		GTGCTGTGCTGTACGACGCTG	0.502																																					p.L155L		Atlas-SNP	.											.	KLHL18	46	.	0			c.G465C						.						129	123	125					3																	47371504		2203	4300	6503	SO:0001819	synonymous_variant	23276	exon4			TGTGCTGTACGAC	AB018338	CCDS33749.1	3p21	2013-01-30	2013-01-30		ENSG00000114648	ENSG00000114648		"Kelch-like", "BTB/POZ domain containing"	29120	protein-coding gene	gene with protein product			"kelch-like 18 (Drosophila)"			9872452	Standard	NM_025010		Approved	KIAA0795, FLJ13703	uc003crd.3	O94889	OTTHUMG00000156522	ENST00000232766.5:c.465G>C	chr3.hg19:g.47371504G>C		67.0	0.0		53.0	16.0	NM_025010	A8K612|Q7Z3E8|Q8N125	Silent	SNP	ENST00000232766.5	hg19	CCDS33749.1																																																																																			.	.		0.502	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344493.1	NM_025010		C	47371504	G	C	47371504	2	2	224	1	0	0	0	0	0	0	0	1	8382	1364	48	4		4	KLHL18	3	47371504	Silent	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	6105368	47371504	150650926	11	31850										
PRR23B	389151	hgsc.bcm.edu	37	chr3	138739004	138739004	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agccggttggggagtccatcCggagctccgggaactcgggg	18	11	0	0	rs376706999		TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr3:138739004C>A	ENST00000329447.5	-	1	764	c.500G>T	c.(499-501)cGg>cTg	p.R167L	MRPS22_ENST00000495075.1_Intron	NM_001013650.2	NP_001013672.1	Q6ZRT6	PR23B_HUMAN	proline rich 23B	167								p.R167Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGAGTCCATCCGGAGCTCCGG	0.647																																					p.R167L		Atlas-SNP	.											PRR23B,NS,carcinoma,0,1	PRR23B	56	.	1	Substitution - Missense(1)	lung(1)	c.G500T						.						31	39	36					3																	138739004		2201	4299	6500	SO:0001583	missense	389151	exon1			TCCATCCGGAGCT	BC137146	CCDS33868.1	3q22.3	2014-06-03			ENSG00000184814	ENSG00000184814			33764	protein-coding gene	gene with protein product							Standard	NM_001013650		Approved	FLJ46116	uc003esy.1	Q6ZRT6	OTTHUMG00000160633	ENST00000329447.5:c.500G>T	chr3.hg19:g.138739004C>A	ENSP00000328768:p.Arg167Leu	139.0	0.0		138.0	15.0	NM_001013650	B2RNV9	Missense_Mutation	SNP	ENST00000329447.5	hg19	CCDS33868.1	.	.	.	.	.	.	.	.	.	.	C	10.49	1.364365	0.24684	.	.	ENSG00000184814	ENST00000329447	.	.	.	3.14	0.243	0.15503	.	1.288490	0.05675	N	0.589327	T	0.30541	0.0768	L	0.34521	1.04	0.09310	N	1	B	0.26744	0.158	B	0.23574	0.047	T	0.25398	-1.0133	9	0.40728	T	0.16	.	5.4872	0.16757	0.0:0.6056:0.0:0.3944	.	167	Q6ZRT6	PR23B_HUMAN	L	167	.	ENSP00000328768:R167L	R	-	2	0	PRR23B	140221694	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.107000	0.10873	0.036000	0.15547	0.456000	0.33151	CGG	.	.		0.647	PRR23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361501.1	NM_001013650		A	138739004	C	A	138739004	3	1	224	1	0	0	0	0	1	0	0	0	12607	652	23	1	301	1	PRR23B	3	138739004	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	91367500	138739004	59283426	12	31851										
TFRC	7037	hgsc.bcm.edu	37	chr3	195787062	195787062	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tatactcacattttgcattgTtttctcaataagcgtataca	4	8	2	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr3:195787062T>C	ENST00000360110.4	-	14	1694	c.1525A>G	c.(1525-1527)Aca>Gca	p.T509A	TFRC_ENST00000535031.1_Missense_Mutation_p.T227A|TFRC_ENST00000465288.1_5'UTR|TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000392396.3_Missense_Mutation_p.T509A|TFRC_ENST00000420415.1_Missense_Mutation_p.T428A	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	509					cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|osteoclast differentiation (GO:0030316)|positive regulation of bone resorption (GO:0045780)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transferrin receptor activity (GO:0004998)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)	Gallium nitrate(DB05260)	TTTTGCATTGTTTTCTCAATA	0.343			T	BCL6	NHL																																p.T509A		Atlas-SNP	.		Dom	yes		3	3q29	7037	"transferrin receptor (p90, CD71)"		L	.	TFRC	54	.	0			c.A1525G						.						139	129	132					3																	195787062		2203	4300	6503	SO:0001583	missense	7037	exon14			GCATTGTTTTCTC	X01060	CCDS3312.1	3q29	2013-09-19	2013-09-19		ENSG00000072274	ENSG00000072274		"CD molecules"	11763	protein-coding gene	gene with protein product		190010	"transferrin receptor (p90, CD71)"				Standard	NM_003234		Approved	CD71, TFR1, p90	uc003fwa.4	P02786	OTTHUMG00000155714	ENST00000360110.4:c.1525A>G	chr3.hg19:g.195787062T>C	ENSP00000353224:p.Thr509Ala	109.0	0.0		88.0	7.0	NM_001128148	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Missense_Mutation	SNP	ENST00000360110.4	hg19	CCDS3312.1	.	.	.	.	.	.	.	.	.	.	T	9.800	1.180235	0.21787	.	.	ENSG00000072274	ENST00000360110;ENST00000420415;ENST00000392396;ENST00000535031	T;T;T;T	0.71103	0.78;0.78;0.78;-0.54	5.44	3.05	0.35203	Peptidase M28 (1);	0.246883	0.47455	D	0.000235	T	0.45895	0.1365	N	0.12569	0.235	0.19575	N	0.999966	B	0.32717	0.381	B	0.32864	0.154	T	0.37103	-0.9720	10	0.07644	T	0.81	0.298	9.1954	0.37224	0.0:0.1462:0.0:0.8538	.	509	P02786	TFR1_HUMAN	A	509;428;509;227	ENSP00000353224:T509A;ENSP00000390133:T428A;ENSP00000376197:T509A;ENSP00000437753:T227A	ENSP00000353224:T509A	T	-	1	0	TFRC	197271459	0.034000	0.19679	0.058000	0.19502	0.685000	0.39939	1.493000	0.35605	0.365000	0.24400	0.533000	0.62120	ACA	.	.		0.343	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1			C	195787062	T	C	195787062	3	2	224	1	0	0	0	0	1	0	0	0	15827	1725	60	2	781	2	TFRC	3	195787062	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10	57048058	195787062	2235368	13	31852										
POLR2B	5431	hgsc.bcm.edu	37	chr4	57871518	57871518	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgttactaaagagaaaagaaTtaaatatgcaaaggaagttt	8	2	0	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr4:57871518T>C	ENST00000381227.1	+	9	1420	c.1007T>C	c.(1006-1008)aTt>aCt	p.I336T	RNU6-998P_ENST00000515894.1_RNA|POLR2B_ENST00000431623.2_Missense_Mutation_p.I261T|POLR2B_ENST00000441246.2_Missense_Mutation_p.I329T|POLR2B_ENST00000314595.5_Missense_Mutation_p.I336T			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	336					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					GAGAAAAGAATTAAATATGCA	0.368																																					p.I336T		Atlas-SNP	.											.	POLR2B	108	.	0			c.T1007C						.						95	97	96					4																	57871518		2203	4299	6502	SO:0001583	missense	5431	exon8			AAAGAATTAAATA		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1007T>C	chr4.hg19:g.57871518T>C	ENSP00000370625:p.Ile336Thr	300.0	0.0		351.0	27.0	NM_000938	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	hg19	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.406979	0.83230	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.77	5.77	0.91146	RNA polymerase, beta subunit, protrusion (1);RNA polymerase Rpb2, domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.75961	0.3921	M	0.86805	2.84	0.80722	D	1	P;P	0.39809	0.62;0.689	P;P	0.47705	0.555;0.555	T	0.79027	-0.1971	10	0.54805	T	0.06	.	16.3818	0.83467	0.0:0.0:0.0:1.0	.	261;336	C9J4M6;P30876	.;RPB2_HUMAN	T	336;261;329;336	ENSP00000370625:I336T;ENSP00000391096:I261T;ENSP00000391452:I329T;ENSP00000312735:I336T	ENSP00000312735:I336T	I	+	2	0	POLR2B	57566275	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.784000	0.85713	2.330000	0.79161	0.528000	0.53228	ATT	.	.		0.368	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		C	57871518	T	C	57871518	3	2	224	1	0	0	0	0	1	0	0	0	12224	1493	52	2	1037	2	POLR2B	4	57871518	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10		57871518	133282758	14	31853										
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77662788	77662788	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cagccccgcagggaggccacGctcctgccggccacagttgc	13	18	0	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr4:77662788G>T	ENST00000296043.6	+	5	4415	c.3462G>T	c.(3460-3462)acG>acT	p.T1154T		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1154					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			GGGAGGCCACGCTCCTGCCGG	0.751																																					p.T1154T		Atlas-SNP	.											.	SHROOM3	134	.	0			c.G3462T						.						3	5	4					4																	77662788		1960	3896	5856	SO:0001819	synonymous_variant	57619	exon5			GGCCACGCTCCTG	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.3462G>T	chr4.hg19:g.77662788G>T		28.0	0.0		35.0	5.0	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	hg19	CCDS3579.2																																																																																			.	.		0.751	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		T	77662788	G	T	77662788	2	4	224	1	0	0	0	0	0	0	0	1	14310	1074	38	1		1	SHROOM3	4	77662788	Silent	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	19791270	77662788	113491488	15	31854										
IL15	3600	hgsc.bcm.edu	37	chr4	142653941	142653941	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaggaactggaggaaaaaaaTattaaagaatttttgcagag	11	2	0	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr4:142653941T>C	ENST00000296545.7	+	8	1273	c.429T>C	c.(427-429)aaT>aaC	p.N143N	IL15_ENST00000514653.1_Silent_p.N116N|IL15_ENST00000394159.1_Silent_p.N116N|IL15_ENST00000529613.1_Silent_p.N143N|IL15_ENST00000477265.1_Silent_p.N116N|IL15_ENST00000320650.4_Silent_p.N143N			P40933	IL15_HUMAN	interleukin 15	143					aging (GO:0007568)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|cellular response to vitamin D (GO:0071305)|extrathymic T cell selection (GO:0045062)|hyaluronan metabolic process (GO:0030212)|immune response (GO:0006955)|inflammatory response (GO:0006954)|lymph node development (GO:0048535)|natural killer cell differentiation (GO:0001779)|negative regulation of smooth muscle cell proliferation (GO:0048662)|NK T cell proliferation (GO:0001866)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immune response (GO:0050778)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of defense response to virus by host (GO:0050691)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_hematologic(180;0.158)					AGGAAAAAAATATTAAAGAAT	0.269																																					p.N143N	Pancreas(10;184 986 25902)	Atlas-SNP	.											.	IL15	17	.	0			c.T429C						.						79	91	87					4																	142653941		2203	4298	6501	SO:0001819	synonymous_variant	3600	exon8			AAAAAATATTAAA	U14407	CCDS3755.1, CCDS3756.1	4q31	2011-07-14			ENSG00000164136	ENSG00000164136		"Interleukins and interleukin receptors"	5977	protein-coding gene	gene with protein product		600554				8178155	Standard	NM_000585		Approved	IL-15, MGC9721	uc003iis.3	P40933	OTTHUMG00000133418	ENST00000296545.7:c.429T>C	chr4.hg19:g.142653941T>C		258.0	0.0		255.0	32.0	NM_000585	D3DNZ2|O00440|O43512|Q495Z8|Q6FGX7|Q93058|Q9UBA3	Silent	SNP	ENST00000296545.7	hg19	CCDS3755.1																																																																																			.	.		0.269	IL15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257278.2	NM_172175		C	142653941	T	C	142653941	2	2	224	1	0	0	0	0	0	0	0	1	7640	1403	49	2		2	IL15	4	142653941	Silent	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10	64991153	142653941	48500335	16	31855										
GUCY1A3	2982	hgsc.bcm.edu	37	chr4	156618214	156618214	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cttcctcaaagaaaaaccagTcggagccgagtctatcttca	7	12	4	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr4:156618214T>A	ENST00000296518.7	+	3	404	c.195T>A	c.(193-195)agT>agA	p.S65R	GUCY1A3_ENST00000513574.1_Missense_Mutation_p.S65R|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.S65R|GUCY1A3_ENST00000393832.3_5'UTR|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.S65R|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.S65R|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.S65R|GUCY1A3_ENST00000515602.1_3'UTR			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	65					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		GAAAAACCAGTCGGAGCCGAG	0.438																																					p.S65R		Atlas-SNP	.											.	GUCY1A3	133	.	0			c.T195A						.						98	101	100					4																	156618214		2203	4300	6503	SO:0001583	missense	2982	exon3			AACCAGTCGGAGC		CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.195T>A	chr4.hg19:g.156618214T>A	ENSP00000296518:p.Ser65Arg	105.0	0.0		112.0	21.0	NM_001130687	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	hg19	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.056645	0.55325	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000296518;ENST00000513574	D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.54;-1.68;-1.68;-1.68	5.93	-1.6	0.08426	.	0.000000	0.85682	D	0.000000	T	0.76004	0.3927	M	0.66939	2.045	0.54753	D	0.999986	B;B;B	0.27013	0.166;0.166;0.166	B;B;B	0.19666	0.026;0.026;0.026	T	0.65384	-0.6181	10	0.13853	T	0.58	.	13.5475	0.61713	0.0:0.6929:0.0:0.3071	.	65;65;65	B3KU69;Q02108;D6RDW3	.;GCYA3_HUMAN;.	R	65	ENSP00000424361:S65R;ENSP00000421493:S65R;ENSP00000426968:S65R;ENSP00000412201:S65R;ENSP00000296518:S65R;ENSP00000426040:S65R	ENSP00000296518:S65R	S	+	3	2	GUCY1A3	156837664	0.737000	0.28175	0.988000	0.46212	0.986000	0.74619	-0.010000	0.12743	-0.141000	0.11374	0.482000	0.46254	AGT	.	.		0.438	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			A	156618214	T	A	156618214	3	1	224	1	0	0	0	0	1	0	0	0	6903	1664	58	4	197	4	GUCY1A3	4	156618214	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10	13964273	156618214	34536062	17	31856										
RGMB	285704	hgsc.bcm.edu	37	chr5	98129071	98129071	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acgaggagagccaggacctgCagctgtgcgtgaacggctgc	16	11	0	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr5:98129071C>A	ENST00000513185.1	+	3	1364	c.928C>A	c.(928-930)Cag>Aag	p.Q310K	RGMB_ENST00000308234.7_Missense_Mutation_p.Q351K			Q6NW40	RGMB_HUMAN	repulsive guidance molecule family member b	310					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell adhesion (GO:0007155)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)	identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	10		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		CCAGGACCTGCAGCTGTGCGT	0.632																																					p.Q351K		Atlas-SNP	.											.	RGMB	29	.	0			c.C1051A						.						38	39	39					5																	98129071		2140	4226	6366	SO:0001583	missense	285704	exon5			GACCTGCAGCTGT	AK074887	CCDS47251.1	5q21.1	2013-11-06	2013-11-06		ENSG00000174136	ENSG00000174136			26896	protein-coding gene	gene with protein product		612687	"RGM domain family, member B"			19324014	Standard	NM_001012761		Approved	FLJ90406, DRAGON	uc003knc.3	Q6NW40	OTTHUMG00000162745	ENST00000513185.1:c.928C>A	chr5.hg19:g.98129071C>A	ENSP00000423256:p.Gln310Lys	58.0	0.0		55.0	5.0	NM_001012761	D6R9A0|Q8NC92	Missense_Mutation	SNP	ENST00000513185.1	hg19		.	.	.	.	.	.	.	.	.	.	C	19.91	3.913805	0.72983	.	.	ENSG00000174136	ENST00000308234;ENST00000513185	D;D	0.85629	-2.01;-2.01	5.78	5.78	0.91487	Repulsive guidance molecule, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92932	0.7751	M	0.81497	2.545	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.91988	0.5600	10	0.45353	T	0.12	-16.4755	19.9851	0.97342	0.0:1.0:0.0:0.0	.	310	Q6NW40	RGMB_HUMAN	K	351;310	ENSP00000308219:Q351K;ENSP00000423256:Q310K	ENSP00000308219:Q351K	Q	+	1	0	RGMB	98156971	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.929000	0.40114	2.727000	0.93392	0.655000	0.94253	CAG	.	.		0.632	RGMB-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370308.1	NM_173670		A	98129071	C	A	98129071	3	1	224	1	0	0	0	0	1	0	0	0	13296	711	25	3	1065	3	RGMB	5	98129071	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10		98129071	82786189	18	31857										
SPINK14	408187	hgsc.bcm.edu	37	chr5	147553855	147553855	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caatggaacggtcaacccctGccctggcttatatcaaccca	7	15	2	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr5:147553855G>T	ENST00000356972.1	+	3	170	c.170G>T	c.(169-171)tGc>tTc	p.C57F	SPINK14_ENST00000562793.1_Intron	NM_001001325.1	NP_001001325.1	Q6IE38	ISK14_HUMAN	serine peptidase inhibitor, Kazal type 14 (putative)	57	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|large_intestine(1)|lung(1)	3						GTCAACCCCTGCCCTGGCTTA	0.413																																					p.C57F		Atlas-SNP	.											.	SPINK14	9	.	0			c.G170T						.						115	115	115					5																	147553855		1501	3128	4629	SO:0001583	missense	408187	exon3			ACCCCTGCCCTGG		CCDS4288.1	5q32	2011-08-31			ENSG00000196800	ENSG00000196800		"Serine peptidase inhibitors, Kazal type"	33825	protein-coding gene	gene with protein product							Standard	NM_001001325		Approved	SPINK5L2	uc031sls.1	Q6IE38	OTTHUMG00000129732	ENST00000356972.1:c.170G>T	chr5.hg19:g.147553855G>T	ENSP00000349459:p.Cys57Phe	154.0	0.0		159.0	26.0	NM_001001325		Missense_Mutation	SNP	ENST00000356972.1	hg19	CCDS4288.1	.	.	.	.	.	.	.	.	.	.	G	15.30	2.793590	0.50102	.	.	ENSG00000196800	ENST00000356972	D	0.98296	-4.85	4.12	4.12	0.48240	Proteinase inhibitor I1, Kazal (3);	0.000000	0.64402	D	0.000015	D	0.98692	0.9561	.	.	.	0.42198	D	0.991754	D	0.89917	1.0	D	0.91635	0.999	D	0.98701	1.0700	9	0.87932	D	0	-16.6243	12.1753	0.54182	0.0:0.0:1.0:0.0	.	57	Q6IE38	ISK14_HUMAN	F	57	ENSP00000349459:C57F	ENSP00000349459:C57F	C	+	2	0	SPINK14	147534048	0.150000	0.22732	0.793000	0.32043	0.788000	0.44548	1.411000	0.34702	2.594000	0.87642	0.655000	0.94253	TGC	.	.		0.413	SPINK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251943.2	NM_001001325		T	147553855	G	T	147553855	3	4	224	1	0	0	0	0	1	0	0	0	15074	1319	46	3	180	3	SPINK14	5	147553855	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	49424784	147553855	33361405	19	31858										
ZKSCAN3	80317	hgsc.bcm.edu	37	chr6	28327497	28327497	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	agatctgggttctgagggctCccgcgagcgcttccgaggct	15	12	2	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr6:28327497C>G	ENST00000377255.3	+	3	431	c.134C>G	c.(133-135)tCc>tGc	p.S45C	ZKSCAN3_ENST00000341464.5_Intron|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.S45C	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	45					autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						TCTGAGGGCTCCCGCGAGCGC	0.632																																					p.S45C		Atlas-SNP	.											.	ZKSCAN3	50	.	0			c.C134G						.						72	81	78					6																	28327497		2203	4300	6503	SO:0001583	missense	80317	exon2			AGGGCTCCCGCGA	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"Zinc fingers, C2H2-type", "-", "-", "-"	13853	protein-coding gene	gene with protein product		612791	"zinc finger protein 306", "zinc finger protein 309"	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.134C>G	chr6.hg19:g.28327497C>G	ENSP00000366465:p.Ser45Cys	97.0	0.0		93.0	11.0	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	hg19	CCDS4650.1	.	.	.	.	.	.	.	.	.	.	.	16.23	3.063438	0.55432	.	.	ENSG00000189298	ENST00000252211;ENST00000454413;ENST00000377255	T;T	0.04654	3.58;3.58	3.83	-2.46	0.06461	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (2);	.	.	.	.	T	0.02688	0.0081	N	0.20845	0.615	0.20703	N	0.999863	D	0.76494	0.999	P	0.62649	0.905	T	0.44452	-0.9327	9	0.32370	T	0.25	.	9.7171	0.40281	0.1535:0.241:0.6054:0.0	.	45	Q9BRR0	ZKSC3_HUMAN	C	45	ENSP00000252211:S45C;ENSP00000366465:S45C	ENSP00000252211:S45C	S	+	2	0	ZKSCAN3	28435476	0.012000	0.17670	0.168000	0.22838	0.436000	0.31835	-0.087000	0.11215	-0.257000	0.09459	0.557000	0.71058	TCC	.	.		0.632	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493		G	28327497	C	G	28327497	3	3	224	1	0	0	0	0	1	0	0	0	17703	855	30	4	136	4	ZKSCAN3	6	28327497	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10		28327497	142787570	20	31859										
CAPN11	11131	hgsc.bcm.edu	37	chr6	44137079	44137079	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aacagccggctcaaggccaaGggcgtgggccagcacgacaa	14	13	1	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr6:44137079G>T	ENST00000398776.1	+	3	188	c.150G>T	c.(148-150)aaG>aaT	p.K50N	CAPN11_ENST00000542245.1_Missense_Mutation_p.K50N	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	50					proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TCAAGGCCAAGGGCGTGGGCC	0.507																																					p.K50N		Atlas-SNP	.											.	CAPN11	66	.	0			c.G150T						.						40	42	41					6																	44137079		1922	4133	6055	SO:0001583	missense	11131	exon3			GGCCAAGGGCGTG	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.150G>T	chr6.hg19:g.44137079G>T	ENSP00000381758:p.Lys50Asn	195.0	0.0		206.0	56.0	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	hg19	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	G	1.764	-0.485979	0.04352	.	.	ENSG00000137225	ENST00000398776;ENST00000542245;ENST00000532171	D;D;T	0.97328	-4.34;-4.34;0.98	4.1	0.0875	0.14451	.	1.652940	0.03073	N	0.157458	D	0.90435	0.7005	L	0.38175	1.15	0.32992	D	0.525041	B	0.18741	0.03	B	0.19946	0.027	T	0.73994	-0.3807	10	0.25106	T	0.35	.	12.7797	0.57471	0.0:0.3365:0.5499:0.1136	.	50	Q9UMQ6	CAN11_HUMAN	N	50;50;80	ENSP00000381758:K50N;ENSP00000441078:K50N;ENSP00000432420:K80N	ENSP00000381758:K50N	K	+	3	2	CAPN11	44245057	0.136000	0.22515	0.143000	0.22291	0.001000	0.01503	0.208000	0.17415	-0.227000	0.09884	-2.547000	0.00178	AAG	.	.		0.507	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			T	44137079	G	T	44137079	3	4	224	1	0	0	0	0	1	0	0	0	2626	991	35	3	160	3	CAPN11	6	44137079	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	15809582	44137079	126977988	21	31860										
PSPH	5723	hgsc.bcm.edu	37	chr7	56084931	56084931	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	actgttaacatcttaccgttAaagtagaatttcagcctatt	5	8	2	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr7:56084931A>G	ENST00000395471.3	-	6	1222	c.417T>C	c.(415-417)ttT>ttC	p.F139F	PSPH_ENST00000275605.3_Silent_p.F139F|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	139					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TCTTACCGTTAAAGTAGAATT	0.383																																					p.F139F		Atlas-SNP	.											.	PSPH	23	.	0			c.T417C						.						102	81	88					7																	56084931		2203	4300	6503	SO:0001819	synonymous_variant	5723	exon6			ACCGTTAAAGTAG	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.417T>C	chr7.hg19:g.56084931A>G		212.0	0.0		225.0	54.0	NM_004577	B2RCR5|Q7Z3S5	Silent	SNP	ENST00000395471.3	hg19	CCDS5522.1																																																																																			.	.		0.383	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577		G	56084931	A	G	56084931	2	3	224	1	0	0	0	0	0	0	0	1	12729	359	13	2		2	PSPH	7	56084931	Silent	SNP	A	TCGA-DD-AAVQ-01A-11D-A40R-10		56084931	103053732	22	31861										
GNAI1	2770	hgsc.bcm.edu	37	chr7	79828588	79828588	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctggagctgctgaagaaggCtttatgactgcagaacttgc	13	8	0	4			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr7:79828588C>T	ENST00000351004.3	+	4	724	c.351C>T	c.(349-351)ggC>ggT	p.G117G	GNAI1_ENST00000457358.2_Silent_p.G65G	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	117					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						CTGAAGAAGGCTTTATGACTG	0.408																																					p.G117G		Atlas-SNP	.											.	GNAI1	44	.	0			c.C351T						.						115	109	111					7																	79828588		2203	4300	6503	SO:0001819	synonymous_variant	2770	exon4			AGAAGGCTTTATG	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"Gi1 protein alpha subunit"	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.351C>T	chr7.hg19:g.79828588C>T		73.0	0.0		104.0	34.0	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Silent	SNP	ENST00000351004.3	hg19	CCDS5595.1																																																																																			.	.		0.408	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		T	79828588	C	T	79828588	2	4	224	1	0	0	0	0	0	0	0	1	6512	784	28	3		3	GNAI1	7	79828588	Silent	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	23743657	79828588	79310075	23	31862										
LHFPL3	375612	hgsc.bcm.edu	37	chr7	103969251	103969251	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cccggagccgccgccgctgcCgccgccgccgccgccgcgat	14	23	0	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr7:103969251C>T	ENST00000535008.1	+	1	148	c.24C>T	c.(22-24)gcC>gcT	p.A8A	LHFPL3_ENST00000424859.1_5'UTR|LHFPL3_ENST00000543266.1_Silent_p.A8A|LHFPL3_ENST00000401970.2_5'UTR			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	8						integral component of membrane (GO:0016021)		p.A8A(1)		kidney(1)|large_intestine(2)|lung(6)	9						ccgccgctgccgccgccgccg	0.721																																					p.A8A		Atlas-SNP	.											LHFPL3,NS,carcinoma,0,1	LHFPL3	24	.	1	Substitution - coding silent(1)	kidney(1)	c.C24T						.						11	14	13					7																	103969251		1949	4092	6041	SO:0001819	synonymous_variant	375612	exon1			CGCTGCCGCCGCC	AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416			6589	protein-coding gene	gene with protein product		609719	"lipoma HMGIC fusion partner-like 4"	LHFPL4		10329012	Standard	NM_199000		Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000535008.1:c.24C>T	chr7.hg19:g.103969251C>T		25.0	0.0		37.0	2.0	NM_199000	A1L383|A4D0Q5	Silent	SNP	ENST00000535008.1	hg19																																																																																				.	.		0.721	LHFPL3-201	KNOWN	basic	protein_coding	protein_coding		NM_199000		T	103969251	C	T	103969251	2	4	224	1	0	0	0	0	0	0	0	1	8775	639	23	1		1	LHFPL3	7	103969251	Silent	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	24140663	103969251	55169412	24	31863										
XPO7	23039	hgsc.bcm.edu	37	chr8	21846524	21846524	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgtcctccagcatcaccaacTtgaagtactggggccgttgt	10	12	1	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr8:21846524T>G	ENST00000252512.9	+	16	1898	c.1798T>G	c.(1798-1800)Ttg>Gtg	p.L600V	XPO7_ENST00000434536.1_Missense_Mutation_p.L609V|XPO7_ENST00000433566.4_Missense_Mutation_p.L601V	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	600					mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		CATCACCAACTTGAAGTACTG	0.438																																					p.L600V		Atlas-SNP	.											.	XPO7	79	.	0			c.T1798G						.						91	93	92					8																	21846524		1881	4122	6003	SO:0001583	missense	23039	exon16			ACCAACTTGAAGT	AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"Exportins"	14108	protein-coding gene	gene with protein product		606140	"RAN binding protein 16"	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.1798T>G	chr8.hg19:g.21846524T>G	ENSP00000252512:p.Leu600Val	76.0	0.0		61.0	18.0	NM_015024	O94846|Q6PJK9|Q8NEK7	Missense_Mutation	SNP	ENST00000252512.9	hg19	CCDS47818.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.570976	0.45798	.	.	ENSG00000130227	ENST00000434536;ENST00000252512;ENST00000433566	T;T;T	0.42900	0.96;0.96;0.96	5.89	1.36	0.22044	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.60766	0.2294	M	0.85041	2.73	0.58432	D	0.999998	D;D;D	0.67145	0.996;0.992;0.974	P;P;P	0.62184	0.844;0.899;0.795	T	0.63363	-0.6654	10	0.59425	D	0.04	-9.0294	10.3925	0.44181	0.0:0.6056:0.0:0.3944	.	601;609;600	E7ESC6;E9PEN8;Q9UIA9	.;.;XPO7_HUMAN	V	609;600;601	ENSP00000404853:L609V;ENSP00000252512:L600V;ENSP00000410249:L601V	ENSP00000252512:L600V	L	+	1	2	XPO7	21902470	0.997000	0.39634	1.000000	0.80357	0.990000	0.78478	0.461000	0.21940	0.242000	0.21303	-0.270000	0.10280	TTG	.	.		0.438	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024		G	21846524	T	G	21846524	3	3	224	1	0	0	0	0	1	0	0	0	17464	1606	56	5	1912	5	XPO7	8	21846524	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10		21846524	124517498	25	31864										
SLCO5A1	81796	hgsc.bcm.edu	37	chr8	70585186	70585186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgcttctgggaagggccccGggtaggtctgtgctgcgcac	16	11	2	0	rs369446842		TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr8:70585186G>A	ENST00000260126.4	-	10	3171	c.2465C>T	c.(2464-2466)cCg>cTg	p.P822L	SLCO5A1_ENST00000530307.1_Missense_Mutation_p.P767L|SLCO5A1_ENST00000524945.1_3'UTR	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	822						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.P824fs*>26(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			GAAGGGCCCCGGGTAGGTCTG	0.587																																					p.P822L		Atlas-SNP	.											.	SLCO5A1	142	.	1	Insertion - Frameshift(1)	lung(1)	c.C2465T						.						57	60	59					8																	70585186		2203	4300	6503	SO:0001583	missense	81796	exon10			GGCCCCGGGTAGG	AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"Solute carriers"	19046	protein-coding gene	gene with protein product		613543	"solute carrier family 21 (organic anion transporter), member 15"	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.2465C>T	chr8.hg19:g.70585186G>A	ENSP00000260126:p.Pro822Leu	63.0	0.0		105.0	10.0	NM_030958	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Missense_Mutation	SNP	ENST00000260126.4	hg19	CCDS6205.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.408609	0.83340	.	.	ENSG00000137571	ENST00000260126;ENST00000530307	T;T	0.54675	0.59;0.56	5.93	5.93	0.95920	.	0.411905	0.24859	N	0.035037	T	0.52322	0.1727	L	0.52573	1.65	0.58432	D	0.999998	B;B	0.17268	0.021;0.021	B;B	0.12156	0.007;0.007	T	0.41627	-0.9498	10	0.44086	T	0.13	.	20.3539	0.98825	0.0:0.0:1.0:0.0	.	767;822	E9PKK5;Q9H2Y9	.;SO5A1_HUMAN	L	822;767	ENSP00000260126:P822L;ENSP00000431611:P767L	ENSP00000260126:P822L	P	-	2	0	SLCO5A1	70747740	1.000000	0.71417	0.661000	0.29709	0.962000	0.63368	8.371000	0.90123	2.826000	0.97356	0.655000	0.94253	CCG	.	.		0.587	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958		A	70585186	G	A	70585186	3	1	224	1	0	0	0	0	1	0	0	0	14746	1116	39	1	85	1	SLCO5A1	8	70585186	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	48738662	70585186	75778836	26	31865										
ESRP1	54845	hgsc.bcm.edu	37	chr8	95686717	95686717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcgaaatggcttatccccacCgccatgtaagttaccatgta	7	12	0	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr8:95686717C>T	ENST00000433389.2	+	12	1824	c.1634C>T	c.(1633-1635)cCg>cTg	p.P545L	ESRP1_ENST00000423620.2_Missense_Mutation_p.P545L|ESRP1_ENST00000358397.5_Missense_Mutation_p.P545L|ESRP1_ENST00000454170.2_Missense_Mutation_p.P545L	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	545					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						TTATCCCCACCGCCATGTAAG	0.438																																					p.P545L		Atlas-SNP	.											.	ESRP1	148	.	0			c.C1634T						.						80	81	81					8																	95686717		1912	4139	6051	SO:0001583	missense	54845	exon12			CCCCACCGCCATG	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"RNA binding motif (RRM) containing"	25966	protein-coding gene	gene with protein product		612959	"RNA binding motif protein 35A"	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.1634C>T	chr8.hg19:g.95686717C>T	ENSP00000405738:p.Pro545Leu	76.0	0.0		109.0	18.0	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Missense_Mutation	SNP	ENST00000433389.2	hg19	CCDS47897.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.405055	0.83230	.	.	ENSG00000104413	ENST00000423620;ENST00000433389;ENST00000358397;ENST00000454170;ENST00000517610	T;T;T;T;T	0.17854	2.54;2.66;2.53;2.72;2.25	5.54	5.54	0.83059	.	0.153256	0.64402	D	0.000014	T	0.43612	0.1255	M	0.66939	2.045	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.999;1.0	D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.965;0.968;1.0	T	0.13202	-1.0518	10	0.52906	T	0.07	-15.8517	19.8585	0.96775	0.0:1.0:0.0:0.0	.	545;545;545;545;545;545	D7PBN3;Q6NXG1-4;Q6NXG1-2;E9PB47;Q6NXG1-3;Q6NXG1	.;.;.;.;.;ESRP1_HUMAN	L	545;545;545;545;404	ENSP00000407349:P545L;ENSP00000405738:P545L;ENSP00000351168:P545L;ENSP00000402766:P545L;ENSP00000429125:P404L	ENSP00000351168:P545L	P	+	2	0	ESRP1	95755893	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.818000	0.86416	2.760000	0.94817	0.655000	0.94253	CCG	.	.		0.438	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697		T	95686717	C	T	95686717	3	4	224	1	0	0	0	0	1	0	0	0	5260	652	23	1	1680	1	ESRP1	8	95686717	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	25101531	95686717	50677305	27	31866										
CYP11B1	1584	hgsc.bcm.edu	37	chr8	143957167	143957167	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccgcacgcagcaagggcagcTcggtggttgccttctgggga	16	12	1	0	rs563321033	byFrequency	TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr8:143957167T>C	ENST00000292427.4	-	6	1114	c.1082A>G	c.(1081-1083)gAg>gGg	p.E361G	CYP11B1_ENST00000517471.1_Missense_Mutation_p.E361G|CYP11B1_ENST00000377675.3_Missense_Mutation_p.E432G	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	361					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	CAAGGGCAGCTCGGTGGTTGC	0.687									Familial Hyperaldosteronism type I				.|||	2	0.000399361	0	0.0029	5008	,	,		16702	0		0	False		,,,				2504	0				p.E361G		Atlas-SNP	.											.	CYP11B1	128	.	0			c.A1082G						.						69	71	70					8																	143957167		2203	4300	6503	SO:0001583	missense	1584	exon6	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	GGCAGCTCGGTGG	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"Cytochrome P450s"	2591	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	610613	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.1082A>G	chr8.hg19:g.143957167T>C	ENSP00000292427:p.Glu361Gly	138.0	0.0		159.0	7.0	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	ENST00000292427.4	hg19	CCDS6392.1	.	.	.	.	.	.	.	.	.	.	.	6.777	0.512273	0.12944	.	.	ENSG00000160882	ENST00000519285;ENST00000292427;ENST00000517471;ENST00000377675	T;T;T;T	0.76316	-1.01;-0.37;2.65;-0.37	4.42	3.15	0.36227	.	0.447704	0.19021	N	0.124839	T	0.71099	0.3300	L	0.56769	1.78	0.28820	N	0.897732	B;B;B;P;B	0.35050	0.094;0.01;0.022;0.482;0.101	B;B;B;B;B	0.37091	0.085;0.06;0.06;0.208;0.241	T	0.63427	-0.6640	10	0.27785	T	0.31	.	8.2956	0.31984	0.0:0.0:0.3459:0.6541	.	432;361;361;361;77	Q4VAR0;Q8TDD0;Q4VAQ9;P15538;Q8N9P8	.;.;.;C11B1_HUMAN;.	G	16;361;361;432	ENSP00000430144:E16G;ENSP00000292427:E361G;ENSP00000428043:E361G;ENSP00000366903:E432G	ENSP00000292427:E361G	E	-	2	0	CYP11B1	143954169	0.000000	0.05858	0.837000	0.33122	0.272000	0.26649	0.155000	0.16362	1.760000	0.52011	0.454000	0.30748	GAG	.	.		0.687	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			C	143957167	T	C	143957167	3	2	224	1	0	0	0	0	1	0	0	0	4147	1551	54	2	445	2	CYP11B1	8	143957167	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10	48270450	143957167	2406855	28	31867										
STXBP1	6812	hgsc.bcm.edu	37	chr9	130423380	130423380	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgtcttttgtcatacttgcaGcttgtccagatgccctgttt	8	10	2	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr9:130423380G>T	ENST00000373299.1	+	6	440		c.e6-1		STXBP1_ENST00000373302.3_Splice_Site	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1						axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)			breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						CATACTTGCAGCTTGTCCAGA	0.408																																					.		Atlas-SNP	.											.	STXBP1	99	.	0			c.326-1G>T						.						102	92	95					9																	130423380		2203	4300	6503	SO:0001630	splice_region_variant	6812	exon6			CTTGCAGCTTGTC	AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"syntaxin-binding protein 1"	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.326-1G>T	chr9.hg19:g.130423380G>T		57.0	0.0		84.0	10.0	NM_001032221	B1AM97|Q28208|Q62759|Q64320|Q96TG8	Splice_Site	SNP	ENST00000373299.1	hg19	CCDS35146.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.363401	0.82353	.	.	ENSG00000136854	ENST00000535154;ENST00000373302;ENST00000373299	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5764	0.87950	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	STXBP1	129463201	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.529000	0.98049	2.746000	0.94184	0.655000	0.94253	.	.	.		0.408	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165	Intron	T	130423380	G	T	130423380	5	4	224	1	0	0	0	0	0	0	1	0	15367	985	34	3	347	3	STXBP1	9	130423380	Splice_Site	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10		130423380	10790051	29	31868										
C1QL3	389941	hgsc.bcm.edu	37	chr10	16556558	16556558	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaataataaatccagaaaacGtgctgtatttgttgttgttt	7	4	0	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr10:16556558G>A	ENST00000298943.3	-	2	1676	c.737C>T	c.(736-738)aCg>aTg	p.T246M		NM_001010908.1	NP_001010908.1	Q5VWW1	C1QL3_HUMAN	complement component 1, q subcomponent-like 3	246	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				regulation of synapse organization (GO:0050807)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)				breast(1)|endometrium(3)|kidney(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	13						TCCAGAAAACGTGCTGTATTT	0.398																																					p.T246M		Atlas-SNP	.											.	C1QL3	27	.	0			c.C737T						.						144	137	139					10																	16556558		2203	4300	6503	SO:0001583	missense	389941	exon2			GAAAACGTGCTGT		CCDS31156.1	10p13	2012-03-26			ENSG00000165985	ENSG00000165985			19359	protein-coding gene	gene with protein product		615227				21378161	Standard	NM_001010908		Approved	K100, C1ql, C1QTNF13, CTRP13	uc001ioj.1	Q5VWW1	OTTHUMG00000017738	ENST00000298943.3:c.737C>T	chr10.hg19:g.16556558G>A	ENSP00000298943:p.Thr246Met	98.0	0.0		87.0	6.0	NM_001010908	A0PJY4|A0PJY5	Missense_Mutation	SNP	ENST00000298943.3	hg19	CCDS31156.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.114609	0.77210	.	.	ENSG00000165985	ENST00000298943;ENST00000448557	T	0.78126	-1.15	5.68	5.68	0.88126	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.000000	0.85682	D	0.000000	D	0.89291	0.6673	M	0.81341	2.54	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89973	0.4095	10	0.87932	D	0	.	19.7873	0.96444	0.0:0.0:1.0:0.0	.	246	Q5VWW1	C1QL3_HUMAN	M	246;223	ENSP00000298943:T246M	ENSP00000298943:T246M	T	-	2	0	C1QL3	16596564	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	9.869000	0.99810	2.673000	0.90976	0.655000	0.94253	ACG	.	.		0.398	C1QL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047003.1	XM_372305		A	16556558	G	A	16556558	3	1	224	1	0	0	0	0	1	0	0	0	1962	1145	40	1	34	1	C1QL3	10	16556558	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10		16556558	118978189	30	31869										
GDF10	2662	hgsc.bcm.edu	37	chr10	48438408	48438408	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttacccagcctggccctgaaGctgcggaccgtgttgccccc	11	17	0	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr10:48438408G>A	ENST00000224605.2	-	1	568	c.303C>T	c.(301-303)agC>agT	p.S101S		NM_004962.3	NP_004953.1	P55107	BMP3B_HUMAN	growth differentiation factor 10	101					fat cell differentiation (GO:0045444)|growth (GO:0040007)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(20)|skin(1)	31						TGGCCCTGAAGCTGCGGACCG	0.642																																					p.S101S		Atlas-SNP	.											.	GDF10	79	.	0			c.C303T						.						21	16	17					10																	48438408		2190	4290	6480	SO:0001819	synonymous_variant	2662	exon1			CCTGAAGCTGCGG	L42113	CCDS73117.1	10q11.22	2014-04-10			ENSG00000107623	ENSG00000266524		"Endogenous ligands"	4215	protein-coding gene	gene with protein product		601361				8679252	Standard	NM_004962		Approved	BMP-3b	uc001jfb.3	P55107	OTTHUMG00000188319	ENST00000224605.2:c.303C>T	chr10.hg19:g.48438408G>A		56.0	0.0		47.0	10.0	NM_004962	Q5VSQ8|Q9UCX6	Silent	SNP	ENST00000224605.2	hg19	CCDS7220.1																																																																																			.	.		0.642	GDF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047884.1	NM_004962		A	48438408	G	A	48438408	2	1	224	1	0	0	0	0	0	0	0	1	6319	962	34	3		3	GDF10	10	48438408	Silent	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	31881850	48438408	87096339	31	31870										
CCDC6	8030	hgsc.bcm.edu	37	chr10	61666139	61666139	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cggccgagctgctgctgttgCcccccgccccgtccgtgtcg	13	19	0	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr10:61666139C>A	ENST00000263102.6	-	1	275	c.44G>T	c.(43-45)gGc>gTc	p.G15V		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	15						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		GCTGCTGTTGCCCCCCGCCCC	0.776			T	RET	NSCLC																																p.G15V		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	CCDC6	44	.	0			c.G44T						.						6	8	8					10																	61666139		1702	3561	5263	SO:0001583	missense	8030	exon1			CTGTTGCCCCCCG	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"	601985	"DNA segment on chromosome 10 (unique) 170"	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.44G>T	chr10.hg19:g.61666139C>A	ENSP00000263102:p.Gly15Val	25.0	0.0		37.0	17.0	NM_005436	Q15250|Q6GSG7	Missense_Mutation	SNP	ENST00000263102.6	hg19	CCDS7257.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.576752	0.65878	.	.	ENSG00000108091	ENST00000263102	D	0.85955	-2.05	3.81	3.81	0.43845	.	0.486350	0.22646	N	0.057387	T	0.79656	0.4483	N	0.22421	0.69	0.80722	D	1	P	0.48998	0.918	P	0.48704	0.587	T	0.78732	-0.2089	10	0.38643	T	0.18	-10.9702	11.4095	0.49917	0.0:1.0:0.0:0.0	.	15	Q16204	CCDC6_HUMAN	V	15	ENSP00000263102:G15V	ENSP00000263102:G15V	G	-	2	0	CCDC6	61336145	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.580000	0.53907	2.127000	0.65507	0.563000	0.77884	GGC	.	.		0.776	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436		A	61666139	C	A	61666139	3	1	224	1	0	0	0	0	1	0	0	0	2832	739	26	3	1416	3	CCDC6	10	61666139	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	13227731	61666139	73868608	32	31871										
GOLGA7B	401647	hgsc.bcm.edu	37	chr10	99623838	99623838	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	catggagacccactatgagaAggtggcccctcccgccccac	10	17	0	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr10:99623838A>T	ENST00000370602.1	+	3	355	c.290A>T	c.(289-291)aAg>aTg	p.K97M		NM_001010917.2	NP_001010917.1	Q2TAP0	GOG7B_HUMAN	golgin A7 family, member B	97						Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|prostate(1)	5						CACTATGAGAAGGTGGCCCCT	0.607																																					p.K97M		Atlas-SNP	.											.	GOLGA7B	11	.	0			c.A290T						.						47	48	48					10																	99623838		2203	4300	6503	SO:0001630	splice_region_variant	401647	exon3			ATGAGAAGGTGGC	BC008047	CCDS31265.1	10q24.2	2011-10-25	2010-02-12	2008-10-03	ENSG00000155265	ENSG00000155265			31668	protein-coding gene	gene with protein product		614189	"chromosome 10 open reading frame 133", "chromosome 10 open reading frame 132", "golgi autoantigen, golgin subfamily a, 7B"	C10orf133, C10orf132			Standard	NM_001010917		Approved	bA459F3.4, bA451M19.3	uc001kos.3	Q2TAP0	OTTHUMG00000018869	ENST00000370602.1:c.291+1A>T	chr10.hg19:g.99623838A>T		77.0	0.0		96.0	26.0	NM_001010917	Q5T4F5	Missense_Mutation	SNP	ENST00000370602.1	hg19	CCDS31265.1	.	.	.	.	.	.	.	.	.	.	A	19.68	3.873689	0.72180	.	.	ENSG00000155265	ENST00000370602	.	.	.	5.17	5.17	0.71159	Golgin subfamily A member 7/ERF4 (1);	0.000000	0.85682	D	0.000000	T	0.79975	0.4539	M	0.86740	2.835	0.80722	D	1	D	0.65815	0.995	D	0.63703	0.917	D	0.83981	0.0332	9	0.87932	D	0	-51.2966	14.1408	0.65318	1.0:0.0:0.0:0.0	.	97	Q2TAP0	GOG7B_HUMAN	M	97	.	ENSP00000359634:K97M	K	+	2	0	GOLGA7B	99613828	1.000000	0.71417	1.000000	0.80357	0.417000	0.31264	9.139000	0.94554	2.189000	0.69895	0.459000	0.35465	AAG	.	.		0.607	GOLGA7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049752.1	NM_001010917	Missense_Mutation	T	99623838	A	T	99623838	5	4	224	1	0	0	0	0	0	0	1	0	6570	86	3	4	300	4	GOLGA7B	10	99623838	Splice_Site	SNP	A	TCGA-DD-AAVQ-01A-11D-A40R-10	37957699	99623838	35910909	33	31872										
COL17A1	1308	hgsc.bcm.edu	37	chr10	105796292	105796292	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	actactcagctctgcatagtCcaaagacaggagggacccat	9	12	2	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr10:105796292C>A	ENST00000353479.5	-	48	3666	c.3376G>T	c.(3376-3378)Gac>Tac	p.D1126Y	COL17A1_ENST00000369733.3_Missense_Mutation_p.D1081Y	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1126	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TCTGCATAGTCCAAAGACAGG	0.592																																					p.D1126Y		Atlas-SNP	.											.	COL17A1	149	.	0			c.G3376T						.						60	55	57					10																	105796292		2203	4300	6503	SO:0001583	missense	1308	exon48			CATAGTCCAAAGA	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.3376G>T	chr10.hg19:g.105796292C>A	ENSP00000340937:p.Asp1126Tyr	67.0	0.0		56.0	14.0	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	hg19	CCDS7554.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695403	0.68386	.	.	ENSG00000065618	ENST00000353479;ENST00000369733	D;D	0.92048	-2.96;-2.93	5.75	4.85	0.62838	.	0.000000	0.48767	D	0.000172	D	0.94324	0.8176	M	0.69248	2.105	0.80722	D	1	D	0.76494	0.999	P	0.60789	0.879	D	0.94521	0.7727	10	0.72032	D	0.01	-23.095	12.8797	0.58010	0.0:0.9254:0.0:0.0746	.	1126	Q9UMD9	COHA1_HUMAN	Y	1126;1081	ENSP00000340937:D1126Y;ENSP00000358748:D1081Y	ENSP00000340937:D1126Y	D	-	1	0	COL17A1	105786282	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.282000	0.43461	1.438000	0.47492	0.549000	0.68633	GAC	.	.		0.592	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		A	105796292	C	A	105796292	3	1	224	1	0	0	0	0	1	0	0	0	3676	855	30	3	1153	3	COL17A1	10	105796292	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	6172454	105796292	29738455	34	31873										
PRKRIR	5612	hgsc.bcm.edu	37	chr11	76062358	76062362	+	Frame_Shift_Del	DEL	CATGA	CATGA	-													0	0	1	0	0	0	1	1	0	gtattgaatttgagttgtccCatgactgagggtaccagaga							TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	CATGA	CATGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr11:76062358_76062362delCATGA	ENST00000260045.3	-	5	1937_1941	c.1832_1836delTCATG	c.(1831-1836)gtcatgfs	p.VM611fs	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	611					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						TGAGTTGTCCCATGACTGAGGGTAC	0.434																																					p.611_613del		Atlas-INDEL	.											.	PRKRIR	65	.	0			c.1833_1837del						.																																			SO:0001589	frameshift_variant	5612	exon5			.	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"THAP (C2CH-type zinc finger) domain containing"	9440	protein-coding gene	gene with protein product	"THAP domain containing 12"	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.1832_1836delTCATG	chr11.hg19:g.76062358_76062362delCATGA	ENSP00000260045:p.Val611fs	125.0	0.0		123.0	28.0	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Frame_Shift_Del	DEL	ENST00000260045.3	hg19	CCDS8243.1																																																																																			.	.		0.434	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705		-	76062362	CATGA	-	76062358	7	5	224	1	0	1	0	1	0	0	0	0	12538	594	21	0	453	0	PRKRIR	11	76062358	Frame_Shift_Del	DEL	CATGA	TCGA-DD-AAVQ-01A-11D-A40R-10		76062358	58944158	35	31874										
VWA5A	4013	hgsc.bcm.edu	37	chr11	123989361	123989361	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggcattgagaaggtccaatcCaactgccccttgagtcctac	9	13	0	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr11:123989361C>T	ENST00000456829.2	+	6	842	c.591C>T	c.(589-591)tcC>tcT	p.S197S	VWA5A_ENST00000361352.5_Silent_p.S197S|VWA5A_ENST00000449321.1_Silent_p.S197S|VWA5A_ENST00000392748.1_Silent_p.S197S|VWA5A_ENST00000392744.4_Silent_p.S213S|VWA5A_ENST00000360334.4_Silent_p.S197S	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	197										autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						AGGTCCAATCCAACTGCCCCT	0.493																																					p.S197S		Atlas-SNP	.											.	VWA5A	102	.	0			c.C591T						.						116	102	107					11																	123989361		2201	4299	6500	SO:0001819	synonymous_variant	4013	exon5			CCAATCCAACTGC	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"loss of heterozygosity, 11, chromosomal region 2, gene A"	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.591C>T	chr11.hg19:g.123989361C>T		77.0	0.0		76.0	25.0	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Silent	SNP	ENST00000456829.2	hg19	CCDS8444.1																																																																																			.	.		0.493	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622		T	123989361	C	T	123989361	2	4	224	1	0	0	0	0	0	0	0	1	17257	581	21	3		3	VWA5A	11	123989361	Silent	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	47927003	123989361	11017155	36	31875										
MLL2	8085	hgsc.bcm.edu	37	chr12	49431178	49431178	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctggggcaaacctggctgtcGggcacctgcaagacccaggg	15	13	0	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr12:49431178G>A	ENST00000301067.7	-	34	9960	c.9961C>T	c.(9961-9963)Cga>Tga	p.R3321*	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3321	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R3051*(1)|p.R3321*(1)									CCTGGCTGTCGGGCACCTGCA	0.622																																					p.R3321X		Atlas-SNP	.											MLL2_ENST00000301067,NS,lymphoid_neoplasm,0,4	MLL2	1173	.	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C9961T						.						18	22	21					12																	49431178		2103	4224	6327	SO:0001587	stop_gained	8085	exon34			GCTGTCGGGCACC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.9961C>T	chr12.hg19:g.49431178G>A	ENSP00000301067:p.Arg3321*	113.0	0.0		120.0	25.0	NM_003482	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	50	17.260850	0.99882	.	.	ENSG00000167548	ENST00000301067	.	.	.	5.61	4.71	0.59529	.	0.000000	0.31721	N	0.007180	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.4258	0.61024	0.0:0.0:0.7155:0.2845	.	.	.	.	X	3321	.	ENSP00000301067:R3321X	R	-	1	2	MLL2	47717445	0.998000	0.40836	0.988000	0.46212	0.838000	0.47535	2.968000	0.49224	1.502000	0.48669	0.655000	0.94253	CGA	.	.		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49431178	G	A	49431178	4	1	224	1	0	0	0	0	0	1	0	0	9630	1124	39	1	6736	1	MLL2	12	49431178	Nonsense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10		49431178	84420717	37	31876										
KRT2	3849	hgsc.bcm.edu	37	chr12	53045638	53045639	+	In_Frame_Ins	INS	-	-	AAAGCCGCTGCCGCCTCC													0	0	1	0	0	0	1	1	0	ccaaagctgctgccgcctccINSaaaaccacctcctctgccac							TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr12:53045638_53045639insAAAGCCGCTGCCGCCTCC	ENST00000309680.3	-	1	309_310	c.288_289insGGAGGCGGCAGCGGCTTT	c.(286-291)tttgga>tttGGAGGCGGCAGCGGCTTTgga	p.96_97FG>FGGGSGFG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	96	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		ctgccgcctccaaaaccacctc	0.619																																					p.G97delinsGGGSGFG		Atlas-INDEL	.											.	KRT2	94	.	0			c.289_290insGGAGGCGGCAGCGGCTTT						.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.288_289insGGAGGCGGCAGCGGCTTT	chr12.hg19:g.53045638_53045639insAAAGCCGCTGCCGCCTCC	ENSP00000310861:p.Phe96_Gly97insGlyGlyGlySerGlyPhe	132.0	0.0		162.0	59.0	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.619	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		AAAGCCGCTGCCGCCTCC	53045639	-	AAAGCCGCTGCCGCCTCC	53045638	7	5	224	1	0	1	1	0	0	0	0	0	8466	603	21	0	1666	0	KRT2	12	53045638	In_Frame_Ins	INS	-	TCGA-DD-AAVQ-01A-11D-A40R-10	3614460	53045638	80806257	38	31877										
APEX1	328	hgsc.bcm.edu	37	chr14	20925369	20925369	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggcacatgaagaaattgaccTtcgcaaccccaaggggaaca	10	11	0	3			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr14:20925369T>C	ENST00000216714.3	+	5	927	c.659T>C	c.(658-660)cTt>cCt	p.L220P	APEX1_ENST00000557365.1_3'UTR|OSGEP_ENST00000556252.1_5'Flank|APEX1_ENST00000557054.1_3'UTR|OSGEP_ENST00000206542.4_5'Flank|APEX1_ENST00000398030.4_Missense_Mutation_p.L220P|APEX1_ENST00000555414.1_Missense_Mutation_p.L220P	NM_001244249.1|NM_001641.3	NP_001231178.1|NP_001632.2	P27695	APEX1_HUMAN	APEX nuclease (multifunctional DNA repair enzyme) 1	220					aging (GO:0007568)|base-excision repair (GO:0006284)|cell redox homeostasis (GO:0045454)|cellular response to cAMP (GO:0071320)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to peptide hormone stimulus (GO:0071375)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA demethylation (GO:0080111)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|negative regulation of smooth muscle cell migration (GO:0014912)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oxidation-reduction process (GO:0055114)|positive regulation of DNA repair (GO:0045739)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribosome (GO:0005840)|transcription factor complex (GO:0005667)	3'-5' exonuclease activity (GO:0008408)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|phosphodiesterase I activity (GO:0004528)|phosphoric diester hydrolase activity (GO:0008081)|poly(A) RNA binding (GO:0044822)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|uracil DNA N-glycosylase activity (GO:0004844)			breast(2)|endometrium(1)|large_intestine(4)|ovary(2)	9	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)	Lucanthone(DB04967)	GAAATTGACCTTCGCAACCCC	0.552								Other BER factors																													p.L220P		Atlas-SNP	.											.	APEX1	23	.	0			c.T659C						.						85	82	83					14																	20925369		2203	4300	6503	SO:0001583	missense	328	exon5			TTGACCTTCGCAA	X59764	CCDS9550.1	14q11.2	2008-02-05	2002-09-11	2002-09-13	ENSG00000100823	ENSG00000100823	4.2.99.18		587	protein-coding gene	gene with protein product		107748	"APEX nuclease (multifunctional DNA repair enzyme)"	APEX			Standard	NM_001641		Approved	APE, REF1, HAP1, APX, APEN, REF-1, APE-1	uc021rnr.1	P27695	OTTHUMG00000029544	ENST00000216714.3:c.659T>C	chr14.hg19:g.20925369T>C	ENSP00000216714:p.Leu220Pro	110.0	0.0		120.0	31.0	NM_080648	Q969L5|Q99775	Missense_Mutation	SNP	ENST00000216714.3	hg19	CCDS9550.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.36|18.36	3.607500|3.607500	0.66558|0.66558	.|.	.|.	ENSG00000100823|ENSG00000100823	ENST00000438886|ENST00000555414;ENST00000216714;ENST00000553681;ENST00000398030;ENST00000555839	.|T;T;T;T;T	.|0.69175	.|-0.21;-0.21;-0.21;-0.21;-0.38	5.79|5.79	5.79|5.79	0.91817|0.91817	.|Endonuclease/exonuclease/phosphatase (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88945|0.88945	0.6575|0.6575	H|H	0.98507|0.98507	4.25|4.25	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.93021|0.93021	0.6440|0.6440	5|10	.|0.87932	.|D	.|0	.|.	15.118|15.118	0.72419|0.72419	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|220	.|P27695	.|APEX1_HUMAN	L|P	147|220;220;220;220;191	.|ENSP00000451979:L220P;ENSP00000216714:L220P;ENSP00000451327:L220P;ENSP00000381111:L220P;ENSP00000452460:L191P	.|ENSP00000216714:L220P	F|L	+|+	1|2	0|0	APEX1|APEX1	19995209|19995209	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.615000|7.615000	0.83006|0.83006	2.207000|2.207000	0.71202|0.71202	0.533000|0.533000	0.62120|0.62120	TTC|CTT	.	.		0.552	APEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073641.3	NM_001641		C	20925369	T	C	20925369	3	2	224	1	0	0	0	0	1	0	0	0	769	1609	56	2	673	2	APEX1	14	20925369	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10		20925369	86424171	39	31878										
SERPINA11	256394	hgsc.bcm.edu	37	chr14	94912770	94912770	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggaggaccagcagcgccaagGcatttcctctgtattctatc	10	12	2	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr14:94912770G>A	ENST00000334708.3	-	3	879	c.815C>T	c.(814-816)gCc>gTc	p.A272V	RP11-349I1.2_ENST00000536735.1_RNA	NM_001080451.1	NP_001073920.1	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	272					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(14)|skin(1)|upper_aerodigestive_tract(1)	24				COAD - Colon adenocarcinoma(157;0.211)		CAGCGCCAAGGCATTTCCTCT	0.552																																					p.A272V		Atlas-SNP	.											.	SERPINA11	53	.	0			c.C815T						.						123	111	115					14																	94912770		2203	4300	6503	SO:0001583	missense	256394	exon3			GCCAAGGCATTTC	BX248259	CCDS32149.1	14q32.13	2014-02-18	2005-08-18		ENSG00000186910	ENSG00000186910		"Serine (or cysteine) peptidase inhibitors"	19193	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11"			15014966, 24172014	Standard	NM_001080451		Approved		uc001ydd.1	Q86U17	OTTHUMG00000171348	ENST00000334708.3:c.815C>T	chr14.hg19:g.94912770G>A	ENSP00000335024:p.Ala272Val	97.0	0.0		116.0	25.0	NM_001080451	B2RV07	Missense_Mutation	SNP	ENST00000334708.3	hg19	CCDS32149.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.609887	0.46527	.	.	ENSG00000186910	ENST00000334708	D	0.82803	-1.65	5.53	4.45	0.53987	Serpin domain (3);	0.000000	0.64402	D	0.000009	D	0.87168	0.6110	L	0.58510	1.815	0.34251	D	0.678785	P	0.44195	0.828	P	0.58391	0.838	D	0.90081	0.4170	10	0.46703	T	0.11	.	13.0161	0.58757	0.1234:0.0:0.8766:0.0	.	272	Q86U17	SPA11_HUMAN	V	272	ENSP00000335024:A272V	ENSP00000335024:A272V	A	-	2	0	SERPINA11	93982523	1.000000	0.71417	0.166000	0.22797	0.262000	0.26303	3.357000	0.52277	2.591000	0.87537	0.555000	0.69702	GCC	.	.		0.552	SERPINA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413091.1	NM_001080451		A	94912770	G	A	94912770	3	1	224	1	0	0	0	0	1	0	0	0	14103	1203	42	3	465	3	SERPINA11	14	94912770	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	73987401	94912770	12436770	40	31879										
HERC2	8924	hgsc.bcm.edu	37	chr15	28412958	28412958	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgcagagggggtcactgcgtCctcagaggaaacaatctagt	13	9	3	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr15:28412958C>A	ENST00000261609.7	-	68	10537	c.10429G>T	c.(10429-10431)Gac>Tac	p.D3477Y		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GTCACTGCGTCCTCAGAGGAA	0.527																																					p.D3477Y		Atlas-SNP	.											.	HERC2	501	.	0			c.G10429T						.						67	69	68					15																	28412958		2203	4300	6503	SO:0001583	missense	8924	exon68			CTGCGTCCTCAGA	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.10429G>T	chr15.hg19:g.28412958C>A	ENSP00000261609:p.Asp3477Tyr	67.0	0.0		86.0	18.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.052115	0.55218	.	.	ENSG00000128731	ENST00000261609	T	0.39406	1.08	5.62	4.7	0.59300	.	0.050966	0.85682	D	0.000000	T	0.46870	0.1415	L	0.57536	1.79	0.80722	D	1	P	0.48503	0.911	P	0.46585	0.521	T	0.51052	-0.8754	10	0.62326	D	0.03	.	14.8081	0.69974	0.0:0.9297:0.0:0.0703	.	3477	O95714	HERC2_HUMAN	Y	3477	ENSP00000261609:D3477Y	ENSP00000261609:D3477Y	D	-	1	0	HERC2	26086553	1.000000	0.71417	1.000000	0.80357	0.070000	0.16714	7.788000	0.85771	2.638000	0.89438	0.591000	0.81541	GAC	.	.		0.527	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28412958	C	A	28412958	3	1	224	1	0	0	0	0	1	0	0	0	7067	855	30	3	4179	3	HERC2	15	28412958	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10		28412958	74118434	41	31880										
TUBGCP4	27229	hgsc.bcm.edu	37	chr15	43668706	43668706	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttgtttgatttcaggatcaCcatccatctcaacagggcca	7	11	3	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr15:43668706C>A	ENST00000260383.7	+	3	467	c.213C>A	c.(211-213)caC>caA	p.H71Q	TUBGCP4_ENST00000570081.1_3'UTR|TUBGCP4_ENST00000399460.3_5'Flank|TUBGCP4_ENST00000564079.1_Missense_Mutation_p.H71Q			Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	71					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|spindle pole (GO:0000922)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(4)|prostate(2)|upper_aerodigestive_tract(2)	21		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		TTCAGGATCACCATCCATCTC	0.468											OREG0023088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H71Q		Atlas-SNP	.											.	TUBGCP4	48	.	0			c.C213A						.						159	149	152					15																	43668706		1891	4121	6012	SO:0001583	missense	27229	exon3			GGATCACCATCCA	AJ249677	CCDS42030.1, CCDS66745.1	15q15.3	2014-08-12			ENSG00000137822	ENSG00000137822			16691	protein-coding gene	gene with protein product		609610				10562286	Standard	NM_001286414		Approved	76P, FLJ14797	uc001zrn.3	Q9UGJ1	OTTHUMG00000176647	ENST00000260383.7:c.213C>A	chr15.hg19:g.43668706C>A	ENSP00000260383:p.His71Gln	94.0	0.0	918	85.0	23.0	NM_014444	B3KNK6|Q969X3|Q9NVF0	Missense_Mutation	SNP	ENST00000260383.7	hg19		.	.	.	.	.	.	.	.	.	.	C	7.070	0.568059	0.13560	.	.	ENSG00000137822	ENST00000260383	T	0.39787	1.06	5.34	1.36	0.22044	.	0.000000	0.85682	D	0.000000	T	0.23572	0.0570	N	0.19112	0.55	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.06881	-1.0802	10	0.14252	T	0.57	-22.7104	10.6915	0.45872	0.0:0.6524:0.0:0.3476	.	71;71	Q9UGJ1;Q9UGJ1-2	GCP4_HUMAN;.	Q	71	ENSP00000260383:H71Q	ENSP00000260383:H71Q	H	+	3	2	TUBGCP4	41455998	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.197000	0.32211	0.353000	0.24079	-0.136000	0.14681	CAC	.	.		0.468	TUBGCP4-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000432970.1	NM_014444		A	43668706	C	A	43668706	3	1	224	1	0	0	0	0	1	0	0	0	16783	506	18	3	223	3	TUBGCP4	15	43668706	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	15255748	43668706	58862686	42	31881										
CRAMP1L	57585	hgsc.bcm.edu	37	chr16	1715078	1715078	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agaacactgctccctagaccAtcggaaaaccagtcccacaa	6	15	0	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr16:1715078A>G	ENST00000397412.3	+	14	2790	c.2691A>G	c.(2689-2691)ccA>ccG	p.P897P	LA16c-431H6.6_ENST00000454337.1_3'UTR|CRAMP1L_ENST00000293925.5_Silent_p.P897P|CRAMP1L_ENST00000262317.4_Silent_p.P275P|CRAMP1L_ENST00000436138.3_Silent_p.P894P			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	897						nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						TCCCTAGACCATCGGAAAACC	0.478																																					p.P897P		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.A2691G						.						127	125	126					16																	1715078		1989	4163	6152	SO:0001819	synonymous_variant	57585	exon13			TAGACCATCGGAA	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"Crm (Cramped Drosophila)-like"				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.2691A>G	chr16.hg19:g.1715078A>G		77.0	0.0		72.0	15.0	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Silent	SNP	ENST00000397412.3	hg19	CCDS10440.2	.	.	.	.	.	.	.	.	.	.	A	2.480	-0.319873	0.05386	.	.	ENSG00000007545	ENST00000415022	.	.	.	5.71	-11.4	0.00090	.	.	.	.	.	T	0.32010	0.0815	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41963	-0.9479	4	.	.	.	-33.4245	2.6208	0.04916	0.4934:0.1631:0.0893:0.2542	.	.	.	.	V	55	.	.	I	+	1	0	CRAMP1L	1655079	0.000000	0.05858	0.329000	0.25429	0.183000	0.23260	-2.981000	0.00662	-1.602000	0.01599	-0.621000	0.04028	ATC	.	.		0.478	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4			G	1715078	A	G	1715078	2	3	224	1	0	0	0	0	0	0	0	1	3848	204	8	2		2	CRAMP1L	16	1715078	Silent	SNP	A	TCGA-DD-AAVQ-01A-11D-A40R-10		1715078	88639675	43	31882										
GRB7	2886	hgsc.bcm.edu	37	chr17	37901708	37901708	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ataataccctggtggccatgGacttctctggccatgctggg	12	11	1	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr17:37901708G>A	ENST00000309156.4	+	11	1383	c.1126G>A	c.(1126-1128)Gac>Aac	p.D376N	GRB7_ENST00000394204.1_Missense_Mutation_p.D376N|GRB7_ENST00000394209.2_Missense_Mutation_p.D376N|GRB7_ENST00000445327.2_Missense_Mutation_p.D399N|GRB7_ENST00000394211.3_Missense_Mutation_p.D376N|GRB7_ENST00000309185.3_Missense_Mutation_p.D376N	NM_005310.3	NP_005301.2	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7	376					blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|leukocyte migration (GO:0050900)|negative regulation of translation (GO:0017148)|positive regulation of cell migration (GO:0030335)|positive regulation of signal transduction (GO:0009967)|stress granule assembly (GO:0034063)	cell projection (GO:0042995)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			GGTGGCCATGGACTTCTCTGG	0.612																																					p.D399N		Atlas-SNP	.											.	GRB7	48	.	0			c.G1195A						.						70	66	67					17																	37901708		2203	4300	6503	SO:0001583	missense	2886	exon11			GCCATGGACTTCT	D43772	CCDS11345.1, CCDS56028.1	17q12	2013-02-14			ENSG00000141738	ENSG00000141738		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4567	protein-coding gene	gene with protein product		601522					Standard	NM_005310		Approved		uc021twu.1	Q14451	OTTHUMG00000133253	ENST00000309156.4:c.1126G>A	chr17.hg19:g.37901708G>A	ENSP00000310771:p.Asp376Asn	53.0	0.0		47.0	8.0	NM_001242442	B2RAV1|B3KNL0|B3KWP9|B7WP75|J3KQM4|Q53YD3|Q92568|Q96DF9|Q9Y220	Missense_Mutation	SNP	ENST00000309156.4	hg19	CCDS11345.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.876208	0.91664	.	.	ENSG00000141738	ENST00000309185;ENST00000309156;ENST00000394211;ENST00000394209;ENST00000445327;ENST00000394204	T;T;T;T;T;T	0.69435	-0.4;0.83;0.83;0.83;0.8;-0.4	5.88	5.88	0.94601	BPS (Between PH and SH2) domain (1);	0.000000	0.85682	D	0.000000	D	0.83977	0.5371	M	0.83223	2.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.83253	-0.0052	10	0.45353	T	0.12	-40.6223	19.8311	0.96636	0.0:0.0:1.0:0.0	.	376;376	Q14451-2;Q14451	.;GRB7_HUMAN	N	376;376;376;376;399;376	ENSP00000311752:D376N;ENSP00000310771:D376N;ENSP00000377761:D376N;ENSP00000377759:D376N;ENSP00000403459:D399N;ENSP00000377754:D376N	ENSP00000310771:D376N	D	+	1	0	GRB7	35155234	1.000000	0.71417	1.000000	0.80357	0.378000	0.30076	9.752000	0.98900	2.790000	0.95986	0.591000	0.81541	GAC	.	.		0.612	GRB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257024.2	NM_005310		A	37901708	G	A	37901708	3	1	224	1	0	0	0	0	1	0	0	0	6768	1174	41	3	1164	3	GRB7	17	37901708	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10		37901708	43293502	44	31883										
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76075532	76075532	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggagcagcacaagccaggacCatgcagcagccgccacagcc	12	16	0	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr17:76075532C>T	ENST00000588061.1	+	12	3994	c.3267C>T	c.(3265-3267)acC>acT	p.T1089T	TNRC6C_ENST00000588847.1_Silent_p.T1086T|TNRC6C_ENST00000335749.4_Silent_p.T1086T|TNRC6C_ENST00000301624.4_Silent_p.T1089T|TNRC6C_ENST00000541771.1_Silent_p.T1089T|TNRC6C_ENST00000544502.1_Silent_p.T1086T			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1089					embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			AAGCCAGGACCATGCAGCAGC	0.547																																					p.T1089T		Atlas-SNP	.											.	TNRC6C	173	.	0			c.C3267T						.						92	104	100					17																	76075532		2155	4260	6415	SO:0001819	synonymous_variant	57690	exon11			CAGGACCATGCAG	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.3267C>T	chr17.hg19:g.76075532C>T		56.0	0.0		57.0	14.0	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Silent	SNP	ENST00000588061.1	hg19	CCDS45798.1																																																																																			.	.		0.547	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		T	76075532	C	T	76075532	2	4	224	1	0	0	0	0	0	0	0	1	16357	581	21	3		3	TNRC6C	17	76075532	Silent	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	38173824	76075532	5119678	45	31884										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3129395	3129395	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgaaggtttgttaggtttgcTgccaagcaaagcatctttct	10	7	2	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr18:3129395T>G	ENST00000356443.4	-	18	2962	c.2629A>C	c.(2629-2631)Agc>Cgc	p.S877R	MYOM1_ENST00000400569.3_Missense_Mutation_p.S877R|MYOM1_ENST00000582016.1_5'UTR|MYOM1_ENST00000261606.7_Intron	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	877					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TTAGGTTTGCTGCCAAGCAAA	0.547											OREG0024838	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S877R		Atlas-SNP	.											.	MYOM1	192	.	0			c.A2629C						.						178	179	178					18																	3129395		1935	4138	6073	SO:0001583	missense	8736	exon18			GTTTGCTGCCAAG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2629A>C	chr18.hg19:g.3129395T>G	ENSP00000348821:p.Ser877Arg	101.0	0.0	608	126.0	12.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	4.012	-0.000417	0.07819	.	.	ENSG00000101605	ENST00000356443;ENST00000400569	T;T	0.43688	0.94;0.95	5.88	0.54	0.17163	.	0.456915	0.25668	N	0.029086	T	0.19208	0.0461	N	0.14661	0.345	0.24952	N	0.991785	B	0.12630	0.006	B	0.10450	0.005	T	0.18587	-1.0332	10	0.15066	T	0.55	.	5.7522	0.18152	0.0:0.2144:0.2453:0.5403	.	877	P52179	MYOM1_HUMAN	R	877	ENSP00000348821:S877R;ENSP00000383413:S877R	ENSP00000348821:S877R	S	-	1	0	MYOM1	3119395	1.000000	0.71417	0.621000	0.29145	0.040000	0.13550	1.688000	0.37690	0.114000	0.18032	-0.290000	0.09829	AGC	.	.		0.547	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		G	3129395	T	G	3129395	3	3	224	1	0	0	0	0	1	0	0	0	10100	1580	55	5	2512	5	MYOM1	18	3129395	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10		3129395	74947853	46	31885										
OSBPL1A	114876	hgsc.bcm.edu	37	chr18	21743143	21743143	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caccctgacttgtatgcattTtaataaatgtcaggcaaatt	6	8	1	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr18:21743143T>C	ENST00000319481.3	-	28	3059	c.2853A>G	c.(2851-2853)taA>taG	p.*951*	OSBPL1A_ENST00000399443.3_Silent_p.*438*|RP11-799B12.4_ENST00000583267.1_lincRNA|OSBPL1A_ENST00000357041.4_Silent_p.*569*	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	0					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					TGTATGCATTTTAATAAATGT	0.348																																					p.X951X		Atlas-SNP	.											.	OSBPL1A	94	.	0			c.A2853G						.						94	91	92					18																	21743143		2203	4300	6503	SO:0001819	synonymous_variant	114876	exon28			TGCATTTTAATAA	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"Oxysterol binding proteins", "Ankyrin repeat domain containing"	16398	protein-coding gene	gene with protein product		606730	"oxysterol binding protein-like 1B"	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.2853A>G	chr18.hg19:g.21743143T>C		82.0	0.0		104.0	14.0	NM_080597	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	hg19	CCDS11884.1																																																																																			.	.		0.348	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		C	21743143	T	C	21743143	2	2	224	1	0	0	0	0	0	0	0	1	11286	1848	64	2		2	OSBPL1A	18	21743143	Silent	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10	18613748	21743143	56334105	47	31886										
MIDN	90007	hgsc.bcm.edu	37	chr19	1257098	1257098	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtagaaaggcccggcgggacGcgcggggtccgtaccactgg	18	12	0	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr19:1257098G>A	ENST00000591446.2	+	7	1643	c.1234G>A	c.(1234-1236)Gcg>Acg	p.A412T	MIDN_ENST00000300952.2_Missense_Mutation_p.A412T|CIRBP_ENST00000588030.1_5'Flank			Q504T8	MIDN_HUMAN	midnolin	412						cytosol (GO:0005829)|nucleolus (GO:0005730)				NS(1)|endometrium(3)|kidney(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCGGCGGGACGCGCGGGGTCC	0.716																																					p.A412T		Atlas-SNP	.											.	MIDN	34	.	0			c.G1234A						.						14	18	17					19																	1257098		2193	4283	6476	SO:0001583	missense	90007	exon8			CGGGACGCGCGGG	AC004221	CCDS32864.1	19p13.3	2013-09-20			ENSG00000167470	ENSG00000167470			16298	protein-coding gene	gene with protein product		606700				10974535	Standard	XM_005259671		Approved		uc002lrp.3	Q504T8	OTTHUMG00000180144	ENST00000591446.2:c.1234G>A	chr19.hg19:g.1257098G>A	ENSP00000467679:p.Ala412Thr	71.0	0.0		78.0	17.0	NM_177401	Q96BW8	Missense_Mutation	SNP	ENST00000591446.2	hg19	CCDS32864.1	.	.	.	.	.	.	.	.	.	.	g	14.62	2.588613	0.46110	.	.	ENSG00000167470	ENST00000300952	.	.	.	3.44	3.44	0.39384	.	0.272597	0.31102	U	0.008253	T	0.26846	0.0657	L	0.34521	1.04	0.29005	N	0.887214	D	0.58970	0.984	P	0.44772	0.46	T	0.08006	-1.0743	9	0.25106	T	0.35	-17.2934	9.2415	0.37500	0.0:0.0:0.7835:0.2165	.	412	Q504T8	MIDN_HUMAN	T	412	.	ENSP00000300952:A412T	A	+	1	0	MIDN	1208098	1.000000	0.71417	0.915000	0.36163	0.164000	0.22412	4.907000	0.63300	1.756000	0.51951	0.486000	0.48141	GCG	.	.		0.716	MIDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449965.2			A	1257098	G	A	1257098	3	1	224	1	0	0	0	0	1	0	0	0	9588	1087	38	1	1260	1	MIDN	19	1257098	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10		1257098	57871885	48	31887										
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11558367	11558367	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaggaggaggaggaggaggaGgaggaagaagaggctgaaga	23	1	0	4			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr19:11558367G>A	ENST00000589838.1	+	10	963	c.963G>A	c.(961-963)gaG>gaA	p.E321E	PRKCSH_ENST00000412601.1_Silent_p.E321E|PRKCSH_ENST00000592741.1_Silent_p.E321E|PRKCSH_ENST00000587327.1_Silent_p.E321E|PRKCSH_ENST00000252455.2_Silent_p.E321E|PRKCSH_ENST00000591462.1_Silent_p.E321E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	321	Glu-rich (acidic).				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)	p.E321_E322delEE(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaggaggaagaag	0.632																																					p.E321E		Atlas-SNP	.											.	PRKCSH	55	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.G963A						.						28	28	28					19																	11558367		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAGGAA		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"EF-hand domain containing"	9411	protein-coding gene	gene with protein product		177060	"polycystic liver disease"	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.963G>A	chr19.hg19:g.11558367G>A		64.0	0.0		91.0	4.0	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	CCDS32911.1																																																																																			.	.		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			A	11558367	G	A	11558367	2	1	224	1	0	0	0	0	0	0	0	1	12528	991	35	3		3	PRKCSH	19	11558367	Silent	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	10301269	11558367	47570616	49	31888										
CALR	811	hgsc.bcm.edu	37	chr19	13054677	13054677	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggaggatgaggaggacaagGaggaagatgaggaggaagat	20	1	0	4			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr19:13054677G>T	ENST00000316448.5	+	9	1277	c.1204G>T	c.(1204-1206)Gag>Tag	p.E402*	RAD23A_ENST00000592268.1_5'Flank|CTC-425F1.4_ENST00000589120.1_RNA|RAD23A_ENST00000586534.1_5'Flank|RAD23A_ENST00000316856.3_5'Flank|RAD23A_ENST00000541222.1_5'Flank	NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	402	Asp/Glu/Lys-rich.|C-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	ggaggacaaggaggaagatga	0.587																																					p.E402X		Atlas-SNP	.											.	CALR	31	.	0			c.G1204T						.						258	199	219					19																	13054677		2203	4299	6502	SO:0001587	stop_gained	811	exon9			GACAAGGAGGAAG	M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"Sicca syndrome antigen A (autoantigen Ro; calreticulin)", "autoantigen Ro"	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.1204G>T	chr19.hg19:g.13054677G>T	ENSP00000320866:p.Glu402*	287.0	0.0		372.0	82.0	NM_004343	Q6IAT4|Q9UDG2	Nonsense_Mutation	SNP	ENST00000316448.5	hg19	CCDS12288.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165549	0.78339	.	.	ENSG00000179218	ENST00000316448;ENST00000539083	.	.	.	5.4	5.4	0.78164	.	0.351696	0.27591	N	0.018696	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-36.9649	11.4462	0.50125	0.0841:0.0:0.9159:0.0	.	.	.	.	X	402;281	.	ENSP00000320866:E402X	E	+	1	0	CALR	12915677	1.000000	0.71417	0.400000	0.26346	0.301000	0.27625	3.720000	0.54933	2.526000	0.85167	0.555000	0.69702	GAG	.	.		0.587	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343		T	13054677	G	T	13054677	4	4	224	1	0	0	0	0	0	1	0	0	2594	1175	41	3	1238	3	CALR	19	13054677	Nonsense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	1496310	13054677	46074306	50	31889										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13616815	13616815	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgaagaggaagagagaccggTtaaccgtgaggcagttctgt	15	6	1	5			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr19:13616815T>A	ENST00000360228.5	-	1	223	c.224A>T	c.(223-225)aAc>aTc	p.N75I	CACNA1A_ENST00000573710.2_Missense_Mutation_p.N75I	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	75					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GAGAGACCGGTTAACCGTGAG	0.562																																					p.N75I		Atlas-SNP	.											.	CACNA1A	715	.	0			c.A224T						.						90	98	96					19																	13616815		2085	4212	6297	SO:0001583	missense	773	exon1			GACCGGTTAACCG	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.224A>T	chr19.hg19:g.13616815T>A	ENSP00000353362:p.Asn75Ile	1039.0	0.0		1101.0	278.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	T	12.22	1.871708	0.33069	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	T	0.53857	0.6	3.36	3.36	0.38483	.	0.000000	0.64402	U	0.000005	T	0.73705	0.3621	M	0.88241	2.94	0.51767	D	0.999935	D;D	0.71674	0.998;0.99	D;D	0.76071	0.987;0.946	T	0.78432	-0.2206	10	0.87932	D	0	.	10.904	0.47069	0.0:0.0:0.0:1.0	.	75;75	O00555;Q9NS88	CAC1A_HUMAN;.	I	75	ENSP00000353362:N75I	ENSP00000317661:N75I	N	-	2	0	CACNA1A	13477815	1.000000	0.71417	1.000000	0.80357	0.186000	0.23388	7.547000	0.82146	1.414000	0.47017	0.416000	0.27883	AAC	.	.		0.562	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13616815	T	A	13616815	3	1	224	1	0	0	0	0	1	0	0	0	2540	1725	60	4	7598	4	CACNA1A	19	13616815	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10	562138	13616815	45512168	51	31890										
TM6SF2	53345	hgsc.bcm.edu	37	chr19	19379472	19379472	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cagcgggttagcgcccggggCtggctgaagaccttcatgcc	15	13	1	2			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr19:19379472C>A	ENST00000389363.4	-	6	648	c.576G>T	c.(574-576)caG>caT	p.Q192H	TM6SF2_ENST00000586107.1_5'Flank|AC138430.4_ENST00000586064.2_RNA	NM_001001524.2	NP_001001524.2	Q9BZW4	TM6S2_HUMAN	transmembrane 6 superfamily member 2	192						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14			Epithelial(12;0.0151)			GCGCCCGGGGCTGGCTGAAGA	0.587																																					p.Q192H		Atlas-SNP	.											.	TM6SF2	39	.	0			c.G576T						.						62	65	64					19																	19379472		1963	4151	6114	SO:0001583	missense	53345	exon6			CCGGGGCTGGCTG	AF255923	CCDS42528.1	19p13.3-p12	2008-02-05							11861	protein-coding gene	gene with protein product		606563				11124529	Standard	NM_001001524		Approved	Lpr4	uc002nmd.1	Q9BZW4		ENST00000389363.4:c.576G>T	chr19.hg19:g.19379472C>A	ENSP00000374014:p.Gln192His	93.0	0.0		118.0	38.0	NM_001001524	Q0IJ64	Missense_Mutation	SNP	ENST00000389363.4	hg19	CCDS42528.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.521455	0.44866	.	.	ENSG00000213996	ENST00000389363;ENST00000269990	T	0.29917	1.55	5.01	5.01	0.66863	.	0.312353	0.22424	U	0.060251	T	0.50565	0.1623	M	0.78049	2.395	0.25777	N	0.984778	D	0.61080	0.989	P	0.56916	0.809	T	0.50180	-0.8858	10	0.62326	D	0.03	-11.931	13.8127	0.63273	0.0:1.0:0.0:0.0	.	192	Q9BZW4	TM6S2_HUMAN	H	192	ENSP00000374014:Q192H	ENSP00000269990:Q192H	Q	-	3	2	TM6SF2	19240472	1.000000	0.71417	0.640000	0.29408	0.384000	0.30261	1.625000	0.37029	2.340000	0.79590	0.650000	0.86243	CAG	.	.		0.587	TM6SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460122.2	NM_203510		A	19379472	C	A	19379472	3	1	224	1	0	0	0	0	1	0	0	0	15988	796	28	3	577	3	TM6SF2	19	19379472	Missense_Mutation	SNP	C	TCGA-DD-AAVQ-01A-11D-A40R-10	5762657	19379472	39749511	52	31891										
C20orf54	113278	hgsc.bcm.edu	37	chr20	746297	746298	+	Missense_Mutation	DNP	GG	GG	AT													0	0	1	0	0	0	1	1	0	tgaccaccgtgaggtaggagGgcaggtaccagccctcgggc							TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr20:746297_746298GG>AT	ENST00000217254.7	-	2	362_363	c.121_122CC>AT	c.(121-123)CCc>ATc	p.P41I	SLC52A3_ENST00000381944.3_Missense_Mutation_p.P41I|SLC52A3_ENST00000473664.1_5'UTR	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	41					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										GAGGTAGGAGGGCAGGTACCAG	0.644																																					p.P41L|p.P41T		Atlas-SNP	.											.	.	.	.	0			c.C122T|c.C121A						.																																			SO:0001583	missense	113278	exon2			TAGGAGGGCAGGT|AGGAGGGCAGGTA	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"Solute carriers"	16187	protein-coding gene	gene with protein product	"hypothetical protein LOC113278"	613350	"chromosome 20 open reading frame 54"	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.121_122delinsAT	chr20.hg19:g.746297_746298delinsAT	ENSP00000217254:p.Pro41Ile	100.0|99.0	0.0		107.0|109.0	32.0	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	hg19	CCDS13007.1																																																																																			.	.		0.644	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409		AT	746298	GG	AT	746297	3	1	224	1	0	0	0	0	1	0	0	0	2116	1232	43	3	1303	3	C20orf54	20	746297	Missense_Mutation	DNP	GG	TCGA-DD-AAVQ-01A-11D-A40R-10		746297	62279223	53	31892										
FAM65C	140876	hgsc.bcm.edu	37	chr20	49247308	49247308	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctgtgcactgctgaagcctGcgaaggaggcgctccggccc	14	14	1	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr20:49247308G>T	ENST00000327979.2	-	2	488	c.77C>A	c.(76-78)gCa>gAa	p.A26E	FAM65C_ENST00000535356.1_Missense_Mutation_p.A30E|FAM65C_ENST00000045083.2_Missense_Mutation_p.A26E			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	26										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GCTGAAGCCTGCGAAGGAGGC	0.662																																					p.A26E		Atlas-SNP	.											.	FAM65C	87	.	0			c.C77A						.						29	25	26					20																	49247308		2203	4300	6503	SO:0001583	missense	140876	exon2			AAGCCTGCGAAGG	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.77C>A	chr20.hg19:g.49247308G>T	ENSP00000332663:p.Ala26Glu	142.0	0.0		176.0	52.0	NM_080829	Q5QPB6|Q9NQQ2	Missense_Mutation	SNP	ENST00000327979.2	hg19	CCDS13431.2	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814019	0.70912	.	.	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	T;T;T	0.20332	2.09;2.09;2.08	4.91	4.91	0.64330	.	0.062145	0.64402	D	0.000005	T	0.46229	0.1382	M	0.77313	2.365	0.43118	D	0.99483	D;D	0.76494	0.999;0.999	D;D	0.69479	0.964;0.964	T	0.50474	-0.8824	10	0.87932	D	0	-11.5365	13.9446	0.64077	0.0:0.0:1.0:0.0	.	30;26	F5H0X2;Q96MK2	.;FA65C_HUMAN	E	26;26;30	ENSP00000332663:A26E;ENSP00000045083:A26E;ENSP00000439802:A30E	ENSP00000045083:A26E	A	-	2	0	FAM65C	48680715	0.996000	0.38824	0.921000	0.36526	0.489000	0.33432	4.426000	0.59882	2.414000	0.81942	0.561000	0.74099	GCA	.	.		0.662	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			T	49247308	G	T	49247308	3	4	224	1	0	0	0	0	1	0	0	0	5609	1319	46	3	2847	3	FAM65C	20	49247308	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	48501011	49247308	13778212	54	31893										
RWDD2B	10069	hgsc.bcm.edu	37	chr21	30380212	30380212	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	attctttcttttgcatttgtTatagatatgatggctgtaga	8	4	2	3			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr21:30380212T>G	ENST00000493196.1	-	4	695	c.595A>C	c.(595-597)Aac>Cac	p.N199H	RWDD2B_ENST00000486719.1_5'UTR	NM_016940.2	NP_058636.1	P57060	RWD2B_HUMAN	RWD domain containing 2B	199										endometrium(1)|kidney(1)|large_intestine(8)|lung(2)	12						TTGCATTTGTTATAGATATGA	0.463																																					p.N199H		Atlas-SNP	.											.	RWDD2B	24	.	0			c.A595C						.						119	117	118					21																	30380212		2203	4300	6503	SO:0001583	missense	10069	exon4			ATTTGTTATAGAT	AF212232	CCDS13582.1	21q22.11	2012-12-07	2007-07-17	2007-07-17	ENSG00000156253	ENSG00000156253			1302	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 6"	C21orf6		10729227	Standard	NM_016940		Approved	GL011	uc002yms.3	P57060	OTTHUMG00000078805	ENST00000493196.1:c.595A>C	chr21.hg19:g.30380212T>G	ENSP00000418693:p.Asn199His	60.0	0.0		75.0	24.0	NM_016940		Missense_Mutation	SNP	ENST00000493196.1	hg19	CCDS13582.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.523035	0.85600	.	.	ENSG00000156253	ENST00000493196	.	.	.	5.41	5.41	0.78517	Domain of unknown function DUF1115 (1);	0.041393	0.85682	D	0.000000	T	0.79964	0.4537	M	0.84219	2.685	0.58432	D	0.999998	D;D	0.76494	0.998;0.999	D;D	0.69654	0.946;0.965	T	0.82827	-0.0265	9	0.62326	D	0.03	-9.9902	15.612	0.76733	0.0:0.0:0.0:1.0	.	199;199	Q53FD2;P57060	.;RWD2B_HUMAN	H	199	.	ENSP00000418693:N199H	N	-	1	0	RWDD2B	29302083	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.846000	0.86887	2.281000	0.76405	0.533000	0.62120	AAC	.	.		0.463	RWDD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171858.1			G	30380212	T	G	30380212	3	3	224	1	0	0	0	0	1	0	0	0	13771	1754	61	5	372	5	RWDD2B	21	30380212	Missense_Mutation	SNP	T	TCGA-DD-AAVQ-01A-11D-A40R-10		30380212	17749683	55	31894										
TRAPPC10	7109	hgsc.bcm.edu	37	chr21	45495012	45495012	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gttgaccttttggcaggtttGggagctgagcgaccagaaac	14	8	0	3			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr21:45495012G>T	ENST00000291574.4	+	9	1453	c.1278G>T	c.(1276-1278)ttG>ttT	p.L426F		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	426					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						TGGCAGGTTTGGGAGCTGAGC	0.433																																					p.L426F		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.G1278T						.						98	88	91					21																	45495012		2203	4300	6503	SO:0001583	missense	7109	exon9			AGGTTTGGGAGCT	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"Trafficking protein particle complex"	11868	protein-coding gene	gene with protein product	"trafficking protein particle complex subunit 130", "TRAPP 130 kDa subunit"	602103	"transmembrane protein 1"	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.1278G>T	chr21.hg19:g.45495012G>T	ENSP00000291574:p.Leu426Phe	63.0	0.0		86.0	4.0	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	hg19	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.576262	0.65878	.	.	ENSG00000160218	ENST00000291574	T	0.47177	0.85	5.21	4.32	0.51571	.	0.000000	0.64402	D	0.000001	T	0.54759	0.1878	L	0.44542	1.39	0.58432	D	0.99999	D	0.76494	0.999	D	0.66716	0.946	T	0.56306	-0.8001	10	0.66056	D	0.02	.	7.2173	0.25967	0.0798:0.0:0.6288:0.2914	.	426	P48553	TPC10_HUMAN	F	426	ENSP00000291574:L426F	ENSP00000291574:L426F	L	+	3	2	TRAPPC10	44319440	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.323000	0.33701	1.297000	0.44761	0.655000	0.94253	TTG	.	.		0.433	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		T	45495012	G	T	45495012	3	4	224	1	0	0	0	0	1	0	0	0	16472	1339	47	3	1312	3	TRAPPC10	21	45495012	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	15114800	45495012	2634883	56	31895										
ZNF280A	129025	hgsc.bcm.edu	37	chr22	22868555	22868555	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggtccttggttttgtgctctAtttcctccttcaacgtcaaa	7	11	3	0			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chr22:22868555A>G	ENST00000302097.3	-	2	1652	c.1400T>C	c.(1399-1401)aTa>aCa	p.I467T		NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	467					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TTTGTGCTCTATTTCCTCCTT	0.438																																					p.I467T		Atlas-SNP	.											.	ZNF280A	67	.	0			c.T1400C						.						120	114	116					22																	22868555		2203	4300	6503	SO:0001583	missense	129025	exon2			TGCTCTATTTCCT	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"zinc finger protein 280", "suppressor of hairy wing homolog 1 (Drosophila)"	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.1400T>C	chr22.hg19:g.22868555A>G	ENSP00000302855:p.Ile467Thr	91.0	0.0		100.0	31.0	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	hg19	CCDS13800.1	.	.	.	.	.	.	.	.	.	.	A	1.064	-0.671898	0.03403	.	.	ENSG00000169548	ENST00000302097	T	0.60299	0.2	3.76	-7.04	0.01578	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.	.	.	.	T	0.30603	0.0770	N	0.11560	0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24261	-1.0165	9	0.21540	T	0.41	-2.1691	10.0285	0.42085	0.2872:0.0:0.5966:0.1162	.	467	P59817	Z280A_HUMAN	T	467	ENSP00000302855:I467T	ENSP00000302855:I467T	I	-	2	0	ZNF280A	21198555	0.616000	0.27035	0.000000	0.03702	0.105000	0.19272	0.308000	0.19314	-1.943000	0.01039	-0.274000	0.10170	ATA	.	.		0.438	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740		G	22868555	A	G	22868555	3	3	224	1	0	0	0	0	1	0	0	0	17829	449	16	2	232	2	ZNF280A	22	22868555	Missense_Mutation	SNP	A	TCGA-DD-AAVQ-01A-11D-A40R-10		22868555	28436011	57	31896										
TLR8	51311	hgsc.bcm.edu	37	chrX	12939521	12939521	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	gagatttccgaagatggatgGatgaacatctgaatgtcaaa	11	5	2	4			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chrX:12939521G>A	ENST00000218032.6	+	2	2449	c.2362G>A	c.(2362-2364)Gat>Aat	p.D788N	TLR8_ENST00000311912.5_Missense_Mutation_p.D806N	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	788	LRRCT.				cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	AAGATGGATGGATGAACATCT	0.443																																					p.D788N		Atlas-SNP	.											.	TLR8	134	.	0			c.G2362A						.						120	101	107					X																	12939521		2203	4300	6503	SO:0001583	missense	51311	exon2			TGGATGGATGAAC	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2362G>A	chrX.hg19:g.12939521G>A	ENSP00000218032:p.Asp788Asn	71.0	0.0		71.0	15.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	G	6.551	0.469899	0.12461	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.28454	1.61;1.79	5.97	5.1	0.69264	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.41938	D	0.000783	T	0.16685	0.0401	N	0.11284	0.12	0.35845	D	0.826347	D;D	0.59767	0.986;0.986	P;P	0.50490	0.642;0.642	T	0.36915	-0.9728	10	0.07325	T	0.83	.	2.955	0.05874	0.1181:0.1669:0.5375:0.1774	.	788;806	Q9NR97;D1CS70	TLR8_HUMAN;.	N	788;806	ENSP00000218032:D788N;ENSP00000312082:D806N	ENSP00000218032:D788N	D	+	1	0	TLR8	12849442	0.144000	0.22641	0.986000	0.45419	0.904000	0.53231	0.653000	0.24902	1.267000	0.44247	0.600000	0.82982	GAT	.	.		0.443	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		A	12939521	G	A	12939521	3	1	224	1	0	0	0	0	1	0	0	0	15972	1174	41	3	2368	3	TLR8	23	12939521	Missense_Mutation	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10		12939521	142331039	58	31897										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24383454	24383454	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttggcaacaggcgctgttcaGatagtgcagccacatccagg	12	11	1	1			TCGA-DD-AAVQ-01A-11D-A40R-10	TCGA-DD-AAVQ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	909a06f3-3314-45ad-a516-b06af0c953a3	8bb6a3ac-5434-4a1d-952d-273baa389e04	g.chrX:24383454G>T								AC004552.1 (16431 upstream) : PDK3 (99883 downstream)																							GCGCTGTTCAGATAGTGCAGC	0.562																																					p.Q859H		Atlas-SNP	.											.	.	.	.	0			c.G2577T						.						91	79	83					X																	24383454		1568	3582	5150	SO:0001628	intergenic_variant	100130302	exon1			TGTTCAGATAGTG																													chrX.hg19:g.24383454G>T		74.0	0.0		55.0	19.0	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.562									T	24383454	G	T	24383454	1	4	224	0	1	0	0	0	0	0	0	0	5581	933	33	3		3	FAM48B1	23	24383454	IGR	SNP	G	TCGA-DD-AAVQ-01A-11D-A40R-10	11443933	24383454	130887106	59	31898										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32131190	32131190	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tcttcttcactcaccggtggGcccggaaagcctggctggcc	12	15	4	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr1:32131190G>A	ENST00000373672.3	-	55	4002	c.3486C>T	c.(3484-3486)ggC>ggT	p.G1162G	COL16A1_ENST00000271069.6_Silent_p.G1162G	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1162	Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TCACCGGTGGGCCCGGAAAGC	0.627																																					p.G1162G	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.C3486T						.						79	85	83					1																	32131190		1972	4150	6122	SO:0001819	synonymous_variant	1307	exon55			CGGTGGGCCCGGA	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.3486C>T	chr1.hg19:g.32131190G>A		50.0	0.0		52.0	10.0	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.		0.627	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		A	32131190	G	A	32131190	2	1	225	1	0	0	0	0	0	0	0	1	3675	1190	42	3		3	COL16A1	1	32131190	Silent	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10		32131190	217119431	1	31899										
RBBP4	5928	hgsc.bcm.edu	37	chr1	33134435	33134435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	caaatctcagtgggcacttaCttagtgcttcagatgaccat	8	10	2	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr1:33134435C>T	ENST00000373493.5	+	5	739	c.580C>T	c.(580-582)Ctt>Ttt	p.L194F	RBBP4_ENST00000458695.2_Missense_Mutation_p.L159F|RBBP4_ENST00000524393.1_3'UTR|RBBP4_ENST00000373485.1_Missense_Mutation_p.L194F|RBBP4_ENST00000544435.1_5'UTR|RBBP4_ENST00000414241.3_Missense_Mutation_p.L193F	NM_001135255.1|NM_005610.2	NP_001128727.1|NP_005601.1	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4	194					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin assembly (GO:0031497)|chromatin remodeling (GO:0006338)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|nucleosome assembly (GO:0006334)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|NURF complex (GO:0016589)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				TGGGCACTTACTTAGTGCTTC	0.488																																					p.L194F		Atlas-SNP	.											.	RBBP4	38	.	0			c.C580T						.						99	88	92					1																	33134435		2203	4300	6503	SO:0001583	missense	5928	exon5			CACTTACTTAGTG	BC053904	CCDS366.1, CCDS44105.1, CCDS44106.1	1p35.1	2014-07-17	2001-11-28		ENSG00000162521	ENSG00000162521		"WD repeat domain containing"	9887	protein-coding gene	gene with protein product		602923	"retinoblastoma-binding protein 4"			8350924, 14609955, 17531812	Standard	NM_005610		Approved	RbAp48, NURF55, lin-53	uc001bvr.3	Q09028	OTTHUMG00000007998	ENST00000373493.5:c.580C>T	chr1.hg19:g.33134435C>T	ENSP00000362592:p.Leu194Phe	75.0	0.0		78.0	17.0	NM_005610	B2R6G9|B4DRH0|D3DPQ3|P31149|Q53H02|Q96BV9	Missense_Mutation	SNP	ENST00000373493.5	hg19	CCDS366.1	.	.	.	.	.	.	.	.	.	.	C	33	5.269434	0.95429	.	.	ENSG00000162521	ENST00000414241;ENST00000373493;ENST00000373485;ENST00000458695	T;T;T;T	0.61510	0.1;0.1;0.1;0.1	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.67524	0.2902	L	0.38531	1.155	0.80722	D	1	D;D	0.58620	0.983;0.973	P;P	0.62382	0.793;0.901	T	0.68614	-0.5362	10	0.72032	D	0.01	.	19.0691	0.93125	0.0:1.0:0.0:0.0	.	193;194	Q09028-2;Q09028	.;RBBP4_HUMAN	F	193;194;194;159	ENSP00000398242:L193F;ENSP00000362592:L194F;ENSP00000362584:L194F;ENSP00000396057:L159F	ENSP00000362584:L194F	L	+	1	0	RBBP4	32907022	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.761000	0.85260	2.835000	0.97688	0.591000	0.81541	CTT	.	.		0.488	RBBP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021957.3	NM_005610		T	33134435	C	T	33134435	3	4	225	1	0	0	0	0	1	0	0	0	13116	565	20	3	598	3	RBBP4	1	33134435	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	1003245	33134435	216116186	2	31900										
ASB17	127247	hgsc.bcm.edu	37	chr1	76397785	76397785	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	atgtaatctgtgagtagtgcGtcaaaaccatccaagtccac	8	10	2	1	rs534539433		TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr1:76397785G>A	ENST00000284142.6	-	1	331	c.192C>T	c.(190-192)gaC>gaT	p.D64D		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	64					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	21						TGAGTAGTGCGTCAAAACCAT	0.393													G|||	1	0.000199681	0	0	5008	,	,		18876	0.001		0	False		,,,				2504	0				p.D64D		Atlas-SNP	.											ASB17,NS,carcinoma,-2,1	ASB17	53	.	0			c.C192T						.						153	140	144					1																	76397785		2203	4300	6503	SO:0001819	synonymous_variant	127247	exon1			TAGTGCGTCAAAA	AF403035	CCDS671.1	1p22.3	2013-01-11	2011-01-25		ENSG00000154007	ENSG00000154007		"Ankyrin repeat domain containing"	19769	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 17"			12076535	Standard	NM_080868		Approved		uc001dhe.2	Q8WXJ9	OTTHUMG00000009787	ENST00000284142.6:c.192C>T	chr1.hg19:g.76397785G>A		180.0	0.0		147.0	19.0	NM_080868	B1APB8|Q8N0X5	Silent	SNP	ENST00000284142.6	hg19	CCDS671.1																																																																																			.	.		0.393	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868		A	76397785	G	A	76397785	2	1	225	1	0	0	0	0	0	0	0	1	1021	1136	40	1		1	ASB17	1	76397785	Silent	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	43263350	76397785	172852836	3	31901										
RPL5	6125	hgsc.bcm.edu	37	chr1	93299205	93299205	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gttcgtgtgacaaacagagaTatcatttgtcaggtaagttg	11	5	2	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr1:93299205T>A	ENST00000370321.3	+	3	267	c.177T>A	c.(175-177)gaT>gaA	p.D59E		NM_000969.3	NP_000960.2	P46777	RL5_HUMAN	ribosomal protein L5	59					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	5S rRNA binding (GO:0008097)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)		CAAACAGAGATATCATTTGTC	0.373																																					p.D59E		Atlas-SNP	.											.,1	RPL5	38	.	0			c.T177A						.						61	67	65					1																	93299205		2203	4300	6503	SO:0001583	missense	6125	exon3			CAGAGATATCATT	U14966	CCDS741.1	1p22.1	2014-06-13			ENSG00000122406	ENSG00000122406		"L ribosomal proteins"	10360	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 135"	603634				7937132, 7772601	Standard	NM_000969		Approved	L5, PPP1R135	uc001doz.3	P46777	OTTHUMG00000010899	ENST00000370321.3:c.177T>A	chr1.hg19:g.93299205T>A	ENSP00000359345:p.Asp59Glu	67.0	0.0		48.0	8.0	NM_000969	Q32LZ3|Q53HH6|Q9H3F4	Missense_Mutation	SNP	ENST00000370321.3	hg19	CCDS741.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.186516	0.78789	.	.	ENSG00000122406	ENST00000432788;ENST00000370321;ENST00000315741	T	0.63744	-0.06	4.69	-0.82	0.10826	.	0.000000	0.85682	D	0.000000	T	0.68485	0.3006	H	0.98466	4.24	0.58432	D	0.999999	B	0.31949	0.348	B	0.40256	0.324	T	0.71656	-0.4527	10	0.56958	D	0.05	.	11.3036	0.49320	0.0:0.5127:0.0:0.4873	.	59	P46777	RL5_HUMAN	E	9;59;9	ENSP00000359345:D59E	ENSP00000359338:D9E	D	+	3	2	RPL5	93071793	0.828000	0.29307	0.998000	0.56505	0.917000	0.54804	-0.054000	0.11826	-0.129000	0.11620	-0.366000	0.07423	GAT	.	.		0.373	RPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030058.2	NM_000969		A	93299205	T	A	93299205	3	1	225	1	0	0	0	0	1	0	0	0	13612	1403	49	4	187	4	RPL5	1	93299205	Missense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	16901420	93299205	155951416	4	31902										
BNIPL	149428	hgsc.bcm.edu	37	chr1	151019153	151019153	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ccgggatctccatggctcagGagggacatagcacaggactg	14	11	2	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr1:151019153G>C	ENST00000368931.3	+	10	1220	c.1064G>C	c.(1063-1065)gGa>gCa	p.G355A	C1orf56_ENST00000368926.5_5'Flank|BNIPL_ENST00000295294.7_Missense_Mutation_p.G273A	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	355					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CATGGCTCAGGAGGGACATAG	0.498																																					p.G355A		Atlas-SNP	.											.	BNIPL	45	.	0			c.G1064C						.						120	106	111					1																	151019153		2203	4300	6503	SO:0001583	missense	149428	exon10			GCTCAGGAGGGAC	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.1064G>C	chr1.hg19:g.151019153G>C	ENSP00000357927:p.Gly355Ala	101.0	0.0		110.0	29.0	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Missense_Mutation	SNP	ENST00000368931.3	hg19	CCDS978.2	.	.	.	.	.	.	.	.	.	.	G	16.02	3.004133	0.54254	.	.	ENSG00000163141	ENST00000368931;ENST00000361277;ENST00000295294	T;T;T	0.53640	1.32;1.31;0.61	5.82	3.9	0.45041	.	0.781797	0.11843	N	0.524093	T	0.15132	0.0365	L	0.31664	0.95	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.24012	-1.0172	10	0.25751	T	0.34	.	8.7024	0.34334	0.0821:0.1503:0.7676:0.0	.	355	Q7Z465	BNIPL_HUMAN	A	355;353;273	ENSP00000357927:G355A;ENSP00000355333:G353A;ENSP00000295294:G273A	ENSP00000295294:G273A	G	+	2	0	BNIPL	149285777	0.998000	0.40836	0.049000	0.19019	0.685000	0.39939	1.925000	0.40074	0.744000	0.32741	0.655000	0.94253	GGA	.	.		0.498	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279		C	151019153	G	C	151019153	3	2	225	1	0	0	0	0	1	0	0	0	1480	1174	41	4	1102	4	BNIPL	1	151019153	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	57719948	151019153	98231468	5	31903										
PLB1	151056	hgsc.bcm.edu	37	chr2	28763246	28763246	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cctgcagccctgcaccagagCcctgtaattgctcagaggag	11	14	1	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr2:28763246C>T	ENST00000327757.5	+	12	756	c.712C>T	c.(712-714)Ccc>Tcc	p.P238S	PLB1_ENST00000422425.2_Missense_Mutation_p.P249S	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	238	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TGCACCAGAGCCCTGTAATTG	0.592																																					p.P249S		Atlas-SNP	.											.	PLB1	255	.	0			c.C745T						.						56	55	56					2																	28763246		2203	4300	6503	SO:0001583	missense	151056	exon12			CCAGAGCCCTGTA		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.712C>T	chr2.hg19:g.28763246C>T	ENSP00000330442:p.Pro238Ser	45.0	0.0		35.0	10.0	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	hg19	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	C	1.439	-0.568150	0.03910	.	.	ENSG00000163803	ENST00000327757;ENST00000422425	T;T	0.11169	2.82;2.8	5.03	-10.1	0.00402	.	1.149250	0.06223	N	0.687149	T	0.07143	0.0181	L	0.54323	1.7	0.09310	N	1	B;B	0.25312	0.123;0.002	B;B	0.30572	0.117;0.007	T	0.35525	-0.9785	10	0.09084	T	0.74	-0.1735	2.0119	0.03489	0.3356:0.1103:0.3529:0.2013	.	249;238	Q6P1J6-3;Q6P1J6	.;PLB1_HUMAN	S	238;249	ENSP00000330442:P238S;ENSP00000416440:P249S	ENSP00000330442:P238S	P	+	1	0	PLB1	28616750	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-4.034000	0.00309	-2.450000	0.00543	-1.147000	0.01851	CCC	.	.		0.592	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			T	28763246	C	T	28763246	3	4	225	1	0	0	0	0	1	0	0	0	12033	739	26	3	791	3	PLB1	2	28763246	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10		28763246	214436127	6	31904										
FSHR	2492	hgsc.bcm.edu	37	chr2	49190880	49190880	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	actctgaggatgttgtacccCatgatatcttcacatgggtt	9	9	3	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr2:49190880C>A	ENST00000406846.2	-	10	1199	c.1080G>T	c.(1078-1080)atG>atT	p.M360I	FSHR_ENST00000541117.1_Missense_Mutation_p.M96I|FSHR_ENST00000304421.4_Missense_Mutation_p.M334I|FSHR_ENST00000346173.3_Missense_Mutation_p.M298I	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	360					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	TGTTGTACCCCATGATATCTT	0.448									Gonadal Dysgenesis, 46 XX																												p.M360I		Atlas-SNP	.											.	FSHR	164	.	0			c.G1080T						.						236	201	213					2																	49190880		2203	4300	6503	SO:0001583	missense	2492	exon10	Familial Cancer Database		GTACCCCATGATA		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.1080G>T	chr2.hg19:g.49190880C>A	ENSP00000384708:p.Met360Ile	147.0	0.0		134.0	12.0	NM_000145	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Missense_Mutation	SNP	ENST00000406846.2	hg19	CCDS1843.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026316	0.75390	.	.	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000541117	D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.91219	0.7233	M	0.66439	2.03	0.80722	D	1	D;D;D	0.56287	0.958;0.975;0.958	D;D;D	0.71656	0.943;0.974;0.943	D	0.90361	0.4373	9	.	.	.	.	17.7465	0.88422	0.0:1.0:0.0:0.0	.	334;298;360	Q05AH0;G5E967;P23945	.;.;FSHR_HUMAN	I	360;298;334;96	ENSP00000384708:M360I;ENSP00000333908:M298I;ENSP00000306780:M334I;ENSP00000444172:M96I	.	M	-	3	0	FSHR	49044384	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.651000	0.83577	2.673000	0.90976	0.561000	0.74099	ATG	.	.		0.448	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2			A	49190880	C	A	49190880	3	1	225	1	0	0	0	0	1	0	0	0	6081	594	21	3	1011	3	FSHR	2	49190880	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	20427634	49190880	194008493	7	31905										
FBLN7	129804	hgsc.bcm.edu	37	chr2	112922614	112922614	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gaacacccccgcagacggcaGaaagtttggaagcaagtact	11	11	0	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr2:112922614G>A	ENST00000331203.2	+	3	543	c.272G>A	c.(271-273)aGa>aAa	p.R91K	FBLN7_ENST00000472377.1_3'UTR|FBLN7_ENST00000409667.3_Missense_Mutation_p.R91K|FBLN7_ENST00000409903.1_Missense_Mutation_p.R91K|FBLN7_ENST00000409450.3_Missense_Mutation_p.R91K	NM_001128165.1|NM_153214.2	NP_001121637.1|NP_694946.2	Q53RD9	FBLN7_HUMAN	fibulin 7	91	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GCAGACGGCAGAAAGTTTGGA	0.547																																					p.R91K		Atlas-SNP	.											.	FBLN7	49	.	0			c.G272A						.						70	68	69					2																	112922614		2203	4300	6503	SO:0001583	missense	129804	exon3			ACGGCAGAAAGTT		CCDS2095.1, CCDS46391.1	2q13	2010-06-15			ENSG00000144152	ENSG00000144152		"Fibulins"	26740	protein-coding gene	gene with protein product		611551				17699513	Standard	NM_153214		Approved	FLJ37440, TM14	uc002tho.1	Q53RD9	OTTHUMG00000153267	ENST00000331203.2:c.272G>A	chr2.hg19:g.112922614G>A	ENSP00000331411:p.Arg91Lys	103.0	0.0		85.0	25.0	NM_153214	A0JNV1|A0JNV2|Q5H9P5|Q8N9G0	Missense_Mutation	SNP	ENST00000331203.2	hg19	CCDS2095.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.486995	0.44249	.	.	ENSG00000144152	ENST00000331203;ENST00000409903;ENST00000409667;ENST00000409450	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.6	3.7	0.42460	Complement control module (2);Sushi/SCR/CCP (3);	0.288868	0.38111	N	0.001818	T	0.42653	0.1212	L	0.31207	0.915	0.23820	N	0.996753	B;B;B;B	0.17465	0.0;0.003;0.022;0.015	B;B;B;B	0.24974	0.001;0.012;0.032;0.057	T	0.31420	-0.9944	10	0.05959	T	0.93	-16.4405	6.959	0.24587	0.3788:0.0:0.6212:0.0	.	91;91;91;91	Q53RD9-4;Q53RD9-2;Q53RD9;B8ZZC1	.;.;FBLN7_HUMAN;.	K	91	ENSP00000331411:R91K;ENSP00000386295:R91K;ENSP00000386822:R91K;ENSP00000387000:R91K	ENSP00000331411:R91K	R	+	2	0	FBLN7	112639085	0.054000	0.20591	0.868000	0.34077	0.958000	0.62258	0.254000	0.18314	0.641000	0.30601	-0.345000	0.07892	AGA	.	.		0.547	FBLN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330505.1	NM_153214		A	112922614	G	A	112922614	3	1	225	1	0	0	0	0	1	0	0	0	5709	942	33	3	282	3	FBLN7	2	112922614	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	63731734	112922614	130276759	8	31906										
NEB	4703	hgsc.bcm.edu	37	chr2	152426620	152426620	+	Frame_Shift_Del	DEL	T	T	-													0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tctgcagttcgtaggccttcTtggcctgaatcacatcgttc							TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr2:152426620delT	ENST00000172853.10	-	81	12449	c.12302delA	c.(12301-12303)aagfs	p.K4102fs	NEB_ENST00000427231.2_Frame_Shift_Del_p.K5803fs|NEB_ENST00000409198.1_Frame_Shift_Del_p.K4102fs|NEB_ENST00000604864.1_Frame_Shift_Del_p.K5803fs|NEB_ENST00000397345.3_Frame_Shift_Del_p.K5803fs|NEB_ENST00000603639.1_Frame_Shift_Del_p.K5803fs			P20929	NEBU_HUMAN	nebulin	4102					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GTAGGCCTTCTTGGCCTGAAT	0.502																																					p.K5802fs		Atlas-INDEL	.											.	NEB	1697	.	0			c.17406delG						.						42	41	41					2																	152426620		2053	4190	6243	SO:0001589	frameshift_variant	4703	exon109			.	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.12302delA	chr2.hg19:g.152426620delT	ENSP00000172853:p.Lys4102fs	57.0	0.0		57.0	13.0	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Frame_Shift_Del	DEL	ENST00000172853.10	hg19																																																																																				.	.		0.502	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		-	152426620	T	-	152426620	7	5	225	1	0	1	0	1	0	0	0	0	10311	1609	56	0	8577	0	NEB	2	152426620	Frame_Shift_Del	DEL	T	TCGA-DD-AAVR-01A-11D-A40R-10	39504006	152426620	90772753	9	31907										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160269055	160269055	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tcaaaagacaccactgcattCccttttaattaacattttat	2	10	1	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr2:160269055C>A	ENST00000392783.2	-	14	2963	c.2468G>T	c.(2467-2469)gGa>gTa	p.G823V	BAZ2B_ENST00000355831.2_Splice_Site_p.G789V|BAZ2B_ENST00000343439.5_Splice_Site_p.G723V|BAZ2B_ENST00000392782.1_Splice_Site_p.G787V	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	823				G -> E (in Ref. 1; BAA89212). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CCACTGCATTCCCTTTTAATT	0.333																																					p.G823V		Atlas-SNP	.											.	BAZ2B	196	.	0			c.G2468T						.						92	74	79					2																	160269055		1817	4071	5888	SO:0001630	splice_region_variant	29994	exon14			TGCATTCCCTTTT	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.2467-1G>T	chr2.hg19:g.160269055C>A		76.0	0.0		77.0	15.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	17.69	3.452484	0.63290	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.61274	0.16;0.19;0.16;0.12	5.49	5.49	0.81192	Methyl-CpG DNA binding (1);DNA-binding, integrase-type (1);	0.000000	0.36374	U	0.002640	T	0.69975	0.3171	L	0.36672	1.1	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.996;1.0;1.0;1.0	T	0.72513	-0.4270	10	0.87932	D	0	-8.5924	19.3616	0.94442	0.0:1.0:0.0:0.0	.	627;723;787;823	Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;BAZ2B_HUMAN	V	787;823;789;723	ENSP00000376533:G787V;ENSP00000376534:G823V;ENSP00000348087:G789V;ENSP00000339670:G723V	ENSP00000339670:G723V	G	-	2	0	BAZ2B	159977301	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.362000	0.79507	2.568000	0.86640	0.650000	0.86243	GGA	.	.		0.333	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		Missense_Mutation	A	160269055	C	A	160269055	5	1	225	1	0	0	0	0	0	0	1	0	1332	869	30	3	4134	3	BAZ2B	2	160269055	Splice_Site	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	7842435	160269055	82930318	10	31908										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168103526	168103526	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gctagccacactcaagtcacTtaaagaatcaagccatcgat	6	12	3	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr2:168103526T>C	ENST00000409195.1	+	9	5713	c.5624T>C	c.(5623-5625)cTt>cCt	p.L1875P	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.L1653P|XIRP2_ENST00000295237.9_Missense_Mutation_p.L1875P|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1700					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CTCAAGTCACTTAAAGAATCA	0.383																																					p.L1875P		Atlas-SNP	.											.	XIRP2	914	.	0			c.T5624C						.						80	72	75					2																	168103526		1884	4120	6004	SO:0001583	missense	129446	exon9			AGTCACTTAAAGA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5624T>C	chr2.hg19:g.168103526T>C	ENSP00000386840:p.Leu1875Pro	181.0	0.0		189.0	52.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.298886	0.60195	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.07021	3.24;3.24;3.23	5.46	5.46	0.80206	.	0.131337	0.52532	D	0.000075	T	0.27594	0.0678	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.71870	0.936;0.971;0.975	T	0.00763	-1.1576	10	0.59425	D	0.04	-9.6873	14.8073	0.69968	0.0:0.0:0.0:1.0	.	1700;1700;1653	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	P	1875;1875;1653	ENSP00000386840:L1875P;ENSP00000295237:L1875P;ENSP00000387255:L1653P	ENSP00000295237:L1875P	L	+	2	0	XIRP2	167811772	1.000000	0.71417	0.972000	0.41901	0.946000	0.59487	7.331000	0.79192	2.199000	0.70637	0.528000	0.53228	CTT	.	.		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		C	168103526	T	C	168103526	3	2	225	1	0	0	0	0	1	0	0	0	17445	1609	56	2	5654	2	XIRP2	2	168103526	Missense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	7834471	168103526	75095847	11	31909										
USP40	55230	hgsc.bcm.edu	37	chr2	234402122	234402122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ccaagacgaagtacagttggTctggtcctgatgactctccc	10	12	2	3	rs368100283		TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr2:234402122T>C	ENST00000427112.2	-	24	2898	c.2863A>G	c.(2863-2865)Acc>Gcc	p.T955A	USP40_ENST00000450966.1_Missense_Mutation_p.T967A|USP40_ENST00000251722.6_Missense_Mutation_p.T955A|USP40_ENST00000409945.1_Missense_Mutation_p.T131A			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	955					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		GTACAGTTGGTCTGGTCCTGA	0.512																																					p.T967A		Atlas-SNP	.											.	USP40	174	.	0			c.A2899G						.	T	ALA/THR	0,3948		0,0,1974	66	68	67		2899	-10.8	0	2		67	1,8307		0,1,4153	no	missense	USP40	NM_018218.2	58	0,1,6127	CC,CT,TT		0.012,0.0,0.0082	benign	967/1248	234402122	1,12255	1974	4154	6128	SO:0001583	missense	55230	exon24			AGTTGGTCTGGTC	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.2863A>G	chr2.hg19:g.234402122T>C	ENSP00000387898:p.Thr955Ala	183.0	0.0		157.0	35.0	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	hg19	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	T	9.535	1.111763	0.20714	0.0	1.2E-4	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112;ENST00000409945	T;T;T	0.04502	3.61;3.61;3.61	5.77	-10.8	0.00216	.	7739.210000	0.00166	N	0.000000	T	0.02727	0.0082	N	0.22421	0.69	0.09310	N	1	B;B;B	0.19817	0.004;0.001;0.039	B;B;B	0.16289	0.012;0.001;0.015	T	0.34453	-0.9828	10	0.08381	T	0.77	.	8.5971	0.33723	0.1825:0.601:0.103:0.1136	.	967;131;615	Q9NVE5-3;Q9NVE5-2;B4DN96	.;.;.	A	967;955;955;131	ENSP00000415434:T967A;ENSP00000251722:T955A;ENSP00000387898:T955A	ENSP00000251722:T955A	T	-	1	0	USP40	234066861	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-1.169000	0.03120	-2.118000	0.00828	0.459000	0.35465	ACC	.	.		0.512	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		C	234402122	T	C	234402122	3	2	225	1	0	0	0	0	1	0	0	0	17087	1667	58	2	876	2	USP40	2	234402122	Missense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	66298596	234402122	8797251	12	31910										
BAP1	8314	hgsc.bcm.edu	37	chr3	52436363	52436363	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ccggtcaggcttccgctgctTgtggagccggccgatgctga	15	13	1	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr3:52436363T>A	ENST00000460680.1	-	17	2602	c.2131A>T	c.(2131-2133)Aag>Tag	p.K711*	BAP1_ENST00000296288.5_Nonsense_Mutation_p.K693*	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TTCCGCTGCTTGTGGAGCCGG	0.652			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.K711X	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.A2131T						.						20	23	22					3																	52436363		2200	4296	6496	SO:0001587	stop_gained	8314	exon17			GCTGCTTGTGGAG	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.2131A>T	chr3.hg19:g.52436363T>A	ENSP00000417132:p.Lys711*	52.0	0.0		60.0	15.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Nonsense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.012645	0.75161	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000478368	.	.	.	5.52	5.52	0.82312	.	0.045134	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6244	0.76840	0.0:0.0:0.0:1.0	.	.	.	.	X	711;693;235	.	ENSP00000296288:K693X	K	-	1	0	BAP1	52411403	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.985000	0.88162	2.093000	0.63338	0.459000	0.35465	AAG	.	.		0.652	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52436363	T	A	52436363	4	1	225	1	0	0	0	0	0	1	0	0	1311	1821	63	4	62	4	BAP1	3	52436363	Nonsense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10		52436363	145586067	13	31911										
BAP1	51533	hgsc.bcm.edu	37	chr3	52442612	52442612	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tttgaacaggaagataaatcCatatacagggctgggggaag	13	5	0	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr3:52442612C>T	ENST00000327906.3	+	0	0				BAP1_ENST00000296288.5_Missense_Mutation_p.G45R|BAP1_ENST00000460680.1_Missense_Mutation_p.G45R|PHF7_ENST00000347025.2_5'Flank	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.G45*(1)		breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		AAGATAAATCCATATACAGGG	0.493																																					p.G45R		Atlas-SNP	.											BAP1,upper_arm,benign_melanocytic_nevus,0,1	BAP1	371	.	1	Substitution - Nonsense(1)	skin(1)	c.G133A						.						31	31	31					3																	52442612		2203	4299	6502	SO:0001631	upstream_gene_variant	8314	exon4			TAAATCCATATAC	AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"Zinc fingers, PHD-type"	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		chr3.hg19:g.52442612C>T	Exception_encountered	132.0	0.0		111.0	30.0	NM_004656	K4DI82	Missense_Mutation	SNP	ENST00000327906.3	hg19	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	C	35	5.432866	0.96150	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.61510	0.1;0.1	5.43	5.43	0.79202	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.099859	0.64402	D	0.000002	D	0.84999	0.5597	H	0.96833	3.89	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90012	0.4122	10	0.87932	D	0	-3.095	19.2289	0.93829	0.0:1.0:0.0:0.0	.	45	Q92560	BAP1_HUMAN	R	45	ENSP00000417132:G45R;ENSP00000296288:G45R	ENSP00000296288:G45R	G	-	1	0	BAP1	52417652	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.783000	0.85696	2.550000	0.86006	0.655000	0.94253	GGA	.	.		0.493	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1	NM_016483		T	52442612	C	T	52442612	1	4	225	0	1	0	0	0	0	0	0	0	1311	603	21	3		3	BAP1	3	52442612	5'Flank	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	6249	52442612	145579818	14	31912										
CCDC54	84692	hgsc.bcm.edu	37	chr3	107096716	107096716	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gtccatatgataccaaaagtCcaggaaaagactgacttgta	8	8	0	3			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr3:107096716C>A	ENST00000261058.1	+	1	529	c.282C>A	c.(280-282)gtC>gtA	p.V94V		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	94										NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						TACCAAAAGTCCAGGAAAAGA	0.378																																					p.V94V		Atlas-SNP	.											.	CCDC54	56	.	0			c.C282A						.						72	70	71					3																	107096716		2203	4300	6503	SO:0001819	synonymous_variant	84692	exon1			AAAAGTCCAGGAA	AF367469	CCDS2949.1	3q13.12	2013-10-11			ENSG00000138483	ENSG00000138483			30703	protein-coding gene	gene with protein product	"sperm protein 17"					15257753	Standard	NM_032600		Approved	NYD-SP17, FLJ25362, SP17	uc003dwi.1	Q8NEL0	OTTHUMG00000159169	ENST00000261058.1:c.282C>A	chr3.hg19:g.107096716C>A		108.0	0.0		118.0	24.0	NM_032600	Q96A43	Silent	SNP	ENST00000261058.1	hg19	CCDS2949.1																																																																																			.	.		0.378	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1	NM_032600		A	107096716	C	A	107096716	2	1	225	1	0	0	0	0	0	0	0	1	2826	842	30	3		3	CCDC54	3	107096716	Silent	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	54654104	107096716	90925714	15	31913										
NDUFB4	4710	hgsc.bcm.edu	37	chr3	120320137	120320137	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	accagatgtttagtatttgaGtgataggttcactttctagg	10	5	2	3			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr3:120320137G>A	ENST00000184266.2	+	2	378				NDUFB4_ENST00000492739.1_Intron|NDUFB4_ENST00000485064.1_Silent_p.E120E	NM_004547.5	NP_004538.2	O95168	NDUB4_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|large_intestine(1)|lung(3)	5				GBM - Glioblastoma multiforme(114;0.14)		TAGTATTTGAGTGATAGGTTC	0.483																																					p.E120E		Atlas-SNP	.											.	NDUFB4	21	.	0			c.G360A						.						101	117	112					3																	120320137		2203	4296	6499	SO:0001627	intron_variant	4710	exon2			ATTTGAGTGATAG	AF044957	CCDS2999.1, CCDS54630.1	3q13.33	2011-07-04	2002-08-29		ENSG00000065518	ENSG00000065518		"Mitochondrial respiratory chain complex / Complex I"	7699	protein-coding gene	gene with protein product	"complex I B15 subunit"	603840	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4 (15kD, B15)"			9878551	Standard	NM_004547		Approved	B15	uc003edu.3	O95168	OTTHUMG00000159442	ENST00000184266.2:c.327+33G>A	chr3.hg19:g.120320137G>A		39.0	0.0		33.0	9.0	NM_001168331	B2RUY3|B9EJC7	Silent	SNP	ENST00000184266.2	hg19	CCDS2999.1																																																																																			.	.		0.483	NDUFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355420.1	NM_004547		A	120320137	G	A	120320137	1	1	225	0	1	0	0	0	0	0	0	0	10292	1020	36	3		3	NDUFB4	3	120320137	Intron	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	13223421	120320137	77702293	16	31914										
ALG1L	200810	hgsc.bcm.edu	37	chr3	125648374	125648374	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gttcttccaaaactggtttaGcttgcctgcaggatcaggaa	10	9	2	0	rs200222793		TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr3:125648374G>C	ENST00000340333.3	-	6	548	c.385C>G	c.(385-387)Cta>Gta	p.L129V	FAM86JP_ENST00000485843.1_RNA	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like	129							transferase activity, transferring glycosyl groups (GO:0016757)			large_intestine(2)|lung(2)	4						AACTGGTTTAGCTTGCCTGCA	0.512																																					p.L149V		Atlas-SNP	.											.	ALG1L	12	.	0			c.C445G						.						42	53	49					3																	125648374		1369	2314	3683	SO:0001583	missense	200810	exon7			GGTTTAGCTTGCC	BC073816	CCDS33840.1, CCDS74998.1	3q21.2	2013-02-22	2013-02-22		ENSG00000189366	ENSG00000189366		"Glycosyltransferase group 1 domain containing"	33721	protein-coding gene	gene with protein product	"asparagine-linked glycosylation 1-like 1"		"asparagine-linked glycosylation 1-like"				Standard	NM_001015050		Approved	ALG1L1	uc003eig.2	Q6GMV1	OTTHUMG00000159588	ENST00000340333.3:c.385C>G	chr3.hg19:g.125648374G>C	ENSP00000340009:p.Leu129Val	143.0	0.0		129.0	31.0	NM_001195223	D3DNA5	Missense_Mutation	SNP	ENST00000340333.3	hg19	CCDS33840.1	.	.	.	.	.	.	.	.	.	.	.	13.73	2.323743	0.41096	.	.	ENSG00000189366	ENST00000340333	T	0.73047	-0.71	2.3	2.3	0.28687	.	0.000000	0.64402	D	0.000001	T	0.70544	0.3236	L	0.41236	1.265	0.80722	D	1	D	0.71674	0.998	P	0.62740	0.906	T	0.70382	-0.4887	10	0.72032	D	0.01	-10.2455	5.0245	0.14378	0.1808:0.0:0.8192:0.0	.	129	Q6GMV1	ALG1L_HUMAN	V	129	ENSP00000340009:L129V	ENSP00000340009:L129V	L	-	1	2	ALG1L	127131064	1.000000	0.71417	0.350000	0.25708	0.050000	0.14768	2.710000	0.47169	1.285000	0.44548	0.184000	0.17185	CTA	.	G|0.999;T|0.001		0.512	ALG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356347.1	NM_001015050		C	125648374	G	C	125648374	3	2	225	1	0	0	0	0	1	0	0	0	517	962	34	4	182	4	ALG1L	3	125648374	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	5328237	125648374	72374056	17	31915										
HTT	3064	hgsc.bcm.edu	37	chr4	3230458	3230458	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ccttcgtcaccacccacgtcTccagtcaactccaggttttc	5	18	3	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr4:3230458T>C	ENST00000355072.5	+	58	8110	c.7965T>C	c.(7963-7965)tcT>tcC	p.S2655S	HTT_ENST00000513806.1_3'UTR	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2655					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CACCCACGTCTCCAGTCAACT	0.493																																					p.S2655S		Atlas-SNP	.											.	HTT	221	.	0			c.T7965C						.						84	88	87					4																	3230458		1992	4173	6165	SO:0001819	synonymous_variant	3064	exon58			CACGTCTCCAGTC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.7965T>C	chr4.hg19:g.3230458T>C		102.0	0.0		94.0	15.0	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	hg19	CCDS43206.1																																																																																			.	.		0.493	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		C	3230458	T	C	3230458	2	2	225	1	0	0	0	0	0	0	0	1	7466	1538	54	2		2	HTT	4	3230458	Silent	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10		3230458	187923818	18	31916										
EVC	2121	hgsc.bcm.edu	37	chr4	5747031	5747031	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	caccctggctgatgtggaaaAgaaggagagagaatactctg	13	7	1	4			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr4:5747031A>G	ENST00000264956.6	+	7	1086	c.902A>G	c.(901-903)aAg>aGg	p.K301R	EVC_ENST00000509451.1_Missense_Mutation_p.K301R|EVC_ENST00000382674.2_Missense_Mutation_p.K301R	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	301					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				GATGTGGAAAAGAAGGAGAGA	0.433																																					p.K301R		Atlas-SNP	.											.	EVC	90	.	0			c.A902G						.						131	128	129					4																	5747031		2203	4300	6503	SO:0001583	missense	2121	exon7			TGGAAAAGAAGGA	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.902A>G	chr4.hg19:g.5747031A>G	ENSP00000264956:p.Lys301Arg	110.0	0.0		110.0	19.0	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	hg19	CCDS3383.1	.	.	.	.	.	.	.	.	.	.	A	0.012	-1.690075	0.00738	.	.	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.41758	0.99;0.99;1.09	5.4	-0.135	0.13477	.	0.225320	0.44902	N	0.000415	T	0.19927	0.0479	N	0.11789	0.175	0.24232	N	0.995391	B	0.06786	0.001	B	0.09377	0.004	T	0.29761	-1.0001	10	0.02654	T	1	.	14.2527	0.66031	0.1562:0.0:0.8438:0.0	.	301	P57679	EVC_HUMAN	R	301	ENSP00000264956:K301R;ENSP00000372120:K301R;ENSP00000426774:K301R	ENSP00000264956:K301R	K	+	2	0	EVC	5797932	1.000000	0.71417	0.600000	0.28864	0.004000	0.04260	0.900000	0.28431	-0.391000	0.07763	-0.385000	0.06624	AAG	.	.		0.433	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			G	5747031	A	G	5747031	3	3	225	1	0	0	0	0	1	0	0	0	5287	72	3	2	928	2	EVC	4	5747031	Missense_Mutation	SNP	A	TCGA-DD-AAVR-01A-11D-A40R-10	2516573	5747031	185407245	19	31917										
NFXL1	152518	hgsc.bcm.edu	37	chr4	47850263	47850263	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gagataatatttatgtttttGccatagtgatagctcaactg	8	5	1	2	rs565045894		TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr4:47850263G>A	ENST00000507489.1	-	23	2829	c.2653C>T	c.(2653-2655)Caa>Taa	p.Q885*	NFXL1_ENST00000381538.3_Nonsense_Mutation_p.Q885*	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	885						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						TTATGTTTTTGCCATAGTGAT	0.368																																					p.Q885X		Atlas-SNP	.											.	NFXL1	79	.	0			c.C2653T						.						164	153	157					4																	47850263		2203	4300	6503	SO:0001587	stop_gained	152518	exon23			GTTTTTGCCATAG	AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"ovarian zinc finger protein"						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.2653C>T	chr4.hg19:g.47850263G>A	ENSP00000422037:p.Gln885*	71.0	0.0		71.0	11.0	NM_152995	B1Q2K1|Q86VG1|Q8WVH1	Nonsense_Mutation	SNP	ENST00000507489.1	hg19	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	G	20.4	3.977014	0.74360	.	.	ENSG00000170448	ENST00000381538;ENST00000507489	.	.	.	5.79	4.92	0.64577	.	0.087565	0.48767	D	0.000174	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	-17.6633	15.9323	0.79672	0.0:0.0:0.8644:0.1356	.	.	.	.	X	885	.	ENSP00000370949:Q885X	Q	-	1	0	NFXL1	47545020	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	4.502000	0.60400	2.727000	0.93392	0.650000	0.86243	CAA	.	.		0.368	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995		A	47850263	G	A	47850263	4	1	225	1	0	0	0	0	0	1	0	0	10397	1328	46	3	86	3	NFXL1	4	47850263	Nonsense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	42103232	47850263	143304013	20	31918										
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90170448	90170448	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gggacatgccgaaggttcgcTagtgaggggggttggttgag	20	5	0	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr4:90170448T>C	ENST00000609438.1	-	2	1332	c.814A>G	c.(814-816)Agc>Ggc	p.S272G	GPRIN3_ENST00000333209.4_Missense_Mutation_p.S272G	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	272										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		GAAGGTTCGCTAGTGAGGGGG	0.562																																					p.S272G		Atlas-SNP	.											.	GPRIN3	90	.	0			c.A814G						.						72	76	75					4																	90170448		2203	4300	6503	SO:0001583	missense	285513	exon2			GTTCGCTAGTGAG	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.814A>G	chr4.hg19:g.90170448T>C	ENSP00000476603:p.Ser272Gly	65.0	0.0		52.0	12.0	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	hg19	CCDS34030.1	.	.	.	.	.	.	.	.	.	.	T	7.866	0.727104	0.15439	.	.	ENSG00000185477	ENST00000333209	T	0.11930	2.73	5.64	3.17	0.36434	.	0.000000	0.40385	N	0.001108	T	0.06872	0.0175	N	0.19112	0.55	0.09310	N	1	B	0.32653	0.379	B	0.27170	0.077	T	0.33548	-0.9864	10	0.26408	T	0.33	-5.0071	5.9496	0.19237	0.0:0.1447:0.1396:0.7158	.	272	Q6ZVF9	GRIN3_HUMAN	G	272	ENSP00000328672:S272G	ENSP00000328672:S272G	S	-	1	0	GPRIN3	90389471	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	-0.230000	0.09083	0.535000	0.28714	0.528000	0.53228	AGC	.	.		0.562	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		C	90170448	T	C	90170448	3	2	225	1	0	0	0	0	1	0	0	0	6740	1522	53	2	1520	2	GPRIN3	4	90170448	Missense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	42320185	90170448	100983828	21	31919										
PET112L	5188	hgsc.bcm.edu	37	chr4	152637251	152637251	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ctcttctccacaggacatgtCgggctccaggaccacctcca	8	17	2	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr4:152637251C>T	ENST00000263985.6	-	5	713	c.673G>A	c.(673-675)Gac>Aac	p.D225N	PET112_ENST00000512306.1_Missense_Mutation_p.D225N|PET112_ENST00000515812.1_Intron	NM_004564.2	NP_004555.1												p.D225N(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						CAGGACATGTCGGGCTCCAGG	0.577																																					p.D225N		Atlas-SNP	.											PET112,NS,carcinoma,0,1	PET112	43	.	1	Substitution - Missense(1)	endometrium(1)	c.G673A						.						53	49	50					4																	152637251		2203	4300	6503	SO:0001583	missense	5188	exon5			ACATGTCGGGCTC																												ENST00000263985.6:c.673G>A	chr4.hg19:g.152637251C>T	ENSP00000263985:p.Asp225Asn	138.0	0.0		125.0	22.0	NM_004564		Missense_Mutation	SNP	ENST00000263985.6	hg19	CCDS3776.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.828700	0.90955	.	.	ENSG00000059691	ENST00000263985;ENST00000512306	T;T	0.53857	0.6;0.65	5.22	5.22	0.72569	Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic (1);	0.100907	0.64402	D	0.000003	T	0.78317	0.4264	H	0.94264	3.515	0.80722	D	1	D;D	0.67145	0.994;0.996	P;P	0.58780	0.671;0.845	D	0.85507	0.1195	10	0.87932	D	0	-23.6428	18.7623	0.91856	0.0:1.0:0.0:0.0	.	225;225	D6RDU9;O75879	.;GATB_HUMAN	N	225	ENSP00000263985:D225N;ENSP00000420831:D225N	ENSP00000263985:D225N	D	-	1	0	PET112	152856701	1.000000	0.71417	0.776000	0.31678	0.889000	0.51656	5.989000	0.70587	2.422000	0.82143	0.655000	0.94253	GAC	.	.		0.577	PET112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365671.1			T	152637251	C	T	152637251	3	4	225	1	0	0	0	0	1	0	0	0	11743	884	31	1	1036	1	PET112L	4	152637251	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	62466803	152637251	38517025	22	31920										
GFM2	84340	hgsc.bcm.edu	37	chr5	74018369	74018369	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	agaggctccaaaacttgcttAtcagctttcttcagagccta	7	11	3	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr5:74018369A>C	ENST00000296805.3	-	20	2503	c.2046T>G	c.(2044-2046)gaT>gaG	p.D682E	RNU6-658P_ENST00000384606.1_RNA|GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000509430.1_Missense_Mutation_p.D682E|GFM2_ENST00000345239.2_Missense_Mutation_p.D635E	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		AAACTTGCTTATCAGCTTTCT	0.358																																					p.D682E		Atlas-SNP	.											.	GFM2	38	.	0			c.T2046G						.						80	81	81					5																	74018369		2203	4300	6503	SO:0001583	missense	84340	exon20			TTGCTTATCAGCT	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.2046T>G	chr5.hg19:g.74018369A>C	ENSP00000296805:p.Asp682Glu	105.0	0.0		109.0	18.0	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	A	10.32	1.317325	0.23908	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000509430	T;T;T	0.41758	0.99;0.99;0.99	5.96	-4.28	0.03732	Ribosomal protein S5 domain 2-type fold (1);Translation elongation factor EFG/EF2, domain IV (2);Translation elongation factor EFG/EF2, C-terminal (1);	0.198488	0.56097	N	0.000039	T	0.20659	0.0497	N	0.17082	0.46	0.80722	D	1	B;B;B	0.21071	0.003;0.051;0.003	B;B;B	0.18871	0.006;0.023;0.01	T	0.01182	-1.1426	10	0.51188	T	0.08	-11.5008	8.4158	0.32670	0.2843:0.294:0.4217:0.0	.	680;635;682	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	E	682;635;682	ENSP00000296805:D682E;ENSP00000296804:D635E;ENSP00000427004:D682E	ENSP00000296805:D682E	D	-	3	2	GFM2	74054125	0.275000	0.24201	0.905000	0.35620	0.854000	0.48673	-0.305000	0.08188	-0.627000	0.05589	-0.297000	0.09499	GAT	.	.		0.358	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		C	74018369	A	C	74018369	3	2	225	1	0	0	0	0	1	0	0	0	6350	446	16	5	301	5	GFM2	5	74018369	Missense_Mutation	SNP	A	TCGA-DD-AAVR-01A-11D-A40R-10		74018369	106896891	23	31921										
SH3PXD2B	285590	hgsc.bcm.edu	37	chr5	171766054	171766054	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tggccccctactgcctggggGccctccccatccaacaagga	10	18	0	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr5:171766054G>A	ENST00000311601.5	-	13	2225	c.2055C>T	c.(2053-2055)ggC>ggT	p.G685G	SH3PXD2B_ENST00000519643.1_Intron	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	685					adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTGCCTGGGGGCCCTCCCCAT	0.642																																					p.G685G		Atlas-SNP	.											.	SH3PXD2B	91	.	0			c.C2055T						.						60	58	58					5																	171766054		2203	4300	6503	SO:0001819	synonymous_variant	285590	exon13			CTGGGGGCCCTCC	AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"KIAA1295"	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.2055C>T	chr5.hg19:g.171766054G>A		71.0	0.0		96.0	16.0	NM_001017995	B6F0V2|Q9P2Q1	Silent	SNP	ENST00000311601.5	hg19	CCDS34291.1																																																																																			.	.		0.642	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963		A	171766054	G	A	171766054	2	1	225	1	0	0	0	0	0	0	0	1	14272	1190	42	3		3	SH3PXD2B	5	171766054	Silent	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	97747685	171766054	9149206	24	31922										
HIST1H4C	8364	hgsc.bcm.edu	37	chr6	26104199	26104199	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tctggtcgcggcaaaggcggAaaaggcttggggaagggtgg	20	6	1	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr6:26104199A>T	ENST00000377803.2	+	1	96	c.24A>T	c.(22-24)ggA>ggT	p.G8G		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	8					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7						GCAAAGGCGGAAAAGGCTTGG	0.517																																					p.G8G		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.A24T						.						56	57	56					6																	26104199		2203	4300	6503	SO:0001819	synonymous_variant	8364	exon1			AGGCGGAAAAGGC	X60486	CCDS4583.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000197061	ENSG00000197061		"Histones / Replication-dependent"	4787	protein-coding gene	gene with protein product		602827	"H4 histone family, member G", "histone 1, H4c"	H4FG		9119399, 12408966	Standard	NM_003542		Approved	H4/g, dJ221C16.1	uc003ngi.3	P62805	OTTHUMG00000014429	ENST00000377803.2:c.24A>T	chr6.hg19:g.26104199A>T		77.0	0.0		93.0	11.0	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377803.2	hg19	CCDS4583.1																																																																																			.	.		0.517	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542		T	26104199	A	T	26104199	2	4	225	1	0	0	0	0	0	0	0	1	7176	233	9	4		4	HIST1H4C	6	26104199	Silent	SNP	A	TCGA-DD-AAVR-01A-11D-A40R-10		26104199	145010868	25	31923										
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156767	26156769	+	In_Frame_Del	DEL	CCT	CCT	-													0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cattactaaagctgttgccgCctccaaggagcgcagcggcg					rs377472965		TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr6:26156767_26156769delCCT	ENST00000304218.3	+	1	209_211	c.149_151delCCT	c.(148-153)gcctcc>gcc	p.S51del	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	51	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						GCTGTTGCCGCCTCCAAGGAGCG	0.606																																					p.50_50del		Atlas-INDEL	.											.	HIST1H1E	69	.	0			c.148_150del						.																																			SO:0001651	inframe_deletion	3008	exon1			.	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"Histones / Replication-dependent"	4718	protein-coding gene	gene with protein product		142220	"H1 histone family, member 4", "histone 1, H1e"	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.149_151delCCT	chr6.hg19:g.26156767_26156769delCCT	ENSP00000307705:p.Ser51del	68.0	0.0		85.0	25.0	NM_005321	Q4VB25	In_Frame_Del	DEL	ENST00000304218.3	hg19	CCDS4586.1																																																																																			.	.		0.606	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		-	26156769	CCT	-	26156767	7	5	225	1	0	1	0	1	0	0	0	0	7135	739	26	0	151	0	HIST1H1E	6	26156767	In_Frame_Del	DEL	CCT	TCGA-DD-AAVR-01A-11D-A40R-10	52568	26156767	144958300	26	31924										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30920202	30920202	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tgggagagaatgattcattcCctgcatgggccatagttatt	11	7	1	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr6:30920202C>T	ENST00000462446.1	+	2	3989	c.3961C>T	c.(3961-3963)Cct>Tct	p.P1321S	DPCR1_ENST00000304311.2_Missense_Mutation_p.P163S|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	445						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						TGATTCATTCCCTGCATGGGC	0.502																																					p.P1321S		Atlas-SNP	.											.	DPCR1	99	.	0			c.C3961T						.						100	76	84					6																	30920202		2203	4300	6503	SO:0001583	missense	135656	exon2			TCATTCCCTGCAT	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.3961C>T	chr6.hg19:g.30920202C>T	ENSP00000417182:p.Pro1321Ser	91.0	0.0		107.0	15.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	C	16.50	3.141384	0.57044	.	.	ENSG00000168631	ENST00000462446;ENST00000450344;ENST00000304311	T;T	0.70516	-0.21;-0.49	3.78	3.78	0.43462	.	.	.	.	.	T	0.72676	0.3490	L	0.52573	1.65	0.33012	D	0.527678	D	0.89917	1.0	D	0.91635	0.999	T	0.73531	-0.3953	9	0.87932	D	0	-13.4067	11.2912	0.49252	0.0:1.0:0.0:0.0	.	1321	E9PEI6	.	S	1321;445;163	ENSP00000417182:P1321S;ENSP00000305948:P163S	ENSP00000305948:P163S	P	+	1	0	DPCR1	31028181	0.419000	0.25449	0.994000	0.49952	0.922000	0.55478	1.884000	0.39668	2.075000	0.62263	0.551000	0.68910	CCT	.	.		0.502	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		T	30920202	C	T	30920202	3	4	225	1	0	0	0	0	1	0	0	0	4714	623	22	3	3967	3	DPCR1	6	30920202	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	4763435	30920202	140194865	27	31925										
UBR2	23304	hgsc.bcm.edu	37	chr6	42637952	42637952	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tcccataatgtgttggggtaGctgcgcgtacaccatccaaa	10	11	0	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr6:42637952G>A	ENST00000372899.1	+	35	4262	c.4004G>A	c.(4003-4005)aGc>aAc	p.S1335N	UBR2_ENST00000372883.3_3'UTR|UBR2_ENST00000372901.1_Missense_Mutation_p.S1335N	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1335					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TGTTGGGGTAGCTGCGCGTAC	0.408																																					p.S1335N		Atlas-SNP	.											.	UBR2	134	.	0			c.G4004A						.						141	120	127					6																	42637952		2203	4300	6503	SO:0001583	missense	23304	exon35			GGGGTAGCTGCGC	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.4004G>A	chr6.hg19:g.42637952G>A	ENSP00000361990:p.Ser1335Asn	152.0	0.0		201.0	27.0	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	hg19	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	G	17.90	3.503097	0.64298	.	.	ENSG00000024048	ENST00000372899;ENST00000372901	T;T	0.58797	0.31;0.31	5.36	4.47	0.54385	.	0.134335	0.64402	D	0.000002	T	0.46737	0.1408	M	0.65498	2.005	0.80722	D	1	P;P	0.40660	0.694;0.726	B;B	0.40864	0.281;0.342	T	0.52335	-0.8589	10	0.45353	T	0.12	-28.1992	15.6784	0.77349	0.0:0.1422:0.8578:0.0	.	1335;1335	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	N	1335	ENSP00000361990:S1335N;ENSP00000361992:S1335N	ENSP00000361990:S1335N	S	+	2	0	UBR2	42745930	1.000000	0.71417	0.959000	0.39883	0.934000	0.57294	6.026000	0.70873	1.215000	0.43411	0.655000	0.94253	AGC	.	.		0.408	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		A	42637952	G	A	42637952	3	1	225	1	0	0	0	0	1	0	0	0	16917	971	34	3	4288	3	UBR2	6	42637952	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	11717750	42637952	128477115	28	31926										
KLHL32	114792	hgsc.bcm.edu	37	chr6	97561870	97561870	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	acagcctgtctggcagactcGcaggaccaaaccacgattcc	9	15	1	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr6:97561870G>T	ENST00000369261.4	+	7	1202	c.839G>T	c.(838-840)cGc>cTc	p.R280L	KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000539200.1_Missense_Mutation_p.R211L|KLHL32_ENST00000536676.1_Missense_Mutation_p.R244L	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	280										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		TGGCAGACTCGCAGGACCAAA	0.527																																					p.R280L		Atlas-SNP	.											.	KLHL32	85	.	0			c.G839T						.						94	80	85					6																	97561870		2203	4300	6503	SO:0001583	missense	114792	exon7			AGACTCGCAGGAC	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"Kelch-like", "BTB/POZ domain containing"	21221	protein-coding gene	gene with protein product			"BTB and kelch domain containing 5", "KIAA1900", "kelch-like 32 (Drosophila)"	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.839G>T	chr6.hg19:g.97561870G>T	ENSP00000358265:p.Arg280Leu	152.0	0.0		130.0	23.0	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	hg19	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.753878	0.31046	.	.	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200	T;T;T	0.73258	-0.69;-0.71;-0.73	5.5	5.5	0.81552	.	0.560131	0.20386	N	0.093355	T	0.45617	0.1351	L	0.46157	1.445	0.36971	D	0.893828	B;B;B;B	0.06786	0.0;0.001;0.0;0.001	B;B;B;B	0.09377	0.001;0.001;0.0;0.004	T	0.27839	-1.0062	10	0.13853	T	0.58	.	11.5958	0.50972	0.0:0.1331:0.7291:0.1379	.	211;244;280;280	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	L	280;244;211	ENSP00000358265:R280L;ENSP00000440382:R244L;ENSP00000441527:R211L	ENSP00000358265:R280L	R	+	2	0	KLHL32	97668591	0.149000	0.22717	0.962000	0.40283	0.945000	0.59286	2.087000	0.41653	2.854000	0.98071	0.655000	0.94253	CGC	.	.		0.527	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		T	97561870	G	T	97561870	3	4	225	1	0	0	0	0	1	0	0	0	8395	1087	38	1	861	1	KLHL32	6	97561870	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	54923918	97561870	73553197	29	31927										
SCIN	85477	hgsc.bcm.edu	37	chr7	12610443	12610443	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	agctataccacgaagagttcGcccgggcgggcaagcaggcg	15	12	0	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr7:12610443G>T	ENST00000297029.5	+	1	132	c.31G>T	c.(31-33)Gcc>Tcc	p.A11S	AC005281.2_ENST00000433040.1_RNA	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	11	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		CGAAGAGTTCGCCCGGGCGGG	0.652																																					p.A11S		Atlas-SNP	.											.	SCIN	105	.	0			c.G31T						.						16	25	22					7																	12610443		692	1590	2282	SO:0001583	missense	85477	exon1			GAGTTCGCCCGGG	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.31G>T	chr7.hg19:g.12610443G>T	ENSP00000297029:p.Ala11Ser	77.0	0.0		84.0	12.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	hg19	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	G	6.796	0.515941	0.12944	.	.	ENSG00000006747	ENST00000297029;ENST00000417018	T;T	0.17213	2.29;2.29	4.89	3.04	0.35103	.	0.309943	0.28130	N	0.016482	T	0.09468	0.0233	N	0.16790	0.44	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.14783	-1.0460	10	0.10111	T	0.7	-6.9749	11.3956	0.49841	0.0:0.1476:0.7154:0.137	.	11	Q9Y6U3	ADSV_HUMAN	S	11	ENSP00000297029:A11S;ENSP00000404380:A11S	ENSP00000297029:A11S	A	+	1	0	SCIN	12576968	0.818000	0.29161	0.264000	0.24511	0.007000	0.05969	2.267000	0.43329	0.619000	0.30197	-0.321000	0.08615	GCC	.	.		0.652	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		T	12610443	G	T	12610443	3	4	225	1	0	0	0	0	1	0	0	0	13920	1087	38	1	33	1	SCIN	7	12610443	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10		12610443	146528220	30	31928										
SP8	221833	hgsc.bcm.edu	37	chr7	20825271	20825271	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cagctggcggaagaagaggaCgaggagcgtttccaggggtg	19	7	0	2	rs145875827		TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr7:20825271C>A	ENST00000361443.4	-	3	348	c.111G>T	c.(109-111)tcG>tcT	p.S37S	SP8_ENST00000418710.2_Silent_p.S55S	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	37	Ser-rich.				dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						AAGAAGAGGACGAGGAGCGTT	0.632																																					p.S55S		Atlas-SNP	.											.	SP8	43	.	0			c.G165T						.						46	47	47					7																	20825271		2203	4300	6503	SO:0001819	synonymous_variant	221833	exon2			AGAGGACGAGGAG		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.111G>T	chr7.hg19:g.20825271C>A		88.0	0.0		77.0	14.0	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	hg19	CCDS5372.1																																																																																			.	C|1.000;T|0.000		0.632	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			A	20825271	C	A	20825271	2	1	225	1	0	0	0	0	0	0	0	1	14985	523	19	1		1	SP8	7	20825271	Silent	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	8214828	20825271	138313392	31	31929										
ELN	2006	hgsc.bcm.edu	37	chr7	73452038	73452038	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tcttctcttccctctgcagcGctggggcctggaggcaaacc	11	15	3	0	rs376512299		TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr7:73452038G>A	ENST00000252034.7	+	4	564	c.165G>A	c.(163-165)gcG>gcA	p.A55A	ELN_ENST00000358929.4_Splice_Site_p.A55A|ELN_ENST00000380575.4_Splice_Site_p.A45A|ELN_ENST00000445912.1_Splice_Site_p.A55A|ELN_ENST00000380562.4_Splice_Site_p.A55A|ELN_ENST00000380576.5_Splice_Site_p.A55A|ELN_ENST00000320399.6_Splice_Site_p.A55A|ELN_ENST00000357036.5_Splice_Site_p.A55A|ELN_ENST00000458204.1_Splice_Site_p.A45A|ELN_ENST00000320492.7_Splice_Site_p.A55A|ELN_ENST00000414324.1_Splice_Site_p.A45A|ELN_ENST00000380553.4_Splice_Site_p.A55A|ELN_ENST00000380584.4_Splice_Site_p.A55A|ELN_ENST00000429192.1_Splice_Site_p.A55A	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	55					blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)	p.A55A(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				CCTCTGCAGCGCTGGGGCCTG	0.587			T	PAX5	B-ALL		"Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"																														p.A55A		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	ELN,NS,haematopoietic_neoplasm,0,1	ELN	81	.	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G165A						.	A	,,,,	3,4403	6.2+/-15.9	0,3,2200	86	63	71		165,135,165,165,165	-10.3	0	7		71	0,8600		0,0,4300	no	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ELN	NM_000501.2,NM_001081752.1,NM_001081753.1,NM_001081754.1,NM_001081755.1	,,,,	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	,,,,	55/725,45/678,55/693,55/712,55/706	73452038	3,13003	2203	4300	6503	SO:0001630	splice_region_variant	2006	exon4			TGCAGCGCTGGGG		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"tropoelastin", "supravalvular aortic stenosis", "Williams-Beuren syndrome"	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.164-1G>A	chr7.hg19:g.73452038G>A		80.0	0.0		100.0	24.0	NM_001081753	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Silent	SNP	ENST00000252034.7	hg19	CCDS5562.2																																																																																			.	.		0.587	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501	Silent	A	73452038	G	A	73452038	5	1	225	1	0	0	0	0	0	0	1	0	5073	1101	38	1	179	1	ELN	7	73452038	Splice_Site	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	52626767	73452038	85686625	32	31930										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88963559	88963559	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gataaaacagaaagagttagCaaaaatgttcaaagacttgt	8	4	1	3			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr7:88963559C>T	ENST00000333190.4	+	4	1872	c.1263C>T	c.(1261-1263)agC>agT	p.S421S		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	421							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AAAGAGTTAGCAAAAATGTTC	0.388										HNSCC(36;0.09)																											p.S421S		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C1263T						.						52	55	54					7																	88963559		2203	4300	6503	SO:0001819	synonymous_variant	219578	exon4			AGTTAGCAAAAAT	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1263C>T	chr7.hg19:g.88963559C>T		86.0	0.0		85.0	17.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	hg19	CCDS5613.1																																																																																			.	.		0.388	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88963559	C	T	88963559	2	4	225	1	0	0	0	0	0	0	0	1	18186	709	25	3		3	ZNF804B	7	88963559	Silent	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	15511521	88963559	70175104	33	31931										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116426762	116426762	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gcttatatttactccagaacCgcagccaatcagcttcactc	5	14	2	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr8:116426762C>T	ENST00000220888.5	-	6	3494	c.3335G>A	c.(3334-3336)cGg>cAg	p.R1112Q	TRPS1_ENST00000520276.1_Missense_Mutation_p.R1116Q|TRPS1_ENST00000519076.1_Missense_Mutation_p.R866Q|TRPS1_ENST00000395715.3_Missense_Mutation_p.R1125Q			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	1112	Mediates interaction with RNF4. {ECO:0000250}.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			ACTCCAGAACCGCAGCCAATC	0.468									Langer-Giedion syndrome																												p.R1125Q		Atlas-SNP	.											TRPS1_ENST00000395715,caecum,carcinoma,0,4	TRPS1	516	.	0			c.G3374A						.						94	92	93					8																	116426762		1911	4131	6042	SO:0001583	missense	7227	exon7	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	CAGAACCGCAGCC	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.3335G>A	chr8.hg19:g.116426762C>T	ENSP00000220888:p.Arg1112Gln	163.0	0.0		214.0	35.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	C	23.7	4.445419	0.84101	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276	D;D;D;D	0.99311	-5.73;-5.71;-5.59;-5.71	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.98817	0.9601	N	0.19112	0.55	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.992;0.996	D	0.99945	1.1458	10	0.87932	D	0	.	19.865	0.96801	0.0:1.0:0.0:0.0	.	1116;1112;1125	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	Q	1125;1112;866;1116	ENSP00000379065:R1125Q;ENSP00000220888:R1112Q;ENSP00000428910:R866Q;ENSP00000428680:R1116Q	ENSP00000220888:R1112Q	R	-	2	0	TRPS1	116495938	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.622000	0.83099	2.685000	0.91497	0.655000	0.94253	CGG	.	.		0.468	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		T	116426762	C	T	116426762	3	4	225	1	0	0	0	0	1	0	0	0	16608	652	23	1	514	1	TRPS1	8	116426762	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10		116426762	29937260	34	31932										
C9orf5	23731	hgsc.bcm.edu	37	chr9	111882014	111882014	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cagcacaggcacacgaacagCacggccccggtgttgtagaa	12	13	0	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr9:111882014C>A	ENST00000374586.3	-	1	211	c.180G>T	c.(178-180)gtG>gtT	p.V60V		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	60						integral component of membrane (GO:0016021)											ACACGAACAGCACGGCCCCGG	0.692																																					p.V60V		Atlas-SNP	.											.	.	.	.	0			c.G180T						.						10	17	15					9																	111882014		1987	4143	6130	SO:0001819	synonymous_variant	23731	exon1			GAACAGCACGGCC	AF153415	CCDS43858.1	9q31	2012-03-06	2012-03-06	2012-03-06	ENSG00000106771	ENSG00000106771			1363	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 5"	C9orf5		10564813	Standard	NM_032012		Approved	CG-2	uc004bdt.4	Q9H330	OTTHUMG00000020469	ENST00000374586.3:c.180G>T	chr9.hg19:g.111882014C>A		49.0	0.0		45.0	16.0	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Silent	SNP	ENST00000374586.3	hg19	CCDS43858.1																																																																																			.	.		0.692	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012		A	111882014	C	A	111882014	2	1	225	1	0	0	0	0	0	0	0	1	2488	697	25	3		3	C9orf5	9	111882014	Silent	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10		111882014	29331417	35	31933										
SETX	23064	hgsc.bcm.edu	37	chr9	135205038	135205038	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	acactgtcttgcactttcatTggttctttagaaaatgttgg	8	7	3	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr9:135205038T>G	ENST00000224140.5	-	10	2129	c.1947A>C	c.(1945-1947)ccA>ccC	p.P649P	SETX_ENST00000393220.1_Silent_p.P649P|SETX_ENST00000372169.2_Silent_p.P649P	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	649					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GCACTTTCATTGGTTCTTTAG	0.353																																					p.P649P		Atlas-SNP	.											.	SETX	234	.	0			c.A1947C						.						99	95	96					9																	135205038		2203	4300	6503	SO:0001819	synonymous_variant	23064	exon10			TTTCATTGGTTCT	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.1947A>C	chr9.hg19:g.135205038T>G		62.0	0.0		68.0	12.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Silent	SNP	ENST00000224140.5	hg19	CCDS6947.1																																																																																			.	.		0.353	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		G	135205038	T	G	135205038	2	3	225	1	0	0	0	0	0	0	0	1	14156	1799	63	5		5	SETX	9	135205038	Silent	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	23323024	135205038	6008393	36	31934										
MUC2	4583	hgsc.bcm.edu	37	chr11	1093075	1093075	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	agaccccaaccccaacagccAtcaccaccaccactacggtg	5	20	1	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr11:1093075A>G	ENST00000441003.2	+	30	4921	c.4894A>G	c.(4894-4896)Atc>Gtc	p.I1632V	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.I1599V	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cccaacagccatcaccaccac	0.632																																					p.I1632V		Atlas-SNP	.											.	MUC2	614	.	0			c.A4894G						.						100	149	132					11																	1093075		1865	3567	5432	SO:0001583	missense	4583	exon30			ACAGCCATCACCA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4894A>G	chr11.hg19:g.1093075A>G	ENSP00000415183:p.Ile1632Val	28.0	0.0		21.0	4.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.873	-0.731385	0.03135	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12255	2.7;3.0	0.703	0.703	0.18116	.	.	.	.	.	T	0.04137	0.0115	.	.	.	0.09310	N	1	B	0.11235	0.004	B	0.01281	0.0	T	0.43766	-0.9371	8	0.02654	T	1	.	3.7866	0.08703	1.0:0.0:0.0:0.0	.	1632	E7EUV1	.	V	1632;1599	ENSP00000415183:I1632V;ENSP00000351956:I1599V	ENSP00000351956:I1599V	I	+	1	0	MUC2	1083075	0.000000	0.05858	0.003000	0.11579	0.018000	0.09664	0.316000	0.19469	0.571000	0.29365	0.102000	0.15555	ATC	.	.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093075	A	G	1093075	3	3	225	1	0	0	0	0	1	0	0	0	9984	217	8	2	5012	2	MUC2	11	1093075	Missense_Mutation	SNP	A	TCGA-DD-AAVR-01A-11D-A40R-10		1093075	133913441	37	31935										
OR4A47	403253	hgsc.bcm.edu	37	chr11	48510973	48510973	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ggcttgcactattgtgtttcTgctcttactcatctcttatg	7	10	4	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr11:48510973T>A	ENST00000446524.1	+	1	705	c.629T>A	c.(628-630)cTg>cAg	p.L210Q		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	210						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						ATTGTGTTTCTGCTCTTACTC	0.463																																					p.L210Q		Atlas-SNP	.											.	OR4A47	72	.	0			c.T629A						.						105	101	103					11																	48510973		2201	4298	6499	SO:0001583	missense	403253	exon1			TGTTTCTGCTCTT	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"GPCR / Class A : Olfactory receptors"	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.629T>A	chr11.hg19:g.48510973T>A	ENSP00000412752:p.Leu210Gln	84.0	0.0		85.0	20.0	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	hg19	CCDS31490.1	.	.	.	.	.	.	.	.	.	.	N	12.73	2.024773	0.35701	.	.	ENSG00000237388	ENST00000446524	T	0.44881	0.91	4.59	3.44	0.39384	GPCR, rhodopsin-like superfamily (1);	0.792028	0.10645	N	0.650501	T	0.69984	0.3172	H	0.96633	3.855	0.09310	N	1	D	0.53745	0.962	P	0.61003	0.882	T	0.58967	-0.7542	10	0.72032	D	0.01	.	4.9005	0.13771	0.0:0.1002:0.1868:0.7129	.	210	Q6IF82	O4A47_HUMAN	Q	210	ENSP00000412752:L210Q	ENSP00000412752:L210Q	L	+	2	0	OR4A47	48467549	0.000000	0.05858	0.155000	0.22561	0.765000	0.43378	0.331000	0.19733	0.599000	0.29845	0.172000	0.16884	CTG	.	.		0.463	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512		A	48510973	T	A	48510973	3	1	225	1	0	0	0	0	1	0	0	0	11051	1580	55	4	631	4	OR4A47	11	48510973	Missense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	47417898	48510973	86495543	38	31936										
OR4D6	219983	hgsc.bcm.edu	37	chr11	59224678	59224678	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tatcaccgtccccaagttccTggtggatcttttatcagaca	7	12	3	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr11:59224678T>A	ENST00000300127.2	+	1	268	c.245T>A	c.(244-246)cTg>cAg	p.L82Q		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						CCCAAGTTCCTGGTGGATCTT	0.453																																					p.L82Q		Atlas-SNP	.											.	OR4D6	65	.	0			c.T245A						.						137	126	130					11																	59224678		2201	4295	6496	SO:0001583	missense	219983	exon1			AGTTCCTGGTGGA	AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"GPCR / Class A : Olfactory receptors"	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.245T>A	chr11.hg19:g.59224678T>A	ENSP00000300127:p.Leu82Gln	143.0	0.0		125.0	34.0	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	hg19	CCDS31562.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.380000	0.82682	.	.	ENSG00000166884	ENST00000300127	T	0.00433	7.43	6.01	6.01	0.97437	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41938	D	0.000782	T	0.02342	0.0072	H	0.97186	3.955	0.38690	D	0.952741	D	0.89917	1.0	D	0.85130	0.997	T	0.06625	-1.0816	10	0.87932	D	0	-8.9509	15.3555	0.74423	0.0:0.0:0.0:1.0	.	82	Q8NGJ1	OR4D6_HUMAN	Q	82	ENSP00000300127:L82Q	ENSP00000300127:L82Q	L	+	2	0	OR4D6	58981254	0.947000	0.32204	1.000000	0.80357	0.968000	0.65278	6.293000	0.72731	2.299000	0.77371	0.533000	0.62120	CTG	.	.		0.453	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708		A	59224678	T	A	59224678	3	1	225	1	0	0	0	0	1	0	0	0	11067	1580	55	4	247	4	OR4D6	11	59224678	Missense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	10713705	59224678	75781838	39	31937										
MAP4K2	5871	hgsc.bcm.edu	37	chr11	64568236	64568236	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cagcagggtgtggcccttacCagcgagtcttatctctcagt	11	12	3	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr11:64568236C>A	ENST00000294066.2	-	10	816	c.725G>T	c.(724-726)tGg>tTg	p.W242L	MAP4K2_ENST00000377350.3_Splice_Site_p.W242L|MAP4K2_ENST00000468062.1_5'UTR	NM_004579.3	NP_004570.2	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase kinase 2	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|immune response (GO:0006955)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|positive regulation of JNK cascade (GO:0046330)|protein phosphorylation (GO:0006468)|vesicle targeting (GO:0006903)	Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(1)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(2)	8						TGGCCCTTACCAGCGAGTCTT	0.637																																					p.W242L		Atlas-SNP	.											.	MAP4K2	83	.	0			c.G725T						.						26	22	23					11																	64568236		2198	4295	6493	SO:0001630	splice_region_variant	5871	exon10			CCTTACCAGCGAG	BC047865	CCDS8082.1	11q13.1	2011-06-09			ENSG00000168067	ENSG00000168067		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6864	protein-coding gene	gene with protein product		603166		RAB8IP		7515885	Standard	NM_004579		Approved	GCK, BL44	uc001obh.3	Q12851	OTTHUMG00000045328	ENST00000294066.2:c.725+1G>T	chr11.hg19:g.64568236C>A		35.0	0.0		37.0	13.0	NM_004579	Q86VU3	Missense_Mutation	SNP	ENST00000294066.2	hg19	CCDS8082.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.721659	0.68959	.	.	ENSG00000168067	ENST00000294066;ENST00000377350;ENST00000439069	T;T;T	0.20332	2.08;2.08;2.08	4.66	4.66	0.58398	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.29684	0.0741	N	0.17838	0.53	0.80722	D	1	P;D	0.64830	0.931;0.994	P;D	0.71870	0.782;0.975	T	0.04373	-1.0956	9	.	.	.	.	15.4664	0.75403	0.0:1.0:0.0:0.0	.	242;242	Q86VU3;Q12851	.;M4K2_HUMAN	L	242;242;198	ENSP00000294066:W242L;ENSP00000366567:W242L;ENSP00000403563:W198L	.	W	-	2	0	MAP4K2	64324812	1.000000	0.71417	0.997000	0.53966	0.259000	0.26198	7.331000	0.79192	2.332000	0.79248	0.456000	0.33151	TGG	.	.		0.637	MAP4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105239.1	NM_004579	Missense_Mutation	A	64568236	C	A	64568236	5	1	225	1	0	0	0	0	0	0	1	0	9269	608	21	3	1829	3	MAP4K2	11	64568236	Splice_Site	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	5343558	64568236	70438280	40	31938										
OVOL1	5017	hgsc.bcm.edu	37	chr11	65562094	65562094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ctaccagcgcatgctgaaccGccacatgaagtgtcacaacg	9	14	1	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr11:65562094G>A	ENST00000335987.3	+	3	756	c.404G>A	c.(403-405)cGc>cAc	p.R135H	RP11-770G2.5_ENST00000531155.1_RNA|OVOL1_ENST00000532448.1_Missense_Mutation_p.R73H	NM_004561.3	NP_004552.2	O14753	OVOL1_HUMAN	ovo-like zinc finger 1	135					cytoskeleton organization (GO:0007010)|epidermal cell differentiation (GO:0009913)|germline cell cycle switching, mitotic to meiotic cell cycle (GO:0051729)|kidney development (GO:0001822)|mesoderm development (GO:0007498)|negative regulation of meiotic cell cycle phase transition (GO:1901994)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6				READ - Rectum adenocarcinoma(159;0.17)		ATGCTGAACCGCCACATGAAG	0.587																																					p.R135H		Atlas-SNP	.											.	OVOL1	15	.	0			c.G404A						.						127	94	105					11																	65562094		2201	4297	6498	SO:0001583	missense	5017	exon3			TGAACCGCCACAT	BC059408	CCDS8112.1	11q13	2013-10-17	2013-10-17		ENSG00000172818	ENSG00000172818		"Zinc fingers, C2H2-type"	8525	protein-coding gene	gene with protein product		602313	"ovo (Drosophila) homolog-like 1", "ovo-like 1(Drosophila)"			9383297	Standard	NM_004561		Approved	HOVO1	uc001ofp.3	O14753	OTTHUMG00000166600	ENST00000335987.3:c.404G>A	chr11.hg19:g.65562094G>A	ENSP00000337862:p.Arg135His	79.0	0.0		85.0	22.0	NM_004561	Q6PCB1	Missense_Mutation	SNP	ENST00000335987.3	hg19	CCDS8112.1	.	.	.	.	.	.	.	.	.	.	G	36	5.639352	0.96693	.	.	ENSG00000172818	ENST00000335987;ENST00000532448	T;T	0.26810	1.71;1.71	5.0	5.0	0.66597	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.081121	0.52532	D	0.000075	T	0.44582	0.1300	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.27773	-1.0064	10	0.48119	T	0.1	-37.3183	15.7757	0.78214	0.0:0.0:1.0:0.0	.	135	O14753	OVOL1_HUMAN	H	135;73	ENSP00000337862:R135H;ENSP00000434220:R73H	ENSP00000337862:R135H	R	+	2	0	OVOL1	65318670	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	9.780000	0.99024	2.313000	0.78055	0.561000	0.74099	CGC	.	.		0.587	OVOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390690.1	NM_004561		A	65562094	G	A	65562094	3	1	225	1	0	0	0	0	1	0	0	0	11335	1087	38	1	414	1	OVOL1	11	65562094	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	993858	65562094	69444422	41	31939										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103026161	103026161	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cttcctagggggactagtctAgagaaactactgtttggtga	12	7	1	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr11:103026161A>G	ENST00000375735.2	+	25	3819	c.3675A>G	c.(3673-3675)ctA>ctG	p.L1225L	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Silent_p.L1225L	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1225	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GGACTAGTCTAGAGAAACTAC	0.413																																					p.L1225L		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A3675G						.						83	82	82					11																	103026161		1831	4083	5914	SO:0001819	synonymous_variant	79659	exon25			TAGTCTAGAGAAA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.3675A>G	chr11.hg19:g.103026161A>G		119.0	0.0		134.0	28.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.413	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103026161	A	G	103026161	2	3	225	1	0	0	0	0	0	0	0	1	4848	407	15	2		2	DYNC2H1	11	103026161	Silent	SNP	A	TCGA-DD-AAVR-01A-11D-A40R-10	37464067	103026161	31980355	42	31940										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19427544	19427545	+	Frame_Shift_Ins	INS	-	-	A													0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	accagagatccaaaacaatcINSaaaaaaacaaggaaatgagc							TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr12:19427544_19427545insA	ENST00000299275.6	+	10	928_929	c.922_923insA	c.(922-924)caafs	p.Q308fs	PLEKHA5_ENST00000538714.1_Frame_Shift_Ins_p.Q308fs|PLEKHA5_ENST00000359180.3_Frame_Shift_Ins_p.Q308fs|PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000543806.1_Frame_Shift_Ins_p.Q200fs|PLEKHA5_ENST00000429027.2_Frame_Shift_Ins_p.Q314fs|PLEKHA5_ENST00000424268.1_Frame_Shift_Ins_p.Q200fs|PLEKHA5_ENST00000355397.3_Frame_Shift_Ins_p.Q308fs|PLEKHA5_ENST00000539256.1_Frame_Shift_Ins_p.Q66fs|PLEKHA5_ENST00000309364.4_Frame_Shift_Ins_p.Q308fs|PLEKHA5_ENST00000317589.4_Frame_Shift_Ins_p.Q308fs	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	308					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					CCAAAACAATCAAAAAAACAAG	0.327																																					p.Q314fs	Pancreas(196;329 2193 11246 14234 19524)	Atlas-INDEL	.											.,2	PLEKHA5	198	.	0			c.940_941insA						.																																			SO:0001589	frameshift_variant	54477	exon11			.	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.929dupA	chr12.hg19:g.19427551_19427551dupA	ENSP00000299275:p.Gln308fs	140.0	0.0		166.0	33.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Frame_Shift_Ins	INS	ENST00000299275.6	hg19	CCDS8682.1																																																																																			.	.		0.327	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		A	19427545	-	A	19427544	7	5	225	1	0	1	1	0	0	0	0	0	12068	827	29	0	960	0	PLEKHA5	12	19427544	Frame_Shift_Ins	INS	-	TCGA-DD-AAVR-01A-11D-A40R-10		19427544	114424351	43	31941										
ARID2	196528	hgsc.bcm.edu	37	chr12	46231303	46231303	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	atggaaattttgggaaatctTtgcaaagcagaagataatgg	11	3	1	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr12:46231303T>G	ENST00000334344.6	+	10	1315	c.1143T>G	c.(1141-1143)ctT>ctG	p.L381L	ARID2_ENST00000444670.1_Silent_p.L10L|ARID2_ENST00000422737.1_Silent_p.L232L|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	381					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TGGGAAATCTTTGCAAAGCAG	0.323			"N, S, F"		hepatocellular carcinoma																																p.L381L		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.T1143G						.						100	98	99					12																	46231303		2203	4300	6503	SO:0001819	synonymous_variant	196528	exon10			AAATCTTTGCAAA		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1143T>G	chr12.hg19:g.46231303T>G		105.0	0.0		112.0	26.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Silent	SNP	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.323	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		G	46231303	T	G	46231303	2	3	225	1	0	0	0	0	0	0	0	1	915	1828	64	5		5	ARID2	12	46231303	Silent	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	26803759	46231303	87620592	44	31942										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48376330	48376330	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ccagctgctcccctctcgccAggcattccctgaagacctgg	9	18	1	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr12:48376330A>C	ENST00000380518.3	-	34	2420	c.2256T>G	c.(2254-2256)ccT>ccG	p.P752P	COL2A1_ENST00000493991.1_5'UTR|COL2A1_ENST00000337299.6_Silent_p.P683P	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	752	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CCCTCTCGCCAGGCATTCCCT	0.627																																					p.P752P		Atlas-SNP	.											.	COL2A1	368	.	0			c.T2256G						.						36	37	37					12																	48376330		2203	4300	6503	SO:0001819	synonymous_variant	1280	exon34			CTCGCCAGGCATT	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.2256T>G	chr12.hg19:g.48376330A>C		94.0	0.0		66.0	18.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	hg19	CCDS41778.1																																																																																			.	.		0.627	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		C	48376330	A	C	48376330	2	2	225	1	0	0	0	0	0	0	0	1	3689	175	7	5		5	COL2A1	12	48376330	Silent	SNP	A	TCGA-DD-AAVR-01A-11D-A40R-10	2145027	48376330	85475565	45	31943										
CS	1431	hgsc.bcm.edu	37	chr12	56669864	56669864	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tggtgaaattgtgagaccagTccaggttagagtcaatggcc	13	7	1	3			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr12:56669864T>C	ENST00000351328.3	-	7	894	c.704A>G	c.(703-705)gAc>gGc	p.D235G	CS_ENST00000548567.1_Missense_Mutation_p.D169G|CS_ENST00000542324.2_Missense_Mutation_p.D222G	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	235					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		GTGAGACCAGTCCAGGTTAGA	0.483																																					p.D235G		Atlas-SNP	.											.	CS	44	.	0			c.A704G						.						157	129	139					12																	56669864		2203	4300	6503	SO:0001583	missense	1431	exon7			GACCAGTCCAGGT		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.704A>G	chr12.hg19:g.56669864T>C	ENSP00000342056:p.Asp235Gly	122.0	0.0		102.0	25.0	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Missense_Mutation	SNP	ENST00000351328.3	hg19	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.022699	0.93462	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000542324	.	.	.	5.41	5.41	0.78517	Citrate synthase-like, large alpha subdomain (1);Citrate synthase-like, core (1);	0.000000	0.85682	D	0.000000	D	0.83649	0.5300	M	0.88842	2.985	0.80722	D	1	D;D;D;D	0.65815	0.98;0.995;0.995;0.995	P;D;D;D	0.68943	0.897;0.961;0.93;0.961	D	0.87020	0.2128	9	0.87932	D	0	-23.7983	14.7325	0.69393	0.0:0.0:0.0:1.0	.	169;222;190;235	B7Z1E1;B4DJV2;B3KTN4;O75390	.;.;.;CISY_HUMAN	G	169;235;222	.	ENSP00000342056:D235G	D	-	2	0	CS	54956131	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.725000	0.84808	2.184000	0.69523	0.454000	0.30748	GAC	.	.		0.483	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077		C	56669864	T	C	56669864	3	2	225	1	0	0	0	0	1	0	0	0	3926	1667	58	2	716	2	CS	12	56669864	Missense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	8293534	56669864	77182031	46	31944										
METAP2	10988	hgsc.bcm.edu	37	chr12	95867960	95867960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cgctctctcgggcaacatggCgggtgtggaggaggtagcgg	19	9	1	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr12:95867960C>T	ENST00000323666.5	+	1	234	c.5C>T	c.(4-6)gCg>gTg	p.A2V	METAP2_ENST00000551840.1_Missense_Mutation_p.A2V|METAP2_ENST00000550777.1_Missense_Mutation_p.A2V|METAP2_ENST00000261220.9_Missense_Mutation_p.A2V|METAP2_ENST00000546753.1_Missense_Mutation_p.A2V	NM_006838.3	NP_006829.1			methionyl aminopeptidase 2											endometrium(3)|large_intestine(2)|lung(7)|prostate(1)	13						GGCAACATGGCGGGTGTGGAG	0.657																																					p.A2V		Atlas-SNP	.											.	METAP2	28	.	0			c.C5T						.						33	41	38					12																	95867960		2201	4297	6498	SO:0001583	missense	10988	exon1			ACATGGCGGGTGT	U13261	CCDS9052.1	12q22	2014-09-04			ENSG00000111142		3.4.11.18		16672	protein-coding gene	gene with protein product	"Peptidase M"	601870				7644482, 8858118	Standard	NM_006838		Approved	MNPEP, p67, MAP2	uc001tec.3	P50579	OTTHUMG00000170280	ENST00000323666.5:c.5C>T	chr12.hg19:g.95867960C>T	ENSP00000325312:p.Ala2Val	147.0	0.0		163.0	32.0	NM_006838		Missense_Mutation	SNP	ENST00000323666.5	hg19	CCDS9052.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.764262	0.89932	.	.	ENSG00000111142	ENST00000323666;ENST00000546753;ENST00000261220;ENST00000549502;ENST00000553151;ENST00000550777;ENST00000551840	.	.	.	5.19	4.28	0.50868	.	0.116232	0.56097	D	0.000022	T	0.50411	0.1614	N	0.08118	0	0.37963	D	0.93302	B;D;D;D;D	0.76494	0.064;0.976;0.999;0.999;0.999	B;D;D;D;D	0.71184	0.02;0.921;0.972;0.972;0.939	T	0.62358	-0.6871	9	0.87932	D	0	-2.6333	11.198	0.48724	0.1837:0.8163:0.0:0.0	.	2;2;2;2;2	B4DUX5;F8VRR3;G3XA91;F8VQZ7;P50579	.;.;.;.;AMPM2_HUMAN	V	2	.	ENSP00000261220:A2V	A	+	2	0	METAP2	94392091	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.704000	0.54815	1.279000	0.44446	0.561000	0.74099	GCG	.	.		0.657	METAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408296.1	NM_006838		T	95867960	C	T	95867960	3	4	225	1	0	0	0	0	1	0	0	0	9496	768	27	1	7	1	METAP2	12	95867960	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	39198096	95867960	37983935	47	31945										
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46563046	46563046	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ctctggggagacgacaaagaAtgtgaaggataaggagaggc	16	5	1	4			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr13:46563046A>G	ENST00000242848.4	-	9	1479	c.1131T>C	c.(1129-1131)caT>caC	p.H377H	ZC3H13_ENST00000282007.3_Silent_p.H377H			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	377	Arg/Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		ACGACAAAGAATGTGAAGGAT	0.483																																					p.H377H	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-SNP	.											.	ZC3H13	197	.	0			c.T1131C						.						151	133	139					13																	46563046		2203	4300	6503	SO:0001819	synonymous_variant	23091	exon9			CAAAGAATGTGAA	AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.1131T>C	chr13.hg19:g.46563046A>G		126.0	0.0		98.0	28.0	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Silent	SNP	ENST00000242848.4	hg19																																																																																				.	.		0.483	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		G	46563046	A	G	46563046	2	3	225	1	0	0	0	0	0	0	0	1	17580	98	4	2		2	ZC3H13	13	46563046	Silent	SNP	A	TCGA-DD-AAVR-01A-11D-A40R-10		46563046	68606832	48	31946										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99640931	99640931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cgtggagaagcgcaggctgcCgttctcggacgagtgctcgg	17	11	1	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr14:99640931C>T	ENST00000357195.3	-	4	2251	c.2242G>A	c.(2242-2244)Ggc>Agc	p.G748S	BCL11B_ENST00000443726.2_Missense_Mutation_p.G554S|BCL11B_ENST00000345514.2_Missense_Mutation_p.G677S	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	748					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		CGCAGGCTGCCGTTCTCGGAC	0.731			T	TLX3	T-ALL																																p.G748S		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	.	BCL11B	108	.	0			c.G2242A						.						10	10	10					14																	99640931		2119	4166	6285	SO:0001583	missense	64919	exon4			GGCTGCCGTTCTC	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.2242G>A	chr14.hg19:g.99640931C>T	ENSP00000349723:p.Gly748Ser	26.0	0.0		29.0	10.0	NM_138576	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	hg19	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.063502	0.76187	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.12984	2.65;2.67;2.63	4.25	4.25	0.50352	.	0.000000	0.64402	D	0.000019	T	0.36358	0.0964	M	0.68952	2.095	0.58432	D	0.999999	D;P	0.89917	1.0;0.705	D;B	0.97110	1.0;0.016	T	0.17198	-1.0377	10	0.51188	T	0.08	-17.2728	17.0216	0.86435	0.0:1.0:0.0:0.0	.	677;748	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	S	748;677;554	ENSP00000349723:G748S;ENSP00000280435:G677S;ENSP00000387419:G554S	ENSP00000280435:G677S	G	-	1	0	BCL11B	98710684	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.069000	0.76755	2.080000	0.62538	0.561000	0.74099	GGC	.	.		0.731	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		T	99640931	C	T	99640931	3	4	225	1	0	0	0	0	1	0	0	0	1364	652	23	1	446	1	BCL11B	14	99640931	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10		99640931	7708609	49	31947										
FURIN	5045	hgsc.bcm.edu	37	chr15	91423406	91423406	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	acatcactcggctggagcacGctcaggcgcggctcaccctg	12	16	3	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr15:91423406G>A	ENST00000268171.3	+	13	1738	c.1459G>A	c.(1459-1461)Gct>Act	p.A487T		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	487					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GCTGGAGCACGCTCAGGCGCG	0.672																																					p.A487T		Atlas-SNP	.											.	FURIN	85	.	0			c.G1459A						.						43	43	43					15																	91423406		2197	4297	6494	SO:0001583	missense	5045	exon13			GAGCACGCTCAGG	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1459G>A	chr15.hg19:g.91423406G>A	ENSP00000268171:p.Ala487Thr	105.0	0.0		82.0	19.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	hg19	CCDS10364.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.048084	0.75846	.	.	ENSG00000140564	ENST00000268171	T	0.63913	-0.07	4.65	3.73	0.42828	Proprotein convertase, P (1);Galactose-binding domain-like (1);	0.122566	0.56097	D	0.000023	T	0.48295	0.1492	N	0.19112	0.55	0.35797	D	0.822878	P	0.41748	0.761	B	0.40199	0.322	T	0.63528	-0.6617	10	0.87932	D	0	-3.5694	13.1447	0.59454	0.0779:0.0:0.9221:0.0	.	487	P09958	FURIN_HUMAN	T	487	ENSP00000268171:A487T	ENSP00000268171:A487T	A	+	1	0	FURIN	89224410	0.998000	0.40836	0.531000	0.27976	0.778000	0.44026	7.682000	0.84083	1.180000	0.42898	0.485000	0.47835	GCT	.	.		0.672	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		A	91423406	G	A	91423406	3	1	225	1	0	0	0	0	1	0	0	0	6107	1087	38	1	1505	1	FURIN	15	91423406	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10		91423406	11107986	50	31948										
GLIS2	84662	hgsc.bcm.edu	37	chr16	4386759	4386759	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cgtctgcccctacgagggctGcaacaagcgctattccaact	9	15	1	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr16:4386759G>A	ENST00000262366.3	+	8	1630	c.809G>A	c.(808-810)tGc>tAc	p.C270Y	GLIS2_ENST00000433375.1_Missense_Mutation_p.C270Y|RP11-295D4.1_ENST00000574705.1_RNA|PAM16_ENST00000577031.1_Intron			Q9BZE0	GLIS2_HUMAN	GLIS family zinc finger 2	270					cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(4)|endometrium(1)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	11						TACGAGGGCTGCAACAAGCGC	0.612																																					p.C270Y		Atlas-SNP	.											.	GLIS2	29	.	0			c.G809A						.						28	26	27					16																	4386759		2195	4293	6488	SO:0001583	missense	84662	exon6			AGGGCTGCAACAA	AF325914	CCDS10511.1	16p13.3	2013-01-08			ENSG00000126603	ENSG00000126603		"Zinc fingers, C2H2-type"	29450	protein-coding gene	gene with protein product	"nephrocystin-7"	608539				11741991, 14500813, 17618285	Standard	NM_032575		Approved	NPHP7	uc002cwc.1	Q9BZE0	OTTHUMG00000129467	ENST00000262366.3:c.809G>A	chr16.hg19:g.4386759G>A	ENSP00000262366:p.Cys270Tyr	116.0	0.0		93.0	6.0	NM_032575	B3KX84	Missense_Mutation	SNP	ENST00000262366.3	hg19	CCDS10511.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.799917	0.90538	.	.	ENSG00000126603	ENST00000262366;ENST00000433375	D;D	0.85861	-2.04;-2.04	5.97	5.97	0.96955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.050475	0.85682	D	0.000000	D	0.94748	0.8305	M	0.93328	3.405	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95307	0.8408	10	0.87932	D	0	.	19.1994	0.93704	0.0:0.0:1.0:0.0	.	270	Q9BZE0	GLIS2_HUMAN	Y	270	ENSP00000262366:C270Y;ENSP00000395547:C270Y	ENSP00000262366:C270Y	C	+	2	0	GLIS2	4326760	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.784000	0.99039	2.837000	0.97791	0.655000	0.94253	TGC	.	.		0.612	GLIS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251630.1	NM_032575		A	4386759	G	A	4386759	3	1	225	1	0	0	0	0	1	0	0	0	6454	1319	46	3	831	3	GLIS2	16	4386759	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10		4386759	85967994	51	31949										
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27709794	27709794	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	agggcgctcctcagcagaaaGgccgagcagccagccagccc	13	16	1	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr16:27709794G>A	ENST00000261588.4	+	9	1105	c.1086G>A	c.(1084-1086)aaG>aaA	p.K362K	CTD-2049O4.1_ENST00000564893.1_RNA|KIAA0556_ENST00000567894.1_3'UTR	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	362						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						TCAGCAGAAAGGCCGAGCAGC	0.642																																					p.K362K		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G1086A						.						26	27	27					16																	27709794		2197	4300	6497	SO:0001819	synonymous_variant	23247	exon9			CAGAAAGGCCGAG	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.1086G>A	chr16.hg19:g.27709794G>A		72.0	0.0		60.0	17.0	NM_015202	A7E2C2	Silent	SNP	ENST00000261588.4	hg19	CCDS32415.1																																																																																			.	.		0.642	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		A	27709794	G	A	27709794	2	1	225	1	0	0	0	0	0	0	0	1	8192	991	35	3		3	KIAA0556	16	27709794	Silent	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	23323035	27709794	62644959	52	31950										
SF3B3	23450	hgsc.bcm.edu	37	chr16	70605100	70605100	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gctcctactacttccctgtgAaggtaggttgggggaatctg	13	9	1	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr16:70605100A>T	ENST00000302516.5	+	25	3722	c.3511A>T	c.(3511-3513)Aag>Tag	p.K1171*		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	1171					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				CTTCCCTGTGAAGGTAGGTTG	0.552																																					p.K1171X		Atlas-SNP	.											.	SF3B3	99	.	0			c.A3511T						.						87	75	79					16																	70605100		2198	4300	6498	SO:0001587	stop_gained	23450	exon25			CCTGTGAAGGTAG	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.3511A>T	chr16.hg19:g.70605100A>T	ENSP00000305790:p.Lys1171*	68.0	0.0		66.0	34.0	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Nonsense_Mutation	SNP	ENST00000302516.5	hg19	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	A	43	10.271615	0.99372	.	.	ENSG00000189091	ENST00000302516	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1146	0.81295	1.0:0.0:0.0:0.0	.	.	.	.	X	1171	.	ENSP00000305790:K1171X	K	+	1	0	SF3B3	69162601	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	9.245000	0.95431	2.200000	0.70718	0.460000	0.39030	AAG	.	.		0.552	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		T	70605100	A	T	70605100	4	4	225	1	0	0	0	0	0	1	0	0	14167	247	9	4	3605	4	SF3B3	16	70605100	Nonsense_Mutation	SNP	A	TCGA-DD-AAVR-01A-11D-A40R-10	42895306	70605100	19749653	53	31951										
KIF1C	10749	hgsc.bcm.edu	37	chr17	4927022	4927022	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gggccggggcggggggctgcGcaggcccccagcccgctttg	20	15	0	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr17:4927022G>A	ENST00000320785.5	+	23	3245	c.2888G>A	c.(2887-2889)cGc>cAc	p.R963H		NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	963					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						GGGGGGCTGCGCAGGCCCCCA	0.697																																					p.R963H	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											.	KIF1C	70	.	0			c.G2888A						.						11	14	13					17																	4927022		2113	4145	6258	SO:0001583	missense	10749	exon23			GGCTGCGCAGGCC	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"Kinesins"	6317	protein-coding gene	gene with protein product		603060	"spastic ataxia 2 (autosomal recessive)"	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.2888G>A	chr17.hg19:g.4927022G>A	ENSP00000320821:p.Arg963His	104.0	0.0		82.0	4.0	NM_006612	D3DTL6|O75186|Q5U618	Missense_Mutation	SNP	ENST00000320785.5	hg19	CCDS11065.1	.	.	.	.	.	.	.	.	.	.	G	17.16	3.318031	0.60524	.	.	ENSG00000129250	ENST00000320785	T	0.73575	-0.76	4.93	4.93	0.64822	.	.	.	.	.	T	0.69513	0.3119	L	0.29908	0.895	0.35110	D	0.766065	D	0.65815	0.995	P	0.50082	0.63	T	0.77148	-0.2694	9	0.54805	T	0.06	.	11.3585	0.49630	0.0:0.1832:0.8168:0.0	.	963	O43896	KIF1C_HUMAN	H	963	ENSP00000320821:R963H	ENSP00000320821:R963H	R	+	2	0	KIF1C	4867746	0.995000	0.38212	1.000000	0.80357	0.964000	0.63967	1.903000	0.39858	2.558000	0.86282	0.655000	0.94253	CGC	.	.		0.697	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1			A	4927022	G	A	4927022	3	1	225	1	0	0	0	0	1	0	0	0	8294	1087	38	1	2970	1	KIF1C	17	4927022	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10		4927022	76268188	54	31952										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37876052	37876052	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	tcctgcagctgtgtggacctGgatgacaagggctgccccgc	14	13	0	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr17:37876052G>A	ENST00000269571.5	+	16	2070	c.1911G>A	c.(1909-1911)ctG>ctA	p.L637L	ERBB2_ENST00000541774.1_Silent_p.L622L|ERBB2_ENST00000445658.2_Silent_p.L361L|ERBB2_ENST00000584601.1_Silent_p.L607L|ERBB2_ENST00000406381.2_Silent_p.L607L|ERBB2_ENST00000540147.1_Silent_p.L607L|ERBB2_ENST00000584450.1_Silent_p.L637L			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	637					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GTGTGGACCTGGATGACAAGG	0.597		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.L637L		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	.	ERBB2	429	.	0			c.G1911A						.						174	142	153					17																	37876052		2203	4300	6503	SO:0001819	synonymous_variant	2064	exon16			GGACCTGGATGAC	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1911G>A	chr17.hg19:g.37876052G>A		97.0	0.0		180.0	43.0	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent	SNP	ENST00000269571.5	hg19	CCDS32642.1																																																																																			.	.		0.597	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			A	37876052	G	A	37876052	2	1	225	1	0	0	0	0	0	0	0	1	5208	1335	47	3		3	ERBB2	17	37876052	Silent	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	32949030	37876052	43319158	55	31953										
KRT10	3858	hgsc.bcm.edu	37	chr17	38975319	38975319	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gccggaactgccgccgtggcCgccgccgtggccgccgccgg	17	19	0	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr17:38975319C>T	ENST00000269576.5	-	7	1477	c.1468G>A	c.(1468-1470)Ggc>Agc	p.G490S	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ccgccgtggccgccgccgtgg	0.791																																					p.G490S		Atlas-SNP	.											.	KRT10	56	.	0			c.G1468A						.																																			SO:0001583	missense	3858	exon7			CGTGGCCGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1468G>A	chr17.hg19:g.38975319C>T	ENSP00000269576:p.Gly490Ser	34.0	0.0		96.0	18.0	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546565	0.86022	.	.	ENSG00000186395	ENST00000269576	D	0.96587	-4.06	4.38	4.38	0.52667	.	0.845686	0.09879	N	0.743932	D	0.94778	0.8314	N	0.08118	0	0.27860	N	0.940431	D	0.89917	1.0	D	0.76071	0.987	D	0.87790	0.2618	10	0.18710	T	0.47	.	12.7512	0.57310	0.0:1.0:0.0:0.0	.	490	P13645	K1C10_HUMAN	S	490	ENSP00000269576:G490S	ENSP00000269576:G490S	G	-	1	0	KRT10	36228845	0.019000	0.18553	0.876000	0.34364	0.184000	0.23303	0.448000	0.21726	2.739000	0.93911	0.603000	0.83216	GGC	.	.		0.791	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		T	38975319	C	T	38975319	3	4	225	1	0	0	0	0	1	0	0	0	8457	652	23	1	294	1	KRT10	17	38975319	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	1099267	38975319	42219891	56	31954										
RAB5C	5878	hgsc.bcm.edu	37	chr17	40277843	40277843	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cggctggctgggttgttctcCtggaggtccacacctcggtt	14	12	1	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr17:40277843C>T	ENST00000346213.4	-	6	821	c.609G>A	c.(607-609)caG>caA	p.Q203Q	CTD-2132N18.3_ENST00000592574.1_Intron|RAB5C_ENST00000393860.3_Silent_p.Q203Q|RAB5C_ENST00000547517.1_Silent_p.Q236Q	NM_004583.3	NP_004574.2	P51148	RAB5C_HUMAN	RAB5C, member RAS oncogene family	203					endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|plasma membrane to endosome transport (GO:0048227)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(4)|prostate(1)|skin(1)	7		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		GGTTGTTCTCCTGGAGGTCCA	0.617																																					p.Q236Q		Atlas-SNP	.											.	RAB5C	20	.	0			c.G708A						.						40	37	38					17																	40277843		2203	4300	6503	SO:0001819	synonymous_variant	5878	exon7			GTTCTCCTGGAGG	U18420	CCDS11419.1, CCDS58551.1	17q21.2	2013-02-15			ENSG00000108774	ENSG00000108774		"RAB, member RAS oncogene"	9785	protein-coding gene	gene with protein product	"RAB, member of RAS oncogene family-like", "RAB5C, member of RAS oncogene family"	604037		RABL		8646882	Standard	NM_004583		Approved	RAB5CL	uc010cxx.3	P51148	OTTHUMG00000169703	ENST00000346213.4:c.609G>A	chr17.hg19:g.40277843C>T		48.0	0.0		48.0	5.0	NM_001252039	F8W1H5|Q6FH55|Q9P0Y5	Silent	SNP	ENST00000346213.4	hg19	CCDS11419.1																																																																																			.	.		0.617	RAB5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405509.1	NM_004583		T	40277843	C	T	40277843	2	4	225	1	0	0	0	0	0	0	0	1	12965	680	24	3		3	RAB5C	17	40277843	Silent	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	1302524	40277843	40917367	57	31955										
NGFR	4804	hgsc.bcm.edu	37	chr17	47590143	47590143	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gaggtggagaagcttctcaaCggctctgcgggggacacctg	16	10	2	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr17:47590143C>T	ENST00000172229.3	+	6	1181	c.1056C>T	c.(1054-1056)aaC>aaT	p.N352N	NGFR_ENST00000504201.1_Silent_p.N258N|RP5-1029K10.2_ENST00000514506.1_RNA	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	352	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					AGCTTCTCAACGGCTCTGCGG	0.667																																					p.N352N		Atlas-SNP	.											.	NGFR	46	.	0			c.C1056T						.						56	62	60					17																	47590143		2202	4298	6500	SO:0001819	synonymous_variant	4804	exon6			TCTCAACGGCTCT	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"Tumor necrosis factor receptor superfamily", "CD molecules"	7809	protein-coding gene	gene with protein product	"low affinity nerve growth factor receptor", "TNFR superfamily, member 16"	162010	"nerve growth factor receptor (TNFR superfamily, member 16)"			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.1056C>T	chr17.hg19:g.47590143C>T		173.0	0.0		172.0	7.0	NM_002507	B2R961|B4E096	Silent	SNP	ENST00000172229.3	hg19	CCDS11549.1																																																																																			.	.		0.667	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1			T	47590143	C	T	47590143	2	4	225	1	0	0	0	0	0	0	0	1	10405	535	19	1		1	NGFR	17	47590143	Silent	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10	7312300	47590143	33605067	58	31956										
KLC3	147700	hgsc.bcm.edu	37	chr19	45848977	45848977	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cgggacagggcccggcagccGgcttggagatgctggaggaa	19	10	0	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr19:45848977G>A	ENST00000391946.2	+	2	280	c.178G>A	c.(178-180)Ggc>Agc	p.G60S	KLC3_ENST00000585434.1_Missense_Mutation_p.G60S|KLC3_ENST00000470402.1_Missense_Mutation_p.G74S	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	60					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		CCCGGCAGCCGGCTTGGAGAT	0.721																																					p.G60S		Atlas-SNP	.											.	KLC3	37	.	0			c.G178A						.						5	8	7					19																	45848977		1841	3919	5760	SO:0001583	missense	147700	exon2			GCAGCCGGCTTGG	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"Tetratricopeptide (TTC) repeat domain containing"	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.178G>A	chr19.hg19:g.45848977G>A	ENSP00000375810:p.Gly60Ser	122.0	0.0		141.0	6.0	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Missense_Mutation	SNP	ENST00000391946.2	hg19	CCDS12660.2	.	.	.	.	.	.	.	.	.	.	G	1.204	-0.631672	0.03584	.	.	ENSG00000104892	ENST00000391946;ENST00000470402	D;D	0.82433	-1.6;-1.61	3.4	1.22	0.21188	.	0.651119	0.13625	N	0.374157	T	0.66577	0.2803	N	0.14661	0.345	0.09310	N	1	B;B;B	0.18013	0.01;0.025;0.014	B;B;B	0.12837	0.008;0.008;0.004	T	0.54159	-0.8335	10	0.38643	T	0.18	-23.0123	7.3856	0.26880	0.2277:0.0:0.7723:0.0	.	60;74;60	Q6P597-2;Q6P597-3;Q6P597	.;.;KLC3_HUMAN	S	60;74	ENSP00000375810:G60S;ENSP00000436019:G74S	ENSP00000375810:G60S	G	+	1	0	KLC3	50540817	0.950000	0.32346	0.006000	0.13384	0.098000	0.18820	2.903000	0.48711	0.280000	0.22209	-0.643000	0.03959	GGC	.	.		0.721	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275		A	45848977	G	A	45848977	3	1	225	1	0	0	0	0	1	0	0	0	8344	1116	39	1	180	1	KLC3	19	45848977	Missense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10		45848977	13280006	59	31957										
RIN2	54453	hgsc.bcm.edu	37	chr20	19955803	19955803	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ggcggtgcaaagaccttgagCggcggccggccgggcgcagg	20	12	0	2	rs370646119		TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr20:19955803C>T	ENST00000255006.6	+	8	1430	c.1281C>T	c.(1279-1281)agC>agT	p.S427S	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Intron	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	378					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						AGACCTTGAGCGGCGGCCGGC	0.692																																					p.S427S		Atlas-SNP	.											.	RIN2	126	.	0			c.C1281T						.	C	,	2,3680		0,2,1839	29	31	30		1281,1134	0.1	0.1	20		30	0,8156		0,0,4078	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	0,2,5917	TT,TC,CC		0.0,0.0543,0.0169	,	427/945,378/896	19955803	2,11836	1841	4078	5919	SO:0001819	synonymous_variant	54453	exon8			CTTGAGCGGCGGC	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.1281C>T	chr20.hg19:g.19955803C>T		728.0	0.0		675.0	47.0	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	hg19	CCDS56182.1																																																																																			.	.		0.692	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			T	19955803	C	T	19955803	2	4	225	1	0	0	0	0	0	0	0	1	13387	767	27	1		1	RIN2	20	19955803	Silent	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10		19955803	43069717	60	31958										
PCIF1	63935	hgsc.bcm.edu	37	chr20	44571777	44571777	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ctttcaaccgctggatgctgGagcgcaaggtggtagacaaa	13	9	1	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr20:44571777G>T	ENST00000372409.3	+	8	1079	c.715G>T	c.(715-717)Gag>Tag	p.E239*		NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	239					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						CTGGATGCTGGAGCGCAAGGT	0.537																																					p.E239X		Atlas-SNP	.											.	PCIF1	51	.	0			c.G715T						.						77	60	66					20																	44571777		2203	4300	6503	SO:0001587	stop_gained	63935	exon8			ATGCTGGAGCGCA	AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 121"		"chromosome 20 open reading frame 67"	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.715G>T	chr20.hg19:g.44571777G>T	ENSP00000361486:p.Glu239*	63.0	0.0		51.0	16.0	NM_022104	E1P5P1|Q54AB9|Q9NT85	Nonsense_Mutation	SNP	ENST00000372409.3	hg19	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	G	40	7.972069	0.98588	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-21.579	17.4916	0.87705	0.0:0.0:1.0:0.0	.	.	.	.	X	239	.	ENSP00000361486:E239X	E	+	1	0	PCIF1	44005184	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.519000	0.98025	2.606000	0.88127	0.655000	0.94253	GAG	.	.		0.537	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104		T	44571777	G	T	44571777	4	4	225	1	0	0	0	0	0	1	0	0	11589	1175	41	3	737	3	PCIF1	20	44571777	Nonsense_Mutation	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	24615974	44571777	18453743	61	31959										
ZBTB46	140685	hgsc.bcm.edu	37	chr20	62421975	62421975	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gctgcccagcaggacgttctTgtgcgccttgaagaccttgc	12	13	1	2			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr20:62421975T>C	ENST00000245663.4	-	2	286	c.136A>G	c.(136-138)Aag>Gag	p.K46E	ZBTB46_ENST00000480766.1_5'Flank|ZBTB46_ENST00000302995.2_Missense_Mutation_p.K46E|ZBTB46_ENST00000395104.1_Missense_Mutation_p.K46E	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	46	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					AGGACGTTCTTGTGCGCCTTG	0.642																																					p.K46E		Atlas-SNP	.											.	ZBTB46	72	.	0			c.A136G						.						70	57	62					20																	62421975		2203	4300	6503	SO:0001583	missense	140685	exon2			CGTTCTTGTGCGC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.136A>G	chr20.hg19:g.62421975T>C	ENSP00000245663:p.Lys46Glu	33.0	0.0		41.0	8.0	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Missense_Mutation	SNP	ENST00000245663.4	hg19	CCDS13538.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.066925	0.76301	.	.	ENSG00000130584	ENST00000245663;ENST00000302995;ENST00000395104	T;T;T	0.78924	-1.22;-1.22;-1.22	5.77	5.77	0.91146	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.052838	0.64402	D	0.000001	D	0.90672	0.7074	M	0.92738	3.34	0.44843	D	0.997857	D	0.89917	1.0	D	0.91635	0.999	D	0.92793	0.6250	10	0.87932	D	0	.	15.2702	0.73696	0.0:0.0:0.0:1.0	.	46	Q86UZ6	ZBT46_HUMAN	E	46	ENSP00000245663:K46E;ENSP00000303102:K46E;ENSP00000378536:K46E	ENSP00000245663:K46E	K	-	1	0	ZBTB46	61892419	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	4.944000	0.63561	2.205000	0.71048	0.533000	0.62120	AAG	.	.		0.642	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		C	62421975	T	C	62421975	3	2	225	1	0	0	0	0	1	0	0	0	17562	1821	63	2	1649	2	ZBTB46	20	62421975	Missense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	17850198	62421975	603545	62	31960										
RWDD2B	10069	hgsc.bcm.edu	37	chr21	30380106	30380106	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	accagaattcttcacaggcaCtttgtgggccttccacacaa	7	13	2	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr21:30380106C>G	ENST00000493196.1	-	4	801	c.701G>C	c.(700-702)aGt>aCt	p.S234T	RWDD2B_ENST00000486719.1_5'UTR	NM_016940.2	NP_058636.1	P57060	RWD2B_HUMAN	RWD domain containing 2B	234										endometrium(1)|kidney(1)|large_intestine(8)|lung(2)	12						TTCACAGGCACTTTGTGGGCC	0.408																																					p.S234T		Atlas-SNP	.											.	RWDD2B	24	.	0			c.G701C						.						75	77	76					21																	30380106		2203	4300	6503	SO:0001583	missense	10069	exon4			CAGGCACTTTGTG	AF212232	CCDS13582.1	21q22.11	2012-12-07	2007-07-17	2007-07-17	ENSG00000156253	ENSG00000156253			1302	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 6"	C21orf6		10729227	Standard	NM_016940		Approved	GL011	uc002yms.3	P57060	OTTHUMG00000078805	ENST00000493196.1:c.701G>C	chr21.hg19:g.30380106C>G	ENSP00000418693:p.Ser234Thr	52.0	0.0		54.0	14.0	NM_016940		Missense_Mutation	SNP	ENST00000493196.1	hg19	CCDS13582.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650602	0.67472	.	.	ENSG00000156253	ENST00000493196	.	.	.	5.65	4.77	0.60923	Domain of unknown function DUF1115 (1);	0.232469	0.52532	D	0.000066	T	0.52661	0.1748	L	0.39326	1.205	0.37913	D	0.931429	B;P	0.47484	0.098;0.896	B;P	0.53224	0.076;0.721	T	0.52808	-0.8526	9	0.22109	T	0.4	-8.6106	10.9956	0.47573	0.0:0.8588:0.0:0.1412	.	234;234	Q53FD2;P57060	.;RWD2B_HUMAN	T	234	.	ENSP00000418693:S234T	S	-	2	0	RWDD2B	29301977	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.022000	0.41030	1.626000	0.50381	0.655000	0.94253	AGT	.	.		0.408	RWDD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171858.1			G	30380106	C	G	30380106	3	3	225	1	0	0	0	0	1	0	0	0	13771	565	20	4	266	4	RWDD2B	21	30380106	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10		30380106	17749789	63	31961										
C22orf33	339669	hgsc.bcm.edu	37	chr22	37395926	37395926	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	gtagccgaggtcatagtagtCtgagaagacggaggagattt	15	5	2	3			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr22:37395926C>T	ENST00000405091.2	-	5	840	c.589G>A	c.(589-591)Gac>Aac	p.D197N	TEX33_ENST00000381821.1_Missense_Mutation_p.D197N|TEX33_ENST00000402860.3_Missense_Mutation_p.D112N			O43247	TEX33_HUMAN	testis expressed 33	197																	TCATAGTAGTCTGAGAAGACG	0.537																																					p.D197N		Atlas-SNP	.											.	TEX33	25	.	0			c.G589A						.						131	122	125					22																	37395926		2203	4300	6503	SO:0001583	missense	339669	exon4			AGTAGTCTGAGAA	BC042635	CCDS13937.1, CCDS54524.1	22q12.3	2013-10-11	2012-02-16	2012-02-16	ENSG00000185264	ENSG00000185264			28568	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 33"	C22orf33		22332119	Standard	NM_178552		Approved	MGC35206, EAN57	uc003aqf.3	O43247	OTTHUMG00000150531	ENST00000405091.2:c.589G>A	chr22.hg19:g.37395926C>T	ENSP00000386118:p.Asp197Asn	53.0	0.0		43.0	7.0	NM_001163857	B1AH46|Q6ICF2|Q8IVQ2|Q9Y4V8	Missense_Mutation	SNP	ENST00000405091.2	hg19	CCDS54524.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.93|11.93	1.786867|1.786867	0.31593|0.31593	.|.	.|.	ENSG00000185264|ENSG00000185264	ENST00000402860;ENST00000405091;ENST00000381821|ENST00000442538	.|.	.|.	.|.	4.86|4.86	4.86|4.86	0.63082|0.63082	.|.	0.329651|.	0.25458|.	N|.	0.030540|.	T|T	0.63745|0.63745	0.2537|0.2537	M|M	0.69823|0.69823	2.125|2.125	0.32343|0.32343	N|N	0.559505|0.559505	D|.	0.57257|.	0.979|.	P|.	0.56563|.	0.801|.	T|T	0.71397|0.71397	-0.4605|-0.4605	9|5	0.37606|.	T|.	0.19|.	-13.7082|-13.7082	13.5338|13.5338	0.61638|0.61638	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	197|.	O43247|.	EAN57_HUMAN|.	N|K	112;197;197|55	.|.	ENSP00000371243:D197N|.	D|R	-|-	1|2	0|0	C22orf33|C22orf33	35725872|35725872	0.992000|0.992000	0.36948|0.36948	0.991000|0.991000	0.47740|0.47740	0.144000|0.144000	0.21451|0.21451	3.828000|3.828000	0.55753|0.55753	2.261000|2.261000	0.74972|0.74972	0.558000|0.558000	0.71614|0.71614	GAC|AGA	.	.		0.537	TEX33-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318778.2	NM_178552		T	37395926	C	T	37395926	3	4	225	1	0	0	0	0	1	0	0	0	2147	913	32	3	265	3	C22orf33	22	37395926	Missense_Mutation	SNP	C	TCGA-DD-AAVR-01A-11D-A40R-10		37395926	13908640	64	31962										
SBF1	6305	hgsc.bcm.edu	37	chr22	50893272	50893272	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ctcgggcgcatacatgtaatTgtggaacacaggcgtcctct	11	11	1	0			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chr22:50893272T>A	ENST00000390679.3	-	34	4889	c.4705A>T	c.(4705-4707)Aat>Tat	p.N1569Y	SBF1_ENST00000348911.6_Missense_Mutation_p.N1570Y|SBF1_ENST00000380817.3_Missense_Mutation_p.N1595Y|SBF1_ENST00000476293.1_5'Flank			O95248	MTMR5_HUMAN	SET binding factor 1	1569	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		TACATGTAATTGTGGAACACA	0.642																																					p.N1595Y		Atlas-SNP	.											.	SBF1	211	.	0			c.A4783T						.						44	50	48					22																	50893272		2072	4195	6267	SO:0001583	missense	6305	exon35			TGTAATTGTGGAA	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.4705A>T	chr22.hg19:g.50893272T>A	ENSP00000375097:p.Asn1569Tyr	64.0	0.0		44.0	17.0	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.47|17.47	3.398530|3.398530	0.62177|0.62177	.|.	.|.	ENSG00000100241|ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000337034;ENST00000390679|ENST00000418590	D;D;D|.	0.94537|.	-3.45;-3.45;-3.45|.	3.74|3.74	3.74|3.74	0.42951|0.42951	Myotubularin phosphatase domain (1);|.	0.054068|.	0.64402|.	D|.	0.000001|.	D|D	0.86239|0.86239	0.5885|0.5885	H|H	0.96518|0.96518	3.835|3.835	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.998;0.998;0.999|.	D|D	0.90033|0.90033	0.4136|0.4136	10|5	0.87932|.	D|.	0|.	.|.	12.5669|12.5669	0.56314|0.56314	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1569;1595;128|.	O95248;O95248-4;A6PVG7|.	MTMR5_HUMAN;.;.|.	Y|L	1595;1570;1605;1569|128	ENSP00000370196:N1595Y;ENSP00000252027:N1570Y;ENSP00000375097:N1569Y|.	ENSP00000336522:N1605Y|.	N|Q	-|-	1|2	0|0	SBF1|SBF1	49240138|49240138	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.481000|0.481000	0.33189|0.33189	7.466000|7.466000	0.80914|0.80914	1.701000|1.701000	0.51217|0.51217	0.379000|0.379000	0.24179|0.24179	AAT|CAA	.	.		0.642	SBF1-201	KNOWN	basic	protein_coding	protein_coding				A	50893272	T	A	50893272	3	1	225	1	0	0	0	0	1	0	0	0	13873	1812	63	4	926	4	SBF1	22	50893272	Missense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	13497346	50893272	411294	65	31963										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12701706	12701706	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	atcatcaacggccaagtgtcGgtgagtttacagtcacctgc	10	11	3	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chrX:12701706G>A	ENST00000380682.1	+	6	1079	c.573G>A	c.(571-573)tcG>tcA	p.S191S		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	191					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.S191S(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						GCCAAGTGTCGGTGAGTTTAC	0.448																																					p.S191S		Atlas-SNP	.											.	FRMPD4	214	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G573A						.						96	73	81					X																	12701706		2203	4300	6503	SO:0001630	splice_region_variant	9758	exon6			AGTGTCGGTGAGT	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.573+1G>A	chrX.hg19:g.12701706G>A		116.0	0.0		101.0	49.0	NM_014728	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	hg19	CCDS35201.1																																																																																			.	.		0.448	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712	Silent	A	12701706	G	A	12701706	5	1	225	1	0	0	0	0	0	0	1	0	6067	1130	39	1	595	1	FRMPD4	23	12701706	Splice_Site	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10		12701706	142568854	66	31964										
MED14	9282	hgsc.bcm.edu	37	chrX	40526016	40526016	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ctggtcctattgagattccaTgcgaggatgggggaggagtt	16	6	0	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chrX:40526016T>C	ENST00000324817.1	-	24	3339	c.3221A>G	c.(3220-3222)cAt>cGt	p.H1074R		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	1074	Pro-rich.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGAGATTCCATGCGAGGATGG	0.473																																					p.H1074R		Atlas-SNP	.											.	MED14	108	.	0			c.A3221G						.						46	39	41					X																	40526016		2203	4300	6503	SO:0001583	missense	9282	exon24			ATTCCATGCGAGG	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.3221A>G	chrX.hg19:g.40526016T>C	ENSP00000323720:p.His1074Arg	183.0	0.0		161.0	72.0	NM_004229	Q4KMR7|Q9UNB3	Missense_Mutation	SNP	ENST00000324817.1	hg19	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	T	12.30	1.895970	0.33442	.	.	ENSG00000180182	ENST00000324817	.	.	.	5.75	5.75	0.90469	.	0.056936	0.64402	D	0.000001	T	0.33760	0.0874	N	0.14661	0.345	0.37914	D	0.931453	B	0.22604	0.072	B	0.25884	0.064	T	0.31530	-0.9940	9	0.25106	T	0.35	.	8.8488	0.35188	0.3082:0.0:0.0:0.6918	.	1074	O60244	MED14_HUMAN	R	1074	.	ENSP00000323720:H1074R	H	-	2	0	MED14	40410960	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.288000	0.72679	1.931000	0.55961	0.402000	0.26972	CAT	.	.		0.473	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		C	40526016	T	C	40526016	3	2	225	1	0	0	0	0	1	0	0	0	9441	1464	51	2	1175	2	MED14	23	40526016	Missense_Mutation	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	27824310	40526016	114744544	67	31965										
FGF16	8823	hgsc.bcm.edu	37	chrX	76711987	76711987	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	cttctaagttgccctccatgTccagagacctctttcactat	5	14	3	1			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chrX:76711987T>C	ENST00000439435.1	+	2	324	c.324T>C	c.(322-324)tgT>tgC	p.C108C				O43320	FGF16_HUMAN	fibroblast growth factor 16	0					cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of brown fat cell proliferation (GO:0070349)|response to temperature stimulus (GO:0009266)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(1)|breast(1)|lung(2)	4						GCCCTCCATGTCCAGAGACCT	0.502																																					p.S109P		Atlas-SNP	.											.	FGF16	16	.	0			c.T325C						.						111	106	107					X																	76711987		1900	4107	6007	SO:0001819	synonymous_variant	8823	exon2			TCCATGTCCAGAG	AB009391	CCDS75996.1	Xq21.1	2014-01-31			ENSG00000196468	ENSG00000196468			3672	protein-coding gene	gene with protein product		300827	"metacarpal 4-5 fusion"	MF4		9473496, 11474196, 23709756	Standard	NM_003868		Approved		uc011mqp.2	O43320	OTTHUMG00000013133	ENST00000439435.1:c.324T>C	chrX.hg19:g.76711987T>C		114.0	0.0		100.0	41.0	NM_003868		Missense_Mutation	SNP	ENST00000439435.1	hg19																																																																																				.	.		0.502	FGF16-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000036814.1	NM_003868		C	76711987	T	C	76711987	2	2	225	1	0	0	0	0	0	0	0	1	5852	1667	58	2		2	FGF16	23	76711987	Silent	SNP	T	TCGA-DD-AAVR-01A-11D-A40R-10	36185971	76711987	78558573	68	31966										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83126541	83126541	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	actccagagaggtacaaatgAtaaatcaagacctttgaaat	7	7	1	4			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chrX:83126541A>T	ENST00000329312.4	+	3	177	c.140A>T	c.(139-141)gAt>gTt	p.D47V		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	47					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						GGTACAAATGATAAATCAAGA	0.294																																					p.D47V		Atlas-SNP	.											.	CYLC1	272	.	0			c.A140T						.						66	60	62					X																	83126541		2203	4296	6499	SO:0001583	missense	1538	exon3			CAAATGATAAATC	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.140A>T	chrX.hg19:g.83126541A>T	ENSP00000331556:p.Asp47Val	372.0	1.0		388.0	190.0	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	hg19	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	a	2.791	-0.251370	0.05867	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.42900	0.96	4.59	2.2	0.27929	.	.	.	.	.	T	0.25494	0.0620	N	0.22421	0.69	0.09310	N	1	B;B	0.25169	0.119;0.119	B;B	0.21917	0.037;0.037	T	0.21759	-1.0236	9	0.62326	D	0.03	0.4273	3.5805	0.07950	0.652:0.229:0.119:0.0	.	47;47	P35663;F5H4V5	CYLC1_HUMAN;.	V	47	ENSP00000331556:D47V	ENSP00000331556:D47V	D	+	2	0	CYLC1	83013197	0.010000	0.17322	0.057000	0.19452	0.001000	0.01503	0.175000	0.16762	0.683000	0.31428	0.486000	0.48141	GAT	.	.		0.294	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		T	83126541	A	T	83126541	3	4	225	1	0	0	0	0	1	0	0	0	4143	333	12	4	150	4	CYLC1	23	83126541	Missense_Mutation	SNP	A	TCGA-DD-AAVR-01A-11D-A40R-10	6414554	83126541	72144019	69	31967										
RAB39B	116442	hgsc.bcm.edu	37	chrX	154493379	154493379	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.482870071105365	0	0.529599432825239	0.333333333333333	1	0	ctgaacctctcttgacccgcGgtatcccagatctggagctt	9	14	2	3			TCGA-DD-AAVR-01A-11D-A40R-10	TCGA-DD-AAVR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de2cbef6-7b85-4ffc-b131-32615e787573	c5cdd91e-522e-444f-9a7e-81c5d13d1a33	g.chrX:154493379G>A	ENST00000369454.3	-	1	495	c.195C>T	c.(193-195)acC>acT	p.T65T		NM_171998.2	NP_741995.1	Q96DA2	RB39B_HUMAN	RAB39B, member RAS oncogene family	65					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|synapse organization (GO:0050808)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)			breast(1)|central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(12)	19	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CTTGACCCGCGGTATCCCAGA	0.617																																					p.T65T		Atlas-SNP	.											.	RAB39B	37	.	0			c.C195T						.						74	60	65					X																	154493379		2203	4300	6503	SO:0001819	synonymous_variant	116442	exon1			ACCCGCGGTATCC	AY052478	CCDS14766.1	Xq28	2014-01-31			ENSG00000155961	ENSG00000155961		"RAB, member RAS oncogene"	16499	protein-coding gene	gene with protein product		300774	"mental retardation, X-linked 72"	MRX72		12438742, 20159109	Standard	NM_171998		Approved		uc004fne.3	Q96DA2	OTTHUMG00000022659	ENST00000369454.3:c.195C>T	chrX.hg19:g.154493379G>A		61.0	0.0		64.0	30.0	NM_171998	Q5JT79|Q8NEX3	Silent	SNP	ENST00000369454.3	hg19	CCDS14766.1																																																																																			.	.		0.617	RAB39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058792.1	NM_171998		A	154493379	G	A	154493379	2	1	225	1	0	0	0	0	0	0	0	1	12945	1103	39	1		1	RAB39B	23	154493379	Silent	SNP	G	TCGA-DD-AAVR-01A-11D-A40R-10	71366838	154493379	777181	70	31968										
HEYL	26508	hgsc.bcm.edu	37	chr1	40092821	40092821	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	cgaaaaccaatgctccggaaGtcaactgccagggctcgggc	12	13	1	0			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr1:40092821G>T	ENST00000372852.3	-	5	664	c.345C>A	c.(343-345)gaC>gaA	p.D115E	HEYL_ENST00000535435.1_Missense_Mutation_p.D87E	NM_014571.3	NP_055386	Q9NQ87	HEYL_HUMAN	hes-related family bHLH transcription factor with YRPW motif-like	115					atrioventricular valve morphogenesis (GO:0003181)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to BMP stimulus (GO:0071773)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|glomerulus development (GO:0032835)|mesenchymal cell development (GO:0014031)|negative regulation of androgen receptor activity (GO:2000824)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|pulmonary valve morphogenesis (GO:0003184)|skeletal muscle cell differentiation (GO:0035914)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-1 domain binding (GO:0050683)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	7	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.1e-18)|Epithelial(16;2.77e-17)|all cancers(16;5.64e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TGCTCCGGAAGTCAACTGCCA	0.607																																					p.D115E		Atlas-SNP	.											.	HEYL	27	.	0			c.C345A						.						27	29	29					1																	40092821		2201	4299	6500	SO:0001583	missense	26508	exon5			CCGGAAGTCAACT	BC006087	CCDS439.1	1p34.3	2013-10-17	2013-10-17		ENSG00000163909	ENSG00000163909		"Basic helix-loop-helix proteins"	4882	protein-coding gene	gene with protein product	"hairy/enhancer-of-split related with YRPW motif 3"	609034	"hairy/enhancer-of-split related with YRPW motif-like"			10415358, 10860664	Standard	NM_014571		Approved	bHLHb33, HEY3, HESR3	uc001cdp.3	Q9NQ87	OTTHUMG00000000458	ENST00000372852.3:c.345C>A	chr1.hg19:g.40092821G>T	ENSP00000361943:p.Asp115Glu	161.0	0.0		85.0	53.0	NM_014571	Q5TG99	Missense_Mutation	SNP	ENST00000372852.3	hg19	CCDS439.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.981283	0.74474	.	.	ENSG00000163909	ENST00000372852;ENST00000535435	T;T	0.43688	0.94;0.94	5.19	3.31	0.37934	Orange subgroup (1);	0.000000	0.85682	D	0.000000	T	0.63604	0.2525	M	0.82517	2.595	0.54753	D	0.999985	D	0.89917	1.0	D	0.97110	1.0	T	0.67364	-0.5689	10	0.87932	D	0	-1.0564	9.7227	0.40313	0.229:0.0:0.771:0.0	.	115	Q9NQ87	HEYL_HUMAN	E	115;87	ENSP00000361943:D115E;ENSP00000439071:D87E	ENSP00000361943:D115E	D	-	3	2	HEYL	39865408	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.445000	0.35079	1.192000	0.43071	0.462000	0.41574	GAC	.	.		0.607	HEYL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001179.2	NM_014571		T	40092821	G	T	40092821	3	4	226	1	0	0	0	0	1	0	0	0	7089	1020	36	3	645	3	HEYL	1	40092821	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10		40092821	209157800	1	31969										
SV2A	9900	hgsc.bcm.edu	37	chr1	149885087	149885087	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ttgcccccagactctgcccgGggaatgccctgatattcccc	9	17	1	2			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr1:149885087G>A	ENST00000369146.3	-	2	796	c.306C>T	c.(304-306)ccC>ccT	p.P102P	SV2A_ENST00000369145.1_Silent_p.P102P	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	102					cellular calcium ion homeostasis (GO:0006874)|neurotransmitter transport (GO:0006836)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane transporter activity (GO:0022857)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	ACTCTGCCCGGGGAATGCCCT	0.627																																					p.P102P		Atlas-SNP	.											.	SV2A	123	.	0			c.C306T						.						108	107	107					1																	149885087		2203	4300	6503	SO:0001819	synonymous_variant	9900	exon2			TGCCCGGGGAATG	AB018279	CCDS940.1	1q21.2	2008-02-05			ENSG00000159164	ENSG00000159164			20566	protein-coding gene	gene with protein product		185860				7681585, 10611374	Standard	NM_014849		Approved	SV2, KIAA0736	uc001etg.3	Q7L0J3	OTTHUMG00000012209	ENST00000369146.3:c.306C>T	chr1.hg19:g.149885087G>A		98.0	0.0		131.0	75.0	NM_014849	D3DUZ7|O94841|Q5QNX8|Q7Z3L6|Q8NBJ6|Q9BVZ9	Silent	SNP	ENST00000369146.3	hg19	CCDS940.1																																																																																			.	.		0.627	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1			A	149885087	G	A	149885087	2	1	226	1	0	0	0	0	0	0	0	1	15432	1219	43	3		3	SV2A	1	149885087	Silent	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	109792266	149885087	99365534	2	31970										
SNX27	81609	hgsc.bcm.edu	37	chr1	151665429	151665429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gggatgagatgcagcgatggGacacagatgaagaagggatg	18	4	0	4			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr1:151665429G>A	ENST00000458013.2	+	10	1552	c.1432G>A	c.(1432-1434)Gac>Aac	p.D478N	SNX27_ENST00000368838.1_Missense_Mutation_p.D385N|SNX27_ENST00000368843.3_Missense_Mutation_p.D478N			Q96L92	SNX27_HUMAN	sorting nexin family member 27	478	FERM-like region F3.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|establishment of natural killer cell polarity (GO:0001770)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to plasma membrane (GO:1990126)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(1)|large_intestine(2)|ovary(2)	5	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCAGCGATGGGACACAGATGA	0.473																																					p.D478N	Colon(46;291 966 40145 41237 41888)	Atlas-SNP	.											.	SNX27	44	.	0			c.G1432A						.						140	139	139					1																	151665429		2203	4300	6503	SO:0001583	missense	81609	exon10			CGATGGGACACAG	AB007957	CCDS1001.1	1q21.3	2008-03-11			ENSG00000143376	ENSG00000143376		"Sorting nexins"	20073	protein-coding gene	gene with protein product		611541				12461558	Standard	XM_005245509		Approved	MY014, KIAA0488, MGC20471	uc001eyn.1	Q96L92	OTTHUMG00000013052	ENST00000458013.2:c.1432G>A	chr1.hg19:g.151665429G>A	ENSP00000400333:p.Asp478Asn	173.0	0.0		236.0	63.0	NM_030918	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	Missense_Mutation	SNP	ENST00000458013.2	hg19		.	.	.	.	.	.	.	.	.	.	G	28.0	4.882795	0.91740	.	.	ENSG00000143376	ENST00000458013;ENST00000368843;ENST00000368838	D;D;D	0.92699	-3.09;-3.09;-3.09	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.87653	0.6231	L	0.51422	1.61	0.80722	D	1	P;P	0.49862	0.757;0.929	B;B	0.42827	0.225;0.399	D	0.87512	0.2440	10	0.39692	T	0.17	.	16.7243	0.85417	0.0:0.0:1.0:0.0	.	478;478	Q96L92;Q96L92-3	SNX27_HUMAN;.	N	478;478;385	ENSP00000400333:D478N;ENSP00000357836:D478N;ENSP00000357831:D385N	ENSP00000357831:D385N	D	+	1	0	SNX27	149932053	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.970000	0.93415	2.726000	0.93360	0.563000	0.77884	GAC	.	.		0.473	SNX27-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000036624.3	NM_030918		A	151665429	G	A	151665429	3	1	226	1	0	0	0	0	1	0	0	0	14912	1174	41	3	1470	3	SNX27	1	151665429	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	1780342	151665429	97585192	3	31971										
HSD11B1	3290	hgsc.bcm.edu	37	chr1	209879256	209879256	+	Frame_Shift_Del	DEL	G	G	-													0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	atgggagcccatgtggtggtGacagcgaggtcaaaagaaac							TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr1:209879256delG	ENST00000367028.2	+	3	358	c.189delG	c.(187-189)gtgfs	p.V63fs	RP1-28O10.1_ENST00000441672.1_RNA|HSD11B1_ENST00000261465.1_Frame_Shift_Del_p.V63fs|HSD11B1_ENST00000367027.3_Frame_Shift_Del_p.V63fs	NM_001206741.1	NP_001193670.1	P28845	DHI1_HUMAN	hydroxysteroid (11-beta) dehydrogenase 1	63					glucocorticoid biosynthetic process (GO:0006704)|lung development (GO:0030324)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	11-beta-hydroxysteroid dehydrogenase (NADP+) activity (GO:0070524)|11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity (GO:0003845)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	16				OV - Ovarian serous cystadenocarcinoma(81;1.04e-55)|Epithelial(68;1.57e-52)|all cancers(67;1.83e-46)|Colorectal(1306;0.115)	Prednisone(DB00635)	ATGTGGTGGTGACAGCGAGGT	0.478																																					p.V63fs		Atlas-INDEL	.											.	HSD11B1	35	.	0			c.188delT						.						159	148	152					1																	209879256		2203	4300	6503	SO:0001589	frameshift_variant	3290	exon3			.	BC012593	CCDS1489.1	1q32-q41	2011-09-20			ENSG00000117594	ENSG00000117594	1.1.1.146	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5208	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 26C, member 1"	600713		HSD11B, HSD11		1885595, 19027726	Standard	NM_005525		Approved	SDR26C1	uc001hhk.3	P28845	OTTHUMG00000036481	ENST00000367028.2:c.189delG	chr1.hg19:g.209879256delG	ENSP00000355995:p.Val63fs	95.0	0.0		124.0	21.0	NM_001206741	B2R9Z1|D3DT89	Frame_Shift_Del	DEL	ENST00000367028.2	hg19	CCDS1489.1																																																																																			.	.		0.478	HSD11B1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088743.2	NM_005525		-	209879256	G	-	209879256	7	5	226	1	0	1	0	1	0	0	0	0	7384	1277	45	0	195	0	HSD11B1	1	209879256	Frame_Shift_Del	DEL	G	TCGA-DD-AAVS-01A-11D-A40R-10	58213827	209879256	39371365	4	31972										
GREB1	9687	hgsc.bcm.edu	37	chr2	11775439	11775439	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tcaacctgcgggtgcacagcGccggcctcctgctctgccgg	13	17	2	0	rs200590869		TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr2:11775439G>T	ENST00000381486.2	+	30	5554	c.5254G>T	c.(5254-5256)Gcc>Tcc	p.A1752S	GREB1_ENST00000396123.1_Missense_Mutation_p.A750S|GREB1_ENST00000234142.5_Missense_Mutation_p.A1752S	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1752						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GGTGCACAGCGCCGGCCTCCT	0.612																																					p.A1752S	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.G5254T						.						63	70	68					2																	11775439		2050	4191	6241	SO:0001583	missense	9687	exon30			CACAGCGCCGGCC		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.5254G>T	chr2.hg19:g.11775439G>T	ENSP00000370896:p.Ala1752Ser	67.0	0.0		62.0	28.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	G	11.64	1.698882	0.30142	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.42900	0.96;0.96;0.96	4.61	4.61	0.57282	.	0.054859	0.64402	D	0.000001	T	0.23451	0.0567	N	0.11724	0.165	0.46678	D	0.99915	B	0.32071	0.355	B	0.35550	0.205	T	0.07195	-1.0785	10	0.05959	T	0.93	-27.4037	12.5377	0.56150	0.0:0.0:0.8334:0.1666	.	1752	Q4ZG55	GREB1_HUMAN	S	1752;1752;750	ENSP00000370896:A1752S;ENSP00000234142:A1752S;ENSP00000379429:A750S	ENSP00000234142:A1752S	A	+	1	0	GREB1	11692890	0.960000	0.32886	1.000000	0.80357	0.991000	0.79684	2.920000	0.48844	2.124000	0.65301	0.563000	0.77884	GCC	.	.		0.612	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		T	11775439	G	T	11775439	3	4	226	1	0	0	0	0	1	0	0	0	6769	1087	38	1	5476	1	GREB1	2	11775439	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10		11775439	231423934	5	31973										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	24021162	24021162	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tgtgaggcatgtaaacaataCtaggtactgttcttcgagct	10	7	1	1			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr2:24021162C>T	ENST00000238789.5	-	19	2829	c.2486G>A	c.(2485-2487)aGt>aAt	p.S829N	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	829						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTAAACAATACTAGGTACTGT	0.363																																					p.S829N		Atlas-SNP	.											.	ATAD2B	110	.	0			c.G2486A						.						60	56	57					2																	24021162		1841	4099	5940	SO:0001583	missense	54454	exon19			ACAATACTAGGTA	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.2486G>A	chr2.hg19:g.24021162C>T	ENSP00000238789:p.Ser829Asn	362.0	1.0		322.0	114.0	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	hg19	CCDS46227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.582972|5.582972	0.96578|0.96578	.|.	.|.	ENSG00000119778|ENSG00000119778	ENST00000238789|ENST00000381024	D|.	0.95342|.	-3.68|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.775342|.	0.12289|.	N|.	0.482158|.	D|D	0.84999|0.84999	0.5597|0.5597	M|M	0.88181|0.88181	2.935|2.935	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.99;0.996|.	D|D	0.86144|0.86144	0.1583|0.1583	10|5	0.87932|.	D|.	0|.	.|.	20.0916|20.0916	0.97822|0.97822	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	829;829|.	Q9ULI0;Q9ULI0-2|.	ATD2B_HUMAN;.|.	N|I	829|110	ENSP00000238789:S829N|.	ENSP00000238789:S829N|.	S|V	-|-	2|1	0|0	ATAD2B|ATAD2B	23874666|23874666	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.651000|7.651000	0.83577|0.83577	2.828000|2.828000	0.97474|0.97474	0.655000|0.655000	0.94253|0.94253	AGT|GTA	.	.		0.363	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		T	24021162	C	T	24021162	3	4	226	1	0	0	0	0	1	0	0	0	1072	565	20	3	1930	3	ATAD2B	2	24021162	Missense_Mutation	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10	12245723	24021162	219178211	6	31974										
CFC1	55997	hgsc.bcm.edu	37	chr2	131356332	131356332	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	cggtgactgtcggtgcttctGagtggcaaccttggtgactt	14	9	1	3			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr2:131356332G>C	ENST00000259216.4	-	3	392	c.130C>G	c.(130-132)Cag>Gag	p.Q44E		NM_032545.3	NP_115934.1	P0CG37	CFC1_HUMAN	cripto, FRL-1, cryptic family 1	44					determination of left/right symmetry (GO:0007368)|gastrulation (GO:0007369)|nodal signaling pathway (GO:0038092)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nodal binding (GO:0038100)			endometrium(1)|lung(4)	5	Colorectal(110;0.1)					CGGTGCTTCTGAGTGGCAACC	0.517																																					p.Q44E		Atlas-SNP	.											.	.	.	.	0			c.C130G						.						16	25	22					2																	131356332		2172	4252	6424	SO:0001583	missense	653275	exon3			GCTTCTGAGTGGC	AF312769	CCDS2162.1, CCDS74573.1, CCDS74574.1	2q21.2	2014-02-04			ENSG00000136698	ENSG00000136698			18292	protein-coding gene	gene with protein product		605194	"heterotaxy 2 (autosomal dominant)"	HTX2		11062482, 10858660	Standard	NM_032545		Approved	CRYPTIC, HTX2	uc002tro.2	P0CG37	OTTHUMG00000131628	ENST00000259216.4:c.130C>G	chr2.hg19:g.131356332G>C	ENSP00000259216:p.Gln44Glu	945.0	0.0		1179.0	177.0	NM_001079530	B2RCY0|B9EJD3|Q53T05|Q9GZR3	Missense_Mutation	SNP	ENST00000259216.4	hg19	CCDS2162.1	.	.	.	.	.	.	.	.	.	.	.	4.579	0.107512	0.08780	.	.	ENSG00000136698	ENST00000259216	D	0.89343	-2.5	1.91	1.91	0.25777	.	1.275020	0.05417	N	0.543449	D	0.84238	0.5428	M	0.61703	1.905	0.09310	N	1	B	0.28470	0.213	B	0.26202	0.067	T	0.68146	-0.5486	10	0.02654	T	1	-5.6354	7.2964	0.26395	0.0:0.0:1.0:0.0	.	44	P0CG37	CFC1_HUMAN	E	44	ENSP00000259216:Q44E	ENSP00000259216:Q44E	Q	-	1	0	CFC1	131072802	0.011000	0.17503	0.063000	0.19743	0.117000	0.20001	2.818000	0.48041	1.379000	0.46325	0.436000	0.28706	CAG	.	.		0.517	CFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333367.1	NM_032545		C	131356332	G	C	131356332	3	2	226	1	0	0	0	0	1	0	0	0	3281	1299	45	4	1253	4	CFC1	2	131356332	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	107335170	131356332	111843041	7	31975										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141294168	141294168	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	accacagtagagcagtttttCatctgatttatctttacagt	6	8	3	2			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr2:141294168C>T	ENST00000389484.3	-	46	8595	c.7624G>A	c.(7624-7626)Gaa>Aaa	p.E2542K		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2542	LDL-receptor class A 11. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AGCAGTTTTTCATCTGATTTA	0.418										TSP Lung(27;0.18)																											p.E2542K	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G7624A						.						150	150	150					2																	141294168		2203	4300	6503	SO:0001583	missense	53353	exon46			GTTTTTCATCTGA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.7624G>A	chr2.hg19:g.141294168C>T	ENSP00000374135:p.Glu2542Lys	130.0	0.0		200.0	42.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	34	5.382062	0.95967	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.99105	-5.43	5.19	5.19	0.71726	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99635	0.9866	H	0.98426	4.23	0.58432	D	0.999999	D	0.76494	0.999	D	0.83275	0.996	D	0.97468	1.0039	10	0.72032	D	0.01	.	18.7053	0.91635	0.0:1.0:0.0:0.0	.	2542	Q9NZR2	LRP1B_HUMAN	K	2542;2480	ENSP00000374135:E2542K	ENSP00000374135:E2542K	E	-	1	0	LRP1B	141010638	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.726000	0.84824	2.430000	0.82344	0.650000	0.86243	GAA	.	.		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141294168	C	T	141294168	3	4	226	1	0	0	0	0	1	0	0	0	8964	835	29	3	6359	3	LRP1B	2	141294168	Missense_Mutation	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10	9937836	141294168	101905205	8	31976										
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172641967	172641967	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	atgcgtgacttaggtgttggTtctgaaccagcgggtttgct	14	7	1	2			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr2:172641967T>C	ENST00000422440.2	-	18	1891	c.1854A>G	c.(1852-1854)gaA>gaG	p.E618E	SLC25A12_ENST00000392592.4_Silent_p.E511E	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	618					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	TAGGTGTTGGTTCTGAACCAG	0.517																																					p.E618E		Atlas-SNP	.											.	SLC25A12	59	.	0			c.A1854G						.						176	157	163					2																	172641967		2203	4300	6503	SO:0001819	synonymous_variant	8604	exon18			TGTTGGTTCTGAA	Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"Solute carriers", "EF-hand domain containing"	10982	protein-coding gene	gene with protein product		603667	"solute carrier family 25 (mitochondrial carrier, Aralar), member 12"			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.1854A>G	chr2.hg19:g.172641967T>C		137.0	0.0		217.0	49.0	NM_003705	B3KR64|Q96AM8	Silent	SNP	ENST00000422440.2	hg19	CCDS33327.1																																																																																			.	.		0.517	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		C	172641967	T	C	172641967	2	2	226	1	0	0	0	0	0	0	0	1	14489	1722	60	2		2	SLC25A12	2	172641967	Silent	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10	31347799	172641967	70557406	9	31977										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098961	178098961	+	Missense_Mutation	SNP	T	T	C													0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tctcgacttactccaagatcTatatcttgcctccaaagtat							TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr2:178098961T>C	ENST00000397062.3	-	2	638	c.84A>G	c.(82-84)atA>atG	p.I28M	NFE2L2_ENST00000446151.2_Missense_Mutation_p.I12M|NFE2L2_ENST00000464747.1_Missense_Mutation_p.I12M|NFE2L2_ENST00000397063.4_Missense_Mutation_p.I12M|NFE2L2_ENST00000423513.1_Missense_Mutation_p.I12M	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	28					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			CTCCAAGATCTATATCTTGCC	0.363			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.I28M		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	.	NFE2L2	225	.	0			c.A84G						.						65	58	60					2																	178098961		1844	4099	5943	SO:0001583	missense	4780	exon2			AAGATCTATATCT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.84A>G	chr2.hg19:g.178098961T>C	ENSP00000380252:p.Ile28Met	57.0	0.0		54.0	11.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	13.97	2.395205	0.42512	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44;1.44	5.78	0.292	0.15737	.	0.042355	0.85682	D	0.000000	T	0.52901	0.1763	M	0.86740	2.835	0.46927	D	0.999257	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.80764	0.972;0.994;0.988;0.972	T	0.52646	-0.8548	10	0.87932	D	0	.	7.0251	0.24936	0.4323:0.0:0.2239:0.3438	.	12;12;12;28	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	M	12;28;12;12;12;12;12	ENSP00000380253:I12M;ENSP00000380252:I28M;ENSP00000411575:I12M;ENSP00000391590:I12M;ENSP00000400073:I12M;ENSP00000412191:I12M;ENSP00000410015:I12M	ENSP00000380252:I28M	I	-	3	3	NFE2L2	177807207	0.997000	0.39634	1.000000	0.80357	0.965000	0.64279	0.326000	0.19646	0.103000	0.17682	-2.000000	0.00444	ATA	.	.		0.363	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		C	178098961	T	C	178098961	3	2	226	1	0	0	0	0	1	0	0	0	10377	1512	53	2	1749	2	NFE2L2	2	178098961	Missense_Mutation	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10	5456994	178098961	65100412	10	31978	165	3								
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098968	178098968	+	Missense_Mutation	SNP	T	T	C													0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ttactccaagatctatatctTgcctccaaagtatgtcaatc							TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr2:178098968T>C	ENST00000397062.3	-	2	631	c.77A>G	c.(76-78)cAa>cGa	p.Q26R	NFE2L2_ENST00000446151.2_Missense_Mutation_p.Q10R|NFE2L2_ENST00000464747.1_Missense_Mutation_p.Q10R|NFE2L2_ENST00000397063.4_Missense_Mutation_p.Q10R|NFE2L2_ENST00000423513.1_Missense_Mutation_p.Q10R	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	26					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q26P(1)|p.Q26L(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ATCTATATCTTGCCTCCAAAG	0.348			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.Q26R		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,-1,2	NFE2L2	225	.	2	Substitution - Missense(2)	lung(2)	c.A77G						.						59	53	55					2																	178098968		1842	4098	5940	SO:0001583	missense	4780	exon2			ATATCTTGCCTCC		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.77A>G	chr2.hg19:g.178098968T>C	ENSP00000380252:p.Gln26Arg	52.0	0.0		50.0	9.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.075082	0.76415	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35;1.35;1.35	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.66025	0.2748	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.76494	0.999;0.993;0.998;0.999	D;D;D;D	0.80764	0.994;0.968;0.994;0.994	T	0.72782	-0.4189	10	0.87932	D	0	.	16.098	0.81144	0.0:0.0:0.0:1.0	.	10;10;10;26	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	R	10;26;10;10;10;10;10	ENSP00000380253:Q10R;ENSP00000380252:Q26R;ENSP00000411575:Q10R;ENSP00000391590:Q10R;ENSP00000400073:Q10R;ENSP00000412191:Q10R;ENSP00000410015:Q10R	ENSP00000380252:Q26R	Q	-	2	0	NFE2L2	177807214	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.698000	0.84413	2.210000	0.71456	0.460000	0.39030	CAA	.	.		0.348	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		C	178098968	T	C	178098968	3	2	226	1	0	0	0	0	1	0	0	0	10377	1812	63	2	1756	2	NFE2L2	2	178098968	Missense_Mutation	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10	7	178098968	65100405	11	31979	165	3								
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098972	178098972	+	Missense_Mutation	SNP	T	T	A													0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tccaagatctatatcttgccTccaaagtatgtcaatcaaat							TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr2:178098972T>A	ENST00000397062.3	-	2	627	c.73A>T	c.(73-75)Agg>Tgg	p.R25W	NFE2L2_ENST00000446151.2_Missense_Mutation_p.R9W|NFE2L2_ENST00000464747.1_Missense_Mutation_p.R9W|NFE2L2_ENST00000397063.4_Missense_Mutation_p.R9W|NFE2L2_ENST00000423513.1_Missense_Mutation_p.R9W	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	25					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ATATCTTGCCTCCAAAGTATG	0.348			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.R25W		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	.	NFE2L2	225	.	0			c.A73T						.						57	51	53					2																	178098972		1838	4097	5935	SO:0001583	missense	4780	exon2			CTTGCCTCCAAAG		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.73A>T	chr2.hg19:g.178098972T>A	ENSP00000380252:p.Arg25Trp	48.0	0.0		47.0	8.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.852272	0.71719	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3;1.3;1.3	5.78	5.78	0.91487	.	0.081400	0.85682	D	0.000000	T	0.65428	0.2690	M	0.85542	2.76	0.54753	D	0.999985	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.87578	0.992;0.998;0.975;0.992	T	0.71570	-0.4553	10	0.87932	D	0	.	16.098	0.81144	0.0:0.0:0.0:1.0	.	9;9;9;25	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	W	9;25;9;9;9;9;9	ENSP00000380253:R9W;ENSP00000380252:R25W;ENSP00000411575:R9W;ENSP00000391590:R9W;ENSP00000400073:R9W;ENSP00000412191:R9W;ENSP00000410015:R9W	ENSP00000380252:R25W	R	-	1	2	NFE2L2	177807218	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.881000	0.69706	2.210000	0.71456	0.460000	0.39030	AGG	.	.		0.348	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		A	178098972	T	A	178098972	3	1	226	1	0	0	0	0	1	0	0	0	10377	1550	54	4	1760	4	NFE2L2	2	178098972	Missense_Mutation	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10	4	178098972	65100401	12	31980	165	3								
PLEKHA3	65977	hgsc.bcm.edu	37	chr2	179365879	179365879	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	cagatacagattcttgtagtGatattcctcttgaagaccca	7	9	2	5			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr2:179365879G>A	ENST00000234453.5	+	7	1153	c.751G>A	c.(751-753)Gat>Aat	p.D251N		NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	251						Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			TTCTTGTAGTGATATTCCTCT	0.413																																					p.D251N		Atlas-SNP	.											.	PLEKHA3	25	.	0			c.G751A						.						88	92	90					2																	179365879		2203	4300	6503	SO:0001583	missense	65977	exon7			TGTAGTGATATTC	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"Pleckstrin homology (PH) domain containing"	14338	protein-coding gene	gene with protein product	"four-phosphate-adaptor protein 1"	607774	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.751G>A	chr2.hg19:g.179365879G>A	ENSP00000234453:p.Asp251Asn	249.0	0.0		333.0	87.0	NM_019091	Q4ZG69|Q86TQ1|Q9NXT3	Missense_Mutation	SNP	ENST00000234453.5	hg19	CCDS33336.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.002626	0.93227	.	.	ENSG00000116095	ENST00000234453;ENST00000421187	T	0.20738	2.05	5.77	5.77	0.91146	.	0.051963	0.64402	D	0.000001	T	0.34774	0.0909	L	0.27053	0.805	0.53688	D	0.999978	D	0.63880	0.993	D	0.74674	0.984	T	0.02307	-1.1179	10	0.23891	T	0.37	-3.391	19.9795	0.97321	0.0:0.0:1.0:0.0	.	251	Q9HB20	PKHA3_HUMAN	N	251;60	ENSP00000234453:D251N	ENSP00000234453:D251N	D	+	1	0	PLEKHA3	179074125	1.000000	0.71417	0.997000	0.53966	0.892000	0.51952	7.539000	0.82063	2.720000	0.93068	0.650000	0.86243	GAT	.	.		0.413	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091		A	179365879	G	A	179365879	3	1	226	1	0	0	0	0	1	0	0	0	12066	1290	45	3	777	3	PLEKHA3	2	179365879	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	1266907	179365879	63833494	13	31981										
CTLA4	1493	hgsc.bcm.edu	37	chr2	204736111	204736111	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tctgttgcagatccagaaccGtgcccagattctgacttcct	8	13	2	4	rs200657280		TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr2:204736111G>A	ENST00000302823.3	+	3	625	c.468G>A	c.(466-468)ccG>ccA	p.P156P	CTLA4_ENST00000427473.2_Intron|CTLA4_ENST00000472206.1_Intron|CTLA4_ENST00000487393.1_Intron|CTLA4_ENST00000295854.6_Intron	NM_005214.4	NP_005205.2	P16410	CTLA4_HUMAN	cytotoxic T-lymphocyte-associated protein 4	156					B cell receptor signaling pathway (GO:0050853)|cellular response to DNA damage stimulus (GO:0006974)|immune response (GO:0006955)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of immune response (GO:0050777)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of apoptotic process (GO:0043065)|T cell costimulation (GO:0031295)	clathrin-coated endocytic vesicle (GO:0045334)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				large_intestine(4)|lung(4)|skin(1)	9					Ipilimumab(DB06186)	ATCCAGAACCGTGCCCAGATT	0.453																																					p.P156P		Atlas-SNP	.											.	CTLA4	24	.	0			c.G468A						.	G	,	1,4405	2.1+/-5.4	0,1,2202	172	162	165		,468	-9.4	1	2		165	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous	CTLA4	NM_001037631.2,NM_005214.4	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	,156/224	204736111	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1493	exon3			AGAACCGTGCCCA		CCDS2362.1, CCDS42803.1	2q33	2014-02-03			ENSG00000163599	ENSG00000163599		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	2505	protein-coding gene	gene with protein product		123890	"celiac disease 3", "insulin-dependent diabetes mellitus 12"	CELIAC3, IDDM12		3220103, 8817351	Standard	NM_005214		Approved	CD152, CD, GSE, CD28, ICOS	uc002vak.2	P16410	OTTHUMG00000132877	ENST00000302823.3:c.468G>A	chr2.hg19:g.204736111G>A		79.0	0.0		54.0	13.0	NM_005214	A0N1S0|E9PDH0|O95653|Q0PP65|Q52MC1|Q53TD5|Q5S005|Q8WXJ1|Q96P43|Q9UKN9	Silent	SNP	ENST00000302823.3	hg19	CCDS2362.1																																																																																			.	G|0.999;A|0.001		0.453	CTLA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256365.1	NM_005214		A	204736111	G	A	204736111	2	1	226	1	0	0	0	0	0	0	0	1	4013	1132	40	1		1	CTLA4	2	204736111	Silent	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	25370232	204736111	38463262	14	31982										
IFT57	55081	hgsc.bcm.edu	37	chr3	107886700	107886700	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tggtgcatttggtcaacatgGattctccaatcctacaggca	9	10	2	0			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr3:107886700G>C	ENST00000264538.3	-	7	1036	c.789C>G	c.(787-789)atC>atG	p.I263M	IFT57_ENST00000468021.1_5'Flank	NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	263					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			GGTCAACATGGATTCTCCAAT	0.353																																					p.I263M		Atlas-SNP	.											.	IFT57	44	.	0			c.C789G						.						198	188	191					3																	107886700		2203	4300	6503	SO:0001583	missense	55081	exon7			AACATGGATTCTC	AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"Intraflagellar transport homologs"	17367	protein-coding gene	gene with protein product		606621	"estrogen-related receptor beta like 1", "intraflagellar transport 57 homolog (Chlamydomonas)"	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.789C>G	chr3.hg19:g.107886700G>C	ENSP00000264538:p.Ile263Met	71.0	0.0		98.0	30.0	NM_018010	Q96DA9	Missense_Mutation	SNP	ENST00000264538.3	hg19	CCDS2951.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.615305	0.46631	.	.	ENSG00000114446	ENST00000264538	.	.	.	5.93	4.14	0.48551	.	0.196743	0.52532	D	0.000066	T	0.56514	0.1990	L	0.37897	1.145	0.45554	D	0.998509	P	0.39480	0.675	P	0.48704	0.587	T	0.54589	-0.8271	9	0.45353	T	0.12	.	11.3385	0.49518	0.2007:0.0:0.7993:0.0	.	263	Q9NWB7	IFT57_HUMAN	M	263	.	ENSP00000264538:I263M	I	-	3	3	IFT57	109369390	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.473000	0.35387	0.831000	0.34780	0.655000	0.94253	ATC	.	.		0.353	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010		C	107886700	G	C	107886700	3	2	226	1	0	0	0	0	1	0	0	0	7571	1164	41	4	520	4	IFT57	3	107886700	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10		107886700	90135730	15	31983										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62598783	62598783	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	taaagtttgatttgcggactAggataaagagtggagaggct	14	3	0	3			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr4:62598783A>T	ENST00000514591.1	+	7	1035	c.706A>T	c.(706-708)Agg>Tgg	p.R236W	LPHN3_ENST00000514996.1_Missense_Mutation_p.R236W|LPHN3_ENST00000545650.1_Missense_Mutation_p.R236W|LPHN3_ENST00000509896.1_Missense_Mutation_p.R304W|LPHN3_ENST00000514157.1_Missense_Mutation_p.R236W|LPHN3_ENST00000506720.1_Missense_Mutation_p.R304W|LPHN3_ENST00000508946.1_Missense_Mutation_p.R236W|LPHN3_ENST00000504896.1_Missense_Mutation_p.R236W|LPHN3_ENST00000507625.1_Missense_Mutation_p.R304W|LPHN3_ENST00000506746.1_Missense_Mutation_p.R304W|LPHN3_ENST00000512091.2_Missense_Mutation_p.R236W|LPHN3_ENST00000507164.1_Missense_Mutation_p.R304W|LPHN3_ENST00000511324.1_Missense_Mutation_p.R304W|LPHN3_ENST00000508693.1_Missense_Mutation_p.R304W|LPHN3_ENST00000506700.1_Missense_Mutation_p.R236W			Q9HAR2	LPHN3_HUMAN	latrophilin 3	236	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						TTTGCGGACTAGGATAAAGAG	0.463																																					p.R236W		Atlas-SNP	.											.	LPHN3	800	.	0			c.A706T						.						79	73	75					4																	62598783		1903	4119	6022	SO:0001583	missense	23284	exon5			CGGACTAGGATAA	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.706A>T	chr4.hg19:g.62598783A>T	ENSP00000422533:p.Arg236Trp	84.0	0.0		79.0	5.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	A	16.38	3.108454	0.56291	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	5.26	4.05	0.47172	.	0.000000	0.85682	D	0.000000	D	0.94837	0.8332	M	0.90198	3.095	0.53005	D	0.999968	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.998;0.992	D	0.94708	0.7889	10	0.87932	D	0	.	11.5444	0.50685	0.8498:0.1502:0.0:0.0	.	236;304;236	E9PE04;E7EN28;Q9HAR2-2	.;.;.	W	236;236;304;304;236;236;236;236;236;304;304;304;236;236;236;304;304;236	ENSP00000423388:R236W;ENSP00000422533:R236W;ENSP00000423787:R304W;ENSP00000425033:R304W;ENSP00000424120:R236W;ENSP00000439831:R236W;ENSP00000421476:R304W;ENSP00000424030:R304W;ENSP00000421372:R304W;ENSP00000425201:R236W;ENSP00000423434:R236W;ENSP00000421627:R236W;ENSP00000420931:R304W;ENSP00000425884:R304W;ENSP00000424258:R236W	ENSP00000280009:R236W	R	+	1	2	LPHN3	62281378	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.504000	0.60414	0.822000	0.34565	-0.472000	0.04984	AGG	.	.		0.463	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			T	62598783	A	T	62598783	3	4	226	1	0	0	0	0	1	0	0	0	8926	411	15	4	724	4	LPHN3	4	62598783	Missense_Mutation	SNP	A	TCGA-DD-AAVS-01A-11D-A40R-10		62598783	128555493	16	31984										
IRF2	3660	hgsc.bcm.edu	37	chr4	185309971	185309971	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tttcttgatgacgctggcccGggtctcccggtctggccgac	13	14	3	2			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr4:185309971G>A	ENST00000393593.3	-	9	1198	c.991C>T	c.(991-993)Cgg>Tgg	p.R331W		NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	331					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		ACGCTGGCCCGGGTCTCCCGG	0.597																																					p.R331W		Atlas-SNP	.											IRF2,colon,carcinoma,0,1	IRF2	53	.	0			c.C991T						.						62	72	68					4																	185309971		2203	4300	6503	SO:0001583	missense	3660	exon9			TGGCCCGGGTCTC		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.991C>T	chr4.hg19:g.185309971G>A	ENSP00000377218:p.Arg331Trp	101.0	0.0		61.0	37.0	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Missense_Mutation	SNP	ENST00000393593.3	hg19	CCDS3835.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611787	0.66558	.	.	ENSG00000168310	ENST00000393593	D	0.99113	-5.44	5.08	3.25	0.37280	.	0.385573	0.22328	N	0.061515	D	0.98927	0.9636	L	0.61218	1.895	0.53688	D	0.999976	D	0.89917	1.0	D	0.91635	0.999	D	0.99107	1.0845	10	0.87932	D	0	-2.7438	12.7538	0.57323	0.0:0.0:0.5362:0.4638	.	331	P14316	IRF2_HUMAN	W	331	ENSP00000377218:R331W	ENSP00000377218:R331W	R	-	1	2	IRF2	185546965	0.992000	0.36948	0.920000	0.36463	0.992000	0.81027	2.124000	0.42006	0.641000	0.30601	0.561000	0.74099	CGG	.	.		0.597	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1			A	185309971	G	A	185309971	3	1	226	1	0	0	0	0	1	0	0	0	7837	1115	39	1	62	1	IRF2	4	185309971	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	122711188	185309971	5844305	17	31985										
IRX1	79192	hgsc.bcm.edu	37	chr5	3600742	3600742	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gagagagacctcgtccccagGccagattcgccggcacagca	12	15	0	3			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr5:3600742G>T	ENST00000302006.3	+	3	1384	c.1332G>T	c.(1330-1332)agG>agT	p.R444S	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	444					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TCGTCCCCAGGCCAGATTCGC	0.617																																					p.R444S		Atlas-SNP	.											.	IRX1	106	.	0			c.G1332T						.						55	59	58					5																	3600742		2203	4300	6503	SO:0001583	missense	79192	exon3			CCCCAGGCCAGAT	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.1332G>T	chr5.hg19:g.3600742G>T	ENSP00000305244:p.Arg444Ser	92.0	0.0		88.0	28.0	NM_024337	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	hg19	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.656142	0.29425	.	.	ENSG00000170549	ENST00000302006	T	0.60920	0.15	4.17	2.33	0.28932	.	0.420300	0.24449	N	0.038438	T	0.68026	0.2956	M	0.62723	1.935	0.44123	D	0.996901	D	0.71674	0.998	D	0.76071	0.987	T	0.64249	-0.6452	10	0.52906	T	0.07	.	7.6322	0.28247	0.3832:0.0:0.6168:0.0	.	444	P78414	IRX1_HUMAN	S	444	ENSP00000305244:R444S	ENSP00000305244:R444S	R	+	3	2	IRX1	3653742	1.000000	0.71417	0.250000	0.24296	0.162000	0.22319	1.322000	0.33689	0.211000	0.20683	0.467000	0.42956	AGG	.	.		0.617	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		T	3600742	G	T	3600742	3	4	226	1	0	0	0	0	1	0	0	0	7852	1194	42	3	1342	3	IRX1	5	3600742	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10		3600742	177314518	18	31986										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38427168	38427168	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gagatcttacgctgcaactcCctggccactggagccccagc	10	16	1	1	rs370628892		TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr5:38427168C>G	ENST00000354891.3	+	14	2214	c.1868C>G	c.(1867-1869)cCc>cGc	p.P623R	EGFLAM_ENST00000336740.6_Missense_Mutation_p.P389R|EGFLAM_ENST00000322350.5_Missense_Mutation_p.P623R|EGFLAM-AS1_ENST00000508986.1_RNA|EGFLAM_ENST00000397202.2_5'UTR	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	623	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					GCTGCAACTCCCTGGCCACTG	0.483																																					p.P623R	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C1868G						.						166	163	164					5																	38427168		2203	4300	6503	SO:0001583	missense	133584	exon14			CAACTCCCTGGCC	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.1868C>G	chr5.hg19:g.38427168C>G	ENSP00000346964:p.Pro623Arg	43.0	0.0		66.0	24.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	hg19	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	C	10.72	1.428998	0.25726	.	.	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000339580	T;T;T	0.70282	-0.47;-0.47;-0.47	5.76	4.87	0.63330	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.056805	0.64402	D	0.000001	T	0.64249	0.2581	L	0.50993	1.605	0.80722	D	1	B;B;B	0.31893	0.122;0.345;0.009	B;B;B	0.32211	0.117;0.142;0.009	T	0.59804	-0.7385	10	0.16896	T	0.51	-11.7169	15.058	0.71930	0.0:0.731:0.269:0.0	.	389;623;623	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	R	623;623;389;389	ENSP00000346964:P623R;ENSP00000313084:P623R;ENSP00000337607:P389R	ENSP00000313084:P623R	P	+	2	0	EGFLAM	38462925	0.976000	0.34144	0.957000	0.39632	0.202000	0.24057	2.957000	0.49137	1.394000	0.46624	0.655000	0.94253	CCC	.	.		0.483	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		G	38427168	C	G	38427168	3	3	226	1	0	0	0	0	1	0	0	0	4968	623	22	4	1936	4	EGFLAM	5	38427168	Missense_Mutation	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10	34826426	38427168	142488092	19	31987										
FNIP1	96459	hgsc.bcm.edu	37	chr5	131013525	131013525	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gactgttggaacccaggcaaGatgattggtcagaactgcag	13	8	1	3			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr5:131013525G>A	ENST00000510461.1	-	13	1485	c.1390C>T	c.(1390-1392)Ctt>Ttt	p.L464F	FNIP1_ENST00000307968.7_Missense_Mutation_p.L436F|FNIP1_ENST00000511848.1_Missense_Mutation_p.L464F|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307954.8_Missense_Mutation_p.L419F	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	464					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		ACCCAGGCAAGATGATTGGTC	0.388																																					p.L464F		Atlas-SNP	.											.	FNIP1	104	.	0			c.C1390T						.						90	87	88					5																	131013525		2203	4300	6503	SO:0001583	missense	96459	exon13			AGGCAAGATGATT	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.1390C>T	chr5.hg19:g.131013525G>A	ENSP00000421985:p.Leu464Phe	91.0	0.0		69.0	18.0	NM_133372	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	hg19	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.972914	0.92919	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461;ENST00000511848	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.45	5.45	0.79879	.	.	.	.	.	T	0.73961	0.3654	M	0.84846	2.72	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.997;0.999;1.0	T	0.77474	-0.2574	9	0.72032	D	0.01	-7.3683	19.6467	0.95778	0.0:0.0:1.0:0.0	.	464;464;436;464	A8K8V8;Q8TF40-2;Q8TF40-3;Q8TF40	.;.;.;FNIP1_HUMAN	F	436;419;224;464;464	ENSP00000309266:L436F;ENSP00000310453:L419F;ENSP00000421985:L464F;ENSP00000425619:L464F	ENSP00000310453:L419F	L	-	1	0	FNIP1	131041424	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.346000	0.72999	2.716000	0.92895	0.655000	0.94253	CTT	.	.		0.388	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		A	131013525	G	A	131013525	3	1	226	1	0	0	0	0	1	0	0	0	5983	942	33	3	2134	3	FNIP1	5	131013525	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	92586357	131013525	49901735	20	31988										
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140166927	140166927	+	Frame_Shift_Del	DEL	C	C	-													0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tgataatgctccagaactggCggtcacttcattgtatttgc							TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr5:140166927delC	ENST00000504120.2	+	1	1052	c.1052delC	c.(1051-1053)gcgfs	p.A351fs	PCDHA1_ENST00000394633.3_Frame_Shift_Del_p.A351fs|PCDHA1_ENST00000378133.3_Frame_Shift_Del_p.A351fs	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	351	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAGAACTGGCGGTCACTTCA	0.488																																					p.A351fs		Atlas-INDEL	.											.	PCDHA1	387	.	0			c.1051delG						.						97	96	97					5																	140166927		2203	4300	6503	SO:0001589	frameshift_variant	56147	exon1			.	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"Cadherins / Protocadherins : Clustered"	8663	other	complex locus constituent	"KIAA0345-like 13"	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1052delC	chr5.hg19:g.140166927delC	ENSP00000420840:p.Ala351fs	126.0	0.0		150.0	50.0	NM_031411	O75288|Q9NRT7	Frame_Shift_Del	DEL	ENST00000504120.2	hg19	CCDS54913.1																																																																																			.	.		0.488	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		-	140166927	C	-	140166927	7	5	226	1	0	1	0	1	0	0	0	0	11528	768	27	0	1054	0	PCDHA1	5	140166927	Frame_Shift_Del	DEL	C	TCGA-DD-AAVS-01A-11D-A40R-10	9153402	140166927	40748333	21	31989										
TNIP1	10318	hgsc.bcm.edu	37	chr5	150415262	150415262	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ctggaagtcctcctcgaagaTcttcacctggtgtggaggga	13	10	2	1			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr5:150415262T>C	ENST00000389378.2	-	14	1990	c.1402A>G	c.(1402-1404)Atc>Gtc	p.I468V	TNIP1_ENST00000521591.1_Missense_Mutation_p.I468V|TNIP1_ENST00000524280.1_Missense_Mutation_p.I468V|TNIP1_ENST00000523200.1_Missense_Mutation_p.I468V|TNIP1_ENST00000518977.1_Missense_Mutation_p.I468V|TNIP1_ENST00000521423.1_Intron|TNIP1_ENST00000520931.1_Missense_Mutation_p.I415V|TNIP1_ENST00000315050.7_Missense_Mutation_p.I468V|TNIP1_ENST00000522226.1_Missense_Mutation_p.I468V|TNIP1_ENST00000523338.1_Missense_Mutation_p.I468V	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	468	Required for inhibitory activity of TNF- induced NF-kappa-B activation. {ECO:0000250}.|Ubiquitin-binding domain (UBD).				defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCTCGAAGATCTTCACCTGG	0.592																																					p.I468V		Atlas-SNP	.											.	TNIP1	51	.	0			c.A1402G						.						82	70	74					5																	150415262		2203	4300	6503	SO:0001583	missense	10318	exon14			CGAAGATCTTCAC	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"virion-associated nuclear-shuttling protein", "Nef-associated factor 1 SNP"	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.1402A>G	chr5.hg19:g.150415262T>C	ENSP00000374029:p.Ile468Val	41.0	0.0		36.0	11.0	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Missense_Mutation	SNP	ENST00000389378.2	hg19	CCDS34280.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.270156	0.80469	.	.	ENSG00000145901	ENST00000520931;ENST00000389378;ENST00000517504;ENST00000315050;ENST00000523338;ENST00000544828;ENST00000417127;ENST00000539213;ENST00000522226;ENST00000521591;ENST00000518977;ENST00000524280;ENST00000523200;ENST00000545840	D;D;D;D;D;D;D;D;D;D	0.96265	-3.96;-3.96;-3.96;-3.96;-3.96;-3.96;-3.96;-3.96;-3.96;-3.96	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.97598	0.9213	M	0.74881	2.28	0.51233	D	0.999911	D;D;D;D;D;D;D	0.89917	0.993;0.997;0.991;0.997;0.997;0.999;1.0	D;D;D;D;D;D;D	0.85130	0.984;0.993;0.978;0.993;0.993;0.997;0.997	D	0.97035	0.9753	10	0.23302	T	0.38	-19.6252	14.8334	0.70164	0.0:0.0:0.0:1.0	.	468;422;422;468;468;468;468	B7Z8K2;A4F1X9;A4F1X7;E7EPY1;E7ET96;A4F1W9;Q15025	.;.;.;.;.;.;TNIP1_HUMAN	V	415;468;81;468;468;425;425;430;468;468;468;468;468;425	ENSP00000429891:I415V;ENSP00000374029:I468V;ENSP00000430739:I81V;ENSP00000317891:I468V;ENSP00000428243:I468V;ENSP00000428187:I468V;ENSP00000430760:I468V;ENSP00000430971:I468V;ENSP00000429912:I468V;ENSP00000431105:I468V	ENSP00000317891:I468V	I	-	1	0	TNIP1	150395455	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	5.613000	0.67688	2.086000	0.62901	0.459000	0.35465	ATC	.	.		0.592	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		C	150415262	T	C	150415262	3	2	226	1	0	0	0	0	1	0	0	0	16329	1435	50	2	528	2	TNIP1	5	150415262	Missense_Mutation	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10	10248335	150415262	30499998	22	31990										
DSP	1832	hgsc.bcm.edu	37	chr6	7580097	7580097	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gaccaccatcaaggagatatCcatgcaaaaagaggatgatt	9	8	1	3			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr6:7580097C>G	ENST00000379802.3	+	23	4015	c.3674C>G	c.(3673-3675)tCc>tGc	p.S1225C	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1225	Central fibrous rod domain.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AAGGAGATATCCATGCAAAAA	0.373																																					p.S1225C		Atlas-SNP	.											.	DSP	306	.	0			c.C3674G						.						75	72	73					6																	7580097		2203	4300	6503	SO:0001583	missense	1832	exon23			AGATATCCATGCA	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.3674C>G	chr6.hg19:g.7580097C>G	ENSP00000369129:p.Ser1225Cys	183.0	0.0		300.0	193.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.265944	0.59540	.	.	ENSG00000096696	ENST00000379802	D	0.92699	-3.09	5.37	5.37	0.77165	.	0.117336	0.38778	N	0.001579	D	0.87341	0.6153	L	0.34521	1.04	0.80722	D	1	P	0.44578	0.838	B	0.43916	0.436	D	0.89031	0.3442	10	0.56958	D	0.05	.	18.7003	0.91618	0.0:1.0:0.0:0.0	.	1225	P15924	DESP_HUMAN	C	1225	ENSP00000369129:S1225C	ENSP00000369129:S1225C	S	+	2	0	DSP	7525096	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.917000	0.63369	2.518000	0.84900	0.557000	0.71058	TCC	.	.		0.373	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		G	7580097	C	G	7580097	3	3	226	1	0	0	0	0	1	0	0	0	4783	855	30	4	3764	4	DSP	6	7580097	Missense_Mutation	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10		7580097	163534970	23	31991										
SLC17A4	10050	hgsc.bcm.edu	37	chr6	25776923	25776923	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ctccagaaaaatcctcagacTcatcaccatcaggaaactct	4	14	5	2			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr6:25776923T>A	ENST00000377905.4	+	9	1207	c.1088T>A	c.(1087-1089)cTc>cAc	p.L363H	SLC17A4_ENST00000439485.2_Missense_Mutation_p.L133H|SLC17A4_ENST00000397076.2_Missense_Mutation_p.L133H	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	363					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			breast(4)|endometrium(1)|kidney(4)|large_intestine(3)|lung(21)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						ATCCTCAGACTCATCACCATC	0.488																																					p.L363H		Atlas-SNP	.											.	SLC17A4	79	.	0			c.T1088A						.						172	159	164					6																	25776923		2203	4300	6503	SO:0001583	missense	10050	exon9			TCAGACTCATCAC	AB020527	CCDS4564.1, CCDS75411.1	6p22.2	2013-07-18	2013-07-18		ENSG00000146039	ENSG00000146039		"Solute carriers"	10932	protein-coding gene	gene with protein product		604216	"solute carrier family 17 (sodium phosphate), member 4"			10319585	Standard	NM_005495		Approved	KIAA2138	uc003nfe.3	Q9Y2C5	OTTHUMG00000014410	ENST00000377905.4:c.1088T>A	chr6.hg19:g.25776923T>A	ENSP00000367137:p.Leu363His	115.0	0.0		173.0	30.0	NM_005495	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Missense_Mutation	SNP	ENST00000377905.4	hg19	CCDS4564.1	.	.	.	.	.	.	.	.	.	.	T	18.80	3.700694	0.68501	.	.	ENSG00000146039	ENST00000377905;ENST00000439485;ENST00000397076	T;T;T	0.61859	0.11;0.14;0.07	5.63	5.63	0.86233	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.45867	D	0.000332	T	0.64951	0.2645	M	0.64676	1.99	0.35717	D	0.816877	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.993;0.984	T	0.69359	-0.5166	10	0.48119	T	0.1	.	12.535	0.56137	0.0:0.0:0.0:1.0	.	133;133;363	E7EPE8;E7EU17;Q9Y2C5	.;.;S17A4_HUMAN	H	363;133;133	ENSP00000367137:L363H;ENSP00000391345:L133H;ENSP00000380266:L133H	ENSP00000367137:L363H	L	+	2	0	SLC17A4	25884902	0.519000	0.26242	0.515000	0.27774	0.996000	0.88848	2.608000	0.46308	2.279000	0.76181	0.533000	0.62120	CTC	.	.		0.488	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1			A	25776923	T	A	25776923	3	1	226	1	0	0	0	0	1	0	0	0	14434	1551	54	4	1118	4	SLC17A4	6	25776923	Missense_Mutation	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10	18196826	25776923	145338144	24	31992										
RUNX2	860	hgsc.bcm.edu	37	chr6	45390466	45390466	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	cagcagcagcagcagcagcaAcagcagcagcagcagcagga	13	13	0	0	rs575896136	byFrequency	TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr6:45390466A>G	ENST00000371438.1	+	2	553	c.195A>G	c.(193-195)caA>caG	p.Q65Q	RUNX2_ENST00000541979.1_Silent_p.Q133Q|RUNX2_ENST00000359524.5_Silent_p.Q51Q|RUNX2_ENST00000371436.6_Silent_p.Q65Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371432.3_Silent_p.Q51Q|RUNX2_ENST00000352853.5_Silent_p.Q133Q|RUNX2_ENST00000465038.2_Silent_p.Q65Q|RUNX2_ENST00000576263.1_Silent_p.Q65Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	65	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcaacagcagcagc	0.731													A|||	8	0.00159744	0.0023	0	5008	,	,		7675	0.002		0	False		,,,				2504	0.0031				p.Q65Q		Atlas-SNP	.											.	RUNX2	128	.	0			c.A195G						.						10	15	14					6																	45390466		1452	3071	4523	SO:0001819	synonymous_variant	860	exon3			GCAGCAACAGCAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.195A>G	chr6.hg19:g.45390466A>G		48.0	0.0		103.0	5.0	NM_001024630	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	hg19	CCDS43467.2																																																																																			.	.		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390466	A	G	45390466	2	3	226	1	0	0	0	0	0	0	0	1	13763	40	2	2		2	RUNX2	6	45390466	Silent	SNP	A	TCGA-DD-AAVS-01A-11D-A40R-10	19613543	45390466	125724601	25	31993										
RP9	6100	hgsc.bcm.edu	37	chr7	33136968	33136968	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ggtgaccatagcgtttgcaaCgccaacctaaaaacgaaaag	9	10	0	1			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr7:33136968C>T	ENST00000297157.3	-	4	337	c.320G>A	c.(319-321)cGt>cAt	p.R107H		NM_203288.1	NP_976033.1	Q8TA86	RP9_HUMAN	retinitis pigmentosa 9 (autosomal dominant)	107	PIM1-binding. {ECO:0000250}.				cognition (GO:0050890)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|signal recognition particle receptor complex (GO:0005785)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|urinary_tract(1)	7			GBM - Glioblastoma multiforme(11;0.0403)			GCGTTTGCAACGCCAACCTAA	0.363																																					p.R107H		Atlas-SNP	.											.	RP9	19	.	0			c.G320A						.						79	75	76					7																	33136968		2203	4300	6503	SO:0001583	missense	6100	exon4			TTGCAACGCCAAC	AX016710	CCDS5440.1	7p14.3	2014-01-28			ENSG00000164610	ENSG00000164610			10288	protein-coding gene	gene with protein product	"Pim-1 kinase associated protein"	607331				8513323	Standard	NM_203288		Approved	PAP-1	uc003tdm.3	Q8TA86	OTTHUMG00000152988	ENST00000297157.3:c.320G>A	chr7.hg19:g.33136968C>T	ENSP00000297157:p.Arg107His	54.0	0.0		59.0	19.0	NM_203288		Missense_Mutation	SNP	ENST00000297157.3	hg19	CCDS5440.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.654263	0.67472	.	.	ENSG00000164610	ENST00000297157;ENST00000448915	D;D	0.83163	-1.69;-1.69	3.77	3.77	0.43336	Zinc finger, CCHC-type (1);	0.000000	0.85682	D	0.000000	T	0.81024	0.4737	M	0.76727	2.345	0.53688	D	0.999979	P	0.40050	0.7	B	0.32583	0.148	D	0.85052	0.0929	10	0.56958	D	0.05	-43.348	16.449	0.83973	0.0:1.0:0.0:0.0	.	107	Q8TA86	RP9_HUMAN	H	107;73	ENSP00000297157:R107H;ENSP00000411577:R73H	ENSP00000297157:R107H	R	-	2	0	RP9	33103493	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.032000	0.76498	2.028000	0.59812	0.400000	0.26472	CGT	.	.		0.363	RP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328914.1	NM_203288		T	33136968	C	T	33136968	3	4	226	1	0	0	0	0	1	0	0	0	13550	536	19	1	357	1	RP9	7	33136968	Missense_Mutation	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10		33136968	126001695	26	31994										
MELK	9833	hgsc.bcm.edu	37	chr9	36589546	36589546	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gtcacagagtgatttgccccGgatcaaaacggagattgagg	13	8	2	4			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr9:36589546G>T	ENST00000298048.2	+	4	342	c.158G>T	c.(157-159)cGg>cTg	p.R53L	MELK_ENST00000536329.1_Intron|MELK_ENST00000543751.1_Missense_Mutation_p.R21L|MELK_ENST00000541717.1_Missense_Mutation_p.R53L|MELK_ENST00000538311.1_5'UTR|MELK_ENST00000487398.1_3'UTR|MELK_ENST00000536987.1_5'UTR|MELK_ENST00000536860.1_Missense_Mutation_p.R53L|MELK_ENST00000545008.1_Missense_Mutation_p.R53L	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	53	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			GATTTGCCCCGGATCAAAACG	0.398																																					p.R53L	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.G158T						.						167	152	158					9																	36589546		2203	4300	6503	SO:0001583	missense	9833	exon4			TGCCCCGGATCAA	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.158G>T	chr9.hg19:g.36589546G>T	ENSP00000298048:p.Arg53Leu	81.0	0.0		63.0	25.0	NM_001256688	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	hg19	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	G	30	5.053502	0.93793	.	.	ENSG00000165304	ENST00000298048;ENST00000545008;ENST00000536860;ENST00000541717;ENST00000543751	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;1.81	5.21	5.21	0.72293	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.72326	0.3446	L	0.33668	1.02	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.998;0.999;0.999;1.0;0.999	T	0.75703	-0.3225	10	0.87932	D	0	-9.8066	18.7878	0.91961	0.0:0.0:1.0:0.0	.	21;53;53;53;21;53	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A7;Q14680	.;.;.;.;.;MELK_HUMAN	L	53;53;53;53;21	ENSP00000298048:R53L;ENSP00000445452:R53L;ENSP00000439792:R53L;ENSP00000437804:R53L;ENSP00000441596:R21L	ENSP00000298048:R53L	R	+	2	0	MELK	36579546	1.000000	0.71417	0.522000	0.27862	0.948000	0.59901	9.142000	0.94618	2.446000	0.82766	0.655000	0.94253	CGG	.	.		0.398	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		T	36589546	G	T	36589546	3	4	226	1	0	0	0	0	1	0	0	0	9479	1116	39	1	168	1	MELK	9	36589546	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10		36589546	104623885	27	31995										
NRP1	8829	hgsc.bcm.edu	37	chr10	33510747	33510747	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gttatcagtggtttggggaaTactgcaaccacaacatctgt	10	8	2	0			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr10:33510747T>C	ENST00000265371.4	-	9	1707	c.1182A>G	c.(1180-1182)gtA>gtG	p.V394V	NRP1_ENST00000374867.2_Silent_p.V394V|NRP1_ENST00000374816.3_Silent_p.V394V|NRP1_ENST00000374821.5_Silent_p.V394V|NRP1_ENST00000374823.5_Silent_p.V394V|NRP1_ENST00000432372.2_Silent_p.V394V|NRP1_ENST00000395995.1_Silent_p.V394V|NRP1_ENST00000374875.1_Silent_p.V213V|NRP1_ENST00000374822.4_Silent_p.V394V			O14786	NRP1_HUMAN	neuropilin 1	394	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	GTTTGGGGAATACTGCAACCA	0.418																																					p.V394V	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.A1182G						.						161	153	156					10																	33510747		2203	4300	6503	SO:0001819	synonymous_variant	8829	exon8			GGGGAATACTGCA	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"CD molecules"	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.1182A>G	chr10.hg19:g.33510747T>C		129.0	0.0		116.0	45.0	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Silent	SNP	ENST00000265371.4	hg19	CCDS7177.1																																																																																			.	.		0.418	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2			C	33510747	T	C	33510747	2	2	226	1	0	0	0	0	0	0	0	1	10669	1393	49	2		2	NRP1	10	33510747	Silent	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10		33510747	102024000	28	31996										
C10orf72	196740	hgsc.bcm.edu	37	chr10	50255074	50255074	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gcagcttcggtttatggaacGtgggggctatcggagctgtg	17	7	0	0			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr10:50255074G>T	ENST00000332853.4	-	7	814	c.791C>A	c.(790-792)aCg>aAg	p.T264K		NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T264R(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						TTTATGGAACGTGGGGGCTAT	0.473																																					p.T264K		Atlas-SNP	.											VSTM4,NS,carcinoma,0,1	VSTM4	83	.	1	Substitution - Missense(1)	lung(1)	c.C791A						.						324	295	305					10																	50255074		2203	4300	6503	SO:0001583	missense	196740	exon7			TGGAACGTGGGGG	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"Immunoglobulin superfamily / V-set domain containing"	26470	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 72"	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.791C>A	chr10.hg19:g.50255074G>T	ENSP00000331062:p.Thr264Lys	128.0	0.0		125.0	38.0	NM_001031746	B4DNI6|Q96MX7	Missense_Mutation	SNP	ENST00000332853.4	hg19	CCDS31198.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.839349	0.32513	.	.	ENSG00000165633	ENST00000332853	T	0.05855	3.38	5.92	5.92	0.95590	.	0.514470	0.21973	N	0.066437	T	0.02649	0.0080	N	0.01352	-0.895	0.80722	D	1	B	0.24768	0.111	B	0.20577	0.03	T	0.56183	-0.8021	10	0.12430	T	0.62	-3.0249	15.8243	0.78686	0.0:0.0:1.0:0.0	.	264	Q8IW00	VSTM4_HUMAN	K	264	ENSP00000331062:T264K	ENSP00000331062:T264K	T	-	2	0	VSTM4	49925080	0.177000	0.23109	0.036000	0.18154	0.071000	0.16799	3.182000	0.50910	2.811000	0.96726	0.555000	0.69702	ACG	.	.		0.473	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984		T	50255074	G	T	50255074	3	4	226	1	0	0	0	0	1	0	0	0	1617	1145	40	1	179	1	C10orf72	10	50255074	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	16744327	50255074	85279673	29	31997										
BTAF1	9044	hgsc.bcm.edu	37	chr10	93744021	93744021	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	atatcctttcagaacatttaTattatgacgaaattgccgtt	5	7	1	2			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr10:93744021T>C	ENST00000265990.6	+	19	2595	c.2287T>C	c.(2287-2289)Tat>Cat	p.Y763H	BTAF1_ENST00000471217.1_3'UTR	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	763					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				AGAACATTTATATTATGACGA	0.353																																					p.Y763H		Atlas-SNP	.											.	BTAF1	148	.	0			c.T2287C						.						103	94	97					10																	93744021		2202	4300	6502	SO:0001583	missense	9044	exon19			CATTTATATTATG	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.2287T>C	chr10.hg19:g.93744021T>C	ENSP00000265990:p.Tyr763His	105.0	0.0		76.0	24.0	NM_003972	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	hg19	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.977054	0.74360	.	.	ENSG00000095564	ENST00000265990	T	0.64803	-0.12	5.67	5.67	0.87782	Domain of unknown function DUF3535 (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.79118	0.4392	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.77731	-0.2478	10	0.27082	T	0.32	-4.614	15.9104	0.79470	0.0:0.0:0.0:1.0	.	763;763	Q2M1V9;O14981	.;BTAF1_HUMAN	H	763	ENSP00000265990:Y763H	ENSP00000265990:Y763H	Y	+	1	0	BTAF1	93734001	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	8.040000	0.89188	2.155000	0.67459	0.528000	0.53228	TAT	.	.		0.353	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		C	93744021	T	C	93744021	3	2	226	1	0	0	0	0	1	0	0	0	1538	1406	49	2	2361	2	BTAF1	10	93744021	Missense_Mutation	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10	43488947	93744021	41790726	30	31998										
TSSC4	10078	hgsc.bcm.edu	37	chr11	2424065	2424065	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gtcctgatgagccgccctcaCccccgtcaggcctcctccca	8	21	2	2			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr11:2424065C>T	ENST00000333256.6	+	3	645	c.202C>T	c.(202-204)Ccc>Tcc	p.P68S	TSSC4_ENST00000380992.1_Intron|AC124057.5_ENST00000433035.1_RNA|TSSC4_ENST00000380996.5_Intron|TSSC4_ENST00000451491.2_Missense_Mutation_p.P68S			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	68										endometrium(3)|large_intestine(1)|lung(4)	8		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCCGCCCTCACCCCCGTCAGG	0.637																																					p.P68S		Atlas-SNP	.											.	TSSC4	19	.	0			c.C202T						.						37	30	32					11																	2424065		2192	4296	6488	SO:0001583	missense	10078	exon2			CCCTCACCCCCGT	AF125568	CCDS7735.1, CCDS73241.1	11p15.5	2008-02-05			ENSG00000184281	ENSG00000184281			12386	protein-coding gene	gene with protein product		603852				10072438	Standard	XM_005252722		Approved		uc001lwl.3	Q9Y5U2	OTTHUMG00000009895	ENST00000333256.6:c.202C>T	chr11.hg19:g.2424065C>T	ENSP00000331087:p.Pro68Ser	80.0	0.0		81.0	33.0	NM_005706	C9JS66|Q86VL2|Q9BRS6	Missense_Mutation	SNP	ENST00000333256.6	hg19	CCDS7735.1	.	.	.	.	.	.	.	.	.	.	C	3.429	-0.116589	0.06838	.	.	ENSG00000184281	ENST00000333256;ENST00000437110;ENST00000435795;ENST00000485682;ENST00000496468;ENST00000451491	T;T;T;T;T;T	0.45276	2.54;1.56;0.9;0.91;1.56;2.54	3.07	0.937	0.19494	.	0.515929	0.16858	U	0.196644	T	0.33030	0.0849	M	0.62723	1.935	0.09310	N	1	B	0.29432	0.244	B	0.27076	0.076	T	0.15867	-1.0422	9	.	.	.	-2.7914	4.7102	0.12868	0.0:0.5819:0.184:0.2342	.	68	Q9Y5U2	TSSC4_HUMAN	S	68	ENSP00000331087:P68S;ENSP00000396925:P68S;ENSP00000403475:P68S;ENSP00000431430:P68S;ENSP00000435013:P68S;ENSP00000411224:P68S	.	P	+	1	0	TSSC4	2380641	0.000000	0.05858	0.001000	0.08648	0.103000	0.19146	-0.004000	0.12878	0.653000	0.30826	0.462000	0.41574	CCC	.	.		0.637	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706		T	2424065	C	T	2424065	3	4	226	1	0	0	0	0	1	0	0	0	16682	507	18	3	204	3	TSSC4	11	2424065	Missense_Mutation	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10		2424065	132582451	31	31999										
OR52B4	143496	hgsc.bcm.edu	37	chr11	4389234	4389234	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gaagagctgagtgatgcaacGatccagggagatgtccccag	14	9	0	4	rs267602877		TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr11:4389234G>A	ENST00000408920.2	-	1	382	c.292C>T	c.(292-294)Cgt>Tgt	p.R98C		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	98					cognition (GO:0050890)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTGATGCAACGATCCAGGGAG	0.527																																					p.R98C		Atlas-SNP	.											.	OR52B4	56	.	0			c.C292T						.						101	104	103					11																	4389234		2145	4245	6390	SO:0001583	missense	143496	exon1			TGCAACGATCCAG	AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"GPCR / Class A : Olfactory receptors"	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.292C>T	chr11.hg19:g.4389234G>A	ENSP00000386160:p.Arg98Cys	137.0	0.0		128.0	49.0	NM_001005161	A6NP68|Q6IFK6	Missense_Mutation	SNP	ENST00000408920.2	hg19	CCDS41609.1	.	.	.	.	.	.	.	.	.	.	G	2.127	-0.400048	0.04865	.	.	ENSG00000221996	ENST00000408920	T	0.03035	4.07	5.28	-10.6	0.00265	GPCR, rhodopsin-like superfamily (1);	1.091190	0.06975	N	0.818824	T	0.01800	0.0057	N	0.11892	0.195	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.48031	-0.9070	10	0.62326	D	0.03	.	5.3366	0.15961	0.5348:0.2427:0.088:0.1345	.	98	Q8NGK2	O52B4_HUMAN	C	98	ENSP00000386160:R98C	ENSP00000386160:R98C	R	-	1	0	OR52B4	4345810	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.536000	0.00438	-2.787000	0.00358	-2.226000	0.00293	CGT	.	.		0.527	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3	NM_001005161		A	4389234	G	A	4389234	3	1	226	1	0	0	0	0	1	0	0	0	11121	1058	37	1	656	1	OR52B4	11	4389234	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	1965169	4389234	130617282	32	32000										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62295933	62295933	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	aggcatggagatcttgggggTcttgaagtgcatctcaggca	15	7	3	2	rs543137707		TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr11:62295933T>C	ENST00000378024.4	-	5	6230	c.5956A>G	c.(5956-5958)Acc>Gcc	p.T1986A	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1986					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				ATCTTGGGGGTCTTGAAGTGC	0.507													T|||	1	0.000199681	8e-04	0	5008	,	,		22609	0		0	False		,,,				2504	0				p.T1986A		Atlas-SNP	.											.	AHNAK	532	.	0			c.A5956G						.						269	276	273					11																	62295933		2202	4299	6501	SO:0001583	missense	79026	exon5			TGGGGGTCTTGAA	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.5956A>G	chr11.hg19:g.62295933T>C	ENSP00000367263:p.Thr1986Ala	102.0	0.0		109.0	8.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	t	0.001	-3.251305	0.00022	.	.	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.00856	5.61	3.78	-1.22	0.09494	.	.	.	.	.	T	0.00300	0.0009	N	0.00459	-1.475	0.09310	N	1	B	0.09022	0.002	B	0.14023	0.01	T	0.42344	-0.9457	9	0.02654	T	1	.	5.0121	0.14317	0.0:0.5779:0.149:0.273	.	1986	Q09666	AHNK_HUMAN	A	75;1986	ENSP00000367263:T1986A	ENSP00000244934:T75A	T	-	1	0	AHNAK	62052509	0.873000	0.30073	0.009000	0.14445	0.052000	0.14988	0.460000	0.21924	-0.580000	0.05944	-0.802000	0.03209	ACC	.	.		0.507	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62295933	T	C	62295933	3	2	226	1	0	0	0	0	1	0	0	0	414	1667	58	2	11836	2	AHNAK	11	62295933	Missense_Mutation	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10	57906699	62295933	72710583	33	32001										
CCDC84	338657	hgsc.bcm.edu	37	chr11	118886070	118886070	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	accgagttggggccaactttGatcacagctccaggaccagt	11	12	1	1			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr11:118886070G>C	ENST00000334418.1	+	10	915	c.859G>C	c.(859-861)Gat>Cat	p.D287H	RPS25_ENST00000528547.1_5'Flank	NM_198489.1	NP_940891.1	Q86UT8	CCD84_HUMAN	coiled-coil domain containing 84	287										breast(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		GGCCAACTTTGATCACAGCTC	0.488																																					p.D287H		Atlas-SNP	.											.	CCDC84	21	.	0			c.G859C						.						39	42	41					11																	118886070		2200	4295	6495	SO:0001583	missense	338657	exon10			AACTTTGATCACA	AB094093	CCDS8405.1	11q23.3	2006-03-13			ENSG00000186166	ENSG00000186166			30460	protein-coding gene	gene with protein product							Standard	NM_198489		Approved	DLNB14	uc001pul.3	Q86UT8	OTTHUMG00000166348	ENST00000334418.1:c.859G>C	chr11.hg19:g.118886070G>C	ENSP00000334767:p.Asp287His	128.0	0.0		118.0	42.0	NM_198489		Missense_Mutation	SNP	ENST00000334418.1	hg19	CCDS8405.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059383	0.93846	.	.	ENSG00000186166	ENST00000334418	T	0.47528	0.84	5.76	5.76	0.90799	.	0.091955	0.64402	D	0.000001	T	0.69655	0.3135	M	0.65498	2.005	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.70817	-0.4769	10	0.87932	D	0	-23.307	19.9738	0.97296	0.0:0.0:1.0:0.0	.	287	Q86UT8	CCD84_HUMAN	H	287	ENSP00000334767:D287H	ENSP00000334767:D287H	D	+	1	0	CCDC84	118391280	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	9.275000	0.95738	2.732000	0.93576	0.655000	0.94253	GAT	.	.		0.488	CCDC84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389315.1	NM_198489		C	118886070	G	C	118886070	3	2	226	1	0	0	0	0	1	0	0	0	2860	1290	45	4	897	4	CCDC84	11	118886070	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	56590137	118886070	16120446	34	32002										
TAS2R50	259296	hgsc.bcm.edu	37	chr12	11138987	11138987	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tcccagtcatgtttccttcaTattcttctgcccacatactc	3	15	4	0			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr12:11138987T>C	ENST00000506868.1	-	1	524	c.473A>G	c.(472-474)tAt>tGt	p.Y158C	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	158					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)	17						GTTTCCTTCATATTCTTCTGC	0.398																																					p.Y158C		Atlas-SNP	.											.	TAS2R50	37	.	0			c.A473G						.						171	164	166					12																	11138987		2203	4300	6503	SO:0001583	missense	259296	exon1			CCTTCATATTCTT	AF494235	CCDS8638.1	12p13.2	2012-08-22			ENSG00000212126	ENSG00000212126		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18882	protein-coding gene	gene with protein product		609627				12379855, 12584440, 16175505	Standard	NM_176890		Approved	T2R51	uc001qzl.2	P59544	OTTHUMG00000162719	ENST00000506868.1:c.473A>G	chr12.hg19:g.11138987T>C	ENSP00000424040:p.Tyr158Cys	120.0	0.0		123.0	41.0	NM_176890	P59545|Q2M255|Q645Y0	Missense_Mutation	SNP	ENST00000506868.1	hg19	CCDS8638.1	.	.	.	.	.	.	.	.	.	.	T	4.909	0.168934	0.09339	.	.	ENSG00000212126	ENST00000506868	T	0.37752	1.18	2.08	-0.897	0.10553	.	1.002760	0.08044	U	0.995590	T	0.31009	0.0783	L	0.58810	1.83	0.09310	N	1	B	0.18013	0.025	B	0.23852	0.049	T	0.36986	-0.9725	10	0.44086	T	0.13	.	3.3518	0.07155	0.0:0.1551:0.2363:0.6086	.	158	P59544	T2R50_HUMAN	C	158	ENSP00000424040:Y158C	ENSP00000424040:Y158C	Y	-	2	0	TAS2R50	11030254	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-0.410000	0.07151	-0.360000	0.08138	0.260000	0.18958	TAT	.	.		0.398	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890		C	11138987	T	C	11138987	3	2	226	1	0	0	0	0	1	0	0	0	15599	1406	49	2	430	2	TAS2R50	12	11138987	Missense_Mutation	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10		11138987	122712908	35	32003										
KRT2	3849	hgsc.bcm.edu	37	chr12	53045636	53045637	+	In_Frame_Ins	INS	-	-	CCAAAGCCGCTGCCGCCT													0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ctccaaagctgctgccgcctINSccaaaaccacctcctctgcc							TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr12:53045636_53045637insCCAAAGCCGCTGCCGCCT	ENST00000309680.3	-	1	311_312	c.290_291insAGGCGGCAGCGGCTTTGG	c.(289-291)gga>ggAGGCGGCAGCGGCTTTGGa	p.97_97G>GGGSGFG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	97	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		tgctgccgcctccaaaaccacc	0.624																																					p.G97delinsGGGSGFG		Atlas-INDEL	.											.,1	KRT2	94	.	0			c.291_292insAGGCGGCAGCGGCTTTGG						.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.290_291insAGGCGGCAGCGGCTTTGG	chr12.hg19:g.53045636_53045637insCCAAAGCCGCTGCCGCCT	Exception_encountered	155.0	0.0		175.0	65.0	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.624	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		CCAAAGCCGCTGCCGCCT	53045637	-	CCAAAGCCGCTGCCGCCT	53045636	7	5	226	1	0	1	1	0	0	0	0	0	8466	1538	54	0	1664	0	KRT2	12	53045636	In_Frame_Ins	INS	-	TCGA-DD-AAVS-01A-11D-A40R-10	41906649	53045636	80806259	36	32004										
PHLDA1	22822	hgsc.bcm.edu	37	chr12	76424919	76424919	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ccctgcccgggctgttgttgCtgctgctgctgctgctgttg	14	13	0	0	rs527917078|rs371223910	byFrequency	TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr12:76424919C>T	ENST00000266671.5	-	1	2793	c.603G>A	c.(601-603)caG>caA	p.Q201Q	RP11-290L1.3_ENST00000552367.1_RNA|PHLDA1_ENST00000602540.1_Silent_p.Q60Q|RP11-290L1.2_ENST00000547721.1_RNA			Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A, member 1	201	PH.|Poly-Gln.				apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634)		p.Q201Q(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	14		Colorectal(145;0.09)				gctgttgttgctgctgctgct	0.642																																					p.Q201Q		Atlas-SNP	.											PHLDA1,caecum,carcinoma,0,2	PHLDA1	39	.	1	Substitution - coding silent(1)	endometrium(1)	c.G603A						.						14	16	16					12																	76424919		2187	4264	6451	SO:0001819	synonymous_variant	22822	exon1			TTGTTGCTGCTGC	Z50194	CCDS31861.1	12q15	2008-08-05				ENSG00000139289			8933	protein-coding gene	gene with protein product	"proline-histidine rich protein"	605335				12384558, 15037619	Standard	NM_007350		Approved	TDAG51, DT1P1B11, PHRIP	uc001sxu.3	Q8WV24		ENST00000266671.5:c.603G>A	chr12.hg19:g.76424919C>T		28.0	0.0		23.0	2.0	NM_007350	A1A4G9|Q15184|Q2TAN2|Q9NZ17	Silent	SNP	ENST00000266671.5	hg19	CCDS31861.1																																																																																			.	.		0.642	PHLDA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405846.2	NM_007350		T	76424919	C	T	76424919	2	4	226	1	0	0	0	0	0	0	0	1	11857	796	28	3		3	PHLDA1	12	76424919	Silent	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10	23379283	76424919	57426976	37	32005										
SH2B3	10019	hgsc.bcm.edu	37	chr12	111885580	111885580	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tcccactcgagtgcggcgccGcctgtgatgtccggctctcc	12	17	1	1	rs74163667		TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr12:111885580G>T	ENST00000341259.2	+	7	1714	c.1357G>T	c.(1357-1359)Gcc>Tcc	p.A453S	SH2B3_ENST00000538307.1_Missense_Mutation_p.A251S	NM_005475.2	NP_005466.1	Q9UQQ2	SH2B3_HUMAN	SH2B adaptor protein 3	453	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic hemopoiesis (GO:0035162)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)	phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	10					Pazopanib(DB06589)	GTGCGGCGCCGCCTGTGATGT	0.642																																					p.A453S		Atlas-SNP	.											.	SH2B3	62	.	0			c.G1357T						.						64	56	59					12																	111885580		2203	4300	6503	SO:0001583	missense	10019	exon7			GGCGCCGCCTGTG	AF055581	CCDS9153.1	12q24.12	2014-09-17				ENSG00000111252		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	29605	protein-coding gene	gene with protein product	"lymphocyte adaptor protein"	605093				10799879	Standard	NM_005475		Approved	LNK, IDDM20	uc001tse.3	Q9UQQ2		ENST00000341259.2:c.1357G>T	chr12.hg19:g.111885580G>T	ENSP00000345492:p.Ala453Ser	57.0	0.0		64.0	4.0	NM_005475	B9EGG5|O95184	Missense_Mutation	SNP	ENST00000341259.2	hg19	CCDS9153.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476594	0.44044	.	.	ENSG00000111252	ENST00000341259;ENST00000551001;ENST00000538307	T;T	0.43294	0.95;0.95	4.96	4.96	0.65561	SH2 motif (1);	0.096959	0.64402	N	0.000001	T	0.22126	0.0533	N	0.08118	0	0.80722	D	1	B;B;P	0.38535	0.386;0.289;0.635	B;B;B	0.41764	0.366;0.201;0.347	T	0.12400	-1.0549	10	0.06236	T	0.91	-2.7783	9.9527	0.41649	0.1278:0.0:0.8722:0.0	.	251;317;453	F5GYM4;Q59H48;Q9UQQ2	.;.;SH2B3_HUMAN	S	453;263;251	ENSP00000345492:A453S;ENSP00000440597:A251S	ENSP00000345492:A453S	A	+	1	0	SH2B3	110369963	1.000000	0.71417	0.946000	0.38457	0.705000	0.40729	6.249000	0.72427	2.474000	0.83562	0.462000	0.41574	GCC	.	.		0.642	SH2B3-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404779.1	NM_005475		T	111885580	G	T	111885580	3	4	226	1	0	0	0	0	1	0	0	0	14244	1087	38	1	1379	1	SH2B3	12	111885580	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	35460661	111885580	21966315	38	32006										
EP400	57634	hgsc.bcm.edu	37	chr12	132512745	132512746	+	Frame_Shift_Del	DEL	CA	CA	-													0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ggaaggaggccgggccagcgCacagttacacttcatcctca							TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr12:132512745_132512746delCA	ENST00000333577.4	+	28	5510_5511	c.5401_5402delCA	c.(5401-5403)cacfs	p.H1801fs	EP400_ENST00000332482.4_Frame_Shift_Del_p.H1728fs|EP400_ENST00000389562.2_Frame_Shift_Del_p.H1764fs|EP400_ENST00000389561.2_Frame_Shift_Del_p.H1765fs|EP400_ENST00000330386.6_Frame_Shift_Del_p.H1684fs			Q96L91	EP400_HUMAN	E1A binding protein p400	1801					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CGGGCCAGCGCACAGTTACACT	0.559																																					p.1764_1765del		Atlas-INDEL	.											.	EP400	370	.	0			c.5292_5293del						.																																			SO:0001589	frameshift_variant	57634	exon27			.	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.5401_5402delCA	chr12.hg19:g.132512747_132512748delCA	ENSP00000333602:p.His1801fs	114.0	0.0		85.0	35.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Frame_Shift_Del	DEL	ENST00000333577.4	hg19																																																																																				.	.		0.559	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		-	132512746	CA	-	132512745	7	5	226	1	0	1	0	1	0	0	0	0	5151	710	25	0	5392	0	EP400	12	132512745	Frame_Shift_Del	DEL	CA	TCGA-DD-AAVS-01A-11D-A40R-10	20627165	132512745	1339150	39	32007										
NPAS3	64067	hgsc.bcm.edu	37	chr14	34269937	34269937	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gtgctcccgctggtgcacagGgtgaccgggaccctggccgc	16	15	0	1			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr14:34269937G>A	ENST00000356141.4	+	12	2424	c.2424G>A	c.(2422-2424)agG>agA	p.R808R	NPAS3_ENST00000346562.2_Silent_p.R776R|NPAS3_ENST00000551492.1_Silent_p.R813R|NPAS3_ENST00000548645.1_Silent_p.R778R|NPAS3_ENST00000357798.5_Silent_p.R795R			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	808					locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		TGGTGCACAGGGTGACCGGGA	0.716																																					p.R808R		Atlas-SNP	.											.	NPAS3	266	.	0			c.G2424A						.						9	9	9					14																	34269937		2159	4216	6375	SO:0001819	synonymous_variant	64067	exon12			GCACAGGGTGACC	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.2424G>A	chr14.hg19:g.34269937G>A		41.0	0.0		39.0	9.0	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Silent	SNP	ENST00000356141.4	hg19	CCDS53891.1																																																																																			.	.		0.716	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			A	34269937	G	A	34269937	2	1	226	1	0	0	0	0	0	0	0	1	10573	1223	43	3		3	NPAS3	14	34269937	Silent	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10		34269937	73079603	40	32008										
RFX7	64864	hgsc.bcm.edu	37	chr15	56388062	56388062	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	agaagcaactgatagagtgaTagtgctttgattattgcctg	11	5	0	5			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr15:56388062T>C	ENST00000559447.2	-	9	1844	c.1573A>G	c.(1573-1575)Atc>Gtc	p.I525V	RFX7_ENST00000423270.1_Missense_Mutation_p.I622V|RFX7_ENST00000422057.1_Missense_Mutation_p.I525V|RFX7_ENST00000317318.6_Missense_Mutation_p.I622V			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	525					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GATAGAGTGATAGTGCTTTGA	0.408																																					p.I622V		Atlas-SNP	.											.	RFX7	170	.	0			c.A1864G						.						91	87	88					15																	56388062		1995	4169	6164	SO:0001583	missense	64864	exon9			GAGTGATAGTGCT			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.1573A>G	chr15.hg19:g.56388062T>C	ENSP00000453281:p.Ile525Val	21.0	0.0		23.0	9.0	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	hg19		.	.	.	.	.	.	.	.	.	.	T	0.153	-1.089567	0.01873	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	T;T;T	0.49432	0.78;0.78;0.78	5.5	-9.57	0.00562	.	1.024190	0.07800	N	0.956385	T	0.15782	0.0380	N	0.03608	-0.345	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42085	-0.9472	10	0.02654	T	1	1.1266	10.5474	0.45068	0.0:0.2693:0.153:0.5777	.	525;525	Q2KHR2;C9JU50	RFX7_HUMAN;.	V	525;622;622	ENSP00000387504:I525V;ENSP00000313299:I622V;ENSP00000397644:I622V	ENSP00000313299:I622V	I	-	1	0	RFX7	54175354	0.524000	0.26282	0.161000	0.22692	0.928000	0.56348	-0.234000	0.09028	-1.265000	0.02449	-1.151000	0.01829	ATC	.	.		0.408	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		C	56388062	T	C	56388062	3	2	226	1	0	0	0	0	1	0	0	0	13283	1406	49	2	2522	2	RFX7	15	56388062	Missense_Mutation	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10		56388062	46143330	41	32009										
HERC1	8925	hgsc.bcm.edu	37	chr15	63916053	63916053	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ttcagcttaactacttgtctCgctatttggacaaaaatagg	7	8	2	0			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr15:63916053C>T	ENST00000443617.2	-	73	13569	c.13482G>A	c.(13480-13482)gcG>gcA	p.A4494A		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4494					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CTACTTGTCTCGCTATTTGGA	0.453																																					p.A4494A		Atlas-SNP	.											.	HERC1	624	.	0			c.G13482A						.						81	80	80					15																	63916053		1943	4142	6085	SO:0001819	synonymous_variant	8925	exon73			TTGTCTCGCTATT	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13482G>A	chr15.hg19:g.63916053C>T		61.0	0.0		72.0	24.0	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.		0.453	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63916053	C	T	63916053	2	4	226	1	0	0	0	0	0	0	0	1	7066	871	31	1		1	HERC1	15	63916053	Silent	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10	7527991	63916053	38615339	42	32010										
AXIN1	8312	hgsc.bcm.edu	37	chr16	354369	354369	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ccgcgtgcgctgcacagcctCcaggcggtggatgagctcct	14	15	0	1			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr16:354369C>A	ENST00000262320.3	-	5	1560	c.1189G>T	c.(1189-1191)Gag>Tag	p.E397*	AXIN1_ENST00000354866.3_Nonsense_Mutation_p.E397*|AXIN1_ENST00000481769.1_5'UTR	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	397	Interaction with GSK3B. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)	p.?(1)		biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				TGCACAGCCTCCAGGCGGTGG	0.706																																					p.E397X		Atlas-SNP	.											.	AXIN1	290	.	1	Unknown(1)	liver(1)	c.G1189T						.						29	29	29					16																	354369		2202	4293	6495	SO:0001587	stop_gained	8312	exon5			CAGCCTCCAGGCG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1189G>T	chr16.hg19:g.354369C>A	ENSP00000262320:p.Glu397*	105.0	0.0		71.0	44.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Nonsense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	C	41	9.002289	0.99033	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-0.2156	18.617	0.91306	0.0:1.0:0.0:0.0	.	.	.	.	X	397	.	ENSP00000262320:E397X	E	-	1	0	AXIN1	294370	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	7.625000	0.83145	2.418000	0.82041	0.563000	0.77884	GAG	.	.		0.706	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	354369	C	A	354369	4	1	226	1	0	0	0	0	0	1	0	0	1236	864	30	3	1427	3	AXIN1	16	354369	Nonsense_Mutation	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10		354369	90000384	43	32011										
RNF167	26001	hgsc.bcm.edu	37	chr17	4848077	4848077	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	acctgccccatttgcaagcaGcctgttcatcggggtcctgg	11	14	1	0			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr17:4848077G>A	ENST00000262482.6	+	10	1475	c.819G>A	c.(817-819)caG>caA	p.Q273Q	RNF167_ENST00000571816.1_Silent_p.Q273Q|RNF167_ENST00000575111.1_Silent_p.Q273Q|RNF167_ENST00000572430.1_Silent_p.Q273Q|RNF167_ENST00000576229.1_Silent_p.Q238Q	NM_015528.1	NP_056343.1	Q9H6Y7	RN167_HUMAN	ring finger protein 167	273					negative regulation of cell cycle (GO:0045786)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(1)	4						TTTGCAAGCAGCCTGTTCATC	0.602																																					p.Q273Q		Atlas-SNP	.											.	RNF167	14	.	0			c.G819A						.						112	111	112					17																	4848077		2203	4300	6503	SO:0001819	synonymous_variant	26001	exon10			CAAGCAGCCTGTT	AL050060	CCDS11060.1	17p13.3	2013-02-21			ENSG00000108523	ENSG00000108523		"RING-type (C3HC4) zinc fingers"	24544	protein-coding gene	gene with protein product		610431				23129617, 23353890	Standard	NM_015528		Approved	DKFZP566H073	uc002fzs.3	Q9H6Y7	OTTHUMG00000099397	ENST00000262482.6:c.819G>A	chr17.hg19:g.4848077G>A		119.0	0.0		114.0	38.0	NM_015528	D3DTK8|Q6XYE0|Q8NDC1|Q9Y3V1	Silent	SNP	ENST00000262482.6	hg19	CCDS11060.1																																																																																			.	.		0.602	RNF167-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216854.3	NM_015528		A	4848077	G	A	4848077	2	1	226	1	0	0	0	0	0	0	0	1	13473	962	34	3		3	RNF167	17	4848077	Silent	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10		4848077	76347133	44	32012										
ALOX15B	247	hgsc.bcm.edu	37	chr17	7951790	7951790	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ttccagagccgcctggcccaGatctcgaggggcatccagga	13	14	1	2			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr17:7951790G>C	ENST00000380183.4	+	14	2077	c.1938G>C	c.(1936-1938)caG>caC	p.Q646H	ALOX15B_ENST00000380173.2_Missense_Mutation_p.Q617H|ALOX15B_ENST00000573359.1_Missense_Mutation_p.Q572H|ALOX15B_ENST00000572022.1_Missense_Mutation_p.Q634H	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	646	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						GCCTGGCCCAGATCTCGAGGG	0.637																																					p.Q646H		Atlas-SNP	.											.	ALOX15B	66	.	0			c.G1938C						.						68	73	71					17																	7951790		2203	4300	6503	SO:0001583	missense	247	exon14			GGCCCAGATCTCG	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"Arachidonate lipoxygenases"	434	protein-coding gene	gene with protein product		603697	"arachidonate 15-lipoxygenase, second type"			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1938G>C	chr17.hg19:g.7951790G>C	ENSP00000369530:p.Gln646His	55.0	0.0		47.0	19.0	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	hg19	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.596515	0.28445	.	.	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	D;D	0.90004	-2.6;-2.6	3.74	2.77	0.32553	Lipoxygenase, C-terminal (3);	0.710389	0.13984	N	0.349250	D	0.92277	0.7550	M	0.72353	2.195	0.29685	N	0.841373	P;P;P;D	0.53619	0.916;0.898;0.898;0.961	P;P;P;P	0.62014	0.852;0.769;0.769;0.897	D	0.86855	0.2026	10	0.62326	D	0.03	-23.1093	10.0815	0.42393	0.1028:0.0:0.8972:0.0	.	634;572;617;646	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	H	617;572;646	ENSP00000369520:Q617H;ENSP00000369530:Q646H	ENSP00000344337:Q572H	Q	+	3	2	ALOX15B	7892515	0.970000	0.33590	1.000000	0.80357	0.147000	0.21601	0.603000	0.24149	0.899000	0.36444	0.561000	0.74099	CAG	.	.		0.637	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2			C	7951790	G	C	7951790	3	2	226	1	0	0	0	0	1	0	0	0	539	933	33	4	1992	4	ALOX15B	17	7951790	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	3103713	7951790	73243420	45	32013										
ZNF830	91603	hgsc.bcm.edu	37	chr17	33288644	33288644	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gcgagtgataaatcaggaagAattgcggcggttaatgaagg	15	4	1	3			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr17:33288644A>G	ENST00000361952.3	+	1	96	c.59A>G	c.(58-60)gAa>gGa	p.E20G	CCT6B_ENST00000436961.3_5'Flank|CCT6B_ENST00000314144.5_5'Flank|CCT6B_ENST00000421975.3_5'Flank	NM_052857.3	NP_443089.3	Q96NB3	ZN830_HUMAN	zinc finger protein 830	20					blastocyst growth (GO:0001832)|mitotic nuclear division (GO:0007067)|nuclear cell cycle DNA replication (GO:0033260)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|liver(2)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(249;0.17)				AATCAGGAAGAATTGCGGCGG	0.567																																					p.E20G		Atlas-SNP	.											.	ZNF830	26	.	0			c.A59G						.						87	93	91					17																	33288644		2203	4300	6503	SO:0001583	missense	91603	exon1			AGGAAGAATTGCG	AK055707	CCDS32618.1	17q12	2013-10-23	2008-03-25	2008-03-25	ENSG00000198783	ENSG00000198783			28291	protein-coding gene	gene with protein product	"orphan maintenance of genome 1"		"coiled-coil domain containing 16"	CCDC16		23066043	Standard	NM_052857		Approved	MGC20398, OMCG1	uc002hih.4	Q96NB3	OTTHUMG00000179771	ENST00000361952.3:c.59A>G	chr17.hg19:g.33288644A>G	ENSP00000354518:p.Glu20Gly	159.0	0.0		144.0	49.0	NM_052857	Q96F60|Q96GZ5|Q9BU38	Missense_Mutation	SNP	ENST00000361952.3	hg19	CCDS32618.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.552719	0.86127	.	.	ENSG00000198783	ENST00000361952	T	0.18016	2.24	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.37865	0.1019	L	0.61218	1.895	0.54753	D	0.999986	D	0.89917	1.0	D	0.85130	0.997	T	0.11817	-1.0572	10	0.72032	D	0.01	-2.7862	11.7947	0.52093	1.0:0.0:0.0:0.0	.	20	Q96NB3	ZN830_HUMAN	G	20	ENSP00000354518:E20G	ENSP00000354518:E20G	E	+	2	0	ZNF830	30312757	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	7.311000	0.78958	2.279000	0.76181	0.533000	0.62120	GAA	.	.		0.567	ZNF830-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448018.1	NM_052857		G	33288644	A	G	33288644	3	3	226	1	0	0	0	0	1	0	0	0	18199	246	9	2	61	2	ZNF830	17	33288644	Missense_Mutation	SNP	A	TCGA-DD-AAVS-01A-11D-A40R-10	25336854	33288644	47906566	46	32014										
WNK4	65266	hgsc.bcm.edu	37	chr17	40947049	40947049	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	ccattctcctccagcacaccCgagtttccggtcccactctc	5	20	2	0			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr17:40947049C>A	ENST00000246914.5	+	14	2631	c.2610C>A	c.(2608-2610)ccC>ccA	p.P870P		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	870					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CCAGCACACCCGAGTTTCCGG	0.572																																					p.P870P	Esophageal Squamous(6;201 374 4964 23855 42828)	Atlas-SNP	.											.	WNK4	182	.	0			c.C2610A						.						186	168	174					17																	40947049		2203	4300	6503	SO:0001819	synonymous_variant	65266	exon14			CACACCCGAGTTT	AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"protein kinase, lysine deficient 4"	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.2610C>A	chr17.hg19:g.40947049C>A		121.0	0.0		122.0	44.0	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Silent	SNP	ENST00000246914.5	hg19	CCDS11439.1																																																																																			.	.		0.572	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1			A	40947049	C	A	40947049	2	1	226	1	0	0	0	0	0	0	0	1	17395	639	23	1		1	WNK4	17	40947049	Silent	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10	7658405	40947049	40248161	47	32015										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3187611	3187612	+	Frame_Shift_Ins	INS	-	-	A													0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tggtcttcattcagcttggcINSatgatatgtctcggtttctt							TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr18:3187611_3187612insA	ENST00000356443.4	-	5	1128_1129	c.795_796insT	c.(793-798)catgccfs	p.A266fs	MYOM1_ENST00000261606.7_Frame_Shift_Ins_p.A266fs|RP13-270P17.2_ENST00000580139.1_RNA|MYOM1_ENST00000400569.3_Frame_Shift_Ins_p.A266fs	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	266					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TTCAGCTTGGCATGATATGTCT	0.361																																					p.A266fs		Atlas-INDEL	.											.	MYOM1	192	.	0			c.796_797insT						.																																			SO:0001589	frameshift_variant	8736	exon5			.	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.796dupT	chr18.hg19:g.3187612_3187612dupA	ENSP00000348821:p.Ala266fs	103.0	0.0		91.0	29.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Frame_Shift_Ins	INS	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.361	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		A	3187612	-	A	3187611	7	5	226	1	0	1	1	0	0	0	0	0	10100	710	25	0	4397	0	MYOM1	18	3187611	Frame_Shift_Ins	INS	-	TCGA-DD-AAVS-01A-11D-A40R-10		3187611	74889637	48	32016										
C18orf45	85019	hgsc.bcm.edu	37	chr18	21001406	21001406	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gtccaccaatgagcgtctgcCacctggaaaggacaaggggc	13	12	1	1			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr18:21001406C>T	ENST00000383233.3	-	3	174	c.122G>A	c.(121-123)tGg>tAg	p.W41*	TMEM241_ENST00000542162.1_Nonsense_Mutation_p.W41*|TMEM241_ENST00000399707.1_Intron|TMEM241_ENST00000450466.2_5'UTR	NM_032933.4	NP_116322.3	Q24JQ0	TM241_HUMAN	transmembrane protein 241	41						integral component of membrane (GO:0016021)											GAGCGTCTGCCACCTGGAAAG	0.493																																					p.W41X		Atlas-SNP	.											.	.	.	.	0			c.G122A						.						99	75	83					18																	21001406		2203	4300	6503	SO:0001587	stop_gained	85019	exon3			GTCTGCCACCTGG	BC082984	CCDS11876.2	18q11.2	2011-11-25	2011-11-25	2011-11-25	ENSG00000134490	ENSG00000134490			31723	protein-coding gene	gene with protein product		615430	"chromosome 18 open reading frame 45"	C18orf45		12477932	Standard	NM_032933		Approved	MGC11386, FLJ44259	uc002kuf.3	Q24JQ0	OTTHUMG00000131771	ENST00000383233.3:c.122G>A	chr18.hg19:g.21001406C>T	ENSP00000372720:p.Trp41*	61.0	0.0		80.0	33.0	NM_032933	I0J130|Q6ZTS7|Q6ZW41	Nonsense_Mutation	SNP	ENST00000383233.3	hg19	CCDS11876.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.690917|5.690917	0.96793|0.96793	.|.	.|.	ENSG00000134490|ENSG00000134490	ENST00000497608|ENST00000383233;ENST00000542162	.|.	.|.	.|.	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	.|0.089767	.|0.50627	.|D	.|0.000106	T|.	0.73133|.	0.3548|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.68973|.	-0.5268|.	4|.	.|0.33141	.|T	.|0.24	-35.7723|-35.7723	18.5659|18.5659	0.91116|0.91116	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	S|X	68|41	.|.	.|ENSP00000372720:W41X	G|W	-|-	1|2	0|0	C18orf45|C18orf45	19255404|19255404	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.877000|0.877000	0.50540|0.50540	5.500000|5.500000	0.66943|0.66943	2.678000|2.678000	0.91216|0.91216	0.643000|0.643000	0.83706|0.83706	GGC|TGG	.	.		0.493	TMEM241-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254702.3	NM_032933		T	21001406	C	T	21001406	4	4	226	1	0	0	0	0	0	1	0	0	1905	595	21	3	820	3	C18orf45	18	21001406	Nonsense_Mutation	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10	17813795	21001406	57075842	49	32017										
CDH19	28513	hgsc.bcm.edu	37	chr18	64212133	64212133	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	gattcagagacagtcaagcgGtataaacctttaaaaacaaa	7	7	2	1			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr18:64212133G>A	ENST00000540086.1	-	6	1029	c.783C>T	c.(781-783)taC>taT	p.Y261Y	CDH19_ENST00000262150.2_Silent_p.Y261Y	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	371	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				CAGTCAAGCGGTATAAACCTT	0.328																																					p.Y261Y		Atlas-SNP	.											.	CDH19	141	.	0			c.C783T						.						73	66	69					18																	64212133		2203	4300	6503	SO:0001819	synonymous_variant	28513	exon6			CAAGCGGTATAAA	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"Cadherins / Major cadherins"	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000540086.1:c.783C>T	chr18.hg19:g.64212133G>A		53.0	0.0		54.0	21.0	NM_021153	O15098	Silent	SNP	ENST00000540086.1	hg19	CCDS59325.1																																																																																			.	.		0.328	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153		A	64212133	G	A	64212133	2	1	226	1	0	0	0	0	0	0	0	1	3106	1256	44	3		3	CDH19	18	64212133	Silent	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	43210727	64212133	13865115	50	32018										
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2413945	2413945	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tcctgagagccctgtggtcaGcacccccaccaaatcgatgc	9	16	1	1			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr19:2413945G>A	ENST00000332578.3	+	9	1400	c.1400G>A	c.(1399-1401)aGc>aAc	p.S467N		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	467					plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGTGGTCAGCACCCCCACC	0.622																																					p.S467N		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.G1400A						.						28	30	29					19																	2413945		2203	4300	6503	SO:0001583	missense	360200	exon9			TGGTCAGCACCCC	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"Serine peptidases / Transmembrane"	30079	protein-coding gene	gene with protein product	"polyserase 1"	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.1400G>A	chr19.hg19:g.2413945G>A	ENSP00000330264:p.Ser467Asn	65.0	0.0		63.0	24.0	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	hg19	CCDS12088.1	.	.	.	.	.	.	.	.	.	.	G	0.234	-1.018527	0.02078	.	.	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.87887	-2.31	3.81	-7.3	0.01446	.	0.666044	0.12640	N	0.451440	T	0.61974	0.2390	N	0.01874	-0.695	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.57171	-0.7857	10	0.13108	T	0.6	.	12.5008	0.55953	0.1482:0.1298:0.722:0.0	.	467;501	Q7Z410;E7EMP4	TMPS9_HUMAN;.	N	501;467	ENSP00000330264:S467N	ENSP00000330264:S467N	S	+	2	0	TMPRSS9	2364945	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.888000	0.01616	-1.172000	0.02762	-0.518000	0.04402	AGC	.	.		0.622	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		A	2413945	G	A	2413945	3	1	226	1	0	0	0	0	1	0	0	0	16268	971	34	3	1434	3	TMPRSS9	19	2413945	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10		2413945	56715038	51	32019										
LGI4	163175	hgsc.bcm.edu	37	chr19	35617194	35617194	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	catggagtccccaatgtagcGtgtgaggcacaggaacacgt	13	10	0	1			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr19:35617194G>A	ENST00000310123.3	-	8	1798	c.1279C>T	c.(1279-1281)Cgc>Tgc	p.R427C	LGI4_ENST00000392225.3_Silent_p.H452H|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	427					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CCAATGTAGCGTGTGAGGCAC	0.617																																					p.R427C		Atlas-SNP	.											.	LGI4	32	.	0			c.C1279T						.						33	29	30					19																	35617194		2203	4300	6503	SO:0001583	missense	163175	exon8			TGTAGCGTGTGAG	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.1279C>T	chr19.hg19:g.35617194G>A	ENSP00000312273:p.Arg427Cys	129.0	0.0		146.0	60.0	NM_139284	B2RN53|B9EGS7|Q5M8T1	Missense_Mutation	SNP	ENST00000310123.3	hg19	CCDS12444.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.140520	0.77775	.	.	ENSG00000153902	ENST00000310123;ENST00000437421	T	0.81163	-1.46	4.66	4.66	0.58398	.	0.000000	0.56097	D	0.000025	D	0.86112	0.5855	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86324	0.1694	10	0.56958	D	0.05	.	10.3441	0.43895	0.0:0.0:0.8037:0.1963	.	338;427	Q658V8;Q8N135	.;LGI4_HUMAN	C	427	ENSP00000312273:R427C	ENSP00000312273:R427C	R	-	1	0	LGI4	40309034	1.000000	0.71417	0.969000	0.41365	0.991000	0.79684	7.729000	0.84864	2.147000	0.66899	0.585000	0.79938	CGC	.	.		0.617	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1			A	35617194	G	A	35617194	3	1	226	1	0	0	0	0	1	0	0	0	8763	1145	40	1	342	1	LGI4	19	35617194	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10	33203249	35617194	23511789	52	32020										
CYP2A7	1549	hgsc.bcm.edu	37	chr19	41383137	41383137	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	aacttggtgtcctttttaacCctgcgggccaaactcatggg	10	11	1	0	rs148915421	byFrequency	TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr19:41383137C>A	ENST00000301146.4	-	7	1660	c.1119G>T	c.(1117-1119)agG>agT	p.R373S	CYP2A7_ENST00000291764.3_Missense_Mutation_p.R322S|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	373						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCTTTTTAACCCTGCGGGCCA	0.542																																					p.R373S		Atlas-SNP	.											.	CYP2A7	71	.	0			c.G1119T						.						103	91	95					19																	41383137		2203	4299	6502	SO:0001583	missense	1549	exon7			TTTAACCCTGCGG	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"Cytochrome P450s"	2611	protein-coding gene	gene with protein product		608054	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.1119G>T	chr19.hg19:g.41383137C>A	ENSP00000301146:p.Arg373Ser	204.0	0.0		207.0	69.0	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	hg19	CCDS12569.1	.	.	.	.	.	.	.	.	.	.	C	2.036	-0.421147	0.04734	.	.	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.68331	-0.32;-0.32	2.29	-1.27	0.09347	.	0.317790	0.30565	U	0.009351	T	0.40247	0.1109	N	0.13168	0.305	0.09310	N	1	B;B;B	0.22541	0.06;0.03;0.071	B;B;B	0.28638	0.062;0.03;0.092	T	0.15321	-1.0441	10	0.23891	T	0.37	.	3.6874	0.08334	0.0:0.3939:0.2017:0.4044	.	373;322;373	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	S	373;322	ENSP00000301146:R373S;ENSP00000291764:R322S	ENSP00000291764:R322S	R	-	3	2	CYP2A7	46074977	0.000000	0.05858	0.000000	0.03702	0.184000	0.23303	-2.901000	0.00704	-0.226000	0.09899	0.184000	0.17185	AGG	.	C|0.978;T|0.022		0.542	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589		A	41383137	C	A	41383137	3	1	226	1	0	0	0	0	1	0	0	0	4165	622	22	3	377	3	CYP2A7	19	41383137	Missense_Mutation	SNP	C	TCGA-DD-AAVS-01A-11D-A40R-10	5765943	41383137	17745846	53	32021										
PAK7	57144	hgsc.bcm.edu	37	chr20	9561354	9561354	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	tcttctccctgtacttttcgGtcgtgtagtcagcagtagta	9	10	3	0			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chr20:9561354G>T	ENST00000378429.3	-	5	974	c.428C>A	c.(427-429)aCc>aAc	p.T143N	PAK7_ENST00000378423.1_Missense_Mutation_p.T143N|PAK7_ENST00000353224.5_Missense_Mutation_p.T143N	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	143	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			GTACTTTTCGGTCGTGTAGTC	0.512																																					p.T143N		Atlas-SNP	.											.	PAK7	194	.	0			c.C428A						.						195	191	192					20																	9561354		2203	4300	6503	SO:0001583	missense	57144	exon4			TTTTCGGTCGTGT	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.428C>A	chr20.hg19:g.9561354G>T	ENSP00000367686:p.Thr143Asn	136.0	0.0		144.0	58.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	G	0.036	-1.304932	0.01353	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.43688	0.94;0.94;0.94	5.31	5.31	0.75309	.	0.658377	0.15738	N	0.247078	T	0.32224	0.0822	L	0.29908	0.895	0.09310	N	1	B;B	0.12013	0.005;0.002	B;B	0.19391	0.025;0.002	T	0.11665	-1.0578	9	.	.	.	.	12.7852	0.57500	0.0853:0.0:0.9147:0.0	.	143;143	B0AZM9;Q9P286	.;PAK7_HUMAN	N	143;143;143;91	ENSP00000367686:T143N;ENSP00000322957:T143N;ENSP00000367679:T143N	.	T	-	2	0	PAK7	9509354	0.133000	0.22466	0.014000	0.15608	0.035000	0.12851	3.119000	0.50422	2.503000	0.84419	0.544000	0.68410	ACC	.	.		0.512	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			T	9561354	G	T	9561354	3	4	226	1	0	0	0	0	1	0	0	0	11414	1261	44	3	1759	3	PAK7	20	9561354	Missense_Mutation	SNP	G	TCGA-DD-AAVS-01A-11D-A40R-10		9561354	53464166	54	32022										
TAF9B	51616	hgsc.bcm.edu	37	chrX	77393271	77393271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.113207547169811	6	1	1.83288888888889	3.81851851851852	1.20584795321637	1	1	0	taattaaggacttcagcctaTagtttggagctgttaagcag	10	6	1	0			TCGA-DD-AAVS-01A-11D-A40R-10	TCGA-DD-AAVS-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb1a12bf-565b-47ad-b538-1b8bdcfb6f98	05aee9b3-772a-4c49-ac5b-c9d25f14da7e	g.chrX:77393271T>C	ENST00000341864.5	-	4	474	c.380A>G	c.(379-381)tAt>tGt	p.Y127C		NM_015975.4	NP_057059.2	Q9HBM6	TAF9B_HUMAN	TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa	127					DNA-templated transcription, initiation (GO:0006352)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell growth (GO:0030307)|programmed cell death (GO:0012501)|protein stabilization (GO:0050821)|response to organic cyclic compound (GO:0014070)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	14						CTTCAGCCTATAGTTTGGAGC	0.373																																					p.Y127C		Atlas-SNP	.											.	TAF9B	30	.	0			c.A380G						.						79	71	74					X																	77393271		2203	4296	6499	SO:0001583	missense	51616	exon4			AGCCTATAGTTTG	AF220509	CCDS35340.1	Xq13.1-q21.1	2010-08-16	2006-01-04	2006-01-04	ENSG00000187325	ENSG00000187325			17306	protein-coding gene	gene with protein product		300754	"TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa"	TAF9L		15899866	Standard	XM_005262142		Approved	TAFII31L, DN-7, DN7, TFIID-31	uc004eda.3	Q9HBM6	OTTHUMG00000021887	ENST00000341864.5:c.380A>G	chrX.hg19:g.77393271T>C	ENSP00000339917:p.Tyr127Cys	233.0	1.0		223.0	170.0	NM_015975	B2RUZ9|Q9Y2S3	Missense_Mutation	SNP	ENST00000341864.5	hg19	CCDS35340.1	.	.	.	.	.	.	.	.	.	.	T	17.59	3.427319	0.62733	.	.	ENSG00000187325	ENST00000341864	T	0.55234	0.53	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.73442	0.3587	M	0.87097	2.86	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77678	-0.2498	10	0.87932	D	0	-6.0938	10.4058	0.44256	0.0:0.0:0.0:1.0	.	127	Q9HBM6	TAF9B_HUMAN	C	127	ENSP00000339917:Y127C	ENSP00000339917:Y127C	Y	-	2	0	TAF9B	77279927	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.249000	0.78278	1.575000	0.49775	0.486000	0.48141	TAT	.	.		0.373	TAF9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057308.1	NM_015975		C	77393271	T	C	77393271	3	2	226	1	0	0	0	0	1	0	0	0	15551	1406	49	2	391	2	TAF9B	23	77393271	Missense_Mutation	SNP	T	TCGA-DD-AAVS-01A-11D-A40R-10		77393271	77877289	55	32023										
DNAJC16	23341	hgsc.bcm.edu	37	chr1	15888720	15888720	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gtcctttgccctggcaaacaCtcaagacacagtgagatttg	9	11	1	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:15888720C>G	ENST00000375847.3	+	9	1402	c.1238C>G	c.(1237-1239)aCt>aGt	p.T413S	DNAJC16_ENST00000483270.1_3'UTR|DNAJC16_ENST00000375849.1_Missense_Mutation_p.T413S|DNAJC16_ENST00000375838.1_Missense_Mutation_p.T413S	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	413					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		CTGGCAAACACTCAAGACACA	0.483																																					p.T413S		Atlas-SNP	.											.	DNAJC16	59	.	0			c.C1238G						.						185	164	171					1																	15888720		2203	4300	6503	SO:0001583	missense	23341	exon9			CAAACACTCAAGA	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.1238C>G	chr1.hg19:g.15888720C>G	ENSP00000365007:p.Thr413Ser	135.0	0.0		127.0	46.0	NM_015291	Q68D57|Q86X32|Q8N5P4	Missense_Mutation	SNP	ENST00000375847.3	hg19	CCDS30606.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.615570	0.28801	.	.	ENSG00000116138	ENST00000375847;ENST00000375838;ENST00000375849;ENST00000546230	T;T;T	0.15718	2.4;2.4;2.4	5.96	5.0	0.66597	.	0.206151	0.50627	N	0.000101	T	0.11965	0.0291	N	0.21097	0.63	0.21967	N	0.999444	B;B	0.11235	0.001;0.004	B;B	0.12156	0.002;0.007	T	0.20605	-1.0270	10	0.07030	T	0.85	-11.3812	17.6403	0.88133	0.0:0.8666:0.1334:0.0	.	413;413	Q9Y2G8;Q5TDG9	DJC16_HUMAN;.	S	413	ENSP00000365007:T413S;ENSP00000364998:T413S;ENSP00000365009:T413S	ENSP00000364998:T413S	T	+	2	0	DNAJC16	15761307	0.995000	0.38212	0.963000	0.40424	0.965000	0.64279	3.336000	0.52113	2.833000	0.97629	0.650000	0.86243	ACT	.	.		0.483	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		G	15888720	C	G	15888720	3	3	227	1	0	0	0	0	1	0	0	0	4637	565	20	4	1268	4	DNAJC16	1	15888720	Missense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10		15888720	233361901	1	32024										
SPEN	23013	hgsc.bcm.edu	37	chr1	16199516	16199516	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gattggatgatacagtttccAtagcatctcgtagtagagag	11	6	1	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:16199516A>G	ENST00000375759.3	+	2	493	c.289A>G	c.(289-291)Ata>Gta	p.I97V		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	97					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TACAGTTTCCATAGCATCTCG	0.522																																					p.I97V		Atlas-SNP	.											.	SPEN	374	.	0			c.A289G						.						124	113	117					1																	16199516		2203	4300	6503	SO:0001583	missense	23013	exon2			GTTTCCATAGCAT		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.289A>G	chr1.hg19:g.16199516A>G	ENSP00000364912:p.Ile97Val	149.0	0.0		155.0	72.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	10.84	1.462943	0.26248	.	.	ENSG00000065526	ENST00000375759	T	0.08282	3.11	5.7	5.7	0.88788	.	.	.	.	.	T	0.06188	0.0160	N	0.19112	0.55	0.46701	D	0.999165	P	0.35844	0.524	B	0.31946	0.138	T	0.42531	-0.9446	9	0.44086	T	0.13	-2.5073	12.2073	0.54358	0.8578:0.1422:0.0:0.0	.	97	Q96T58	MINT_HUMAN	V	97	ENSP00000364912:I97V	ENSP00000364912:I97V	I	+	1	0	SPEN	16072103	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.778000	0.55371	2.184000	0.69523	0.528000	0.53228	ATA	.	.		0.522	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16199516	A	G	16199516	3	3	227	1	0	0	0	0	1	0	0	0	15053	217	8	2	295	2	SPEN	1	16199516	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	310796	16199516	233051105	2	32025										
PADI1	29943	hgsc.bcm.edu	37	chr1	17559395	17559395	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ccttcggcaacctggacgtcAgcccgcccgtcacggtgggc	13	17	2	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:17559395A>T	ENST00000375471.4	+	11	1335	c.1243A>T	c.(1243-1245)Agc>Tgc	p.S415C	PADI1_ENST00000536552.1_5'Flank|PADI1_ENST00000537499.1_5'Flank|PADI1_ENST00000413717.2_5'Flank	NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	415					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	CCTGGACGTCAGCCCGCCCGT	0.662																																					p.S415C	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.A1243T						.						30	29	29					1																	17559395		2203	4300	6503	SO:0001583	missense	29943	exon11			GACGTCAGCCCGC	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"Peptidyl arginine deiminases"	18367	protein-coding gene	gene with protein product	"peptidylarginine deiminase type I", "protein-arginine deiminase type-1", "hPAD-colony 10"	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.1243A>T	chr1.hg19:g.17559395A>T	ENSP00000364620:p.Ser415Cys	76.0	0.0		54.0	21.0	NM_013358	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	hg19	CCDS178.1	.	.	.	.	.	.	.	.	.	.	A	16.29	3.081213	0.55753	.	.	ENSG00000142623	ENST00000375471	T	0.32988	1.43	4.86	4.86	0.63082	Protein-arginine deiminase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.61899	0.2384	M	0.90198	3.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70579	-0.4833	10	0.72032	D	0.01	-35.5692	13.4182	0.60980	1.0:0.0:0.0:0.0	.	415	Q9ULC6	PADI1_HUMAN	C	415	ENSP00000364620:S415C	ENSP00000364620:S415C	S	+	1	0	PADI1	17431982	1.000000	0.71417	1.000000	0.80357	0.171000	0.22731	6.501000	0.73691	2.040000	0.60383	0.379000	0.24179	AGC	.	.		0.662	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		T	17559395	A	T	17559395	3	4	227	1	0	0	0	0	1	0	0	0	11386	188	7	4	1285	4	PADI1	1	17559395	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	1359879	17559395	231691226	3	32026										
LRRC8C	84230	hgsc.bcm.edu	37	chr1	90178412	90178412	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctgctaaccccatcactgtgGaaatgaaaggcctgaagaca	9	11	1	3			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:90178412G>A	ENST00000370454.4	+	3	538	c.283G>A	c.(283-285)Gaa>Aaa	p.E95K	RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	95					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		CATCACTGTGGAAATGAAAGG	0.483																																					p.E95K		Atlas-SNP	.											.	LRRC8C	73	.	0			c.G283A						.						113	105	108					1																	90178412		2203	4300	6503	SO:0001583	missense	84230	exon3			ACTGTGGAAATGA		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"hypothetical protein AD158"	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.283G>A	chr1.hg19:g.90178412G>A	ENSP00000359483:p.Glu95Lys	216.0	0.0		244.0	15.0	NM_032270	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	hg19	CCDS725.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.762732	0.89932	.	.	ENSG00000171488	ENST00000370454	T	0.24908	1.83	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.11537	0.0281	N	0.08118	0	0.58432	D	0.999997	B	0.31968	0.349	B	0.39379	0.298	T	0.24368	-1.0162	10	0.30078	T	0.28	.	20.4008	0.98991	0.0:0.0:1.0:0.0	.	95	Q8TDW0	LRC8C_HUMAN	K	95	ENSP00000359483:E95K	ENSP00000359483:E95K	E	+	1	0	LRRC8C	89951000	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	9.635000	0.98437	2.826000	0.97356	0.655000	0.94253	GAA	.	.		0.483	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		A	90178412	G	A	90178412	3	1	227	1	0	0	0	0	1	0	0	0	9032	1175	41	3	289	3	LRRC8C	1	90178412	Missense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	72619017	90178412	159072209	4	32027										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103348775	103348775	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	tccctcagattttttgtctgGataaatgcaagtctcaccac	6	11	3	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:103348775G>A	ENST00000370096.3	-	64	5263	c.4951C>T	c.(4951-4953)Cca>Tca	p.P1651S	COL11A1_ENST00000358392.2_Missense_Mutation_p.P1663S|COL11A1_ENST00000512756.1_Missense_Mutation_p.P1535S|COL11A1_ENST00000353414.4_Missense_Mutation_p.P1612S	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1651	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTTTTGTCTGGATAAATGCAA	0.378																																					p.P1663S		Atlas-SNP	.											.	COL11A1	972	.	0			c.C4987T						.						140	136	137					1																	103348775		2203	4300	6503	SO:0001583	missense	1301	exon64			TGTCTGGATAAAT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.4951C>T	chr1.hg19:g.103348775G>A	ENSP00000359114:p.Pro1651Ser	87.0	0.0		89.0	46.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.001419	0.74818	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09	5.52	5.52	0.82312	Fibrillar collagen, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.89770	0.6811	M	0.89715	3.055	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.998;0.998;0.999;0.998	D	0.91278	0.5049	10	0.87932	D	0	.	19.4353	0.94792	0.0:0.0:1.0:0.0	.	1535;1612;1663;1651;871	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	S	1651;1663;1612;871;1535	ENSP00000359114:P1651S;ENSP00000351163:P1663S;ENSP00000302551:P1612S;ENSP00000426533:P1535S	ENSP00000302551:P1612S	P	-	1	0	COL11A1	103121363	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.603000	0.88011	0.591000	0.81541	CCA	.	.		0.378	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103348775	G	A	103348775	3	1	227	1	0	0	0	0	1	0	0	0	3669	1174	41	3	485	3	COL11A1	1	103348775	Missense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	13170363	103348775	145901846	5	32028										
TCHH	7062	hgsc.bcm.edu	37	chr1	152084174	152084174	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctcctcttgctcccgccttaGttgctgctcgcgcctctcct	7	19	2	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:152084174G>C	ENST00000368804.1	-	2	1518	c.1519C>G	c.(1519-1521)Cta>Gta	p.L507V		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	507	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCCGCCTTAGTTGCTGCTCG	0.652																																					p.L507V		Atlas-SNP	.											.	TCHH	275	.	0			c.C1519G						.						63	70	67					1																	152084174		2062	4193	6255	SO:0001583	missense	7062	exon3			GCCTTAGTTGCTG	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1519C>G	chr1.hg19:g.152084174G>C	ENSP00000357794:p.Leu507Val	33.0	0.0		37.0	8.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	g	7.583	0.669162	0.14776	.	.	ENSG00000159450	ENST00000368804	T	0.06528	3.29	1.93	0.956	0.19608	.	.	.	.	.	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	B	0.25904	0.137	B	0.29440	0.102	T	0.48305	-0.9047	9	0.29301	T	0.29	.	7.6375	0.28274	0.0:0.0:0.7453:0.2547	.	507	Q07283	TRHY_HUMAN	V	507	ENSP00000357794:L507V	ENSP00000357794:L507V	L	-	1	2	TCHH	150350798	0.000000	0.05858	0.002000	0.10522	0.099000	0.18886	0.376000	0.20535	0.398000	0.25338	0.109000	0.15622	CTA	.	.		0.652	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084174	G	C	152084174	3	2	227	1	0	0	0	0	1	0	0	0	15715	1020	36	4	4316	4	TCHH	1	152084174	Missense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	48735399	152084174	97166447	6	32029										
TCHH	7062	hgsc.bcm.edu	37	chr1	152084221	152084221	+	Missense_Mutation	SNP	A	A	C													0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	cgcgcctctcctcctcctcgAgcttcagccaacgttcgcgc					rs202112040		TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:152084221A>C	ENST00000368804.1	-	2	1471	c.1472T>G	c.(1471-1473)cTc>cGc	p.L491R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	491	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCTCCTCGAGCTTCAGCCA	0.672																																					p.L491R		Atlas-SNP	.											.	TCHH	275	.	0			c.T1472G						.						63	70	68					1																	152084221		2106	4220	6326	SO:0001583	missense	7062	exon3			TCCTCGAGCTTCA	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1472T>G	chr1.hg19:g.152084221A>C	ENSP00000357794:p.Leu491Arg	23.0	0.0		40.0	13.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	a	0.064	-1.216147	0.01542	.	.	ENSG00000159450	ENST00000368804	T	0.04603	3.59	2.11	-4.23	0.03789	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43491	-0.9388	9	0.12430	T	0.62	.	7.0185	0.24900	0.2982:0.5613:0.0:0.1406	.	491	Q07283	TRHY_HUMAN	R	491	ENSP00000357794:L491R	ENSP00000357794:L491R	L	-	2	0	TCHH	150350845	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-1.154000	0.03166	-2.764000	0.00368	-1.533000	0.00918	CTC	.	.		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084221	A	C	152084221	3	2	227	1	0	0	0	0	1	0	0	0	15715	304	11	5	4363	5	TCHH	1	152084221	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	47	152084221	97166400	7	32030	166	2								
TCHH	7062	hgsc.bcm.edu	37	chr1	152084224	152084224	+	Missense_Mutation	SNP	T	T	C													0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gcctctcctcctcctcgagcTtcagccaacgttcgcgcctc							TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:152084224T>C	ENST00000368804.1	-	2	1468	c.1469A>G	c.(1468-1470)aAg>aGg	p.K490R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	490	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCTCGAGCTTCAGCCAACG	0.672																																					p.K490R		Atlas-SNP	.											.	TCHH	275	.	0			c.A1469G						.						65	71	69					1																	152084224		2109	4224	6333	SO:0001583	missense	7062	exon3			TCGAGCTTCAGCC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1469A>G	chr1.hg19:g.152084224T>C	ENSP00000357794:p.Lys490Arg	25.0	0.0		40.0	12.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	t	8.419	0.845945	0.16963	.	.	ENSG00000159450	ENST00000368804	T	0.04654	3.58	2.98	-5.97	0.02227	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.09590	T	0.72	.	5.0277	0.14393	0.1398:0.4054:0.0:0.4548	.	490	Q07283	TRHY_HUMAN	R	490	ENSP00000357794:K490R	ENSP00000357794:K490R	K	-	2	0	TCHH	150350848	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.247000	0.00266	-1.053000	0.03218	-1.396000	0.01147	AAG	.	.		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084224	T	C	152084224	3	2	227	1	0	0	0	0	1	0	0	0	15715	1609	56	2	4366	2	TCHH	1	152084224	Missense_Mutation	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10	3	152084224	97166397	8	32031	166	2								
IVL	3713	hgsc.bcm.edu	37	chr1	152883756	152883756	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	cacagctggagctcccagagCagcaggtaggacagccaaag	13	12	0	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:152883756C>T	ENST00000368764.3	+	2	1547	c.1483C>T	c.(1483-1485)Cag>Tag	p.Q495*	IVL_ENST00000392667.2_Nonsense_Mutation_p.Q349*			P07476	INVO_HUMAN	involucrin	495	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCTCCCAGagcagcaggtagg	0.592																																					p.Q495X		Atlas-SNP	.											.	IVL	100	.	0			c.C1483T						.						69	67	68					1																	152883756		2173	4267	6440	SO:0001587	stop_gained	3713	exon2			CCAGAGCAGCAGG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1483C>T	chr1.hg19:g.152883756C>T	ENSP00000357753:p.Gln495*	138.0	0.0		125.0	45.0	NM_005547	Q5T7P4	Nonsense_Mutation	SNP	ENST00000368764.3	hg19	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	C	16.92	3.255751	0.59321	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	.	.	.	3.33	-0.241	0.13043	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	7.7917	0.29125	0.1659:0.5314:0.3027:0.0	.	.	.	.	X	495;349	.	ENSP00000357753:Q495X	Q	+	1	0	IVL	151150380	0.000000	0.05858	0.002000	0.10522	0.023000	0.10783	-3.342000	0.00505	-0.138000	0.11434	0.514000	0.50259	CAG	.	.		0.592	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		T	152883756	C	T	152883756	4	4	227	1	0	0	0	0	0	1	0	0	7938	711	25	3	1485	3	IVL	1	152883756	Nonsense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	799532	152883756	96366865	9	32032										
ATP8B2	57198	hgsc.bcm.edu	37	chr1	154306627	154306627	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	acaacaaactggacaaattcAgcggaaccctctactggaag	8	11	2	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:154306627A>C	ENST00000368489.3	+	10	733	c.733A>C	c.(733-735)Agc>Cgc	p.S245R	ATP8B2_ENST00000368487.3_Missense_Mutation_p.S212R|ATP8B2_ENST00000341822.2_Missense_Mutation_p.S231R|ATP8B2_ENST00000426445.1_3'UTR	NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	231					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GGACAAATTCAGCGGAACCCT	0.507																																					p.S245R		Atlas-SNP	.											.	ATP8B2	158	.	0			c.A733C						.						232	244	240					1																	154306627		2203	4300	6503	SO:0001583	missense	57198	exon10			AAATTCAGCGGAA	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.733A>C	chr1.hg19:g.154306627A>C	ENSP00000357475:p.Ser245Arg	129.0	0.0		124.0	43.0	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	hg19	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	A	12.87	2.068093	0.36470	.	.	ENSG00000143515	ENST00000368487;ENST00000368489;ENST00000341822	T;T;T	0.74737	-0.87;-0.87;-0.87	5.3	5.3	0.74995	ATPase, P-type, ATPase-associated domain (1);	0.168925	0.52532	D	0.000065	T	0.56187	0.1968	L	0.37850	1.14	0.33332	D	0.568758	P;B;B	0.45428	0.858;0.001;0.0	P;B;B	0.49387	0.609;0.005;0.008	T	0.55976	-0.8055	10	0.17832	T	0.49	.	9.3671	0.38230	0.9169:0.0:0.0831:0.0	.	231;245;212	P98198;P98198-3;P98198-4	AT8B2_HUMAN;.;.	R	212;245;231	ENSP00000357472:S212R;ENSP00000357475:S245R;ENSP00000340448:S231R	ENSP00000340448:S231R	S	+	1	0	ATP8B2	152573251	0.999000	0.42202	0.998000	0.56505	0.976000	0.68499	2.515000	0.45512	2.228000	0.72767	0.482000	0.46254	AGC	.	.		0.507	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		C	154306627	A	C	154306627	3	2	227	1	0	0	0	0	1	0	0	0	1195	188	7	5	771	5	ATP8B2	1	154306627	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	1422871	154306627	94943994	10	32033										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228475833	228475833	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gggccacggccacgctgcggTgtgagctgagcaaggcagcc	17	13	0	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:228475833T>C	ENST00000422127.1	+	37	9927	c.9883T>C	c.(9883-9885)Tgt>Cgt	p.C3295R	OBSCN_ENST00000366707.4_Missense_Mutation_p.C414R|OBSCN_ENST00000570156.2_Missense_Mutation_p.C3724R|OBSCN_ENST00000284548.11_Missense_Mutation_p.C3295R|OBSCN_ENST00000366709.4_Missense_Mutation_p.C414R|OBSCN_ENST00000359599.6_Missense_Mutation_p.C2142R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3295	Ig-like 33.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CACGCTGCGGTGTGAGCTGAG	0.607																																					p.C3724R		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T11170C						.						85	90	88					1																	228475833		2050	4187	6237	SO:0001583	missense	84033	exon42			CTGCGGTGTGAGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.9883T>C	chr1.hg19:g.228475833T>C	ENSP00000409493:p.Cys3295Arg	136.0	0.0		132.0	70.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420768	0.83559	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44;-1.44	4.99	4.99	0.66335	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93893	0.8046	H	0.98738	4.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96230	0.9167	10	0.87932	D	0	.	14.8356	0.70180	0.0:0.0:0.0:1.0	.	3295;3295	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	R	3295;3295;414;414;2142	ENSP00000284548:C3295R;ENSP00000409493:C3295R;ENSP00000355668:C414R;ENSP00000355670:C414R;ENSP00000352613:C2142R	ENSP00000284548:C3295R	C	+	1	0	OBSCN	226542456	1.000000	0.71417	0.993000	0.49108	0.951000	0.60555	6.031000	0.70911	2.105000	0.64084	0.459000	0.35465	TGT	.	.		0.607	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228475833	T	C	228475833	3	2	227	1	0	0	0	0	1	0	0	0	10821	1696	59	2	10025	2	OBSCN	1	228475833	Missense_Mutation	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10	74169206	228475833	20774788	11	32034										
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233270849	233270849	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	tggaaaaagatgacagtgaaGctcaagttaataaactggta	10	4	1	3			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr1:233270849G>T	ENST00000258229.9	-	21	3981	c.3747C>A	c.(3745-3747)agC>agA	p.S1249R	PCNXL2_ENST00000520463.1_5'UTR|PCNXL2_ENST00000488780.2_Missense_Mutation_p.S382R	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1249						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				TGACAGTGAAGCTCAAGTTAA	0.393																																					p.S1249R		Atlas-SNP	.											.	PCNXL2	204	.	0			c.C3747A						.						79	79	79					1																	233270849		1865	4110	5975	SO:0001583	missense	80003	exon21			AGTGAAGCTCAAG	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.3747C>A	chr1.hg19:g.233270849G>T	ENSP00000258229:p.Ser1249Arg	265.0	1.0		225.0	97.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.192282	0.38707	.	.	ENSG00000135749	ENST00000258229;ENST00000484347;ENST00000488780	T	0.08807	3.05	5.63	0.491	0.16867	.	0.500314	0.24912	N	0.034605	T	0.06005	0.0156	N	0.22421	0.69	0.80722	D	1	B	0.31009	0.303	B	0.35859	0.212	T	0.40156	-0.9578	10	0.51188	T	0.08	.	6.534	0.22341	0.463:0.0:0.4221:0.1148	.	1249	A6NKB5	PCX2_HUMAN	R	1249;85;382	ENSP00000258229:S1249R	ENSP00000258229:S1249R	S	-	3	2	PCNXL2	231337472	1.000000	0.71417	0.711000	0.30485	0.746000	0.42486	1.715000	0.37971	-0.077000	0.12752	-0.156000	0.13503	AGC	.	.		0.393	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		T	233270849	G	T	233270849	3	4	227	1	0	0	0	0	1	0	0	0	11601	962	34	3	2722	3	PCNXL2	1	233270849	Missense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	4795016	233270849	15979772	12	32035										
RPS7	6201	hgsc.bcm.edu	37	chr2	3624107	3624107	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ttggtggtggtcggaaagctAtcataatctttgttcccgtt	11	7	2	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr2:3624107A>G	ENST00000304921.5	+	4	342	c.178A>G	c.(178-180)Atc>Gtc	p.I60V	RPS7_ENST00000407445.3_Missense_Mutation_p.I60V|RPS7_ENST00000406376.1_Missense_Mutation_p.I60V|RPS7_ENST00000403564.1_Missense_Mutation_p.I60V	NM_001011.3	NP_001002.1	P62081	RS7_HUMAN	ribosomal protein S7	60					cellular protein metabolic process (GO:0044267)|cytoplasmic translation (GO:0002181)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ribosome (GO:0005840)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|lung(2)|urinary_tract(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0963)|Epithelial(75;0.208)		TCGGAAAGCTATCATAATCTT	0.398																																					p.I60V		Atlas-SNP	.											.	RPS7	13	.	0			c.A178G						.						96	104	101					2																	3624107		2203	4300	6503	SO:0001583	missense	6201	exon4			AAAGCTATCATAA		CCDS1648.1	2p25	2011-04-05			ENSG00000171863	ENSG00000171863		"S ribosomal proteins"	10440	protein-coding gene	gene with protein product		603658				8522193, 10625621	Standard	NM_001011		Approved	S7	uc002qxw.3	P62081	OTTHUMG00000090305	ENST00000304921.5:c.178A>G	chr2.hg19:g.3624107A>G	ENSP00000339095:p.Ile60Val	393.0	0.0		385.0	199.0	NM_001011	P23821|P24818|Q57Z92|Q6IPH1	Missense_Mutation	SNP	ENST00000304921.5	hg19	CCDS1648.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.162232	0.38217	.	.	ENSG00000171863	ENST00000304921;ENST00000407445;ENST00000403564;ENST00000406376	.	.	.	4.2	4.2	0.49525	.	0.055074	0.64402	U	0.000001	T	0.49795	0.1578	L	0.35414	1.06	0.58432	D	0.999995	B;B	0.12013	0.005;0.001	B;B	0.24269	0.052;0.015	T	0.41520	-0.9504	9	0.18710	T	0.47	.	12.7429	0.57264	1.0:0.0:0.0:0.0	.	60;60	B5MCP9;P62081	.;RS7_HUMAN	V	60	.	ENSP00000339095:I60V	I	+	1	0	RPS7	3601982	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	9.061000	0.93913	1.651000	0.50673	0.460000	0.39030	ATC	.	.		0.398	RPS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206667.1	NM_001011		G	3624107	A	G	3624107	3	3	227	1	0	0	0	0	1	0	0	0	13675	449	16	2	188	2	RPS7	2	3624107	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10		3624107	239575266	13	32036										
C2orf89	129293	hgsc.bcm.edu	37	chr2	85049140	85049140	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctggccaccatctggctgtgGtgggaatgcccacggcgagg	16	12	1	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr2:85049140G>C	ENST00000409520.2	-	7	1461	c.1419C>G	c.(1417-1419)caC>caG	p.H473Q	TRABD2A_ENST00000479944.1_5'UTR|TRABD2A_ENST00000335459.5_Missense_Mutation_p.H424Q	NM_001277053.1	NP_001263982.1	Q86V40	TIKI1_HUMAN	TraB domain containing 2A	473					head development (GO:0060322)|metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|Wnt-protein binding (GO:0017147)										TCTGGCTGTGGTGGGAATGCC	0.597																																					p.G424G		Atlas-SNP	.											.	.	.	.	0			c.C1272G						.						34	39	37					2																	85049140		2063	4230	6293	SO:0001583	missense	129293	exon6			GCTGTGGTGGGAA	BC049209	CCDS46349.1, CCDS62946.1	2p11.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000186854	ENSG00000186854			27013	protein-coding gene	gene with protein product		614912	"chromosome 2 open reading frame 89"	C2orf89		12477932	Standard	NM_001080824		Approved		uc010ysl.3	Q86V40	OTTHUMG00000152922	ENST00000409520.2:c.1419C>G	chr2.hg19:g.85049140G>C	ENSP00000387075:p.His473Gln	132.0	0.0		108.0	47.0	NM_001080824	B4DKK8|I6UMB9	Silent	SNP	ENST00000409520.2	hg19		.	.	.	.	.	.	.	.	.	.	G	6.837	0.523603	0.13066	.	.	ENSG00000186854	ENST00000335459;ENST00000409520	T;T	0.20598	2.06;2.06	4.44	0.28	0.15682	.	1.078140	0.07285	N	0.871403	T	0.12987	0.0315	.	.	.	0.09310	N	1	B;B	0.15141	0.004;0.012	B;B	0.14023	0.003;0.01	T	0.34850	-0.9812	9	0.33141	T	0.24	.	5.0552	0.14529	0.1953:0.3267:0.478:0.0	.	473;424	Q86V40;Q86V40-2	CB089_HUMAN;.	Q	424;473	ENSP00000335004:H424Q;ENSP00000387075:H473Q	ENSP00000335004:H424Q	H	-	3	2	C2orf89	84902651	0.047000	0.20315	0.211000	0.23655	0.552000	0.35366	0.408000	0.21065	0.110000	0.17919	-0.302000	0.09304	CAC	.	.		0.597	TRABD2A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001080824		C	85049140	G	C	85049140	3	2	227	1	0	0	0	0	1	0	0	0	2205	1252	44	4	102	4	C2orf89	2	85049140	Missense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	81425033	85049140	158150233	14	32037										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098862	178098862	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ttctcttgctccttttggagTtgttcttgtctttccttttc	6	10	3	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr2:178098862T>G	ENST00000397062.3	-	2	737	c.183A>C	c.(181-183)caA>caC	p.Q61H	NFE2L2_ENST00000423513.1_Missense_Mutation_p.Q45H|NFE2L2_ENST00000446151.2_Missense_Mutation_p.Q45H|NFE2L2_ENST00000464747.1_Missense_Mutation_p.Q45H|NFE2L2_ENST00000397063.4_Missense_Mutation_p.Q45H	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	61					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			CCTTTTGGAGTTGTTCTTGTC	0.423			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.Q61H		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	.	NFE2L2	225	.	0			c.A183C						.						154	148	150					2																	178098862		1879	4103	5982	SO:0001583	missense	4780	exon2			TTGGAGTTGTTCT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.183A>C	chr2.hg19:g.178098862T>G	ENSP00000380252:p.Gln61His	94.0	0.0		61.0	14.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	17.58	3.425750	0.62733	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44;1.44	5.78	4.63	0.57726	.	0.118071	0.64402	D	0.000015	T	0.46328	0.1387	M	0.65975	2.015	0.45183	D	0.998196	D;D;D;D	0.76494	0.999;0.998;0.998;0.999	D;D;D;D	0.79784	0.921;0.993;0.951;0.921	T	0.45745	-0.9240	10	0.42905	T	0.14	.	4.7051	0.12846	0.0:0.2637:0.0:0.7363	.	45;45;45;61	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	H	45;61;45;45;45;45;45	ENSP00000380253:Q45H;ENSP00000380252:Q61H;ENSP00000411575:Q45H;ENSP00000391590:Q45H;ENSP00000400073:Q45H;ENSP00000412191:Q45H;ENSP00000410015:Q45H	ENSP00000380252:Q61H	Q	-	3	2	NFE2L2	177807108	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.575000	0.53870	2.210000	0.71456	0.460000	0.39030	CAA	.	.		0.423	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		G	178098862	T	G	178098862	3	3	227	1	0	0	0	0	1	0	0	0	10377	1722	60	5	1650	5	NFE2L2	2	178098862	Missense_Mutation	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10	93049722	178098862	65100511	15	32038										
TTN	7273	hgsc.bcm.edu	37	chr2	179435762	179435762	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	agtgatcttgcttccaccgtCataggtgggtttcttccact	9	11	3	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr2:179435762C>G	ENST00000591111.1	-	276	70398	c.70174G>C	c.(70174-70176)Gac>Cac	p.D23392H	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D16093H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D16160H|TTN_ENST00000589042.1_Missense_Mutation_p.D25033H|TTN_ENST00000342992.6_Missense_Mutation_p.D22465H|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D15968H|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23392	Fibronectin type-III 70. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTCCACCGTCATAGGTGGGT	0.438																																					p.D25033H		Atlas-SNP	.											.	TTN	18412	.	0			c.G75097C						.						152	155	154					2																	179435762		1907	4116	6023	SO:0001583	missense	7273	exon326			CACCGTCATAGGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.70174G>C	chr2.hg19:g.179435762C>G	ENSP00000465570:p.Asp23392His	76.0	0.0		71.0	33.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.74	2.327894	0.41197	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	5.28	5.28	0.74379	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.82545	0.5060	M	0.92555	3.32	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.86678	0.1915	9	0.87932	D	0	.	19.2734	0.94019	0.0:1.0:0.0:0.0	.	15968;16093;16160;23392	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	22465;15968;16160;16093;15966	ENSP00000343764:D22465H;ENSP00000434586:D15968H;ENSP00000340554:D16160H;ENSP00000352154:D16093H	ENSP00000340554:D16160H	D	-	1	0	TTN	179144008	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.776000	0.85560	2.630000	0.89119	0.650000	0.86243	GAC	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179435762	C	G	179435762	3	3	227	1	0	0	0	0	1	0	0	0	16750	826	29	4	33030	4	TTN	2	179435762	Missense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	1336900	179435762	63763611	16	32039										
GULP1	51454	hgsc.bcm.edu	37	chr2	189449050	189449050	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctttgatatgattccattttCtccaatatcacaccagtctt	3	11	3	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr2:189449050C>T	ENST00000409580.1	+	11	1382	c.668C>T	c.(667-669)tCt>tTt	p.S223F	GULP1_ENST00000409609.1_Missense_Mutation_p.S223F|GULP1_ENST00000409805.1_Missense_Mutation_p.S120F|GULP1_ENST00000409843.1_Missense_Mutation_p.S223F|GULP1_ENST00000359135.3_Missense_Mutation_p.S223F|GULP1_ENST00000409830.1_Missense_Mutation_p.S223F			Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing 1	223					apoptotic process (GO:0006915)|lipid transport (GO:0006869)|phagocytosis, engulfment (GO:0006911)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			ATTCCATTTTCTCCAATATCA	0.408																																					p.S223F	Pancreas(178;563 2065 20199 42378 52815)	Atlas-SNP	.											.	GULP1	35	.	0			c.C668T						.						231	197	209					2																	189449050		2203	4300	6503	SO:0001583	missense	51454	exon10			CATTTTCTCCAAT	AF191771	CCDS2295.1, CCDS58742.1, CCDS58743.1	2q32.3-q33	2008-02-05			ENSG00000144366	ENSG00000144366			18649	protein-coding gene	gene with protein product		608165				11729193	Standard	NM_001252668		Approved	CED6, CED-6, GULP	uc010fru.3	Q9UBP9	OTTHUMG00000132647	ENST00000409580.1:c.668C>T	chr2.hg19:g.189449050C>T	ENSP00000386289:p.Ser223Phe	243.0	0.0		267.0	114.0	NM_016315	B2RB51|B4DQ40|B8ZZ72|D3DPH1|E9PB86|Q53PC1|Q53RF3|Q9BVL3	Missense_Mutation	SNP	ENST00000409580.1	hg19	CCDS2295.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.7|29.7	5.031842|5.031842	0.93575|0.93575	.|.	.|.	ENSG00000144366|ENSG00000144366	ENST00000451191;ENST00000433052|ENST00000409843;ENST00000409830;ENST00000409805;ENST00000359135;ENST00000409580;ENST00000409609	.|T;T;T;T;T	.|0.49139	.|0.81;0.79;0.79;0.79;0.79	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.67961|0.67961	0.2949|0.2949	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	.|D;D;D;P	.|0.89917	.|0.999;1.0;0.966;0.93	.|D;D;P;P	.|0.91635	.|0.974;0.999;0.691;0.459	T|T	0.68603|0.68603	-0.5365|-0.5365	5|10	.|0.62326	.|D	.|0.03	-8.8574|-8.8574	18.6501|18.6501	0.91428|0.91428	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|120;47;223;223	.|E9PB86;Q59EC1;Q9UBP9;B8ZZ72	.|.;.;GULP1_HUMAN;.	F|F	48;108|223;223;120;223;223;223	.|ENSP00000387144:S223F;ENSP00000386732:S223F;ENSP00000352047:S223F;ENSP00000386289:S223F;ENSP00000386867:S223F	.|ENSP00000352047:S223F	L|S	+|+	1|2	0|0	GULP1|GULP1	189157295|189157295	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	6.770000|6.770000	0.74990|0.74990	2.659000|2.659000	0.90383|0.90383	0.650000|0.650000	0.86243|0.86243	CTC|TCT	.	.		0.408	GULP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335722.1	NM_016315		T	189449050	C	T	189449050	3	4	227	1	0	0	0	0	1	0	0	0	6910	913	32	3	698	3	GULP1	2	189449050	Missense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	10013288	189449050	53750323	17	32040										
SUMF1	285362	hgsc.bcm.edu	37	chr3	4508802	4508802	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	aagaacccgcaagggaccccGcgcccgcaccggtcccggcc	12	20	0	1	rs200789939	byFrequency	TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr3:4508802G>T	ENST00000272902.5	-	1	163	c.128C>A	c.(127-129)gCg>gAg	p.A43E	SUMF1_ENST00000458465.2_Missense_Mutation_p.A43E|SUMF1_ENST00000534863.1_Missense_Mutation_p.A43E|SUMF1_ENST00000383843.5_Missense_Mutation_p.A43E|SUMF1_ENST00000405420.2_Missense_Mutation_p.A43E	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	43					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(3)	13		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		AAGGGACCCCGCGCCCGCACC	0.711																																					p.A43E		Atlas-SNP	.											.	SUMF1	23	.	0			c.C128A						.						5	7	6					3																	4508802		2089	4113	6202	SO:0001583	missense	285362	exon1			GACCCCGCGCCCG	BC017005	CCDS2564.1, CCDS54548.1, CCDS54549.1	3p26.1	2009-07-23			ENSG00000144455	ENSG00000144455			20376	protein-coding gene	gene with protein product		607939				12757705, 12757706	Standard	NM_182760		Approved	FGE, UNQ3037	uc003bpz.2	Q8NBK3	OTTHUMG00000090269	ENST00000272902.5:c.128C>A	chr3.hg19:g.4508802G>T	ENSP00000272902:p.Ala43Glu	129.0	0.0		95.0	37.0	NM_001164675	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Missense_Mutation	SNP	ENST00000272902.5	hg19	CCDS2564.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.454038	0.43634	.	.	ENSG00000144455	ENST00000534982;ENST00000534863;ENST00000272902;ENST00000383843;ENST00000458465;ENST00000405420	D;D;D;D;D	0.92699	-2.66;-3.08;-3.04;-2.26;-3.09	4.54	2.71	0.32032	.	0.485588	0.20903	N	0.083614	D	0.86251	0.5888	L	0.59436	1.845	0.09310	N	1	B;B;B;B	0.20368	0.044;0.011;0.006;0.006	B;B;B;B	0.17722	0.016;0.019;0.009;0.009	T	0.67917	-0.5546	10	0.09590	T	0.72	-14.8698	5.3757	0.16164	0.1034:0.0:0.6962:0.2003	.	43;43;43;43	E9PF05;G5E9B0;E9PGL0;Q8NBK3	.;.;.;SUMF1_HUMAN	E	43	ENSP00000440421:A43E;ENSP00000272902:A43E;ENSP00000373355:A43E;ENSP00000410060:A43E;ENSP00000384977:A43E	ENSP00000272902:A43E	A	-	2	0	SUMF1	4483802	0.027000	0.19231	0.013000	0.15412	0.135000	0.20990	1.099000	0.31013	0.615000	0.30124	0.591000	0.81541	GCG	.	G|0.999;A|0.001		0.711	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760		T	4508802	G	T	4508802	3	4	227	1	0	0	0	0	1	0	0	0	15400	1087	38	1	1032	1	SUMF1	3	4508802	Missense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10		4508802	193513628	18	32041										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48678931	48678931	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctcccccagggctggccagtAggacaggaggtcattgccat	13	13	1	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr3:48678931A>G	ENST00000164024.4	-	33	9131	c.8851T>C	c.(8851-8853)Tac>Cac	p.Y2951H	MIR4793_ENST00000577502.1_RNA|CELSR3_ENST00000544264.1_Missense_Mutation_p.Y2956H	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	2951					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GCTGGCCAGTAGGACAGGAGG	0.607																																					p.Y2951H		Atlas-SNP	.											.	CELSR3	237	.	0			c.T8851C						.						42	47	46					3																	48678931		2203	4296	6499	SO:0001583	missense	1951	exon33			GCCAGTAGGACAG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.8851T>C	chr3.hg19:g.48678931A>G	ENSP00000164024:p.Tyr2951His	122.0	0.0		104.0	36.0	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	A	17.04	3.287284	0.59867	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.71698	-0.59;-0.58	5.22	5.22	0.72569	.	.	.	.	.	T	0.79782	0.4505	M	0.72894	2.215	0.53688	D	0.999975	B;B;D	0.71674	0.001;0.001;0.998	B;B;P	0.61477	0.004;0.002;0.889	T	0.77021	-0.2742	9	0.17832	T	0.49	.	15.1004	0.72269	1.0:0.0:0.0:0.0	.	2956;2951;3049	Q9NYQ7-2;Q9NYQ7;Q5Y190	.;CELR3_HUMAN;.	H	2951;2956	ENSP00000164024:Y2951H;ENSP00000445694:Y2956H	ENSP00000164024:Y2951H	Y	-	1	0	CELSR3	48653935	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.591000	0.90824	1.972000	0.57404	0.421000	0.28195	TAC	.	.		0.607	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		G	48678931	A	G	48678931	3	3	227	1	0	0	0	0	1	0	0	0	3225	420	15	2	1099	2	CELSR3	3	48678931	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	44170129	48678931	149343499	19	32042										
FGFBP1	9982	hgsc.bcm.edu	37	chr4	15937929	15937929	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	acttgtttccaatagactctCtcatccttgagctttaggca	6	11	2	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr4:15937929C>A	ENST00000382333.1	-	3	621	c.327G>T	c.(325-327)gaG>gaT	p.E109D	FGFBP1_ENST00000259988.2_Missense_Mutation_p.E109D	NM_005130.4	NP_005121.1	Q14512	FGFP1_HUMAN	fibroblast growth factor binding protein 1	109					cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|prostate(2)|skin(1)	10						AATAGACTCTCTCATCCTTGA	0.458																																					p.E109D		Atlas-SNP	.											.	FGFBP1	26	.	0			c.G327T						.						107	103	105					4																	15937929		2203	4300	6503	SO:0001583	missense	9982	exon3			GACTCTCTCATCC	M60047	CCDS3418.1	4p15.32	2008-02-05			ENSG00000137440	ENSG00000137440			19695	protein-coding gene	gene with protein product		607737				11148217, 1885605	Standard	NM_005130		Approved	HBP17, FGFBP	uc003gom.3	Q14512	OTTHUMG00000097745	ENST00000382333.1:c.327G>T	chr4.hg19:g.15937929C>A	ENSP00000371770:p.Glu109Asp	95.0	0.0		39.0	18.0	NM_005130	A8K5J2	Missense_Mutation	SNP	ENST00000382333.1	hg19	CCDS3418.1	.	.	.	.	.	.	.	.	.	.	C	8.954	0.968816	0.18659	.	.	ENSG00000137440	ENST00000382333;ENST00000259988	T;T	0.14640	2.49;2.49	5.42	-6.62	0.01813	.	1.100300	0.06732	N	0.776804	T	0.04318	0.0119	N	0.04018	-0.295	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.41197	-0.9522	10	0.17369	T	0.5	-0.1104	3.9323	0.09292	0.0866:0.2675:0.3858:0.26	.	109	Q14512	FGFP1_HUMAN	D	109	ENSP00000371770:E109D;ENSP00000259988:E109D	ENSP00000259988:E109D	E	-	3	2	FGFBP1	15547027	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.907000	0.04067	-1.247000	0.02507	-0.512000	0.04463	GAG	.	.		0.458	FGFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214974.1	NM_005130		A	15937929	C	A	15937929	3	1	227	1	0	0	0	0	1	0	0	0	5868	912	32	3	381	3	FGFBP1	4	15937929	Missense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10		15937929	175216347	20	32043										
CENPC1	1060	hgsc.bcm.edu	37	chr4	68379975	68379976	+	Frame_Shift_Ins	INS	-	-	T													0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gccatgaattttcttctctgINStttttgttttatagtccttt							TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr4:68379975_68379976insT	ENST00000273853.6	-	8	1510_1511	c.1260_1261insA	c.(1258-1263)aaacagfs	p.Q421fs		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	421					chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										TTTCTTCTCTGTTTTTGTTTTA	0.322																																					p.Q421fs		Atlas-INDEL	.											.	CENPC1	66	.	0			c.1261_1262insA						.																																			SO:0001589	frameshift_variant	1060	exon8			.	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"centromere protein C 1"	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.1261dupA	chr4.hg19:g.68379980_68379980dupT	ENSP00000273853:p.Gln421fs	79.0	0.0		43.0	15.0	NM_001812	Q8IW27|Q9P0M5	Frame_Shift_Ins	INS	ENST00000273853.6	hg19	CCDS47063.1																																																																																			.	.		0.322	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2			T	68379976	-	T	68379975	7	5	227	1	0	1	1	0	0	0	0	0	3231	1386	48	0	1618	0	CENPC1	4	68379975	Frame_Shift_Ins	INS	-	TCGA-DD-AAVU-01A-11D-A40R-10	52442046	68379975	122774301	21	32044										
ALB	213	hgsc.bcm.edu	37	chr4	74274521	74274524	+	Splice_Site	DEL	AAGT	AAGT	-													0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	atgaagagacatttttgaaaAagtaagtaatcagatgttta					rs17853494		TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr4:74274521_74274524delAAGT	ENST00000295897.4	+	4	570_571	c.481_482delAAGT	c.(481-483)aag>g	p.K161fs	ALB_ENST00000509063.1_Splice_Site_p.K161fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000503124.1_Intron|ALB_ENST00000415165.2_Intron|ALB_ENST00000401494.3_Intron	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATTTTTGAAAAAGTAAGTAATCAG	0.348																																					p.160_161del		Atlas-INDEL	.											.	ALB	132	.	0			c.480_482del						.																																			SO:0001630	splice_region_variant	213	exon4			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.482+1AAGT>-	chr4.hg19:g.74274525_74274528delAAGT		119.0	0.0		62.0	22.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	In_Frame_Del	DEL	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.348	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477	Frame_Shift_Del	-	74274524	AAGT	-	74274521	8	5	227	1	0	1	0	1	0	0	1	0	486	28	1	0	495	0	ALB	4	74274521	Splice_Site	DEL	AAGT	TCGA-DD-AAVU-01A-11D-A40R-10	5894546	74274521	116879755	22	32045										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79340185	79340185	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gccaagtggaaagattgtctAcaacatcactctacctctgc	7	12	4	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr4:79340185A>T	ENST00000325942.6	+	33	4948	c.4508A>T	c.(4507-4509)tAc>tTc	p.Y1503F	FRAS1_ENST00000264895.6_Missense_Mutation_p.Y1503F	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1503					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AAGATTGTCTACAACATCACT	0.363																																					p.Y1503F		Atlas-SNP	.											.	FRAS1	779	.	0			c.A4508T						.						180	173	175					4																	79340185		1881	4114	5995	SO:0001583	missense	80144	exon33			TTGTCTACAACAT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.4508A>T	chr4.hg19:g.79340185A>T	ENSP00000326330:p.Tyr1503Phe	73.0	0.0		44.0	18.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	A	10.18	1.278996	0.23307	.	.	ENSG00000138759	ENST00000325942;ENST00000264895	T;T	0.40225	1.04;1.04	5.22	5.22	0.72569	.	0.069181	0.64402	D	0.000012	T	0.39572	0.1083	M	0.64260	1.97	0.80722	D	1	P;B	0.35982	0.531;0.341	B;B	0.34452	0.183;0.137	T	0.33548	-0.9864	10	0.42905	T	0.14	.	11.1482	0.48442	0.8621:0.0:0.0:0.1379	.	1503;1503	E9PHH6;A2RRR8	.;.	F	1503	ENSP00000326330:Y1503F;ENSP00000264895:Y1503F	ENSP00000264895:Y1503F	Y	+	2	0	FRAS1	79559209	0.998000	0.40836	0.720000	0.30636	0.017000	0.09413	2.789000	0.47813	2.099000	0.63709	0.533000	0.62120	TAC	.	.		0.363	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			T	79340185	A	T	79340185	3	4	227	1	0	0	0	0	1	0	0	0	6050	391	14	4	4638	4	FRAS1	4	79340185	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	5065664	79340185	111814091	23	32046										
CDH9	1007	hgsc.bcm.edu	37	chr5	26885790	26885790	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctcaggccggctgaaaggatCagggcttctgcggtgcagga	16	10	3	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr5:26885790C>A	ENST00000231021.4	-	11	1987	c.1815G>T	c.(1813-1815)ctG>ctT	p.L605L		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	605	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CTGAAAGGATCAGGGCTTCTG	0.498																																					p.L605L	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.G1815T						.						84	69	74					5																	26885790		2203	4300	6503	SO:0001819	synonymous_variant	1007	exon11			AAGGATCAGGGCT	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1815G>T	chr5.hg19:g.26885790C>A		188.0	0.0		206.0	98.0	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	hg19	CCDS3893.1																																																																																			.	.		0.498	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26885790	C	A	26885790	2	1	227	1	0	0	0	0	0	0	0	1	3119	813	29	3		3	CDH9	5	26885790	Silent	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10		26885790	154029470	24	32047										
SNX18	112574	hgsc.bcm.edu	37	chr5	53839038	53839038	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ccaaagtcaaggagagtaggCgacacgtggaggaagggaag	17	6	1	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr5:53839038C>T	ENST00000381410.4	+	2	1841	c.1651C>T	c.(1651-1653)Cga>Tga	p.R551*	SNX18_ENST00000343017.6_3'UTR	NM_001102575.1	NP_001096045.1	Q96RF0	SNX18_HUMAN	sorting nexin 18	0	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				GGAGAGTAGGCGACACGTGGA	0.398																																					p.R551X		Atlas-SNP	.											.	SNX18	102	.	0			c.C1651T						.						92	90	90					5																	53839038		1904	4113	6017	SO:0001587	stop_gained	112574	exon2			AGTAGGCGACACG	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"Sorting nexins"	19245	protein-coding gene	gene with protein product			"sorting nexin associated golgi protein 1"	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000381410.4:c.1651C>T	chr5.hg19:g.53839038C>T	ENSP00000370817:p.Arg551*	265.0	0.0		275.0	117.0	NM_001102575	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Nonsense_Mutation	SNP	ENST00000381410.4	hg19	CCDS43317.1	.	.	.	.	.	.	.	.	.	.	C	39	7.430029	0.98279	.	.	ENSG00000178996	ENST00000381410	.	.	.	5.72	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7453	0.62872	0.2803:0.7197:0.0:0.0	.	.	.	.	X	551	.	ENSP00000370817:R551X	R	+	1	2	SNX18	53874795	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.969000	0.40510	1.379000	0.46325	0.655000	0.94253	CGA	.	.		0.398	SNX18-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214073.2			T	53839038	C	T	53839038	4	4	227	1	0	0	0	0	0	1	0	0	14904	760	27	1	1923	1	SNX18	5	53839038	Nonsense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	26953248	53839038	127076222	25	32048										
ZNF608	57507	hgsc.bcm.edu	37	chr5	124080294	124080294	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gcctcttgccagtgctgctgAtctcgggaatcccatacaag	10	13	2	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr5:124080294A>T	ENST00000306315.5	-	1	824	c.389T>A	c.(388-390)aTc>aAc	p.I130N	ZNF608_ENST00000504926.1_5'Flank	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	130							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		AGTGCTGCTGATCTCGGGAAT	0.522																																					p.I130N		Atlas-SNP	.											.	ZNF608	117	.	0			c.T389A						.						75	74	74					5																	124080294		2203	4300	6503	SO:0001583	missense	57507	exon1			CTGCTGATCTCGG	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.389T>A	chr5.hg19:g.124080294A>T	ENSP00000307746:p.Ile130Asn	84.0	0.0		74.0	45.0	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	hg19	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	A	13.70	2.316022	0.40996	.	.	ENSG00000168916	ENST00000306315;ENST00000509799;ENST00000513986	T	0.42900	0.96	5.07	3.89	0.44902	.	0.000000	0.64402	D	0.000014	T	0.44767	0.1309	L	0.51422	1.61	0.39589	D	0.96955	D	0.56968	0.978	P	0.50049	0.629	T	0.38156	-0.9674	10	0.36615	T	0.2	-6.4651	12.049	0.53495	0.8556:0.1444:0.0:0.0	.	130	Q9ULD9	ZN608_HUMAN	N	130	ENSP00000307746:I130N	ENSP00000307746:I130N	I	-	2	0	ZNF608	124108193	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.809000	0.47971	0.859000	0.35456	0.533000	0.62120	ATC	.	.		0.522	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		T	124080294	A	T	124080294	3	4	227	1	0	0	0	0	1	0	0	0	18049	333	12	4	4185	4	ZNF608	5	124080294	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	70241256	124080294	56834966	26	32049										
PCDHB7	56129	hgsc.bcm.edu	37	chr5	140554567	140554567	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctgtgcaggaggagcagggcGgccccggtgggtcgctgctc	19	12	0	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr5:140554567G>C	ENST00000231137.3	+	1	2325	c.2151G>C	c.(2149-2151)gcG>gcC	p.A717A	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	717					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGAGCAGGGCGGCCCCGGTGG	0.662																																					p.A717A		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G2151C						.						72	122	105					5																	140554567		2203	4298	6501	SO:0001819	synonymous_variant	56129	exon1			CAGGGCGGCCCCG	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.2151G>C	chr5.hg19:g.140554567G>C		139.0	0.0		142.0	62.0	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	hg19	CCDS4249.1																																																																																			.	.		0.662	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		C	140554567	G	C	140554567	2	2	227	1	0	0	0	0	0	0	0	1	11556	1103	39	4		4	PCDHB7	5	140554567	Silent	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	16474273	140554567	40360693	27	32050										
MRS2	57380	hgsc.bcm.edu	37	chr6	24412501	24412501	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ttctgatattagattatcgtAatttaaacttagagcaatgg	7	4	1	3			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr6:24412501A>G	ENST00000378386.3	+	5	559	c.466A>G	c.(466-468)Aat>Gat	p.N156D	MRS2_ENST00000378353.1_Missense_Mutation_p.N156D|MRS2_ENST00000543597.1_5'UTR|MRS2_ENST00000274747.7_Silent_p.*118*|MRS2_ENST00000443868.2_Intron|MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000535061.1_Missense_Mutation_p.N106D	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	156						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12						AGATTATCGTAATTTAAACTT	0.348																																					p.N156D		Atlas-SNP	.											.	MRS2	31	.	0			c.A466G						.						92	89	90					6																	24412501		2203	4300	6503	SO:0001583	missense	57380	exon5			TATCGTAATTTAA	AF288288	CCDS4552.1, CCDS69055.1, CCDS69056.1, CCDS75408.1	6p22.3-p22.1	2013-05-03	2013-05-03	2008-01-18	ENSG00000124532	ENSG00000124532			13785	protein-coding gene	gene with protein product			"MRS2-like, magnesium homeostasis factor (S. cerevisiae)", "MRS2 magnesium homeostasis factor homolog (S. cerevisiae)"	MRS2L			Standard	XM_005249242		Approved		uc003neb.3	Q9HD23	OTTHUMG00000014355	ENST00000378386.3:c.466A>G	chr6.hg19:g.24412501A>G	ENSP00000367637:p.Asn156Asp	223.0	0.0		205.0	98.0	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Missense_Mutation	SNP	ENST00000378386.3	hg19	CCDS4552.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.317485	0.40996	.	.	ENSG00000124532	ENST00000535061;ENST00000378386;ENST00000378353	T;T;T	0.43294	1.47;1.54;0.95	5.46	2.88	0.33553	.	0.165679	0.53938	D	0.000046	T	0.09555	0.0235	N	0.12887	0.27	0.80722	D	1	B;B;B	0.18166	0.005;0.026;0.005	B;B;B	0.22152	0.005;0.038;0.009	T	0.10894	-1.0610	10	0.10111	T	0.7	.	11.9533	0.52966	0.7253:0.2746:0.0:0.0	.	106;156;156	F5GWH3;Q9HD23;Q9HD23-2	.;MRS2_HUMAN;.	D	106;156;156	ENSP00000441839:N106D;ENSP00000367637:N156D;ENSP00000367604:N156D	ENSP00000367604:N156D	N	+	1	0	MRS2	24520480	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	1.492000	0.35594	0.881000	0.35993	0.379000	0.24179	AAT	.	.		0.348	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1			G	24412501	A	G	24412501	3	3	227	1	0	0	0	0	1	0	0	0	9860	362	13	2	484	2	MRS2	6	24412501	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10		24412501	146702566	28	32051										
HIST1H2AE	3012	hgsc.bcm.edu	37	chr6	26217258	26217258	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ggcaaaagctaaaacgcgttCttccagggccggtcttcagt	11	11	3	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr6:26217258C>T	ENST00000303910.2	+	1	94	c.56C>T	c.(55-57)tCt>tTt	p.S19F	HIST1H2BG_ENST00000244601.3_5'Flank	NM_021052.2	NP_066390.1	P04908	H2A1B_HUMAN	histone cluster 1, H2ae	19						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	10		all_hematologic(11;0.196)				AAAACGCGTTCTTCCAGGGCC	0.557																																					p.S19F		Atlas-SNP	.											.	HIST1H2AE	25	.	0			c.C56T						.						67	57	60					6																	26217258		2203	4299	6502	SO:0001583	missense	3012	exon1			CGCGTTCTTCCAG	M60752	CCDS4595.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000168274	ENSG00000277075		"Histones / Replication-dependent"	4724	protein-coding gene	gene with protein product		602786	"H2A histone family, member A", "histone 1, H2ae"	H2AFA		9119399, 1916825, 12408966	Standard	NM_021052		Approved	H2A/a, H2A.1	uc003nha.1	P04908	OTTHUMG00000014440	ENST00000303910.2:c.56C>T	chr6.hg19:g.26217258C>T	ENSP00000303373:p.Ser19Phe	141.0	0.0		139.0	59.0	NM_021052	P28001|Q76P63	Missense_Mutation	SNP	ENST00000303910.2	hg19	CCDS4595.1	.	.	.	.	.	.	.	.	.	.	.	9.131	1.011378	0.19277	.	.	ENSG00000168274	ENST00000303910	T	0.71698	-0.59	3.99	3.99	0.46301	.	0.000000	0.33110	U	0.005279	D	0.91099	0.7198	H	0.99929	4.97	0.53688	D	0.999971	.	.	.	.	.	.	D	0.95024	0.8163	8	0.87932	D	0	.	15.5885	0.76506	0.0:1.0:0.0:0.0	.	.	.	.	F	19	ENSP00000303373:S19F	ENSP00000303373:S19F	S	+	2	0	HIST1H2AE	26325237	1.000000	0.71417	0.027000	0.17364	0.125000	0.20455	7.473000	0.81007	2.219000	0.72066	0.591000	0.81541	TCT	.	.		0.557	HIST1H2AE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040103.1	NM_021052		T	26217258	C	T	26217258	3	4	227	1	0	0	0	0	1	0	0	0	7141	913	32	3	58	3	HIST1H2AE	6	26217258	Missense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	1804757	26217258	144897809	29	32052										
TBX18	9096	hgsc.bcm.edu	37	chr6	85446717	85446717	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	agtggcgaaggcattgctggAgggtgatggcatgatatact	16	5	0	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr6:85446717A>T	ENST00000369663.5	-	8	1847	c.1510T>A	c.(1510-1512)Tcc>Acc	p.S504T	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	504					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		GCATTGCTGGAGGGTGATGGC	0.507																																					p.S504T		Atlas-SNP	.											.	TBX18	131	.	0			c.T1510A						.						165	173	170					6																	85446717		2203	4300	6503	SO:0001583	missense	9096	exon8			TGCTGGAGGGTGA	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"T-boxes"	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1510T>A	chr6.hg19:g.85446717A>T	ENSP00000358677:p.Ser504Thr	111.0	0.0		115.0	55.0	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Missense_Mutation	SNP	ENST00000369663.5	hg19	CCDS34495.1	.	.	.	.	.	.	.	.	.	.	A	8.114	0.779463	0.16120	.	.	ENSG00000112837	ENST00000369663	D	0.88664	-2.41	5.48	1.5	0.22942	.	0.127443	0.53938	D	0.000048	T	0.56717	0.2004	N	0.17082	0.46	0.28197	N	0.927514	B	0.15473	0.013	B	0.12156	0.007	T	0.48917	-0.8992	10	0.22706	T	0.39	.	3.891	0.09119	0.59:0.0:0.1505:0.2595	.	504	O95935	TBX18_HUMAN	T	504	ENSP00000358677:S504T	ENSP00000358677:S504T	S	-	1	0	TBX18	85503436	0.849000	0.29639	0.992000	0.48379	0.633000	0.38033	1.026000	0.30103	0.015000	0.14971	-0.334000	0.08254	TCC	.	.		0.507	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508		T	85446717	A	T	85446717	3	4	227	1	0	0	0	0	1	0	0	0	15668	304	11	4	317	4	TBX18	6	85446717	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	59229459	85446717	85668350	30	32053										
BACH2	60468	hgsc.bcm.edu	37	chr6	90661177	90661177	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	tccttttctgagctctccttGgtgtctgtgggcacgtcagg	12	11	4	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr6:90661177G>A	ENST00000257749.4	-	7	1355	c.648C>T	c.(646-648)acC>acT	p.T216T	BACH2_ENST00000343122.3_Silent_p.T216T|RP3-512E2.2_ENST00000445838.1_RNA|BACH2_ENST00000537989.1_Silent_p.T216T|RP3-512E2.2_ENST00000413986.1_RNA	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	216						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		AGCTCTCCTTGGTGTCTGTGG	0.532																																					p.T216T		Atlas-SNP	.											.	BACH2	224	.	0			c.C648T						.						139	130	133					6																	90661177		2203	4300	6503	SO:0001819	synonymous_variant	60468	exon7			CTCCTTGGTGTCT	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.648C>T	chr6.hg19:g.90661177G>A		104.0	0.0		77.0	31.0	NM_021813	E1P518|Q59H70|Q5T793|Q9NTS5	Silent	SNP	ENST00000257749.4	hg19	CCDS5026.1																																																																																			.	.		0.532	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		A	90661177	G	A	90661177	2	1	227	1	0	0	0	0	0	0	0	1	1284	1335	47	3		3	BACH2	6	90661177	Silent	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	5214460	90661177	80453890	31	32054										
EPHA7	2045	hgsc.bcm.edu	37	chr6	94120371	94120371	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	atgtccctcgaacctcgactAaagaggaaaattctgaacca	7	11	1	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr6:94120371A>G	ENST00000369303.4	-	3	864	c.680T>C	c.(679-681)tTa>tCa	p.L227S	EPHA7_ENST00000369297.1_Missense_Mutation_p.L227S	NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	227	Cys-rich.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		AACCTCGACTAAAGAGGAAAA	0.468																																					p.L227S		Atlas-SNP	.											.	EPHA7	251	.	0			c.T680C						.						69	71	70					6																	94120371		2203	4300	6503	SO:0001583	missense	2045	exon3			TCGACTAAAGAGG	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.680T>C	chr6.hg19:g.94120371A>G	ENSP00000358309:p.Leu227Ser	174.0	0.0		154.0	64.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.218328	0.79464	.	.	ENSG00000135333	ENST00000369303;ENST00000369297	T;T	0.75704	-0.96;4.0	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000001	D	0.87752	0.6256	M	0.92169	3.28	0.51482	D	0.999923	D;D;D;D	0.89917	0.997;1.0;1.0;1.0	D;D;D;D	0.97110	0.986;1.0;0.999;0.998	D	0.90843	0.4725	10	0.87932	D	0	.	15.8204	0.78638	1.0:0.0:0.0:0.0	.	227;227;227;227	Q15375-4;Q15375-3;Q15375-2;Q15375	.;.;.;EPHA7_HUMAN	S	227	ENSP00000358309:L227S;ENSP00000358303:L227S	ENSP00000358303:L227S	L	-	2	0	EPHA7	94177092	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.287000	0.95975	2.196000	0.70406	0.533000	0.62120	TTA	.	.		0.468	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			G	94120371	A	G	94120371	3	3	227	1	0	0	0	0	1	0	0	0	5174	372	13	2	2376	2	EPHA7	6	94120371	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	3459194	94120371	76994696	32	32055										
ANK1	286	hgsc.bcm.edu	37	chr8	41550170	41550170	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ggcccagccctgttacctctAtgtccctgctccgggccacc	9	19	1	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr8:41550170A>T	ENST00000347528.4	-	31	3937	c.3854T>A	c.(3853-3855)aTa>aAa	p.I1285K	ANK1_ENST00000265709.8_Missense_Mutation_p.I1326K|ANK1_ENST00000379758.2_Missense_Mutation_p.I1285K|ANK1_ENST00000289734.7_Missense_Mutation_p.I1285K|ANK1_ENST00000352337.4_Missense_Mutation_p.I1285K|ANK1_ENST00000396942.1_Missense_Mutation_p.I1285K|ANK1_ENST00000396945.1_Missense_Mutation_p.I1285K	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1285	UPA domain. {ECO:0000250}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			TGTTACCTCTATGTCCCTGCT	0.602																																					p.I1326K		Atlas-SNP	.											.	ANK1	497	.	0			c.T3977A						.						153	175	167					8																	41550170		2203	4300	6503	SO:0001583	missense	286	exon32			ACCTCTATGTCCC	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.3854T>A	chr8.hg19:g.41550170A>T	ENSP00000339620:p.Ile1285Lys	46.0	0.0		79.0	10.0	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	hg19	CCDS6119.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.0|28.0	4.880070|4.880070	0.91740|0.91740	.|.	.|.	ENSG00000029534|ENSG00000029534	ENST00000520299|ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	.|T;T;T;T;T;T;T	.|0.26810	.|1.71;1.71;1.71;1.71;1.71;1.71;1.71	4.26|4.26	4.26|4.26	0.50523|0.50523	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.48466|0.48466	0.1501|0.1501	M|M	0.76838|0.76838	2.35|2.35	0.80722|0.80722	D|D	1|1	.|P;P;D;D;P;D	.|0.71674	.|0.954;0.9;0.991;0.998;0.954;0.994	.|P;B;P;P;P;P	.|0.62089	.|0.804;0.386;0.898;0.891;0.804;0.825	T|T	0.55970|0.55970	-0.8056|-0.8056	5|10	.|0.87932	.|D	.|0	.|.	13.8755|13.8755	0.63651|0.63651	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1326;1285;1285;1285;1285;601	.|P16157-21;P16157-4;P16157;P16157-5;P16157-3;B3KX39	.|.;.;ANK1_HUMAN;.;.;.	Q|K	606|1285;1285;1285;1285;1285;1285;1326;1285	.|ENSP00000339620:I1285K;ENSP00000289734:I1285K;ENSP00000369082:I1285K;ENSP00000380149:I1285K;ENSP00000380147:I1285K;ENSP00000309131:I1285K;ENSP00000265709:I1326K	.|ENSP00000265709:I1326K	H|I	-|-	3|2	2|0	ANK1|ANK1	41669327|41669327	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.942000|0.942000	0.58702|0.58702	9.119000|9.119000	0.94362|0.94362	1.933000|1.933000	0.56026|0.56026	0.383000|0.383000	0.25322|0.25322	CAT|ATA	.	.		0.602	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		T	41550170	A	T	41550170	3	4	227	1	0	0	0	0	1	0	0	0	620	449	16	4	2165	4	ANK1	8	41550170	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10		41550170	104813852	33	32056										
ODF1	4956	hgsc.bcm.edu	37	chr8	103573034	103573042	+	In_Frame_Del	DEL	CCCGTGCAG	CCCGTGCAG	-													0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	aacccctgcagcccctgcaaCccgtgcagcccatatgatcc					rs143802899|rs199994329|rs568456031|rs372688769|rs59109601|rs377699584|rs11992195|rs62523273|rs386728348|rs58232162	byFrequency	TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	CCCGTGCAG	CCCGTGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr8:103573034_103573042delCCCGTGCAG	ENST00000285402.3	+	2	831_839	c.675_683delCCCGTGCAG	c.(673-684)aacccgtgcagc>aac	p.PCS226del	ODF1_ENST00000518835.1_In_Frame_Del_p.PCS19del	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	226	C-X-P repeat region.		Missing. {ECO:0000269|PubMed:8111388}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.C218_P226delCNPCSPCNP(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			gcccctgcaacccgtgcagcccATATGAT	0.541																																					p.225_228del		Atlas-INDEL	.											ODF1,NS,carcinoma,0,1	ODF1	55	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.674_682del						.																																			SO:0001651	inframe_deletion	4956	exon2			.	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"Heat shock proteins / HSPB"	8113	protein-coding gene	gene with protein product	"cancer/testis antigen 133"	182878	"outer dense fibre of sperm tails 1"			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.675_683delCCCGTGCAG	chr8.hg19:g.103573034_103573042delCCCGTGCAG	ENSP00000285402:p.Pro226_Ser228del	59.0	0.0		78.0	58.0	NM_024410	Q3SX72	In_Frame_Del	DEL	ENST00000285402.3	hg19	CCDS6293.1																																																																																			.	.		0.541	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1			-	103573042	CCCGTGCAG	-	103573034	7	5	227	1	0	1	0	1	0	0	0	0	10835	506	18	0	681	0	ODF1	8	103573034	In_Frame_Del	DEL	CCCGTGCAG	TCGA-DD-AAVU-01A-11D-A40R-10	62022864	103573034	42790988	34	32057										
RIMS2	9699	hgsc.bcm.edu	37	chr8	104973332	104973332	+	Frame_Shift_Del	DEL	A	A	-													0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	tagtgaagtctctgactatgActgtgatgatggaattggtg							TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr8:104973332delA	ENST00000436393.2	+	13	2316	c.2075delA	c.(2074-2076)gacfs	p.D692fs	RIMS2_ENST00000507740.1_Frame_Shift_Del_p.D706fs|RIMS2_ENST00000262231.10_Frame_Shift_Del_p.D753fs|RIMS2_ENST00000406091.3_Frame_Shift_Del_p.D914fs			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	976	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TCTGACTATGACTGTGATGAT	0.289										HNSCC(12;0.0054)																											p.D914fs		Atlas-INDEL	.											.	RIMS2	1357	.	0			c.2740delG						.						106	114	112					8																	104973332		1799	4058	5857	SO:0001589	frameshift_variant	9699	exon15			.	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.2075delA	chr8.hg19:g.104973332delA	ENSP00000390665:p.Asp692fs	132.0	0.0		178.0	142.0	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Frame_Shift_Del	DEL	ENST00000436393.2	hg19																																																																																				.	.		0.289	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		-	104973332	A	-	104973332	7	5	227	1	0	1	0	1	0	0	0	0	13383	275	10	0	2925	0	RIMS2	8	104973332	Frame_Shift_Del	DEL	A	TCGA-DD-AAVU-01A-11D-A40R-10	1400298	104973332	41390690	35	32058										
KANK1	23189	hgsc.bcm.edu	37	chr9	711611	711611	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ggagctggaggagcaggtgcGaaccatccctgtgctccagg	16	11	0	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr9:711611G>A	ENST00000382303.1	+	7	1497	c.845G>A	c.(844-846)cGa>cAa	p.R282Q	KANK1_ENST00000382297.2_Missense_Mutation_p.R282Q|KANK1_ENST00000382293.3_Missense_Mutation_p.R124Q|KANK1_ENST00000489369.1_3'UTR	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	282					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GAGCAGGTGCGAACCATCCCT	0.547																																					p.R282Q		Atlas-SNP	.											.	KANK1	231	.	0			c.G845A						.						87	81	83					9																	711611		2203	4300	6503	SO:0001583	missense	23189	exon7			AGGTGCGAACCAT	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.845G>A	chr9.hg19:g.711611G>A	ENSP00000371740:p.Arg282Gln	95.0	0.0		41.0	29.0	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	hg19	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.642865	0.67244	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.00816	5.66;5.66;5.66	5.93	5.93	0.95920	.	0.000000	0.49305	D	0.000149	T	0.00936	0.0031	N	0.14661	0.345	0.80722	D	1	D;D	0.54601	0.963;0.967	P;B	0.46299	0.511;0.229	T	0.76318	-0.3003	10	0.46703	T	0.11	-1.3225	7.779	0.29054	0.188:0.0:0.812:0.0	.	282;282	Q5W0W1;Q14678	.;KANK1_HUMAN	Q	282;282;282;124	ENSP00000371740:R282Q;ENSP00000371734:R282Q;ENSP00000371730:R124Q	ENSP00000346479:R282Q	R	+	2	0	KANK1	701611	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.128000	0.77217	2.826000	0.97356	0.655000	0.94253	CGA	.	.		0.547	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		A	711611	G	A	711611	3	1	227	1	0	0	0	0	1	0	0	0	7985	1058	37	1	851	1	KANK1	9	711611	Missense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10		711611	140501820	36	32059										
SLC44A1	23446	hgsc.bcm.edu	37	chr9	108126972	108126972	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	tgtcagcagatgacagtggcAggagctgtggtaacatacta	13	7	1	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr9:108126972A>C	ENST00000374720.3	+	10	1471	c.1224A>C	c.(1222-1224)gcA>gcC	p.A408A	SLC44A1_ENST00000343170.7_Silent_p.A200A|SLC44A1_ENST00000374723.1_Silent_p.A408A|SLC44A1_ENST00000374724.1_Silent_p.A408A	NM_080546.3	NP_536856.2	Q8WWI5	CTL1_HUMAN	solute carrier family 44 (choline transporter), member 1	408					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	38					Choline(DB00122)	TGACAGTGGCAGGAGCTGTGG	0.453																																					p.A408A		Atlas-SNP	.											.	SLC44A1	61	.	0			c.A1224C						.						137	126	130					9																	108126972		2203	4300	6503	SO:0001819	synonymous_variant	23446	exon10			AGTGGCAGGAGCT	AJ420812	CCDS6763.1, CCDS75868.1	9q31.2	2014-01-28	2013-07-17	2005-09-06	ENSG00000070214	ENSG00000070214		"CD molecules", "Solute carriers"	18798	protein-coding gene	gene with protein product		606105	"CDW92 antigen"	CDW92		11698453, 10677542	Standard	NM_080546		Approved	CDw92, CTL1, CHTL1, CD92	uc004bcn.3	Q8WWI5	OTTHUMG00000020421	ENST00000374720.3:c.1224A>C	chr9.hg19:g.108126972A>C		143.0	0.0		88.0	81.0	NM_080546	A6NLZ9|Q5VUB3|Q8WVB0|Q96KU3|Q9NY69	Silent	SNP	ENST00000374720.3	hg19	CCDS6763.1																																																																																			.	.		0.453	SLC44A1-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053500.1	NM_080546		C	108126972	A	C	108126972	2	2	227	1	0	0	0	0	0	0	0	1	14650	175	7	5		5	SLC44A1	9	108126972	Silent	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	107415361	108126972	33086459	37	32060										
ASTN2	23245	hgsc.bcm.edu	37	chr9	119249699	119249699	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gtagatactgacttcagggaCctctccatggcttcgaccag	10	12	2	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr9:119249699C>A	ENST00000313400.4	-	20	3536	c.3436G>T	c.(3436-3438)Gtc>Ttc	p.V1146F	ASTN2_ENST00000361477.3_Missense_Mutation_p.V198F|ASTN2_ENST00000373996.3_Missense_Mutation_p.V1142F|ASTN2_ENST00000288520.5_Missense_Mutation_p.V247F|ASTN2_ENST00000341734.4_Missense_Mutation_p.V198F|ASTN2_ENST00000361209.2_Missense_Mutation_p.V1095F			O75129	ASTN2_HUMAN	astrotactin 2	1146	Fibronectin type-III.				negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						ACTTCAGGGACCTCTCCATGG	0.502																																					p.V1095F		Atlas-SNP	.											.	ASTN2	307	.	0			c.G3283T						.						111	100	104					9																	119249699		2203	4300	6503	SO:0001583	missense	23245	exon19			CAGGGACCTCTCC	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.3436G>T	chr9.hg19:g.119249699C>A	ENSP00000314038:p.Val1146Phe	78.0	0.0		40.0	33.0	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	hg19		.	.	.	.	.	.	.	.	.	.	C	15.13	2.743335	0.49151	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000288520;ENST00000341734;ENST00000373986;ENST00000361209;ENST00000361477	T;T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77;0.77	5.49	3.62	0.41486	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.574679	0.19379	N	0.115713	T	0.36413	0.0966	N	0.24115	0.695	0.27369	N	0.955756	B;B;B;B;P;B;B	0.37398	0.073;0.073;0.058;0.09;0.593;0.073;0.062	B;B;B;B;B;B;B	0.40506	0.041;0.041;0.007;0.02;0.331;0.041;0.034	T	0.31475	-0.9942	10	0.66056	D	0.02	-22.2596	10.4469	0.44499	0.0:0.7913:0.0:0.2087	.	198;198;1095;1146;1142;198;247	B7ZKP4;B7ZKP5;O75129-2;O75129;O75129-3;O75129-6;O75129-4	.;.;.;ASTN2_HUMAN;.;.;.	F	1146;1142;247;198;869;1095;198	ENSP00000314038:V1146F;ENSP00000363108:V1142F;ENSP00000288520:V247F;ENSP00000339925:V198F;ENSP00000363098:V869F;ENSP00000354504:V1095F;ENSP00000355116:V198F	ENSP00000288520:V247F	V	-	1	0	ASTN2	118289520	0.613000	0.27009	1.000000	0.80357	0.997000	0.91878	0.497000	0.22514	1.476000	0.48215	-0.122000	0.15005	GTC	.	.		0.502	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		A	119249699	C	A	119249699	3	1	227	1	0	0	0	0	1	0	0	0	1065	507	18	3	640	3	ASTN2	9	119249699	Missense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	11122727	119249699	21963732	38	32061										
CPEB3	22849	hgsc.bcm.edu	37	chr10	93904825	93904825	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	caaggcttgatcaccatggcTatcatccaggaaggcatctt	9	11	3	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr10:93904825T>A	ENST00000265997.4	-	5	1412	c.1240A>T	c.(1240-1242)Agc>Tgc	p.S414C	CPEB3_ENST00000412050.4_Missense_Mutation_p.S400C	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	414					3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				TCACCATGGCTATCATCCAGG	0.423																																					p.S414C		Atlas-SNP	.											.	CPEB3	43	.	0			c.A1240T						.						102	91	95					10																	93904825		2203	4300	6503	SO:0001583	missense	22849	exon5			CATGGCTATCATC	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.1240A>T	chr10.hg19:g.93904825T>A	ENSP00000265997:p.Ser414Cys	112.0	0.0		115.0	36.0	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	hg19	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.993817	0.74703	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.47177	0.85;0.86	5.39	4.26	0.50523	.	0.190023	0.64402	D	0.000014	T	0.44244	0.1284	N	0.22421	0.69	0.38958	D	0.958499	D;D;D	0.62365	0.991;0.964;0.979	P;B;P	0.54759	0.76;0.338;0.634	T	0.48091	-0.9065	10	0.72032	D	0.01	-2.4026	8.4764	0.33016	0.0:0.1499:0.0:0.8501	.	414;400;400	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	C	400;400;414	ENSP00000398310:S400C;ENSP00000265997:S414C	ENSP00000265997:S414C	S	-	1	0	CPEB3	93894805	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	2.583000	0.46094	0.891000	0.36235	-0.256000	0.11100	AGC	.	.		0.423	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		A	93904825	T	A	93904825	3	1	227	1	0	0	0	0	1	0	0	0	3804	1522	53	4	880	4	CPEB3	10	93904825	Missense_Mutation	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10		93904825	41629922	39	32062										
LRDD	55367	hgsc.bcm.edu	37	chr11	802041	802041	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gggtcctgaccaccacttcaCggcagcgccgggcctgcggt	14	16	1	1	rs554590814		TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr11:802041C>T	ENST00000347755.5	-	7	1367	c.1226G>A	c.(1225-1227)cGt>cAt	p.R409H	PIDD_ENST00000534649.1_5'Flank|PIDD_ENST00000411829.2_Missense_Mutation_p.R409H	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2																					CACCACTTCACGGCAGCGCCG	0.677													C|||	1	0.000199681	0	0.0014	5008	,	,		13336	0		0	False		,,,				2504	0				p.R409H		Atlas-SNP	.											.	PIDD	76	.	0			c.G1226A						.						24	22	23					11																	802041		2194	4290	6484	SO:0001583	missense	55367	exon7			ACTTCACGGCAGC																												ENST00000347755.5:c.1226G>A	chr11.hg19:g.802041C>T	ENSP00000337797:p.Arg409His	91.0	0.0		71.0	30.0	NM_145887		Missense_Mutation	SNP	ENST00000347755.5	hg19	CCDS7716.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.422422	0.25639	.	.	ENSG00000177595	ENST00000411829;ENST00000347755	T;T	0.42900	0.96;0.96	4.16	1.03	0.20045	ZU5 (2);	0.173432	0.35207	N	0.003377	T	0.25901	0.0631	L	0.32530	0.975	0.09310	N	1	B;B;B	0.27264	0.173;0.108;0.116	B;B;B	0.19946	0.027;0.012;0.017	T	0.16158	-1.0412	10	0.62326	D	0.03	.	5.4151	0.16370	0.1406:0.6151:0.0:0.2442	.	409;263;409	Q9HB75;Q9HB75-3;Q9HB75-2	PIDD_HUMAN;.;.	H	409	ENSP00000416801:R409H;ENSP00000337797:R409H	ENSP00000337797:R409H	R	-	2	0	PIDD	792041	0.061000	0.20836	0.695000	0.30226	0.309000	0.27889	1.204000	0.32296	0.413000	0.25759	0.561000	0.74099	CGT	.	.		0.677	PIDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257103.1			T	802041	C	T	802041	3	4	227	1	0	0	0	0	1	0	0	0	8945	536	19	1	1546	1	LRDD	11	802041	Missense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10		802041	134204475	40	32063										
MUC2	4583	hgsc.bcm.edu	37	chr11	1092675	1092675	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	accacccctccaccaaccacCactcccagccctccaacgac	2	25	0	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr11:1092675C>A	ENST00000441003.2	+	30	4521	c.4494C>A	c.(4492-4494)acC>acA	p.T1498T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1499T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4233	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caccaaccaccactcccagcc	0.627																																					p.T1498T		Atlas-SNP	.											.	MUC2	614	.	0			c.C4494A						.						376	554	492					11																	1092675		1763	3316	5079	SO:0001819	synonymous_variant	4583	exon30			AACCACCACTCCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4494C>A	chr11.hg19:g.1092675C>A		257.0	0.0		198.0	19.0	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1092675	C	A	1092675	2	1	227	1	0	0	0	0	0	0	0	1	9984	581	21	3		3	MUC2	11	1092675	Silent	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	290634	1092675	133913841	41	32064										
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46456546	46456546	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	agaaatgtcacagctggcatCattgtagatcttgcagttct	9	8	4	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr11:46456546C>T	ENST00000458649.2	-	13	3092	c.2674G>A	c.(2674-2676)Gat>Aat	p.D892N	AMBRA1_ENST00000426438.1_Missense_Mutation_p.D863N|AMBRA1_ENST00000534300.1_Missense_Mutation_p.D832N|AMBRA1_ENST00000533727.1_Missense_Mutation_p.D773N|AMBRA1_ENST00000314845.3_Missense_Mutation_p.D802N|AMBRA1_ENST00000528950.1_Missense_Mutation_p.D863N|AMBRA1_ENST00000298834.3_Missense_Mutation_p.D832N			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	892					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		CAGCTGGCATCATTGTAGATC	0.478																																					p.D895N		Atlas-SNP	.											.	AMBRA1	201	.	0			c.G2683A						.						42	38	39					11																	46456546		2201	4299	6500	SO:0001583	missense	55626	exon15			TGGCATCATTGTA	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	25990	protein-coding gene	gene with protein product	"WD repeat domain 94", "DDB1 and CUL4 associated factor 3"	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.2674G>A	chr11.hg19:g.46456546C>T	ENSP00000415327:p.Asp892Asn	101.0	0.0		105.0	50.0	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.861776	0.97036	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.05447	3.44;3.44;3.44;3.44;3.44;3.44;3.44	5.86	5.86	0.93980	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.27697	0.0681	M	0.71036	2.16	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	0.997;1.0;1.0;0.998;0.998;0.998	D;D;D;D;D;D	0.87578	0.989;0.998;0.998;0.995;0.995;0.995	T	0.00121	-1.2028	10	0.87932	D	0	.	20.1772	0.98182	0.0:1.0:0.0:0.0	.	892;863;832;773;895;802	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	N	802;773;832;863;832;892;863	ENSP00000318313:D802N;ENSP00000433372:D773N;ENSP00000431926:D832N;ENSP00000410899:D863N;ENSP00000298834:D832N;ENSP00000415327:D892N;ENSP00000433945:D863N	ENSP00000298834:D832N	D	-	1	0	AMBRA1	46413122	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.636000	0.83301	2.778000	0.95560	0.655000	0.94253	GAT	.	.		0.478	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		T	46456546	C	T	46456546	3	4	227	1	0	0	0	0	1	0	0	0	565	826	29	3	1246	3	AMBRA1	11	46456546	Missense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	45363871	46456546	88549970	42	32065										
FOLR4	390243	hgsc.bcm.edu	37	chr11	94040366	94040366	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	cagggagagcgagttgtgaaTgtgccgctgtgccaggagga	18	7	0	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr11:94040366T>C	ENST00000440961.2	+	3	407	c.363T>C	c.(361-363)aaT>aaC	p.N121N		NM_001199206.1	NP_001186135.1	A6ND01	JUNO_HUMAN	folate receptor 4, delta (putative)	128					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.N122K(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14						GAGTTGTGAATGTGCCGCTGT	0.537																																					p.N128N		Atlas-SNP	.											FOLR4,NS,carcinoma,0,1	FOLR4	31	.	1	Substitution - Missense(1)	ovary(1)	c.T384C						.						93	100	98					11																	94040366		2185	4286	6471	SO:0001819	synonymous_variant	390243	exon3			TGTGAATGTGCCG			11q14	2014-07-23	2012-12-07		ENSG00000183560	ENSG00000183560			32565	protein-coding gene	gene with protein product		615737	"folate receptor 4 (delta) homolog (mouse)"			11111049, 24739963	Standard	NM_001199206		Approved	Folbp3, JUNO	uc021qou.1	A6ND01		ENST00000440961.2:c.363T>C	chr11.hg19:g.94040366T>C		112.0	0.0		104.0	50.0	NM_001199206		Silent	SNP	ENST00000440961.2	hg19		.	.	.	.	.	.	.	.	.	.	T	4.151	0.026365	0.08054	.	.	ENSG00000183560	ENST00000328458	.	.	.	4.57	-6.96	0.01622	.	.	.	.	.	T	0.30448	0.0765	.	.	.	0.34156	D	0.668073	.	.	.	.	.	.	T	0.37526	-0.9702	4	.	.	.	-15.711	3.8329	0.08882	0.1055:0.2616:0.1047:0.5283	.	.	.	.	T	122	.	.	M	+	2	0	FOLR4	93680014	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.849000	0.01672	-1.309000	0.02315	0.402000	0.26972	ATG	.	.		0.537	FOLR4-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000396420.1	NM_001080486		C	94040366	T	C	94040366	2	2	227	1	0	0	0	0	0	0	0	1	5992	1461	51	2		2	FOLR4	11	94040366	Silent	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10	47583820	94040366	40966150	43	32066										
DRD2	1813	hgsc.bcm.edu	37	chr11	113288785	113288785	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	cacacaagttcaggatgctcGccgtgcacatcatgacgtcc	9	14	2	1	rs201724929		TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr11:113288785G>A	ENST00000362072.3	-	3	703	c.359C>T	c.(358-360)gCg>gTg	p.A120V	DRD2_ENST00000538967.1_Missense_Mutation_p.A120V|DRD2_ENST00000544518.1_Missense_Mutation_p.A119V|DRD2_ENST00000346454.3_Missense_Mutation_p.A120V|DRD2_ENST00000535984.1_5'UTR|DRD2_ENST00000542968.1_Missense_Mutation_p.A120V|DRD2_ENST00000355319.2_Missense_Mutation_p.A120V	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	120					activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CAGGATGCTCGCCGTGCACAT	0.542																																					p.A120V		Atlas-SNP	.											.	DRD2	98	.	0			c.C359T						.						173	120	138					11																	113288785		2201	4296	6497	SO:0001583	missense	1813	exon3			ATGCTCGCCGTGC	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.359C>T	chr11.hg19:g.113288785G>A	ENSP00000354859:p.Ala120Val	68.0	0.0		58.0	21.0	NM_016574	Q9NZR3|Q9UPA9	Missense_Mutation	SNP	ENST00000362072.3	hg19	CCDS8361.1	.	.	.	.	.	.	.	.	.	.	G	35	5.457579	0.96240	.	.	ENSG00000149295	ENST00000355319;ENST00000346454;ENST00000362072;ENST00000544518;ENST00000542968;ENST00000538967;ENST00000543292	T;T;T;T;T;T;T	0.75704	-0.96;-0.96;-0.96;-0.96;-0.96;-0.96;-0.96	5.23	5.23	0.72850	GPCR, rhodopsin-like superfamily (1);	0.146095	0.64402	D	0.000008	D	0.89705	0.6792	M	0.92555	3.32	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.78314	0.977;0.977;0.977;0.991	D	0.91984	0.5597	10	0.87932	D	0	.	18.7905	0.91973	0.0:0.0:1.0:0.0	.	119;120;120;120	F8VUV1;P14416-3;P14416-2;P14416	.;.;.;DRD2_HUMAN	V	120;120;120;119;120;120;120	ENSP00000347474:A120V;ENSP00000278597:A120V;ENSP00000354859:A120V;ENSP00000441068:A119V;ENSP00000442172:A120V;ENSP00000438215:A120V;ENSP00000438419:A120V	ENSP00000278597:A120V	A	-	2	0	DRD2	112793995	1.000000	0.71417	0.994000	0.49952	0.877000	0.50540	9.768000	0.98965	2.591000	0.87537	0.655000	0.94253	GCG	.	.		0.542	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		A	113288785	G	A	113288785	3	1	227	1	0	0	0	0	1	0	0	0	4759	1087	38	1	996	1	DRD2	11	113288785	Missense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	19248419	113288785	21717731	44	32067										
TARBP2	8620	hgsc.bcm.edu	37	chr12	53899546	53899546	+	IGR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctccgcagttgctccctgggCtccctgggtgccctgggccc	13	18	0	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr12:53899546C>G	ENST00000267017.3	-	0	592				TARBP2_ENST00000456234.2_Silent_p.G264G|TARBP2_ENST00000552857.1_Missense_Mutation_p.L152V|TARBP2_ENST00000266987.2_Silent_p.G285G|TARBP2_ENST00000394357.2_Silent_p.G264G	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor						acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						GCTCCCTGGGCTCCCTGGGTG	0.597																																					p.G285G		Atlas-SNP	.											.	TARBP2	35	.	0			c.C855G						.						79	82	81					12																	53899546		2203	4300	6503	SO:0001628	intergenic_variant	6895	exon8			CCTGGGCTCCCTG	AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"Endogenous ligands"	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856		chr12.hg19:g.53899546C>G		69.0	0.0		25.0	21.0	NM_134323	Q3SXL4	Silent	SNP	ENST00000267017.3	hg19	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	C	9.802	1.180730	0.21787	.	.	ENSG00000139546	ENST00000552857;ENST00000550407	.	.	.	4.98	0.906	0.19314	.	.	.	.	.	T	0.30070	0.0753	.	.	.	0.53005	D	0.999967	.	.	.	.	.	.	T	0.08493	-1.0719	5	0.06757	T	0.87	-6.723	7.4954	0.27485	0.0:0.4611:0.3861:0.1528	.	.	.	.	V	152;144	.	ENSP00000447767:L144V	L	+	1	0	TARBP2	52185813	0.000000	0.05858	0.684000	0.30055	0.993000	0.82548	-0.368000	0.07543	0.062000	0.16340	0.561000	0.74099	CTC	.	.		0.597	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717		G	53899546	C	G	53899546	1	3	227	0	1	0	0	0	0	0	0	0	15571	784	28	4		4	TARBP2	12	53899546	IGR	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10		53899546	79952349	45	32068										
ACACB	32	hgsc.bcm.edu	37	chr12	109692040	109692040	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ataatcacagccctgtccctAtcatcacacccactgacccc	3	19	3	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr12:109692040A>G	ENST00000338432.7	+	44	6186	c.6067A>G	c.(6067-6069)Atc>Gtc	p.I2023V	ACACB_ENST00000543201.1_Missense_Mutation_p.I689V|ACACB_ENST00000377854.5_Missense_Mutation_p.I1953V|ACACB_ENST00000377848.3_Missense_Mutation_p.I2023V			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2023	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	CCCTGTCCCTATCATCACACC	0.498																																					p.I2023V		Atlas-SNP	.											.	ACACB	330	.	0			c.A6067G						.						255	240	245					12																	109692040		2203	4300	6503	SO:0001583	missense	32	exon43			GTCCCTATCATCA	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.6067A>G	chr12.hg19:g.109692040A>G	ENSP00000341044:p.Ile2023Val	132.0	0.0		66.0	52.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	A	10.35	1.325474	0.24080	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027;ENST00000543201	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	5.27	2.9	0.33743	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.239612	0.45126	N	0.000387	T	0.21590	0.0520	L	0.38175	1.15	0.30748	N	0.745382	B	0.02656	0.0	B	0.09377	0.004	T	0.12502	-1.0545	10	0.33141	T	0.24	.	8.3136	0.32086	0.6995:0.0:0.3005:0.0	.	2023	O00763	ACACB_HUMAN	V	2023;2023;1953;1254;689	ENSP00000341044:I2023V;ENSP00000367079:I2023V;ENSP00000367085:I1953V;ENSP00000444075:I689V	ENSP00000341044:I2023V	I	+	1	0	ACACB	108176423	0.152000	0.22762	0.678000	0.29963	0.985000	0.73830	0.614000	0.24314	0.416000	0.25844	-0.290000	0.09829	ATC	.	.		0.498	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		G	109692040	A	G	109692040	3	3	227	1	0	0	0	0	1	0	0	0	107	449	16	2	6237	2	ACACB	12	109692040	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	55792494	109692040	24159855	46	32069										
RPGRIP1	57096	hgsc.bcm.edu	37	chr14	21769132	21769132	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	tatttgtccacaggctgaggAccaccttgctgcggttgacc	11	12	0	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr14:21769132A>T	ENST00000400017.2	+	3	226	c.226A>T	c.(226-228)Acc>Tcc	p.T76S	RPGRIP1_ENST00000556336.1_Missense_Mutation_p.T76S|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.T76S|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.T76S	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	76					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		CAGGCTGAGGACCACCTTGCT	0.567																																					p.T76S		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.A226T						.						53	57	56					14																	21769132		1896	4060	5956	SO:0001583	missense	57096	exon3			CTGAGGACCACCT	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.226A>T	chr14.hg19:g.21769132A>T	ENSP00000382895:p.Thr76Ser	126.0	0.0		86.0	17.0	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	hg19	CCDS45080.1	.	.	.	.	.	.	.	.	.	.	a	15.33	2.801322	0.50315	.	.	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660	D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05	3.86	3.86	0.44501	.	0.401084	0.23608	N	0.046379	T	0.81059	0.4744	L	0.61218	1.895	0.80722	D	1	B	0.25719	0.132	B	0.17433	0.018	T	0.80238	-0.1465	10	0.62326	D	0.03	-0.5253	9.2661	0.37641	1.0:0.0:0.0:0.0	.	76	Q96KN7	RPGR1_HUMAN	S	76	ENSP00000450445:T76S;ENSP00000451219:T76S;ENSP00000382895:T76S;ENSP00000206660:T76S	ENSP00000206660:T76S	T	+	1	0	RPGRIP1	20838972	0.825000	0.29262	0.932000	0.37286	0.067000	0.16453	2.234000	0.43035	1.761000	0.52028	0.369000	0.22263	ACC	.	.		0.567	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		T	21769132	A	T	21769132	3	4	227	1	0	0	0	0	1	0	0	0	13564	275	10	4	236	4	RPGRIP1	14	21769132	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10		21769132	85580408	47	32070										
CHD8	57680	hgsc.bcm.edu	37	chr14	21896309	21896309	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	tccattcctgtctttcccccCgaatgaggagcagagcttgc	9	14	1	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr14:21896309C>T	ENST00000557364.1	-	4	1583	c.1320G>A	c.(1318-1320)tcG>tcA	p.S440S	CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Silent_p.S161S|CHD8_ENST00000399982.2_Silent_p.S440S|RN7SL650P_ENST00000583681.1_RNA			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	440					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		TCTTTCCCCCCGAATGAGGAG	0.527																																					p.S440S		Atlas-SNP	.											.	CHD8	339	.	0			c.G1320A						.						182	176	178					14																	21896309		1957	4143	6100	SO:0001819	synonymous_variant	57680	exon3			TCCCCCCGAATGA	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.1320G>A	chr14.hg19:g.21896309C>T		125.0	0.0		93.0	31.0	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	hg19	CCDS53885.1																																																																																			.	.		0.527	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		T	21896309	C	T	21896309	2	4	227	1	0	0	0	0	0	0	0	1	3333	639	23	1		1	CHD8	14	21896309	Silent	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	127177	21896309	85453231	48	32071										
NRXN3	9369	hgsc.bcm.edu	37	chr14	79434578	79434578	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	acctcccaaagctcgtggccTctcgagatggctttcagggc	11	14	2	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr14:79434578T>A	ENST00000554719.1	+	11	2403	c.1912T>A	c.(1912-1914)Tct>Act	p.S638T	NRXN3_ENST00000335750.5_Missense_Mutation_p.S638T	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	244					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		GCTCGTGGCCTCTCGAGATGG	0.507																																					p.S638T		Atlas-SNP	.											.	NRXN3	342	.	0			c.T1912A						.						133	116	122					14																	79434578		2203	4300	6503	SO:0001583	missense	9369	exon11			GTGGCCTCTCGAG	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.1912T>A	chr14.hg19:g.79434578T>A	ENSP00000451648:p.Ser638Thr	124.0	0.0		103.0	66.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	hg19	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.760307	0.89932	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750	T;T	0.76578	-1.03;-1.03	6.03	6.03	0.97812	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	T	0.82157	0.4976	.	.	.	0.58432	D	0.999993	D;P	0.53462	0.96;0.837	P;B	0.51657	0.676;0.356	T	0.81982	-0.0683	8	.	.	.	.	16.5655	0.84588	0.0:0.0:0.0:1.0	.	1011;638	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	T	1011;1000;638;638	ENSP00000451648:S638T;ENSP00000338349:S638T	.	S	+	1	0	NRXN3	78504331	1.000000	0.71417	0.998000	0.56505	0.935000	0.57460	6.248000	0.72418	2.302000	0.77476	0.533000	0.62120	TCT	.	.		0.507	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250		A	79434578	T	A	79434578	3	1	227	1	0	0	0	0	1	0	0	0	10676	1551	54	4	1946	4	NRXN3	14	79434578	Missense_Mutation	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10	57538269	79434578	27914962	49	32072										
SERPINA5	5104	hgsc.bcm.edu	37	chr14	95053895	95053895	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctgcccccagccagagcatcTtcttctcccctgtgagcatc	7	18	3	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr14:95053895T>G	ENST00000554866.1	+	2	310	c.196T>G	c.(196-198)Ttc>Gtc	p.F66V	SERPINA5_ENST00000553780.1_Missense_Mutation_p.F66V|SERPINA5_ENST00000329597.7_Missense_Mutation_p.F66V|SERPINA5_ENST00000554276.1_Missense_Mutation_p.F66V			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	66					fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CCAGAGCATCTTCTTCTCCCC	0.622																																					p.F66V		Atlas-SNP	.											.	SERPINA5	69	.	0			c.T196G						.						35	34	35					14																	95053895		2203	4300	6503	SO:0001583	missense	5104	exon3			AGCATCTTCTTCT	M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"Serine (or cysteine) peptidase inhibitors"	8723	protein-coding gene	gene with protein product		601841	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.196T>G	chr14.hg19:g.95053895T>G	ENSP00000451126:p.Phe66Val	95.0	0.0		82.0	49.0	NM_000624	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	hg19	CCDS9928.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.548933	0.45383	.	.	ENSG00000188488	ENST00000554220;ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000553511;ENST00000554633;ENST00000555681;ENST00000554276;ENST00000557598	D;D;D;D;D;D;D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79;-1.79;-1.79;-1.79;-1.79;-1.79;-1.79	4.11	-0.223	0.13118	Serpin domain (3);	0.084800	0.50627	D	0.000118	T	0.76786	0.4036	M	0.67517	2.055	0.41583	D	0.988756	B;B	0.19331	0.028;0.035	B;B	0.25884	0.064;0.035	T	0.63897	-0.6533	10	0.17369	T	0.5	.	9.1347	0.36866	0.4507:0.0:0.0:0.5493	.	66;66	G3V5Q9;P05154	.;IPSP_HUMAN	V	66	ENSP00000450484:F66V;ENSP00000450837:F66V;ENSP00000452469:F66V;ENSP00000451126:F66V;ENSP00000333203:F66V;ENSP00000450745:F66V;ENSP00000451215:F66V;ENSP00000451697:F66V;ENSP00000451650:F66V;ENSP00000451610:F66V;ENSP00000450485:F66V	ENSP00000333203:F66V	F	+	1	0	SERPINA5	94123648	1.000000	0.71417	0.966000	0.40874	0.206000	0.24218	0.976000	0.29462	0.180000	0.19960	0.459000	0.35465	TTC	.	.		0.622	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624		G	95053895	T	G	95053895	3	3	227	1	0	0	0	0	1	0	0	0	14107	1609	56	5	198	5	SERPINA5	14	95053895	Missense_Mutation	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10	15619317	95053895	12295645	50	32073										
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32925232	32925232	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	cagagttcactctctcctgtActcattggtggaaaccattt	7	11	3	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr15:32925232A>G	ENST00000361627.3	+	9	1880	c.1158A>G	c.(1156-1158)gtA>gtG	p.V386V	ARHGAP11A_ENST00000543522.1_Silent_p.V197V|ARHGAP11A_ENST00000565905.1_Silent_p.V197V|ARHGAP11A_ENST00000563864.1_Intron|ARHGAP11A_ENST00000567348.1_Silent_p.V386V	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	386					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		TCTCTCCTGTACTCATTGGTG	0.393																																					p.V386V	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.A1158G						.						157	152	154					15																	32925232		2201	4300	6501	SO:0001819	synonymous_variant	9824	exon9			TCCTGTACTCATT	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1158A>G	chr15.hg19:g.32925232A>G		134.0	0.0		154.0	72.0	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	hg19	CCDS10028.1																																																																																			.	.		0.393	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		G	32925232	A	G	32925232	2	3	227	1	0	0	0	0	0	0	0	1	863	378	14	2		2	ARHGAP11A	15	32925232	Silent	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10		32925232	69606160	51	32074										
TLN2	83660	hgsc.bcm.edu	37	chr15	62990037	62990037	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	cagcagcaggtcatggttggGcagatgcaccgaggccacat	14	11	1	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr15:62990037G>T	ENST00000561311.1	+	14	1673	c.1443G>T	c.(1441-1443)ggG>ggT	p.G481G	TLN2_ENST00000306829.6_Silent_p.G481G			Q9Y4G6	TLN2_HUMAN	talin 2	481					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						TCATGGTTGGGCAGATGCACC	0.672																																					p.G481G		Atlas-SNP	.											.	TLN2	253	.	0			c.G1443T						.						34	32	32					15																	62990037		2202	4299	6501	SO:0001819	synonymous_variant	83660	exon12			GGTTGGGCAGATG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.1443G>T	chr15.hg19:g.62990037G>T		111.0	0.0		81.0	37.0	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	hg19	CCDS32261.1																																																																																			.	.		0.672	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	62990037	G	T	62990037	2	4	227	1	0	0	0	0	0	0	0	1	15963	1190	42	3		3	TLN2	15	62990037	Silent	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	30064805	62990037	39541355	52	32075										
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65689263	65689263	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	acgccggagtgccagggctgCgcgttggcaattagtaggtt	16	9	0	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr15:65689263C>T	ENST00000352385.2	-	6	1115	c.906G>A	c.(904-906)gcG>gcA	p.A302A		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	302	Ig-like C2-type 3.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						GCCAGGGCTGCGCGTTGGCAA	0.672																																					p.A302A		Atlas-SNP	.											.	IGDCC4	95	.	0			c.G906A						.						38	36	37					15																	65689263		2190	4289	6479	SO:0001819	synonymous_variant	57722	exon6			GGGCTGCGCGTTG		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.906G>A	chr15.hg19:g.65689263C>T		128.0	0.0		128.0	68.0	NM_020962	Q9HCE4	Silent	SNP	ENST00000352385.2	hg19	CCDS10206.1																																																																																			.	.		0.672	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		T	65689263	C	T	65689263	2	4	227	1	0	0	0	0	0	0	0	1	7578	755	27	1		1	IGDCC4	15	65689263	Silent	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	2699226	65689263	36842129	53	32076										
GOLGA6B	55889	hgsc.bcm.edu	37	chr15	72955008	72955008	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	aggctgtggaagaaggaggaGaggctacaaaagcaggagga	18	4	0	2	rs199550549	byFrequency	TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr15:72955008G>C	ENST00000421285.3	+	11	1263	c.1263G>C	c.(1261-1263)gaG>gaC	p.E421D	RN7SL853P_ENST00000477951.2_RNA	NM_018652.4	NP_061122.4	A6NDN3	GOG6B_HUMAN	golgin A6 family, member B	421						Golgi apparatus (GO:0005794)		p.E421D(1)		NS(1)|breast(1)|endometrium(1)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	16						AGAAGGAGGAGAGGCTACAAA	0.587																																					p.E421D		Atlas-SNP	.											GOLGA6B,NS,malignant_melanoma,0,1	GOLGA6B	30	.	1	Substitution - Missense(1)	NS(1)	c.G1263C						.						1	1	1					15																	72955008		108	305	413	SO:0001583	missense	55889	exon11			GGAGGAGAGGCTA		CCDS10245.2	15q24.1	2011-10-25	2010-02-12		ENSG00000215186	ENSG00000215186			32205	protein-coding gene	gene with protein product			"golgi autoantigen, golgin subfamily a, 6B"				Standard	XM_006720604		Approved		uc010uks.1	A6NDN3	OTTHUMG00000133511	ENST00000421285.3:c.1263G>C	chr15.hg19:g.72955008G>C	ENSP00000408132:p.Glu421Asp	53.0	0.0		66.0	3.0	NM_018652	A8MYY7	Missense_Mutation	SNP	ENST00000421285.3	hg19	CCDS10245.2	.	.	.	.	.	.	.	.	.	.	.	3.065	-0.192360	0.06259	.	.	ENSG00000215186	ENST00000421285	T	0.07444	3.19	.	.	.	.	.	.	.	.	T	0.06962	0.0177	L	0.47190	1.495	0.22888	N	0.99861	P	0.49961	0.93	B	0.40444	0.329	T	0.30208	-0.9986	8	0.62326	D	0.03	.	2.6645	0.05037	0.4931:0.0:0.5069:0.0	.	421	A6NDN3	GOG6B_HUMAN	D	421	ENSP00000408132:E421D	ENSP00000408132:E421D	E	+	3	2	GOLGA6B	70742062	0.998000	0.40836	0.134000	0.22075	0.265000	0.26407	0.636000	0.24644	0.088000	0.17205	0.089000	0.15464	GAG	.	G|1.000;|0.000		0.587	GOLGA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257474.4	NM_018652		C	72955008	G	C	72955008	3	2	227	1	0	0	0	0	1	0	0	0	6566	933	33	4	1305	4	GOLGA6B	15	72955008	Missense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	7265745	72955008	29576384	54	32077										
AXIN1	8312	hgsc.bcm.edu	37	chr16	360038	360038	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctgcatctccctgcggtgctGcttacggatcctgtatgggg	13	12	1	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr16:360038G>A	ENST00000262320.3	-	4	1422	c.1051C>T	c.(1051-1053)Cag>Tag	p.Q351*	AXIN1_ENST00000481769.1_5'UTR|AXIN1_ENST00000354866.3_Nonsense_Mutation_p.Q351*	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	351	Interaction with GSK3B. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CTGCGGTGCTGCTTACGGATC	0.612																																					p.Q351X		Atlas-SNP	.											.	AXIN1	290	.	0			c.C1051T						.						86	55	65					16																	360038		2203	4300	6503	SO:0001587	stop_gained	8312	exon4			GGTGCTGCTTACG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1051C>T	chr16.hg19:g.360038G>A	ENSP00000262320:p.Gln351*	81.0	0.0		48.0	39.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Nonsense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	G	38	7.226415	0.98146	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	4.84	4.84	0.62591	.	0.287890	0.34959	N	0.003549	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	17.9962	0.89185	0.0:0.0:1.0:0.0	.	.	.	.	X	351	.	ENSP00000262320:Q351X	Q	-	1	0	AXIN1	300039	1.000000	0.71417	0.995000	0.50966	0.471000	0.32888	9.476000	0.97823	2.257000	0.74773	0.456000	0.33151	CAG	.	.		0.612	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	360038	G	A	360038	4	1	227	1	0	0	0	0	0	1	0	0	1236	1328	46	3	1569	3	AXIN1	16	360038	Nonsense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10		360038	89994715	55	32078										
SERPINF1	5176	hgsc.bcm.edu	37	chr17	1678371	1678371	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gggcagtgggtaacaaagttTgactccagaaagacttccct	11	9	0	3			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr17:1678371T>C	ENST00000254722.4	+	6	826	c.663T>C	c.(661-663)ttT>ttC	p.F221F		NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	221					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						TAACAAAGTTTGACTCCAGAA	0.522																																					p.F221F		Atlas-SNP	.											.	SERPINF1	31	.	0			c.T663C						.						88	87	87					17																	1678371		2203	4300	6503	SO:0001819	synonymous_variant	5176	exon6			AAAGTTTGACTCC	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"Serine (or cysteine) peptidase inhibitors"	8824	protein-coding gene	gene with protein product	"pigment epithelium-derived factor", "proliferation-inducing protein 35"	172860	"serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.663T>C	chr17.hg19:g.1678371T>C		100.0	0.0		43.0	35.0	NM_002615	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Silent	SNP	ENST00000254722.4	hg19	CCDS11012.1																																																																																			.	.		0.522	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615		C	1678371	T	C	1678371	2	2	227	1	0	0	0	0	0	0	0	1	14129	1809	63	2		2	SERPINF1	17	1678371	Silent	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10		1678371	79516839	56	32079										
TP53	7157	hgsc.bcm.edu	37	chr17	7578268	7578268	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	aatttccttccactcggataAgatgctgaggaggggccaga	12	9	0	3			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr17:7578268A>C	ENST00000269305.4	-	6	770	c.581T>G	c.(580-582)cTt>cGt	p.L194R	TP53_ENST00000413465.2_Missense_Mutation_p.L194R|TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.L194R|TP53_ENST00000455263.2_Missense_Mutation_p.L194R|TP53_ENST00000420246.2_Missense_Mutation_p.L194R|TP53_ENST00000359597.4_Missense_Mutation_p.L194R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	194	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		L -> F (in sporadic cancers; somatic mutation).|L -> H (in sporadic cancers; somatic mutation).|L -> I (in sporadic cancers; somatic mutation).|L -> P (in sporadic cancers; somatic mutation).|L -> R (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763}.|L -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.L194R(47)|p.L194P(8)|p.L194H(8)|p.0?(8)|p.?(6)|p.L101R(5)|p.L62R(5)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.L194fs*15(1)|p.L194fs*14(1)|p.L101H(1)|p.L194fs*52(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.L62H(1)|p.I195fs*52(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CACTCGGATAAGATGCTGAGG	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.L194R	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,colon,carcinoma,-1,1	TP53	33396	.	108	Substitution - Missense(75)|Whole gene deletion(8)|Deletion - Frameshift(6)|Complex - deletion inframe(6)|Unknown(6)|Deletion - In frame(5)|Insertion - Frameshift(1)|Complex - frameshift(1)	breast(19)|lung(14)|ovary(14)|large_intestine(11)|haematopoietic_and_lymphoid_tissue(10)|urinary_tract(6)|oesophagus(6)|biliary_tract(5)|skin(5)|bone(4)|upper_aerodigestive_tract(3)|stomach(3)|central_nervous_system(2)|pancreas(2)|liver(2)|soft_tissue(1)|prostate(1)	c.T581G						.						97	87	90					17																	7578268		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CGGATAAGATGCT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.581T>G	chr17.hg19:g.7578268A>C	ENSP00000269305:p.Leu194Arg	183.0	1.0		117.0	105.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.029856	0.54790	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99856	-7.21;-7.21;-7.21;-7.21;-7.21;-7.21;-7.21;-7.21	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99869	0.9938	M	0.90425	3.115	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.984;1.0;1.0;1.0;1.0	D	0.96375	0.9277	10	0.87932	D	0	-29.6709	13.709	0.62656	1.0:0.0:0.0:0.0	.	155;194;194;101;194;194;194	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	194;194;194;194;194;194;183;101;62;101;62	ENSP00000410739:L194R;ENSP00000352610:L194R;ENSP00000269305:L194R;ENSP00000398846:L194R;ENSP00000391127:L194R;ENSP00000391478:L194R;ENSP00000425104:L62R;ENSP00000423862:L101R	ENSP00000269305:L194R	L	-	2	0	TP53	7518993	1.000000	0.71417	0.300000	0.25030	0.031000	0.12232	9.287000	0.95975	2.183000	0.69458	0.533000	0.62120	CTT	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578268	A	C	7578268	3	2	227	1	0	0	0	0	1	0	0	0	16396	72	3	5	713	5	TP53	17	7578268	Missense_Mutation	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	5899897	7578268	73616942	57	32080										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7720679	7720679	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gccttcctgtcctacatgggAcccttcctgaccaactaccg	7	17	0	1	rs375895814		TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr17:7720679A>G	ENST00000572933.1	+	65	11426	c.9966A>G	c.(9964-9966)ggA>ggG	p.G3322G	DNAH2_ENST00000389173.2_Silent_p.G3322G			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3322					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.G3322G(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CCTACATGGGACCCTTCCTGA	0.607																																					p.G3322G		Atlas-SNP	.											DNAH2,colon,carcinoma,0,1	DNAH2	498	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A9966G						.						83	87	86					17																	7720679		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon64			CATGGGACCCTTC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.9966A>G	chr17.hg19:g.7720679A>G		46.0	0.0		31.0	26.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.		0.607	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		G	7720679	A	G	7720679	2	3	227	1	0	0	0	0	0	0	0	1	4604	262	10	2		2	DNAH2	17	7720679	Silent	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	142411	7720679	73474531	58	32081										
TNFRSF13B	23495	hgsc.bcm.edu	37	chr17	16843680	16843680	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	ctttgacggggccttgagcgGggctggcaggagcagggatc	19	9	0	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr17:16843680G>A	ENST00000261652.2	-	4	603	c.591C>T	c.(589-591)ccC>ccT	p.P197P	TNFRSF13B_ENST00000583789.1_Silent_p.P151P|TNFRSF13B_ENST00000437538.2_Silent_p.P151P|TNFRSF13B_ENST00000579315.1_Intron|TNFRSF13B_ENST00000581616.2_5'Flank	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	197					B cell homeostasis (GO:0001782)|cell surface receptor signaling pathway (GO:0007166)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of B cell proliferation (GO:0030889)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|skin(1)	16						GCCTTGAGCGGGGCTGGCAGG	0.657									IgA Deficiency, Selective																												p.P197P		Atlas-SNP	.											.	TNFRSF13B	34	.	0			c.C591T						.						89	94	92					17																	16843680		2203	4300	6503	SO:0001819	synonymous_variant	23495	exon4	Familial Cancer Database	IGAD1, IGAD2	TGAGCGGGGCTGG	AF023614	CCDS11181.1	17p11.2	2014-09-17			ENSG00000240505	ENSG00000240505		"Tumor necrosis factor receptor superfamily", "CD molecules"	18153	protein-coding gene	gene with protein product		604907				9311921	Standard	NM_012452		Approved	TACI, CD267	uc002gqs.1	O14836	OTTHUMG00000059262	ENST00000261652.2:c.591C>T	chr17.hg19:g.16843680G>A		121.0	0.0		41.0	4.0	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Silent	SNP	ENST00000261652.2	hg19	CCDS11181.1																																																																																			.	.		0.657	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2			A	16843680	G	A	16843680	2	1	227	1	0	0	0	0	0	0	0	1	16302	1219	43	3		3	TNFRSF13B	17	16843680	Silent	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	9123001	16843680	64351530	59	32082										
PLCD3	113026	hgsc.bcm.edu	37	chr17	43190626	43190626	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	agctgctgtgcagtcagcacCtgtgggtgagggagggagtg	19	7	1	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr17:43190626C>T	ENST00000540511.1	-	13	2082		c.e13-1		PLCD3_ENST00000322765.5_Splice_Site			Q8N3E9	PLCD3_HUMAN	phospholipase C, delta 3						angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	17						CAGTCAGCACCTGTGGGTGAG	0.632																																					.		Atlas-SNP	.											.	PLCD3	78	.	0			c.1995-1G>A						.						13	14	13					17																	43190626		2093	4214	6307	SO:0001630	splice_region_variant	113026	exon14			CAGCACCTGTGGG	AC002117	CCDS74077.1	17q21	2012-04-20			ENSG00000161714	ENSG00000161714	3.1.4.11		9061	protein-coding gene	gene with protein product		608795				10702670, 9056492	Standard	NM_133373		Approved		uc002iib.3	Q8N3E9	OTTHUMG00000168029	ENST00000540511.1:c.4025-1G>A	chr17.hg19:g.43190626C>T		49.0	0.0		42.0	18.0	NM_133373	Q8TEC1|Q8TF37|Q96FL6	Splice_Site	SNP	ENST00000540511.1	hg19		.	.	.	.	.	.	.	.	.	.	C	19.76	3.887551	0.72410	.	.	ENSG00000161714	ENST00000322765;ENST00000539433	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8544	0.88758	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PLCD3	40546152	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	7.609000	0.82925	2.615000	0.88500	0.555000	0.69702	.	.	.		0.632	PLCD3-001	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000397579.1	NM_133373	Intron	T	43190626	C	T	43190626	5	4	227	1	0	0	0	0	0	0	1	0	12041	695	24	3	386	3	PLCD3	17	43190626	Splice_Site	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	26346946	43190626	38004584	60	32083										
SCRN2	90507	hgsc.bcm.edu	37	chr17	45915690	45915690	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	tgtccacggtagagggtatgCcgacgatctacctgagtctg	13	10	2	2			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr17:45915690C>T	ENST00000290216.9	-	7	1190	c.1065G>A	c.(1063-1065)cgG>cgA	p.R355R	SCRN2_ENST00000407215.3_Silent_p.R355R|SCRN2_ENST00000584123.1_Silent_p.R363R	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	355						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						AGAGGGTATGCCGACGATCTA	0.627																																					p.R355R		Atlas-SNP	.											.	SCRN2	35	.	0			c.G1065A						.						67	70	69					17																	45915690		2203	4300	6503	SO:0001819	synonymous_variant	90507	exon7			GGTATGCCGACGA	BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.1065G>A	chr17.hg19:g.45915690C>T		129.0	0.0		121.0	47.0	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	hg19	CCDS11519.1																																																																																			.	.		0.627	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		T	45915690	C	T	45915690	2	4	227	1	0	0	0	0	0	0	0	1	13954	726	26	3		3	SCRN2	17	45915690	Silent	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10	2725064	45915690	35279520	61	32084										
DCC	1630	hgsc.bcm.edu	37	chr18	50731599	50731599	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	tatacagtgcaagttccaggGccagtagaaaacctgcaagc	10	10	0	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr18:50731599G>C	ENST00000442544.2	+	10	2203	c.1587G>C	c.(1585-1587)ggG>ggC	p.G529G	DCC_ENST00000412726.1_Silent_p.G377G|DCC_ENST00000581580.1_Silent_p.G184G	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	529					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		AAGTTCCAGGGCCAGTAGAAA	0.378																																					p.G529G		Atlas-SNP	.											.	DCC	360	.	0			c.G1587C						.						152	159	157					18																	50731599		2203	4300	6503	SO:0001819	synonymous_variant	1630	exon10			TCCAGGGCCAGTA	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.1587G>C	chr18.hg19:g.50731599G>C		88.0	0.0		105.0	37.0	NM_005215		Silent	SNP	ENST00000442544.2	hg19	CCDS11952.1																																																																																			.	.		0.378	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		C	50731599	G	C	50731599	2	2	227	1	0	0	0	0	0	0	0	1	4284	1190	42	4		4	DCC	18	50731599	Silent	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10		50731599	27345649	62	32085										
TNFRSF11A	8792	hgsc.bcm.edu	37	chr18	60028929	60028929	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	acagaaccccatgtttacttGcccggtttaataattctgct	6	11	1	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr18:60028929G>A	ENST00000586569.1	+	7	671	c.633G>A	c.(631-633)ttG>ttA	p.L211L	TNFRSF11A_ENST00000269485.7_Intron	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	211					adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				ATGTTTACTTGCCCGGTTTAA	0.408																																					p.L211L		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.G633A						.						247	245	246					18																	60028929		2203	4300	6503	SO:0001819	synonymous_variant	8792	exon7			TTACTTGCCCGGT	AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"Tumor necrosis factor receptor superfamily", "CD molecules"	11908	protein-coding gene	gene with protein product		603499	"tumor necrosis factor receptor superfamily, member 11a, activator of NFKB", "Paget disease of bone 2", "loss of heterozygosity, 18, chromosomal region 1"	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.633G>A	chr18.hg19:g.60028929G>A		175.0	0.0		160.0	75.0	NM_001270949	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Silent	SNP	ENST00000586569.1	hg19	CCDS11980.1																																																																																			.	.		0.408	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2			A	60028929	G	A	60028929	2	1	227	1	0	0	0	0	0	0	0	1	16299	1310	46	3		3	TNFRSF11A	18	60028929	Silent	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	9297330	60028929	18048319	63	32086										
PTBP1	5725	hgsc.bcm.edu	37	chr19	804891	804891	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	accaagaacaaccagttccaGgccctgctgcagtatgcgga	10	13	0	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr19:804891G>A	ENST00000349038.4	+	7	742	c.669G>A	c.(667-669)caG>caA	p.Q223Q	MIR4745_ENST00000577608.1_RNA|PTBP1_ENST00000394601.4_Silent_p.Q223Q|PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000356948.6_Silent_p.Q223Q	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	223	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCAGTTCCAGGCCCTGCTGC	0.657																																					p.Q223Q		Atlas-SNP	.											.	PTBP1	43	.	0			c.G669A						.						96	88	91					19																	804891		2203	4300	6503	SO:0001819	synonymous_variant	5725	exon7			GTTCCAGGCCCTG	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"RNA binding motif (RRM) containing"	9583	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein I"	600693	"polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.669G>A	chr19.hg19:g.804891G>A		103.0	0.0		69.0	34.0	NM_031990	Q9BUQ0	Silent	SNP	ENST00000349038.4	hg19	CCDS32859.1																																																																																			.	.		0.657	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1			A	804891	G	A	804891	2	1	227	1	0	0	0	0	0	0	0	1	12737	991	35	3		3	PTBP1	19	804891	Silent	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10		804891	58324092	64	32087										
EMR1	2015	hgsc.bcm.edu	37	chr19	6896547	6896547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	caaggatccaggagtgcgatGcaaaggtgagttcatgtccc	13	9	1	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr19:6896547G>A	ENST00000312053.4	+	3	270	c.233G>A	c.(232-234)tGc>tAc	p.C78Y	EMR1_ENST00000381407.5_Missense_Mutation_p.C78Y|EMR1_ENST00000450315.3_Missense_Mutation_p.C78Y|EMR1_ENST00000601198.1_3'UTR|EMR1_ENST00000250572.8_Missense_Mutation_p.C78Y|EMR1_ENST00000381404.4_Missense_Mutation_p.C78Y|AC020895.1_ENST00000580648.1_RNA	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	78	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					GGAGTGCGATGCAAAGGTGAG	0.498																																					p.C78Y		Atlas-SNP	.											.	EMR1	153	.	0			c.G233A						.						116	84	95					19																	6896547		2203	4300	6503	SO:0001583	missense	2015	exon3			TGCGATGCAAAGG	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.233G>A	chr19.hg19:g.6896547G>A	ENSP00000311545:p.Cys78Tyr	104.0	0.0		104.0	49.0	NM_001256252	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	hg19	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210817	0.39102	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	D;D;D;D;D	0.92965	-1.71;-2.46;-1.71;-3.14;-1.71	3.91	3.91	0.45181	Epidermal growth factor-like (1);	.	.	.	.	D	0.96399	0.8825	M	0.89715	3.055	0.09310	N	0.999996	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.991;0.999	D;D;D;P;D	0.91635	0.998;0.999;0.999;0.872;0.983	D	0.89870	0.4022	9	0.87932	D	0	.	11.748	0.51832	0.0:0.0:1.0:0.0	.	78;78;78;78;78	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	Y	78	ENSP00000311545:C78Y;ENSP00000370811:C78Y;ENSP00000250572:C78Y;ENSP00000370814:C78Y;ENSP00000405974:C78Y	ENSP00000250572:C78Y	C	+	2	0	EMR1	6847547	0.794000	0.28838	0.013000	0.15412	0.033000	0.12548	2.674000	0.46867	1.877000	0.54381	0.543000	0.68304	TGC	.	.		0.498	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			A	6896547	G	A	6896547	3	1	227	1	0	0	0	0	1	0	0	0	5106	1319	46	3	243	3	EMR1	19	6896547	Missense_Mutation	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	6091656	6896547	52232436	65	32088										
PCP2	126006	hgsc.bcm.edu	37	chr19	7697616	7697616	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gctcacggctcttggtggtcTggcccggcccggcttgcagt	15	14	3	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr19:7697616T>A	ENST00000311069.5	-	2	442	c.152A>T	c.(151-153)cAg>cTg	p.Q51L	CTD-3214H19.4_ENST00000595866.1_Intron|CTD-3214H19.6_ENST00000601797.1_RNA|PCP2_ENST00000598935.1_Missense_Mutation_p.Q35L	NM_174895.1	NP_777555.1	Q8IVA1	PCP2_HUMAN	Purkinje cell protein 2	51					rhodopsin mediated signaling pathway (GO:0016056)	neuronal cell body (GO:0043025)	GTPase regulator activity (GO:0030695)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|urinary_tract(1)	2						CTTGGTGGTCTGGCCCGGCCC	0.682																																					p.Q51L		Atlas-SNP	.											.	PCP2	6	.	0			c.A152T						.						31	28	29					19																	7697616		2191	4292	6483	SO:0001583	missense	126006	exon2			GTGGTCTGGCCCG	BC025387	CCDS32893.1, CCDS62521.1	19p13.3	2008-02-05				ENSG00000174788			30209	protein-coding gene	gene with protein product						12477932	Standard	NM_174895		Approved	MGC41903, GPSM4	uc031rjd.1	Q8IVA1		ENST00000311069.5:c.152A>T	chr19.hg19:g.7697616T>A	ENSP00000310585:p.Gln51Leu	43.0	0.0		32.0	16.0	NM_174895	M0R2R7|Q3KRG7	Missense_Mutation	SNP	ENST00000311069.5	hg19	CCDS32893.1	.	.	.	.	.	.	.	.	.	.	T	12.53	1.966344	0.34659	.	.	ENSG00000174788	ENST00000311069	.	.	.	4.52	-2.23	0.06930	.	0.776961	0.10520	N	0.665045	T	0.25975	0.0633	N	0.19112	0.55	0.09310	N	1	B	0.23650	0.089	B	0.16289	0.015	T	0.16158	-1.0412	9	0.25751	T	0.34	-0.0355	14.0196	0.64545	0.0:0.0:0.1789:0.8211	.	51	Q8IVA1	PCP2_HUMAN	L	51	.	ENSP00000310585:Q51L	Q	-	2	0	PCP2	7603616	0.038000	0.19896	0.000000	0.03702	0.473000	0.32948	0.082000	0.14847	-0.223000	0.09943	0.459000	0.35465	CAG	.	.		0.682	PCP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461026.2	XM_058956		A	7697616	T	A	7697616	3	1	227	1	0	0	0	0	1	0	0	0	11606	1580	55	4	270	4	PCP2	19	7697616	Missense_Mutation	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10	801069	7697616	51431367	66	32089										
OLFM2	93145	hgsc.bcm.edu	37	chr19	9968430	9968430	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	agggacccatcagctgcccgGagccgcgcatccaggctccg	13	17	1	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr19:9968430G>A	ENST00000264833.4	-	3	506	c.321C>T	c.(319-321)ctC>ctT	p.L107L	OLFM2_ENST00000590841.1_Silent_p.L29L	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	107					protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						CAGCTGCCCGGAGCCGCGCAT	0.592																																					p.L107L		Atlas-SNP	.											.	OLFM2	42	.	0			c.C321T						.						43	47	45					19																	9968430		2203	4300	6503	SO:0001819	synonymous_variant	93145	exon3			TGCCCGGAGCCGC	AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"noelin 2"						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.321C>T	chr19.hg19:g.9968430G>A		103.0	0.0		119.0	60.0	NM_058164	Q6IMJ3|Q96FC2	Silent	SNP	ENST00000264833.4	hg19	CCDS12221.1																																																																																			.	.		0.592	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1			A	9968430	G	A	9968430	2	1	227	1	0	0	0	0	0	0	0	1	10862	1161	41	3		3	OLFM2	19	9968430	Silent	SNP	G	TCGA-DD-AAVU-01A-11D-A40R-10	2270814	9968430	49160553	67	32090										
ZNF793	390927	hgsc.bcm.edu	37	chr19	38024289	38024289	+	Frame_Shift_Del	DEL	G	G	-													0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	attggtgaggcagcatgcccGggctgccactgttggggtaa					rs370904763		TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr19:38024289delG	ENST00000587143.1	+	5	457	c.222delG	c.(220-222)ccgfs	p.P74fs	ZNF793_ENST00000542455.1_Frame_Shift_Del_p.P74fs|ZNF793_ENST00000587986.1_Frame_Shift_Del_p.P74fs|ZNF793_ENST00000588578.1_Frame_Shift_Del_p.P74fs|ZNF793_ENST00000589319.1_Frame_Shift_Del_p.P74fs|ZNF793_ENST00000445217.1_Frame_Shift_Del_p.P74fs			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	74	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAGCATGCCCGGGCTGCCACT	0.498																																					p.P74fs	Melanoma(44;400 1431 1499 19093)	Atlas-INDEL	.											.	ZNF793	50	.	0			c.221delC						.						71	74	73					19																	38024289		1936	4128	6064	SO:0001589	frameshift_variant	390927	exon7			.	AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.222delG	chr19.hg19:g.38024289delG	ENSP00000468605:p.Pro74fs	136.0	0.0		131.0	58.0	NM_001013659	E9PGN4|Q7Z3Q9	Frame_Shift_Del	DEL	ENST00000587143.1	hg19	CCDS46062.1																																																																																			.	.		0.498	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		-	38024289	G	-	38024289	7	5	227	1	0	1	0	1	0	0	0	0	18180	1103	39	0	232	0	ZNF793	19	38024289	Frame_Shift_Del	DEL	G	TCGA-DD-AAVU-01A-11D-A40R-10	28055859	38024289	21104694	68	32091										
ZNF765	91661	hgsc.bcm.edu	37	chr19	53911921	53911921	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	agtcggaagtcacattttacAtgccatcatagagttcatac	7	9	3	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr19:53911921A>G	ENST00000396408.3	+	4	1230	c.1113A>G	c.(1111-1113)acA>acG	p.T371T	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	371					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		CACATTTTACATGCCATCATA	0.413																																					p.T371T		Atlas-SNP	.											.	ZNF765	61	.	0			c.A1113G						.						116	118	117					19																	53911921		2203	4300	6503	SO:0001819	synonymous_variant	91661	exon4			TTTTACATGCCAT	BC017357	CCDS46171.1	19q13.41	2013-01-08				ENSG00000196417		"Zinc fingers, C2H2-type", "-"	25092	protein-coding gene	gene with protein product						12477932	Standard	XR_430215		Approved		uc002qbm.3	Q7L2R6		ENST00000396408.3:c.1113A>G	chr19.hg19:g.53911921A>G		118.0	0.0		125.0	46.0	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Silent	SNP	ENST00000396408.3	hg19	CCDS46171.1																																																																																			.	.		0.413	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372		G	53911921	A	G	53911921	2	3	227	1	0	0	0	0	0	0	0	1	18154	204	8	2		2	ZNF765	19	53911921	Silent	SNP	A	TCGA-DD-AAVU-01A-11D-A40R-10	15887632	53911921	5217062	69	32092										
DEFB123	245936	hgsc.bcm.edu	37	chr20	30037860	30037860	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	caaagatgctggaatctttaTggcaaatgccgttacagatg	10	7	1	2	rs377702716		TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr20:30037860T>C	ENST00000376309.3	+	2	267	c.87T>C	c.(85-87)taT>taC	p.Y29Y		NM_153324.2	NP_697019.1	Q8N688	DB123_HUMAN	defensin, beta 123	29					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.Y29*(1)|p.Y29Y(1)		kidney(1)|lung(2)	3	Lung NSC(7;0.000139)|all_lung(7;0.000197)|all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			GGAATCTTTATGGCAAATGCC	0.428																																					p.Y29Y		Atlas-SNP	.											DEFB123,NS,carcinoma,0,2	DEFB123	7	.	2	Substitution - Nonsense(1)|Substitution - coding silent(1)	lung(1)|kidney(1)	c.T87C						.	T		1,4405	2.1+/-5.4	0,1,2202	152	150	151		87	-2	0.6	20		151	0,8600		0,0,4300	no	coding-synonymous	DEFB123	NM_153324.2		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		29/68	30037860	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	245936	exon2			TCTTTATGGCAAA	AA933749	CCDS13180.1	20q11.1	2008-07-17			ENSG00000180424	ENSG00000180424		"Defensins, beta"	18103	protein-coding gene	gene with protein product	"beta defensin 23"					11854508	Standard	NM_153324		Approved	DEFB-23	uc002wvy.3	Q8N688	OTTHUMG00000032170	ENST00000376309.3:c.87T>C	chr20.hg19:g.30037860T>C		85.0	0.0		99.0	40.0	NM_153324		Silent	SNP	ENST00000376309.3	hg19	CCDS13180.1																																																																																			.	.		0.428	DEFB123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078510.2	NM_153324		C	30037860	T	C	30037860	2	2	227	1	0	0	0	0	0	0	0	1	4411	1471	51	2		2	DEFB123	20	30037860	Silent	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10		30037860	32987660	70	32093										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46888354	46888354	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	gttccacatccggccagccaCagagggcccaggggtgctgt	14	14	0	1			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr21:46888354C>T	ENST00000359759.4	+	2	1571	c.1550C>T	c.(1549-1551)aCa>aTa	p.T517I	COL18A1_ENST00000400337.2_Missense_Mutation_p.T102I|COL18A1_ENST00000355480.5_Missense_Mutation_p.T282I			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	517	Laminin G-like.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CGGCCAGCCACAGAGGGCCCA	0.637																																					p.T282I		Atlas-SNP	.											.	COL18A1	129	.	0			c.C845T						.						70	83	79					21																	46888354		2112	4231	6343	SO:0001583	missense	80781	exon2			CAGCCACAGAGGG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.1550C>T	chr21.hg19:g.46888354C>T	ENSP00000352798:p.Thr517Ile	88.0	0.0		71.0	23.0	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	hg19		.	.	.	.	.	.	.	.	.	.	C	11.55	1.672545	0.29693	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	T;T;T	0.47528	0.84;0.84;0.84	4.65	3.71	0.42584	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.261461	0.37437	N	0.002093	T	0.61825	0.2378	L	0.59436	1.845	0.41290	D	0.986975	D;D;D	0.62365	0.991;0.989;0.98	D;P;P	0.64877	0.93;0.885;0.731	T	0.67260	-0.5715	10	0.87932	D	0	.	14.168	0.65490	0.0:0.8495:0.1505:0.0	.	517;282;102	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	I	102;102;282;517;517	ENSP00000383191:T102I;ENSP00000347665:T282I;ENSP00000352798:T517I	ENSP00000347665:T282I	T	+	2	0	COL18A1	45712782	0.989000	0.36119	0.052000	0.19188	0.011000	0.07611	5.527000	0.67123	2.289000	0.77006	0.655000	0.94253	ACA	.	.		0.637	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			T	46888354	C	T	46888354	3	4	227	1	0	0	0	0	1	0	0	0	3677	478	17	3	1670	3	COL18A1	21	46888354	Missense_Mutation	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10		46888354	1241541	71	32094										
NCF4	4689	hgsc.bcm.edu	37	chr22	37272068	37272068	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	actccagcctgtcaccccctTagggacatcgcggtggagga	12	14	1	0			TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chr22:37272068T>A	ENST00000248899.6	+	9	942				NCF4_ENST00000397147.4_Nonsense_Mutation_p.L334*	NM_000631.4	NP_000622.2	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4, 40kDa						antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of catalytic activity (GO:0043085)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|membrane (GO:0016020)|NADPH oxidase complex (GO:0043020)|phagolysosome (GO:0032010)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein dimerization activity (GO:0046983)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16					Dextromethorphan(DB00514)	GTCACCCCCTTAGGGACATCG	0.612																																					p.L334X		Atlas-SNP	.											.	NCF4	66	.	0			c.T1001A						.						31	30	31					22																	37272068		2203	4300	6503	SO:0001627	intron_variant	4689	exon8			CCCCCTTAGGGAC	X77094	CCDS13934.1, CCDS13935.1	22q13.1	2014-09-17	2002-08-29		ENSG00000100365	ENSG00000100365			7662	protein-coding gene	gene with protein product	"neutrophil NADPH oxidase factor 4"	601488	"neutrophil cytosolic factor 4 (40kD)"			8839867	Standard	NM_013416		Approved	p40phox, SH3PXD4	uc003apy.4	Q15080	OTTHUMG00000150548	ENST00000248899.6:c.759-3T>A	chr22.hg19:g.37272068T>A		154.0	0.0		140.0	51.0	NM_013416	A8K4F9|O60808|Q86U56|Q9BU98|Q9NP45	Nonsense_Mutation	SNP	ENST00000248899.6	hg19	CCDS13934.1	.	.	.	.	.	.	.	.	.	.	T	14.40	2.524790	0.44969	.	.	ENSG00000100365	ENST00000397147	.	.	.	5.05	-1.04	0.10068	.	3.473280	0.01360	N	0.012219	.	.	.	.	.	.	0.48236	A	0.99961	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.3677	9.407	0.38469	0.0:0.4026:0.0:0.5974	.	.	.	.	X	334	.	.	L	+	2	0	NCF4	35602014	0.484000	0.25964	0.010000	0.14722	0.001000	0.01503	0.592000	0.23984	-0.627000	0.05589	-0.973000	0.02599	TTA	.	.		0.612	NCF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318863.1	NM_000631		A	37272068	T	A	37272068	1	1	227	0	1	0	0	0	0	0	0	0	10227	1764	61	4		4	NCF4	22	37272068	Intron	SNP	T	TCGA-DD-AAVU-01A-11D-A40R-10		37272068	14032498	72	32095										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24381762	24381762	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.4496812825961	2.24700598802395	1.17235095027337	1	1	0	tgtgtagacacgtggaaaggCagaccctgtgatttggccgt	14	8	0	3	rs368897164		TCGA-DD-AAVU-01A-11D-A40R-10	TCGA-DD-AAVU-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c522957e-6571-4b4e-9ab2-8726a74d13e6	ae0c3d36-3ce4-478c-9a80-7446e1da38b1	g.chrX:24381762C>T								AC004552.1 (14739 upstream) : PDK3 (101575 downstream)																							CGTGGAAAGGCAGACCCTGTG	0.502																																					p.G295G		Atlas-SNP	.											.	.	.	.	0			c.C885T						.	C		0,2627		0,0,0,1059,509	154	126	135		885	-1.4	0	X		135	1,5497		0,0,1,1916,1665	no	coding-synonymous	FAM48B1	NM_001136234.1		0,0,1,2975,2174	TT,TC,T,CC,C		0.0182,0.0,0.0123		295/888	24381762	1,8124	1568	3582	5150	SO:0001628	intergenic_variant	100130302	exon1			GAAAGGCAGACCC																													chrX.hg19:g.24381762C>T		292.0	0.0		269.0	229.0	NM_001136234		Silent	SNP		hg19																																																																																				.	.	0	0.502									T	24381762	C	T	24381762	1	4	227	0	1	0	0	0	0	0	0	0	5581	697	25	3		3	FAM48B1	23	24381762	IGR	SNP	C	TCGA-DD-AAVU-01A-11D-A40R-10		24381762	130888798	73	32096										
INPP5B	3633	hgsc.bcm.edu	37	chr1	38357094	38357094	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gtccataggcactcccttccCatttggtctcaaaccatcaa	5	15	2	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:38357094C>T	ENST00000373026.1	-	7	805	c.805G>A	c.(805-807)Ggg>Agg	p.G269R	INPP5B_ENST00000373027.1_Missense_Mutation_p.G25R|INPP5B_ENST00000373024.3_Missense_Mutation_p.G189R|INPP5B_ENST00000373023.2_Missense_Mutation_p.G269R|INPP5B_ENST00000458109.2_5'Flank			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	269					in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				ACTCCCTTCCCATTTGGTCTC	0.448																																					p.G189R		Atlas-SNP	.											.	INPP5B	76	.	0			c.G565A						.						171	173	172					1																	38357094		1893	4106	5999	SO:0001583	missense	3633	exon8			CCTTCCCATTTGG	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"inositol polyphosphate-5-phosphatase, 75kD"			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.805G>A	chr1.hg19:g.38357094C>T	ENSP00000362117:p.Gly269Arg	106.0	0.0		91.0	9.0	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.412	1.080806	0.20309	.	.	ENSG00000204084	ENST00000373027;ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024	D;D;D;D	0.93189	-3.18;-3.05;-3.05;-3.06	5.38	4.47	0.54385	.	903.776000	0.00166	N	0.000000	D	0.93374	0.7887	M	0.65498	2.005	0.80722	D	1	B;P	0.41929	0.045;0.765	B;B	0.42593	0.014;0.392	T	0.81040	-0.1113	10	0.21014	T	0.42	.	10.3144	0.43727	0.0:0.9087:0.0:0.0913	.	269;189	P32019;P32019-2	I5P2_HUMAN;.	R	25;269;269;269;189	ENSP00000362118:G25R;ENSP00000362114:G269R;ENSP00000362117:G269R;ENSP00000362115:G189R	ENSP00000362114:G269R	G	-	1	0	INPP5B	38129681	1.000000	0.71417	0.746000	0.31095	0.118000	0.20060	1.497000	0.35649	1.404000	0.46819	0.650000	0.86243	GGG	.	.		0.448	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		T	38357094	C	T	38357094	3	4	228	1	0	0	0	0	1	0	0	0	7764	594	21	3	2244	3	INPP5B	1	38357094	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10		38357094	210893527	1	32097										
NRD1	4898	hgsc.bcm.edu	37	chr1	52306125	52306125	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tgttgtatttcctgttttacCttccatattacttaggtctg	6	8	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:52306125C>G	ENST00000354831.7	-	2	592	c.403G>C	c.(403-405)Ggt>Cgt	p.G135R	NRD1_ENST00000544028.1_Missense_Mutation_p.G3R|NRD1_ENST00000539524.1_Missense_Mutation_p.G3R|NRD1_ENST00000352171.7_Missense_Mutation_p.G135R|NRD1_ENST00000485608.1_5'UTR	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	135					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						CCTGTTTTACCTTCCATATTA	0.383																																					p.G135R		Atlas-SNP	.											.	NRD1	89	.	0			c.G403C						.						99	94	96					1																	52306125		2203	4300	6503	SO:0001583	missense	4898	exon2			TTTTACCTTCCAT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.403G>C	chr1.hg19:g.52306125C>G	ENSP00000346890:p.Gly135Arg	100.0	0.0		95.0	15.0	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.285951	0.40394	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.39787	1.52;3.76;1.06;1.39	5.57	4.46	0.54185	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.647627	0.16001	N	0.234318	T	0.35335	0.0928	N	0.24115	0.695	0.38173	D	0.939382	P;P;P	0.50272	0.933;0.89;0.89	P;B;P	0.47470	0.548;0.42;0.544	T	0.08764	-1.0706	10	0.26408	T	0.33	-4.142	13.2931	0.60282	0.0:0.9117:0.0:0.0883	.	135;135;135	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	R	135;135;3;135;3	ENSP00000262679:G135R;ENSP00000346890:G135R;ENSP00000444416:G3R;ENSP00000442262:G3R	ENSP00000262679:G135R	G	-	1	0	NRD1	52078713	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	3.237000	0.51344	2.608000	0.88229	0.555000	0.69702	GGT	.	.		0.383	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		G	52306125	C	G	52306125	3	3	228	1	0	0	0	0	1	0	0	0	10654	681	24	4	3384	4	NRD1	1	52306125	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	13949031	52306125	196944496	2	32098										
WDR63	126820	hgsc.bcm.edu	37	chr1	85589863	85589863	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ctgtccacactattcagagaTcacctttctacaacgacatt	4	13	3	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:85589863T>C	ENST00000294664.6	+	19	2221	c.2041T>C	c.(2041-2043)Tca>Cca	p.S681P	WDR63_ENST00000326813.8_Missense_Mutation_p.S642P|WDR63_ENST00000370596.1_Missense_Mutation_p.S642P	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	681										NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		TATTCAGAGATCACCTTTCTA	0.443																																					p.S681P		Atlas-SNP	.											.	WDR63	91	.	0			c.T2041C						.						371	293	320					1																	85589863		2203	4300	6503	SO:0001583	missense	126820	exon19			CAGAGATCACCTT		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"WD repeat domain containing"	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.2041T>C	chr1.hg19:g.85589863T>C	ENSP00000294664:p.Ser681Pro	112.0	0.0		108.0	41.0	NM_145172	A8K988|Q96L72|Q96NU4	Missense_Mutation	SNP	ENST00000294664.6	hg19	CCDS702.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.281164	0.80692	.	.	ENSG00000162643	ENST00000370596;ENST00000326813;ENST00000294664	T;T;T	0.71817	-0.6;-0.6;-0.6	5.44	5.44	0.79542	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.059390	0.64402	N	0.000001	D	0.82935	0.5145	M	0.84683	2.71	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	D	0.86103	0.1557	10	0.72032	D	0.01	-16.4183	15.4425	0.75195	0.0:0.0:0.0:1.0	.	642;681	Q8IWG1-2;Q8IWG1	.;WDR63_HUMAN	P	642;642;681	ENSP00000359628:S642P;ENSP00000317463:S642P;ENSP00000294664:S681P	ENSP00000294664:S681P	S	+	1	0	WDR63	85362451	1.000000	0.71417	0.990000	0.47175	0.837000	0.47467	6.815000	0.75242	2.188000	0.69820	0.482000	0.46254	TCA	.	.		0.443	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172		C	85589863	T	C	85589863	3	2	228	1	0	0	0	0	1	0	0	0	17329	1435	50	2	2111	2	WDR63	1	85589863	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	33283738	85589863	163660758	3	32099										
GFI1	2672	hgsc.bcm.edu	37	chr1	92944171	92944171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ggatgaaagtgtgtttcttcAtgtctgacttctggtggaac	12	6	4	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:92944171A>G	ENST00000370332.1	-	6	1382	c.1064T>C	c.(1063-1065)aTg>aCg	p.M355T	GFI1_ENST00000294702.5_Missense_Mutation_p.M355T|GFI1_ENST00000427103.1_Missense_Mutation_p.M355T	NM_001127215.1	NP_001120687.1	Q99684	GFI1_HUMAN	growth factor independent 1 transcription repressor	355					auditory receptor cell differentiation (GO:0042491)|cell fate commitment (GO:0045165)|cellular response to lipopolysaccharide (GO:0071222)|inner ear morphogenesis (GO:0042472)|mechanosensory behavior (GO:0007638)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell fate specification (GO:0009996)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vitamin D biosynthetic process (GO:0010957)|positive regulation of cell fate specification (GO:0042660)|positive regulation of interleukin-6-mediated signaling pathway (GO:0070105)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|viral process (GO:0016032)	nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)		GTGTTTCTTCATGTCTGACTT	0.502																																					p.M355T		Atlas-SNP	.											.	GFI1	41	.	0			c.T1064C						.						222	191	201					1																	92944171		2203	4300	6503	SO:0001583	missense	2672	exon6			TTCTTCATGTCTG	U67369	CCDS30773.1	1p22	2014-09-17	2007-10-04		ENSG00000162676	ENSG00000162676		"Zinc fingers, C2H2-type"	4237	protein-coding gene	gene with protein product		600871	"growth factor independent 1"	ZNF163		7789186	Standard	NM_005263		Approved	GFI1A, GFI-1	uc001dov.4	Q99684	OTTHUMG00000010897	ENST00000370332.1:c.1064T>C	chr1.hg19:g.92944171A>G	ENSP00000359357:p.Met355Thr	162.0	0.0		182.0	9.0	NM_005263	Q8N564	Missense_Mutation	SNP	ENST00000370332.1	hg19	CCDS30773.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990322	0.74589	.	.	ENSG00000162676	ENST00000370332;ENST00000427103;ENST00000294702	T;T;T	0.18174	2.23;2.23;2.23	5.39	5.39	0.77823	Zinc finger, C2H2-like (1);Zinc finger, CCHC-type (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.30541	0.0768	M	0.64997	1.995	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.06698	-1.0812	10	0.87932	D	0	-32.7457	15.4083	0.74897	1.0:0.0:0.0:0.0	.	355	Q99684	GFI1_HUMAN	T	355	ENSP00000359357:M355T;ENSP00000399719:M355T;ENSP00000294702:M355T	ENSP00000294702:M355T	M	-	2	0	GFI1	92716759	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.339000	0.96797	2.046000	0.60703	0.254000	0.18369	ATG	.	.		0.502	GFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030054.1	NM_005263		G	92944171	A	G	92944171	3	3	228	1	0	0	0	0	1	0	0	0	6347	217	8	2	212	2	GFI1	1	92944171	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	7354308	92944171	156306450	4	32100										
CCDC18	343099	hgsc.bcm.edu	37	chr1	93704961	93704961	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gagatggagaaaataaagcaAtgcacctctctcaattagat	8	7	2	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:93704961A>G	ENST00000343253.7	+	20	3197	c.2695A>G	c.(2695-2697)Atg>Gtg	p.M899V	CCDC18_ENST00000401026.3_Missense_Mutation_p.M900V|CCDC18_ENST00000557479.1_Missense_Mutation_p.M1018V|CCDC18_ENST00000334652.5_Missense_Mutation_p.M195V|CCDC18_ENST00000421014.2_3'UTR|CCDC18_ENST00000338949.4_Missense_Mutation_p.M655V			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	899										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		AAATAAAGCAATGCACCTCTC	0.363																																					p.M900V		Atlas-SNP	.											.	CCDC18	93	.	0			c.A2698G						.						112	103	105					1																	93704961		1854	4090	5944	SO:0001583	missense	343099	exon20			AAAGCAATGCACC			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.2695A>G	chr1.hg19:g.93704961A>G	ENSP00000343377:p.Met899Val	401.0	0.0		421.0	17.0	NM_206886	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	hg19		.	.	.	.	.	.	.	.	.	.	A	0.017	-1.502820	0.00992	.	.	ENSG00000122483	ENST00000343253;ENST00000401026;ENST00000557479;ENST00000338949;ENST00000334652;ENST00000455267	T;T;T	0.77750	-1.12;-1.12;1.06	5.26	1.49	0.22878	.	0.793259	0.12376	N	0.474351	T	0.29850	0.0746	N	0.08118	0	0.09310	N	1	B;B	0.11235	0.0;0.004	B;B	0.10450	0.0;0.005	T	0.19614	-1.0300	10	0.24483	T	0.36	.	3.1048	0.06337	0.5697:0.1179:0.0673:0.2451	.	899;1018	Q5T9S5;G3V388	CCD18_HUMAN;.	V	899;900;1018;655;195;575	ENSP00000383808:M900V;ENSP00000451099:M1018V;ENSP00000334084:M195V	ENSP00000334084:M195V	M	+	1	0	CCDC18	93477549	0.278000	0.24230	0.331000	0.25455	0.666000	0.39218	0.950000	0.29122	0.285000	0.22329	-0.490000	0.04691	ATG	.	.		0.363	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		G	93704961	A	G	93704961	3	3	228	1	0	0	0	0	1	0	0	0	2796	101	4	2	3130	2	CCDC18	1	93704961	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	760790	93704961	155545660	5	32101										
CNN3	1266	hgsc.bcm.edu	37	chr1	95363516	95363516	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cccaagcccatacacactcaTtcctttctgggaagcaactt	5	15	2	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:95363516T>C	ENST00000370206.4	-	7	1155	c.772A>G	c.(772-774)Atg>Gtg	p.M258V	CNN3_ENST00000538964.1_Missense_Mutation_p.M258V|CNN3_ENST00000487539.1_5'UTR|CNN3_ENST00000545882.1_Missense_Mutation_p.M217V|CNN3_ENST00000394202.4_Missense_Mutation_p.M212V	NM_001839.3	NP_001830.1	Q15417	CNN3_HUMAN	calponin 3, acidic	258					actomyosin structure organization (GO:0031032)|epithelial cell differentiation (GO:0030855)	focal adhesion (GO:0005925)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|stomach(1)|urinary_tract(2)	18		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)		TACACACTCATTCCTTTCTGG	0.463																																					p.M258V		Atlas-SNP	.											.	CNN3	23	.	0			c.A772G						.						202	193	196					1																	95363516		2203	4300	6503	SO:0001583	missense	1266	exon7			CACTCATTCCTTT	BC025372	CCDS30775.1, CCDS65592.1, CCDS65593.1	1p22-p21	2010-07-08			ENSG00000117519	ENSG00000117519			2157	protein-coding gene	gene with protein product		602374				8526917	Standard	NM_001839		Approved		uc001dqz.4	Q15417	OTTHUMG00000010783	ENST00000370206.4:c.772A>G	chr1.hg19:g.95363516T>C	ENSP00000359225:p.Met258Val	142.0	0.0		147.0	32.0	NM_001839	B4DFK6|B4DP09|F8WA86|Q6FHA7	Missense_Mutation	SNP	ENST00000370206.4	hg19	CCDS30775.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.380639	0.61845	.	.	ENSG00000117519	ENST00000370206;ENST00000538964;ENST00000394202;ENST00000545882	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.55593	0.1930	M	0.81341	2.54	0.46011	D	0.998819	P;B	0.40083	0.702;0.001	P;B	0.45449	0.481;0.003	T	0.61662	-0.7017	10	0.54805	T	0.06	-16.4132	16.8222	0.85835	0.0:0.0:0.0:1.0	.	212;258	F8WA86;Q15417	.;CNN3_HUMAN	V	258;258;212;217	ENSP00000359225:M258V;ENSP00000437665:M258V;ENSP00000377752:M212V;ENSP00000440081:M217V	ENSP00000359225:M258V	M	-	1	0	CNN3	95136104	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.675000	0.61619	2.371000	0.80710	0.533000	0.62120	ATG	.	.		0.463	CNN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029702.2	NM_001839		C	95363516	T	C	95363516	3	2	228	1	0	0	0	0	1	0	0	0	3613	1493	52	2	221	2	CNN3	1	95363516	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	1658555	95363516	153887105	6	32102										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103491357	103491357	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	attgctttttcttcgctaccTttacccctagtttggctttt	5	11	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:103491357T>A	ENST00000370096.3	-	7	1210				COL11A1_ENST00000512756.1_Intron|COL11A1_ENST00000353414.4_Intron|COL11A1_ENST00000358392.2_Splice_Site_p.K311M	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1						cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CTTCGCTACCTTTACCCCTAG	0.363																																					p.K311M		Atlas-SNP	.											.	COL11A1	972	.	0			c.A932T						.						159	152	154					1																	103491357		2203	4300	6503	SO:0001627	intron_variant	1301	exon6			GCTACCTTTACCC	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.898-188A>T	chr1.hg19:g.103491357T>A		61.0	0.0		63.0	18.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	11.30	1.598020	0.28445	.	.	ENSG00000060718	ENST00000358392;ENST00000427239	T;T	0.72942	-0.67;-0.7	5.5	4.31	0.51392	.	1.072480	0.07007	N	0.824529	T	0.36908	0.0984	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.10520	-1.0626	10	0.42905	T	0.14	.	10.6667	0.45734	0.2424:0.0:0.0:0.7576	.	311	P12107-2	.	M	311	ENSP00000351163:K311M;ENSP00000408640:K311M	ENSP00000351163:K311M	K	-	2	0	COL11A1	103263945	1.000000	0.71417	0.939000	0.37840	0.968000	0.65278	2.249000	0.43169	2.106000	0.64143	0.519000	0.50382	AAG	.	.		0.363	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103491357	T	A	103491357	1	1	228	0	1	0	0	0	0	0	0	0	3669	1623	56	4		4	COL11A1	1	103491357	Intron	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	8127841	103491357	145759264	7	32103										
HSD3B1	3283	hgsc.bcm.edu	37	chr1	120057095	120057095	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cctatcgaccgcccttcaacCgccacatagtcacattgtca	5	17	3	0	rs587764853		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:120057095C>T	ENST00000369413.3	+	4	1094	c.949C>T	c.(949-951)Cgc>Tgc	p.R317C	HSD3B1_ENST00000528909.1_Missense_Mutation_p.R317C|HSD3B1_ENST00000235547.6_Missense_Mutation_p.R319C			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	317					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	GCCCTTCAACCGCCACATAGT	0.473													C|||	1	0.000199681	8e-04	0	5008	,	,		21606	0		0	False		,,,				2504	0				p.R317C		Atlas-SNP	.											.	HSD3B1	53	.	0			c.C949T						.						120	117	118					1																	120057095		2203	4300	6503	SO:0001583	missense	3283	exon4			TTCAACCGCCACA	S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	5217	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 11E, member 1"	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.949C>T	chr1.hg19:g.120057095C>T	ENSP00000358421:p.Arg317Cys	129.0	0.0		162.0	39.0	NM_000862	A8K691|Q14545|Q8IV65	Missense_Mutation	SNP	ENST00000369413.3	hg19	CCDS903.1	.	.	.	.	.	.	.	.	.	.	C	6.817	0.519780	0.13005	.	.	ENSG00000203857	ENST00000369413;ENST00000235547;ENST00000528909	T;T;T	0.71579	-0.58;-0.58;-0.58	3.26	2.31	0.28768	.	0.052103	0.85682	N	0.000000	T	0.63988	0.2558	H	0.94306	3.52	0.80722	D	1	P;B	0.39665	0.682;0.12	B;B	0.34385	0.181;0.04	T	0.69569	-0.5110	10	0.66056	D	0.02	0.9198	8.7277	0.34480	0.0:0.8787:0.0:0.1213	.	319;317	Q5TDG2;P14060	.;3BHS1_HUMAN	C	317;319;317	ENSP00000358421:R317C;ENSP00000235547:R319C;ENSP00000432268:R317C	ENSP00000235547:R319C	R	+	1	0	HSD3B1	119858618	0.785000	0.28726	0.440000	0.26846	0.008000	0.06430	1.417000	0.34770	0.653000	0.30826	0.313000	0.20887	CGC	.	.		0.473	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862		T	120057095	C	T	120057095	3	4	228	1	0	0	0	0	1	0	0	0	7399	652	23	1	959	1	HSD3B1	1	120057095	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	16565738	120057095	129193526	8	32104										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179504037	179504037	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gagaagtaaaagaagaagaaGaacaacaagaagaagaagaa	11	2	0	9	rs200097954|rs368406759|rs6425573	byFrequency	TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:179504037G>C	ENST00000367618.3	+	25	3358	c.2971G>C	c.(2971-2973)Gaa>Caa	p.E991Q		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	991	Glu-rich.		E -> Q (in dbSNP:rs6425573).					p.E991_Q992delEQ(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agaagaagaagaacaacaaga	0.318													G|||	14	0.00279553	0	0.0058	5008	,	,		17137	0.002		0.004	False		,,,				2504	0.0041				p.E991Q		Atlas-SNP	.											.	AXDND1	142	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2971C						.						49	51	50					1																	179504037		2152	4286	6438	SO:0001583	missense	126859	exon25			GAAGAAGAACAAC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2971G>C	chr1.hg19:g.179504037G>C	ENSP00000356590:p.Glu991Gln	342.0	0.0		523.0	28.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	G	9.300	1.052898	0.19907	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.19105	2.17;2.17	4.89	-6.02	0.02192	.	0.508747	0.16499	N	0.211773	T	0.08980	0.0222	N	0.24115	0.695	0.09310	N	1	B;B	0.24186	0.099;0.099	B;B	0.10450	0.003;0.005	T	0.15838	-1.0423	10	0.28530	T	0.3	-2.8152	6.1976	0.20557	0.4456:0.3814:0.173:0.0	rs6425573	875;991	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	Q	991;875;851	ENSP00000356590:E991Q;ENSP00000391716:E851Q	ENSP00000353471:E875Q	E	+	1	0	AXDND1	177770660	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.365000	0.20348	-1.164000	0.02790	-1.047000	0.02352	GAA	.	G|1.000;|0.000		0.318	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179504037	G	C	179504037	3	2	228	1	0	0	0	0	1	0	0	0	1995	943	33	4	3065	4	C1orf125	1	179504037	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	59446942	179504037	69746584	9	32105										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179561766	179561766	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gcacaatgtctgaacaagagCgtatacaggaatgtctgcgg	12	8	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:179561766C>G	ENST00000367614.1	+	2	375	c.16C>G	c.(16-18)Cgt>Ggt	p.R6G	TDRD5_ENST00000444136.1_Missense_Mutation_p.R6G|RP11-545A16.4_ENST00000567150.1_RNA|TDRD5_ENST00000294848.8_Missense_Mutation_p.R6G	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	6					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						TGAACAAGAGCGTATACAGGA	0.438																																					p.R6G		Atlas-SNP	.											.	TDRD5	149	.	0			c.C16G						.						137	131	133					1																	179561766		2203	4300	6503	SO:0001583	missense	163589	exon2			CAAGAGCGTATAC	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.16C>G	chr1.hg19:g.179561766C>G	ENSP00000356586:p.Arg6Gly	71.0	0.0		91.0	5.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	C	17.14	3.313125	0.60414	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.12672	2.66;2.66;2.84	5.91	3.79	0.43588	.	0.294107	0.32328	N	0.006241	T	0.31482	0.0798	L	0.51422	1.61	0.34761	D	0.732786	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.988	T	0.47849	-0.9085	10	0.62326	D	0.03	1.786	15.7448	0.77929	0.2675:0.7325:0.0:0.0	.	6;6	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	G	6	ENSP00000356586:R6G;ENSP00000294848:R6G;ENSP00000406052:R6G	ENSP00000294848:R6G	R	+	1	0	TDRD5	177828389	0.109000	0.22037	0.846000	0.33378	0.857000	0.48899	0.475000	0.22164	1.418000	0.47098	0.655000	0.94253	CGT	.	.		0.438	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		G	179561766	C	G	179561766	3	3	228	1	0	0	0	0	1	0	0	0	15748	768	27	4	18	4	TDRD5	1	179561766	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	57729	179561766	69688855	10	32106										
RGS18	64407	hgsc.bcm.edu	37	chr1	192153515	192153515	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tgatgctgcacaaagcagagTgtatcagctcatggaacaag	11	8	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:192153515T>A	ENST00000367460.3	+	5	720	c.539T>A	c.(538-540)gTg>gAg	p.V180E		NM_130782.2	NP_570138.1	Q9NS28	RGS18_HUMAN	regulator of G-protein signaling 18	180	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			kidney(1)|large_intestine(2)|lung(15)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CAAAGCAGAGTGTATCAGCTC	0.398																																					p.V180E		Atlas-SNP	.											.	RGS18	54	.	0			c.T539A						.						144	135	138					1																	192153515		2203	4300	6503	SO:0001583	missense	64407	exon5			GCAGAGTGTATCA	AF268036	CCDS1374.1	1q31.2	2008-02-05	2007-08-14		ENSG00000150681	ENSG00000150681		"Regulators of G-protein signaling"	14261	protein-coding gene	gene with protein product		607192	"regulator of G-protein signalling 18"			11042171	Standard	NM_130782		Approved	RGS13	uc001gsg.3	Q9NS28	OTTHUMG00000035592	ENST00000367460.3:c.539T>A	chr1.hg19:g.192153515T>A	ENSP00000356430:p.Val180Glu	191.0	0.0		266.0	38.0	NM_130782	B2RD23	Missense_Mutation	SNP	ENST00000367460.3	hg19	CCDS1374.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.611330	0.87258	.	.	ENSG00000150681	ENST00000367460	T	0.72725	-0.68	5.62	5.62	0.85841	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.106857	0.64402	D	0.000004	D	0.87775	0.6262	M	0.93420	3.415	0.58432	D	0.999999	D	0.76494	0.999	D	0.78314	0.991	D	0.90862	0.4739	10	0.87932	D	0	.	14.661	0.68870	0.0:0.0:0.0:1.0	.	180	Q9NS28	RGS18_HUMAN	E	180	ENSP00000356430:V180E	ENSP00000356430:V180E	V	+	2	0	RGS18	190420138	1.000000	0.71417	0.955000	0.39395	0.968000	0.65278	7.534000	0.82004	2.140000	0.66376	0.460000	0.39030	GTG	.	.		0.398	RGS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086382.1	NM_130782		A	192153515	T	A	192153515	3	1	228	1	0	0	0	0	1	0	0	0	13315	1696	59	4	557	4	RGS18	1	192153515	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	12591749	192153515	57097106	11	32107										
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200827018	200827018	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gataggccctaaatctatcaCtaaaaaaatgattgaaggac	7	7	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:200827018C>T	ENST00000236925.4	+	18	4350	c.4301C>T	c.(4300-4302)aCt>aTt	p.T1434I	CAMSAP2_ENST00000413307.2_Missense_Mutation_p.T1407I|CAMSAP2_ENST00000358823.2_Missense_Mutation_p.T1423I			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	1434	CKK. {ECO:0000255|PROSITE- ProRule:PRU00841}.				microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										AAATCTATCACTAAAAAAATG	0.373																																					p.T1423I		Atlas-SNP	.											.	.	.	.	0			c.C4268T						.						68	72	71					1																	200827018		2203	4300	6503	SO:0001583	missense	23271	exon17			CTATCACTAAAAA	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.4301C>T	chr1.hg19:g.200827018C>T	ENSP00000236925:p.Thr1434Ile	271.0	0.0		436.0	71.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Missense_Mutation	SNP	ENST00000236925.4	hg19		.	.	.	.	.	.	.	.	.	.	C	13.21	2.169395	0.38315	.	.	ENSG00000118200	ENST00000358823;ENST00000413307;ENST00000236925	T;T;T	0.17528	2.28;2.27;2.28	5.34	4.42	0.53409	PRC-barrel-like (1);Microtubule-binding calmodulin-regulated spectrin-associated, C-terminal (2);	0.198232	0.53938	D	0.000050	T	0.30479	0.0766	L	0.56769	1.78	0.48341	D	0.999631	B;B;P	0.45672	0.25;0.294;0.864	B;P;P	0.51895	0.145;0.514;0.683	T	0.04333	-1.0959	10	0.59425	D	0.04	-24.5764	15.4309	0.75099	0.0:0.737:0.263:0.0	.	1407;1434;1423	Q08AD1-2;Q08AD1;Q08AD1-3	.;CAMP2_HUMAN;.	I	1423;1407;1434	ENSP00000351684:T1423I;ENSP00000416800:T1407I;ENSP00000236925:T1434I	ENSP00000236925:T1434I	T	+	2	0	CAMSAP1L1	199093641	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.066000	0.41452	1.356000	0.45884	0.563000	0.77884	ACT	.	.		0.373	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		T	200827018	C	T	200827018	3	4	228	1	0	0	0	0	1	0	0	0	2614	565	20	3	4334	3	CAMSAP1L1	1	200827018	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	8673503	200827018	48423603	12	32108										
SYT2	127833	hgsc.bcm.edu	37	chr1	202568364	202568364	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	acctgaatctgctcgaagggGatctcaaagctgaaggactc	11	10	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:202568364G>A	ENST00000367267.1	-	8	1227	c.1035C>T	c.(1033-1035)atC>atT	p.I345I	SYT2_ENST00000367268.4_Silent_p.I345I	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	345	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000250}.				neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	GCTCGAAGGGGATCTCAAAGC	0.522																																					p.I345I		Atlas-SNP	.											.	SYT2	51	.	0			c.C1035T						.						277	267	270					1																	202568364		2203	4300	6503	SO:0001819	synonymous_variant	127833	exon8			GAAGGGGATCTCA	AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"Synaptotagmins"	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.1035C>T	chr1.hg19:g.202568364G>A		82.0	0.0		115.0	16.0	NM_177402	Q496K5|Q8NBE5	Silent	SNP	ENST00000367267.1	hg19	CCDS1427.1																																																																																			.	.		0.522	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402		A	202568364	G	A	202568364	2	1	228	1	0	0	0	0	0	0	0	1	15489	1164	41	3		3	SYT2	1	202568364	Silent	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	1741346	202568364	46682257	13	32109										
MDM4	4194	hgsc.bcm.edu	37	chr1	204513690	204513690	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gtactgccattgtttcagatActacagatgacttgtggttt	9	7	1	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:204513690A>T	ENST00000367182.3	+	9	862	c.700A>T	c.(700-702)Act>Tct	p.T234S	MDM4_ENST00000391947.2_3'UTR|MDM4_ENST00000507825.2_Intron|MDM4_ENST00000454264.2_Intron|MDM4_ENST00000463049.1_3'UTR|MDM4_ENST00000367183.3_Intron	NM_001204171.1|NM_001278516.1|NM_001278517.1|NM_001278518.1|NM_001278519.1|NM_002393.4	NP_001191100.1|NP_001265445.1|NP_001265446.1|NP_001265447.1|NP_001265448.1|NP_002384.2	O15151	MDM4_HUMAN	MDM4, p53 regulator	234					cell proliferation (GO:0008283)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|G0 to G1 transition (GO:0045023)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)	nucleus (GO:0005634)	enzyme binding (GO:0019899)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)			TGTTTCAGATACTACAGATGA	0.358			A		"GBM, bladder, retinoblastoma"																																p.T234S		Atlas-SNP	.		Dom	yes		1	1q32	4194	Mdm4 p53 binding protein homolog		M	.	MDM4	57	.	0			c.A700T						.						142	133	136					1																	204513690		2203	4300	6503	SO:0001583	missense	4194	exon9			TCAGATACTACAG	AF007111	CCDS1447.1, CCDS55674.1, CCDS55675.1, CCDS60396.1, CCDS73007.1, CCDS73008.1, CCDS73009.1	1q32	2014-03-03	2014-03-03		ENSG00000198625	ENSG00000198625			6974	protein-coding gene	gene with protein product		602704	"mouse double minute 4, human homolog of; p53-binding protein", "Mdm4, transformed 3T3 cell double minute 4, p53 binding protein (mouse)", "Mdm4 p53 binding protein homolog (mouse)"			9226370, 14660608	Standard	NM_002393		Approved	MDMX, HDMX	uc001hba.3	O15151	OTTHUMG00000035877	ENST00000367182.3:c.700A>T	chr1.hg19:g.204513690A>T	ENSP00000356150:p.Thr234Ser	110.0	0.0		138.0	6.0	NM_002393	Q2M2Y2|Q32SL2|Q6GS18|Q8IV83	Missense_Mutation	SNP	ENST00000367182.3	hg19	CCDS1447.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.954273	0.73902	.	.	ENSG00000198625	ENST00000367182;ENST00000367179	T;T	0.09817	2.94;2.94	5.62	4.5	0.54988	.	0.133960	0.64402	D	0.000002	T	0.21186	0.0510	L	0.47190	1.495	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.05971	-1.0853	10	0.15499	T	0.54	-1.6684	10.0491	0.42205	0.9229:0.0:0.0771:0.0	.	234	O15151	MDM4_HUMAN	S	234;119	ENSP00000356150:T234S;ENSP00000356147:T119S	ENSP00000356147:T119S	T	+	1	0	MDM4	202780313	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	5.221000	0.65272	0.992000	0.38840	-0.404000	0.06349	ACT	.	.		0.358	MDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087415.2	NM_002393		T	204513690	A	T	204513690	3	4	228	1	0	0	0	0	1	0	0	0	9423	391	14	4	730	4	MDM4	1	204513690	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	1945326	204513690	44736931	14	32110										
KLHDC8A	55220	hgsc.bcm.edu	37	chr1	205308358	205308358	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cacgtccatcgtccgcaggaActtgggctgccggtagaggc	14	13	0	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:205308358A>G	ENST00000367156.3	-	7	1537	c.721T>C	c.(721-723)Ttc>Ctc	p.F241L	KLHDC8A_ENST00000539253.1_Missense_Mutation_p.F241L|KLHDC8A_ENST00000460687.1_Missense_Mutation_p.F107L|KLHDC8A_ENST00000537168.1_Missense_Mutation_p.F128L|KLHDC8A_ENST00000367155.3_Missense_Mutation_p.F241L	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	241										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GTCCGCAGGAACTTGGGCTGC	0.612																																					p.F241L		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.T721C						.						52	46	48					1																	205308358		2203	4300	6503	SO:0001583	missense	55220	exon4			GCAGGAACTTGGG		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.721T>C	chr1.hg19:g.205308358A>G	ENSP00000356124:p.Phe241Leu	95.0	0.0		121.0	26.0	NM_018203	B3KU70|Q9NVG5	Missense_Mutation	SNP	ENST00000367156.3	hg19	CCDS30985.1	.	.	.	.	.	.	.	.	.	.	A	33	5.211477	0.95069	.	.	ENSG00000162873	ENST00000367155;ENST00000367156;ENST00000539253;ENST00000537168	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	5.43	5.43	0.79202	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.79964	0.4537	L	0.58810	1.83	0.58432	D	0.999996	D;P	0.67145	0.996;0.956	D;D	0.73380	0.98;0.931	T	0.76534	-0.2924	10	0.21014	T	0.42	-26.2882	15.1399	0.72601	1.0:0.0:0.0:0.0	.	128;241	F5H5F1;Q8IYD2	.;KLD8A_HUMAN	L	241;241;241;128	ENSP00000356123:F241L;ENSP00000356124:F241L;ENSP00000442229:F241L;ENSP00000443447:F128L	ENSP00000356123:F241L	F	-	1	0	KLHDC8A	203574981	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.300000	0.96151	2.063000	0.61619	0.533000	0.62120	TTC	.	.		0.612	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203		G	205308358	A	G	205308358	3	3	228	1	0	0	0	0	1	0	0	0	8371	43	2	2	343	2	KLHDC8A	1	205308358	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	794668	205308358	43942263	15	32111										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228444576	228444576	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gccaggcggtcgccggggagTacagctgcgaggcggggagc	21	11	0	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:228444576T>C	ENST00000422127.1	+	15	4578	c.4534T>C	c.(4534-4536)Tac>Cac	p.Y1512H	OBSCN_ENST00000359599.6_Missense_Mutation_p.Y76H|OBSCN_ENST00000570156.2_Missense_Mutation_p.Y1604H|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.Y1512H	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1512	Ig-like 15.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CGCCGGGGAGTACAGCTGCGA	0.647																																					p.Y1604H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T4810C						.						40	48	45					1																	228444576		2045	4176	6221	SO:0001583	missense	84033	exon16			GGGGAGTACAGCT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.4534T>C	chr1.hg19:g.228444576T>C	ENSP00000409493:p.Tyr1512His	197.0	0.0		322.0	81.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	16.23	3.063488	0.55432	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;D	0.87491	1.74;1.74;-2.26	4.6	4.6	0.57074	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000007	D	0.95730	0.8611	H	0.97659	4.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97099	0.9796	10	0.87932	D	0	.	13.9628	0.64191	0.0:0.0:0.0:1.0	.	1512;1512	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	H	1512;1512;76	ENSP00000284548:Y1512H;ENSP00000409493:Y1512H;ENSP00000352613:Y76H	ENSP00000284548:Y1512H	Y	+	1	0	OBSCN	226511199	1.000000	0.71417	1.000000	0.80357	0.051000	0.14879	7.178000	0.77657	1.704000	0.51252	0.402000	0.26972	TAC	.	.		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228444576	T	C	228444576	3	2	228	1	0	0	0	0	1	0	0	0	10821	1638	57	2	4588	2	OBSCN	1	228444576	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	23136218	228444576	20806045	16	32112										
CHRM3	1131	hgsc.bcm.edu	37	chr1	240071874	240071874	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tgctcaagcttccgggtcacAgcaccatcctcaactccacc	6	18	3	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:240071874A>C	ENST00000255380.4	+	5	1902	c.1123A>C	c.(1123-1125)Agc>Cgc	p.S375R		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	375					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TCCGGGTCACAGCACCATCCT	0.597																																					p.S375R		Atlas-SNP	.											.	CHRM3	118	.	0			c.A1123C						.						34	27	29					1																	240071874		2203	4300	6503	SO:0001583	missense	1131	exon5			GGTCACAGCACCA	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.1123A>C	chr1.hg19:g.240071874A>C	ENSP00000255380:p.Ser375Arg	214.0	0.0		397.0	24.0	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	hg19	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	A	11.50	1.658630	0.29515	.	.	ENSG00000133019	ENST00000255380	T	0.59224	0.28	5.97	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.326816	0.37136	N	0.002237	T	0.29588	0.0738	N	0.05230	-0.09	0.39017	D	0.959672	P	0.40360	0.714	B	0.33960	0.173	T	0.13229	-1.0517	10	0.23891	T	0.37	-28.8937	9.814	0.40840	0.8623:0.0:0.1377:0.0	.	375	P20309	ACM3_HUMAN	R	375	ENSP00000255380:S375R	ENSP00000255380:S375R	S	+	1	0	CHRM3	238138497	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	6.338000	0.72963	1.074000	0.40909	0.533000	0.62120	AGC	.	.		0.597	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		C	240071874	A	C	240071874	3	2	228	1	0	0	0	0	1	0	0	0	3380	188	7	5	1125	5	CHRM3	1	240071874	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	11627298	240071874	9178747	17	32113										
OR2M3	127062	hgsc.bcm.edu	37	chr1	248367250	248367250	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cctcatctacagcctccgcaAcaaggaggtgaccagagcat	9	14	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr1:248367250A>G	ENST00000456743.1	+	1	919	c.881A>G	c.(880-882)aAc>aGc	p.N294S		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	294						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			AGCCTCCGCAACAAGGAGGTG	0.478																																					p.N294S		Atlas-SNP	.											OR2M3,NS,carcinoma,0,1	OR2M3	116	.	0			c.A881G						.						112	105	107					1																	248367250		2203	4300	6503	SO:0001583	missense	127062	exon1			TCCGCAACAAGGA		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"GPCR / Class A : Olfactory receptors"	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.881A>G	chr1.hg19:g.248367250A>G	ENSP00000389625:p.Asn294Ser	96.0	0.0		156.0	7.0	NM_001004689	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	hg19	CCDS31107.1	.	.	.	.	.	.	.	.	.	.	A	9.927	1.213667	0.22289	.	.	ENSG00000228198	ENST00000456743	T	0.39997	1.05	2.7	2.7	0.31948	.	.	.	.	.	T	0.65533	0.2700	H	0.96777	3.88	0.09310	N	1	P	0.44690	0.841	P	0.49140	0.601	T	0.62407	-0.6861	9	0.87932	D	0	.	10.7308	0.46096	1.0:0.0:0.0:0.0	.	294	Q8NG83	OR2M3_HUMAN	S	294	ENSP00000389625:N294S	ENSP00000389625:N294S	N	+	2	0	OR2M3	246433873	0.023000	0.18921	0.045000	0.18777	0.020000	0.10135	0.687000	0.25407	1.237000	0.43756	0.433000	0.28618	AAC	.	.		0.478	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		G	248367250	A	G	248367250	3	3	228	1	0	0	0	0	1	0	0	0	11020	43	2	2	883	2	OR2M3	1	248367250	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	8295376	248367250	883371	18	32114										
GREB1	9687	hgsc.bcm.edu	37	chr2	11773162	11773162	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cgtgatgtggaacgtggtggAtgtcaactctgctggggaga	17	6	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:11773162A>G	ENST00000381486.2	+	28	5264	c.4964A>G	c.(4963-4965)gAt>gGt	p.D1655G	GREB1_ENST00000234142.5_Missense_Mutation_p.D1655G|GREB1_ENST00000396123.1_Missense_Mutation_p.D653G	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1655						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		AACGTGGTGGATGTCAACTCT	0.562																																					p.D1655G	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.A4964G						.						125	136	133					2																	11773162		2159	4252	6411	SO:0001583	missense	9687	exon28			TGGTGGATGTCAA		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.4964A>G	chr2.hg19:g.11773162A>G	ENSP00000370896:p.Asp1655Gly	116.0	0.0		68.0	7.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	A	14.23	2.474159	0.43942	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.49139	0.79;0.79;0.79	5.3	5.3	0.74995	.	0.047110	0.85682	D	0.000000	T	0.47002	0.1422	L	0.55481	1.735	0.80722	D	1	B	0.17465	0.022	B	0.23716	0.048	T	0.42982	-0.9419	10	0.51188	T	0.08	-25.1792	15.224	0.73336	1.0:0.0:0.0:0.0	.	1655	Q4ZG55	GREB1_HUMAN	G	1655;1655;653	ENSP00000370896:D1655G;ENSP00000234142:D1655G;ENSP00000379429:D653G	ENSP00000234142:D1655G	D	+	2	0	GREB1	11690613	1.000000	0.71417	0.290000	0.24890	0.054000	0.15201	6.604000	0.74150	1.998000	0.58463	0.455000	0.32223	GAT	.	.		0.562	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		G	11773162	A	G	11773162	3	3	228	1	0	0	0	0	1	0	0	0	6769	333	12	2	5178	2	GREB1	2	11773162	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10		11773162	231426211	19	32115										
LPIN1	23175	hgsc.bcm.edu	37	chr2	11911691	11911691	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gagaagaaaaaggaggagaaAgtcacagctggacagcctga	14	6	1	4			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:11911691A>G	ENST00000256720.2	+	4	575	c.482A>G	c.(481-483)aAg>aGg	p.K161R	LPIN1_ENST00000396099.1_Missense_Mutation_p.K167R|LPIN1_ENST00000425416.2_Missense_Mutation_p.K167R|LPIN1_ENST00000396098.1_Missense_Mutation_p.K167R|LPIN1_ENST00000449576.2_Missense_Mutation_p.K210R	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	161					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		AGGAGGAGAAAGTCACAGCTG	0.542																																					p.K210R		Atlas-SNP	.											.	LPIN1	99	.	0			c.A629G						.						68	54	59					2																	11911691		2203	4300	6503	SO:0001583	missense	23175	exon5			GGAGAAAGTCACA	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.482A>G	chr2.hg19:g.11911691A>G	ENSP00000256720:p.Lys161Arg	172.0	0.0		161.0	24.0	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	hg19	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.520378	0.64747	.	.	ENSG00000134324	ENST00000449576;ENST00000396098;ENST00000396099;ENST00000425416;ENST00000256720	D;D;D;D;D	0.91011	-1.71;-2.77;-1.68;-1.55;-1.55	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.93736	0.7998	M	0.63428	1.95	0.80722	D	1	D;P;D	0.64830	0.994;0.948;0.977	D;P;P	0.74348	0.983;0.591;0.751	D	0.91716	0.5385	10	0.17832	T	0.49	-35.8192	16.1502	0.81611	1.0:0.0:0.0:0.0	.	210;161;167	F5GY24;Q14693;A8MU38	.;LPIN1_HUMAN;.	R	210;167;167;167;161	ENSP00000397908:K210R;ENSP00000379405:K167R;ENSP00000379406:K167R;ENSP00000401522:K167R;ENSP00000256720:K161R	ENSP00000256720:K161R	K	+	2	0	LPIN1	11829142	1.000000	0.71417	0.991000	0.47740	0.585000	0.36419	8.850000	0.92190	2.224000	0.72417	0.533000	0.62120	AAG	.	.		0.542	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		G	11911691	A	G	11911691	3	3	228	1	0	0	0	0	1	0	0	0	8927	72	3	2	492	2	LPIN1	2	11911691	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	138529	11911691	231287682	20	32116										
RHOB	388	hgsc.bcm.edu	37	chr2	20647549	20647549	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cgaggtgaagcacttctgtcCcaatgtgcccatcatcctgg	10	13	2	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:20647549C>T	ENST00000272233.4	+	1	715	c.323C>T	c.(322-324)cCc>cTc	p.P108L		NM_004040.2	NP_004031.1	P62745	RHOB_HUMAN	ras homolog family member B	108					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|GTP catabolic process (GO:0006184)|negative regulation of cell cycle (GO:0045786)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|transformed cell apoptotic process (GO:0006927)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|kidney(1)|lung(2)|ovary(1)|urinary_tract(2)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)	all_epithelial(98;4.19e-09)|Lung NSC(108;0.00452)|Ovarian(717;0.0164)		OV - Ovarian serous cystadenocarcinoma(76;1.14e-22)|Epithelial(75;7.84e-19)	Botulinum Toxin Type A(DB00083)	CACTTCTGTCCCAATGTGCCC	0.612																																					p.P108L		Atlas-SNP	.											RHOB,NS,carcinoma,0,1	RHOB	18	.	0			c.C323T						.						84	93	90					2																	20647549		2203	4300	6503	SO:0001583	missense	388	exon1			TCTGTCCCAATGT		CCDS1699.1	2p24	2012-02-27	2012-02-27	2004-03-24	ENSG00000143878	ENSG00000143878			668	protein-coding gene	gene with protein product	"oncogene RHO H6"	165370	"ras homolog gene family, member B"	ARH6, ARHB		3283705, 16278215	Standard	NM_004040		Approved	RhoB, RHOH6, MST081	uc002rdv.3	P62745	OTTHUMG00000090755	ENST00000272233.4:c.323C>T	chr2.hg19:g.20647549C>T	ENSP00000272233:p.Pro108Leu	229.0	0.0		161.0	9.0	NM_004040	B2R692|P01121|Q5U0H6|Q7RTN5|Q7RTR9|Q9CUV7	Missense_Mutation	SNP	ENST00000272233.4	hg19	CCDS1699.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.056970	0.76074	.	.	ENSG00000143878	ENST00000272233	T	0.76968	-1.06	5.39	5.39	0.77823	Small GTP-binding protein domain (1);	0.000000	0.85682	U	0.000000	D	0.89928	0.6857	M	0.87682	2.9	0.80722	D	1	D	0.67145	0.996	D	0.72075	0.976	D	0.91181	0.4976	10	0.87932	D	0	-11.2596	19.5316	0.95231	0.0:1.0:0.0:0.0	.	108	P62745	RHOB_HUMAN	L	108	ENSP00000272233:P108L	ENSP00000272233:P108L	P	+	2	0	RHOB	20511030	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	7.665000	0.83852	2.690000	0.91761	0.650000	0.86243	CCC	.	.		0.612	RHOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207500.1	NM_004040		T	20647549	C	T	20647549	3	4	228	1	0	0	0	0	1	0	0	0	13347	623	22	3	325	3	RHOB	2	20647549	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	8735858	20647549	222551824	21	32117										
EHD3	30845	hgsc.bcm.edu	37	chr2	31489355	31489355	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tggatggcaagatcacaggcGctaatgccaagaaggagatg	14	7	1	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:31489355G>A	ENST00000322054.5	+	6	1678	c.1393G>A	c.(1393-1395)Gct>Act	p.A465T	EHD3_ENST00000541626.1_3'UTR	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	465	EH. {ECO:0000255|PROSITE- ProRule:PRU00077}.				blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					GATCACAGGCGCTAATGCCAA	0.562																																					p.A465T		Atlas-SNP	.											EHD3,NS,carcinoma,0,1	EHD3	90	.	0			c.G1393A						.						106	88	94					2																	31489355		2203	4300	6503	SO:0001583	missense	30845	exon6			ACAGGCGCTAATG	AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"EF-hand domain containing"	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.1393G>A	chr2.hg19:g.31489355G>A	ENSP00000327116:p.Ala465Thr	99.0	0.0		82.0	22.0	NM_014600	B4DFR5|D6W574|Q8N514|Q9NZB3	Missense_Mutation	SNP	ENST00000322054.5	hg19	CCDS1774.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.872563	0.72180	.	.	ENSG00000013016	ENST00000322054	T	0.30182	1.54	5.71	5.71	0.89125	EPS15 homology (EH) (2);EF-hand-like domain (1);	0.044640	0.85682	D	0.000000	T	0.32734	0.0839	L	0.48986	1.54	0.80722	D	1	B	0.22003	0.063	B	0.18263	0.021	T	0.04191	-1.0970	10	0.29301	T	0.29	-17.9785	19.8586	0.96775	0.0:0.0:1.0:0.0	.	465	Q9NZN3	EHD3_HUMAN	T	465	ENSP00000327116:A465T	ENSP00000327116:A465T	A	+	1	0	EHD3	31342859	1.000000	0.71417	0.947000	0.38551	0.991000	0.79684	8.004000	0.88535	2.701000	0.92244	0.462000	0.41574	GCT	.	.		0.562	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600		A	31489355	G	A	31489355	3	1	228	1	0	0	0	0	1	0	0	0	4981	1087	38	1	1415	1	EHD3	2	31489355	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	10841806	31489355	211710018	22	32118										
VRK2	7444	hgsc.bcm.edu	37	chr2	58386637	58386637	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cagatatattcaagaagtcaAgatctccatcttggtataaa	6	7	4	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:58386637A>C	ENST00000435505.2	+	16	2081	c.1336A>C	c.(1336-1338)Aga>Cga	p.R446R	VRK2_ENST00000417641.2_3'UTR|FANCL_ENST00000402135.3_3'UTR|VRK2_ENST00000340157.4_Silent_p.R446R|VRK2_ENST00000412104.2_3'UTR|FANCL_ENST00000403295.3_3'UTR|FANCL_ENST00000233741.4_3'UTR|VRK2_ENST00000440705.2_Silent_p.R423R			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	446	Interaction with MAP3K7.				cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						CAAGAAGTCAAGATCTCCATC	0.383																																					p.R446R		Atlas-SNP	.											.	VRK2	46	.	0			c.A1336C						.						78	78	78					2																	58386637		2203	4300	6503	SO:0001819	synonymous_variant	7444	exon13			AAGTCAAGATCTC	AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.1336A>C	chr2.hg19:g.58386637A>C		169.0	0.0		159.0	21.0	NM_001130480	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Silent	SNP	ENST00000435505.2	hg19	CCDS1859.1																																																																																			.	.		0.383	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296		C	58386637	A	C	58386637	2	2	228	1	0	0	0	0	0	0	0	1	17235	64	3	5		5	VRK2	2	58386637	Silent	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	26897282	58386637	184812736	23	32119										
BCL11A	53335	hgsc.bcm.edu	37	chr2	60688438	60688438	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cagggcgcggctctcgtcgcCcacgcccacgaccgcgcccc	12	22	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:60688438C>T	ENST00000335712.6	-	4	1836	c.1609G>A	c.(1609-1611)Ggc>Agc	p.G537S	BCL11A_ENST00000538214.1_Missense_Mutation_p.G503S|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000356842.4_Missense_Mutation_p.G537S|BCL11A_ENST00000537768.1_Missense_Mutation_p.G206S|BCL11A_ENST00000358510.4_Missense_Mutation_p.G503S	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	537					B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			CTCTCGTCGCCCACGCCCACG	0.701			T	IGH@	B-CLL																																p.G537S		Atlas-SNP	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.G1609A						.						14	14	14					2																	60688438		2193	4279	6472	SO:0001583	missense	53335	exon4			CGTCGCCCACGCC	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"Zinc fingers, C2H2-type"	13221	protein-coding gene	gene with protein product		606557	"ecotropic viral integration site 9"	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.1609G>A	chr2.hg19:g.60688438C>T	ENSP00000338774:p.Gly537Ser	72.0	0.0		38.0	8.0	NM_018014	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	hg19	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	C	2.644	-0.283581	0.05642	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000537768;ENST00000335712;ENST00000358510	T;T;T;T;T	0.08102	3.13;3.42;3.29;3.44;3.37	5.19	4.3	0.51218	.	1.710350	0.02984	N	0.146061	T	0.08044	0.0201	L	0.31664	0.95	0.37417	D	0.913468	B;B;B;B;B	0.25667	0.001;0.131;0.093;0.102;0.126	B;B;B;B;B	0.29440	0.002;0.064;0.102;0.05;0.055	T	0.40289	-0.9571	10	0.10902	T	0.67	-2.9045	5.8478	0.18675	0.1608:0.6845:0.0:0.1547	.	503;206;503;537;537	F5H2Y4;B4DT16;Q9H165-6;Q9H165;D9YZV9	.;.;.;BC11A_HUMAN;.	S	537;562;503;206;537;503	ENSP00000349300:G537S;ENSP00000438303:G503S;ENSP00000443712:G206S;ENSP00000338774:G537S;ENSP00000351307:G503S	ENSP00000338774:G537S	G	-	1	0	BCL11A	60541942	0.968000	0.33430	0.997000	0.53966	0.298000	0.27526	1.622000	0.36997	1.168000	0.42723	-0.188000	0.12872	GGC	.	.		0.701	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		T	60688438	C	T	60688438	3	4	228	1	0	0	0	0	1	0	0	0	1363	623	22	3	1008	3	BCL11A	2	60688438	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	2301801	60688438	182510935	24	32120										
PNO1	56902	hgsc.bcm.edu	37	chr2	68385547	68385547	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	acaaggaaaattccagtcccAgctaacagatacacaccatt	5	12	0	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:68385547A>C	ENST00000263657.2	+	2	334	c.243A>C	c.(241-243)ccA>ccC	p.P81P	WDR92_ENST00000492039.2_5'Flank|WDR92_ENST00000409164.1_5'Flank|WDR92_ENST00000406245.2_5'Flank|WDR92_ENST00000295121.6_5'Flank|RP11-474G23.1_ENST00000406334.3_Intron	NM_020143.2	NP_064528.1	Q9NRX1	PNO1_HUMAN	partner of NOB1 homolog (S. cerevisiae)	81						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						TTCCAGTCCCAGCTAACAGAT	0.383																																					p.P81P	NSCLC(83;642 1410 13044 32832 40058)	Atlas-SNP	.											.	PNO1	17	.	0			c.A243C						.						111	114	113					2																	68385547		2203	4300	6503	SO:0001819	synonymous_variant	56902	exon2			AGTCCCAGCTAAC	AF164799	CCDS1885.1	2p14	2010-07-06			ENSG00000115946	ENSG00000115946			32790	protein-coding gene	gene with protein product	"RNA binding protein"		"KH-type RNA binding protein 1", "KH-type RNA-binding protein 1"	KHRBP1		15497447	Standard	NM_020143		Approved	RRP20	uc002seh.3	Q9NRX1	OTTHUMG00000129563	ENST00000263657.2:c.243A>C	chr2.hg19:g.68385547A>C		155.0	0.0		108.0	29.0	NM_020143	A8K6Q0|Q53G13|Q8WVB8	Silent	SNP	ENST00000263657.2	hg19	CCDS1885.1																																																																																			.	.		0.383	PNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251756.1	NM_020143		C	68385547	A	C	68385547	2	2	228	1	0	0	0	0	0	0	0	1	12170	175	7	5		5	PNO1	2	68385547	Silent	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	7697109	68385547	174813826	25	32121										
GALNT5	11227	hgsc.bcm.edu	37	chr2	158115035	158115035	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	aagcagaagacagacgggagAggcaccaaacctgaagcctc	12	11	0	5			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:158115035A>G	ENST00000259056.4	+	1	926	c.441A>G	c.(439-441)agA>agG	p.R147R		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	147					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						CAGACGGGAGAGGCACCAAAC	0.562																																					p.R147R		Atlas-SNP	.											.	GALNT5	112	.	0			c.A441G						.						66	68	67					2																	158115035		2203	4300	6503	SO:0001819	synonymous_variant	11227	exon1			CGGGAGAGGCACC	AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.441A>G	chr2.hg19:g.158115035A>G		81.0	0.0		83.0	10.0	NM_014568	A5PKZ1|Q9UGK7|Q9UHL6	Silent	SNP	ENST00000259056.4	hg19	CCDS2203.1																																																																																			.	.		0.562	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		G	158115035	A	G	158115035	2	3	228	1	0	0	0	0	0	0	0	1	6224	301	11	2		2	GALNT5	2	158115035	Silent	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	89729488	158115035	85084338	26	32122										
IDH1	3417	hgsc.bcm.edu	37	chr2	209108256	209108256	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	aacccttagacagagccattTggaaggaactgtgtgcaaaa	10	8	0	2	rs374340555		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:209108256T>G	ENST00000415913.1	-	6	974	c.593A>C	c.(592-594)cAa>cCa	p.Q198P	IDH1_ENST00000345146.2_Missense_Mutation_p.Q198P|IDH1_ENST00000446179.1_Missense_Mutation_p.Q198P	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	198					2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		CAGAGCCATTTGGAAGGAACT	0.408			Mis		gliobastoma																																p.Q198P	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	.	IDH1	6310	.	0			c.A593C						.						106	102	103					2																	209108256		2203	4300	6503	SO:0001583	missense	3417	exon6			GCCATTTGGAAGG		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.593A>C	chr2.hg19:g.209108256T>G	ENSP00000390265:p.Gln198Pro	65.0	0.0		56.0	13.0	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	hg19	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.008438	0.75046	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913	T;T;T	0.78364	-1.17;-1.17;-1.17	5.91	3.49	0.39957	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.85392	0.5686	M	0.93062	3.375	0.80722	D	1	P	0.38335	0.627	P	0.46320	0.512	D	0.84940	0.0865	10	0.56958	D	0.05	-7.9797	11.4134	0.49939	0.2411:0.0:0.0:0.7589	.	198	O75874	IDHC_HUMAN	P	198	ENSP00000260985:Q198P;ENSP00000410513:Q198P;ENSP00000390265:Q198P	ENSP00000260985:Q198P	Q	-	2	0	IDH1	208816501	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.293000	0.72731	0.468000	0.27243	0.454000	0.30748	CAA	.	.		0.408	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			G	209108256	T	G	209108256	3	3	228	1	0	0	0	0	1	0	0	0	7503	1812	63	5	671	5	IDH1	2	209108256	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	50993221	209108256	34091117	27	32123										
TNS1	7145	hgsc.bcm.edu	37	chr2	218713775	218713775	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cttcaccttagcatacaggcTcccatctagtggcccctgcg	8	16	2	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:218713775T>A	ENST00000171887.4	-	17	1542	c.1090A>T	c.(1090-1092)Agc>Tgc	p.S364C	TNS1_ENST00000419504.1_Missense_Mutation_p.S364C|TNS1_ENST00000430930.1_Missense_Mutation_p.S364C|TNS1_ENST00000480665.1_5'UTR	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	364					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GCATACAGGCTCCCATCTAGT	0.597																																					p.S364C		Atlas-SNP	.											.	TNS1	251	.	0			c.A1090T						.						117	114	115					2																	218713775		2203	4300	6503	SO:0001583	missense	7145	exon17			ACAGGCTCCCATC	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1090A>T	chr2.hg19:g.218713775T>A	ENSP00000171887:p.Ser364Cys	58.0	0.0		65.0	14.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.040514	0.75732	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554	D;D;D;D;D	0.96232	-3.31;-3.3;-3.32;-3.71;-3.95	5.22	5.22	0.72569	.	0.126908	0.64402	D	0.000001	D	0.97952	0.9326	M	0.81942	2.565	0.80722	D	1	D;P;D;D;D	0.89917	1.0;0.953;0.972;1.0;1.0	D;P;P;D;D	0.76071	0.987;0.627;0.614;0.972;0.972	D	0.98900	1.0776	10	0.87932	D	0	.	15.265	0.73654	0.0:0.0:0.0:1.0	.	364;418;364;364;364	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	C	364;364;364;489;432	ENSP00000171887:S364C;ENSP00000408724:S364C;ENSP00000406016:S364C;ENSP00000405460:S489C;ENSP00000400383:S432C	ENSP00000171887:S364C	S	-	1	0	TNS1	218422020	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	7.827000	0.86722	2.188000	0.69820	0.533000	0.62120	AGC	.	.		0.597	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218713775	T	A	218713775	3	1	228	1	0	0	0	0	1	0	0	0	16358	1551	54	4	4185	4	TNS1	2	218713775	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	9605519	218713775	24485598	28	32124										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227920768	227920768	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gtcctgggagtccggggaggCctttcattccagctggcccg	15	13	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr2:227920768C>A	ENST00000396625.3	-	30	2816	c.2609G>T	c.(2608-2610)gGc>gTc	p.G870V	COL4A4_ENST00000329662.7_Missense_Mutation_p.G870V	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	870	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TCCGGGGAGGCCTTTCATTCC	0.632																																					p.G870V		Atlas-SNP	.											.	COL4A4	215	.	0			c.G2609T						.						42	45	44					2																	227920768		1857	4084	5941	SO:0001583	missense	1286	exon30			GGGAGGCCTTTCA		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.2609G>T	chr2.hg19:g.227920768C>A	ENSP00000379866:p.Gly870Val	134.0	0.0		103.0	5.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	hg19	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.481060	0.44147	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.99353	-5.77;-5.77	5.64	5.64	0.86602	.	.	.	.	.	D	0.99635	0.9866	H	0.95950	3.745	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97808	1.0249	9	0.87932	D	0	.	17.476	0.87659	0.0:1.0:0.0:0.0	.	870	P53420	CO4A4_HUMAN	V	870	ENSP00000379866:G870V;ENSP00000328553:G870V	ENSP00000328553:G870V	G	-	2	0	COL4A4	227629012	1.000000	0.71417	0.985000	0.45067	0.311000	0.27955	5.917000	0.69989	2.660000	0.90430	0.655000	0.94253	GGC	.	.		0.632	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		A	227920768	C	A	227920768	3	1	228	1	0	0	0	0	1	0	0	0	3695	739	26	3	2539	3	COL4A4	2	227920768	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	9206993	227920768	15278605	29	32125										
CNTN4	152330	hgsc.bcm.edu	37	chr3	2777928	2777928	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cactgcatggcccgatttttAttcaagaaccaagtcctgta	7	11	1	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr3:2777928A>G	ENST00000397461.1	+	4	469	c.85A>G	c.(85-87)Att>Gtt	p.I29V	CNTN4_ENST00000418658.1_Missense_Mutation_p.I29V|CNTN4_ENST00000427331.1_Missense_Mutation_p.I29V	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	29					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		CCCGATTTTTATTCAAGAACC	0.373																																					p.I29V		Atlas-SNP	.											.	CNTN4	335	.	0			c.A85G						.						173	164	167					3																	2777928		1827	4081	5908	SO:0001583	missense	152330	exon5			ATTTTTATTCAAG	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.85A>G	chr3.hg19:g.2777928A>G	ENSP00000380602:p.Ile29Val	104.0	0.0		80.0	14.0	NM_175607	B2RAX3|Q8IX14|Q8TC35	Missense_Mutation	SNP	ENST00000397461.1	hg19	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	A	10.37	1.332566	0.24167	.	.	ENSG00000144619	ENST00000422330;ENST00000455083;ENST00000418658;ENST00000397461;ENST00000434053;ENST00000427331	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	6.07	-3.9	0.04181	Immunoglobulin-like fold (1);	0.723211	0.13014	N	0.420610	T	0.22003	0.0530	L	0.28776	0.89	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.33394	-0.9870	10	0.10377	T	0.69	.	7.4138	0.27032	0.3362:0.3286:0.3353:0.0	.	29;29	B3KTK4;Q8IWV2	.;CNTN4_HUMAN	V	29;29;29;29;47;29	ENSP00000408594:I29V;ENSP00000396010:I29V;ENSP00000380602:I29V;ENSP00000404085:I47V;ENSP00000413642:I29V	ENSP00000380602:I29V	I	+	1	0	CNTN4	2752928	0.023000	0.18921	0.001000	0.08648	0.979000	0.70002	0.353000	0.20130	-0.934000	0.03733	0.533000	0.62120	ATT	.	.		0.373	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			G	2777928	A	G	2777928	3	3	228	1	0	0	0	0	1	0	0	0	3645	449	16	2	91	2	CNTN4	3	2777928	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10		2777928	195244502	30	32126										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57445491	57445491	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	catcaattgtttcttgtattCgaatcaagcggtcctcccag	7	11	3	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr3:57445491C>A	ENST00000351747.2	-	20	2870	c.2690G>T	c.(2689-2691)cGa>cTa	p.R897L		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	897	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TTCTTGTATTCGAATCAAGCG	0.348																																					p.R897L		Atlas-SNP	.											DNAH12,colon,carcinoma,0,1	DNAH12	182	.	0			c.G2690T						.						158	121	132					3																	57445491		692	1591	2283	SO:0001583	missense	201625	exon20			TGTATTCGAATCA	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.2690G>T	chr3.hg19:g.57445491C>A	ENSP00000295937:p.Arg897Leu	54.0	0.0		57.0	15.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	hg19		.	.	.	.	.	.	.	.	.	.	C	6.624	0.483655	0.12581	.	.	ENSG00000174844	ENST00000351747;ENST00000495027	T;T	0.60171	0.21;0.21	5.36	5.36	0.76844	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.37865	0.1019	N	0.04746	-0.17	0.80722	D	1	P	0.48503	0.911	P	0.48063	0.565	T	0.40720	-0.9548	9	0.02654	T	1	.	12.8732	0.57977	0.0:0.9156:0.0:0.0844	.	897	Q6ZR08	DYH12_HUMAN	L	897;920	ENSP00000295937:R897L;ENSP00000418137:R920L	ENSP00000295937:R897L	R	-	2	0	DNAH12	57420531	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.820000	0.39032	2.509000	0.84616	0.655000	0.94253	CGA	.	.		0.348	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		A	57445491	C	A	57445491	3	1	228	1	0	0	0	0	1	0	0	0	4602	884	31	1	6748	1	DNAH12	3	57445491	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	54667563	57445491	140576939	31	32127										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89156944	89156944	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tccttctcagctgctctgttCtcgacagcttcggggaactg	10	13	3	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr3:89156944C>G	ENST00000336596.2	+	1	271	c.46C>G	c.(46-48)Ctc>Gtc	p.L16V	EPHA3_ENST00000494014.1_Missense_Mutation_p.L16V|EPHA3_ENST00000452448.2_Missense_Mutation_p.L16V	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	16					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CTGCTCTGTTCTCGACAGCTT	0.577										TSP Lung(6;0.00050)																											p.L16V		Atlas-SNP	.											.	EPHA3	501	.	0			c.C46G						.						170	130	144					3																	89156944		2203	4300	6503	SO:0001583	missense	2042	exon1			TCTGTTCTCGACA	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.46C>G	chr3.hg19:g.89156944C>G	ENSP00000337451:p.Leu16Val	72.0	0.0		55.0	6.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	C	5.616	0.298298	0.10622	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.73469	-0.73;2.65;-0.75	5.59	4.72	0.59763	.	0.329134	0.28901	N	0.013763	T	0.63248	0.2495	L	0.29908	0.895	0.19300	N	0.999973	B;B	0.21606	0.005;0.058	B;B	0.23574	0.007;0.047	T	0.49899	-0.8890	9	.	.	.	.	13.9221	0.63937	0.0:0.926:0.0:0.0739	.	16;16	P29320;P29320-2	EPHA3_HUMAN;.	V	16	ENSP00000337451:L16V;ENSP00000399926:L16V;ENSP00000419190:L16V	.	L	+	1	0	EPHA3	89239634	0.738000	0.28186	0.079000	0.20413	0.004000	0.04260	1.640000	0.37186	1.363000	0.46019	0.561000	0.74099	CTC	.	.		0.577	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		G	89156944	C	G	89156944	3	3	228	1	0	0	0	0	1	0	0	0	5170	913	32	4	48	4	EPHA3	3	89156944	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	31711453	89156944	108865486	32	32128										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89478259	89478259	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	atttactgtatatctaggtaAgccagttatgattgtcacag	8	6	2	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr3:89478259A>G	ENST00000336596.2	+	12	2303	c.2078A>G	c.(2077-2079)aAg>aGg	p.K693R	EPHA3_ENST00000494014.1_Missense_Mutation_p.K693R	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	693	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TATCTAGGTAAGCCAGTTATG	0.299										TSP Lung(6;0.00050)																											p.K693R		Atlas-SNP	.											.	EPHA3	501	.	0			c.A2078G						.						95	100	98					3																	89478259		2203	4300	6503	SO:0001583	missense	2042	exon12			TAGGTAAGCCAGT	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2078A>G	chr3.hg19:g.89478259A>G	ENSP00000337451:p.Lys693Arg	122.0	0.0		96.0	8.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	15.59	2.878195	0.51801	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.62364	0.03;0.03	5.68	5.68	0.88126	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56337	0.1978	N	0.02345	-0.59	0.80722	D	1	D	0.60160	0.987	D	0.73380	0.98	T	0.63972	-0.6516	9	.	.	.	.	16.2237	0.82280	1.0:0.0:0.0:0.0	.	693	P29320	EPHA3_HUMAN	R	693	ENSP00000337451:K693R;ENSP00000419190:K693R	.	K	+	2	0	EPHA3	89560949	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.287000	0.95975	2.289000	0.77006	0.482000	0.46254	AAG	.	.		0.299	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		G	89478259	A	G	89478259	3	3	228	1	0	0	0	0	1	0	0	0	5170	72	3	2	2150	2	EPHA3	3	89478259	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	321315	89478259	108544171	33	32129										
KALRN	8997	hgsc.bcm.edu	37	chr3	124438224	124438224	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ctggacacctcccgcctagcAtgcttcatagaacgtcgcaa	8	15	1	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr3:124438224A>G	ENST00000291478.5	+	27	3940	c.3777A>G	c.(3775-3777)gcA>gcG	p.A1259A	KALRN_ENST00000428018.2_Silent_p.A1227A|KALRN_ENST00000360013.3_Silent_p.A2956A	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2955					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						CCCGCCTAGCATGCTTCATAG	0.562																																					p.A2956A		Atlas-SNP	.											.	KALRN	556	.	0			c.A8868G						.						57	59	58					3																	124438224		2200	4299	6499	SO:0001819	synonymous_variant	8997	exon60			CCTAGCATGCTTC	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.3777A>G	chr3.hg19:g.124438224A>G		135.0	0.0		108.0	31.0	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	hg19	CCDS3028.1	.	.	.	.	.	.	.	.	.	.	A	6.955	0.546063	0.13312	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.3	-10.0	0.00425	.	.	.	.	.	T	0.34600	0.0903	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41787	-0.9489	4	.	.	.	.	3.3715	0.07223	0.5127:0.1749:0.1801:0.1324	.	.	.	.	R	2925	.	.	H	+	2	0	KALRN	125920914	0.000000	0.05858	0.626000	0.29213	0.983000	0.72400	-1.636000	0.02016	-1.789000	0.01264	-0.376000	0.06991	CAT	.	.		0.562	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947		G	124438224	A	G	124438224	2	3	228	1	0	0	0	0	0	0	0	1	7984	204	8	2		2	KALRN	3	124438224	Silent	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	34959965	124438224	73584206	34	32130										
TIPARP	25976	hgsc.bcm.edu	37	chr3	156396043	156396043	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	caaagtcatagattatgttcCaggcattttccaagaaaaca	6	8	1	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr3:156396043C>T	ENST00000461166.1	+	2	1145	c.557C>T	c.(556-558)cCa>cTa	p.P186L	TIPARP_ENST00000542783.1_Missense_Mutation_p.P186L|TIPARP_ENST00000486483.1_Missense_Mutation_p.P186L|TIPARP_ENST00000295924.7_Missense_Mutation_p.P186L	NM_001184717.1	NP_001171646.1	Q7Z3E1	PARPT_HUMAN	TCDD-inducible poly(ADP-ribose) polymerase	186					androgen metabolic process (GO:0008209)|cellular response to organic cyclic compound (GO:0071407)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|multicellular organismal metabolic process (GO:0044236)|negative regulation of gene expression (GO:0010629)|nitrogen compound metabolic process (GO:0006807)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of protein catabolic process (GO:0045732)|post-embryonic development (GO:0009791)|protein ADP-ribosylation (GO:0006471)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculogenesis (GO:0001570)	nucleus (GO:0005634)	enhancer binding (GO:0035326)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GATTATGTTCCAGGCATTTTC	0.423																																					p.P186L	Ovarian(171;276 1987 3319 6837 11197)	Atlas-SNP	.											.	TIPARP	50	.	0			c.C557T						.						119	121	120					3																	156396043		2203	4300	6503	SO:0001583	missense	25976	exon2			ATGTTCCAGGCAT	BX537965	CCDS3177.1	3q25.31	2011-06-22			ENSG00000163659	ENSG00000163659		"Poly (ADP-ribose) polymerases"	23696	protein-coding gene	gene with protein product		612480				12851707	Standard	NM_001184717		Approved	DKFZP434J214, DKFZp686N0351, DDF1, PARP7, PARP-7, PARP-1, pART14, RM1	uc021xgg.1	Q7Z3E1	OTTHUMG00000158646	ENST00000461166.1:c.557C>T	chr3.hg19:g.156396043C>T	ENSP00000420612:p.Pro186Leu	113.0	0.0		123.0	6.0	NM_015508	D3DNK6|Q68CY9|Q86VP4|Q9Y4P7	Missense_Mutation	SNP	ENST00000461166.1	hg19	CCDS3177.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.942230	0.34283	.	.	ENSG00000163659	ENST00000486483;ENST00000295924;ENST00000461166;ENST00000473702;ENST00000481853;ENST00000542783	T;T;T;T;T;T	0.24723	2.87;2.87;2.87;1.84;2.87;2.87	5.11	5.11	0.69529	.	0.222920	0.37095	N	0.002254	T	0.18130	0.0435	N	0.14661	0.345	0.49213	D	0.999769	B	0.29432	0.244	B	0.22386	0.039	T	0.07009	-1.0795	10	0.87932	D	0	.	18.1531	0.89682	0.0:1.0:0.0:0.0	.	186	Q7Z3E1	PARPT_HUMAN	L	186	ENSP00000418757:P186L;ENSP00000295924:P186L;ENSP00000420612:P186L;ENSP00000419982:P186L;ENSP00000418829:P186L;ENSP00000438345:P186L	ENSP00000295924:P186L	P	+	2	0	TIPARP	157878737	1.000000	0.71417	1.000000	0.80357	0.652000	0.38707	3.739000	0.55075	2.390000	0.81377	0.563000	0.77884	CCA	.	.		0.423	TIPARP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351618.1	NM_015508		T	156396043	C	T	156396043	3	4	228	1	0	0	0	0	1	0	0	0	15939	594	21	3	559	3	TIPARP	3	156396043	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	31957819	156396043	41626387	35	32131										
WDR49	151790	hgsc.bcm.edu	37	chr3	167196762	167196762	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tccttgggaaacaggtttttCtcatcaaatacagctttcaa	6	9	3	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr3:167196762C>A	ENST00000308378.3	-	15	2303	c.1998G>T	c.(1996-1998)gaG>gaT	p.E666D	WDR49_ENST00000453925.2_Missense_Mutation_p.E631D|WDR49_ENST00000479765.1_3'UTR|WDR49_ENST00000476376.1_Missense_Mutation_p.E491D|SERPINI2_ENST00000476257.1_5'UTR	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	666										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						ACAGGTTTTTCTCATCAAATA	0.313																																					p.E666D		Atlas-SNP	.											.	WDR49	188	.	0			c.G1998T						.						67	64	65					3																	167196762		2201	4296	6497	SO:0001583	missense	151790	exon15			GTTTTTCTCATCA	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"WD repeat domain containing"	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.1998G>T	chr3.hg19:g.167196762C>A	ENSP00000311343:p.Glu666Asp	59.0	0.0		80.0	16.0	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	hg19	CCDS3201.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.35|11.35	1.612536|1.612536	0.28712|0.28712	.|.	.|.	ENSG00000174776|ENSG00000174776	ENST00000308378;ENST00000476376;ENST00000453925|ENST00000472600	T;T;T|.	0.62639|.	0.01;1.25;0.14|.	5.61|5.61	1.9|1.9	0.25705|0.25705	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|T	0.51126|0.51126	0.1656|0.1656	M|M	0.66939|0.66939	2.045|2.045	0.20307|0.20307	N|N	0.999917|0.999917	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.78314|.	0.991;0.991|.	T|T	0.40979|0.40979	-0.9534|-0.9534	10|5	0.49607|.	T|.	0.09|.	.|.	8.8004|8.8004	0.34905|0.34905	0.0:0.6197:0.0:0.3803|0.0:0.6197:0.0:0.3803	.|.	631;666|.	E7EQK3;Q8IV35|.	.;WDR49_HUMAN|.	D|I	666;491;631|643	ENSP00000311343:E666D;ENSP00000420508:E491D;ENSP00000410863:E631D|.	ENSP00000311343:E666D|.	E|R	-|-	3|2	2|0	WDR49|WDR49	168679456|168679456	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.249000|0.249000	0.25844|0.25844	1.135000|1.135000	0.31454|0.31454	0.074000|0.074000	0.16767|0.16767	-0.136000|-0.136000	0.14681|0.14681	GAG|AGA	.	.		0.313	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		A	167196762	C	A	167196762	3	1	228	1	0	0	0	0	1	0	0	0	17317	912	32	3	99	3	WDR49	3	167196762	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	10800719	167196762	30825668	36	32132										
UGT2B11	10720	hgsc.bcm.edu	37	chr4	70079851	70079851	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gatcacttaattttgacataAcaataggtatgtaggaagga	9	4	1	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr4:70079851A>G	ENST00000446444.1	-	1	598	c.590T>C	c.(589-591)gTt>gCt	p.V197A	RP11-704M14.1_ENST00000505646.1_RNA|RP11-704M14.1_ENST00000504301.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	197					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.V197G(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						TTTTGACATAACAATAGGTAT	0.373																																					p.V197A		Atlas-SNP	.											UGT2B11,colon,carcinoma,0,1	UGT2B11	92	.	1	Substitution - Missense(1)	large_intestine(1)	c.T590C						.						64	64	64					4																	70079851		2202	4295	6497	SO:0001583	missense	10720	exon1			GACATAACAATAG	AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"UDP glucuronosyltransferases"	12545	protein-coding gene	gene with protein product		603064	"UDP glycosyltransferase 2 family, polypeptide B11"			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.590T>C	chr4.hg19:g.70079851A>G	ENSP00000387683:p.Val197Ala	196.0	0.0		165.0	8.0	NM_001073	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	hg19	CCDS3527.1	.	.	.	.	.	.	.	.	.	.	-	0.015	-1.542083	0.00934	.	.	ENSG00000213759	ENST00000446444	T	0.60424	0.19	1.96	0.78	0.18556	.	1.185740	0.06681	U	0.767952	T	0.36441	0.0967	N	0.20610	0.595	0.09310	N	1	B	0.09022	0.002	B	0.15484	0.013	T	0.23833	-1.0177	10	0.16420	T	0.52	.	3.4697	0.07562	0.592:0.0:0.408:0.0	.	197	O75310	UDB11_HUMAN	A	197	ENSP00000387683:V197A	ENSP00000387683:V197A	V	-	2	0	UGT2B11	70114440	0.000000	0.05858	0.027000	0.17364	0.141000	0.21300	-0.772000	0.04694	0.898000	0.36418	0.155000	0.16302	GTT	.	.		0.373	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073		G	70079851	A	G	70079851	3	3	228	1	0	0	0	0	1	0	0	0	16972	43	2	2	1023	2	UGT2B11	4	70079851	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10		70079851	121074425	37	32133										
LIN54	132660	hgsc.bcm.edu	37	chr4	83861045	83861045	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	agttatgtgatacttacttgTttgacagcctgagctgagac	10	7	0	4			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr4:83861045T>C	ENST00000340417.3	-	6	1616	c.1239A>G	c.(1237-1239)aaA>aaG	p.K413K	LIN54_ENST00000442461.2_Silent_p.K192K|LIN54_ENST00000395283.2_Silent_p.K324K|LIN54_ENST00000446851.2_Silent_p.K192K|LIN54_ENST00000510557.1_Silent_p.K192K|LIN54_ENST00000395282.2_3'UTR|LIN54_ENST00000505397.1_Silent_p.K413K|LIN54_ENST00000506560.1_Silent_p.K324K	NM_194282.2	NP_919258.2	Q6MZP7	LIN54_HUMAN	lin-54 DREAM MuvB core complex component	413					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)	14		Hepatocellular(203;0.114)				TACTTACTTGTTTGACAGCCT	0.348																																					p.K413K		Atlas-SNP	.											.	LIN54	50	.	0			c.A1239G						.						131	140	137					4																	83861045		2203	4300	6503	SO:0001819	synonymous_variant	132660	exon6			TACTTGTTTGACA	BX537919	CCDS3599.1, CCDS47089.1, CCDS75157.1	4q21.22	2014-07-17	2014-07-17		ENSG00000189308	ENSG00000189308			25397	protein-coding gene	gene with protein product	"CXC domain containing 1"	613367	"lin-54 homolog (C. elegans)"			21498570	Standard	XM_005262749		Approved	MIP120, DKFZp686L1814, JC8.6, CXCDC1	uc003hnx.3	Q6MZP7	OTTHUMG00000130287	ENST00000340417.3:c.1239A>G	chr4.hg19:g.83861045T>C		174.0	0.0		127.0	11.0	NM_194282	Q32M68|Q32M69|Q6N071|Q76B60	Silent	SNP	ENST00000340417.3	hg19	CCDS3599.1																																																																																			.	.		0.348	LIN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252626.2	NM_194282		C	83861045	T	C	83861045	2	2	228	1	0	0	0	0	0	0	0	1	8818	1722	60	2		2	LIN54	4	83861045	Silent	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	13781194	83861045	107293231	38	32134										
FAT4	79633	hgsc.bcm.edu	37	chr4	126240520	126240520	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tagtgtcatcttaacagtttAtgtccatgatgtaaatgaca	7	6	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr4:126240520A>C	ENST00000394329.3	+	1	2967	c.2954A>C	c.(2953-2955)tAt>tCt	p.Y985S		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	985	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TTAACAGTTTATGTCCATGAT	0.438																																					p.Y985S		Atlas-SNP	.											.	FAT4	1752	.	0			c.A2954C						.						104	101	102					4																	126240520		1950	4140	6090	SO:0001583	missense	79633	exon1			CAGTTTATGTCCA	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.2954A>C	chr4.hg19:g.126240520A>C	ENSP00000377862:p.Tyr985Ser	59.0	0.0		65.0	6.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	0.079	-1.187918	0.01607	.	.	ENSG00000196159	ENST00000394329	T	0.01560	4.77	5.1	1.3	0.21679	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	0.275088	0.19205	U	0.120080	T	0.00724	0.0024	N	0.02775	-0.495	0.54753	D	0.999988	B	0.02656	0.0	B	0.06405	0.002	T	0.47142	-0.9140	10	0.06099	T	0.92	.	5.8147	0.18486	0.5054:0.3124:0.1823:0.0	.	985	Q6V0I7	FAT4_HUMAN	S	985	ENSP00000377862:Y985S	ENSP00000377862:Y985S	Y	+	2	0	FAT4	126459970	1.000000	0.71417	0.544000	0.28141	0.326000	0.28443	2.648000	0.46647	0.419000	0.25927	-0.250000	0.11733	TAT	.	.		0.438	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126240520	A	C	126240520	3	2	228	1	0	0	0	0	1	0	0	0	5700	449	16	5	2956	5	FAT4	4	126240520	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	42379475	126240520	64913756	39	32135										
FAT4	79633	hgsc.bcm.edu	37	chr4	126242187	126242187	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cccttgctgcagacccatcaGctgtgattggttccgttctg	10	13	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr4:126242187G>T	ENST00000394329.3	+	1	4634	c.4621G>T	c.(4621-4623)Gct>Tct	p.A1541S		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1541	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AGACCCATCAGCTGTGATTGG	0.443																																					p.A1541S		Atlas-SNP	.											.	FAT4	1752	.	0			c.G4621T						.						150	139	143					4																	126242187		1959	4165	6124	SO:0001583	missense	79633	exon1			CCATCAGCTGTGA	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.4621G>T	chr4.hg19:g.126242187G>T	ENSP00000377862:p.Ala1541Ser	130.0	0.0		91.0	4.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	10.25	1.297405	0.23650	.	.	ENSG00000196159	ENST00000394329	T	0.54479	0.57	4.35	3.5	0.40072	Cadherin (2);Cadherin-like (1);	0.236802	0.20899	U	0.083677	T	0.39911	0.1096	L	0.28556	0.865	0.52501	D	0.99995	B	0.29862	0.259	B	0.35859	0.212	T	0.15407	-1.0438	10	0.25751	T	0.34	.	8.3353	0.32211	0.0833:0.1559:0.7608:0.0	.	1541	Q6V0I7	FAT4_HUMAN	S	1541	ENSP00000377862:A1541S	ENSP00000377862:A1541S	A	+	1	0	FAT4	126461637	0.994000	0.37717	0.666000	0.29783	0.988000	0.76386	3.084000	0.50143	1.186000	0.42985	0.655000	0.94253	GCT	.	.		0.443	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126242187	G	T	126242187	3	4	228	1	0	0	0	0	1	0	0	0	5700	971	34	3	4623	3	FAT4	4	126242187	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	1667	126242187	64912089	40	32136										
F11	2160	hgsc.bcm.edu	37	chr4	187201692	187201692	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	aaatacttcacgggagaggaGgcatctctggatacacatta	10	8	2	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr4:187201692G>A	ENST00000403665.2	+	10	1445	c.1093G>A	c.(1093-1095)Ggc>Agc	p.G365S	F11_ENST00000264692.4_Missense_Mutation_p.G313S	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	365	Apple 4. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	32		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	CGGGAGAGGAGGCATCTCTGG	0.368																																					p.G365S		Atlas-SNP	.											.	F11	65	.	0			c.G1093A						.						100	95	96					4																	187201692		2203	4300	6503	SO:0001583	missense	2160	exon10			AGAGGAGGCATCT	M13142	CCDS3847.1	4q35	2008-08-01	2008-08-01		ENSG00000088926	ENSG00000088926	3.4.21.27		3529	protein-coding gene	gene with protein product	"plasma thromboplastin antecedent"	264900					Standard	NM_000128		Approved	FXI	uc003iza.1	P03951	OTTHUMG00000150311	ENST00000403665.2:c.1093G>A	chr4.hg19:g.187201692G>A	ENSP00000384957:p.Gly365Ser	218.0	0.0		178.0	18.0	NM_000128	D3DP64|Q4W5C2|Q9Y495	Missense_Mutation	SNP	ENST00000403665.2	hg19	CCDS3847.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.180702	0.57800	.	.	ENSG00000088926	ENST00000403665;ENST00000264692	D;D	0.88586	-2.4;-2.4	5.37	2.65	0.31530	Apple domain (2);PAN-1 domain (1);Apple-like (1);	0.446139	0.22798	N	0.055505	D	0.83505	0.5269	L	0.50333	1.59	0.27106	N	0.962503	B	0.15719	0.014	B	0.30401	0.115	T	0.65051	-0.6262	10	0.08599	T	0.76	.	8.3232	0.32140	0.4049:0.0:0.5951:0.0	.	365	P03951	FA11_HUMAN	S	365;313	ENSP00000384957:G365S;ENSP00000264692:G313S	ENSP00000264692:G313S	G	+	1	0	F11	187438686	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	1.354000	0.34056	0.310000	0.22990	0.655000	0.94253	GGC	.	.		0.368	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4			A	187201692	G	A	187201692	3	1	228	1	0	0	0	0	1	0	0	0	5339	1000	35	3	1127	3	F11	4	187201692	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	60959505	187201692	3952584	41	32137										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5464791	5464791	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tcacacgaggtccgcctgctGactgtaagaatttaccggga	11	11	1	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:5464791G>C	ENST00000296564.7	+	13	5566	c.5344G>C	c.(5344-5346)Gac>Cac	p.D1782H		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1782					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						TCCGCCTGCTGACTGTAAGAA	0.493																																					p.D1782H		Atlas-SNP	.											KIAA0947_ENST00000296564,right_upper_lobe,carcinoma,0,1	KIAA0947	301	.	0			c.G5344C						.						29	30	30					5																	5464791		1923	4125	6048	SO:0001583	missense	23379	exon13			CCTGCTGACTGTA																												ENST00000296564.7:c.5344G>C	chr5.hg19:g.5464791G>C	ENSP00000296564:p.Asp1782His	144.0	0.0		202.0	42.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.477002	0.63849	.	.	ENSG00000164151	ENST00000296564	T	0.14640	2.49	5.41	3.62	0.41486	.	.	.	.	.	T	0.27454	0.0674	L	0.47716	1.5	0.09310	N	0.999997	D	0.76494	0.999	D	0.71870	0.975	T	0.03534	-1.1027	9	0.72032	D	0.01	-9.2346	9.3324	0.38030	0.1737:0.0:0.8263:0.0	.	1782	Q9Y2F5	K0947_HUMAN	H	1782	ENSP00000296564:D1782H	ENSP00000296564:D1782H	D	+	1	0	KIAA0947	5517791	1.000000	0.71417	0.036000	0.18154	0.429000	0.31625	4.908000	0.63307	1.282000	0.44496	0.467000	0.42956	GAC	.	.		0.493	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			C	5464791	G	C	5464791	3	2	228	1	0	0	0	0	1	0	0	0	8211	1290	45	4	5394	4	KIAA0947	5	5464791	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		5464791	175450469	42	32138										
SLC1A3	6507	hgsc.bcm.edu	37	chr5	36629633	36629633	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ctcctttcctggggaacttcTgatgaggatgttacagatgc	11	9	1	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:36629633T>C	ENST00000265113.4	+	3	739	c.263T>C	c.(262-264)cTg>cCg	p.L88P	SLC1A3_ENST00000381918.3_Missense_Mutation_p.L88P	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	88					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GGGGAACTTCTGATGAGGATG	0.413																																					p.L88P		Atlas-SNP	.											.	SLC1A3	88	.	0			c.T263C						.						266	245	252					5																	36629633		2203	4300	6503	SO:0001583	missense	6507	exon3			AACTTCTGATGAG		CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"Solute carriers"	10941	protein-coding gene	gene with protein product	"glutamate transporter variant EAAT1ex9skip"	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.263T>C	chr5.hg19:g.36629633T>C	ENSP00000265113:p.Leu88Pro	133.0	0.0		146.0	44.0	NM_004172	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	hg19	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.225763	0.79576	.	.	ENSG00000079215	ENST00000265113;ENST00000513903;ENST00000505202;ENST00000513646;ENST00000381918	T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17	5.77	5.77	0.91146	Sodium:dicarboxylate symporter, conserved site (1);	0.000000	0.64402	D	0.000001	T	0.81351	0.4804	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.99;0.998	D	0.85795	0.1370	10	0.87932	D	0	-9.3688	16.0914	0.81091	0.0:0.0:0.0:1.0	.	88;88	Q4JCQ8;P43003	.;EAA1_HUMAN	P	88	ENSP00000265113:L88P;ENSP00000427203:L88P;ENSP00000424986:L88P;ENSP00000420992:L88P;ENSP00000371343:L88P	ENSP00000265113:L88P	L	+	2	0	SLC1A3	36665390	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.669000	0.83911	2.184000	0.69523	0.533000	0.62120	CTG	.	.		0.413	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172		C	36629633	T	C	36629633	3	2	228	1	0	0	0	0	1	0	0	0	14448	1580	55	2	286	2	SLC1A3	5	36629633	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	31164842	36629633	144285627	43	32139										
NIPBL	25836	hgsc.bcm.edu	37	chr5	36976040	36976040	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gcagagtgagaaagcggcaaTgtatgatataattagttctc	11	5	1	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:36976040T>C	ENST00000282516.8	+	9	1530	c.1031T>C	c.(1030-1032)aTg>aCg	p.M344T	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Missense_Mutation_p.M344T	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	344					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			AAAGCGGCAATGTATGATATA	0.378																																					p.M344T		Atlas-SNP	.											.	NIPBL	513	.	0			c.T1031C						.						105	111	109					5																	36976040		2203	4300	6503	SO:0001583	missense	25836	exon9			CGGCAATGTATGA	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.1031T>C	chr5.hg19:g.36976040T>C	ENSP00000282516:p.Met344Thr	231.0	0.0		246.0	70.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	hg19	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.629755	0.46944	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.94092	-3.35;-3.35	5.14	5.14	0.70334	.	0.044753	0.85682	D	0.000000	D	0.87981	0.6315	N	0.24115	0.695	0.49798	D	0.999827	P;P	0.40834	0.61;0.73	B;B	0.38020	0.135;0.263	D	0.88167	0.2861	10	0.40728	T	0.16	.	14.9485	0.71050	0.0:0.0:0.0:1.0	.	344;344	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	T	344	ENSP00000282516:M344T;ENSP00000406266:M344T	ENSP00000282516:M344T	M	+	2	0	NIPBL	37011797	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.698000	0.84413	1.935000	0.56089	0.383000	0.25322	ATG	.	.		0.378	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		C	36976040	T	C	36976040	3	2	228	1	0	0	0	0	1	0	0	0	10437	1464	51	2	1061	2	NIPBL	5	36976040	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	346407	36976040	143939220	44	32140										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38435262	38435262	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ggcttcacacagattaagtgCaacacagacattttcattgg	8	9	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:38435262C>T	ENST00000354891.3	+	16	2536	c.2190C>T	c.(2188-2190)tgC>tgT	p.C730C	EGFLAM_ENST00000336740.6_Silent_p.C496C|EGFLAM_ENST00000397202.2_Silent_p.C96C|EGFLAM_ENST00000322350.5_Silent_p.C730C	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	730	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					AGATTAAGTGCAACACAGACA	0.423																																					p.C730C	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C2190T						.						104	103	104					5																	38435262		2203	4300	6503	SO:0001819	synonymous_variant	133584	exon16			TAAGTGCAACACA	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.2190C>T	chr5.hg19:g.38435262C>T		85.0	0.0		117.0	35.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	hg19	CCDS56363.1																																																																																			.	.		0.423	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		T	38435262	C	T	38435262	2	4	228	1	0	0	0	0	0	0	0	1	4968	718	25	3		3	EGFLAM	5	38435262	Silent	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	1459222	38435262	142479998	45	32141										
POLK	51426	hgsc.bcm.edu	37	chr5	74880726	74880726	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	atttccttcatatctccttgGgtctaggttcaacacacctg	6	12	4	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:74880726G>T	ENST00000241436.4	+	9	1373	c.1201G>T	c.(1201-1203)Ggt>Tgt	p.G401C	POLK_ENST00000504026.1_Missense_Mutation_p.G401C|POLK_ENST00000515295.1_Missense_Mutation_p.G401C|POLK_ENST00000380481.3_Missense_Mutation_p.G311C|POLK_ENST00000352007.5_Intron|POLK_ENST00000506928.1_3'UTR|POLK_ENST00000508526.1_Intron	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	401					DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		TATCTCCTTGGGTCTAGGTTC	0.388								DNA polymerases (catalytic subunits)																													p.G401C		Atlas-SNP	.											.	POLK	123	.	0			c.G1201T						.						202	196	198					5																	74880726		2203	4300	6503	SO:0001583	missense	51426	exon9			TCCTTGGGTCTAG	AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"DNA polymerases"	9183	protein-coding gene	gene with protein product	"polymerase (DNA-directed) kappa", "DINB protein", "DNA polymerase kappa"	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.1201G>T	chr5.hg19:g.74880726G>T	ENSP00000241436:p.Gly401Cys	199.0	0.0		185.0	42.0	NM_016218	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Missense_Mutation	SNP	ENST00000241436.4	hg19	CCDS4030.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990151	0.74589	.	.	ENSG00000122008	ENST00000241436;ENST00000515295;ENST00000504026;ENST00000380481	D;D;D;D	0.94046	-3.34;-3.34;-3.34;-3.34	5.25	5.25	0.73442	DNA polymerase, Y-family, little finger domain (1);	0.000000	0.85682	D	0.000000	D	0.97971	0.9332	H	0.95850	3.73	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99044	1.0825	10	0.87932	D	0	-18.937	19.2037	0.93722	0.0:0.0:1.0:0.0	.	401;401;401	Q5Q9G5;Q9UBT6-2;Q9UBT6	.;.;POLK_HUMAN	C	401;401;401;311	ENSP00000241436:G401C;ENSP00000424174:G401C;ENSP00000425075:G401C;ENSP00000369848:G311C	ENSP00000241436:G401C	G	+	1	0	POLK	74916482	1.000000	0.71417	0.999000	0.59377	0.485000	0.33311	9.792000	0.99085	2.606000	0.88127	0.491000	0.48974	GGT	.	.		0.388	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218		T	74880726	G	T	74880726	3	4	228	1	0	0	0	0	1	0	0	0	12213	1232	43	3	1231	3	POLK	5	74880726	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	36445464	74880726	106034534	46	32142										
MCTP1	79772	hgsc.bcm.edu	37	chr5	94204080	94204081	+	Nonsense_Mutation	DNP	GC	GC	TT													0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gggggtgaatcccaatcaaaGcaactattaacgtagtatgc							TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:94204080_94204081GC>TT	ENST00000515393.1	-	17	2392_2393	c.2393_2394GC>AA	c.(2392-2394)tGC>tAA	p.C798*	MCTP1_ENST00000312216.8_Nonsense_Mutation_p.C577*|MCTP1_ENST00000505208.1_Nonsense_Mutation_p.C577*|MCTP1_ENST00000505078.1_Nonsense_Mutation_p.C314*|MCTP1_ENST00000429576.2_Nonsense_Mutation_p.C531*	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	798					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.C798C(1)		breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		CCCAATCAAAGCAACTATTAAC	0.356																																					p.C798X|p.C798Y		Atlas-SNP	.											MCTP1,NS,carcinoma,0,2|.	MCTP1	110	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2394A|c.G2393A						.																																			SO:0001587	stop_gained	79772	exon17			ATCAAAGCAACTA|TCAAAGCAACTAT		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.2393_2394delinsTT	chr5.hg19:g.94204080_94204081delinsTT	ENSP00000424126:p.Cys798*	110.0|111.0	0.0		111.0|109.0	22.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000515393.1	hg19	CCDS34203.1																																																																																			.	.		0.356	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		TT	94204081	GC	TT	94204080	4	4	228	1	0	0	0	0	0	1	0	0	9409	963	34	3	633	3	MCTP1	5	94204080	Nonsense_Mutation	DNP	GC	TCGA-DD-AAVV-01A-11D-A40R-10	19323354	94204080	86711180	47	32143										
FBN2	2201	hgsc.bcm.edu	37	chr5	127610297	127610297	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gctgtgtgaaaccaggtggaCatttacaggtaaaccccccc	10	12	0	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:127610297C>T	ENST00000508053.1	-	66	8647	c.7673G>A	c.(7672-7674)tGt>tAt	p.C2558Y	FBN2_ENST00000262464.4_Missense_Mutation_p.C2558Y			P35556	FBN2_HUMAN	fibrillin 2	2558	EGF-like 43; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ACCAGGTGGACATTTACAGGT	0.398																																					p.C2558Y		Atlas-SNP	.											.	FBN2	858	.	0			c.G7673A						.						99	95	97					5																	127610297		2203	4300	6503	SO:0001583	missense	2201	exon60			GGTGGACATTTAC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.7673G>A	chr5.hg19:g.127610297C>T	ENSP00000424571:p.Cys2558Tyr	169.0	0.0		127.0	6.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.709294	0.89018	.	.	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.99445	-5.91;-5.91	4.92	4.92	0.64577	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000004	D	0.99743	0.9898	H	0.97214	3.96	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	D	0.97148	0.9829	10	0.87932	D	0	.	18.6729	0.91518	0.0:1.0:0.0:0.0	.	2558	P35556	FBN2_HUMAN	Y	2558	ENSP00000262464:C2558Y;ENSP00000424571:C2558Y	ENSP00000262464:C2558Y	C	-	2	0	FBN2	127638196	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.609000	0.82925	2.701000	0.92244	0.585000	0.79938	TGT	.	.		0.398	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127610297	C	T	127610297	3	4	228	1	0	0	0	0	1	0	0	0	5711	478	17	3	1089	3	FBN2	5	127610297	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	33406217	127610297	53304963	48	32144										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153144134	153144134	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gagtgcagaggacctagcgaAgcagacagaaattgcctacg	13	9	0	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:153144134A>G	ENST00000285900.5	+	12	2307	c.1964A>G	c.(1963-1965)aAg>aGg	p.K655R	GRIA1_ENST00000340592.5_Missense_Mutation_p.K655R|GRIA1_ENST00000518783.1_Missense_Mutation_p.K665R|GRIA1_ENST00000521843.2_Missense_Mutation_p.K586R|GRIA1_ENST00000448073.4_Missense_Mutation_p.K665R|GRIA1_ENST00000518142.1_Missense_Mutation_p.K575R	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	655					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	GACCTAGCGAAGCAGACAGAA	0.502																																					p.K665R		Atlas-SNP	.											.	GRIA1	321	.	0			c.A1994G						.						117	97	104					5																	153144134		2203	4300	6503	SO:0001583	missense	2890	exon12			TAGCGAAGCAGAC		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.1964A>G	chr5.hg19:g.153144134A>G	ENSP00000285900:p.Lys655Arg	109.0	0.0		121.0	12.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.573999	0.86542	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.38401	1.68;1.68;1.14;1.68;1.68;1.68;1.14	5.27	5.27	0.74061	Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.46521	0.1397	N	0.21142	0.635	0.80722	D	1	D;D;B;D;D	0.76494	0.999;0.999;0.022;0.999;0.997	D;D;B;D;D	0.85130	0.997;0.997;0.071;0.995;0.951	T	0.51317	-0.8721	10	0.87932	D	0	.	14.3539	0.66722	1.0:0.0:0.0:0.0	.	665;665;575;655;655	E7ESV8;B7Z9G9;B7Z3F6;P42261-2;P42261	.;.;.;.;GRIA1_HUMAN	R	655;655;575;609;655;588;586;665;665	ENSP00000285900:K655R;ENSP00000427920:K575R;ENSP00000339343:K655R;ENSP00000427864:K588R;ENSP00000442108:K586R;ENSP00000428994:K665R;ENSP00000415569:K665R	ENSP00000285900:K655R	K	+	2	0	GRIA1	153124327	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.125000	0.94402	1.980000	0.57719	0.459000	0.35465	AAG	.	.		0.502	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			G	153144134	A	G	153144134	3	3	228	1	0	0	0	0	1	0	0	0	6776	72	3	2	2010	2	GRIA1	5	153144134	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	25533837	153144134	27771126	49	32145										
KIF4B	285643	hgsc.bcm.edu	37	chr5	154393731	154393731	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	atgggaggtgcatacactgcGgagcaggagaatgaaccaac	14	8	0	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:154393731G>A	ENST00000435029.4	+	1	472	c.312G>A	c.(310-312)gcG>gcA	p.A104A		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	104	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CATACACTGCGGAGCAGGAGA	0.413																																					p.A104A		Atlas-SNP	.											.	KIF4B	307	.	0			c.G312A						.						100	106	104					5																	154393731		2203	4300	6503	SO:0001819	synonymous_variant	285643	exon1			CACTGCGGAGCAG	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"Kinesins"	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.312G>A	chr5.hg19:g.154393731G>A		296.0	0.0		322.0	24.0	NM_001099293		Silent	SNP	ENST00000435029.4	hg19	CCDS47324.1																																																																																			.	.		0.413	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			A	154393731	G	A	154393731	2	1	228	1	0	0	0	0	0	0	0	1	8313	1103	39	1		1	KIF4B	5	154393731	Silent	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	1249597	154393731	26521529	50	32146										
SH3PXD2B	285590	hgsc.bcm.edu	37	chr5	171766310	171766310	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cttccttggccaagaccttgTggccacactccagccccatg	8	17	0	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:171766310T>G	ENST00000311601.5	-	13	1969	c.1799A>C	c.(1798-1800)cAc>cCc	p.H600P	SH3PXD2B_ENST00000519643.1_Intron	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	600					adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CAAGACCTTGTGGCCACACTC	0.557																																					p.H600P		Atlas-SNP	.											.	SH3PXD2B	91	.	0			c.A1799C						.						54	62	59					5																	171766310		2200	4300	6500	SO:0001583	missense	285590	exon13			ACCTTGTGGCCAC	AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"KIAA1295"	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.1799A>C	chr5.hg19:g.171766310T>G	ENSP00000309714:p.His600Pro	70.0	0.0		77.0	23.0	NM_001017995	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	hg19	CCDS34291.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735696	0.69189	.	.	ENSG00000174705	ENST00000311601	T	0.65178	-0.14	5.74	5.74	0.90152	.	2.017670	0.02558	N	0.096410	T	0.75903	0.3913	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.55173	-0.8182	9	.	.	.	-34.7274	13.975	0.64268	0.0:0.0:0.0:1.0	.	600	A1X283	SPD2B_HUMAN	P	600	ENSP00000309714:H600P	.	H	-	2	0	SH3PXD2B	171698915	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.843000	0.69424	2.189000	0.69895	0.459000	0.35465	CAC	.	.		0.557	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963		G	171766310	T	G	171766310	3	3	228	1	0	0	0	0	1	0	0	0	14272	1696	59	5	940	5	SH3PXD2B	5	171766310	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	17372579	171766310	9148950	51	32147										
RASGEF1C	255426	hgsc.bcm.edu	37	chr5	179555536	179555536	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ttgtcggcacccaccagaccTtctggcccctggcgcagagc	11	17	1	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr5:179555536T>G	ENST00000393371.2	-	4	809	c.513A>C	c.(511-513)gaA>gaC	p.E171D	RASGEF1C_ENST00000519883.1_5'UTR|RASGEF1C_ENST00000522500.1_Missense_Mutation_p.E20D|RASGEF1C_ENST00000361132.4_Missense_Mutation_p.E171D			Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C	171					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	12	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCACCAGACCTTCTGGCCCCT	0.627																																					p.E171D		Atlas-SNP	.											.	RASGEF1C	81	.	0			c.A513C						.						73	63	67					5																	179555536		2203	4300	6503	SO:0001583	missense	255426	exon5			CAGACCTTCTGGC	AK093160	CCDS4452.1	5q35.3	2005-08-16			ENSG00000146090	ENSG00000146090			27400	protein-coding gene	gene with protein product						12477932	Standard	XM_006714839		Approved	FLJ35841	uc003mlr.3	Q8N431	OTTHUMG00000130914	ENST00000393371.2:c.513A>C	chr5.hg19:g.179555536T>G	ENSP00000377037:p.Glu171Asp	90.0	0.0		81.0	5.0	NM_175062	D3DWQ7|Q7Z4T0|Q8NA49	Missense_Mutation	SNP	ENST00000393371.2	hg19	CCDS4452.1	.	.	.	.	.	.	.	.	.	.	T	11.96	1.794274	0.31777	.	.	ENSG00000146090	ENST00000361132;ENST00000393371;ENST00000522500	T;T;T	0.29655	1.56;1.56;1.56	4.31	3.09	0.35607	Ras guanine nucleotide exchange factor, domain (1);	0.058075	0.64402	N	0.000002	T	0.32496	0.0831	M	0.69823	2.125	0.41724	D	0.98952	B	0.25235	0.121	B	0.31751	0.135	T	0.06954	-1.0798	10	0.26408	T	0.33	.	9.057	0.36412	0.165:0.0:0.0:0.835	.	171	Q8N431	RGF1C_HUMAN	D	171;171;20	ENSP00000354963:E171D;ENSP00000377037:E171D;ENSP00000429114:E20D	ENSP00000354963:E171D	E	-	3	2	RASGEF1C	179488142	1.000000	0.71417	0.438000	0.26821	0.077000	0.17291	1.678000	0.37586	0.595000	0.29777	0.402000	0.26972	GAA	.	.		0.627	RASGEF1C-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253506.2	NM_175062		G	179555536	T	G	179555536	3	3	228	1	0	0	0	0	1	0	0	0	13086	1606	56	5	927	5	RASGEF1C	5	179555536	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	7789226	179555536	1359724	52	32148										
SLC44A4	80736	hgsc.bcm.edu	37	chr6	31839271	31839271	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ctgatcccctgctgtatggtGgtgtcattggtgatccctgg	13	10	1	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr6:31839271G>A	ENST00000229729.6	-	8	617	c.597C>T	c.(595-597)acC>acT	p.T199T	SLC44A4_ENST00000544672.1_Silent_p.T123T|SLC44A4_ENST00000375562.4_Silent_p.T157T	NM_025257.2	NP_079533.2	Q53GD3	CTL4_HUMAN	solute carrier family 44, member 4	199					acetylcholine biosynthetic process (GO:0008292)|acetylcholine secretion (GO:0061526)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of cell growth (GO:0030307)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(1)|urinary_tract(2)	35					Choline(DB00122)	GCTGTATGGTGGTGTCATTGG	0.642																																					p.T199T		Atlas-SNP	.											.	SLC44A4	67	.	0			c.C597T						.						163	139	147					6																	31839271		2203	4300	6503	SO:0001819	synonymous_variant	80736	exon8			TATGGTGGTGTCA	AF134726	CCDS4724.2, CCDS54989.1, CCDS54990.1	6p21.3	2014-02-17	2005-09-06	2005-09-06	ENSG00000204385	ENSG00000204385		"Solute carriers"	13941	protein-coding gene	gene with protein product		606107	"chromosome 6 open reading frame 29"	C6orf29		10677542, 15715662, 24379411	Standard	NM_025257		Approved	NG22, CTL4, FLJ14491, TPPT	uc010jti.3	Q53GD3	OTTHUMG00000031133	ENST00000229729.6:c.597C>T	chr6.hg19:g.31839271G>A		114.0	0.0		104.0	5.0	NM_025257	A2BED3|B0UXX8|B0UZY8|B4DU94|B4DWM2|E9PEK7|Q5JP84|Q5JQ93|Q658S8|Q6UX89|Q8TEW4|Q96C58|Q96K59|Q9Y332	Silent	SNP	ENST00000229729.6	hg19	CCDS4724.2	.	.	.	.	.	.	.	.	.	.	G	3.640	-0.073786	0.07184	.	.	ENSG00000204385	ENST00000414427	.	.	.	4.07	-1.19	0.09585	.	.	.	.	.	T	0.07324	0.0185	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35822	-0.9773	4	.	.	.	-3.2465	1.5687	0.02610	0.1916:0.2999:0.3552:0.1533	.	.	.	.	L	195	.	.	P	-	2	0	SLC44A4	31947250	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.391000	0.07323	-0.192000	0.10432	0.491000	0.48974	CCA	.	.		0.642	SLC44A4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076234.3			A	31839271	G	A	31839271	2	1	228	1	0	0	0	0	0	0	0	1	14653	1335	47	3		3	SLC44A4	6	31839271	Silent	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		31839271	139275796	53	32149										
EPHA7	2045	hgsc.bcm.edu	37	chr6	93956641	93956641	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	caatccaacattagctggtgAaggccagctgggcagtccat	11	11	0	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr6:93956641A>T	ENST00000369303.4	-	15	2779	c.2595T>A	c.(2593-2595)ctT>ctA	p.L865L		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	865	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TTAGCTGGTGAAGGCCAGCTG	0.388																																					p.L865L		Atlas-SNP	.											.	EPHA7	251	.	0			c.T2595A						.						94	93	94					6																	93956641		2203	4300	6503	SO:0001819	synonymous_variant	2045	exon15			CTGGTGAAGGCCA	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2595T>A	chr6.hg19:g.93956641A>T		171.0	0.0		162.0	7.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Silent	SNP	ENST00000369303.4	hg19	CCDS5031.1																																																																																			.	.		0.388	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			T	93956641	A	T	93956641	2	4	228	1	0	0	0	0	0	0	0	1	5174	233	9	4		4	EPHA7	6	93956641	Silent	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	62117370	93956641	77158426	54	32150										
KIAA1919	91749	hgsc.bcm.edu	37	chr6	111587870	111587870	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cttccctgggagaaatggctAttcctgcagtcattggaatt	10	9	1	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr6:111587870A>G	ENST00000368847.4	+	4	1458	c.1105A>G	c.(1105-1107)Att>Gtt	p.I369V		NM_153369.2	NP_699200.2	Q5TF39	NAGT1_HUMAN	KIAA1919	369					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			large_intestine(3)|lung(2)|ovary(4)|skin(3)	12		all_cancers(87;2.35e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.055)|all cancers(137;0.0871)|Epithelial(106;0.0884)		AGAAATGGCTATTCCTGCAGT	0.423																																					p.I369V		Atlas-SNP	.											.	KIAA1919	54	.	0			c.A1105G						.						102	104	103					6																	111587870		2203	4300	6503	SO:0001583	missense	91749	exon4			ATGGCTATTCCTG	BC036115	CCDS5090.1	6q22	2013-10-02			ENSG00000173214	ENSG00000173214			21053	protein-coding gene	gene with protein product							Standard	NM_153369		Approved	MGC33953, MFSD4B	uc003puv.4	Q5TF39	OTTHUMG00000015372	ENST00000368847.4:c.1105A>G	chr6.hg19:g.111587870A>G	ENSP00000357840:p.Ile369Val	113.0	0.0		98.0	24.0	NM_153369	A8K9M0|Q8IYB6|Q96PW9|Q9P0D6	Missense_Mutation	SNP	ENST00000368847.4	hg19	CCDS5090.1	.	.	.	.	.	.	.	.	.	.	A	13.41	2.229792	0.39399	.	.	ENSG00000173214	ENST00000368847	T	0.80566	-1.39	5.92	5.92	0.95590	Major facilitator superfamily domain, general substrate transporter (1);	0.106561	0.64402	D	0.000003	T	0.69196	0.3084	L	0.58428	1.81	0.35933	D	0.832676	B	0.21606	0.058	B	0.18871	0.023	T	0.68731	-0.5331	10	0.39692	T	0.17	-14.5832	16.3615	0.83270	1.0:0.0:0.0:0.0	.	369	Q5TF39	NAGT1_HUMAN	V	369	ENSP00000357840:I369V	ENSP00000357840:I369V	I	+	1	0	KIAA1919	111694563	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.017000	0.64047	2.264000	0.75181	0.450000	0.29827	ATT	.	.		0.423	KIAA1919-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041827.1	NM_153369		G	111587870	A	G	111587870	3	3	228	1	0	0	0	0	1	0	0	0	8271	449	16	2	1119	2	KIAA1919	6	111587870	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	17631229	111587870	59527197	55	32151										
TCF21	6943	hgsc.bcm.edu	37	chr6	134210652	134210652	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	acttccaacgagagcaccgaGgagagctccaactgcgagaa	11	12	0	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr6:134210652G>A	ENST00000367882.4	+	1	377	c.117G>A	c.(115-117)gaG>gaA	p.E39E	TCF21_ENST00000237316.3_Silent_p.E39E|RP3-323P13.2_ENST00000606544.1_RNA|RP3-323P13.2_ENST00000607573.1_RNA|RP3-323P13.2_ENST00000607641.1_RNA|RP3-323P13.2_ENST00000607033.1_RNA	NM_003206.3	NP_003197.2	O43680	TCF21_HUMAN	transcription factor 21	39					branching involved in ureteric bud morphogenesis (GO:0001658)|branchiomeric skeletal muscle development (GO:0014707)|bronchiole development (GO:0060435)|diaphragm development (GO:0060539)|embryonic digestive tract morphogenesis (GO:0048557)|epithelial cell differentiation (GO:0030855)|gland development (GO:0048732)|glomerulus development (GO:0032835)|kidney development (GO:0001822)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lung vasculature development (GO:0060426)|metanephric glomerular capillary formation (GO:0072277)|metanephric mesenchymal cell differentiation (GO:0072162)|morphogenesis of a branching structure (GO:0001763)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|reproductive structure development (GO:0048608)|respiratory system development (GO:0060541)|Sertoli cell differentiation (GO:0060008)|sex determination (GO:0007530)|spleen development (GO:0048536)|ureteric bud development (GO:0001657)|vasculature development (GO:0001944)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	13	Colorectal(23;0.221)|Breast(56;0.247)			GBM - Glioblastoma multiforme(68;0.00518)|OV - Ovarian serous cystadenocarcinoma(155;0.00783)		AGAGCACCGAGGAGAGCTCCA	0.582																																					p.E39E		Atlas-SNP	.											.	TCF21	30	.	0			c.G117A						.						53	61	58					6																	134210652		2203	4300	6503	SO:0001819	synonymous_variant	6943	exon1			CACCGAGGAGAGC	AF047419	CCDS5167.1	6q23.2	2014-09-17			ENSG00000118526	ENSG00000118526		"Basic helix-loop-helix proteins"	11632	protein-coding gene	gene with protein product		603306				9507058	Standard	NM_198392		Approved	POD1, bHLHa23	uc003qei.4	O43680	OTTHUMG00000015608	ENST00000367882.4:c.117G>A	chr6.hg19:g.134210652G>A		183.0	0.0		159.0	34.0	NM_003206	E1P581|O43545|Q6ICV0|Q9BZ14	Silent	SNP	ENST00000367882.4	hg19	CCDS5167.1																																																																																			.	.		0.582	TCF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042292.1	NM_198392		A	134210652	G	A	134210652	2	1	228	1	0	0	0	0	0	0	0	1	15706	991	35	3		3	TCF21	6	134210652	Silent	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	22622782	134210652	36904415	56	32152										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159646690	159646690	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gtgtatgaatttgcagtccgTatttcacagggtgaaagaga	12	5	1	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr6:159646690T>C	ENST00000297267.9	+	8	1208	c.1008T>C	c.(1006-1008)cgT>cgC	p.R336R	FNDC1_ENST00000480856.1_3'UTR|FNDC1_ENST00000340366.6_Silent_p.R336R	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	336	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TTGCAGTCCGTATTTCACAGG	0.438																																					p.R336R		Atlas-SNP	.											FNDC1,NS,carcinoma,+2,1	FNDC1	250	.	0			c.T1008C						.						157	159	159					6																	159646690		1925	4128	6053	SO:0001819	synonymous_variant	84624	exon8			AGTCCGTATTTCA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.1008T>C	chr6.hg19:g.159646690T>C		97.0	0.0		122.0	10.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	hg19	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	T	10.06	1.247955	0.22880	.	.	ENSG00000164694	ENST00000329629	.	.	.	5.75	-8.09	0.01090	.	.	.	.	.	T	0.20170	0.0485	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40646	-0.9552	4	.	.	.	-17.9844	3.6242	0.08107	0.1139:0.3912:0.2554:0.2395	.	.	.	.	H	295	.	.	Y	+	1	0	FNDC1	159566678	0.000000	0.05858	0.310000	0.25168	0.981000	0.71138	-2.427000	0.01026	-1.615000	0.01573	-0.389000	0.06534	TAT	.	.		0.438	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		C	159646690	T	C	159646690	2	2	228	1	0	0	0	0	0	0	0	1	5976	1625	57	2		2	FNDC1	6	159646690	Silent	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	25436038	159646690	11468377	57	32153										
C6orf70	55780	hgsc.bcm.edu	37	chr6	170156445	170156445	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tgtaaatagttatttcctgaAatatttgatgccttggaaag	8	4	0	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr6:170156445A>G	ENST00000366773.3	+	4	360	c.327A>G	c.(325-327)gaA>gaG	p.E109E	ERMARD_ENST00000392095.4_5'UTR|ERMARD_ENST00000588451.1_5'UTR|ERMARD_ENST00000366772.2_Silent_p.E109E|ERMARD_ENST00000418781.3_Silent_p.E109E	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	109					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TATTTCCTGAAATATTTGATG	0.338																																					p.E109E		Atlas-SNP	.											.	C6orf70	63	.	0			c.A327G						.						97	95	96					6																	170156445		2203	4300	6503	SO:0001819	synonymous_variant	55780	exon4			TCCTGAAATATTT	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"chromosome 6 open reading frame 70"	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.327A>G	chr6.hg19:g.170156445A>G		112.0	0.0		118.0	12.0	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Silent	SNP	ENST00000366773.3	hg19	CCDS34576.1																																																																																			.	.		0.338	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341		G	170156445	A	G	170156445	2	3	228	1	0	0	0	0	0	0	0	1	2372	11	1	2		2	C6orf70	6	170156445	Silent	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	10509755	170156445	958622	58	32154										
CHST12	55501	hgsc.bcm.edu	37	chr7	2473077	2473077	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ggagaacgaggagttctaccGcaagttcgccgtgcccatgc	13	12	1	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr7:2473077G>T	ENST00000258711.6	+	2	938	c.803G>T	c.(802-804)cGc>cTc	p.R268L		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	268					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		GAGTTCTACCGCAAGTTCGCC	0.647																																					p.R268L		Atlas-SNP	.											CHST12,NS,carcinoma,0,1	CHST12	39	.	0			c.G803T						.						67	59	62					7																	2473077		2203	4299	6502	SO:0001583	missense	55501	exon2			TCTACCGCAAGTT	AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"Sulfotransferases, membrane-bound"	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.803G>T	chr7.hg19:g.2473077G>T	ENSP00000258711:p.Arg268Leu	44.0	0.0		39.0	2.0	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	hg19	CCDS5333.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.134208	0.56828	.	.	ENSG00000136213	ENST00000258711	T	0.74315	-0.83	5.27	3.34	0.38264	.	0.206543	0.40469	N	0.001098	T	0.75591	0.3870	L	0.51422	1.61	0.45097	D	0.998116	D	0.54397	0.966	P	0.54270	0.747	T	0.74352	-0.3693	10	0.41790	T	0.15	-4.7691	10.7909	0.46432	0.1619:0.0:0.8381:0.0	.	268	Q9NRB3	CHSTC_HUMAN	L	268	ENSP00000258711:R268L	ENSP00000258711:R268L	R	+	2	0	CHST12	2439603	1.000000	0.71417	0.818000	0.32626	0.982000	0.71751	2.055000	0.41345	1.111000	0.41721	0.462000	0.41574	CGC	.	.		0.647	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641		T	2473077	G	T	2473077	3	4	228	1	0	0	0	0	1	0	0	0	3402	1087	38	1	805	1	CHST12	7	2473077	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		2473077	156665586	59	32155										
DGKI	9162	hgsc.bcm.edu	37	chr7	137092695	137092695	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gaaggagtgaacagtggtctGgtccctgaattagcagactg	14	7	1	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr7:137092695G>T	ENST00000288490.5	-	31	2870	c.2870C>A	c.(2869-2871)cCa>cAa	p.P957Q	DGKI_ENST00000446122.1_Missense_Mutation_p.P939Q|DGKI_ENST00000424189.2_Missense_Mutation_p.P970Q|DGKI_ENST00000494390.1_5'UTR|DGKI_ENST00000453654.2_Missense_Mutation_p.P626Q	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	957					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						ACAGTGGTCTGGTCCCTGAAT	0.433																																					p.P957Q		Atlas-SNP	.											.	DGKI	335	.	0			c.C2870A						.						198	175	183					7																	137092695		2203	4300	6503	SO:0001583	missense	9162	exon31			TGGTCTGGTCCCT	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2870C>A	chr7.hg19:g.137092695G>T	ENSP00000288490:p.Pro957Gln	154.0	0.0		129.0	9.0	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	hg19	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	G	12.68	2.010151	0.35415	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.33654	1.4;1.4;1.4	5.7	5.7	0.88788	Ankyrin repeat-containing domain (2);	0.169399	0.53938	D	0.000047	T	0.21590	0.0520	N	0.08118	0	0.46927	D	0.999257	B;B	0.16396	0.002;0.017	B;B	0.12837	0.004;0.008	T	0.09773	-1.0659	10	0.14656	T	0.56	.	18.0216	0.89257	0.0:0.0:1.0:0.0	.	626;957	E9PFX6;O75912	.;DGKI_HUMAN	Q	626;874;960;957;939	ENSP00000392161:P626Q;ENSP00000288490:P957Q;ENSP00000399131:P939Q	ENSP00000288490:P957Q	P	-	2	0	DGKI	136743235	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.370000	0.73114	2.683000	0.91414	0.655000	0.94253	CCA	.	.		0.433	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		T	137092695	G	T	137092695	3	4	228	1	0	0	0	0	1	0	0	0	4473	1348	47	3	343	3	DGKI	7	137092695	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	134619618	137092695	22045968	60	32156										
AGAP3	116988	hgsc.bcm.edu	37	chr7	150814237	150814237	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cctggtgcaccgctatctgaCggggacctatgtccaggagg	14	12	1	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr7:150814237C>T	ENST00000397238.2	+	3	446	c.446C>T	c.(445-447)aCg>aTg	p.T149M	AGAP3_ENST00000473312.1_Missense_Mutation_p.T149M|AGAP3_ENST00000479901.1_Missense_Mutation_p.T149M|AGAP3_ENST00000463381.1_5'UTR|AGAP3_ENST00000335367.3_Missense_Mutation_p.T329M|AGAP3_ENST00000476375.1_3'UTR	NM_031946.4	NP_114152.3	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	113	Small GTPase-like.				cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						CGCTATCTGACGGGGACCTAT	0.667																																					p.T149M		Atlas-SNP	.											.	AGAP3	121	.	0			c.C446T						.						57	61	60					7																	150814237		2099	4266	6365	SO:0001583	missense	116988	exon3			ATCTGACGGGGAC	AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16923	protein-coding gene	gene with protein product			"centaurin, gamma 3"	CENTG3			Standard	NM_001042535		Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000397238.2:c.446C>T	chr7.hg19:g.150814237C>T	ENSP00000380413:p.Thr149Met	115.0	0.0		114.0	21.0	NM_001042535	B3KNZ8|E9PAL8|Q59EN0|Q96RK3	Missense_Mutation	SNP	ENST00000397238.2	hg19	CCDS43681.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.7|24.7	4.561984|4.561984	0.86335|0.86335	.|.	.|.	ENSG00000133612|ENSG00000133612	ENST00000469901|ENST00000473312;ENST00000479901;ENST00000397238;ENST00000335355;ENST00000335367	.|T;T;T;T	.|0.23552	.|1.9;1.9;1.9;1.9	4.42|4.42	3.52|3.52	0.40303|0.40303	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.57621|0.57621	0.2066|0.2066	M|M	0.91717|0.91717	3.235|3.235	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.81914	.|0.989;0.974;0.955;0.995	T|T	0.68588|0.68588	-0.5369|-0.5369	5|10	.|0.87932	.|D	.|0	.|.	13.4421|13.4421	0.61119|0.61119	0.0:0.8416:0.1584:0.0|0.0:0.8416:0.1584:0.0	.|.	.|149;329;149;149	.|C9J975;E7ESL9;Q96P47-4;E9PAL8	.|.;.;.;.	W|M	85|149;149;149;113;329	.|ENSP00000418921:T149M;ENSP00000418125:T149M;ENSP00000380413:T149M;ENSP00000335589:T329M	.|ENSP00000334157:T113M	R|T	+|+	1|2	2|0	AGAP3|AGAP3	150445170|150445170	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.985000|0.985000	0.73830|0.73830	7.569000|7.569000	0.82380|0.82380	1.070000|1.070000	0.40811|0.40811	0.407000|0.407000	0.27541|0.27541	CGG|ACG	.	.		0.667	AGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351908.3	NM_031946		T	150814237	C	T	150814237	3	4	228	1	0	0	0	0	1	0	0	0	369	536	19	1	456	1	AGAP3	7	150814237	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	13721542	150814237	8324426	61	32157										
REEP4	80346	hgsc.bcm.edu	37	chr8	21998971	21998971	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cggccatactcacaccaccaGgcgacagatcatccaggaca	8	16	2	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr8:21998971G>T	ENST00000306306.3	-	1	493	c.25C>A	c.(25-27)Ctg>Atg	p.L9M	REEP4_ENST00000523293.1_Missense_Mutation_p.L9M|REEP4_ENST00000334530.5_Missense_Mutation_p.L9M	NM_025232.2	NP_079508.2	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	9					mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|nuclear envelope organization (GO:0006998)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)	microtubule binding (GO:0008017)			kidney(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	7				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)		CACACCACCAGGCGACAGATC	0.642																																					p.L9M		Atlas-SNP	.											.	REEP4	13	.	0			c.C25A						.						133	128	130					8																	21998971		2203	4300	6503	SO:0001583	missense	80346	exon1			CCACCAGGCGACA	BC013048	CCDS6024.1	8p21.3	2008-05-02	2006-02-07	2006-02-07	ENSG00000168476	ENSG00000168476		"Receptor accessory proteins"	26176	protein-coding gene	gene with protein product		609349	"chromosome 8 open reading frame 20"	C8orf20		16271481, 15550249	Standard	NM_025232		Approved	FLJ22246, FLJ22277, PP432	uc003xau.1	Q9H6H4	OTTHUMG00000131491	ENST00000306306.3:c.25C>A	chr8.hg19:g.21998971G>T	ENSP00000303482:p.Leu9Met	113.0	0.0		129.0	29.0	NM_025232	D3DSQ9|Q86VL1|Q9H6I5|Q9HBP4	Missense_Mutation	SNP	ENST00000306306.3	hg19	CCDS6024.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.561571	0.65538	.	.	ENSG00000168476	ENST00000334530;ENST00000306306;ENST00000523293;ENST00000518664;ENST00000521744	D;D;D;D;D	0.94184	-3.37;-3.37;-3.37;-3.37;-3.37	5.48	2.68	0.31781	.	0.000000	0.35805	N	0.002973	D	0.96207	0.8763	M	0.93016	3.37	0.35947	D	0.833635	D;P;P	0.54964	0.969;0.553;0.8	P;B;B	0.61275	0.886;0.26;0.404	D	0.96684	0.9506	10	0.66056	D	0.02	-15.4853	7.1705	0.25717	0.2624:0.0:0.7376:0.0	.	9;9;9	B4DYB6;Q9H6H4-2;Q9H6H4	.;.;REEP4_HUMAN	M	9	ENSP00000333889:L9M;ENSP00000303482:L9M;ENSP00000428709:L9M;ENSP00000428160:L9M;ENSP00000429451:L9M	ENSP00000303482:L9M	L	-	1	2	REEP4	22054916	0.977000	0.34250	1.000000	0.80357	0.993000	0.82548	0.215000	0.17562	1.317000	0.45149	0.511000	0.50034	CTG	.	.		0.642	REEP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254337.2	NM_025232		T	21998971	G	T	21998971	3	4	228	1	0	0	0	0	1	0	0	0	13222	991	35	3	780	3	REEP4	8	21998971	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		21998971	124365051	62	32158										
PREX2	80243	hgsc.bcm.edu	37	chr8	69021855	69021855	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gatgtgtgtttgtcaaatagAtgagtaagtgttttgtacta	11	2	1	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr8:69021855A>T	ENST00000288368.4	+	25	3420	c.3143A>T	c.(3142-3144)gAt>gTt	p.D1048V		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1048					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TGTCAAATAGATGAGTAAGTG	0.343																																					p.D1048V		Atlas-SNP	.											.	PREX2	614	.	0			c.A3143T						.						103	101	102					8																	69021855		2203	4300	6503	SO:0001583	missense	80243	exon25			AAATAGATGAGTA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3143A>T	chr8.hg19:g.69021855A>T	ENSP00000288368:p.Asp1048Val	155.0	0.0		185.0	25.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.652602	0.88056	.	.	ENSG00000046889	ENST00000288368	T	0.60171	0.21	5.72	5.72	0.89469	.	.	.	.	.	T	0.53883	0.1824	L	0.29908	0.895	0.80722	D	1	P	0.49090	0.919	P	0.46543	0.52	T	0.59830	-0.7380	9	0.87932	D	0	.	16.0037	0.80327	1.0:0.0:0.0:0.0	.	1048	Q70Z35	PREX2_HUMAN	V	1048	ENSP00000288368:D1048V	ENSP00000288368:D1048V	D	+	2	0	PREX2	69184409	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.730000	0.91510	2.184000	0.69523	0.533000	0.62120	GAT	.	.		0.343	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	69021855	A	T	69021855	3	4	228	1	0	0	0	0	1	0	0	0	12489	333	12	4	3470	4	PREX2	8	69021855	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	47022884	69021855	77342167	63	32159										
EIF3H	8667	hgsc.bcm.edu	37	chr8	117671203	117671203	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tggcgaaggctccgcatcatTtccatctgatattggactgg	11	10	2	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr8:117671203T>G	ENST00000276682.4	-	5	1114	c.348A>C	c.(346-348)gaA>gaC	p.E116D	EIF3H_ENST00000521861.1_Missense_Mutation_p.E102D					eukaryotic translation initiation factor 3, subunit H											large_intestine(2)|lung(10)|skin(1)	13	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)					TCCGCATCATTTCCATCTGAT	0.418																																					p.E102D		Atlas-SNP	.											.	EIF3H	28	.	0			c.A306C						.						99	88	92					8																	117671203		2203	4300	6503	SO:0001583	missense	8667	exon3			CATCATTTCCATC	U54559	CCDS6319.1	8q24.11	2007-07-27	2007-07-27	2007-07-27	ENSG00000147677	ENSG00000147677			3273	protein-coding gene	gene with protein product		603912	"eukaryotic translation initiation factor 3, subunit 3 gamma, 40kDa"	EIF3S3		9341143	Standard	NM_003756		Approved	eIF3-gamma, eIF3-p40, eIF3h	uc003yoa.3	O15372	OTTHUMG00000164919	ENST00000276682.4:c.348A>C	chr8.hg19:g.117671203T>G	ENSP00000276682:p.Glu116Asp	159.0	0.0		160.0	22.0	NM_003756		Missense_Mutation	SNP	ENST00000276682.4	hg19		.	.	.	.	.	.	.	.	.	.	T	12.50	1.956634	0.34565	.	.	ENSG00000147677	ENST00000521861;ENST00000276682;ENST00000518949;ENST00000518995;ENST00000522453	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	6.17	-1.6	0.08426	.	0.000000	0.85682	D	0.000000	T	0.43634	0.1256	N	0.20881	0.62	0.53688	D	0.999974	B;P;P	0.41978	0.003;0.767;0.767	B;P;P	0.49752	0.018;0.621;0.621	T	0.23048	-1.0199	10	0.39692	T	0.17	-28.2358	11.0707	0.48002	0.0:0.3826:0.0:0.6174	.	102;116;102	B4DJN9;B3KS98;O15372	.;.;EIF3H_HUMAN	D	102;116;70;118;126	ENSP00000429931:E102D;ENSP00000276682:E116D;ENSP00000428195:E70D;ENSP00000428669:E118D	ENSP00000276682:E116D	E	-	3	2	EIF3H	117740384	1.000000	0.71417	0.980000	0.43619	0.942000	0.58702	2.028000	0.41088	-0.494000	0.06669	-0.250000	0.11733	GAA	.	.		0.418	EIF3H-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000380913.1	NM_003756		G	117671203	T	G	117671203	3	3	228	1	0	0	0	0	1	0	0	0	5020	1838	64	5	776	5	EIF3H	8	117671203	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	48649348	117671203	28692819	64	32160										
MED30	90390	hgsc.bcm.edu	37	chr8	118540924	118540924	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cacttaccacactggaacatAtcaagaccggttaacaaagc	6	12	1	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr8:118540924A>T	ENST00000297347.3	+	2	376	c.212A>T	c.(211-213)tAt>tTt	p.Y71F	MED30_ENST00000522839.1_Missense_Mutation_p.Y71F	NM_080651.2	NP_542382.1	Q96HR3	MED30_HUMAN	mediator complex subunit 30	71					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			kidney(1)|lung(3)|prostate(3)	7	all_cancers(13;3.41e-25)|Lung NSC(37;3.02e-05)|Ovarian(258;0.00163)		STAD - Stomach adenocarcinoma(47;0.0266)			ACTGGAACATATCAAGACCGG	0.343																																					p.Y71F	Melanoma(81;817 1341 9674 26244 29255)	Atlas-SNP	.											.	MED30	15	.	0			c.A212T						.						116	110	112					8																	118540924		2203	4300	6503	SO:0001583	missense	90390	exon2			GAACATATCAAGA	AY083305	CCDS6323.1, CCDS64959.1	8q24.11	2007-07-30	2007-07-30	2007-07-30	ENSG00000164758	ENSG00000164758			23032	protein-coding gene	gene with protein product		610237	"thyroid hormone receptor associated protein 6"	THRAP6			Standard	NM_080651		Approved	TRAP25	uc003yoj.3	Q96HR3	OTTHUMG00000164920	ENST00000297347.3:c.212A>T	chr8.hg19:g.118540924A>T	ENSP00000297347:p.Tyr71Phe	150.0	0.0		160.0	9.0	NM_080651	C6GKU9	Missense_Mutation	SNP	ENST00000297347.3	hg19	CCDS6323.1	.	.	.	.	.	.	.	.	.	.	A	16.20	3.056900	0.55325	.	.	ENSG00000164758	ENST00000297347;ENST00000522839	.	.	.	5.95	5.95	0.96441	Mediator complex, subunit Med30, metazoa (1);	0.112845	0.64402	D	0.000009	T	0.49406	0.1555	L	0.36672	1.1	0.46927	D	0.999259	P;P	0.37176	0.586;0.586	B;B	0.37015	0.239;0.239	T	0.45848	-0.9233	9	0.29301	T	0.29	-2.2429	15.5881	0.76502	1.0:0.0:0.0:0.0	.	71;71	C6GKU9;Q96HR3	.;MED30_HUMAN	F	71	.	ENSP00000297347:Y71F	Y	+	2	0	MED30	118610105	1.000000	0.71417	0.035000	0.18076	0.312000	0.27988	8.896000	0.92521	2.272000	0.75746	0.460000	0.39030	TAT	.	.		0.343	MED30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380923.1	NM_080651		T	118540924	A	T	118540924	3	4	228	1	0	0	0	0	1	0	0	0	9457	449	16	4	218	4	MED30	8	118540924	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	869721	118540924	27823098	65	32161										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144942098	144942098	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cagttctggattgcaacacgTgtctcgtggcctcattgatg	11	10	3	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr8:144942098T>C	ENST00000525985.1	-	2	5395	c.5324A>G	c.(5323-5325)cAc>cGc	p.H1775R				P58107	EPIPL_HUMAN	epiplakin 1	1775						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TTGCAACACGTGTCTCGTGGC	0.527																																					p.H1775R		Atlas-SNP	.											EPPK1,NS,NS,0,1	EPPK1	199	.	0			c.A5324G						.						124	120	122					8																	144942098		1984	4171	6155	SO:0001583	missense	83481	exon1			AACACGTGTCTCG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.5324A>G	chr8.hg19:g.144942098T>C	ENSP00000436337:p.His1775Arg	123.0	0.0		177.0	33.0	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	T	3.728	-0.056063	0.07362	.	.	ENSG00000227184	ENST00000525985	T	0.64260	-0.09	5.1	-0.169	0.13339	.	.	.	.	.	T	0.26810	0.0656	N	0.01874	-0.695	0.09310	N	1	B	0.26318	0.146	B	0.19148	0.024	T	0.19160	-1.0314	9	0.15066	T	0.55	.	4.968	0.14100	0.0:0.3454:0.1605:0.4941	.	1775	E9PPU0	.	R	1775	ENSP00000436337:H1775R	ENSP00000436337:H1775R	H	-	2	0	EPPK1	145014086	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.438000	0.06905	-0.156000	0.11079	0.477000	0.44152	CAC	.	.		0.527	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		C	144942098	T	C	144942098	3	2	228	1	0	0	0	0	1	0	0	0	5192	1696	59	2	1942	2	EPPK1	8	144942098	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	26401174	144942098	1421924	66	32162										
OPLAH	26873	hgsc.bcm.edu	37	chr8	145114666	145114666	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	atgactggagtccagcggctGgtcccggggcaggagcatgc	17	11	0	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr8:145114666G>A	ENST00000426825.1	-	3	280	c.199C>T	c.(199-201)Cag>Tag	p.Q67*	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	67					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCCAGCGGCTGGTCCCGGGGC	0.706																																					p.Q67X		Atlas-SNP	.											.	OPLAH	78	.	0			c.C199T						.						20	27	25					8																	145114666		2156	4238	6394	SO:0001587	stop_gained	26873	exon3			GCGGCTGGTCCCG	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.199C>T	chr8.hg19:g.145114666G>A	ENSP00000475943:p.Gln67*	37.0	0.0		48.0	10.0	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Nonsense_Mutation	SNP	ENST00000426825.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.04	1.521209	0.27211	.	.	ENSG00000178814	ENST00000426825	.	.	.	5.24	3.31	0.37934	.	0.441737	0.25538	N	0.029986	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	12.1388	0.53986	0.0:0.0:0.691:0.309	.	.	.	.	X	67	.	ENSP00000412071:Q67X	Q	-	1	0	OPLAH	145186654	0.969000	0.33509	0.965000	0.40720	0.206000	0.24218	2.964000	0.49192	1.157000	0.42530	0.462000	0.41574	CAG	.	.		0.706	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		A	145114666	G	A	145114666	4	1	228	1	0	0	0	0	0	1	0	0	10885	1357	47	3	3769	3	OPLAH	8	145114666	Nonsense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	172568	145114666	1249356	67	32163										
RECQL4	9401	hgsc.bcm.edu	37	chr8	145739845	145739845	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ccttctgcaggacagattccCgttgcttcctggtcatgccc	9	15	2	1	rs375562152		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr8:145739845C>T	ENST00000428558.2	-	10	1726	c.1685G>A	c.(1684-1686)cGg>cAg	p.R562Q	CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000532237.1_5'UTR	NM_004260.3	NP_004251.3	O94761	RECQ4_HUMAN	RecQ protein-like 4	562	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|bubble DNA binding (GO:0000405)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	26	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GACAGATTCCCGTTGCTTCCT	0.637			"N, F, S"			"osteosarcoma, skin basal and sqamous cell"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Rothmund-Thomson syndrome;RAPADILINO syndrome;Baller-Gerold syndrome																												p.R562Q		Atlas-SNP	.	yes	Rec		Rothmund-Thompson Syndrome	8	8q24.3	9401	RecQ protein-like 4		M	.	RECQL4	75	.	0			c.G1685A						.	C	GLN/ARG	2,4144		0,2,2071	46	50	48		1685	2.5	0	8		48	0,8394		0,0,4197	no	missense	RECQL4	NM_004260.3	43	0,2,6268	TT,TC,CC		0.0,0.0482,0.0159	possibly-damaging	562/1209	145739845	2,12538	2073	4197	6270	SO:0001583	missense	9401	exon10	Familial Cancer Database	RTS, Poikiloderma Atrophicans and Cataract, Congenital Poikiloderma; ;Craniosynostosis with Radial Defects	GATTCCCGTTGCT	AB006532	CCDS75804.1	8q24.3	2014-09-17	2014-03-07	2014-03-07		ENSG00000160957			9949	protein-coding gene	gene with protein product		603780				9878247, 15960976	Standard	NM_004260		Approved	RecQ4	uc003zdj.3	O94761		ENST00000428558.2:c.1685G>A	chr8.hg19:g.145739845C>T	ENSP00000475456:p.Arg562Gln	67.0	0.0		70.0	27.0	NM_004260	Q3Y424|Q96DW2|Q96F55	Missense_Mutation	SNP	ENST00000428558.2	hg19																																																																																				.	.		0.637	RECQL4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_004260		T	145739845	C	T	145739845	3	4	228	1	0	0	0	0	1	0	0	0	13217	652	23	1	1990	1	RECQL4	8	145739845	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	625179	145739845	624177	68	32164										
RLN1	6013	hgsc.bcm.edu	37	chr9	5335462	5335462	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tggaatcctttaatgcaggtAcatactgctgtagctctggt	10	8	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr9:5335462A>T	ENST00000223862.1	-	2	473	c.347T>A	c.(346-348)gTa>gAa	p.V116E	RLN1_ENST00000487557.2_5'UTR|RLN1_ENST00000223858.4_3'UTR	NM_006911.2	NP_008842.1	P04808	REL1_HUMAN	relaxin 1	116					female pregnancy (GO:0007565)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			large_intestine(1)|lung(4)	5	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.02)|Lung(218;0.0984)		TAATGCAGGTACATACTGCTG	0.398																																					p.V116E		Atlas-SNP	.											.	RLN1	16	.	0			c.T347A						.						110	106	107					9																	5335462		2203	4300	6503	SO:0001583	missense	6013	exon2			GCAGGTACATACT		CCDS6462.1	9p24.1	2013-02-26	2004-11-15		ENSG00000107018	ENSG00000107018		"Endogenous ligands"	10026	protein-coding gene	gene with protein product	"prorelaxin H1"	179730	"relaxin 1 (H1)"				Standard	NM_006911		Approved	H1	uc003zjb.2	P04808	OTTHUMG00000019495	ENST00000223862.1:c.347T>A	chr9.hg19:g.5335462A>T	ENSP00000223862:p.Val116Glu	73.0	0.0		79.0	9.0	NM_006911	Q99936|Q9UQJ1	Missense_Mutation	SNP	ENST00000223862.1	hg19	CCDS6462.1	.	.	.	.	.	.	.	.	.	.	A	10.11	1.260126	0.23051	.	.	ENSG00000107018	ENST00000223862	T	0.19532	2.14	1.38	-1.67	0.08238	Insulin-like (3);	7.519490	0.00166	N	0.000004	T	0.16171	0.0389	L	0.50333	1.59	0.09310	N	1	P	0.45594	0.862	B	0.41988	0.372	T	0.27938	-1.0059	10	0.05721	T	0.95	.	2.195	0.03908	0.4306:0.3207:0.2487:0.0	.	116	P04808	REL1_HUMAN	E	116	ENSP00000223862:V116E	ENSP00000223862:V116E	V	-	2	0	RLN1	5325462	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.238000	0.02919	-0.401000	0.07644	-0.986000	0.02555	GTA	.	.		0.398	RLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051617.1			T	5335462	A	T	5335462	3	4	228	1	0	0	0	0	1	0	0	0	13406	391	14	4	214	4	RLN1	9	5335462	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10		5335462	135877969	69	32165										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32632416	32632416	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ccctctccagaatgagcctgTtctgttgacattgtgcgcac	9	13	2	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr9:32632416T>A	ENST00000242310.4	-	1	3251	c.3162A>T	c.(3160-3162)gaA>gaT	p.E1054D	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1054					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		AATGAGCCTGTTCTGTTGACA	0.473																																					p.E1054D		Atlas-SNP	.											.	TAF1L	382	.	0			c.A3162T						.						222	220	221					9																	32632416		2203	4300	6503	SO:0001583	missense	138474	exon1			AGCCTGTTCTGTT	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3162A>T	chr9.hg19:g.32632416T>A	ENSP00000418379:p.Glu1054Asp	171.0	0.0		181.0	37.0	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	hg19	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	19.17	3.776719	0.70107	.	.	ENSG00000122728	ENST00000242310	T	0.20069	2.1	0.479	0.479	0.16796	.	0.000000	0.85682	D	0.000000	T	0.38108	0.1028	M	0.79805	2.47	0.48452	D	0.999659	D	0.63880	0.993	D	0.64506	0.926	T	0.17930	-1.0353	10	0.72032	D	0.01	.	5.1959	0.15236	0.0:1.0E-4:0.0:0.9999	.	1054	Q8IZX4	TAF1L_HUMAN	D	1054	ENSP00000418379:E1054D	ENSP00000418379:E1054D	E	-	3	2	TAF1L	32622416	1.000000	0.71417	0.986000	0.45419	0.847000	0.48162	1.724000	0.38064	0.426000	0.26116	0.164000	0.16699	GAA	.	.		0.473	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32632416	T	A	32632416	3	1	228	1	0	0	0	0	1	0	0	0	15538	1722	60	4	2322	4	TAF1L	9	32632416	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	27296954	32632416	108581015	70	32166										
FAM75C1	441452	hgsc.bcm.edu	37	chr9	90534168	90534168	+	RNA	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ctcgccatttcttgtctcccAgcgtcatcttgtctcccagc	6	17	5	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr9:90534168A>C	ENST00000602681.1	+	0	914							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTTGTCTCCCAGCGTCATCTT	0.597																																					.		Atlas-SNP	.											.	.	.	.	0			c.190-2A>C						.						99	84	89					9																	90534168		692	1591	2283			441452	exon2			TCTCCCAGCGTCA	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"family with sequence similarity 75, member C1"	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		chr9.hg19:g.90534168A>C		352.0	0.0		302.0	15.0	NM_001145124		Splice_Site	SNP	ENST00000602681.1	hg19																																																																																				.	.		0.597	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124		C	90534168	A	C	90534168	1	2	228	0	1	0	0	0	0	0	0	0	5631	202	7	5		5	FAM75C1	9	90534168	RNA	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	57901752	90534168	50679263	71	32167										
OR13C5	138799	hgsc.bcm.edu	37	chr9	107360936	107360936	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	atgtacatgaggaagatggtCccacagaatgttatcaccac	9	9	1	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr9:107360936C>A	ENST00000374779.2	-	1	852	c.759G>T	c.(757-759)ggG>ggT	p.G253G		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						GGAAGATGGTCCCACAGAATG	0.428																																					p.G253G		Atlas-SNP	.											.	OR13C5	60	.	0			c.G759T						.						140	125	130					9																	107360936		2203	4300	6503	SO:0001819	synonymous_variant	138799	exon1			GATGGTCCCACAG		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"GPCR / Class A : Olfactory receptors"	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.759G>T	chr9.hg19:g.107360936C>A		164.0	0.0		126.0	33.0	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	hg19	CCDS35091.1																																																																																			.	.		0.428	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482		A	107360936	C	A	107360936	2	1	228	1	0	0	0	0	0	0	0	1	10946	842	30	3		3	OR13C5	9	107360936	Silent	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	16826768	107360936	33852495	72	32168										
PTPN3	5774	hgsc.bcm.edu	37	chr9	112151605	112151606	+	Frame_Shift_Del	DEL	GG	GG	-													0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ctgtgcacaggtatgcggcaGgggcccctgagtggcgatgt							TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr9:112151605_112151606delGG	ENST00000374541.2	-	22	2264_2265	c.2160_2161delCC	c.(2158-2163)cccctgfs	p.L721fs	PTPN3_ENST00000497739.1_5'UTR|PTPN3_ENST00000446349.1_Frame_Shift_Del_p.L545fs|PTPN3_ENST00000412145.1_Frame_Shift_Del_p.L590fs|PTPN3_ENST00000262539.3_Frame_Shift_Del_p.L567fs|PTPN3_ENST00000394827.3_Frame_Shift_Del_p.L189fs	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	721	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						GTATGCGGCAGGGGCCCCTGAG	0.495																																					p.721_721del		Atlas-INDEL	.											.	PTPN3	106	.	0			c.2161_2162del						.																																			SO:0001589	frameshift_variant	5774	exon22			.		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.2160_2161delCC	chr9.hg19:g.112151607_112151608delGG	ENSP00000363667:p.Leu721fs	73.0	0.0		74.0	18.0	NM_002829	A0AUW9|E7EN99|E9PGU7	Frame_Shift_Del	DEL	ENST00000374541.2	hg19	CCDS6776.1																																																																																			.	.		0.495	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			-	112151606	GG	-	112151605	7	5	228	1	0	1	0	1	0	0	0	0	12804	991	35	0	600	0	PTPN3	9	112151605	Frame_Shift_Del	DEL	GG	TCGA-DD-AAVV-01A-11D-A40R-10	4790669	112151605	29061826	73	32169										
OR1Q1	158131	hgsc.bcm.edu	37	chr9	125377800	125377800	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tcagttgggtctacttccggCccctttccagctattcagtg	9	13	3	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr9:125377800C>A	ENST00000297913.2	+	1	853	c.784C>A	c.(784-786)Ccc>Acc	p.P262T	RP11-64P14.7_ENST00000431442.1_RNA	NM_012364.1	NP_036496.1	Q15612	OR1Q1_HUMAN	olfactory receptor, family 1, subfamily Q, member 1	262					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	17						CTACTTCCGGCCCCTTTCCAG	0.547																																					p.P262T		Atlas-SNP	.											.	OR1Q1	46	.	0			c.C784A						.						63	64	64					9																	125377800		2203	4300	6503	SO:0001583	missense	158131	exon1			TTCCGGCCCCTTT		CCDS35125.1	9q33.2	2013-09-20			ENSG00000165202	ENSG00000165202		"GPCR / Class A : Olfactory receptors"	8223	protein-coding gene	gene with protein product				OR1Q2, OR1Q3			Standard	NM_012364		Approved	OST226, OR9-A, HSTPCR106, OST226OR9-A, TPCR106	uc011lyy.2	Q15612	OTTHUMG00000020615	ENST00000297913.2:c.784C>A	chr9.hg19:g.125377800C>A	ENSP00000297913:p.Pro262Thr	138.0	0.0		128.0	29.0	NM_012364	Q6IFN4|Q8NGR7|Q96R82	Missense_Mutation	SNP	ENST00000297913.2	hg19	CCDS35125.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.208968	0.58343	.	.	ENSG00000165202	ENST00000297913	T	0.00274	8.35	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000157	T	0.01092	0.0036	M	0.93978	3.48	0.09310	N	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.27971	-1.0058	10	0.87932	D	0	-18.8882	18.1511	0.89675	0.0:1.0:0.0:0.0	.	262	Q15612	OR1Q1_HUMAN	T	262	ENSP00000297913:P262T	ENSP00000297913:P262T	P	+	1	0	OR1Q1	124417621	0.306000	0.24490	0.989000	0.46669	0.953000	0.61014	4.529000	0.60588	2.826000	0.97356	0.650000	0.86243	CCC	.	.		0.547	OR1Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053946.1			A	125377800	C	A	125377800	3	1	228	1	0	0	0	0	1	0	0	0	10980	739	26	3	786	3	OR1Q1	9	125377800	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	13226195	125377800	15835631	74	32170										
SVIL	6840	hgsc.bcm.edu	37	chr10	29822162	29822162	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ggggtttctggcgtcactagCttggcggtgtgaccggtatc	16	9	2	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr10:29822162C>T	ENST00000355867.4	-	8	1886	c.1134G>A	c.(1132-1134)aaG>aaA	p.K378K	SVIL_ENST00000375398.2_Silent_p.K378K|SVIL_ENST00000375400.3_Intron	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	378					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GCGTCACTAGCTTGGCGGTGT	0.562																																					p.K378K		Atlas-SNP	.											.	SVIL	226	.	0			c.G1134A						.						89	75	79					10																	29822162		2203	4300	6503	SO:0001819	synonymous_variant	6840	exon8			CACTAGCTTGGCG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1134G>A	chr10.hg19:g.29822162C>T		105.0	0.0		69.0	7.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	hg19	CCDS7164.1																																																																																			.	.		0.562	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			T	29822162	C	T	29822162	2	4	228	1	0	0	0	0	0	0	0	1	15436	796	28	3		3	SVIL	10	29822162	Silent	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10		29822162	105712585	75	32171										
PRKG1	5592	hgsc.bcm.edu	37	chr10	53822361	53822362	+	Missense_Mutation	DNP	GA	GA	TT													0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tcttagaactttaggaaaagGagactggtttggagagaaag					rs145917628	byFrequency	TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr10:53822361_53822362GA>TT	ENST00000401604.2	+	7	1054_1055	c.860_861GA>TT	c.(859-861)gGA>gTT	p.G287V	PRKG1_ENST00000373985.1_Missense_Mutation_p.G275V|PRKG1_ENST00000373975.2_5'UTR|PRKG1_ENST00000373980.4_Missense_Mutation_p.G302V			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	287	cGMP-binding, low affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTAGGAAAAGGAGACTGGTTTG	0.401																																					p.G302V|p.G302G		Atlas-SNP	.											.	PRKG1	167	.	0			c.G905T|c.A906T						.																																			SO:0001583	missense	5592	exon7			GAAAAGGAGACTG|AAAAGGAGACTGG		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	Exception_encountered	chr10.hg19:g.53822361_53822362delinsTT	ENSP00000384200:p.Gly287Val	144.0|146.0	0.0		136.0	30.0	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation|Silent	SNP	ENST00000401604.2	hg19	CCDS44399.1																																																																																			.	.|A|0.998;C|0.002		0.401	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				TT	53822362	GA	TT	53822361	3	4	228	1	0	0	0	0	1	0	0	0	12534	1174	41	3	1201	3	PRKG1	10	53822361	Missense_Mutation	DNP	GA	TCGA-DD-AAVV-01A-11D-A40R-10	24000199	53822361	81712386	76	32172										
LIPF	8513	hgsc.bcm.edu	37	chr10	90435976	90435976	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tctatgttaggctgttaagtCtgggaaattccaagcttatg	10	6	2	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr10:90435976C>A	ENST00000238983.4	+	9	945	c.899C>A	c.(898-900)tCt>tAt	p.S300Y	LIPF_ENST00000608620.1_Missense_Mutation_p.S267Y|LIPF_ENST00000355843.2_Missense_Mutation_p.S277Y|LIPF_ENST00000394375.3_Missense_Mutation_p.S310Y	NM_004190.3	NP_004181.1	P07098	LIPG_HUMAN	lipase, gastric	300					lipid catabolic process (GO:0016042)|malate metabolic process (GO:0006108)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)	lipid binding (GO:0008289)|malate dehydrogenase activity (GO:0016615)|triglyceride lipase activity (GO:0004806)			NS(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(6)	13		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)	Orlistat(DB01083)	GCTGTTAAGTCTGGGAAATTC	0.303																																					p.S310Y		Atlas-SNP	.											.	LIPF	62	.	0			c.C929A						.						64	63	63					10																	90435976		2203	4299	6502	SO:0001583	missense	8513	exon10			TTAAGTCTGGGAA	X05997	CCDS7389.1, CCDS55718.1, CCDS55719.1, CCDS65896.1	10q23	2005-10-30			ENSG00000182333	ENSG00000182333	3.1.1.3		6622	protein-coding gene	gene with protein product		601980				3304425, 9186906	Standard	NM_004190		Approved	HGL, HLAL	uc010qmt.2	P07098	OTTHUMG00000018695	ENST00000238983.4:c.899C>A	chr10.hg19:g.90435976C>A	ENSP00000238983:p.Ser300Tyr	216.0	0.0		187.0	58.0	NM_001198829	B7Z723|F5H1P4|Q2M1P6|Q5VXI7|Q5VXI8|Q658L8	Missense_Mutation	SNP	ENST00000238983.4	hg19	CCDS7389.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.938676	0.34189	.	.	ENSG00000182333	ENST00000394375;ENST00000238983;ENST00000355843	T;T;T	0.72725	-0.68;-0.68;-0.68	4.88	3.93	0.45458	Alpha/beta hydrolase fold-1 (1);	0.378707	0.23041	N	0.052602	D	0.83427	0.5252	M	0.85099	2.735	0.32362	N	0.556991	B;D;B;D	0.89917	0.347;1.0;0.31;1.0	B;D;B;D	0.77557	0.248;0.983;0.168;0.99	D	0.85522	0.1204	10	0.52906	T	0.07	-17.2739	11.2164	0.48830	0.0:0.8156:0.1844:0.0	.	267;310;277;300	Q5VXI8;F5H1P4;Q658L8;P07098	.;.;.;LIPG_HUMAN	Y	310;300;267	ENSP00000377900:S310Y;ENSP00000238983:S300Y;ENSP00000348101:S267Y	ENSP00000238983:S300Y	S	+	2	0	LIPF	90425956	0.001000	0.12720	0.745000	0.31077	0.347000	0.29111	0.091000	0.15046	2.528000	0.85240	0.551000	0.68910	TCT	.	.		0.303	LIPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049256.1			A	90435976	C	A	90435976	3	1	228	1	0	0	0	0	1	0	0	0	8831	913	32	3	929	3	LIPF	10	90435976	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	36613615	90435976	45098771	77	32173										
MUC2	4583	hgsc.bcm.edu	37	chr11	1092362	1092362	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ttgttgctggcccatggataAgtgtatcaccactcccagcc	9	13	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:1092362A>T	ENST00000441003.2	+	30	4208	c.4181A>T	c.(4180-4182)aAg>aTg	p.K1394M	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.K1395M|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1394					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCCATGGATAAGTGTATCACC	0.532																																					p.K1394M		Atlas-SNP	.											.	MUC2	614	.	0			c.A4181T						.						157	198	184					11																	1092362		2145	4218	6363	SO:0001583	missense	4583	exon30			TGGATAAGTGTAT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4181A>T	chr11.hg19:g.1092362A>T	ENSP00000415183:p.Lys1394Met	153.0	0.0		131.0	8.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	a	1.529	-0.544746	0.04024	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13538	2.61;2.58	2.27	1.0	0.19881	.	0.642064	0.11985	U	0.510401	T	0.05135	0.0137	N	0.14661	0.345	0.09310	N	1	P	0.44659	0.84	B	0.29176	0.099	T	0.34875	-0.9811	10	0.35671	T	0.21	.	5.3746	0.16158	0.7073:0.2927:0.0:0.0	.	1394	E7EUV1	.	M	1394;1395	ENSP00000415183:K1394M;ENSP00000351956:K1395M	ENSP00000351956:K1395M	K	+	2	0	MUC2	1082362	0.000000	0.05858	0.001000	0.08648	0.273000	0.26683	-1.729000	0.01856	0.123000	0.18342	0.063000	0.15292	AAG	.	.		0.532	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092362	A	T	1092362	3	4	228	1	0	0	0	0	1	0	0	0	9984	72	3	4	4299	4	MUC2	11	1092362	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10		1092362	133914154	78	32174										
IGF2	3481	hgsc.bcm.edu	37	chr11	2154351	2154351	+	Frame_Shift_Del	DEL	G	G	-													0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ggcgagcacgtgaccccggcGggcacgcaggagggcaggca							TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:2154351delG	ENST00000416167.2	-	4	1575	c.409delC	c.(409-411)cgcfs	p.R138fs	IGF2_ENST00000434045.2_Frame_Shift_Del_p.R194fs|IGF2_ENST00000381395.1_Frame_Shift_Del_p.R138fs|IGF2_ENST00000300632.5_Frame_Shift_Del_p.R138fs|IGF2_ENST00000381392.1_Frame_Shift_Del_p.R141fs|IGF2_ENST00000381406.4_Frame_Shift_Del_p.R141fs|IGF2_ENST00000418738.2_Frame_Shift_Del_p.R138fs|IGF2_ENST00000381389.1_Frame_Shift_Del_p.R138fs|MIR483_ENST00000385070.1_RNA			P01344	IGF2_HUMAN	insulin-like growth factor 2	138					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|exocrine pancreas development (GO:0031017)|female pregnancy (GO:0007565)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to nicotine (GO:0035094)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|striated muscle cell differentiation (GO:0051146)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	growth factor activity (GO:0008083)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|protein serine/threonine kinase activator activity (GO:0043539)|receptor activator activity (GO:0030546)			central_nervous_system(1)|kidney(1)|lung(1)|pancreas(1)|skin(1)|urinary_tract(1)	6		all_epithelial(84;5.04e-06)|Breast(177;0.000777)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.0179)|COAD - Colon adenocarcinoma(6;0.029)	BRCA - Breast invasive adenocarcinoma(625;1.09e-05)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		TGACCCCGGCGGGCACGCAGG	0.667																																					p.R193fs		Atlas-INDEL	.											.	IGF2	54	.	0			c.578delG						.						33	33	33					11																	2154351		2201	4298	6499	SO:0001589	frameshift_variant	3481	exon5			.	M29645, AK025719	CCDS7728.1, CCDS44517.1	11p15.5	2014-09-16	2014-09-16		ENSG00000167244	ENSG00000167244			5466	protein-coding gene	gene with protein product	"somatomedin A"	147470	"chromosome 11 open reading frame 43"	C11orf43		2450353, 3167054	Standard	NM_000612		Approved	FLJ44734, IGF-II	uc009ydf.3	P01344	OTTHUMG00000009395	ENST00000416167.2:c.409delC	chr11.hg19:g.2154351delG	ENSP00000414497:p.Arg138fs	185.0	0.0		147.0	32.0	NM_001127598	B3KX48|B7WP08|C9JAF2|E3UN45|P78449|Q14299|Q1WM26|Q9UC68|Q9UC69	Frame_Shift_Del	DEL	ENST00000416167.2	hg19	CCDS7728.1																																																																																			.	.		0.667	IGF2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026053.2	NM_000612		-	2154351	G	-	2154351	7	5	228	1	0	1	0	1	0	0	0	0	7581	1116	39	0	137	0	IGF2	11	2154351	Frame_Shift_Del	DEL	G	TCGA-DD-AAVV-01A-11D-A40R-10	1061989	2154351	132852165	79	32175										
OR51L1	119682	hgsc.bcm.edu	37	chr11	5020271	5020271	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	atttatcctgaggggttttcCtggactggagtatgttcatt	11	6	1	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:5020271C>T	ENST00000321543.1	+	1	59	c.59C>T	c.(58-60)cCt>cTt	p.P20L		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P20L(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGGGGTTTTCCTGGACTGGAG	0.428																																					p.P20L		Atlas-SNP	.											OR51L1,NS,carcinoma,0,1	OR51L1	60	.	1	Substitution - Missense(1)	lung(1)	c.C59T						.						215	204	208					11																	5020271		2201	4298	6499	SO:0001583	missense	119682	exon1			GTTTTCCTGGACT	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"GPCR / Class A : Olfactory receptors"	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.59C>T	chr11.hg19:g.5020271C>T	ENSP00000322156:p.Pro20Leu	134.0	0.0		138.0	12.0	NM_001004755	Q6IFE5	Missense_Mutation	SNP	ENST00000321543.1	hg19	CCDS31369.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.591576	0.46214	.	.	ENSG00000176798	ENST00000321543	T	0.00493	7.0	5.58	4.67	0.58626	.	0.000000	0.43919	D	0.000507	T	0.00845	0.0028	M	0.88775	2.98	0.36136	D	0.846497	P	0.43287	0.802	B	0.34489	0.184	T	0.57481	-0.7804	10	0.72032	D	0.01	.	14.7839	0.69787	0.1453:0.8547:0.0:0.0	.	20	Q8NGJ5	O51L1_HUMAN	L	20	ENSP00000322156:P20L	ENSP00000322156:P20L	P	+	2	0	OR51L1	4976847	0.161000	0.22892	0.972000	0.41901	0.492000	0.33523	1.815000	0.38981	1.580000	0.49851	0.655000	0.94253	CCT	.	.		0.428	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755		T	5020271	C	T	5020271	3	4	228	1	0	0	0	0	1	0	0	0	11111	681	24	3	61	3	OR51L1	11	5020271	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	2865920	5020271	129986245	80	32176										
OR2AG1	144125	hgsc.bcm.edu	37	chr11	6806278	6806278	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gaaaccacagcatggagctcTggaacttcaccttgggaagt	11	10	2	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:6806278T>C	ENST00000307401.4	+	1	31	c.10T>C	c.(10-12)Tgg>Cgg	p.W4R		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATGGAGCTCTGGAACTTCAC	0.408																																					p.W4R		Atlas-SNP	.											.	OR2AG1	57	.	0			c.T10C						.						103	99	100					11																	6806278		2201	4296	6497	SO:0001583	missense	144125	exon1			GAGCTCTGGAACT	AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"GPCR / Class A : Olfactory receptors"	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.10T>C	chr11.hg19:g.6806278T>C	ENSP00000307447:p.Trp4Arg	93.0	0.0		89.0	10.0	NM_001004489	B9EKV7|Q6IFG7|Q96R26	Missense_Mutation	SNP	ENST00000307401.4	hg19	CCDS31414.1	.	.	.	.	.	.	.	.	.	.	T	0.034	-1.316255	0.01331	.	.	ENSG00000170803	ENST00000307401	T	0.19105	2.17	4.25	0.383	0.16239	.	0.616819	0.14159	N	0.337530	T	0.07548	0.0190	N	0.05078	-0.115	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.40572	-0.9556	10	0.11485	T	0.65	.	5.2336	0.15436	0.0:0.1828:0.1536:0.6636	.	4	Q9H205	O2AG1_HUMAN	R	4	ENSP00000307447:W4R	ENSP00000307447:W4R	W	+	1	0	OR2AG1	6762854	0.071000	0.21146	0.103000	0.21229	0.012000	0.07955	0.219000	0.17641	-0.024000	0.13941	-1.541000	0.00910	TGG	.	.		0.408	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385980.1	NM_001004489		C	6806278	T	C	6806278	3	2	228	1	0	0	0	0	1	0	0	0	10993	1580	55	2	12	2	OR2AG1	11	6806278	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	1786007	6806278	128200238	81	32177										
SVIP	258010	hgsc.bcm.edu	37	chr11	22851254	22851254	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tactcaccaggtccggcgtgGgaggcgcggactccccggga	16	14	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:22851254G>T	ENST00000354193.4	-	1	157	c.41C>A	c.(40-42)cCc>cAc	p.P14H	RP11-17A1.3_ENST00000499625.1_RNA|RP11-17A1.3_ENST00000525963.1_RNA|SVIP_ENST00000533774.1_5'Flank|RP11-17A1.3_ENST00000528701.1_RNA	NM_148893.1	NP_683691.1	Q8NHG7	SVIP_HUMAN	small VCP/p97-interacting protein	14					negative regulation of ER-associated ubiquitin-dependent protein catabolic process (GO:1903070)|negative regulation of protein complex assembly (GO:0031333)|positive regulation of autophagy (GO:0010508)|positive regulation of protein lipidation (GO:1903061)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	protein self-association (GO:0043621)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	3						GTCCGGCGTGGGAGGCGCGGA	0.701																																					p.P14H		Atlas-SNP	.											.	SVIP	10	.	0			c.C41A						.						12	16	15					11																	22851254		1861	4075	5936	SO:0001583	missense	258010	exon1			GGCGTGGGAGGCG	AF527534	CCDS41627.1	11p14.2	2009-03-10				ENSG00000198168			25238	protein-coding gene	gene with protein product						18793143, 17872946, 12529442	Standard	NM_148893		Approved	DKFZp313A2432	uc001mqp.4	Q8NHG7		ENST00000354193.4:c.41C>A	chr11.hg19:g.22851254G>T	ENSP00000346130:p.Pro14His	292.0	0.0		219.0	41.0	NM_148893		Missense_Mutation	SNP	ENST00000354193.4	hg19	CCDS41627.1	.	.	.	.	.	.	.	.	.	.	G	6.846	0.525399	0.13066	.	.	ENSG00000198168	ENST00000354193	.	.	.	3.98	3.06	0.35304	.	0.222161	0.23083	N	0.052125	T	0.27731	0.0682	.	.	.	0.09310	N	1	P	0.37276	0.589	B	0.37144	0.242	T	0.15838	-1.0423	8	0.62326	D	0.03	-1.9713	7.5771	0.27942	0.1193:0.0:0.8807:0.0	.	14	Q8NHG7	SVIP_HUMAN	H	14	.	ENSP00000346130:P14H	P	-	2	0	SVIP	22807830	0.308000	0.24509	0.020000	0.16555	0.443000	0.32047	1.076000	0.30729	1.007000	0.39238	-0.339000	0.08088	CCC	.	.		0.701	SVIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387725.2	NM_148893		T	22851254	G	T	22851254	3	4	228	1	0	0	0	0	1	0	0	0	15437	1232	43	3	208	3	SVIP	11	22851254	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	16044976	22851254	112155262	82	32178										
OR5J2	282775	hgsc.bcm.edu	37	chr11	55944169	55944169	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	atcatgctgaactaaaagctGtgctttttgtggtgttcctg	10	7	1	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:55944169G>T	ENST00000312298.1	+	1	76	c.76G>T	c.(76-78)Gtg>Ttg	p.V26L		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	26						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	44	Esophageal squamous(21;0.00693)					ACTAAAAGCTGTGCTTTTTGT	0.388																																					p.V26L		Atlas-SNP	.											.	OR5J2	98	.	0			c.G76T						.						170	163	165					11																	55944169		2201	4295	6496	SO:0001583	missense	282775	exon1			AAAGCTGTGCTTT	AB065595	CCDS31522.1	11q11	2012-08-09			ENSG00000174957	ENSG00000174957		"GPCR / Class A : Olfactory receptors"	19612	protein-coding gene	gene with protein product							Standard	NM_001005492		Approved		uc010rjb.2	Q8NH18	OTTHUMG00000166835	ENST00000312298.1:c.76G>T	chr11.hg19:g.55944169G>T	ENSP00000310788:p.Val26Leu	111.0	0.0		71.0	10.0	NM_001005492	Q6IEU5	Missense_Mutation	SNP	ENST00000312298.1	hg19	CCDS31522.1	.	.	.	.	.	.	.	.	.	.	G	0.790	-0.759158	0.03019	.	.	ENSG00000174957	ENST00000312298	T	0.00063	8.78	4.32	-8.38	0.00973	.	1.628360	0.03583	N	0.230428	T	0.00039	0.0001	N	0.03238	-0.38	0.09310	N	1	B	0.19583	0.037	B	0.17098	0.017	T	0.37911	-0.9685	10	0.06236	T	0.91	.	2.8179	0.05463	0.1185:0.3675:0.1343:0.3796	.	26	Q8NH18	OR5J2_HUMAN	L	26	ENSP00000310788:V26L	ENSP00000310788:V26L	V	+	1	0	OR5J2	55700745	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.136000	0.00588	-0.952000	0.03649	-0.294000	0.09567	GTG	.	.		0.388	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492		T	55944169	G	T	55944169	3	4	228	1	0	0	0	0	1	0	0	0	11174	1377	48	3	78	3	OR5J2	11	55944169	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	33092915	55944169	79062347	83	32179										
OR8K3	219473	hgsc.bcm.edu	37	chr11	56086057	56086057	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tgttgtggataagaatataaTttcttattatttttgtgcaa	7	2	1	1	rs141217471		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:56086057T>G	ENST00000312711.1	+	1	275	c.275T>G	c.(274-276)aTt>aGt	p.I92S		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	92						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					AAGAATATAATTTCTTATTAT	0.358																																					p.I92S		Atlas-SNP	.											.	OR8K3	92	.	0			c.T275G						.						74	80	78					11																	56086057		2201	4296	6497	SO:0001583	missense	219473	exon1			ATATAATTTCTTA	AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"GPCR / Class A : Olfactory receptors"	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.275T>G	chr11.hg19:g.56086057T>G	ENSP00000323555:p.Ile92Ser	147.0	0.0		144.0	6.0	NM_001005202	Q6IFC4	Missense_Mutation	SNP	ENST00000312711.1	hg19	CCDS31527.1	.	.	.	.	.	.	.	.	.	.	T	13.01	2.110663	0.37242	.	.	ENSG00000181689	ENST00000312711	T	0.01359	4.98	4.65	4.65	0.58169	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000007	T	0.11793	0.0287	H	0.94542	3.55	0.35935	D	0.832798	D	0.63880	0.993	D	0.64410	0.925	T	0.13845	-1.0494	10	0.87932	D	0	.	13.7071	0.62646	0.0:0.0:0.0:1.0	.	92	Q8NH51	OR8K3_HUMAN	S	92	ENSP00000323555:I92S	ENSP00000323555:I92S	I	+	2	0	OR8K3	55842633	1.000000	0.71417	0.053000	0.19242	0.001000	0.01503	5.351000	0.66022	2.074000	0.62210	0.519000	0.50382	ATT	.	T|1.000;A|0.000		0.358	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	NM_001005202		G	56086057	T	G	56086057	3	3	228	1	0	0	0	0	1	0	0	0	11253	1493	52	5	277	5	OR8K3	11	56086057	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	141888	56086057	78920459	84	32180										
MS4A4A	51338	hgsc.bcm.edu	37	chr11	60068517	60068517	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	aattgcagcaggaattagaaCtacaaaaggcctggtgagta	11	6	0	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:60068517C>G	ENST00000337908.4	+	4	464	c.374C>G	c.(373-375)aCt>aGt	p.T125S	MS4A4A_ENST00000355131.3_Missense_Mutation_p.T106S|MS4A4A_ENST00000532114.1_Missense_Mutation_p.T125S|MS4A4A_ENST00000395016.3_Missense_Mutation_p.T106S	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	125						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						GGAATTAGAACTACAAAAGGC	0.308																																					p.T125S		Atlas-SNP	.											.	MS4A4A	76	.	0			c.C374G						.						73	74	74					11																	60068517		2203	4298	6501	SO:0001583	missense	51338	exon4			TTAGAACTACAAA	AB013102	CCDS7982.1, CCDS58135.1	11q12	2012-02-28	2012-02-28		ENSG00000110079	ENSG00000110079			13371	protein-coding gene	gene with protein product		606547	"membrane-spanning 4-domains, subfamily A, member 4"	MS4A4		11245982, 11401424	Standard	NM_148975		Approved	CD20L1, MS4A7	uc001noz.3	Q96JQ5	OTTHUMG00000154949	ENST00000337908.4:c.374C>G	chr11.hg19:g.60068517C>G	ENSP00000338648:p.Thr125Ser	38.0	0.0		29.0	8.0	NM_148975	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Missense_Mutation	SNP	ENST00000337908.4	hg19	CCDS7982.1	.	.	.	.	.	.	.	.	.	.	C	11.28	1.593060	0.28357	.	.	ENSG00000110079	ENST00000532114;ENST00000337908;ENST00000355131;ENST00000395016	T;T;T;T	0.02158	4.42;4.42;4.42;4.42	4.3	0.305	0.15801	.	0.806785	0.10939	N	0.617534	T	0.02494	0.0076	L	0.39085	1.19	0.21802	N	0.999534	P;P	0.46142	0.873;0.793	P;B	0.47673	0.554;0.354	T	0.30090	-0.9990	10	0.07325	T	0.83	-2.0932	6.5799	0.22588	0.0:0.5889:0.0:0.4111	.	125;125	Q96JQ5-2;Q96JQ5	.;M4A4A_HUMAN	S	125;125;106;106	ENSP00000434506:T125S;ENSP00000338648:T125S;ENSP00000347252:T106S;ENSP00000378462:T106S	ENSP00000338648:T125S	T	+	2	0	MS4A4A	59825093	0.159000	0.22864	0.838000	0.33150	0.790000	0.44656	0.291000	0.18994	-0.022000	0.13986	-0.373000	0.07131	ACT	.	.		0.308	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2			G	60068517	C	G	60068517	3	3	228	1	0	0	0	0	1	0	0	0	9871	565	20	4	388	4	MS4A4A	11	60068517	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	3982460	60068517	74937999	85	32181										
MS4A10	341116	hgsc.bcm.edu	37	chr11	60563034	60563034	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ctctaccctctcaggtccacAtccagaggctggagctggcc	10	16	2	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:60563034A>C	ENST00000308287.1	+	6	595	c.499A>C	c.(499-501)Atc>Ctc	p.I167L		NM_206893.3	NP_996776.2	Q96PG2	M4A10_HUMAN	membrane-spanning 4-domains, subfamily A, member 10	167						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|skin(2)	21						TCAGGTCCACATCCAGAGGCT	0.617																																					p.I167L		Atlas-SNP	.											.	MS4A10	38	.	0			c.A499C						.						86	63	71					11																	60563034		2203	4299	6502	SO:0001583	missense	341116	exon6			GTCCACATCCAGA	AK122633	CCDS7992.1	11q12.2	2008-02-05				ENSG00000172689			13368	protein-coding gene	gene with protein product		608403				11486273, 11401424	Standard	NM_206893		Approved	CD20L7, MS4A9	uc001npz.1	Q96PG2		ENST00000308287.1:c.499A>C	chr11.hg19:g.60563034A>C	ENSP00000311862:p.Ile167Leu	57.0	0.0		41.0	7.0	NM_206893	B2RP45|Q96PG3	Missense_Mutation	SNP	ENST00000308287.1	hg19	CCDS7992.1	.	.	.	.	.	.	.	.	.	.	A	12.22	1.872317	0.33069	.	.	ENSG00000172689	ENST00000308287	T	0.01902	4.57	4.01	-0.103	0.13609	.	0.427442	0.17384	N	0.176188	T	0.02807	0.0084	L	0.60455	1.87	0.23607	N	0.997302	B	0.31256	0.316	B	0.36666	0.23	T	0.40905	-0.9538	10	0.27785	T	0.31	-11.3484	4.405	0.11406	0.4777:0.4074:0.1149:0.0	.	167	Q96PG2	M4A10_HUMAN	L	167	ENSP00000311862:I167L	ENSP00000311862:I167L	I	+	1	0	MS4A10	60319610	0.812000	0.29077	0.938000	0.37757	0.404000	0.30871	0.489000	0.22387	0.189000	0.20188	0.533000	0.62120	ATC	.	.		0.617	MS4A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395619.1	NM_206893		C	60563034	A	C	60563034	3	2	228	1	0	0	0	0	1	0	0	0	9864	217	8	5	517	5	MS4A10	11	60563034	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	494517	60563034	74443482	86	32182										
FAU	740	hgsc.bcm.edu	37	chr11	64888473	64888473	+	5'Flank	DEL	C	C	-													0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cttaggagtctgacctctcaCttttccagcacgggccaggg							TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:64888473delC	ENST00000279242.2	+	0	0				MRPL49_ENST00000526171.1_5'Flank|FAU_ENST00000525297.1_Frame_Shift_Del_p.V51fs|FAU_ENST00000527548.1_Frame_Shift_Del_p.V86fs|FAU_ENST00000529259.1_3'UTR|FAU_ENST00000529639.1_Frame_Shift_Del_p.V86fs|MRPL49_ENST00000534078.1_5'Flank|FAU_ENST00000531743.1_Frame_Shift_Del_p.V86fs|FAU_ENST00000279259.3_Intron|MRPL49_ENST00000531705.1_5'Flank	NM_004927.3	NP_004918.1	Q13405	RM49_HUMAN	mitochondrial ribosomal protein L49						translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			endometrium(1)|ovary(1)	2						TGACCTCTCACTTTTCCAGCA	0.512																																					p.V86fs		Atlas-INDEL	.											.	FAU	17	.	0			c.257delT						.						220	216	217					11																	64888473		2201	4297	6498	SO:0001631	upstream_gene_variant	2197	exon4			.		CCDS8096.1	11q13.1	2012-11-14	2001-10-16	2001-10-19	ENSG00000149792	ENSG00000149792		"Mitochondrial ribosomal proteins / large subunits"	1176	protein-coding gene	gene with protein product	"neighbor of FAU", "next to FAU"	606866	"chromosome 11 open reading frame 4"	C11orf4		8786148	Standard	NM_004927		Approved	NOF, NOF1, L49mt	uc001oda.2	Q13405	OTTHUMG00000165608		chr11.hg19:g.64888473delC	Exception_encountered	145.0	0.0		119.0	15.0	NM_001997	B2R4G6	Frame_Shift_Del	DEL	ENST00000279242.2	hg19	CCDS8096.1																																																																																			.	.		0.512	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		-	64888473	C	-	64888473	6	5	228	0	1	1	0	1	0	0	0	0	5702	565	20	0		0	FAU	11	64888473	5'Flank	DEL	C	TCGA-DD-AAVV-01A-11D-A40R-10	4325439	64888473	70118043	87	32183										
GAB2	9846	hgsc.bcm.edu	37	chr11	77991812	77991812	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cttgttaaaggtcaggcctgCatctacctgctcacagaagt	9	11	3	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:77991812C>T	ENST00000361507.4	-	2	296	c.211G>A	c.(211-213)Gca>Aca	p.A71T	GAB2_ENST00000526030.1_5'UTR|GAB2_ENST00000340149.2_Missense_Mutation_p.A33T	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	71	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			GTCAGGCCTGCATCTACCTGC	0.493																																					p.A71T		Atlas-SNP	.											.	GAB2	63	.	0			c.G211A						.						153	135	141					11																	77991812		2200	4292	6492	SO:0001583	missense	9846	exon2			GGCCTGCATCTAC	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"Pleckstrin homology (PH) domain containing"	14458	protein-coding gene	gene with protein product	"Grb2-associated binder 2"	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.211G>A	chr11.hg19:g.77991812C>T	ENSP00000354952:p.Ala71Thr	99.0	0.0		99.0	14.0	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Missense_Mutation	SNP	ENST00000361507.4	hg19	CCDS8259.1	.	.	.	.	.	.	.	.	.	.	C	34	5.394558	0.96009	.	.	ENSG00000033327	ENST00000340149;ENST00000361507;ENST00000528886;ENST00000530915	T;T;T;T	0.77358	-1.09;2.64;-1.09;-1.09	5.37	5.37	0.77165	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.64402	U	0.000001	D	0.85461	0.5702	L	0.46670	1.46	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.86228	0.1635	10	0.72032	D	0.01	-9.0531	19.4818	0.95013	0.0:1.0:0.0:0.0	.	71	Q9UQC2	GAB2_HUMAN	T	33;71;33;33	ENSP00000343959:A33T;ENSP00000354952:A71T;ENSP00000433762:A33T;ENSP00000431868:A33T	ENSP00000343959:A33T	A	-	1	0	GAB2	77669460	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.880000	0.69698	2.667000	0.90743	0.563000	0.77884	GCA	.	.		0.493	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		T	77991812	C	T	77991812	3	4	228	1	0	0	0	0	1	0	0	0	6157	710	25	3	1855	3	GAB2	11	77991812	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	13103339	77991812	57014704	88	32184										
PRDM10	56980	hgsc.bcm.edu	37	chr11	129801056	129801056	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gggtttcctgtggcagctgaGggattgggatagtggtctgt	18	5	1	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr11:129801056G>A	ENST00000360871.3	-	11	1616	c.1385C>T	c.(1384-1386)cCt>cTt	p.P462L	PRDM10_ENST00000358825.5_Missense_Mutation_p.P462L|PRDM10_ENST00000526082.1_Missense_Mutation_p.P376L|PRDM10_ENST00000423662.2_Missense_Mutation_p.P376L|PRDM10_ENST00000528746.1_Missense_Mutation_p.P436L|PRDM10_ENST00000304538.6_Missense_Mutation_p.P376L	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	462					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TGGCAGCTGAGGGATTGGGAT	0.542																																					p.P462L		Atlas-SNP	.											.	PRDM10	120	.	0			c.C1385T						.						180	179	179					11																	129801056		2201	4297	6498	SO:0001583	missense	56980	exon11			AGCTGAGGGATTG	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"Zinc fingers, C2H2-type"	13995	protein-coding gene	gene with protein product	"PRDM zinc finger transcription factor", "PR-domain family member 7", "tristanin"					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.1385C>T	chr11.hg19:g.129801056G>A	ENSP00000354118:p.Pro462Leu	85.0	0.0		69.0	6.0	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	hg19	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.040970	0.75732	.	.	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082;ENST00000533431	T;T;T;T;T;T;T	0.10763	2.86;2.84;2.85;2.85;2.9;2.84;2.94	4.97	4.97	0.65823	.	0.277127	0.36134	N	0.002766	T	0.12902	0.0313	N	0.24115	0.695	0.47905	D	0.999544	B;D;P;B;P;P;P	0.57571	0.437;0.98;0.573;0.437;0.573;0.612;0.573	B;P;B;B;B;B;B	0.49085	0.098;0.6;0.199;0.098;0.199;0.138;0.199	T	0.02431	-1.1160	10	0.56958	D	0.05	-16.3028	16.09	0.81086	0.0:0.0:1.0:0.0	.	376;462;462;462;376;376;376	B7ZL72;Q9NQV6-4;G3XAE5;Q9NQV6;Q9NQV6-5;Q9NQV6-2;Q9NQV6-1	.;.;.;PRD10_HUMAN;.;.;.	L	462;376;462;376;436;376;179	ENSP00000351686:P462L;ENSP00000302669:P376L;ENSP00000354118:P462L;ENSP00000398431:P376L;ENSP00000431262:P436L;ENSP00000432237:P376L;ENSP00000435940:P179L	ENSP00000302669:P376L	P	-	2	0	PRDM10	129306266	1.000000	0.71417	0.962000	0.40283	0.972000	0.66771	5.558000	0.67319	2.461000	0.83175	0.585000	0.79938	CCT	.	.		0.542	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		A	129801056	G	A	129801056	3	1	228	1	0	0	0	0	1	0	0	0	12463	1000	35	3	2145	3	PRDM10	11	129801056	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	51809244	129801056	5205460	89	32185										
ZNF384	171017	hgsc.bcm.edu	37	chr12	6787319	6787319	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gtcttgccgtctttctgatgGtcatcatcatcctcagggga	10	11	7	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr12:6787319G>T	ENST00000396801.3	-	6	867	c.660C>A	c.(658-660)gaC>gaA	p.D220E	ZNF384_ENST00000355772.4_Missense_Mutation_p.D165E|ZNF384_ENST00000319770.3_Missense_Mutation_p.D204E|ZNF384_ENST00000396795.1_Missense_Mutation_p.D220E|ZNF384_ENST00000396799.2_Missense_Mutation_p.D220E|ZNF384_ENST00000361959.3_Missense_Mutation_p.D220E	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	220					nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)		EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						CTTTCTGATGGTCATCATCAT	0.572			T	"EWSR1, TAF15 "	ALL																																p.D220E		Atlas-SNP	.		Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	.	ZNF384	102	.	0			c.C660A						.						159	149	152					12																	6787319		2203	4300	6503	SO:0001583	missense	171017	exon6			CTGATGGTCATCA	U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"Zinc fingers, C2H2-type"	11955	protein-coding gene	gene with protein product		609951	"trinucleotide repeat containing 1"	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.660C>A	chr12.hg19:g.6787319G>T	ENSP00000380019:p.Asp220Glu	46.0	0.0		29.0	8.0	NM_133476	O15407|Q7Z722|Q8N938	Missense_Mutation	SNP	ENST00000396801.3	hg19	CCDS44817.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.528617	0.27299	.	.	ENSG00000126746	ENST00000319770;ENST00000396795;ENST00000396801;ENST00000361959;ENST00000355772;ENST00000396799;ENST00000417772;ENST00000436774;ENST00000542796	T;T;T;T;T;T;T	0.76186	3.27;3.2;-1.0;-1.0;3.26;3.2;3.56	5.48	4.6	0.57074	.	0.353173	0.29113	N	0.013103	T	0.52725	0.1752	N	0.04508	-0.205	0.36089	D	0.843333	B;P;B;B;B	0.35894	0.145;0.526;0.049;0.165;0.165	B;B;B;B;B	0.37601	0.048;0.254;0.028;0.069;0.069	T	0.59311	-0.7478	10	0.19590	T	0.45	-15.1413	12.5638	0.56297	0.0768:0.0:0.9232:0.0	.	220;220;165;204;220	Q8TF68;E9PHB3;Q8TF68-3;F8W6Q3;Q8TF68-2	ZN384_HUMAN;.;.;.;.	E	204;220;220;220;165;220;220;204;204	ENSP00000321650:D204E;ENSP00000380013:D220E;ENSP00000380019:D220E;ENSP00000354592:D220E;ENSP00000348018:D165E;ENSP00000380017:D220E;ENSP00000412911:D204E	ENSP00000321650:D204E	D	-	3	2	ZNF384	6657580	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.274000	0.65569	1.310000	0.45006	0.591000	0.81541	GAC	.	.		0.572	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400712.1			T	6787319	G	T	6787319	3	4	228	1	0	0	0	0	1	0	0	0	17890	1252	44	3	1097	3	ZNF384	12	6787319	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		6787319	127064576	90	32186										
TAS2R7	50837	hgsc.bcm.edu	37	chr12	10955114	10955114	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	atgcattccctaagatccccActgaaaactctccaactgct	4	15	1	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr12:10955114A>T	ENST00000240687.2	-	1	112	c.56T>A	c.(55-57)gTg>gAg	p.V19E		NM_023919.2	NP_076408.1	Q9NYW3	TA2R7_HUMAN	taste receptor, type 2, member 7	19					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			kidney(1)|large_intestine(1)|lung(3)|skin(2)|stomach(3)	10						TAAGATCCCCACTGAAAACTC	0.403																																					p.V19E		Atlas-SNP	.											.	TAS2R7	35	.	0			c.T56A						.						113	118	116					12																	10955114		2203	4300	6503	SO:0001583	missense	50837	exon1			ATCCCCACTGAAA	AF227133	CCDS8631.1	12p13	2012-08-22			ENSG00000121377	ENSG00000121377		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14913	protein-coding gene	gene with protein product		604793				10761934, 10766242	Standard	NM_023919		Approved	T2R7, TRB4	uc001qyv.3	Q9NYW3	OTTHUMG00000168505	ENST00000240687.2:c.56T>A	chr12.hg19:g.10955114A>T	ENSP00000240687:p.Val19Glu	119.0	0.0		95.0	13.0	NM_023919	Q645Y1	Missense_Mutation	SNP	ENST00000240687.2	hg19	CCDS8631.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.854547	0.32791	.	.	ENSG00000121377	ENST00000240687	T	0.44881	0.91	5.36	4.2	0.49525	.	0.475878	0.18998	N	0.125423	T	0.57858	0.2082	M	0.78049	2.395	0.21675	N	0.999593	P	0.52463	0.953	P	0.56865	0.808	T	0.53078	-0.8489	10	0.87932	D	0	.	9.9143	0.41425	0.8476:0.0:0.0:0.1524	.	19	Q9NYW3	TA2R7_HUMAN	E	19	ENSP00000240687:V19E	ENSP00000240687:V19E	V	-	2	0	TAS2R7	10846381	0.001000	0.12720	0.022000	0.16811	0.011000	0.07611	1.165000	0.31822	1.026000	0.39733	0.455000	0.32223	GTG	.	.		0.403	TAS2R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399931.1			T	10955114	A	T	10955114	3	4	228	1	0	0	0	0	1	0	0	0	15601	159	6	4	904	4	TAS2R7	12	10955114	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	4167795	10955114	122896781	91	32187										
CEP290	80184	hgsc.bcm.edu	37	chr12	88508214	88508214	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tacattaactagtctttcaaGgctagggataattagagatg	9	5	2	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr12:88508214G>T	ENST00000552810.1	-	20	2378	c.2035C>A	c.(2035-2037)Ctt>Att	p.L679I	CEP290_ENST00000397838.3_5'UTR|CEP290_ENST00000309041.7_Missense_Mutation_p.L681I	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	679					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						AGTCTTTCAAGGCTAGGGATA	0.338																																					p.L679I		Atlas-SNP	.											.	CEP290	195	.	0			c.C2035A						.						156	138	144					12																	88508214		1602	3564	5166	SO:0001583	missense	80184	exon20			TTTCAAGGCTAGG	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.2035C>A	chr12.hg19:g.88508214G>T	ENSP00000448012:p.Leu679Ile	76.0	0.0		84.0	4.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.995407	0.74703	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998	T;T	0.79352	-1.26;-1.26	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000001	D	0.84750	0.5541	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.78314	0.945;0.991	T	0.82500	-0.0426	10	0.34782	T	0.22	.	11.8573	0.52446	0.1342:0.0:0.8658:0.0	.	679;679	Q05BJ6;O15078	.;CE290_HUMAN	I	679;681;679	ENSP00000448012:L679I;ENSP00000308021:L681I	ENSP00000308021:L681I	L	-	1	0	CEP290	87032345	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.264000	0.58859	2.880000	0.98712	0.650000	0.86243	CTT	.	.		0.338	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		T	88508214	G	T	88508214	3	4	228	1	0	0	0	0	1	0	0	0	3255	1000	35	3	5544	3	CEP290	12	88508214	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	77553100	88508214	45343681	92	32188										
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94697637	94697637	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	atttgcctccattgtcatccTcagaaatggaagaattttta	6	8	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr12:94697637T>G	ENST00000258526.4	+	29	4741	c.4492T>G	c.(4492-4494)Tca>Gca	p.S1498A	PLXNC1_ENST00000547057.1_Missense_Mutation_p.S545A|PLXNC1_ENST00000545312.1_Missense_Mutation_p.S237A	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1498					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						ATTGTCATCCTCAGAAATGGA	0.343																																					p.S1498A		Atlas-SNP	.											.	PLXNC1	135	.	0			c.T4492G						.						83	86	85					12																	94697637		2203	4300	6503	SO:0001583	missense	10154	exon29			TCATCCTCAGAAA	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.4492T>G	chr12.hg19:g.94697637T>G	ENSP00000258526:p.Ser1498Ala	310.0	0.0		243.0	23.0	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	T	11.58	1.679831	0.29783	.	.	ENSG00000136040	ENST00000258526;ENST00000547057;ENST00000545312	T;T;T	0.11495	2.77;2.77;2.77	5.27	4.12	0.48240	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.479350	0.22467	N	0.059664	T	0.04543	0.0124	N	0.03608	-0.345	0.25912	N	0.983229	B;B	0.13594	0.0;0.008	B;B	0.15870	0.0;0.014	T	0.36456	-0.9747	10	0.31617	T	0.26	.	7.0673	0.25159	0.0:0.0739:0.2727:0.6534	.	545;1498	B4DHQ7;O60486	.;PLXC1_HUMAN	A	1498;545;237	ENSP00000258526:S1498A;ENSP00000446720:S545A;ENSP00000439225:S237A	ENSP00000258526:S1498A	S	+	1	0	PLXNC1	93221768	0.259000	0.24043	1.000000	0.80357	0.994000	0.84299	0.697000	0.25556	0.839000	0.34971	0.533000	0.62120	TCA	.	.		0.343	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			G	94697637	T	G	94697637	3	3	228	1	0	0	0	0	1	0	0	0	12135	1551	54	5	4606	5	PLXNC1	12	94697637	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	6189423	94697637	39154258	93	32189										
CCDC63	160762	hgsc.bcm.edu	37	chr12	111345215	111345215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	aggagaatcggagtaaggaaGtgcgcggagacagcctgcct	16	8	0	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr12:111345215G>A	ENST00000308208.5	+	12	1869	c.1627G>A	c.(1627-1629)Gtg>Atg	p.V543M	CCDC63_ENST00000552694.1_Missense_Mutation_p.V464M|CCDC63_ENST00000545036.1_Missense_Mutation_p.V503M	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	543										NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						GAGTAAGGAAGTGCGCGGAGA	0.527																																					p.V543M		Atlas-SNP	.											.	CCDC63	89	.	0			c.G1627A						.						95	74	81					12																	111345215		2203	4300	6503	SO:0001583	missense	160762	exon12			AAGGAAGTGCGCG	AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"outer row dynein assembly 5 homolog (Chlamydomonas)"						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1627G>A	chr12.hg19:g.111345215G>A	ENSP00000312399:p.Val543Met	97.0	0.0		79.0	6.0	NM_152591	B4DY03|Q0P603|Q6P2E1	Missense_Mutation	SNP	ENST00000308208.5	hg19	CCDS9151.1	.	.	.	.	.	.	.	.	.	.	G	2.280	-0.365001	0.05103	.	.	ENSG00000173093	ENST00000545036;ENST00000308208;ENST00000552694	T;T;T	0.32272	1.46;1.46;1.46	3.21	-6.43	0.01926	.	2.903520	0.01240	N	0.008599	T	0.12944	0.0314	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.09377	0.004	T	0.13361	-1.0512	10	0.30078	T	0.28	.	2.1649	0.03834	0.18:0.2014:0.4094:0.2092	.	543	Q8NA47	CCD63_HUMAN	M	503;543;464	ENSP00000445881:V503M;ENSP00000312399:V543M;ENSP00000450217:V464M	ENSP00000312399:V543M	V	+	1	0	CCDC63	109829598	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-5.477000	0.00119	-3.043000	0.00262	-0.511000	0.04467	GTG	.	.		0.527	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591		A	111345215	G	A	111345215	3	1	228	1	0	0	0	0	1	0	0	0	2836	1029	36	3	1669	3	CCDC63	12	111345215	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	16647578	111345215	22506680	94	32190										
FLT1	2321	hgsc.bcm.edu	37	chr13	29041086	29041086	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tctgtttccttcttctttgaAgtaggtacagctagatattt	7	7	3	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr13:29041086A>G	ENST00000282397.4	-	3	593	c.342T>C	c.(340-342)acT>acC	p.T114T	FLT1_ENST00000541932.1_Silent_p.T114T|FLT1_ENST00000539099.1_Silent_p.T114T	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	114	Ig-like C2-type 1.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCTTCTTTGAAGTAGGTACAG	0.368																																					p.T114T		Atlas-SNP	.											.	FLT1	393	.	0			c.T342C						.						143	137	139					13																	29041086		2203	4300	6503	SO:0001819	synonymous_variant	2321	exon3			CTTTGAAGTAGGT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.342T>C	chr13.hg19:g.29041086A>G		100.0	0.0		71.0	7.0	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.		0.368	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			G	29041086	A	G	29041086	2	3	228	1	0	0	0	0	0	0	0	1	5949	59	3	2		2	FLT1	13	29041086	Silent	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10		29041086	86128792	95	32191										
FNDC3A	22862	hgsc.bcm.edu	37	chr13	49649455	49649455	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tacaagttaacccaggagaaGcatttacaataagaagagaa	8	6	0	3			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr13:49649455G>A	ENST00000492622.2	+	3	435	c.130G>A	c.(130-132)Gca>Aca	p.A44T	FNDC3A_ENST00000541916.1_Missense_Mutation_p.A44T	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	44					fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		CCCAGGAGAAGCATTTACAAT	0.303																																					p.A44T		Atlas-SNP	.											.	FNDC3A	93	.	0			c.G130A						.						151	151	151					13																	49649455		1820	4076	5896	SO:0001583	missense	22862	exon3			GGAGAAGCATTTA	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"Fibronectin type III domain containing"	20296	protein-coding gene	gene with protein product		615794	"fibronectin type III domain containing 3"	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.130G>A	chr13.hg19:g.49649455G>A	ENSP00000417257:p.Ala44Thr	404.0	0.0		280.0	16.0	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	hg19	CCDS41886.1	.	.	.	.	.	.	.	.	.	.	G	10.10	1.256911	0.22965	.	.	ENSG00000102531	ENST00000492622;ENST00000541916	T;T	0.32272	1.46;1.46	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000002	T	0.17577	0.0422	N	0.11154	0.105	0.49299	D	0.999776	B	0.21225	0.053	B	0.19666	0.026	T	0.08493	-1.0719	10	0.02654	T	1	-8.388	18.8844	0.92370	0.0:0.0:1.0:0.0	.	44	Q9Y2H6	FND3A_HUMAN	T	44	ENSP00000417257:A44T;ENSP00000441831:A44T	ENSP00000420275:A44T	A	+	1	0	FNDC3A	48547456	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	5.980000	0.70516	2.809000	0.96659	0.655000	0.94253	GCA	.	.		0.303	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		A	49649455	G	A	49649455	3	1	228	1	0	0	0	0	1	0	0	0	5977	971	34	3	136	3	FNDC3A	13	49649455	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	20608369	49649455	65520423	96	32192										
OR4K1	79544	hgsc.bcm.edu	37	chr14	20403852	20403852	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cacacaaatgaatcgatggtGtctgagtttgtacttttggg	11	6	1	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr14:20403852G>A	ENST00000285600.4	+	1	86	c.27G>A	c.(25-27)gtG>gtA	p.V9V		NM_001004063.2	NP_001004063.2	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K, member 1	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(24)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		AATCGATGGTGTCTGAGTTTG	0.368																																					p.V9V		Atlas-SNP	.											.	OR4K1	108	.	0			c.G27A						.						339	379	366					14																	20403852		2203	4300	6503	SO:0001819	synonymous_variant	79544	exon1			GATGGTGTCTGAG		CCDS32025.1	14q11.2	2013-09-23			ENSG00000155249	ENSG00000155249		"GPCR / Class A : Olfactory receptors"	14726	protein-coding gene	gene with protein product							Standard	NM_001004063		Approved		uc001vwj.2	Q8NGD4	OTTHUMG00000170633	ENST00000285600.4:c.27G>A	chr14.hg19:g.20403852G>A		93.0	0.0		97.0	39.0	NM_001004063	B9EKV9|Q8NGD6|Q96R73	Silent	SNP	ENST00000285600.4	hg19	CCDS32025.1																																																																																			.	.		0.368	OR4K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409881.1			A	20403852	G	A	20403852	2	1	228	1	0	0	0	0	0	0	0	1	11076	1364	48	3		3	OR4K1	14	20403852	Silent	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		20403852	86945688	97	32193										
VIPAR	63894	hgsc.bcm.edu	37	chr14	77919642	77919642	+	Splice_Site	DEL	T	T	-													0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ctagggactcttctacttacTtcccacaggttccccactcc							TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr14:77919642delT	ENST00000553888.1	-	3	706	c.196delA	c.(196-198)agt>gt	p.S66fs	VIPAS39_ENST00000557658.1_Splice_Site_p.S66fs|VIPAS39_ENST00000327028.4_Splice_Site_p.S66fs|VIPAS39_ENST00000343765.2_Splice_Site_p.S66fs|VIPAS39_ENST00000448935.2_Splice_Site_p.S66fs|VIPAS39_ENST00000556412.1_Splice_Site_p.S92fs	NM_001193314.1|NM_001193317.1|NM_022067.3	NP_001180243.1|NP_001180246.1|NP_071350.2	Q9H9C1	SPE39_HUMAN	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	66					cell differentiation (GO:0030154)|endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|late endosome (GO:0005770)|recycling endosome (GO:0055037)											TTCTACTTACTTCCCACAGGT	0.498																																					.		Atlas-INDEL	.											.	.	.	.	0			c.196+1A>-						.						268	263	265					14																	77919642		2203	4300	6503	SO:0001630	splice_region_variant	63894	exon4			.	AK022925	CCDS9862.1, CCDS53905.1	14q24.3-q31	2013-08-14	2012-07-24	2012-07-24	ENSG00000151445	ENSG00000151445			20347	protein-coding gene	gene with protein product	"VPS33B interacting protein, apical-basolateral polarity regulator"	613401	"chromosome 14 open reading frame 133"	C14orf133		20190753, 19109425, 22753090, 23002115, 23918659	Standard	NM_022067		Approved	VIPAR, VPS16B, SPE-39, SPE39, hSPE-39	uc001xtu.2	Q9H9C1		ENST00000553888.1:c.196+1A>-	chr14.hg19:g.77919642delT		86.0	0.0		72.0	27.0	NM_001193316	B4DPI6|O95434|Q9H7E1|Q9H9I9	Splice_Site	DEL	ENST00000553888.1	hg19	CCDS9862.1																																																																																			.	.		0.498	VIPAS39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414008.1	NM_022067	Frame_Shift_Del	-	77919642	T	-	77919642	8	5	228	1	0	1	0	1	0	0	1	0	17183	1623	56	0	1357	0	VIPAR	14	77919642	Splice_Site	DEL	T	TCGA-DD-AAVV-01A-11D-A40R-10	57515790	77919642	29429898	98	32194										
FSIP1	161835	hgsc.bcm.edu	37	chr15	40005705	40005705	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ctcagccgattatgcagatcGcgttgctctttggtgttcct	10	11	2	1	rs557574177	byFrequency	TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr15:40005705G>C	ENST00000350221.3	-	10	1337	c.1128C>G	c.(1126-1128)cgC>cgG	p.R376R		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	376										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TATGCAGATCGCGTTGCTCTT	0.313																																					p.R376R		Atlas-SNP	.											.	FSIP1	53	.	0			c.C1128G						.						232	231	232					15																	40005705		2203	4300	6503	SO:0001819	synonymous_variant	161835	exon10			CAGATCGCGTTGC	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1128C>G	chr15.hg19:g.40005705G>C		98.0	0.0		104.0	31.0	NM_152597	Q6X2C8|Q86Y89	Silent	SNP	ENST00000350221.3	hg19	CCDS10050.1																																																																																			.	.		0.313	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		C	40005705	G	C	40005705	2	2	228	1	0	0	0	0	0	0	0	1	6082	1074	38	4		4	FSIP1	15	40005705	Silent	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		40005705	62525687	99	32195										
HERC1	8925	hgsc.bcm.edu	37	chr15	63970130	63970130	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	agcagcgtggcatggcgcccAgtttgcttgtgaacacaccg	13	12	0	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr15:63970130A>G	ENST00000443617.2	-	37	7071	c.6984T>C	c.(6982-6984)acT>acC	p.T2328T	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2328					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CATGGCGCCCAGTTTGCTTGT	0.532																																					p.T2328T		Atlas-SNP	.											.	HERC1	624	.	0			c.T6984C						.						153	159	157					15																	63970130		2149	4256	6405	SO:0001819	synonymous_variant	8925	exon37			GCGCCCAGTTTGC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.6984T>C	chr15.hg19:g.63970130A>G		87.0	0.0		59.0	4.0	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.		0.532	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		G	63970130	A	G	63970130	2	3	228	1	0	0	0	0	0	0	0	1	7066	175	7	2		2	HERC1	15	63970130	Silent	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	23964425	63970130	38561262	100	32196										
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65694784	65694784	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ggcctgcatcactctcctgaAcatccaggatctgaaggacg	10	13	3	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr15:65694784A>G	ENST00000352385.2	-	4	814	c.605T>C	c.(604-606)gTt>gCt	p.V202A		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	202	Ig-like C2-type 2.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						ACTCTCCTGAACATCCAGGAT	0.637																																					p.V202A		Atlas-SNP	.											.	IGDCC4	95	.	0			c.T605C						.						48	41	44					15																	65694784		2196	4291	6487	SO:0001583	missense	57722	exon4			TCCTGAACATCCA		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.605T>C	chr15.hg19:g.65694784A>G	ENSP00000319623:p.Val202Ala	98.0	0.0		74.0	9.0	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.545597	0.86022	.	.	ENSG00000103742	ENST00000352385	T	0.68624	-0.34	5.17	5.17	0.71159	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.203210	0.41605	D	0.000850	T	0.72399	0.3455	L	0.41356	1.27	0.53688	D	0.99997	P	0.52692	0.955	P	0.60173	0.87	T	0.74970	-0.3482	10	0.62326	D	0.03	-2.7325	13.9984	0.64416	1.0:0.0:0.0:0.0	.	202	Q8TDY8	IGDC4_HUMAN	A	202	ENSP00000319623:V202A	ENSP00000319623:V202A	V	-	2	0	IGDCC4	63481837	0.999000	0.42202	0.165000	0.22776	0.944000	0.59088	8.393000	0.90182	1.946000	0.56461	0.459000	0.35465	GTT	.	.		0.637	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		G	65694784	A	G	65694784	3	3	228	1	0	0	0	0	1	0	0	0	7578	43	2	2	3215	2	IGDCC4	15	65694784	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	1724654	65694784	36836608	101	32197										
CRAMP1L	57585	hgsc.bcm.edu	37	chr16	1706116	1706116	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gatcctgggcatccagagtgGgcagggcacggcccggggcc	18	13	0	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr16:1706116G>C	ENST00000397412.3	+	10	1457	c.1358G>C	c.(1357-1359)gGg>gCg	p.G453A	CRAMP1L_ENST00000262317.4_Intron|CRAMP1L_ENST00000436138.3_Missense_Mutation_p.G450A|LA16c-431H6.6_ENST00000454337.1_Intron|CRAMP1L_ENST00000293925.5_Missense_Mutation_p.G453A			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	453						nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						ATCCAGAGTGGGCAGGGCACG	0.716																																					p.G453A		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.G1358C						.						9	12	11					16																	1706116		1904	4060	5964	SO:0001583	missense	57585	exon9			AGAGTGGGCAGGG	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"Crm (Cramped Drosophila)-like"				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.1358G>C	chr16.hg19:g.1706116G>C	ENSP00000380559:p.Gly453Ala	142.0	0.0		132.0	6.0	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Missense_Mutation	SNP	ENST00000397412.3	hg19	CCDS10440.2	.	.	.	.	.	.	.	.	.	.	G	9.846	1.192246	0.21954	.	.	ENSG00000007545	ENST00000397412;ENST00000293925;ENST00000436138	.	.	.	5.02	5.02	0.67125	.	0.062767	0.64402	D	0.000006	T	0.50326	0.1609	N	0.17082	0.46	0.80722	D	1	P	0.36110	0.537	B	0.42555	0.391	T	0.52351	-0.8587	9	0.41790	T	0.15	-34.9142	18.5282	0.90981	0.0:0.0:1.0:0.0	.	453	Q96RY5	CRML_HUMAN	A	453;453;450	.	ENSP00000293925:G453A	G	+	2	0	CRAMP1L	1646117	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	5.129000	0.64739	2.592000	0.87571	0.655000	0.94253	GGG	.	.		0.716	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4			C	1706116	G	C	1706116	3	2	228	1	0	0	0	0	1	0	0	0	3848	1232	43	4	1392	4	CRAMP1L	16	1706116	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		1706116	88648637	102	32198										
TP53	7157	hgsc.bcm.edu	37	chr17	7578461	7578461	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gtagatggccatggcgcggaCgcgggtgccgggcgggggtg	23	9	0	1	rs121912654		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr17:7578461C>A	ENST00000269305.4	-	5	658	c.469G>T	c.(469-471)Gtc>Ttc	p.V157F	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.V157F|TP53_ENST00000445888.2_Missense_Mutation_p.V157F|TP53_ENST00000420246.2_Missense_Mutation_p.V157F|TP53_ENST00000455263.2_Missense_Mutation_p.V157F|TP53_ENST00000413465.2_Missense_Mutation_p.V157F	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	157	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> A (in sporadic cancers; somatic mutation).|V -> D (in sporadic cancers; somatic mutation).|V -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|V -> G (in sporadic cancers; somatic mutation).|V -> I (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9419979}.|V -> L (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V157F(161)|p.V157I(10)|p.0?(8)|p.V157L(6)|p.V64F(6)|p.V25F(6)|p.R156_I162delRVRAMAI(2)|p.T155fs*23(2)|p.V157del(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.V157fs*22(2)|p.V157fs*24(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156_V157del(1)|p.R156_V157insV(1)|p.R156_R158delRVR(1)|p.R156fs*12(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.V157_M160delVRAM(1)|p.D148fs*23(1)|p.V157_R158delVR(1)|p.S149fs*72(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*20(1)|p.V157_I162delVRAMAI(1)|p.V157fs*23(1)|p.V157fs*21(1)|p.V157fs*25(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGCGCGGACGCGGGTGCCG	0.617		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.V157F	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,+1,5	TP53	33396	.	231	Substitution - Missense(189)|Deletion - Frameshift(15)|Deletion - In frame(14)|Whole gene deletion(8)|Insertion - Frameshift(3)|Insertion - In frame(1)|Complex - frameshift(1)	lung(69)|liver(30)|upper_aerodigestive_tract(26)|breast(19)|oesophagus(14)|ovary(13)|stomach(9)|large_intestine(7)|haematopoietic_and_lymphoid_tissue(7)|central_nervous_system(6)|bone(5)|vulva(4)|urinary_tract(4)|skin(3)|pancreas(3)|endometrium(2)|kidney(2)|biliary_tract(2)|soft_tissue(2)|prostate(1)|adrenal_gland(1)|salivary_gland(1)|thymus(1)	c.G469T						.						50	52	51					17																	7578461		2202	4300	6502	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CGCGGACGCGGGT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.469G>T	chr17.hg19:g.7578461C>A	ENSP00000269305:p.Val157Phe	118.0	0.0		111.0	48.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.865109	0.32977	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99822	-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94	5.47	2.42	0.29668	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.216722	0.39210	N	0.001429	D	0.99718	0.9891	M	0.86420	2.815	0.33606	D	0.603	D;D;D;D;D;D;D	0.89917	1.0;0.998;0.999;0.999;0.999;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.997;0.994;0.984;0.981;0.996;0.998;0.996	D	0.97998	1.0358	10	0.72032	D	0.01	-16.7152	5.3541	0.16051	0.0:0.6119:0.146:0.2421	.	118;157;157;64;157;157;157	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	F	157;157;157;157;157;157;146;64;25;64;25;157	ENSP00000410739:V157F;ENSP00000352610:V157F;ENSP00000269305:V157F;ENSP00000398846:V157F;ENSP00000391127:V157F;ENSP00000391478:V157F;ENSP00000425104:V25F;ENSP00000423862:V64F;ENSP00000424104:V157F	ENSP00000269305:V157F	V	-	1	0	TP53	7519186	0.137000	0.22531	0.013000	0.15412	0.150000	0.21749	0.548000	0.23314	0.386000	0.24997	-0.253000	0.11424	GTC	.	.		0.617	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578461	C	A	7578461	3	1	228	1	0	0	0	0	1	0	0	0	16396	536	19	1	829	1	TP53	17	7578461	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10		7578461	73616749	103	32199										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11783485	11783485	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	attgatcctgttctgggaccCctgcttgggagagaagtcat	12	9	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr17:11783485C>T	ENST00000262442.4	+	54	10637	c.10569C>T	c.(10567-10569)ccC>ccT	p.P3523P	DNAH9_ENST00000454412.2_Silent_p.P3523P|DNAH9_ENST00000608377.1_5'Flank	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3523	AAA 5. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TTCTGGGACCCCTGCTTGGGA	0.507																																					p.P3523P		Atlas-SNP	.											.	DNAH9	695	.	0			c.C10569T						.						100	99	99					17																	11783485		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon54			GGGACCCCTGCTT	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10569C>T	chr17.hg19:g.11783485C>T		83.0	0.0		74.0	4.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	hg19	CCDS11160.1																																																																																			.	.		0.507	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11783485	C	T	11783485	2	4	228	1	0	0	0	0	0	0	0	1	4610	610	22	3		3	DNAH9	17	11783485	Silent	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	4205024	11783485	69411725	104	32200										
GPR179	440435	hgsc.bcm.edu	37	chr17	36486669	36486669	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gcctgatgggtggatgaggcAgccttctcctagcctcctca	12	13	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr17:36486669A>T	ENST00000342292.4	-	11	2803	c.2783T>A	c.(2782-2784)cTg>cAg	p.L928Q	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	928					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TGGATGAGGCAGCCTTCTCCT	0.632																																					p.L928Q		Atlas-SNP	.											.	GPR179	170	.	0			c.T2783A						.						15	17	17					17																	36486669		2112	4237	6349	SO:0001583	missense	440435	exon11			TGAGGCAGCCTTC		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.2783T>A	chr17.hg19:g.36486669A>T	ENSP00000345060:p.Leu928Gln	44.0	0.0		53.0	11.0	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	A	9.380	1.072728	0.20147	.	.	ENSG00000188888	ENST00000342292	T	0.56611	0.45	4.98	1.51	0.23008	.	0.565570	0.15109	N	0.280073	T	0.30947	0.0781	L	0.29908	0.895	0.09310	N	1	P	0.40083	0.702	B	0.34418	0.182	T	0.10177	-1.0641	10	0.19147	T	0.46	0.0032	5.776	0.18279	0.5798:0.0:0.4202:0.0	.	928	Q6PRD1	GP179_HUMAN	Q	928	ENSP00000345060:L928Q	ENSP00000345060:L928Q	L	-	2	0	GPR179	33740195	0.113000	0.22115	0.211000	0.23655	0.161000	0.22273	0.627000	0.24506	0.413000	0.25759	0.459000	0.35465	CTG	.	.		0.632	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			T	36486669	A	T	36486669	3	4	228	1	0	0	0	0	1	0	0	0	6682	188	7	4	4324	4	GPR179	17	36486669	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	24703184	36486669	44708541	105	32201										
EXOC7	23265	hgsc.bcm.edu	37	chr17	74084172	74084172	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gctcgtgtacggtgccgtccTtcggcatgttgtactccttg	12	12	0	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr17:74084172T>C	ENST00000335146.7	-	12	1537	c.1484A>G	c.(1483-1485)aAg>aGg	p.K495R	EXOC7_ENST00000332065.5_Missense_Mutation_p.K413R|EXOC7_ENST00000607838.1_Missense_Mutation_p.K467R|EXOC7_ENST00000405575.4_Missense_Mutation_p.K467R|EXOC7_ENST00000589210.1_Missense_Mutation_p.K444R|EXOC7_ENST00000411744.2_Missense_Mutation_p.K436R|EXOC7_ENST00000467929.2_Missense_Mutation_p.K403R			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	495					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			GGTGCCGTCCTTCGGCATGTT	0.647																																					p.K495R		Atlas-SNP	.											.	EXOC7	47	.	0			c.A1484G						.						125	107	113					17																	74084172		2203	4300	6503	SO:0001583	missense	23265	exon12			CCGTCCTTCGGCA	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1484A>G	chr17.hg19:g.74084172T>C	ENSP00000334100:p.Lys495Arg	66.0	0.0		64.0	19.0	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145341	0.77888	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.86	4.86	0.63082	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.39860	0.1094	L	0.33485	1.01	0.80722	D	1	B;B;B;B;B;P;B	0.40230	0.218;0.007;0.368;0.035;0.034;0.708;0.063	B;B;B;B;B;B;B	0.36534	0.087;0.009;0.199;0.029;0.05;0.227;0.037	T	0.20773	-1.0265	9	0.18710	T	0.47	-27.8942	14.4628	0.67462	0.0:0.0:0.0:1.0	.	436;467;403;403;495;413;444	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	R	413;333;467;495;444;403;436	.	ENSP00000333806:K413R	K	-	2	0	EXOC7	71595767	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.720000	0.84759	1.807000	0.52817	0.528000	0.53228	AAG	.	.		0.647	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		C	74084172	T	C	74084172	3	2	228	1	0	0	0	0	1	0	0	0	5312	1609	56	2	759	2	EXOC7	17	74084172	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	37597503	74084172	7111038	106	32202										
FASN	2194	hgsc.bcm.edu	37	chr17	80038728	80038728	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gggccctccgggttcaccagCagggagcgcaggttcagctg	16	13	2	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr17:80038728C>A	ENST00000306749.2	-	39	6884	c.6666G>T	c.(6664-6666)ctG>ctT	p.L2222L	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2222	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GGTTCACCAGCAGGGAGCGCA	0.672																																					p.L2222L	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G6666T						.						24	28	26					17																	80038728		2198	4294	6492	SO:0001819	synonymous_variant	2194	exon39			CACCAGCAGGGAG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6666G>T	chr17.hg19:g.80038728C>A		111.0	0.0		96.0	9.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.672	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80038728	C	A	80038728	2	1	228	1	0	0	0	0	0	0	0	1	5691	697	25	3		3	FASN	17	80038728	Silent	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	5954556	80038728	1156482	107	32203										
RNF152	220441	hgsc.bcm.edu	37	chr18	59483459	59483459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ttcggaagtgtgtggaatggCgatgacagccaggacctccg	15	9	0	1	rs561051015	byFrequency	TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr18:59483459C>T	ENST00000312828.3	-	2	1337	c.238G>A	c.(238-240)Gcc>Acc	p.A80T		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	80					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				TGTGGAATGGCGATGACAGCC	0.637													C|||	2	0.000399361	0	0.0029	5008	,	,		18371	0		0	False		,,,				2504	0				p.A80T		Atlas-SNP	.											.	RNF152	37	.	0			c.G238A						.						85	92	90					18																	59483459		2203	4300	6503	SO:0001583	missense	220441	exon2			GAATGGCGATGAC	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"RING-type (C3HC4) zinc fingers"	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.238G>A	chr18.hg19:g.59483459C>T	ENSP00000316628:p.Ala80Thr	123.0	0.0		85.0	7.0	NM_173557	B3KV99|Q52LA4	Missense_Mutation	SNP	ENST00000312828.3	hg19	CCDS11978.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.163620	0.57476	.	.	ENSG00000176641	ENST00000312828	D	0.83419	-1.72	4.97	4.97	0.65823	.	0.122835	0.53938	D	0.000044	T	0.69895	0.3162	N	0.12182	0.205	0.49213	D	0.999769	B	0.10296	0.003	B	0.04013	0.001	T	0.64462	-0.6402	10	0.13470	T	0.59	-3.2112	18.4187	0.90579	0.0:1.0:0.0:0.0	.	80	Q8N8N0	RN152_HUMAN	T	80	ENSP00000316628:A80T	ENSP00000316628:A80T	A	-	1	0	RNF152	57634439	0.999000	0.42202	0.997000	0.53966	0.898000	0.52572	4.107000	0.57811	2.600000	0.87896	0.655000	0.94253	GCC	.	.		0.637	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557		T	59483459	C	T	59483459	3	4	228	1	0	0	0	0	1	0	0	0	13468	768	27	1	377	1	RNF152	18	59483459	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10		59483459	18593789	108	32204										
FZR1	51343	hgsc.bcm.edu	37	chr19	3531921	3531921	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gcctccaggggcgctggcctGgaatgctgagcagctgtcgt	16	12	0	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr19:3531921G>A	ENST00000395095.3	+	9	836	c.836G>A	c.(835-837)tGg>tAg	p.W279*	FZR1_ENST00000441788.2_Nonsense_Mutation_p.W279*|FZR1_ENST00000313639.8_Nonsense_Mutation_p.W190*	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	279					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGCTGGCCTGGAATGCTGAG	0.721																																					p.W279X		Atlas-SNP	.											.	FZR1	42	.	0			c.G836A						.						12	16	15					19																	3531921		2190	4282	6472	SO:0001587	stop_gained	51343	exon9			TGGCCTGGAATGC	AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"WD repeat domain containing"	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.836G>A	chr19.hg19:g.3531921G>A	ENSP00000378529:p.Trp279*	76.0	0.0		58.0	5.0	NM_001136198	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Nonsense_Mutation	SNP	ENST00000395095.3	hg19	CCDS45916.1	.	.	.	.	.	.	.	.	.	.	G	37	6.052137	0.97236	.	.	ENSG00000105325	ENST00000441788;ENST00000395095;ENST00000313639	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.2653	16.6845	0.85301	0.0:0.0:1.0:0.0	.	.	.	.	X	279;279;190	.	ENSP00000321800:W190X	W	+	2	0	FZR1	3482921	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	7.689000	0.84165	2.544000	0.85801	0.561000	0.74099	TGG	.	.		0.721	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		A	3531921	G	A	3531921	4	1	228	1	0	0	0	0	0	1	0	0	6146	1357	47	3	870	3	FZR1	19	3531921	Nonsense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		3531921	55597062	109	32205										
TMEM146	257062	hgsc.bcm.edu	37	chr19	5778649	5778649	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	caggcacagagcccccgggaCgccaccgcactcctcacgga	11	19	1	1	rs373865922		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr19:5778649C>T	ENST00000381624.3	+	22	2420	c.2359C>T	c.(2359-2361)Cgc>Tgc	p.R787C	CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	787					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											GCCCCCGGGACGCCACCGCAC	0.582																																					p.R787C		Atlas-SNP	.											.	.	.	.	0			c.C2359T						.	C	CYS/ARG	0,4240		0,0,2120	44	50	48		2359	-2.2	0	19		48	1,8451		0,1,4225	no	missense	TMEM146	NM_152784.3	180	0,1,6345	TT,TC,CC		0.0118,0.0,0.0079	probably-damaging	787/799	5778649	1,12691	2120	4226	6346	SO:0001583	missense	257062	exon22			CCGGGACGCCACC	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.2359C>T	chr19.hg19:g.5778649C>T	ENSP00000371037:p.Arg787Cys	184.0	0.0		140.0	10.0	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	hg19	CCDS12149.2	.	.	.	.	.	.	.	.	.	.	C	5.711	0.315605	0.10789	0.0	1.18E-4	ENSG00000174898	ENST00000381624;ENST00000381613	T	0.26373	1.74	1.09	-2.19	0.07015	.	.	.	.	.	T	0.11537	0.0281	L	0.29908	0.895	0.09310	N	1	P	0.46512	0.879	B	0.28553	0.091	T	0.13818	-1.0495	9	0.87932	D	0	.	5.3079	0.15813	0.4202:0.5798:0.0:0.0	.	787	Q86XM0	TM146_HUMAN	C	787;456	ENSP00000371037:R787C	ENSP00000371026:R456C	R	+	1	0	TMEM146	5729649	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.438000	0.06905	-0.731000	0.04862	-0.410000	0.06199	CGC	.	.		0.582	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		T	5778649	C	T	5778649	3	4	228	1	0	0	0	0	1	0	0	0	16075	536	19	1	2445	1	TMEM146	19	5778649	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	2246728	5778649	53350334	110	32206										
SH2D3A	10045	hgsc.bcm.edu	37	chr19	6755043	6755043	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tcttcctcctcatcctcctcGgcctcccaccatggggcctc	6	21	2	0	rs145201987		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr19:6755043G>A	ENST00000245908.6	-	5	1049	c.780C>T	c.(778-780)gcC>gcT	p.A260A	SH2D3A_ENST00000599563.1_5'UTR|SH2D3A_ENST00000437152.3_Silent_p.A138A	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	260	Poly-Glu.				JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						CATCCTCCTCGGCCTCCCACC	0.627																																					p.A260A		Atlas-SNP	.											.	SH2D3A	53	.	0			c.C780T						.	G		0,4406		0,0,2203	160	183	175		780	-9.1	0	19	dbSNP_134	175	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	SH2D3A	NM_005490.2		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		260/577	6755043	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	10045	exon5			CTCCTCGGCCTCC	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"SH2 domain containing"	16885	protein-coding gene	gene with protein product		604721	"SH2 domain-containing 3A"			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.780C>T	chr19.hg19:g.6755043G>A		77.0	0.0		53.0	16.0	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Silent	SNP	ENST00000245908.6	hg19	CCDS12173.1																																																																																			.	G|1.000;A|0.000		0.627	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490		A	6755043	G	A	6755043	2	1	228	1	0	0	0	0	0	0	0	1	14248	1103	39	1		1	SH2D3A	19	6755043	Silent	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	976394	6755043	52373940	111	32207										
DPY19L3	147991	hgsc.bcm.edu	37	chr19	32930029	32930029	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tttgtgcagaatagataccaCaagagttgagtttaccatcc	8	8	0	4			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr19:32930029C>T	ENST00000342179.5	+	7	823	c.608C>T	c.(607-609)aCa>aTa	p.T203I	DPY19L3_ENST00000392250.2_Missense_Mutation_p.T203I|DPY19L3_ENST00000586987.1_Missense_Mutation_p.T203I	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	203						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					ATAGATACCACAAGAGTTGAG	0.378																																					p.T203I		Atlas-SNP	.											.	DPY19L3	70	.	0			c.C608T						.						178	172	174					19																	32930029		2203	4300	6503	SO:0001583	missense	147991	exon7			ATACCACAAGAGT		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.608C>T	chr19.hg19:g.32930029C>T	ENSP00000344937:p.Thr203Ile	88.0	0.0		117.0	23.0	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Missense_Mutation	SNP	ENST00000342179.5	hg19	CCDS12422.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599513	0.87055	.	.	ENSG00000178904	ENST00000392250;ENST00000319326;ENST00000342179	T;T	0.59083	0.29;0.29	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.79335	0.4428	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80632	-0.1296	10	0.54805	T	0.06	-20.3538	19.4882	0.95039	0.0:1.0:0.0:0.0	.	203	Q6ZPD9	D19L3_HUMAN	I	203	ENSP00000376081:T203I;ENSP00000344937:T203I	ENSP00000315672:T203I	T	+	2	0	DPY19L3	37621869	1.000000	0.71417	0.974000	0.42286	0.996000	0.88848	7.601000	0.82783	2.618000	0.88619	0.563000	0.77884	ACA	.	.		0.378	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325		T	32930029	C	T	32930029	3	4	228	1	0	0	0	0	1	0	0	0	4744	478	17	3	630	3	DPY19L3	19	32930029	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	26174986	32930029	26198954	112	32208										
RYR1	6261	hgsc.bcm.edu	37	chr19	38960049	38960049	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ccatctgtggcctccaggaaGgcttcgagccatttgccatc	10	14	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr19:38960049G>T	ENST00000359596.3	+	27	3661	c.3661G>T	c.(3661-3663)Ggc>Tgc	p.G1221C	RYR1_ENST00000360985.3_Missense_Mutation_p.G1221C|RYR1_ENST00000355481.4_Missense_Mutation_p.G1221C			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1221	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCTCCAGGAAGGCTTCGAGCC	0.602																																					p.G1221C		Atlas-SNP	.											.	RYR1	708	.	0			c.G3661T						.						149	141	144					19																	38960049		2203	4300	6503	SO:0001583	missense	6261	exon27			CAGGAAGGCTTCG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.3661G>T	chr19.hg19:g.38960049G>T	ENSP00000352608:p.Gly1221Cys	75.0	0.0		96.0	36.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	g	16.57	3.160975	0.57368	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98684	-5.06;-5.06;-5.07	3.48	3.48	0.39840	.	0.000000	0.64402	U	0.000008	D	0.98795	0.9594	M	0.68952	2.095	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.83275	0.991;0.996	D	0.99525	1.0959	10	0.87932	D	0	.	14.86	0.70372	0.0:0.0:1.0:0.0	.	1221;1221	P21817-2;P21817	.;RYR1_HUMAN	C	1221	ENSP00000352608:G1221C;ENSP00000347667:G1221C;ENSP00000354254:G1221C	ENSP00000347667:G1221C	G	+	1	0	RYR1	43651889	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.278000	0.95766	1.816000	0.52996	0.434000	0.28630	GGC	.	.		0.602	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38960049	G	T	38960049	3	4	228	1	0	0	0	0	1	0	0	0	13783	1000	35	3	3767	3	RYR1	19	38960049	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	6030020	38960049	20168934	113	32209										
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48185376	48185376	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ggcctcggccctcaggccccCgacagccaggcttccccggc	12	21	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr19:48185376C>G	ENST00000396720.3	+	7	2444	c.2250C>G	c.(2248-2250)ccC>ccG	p.P750P	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	750										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		CTCAGGCCCCCGACAGCCAGG	0.746																																					p.P750P		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.C2250G						.						4	6	5					19																	48185376		1808	3914	5722	SO:0001819	synonymous_variant	29998	exon7			GGCCCCCGACAGC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.2250C>G	chr19.hg19:g.48185376C>G		97.0	0.0		115.0	20.0	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	hg19	CCDS46134.1																																																																																			.	.		0.746	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		G	48185376	C	G	48185376	2	3	228	1	0	0	0	0	0	0	0	1	6482	639	23	4		4	GLTSCR1	19	48185376	Silent	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	9225327	48185376	10943607	114	32210										
IL4I1	259307	hgsc.bcm.edu	37	chr19	50397537	50397537	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gtacccacctggttgagagcCatctggtagatgtcttcggg	13	10	2	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr19:50397537C>A	ENST00000391826.2	-	5	697	c.555G>T	c.(553-555)atG>atT	p.M185I	IL4I1_ENST00000341114.3_Missense_Mutation_p.M207I|IL4I1_ENST00000595948.1_Missense_Mutation_p.M207I	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	185						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	GGTTGAGAGCCATCTGGTAGA	0.617																																					p.M207I		Atlas-SNP	.											.	IL4I1	50	.	0			c.G621T						.						92	89	90					19																	50397537		2203	4300	6503	SO:0001583	missense	259307	exon7			GAGAGCCATCTGG	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.555G>T	chr19.hg19:g.50397537C>A	ENSP00000375702:p.Met185Ile	71.0	0.0		82.0	23.0	NM_172374	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Missense_Mutation	SNP	ENST00000391826.2	hg19	CCDS12787.1	.	.	.	.	.	.	.	.	.	.	C	10.78	1.445856	0.25987	.	.	ENSG00000104951	ENST00000341114;ENST00000391826	D;D	0.92048	-2.96;-2.96	5.38	5.38	0.77491	Amine oxidase (1);	0.433635	0.28647	N	0.014620	D	0.89153	0.6634	L	0.54323	1.7	0.35942	D	0.833319	P;P;P	0.44521	0.804;0.837;0.837	B;B;B	0.38755	0.184;0.281;0.281	D	0.91209	0.4997	10	0.34782	T	0.22	-44.905	14.6045	0.68466	0.0:1.0:0.0:0.0	.	207;207;185	Q96RQ9-2;Q1WMJ3;Q96RQ9	.;.;OXLA_HUMAN	I	207;185	ENSP00000342557:M207I;ENSP00000375702:M185I	ENSP00000342557:M207I	M	-	3	0	IL4I1	55089349	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	0.759000	0.26461	2.521000	0.84997	0.491000	0.48974	ATG	.	.		0.617	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			A	50397537	C	A	50397537	3	1	228	1	0	0	0	0	1	0	0	0	7706	594	21	3	1164	3	IL4I1	19	50397537	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	2212161	50397537	8731446	115	32211										
KLK6	5653	hgsc.bcm.edu	37	chr19	51466671	51466671	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gtttggctgggcgtgccaggCgcaacagcatgatgtcctgg	16	10	0	1	rs553226234		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr19:51466671C>A	ENST00000376851.3	-	4	771	c.332G>T	c.(331-333)cGc>cTc	p.R111L	KLK6_ENST00000376853.4_Intron|KLK6_ENST00000310157.2_Missense_Mutation_p.R111L|KLK6_ENST00000456750.2_Missense_Mutation_p.R4L|KLK6_ENST00000391808.1_Missense_Mutation_p.R4L|CTB-147C22.8_ENST00000601506.1_RNA|KLK6_ENST00000594641.1_Missense_Mutation_p.R111L	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	111	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		GCGTGCCAGGCGCAACAGCAT	0.617																																					p.R111L		Atlas-SNP	.											KLK6,NS,carcinoma,0,1	KLK6	35	.	0			c.G332T						.						90	64	73					19																	51466671		2203	4300	6503	SO:0001583	missense	5653	exon4			GCCAGGCGCAACA	U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"Kallikreins", "Serine peptidases / Serine peptidases"	6367	protein-coding gene	gene with protein product		602652	"protease, serine, 18", "kallikrein 6 (neurosin, zyme)"	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.332G>T	chr19.hg19:g.51466671C>A	ENSP00000366047:p.Arg111Leu	72.0	0.0		100.0	20.0	NM_001012964	A6NJA1|A8MW09|Q6H301	Missense_Mutation	SNP	ENST00000376851.3	hg19	CCDS12811.1	.	.	.	.	.	.	.	.	.	.	N	24.5	4.536267	0.85812	.	.	ENSG00000167755	ENST00000310157;ENST00000376851;ENST00000391808;ENST00000456750	D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58	4.69	-0.0942	0.13646	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.185873	0.26723	N	0.022831	D	0.88250	0.6386	L	0.61387	1.9	0.09310	N	1	D;P	0.56968	0.978;0.678	P;B	0.55222	0.771;0.071	T	0.79586	-0.1742	10	0.87932	D	0	.	3.6265	0.08114	0.1695:0.4454:0.0:0.3851	.	111;4	Q92876;Q92876-2	KLK6_HUMAN;.	L	111;111;4;4	ENSP00000309148:R111L;ENSP00000366047:R111L;ENSP00000375684:R4L;ENSP00000409241:R4L	ENSP00000309148:R111L	R	-	2	0	KLK6	56158483	0.093000	0.21703	0.396000	0.26296	0.892000	0.51952	0.379000	0.20585	0.178000	0.19917	0.486000	0.48141	CGC	.	.		0.617	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774		A	51466671	C	A	51466671	3	1	228	1	0	0	0	0	1	0	0	0	8417	768	27	1	414	1	KLK6	19	51466671	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	1069134	51466671	7662312	116	32212										
ZNF616	90317	hgsc.bcm.edu	37	chr19	52618477	52618477	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cagtctgatgaagtctaagaTggacacgctgactaaaggaa	11	7	2	4			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr19:52618477T>C	ENST00000600228.1	-	4	2201	c.1940A>G	c.(1939-1941)cAt>cGt	p.H647R	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	647					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		AAGTCTAAGATGGACACGCTG	0.423																																					p.H647R		Atlas-SNP	.											.	ZNF616	109	.	0			c.A1940G						.						123	116	118					19																	52618477		2203	4300	6503	SO:0001583	missense	90317	exon4			CTAAGATGGACAC	AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"Zinc fingers, C2H2-type", "-"	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.1940A>G	chr19.hg19:g.52618477T>C	ENSP00000471000:p.His647Arg	96.0	0.0		107.0	11.0	NM_178523	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	hg19	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.549047	0.00926	.	.	ENSG00000204611	ENST00000330123	.	.	.	1.93	-1.05	0.10036	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24431	0.0592	L	0.41027	1.25	0.09310	N	1	B	0.16396	0.017	B	0.10450	0.005	T	0.24621	-1.0155	8	0.17369	T	0.5	.	0.6266	0.00787	0.1979:0.1454:0.2006:0.456	.	647	Q08AN1	ZN616_HUMAN	R	647	.	ENSP00000328722:H647R	H	-	2	0	ZNF616	57310289	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.579000	0.05834	-0.006000	0.14370	-0.686000	0.03744	CAT	.	.		0.423	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892		C	52618477	T	C	52618477	3	2	228	1	0	0	0	0	1	0	0	0	18056	1464	51	2	409	2	ZNF616	19	52618477	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	1151806	52618477	6510506	117	32213										
MYH7B	57644	hgsc.bcm.edu	37	chr20	33575452	33575452	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tgcgtgtagggaacgagtacGtgaccaagggccagagtgtg	17	7	0	2	rs371353626		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr20:33575452G>A	ENST00000262873.7	+	15	1458	c.1366G>A	c.(1366-1368)Gtg>Atg	p.V456M	MIR499A_ENST00000384903.1_RNA	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	414	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GAACGAGTACGTGACCAAGGG	0.662																																					p.V456M		Atlas-SNP	.											.	MYH7B	145	.	0			c.G1366A						.	G	MET/VAL	0,4150		0,0,2075	98	108	105		1366	3.5	1	20		105	1,8409		0,1,4204	no	missense	MYH7B	NM_020884.3	21	0,1,6279	AA,AG,GG		0.0119,0.0,0.0080	probably-damaging	456/1984	33575452	1,12559	2075	4205	6280	SO:0001583	missense	57644	exon17			GAGTACGTGACCA	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.1366G>A	chr20.hg19:g.33575452G>A	ENSP00000262873:p.Val456Met	167.0	0.0		132.0	27.0	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	hg19	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	G	18.48	3.632777	0.67015	0.0	1.19E-4	ENSG00000078814	ENST00000262873	D	0.90324	-2.65	3.53	3.53	0.40419	Myosin head, motor domain (2);	0.000000	0.32624	N	0.005849	D	0.95674	0.8593	M	0.93197	3.39	0.53688	D	0.999977	D	0.60160	0.987	P	0.58660	0.843	D	0.97087	0.9788	10	0.87932	D	0	.	16.3928	0.83545	0.0:0.0:1.0:0.0	.	414	A7E2Y1	MYH7B_HUMAN	M	456	ENSP00000262873:V456M	ENSP00000262873:V456M	V	+	1	0	MYH7B	33039113	1.000000	0.71417	0.983000	0.44433	0.774000	0.43823	4.655000	0.61476	2.279000	0.76181	0.561000	0.74099	GTG	.	.		0.662	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		A	33575452	G	A	33575452	3	1	228	1	0	0	0	0	1	0	0	0	10049	1145	40	1	1424	1	MYH7B	20	33575452	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		33575452	29450068	118	32214										
TOX2	84969	hgsc.bcm.edu	37	chr20	42697300	42697300	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tctctcacagcctgctccccAgggacaaatcgctctacctc	6	18	3	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr20:42697300A>T	ENST00000358131.5	+	8	1649	c.1441A>T	c.(1441-1443)Agg>Tgg	p.R481W	TOX2_ENST00000341197.4_Missense_Mutation_p.R499W|TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000372999.1_Missense_Mutation_p.R457W|TOX2_ENST00000423191.2_Missense_Mutation_p.R457W	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	481					female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			CCTGCTCCCCAGGGACAAATC	0.627																																					p.R499W		Atlas-SNP	.											.	TOX2	158	.	0			c.A1495T						.						187	141	157					20																	42697300		2203	4300	6503	SO:0001583	missense	84969	exon9			CTCCCCAGGGACA	BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"granulosa cell HMG box 1"	611163	"chromosome 20 open reading frame 100"	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.1441A>T	chr20.hg19:g.42697300A>T	ENSP00000350849:p.Arg481Trp	107.0	0.0		78.0	16.0	NM_001098797	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Missense_Mutation	SNP	ENST00000358131.5	hg19	CCDS42875.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.129675	0.77549	.	.	ENSG00000124191	ENST00000341197;ENST00000423191;ENST00000372999;ENST00000358131;ENST00000435864	T;T;T;T;T	0.38560	1.59;1.63;1.63;1.35;1.13	5.05	5.05	0.67936	.	0.133094	0.33732	N	0.004601	T	0.61464	0.2349	M	0.61703	1.905	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.993	D;D;D;P	0.85130	0.997;0.997;0.99;0.849	T	0.65413	-0.6174	10	0.87932	D	0	.	13.9946	0.64388	1.0:0.0:0.0:0.0	.	377;499;481;457	B4DQV8;G3XAC7;Q96NM4;E1P5X0	.;.;TOX2_HUMAN;.	W	499;457;457;481;377	ENSP00000344724:R499W;ENSP00000390278:R457W;ENSP00000362090:R457W;ENSP00000350849:R481W;ENSP00000396777:R377W	ENSP00000344724:R499W	R	+	1	2	TOX2	42130714	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	3.545000	0.53648	1.900000	0.55004	0.533000	0.62120	AGG	.	.		0.627	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2			T	42697300	A	T	42697300	3	4	228	1	0	0	0	0	1	0	0	0	16393	179	7	4	1659	4	TOX2	20	42697300	Missense_Mutation	SNP	A	TCGA-DD-AAVV-01A-11D-A40R-10	9121848	42697300	20328220	119	32215										
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57276110	57276110	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	aagccgccctgcatcccccaGccctggccgtcctcagccac	8	22	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr20:57276110G>T	ENST00000356091.6	+	6	1006	c.718G>T	c.(718-720)Gcc>Tcc	p.A240S	NPEPL1_ENST00000525967.1_Missense_Mutation_p.A212S|NPEPL1_ENST00000525817.1_Missense_Mutation_p.A192S|STX16-NPEPL1_ENST00000530122.1_3'UTR	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	240						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			GCATCCCCCAGCCCTGGCCGT	0.622																																					p.A240S		Atlas-SNP	.											.	NPEPL1	36	.	0			c.G718T						.						21	24	23					20																	57276110		1988	4150	6138	SO:0001583	missense	79716	exon6			CCCCCAGCCCTGG	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.718G>T	chr20.hg19:g.57276110G>T	ENSP00000348395:p.Ala240Ser	111.0	0.0		146.0	7.0	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	hg19	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.187283	0.57909	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.42513	0.97;0.97;0.97	5.11	5.11	0.69529	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.65407	0.2688	M	0.77406	2.37	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.988;0.979;0.997;0.996	T	0.67138	-0.5746	10	0.46703	T	0.11	-16.1524	15.6983	0.77517	0.0:0.0:1.0:0.0	.	240;192;212;240	Q8NDH3;G5EA34;E9PN47;Q8NDH3-3	PEPL1_HUMAN;.;.;.	S	212;192;240	ENSP00000434810:A212S;ENSP00000437112:A192S;ENSP00000348395:A240S	ENSP00000348395:A240S	A	+	1	0	NPEPL1	56709517	1.000000	0.71417	0.113000	0.21522	0.023000	0.10783	9.375000	0.97178	2.365000	0.80145	0.655000	0.94253	GCC	.	.		0.622	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		T	57276110	G	T	57276110	3	4	228	1	0	0	0	0	1	0	0	0	10583	971	34	3	586	3	NPEPL1	20	57276110	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	14578810	57276110	5749410	120	32216										
COL9A3	1299	hgsc.bcm.edu	37	chr20	61453479	61453479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	ccagggaccttctggactccCcggcctccctggtcccccag	10	20	1	0	rs373399710		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr20:61453479C>T	ENST00000343916.3	+	9	443	c.440C>T	c.(439-441)cCc>cTc	p.P147L		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	147	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					TCTGGACTCCCCGGCCTCCCT	0.647																																					p.P147L		Atlas-SNP	.											.	COL9A3	70	.	0			c.C440T						.						61	65	63					20																	61453479		2203	4299	6502	SO:0001583	missense	1299	exon9			GACTCCCCGGCCT	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2219	protein-coding gene	gene with protein product	"collagen type IX proteoglycan"	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.440C>T	chr20.hg19:g.61453479C>T	ENSP00000341640:p.Pro147Leu	319.0	0.0		406.0	73.0	NM_001853	Q13681|Q9H4G9|Q9UPE2	Missense_Mutation	SNP	ENST00000343916.3	hg19	CCDS13505.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.863005	0.32884	.	.	ENSG00000092758	ENST00000343916;ENST00000452372;ENST00000537652	D;D	0.96885	-4.16;-3.08	5.18	5.18	0.71444	.	0.000000	0.85682	U	0.000000	D	0.97851	0.9294	M	0.85041	2.73	0.80722	D	1	D	0.71674	0.998	D	0.67900	0.954	D	0.97905	1.0305	10	0.51188	T	0.08	.	13.0729	0.59072	0.0:0.8382:0.1618:0.0	.	147	Q14050	CO9A3_HUMAN	L	147;110;110	ENSP00000341640:P147L;ENSP00000394280:P110L	ENSP00000341640:P147L	P	+	2	0	COL9A3	60923924	0.367000	0.25023	0.871000	0.34182	0.232000	0.25224	1.840000	0.39230	2.412000	0.81896	0.591000	0.81541	CCC	.	.		0.647	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853		T	61453479	C	T	61453479	3	4	228	1	0	0	0	0	1	0	0	0	3711	623	22	3	474	3	COL9A3	20	61453479	Missense_Mutation	SNP	C	TCGA-DD-AAVV-01A-11D-A40R-10	4177369	61453479	1572041	121	32217										
BCL2L13	23786	hgsc.bcm.edu	37	chr22	18171844	18171844	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	aagactgcttggcccatcttGgagaaaaagtgtcccaggaa	11	9	1	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr22:18171844G>C	ENST00000317582.5	+	4	669	c.322G>C	c.(322-324)Gga>Cga	p.G108R	BCL2L13_ENST00000399782.1_Missense_Mutation_p.G108R|BCL2L13_ENST00000337612.5_Intron|BCL2L13_ENST00000543133.1_Intron|BCL2L13_ENST00000418951.2_3'UTR|BCL2L13_ENST00000493680.1_Missense_Mutation_p.G108R|BCL2L13_ENST00000538149.1_Intron|BCL2L13_ENST00000355028.3_Missense_Mutation_p.G108R	NM_015367.3	NP_056182.2	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	108					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		GGCCCATCTTGGAGAAAAAGT	0.493																																					p.G132R		Atlas-SNP	.											.	BCL2L13	27	.	0			c.G394C						.						97	86	90					22																	18171844		2203	4300	6503	SO:0001583	missense	23786	exon3			CATCTTGGAGAAA	AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968			17164	protein-coding gene	gene with protein product						11262395, 11381032	Standard	NM_015367		Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000317582.5:c.322G>C	chr22.hg19:g.18171844G>C	ENSP00000318883:p.Gly108Arg	124.0	0.0		121.0	6.0	NM_001270726	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	Missense_Mutation	SNP	ENST00000317582.5	hg19	CCDS13746.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546642	0.86022	.	.	ENSG00000099968	ENST00000399782;ENST00000317582;ENST00000493680;ENST00000355028	T;T;T;T	0.10860	2.83;2.83;2.83;2.83	5.7	5.7	0.88788	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (2);	0.054761	0.64402	D	0.000001	T	0.32734	0.0839	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.991;0.997;0.995	T	0.01143	-1.1438	10	0.72032	D	0.01	-19.6057	14.6525	0.68808	0.0:0.0:0.8547:0.1453	.	108;108;108	E9PDD6;Q9BXK5;Q9BXK5-2	.;B2L13_HUMAN;.	R	108	ENSP00000382682:G108R;ENSP00000318883:G108R;ENSP00000434764:G108R;ENSP00000347133:G108R	ENSP00000318883:G108R	G	+	1	0	BCL2L13	16551844	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.897000	0.75671	2.683000	0.91414	0.650000	0.86243	GGA	.	.		0.493	BCL2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316184.1	NM_015367		C	18171844	G	C	18171844	3	2	228	1	0	0	0	0	1	0	0	0	1371	1349	47	4	332	4	BCL2L13	22	18171844	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10		18171844	33132722	122	32218										
PIWIL3	440822	hgsc.bcm.edu	37	chr22	25144937	25144937	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cccgggacggacaaaaaattGgtatcaaatttcaaatccca	7	10	2	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr22:25144937G>T	ENST00000332271.5	-	12	1802	c.1386C>A	c.(1384-1386)acC>acA	p.T462T	PIWIL3_ENST00000527701.1_Silent_p.T353T|PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000533313.1_Silent_p.T353T	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	462					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						ACAAAAAATTGGTATCAAATT	0.353																																					p.T462T		Atlas-SNP	.											.	PIWIL3	115	.	0			c.C1386A						.						95	91	93					22																	25144937		2202	4300	6502	SO:0001819	synonymous_variant	440822	exon12			AAAATTGGTATCA	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.1386C>A	chr22.hg19:g.25144937G>T		84.0	0.0		68.0	7.0	NM_001008496		Silent	SNP	ENST00000332271.5	hg19	CCDS33623.1																																																																																			.	.		0.353	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		T	25144937	G	T	25144937	2	4	228	1	0	0	0	0	0	0	0	1	11968	1335	47	3		3	PIWIL3	22	25144937	Silent	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	6973093	25144937	26159629	123	32219										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26222449	26222449	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	caggaactctttgcggctgtGgtctcactcatcaacaggta	10	11	4	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr22:26222449G>C	ENST00000407587.2	+	14	2938	c.2769G>C	c.(2767-2769)gtG>gtC	p.V923V	MYO18B_ENST00000536101.1_Silent_p.V923V|MYO18B_ENST00000335473.7_Silent_p.V923V			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	923	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TTGCGGCTGTGGTCTCACTCA	0.542																																					p.V923V		Atlas-SNP	.											.	MYO18B	322	.	0			c.G2769C						.						164	157	159					22																	26222449		1959	4155	6114	SO:0001819	synonymous_variant	84700	exon14			GGCTGTGGTCTCA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.2769G>C	chr22.hg19:g.26222449G>C		91.0	0.0		92.0	15.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.		0.542	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		C	26222449	G	C	26222449	2	2	228	1	0	0	0	0	0	0	0	1	10075	1335	47	4		4	MYO18B	22	26222449	Silent	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	1077512	26222449	25082117	124	32220										
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50664306	50664306	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	acagtccttctcaatctcctTcaactcctcaagggagaaaa	5	13	4	1			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chr22:50664306T>C	ENST00000248846.5	-	10	2004	c.1900A>G	c.(1900-1902)Aag>Gag	p.K634E	TUBGCP6_ENST00000439308.2_Missense_Mutation_p.K634E|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	634					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TCAATCTCCTTCAACTCCTCA	0.597																																					p.K634E		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.A1900G						.						76	70	72					22																	50664306		2203	4300	6503	SO:0001583	missense	85378	exon10			TCTCCTTCAACTC	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.1900A>G	chr22.hg19:g.50664306T>C	ENSP00000248846:p.Lys634Glu	116.0	0.0		89.0	6.0	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	hg19	CCDS14087.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.939131	0.73557	.	.	ENSG00000128159	ENST00000248846;ENST00000439308	T;T	0.12879	2.98;2.64	5.19	5.19	0.71726	.	0.832577	0.11242	N	0.584580	T	0.22205	0.0535	L	0.47716	1.5	0.40156	D	0.977009	P;P	0.40282	0.711;0.649	P;B	0.46917	0.531;0.336	T	0.01914	-1.1248	10	0.33141	T	0.24	.	15.0451	0.71822	0.0:0.0:0.0:1.0	.	634;634	B2RWN4;Q96RT7	.;GCP6_HUMAN	E	634	ENSP00000248846:K634E;ENSP00000397387:K634E	ENSP00000248846:K634E	K	-	1	0	TUBGCP6	49006433	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	4.445000	0.60007	1.967000	0.57214	0.379000	0.24179	AAG	.	.		0.597	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		C	50664306	T	C	50664306	3	2	228	1	0	0	0	0	1	0	0	0	16785	1792	62	2	3623	2	TUBGCP6	22	50664306	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	24441857	50664306	640260	125	32221										
RBM10	8241	hgsc.bcm.edu	37	chrX	47030585	47030585	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gaggaggaggaggaggaggaTgaggaggaggaggagaaggc	25	1	0	2	rs377667483		TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chrX:47030585T>G	ENST00000377604.3	+	4	1102	c.360T>G	c.(358-360)gaT>gaG	p.D120E	RBM10_ENST00000329236.7_Intron|RBM10_ENST00000345781.6_Intron	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	120	Poly-Glu.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						aggaggaggatgaggaggagg	0.667													T|||	2	0.000529801	0	0	3775	,	,		8316	0.002		0	False		,,,				2504	0				p.D185E	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.T555G						.						20	19	20					X																	47030585		2202	4297	6499	SO:0001583	missense	8241	exon4			GGAGGATGAGGAG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.360T>G	chrX.hg19:g.47030585T>G	ENSP00000366829:p.Asp120Glu	54.0	0.0		72.0	5.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	T	1.034	-0.680868	0.03353	.	.	ENSG00000182872	ENST00000377604	T	0.10960	2.82	2.89	-2.28	0.06826	Nucleotide-binding, alpha-beta plait (1);	0.397395	0.18197	N	0.148658	T	0.03783	0.0107	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.49153	-0.8969	10	0.02654	T	1	-3.1034	10.6013	0.45369	0.0:0.0:0.7699:0.2301	.	185;120;120	Q7Z3D7;P98175-2;P98175	.;.;RBM10_HUMAN	E	120	ENSP00000366829:D120E	ENSP00000366829:D120E	D	+	3	2	RBM10	46915529	0.996000	0.38824	0.881000	0.34555	0.930000	0.56654	-0.096000	0.11059	-0.655000	0.05387	-0.549000	0.04216	GAT	.	.		0.667	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		G	47030585	T	G	47030585	3	3	228	1	0	0	0	0	1	0	0	0	13126	1461	51	5	370	5	RBM10	23	47030585	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10		47030585	108239975	126	32222										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91137937	91137937	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	gacatcaactattgaaatctGcagtgagatataactttcta	6	7	3	2			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chrX:91137937G>A	ENST00000373094.1	+	2	3878				PCDH11X_ENST00000504220.2_Intron|PCDH11X_ENST00000406881.1_Intron|PCDH11X_ENST00000361655.2_Intron|PCDH11X_ENST00000298274.8_Intron|PCDH11X_ENST00000395337.2_Missense_Mutation_p.C1022Y|PCDH11X_ENST00000373097.1_Intron|PCDH11X_ENST00000373088.1_Intron	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked						homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						ATTGAAATCTGCAGTGAGATA	0.328																																					p.C1022Y	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.G3065A						.						154	137	143					X																	91137937		2203	4300	6503	SO:0001627	intron_variant	27328	exon6			AAATCTGCAGTGA	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3033+3665G>A	chrX.hg19:g.91137937G>A		421.0	1.0		460.0	271.0	NM_032967	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	hg19	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	G	4.232	0.041892	0.08196	.	.	ENSG00000102290	ENST00000395337	T	0.52754	0.65	3.42	0.464	0.16706	.	.	.	.	.	T	0.22003	0.0530	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10382	-1.0632	8	0.11182	T	0.66	.	2.3067	0.04176	0.3074:0.0:0.4504:0.2421	.	1022	Q9BZA7-2	.	Y	1022	ENSP00000378746:C1022Y	ENSP00000378746:C1022Y	C	+	2	0	PCDH11X	91024593	1.000000	0.71417	0.998000	0.56505	0.335000	0.28730	1.212000	0.32394	-0.030000	0.13804	-0.365000	0.07479	TGC	.	.		0.328	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		A	91137937	G	A	91137937	1	1	228	0	1	0	0	0	0	0	0	0	11517	1319	46	3		3	PCDH11X	23	91137937	Intron	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	44107352	91137937	64132623	127	32223										
GLA	2717	hgsc.bcm.edu	37	chrX	100662799	100662799	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cttgccaatccattgtccagTgctctagccccagggatgtc	9	14	1	0			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chrX:100662799T>A	ENST00000218516.3	-	1	114	c.93A>T	c.(91-93)gcA>gcT	p.A31A	RPL36A-HNRNPH2_ENST00000409170.3_Intron|GLA_ENST00000479445.1_5'UTR|HNRNPH2_ENST00000316594.5_5'Flank	NM_000169.2	NP_000160.1	P06280	AGAL_HUMAN	galactosidase, alpha	31			A -> V (in FD). {ECO:0000269|PubMed:15712228, ECO:0000269|PubMed:9100224}.		glycoside catabolic process (GO:0016139)|glycosphingolipid catabolic process (GO:0046479)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide catabolic process (GO:0046477)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|oligosaccharide metabolic process (GO:0009311)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|catalytic activity (GO:0003824)|galactoside binding (GO:0016936)|hydrolase activity (GO:0016787)|protein homodimerization activity (GO:0042803)|raffinose alpha-galactosidase activity (GO:0052692)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						CATTGTCCAGTGCTCTAGCCC	0.592																																					p.A31A	Colon(193;776 2816 31189 44474)	Atlas-SNP	.											.	GLA	43	.	0			c.A93T						.						99	98	98					X																	100662799		2203	4300	6503	SO:0001819	synonymous_variant	2717	exon1			GTCCAGTGCTCTA	X16889	CCDS14484.1	Xq21.3-q22	2014-09-17			ENSG00000102393	ENSG00000102393	3.2.1.22		4296	protein-coding gene	gene with protein product		300644					Standard	NM_000169		Approved	GALA	uc004ehl.1	P06280	OTTHUMG00000022026	ENST00000218516.3:c.93A>T	chrX.hg19:g.100662799T>A		140.0	0.0		222.0	12.0	NM_000169	Q6LER7	Silent	SNP	ENST00000218516.3	hg19	CCDS14484.1																																																																																			.	.		0.592	GLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057540.1			A	100662799	T	A	100662799	2	1	228	1	0	0	0	0	0	0	0	1	6434	1683	59	4		4	GLA	23	100662799	Silent	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	9524862	100662799	54607761	128	32224										
IGSF1	3547	hgsc.bcm.edu	37	chrX	130420435	130420435	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	tgatgtcatacccagactcaTccctgaaaagagagattatg	8	9	2	5			TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chrX:130420435T>G	ENST00000361420.3	-	3	152	c.73A>C	c.(73-75)Atg>Ctg	p.M25L	IGSF1_ENST00000370900.1_Missense_Mutation_p.M25L|IGSF1_ENST00000370901.4_Missense_Mutation_p.M25L|IGSF1_ENST00000370910.1_Intron|IGSF1_ENST00000370904.1_Intron|IGSF1_ENST00000370903.3_Missense_Mutation_p.M25L			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	25					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						CCCAGACTCATCCCTGAAAAG	0.498																																					p.M25L		Atlas-SNP	.											.	IGSF1	231	.	0			c.A73C						.						128	100	109					X																	130420435		2203	4300	6503	SO:0001583	missense	3547	exon3			GACTCATCCCTGA	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.73A>C	chrX.hg19:g.130420435T>G	ENSP00000355010:p.Met25Leu	73.0	0.0		109.0	5.0	NM_001555	B5MEG2|H9KV64|O15070|Q9NTC8	Missense_Mutation	SNP	ENST00000361420.3	hg19	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.518450	0.00967	.	.	ENSG00000147255	ENST00000361420;ENST00000370903;ENST00000370901;ENST00000370900	T;T;T;T	0.00585	6.39;6.39;6.8;6.8	4.15	1.31	0.21738	.	.	.	.	.	T	0.00271	0.0008	N	0.02539	-0.55	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40608	-0.9554	9	0.02654	T	1	.	4.2705	0.10783	0.1161:0.0:0.4603:0.4236	.	25;25	Q8N6C5-3;Q8N6C5	.;IGSF1_HUMAN	L	25	ENSP00000355010:M25L;ENSP00000359940:M25L;ENSP00000359938:M25L;ENSP00000359937:M25L	ENSP00000355010:M25L	M	-	1	0	IGSF1	130248116	0.999000	0.42202	0.718000	0.30602	0.521000	0.34408	0.283000	0.18846	0.140000	0.18849	-0.269000	0.10298	ATG	.	.		0.498	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			G	130420435	T	G	130420435	3	3	228	1	0	0	0	0	1	0	0	0	7605	1435	50	5	4086	5	IGSF1	23	130420435	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	29757636	130420435	24850125	129	32225										
ARHGAP4	393	hgsc.bcm.edu	37	chrX	153173335	153173335	+	Missense_Mutation	SNP	T	T	A													0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	cccaggactgggagaggtggTagatgctggcccaaggccct							TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chrX:153173335T>A	ENST00000350060.5	-	22	2730	c.2689A>T	c.(2689-2691)Acc>Tcc	p.T897S	ARHGAP4_ENST00000537206.1_Missense_Mutation_p.T874S|ARHGAP4_ENST00000370016.1_Missense_Mutation_p.T876S|ARHGAP4_ENST00000370028.3_Missense_Mutation_p.T937S|ARHGAP4_ENST00000393721.1_Missense_Mutation_p.T719S|ARHGAP4_ENST00000467421.1_5'Flank	NM_001666.4	NP_001657.3	P98171	RHG04_HUMAN	Rho GTPase activating protein 4	897					apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|negative regulation of axon extension (GO:0030517)|negative regulation of fibroblast migration (GO:0010764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)	Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGAGAGGTGGTAGATGCTGGC	0.647																																					p.T937S		Atlas-SNP	.											.	ARHGAP4	103	.	0			c.A2809T						.						48	53	52					X																	153173335		2203	4299	6502	SO:0001583	missense	393	exon23			AGGTGGTAGATGC	X78817	CCDS14736.1, CCDS55540.1	Xq28	2010-02-09			ENSG00000089820	ENSG00000089820		"Rho GTPase activating proteins"	674	protein-coding gene	gene with protein product	"Rho-GAP hematopoietic protein C1"	300023				8570618	Standard	NM_001666		Approved	KIAA0131, C1, p115, RhoGAP4, SrGAP4	uc004fjk.2	P98171	OTTHUMG00000024226	ENST00000350060.5:c.2689A>T	chrX.hg19:g.153173335T>A	ENSP00000203786:p.Thr897Ser	139.0	0.0		114.0	12.0	NM_001164741	Q14144|Q86UY3	Missense_Mutation	SNP	ENST00000350060.5	hg19	CCDS14736.1	.	.	.	.	.	.	.	.	.	.	c	11.70	1.716606	0.30413	.	.	ENSG00000089820	ENST00000393721;ENST00000370028;ENST00000350060;ENST00000370016;ENST00000537206	T;T;T;T;T	0.10382	2.88;2.89;2.89;2.88;2.89	4.33	-5.22	0.02806	.	.	.	.	.	T	0.05502	0.0145	N	0.24115	0.695	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.15870	0.014;0.014	T	0.45687	-0.9244	9	0.15952	T	0.53	.	7.2357	0.26067	0.0:0.3153:0.2472:0.4375	.	937;897	Q86UY3;P98171	.;RHG04_HUMAN	S	719;937;897;876;874	ENSP00000377322:T719S;ENSP00000359045:T937S;ENSP00000203786:T897S;ENSP00000359033:T876S;ENSP00000444169:T874S	ENSP00000203786:T897S	T	-	1	0	ARHGAP4	152826529	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.210000	0.09345	-0.760000	0.04677	-0.283000	0.09986	ACC	.	.		0.647	ARHGAP4-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061119.1	NM_001666		A	153173335	T	A	153173335	3	1	228	1	0	0	0	0	1	0	0	0	885	1638	57	4	155	4	ARHGAP4	23	153173335	Missense_Mutation	SNP	T	TCGA-DD-AAVV-01A-11D-A40R-10	22752900	153173335	2097225	130	32226	167	2								
ARHGAP4	393	hgsc.bcm.edu	37	chrX	153173337	153173337	+	Missense_Mutation	SNP	G	G	A													0.0230769230769231	3	1	0.491175723717623	1.96470289487049	0	0.166666666666667	0.751940625889747	0	caggactgggagaggtggtaGatgctggcccaaggccctgg							TCGA-DD-AAVV-01A-11D-A40R-10	TCGA-DD-AAVV-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9d4bac19-b9ce-4a48-8dad-da0dd93ff952	332d7d8c-8386-44c8-8720-3e2ba050cbdf	g.chrX:153173337G>A	ENST00000350060.5	-	22	2728	c.2687C>T	c.(2686-2688)tCt>tTt	p.S896F	ARHGAP4_ENST00000537206.1_Missense_Mutation_p.S873F|ARHGAP4_ENST00000370016.1_Missense_Mutation_p.S875F|ARHGAP4_ENST00000370028.3_Missense_Mutation_p.S936F|ARHGAP4_ENST00000393721.1_Missense_Mutation_p.S718F|ARHGAP4_ENST00000467421.1_5'Flank	NM_001666.4	NP_001657.3	P98171	RHG04_HUMAN	Rho GTPase activating protein 4	896					apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|negative regulation of axon extension (GO:0030517)|negative regulation of fibroblast migration (GO:0010764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)	Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)	p.S896C(1)|p.S936C(1)		central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGAGGTGGTAGATGCTGGCCC	0.652																																					p.S936F		Atlas-SNP	.											.	ARHGAP4	103	.	2	Substitution - Missense(2)	lung(2)	c.C2807T						.						50	54	53					X																	153173337		2203	4300	6503	SO:0001583	missense	393	exon23			GTGGTAGATGCTG	X78817	CCDS14736.1, CCDS55540.1	Xq28	2010-02-09			ENSG00000089820	ENSG00000089820		"Rho GTPase activating proteins"	674	protein-coding gene	gene with protein product	"Rho-GAP hematopoietic protein C1"	300023				8570618	Standard	NM_001666		Approved	KIAA0131, C1, p115, RhoGAP4, SrGAP4	uc004fjk.2	P98171	OTTHUMG00000024226	ENST00000350060.5:c.2687C>T	chrX.hg19:g.153173337G>A	ENSP00000203786:p.Ser896Phe	144.0	0.0		115.0	8.0	NM_001164741	Q14144|Q86UY3	Missense_Mutation	SNP	ENST00000350060.5	hg19	CCDS14736.1	.	.	.	.	.	.	.	.	.	.	g	13.04	2.117537	0.37339	.	.	ENSG00000089820	ENST00000393721;ENST00000370028;ENST00000350060;ENST00000370016;ENST00000537206	T;T;T;T;T	0.11930	2.73;2.73;2.73;2.73;2.73	4.01	3.14	0.36123	.	1.074070	0.07411	N	0.892394	T	0.11495	0.0280	N	0.19112	0.55	0.09310	N	1	P;B	0.37955	0.612;0.303	B;B	0.37833	0.259;0.172	T	0.36359	-0.9751	10	0.59425	D	0.04	.	10.2604	0.43423	0.1043:0.0:0.8957:0.0	.	936;896	Q86UY3;P98171	.;RHG04_HUMAN	F	718;936;896;875;873	ENSP00000377322:S718F;ENSP00000359045:S936F;ENSP00000203786:S896F;ENSP00000359033:S875F;ENSP00000444169:S873F	ENSP00000203786:S896F	S	-	2	0	ARHGAP4	152826531	0.005000	0.15991	0.000000	0.03702	0.015000	0.08874	1.381000	0.34362	0.549000	0.28973	0.513000	0.50165	TCT	.	.		0.652	ARHGAP4-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061119.1	NM_001666		A	153173337	G	A	153173337	3	1	228	1	0	0	0	0	1	0	0	0	885	942	33	3	157	3	ARHGAP4	23	153173337	Missense_Mutation	SNP	G	TCGA-DD-AAVV-01A-11D-A40R-10	2	153173337	2097223	131	32227	167	2								
MAP7D1	55700	hgsc.bcm.edu	37	chr1	36643703	36643703	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	agcgcagggccagtaacgagAaggagtcagcagccccagcc	14	13	1	1	rs3045695|rs141305015|rs200892098	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr1:36643703A>G	ENST00000373151.2	+	9	1825	c.1609A>G	c.(1609-1611)Aag>Gag	p.K537E	MAP7D1_ENST00000316156.4_Missense_Mutation_p.K500E|MAP7D1_ENST00000373150.4_Missense_Mutation_p.K505E|MAP7D1_ENST00000373148.4_Missense_Mutation_p.K83E	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	537	Pro-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CAGTAACGAGAAGGAGTCAGC	0.721																																					p.K537E		Atlas-SNP	.											.,2	MAP7D1	62	.	0			c.A1609G						.						29	29	29					1																	36643703		2192	4270	6462	SO:0001583	missense	55700	exon9			AACGAGAAGGAGT	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"proline arginine rich coiled coil 1", "arginine/proline rich coiled-coil 1"	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.1609A>G	chr1.hg19:g.36643703A>G	ENSP00000362244:p.Lys537Glu	1.0	1.0		7.0	7.0	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Missense_Mutation	SNP	ENST00000373151.2	hg19	CCDS30673.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.555|6.555	0.470598|0.470598	0.12461|0.12461	.|.	.|.	ENSG00000116871|ENSG00000116871	ENST00000530975|ENST00000316156;ENST00000373150;ENST00000373151;ENST00000373148	T|T;T;T;T	0.57752|0.49720	0.38|0.77;0.77;0.77;0.77	5.03|5.03	2.66|2.66	0.31614|0.31614	.|.	.|0.493263	.|0.17209	.|N	.|0.182837	T|T	0.36358|0.36358	0.0964|0.0964	L|L	0.50333|0.50333	1.59|1.59	0.31867|0.31867	N|N	0.620209|0.620209	.|B;B;B;B;B	.|0.12013	.|0.001;0.001;0.005;0.002;0.001	.|B;B;B;B;B	.|0.08055	.|0.003;0.001;0.003;0.003;0.001	T|T	0.34875|0.34875	-0.9811|-0.9811	7|10	0.62326|0.19147	D|T	0.03|0.46	-11.1212|-11.1212	7.538|7.538	0.27721|0.27721	0.8218:0.0:0.1782:0.0|0.8218:0.0:0.1782:0.0	.|.	.|83;537;500;505;537	.|Q3KQU3-3;D3DPS3;Q3KQU3-2;Q3KQU3-4;Q3KQU3	.|.;.;.;.;MA7D1_HUMAN	G|E	119|500;505;537;83	ENSP00000437046:E119G|ENSP00000320228:K500E;ENSP00000362243:K505E;ENSP00000362244:K537E;ENSP00000362241:K83E	ENSP00000437046:E119G|ENSP00000320228:K500E	E|K	+|+	2|1	0|0	MAP7D1|MAP7D1	36416290|36416290	0.997000|0.997000	0.39634|0.39634	0.990000|0.990000	0.47175|0.47175	0.119000|0.119000	0.20118|0.20118	1.102000|1.102000	0.31050|0.31050	0.951000|0.951000	0.37770|0.37770	0.528000|0.528000	0.53228|0.53228	GAA|AAG	.	.		0.721	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067		G	36643703	A	G	36643703	3	3	229	1	0	0	0	0	1	0	0	0	9276	247	9	2	1643	2	MAP7D1	1	36643703	Missense_Mutation	SNP	A	TCGA-DD-AAVW-01A-11D-A40R-10		36643703	212606918	1	32228										
CCDC18	343099	hgsc.bcm.edu	37	chr1	93672688	93672690	+	In_Frame_Del	DEL	CGG	CGG	-													0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ttaaaagaagaaaataacaaCggaaaagaaaaattaaggat					rs2783499	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr1:93672688_93672690delCGG	ENST00000343253.7	+	9	1444_1446	c.942_944delCGG	c.(940-945)aacgga>aaa	p.314_315NG>K	CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000401026.3_In_Frame_Del_p.314_315NG>K|CCDC18_ENST00000557479.1_In_Frame_Del_p.432_433NG>K|CCDC18_ENST00000338949.4_In_Frame_Del_p.113_114NG>K			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	314										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		AAAATAACAACGGAAAAGAAAAA	0.276																																					p.314_315del		Atlas-INDEL	.											.	CCDC18	93	.	0			c.941_943del						.																																			SO:0001651	inframe_deletion	343099	exon9			.			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.942_944delCGG	chr1.hg19:g.93672688_93672690delCGG	ENSP00000343377:p.Asn314_Gly315delinsLys	479.0	0.0		115.0	12.0	NM_206886	Q6ZU17	In_Frame_Del	DEL	ENST00000343253.7	hg19																																																																																				.	.		0.276	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		-	93672690	CGG	-	93672688	7	5	229	1	0	1	0	1	0	0	0	0	2796	535	19	0	1330	0	CCDC18	1	93672688	In_Frame_Del	DEL	CGG	TCGA-DD-AAVW-01A-11D-A40R-10	57028985	93672688	155577933	2	32229										
ITGA10	8515	hgsc.bcm.edu	37	chr1	145537466	145537466	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gtggccggcggaaagtgctgGtatctacaactctggagaac	14	9	2	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr1:145537466G>C	ENST00000369304.3	+	20	2651	c.2476G>C	c.(2476-2478)Gta>Cta	p.V826L	ITGA10_ENST00000539363.1_Missense_Mutation_p.V683L|ITGA10_ENST00000538811.1_Missense_Mutation_p.V695L	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	826					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GAAAGTGCTGGTATCTACAAC	0.517																																					p.V826L		Atlas-SNP	.											.	ITGA10	131	.	0			c.G2476C						.						193	205	201					1																	145537466		2203	4300	6503	SO:0001583	missense	8515	exon20			GTGCTGGTATCTA	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.2476G>C	chr1.hg19:g.145537466G>C	ENSP00000358310:p.Val826Leu	110.0	0.0		68.0	6.0	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.780770	0.49891	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.41758	0.99;0.99;0.99	5.07	5.07	0.68467	Integrin alpha-2 (1);	0.000000	0.64402	D	0.000001	T	0.31949	0.0813	L	0.34521	1.04	0.58432	D	0.999999	B;B;P;B	0.36354	0.155;0.073;0.549;0.388	B;B;P;B	0.45753	0.17;0.076;0.492;0.189	T	0.12477	-1.0546	10	0.45353	T	0.12	.	15.9866	0.80157	0.0:0.0:1.0:0.0	.	792;695;683;826	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	L	826;792;683;695	ENSP00000358310:V826L;ENSP00000439894:V683L;ENSP00000440011:V695L	ENSP00000358310:V826L	V	+	1	0	ITGA10	144248823	1.000000	0.71417	0.977000	0.42913	0.610000	0.37248	7.282000	0.78630	2.645000	0.89757	0.655000	0.94253	GTA	.	.		0.517	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		C	145537466	G	C	145537466	3	2	229	1	0	0	0	0	1	0	0	0	7882	1261	44	4	2554	4	ITGA10	1	145537466	Missense_Mutation	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10	51864778	145537466	103713155	3	32230										
CENPF	1063	hgsc.bcm.edu	37	chr1	214819555	214819558	+	Frame_Shift_Del	DEL	TCTG	TCTG	-													0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ttaaggtctgaaaaagaaaaTctgacaaaacaaatacaaga					rs565584032		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	TCTG	TCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr1:214819555_214819558delTCTG	ENST00000366955.3	+	13	6810_6813	c.6642_6645delTCTG	c.(6640-6645)aatctgfs	p.NL2214fs		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2310	2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AAAAAGAAAATCTGACAAAACAAA	0.353																																					p.2214_2215del	Colon(80;575 1284 11000 14801 43496)	Atlas-INDEL	.											.	CENPF	321	.	0			c.6641_6644del						.																																			SO:0001589	frameshift_variant	1063	exon13			.	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.6642_6645delTCTG	chr1.hg19:g.214819555_214819558delTCTG	ENSP00000355922:p.Asn2214fs	332.0	0.0		223.0	14.0	NM_016343	Q13171|Q13246|Q5VVM7	Frame_Shift_Del	DEL	ENST00000366955.3	hg19	CCDS31023.1																																																																																			.	.		0.353	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		-	214819558	TCTG	-	214819555	7	5	229	1	0	1	0	1	0	0	0	0	3233	1432	50	0	6688	0	CENPF	1	214819555	Frame_Shift_Del	DEL	TCTG	TCGA-DD-AAVW-01A-11D-A40R-10	69282089	214819555	34431066	4	32231										
ATL2	64225	hgsc.bcm.edu	37	chr2	38604337	38604337	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gcggcgcttgggtcgctggtCcgtcgccggcgccacagccc	16	17	0	0			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:38604337C>T	ENST00000378954.4	-	1	67	c.66G>A	c.(64-66)cgG>cgA	p.R22R	ATL2_ENST00000539122.1_5'UTR|ATL2_ENST00000419554.2_Silent_p.R22R|ATL2_ENST00000452935.2_5'Flank|ATL2_ENST00000332337.4_5'Flank|ATL2_ENST00000406122.1_5'UTR|ATL2_ENST00000402054.1_5'Flank|ATL2_ENST00000546051.1_5'Flank	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	22					endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						GGTCGCTGGTCCGTCGCCGGC	0.672																																					p.R22R		Atlas-SNP	.											.	ATL2	49	.	0			c.G66A						.						20	26	24					2																	38604337		2202	4291	6493	SO:0001819	synonymous_variant	64225	exon1			GCTGGTCCGTCGC		CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787			24047	protein-coding gene	gene with protein product		609368	"ADP-ribosylation factor-like 6 interacting protein 2"	ARL6IP2		10508919, 18270207	Standard	NM_022374		Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.66G>A	chr2.hg19:g.38604337C>T		151.0	0.0		162.0	15.0	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Silent	SNP	ENST00000378954.4	hg19	CCDS46260.1	.	.	.	.	.	.	.	.	.	.	C	4.189	0.033727	0.08101	.	.	ENSG00000119787	ENST00000443098	.	.	.	3.68	2.78	0.32641	.	.	.	.	.	T	0.56381	0.1981	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50701	-0.8797	4	.	.	.	-2.2579	8.0452	0.30545	0.0:0.8784:0.0:0.1216	.	.	.	.	E	21	.	.	G	-	2	0	ATL2	38457841	1.000000	0.71417	0.966000	0.40874	0.040000	0.13550	0.826000	0.27407	0.812000	0.34326	0.650000	0.86243	GGA	.	.		0.672	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374		T	38604337	C	T	38604337	2	4	229	1	0	0	0	0	0	0	0	1	1107	842	30	3		3	ATL2	2	38604337	Silent	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10		38604337	204595036	5	32232										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	catggccgggcgagctggagGaggaggaggaggaggaggag	24	5	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						.						3	4	4					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	191.0	0.0		331.0	31.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73613036	G	C	73613036	3	2	229	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10	35008699	73613036	169586337	6	32233										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168105575	168105577	+	In_Frame_Del	DEL	TTG	TTG	-													0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	tagacaacaaaaagaagaaaTtgaaaaacagaaacaggaga					rs533159553		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:168105575_168105577delTTG	ENST00000409195.1	+	9	7762_7764	c.7673_7675delTTG	c.(7672-7677)attgaa>aaa	p.2558_2559IE>K	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_In_Frame_Del_p.2558_2559IE>K|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_In_Frame_Del_p.2336_2337IE>K|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2383					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAAGAAGAAATTGAAAAACAGAA	0.315																																					p.2558_2558del		Atlas-INDEL	.											.	XIRP2	914	.	0			c.7672_7674del						.																																			SO:0001651	inframe_deletion	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.7673_7675delTTG	chr2.hg19:g.168105575_168105577delTTG	ENSP00000386840:p.Ile2558_Glu2559delinsLys	299.0	0.0		140.0	12.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	In_Frame_Del	DEL	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.315	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		-	168105577	TTG	-	168105575	7	5	229	1	0	1	0	1	0	0	0	0	17445	1493	52	0	7703	0	XIRP2	2	168105575	In_Frame_Del	DEL	TTG	TCGA-DD-AAVW-01A-11D-A40R-10	94492539	168105575	75093798	7	32234										
C2orf66	401027	hgsc.bcm.edu	37	chr2	197672293	197672293	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gtggggaaaggatttggaaaTgttccaagatcaagacctct	12	6	2	2			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:197672293T>A	ENST00000342506.2	-	2	1116	c.228A>T	c.(226-228)acA>acT	p.T76T		NM_213608.2	NP_998773.1	Q6UXQ4	CB066_HUMAN	chromosome 2 open reading frame 66	76						extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|ovary(1)	9						GATTTGGAAATGTTCCAAGAT	0.393																																					p.T76T		Atlas-SNP	.											.	C2orf66	15	.	0			c.A228T						.						134	141	139					2																	197672293		2203	4300	6503	SO:0001819	synonymous_variant	401027	exon2			TGGAAATGTTCCA		CCDS2317.1	2q33.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000187944	ENSG00000187944			33809	protein-coding gene	gene with protein product							Standard	NM_213608		Approved	UNQ6411	uc002utv.3	Q6UXQ4	OTTHUMG00000132742	ENST00000342506.2:c.228A>T	chr2.hg19:g.197672293T>A		150.0	0.0		36.0	6.0	NM_213608	B2RNW3	Silent	SNP	ENST00000342506.2	hg19	CCDS2317.1																																																																																			.	.		0.393	C2orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256102.1	NM_213608		A	197672293	T	A	197672293	2	1	229	1	0	0	0	0	0	0	0	1	2187	1451	51	4		4	C2orf66	2	197672293	Silent	SNP	T	TCGA-DD-AAVW-01A-11D-A40R-10	29566718	197672293	45527080	8	32235										
IQCA1	79781	hgsc.bcm.edu	37	chr2	237327828	237327830	+	In_Frame_Del	DEL	GGC	GGC	-													0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gttcctttcttttgttttttGgctttcttgggttgtttttc					rs559244816		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	GGC	GGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:237327828_237327830delGGC	ENST00000409907.3	-	8	1370_1372	c.1096_1098delGCC	c.(1096-1098)gccdel	p.A366del	IQCA1_ENST00000465621.1_5'UTR|IQCA1_ENST00000309507.5_In_Frame_Del_p.A362del|IQCA1_ENST00000431676.2_Intron	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	366	Lys-rich.						ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						TTTGTTTTTTGGCTTTCTTGGGT	0.271																																					p.373_374del		Atlas-INDEL	.											.	IQCA1	170	.	0			c.1118_1120del						.																																			SO:0001651	inframe_deletion	79781	exon8			.	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"ATPases / AAA-type"	26195	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 11"		"IQ motif containing with AAA domain"	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.1096_1098delGCC	chr2.hg19:g.237327828_237327830delGGC	ENSP00000387347:p.Ala366del	508.0	0.0		275.0	17.0	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	In_Frame_Del	DEL	ENST00000409907.3	hg19	CCDS46549.1																																																																																			.	.		0.271	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		-	237327830	GGC	-	237327828	7	5	229	1	0	1	0	1	0	0	0	0	7811	1335	47	0	1418	0	IQCA1	2	237327828	In_Frame_Del	DEL	GGC	TCGA-DD-AAVW-01A-11D-A40R-10	39655535	237327828	5871545	9	32236	168	2								
IQCA1	79781	hgsc.bcm.edu	37	chr2	237327837	237327839	+	In_Frame_Del	DEL	GGG	GGG	-													0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ttttgttttttggctttcttGggttgtttttcctttttctt							TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	GGG	GGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:237327837_237327839delGGG	ENST00000409907.3	-	8	1361_1363	c.1087_1089delCCC	c.(1087-1089)cccdel	p.P363del	IQCA1_ENST00000465621.1_5'UTR|IQCA1_ENST00000309507.5_In_Frame_Del_p.P359del|IQCA1_ENST00000431676.2_Intron	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	363	Lys-rich.						ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						TGGCTTTCTTGGGTTGTttttcc	0.266																																					p.370_371del		Atlas-INDEL	.											.	IQCA1	170	.	0			c.1109_1111del						.																																			SO:0001651	inframe_deletion	79781	exon8			.	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"ATPases / AAA-type"	26195	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 11"		"IQ motif containing with AAA domain"	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.1087_1089delCCC	chr2.hg19:g.237327837_237327839delGGG	ENSP00000387347:p.Pro363del	501.0	0.0		260.0	17.0	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	In_Frame_Del	DEL	ENST00000409907.3	hg19	CCDS46549.1																																																																																			.	.		0.266	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		-	237327839	GGG	-	237327837	7	5	229	1	0	1	0	1	0	0	0	0	7811	1335	47	0	1427	0	IQCA1	2	237327837	In_Frame_Del	DEL	GGG	TCGA-DD-AAVW-01A-11D-A40R-10	9	237327837	5871536	10	32237	168	2								
PRRT3	285368	hgsc.bcm.edu	37	chr3	9989661	9989661	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ctgggggatggctttgggggCgccccggccactcctcggct	17	14	0	0			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr3:9989661C>T	ENST00000412055.1	-	4	1325	c.1196G>A	c.(1195-1197)cGc>cAc	p.R399H	PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	399	Pro-rich.					integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						GCTTTGGGGGCGCCCCGGCCA	0.577																																					p.R399H		Atlas-SNP	.											.	PRRT3	35	.	0			c.G1196A						.						4	5	5					3																	9989661		1759	3881	5640	SO:0001583	missense	285368	exon4			TGGGGGCGCCCCG	AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"Proline-rich transmembrane proteins"	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.1196G>A	chr3.hg19:g.9989661C>T	ENSP00000392511:p.Arg399His	60.0	0.0		50.0	12.0	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Missense_Mutation	SNP	ENST00000412055.1	hg19	CCDS43049.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671840	0.67928	.	.	ENSG00000163704	ENST00000412055	T	0.17370	2.28	4.89	3.98	0.46160	.	0.241759	0.28241	N	0.016072	T	0.20373	0.0490	L	0.27053	0.805	0.80722	D	1	D	0.64830	0.994	P	0.56916	0.809	T	0.00628	-1.1637	9	.	.	.	-9.6073	10.9219	0.47169	0.0:0.7032:0.2968:0.0	.	399	Q5FWE3	PRRT3_HUMAN	H	399	ENSP00000392511:R399H	.	R	-	2	0	PRRT3	9964661	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	2.125000	0.42016	2.527000	0.85204	0.655000	0.94253	CGC	.	.		0.577	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351		T	9989661	C	T	9989661	3	4	229	1	0	0	0	0	1	0	0	0	12623	768	27	1	1753	1	PRRT3	3	9989661	Missense_Mutation	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10		9989661	188032769	11	32238										
ZNF35	7584	hgsc.bcm.edu	37	chr3	44692628	44692628	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gtgaaggtgaaaaaggaggaGgaagaagaagaaaacttccc	14	4	0	5			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr3:44692628G>A	ENST00000396056.2	+	2	304	c.69G>A	c.(67-69)gaG>gaA	p.E23E	ZNF35_ENST00000296092.3_Silent_p.E23E|ZNF35_ENST00000542250.1_5'UTR|ZNF35_ENST00000453164.1_Silent_p.E23E|RP11-944L7.4_ENST00000457331.1_RNA|ZNF35_ENST00000399560.2_Silent_p.E23E	NM_003420.3	NP_003411.3	P13682	ZNF35_HUMAN	zinc finger protein 35	23	Globular domain.|Poly-Glu.				cellular response to retinoic acid (GO:0071300)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cell (GO:0005623)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12		Ovarian(412;0.0228)		OV - Ovarian serous cystadenocarcinoma(275;2.49e-27)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)		AAAAGGAGGAGGAAGAAGAAG	0.542																																					p.E23E		Atlas-SNP	.											.	ZNF35	34	.	0			c.G69A						.						57	57	57					3																	44692628		2203	4300	6503	SO:0001819	synonymous_variant	7584	exon2			GGAGGAGGAAGAA	X07289	CCDS2718.2	3p21.32	2013-01-08	2006-05-11		ENSG00000169981	ENSG00000169981		"Zinc fingers, C2H2-type"	13099	protein-coding gene	gene with protein product		194533	"zinc finger protein 35 (clone HF.10)"			2108922, 1572646	Standard	NM_003420		Approved	HF.10, HF10, Zfp105	uc003cnq.3	P13682	OTTHUMG00000133091	ENST00000396056.2:c.69G>A	chr3.hg19:g.44692628G>A		295.0	0.0		158.0	16.0	NM_003420	B2RBU6|Q53Y54|Q96D01	Silent	SNP	ENST00000396056.2	hg19	CCDS2718.2																																																																																			.	.		0.542	ZNF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256749.4	NM_003420		A	44692628	G	A	44692628	2	1	229	1	0	0	0	0	0	0	0	1	17877	991	35	3		3	ZNF35	3	44692628	Silent	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10	34702967	44692628	153329802	12	32239										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111940054	111940054	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ggacagaatctcattcctgtAttgtctctggtagcttgcct	9	10	2	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr3:111940054A>G	ENST00000305815.5	-	14	1843	c.1591T>C	c.(1591-1593)Tac>Cac	p.Y531H	SLC9C1_ENST00000487372.1_Missense_Mutation_p.Y483H	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	531					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TCATTCCTGTATTGTCTCTGG	0.368																																					p.Y531H		Atlas-SNP	.											.	.	.	.	0			c.T1591C						.						105	103	104					3																	111940054		2203	4300	6503	SO:0001583	missense	285335	exon14			TCCTGTATTGTCT	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.1591T>C	chr3.hg19:g.111940054A>G	ENSP00000306627:p.Tyr531His	60.0	0.0		30.0	5.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	A	14.56	2.572014	0.45798	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.81330	-1.41;-1.48	5.7	5.7	0.88788	.	0.246358	0.29260	N	0.012677	D	0.83312	0.5227	L	0.32530	0.975	0.34533	D	0.709464	D;D	0.89917	0.999;1.0	D;D	0.77557	0.99;0.983	D	0.86396	0.1739	10	0.37606	T	0.19	.	12.3536	0.55163	1.0:0.0:0.0:0.0	.	483;531	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	H	531;483	ENSP00000306627:Y531H;ENSP00000420688:Y483H	ENSP00000306627:Y531H	Y	-	1	0	SLC9A10	113422744	1.000000	0.71417	0.996000	0.52242	0.728000	0.41692	4.551000	0.60740	2.170000	0.68504	0.482000	0.46254	TAC	.	.		0.368	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		G	111940054	A	G	111940054	3	3	229	1	0	0	0	0	1	0	0	0	14725	449	16	2	2006	2	SLC9A10	3	111940054	Missense_Mutation	SNP	A	TCGA-DD-AAVW-01A-11D-A40R-10	67247426	111940054	86082376	13	32240										
COPG	22820	hgsc.bcm.edu	37	chr3	128986867	128986867	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	aagcagaaggcccttaatgcAggctatatcctaaatggtga	10	8	0	2			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr3:128986867A>G	ENST00000314797.6	+	16	1736	c.1632A>G	c.(1630-1632)gcA>gcG	p.A544A		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	544					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										CCCTTAATGCAGGCTATATCC	0.517																																					p.A544A		Atlas-SNP	.											.	.	.	.	0			c.A1632G						.						153	127	136					3																	128986867		2203	4300	6503	SO:0001819	synonymous_variant	22820	exon16			TAATGCAGGCTAT	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"coat protein gamma-cop"	615525	"coatomer protein complex, subunit gamma"	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.1632A>G	chr3.hg19:g.128986867A>G		94.0	0.0		52.0	20.0	NM_016128	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	hg19	CCDS33851.1																																																																																			.	.		0.517	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128		G	128986867	A	G	128986867	2	3	229	1	0	0	0	0	0	0	0	1	3733	175	7	2		2	COPG	3	128986867	Silent	SNP	A	TCGA-DD-AAVW-01A-11D-A40R-10	17046813	128986867	69035563	14	32241										
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6611736	6611736	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	acaacggctaccagatgcagCggaggccctacgtttcctat	10	13	0	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr4:6611736C>T	ENST00000285599.3	+	13	2254	c.2218C>T	c.(2218-2220)Cgg>Tgg	p.R740W	MAN2B2_ENST00000504960.1_3'UTR|MAN2B2_ENST00000504248.1_Missense_Mutation_p.R689W	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	740					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CCAGATGCAGCGGAGGCCCTA	0.582																																					p.R740W		Atlas-SNP	.											MAN2B2,colon,carcinoma,0,1	MAN2B2	80	.	0			c.C2218T						.						94	86	89					4																	6611736		2203	4300	6503	SO:0001583	missense	23324	exon13			ATGCAGCGGAGGC	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"core-specific lysosomal alpha-1,6-Mannosidase"					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.2218C>T	chr4.hg19:g.6611736C>T	ENSP00000285599:p.Arg740Trp	132.0	0.0		82.0	21.0	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	hg19	CCDS33951.1	.	.	.	.	.	.	.	.	.	.	c	18.48	3.632545	0.67015	.	.	ENSG00000013288	ENST00000285599;ENST00000504248	D;D	0.85013	-1.93;-1.93	3.98	2.94	0.34122	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.217789	0.40818	N	0.001011	D	0.90345	0.6979	M	0.79475	2.455	0.36909	D	0.890791	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.75484	0.986;0.981;0.963	D	0.91764	0.5422	10	0.87932	D	0	-41.6707	8.7335	0.34514	0.4731:0.5269:0.0:0.0	.	689;740;740	E9PCD7;Q9Y2E5;Q9Y2E5-2	.;MA2B2_HUMAN;.	W	740;689	ENSP00000285599:R740W;ENSP00000423129:R689W	ENSP00000285599:R740W	R	+	1	2	MAN2B2	6662637	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.635000	0.54309	1.930000	0.55929	0.558000	0.71614	CGG	.	.		0.582	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		T	6611736	C	T	6611736	3	4	229	1	0	0	0	0	1	0	0	0	9226	759	27	1	2268	1	MAN2B2	4	6611736	Missense_Mutation	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10		6611736	184542540	15	32242										
PCDHGB2	56103	hgsc.bcm.edu	37	chr5	140741078	140741078	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ccaacagacttcctacatggTtcacgtggcagagaacaatc	8	12	1	2			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr5:140741078T>C	ENST00000522605.1	+	1	1376	c.1376T>C	c.(1375-1377)gTt>gCt	p.V459A	PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	459	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTACATGGTTCACGTGGCA	0.557																																					p.V459A		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.T1376C						.						93	95	94					5																	140741078		2044	4195	6239	SO:0001583	missense	56103	exon1			ACATGGTTCACGT	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"Cadherins / Protocadherins : Clustered"	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.1376T>C	chr5.hg19:g.140741078T>C	ENSP00000429018:p.Val459Ala	118.0	0.0		81.0	19.0	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	hg19	CCDS54924.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.091274	0.00367	.	.	ENSG00000253910	ENST00000522605	T	0.01804	4.63	5.41	2.76	0.32466	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.02571	0.0078	N	0.17082	0.46	0.09310	N	0.999999	P;D	0.69078	0.675;0.997	B;D	0.72075	0.254;0.976	T	0.37502	-0.9703	9	0.06757	T	0.87	.	4.8317	0.13443	0.0:0.4297:0.0:0.5703	.	459;459	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	A	459	ENSP00000429018:V459A	ENSP00000429018:V459A	V	+	2	0	PCDHGB2	140721262	0.023000	0.18921	0.997000	0.53966	0.211000	0.24417	0.343000	0.19944	0.995000	0.38917	0.460000	0.39030	GTT	.	.		0.557	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		C	140741078	T	C	140741078	3	2	229	1	0	0	0	0	1	0	0	0	11572	1725	60	2	1378	2	PCDHGB2	5	140741078	Missense_Mutation	SNP	T	TCGA-DD-AAVW-01A-11D-A40R-10		140741078	40174182	16	32243										
PCDHGA6	56109	hgsc.bcm.edu	37	chr5	140755848	140755848	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ggcttcgggaggtggcttagCgagcatgcccggctcgcact	16	12	0	0			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr5:140755848C>T	ENST00000517434.1	+	1	2198	c.2198C>T	c.(2197-2199)gCg>gTg	p.A733V	PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	733					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGCTTAGCGAGCATGCCC	0.622																																					p.A733V		Atlas-SNP	.											.	PCDHGA6	219	.	0			c.C2198T						.						74	80	78					5																	140755848		2203	4300	6503	SO:0001583	missense	56109	exon1			GCTTAGCGAGCAT	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"Cadherins / Protocadherins : Clustered"	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.2198C>T	chr5.hg19:g.140755848C>T	ENSP00000429601:p.Ala733Val	149.0	0.0		141.0	36.0	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	hg19	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	6.378	0.437859	0.12104	.	.	ENSG00000253731	ENST00000517434	T	0.44482	0.92	5.15	0.115	0.14643	.	0.925107	0.08507	U	0.935524	T	0.25791	0.0628	L	0.37630	1.12	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.09377	0.003;0.004	T	0.29119	-1.0022	10	0.06891	T	0.86	.	5.305	0.15799	0.0:0.4676:0.2001:0.3324	.	733;733	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	V	733	ENSP00000429601:A733V	ENSP00000429601:A733V	A	+	2	0	PCDHGA6	140736032	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.582000	0.05814	0.150000	0.19136	-0.136000	0.14681	GCG	.	.		0.622	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		T	140755848	C	T	140755848	3	4	229	1	0	0	0	0	1	0	0	0	11567	768	27	1	2200	1	PCDHGA6	5	140755848	Missense_Mutation	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10	14770	140755848	40159412	17	32244										
OR2J3	442186	hgsc.bcm.edu	37	chr6	29080267	29080267	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gatacccatgtcaatgagctGaccctcatgatcacaagctc	7	13	3	3			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr6:29080267G>T	ENST00000377169.1	+	1	600	c.600G>T	c.(598-600)ctG>ctT	p.L200L		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						TCAATGAGCTGACCCTCATGA	0.463																																					p.L200L		Atlas-SNP	.											.	OR2J3	53	.	0			c.G600T						.						100	112	108					6																	29080267		1339	2597	3936	SO:0001819	synonymous_variant	442186	exon1			TGAGCTGACCCTC		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"GPCR / Class A : Olfactory receptors"	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.600G>T	chr6.hg19:g.29080267G>T		129.0	0.0		50.0	14.0	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Silent	SNP	ENST00000377169.1	hg19	CCDS43433.1																																																																																			.	.		0.463	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			T	29080267	G	T	29080267	2	4	229	1	0	0	0	0	0	0	0	1	11013	1277	45	3		3	OR2J3	6	29080267	Silent	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10		29080267	142034800	18	32245										
TRIM10	10107	hgsc.bcm.edu	37	chr6	30121906	30121906	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	caagagacaccctcacctgcCggggctgctccttcagggtc	11	16	2	1	rs137941157	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr6:30121906C>T	ENST00000449742.2	-	7	1361	c.1286G>A	c.(1285-1287)cGg>cAg	p.R429Q	TRIM10_ENST00000376704.3_Intron	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	429	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.R429L(1)		ovary(1)	1						CCTCACCTGCCGGGGCTGCTC	0.642																																					p.R429Q		Atlas-SNP	.											.	TRIM10	65	.	1	Substitution - Missense(1)	lung(1)	c.G1286A						.						43	39	41					6																	30121906		1509	2708	4217	SO:0001583	missense	10107	exon7			ACCTGCCGGGGCT	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10072	protein-coding gene	gene with protein product		605701	"tripartite motif-containing 10"	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.1286G>A	chr6.hg19:g.30121906C>T	ENSP00000397073:p.Arg429Gln	132.0	0.0		93.0	16.0	NM_006778	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Missense_Mutation	SNP	ENST00000449742.2	hg19	CCDS34375.1	.	.	.	.	.	.	.	.	.	.	C	7.712	0.695347	0.15106	.	.	ENSG00000204613	ENST00000449742;ENST00000376706	T	0.70516	-0.49	6.01	-3.21	0.05140	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	1.261850	0.05437	N	0.547066	T	0.30070	0.0753	N	0.16166	0.38	0.09310	N	1	B	0.19583	0.037	B	0.09377	0.004	T	0.14420	-1.0473	10	0.23302	T	0.38	.	13.6023	0.62026	0.0:0.3426:0.0:0.6574	.	429	Q9UDY6	TRI10_HUMAN	Q	429	ENSP00000397073:R429Q	ENSP00000365896:R429Q	R	-	2	0	TRIM10	30229885	0.000000	0.05858	0.260000	0.24451	0.100000	0.18952	-0.606000	0.05654	-0.710000	0.05001	-1.157000	0.01802	CGG	.	C|1.000;A|0.000		0.642	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1			T	30121906	C	T	30121906	3	4	229	1	0	0	0	0	1	0	0	0	16501	652	23	1	251	1	TRIM10	6	30121906	Missense_Mutation	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10	1041639	30121906	140993161	19	32246										
EYS	346007	hgsc.bcm.edu	37	chr6	66042220	66042220	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	aagccactaaatcaaacttaTattcttacgataaatcccac	2	11	2	0			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr6:66042220T>A	ENST00000370621.3	-	11	2293				EYS_ENST00000503581.1_Intron|EYS_ENST00000393380.2_Silent_p.I619I|EYS_ENST00000370616.2_Intron			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)						detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						atcaaacttatattcttacga	0.294																																					p.I619I		Atlas-SNP	.											.	EYS	527	.	0			c.A1857T						.						173	152	159					6																	66042220		692	1590	2282	SO:0001627	intron_variant	346007	exon12			AACTTATATTCTT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1766+2652A>T	chr6.hg19:g.66042220T>A		70.0	0.0		29.0	6.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	hg19																																																																																				.	.		0.294	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	66042220	T	A	66042220	1	1	229	0	1	0	0	0	0	0	0	0	5334	1396	49	4		4	EYS	6	66042220	Intron	SNP	T	TCGA-DD-AAVW-01A-11D-A40R-10	35920314	66042220	105072847	20	32247										
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	10	12	0	0			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		61.0	0.0		36.0	8.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	229	1	0	0	0	0	0	0	0	1	15659	962	34	3		3	TBP	6	170871004	Silent	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10	104828784	170871004	244063	21	32248										
RSBN1L	222194	hgsc.bcm.edu	37	chr7	77326048	77326048	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gcagccccgcgtcttggagcTttgcccctctgtctgctgct	11	16	3	0			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr7:77326048T>G	ENST00000334955.8	+	1	289	c.262T>G	c.(262-264)Ttt>Gtt	p.F88V	RSBN1L_ENST00000445288.1_5'Flank|RSBN1L-AS1_ENST00000440088.1_lincRNA	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	88	Ser-rich.					nucleus (GO:0005634)				central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTCTTGGAGCTTTGCCCCTCT	0.657																																					p.F88V		Atlas-SNP	.											.	RSBN1L	74	.	0			c.T262G						.						23	32	29					7																	77326048		2021	4178	6199	SO:0001583	missense	222194	exon1			TGGAGCTTTGCCC	AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.262T>G	chr7.hg19:g.77326048T>G	ENSP00000334040:p.Phe88Val	75.0	0.0		81.0	27.0	NM_198467	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Missense_Mutation	SNP	ENST00000334955.8	hg19	CCDS43607.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.503703	0.44558	.	.	ENSG00000187257	ENST00000334955	.	.	.	3.84	0.104	0.14531	.	0.553074	0.16943	N	0.193215	T	0.33000	0.0848	L	0.27053	0.805	0.80722	D	1	B	0.28291	0.206	B	0.22601	0.04	T	0.06023	-1.0850	9	0.54805	T	0.06	-2.5694	6.4576	0.21938	0.0:0.3033:0.0:0.6967	.	88	Q6PCB5	RSBNL_HUMAN	V	88	.	ENSP00000334040:F88V	F	+	1	0	RSBN1L	77163984	1.000000	0.71417	0.950000	0.38849	0.664000	0.39144	1.572000	0.36461	-0.075000	0.12798	0.260000	0.18958	TTT	.	.		0.657	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467		G	77326048	T	G	77326048	3	3	229	1	0	0	0	0	1	0	0	0	13712	1609	56	5	264	5	RSBN1L	7	77326048	Missense_Mutation	SNP	T	TCGA-DD-AAVW-01A-11D-A40R-10		77326048	81812615	22	32249										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	93003968	93003968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	catccaaacggtaatgctgaGgtggaggtggggtagggtga	18	5	0	2			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr8:93003968G>A	ENST00000523629.1	-	7	1344	c.890C>T	c.(889-891)cCt>cTt	p.P297L	RUNX1T1_ENST00000265814.3_Missense_Mutation_p.P297L|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.P308L|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.P260L|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.P260L|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.P270L|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.P270L|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.P260L	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	297	Poly-Pro.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			GTAATGCTGAGGTGGAGGTGG	0.562																																					p.P356L		Atlas-SNP	.											.	RUNX1T1	516	.	0			c.C1067T						.						218	176	190					8																	93003968		2203	4300	6503	SO:0001583	missense	862	exon7			TGCTGAGGTGGAG	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.890C>T	chr8.hg19:g.93003968G>A	ENSP00000428543:p.Pro297Leu	119.0	0.0		101.0	35.0	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	hg19	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.847410	0.32606	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.29655	1.56;1.57;1.56;1.57;1.57;1.57;1.56;1.57	6.17	6.17	0.99709	.	0.094035	0.85682	D	0.000000	T	0.28234	0.0697	L	0.36672	1.1	0.80722	D	1	B;B;B	0.16802	0.001;0.0;0.019	B;B;B	0.25405	0.002;0.002;0.06	T	0.12604	-1.0541	10	0.07813	T	0.8	-12.043	20.4745	0.99168	0.0:0.0:1.0:0.0	.	308;297;270	E7EPN4;Q06455;Q06455-2	.;MTG8_HUMAN;.	L	297;270;297;260;260;260;308;270	ENSP00000428543:P297L;ENSP00000379520:P270L;ENSP00000265814:P297L;ENSP00000353504:P260L;ENSP00000390137:P260L;ENSP00000428742:P260L;ENSP00000402257:P308L;ENSP00000430728:P270L	ENSP00000265814:P297L	P	-	2	0	RUNX1T1	93073144	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.375000	0.73137	2.941000	0.99782	0.655000	0.94253	CCT	.	.		0.562	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		A	93003968	G	A	93003968	3	1	229	1	0	0	0	0	1	0	0	0	13762	1000	35	3	948	3	RUNX1T1	8	93003968	Missense_Mutation	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10		93003968	53360054	23	32250										
TSPYL5	85453	hgsc.bcm.edu	37	chr8	98289975	98289975	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gtgaagggtccgggtcgcgcGgggcgtcgtccggagcaggg	22	10	0	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr8:98289975G>A	ENST00000322128.3	-	1	201	c.98C>T	c.(97-99)cCg>cTg	p.P33L		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	33					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					CGGGTCGCGCGGGGCGTCGTC	0.711																																					p.P33L		Atlas-SNP	.											.	TSPYL5	48	.	0			c.C98T						.						8	10	9					8																	98289975		2131	4131	6262	SO:0001583	missense	85453	exon1			TCGCGCGGGGCGT	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.98C>T	chr8.hg19:g.98289975G>A	ENSP00000322802:p.Pro33Leu	61.0	0.0		144.0	22.0	NM_033512	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	hg19	CCDS34927.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.344730	0.24426	.	.	ENSG00000180543	ENST00000322128	T	0.48836	0.8	3.82	0.903	0.19296	.	0.813650	0.10113	N	0.714458	T	0.37839	0.1018	L	0.52011	1.625	0.09310	N	1	B	0.19583	0.037	B	0.06405	0.002	T	0.28459	-1.0043	10	0.40728	T	0.16	-0.2151	5.9128	0.19037	0.1124:0.3597:0.5279:0.0	.	33	Q86VY4	TSYL5_HUMAN	L	33	ENSP00000322802:P33L	ENSP00000322802:P33L	P	-	2	0	TSPYL5	98359151	0.052000	0.20516	0.001000	0.08648	0.272000	0.26649	0.680000	0.25306	0.172000	0.19760	0.561000	0.74099	CCG	.	.		0.711	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512		A	98289975	G	A	98289975	3	1	229	1	0	0	0	0	1	0	0	0	16677	1116	39	1	1159	1	TSPYL5	8	98289975	Missense_Mutation	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10	5286007	98289975	48074047	24	32251										
COL15A1	1306	hgsc.bcm.edu	37	chr9	101816900	101816900	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ctggggtcttcctggctcaaAgggagaaaaaggcgaccagg	15	9	2	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr9:101816900A>G	ENST00000375001.3	+	32	3416	c.2993A>G	c.(2992-2994)aAg>aGg	p.K998R		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	998	Triple-helical region 6 (COL6).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CCTGGCTCAAAGGGAGAAAAA	0.438																																					p.K998R		Atlas-SNP	.											.	COL15A1	211	.	0			c.A2993G						.						83	89	87					9																	101816900		2203	4300	6503	SO:0001583	missense	1306	exon32			GCTCAAAGGGAGA	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2993A>G	chr9.hg19:g.101816900A>G	ENSP00000364140:p.Lys998Arg	218.0	0.0		83.0	4.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	hg19	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.401480	0.62288	.	.	ENSG00000204291	ENST00000375001	T	0.30981	1.51	5.67	5.67	0.87782	C-type lectin fold (1);	0.188258	0.46758	D	0.000274	T	0.47820	0.1466	L	0.54863	1.705	0.45747	D	0.998644	D	0.63880	0.993	D	0.72625	0.978	T	0.31308	-0.9948	10	0.28530	T	0.3	-17.9351	12.5857	0.56416	1.0:0.0:0.0:0.0	.	998	P39059	COFA1_HUMAN	R	998	ENSP00000364140:K998R	ENSP00000364140:K998R	K	+	2	0	COL15A1	100856721	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.419000	0.66435	2.288000	0.76882	0.533000	0.62120	AAG	.	.		0.438	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		G	101816900	A	G	101816900	3	3	229	1	0	0	0	0	1	0	0	0	3674	72	3	2	3119	2	COL15A1	9	101816900	Missense_Mutation	SNP	A	TCGA-DD-AAVW-01A-11D-A40R-10		101816900	39396531	25	32252										
C9orf30	91283	hgsc.bcm.edu	37	chr9	103204372	103204372	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	taagcagcgtacctggcaggCgctggcccacgaatacaact	11	13	0	0	rs139409577	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr9:103204372C>T	ENST00000395067.2	+	2	423	c.152C>T	c.(151-153)gCg>gTg	p.A51V	MSANTD3-TMEFF1_ENST00000502978.1_5'Flank|MSANTD3_ENST00000374885.1_Missense_Mutation_p.A51V|TMEFF1_ENST00000334943.6_5'Flank	NM_001198805.1|NM_001198806.1|NM_080655.2	NP_001185734.1|NP_001185735.1|NP_542386.1	Q96H12	MSD3_HUMAN	Myb/SANT-like DNA-binding domain containing 3	51	Myb-like.									endometrium(2)|lung(2)	4						ACCTGGCAGGCGCTGGCCCAC	0.483																																					p.A51V		Atlas-SNP	.											.	MSANTD3	10	.	0			c.C152T						.						42	43	43					9																	103204372		2203	4300	6503	SO:0001583	missense	91283	exon2			GGCAGGCGCTGGC	BC008993	CCDS6749.1, CCDS56579.1	9q31.1	2012-03-13	2012-03-13	2012-03-13	ENSG00000066697	ENSG00000066697			23370	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 30"	C9orf30			Standard	NM_080655		Approved	MGC17337		Q96H12	OTTHUMG00000020365	ENST00000395067.2:c.152C>T	chr9.hg19:g.103204372C>T	ENSP00000378506:p.Ala51Val	90.0	0.0		33.0	13.0	NM_001198805	B2RC35|Q5T726|Q5T727|Q5T728	Missense_Mutation	SNP	ENST00000395067.2	hg19	CCDS6749.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.743003	0.89663	.	.	ENSG00000066697	ENST00000395067;ENST00000398977;ENST00000374885;ENST00000374886	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	T	0.45875	0.1364	N	0.08118	0	0.48830	D	0.99971	D	0.56746	0.977	P	0.51806	0.68	T	0.44682	-0.9312	8	0.30078	T	0.28	-4.2443	19.1261	0.93384	0.0:1.0:0.0:0.0	.	51	Q96H12	CI030_HUMAN	V	51	.	ENSP00000364020:A51V	A	+	2	0	C9orf30	102244193	0.997000	0.39634	0.983000	0.44433	0.977000	0.68977	3.765000	0.55272	2.779000	0.95612	0.655000	0.94253	GCG	.	C|1.000;T|0.000		0.483	MSANTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053410.1	NM_080655		T	103204372	C	T	103204372	3	4	229	1	0	0	0	0	1	0	0	0	2480	768	27	1	154	1	C9orf30	9	103204372	Missense_Mutation	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10	1387472	103204372	38009059	26	32253										
GPR158	57512	hgsc.bcm.edu	37	chr10	25887911	25887911	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gtgtgctgggcagagcgaagAactgccccccaaagctgtag	14	11	0	2			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr10:25887911A>C	ENST00000376351.3	+	11	3715	c.3356A>C	c.(3355-3357)gAa>gCa	p.E1119A	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1119					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CAGAGCGAAGAACTGCCCCCC	0.478																																					p.E1119A		Atlas-SNP	.											.	GPR158	255	.	0			c.A3356C						.						87	90	89					10																	25887911		2203	4300	6503	SO:0001583	missense	57512	exon11			GCGAAGAACTGCC	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3356A>C	chr10.hg19:g.25887911A>C	ENSP00000365529:p.Glu1119Ala	108.0	0.0		46.0	19.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	A	9.726	1.161006	0.21538	.	.	ENSG00000151025	ENST00000376351	T	0.67698	-0.28	5.69	5.69	0.88448	.	0.240296	0.35555	N	0.003129	T	0.62792	0.2457	L	0.29908	0.895	0.50632	D	0.999889	P	0.52316	0.952	P	0.49477	0.612	T	0.62134	-0.6918	10	0.33940	T	0.23	.	14.5105	0.67784	1.0:0.0:0.0:0.0	.	1119	Q5T848	GP158_HUMAN	A	1119	ENSP00000365529:E1119A	ENSP00000365529:E1119A	E	+	2	0	GPR158	25927917	1.000000	0.71417	0.208000	0.23602	0.083000	0.17756	7.984000	0.88150	2.162000	0.67917	0.533000	0.62120	GAA	.	.		0.478	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		C	25887911	A	C	25887911	3	2	229	1	0	0	0	0	1	0	0	0	6671	246	9	5	3398	5	GPR158	10	25887911	Missense_Mutation	SNP	A	TCGA-DD-AAVW-01A-11D-A40R-10		25887911	109646836	27	32254										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105203771	105203771	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ttctgcggaggagccaggctGcagccagtcaccgcgtgctg	15	13	2	0			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr10:105203771G>T	ENST00000369797.3	+	34	5318	c.5224G>T	c.(5224-5226)Gca>Tca	p.A1742S		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1742					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GAGCCAGGCTGCAGCCAGTCA	0.607																																					p.A1742S		Atlas-SNP	.											.	PDCD11	160	.	0			c.G5224T						.						43	45	44					10																	105203771		2203	4300	6503	SO:0001583	missense	22984	exon34			CAGGCTGCAGCCA	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5224G>T	chr10.hg19:g.105203771G>T	ENSP00000358812:p.Ala1742Ser	79.0	0.0		42.0	12.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	hg19	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812101	0.70797	.	.	ENSG00000148843	ENST00000369797	T	0.41065	1.01	5.67	5.67	0.87782	Tetratricopeptide-like helical (1);Suppressor of forked (1);Tetratricopeptide repeat-containing (1);	0.258158	0.45361	D	0.000363	T	0.31857	0.0810	N	0.14661	0.345	0.28154	N	0.929268	B	0.06786	0.001	B	0.04013	0.001	T	0.21552	-1.0242	10	0.51188	T	0.08	-6.3898	19.7629	0.96329	0.0:0.0:1.0:0.0	.	1742	Q14690	RRP5_HUMAN	S	1742	ENSP00000358812:A1742S	ENSP00000358812:A1742S	A	+	1	0	PDCD11	105193761	1.000000	0.71417	0.403000	0.26384	0.834000	0.47266	5.643000	0.67895	2.666000	0.90696	0.561000	0.74099	GCA	.	.		0.607	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			T	105203771	G	T	105203771	3	4	229	1	0	0	0	0	1	0	0	0	11626	1319	46	3	5354	3	PDCD11	10	105203771	Missense_Mutation	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10	79315860	105203771	30330976	28	32255										
MKI67	4288	hgsc.bcm.edu	37	chr10	129914055	129914055	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	tcactaatttaacgctggaaAtttctttaaaatccccagaa	4	9	2	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr10:129914055A>G	ENST00000368654.3	-	7	992	c.617T>C	c.(616-618)aTt>aCt	p.I206T	MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	206					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				AACGCTGGAAATTTCTTTAAA	0.403																																					p.I206T		Atlas-SNP	.											.	MKI67	363	.	0			c.T617C						.						94	95	95					10																	129914055		2203	4300	6503	SO:0001583	missense	4288	exon7			CTGGAAATTTCTT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.617T>C	chr10.hg19:g.129914055A>G	ENSP00000357643:p.Ile206Thr	44.0	0.0		24.0	4.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	A	6.685	0.495074	0.12762	.	.	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.20881	2.04	3.69	-1.44	0.08856	.	1.520410	0.03934	N	0.285756	T	0.10165	0.0249	N	0.14661	0.345	0.09310	N	0.999999	B	0.23377	0.084	B	0.18561	0.022	T	0.19257	-1.0311	9	.	.	.	.	1.0409	0.01559	0.1777:0.3431:0.1655:0.3137	.	206	P46013	KI67_HUMAN	T	206	ENSP00000357643:I206T	.	I	-	2	0	MKI67	129804045	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.148000	0.10219	-0.267000	0.09325	-0.339000	0.08088	ATT	.	.		0.403	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		G	129914055	A	G	129914055	3	3	229	1	0	0	0	0	1	0	0	0	9607	101	4	2	9189	2	MKI67	10	129914055	Missense_Mutation	SNP	A	TCGA-DD-AAVW-01A-11D-A40R-10	24710284	129914055	5620692	29	32256										
PYGM	5837	hgsc.bcm.edu	37	chr11	64518935	64518935	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ggccatgtggtacccaggtgCagcctgaggggacaaagtct	15	10	1	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr11:64518935C>T	ENST00000164139.3	-	16	2229	c.1831G>A	c.(1831-1833)Gca>Aca	p.A611T	PYGM_ENST00000377432.3_Missense_Mutation_p.A523T|PYGM_ENST00000462303.1_5'UTR	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	611					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TACCCAGGTGCAGCCTGAGGG	0.592																																					p.A611T		Atlas-SNP	.											.	PYGM	77	.	0			c.G1831A						.						92	97	95					11																	64518935		2201	4297	6498	SO:0001583	missense	5837	exon16			CAGGTGCAGCCTG		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.1831G>A	chr11.hg19:g.64518935C>T	ENSP00000164139:p.Ala611Thr	90.0	0.0		70.0	21.0	NM_005609	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	hg19	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	C	38	6.677460	0.97755	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.94184	-3.37;-3.37	5.25	5.25	0.73442	.	0.000000	0.64402	D	0.000019	D	0.98169	0.9395	H	0.98802	4.335	0.80722	D	1	P;D	0.56521	0.946;0.976	D;D	0.71870	0.975;0.922	D	0.99211	1.0876	10	0.87932	D	0	-16.4427	16.3883	0.83523	0.0:1.0:0.0:0.0	.	523;611	A6NDY6;P11217	.;PYGM_HUMAN	T	523;611;592	ENSP00000366650:A523T;ENSP00000164139:A611T	ENSP00000164139:A611T	A	-	1	0	PYGM	64275511	1.000000	0.71417	0.576000	0.28549	0.910000	0.53928	7.616000	0.83018	2.739000	0.93911	0.561000	0.74099	GCA	.	.		0.592	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		T	64518935	C	T	64518935	3	4	229	1	0	0	0	0	1	0	0	0	12877	710	25	3	717	3	PYGM	11	64518935	Missense_Mutation	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10		64518935	70487581	30	32257										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2800310	2800310	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gggctgtgtgcgcgcgcgggGtcgaccgagtgaggaggagc	22	9	0	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr12:2800310G>T	ENST00000347598.4	+	49	6506	c.6506G>T	c.(6505-6507)gGt>gTt	p.G2169V	CACNA1C_ENST00000399644.1_Missense_Mutation_p.G2121V|CACNA1C_ENST00000399621.1_Missense_Mutation_p.G2140V|CACNA1C_ENST00000399638.1_Missense_Mutation_p.G2149V|CACNA1C_ENST00000399637.1_Missense_Mutation_p.G2140V|CACNA1C_ENST00000399601.1_Missense_Mutation_p.G2121V|CACNA1C-AS1_ENST00000544517.1_RNA|CACNA1C_ENST00000399606.1_Missense_Mutation_p.G2141V|CACNA1C_ENST00000399634.1_Missense_Mutation_p.G2192V|CACNA1C_ENST00000399641.1_Missense_Mutation_p.G2121V|CACNA1C_ENST00000406454.3_Missense_Mutation_p.G2192V|CACNA1C_ENST00000399649.1_Missense_Mutation_p.G2127V|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000402845.3_Missense_Mutation_p.G2140V|CACNA1C_ENST00000335762.5_Missense_Mutation_p.G2146V|CACNA1C_ENST00000344100.3_Missense_Mutation_p.G2162V|CACNA1C_ENST00000327702.7_Missense_Mutation_p.G2156V|CACNA1C_ENST00000399591.1_Missense_Mutation_p.G2129V|CACNA1C_ENST00000399603.1_Missense_Mutation_p.G2121V|CACNA1C_ENST00000399655.1_Missense_Mutation_p.G2121V|CACNA1C-AS1_ENST00000541673.1_RNA|CACNA1C_ENST00000399617.1_Missense_Mutation_p.G2156V|CACNA1C_ENST00000399629.1_Missense_Mutation_p.G2138V|CACNA1C_ENST00000399597.1_Missense_Mutation_p.G2121V|CACNA1C_ENST00000399595.1_Missense_Mutation_p.G2129V	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	2204			A -> T.		adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGCGCGCGGGGTCGACCGAGT	0.632																																					p.G2204V		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.G6611T						.						21	28	26					12																	2800310		1962	4124	6086	SO:0001583	missense	775	exon50			CGCGGGGTCGACC	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.6506G>T	chr12.hg19:g.2800310G>T	ENSP00000266376:p.Gly2169Val	175.0	0.0		114.0	34.0	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	2.365	-0.345696	0.05208	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43	4.49	1.08	0.20341	.	0.941163	0.08901	N	0.877252	T	0.32346	0.0826	N	0.08118	0	0.20403	N	0.999908	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.31548	0.0;0.002;0.02;0.001;0.0;0.098;0.078;0.001;0.029;0.001;0.098;0.069;0.02;0.001;0.041;0.148;0.02;0.002;0.0;0.0;0.145;0.0;0.328;0.13;0.02	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.37239	0.001;0.004;0.023;0.001;0.004;0.107;0.053;0.004;0.03;0.001;0.107;0.055;0.034;0.004;0.01;0.046;0.034;0.004;0.002;0.0;0.099;0.001;0.244;0.101;0.023	T	0.32214	-0.9915	10	0.46703	T	0.11	.	4.4188	0.11470	0.4164:0.4475:0.1361:0.0	.	812;2162;2118;2204;2156;2140;2121;2138;2149;2121;2141;2121;2152;2169;2121;2156;2192;2129;2127;2129;2110;2140;2140;2121;2121	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	V	2146;2121;2121;2149;2121;2140;2140;2129;2121;2169;2141;2121;2162;2138;2156;2127;2140;2121;2192;2156;2192;2129;2022	ENSP00000336982:G2146V;ENSP00000382563:G2121V;ENSP00000382552:G2121V;ENSP00000382547:G2149V;ENSP00000382506:G2121V;ENSP00000382530:G2140V;ENSP00000382546:G2140V;ENSP00000382500:G2129V;ENSP00000382549:G2121V;ENSP00000266376:G2169V;ENSP00000382515:G2141V;ENSP00000382510:G2121V;ENSP00000341092:G2162V;ENSP00000382537:G2138V;ENSP00000329877:G2156V;ENSP00000382557:G2127V;ENSP00000385724:G2140V;ENSP00000382512:G2121V;ENSP00000382542:G2192V;ENSP00000382526:G2156V;ENSP00000385896:G2192V;ENSP00000382504:G2129V	ENSP00000323129:G2022V	G	+	2	0	CACNA1C	2670571	1.000000	0.71417	0.004000	0.12327	0.024000	0.10985	1.395000	0.34520	0.108000	0.17862	0.591000	0.81541	GGT	.	.		0.632	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2800310	G	T	2800310	3	4	229	1	0	0	0	0	1	0	0	0	2542	1261	44	3	7257	3	CACNA1C	12	2800310	Missense_Mutation	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10		2800310	131051585	31	32258										
NACA	4666	hgsc.bcm.edu	37	chr12	57113526	57113526	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ttacctatagggagaggctcCccaaggcttttctttgctag	10	10	1	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr12:57113526C>T	ENST00000454682.1	-	3	2069	c.1788G>A	c.(1786-1788)ggG>ggA	p.G596G	NACA_ENST00000356769.3_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000550952.1_Silent_p.G596G|NACA_ENST00000552540.1_Intron|NACA_ENST00000548563.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	596	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GGAGAGGCTCCCCAAGGCTTT	0.512			T	BCL6	NHL																																p.G596G		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.G1788A						.						45	46	46					12																	57113526		1568	3582	5150	SO:0001819	synonymous_variant	4666	exon3			AGGCTCCCCAAGG	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.1788G>A	chr12.hg19:g.57113526C>T		159.0	0.0		77.0	16.0	NM_001113203		Silent	SNP	ENST00000454682.1	hg19																																																																																				.	.		0.512	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		T	57113526	C	T	57113526	2	4	229	1	0	0	0	0	0	0	0	1	10142	610	22	3		3	NACA	12	57113526	Silent	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10	54313216	57113526	76738369	32	32259										
CUX2	23316	hgsc.bcm.edu	37	chr12	111772269	111772269	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	tcccacagaaccaaggtcctCaccatccccaccccccagcc	4	23	1	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr12:111772269C>T	ENST00000261726.6	+	19	3105	c.2951C>T	c.(2950-2952)tCa>tTa	p.S984L		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	984					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						CCAAGGTCCTCACCATCCCCA	0.592																																					p.S984L		Atlas-SNP	.											.	CUX2	145	.	0			c.C2951T						.						29	37	34					12																	111772269		1946	4130	6076	SO:0001583	missense	23316	exon19			GGTCCTCACCATC	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.2951C>T	chr12.hg19:g.111772269C>T	ENSP00000261726:p.Ser984Leu	126.0	0.0		76.0	11.0	NM_015267	A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	hg19	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.723477	0.68959	.	.	ENSG00000111249	ENST00000261726	T	0.53206	0.63	5.09	5.09	0.68999	.	0.060756	0.64402	D	0.000002	T	0.41719	0.1171	L	0.32530	0.975	0.80722	D	1	P	0.39060	0.657	B	0.37650	0.255	T	0.41840	-0.9486	10	0.52906	T	0.07	-10.7296	18.4597	0.90734	0.0:1.0:0.0:0.0	.	984	O14529	CUX2_HUMAN	L	984	ENSP00000261726:S984L	ENSP00000261726:S984L	S	+	2	0	CUX2	110256652	1.000000	0.71417	0.956000	0.39512	0.642000	0.38348	5.903000	0.69877	2.530000	0.85305	0.655000	0.94253	TCA	.	.		0.592	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		T	111772269	C	T	111772269	3	4	229	1	0	0	0	0	1	0	0	0	4067	838	29	3	3025	3	CUX2	12	111772269	Missense_Mutation	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10	54658743	111772269	22079626	33	32260										
SPERT	220082	hgsc.bcm.edu	37	chr13	46287798	46287798	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gctgggccgagaggagagccGggccccctcgccactgctgc	16	16	0	2			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr13:46287798G>A	ENST00000310521.1	+	3	718	c.638G>A	c.(637-639)cGg>cAg	p.R213Q	SPERT_ENST00000378966.3_Missense_Mutation_p.R177Q	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	213						cytoplasmic membrane-bounded vesicle (GO:0016023)				NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		GAGGAGAGCCGGGCCCCCTCG	0.652																																					p.R213Q		Atlas-SNP	.											.	SPERT	54	.	0			c.G638A						.						41	41	41					13																	46287798		2203	4300	6503	SO:0001583	missense	220082	exon3			AGAGCCGGGCCCC	AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"spermatid flower-like structure protein", "testis specific leucine zipper protein nurit", "chibby homolog 2 (Drosophila)"					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.638G>A	chr13.hg19:g.46287798G>A	ENSP00000309189:p.Arg213Gln	38.0	0.0		38.0	9.0	NM_152719	A8K8I5|Q8NHV2	Missense_Mutation	SNP	ENST00000310521.1	hg19	CCDS9399.1	.	.	.	.	.	.	.	.	.	.	G	0.735	-0.778610	0.02929	.	.	ENSG00000174015	ENST00000310521;ENST00000378966	T;T	0.41400	1.0;1.0	5.31	2.5	0.30297	.	0.533809	0.17062	N	0.188531	T	0.18509	0.0444	N	0.14661	0.345	0.09310	N	1	B;B	0.27971	0.196;0.043	B;B	0.14578	0.011;0.002	T	0.12142	-1.0559	10	0.17832	T	0.49	.	4.1666	0.10310	0.291:0.1885:0.5204:0.0	.	177;213	Q8NA61-2;Q8NA61	.;SPERT_HUMAN	Q	213;177	ENSP00000309189:R213Q;ENSP00000368249:R177Q	ENSP00000309189:R213Q	R	+	2	0	SPERT	45185799	0.005000	0.15991	0.022000	0.16811	0.109000	0.19521	1.176000	0.31957	0.800000	0.34041	0.609000	0.83330	CGG	.	.		0.652	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719		A	46287798	G	A	46287798	3	1	229	1	0	0	0	0	1	0	0	0	15054	1116	39	1	648	1	SPERT	13	46287798	Missense_Mutation	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10		46287798	68882080	34	32261										
WDR90	197335	hgsc.bcm.edu	37	chr16	717526	717526	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	ctgtgcaggtttacaccgtcCgccaggctgctcttcacggc	11	15	2	0	rs373944645		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr16:717526C>T	ENST00000293879.4	+	41	5184	c.5184C>T	c.(5182-5184)tcC>tcT	p.S1728S	WDR90_ENST00000549091.1_Silent_p.S1730S|WDR90_ENST00000315764.4_Silent_p.S279S|RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000547944.1_Silent_p.S327S			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1728										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				TTACACCGTCCGCCAGGCTGC	0.637													C|||	1	0.000199681	0	0.0014	5008	,	,		19457	0		0	False		,,,				2504	0				p.S1728S		Atlas-SNP	.											.	WDR90	107	.	0			c.C5184T						.	C		0,4264		0,0,2132	50	57	55		5184	-9.8	0	16		55	1,8449		0,1,4224	no	coding-synonymous	WDR90	NM_145294.4		0,1,6356	TT,TC,CC		0.0118,0.0,0.0079		1728/1749	717526	1,12713	2132	4225	6357	SO:0001819	synonymous_variant	197335	exon41			ACCGTCCGCCAGG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.5184C>T	chr16.hg19:g.717526C>T		33.0	0.0		23.0	10.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	C	3.305	-0.141970	0.06669	0.0	1.18E-4	ENSG00000161996	ENST00000546896	.	.	.	4.9	-9.79	0.00494	.	.	.	.	.	T	0.63908	0.2551	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.81716	-0.0806	5	0.87932	D	0	.	10.4405	0.44462	0.1527:0.5885:0.0772:0.1816	.	.	.	.	L	31	.	ENSP00000447915:P31L	P	+	2	0	WDR90	657527	0.000000	0.05858	0.000000	0.03702	0.125000	0.20455	-7.334000	0.00038	-4.518000	0.00044	-2.126000	0.00345	CCG	.	.		0.637	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		T	717526	C	T	717526	2	4	229	1	0	0	0	0	0	0	0	1	17352	639	23	1		1	WDR90	16	717526	Silent	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10		717526	89637227	35	32262										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33513464	33513464	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gagagtgagctgctggagatCctgactgtggtgggcaaaca	16	7	0	4			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr17:33513464C>G	ENST00000268876.5	+	20	2779	c.2682C>G	c.(2680-2682)atC>atG	p.I894M	UNC45B_ENST00000591048.1_Missense_Mutation_p.I813M|UNC45B_ENST00000394570.2_Missense_Mutation_p.I892M|UNC45B_ENST00000433649.1_Missense_Mutation_p.I892M|UNC45B_ENST00000378449.1_Missense_Mutation_p.I813M|RP11-799D4.2_ENST00000590144.1_RNA	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	894					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TGCTGGAGATCCTGACTGTGG	0.537																																					p.I894M		Atlas-SNP	.											.	UNC45B	133	.	0			c.C2682G						.						121	100	107					17																	33513464		2203	4300	6503	SO:0001583	missense	146862	exon20			GGAGATCCTGACT	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.2682C>G	chr17.hg19:g.33513464C>G	ENSP00000268876:p.Ile894Met	127.0	0.0		66.0	15.0	NM_173167	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	hg19	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.678120	0.47886	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T	0.33216	3.52;1.42;2.9	6.02	2.68	0.31781	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.47857	0.1468	M	0.68952	2.095	0.43771	D	0.996295	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.996;0.999;0.987	T	0.40384	-0.9566	10	0.56958	D	0.05	-26.3805	7.3734	0.26815	0.1302:0.716:0.0:0.1539	.	813;892;894	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	M	894;894;892;813	ENSP00000268876:I894M;ENSP00000412840:I892M;ENSP00000367710:I813M	ENSP00000268876:I894M	I	+	3	3	UNC45B	30537577	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.548000	0.36201	0.737000	0.32582	0.655000	0.94253	ATC	.	.		0.537	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		G	33513464	C	G	33513464	3	3	229	1	0	0	0	0	1	0	0	0	17004	845	30	4	2756	4	UNC45B	17	33513464	Missense_Mutation	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10		33513464	47681746	36	32263										
KRT24	192666	hgsc.bcm.edu	37	chr17	38858134	38858135	+	Missense_Mutation	DNP	CA	CA	GC													0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gtcatcagcagccaatctggCattgtcaatgtgcaaaatga					rs201305125|rs11309872	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr17:38858134_38858135CA>GC	ENST00000264651.2	-	2	722_723	c.666_667TG>GC	c.(664-669)aaTGcc>aaGCcc	p.222_223NA>KP		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	222	Coil 1B.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				GCCAATCTGGCATTGTCAATGT	0.332																																					p.A223P|p.N222K	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											KRT24,NS,lymphoid_neoplasm,0,1|.,1	KRT24	60	.	0			c.G667C|c.T666G						.																																			SO:0001583	missense	192666	exon2			ATCTGGCATTGTC|TCTGGCATTGTCA		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"-", "Intermediate filaments type I, keratins (acidic)"	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.666_667delinsGC	chr17.hg19:g.38858134_38858135delinsGC	ENSP00000264651:p.N222_A223delinsKP	500.0|496.0	0.0		188.0|190.0	12.0|15.0	NM_019016	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	hg19	CCDS11372.1																																																																																			.	.		0.332	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		GC	38858135	CA	GC	38858134	3	3	229	1	0	0	0	0	1	0	0	0	8470	710	25	4	938	4	KRT24	17	38858134	Missense_Mutation	DNP	CA	TCGA-DD-AAVW-01A-11D-A40R-10	5344670	38858134	42337076	37	32264										
RPTOR	57521	hgsc.bcm.edu	37	chr17	78796082	78796082	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gccatcacagacaccatcgcGtggaacgtgctcccccgggg	12	16	1	1	rs375226529		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr17:78796082G>A	ENST00000306801.3	+	8	1334	c.972G>A	c.(970-972)gcG>gcA	p.A324A	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000570891.1_Silent_p.A324A|RPTOR_ENST00000537330.1_Silent_p.A139A|RPTOR_ENST00000544334.2_Silent_p.A324A	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	324					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						ACACCATCGCGTGGAACGTGC	0.647																																					p.A324A		Atlas-SNP	.											.	RPTOR	122	.	0			c.G972A						.	G	,	1,4405	2.1+/-5.4	0,1,2202	154	152	153		972,972	-9.8	0.3	17		153	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	324/1178,324/1336	78796082	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon8			CATCGCGTGGAAC		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.972G>A	chr17.hg19:g.78796082G>A		95.0	0.0		94.0	29.0	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	hg19	CCDS11773.1																																																																																			.	.		0.647	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		A	78796082	G	A	78796082	2	1	229	1	0	0	0	0	0	0	0	1	13680	1132	40	1		1	RPTOR	17	78796082	Silent	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10	39937948	78796082	2399128	38	32265										
C3	718	hgsc.bcm.edu	37	chr19	6713207	6713207	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gactgggcctcacctgagtgCaagatgacggtggcagacac	14	11	1	4			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr19:6713207C>T	ENST00000245907.6	-	9	1088	c.996G>A	c.(994-996)ttG>ttA	p.L332L		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	332					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CACCTGAGTGCAAGATGACGG	0.597																																					p.L332L		Atlas-SNP	.											.	C3	192	.	0			c.G996A						.						58	52	54					19																	6713207		2203	4300	6503	SO:0001819	synonymous_variant	718	exon9			TGAGTGCAAGATG	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.996G>A	chr19.hg19:g.6713207C>T		95.0	0.0		72.0	19.0	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	hg19	CCDS32883.1																																																																																			.	.		0.597	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		T	6713207	C	T	6713207	2	4	229	1	0	0	0	0	0	0	0	1	2206	709	25	3		3	C3	19	6713207	Silent	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10		6713207	52415776	39	32266										
HOOK2	29911	hgsc.bcm.edu	37	chr19	12880808	12880808	+	Frame_Shift_Del	DEL	C	C	-													0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	gcgttcctccagctgccgcaCctgccgccgcagctccctca							TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr19:12880808delC	ENST00000397668.3	-	11	1064	c.991delG	c.(991-993)gtgfs	p.V331fs	HOOK2_ENST00000264827.5_Frame_Shift_Del_p.V331fs|HOOK2_ENST00000589965.1_Intron	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	331	Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						AGCTGCCGCACCTGCCGCCGC	0.726																																					p.V331fs		Atlas-INDEL	.											.	HOOK2	73	.	0			c.992delT						.						3	3	3					19																	12880808		1798	3738	5536	SO:0001589	frameshift_variant	29911	exon11			.	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"hook homolog 2 (Drosophila)"			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.991delG	chr19.hg19:g.12880808delC	ENSP00000380785:p.Val331fs	41.0	0.0		59.0	13.0	NM_001100176	O60562	Frame_Shift_Del	DEL	ENST00000397668.3	hg19	CCDS42508.1																																																																																			.	.		0.726	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312		-	12880808	C	-	12880808	7	5	229	1	0	1	0	1	0	0	0	0	7292	507	18	0	1220	0	HOOK2	19	12880808	Frame_Shift_Del	DEL	C	TCGA-DD-AAVW-01A-11D-A40R-10	6167601	12880808	46248175	40	32267										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13318671	13318671	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	cccggcccggcctggccaccGcctgctgctgctgctgctgc	13	20	0	0			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr19:13318671G>T	ENST00000360228.5	-	47	6976	c.6977C>A	c.(6976-6978)gCg>gAg	p.A2326E	CACNA1A_ENST00000573710.2_3'UTR	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	2325					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CCTGGCCACCGCctgctgctg	0.766																																					p.A2326E		Atlas-SNP	.											.	CACNA1A	715	.	0			c.C6977A						.						1	1	1					19																	13318671		333	860	1193	SO:0001583	missense	773	exon47			GCCACCGCCTGCT	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.6977C>A	chr19.hg19:g.13318671G>T	ENSP00000353362:p.Ala2326Glu	425.0	0.0		482.0	23.0	NM_001127222	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	g	5.356	0.250903	0.10130	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018	D	0.95690	-3.78	2.6	0.109	0.14578	.	0.390690	0.08080	U	1.000000	D	0.85915	0.5808	N	0.08118	0	0.09310	N	0.999993	B;B;B	0.13145	0.007;0.0;0.004	B;B;B	0.08055	0.003;0.001;0.001	T	0.73642	-0.3918	10	0.19590	T	0.45	.	3.0397	0.06134	0.275:0.0:0.5237:0.2013	.	2332;2326;2315	E9PD31;Q9NS88;E7EVF2	.;.;.	E	2326;2332;2315	ENSP00000353362:A2326E	ENSP00000349520:A2315E	A	-	2	0	CACNA1A	13179671	0.977000	0.34250	0.145000	0.22337	0.879000	0.50718	0.936000	0.28938	-0.367000	0.08052	0.281000	0.19383	GCG	.	.		0.766	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13318671	G	T	13318671	3	4	229	1	0	0	0	0	1	0	0	0	2540	1087	38	1	547	1	CACNA1A	19	13318671	Missense_Mutation	SNP	G	TCGA-DD-AAVW-01A-11D-A40R-10	437863	13318671	45810312	41	32268										
RYR1	6261	hgsc.bcm.edu	37	chr19	38976748	38976748	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	actgaggatgctgggggaggCggtgcgcgacggtgggcagc	22	8	0	1			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr19:38976748C>T	ENST00000359596.3	+	34	5453	c.5453C>T	c.(5452-5454)gCg>gTg	p.A1818V	RYR1_ENST00000360985.3_Missense_Mutation_p.A1818V|RYR1_ENST00000355481.4_Missense_Mutation_p.A1818V			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1818	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.A1818G(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTGGGGGAGGCGGTGCGCGAC	0.706																																					p.A1818V		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	.	1	Substitution - Missense(1)	lung(1)	c.C5453T						.						52	52	52					19																	38976748		2201	4292	6493	SO:0001583	missense	6261	exon34			GGGAGGCGGTGCG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5453C>T	chr19.hg19:g.38976748C>T	ENSP00000352608:p.Ala1818Val	99.0	0.0		49.0	6.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.840101	0.71488	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.74737	-0.87;-0.87;-0.87	3.7	3.7	0.42460	.	0.000000	0.64402	U	0.000005	D	0.85617	0.5738	M	0.81341	2.54	0.52501	D	0.999957	D;P	0.89917	1.0;0.909	D;B	0.71656	0.974;0.432	D	0.88490	0.3075	10	0.87932	D	0	.	15.2171	0.73277	0.0:1.0:0.0:0.0	.	1818;1818	P21817-2;P21817	.;RYR1_HUMAN	V	1818	ENSP00000352608:A1818V;ENSP00000347667:A1818V;ENSP00000354254:A1818V	ENSP00000347667:A1818V	A	+	2	0	RYR1	43668588	1.000000	0.71417	0.992000	0.48379	0.898000	0.52572	5.840000	0.69402	1.886000	0.54624	0.585000	0.79938	GCG	.	.		0.706	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38976748	C	T	38976748	3	4	229	1	0	0	0	0	1	0	0	0	13783	768	27	1	5587	1	RYR1	19	38976748	Missense_Mutation	SNP	C	TCGA-DD-AAVW-01A-11D-A40R-10	25658077	38976748	20152235	42	32269										
APP	351	hgsc.bcm.edu	37	chr21	27369713	27369713	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	caagaggttcctgggtagtcTtgagtaaactttgggacact	12	7	1	2			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr21:27369713T>C	ENST00000346798.3	-	8	1085	c.1052A>G	c.(1051-1053)aAg>aGg	p.K351R	APP_ENST00000440126.3_Intron|APP_ENST00000348990.5_Intron|APP_ENST00000448388.2_Intron|APP_ENST00000359726.3_Missense_Mutation_p.K295R|APP_ENST00000439274.2_Missense_Mutation_p.K295R|APP_ENST00000357903.3_Intron|APP_ENST00000358918.3_Missense_Mutation_p.K351R|APP_ENST00000354192.3_Intron	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	351					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				CTGGGTAGTCTTGAGTAAACT	0.438																																					p.K351R		Atlas-SNP	.											.	APP	90	.	0			c.A1052G						.						107	100	103					21																	27369713		2203	4300	6503	SO:0001583	missense	351	exon8			GTAGTCTTGAGTA	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1052A>G	chr21.hg19:g.27369713T>C	ENSP00000284981:p.Lys351Arg	137.0	0.0		60.0	11.0	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	hg19	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.812066	0.32053	.	.	ENSG00000142192	ENST00000346798;ENST00000358918;ENST00000359726;ENST00000439274	D;D;D;D	0.96232	-2.02;-1.87;-3.95;-2.02	4.35	4.35	0.52113	.	0.342318	0.26023	N	0.026820	D	0.95277	0.8468	L	0.41710	1.295	0.80722	D	1	P;P	0.34587	0.458;0.458	P;P	0.51742	0.678;0.678	D	0.91420	0.5158	10	0.11794	T	0.64	-34.2354	10.2299	0.43250	0.0:0.0:0.0:1.0	.	295;351	E9PG40;P05067	.;A4_HUMAN	R	351;351;295;295	ENSP00000284981:K351R;ENSP00000351796:K351R;ENSP00000352760:K295R;ENSP00000398879:K295R	ENSP00000284981:K351R	K	-	2	0	APP	26291584	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.093000	0.50217	2.198000	0.70561	0.533000	0.62120	AAG	.	.		0.438	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		C	27369713	T	C	27369713	3	2	229	1	0	0	0	0	1	0	0	0	815	1609	56	2	1304	2	APP	21	27369713	Missense_Mutation	SNP	T	TCGA-DD-AAVW-01A-11D-A40R-10		27369713	20760182	43	32270										
LSS	4047	hgsc.bcm.edu	37	chr21	47647474	47647475	+	Frame_Shift_Ins	INS	-	-	T													0.0232558139534884	1	1	0.553884711779449	0	0.646198830409357	1	1	0	catactcctacctggcaggaINSggaaaagtgggccaccataa							TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr21:47647474_47647475insT	ENST00000397728.3	-	3	388_389	c.310_311insA	c.(310-312)ctcfs	p.L104fs	MCM3AP-AS1_ENST00000591223.1_RNA|LSS_ENST00000464357.1_5'UTR|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000420074.1_RNA|LSS_ENST00000522411.1_Frame_Shift_Ins_p.L104fs|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA|LSS_ENST00000457828.2_Frame_Shift_Ins_p.L24fs|LSS_ENST00000356396.4_Frame_Shift_Ins_p.L104fs|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	104					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					ACCTGGCAGGAGGAAAAGTGGG	0.594																																					p.L104fs	Pancreas(114;955 2313 34923 50507)	Atlas-INDEL	.											.	LSS	50	.	0			c.311_312insA						.																																			SO:0001589	frameshift_variant	4047	exon3			.	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.310_311insA	chr21.hg19:g.47647474_47647475insT	ENSP00000380837:p.Leu104fs	119.0	0.0		56.0	13.0	NM_001145436	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Frame_Shift_Ins	INS	ENST00000397728.3	hg19	CCDS13733.1																																																																																			.	.		0.594	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			T	47647475	-	T	47647474	7	5	229	1	0	1	1	0	0	0	0	0	9074	304	11	0	1967	0	LSS	21	47647474	Frame_Shift_Ins	INS	-	TCGA-DD-AAVW-01A-11D-A40R-10	20277761	47647474	482421	44	32271										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27106484	27106484	+	Frame_Shift_Del	DEL	A	A	-													0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gcaggcaccactaacttatgAaaaggaggaggaacaggacc							TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:27106484delA	ENST00000324856.7	+	20	6466	c.6095delA	c.(6094-6096)gaafs	p.E2032fs	ARID1A_ENST00000457599.2_Frame_Shift_Del_p.E1815fs|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.E1649fs|ARID1A_ENST00000540690.1_Frame_Shift_Del_p.E360fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2032					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CTAACTTATGAAAAGGAGGAG	0.552			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.E2032fs		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	ARID1A,NS,carcinoma,0,1	ARID1A	842	.	0			c.6094delG						.						134	128	130					1																	27106484		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.6095delA	chr1.hg19:g.27106484delA	ENSP00000320485:p.Glu2032fs	130.0	0.0		103.0	69.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.552	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27106484	A	-	27106484	7	5	230	1	0	1	0	1	0	0	0	0	913	246	9	0	6173	0	ARID1A	1	27106484	Frame_Shift_Del	DEL	A	TCGA-DD-AAVX-01A-11D-A40R-10		27106484	222144137	1	32272										
TMEM39B	55116	hgsc.bcm.edu	37	chr1	32540608	32540608	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gaaatccgctctgtgagccgGgatcctcggggggctctagt	15	11	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:32540608G>T	ENST00000336294.5	+	2	207	c.61G>T	c.(61-63)Gga>Tga	p.G21*	TMEM39B_ENST00000487305.1_3'UTR|TMEM39B_ENST00000427288.1_5'UTR|RP11-277A4.4_ENST00000366152.3_RNA|TMEM39B_ENST00000456834.2_Nonsense_Mutation_p.G21*|TMEM39B_ENST00000373634.4_5'UTR	NM_018056.2	NP_060526.2	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	21						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(5)|ovary(1)|prostate(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				CTGTGAGCCGGGATCCTCGGG	0.567																																					p.G21X		Atlas-SNP	.											.	TMEM39B	66	.	0			c.G61T						.						45	51	49					1																	32540608		692	1591	2283	SO:0001587	stop_gained	55116	exon2			GAGCCGGGATCCT	AL136695	CCDS351.2	1p35.1	2008-02-05			ENSG00000121775	ENSG00000121775			25510	protein-coding gene	gene with protein product						12477932	Standard	NM_018056		Approved	FLJ10315	uc010ogv.2	Q9GZU3	OTTHUMG00000004020	ENST00000336294.5:c.61G>T	chr1.hg19:g.32540608G>T	ENSP00000338165:p.Gly21*	62.0	0.0		68.0	44.0	NM_018056	B4DKN8|B4DQE6|B4DTN8|D3DPP4|Q6IA44	Nonsense_Mutation	SNP	ENST00000336294.5	hg19	CCDS351.2	.	.	.	.	.	.	.	.	.	.	G	35	5.543470	0.96474	.	.	ENSG00000121775	ENST00000336294;ENST00000373633;ENST00000438825;ENST00000456834	.	.	.	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-5.1175	18.2567	0.90022	0.0:0.0:1.0:0.0	.	.	.	.	X	21	.	ENSP00000338165:G21X	G	+	1	0	TMEM39B	32313195	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.733000	0.84916	2.384000	0.81235	0.655000	0.94253	GGA	.	.		0.567	TMEM39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011489.2	NM_018056		T	32540608	G	T	32540608	4	4	230	1	0	0	0	0	0	1	0	0	16177	1233	43	3	67	3	TMEM39B	1	32540608	Nonsense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	5434124	32540608	216710013	2	32273										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34238304	34238304	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gaaaccgggagccttccctcCggccatatgcaggtatgcca	11	14	0	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:34238304C>T	ENST00000338325.1	-	7	948	c.536G>A	c.(535-537)cGg>cAg	p.R179Q	CSMD2_ENST00000373381.4_Missense_Mutation_p.R571Q			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	531	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GCCTTCCCTCCGGCCATATGC	0.522																																					p.R531Q		Atlas-SNP	.											CSMD2_ENST00000373381,colon,carcinoma,-1,2	CSMD2	946	.	0			c.G1592A						.						93	91	92					1																	34238304		2203	4300	6503	SO:0001583	missense	114784	exon13			TCCCTCCGGCCAT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000338325.1:c.536G>A	chr1.hg19:g.34238304C>T	ENSP00000340311:p.Arg179Gln	60.0	0.0		50.0	39.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000338325.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.21	2.467050	0.43839	.	.	ENSG00000121904	ENST00000373381;ENST00000338325	T;T	0.63255	-0.03;-0.03	6.06	0.689	0.18033	Complement control module (2);Sushi/SCR/CCP (3);	0.190177	0.44097	N	0.000482	T	0.46171	0.1379	L	0.48935	1.535	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.13407	0.009;0.005	T	0.14337	-1.0476	10	0.27082	T	0.32	.	3.8697	0.09031	0.2561:0.4376:0.0:0.3063	.	531;571	Q7Z408;E7EUA6	CSMD2_HUMAN;.	Q	571;179	ENSP00000362479:R571Q;ENSP00000340311:R179Q	ENSP00000241312:R531Q	R	-	2	0	CSMD2	34010891	0.761000	0.28439	0.987000	0.45799	0.987000	0.75469	0.464000	0.21988	-0.117000	0.11872	-0.137000	0.14449	CGG	.	.		0.522	CSMD2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000036404.2	NM_052896		T	34238304	C	T	34238304	3	4	230	1	0	0	0	0	1	0	0	0	3947	652	23	1	9099	1	CSMD2	1	34238304	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	1697696	34238304	215012317	3	32274										
JAK1	3716	hgsc.bcm.edu	37	chr1	65310503	65310503	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gatgaatgggccacactcacTgtcgatgccctcacgggcca	11	14	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:65310503T>A	ENST00000342505.4	-	16	2433	c.2185A>T	c.(2185-2187)Agt>Tgt	p.S729C	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	729	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CCACACTCACTGTCGATGCCC	0.547			Mis		ALL																																p.S729C		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	JAK1,NS,carcinoma,0,2	JAK1	209	.	0			c.A2185T						.						96	113	107					1																	65310503		2115	4222	6337	SO:0001583	missense	3716	exon16			ACTCACTGTCGAT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2185A>T	chr1.hg19:g.65310503T>A	ENSP00000343204:p.Ser729Cys	125.0	0.0		96.0	72.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.814614	0.50527	.	.	ENSG00000162434	ENST00000342505	T	0.76839	-1.05	5.0	2.65	0.31530	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.65312	0.2679	L	0.54965	1.715	0.22552	N	0.998997	P	0.46142	0.873	P	0.46850	0.529	T	0.57177	-0.7856	9	0.72032	D	0.01	-5.9131	9.7115	0.40247	0.0:0.1625:0.0:0.8375	.	729	P23458	JAK1_HUMAN	C	729	ENSP00000343204:S729C	ENSP00000343204:S729C	S	-	1	0	JAK1	65083091	0.100000	0.21855	0.477000	0.27303	0.441000	0.31987	2.149000	0.42244	0.940000	0.37473	0.460000	0.39030	AGT	.	.		0.547	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		A	65310503	T	A	65310503	3	1	230	1	0	0	0	0	1	0	0	0	7946	1580	55	4	1319	4	JAK1	1	65310503	Missense_Mutation	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	31072199	65310503	183940118	4	32275										
LHX8	431707	hgsc.bcm.edu	37	chr1	75602886	75602886	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gcctcgggctccggctgcccTcctggcaagtgtgtgtgcaa	14	14	0	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:75602886T>A	ENST00000294638.5	+	4	871	c.207T>A	c.(205-207)ccT>ccA	p.P69P	LHX8_ENST00000356261.3_Silent_p.P59P|LHX8_ENST00000559413.1_3'UTR	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8	69					female gonad development (GO:0008585)|forebrain neuron development (GO:0021884)|learning or memory (GO:0007611)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	female germ cell nucleus (GO:0001674)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(18)|ovary(3)|urinary_tract(1)	30						CCGGCTGCCCTCCTGGCAAGT	0.687																																					p.P69P		Atlas-SNP	.											.	LHX8	73	.	0			c.T207A						.						26	28	28					1																	75602886		2203	4300	6503	SO:0001819	synonymous_variant	431707	exon4			CTGCCCTCCTGGC	AB050476	CCDS30756.1, CCDS58008.1	1p31.1	2011-06-20			ENSG00000162624	ENSG00000162624		"Homeoboxes / LIM class"	28838	protein-coding gene	gene with protein product		604425				9598319	Standard	NM_001256114		Approved	Lhx7	uc031pmx.1	Q68G74	OTTHUMG00000009692	ENST00000294638.5:c.207T>A	chr1.hg19:g.75602886T>A		219.0	0.0		153.0	69.0	NM_001001933	E9PGE3	Silent	SNP	ENST00000294638.5	hg19	CCDS30756.1																																																																																			.	.		0.687	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	NM_001001933		A	75602886	T	A	75602886	2	1	230	1	0	0	0	0	0	0	0	1	8785	1538	54	4		4	LHX8	1	75602886	Silent	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	10292383	75602886	173647735	5	32276										
C1orf104	23623	hgsc.bcm.edu	37	chr1	155291207	155291207	+	Intron	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	ggaggtccattctgggcccgGacctcttccaggcccccgcc	12	18	2	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:155291207G>C	ENST00000368352.5	+	2	65				RUSC1-AS1_ENST00000543656.1_RNA|RUSC1_ENST00000368347.4_5'Flank|RUSC1-AS1_ENST00000450199.1_RNA|RUSC1_ENST00000368354.3_Intron|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1						positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			TCTGGGCCCGGACCTCTTCCA	0.672																																					p.P25A		Atlas-SNP	.											.	.	.	.	0			c.C73G						.						12	14	13					1																	155291207		1834	4079	5913	SO:0001627	intron_variant	284618	exon2			GGCCCGGACCTCT	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.-86-272G>C	chr1.hg19:g.155291207G>C		127.0	0.0		109.0	39.0	NM_001039517	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Missense_Mutation	SNP	ENST00000368352.5	hg19	CCDS41410.1																																																																																			.	.		0.672	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			C	155291207	G	C	155291207	1	2	230	0	1	0	0	0	0	0	0	0	1980	1174	41	4		4	C1orf104	1	155291207	Intron	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	79688321	155291207	93959414	6	32277										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179632575	179632575	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	aaagtagaagttcataagccAgaagtactgggtgctcagga	12	6	2	2	rs147178825		TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:179632575A>G	ENST00000367614.1	+	15	2795	c.2436A>G	c.(2434-2436)ccA>ccG	p.P812P	TDRD5_ENST00000294848.8_Silent_p.P812P|TDRD5_ENST00000444136.1_Silent_p.P866P	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	812					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						TTCATAAGCCAGAAGTACTGG	0.418																																					p.P866P		Atlas-SNP	.											.	TDRD5	149	.	0			c.A2598G						.	A	,,,,	1,4405	2.1+/-5.4	0,1,2202	83	80	81		2598,2598,2436,1101,2436	1	0.2	1	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_001199092.1,NM_173533.3	,,,,	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	,,,,	866/1036,866/1036,812/982,367/537,812/982	179632575	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	163589	exon16			TAAGCCAGAAGTA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2436A>G	chr1.hg19:g.179632575A>G		126.0	0.0		93.0	29.0	NM_001199085	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	A|1.000;G|0.000		0.418	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		G	179632575	A	G	179632575	2	3	230	1	0	0	0	0	0	0	0	1	15748	175	7	2		2	TDRD5	1	179632575	Silent	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10	24341368	179632575	69618046	7	32278										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190250879	190250879	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tactttccagcggccaaactCcctgaaaagcaaatttattt	5	11	0	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:190250879C>T	ENST00000367462.3	-	3	469	c.238G>A	c.(238-240)Gag>Aag	p.E80K	RP11-547I7.1_ENST00000452178.1_RNA|BRINP3_ENST00000534846.1_Intron	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	80	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											CGGCCAAACTCCCTGAAAAGC	0.393																																					p.E80K		Atlas-SNP	.											.	FAM5C	343	.	0			c.G238A						.						53	53	53					1																	190250879		2203	4300	6503	SO:0001630	splice_region_variant	339479	exon3			CAAACTCCCTGAA	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.237-1G>A	chr1.hg19:g.190250879C>T		224.0	0.0		184.0	69.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	C	34	5.329455	0.95733	.	.	ENSG00000162670	ENST00000367462	D	0.83755	-1.76	5.67	5.67	0.87782	Membrane attack complex component/perforin (MACPF) domain (2);	0.000000	0.85682	D	0.000000	D	0.90532	0.7033	M	0.71581	2.175	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	D	0.91027	0.4861	10	0.72032	D	0.01	.	17.2529	0.87047	0.0:1.0:0.0:0.0	.	80	Q76B58	FAM5C_HUMAN	K	80	ENSP00000356432:E80K	ENSP00000356432:E80K	E	-	1	0	FAM5C	188517502	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.794000	0.85869	2.677000	0.91161	0.585000	0.79938	GAG	.	.		0.393	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051	Missense_Mutation	T	190250879	C	T	190250879	5	4	230	1	0	0	0	0	0	0	1	0	5602	869	30	3	2086	3	FAM5C	1	190250879	Splice_Site	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	10618304	190250879	58999742	8	32279										
CENPF	1063	hgsc.bcm.edu	37	chr1	214816385	214816385	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tccctcgagaagctagaagaGaaaatggaaagtcaagggat	12	6	1	3			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:214816385G>T	ENST00000366955.3	+	12	4872	c.4704G>T	c.(4702-4704)gaG>gaT	p.E1568D		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	1664	2 X 96 AA approximate tandem repeats.		Missing. {ECO:0000269|PubMed:7651420}.		cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.E1568D(2)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGCTAGAAGAGAAAATGGAAA	0.473																																					p.E1568D	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,NS,carcinoma,0,2	CENPF	321	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G4704T						.						49	53	52					1																	214816385		2203	4300	6503	SO:0001583	missense	1063	exon12			AGAAGAGAAAATG	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.4704G>T	chr1.hg19:g.214816385G>T	ENSP00000355922:p.Glu1568Asp	138.0	0.0		125.0	33.0	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	G	6.808	0.518239	0.13005	.	.	ENSG00000117724	ENST00000366955	T	0.03635	3.86	4.9	1.75	0.24633	.	0.694331	0.11888	N	0.519839	T	0.01695	0.0054	N	0.05306	-0.075	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.49143	-0.8970	10	0.19147	T	0.46	.	3.1187	0.06383	0.1682:0.2768:0.4361:0.1189	.	1664	P49454	CENPF_HUMAN	D	1568	ENSP00000355922:E1568D	ENSP00000355922:E1568D	E	+	3	2	CENPF	212883008	0.241000	0.23857	0.964000	0.40570	0.972000	0.66771	-0.553000	0.06012	0.436000	0.26393	0.655000	0.94253	GAG	.	.		0.473	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214816385	G	T	214816385	3	4	230	1	0	0	0	0	1	0	0	0	3233	933	33	3	4746	3	CENPF	1	214816385	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	24565506	214816385	34434236	9	32280										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228537683	228537683	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tggacagcctgaccggtgtgGactctggccagtacatgtgc	14	11	1	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:228537683G>T	ENST00000422127.1	+	76	18285	c.18241G>T	c.(18241-18243)Gac>Tac	p.D6081Y	OBSCN_ENST00000366707.4_Missense_Mutation_p.D3715Y|OBSCN_ENST00000284548.11_Missense_Mutation_p.D6081Y|OBSCN_ENST00000366709.4_Missense_Mutation_p.D3200Y|OBSCN_ENST00000570156.2_Missense_Mutation_p.D7038Y	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6081	Ig-like 52.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GACCGGTGTGGACTCTGGCCA	0.607																																					p.D7038Y		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G21112T						.						34	42	39					1																	228537683		2101	4126	6227	SO:0001583	missense	84033	exon87			GGTGTGGACTCTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18241G>T	chr1.hg19:g.228537683G>T	ENSP00000409493:p.Asp6081Tyr	51.0	0.0		43.0	15.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.94|17.94	3.512604|3.512604	0.64522|0.64522	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709|ENST00000441106	D;D;D;D|.	0.81821|.	-1.54;-1.54;-1.54;-1.54|.	5.39|5.39	5.39|5.39	0.77823|0.77823	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.000000|.	0.64402|.	D|.	0.000001|.	D|D	0.87892|0.87892	0.6292|0.6292	H|H	0.95712|0.95712	3.71|3.71	0.53005|0.53005	D|D	0.999969|0.999969	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.81914|.	0.995;0.992|.	D|D	0.91351|0.91351	0.5104|0.5104	10|5	0.87932|.	D|.	0|.	.|.	19.1538|19.1538	0.93502|0.93502	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	6081;6081|.	Q5VST9;Q5VST9-3|.	OBSCN_HUMAN;.|.	Y|V	6081;6081;3715;3200|697	ENSP00000284548:D6081Y;ENSP00000409493:D6081Y;ENSP00000355668:D3715Y;ENSP00000355670:D3200Y|.	ENSP00000284548:D6081Y|.	D|G	+|+	1|2	0|0	OBSCN|OBSCN	226604306|226604306	1.000000|1.000000	0.71417|0.71417	0.897000|0.897000	0.35233|0.35233	0.050000|0.050000	0.14768|0.14768	9.692000|9.692000	0.98682|0.98682	2.517000|2.517000	0.84864|0.84864	0.491000|0.491000	0.48974|0.48974	GAC|GGA	.	.		0.607	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228537683	G	T	228537683	3	4	230	1	0	0	0	0	1	0	0	0	10821	1174	41	3	18539	3	OBSCN	1	228537683	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	13721298	228537683	20712938	10	32281										
SMYD3	64754	hgsc.bcm.edu	37	chr1	245912933	245912933	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	atcttcaatcaggctgtgttCtctgccatgtgtcactctca	7	12	6	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:245912933C>T	ENST00000388985.4	-	12	1218	c.1219G>A	c.(1219-1221)Gaa>Aaa	p.E407K	SMYD3_ENST00000366517.1_5'UTR|SMYD3_ENST00000541742.1_Missense_Mutation_p.E348K|SMYD3_ENST00000490107.1_Missense_Mutation_p.E348K			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	407					cellular response to dexamethasone stimulus (GO:0071549)|establishment of protein localization (GO:0045184)|myotube cell development (GO:0014904)|negative regulation of protein kinase activity (GO:0006469)|nucleosome assembly (GO:0006334)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)			breast(3)|large_intestine(5)|lung(8)|skin(1)	17	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		AGGCTGTGTTCTCTGCCATGT	0.458																																					p.E407K		Atlas-SNP	.											.	SMYD3	77	.	0			c.G1219A						.						139	114	122					1																	245912933		2203	4300	6503	SO:0001583	missense	64754	exon12			TGTGTTCTCTGCC	AK023594	CCDS31083.1	1q44	2011-07-01	2003-05-14	2003-05-16	ENSG00000185420	ENSG00000185420		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	15513	protein-coding gene	gene with protein product		608783	"zinc finger, MYND domain containing 1"	ZNFN3A1, ZMYND1			Standard	NM_022743		Approved	KMT3E	uc001ibl.3	Q9H7B4	OTTHUMG00000040508	ENST00000388985.4:c.1219G>A	chr1.hg19:g.245912933C>T	ENSP00000373637:p.Glu407Lys	63.0	0.0		42.0	10.0	NM_001167740	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Missense_Mutation	SNP	ENST00000388985.4	hg19	CCDS53486.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.365464	0.61513	.	.	ENSG00000185420	ENST00000541742;ENST00000490107;ENST00000544586;ENST00000388985	T;T;T	0.21932	1.98;1.98;1.98	5.41	4.5	0.54988	.	0.215542	0.41605	D	0.000842	T	0.11196	0.0273	N	0.12746	0.255	0.38254	D	0.94169	B	0.09022	0.002	B	0.06405	0.002	T	0.17440	-1.0369	10	0.16420	T	0.52	-0.2064	11.865	0.52488	0.0:0.9198:0.0:0.0802	.	407	Q9H7B4	SMYD3_HUMAN	K	348;348;237;407	ENSP00000444184:E348K;ENSP00000419184:E348K;ENSP00000373637:E407K	ENSP00000373637:E407K	E	-	1	0	SMYD3	243979556	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.222000	0.51223	2.538000	0.85594	0.563000	0.77884	GAA	.	.		0.458	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743		T	245912933	C	T	245912933	3	4	230	1	0	0	0	0	1	0	0	0	14838	922	32	3	71	3	SMYD3	1	245912933	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	17375250	245912933	3337688	11	32282										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247071004	247071004	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cagatggcgcccttgtctcaTtacactttctctaatgtgtg	8	11	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:247071004T>C	ENST00000391829.2	-	5	736	c.613A>G	c.(613-615)Atg>Gtg	p.M205V	AHCTF1_ENST00000366508.1_Missense_Mutation_p.M240V|AHCTF1_ENST00000326225.3_Missense_Mutation_p.M214V			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	205	Necessary for cytoplasmic localization. {ECO:0000250}.|Seven-bladed beta propeller repeats. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CCTTGTCTCATTACACTTTCT	0.388																																					p.M214V	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.A640G						.						129	121	124					1																	247071004		2203	4300	6503	SO:0001583	missense	25909	exon5			GTCTCATTACACT		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.613A>G	chr1.hg19:g.247071004T>C	ENSP00000375705:p.Met205Val	207.0	0.0		153.0	40.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	hg19		.	.	.	.	.	.	.	.	.	.	T	6.556	0.470887	0.12461	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.39229	1.09;1.09;1.09	5.76	5.76	0.90799	.	0.135213	0.64402	D	0.000002	T	0.26882	0.0658	N	0.14661	0.345	0.32138	N	0.585823	B;B	0.21225	0.053;0.04	B;B	0.18561	0.022;0.008	T	0.27673	-1.0067	10	0.52906	T	0.07	-10.9719	10.6901	0.45867	0.0:0.0712:0.0:0.9288	.	240;205	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	V	240;214;205	ENSP00000355464:M240V;ENSP00000355465:M214V;ENSP00000375705:M205V	ENSP00000355465:M214V	M	-	1	0	AHCTF1	245137627	1.000000	0.71417	0.996000	0.52242	0.979000	0.70002	3.893000	0.56243	2.323000	0.78572	0.528000	0.53228	ATG	.	.		0.388	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		C	247071004	T	C	247071004	3	2	230	1	0	0	0	0	1	0	0	0	408	1493	52	2	6315	2	AHCTF1	1	247071004	Missense_Mutation	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	1158071	247071004	2179617	12	32283										
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112399	248112399	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tccaccattgttcctaagatGgcatctgattttctgcatgg	8	10	2	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr1:248112399G>A	ENST00000357191.3	+	1	240	c.240G>A	c.(238-240)atG>atA	p.M80I	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TTCCTAAGATGGCATCTGATT	0.443																																					p.M80I		Atlas-SNP	.											.	OR2L8	92	.	0			c.G240A						.						298	263	275					1																	248112399		2203	4297	6500	SO:0001583	missense	391190	exon1			TAAGATGGCATCT	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.240G>A	chr1.hg19:g.248112399G>A	ENSP00000349719:p.Met80Ile	99.0	0.0		44.0	18.0	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	hg19	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	G	9.559	1.118018	0.20877	.	.	ENSG00000196936	ENST00000357191	T	0.05513	3.43	1.64	1.64	0.23874	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38272	U	0.001749	T	0.09905	0.0243	M	0.64404	1.975	0.09310	N	0.999999	P	0.39391	0.671	B	0.44163	0.443	T	0.07751	-1.0756	10	0.66056	D	0.02	.	7.9631	0.30083	0.0:0.5367:0.4633:0.0	.	80	Q8NGY9	OR2L8_HUMAN	I	80	ENSP00000349719:M80I	ENSP00000349719:M80I	M	+	3	0	OR2L8	246179022	0.000000	0.05858	0.478000	0.27316	0.189000	0.23516	-1.430000	0.02434	0.905000	0.36596	0.479000	0.44913	ATG	.	.		0.443	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			A	248112399	G	A	248112399	3	1	230	1	0	0	0	0	1	0	0	0	11018	1348	47	3	242	3	OR2L8	1	248112399	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	1041395	248112399	1138222	13	32284										
CCDC142	84865	hgsc.bcm.edu	37	chr2	74709806	74709806	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	ggcgtcggccaccacggcgtCcctccagaagttccgctcgg	13	17	0	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr2:74709806C>T	ENST00000393965.3	-	1	555	c.159G>A	c.(157-159)ggG>ggA	p.G53G	CCDC142_ENST00000290418.4_Silent_p.G53G|CCDC142_ENST00000471713.1_Intron|TTC31_ENST00000410003.1_5'Flank|TTC31_ENST00000442235.2_5'Flank|TTC31_ENST00000233623.5_5'Flank	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	53										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						ACCACGGCGTCCCTCCAGAAG	0.721																																					p.G53G		Atlas-SNP	.											.	CCDC142	40	.	0			c.G159A						.						39	39	39					2																	74709806		2171	4265	6436	SO:0001819	synonymous_variant	84865	exon1			CGGCGTCCCTCCA	AK075543	CCDS1945.1	2p13.1	2008-02-05			ENSG00000135637	ENSG00000135637			25889	protein-coding gene	gene with protein product							Standard	NM_032779		Approved	FLJ14397	uc002slq.3	Q17RM4	OTTHUMG00000129962	ENST00000393965.3:c.159G>A	chr2.hg19:g.74709806C>T		90.0	0.0		59.0	21.0	NM_032779	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Silent	SNP	ENST00000393965.3	hg19																																																																																				.	.		0.721	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779		T	74709806	C	T	74709806	2	4	230	1	0	0	0	0	0	0	0	1	2778	842	30	3		3	CCDC142	2	74709806	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		74709806	168489567	14	32285										
MAP4K4	9448	hgsc.bcm.edu	37	chr2	102477449	102477449	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	agagaccagcggagccacagGtagcgacagccagctttgct	13	12	0	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr2:102477449G>T	ENST00000347699.4	+	16	1866		c.e16+1		MAP4K4_ENST00000350878.4_Intron|MAP4K4_ENST00000413150.2_Intron|MAP4K4_ENST00000350198.4_Intron|MAP4K4_ENST00000456652.1_Intron|MAP4K4_ENST00000302217.5_Intron|MAP4K4_ENST00000324219.4_Splice_Site|MAP4K4_ENST00000425019.1_Splice_Site	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4						intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GGAGCCACAGGTAGCGACAGC	0.557																																					.		Atlas-SNP	.											.	MAP4K4	111	.	0			c.1773+1G>T						.						27	25	26					2																	102477449		2018	4188	6206	SO:0001630	splice_region_variant	9448	exon16			CCACAGGTAGCGA	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.1866+1G>T	chr2.hg19:g.102477449G>T		37.0	0.0		29.0	8.0	NM_145686	O75172|Q9NST7	Splice_Site	SNP	ENST00000347699.4	hg19	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.897335	0.91962	.	.	ENSG00000071054	ENST00000425019;ENST00000324219;ENST00000347699;ENST00000417294;ENST00000421882	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1865	0.98220	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MAP4K4	101843881	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.017000	0.93651	2.775000	0.95449	0.655000	0.94253	.	.	.		0.557	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	Intron	T	102477449	G	T	102477449	5	4	230	1	0	0	0	0	0	0	1	0	9271	1275	44	3	1929	3	MAP4K4	2	102477449	Splice_Site	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	27767643	102477449	140721924	15	32286										
PRPF40A	55660	hgsc.bcm.edu	37	chr2	153526802	153526802	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	catcagatactgctgggcttCagaccaagtggtagagtatg	12	8	2	3			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr2:153526802C>A	ENST00000410080.1	-	15	2114	c.1573G>T	c.(1573-1575)Gaa>Taa	p.E525*		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	552					cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|mRNA processing (GO:0006397)|regulation of cell shape (GO:0008360)|regulation of cytokinesis (GO:0032465)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|urinary_tract(1)	21						TGCTGGGCTTCAGACCAAGTG	0.378																																					p.E525X		Atlas-SNP	.											.	PRPF40A	149	.	0			c.G1573T						.						148	132	137					2																	153526802		1847	4112	5959	SO:0001587	stop_gained	55660	exon15			GGGCTTCAGACCA	AF049523	CCDS46430.1	2q23.3	2010-01-25	2007-01-12	2006-01-13	ENSG00000196504	ENSG00000196504			16463	protein-coding gene	gene with protein product		612941	"formin-binding protein 3", "formin binding protein 3", "PRP40 pre-mRNA processing factor 40 homolog A (yeast)"	FNBP3		9724750, 12460579	Standard	NM_017892		Approved	FLJ20585, FBP11, HYPA, NY-REN-6, HIP10, FBP-11, FLAF1, Prp40	uc002tyh.4	O75400	OTTHUMG00000154031	ENST00000410080.1:c.1573G>T	chr2.hg19:g.153526802C>A	ENSP00000386458:p.Glu525*	87.0	0.0		80.0	26.0	NM_017892	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	Nonsense_Mutation	SNP	ENST00000410080.1	hg19	CCDS46430.1	.	.	.	.	.	.	.	.	.	.	C	44	10.859167	0.99479	.	.	ENSG00000196504	ENST00000410080;ENST00000356402;ENST00000440252;ENST00000359961	.	.	.	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-25.4456	19.1932	0.93675	0.0:1.0:0.0:0.0	.	.	.	.	X	525;534;421;472	.	ENSP00000348770:E534X	E	-	1	0	PRPF40A	153235048	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.754000	0.85163	2.603000	0.88011	0.555000	0.69702	GAA	.	.		0.378	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575		A	153526802	C	A	153526802	4	1	230	1	0	0	0	0	0	1	0	0	12583	835	29	3	1267	3	PRPF40A	2	153526802	Nonsense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	51049353	153526802	89672571	16	32287										
GRB14	2888	hgsc.bcm.edu	37	chr2	165381556	165381556	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	atttcaccattggtttcagtTgcaaaagataccatatgctc	6	9	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr2:165381556T>A	ENST00000263915.3	-	5	1174	c.636A>T	c.(634-636)gcA>gcT	p.A212A	GRB14_ENST00000543549.1_Silent_p.A125A	NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	212					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						TGGTTTCAGTTGCAAAAGATA	0.269																																					p.A212A		Atlas-SNP	.											.	GRB14	73	.	0			c.A636T						.						66	72	70					2																	165381556		2202	4298	6500	SO:0001819	synonymous_variant	2888	exon5			TTCAGTTGCAAAA		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.636A>T	chr2.hg19:g.165381556T>A		431.0	0.0		323.0	98.0	NM_004490	B7Z7F9|Q7Z6I1	Silent	SNP	ENST00000263915.3	hg19	CCDS2222.1																																																																																			.	.		0.269	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			A	165381556	T	A	165381556	2	1	230	1	0	0	0	0	0	0	0	1	6766	1799	63	4		4	GRB14	2	165381556	Silent	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	11854754	165381556	77817817	17	32288										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189859318	189859318	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	agcccggaccacgtggtgaaCgcgtaagttttactgcaaca	11	11	0	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr2:189859318C>T	ENST00000304636.3	+	19	1515	c.1345C>T	c.(1345-1347)Cgc>Tgc	p.R449C	COL3A1_ENST00000317840.5_Missense_Mutation_p.R449C	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	449	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.R449C(1)		NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	ACGTGGTGAACGCGTAAGTTT	0.388																																					p.R449C		Atlas-SNP	.											COL3A1,NS,carcinoma,-1,1	COL3A1	292	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.C1345T						.						100	99	100					2																	189859318		2203	4300	6503	SO:0001583	missense	1281	exon19			GGTGAACGCGTAA	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.1345C>T	chr2.hg19:g.189859318C>T	ENSP00000304408:p.Arg449Cys	210.0	0.0		180.0	63.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	hg19	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.215950	0.58452	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.83755	-1.76;-1.76	6.17	6.17	0.99709	.	0.000000	0.51477	D	0.000094	D	0.88706	0.6509	M	0.79926	2.475	0.58432	D	0.999999	D	0.69078	0.997	P	0.53593	0.73	D	0.89397	0.3693	10	0.66056	D	0.02	.	15.581	0.76439	0.1377:0.8623:0.0:0.0	.	449	P02461	CO3A1_HUMAN	C	449	ENSP00000304408:R449C;ENSP00000315243:R449C	ENSP00000304408:R449C	R	+	1	0	COL3A1	189567563	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	3.010000	0.49559	2.941000	0.99782	0.655000	0.94253	CGC	.	.		0.388	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		T	189859318	C	T	189859318	3	4	230	1	0	0	0	0	1	0	0	0	3690	536	19	1	1419	1	COL3A1	2	189859318	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	24477762	189859318	53340055	18	32289										
NAB1	4664	hgsc.bcm.edu	37	chr2	191548503	191548503	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	aggattctgtgcaaacactcTtccagcaggctagagctaag	10	10	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr2:191548503T>C	ENST00000337386.5	+	7	1506	c.1045T>C	c.(1045-1047)Ttc>Ctc	p.F349L	NAB1_ENST00000409581.1_Missense_Mutation_p.F349L|AC006460.2_ENST00000421437.1_RNA|NAB1_ENST00000357215.5_Intron|NAB1_ENST00000484774.1_3'UTR|NAB1_ENST00000545490.1_Intron|NAB1_ENST00000409641.1_Missense_Mutation_p.F349L|AC006460.2_ENST00000411949.1_RNA|AC006460.2_ENST00000428032.1_RNA	NM_005966.3	NP_005957.2	Q13506	NAB1_HUMAN	NGFI-A binding protein 1 (EGR1 binding protein 1)	349					endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of epidermis development (GO:0045682)|regulation of transcription, DNA-templated (GO:0006355)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)			GCAAACACTCTTCCAGCAGGC	0.358																																					p.F349L		Atlas-SNP	.											.	NAB1	31	.	0			c.T1045C						.						76	76	76					2																	191548503		2203	4300	6503	SO:0001583	missense	4664	exon7			ACACTCTTCCAGC		CCDS2307.1	2q32.3-q33	2008-05-23			ENSG00000138386	ENSG00000138386			7626	protein-coding gene	gene with protein product	"EGR1 binding protein 1"	600800				7624335, 8668170, 9418898	Standard	XM_005246579		Approved		uc002usb.3	Q13506	OTTHUMG00000132689	ENST00000337386.5:c.1045T>C	chr2.hg19:g.191548503T>C	ENSP00000336894:p.Phe349Leu	62.0	0.0		44.0	14.0	NM_005966	O75383|O75384|Q6GTU1|Q9UEV1	Missense_Mutation	SNP	ENST00000337386.5	hg19	CCDS2307.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.212113	0.39102	.	.	ENSG00000138386	ENST00000409581;ENST00000337386;ENST00000409641	.	.	.	5.34	4.15	0.48705	Nab1, C-terminal (1);	0.115720	0.64402	D	0.000015	T	0.28499	0.0705	N	0.08118	0	0.80722	D	1	B;B	0.23650	0.089;0.089	B;B	0.25614	0.062;0.062	T	0.06006	-1.0851	9	0.11182	T	0.66	-12.3801	9.5719	0.39433	0.1562:0.0:0.0:0.8438	.	349;349	B8ZZS2;Q13506	.;NAB1_HUMAN	L	349	.	ENSP00000336894:F349L	F	+	1	0	NAB1	191256748	1.000000	0.71417	0.998000	0.56505	0.784000	0.44337	2.515000	0.45512	1.007000	0.39238	0.528000	0.53228	TTC	.	.		0.358	NAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255986.1	NM_005966		C	191548503	T	C	191548503	3	2	230	1	0	0	0	0	1	0	0	0	10140	1609	56	2	1059	2	NAB1	2	191548503	Missense_Mutation	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	1689185	191548503	51650870	19	32290										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266101	41266101	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gcaacagtcttacctggactCtggaatccattctggtgcca	9	12	3	0	rs121913416|rs121913400		TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr3:41266101C>G	ENST00000349496.5	+	3	378	c.98C>G	c.(97-99)tCt>tGt	p.S33C	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33C|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33C|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33C|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26C	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33C	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,359	CTNNB1	4904	.	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98G						.						92	77	82					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>G	chr3.hg19:g.41266101C>G	ENSP00000344456:p.Ser33Cys	136.0	0.0		92.0	38.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.381716	0.82792	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	C	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26C;ENSP00000385604:S33C;ENSP00000412219:S33C;ENSP00000379486:S33C;ENSP00000344456:S33C;ENSP00000411226:S26C;ENSP00000379488:S33C;ENSP00000409302:S33C;ENSP00000401599:S33C	ENSP00000344456:S33C	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266101	C	G	41266101	3	3	230	1	0	0	0	0	1	0	0	0	4018	913	32	4	104	4	CTNNB1	3	41266101	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		41266101	156756329	20	32291										
LTF	4057	hgsc.bcm.edu	37	chr3	46501175	46501175	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	ctggatacactggatgggggAgtctctctttatgcagctga	13	8	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr3:46501175A>G	ENST00000231751.4	-	2	473	c.178T>C	c.(178-180)Tcc>Ccc	p.S60P	LTF_ENST00000417439.1_Missense_Mutation_p.S60P|LTF_ENST00000426532.2_Missense_Mutation_p.S16P	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	60	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		TGGATGGGGGAGTCTCTCTTT	0.522																																					p.S60P		Atlas-SNP	.											LTF,rectum,carcinoma,0,1	LTF	98	.	0			c.T178C						.						124	115	118					3																	46501175		2203	4300	6503	SO:0001583	missense	4057	exon2			TGGGGGAGTCTCT		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.178T>C	chr3.hg19:g.46501175A>G	ENSP00000231751:p.Ser60Pro	89.0	2.0		73.0	4.0	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Missense_Mutation	SNP	ENST00000231751.4	hg19	CCDS33747.1	.	.	.	.	.	.	.	.	.	.	A	15.32	2.799070	0.50208	.	.	ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496;ENST00000443743;ENST00000431944;ENST00000415180	T;T;T;T;T;T	0.36878	2.25;2.25;2.25;2.25;1.23;1.23	4.62	3.42	0.39159	.	0.334073	0.32769	N	0.005661	T	0.64583	0.2611	M	0.93898	3.47	0.09310	N	1	D;D;D	0.65815	0.994;0.995;0.994	D;D;D	0.72625	0.978;0.946;0.978	T	0.59064	-0.7524	10	0.72032	D	0.01	-23.6303	8.032	0.30470	0.8192:0.0:0.0:0.1808	.	60;47;60	E7ER44;E7EQB2;P02788	.;.;TRFL_HUMAN	P	60;16;60;47;60;71;16	ENSP00000231751:S60P;ENSP00000405719:S16P;ENSP00000405546:S60P;ENSP00000397427:S47P;ENSP00000395234:S71P;ENSP00000400254:S16P	ENSP00000231751:S60P	S	-	1	0	LTF	46476179	0.136000	0.22515	0.002000	0.10522	0.006000	0.05464	1.447000	0.35101	0.839000	0.34971	0.528000	0.53228	TCC	.	.		0.522	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		G	46501175	A	G	46501175	3	3	230	1	0	0	0	0	1	0	0	0	9088	304	11	2	2018	2	LTF	3	46501175	Missense_Mutation	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10	5235074	46501175	151521255	21	32292										
ALS2CL	259173	hgsc.bcm.edu	37	chr3	46722032	46722032	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tgccaatgtagcgctcacctCtggaaggagaggaatgtggc	14	9	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr3:46722032C>A	ENST00000318962.4	-	14	1520		c.e14-1		ALS2CL_ENST00000415953.1_Splice_Site	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like						endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		GCGCTCACCTCTGGAAGGAGA	0.632																																					.		Atlas-SNP	.											.	ALS2CL	78	.	0			c.1437-1G>T						.						65	60	62					3																	46722032		2203	4300	6503	SO:0001630	splice_region_variant	259173	exon15			TCACCTCTGGAAG	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.1437-1G>T	chr3.hg19:g.46722032C>A		20.0	0.0		13.0	4.0	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Splice_Site	SNP	ENST00000318962.4	hg19	CCDS2743.1	.	.	.	.	.	.	.	.	.	.	C	11.46	1.646713	0.29246	.	.	ENSG00000178038	ENST00000318962;ENST00000415953	.	.	.	4.55	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8401	0.70217	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ALS2CL	46697036	1.000000	0.71417	0.997000	0.53966	0.082000	0.17680	6.497000	0.73674	2.355000	0.79922	0.462000	0.41574	.	.	.		0.632	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	Intron	A	46722032	C	A	46722032	5	1	230	1	0	0	0	0	0	0	1	0	551	927	32	3	1477	3	ALS2CL	3	46722032	Splice_Site	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	220857	46722032	151300398	22	32293										
CCDC66	285331	hgsc.bcm.edu	37	chr3	56627035	56627035	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gcaccctttcagtgctgtgaAacaagaactgcaaagaaaat	8	9	1	3			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr3:56627035A>C	ENST00000394672.3	+	8	1044	c.974A>C	c.(973-975)aAa>aCa	p.K325T	CCDC66_ENST00000326595.7_Missense_Mutation_p.K291T|CCDC66_ENST00000436465.2_Missense_Mutation_p.K325T	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	325					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		AGTGCTGTGAAACAAGAACTG	0.338																																					p.K325T		Atlas-SNP	.											.	CCDC66	145	.	0			c.A974C						.						103	111	109					3																	56627035		2203	4300	6503	SO:0001583	missense	285331	exon8			CTGTGAAACAAGA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.974A>C	chr3.hg19:g.56627035A>C	ENSP00000378167:p.Lys325Thr	161.0	0.0		130.0	48.0	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	hg19	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	A	14.56	2.572501	0.45798	.	.	ENSG00000180376	ENST00000394672;ENST00000326595;ENST00000436465	T;T;T	0.32023	1.47;1.48;1.47	5.5	1.73	0.24493	.	0.274651	0.34959	N	0.003556	T	0.39600	0.1084	M	0.75264	2.295	0.80722	D	1	P	0.51351	0.944	P	0.52957	0.714	T	0.20009	-1.0288	10	0.66056	D	0.02	-15.4739	4.6077	0.12385	0.7009:0.0:0.1584:0.1407	.	325	A2RUB6	CCD66_HUMAN	T	325;291;325	ENSP00000378167:K325T;ENSP00000326050:K291T;ENSP00000404320:K325T	ENSP00000326050:K291T	K	+	2	0	CCDC66	56602075	0.992000	0.36948	0.607000	0.28956	0.908000	0.53690	1.559000	0.36320	0.375000	0.24679	-0.333000	0.08304	AAA	.	.		0.338	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		C	56627035	A	C	56627035	3	2	230	1	0	0	0	0	1	0	0	0	2840	14	1	5	1004	5	CCDC66	3	56627035	Missense_Mutation	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10	9905003	56627035	141395395	23	32294										
ETV5	2119	hgsc.bcm.edu	37	chr3	185797732	185797732	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gaagcgaatggggggcggggGcggggcccacaccttgaact	19	10	0	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr3:185797732G>A	ENST00000306376.5	-	7	770	c.524C>T	c.(523-525)gCc>gTc	p.A175V	ETV5_ENST00000434744.1_Missense_Mutation_p.A175V|ETV5_ENST00000537818.1_Missense_Mutation_p.A217V|ETV5-AS1_ENST00000453370.1_RNA	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	175					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			GGGGGCGGGGGCGGGGCCCAC	0.632			T	"TMPRSS2, SCL45A3"	Prostate																																p.A175V		Atlas-SNP	.		Dom	yes		3	3q28	2119	ets variant gene 5		E	.	ETV5	106	.	0			c.C524T						.						39	48	45					3																	185797732		2203	4300	6503	SO:0001583	missense	2119	exon7			GCGGGGGCGGGGC	BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"ets-related molecule"	601600	"ets variant gene 5 (ets-related molecule)"			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.524C>T	chr3.hg19:g.185797732G>A	ENSP00000306894:p.Ala175Val	53.0	0.0		43.0	15.0	NM_004454	A6NH46|B7Z7D7|Q6IBN5	Missense_Mutation	SNP	ENST00000306376.5	hg19	CCDS33906.1	.	.	.	.	.	.	.	.	.	.	G	3.829	-0.036156	0.07497	.	.	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818	T;T;T	0.10005	2.94;2.94;2.92	5.19	0.569	0.17340	PEA3-type ETS-domain transcription factor, N-terminal (1);	1.096050	0.06836	N	0.794816	T	0.09598	0.0236	L	0.38531	1.155	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38308	-0.9667	10	0.45353	T	0.12	.	7.0571	0.25106	0.1759:0.2676:0.5565:0.0	.	175;217	P41161;B7Z7D7	ETV5_HUMAN;.	V	175;175;217	ENSP00000306894:A175V;ENSP00000413755:A175V;ENSP00000441737:A217V	ENSP00000306894:A175V	A	-	2	0	ETV5	187280426	0.538000	0.26394	0.026000	0.17262	0.029000	0.11900	2.650000	0.46665	0.171000	0.19730	-0.499000	0.04595	GCC	.	.		0.632	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454		A	185797732	G	A	185797732	3	1	230	1	0	0	0	0	1	0	0	0	5284	1203	42	3	1036	3	ETV5	3	185797732	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	129170697	185797732	12224698	24	32295										
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25676185	25676185	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	acgctgggctccaacatcggCaccaccaccaccgccatcct	7	20	0	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr4:25676185C>G	ENST00000382051.3	+	12	1442	c.1392C>G	c.(1390-1392)ggC>ggG	p.G464G	SLC34A2_ENST00000504570.1_Silent_p.G463G|SLC34A2_ENST00000503434.1_Silent_p.G463G	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	464	Poly-Thr.				aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				CCAACATCGGCACCACCACCA	0.592			T	ROS1	NSCLC																																p.G464G		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	.	SLC34A2	93	.	0			c.C1392G						.						92	87	89					4																	25676185		2203	4300	6503	SO:0001819	synonymous_variant	10568	exon12			CATCGGCACCACC	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.1392C>G	chr4.hg19:g.25676185C>G		161.0	0.0		116.0	47.0	NM_006424	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Silent	SNP	ENST00000382051.3	hg19	CCDS3435.1																																																																																			.	.		0.592	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		G	25676185	C	G	25676185	2	3	230	1	0	0	0	0	0	0	0	1	14583	697	25	4		4	SLC34A2	4	25676185	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		25676185	165478091	25	32296										
GYPA	2994	hgsc.bcm.edu	37	chr4	145035877	145035877	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	caacagaacttaaaggcacgTctgtgtcaggtgaggggaga	14	7	2	3			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr4:145035877T>A	ENST00000283126.7	-	1	93				GYPA_ENST00000503627.1_Missense_Mutation_p.D89V|GYPA_ENST00000360771.4_Missense_Mutation_p.D134V|GYPA_ENST00000512789.1_Missense_Mutation_p.D69V|GYPA_ENST00000324022.10_Missense_Mutation_p.D101V|GYPA_ENST00000535709.1_Missense_Mutation_p.D108V|RP11-673E1.4_ENST00000506982.1_RNA|GYPA_ENST00000504786.1_Missense_Mutation_p.D102V|GYPA_ENST00000512064.1_Missense_Mutation_p.D121V			P06028	GLPB_HUMAN	glycophorin B (MNS blood group)							integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|skin(1)	4	all_hematologic(180;0.158)					TAAAGGCACGTCTGTGTCAGG	0.338																																					p.D134V		Atlas-SNP	.											.	GYPA	27	.	0			c.A401T						.						81	83	83					4																	145035877		2203	4300	6503	SO:0001627	intron_variant	2993	exon6			GGCACGTCTGTGT		CCDS54809.1	4q31.21	2014-09-17	2006-02-23			ENSG00000250361		"CD molecules", "Blood group antigens"	4703	protein-coding gene	gene with protein product		111740	"glycophorin B (includes Ss blood group)", "glycophorin B (Ss blood group)"	MNS			Standard	NM_002100		Approved	GPB, SS, CD235b		P06028		ENST00000283126.7:c.37+25874A>T	chr4.hg19:g.145035877T>A		104.0	0.0		64.0	27.0	NM_002099	B8Q174|E2QBW7|Q0VAF4|Q58HE9|Q58HF0|Q58HF1|Q9UCH7	Missense_Mutation	SNP	ENST00000283126.7	hg19		.	.	.	.	.	.	.	.	.	.	T	13.63	2.293261	0.40594	.	.	ENSG00000170180	ENST00000360771;ENST00000324022;ENST00000535709;ENST00000512064;ENST00000512789;ENST00000504786;ENST00000503627	T;T;T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21;2.21;2.21	4.72	-7.29	0.01451	.	2.245640	0.01908	N	0.039644	T	0.17619	0.0423	L	0.53249	1.67	0.09310	N	1	B;B;B;B;B	0.21688	0.059;0.019;0.059;0.033;0.059	B;B;B;B;B	0.22880	0.042;0.029;0.042;0.029;0.042	T	0.38757	-0.9646	10	0.87932	D	0	0.3478	9.7604	0.40528	0.1153:0.1589:0.0:0.7258	.	101;69;121;102;134	B8Q185;Q13030;E9PD10;E7EQF3;P02724	.;.;.;.;GLPA_HUMAN	V	134;101;108;121;69;102;89	ENSP00000354003:D134V;ENSP00000324483:D101V;ENSP00000445398:D108V;ENSP00000426130:D121V;ENSP00000425193:D69V;ENSP00000425549:D102V;ENSP00000421243:D89V	ENSP00000324483:D101V	D	-	2	0	GYPA	145255327	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.807000	0.00361	-1.430000	0.01985	-0.472000	0.04984	GAC	.	.		0.338	GYPB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002100		A	145035877	T	A	145035877	1	1	230	0	1	0	0	0	0	0	0	0	6917	1667	58	4		4	GYPA	4	145035877	Intron	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	119359692	145035877	46118399	26	32297										
RXFP1	59350	hgsc.bcm.edu	37	chr4	159568206	159568206	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cagttctgattctcatttggAttactggttttatagtggct	9	6	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr4:159568206A>G	ENST00000307765.5	+	16	1860	c.1609A>G	c.(1609-1611)Att>Gtt	p.I537V	RXFP1_ENST00000460056.2_Missense_Mutation_p.I456V|RXFP1_ENST00000343542.5_Missense_Mutation_p.I489V|RXFP1_ENST00000470033.1_Missense_Mutation_p.I504V|RXFP1_ENST00000448688.2_Missense_Mutation_p.I432V	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	537					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		TCTCATTTGGATTACTGGTTT	0.353																																					p.I564V		Atlas-SNP	.											.	RXFP1	98	.	0			c.A1690G						.						105	99	101					4																	159568206		1846	4090	5936	SO:0001583	missense	59350	exon16			ATTTGGATTACTG	AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"GPCR / Class A : Relaxin family peptide receptors"	19718	protein-coding gene	gene with protein product		606654	"leucine-rich repeat-containing G protein-coupled receptor 7"	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.1609A>G	chr4.hg19:g.159568206A>G	ENSP00000303248:p.Ile537Val	79.0	0.0		71.0	33.0	NM_001253727	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Missense_Mutation	SNP	ENST00000307765.5	hg19	CCDS43276.1	.	.	.	.	.	.	.	.	.	.	A	8.057	0.767314	0.15983	.	.	ENSG00000171509	ENST00000460056;ENST00000307765;ENST00000448688;ENST00000343542;ENST00000470033;ENST00000440678	T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22	5.6	5.6	0.85130	GPCR, rhodopsin-like superfamily (1);	0.473362	0.24985	N	0.034030	T	0.18215	0.0437	N	0.12443	0.215	0.36487	D	0.868187	B;B;B;B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B;B;B	0.11329	0.004;0.006;0.002;0.002;0.002;0.005;0.004;0.004	T	0.20739	-1.0266	10	0.10377	T	0.69	.	8.2529	0.31737	0.7945:0.1345:0.071:0.0	.	548;564;432;489;504;456;407;537	B3KV27;B4DGP2;B4DHD1;Q9HBX9-4;Q9HBX9-2;E9PCA3;Q59H16;Q9HBX9	.;.;.;.;.;.;.;RXFP1_HUMAN	V	456;537;432;489;504;407	ENSP00000423306:I456V;ENSP00000303248:I537V;ENSP00000414885:I432V;ENSP00000345889:I489V;ENSP00000420712:I504V	ENSP00000303248:I537V	I	+	1	0	RXFP1	159787656	1.000000	0.71417	0.972000	0.41901	0.893000	0.52053	1.792000	0.38754	2.128000	0.65567	0.528000	0.53228	ATT	.	.		0.353	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634		G	159568206	A	G	159568206	3	3	230	1	0	0	0	0	1	0	0	0	13774	333	12	2	1671	2	RXFP1	4	159568206	Missense_Mutation	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10	14532329	159568206	31586070	27	32298										
ZNF608	57507	hgsc.bcm.edu	37	chr5	123980027	123980028	+	Missense_Mutation	DNP	AC	AC	TA													0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gtaaggataagcatgcaagtActgtatgtatgactgatgct							TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr5:123980027_123980028AC>TA	ENST00000306315.5	-	5	4467_4468	c.4032_4033GT>TA	c.(4030-4035)caGTac>caTAac	p.1344_1345QY>HN	ZNF608_ENST00000513985.1_5'UTR|ZNF608_ENST00000504926.1_Missense_Mutation_p.917_918QY>HN	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1344							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		GCATGCAAGTACTGTATGTATG	0.495																																					p.Y1345N|p.Q1344H		Atlas-SNP	.											.	ZNF608	117	.	0			c.T4033A|c.G4032T						.																																			SO:0001583	missense	57507	exon5			GCAAGTACTGTAT|CAAGTACTGTATG	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.4032_4033delinsTA	chr5.hg19:g.123980027_123980028delinsTA	ENSP00000307746:p.Q1344_Y1345delinsHN	108.0	0.0		106.0|108.0	24.0	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	hg19	CCDS34219.1																																																																																			.	.		0.495	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		TA	123980028	AC	TA	123980027	3	4	230	1	0	0	0	0	1	0	0	0	18049	391	14	4	525	4	ZNF608	5	123980027	Missense_Mutation	DNP	AC	TCGA-DD-AAVX-01A-11D-A40R-10		123980027	56935233	28	32299										
PCDHGB3	56102	hgsc.bcm.edu	37	chr5	140750610	140750610	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tggtcctcacagctgtggatGggggcgagccctccagaagc	15	12	1	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr5:140750610G>A	ENST00000576222.1	+	1	780	c.649G>A	c.(649-651)Ggg>Agg	p.G217R	PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	217	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTGTGGATGGGGGCGAGCC	0.547																																					p.G217R		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.G649A						.						49	52	51					5																	140750610		2025	4204	6229	SO:0001583	missense	56102	exon1			GTGGATGGGGGCG	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.649G>A	chr5.hg19:g.140750610G>A	ENSP00000461862:p.Gly217Arg	92.0	0.0		94.0	21.0	NM_018924	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.		0.547	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140750610	G	A	140750610	3	1	230	1	0	0	0	0	1	0	0	0	11573	1348	47	3	651	3	PCDHGB3	5	140750610	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	16770583	140750610	40164650	29	32300										
GPLD1	2822	hgsc.bcm.edu	37	chr6	24429303	24429303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cgtgaagtgccccggagagtCgggctcccaaagaactcctt	12	13	0	3			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr6:24429303C>T	ENST00000230036.1	-	25	2590	c.2480G>A	c.(2479-2481)cGa>cAa	p.R827Q		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	827					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						CCCGGAGAGTCGGGCTCCCAA	0.483																																					p.R827Q		Atlas-SNP	.											.	GPLD1	91	.	0			c.G2480A						.						93	82	86					6																	24429303		2203	4300	6503	SO:0001583	missense	2822	exon25			GAGAGTCGGGCTC	L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.2480G>A	chr6.hg19:g.24429303C>T	ENSP00000230036:p.Arg827Gln	65.0	0.0		59.0	11.0	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	hg19	CCDS4553.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.385727	0.61956	.	.	ENSG00000112293	ENST00000230036	T	0.67698	-0.28	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000009	T	0.66499	0.2795	M	0.73962	2.25	0.80722	D	1	D	0.71674	0.998	P	0.49502	0.613	T	0.65080	-0.6255	10	0.29301	T	0.29	-19.612	17.8579	0.88771	0.0:1.0:0.0:0.0	.	827	P80108	PHLD_HUMAN	Q	827	ENSP00000230036:R827Q	ENSP00000230036:R827Q	R	-	2	0	GPLD1	24537282	1.000000	0.71417	0.999000	0.59377	0.619000	0.37552	4.423000	0.59861	2.744000	0.94065	0.655000	0.94253	CGA	.	.		0.483	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503		T	24429303	C	T	24429303	3	4	230	1	0	0	0	0	1	0	0	0	6622	884	31	1	46	1	GPLD1	6	24429303	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		24429303	146685764	30	32301										
HIST1H2AG	8969	hgsc.bcm.edu	37	chr6	27101233	27101233	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tgagagccaccacaaggcgaAgggcaagtaactatctgtac	11	10	1	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr6:27101233A>T	ENST00000359193.2	+	1	402	c.383A>T	c.(382-384)aAg>aTg	p.K128M	HIST1H2BJ_ENST00000607124.1_5'Flank|HIST1H2BJ_ENST00000339812.2_5'Flank|HIST1H2BJ_ENST00000541790.1_5'Flank	NM_021064.4	NP_066408.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ag	128						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	17						CACAAGGCGAAGGGCAAGTAA	0.517																																					p.K128M		Atlas-SNP	.											.	HIST1H2AG	37	.	0			c.A383T						.						65	63	64					6																	27101233		2203	4300	6503	SO:0001583	missense	8969	exon1			AGGCGAAGGGCAA	L19778	CCDS4619.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000196787	ENSG00000196787		"Histones / Replication-dependent"	4737	protein-coding gene	gene with protein product		615012	"H2A histone family, member P", "histone 1, H2ag"	H2AFP		8179821, 12408966	Standard	NM_021064		Approved	pH2A/f, H2A/p, H2A.1b	uc003niw.3	P0C0S8	OTTHUMG00000014469	ENST00000359193.2:c.383A>T	chr6.hg19:g.27101233A>T	ENSP00000352119:p.Lys128Met	203.0	0.0		133.0	43.0	NM_021064	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000359193.2	hg19	CCDS4619.1	.	.	.	.	.	.	.	.	.	.	.	13.89	2.371254	0.42003	.	.	ENSG00000196787	ENST00000359193	T	0.47869	0.83	4.08	4.08	0.47627	.	0.000000	0.41938	D	0.000781	T	0.26521	0.0648	.	.	.	0.34292	D	0.683351	B	0.26547	0.152	B	0.28991	0.097	T	0.33163	-0.9879	9	0.87932	D	0	.	11.6705	0.51399	1.0:0.0:0.0:0.0	.	128	P0C0S8	H2A1_HUMAN	M	128	ENSP00000352119:K128M	ENSP00000352119:K128M	K	+	2	0	HIST1H2AG	27209212	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	8.002000	0.88514	1.801000	0.52704	0.533000	0.62120	AAG	.	.		0.517	HIST1H2AG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040137.1	NM_021064		T	27101233	A	T	27101233	3	4	230	1	0	0	0	0	1	0	0	0	7142	72	3	4	385	4	HIST1H2AG	6	27101233	Missense_Mutation	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10	2671930	27101233	144013834	31	32302										
NRM	11270	hgsc.bcm.edu	37	chr6	30656498	30656498	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	agttttctttgtagctgggcCcggaggtagcggaggtcttg	16	7	2	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr6:30656498C>A	ENST00000259953.4	-	5	1080	c.729G>T	c.(727-729)cgG>cgT	p.R243R	NRM_ENST00000376420.5_Silent_p.R184R|PPP1R18_ENST00000488324.1_5'Flank|NRM_ENST00000470733.1_5'UTR|NRM_ENST00000376421.5_Silent_p.R243R|PPP1R18_ENST00000399199.3_5'Flank|PPP1R18_ENST00000274853.3_5'Flank	NM_007243.2	NP_009174.1	Q8IXM6	NRM_HUMAN	nurim (nuclear envelope membrane protein)	243	Leu-rich.					integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)				large_intestine(1)|lung(2)	3						GTAGCTGGGCCCGGAGGTAGC	0.607																																					p.R249R		Atlas-SNP	.											.	NRM	7	.	0			c.G747T						.						53	58	56					6																	30656498		2203	4300	6503	SO:0001819	synonymous_variant	11270	exon4			CTGGGCCCGGAGG	AF143676	CCDS4686.1, CCDS59498.1	6p21.3	2010-02-17			ENSG00000137404	ENSG00000137404			8003	protein-coding gene	gene with protein product						10402458, 17517639	Standard	NM_007243		Approved	NRM29	uc031sng.1	Q8IXM6	OTTHUMG00000031223	ENST00000259953.4:c.729G>T	chr6.hg19:g.30656498C>A		109.0	0.0		85.0	21.0	NM_001270707	B0S7R0|B0S7R1|I3XIE2|I3XIE3|Q5JP57|Q5JP58|Q5JP59|Q5JP60|Q8WU45|Q9BSX3|Q9UN92	Silent	SNP	ENST00000259953.4	hg19	CCDS4686.1	.	.	.	.	.	.	.	.	.	.	C	7.108	0.575416	0.13623	.	.	ENSG00000137404	ENST00000444096	.	.	.	5.26	2.13	0.27403	.	.	.	.	.	T	0.30792	0.0776	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.14420	-1.0473	4	.	.	.	-18.1619	4.1973	0.10450	0.2804:0.5101:0.125:0.0845	.	.	.	.	C	243	.	.	G	-	1	0	NRM	30764477	0.808000	0.29022	0.990000	0.47175	0.643000	0.38383	-0.117000	0.10708	0.603000	0.29913	-0.169000	0.13324	GGC	.	.		0.607	NRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076466.2			A	30656498	C	A	30656498	2	1	230	1	0	0	0	0	0	0	0	1	10666	610	22	3		3	NRM	6	30656498	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	3555265	30656498	140458569	32	32303										
TNXB	7148	hgsc.bcm.edu	37	chr6	32036842	32036842	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cgtggcctcctccactgtcaActccccgaggtggggctcag	12	16	2	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr6:32036842A>G	ENST00000375244.3	-	16	5860	c.5659T>C	c.(5659-5661)Ttg>Ctg	p.L1887L	TNXB_ENST00000375247.2_Silent_p.L1887L			P22105	TENX_HUMAN	tenascin XB	1969	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TCCACTGTCAACTCCCCGAGG	0.582																																					p.L1887L		Atlas-SNP	.											.	TNXB	553	.	0			c.T5659C						.						57	64	61					6																	32036842		1306	2575	3881	SO:0001819	synonymous_variant	7148	exon16			CTGTCAACTCCCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5659T>C	chr6.hg19:g.32036842A>G		71.0	0.0		63.0	22.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	hg19																																																																																				.	.		0.582	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		G	32036842	A	G	32036842	2	3	230	1	0	0	0	0	0	0	0	1	16361	40	2	2		2	TNXB	6	32036842	Silent	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10	1380344	32036842	139078225	33	32304										
PXT1	222659	hgsc.bcm.edu	37	chr6	36359627	36359627	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gaagacaaaatgatctagtgCatctctgccatcctgttgaa	8	9	2	3			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr6:36359627C>T	ENST00000454782.2	-	5	808	c.325G>A	c.(325-327)Gca>Aca	p.A109T	RP1-50J22.4_ENST00000411643.1_RNA	NM_152990.3	NP_694535.2	Q8NFP0	PXT1_HUMAN	peroxisomal, testis specific 1	109					positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|peroxisome (GO:0005777)											TGATCTAGTGCATCTCTGCCA	0.323																																					p.A109T		Atlas-SNP	.											.	PXT1	6	.	0			c.G325A						.						101	103	102					6																	36359627		2203	4300	6503	SO:0001583	missense	222659	exon5			CTAGTGCATCTCT	AF486827	CCDS4820.2	6p21.31	2004-04-30			ENSG00000179165	ENSG00000179165			18312	protein-coding gene	gene with protein product							Standard	NM_152990		Approved	STEPP	uc003omd.2	Q8NFP0	OTTHUMG00000159815	ENST00000454782.2:c.325G>A	chr6.hg19:g.36359627C>T	ENSP00000419944:p.Ala109Thr	84.0	0.0		80.0	17.0	NM_152990	J3KR74	Missense_Mutation	SNP	ENST00000454782.2	hg19	CCDS4820.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.98|10.98	1.505291|1.505291	0.26949|0.26949	.|.	.|.	ENSG00000179165|ENSG00000179165	ENST00000454782;ENST00000538109|ENST00000459696	.|.	.|.	.|.	4.84|4.84	0.817|0.817	0.18773|0.18773	.|.	0.885835|.	0.09360|.	N|.	0.812898|.	T|T	0.15089|0.15089	0.0364|0.0364	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	P|.	0.51351|.	0.944|.	P|.	0.52957|.	0.714|.	T|T	0.29671|0.29671	-1.0004|-1.0004	8|4	0.23891|.	T|.	0.37|.	3.3413|3.3413	7.9695|7.9695	0.30119|0.30119	0.0:0.4374:0.4695:0.0931|0.0:0.4374:0.4695:0.0931	.|.	26|.	Q8NFP0|.	PXT1_HUMAN|.	T|I	109;26|32	.|.	ENSP00000419944:A109T|.	A|M	-|-	1|3	0|0	PXT1|PXT1	36467605|36467605	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.306000|-0.306000	0.08178|0.08178	0.020000|0.020000	0.15106|0.15106	-0.165000|-0.165000	0.13383|0.13383	GCA|ATG	.	.		0.323	PXT1-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357516.2	NM_152990		T	36359627	C	T	36359627	3	4	230	1	0	0	0	0	1	0	0	0	12868	710	25	3	83	3	PXT1	6	36359627	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	4322785	36359627	134755440	34	32305										
CRISP1	167	hgsc.bcm.edu	37	chr6	49814359	49814359	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	acaggataagatgtcatatgCatattttctccacaaaaggt	7	7	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr6:49814359C>T	ENST00000335847.4	-	5	410	c.309G>A	c.(307-309)atG>atA	p.M103I	CRISP1_ENST00000355791.2_Missense_Mutation_p.M103I|CRISP1_ENST00000505118.1_Missense_Mutation_p.M103I|CRISP1_ENST00000507853.1_Missense_Mutation_p.M103I|CRISP1_ENST00000329411.5_Missense_Mutation_p.M103I|CRISP1_ENST00000536021.1_Missense_Mutation_p.M103I	NM_001131.2	NP_001122.2	P54107	CRIS1_HUMAN	cysteine-rich secretory protein 1	103	SCP.				binding of sperm to zona pellucida (GO:0007339)|fusion of sperm to egg plasma membrane (GO:0007342)|regulation of acrosome reaction (GO:0060046)	extracellular space (GO:0005615)|nucleus (GO:0005634)	calcium channel regulator activity (GO:0005246)			endometrium(1)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0358)					ATGTCATATGCATATTTTCTC	0.378																																					p.M103I		Atlas-SNP	.											.	CRISP1	45	.	0			c.G309A						.						184	157	166					6																	49814359		2203	4300	6503	SO:0001583	missense	167	exon5			CATATGCATATTT	D38451	CCDS4931.1, CCDS4932.1	6p21.2-p21.1	2008-02-05	2003-09-03	2003-09-05	ENSG00000124812	ENSG00000124812			304	protein-coding gene	gene with protein product		601193	"acidic epididymal glycoprotein-like 1"	AEGL1		8838800	Standard	NM_001131		Approved	CRISP-1, ARP, HUMARP, HSCRISP1D, HSCRISP1G	uc003ozw.2	P54107	OTTHUMG00000014827	ENST00000335847.4:c.309G>A	chr6.hg19:g.49814359C>T	ENSP00000338276:p.Met103Ile	72.0	0.0		73.0	27.0	NM_001205220	B5BU98|O00698|Q13248|Q14082|Q96SF6	Missense_Mutation	SNP	ENST00000335847.4	hg19	CCDS4931.1	.	.	.	.	.	.	.	.	.	.	C	10.18	1.278026	0.23307	.	.	ENSG00000124812	ENST00000507853;ENST00000335847;ENST00000355791;ENST00000329411;ENST00000505118;ENST00000536021	T;T;T;T;T;T	0.06768	3.26;3.26;3.26;3.26;3.26;3.26	5.34	2.52	0.30459	CAP domain (3);	0.558033	0.18817	N	0.130353	T	0.00815	0.0027	N	0.03194	-0.395	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.002	T	0.47623	-0.9103	9	.	.	.	.	4.7058	0.12849	0.1868:0.6303:0.0:0.1829	.	103;103	P54107-2;P54107	.;CRIS1_HUMAN	I	103	ENSP00000425020:M103I;ENSP00000338276:M103I;ENSP00000348044:M103I;ENSP00000331317:M103I;ENSP00000427589:M103I;ENSP00000441798:M103I	.	M	-	3	0	CRISP1	49922318	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.244000	0.08903	0.209000	0.20645	-0.145000	0.13849	ATG	.	.		0.378	CRISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040875.2	NM_001131		T	49814359	C	T	49814359	3	4	230	1	0	0	0	0	1	0	0	0	3881	710	25	3	456	3	CRISP1	6	49814359	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	13454732	49814359	121300708	35	32306										
VGLL2	245806	hgsc.bcm.edu	37	chr6	117589350	117589350	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tctctctctgaacagaaactAgcctattattccaaaatgca	4	11	2	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr6:117589350A>C	ENST00000326274.5	+	2	277	c.87A>C	c.(85-87)ctA>ctC	p.L29L	VGLL2_ENST00000352536.3_Silent_p.L29L	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	29					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|kidney(1)|lung(3)	5				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)		AACAGAAACTAGCCTATTATT	0.468																																					p.L29L		Atlas-SNP	.											.	VGLL2	18	.	0			c.A87C						.						124	151	142					6																	117589350		2202	4300	6502	SO:0001819	synonymous_variant	245806	exon2			GAAACTAGCCTAT	AY056583	CCDS5114.1, CCDS5115.1	6q22.31	2014-03-03	2014-03-03		ENSG00000170162	ENSG00000170162			20232	protein-coding gene	gene with protein product		609979	"vestigial like 2 (Drosophila)"			12376544	Standard	NM_153453		Approved		uc003pxn.3	Q8N8G2	OTTHUMG00000015451	ENST00000326274.5:c.87A>C	chr6.hg19:g.117589350A>C		193.0	0.0		159.0	56.0	NM_182645	Q8WWX1	Silent	SNP	ENST00000326274.5	hg19	CCDS5115.1																																																																																			.	.		0.468	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453		C	117589350	A	C	117589350	2	2	230	1	0	0	0	0	0	0	0	1	17174	407	15	5		5	VGLL2	6	117589350	Silent	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10	67774991	117589350	53525717	36	32307										
HSF2	3298	hgsc.bcm.edu	37	chr6	122749064	122749064	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tcagcttttcactagttctgTgcagatgaatcccacagatt	7	10	3	3			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr6:122749064T>C	ENST00000368455.4	+	11	1385	c.1193T>C	c.(1192-1194)gTg>gCg	p.V398A	HSF2_ENST00000452194.1_Intron	NM_004506.3	NP_004497.1	Q03933	HSF2_HUMAN	heat shock transcription factor 2	398					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stress (GO:0006950)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			large_intestine(4)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(136;0.00371)|all cancers(137;0.0299)|GBM - Glioblastoma multiforme(226;0.0586)		ACTAGTTCTGTGCAGATGAAT	0.294																																					p.V398A		Atlas-SNP	.											.	HSF2	43	.	0			c.T1193C						.						71	68	69					6																	122749064		2203	4299	6502	SO:0001583	missense	3298	exon11			GTTCTGTGCAGAT	M65217	CCDS5124.1, CCDS47470.1	6q22	2008-08-29			ENSG00000025156	ENSG00000025156			5225	protein-coding gene	gene with protein product		140581				1871106	Standard	NM_004506		Approved		uc003pyu.2	Q03933	OTTHUMG00000016216	ENST00000368455.4:c.1193T>C	chr6.hg19:g.122749064T>C	ENSP00000357440:p.Val398Ala	216.0	0.0		156.0	55.0	NM_004506	B4DGJ4|Q0VAH9|Q2M1K4|Q9H445	Missense_Mutation	SNP	ENST00000368455.4	hg19	CCDS5124.1	.	.	.	.	.	.	.	.	.	.	T	17.43	3.387601	0.61956	.	.	ENSG00000025156	ENST00000368455	.	.	.	5.87	4.71	0.59529	Vertebrate heat shock transcription factor (1);	0.312857	0.25302	N	0.031646	T	0.28566	0.0707	L	0.50333	1.59	0.80722	D	1	B	0.27416	0.178	B	0.28991	0.097	T	0.12400	-1.0549	9	0.08179	T	0.78	-2.0516	10.4216	0.44354	0.0:0.0735:0.0:0.9265	.	398	Q03933	HSF2_HUMAN	A	398	.	ENSP00000357440:V398A	V	+	2	0	HSF2	122790763	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.172000	0.65003	1.051000	0.40369	0.528000	0.53228	GTG	.	.		0.294	HSF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043520.1	NM_004506		C	122749064	T	C	122749064	3	2	230	1	0	0	0	0	1	0	0	0	7405	1696	59	2	1235	2	HSF2	6	122749064	Missense_Mutation	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	5159714	122749064	48366003	37	32308										
IGFBP1	3484	hgsc.bcm.edu	37	chr7	45931536	45931536	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	aagttattctcttaggagccCtgccgaatagaactctacag	8	10	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr7:45931536C>G	ENST00000275525.3	+	3	821	c.525C>G	c.(523-525)ccC>ccG	p.P175P	IGFBP1_ENST00000457280.1_Silent_p.P175P|IGFBP1_ENST00000468955.1_Intron	NM_000596.2	NP_000587.1	P08833	IBP1_HUMAN	insulin-like growth factor binding protein 1	175	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)|tissue regeneration (GO:0042246)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	insulin-like growth factor binding (GO:0005520)	p.P175P(1)		large_intestine(2)|lung(4)	6						CTTAGGAGCCCTGCCGAATAG	0.418											OREG0018048	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P175P		Atlas-SNP	.											IGFBP1,NS,carcinoma,0,1	IGFBP1	19	.	1	Substitution - coding silent(1)	lung(1)	c.C525G						.						65	64	64					7																	45931536		2203	4300	6503	SO:0001819	synonymous_variant	3484	exon3			GGAGCCCTGCCGA		CCDS5504.1	7p12.3	2014-09-16			ENSG00000146678	ENSG00000146678			5469	protein-coding gene	gene with protein product	"placental protein 12", "amniotic fluid binding protein", "alpha-pregnancy-associated endometrial globulin", "growth hormone independent-binding protein", "binding protein-28", "binding protein-26", "binding protein-25", "IGF-binding protein 1"	146730		IBP1		2461294	Standard	NM_000596		Approved	IGF-BP25, AFBP, hIGFBP-1, PP12	uc003tnp.3	P08833	OTTHUMG00000152343	ENST00000275525.3:c.525C>G	chr7.hg19:g.45931536C>G		72.0	0.0	935	48.0	19.0	NM_000596	A4D2F4|D3DVL9|Q8IYP5	Silent	SNP	ENST00000275525.3	hg19	CCDS5504.1																																																																																			.	.		0.418	IGFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251355.2	NM_000596		G	45931536	C	G	45931536	2	3	230	1	0	0	0	0	0	0	0	1	7587	668	24	4		4	IGFBP1	7	45931536	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		45931536	113207127	38	32309										
TRIM56	81844	hgsc.bcm.edu	37	chr7	100731596	100731596	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tcgcacagcggctcaggcagCtgcagggctgcccctgggca	15	15	1	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr7:100731596C>T	ENST00000306085.6	+	3	1300	c.1003C>T	c.(1003-1005)Ctg>Ttg	p.L335L		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	335					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					GCTCAGGCAGCTGCAGGGCTG	0.716																																					p.L335L	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.C1003T						.						11	13	12					7																	100731596		1913	4108	6021	SO:0001819	synonymous_variant	81844	exon3			AGGCAGCTGCAGG	BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19028	protein-coding gene	gene with protein product			"tripartite motif-containing 56"				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.1003C>T	chr7.hg19:g.100731596C>T		26.0	0.0		48.0	11.0	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	hg19	CCDS43625.1																																																																																			.	.		0.716	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961		T	100731596	C	T	100731596	2	4	230	1	0	0	0	0	0	0	0	1	16545	796	28	3		3	TRIM56	7	100731596	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	54800060	100731596	58407067	39	32310										
PDP1	54704	hgsc.bcm.edu	37	chr8	94935709	94935709	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	aaaatgtcctcggtatttgaGgatcagaacgcagcaaccca	9	10	1	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr8:94935709G>A	ENST00000297598.4	+	2	1691	c.1422G>A	c.(1420-1422)gaG>gaA	p.E474E	PDP1_ENST00000520728.1_Silent_p.E474E|PDP1_ENST00000517764.1_Silent_p.E474E|PDP1_ENST00000396200.3_Silent_p.E499E	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	474					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						CGGTATTTGAGGATCAGAACG	0.488																																					p.E499E		Atlas-SNP	.											.	PDP1	97	.	0			c.G1497A						.						141	130	134					8																	94935709		2203	4300	6503	SO:0001819	synonymous_variant	54704	exon3			ATTTGAGGATCAG	AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9279	protein-coding gene	gene with protein product		605993	"protein phosphatase 2C, magnesium-dependent, catalytic subunit"	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.1422G>A	chr8.hg19:g.94935709G>A		71.0	0.0		122.0	72.0	NM_001161780	B3KX71|J3KPU0|Q5U5K1	Silent	SNP	ENST00000297598.4	hg19	CCDS6259.1																																																																																			.	.		0.488	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		A	94935709	G	A	94935709	2	1	230	1	0	0	0	0	0	0	0	1	11694	991	35	3		3	PDP1	8	94935709	Silent	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10		94935709	51428313	40	32311										
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145666384	145666384	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	ctcagctgccctgggaaagtCtcctgccttggagaagaggt	13	11	2	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr8:145666384C>G	ENST00000409379.3	-	8	1005	c.976G>C	c.(976-978)Gac>Cac	p.D326H	AC084125.4_ENST00000544423.1_RNA|AC084125.4_ENST00000442850.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	326					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						CTGGGAAAGTCTCCTGCCTTG	0.647																																					p.D326H		Atlas-SNP	.											.	TONSL	128	.	0			c.G976C						.						99	96	97					8																	145666384		2203	4300	6503	SO:0001583	missense	4796	exon8			GAAAGTCTCCTGC		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.976G>C	chr8.hg19:g.145666384C>G	ENSP00000386239:p.Asp326His	74.0	0.0		110.0	49.0	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	hg19	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	C	12.31	1.899950	0.33535	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.77489	-1.1	5.45	3.62	0.41486	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.247196	0.47852	D	0.000213	T	0.81273	0.4788	L	0.60455	1.87	0.26142	N	0.980262	D	0.89917	1.0	D	0.68192	0.956	T	0.70371	-0.4890	10	0.45353	T	0.12	-38.2468	4.2365	0.10628	0.163:0.5937:0.1577:0.0856	.	326	Q96HA7	TONSL_HUMAN	H	326	ENSP00000386239:D326H	ENSP00000386239:D326H	D	-	1	0	TONSL	145637192	0.992000	0.36948	0.633000	0.29310	0.501000	0.33797	3.102000	0.50291	0.649000	0.30751	0.561000	0.74099	GAC	.	.		0.647	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		G	145666384	C	G	145666384	3	3	230	1	0	0	0	0	1	0	0	0	10391	913	32	4	3236	4	NFKBIL2	8	145666384	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	50730675	145666384	697638	41	32312										
ACO1	48	hgsc.bcm.edu	37	chr9	32431729	32431729	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	ttccccaggagtaaatgcaaAgggacagcaggtatttctga	11	8	1	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr9:32431729A>G	ENST00000309951.6	+	15	1877	c.1739A>G	c.(1738-1740)aAg>aGg	p.K580R	ACO1_ENST00000541043.1_Missense_Mutation_p.K481R|ACO1_ENST00000379923.1_Missense_Mutation_p.K580R	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	580					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		GTAAATGCAAAGGGACAGCAG	0.418																																					p.K580R		Atlas-SNP	.											.	ACO1	149	.	0			c.A1739G						.						99	95	96					9																	32431729		2203	4300	6503	SO:0001583	missense	48	exon15			ATGCAAAGGGACA	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1739A>G	chr9.hg19:g.32431729A>G	ENSP00000309477:p.Lys580Arg	102.0	0.0		78.0	37.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	hg19	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	A	15.73	2.918383	0.52546	.	.	ENSG00000122729	ENST00000432017;ENST00000309951;ENST00000379923;ENST00000541043	T;T;T	0.17528	2.27;2.27;2.27	5.49	4.35	0.52113	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (1);	0.440276	0.27008	N	0.021391	T	0.12433	0.0302	N	0.21282	0.65	0.29079	N	0.882805	B;B	0.12013	0.005;0.001	B;B	0.12156	0.007;0.002	T	0.09378	-1.0677	10	0.59425	D	0.04	-10.1376	10.9111	0.47110	0.925:0.0:0.075:0.0	.	616;580	Q59FI0;P21399	.;ACOC_HUMAN	R	616;580;580;481	ENSP00000309477:K580R;ENSP00000369255:K580R;ENSP00000438733:K481R	ENSP00000309477:K580R	K	+	2	0	ACO1	32421729	1.000000	0.71417	0.992000	0.48379	0.910000	0.53928	4.321000	0.59209	1.027000	0.39758	-0.264000	0.10439	AAG	.	.		0.418	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		G	32431729	A	G	32431729	3	3	230	1	0	0	0	0	1	0	0	0	146	72	3	2	1793	2	ACO1	9	32431729	Missense_Mutation	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10		32431729	108781702	42	32313										
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139395113	139395113	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	ccagcaggcgcttggcggcaTcagagcgtgagtagcgggcg	18	11	1	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr9:139395113T>A	ENST00000277541.6	-	31	5900	c.5825A>T	c.(5824-5826)gAt>gTt	p.D1942V		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1942					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		CTTGGCGGCATCAGAGCGTGA	0.662			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.D1942V		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.A5825T						.						90	109	103					9																	139395113		2197	4297	6494	SO:0001583	missense	4851	exon31			GCGGCATCAGAGC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5825A>T	chr9.hg19:g.139395113T>A	ENSP00000277541:p.Asp1942Val	55.0	0.0		46.0	10.0	NM_017617	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	hg19	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.392163	0.83011	.	.	ENSG00000148400	ENST00000277541	T	0.58060	0.36	4.68	4.68	0.58851	Ankyrin repeat-containing domain (3);	0.100236	0.64402	D	0.000003	T	0.61726	0.2370	M	0.72576	2.205	0.80722	D	1	P	0.51933	0.949	P	0.50970	0.655	T	0.66236	-0.5974	10	0.52906	T	0.07	.	13.646	0.62281	0.0:0.0:0.0:1.0	.	1942	P46531	NOTC1_HUMAN	V	1942	ENSP00000277541:D1942V	ENSP00000277541:D1942V	D	-	2	0	NOTCH1	138514934	1.000000	0.71417	0.442000	0.26870	0.930000	0.56654	7.797000	0.85911	1.881000	0.54492	0.454000	0.30748	GAT	.	.		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139395113	T	A	139395113	3	1	230	1	0	0	0	0	1	0	0	0	10556	1435	50	4	1858	4	NOTCH1	9	139395113	Missense_Mutation	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	106963384	139395113	1818318	43	32314										
MASTL	84930	hgsc.bcm.edu	37	chr10	27454042	27454042	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	ccatcaatggcaaaacctagAcaagattattcaagaacccc	5	12	2	3			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr10:27454042A>G	ENST00000375940.4	+	5	660	c.603A>G	c.(601-603)agA>agG	p.R201R	MASTL_ENST00000342386.6_Silent_p.R201R|MASTL_ENST00000375946.4_Silent_p.R201R			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	201	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CAAAACCTAGACAAGATTATT	0.343																																					p.R201R		Atlas-SNP	.											.	MASTL	81	.	0			c.A603G						.						105	104	104					10																	27454042		2203	4300	6503	SO:0001819	synonymous_variant	84930	exon5			ACCTAGACAAGAT	BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.603A>G	chr10.hg19:g.27454042A>G		173.0	0.0		124.0	34.0	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Silent	SNP	ENST00000375940.4	hg19	CCDS53502.1																																																																																			.	.		0.343	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		G	27454042	A	G	27454042	2	3	230	1	0	0	0	0	0	0	0	1	9337	272	10	2		2	MASTL	10	27454042	Silent	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10		27454042	108080705	44	32315										
NRG3	10718	hgsc.bcm.edu	37	chr10	84745207	84745207	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	aattctgactgatgccagacGgtcagaagactacgaactgg	11	9	2	5	rs150401464	byFrequency	TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr10:84745207G>T	ENST00000404547.1	+	10	2009	c.2009G>T	c.(2008-2010)cGg>cTg	p.R670L	NRG3_ENST00000372141.2_Missense_Mutation_p.R646L|NRG3_ENST00000537893.1_Missense_Mutation_p.R296L|NRG3_ENST00000404576.2_Missense_Mutation_p.R450L|NRG3_ENST00000545131.1_Missense_Mutation_p.R296L|NRG3_ENST00000556918.1_Missense_Mutation_p.R476L|NRG3_ENST00000372142.2_Missense_Mutation_p.R449L			P56975	NRG3_HUMAN	neuregulin 3	670					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		GATGCCAGACGGTCAGAAGAC	0.483																																					p.R646L		Atlas-SNP	.											.	NRG3	301	.	0			c.G1937T						.						72	69	70					10																	84745207		2203	4300	6503	SO:0001583	missense	10718	exon9			CCAGACGGTCAGA	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.2009G>T	chr10.hg19:g.84745207G>T	ENSP00000384796:p.Arg670Leu	105.0	0.0		67.0	26.0	NM_001010848	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	hg19	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.190993	0.58017	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287;ENST00000372142;ENST00000404576;ENST00000556918;ENST00000545131;ENST00000537893	T;T;T;T;T;T;T	0.68903	0.27;0.44;0.5;-0.36;0.21;-0.18;-0.18	5.54	4.63	0.57726	.	0.071482	0.52532	D	0.000073	T	0.75874	0.3909	L	0.53249	1.67	0.53688	D	0.999976	B;D;P;D	0.71674	0.364;0.997;0.841;0.998	B;D;B;D	0.65987	0.168;0.919;0.358;0.94	T	0.78127	-0.2325	10	0.87932	D	0	-32.1113	12.5326	0.56124	0.0814:0.0:0.9186:0.0	.	645;670;449;646	B9EGV5;P56975;P56975-3;P56975-4	.;NRG3_HUMAN;.;.	L	646;670;645;449;450;476;296;296	ENSP00000361214:R646L;ENSP00000384796:R670L;ENSP00000361215:R449L;ENSP00000385804:R450L;ENSP00000451376:R476L;ENSP00000441201:R296L;ENSP00000440377:R296L	ENSP00000361214:R646L	R	+	2	0	NRG3	84735187	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.005000	0.63972	1.334000	0.45468	0.655000	0.94253	CGG	.	G|1.000;A|0.000		0.483	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		T	84745207	G	T	84745207	3	4	230	1	0	0	0	0	1	0	0	0	10658	1116	39	1	2215	1	NRG3	10	84745207	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	57291165	84745207	50789540	45	32316										
TBC1D12	23232	hgsc.bcm.edu	37	chr10	96162647	96162647	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gctactgtccgctccccgctGgccaggccggcgccccgccg	13	21	0	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr10:96162647G>A	ENST00000225235.4	+	1	387	c.277G>A	c.(277-279)Ggc>Agc	p.G93S		NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	93							Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	20		Colorectal(252;0.0429)				GCTCCCCGCTGGCCAGGCCGG	0.761																																					p.G93S		Atlas-SNP	.											.	TBC1D12	51	.	0			c.G277A						.						2	2	2					10																	96162647		832	2135	2967	SO:0001583	missense	23232	exon1			CCCGCTGGCCAGG	AB011180	CCDS41553.1	10q23.33	2013-09-20			ENSG00000108239	ENSG00000108239			29082	protein-coding gene	gene with protein product						9628581	Standard	NM_015188		Approved	KIAA0608	uc001kjr.2	O60347	OTTHUMG00000018794	ENST00000225235.4:c.277G>A	chr10.hg19:g.96162647G>A	ENSP00000225235:p.Gly93Ser	34.0	0.0		30.0	11.0	NM_015188	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Missense_Mutation	SNP	ENST00000225235.4	hg19	CCDS41553.1	.	.	.	.	.	.	.	.	.	.	G	7.829	0.719332	0.15372	.	.	ENSG00000108239	ENST00000225235	T	0.04194	3.68	3.2	1.22	0.21188	.	4.432070	0.01305	U	0.010416	T	0.04182	0.0116	N	0.19112	0.55	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.37686	-0.9695	10	0.27082	T	0.32	-0.033	5.8994	0.18957	0.1241:0.203:0.6728:0.0	.	93	O60347	TBC12_HUMAN	S	93	ENSP00000225235:G93S	ENSP00000225235:G93S	G	+	1	0	TBC1D12	96152637	0.390000	0.25213	0.187000	0.23214	0.547000	0.35210	0.977000	0.29475	0.662000	0.31006	0.298000	0.19748	GGC	.	.		0.761	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2			A	96162647	G	A	96162647	3	1	230	1	0	0	0	0	1	0	0	0	15616	1348	47	3	279	3	TBC1D12	10	96162647	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	11417440	96162647	39372100	46	32317										
CYP2C8	1558	hgsc.bcm.edu	37	chr10	96826978	96826978	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cacccacccttggtttttctCaactcctccacaaggcagtg	6	16	1	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr10:96826978C>G	ENST00000371270.3	-	3	562	c.468G>C	c.(466-468)ttG>ttC	p.L156F	CYP2C8_ENST00000539050.1_Missense_Mutation_p.L70F|CYP2C8_ENST00000535898.1_Missense_Mutation_p.L54F	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	156					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	TGGTTTTTCTCAACTCCTCCA	0.517																																					p.L156F		Atlas-SNP	.											.	CYP2C8	73	.	0			c.G468C						.						240	216	224					10																	96826978		2203	4300	6503	SO:0001583	missense	1558	exon3			TTTTCTCAACTCC	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"Cytochrome P450s"	2622	protein-coding gene	gene with protein product		601129	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.468G>C	chr10.hg19:g.96826978C>G	ENSP00000360317:p.Leu156Phe	117.0	0.0		106.0	25.0	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	hg19	CCDS7438.1	.	.	.	.	.	.	.	.	.	.	c	10.95	1.494613	0.26774	.	.	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.73575	-0.76;-0.76;-0.76	4.64	-2.0	0.07433	.	0.353824	0.23879	U	0.043675	T	0.58206	0.2106	L	0.35644	1.08	0.09310	N	1	B;B;B;B	0.27765	0.156;0.075;0.188;0.188	B;B;B;B	0.34418	0.114;0.113;0.182;0.182	T	0.46373	-0.9196	10	0.22706	T	0.39	.	5.8812	0.18856	0.0:0.3175:0.2401:0.4423	.	70;54;124;156	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	F	156;123;54;70	ENSP00000360317:L156F;ENSP00000445062:L54F;ENSP00000442343:L70F	ENSP00000360317:L156F	L	-	3	2	CYP2C8	96816968	0.000000	0.05858	0.081000	0.20488	0.956000	0.61745	-2.103000	0.01341	-0.024000	0.13941	-0.215000	0.12644	TTG	.	.		0.517	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770		G	96826978	C	G	96826978	3	3	230	1	0	0	0	0	1	0	0	0	4169	825	29	4	1032	4	CYP2C8	10	96826978	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	664331	96826978	38707769	47	32318										
ZFYVE27	118813	hgsc.bcm.edu	37	chr10	99509255	99509255	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tatggggctcttctgggcacAgtctgcatgctgtatttgct	12	9	3	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr10:99509255A>T	ENST00000393677.4	+	6	780	c.576A>T	c.(574-576)acA>acT	p.T192T	ZFYVE27_ENST00000357540.4_Silent_p.T106T|ZFYVE27_ENST00000370613.3_Silent_p.T74T|ZFYVE27_ENST00000370610.3_Silent_p.T94T|ZFYVE27_ENST00000453958.2_Silent_p.T192T|ZFYVE27_ENST00000337540.7_Silent_p.T160T|ZFYVE27_ENST00000356257.4_Silent_p.T192T|ZFYVE27_ENST00000359980.3_Silent_p.T192T	NM_144588.6	NP_653189.3	Q5T4F4	ZFY27_HUMAN	zinc finger, FYVE domain containing 27	192					cell death (GO:0008219)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein localization to plasma membrane (GO:0072659)	axon (GO:0030424)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)	metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	8		Colorectal(252;0.0846)		Epithelial(162;7.08e-10)|all cancers(201;5.18e-08)		TTCTGGGCACAGTCTGCATGC	0.517																																					p.T192T		Atlas-SNP	.											.	ZFYVE27	31	.	0			c.A576T						.						142	118	126					10																	99509255		2203	4300	6503	SO:0001819	synonymous_variant	118813	exon5			GGGCACAGTCTGC	BC030621	CCDS31263.1, CCDS31264.1, CCDS53562.1, CCDS53563.1, CCDS53564.1, CCDS53565.1	10q24.2	2013-09-11			ENSG00000155256	ENSG00000155256		"Zinc fingers, FYVE domain containing"	26559	protein-coding gene	gene with protein product	"protrudin"	610243				14702039	Standard	NM_144588		Approved	FLJ32919, SPG33	uc001kol.2	Q5T4F4	OTTHUMG00000018867	ENST00000393677.4:c.576A>T	chr10.hg19:g.99509255A>T		58.0	0.0		51.0	21.0	NM_001002261	B7Z3S0|B7Z404|B7Z626|G8JLC3|G8JLF0|J3KP98|Q5T4F1|Q5T4F2|Q5T4F3|Q8N1K0|Q8N6D6|Q8NCA0|Q8NDE4|Q96M08	Silent	SNP	ENST00000393677.4	hg19	CCDS31263.1																																																																																			.	.		0.517	ZFYVE27-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049745.2	NM_144588		T	99509255	A	T	99509255	2	4	230	1	0	0	0	0	0	0	0	1	17684	175	7	4		4	ZFYVE27	10	99509255	Silent	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10	2682277	99509255	36025492	48	32319										
MKI67	4288	hgsc.bcm.edu	37	chr10	129903317	129903317	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gggtgtgtccatagctttccCtactgatggtgttcgtttcc	11	10	0	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr10:129903317C>A	ENST00000368654.3	-	13	7162	c.6787G>T	c.(6787-6789)Ggg>Tgg	p.G2263W	MKI67_ENST00000368653.3_Missense_Mutation_p.G1903W	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2263	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				ATAGCTTTCCCTACTGATGGT	0.473																																					p.G2263W		Atlas-SNP	.											.	MKI67	363	.	0			c.G6787T						.						318	289	299					10																	129903317		2203	4300	6503	SO:0001583	missense	4288	exon13			CTTTCCCTACTGA	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.6787G>T	chr10.hg19:g.129903317C>A	ENSP00000357643:p.Gly2263Trp	82.0	0.0		68.0	22.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687573	0.29962	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.04360	3.64;3.64	2.65	-0.558	0.11796	.	2.301870	0.02101	N	0.053950	T	0.17365	0.0417	M	0.68952	2.095	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.999;0.999	T	0.11891	-1.0569	10	0.66056	D	0.02	.	3.705	0.08397	0.0:0.2846:0.4109:0.3045	.	2262;1903;2263	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	W	2263;1903;2262	ENSP00000357643:G2263W;ENSP00000357642:G1903W	ENSP00000357642:G1903W	G	-	1	0	MKI67	129793307	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.329000	0.02677	-0.109000	0.12044	-0.136000	0.14681	GGG	.	.		0.473	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		A	129903317	C	A	129903317	3	1	230	1	0	0	0	0	1	0	0	0	9607	681	24	3	2995	3	MKI67	10	129903317	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	30394062	129903317	5631430	49	32320										
POU2AF1	5450	hgsc.bcm.edu	37	chr11	111228301	111228301	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gctgacagcttcatggggcaCatactcggtgtaaggtgtcc	13	10	1	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr11:111228301C>T	ENST00000393067.3	-	4	839	c.325G>A	c.(325-327)Gtg>Atg	p.V109M		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	109					humoral immune response (GO:0006959)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(2)|lung(2)	5		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		TCATGGGGCACATACTCGGTG	0.647			T	BCL6	NHL																																p.V109M		Atlas-SNP	.		Dom	yes		11	11q23.1	5450	"POU domain, class 2, associating factor 1 (OBF1)"		L	.	POU2AF1	23	.	0			c.G325A						.						48	46	47					11																	111228301		2201	4297	6498	SO:0001583	missense	5450	exon4			GGGGCACATACTC		CCDS31675.1	11q23.1	2011-06-01	2007-07-13			ENSG00000110777			9211	protein-coding gene	gene with protein product		601206	"POU domain class 2, associating factor 1"			8617501	Standard	NM_006235		Approved	OBF1	uc001plg.4	Q16633		ENST00000393067.3:c.325G>A	chr11.hg19:g.111228301C>T	ENSP00000376786:p.Val109Met	178.0	0.0		130.0	45.0	NM_006235	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	hg19	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.409405	0.25378	.	.	ENSG00000110777	ENST00000393067;ENST00000531398	T;T	0.35421	1.31;1.31	4.87	2.67	0.31697	.	0.545614	0.19102	N	0.122673	T	0.18257	0.0438	N	0.12182	0.205	0.28599	N	0.909276	B	0.22541	0.071	B	0.22152	0.038	T	0.06058	-1.0848	10	0.45353	T	0.12	.	6.008	0.19557	0.1683:0.6612:0.0:0.1706	.	109	Q16633	OBF1_HUMAN	M	109;111	ENSP00000376786:V109M;ENSP00000433527:V111M	ENSP00000376786:V109M	V	-	1	0	POU2AF1	110733511	0.658000	0.27402	1.000000	0.80357	0.711000	0.40976	0.464000	0.21988	2.249000	0.74217	0.498000	0.49722	GTG	.	.		0.647	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235		T	111228301	C	T	111228301	3	4	230	1	0	0	0	0	1	0	0	0	12279	478	17	3	453	3	POU2AF1	11	111228301	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		111228301	23778215	50	32321										
AMICA1	120425	hgsc.bcm.edu	37	chr11	118067460	118067460	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tcattctcaccatggtcatgTaggtggcctctgatttttca	8	10	5	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr11:118067460T>C	ENST00000356289.5	-	9	1255	c.1082A>G	c.(1081-1083)tAc>tGc	p.Y361C	AMICA1_ENST00000526620.1_Missense_Mutation_p.Y322C|AMICA1_ENST00000292067.7_Missense_Mutation_p.Y351C|AMICA1_ENST00000533261.1_Missense_Mutation_p.Y350C	NM_001098526.1	NP_001091996.1	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen 1	361					blood coagulation (GO:0007596)|gamma-delta T cell activation (GO:0046629)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte migration (GO:0050900)|monocyte extravasation (GO:0035696)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|stomach(2)	20	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CATGGTCATGTAGGTGGCCTC	0.522																																					p.Y361C		Atlas-SNP	.											.	AMICA1	49	.	0			c.A1082G						.						232	192	205					11																	118067460		2200	4296	6496	SO:0001583	missense	120425	exon9			GTCATGTAGGTGG	AY138965, AY358362	CCDS8391.1, CCDS41723.1, CCDS66240.1	11q23.3	2013-01-11				ENSG00000160593		"Immunoglobulin superfamily / V-set domain containing"	19084	protein-coding gene	gene with protein product		609770				12975309	Standard	NM_001098526		Approved	Gm638, AMICA	uc001psk.2	Q86YT9		ENST00000356289.5:c.1082A>G	chr11.hg19:g.118067460T>C	ENSP00000348635:p.Tyr361Cys	68.0	0.0		52.0	15.0	NM_001098526	B0YIV1|B0YIV2|Q496M1|Q5DTC6|Q7Z499|Q8N9I7|Q8NF70	Missense_Mutation	SNP	ENST00000356289.5	hg19	CCDS41723.1	.	.	.	.	.	.	.	.	.	.	T	17.62	3.435333	0.62955	.	.	ENSG00000160593	ENST00000356289;ENST00000292067;ENST00000533261;ENST00000526620	D;D;D;D	0.99319	-5.23;-5.22;-5.41;-5.74	5.19	5.19	0.71726	.	0.000000	0.39544	N	0.001325	D	0.98738	0.9576	L	0.34521	1.04	0.41522	D	0.988405	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.997;0.999	D	0.99264	1.0891	10	0.87932	D	0	-16.9565	11.3658	0.49671	0.0:0.0:0.0:1.0	.	361;350;351	Q86YT9;E9PR26;Q86YT9-2	JAML1_HUMAN;.;.	C	361;351;350;322	ENSP00000348635:Y361C;ENSP00000292067:Y351C;ENSP00000436117:Y350C;ENSP00000431218:Y322C	ENSP00000292067:Y351C	Y	-	2	0	AMICA1	117572670	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	3.432000	0.52824	2.179000	0.69175	0.482000	0.46254	TAC	.	.		0.522	AMICA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392105.2	NM_153206		C	118067460	T	C	118067460	3	2	230	1	0	0	0	0	1	0	0	0	574	1638	57	2	110	2	AMICA1	11	118067460	Missense_Mutation	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	6839159	118067460	16939056	51	32322										
PANX3	116337	hgsc.bcm.edu	37	chr11	124489377	124489377	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cttccaggaagaattcagctGctccatcaagacagggctgc	10	12	2	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr11:124489377G>A	ENST00000284288.2	+	4	792	c.725G>A	c.(724-726)tGc>tAc	p.C242Y		NM_052959.2	NP_443191.1	Q96QZ0	PANX3_HUMAN	pannexin 3	242					cell-cell signaling (GO:0007267)|ion transport (GO:0006811)|protein hexamerization (GO:0034214)|transmembrane transport (GO:0055085)	gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|urinary_tract(1)	26	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)		GAATTCAGCTGCTCCATCAAG	0.493																																					p.C242Y		Atlas-SNP	.											.	PANX3	52	.	0			c.G725A						.						114	94	101					11																	124489377		2201	4299	6500	SO:0001583	missense	116337	exon4			TCAGCTGCTCCAT	AF406650	CCDS8447.1	11q24.2	2011-12-02			ENSG00000154143	ENSG00000154143		"Ion channels / Pannexins"	20573	protein-coding gene	gene with protein product		608422					Standard	NM_052959		Approved	Px3	uc001qah.3	Q96QZ0	OTTHUMG00000165925	ENST00000284288.2:c.725G>A	chr11.hg19:g.124489377G>A	ENSP00000284288:p.Cys242Tyr	104.0	0.0		85.0	26.0	NM_052959		Missense_Mutation	SNP	ENST00000284288.2	hg19	CCDS8447.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.202208	0.79127	.	.	ENSG00000154143	ENST00000284288	T	0.28454	1.61	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.61476	0.2350	M	0.82323	2.585	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.67530	-0.5647	10	0.87932	D	0	-14.9584	18.8151	0.92073	0.0:0.0:1.0:0.0	.	242	Q96QZ0	PANX3_HUMAN	Y	242	ENSP00000284288:C242Y	ENSP00000284288:C242Y	C	+	2	0	PANX3	123994587	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.234000	0.95347	2.459000	0.83118	0.561000	0.74099	TGC	.	.		0.493	PANX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387064.1			A	124489377	G	A	124489377	3	1	230	1	0	0	0	0	1	0	0	0	11431	1319	46	3	739	3	PANX3	11	124489377	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	6421917	124489377	10517139	52	32323										
DENND5B	160518	hgsc.bcm.edu	37	chr12	31586180	31586180	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tggcactccgacttacccagCgactgaaacaatcaaattat	6	12	1	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr12:31586180C>T	ENST00000389082.5	-	8	2279	c.2015G>A	c.(2014-2016)cGc>cAc	p.R672H	DENND5B_ENST00000536562.1_Missense_Mutation_p.R707H|DENND5B_ENST00000306833.6_Missense_Mutation_p.R707H|DENND5B_ENST00000354285.4_Missense_Mutation_p.R694H	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	672					positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						ACTTACCCAGCGACTGAAACA	0.418																																					p.R672H		Atlas-SNP	.											.	DENND5B	114	.	0			c.G2015A						.						132	136	135					12																	31586180		2058	4214	6272	SO:0001583	missense	160518	exon8			ACCCAGCGACTGA	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.2015G>A	chr12.hg19:g.31586180C>T	ENSP00000373734:p.Arg672His	77.0	0.0		49.0	13.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	hg19	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.000420	0.93227	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285	T;T;T;T	0.09350	3.64;3.74;3.74;2.99	4.13	4.13	0.48395	.	0.165830	0.40554	N	0.001071	T	0.24624	0.0597	L	0.47716	1.5	0.52501	D	0.999958	D;D;D	0.71674	0.998;0.996;0.996	D;P;P	0.64877	0.93;0.742;0.852	T	0.01309	-1.1389	10	0.42905	T	0.14	-10.7244	16.6004	0.84815	0.0:1.0:0.0:0.0	.	694;672;707	Q6ZUT9-4;Q6ZUT9;G3V1S3	.;DEN5B_HUMAN;.	H	672;707;707;694	ENSP00000373734:R672H;ENSP00000306482:R707H;ENSP00000444889:R707H;ENSP00000346238:R694H	ENSP00000306482:R707H	R	-	2	0	DENND5B	31477447	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.306000	0.65756	2.131000	0.65755	0.655000	0.94253	CGC	.	.		0.418	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		T	31586180	C	T	31586180	3	4	230	1	0	0	0	0	1	0	0	0	4439	768	27	1	1865	1	DENND5B	12	31586180	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		31586180	102265715	53	32324										
KRT81	3887	hgsc.bcm.edu	37	chr12	52681031	52681031	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	ggcgccctccagctcggccaGcttgcagcgggcatcactga	13	16	1	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr12:52681031G>A	ENST00000327741.5	-	7	1170	c.1102C>T	c.(1102-1104)Ctg>Ttg	p.L368L	KRT86_ENST00000423955.2_Intron|KRT86_ENST00000544024.1_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	368	Coil 2.|Rod.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		AGCTCGGCCAGCTTGCAGCGG	0.622																																					p.L368L		Atlas-SNP	.											KRT81,NS,carcinoma,0,1	KRT81	46	.	0			c.C1102T						.						43	41	42					12																	52681031		2203	4297	6500	SO:0001819	synonymous_variant	3887	exon7			CGGCCAGCTTGCA	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"-", "Intermediate filaments type II, keratins (basic)"	6458	protein-coding gene	gene with protein product	"hard keratin type II 1"	602153	"keratin, hair, basic, 1"	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.1102C>T	chr12.hg19:g.52681031G>A		95.0	0.0		68.0	29.0	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Silent	SNP	ENST00000327741.5	hg19	CCDS31805.1																																																																																			.	.		0.622	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281		A	52681031	G	A	52681031	2	1	230	1	0	0	0	0	0	0	0	1	8504	962	34	3		3	KRT81	12	52681031	Silent	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	21094851	52681031	81170864	54	32325										
ZNF140	7699	hgsc.bcm.edu	37	chr12	133682814	133682814	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cgccgtttctcacaccttacTcgacatcagagcatccatac	5	16	2	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr12:133682814T>G	ENST00000355557.2	+	5	2234	c.951T>G	c.(949-951)acT>acG	p.T317T	ZNF140_ENST00000544426.1_Silent_p.T214T|ZNF140_ENST00000440550.2_3'UTR	NM_003440.2	NP_003431.2	P52738	ZN140_HUMAN	zinc finger protein 140	317					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.114)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CACACCTTACTCGACATCAGA	0.423																																					p.T317T		Atlas-SNP	.											.	ZNF140	18	.	0			c.T951G						.						116	107	110					12																	133682814		2203	4300	6503	SO:0001819	synonymous_variant	7699	exon5			CCTTACTCGACAT	U09368	CCDS9282.1, CCDS73550.1	12q24.33	2013-01-08	2006-06-13		ENSG00000196387	ENSG00000196387		"Zinc fingers, C2H2-type", "-"	12925	protein-coding gene	gene with protein product		604082	"zinc finger protein 140 (clone pHZ-39)"			7557990	Standard	XR_245353		Approved	pHZ-39	uc001ulo.3	P52738	OTTHUMG00000167942	ENST00000355557.2:c.951T>G	chr12.hg19:g.133682814T>G		91.0	0.0		98.0	31.0	NM_003440	D3DXJ3|Q05CP6|Q8IV75	Silent	SNP	ENST00000355557.2	hg19	CCDS9282.1																																																																																			.	.		0.423	ZNF140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397169.1	NM_003440		G	133682814	T	G	133682814	2	3	230	1	0	0	0	0	0	0	0	1	17744	1538	54	5		5	ZNF140	12	133682814	Silent	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	81001783	133682814	169081	55	32326										
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46541986	46541986	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gccaatctttatcagcatctCggtcccattctctctgcctc	5	16	5	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr13:46541986C>A	ENST00000242848.4	-	15	4322	c.3974G>T	c.(3973-3975)cGa>cTa	p.R1325L	ZC3H13_ENST00000378921.2_Missense_Mutation_p.R281L|ZC3H13_ENST00000282007.3_Missense_Mutation_p.R1325L			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1325							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		atcagcatctcggtcccattc	0.488																																					p.R1325L	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-SNP	.											.	ZC3H13	197	.	0			c.G3974T						.						314	210	246					13																	46541986		2203	4300	6503	SO:0001583	missense	23091	exon15			GCATCTCGGTCCC	AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.3974G>T	chr13.hg19:g.46541986C>A	ENSP00000242848:p.Arg1325Leu	52.0	0.0		62.0	27.0	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	hg19		.	.	.	.	.	.	.	.	.	.	C	16.16	3.045346	0.55110	.	.	ENSG00000123200	ENST00000242848;ENST00000378921;ENST00000282007	T;T;T	0.37915	2.19;1.91;1.17	5.28	5.28	0.74379	.	0.000000	0.45606	D	0.000345	T	0.57475	0.2056	L	0.55481	1.735	0.58432	D	0.999998	D;D	0.67145	0.993;0.996	D;D	0.79108	0.982;0.992	T	0.59526	-0.7438	10	0.72032	D	0.01	.	18.5206	0.90951	0.0:1.0:0.0:0.0	.	1325;1325	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	L	1325;281;1325	ENSP00000242848:R1325L;ENSP00000368201:R281L;ENSP00000282007:R1325L	ENSP00000242848:R1325L	R	-	2	0	ZC3H13	45439987	1.000000	0.71417	0.928000	0.36995	0.570000	0.35934	5.336000	0.65935	2.461000	0.83175	0.591000	0.81541	CGA	.	.		0.488	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46541986	C	A	46541986	3	1	230	1	0	0	0	0	1	0	0	0	17580	884	31	1	732	1	ZC3H13	13	46541986	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		46541986	68627892	56	32327										
YLPM1	56252	hgsc.bcm.edu	37	chr14	75248349	75248357	+	In_Frame_Del	DEL	CCTCCAGTG	CCTCCAGTG	-													0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cacctctacctacaatgcccCctccagtgttgcctccttca					rs549952937		TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	CCTCCAGTG	CCTCCAGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr14:75248349_75248357delCCTCCAGTG	ENST00000552421.1	+	4	1727_1735	c.1603_1611delCCTCCAGTG	c.(1603-1611)cctccagtgdel	p.PPV535del	YLPM1_ENST00000325680.7_In_Frame_Del_p.PPV535del|YLPM1_ENST00000238571.3_Intron			P49750	YLPM1_HUMAN	YLP motif containing 1	0					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		TACAATGCCCCCTCCAGTGTTGCCTCCTT	0.526																																					p.534_537del		Atlas-INDEL	.											.	YLPM1	298	.	0			c.1602_1610del						.																																			SO:0001651	inframe_deletion	56252	exon4			.	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.1603_1611delCCTCCAGTG	chr14.hg19:g.75248349_75248357delCCTCCAGTG	ENSP00000447921:p.Pro535_Val537del	63.0	0.0		59.0	16.0	NM_019589	P49752|Q96I64|Q9P1V7	In_Frame_Del	DEL	ENST00000552421.1	hg19																																																																																				.	.		0.526	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		-	75248357	CCTCCAGTG	-	75248349	7	5	230	1	0	1	0	1	0	0	0	0	17501	623	22	0	1617	0	YLPM1	14	75248349	In_Frame_Del	DEL	CCTCCAGTG	TCGA-DD-AAVX-01A-11D-A40R-10		75248349	32101191	57	32328										
VIPAR	63894	hgsc.bcm.edu	37	chr14	77900204	77900204	+	Missense_Mutation	SNP	T	T	C													0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cctttgtggtgaatagggcaTctacatcattccaggctcga							TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr14:77900204T>C	ENST00000553888.1	-	16	1670	c.1160A>G	c.(1159-1161)gAt>gGt	p.D387G	VIPAS39_ENST00000557658.1_Missense_Mutation_p.D387G|VIPAS39_ENST00000327028.4_Missense_Mutation_p.D374G|VIPAS39_ENST00000343765.2_Missense_Mutation_p.D387G|VIPAS39_ENST00000448935.2_Missense_Mutation_p.D338G|VIPAS39_ENST00000556412.1_Missense_Mutation_p.D413G	NM_001193314.1|NM_001193317.1|NM_022067.3	NP_001180243.1|NP_001180246.1|NP_071350.2	Q9H9C1	SPE39_HUMAN	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	387					cell differentiation (GO:0030154)|endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|late endosome (GO:0005770)|recycling endosome (GO:0055037)											GAATAGGGCATCTACATCATT	0.498																																					p.D387G		Atlas-SNP	.											.	.	.	.	0			c.A1160G						.						106	94	98					14																	77900204		2203	4300	6503	SO:0001583	missense	63894	exon16			AGGGCATCTACAT	AK022925	CCDS9862.1, CCDS53905.1	14q24.3-q31	2013-08-14	2012-07-24	2012-07-24	ENSG00000151445	ENSG00000151445			20347	protein-coding gene	gene with protein product	"VPS33B interacting protein, apical-basolateral polarity regulator"	613401	"chromosome 14 open reading frame 133"	C14orf133		20190753, 19109425, 22753090, 23002115, 23918659	Standard	NM_022067		Approved	VIPAR, VPS16B, SPE-39, SPE39, hSPE-39	uc001xtu.2	Q9H9C1		ENST00000553888.1:c.1160A>G	chr14.hg19:g.77900204T>C	ENSP00000452181:p.Asp387Gly	198.0	0.0		174.0	51.0	NM_001193314	B4DPI6|O95434|Q9H7E1|Q9H9I9	Missense_Mutation	SNP	ENST00000553888.1	hg19	CCDS9862.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.436693	0.83885	.	.	ENSG00000151445	ENST00000343765;ENST00000553888;ENST00000327028;ENST00000557658;ENST00000448935;ENST00000556412	T;T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;0.4;0.4	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.68860	0.3047	L	0.56769	1.78	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.982	T	0.72293	-0.4336	10	0.87932	D	0	-16.3086	15.0021	0.71483	0.0:0.0:0.0:1.0	.	338;387	B4DPI6;Q9H9C1	.;VIPAR_HUMAN	G	387;387;374;387;338;413	ENSP00000339122:D387G;ENSP00000452181:D387G;ENSP00000313098:D374G;ENSP00000452191:D387G;ENSP00000404815:D338G;ENSP00000451857:D413G	ENSP00000313098:D374G	D	-	2	0	VIPAR	76969957	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	6.964000	0.76061	2.034000	0.60081	0.482000	0.46254	GAT	.	.		0.498	VIPAS39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414008.1	NM_022067		C	77900204	T	C	77900204	3	2	230	1	0	0	0	0	1	0	0	0	17183	1435	50	2	341	2	VIPAR	14	77900204	Missense_Mutation	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	2651855	77900204	29449336	58	32329	169	2								
VIPAR	63894	hgsc.bcm.edu	37	chr14	77900210	77900210	+	Missense_Mutation	SNP	T	T	G													0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tggtgaatagggcatctacaTcattccaggctcgaagcttg							TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr14:77900210T>G	ENST00000553888.1	-	16	1664	c.1154A>C	c.(1153-1155)gAt>gCt	p.D385A	VIPAS39_ENST00000557658.1_Missense_Mutation_p.D385A|VIPAS39_ENST00000327028.4_Missense_Mutation_p.D372A|VIPAS39_ENST00000343765.2_Missense_Mutation_p.D385A|VIPAS39_ENST00000448935.2_Missense_Mutation_p.D336A|VIPAS39_ENST00000556412.1_Missense_Mutation_p.D411A	NM_001193314.1|NM_001193317.1|NM_022067.3	NP_001180243.1|NP_001180246.1|NP_071350.2	Q9H9C1	SPE39_HUMAN	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	385					cell differentiation (GO:0030154)|endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|late endosome (GO:0005770)|recycling endosome (GO:0055037)											GGCATCTACATCATTCCAGGC	0.502																																					p.D385A		Atlas-SNP	.											.	.	.	.	0			c.A1154C						.						107	95	99					14																	77900210		2203	4300	6503	SO:0001583	missense	63894	exon16			TCTACATCATTCC	AK022925	CCDS9862.1, CCDS53905.1	14q24.3-q31	2013-08-14	2012-07-24	2012-07-24	ENSG00000151445	ENSG00000151445			20347	protein-coding gene	gene with protein product	"VPS33B interacting protein, apical-basolateral polarity regulator"	613401	"chromosome 14 open reading frame 133"	C14orf133		20190753, 19109425, 22753090, 23002115, 23918659	Standard	NM_022067		Approved	VIPAR, VPS16B, SPE-39, SPE39, hSPE-39	uc001xtu.2	Q9H9C1		ENST00000553888.1:c.1154A>C	chr14.hg19:g.77900210T>G	ENSP00000452181:p.Asp385Ala	202.0	0.0		172.0	52.0	NM_001193314	B4DPI6|O95434|Q9H7E1|Q9H9I9	Missense_Mutation	SNP	ENST00000553888.1	hg19	CCDS9862.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.785578	0.70337	.	.	ENSG00000151445	ENST00000343765;ENST00000553888;ENST00000327028;ENST00000557658;ENST00000448935;ENST00000556412	T;T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03;-0.03	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.62097	0.2400	L	0.55481	1.735	0.80722	D	1	B;P	0.39696	0.437;0.683	B;B	0.42798	0.17;0.398	T	0.61138	-0.7123	10	0.32370	T	0.25	-16.3401	15.0021	0.71483	0.0:0.0:0.0:1.0	.	336;385	B4DPI6;Q9H9C1	.;VIPAR_HUMAN	A	385;385;372;385;336;411	ENSP00000339122:D385A;ENSP00000452181:D385A;ENSP00000313098:D372A;ENSP00000452191:D385A;ENSP00000404815:D336A;ENSP00000451857:D411A	ENSP00000313098:D372A	D	-	2	0	VIPAR	76969963	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	6.964000	0.76061	2.034000	0.60081	0.482000	0.46254	GAT	.	.		0.502	VIPAS39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414008.1	NM_022067		G	77900210	T	G	77900210	3	3	230	1	0	0	0	0	1	0	0	0	17183	1435	50	5	347	5	VIPAR	14	77900210	Missense_Mutation	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	6	77900210	29449330	59	32330	169	2								
PPP2R5C	5527	hgsc.bcm.edu	37	chr14	102285330	102285330	+	Intron	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	aagttatgtttcactctaggGaacaagtcctgaagaaccct	8	9	2	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr14:102285330G>A	ENST00000334743.5	+	1	142				PPP2R5C_ENST00000445439.3_Intron|PPP2R5C_ENST00000350249.3_Intron|PPP2R5C_ENST00000328724.5_Intron|PPP2R5C_ENST00000557714.1_Intron|PPP2R5C_ENST00000422945.2_Splice_Site_p.G32E|PPP2R5C_ENST00000557095.1_Intron|PPP2R5C_ENST00000556068.1_3'UTR|PPP2R5C_ENST00000554442.1_Intron|PPP2R5C_ENST00000556946.1_Intron	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						TCACTCTAGGGAACAAGTCCT	0.403																																					p.G32E		Atlas-SNP	.											.	PPP2R5C	74	.	0			c.G95A						.						121	101	107					14																	102285330		692	1591	2283	SO:0001627	intron_variant	5527	exon3			TCTAGGGAACAAG	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.94+8957G>A	chr14.hg19:g.102285330G>A		77.0	0.0		68.0	16.0	NM_001161725	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Missense_Mutation	SNP	ENST00000334743.5	hg19	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	G	0.163	-1.078923	0.01903	.	.	ENSG00000078304	ENST00000422945;ENST00000557268	T;T	0.41065	1.04;1.01	3.38	2.49	0.30216	.	.	.	.	.	T	0.24736	0.0600	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31194	-0.9952	9	0.02654	T	1	.	6.8767	0.24151	0.1274:0.0:0.8726:0.0	.	32	F5GWP3	.	E	32;30	ENSP00000412324:G32E;ENSP00000450931:G30E	ENSP00000412324:G32E	G	+	2	0	PPP2R5C	101355083	0.004000	0.15560	0.004000	0.12327	0.103000	0.19146	0.519000	0.22862	1.003000	0.39130	-0.137000	0.14449	GGA	.	.		0.403	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719		A	102285330	G	A	102285330	1	1	230	0	1	0	0	0	0	0	0	0	12406	1188	41	3		3	PPP2R5C	14	102285330	Intron	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	24385120	102285330	5064210	60	32331										
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105359964	105359964	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	atgaacgacagctgtgaggaCgccctggccaacaagacgcg	13	12	0	3			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr14:105359964C>T	ENST00000414716.3	+	15	4371	c.4143C>T	c.(4141-4143)gaC>gaT	p.D1381D	CEP170B_ENST00000418279.1_Silent_p.D1311D|CEP170B_ENST00000453495.1_Silent_p.D1417D|CEP170B_ENST00000556508.1_Silent_p.D1346D	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	1416						cytoplasm (GO:0005737)|microtubule (GO:0005874)											GCTGTGAGGACGCCCTGGCCA	0.672																																					p.D1381D		Atlas-SNP	.											.	.	.	.	0			c.C4143T						.						15	19	17					14																	105359964		2133	4221	6354	SO:0001819	synonymous_variant	283638	exon15			TGAGGACGCCCTG	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.4143C>T	chr14.hg19:g.105359964C>T		118.0	0.0		125.0	11.0	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	hg19	CCDS45175.1																																																																																			.	.		0.672	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		T	105359964	C	T	105359964	2	4	230	1	0	0	0	0	0	0	0	1	8175	535	19	1		1	KIAA0284	14	105359964	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	3074634	105359964	1989576	61	32332										
SLC24A5	283652	hgsc.bcm.edu	37	chr15	48431227	48431227	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	agaattttttgggtattatcCcttcctattattacattact	4	7	0	1	rs112771038		TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr15:48431227C>T	ENST00000341459.3	+	7	1006	c.933C>T	c.(931-933)tcC>tcT	p.S311S	SLC24A5_ENST00000449382.2_Silent_p.S251S	NM_205850.2	NP_995322.1	Q71RS6	NCKX5_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 5	311					ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|negative regulation of melanin biosynthetic process (GO:0048022)|response to stimulus (GO:0050896)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|skin(1)|upper_aerodigestive_tract(1)	27		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		GGGTATTATCCCTTCCTATTA	0.318																																					p.S311S		Atlas-SNP	.											.	SLC24A5	64	.	0			c.C933T						.						61	63	62					15																	48431227		2197	4292	6489	SO:0001819	synonymous_variant	283652	exon7			ATTATCCCTTCCT	AF348468	CCDS10128.1	15q21.1	2014-01-28	2013-07-18		ENSG00000188467	ENSG00000188467		"Solute carriers"	20611	protein-coding gene	gene with protein product	"oculocutaneous albinism 6 (autosomal recessive)"	609802	"solute carrier family 24, member 5"			23364476	Standard	XM_005254308		Approved	JSX, OCA6	uc001zwe.3	Q71RS6	OTTHUMG00000131494	ENST00000341459.3:c.933C>T	chr15.hg19:g.48431227C>T		229.0	0.0		172.0	53.0	NM_205850	A5X8Z8|A5X8Z9|Q14CT4|Q6DKH3	Silent	SNP	ENST00000341459.3	hg19	CCDS10128.1																																																																																			.	T|1.000;|0.000		0.318	SLC24A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254340.2	NM_205850		T	48431227	C	T	48431227	2	4	230	1	0	0	0	0	0	0	0	1	14484	610	22	3		3	SLC24A5	15	48431227	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		48431227	54100165	62	32333										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54542554	54542554	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tgtgaagggctcctgtggggCattgcaaggcaaggcatgaa	16	7	0	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr15:54542554C>T	ENST00000260323.11	+	7	3360	c.3360C>T	c.(3358-3360)ggC>ggT	p.G1120G	UNC13C_ENST00000537900.1_Silent_p.G1118G|UNC13C_ENST00000545554.1_Silent_p.G1120G	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1120					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCCTGTGGGGCATTGCAAGGC	0.512																																					p.G1120G		Atlas-SNP	.											.	UNC13C	674	.	0			c.C3360T						.						102	100	101					15																	54542554		2145	4280	6425	SO:0001819	synonymous_variant	440279	exon6			GTGGGGCATTGCA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.3360C>T	chr15.hg19:g.54542554C>T		76.0	0.0		77.0	21.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.512	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54542554	C	T	54542554	2	4	230	1	0	0	0	0	0	0	0	1	17001	697	25	3		3	UNC13C	15	54542554	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	6111327	54542554	47988838	63	32334										
ZNF768	79724	hgsc.bcm.edu	37	chr16	30536644	30536644	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gtgctggatcagggtggagcCccgcccgaagctcttcccgc	14	15	2	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr16:30536644C>T	ENST00000380412.5	-	2	992	c.817G>A	c.(817-819)Ggc>Agc	p.G273S	ZNF768_ENST00000562803.1_Missense_Mutation_p.G242S	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	273					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	DNA-directed RNA polymerase II, core complex (GO:0005665)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						AGGGTGGAGCCCCGCCCGAAG	0.652																																					p.G273S		Atlas-SNP	.											.	ZNF768	28	.	0			c.G817A						.						56	56	56					16																	30536644		2197	4300	6497	SO:0001583	missense	79724	exon2			TGGAGCCCCGCCC	BC013760	CCDS10681.2	16p11.2	2013-01-08			ENSG00000169957	ENSG00000169957		"Zinc fingers, C2H2-type"	26273	protein-coding gene	gene with protein product						12477932	Standard	NM_024671		Approved	FLJ23436	uc002dyk.4	Q9H5H4	OTTHUMG00000132392	ENST00000380412.5:c.817G>A	chr16.hg19:g.30536644C>T	ENSP00000369777:p.Gly273Ser	40.0	0.0		42.0	19.0	NM_024671	Q569L7|Q96CX4	Missense_Mutation	SNP	ENST00000380412.5	hg19	CCDS10681.2	.	.	.	.	.	.	.	.	.	.	C	11.35	1.611572	0.28712	.	.	ENSG00000169957	ENST00000380412;ENST00000538507	T	0.07114	3.22	4.99	4.99	0.66335	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.139827	0.33438	N	0.004919	T	0.02083	0.0065	N	0.01091	-1.02	0.22693	N	0.998843	B	0.30326	0.276	B	0.29267	0.1	T	0.45071	-0.9286	10	0.02654	T	1	-13.8205	7.4079	0.27001	0.0:0.8227:0.0:0.1773	.	273	Q9H5H4	ZN768_HUMAN	S	273;242	ENSP00000369777:G273S	ENSP00000369777:G273S	G	-	1	0	ZNF768	30444145	0.000000	0.05858	1.000000	0.80357	0.646000	0.38490	0.329000	0.19698	2.601000	0.87937	0.462000	0.41574	GGC	.	.		0.652	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671		T	30536644	C	T	30536644	3	4	230	1	0	0	0	0	1	0	0	0	18156	623	22	3	809	3	ZNF768	16	30536644	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		30536644	59818109	64	32335										
SPG7	6687	hgsc.bcm.edu	37	chr16	89620237	89620237	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tgaggaaggtcacccgcatcGcctactccatggtgaagcag	12	12	1	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr16:89620237G>T	ENST00000268704.2	+	15	1987	c.1972G>T	c.(1972-1974)Gcc>Tcc	p.A658S		NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	658					anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		CACCCGCATCGCCTACTCCAT	0.672																																					p.A658S		Atlas-SNP	.											.	SPG7	75	.	0			c.G1972T						.						96	76	83					16																	89620237		2198	4300	6498	SO:0001583	missense	6687	exon15			CGCATCGCCTACT	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"ATPases / AAA-type"	11237	protein-coding gene	gene with protein product	"paraplegin"	602783	"cell matrix adhesion regulator"	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.1972G>T	chr16.hg19:g.89620237G>T	ENSP00000268704:p.Ala658Ser	102.0	0.0		68.0	4.0	NM_003119	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	hg19	CCDS10977.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.834236	0.91036	.	.	ENSG00000197912	ENST00000268704	D	0.90788	-2.73	5.06	5.06	0.68205	Peptidase M41 (1);Peptidase M41, FtsH (2);	0.000000	0.85682	D	0.000000	D	0.96608	0.8893	M	0.93241	3.395	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97636	1.0145	10	0.72032	D	0.01	.	17.4535	0.87599	0.0:0.0:1.0:0.0	.	658	Q9UQ90	SPG7_HUMAN	S	658	ENSP00000268704:A658S	ENSP00000268704:A658S	A	+	1	0	SPG7	88147738	1.000000	0.71417	0.928000	0.36995	0.675000	0.39556	9.423000	0.97461	2.342000	0.79632	0.563000	0.77884	GCC	.	.		0.672	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119		T	89620237	G	T	89620237	3	4	230	1	0	0	0	0	1	0	0	0	15059	1087	38	1	2180	1	SPG7	16	89620237	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	59083593	89620237	734516	65	32336										
ZZEF1	23140	hgsc.bcm.edu	37	chr17	4016072	4016072	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gccactgcaatggacaggtgCctaagcacaacatctggctt	10	12	1	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr17:4016072C>T	ENST00000381638.2	-	5	1021	c.897G>A	c.(895-897)agG>agA	p.R299R	ZZEF1_ENST00000574474.1_5'UTR|snoU13_ENST00000459263.1_RNA	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	299	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.						calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						TGGACAGGTGCCTAAGCACAA	0.473																																					p.R299R		Atlas-SNP	.											.	ZZEF1	195	.	0			c.G897A						.						58	44	49					17																	4016072		2203	4300	6503	SO:0001819	synonymous_variant	23140	exon5			CAGGTGCCTAAGC	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.897G>A	chr17.hg19:g.4016072C>T		60.0	0.0		41.0	13.0	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	hg19	CCDS11043.1																																																																																			.	.		0.473	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		T	4016072	C	T	4016072	2	4	230	1	0	0	0	0	0	0	0	1	18270	738	26	3		3	ZZEF1	17	4016072	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		4016072	77179138	66	32337										
C17orf39	79018	hgsc.bcm.edu	37	chr17	17962265	17962265	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gagctgaagaatggagactaCgtcttcatgaggtggaaggt	15	5	2	4			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr17:17962265C>T	ENST00000268719.4	+	4	863	c.690C>T	c.(688-690)taC>taT	p.Y230Y		NM_024052.4	NP_076957.3	Q8IVV7	GID4_HUMAN	GID complex subunit 4	230								p.Y230Y(1)									ATGGAGACTACGTCTTCATGA	0.463																																					p.Y230Y		Atlas-SNP	.											C17orf39,NS,carcinoma,0,1	.	.	.	1	Substitution - coding silent(1)	ovary(1)	c.C690T						.						74	67	70					17																	17962265		2203	4300	6503	SO:0001819	synonymous_variant	79018	exon4			AGACTACGTCTTC	AK127580	CCDS11190.1	17p11.2	2013-07-31	2013-07-31	2012-07-20	ENSG00000141034	ENSG00000141034			28453	protein-coding gene	gene with protein product	"vacuolar import and degradation 24"		"chromosome 17 open reading frame 39", "GID complex subunit 4, VID24 homolog (S. cerevisiae)"	C17orf39		11997338	Standard	NM_024052		Approved	VID24	uc002gsg.1	Q8IVV7	OTTHUMG00000059398	ENST00000268719.4:c.690C>T	chr17.hg19:g.17962265C>T		87.0	0.0		82.0	4.0	NM_024052	Q8TEB5|Q9BW50	Silent	SNP	ENST00000268719.4	hg19	CCDS11190.1																																																																																			.	.		0.463	GID4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132071.2	NM_024052		T	17962265	C	T	17962265	2	4	230	1	0	0	0	0	0	0	0	1	1857	547	19	1		1	C17orf39	17	17962265	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	13946193	17962265	63232945	67	32338										
AANAT	15	hgsc.bcm.edu	37	chr17	74465835	74465835	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cttccggcagcagggcagggGccccatcctgctgtggcgct	15	15	0	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr17:74465835G>A	ENST00000392492.3	+	4	641	c.407G>A	c.(406-408)gGc>gAc	p.G136D	AANAT_ENST00000250615.3_Missense_Mutation_p.G181D	NM_001088.2	NP_001079.1	Q16613	SNAT_HUMAN	aralkylamine N-acetyltransferase	136	Acetyl-CoA binding. {ECO:0000250}.|N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|melatonin biosynthetic process (GO:0030187)|N-terminal protein amino acid acetylation (GO:0006474)|response to calcium ion (GO:0051592)|response to copper ion (GO:0046688)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to insulin (GO:0032868)|response to light stimulus (GO:0009416)|response to prostaglandin E (GO:0034695)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)	aralkylamine N-acetyltransferase activity (GO:0004059)|arylamine N-acetyltransferase activity (GO:0004060)			lung(1)	1						CAGGGCAGGGGCCCCATCCTG	0.706																																					p.G181D		Atlas-SNP	.											.	AANAT	7	.	0			c.G542A						.						8	8	8					17																	74465835		2174	4251	6425	SO:0001583	missense	15	exon7			GCAGGGGCCCCAT	U40347	CCDS11745.1, CCDS54169.1	17q25.1	2013-10-15	2010-05-07		ENSG00000129673	ENSG00000129673	2.3.1.87		19	protein-coding gene	gene with protein product	"serotonin N-acetyltransferase"	600950	"arylalkylamine N-acetyltransferase"			8661026	Standard	NM_001088		Approved	SNAT	uc002jro.3	Q16613	OTTHUMG00000180179	ENST00000392492.3:c.407G>A	chr17.hg19:g.74465835G>A	ENSP00000376282:p.Gly136Asp	63.0	0.0		46.0	13.0	NM_001166579	A0AVF2|J3KMZ5|Q562F4	Missense_Mutation	SNP	ENST00000392492.3	hg19	CCDS11745.1	.	.	.	.	.	.	.	.	.	.	G	31	5.065866	0.93898	.	.	ENSG00000129673	ENST00000250615;ENST00000392492	T;T	0.57436	0.4;0.4	5.13	5.13	0.70059	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.83552	0.5279	H	0.98068	4.14	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90212	0.4265	10	0.87932	D	0	-7.8365	18.5824	0.91176	0.0:0.0:1.0:0.0	.	136	Q16613	SNAT_HUMAN	D	181;136	ENSP00000250615:G181D;ENSP00000376282:G136D	ENSP00000250615:G181D	G	+	2	0	AANAT	71977430	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	9.252000	0.95491	2.380000	0.81148	0.462000	0.41574	GGC	.	.		0.706	AANAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450130.1	NM_001088		A	74465835	G	A	74465835	3	1	230	1	0	0	0	0	1	0	0	0	18	1203	42	3	556	3	AANAT	17	74465835	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	56503570	74465835	6729375	68	32339										
TMC6	11322	hgsc.bcm.edu	37	chr17	76120700	76120700	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gcccatgatgaaggccaccaGcagcagcagcaggagggcat	14	12	0	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr17:76120700G>C	ENST00000590602.1	-	8	955	c.796C>G	c.(796-798)Ctg>Gtg	p.L266V	TMC6_ENST00000592076.1_5'Flank|TMC6_ENST00000322914.3_Missense_Mutation_p.L266V|TMC6_ENST00000392467.3_Missense_Mutation_p.L266V|TMC6_ENST00000591436.1_5'Flank|TMC6_ENST00000589553.1_Missense_Mutation_p.L39V|TMC6_ENST00000306591.7_Missense_Mutation_p.L266V|TMC6_ENST00000322933.4_5'UTR			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	266				L -> P (in Ref. 2; AAP69874). {ECO:0000305}.	ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			AAGGCCACCAGCAGCAGCAGC	0.672																																					p.L266V		Atlas-SNP	.											.	TMC6	42	.	0			c.C796G						.						19	19	19					17																	76120700		2183	4244	6427	SO:0001583	missense	11322	exon8			CCACCAGCAGCAG	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"epidermodysplasia verruciformis 1"	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.796C>G	chr17.hg19:g.76120700G>C	ENSP00000465261:p.Leu266Val	73.0	0.0		74.0	4.0	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	hg19	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.650996	0.29336	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000306591	T;T;T	0.54279	0.58;0.58;0.58	3.64	1.38	0.22167	.	1.022600	0.07798	N	0.955959	T	0.53498	0.1800	L	0.53249	1.67	0.33038	D	0.531028	P;D;D;D;B	0.58268	0.713;0.981;0.981;0.982;0.23	B;P;P;P;B	0.57101	0.246;0.813;0.761;0.664;0.082	T	0.56974	-0.7890	10	0.06891	T	0.86	-10.1151	4.5808	0.12257	0.211:0.184:0.605:0.0	.	103;266;39;266;266	B4E003;Q7Z403-2;Q7Z403-4;B3KTU5;Q7Z403	.;.;.;.;TMC6_HUMAN	V	266	ENSP00000313408:L266V;ENSP00000376260:L266V;ENSP00000306405:L266V	ENSP00000306405:L266V	L	-	1	2	TMC6	73632295	0.228000	0.23718	0.981000	0.43875	0.146000	0.21551	0.651000	0.24873	0.497000	0.27926	0.462000	0.41574	CTG	.	.		0.672	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			C	76120700	G	C	76120700	3	2	230	1	0	0	0	0	1	0	0	0	16004	962	34	4	1673	4	TMC6	17	76120700	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	1654865	76120700	5074510	69	32340										
PRODH2	58510	hgsc.bcm.edu	37	chr19	36291013	36291013	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tgagcagctcctgttccctgCgggcaccctgaagcacgctc	11	16	0	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr19:36291013C>T	ENST00000301175.3	-	11	1555	c.1538G>A	c.(1537-1539)cGc>cAc	p.R513H	AC002398.5_ENST00000433059.1_lincRNA	NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	513					proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTGTTCCCTGCGGGCACCCTG	0.597																																					p.R513H		Atlas-SNP	.											.	PRODH2	68	.	0			c.G1538A						.						36	29	31					19																	36291013		2203	4299	6502	SO:0001583	missense	58510	exon11			TCCCTGCGGGCAC	U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.1538G>A	chr19.hg19:g.36291013C>T	ENSP00000301175:p.Arg513His	72.0	0.0		50.0	4.0	NM_021232		Missense_Mutation	SNP	ENST00000301175.3	hg19	CCDS12478.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.399030	0.83120	.	.	ENSG00000250799	ENST00000301175	T	0.33438	1.41	5.26	4.21	0.49690	Proline dehydrogenase (1);	.	.	.	.	T	0.53916	0.1826	M	0.80508	2.5	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.53542	-0.8424	9	0.46703	T	0.11	.	12.0582	0.53548	0.0:0.9145:0.0:0.0855	.	513	Q9UF12	PROD2_HUMAN	H	513	ENSP00000301175:R513H	ENSP00000301175:R513H	R	-	2	0	PRODH2	40982853	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.796000	0.38794	2.766000	0.95052	0.650000	0.86243	CGC	.	.		0.597	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232		T	36291013	C	T	36291013	3	4	230	1	0	0	0	0	1	0	0	0	12561	768	27	1	76	1	PRODH2	19	36291013	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		36291013	22837970	70	32341										
SIGLEC9	27180	hgsc.bcm.edu	37	chr19	51630327	51630327	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	ggctcatctctgtcactcccAgagggccagtctctgcgcct	10	16	4	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr19:51630327A>G	ENST00000250360.3	+	4	856	c.789A>G	c.(787-789)ccA>ccG	p.P263P	SIGLEC9_ENST00000440804.3_Silent_p.P263P	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	263	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		TGTCACTCCCAGAGGGCCAGT	0.537																																					p.P263P		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.A789G						.						99	97	97					19																	51630327		2203	4300	6503	SO:0001819	synonymous_variant	27180	exon4			ACTCCCAGAGGGC	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.789A>G	chr19.hg19:g.51630327A>G		64.0	0.0		46.0	16.0	NM_001198558	Q6GTU4|Q9BYI9	Silent	SNP	ENST00000250360.3	hg19	CCDS12825.1																																																																																			.	.		0.537	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		G	51630327	A	G	51630327	2	3	230	1	0	0	0	0	0	0	0	1	14330	175	7	2		2	SIGLEC9	19	51630327	Silent	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10	15339314	51630327	7498656	71	32342										
ZNF808	388558	hgsc.bcm.edu	37	chr19	53058362	53058362	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	catcgtagaattcatagtggTgagaaaccttacaagtgtag	10	6	1	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr19:53058362T>A	ENST00000359798.4	+	5	2373	c.2193T>A	c.(2191-2193)ggT>ggA	p.G731G		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	731					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		TTCATAGTGGTGAGAAACCTT	0.433																																					p.G731G		Atlas-SNP	.											.	ZNF808	81	.	0			c.T2193A						.						197	193	194					19																	53058362		2203	4300	6503	SO:0001819	synonymous_variant	388558	exon5			TAGTGGTGAGAAA	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.2193T>A	chr19.hg19:g.53058362T>A		134.0	0.0		95.0	27.0	NM_001039886	Q68CN7	Silent	SNP	ENST00000359798.4	hg19	CCDS46167.1																																																																																			.	.		0.433	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		A	53058362	T	A	53058362	2	1	230	1	0	0	0	0	0	0	0	1	18188	1683	59	4		4	ZNF808	19	53058362	Silent	SNP	T	TCGA-DD-AAVX-01A-11D-A40R-10	1428035	53058362	6070621	72	32343										
SLC2A10	81031	hgsc.bcm.edu	37	chr20	45354676	45354676	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	aagctgtctggctgtgcccaAtgccaccgggcagacaggcc	13	14	1	1			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr20:45354676A>G	ENST00000359271.2	+	2	1251	c.1001A>G	c.(1000-1002)aAt>aGt	p.N334S		NM_030777.3	NP_110404.1	O95528	GTR10_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 10	334					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sugar:proton symporter activity (GO:0005351)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	34		Myeloproliferative disorder(115;0.0122)				GCTGTGCCCAATGCCACCGGG	0.622																																					p.N334S		Atlas-SNP	.											.	SLC2A10	75	.	0			c.A1001G						.						58	54	55					20																	45354676		2203	4300	6503	SO:0001583	missense	81031	exon2			TGCCCAATGCCAC	AL137188	CCDS13402.1	20q13.12	2013-05-22			ENSG00000197496	ENSG00000197496		"Solute carriers"	13444	protein-coding gene	gene with protein product		606145				11247674	Standard	NM_030777		Approved	GLUT10	uc002xsl.3	O95528	OTTHUMG00000032657	ENST00000359271.2:c.1001A>G	chr20.hg19:g.45354676A>G	ENSP00000352216:p.Asn334Ser	34.0	0.0		35.0	11.0	NM_030777	A8K4J6|Q3MIX5|Q9H4I6	Missense_Mutation	SNP	ENST00000359271.2	hg19	CCDS13402.1	.	.	.	.	.	.	.	.	.	.	A	5.952	0.359626	0.11239	.	.	ENSG00000197496	ENST00000359271	T	0.81415	-1.49	5.86	4.7	0.59300	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	7.882870	0.00166	N	0.000000	T	0.65657	0.2712	N	0.08118	0	0.24389	N	0.994754	B	0.22346	0.068	B	0.13407	0.009	T	0.56001	-0.8051	10	0.14656	T	0.56	0.9681	8.8693	0.35305	0.7909:0.1384:0.0707:0.0	.	334	O95528	GTR10_HUMAN	S	334	ENSP00000352216:N334S	ENSP00000352216:N334S	N	+	2	0	SLC2A10	44788083	0.986000	0.35501	0.980000	0.43619	0.410000	0.31052	2.777000	0.47717	2.240000	0.73641	0.533000	0.62120	AAT	.	.		0.622	SLC2A10-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079578.2			G	45354676	A	G	45354676	3	3	230	1	0	0	0	0	1	0	0	0	14554	101	4	2	1007	2	SLC2A10	20	45354676	Missense_Mutation	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10		45354676	17670844	73	32344										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46265302	46265303	+	Nonsense_Mutation	DNP	GG	GG	TT													0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gacggaaatgttgtcaagcaGgagcagctaagtcctaagaa							TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr20:46265302_46265303GG>TT	ENST00000371998.3	+	12	2363_2364	c.2172_2173GG>TT	c.(2170-2175)caGGag>caTTag	p.724_725QE>H*	NCOA3_ENST00000372004.3_Nonsense_Mutation_p.724_725QE>H*|NCOA3_ENST00000341724.6_Nonsense_Mutation_p.734_735QE>H*|NCOA3_ENST00000371997.3_Nonsense_Mutation_p.734_735QE>H*			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	724					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TTGTCAAGCAGGAGCAGCTAAG	0.47																																					p.Q734H|p.E735X		Atlas-SNP	.											.	NCOA3	156	.	0			c.G2202T|c.G2203T						.																																			SO:0001587	stop_gained	8202	exon12			CAAGCAGGAGCAG|AAGCAGGAGCAGC	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	Exception_encountered	chr20.hg19:g.46265302_46265303delinsTT	ENSP00000361066:p.Q724_E725delinsH*	140.0|143.0	0.0		130.0|129.0	39.0|38.0	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.		0.47	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		TT	46265303	GG	TT	46265302	4	4	230	1	0	0	0	0	0	1	0	0	10239	991	35	3	2240	3	NCOA3	20	46265302	Nonsense_Mutation	DNP	GG	TCGA-DD-AAVX-01A-11D-A40R-10	910626	46265302	16760218	74	32345										
SEPT5	5413	hgsc.bcm.edu	37	chr22	19707954	19707954	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	cgagtgcactgctgcctataCttcatctcccccttcgggca	8	16	2	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr22:19707954C>T	ENST00000455784.2	+	6	599	c.474C>T	c.(472-474)taC>taT	p.Y158Y	SEPT5_ENST00000383045.3_Silent_p.Y167Y|GP1BB_ENST00000366425.3_5'Flank|SEPT5_ENST00000438754.2_Silent_p.Y167Y|SEPT5_ENST00000406395.1_Silent_p.Y158Y	NM_002688.5	NP_002679.2	Q99719	SEPT5_HUMAN	septin 5	158	Septin-type G.				cytokinesis (GO:0000910)|GTP catabolic process (GO:0006184)|regulation of exocytosis (GO:0017157)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic vesicle targeting (GO:0016080)	plasma membrane (GO:0005886)|septin complex (GO:0031105)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			lung(1)|upper_aerodigestive_tract(1)	2	Colorectal(54;0.0993)					GCTGCCTATACTTCATCTCCC	0.592																																					p.Y167Y		Atlas-SNP	.											.	SEPT5	32	.	0			c.C501T						.						112	107	108					22																	19707954		2203	4298	6501	SO:0001819	synonymous_variant	5413	exon5			CCTATACTTCATC	Y11593	CCDS13764.1, CCDS56224.1	22q11.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000184702	ENSG00000184702		"Septins"	9164	protein-coding gene	gene with protein product		602724	"peanut-like 1 (Drosophila)"	PNUTL1		9385360, 9611266	Standard	NM_002688		Approved	HCDCREL-1, H5		Q99719	OTTHUMG00000150399	ENST00000455784.2:c.474C>T	chr22.hg19:g.19707954C>T		99.0	0.0		79.0	24.0	NM_001009939	O15251|Q96MY5	Silent	SNP	ENST00000455784.2	hg19	CCDS13764.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.379782	0.24944	.	.	ENSG00000184702	ENST00000413258	.	.	.	3.6	1.45	0.22620	.	.	.	.	.	T	0.55673	0.1935	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47446	-0.9117	4	.	.	.	.	8.1217	0.30976	0.0:0.7258:0.0:0.2742	.	.	.	.	F	55	.	.	L	+	1	0	SEPT5	18087954	1.000000	0.71417	0.993000	0.49108	0.957000	0.61999	0.864000	0.27926	0.322000	0.23283	0.313000	0.20887	CTT	.	.		0.592	SEPT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317937.1	NM_002688		T	19707954	C	T	19707954	2	4	230	1	0	0	0	0	0	0	0	1	14082	576	20	3		3	SEPT5	22	19707954	Silent	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10		19707954	31596612	75	32346										
ZNF280B	140883	hgsc.bcm.edu	37	chr22	22842882	22842882	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	agtcactaagtaacacaatgGgattttctttcttgggatca	8	7	4	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr22:22842882G>A	ENST00000406426.1	-	4	1584	c.842C>T	c.(841-843)cCc>cTc	p.P281L	ZNF280B_ENST00000360412.2_Missense_Mutation_p.P281L			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	281					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TAACACAATGGGATTTTCTTT	0.388																																					p.P281L		Atlas-SNP	.											.	ZNF280B	67	.	0			c.C842T						.						119	111	114					22																	22842882		2203	4300	6503	SO:0001583	missense	140883	exon4			ACAATGGGATTTT	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"zinc finger protein 279", "suppressor of hairy wing homolog 2 (Drosophila)"	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.842C>T	chr22.hg19:g.22842882G>A	ENSP00000385998:p.Pro281Leu	96.0	0.0		71.0	35.0	NM_080764		Missense_Mutation	SNP	ENST00000406426.1	hg19	CCDS13799.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.642443	0.00112	.	.	ENSG00000198477	ENST00000406426;ENST00000360412	T;T	0.02216	4.39;4.39	4.43	2.14	0.27477	.	.	.	.	.	T	0.00552	0.0018	N	0.00186	-1.895	0.34395	D	0.69463	B	0.02656	0.0	B	0.01281	0.0	T	0.34551	-0.9824	9	0.02654	T	1	-0.7367	4.5432	0.12067	0.7234:0.0:0.1044:0.1722	.	281	Q86YH2	Z280B_HUMAN	L	281	ENSP00000385998:P281L;ENSP00000353586:P281L	ENSP00000353586:P281L	P	-	2	0	ZNF280B	21172882	1.000000	0.71417	0.010000	0.14722	0.076000	0.17211	2.654000	0.46699	0.860000	0.35481	-0.302000	0.09304	CCC	.	.		0.388	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764		A	22842882	G	A	22842882	3	1	230	1	0	0	0	0	1	0	0	0	17830	1232	43	3	793	3	ZNF280B	22	22842882	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	3134928	22842882	28461684	76	32347										
MPPED1	758	hgsc.bcm.edu	37	chr22	43870642	43870642	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	tgccctacgagtacaagatcGtgatcgcaggcaaccacgag	11	12	0	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chr22:43870642G>C	ENST00000417669.2	+	4	877	c.433G>C	c.(433-435)Gtg>Ctg	p.V145L	MPPED1_ENST00000443721.1_Missense_Mutation_p.V145L|MPPED1_ENST00000542779.1_Missense_Mutation_p.V145L|MPPED1_ENST00000538182.1_Missense_Mutation_p.V178L|MPPED1_ENST00000439548.1_5'UTR|MPPED1_ENST00000414469.2_Missense_Mutation_p.V39L			O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1	145							hydrolase activity (GO:0016787)			endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|skin(1)	13		all_neural(38;0.0244)|Ovarian(80;0.0694)				GTACAAGATCGTGATCGCAGG	0.567																																					p.V145L		Atlas-SNP	.											.	MPPED1	59	.	0			c.G433C						.						119	121	121					22																	43870642		2115	4252	6367	SO:0001583	missense	758	exon4			AAGATCGTGATCG	U84894	CCDS46723.1	22q13.2	2013-09-20	2005-10-10	2005-10-10	ENSG00000186732	ENSG00000186732			1306	protein-coding gene	gene with protein product		602112	"chromosome 22 open reading frame 1"	C22orf1		9266672, 10591208	Standard	NM_001044370		Approved	239AB, FAM1A	uc011apv.2	O15442	OTTHUMG00000150566	ENST00000417669.2:c.433G>C	chr22.hg19:g.43870642G>C	ENSP00000388137:p.Val145Leu	54.0	0.0		50.0	23.0	NM_001044370	A8K159|B7Z2S9|Q8N361	Missense_Mutation	SNP	ENST00000417669.2	hg19	CCDS46723.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.980655	0.92982	.	.	ENSG00000186732	ENST00000417669;ENST00000443721;ENST00000545165;ENST00000414469;ENST00000542779;ENST00000538182	T;T;D;T;T	0.83755	0.77;0.77;-1.76;0.77;0.77	5.08	5.08	0.68730	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	D	0.86003	0.5829	M	0.64567	1.98	0.80722	D	1	D;P	0.53619	0.961;0.895	P;P	0.50136	0.632;0.632	D	0.86675	0.1913	10	0.48119	T	0.1	-35.2044	18.5263	0.90974	0.0:0.0:1.0:0.0	.	178;145	B7Z2S9;O15442	.;MPPD1_HUMAN	L	145;145;123;39;145;178	ENSP00000388137:V145L;ENSP00000400686:V145L;ENSP00000388245:V39L;ENSP00000444532:V145L;ENSP00000438335:V178L	ENSP00000388245:V39L	V	+	1	0	MPPED1	42200586	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	9.457000	0.97630	2.365000	0.80145	0.551000	0.68910	GTG	.	.		0.567	MPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318938.2	NM_001044370		C	43870642	G	C	43870642	3	2	230	1	0	0	0	0	1	0	0	0	9750	1145	40	4	443	4	MPPED1	22	43870642	Missense_Mutation	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	21027760	43870642	7433924	77	32348										
WNK3	65267	hgsc.bcm.edu	37	chrX	54321102	54321102	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gctgagcgggagcaaggggtAaagttgtattctggggctga	18	5	1	2			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chrX:54321102A>G	ENST00000375159.2	-	7	1576	c.1577T>C	c.(1576-1578)tTa>tCa	p.L526S	WNK3_ENST00000354646.2_Missense_Mutation_p.L526S|WNK3_ENST00000375169.3_Missense_Mutation_p.L526S			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	526					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AGCAAGGGGTAAAGTTGTATT	0.473																																					p.L526S		Atlas-SNP	.											.	WNK3	218	.	0			c.T1577C						.						84	73	77					X																	54321102		2203	4300	6503	SO:0001583	missense	65267	exon8			AGGGGTAAAGTTG	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.1577T>C	chrX.hg19:g.54321102A>G	ENSP00000364301:p.Leu526Ser	42.0	0.0		43.0	27.0	NM_001002838	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	hg19	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	A	0.909	-0.719772	0.03182	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.71222	-0.53;-0.55;-0.55	3.66	2.5	0.30297	.	0.420263	0.17020	N	0.190176	T	0.53029	0.1771	L	0.32530	0.975	0.09310	N	1	B;B	0.29085	0.232;0.069	B;B	0.30251	0.113;0.053	T	0.33214	-0.9877	10	0.15499	T	0.54	0.0899	5.8579	0.18730	0.7614:0.0:0.2386:0.0	.	526;526	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	S	526	ENSP00000364312:L526S;ENSP00000346667:L526S;ENSP00000364301:L526S	ENSP00000346667:L526S	L	-	2	0	WNK3	54337827	0.012000	0.17670	0.017000	0.16124	0.464000	0.32679	1.405000	0.34635	0.603000	0.29913	0.481000	0.45027	TTA	.	.		0.473	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		G	54321102	A	G	54321102	3	3	230	1	0	0	0	0	1	0	0	0	17394	372	13	2	3893	2	WNK3	23	54321102	Missense_Mutation	SNP	A	TCGA-DD-AAVX-01A-11D-A40R-10		54321102	100949458	78	32349										
AVPR2	554	hgsc.bcm.edu	37	chrX	153171432	153171432	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	gaagtggggctcactggaacCggccggtgctagtggcttgg	18	9	1	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chrX:153171432C>T	ENST00000358927.2	+	3	681	c.472C>T	c.(472-474)Cgg>Tgg	p.R158W	AVPR2_ENST00000370049.1_Missense_Mutation_p.R158W|AVPR2_ENST00000337474.5_Missense_Mutation_p.R158W			P30518	V2R_HUMAN	arginine vasopressin receptor 2	158					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|excretion (GO:0007588)|hemostasis (GO:0007599)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-gamma production (GO:0032609)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of systemic arterial blood pressure (GO:0003084)|response to cytokine (GO:0034097)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	vasopressin receptor activity (GO:0005000)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	26	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Conivaptan(DB00872)|Desmopressin(DB00035)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	TCACTGGAACCGGCCGGTGCT	0.647																																					p.R158W		Atlas-SNP	.											.	AVPR2	43	.	0			c.C472T						.						60	45	50					X																	153171432		2203	4300	6503	SO:0001583	missense	554	exon2			TGGAACCGGCCGG	Z11687	CCDS14735.1, CCDS55539.1	Xq28	2014-09-17	2008-08-01		ENSG00000126895	ENSG00000126895		"GPCR / Class A : Vasopressin and oxytocin receptors"	897	protein-coding gene	gene with protein product	"nephrogenic diabetes insipidus"	300538		DIR3, DIR		1324225	Standard	NM_000054		Approved	V2R	uc004fjh.4	P30518	OTTHUMG00000024227	ENST00000358927.2:c.472C>T	chrX.hg19:g.153171432C>T	ENSP00000351805:p.Arg158Trp	18.0	0.0		16.0	12.0	NM_001146151	C5HF20|O43192|Q3MJD3|Q9UCV9	Missense_Mutation	SNP	ENST00000358927.2	hg19	CCDS14735.1	.	.	.	.	.	.	.	.	.	.	C	12.26	1.883490	0.33255	.	.	ENSG00000126895	ENST00000358927;ENST00000430697;ENST00000337474;ENST00000370049	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	3.54	1.36	0.22044	GPCR, rhodopsin-like superfamily (1);	0.514798	0.19600	N	0.110416	T	0.76449	0.3989	M	0.72894	2.215	0.34355	D	0.690286	D;D	0.69078	0.997;0.996	P;P	0.58970	0.764;0.849	T	0.79315	-0.1854	10	0.37606	T	0.19	-19.1325	9.3327	0.38032	0.5202:0.4797:0.0:0.0	.	158;158	P30518-2;P30518	.;V2R_HUMAN	W	158	ENSP00000351805:R158W;ENSP00000393513:R158W;ENSP00000338072:R158W;ENSP00000359066:R158W	ENSP00000338072:R158W	R	+	1	2	AVPR2	152824626	0.021000	0.18746	1.000000	0.80357	0.211000	0.24417	0.176000	0.16782	0.569000	0.29329	0.279000	0.19357	CGG	.	.		0.647	AVPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061127.2			T	153171432	C	T	153171432	3	4	230	1	0	0	0	0	1	0	0	0	1233	643	23	1	478	1	AVPR2	23	153171432	Missense_Mutation	SNP	C	TCGA-DD-AAVX-01A-11D-A40R-10	98850330	153171432	2099128	79	32350										
PLXNA3	55558	hgsc.bcm.edu	37	chrX	153691734	153691734	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0506329113924051	4	1	0.84984520123839	3.02757352941176	0.269117647058824	0.559440559440559	1	0	aggctggtcttgtggctcagGtgcgggtcgatggcttccag	17	9	2	0			TCGA-DD-AAVX-01A-11D-A40R-10	TCGA-DD-AAVX-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e8170e1d-9a50-4822-84ec-8750c4a174cb	65b44904-6523-4508-b745-d3af723355fc	g.chrX:153691734G>T	ENST00000369682.3	+	5	1493	c.1318G>T	c.(1318-1320)Gtg>Ttg	p.V440L		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	440	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGTGGCTCAGGTGCGGGTCGA	0.617																																					p.V440L		Atlas-SNP	.											.	PLXNA3	156	.	0			c.G1318T						.						142	133	136					X																	153691734		2203	4300	6503	SO:0001630	splice_region_variant	55558	exon5			GCTCAGGTGCGGG	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"Plexins"	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.1318-1G>T	chrX.hg19:g.153691734G>T		36.0	0.0		33.0	21.0	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	hg19	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650243	0.47362	.	.	ENSG00000130827	ENST00000369682	T	0.07327	3.2	4.8	4.8	0.61643	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.059469	0.64402	D	0.000003	T	0.12603	0.0306	M	0.80982	2.52	0.44627	D	0.997609	B	0.06786	0.001	B	0.15484	0.013	T	0.03051	-1.1078	9	.	.	.	.	9.5302	0.39189	0.1003:0.0:0.8997:0.0	.	440	P51805	PLXA3_HUMAN	L	440	ENSP00000358696:V440L	.	V	+	1	0	PLXNA3	153344928	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	3.760000	0.55235	2.229000	0.72834	0.525000	0.51046	GTG	.	.		0.617	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	Missense_Mutation	T	153691734	G	T	153691734	5	4	230	1	0	0	0	0	0	0	1	0	12130	1275	44	3	1332	3	PLXNA3	23	153691734	Splice_Site	SNP	G	TCGA-DD-AAVX-01A-11D-A40R-10	520302	153691734	1578826	80	32351										
MIB2	142678	hgsc.bcm.edu	37	chr1	1560565	1560565	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggaccacctcccaaggctcGgtatgaggctgtcacactga	11	13	1	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr1:1560565G>C	ENST00000357210.4	+	6	1111	c.895G>C	c.(895-897)Ggc>Cgc	p.G299R	MIB2_ENST00000505820.2_Splice_Site_p.G356R|MIB2_ENST00000520777.1_Splice_Site_p.G356R|MIB2_ENST00000360522.4_Splice_Site_p.G299R|MIB2_ENST00000378710.3_Splice_Site_p.G299R|MIB2_ENST00000378708.1_Splice_Site_p.G241R|MIB2_ENST00000378712.1_Intron|MIB2_ENST00000504599.1_Splice_Site_p.G255R|MIB2_ENST00000355826.5_Splice_Site_p.G342R|MIB2_ENST00000518681.1_Intron	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	299					Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CCCAAGGCTCGGTATGAGGCT	0.642																																					p.G356R		Atlas-SNP	.											.	MIB2	62	.	0			c.G1066C						.						54	59	57					1																	1560565		2193	4285	6478	SO:0001630	splice_region_variant	142678	exon6			AGGCTCGGTATGA	AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	30577	protein-coding gene	gene with protein product		611141	"zinc finger, ZZ type with ankyrin repeat domain 1", "mindbomb homolog 2 (Drosophila)"	ZZANK1		12761501	Standard	NM_080875		Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000357210.4:c.895+1G>C	chr1.hg19:g.1560565G>C		39.0	0.0		36.0	17.0	NM_001170686	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	Missense_Mutation	SNP	ENST00000357210.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.62|19.62	3.862378|3.862378	0.71949|0.71949	.|.	.|.	ENSG00000197530|ENSG00000197530	ENST00000520777;ENST00000357210;ENST00000360522;ENST00000378710;ENST00000355826;ENST00000505820;ENST00000504599;ENST00000378708|ENST00000514234	T;T;T;T;T;T;T;T|.	0.53857|.	0.6;0.65;0.71;0.7;0.64;0.6;0.68;0.76|.	4.74|4.74	4.74|4.74	0.60224|0.60224	.|.	0.057194|.	0.64402|.	D|.	0.000001|.	T|T	0.74199|0.74199	0.3685|0.3685	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	D;D;P;P|.	0.76494|.	0.999;0.968;0.953;0.947|.	D;P;P;D|.	0.70487|.	0.969;0.773;0.825;0.933|.	T|T	0.75016|0.75016	-0.3466|-0.3466	10|5	0.87932|.	D|.	0|.	-31.4742|-31.4742	16.6859|16.6859	0.85306|0.85306	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	299;356;285;299|.	Q96AX9-5;E9PGU1;Q96AX9-2;Q96AX9|.	.;.;.;MIB2_HUMAN|.	R|P	356;299;299;299;342;356;255;241|149	ENSP00000428660:G356R;ENSP00000349741:G299R;ENSP00000353713:G299R;ENSP00000367982:G299R;ENSP00000348081:G342R;ENSP00000426103:G356R;ENSP00000426128:G255R;ENSP00000367980:G241R|.	ENSP00000348081:G342R|.	G|R	+|+	1|2	0|0	MIB2|MIB2	1550428|1550428	1.000000|1.000000	0.71417|0.71417	0.731000|0.731000	0.30826|0.30826	0.320000|0.320000	0.28249|0.28249	9.327000|9.327000	0.96396|0.96396	2.180000|2.180000	0.69256|0.69256	0.455000|0.455000	0.32223|0.32223	GGC|CGG	.	.		0.642	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875	Missense_Mutation	C	1560565	G	C	1560565	5	2	231	1	0	0	0	0	0	0	1	0	9576	1130	39	4	1088	4	MIB2	1	1560565	Splice_Site	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10		1560565	247690056	1	32352										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32133217	32133217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tgacccggtgtagccacgctCccccttgatgccctgacaag	10	16	0	3			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr1:32133217C>T	ENST00000373672.3	-	52	3832	c.3316G>A	c.(3316-3318)Gag>Aag	p.E1106K	COL16A1_ENST00000271069.6_Missense_Mutation_p.E1106K	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1106	Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TAGCCACGCTCCCCCTTGATG	0.622																																					p.E1106K	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.G3316A						.						21	26	25					1																	32133217		2124	4245	6369	SO:0001583	missense	1307	exon52			CACGCTCCCCCTT	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.3316G>A	chr1.hg19:g.32133217C>T	ENSP00000362776:p.Glu1106Lys	119.0	0.0		83.0	41.0	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.847933	0.51164	.	.	ENSG00000084636	ENST00000373672;ENST00000271069	D;D	0.93247	-3.19;-3.19	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	D	0.94594	0.8258	L	0.61036	1.89	0.40248	D	0.978037	D;D	0.67145	0.993;0.996	D;D	0.73708	0.956;0.981	D	0.92248	0.5806	10	0.07030	T	0.85	.	13.4522	0.61178	0.0:1.0:0.0:0.0	.	1106;1105	Q07092;Q07092-2	COGA1_HUMAN;.	K	1106	ENSP00000362776:E1106K;ENSP00000271069:E1106K	ENSP00000271069:E1106K	E	-	1	0	COL16A1	31905804	0.042000	0.20092	0.624000	0.29186	0.566000	0.35808	1.102000	0.31050	2.323000	0.78572	0.563000	0.77884	GAG	.	.		0.622	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		T	32133217	C	T	32133217	3	4	231	1	0	0	0	0	1	0	0	0	3675	864	30	3	1578	3	COL16A1	1	32133217	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	30572652	32133217	217117404	2	32353										
ZBTB7B	51043	hgsc.bcm.edu	37	chr1	154987493	154987493	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	accagcagcgccaacatgccAgctgtgctccaggctgcccg	11	17	0	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr1:154987493A>G	ENST00000368426.3	+	3	494	c.357A>G	c.(355-357)ccA>ccG	p.P119P	ZBTB7B_ENST00000417934.2_Silent_p.P153P|ZBTB7B_ENST00000487542.1_3'UTR|ZBTB7B_ENST00000535420.1_Silent_p.P119P|ZBTB7B_ENST00000292176.2_Silent_p.P119P	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	119					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CCAACATGCCAGCTGTGCTCC	0.617																																					p.P153P		Atlas-SNP	.											.	ZBTB7B	69	.	0			c.A459G						.						34	38	37					1																	154987493		2203	4300	6503	SO:0001819	synonymous_variant	51043	exon4			CATGCCAGCTGTG	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	18668	protein-coding gene	gene with protein product	"zinc finger and BTB domain containing 15"	607646	"zinc finger protein 67 homolog (mouse)"	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.357A>G	chr1.hg19:g.154987493A>G		76.0	0.0		125.0	38.0	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Silent	SNP	ENST00000368426.3	hg19	CCDS1081.1																																																																																			.	.		0.617	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872		G	154987493	A	G	154987493	2	3	231	1	0	0	0	0	0	0	0	1	17569	175	7	2		2	ZBTB7B	1	154987493	Silent	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	122854276	154987493	94263128	3	32354										
GPR37L1	9283	hgsc.bcm.edu	37	chr1	202097337	202097337	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccgtggtgggcctgaccgtgGtctacgccttctgcaccctc	12	16	2	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr1:202097337G>A	ENST00000367282.5	+	2	1205	c.1099G>A	c.(1099-1101)Gtc>Atc	p.V367I		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	367					negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.V367F(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						CCTGACCGTGGTCTACGCCTT	0.652																																					p.V367I		Atlas-SNP	.											GPR37L1,NS,carcinoma,0,1	GPR37L1	33	.	1	Substitution - Missense(1)	lung(1)	c.G1099A						.						149	132	138					1																	202097337		2203	4300	6503	SO:0001583	missense	9283	exon2			ACCGTGGTCTACG	AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"GPCR / Class A : Orphans"	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.1099G>A	chr1.hg19:g.202097337G>A	ENSP00000356251:p.Val367Ile	62.0	0.0		104.0	56.0	NM_004767	B2R7M9|Q5SXP7|Q86VP7	Missense_Mutation	SNP	ENST00000367282.5	hg19	CCDS1420.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.472533	0.43942	.	.	ENSG00000170075	ENST00000541334;ENST00000367282	T	0.75154	-0.91	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.133801	0.50627	D	0.000120	T	0.59528	0.2200	N	0.17474	0.49	0.44547	D	0.9975	B	0.31893	0.345	B	0.39119	0.291	T	0.55147	-0.8186	10	0.12430	T	0.62	-48.8695	9.9678	0.41734	0.1256:0.0:0.8744:0.0	.	367	O60883	ETBR2_HUMAN	I	234;367	ENSP00000356251:V367I	ENSP00000356251:V367I	V	+	1	0	GPR37L1	200363960	0.775000	0.28604	0.999000	0.59377	0.920000	0.55202	0.799000	0.27028	2.437000	0.82529	0.561000	0.74099	GTC	.	.		0.652	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2	NM_004767		A	202097337	G	A	202097337	3	1	231	1	0	0	0	0	1	0	0	0	6700	1261	44	3	1105	3	GPR37L1	1	202097337	Missense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	47109844	202097337	47153284	4	32355										
SLC41A1	254428	hgsc.bcm.edu	37	chr1	205764544	205764544	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agagttctctccgggcattcCattcatgtgcaggaaggtgg	13	9	2	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr1:205764544C>T	ENST00000367137.3	-	9	2149	c.1135G>A	c.(1135-1137)Gga>Aga	p.G379R	SLC41A1_ENST00000468057.1_5'UTR	NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	379					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	17	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			CCGGGCATTCCATTCATGTGC	0.592																																					p.G379R		Atlas-SNP	.											.	SLC41A1	46	.	0			c.G1135A						.						78	64	69					1																	205764544		2203	4300	6503	SO:0001583	missense	254428	exon9			GCATTCCATTCAT	AJ514402	CCDS30988.1	1q32.1	2013-07-17	2013-07-17		ENSG00000133065	ENSG00000133065		"Solute carriers"	19429	protein-coding gene	gene with protein product		610801				12810078, 18367447	Standard	NM_173854		Approved	MgtE	uc001hdh.1	Q8IVJ1	OTTHUMG00000036000	ENST00000367137.3:c.1135G>A	chr1.hg19:g.205764544C>T	ENSP00000356105:p.Gly379Arg	155.0	0.0		247.0	48.0	NM_173854	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Missense_Mutation	SNP	ENST00000367137.3	hg19	CCDS30988.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.641874	0.47153	.	.	ENSG00000133065	ENST00000367137	T	0.28666	1.6	5.35	4.44	0.53790	MgtE magnesium transporter, integral membrane (1);	0.053284	0.85682	D	0.000000	T	0.26048	0.0635	L	0.40543	1.245	0.53688	D	0.999979	B	0.29270	0.24	B	0.35727	0.209	T	0.04900	-1.0919	10	0.17832	T	0.49	-2.0629	10.1077	0.42544	0.0:0.846:0.0:0.154	.	379	Q8IVJ1	S41A1_HUMAN	R	379	ENSP00000356105:G379R	ENSP00000356105:G379R	G	-	1	0	SLC41A1	204031167	1.000000	0.71417	0.925000	0.36789	0.008000	0.06430	5.620000	0.67736	1.489000	0.48450	-0.140000	0.14226	GGA	.	.		0.592	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1			T	205764544	C	T	205764544	3	4	231	1	0	0	0	0	1	0	0	0	14644	603	21	3	418	3	SLC41A1	1	205764544	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	3667207	205764544	43486077	5	32356										
USH2A	7399	hgsc.bcm.edu	37	chr1	215914870	215914870	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caaacatcctactgctaactCcacaacttccttgaaaaaaa	2	13	0	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr1:215914870C>A	ENST00000307340.3	-	60	11944	c.11558G>T	c.(11557-11559)gGa>gTa	p.G3853V	USH2A_ENST00000366943.2_Missense_Mutation_p.G3853V	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3853	Fibronectin type-III 23. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACTGCTAACTCCACAACTTCC	0.358										HNSCC(13;0.011)																											p.G3853V		Atlas-SNP	.											.	USH2A	1168	.	0			c.G11558T						.						73	76	75					1																	215914870		2203	4300	6503	SO:0001583	missense	7399	exon60			CTAACTCCACAAC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.11558G>T	chr1.hg19:g.215914870C>A	ENSP00000305941:p.Gly3853Val	87.0	0.0		117.0	35.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.620019	0.46736	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.63744	-0.06;-0.06	5.38	4.47	0.54385	Fibronectin, type III (5);Immunoglobulin-like fold (1);	0.000000	0.43919	D	0.000511	T	0.78654	0.4317	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81940	-0.0703	10	0.87932	D	0	.	13.8693	0.63608	0.0:0.9278:0.0:0.0722	.	3853	O75445	USH2A_HUMAN	V	3853	ENSP00000305941:G3853V;ENSP00000355910:G3853V	ENSP00000305941:G3853V	G	-	2	0	USH2A	213981493	1.000000	0.71417	1.000000	0.80357	0.433000	0.31745	4.286000	0.58995	1.502000	0.48669	0.655000	0.94253	GGA	.	.		0.358	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	215914870	C	A	215914870	3	1	231	1	0	0	0	0	1	0	0	0	17051	855	30	3	4102	3	USH2A	1	215914870	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	10150326	215914870	33335751	6	32357										
GEMIN6	79833	hgsc.bcm.edu	37	chr2	39006178	39006178	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccttagaatggcaagattacAtttacaaagaggtccgagtg	10	7	0	3			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr2:39006178A>G	ENST00000281950.3	+	2	162	c.46A>G	c.(46-48)Att>Gtt	p.I16V	GEMIN6_ENST00000409011.1_Missense_Mutation_p.I16V|GEMIN6_ENST00000409566.1_Missense_Mutation_p.I16V	NM_024775.9	NP_079051.9	Q8WXD5	GEMI6_HUMAN	gem (nuclear organelle) associated protein 6	16					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				kidney(1)|large_intestine(3)|pancreas(1)	5		all_hematologic(82;0.21)				GCAAGATTACATTTACAAAGA	0.433																																					p.I16V		Atlas-SNP	.											.	GEMIN6	13	.	0			c.A46G						.						138	135	136					2																	39006178		2203	4300	6503	SO:0001583	missense	79833	exon2			GATTACATTTACA	AF453443	CCDS1799.1	2p22.1	2014-05-14			ENSG00000152147	ENSG00000152147			20044	protein-coding gene	gene with protein product		607006				11748230	Standard	NM_024775		Approved	FLJ23459	uc002rrc.3	Q8WXD5	OTTHUMG00000128588	ENST00000281950.3:c.46A>G	chr2.hg19:g.39006178A>G	ENSP00000281950:p.Ile16Val	188.0	0.0		145.0	70.0	NM_024775	B2RDP8|Q53SI5|Q8WVB4|Q9H5G6	Missense_Mutation	SNP	ENST00000281950.3	hg19	CCDS1799.1	.	.	.	.	.	.	.	.	.	.	A	2.942	-0.218659	0.06101	.	.	ENSG00000152147	ENST00000409011;ENST00000281950;ENST00000409566	T;T;T	0.37584	1.19;1.19;1.19	5.01	-1.72	0.08107	.	0.546567	0.18981	N	0.125871	T	0.06826	0.0174	N	0.00325	-1.645	0.21675	N	0.999594	B	0.02656	0.0	B	0.04013	0.001	T	0.41805	-0.9488	10	0.02654	T	1	-0.4869	8.6224	0.33868	0.1972:0.0:0.6543:0.1484	.	16	Q8WXD5	GEMI6_HUMAN	V	16	ENSP00000387191:I16V;ENSP00000281950:I16V;ENSP00000386613:I16V	ENSP00000281950:I16V	I	+	1	0	GEMIN6	38859682	0.421000	0.25465	0.992000	0.48379	0.987000	0.75469	0.186000	0.16978	-0.155000	0.11098	-0.256000	0.11100	ATT	.	.		0.433	GEMIN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250441.3			G	39006178	A	G	39006178	3	3	231	1	0	0	0	0	1	0	0	0	6340	217	8	2	48	2	GEMIN6	2	39006178	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10		39006178	204193195	7	32358										
SLC35F5	80255	hgsc.bcm.edu	37	chr2	114500441	114500441	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgatattactgaacctcacaCgagactttttgggggcttaa	9	8	1	3			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr2:114500441C>A	ENST00000245680.2	-	7	991	c.578G>T	c.(577-579)cGt>cTt	p.R193L	SLC35F5_ENST00000409342.1_Missense_Mutation_p.R187L	NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	193					transport (GO:0006810)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						GAACCTCACACGAGACTTTTT	0.353																																					p.R193L		Atlas-SNP	.											.	SLC35F5	60	.	0			c.G578T						.						102	94	97					2																	114500441		2203	4300	6503	SO:0001583	missense	80255	exon7			CTCACACGAGACT	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"Solute carriers"	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.578G>T	chr2.hg19:g.114500441C>A	ENSP00000245680:p.Arg193Leu	86.0	0.0		52.0	18.0	NM_025181	Q9H6P8|Q9H7D8	Missense_Mutation	SNP	ENST00000245680.2	hg19	CCDS2119.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.622275	0.87460	.	.	ENSG00000115084	ENST00000245680;ENST00000409106;ENST00000409342	T;T	0.50277	0.75;0.76	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.57829	0.2080	L	0.34521	1.04	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.993	D;D;D	0.81914	0.995;0.986;0.982	T	0.49952	-0.8884	10	0.23302	T	0.38	-2.6917	18.5881	0.91197	0.0:1.0:0.0:0.0	.	193;187;193	B2RDY0;B8ZZV6;Q8WV83	.;.;S35F5_HUMAN	L	193;187;187	ENSP00000245680:R193L;ENSP00000386754:R187L	ENSP00000245680:R193L	R	-	2	0	SLC35F5	114216911	1.000000	0.71417	0.998000	0.56505	0.676000	0.39594	7.010000	0.76353	2.692000	0.91855	0.655000	0.94253	CGT	.	.		0.353	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181		A	114500441	C	A	114500441	3	1	231	1	0	0	0	0	1	0	0	0	14607	536	19	1	1029	1	SLC35F5	2	114500441	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	75494263	114500441	128698932	8	32359										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098804	178098804	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgaattgggagaaattcacCtgtctcttcatctagttgta	8	8	4	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr2:178098804C>G	ENST00000397062.3	-	2	795	c.241G>C	c.(241-243)Ggt>Cgt	p.G81R	NFE2L2_ENST00000464747.1_Missense_Mutation_p.G65R|NFE2L2_ENST00000423513.1_Missense_Mutation_p.G65R|NFE2L2_ENST00000446151.2_Missense_Mutation_p.G65R|NFE2L2_ENST00000397063.4_Missense_Mutation_p.G65R	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	81					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G81S(2)|p.G81_F83delGEF(1)|p.G81C(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AGAAATTCACCTGTCTCTTCA	0.438			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.G81R		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,0,4	NFE2L2	225	.	4	Substitution - Missense(3)|Deletion - In frame(1)	lung(2)|liver(1)|endometrium(1)	c.G241C						.						143	142	142					2																	178098804		1901	4105	6006	SO:0001583	missense	4780	exon2			ATTCACCTGTCTC		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.241G>C	chr2.hg19:g.178098804C>G	ENSP00000380252:p.Gly81Arg	83.0	0.0		51.0	28.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.1|20.1	3.933163|3.933163	0.73442|0.73442	.|.	.|.	ENSG00000116044|ENSG00000116044	ENST00000449627|ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	T|T;T;T;T;T;T	0.27890|0.52983	1.64|1.2;1.2;1.2;0.64;0.64;1.2	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75110|0.75110	0.3805|0.3805	M|M	0.87180|0.87180	2.865|2.865	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.999;0.999;1.0;0.999	T|T	0.78563|0.78563	-0.2156|-0.2156	7|10	0.18710|0.87932	T|D	0.47|0	.|.	19.9976|19.9976	0.97389|0.97389	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|65;65;65;81	.|E9PGJ7;B4DNB0;C9JFL6;Q16236	.|.;.;.;NF2L2_HUMAN	P|R	65|65;81;65;65;65;65	ENSP00000391590:A65P|ENSP00000380253:G65R;ENSP00000380252:G81R;ENSP00000411575:G65R;ENSP00000400073:G65R;ENSP00000412191:G65R;ENSP00000410015:G65R	ENSP00000391590:A65P|ENSP00000380252:G81R	A|G	-|-	1|1	0|0	NFE2L2|NFE2L2	177807050|177807050	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.995000|0.995000	0.86356|0.86356	7.298000|7.298000	0.78815|0.78815	2.737000|2.737000	0.93849|0.93849	0.563000|0.563000	0.77884|0.77884	GCA|GGT	.	.		0.438	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		G	178098804	C	G	178098804	3	3	231	1	0	0	0	0	1	0	0	0	10377	681	24	4	1592	4	NFE2L2	2	178098804	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	63598363	178098804	65100569	9	32360										
SLC39A10	57181	hgsc.bcm.edu	37	chr2	196573489	196573489	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgatgctgtattgaaaggacTtgttgctctaggaggcattt	12	5	1	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr2:196573489T>G	ENST00000409086.3	+	5	1771	c.1496T>G	c.(1495-1497)cTt>cGt	p.L499R	SLC39A10_ENST00000541054.1_Missense_Mutation_p.L49R|SLC39A10_ENST00000359634.5_Missense_Mutation_p.L499R	NM_001127257.1	NP_001120729.1	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter), member 10	499					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(16)|pancreas(1)|prostate(1)|skin(2)	34			OV - Ovarian serous cystadenocarcinoma(117;0.221)			TTGAAAGGACTTGTTGCTCTA	0.348																																					p.L499R		Atlas-SNP	.											.	SLC39A10	89	.	0			c.T1496G						.						121	111	114					2																	196573489		2203	4300	6503	SO:0001583	missense	57181	exon5			AAGGACTTGTTGC		CCDS33353.1	2q33.1	2013-05-22			ENSG00000196950	ENSG00000196950		"Solute carriers"	20861	protein-coding gene	gene with protein product		608733	"solute carrier family 39 (metal ion transporter), member 10"			12659941	Standard	NM_020342		Approved	KIAA1265, FLJ90515, DKFZp564L2123	uc002utg.4	Q9ULF5	OTTHUMG00000154380	ENST00000409086.3:c.1496T>G	chr2.hg19:g.196573489T>G	ENSP00000386766:p.Leu499Arg	141.0	0.0		114.0	18.0	NM_020342	A8K5C6|B4DGU0|Q3MJA4|Q68CR5|Q6DKH6|Q9Y3Z1	Missense_Mutation	SNP	ENST00000409086.3	hg19	CCDS33353.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.468444	0.84533	.	.	ENSG00000196950	ENST00000409086;ENST00000359634;ENST00000541054	T;T;T	0.57752	0.38;0.38;0.38	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.74321	0.3701	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79212	-0.1896	10	0.87932	D	0	.	14.9168	0.70805	0.0:0.0:0.0:1.0	.	499	Q9ULF5	S39AA_HUMAN	R	499;499;49	ENSP00000386766:L499R;ENSP00000352655:L499R;ENSP00000437787:L49R	ENSP00000352655:L499R	L	+	2	0	SLC39A10	196281734	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.819000	0.86621	2.124000	0.65301	0.528000	0.53228	CTT	.	.		0.348	SLC39A10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335186.1	XM_047707		G	196573489	T	G	196573489	3	3	231	1	0	0	0	0	1	0	0	0	14628	1609	56	5	1510	5	SLC39A10	2	196573489	Missense_Mutation	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	18474685	196573489	46625884	10	32361										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	203996824	203996824	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cttgttaatacttctcttatTaaaaacctcacccatcaaat	1	11	3	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr2:203996824T>G	ENST00000449802.1	+	25	3939	c.3606T>G	c.(3604-3606)atT>atG	p.I1202M		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1202										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						CTTCTCTTATTAAAAACCTCA	0.333																																					p.I1202M		Atlas-SNP	.											.	NBEAL1	266	.	0			c.T3606G						.						103	89	93					2																	203996824		692	1591	2283	SO:0001583	missense	65065	exon25			TCTTATTAAAAAC	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.3606T>G	chr2.hg19:g.203996824T>G	ENSP00000399903:p.Ile1202Met	347.0	0.0		233.0	108.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	T	12.98	2.100680	0.37048	.	.	ENSG00000144426	ENST00000449802;ENST00000340268	T	0.56941	0.43	5.09	-1.14	0.09741	.	.	.	.	.	T	0.39517	0.1081	L	0.50333	1.59	0.38097	D	0.937143	B	0.32526	0.374	B	0.35470	0.203	T	0.33420	-0.9869	9	0.45353	T	0.12	.	1.8039	0.03076	0.3123:0.0719:0.2448:0.371	.	1202	Q6ZS30	NBEL1_HUMAN	M	1202	ENSP00000399903:I1202M	ENSP00000344985:I1202M	I	+	3	3	NBEAL1	203705069	0.981000	0.34729	0.983000	0.44433	0.765000	0.43378	0.069000	0.14552	-0.013000	0.14199	0.260000	0.18958	ATT	.	.		0.333	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			G	203996824	T	G	203996824	3	3	231	1	0	0	0	0	1	0	0	0	10197	1742	61	5	3700	5	NBEAL1	2	203996824	Missense_Mutation	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	7423335	203996824	39202549	11	32362										
CPS1	1373	hgsc.bcm.edu	37	chr2	211465358	211465358	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcagttgagtccattatggcTacggaagacaggcagctgtt	12	8	1	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr2:211465358T>C	ENST00000233072.5	+	15	1825	c.1629T>C	c.(1627-1629)gcT>gcC	p.A543A	CPS1_ENST00000430249.2_Silent_p.A549A|CPS1_ENST00000451903.2_Silent_p.A92A	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	543					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	CCATTATGGCTACGGAAGACA	0.408																																					p.A549A		Atlas-SNP	.											.	CPS1	485	.	0			c.T1647C						.						119	118	119					2																	211465358		2203	4300	6503	SO:0001819	synonymous_variant	1373	exon16			TATGGCTACGGAA	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.1629T>C	chr2.hg19:g.211465358T>C		211.0	1.0		128.0	65.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	hg19	CCDS2393.1																																																																																			.	.		0.408	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			C	211465358	T	C	211465358	2	2	231	1	0	0	0	0	0	0	0	1	3825	1509	53	2		2	CPS1	2	211465358	Silent	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	7468534	211465358	31734015	12	32363										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215880217	215880217	+	Frame_Shift_Del	DEL	G	G	-													0	0	1	0	0	0	1	1	0	aaccaacagcaacttgccttGtatgtgaagttgtaaatgtt							TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr2:215880217delG	ENST00000272895.7	-	15	2172	c.1953delC	c.(1951-1953)tacfs	p.Y651fs	ABCA12_ENST00000389661.4_Frame_Shift_Del_p.Y333fs	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	651				Y -> D (in Ref. 1; AAP21093). {ECO:0000305}.	cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AACTTGCCTTGTATGTGAAGT	0.358																																					p.K652fs	Ovarian(66;664 1488 5121 34295)	Atlas-INDEL	.											.	ABCA12	368	.	0			c.1954delA						.						76	73	74					2																	215880217		2203	4300	6503	SO:0001589	frameshift_variant	26154	exon15			.	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.1953delC	chr2.hg19:g.215880217delG	ENSP00000272895:p.Tyr651fs	161.0	0.0		110.0	52.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Frame_Shift_Del	DEL	ENST00000272895.7	hg19	CCDS33372.1																																																																																			.	.		0.358	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		-	215880217	G	-	215880217	7	5	231	1	0	1	0	1	0	0	0	0	30	1372	48	0	5990	0	ABCA12	2	215880217	Frame_Shift_Del	DEL	G	TCGA-DD-AAVY-01A-11D-A40R-10	4414859	215880217	27319156	13	32364										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38127869	38127870	+	Splice_Site	DEL	GT	GT	-													0	0	1	0	0	0	1	1	0	ggccaccactaagtttcaagGtgagtgatcacaggttgcta							TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr3:38127869_38127870delGT	ENST00000308059.6	+	9	1593		c.e9+1		DLEC1_ENST00000452631.2_Splice_Site|DLEC1_ENST00000346219.3_Splice_Site					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		AAGTTTCAAGGTGAGTGATCAC	0.431																																					p.524_524del		Atlas-INDEL	.											.	DLEC1	278	.	0			c.1572_1572del						.																																			SO:0001630	splice_region_variant	9940	exon9			.	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1572+1GT>-	chr3.hg19:g.38127869_38127870delGT		138.0	0.0		88.0	40.0	NM_007335		Frame_Shift_Del	DEL	ENST00000308059.6	hg19	CCDS2672.2																																																																																			.	.		0.431	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	Intron	-	38127870	GT	-	38127869	8	5	231	1	0	1	0	1	0	0	1	0	4554	1275	44	0	1607	0	DLEC1	3	38127869	Splice_Site	DEL	GT	TCGA-DD-AAVY-01A-11D-A40R-10		38127869	159894561	14	32365										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266097	41266097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ggcagcaacagtcttacctgGactctggaatccattctggt	10	11	3	0	rs28931588|rs121913416|rs121913417		TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr3:41266097G>A	ENST00000349496.5	+	3	374	c.94G>A	c.(94-96)Gac>Aac	p.D32N	CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32N|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25N|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32N|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32N	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32Y(128)|p.D32N(82)|p.A5_A80del(53)|p.D32H(40)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.Q28fs*20(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.D32fs*9(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GTCTTACCTGGACTCTGGAAT	0.478	D32N(KE39_STOMACH)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32N	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,2	CTNNB1	4904	.	397	Substitution - Missense(250)|Deletion - In frame(120)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Complex - frameshift(1)	liver(155)|central_nervous_system(55)|endometrium(40)|stomach(36)|pancreas(28)|large_intestine(22)|pituitary(22)|skin(11)|ovary(9)|soft_tissue(4)|prostate(4)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|adrenal_gland(1)|biliary_tract(1)|urinary_tract(1)|lung(1)|NS(1)	c.G94A						.						92	77	82					3																	41266097		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TACCTGGACTCTG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.94G>A	chr3.hg19:g.41266097G>A	ENSP00000344456:p.Asp32Asn	173.0	0.0		127.0	53.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	30	5.054970	0.93793	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.71567	0.3355	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.73824	-0.3861	10	0.87932	D	0	0.3843	19.9596	0.97236	0.0:0.0:1.0:0.0	.	32	P35222	CTNB1_HUMAN	N	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25N;ENSP00000385604:D32N;ENSP00000412219:D32N;ENSP00000379486:D32N;ENSP00000344456:D32N;ENSP00000411226:D25N;ENSP00000379488:D32N;ENSP00000409302:D32N;ENSP00000401599:D32N	ENSP00000344456:D32N	D	+	1	0	CTNNB1	41241101	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GAC	.	.		0.478	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266097	G	A	41266097	3	1	231	1	0	0	0	0	1	0	0	0	4018	1174	41	3	100	3	CTNNB1	3	41266097	Missense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	3138228	41266097	156756333	15	32366										
MCM2	4171	hgsc.bcm.edu	37	chr3	127336848	127336848	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctcgctgactttctctgagaAcgtggacctcacagagccca	9	14	2	3			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr3:127336848A>G	ENST00000265056.7	+	12	2181	c.1937A>G	c.(1936-1938)aAc>aGc	p.N646S	MCM2_ENST00000468414.1_3'UTR	NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	646	MCM.				cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						TTCTCTGAGAACGTGGACCTC	0.582																																					p.N646S		Atlas-SNP	.											.	MCM2	79	.	0			c.A1937G						.						106	78	88					3																	127336848		2203	4300	6503	SO:0001583	missense	4171	exon12			CTGAGAACGTGGA	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"mitotin"	116945	"minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)", "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.1937A>G	chr3.hg19:g.127336848A>G	ENSP00000265056:p.Asn646Ser	55.0	0.0		37.0	19.0	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	hg19	CCDS3043.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	29.2|29.2	4.987677|4.987677	0.93106|0.93106	.|.	.|.	ENSG00000073111|ENSG00000073111	ENST00000265056;ENST00000539922;ENST00000543142|ENST00000491422	T|.	0.09255|.	3.0|.	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88415|0.88415	0.6430|0.6430	H|H	0.97635|0.97635	4.045|4.045	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;1.0;1.0|.	D;D;D|.	0.97110|.	0.991;1.0;1.0|.	D|D	0.92399|0.92399	0.5928|0.5928	10|5	0.87932|.	D|.	0|.	-51.1147|-51.1147	15.8646|15.8646	0.79055|0.79055	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	696;516;646|.	F5H1E9;B4DSV5;P49736|.	.;.;MCM2_HUMAN|.	S|A	646;550;696|578	ENSP00000265056:N646S|.	ENSP00000265056:N646S|.	N|T	+|+	2|1	0|0	MCM2|MCM2	128819538|128819538	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.874000|0.874000	0.50279|0.50279	9.118000|9.118000	0.94355|0.94355	2.226000|2.226000	0.72624|0.72624	0.482000|0.482000	0.46254|0.46254	AAC|ACG	.	.		0.582	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			G	127336848	A	G	127336848	3	3	231	1	0	0	0	0	1	0	0	0	9395	43	2	2	1983	2	MCM2	3	127336848	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	86070751	127336848	70685582	16	32367										
COPG	22820	hgsc.bcm.edu	37	chr3	128987352	128987352	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctccaggtctgactgtgtccAtccctggtctggagagggct	13	12	2	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr3:128987352A>T	ENST00000314797.6	+	17	1767	c.1663A>T	c.(1663-1665)Atc>Ttc	p.I555F		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	555					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										GACTGTGTCCATCCCTGGTCT	0.577																																					p.I555F		Atlas-SNP	.											.	.	.	.	0			c.A1663T						.						84	77	79					3																	128987352		2203	4300	6503	SO:0001583	missense	22820	exon17			GTGTCCATCCCTG	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"coat protein gamma-cop"	615525	"coatomer protein complex, subunit gamma"	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.1663A>T	chr3.hg19:g.128987352A>T	ENSP00000325002:p.Ile555Phe	87.0	0.0		73.0	33.0	NM_016128	A8K6M8|B3KMF6|Q54AC4	Missense_Mutation	SNP	ENST00000314797.6	hg19	CCDS33851.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.361635	0.24684	.	.	ENSG00000181789	ENST00000314797	T	0.18174	2.23	6.07	2.39	0.29439	Armadillo-like helical (1);	0.070878	0.64402	D	0.000011	T	0.11665	0.0284	L	0.28014	0.82	0.46222	D	0.998932	B	0.29085	0.232	B	0.32533	0.147	T	0.17167	-1.0378	10	0.33141	T	0.24	-15.7601	8.0081	0.30336	0.6905:0.0:0.3095:0.0	.	555	Q9Y678	COPG_HUMAN	F	555	ENSP00000325002:I555F	ENSP00000325002:I555F	I	+	1	0	COPG	130470042	1.000000	0.71417	0.993000	0.49108	0.172000	0.22775	3.636000	0.54317	0.178000	0.19917	-0.290000	0.09829	ATC	.	.		0.577	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128		T	128987352	A	T	128987352	3	4	231	1	0	0	0	0	1	0	0	0	3733	217	8	4	1729	4	COPG	3	128987352	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	1650504	128987352	69035078	17	32368										
BCHE	590	hgsc.bcm.edu	37	chr3	165548042	165548042	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcttcataaagagatgttacCgcccaaggagcattaaagga	10	8	1	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr3:165548042C>T	ENST00000264381.3	-	2	946	c.780G>A	c.(778-780)gcG>gcA	p.A260A	BCHE_ENST00000540653.1_Intron	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	260					cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	GAGATGTTACCGCCCAAGGAG	0.428																																					p.A260A		Atlas-SNP	.											.	BCHE	136	.	0			c.G780A						.						98	102	101					3																	165548042		2203	4300	6503	SO:0001819	synonymous_variant	590	exon2			TGTTACCGCCCAA	M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"cholinesterase 1", "cholinesterase (serum) 2"	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.780G>A	chr3.hg19:g.165548042C>T		212.0	0.0		184.0	76.0	NM_000055	A8K7P8	Silent	SNP	ENST00000264381.3	hg19	CCDS3198.1																																																																																			.	.		0.428	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350254.1			T	165548042	C	T	165548042	2	4	231	1	0	0	0	0	0	0	0	1	1358	639	23	1		1	BCHE	3	165548042	Silent	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	36560690	165548042	32474388	18	32369										
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54256024	54256024	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aacatcaagacagggggaagAgtttatggaactacaggtaa	12	5	1	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr4:54256024A>G	ENST00000337488.6	+	6	575	c.381A>G	c.(379-381)agA>agG	p.R127R	FIP1L1_ENST00000507922.1_Silent_p.R112R|FIP1L1_ENST00000507166.1_Silent_p.R127R|FIP1L1_ENST00000306932.6_Silent_p.R112R|FIP1L1_ENST00000358575.5_Silent_p.R112R	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	127	Necessary for stimulating PAPOLA activity.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CAGGGGGAAGAGTTTATGGAA	0.313			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.R127R		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.A381G						.						108	119	115					4																	54256024		2203	4300	6503	SO:0001819	synonymous_variant	81608	exon6			GGGAAGAGTTTAT	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.381A>G	chr4.hg19:g.54256024A>G		124.0	0.0		96.0	40.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Silent	SNP	ENST00000337488.6	hg19	CCDS3491.1																																																																																			.	.		0.313	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		G	54256024	A	G	54256024	2	3	231	1	0	0	0	0	0	0	0	1	5904	301	11	2		2	FIP1L1	4	54256024	Silent	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10		54256024	136898252	19	32370										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85663028	85663028	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	taaaacacattgttcaccaaTacctggtagcttcctccact	4	13	1	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr4:85663028T>C	ENST00000295888.4	-	38	6527	c.6120A>G	c.(6118-6120)gtA>gtG	p.V2040V	WDFY3_ENST00000322366.6_Silent_p.V2040V	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2040					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TGTTCACCAATACCTGGTAGC	0.378																																					p.V2040V		Atlas-SNP	.											.	WDFY3	314	.	0			c.A6120G						.						79	80	80					4																	85663028		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon38			CACCAATACCTGG	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.6120A>G	chr4.hg19:g.85663028T>C		253.0	1.0		227.0	96.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.		0.378	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		C	85663028	T	C	85663028	2	2	231	1	0	0	0	0	0	0	0	1	17285	1393	49	2		2	WDFY3	4	85663028	Silent	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	31407004	85663028	105491248	20	32371										
HHIP	64399	hgsc.bcm.edu	37	chr4	145567951	145567951	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggaggagaaggtgcctgaatGggaaccccccgaagcgcctg	16	11	0	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr4:145567951G>T	ENST00000296575.3	+	1	779	c.124G>T	c.(124-126)Ggg>Tgg	p.G42W	HHIP-AS1_ENST00000503066.1_RNA|HHIP-AS1_ENST00000508269.1_RNA|HHIP-AS1_ENST00000512359.1_RNA|HHIP_ENST00000434550.2_Missense_Mutation_p.G42W	NM_022475.2	NP_071920.1	Q96QV1	HHIP_HUMAN	hedgehog interacting protein	42	Arg-rich.				carbohydrate metabolic process (GO:0005975)|dorsal/ventral pattern formation (GO:0009953)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|negative regulation of signal transduction (GO:0009968)|negative regulation of smoothened signaling pathway (GO:0045879)|neuroblast proliferation (GO:0007405)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|skeletal system morphogenesis (GO:0048705)|smoothened signaling pathway (GO:0007224)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	hedgehog family protein binding (GO:0097108)|oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		GTGCCTGAATGGGAACCCCCC	0.592																																					p.G42W		Atlas-SNP	.											.	HHIP	100	.	0			c.G124T						.						82	90	87					4																	145567951		2203	4300	6503	SO:0001583	missense	64399	exon1			CTGAATGGGAACC	AK024645	CCDS3762.1	4q31.21-q31.3	2008-08-29	2001-11-29		ENSG00000164161	ENSG00000164161			14866	protein-coding gene	gene with protein product		606178	"hedgehog-interacting protein"			11435703, 11731473	Standard	NM_022475		Approved	HIP, FLJ20992	uc003ijs.2	Q96QV1	OTTHUMG00000161428	ENST00000296575.3:c.124G>T	chr4.hg19:g.145567951G>T	ENSP00000296575:p.Gly42Trp	209.0	0.0		170.0	85.0	NM_022475	Q6PK09|Q8NCI7|Q9BXK3|Q9H1J4|Q9H7E7	Missense_Mutation	SNP	ENST00000296575.3	hg19	CCDS3762.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559029	0.65538	.	.	ENSG00000164161	ENST00000296575;ENST00000434550	T;T	0.78246	-1.16;-1.16	5.11	5.11	0.69529	Folate receptor-like (1);	0.000000	0.85682	D	0.000000	D	0.86522	0.5953	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85183	0.1005	10	0.35671	T	0.21	-10.106	18.5565	0.91086	0.0:0.0:1.0:0.0	.	42;42	Q96QV1;Q96QV1-2	HHIP_HUMAN;.	W	42	ENSP00000296575:G42W;ENSP00000408587:G42W	ENSP00000296575:G42W	G	+	1	0	HHIP	145787401	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	8.162000	0.89657	2.373000	0.80994	0.650000	0.86243	GGG	.	.		0.592	HHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364887.2			T	145567951	G	T	145567951	3	4	231	1	0	0	0	0	1	0	0	0	7101	1348	47	3	126	3	HHIP	4	145567951	Missense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	59904923	145567951	45586325	21	32372										
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1221377	1221377	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	atcatcttcctcttcttcttCgtggtagaggtcagtcagga	9	10	7	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr5:1221377C>T	ENST00000304460.10	+	11	1706	c.1650C>T	c.(1648-1650)ttC>ttT	p.F550F		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	550					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			TCTTCTTCTTCGTGGTAGAGG	0.582																																					p.F550F		Atlas-SNP	.											.	SLC6A19	99	.	0			c.C1650T						.						158	117	131					5																	1221377		2203	4300	6503	SO:0001819	synonymous_variant	340024	exon11			CTTCTTCGTGGTA	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1650C>T	chr5.hg19:g.1221377C>T		55.0	0.0		54.0	16.0	NM_001003841	A8K446	Silent	SNP	ENST00000304460.10	hg19	CCDS34130.1																																																																																			.	.		0.582	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		T	1221377	C	T	1221377	2	4	231	1	0	0	0	0	0	0	0	1	14697	883	31	1		1	SLC6A19	5	1221377	Silent	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10		1221377	179693883	22	32373										
CDH18	1016	hgsc.bcm.edu	37	chr5	19473502	19473502	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	accctcataggcataagtctGaagagagtcataagggggaa	12	7	3	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr5:19473502G>T	ENST00000507958.1	-	15	3196	c.2206C>A	c.(2206-2208)Cag>Aag	p.Q736K	CDH18_ENST00000274170.4_Missense_Mutation_p.Q736K|CDH18_ENST00000510297.1_5'UTR|CDH18_ENST00000382275.1_Missense_Mutation_p.Q736K			Q13634	CAD18_HUMAN	cadherin 18, type 2	736					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					GCATAAGTCTGAAGAGAGTCA	0.473																																					p.Q736K		Atlas-SNP	.											.	CDH18	561	.	0			c.C2206A						.						123	120	121					5																	19473502		2203	4300	6503	SO:0001583	missense	1016	exon13			AAGTCTGAAGAGA	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.2206C>A	chr5.hg19:g.19473502G>T	ENSP00000425093:p.Gln736Lys	156.0	0.0		167.0	51.0	NM_004934	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.902893	0.92035	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170	T;T;T	0.76968	-1.06;-1.06;-1.06	6.01	6.01	0.97437	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.87533	0.6201	M	0.70842	2.15	0.58432	D	0.999997	D	0.67145	0.996	D	0.70016	0.967	D	0.86056	0.1529	9	.	.	.	.	19.085	0.93200	0.0:0.0:1.0:0.0	.	736	Q13634	CAD18_HUMAN	K	736	ENSP00000371710:Q736K;ENSP00000425093:Q736K;ENSP00000274170:Q736K	.	Q	-	1	0	CDH18	19509259	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.863000	0.99569	2.861000	0.98227	0.650000	0.86243	CAG	.	.		0.473	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		T	19473502	G	T	19473502	3	4	231	1	0	0	0	0	1	0	0	0	3105	1299	45	3	170	3	CDH18	5	19473502	Missense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	18252125	19473502	161441758	23	32374										
CDH9	1007	hgsc.bcm.edu	37	chr5	26881347	26881348	+	Missense_Mutation	DNP	GA	GA	TT													0	0	1	0	0	0	1	1	0	tcttggttacaatcagctgtGagagattccaaagaactgag							TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr5:26881347_26881348GA>TT	ENST00000231021.4	-	12	2439_2440	c.2267_2268TC>AA	c.(2266-2268)cTC>cAA	p.L756Q		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	756					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						AATCAGCTGTGAGAGATTCCAA	0.465																																					p.L756L|p.L756H	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.C2268A|c.T2267A						.																																			SO:0001583	missense	1007	exon12			AGCTGTGAGAGAT|GCTGTGAGAGATT	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.2267_2268delinsTT	chr5.hg19:g.26881347_26881348delinsTT	ENSP00000231021:p.Leu756Gln	118.0	0.0		152.0|153.0	61.0|62.0	NM_016279	Q3B7I5	Silent|Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1																																																																																			.	.		0.465	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		TT	26881348	GA	TT	26881347	3	4	231	1	0	0	0	0	1	0	0	0	3119	1277	45	3	105	3	CDH9	5	26881347	Missense_Mutation	DNP	GA	TCGA-DD-AAVY-01A-11D-A40R-10	7407845	26881347	154033913	24	32375										
NUP153	9972	hgsc.bcm.edu	37	chr6	17628999	17628999	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atgtggactttgaagaattcTcatctttggtttgctctgaa	9	6	3	3			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr6:17628999T>C	ENST00000262077.2	-	18	3430	c.3431A>G	c.(3430-3432)gAg>gGg	p.E1144G	NUP153_ENST00000537253.1_Missense_Mutation_p.E1175G	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	1144					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			TGAAGAATTCTCATCTTTGGT	0.403																																					p.E1144G		Atlas-SNP	.											.	NUP153	116	.	0			c.A3431G						.						96	98	97					6																	17628999		2203	4300	6503	SO:0001583	missense	9972	exon18			GAATTCTCATCTT	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"nucleoporin 153kD"			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.3431A>G	chr6.hg19:g.17628999T>C	ENSP00000262077:p.Glu1144Gly	86.0	0.0		126.0	90.0	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	hg19	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.148919	0.57151	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.07567	3.18;3.18	5.75	5.75	0.90469	.	0.000000	0.50627	D	0.000112	T	0.12475	0.0303	M	0.68317	2.08	0.38685	D	0.952632	D;P;P	0.65815	0.995;0.846;0.7	P;B;B	0.61658	0.892;0.374;0.181	T	0.09487	-1.0672	10	0.26408	T	0.33	-16.2498	11.1491	0.48447	0.0:0.0713:0.0:0.9287	.	1175;1124;1144	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	G	1144;1124;1175	ENSP00000262077:E1144G;ENSP00000444029:E1175G	ENSP00000262077:E1144G	E	-	2	0	NUP153	17736978	0.999000	0.42202	1.000000	0.80357	0.979000	0.70002	3.701000	0.54793	2.195000	0.70347	0.533000	0.62120	GAG	.	.		0.403	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			C	17628999	T	C	17628999	3	2	231	1	0	0	0	0	1	0	0	0	10764	1551	54	2	1016	2	NUP153	6	17628999	Missense_Mutation	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10		17628999	153486068	25	32376										
MRPL14	64928	hgsc.bcm.edu	37	chr6	44081735	44081735	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtcgaatctgggggtcattcGggggccaggcatgcagtgcc	17	10	2	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr6:44081735G>A	ENST00000372014.3	-	3	414	c.283C>T	c.(283-285)Cga>Tga	p.R95*		NM_032111.2	NP_115487.2	Q6P1L8	RM14_HUMAN	mitochondrial ribosomal protein L14	95					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	12	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0181)			GGGGTCATTCGGGGGCCAGGC	0.567																																					p.R95X		Atlas-SNP	.											.	MRPL14	15	.	0			c.C283T						.						114	118	116					6																	44081735		2203	4300	6503	SO:0001587	stop_gained	64928	exon3			TCATTCGGGGGCC	AB051339	CCDS34460.1	6p21.3	2012-09-13			ENSG00000180992	ENSG00000180992		"Mitochondrial ribosomal proteins / large subunits"	14279	protein-coding gene	gene with protein product		611827					Standard	XM_005249300		Approved	RPML32, MRP-L32	uc003owp.3	Q6P1L8	OTTHUMG00000014756	ENST00000372014.3:c.283C>T	chr6.hg19:g.44081735G>A	ENSP00000361084:p.Arg95*	107.0	0.0		186.0	34.0	NM_032111	B2R575|Q96Q72	Nonsense_Mutation	SNP	ENST00000372014.3	hg19	CCDS34460.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.924330	0.52653	.	.	ENSG00000180992	ENST00000372014	.	.	.	5.69	2.77	0.32553	.	0.692312	0.14538	N	0.313477	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.3243	0.07061	0.1308:0.1183:0.4923:0.2586	.	.	.	.	X	95	.	ENSP00000361084:R95X	R	-	1	2	MRPL14	44189713	0.987000	0.35691	0.377000	0.26055	0.338000	0.28826	2.468000	0.45102	1.373000	0.46208	0.561000	0.74099	CGA	.	.		0.567	MRPL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040707.1	NM_032111		A	44081735	G	A	44081735	4	1	231	1	0	0	0	0	0	1	0	0	9788	1124	39	1	158	1	MRPL14	6	44081735	Nonsense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	26452736	44081735	127033332	26	32377										
MANEA	79694	hgsc.bcm.edu	37	chr6	96034647	96034647	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgtattttattacagttggtAtggaaatccacaatttgatg	8	4	0	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr6:96034647A>G	ENST00000358812.4	+	2	466	c.332A>G	c.(331-333)tAt>tGt	p.Y111C	MANEA_ENST00000369293.1_Missense_Mutation_p.Y111C	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	111	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		TACAGTTGGTATGGAAATCCA	0.368																																					p.Y111C		Atlas-SNP	.											.	MANEA	58	.	0			c.A332G						.						95	98	97					6																	96034647		2203	4300	6503	SO:0001583	missense	79694	exon2			GTTGGTATGGAAA	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.332A>G	chr6.hg19:g.96034647A>G	ENSP00000351669:p.Tyr111Cys	155.0	0.0		66.0	57.0	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Missense_Mutation	SNP	ENST00000358812.4	hg19	CCDS5032.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.110968	0.56398	.	.	ENSG00000172469	ENST00000358812;ENST00000369293;ENST00000542500	.	.	.	5.98	4.76	0.60689	.	0.233296	0.45606	D	0.000357	T	0.75170	0.3813	M	0.88979	2.995	0.44825	D	0.997832	D;D	0.89917	0.997;1.0	P;D	0.68943	0.874;0.961	T	0.80111	-0.1519	9	0.87932	D	0	-20.1259	10.1819	0.42972	0.7209:0.0:0.0:0.2791	.	111;111	Q5SRI9;Q8WWX4	MANEA_HUMAN;.	C	111	.	ENSP00000351669:Y111C	Y	+	2	0	MANEA	96141368	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.537000	0.45702	2.288000	0.76882	0.528000	0.53228	TAT	.	.		0.368	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641		G	96034647	A	G	96034647	3	3	231	1	0	0	0	0	1	0	0	0	9230	449	16	2	334	2	MANEA	6	96034647	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	51952912	96034647	75080420	27	32378										
GRM1	2911	hgsc.bcm.edu	37	chr6	146480653	146480653	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctagagtggtggtctgcttCtgtgaaggcatgacagtgcg	16	7	2	3			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr6:146480653C>A	ENST00000282753.1	+	2	1105	c.870C>A	c.(868-870)ttC>ttA	p.F290L	GRM1_ENST00000492807.2_Missense_Mutation_p.F290L|GRM1_ENST00000507907.1_Missense_Mutation_p.F290L|GRM1_ENST00000355289.4_Missense_Mutation_p.F290L|GRM1_ENST00000392299.2_Missense_Mutation_p.F290L|GRM1_ENST00000361719.2_Missense_Mutation_p.F290L			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	290					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		TGGTCTGCTTCTGTGAAGGCA	0.547																																					p.F290L		Atlas-SNP	.											.	GRM1	419	.	0			c.C870A						.						89	82	84					6																	146480653		2203	4300	6503	SO:0001583	missense	2911	exon3			CTGCTTCTGTGAA	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.870C>A	chr6.hg19:g.146480653C>A	ENSP00000282753:p.Phe290Leu	100.0	0.0		39.0	37.0	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	hg19	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.567417	0.86439	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77;-1.77	5.32	3.55	0.40652	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.88332	0.6408	M	0.87038	2.855	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.83275	0.992;0.992;0.996;0.987	D	0.88762	0.3258	10	0.87932	D	0	.	9.1072	0.36705	0.0:0.7769:0.0:0.2231	.	290;290;285;290	F8W805;Q13255;Q59HC2;Q13255-2	.;GRM1_HUMAN;.;.	L	290	ENSP00000354896:F290L;ENSP00000376119:F290L;ENSP00000424095:F290L;ENSP00000282753:F290L;ENSP00000347437:F290L;ENSP00000425599:F290L	ENSP00000282753:F290L	F	+	3	2	GRM1	146522346	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.801000	0.55545	0.643000	0.30638	0.655000	0.94253	TTC	.	.		0.547	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		A	146480653	C	A	146480653	3	1	231	1	0	0	0	0	1	0	0	0	6805	912	32	3	876	3	GRM1	6	146480653	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	50446006	146480653	24634414	28	32379										
ACAT2	39	hgsc.bcm.edu	37	chr6	160188168	160188168	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgcagtccagtcaatagggAtaggagactccagcattgtg	12	8	1	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr6:160188168A>G	ENST00000367048.4	+	3	2082	c.322A>G	c.(322-324)Ata>Gta	p.I108V	ACAT2_ENST00000541436.1_Missense_Mutation_p.I137V	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	108					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		GTCAATAGGGATAGGAGACTC	0.512																																					p.I108V		Atlas-SNP	.											.	ACAT2	32	.	0			c.A322G						.						174	151	159					6																	160188168		2203	4300	6503	SO:0001583	missense	39	exon3			ATAGGGATAGGAG	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	100678	"acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)", "acetyl-Coenzyme A acetyltransferase 2"			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.322A>G	chr6.hg19:g.160188168A>G	ENSP00000356015:p.Ile108Val	150.0	0.0		56.0	50.0	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Missense_Mutation	SNP	ENST00000367048.4	hg19	CCDS5268.1	.	.	.	.	.	.	.	.	.	.	A	2.916	-0.224373	0.06061	.	.	ENSG00000120437	ENST00000367048;ENST00000541436	T;T	0.40756	1.02;1.02	5.46	-10.0	0.00425	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	1.054170	0.07364	N	0.884580	T	0.03136	0.0092	N	0.02111	-0.68	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.29336	-1.0015	10	0.33940	T	0.23	-2.4897	0.9502	0.01374	0.3266:0.1962:0.2872:0.19	.	137;108	B7Z233;Q9BWD1	.;THIC_HUMAN	V	108;137	ENSP00000356015:I108V;ENSP00000437850:I137V	ENSP00000356015:I108V	I	+	1	0	ACAT2	160108158	0.000000	0.05858	0.000000	0.03702	0.995000	0.86356	-0.119000	0.10676	-1.523000	0.01767	-0.327000	0.08410	ATA	.	.		0.512	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891		G	160188168	A	G	160188168	3	3	231	1	0	0	0	0	1	0	0	0	122	333	12	2	332	2	ACAT2	6	160188168	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	13707515	160188168	10926899	29	32380										
MLLT4	4301	hgsc.bcm.edu	37	chr6	168319445	168319445	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaaatgtagtgactgtggctGaaaacactgccgatgagctg	12	7	0	3			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr6:168319445G>T	ENST00000447894.2	+	20	2719	c.2719G>T	c.(2719-2721)Gaa>Taa	p.E907*	MLLT4_ENST00000366806.2_Nonsense_Mutation_p.E907*|MLLT4_ENST00000392112.1_Nonsense_Mutation_p.E891*|MLLT4_ENST00000351017.4_Nonsense_Mutation_p.E914*|MLLT4_ENST00000400822.3_Nonsense_Mutation_p.E906*|MLLT4_ENST00000344191.4_Nonsense_Mutation_p.E907*|MLLT4_ENST00000392108.3_Nonsense_Mutation_p.E907*			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	907	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GACTGTGGCTGAAAACACTGC	0.463			T	MLL	AL																																p.E907X		Atlas-SNP	.		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	.	MLLT4	351	.	0			c.G2719T						.						99	93	95					6																	168319445		2203	4300	6503	SO:0001587	stop_gained	4301	exon20			GTGGCTGAAAACA	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.2719G>T	chr6.hg19:g.168319445G>T	ENSP00000404595:p.Glu907*	118.0	0.0		47.0	43.0	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Nonsense_Mutation	SNP	ENST00000447894.2	hg19		.	.	.	.	.	.	.	.	.	.	G	42	9.621894	0.99221	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894;ENST00000497596	.	.	.	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-39.8268	19.4438	0.94838	0.0:0.0:1.0:0.0	.	.	.	.	X	907;914;907;907;891;907;906;907;70	.	ENSP00000345834:E907X	E	+	1	0	MLLT4	168062294	1.000000	0.71417	0.982000	0.44146	0.733000	0.41908	9.217000	0.95160	2.655000	0.90218	0.655000	0.94253	GAA	.	.		0.463	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		T	168319445	G	T	168319445	4	4	231	1	0	0	0	0	0	1	0	0	9638	1291	45	3	2797	3	MLLT4	6	168319445	Nonsense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	8131277	168319445	2795622	30	32381										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11416274	11416274	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acaccgtaaacccaggtcttTagtctcccatctaagaagaa	6	12	3	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr7:11416274T>C	ENST00000423059.4	-	27	5063	c.4812A>G	c.(4810-4812)ctA>ctG	p.L1604L	AC004538.3_ENST00000445839.1_RNA|AC004538.3_ENST00000428967.1_RNA|AC004538.3_ENST00000595972.1_RNA|AC004538.3_ENST00000599875.1_RNA|AC004538.3_ENST00000421121.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1604					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CCCAGGTCTTTAGTCTCCCAT	0.343										HNSCC(18;0.044)																											p.L1604L		Atlas-SNP	.											.	THSD7A	219	.	0			c.A4812G						.						52	55	54					7																	11416274		1857	4092	5949	SO:0001819	synonymous_variant	221981	exon26			GGTCTTTAGTCTC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.4812A>G	chr7.hg19:g.11416274T>C		55.0	0.0		61.0	40.0	NM_015204		Silent	SNP	ENST00000423059.4	hg19	CCDS47543.1																																																																																			.	.		0.343	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		C	11416274	T	C	11416274	2	2	231	1	0	0	0	0	0	0	0	1	15894	1741	61	2		2	THSD7A	7	11416274	Silent	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10		11416274	147722389	31	32382										
RELN	5649	hgsc.bcm.edu	37	chr7	103214576	103214576	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	cagagggaccgtccgggcttCccttttcccagggccattga	12	14	0	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr7:103214576C>T	ENST00000428762.1	-	30	4633	c.4474G>A	c.(4474-4476)Gaa>Aaa	p.E1492K	RELN_ENST00000343529.5_Missense_Mutation_p.E1492K|RELN_ENST00000424685.2_Missense_Mutation_p.E1492K	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1492					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GTCCGGGCTTCCCTTTTCCCA	0.458																																					p.E1492K	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.G4474A						.						129	126	127					7																	103214576		2203	4300	6503	SO:0001583	missense	5649	exon30			GGGCTTCCCTTTT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.4474G>A	chr7.hg19:g.103214576C>T	ENSP00000392423:p.Glu1492Lys	180.0	0.0		121.0	53.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079334	0.94050	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.44083	1.81;0.93;1.81	5.62	5.62	0.85841	.	0.110120	0.64402	D	0.000008	T	0.56352	0.1979	L	0.40543	1.245	0.58432	D	0.999999	D;D	0.67145	0.994;0.996	D;P	0.64144	0.922;0.807	T	0.52079	-0.8623	10	0.48119	T	0.1	.	20.024	0.97514	0.0:1.0:0.0:0.0	.	1492;1492	P78509-2;P78509	.;RELN_HUMAN	K	1492	ENSP00000392423:E1492K;ENSP00000345694:E1492K;ENSP00000388446:E1492K	ENSP00000345694:E1492K	E	-	1	0	RELN	103001812	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.445000	0.80570	2.809000	0.96659	0.655000	0.94253	GAA	.	.		0.458	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103214576	C	T	103214576	3	4	231	1	0	0	0	0	1	0	0	0	13235	864	30	3	6052	3	RELN	7	103214576	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	91798302	103214576	55924087	32	32383										
RINT1	60561	hgsc.bcm.edu	37	chr7	105183036	105183036	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tggaaccatgattagccagaTtgaagagatcgaacgtcatc	10	8	1	4			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr7:105183036T>A	ENST00000257700.2	+	4	686	c.455T>A	c.(454-456)aTt>aAt	p.I152N		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	152					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.I152T(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						ATTAGCCAGATTGAAGAGATC	0.418																																					p.I152N		Atlas-SNP	.											RINT1,rectum,carcinoma,-1,1	RINT1	65	.	1	Substitution - Missense(1)	ovary(1)	c.T455A						.						130	115	120					7																	105183036		2203	4300	6503	SO:0001583	missense	60561	exon4			GCCAGATTGAAGA	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.455T>A	chr7.hg19:g.105183036T>A	ENSP00000257700:p.Ile152Asn	189.0	0.0		137.0	66.0	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	hg19	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.742156	0.69418	.	.	ENSG00000135249	ENST00000257700;ENST00000493041	T	0.33654	1.4	5.16	5.16	0.70880	.	0.335699	0.33959	N	0.004385	T	0.35653	0.0939	L	0.46157	1.445	0.45806	D	0.998687	P	0.44478	0.836	B	0.41088	0.347	T	0.28004	-1.0057	10	0.66056	D	0.02	-9.2808	14.9865	0.71351	0.0:0.0:0.0:1.0	.	152	Q6NUQ1	RINT1_HUMAN	N	152;121	ENSP00000257700:I152N	ENSP00000257700:I152N	I	+	2	0	RINT1	104970272	1.000000	0.71417	0.835000	0.33067	0.434000	0.31775	7.287000	0.78681	1.929000	0.55896	0.379000	0.24179	ATT	.	.		0.418	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		A	105183036	T	A	105183036	3	1	231	1	0	0	0	0	1	0	0	0	13391	1493	52	4	469	4	RINT1	7	105183036	Missense_Mutation	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	1968460	105183036	53955627	33	32384										
GCC1	79571	hgsc.bcm.edu	37	chr7	127222825	127222825	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acttctccttcagctctgcaAgctgttcctgggctgcctcc	8	16	3	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr7:127222825A>C	ENST00000321407.2	-	2	1995	c.1571T>G	c.(1570-1572)cTt>cGt	p.L524R	GCC1_ENST00000497650.1_5'Flank	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	524					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CAGCTCTGCAAGCTGTTCCTG	0.547																																					p.L524R		Atlas-SNP	.											.	GCC1	83	.	0			c.T1571G						.						75	72	73					7																	127222825		2203	4300	6503	SO:0001583	missense	79571	exon2			TCTGCAAGCTGTT	AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"golgi coiled-coil 1"			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.1571T>G	chr7.hg19:g.127222825A>C	ENSP00000318821:p.Leu524Arg	101.0	0.0		88.0	41.0	NM_024523	Q9H6N7	Missense_Mutation	SNP	ENST00000321407.2	hg19	CCDS5796.1	.	.	.	.	.	.	.	.	.	.	A	17.01	3.279090	0.59758	.	.	ENSG00000179562	ENST00000321407	T	0.15718	2.4	5.29	5.29	0.74685	.	0.063696	0.64402	D	0.000004	T	0.39145	0.1067	M	0.68952	2.095	0.54753	D	0.999984	D	0.89917	1.0	D	0.73380	0.98	T	0.16541	-1.0399	10	0.59425	D	0.04	-8.9467	13.4815	0.61338	1.0:0.0:0.0:0.0	.	524	Q96CN9	GCC1_HUMAN	R	524	ENSP00000318821:L524R	ENSP00000318821:L524R	L	-	2	0	GCC1	127010061	1.000000	0.71417	0.984000	0.44739	0.962000	0.63368	5.574000	0.67424	2.123000	0.65237	0.533000	0.62120	CTT	.	.		0.547	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523		C	127222825	A	C	127222825	3	2	231	1	0	0	0	0	1	0	0	0	6293	72	3	5	760	5	GCC1	7	127222825	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	22039789	127222825	31915838	34	32385										
TMEM140	55281	hgsc.bcm.edu	37	chr7	134849312	134849312	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgggaggctggcaacctcaCtgacctgcccaacctgagaa	11	14	1	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr7:134849312C>G	ENST00000275767.3	+	2	342	c.119C>G	c.(118-120)aCt>aGt	p.T40S	C7orf49_ENST00000459937.1_Intron	NM_018295.3	NP_060765.4	Q9NV12	TM140_HUMAN	transmembrane protein 140	40						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)	5						GGCAACCTCACTGACCTGCCC	0.552																																					p.T40S		Atlas-SNP	.											.	TMEM140	18	.	0			c.C119G						.						151	137	142					7																	134849312		2203	4300	6503	SO:0001583	missense	55281	exon2			ACCTCACTGACCT	AK001862	CCDS5837.1	7q33	2006-03-17			ENSG00000146859	ENSG00000146859			21870	protein-coding gene	gene with protein product							Standard	NM_018295		Approved	FLJ11000	uc003vsi.3	Q9NV12	OTTHUMG00000155413	ENST00000275767.3:c.119C>G	chr7.hg19:g.134849312C>G	ENSP00000275767:p.Thr40Ser	119.0	0.0		107.0	13.0	NM_018295	A4D1P9|Q8WUC3	Missense_Mutation	SNP	ENST00000275767.3	hg19	CCDS5837.1	.	.	.	.	.	.	.	.	.	.	C	8.843	0.942814	0.18281	.	.	ENSG00000146859	ENST00000275767;ENST00000456488	T	0.22743	1.94	5.81	-7.01	0.01594	.	1.512540	0.03660	N	0.242408	T	0.23249	0.0562	L	0.54323	1.7	0.09310	N	1	B	0.30439	0.279	B	0.28011	0.085	T	0.28138	-1.0053	10	0.56958	D	0.05	0.1759	16.7955	0.85601	0.0:0.2503:0.0:0.7497	.	40	Q9NV12	TM140_HUMAN	S	40	ENSP00000275767:T40S	ENSP00000275767:T40S	T	+	2	0	TMEM140	134499852	0.000000	0.05858	0.000000	0.03702	0.311000	0.27955	-0.848000	0.04326	-1.756000	0.01318	-0.797000	0.03246	ACT	.	.		0.552	TMEM140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340017.2	NM_018295		G	134849312	C	G	134849312	3	3	231	1	0	0	0	0	1	0	0	0	16070	565	20	4	121	4	TMEM140	7	134849312	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	7626487	134849312	24289351	35	32386										
FAM167A	83648	hgsc.bcm.edu	37	chr8	11301674	11301674	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cccagcctctctcagggggaGcaagggctcctgccccccac	11	19	2	0	rs376899787		TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr8:11301674G>T	ENST00000528897.1	-	2	866	c.247C>A	c.(247-249)Ctc>Atc	p.L83I	FAM167A_ENST00000534308.1_Missense_Mutation_p.L83I|FAM167A_ENST00000531564.1_5'Flank|FAM167A_ENST00000284486.4_Missense_Mutation_p.L83I			Q96KS9	F167A_HUMAN	family with sequence similarity 167, member A	83										breast(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)	9						CTCAGGGGGAGCAAGGGCTCC	0.687																																					p.L83I		Atlas-SNP	.											.	FAM167A	21	.	0			c.C247A						.	G	ILE/LEU	0,4382		0,0,2191	23	28	26		247	0.6	0	8		26	1,8569		0,1,4284	no	missense	FAM167A	NM_053279.2	5	0,1,6475	TT,TG,GG		0.0117,0.0,0.0077	benign	83/215	11301674	1,12951	2191	4285	6476	SO:0001583	missense	83648	exon2			GGGGGAGCAAGGG		CCDS5981.1	8p23-p22	2010-08-27	2008-06-11	2008-06-11	ENSG00000154319	ENSG00000154319			15549	protein-coding gene	gene with protein product		610085	"chromosome 8 open reading frame 13"	C8orf13			Standard	NM_053279		Approved		uc003wtw.2	Q96KS9	OTTHUMG00000129361	ENST00000528897.1:c.247C>A	chr8.hg19:g.11301674G>T	ENSP00000436655:p.Leu83Ile	84.0	0.0		22.0	17.0	NM_053279	A8K3T9|Q3SXY1|Q3SXY3|Q8N3M3|Q9NSR0	Missense_Mutation	SNP	ENST00000528897.1	hg19	CCDS5981.1	.	.	.	.	.	.	.	.	.	.	G	6.976	0.550098	0.13374	0.0	1.17E-4	ENSG00000154319	ENST00000284486;ENST00000534308;ENST00000528897;ENST00000531804	T;T;T;T	0.43688	3.09;3.09;3.09;0.94	4.78	0.606	0.17559	.	1.281020	0.05480	N	0.554563	T	0.24890	0.0604	N	0.22421	0.69	0.09310	N	1	B	0.24186	0.099	B	0.22601	0.04	T	0.18650	-1.0330	10	0.13108	T	0.6	-11.1218	3.6385	0.08158	0.403:0.0:0.4193:0.1777	.	83	Q96KS9	F167A_HUMAN	I	83	ENSP00000284486:L83I;ENSP00000432232:L83I;ENSP00000436655:L83I;ENSP00000431951:L83I	ENSP00000284486:L83I	L	-	1	0	FAM167A	11339084	0.008000	0.16893	0.000000	0.03702	0.035000	0.12851	0.869000	0.27996	0.163000	0.19507	0.655000	0.94253	CTC	.	.		0.687	FAM167A-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000383901.1			T	11301674	G	T	11301674	3	4	231	1	0	0	0	0	1	0	0	0	5488	971	34	3	405	3	FAM167A	8	11301674	Missense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10		11301674	135062348	36	32387										
PTK2B	2185	hgsc.bcm.edu	37	chr8	27315938	27315938	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcagatgctgacggcttcacAcaccctggctgtggacgcca	12	14	1	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr8:27315938A>G	ENST00000397501.1	+	36	3750	c.2942A>G	c.(2941-2943)cAc>cGc	p.H981R	PTK2B_ENST00000544172.1_Missense_Mutation_p.H981R|PTK2B_ENST00000346049.5_Missense_Mutation_p.H981R|PTK2B_ENST00000517339.1_Missense_Mutation_p.H939R|PTK2B_ENST00000338238.4_Missense_Mutation_p.H939R|PTK2B_ENST00000420218.2_Missense_Mutation_p.H939R	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	981	Focal adhesion targeting (FAT).|Interaction with TGFB1I1. {ECO:0000250}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	ACGGCTTCACACACCCTGGCT	0.612																																					p.H981R		Atlas-SNP	.											.	PTK2B	304	.	0			c.A2942G						.						74	50	58					8																	27315938		2203	4300	6503	SO:0001583	missense	2185	exon36			CTTCACACACCCT	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"protein tyrosine kinase 2 beta", "PTK2B protein tyrosine kinase 2 beta"	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.2942A>G	chr8.hg19:g.27315938A>G	ENSP00000380638:p.His981Arg	130.0	0.0		51.0	42.0	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Missense_Mutation	SNP	ENST00000397501.1	hg19	CCDS6057.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.444576	0.83993	.	.	ENSG00000120899	ENST00000397501;ENST00000338238;ENST00000544172;ENST00000346049;ENST00000420218;ENST00000517339	T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79	4.91	4.91	0.64330	Focal adhesion kinase, targeting (FAT) domain (3);	0.000000	0.85682	D	0.000000	T	0.70193	0.3196	M	0.85462	2.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.984;0.995	T	0.75769	-0.3201	10	0.87932	D	0	.	12.5376	0.56150	1.0:0.0:0.0:0.0	.	939;981	Q14289-2;Q14289	.;FAK2_HUMAN	R	981;939;981;981;939;939	ENSP00000380638:H981R;ENSP00000342242:H939R;ENSP00000440926:H981R;ENSP00000332816:H981R;ENSP00000391995:H939R;ENSP00000427931:H939R	ENSP00000342242:H939R	H	+	2	0	PTK2B	27371855	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.131000	0.94446	2.048000	0.60808	0.460000	0.39030	CAC	.	.		0.612	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103		G	27315938	A	G	27315938	3	3	231	1	0	0	0	0	1	0	0	0	12776	159	6	2	3060	2	PTK2B	8	27315938	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	16014264	27315938	119048084	37	32388										
MRPL15	29088	hgsc.bcm.edu	37	chr8	55055240	55055240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cagggtgctgacacctttacGgcaaaagttaatattgaagt	10	7	0	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr8:55055240G>A	ENST00000260102.4	+	4	521	c.447G>A	c.(445-447)acG>acA	p.T149T		NM_014175.3	NP_054894.1	Q9P015	RM15_HUMAN	mitochondrial ribosomal protein L15	149					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)|skin(3)	10		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)			ACACCTTTACGGCAAAAGTTA	0.368																																					p.T149T		Atlas-SNP	.											.	MRPL15	26	.	0			c.G447A						.						91	84	86					8																	55055240		2203	4300	6503	SO:0001819	synonymous_variant	29088	exon4			CTTTACGGCAAAA	AB051619	CCDS6158.1	8q11.2-q13	2012-09-13			ENSG00000137547	ENSG00000137547		"Mitochondrial ribosomal proteins / large subunits"	14054	protein-coding gene	gene with protein product		611828				11543634	Standard	NM_014175		Approved	RPML7, MRP-L7, HSPC145, L15mt, MRP-L15	uc003xsa.2	Q9P015	OTTHUMG00000164315	ENST00000260102.4:c.447G>A	chr8.hg19:g.55055240G>A		243.0	0.0		373.0	31.0	NM_014175	Q96Q54|Q9H0Y1	Silent	SNP	ENST00000260102.4	hg19	CCDS6158.1																																																																																			.	.		0.368	MRPL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378254.1	NM_014175		A	55055240	G	A	55055240	2	1	231	1	0	0	0	0	0	0	0	1	9789	1103	39	1		1	MRPL15	8	55055240	Silent	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	27739302	55055240	91308782	38	32389										
TMEM8B	51754	hgsc.bcm.edu	37	chr9	35853536	35853536	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccgccgccggcactgctaccCacccacgtggcgccgctggc	12	21	0	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr9:35853536C>T	ENST00000377991.4	+	14	2133	c.1118C>T	c.(1117-1119)cCa>cTa	p.P373L	TMEM8B_ENST00000377988.2_Missense_Mutation_p.P373L	NM_001042589.2	NP_001036054.1	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B	373					cell-matrix adhesion (GO:0007160)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle (GO:0007346)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	7						CACTGCTACCCACCCACGTGG	0.617																																					p.P373L		Atlas-SNP	.											.	TMEM8B	53	.	0			c.C1118T						.						52	53	53					9																	35853536		2039	4168	6207	SO:0001583	missense	51754	exon13			GCTACCCACCCAC	BC043384	CCDS6595.1, CCDS43800.1	9p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000137103	ENSG00000137103			21427	protein-coding gene	gene with protein product	"nasopharyngeal carcinoma expressed 6"		"chromosome 9 open reading frame 127"	C9orf127		12918109, 8619474	Standard	NM_016446		Approved	NAG-5, NGX6	uc003zym.4	A6NDV4	OTTHUMG00000019885	ENST00000377991.4:c.1118C>T	chr9.hg19:g.35853536C>T	ENSP00000367230:p.Pro373Leu	74.0	0.0		46.0	18.0	NM_001042590	B3KQF3|O75539|Q49AB1|Q4KMX5|Q5TCW5|Q9HBY2|Q9P0U7	Missense_Mutation	SNP	ENST00000377991.4	hg19	CCDS43800.1	.	.	.	.	.	.	.	.	.	.	C	32	5.150412	0.94645	.	.	ENSG00000137103	ENST00000377991;ENST00000377988	T;T	0.45668	0.89;0.89	5.28	5.28	0.74379	.	.	.	.	.	T	0.69043	0.3067	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72737	-0.4203	9	0.51188	T	0.08	.	17.5022	0.87735	0.0:1.0:0.0:0.0	.	373	A6NDV4	TMM8B_HUMAN	L	373	ENSP00000367230:P373L;ENSP00000367227:P373L	ENSP00000367227:P373L	P	+	2	0	TMEM8B	35843536	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.006000	0.70724	2.473000	0.83533	0.555000	0.69702	CCA	.	.		0.617	TMEM8B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052388.2	NM_016446		T	35853536	C	T	35853536	3	4	231	1	0	0	0	0	1	0	0	0	16230	594	21	3	1346	3	TMEM8B	9	35853536	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10		35853536	105359895	39	32390										
TMC1	117531	hgsc.bcm.edu	37	chr9	75407157	75407157	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	attaccctttgggaagccaaTatgatcaaggcctacaatgc	8	10	1	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr9:75407157T>C	ENST00000297784.5	+	17	1995	c.1455T>C	c.(1453-1455)aaT>aaC	p.N485N	TMC1_ENST00000396237.3_Silent_p.N485N|TMC1_ENST00000340019.3_Silent_p.N485N|TMC1_ENST00000486417.1_3'UTR	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	485					auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						GGGAAGCCAATATGATCAAGG	0.408																																					p.N485N	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.T1455C						.						239	222	228					9																	75407157		2203	4300	6503	SO:0001819	synonymous_variant	117531	exon17			AGCCAATATGATC	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"transmembrane, cochlear expressed, 1"	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.1455T>C	chr9.hg19:g.75407157T>C		197.0	0.0		140.0	57.0	NM_138691	A8MVZ2|B1AM91	Silent	SNP	ENST00000297784.5	hg19	CCDS6643.1																																																																																			.	.		0.408	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1			C	75407157	T	C	75407157	2	2	231	1	0	0	0	0	0	0	0	1	15999	1403	49	2		2	TMC1	9	75407157	Silent	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	39553621	75407157	65806274	40	32391										
C9orf95	54981	hgsc.bcm.edu	37	chr9	77681717	77681717	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttagatcttcatatacttgcAaaaagaggtcctcttcagat	6	8	4	3			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr9:77681717A>G	ENST00000361092.4	-	8	772	c.536T>C	c.(535-537)tTg>tCg	p.L179S	NMRK1_ENST00000482537.1_5'UTR|NMRK1_ENST00000376811.1_Missense_Mutation_p.L183S|NMRK1_ENST00000376808.4_Missense_Mutation_p.L155S	NM_017881.2	NP_060351.1	Q9NWW6	NRK1_HUMAN	nicotinamide riboside kinase 1	179					NAD biosynthetic process (GO:0009435)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|ribosylnicotinamide kinase activity (GO:0050262)										ATATACTTGCAAAAAGAGGTC	0.368																																					p.L179S		Atlas-SNP	.											.	.	.	.	0			c.T536C						.						156	147	150					9																	77681717		2203	4300	6503	SO:0001583	missense	54981	exon8			ACTTGCAAAAAGA	AK097144	CCDS6650.1, CCDS47981.1	9q21.31	2012-03-30	2012-03-30	2012-03-30	ENSG00000106733	ENSG00000106733			26057	protein-coding gene	gene with protein product		608704	"chromosome 9 open reading frame 95"	C9orf95		15137942	Standard	NM_017881		Approved	FLJ20559, NRK1, bA235O14.2	uc004ajr.4	Q9NWW6	OTTHUMG00000020034	ENST00000361092.4:c.536T>C	chr9.hg19:g.77681717A>G	ENSP00000354387:p.Leu179Ser	132.0	0.0		127.0	54.0	NM_017881	Q5W124|Q8N430	Missense_Mutation	SNP	ENST00000361092.4	hg19	CCDS6650.1	.	.	.	.	.	.	.	.	.	.	A	0.693	-0.793848	0.02862	.	.	ENSG00000106733	ENST00000376811;ENST00000376794;ENST00000361092;ENST00000376808	T;T;T	0.26518	1.73;1.73;1.73	5.45	2.56	0.30785	.	0.789352	0.11813	N	0.526960	T	0.06325	0.0163	N	0.00483	-1.445	0.23537	N	0.997465	B;B;B	0.12013	0.0;0.005;0.001	B;B;B	0.06405	0.0;0.002;0.002	T	0.31447	-0.9943	10	0.07175	T	0.84	-10.7153	8.9807	0.35964	0.2368:0.0:0.7632:0.0	.	155;183;179	Q9NWW6-2;Q5W125;Q9NWW6	.;.;NRK1_HUMAN	S	183;183;179;155	ENSP00000366007:L183S;ENSP00000354387:L179S;ENSP00000366004:L155S	ENSP00000354387:L179S	L	-	2	0	C9orf95	76871537	0.311000	0.24536	0.964000	0.40570	0.446000	0.32137	1.317000	0.33631	1.286000	0.44565	-0.248000	0.11899	TTG	.	.		0.368	NMRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052705.1	NM_017881		G	77681717	A	G	77681717	3	3	231	1	0	0	0	0	1	0	0	0	2509	131	5	2	71	2	C9orf95	9	77681717	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	2274560	77681717	63531714	41	32392										
FAM171A1	221061	hgsc.bcm.edu	37	chr10	15255031	15255031	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcctcgtgggcagatcttctCtggtgggggctggctgctgg	17	10	2	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr10:15255031C>A	ENST00000378116.4	-	8	2562	c.2556G>T	c.(2554-2556)caG>caT	p.Q852H	FAM171A1_ENST00000477161.1_5'Flank	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	852						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						CAGATCTTCTCTGGTGGGGGC	0.622																																					p.Q852H		Atlas-SNP	.											.	FAM171A1	252	.	0			c.G2556T						.						123	129	127					10																	15255031		2203	4300	6503	SO:0001583	missense	221061	exon8			TCTTCTCTGGTGG	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 38"	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.2556G>T	chr10.hg19:g.15255031C>A	ENSP00000367356:p.Gln852His	51.0	0.0		62.0	39.0	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	hg19	CCDS31154.1	.	.	.	.	.	.	.	.	.	.	C	1.268	-0.613806	0.03690	.	.	ENSG00000148468	ENST00000378116;ENST00000396781	T	0.30714	1.52	5.1	0.752	0.18398	.	0.873151	0.10347	N	0.685629	T	0.12689	0.0308	N	0.03115	-0.41	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30446	-0.9978	10	0.27785	T	0.31	-1.244	7.4545	0.27258	0.3847:0.2511:0.3642:0.0	.	852	Q5VUB5	F1711_HUMAN	H	852;851	ENSP00000367356:Q852H	ENSP00000367356:Q852H	Q	-	3	2	FAM171A1	15295037	0.420000	0.25457	0.041000	0.18516	0.503000	0.33858	0.763000	0.26517	0.282000	0.22254	0.563000	0.77884	CAG	.	.		0.622	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		A	15255031	C	A	15255031	3	1	231	1	0	0	0	0	1	0	0	0	5495	912	32	3	120	3	FAM171A1	10	15255031	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10		15255031	120279716	42	32393										
KCNC1	3746	hgsc.bcm.edu	37	chr11	17758086	17758086	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cagccgcgcatctgggcgctCttcgaggacccgtactcgtc	12	16	2	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr11:17758086C>A	ENST00000379472.3	+	1	567	c.537C>A	c.(535-537)ctC>ctA	p.L179L	KCNC1_ENST00000265969.6_Silent_p.L179L	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	179					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(7)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33					Dalfampridine(DB06637)	TCTGGGCGCTCTTCGAGGACC	0.682																																					p.L179L		Atlas-SNP	.											.	KCNC1	149	.	0			c.C537A						.						5	6	5					11																	17758086		1996	3948	5944	SO:0001819	synonymous_variant	3746	exon1			GGCGCTCTTCGAG	M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.537C>A	chr11.hg19:g.17758086C>A		71.0	0.0		67.0	29.0	NM_004976	K4DI87	Silent	SNP	ENST00000379472.3	hg19	CCDS7827.1																																																																																			.	.		0.682	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976		A	17758086	C	A	17758086	2	1	231	1	0	0	0	0	0	0	0	1	8023	900	32	3		3	KCNC1	11	17758086	Silent	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10		17758086	117248430	43	32394										
OR5M3	219482	hgsc.bcm.edu	37	chr11	56237301	56237301	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tccttctgctgagcgcattcGcagaatggcaatgaggatga	12	9	1	4	rs138643585		TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr11:56237301G>A	ENST00000312240.2	-	1	713	c.673C>T	c.(673-675)Cga>Tga	p.R225*		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					GAGCGCATTCGCAGAATGGCA	0.403													g|||	1	0.000199681	0	0	5008	,	,		21550	0		0.001	False		,,,				2504	0				p.R225X		Atlas-SNP	.											.	OR5M3	103	.	0			c.C673T						.						65	64	64					11																	56237301		2201	4292	6493	SO:0001587	stop_gained	219482	exon1			GCATTCGCAGAAT	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"GPCR / Class A : Olfactory receptors"	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.673C>T	chr11.hg19:g.56237301G>A	ENSP00000312208:p.Arg225*	230.0	0.0		197.0	86.0	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Nonsense_Mutation	SNP	ENST00000312240.2	hg19	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	G	4.951	0.176628	0.09443	.	.	ENSG00000174937	ENST00000312240	.	.	.	5.08	-10.2	0.00374	.	0.207799	0.23698	N	0.045442	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.0585	5.4574	0.16598	0.1327:0.0774:0.1742:0.6158	.	.	.	.	X	225	.	ENSP00000312208:R225X	R	-	1	2	OR5M3	55993877	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-3.344000	0.00504	-2.305000	0.00654	-0.235000	0.12190	CGA	.	G|1.000;C|0.000		0.403	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		A	56237301	G	A	56237301	4	1	231	1	0	0	0	0	0	1	0	0	11184	1095	38	1	252	1	OR5M3	11	56237301	Nonsense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	38479215	56237301	78769215	44	32395										
MS4A14	84689	hgsc.bcm.edu	37	chr11	60184358	60184358	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtggagaaagtgccaaaactGttatgccaagattcagaatc	10	7	1	3	rs375353153		TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr11:60184358G>T	ENST00000300187.6	+	5	2194	c.1917G>T	c.(1915-1917)ctG>ctT	p.L639L	MS4A14_ENST00000531783.1_Silent_p.L672L|MS4A14_ENST00000395005.2_Silent_p.L622L|MS4A14_ENST00000531787.1_Silent_p.L527L	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	639	Gln-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						TGCCAAAACTGTTATGCCAAG	0.473																																					p.L672L		Atlas-SNP	.											.	MS4A14	120	.	0			c.G2016T						.						84	84	84					11																	60184358		2203	4300	6503	SO:0001819	synonymous_variant	84689	exon6			AAAACTGTTATGC	AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"membrane-spanning 4-domains, subfamily A, member 16"	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.1917G>T	chr11.hg19:g.60184358G>T		120.0	0.0		102.0	50.0	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Silent	SNP	ENST00000300187.6	hg19	CCDS31569.1																																																																																			.	.		0.473	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			T	60184358	G	T	60184358	2	4	231	1	0	0	0	0	0	0	0	1	9867	1364	48	3		3	MS4A14	11	60184358	Silent	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	3947057	60184358	74822158	45	32396										
ME3	10873	hgsc.bcm.edu	37	chr11	86267694	86267694	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	ccacgtccgaagtcagcactCggtagaagagcttctcgttc	10	13	2	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr11:86267694C>T	ENST00000393324.3	-	3	621	c.368G>A	c.(367-369)cGa>cAa	p.R123Q	ME3_ENST00000359636.2_Missense_Mutation_p.R123Q|ME3_ENST00000543262.1_Missense_Mutation_p.R123Q|ME3_ENST00000323418.6_Missense_Mutation_p.R61Q|RP11-317J19.1_ENST00000524610.1_RNA	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	123					aerobic respiration (GO:0009060)|malate metabolic process (GO:0006108)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|pyruvate metabolic process (GO:0006090)	mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)			endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|skin(3)|stomach(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)				AGTCAGCACTCGGTAGAAGAG	0.547																																					p.R123Q		Atlas-SNP	.											.	ME3	70	.	0			c.G368A						.						122	99	107					11																	86267694		2202	4299	6501	SO:0001583	missense	10873	exon4			AGCACTCGGTAGA	X79440	CCDS8277.1	11q14.2	2012-09-20			ENSG00000151376	ENSG00000151376	1.1.1.40		6985	protein-coding gene	gene with protein product		604626				7818469	Standard	NM_001161586		Approved		uc001pbz.3	Q16798	OTTHUMG00000167217	ENST00000393324.3:c.368G>A	chr11.hg19:g.86267694C>T	ENSP00000376998:p.Arg123Gln	93.0	0.0		68.0	23.0	NM_006680	B7Z6V0|Q8TBJ0	Missense_Mutation	SNP	ENST00000393324.3	hg19	CCDS8277.1	.	.	.	.	.	.	.	.	.	.	C	36	5.609640	0.96637	.	.	ENSG00000151376	ENST00000359636;ENST00000543262;ENST00000393324;ENST00000524826;ENST00000545395;ENST00000323418;ENST00000530335	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	5.96	5.96	0.96718	Malic enzyme, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.63390	0.2507	M	0.87269	2.87	0.80722	D	1	D	0.63046	0.992	P	0.51550	0.673	T	0.67860	-0.5561	9	.	.	.	.	20.422	0.99049	0.0:1.0:0.0:0.0	.	123	Q16798	MAON_HUMAN	Q	123;123;123;123;61;61;123	ENSP00000352657:R123Q;ENSP00000440246:R123Q;ENSP00000376998:R123Q;ENSP00000431182:R123Q;ENSP00000315255:R61Q;ENSP00000434690:R123Q	.	R	-	2	0	ME3	85945342	1.000000	0.71417	0.951000	0.38953	0.956000	0.61745	4.898000	0.63238	2.832000	0.97577	0.655000	0.94253	CGA	.	.		0.547	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2			T	86267694	C	T	86267694	3	4	231	1	0	0	0	0	1	0	0	0	9428	884	31	1	1494	1	ME3	11	86267694	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	26083336	86267694	48738822	46	32397										
FAT3	120114	hgsc.bcm.edu	37	chr11	92533328	92533328	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaggttctcgttcatatctaCatctctgatgtaaatgacaa	7	8	4	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr11:92533328C>T	ENST00000298047.6	+	9	7166	c.7149C>T	c.(7147-7149)taC>taT	p.Y2383Y	FAT3_ENST00000409404.2_Silent_p.Y2383Y|FAT3_ENST00000525166.1_Silent_p.Y2233Y			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2383	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TTCATATCTACATCTCTGATG	0.428										TCGA Ovarian(4;0.039)																											p.Y2383Y		Atlas-SNP	.											.	FAT3	1822	.	0			c.C7149T						.						129	128	128					11																	92533328		1894	4110	6004	SO:0001819	synonymous_variant	120114	exon9			TATCTACATCTCT	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.7149C>T	chr11.hg19:g.92533328C>T		98.0	0.0		78.0	50.0	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	hg19																																																																																				.	.		0.428	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92533328	C	T	92533328	2	4	231	1	0	0	0	0	0	0	0	1	5699	489	17	3		3	FAT3	11	92533328	Silent	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	6265634	92533328	42473188	47	32398										
EXPH5	23086	hgsc.bcm.edu	37	chr11	108385423	108385423	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tggtcttaggatgtcatagaTagacatattggaagtttcat	10	4	3	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr11:108385423T>C	ENST00000265843.4	-	6	921	c.811A>G	c.(811-813)Atc>Gtc	p.I271V	EXPH5_ENST00000443411.1_Missense_Mutation_p.I83V|EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Missense_Mutation_p.I195V|EXPH5_ENST00000525344.1_Missense_Mutation_p.I264V	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	271					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		ATGTCATAGATAGACATATTG	0.383																																					p.I271V		Atlas-SNP	.											.	EXPH5	193	.	0			c.A811G						.						133	124	127					11																	108385423		2201	4298	6499	SO:0001583	missense	23086	exon6			CATAGATAGACAT		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.811A>G	chr11.hg19:g.108385423T>C	ENSP00000265843:p.Ile271Val	114.0	0.0		75.0	33.0	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	hg19	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	T	13.58	2.278281	0.40294	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.06218	3.9;3.82;3.67;3.9;3.71;3.33	5.67	4.54	0.55810	.	0.100838	0.43919	N	0.000517	T	0.09862	0.0242	M	0.71581	2.175	0.27942	N	0.937463	B	0.31193	0.312	B	0.29524	0.103	T	0.06844	-1.0804	10	0.56958	D	0.05	-8.7832	11.2781	0.49178	0.0:0.0721:0.0:0.9279	.	271	Q8NEV8	EXPH5_HUMAN	V	271;195;83;264;115;195;83	ENSP00000265843:I271V;ENSP00000391966:I195V;ENSP00000411390:I83V;ENSP00000432546:I264V;ENSP00000432683:I195V;ENSP00000446434:I83V	ENSP00000265843:I271V	I	-	1	0	EXPH5	107890633	0.975000	0.34042	0.997000	0.53966	0.998000	0.95712	1.437000	0.34991	0.976000	0.38417	0.533000	0.62120	ATC	.	.		0.383	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		C	108385423	T	C	108385423	3	2	231	1	0	0	0	0	1	0	0	0	5324	1406	49	2	5162	2	EXPH5	11	108385423	Missense_Mutation	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	15852095	108385423	26621093	48	32399										
ABCG4	64137	hgsc.bcm.edu	37	chr11	119025597	119025597	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tggagctggtcaacaacccgCctgtcatgttctttgatgag	11	10	3	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr11:119025597C>T	ENST00000449422.2	+	6	846	c.658C>T	c.(658-660)Cct>Tct	p.P220S	ABCG4_ENST00000307417.3_Missense_Mutation_p.P220S|ABCG4_ENST00000531739.1_Missense_Mutation_p.P220S	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	220	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CAACAACCCGCCTGTCATGTT	0.632																																					p.P220S		Atlas-SNP	.											.	ABCG4	77	.	0			c.C658T						.						158	147	151					11																	119025597		2200	4295	6495	SO:0001583	missense	64137	exon6			AACCCGCCTGTCA	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"ATP binding cassette transporters / subfamily G"	13884	protein-coding gene	gene with protein product	"putative ABC transporter", "ATP-binding cassette, subfamily G, member 4"	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.658C>T	chr11.hg19:g.119025597C>T	ENSP00000406874:p.Pro220Ser	97.0	0.0		78.0	24.0	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647577	0.87958	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739	T;T;T	0.25912	1.77;1.77;1.77	4.48	4.48	0.54585	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.106898	0.64402	D	0.000003	T	0.27063	0.0663	N	0.03050	-0.425	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.48019	-0.9071	10	0.36615	T	0.2	-12.1481	17.3381	0.87288	0.0:1.0:0.0:0.0	.	220	Q9H172	ABCG4_HUMAN	S	220	ENSP00000304111:P220S;ENSP00000406874:P220S;ENSP00000434318:P220S	ENSP00000304111:P220S	P	+	1	0	ABCG4	118530807	1.000000	0.71417	0.801000	0.32222	0.981000	0.71138	7.645000	0.83430	2.339000	0.79563	0.491000	0.48974	CCT	.	.		0.632	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		T	119025597	C	T	119025597	3	4	231	1	0	0	0	0	1	0	0	0	70	739	26	3	676	3	ABCG4	11	119025597	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	10640174	119025597	15980919	49	32400										
WBP11	51729	hgsc.bcm.edu	37	chr12	14948022	14948022	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcaaaggaatactctccactTccacatgctgagcattctga	7	12	2	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr12:14948022T>A	ENST00000261167.2	-	6	637	c.404A>T	c.(403-405)gAa>gTa	p.E135V		NM_016312.2	NP_057396.1	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	135					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein phosphatase type 1 regulator activity (GO:0008599)|single-stranded DNA binding (GO:0003697)|WW domain binding (GO:0050699)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)	30						ACTCTCCACTTCCACATGCTG	0.418																																					p.E135V		Atlas-SNP	.											.	WBP11	66	.	0			c.A404T						.						97	88	91					12																	14948022		2203	4300	6503	SO:0001583	missense	51729	exon6			TCCACTTCCACAT	AB029309	CCDS8666.1	12p12.3	2014-06-13			ENSG00000084463	ENSG00000084463			16461	protein-coding gene	gene with protein product	"splicing factor, PQBP1 and PP1 interacting", "protein phosphatase 1, regulatory subunit 165"					10593949	Standard	NM_016312		Approved	NPWBP, SIPP1, PPP1R165	uc001rci.3	Q9Y2W2	OTTHUMG00000168737	ENST00000261167.2:c.404A>T	chr12.hg19:g.14948022T>A	ENSP00000261167:p.Glu135Val	49.0	0.0		46.0	24.0	NM_016312	Q96AY8	Missense_Mutation	SNP	ENST00000261167.2	hg19	CCDS8666.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.717052	0.68844	.	.	ENSG00000084463	ENST00000261167;ENST00000537574	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.74756	0.3758	L	0.59436	1.845	0.80722	D	1	D	0.71674	0.998	D	0.73708	0.981	T	0.77536	-0.2551	9	0.87932	D	0	-22.0807	13.2723	0.60167	0.0:0.0:0.0:1.0	.	135	Q9Y2W2	WBP11_HUMAN	V	135	.	ENSP00000261167:E135V	E	-	2	0	WBP11	14839289	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.791000	0.85805	2.030000	0.59900	0.533000	0.62120	GAA	.	.		0.418	WBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400850.1	NM_016312		A	14948022	T	A	14948022	3	1	231	1	0	0	0	0	1	0	0	0	17273	1783	62	4	1549	4	WBP11	12	14948022	Missense_Mutation	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10		14948022	118903873	50	32401										
HELB	92797	hgsc.bcm.edu	37	chr12	66731799	66731799	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggtgggagaatctccacaaGtgtcttccagacttcagaat	10	9	3	3			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr12:66731799G>C	ENST00000247815.4	+	13	3240	c.3181G>C	c.(3181-3183)Gtg>Ctg	p.V1061L		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	1061					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		ATCTCCACAAGTGTCTTCCAG	0.338																																					p.V1061L		Atlas-SNP	.											.	HELB	90	.	0			c.G3181C						.						59	61	60					12																	66731799		2203	4299	6502	SO:0001583	missense	92797	exon13			CCACAAGTGTCTT	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.3181G>C	chr12.hg19:g.66731799G>C	ENSP00000247815:p.Val1061Leu	117.0	0.0		70.0	37.0	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	hg19	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.966614	0.74131	.	.	ENSG00000127311	ENST00000247815	T	0.17054	2.3	5.5	4.61	0.57282	.	0.197175	0.30410	N	0.009691	T	0.17195	0.0413	M	0.64997	1.995	0.35656	D	0.812173	P	0.48407	0.91	B	0.35182	0.197	T	0.30736	-0.9968	9	.	.	.	-13.8094	14.1357	0.65287	0.0722:0.0:0.9278:0.0	.	1061	Q8NG08	HELB_HUMAN	L	1061	ENSP00000247815:V1061L	.	V	+	1	0	HELB	65018066	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.753000	0.55180	1.304000	0.44892	0.655000	0.94253	GTG	.	.		0.338	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1			C	66731799	G	C	66731799	3	2	231	1	0	0	0	0	1	0	0	0	7054	1029	36	4	3231	4	HELB	12	66731799	Missense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	51783777	66731799	67120096	51	32402										
CAND1	55832	hgsc.bcm.edu	37	chr12	67705572	67705572	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agccattacgtgcaacatgtAcaactaaggtaagaaatgat	8	7	0	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr12:67705572A>G	ENST00000545606.1	+	14	3897	c.3460A>G	c.(3460-3462)Aca>Gca	p.T1154A		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	1154					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TGCAACATGTACAACTAAGGT	0.408																																					p.T1154A		Atlas-SNP	.											.	CAND1	100	.	0			c.A3460G						.						128	113	118					12																	67705572		2203	4300	6503	SO:0001583	missense	55832	exon14			ACATGTACAACTA		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.3460A>G	chr12.hg19:g.67705572A>G	ENSP00000442318:p.Thr1154Ala	142.0	0.0		127.0	64.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.604299	0.46423	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000544619	T;T	0.65549	-0.16;-0.16	5.93	4.76	0.60689	TATA-binding protein interacting (TIP20) (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.046490	0.85682	D	0.000000	T	0.62159	0.2405	M	0.75884	2.315	0.80722	D	1	B;B	0.23442	0.085;0.078	B;B	0.24974	0.028;0.057	T	0.57888	-0.7733	9	.	.	.	-13.2711	13.1441	0.59450	0.8664:0.1336:0.0:0.0	.	986;1154	Q86VP6-2;Q86VP6	.;CAND1_HUMAN	A	1154;1154;694	ENSP00000442318:T1154A;ENSP00000444089:T694A	.	T	+	1	0	CAND1	65991839	1.000000	0.71417	0.992000	0.48379	0.319000	0.28217	7.222000	0.78025	1.036000	0.39998	0.482000	0.46254	ACA	.	.		0.408	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		G	67705572	A	G	67705572	3	3	231	1	0	0	0	0	1	0	0	0	2617	391	14	2	3514	2	CAND1	12	67705572	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	973773	67705572	66146323	52	32403										
MED13L	23389	hgsc.bcm.edu	37	chr12	116444191	116444191	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aatgacctggtgtagtgacaTccttggtaccaaatccatcc	8	11	0	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr12:116444191T>C	ENST00000281928.3	-	12	2470	c.2264A>G	c.(2263-2265)gAt>gGt	p.D755G		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	755						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TGTAGTGACATCCTTGGTACC	0.408																																					p.D755G		Atlas-SNP	.											.	MED13L	193	.	0			c.A2264G						.						101	97	98					12																	116444191		2203	4300	6503	SO:0001583	missense	23389	exon12			GTGACATCCTTGG	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.2264A>G	chr12.hg19:g.116444191T>C	ENSP00000281928:p.Asp755Gly	125.0	0.0		103.0	48.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	T	15.19	2.760142	0.49468	.	.	ENSG00000123066	ENST00000281928	T	0.74106	-0.81	5.83	5.83	0.93111	.	0.175735	0.49305	D	0.000158	T	0.56834	0.2012	N	0.08118	0	0.42120	D	0.991425	B	0.23316	0.083	B	0.19391	0.025	T	0.54754	-0.8246	10	0.26408	T	0.33	.	16.1952	0.82023	0.0:0.0:0.0:1.0	.	755	Q71F56	MD13L_HUMAN	G	755	ENSP00000281928:D755G	ENSP00000281928:D755G	D	-	2	0	MED13L	114928574	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.154000	0.71826	2.236000	0.73375	0.482000	0.46254	GAT	.	.		0.408	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			C	116444191	T	C	116444191	3	2	231	1	0	0	0	0	1	0	0	0	9440	1435	50	2	4448	2	MED13L	12	116444191	Missense_Mutation	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	48738619	116444191	17407704	53	32404										
RPLP0	6175	hgsc.bcm.edu	37	chr12	120634712	120634715	+	Frame_Shift_Del	DEL	GATG	GATG	-													0	0	1	0	0	0	1	1	0	gggcagcagccacaaaggcaGatggatcagccaagaaggcc							TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	GATG	GATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr12:120634712_120634715delGATG	ENST00000551150.1	-	7	1130_1133	c.815_818delCATC	c.(814-819)ccatctfs	p.PS272fs	RPLP0_ENST00000552292.1_Frame_Shift_Del_p.PS62fs|RPLP0_ENST00000550296.1_5'Flank|RPLP0_ENST00000392514.4_Frame_Shift_Del_p.PS272fs|GCN1L1_ENST00000300648.6_5'Flank|RPLP0_ENST00000228306.4_Frame_Shift_Del_p.PS272fs|RPLP0_ENST00000546989.1_Frame_Shift_Del_p.PS236fs|RPLP0_ENST00000313104.5_Frame_Shift_Del_p.PS210fs			P05388	RLA0_HUMAN	ribosomal protein, large, P0	272					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CACAAAGGCAGATGGATCAGCCAA	0.578																																					p.272_273del		Atlas-INDEL	.											.	RPLP0	27	.	0			c.816_819del						.																																			SO:0001589	frameshift_variant	6175	exon8			.	AB007187	CCDS9193.1	12q24.2	2011-07-29			ENSG00000089157	ENSG00000089157		"L ribosomal proteins"	10371	protein-coding gene	gene with protein product	"acidic ribosomal phosphoprotein P0"	180510				9582194	Standard	NM_053275		Approved	PRLP0, P0, L10E, RPP0, LP0	uc001txq.3	P05388	OTTHUMG00000169317	ENST00000551150.1:c.815_818delCATC	chr12.hg19:g.120634712_120634715delGATG	ENSP00000449328:p.Pro272fs	367.0	0.0		236.0	81.0	NM_053275	Q3B7A4|Q9BVK4	Frame_Shift_Del	DEL	ENST00000551150.1	hg19	CCDS9193.1																																																																																			.	.		0.578	RPLP0-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403448.3	NM_053275		-	120634715	GATG	-	120634712	7	5	231	1	0	1	0	1	0	0	0	0	13619	942	33	0	139	0	RPLP0	12	120634712	Frame_Shift_Del	DEL	GATG	TCGA-DD-AAVY-01A-11D-A40R-10	4190521	120634712	13217183	54	32405										
GPR109A	338442	hgsc.bcm.edu	37	chr12	123186897	123186897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgtcatcttcctctggaggcAgcggttgatcaaagtggaga	13	8	4	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr12:123186897A>G	ENST00000328880.5	-	1	993	c.934T>C	c.(934-936)Tgc>Cgc	p.C312R	HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	312					negative regulation of lipid catabolic process (GO:0050995)|neutrophil apoptotic process (GO:0001781)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of neutrophil apoptotic process (GO:0033031)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nicotinic acid receptor activity (GO:0070553)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	15					Niacin(DB00627)	CTCTGGAGGCAGCGGTTGATC	0.552																																					p.C312R		Atlas-SNP	.											.	HCAR2	36	.	0			c.T934C						.						133	107	116					12																	123186897		2203	4300	6503	SO:0001583	missense	338442	exon1			GGAGGCAGCGGTT	AY148884	CCDS9235.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000182782	ENSG00000182782		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	24827	protein-coding gene	gene with protein product	"niacin receptor 1"	609163	"G protein-coupled receptor 109A"	GPR109A		21167710, 12522134, 12646212, 19141678, 18983141, 21454438	Standard	NM_177551		Approved	HCA2, HM74A, PUMAG, Puma-g, NIACR1	uc001ucx.1	Q8TDS4	OTTHUMG00000162722	ENST00000328880.5:c.934T>C	chr12.hg19:g.123186897A>G	ENSP00000375066:p.Cys312Arg	261.0	0.0		212.0	54.0	NM_177551	A0PJL5|A7LGG3	Missense_Mutation	SNP	ENST00000328880.5	hg19	CCDS9235.1	.	.	.	.	.	.	.	.	.	.	A	8.755	0.922293	0.17982	.	.	ENSG00000182782	ENST00000328880;ENST00000536970	T	0.36157	1.27	5.6	4.46	0.54185	.	0.295501	0.24240	U	0.040270	T	0.29061	0.0722	L	0.53249	1.67	0.52501	D	0.99995	B	0.11235	0.004	B	0.06405	0.002	T	0.11470	-1.0586	10	0.24483	T	0.36	-28.934	6.4677	0.21991	0.8292:0.0:0.1708:0.0	.	312	Q8TDS4	HCAR2_HUMAN	R	312	ENSP00000375066:C312R	ENSP00000375066:C312R	C	-	1	0	HCAR2	121752850	0.999000	0.42202	1.000000	0.80357	0.781000	0.44180	1.470000	0.35354	2.248000	0.74166	0.460000	0.39030	TGC	.	.		0.552	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551		G	123186897	A	G	123186897	3	3	231	1	0	0	0	0	1	0	0	0	6633	188	7	2	161	2	GPR109A	12	123186897	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	2552185	123186897	10664998	55	32406										
HSPA2	3306	hgsc.bcm.edu	37	chr14	65008434	65008434	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcgagcatcgagatcgactcGctctacgagggcgtggactt	14	11	1	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr14:65008434G>A	ENST00000394709.1	+	2	943	c.867G>A	c.(865-867)tcG>tcA	p.S289S	HSPA2_ENST00000247207.6_Silent_p.S289S|RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	289					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		AGATCGACTCGCTCTACGAGG	0.672																																					p.S289S	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-SNP	.											.	HSPA2	83	.	0			c.G867A						.						20	20	20					14																	65008434		2201	4299	6500	SO:0001819	synonymous_variant	3306	exon1			CGACTCGCTCTAC	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"Heat shock proteins / HSP70"	5235	protein-coding gene	gene with protein product		140560	"heat shock 70kD protein 2"				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.867G>A	chr14.hg19:g.65008434G>A		59.0	0.0		40.0	21.0	NM_021979	Q15508|Q53XM3|Q9UE78	Silent	SNP	ENST00000394709.1	hg19	CCDS9766.1																																																																																			.	.		0.672	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			A	65008434	G	A	65008434	2	1	231	1	0	0	0	0	0	0	0	1	7420	1074	38	1		1	HSPA2	14	65008434	Silent	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10		65008434	42341106	56	32407										
LTBP2	4053	hgsc.bcm.edu	37	chr14	74988710	74988710	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gttgatgcagcgcccttttcCcttgcaggggtccctcagac	11	14	1	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr14:74988710C>A	ENST00000261978.4	-	17	3078	c.2692G>T	c.(2692-2694)Gga>Tga	p.G898*	LTBP2_ENST00000556690.1_Nonsense_Mutation_p.G898*	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	898	Cys-rich.|EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CGCCCTTTTCCCTTGCAGGGG	0.617																																					p.G898X		Atlas-SNP	.											.	LTBP2	158	.	0			c.G2692T						.						71	64	66					14																	74988710		2203	4300	6503	SO:0001587	stop_gained	4053	exon17			CTTTTCCCTTGCA		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.2692G>T	chr14.hg19:g.74988710C>A	ENSP00000261978:p.Gly898*	103.0	0.0		96.0	16.0	NM_000428	Q99907|Q9NS51	Nonsense_Mutation	SNP	ENST00000261978.4	hg19	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	C	43	9.943815	0.99302	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	.	.	.	3.99	3.99	0.46301	.	0.189851	0.25616	N	0.029453	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	13.9681	0.64221	0.0:1.0:0.0:0.0	.	.	.	.	X	898	.	ENSP00000261978:G898X	G	-	1	0	LTBP2	74058463	0.998000	0.40836	0.220000	0.23810	0.691000	0.40173	5.806000	0.69150	2.214000	0.71695	0.462000	0.41574	GGA	.	.		0.617	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		A	74988710	C	A	74988710	4	1	231	1	0	0	0	0	0	1	0	0	9083	632	22	3	2853	3	LTBP2	14	74988710	Nonsense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	9980276	74988710	32360830	57	32408										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089396	86089396	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caccatttgttcagaggccaCcacccatgcctcctatctga	6	16	2	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr14:86089396C>A	ENST00000330753.4	+	2	2305	c.1538C>A	c.(1537-1539)aCc>aAc	p.T513N	FLRT2_ENST00000554746.1_Missense_Mutation_p.T513N	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	513	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TCAGAGGCCACCACCCATGCC	0.557																																					p.T513N		Atlas-SNP	.											.	FLRT2	168	.	0			c.C1538A						.						120	113	115					14																	86089396		2203	4300	6503	SO:0001583	missense	23768	exon2			AGGCCACCACCCA	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1538C>A	chr14.hg19:g.86089396C>A	ENSP00000332879:p.Thr513Asn	139.0	0.0		119.0	49.0	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	hg19	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	C	10.62	1.401811	0.25291	.	.	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.55930	0.49;0.49	6.17	6.17	0.99709	.	0.201639	0.51477	D	0.000083	T	0.34774	0.0909	N	0.19112	0.55	0.37130	D	0.901206	B	0.33073	0.396	B	0.21360	0.034	T	0.36114	-0.9761	10	0.32370	T	0.25	-24.1914	13.9957	0.64397	0.0:0.9315:0.0:0.0685	.	513	O43155	FLRT2_HUMAN	N	513;513;166	ENSP00000332879:T513N;ENSP00000451050:T513N	ENSP00000332879:T513N	T	+	2	0	FLRT2	85159149	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	2.121000	0.41977	2.941000	0.99782	0.655000	0.94253	ACC	.	.		0.557	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			A	86089396	C	A	86089396	3	1	231	1	0	0	0	0	1	0	0	0	5947	507	18	3	1540	3	FLRT2	14	86089396	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	11100686	86089396	21260144	58	32409										
ITGAM	3684	hgsc.bcm.edu	37	chr16	31341476	31341476	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctggctgagcttcggaaggcCcccgtggtggtgagaagcta	16	10	0	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr16:31341476C>G	ENST00000287497.8	+	26	3126	c.3051C>G	c.(3049-3051)gcC>gcG	p.A1017A	ITGAM_ENST00000544665.3_Silent_p.A1018A			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	1017					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						TTCGGAAGGCCCCCGTGGTGG	0.602																																					p.A1018A		Atlas-SNP	.											.	ITGAM	137	.	0			c.C3054G						.						30	32	32					16																	31341476		2020	4160	6180	SO:0001819	synonymous_variant	3684	exon26			GAAGGCCCCCGTG	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.3051C>G	chr16.hg19:g.31341476C>G		97.0	0.0		67.0	27.0	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Silent	SNP	ENST00000287497.8	hg19	CCDS45470.1																																																																																			.	.		0.602	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		G	31341476	C	G	31341476	2	3	231	1	0	0	0	0	0	0	0	1	7896	610	22	4		4	ITGAM	16	31341476	Silent	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10		31341476	59013277	59	32410										
FAM65A	79567	hgsc.bcm.edu	37	chr16	67579380	67579380	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcttccagttctggagttttGtggaaaccttggacagcccc	10	11	2	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr16:67579380G>C	ENST00000379312.3	+	18	3266	c.3145G>C	c.(3145-3147)Gtg>Ctg	p.V1049L	CTD-2012K14.4_ENST00000564717.1_RNA|CTD-2012K14.3_ENST00000563083.1_RNA|FAM65A_ENST00000540839.3_Missense_Mutation_p.V1064L|FAM65A_ENST00000042381.4_Missense_Mutation_p.V1045L|FAM65A_ENST00000422602.2_Missense_Mutation_p.V1065L|FAM65A_ENST00000428437.2_Missense_Mutation_p.V1059L	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	1049						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		CTGGAGTTTTGTGGAAACCTT	0.612																																					p.V1065L		Atlas-SNP	.											.	FAM65A	104	.	0			c.G3193C						.						54	60	58					16																	67579380		2198	4300	6498	SO:0001583	missense	79567	exon18			AGTTTTGTGGAAA	AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.3145G>C	chr16.hg19:g.67579380G>C	ENSP00000368614:p.Val1049Leu	169.0	0.0		113.0	54.0	NM_001193523	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	hg19	CCDS54028.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.114|8.114	0.779446|0.779446	0.16120|0.16120	.|.	.|.	ENSG00000039523|ENSG00000039523	ENST00000428437|ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	.|T;T;T	.|0.71934	.|-0.61;-0.61;-0.61	5.63|5.63	-1.82|-1.82	0.07857|0.07857	.|.	.|0.333489	.|0.31566	.|N	.|0.007440	T|T	0.28732|0.28732	0.0712|0.0712	N|N	0.01352|0.01352	-0.895|-0.895	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.22346	.|0.068;0.068;0.068	.|B;B;B	.|0.23150	.|0.044;0.044;0.044	T|T	0.27400|0.27400	-1.0075|-1.0075	5|10	.|0.13108	.|T	.|0.6	-1.6938|-1.6938	1.0646|1.0646	0.01608|0.01608	0.3738:0.0952:0.1936:0.3373|0.3738:0.0952:0.1936:0.3373	.|.	.|1059;1065;1049	.|B4DIM2;E9PBS3;Q6ZS17	.|.;.;FA65A_HUMAN	S|L	1038|1049;1045;1065;1059	.|ENSP00000368614:V1049L;ENSP00000042381:V1045L;ENSP00000400099:V1065L	.|ENSP00000042381:V1045L	C|V	+|+	2|1	0|0	FAM65A|FAM65A	66136881|66136881	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.714000|0.714000	0.41099|0.41099	-0.043000|-0.043000	0.12043|0.12043	-0.128000|-0.128000	0.11641|0.11641	0.655000|0.655000	0.94253|0.94253	TGT|GTG	.	.		0.612	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		C	67579380	G	C	67579380	3	2	231	1	0	0	0	0	1	0	0	0	5607	1377	48	4	3199	4	FAM65A	16	67579380	Missense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	36237904	67579380	22775373	60	32411										
PLA2G15	23659	hgsc.bcm.edu	37	chr16	68289848	68289848	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggccttcgtgtcactgggtGcgccctgggggggcgtggcc	20	12	1	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr16:68289848G>A	ENST00000219345.5	+	5	765	c.682G>A	c.(682-684)Gcg>Acg	p.A228T	PLA2G15_ENST00000413021.2_Missense_Mutation_p.A134T|RP11-96D1.7_ENST00000563175.1_RNA|PLA2G15_ENST00000566188.1_Missense_Mutation_p.C186Y|RP11-96D1.7_ENST00000569843.1_RNA|PLA2G15_ENST00000444212.2_Intron	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	228					ceramide metabolic process (GO:0006672)|fatty acid catabolic process (GO:0009062)|phosphatidylcholine metabolic process (GO:0046470)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)|O-acyltransferase activity (GO:0008374)|phospholipid binding (GO:0005543)			kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						GTCACTGGGTGCGCCCTGGGG	0.637																																					p.A228T		Atlas-SNP	.											.	PLA2G15	30	.	0			c.G682A						.						29	32	31					16																	68289848		2198	4300	6498	SO:0001583	missense	23659	exon5			CTGGGTGCGCCCT	AB017494	CCDS10864.1	16q22.1	2008-09-19	2008-09-19	2008-09-19	ENSG00000103066	ENSG00000103066			17163	protein-coding gene	gene with protein product		609362	"lysophospholipase 3 (lysosomal phospholipase A2)"	LYPLA3		10092508, 16973413	Standard	XM_005255886		Approved	LLPL, GXVPLA2	uc002evr.3	Q8NCC3	OTTHUMG00000137554	ENST00000219345.5:c.682G>A	chr16.hg19:g.68289848G>A	ENSP00000219345:p.Ala228Thr	88.0	0.0		85.0	36.0	NM_012320	B3KMF3|B4DUD1|Q53GZ1|Q9NPQ6|Q9UG04|Q9Y2B3	Missense_Mutation	SNP	ENST00000219345.5	hg19	CCDS10864.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.662937	0.88251	.	.	ENSG00000103066	ENST00000413021;ENST00000219345	D;D	0.94687	-3.49;-3.49	5.61	4.65	0.58169	.	0.151409	0.64402	D	0.000014	D	0.95230	0.8453	L	0.48935	1.535	0.80722	D	1	D;D	0.69078	0.997;0.978	D;P	0.64776	0.929;0.875	D	0.93463	0.6812	10	0.20046	T	0.44	-30.5189	16.0158	0.80439	0.0:0.1413:0.8587:0.0	.	134;228	B4DUD1;Q8NCC3	.;PAG15_HUMAN	T	134;228	ENSP00000394197:A134T;ENSP00000219345:A228T	ENSP00000219345:A228T	A	+	1	0	PLA2G15	66847349	0.999000	0.42202	0.955000	0.39395	0.991000	0.79684	3.210000	0.51129	1.361000	0.45981	0.591000	0.81541	GCG	.	.		0.637	PLA2G15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268888.2	NM_012320		A	68289848	G	A	68289848	3	1	231	1	0	0	0	0	1	0	0	0	12001	1319	46	3	700	3	PLA2G15	16	68289848	Missense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	710468	68289848	22064905	61	32412										
ITGAE	3682	hgsc.bcm.edu	37	chr17	3664407	3664407	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgttcacatcgtcttctccAccgccttctttgttgctgta	7	13	4	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr17:3664407A>G	ENST00000263087.4	-	6	596	c.498T>C	c.(496-498)ggT>ggC	p.G166G		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	166	X-domain (extra domain).				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		CGTCTTCTCCACCGCCTTCTT	0.537																																					p.G166G	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.T498C						.						207	197	200					17																	3664407		2203	4300	6503	SO:0001819	synonymous_variant	3682	exon6			TTCTCCACCGCCT	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"CD molecules", "Integrins"	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.498T>C	chr17.hg19:g.3664407A>G		38.0	0.0		32.0	19.0	NM_002208	Q17RS6|Q9NZU9	Silent	SNP	ENST00000263087.4	hg19	CCDS32531.1																																																																																			.	.		0.537	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208		G	3664407	A	G	3664407	2	3	231	1	0	0	0	0	0	0	0	1	7894	146	6	2		2	ITGAE	17	3664407	Silent	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10		3664407	77530803	62	32413										
ANKFY1	51479	hgsc.bcm.edu	37	chr17	4080548	4080548	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggaacagcacactttcaataTcagagttctgaactgccaca	7	11	3	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr17:4080548T>C	ENST00000341657.4	-	19	2683	c.2648A>G	c.(2647-2649)gAt>gGt	p.D883G	ANKFY1_ENST00000574367.1_Missense_Mutation_p.D884G|CYB5D2_ENST00000573984.1_Intron|ANKFY1_ENST00000570535.1_Missense_Mutation_p.D925G	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	883					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						ACTTTCAATATCAGAGTTCTG	0.473																																					p.D925G		Atlas-SNP	.											.	ANKFY1	81	.	0			c.A2774G						.						144	135	138					17																	4080548		1985	4164	6149	SO:0001583	missense	51479	exon19			TCAATATCAGAGT	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"Zinc fingers, FYVE domain containing", "BTB/POZ domain containing", "Ankyrin repeat domain containing"	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.2648A>G	chr17.hg19:g.4080548T>C	ENSP00000343362:p.Asp883Gly	190.0	0.0		140.0	71.0	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	hg19		.	.	.	.	.	.	.	.	.	.	T	24.2	4.500281	0.85176	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	.	.	.	5.95	5.95	0.96441	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.78162	0.4240	M	0.72118	2.19	0.80722	D	1	D;D;D;D	0.89917	0.998;0.999;1.0;1.0	D;D;D;D	0.87578	0.995;0.986;0.998;0.998	T	0.78422	-0.2210	9	0.46703	T	0.11	-26.3638	15.5912	0.76530	0.0:0.0:0.0:1.0	.	825;883;884;925	F5H754;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;ANFY1_HUMAN;.;.	G	884;825	.	ENSP00000343362:D884G	D	-	2	0	ANKFY1	4027297	1.000000	0.71417	0.995000	0.50966	0.716000	0.41182	7.831000	0.86748	2.280000	0.76307	0.460000	0.39030	GAT	.	.		0.473	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		C	4080548	T	C	4080548	3	2	231	1	0	0	0	0	1	0	0	0	626	1435	50	2	889	2	ANKFY1	17	4080548	Missense_Mutation	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	416141	4080548	77114662	63	32414										
GGNBP2	79893	hgsc.bcm.edu	37	chr17	34945708	34945708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aatacagtcatttatggctaAtaaccagtctttctacagca	5	9	3	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr17:34945708A>G	ENST00000304718.4	+	14	2277	c.1961A>G	c.(1960-1962)aAt>aGt	p.N654S	DHRS11_ENST00000251312.5_5'Flank|DHRS11_ENST00000590554.1_5'Flank	NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	654					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		TTTATGGCTAATAACCAGTCT	0.358																																					p.N654S		Atlas-SNP	.											.	GGNBP2	72	.	0			c.A1961G						.						147	163	158					17																	34945708		2203	4300	6503	SO:0001583	missense	79893	exon14			TGGCTAATAACCA	AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.1961A>G	chr17.hg19:g.34945708A>G	ENSP00000307617:p.Asn654Ser	140.0	0.0		112.0	38.0	NM_024835	B2RPK7|Q96T90|Q9GZR8|Q9H767	Missense_Mutation	SNP	ENST00000304718.4	hg19	CCDS11314.1	.	.	.	.	.	.	.	.	.	.	A	4.859	0.159701	0.09287	.	.	ENSG00000005955	ENST00000304718	.	.	.	5.85	5.85	0.93711	.	0.207165	0.51477	D	0.000099	T	0.37679	0.1012	N	0.08118	0	0.80722	D	1	B	0.14012	0.009	B	0.15484	0.013	T	0.23440	-1.0188	9	0.41790	T	0.15	-19.1435	12.1411	0.53998	0.8573:0.1427:0.0:0.0	.	654	Q9H3C7	GGNB2_HUMAN	S	654	.	ENSP00000307617:N654S	N	+	2	0	GGNBP2	32019821	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.644000	0.54381	2.237000	0.73441	0.459000	0.35465	AAT	.	.		0.358	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		G	34945708	A	G	34945708	3	3	231	1	0	0	0	0	1	0	0	0	6367	101	4	2	2011	2	GGNBP2	17	34945708	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	30865160	34945708	46249502	64	32415										
KRT20	54474	hgsc.bcm.edu	37	chr17	39036074	39036074	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atatgctttaccatgctgagAtgggactggagttctatctc	10	8	2	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr17:39036074A>G	ENST00000167588.3	-	5	950	c.909T>C	c.(907-909)caT>caC	p.H303H		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	303	Coil 2.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				CCATGCTGAGATGGGACTGGA	0.418																																					p.H303H		Atlas-SNP	.											.	KRT20	38	.	0			c.T909C						.						110	99	103					17																	39036074		2203	4300	6503	SO:0001819	synonymous_variant	54474	exon5			GCTGAGATGGGAC	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"-", "Intermediate filaments type I, keratins (acidic)"	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.909T>C	chr17.hg19:g.39036074A>G		78.0	0.0		59.0	26.0	NM_019010	B2R6W7	Silent	SNP	ENST00000167588.3	hg19	CCDS11379.1																																																																																			.	.		0.418	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2			G	39036074	A	G	39036074	2	3	231	1	0	0	0	0	0	0	0	1	8467	330	12	2		2	KRT20	17	39036074	Silent	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	4090366	39036074	42159136	65	32416										
KRT38	8687	hgsc.bcm.edu	37	chr17	39593759	39593759	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agcacagggggcagtcacgcAggagggagacgtggagcacg	19	9	1	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr17:39593759A>T	ENST00000246646.3	-	7	1275	c.1276T>A	c.(1276-1278)Tgc>Agc	p.C426S		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	426	Tail.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				GCAGTCACGCAGGAGGGAGAC	0.622																																					p.C426S		Atlas-SNP	.											.	KRT38	63	.	0			c.T1276A						.						34	29	31					17																	39593759		2203	4299	6502	SO:0001583	missense	8687	exon7			TCACGCAGGAGGG	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"-", "Intermediate filaments type I, keratins (acidic)"	6456	protein-coding gene	gene with protein product		604542	"keratin, hair, acidic, 8"	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.1276T>A	chr17.hg19:g.39593759A>T	ENSP00000246646:p.Cys426Ser	248.0	0.0		192.0	83.0	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	hg19	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	.	6.670	0.492139	0.12702	.	.	ENSG00000171360	ENST00000246646	D	0.81579	-1.51	2.36	1.24	0.21308	.	0.254426	0.28230	N	0.016101	T	0.52869	0.1761	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34428	-0.9829	10	0.07990	T	0.79	.	4.5883	0.12294	0.7141:0.0:0.0:0.2859	.	426	O76015	KRT38_HUMAN	S	426	ENSP00000246646:C426S	ENSP00000246646:C426S	C	-	1	0	KRT38	36847285	0.365000	0.25006	0.009000	0.14445	0.226000	0.24999	0.932000	0.28884	0.331000	0.23511	0.459000	0.35465	TGC	.	.		0.622	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		T	39593759	A	T	39593759	3	4	231	1	0	0	0	0	1	0	0	0	8484	188	7	4	98	4	KRT38	17	39593759	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	557685	39593759	41601451	66	32417										
PTRF	284119	hgsc.bcm.edu	37	chr17	40575009	40575009	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctcttctgagccggcccccGacggctcctccgctgcctga	11	19	2	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr17:40575009G>T	ENST00000357037.5	-	1	526	c.107C>A	c.(106-108)tCg>tAg	p.S36*		NM_012232.5	NP_036364.2			polymerase I and transcript release factor											breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		GCCGGCCCCCGACGGCTCCTC	0.672																																					p.S36X		Atlas-SNP	.											.	PTRF	48	.	0			c.C107A						.						18	18	18					17																	40575009		2196	4282	6478	SO:0001587	stop_gained	284119	exon1			GCCCCCGACGGCT	AF000421	CCDS11425.1	17q21.31	2011-04-20				ENSG00000177469			9688	protein-coding gene	gene with protein product		603198				9582279	Standard	NM_012232		Approved	cavin-1, CAVIN1	uc002hzo.3	Q6NZI2		ENST00000357037.5:c.107C>A	chr17.hg19:g.40575009G>T	ENSP00000349541:p.Ser36*	126.0	0.0		110.0	47.0	NM_012232		Nonsense_Mutation	SNP	ENST00000357037.5	hg19	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	G	36	5.698984	0.96802	.	.	ENSG00000177469	ENST00000357037	.	.	.	5.13	5.13	0.70059	.	0.744958	0.11938	N	0.514971	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3283	13.9417	0.64059	0.0761:0.0:0.9239:0.0	.	.	.	.	X	36	.	ENSP00000349541:S36X	S	-	2	0	PTRF	37828535	0.905000	0.30787	1.000000	0.80357	0.546000	0.35178	2.121000	0.41977	2.373000	0.80994	0.561000	0.74099	TCG	.	.		0.672	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232		T	40575009	G	T	40575009	4	4	231	1	0	0	0	0	0	1	0	0	12830	1059	37	1	1073	1	PTRF	17	40575009	Nonsense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	981250	40575009	40620201	67	32418										
PCYT2	5833	hgsc.bcm.edu	37	chr17	79862774	79862775	+	Missense_Mutation	DNP	CC	CC	AG													0	0	1	0	0	0	1	1	0	cctggcagcctccaggaaggCcagctccttggcttccttct							TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr17:79862774_79862775CC>AG	ENST00000538936.2	-	13	1212_1213	c.1104_1105GG>CT	c.(1102-1107)ctGGcc>ctCTcc	p.A369S	PCYT2_ENST00000331285.3_Missense_Mutation_p.A291S|PCYT2_ENST00000570391.1_Missense_Mutation_p.A337S|PCYT2_ENST00000571105.1_Missense_Mutation_p.A347S|PCYT2_ENST00000538721.2_Missense_Mutation_p.A387S|PCYT2_ENST00000570388.1_Missense_Mutation_p.A291S	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine	369					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)	ethanolamine-phosphate cytidylyltransferase activity (GO:0004306)			breast(2)|endometrium(1)|lung(4)|ovary(1)	8	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		Lamivudine(DB00709)	TCCAGGAAGGCCAGCTCCTTGG	0.668																																					p.A387S|p.L386L		Atlas-SNP	.											.	PCYT2	23	.	0			c.G1159T|c.G1158C						.																																			SO:0001583	missense	5833	exon14			GGAAGGCCAGCTC|GAAGGCCAGCTCC	D84307	CCDS11791.1, CCDS54178.1, CCDS58610.1, CCDS62364.1	17q25.3	2008-07-18				ENSG00000185813			8756	protein-coding gene	gene with protein product		602679				9083101	Standard	XM_005256386		Approved	ET	uc002kch.2	Q99447		ENST00000538936.2:c.1104_1105delinsAG	chr17.hg19:g.79862774_79862775delinsAG	ENSP00000439245:p.Ala369Ser	71.0|73.0	0.0		58.0|59.0	24.0	NM_001184917	B7Z7A5|B7ZAS0|F5H8B1|Q6IBM3|Q96G08	Missense_Mutation|Silent	SNP	ENST00000538936.2	hg19	CCDS11791.1																																																																																			.	.		0.668	PCYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439939.1	NM_002861		AG	79862775	CC	AG	79862774	3	1	231	1	0	0	0	0	1	0	0	0	11621	739	26	3	68	3	PCYT2	17	79862774	Missense_Mutation	DNP	CC	TCGA-DD-AAVY-01A-11D-A40R-10	39287765	79862774	1332436	68	32419										
ZNF750	79755	hgsc.bcm.edu	37	chr17	80789233	80789233	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttctgttggggtccgaaggGtttaacctggaaggactcga	14	7	1	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr17:80789233G>T	ENST00000269394.3	-	2	1931	c.1098C>A	c.(1096-1098)aaC>aaA	p.N366K	TBCD_ENST00000355528.4_Intron|TBCD_ENST00000397466.2_Intron|TBCD_ENST00000539345.2_Intron|ZNF750_ENST00000572562.1_5'UTR	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	366					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			GGTCCGAAGGGTTTAACCTGG	0.547																																					p.N366K		Atlas-SNP	.											.	ZNF750	60	.	0			c.C1098A						.						103	112	109					17																	80789233		2203	4300	6503	SO:0001583	missense	79755	exon2			CGAAGGGTTTAAC	AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.1098C>A	chr17.hg19:g.80789233G>T	ENSP00000269394:p.Asn366Lys	74.0	0.0		60.0	29.0	NM_024702	Q9H899	Missense_Mutation	SNP	ENST00000269394.3	hg19	CCDS11819.1	.	.	.	.	.	.	.	.	.	.	G	2.774	-0.254934	0.05829	.	.	ENSG00000141579	ENST00000269394	T	0.21932	1.98	4.61	0.0378	0.14198	.	0.278860	0.30159	N	0.010277	T	0.15912	0.0383	L	0.54323	1.7	0.09310	N	0.999998	B	0.32160	0.358	B	0.25140	0.058	T	0.15206	-1.0445	9	.	.	.	-20.6767	9.6525	0.39906	0.5044:0.0:0.4956:0.0	.	366	Q32MQ0	ZN750_HUMAN	K	366	ENSP00000269394:N366K	.	N	-	3	2	ZNF750	78382522	0.074000	0.21230	0.001000	0.08648	0.107000	0.19398	0.708000	0.25719	0.101000	0.17610	0.557000	0.71058	AAC	.	.		0.547	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702		T	80789233	G	T	80789233	3	4	231	1	0	0	0	0	1	0	0	0	18147	1252	44	3	1081	3	ZNF750	17	80789233	Missense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	926459	80789233	405977	69	32420										
MUC16	94025	hgsc.bcm.edu	37	chr19	9056223	9056223	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	gataagcacttgtcactgttCccagctcaacgctctctgtc	7	14	3	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr19:9056223C>T	ENST00000397910.4	-	3	31426	c.31223G>A	c.(31222-31224)gGa>gAa	p.G10408E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10410	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGTCACTGTTCCCAGCTCAAC	0.478																																					p.G10408E		Atlas-SNP	.											.	MUC16	4315	.	0			c.G31223A						.						201	199	200					19																	9056223		2019	4185	6204	SO:0001583	missense	94025	exon3			ACTGTTCCCAGCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31223G>A	chr19.hg19:g.9056223C>T	ENSP00000381008:p.Gly10408Glu	106.0	0.0		71.0	27.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	7.977	0.750294	0.15778	.	.	ENSG00000181143	ENST00000397910	T	0.03553	3.89	3.94	-5.11	0.02901	.	.	.	.	.	T	0.01627	0.0052	N	0.12182	0.205	.	.	.	P	0.46142	0.873	B	0.36959	0.237	T	0.38564	-0.9655	8	0.87932	D	0	.	1.6852	0.02840	0.1438:0.2584:0.1411:0.4567	.	10408	B5ME49	.	E	10408	ENSP00000381008:G10408E	ENSP00000381008:G10408E	G	-	2	0	MUC16	8917223	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.018000	0.03626	-0.905000	0.03871	-0.890000	0.02929	GGA	.	.		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9056223	C	T	9056223	3	4	231	1	0	0	0	0	1	0	0	0	9982	855	30	3	12628	3	MUC16	19	9056223	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10		9056223	50072760	70	32421										
GLT25D1	79709	hgsc.bcm.edu	37	chr19	17691643	17691643	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caaggcgcccgcaaactgctGgctgctgagccgctctccaa	11	16	1	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr19:17691643G>T	ENST00000252599.4	+	11	1650	c.1530G>T	c.(1528-1530)ctG>ctT	p.L510L		NM_024656.2	NP_078932.2	Q8NBJ5	GT251_HUMAN	collagen beta(1-O)galactosyltransferase 1	510					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	procollagen galactosyltransferase activity (GO:0050211)										GCAAACTGCTGGCTGCTGAGC	0.637																																					p.L510L		Atlas-SNP	.											.	.	.	.	0			c.G1530T						.						67	61	63					19																	17691643		2203	4300	6503	SO:0001819	synonymous_variant	79709	exon11			ACTGCTGGCTGCT	AK075541	CCDS12363.1	19p13.11	2013-02-27	2013-02-27	2013-02-27	ENSG00000130309	ENSG00000130309			26182	protein-coding gene	gene with protein product			"glycosyltransferase 25 domain containing 1"	GLT25D1		19075007	Standard	NM_024656		Approved	FLJ22329	uc002nhc.1	Q8NBJ5		ENST00000252599.4:c.1530G>T	chr19.hg19:g.17691643G>T		69.0	0.0		60.0	30.0	NM_024656	Q8NC64	Silent	SNP	ENST00000252599.4	hg19	CCDS12363.1																																																																																			.	.		0.637	COLGALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464216.1	NM_024656		T	17691643	G	T	17691643	2	4	231	1	0	0	0	0	0	0	0	1	6474	1335	47	3		3	GLT25D1	19	17691643	Silent	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	8635420	17691643	41437340	71	32422										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42880311	42880311	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gggcctgctcttcttccggcAggaccaggcccacattgacc	11	16	2	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr19:42880311A>G	ENST00000251268.6	+	42	7922	c.7922A>G	c.(7921-7923)cAg>cGg	p.Q2641R	MEGF8_ENST00000334370.4_Missense_Mutation_p.Q2574R|MEGF8_ENST00000378073.4_Missense_Mutation_p.Q235R	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2641					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				TTCTTCCGGCAGGACCAGGCC	0.612																																					p.Q2641R		Atlas-SNP	.											.	MEGF8	358	.	0			c.A7922G						.						28	26	26					19																	42880311		2203	4298	6501	SO:0001583	missense	1954	exon42			TCCGGCAGGACCA	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.7922A>G	chr19.hg19:g.42880311A>G	ENSP00000251268:p.Gln2641Arg	57.0	0.0		53.0	19.0	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	A	21.9	4.221361	0.79464	.	.	ENSG00000105429	ENST00000334370;ENST00000251268;ENST00000378073	T;T;T	0.42131	0.99;0.98;1.12	4.8	4.8	0.61643	.	0.000000	0.64402	D	0.000003	T	0.63438	0.2511	M	0.75884	2.315	0.80722	D	1	D;D;D	0.63880	0.989;0.993;0.989	D;D;D	0.72982	0.969;0.958;0.979	T	0.68398	-0.5419	10	0.87932	D	0	-4.1057	13.6587	0.62354	1.0:0.0:0.0:0.0	.	235;2641;2574	F5GZG7;Q7Z7M0;Q7Z7M0-2	.;MEGF8_HUMAN;.	R	2574;2641;235	ENSP00000334219:Q2574R;ENSP00000251268:Q2641R;ENSP00000367313:Q235R	ENSP00000251268:Q2641R	Q	+	2	0	MEGF8	47572151	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.524000	0.90579	1.941000	0.56285	0.459000	0.35465	CAG	.	.		0.612	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		G	42880311	A	G	42880311	3	3	231	1	0	0	0	0	1	0	0	0	9472	188	7	2	7883	2	MEGF8	19	42880311	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	25188668	42880311	16248672	72	32423										
ZNF296	162979	hgsc.bcm.edu	37	chr19	45575426	45575426	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgtcggccatgagggggctCtggggcggcacctgccggtg	20	11	1	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr19:45575426C>A	ENST00000303809.2	-	3	1075	c.861G>T	c.(859-861)caG>caT	p.Q287H		NM_145288.1	NP_660331.1	Q8WUU4	ZN296_HUMAN	zinc finger protein 296	287					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|lung(3)|prostate(1)|urinary_tract(2)	7						TGAGGGGGCTCTGGGGCGGCA	0.697																																					p.Q287H		Atlas-SNP	.											.	ZNF296	22	.	0			c.G861T						.						31	40	37					19																	45575426		2198	4290	6488	SO:0001583	missense	162979	exon3			GGGGCTCTGGGGC	BC019352	CCDS12653.1	19q13.32	2013-01-08	2008-06-24	2008-06-24		ENSG00000170684		"Zinc fingers, C2H2-type"	15981	protein-coding gene	gene with protein product		613226	"zinc finger protein 342"	ZNF342		11063263, 14633674	Standard	NM_145288		Approved		uc002pao.3	Q8WUU4		ENST00000303809.2:c.861G>T	chr19.hg19:g.45575426C>A	ENSP00000302770:p.Gln287His	106.0	0.0		87.0	42.0	NM_145288		Missense_Mutation	SNP	ENST00000303809.2	hg19	CCDS12653.1	.	.	.	.	.	.	.	.	.	.	C	8.659	0.899976	0.17686	.	.	ENSG00000170684	ENST00000303809;ENST00000545481	T	0.05025	3.51	5.47	-2.97	0.05530	.	1.087690	0.07054	N	0.832555	T	0.05960	0.0155	N	0.24115	0.695	0.09310	N	1	P	0.48162	0.906	P	0.44732	0.459	T	0.43507	-0.9387	10	0.59425	D	0.04	-3.8448	9.6673	0.39992	0.0:0.401:0.0:0.599	.	287	Q8WUU4	ZN296_HUMAN	H	287;263	ENSP00000302770:Q287H	ENSP00000302770:Q287H	Q	-	3	2	ZNF296	50267266	0.000000	0.05858	0.015000	0.15790	0.000000	0.00434	-0.536000	0.06135	-0.323000	0.08602	-0.768000	0.03414	CAG	.	.		0.697	ZNF296-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457529.1	NM_145288		A	45575426	C	A	45575426	3	1	231	1	0	0	0	0	1	0	0	0	17843	912	32	3	570	3	ZNF296	19	45575426	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	2695115	45575426	13553557	73	32424										
KLK13	26085	hgsc.bcm.edu	37	chr19	51563812	51563812	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gagtgggggaagcaggtgtaGccacctgggagaaacccact	16	9	0	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr19:51563812G>A	ENST00000595793.1	-	2	159	c.117C>T	c.(115-117)ggC>ggT	p.G39G	KLK13_ENST00000596955.1_Silent_p.G39G|KLK13_ENST00000595547.1_Silent_p.G39G|KLK13_ENST00000335422.3_Intron	NM_015596.1	NP_056411.1	Q9UKR3	KLK13_HUMAN	kallikrein-related peptidase 13	39	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				protein processing (GO:0016485)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)	hydrolase activity (GO:0016787)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	16		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00432)		AGCAGGTGTAGCCACCTGGGA	0.567																																					p.G39G		Atlas-SNP	.											.	KLK13	40	.	0			c.C117T						.						100	104	102					19																	51563812		2203	4300	6503	SO:0001819	synonymous_variant	26085	exon2			GGTGTAGCCACCT		CCDS12822.1	19q13.33	2008-02-05	2006-10-27			ENSG00000167759		"Kallikreins"	6361	protein-coding gene	gene with protein product		605505	"kallikrein 13"			16800724, 16800723	Standard	NM_015596		Approved	KLK-L4	uc002pvn.3	Q9UKR3		ENST00000595793.1:c.117C>T	chr19.hg19:g.51563812G>A		147.0	0.0		131.0	8.0	NM_015596	A7UNK6|Q86VI8|Q9Y433	Silent	SNP	ENST00000595793.1	hg19	CCDS12822.1																																																																																			.	.		0.567	KLK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464298.2	NM_015596		A	51563812	G	A	51563812	2	1	231	1	0	0	0	0	0	0	0	1	8410	958	34	3		3	KLK13	19	51563812	Silent	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10	5988386	51563812	7565171	74	32425										
ZNF471	57573	hgsc.bcm.edu	37	chr19	57027696	57027696	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttttcccaggaagaatggcAatggatgaaccctgctcaga	10	9	1	3	rs150191675		TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr19:57027696A>C	ENST00000308031.5	+	3	219	c.86A>C	c.(85-87)cAa>cCa	p.Q29P	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_Missense_Mutation_p.Q29P	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	29	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		GAAGAATGGCAATGGATGAAC	0.423																																					p.Q29P	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.A86C						.						161	146	151					19																	57027696		2203	4300	6503	SO:0001583	missense	57573	exon3			AATGGCAATGGAT	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.86A>C	chr19.hg19:g.57027696A>C	ENSP00000309161:p.Gln29Pro	190.0	0.0		128.0	64.0	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	hg19	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.582547	0.28180	.	.	ENSG00000196263	ENST00000308031	T	0.01887	4.58	3.77	0.448	0.16614	Krueppel-associated box (4);	.	.	.	.	T	0.03053	0.0090	M	0.64260	1.97	0.09310	N	0.999996	B	0.31383	0.321	B	0.32677	0.15	T	0.39418	-0.9615	9	0.52906	T	0.07	.	4.0047	0.09595	0.596:0.1867:0.2173:0.0	.	29	Q9BX82	ZN471_HUMAN	P	29	ENSP00000309161:Q29P	ENSP00000309161:Q29P	Q	+	2	0	ZNF471	61719508	0.022000	0.18835	0.993000	0.49108	0.998000	0.95712	0.093000	0.15086	0.152000	0.19188	0.528000	0.53228	CAA	.	A|1.000;T|0.000		0.423	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		C	57027696	A	C	57027696	3	2	231	1	0	0	0	0	1	0	0	0	17945	130	5	5	92	5	ZNF471	19	57027696	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	5463884	57027696	2101287	75	32426										
ZNF606	80095	hgsc.bcm.edu	37	chr19	58489957	58489957	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccagtatgagttctccggtgTgcaatgaggtgagaactaca	12	8	1	3			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr19:58489957T>C	ENST00000341164.4	-	7	2711	c.2091A>G	c.(2089-2091)gcA>gcG	p.A697A	ZNF606_ENST00000536132.1_Silent_p.A607A	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	697					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		TTCTCCGGTGTGCAATGAGGT	0.408																																					p.A697A		Atlas-SNP	.											.	ZNF606	155	.	0			c.A2091G						.						99	98	99					19																	58489957		2203	4300	6503	SO:0001819	synonymous_variant	80095	exon7			CCGGTGTGCAATG	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"Zinc fingers, C2H2-type", "-"	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.2091A>G	chr19.hg19:g.58489957T>C		161.0	0.0		112.0	52.0	NM_025027	A8KAN2|Q8NE04|Q96JH5	Silent	SNP	ENST00000341164.4	hg19	CCDS12968.1																																																																																			.	.		0.408	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		C	58489957	T	C	58489957	2	2	231	1	0	0	0	0	0	0	0	1	18047	1683	59	2		2	ZNF606	19	58489957	Silent	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	1462261	58489957	639026	76	32427										
REM1	28954	hgsc.bcm.edu	37	chr20	30064277	30064277	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caacaccgagcaggaagcaaAgacccctctgcaccggcgag	11	15	1	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr20:30064277A>G	ENST00000201979.2	+	2	322	c.29A>G	c.(28-30)aAg>aGg	p.K10R	DEFB124_ENST00000481595.1_Intron	NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	10					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			CAGGAAGCAAAGACCCCTCTG	0.597																																					p.K10R		Atlas-SNP	.											.	REM1	54	.	0			c.A29G						.						103	117	112					20																	30064277		2203	4300	6503	SO:0001583	missense	28954	exon2			AAGCAAAGACCCC	AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"GTPase GES"	610388	"RAS (RAD and GEM)-like GTP-binding"	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.29A>G	chr20.hg19:g.30064277A>G	ENSP00000201979:p.Lys10Arg	164.0	0.0		149.0	63.0	NM_014012	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Missense_Mutation	SNP	ENST00000201979.2	hg19	CCDS13181.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.879027	0.33162	.	.	ENSG00000088320	ENST00000201979	T	0.65732	-0.17	4.55	4.55	0.56014	.	0.302146	0.25270	N	0.031896	T	0.39253	0.1071	N	0.17082	0.46	0.32009	N	0.60234	B	0.19445	0.036	B	0.15052	0.012	T	0.39292	-0.9621	10	0.14656	T	0.56	.	6.7031	0.23236	0.8966:0.0:0.1034:0.0	.	10	O75628	REM1_HUMAN	R	10	ENSP00000201979:K10R	ENSP00000201979:K10R	K	+	2	0	REM1	29527938	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.097000	0.57741	1.905000	0.55150	0.533000	0.62120	AAG	.	.		0.597	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012		G	30064277	A	G	30064277	3	3	231	1	0	0	0	0	1	0	0	0	13237	72	3	2	31	2	REM1	20	30064277	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10		30064277	32961243	77	32428										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44678266	44678266	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctgcacactcttcaggccacAgctgctggtgctggtgcgtg	13	13	2	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr20:44678266A>T	ENST00000454036.2	+	17	2136	c.2087A>T	c.(2086-2088)cAg>cTg	p.Q696L	SLC12A5_ENST00000243964.3_Missense_Mutation_p.Q673L	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	696					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	TTCAGGCCACAGCTGCTGGTG	0.567																																					p.Q696L		Atlas-SNP	.											.	SLC12A5	181	.	0			c.A2087T						.						48	37	41					20																	44678266		2203	4300	6503	SO:0001583	missense	57468	exon17			GGCCACAGCTGCT	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.2087A>T	chr20.hg19:g.44678266A>T	ENSP00000387694:p.Gln696Leu	77.0	0.0		44.0	19.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	hg19	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	A	15.22	2.767447	0.49574	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	D;D	0.98862	-5.19;-5.19	4.34	4.34	0.51931	Amino acid permease domain (1);	0.151012	0.46145	D	0.000312	D	0.99432	0.9799	H	0.97896	4.1	0.80722	D	1	B;D	0.89917	0.081;1.0	B;D	0.91635	0.174;0.999	D	0.98264	1.0500	10	0.87932	D	0	.	12.4905	0.55897	1.0:0.0:0.0:0.0	.	696;673	Q9H2X9;Q9H2X9-2	S12A5_HUMAN;.	L	696;673	ENSP00000387694:Q696L;ENSP00000243964:Q673L	ENSP00000243964:Q673L	Q	+	2	0	SLC12A5	44111673	1.000000	0.71417	1.000000	0.80357	0.372000	0.29890	9.097000	0.94193	1.812000	0.52913	0.377000	0.23210	CAG	.	.		0.567	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			T	44678266	A	T	44678266	3	4	231	1	0	0	0	0	1	0	0	0	14401	188	7	4	2209	4	SLC12A5	20	44678266	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	14613989	44678266	18347254	78	32429										
COL20A1	57642	hgsc.bcm.edu	37	chr20	61948009	61948009	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgggaccccgaccttcacgCtcttcaaggacgcccagctg	11	16	3	0			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr20:61948009C>T	ENST00000358894.6	+	21	2729	c.2629C>T	c.(2629-2631)Ctc>Ttc	p.L877F	COL20A1_ENST00000326996.6_Missense_Mutation_p.L877F|COL20A1_ENST00000435874.1_Missense_Mutation_p.L884F|COL20A1_ENST00000422202.1_Missense_Mutation_p.L884F	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	877	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GACCTTCACGCTCTTCAAGGA	0.637																																					p.L877F		Atlas-SNP	.											.	COL20A1	137	.	0			c.C2629T						.						23	26	25					20																	61948009		1982	4133	6115	SO:0001583	missense	57642	exon21			TTCACGCTCTTCA	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.2629C>T	chr20.hg19:g.61948009C>T	ENSP00000351767:p.Leu877Phe	52.0	0.0		43.0	5.0	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	hg19	CCDS46628.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.824388	0.71143	.	.	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	T;T;T;T	0.01725	4.67;4.67;4.67;4.67	4.22	3.26	0.37387	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.081539	0.51477	D	0.000096	T	0.08582	0.0213	M	0.81497	2.545	0.40869	D	0.983893	D;D	0.63880	0.993;0.989	D;P	0.64506	0.926;0.845	T	0.01375	-1.1371	10	0.62326	D	0.03	.	10.629	0.45525	0.1926:0.8074:0.0:0.0	.	884;877	Q9P218-2;Q9P218	.;COKA1_HUMAN	F	877;877;884;884	ENSP00000351767:L877F;ENSP00000323077:L877F;ENSP00000408690:L884F;ENSP00000414753:L884F	ENSP00000323077:L877F	L	+	1	0	COL20A1	61418454	0.980000	0.34600	0.951000	0.38953	0.523000	0.34469	2.527000	0.45615	0.761000	0.33130	0.289000	0.19496	CTC	.	.		0.637	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		T	61948009	C	T	61948009	3	4	231	1	0	0	0	0	1	0	0	0	3681	797	28	3	2707	3	COL20A1	20	61948009	Missense_Mutation	SNP	C	TCGA-DD-AAVY-01A-11D-A40R-10	17269743	61948009	1077511	79	32430										
XBP1	7494	hgsc.bcm.edu	37	chr22	29196386	29196386	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctccgggctggcccctctctGggctggcaccatgagcggca	14	16	1	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chr22:29196386G>A	ENST00000216037.6	-	1	199	c.127C>T	c.(127-129)Cag>Tag	p.Q43*	XBP1_ENST00000405219.3_5'Flank|CTA-292E10.6_ENST00000585003.1_RNA|CTA-292E10.6_ENST00000418292.1_RNA|CTA-292E10.6_ENST00000458080.1_RNA|XBP1_ENST00000344347.5_Nonsense_Mutation_p.Q43*|CTA-292E10.6_ENST00000451486.1_RNA|XBP1_ENST00000403532.3_Nonsense_Mutation_p.Q43*	NM_001079539.1|NM_005080.3	NP_001073007.1|NP_005071.2	P17861	XBP1_HUMAN	X-box binding protein 1	43					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial cell maturation involved in salivary gland development (GO:0060691)|exocrine pancreas development (GO:0031017)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|serotonin secretion, neurotransmission (GO:0060096)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|large_intestine(1)|lung(1)	5						GCCCCTCTCTGGGCTGGCACC	0.761																																					p.Q43X		Atlas-SNP	.											.	XBP1	37	.	0			c.C127T						.						2	3	2					22																	29196386		1448	3100	4548	SO:0001587	stop_gained	7494	exon1			CTCTCTGGGCTGG	M31627	CCDS13847.1	22q12.1	2013-01-10			ENSG00000100219	ENSG00000100219		"basic leucine zipper proteins"	12801	protein-coding gene	gene with protein product		194355		XBP2		1718857, 2196176	Standard	NM_001079539		Approved		uc003aec.3	P17861	OTTHUMG00000151094	ENST00000216037.6:c.127C>T	chr22.hg19:g.29196386G>A	ENSP00000216037:p.Gln43*	78.0	0.0		74.0	52.0	NM_001079539	Q8WYK6|Q969P1|Q96BD7	Nonsense_Mutation	SNP	ENST00000216037.6	hg19	CCDS13847.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.724567	0.68959	.	.	ENSG00000100219	ENST00000216037;ENST00000403532;ENST00000344347	.	.	.	3.65	1.44	0.22558	.	0.440036	0.21629	N	0.071510	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	.	8.0386	0.30508	0.0:0.1746:0.6451:0.1802	.	.	.	.	X	43	.	ENSP00000216037:Q43X	Q	-	1	0	XBP1	27526386	0.975000	0.34042	0.031000	0.17742	0.616000	0.37450	3.219000	0.51200	0.481000	0.27557	-0.309000	0.09137	CAG	.	.		0.761	XBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321274.1	NM_005080		A	29196386	G	A	29196386	4	1	231	1	0	0	0	0	0	1	0	0	17437	1357	47	3	1049	3	XBP1	22	29196386	Nonsense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10		29196386	22108180	80	32431										
MAP3K15	389840	hgsc.bcm.edu	37	chrX	19416359	19416359	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cttgcctgctatctctctccGggatttctttgatggctatt	8	11	3	1			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chrX:19416359G>C	ENST00000338883.4	-	15	2050	c.2051C>G	c.(2050-2052)cCg>cGg	p.P684R	MAP3K15_ENST00000469203.2_Missense_Mutation_p.P516R|MAP3K15_ENST00000518578.1_5'UTR|MAP3K15_ENST00000359173.3_Missense_Mutation_p.P119R	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	684	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					ATCTCTCTCCGGGATTTCTTT	0.547																																					p.P684R		Atlas-SNP	.											.	MAP3K15	108	.	0			c.C2051G						.						174	162	166					X																	19416359		2203	4300	6503	SO:0001583	missense	389840	exon15			CTCTCCGGGATTT	AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.2051C>G	chrX.hg19:g.19416359G>C	ENSP00000345629:p.Pro684Arg	49.0	0.0		38.0	35.0	NM_001001671	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Missense_Mutation	SNP	ENST00000338883.4	hg19		.	.	.	.	.	.	.	.	.	.	G	22.1	4.244085	0.79912	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	T;T;T	0.64260	-0.09;-0.09;-0.09	5.32	5.32	0.75619	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.100126	0.64402	D	0.000001	T	0.65037	0.2653	N	0.11818	0.18	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.69654	0.965;0.944	T	0.71048	-0.4705	10	0.51188	T	0.08	.	18.1681	0.89734	0.0:0.0:1.0:0.0	.	159;684	Q6ZN16-3;Q6ZN16	.;M3K15_HUMAN	R	684;119;516	ENSP00000345629:P684R;ENSP00000352093:P119R;ENSP00000428356:P516R	ENSP00000345629:P684R	P	-	2	0	MAP3K15	19326280	1.000000	0.71417	0.998000	0.56505	0.924000	0.55760	9.382000	0.97209	2.227000	0.72691	0.519000	0.50382	CCG	.	.		0.547	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671		C	19416359	G	C	19416359	3	2	231	1	0	0	0	0	1	0	0	0	9258	1116	39	4	1950	4	MAP3K15	23	19416359	Missense_Mutation	SNP	G	TCGA-DD-AAVY-01A-11D-A40R-10		19416359	135854201	81	32432										
ARMCX3	51566	hgsc.bcm.edu	37	chrX	100880445	100880445	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgcatttaacagagatattaTtcgtgatctgggtggtctcc	10	7	2	2			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chrX:100880445T>A	ENST00000341189.4	+	5	1342	c.476T>A	c.(475-477)aTt>aAt	p.I159N	RP4-545K15.5_ENST00000564612.1_RNA|ARMCX3_ENST00000537169.1_Missense_Mutation_p.I159N|ARMCX3_ENST00000471229.2_Missense_Mutation_p.I159N|ARMCX3-AS1_ENST00000454228.1_RNA	NM_016607.3	NP_057691.1	Q9UH62	ARMX3_HUMAN	armadillo repeat containing, X-linked 3	159					cellular protein localization (GO:0034613)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of mitochondrial outer membrane (GO:0031307)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11						AGAGATATTATTCGTGATCTG	0.393																																					p.I159N		Atlas-SNP	.											.	ARMCX3	33	.	0			c.T476A						.						84	82	83					X																	100880445		2203	4297	6500	SO:0001583	missense	51566	exon5			ATATTATTCGTGA	AY359079	CCDS14489.1	Xq22.1	2014-03-21			ENSG00000102401	ENSG00000102401		"Armadillo repeat containing"	24065	protein-coding gene	gene with protein product		300364				11162520, 11042152, 19304657, 16221301, 22569362	Standard	NM_016607		Approved	ALEX3, GASP6	uc004eia.1	Q9UH62	OTTHUMG00000022035	ENST00000341189.4:c.476T>A	chrX.hg19:g.100880445T>A	ENSP00000340672:p.Ile159Asn	115.0	0.0		188.0	89.0	NM_016607	Q53HC6|Q7LCF5|Q9NPE4	Missense_Mutation	SNP	ENST00000341189.4	hg19	CCDS14489.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.620372	0.46736	.	.	ENSG00000102401	ENST00000341189;ENST00000537169	T;T	0.42900	0.96;0.96	4.29	4.29	0.51040	Armadillo-like helical (1);Armadillo-type fold (1);	0.048223	0.85682	D	0.000000	T	0.53722	0.1814	L	0.49571	1.57	0.45035	D	0.998057	D	0.89917	1.0	D	0.97110	1.0	T	0.51379	-0.8713	9	.	.	.	-19.302	8.882	0.35380	0.0:0.0:0.0:1.0	.	159	Q9UH62	ARMX3_HUMAN	N	159	ENSP00000340672:I159N;ENSP00000439032:I159N	.	I	+	2	0	ARMCX3	100767101	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.714000	0.47202	1.919000	0.55581	0.430000	0.28490	ATT	.	.		0.393	ARMCX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057568.2	NM_016607		A	100880445	T	A	100880445	3	1	231	1	0	0	0	0	1	0	0	0	961	1493	52	4	478	4	ARMCX3	23	100880445	Missense_Mutation	SNP	T	TCGA-DD-AAVY-01A-11D-A40R-10	81464086	100880445	54390115	82	32433										
PLP1	5354	hgsc.bcm.edu	37	chrX	103041449	103041449	+	Frame_Shift_Del	DEL	G	G	-													0	0	1	0	0	0	1	1	0	cctctttcttcttcctttatGgggccctcctgctggctgag							TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chrX:103041449delG	ENST00000303958.2	+	3	393	c.247delG	c.(247-249)gggfs	p.G83fs	PLP1_ENST00000361621.2_Frame_Shift_Del_p.G83fs|PLP1_ENST00000418604.1_Frame_Shift_Del_p.G83fs	NM_000533.3	NP_000524.3	P60201	MYPR_HUMAN	proteolipid protein 1	83					astrocyte development (GO:0014002)|axon development (GO:0061564)|axon ensheathment (GO:0008366)|cell death (GO:0008219)|cell maturation (GO:0048469)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|long-chain fatty acid biosynthetic process (GO:0042759)|positive regulation of gene expression (GO:0010628)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	structural constituent of myelin sheath (GO:0019911)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	17						CTTCCTTTATGGGGCCCTCCT	0.522																																					p.Y82X		Atlas-INDEL	.											.	PLP1	37	.	0			c.246delT						.						120	114	116					X																	103041449		2203	4300	6503	SO:0001589	frameshift_variant	5354	exon3			.	M27110	CCDS14513.1, CCDS14514.1	Xq22	2013-05-14	2008-07-28		ENSG00000123560	ENSG00000123560			9086	protein-coding gene	gene with protein product	"Pelizaeus-Merzbacher disease"	300401	"spastic paraplegia 2, uncomplicated"	SPG2, PLP			Standard	NM_001128834		Approved	GPM6C	uc004elk.3	P60201	OTTHUMG00000022111	ENST00000303958.2:c.247delG	chrX.hg19:g.103041449delG	ENSP00000305152:p.Gly83fs	198.0	0.0		239.0	110.0	NM_199478	P04400|P06905|Q502Y1|Q6FHZ6	Frame_Shift_Del	DEL	ENST00000303958.2	hg19	CCDS14513.1																																																																																			.	.		0.522	PLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057743.2			-	103041449	G	-	103041449	7	5	231	1	0	1	0	1	0	0	0	0	12113	1348	47	0	257	0	PLP1	23	103041449	Frame_Shift_Del	DEL	G	TCGA-DD-AAVY-01A-11D-A40R-10	2161004	103041449	52229111	83	32434										
GPR101	83550	hgsc.bcm.edu	37	chrX	136113550	136113550	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggctgttgaggggccagaagAgaggcacagaggtggccacc	18	9	0	4			TCGA-DD-AAVY-01A-11D-A40R-10	TCGA-DD-AAVY-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a40648e-66fb-456f-bb65-eb211084f42c	6cc223ac-a900-47e6-95c6-bef64dca1158	g.chrX:136113550A>G	ENST00000298110.1	-	1	283	c.284T>C	c.(283-285)cTc>cCc	p.L95P		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	95						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					GGGCCAGAAGAGAGGCACAGA	0.597																																					p.L95P		Atlas-SNP	.											.	GPR101	96	.	0			c.T284C						.						56	48	51					X																	136113550		2203	4300	6503	SO:0001583	missense	83550	exon1			CAGAAGAGAGGCA	AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"GPCR / Class A : Orphans"	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.284T>C	chrX.hg19:g.136113550A>G	ENSP00000298110:p.Leu95Pro	67.0	0.0		126.0	122.0	NM_054021	Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	hg19	CCDS14662.1	.	.	.	.	.	.	.	.	.	.	A	6.684	0.494762	0.12702	.	.	ENSG00000165370	ENST00000298110	T	0.19806	2.12	4.85	3.71	0.42584	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.14227	0.0344	L	0.33137	0.985	0.21064	N	0.999796	B	0.15141	0.012	B	0.16722	0.016	T	0.21895	-1.0232	9	0.66056	D	0.02	-3.8782	1.7199	0.02909	0.5246:0.0:0.189:0.2864	.	95	Q96P66	GP101_HUMAN	P	95	ENSP00000298110:L95P	ENSP00000298110:L95P	L	-	2	0	GPR101	135941216	0.051000	0.20477	0.885000	0.34714	0.995000	0.86356	0.615000	0.24329	1.595000	0.50050	0.441000	0.28932	CTC	.	.		0.597	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			G	136113550	A	G	136113550	3	3	231	1	0	0	0	0	1	0	0	0	6630	304	11	2	1245	2	GPR101	23	136113550	Missense_Mutation	SNP	A	TCGA-DD-AAVY-01A-11D-A40R-10	33072101	136113550	19157010	84	32435										
PRKCZ	5590	hgsc.bcm.edu	37	chr1	2082320	2082320	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	cctaatcagagtcatcgggcGcgggagctacgccaaggttc	13	12	2	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr1:2082320G>A	ENST00000400921.2	+	6	913	c.230G>A	c.(229-231)cGc>cAc	p.R77H	PRKCZ_ENST00000400920.1_Missense_Mutation_p.R77H|PRKCZ_ENST00000479263.1_3'UTR	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta	260	OPR.				actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.R260H(1)		breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	GTCATCGGGCGCGGGAGCTAC	0.512																																					p.R260H		Atlas-SNP	.											PRKCZ_ENST00000378567,colon,carcinoma,+1,1	PRKCZ	84	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G779A						.						79	77	78					1																	2082320		2203	4300	6503	SO:0001583	missense	5590	exon9			TCGGGCGCGGGAG	BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.230G>A	chr1.hg19:g.2082320G>A	ENSP00000383712:p.Arg77His	113.0	0.0		63.0	42.0	NM_002744	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Missense_Mutation	SNP	ENST00000400921.2	hg19	CCDS41229.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.747721	0.89663	.	.	ENSG00000067606	ENST00000378567;ENST00000400921;ENST00000461106;ENST00000470596;ENST00000400920;ENST00000486681;ENST00000470986;ENST00000470511;ENST00000497183	T;T;T;T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;1.88;-0.24;-0.24;-0.24;-0.24	4.8	4.8	0.61643	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.80639	0.4661	M	0.69358	2.11	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.82908	-0.0224	10	0.87932	D	0	.	17.0179	0.86424	0.0:0.0:1.0:0.0	.	156;84;260	E9PCW2;B3KUN5;Q05513	.;.;KPCZ_HUMAN	H	260;77;156;77;77;73;77;77;73	ENSP00000367830:R260H;ENSP00000383712:R77H;ENSP00000426412:R156H;ENSP00000424228:R77H;ENSP00000383711:R77H;ENSP00000424763:R73H;ENSP00000421219:R77H;ENSP00000422764:R73H	ENSP00000367830:R260H	R	+	2	0	PRKCZ	2072180	1.000000	0.71417	0.987000	0.45799	0.679000	0.39708	8.977000	0.93446	2.493000	0.84123	0.591000	0.81541	CGC	.	.		0.512	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		A	2082320	G	A	2082320	3	1	232	1	0	0	0	0	1	0	0	0	12529	1087	38	1	813	1	PRKCZ	1	2082320	Missense_Mutation	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10		2082320	247168301	1	32436										
CELA2A	63036	hgsc.bcm.edu	37	chr1	15793937	15793937	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gacggccggtggcaggtgcaCggcatcgtcagcttcgggtc	17	12	1	0	rs201638508		TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr1:15793937C>T	ENST00000359621.4	+	7	721	c.696C>T	c.(694-696)caC>caT	p.H232H	CELA2B_ENST00000494280.1_3'UTR	NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	232	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|keratohyalin granule (GO:0036457)	serine hydrolase activity (GO:0017171)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						GGCAGGTGCACGGCATCGTCA	0.592													T|||	1	0.000199681	0	0	5008	,	,		16971	0.001		0	False		,,,				2504	0				p.H232H		Atlas-SNP	.											.	CELA2A	32	.	0			c.C696T						.	T		0,4406		0,0,2203	71	67	68		696	-1.5	0.4	1		68	1,8599	818.9+/-406.8	0,1,4299	no	coding-synonymous	CELA2A	NM_033440.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		232/270	15793937	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	63036	exon7			GGTGCACGGCATC		CCDS157.1	1p36.21	2009-07-09			ENSG00000142615	ENSG00000142615	3.4.21.71		24609	protein-coding gene	gene with protein product	"elastase 2A"	609443				3646943, 2834346	Standard	NM_033440		Approved	ELA2A	uc001awk.3	P08217	OTTHUMG00000002258	ENST00000359621.4:c.696C>T	chr1.hg19:g.15793937C>T		79.0	0.0		65.0	40.0	NM_033440	B2R5I4|Q14243	Silent	SNP	ENST00000359621.4	hg19	CCDS157.1																																																																																			.	C|0.999;T|0.001		0.592	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440		T	15793937	C	T	15793937	2	4	232	1	0	0	0	0	0	0	0	1	3213	535	19	1		1	CELA2A	1	15793937	Silent	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	13711617	15793937	233456684	2	32437										
NFIA	4774	hgsc.bcm.edu	37	chr1	61743211	61743212	+	Frame_Shift_Ins	INS	-	-	C													0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	attcaagtcaatctgaaagtINScccagccagccaagtgacgc							TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr1:61743211_61743212insC	ENST00000403491.3	+	3	1063_1064	c.579_580insC	c.(580-582)cccfs	p.P194fs	NFIA_ENST00000371187.3_Frame_Shift_Ins_p.P194fs|NFIA_ENST00000407417.3_Frame_Shift_Ins_p.P186fs|NFIA_ENST00000371191.1_Frame_Shift_Ins_p.P217fs|NFIA_ENST00000371189.4_Frame_Shift_Ins_p.P239fs|NFIA_ENST00000371185.2_Intron|NFIA_ENST00000479364.1_3'UTR|NFIA_ENST00000485903.2_Frame_Shift_Ins_p.P194fs|NFIA_ENST00000371184.2_Intron	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	194					DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						AATCTGAAAGTCCCAGCCAGCC	0.46																																					p.S238fs		Atlas-INDEL	.											.	NFIA	76	.	0			c.714_715insC						.																																			SO:0001589	frameshift_variant	4774	exon4			.	U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599			7784	protein-coding gene	gene with protein product		600727				7590749	Standard	NM_001134673		Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.582dupC	chr1.hg19:g.61743214_61743214dupC	ENSP00000384523:p.Pro194fs	218.0	0.0		143.0	85.0	NM_001145512	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	Frame_Shift_Ins	INS	ENST00000403491.3	hg19	CCDS44156.1																																																																																			.	.		0.46	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023799.3	NM_005595		C	61743212	-	C	61743211	7	5	232	1	0	1	1	0	0	0	0	0	10379	1664	58	0	735	0	NFIA	1	61743211	Frame_Shift_Ins	INS	-	TCGA-DD-AAVZ-01A-11D-A40R-10	45949274	61743211	187507410	3	32438										
DENND2D	79961	hgsc.bcm.edu	37	chr1	111730233	111730233	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	attcaccacagctcttatttCacagttttttcccttggttt	4	11	3	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr1:111730233C>T	ENST00000357640.4	-	12	1639	c.1410G>A	c.(1408-1410)gtG>gtA	p.V470V	RP5-1180E21.5_ENST00000610049.1_RNA|DENND2D_ENST00000369752.5_Silent_p.V467V	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	470					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(1)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		GCTCTTATTTCACAGTTTTTT	0.433																																					p.V470V		Atlas-SNP	.											.	DENND2D	50	.	0			c.G1410A						.						244	202	216					1																	111730233		2202	4300	6502	SO:0001819	synonymous_variant	79961	exon12			TTATTTCACAGTT		CCDS831.1, CCDS60219.1	1p13.3	2014-02-12	2005-08-17		ENSG00000162777	ENSG00000162777		"DENN/MADD domain containing"	26192	protein-coding gene	gene with protein product		615111				12477932	Standard	NM_024901		Approved	FLJ22457, RP5-1180E21.2	uc001eal.2	Q9H6A0	OTTHUMG00000012356	ENST00000357640.4:c.1410G>A	chr1.hg19:g.111730233C>T		81.0	0.0		151.0	72.0	NM_024901	Q5T5V6|Q9BSU0	Silent	SNP	ENST00000357640.4	hg19	CCDS831.1																																																																																			.	.		0.433	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1	NM_024901		T	111730233	C	T	111730233	2	4	232	1	0	0	0	0	0	0	0	1	4433	813	29	3		3	DENND2D	1	111730233	Silent	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	49987022	111730233	137520388	4	32439										
ADORA3	140	hgsc.bcm.edu	37	chr1	112042811	112042811	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	taaaggcagccatgacagagCaaacaagaaaagaaccagaa	9	8	0	5			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr1:112042811C>T	ENST00000241356.4	-	2	1123	c.718G>A	c.(718-720)Gct>Act	p.A240T	ADORA3_ENST00000369717.4_Intron|ADORA3_ENST00000486342.1_5'Flank|ADORA3_ENST00000369716.4_Intron	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	240					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	CATGACAGAGCAAACAAGAAA	0.448																																					p.A240T		Atlas-SNP	.											ADORA3,colon,carcinoma,0,1	ADORA3	104	.	0			c.G718A						.						127	123	124					1																	112042811		2203	4300	6503	SO:0001583	missense	140	exon2			ACAGAGCAAACAA	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"GPCR / Class A : Adenosine receptors", "Immunoglobulin superfamily / V-set domain containing"	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.718G>A	chr1.hg19:g.112042811C>T	ENSP00000241356:p.Ala240Thr	197.0	0.0		238.0	105.0	NM_000677	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000241356.4	hg19	CCDS839.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.703716	0.68501	.	.	ENSG00000121933	ENST00000241356	T	0.72394	-0.65	4.91	4.91	0.64330	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.52338	0.1728	L	0.43757	1.38	0.45015	D	0.99803	B	0.14805	0.011	B	0.25614	0.062	T	0.51164	-0.8740	9	0.20519	T	0.43	.	18.0377	0.89309	0.0:1.0:0.0:0.0	.	240	P33765	AA3R_HUMAN	T	240	ENSP00000241356:A240T	ENSP00000241356:A240T	A	-	1	0	ADORA3	111844334	1.000000	0.71417	0.997000	0.53966	0.716000	0.41182	7.442000	0.80503	2.431000	0.82371	0.650000	0.86243	GCT	.	.		0.448	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683		T	112042811	C	T	112042811	3	4	232	1	0	0	0	0	1	0	0	0	329	710	25	3	956	3	ADORA3	1	112042811	Missense_Mutation	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	312578	112042811	137207810	5	32440										
C1orf26	54823	hgsc.bcm.edu	37	chr1	185259914	185259914	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	aacaggggatggtgtgaagaCatgctcaactataggatata	12	5	1	2			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr1:185259914C>T	ENST00000367500.4	+	19	2847	c.2682C>T	c.(2680-2682)gaC>gaT	p.D894D	SWT1_ENST00000367501.3_Silent_p.D894D	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	894										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						GGTGTGAAGACATGCTCAACT	0.398																																					p.D894D		Atlas-SNP	.											.	SWT1	88	.	0			c.C2682T						.						91	89	90					1																	185259914		2203	4300	6503	SO:0001819	synonymous_variant	54823	exon19			TGAAGACATGCTC	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.2682C>T	chr1.hg19:g.185259914C>T		97.0	0.0		183.0	32.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Silent	SNP	ENST00000367500.4	hg19	CCDS1367.1																																																																																			.	.		0.398	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		T	185259914	C	T	185259914	2	4	232	1	0	0	0	0	0	0	0	1	2037	477	17	3		3	C1orf26	1	185259914	Silent	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	73217103	185259914	63990707	6	32441										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185892673	185892673	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	ccttatggcatatggaatatTtctgactttgtaccaccaaa	6	9	1	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr1:185892673T>A	ENST00000271588.4	+	8	1402	c.1173T>A	c.(1171-1173)atT>atA	p.I391I	HMCN1_ENST00000367492.2_Silent_p.I391I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	391					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TATGGAATATTTCTGACTTTG	0.343																																					p.I391I		Atlas-SNP	.											.	HMCN1	797	.	0			c.T1173A						.						122	121	122					1																	185892673		2203	4299	6502	SO:0001819	synonymous_variant	83872	exon8			GAATATTTCTGAC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.1173T>A	chr1.hg19:g.185892673T>A		102.0	0.0		166.0	28.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.343	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	185892673	T	A	185892673	2	1	232	1	0	0	0	0	0	0	0	1	7229	1829	64	4		4	HMCN1	1	185892673	Silent	SNP	T	TCGA-DD-AAVZ-01A-11D-A40R-10	632759	185892673	63357948	7	32442										
KIF14	9928	hgsc.bcm.edu	37	chr1	200522763	200522764	+	Frame_Shift_Del	DEL	AC	AC	-													0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gagattctagttcctggtggAcaatgtgagttactctactc					rs547771811		TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr1:200522763_200522764delAC	ENST00000367350.4	-	30	5137_5138	c.4699_4700delGT	c.(4699-4701)gtcfs	p.V1567fs		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1567	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						TTCCTGGTGGACAATGTGAGTT	0.396																																					p.1567_1567del		Atlas-INDEL	.											.	KIF14	156	.	0			c.4700_4701del						.																																			SO:0001589	frameshift_variant	9928	exon30			.	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.4699_4700delGT	chr1.hg19:g.200522763_200522764delAC	ENSP00000356319:p.Val1567fs	213.0	0.0		318.0	195.0	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Frame_Shift_Del	DEL	ENST00000367350.4	hg19	CCDS30963.1																																																																																			.	.		0.396	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		-	200522764	AC	-	200522763	7	5	232	1	0	1	0	1	0	0	0	0	8285	275	10	0	250	0	KIF14	1	200522763	Frame_Shift_Del	DEL	AC	TCGA-DD-AAVZ-01A-11D-A40R-10	14630090	200522763	48727858	8	32443										
DDX59	83479	hgsc.bcm.edu	37	chr1	200635154	200635154	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	ggccagaatgtctcttcccaGaagtcccacaggaatcatct	8	13	3	2			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr1:200635154G>T	ENST00000331314.6	-	2	928	c.715C>A	c.(715-717)Ctg>Atg	p.L239M	DDX59_ENST00000447706.2_Missense_Mutation_p.L239M|DDX59_ENST00000367348.3_Missense_Mutation_p.L239M	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	239	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						TCTCTTCCCAGAAGTCCCACA	0.438																																					p.L239M		Atlas-SNP	.											.	DDX59	117	.	0			c.C715A						.						115	116	116					1																	200635154		2203	4300	6503	SO:0001583	missense	83479	exon2			TTCCCAGAAGTCC	BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"Zinc fingers, HIT-type", "DEAD-boxes"	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.715C>A	chr1.hg19:g.200635154G>T	ENSP00000330460:p.Leu239Met	243.0	0.0		389.0	90.0	NM_001031725	Q6PJL2|Q8IVW3|Q9H0W3	Missense_Mutation	SNP	ENST00000331314.6	hg19	CCDS30964.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.773351	0.31411	.	.	ENSG00000118197	ENST00000447706;ENST00000367348;ENST00000331314	T;T;T	0.14893	2.47;2.47;2.47	5.33	4.21	0.49690	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.207232	0.40144	N	0.001175	T	0.12603	0.0306	N	0.25380	0.74	0.27310	N	0.957321	B;B	0.22414	0.069;0.04	B;B	0.31016	0.123;0.048	T	0.09357	-1.0678	10	0.48119	T	0.1	-11.577	7.4454	0.27209	0.1253:0.0:0.7067:0.168	.	239;239	B7Z5N6;Q5T1V6	.;DDX59_HUMAN	M	239	ENSP00000394367:L239M;ENSP00000356317:L239M;ENSP00000330460:L239M	ENSP00000330460:L239M	L	-	1	2	DDX59	198901777	0.816000	0.29132	0.989000	0.46669	0.998000	0.95712	1.259000	0.32956	2.498000	0.84270	0.650000	0.86243	CTG	.	.		0.438	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4		T	200635154	G	T	200635154	3	4	232	1	0	0	0	0	1	0	0	0	4378	933	33	3	1172	3	DDX59	1	200635154	Missense_Mutation	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10	112391	200635154	48615467	9	32444										
FMN2	56776	hgsc.bcm.edu	37	chr1	240371876	240371876	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	agttgggagtagcactttacCaaccccacaggtgtgtggat	12	9	0	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr1:240371876C>G	ENST00000319653.9	+	5	3994	c.3764C>G	c.(3763-3765)cCa>cGa	p.P1255R		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1255	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AGCACTTTACCAACCCCACAG	0.562																																					p.P1255R		Atlas-SNP	.											.	FMN2	451	.	0			c.C3764G						.						65	60	62					1																	240371876		2203	4300	6503	SO:0001583	missense	56776	exon5			CTTTACCAACCCC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3764C>G	chr1.hg19:g.240371876C>G	ENSP00000318884:p.Pro1255Arg	137.0	0.0		287.0	49.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	c	7.924	0.739169	0.15642	.	.	ENSG00000155816	ENST00000319653	T	0.65732	-0.17	4.6	3.67	0.42095	Actin-binding FH2 (1);Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	0.540328	0.15894	U	0.239405	T	0.58047	0.2095	M	0.61703	1.905	0.19575	N	0.999964	P	0.38395	0.629	B	0.41619	0.361	T	0.51513	-0.8696	9	.	.	.	.	5.3112	0.15831	0.1668:0.6673:0.0:0.1659	.	1255	Q9NZ56	FMN2_HUMAN	R	1255	ENSP00000318884:P1255R	.	P	+	2	0	FMN2	238438499	0.764000	0.28473	0.014000	0.15608	0.596000	0.36781	3.296000	0.51802	0.893000	0.36288	0.472000	0.43445	CCA	.	.		0.562	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		G	240371876	C	G	240371876	3	3	232	1	0	0	0	0	1	0	0	0	5958	594	21	4	3782	4	FMN2	1	240371876	Missense_Mutation	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	39736722	240371876	8878745	10	32445										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71577248	71577248	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	cggtctccctttggtattgtGaaagcatcctggctaccaaa	9	11	1	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr2:71577248G>A	ENST00000409544.1	+	2	1794	c.1164G>A	c.(1162-1164)gtG>gtA	p.V388V	ZNF638_ENST00000355812.3_Silent_p.V388V|ZNF638_ENST00000264447.4_Silent_p.V388V|ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000377802.2_Silent_p.V388V	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	388					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TTGGTATTGTGAAAGCATCCT	0.408																																					p.V388V		Atlas-SNP	.											.	ZNF638	179	.	0			c.G1164A						.						141	137	138					2																	71577248		2203	4300	6503	SO:0001819	synonymous_variant	27332	exon2			TATTGTGAAAGCA	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.1164G>A	chr2.hg19:g.71577248G>A		68.0	0.0		55.0	21.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	hg19	CCDS1917.1																																																																																			.	.		0.408	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		A	71577248	G	A	71577248	2	1	232	1	0	0	0	0	0	0	0	1	18070	1277	45	3		3	ZNF638	2	71577248	Silent	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10		71577248	171622125	11	32446										
VWA3B	200403	hgsc.bcm.edu	37	chr2	98887262	98887262	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	tcgatgctggaaagtgaaatCctagctgggaaaatgtacat	11	6	0	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr2:98887262C>A	ENST00000477737.1	+	22	3165	c.2961C>A	c.(2959-2961)atC>atA	p.I987I	VWA3B_ENST00000490947.2_3'UTR	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	987										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AAAGTGAAATCCTAGCTGGGA	0.483																																					p.I987I		Atlas-SNP	.											.	VWA3B	138	.	0			c.C2961A						.						135	133	134					2																	98887262		1863	4104	5967	SO:0001819	synonymous_variant	200403	exon22			TGAAATCCTAGCT	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.2961C>A	chr2.hg19:g.98887262C>A		378.0	1.0		407.0	151.0	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Silent	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	4.661	0.122892	0.08931	.	.	ENSG00000168658	ENST00000473149	.	.	.	4.82	3.94	0.45596	.	.	.	.	.	T	0.56247	0.1972	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52873	-0.8517	4	.	.	.	.	7.0936	0.25297	0.0:0.8025:0.0:0.1975	.	.	.	.	T	398	.	.	P	+	1	0	VWA3B	98253694	0.987000	0.35691	0.957000	0.39632	0.556000	0.35491	0.267000	0.18552	1.252000	0.44001	0.655000	0.94253	CCT	.	.		0.483	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		A	98887262	C	A	98887262	2	1	232	1	0	0	0	0	0	0	0	1	17256	845	30	3		3	VWA3B	2	98887262	Silent	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	27310014	98887262	144312111	12	32447										
RAB3GAP1	22930	hgsc.bcm.edu	37	chr2	135809890	135809890	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	tcctcaagatggctgccgacAgtgaggtgatttctttgctc	11	10	2	3			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr2:135809890A>G	ENST00000264158.8	+	1	56	c.13A>G	c.(13-15)Agt>Ggt	p.S5G	RAB3GAP1_ENST00000539493.1_5'UTR|RAB3GAP1_ENST00000425393.1_Missense_Mutation_p.S5G|RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.S5G	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	5					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		GGCTGCCGACAGTGAGGTGAT	0.582																																					p.S5G		Atlas-SNP	.											.	RAB3GAP1	87	.	0			c.A13G						.						98	89	92					2																	135809890		2203	4300	6503	SO:0001583	missense	22930	exon1			GCCGACAGTGAGG	D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.13A>G	chr2.hg19:g.135809890A>G	ENSP00000264158:p.Ser5Gly	104.0	0.0		86.0	30.0	NM_001172435	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	hg19	CCDS33294.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.093703	0.56075	.	.	ENSG00000115839	ENST00000264158;ENST00000442034;ENST00000425393	T;T	0.47528	0.84;0.87	4.37	3.22	0.36961	.	0.048805	0.85682	N	0.000000	T	0.36303	0.0962	L	0.34521	1.04	0.80722	D	1	P;P	0.52170	0.951;0.882	P;B	0.46026	0.501;0.404	T	0.05666	-1.0871	10	0.26408	T	0.33	-2.4557	7.5345	0.27702	0.8992:0.0:0.1008:0.0	.	5;5	C9J837;Q15042	.;RB3GP_HUMAN	G	5	ENSP00000264158:S5G;ENSP00000411418:S5G	ENSP00000264158:S5G	S	+	1	0	RAB3GAP1	135526360	1.000000	0.71417	1.000000	0.80357	0.395000	0.30598	4.566000	0.60843	0.837000	0.34925	0.408000	0.27601	AGT	.	.		0.582	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233		G	135809890	A	G	135809890	3	3	232	1	0	0	0	0	1	0	0	0	12950	188	7	2	15	2	RAB3GAP1	2	135809890	Missense_Mutation	SNP	A	TCGA-DD-AAVZ-01A-11D-A40R-10	36922628	135809890	107389483	13	32448										
FN1	2335	hgsc.bcm.edu	37	chr2	216241231	216241231	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gttccctgacctgtgatggtGtagcttctgacatctggctt	11	10	2	3			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr2:216241231G>A	ENST00000359671.1	-	35	5869	c.5604C>T	c.(5602-5604)taC>taT	p.Y1868Y	FN1_ENST00000336916.4_Silent_p.Y1868Y|FN1_ENST00000346544.3_Silent_p.Y1868Y|FN1_ENST00000357009.2_Silent_p.Y1868Y|FN1_ENST00000421182.1_Silent_p.Y1778Y|FN1_ENST00000345488.5_Silent_p.Y1868Y|FN1_ENST00000357867.4_Silent_p.Y1778Y|FN1_ENST00000446046.1_Silent_p.Y1868Y|FN1_ENST00000443816.1_Silent_p.Y1778Y|FN1_ENST00000356005.4_Silent_p.Y1778Y|FN1_ENST00000354785.4_Silent_p.Y1959Y|FN1_ENST00000323926.6_Silent_p.Y1959Y|FN1_ENST00000432072.2_Silent_p.Y1869Y|FN1_ENST00000490833.1_5'Flank			P02751	FINC_HUMAN	fibronectin 1	1868	Binds to FBLN1.|Fibronectin type-III 14. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Heparin-binding 2.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	CTGTGATGGTGTAGCTTCTGA	0.458																																					p.Y1959Y		Atlas-SNP	.											FN1_ENST00000354785,NS,carcinoma,0,2	FN1	521	.	0			c.C5877T						.						199	159	173					2																	216241231		2203	4300	6503	SO:0001819	synonymous_variant	2335	exon36			GATGGTGTAGCTT		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.5604C>T	chr2.hg19:g.216241231G>A		86.0	0.0		92.0	42.0	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	hg19																																																																																				.	.		0.458	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		A	216241231	G	A	216241231	2	1	232	1	0	0	0	0	0	0	0	1	5970	1372	48	3		3	FN1	2	216241231	Silent	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10	80431341	216241231	26958142	14	32449										
ABCB6	10058	hgsc.bcm.edu	37	chr2	220080755	220080755	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	cactggatgtgccccgatccGcgatccgcagcacctcccct	9	19	0	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr2:220080755G>A	ENST00000265316.3	-	5	1434	c.1118C>T	c.(1117-1119)gCg>gTg	p.A373V	ABCB6_ENST00000439002.2_Missense_Mutation_p.A327V	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	373	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCCCGATCCGCGATCCGCAG	0.677																																					p.A373V		Atlas-SNP	.											.	ABCB6	76	.	0			c.C1118T						.						19	23	22					2																	220080755		2201	4300	6501	SO:0001583	missense	10058	exon5			CGATCCGCGATCC	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.1118C>T	chr2.hg19:g.220080755G>A	ENSP00000265316:p.Ala373Val	103.0	0.0		96.0	24.0	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	SNP	ENST00000265316.3	hg19	CCDS2436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.35|10.35	1.326377|1.326377	0.24080|0.24080	.|.	.|.	ENSG00000115657|ENSG00000115657	ENST00000265316;ENST00000439002|ENST00000295750	D;D|.	0.94376|.	-3.41;-2.3|.	5.08|5.08	3.94|3.94	0.45596|0.45596	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);|.	0.120411|.	0.56097|.	N|.	0.000027|.	T|T	0.07548|0.07548	0.0190|0.0190	N|N	0.00028|0.00028	-2.63|-2.63	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.17107|0.17107	-1.0380|-1.0380	10|5	0.35671|.	T|.	0.21|.	-15.6538|-15.6538	10.4037|10.4037	0.44243|0.44243	0.9219:0.0:0.078:0.0|0.9219:0.0:0.078:0.0	.|.	327;373|.	Q9NP58-4;Q9NP58|.	.;ABCB6_HUMAN|.	V|W	373;327|221	ENSP00000265316:A373V;ENSP00000394333:A327V|.	ENSP00000265316:A373V|.	A|R	-|-	2|1	0|2	ABCB6|ABCB6	219788999|219788999	1.000000|1.000000	0.71417|0.71417	0.871000|0.871000	0.34182|0.34182	0.961000|0.961000	0.63080|0.63080	7.120000|7.120000	0.77153|0.77153	1.068000|1.068000	0.40764|0.40764	-0.302000|-0.302000	0.09304|0.09304	GCG|CGG	.	.		0.677	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		A	220080755	G	A	220080755	3	1	232	1	0	0	0	0	1	0	0	0	45	1087	38	1	1470	1	ABCB6	2	220080755	Missense_Mutation	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10	3839524	220080755	23118618	15	32450										
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241494429	241494429	+	5'UTR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gtcctgcgccctcagcgggcCctcagcttcctcctcttcct	8	20	3	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr2:241494429C>A	ENST00000272972.3	-	0	137				ANKMY1_ENST00000462004.1_5'UTR|ANKMY1_ENST00000405002.1_5'UTR|ANKMY1_ENST00000403283.1_Missense_Mutation_p.G143C|ANKMY1_ENST00000406958.1_Missense_Mutation_p.G64C|ANKMY1_ENST00000373320.4_5'UTR|ANKMY1_ENST00000401804.1_Missense_Mutation_p.G64C|ANKMY1_ENST00000391987.1_5'UTR|ANKMY1_ENST00000536462.1_Missense_Mutation_p.G17C|ANKMY1_ENST00000405523.3_Missense_Mutation_p.G64C|ANKMY1_ENST00000361678.4_Missense_Mutation_p.G64C|ANKMY1_ENST00000373318.2_Missense_Mutation_p.G64C	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1								metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		CTCAGCGGGCCCTCAGCTTCC	0.587																																					p.G64C		Atlas-SNP	.											.	ANKMY1	112	.	0			c.G190T						.						110	112	111					2																	241494429		2203	4300	6503	SO:0001623	5_prime_UTR_variant	51281	exon3			GCGGGCCCTCAGC	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.-78G>T	chr2.hg19:g.241494429C>A		109.0	0.0		100.0	5.0	NM_017844	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	hg19	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.576996	0.28092	.	.	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000361678;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000441168;ENST00000411765	T;T;T;T;T;T;T;T	0.57907	2.82;3.5;2.14;2.3;0.37;2.16;2.11;1.44	3.85	2.97	0.34412	.	.	.	.	.	T	0.55955	0.1953	N	0.24115	0.695	0.09310	N	1	D;D;D	0.89917	0.999;0.999;1.0	D;P;D	0.70935	0.936;0.908;0.971	T	0.44298	-0.9337	9	0.72032	D	0.01	.	9.8639	0.41131	0.0:0.896:0.0:0.104	.	64;64;64	Q6GPI0;B5MBY4;Q9P2S6-2	.;.;.	C	64;64;64;143;64;17;64;17;64	ENSP00000362415:G64C;ENSP00000384555:G64C;ENSP00000355097:G64C;ENSP00000383968:G143C;ENSP00000385887:G64C;ENSP00000444707:G17C;ENSP00000385635:G64C;ENSP00000405938:G17C	ENSP00000355097:G64C	G	-	1	0	ANKMY1	241143102	0.003000	0.15002	0.044000	0.18714	0.073000	0.16967	0.919000	0.28692	1.200000	0.43188	0.655000	0.94253	GGC	.	.		0.587	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		A	241494429	C	A	241494429	1	1	232	0	1	0	0	0	0	0	0	0	634	623	22	3		3	ANKMY1	2	241494429	5'UTR	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	21413674	241494429	1704944	16	32451										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38739634	38739634	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gatgcctacggctgggctccCacagtcccctctggtgccat	11	16	1	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr3:38739634C>T	ENST00000449082.2	-	27	5076	c.5077G>A	c.(5077-5079)Ggg>Agg	p.G1693R		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1693					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GCTGGGCTCCCACAGTCCCCT	0.562																																					p.G1693R		Atlas-SNP	.											.	SCN10A	359	.	0			c.G5077A						.						93	91	92					3																	38739634		2203	4300	6503	SO:0001583	missense	6336	exon27			GGCTCCCACAGTC	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.5077G>A	chr3.hg19:g.38739634C>T	ENSP00000390600:p.Gly1693Arg	119.0	0.0		140.0	61.0	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	hg19	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.100457	0.76983	.	.	ENSG00000185313	ENST00000449082	D	0.98512	-4.97	5.38	5.38	0.77491	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99486	0.9817	H	0.99042	4.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98034	1.0378	10	0.87932	D	0	.	19.3209	0.94237	0.0:1.0:0.0:0.0	.	1693	Q9Y5Y9	SCNAA_HUMAN	R	1693	ENSP00000390600:G1693R	ENSP00000390600:G1693R	G	-	1	0	SCN10A	38714638	1.000000	0.71417	0.986000	0.45419	0.726000	0.41606	7.651000	0.83577	2.800000	0.96347	0.655000	0.94253	GGG	.	.		0.562	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38739634	C	T	38739634	3	4	232	1	0	0	0	0	1	0	0	0	13927	594	21	3	797	3	SCN10A	3	38739634	Missense_Mutation	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10		38739634	159282796	17	32452										
ITGB5	3693	hgsc.bcm.edu	37	chr3	124560396	124560396	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	cgcaatttggaaacaacttgTaactagagaggaagaagaga	11	5	0	3			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr3:124560396T>G	ENST00000296181.4	-	5	910	c.614A>C	c.(613-615)tAc>tCc	p.Y205S		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	205	VWFA.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		AAACAACTTGTAACTAGAGAG	0.463																																					p.Y205S		Atlas-SNP	.											.	ITGB5	66	.	0			c.A614C						.						65	59	61					3																	124560396		2203	4300	6503	SO:0001583	missense	3693	exon5			AACTTGTAACTAG	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.614A>C	chr3.hg19:g.124560396T>G	ENSP00000296181:p.Tyr205Ser	73.0	0.0		66.0	28.0	NM_002213	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	hg19	CCDS3030.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.0|21.0	4.075961|4.075961	0.76415|0.76415	.|.	.|.	ENSG00000082781|ENSG00000082781	ENST00000496703|ENST00000296181	.|D	.|0.97752	.|-4.52	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	.|0.060984	.|0.64402	.|D	.|0.000002	D|D	0.97377|0.97377	0.9142|0.9142	L|L	0.31371|0.31371	0.925|0.925	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.73708	.|0.981	D|D	0.97059|0.97059	0.9769|0.9769	5|10	.|0.31617	.|T	.|0.26	.|.	16.0399|16.0399	0.80667|0.80667	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|205	.|P18084	.|ITB5_HUMAN	F|S	1|205	.|ENSP00000296181:Y205S	.|ENSP00000296181:Y205S	L|Y	-|-	3|2	2|0	ITGB5|ITGB5	126043086|126043086	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	5.734000|5.734000	0.68580|0.68580	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	TTA|TAC	.	.		0.463	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		G	124560396	T	G	124560396	3	3	232	1	0	0	0	0	1	0	0	0	7907	1638	57	5	1829	5	ITGB5	3	124560396	Missense_Mutation	SNP	T	TCGA-DD-AAVZ-01A-11D-A40R-10	85820762	124560396	73462034	18	32453										
FOXL2	668	hgsc.bcm.edu	37	chr3	138664931	138664931	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gcaggaggcatagggcatggGtgagggaggctgcggtagcg	22	6	0	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr3:138664931G>C	ENST00000330315.3	-	1	1051	c.634C>G	c.(634-636)Ccc>Gcc	p.P212A	RP11-548O1.3_ENST00000495287.1_lincRNA|C3orf72_ENST00000383165.3_5'Flank	NM_023067.3	NP_075555.1	P58012	FOXL2_HUMAN	forkhead box L2	212					apoptotic DNA fragmentation (GO:0006309)|cell differentiation (GO:0030154)|embryonic eye morphogenesis (GO:0048048)|extraocular skeletal muscle development (GO:0002074)|female somatic sex determination (GO:0019101)|granulosa cell differentiation (GO:0060014)|menstruation (GO:0042703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	cysteine-type endopeptidase regulator activity involved in apoptotic process (GO:0043028)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin conjugating enzyme binding (GO:0031624)			large_intestine(1)|lung(1)|ovary(333)|skin(1)	336						TAGGGCATGGGTGAGGGAGGC	0.736			Mis		granulosa-cell tumour of the ovary		"Blepharophimosis, ptosis and epicanthus inversus Types I, II; Premature ovarian failure type III"																														p.P212A		Atlas-SNP	.		Dom	yes		3	3q23	668	forkhead box L2	yes	O	.	FOXL2	408	.	0			c.C634G						.						10	4	6					3																	138664931		1217	2299	3516	SO:0001583	missense	668	exon1			GCATGGGTGAGGG	AF301906	CCDS3105.1	3q23	2008-04-10			ENSG00000183770	ENSG00000183770		"Forkhead boxes"	1092	protein-coding gene	gene with protein product		605597		BPES		1941972	Standard	NM_023067		Approved	BPES1	uc003esw.3	P58012	OTTHUMG00000159889	ENST00000330315.3:c.634C>G	chr3.hg19:g.138664931G>C	ENSP00000333188:p.Pro212Ala	508.0	0.0		435.0	25.0	NM_023067	Q4ZGJ3	Missense_Mutation	SNP	ENST00000330315.3	hg19	CCDS3105.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.800356	0.70567	.	.	ENSG00000183770	ENST00000330315;ENST00000542203	D	0.94613	-3.47	3.66	3.66	0.41972	.	0.257379	0.31484	U	0.007562	D	0.95516	0.8543	L	0.42245	1.32	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	D	0.95975	0.8973	10	0.62326	D	0.03	.	15.7039	0.77563	0.0:0.0:1.0:0.0	.	212	P58012	FOXL2_HUMAN	A	212	ENSP00000333188:P212A	ENSP00000333188:P212A	P	-	1	0	FOXL2	140147621	1.000000	0.71417	0.990000	0.47175	0.895000	0.52256	5.096000	0.64535	1.742000	0.51746	0.505000	0.49811	CCC	.	.		0.736	FOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357999.1			C	138664931	G	C	138664931	3	2	232	1	0	0	0	0	1	0	0	0	6025	1261	44	4	500	4	FOXL2	3	138664931	Missense_Mutation	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10	14104535	138664931	59357499	19	32454										
ELF2	1998	hgsc.bcm.edu	37	chr4	139994674	139994674	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	cagggcttcagcagcttcaaTtgtcttatctgtacagtgtg	10	9	4	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr4:139994674T>C	ENST00000394235.2	-	5	788	c.286A>G	c.(286-288)Att>Gtt	p.I96V	ELF2_ENST00000265495.4_Missense_Mutation_p.I96V|ELF2_ENST00000510408.1_Missense_Mutation_p.I36V|ELF2_ENST00000379550.1_Missense_Mutation_p.I96V|ELF2_ENST00000379549.2_Missense_Mutation_p.I36V|ELF2_ENST00000358635.3_Missense_Mutation_p.I36V	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)											endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					GCAGCTTCAATTGTCTTATCT	0.383																																					p.H96D		Atlas-SNP	.											.	ELF2	43	.	0			c.C286G						.						116	105	109					4																	139994674		2203	4300	6503	SO:0001583	missense	1998	exon4			CTTCAATTGTCTT	AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.286A>G	chr4.hg19:g.139994674T>C	ENSP00000377782:p.Ile96Val	236.0	0.0		219.0	77.0	NM_201999		Missense_Mutation	SNP	ENST00000394235.2	hg19	CCDS3744.1	.	.	.	.	.	.	.	.	.	.	T	19.51	3.841831	0.71488	.	.	ENSG00000109381	ENST00000358635;ENST00000394235;ENST00000379550;ENST00000265495;ENST00000379549;ENST00000510408;ENST00000420916;ENST00000512627	T;T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.21	5.21	0.72293	.	0.111315	0.64402	D	0.000014	T	0.56187	0.1968	L	0.52126	1.63	0.44155	D	0.996959	P;D;P;P;P	0.53885	0.699;0.963;0.592;0.953;0.954	P;P;P;P;P	0.55087	0.768;0.678;0.475;0.76;0.718	T	0.54879	-0.8227	9	.	.	.	.	15.0854	0.72148	0.0:0.0:0.0:1.0	.	36;96;36;36;36	B0KYV4;Q15723-1;E9PCX3;B7Z720;Q15723-3	.;.;.;.;.	V	36;96;96;96;36;36;36;36	ENSP00000351458:I36V;ENSP00000377782:I96V;ENSP00000368868:I96V;ENSP00000265495:I96V;ENSP00000368867:I36V;ENSP00000426997:I36V;ENSP00000397796:I36V;ENSP00000426087:I36V	.	I	-	1	0	ELF2	140214124	1.000000	0.71417	0.917000	0.36280	0.972000	0.66771	4.905000	0.63286	1.982000	0.57802	0.455000	0.32223	ATT	.	.		0.383	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874		C	139994674	T	C	139994674	3	2	232	1	0	0	0	0	1	0	0	0	5056	1493	52	2	1519	2	ELF2	4	139994674	Missense_Mutation	SNP	T	TCGA-DD-AAVZ-01A-11D-A40R-10		139994674	51159602	20	32455										
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65309395	65309395	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	aggctccctgatggattttcTcagctgttaaacctaaccca	7	12	1	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr5:65309395T>C	ENST00000284037.5	+	6	794	c.405T>C	c.(403-405)tcT>tcC	p.S135S	ERBB2IP_ENST00000416865.2_Silent_p.S135S|ERBB2IP_ENST00000508515.1_Silent_p.S135S|ERBB2IP_ENST00000506030.1_Silent_p.S135S|ERBB2IP_ENST00000380938.2_Silent_p.S135S|ERBB2IP_ENST00000511297.1_Silent_p.S135S|ERBB2IP_ENST00000380939.2_Silent_p.S135S|ERBB2IP_ENST00000380935.1_Silent_p.S135S|ERBB2IP_ENST00000380943.2_Silent_p.S135S|ERBB2IP_ENST00000380936.1_Silent_p.S135S	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	135					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		ATGGATTTTCTCAGCTGTTAA	0.323																																					p.S135S		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.T405C						.						153	157	155					5																	65309395		2203	4300	6503	SO:0001819	synonymous_variant	55914	exon6			ATTTTCTCAGCTG		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"densin-180-like protein", "ERBB2-interacting protein"	606944	"erbb2-interacting protein"			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.405T>C	chr5.hg19:g.65309395T>C		102.0	0.0		108.0	11.0	NM_001253701	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Silent	SNP	ENST00000284037.5	hg19	CCDS58953.1																																																																																			.	.		0.323	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		C	65309395	T	C	65309395	2	2	232	1	0	0	0	0	0	0	0	1	5209	1538	54	2		2	ERBB2IP	5	65309395	Silent	SNP	T	TCGA-DD-AAVZ-01A-11D-A40R-10		65309395	115605865	21	32456										
SLC12A2	6558	hgsc.bcm.edu	37	chr5	127483354	127483354	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	atttacaccactaatttctgCaggtatattttcagccactc	4	11	2	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr5:127483354C>G	ENST00000262461.2	+	11	2003	c.1814C>G	c.(1813-1815)gCa>gGa	p.A605G	SLC12A2_ENST00000343225.4_Missense_Mutation_p.A605G	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	605					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	CTAATTTCTGCAGGTATATTT	0.323																																					p.A605G		Atlas-SNP	.											.	SLC12A2	119	.	0			c.C1814G						.						127	125	126					5																	127483354		2203	4297	6500	SO:0001583	missense	6558	exon11			TTTCTGCAGGTAT		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.1814C>G	chr5.hg19:g.127483354C>G	ENSP00000262461:p.Ala605Gly	161.0	0.0		103.0	32.0	NM_001046	Q8N713|Q8WWH7	Missense_Mutation	SNP	ENST00000262461.2	hg19	CCDS4144.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.506570	0.85282	.	.	ENSG00000064651	ENST00000262461;ENST00000343225	D;D	0.99014	-5.33;-5.33	5.06	5.06	0.68205	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99333	0.9766	M	0.85462	2.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99139	1.0855	10	0.62326	D	0.03	.	18.6192	0.91315	0.0:1.0:0.0:0.0	.	605;605	P55011-3;P55011	.;S12A2_HUMAN	G	605	ENSP00000262461:A605G;ENSP00000340878:A605G	ENSP00000262461:A605G	A	+	2	0	SLC12A2	127511253	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.212000	0.77941	2.638000	0.89438	0.585000	0.79938	GCA	.	.		0.323	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		G	127483354	C	G	127483354	3	3	232	1	0	0	0	0	1	0	0	0	14398	710	25	4	1856	4	SLC12A2	5	127483354	Missense_Mutation	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	62173959	127483354	53431906	22	32457										
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140516627	140516627	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	ggagccacagaccgcggctcCccggcgctgagcagcgaggc	16	16	0	2			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr5:140516627C>T	ENST00000231134.5	+	1	1828	c.1611C>T	c.(1609-1611)tcC>tcT	p.S537S		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	537	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACCGCGGCTCCCCGGCGCTGA	0.682																																					p.S537S		Atlas-SNP	.											.	PCDHB5	184	.	0			c.C1611T						.						41	47	45					5																	140516627		2203	4299	6502	SO:0001819	synonymous_variant	26167	exon1			CGGCTCCCCGGCG	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.1611C>T	chr5.hg19:g.140516627C>T		126.0	0.0		182.0	77.0	NM_015669	Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	hg19	CCDS4247.1																																																																																			.	.		0.682	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		T	140516627	C	T	140516627	2	4	232	1	0	0	0	0	0	0	0	1	11554	610	22	3		3	PCDHB5	5	140516627	Silent	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	13033273	140516627	40398633	23	32458										
BAI3	577	hgsc.bcm.edu	37	chr6	70037730	70037730	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	aggtttaccagcattagtagTggccacatcagtaggcttca	10	9	2	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr6:70037730T>G	ENST00000370598.1	+	22	3805	c.2984T>G	c.(2983-2985)gTg>gGg	p.V995G	BAI3_ENST00000238918.8_Missense_Mutation_p.V201G	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	995					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V995A(2)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				GCATTAGTAGTGGCCACATCA	0.383																																					p.V995G		Atlas-SNP	.											BAI3,colon,carcinoma,0,3	BAI3	451	.	2	Substitution - Missense(2)	lung(2)	c.T2984G						.						135	114	121					6																	70037730		2203	4300	6503	SO:0001583	missense	577	exon22			TAGTAGTGGCCAC	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.2984T>G	chr6.hg19:g.70037730T>G	ENSP00000359630:p.Val995Gly	101.0	0.0		117.0	55.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.132426	0.77662	.	.	ENSG00000135298	ENST00000370598;ENST00000238918	T;T	0.59083	0.29;0.29	5.75	4.58	0.56647	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.77405	0.4125	H	0.95745	3.715	0.80722	D	1	P;P;D	0.89917	0.948;0.901;1.0	P;P;D	0.97110	0.765;0.636;1.0	D	0.83731	0.0198	10	0.87932	D	0	.	11.7912	0.52070	0.0:0.0688:0.0:0.9312	.	201;995;995	B7Z356;A8K0Y1;O60242	.;.;BAI3_HUMAN	G	995;201	ENSP00000359630:V995G;ENSP00000238918:V201G	ENSP00000238918:V201G	V	+	2	0	BAI3	70094451	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.040000	0.89188	1.002000	0.39104	0.533000	0.62120	GTG	.	.		0.383	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			G	70037730	T	G	70037730	3	3	232	1	0	0	0	0	1	0	0	0	1300	1696	59	5	3062	5	BAI3	6	70037730	Missense_Mutation	SNP	T	TCGA-DD-AAVZ-01A-11D-A40R-10		70037730	101077337	24	32459										
KIAA1324L	222223	hgsc.bcm.edu	37	chr7	86554856	86554856	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gaacttaccattcattccatCgcactttgaattcccaacat	3	13	1	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr7:86554856C>T	ENST00000450689.2	-	10	1572	c.1387G>A	c.(1387-1389)Gat>Aat	p.D463N	KIAA1324L_ENST00000297222.6_Missense_Mutation_p.D223N|KIAA1324L_ENST00000444627.1_Missense_Mutation_p.D463N|KIAA1324L_ENST00000416314.1_Missense_Mutation_p.D296N	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	463						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					TTCATTCCATCGCACTTTGAA	0.393																																					p.D463N		Atlas-SNP	.											.	KIAA1324L	225	.	0			c.G1387A						.						127	111	116					7																	86554856		2203	4300	6503	SO:0001583	missense	222223	exon10			TTCCATCGCACTT	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.1387G>A	chr7.hg19:g.86554856C>T	ENSP00000413445:p.Asp463Asn	115.0	0.0		107.0	38.0	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Missense_Mutation	SNP	ENST00000450689.2	hg19	CCDS47632.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.2|20.2	3.953897|3.953897	0.73902|0.73902	.|.	.|.	ENSG00000164659|ENSG00000164659	ENST00000450689;ENST00000297222;ENST00000444627;ENST00000416314|ENST00000423294	T;T;T;T|.	0.41400|.	1.0;1.0;1.0;1.0|.	5.7|5.7	5.7|5.7	0.88788|0.88788	Growth factor, receptor (1);|.	0.045007|.	0.85682|.	D|.	0.000000|.	T|T	0.72779|0.72779	0.3503|0.3503	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	D;D;D|.	0.69078|.	0.99;0.997;0.997|.	P;P;P|.	0.60886|.	0.812;0.88;0.759|.	T|T	0.69273|0.69273	-0.5188|-0.5188	10|5	0.21014|.	T|.	0.42|.	.|.	18.8137|18.8137	0.92070|0.92070	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	463;223;296|.	A8MWY0;A8MWY0-2;B4DJV3|.	K132L_HUMAN;.;.|.	N|Q	463;223;463;296|423	ENSP00000413445:D463N;ENSP00000297222:D223N;ENSP00000397377:D463N;ENSP00000402390:D296N|.	ENSP00000297222:D223N|.	D|R	-|-	1|2	0|0	KIAA1324L|KIAA1324L	86392792|86392792	1.000000|1.000000	0.71417|0.71417	0.909000|0.909000	0.35828|0.35828	0.404000|0.404000	0.30871|0.30871	7.793000|7.793000	0.85851|0.85851	2.698000|2.698000	0.92095|0.92095	0.563000|0.563000	0.77884|0.77884	GAT|CGA	.	.		0.393	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		T	86554856	C	T	86554856	3	4	232	1	0	0	0	0	1	0	0	0	8233	884	31	1	1754	1	KIAA1324L	7	86554856	Missense_Mutation	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10		86554856	72583807	25	32460										
CHRNB3	1142	hgsc.bcm.edu	37	chr8	42586871	42586871	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	tcgtgaaatcaaacggaactGttgtctggacccctcccgcc	9	14	2	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr8:42586871G>C	ENST00000289957.2	+	5	549	c.421G>C	c.(421-423)Gtt>Ctt	p.V141L		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	141					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	AAACGGAACTGTTGTCTGGAC	0.542																																					p.V141L		Atlas-SNP	.											.	CHRNB3	74	.	0			c.G421C						.						62	55	57					8																	42586871		2203	4300	6503	SO:0001583	missense	1142	exon5			GGAACTGTTGTCT	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.421G>C	chr8.hg19:g.42586871G>C	ENSP00000289957:p.Val141Leu	165.0	1.0		286.0	190.0	NM_000749	Q15827	Missense_Mutation	SNP	ENST00000289957.2	hg19	CCDS6134.1	.	.	.	.	.	.	.	.	.	.	g	12.34	1.907703	0.33721	.	.	ENSG00000147432	ENST00000289957	D	0.84070	-1.8	5.35	2.08	0.27032	Neurotransmitter-gated ion-channel ligand-binding (3);	0.155822	0.56097	D	0.000031	D	0.83096	0.5180	M	0.78456	2.415	0.29239	N	0.872747	B	0.24823	0.112	B	0.37422	0.249	T	0.79169	-0.1914	10	0.66056	D	0.02	.	6.9631	0.24608	0.4119:0.0:0.5881:0.0	.	141	Q05901	ACHB3_HUMAN	L	141	ENSP00000289957:V141L	ENSP00000289957:V141L	V	+	1	0	CHRNB3	42706028	0.253000	0.23982	0.007000	0.13788	0.015000	0.08874	0.872000	0.28037	0.762000	0.33152	-0.145000	0.13849	GTT	.	.		0.542	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			C	42586871	G	C	42586871	3	2	232	1	0	0	0	0	1	0	0	0	3394	1377	48	4	439	4	CHRNB3	8	42586871	Missense_Mutation	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10		42586871	103777151	26	32461										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113293433	113293433	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	aggtaaagttccagaccatgTtccattggctgtgcactgtc	10	10	0	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr8:113293433T>C	ENST00000297405.5	-	59	9722	c.9478A>G	c.(9478-9480)Aca>Gca	p.T3160A	CSMD3_ENST00000343508.3_Missense_Mutation_p.T3120A|CSMD3_ENST00000455883.2_Missense_Mutation_p.T2991A|CSMD3_ENST00000352409.3_Missense_Mutation_p.T3090A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3160	Sushi 23. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CCAGACCATGTTCCATTGGCT	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.T3160A		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A9478G						.						116	110	112					8																	113293433		2203	4300	6503	SO:0001583	missense	114788	exon59			ACCATGTTCCATT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9478A>G	chr8.hg19:g.113293433T>C	ENSP00000297405:p.Thr3160Ala	155.0	0.0		171.0	22.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.856844	0.91433	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	5.67	5.67	0.87782	Complement control module (2);Sushi/SCR/CCP (3);	0.066283	0.64402	D	0.000014	T	0.77226	0.4099	M	0.74389	2.26	0.58432	D	0.999991	D;P;P	0.57899	0.981;0.478;0.748	D;P;P	0.65010	0.931;0.491;0.511	T	0.76675	-0.2872	10	0.36615	T	0.2	.	15.9699	0.80004	0.0:0.0:0.0:1.0	.	2991;3160;3120	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	A	3120;3160;2430;2991;3090	ENSP00000345799:T3120A;ENSP00000297405:T3160A;ENSP00000341558:T2430A;ENSP00000412263:T2991A;ENSP00000343124:T3090A	ENSP00000297405:T3160A	T	-	1	0	CSMD3	113362609	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.946000	0.87746	2.170000	0.68504	0.524000	0.50904	ACA	.	.		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113293433	T	C	113293433	3	2	232	1	0	0	0	0	1	0	0	0	3948	1725	60	2	1697	2	CSMD3	8	113293433	Missense_Mutation	SNP	T	TCGA-DD-AAVZ-01A-11D-A40R-10	70706562	113293433	33070589	27	32462										
SNAPC4	6621	hgsc.bcm.edu	37	chr9	139272186	139272186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	ggctgccaggaaccgcgcccGcaacaggaggtaggccgggt	17	13	0	0	rs372472067		TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr9:139272186G>A	ENST00000298532.2	-	21	4461	c.4093C>T	c.(4093-4095)Cgg>Tgg	p.R1365W		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		AACCGCGCCCGCAACAGGAGG	0.726																																					p.R1365W		Atlas-SNP	.											.	SNAPC4	82	.	0			c.C4093T						.		TRP/ARG	0,4390		0,0,2195	21	23	23		4093	1.7	0	9		23	2,8586		0,2,4292	no	missense	SNAPC4	NM_003086.2	101	0,2,6487	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	1365/1470	139272186	2,12976	2195	4294	6489	SO:0001583	missense	6621	exon21			GCGCCCGCAACAG	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"small nuclear RNA activating complex, polypeptide 4, 190kD"			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.4093C>T	chr9.hg19:g.139272186G>A	ENSP00000298532:p.Arg1365Trp	112.0	0.0		133.0	47.0	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	hg19	CCDS6998.1	.	.	.	.	.	.	.	.	.	.	g	11.34	1.610741	0.28712	0.0	2.33E-4	ENSG00000165684	ENST00000298532	T	0.24908	1.83	4.06	1.66	0.24008	.	0.196559	0.34507	N	0.003920	T	0.19167	0.0460	L	0.40543	1.245	0.09310	N	1	B	0.26081	0.141	B	0.14023	0.01	T	0.15694	-1.0428	10	0.87932	D	0	-13.5129	10.0768	0.42366	0.0:0.0:0.3652:0.6348	.	1365	Q5SXM2	SNPC4_HUMAN	W	1365	ENSP00000298532:R1365W	ENSP00000298532:R1365W	R	-	1	2	SNAPC4	138392007	0.983000	0.35010	0.012000	0.15200	0.005000	0.04900	1.417000	0.34770	0.044000	0.15775	-0.408000	0.06270	CGG	.	.		0.726	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086		A	139272186	G	A	139272186	3	1	232	1	0	0	0	0	1	0	0	0	14852	1086	38	1	324	1	SNAPC4	9	139272186	Missense_Mutation	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10		139272186	1941245	28	32463										
GPR158	57512	hgsc.bcm.edu	37	chr10	25464914	25464914	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	cgctgtccgcaccggccccaCaggtcttcctccaggccacg	10	20	1	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr10:25464914C>A	ENST00000376351.3	+	1	924	c.565C>A	c.(565-567)Cag>Aag	p.Q189K	GPR158-AS1_ENST00000449643.1_RNA	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	189					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						ACCGGCCCCACAGGTCTTCCT	0.677																																					p.Q189K		Atlas-SNP	.											.	GPR158	255	.	0			c.C565A						.						34	31	32					10																	25464914		2202	4299	6501	SO:0001583	missense	57512	exon1			GCCCCACAGGTCT	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.565C>A	chr10.hg19:g.25464914C>A	ENSP00000365529:p.Gln189Lys	63.0	0.0		86.0	33.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	C	19.21	3.782708	0.70222	.	.	ENSG00000151025	ENST00000376351	T	0.77620	-1.11	4.77	4.77	0.60923	.	0.160748	0.41605	D	0.000860	D	0.84129	0.5404	M	0.71036	2.16	0.34689	D	0.725483	P	0.47910	0.902	P	0.53006	0.715	D	0.89589	0.3826	10	0.59425	D	0.04	.	17.9839	0.89150	0.0:1.0:0.0:0.0	.	189	Q5T848	GP158_HUMAN	K	189	ENSP00000365529:Q189K	ENSP00000365529:Q189K	Q	+	1	0	GPR158	25504920	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.846000	0.39289	2.485000	0.83878	0.591000	0.81541	CAG	.	.		0.677	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		A	25464914	C	A	25464914	3	1	232	1	0	0	0	0	1	0	0	0	6671	479	17	3	567	3	GPR158	10	25464914	Missense_Mutation	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10		25464914	110069833	29	32464										
ZNF248	57209	hgsc.bcm.edu	37	chr10	38121102	38121102	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	ttctctgatgttgagtgaggTttgacttctcccagaaggtt	11	7	2	5			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr10:38121102T>C	ENST00000395867.3	-	6	1731	c.1181A>G	c.(1180-1182)aAc>aGc	p.N394S	ZNF248_ENST00000357328.4_Missense_Mutation_p.N394S|ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000494133.1_Intron|AL135791.1_ENST00000583461.1_RNA	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TTGAGTGAGGTTTGACTTCTC	0.463																																					p.N394S		Atlas-SNP	.											.	ZNF248	61	.	0			c.A1181G						.						100	100	100					10																	38121102		2203	4299	6502	SO:0001583	missense	57209	exon6			GTGAGGTTTGACT	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"Zinc fingers, C2H2-type", "-"	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.1181A>G	chr10.hg19:g.38121102T>C	ENSP00000379208:p.Asn394Ser	114.0	0.0		99.0	37.0	NM_001267597	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	hg19	CCDS7194.1	.	.	.	.	.	.	.	.	.	.	T	11.36	1.617182	0.28801	.	.	ENSG00000198105	ENST00000395867;ENST00000357328	T;T	0.19938	2.11;2.11	4.04	4.04	0.47022	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000050	T	0.12944	0.0314	N	0.10733	0.035	0.36694	D	0.879722	D	0.56035	0.974	P	0.49665	0.618	T	0.07195	-1.0785	10	0.07482	T	0.82	.	11.5902	0.50941	0.0:0.0:0.0:1.0	.	394	Q8NDW4	ZN248_HUMAN	S	394	ENSP00000379208:N394S;ENSP00000349882:N394S	ENSP00000349882:N394S	N	-	2	0	ZNF248	38161108	0.000000	0.05858	1.000000	0.80357	0.985000	0.73830	0.016000	0.13377	2.062000	0.61559	0.455000	0.32223	AAC	.	.		0.463	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		C	38121102	T	C	38121102	3	2	232	1	0	0	0	0	1	0	0	0	17808	1725	60	2	562	2	ZNF248	10	38121102	Missense_Mutation	SNP	T	TCGA-DD-AAVZ-01A-11D-A40R-10	12656188	38121102	97413645	30	32465										
LOXL4	84171	hgsc.bcm.edu	37	chr10	100017527	100017527	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	agggtccgctcatatcccctGcagcgcacctcactcaggtg	10	16	3	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr10:100017527G>A	ENST00000260702.3	-	8	1290	c.1140C>T	c.(1138-1140)tgC>tgT	p.C380C	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	380	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		CATATCCCCTGCAGCGCACCT	0.602																																					p.C380C		Atlas-SNP	.											.	LOXL4	60	.	0			c.C1140T						.						100	85	90					10																	100017527		2203	4300	6503	SO:0001819	synonymous_variant	84171	exon8			TCCCCTGCAGCGC	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.1140C>T	chr10.hg19:g.100017527G>A		69.0	0.0		85.0	36.0	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Silent	SNP	ENST00000260702.3	hg19	CCDS7473.1																																																																																			.	.		0.602	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211		A	100017527	G	A	100017527	2	1	232	1	0	0	0	0	0	0	0	1	8911	1311	46	3		3	LOXL4	10	100017527	Silent	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10	61896425	100017527	35517220	31	32466										
OR8H1	219469	hgsc.bcm.edu	37	chr11	56057636	56057636	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	tgtcttctctgcatgactctAatgagagcatttttaacttc	6	9	3	2			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr11:56057636A>G	ENST00000313022.2	-	1	930	c.903T>C	c.(901-903)atT>atC	p.I301I		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	301						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					GCATGACTCTAATGAGAGCAT	0.348																																					p.I301I		Atlas-SNP	.											.	OR8H1	89	.	0			c.T903C						.						90	102	98					11																	56057636		2201	4294	6495	SO:0001819	synonymous_variant	219469	exon1			GACTCTAATGAGA	AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"GPCR / Class A : Olfactory receptors"	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.903T>C	chr11.hg19:g.56057636A>G		192.0	0.0		170.0	65.0	NM_001005199	B2RNI7|Q6IFC5	Silent	SNP	ENST00000313022.2	hg19	CCDS31526.1																																																																																			.	.		0.348	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199		G	56057636	A	G	56057636	2	3	232	1	0	0	0	0	0	0	0	1	11246	358	13	2		2	OR8H1	11	56057636	Silent	SNP	A	TCGA-DD-AAVZ-01A-11D-A40R-10		56057636	78948880	32	32467										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73849880	73849880	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gaactgttcagaagggacatCtgcttccgtggagctctgcc	12	11	3	1	rs139995248		TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr11:73849880C>A	ENST00000334126.7	-	5	1066	c.840G>T	c.(838-840)caG>caT	p.Q280H	C2CD3_ENST00000539061.1_Missense_Mutation_p.Q280H|C2CD3_ENST00000313663.7_Missense_Mutation_p.Q280H			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	280					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GAAGGGACATCTGCTTCCGTG	0.433																																					p.Q280H		Atlas-SNP	.											C2CD3_ENST00000334126,NS,carcinoma,0,2	C2CD3	288	.	0			c.G840T						.						143	125	131					11																	73849880		2200	4293	6493	SO:0001583	missense	26005	exon5			GGACATCTGCTTC	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.840G>T	chr11.hg19:g.73849880C>A	ENSP00000334379:p.Gln280His	89.0	0.0		104.0	37.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	14.20	2.465221	0.43839	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000289350;ENST00000539061	T;T	0.11063	2.81;2.85	5.99	2.96	0.34315	.	0.235228	0.35349	N	0.003274	T	0.11879	0.0289	M	0.72118	2.19	0.28356	N	0.920679	B;B	0.21821	0.061;0.06	B;B	0.22386	0.039;0.037	T	0.17806	-1.0357	10	0.42905	T	0.14	-1.9468	4.5098	0.11906	0.3028:0.5252:0.0:0.172	.	280;280	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	H	280	ENSP00000334379:Q280H;ENSP00000323339:Q280H	ENSP00000289350:Q280H	Q	-	3	2	C2CD3	73527528	0.661000	0.27430	0.998000	0.56505	0.935000	0.57460	0.136000	0.15974	0.349000	0.23975	-0.345000	0.07892	CAG	.	C|1.000;T|0.000		0.433	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		A	73849880	C	A	73849880	3	1	232	1	0	0	0	0	1	0	0	0	2156	912	32	3	5159	3	C2CD3	11	73849880	Missense_Mutation	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	17792244	73849880	61156636	33	32468										
GXYLT1	283464	hgsc.bcm.edu	37	chr12	42503406	42503407	+	Frame_Shift_Ins	INS	-	-	T													0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gaagcacatggtttaaagagINSttttttccactctgctgcat							TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr12:42503406_42503407insT	ENST00000398675.3	-	4	805_806	c.573_574insA	c.(571-576)aaactcfs	p.L192fs	GXYLT1_ENST00000280876.6_Frame_Shift_Ins_p.L161fs	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	192					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						GGTTTAAAGAGTTTTTTCCACT	0.317																																					p.L192fs		Atlas-INDEL	.											.	GXYLT1	47	.	0			c.574_575insA						.																																			SO:0001589	frameshift_variant	283464	exon4			.	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"Glycosyltransferase family 8 domain containing"	27482	protein-coding gene	gene with protein product		613321	"glycosyltransferase 8 domain containing 3"	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.574dupA	chr12.hg19:g.42503412_42503412dupT	ENSP00000381666:p.Leu192fs	357.0	0.0		315.0	101.0	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Frame_Shift_Ins	INS	ENST00000398675.3	hg19	CCDS41772.1																																																																																			.	.		0.317	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597		T	42503407	-	T	42503406	7	5	232	1	0	1	1	0	0	0	0	0	6912	1029	36	0	768	0	GXYLT1	12	42503406	Frame_Shift_Ins	INS	-	TCGA-DD-AAVZ-01A-11D-A40R-10		42503406	91348489	34	32469										
TROAP	10024	hgsc.bcm.edu	37	chr12	49719613	49719613	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gcttcctgcttctctaggctGgagggaccaggacctcgagg	14	12	1	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr12:49719613G>A	ENST00000257909.3	+	5	655	c.579G>A	c.(577-579)ctG>ctA	p.L193L	TROAP_ENST00000547923.1_5'Flank|RP11-161H23.9_ENST00000553259.1_RNA|TROAP_ENST00000551245.1_Silent_p.L193L	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	193					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						TCTCTAGGCTGGAGGGACCAG	0.637																																					p.L193L		Atlas-SNP	.											.	TROAP	80	.	0			c.G579A						.						35	38	37					12																	49719613		2203	4300	6503	SO:0001819	synonymous_variant	10024	exon5			TAGGCTGGAGGGA	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"tastin"	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.579G>A	chr12.hg19:g.49719613G>A		59.0	0.0		54.0	21.0	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Silent	SNP	ENST00000257909.3	hg19	CCDS8784.1																																																																																			.	.		0.637	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480		A	49719613	G	A	49719613	2	1	232	1	0	0	0	0	0	0	0	1	16590	1335	47	3		3	TROAP	12	49719613	Silent	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10	7216207	49719613	84132282	35	32470										
LASS5	91012	hgsc.bcm.edu	37	chr12	50537811	50537811	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gaccactgtcctcgatgccaAtacagagtgcacagggtttg	11	11	0	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr12:50537811A>G	ENST00000317551.6	-	2	351	c.227T>C	c.(226-228)aTt>aCt	p.I76T	CERS5_ENST00000422340.2_Missense_Mutation_p.I18T	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	76					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										CTCGATGCCAATACAGAGTGC	0.393																																					p.I76T		Atlas-SNP	.											.	.	.	.	0			c.T227C						.						133	128	130					12																	50537811		2203	4300	6503	SO:0001583	missense	91012	exon2			ATGCCAATACAGA		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"Homeoboxes / CERS class"	23749	protein-coding gene	gene with protein product		615335	"LAG1 longevity assurance homolog 5 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 5"	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.227T>C	chr12.hg19:g.50537811A>G	ENSP00000325485:p.Ile76Thr	67.0	0.0		72.0	4.0	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	hg19	CCDS8801.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.267187	0.59540	.	.	ENSG00000139624	ENST00000317551;ENST00000422340	T;T	0.20738	2.05;2.73	4.0	4.0	0.46444	.	0.359234	0.28841	N	0.013962	T	0.19846	0.0477	L	0.39898	1.24	0.35543	D	0.80318	B;B	0.21821	0.061;0.036	B;B	0.23150	0.044;0.028	T	0.22977	-1.0201	10	0.72032	D	0.01	-4.0757	13.9595	0.64170	1.0:0.0:0.0:0.0	.	18;76	B4DV54;Q8N5B7	.;CERS5_HUMAN	T	76;18	ENSP00000325485:I76T;ENSP00000389050:I18T	ENSP00000325485:I76T	I	-	2	0	CERS5	48824078	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	8.565000	0.90730	2.037000	0.60232	0.533000	0.62120	ATT	.	.		0.393	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190		G	50537811	A	G	50537811	3	3	232	1	0	0	0	0	1	0	0	0	8651	101	4	2	987	2	LASS5	12	50537811	Missense_Mutation	SNP	A	TCGA-DD-AAVZ-01A-11D-A40R-10	818198	50537811	83314084	36	32471										
BEST3	144453	hgsc.bcm.edu	37	chr12	70088201	70088201	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	atatctgtcacagtaaattgAtaatttttcaaagtaacgtt	5	5	3	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr12:70088201A>G	ENST00000330891.5	-	3	422	c.196T>C	c.(196-198)Tca>Cca	p.S66P	BEST3_ENST00000533674.1_5'UTR|BEST3_ENST00000266661.4_Intron|BEST3_ENST00000331471.4_Missense_Mutation_p.S66P|BEST3_ENST00000393365.1_5'UTR|BEST3_ENST00000476098.1_Intron|BEST3_ENST00000553096.1_Intron|BEST3_ENST00000551160.1_5'UTR	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	66					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			CAGTAAATTGATAATTTTTCA	0.378																																					p.S66P		Atlas-SNP	.											.	BEST3	129	.	0			c.T196C						.						109	108	108					12																	70088201		1930	4140	6070	SO:0001583	missense	144453	exon3			AAATTGATAATTT	AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17105	protein-coding gene	gene with protein product		607337	"vitelliform macular dystrophy 2-like 3"	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.196T>C	chr12.hg19:g.70088201A>G	ENSP00000332413:p.Ser66Pro	120.0	0.0		138.0	46.0	NM_032735	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Missense_Mutation	SNP	ENST00000330891.5	hg19	CCDS8992.2	.	.	.	.	.	.	.	.	.	.	A	18.30	3.592776	0.66219	.	.	ENSG00000127325	ENST00000331471;ENST00000330891;ENST00000548658	D;D;D	0.98585	-5.01;-5.01;-5.01	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.98707	0.9566	M	0.75777	2.31	0.80722	D	1	D;P	0.76494	0.999;0.886	D;P	0.72982	0.979;0.615	D	0.99297	1.0900	10	0.34782	T	0.22	-16.0534	16.4608	0.84044	1.0:0.0:0.0:0.0	.	66;66	Q8N1M1;Q8N1M1-1	BEST3_HUMAN;.	P	66	ENSP00000329064:S66P;ENSP00000332413:S66P;ENSP00000446575:S66P	ENSP00000332413:S66P	S	-	1	0	BEST3	68374468	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.438000	0.59961	2.288000	0.76882	0.533000	0.62120	TCA	.	.		0.378	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439		G	70088201	A	G	70088201	3	3	232	1	0	0	0	0	1	0	0	0	1406	333	12	2	1842	2	BEST3	12	70088201	Missense_Mutation	SNP	A	TCGA-DD-AAVZ-01A-11D-A40R-10	19550390	70088201	63763694	37	32472										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80732976	80732977	+	Frame_Shift_Ins	INS	-	-	C													0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	atcataaagtggtctcatctINStacaggaatcatagacattc							TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr12:80732976_80732977insC	ENST00000547103.1	+	42	4925_4926	c.4919_4920insC	c.(4918-4923)cttacafs	p.T1641fs	OTOGL_ENST00000458043.2_Frame_Shift_Ins_p.T1653fs			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1641	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TGGTCTCATCTTACAGGAATCA	0.421																																					p.L1652fs		Atlas-INDEL	.											.	OTOGL	235	.	0			c.4955_4956insC						.																																			SO:0001589	frameshift_variant	283310	exon42			.	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	Exception_encountered	chr12.hg19:g.80732976_80732977insC	ENSP00000447211:p.Thr1641fs	115.0	0.0		109.0	47.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Frame_Shift_Ins	INS	ENST00000547103.1	hg19																																																																																				.	.		0.421	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		C	80732977	-	C	80732976	7	5	232	1	0	1	1	0	0	0	0	0	1709	1609	56	0	5121	0	C12orf64	12	80732976	Frame_Shift_Ins	INS	-	TCGA-DD-AAVZ-01A-11D-A40R-10	10644775	80732976	53118919	38	32473										
ASB2	51676	hgsc.bcm.edu	37	chr14	94420805	94420805	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	tcttcatcgccatccttgatGgcctttatcaaggggtccgc	9	13	3	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr14:94420805G>A	ENST00000315988.4	-	2	680	c.192C>T	c.(190-192)gcC>gcT	p.A64A	ASB2_ENST00000556337.1_Intron|ASB2_ENST00000555019.1_Silent_p.A112A	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	64					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		CATCCTTGATGGCCTTTATCA	0.607																																					p.A112A		Atlas-SNP	.											.	ASB2	71	.	0			c.C336T						.						85	72	76					14																	94420805		2203	4300	6503	SO:0001819	synonymous_variant	51676	exon4			CTTGATGGCCTTT	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"Ankyrin repeat domain containing"	16012	protein-coding gene	gene with protein product		605759	"ankyrin repeat and SOCS box-containing 2"				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.192C>T	chr14.hg19:g.94420805G>A		55.0	0.0		71.0	29.0	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Silent	SNP	ENST00000315988.4	hg19	CCDS9915.1																																																																																			.	.		0.607	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1			A	94420805	G	A	94420805	2	1	232	1	0	0	0	0	0	0	0	1	1023	1335	47	3		3	ASB2	14	94420805	Silent	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10		94420805	12928735	39	32474										
EIF5	1983	hgsc.bcm.edu	37	chr14	103806063	103806063	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	atcaagctcagcttatctccAagattccacatatcttgaag	5	11	4	2			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr14:103806063A>T	ENST00000216554.3	+	10	1670	c.994A>T	c.(994-996)Aag>Tag	p.K332*	EIF5_ENST00000558506.1_Nonsense_Mutation_p.K332*|EIF5_ENST00000392715.2_Nonsense_Mutation_p.K332*|SNORA28_ENST00000606769.1_RNA	NM_001969.4	NP_001960.2	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	332	W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(3)|kidney(2)|large_intestine(3)|lung(5)|pancreas(2)|skin(2)|upper_aerodigestive_tract(1)	18		Melanoma(154;0.155)	Epithelial(46;0.182)			GCTTATCTCCAAGATTCCACA	0.443																																					p.K332X		Atlas-SNP	.											.	EIF5	40	.	0			c.A994T						.						112	97	102					14																	103806063		2203	4300	6503	SO:0001587	stop_gained	1983	exon10			ATCTCCAAGATTC	U49436	CCDS9980.1	14q32.32	2006-05-11				ENSG00000100664			3299	protein-coding gene	gene with protein product		601710				8663286	Standard	NM_001969		Approved		uc001ymq.4	P55010		ENST00000216554.3:c.994A>T	chr14.hg19:g.103806063A>T	ENSP00000216554:p.Lys332*	96.0	0.0		101.0	41.0	NM_001969	Q53XB3|Q9H5N2|Q9UG48	Nonsense_Mutation	SNP	ENST00000216554.3	hg19	CCDS9980.1	.	.	.	.	.	.	.	.	.	.	.	45	11.304472	0.99544	.	.	ENSG00000100664	ENST00000216554;ENST00000392715	.	.	.	5.89	5.89	0.94794	.	0.050558	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.1273	14.8867	0.70575	1.0:0.0:0.0:0.0	.	.	.	.	X	332	.	ENSP00000216554:K332X	K	+	1	0	EIF5	102875816	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.933000	0.75874	2.245000	0.73994	0.455000	0.32223	AAG	.	.		0.443	EIF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415329.2	NM_001969		T	103806063	A	T	103806063	4	4	232	1	0	0	0	0	0	1	0	0	5042	131	5	4	1024	4	EIF5	14	103806063	Nonsense_Mutation	SNP	A	TCGA-DD-AAVZ-01A-11D-A40R-10	9385258	103806063	3543477	40	32475										
PDCD7	10081	hgsc.bcm.edu	37	chr15	65412278	65412278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	aaaagtctcatctgctgaggCtggaggacagacccctgggc	13	11	2	2			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr15:65412278C>T	ENST00000204549.4	-	3	1078	c.1024G>A	c.(1024-1026)Gcc>Acc	p.A342T		NM_005707.1	NP_005698.1	Q8N8D1	PDCD7_HUMAN	programmed cell death 7	342					apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of T cell apoptotic process (GO:0070234)|response to glucocorticoid (GO:0051384)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)				endometrium(4)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	7						TCTGCTGAGGCTGGAGGACAG	0.463																																					p.A342T		Atlas-SNP	.											.	PDCD7	22	.	0			c.G1024A						.						116	136	129					15																	65412278		2202	4299	6501	SO:0001583	missense	10081	exon3			CTGAGGCTGGAGG	AF083930	CCDS10201.1	15q22.2	2012-06-07			ENSG00000090470	ENSG00000090470			8767	protein-coding gene	gene with protein product	"U11/U12 snRNP 59K"	608138				10037816	Standard	NM_005707		Approved	HES18, ES18	uc002aol.3	Q8N8D1	OTTHUMG00000133117	ENST00000204549.4:c.1024G>A	chr15.hg19:g.65412278C>T	ENSP00000204549:p.Ala342Thr	132.0	0.0		97.0	41.0	NM_005707	Q96AK8|Q9Y6D7	Missense_Mutation	SNP	ENST00000204549.4	hg19	CCDS10201.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.329723	0.24167	.	.	ENSG00000090470	ENST00000204549;ENST00000431964;ENST00000380204	.	.	.	5.33	4.4	0.53042	.	0.411976	0.22847	N	0.054914	T	0.37598	0.1009	L	0.51422	1.61	0.28577	N	0.910335	B	0.18461	0.028	B	0.15870	0.014	T	0.26052	-1.0114	9	0.13470	T	0.59	-3.8902	9.5014	0.39019	0.0:0.6322:0.293:0.0749	.	342	Q8N8D1	PDCD7_HUMAN	T	342;127;136	.	ENSP00000204549:A342T	A	-	1	0	PDCD7	63199331	0.922000	0.31269	0.997000	0.53966	0.436000	0.31835	1.595000	0.36708	1.353000	0.45828	-0.302000	0.09304	GCC	.	.		0.463	PDCD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256784.2	NM_005707		T	65412278	C	T	65412278	3	4	232	1	0	0	0	0	1	0	0	0	11634	797	28	3	445	3	PDCD7	15	65412278	Missense_Mutation	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10		65412278	37119114	41	32476										
AXIN1	8312	hgsc.bcm.edu	37	chr16	347839	347843	+	Frame_Shift_Del	DEL	CGGGT	CGGGT	-													0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	cgaagctgctctgggccctgCgggtggcctcggcctccacc							TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	CGGGT	CGGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr16:347839_347843delCGGGT	ENST00000262320.3	-	6	2034_2038	c.1663_1667delACCCG	c.(1663-1668)acccgcfs	p.TR555fs	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Frame_Shift_Del_p.TR555fs	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	555	Interaction with RNF111.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CTGGGCCCTGCGGGTGGCCTCGGCC	0.702																																					p.555_556del		Atlas-INDEL	.											.	AXIN1	290	.	0			c.1664_1668del						.																																			SO:0001589	frameshift_variant	8312	exon6			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1663_1667delACCCG	chr16.hg19:g.347839_347843delCGGGT	ENSP00000262320:p.Thr555fs	55.0	0.0		26.0	14.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Del	DEL	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.702	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			-	347843	CGGGT	-	347839	7	5	232	1	0	1	0	1	0	0	0	0	1236	768	27	0	945	0	AXIN1	16	347839	Frame_Shift_Del	DEL	CGGGT	TCGA-DD-AAVZ-01A-11D-A40R-10		347839	90006914	42	32477										
BRCA1	672	hgsc.bcm.edu	37	chr17	41245576	41245576	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	tctgctgtgcctgactggcaTttggttgtacttttttttct	9	8	2	1	rs397507195|rs55932871		TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr17:41245576T>C	ENST00000357654.3	-	10	2090	c.1972A>G	c.(1972-1974)Atg>Gtg	p.M658V	BRCA1_ENST00000354071.3_Missense_Mutation_p.M658V|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.M611V|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.M362V|BRCA1_ENST00000346315.3_Missense_Mutation_p.M658V|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.M658V	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	658					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CTGACTGGCATTTGGTTGTAC	0.388			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.M658V		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.A1972G						.						116	102	107					17																	41245576		2202	4300	6502	SO:0001583	missense	672	exon10	Familial Cancer Database		CTGGCATTTGGTT	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.1972A>G	chr17.hg19:g.41245576T>C	ENSP00000350283:p.Met658Val	105.0	0.0		87.0	30.0	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	hg19	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	T	2.507	-0.313796	0.05422	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3	5.15	0.357	0.16079	.	1.476590	0.03689	N	0.246844	T	0.72859	0.3513	L	0.43598	1.365	0.09310	N	1	B;B;B;B;B;B	0.16166	0.0;0.002;0.003;0.016;0.001;0.003	B;B;B;B;B;B	0.17979	0.003;0.003;0.015;0.015;0.01;0.02	T	0.50021	-0.8876	10	0.29301	T	0.29	.	5.2752	0.15645	0.0:0.2213:0.1387:0.64	rs55932871	658;617;658;658;658;658	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	V	658;658;658;658;362;658;611	ENSP00000350283:M658V;ENSP00000326002:M658V;ENSP00000246907:M658V;ENSP00000310938:M362V;ENSP00000418960:M658V;ENSP00000418775:M611V	ENSP00000310938:M362V	M	-	1	0	BRCA1	38499102	0.000000	0.05858	0.199000	0.23439	0.575000	0.36095	0.150000	0.16263	-0.137000	0.11455	0.459000	0.35465	ATG	.	.		0.388	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		C	41245576	T	C	41245576	3	2	232	1	0	0	0	0	1	0	0	0	1500	1493	52	2	3745	2	BRCA1	17	41245576	Missense_Mutation	SNP	T	TCGA-DD-AAVZ-01A-11D-A40R-10		41245576	39949634	43	32478										
LONP1	257062	hgsc.bcm.edu	37	chr19	5719971	5719971	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	attggcccccaattgccgggCctcggccccacagtgcccaa	10	18	0	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr19:5719971C>T	ENST00000381624.3	+	0	0				CATSPERD_ENST00000381614.2_5'Flank|LONP1_ENST00000590511.1_5'UTR|LONP1_ENST00000590729.1_5'Flank|LONP1_ENST00000585374.1_Intron|LONP1_ENST00000540670.2_Intron|LONP1_ENST00000360614.3_Missense_Mutation_p.G58D|LONP1_ENST00000593119.1_Intron	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta						multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											AATTGCCGGGCCTCGGCCCCA	0.751																																					p.G58D		Atlas-SNP	.											.	LONP1	66	.	0			c.G173A						.						4	5	4					19																	5719971		1907	3844	5751	SO:0001631	upstream_gene_variant	9361	exon1			GCCGGGCCTCGGC	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036		chr19.hg19:g.5719971C>T	Exception_encountered	163.0	0.0		183.0	9.0	NM_004793	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	hg19	CCDS12149.2	.	.	.	.	.	.	.	.	.	.	C	12.23	1.874298	0.33069	.	.	ENSG00000196365	ENST00000360614;ENST00000358403	T	0.19532	2.14	4.27	2.08	0.27032	.	0.396421	0.18147	N	0.150223	T	0.10035	0.0246	N	0.24115	0.695	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37103	-0.9720	10	0.07813	T	0.8	-6.9898	5.0333	0.14421	0.2152:0.6755:0.0:0.1093	.	58;58	E5KMH8;P36776	.;LONM_HUMAN	D	58	ENSP00000353826:G58D	ENSP00000351177:G58D	G	-	2	0	LONP1	5670971	0.007000	0.16637	0.033000	0.17914	0.859000	0.49053	1.335000	0.33839	0.506000	0.28125	0.655000	0.94253	GGC	.	.		0.751	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		T	5719971	C	T	5719971	1	4	232	0	1	0	0	0	0	0	0	0	8901	739	26	3		3	LONP1	19	5719971	5'Flank	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10		5719971	53409012	44	32479										
ZNF581	51545	hgsc.bcm.edu	37	chr19	56156193	56156193	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	gggctccaggccagaaaaagTgctacagctgccccgtgtgc	13	13	0	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr19:56156193T>C	ENST00000587252.1	+	2	529	c.256T>C	c.(256-258)Tgc>Cgc	p.C86R	ZNF581_ENST00000270451.5_Missense_Mutation_p.C86R|ZNF581_ENST00000588537.1_Missense_Mutation_p.C86R			Q9P0T4	ZN581_HUMAN	zinc finger protein 581	86					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)|ovary(1)	3		Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		CCAGAAAAAGTGCTACAGCTG	0.577																																					p.C86R		Atlas-SNP	.											.	ZNF581	13	.	0			c.T256C						.						58	55	56					19																	56156193		2203	4300	6503	SO:0001583	missense	51545	exon2			AAAAAGTGCTACA	AK026203	CCDS12932.1	19q13.42	2013-09-20			ENSG00000171425	ENSG00000171425		"Zinc fingers, C2H2-type"	25017	protein-coding gene	gene with protein product						11042152	Standard	NM_016535		Approved	HSPC189, FLJ22550	uc002qlq.3	Q9P0T4	OTTHUMG00000180869	ENST00000587252.1:c.256T>C	chr19.hg19:g.56156193T>C	ENSP00000466047:p.Cys86Arg	135.0	0.0		116.0	42.0	NM_016535	B2RDM6	Missense_Mutation	SNP	ENST00000587252.1	hg19	CCDS12932.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.936690	0.52972	.	.	ENSG00000171425	ENST00000270451	T	0.07114	3.22	3.2	-1.78	0.07957	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05044	0.0135	N	0.14661	0.345	0.80722	D	1	D	0.53151	0.958	P	0.46275	0.51	T	0.49716	-0.8910	9	0.87932	D	0	.	3.5017	0.07676	0.26:0.1844:0.0:0.5556	.	86	Q9P0T4	ZN581_HUMAN	R	86	ENSP00000270451:C86R	ENSP00000270451:C86R	C	+	1	0	ZNF581	60848005	0.053000	0.20554	0.580000	0.28601	0.862000	0.49288	-0.572000	0.05881	-0.490000	0.06707	0.334000	0.21626	TGC	.	.		0.577	ZNF581-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453430.1	NM_016535		C	56156193	T	C	56156193	3	2	232	1	0	0	0	0	1	0	0	0	18028	1696	59	2	258	2	ZNF581	19	56156193	Missense_Mutation	SNP	T	TCGA-DD-AAVZ-01A-11D-A40R-10	50436222	56156193	2972790	45	32480										
BRWD1	54014	hgsc.bcm.edu	37	chr21	40558988	40558988	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	ttccaggatctgaaccccctTaaaaaaagcatttttctatt	4	10	2	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chr21:40558988T>G	ENST00000333229.2	-	42	7254	c.6927A>C	c.(6925-6927)ttA>ttC	p.L2309F	AF129408.17_ENST00000608767.1_RNA	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2309					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TGAACCCCCTTAAAAAAAGCA	0.318																																					p.L2309F	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A6927C						.						73	75	74					21																	40558988		2202	4297	6499	SO:0001583	missense	54014	exon42			CCCCCTTAAAAAA	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.6927A>C	chr21.hg19:g.40558988T>G	ENSP00000330753:p.Leu2309Phe	238.0	0.0		214.0	86.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	hg19	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	T	3.504	-0.101220	0.06967	.	.	ENSG00000185658	ENST00000333229	T	0.59083	0.29	4.71	-4.64	0.03349	.	1.823850	0.02474	N	0.087812	T	0.47691	0.1459	L	0.50333	1.59	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.23762	-1.0179	10	0.30854	T	0.27	-0.0027	6.4579	0.21940	0.466:0.1179:0.0:0.4161	.	2309	Q9NSI6	BRWD1_HUMAN	F	2309	ENSP00000330753:L2309F	ENSP00000330753:L2309F	L	-	3	2	BRWD1	39480858	0.000000	0.05858	0.034000	0.17996	0.736000	0.42039	-0.720000	0.04969	-0.651000	0.05415	0.528000	0.53228	TTA	.	.		0.318	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		G	40558988	T	G	40558988	3	3	232	1	0	0	0	0	1	0	0	0	1527	1751	61	5	39	5	BRWD1	21	40558988	Missense_Mutation	SNP	T	TCGA-DD-AAVZ-01A-11D-A40R-10		40558988	7570907	46	32481										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37027755	37027755	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	cctcccaagattggagtgtcCcatctctgcctggagcctcc	9	16	1	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chrX:37027755C>G	ENST00000358047.3	+	1	1324	c.1272C>G	c.(1270-1272)tcC>tcG	p.S424S		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	424										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						TTGGAGTGTCCCATCTCTGCC	0.607																																					p.S424S		Atlas-SNP	.											.	FAM47C	267	.	0			c.C1272G						.						60	59	60					X																	37027755		2202	4300	6502	SO:0001819	synonymous_variant	442444	exon1			AGTGTCCCATCTC	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.1272C>G	chrX.hg19:g.37027755C>G		66.0	0.0		54.0	41.0	NM_001013736	Q6ZU46	Silent	SNP	ENST00000358047.3	hg19	CCDS35227.1																																																																																			.	.		0.607	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		G	37027755	C	G	37027755	2	3	232	1	0	0	0	0	0	0	0	1	5579	610	22	4		4	FAM47C	23	37027755	Silent	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10		37027755	118242805	47	32482										
IGBP1	3476	hgsc.bcm.edu	37	chrX	69353836	69353836	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	ttacagctgccgcggctcccCgagctgttcgaaactggtag	12	13	0	0			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chrX:69353836C>A	ENST00000342206.6	+	1	538	c.39C>A	c.(37-39)ccC>ccA	p.P13P	IGBP1_ENST00000356413.4_Silent_p.P13P			P78318	IGBP1_HUMAN	immunoglobulin (CD79A) binding protein 1	13					B cell activation (GO:0042113)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein dephosphorylation (GO:0035308)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dephosphorylation (GO:0035306)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microtubule-based movement (GO:0060632)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	protein phosphatase type 2A regulator activity (GO:0008601)			kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(2)	11						CGCGGCTCCCCGAGCTGTTCG	0.557											OREG0019849	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P13P	NSCLC(167;1189 1558 6576 8216 30387 37980 41450)	Atlas-SNP	.											.	IGBP1	33	.	0			c.C39A						.						27	25	26					X																	69353836		2203	4300	6503	SO:0001819	synonymous_variant	3476	exon2			GCTCCCCGAGCTG	Y08915	CCDS14396.1	Xq13.1-q13.3	2008-02-05			ENSG00000089289	ENSG00000089289			5461	protein-coding gene	gene with protein product	"alpha 4"	300139		IBP1		9441740	Standard	NM_001551		Approved		uc004dxw.3	P78318	OTTHUMG00000021767	ENST00000342206.6:c.39C>A	chrX.hg19:g.69353836C>A		80.0	0.0	1114	71.0	51.0	NM_001551	Q8TAB2	Silent	SNP	ENST00000342206.6	hg19	CCDS14396.1																																																																																			.	.		0.557	IGBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057052.1			A	69353836	C	A	69353836	2	1	232	1	0	0	0	0	0	0	0	1	7576	639	23	1		1	IGBP1	23	69353836	Silent	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	32326081	69353836	85916724	48	32483										
ARR3	407	hgsc.bcm.edu	37	chrX	69498423	69498423	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	ccaatcctggctgccagctgCcagaaacggggcctggcact	12	15	0	1			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chrX:69498423C>A	ENST00000307959.8	+	12	888	c.837C>A	c.(835-837)tgC>tgA	p.C279*	ARR3_ENST00000374495.3_Nonsense_Mutation_p.C279*	NM_004312.2	NP_004303.2	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	279					endocytosis (GO:0006897)|regulation of protein phosphorylation (GO:0001932)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)				endometrium(3)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	16						CTGCCAGCTGCCAGAAACGGG	0.478																																					p.C279X		Atlas-SNP	.											.	ARR3	41	.	0			c.C837A						.						67	61	63					X																	69498423		2203	4300	6503	SO:0001587	stop_gained	407	exon12			CAGCTGCCAGAAA		CCDS14399.1	Xq13.1	2013-10-11			ENSG00000120500	ENSG00000120500			710	protein-coding gene	gene with protein product	"arrestin 4"	301770				8224247	Standard	NM_004312		Approved	ARRX	uc004dyb.2	P36575	OTTHUMG00000021768	ENST00000307959.8:c.837C>A	chrX.hg19:g.69498423C>A	ENSP00000311538:p.Cys279*	216.0	1.0		210.0	159.0	NM_004312	B5B0B9|Q5JT23|Q5JT24|Q6IBF5|Q96EN2	Nonsense_Mutation	SNP	ENST00000307959.8	hg19	CCDS14399.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.211327	0.79240	.	.	ENSG00000120500	ENST00000374495;ENST00000374480;ENST00000307959	.	.	.	3.92	-2.04	0.07343	.	0.287468	0.35235	N	0.003360	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	5.745	0.18114	0.0:0.3245:0.2272:0.4483	.	.	.	.	X	279	.	ENSP00000311538:C279X	C	+	3	2	ARR3	69415148	0.004000	0.15560	0.028000	0.17463	0.991000	0.79684	-1.769000	0.01792	-0.496000	0.06650	0.513000	0.50165	TGC	.	.		0.478	ARR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057055.2	NM_004312		A	69498423	C	A	69498423	4	1	232	1	0	0	0	0	0	1	0	0	979	747	26	3	879	3	ARR3	23	69498423	Nonsense_Mutation	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10	144587	69498423	85772137	49	32484										
SPRY3	10251	hgsc.bcm.edu	37	chrX	155004171	155004171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	tgctgatgagccctgctcttGtgggcctagttcttgctttg	12	10	2	2			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chrX:155004171G>A	ENST00000302805.2	+	2	1069	c.638G>A	c.(637-639)tGt>tAt	p.C213Y		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	213	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)						all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCCTGCTCTTGTGGGCCTAGT	0.562																																					p.C213Y		Atlas-SNP	.											.	SPRY3	52	.	0			c.G638A						.						263	233	243					X																	155004171		2203	4296	6499	SO:0001583	missense	10251	exon2			GCTCTTGTGGGCC	AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"Pseudoautosomal regions / PAR2"	11271	protein-coding gene	gene with protein product	"antagonist of FGF signaling"	300531	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.638G>A	chrX.hg19:g.155004171G>A	ENSP00000302978:p.Cys213Tyr	135.0	0.0		111.0	13.0	NM_005840	A8K0H8	Missense_Mutation	SNP	ENST00000302805.2	hg19	CCDS14769.4	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.84|13.84	2.355678|2.355678	0.41700|0.41700	.|.	.|.	ENSG00000168939|ENSG00000168939	ENST00000302805|ENST00000369437	T|.	0.71103|.	-0.54|.	2.94|2.94	2.94|2.94	0.34122|0.34122	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.46483|0.46483	0.1395|0.1395	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999999|0.999999	D|.	0.63880|.	0.993|.	D|.	0.81914|.	0.995|.	T|T	0.40213|0.40213	-0.9575|-0.9575	9|5	0.87932|0.87932	D|D	0|0	-25.9166|-25.9166	10.9825|10.9825	0.47504|0.47504	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	213|.	O43610|.	SPY3_HUMAN|.	Y|M	213|114	ENSP00000302978:C213Y|.	ENSP00000302978:C213Y|ENSP00000358445:V114M	C|V	+|+	2|1	0|0	SPRY3|SPRY3	154657365|154657365	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.888000|0.888000	0.51559|0.51559	7.231000|7.231000	0.78106|0.78106	1.494000|1.494000	0.48533|0.48533	0.279000|0.279000	0.19357|0.19357	TGT|GTG	.	.		0.562	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840		A	155004171	G	A	155004171	3	1	232	1	0	0	0	0	1	0	0	0	15122	1377	48	3	640	3	SPRY3	23	155004171	Missense_Mutation	SNP	G	TCGA-DD-AAVZ-01A-11D-A40R-10	85505748	155004171	266389	50	32485										
UTY	7404	hgsc.bcm.edu	37	chrY	15447912	15447912	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0588235294117647	3	1	1.04201680672269	0	1.31623175586024	0.166666666666667	0.751940625889747	0	attagaaagtcccttgacatCagcacagccattagatgtgt	8	9	1	3			TCGA-DD-AAVZ-01A-11D-A40R-10	TCGA-DD-AAVZ-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	468bffe1-0c0a-44f6-bc8d-3f1961116b91	77a16e4e-a1bc-4dc1-ae4a-88342f6c99c4	g.chrY:15447912C>T	ENST00000331397.4	-	16	3081	c.2074G>A	c.(2074-2076)Gat>Aat	p.D692N	UTY_ENST00000382896.4_Missense_Mutation_p.D737N|UTY_ENST00000537580.1_Missense_Mutation_p.D613N|UTY_ENST00000538878.1_Missense_Mutation_p.D659N|UTY_ENST00000329134.5_Missense_Mutation_p.D692N|UTY_ENST00000545955.1_Missense_Mutation_p.D767N|UTY_ENST00000362096.4_Missense_Mutation_p.D692N|UTY_ENST00000540140.1_Missense_Mutation_p.D689N	NM_001258267.1|NM_007125.4	NP_001245196.1|NP_009056.3	O14607	UTY_HUMAN	ubiquitously transcribed tetratricopeptide repeat containing, Y-linked	692					regulation of gene expression (GO:0010468)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)			kidney(1)|lung(6)	7						CCCTTGACATCAGCACAGCCA	0.408																																					p.D789N	Colon(103;1740 2135 40732 45171)	Atlas-SNP	.											.	UTY	45	.	0			c.G2365A						.						108	99	101					Y																	15447912		623	1992	2615	SO:0001583	missense	7404	exon18			TGACATCAGCACA	AF000994	CCDS14783.1, CCDS14784.1, CCDS14785.1, CCDS59184.1, CCDS76073.1, CCDS76074.1, CCDS76075.1, CCDS76076.1, CCDS76077.1, CCDS76078.1, CCDS76079.1	Yq11.221	2013-11-04	2012-11-15		ENSG00000183878	ENSG00000183878		"Tetratricopeptide (TTC) repeat domain containing"	12638	protein-coding gene	gene with protein product		400009	"ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome", "ubiquitously transcribed tetratricopeptide repeat gene, Y-linked"			8944031, 9499428	Standard	NM_182659		Approved	KDM6AL	uc022ckf.2	O14607	OTTHUMG00000036319	ENST00000331397.4:c.2074G>A	chrY.hg19:g.15447912C>T	ENSP00000328939:p.Asp692Asn	80.0	0.0		91.0	70.0	NM_001258249	A8K9Z3|E1U199|E1U1A0|F5H4V7|F8W8R7|O14608	Missense_Mutation	SNP	ENST00000331397.4	hg19	CCDS14783.1																																																																																			.	.		0.408	UTY-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088394.1	NM_182660		T	15447912	C	T	15447912	3	4	232	1	0	0	0	0	1	0	0	0	17122	826	29	3	2284	3	UTY	24	15447912	Missense_Mutation	SNP	C	TCGA-DD-AAVZ-01A-11D-A40R-10		15447912	43925654	51	32486										
FBXO44	93611	hgsc.bcm.edu	37	chr1	11721248	11721248	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	catctggtttcagcacggcgGcgtggacactcattactggg	13	11	3	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr1:11721248G>A	ENST00000251547.5	+	6	768	c.686G>A	c.(685-687)gGc>gAc	p.G229D	FBXO44_ENST00000376770.1_Missense_Mutation_p.G229D|FBXO44_ENST00000251546.4_Silent_p.R187R|FBXO44_ENST00000376768.1_Silent_p.R219R|FBXO6_ENST00000376753.4_5'Flank|FBXO44_ENST00000376762.4_Silent_p.R187R|FBXO44_ENST00000376760.1_Silent_p.R187R	NM_033182.5	NP_149438.2	Q9H4M3	FBX44_HUMAN	F-box protein 44	229	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.41e-06)|COAD - Colon adenocarcinoma(227;0.000255)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000758)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCACGGCGGCGTGGACACT	0.657																																					p.G229D		Atlas-SNP	.											.	FBXO44	20	.	0			c.G686A						.						90	90	90					1																	11721248		2203	4300	6503	SO:0001583	missense	93611	exon6			ACGGCGGCGTGGA	AY040878	CCDS131.1, CCDS132.1	1p36.21	2008-03-26			ENSG00000132879	ENSG00000132879		"F-boxes /  "other""	24847	protein-coding gene	gene with protein product		609111				12383498	Standard	XM_005263535		Approved	FBX30, FBG3, MGC14140, Fbxo6a, Fbx44	uc001asm.3	Q9H4M3	OTTHUMG00000002071	ENST00000251547.5:c.686G>A	chr1.hg19:g.11721248G>A	ENSP00000251547:p.Gly229Asp	54.0	0.0		63.0	14.0	NM_033182	B3KNZ2|B7Z743|Q5TGX2|Q5TGX4|Q5TGX5|Q68DJ9|Q8WWY2	Missense_Mutation	SNP	ENST00000251547.5	hg19	CCDS132.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.770421	0.90108	.	.	ENSG00000132879	ENST00000376770;ENST00000251547	T;T	0.35973	1.28;1.28	4.82	4.82	0.62117	Galactose-binding domain-like (1);F-box associated (FBA) domain (2);	.	.	.	.	T	0.61299	0.2336	.	.	.	0.41476	D	0.988139	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.67205	-0.5729	8	0.72032	D	0.01	-25.2829	15.0549	0.71908	0.0:0.0:1.0:0.0	.	89;229	B7Z3K4;Q9H4M3	.;FBX44_HUMAN	D	229	ENSP00000365961:G229D;ENSP00000251547:G229D	ENSP00000251547:G229D	G	+	2	0	FBXO44	11643835	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.613000	0.82986	2.228000	0.72767	0.561000	0.74099	GGC	.	.		0.657	FBXO44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005761.1	NM_183412		A	11721248	G	A	11721248	3	1	233	1	0	0	0	0	1	0	0	0	5761	1203	42	3	704	3	FBXO44	1	11721248	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10		11721248	237529373	1	32487										
HEYL	26508	hgsc.bcm.edu	37	chr1	40092692	40092692	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gtgggcgaaggctccatctcGgctgcgtagctgttgaggtg	17	9	1	1	rs372712511		TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr1:40092692G>A	ENST00000372852.3	-	5	793	c.474C>T	c.(472-474)gcC>gcT	p.A158A	HEYL_ENST00000535435.1_Silent_p.A130A	NM_014571.3	NP_055386	Q9NQ87	HEYL_HUMAN	hes-related family bHLH transcription factor with YRPW motif-like	158					atrioventricular valve morphogenesis (GO:0003181)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to BMP stimulus (GO:0071773)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|glomerulus development (GO:0032835)|mesenchymal cell development (GO:0014031)|negative regulation of androgen receptor activity (GO:2000824)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|pulmonary valve morphogenesis (GO:0003184)|skeletal muscle cell differentiation (GO:0035914)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-1 domain binding (GO:0050683)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	7	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.1e-18)|Epithelial(16;2.77e-17)|all cancers(16;5.64e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GCTCCATCTCGGCTGCGTAGC	0.642																																					p.A158A		Atlas-SNP	.											HEYL,colon,carcinoma,0,1	HEYL	27	.	0			c.C474T						.	G		0,4406		0,0,2203	64	58	60		474	-9.9	0.9	1		60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	HEYL	NM_014571.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		158/329	40092692	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	26508	exon5			CATCTCGGCTGCG	BC006087	CCDS439.1	1p34.3	2013-10-17	2013-10-17		ENSG00000163909	ENSG00000163909		"Basic helix-loop-helix proteins"	4882	protein-coding gene	gene with protein product	"hairy/enhancer-of-split related with YRPW motif 3"	609034	"hairy/enhancer-of-split related with YRPW motif-like"			10415358, 10860664	Standard	NM_014571		Approved	bHLHb33, HEY3, HESR3	uc001cdp.3	Q9NQ87	OTTHUMG00000000458	ENST00000372852.3:c.474C>T	chr1.hg19:g.40092692G>A		157.0	0.0		171.0	11.0	NM_014571	Q5TG99	Silent	SNP	ENST00000372852.3	hg19	CCDS439.1																																																																																			.	.		0.642	HEYL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001179.2	NM_014571		A	40092692	G	A	40092692	2	1	233	1	0	0	0	0	0	0	0	1	7089	1103	39	1		1	HEYL	1	40092692	Silent	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	28371444	40092692	209157929	2	32488										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70502269	70502269	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gtggggtccttgcagacaacAgctaaagatgcagtacataa	11	8	0	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr1:70502269A>T	ENST00000035383.5	+	18	2166	c.2136A>T	c.(2134-2136)acA>acT	p.T712T	LRRC7_ENST00000415775.2_Intron|LRRC7_ENST00000310961.5_Silent_p.T717T	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	712						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TGCAGACAACAGCTAAAGATG	0.423																																					p.T712T		Atlas-SNP	.											.	LRRC7	400	.	0			c.A2136T						.						134	147	142					1																	70502269		2203	4300	6503	SO:0001819	synonymous_variant	57554	exon18			GACAACAGCTAAA		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2136A>T	chr1.hg19:g.70502269A>T		117.0	0.0		174.0	35.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Silent	SNP	ENST00000035383.5	hg19	CCDS645.1																																																																																			.	.		0.423	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		T	70502269	A	T	70502269	2	4	233	1	0	0	0	0	0	0	0	1	9029	175	7	4		4	LRRC7	1	70502269	Silent	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	30409577	70502269	178748352	3	32489										
PSMA5	5686	hgsc.bcm.edu	37	chr1	109944673	109944673	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ctcttcaagttcttcctttgTgaacatgtggaaattctggc	8	9	4	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr1:109944673T>A	ENST00000271308.4	-	9	708	c.688A>T	c.(688-690)Aca>Tca	p.T230S	PSMA5_ENST00000490870.1_5'UTR|PSMA5_ENST00000538610.1_Missense_Mutation_p.T172S	NM_002790.3	NP_002781.2	P28066	PSA5_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 5	230					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)	5		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.045)|Colorectal(144;0.116)|Epithelial(280;0.187)|all cancers(265;0.196)|LUSC - Lung squamous cell carcinoma(189;0.235)		TCTTCCTTTGTGAACATGTGG	0.428																																					p.T230S		Atlas-SNP	.											.	PSMA5	14	.	0			c.A688T						.						137	136	137					1																	109944673		2203	4300	6503	SO:0001583	missense	5686	exon9			CCTTTGTGAACAT	X61970	CCDS799.1, CCDS55619.1	1p13	2008-02-05			ENSG00000143106	ENSG00000143106		"Proteasome (prosome, macropain) subunits"	9534	protein-coding gene	gene with protein product		176844				1888762	Standard	NM_002790		Approved	ZETA	uc001dxn.3	P28066	OTTHUMG00000012001	ENST00000271308.4:c.688A>T	chr1.hg19:g.109944673T>A	ENSP00000271308:p.Thr230Ser	49.0	0.0		51.0	12.0	NM_002790	B2R8F6|B4E2V4|Q3T1C1|Q6IBF7	Missense_Mutation	SNP	ENST00000271308.4	hg19	CCDS799.1	.	.	.	.	.	.	.	.	.	.	T	8.614	0.889832	0.17540	.	.	ENSG00000143106	ENST00000538610;ENST00000271308	T;T	0.63096	-0.02;1.02	5.53	4.41	0.53225	.	0.117922	0.56097	D	0.000028	T	0.17534	0.0421	N	0.16233	0.39	0.42692	D	0.993584	B	0.02656	0.0	B	0.01281	0.0	T	0.19679	-1.0298	10	0.06625	T	0.88	-11.8279	5.7885	0.18347	0.1485:0.0791:0.0:0.7724	.	230	P28066	PSA5_HUMAN	S	172;230	ENSP00000440618:T172S;ENSP00000271308:T230S	ENSP00000271308:T230S	T	-	1	0	PSMA5	109746196	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.902000	0.56310	1.126000	0.42016	0.533000	0.62120	ACA	.	.		0.428	PSMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033192.2	NM_002790		A	109944673	T	A	109944673	3	1	233	1	0	0	0	0	1	0	0	0	12682	1696	59	4	41	4	PSMA5	1	109944673	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	39442404	109944673	139305948	4	32490										
C1orf14	81626	hgsc.bcm.edu	37	chr1	182920459	182920459	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	taaaatttatttacctcaacCaatataccaacaaaagggat	3	8	1	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr1:182920459C>A	ENST00000367547.3	-	2	785	c.549G>T	c.(547-549)ttG>ttT	p.L183F	SHCBP1L_ENST00000423786.1_Missense_Mutation_p.L64F|SHCBP1L_ENST00000488956.1_5'UTR	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	255										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						TTACCTCAACCAATATACCAA	0.294																																					p.L183F		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.G549T						.						48	50	49					1																	182920459		2202	4295	6497	SO:0001583	missense	81626	exon2			CTCAACCAATATA	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.549G>T	chr1.hg19:g.182920459C>A	ENSP00000356518:p.Leu183Phe	221.0	0.0		407.0	47.0	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	hg19	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.395843	0.42512	.	.	ENSG00000157060	ENST00000367547;ENST00000287709;ENST00000423786	T;T	0.58506	0.33;0.48	5.58	-0.551	0.11822	.	0.289408	0.24330	N	0.039469	T	0.48040	0.1478	M	0.66939	2.045	0.29710	N	0.839469	B;B	0.24186	0.099;0.099	B;B	0.26202	0.067;0.067	T	0.46373	-0.9196	10	0.59425	D	0.04	-15.1293	3.8021	0.08763	0.3028:0.4067:0.2129:0.0776	.	64;183	Q9BZQ2-2;Q9BZQ2-3	.;.	F	183;252;64	ENSP00000356518:L183F;ENSP00000397308:L64F	ENSP00000287709:L252F	L	-	3	2	SHCBP1L	181187082	0.485000	0.25972	0.996000	0.52242	0.992000	0.81027	-0.837000	0.04377	0.023000	0.15187	0.655000	0.94253	TTG	.	.		0.294	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		A	182920459	C	A	182920459	3	1	233	1	0	0	0	0	1	0	0	0	2002	593	21	3	1448	3	C1orf14	1	182920459	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	72975786	182920459	66330162	5	32491										
MARK1	4139	hgsc.bcm.edu	37	chr1	220826619	220826619	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tgcttcaccatcccatgaaaCgggtgcatttgcacatgcca	8	13	1	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr1:220826619C>T	ENST00000366917.4	+	16	2179	c.1913C>T	c.(1912-1914)aCg>aTg	p.T638M	MARK1_ENST00000366918.4_Missense_Mutation_p.T616M|MARK1_ENST00000402574.1_Missense_Mutation_p.T503M					MAP/microtubule affinity-regulating kinase 1											central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		TCCCATGAAACGGGTGCATTT	0.512																																					p.T638M		Atlas-SNP	.											.	MARK1	161	.	0			c.C1913T						.						86	82	84					1																	220826619		2203	4300	6503	SO:0001583	missense	4139	exon16			ATGAAACGGGTGC	AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1913C>T	chr1.hg19:g.220826619C>T	ENSP00000355884:p.Thr638Met	141.0	0.0		291.0	12.0	NM_018650		Missense_Mutation	SNP	ENST00000366917.4	hg19	CCDS31029.2	.	.	.	.	.	.	.	.	.	.	C	20.6	4.017294	0.75161	.	.	ENSG00000116141	ENST00000402574;ENST00000366918;ENST00000366917	T;T;T	0.73469	-0.63;-0.42;-0.75	4.94	4.94	0.65067	.	0.120309	0.56097	D	0.000034	T	0.73953	0.3653	M	0.64997	1.995	0.45914	D	0.998752	P;B;B;B	0.52170	0.951;0.131;0.022;0.037	P;B;B;B	0.46237	0.508;0.102;0.018;0.041	T	0.76812	-0.2821	10	0.54805	T	0.06	.	11.6333	0.51189	0.0:0.9178:0.0:0.0822	.	638;503;638;616	B4DIB3;Q9P0L2-2;Q9P0L2;Q9P0L2-3	.;.;MARK1_HUMAN;.	M	503;616;638	ENSP00000386017:T503M;ENSP00000355885:T616M;ENSP00000355884:T638M	ENSP00000355884:T638M	T	+	2	0	MARK1	218893242	0.589000	0.26807	0.005000	0.12908	0.979000	0.70002	5.859000	0.69539	2.267000	0.75376	0.462000	0.41574	ACG	.	.		0.512	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			T	220826619	C	T	220826619	3	4	233	1	0	0	0	0	1	0	0	0	9321	536	19	1	1975	1	MARK1	1	220826619	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	37906160	220826619	28424002	6	32492										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1842975	1842975	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ctgagccgtcgcatcctggcGtggggcaggacatgccttcc	14	14	0	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr2:1842975G>T	ENST00000399161.2	-	21	3773	c.3026C>A	c.(3025-3027)aCg>aAg	p.T1009K	MYT1L_ENST00000471668.1_5'UTR|MYT1L_ENST00000407844.1_Missense_Mutation_p.T5K|MYT1L_ENST00000428368.2_Missense_Mutation_p.T1007K	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1009					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GCATCCTGGCGTGGGGCAGGA	0.667																																					p.T1007K		Atlas-SNP	.											MYT1L,NS,carcinoma,0,1	MYT1L	241	.	0			c.C3020A						.						29	35	33					2																	1842975		2046	4189	6235	SO:0001583	missense	23040	exon21			CCTGGCGTGGGGC	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.3026C>A	chr2.hg19:g.1842975G>T	ENSP00000382114:p.Thr1009Lys	135.0	0.0		167.0	35.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.327901	0.95733	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000407844;ENST00000399157;ENST00000428368	T;T	0.59772	0.25;0.24	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.81044	0.4741	M	0.88775	2.98	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.969;1.0;0.999	T	0.82991	-0.0182	10	0.52906	T	0.07	-32.9984	19.5365	0.95255	0.0:0.0:1.0:0.0	.	5;1009;1007	Q9UL68-3;Q9UL68;Q9UL68-4	.;MYT1L_HUMAN;.	K	1009;955;5;63;1007	ENSP00000382114:T1009K;ENSP00000396103:T1007K	ENSP00000295067:T955K	T	-	2	0	MYT1L	1821982	1.000000	0.71417	0.967000	0.41034	0.927000	0.56198	9.780000	0.99024	2.618000	0.88619	0.563000	0.77884	ACG	.	.		0.667	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		T	1842975	G	T	1842975	3	4	233	1	0	0	0	0	1	0	0	0	10116	1145	40	1	554	1	MYT1L	2	1842975	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10		1842975	241356398	7	32493										
ASXL2	55252	hgsc.bcm.edu	37	chr2	25966307	25966307	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ggtgagaggtttaggcagaaTttgctccatgggaacatctt	13	6	1	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr2:25966307T>C	ENST00000435504.4	-	13	3192	c.2899A>G	c.(2899-2901)Att>Gtt	p.I967V	ASXL2_ENST00000404843.1_Intron|ASXL2_ENST00000272341.4_Intron|ASXL2_ENST00000336112.4_Missense_Mutation_p.I939V			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	967					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTAGGCAGAATTTGCTCCATG	0.448																																					p.I967V		Atlas-SNP	.											.	ASXL2	217	.	0			c.A2899G						.						154	148	150					2																	25966307		1889	4110	5999	SO:0001583	missense	55252	exon12			GCAGAATTTGCTC			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.2899A>G	chr2.hg19:g.25966307T>C	ENSP00000391447:p.Ile967Val	59.0	0.0		69.0	26.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	hg19		.	.	.	.	.	.	.	.	.	.	T	16.00	2.998443	0.54147	.	.	ENSG00000143970	ENST00000435504;ENST00000336112	T;T	0.26223	1.75;1.75	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.49490	0.1560	M	0.74258	2.255	0.80722	D	1	P	0.48640	0.913	P	0.61592	0.891	T	0.52381	-0.8583	10	0.87932	D	0	-16.8414	14.5345	0.67950	0.0:0.0:0.0:1.0	.	967	Q76L83	ASXL2_HUMAN	V	967;939	ENSP00000391447:I967V;ENSP00000337250:I939V	ENSP00000337250:I939V	I	-	1	0	ASXL2	25819811	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.451000	0.80668	2.112000	0.64535	0.460000	0.39030	ATT	.	.		0.448	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		C	25966307	T	C	25966307	3	2	233	1	0	0	0	0	1	0	0	0	1067	1493	52	2	1412	2	ASXL2	2	25966307	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	24123332	25966307	217233066	8	32494										
GALNT14	79623	hgsc.bcm.edu	37	chr2	31154985	31154985	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	aaacgtaggggtgcttcttcCggaagacgtgccccactcgg	13	12	1	1	rs368328840		TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr2:31154985C>T	ENST00000349752.5	-	10	1646	c.1007G>A	c.(1006-1008)cGg>cAg	p.R336Q	GALNT14_ENST00000324589.5_Missense_Mutation_p.R341Q|GALNT14_ENST00000356174.3_Missense_Mutation_p.R303Q|GALNT14_ENST00000420311.2_Missense_Mutation_p.R301Q|GALNT14_ENST00000486564.1_5'UTR|GALNT14_ENST00000406653.1_Missense_Mutation_p.R316Q	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	336	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					GTGCTTCTTCCGGAAGACGTG	0.592																																					p.R341Q		Atlas-SNP	.											.	GALNT14	103	.	0			c.G1022A						.	C	GLN/ARG	0,4406		0,0,2203	96	89	91		1007	5	1	2		91	1,8599	1.2+/-3.3	0,1,4299	no	missense	GALNT14	NM_024572.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	336/553	31154985	1,13005	2203	4300	6503	SO:0001583	missense	79623	exon11			TTCTTCCGGAAGA	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"Glycosyltransferase family 2 domain containing"	22946	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 14"	608225	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.1007G>A	chr2.hg19:g.31154985C>T	ENSP00000288988:p.Arg336Gln	69.0	0.0		90.0	22.0	NM_001253826	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	hg19	CCDS1773.2	.	.	.	.	.	.	.	.	.	.	C	36	5.858980	0.97036	0.0	1.16E-4	ENSG00000158089	ENST00000349752;ENST00000324589;ENST00000406653;ENST00000356174;ENST00000420311;ENST00000430167	T;T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33;-0.33	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.87188	0.6115	H	0.94222	3.51	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.996;0.999;1.0;0.999	D	0.91118	0.4927	10	0.87932	D	0	.	18.2582	0.90025	0.0:1.0:0.0:0.0	.	301;303;341;336;316	F5H263;Q96FL9-2;Q96FL9-3;Q96FL9;B3KV89	.;.;.;GLT14_HUMAN;.	Q	336;341;316;303;301;303	ENSP00000288988:R336Q;ENSP00000314500:R341Q;ENSP00000385435:R316Q;ENSP00000348497:R303Q;ENSP00000415514:R301Q;ENSP00000406399:R303Q	ENSP00000314500:R341Q	R	-	2	0	GALNT14	31008489	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.315000	0.78130	0.561000	0.74099	CGG	.	.		0.592	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572		T	31154985	C	T	31154985	3	4	233	1	0	0	0	0	1	0	0	0	6220	652	23	1	675	1	GALNT14	2	31154985	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	5188678	31154985	212044388	9	32495										
AFTPH	54812	hgsc.bcm.edu	37	chr2	64779969	64779969	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ttttgttactggtactcaagAttcaatgagtgatgccactt	8	7	2	3			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr2:64779969A>G	ENST00000422803.1	+	2	1675	c.1361A>G	c.(1360-1362)gAt>gGt	p.D454G	AFTPH_ENST00000238855.7_Missense_Mutation_p.D454G|AFTPH_ENST00000238856.4_Missense_Mutation_p.D454G|AFTPH_ENST00000409183.1_Missense_Mutation_p.D85G|AFTPH_ENST00000409933.1_Missense_Mutation_p.D454G			Q6ULP2	AFTIN_HUMAN	aftiphilin	454					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						GGTACTCAAGATTCAATGAGT	0.398																																					p.D454G		Atlas-SNP	.											.	AFTPH	117	.	0			c.A1361G						.						175	167	170					2																	64779969		2203	4300	6503	SO:0001583	missense	54812	exon2			CTCAAGATTCAAT	AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.1361A>G	chr2.hg19:g.64779969A>G	ENSP00000397726:p.Asp454Gly	112.0	0.0		151.0	39.0	NM_017657	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Missense_Mutation	SNP	ENST00000422803.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.42	2.530860	0.45073	.	.	ENSG00000119844	ENST00000238856;ENST00000422803;ENST00000238855;ENST00000409933;ENST00000409183	T;T;T;T;T	0.52526	1.64;1.64;1.63;1.63;0.66	5.8	4.64	0.57946	.	0.326289	0.32503	N	0.006018	T	0.60143	0.2246	L	0.60455	1.87	0.35589	D	0.806924	B;B;D;D	0.71674	0.275;0.275;0.998;0.998	B;B;D;D	0.81914	0.055;0.12;0.995;0.995	T	0.68108	-0.5496	10	0.48119	T	0.1	-4.2067	8.3905	0.32526	0.7984:0.1309:0.0707:0.0	.	454;454;454;454	Q6ULP2;Q6ULP2-2;Q6ULP2-5;Q6ULP2-4	AFTIN_HUMAN;.;.;.	G	454;454;454;454;85	ENSP00000238856:D454G;ENSP00000397726:D454G;ENSP00000238855:D454G;ENSP00000387071:D454G;ENSP00000386913:D85G	ENSP00000238855:D454G	D	+	2	0	AFTPH	64633473	0.970000	0.33590	1.000000	0.80357	0.958000	0.62258	2.369000	0.44231	2.213000	0.71641	0.528000	0.53228	GAT	.	.		0.398	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657		G	64779969	A	G	64779969	3	3	233	1	0	0	0	0	1	0	0	0	364	333	12	2	1363	2	AFTPH	2	64779969	Missense_Mutation	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	33624984	64779969	178419404	10	32496										
CD207	50489	hgsc.bcm.edu	37	chr2	71060827	71060827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ccaagctgccctggagtgccCggatctttgtatttaaagca	10	11	1	0	rs567546839	byFrequency	TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr2:71060827C>T	ENST00000410009.3	-	3	560	c.515G>A	c.(514-516)cGg>cAg	p.R172Q		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	172					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						CTGGAGTGCCCGGATCTTTGT	0.428													C|||	13	0.00259585	0	0	5008	,	,		20139	0		0	False		,,,				2504	0.0133				p.R172Q		Atlas-SNP	.											.	CD207	47	.	0			c.G515A						.						81	72	75					2																	71060827		1862	4104	5966	SO:0001583	missense	50489	exon3			AGTGCCCGGATCT	AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"C-type lectin domain containing", "CD molecules"	17935	protein-coding gene	gene with protein product		604862	"CD207 antigen, langerin"			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.515G>A	chr2.hg19:g.71060827C>T	ENSP00000386378:p.Arg172Gln	89.0	0.0		106.0	19.0	NM_015717		Missense_Mutation	SNP	ENST00000410009.3	hg19		.	.	.	.	.	.	.	.	.	.	C	0.319	-0.962903	0.02249	.	.	ENSG00000116031	ENST00000410009	T	0.28069	1.63	4.12	-3.86	0.04230	.	1.382280	0.04510	N	0.382668	T	0.12263	0.0298	N	0.04245	-0.25	0.09310	N	1	B	0.14012	0.009	B	0.01281	0.0	T	0.21552	-1.0242	10	0.15499	T	0.54	.	6.1748	0.20437	0.1481:0.2122:0.0:0.6397	.	172	Q9UJ71	CLC4K_HUMAN	Q	172	ENSP00000386378:R172Q	ENSP00000386378:R172Q	R	-	2	0	CD207	70914335	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.572000	0.05881	-0.912000	0.03837	-0.181000	0.13052	CGG	.	.		0.428	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717		T	71060827	C	T	71060827	3	4	233	1	0	0	0	0	1	0	0	0	2985	652	23	1	487	1	CD207	2	71060827	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	6280858	71060827	172138546	11	32497										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	79971559	79971559	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	caaaggcccatctggtaaaaAgaaagggaggtcaaagaaag	12	6	2	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr2:79971559A>C	ENST00000402739.4	+	2	154	c.149A>C	c.(148-150)aAg>aCg	p.K50T	CTNNA2_ENST00000466387.1_Missense_Mutation_p.K50T|CTNNA2_ENST00000496558.1_Missense_Mutation_p.K50T|CTNNA2_ENST00000541047.1_Missense_Mutation_p.K50T|CTNNA2_ENST00000361291.4_Missense_Mutation_p.K84T|CTNNA2_ENST00000540488.1_Missense_Mutation_p.K50T	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	50					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						TCTGGTAAAAAGAAAGGGAGG	0.408																																					p.K50T		Atlas-SNP	.											.	CTNNA2	462	.	0			c.A149C						.						73	70	71					2																	79971559		1868	4112	5980	SO:0001583	missense	1496	exon3			GTAAAAAGAAAGG		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.149A>C	chr2.hg19:g.79971559A>C	ENSP00000384638:p.Lys50Thr	223.0	0.0		253.0	67.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	A	25.7	4.669299	0.88348	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000451966;ENST00000409971;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T;T;T	0.38240	1.15;1.15;1.15;1.15;1.15;1.15;1.15;1.15	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.61949	0.2388	M	0.89095	3.005	0.80722	D	1	P;D;D	0.56035	0.775;0.974;0.974	P;P;P	0.60609	0.665;0.877;0.877	T	0.67389	-0.5683	10	0.45353	T	0.12	.	13.5353	0.61644	1.0:0.0:0.0:0.0	.	50;50;50	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	T	50;50;50;50;84;50;50;50	ENSP00000418191:K50T;ENSP00000419295:K50T;ENSP00000400105:K50T;ENSP00000387073:K50T;ENSP00000355398:K84T;ENSP00000384638:K50T;ENSP00000444675:K50T;ENSP00000441705:K50T	ENSP00000355398:K84T	K	+	2	0	CTNNA2	79825067	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.087000	0.62958	0.377000	0.23210	AAG	.	.		0.408	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		C	79971559	A	C	79971559	3	2	233	1	0	0	0	0	1	0	0	0	4015	72	3	5	155	5	CTNNA2	2	79971559	Missense_Mutation	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	8910732	79971559	163227814	12	32498										
FAM178B	51252	hgsc.bcm.edu	37	chr2	97637835	97637835	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ggcctcccgactggcctgcaGcaccctcgggttgaggaatt	13	14	0	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr2:97637835G>T	ENST00000417561.3	-	7	810	c.811C>A	c.(811-813)Ctg>Atg	p.L271M	FAM178B_ENST00000327896.3_Missense_Mutation_p.L91M|FAM178B_ENST00000490605.2_Missense_Mutation_p.L123M			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	271										large_intestine(1)|ovary(1)	2						CTGGCCTGCAGCACCCTCGGG	0.667																																					p.L123M		Atlas-SNP	.											.	FAM178B	35	.	0			c.C367A						.						4	7	6					2																	97637835		675	1553	2228	SO:0001583	missense	51252	exon3			CCTGCAGCACCCT	AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.811C>A	chr2.hg19:g.97637835G>T	ENSP00000413245:p.Leu271Met	303.0	0.0		373.0	88.0	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Missense_Mutation	SNP	ENST00000417561.3	hg19		.	.	.	.	.	.	.	.	.	.	G	12.00	1.806872	0.31961	.	.	ENSG00000168754	ENST00000417561;ENST00000327896;ENST00000490605	T;T;T	0.51071	0.72;0.81;0.78	3.18	1.24	0.21308	.	.	.	.	.	T	0.32556	0.0833	N	0.14661	0.345	0.09310	N	1	.	.	.	.	.	.	T	0.27673	-1.0067	7	0.48119	T	0.1	0.113	9.0114	0.36144	0.0:0.4492:0.5507:0.0	.	.	.	.	M	271;91;123	ENSP00000413245:L271M;ENSP00000333553:L91M;ENSP00000429896:L123M	ENSP00000333553:L91M	L	-	1	2	FAM178B	97001562	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.451000	0.21779	0.326000	0.23384	-0.175000	0.13238	CTG	.	.		0.667	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490		T	97637835	G	T	97637835	3	4	233	1	0	0	0	0	1	0	0	0	5509	962	34	3	1763	3	FAM178B	2	97637835	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	17666276	97637835	145561538	13	32499										
PRRT3	285368	hgsc.bcm.edu	37	chr3	9988877	9988877	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	cggcctgggcccgggtacagCcagagcgcagccgccagctg	16	16	0	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr3:9988877C>T	ENST00000412055.1	-	4	2109	c.1980G>A	c.(1978-1980)tgG>tgA	p.W660*	PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	660						integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						CCGGGTACAGCCAGAGCGCAG	0.751																																					p.W660X		Atlas-SNP	.											.	PRRT3	35	.	0			c.G1980A						.						1	1	1					3																	9988877		1069	2388	3457	SO:0001587	stop_gained	285368	exon4			GTACAGCCAGAGC	AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"Proline-rich transmembrane proteins"	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.1980G>A	chr3.hg19:g.9988877C>T	ENSP00000392511:p.Trp660*	32.0	0.0		35.0	8.0	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Nonsense_Mutation	SNP	ENST00000412055.1	hg19	CCDS43049.1	.	.	.	.	.	.	.	.	.	.	C	39	7.548770	0.98352	.	.	ENSG00000163704	ENST00000412055	.	.	.	4.16	4.16	0.48862	.	0.000000	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-9.3143	14.006	0.64463	0.0:1.0:0.0:0.0	.	.	.	.	X	660	.	.	W	-	3	0	PRRT3	9963877	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	3.636000	0.54317	2.144000	0.66660	0.313000	0.20887	TGG	.	.		0.751	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351		T	9988877	C	T	9988877	4	4	233	1	0	0	0	0	0	1	0	0	12623	740	26	3	969	3	PRRT3	3	9988877	Nonsense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10		9988877	188033553	14	32500										
VILL	50853	hgsc.bcm.edu	37	chr3	38043300	38043300	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gagcatgtgaccatgggcagCgagcccccccacttcctcgc	11	17	0	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr3:38043300C>T	ENST00000283713.6	+	13	1694	c.1428C>T	c.(1426-1428)agC>agT	p.S476S	VILL_ENST00000465644.1_Silent_p.S194S|VILL_ENST00000383759.2_Silent_p.S476S			O15195	VILL_HUMAN	villin-like	476					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		CCATGGGCAGCGAGCCCCCCC	0.592																																					p.S476S		Atlas-SNP	.											.	VILL	61	.	0			c.C1428T						.						144	123	130					3																	38043300		2203	4300	6503	SO:0001819	synonymous_variant	50853	exon12			GGGCAGCGAGCCC		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.1428C>T	chr3.hg19:g.38043300C>T		94.0	0.0		104.0	30.0	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Silent	SNP	ENST00000283713.6	hg19	CCDS2670.2																																																																																			.	.		0.592	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873		T	38043300	C	T	38043300	2	4	233	1	0	0	0	0	0	0	0	1	17180	767	27	1		1	VILL	3	38043300	Silent	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	28054423	38043300	159979130	15	32501										
ERC2	26059	hgsc.bcm.edu	37	chr3	56026116	56026116	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tgcgatcttcttgtccttgtCattcttctcattctccacct	4	14	6	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr3:56026116C>G	ENST00000288221.6	-	11	2479	c.2224G>C	c.(2224-2226)Gac>Cac	p.D742H		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	742						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		TTGTCCTTGTCATTCTTCTCA	0.498																																					p.D742H		Atlas-SNP	.											.	ERC2	221	.	0			c.G2224C						.						201	201	201					3																	56026116		1951	4143	6094	SO:0001583	missense	26059	exon11			CCTTGTCATTCTT	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2224G>C	chr3.hg19:g.56026116C>G	ENSP00000288221:p.Asp742His	111.0	0.0		139.0	34.0	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	hg19	CCDS46851.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.3|20.3	3.959686|3.959686	0.74016|0.74016	.|.	.|.	ENSG00000187672|ENSG00000187672	ENST00000288221|ENST00000492584	T|.	0.48836|.	0.8|.	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76579|0.76579	0.4007|0.4007	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|T	0.74466|0.74466	-0.3656|-0.3656	10|5	0.72032|.	D|.	0.01|.	-23.7434|-23.7434	19.824|19.824	0.96608|0.96608	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	742|.	O15083|.	ERC2_HUMAN|.	H|I	742|392	ENSP00000288221:D742H|.	ENSP00000288221:D742H|.	D|M	-|-	1|3	0|0	ERC2|ERC2	56001156|56001156	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.928000|0.928000	0.56348|0.56348	7.818000|7.818000	0.86416|0.86416	2.699000|2.699000	0.92147|0.92147	0.591000|0.591000	0.81541|0.81541	GAC|ATG	.	.		0.498	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		G	56026116	C	G	56026116	3	3	233	1	0	0	0	0	1	0	0	0	5213	826	29	4	667	4	ERC2	3	56026116	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	17982816	56026116	141996314	16	32502										
SHQ1	55164	hgsc.bcm.edu	37	chr3	72799710	72799710	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	accttgcaaagaactgactgTctcagatggactatctttga	8	9	2	4			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr3:72799710T>C	ENST00000325599.8	-	11	1598	c.1459A>G	c.(1459-1461)Aca>Gca	p.T487A	SHQ1_ENST00000463369.1_Missense_Mutation_p.T459A|SHQ1_ENST00000468371.1_5'UTR	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	487	Ser-rich.				negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		GAACTGACTGTCTCAGATGGA	0.473																																					p.T487A		Atlas-SNP	.											.	SHQ1	60	.	0			c.A1459G						.						122	117	119					3																	72799710		2203	4300	6503	SO:0001583	missense	55164	exon11			TGACTGTCTCAGA	BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"SHQ1 homolog (S. cerevisiae)"			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.1459A>G	chr3.hg19:g.72799710T>C	ENSP00000315182:p.Thr487Ala	93.0	0.0		97.0	19.0	NM_018130	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Missense_Mutation	SNP	ENST00000325599.8	hg19	CCDS33788.1	.	.	.	.	.	.	.	.	.	.	T	3.669	-0.067834	0.07228	.	.	ENSG00000144736	ENST00000325599;ENST00000463369	T;T	0.28895	1.6;1.59	5.52	-10.3	0.00346	.	1.051930	0.07459	N	0.900307	T	0.12860	0.0312	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18304	-1.0341	10	0.08381	T	0.77	-1.4086	4.418	0.11466	0.1545:0.4539:0.188:0.2036	.	487	Q6PI26	SHQ1_HUMAN	A	487;459	ENSP00000315182:T487A;ENSP00000417452:T459A	ENSP00000315182:T487A	T	-	1	0	SHQ1	72882400	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.330000	0.02675	-2.208000	0.00740	-0.290000	0.09829	ACA	.	.		0.473	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130		C	72799710	T	C	72799710	3	2	233	1	0	0	0	0	1	0	0	0	14307	1667	58	2	278	2	SHQ1	3	72799710	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	16773594	72799710	125222720	17	32503										
PPP4R2	151987	hgsc.bcm.edu	37	chr3	73046215	73046215	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gtcgagaggctccaggaggcGctgaaaggtgggggtagctg	20	7	0	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr3:73046215G>T	ENST00000356692.5	+	1	280	c.27G>T	c.(25-27)gcG>gcT	p.A9A	PPP4R2_ENST00000394284.3_Silent_p.A9A|PPP4R2_ENST00000495566.1_Silent_p.A9A|PPP4R2_ENST00000295862.9_5'UTR			Q9NY27	PP4R2_HUMAN	protein phosphatase 4, regulatory subunit 2	9					cellular protein modification process (GO:0006464)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA processing (GO:0006397)|regulation of catalytic activity (GO:0050790)|regulation of double-strand break repair via homologous recombination (GO:0010569)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)	protein binding, bridging (GO:0030674)|protein phosphatase type 4 regulator activity (GO:0030362)			breast(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|stomach(1)|urinary_tract(2)	12		Prostate(10;0.0187)|Lung SC(41;0.236)		Epithelial(33;1.76e-07)|BRCA - Breast invasive adenocarcinoma(55;9.42e-05)|LUSC - Lung squamous cell carcinoma(21;0.00211)|Lung(16;0.00643)|KIRC - Kidney renal clear cell carcinoma(39;0.0164)|Kidney(39;0.0193)|OV - Ovarian serous cystadenocarcinoma(275;0.031)		TCCAGGAGGCGCTGAAAGGTG	0.692																																					p.A9A		Atlas-SNP	.											.	PPP4R2	30	.	0			c.G27T						.						32	32	32					3																	73046215		1821	3381	5202	SO:0001819	synonymous_variant	151987	exon1			GGAGGCGCTGAAA	AJ271448	CCDS2917.1	3q29	2010-06-18			ENSG00000163605	ENSG00000163605		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	18296	protein-coding gene	gene with protein product		613822				10769191	Standard	NM_174907		Approved		uc003dph.1	Q9NY27	OTTHUMG00000158816	ENST00000356692.5:c.27G>T	chr3.hg19:g.73046215G>T		232.0	0.0		275.0	72.0	NM_174907	A8K1I6|Q2TAJ9|Q498B8|Q8WXX6	Silent	SNP	ENST00000356692.5	hg19	CCDS2917.1																																																																																			.	.		0.692	PPP4R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352321.1	NM_174907		T	73046215	G	T	73046215	2	4	233	1	0	0	0	0	0	0	0	1	12416	1074	38	1		1	PPP4R2	3	73046215	Silent	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	246505	73046215	124976215	18	32504										
OR5H14	403273	hgsc.bcm.edu	37	chr3	97868486	97868486	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gaagatgctgatcaacttctTagctaagagtaagatgatat	9	5	2	5			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr3:97868486T>C	ENST00000437310.1	+	1	317	c.257T>C	c.(256-258)tTa>tCa	p.L86S	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						ATCAACTTCTTAGCTAAGAGT	0.393																																					p.L86S		Atlas-SNP	.											.	OR5H14	56	.	0			c.T257C						.						244	244	244					3																	97868486		2203	4298	6501	SO:0001583	missense	403273	exon1			ACTTCTTAGCTAA		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"GPCR / Class A : Olfactory receptors"	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.257T>C	chr3.hg19:g.97868486T>C	ENSP00000401706:p.Leu86Ser	201.0	0.0		265.0	66.0	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	hg19	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	T	8.975	0.973948	0.18736	.	.	ENSG00000236032	ENST00000437310	T	0.00540	6.7	2.49	1.2	0.21068	GPCR, rhodopsin-like superfamily (1);	1.060770	0.07510	N	0.908663	T	0.00936	0.0031	M	0.84156	2.68	0.09310	N	1	B	0.20671	0.047	B	0.21151	0.033	T	0.42599	-0.9442	10	0.87932	D	0	.	6.5981	0.22685	0.0:0.0:0.2461:0.7539	.	86	A6NHG9	O5H14_HUMAN	S	86	ENSP00000401706:L86S	ENSP00000401706:L86S	L	+	2	0	OR5H14	99351176	0.123000	0.22298	0.003000	0.11579	0.083000	0.17756	2.548000	0.45794	0.165000	0.19558	0.164000	0.16699	TTA	.	.		0.393	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			C	97868486	T	C	97868486	3	2	233	1	0	0	0	0	1	0	0	0	11169	1764	61	2	259	2	OR5H14	3	97868486	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	24822271	97868486	100153944	19	32505										
GTF2E1	2960	hgsc.bcm.edu	37	chr3	120500204	120500204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tcatggtggctggccgtccgTtctcctacagtgaagtgagc	13	11	2	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr3:120500204T>C	ENST00000283875.5	+	5	1300	c.1207T>C	c.(1207-1209)Ttc>Ctc	p.F403L		NM_005513.2	NP_005504.2	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1, alpha 56kDa	403					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)	22				GBM - Glioblastoma multiforme(114;0.159)		TGGCCGTCCGTTCTCCTACAG	0.507																																					p.F403L		Atlas-SNP	.											.	GTF2E1	52	.	0			c.T1207C						.						149	148	148					3																	120500204		2203	4300	6503	SO:0001583	missense	2960	exon5			CGTCCGTTCTCCT	S67859	CCDS3002.1	3q21-q24	2010-03-23	2002-08-29		ENSG00000153767	ENSG00000153767		"General transcription factors"	4650	protein-coding gene	gene with protein product		189962	"general transcription factor IIE, polypeptide 1 (alpha subunit, 56kD)"			1454543, 8162052	Standard	NM_005513		Approved	TFIIE-A, FE	uc003edz.4	P29083	OTTHUMG00000159667	ENST00000283875.5:c.1207T>C	chr3.hg19:g.120500204T>C	ENSP00000283875:p.Phe403Leu	194.0	0.0		213.0	38.0	NM_005513	Q16103	Missense_Mutation	SNP	ENST00000283875.5	hg19	CCDS3002.1	.	.	.	.	.	.	.	.	.	.	T	16.29	3.082794	0.55861	.	.	ENSG00000153767	ENST00000283875	T	0.53423	0.62	5.39	4.2	0.49525	.	0.257074	0.46442	D	0.000300	T	0.38639	0.1048	L	0.50919	1.6	0.43499	D	0.99574	B	0.25206	0.12	B	0.27500	0.08	T	0.25187	-1.0139	10	0.40728	T	0.16	-31.3621	5.5133	0.16892	0.1557:0.0863:0.0:0.758	.	403	P29083	T2EA_HUMAN	L	403	ENSP00000283875:F403L	ENSP00000283875:F403L	F	+	1	0	GTF2E1	121982894	1.000000	0.71417	0.967000	0.41034	0.953000	0.61014	5.707000	0.68370	1.027000	0.39758	0.528000	0.53228	TTC	.	.		0.507	GTF2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356770.1	NM_005513		C	120500204	T	C	120500204	3	2	233	1	0	0	0	0	1	0	0	0	6865	1725	60	2	1221	2	GTF2E1	3	120500204	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	22631718	120500204	77522226	20	32506										
FETUB	26998	hgsc.bcm.edu	37	chr3	186360348	186360349	+	Splice_Site	INS	-	-	T													0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	aactgtactcttcgcccaggINStaagaaatcactacgatttt					rs147011769	byFrequency	TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr3:186360348_186360349insT	ENST00000265029.3	+	3	525		c.e3+1		FETUB_ENST00000382134.3_Intron|RP11-134F2.2_ENST00000428501.1_RNA|FETUB_ENST00000539949.1_Intron|FETUB_ENST00000450521.1_Splice_Site|FETUB_ENST00000488561.1_Intron|FETUB_ENST00000382136.3_Splice_Site|RP11-134F2.2_ENST00000455926.1_RNA	NM_014375.2	NP_055190.2	Q9UGM5	FETUB_HUMAN	fetuin B						binding of sperm to zona pellucida (GO:0007339)|negative regulation of endopeptidase activity (GO:0010951)|single fertilization (GO:0007338)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)	20	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		CTTCGCCCAGGTAAGAAATCAC	0.342																																					.		Atlas-INDEL	.											.	FETUB	53	.	0			c.424+1->T						.																																			SO:0001630	splice_region_variant	26998	exon3			.	AJ242928	CCDS3279.1	3q27.3	2008-05-15			ENSG00000090512	ENSG00000090512			3658	protein-coding gene	gene with protein product		605954				10947975	Standard	XM_005247350		Approved		uc003fqn.3	Q9UGM5	OTTHUMG00000156586	ENST00000265029.3:c.424+1->T	chr3.hg19:g.186360349_186360349dupT		125.0	0.0		227.0	52.0	NM_014375	B2RCW6|E9PG06|Q1RMZ0|Q5J876|Q6DK58|Q6GRB6|Q9Y6Z0	Splice_Site	INS	ENST00000265029.3	hg19	CCDS3279.1																																																																																			.	.		0.342	FETUB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344679.1	NM_014375	Intron	T	186360349	-	T	186360348	8	5	233	1	0	1	1	0	0	0	1	0	5829	1275	44	0	435	0	FETUB	3	186360348	Splice_Site	INS	-	TCGA-DD-AAW0-01A-11D-A40R-10	65860144	186360348	11662082	21	32507										
ALB	213	hgsc.bcm.edu	37	chr4	74285302	74285311	+	Frame_Shift_Del	DEL	TTTTGTAGAG	TTTTGTAGAG	-													0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gttatggatgatttcgcagcTtttgtagagaagtgctgcaa					rs564649737		TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	TTTTGTAGAG	TTTTGTAGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr4:74285302_74285311delTTTTGTAGAG	ENST00000503124.1	+	11	1488_1497	c.1281_1290delTTTTGTAGAG	c.(1279-1290)gcttttgtagagfs	p.AFVE427fs	ALB_ENST00000295897.4_Frame_Shift_Del_p.AFVE577fs|ALB_ENST00000509063.1_Frame_Shift_Del_p.AFVE577fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Frame_Shift_Del_p.AFVE462fs|ALB_ENST00000415165.2_Frame_Shift_Del_p.AFVE385fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATTTCGCAGCTTTTGTAGAGAAGTGCTGCA	0.419																																					p.577_580del		Atlas-INDEL	.											.	ALB	132	.	0			c.1730_1739del						.																																			SO:0001589	frameshift_variant	213	exon13			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1281_1290delTTTTGTAGAG	chr4.hg19:g.74285302_74285311delTTTTGTAGAG	ENSP00000421027:p.Ala427fs	106.0	0.0		99.0	15.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.419	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74285311	TTTTGTAGAG	-	74285302	7	5	233	1	0	1	0	1	0	0	0	0	486	1596	56	0	1781	0	ALB	4	74285302	Frame_Shift_Del	DEL	TTTTGTAGAG	TCGA-DD-AAW0-01A-11D-A40R-10		74285302	116868974	22	32508										
CNOT6L	246175	hgsc.bcm.edu	37	chr4	78694248	78694248	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	cacttacctttcaaacctagAgtttgtagctggaagagccg	9	10	1	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr4:78694248A>G	ENST00000504123.1	-	4	517	c.387T>C	c.(385-387)acT>acC	p.T129T	CNOT6L_ENST00000264903.4_Silent_p.T129T|CNOT6L_ENST00000506166.1_5'UTR			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	129	Required for interaction with CNOT1, CNOT3 and CNOT7.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						TCAAACCTAGAGTTTGTAGCT	0.318																																					p.T129T		Atlas-SNP	.											.	CNOT6L	57	.	0			c.T387C						.						42	42	42					4																	78694248		1797	4073	5870	SO:0001819	synonymous_variant	246175	exon4			ACCTAGAGTTTGT	AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.387T>C	chr4.hg19:g.78694248A>G		558.0	0.0		549.0	165.0	NM_144571	Q9UF92	Silent	SNP	ENST00000504123.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.392	1.075869	0.20227	.	.	ENSG00000138767	ENST00000515506	.	.	.	4.78	2.18	0.27775	.	.	.	.	.	T	0.41373	0.1156	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41805	-0.9488	4	.	.	.	-10.062	0.6411	0.00810	0.4491:0.1804:0.1952:0.1754	.	.	.	.	P	158	.	.	S	-	1	0	CNOT6L	78913272	0.945000	0.32115	1.000000	0.80357	0.997000	0.91878	0.163000	0.16520	1.779000	0.52309	0.454000	0.30748	TCT	.	.		0.318	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1			G	78694248	A	G	78694248	2	3	233	1	0	0	0	0	0	0	0	1	3625	291	11	2		2	CNOT6L	4	78694248	Silent	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	4408946	78694248	112460028	23	32509										
BANK1	55024	hgsc.bcm.edu	37	chr4	102839251	102839251	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	aatgttcaggagcaacctggGcatctaagatgaaaaatatg	10	6	2	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr4:102839251G>C	ENST00000322953.4	+	7	1385	c.1111G>C	c.(1111-1113)Gca>Cca	p.A371P	BANK1_ENST00000508653.1_Missense_Mutation_p.A238P|BANK1_ENST00000504592.1_Missense_Mutation_p.A356P|BANK1_ENST00000428908.1_Missense_Mutation_p.A238P|BANK1_ENST00000444316.2_Missense_Mutation_p.A341P	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	371					B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		AGCAACCTGGGCATCTAAGAT	0.408																																					p.A371P		Atlas-SNP	.											.	BANK1	95	.	0			c.G1111C						.						82	83	82					4																	102839251		2203	4298	6501	SO:0001583	missense	55024	exon7			ACCTGGGCATCTA	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.1111G>C	chr4.hg19:g.102839251G>C	ENSP00000320509:p.Ala371Pro	318.0	0.0		317.0	100.0	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	hg19	CCDS34038.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111316	0.77210	.	.	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	4.66	4.66	0.58398	Ankyrin repeat-containing domain (1);	0.191497	0.32868	N	0.005558	T	0.66436	0.2789	M	0.68317	2.08	0.44261	D	0.997113	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;1.0	T	0.69363	-0.5165	10	0.62326	D	0.03	.	15.1095	0.72343	0.0:0.0:1.0:0.0	.	238;371;356	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	P	356;371;238;238;341	ENSP00000421443:A356P;ENSP00000320509:A371P;ENSP00000412748:A238P;ENSP00000422314:A238P;ENSP00000388817:A341P	ENSP00000320509:A371P	A	+	1	0	BANK1	103058274	1.000000	0.71417	0.980000	0.43619	0.986000	0.74619	4.846000	0.62860	2.409000	0.81822	0.655000	0.94253	GCA	.	.		0.408	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		C	102839251	G	C	102839251	3	2	233	1	0	0	0	0	1	0	0	0	1309	1203	42	4	1137	4	BANK1	4	102839251	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	24145003	102839251	88315025	24	32510										
TRPC3	7222	hgsc.bcm.edu	37	chr4	122828649	122828649	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	atgtacgcaatccgagagaaGctgagcacaacagctatggc	11	10	0	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr4:122828649G>C	ENST00000379645.3	-	7	1939	c.1866C>G	c.(1864-1866)agC>agG	p.S622R	TRPC3_ENST00000513531.1_Missense_Mutation_p.S494R|TRPC3_ENST00000264811.5_Missense_Mutation_p.S549R	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	537					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						TCCGAGAGAAGCTGAGCACAA	0.448																																					p.S622R		Atlas-SNP	.											.	TRPC3	201	.	0			c.C1866G						.						98	97	97					4																	122828649		2203	4299	6502	SO:0001583	missense	7222	exon7			AGAGAAGCTGAGC	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.1866C>G	chr4.hg19:g.122828649G>C	ENSP00000368966:p.Ser622Arg	361.0	0.0		301.0	81.0	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	hg19	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.078863	0.76528	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	D;D;D	0.97256	-4.31;-4.31;-4.31	5.3	5.3	0.74995	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98957	0.9645	M	0.94142	3.5	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.99568	1.0970	10	0.87932	D	0	-23.1109	18.9622	0.92681	0.0:0.0:1.0:0.0	.	537;494;622	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	R	549;622;494	ENSP00000264811:S549R;ENSP00000368966:S622R;ENSP00000426899:S494R	ENSP00000264811:S549R	S	-	3	2	TRPC3	123048099	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.145000	0.31577	2.465000	0.83290	0.655000	0.94253	AGC	.	.		0.448	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		C	122828649	G	C	122828649	3	2	233	1	0	0	0	0	1	0	0	0	16594	962	34	4	923	4	TRPC3	4	122828649	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	19989398	122828649	68325627	25	32511										
CLGN	1047	hgsc.bcm.edu	37	chr4	141323176	141323176	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tgtctgctaggagtttaatgTatgcacctccacaatcaata	7	9	2	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr4:141323176T>C	ENST00000325617.5	-	6	904	c.464A>G	c.(463-465)tAc>tGc	p.Y155C	CLGN_ENST00000414773.1_Missense_Mutation_p.Y155C|CLGN_ENST00000537281.1_Missense_Mutation_p.Y155C	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	155					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					GAGTTTAATGTATGCACCTCC	0.274																																					p.Y155C		Atlas-SNP	.											.	CLGN	76	.	0			c.A464G						.						63	68	66					4																	141323176		2202	4283	6485	SO:0001583	missense	1047	exon7			TTAATGTATGCAC	D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.464A>G	chr4.hg19:g.141323176T>C	ENSP00000326699:p.Tyr155Cys	529.0	0.0		453.0	144.0	NM_001130675	B3KS90|B4DXV8|D3DNY8	Missense_Mutation	SNP	ENST00000325617.5	hg19	CCDS3751.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.364046	0.82353	.	.	ENSG00000153132	ENST00000325617;ENST00000414773;ENST00000537281;ENST00000545667;ENST00000509477	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	5.44	5.44	0.79542	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Calreticulin/calnexin, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.85669	0.5750	H	0.96460	3.825	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90356	0.4370	10	0.87932	D	0	-8.9119	15.8087	0.78538	0.0:0.0:0.0:1.0	.	155	O14967	CLGN_HUMAN	C	155;155;155;72;155	ENSP00000326699:Y155C;ENSP00000392782:Y155C;ENSP00000439381:Y155C;ENSP00000424593:Y155C	ENSP00000326699:Y155C	Y	-	2	0	CLGN	141542626	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.191000	0.70037	0.528000	0.53228	TAC	.	.		0.274	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362		C	141323176	T	C	141323176	3	2	233	1	0	0	0	0	1	0	0	0	3526	1638	57	2	1408	2	CLGN	4	141323176	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	18494527	141323176	49831100	26	32512										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155410671	155410702	+	Frame_Shift_Del	DEL	CGCTTTCGGAATCAATGGCAAAAGATGGTCCA	CGCTTTCGGAATCAATGGCAAAAGATGGTCCA	-													0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ccggatagtgctgatcgcacCgctttcggaatcaatggcaa					rs371502851	byFrequency	TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	CGCTTTCGGAATCAATGGCAAAAGATGGTCCA	CGCTTTCGGAATCAATGGCAAAAGATGGTCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr4:155410671_155410702delCGCTTTCGGAATCAATGGCAAAAGATGGTCCA	ENST00000339452.1	-	1	2166_2197	c.1806_1837delTGGACCATCTTTTGCCATTGATTCCGAAAGCG	c.(1804-1839)tgtggaccatcttttgccattgattccgaaagcggtfs	p.CGPSFAIDSESG602fs	DCHS2_ENST00000443500.1_Frame_Shift_Del_p.CGPSFAIDSESG602fs|DCHS2_ENST00000456341.2_Frame_Shift_Del_p.CGPSFAIDSESG595fs	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1724	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CTGATCGCACCGCTTTCGGAATCAATGGCAAAAGATGGTCCACACTCTGCGG	0.595																																					p.603_613del		Atlas-INDEL	.											.	DCHS2	594	.	0			c.1807_1838del						.																																			SO:0001589	frameshift_variant	54798	exon1			.	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.1806_1837delTGGACCATCTTTTGCCATTGATTCCGAAAGCG	chr4.hg19:g.155410671_155410702delCGCTTTCGGAATCAATGGCAAAAGATGGTCCA	ENSP00000345062:p.Cys602fs	102.0	0.0		108.0	15.0	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Frame_Shift_Del	DEL	ENST00000339452.1	hg19	CCDS47150.1																																																																																			.	.		0.595	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552		-	155410702	CGCTTTCGGAATCAATGGCAAAAGATGGTCCA	-	155410671	7	5	233	1	0	1	0	1	0	0	0	0	4290	652	23	0	9247	0	DCHS2	4	155410671	Frame_Shift_Del	DEL	CGCTTTCGGAATCAATGGCAAAAGATGGTCCA	TCGA-DD-AAW0-01A-11D-A40R-10	14087495	155410671	35743605	27	32513										
EMB	133418	hgsc.bcm.edu	37	chr5	49701580	49701580	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tttacactcccattactactGtaccaggtccaatttaaagg	5	11	0	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr5:49701580G>A	ENST00000303221.5	-	5	794	c.579C>T	c.(577-579)taC>taT	p.Y193Y	EMB_ENST00000508934.1_Silent_p.Y139Y|EMB_ENST00000514111.1_Silent_p.Y143Y|EMB_ENST00000506190.1_5'UTR	NM_198449.2	NP_940851.1	Q6PCB8	EMB_HUMAN	embigin	193	Ig-like V-type 2.				cell adhesion (GO:0007155)|plasma membrane lactate transport (GO:0035879)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	organic cyclic compound binding (GO:0097159)			breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	15	Lung SC(58;0.218)	Lung NSC(810;0.0795)				CATTACTACTGTACCAGGTCC	0.323																																					p.Y193Y		Atlas-SNP	.											.	EMB	42	.	0			c.C579T						.						58	60	60					5																	49701580		2203	4291	6494	SO:0001819	synonymous_variant	133418	exon5			ACTACTGTACCAG	BC059398	CCDS3953.1	5q11.1	2013-01-29	2010-06-24		ENSG00000170571	ENSG00000170571		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30465	protein-coding gene	gene with protein product		615669	"embigin homolog (mouse)"			9438341	Standard	NM_198449		Approved	MGC71745	uc003jom.3	Q6PCB8	OTTHUMG00000131161	ENST00000303221.5:c.579C>T	chr5.hg19:g.49701580G>A		653.0	0.0		767.0	43.0	NM_198449	B7Z6S3|B7Z902	Silent	SNP	ENST00000303221.5	hg19	CCDS3953.1																																																																																			.	.		0.323	EMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253853.1	NM_198449		A	49701580	G	A	49701580	2	1	233	1	0	0	0	0	0	0	0	1	5087	1372	48	3		3	EMB	5	49701580	Silent	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10		49701580	131213680	28	32514										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54701259	54701259	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ttcatgtgctttagattgcaAtagatattaaatctgcaaag	7	5	2	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr5:54701259A>G	ENST00000230640.5	+	22	2742	c.2488A>G	c.(2488-2490)Ata>Gta	p.I830V	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.I729V	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	830					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TTAGATTGCAATAGATATTAA	0.299																																					p.I830V	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.A2488G						.						65	66	66					5																	54701259		2203	4300	6503	SO:0001583	missense	23517	exon22			ATTGCAATAGATA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.2488A>G	chr5.hg19:g.54701259A>G	ENSP00000230640:p.Ile830Val	114.0	0.0		154.0	42.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	hg19	CCDS3967.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.535582	0.27475	.	.	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.28895	1.59;1.59	5.51	-5.59	0.02505	.	0.783353	0.13050	N	0.417768	T	0.11196	0.0273	N	0.12746	0.255	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.15093	-1.0449	10	0.30854	T	0.27	-34.3256	3.252	0.06818	0.2805:0.2239:0.3928:0.1028	.	729;830	F5H7E2;P42285	.;SK2L2_HUMAN	V	830;729	ENSP00000230640:I830V;ENSP00000442583:I729V	ENSP00000230640:I830V	I	+	1	0	SKIV2L2	54737016	0.248000	0.23930	0.808000	0.32385	0.913000	0.54294	0.689000	0.25437	-0.779000	0.04560	0.383000	0.25322	ATA	.	.		0.299	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			G	54701259	A	G	54701259	3	3	233	1	0	0	0	0	1	0	0	0	14375	101	4	2	2574	2	SKIV2L2	5	54701259	Missense_Mutation	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	4999679	54701259	126214001	29	32515										
SLC38A9	153129	hgsc.bcm.edu	37	chr5	54965110	54965110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gcaataaagtgttaaaaggcCcatcagtatgatgacacaca	8	8	1	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr5:54965110C>T	ENST00000396865.2	-	7	1063	c.472G>A	c.(472-474)Ggc>Agc	p.G158S	SLC38A9_ENST00000416547.2_Missense_Mutation_p.G34S|SLC38A9_ENST00000515629.1_Missense_Mutation_p.G95S|SLC38A9_ENST00000318672.3_Missense_Mutation_p.G158S|SLC38A9_ENST00000539768.1_Missense_Mutation_p.G158S|SLC38A9_ENST00000512595.1_Missense_Mutation_p.G131S	NM_173514.3	NP_775785.2	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	158					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				GTTAAAAGGCCCATCAGTATG	0.328																																					p.G158S		Atlas-SNP	.											.	SLC38A9	50	.	0			c.G472A						.						186	190	189					5																	54965110		2203	4300	6503	SO:0001583	missense	153129	exon7			AAAGGCCCATCAG		CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058		"Solute carriers"	26907	protein-coding gene	gene with protein product							Standard	NM_173514		Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000396865.2:c.472G>A	chr5.hg19:g.54965110C>T	ENSP00000380074:p.Gly158Ser	97.0	0.0		101.0	22.0	NM_173514	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	Missense_Mutation	SNP	ENST00000396865.2	hg19	CCDS3968.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.957368	0.92726	.	.	ENSG00000177058	ENST00000396865;ENST00000318672;ENST00000539768;ENST00000515629;ENST00000416547;ENST00000512595;ENST00000511233;ENST00000512208;ENST00000503817	T;T;T;T;T;T;T;T;T	0.02787	4.16;4.16;4.16;4.16;4.16;4.16;4.16;4.16;4.16	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.12008	0.0292	L	0.50919	1.6	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.87578	0.952;0.998	T	0.12734	-1.0536	10	0.29301	T	0.29	-18.6055	19.3048	0.94157	0.0:1.0:0.0:0.0	.	131;158	B3KXV1;Q8NBW4	.;S38A9_HUMAN	S	158;158;158;95;34;131;158;95;95	ENSP00000380074:G158S;ENSP00000316596:G158S;ENSP00000437771:G158S;ENSP00000420934:G95S;ENSP00000397429:G34S;ENSP00000427335:G131S;ENSP00000423219:G158S;ENSP00000426413:G95S;ENSP00000424918:G95S	ENSP00000316596:G158S	G	-	1	0	SLC38A9	55000867	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.065000	0.76727	2.622000	0.88805	0.650000	0.86243	GGC	.	.		0.328	SLC38A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253912.2	NM_173514		T	54965110	C	T	54965110	3	4	233	1	0	0	0	0	1	0	0	0	14626	623	22	3	1253	3	SLC38A9	5	54965110	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	263851	54965110	125950150	30	32516										
MCCC2	64087	hgsc.bcm.edu	37	chr5	70952644	70952644	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	cagttttagtgcagccctcaAcgcaccaatagagaagactg	9	11	1	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr5:70952644A>G	ENST00000340941.6	+	17	1778	c.1649A>G	c.(1648-1650)aAc>aGc	p.N550S	MCCC2_ENST00000323375.8_Missense_Mutation_p.N512S	NM_022132.4	NP_071415.1	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-CoA carboxylase 2 (beta)	550	Carboxyltransferase.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|coenzyme A metabolic process (GO:0015936)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			endometrium(2)|kidney(15)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	30		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	GCAGCCCTCAACGCACCAATA	0.418																																					p.N550S		Atlas-SNP	.											.	MCCC2	47	.	0			c.A1649G						.						227	207	214					5																	70952644		2203	4300	6503	SO:0001583	missense	64087	exon17			CCCTCAACGCACC	AF310971	CCDS34184.1	5q12-q13	2010-04-30	2010-04-30		ENSG00000131844	ENSG00000131844	6.4.1.4		6937	protein-coding gene	gene with protein product		609014	"methylcrotonoyl-Coenzyme A carboxylase 2 (beta)"				Standard	NM_022132		Approved	MCCB	uc003kbs.4	Q9HCC0	OTTHUMG00000162505	ENST00000340941.6:c.1649A>G	chr5.hg19:g.70952644A>G	ENSP00000343657:p.Asn550Ser	110.0	0.0		175.0	34.0	NM_022132	A6NIY9|Q96C27|Q9Y4L7	Missense_Mutation	SNP	ENST00000340941.6	hg19	CCDS34184.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.076929	0.76415	.	.	ENSG00000131844	ENST00000340941;ENST00000323375	D;D	0.97378	-4.36;-4.36	4.94	4.94	0.65067	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.000000	0.85682	D	0.000000	D	0.95645	0.8584	L	0.55990	1.75	0.80722	D	1	P	0.45126	0.851	B	0.43251	0.413	D	0.95765	0.8804	10	0.72032	D	0.01	-12.0809	13.617	0.62115	1.0:0.0:0.0:0.0	.	550	Q9HCC0	MCCB_HUMAN	S	550;512	ENSP00000343657:N550S;ENSP00000327308:N512S	ENSP00000327308:N512S	N	+	2	0	MCCC2	70988400	1.000000	0.71417	0.986000	0.45419	0.679000	0.39708	9.240000	0.95396	1.867000	0.54127	0.528000	0.53228	AAC	.	.		0.418	MCCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369243.4			G	70952644	A	G	70952644	3	3	233	1	0	0	0	0	1	0	0	0	9384	43	2	2	1715	2	MCCC2	5	70952644	Missense_Mutation	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	15987534	70952644	109962616	31	32517										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72189057	72189058	+	Frame_Shift_Del	DEL	CT	CT	-													0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tgtaaacctagtacagaagaCtcttgcacaagccatggtaa							TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr5:72189057_72189058delCT	ENST00000337273.5	+	16	2306_2307	c.1880_1881delCT	c.(1879-1881)actfs	p.T627fs	TNPO1_ENST00000523768.1_Frame_Shift_Del_p.T577fs|TNPO1_ENST00000454282.1_Frame_Shift_Del_p.T577fs|TNPO1_ENST00000506351.2_Frame_Shift_Del_p.T619fs	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	627					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		GTACAGAAGACTCTTGCACAAG	0.391																																					p.627_627del		Atlas-INDEL	.											.	TNPO1	90	.	0			c.1879_1880del						.																																			SO:0001589	frameshift_variant	3842	exon16			.	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.1880_1881delCT	chr5.hg19:g.72189059_72189060delCT	ENSP00000336712:p.Thr627fs	87.0	0.0		122.0	29.0	NM_002270	B4DVC6|Q92957|Q92975	Frame_Shift_Del	DEL	ENST00000337273.5	hg19	CCDS43329.1																																																																																			.	.		0.391	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		-	72189058	CT	-	72189057	7	5	233	1	0	1	0	1	0	0	0	0	16350	565	20	0	1942	0	TNPO1	5	72189057	Frame_Shift_Del	DEL	CT	TCGA-DD-AAW0-01A-11D-A40R-10	1236413	72189057	108726203	32	32518										
FBN2	2201	hgsc.bcm.edu	37	chr5	127670429	127670429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	acctgtacatcctgtggtccCcttcttcactgagtaaccca	6	15	2	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr5:127670429C>T	ENST00000508053.1	-	37	5055	c.4081G>A	c.(4081-4083)Ggg>Agg	p.G1361R	FBN2_ENST00000262464.4_Missense_Mutation_p.G1361R|FBN2_ENST00000508989.1_Missense_Mutation_p.G1328R|FBN2_ENST00000507835.1_Missense_Mutation_p.G211R			P35556	FBN2_HUMAN	fibrillin 2	1361	EGF-like 21; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CCTGTGGTCCCCTTCTTCACT	0.423																																					p.G1361R		Atlas-SNP	.											.	FBN2	858	.	0			c.G4081A						.						146	129	135					5																	127670429		2203	4300	6503	SO:0001583	missense	2201	exon31			TGGTCCCCTTCTT	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.4081G>A	chr5.hg19:g.127670429C>T	ENSP00000424571:p.Gly1361Arg	70.0	0.0		94.0	18.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.951140	0.92660	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000507835;ENST00000508989	D;D;D;D	0.92249	-3.0;-3.0;-3.0;-3.0	4.96	4.96	0.65561	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.224079	0.32593	N	0.005887	D	0.94712	0.8294	L	0.48935	1.535	0.52501	D	0.999951	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.94977	0.8122	10	0.72032	D	0.01	.	18.8164	0.92079	0.0:1.0:0.0:0.0	.	1328;1361	D6RJI3;P35556	.;FBN2_HUMAN	R	1361;1361;211;1328	ENSP00000262464:G1361R;ENSP00000424571:G1361R;ENSP00000426839:G211R;ENSP00000425596:G1328R	ENSP00000262464:G1361R	G	-	1	0	FBN2	127698328	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.609000	0.82925	2.743000	0.94032	0.650000	0.86243	GGG	.	.		0.423	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127670429	C	T	127670429	3	4	233	1	0	0	0	0	1	0	0	0	5711	623	22	3	4797	3	FBN2	5	127670429	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	55481372	127670429	53244831	33	32519										
AFAP1L1	134265	hgsc.bcm.edu	37	chr5	148695457	148695457	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	caactgttctacccttggccGccgggagacctgtgatcacg	11	14	2	2	rs371511486		TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr5:148695457G>A	ENST00000296721.4	+	10	1192	c.1094G>A	c.(1093-1095)cGc>cAc	p.R365H	AFAP1L1_ENST00000515000.1_Missense_Mutation_p.R365H	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	365						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCCTTGGCCGCCGGGAGACC	0.632																																					p.R365H		Atlas-SNP	.											AFAP1L1,colon,carcinoma,0,1	AFAP1L1	86	.	0			c.G1094A						.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	75	67	70		1094,1094	4.6	1	5		70	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	AFAP1L1	NM_001146337.1,NM_152406.2	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	365/726,365/769	148695457	1,13005	2203	4300	6503	SO:0001583	missense	134265	exon10			TTGGCCGCCGGGA	AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"Pleckstrin homology (PH) domain containing"	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.1094G>A	chr5.hg19:g.148695457G>A	ENSP00000296721:p.Arg365His	114.0	0.0		160.0	25.0	NM_001146337	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	hg19	CCDS34274.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.311870	0.23821	0.0	1.16E-4	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.11821	2.74;2.74	5.46	4.58	0.56647	.	0.239927	0.44285	D	0.000477	T	0.09379	0.0231	L	0.33485	1.01	0.40845	D	0.983701	B;B	0.19706	0.038;0.032	B;B	0.16722	0.016;0.005	T	0.05419	-1.0886	10	0.02654	T	1	-17.0073	12.8176	0.57675	0.0767:0.0:0.9233:0.0	.	365;365	Q8TED9-2;Q8TED9	.;AF1L1_HUMAN	H	365	ENSP00000296721:R365H;ENSP00000424427:R365H	ENSP00000296721:R365H	R	+	2	0	AFAP1L1	148675650	0.977000	0.34250	1.000000	0.80357	0.411000	0.31082	2.625000	0.46452	2.556000	0.86216	0.561000	0.74099	CGC	.	.		0.632	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		A	148695457	G	A	148695457	3	1	233	1	0	0	0	0	1	0	0	0	354	1087	38	1	1132	1	AFAP1L1	5	148695457	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	21025028	148695457	32219803	34	32520										
HMMR	3161	hgsc.bcm.edu	37	chr5	162901124	162901124	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	aatgcagagatgcaaaacttAaaacagaagtttattcttga	7	5	1	3			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr5:162901124A>T	ENST00000358715.3	+	10	999	c.963A>T	c.(961-963)ttA>ttT	p.L321F	HMMR_ENST00000393915.4_Missense_Mutation_p.L322F|HMMR_ENST00000432118.2_Missense_Mutation_p.L235F|HMMR_ENST00000353866.3_Missense_Mutation_p.L306F			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	321					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	TGCAAAACTTAAAACAGAAGT	0.328																																					p.L322F		Atlas-SNP	.											.	HMMR	64	.	0			c.A966T						.						80	77	78					5																	162901124		2203	4300	6503	SO:0001583	missense	3161	exon10			AAACTTAAAACAG	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"CD molecules"	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.963A>T	chr5.hg19:g.162901124A>T	ENSP00000351554:p.Leu321Phe	568.0	0.0		934.0	165.0	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	hg19	CCDS4362.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.134729	0.37728	.	.	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000434157;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18	5.77	1.65	0.23941	.	0.254173	0.32719	N	0.005734	T	0.21022	0.0506	M	0.69823	2.125	0.21290	N	0.999733	D;D;D;D	0.76494	0.999;0.992;0.999;0.999	D;P;D;D	0.70016	0.967;0.9;0.967;0.967	T	0.02156	-1.1204	10	0.41790	T	0.15	-6.7995	7.8407	0.29397	0.6974:0.0:0.3026:0.0	.	235;322;306;321	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	F	207;306;306;322;298;235;321	ENSP00000400527:L207F;ENSP00000185942:L306F;ENSP00000377492:L322F;ENSP00000402673:L235F;ENSP00000351554:L321F	ENSP00000185942:L306F	L	+	3	2	HMMR	162833702	0.996000	0.38824	0.084000	0.20598	0.457000	0.32468	0.537000	0.23144	0.507000	0.28148	0.533000	0.62120	TTA	.	.		0.328	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484		T	162901124	A	T	162901124	3	4	233	1	0	0	0	0	1	0	0	0	7251	359	13	4	1004	4	HMMR	5	162901124	Missense_Mutation	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	14205667	162901124	18014136	35	32521										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168176483	168176483	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	cacagccttcttaccatcacAggtgaagtcctggatggcca	9	13	2	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr5:168176483A>T	ENST00000519560.1	-	19	2550	c.2131T>A	c.(2131-2133)Tgt>Agt	p.C711S	SLIT3_ENST00000332966.8_Missense_Mutation_p.C711S|SLIT3_ENST00000404867.3_Missense_Mutation_p.C711S	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	711	LRRCT 3.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTACCATCACAGGTGAAGTCC	0.542																																					p.C711S	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.T2131A						.						85	82	83					5																	168176483		2203	4300	6503	SO:0001583	missense	6586	exon19			CATCACAGGTGAA	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.2131T>A	chr5.hg19:g.168176483A>T	ENSP00000430333:p.Cys711Ser	93.0	0.0		121.0	27.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	hg19	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.671184	0.88348	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.79033	-1.23;-1.23;-1.22	5.42	5.42	0.78866	Cysteine-rich flanking region, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.91794	0.7404	H	0.96208	3.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94324	0.7556	10	0.87932	D	0	.	15.4652	0.75394	1.0:0.0:0.0:0.0	.	711	O75094	SLIT3_HUMAN	S	711	ENSP00000430333:C711S;ENSP00000332164:C711S;ENSP00000384890:C711S	ENSP00000332164:C711S	C	-	1	0	SLIT3	168109061	1.000000	0.71417	0.998000	0.56505	0.893000	0.52053	8.855000	0.92236	2.043000	0.60533	0.533000	0.62120	TGT	.	.		0.542	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		T	168176483	A	T	168176483	3	4	233	1	0	0	0	0	1	0	0	0	14756	188	7	4	2512	4	SLIT3	5	168176483	Missense_Mutation	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	5275359	168176483	12738777	36	32522										
SYCP2L	221711	hgsc.bcm.edu	37	chr6	10911072	10911072	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tgcagggtgtattcatttccGtgtattgctgcttttgctga	11	7	1	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr6:10911072G>T	ENST00000283141.6	+	12	1184	c.888G>T	c.(886-888)ccG>ccT	p.P296P	SYCP2L_ENST00000543878.1_Silent_p.P137P|RP11-637O19.3_ENST00000480294.1_3'UTR	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	296						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			ATTCATTTCCGTGTATTGCTG	0.413																																					p.P296P		Atlas-SNP	.											.	SYCP2L	101	.	0			c.G888T						.						271	247	255					6																	10911072		1921	4126	6047	SO:0001819	synonymous_variant	221711	exon12			ATTTCCGTGTATT	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 177"	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.888G>T	chr6.hg19:g.10911072G>T		60.0	0.0		78.0	29.0	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Silent	SNP	ENST00000283141.6	hg19	CCDS43423.1																																																																																			.	.		0.413	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		T	10911072	G	T	10911072	2	4	233	1	0	0	0	0	0	0	0	1	15448	1132	40	1		1	SYCP2L	6	10911072	Silent	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10		10911072	160203995	37	32523										
ATF6B	1388	hgsc.bcm.edu	37	chr6	32093947	32093947	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tctggacggtttcaaatgagGatgttgggtcatctcccagg	13	8	4	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr6:32093947G>T	ENST00000375203.3	-	5	457	c.425C>A	c.(424-426)tCc>tAc	p.S142Y	ATF6B_ENST00000375201.4_Missense_Mutation_p.S139Y|ATF6B_ENST00000468502.1_5'UTR	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	142					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						TTCAAATGAGGATGTTGGGTC	0.532																																					p.S142Y		Atlas-SNP	.											.	ATF6B	40	.	0			c.C425A						.						138	121	127					6																	32093947		2203	4300	6503	SO:0001583	missense	1388	exon5			AATGAGGATGTTG		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"basic leucine zipper proteins"	2349	protein-coding gene	gene with protein product		600984	"cAMP responsive element binding protein-like 1"	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.425C>A	chr6.hg19:g.32093947G>T	ENSP00000364349:p.Ser142Tyr	77.0	0.0		100.0	19.0	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Missense_Mutation	SNP	ENST00000375203.3	hg19	CCDS4737.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.321906	0.41096	.	.	ENSG00000213676	ENST00000375203;ENST00000375201	T;T	0.57107	0.42;1.16	5.25	3.46	0.39613	.	0.276444	0.29473	U	0.012047	T	0.19765	0.0475	L	0.56769	1.78	0.25642	N	0.986194	B;B;B	0.28636	0.218;0.178;0.112	B;B;B	0.30495	0.116;0.074;0.034	T	0.35475	-0.9787	10	0.02654	T	1	-1.9902	8.2551	0.31751	0.1806:0.0:0.8194:0.0	.	142;139;142	Q96QL7;Q99941-2;Q99941	.;.;ATF6B_HUMAN	Y	142;139	ENSP00000364349:S142Y;ENSP00000364347:S139Y	ENSP00000364347:S139Y	S	-	2	0	ATF6B	32201925	1.000000	0.71417	0.962000	0.40283	0.911000	0.54048	2.445000	0.44899	0.779000	0.33543	0.650000	0.86243	TCC	.	.		0.532	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2			T	32093947	G	T	32093947	3	4	233	1	0	0	0	0	1	0	0	0	1085	1174	41	3	1742	3	ATF6B	6	32093947	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	21182875	32093947	139021120	38	32524										
RUNX2	860	hgsc.bcm.edu	37	chr6	45514837	45514837	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tggcacttcgtcaggatcctAtcagtttcccatggtgccgg	11	12	2	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr6:45514837A>G	ENST00000371438.1	+	8	1719	c.1361A>G	c.(1360-1362)tAt>tGt	p.Y454C	RUNX2_ENST00000359524.5_Missense_Mutation_p.Y440C|RUNX2_ENST00000352853.5_Missense_Mutation_p.Y522C|RUNX2_ENST00000576263.1_Intron|RUNX2_ENST00000465038.2_Missense_Mutation_p.Y454C|RUNX2_ENST00000541979.1_Missense_Mutation_p.Y500C|RUNX2_ENST00000371436.6_Missense_Mutation_p.Y432C|RUNX2_ENST00000371432.3_Missense_Mutation_p.Y418C	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	454	Interaction with KAT6B.|Pro/Ser/Thr-rich.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						TCAGGATCCTATCAGTTTCCC	0.557																																					p.Y454C		Atlas-SNP	.											.	RUNX2	128	.	0			c.A1361G						.						93	83	86					6																	45514837		2203	4300	6503	SO:0001583	missense	860	exon9			GATCCTATCAGTT	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.1361A>G	chr6.hg19:g.45514837A>G	ENSP00000360493:p.Tyr454Cys	114.0	0.0		174.0	47.0	NM_001024630	O14614|O14615|O95181	Missense_Mutation	SNP	ENST00000371438.1	hg19	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	A	17.52	3.411255	0.62399	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	T;T;T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64;0.64;0.64	5.77	5.77	0.91146	Runx inhibition (1);	0.000000	0.85682	D	0.000000	T	0.63757	0.2538	M	0.75777	2.31	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.68731	-0.5331	10	0.87932	D	0	-4.7797	16.3948	0.83586	1.0:0.0:0.0:0.0	.	500;454;440	F6RGB9;Q13950;Q13950-2	.;RUNX2_HUMAN;.	C	454;522;500;454;432;440;418	ENSP00000420707:Y454C;ENSP00000319087:Y522C;ENSP00000446290:Y500C;ENSP00000360493:Y454C;ENSP00000360491:Y432C;ENSP00000352514:Y440C;ENSP00000360486:Y418C	ENSP00000319087:Y522C	Y	+	2	0	RUNX2	45622815	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.910000	0.92685	2.326000	0.78906	0.533000	0.62120	TAT	.	.		0.557	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45514837	A	G	45514837	3	3	233	1	0	0	0	0	1	0	0	0	13763	449	16	2	1407	2	RUNX2	6	45514837	Missense_Mutation	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	13420890	45514837	125600230	39	32525										
MYO6	4646	hgsc.bcm.edu	37	chr6	76538320	76538320	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	caaagttcgatatagtaaagAcagaatttatgtaagtattt	7	3	0	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr6:76538320A>T	ENST00000369977.3	+	4	390	c.251A>T	c.(250-252)gAc>gTc	p.D84V	MYO6_ENST00000369975.1_Missense_Mutation_p.D84V|MYO6_ENST00000369985.4_Missense_Mutation_p.D84V|MYO6_ENST00000369981.3_Missense_Mutation_p.D84V	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	84	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		TATAGTAAAGACAGAATTTAT	0.289																																					p.D84V		Atlas-SNP	.											.	MYO6	124	.	0			c.A251T						.						87	96	93					6																	76538320		2203	4299	6502	SO:0001583	missense	4646	exon4			GTAAAGACAGAAT	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.251A>T	chr6.hg19:g.76538320A>T	ENSP00000358994:p.Asp84Val	211.0	0.0		269.0	64.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	hg19	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.376238	0.82682	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	T;T;T;T	0.73681	-0.77;-0.77;-0.77;-0.77	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.89487	0.6729	H	0.97051	3.93	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.81914	0.94;0.995	D	0.92940	0.6371	10	0.72032	D	0.01	.	15.6234	0.76829	1.0:0.0:0.0:0.0	.	84;84	Q9UM54-2;Q9UM54-1	.;.	V	84	ENSP00000358998:D84V;ENSP00000359002:D84V;ENSP00000358994:D84V;ENSP00000358992:D84V	ENSP00000358992:D84V	D	+	2	0	MYO6	76595040	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.700000	0.91322	2.097000	0.63578	0.460000	0.39030	GAC	.	.		0.289	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		T	76538320	A	T	76538320	3	4	233	1	0	0	0	0	1	0	0	0	10090	275	10	4	261	4	MYO6	6	76538320	Missense_Mutation	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	31023483	76538320	94576747	40	32526										
AIM1	202	hgsc.bcm.edu	37	chr6	106967341	106967341	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	aactgctatagaaaccaaagTtaccgtctcggaagaagaga	9	8	1	3			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr6:106967341T>G	ENST00000369066.3	+	2	1521	c.1034T>G	c.(1033-1035)gTt>gGt	p.V345G		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GAAACCAAAGTTACCGTCTCG	0.438																																					p.V345G		Atlas-SNP	.											.	AIM1	161	.	0			c.T1034G						.						81	87	85					6																	106967341		2203	4300	6503	SO:0001583	missense	202	exon2			CCAAAGTTACCGT	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1034T>G	chr6.hg19:g.106967341T>G	ENSP00000358062:p.Val345Gly	147.0	0.0		261.0	62.0	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	T	10.78	1.447998	0.26074	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.74947	-0.89	5.4	-2.79	0.05841	.	0.760913	0.11214	N	0.587373	T	0.32436	0.0829	L	0.40543	1.245	0.09310	N	0.999995	B	0.06786	0.001	B	0.08055	0.003	T	0.11792	-1.0573	10	0.15499	T	0.54	.	2.6365	0.04959	0.1022:0.3346:0.2286:0.3346	.	345	Q9Y4K1	AIM1_HUMAN	G	753;345	ENSP00000358062:V345G	ENSP00000285105:V753G	V	+	2	0	AIM1	107074034	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	-0.782000	0.04643	-0.072000	0.12864	-0.256000	0.11100	GTT	.	.		0.438	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			G	106967341	T	G	106967341	3	3	233	1	0	0	0	0	1	0	0	0	430	1725	60	5	1040	5	AIM1	6	106967341	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	30429021	106967341	64147726	41	32527										
SMPD2	6610	hgsc.bcm.edu	37	chr6	109764501	109764501	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gttttacatctcctgtaagaGttttgaaaccactacaggct	7	9	1	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr6:109764501G>A	ENST00000258052.3	+	9	1120	c.761G>A	c.(760-762)aGt>aAt	p.S254N	PPIL6_ENST00000521072.2_5'Flank|PPIL6_ENST00000440797.2_5'Flank|PPIL6_ENST00000424445.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	254					apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		TCCTGTAAGAGTTTTGAAACC	0.527																																					p.S254N		Atlas-SNP	.											.	SMPD2	25	.	0			c.G761A						.						94	102	99					6																	109764501		2203	4300	6503	SO:0001583	missense	6610	exon9			GTAAGAGTTTTGA	AJ222801	CCDS5075.1	6q21	2009-10-23			ENSG00000135587	ENSG00000135587	3.1.4.12		11121	protein-coding gene	gene with protein product		603498				9520418	Standard	XM_005267109		Approved	nSMase, ISC1	uc003pti.3	O60906	OTTHUMG00000015348	ENST00000258052.3:c.761G>A	chr6.hg19:g.109764501G>A	ENSP00000258052:p.Ser254Asn	102.0	0.0		107.0	23.0	NM_003080	Q5TED1|Q9BWR3	Missense_Mutation	SNP	ENST00000258052.3	hg19	CCDS5075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.229|3.229	-0.157778|-0.157778	0.06544|0.06544	.|.	.|.	ENSG00000135587|ENSG00000135587	ENST00000258052|ENST00000458487	T|.	0.31247|.	1.5|.	5.95|5.95	3.16|3.16	0.36331|0.36331	Endonuclease/exonuclease/phosphatase (2);|.	0.609348|.	0.19428|.	N|.	0.114521|.	T|T	0.08802|0.08802	0.0218|0.0218	N|N	0.16166|0.16166	0.38|0.38	0.23492|0.23492	N|N	0.997564|0.997564	B|.	0.02656|.	0.0|.	B|.	0.06405|.	0.002|.	T|T	0.35748|0.35748	-0.9776|-0.9776	10|5	0.15499|.	T|.	0.54|.	-8.1966|-8.1966	9.2681|9.2681	0.37654|0.37654	0.1584:0.5431:0.2985:0.0|0.1584:0.5431:0.2985:0.0	.|.	254|.	O60906|.	NSMA_HUMAN|.	N|I	254|151	ENSP00000258052:S254N|.	ENSP00000258052:S254N|.	S|V	+|+	2|1	0|0	SMPD2|SMPD2	109871194|109871194	0.801000|0.801000	0.28930|0.28930	0.865000|0.865000	0.33974|0.33974	0.615000|0.615000	0.37417|0.37417	0.784000|0.784000	0.26816|0.26816	0.381000|0.381000	0.24851|0.24851	-0.165000|-0.165000	0.13383|0.13383	AGT|GTT	.	.		0.527	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1			A	109764501	G	A	109764501	3	1	233	1	0	0	0	0	1	0	0	0	14820	1029	36	3	795	3	SMPD2	6	109764501	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	2797160	109764501	61350566	42	32528										
RGS17	26575	hgsc.bcm.edu	37	chr6	153332802	153332802	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	aaagaatctctgtgcattaaAgtatatatctgaagttgggc	9	5	2	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr6:153332802A>C	ENST00000367225.2	-	4	564	c.540T>G	c.(538-540)acT>acG	p.T180T	RGS17_ENST00000206262.1_Silent_p.T180T			Q9UGC6	RGS17_HUMAN	regulator of G-protein signaling 17	180	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(2)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	14		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)		TGTGCATTAAAGTATATATCT	0.353																																					p.T180T	Esophageal Squamous(78;500 1236 6775 24364 49058)	Atlas-SNP	.											.	RGS17	32	.	0			c.T540G						.						59	60	59					6																	153332802		2203	4300	6503	SO:0001819	synonymous_variant	26575	exon5			CATTAAAGTATAT	AF202257	CCDS5244.1	6q25-q26	2009-05-29	2007-08-14		ENSG00000091844	ENSG00000091844		"Regulators of G-protein signaling"	14088	protein-coding gene	gene with protein product		607191	"regulator of G-protein signalling 17"			10419452	Standard	NM_012419		Approved	RGSZ2, RGS-17	uc003qpm.3	Q9UGC6	OTTHUMG00000015858	ENST00000367225.2:c.540T>G	chr6.hg19:g.153332802A>C		233.0	0.0		209.0	17.0	NM_012419	Q5TF49|Q8TD61|Q9UJS8	Silent	SNP	ENST00000367225.2	hg19	CCDS5244.1																																																																																			.	.		0.353	RGS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042773.2			C	153332802	A	C	153332802	2	2	233	1	0	0	0	0	0	0	0	1	13314	59	3	5		5	RGS17	6	153332802	Silent	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	43568301	153332802	17782265	43	32529										
SDK1	221935	hgsc.bcm.edu	37	chr7	4245519	4245519	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ctctttcctcagccccggccAtggccccgcagaacgtgcag	10	18	2	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr7:4245519A>G	ENST00000404826.2	+	36	5246	c.5107A>G	c.(5107-5109)Atg>Gtg	p.M1703V	SDK1_ENST00000389531.3_Missense_Mutation_p.M1683V	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1703					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AGCCCCGGCCATGGCCCCGCA	0.662																																					p.M1703V		Atlas-SNP	.											.	SDK1	361	.	0			c.A5107G						.						44	36	39					7																	4245519		2145	4229	6374	SO:0001583	missense	221935	exon36			CCGGCCATGGCCC	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.5107A>G	chr7.hg19:g.4245519A>G	ENSP00000385899:p.Met1703Val	93.0	0.0		119.0	29.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	A	3.942	-0.014093	0.07681	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.52983	0.64;0.64	5.46	1.56	0.23342	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.258281	0.37761	N	0.001956	T	0.17916	0.0430	N	0.02266	-0.62	0.26122	N	0.980538	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.09377	0.002;0.004;0.002	T	0.11916	-1.0568	10	0.38643	T	0.18	.	4.1767	0.10355	0.4302:0.3811:0.0667:0.1221	.	1683;190;1703	F8W6X9;F2Z3E9;Q7Z5N4	.;.;SDK1_HUMAN	V	1703;1683	ENSP00000385899:M1703V;ENSP00000374182:M1683V	ENSP00000374182:M1683V	M	+	1	0	SDK1	4212045	0.961000	0.32948	0.258000	0.24420	0.067000	0.16453	2.026000	0.41069	0.021000	0.15133	0.533000	0.62120	ATG	.	.		0.662	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		G	4245519	A	G	4245519	3	3	233	1	0	0	0	0	1	0	0	0	13983	217	8	2	5249	2	SDK1	7	4245519	Missense_Mutation	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10		4245519	154893144	44	32530										
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725803	15725803	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tgctgatggtggtgatggtgGtggtggtggtggtggtggtg	24	1	0	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr7:15725803G>A	ENST00000262041.5	-	1	634	c.225C>T	c.(223-225)caC>caT	p.H75H	AC005550.5_ENST00000438923.1_lincRNA|AC005550.4_ENST00000442176.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	75	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		ggtgatggtggtggtggtggt	0.602																																					p.H75H	Esophageal Squamous(140;197 1769 16409 18257 29929)	Atlas-SNP	.											MEOX2,caecum,carcinoma,0,1	MEOX2	68	.	0			c.C225T						.						21	22	22					7																	15725803		2203	4299	6502	SO:0001819	synonymous_variant	4223	exon1			ATGGTGGTGGTGG		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.225C>T	chr7.hg19:g.15725803G>A		56.0	1.0		58.0	5.0	NM_005924	B2R8I7|O75263|Q9UPL6	Silent	SNP	ENST00000262041.5	hg19	CCDS34605.1																																																																																			.	.		0.602	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		A	15725803	G	A	15725803	2	1	233	1	0	0	0	0	0	0	0	1	9483	1252	44	3		3	MEOX2	7	15725803	Silent	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	11480284	15725803	143412860	45	32531										
HECW1	23072	hgsc.bcm.edu	37	chr7	43447201	43447201	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	aagaaagggatgtttttcaaCccagacccttatctgaagat	8	8	2	4			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr7:43447201C>T	ENST00000395891.2	+	8	1277	c.672C>T	c.(670-672)aaC>aaT	p.N224N	HECW1_ENST00000471043.1_3'UTR|HECW1_ENST00000453890.1_Silent_p.N224N	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	224	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TGTTTTTCAACCCAGACCCTT	0.428																																					p.N224N		Atlas-SNP	.											.	HECW1	540	.	0			c.C672T						.						50	48	49					7																	43447201		1874	4106	5980	SO:0001819	synonymous_variant	23072	exon8			TTTCAACCCAGAC	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.672C>T	chr7.hg19:g.43447201C>T		242.0	0.0		279.0	22.0	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	hg19	CCDS5469.2																																																																																			.	.		0.428	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		T	43447201	C	T	43447201	2	4	233	1	0	0	0	0	0	0	0	1	7051	506	18	3		3	HECW1	7	43447201	Silent	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	27721398	43447201	115691462	46	32532										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81603858	81603858	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	atccgatattttcaggtcatTgcagtaatctctgaaaaaaa	6	7	3	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr7:81603858T>G	ENST00000356253.5	-	25	2257	c.2002A>C	c.(2002-2004)Aat>Cat	p.N668H	CACNA2D1_ENST00000356860.3_Missense_Mutation_p.N656H			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	668					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TTCAGGTCATTGCAGTAATCT	0.254																																					p.N656H		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A1966C						.						48	47	47					7																	81603858		2196	4279	6475	SO:0001583	missense	781	exon25			GGTCATTGCAGTA	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2002A>C	chr7.hg19:g.81603858T>G	ENSP00000348589:p.Asn668His	94.0	0.0		99.0	21.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	hg19		.	.	.	.	.	.	.	.	.	.	T	12.43	1.934787	0.34189	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253	T;T	0.07444	3.24;3.19	4.87	4.87	0.63330	.	0.261789	0.43110	D	0.000608	T	0.13030	0.0316	L	0.34521	1.04	0.80722	D	1	P	0.50943	0.94	P	0.52267	0.694	T	0.02294	-1.1181	10	0.49607	T	0.09	-7.4741	13.9351	0.64021	0.0:0.0:0.0:1.0	.	656	P54289-2	.	H	656;675;668	ENSP00000349320:N656H;ENSP00000348589:N668H	ENSP00000284088:N675H	N	-	1	0	CACNA2D1	81441794	1.000000	0.71417	0.997000	0.53966	0.135000	0.20990	4.445000	0.60007	1.949000	0.56562	0.482000	0.46254	AAT	.	.		0.254	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				G	81603858	T	G	81603858	3	3	233	1	0	0	0	0	1	0	0	0	2550	1812	63	5	1369	5	CACNA2D1	7	81603858	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	38156657	81603858	77534805	47	32533										
KIAA1324L	222223	hgsc.bcm.edu	37	chr7	86567441	86567441	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ttgatgcaacactgctggtaCctttccttcttcatcacatg	6	12	3	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr7:86567441C>G	ENST00000450689.2	-	8	1275		c.e8+1		KIAA1324L_ENST00000444627.1_Splice_Site|KIAA1324L_ENST00000297222.6_Splice_Site|KIAA1324L_ENST00000416314.1_Splice_Site	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like							integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					ACTGCTGGTACCTTTCCTTCT	0.428																																					.		Atlas-SNP	.											.	KIAA1324L	225	.	0			c.1089+1G>C						.						159	137	144					7																	86567441		2174	4232	6406	SO:0001630	splice_region_variant	222223	exon9			CTGGTACCTTTCC	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.1089+1G>C	chr7.hg19:g.86567441C>G		68.0	0.0		65.0	13.0	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Splice_Site	SNP	ENST00000450689.2	hg19	CCDS47632.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.931219	0.73327	.	.	ENSG00000164659	ENST00000450689;ENST00000297222;ENST00000444627;ENST00000416314;ENST00000423294	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.348	0.90328	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA1324L	86405377	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	7.571000	0.82399	2.565000	0.86533	0.563000	0.77884	.	.	.		0.428	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748	Intron	G	86567441	C	G	86567441	5	3	233	1	0	0	0	0	0	0	1	0	8233	521	18	4	2059	4	KIAA1324L	7	86567441	Splice_Site	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	4963583	86567441	72571222	48	32534										
OPLAH	26873	hgsc.bcm.edu	37	chr8	145113729	145113729	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	cggatgcctcgagatagcagCccctccagcttcccacgcag	10	17	0	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr8:145113729C>T	ENST00000426825.1	-	5	615	c.534G>A	c.(532-534)ggG>ggA	p.G178G	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	178					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GAGATAGCAGCCCCTCCAGCT	0.677																																					p.G178G		Atlas-SNP	.											.	OPLAH	78	.	0			c.G534A						.						17	23	21					8																	145113729		2065	4187	6252	SO:0001819	synonymous_variant	26873	exon5			TAGCAGCCCCTCC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.534G>A	chr8.hg19:g.145113729C>T		91.0	0.0		117.0	50.0	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Silent	SNP	ENST00000426825.1	hg19																																																																																				.	.		0.677	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		T	145113729	C	T	145113729	2	4	233	1	0	0	0	0	0	0	0	1	10885	726	26	3		3	OPLAH	8	145113729	Silent	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10		145113729	1250293	49	32535										
DOCK8	81704	hgsc.bcm.edu	37	chr9	328171	328171	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gacatctacctggtagtcaaGgtaattcagtacgatctgat	9	8	4	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr9:328171G>C	ENST00000453981.1	+	9	1156	c.1044G>C	c.(1042-1044)aaG>aaC	p.K348N	DOCK8_ENST00000432829.2_Splice_Site_p.K280N|DOCK8_ENST00000469391.1_Splice_Site_p.K280N			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	348					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TGGTAGTCAAGGTAATTCAGT	0.498																																					p.K348N		Atlas-SNP	.											.	DOCK8	401	.	0			c.G1044C						.						78	64	69					9																	328171		2203	4300	6503	SO:0001630	splice_region_variant	81704	exon9			AGTCAAGGTAATT	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.1044+1G>C	chr9.hg19:g.328171G>C		76.0	0.0		60.0	12.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	21.8	4.208845	0.79240	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391	T;T;T	0.44881	0.91;0.91;0.91	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.70211	0.3198	M	0.85945	2.785	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.73380	0.98;0.98	T	0.74150	-0.3758	10	0.87932	D	0	.	19.5736	0.95432	0.0:0.0:1.0:0.0	.	280;348	E9PH09;Q8NF50	.;DOCK8_HUMAN	N	348;348;280;280	ENSP00000408464:K348N;ENSP00000394888:K280N;ENSP00000419438:K280N	ENSP00000287364:K348N	K	+	3	2	DOCK8	318171	1.000000	0.71417	1.000000	0.80357	0.365000	0.29674	9.243000	0.95416	2.729000	0.93468	0.555000	0.69702	AAG	.	.		0.498	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	Missense_Mutation	C	328171	G	C	328171	5	2	233	1	0	0	0	0	0	0	1	0	4695	1014	35	4	1078	4	DOCK8	9	328171	Splice_Site	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10		328171	140885260	50	32536										
MEGF9	1955	hgsc.bcm.edu	37	chr9	123476253	123476253	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gtcgaagtgcgttccgccgcCggaggggtggtcggcgaggg	21	10	0	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr9:123476253C>T	ENST00000373930.3	-	1	495	c.384G>A	c.(382-384)ccG>ccA	p.P128P	MEGF9_ENST00000426959.1_Silent_p.P120P	NM_001080497.2	NP_001073966.2	Q9H1U4	MEGF9_HUMAN	multiple EGF-like-domains 9	128	Pro-rich.					integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	16						GTTCCGCCGCCGGAGGGGTGG	0.716																																					p.P128P		Atlas-SNP	.											.	MEGF9	33	.	0			c.G384A						.						15	22	20					9																	123476253		1870	4076	5946	SO:0001819	synonymous_variant	1955	exon1			CGCCGCCGGAGGG	AB011542	CCDS48010.1, CCDS48010.2	9q32-q33.3	2008-07-21	2006-03-31	2006-03-31	ENSG00000106780	ENSG00000106780			3234	protein-coding gene	gene with protein product		604268	"EGF-like-domain, multiple 5"	EGFL5		9693030	Standard	NM_001080497		Approved		uc022bms.1	Q9H1U4	OTTHUMG00000021039	ENST00000373930.3:c.384G>A	chr9.hg19:g.123476253C>T		120.0	0.0		110.0	29.0	NM_001080497	B7Z315|O75098	Silent	SNP	ENST00000373930.3	hg19	CCDS48010.2																																																																																			.	.		0.716	MEGF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055513.1	NM_001080497		T	123476253	C	T	123476253	2	4	233	1	0	0	0	0	0	0	0	1	9473	639	23	1		1	MEGF9	9	123476253	Silent	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	123148082	123476253	17737178	51	32537										
C9orf142	286257	hgsc.bcm.edu	37	chr9	139886992	139886992	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gggaggaaagcggggaggggGaccgcggcggcttcaacctc	20	10	1	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr9:139886992G>C	ENST00000371620.3	+	1	123	c.97G>C	c.(97-99)Gac>Cac	p.D33H	C9orf142_ENST00000493968.1_3'UTR|CLIC3_ENST00000480181.1_5'Flank	NM_183241.1	NP_899064.1	Q9BUH6	CI142_HUMAN	chromosome 9 open reading frame 142	33						extracellular vesicular exosome (GO:0070062)						all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CGGGGAGGGGGACCGCGGCGG	0.746																																					p.D33H		Atlas-SNP	.											.	C9orf142	8	.	0			c.G97C						.						2	2	2					9																	139886992		1265	2625	3890	SO:0001583	missense	286257	exon1			GAGGGGGACCGCG	BC002613	CCDS7020.1	9q34.3	2008-02-05			ENSG00000148362	ENSG00000148362			27849	protein-coding gene	gene with protein product							Standard	NM_183241		Approved		uc004cki.3	Q9BUH6	OTTHUMG00000020971	ENST00000371620.3:c.97G>C	chr9.hg19:g.139886992G>C	ENSP00000360682:p.Asp33His	39.0	0.0		43.0	5.0	NM_183241	Q8IY19	Missense_Mutation	SNP	ENST00000371620.3	hg19	CCDS7020.1	.	.	.	.	.	.	.	.	.	.	g	16.22	3.062984	0.55432	.	.	ENSG00000148362	ENST00000371620	.	.	.	3.4	2.49	0.30216	.	1.653770	0.03482	N	0.215257	T	0.39091	0.1065	L	0.29908	0.895	0.09310	N	1	P	0.35656	0.514	B	0.40329	0.326	T	0.40646	-0.9552	9	0.54805	T	0.06	-13.2313	8.2554	0.31754	0.1188:0.0:0.8812:0.0	.	33	Q9BUH6	CI142_HUMAN	H	33	.	ENSP00000360682:D33H	D	+	1	0	C9orf142	139006813	0.057000	0.20700	0.001000	0.08648	0.039000	0.13416	3.119000	0.50422	0.990000	0.38787	0.556000	0.70494	GAC	.	.		0.746	C9orf142-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055255.1	NM_183241		C	139886992	G	C	139886992	3	2	233	1	0	0	0	0	1	0	0	0	2463	1174	41	4	99	4	C9orf142	9	139886992	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	16410739	139886992	1326439	52	32538										
WAC	51322	hgsc.bcm.edu	37	chr10	28897314	28897314	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	cttcctgctttgcaagccacGctgcagcttaataattctaa	6	12	1	0	rs377502318		TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr10:28897314G>A	ENST00000354911.4	+	8	1280	c.1119G>A	c.(1117-1119)acG>acA	p.T373T	WAC_ENST00000428935.1_Silent_p.T328T|WAC_ENST00000375646.1_Silent_p.T225T|WAC_ENST00000347934.4_Silent_p.T270T|WAC_ENST00000375664.4_Silent_p.T328T	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	373					cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						TGCAAGCCACGCTGCAGCTTA	0.378																																					p.T373T		Atlas-SNP	.											.	WAC	77	.	0			c.G1119A						.	G	,	0,4406		0,0,2203	40	37	38		1119,810	-10	0.5	10		38	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	WAC	NM_016628.4,NM_100486.3	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	373/648,270/545	28897314	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51322	exon8			AGCCACGCTGCAG	AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"WW domain-containing adaptor with coiled coil"			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.1119G>A	chr10.hg19:g.28897314G>A		122.0	0.0		126.0	31.0	NM_016628	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Silent	SNP	ENST00000354911.4	hg19	CCDS7159.1																																																																																			.	.		0.378	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264		A	28897314	G	A	28897314	2	1	233	1	0	0	0	0	0	0	0	1	17262	1074	38	1		1	WAC	10	28897314	Silent	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10		28897314	106637433	53	32539										
NFKB2	4791	hgsc.bcm.edu	37	chr10	104156557	104156557	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gtgcctccagtgagaagggcCgaaagacctatcccactgtc	11	13	0	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr10:104156557C>G	ENST00000369966.3	+	5	470	c.220C>G	c.(220-222)Cga>Gga	p.R74G	NFKB2_ENST00000189444.6_Missense_Mutation_p.R74G|NFKB2_ENST00000428099.1_Missense_Mutation_p.R74G	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	74	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	TGAGAAGGGCCGAAAGACCTA	0.597			T	IGH@	B-NHL																																p.R74G		Atlas-SNP	.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	.	NFKB2	48	.	0			c.C220G						.						84	86	85					10																	104156557		2068	4205	6273	SO:0001583	missense	4791	exon5			AAGGGCCGAAAGA	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"Ankyrin repeat domain containing"	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.220C>G	chr10.hg19:g.104156557C>G	ENSP00000358983:p.Arg74Gly	65.0	0.0		119.0	27.0	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	hg19	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.523734	0.64747	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.41065	1.01;1.01;1.01	5.15	4.22	0.49857	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.103207	0.64402	D	0.000006	T	0.50905	0.1643	L	0.49778	1.585	0.41585	D	0.98876	P;P;P	0.40875	0.731;0.661;0.528	P;P;P	0.51657	0.676;0.588;0.653	T	0.53837	-0.8382	10	0.66056	D	0.02	.	13.1379	0.59419	0.1603:0.8397:0.0:0.0	.	74;74;74	D3DR86;Q00653;A8K9D9	.;NFKB2_HUMAN;.	G	74	ENSP00000410256:R74G;ENSP00000358983:R74G;ENSP00000189444:R74G	ENSP00000189444:R74G	R	+	1	2	NFKB2	104146547	0.334000	0.24739	1.000000	0.80357	0.979000	0.70002	0.957000	0.29215	1.099000	0.41499	0.561000	0.74099	CGA	.	.		0.597	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			G	104156557	C	G	104156557	3	3	233	1	0	0	0	0	1	0	0	0	10385	644	23	4	234	4	NFKB2	10	104156557	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	75259243	104156557	31378190	54	32540										
ACSL5	51703	hgsc.bcm.edu	37	chr10	114169431	114169431	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ggaattgagatcttatccctAtatgatgctgaggtatggat	11	5	1	3			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr10:114169431A>T	ENST00000393081.1	+	7	1006	c.699A>T	c.(697-699)ctA>ctT	p.L233L	RP11-324O2.3_ENST00000594870.2_RNA|ACSL5_ENST00000369410.3_5'UTR|RP11-324O2.6_ENST00000424422.1_RNA|RP11-324O2.3_ENST00000449782.2_RNA|ACSL5_ENST00000354273.4_Silent_p.L233L|ACSL5_ENST00000356116.1_Silent_p.L289L|ACSL5_ENST00000354655.4_Silent_p.L233L|ACSL5_ENST00000433418.1_Silent_p.L233L|RP11-324O2.3_ENST00000598447.1_RNA	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	233					cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		TCTTATCCCTATATGATGCTG	0.473																																					p.L289L		Atlas-SNP	.											.	ACSL5	51	.	0			c.A867T						.						158	140	146					10																	114169431		2203	4300	6503	SO:0001819	synonymous_variant	51703	exon7			ATCCCTATATGAT	AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142		"Acyl-CoA synthetase family"	16526	protein-coding gene	gene with protein product	"FACL5 for fatty acid coenzyme A ligase 5", "long-chain acyl-CoA synthetase 5", "long-chain fatty acid coenzyme A ligase 5", "fatty-acid-Coenzyme A ligase, long-chain 5"	605677	"fatty-acid-Coenzyme A ligase, long-chain 5"	FACL5		11127823	Standard	NM_016234		Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.699A>T	chr10.hg19:g.114169431A>T		87.0	0.0		124.0	25.0	NM_016234	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Silent	SNP	ENST00000393081.1	hg19	CCDS7573.1																																																																																			.	.		0.473	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1	NM_016234		T	114169431	A	T	114169431	2	4	233	1	0	0	0	0	0	0	0	1	180	436	16	4		4	ACSL5	10	114169431	Silent	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	10012874	114169431	21365316	55	32541										
FANCF	2188	hgsc.bcm.edu	37	chr11	22646577	22646577	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tggcggctagtcactaaagtCaaaagcccggctgggagggc	15	10	2	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr11:22646577C>T	ENST00000327470.3	-	1	810	c.780G>A	c.(778-780)ttG>ttA	p.L260L	AC103801.2_ENST00000428556.2_5'Flank	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	260					DNA repair (GO:0006281)|ovarian follicle development (GO:0001541)|spermatogenesis (GO:0007283)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						TCACTAAAGTCAAAAGCCCGG	0.542			"N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L260L		Atlas-SNP	.	yes	Rec		Fanconi anaemia F	11	11p15	2188	"Fanconi anemia, complementation group F"		L	.	FANCF	24	.	0			c.G780A						.						52	62	59					11																	22646577		2203	4300	6503	SO:0001819	synonymous_variant	2188	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TAAAGTCAAAAGC		CCDS7857.1	11p15	2014-09-17				ENSG00000183161		"Fanconi anemia, complementation groups"	3587	protein-coding gene	gene with protein product		613897				9382107	Standard	NM_022725		Approved	FAF	uc001mql.1	Q9NPI8		ENST00000327470.3:c.780G>A	chr11.hg19:g.22646577C>T		113.0	0.0	757	132.0	18.0	NM_022725	Q52LM0	Silent	SNP	ENST00000327470.3	hg19	CCDS7857.1																																																																																			.	.		0.542	FANCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387712.2	NM_022725		T	22646577	C	T	22646577	2	4	233	1	0	0	0	0	0	0	0	1	5675	825	29	3		3	FANCF	11	22646577	Silent	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10		22646577	112359939	56	32542										
KDM2A	22992	hgsc.bcm.edu	37	chr11	67015791	67015791	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ttaacgaagaattgccaaatTgctgggaatgtccaaagtgc	10	7	0	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr11:67015791T>A	ENST00000529006.2	+	16	2451	c.2005T>A	c.(2005-2007)Tgc>Agc	p.C669S	KDM2A_ENST00000308783.5_Missense_Mutation_p.C127S|KDM2A_ENST00000530342.1_Missense_Mutation_p.C230S|KDM2A_ENST00000398645.2_Missense_Mutation_p.C669S|KDM2A_ENST00000526258.1_3'UTR	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	669					histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						ATTGCCAAATTGCTGGGAATG	0.443																																					p.C669S		Atlas-SNP	.											.	KDM2A	80	.	0			c.T2005A						.						75	70	72					11																	67015791		1919	4121	6040	SO:0001583	missense	22992	exon16			CCAAATTGCTGGG	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13606	protein-coding gene	gene with protein product	"F-box protein FBL11", "jumonji C domain-containing histone demethylase 1A"	605657	"F-box and leucine-rich repeat protein 11"	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.2005T>A	chr11.hg19:g.67015791T>A	ENSP00000432786:p.Cys669Ser	176.0	0.0		206.0	36.0	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Missense_Mutation	SNP	ENST00000529006.2	hg19	CCDS44657.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.458811	0.84317	.	.	ENSG00000173120	ENST00000398645;ENST00000529006;ENST00000530342;ENST00000446134;ENST00000308783	D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13	5.16	5.16	0.70880	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.89729	0.6799	L	0.40543	1.245	0.54753	D	0.999985	D;D	0.76494	0.993;0.999	P;D	0.70227	0.796;0.968	D	0.88441	0.3042	10	0.32370	T	0.25	-12.2836	15.1664	0.72828	0.0:0.0:0.0:1.0	.	127;669	D4QA03;Q9Y2K7	.;KDM2A_HUMAN	S	669;669;230;230;127	ENSP00000381640:C669S;ENSP00000432786:C669S;ENSP00000435776:C230S;ENSP00000309302:C127S	ENSP00000309302:C127S	C	+	1	0	KDM2A	66772367	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.841000	0.86834	2.173000	0.68751	0.533000	0.62120	TGC	.	.		0.443	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308		A	67015791	T	A	67015791	3	1	233	1	0	0	0	0	1	0	0	0	8133	1812	63	4	2063	4	KDM2A	11	67015791	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	44369214	67015791	67990725	57	32543										
CDON	50937	hgsc.bcm.edu	37	chr11	125830853	125830853	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gtcctcaggtttcccggggcTgctgaaggacctctgtcggg	15	12	2	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr11:125830853T>A	ENST00000392693.3	-	20	3975	c.3848A>T	c.(3847-3849)cAg>cTg	p.Q1283L	RP11-680F20.12_ENST00000582823.1_RNA|CDON_ENST00000263577.7_Missense_Mutation_p.Q1260L|CDON_ENST00000531738.1_Missense_Mutation_p.Q637L	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1283					anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		TTCCCGGGGCTGCTGAAGGAC	0.542																																					p.Q1283L		Atlas-SNP	.											.	CDON	137	.	0			c.A3848T						.						115	117	116					11																	125830853		2201	4299	6500	SO:0001583	missense	50937	exon20			CGGGGCTGCTGAA	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17104	protein-coding gene	gene with protein product	"cell adhesion molecule-related/down-regulated by oncogenes"	608707	"Cdon homolog (mouse)"			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.3848A>T	chr11.hg19:g.125830853T>A	ENSP00000376458:p.Gln1283Leu	144.0	0.0		194.0	45.0	NM_001243597	O14631	Missense_Mutation	SNP	ENST00000392693.3	hg19	CCDS58192.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.878723	0.33162	.	.	ENSG00000064309	ENST00000392693;ENST00000531738;ENST00000263577	T;T;T	0.74526	-0.85;-0.25;-0.82	5.31	2.99	0.34606	.	0.170681	0.28031	N	0.016877	T	0.81408	0.4816	M	0.62723	1.935	0.09310	N	0.999999	D;D;D	0.63046	0.987;0.992;0.985	D;D;P	0.72982	0.953;0.979;0.643	T	0.71196	-0.4664	10	0.87932	D	0	-2.4337	8.4566	0.32903	0.0:0.1548:0.0:0.8452	.	1283;1260;637	Q4KMG0;Q4KMG0-2;E9PN78	CDON_HUMAN;.;.	L	1283;637;1260	ENSP00000376458:Q1283L;ENSP00000432901:Q637L;ENSP00000263577:Q1260L	ENSP00000263577:Q1260L	Q	-	2	0	CDON	125336063	0.983000	0.35010	0.133000	0.22050	0.005000	0.04900	2.220000	0.42908	0.466000	0.27193	-0.290000	0.09829	CAG	.	.		0.542	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		A	125830853	T	A	125830853	3	1	233	1	0	0	0	0	1	0	0	0	3172	1580	55	4	19	4	CDON	11	125830853	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	58815062	125830853	9175663	58	32544										
EMP1	2012	hgsc.bcm.edu	37	chr12	13366426	13366426	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gtttcaggtctggttggtttCcaatacggtagatgcatcag	12	7	3	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr12:13366426C>A	ENST00000256951.5	+	3	291	c.92C>A	c.(91-93)tCc>tAc	p.S31Y	EMP1_ENST00000544053.1_5'UTR|EMP1_ENST00000542289.1_Intron|EMP1_ENST00000537612.1_Missense_Mutation_p.S31Y|EMP1_ENST00000431267.2_Intron|EMP1_ENST00000396301.3_Missense_Mutation_p.S31Y	NM_001423.2	NP_001414.1	P54849	EMP1_HUMAN	epithelial membrane protein 1	31					cell growth (GO:0016049)|cell proliferation (GO:0008283)|epidermis development (GO:0008544)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)							Prostate(47;0.194)		BRCA - Breast invasive adenocarcinoma(232;0.153)		TGGTTGGTTTCCAATACGGTA	0.383																																					p.S31Y		Atlas-SNP	.											.	EMP1	14	.	0			c.C92A						.						158	153	155					12																	13366426		2203	4300	6503	SO:0001583	missense	2012	exon3			TGGTTTCCAATAC	U43916	CCDS8660.1	12p12.3	2008-08-04				ENSG00000134531			3333	protein-coding gene	gene with protein product		602333				8996089, 9126480	Standard	NM_001423		Approved	TMP, CL-20	uc001rbr.3	P54849		ENST00000256951.5:c.92C>A	chr12.hg19:g.13366426C>A	ENSP00000256951:p.Ser31Tyr	163.0	0.0		215.0	39.0	NM_001423	B2R5N1|B4DRR1|O00681|Q13481|Q13834	Missense_Mutation	SNP	ENST00000256951.5	hg19	CCDS8660.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.168324	0.38315	.	.	ENSG00000134531	ENST00000256951;ENST00000538364;ENST00000396301;ENST00000537612	D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.64	5.78	3.88	0.44766	.	1.084740	0.07112	N	0.842346	D	0.88153	0.6360	N	0.17082	0.46	0.09310	N	1	D;D	0.61080	0.989;0.979	P;P	0.58331	0.837;0.837	T	0.72802	-0.4183	10	0.02654	T	1	-1.1021	11.7436	0.51807	0.1252:0.5102:0.3646:0.0	.	31;31	B4DRR1;P54849	.;EMP1_HUMAN	Y	31	ENSP00000256951:S31Y;ENSP00000441223:S31Y;ENSP00000379595:S31Y;ENSP00000445319:S31Y	ENSP00000256951:S31Y	S	+	2	0	EMP1	13257693	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	0.123000	0.15708	0.843000	0.35070	0.655000	0.94253	TCC	.	.		0.383	EMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401019.1	NM_001423		A	13366426	C	A	13366426	3	1	233	1	0	0	0	0	1	0	0	0	5103	855	30	3	98	3	EMP1	12	13366426	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10		13366426	120485469	59	32545										
PFDN5	5204	hgsc.bcm.edu	37	chr12	53689386	53689386	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	taacatcacggagctgaatcTgccgcagctagaaatgctca	9	11	3	2	rs199718276		TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr12:53689386T>A	ENST00000551018.1	+	1	312	c.35T>A	c.(34-36)cTg>cAg	p.L12Q	PFDN5_ENST00000550846.1_Missense_Mutation_p.L12Q|PFDN5_ENST00000334478.4_Missense_Mutation_p.L12Q|PFDN5_ENST00000351500.3_Missense_Mutation_p.L12Q	NM_002624.3	NP_002615.2	Q99471	PFD5_HUMAN	prefoldin subunit 5	12					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	transcription corepressor activity (GO:0003714)			kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)	8						GAGCTGAATCTGCCGCAGCTA	0.587																																					p.L12Q		Atlas-SNP	.											PFDN5,NS,carcinoma,0,2	PFDN5	16	.	0			c.T35A						.						109	106	107					12																	53689386		2203	4300	6503	SO:0001583	missense	5204	exon1			TGAATCTGCCGCA	D89667	CCDS8853.1, CCDS8854.1	12q13.13	2008-05-14	2006-02-24						8869	protein-coding gene	gene with protein product		604899	"prefoldin 5"			9630229, 9792694	Standard	NM_002624		Approved	PFD5, MM-1	uc001scl.3	Q99471	OTTHUMG00000169675	ENST00000551018.1:c.35T>A	chr12.hg19:g.53689386T>A	ENSP00000447942:p.Leu12Gln	76.0	0.0		150.0	42.0	NM_002624	A8K9A8|Q54AA8|Q9C083|Q9C084	Missense_Mutation	SNP	ENST00000551018.1	hg19	CCDS8853.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.941641	0.92526	.	.	ENSG00000123349	ENST00000551018;ENST00000351500;ENST00000334478	D;T;D	0.82344	-1.6;-1.2;-1.6	5.73	5.73	0.89815	Prefoldin (1);	0.000000	0.64402	D	0.000001	D	0.91355	0.7273	M	0.84948	2.725	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.69824	0.966;0.915	D	0.92579	0.6073	10	0.87932	D	0	.	14.2815	0.66216	0.0:0.0:0.0:1.0	.	12;12	Q9C083;Q99471	.;PFD5_HUMAN	Q	12	ENSP00000447942:L12Q;ENSP00000266964:L12Q;ENSP00000334188:L12Q	ENSP00000243040:L12Q	L	+	2	0	PFDN5	51975653	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	6.030000	0.70903	2.324000	0.78689	0.533000	0.62120	CTG	.	.		0.587	PFDN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405368.2			A	53689386	T	A	53689386	3	1	233	1	0	0	0	0	1	0	0	0	11767	1580	55	4	37	4	PFDN5	12	53689386	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	40322960	53689386	80162509	60	32546										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56495091	56495091	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ttaccccactctccccacccGggttagaggaagaggatgtc	10	14	1	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr12:56495091G>C	ENST00000267101.3	+	27	3888	c.3448G>C	c.(3448-3450)Ggg>Cgg	p.G1150R	RP11-603J24.9_ENST00000548861.1_5'Flank|ERBB3_ENST00000549832.1_Missense_Mutation_p.G270R|ERBB3_ENST00000450146.2_Missense_Mutation_p.G507R|ERBB3_ENST00000553131.1_Missense_Mutation_p.G391R|ERBB3_ENST00000415288.2_Missense_Mutation_p.G1091R	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	1150					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CTCCCCACCCGGGTTAGAGGA	0.572																																					p.G1150R		Atlas-SNP	.											.	ERBB3	350	.	0			c.G3448C						.						56	56	56					12																	56495091		2203	4300	6503	SO:0001583	missense	2065	exon27			CCACCCGGGTTAG	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.3448G>C	chr12.hg19:g.56495091G>C	ENSP00000267101:p.Gly1150Arg	108.0	0.0		140.0	32.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.140072	0.37728	.	.	ENSG00000065361	ENST00000267101;ENST00000450146;ENST00000415288;ENST00000550070;ENST00000553131;ENST00000549832	T;D;T;D;D	0.84298	-1.48;-1.6;-1.46;-1.83;-1.7	6.17	5.29	0.74685	.	0.101741	0.44285	N	0.000467	T	0.75708	0.3886	L	0.27053	0.805	0.38516	D	0.948604	B;B;B	0.29612	0.251;0.163;0.017	B;B;B	0.27170	0.077;0.035;0.013	T	0.73675	-0.3908	10	0.26408	T	0.33	.	12.5573	0.56261	0.0769:0.0:0.9231:0.0	.	1091;270;1150	P21860-4;B3KWG5;P21860	.;.;ERBB3_HUMAN	R	1150;507;1091;273;391;270	ENSP00000267101:G1150R;ENSP00000399178:G507R;ENSP00000408340:G1091R;ENSP00000449129:G391R;ENSP00000448729:G270R	ENSP00000267101:G1150R	G	+	1	0	ERBB3	54781358	1.000000	0.71417	0.644000	0.29465	0.956000	0.61745	4.269000	0.58890	1.630000	0.50440	0.655000	0.94253	GGG	.	.		0.572	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			C	56495091	G	C	56495091	3	2	233	1	0	0	0	0	1	0	0	0	5210	1116	39	4	3685	4	ERBB3	12	56495091	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	2805705	56495091	77356804	61	32547										
LRP1	4035	hgsc.bcm.edu	37	chr12	57591115	57591115	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tctgatcttcgccaaccggtActacctgcgcaagctcaacc	7	16	3	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr12:57591115A>G	ENST00000243077.3	+	57	9576	c.9110A>G	c.(9109-9111)tAc>tGc	p.Y3037C	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3037					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GCCAACCGGTACTACCTGCGC	0.597																																					p.Y3037C		Atlas-SNP	.											.	LRP1	428	.	0			c.A9110G						.						209	198	202					12																	57591115		2203	4300	6503	SO:0001583	missense	4035	exon57			ACCGGTACTACCT	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.9110A>G	chr12.hg19:g.57591115A>G	ENSP00000243077:p.Tyr3037Cys	115.0	0.0		136.0	38.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	A	17.21	3.331124	0.60853	.	.	ENSG00000123384	ENST00000243077	D	0.91180	-2.8	5.01	5.01	0.66863	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.64402	D	0.000011	D	0.94938	0.8363	M	0.81682	2.555	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94828	0.7993	10	0.48119	T	0.1	.	13.8388	0.63426	1.0:0.0:0.0:0.0	.	3037	Q07954	LRP1_HUMAN	C	3037	ENSP00000243077:Y3037C	ENSP00000243077:Y3037C	Y	+	2	0	LRP1	55877382	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	8.997000	0.93544	2.100000	0.63781	0.418000	0.28097	TAC	.	.		0.597	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		G	57591115	A	G	57591115	3	3	233	1	0	0	0	0	1	0	0	0	8960	391	14	2	9336	2	LRP1	12	57591115	Missense_Mutation	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	1096024	57591115	76260780	62	32548										
SLC5A8	160728	hgsc.bcm.edu	37	chr12	101573838	101573838	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ctcccataagtgacgccagcGcagccattccaatacacagg	8	15	0	1	rs200408412		TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr12:101573838G>A	ENST00000536262.2	-	10	1760	c.1202C>T	c.(1201-1203)gCg>gTg	p.A401V		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TGACGCCAGCGCAGCCATTCC	0.433																																					p.A401V	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.C1202T						.						168	166	167					12																	101573838		2203	4300	6503	SO:0001583	missense	160728	exon10			GCCAGCGCAGCCA	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1202C>T	chr12.hg19:g.101573838G>A	ENSP00000445340:p.Ala401Val	120.0	0.0		197.0	36.0	NM_145913		Missense_Mutation	SNP	ENST00000536262.2	hg19	CCDS9080.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.361241	0.24684	.	.	ENSG00000256870	ENST00000536262	D	0.86497	-2.13	5.85	3.97	0.46021	.	0.114043	0.64402	N	0.000010	T	0.78451	0.4285	L	0.37561	1.115	0.40320	D	0.978812	B	0.24963	0.115	B	0.23150	0.044	T	0.71533	-0.4564	10	0.15952	T	0.53	.	9.8809	0.41233	0.0703:0.2586:0.6711:0.0	.	401	Q8N695	SC5A8_HUMAN	V	401	ENSP00000445340:A401V	ENSP00000445340:A401V	A	-	2	0	SLC5A8	100097969	0.982000	0.34865	0.895000	0.35142	0.434000	0.31775	1.993000	0.40747	1.484000	0.48361	0.650000	0.86243	GCG	.	G|0.999;A|0.001		0.433	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		A	101573838	G	A	101573838	3	1	233	1	0	0	0	0	1	0	0	0	14686	1087	38	1	654	1	SLC5A8	12	101573838	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	43982723	101573838	32278057	63	32549										
UBC	7316	hgsc.bcm.edu	37	chr12	125397889	125397889	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ctgagacggagcaccaggtgCagggtagactctttctggat	14	9	2	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr12:125397889C>A	ENST00000538617.1	-	3	745	c.429G>T	c.(427-429)ctG>ctT	p.L143L	UBC_ENST00000536769.1_Silent_p.L143L|UBC_ENST00000546120.1_Intron|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000339647.5_Silent_p.L143L|UBC_ENST00000536661.1_5'Flank			P0CG48	UBC_HUMAN	ubiquitin C	523	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		GCACCAGGTGCAGGGTAGACT	0.557																																					p.L143L		Atlas-SNP	.											.	UBC	79	.	0			c.G429T						.						102	102	102					12																	125397889		2203	4297	6500	SO:0001819	synonymous_variant	7316	exon2			CAGGTGCAGGGTA		CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"polyubiquitin-C"	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000538617.1:c.429G>T	chr12.hg19:g.125397889C>A		118.0	0.0		145.0	32.0	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000538617.1	hg19																																																																																				.	.		0.557	UBC-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000400179.1	NM_021009		A	125397889	C	A	125397889	2	1	233	1	0	0	0	0	0	0	0	1	16857	697	25	3		3	UBC	12	125397889	Silent	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	23824051	125397889	8454006	64	32550										
EPSTI1	94240	hgsc.bcm.edu	37	chr13	43566216	43566216	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ggctcagctccccttgccgcCcagaagggtcctggggatcc	13	16	1	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr13:43566216C>T	ENST00000398762.3	-	1	85	c.86G>A	c.(85-87)gGg>gAg	p.G29E	EPSTI1_ENST00000313640.7_Missense_Mutation_p.G29E|EPSTI1_ENST00000476830.2_5'UTR|EPSTI1_ENST00000313624.7_Missense_Mutation_p.G29E			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)	29										endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		CCCTTGCCGCCCAGAAGGGTC	0.697																																					p.G29E		Atlas-SNP	.											.	EPSTI1	47	.	0			c.G86A						.						23	29	27					13																	43566216		2188	4283	6471	SO:0001583	missense	94240	exon1			TGCCGCCCAGAAG	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"epithelial stromal interaction protein 1"	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814	ENST00000398762.3:c.86G>A	chr13.hg19:g.43566216C>T	ENSP00000381746:p.Gly29Glu	207.0	0.0		324.0	86.0	NM_001002264	Q8IVC7|Q8NDQ7	Missense_Mutation	SNP	ENST00000398762.3	hg19	CCDS9387.1	.	.	.	.	.	.	.	.	.	.	C	8.049	0.765557	0.15914	.	.	ENSG00000133106	ENST00000313640;ENST00000313624;ENST00000398762	.	.	.	0.757	0.757	0.18427	.	1.221540	0.05757	N	0.604161	T	0.41673	0.1169	L	0.54323	1.7	0.09310	N	1	B;B	0.13145	0.004;0.007	B;B	0.11329	0.006;0.005	T	0.38090	-0.9677	9	0.49607	T	0.09	0.0925	4.7802	0.13199	0.0:1.0:0.0:0.0	.	29;29	Q96J88-2;Q96J88-3	.;.	E	29	.	ENSP00000318643:G29E	G	-	2	0	EPSTI1	42464216	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	-1.394000	0.02518	0.683000	0.31428	0.305000	0.20034	GGG	.	.		0.697	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264		T	43566216	C	T	43566216	3	4	233	1	0	0	0	0	1	0	0	0	5200	623	22	3	1198	3	EPSTI1	13	43566216	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10		43566216	71603662	65	32551										
RNF219	79596	hgsc.bcm.edu	37	chr13	79190261	79190261	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ttgctgttgtctgactctgaCatcattgaatccaactcaga	7	10	4	4			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr13:79190261C>T	ENST00000282003.6	-	6	1693	c.1635G>A	c.(1633-1635)atG>atA	p.M545I	RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000560209.2_RNA	NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	545	Ser-rich.						zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		CTGACTCTGACATCATTGAAT	0.413																																					p.M545I		Atlas-SNP	.											.	RNF219	94	.	0			c.G1635A						.						147	147	147					13																	79190261		2203	4300	6503	SO:0001583	missense	79596	exon6			CTCTGACATCATT	BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.1635G>A	chr13.hg19:g.79190261C>T	ENSP00000282003:p.Met545Ile	93.0	0.0		112.0	33.0	NM_024546	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	hg19	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.234007	0.79688	.	.	ENSG00000152193	ENST00000282003	T	0.14022	2.54	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.37625	0.1010	M	0.61703	1.905	0.58432	D	0.999994	D	0.69078	0.997	D	0.73380	0.98	T	0.00907	-1.1519	10	0.48119	T	0.1	-22.7	20.2019	0.98263	0.0:1.0:0.0:0.0	.	545	Q5W0B1	RN219_HUMAN	I	545	ENSP00000282003:M545I	ENSP00000282003:M545I	M	-	3	0	RNF219	78088262	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.424000	0.66464	2.776000	0.95493	0.655000	0.94253	ATG	.	.		0.413	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		T	79190261	C	T	79190261	3	4	233	1	0	0	0	0	1	0	0	0	13497	478	17	3	549	3	RNF219	13	79190261	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	35624045	79190261	35979617	66	32552										
KLHL28	54813	hgsc.bcm.edu	37	chr14	45403543	45403543	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	caagagtacttcggctttcaTtcattctctctagagaagtc	7	10	4	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr14:45403543T>C	ENST00000396128.4	-	3	1237	c.1118A>G	c.(1117-1119)aAt>aGt	p.N373S	KLHL28_ENST00000355081.2_Missense_Mutation_p.N387S	NM_017658.3	NP_060128.2	Q9NXS3	KLH28_HUMAN	kelch-like family member 28	373										breast(2)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TCGGCTTTCATTCATTCTCTC	0.398																																					p.N373S		Atlas-SNP	.											.	KLHL28	53	.	0			c.A1118G						.						130	120	124					14																	45403543		2203	4300	6503	SO:0001583	missense	54813	exon3			CTTTCATTCATTC	AK000088	CCDS9680.1	14q21.1	2013-02-22	2013-02-22	2007-01-09	ENSG00000179454	ENSG00000179454		"Kelch-like", "BTB/POZ domain containing"	19741	protein-coding gene	gene with protein product			"BTB (POZ) domain containing 5", "kelch-like 28 (Drosophila)"	BTBD5			Standard	NM_017658		Approved	FLJ20081	uc001wvr.3	Q9NXS3	OTTHUMG00000140263	ENST00000396128.4:c.1118A>G	chr14.hg19:g.45403543T>C	ENSP00000379434:p.Asn373Ser	169.0	0.0		169.0	45.0	NM_017658	Q0VAL5	Missense_Mutation	SNP	ENST00000396128.4	hg19	CCDS9680.1	.	.	.	.	.	.	.	.	.	.	T	1.283	-0.609703	0.03690	.	.	ENSG00000179454	ENST00000396128;ENST00000355081	T;T	0.73469	-0.75;-0.75	5.38	5.38	0.77491	Kelch-type beta propeller (1);	0.379360	0.32563	N	0.005921	T	0.54287	0.1849	L	0.33137	0.985	0.27761	N	0.943838	B	0.02656	0.0	B	0.06405	0.002	T	0.47355	-0.9124	10	0.02654	T	1	.	4.8494	0.13530	0.2666:0.0802:0.0:0.6531	.	373	Q9NXS3	KLH28_HUMAN	S	373;387	ENSP00000379434:N373S;ENSP00000347193:N387S	ENSP00000347193:N387S	N	-	2	0	KLHL28	44473293	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.492000	0.45311	2.157000	0.67596	0.455000	0.32223	AAT	.	.		0.398	KLHL28-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276790.3			C	45403543	T	C	45403543	3	2	233	1	0	0	0	0	1	0	0	0	8391	1493	52	2	609	2	KLHL28	14	45403543	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10		45403543	61945997	67	32553										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414494	105414495	+	In_Frame_Ins	INS	-	-	TTT													0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	atcacgtccgtcttggggccINStttcaggtccagcttggggc							TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr14:105414494_105414495insTTT	ENST00000333244.5	-	7	7412_7413	c.7293_7294insAAA	c.(7291-7296)aaaggc>aaaAAAggc	p.2431_2432insK	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2431						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GTCTTGGGGCCTTTCAGGTCCA	0.624																																					p.G2432delinsKG		Atlas-INDEL	.											.	AHNAK2	719	.	0			c.7294_7295insAAA						.																																			SO:0001652	inframe_insertion	113146	exon7			.	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7291_7293dupAAA	chr14.hg19:g.105414495_105414497dupTTT	ENSP00000353114:p.Lys2431_Lys2431dup	140.0	0.0		197.0	42.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	In_Frame_Ins	INS	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.624	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		TTT	105414495	-	TTT	105414494	7	5	233	1	0	1	1	0	0	0	0	0	415	681	24	0	10097	0	AHNAK2	14	105414494	In_Frame_Ins	INS	-	TCGA-DD-AAW0-01A-11D-A40R-10	60010951	105414494	1935046	68	32554										
HERC2	8924	hgsc.bcm.edu	37	chr15	28516001	28516001	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	aactctcattggggctcagaGggccagacaaaagctagaaa	11	9	2	3			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr15:28516001G>A	ENST00000261609.7	-	10	1205	c.1097C>T	c.(1096-1098)cCt>cTt	p.P366L		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GGGGCTCAGAGGGCCAGACAA	0.428																																					p.P366L		Atlas-SNP	.											.	HERC2	501	.	0			c.C1097T						.						36	33	34					15																	28516001		2203	4300	6503	SO:0001583	missense	8924	exon10			CTCAGAGGGCCAG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.1097C>T	chr15.hg19:g.28516001G>A	ENSP00000261609:p.Pro366Leu	141.0	0.0		178.0	39.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.676326	0.29783	.	.	ENSG00000128731	ENST00000261609	T	0.38401	1.14	5.74	5.74	0.90152	.	0.118259	0.64402	D	0.000018	T	0.23532	0.0569	N	0.19112	0.55	0.58432	D	0.999999	B	0.27498	0.18	B	0.21917	0.037	T	0.07424	-1.0773	10	0.16420	T	0.52	.	14.7248	0.69336	0.0:0.0:0.8552:0.1448	.	366	O95714	HERC2_HUMAN	L	366	ENSP00000261609:P366L	ENSP00000261609:P366L	P	-	2	0	HERC2	26189596	1.000000	0.71417	0.993000	0.49108	0.373000	0.29922	5.585000	0.67497	2.706000	0.92434	0.650000	0.86243	CCT	.	.		0.428	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28516001	G	A	28516001	3	1	233	1	0	0	0	0	1	0	0	0	7067	1000	35	3	13743	3	HERC2	15	28516001	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10		28516001	74015391	69	32555										
DENND4A	10260	hgsc.bcm.edu	37	chr15	65957785	65957785	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	atatttgctatcttcagacaTacagtggcggggaatctgtg	11	7	3	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr15:65957785T>C	ENST00000431932.2	-	29	5333	c.5125A>G	c.(5125-5127)Atg>Gtg	p.M1709V	DENND4A_ENST00000443035.3_Missense_Mutation_p.M1752V	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1709					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						TCTTCAGACATACAGTGGCGG	0.303																																					p.M1752V		Atlas-SNP	.											.	DENND4A	217	.	0			c.A5254G						.						110	109	109					15																	65957785		1865	4115	5980	SO:0001583	missense	10260	exon30			CAGACATACAGTG	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.5125A>G	chr15.hg19:g.65957785T>C	ENSP00000396830:p.Met1709Val	104.0	0.0		101.0	28.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	hg19	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	T	13.38	2.219359	0.39201	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.04654	3.6;3.58	5.71	5.71	0.89125	.	0.200060	0.53938	D	0.000057	T	0.08403	0.0209	L	0.44542	1.39	0.46654	D	0.999145	P;D	0.53745	0.691;0.962	B;P	0.46885	0.329;0.53	T	0.31641	-0.9936	10	0.33141	T	0.24	.	15.9781	0.80086	0.0:0.0:0.0:1.0	.	1752;1709	E7EPL3;Q7Z401	.;MYCPP_HUMAN	V	1752;1709	ENSP00000391167:M1752V;ENSP00000396830:M1709V	ENSP00000396830:M1709V	M	-	1	0	DENND4A	63744839	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	3.531000	0.53546	2.171000	0.68590	0.533000	0.62120	ATG	.	.		0.303	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		C	65957785	T	C	65957785	3	2	233	1	0	0	0	0	1	0	0	0	4435	1406	49	2	482	2	DENND4A	15	65957785	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	37441784	65957785	36573607	70	32556										
PSTPIP1	9051	hgsc.bcm.edu	37	chr15	77320928	77320928	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	acgagcagaagtgccgggacGcggacgacgcggagcaggcc	18	12	0	1	rs1141043		TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr15:77320928G>T	ENST00000558012.1	+	7	940	c.451G>T	c.(451-453)Gcg>Tcg	p.A151S	PSTPIP1_ENST00000557995.1_3'UTR|PSTPIP1_ENST00000267939.5_Missense_Mutation_p.A150S|PSTPIP1_ENST00000379595.3_Missense_Mutation_p.A151S|PSTPIP1_ENST00000559295.1_Missense_Mutation_p.A151S	NM_003978.3	NP_003969.2	O43586	PPIP1_HUMAN	proline-serine-threonine phosphatase interacting protein 1	151			A -> S (in dbSNP:rs1141043). {ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|signal transduction (GO:0007165)	actomyosin contractile ring (GO:0005826)|cell projection (GO:0042995)|cleavage furrow (GO:0032154)|cytosol (GO:0005829)|membrane (GO:0016020)|stress fiber (GO:0001725)				breast(1)|endometrium(3)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						GTGCCGGGACGCGGACGACGC	0.677																																					p.A151S		Atlas-SNP	.											.	PSTPIP1	50	.	0			c.G451T						.						18	22	20					15																	77320928		2039	4165	6204	SO:0001583	missense	9051	exon7			CGGGACGCGGACG	U94778	CCDS45312.1	15q24.3	2014-09-17			ENSG00000140368	ENSG00000140368			9580	protein-coding gene	gene with protein product	"CD2 cytoplasmic tail-binding protein", "CD2 antigen-binding protein 1", "PEST phosphatase-interacting protein 1"	606347				9857189	Standard	NM_003978		Approved	PSTPIP, CD2BP1L, CD2BP1, CD2BP1S, H-PIP, PAPAS	uc002bcf.2	O43586	OTTHUMG00000172594	ENST00000558012.1:c.451G>T	chr15.hg19:g.77320928G>T	ENSP00000452746:p.Ala151Ser	274.0	0.0		366.0	93.0	NM_003978	B5BU74|B5BUK4|O43585|O95657	Missense_Mutation	SNP	ENST00000558012.1	hg19	CCDS45312.1	.	.	.	.	.	.	.	.	.	.	g	15.55	2.865813	0.51588	.	.	ENSG00000140368	ENST00000379595;ENST00000267939	T;T	0.47177	0.85;2.44	4.55	4.55	0.56014	Prismane-like (1);	0.000000	0.85682	D	0.000000	T	0.60508	0.2274	M	0.68317	2.08	0.58432	D	0.999998	D;P;D;P	0.64830	0.994;0.886;0.983;0.585	P;P;P;B	0.58454	0.839;0.72;0.752;0.235	T	0.58014	-0.7711	10	0.20519	T	0.43	-9.7098	16.0972	0.81135	0.0:0.0:1.0:0.0	rs1141043	29;151;150;151	B4DQC0;O43586-2;C9K004;O43586	.;.;.;PPIP1_HUMAN	S	151;150	ENSP00000368914:A151S;ENSP00000267939:A150S	ENSP00000267939:A150S	A	+	1	0	PSTPIP1	75107983	0.988000	0.35896	0.699000	0.30290	0.158000	0.22134	3.301000	0.51842	2.088000	0.63022	0.443000	0.29094	GCG	.	G|1.000;|0.000		0.677	PSTPIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419373.2	NM_003978		T	77320928	G	T	77320928	3	4	233	1	0	0	0	0	1	0	0	0	12733	1087	38	1	477	1	PSTPIP1	15	77320928	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	11363143	77320928	25210464	71	32557										
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81224345	81224347	+	In_Frame_Del	DEL	AAC	AAC	-													0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	cctggcagagctgcccccatAacaacgtgaccggcattgcc							TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr15:81224345_81224347delAAC	ENST00000394685.3	+	22	3177_3179	c.2758_2760delAAC	c.(2758-2760)aacdel	p.N921del	KIAA1199_ENST00000220244.3_In_Frame_Del_p.N921del|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_In_Frame_Del_p.N921del			Q8WUJ3	CEMIP_HUMAN		921					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CTGCCCCCATAACAACGTGACCG	0.596																																					p.919_920del		Atlas-INDEL	.											.	KIAA1199	118	.	0			c.2757_2759del						.																																			SO:0001651	inframe_deletion	57214	exon21			.																												ENST00000394685.3:c.2758_2760delAAC	chr15.hg19:g.81224348_81224350delAAC	ENSP00000378177:p.Asn921del	43.0	0.0		60.0	18.0	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	In_Frame_Del	DEL	ENST00000394685.3	hg19	CCDS10315.1																																																																																			.	.		0.596	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			-	81224347	AAC	-	81224345	7	5	233	1	0	1	0	1	0	0	0	0	8222	362	13	0	2836	0	KIAA1199	15	81224345	In_Frame_Del	DEL	AAC	TCGA-DD-AAW0-01A-11D-A40R-10	3903417	81224345	21307047	72	32558										
C16orf42	84572	hgsc.bcm.edu	37	chr16	1399610	1399610	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	catcagtgtccgagggcagcCtgggagaggagggggagcac	19	9	1	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr16:1399610C>T	ENST00000204679.4	+	0	0				TSR3_ENST00000007390.2_Splice_Site	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit						carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				CGAGGGCAGCCTGGGAGAGGA	0.627																																					.		Atlas-SNP	.											.	.	.	.	0			c.768-1G>A						.						30	35	34					16																	1399610		2198	4299	6497	SO:0001631	upstream_gene_variant	115939	exon7			GGCAGCCTGGGAG	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"GlcNAc-phosphotransferase gamma-subunit"	607838	"N-acetylglucosamine-1-phosphotransferase, gamma subunit", "chromosome 16 open reading frame 27"	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835		chr16.hg19:g.1399610C>T	Exception_encountered	101.0	0.0		142.0	20.0	NM_001001410	B2R556|Q6XYD7|Q96L13	Splice_Site	SNP	ENST00000204679.4	hg19	CCDS10436.1	.	.	.	.	.	.	.	.	.	.	C	8.328	0.825766	0.16749	.	.	ENSG00000007520	ENST00000007390	.	.	.	4.38	2.26	0.28386	.	.	.	.	.	.	.	.	.	.	.	0.22330	N	0.999195	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.8635	0.18762	0.1888:0.7032:0.0:0.108	.	.	.	.	.	-1	.	.	.	-	.	.	C16orf42	1339611	0.589000	0.26807	0.058000	0.19502	0.342000	0.28953	1.386000	0.34419	0.973000	0.38340	0.561000	0.74099	.	.	.		0.627	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520		T	1399610	C	T	1399610	1	4	233	0	1	0	0	0	0	0	0	0	1815	695	24	3		3	C16orf42	16	1399610	5'Flank	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10		1399610	88955143	73	32559										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2815588	2815588	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ccaagtctcgtacaccacctCgacgtcgcagctctcgatca	7	17	3	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr16:2815588C>T	ENST00000301740.8	+	11	5608	c.5059C>T	c.(5059-5061)Cga>Tga	p.R1687*		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1687	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						TACACCACCTCGACGTCGCAG	0.567																																					p.R1687X		Atlas-SNP	.											.	SRRM2	263	.	0			c.C5059T						.						104	83	90					16																	2815588		2198	4300	6498	SO:0001587	stop_gained	23524	exon11			CCACCTCGACGTC	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.5059C>T	chr16.hg19:g.2815588C>T	ENSP00000301740:p.Arg1687*	81.0	0.0		87.0	37.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Nonsense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	44	10.861450	0.99479	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	.	.	.	5.47	5.47	0.80525	.	0.000000	0.53938	D	0.000046	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.8877	11.8538	0.52425	0.1747:0.8253:0.0:0.0	.	.	.	.	X	1687;1687;939	.	ENSP00000301740:R1687X	R	+	1	2	SRRM2	2755589	0.997000	0.39634	1.000000	0.80357	0.978000	0.69477	0.858000	0.27845	2.566000	0.86566	0.655000	0.94253	CGA	.	.		0.567	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2815588	C	T	2815588	4	4	233	1	0	0	0	0	0	1	0	0	15184	876	31	1	5097	1	SRRM2	16	2815588	Nonsense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	1415978	2815588	87539165	74	32560										
MYH10	4628	hgsc.bcm.edu	37	chr17	8424298	8424298	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gaagctgatctaggactaggTgtggatccaattttccagcc	11	9	1	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr17:8424298T>A	ENST00000269243.4	-	17	2216	c.2078A>T	c.(2077-2079)cAc>cTc	p.H693L	MYH10_ENST00000360416.3_Missense_Mutation_p.H724L|MYH10_ENST00000396239.1_Missense_Mutation_p.H714L|MYH10_ENST00000379980.4_Missense_Mutation_p.H709L	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	693	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						TAGGACTAGGTGTGGATCCAA	0.428																																					p.H724L		Atlas-SNP	.											.	MYH10	148	.	0			c.A2171T						.						77	69	72					17																	8424298		2203	4300	6503	SO:0001583	missense	4628	exon19			ACTAGGTGTGGAT	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2078A>T	chr17.hg19:g.8424298T>A	ENSP00000269243:p.His693Leu	180.0	0.0		223.0	44.0	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	hg19	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.135891	0.77662	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.19	5.19	0.71726	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.86602	0.5972	L	0.47078	1.49	0.80722	D	1	P;P;P	0.44946	0.846;0.717;0.846	P;P;P	0.50314	0.614;0.637;0.614	T	0.83269	-0.0044	10	0.12103	T	0.63	.	15.2135	0.73244	0.0:0.0:0.0:1.0	.	702;724;693	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	L	693;724;714;709	ENSP00000269243:H693L;ENSP00000353590:H724L;ENSP00000379539:H714L;ENSP00000369315:H709L	ENSP00000269243:H693L	H	-	2	0	MYH10	8365023	1.000000	0.71417	0.251000	0.24312	0.895000	0.52256	7.714000	0.84703	2.188000	0.69820	0.533000	0.62120	CAC	.	.		0.428	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			A	8424298	T	A	8424298	3	1	233	1	0	0	0	0	1	0	0	0	10039	1696	59	4	3952	4	MYH10	17	8424298	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10		8424298	72770912	75	32561										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27442372	27442372	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tcctgcctggcactcacctaTtcaccagggagacgagaagg	11	13	2	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr17:27442372T>C	ENST00000527372.1	-	13	2495	c.2315A>G	c.(2314-2316)aAt>aGt	p.N772S	MYO18A_ENST00000354329.4_Missense_Mutation_p.N772S|MYO18A_ENST00000531253.1_Missense_Mutation_p.N772S|MYO18A_ENST00000533112.1_Missense_Mutation_p.N772S	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	772	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CACTCACCTATTCACCAGGGA	0.617																																					p.N772S	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.A2315G						.						39	47	44					17																	27442372		1993	4164	6157	SO:0001583	missense	399687	exon13			CACCTATTCACCA	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.2315A>G	chr17.hg19:g.27442372T>C	ENSP00000437073:p.Asn772Ser	103.0	0.0		157.0	31.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.904880	0.92035	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000458428	D;D;D;D	0.96651	-4.08;-4.08;-4.08;-4.08	5.43	5.43	0.79202	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.98686	0.9559	H	0.95816	3.725	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.998;0.998;0.998;1.0	D;D;D;D;D	0.91635	0.998;0.994;0.994;0.994;0.999	D	0.99774	1.1025	10	0.87932	D	0	.	15.4894	0.75593	0.0:0.0:0.0:1.0	.	441;384;772;772;772	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	S	772;772;772;772;772;384	ENSP00000346291:N772S;ENSP00000435932:N772S;ENSP00000434228:N772S;ENSP00000437073:N772S	ENSP00000346291:N772S	N	-	2	0	MYO18A	24466498	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	5.857000	0.69525	2.070000	0.61991	0.533000	0.62120	AAT	.	.		0.617	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		C	27442372	T	C	27442372	3	2	233	1	0	0	0	0	1	0	0	0	10074	1493	52	2	3969	2	MYO18A	17	27442372	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	19018074	27442372	53752838	76	32562										
ANKRD13B	124930	hgsc.bcm.edu	37	chr17	27939496	27939496	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tgcgacgaaccggtgccatcGgtgcgaggcagccccagcag	15	14	0	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr17:27939496G>A	ENST00000394859.3	+	12	1489	c.1335G>A	c.(1333-1335)tcG>tcA	p.S445S	RP11-68I3.2_ENST00000581474.1_RNA	NM_152345.4	NP_689558.4	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	445	Ser-rich.					endosome (GO:0005768)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	16						CGGTGCCATCGGTGCGAGGCA	0.642																																					p.S445S		Atlas-SNP	.											.	ANKRD13B	39	.	0			c.G1335A						.						27	27	27					17																	27939496		2200	4296	6496	SO:0001819	synonymous_variant	124930	exon12			GCCATCGGTGCGA	AK092673	CCDS11251.1	17q11.2	2013-01-10			ENSG00000198720	ENSG00000198720		"Ankyrin repeat domain containing"	26363	protein-coding gene	gene with protein product		615124					Standard	NM_152345		Approved	FLJ25555	uc002hei.3	Q86YJ7	OTTHUMG00000132731	ENST00000394859.3:c.1335G>A	chr17.hg19:g.27939496G>A		221.0	0.0		237.0	61.0	NM_152345	Q8N7S9	Silent	SNP	ENST00000394859.3	hg19	CCDS11251.1																																																																																			.	.		0.642	ANKRD13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256077.1	NM_152345		A	27939496	G	A	27939496	2	1	233	1	0	0	0	0	0	0	0	1	642	1103	39	1		1	ANKRD13B	17	27939496	Silent	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	497124	27939496	53255714	77	32563										
KRT10	3858	hgsc.bcm.edu	37	chr17	38975319	38975319	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gccggaactgccgccgtggcCgccgccgtggccgccgccgg	17	19	0	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr17:38975319C>T	ENST00000269576.5	-	7	1477	c.1468G>A	c.(1468-1470)Ggc>Agc	p.G490S	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ccgccgtggccgccgccgtgg	0.791																																					p.G490S		Atlas-SNP	.											.	KRT10	56	.	0			c.G1468A						.																																			SO:0001583	missense	3858	exon7			CGTGGCCGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1468G>A	chr17.hg19:g.38975319C>T	ENSP00000269576:p.Gly490Ser	29.0	0.0		65.0	5.0	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546565	0.86022	.	.	ENSG00000186395	ENST00000269576	D	0.96587	-4.06	4.38	4.38	0.52667	.	0.845686	0.09879	N	0.743932	D	0.94778	0.8314	N	0.08118	0	0.27860	N	0.940431	D	0.89917	1.0	D	0.76071	0.987	D	0.87790	0.2618	10	0.18710	T	0.47	.	12.7512	0.57310	0.0:1.0:0.0:0.0	.	490	P13645	K1C10_HUMAN	S	490	ENSP00000269576:G490S	ENSP00000269576:G490S	G	-	1	0	KRT10	36228845	0.019000	0.18553	0.876000	0.34364	0.184000	0.23303	0.448000	0.21726	2.739000	0.93911	0.603000	0.83216	GGC	.	.		0.791	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		T	38975319	C	T	38975319	3	4	233	1	0	0	0	0	1	0	0	0	8457	652	23	1	294	1	KRT10	17	38975319	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	11035823	38975319	42219891	78	32564										
KRT12	3859	hgsc.bcm.edu	37	chr17	39018821	39018821	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tagggtttctgcatacctttAgaggaatcagttgactgtgc	11	7	2	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr17:39018821A>G	ENST00000251643.4	-	7	1406	c.1383T>C	c.(1381-1383)tcT>tcC	p.S461S	RP5-1110E20.1_ENST00000579136.1_RNA	NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN	keratin 12	461	Tail.				visual perception (GO:0007601)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	15		Breast(137;0.000301)			Griseofulvin(DB00400)	GCATACCTTTAGAGGAATCAG	0.353																																					p.S461S		Atlas-SNP	.											.	KRT12	53	.	0			c.T1383C						.						142	134	137					17																	39018821		2203	4300	6503	SO:0001819	synonymous_variant	3859	exon7			ACCTTTAGAGGAA		CCDS11378.1	17q21.2	2013-06-20	2008-08-01		ENSG00000187242	ENSG00000187242		"-", "Intermediate filaments type I, keratins (acidic)"	6414	protein-coding gene	gene with protein product	"Meesmann corneal dystrophy"	601687				9171831, 16831889	Standard	NM_000223		Approved	K12	uc002hvk.2	Q99456	OTTHUMG00000133369	ENST00000251643.4:c.1383T>C	chr17.hg19:g.39018821A>G		101.0	0.0		120.0	25.0	NM_000223	B2R9E0	Silent	SNP	ENST00000251643.4	hg19	CCDS11378.1																																																																																			.	.		0.353	KRT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257214.2	NM_000223		G	39018821	A	G	39018821	2	3	233	1	0	0	0	0	0	0	0	1	8458	407	15	2		2	KRT12	17	39018821	Silent	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	43502	39018821	42176389	79	32565										
TUBD1	51174	hgsc.bcm.edu	37	chr17	57963509	57963509	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gcatgttgaccatatttccaTtggccagactgggcagcctt	10	11	0	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr17:57963509T>G	ENST00000592426.1	-	2	255	c.255A>C	c.(253-255)caA>caC	p.Q85H	TUBD1_ENST00000394239.3_Missense_Mutation_p.Q85H|TUBD1_ENST00000539018.1_Intron|TUBD1_ENST00000346141.6_Intron|TUBD1_ENST00000325752.3_Missense_Mutation_p.Q85H|TUBD1_ENST00000340993.6_Missense_Mutation_p.Q85H|TUBD1_ENST00000376094.4_Missense_Mutation_p.Q85H|TUBD1_ENST00000591611.1_5'UTR			Q9UJT1	TBD_HUMAN	tubulin, delta 1	85					cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|protein polymerization (GO:0051258)|spermatogenesis (GO:0007283)	centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(2)	21	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)		Vinblastine(DB00570)	CATATTTCCATTGGCCAGACT	0.418																																					p.Q85H		Atlas-SNP	.											.	TUBD1	38	.	0			c.A255C						.						127	124	125					17																	57963509		2203	4300	6503	SO:0001583	missense	51174	exon3			TTTCCATTGGCCA	AF201333	CCDS11620.1, CCDS54151.1, CCDS54152.1, CCDS54153.1, CCDS54154.1	17q23.1	2007-03-16						"Tubulins"	16811	protein-coding gene	gene with protein product		607344				10620804	Standard	NM_016261		Approved	FLJ12709, TUBD	uc002ixw.2	Q9UJT1		ENST00000592426.1:c.255A>C	chr17.hg19:g.57963509T>G	ENSP00000468518:p.Gln85His	122.0	0.0		175.0	58.0	NM_016261	B4DPT8|B4DW01|D3DU02|E9PCA7|E9PCQ8|Q5KU36|Q9BWG9|Q9H7Z8	Missense_Mutation	SNP	ENST00000592426.1	hg19	CCDS11620.1	.	.	.	.	.	.	.	.	.	.	T	13.49	2.251660	0.39797	.	.	ENSG00000108423	ENST00000325752;ENST00000340993;ENST00000394239;ENST00000376094	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	6.08	2.67	0.31697	Tubulin/FtsZ, GTPase domain (4);	0.528179	0.20747	N	0.086425	T	0.44117	0.1278	N	0.17474	0.49	0.80722	D	1	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.15484	0.003;0.001;0.0;0.013	T	0.21280	-1.0250	10	0.48119	T	0.1	-0.345	2.9007	0.05705	0.1042:0.1353:0.1539:0.6065	.	85;85;85;85	E9PCA7;E9PCQ8;Q9UJT1-2;Q9UJT1	.;.;.;TBD_HUMAN	H	85	ENSP00000320797:Q85H;ENSP00000342399:Q85H;ENSP00000377785:Q85H;ENSP00000365262:Q85H	ENSP00000320797:Q85H	Q	-	3	2	TUBD1	55318291	0.061000	0.20836	0.938000	0.37757	0.990000	0.78478	0.351000	0.20096	0.179000	0.19938	-0.264000	0.10439	CAA	.	.		0.418	TUBD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448815.1	NM_016261		G	57963509	T	G	57963509	3	3	233	1	0	0	0	0	1	0	0	0	16777	1490	52	5	1134	5	TUBD1	17	57963509	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	18944688	57963509	23231701	80	32566										
INTS2	57508	hgsc.bcm.edu	37	chr17	59968916	59968916	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ttgagtatctcctgttctgtGactggctgatttgtggcttc	11	8	2	3			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr17:59968916G>T	ENST00000444766.3	-	14	1932	c.1857C>A	c.(1855-1857)gtC>gtA	p.V619V	INTS2_ENST00000251334.6_Silent_p.V611V	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	619					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						CCTGTTCTGTGACTGGCTGAT	0.343																																					p.V619V		Atlas-SNP	.											.	INTS2	89	.	0			c.C1857A						.						152	152	152					17																	59968916		1869	4095	5964	SO:0001819	synonymous_variant	57508	exon14			TTCTGTGACTGGC	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.1857C>A	chr17.hg19:g.59968916G>T		156.0	0.0		190.0	14.0	NM_020748	Q9ULD3	Silent	SNP	ENST00000444766.3	hg19	CCDS45750.1																																																																																			.	.		0.343	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		T	59968916	G	T	59968916	2	4	233	1	0	0	0	0	0	0	0	1	7787	1277	45	3		3	INTS2	17	59968916	Silent	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	2005407	59968916	21226294	81	32567										
DDX5	1655	hgsc.bcm.edu	37	chr17	62496761	62496761	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	aggtcgctcacttgctttatGttattaggtgtaaagaaagt	10	5	1	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr17:62496761G>A	ENST00000225792.5	-	12	1748	c.1347C>T	c.(1345-1347)aaC>aaT	p.N449N	DDX5_ENST00000450599.2_Silent_p.N370N|MIR5047_ENST00000579212.1_RNA|MIR3064_ENST00000581130.1_RNA|DDX5_ENST00000580026.1_5'UTR|DDX5_ENST00000578804.1_Silent_p.N449N	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	449	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			CTTGCTTTATGTTATTAGGTG	0.423			T	ETV4	prostate																																p.N449N	NSCLC(22;406 813 4871 19580 40307)	Atlas-SNP	.		Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	.	DDX5	101	.	0			c.C1347T						.						162	144	150					17																	62496761		2203	4300	6503	SO:0001819	synonymous_variant	1655	exon12			CTTTATGTTATTA	AF015812	CCDS11659.1	17q21	2012-07-27	2012-02-23		ENSG00000108654	ENSG00000108654		"DEAD-boxes"	2746	protein-coding gene	gene with protein product		180630	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 5"	HLR1, G17P1		22156369, 18698352	Standard	NM_004396		Approved	p68	uc002jek.2	P17844	OTTHUMG00000178936	ENST00000225792.5:c.1347C>T	chr17.hg19:g.62496761G>A		132.0	0.0		167.0	47.0	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Silent	SNP	ENST00000225792.5	hg19	CCDS11659.1																																																																																			.	.		0.423	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		A	62496761	G	A	62496761	2	1	233	1	0	0	0	0	0	0	0	1	4369	1368	48	3		3	DDX5	17	62496761	Silent	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	2527845	62496761	18698449	82	32568										
MIB1	57534	hgsc.bcm.edu	37	chr18	19399526	19399526	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tgatatcctagcagttctttTggaagctggagcagatgtta	11	6	1	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr18:19399526T>G	ENST00000261537.6	+	12	2012	c.1748T>G	c.(1747-1749)tTg>tGg	p.L583W	SNORA73_ENST00000363107.1_RNA|MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	583					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			GCAGTTCTTTTGGAAGCTGGA	0.383																																					p.L583W		Atlas-SNP	.											.	MIB1	87	.	0			c.T1748G						.						149	141	144					18																	19399526		2203	4300	6503	SO:0001583	missense	57534	exon12			TTCTTTTGGAAGC	AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.1748T>G	chr18.hg19:g.19399526T>G	ENSP00000261537:p.Leu583Trp	101.0	0.0		126.0	36.0	NM_020774	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	hg19	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.953391	0.92660	.	.	ENSG00000101752	ENST00000261537	T	0.19938	2.11	5.4	5.4	0.78164	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000001	T	0.62441	0.2428	H	0.98027	4.13	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	T	0.78316	-0.2251	10	0.87932	D	0	-7.3818	15.4268	0.75059	0.0:0.0:0.0:1.0	.	583	Q86YT6	MIB1_HUMAN	W	583	ENSP00000261537:L583W	ENSP00000261537:L583W	L	+	2	0	MIB1	17653524	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.057000	0.61298	0.460000	0.39030	TTG	.	.		0.383	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		G	19399526	T	G	19399526	3	3	233	1	0	0	0	0	1	0	0	0	9575	1821	63	5	1794	5	MIB1	18	19399526	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10		19399526	58677722	83	32569										
MCART2	147407	hgsc.bcm.edu	37	chr18	29339948	29339948	+	Frame_Shift_Del	DEL	C	C	-													0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	taattggaaaacacaagaatCccaacatggcacccaataga							TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr18:29339948delC	ENST00000579441.2	-	1	676	c.677delG	c.(676-678)ggafs	p.G226fs	SLC25A52_ENST00000269205.5_Frame_Shift_Del_p.G236fs			Q3SY17	S2552_HUMAN	solute carrier family 25, member 52	226					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											ACACAAGAATCCCAACATGGC	0.448																																					p.G236fs		Atlas-INDEL	.											.	.	.	.	0			c.708delA						.						62	61	61					18																	29339948		2203	4300	6503	SO:0001589	frameshift_variant	147407	exon1			.		CCDS32812.1, CCDS32812.2	18q12.1	2013-07-15	2012-03-29	2012-03-29	ENSG00000141437	ENSG00000141437		"Solute carriers"	23324	protein-coding gene	gene with protein product			"mitochondrial carrier triple repeat 2"	MCART2			Standard	NM_001034172		Approved		uc002kxa.3	Q3SY17	OTTHUMG00000179617	ENST00000579441.2:c.677delG	chr18.hg19:g.29339948delC	ENSP00000462754:p.Gly226fs	346.0	0.0		483.0	122.0	NM_001034172		Frame_Shift_Del	DEL	ENST00000579441.2	hg19																																																																																				.	.		0.448	SLC25A52-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_084000		-	29339948	C	-	29339948	7	5	233	1	0	1	0	1	0	0	0	0	9379	855	30	0	220	0	MCART2	18	29339948	Frame_Shift_Del	DEL	C	TCGA-DD-AAW0-01A-11D-A40R-10	9940422	29339948	48737300	84	32570										
DCC	1630	hgsc.bcm.edu	37	chr18	50450079	50450079	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	tgtgttttcccctcatagatCcaggactgcatagacagctg	9	11	1	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr18:50450079C>T	ENST00000442544.2	+	4	1316	c.700C>T	c.(700-702)Cca>Tca	p.P234S	DCC_ENST00000412726.1_Missense_Mutation_p.P82S	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	234	Ig-like C2-type 3.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CCTCATAGATCCAGGACTGCA	0.348																																					p.P234S		Atlas-SNP	.											DCC,NS,carcinoma,0,1	DCC	360	.	0			c.C700T						.						107	93	98					18																	50450079		2203	4300	6503	SO:0001583	missense	1630	exon4			ATAGATCCAGGAC	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.700C>T	chr18.hg19:g.50450079C>T	ENSP00000389140:p.Pro234Ser	120.0	2.0		154.0	32.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.465056	0.26335	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.62364	0.03;0.03	5.67	5.67	0.87782	Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.45094	0.1325	N	0.20574	0.59	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.34104	-0.9842	10	0.21014	T	0.42	.	11.9488	0.52944	0.0:0.9196:0.0:0.0804	.	82;234	E7EQM8;P43146	.;DCC_HUMAN	S	234;167;82	ENSP00000389140:P234S;ENSP00000397322:P82S	ENSP00000304146:P167S	P	+	1	0	DCC	48704077	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	4.027000	0.57239	2.679000	0.91253	0.655000	0.94253	CCA	.	.		0.348	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	50450079	C	T	50450079	3	4	233	1	0	0	0	0	1	0	0	0	4284	855	30	3	714	3	DCC	18	50450079	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	21110131	50450079	27627169	85	32571										
SALL3	27164	hgsc.bcm.edu	37	chr18	76753827	76753827	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gccagggccggggacgctccCgtgggcgcgcaggctagcgc	19	15	0	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr18:76753827C>A	ENST00000537592.2	+	2	1836	c.1836C>A	c.(1834-1836)ccC>ccA	p.P612P	SALL3_ENST00000575389.2_Silent_p.P612P|SALL3_ENST00000536229.3_Silent_p.P479P	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	612					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		GGGACGCTCCCGTGGGCGCGC	0.751																																					p.P612P		Atlas-SNP	.											.	SALL3	162	.	0			c.C1836A						.						4	5	5					18																	76753827		1884	3761	5645	SO:0001819	synonymous_variant	27164	exon2			CGCTCCCGTGGGC	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.1836C>A	chr18.hg19:g.76753827C>A		48.0	0.0		60.0	13.0	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	hg19	CCDS12013.1																																																																																			.	.		0.751	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		A	76753827	C	A	76753827	2	1	233	1	0	0	0	0	0	0	0	1	13827	639	23	1		1	SALL3	18	76753827	Silent	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10	26303748	76753827	1323421	86	32572										
CYP2B6	1555	hgsc.bcm.edu	37	chr19	41518307	41518307	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	aggcagtcatctatgagattCagagattttccgaccttctc	8	10	4	2			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr19:41518307C>T	ENST00000324071.4	+	7	1076	c.1069C>T	c.(1069-1071)Cag>Tag	p.Q357*	CYP2B6_ENST00000330446.5_Nonsense_Mutation_p.Q157*|CYP2B6_ENST00000593831.1_Nonsense_Mutation_p.Q121*	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	357					cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	CTATGAGATTCAGAGATTTTC	0.532																																					p.Q357X		Atlas-SNP	.											.	CYP2B6	79	.	0			c.C1069T						.						123	97	106					19																	41518307		2203	4300	6503	SO:0001587	stop_gained	1555	exon7			GAGATTCAGAGAT	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"Cytochrome P450s"	2615	protein-coding gene	gene with protein product		123930	"cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6", "cytochrome P450, family 2, subfamily B", "cytochrome P450, subfamily IIB (phenobarbital-inducible)"	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.1069C>T	chr19.hg19:g.41518307C>T	ENSP00000324648:p.Gln357*	65.0	0.0		90.0	20.0	NM_000767	B4DWP3|Q2V565|Q9UK46	Nonsense_Mutation	SNP	ENST00000324071.4	hg19	CCDS12570.1	.	.	.	.	.	.	.	.	.	.	.	17.29	3.352729	0.61293	.	.	ENSG00000197408	ENST00000324071;ENST00000330446	.	.	.	4.3	4.3	0.51218	.	0.062472	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.32	0.66479	0.0:1.0:0.0:0.0	.	.	.	.	X	357;157	.	ENSP00000324648:Q357X	Q	+	1	0	CYP2B6	46210147	1.000000	0.71417	1.000000	0.80357	0.243000	0.25628	7.136000	0.77285	2.219000	0.72066	0.298000	0.19748	CAG	.	.		0.532	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767		T	41518307	C	T	41518307	4	4	233	1	0	0	0	0	0	1	0	0	4166	827	29	3	1095	3	CYP2B6	19	41518307	Nonsense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10		41518307	17610676	87	32573										
ZNF211	10520	hgsc.bcm.edu	37	chr19	58152529	58152529	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gcggtggccttttacagtggAaaaagtcatcacaactgggg	13	8	2	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr19:58152529A>G	ENST00000347302.3	+	3	854	c.675A>G	c.(673-675)ggA>ggG	p.G225G	ZNF211_ENST00000541801.1_Silent_p.G216G|ZNF211_ENST00000254182.7_Silent_p.G216G|ZNF211_ENST00000420680.1_Silent_p.G229G|ZNF211_ENST00000240731.4_Silent_p.G238G|ZNF211_ENST00000544273.1_Silent_p.G237G|ZNF211_ENST00000299871.5_Silent_p.G290G|ZNF211_ENST00000391703.3_Silent_p.G164G	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	225					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTTACAGTGGAAAAAGTCATC	0.453																																					p.G290G		Atlas-SNP	.											.	ZNF211	78	.	0			c.A870G						.						68	69	69					19																	58152529		2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			CAGTGGAAAAAGT	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"Zinc fingers, C2H2-type", "-"	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.675A>G	chr19.hg19:g.58152529A>G		106.0	0.0		136.0	32.0	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	hg19	CCDS12957.1	.	.	.	.	.	.	.	.	.	.	A	5.174	0.217740	0.09810	.	.	ENSG00000121417	ENST00000407202	.	.	.	3.8	-1.57	0.08506	.	.	.	.	.	T	0.32882	0.0844	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.34179	-0.9839	4	.	.	.	.	9.7393	0.40409	0.4824:0.0:0.5176:0.0	.	.	.	.	E	229	.	.	K	+	1	0	ZNF211	62844341	0.000000	0.05858	0.000000	0.03702	0.120000	0.20174	-1.932000	0.01554	-0.503000	0.06586	0.482000	0.46254	AAA	.	.		0.453	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1			G	58152529	A	G	58152529	2	3	233	1	0	0	0	0	0	0	0	1	17782	233	9	2		2	ZNF211	19	58152529	Silent	SNP	A	TCGA-DD-AAW0-01A-11D-A40R-10	16634222	58152529	976454	88	32574										
DLGAP4	22839	hgsc.bcm.edu	37	chr20	35128903	35128903	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	cggcacagccaggggcctgcCgccgagacggctactggttc	15	15	0	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr20:35128903C>T	ENST00000373907.2	+	9	2600	c.2401C>T	c.(2401-2403)Cgc>Tgc	p.R801C	DLGAP4_ENST00000339266.5_Missense_Mutation_p.R801C|DLGAP4_ENST00000373913.3_Missense_Mutation_p.R798C|DLGAP4_ENST00000340491.4_Missense_Mutation_p.R262C|DLGAP4_ENST00000475894.1_3'UTR|DLGAP4_ENST00000401952.2_Missense_Mutation_p.R798C			Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4	801					cell-cell signaling (GO:0007267)	membrane (GO:0016020)|synapse (GO:0045202)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				AGGGGCCTGCCGCCGAGACGG	0.652																																					p.R798C		Atlas-SNP	.											.	DLGAP4	111	.	0			c.C2392T						.						25	29	27					20																	35128903		2144	4226	6370	SO:0001583	missense	22839	exon9			GCCTGCCGCCGAG	AF088030	CCDS13274.1, CCDS13275.1	20q11.23	2010-02-05			ENSG00000080845	ENSG00000080845			24476	protein-coding gene	gene with protein product						9115257	Standard	XM_005260329		Approved	DAP4, KIAA0964, SAPAP4	uc010zvp.2	Q9Y2H0	OTTHUMG00000032390	ENST00000373907.2:c.2401C>T	chr20.hg19:g.35128903C>T	ENSP00000363014:p.Arg801Cys	136.0	0.0		192.0	33.0	NM_014902	E1P5T5|Q5QPG4|Q5T2Y4|Q5T2Y5|Q9H137|Q9H138|Q9H1L7	Missense_Mutation	SNP	ENST00000373907.2	hg19		.	.	.	.	.	.	.	.	.	.	C	19.28	3.797198	0.70567	.	.	ENSG00000080845	ENST00000373913;ENST00000401952;ENST00000373907;ENST00000339266;ENST00000340491	T;T;T;T;T	0.20332	2.08;2.08;2.08;2.08;2.08	5.62	4.62	0.57501	.	0.048466	0.85682	D	0.000000	T	0.46249	0.1383	M	0.80183	2.485	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;0.997	D;D;P;D	0.65010	0.931;0.921;0.861;0.924	T	0.49351	-0.8949	10	0.72032	D	0.01	.	14.4348	0.67274	0.1477:0.8523:0.0:0.0	.	107;262;801;798	F8WF49;Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1	.;.;DLGP4_HUMAN;.	C	798;798;801;801;262	ENSP00000363023:R798C;ENSP00000384954:R798C;ENSP00000363014:R801C;ENSP00000341633:R801C;ENSP00000345700:R262C	ENSP00000341633:R801C	R	+	1	0	DLGAP4	34562317	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.718000	0.38001	2.659000	0.90383	0.655000	0.94253	CGC	.	.		0.652	DLGAP4-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000079025.2	NM_014902		T	35128903	C	T	35128903	3	4	233	1	0	0	0	0	1	0	0	0	4564	652	23	1	2550	1	DLGAP4	20	35128903	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10		35128903	27896617	89	32575										
KRTAP24-1	643803	hgsc.bcm.edu	37	chr21	31654604	31654604	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	agctcagtggtcggcagctcGtaggcctgtagcttgaatag	14	9	1	1			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr21:31654604G>A	ENST00000340345.4	-	1	672	c.647C>T	c.(646-648)aCg>aTg	p.T216M		NM_001085455.1	NP_001078924.1	Q3LI83	KR241_HUMAN	keratin associated protein 24-1	216	6 X 10 AA repeats of Y-[ILR]-[SVPC]- [NRTS]-[SNTG]-X-[QHRP]-[PSY]-[QSL]-[SRK].					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|large_intestine(3)|lung(7)|urinary_tract(3)	14						TCGGCAGCTCGTAGGCCTGTA	0.438																																					p.T216M		Atlas-SNP	.											.	KRTAP24-1	44	.	0			c.C647T						.						100	97	98					21																	31654604		1860	4099	5959	SO:0001583	missense	643803	exon1			CAGCTCGTAGGCC	AB096935	CCDS42915.1	21q22.11	2007-11-23			ENSG00000188694	ENSG00000188694		"Keratin associated proteins"	33902	protein-coding gene	gene with protein product							Standard	NM_001085455		Approved	KAP24.1	uc002ynv.3	Q3LI83	OTTHUMG00000125483	ENST00000340345.4:c.647C>T	chr21.hg19:g.31654604G>A	ENSP00000339238:p.Thr216Met	93.0	0.0		141.0	18.0	NM_001085455	Q1XDX0	Missense_Mutation	SNP	ENST00000340345.4	hg19	CCDS42915.1	.	.	.	.	.	.	.	.	.	.	G	5.319	0.244163	0.10077	.	.	ENSG00000188694	ENST00000340345	T	0.30714	1.52	3.63	-4.66	0.03329	.	1.491660	0.04449	N	0.372265	T	0.12860	0.0312	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.26538	-1.0100	10	0.49607	T	0.09	4.086	4.6583	0.12630	0.281:0.3598:0.3592:0.0	.	216	Q3LI83	KR241_HUMAN	M	216	ENSP00000339238:T216M	ENSP00000339238:T216M	T	-	2	0	KRTAP24-1	30576475	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-1.104000	0.03326	-0.515000	0.06479	-0.440000	0.05779	ACG	.	.		0.438	KRTAP24-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246806.2	NM_001085455		A	31654604	G	A	31654604	3	1	233	1	0	0	0	0	1	0	0	0	8551	1145	40	1	121	1	KRTAP24-1	21	31654604	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10		31654604	16475291	90	32576										
RIMBP3	85376	hgsc.bcm.edu	37	chr22	20457887	20457887	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gctcccagcagtggcatcggCgacctcacaaaccttaagcc	9	16	1	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr22:20457887C>A	ENST00000426804.1	-	1	3899	c.3415G>T	c.(3415-3417)Gcc>Tcc	p.A1139S	SCARNA17_ENST00000516762.1_RNA|SCARNA18_ENST00000516215.1_RNA|RN7SKP131_ENST00000363006.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1139	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.									breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			GTGGCATCGGCGACCTCACAA	0.562																																					p.A1139S		Atlas-SNP	.											.	RIMBP3	42	.	0			c.G3415T						.						75	78	77					22																	20457887		2052	4210	6262	SO:0001583	missense	85376	exon1			CATCGGCGACCTC	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3415G>T	chr22.hg19:g.20457887C>A	ENSP00000391564:p.Ala1139Ser	802.0	0.0		1070.0	97.0	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	hg19	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	C	10.32	1.316786	0.23908	.	.	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.37915	1.17	3.42	-6.84	0.01687	Fibronectin, type III (2);	0.426528	0.23556	N	0.046913	T	0.17280	0.0415	L	0.41027	1.25	0.09310	N	1	P	0.35821	0.523	B	0.33890	0.172	T	0.06752	-1.0809	10	0.34782	T	0.22	1.6997	2.317	0.04201	0.1093:0.1783:0.3527:0.3598	.	1045	Q9UFD9	RIM3A_HUMAN	S	1045;1139	ENSP00000391564:A1139S	ENSP00000347318:A1045S	A	-	1	0	RIMBP3	18837887	0.000000	0.05858	0.000000	0.03702	0.592000	0.36648	-3.329000	0.00510	-1.591000	0.01621	-1.109000	0.02080	GCC	.	.		0.562	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672		A	20457887	C	A	20457887	3	1	233	1	0	0	0	0	1	0	0	0	13379	768	27	1	1508	1	RIMBP3	22	20457887	Missense_Mutation	SNP	C	TCGA-DD-AAW0-01A-11D-A40R-10		20457887	30846679	91	32577										
SUSD2	56241	hgsc.bcm.edu	37	chr22	24581177	24581177	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	gccaggcctgggaggagctgGaggatcagctgcccaacttc	15	12	1	0			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chr22:24581177G>A	ENST00000358321.3	+	6	1159	c.898G>A	c.(898-900)Gag>Aag	p.E300K		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	300	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.E300Q(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						GGAGGAGCTGGAGGATCAGCT	0.672																																					p.E300K		Atlas-SNP	.											SUSD2,NS,carcinoma,0,1	SUSD2	68	.	1	Substitution - Missense(1)	prostate(1)	c.G898A						.						28	28	28					22																	24581177		2203	4300	6503	SO:0001583	missense	56241	exon6			GAGCTGGAGGATC	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.898G>A	chr22.hg19:g.24581177G>A	ENSP00000351075:p.Glu300Lys	60.0	1.0		93.0	18.0	NM_019601	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	hg19	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.513687	0.85389	.	.	ENSG00000099994	ENST00000358321	T	0.22539	1.95	4.27	4.27	0.50696	AMOP (3);	0.182147	0.46758	D	0.000261	T	0.36663	0.0975	M	0.77820	2.39	0.39316	D	0.965161	P	0.50819	0.939	P	0.51453	0.67	T	0.42464	-0.9450	10	0.72032	D	0.01	-18.4309	12.6244	0.56622	0.0:0.0:1.0:0.0	.	300	Q9UGT4	SUSD2_HUMAN	K	300	ENSP00000351075:E300K	ENSP00000351075:E300K	E	+	1	0	SUSD2	22911177	1.000000	0.71417	0.911000	0.35937	0.561000	0.35649	7.216000	0.77974	2.102000	0.63906	0.437000	0.28790	GAG	.	.		0.672	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		A	24581177	G	A	24581177	3	1	233	1	0	0	0	0	1	0	0	0	15423	1175	41	3	920	3	SUSD2	22	24581177	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10	4123290	24581177	26723389	92	32578										
STS	412	hgsc.bcm.edu	37	chrX	7252038	7252038	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	atcccacaggatcattgatgGacgtgatctgatgcccctgc	10	12	2	3			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chrX:7252038G>A	ENST00000217961.4	+	9	1488	c.1268G>A	c.(1267-1269)gGa>gAa	p.G423E		NM_000351.4	NP_000342.2	P08842	STS_HUMAN	steroid sulfatase (microsomal), isozyme S	423					cellular protein metabolic process (GO:0044267)|epidermis development (GO:0008544)|female pregnancy (GO:0007565)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|steroid catabolic process (GO:0006706)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|steryl-sulfatase activity (GO:0004773)|sulfuric ester hydrolase activity (GO:0008484)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(1)	27		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Norelgestromin(DB06713)	ATCATTGATGGACGTGATCTG	0.488									Ichthyosis																												p.G423E		Atlas-SNP	.											.	STS	64	.	0			c.G1268A						.						124	93	103					X																	7252038		2203	4299	6502	SO:0001583	missense	412	exon9	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTGATGGACGTGA	M16505	CCDS14127.1	Xp22.32	2013-06-10	2007-07-19		ENSG00000101846	ENSG00000101846	3.1.6.2	"Arylsulfatase family"	11425	protein-coding gene	gene with protein product	"arylsulfatase C"	300747	"steroid sulfatase (microsomal), arylsulfatase C, isozyme S"	ARSC1			Standard	NM_000351		Approved	ARSC	uc004cry.4	P08842	OTTHUMG00000021102	ENST00000217961.4:c.1268G>A	chrX.hg19:g.7252038G>A	ENSP00000217961:p.Gly423Glu	58.0	0.0		75.0	24.0	NM_000351	B2RA47	Missense_Mutation	SNP	ENST00000217961.4	hg19	CCDS14127.1	.	.	.	.	.	.	.	.	.	.	G	19.98	3.926303	0.73327	.	.	ENSG00000101846	ENST00000217961	D	0.99698	-6.44	3.95	3.95	0.45737	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.99869	0.9938	H	0.99783	4.775	0.50467	D	0.999872	D	0.89917	1.0	D	0.97110	1.0	D	0.96309	0.9227	10	0.87932	D	0	.	12.8957	0.58098	0.0:0.0:1.0:0.0	.	423	P08842	STS_HUMAN	E	423	ENSP00000217961:G423E	ENSP00000217961:G423E	G	+	2	0	STS	7262038	1.000000	0.71417	0.012000	0.15200	0.117000	0.20001	7.637000	0.83313	1.586000	0.49944	0.513000	0.50165	GGA	.	.		0.488	STS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055686.1	NM_000351		A	7252038	G	A	7252038	3	1	233	1	0	0	0	0	1	0	0	0	15347	1174	41	3	1302	3	STS	23	7252038	Missense_Mutation	SNP	G	TCGA-DD-AAW0-01A-11D-A40R-10		7252038	148018522	93	32579										
CAPN6	827	hgsc.bcm.edu	37	chrX	110495540	110495540	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0319148936170213	3	1	0.528772865853659	0.9033203125	0.437973484848485	1	1	0	ttcatgagtacaaacctcaaTggaacagcagatcagaccac	7	11	3	3			TCGA-DD-AAW0-01A-11D-A40R-10	TCGA-DD-AAW0-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fe50376-65f7-435c-aa48-38e821e121b3	16c90d4a-6a13-4147-9135-3e66190c927f	g.chrX:110495540T>C	ENST00000324068.1	-	5	861	c.694A>G	c.(694-696)Att>Gtt	p.I232V	CAPN6_ENST00000541758.1_Intron	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	232	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						CAAACCTCAATGGAACAGCAG	0.428																																					p.I232V		Atlas-SNP	.											.	CAPN6	120	.	0			c.A694G						.						122	94	103					X																	110495540		2203	4300	6503	SO:0001583	missense	827	exon5			CCTCAATGGAACA	AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.694A>G	chrX.hg19:g.110495540T>C	ENSP00000317214:p.Ile232Val	51.0	0.0		51.0	22.0	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Missense_Mutation	SNP	ENST00000324068.1	hg19	CCDS14555.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.580529	0.86645	.	.	ENSG00000077274	ENST00000324068	T	0.42900	0.96	5.97	5.97	0.96955	Peptidase C2, calpain, catalytic domain (3);	0.094708	0.64402	D	0.000001	T	0.66436	0.2789	M	0.78344	2.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70659	-0.4811	10	0.72032	D	0.01	.	15.388	0.74718	0.0:0.0:0.0:1.0	.	232	Q9Y6Q1	CAN6_HUMAN	V	232	ENSP00000317214:I232V	ENSP00000317214:I232V	I	-	1	0	CAPN6	110382196	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.622000	0.61240	2.018000	0.59344	0.486000	0.48141	ATT	.	.		0.428	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			C	110495540	T	C	110495540	3	2	233	1	0	0	0	0	1	0	0	0	2632	1464	51	2	1267	2	CAPN6	23	110495540	Missense_Mutation	SNP	T	TCGA-DD-AAW0-01A-11D-A40R-10	103243502	110495540	44775020	94	32580										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11591031	11591031	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gcacctgtgtcacctctgcaAggccatcgcagccaactccg	9	17	2	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:11591031A>T	ENST00000294484.6	+	16	3308	c.3170A>T	c.(3169-3171)aAg>aTg	p.K1057M	PTCHD2_ENST00000304391.6_5'Flank|PTCHD2_ENST00000389575.3_Missense_Mutation_p.K1057M	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	1057					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CACCTCTGCAAGGCCATCGCA	0.622																																					p.K1057M		Atlas-SNP	.											.	PTCHD2	193	.	0			c.A3170T						.						88	101	97					1																	11591031		2078	4203	6281	SO:0001583	missense	57540	exon16			TCTGCAAGGCCAT	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.3170A>T	chr1.hg19:g.11591031A>T	ENSP00000294484:p.Lys1057Met	70.0	0.0		80.0	35.0	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	hg19	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.247580	0.80024	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	D;D	0.92699	-3.04;-3.09	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.93278	0.7858	L	0.32530	0.975	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.94154	0.7408	10	0.87932	D	0	-27.4336	13.8596	0.63552	1.0:0.0:0.0:0.0	.	1057	Q9P2K9	PTHD2_HUMAN	M	1057	ENSP00000294484:K1057M;ENSP00000374226:K1057M	ENSP00000294484:K1057M	K	+	2	0	PTCHD2	11513618	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	9.078000	0.94023	1.878000	0.54408	0.482000	0.46254	AAG	.	.		0.622	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11591031	A	T	11591031	3	4	234	1	0	0	0	0	1	0	0	0	12745	72	3	4	3228	4	PTCHD2	1	11591031	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10		11591031	237659590	1	32581										
ZBTB17	7709	hgsc.bcm.edu	37	chr1	16271442	16271442	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tctccctcacctcgcacttgTggatgacggagccgtaggcc	11	15	2	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:16271442T>C	ENST00000375743.4	-	7	1149	c.917A>G	c.(916-918)cAc>cGc	p.H306R	ZBTB17_ENST00000375733.2_Missense_Mutation_p.H306R|ZBTB17_ENST00000537142.1_Missense_Mutation_p.H224R|ZBTB17_ENST00000448462.2_Missense_Mutation_p.H243R|ZBTB17_ENST00000479282.1_5'Flank	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17	306	Interaction with MYC.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|ectoderm development (GO:0007398)|endoplasmic reticulum unfolded protein response (GO:0030968)|gastrulation with mouth forming second (GO:0001702)|negative regulation of cell cycle (GO:0045786)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)	15		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		CTCGCACTTGTGGATGACGGA	0.716																																					p.H306R		Atlas-SNP	.											.	ZBTB17	45	.	0			c.A917G						.						28	33	31					1																	16271442		2197	4292	6489	SO:0001583	missense	7709	exon7			CACTTGTGGATGA	U20647	CCDS165.1, CCDS55576.1, CCDS72712.1	1p36.13	2013-01-08	2004-07-16	2004-07-16	ENSG00000116809	ENSG00000116809		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12936	protein-coding gene	gene with protein product		604084	"zinc finger protein 151 (pHZ-67)", "zinc finger protein 60"	ZNF151, ZNF60			Standard	NM_003443		Approved	MIZ1, pHZ-67	uc001axl.4	Q13105	OTTHUMG00000009377	ENST00000375743.4:c.917A>G	chr1.hg19:g.16271442T>C	ENSP00000364895:p.His306Arg	32.0	0.0		33.0	14.0	NM_003443	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Missense_Mutation	SNP	ENST00000375743.4	hg19	CCDS165.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.414375	0.83449	.	.	ENSG00000116809	ENST00000375743;ENST00000375733;ENST00000444654;ENST00000537142;ENST00000448462	T;T;T;T	0.77750	-1.12;-1.12;-1.12;1.55	5.06	3.88	0.44766	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.80854	0.4703	L	0.34521	1.04	0.54753	D	0.99998	D;D;D;D;D;D	0.89917	0.991;0.978;0.996;0.999;1.0;0.997	D;D;D;D;D;D	0.80764	0.989;0.942;0.99;0.971;0.994;0.915	T	0.82559	-0.0397	10	0.72032	D	0.01	.	11.9656	0.53033	0.0:0.0:0.1448:0.8552	.	230;243;306;224;306;306	B4DYU5;E7EPQ4;Q13105-2;F5H411;B2RCP2;Q13105	.;.;.;.;.;ZBT17_HUMAN	R	306;306;225;224;243	ENSP00000364895:H306R;ENSP00000364885:H306R;ENSP00000438529:H224R;ENSP00000391002:H243R	ENSP00000364885:H306R	H	-	2	0	ZBTB17	16144029	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.819000	0.62664	1.898000	0.54952	0.459000	0.35465	CAC	.	.		0.716	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443		C	16271442	T	C	16271442	3	2	234	1	0	0	0	0	1	0	0	0	17542	1696	59	2	1534	2	ZBTB17	1	16271442	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	4680411	16271442	232979179	2	32582										
PADI4	23569	hgsc.bcm.edu	37	chr1	17690224	17690224	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tgcgcagaaagcccttctccTtcaagtggtggaacatggtg	12	10	2	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:17690224T>A	ENST00000375448.4	+	16	1992	c.1966T>A	c.(1966-1968)Ttc>Atc	p.F656I		NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	656					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	GCCCTTCTCCTTCAAGTGGTG	0.597																																					p.F656I		Atlas-SNP	.											.	PADI4	70	.	0			c.T1966A						.						82	68	73					1																	17690224		2203	4300	6503	SO:0001583	missense	23569	exon16			TTCTCCTTCAAGT	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"Peptidyl arginine deiminases"	18368	protein-coding gene	gene with protein product		605347	"peptidyl arginine deiminase, type V"	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.1966T>A	chr1.hg19:g.17690224T>A	ENSP00000364597:p.Phe656Ile	134.0	0.0		129.0	52.0	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	hg19	CCDS180.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.952279	0.73787	.	.	ENSG00000159339	ENST00000375448	T	0.32753	1.44	4.62	3.46	0.39613	Protein-arginine deiminase, C-terminal (1);	0.123147	0.56097	D	0.000036	T	0.52092	0.1713	M	0.92459	3.31	0.33086	D	0.537281	D	0.53619	0.961	P	0.55508	0.777	T	0.65623	-0.6123	10	0.59425	D	0.04	-25.0211	5.6269	0.17487	0.0:0.0899:0.174:0.736	.	656	Q9UM07	PADI4_HUMAN	I	656	ENSP00000364597:F656I	ENSP00000364597:F656I	F	+	1	0	PADI4	17562811	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	3.157000	0.50716	0.691000	0.31592	0.459000	0.35465	TTC	.	.		0.597	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387		A	17690224	T	A	17690224	3	1	234	1	0	0	0	0	1	0	0	0	11389	1609	56	4	2028	4	PADI4	1	17690224	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	1418782	17690224	231560397	3	32583										
PAX7	5081	hgsc.bcm.edu	37	chr1	19018334	19018334	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gacgcagtcggaccacattcAcggccgagcagctggaggag	15	12	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:19018334A>T	ENST00000375375.3	+	5	1271	c.673A>T	c.(673-675)Acg>Tcg	p.T225S	PAX7_ENST00000400661.3_Missense_Mutation_p.T223S|PAX7_ENST00000420770.2_Missense_Mutation_p.T225S	NM_002584.2|NM_013945.2	NP_002575.1|NP_039236.1	P23759	PAX7_HUMAN	paired box 7	225					anatomical structure morphogenesis (GO:0009653)|cartilage development (GO:0051216)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic skeletal system development (GO:0048706)|muscle tissue morphogenesis (GO:0060415)|negative regulation of apoptotic process (GO:0043066)|neuron fate commitment (GO:0048663)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell fate commitment (GO:0010453)|regulation of protein binding (GO:0043393)|skeletal muscle satellite cell commitment (GO:0014813)|skeletal muscle tissue regeneration (GO:0043403)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX7/FOXO1(197)	breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)	31		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		GACCACATTCACGGCCGAGCA	0.627			T	FOXO1A	alveolar rhabdomyosarcoma																																p.T225S		Atlas-SNP	.		Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	.	PAX7	127	.	0			c.A673T						.						42	36	38					1																	19018334		2202	4300	6502	SO:0001583	missense	5081	exon5			ACATTCACGGCCG	X96743	CCDS186.1, CCDS44074.1, CCDS44075.1	1p36.13	2011-06-20	2007-07-12		ENSG00000009709	ENSG00000009709		"Paired boxes", "Homeoboxes / PRD class"	8621	protein-coding gene	gene with protein product		167410	"paired box gene 7"			7981748, 8431641	Standard	NM_001135254		Approved	Hup1	uc001bay.3	P23759	OTTHUMG00000002433	ENST00000375375.3:c.673A>T	chr1.hg19:g.19018334A>T	ENSP00000364524:p.Thr225Ser	158.0	0.0		165.0	53.0	NM_002584	E9PFV9|Q0VA99|Q2PJS5	Missense_Mutation	SNP	ENST00000375375.3	hg19	CCDS186.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.406392	0.83230	.	.	ENSG00000009709	ENST00000375375;ENST00000420770;ENST00000400661	D;D;D	0.96774	-4.12;-4.12;-4.12	4.98	4.98	0.66077	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.95771	0.8624	N	0.22421	0.69	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.996;0.994;0.999	D	0.94598	0.7793	10	0.27082	T	0.32	.	13.4979	0.61436	1.0:0.0:0.0:0.0	.	225;223;225	E9PFV9;P23759-2;P23759	.;.;PAX7_HUMAN	S	225;225;223	ENSP00000364524:T225S;ENSP00000403389:T225S;ENSP00000383502:T223S	ENSP00000364524:T225S	T	+	1	0	PAX7	18890921	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.297000	0.96120	1.875000	0.54330	0.533000	0.62120	ACG	.	.		0.627	PAX7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006928.1	NM_002584		T	19018334	A	T	19018334	3	4	234	1	0	0	0	0	1	0	0	0	11493	159	6	4	691	4	PAX7	1	19018334	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	1328110	19018334	230232287	4	32584										
CSMD2	114784	hgsc.bcm.edu	37	chr1	33985196	33985196	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gtgggctggatgttgcggtcGtacattgggttctcaaatgt	15	6	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:33985196G>A	ENST00000373381.4	-	70	10994	c.10818C>T	c.(10816-10818)taC>taT	p.Y3606Y		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3462						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TGTTGCGGTCGTACATTGGGT	0.557																																					p.Y3462Y		Atlas-SNP	.											.	CSMD2	946	.	0			c.C10386T						.						320	270	287					1																	33985196		2203	4300	6503	SO:0001819	synonymous_variant	114784	exon69			GCGGTCGTACATT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.10818C>T	chr1.hg19:g.33985196G>A		73.0	0.0		124.0	55.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	hg19																																																																																				.	.		0.557	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	33985196	G	A	33985196	2	1	234	1	0	0	0	0	0	0	0	1	3947	1140	40	1		1	CSMD2	1	33985196	Silent	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	14966862	33985196	215265425	5	32585										
SLC2A1	6513	hgsc.bcm.edu	37	chr1	43393339	43393339	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	cagttggagaagcctgcaacGgcaatggcagctggacgtgg	16	9	0	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:43393339G>A	ENST00000426263.3	-	9	1393	c.1215C>T	c.(1213-1215)gcC>gcT	p.A405A	SLC2A1_ENST00000475162.1_Intron	NM_006516.2	NP_006507.2	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 1	405			A -> D (in GLUT1DS1). {ECO:0000269|PubMed:20129935}.		carbohydrate metabolic process (GO:0005975)|cellular response to glucose starvation (GO:0042149)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|protein complex assembly (GO:0006461)|regulation of insulin secretion (GO:0050796)|response to osmotic stress (GO:0006970)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|female pronucleus (GO:0001939)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|midbody (GO:0030496)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|identical protein binding (GO:0042802)|protein self-association (GO:0043621)|xenobiotic transporter activity (GO:0042910)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|pancreas(2)	13	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)	AGCCTGCAACGGCAATGGCAG	0.552																																					p.A405A		Atlas-SNP	.											.	SLC2A1	36	.	0			c.C1215T						.						69	65	66					1																	43393339		2203	4300	6503	SO:0001819	synonymous_variant	6513	exon9			TGCAACGGCAATG	K03195	CCDS477.1	1p34.2	2013-05-22			ENSG00000117394	ENSG00000117394		"Solute carriers"	11005	protein-coding gene	gene with protein product		138140	"human T-cell leukemia virus (I and II) receptor"	GLUT1, GLUT, HTLVR		8839927, 14622599, 18451999	Standard	NM_006516		Approved	DYT18	uc001cik.2	P11166	OTTHUMG00000007657	ENST00000426263.3:c.1215C>T	chr1.hg19:g.43393339G>A		179.0	0.0		213.0	88.0	NM_006516	A8K9S6|B2R620|D3DPX0|O75535|Q147X2	Silent	SNP	ENST00000426263.3	hg19	CCDS477.1																																																																																			.	.		0.552	SLC2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020358.2	NM_006516		A	43393339	G	A	43393339	2	1	234	1	0	0	0	0	0	0	0	1	14553	1103	39	1		1	SLC2A1	1	43393339	Silent	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	9408143	43393339	205857282	6	32586										
CYP4B1	1580	hgsc.bcm.edu	37	chr1	47278257	47278257	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	attatgatgtgctgaagcccTatgtggccgtgttcactgag	12	8	1	3	rs539678720		TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:47278257T>A	ENST00000271153.4	+	4	493	c.457T>A	c.(457-459)Tat>Aat	p.Y153N	CYP4B1_ENST00000371923.4_Missense_Mutation_p.Y153N|CYP4B1_ENST00000371919.4_Missense_Mutation_p.Y138N|CYP4B1_ENST00000452782.2_De_novo_Start_OutOfFrame			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	153					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	GCTGAAGCCCTATGTGGCCGT	0.592																																					p.Y153N		Atlas-SNP	.											.	CYP4B1	81	.	0			c.T457A						.						163	132	143					1																	47278257		2203	4300	6503	SO:0001583	missense	1580	exon4			AAGCCCTATGTGG	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"Cytochrome P450s"	2644	protein-coding gene	gene with protein product		124075	"cytochrome P450, subfamily IVB, polypeptide 1"				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.457T>A	chr1.hg19:g.47278257T>A	ENSP00000271153:p.Tyr153Asn	118.0	0.0		128.0	41.0	NM_000779	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Missense_Mutation	SNP	ENST00000271153.4	hg19	CCDS542.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.800886	0.90538	.	.	ENSG00000142973	ENST00000371923;ENST00000271153;ENST00000371919	T;T;T	0.70282	-0.47;-0.47;-0.47	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.87188	0.6115	M	0.90705	3.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;0.998	D	0.89728	0.3924	10	0.87932	D	0	.	16.3337	0.83051	0.0:0.0:0.0:1.0	.	138;153;153	Q8IZB0;P13584-2;P13584	.;.;CP4B1_HUMAN	N	153;153;138	ENSP00000360991:Y153N;ENSP00000271153:Y153N;ENSP00000360987:Y138N	ENSP00000271153:Y153N	Y	+	1	0	CYP4B1	47050844	1.000000	0.71417	0.994000	0.49952	0.853000	0.48598	5.968000	0.70413	2.260000	0.74910	0.482000	0.46254	TAT	.	.		0.592	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779		A	47278257	T	A	47278257	3	1	234	1	0	0	0	0	1	0	0	0	4187	1522	53	4	471	4	CYP4B1	1	47278257	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	3884918	47278257	201972364	7	32587										
PYGO2	90780	hgsc.bcm.edu	37	chr1	154931788	154931788	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gctggggagcccctgaccagGtctctggagaggagaagggc	18	10	1	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:154931788G>A	ENST00000368457.2	-	3	859	c.688C>T	c.(688-690)Cct>Tct	p.P230S	RP11-307C12.12_ENST00000605085.1_RNA|PYGO2_ENST00000483463.1_5'Flank|PYGO2_ENST00000368456.1_Missense_Mutation_p.P193S	NM_138300.3	NP_612157.1	Q9BRQ0	PYGO2_HUMAN	pygopus family PHD finger 2	230	Pro-rich.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|developmental growth (GO:0048589)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mammary gland development (GO:0030879)|palate development (GO:0060021)|positive regulation of chromatin binding (GO:0035563)|post-embryonic development (GO:0009791)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|spermatid nucleus differentiation (GO:0007289)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase regulator activity (GO:0035034)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)|skin(2)|urinary_tract(1)	10	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CCCTGACCAGGTCTCTGGAGA	0.637																																					p.P230S	NSCLC(87;357 1460 1955 21029 23522)	Atlas-SNP	.											.	PYGO2	32	.	0			c.C688T						.						28	33	31					1																	154931788		2203	4300	6503	SO:0001583	missense	90780	exon3			GACCAGGTCTCTG	BC006132	CCDS1075.1	1q22	2013-10-09	2013-10-09		ENSG00000163348	ENSG00000163348		"Zinc fingers, PHD-type"	30257	protein-coding gene	gene with protein product		606903	"pygopus homolog 2 (Drosophila)"			11988739	Standard	NM_138300		Approved		uc001fft.3	Q9BRQ0	OTTHUMG00000037370	ENST00000368457.2:c.688C>T	chr1.hg19:g.154931788G>A	ENSP00000357442:p.Pro230Ser	124.0	0.0		211.0	119.0	NM_138300	Q8WYZ4|Q96CY2	Missense_Mutation	SNP	ENST00000368457.2	hg19	CCDS1075.1	.	.	.	.	.	.	.	.	.	.	G	7.696	0.691987	0.15039	.	.	ENSG00000163348	ENST00000368457;ENST00000368456	T;T	0.43294	0.95;0.97	4.72	4.72	0.59763	.	0.475485	0.19349	N	0.116460	T	0.30355	0.0762	N	0.19112	0.55	0.39525	D	0.968574	D	0.69078	0.997	P	0.57911	0.829	T	0.03259	-1.1055	10	0.22109	T	0.4	-3.6966	14.7378	0.69430	0.0:0.0:1.0:0.0	.	230	Q9BRQ0	PYGO2_HUMAN	S	230;193	ENSP00000357442:P230S;ENSP00000357441:P193S	ENSP00000357441:P193S	P	-	1	0	PYGO2	153198412	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.146000	0.64845	2.454000	0.82982	0.462000	0.41574	CCT	.	.		0.637	PYGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090949.1	NM_138300		A	154931788	G	A	154931788	3	1	234	1	0	0	0	0	1	0	0	0	12879	1261	44	3	536	3	PYGO2	1	154931788	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	107653531	154931788	94318833	8	32588										
CLK2	1196	hgsc.bcm.edu	37	chr1	155239305	155239305	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tgagcggctaaatgtccggcTgcgcctcctccgccgtctgt	12	15	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:155239305T>A	ENST00000368361.4	-	3	688	c.373A>T	c.(373-375)Agc>Tgc	p.S125C	CLK2_ENST00000536801.1_Missense_Mutation_p.S125C|CLK2_ENST00000355560.4_Missense_Mutation_p.S124C|CLK2_ENST00000497188.1_5'Flank|CLK2_ENST00000361168.5_Missense_Mutation_p.S125C			P49760	CLK2_HUMAN	CDC-like kinase 2	125					negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			AATGTCCGGCTGCGCCTCCTC	0.592								Other conserved DNA damage response genes																													p.S125C		Atlas-SNP	.											.	CLK2	55	.	0			c.A373T						.						71	65	67					1																	155239305		2203	4300	6503	SO:0001583	missense	1196	exon3			TCCGGCTGCGCCT	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"CDC-like kinases"	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.373A>T	chr1.hg19:g.155239305T>A	ENSP00000357345:p.Ser125Cys	47.0	0.0		77.0	46.0	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Missense_Mutation	SNP	ENST00000368361.4	hg19		.	.	.	.	.	.	.	.	.	.	.	19.80	3.895106	0.72639	.	.	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000536801	T;T;T;T	0.56275	0.47;0.47;0.47;0.47	4.96	4.96	0.65561	.	0.583777	0.19910	N	0.103315	T	0.31638	0.0803	N	0.21282	0.65	0.49483	D	0.999798	P;D	0.54964	0.947;0.969	B;P	0.47162	0.339;0.54	T	0.08932	-1.0698	10	0.34782	T	0.22	.	13.6318	0.62200	0.0:0.0:0.0:1.0	.	125;125	P49760;P49760-3	CLK2_HUMAN;.	C	125;125;124;125	ENSP00000354856:S125C;ENSP00000357345:S125C;ENSP00000347759:S124C;ENSP00000441023:S125C	ENSP00000347759:S124C	S	-	1	0	CLK2	153505929	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.637000	0.83313	2.099000	0.63709	0.529000	0.55759	AGC	.	.		0.592	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993		A	155239305	T	A	155239305	3	1	234	1	0	0	0	0	1	0	0	0	3539	1580	55	4	1167	4	CLK2	1	155239305	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	307517	155239305	94011316	9	32589										
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161021132	161021132	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ccagggccaaggccagggccAgggccagggccagaggcagg	19	13	0	1	rs144785706	byFrequency	TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:161021132A>T	ENST00000368013.3	-	10	1712	c.1392T>A	c.(1390-1392)ccT>ccA	p.P464P	ARHGAP30_ENST00000368015.1_Silent_p.P287P|ARHGAP30_ENST00000368016.3_Silent_p.P464P	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	464					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			ggccagggccagggccagggc	0.622																																					p.P464P		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.T1392A						.						30	32	31					1																	161021132		2203	4299	6502	SO:0001819	synonymous_variant	257106	exon10			AGGGCCAGGGCCA	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"Rho GTPase activating proteins"	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.1392T>A	chr1.hg19:g.161021132A>T		66.0	0.0		103.0	33.0	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Silent	SNP	ENST00000368013.3	hg19	CCDS30918.1																																																																																			.	A|0.999;G|0.001		0.622	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		T	161021132	A	T	161021132	2	4	234	1	0	0	0	0	0	0	0	1	879	175	7	4		4	ARHGAP30	1	161021132	Silent	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	5781827	161021132	88229489	10	32590										
C1orf129	80133	hgsc.bcm.edu	37	chr1	170967477	170967477	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tttcttacccaaatttaaatCaaaattccagtttctcgtat	2	9	3	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:170967477C>A	ENST00000367758.3	+	15	1757	c.1658C>A	c.(1657-1659)tCa>tAa	p.S553*	MROH9_ENST00000367759.4_Intron	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	553																	AAATTTAAATCAAAATTCCAG	0.388																																					p.S553X		Atlas-SNP	.											.	.	.	.	0			c.C1658A						.						184	161	168					1																	170967477		1834	4085	5919	SO:0001587	stop_gained	80133	exon15			TTAAATCAAAATT	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"maestro heat-like repeat containing"	26287	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 129"	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.1658C>A	chr1.hg19:g.170967477C>A	ENSP00000356732:p.Ser553*	61.0	0.0		91.0	28.0	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Nonsense_Mutation	SNP	ENST00000367758.3	hg19	CCDS41436.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552741	0.65425	.	.	ENSG00000117501	ENST00000367758	.	.	.	3.5	0.416	0.16416	.	1.170700	0.06403	N	0.719257	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	2.8232	5.62	0.17451	0.0:0.6075:0.0:0.3925	.	.	.	.	X	553	.	ENSP00000356732:S553X	S	+	2	0	C1orf129	169234101	0.001000	0.12720	0.000000	0.03702	0.031000	0.12232	1.013000	0.29937	-0.018000	0.14079	0.446000	0.29264	TCA	.	.		0.388	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		A	170967477	C	A	170967477	4	1	234	1	0	0	0	0	0	1	0	0	1998	838	29	3	1712	3	C1orf129	1	170967477	Nonsense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	9946345	170967477	78283144	11	32591										
TNN	63923	hgsc.bcm.edu	37	chr1	175053028	175053028	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	caggaggtagctgaggtcacTgtgcccaagagcagtgaccc	14	11	1	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:175053028T>A	ENST00000239462.4	+	5	1304	c.1191T>A	c.(1189-1191)acT>acA	p.T397T		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	397	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		CTGAGGTCACTGTGCCCAAGA	0.532																																					p.T397T		Atlas-SNP	.											.	TNN	297	.	0			c.T1191A						.						133	108	116					1																	175053028		2203	4300	6503	SO:0001819	synonymous_variant	63923	exon5			GGTCACTGTGCCC	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1191T>A	chr1.hg19:g.175053028T>A		93.0	0.0		140.0	85.0	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	hg19	CCDS30943.1																																																																																			.	.		0.532	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		A	175053028	T	A	175053028	2	1	234	1	0	0	0	0	0	0	0	1	16338	1567	55	4		4	TNN	1	175053028	Silent	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	4085551	175053028	74197593	12	32592										
KIF14	9928	hgsc.bcm.edu	37	chr1	200558393	200558393	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aatcgctttttgttgacataTatttcctgttcaagatgctg	7	7	1	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:200558393T>C	ENST00000367350.4	-	18	3504	c.3066A>G	c.(3064-3066)atA>atG	p.I1022M		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1022	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						TGTTGACATATATTTCCTGTT	0.323																																					p.I1022M		Atlas-SNP	.											.	KIF14	156	.	0			c.A3066G						.						158	149	152					1																	200558393		2202	4300	6502	SO:0001583	missense	9928	exon18			GACATATATTTCC	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.3066A>G	chr1.hg19:g.200558393T>C	ENSP00000356319:p.Ile1022Met	89.0	0.0		122.0	70.0	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	hg19	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	T	13.06	2.123903	0.37533	.	.	ENSG00000118193	ENST00000367350	T	0.17054	2.3	5.25	-7.71	0.01254	.	0.360755	0.24630	N	0.036888	T	0.10078	0.0247	L	0.58101	1.795	0.09310	N	1	B	0.27625	0.183	B	0.25884	0.064	T	0.11616	-1.0580	10	0.48119	T	0.1	.	2.0133	0.03493	0.2909:0.2749:0.3139:0.1203	.	1022	Q15058	KIF14_HUMAN	M	1022	ENSP00000356319:I1022M	ENSP00000356319:I1022M	I	-	3	3	KIF14	198825016	0.000000	0.05858	0.000000	0.03702	0.946000	0.59487	-1.756000	0.01813	-1.000000	0.03438	0.454000	0.30748	ATA	.	.		0.323	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		C	200558393	T	C	200558393	3	2	234	1	0	0	0	0	1	0	0	0	8285	1396	49	2	1932	2	KIF14	1	200558393	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	25505365	200558393	48692228	13	32593										
SMYD2	56950	hgsc.bcm.edu	37	chr1	214504364	214504364	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gccatccgagacatggtcagAtatgcacgcaacgtcattga	10	11	2	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr1:214504364A>T	ENST00000366957.5	+	9	910	c.888A>T	c.(886-888)agA>agT	p.R296S	SMYD2_ENST00000491455.1_3'UTR|SMYD2_ENST00000415093.2_Intron	NM_020197.2	NP_064582.2	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	296					negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|RNA polymerase II core binding (GO:0000993)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		ACATGGTCAGATATGCACGCA	0.507																																					p.R296S		Atlas-SNP	.											.	SMYD2	40	.	0			c.A888T						.						138	135	136					1																	214504364		2203	4300	6503	SO:0001583	missense	56950	exon9			GGTCAGATATGCA	AF226053	CCDS31022.1	1q32.3	2011-07-01			ENSG00000143499	ENSG00000143499		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	20982	protein-coding gene	gene with protein product		610663					Standard	NM_020197		Approved	HSKM-B, ZMYND14, KMT3C	uc021pix.1	Q9NRG4	OTTHUMG00000037066	ENST00000366957.5:c.888A>T	chr1.hg19:g.214504364A>T	ENSP00000355924:p.Arg296Ser	156.0	0.0		177.0	52.0	NM_020197	B2R9P9|I6L9H7|Q4V765|Q5VSH9|Q96AI4	Missense_Mutation	SNP	ENST00000366957.5	hg19	CCDS31022.1	.	.	.	.	.	.	.	.	.	.	A	17.13	3.310795	0.60414	.	.	ENSG00000143499	ENST00000366957;ENST00000416415	T	0.17528	2.27	5.84	2.32	0.28847	.	0.687749	0.15232	N	0.273343	T	0.10637	0.0260	L	0.36672	1.1	0.80722	D	1	B;B	0.26902	0.068;0.163	B;B	0.18263	0.011;0.021	T	0.14090	-1.0485	10	0.08599	T	0.76	-1.9832	8.1984	0.31411	0.781:0.0:0.219:0.0	.	296;280	Q9NRG4;Q05C86	SMYD2_HUMAN;.	S	296;15	ENSP00000355924:R296S	ENSP00000355924:R296S	R	+	3	2	SMYD2	212570987	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	1.064000	0.30579	0.148000	0.19059	0.533000	0.62120	AGA	.	.		0.507	SMYD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089998.1	NM_020197		T	214504364	A	T	214504364	3	4	234	1	0	0	0	0	1	0	0	0	14837	330	12	4	922	4	SMYD2	1	214504364	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	13945971	214504364	34746257	14	32594										
PXDN	7837	hgsc.bcm.edu	37	chr2	1652300	1652300	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	atgggctggaagttctcgtcCagccggtaaagcagtgggtt	15	8	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:1652300C>T	ENST00000252804.4	-	17	3302	c.3252G>A	c.(3250-3252)ctG>ctA	p.L1084L		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1084					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		AGTTCTCGTCCAGCCGGTAAA	0.577																																					p.L1084L		Atlas-SNP	.											.	PXDN	255	.	0			c.G3252A						.						47	57	54					2																	1652300		2163	4263	6426	SO:0001819	synonymous_variant	7837	exon17			CTCGTCCAGCCGG	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.3252G>A	chr2.hg19:g.1652300C>T		70.0	0.0		75.0	32.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	hg19	CCDS46221.1																																																																																			.	.		0.577	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1652300	C	T	1652300	2	4	234	1	0	0	0	0	0	0	0	1	12862	581	21	3		3	PXDN	2	1652300	Silent	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10		1652300	241547073	15	32595										
DNAJC27	51277	hgsc.bcm.edu	37	chr2	25179973	25179973	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tttcaaagtacaggaaccctTtgctttcagcccaaagacgt	7	11	2	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:25179973T>G	ENST00000264711.2	-	5	656	c.467A>C	c.(466-468)aAa>aCa	p.K156T	DNAJC27_ENST00000468467.1_5'Flank|DNAJC27_ENST00000534855.1_Missense_Mutation_p.K85T	NM_001198559.1|NM_016544.2	NP_001185488.1|NP_057628.1	Q9NZQ0	DJC27_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 27	156					small GTPase mediated signal transduction (GO:0007264)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						CAGGAACCCTTTGCTTTCAGC	0.423																																					p.K156T		Atlas-SNP	.											.	DNAJC27	37	.	0			c.A467C						.						154	145	148					2																	25179973		2203	4300	6503	SO:0001583	missense	51277	exon5			AACCCTTTGCTTT		CCDS1716.1, CCDS74493.1	2p23.3	2011-09-02	2008-08-20	2008-08-20	ENSG00000115137	ENSG00000115137		"Heat shock proteins / DNAJ (HSP40)"	30290	protein-coding gene	gene with protein product		613527	"rab and DnaJ domain containing"	RBJ		14980719	Standard	NM_016544		Approved	RabJS	uc002rft.2	Q9NZQ0	OTTHUMG00000125524	ENST00000264711.2:c.467A>C	chr2.hg19:g.25179973T>G	ENSP00000264711:p.Lys156Thr	118.0	0.0		127.0	50.0	NM_016544	Q5JV88|Q86Y24	Missense_Mutation	SNP	ENST00000264711.2	hg19	CCDS1716.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.020881	0.54576	.	.	ENSG00000115137	ENST00000264711;ENST00000534855	T;T	0.76968	-1.06;-0.8	5.8	-0.989	0.10242	Small GTP-binding protein domain (1);	0.216129	0.53938	D	0.000056	T	0.74253	0.3692	M	0.65498	2.005	0.32586	N	0.527858	B;B	0.20780	0.039;0.048	B;B	0.34873	0.06;0.191	T	0.69982	-0.4997	10	0.32370	T	0.25	-12.6012	10.2276	0.43236	0.0:0.4994:0.0:0.5006	.	156;156	Q9NZQ0-3;Q9NZQ0	.;DJC27_HUMAN	T	156;85	ENSP00000264711:K156T;ENSP00000440086:K85T	ENSP00000264711:K156T	K	-	2	0	DNAJC27	25033477	0.925000	0.31364	0.990000	0.47175	0.996000	0.88848	1.217000	0.32455	-0.113000	0.11958	0.528000	0.53228	AAA	.	.		0.423	DNAJC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246855.3	NM_016544		G	25179973	T	G	25179973	3	3	234	1	0	0	0	0	1	0	0	0	4647	1841	64	5	366	5	DNAJC27	2	25179973	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	23527673	25179973	218019400	16	32596										
C2orf70	339778	hgsc.bcm.edu	37	chr2	26798930	26798930	+	Frame_Shift_Del	DEL	A	A	-													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ccatcttctccaccaaccccAacctcctgctgatggagcgc							TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:26798930delA	ENST00000329615.3	+	2	266	c.235delA	c.(235-237)aacfs	p.N79fs	C2orf70_ENST00000409392.1_Frame_Shift_Del_p.Q66fs	NM_001105519.1	NP_001098989.1	A6NJV1	CB070_HUMAN	chromosome 2 open reading frame 70	79						nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	13						CACCAACCCCAACCTCCTGCT	0.612																																					p.P78fs		Atlas-INDEL	.											.	C2orf70	26	.	0			c.234delC						.						114	125	121					2																	26798930		2079	4207	6286	SO:0001589	frameshift_variant	339778	exon2			.		CCDS42661.1	2p23.3	2011-05-09			ENSG00000173557	ENSG00000173557			27938	protein-coding gene	gene with protein product	"hypothetical protein LOC339778"						Standard	NM_001105519		Approved	LOC339778	uc010eyn.3	A6NJV1	OTTHUMG00000151994	ENST00000329615.3:c.235delA	chr2.hg19:g.26798930delA	ENSP00000332875:p.Asn79fs	121.0	0.0		123.0	45.0	NM_001105519		Frame_Shift_Del	DEL	ENST00000329615.3	hg19	CCDS42661.1																																																																																			.	.		0.612	C2orf70-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353258.1	NM_001105519		-	26798930	A	-	26798930	7	5	234	1	0	1	0	1	0	0	0	0	2192	130	5	0	241	0	C2orf70	2	26798930	Frame_Shift_Del	DEL	A	TCGA-DD-AAW1-01A-11D-A40P-10	1618957	26798930	216400443	17	32597										
TMEM131	23505	hgsc.bcm.edu	37	chr2	98543941	98543941	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	cttctattatgctctctgacTgaacgaatgctgtgaagaaa	8	8	2	4			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:98543941T>A	ENST00000186436.5	-	2	425	c.197A>T	c.(196-198)cAg>cTg	p.Q66L	TMEM131_ENST00000425805.2_Missense_Mutation_p.Q17L	NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	66						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						GCTCTCTGACTGAACGAATGC	0.289																																					p.Q66L		Atlas-SNP	.											.	TMEM131	258	.	0			c.A197T						.						72	67	69					2																	98543941		1871	4097	5968	SO:0001583	missense	23505	exon2			TCTGACTGAACGA	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.197A>T	chr2.hg19:g.98543941T>A	ENSP00000186436:p.Gln66Leu	904.0	1.0		870.0	353.0	NM_015348		Missense_Mutation	SNP	ENST00000186436.5	hg19	CCDS46368.1	.	.	.	.	.	.	.	.	.	.	T	14.46	2.542423	0.45280	.	.	ENSG00000075568	ENST00000186436;ENST00000425805	T	0.33654	1.4	5.16	3.98	0.46160	.	.	.	.	.	T	0.42832	0.1220	L	0.43923	1.385	0.37148	D	0.902029	D;B	0.58268	0.982;0.0	P;B	0.55545	0.778;0.002	T	0.45716	-0.9242	9	0.42905	T	0.14	.	11.3129	0.49375	0.0:0.0:0.153:0.847	.	17;66	B4DMG2;Q92545	.;TM131_HUMAN	L	66;17	ENSP00000186436:Q66L	ENSP00000186436:Q66L	Q	-	2	0	TMEM131	97910373	1.000000	0.71417	0.995000	0.50966	0.884000	0.51177	4.064000	0.57506	0.964000	0.38108	0.455000	0.32223	CAG	.	.		0.289	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		A	98543941	T	A	98543941	3	1	234	1	0	0	0	0	1	0	0	0	16059	1580	55	4	5614	4	TMEM131	2	98543941	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	71745011	98543941	144655432	18	32598										
DDX18	8886	hgsc.bcm.edu	37	chr2	118577227	118577227	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tgtcttttaaaaccaaagatAcgaaaaaagcaaaaactgaa	5	6	1	2	rs375147442		TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:118577227A>T	ENST00000263239.2	+	3	501	c.373A>T	c.(373-375)Acg>Tcg	p.T125S	DDX18_ENST00000474694.1_3'UTR	NM_006773.3	NP_006764.3	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	125					ATP catabolic process (GO:0006200)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AACCAAAGATACGAAAAAAGC	0.303											OREG0003814	type=REGULATORY REGION|Gene=DDX18|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T125S		Atlas-SNP	.											.	DDX18	79	.	0			c.A373T						.						40	39	39					2																	118577227		2203	4300	6503	SO:0001583	missense	8886	exon3			AAAGATACGAAAA	X98743	CCDS2120.1	2q21.2	2008-02-05	2003-06-13		ENSG00000088205	ENSG00000088205		"DEAD-boxes"	2741	protein-coding gene	gene with protein product		606355	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-regulated)"			8861962	Standard	NM_006773		Approved	MrDb	uc002tlh.1	Q9NVP1	OTTHUMG00000058521	ENST00000263239.2:c.373A>T	chr2.hg19:g.118577227A>T	ENSP00000263239:p.Thr125Ser	586.0	0.0	1489	528.0	204.0	NM_006773	Q6GTZ9|Q6IAU4|Q92732|Q9BQB7	Missense_Mutation	SNP	ENST00000263239.2	hg19	CCDS2120.1	.	.	.	.	.	.	.	.	.	.	A	0.014	-1.602732	0.00849	.	.	ENSG00000088205	ENST00000263239	T	0.22743	1.94	3.49	-6.8	0.01709	.	4.794660	0.00397	N	0.000041	T	0.10551	0.0258	N	0.25647	0.755	0.09310	N	0.999996	B	0.02656	0.0	B	0.06405	0.002	T	0.27536	-1.0071	10	0.09084	T	0.74	3.6558	2.7859	0.05374	0.4351:0.1098:0.3381:0.1169	.	125	Q9NVP1	DDX18_HUMAN	S	125	ENSP00000263239:T125S	ENSP00000263239:T125S	T	+	1	0	DDX18	118293697	0.001000	0.12720	0.019000	0.16419	0.030000	0.12068	-0.321000	0.08018	-2.018000	0.00943	-1.699000	0.00722	ACG	.	.		0.303	DDX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129632.3	NM_006773		T	118577227	A	T	118577227	3	4	234	1	0	0	0	0	1	0	0	0	4347	391	14	4	383	4	DDX18	2	118577227	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	20033286	118577227	124622146	19	32599										
MMADHC	27249	hgsc.bcm.edu	37	chr2	150435994	150435994	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	caaactcatgtctttcacttGataaaggttctgctagaaca	6	9	4	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:150435994G>A	ENST00000428879.1	-	3	827	c.323C>T	c.(322-324)tCa>tTa	p.S108L	MMADHC_ENST00000303319.5_Missense_Mutation_p.S108L|MMADHC_ENST00000422782.2_Missense_Mutation_p.S108L			Q9H3L0	MMAD_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria	108			S -> SLAEPLS (in MMAHCD; cblD variant 2).		cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(2)	11						TCTTTCACTTGATAAAGGTTC	0.368																																					p.S108L		Atlas-SNP	.											.	MMADHC	20	.	0			c.C323T						.						96	94	95					2																	150435994		2203	4300	6503	SO:0001583	missense	27249	exon4			TCACTTGATAAAG	BC023995	CCDS2189.1	2q23	2011-05-12	2009-01-08	2009-01-08	ENSG00000168288	ENSG00000168288			25221	protein-coding gene	gene with protein product		611935	"chromosome 2 open reading frame 25"	C2orf25		18385497	Standard	NM_015702		Approved	CL25022, cblD	uc002txc.3	Q9H3L0	OTTHUMG00000155558	ENST00000428879.1:c.323C>T	chr2.hg19:g.150435994G>A	ENSP00000389060:p.Ser108Leu	156.0	0.0		171.0	8.0	NM_015702	B2R895|D3DP91|O95891	Missense_Mutation	SNP	ENST00000428879.1	hg19	CCDS2189.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551154	0.65311	.	.	ENSG00000168288	ENST00000303319;ENST00000428879;ENST00000422782	D;D;D	0.89196	-2.48;-2.48;-2.48	5.19	5.19	0.71726	.	0.467513	0.23008	N	0.052992	D	0.88559	0.6469	M	0.63428	1.95	0.38452	D	0.946974	P;B	0.36392	0.551;0.298	B;B	0.37833	0.23;0.259	D	0.88849	0.3318	10	0.39692	T	0.17	-15.3331	18.0635	0.89384	0.0:0.0:1.0:0.0	.	108;108	F8WEC0;Q9H3L0	.;MMAD_HUMAN	L	108	ENSP00000301920:S108L;ENSP00000389060:S108L;ENSP00000408331:S108L	ENSP00000301920:S108L	S	-	2	0	MMADHC	150144240	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.694000	0.68272	2.570000	0.86706	0.557000	0.71058	TCA	.	.		0.368	MMADHC-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332312.1	NM_015702		A	150435994	G	A	150435994	3	1	234	1	0	0	0	0	1	0	0	0	9651	1294	45	3	587	3	MMADHC	2	150435994	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	31858767	150435994	92763379	20	32600										
KCNH7	90134	hgsc.bcm.edu	37	chr2	163292032	163292032	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	agcagcgccatattctgaatAtcgatccagtttcctggcca	8	12	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:163292032A>T	ENST00000332142.5	-	8	1729	c.1630T>A	c.(1630-1632)Tat>Aat	p.Y544N	KCNH7_ENST00000328032.4_Missense_Mutation_p.Y537N	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	544					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TATTCTGAATATCGATCCAGT	0.453																																					p.Y544N	GBM(196;1492 2208 17507 24132 45496)	Atlas-SNP	.											.	KCNH7	378	.	0			c.T1630A						.						76	73	74					2																	163292032		2203	4300	6503	SO:0001583	missense	90134	exon8			CTGAATATCGATC	AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.1630T>A	chr2.hg19:g.163292032A>T	ENSP00000331727:p.Tyr544Asn	98.0	0.0		86.0	26.0	NM_033272	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	hg19	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	A	31	5.059558	0.93846	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.98512	-4.97;-4.97	6.16	6.16	0.99307	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98661	0.9551	M	0.64404	1.975	0.80722	D	1	D;P	0.89917	1.0;0.873	D;P	0.97110	1.0;0.588	D	0.99871	1.1096	10	0.66056	D	0.02	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	537;544	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	N	544;537	ENSP00000331727:Y544N;ENSP00000333781:Y537N	ENSP00000333781:Y537N	Y	-	1	0	KCNH7	163000278	1.000000	0.71417	0.992000	0.48379	0.953000	0.61014	9.339000	0.96797	2.367000	0.80283	0.528000	0.53228	TAT	.	.		0.453	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		T	163292032	A	T	163292032	3	4	234	1	0	0	0	0	1	0	0	0	8046	449	16	4	2062	4	KCNH7	2	163292032	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	12856038	163292032	79907341	21	32601										
DYNC1I2	1781	hgsc.bcm.edu	37	chr2	172563798	172563799	+	Splice_Site	INS	-	-	CCT													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gtctatttcactatttagtcINScctcctcctatgtctccatc							TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:172563798_172563799insCCT	ENST00000397119.3	+	5	413_414	c.246_247insCCT	c.(247-249)cct>CCTcct	p.83_83P>PP	DYNC1I2_ENST00000508530.1_Splice_Site_p.77_77P>PP|DYNC1I2_ENST00000263811.4_Splice_Site_p.77_77P>PP|DYNC1I2_ENST00000340296.4_Splice_Site_p.77_77P>PP|DYNC1I2_ENST00000358002.6_In_Frame_Ins_p.95_95P>PP|DYNC1I2_ENST00000409317.1_Splice_Site_p.77_77P>PP|DYNC1I2_ENST00000534253.2_In_Frame_Ins_p.83_83P>PP|DYNC1I2_ENST00000409453.1_Splice_Site_p.83_83P>PP|DYNC1I2_ENST00000409197.1_Splice_Site_p.77_77P>PP|DYNC1I2_ENST00000410079.3_In_Frame_Ins_p.95_95P>PP|DYNC1I2_ENST00000409773.1_Splice_Site_p.83_83P>PP|AC068039.1_ENST00000598148.1_Intron	NM_001378.1	NP_001369.1	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2	83					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|G2/M transition of mitotic cell cycle (GO:0000086)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|microtubule (GO:0005874)|vesicle (GO:0031982)	microtubule motor activity (GO:0003777)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.198)			ACTATTTAGTCCCTCCTCCTAT	0.421																																					p.V94delinsVP		Atlas-INDEL	.											.	DYNC1I2	43	.	0			c.282_283insCCT						.																																			SO:0001630	splice_region_variant	1781	exon4			.	AK055491	CCDS46450.1, CCDS63054.1, CCDS63056.1, CCDS63057.1	2q31.1	2013-01-10	2005-11-24	2005-11-24	ENSG00000077380	ENSG00000077380		"Cytoplasmic dyneins", "WD repeat domain containing"	2964	protein-coding gene	gene with protein product		603331	"dynein, cytoplasmic, intermediate polypeptide 2"	DNCI2		10049579, 16260502	Standard	NM_001378		Approved		uc002uha.2	Q13409	OTTHUMG00000154061	ENST00000397119.3:c.245-1->CCT	chr2.hg19:g.172563805_172563807dupCCT		277.0	0.0		269.0	91.0	NM_001271786	B7ZA04|D3DPD4|D3DPD5|D3DPD6|Q32LY9|Q53S84|Q5BJF8|Q7Z4X1|Q96NG7|Q96S87|Q9BXZ5|Q9NT58	In_Frame_Ins	INS	ENST00000397119.3	hg19	CCDS46450.1																																																																																			.	.		0.421	DYNC1I2-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333683.2	NM_001378	In_Frame_Ins	CCT	172563799	-	CCT	172563798	8	5	234	1	0	1	1	0	0	0	1	0	4845	869	30	0	260	0	DYNC1I2	2	172563798	Splice_Site	INS	-	TCGA-DD-AAW1-01A-11D-A40P-10	9271766	172563798	70635575	22	32602										
PLCL1	5334	hgsc.bcm.edu	37	chr2	198950034	198950034	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ttgtaaatctgttcaatacaGggattttgaactatctatga	7	5	3	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:198950034G>A	ENST00000428675.1	+	2	2191	c.1793G>A	c.(1792-1794)aGg>aAg	p.R598K	PLCL1_ENST00000437704.2_Missense_Mutation_p.R500K	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	598	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	GTTCAATACAGGGATTTTGAA	0.408																																					p.R598K		Atlas-SNP	.											PLCL1_ENST00000428675,NS,carcinoma,0,2	PLCL1	358	.	0			c.G1793A						.						67	70	69					2																	198950034		2203	4300	6503	SO:0001583	missense	5334	exon2			AATACAGGGATTT	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.1793G>A	chr2.hg19:g.198950034G>A	ENSP00000402861:p.Arg598Lys	119.0	0.0		127.0	59.0	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	hg19	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	G	0.280	-0.986934	0.02180	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.66099	-0.19;-0.19	5.36	5.36	0.76844	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.075564	0.56097	D	0.000027	T	0.35068	0.0919	N	0.04636	-0.2	0.38370	D	0.94485	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.34925	-0.9809	9	.	.	.	.	8.925	0.35634	0.0839:0.1536:0.7625:0.0	.	598;524	Q15111;B4DYZ4	PLCL1_HUMAN;.	K	598;500	ENSP00000402861:R598K;ENSP00000414138:R500K	.	R	+	2	0	PLCL1	198658279	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.751000	0.55165	2.793000	0.96121	0.561000	0.74099	AGG	.	.		0.408	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		A	198950034	G	A	198950034	3	1	234	1	0	0	0	0	1	0	0	0	12048	1000	35	3	1799	3	PLCL1	2	198950034	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	26386236	198950034	44249339	23	32603										
ZNF142	7701	hgsc.bcm.edu	37	chr2	219513536	219513536	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	agctcttcactgccagggtgGccctgcttcttgtgtttacg	11	12	3	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:219513536G>T	ENST00000449707.1	-	6	1516	c.1095C>A	c.(1093-1095)ggC>ggA	p.G365G	ZNF142_ENST00000411696.2_Silent_p.G365G	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	365					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		TGCCAGGGTGGCCCTGCTTCT	0.537											OREG0015202	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G365G	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.C1095A						.						69	68	69					2																	219513536		2078	4228	6306	SO:0001819	synonymous_variant	7701	exon6			AGGGTGGCCCTGC	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.1095C>A	chr2.hg19:g.219513536G>T		126.0	0.0	2259	121.0	49.0	NM_001105537	Q92510	Silent	SNP	ENST00000449707.1	hg19	CCDS42817.1																																																																																			.	.		0.537	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		T	219513536	G	T	219513536	2	4	234	1	0	0	0	0	0	0	0	1	17746	1190	42	3		3	ZNF142	2	219513536	Silent	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	20563502	219513536	23685837	24	32604										
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233709080	233709080	+	Splice_Site	DEL	A	A	-													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ttctctttttctttaacagcAttccaacctgcacaccagca							TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr2:233709080delA	ENST00000409547.1	+	27	3412	c.3101delA	c.(3100-3102)cat>ct	p.H1034fs	GIGYF2_ENST00000409451.3_Splice_Site_p.H1055fs|GIGYF2_ENST00000409196.3_Splice_Site_p.H1028fs|GIGYF2_ENST00000373563.4_Splice_Site_p.H1034fs|GIGYF2_ENST00000452341.2_3'UTR|GIGYF2_ENST00000373566.3_Splice_Site_p.H1056fs|GIGYF2_ENST00000409480.1_Splice_Site_p.H1056fs	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1034					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		CTTTAACAGCATTCCAACCTG	0.388																																					p.H1055fs		Atlas-INDEL	.											.	GIGYF2	288	.	0			c.3163delC						.						76	75	75					2																	233709080		2203	4300	6503	SO:0001630	splice_region_variant	26058	exon27			.	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3100-1A>-	chr2.hg19:g.233709080delA		107.0	0.0		108.0	50.0	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Frame_Shift_Del	DEL	ENST00000409547.1	hg19	CCDS33401.1																																																																																			.	.		0.388	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	Frame_Shift_Del	-	233709080	A	-	233709080	8	5	234	1	0	1	0	1	0	0	1	0	6386	231	8	0	3261	0	GIGYF2	2	233709080	Splice_Site	DEL	A	TCGA-DD-AAW1-01A-11D-A40P-10	14195544	233709080	9490293	25	32605										
NR2C2	7182	hgsc.bcm.edu	37	chr3	15084400	15084400	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gatgagctccaacataacagAagaacttttttttactggtc	7	8	0	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr3:15084400A>G	ENST00000425241.1	+	14	2038	c.1676A>G	c.(1675-1677)gAa>gGa	p.E559G	NR2C2_ENST00000393102.3_Missense_Mutation_p.E559G|NR2C2_ENST00000406272.2_Missense_Mutation_p.E559G|MRPS25_ENST00000496484.1_5'UTR|NR2C2_ENST00000323373.6_Missense_Mutation_p.E578G|NR2C2_ENST00000478572.1_3'UTR			P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2	559					cell differentiation (GO:0030154)|gene expression (GO:0010467)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						AACATAACAGAAGAACTTTTT	0.458																																					p.E578G		Atlas-SNP	.											.	NR2C2	44	.	0			c.A1733G						.						86	76	80					3																	15084400		2203	4300	6503	SO:0001583	missense	7182	exon15			TAACAGAAGAACT	L27586	CCDS2621.1, CCDS74905.1	3p25	2013-01-16			ENSG00000177463	ENSG00000177463		"Nuclear hormone receptors"	7972	protein-coding gene	gene with protein product		601426		TR4		8661150, 8016112	Standard	XM_005265428		Approved	TAK1, TR2R1, hTAK1	uc003bzi.3	P49116	OTTHUMG00000129839	ENST00000425241.1:c.1676A>G	chr3.hg19:g.15084400A>G	ENSP00000388387:p.Glu559Gly	222.0	0.0		229.0	106.0	NM_003298	A8K3H5|B6ZGT8|P55092	Missense_Mutation	SNP	ENST00000425241.1	hg19		.	.	.	.	.	.	.	.	.	.	A	24.4	4.531998	0.85812	.	.	ENSG00000177463	ENST00000425241;ENST00000323373;ENST00000393102;ENST00000406272	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	5.76	5.76	0.90799	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.000000	0.85682	D	0.000000	T	0.81403	0.4815	M	0.91612	3.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.85721	0.1325	10	0.87932	D	0	.	16.3634	0.83296	1.0:0.0:0.0:0.0	.	559;578	P49116;F2YGU2	NR2C2_HUMAN;.	G	559;578;559;559	ENSP00000388387:E559G;ENSP00000320447:E578G;ENSP00000376814:E559G;ENSP00000384463:E559G	ENSP00000320447:E578G	E	+	2	0	NR2C2	15059404	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	9.334000	0.96470	2.324000	0.78689	0.533000	0.62120	GAA	.	.		0.458	NR2C2-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000340729.1	NM_003298		G	15084400	A	G	15084400	3	3	234	1	0	0	0	0	1	0	0	0	10632	246	9	2	1787	2	NR2C2	3	15084400	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10		15084400	182938030	26	32606										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr3:41266098A>G	ENST00000349496.5	+	3	375	c.95A>G	c.(94-96)gAc>gGc	p.D32G	CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95G						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>G	chr3.hg19:g.41266098A>G	ENSP00000344456:p.Asp32Gly	189.0	1.0		197.0	98.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308122	0.81247	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69788	0.3150	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.74137	-0.3762	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	G	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25G;ENSP00000385604:D32G;ENSP00000412219:D32G;ENSP00000379486:D32G;ENSP00000344456:D32G;ENSP00000411226:D25G;ENSP00000379488:D32G;ENSP00000409302:D32G;ENSP00000401599:D32G	ENSP00000344456:D32G	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266098	A	G	41266098	3	3	234	1	0	0	0	0	1	0	0	0	4018	275	10	2	101	2	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	26181698	41266098	156756332	27	32607										
MST1	327	hgsc.bcm.edu	37	chr3	49721754	49721754	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ccctgccaccaacctcacagGcccccacaggggccaacagt	8	20	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr3:49721754G>A	ENST00000296456.5	+	0	3220				MST1_ENST00000449682.2_Missense_Mutation_p.A670V|AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		AACCTCACAGGCCCCCACAGG	0.567																																					p.A670V		Atlas-SNP	.											.	MST1	84	.	0			c.C2009T						.						25	30	28					3																	49721754		2199	4290	6489	SO:0001628	intergenic_variant	4485	exon17			TCACAGGCCCCCA	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		chr3.hg19:g.49721754G>A		193.0	0.0		204.0	72.0	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.009361	0.93346	.	.	ENSG00000173531	ENST00000449682	D	0.93426	-3.22	5.59	5.59	0.84812	.	0.000000	0.42172	D	0.000758	D	0.95689	0.8598	L	0.52759	1.655	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94744	0.7921	10	0.39692	T	0.17	.	19.5863	0.95490	0.0:0.0:1.0:0.0	.	670	G3XAK1	.	V	670	ENSP00000414287:A670V	ENSP00000414287:A670V	A	-	2	0	MST1	49696758	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.932000	0.92897	2.621000	0.88768	0.655000	0.94253	GCC	.	.		0.567	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			A	49721754	G	A	49721754	1	1	234	0	1	0	0	0	0	0	0	0	9899	1203	42	3		3	MST1	3	49721754	IGR	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	8455656	49721754	148300676	28	32608										
EPHA6	285220	hgsc.bcm.edu	37	chr3	97367160	97367160	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aaactctaacacttaacctcTgctattctgcataaattctg	3	11	4	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr3:97367160T>A	ENST00000514100.1	+	13	1425	c.1183T>A	c.(1183-1185)Tgc>Agc	p.C395S	EPHA6_ENST00000389672.5_Intron|EPHA6_ENST00000502694.1_Missense_Mutation_p.C331S	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	0	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						ACTTAACCTCTGCTATTCTGC	0.328																																					p.C331S		Atlas-SNP	.											.	EPHA6	439	.	0			c.T991A						.						100	92	94					3																	97367160		1814	4083	5897	SO:0001583	missense	285220	exon13			AACCTCTGCTATT	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000514100.1:c.1183T>A	chr3.hg19:g.97367160T>A	ENSP00000421711:p.Cys395Ser	128.0	0.0		82.0	40.0	NM_173655	D6RAL5	Missense_Mutation	SNP	ENST00000514100.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.18	1.280165	0.23392	.	.	ENSG00000080224	ENST00000514100;ENST00000502694	D;T	0.81499	-1.5;-1.37	3.77	-3.32	0.04973	.	.	.	.	.	T	0.67116	0.2859	.	.	.	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.54549	-0.8277	8	0.87932	D	0	.	5.1581	0.15046	0.1541:0.2544:0.0:0.5916	.	331;395	Q9UF33-2;D6RAL5	.;.	S	395;331	ENSP00000421711:C395S;ENSP00000423950:C331S	ENSP00000423950:C331S	C	+	1	0	EPHA6	98849850	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.804000	0.04535	-0.807000	0.04393	-1.414000	0.01117	TGC	.	.		0.328	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448		A	97367160	T	A	97367160	3	1	234	1	0	0	0	0	1	0	0	0	5173	1580	55	4	2941	4	EPHA6	3	97367160	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	47645406	97367160	100655270	29	32609										
WDR52	55779	hgsc.bcm.edu	37	chr3	113120468	113120468	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tatttccagtttcattcattTttatcatagagaagagattc	5	6	3	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr3:113120468T>A	ENST00000295868.2	-	10	1451	c.1289A>T	c.(1288-1290)aAa>aTa	p.K430I	WDR52-AS1_ENST00000498480.1_RNA|WDR52-AS1_ENST00000473329.1_RNA|WDR52_ENST00000393845.2_Missense_Mutation_p.K430I	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						TTCATTCATTTTTATCATAGA	0.348																																					p.K430I		Atlas-SNP	.											.	WDR52	151	.	0			c.A1289T						.						122	121	121					3																	113120468		2203	4300	6503	SO:0001583	missense	55779	exon10			TTCATTTTTATCA																												ENST00000295868.2:c.1289A>T	chr3.hg19:g.113120468T>A	ENSP00000295868:p.Lys430Ile	171.0	0.0		190.0	84.0	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	hg19	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.072432	0.76415	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.50813	2.62;0.73	5.47	5.47	0.80525	WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.68650	0.3024	M	0.77820	2.39	0.80722	D	1	D	0.76494	0.999	D	0.66716	0.946	T	0.73649	-0.3916	9	0.87932	D	0	.	15.5536	0.76173	0.0:0.0:0.0:1.0	.	430	Q96MT7	WDR52_HUMAN	I	430	ENSP00000377428:K430I;ENSP00000295868:K430I	ENSP00000295868:K430I	K	-	2	0	WDR52	114603158	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	3.465000	0.53064	2.066000	0.61787	0.533000	0.62120	AAA	.	.		0.348	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			A	113120468	T	A	113120468	3	1	234	1	0	0	0	0	1	0	0	0	17319	1841	64	4	4394	4	WDR52	3	113120468	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	15753308	113120468	84901962	30	32610										
ZBTB38	253461	hgsc.bcm.edu	37	chr3	141163168	141163168	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gacatacccacttctgccaaTgtacaaaatgcagagggtac	8	11	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr3:141163168T>C	ENST00000514251.1	+	4	2217	c.1938T>C	c.(1936-1938)aaT>aaC	p.N646N	ZBTB38_ENST00000321464.5_Silent_p.N647N|ZBTB38_ENST00000441582.2_Silent_p.N646N					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						CTTCTGCCAATGTACAAAATG	0.433																																					p.N646N		Atlas-SNP	.											.	ZBTB38	92	.	0			c.T1938C						.						94	91	92					3																	141163168		1919	4138	6057	SO:0001819	synonymous_variant	253461	exon8			TGCCAATGTACAA	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	26636	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 171"	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.1938T>C	chr3.hg19:g.141163168T>C		92.0	0.0		69.0	28.0	NM_001080412		Silent	SNP	ENST00000514251.1	hg19	CCDS43157.1																																																																																			.	.		0.433	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2			C	141163168	T	C	141163168	2	2	234	1	0	0	0	0	0	0	0	1	17554	1461	51	2		2	ZBTB38	3	141163168	Silent	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	28042700	141163168	56859262	31	32611										
C3orf58	205428	hgsc.bcm.edu	37	chr3	143704424	143704424	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gttggccatttgcaaagtatCttggagcttgtggaagaatg	13	5	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr3:143704424C>G	ENST00000315691.3	+	2	1232	c.697C>G	c.(697-699)Ctt>Gtt	p.L233V	C3orf58_ENST00000493396.1_Intron|C3orf58_ENST00000495414.1_Missense_Mutation_p.L24V|C3orf58_ENST00000441925.2_5'UTR	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	233					cardiac muscle cell proliferation (GO:0060038)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	COPI vesicle coat (GO:0030126)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TGCAAAGTATCTTGGAGCTTG	0.393																																					p.L233V		Atlas-SNP	.											.	C3orf58	36	.	0			c.C697G						.						152	151	152					3																	143704424		2203	4300	6503	SO:0001583	missense	205428	exon2			AAGTATCTTGGAG	AK095161	CCDS3130.1, CCDS46929.1	3q24	2013-12-06			ENSG00000181744	ENSG00000181744			28490	protein-coding gene	gene with protein product	"deleted in autism 1", "hypoxia and Akt induced stem cell factor"	612200				21283809, 23784961, 24269490	Standard	NM_173552		Approved	MGC33365, DIA1, HASF	uc003evo.3	Q8NDZ4	OTTHUMG00000159380	ENST00000315691.3:c.697C>G	chr3.hg19:g.143704424C>G	ENSP00000320081:p.Leu233Val	167.0	0.0		186.0	66.0	NM_173552	B2RCF2|B7Z1W3	Missense_Mutation	SNP	ENST00000315691.3	hg19	CCDS3130.1	.	.	.	.	.	.	.	.	.	.	C	14.57	2.573485	0.45902	.	.	ENSG00000181744	ENST00000315691;ENST00000495414;ENST00000492452	T	0.36878	1.23	5.24	4.37	0.52481	.	0.000000	0.64402	D	0.000001	T	0.46698	0.1406	M	0.73217	2.22	0.80722	D	1	P;D	0.56287	0.915;0.975	P;P	0.52957	0.596;0.714	T	0.45731	-0.9241	10	0.51188	T	0.08	.	8.7331	0.34512	0.0:0.7811:0.0:0.2189	.	24;233	B7Z1W3;Q8NDZ4	.;CC058_HUMAN	V	233;24;39	ENSP00000320081:L233V	ENSP00000320081:L233V	L	+	1	0	C3orf58	145187114	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.837000	0.55820	1.228000	0.43614	-0.136000	0.14681	CTT	.	.		0.393	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552		G	143704424	C	G	143704424	3	3	234	1	0	0	0	0	1	0	0	0	2238	913	32	4	737	4	C3orf58	3	143704424	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	2541256	143704424	54318006	32	32612										
CCDC39	339829	hgsc.bcm.edu	37	chr3	180378364	180378364	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ttgtaatttctcaccctgatTttattatcatcttgttgtgc	5	8	3	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr3:180378364T>G	ENST00000442201.2	-	4	629	c.510A>C	c.(508-510)aaA>aaC	p.K170N	CCDC39_ENST00000273654.4_Missense_Mutation_p.K254N	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	170					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TCACCCTGATTTTATTATCAT	0.373																																					p.K170N		Atlas-SNP	.											.	CCDC39	242	.	0			c.A510C						.						108	101	103					3																	180378364		1842	4087	5929	SO:0001583	missense	339829	exon4			CCTGATTTTATTA	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.510A>C	chr3.hg19:g.180378364T>G	ENSP00000405708:p.Lys170Asn	121.0	0.0		103.0	39.0	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	hg19	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.526912	0.64860	.	.	ENSG00000145075	ENST00000273654;ENST00000442201	T;T	0.22336	1.96;1.96	5.6	3.17	0.36434	.	0.136287	0.64402	D	0.000004	T	0.44030	0.1274	M	0.81341	2.54	0.41505	D	0.988306	D	0.76494	0.999	D	0.70935	0.971	T	0.30416	-0.9979	10	0.48119	T	0.1	-32.7871	10.1634	0.42866	0.0:0.1265:0.0:0.8735	.	170	Q9UFE4	CCD39_HUMAN	N	254;170	ENSP00000273654:K254N;ENSP00000405708:K170N	ENSP00000273654:K254N	K	-	3	2	CCDC39	181861058	1.000000	0.71417	0.998000	0.56505	0.761000	0.43186	1.066000	0.30604	0.399000	0.25367	0.477000	0.44152	AAA	.	.		0.373	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		G	180378364	T	G	180378364	3	3	234	1	0	0	0	0	1	0	0	0	2813	1838	64	5	2383	5	CCDC39	3	180378364	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	36673940	180378364	17644066	33	32613										
ADIPOQ	9370	hgsc.bcm.edu	37	chr3	186572279	186572279	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tatgaaggatgtgaaggtcaGcctcttcaagaaggacaagg	13	6	3	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr3:186572279G>A	ENST00000412955.2	+	3	662	c.521G>A	c.(520-522)aGc>aAc	p.S174N	ADIPOQ_ENST00000320741.2_Missense_Mutation_p.S174N|ADIPOQ_ENST00000444204.2_Missense_Mutation_p.S174N|ADIPOQ-AS1_ENST00000422718.1_RNA			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	174	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				adiponectin-activated signaling pathway (GO:0033211)|brown fat cell differentiation (GO:0050873)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to insulin stimulus (GO:0032869)|circadian rhythm (GO:0007623)|detection of oxidative stress (GO:0070994)|fatty acid beta-oxidation (GO:0006635)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|low-density lipoprotein particle clearance (GO:0034383)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of hormone secretion (GO:0046888)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular protein transport (GO:0090317)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metanephric mesenchymal cell migration (GO:2000590)|negative regulation of phagocytosis (GO:0050765)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of receptor binding (GO:1900121)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of synaptic transmission (GO:0050805)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|positive regulation of blood pressure (GO:0045777)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of metanephric glomerular visceral epithelial cell development (GO:2000478)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myeloid cell apoptotic process (GO:0033034)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal albumin absorption (GO:2000534)|positive regulation of signal transduction (GO:0009967)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|regulation of glucose metabolic process (GO:0010906)|response to activity (GO:0014823)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to linoleic acid (GO:0070543)|response to nutrient (GO:0007584)|response to sucrose (GO:0009744)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|sialic acid binding (GO:0033691)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(2)	16	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)		GTGAAGGTCAGCCTCTTCAAG	0.488																																					p.S174N		Atlas-SNP	.											.	ADIPOQ	35	.	0			c.G521A						.						146	130	136					3																	186572279		2203	4300	6503	SO:0001583	missense	9370	exon4			AGGTCAGCCTCTT	D45371	CCDS3284.1	3q27	2013-02-26	2005-01-24	2005-01-27	ENSG00000181092	ENSG00000181092		"Endogenous ligands"	13633	protein-coding gene	gene with protein product	"adipose most abundant gene transcript 1", "adiponectin precursor"	605441	"adipocyte, C1Q and collagen domain containing"	ACDC		7592907, 8631877	Standard	NM_001177800		Approved	ACRP30, AdipoQ, apM1, GBP28, adiponectin	uc003fra.3	Q15848	OTTHUMG00000156521	ENST00000412955.2:c.521G>A	chr3.hg19:g.186572279G>A	ENSP00000405611:p.Ser174Asn	130.0	0.0		158.0	74.0	NM_001177800	Q58EX9	Missense_Mutation	SNP	ENST00000412955.2	hg19	CCDS3284.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.928388	0.73327	.	.	ENSG00000181092	ENST00000412955;ENST00000320741;ENST00000444204	T;T;T	0.75477	-0.94;-0.94;-0.94	5.38	5.38	0.77491	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.054006	0.64402	D	0.000001	T	0.81880	0.4916	L	0.53671	1.685	0.46631	D	0.999134	D	0.67145	0.996	D	0.68353	0.957	T	0.76934	-0.2775	10	0.20046	T	0.44	.	16.9985	0.86375	0.0:0.0:1.0:0.0	.	174	Q15848	ADIPO_HUMAN	N	174	ENSP00000405611:S174N;ENSP00000320709:S174N;ENSP00000389814:S174N	ENSP00000320709:S174N	S	+	2	0	ADIPOQ	188054973	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.222000	0.65277	2.700000	0.92200	0.655000	0.94253	AGC	.	.		0.488	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344490.2	NM_004797		A	186572279	G	A	186572279	3	1	234	1	0	0	0	0	1	0	0	0	317	971	34	3	527	3	ADIPOQ	3	186572279	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	6193915	186572279	11450151	34	32614										
TMEM44	93109	hgsc.bcm.edu	37	chr3	194349215	194349215	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	actggtcctgtctgggtttcTgtgcacatctcagatagaga	11	9	3	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr3:194349215T>A	ENST00000392432.2	-	2	366	c.161A>T	c.(160-162)cAg>cTg	p.Q54L	TMEM44_ENST00000273580.7_Missense_Mutation_p.Q54L|TMEM44_ENST00000330115.3_5'UTR|TMEM44_ENST00000473092.1_Missense_Mutation_p.Q54L|TMEM44_ENST00000381975.3_Missense_Mutation_p.Q54L|TMEM44_ENST00000347147.4_Missense_Mutation_p.Q54L	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	54						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|urinary_tract(1)	8	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)		TCTGGGTTTCTGTGCACATCT	0.552																																					p.Q54L		Atlas-SNP	.											.	TMEM44	42	.	0			c.A161T						.						66	60	62					3																	194349215		2203	4300	6503	SO:0001583	missense	93109	exon2			GGTTTCTGTGCAC	AL833026	CCDS3308.1, CCDS33921.1, CCDS3308.2, CCDS54698.1, CCDS54699.1	3q29	2005-08-16			ENSG00000145014	ENSG00000145014			25120	protein-coding gene	gene with protein product							Standard	NM_138399		Approved	DKFZp686O18124	uc010hzn.3	Q2T9K0	OTTHUMG00000156023	ENST00000392432.2:c.161A>T	chr3.hg19:g.194349215T>A	ENSP00000376227:p.Gln54Leu	93.0	0.0		80.0	32.0	NM_138399	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	hg19	CCDS54699.1	.	.	.	.	.	.	.	.	.	.	T	10.61	1.397505	0.25205	.	.	ENSG00000145014	ENST00000392432;ENST00000273580;ENST00000347147;ENST00000381975;ENST00000473092	T;T;T;T;T	0.30981	1.94;1.52;1.52;1.51;1.52	5.23	1.3	0.21679	.	0.695149	0.13367	N	0.393223	T	0.13884	0.0336	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.20368	0.007;0.044;0.007;0.007;0.007	B;B;B;B;B	0.17979	0.009;0.02;0.013;0.009;0.009	T	0.20538	-1.0272	10	0.51188	T	0.08	-4.488	4.503	0.11874	0.0:0.1796:0.1661:0.6543	.	54;54;54;54;54	E9PGA9;Q2T9K0;Q2T9K0-4;Q2T9K0-2;Q2T9K0-6	.;TMM44_HUMAN;.;.;.	L	54	ENSP00000376227:Q54L;ENSP00000273580:Q54L;ENSP00000333355:Q54L;ENSP00000371402:Q54L;ENSP00000418674:Q54L	ENSP00000273580:Q54L	Q	-	2	0	TMEM44	195830504	0.194000	0.23325	0.020000	0.16555	0.394000	0.30568	0.091000	0.15046	-0.017000	0.14103	0.459000	0.35465	CAG	.	.		0.552	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399		A	194349215	T	A	194349215	3	1	234	1	0	0	0	0	1	0	0	0	16183	1580	55	4	1340	4	TMEM44	3	194349215	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	7776936	194349215	3673215	35	32615										
ZNF595	152687	hgsc.bcm.edu	37	chr4	53384	53384	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gataccctgaagtcgggaaaTggtgagtgtgcggggcaggg	19	6	0	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr4:53384T>A	ENST00000509152.2	+	1	187	c.2T>A	c.(1-3)aTg>aAg	p.M1K	ZNF595_ENST00000339368.6_3'UTR|ZNF595_ENST00000526473.2_Splice_Site_p.M1K			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	1					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		AGTCGGGAAATGGTGAGTGTG	0.642																																					p.M1K		Atlas-SNP	.											.	.	.	.	0			c.T2A						.						205	234	224					4																	53384		2203	4300	6503	SO:0001630	splice_region_variant	255403	exon1			GGGAAATGGTGAG	BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"Zinc fingers, C2H2-type", "-"	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.3+1T>A	chr4.hg19:g.53384T>A		88.0	0.0		119.0	6.0	NM_001039127		Missense_Mutation	SNP	ENST00000509152.2	hg19		.	.	.	.	.	.	.	.	.	.	T	13.72	2.321870	0.41096	.	.	ENSG00000197701	ENST00000509152;ENST00000526473	T;T	0.01092	5.35;5.41	0.51	0.51	0.16983	.	.	.	.	.	T	0.01320	0.0043	.	.	.	0.80722	D	1	B;B	0.22003	0.061;0.063	B;B	0.20577	0.03;0.026	T	0.54964	-0.8214	7	0.87932	D	0	.	.	.	.	.	1;1	Q8IYB9;Q3SXZ3	ZN595_HUMAN;ZN718_HUMAN	K	1	ENSP00000434858:M1K;ENSP00000437878:M1K	ENSP00000434858:M1K	M	+	2	0	ZNF595	43384	0.013000	0.17824	0.112000	0.21494	0.021000	0.10359	0.310000	0.19356	0.436000	0.26393	0.260000	0.18958	ATG	.	.		0.642	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000357817.2	NM_182524	Missense_Mutation	A	53384	T	A	53384	5	1	234	1	0	0	0	0	0	0	1	0	18040	1478	51	4	4	4	ZNF595	4	53384	Splice_Site	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10		53384	191100892	36	32616										
CLNK	116449	hgsc.bcm.edu	37	chr4	10522420	10522420	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tgaaagtgctcttacctctgTtttgcacactgtggttgctt	9	9	2	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr4:10522420T>C	ENST00000226951.6	-	15	1006	c.767A>G	c.(766-768)aAc>aGc	p.N256S		NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	256					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						CTTACCTCTGTTTTGCACACT	0.378																																					p.N256S	GBM(87;402 1286 6949 13902 35851)	Atlas-SNP	.											.	CLNK	85	.	0			c.A767G						.						140	125	130					4																	10522420		1858	4107	5965	SO:0001583	missense	116449	exon15			CCTCTGTTTTGCA	AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"SH2 domain containing"	17438	protein-coding gene	gene with protein product	"mast cell immunoreceptor signal transducer"	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.767A>G	chr4.hg19:g.10522420T>C	ENSP00000226951:p.Asn256Ser	128.0	0.0		109.0	45.0	NM_052964	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	hg19	CCDS47024.1	.	.	.	.	.	.	.	.	.	.	T	1.473	-0.559360	0.03967	.	.	ENSG00000109684	ENST00000226951;ENST00000429087	T	0.20463	2.07	3.58	-1.9	0.07665	.	1.529250	0.03878	N	0.276734	T	0.11110	0.0271	N	0.24115	0.695	0.35541	D	0.803033	B	0.02656	0.0	B	0.01281	0.0	T	0.45011	-0.9290	10	0.06365	T	0.9	-4.8736	4.3691	0.11239	0.0:0.4209:0.2125:0.3666	.	256	Q7Z7G1	CLNK_HUMAN	S	256;220	ENSP00000226951:N256S	ENSP00000226951:N256S	N	-	2	0	CLNK	10131518	0.002000	0.14202	0.585000	0.28666	0.534000	0.34807	-0.658000	0.05329	-0.327000	0.08551	0.379000	0.24179	AAC	.	.		0.378	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964		C	10522420	T	C	10522420	3	2	234	1	0	0	0	0	1	0	0	0	3549	1725	60	2	539	2	CLNK	4	10522420	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	10469036	10522420	180631856	37	32617										
HELQ	113510	hgsc.bcm.edu	37	chr4	84361091	84361091	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gacaaaaaactaagcaggaaTaattgggaataacttctgtc	8	6	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr4:84361091T>A	ENST00000295488.3	-	8	1895	c.1733A>T	c.(1732-1734)tAt>tTt	p.Y578F	HELQ_ENST00000510985.1_Missense_Mutation_p.Y511F	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	578	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						TAAGCAGGAATAATTGGGAAT	0.323								Other identified genes with known or suspected DNA repair function																													p.Y578F		Atlas-SNP	.											.	HELQ	95	.	0			c.A1733T						.						78	80	79					4																	84361091		2203	4299	6502	SO:0001583	missense	113510	exon8			CAGGAATAATTGG	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1733A>T	chr4.hg19:g.84361091T>A	ENSP00000295488:p.Tyr578Phe	648.0	2.0		718.0	287.0	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	hg19	CCDS3603.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.248743	0.39797	.	.	ENSG00000163312	ENST00000295488;ENST00000510985	T;D	0.91180	-0.52;-2.8	5.68	5.68	0.88126	Helicase, C-terminal (1);	0.429052	0.27567	N	0.018797	D	0.86016	0.5832	L	0.45352	1.415	0.47584	D	0.999463	P;B	0.36086	0.536;0.009	B;B	0.29862	0.108;0.011	D	0.84904	0.0844	10	0.32370	T	0.25	.	15.9199	0.79556	0.0:0.0:0.0:1.0	.	511;578	E3W980;Q8TDG4	.;HELQ_HUMAN	F	578;511	ENSP00000295488:Y578F;ENSP00000424539:Y511F	ENSP00000295488:Y578F	Y	-	2	0	HELQ	84580115	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.015000	0.88690	2.161000	0.67846	0.533000	0.62120	TAT	.	.		0.323	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		A	84361091	T	A	84361091	3	1	234	1	0	0	0	0	1	0	0	0	7056	1406	49	4	1616	4	HELQ	4	84361091	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	73838671	84361091	106793185	38	32618										
CDS1	1040	hgsc.bcm.edu	37	chr4	85564293	85564293	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ttcaaaagagccttcaaaatCaaggtgtgtgtttagattct	8	6	4	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr4:85564293C>A	ENST00000295887.5	+	11	1572	c.1149C>A	c.(1147-1149)atC>atA	p.I383I		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		CCTTCAAAATCAAGGTGTGTG	0.383																																					p.I383I		Atlas-SNP	.											.	CDS1	58	.	0			c.C1149A						.						109	116	113					4																	85564293		2203	4300	6503	SO:0001819	synonymous_variant	1040	exon11			CAAAATCAAGGTG	U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.1149C>A	chr4.hg19:g.85564293C>A		86.0	0.0		58.0	20.0	NM_001263	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000295887.5	hg19	CCDS3608.1																																																																																			.	.		0.383	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2			A	85564293	C	A	85564293	2	1	234	1	0	0	0	0	0	0	0	1	3179	816	29	3		3	CDS1	4	85564293	Silent	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	1203202	85564293	105589983	39	32619										
MEF2C	4208	hgsc.bcm.edu	37	chr5	88056848	88056849	+	Intron	INS	-	-	T													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	attatcaaattcttcattaaINStttttttgtatttttcttca							TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr5:88056848_88056849insT	ENST00000437473.2	-	4	820				MEF2C_ENST00000514015.1_Intron|MEF2C_ENST00000539796.1_Intron|MEF2C_ENST00000508569.1_Intron|MEF2C_ENST00000510942.1_Intron|MEF2C_ENST00000424173.2_Frame_Shift_Ins_p.I118fs|MEF2C_ENST00000340208.5_Frame_Shift_Ins_p.I138fs|MEF2C_ENST00000503554.1_Intron|MEF2C_ENST00000514028.1_Intron|MEF2C_ENST00000506554.1_Intron|MEF2C_ENST00000504921.2_Intron	NM_001193350.1|NM_002397.4	NP_001180279.1|NP_002388.2	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C						apoptotic process (GO:0006915)|B cell homeostasis (GO:0001782)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac ventricle formation (GO:0003211)|cartilage morphogenesis (GO:0060536)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to fluid shear stress (GO:0071498)|cellular response to glucose stimulus (GO:0071333)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to trichostatin A (GO:0035984)|chondrocyte differentiation (GO:0002062)|dentate gyrus development (GO:0021542)|embryonic viscerocranium morphogenesis (GO:0048703)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|germinal center formation (GO:0002467)|glomerulus morphogenesis (GO:0072102)|heart development (GO:0007507)|heart looping (GO:0001947)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|MAPK cascade (GO:0000165)|melanocyte differentiation (GO:0030318)|monocyte differentiation (GO:0030224)|muscle cell differentiation (GO:0042692)|muscle cell fate determination (GO:0007521)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myotube differentiation (GO:0014902)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nephron tubule epithelial cell differentiation (GO:0072160)|nervous system development (GO:0007399)|neural crest cell differentiation (GO:0014033)|neuron development (GO:0048666)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|platelet formation (GO:0030220)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primary heart field specification (GO:0003138)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of dendritic spine development (GO:0060998)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of germinal center formation (GO:0002634)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron apoptotic process (GO:0043523)|regulation of neurotransmitter secretion (GO:0046928)|regulation of sarcomere organization (GO:0060297)|regulation of synapse assembly (GO:0051963)|regulation of synaptic activity (GO:0060025)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|renal tubule morphogenesis (GO:0061333)|response to ischemia (GO:0002931)|response to virus (GO:0009615)|response to vitamin E (GO:0033197)|secondary heart field specification (GO:0003139)|sinoatrial valve morphogenesis (GO:0003185)|skeletal muscle tissue development (GO:0007519)|smooth muscle cell differentiation (GO:0051145)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|sarcomere (GO:0030017)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|miRNA binding (GO:0035198)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	40		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		TTCTTCATTAATTTTTTTGTAT	0.401										HNSCC(66;0.2)																											p.I138fs		Atlas-INDEL	.											MEF2C_ENST00000424173,caecum,carcinoma,0,2	MEF2C	184	.	0			c.413_414insA						.																																			SO:0001627	intron_variant	4208	exon6			.	AL833268	CCDS47244.1, CCDS47245.1, CCDS54877.1, CCDS54878.1	5q14.3	2013-07-03	2007-04-24		ENSG00000081189	ENSG00000081189		"Myocyte enhancer factors"	6996	protein-coding gene	gene with protein product		600662				8455629	Standard	NM_002397		Approved		uc003kjl.3	Q06413	OTTHUMG00000162634	ENST00000437473.2:c.402+152->A	chr5.hg19:g.88056855_88056855dupT		203.0	0.0		174.0	59.0	NM_001193347	C9JMZ0|D7F7N5|F8W7V7	Frame_Shift_Ins	INS	ENST00000437473.2	hg19	CCDS47245.1																																																																																			.	.		0.401	MEF2C-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369817.1	NM_002397		T	88056849	-	T	88056848	6	5	234	0	1	1	1	0	0	0	0	0	9466	101	4	0		0	MEF2C	5	88056848	Intron	INS	-	TCGA-DD-AAW1-01A-11D-A40P-10		88056848	92858412	40	32620										
PAM	5066	hgsc.bcm.edu	37	chr5	102360941	102360941	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aaagagccaggctcgggagtGcctgttgttctcattacaac	11	10	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr5:102360941G>T	ENST00000438793.3	+	23	3062	c.2592G>T	c.(2590-2592)gtG>gtT	p.V864V	PAM_ENST00000379787.4_Silent_p.V244V|PAM_ENST00000455264.2_Intron|PAM_ENST00000274392.9_Silent_p.V766V|PAM_ENST00000346918.2_Intron|PAM_ENST00000348126.2_Silent_p.V757V|PAM_ENST00000304400.7_Silent_p.V864V	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	864					central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	GCTCGGGAGTGCCTGTTGTTC	0.468																																					p.V864V		Atlas-SNP	.											.	PAM	180	.	0			c.G2592T						.						111	123	119					5																	102360941		2203	4300	6503	SO:0001819	synonymous_variant	5066	exon23			GGGAGTGCCTGTT	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.2592G>T	chr5.hg19:g.102360941G>T		198.0	0.0		200.0	89.0	NM_001177306	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Silent	SNP	ENST00000438793.3	hg19	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	G	3.524	-0.097064	0.07010	.	.	ENSG00000145730	ENST00000504691	.	.	.	5.69	1.52	0.23074	.	.	.	.	.	T	0.46737	0.1408	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32134	-0.9918	4	.	.	.	.	4.5002	0.11860	0.1416:0.0922:0.5848:0.1814	.	.	.	.	F	159	.	.	C	+	2	0	PAM	102388840	0.998000	0.40836	0.995000	0.50966	0.483000	0.33249	0.558000	0.23469	0.758000	0.33059	-0.205000	0.12727	TGC	.	.		0.468	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		T	102360941	G	T	102360941	2	4	234	1	0	0	0	0	0	0	0	1	11421	1306	46	3		3	PAM	5	102360941	Silent	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	14304093	102360941	78554319	41	32621										
PCDHGB7	56099	hgsc.bcm.edu	37	chr5	140799184	140799184	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	cgggccgcgcagccaggctaCctggtgaccaaggtggtggc	17	13	0	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr5:140799184C>T	ENST00000398594.2	+	1	1758	c.1758C>T	c.(1756-1758)taC>taT	p.Y586Y	PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	586	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCAGGCTACCTGGTGACCA	0.701																																					p.Y586Y		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.C1758T						.						28	33	31					5																	140799184		2195	4294	6489	SO:0001819	synonymous_variant	56099	exon1			AGGCTACCTGGTG	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1758C>T	chr5.hg19:g.140799184C>T		71.0	0.0		98.0	42.0	NM_018927	Q9UN63	Silent	SNP	ENST00000398594.2	hg19	CCDS47293.1																																																																																			.	.		0.701	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		T	140799184	C	T	140799184	2	4	234	1	0	0	0	0	0	0	0	1	11577	518	18	3		3	PCDHGB7	5	140799184	Silent	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	38438243	140799184	40116076	42	32622										
MYLIP	29116	hgsc.bcm.edu	37	chr6	16143347	16143347	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gcaatggaaaactatggcatAgaatggcattctgtgcggga	13	6	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr6:16143347A>T	ENST00000356840.3	+	4	759	c.561A>T	c.(559-561)atA>atT	p.I187I	MYLIP_ENST00000349606.4_Silent_p.I6I|MIR4639_ENST00000584938.1_RNA	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	187	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			ACTATGGCATAGAATGGCATT	0.453																																					p.I187I		Atlas-SNP	.											.	MYLIP	44	.	0			c.A561T						.						144	137	140					6																	16143347		2203	4300	6503	SO:0001819	synonymous_variant	29116	exon4			TGGCATAGAATGG	AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.561A>T	chr6.hg19:g.16143347A>T		154.0	0.0		177.0	75.0	NM_013262	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Silent	SNP	ENST00000356840.3	hg19	CCDS4536.1																																																																																			.	.		0.453	MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043864.1	NM_013262		T	16143347	A	T	16143347	2	4	234	1	0	0	0	0	0	0	0	1	10064	410	15	4		4	MYLIP	6	16143347	Silent	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10		16143347	154971720	43	32623										
CCHCR1	54535	hgsc.bcm.edu	37	chr6	31110818	31110818	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tggaggcctggggctggacaCcacagatttcttcttatcca	11	11	2	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr6:31110818C>A	ENST00000376266.5	-	17	2268	c.2146G>T	c.(2146-2148)Gtg>Ttg	p.V716L	CCHCR1_ENST00000396263.2_Missense_Mutation_p.V663L|CCHCR1_ENST00000451521.2_Missense_Mutation_p.V769L|CCHCR1_ENST00000396268.3_Missense_Mutation_p.V805L	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	716					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						GGGCTGGACACCACAGATTTC	0.557																																					p.V805L		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G2413T						.						236	275	261					6																	31110818		1511	2709	4220	SO:0001583	missense	54535	exon17			TGGACACCACAGA	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"chromosome 6 open reading frame 18"	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.2146G>T	chr6.hg19:g.31110818C>A	ENSP00000365442:p.Val716Leu	173.0	0.0		210.0	84.0	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	hg19	CCDS4695.1	.	.	.	.	.	.	.	.	.	.	C	10.27	1.304523	0.23736	.	.	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521	T;T;T;T	0.03358	3.96;3.98;3.96;3.96	4.9	4.02	0.46733	.	0.800888	0.10538	N	0.663055	T	0.01092	0.0036	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.26775	0.038;0.054;0.159;0.031	B;B;B;B	0.24541	0.05;0.054;0.054;0.03	T	0.47394	-0.9121	10	0.28530	T	0.3	-0.065	11.0522	0.47896	0.0:0.8124:0.1876:0.0	.	702;716;769;805	B4DIA2;Q8TD31;E9PE84;Q8TD31-2	.;CCHCR_HUMAN;.;.	L	805;716;663;702;769	ENSP00000379566:V805L;ENSP00000365442:V716L;ENSP00000379561:V663L;ENSP00000401039:V769L	ENSP00000365442:V716L	V	-	1	0	CCHCR1	31218797	0.000000	0.05858	0.005000	0.12908	0.035000	0.12851	0.467000	0.22035	1.258000	0.44101	0.549000	0.68633	GTG	.	.		0.557	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052		A	31110818	C	A	31110818	3	1	234	1	0	0	0	0	1	0	0	0	2879	507	18	3	210	3	CCHCR1	6	31110818	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	14967471	31110818	140004249	44	32624										
COL19A1	1310	hgsc.bcm.edu	37	chr6	70890392	70890392	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gagatataggtttccctggaCcagaaggaccctcaggaaag	12	9	1	2	rs369271643		TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr6:70890392C>G	ENST00000322773.4	+	44	2854	c.2752C>G	c.(2752-2754)Cca>Gca	p.P918A	COL19A1_ENST00000393344.1_Missense_Mutation_p.P540A	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	918	Collagen-like 10.|Triple-helical region 5 (COL5).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)	p.P918T(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						TTTCCCTGGACCAGAAGGACC	0.408																																					p.P918A		Atlas-SNP	.											COL19A1,NS,carcinoma,0,1	COL19A1	232	.	1	Substitution - Missense(1)	lung(1)	c.C2752G						.	C	ALA/PRO	0,4406		0,0,2203	149	149	149		2752	5.5	1	6		149	1,8599		0,1,4299	no	missense	COL19A1	NM_001858.4	27	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	probably-damaging	918/1143	70890392	1,13005	2203	4300	6503	SO:0001583	missense	1310	exon44			CCTGGACCAGAAG		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.2752C>G	chr6.hg19:g.70890392C>G	ENSP00000316030:p.Pro918Ala	143.0	0.0		124.0	49.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	hg19	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.365675	0.61513	0.0	1.16E-4	ENSG00000082293	ENST00000322773;ENST00000393344	D;D	0.98633	-5.04;-1.53	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000001	D	0.98134	0.9384	L	0.58101	1.795	0.51482	D	0.999921	D	0.89917	1.0	D	0.87578	0.998	D	0.97929	1.0319	10	0.05721	T	0.95	.	17.591	0.87997	0.0:1.0:0.0:0.0	.	918	Q14993	COJA1_HUMAN	A	918;540	ENSP00000316030:P918A;ENSP00000377013:P540A	ENSP00000316030:P918A	P	+	1	0	COL19A1	70947113	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.485000	0.53208	2.590000	0.87494	0.484000	0.47621	CCA	.	.		0.408	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			G	70890392	C	G	70890392	3	3	234	1	0	0	0	0	1	0	0	0	3678	507	18	4	2922	4	COL19A1	6	70890392	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	39779574	70890392	100224675	45	32625										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136582573	136582573	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aaaagtaccacgacctcttcCtcttttggcccaataatcca	4	14	2	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr6:136582573C>T	ENST00000531224.1	-	12	2839	c.2587G>A	c.(2587-2589)Gga>Aga	p.G863R	BCLAF1_ENST00000527759.1_Missense_Mutation_p.G861R|BCLAF1_ENST00000527536.1_Missense_Mutation_p.G814R|BCLAF1_ENST00000353331.4_Missense_Mutation_p.G812R|BCLAF1_ENST00000530767.1_Missense_Mutation_p.G690R|BCLAF1_ENST00000392348.2_Missense_Mutation_p.G812R|BCLAF1_ENST00000031135.9_Missense_Mutation_p.G81R|BCLAF1_ENST00000529917.1_5'UTR	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	863					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		CGACCTCTTCCTCTTTTGGCC	0.408																																					p.G863R	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.G2587A						.						197	198	197					6																	136582573		2203	4300	6503	SO:0001583	missense	9774	exon12			CTCTTCCTCTTTT	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.2587G>A	chr6.hg19:g.136582573C>T	ENSP00000435210:p.Gly863Arg	115.0	0.0		133.0	40.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.9|21.9	4.223322|4.223322	0.79464|0.79464	.|.	.|.	ENSG00000029363|ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000031135;ENST00000392348|ENST00000534762	T;T;T;T;T;T;T|T	0.57436|0.50813	2.08;1.61;1.62;1.88;2.07;0.4;1.61|0.73	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	0.000000|.	0.64402|.	D|.	0.000006|.	T|T	0.55832|0.55832	0.1945|0.1945	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	0.999;1.0;0.999;0.999;0.999|.	T|T	0.57283|0.57283	-0.7838|-0.7838	10|7	0.52906|0.62326	T|D	0.07|0.03	-18.0574|-18.0574	19.3961|19.3961	0.94607|0.94607	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	861;142;812;863;690|.	Q9NYF8-2;B7Z8J9;Q9NYF8-3;Q9NYF8;Q9NYF8-4|.	.;.;.;BCLF1_HUMAN;.|.	R|K	863;812;814;690;861;81;812|129	ENSP00000435210:G863R;ENSP00000229446:G812R;ENSP00000435441:G814R;ENSP00000436501:G690R;ENSP00000434826:G861R;ENSP00000031135:G81R;ENSP00000376159:G812R|ENSP00000437018:R129K	ENSP00000031135:G81R|ENSP00000437018:R129K	G|R	-|-	1|2	0|0	BCLAF1|BCLAF1	136624266|136624266	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.778000|4.778000	0.62368|0.62368	2.581000|2.581000	0.87130|0.87130	0.655000|0.655000	0.94253|0.94253	GGA|AGG	.	.		0.408	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		T	136582573	C	T	136582573	3	4	234	1	0	0	0	0	1	0	0	0	1383	690	24	3	183	3	BCLAF1	6	136582573	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	65692181	136582573	34532494	46	32626										
IKZF1	10320	hgsc.bcm.edu	37	chr7	50468300	50468300	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ctcgtcgcacataacgcgagGggagcaccgcttccacatga	11	14	0	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:50468300G>A	ENST00000331340.3	+	8	1690	c.1535G>A	c.(1534-1536)gGg>gAg	p.G512E	IKZF1_ENST00000357364.4_Missense_Mutation_p.G425E|IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000438033.1_Missense_Mutation_p.G425E|IKZF1_ENST00000439701.1_Missense_Mutation_p.G470E|IKZF1_ENST00000359197.5_Missense_Mutation_p.G470E|IKZF1_ENST00000346667.4_Missense_Mutation_p.G282E|IKZF1_ENST00000349824.4_Missense_Mutation_p.G369E|IKZF1_ENST00000343574.5_Missense_Mutation_p.G425E	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	512					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(28)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				ATAACGCGAGGGGAGCACCGC	0.632			"D,T"	BCL6	"ALL, DLBCL"																																p.G512E		Atlas-SNP	.		"Rec,Dom"	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	28	Unknown(28)	haematopoietic_and_lymphoid_tissue(28)	c.G1535A						.						47	48	48					7																	50468300		2151	4265	6416	SO:0001583	missense	10320	exon8			CGCGAGGGGAGCA	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13176	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 92"	603023	"zinc finger protein, subfamily 1A, 1 (Ikaros)"	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.1535G>A	chr7.hg19:g.50468300G>A	ENSP00000331614:p.Gly512Glu	51.0	0.0		43.0	14.0	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	hg19		.	.	.	.	.	.	.	.	.	.	G	33	5.239947	0.95240	.	.	ENSG00000185811	ENST00000346667;ENST00000343574;ENST00000359197;ENST00000349824;ENST00000357364;ENST00000331340;ENST00000438033;ENST00000439701	T;T;T;T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05;1.05;1.05;1.05	5.75	5.75	0.90469	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.69260	0.3091	.	.	.	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.72097	-0.4393	9	0.87932	D	0	-16.1653	19.9376	0.97146	0.0:0.0:1.0:0.0	.	425;282;425;470;512	Q13422-2;Q13422-6;Q13422-3;Q13422-7;Q13422	.;.;.;.;IKZF1_HUMAN	E	282;425;470;369;425;512;425;470	ENSP00000340080:G282E;ENSP00000342750:G425E;ENSP00000352123:G470E;ENSP00000342485:G369E;ENSP00000349928:G425E;ENSP00000331614:G512E;ENSP00000396554:G425E;ENSP00000413025:G470E	ENSP00000331614:G512E	G	+	2	0	IKZF1	50435794	1.000000	0.71417	0.728000	0.30774	0.925000	0.55904	9.758000	0.98927	2.711000	0.92665	0.655000	0.94253	GGG	.	.		0.632	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060		A	50468300	G	A	50468300	3	1	234	1	0	0	0	0	1	0	0	0	7623	1232	43	3	1561	3	IKZF1	7	50468300	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10		50468300	108670363	47	32627										
CHCHD2	51142	hgsc.bcm.edu	37	chr7	56170565	56170565	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ggacaaattacctaccgtttGcaagtcggcactgtttcagc	9	11	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:56170565G>C	ENST00000395422.3	-	3	602	c.440C>G	c.(439-441)gCa>gGa	p.A147G	snoU13_ENST00000458988.1_RNA	NM_016139.2	NP_057223.1	Q9Y6H1	CHCH2_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 2	147	CHCH.					mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(3)	5	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CCTACCGTTTGCAAGTCGGCA	0.423																																					p.A147G		Atlas-SNP	.											.	CHCHD2	10	.	0			c.C440G						.						75	69	71					7																	56170565		2203	4300	6503	SO:0001583	missense	51142	exon3			CCGTTTGCAAGTC	AF078845	CCDS5526.1	7p11.2	2014-07-14	2004-01-19	2004-01-21	ENSG00000106153	ENSG00000106153		"Coiled-coil-helix-coiled-coil-helix domain containing"	21645	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 17"	C7orf17		23303788	Standard	NM_016139		Approved		uc003tsa.3	Q9Y6H1	OTTHUMG00000129429	ENST00000395422.3:c.440C>G	chr7.hg19:g.56170565G>C	ENSP00000378812:p.Ala147Gly	68.0	0.0		69.0	25.0	NM_016139	Q498C3|Q6NZ50	Missense_Mutation	SNP	ENST00000395422.3	hg19	CCDS5526.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.346236	0.82022	.	.	ENSG00000106153	ENST00000395422	T	0.51574	0.7	5.35	5.35	0.76521	.	0.233360	0.42294	D	0.000731	T	0.74604	0.3738	M	0.92507	3.315	0.52099	D	0.999949	D	0.61697	0.99	D	0.66196	0.942	T	0.77365	-0.2615	10	0.32370	T	0.25	.	18.0268	0.89271	0.0:0.0:1.0:0.0	.	147	Q9Y6H1	CHCH2_HUMAN	G	147	ENSP00000378812:A147G	ENSP00000378812:A147G	A	-	2	0	CHCHD2	56138059	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	6.268000	0.72552	2.498000	0.84270	0.557000	0.71058	GCA	.	.		0.423	CHCHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251589.1	NM_016139		C	56170565	G	C	56170565	3	2	234	1	0	0	0	0	1	0	0	0	3318	1319	46	4	23	4	CHCHD2	7	56170565	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	5702265	56170565	102968098	48	32628										
CLIP2	7461	hgsc.bcm.edu	37	chr7	73790427	73790427	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	agagtggggtgctgcgggatAaatacgagaaggccctgaag	17	6	0	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:73790427A>T	ENST00000395060.1	+	9	1696	c.1696A>T	c.(1696-1698)Aaa>Taa	p.K566*	CLIP2_ENST00000361545.5_Nonsense_Mutation_p.K531*|CLIP2_ENST00000223398.6_Nonsense_Mutation_p.K566*			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	566						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						GCTGCGGGATAAATACGAGAA	0.657																																					p.K566X		Atlas-SNP	.											.	CLIP2	134	.	0			c.A1696T						.						28	31	30					7																	73790427		2203	4300	6503	SO:0001587	stop_gained	7461	exon10			CGGGATAAATACG	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"cytoplasmic linker 2", "Williams-Beuren syndrome chromosome region 3"	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.1696A>T	chr7.hg19:g.73790427A>T	ENSP00000378500:p.Lys566*	202.0	0.0		193.0	73.0	NM_003388	O14527|O43611	Nonsense_Mutation	SNP	ENST00000395060.1	hg19	CCDS5569.1	.	.	.	.	.	.	.	.	.	.	A	39	7.566374	0.98361	.	.	ENSG00000106665	ENST00000539676;ENST00000223398;ENST00000361545;ENST00000395060	.	.	.	5.02	5.02	0.67125	.	0.292075	0.37348	N	0.002131	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.6181	13.6265	0.62168	1.0:0.0:0.0:0.0	.	.	.	.	X	566;566;531;566	.	ENSP00000223398:K566X	K	+	1	0	CLIP2	73428363	1.000000	0.71417	0.997000	0.53966	0.946000	0.59487	5.963000	0.70372	1.894000	0.54839	0.456000	0.33151	AAA	.	.		0.657	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388		T	73790427	A	T	73790427	4	4	234	1	0	0	0	0	0	1	0	0	3535	363	13	4	1730	4	CLIP2	7	73790427	Nonsense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	17619862	73790427	85348236	49	32629										
PCLO	27445	hgsc.bcm.edu	37	chr7	82435068	82435068	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gcttccttcactgtccacgcTatacccactgccaaagctgc	6	17	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:82435068T>C	ENST00000333891.9	-	21	15206	c.14869A>G	c.(14869-14871)Agc>Ggc	p.S4957G		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTGTCCACGCTATACCCACTG	0.517																																					p.S4957G		Atlas-SNP	.											.	PCLO	1506	.	0			c.A14869G						.						56	57	57					7																	82435068		2039	4200	6239	SO:0001583	missense	27445	exon21			CCACGCTATACCC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14869A>G	chr7.hg19:g.82435068T>C	ENSP00000334319:p.Ser4957Gly	136.0	0.0		114.0	42.0	NM_033026		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.240496	0.39598	.	.	ENSG00000186472	ENST00000333891	T	0.20738	2.05	5.69	5.69	0.88448	.	.	.	.	.	T	0.17152	0.0412	L	0.29908	0.895	0.80722	D	1	B	0.20368	0.044	B	0.22753	0.041	T	0.03630	-1.1018	9	0.87932	D	0	.	10.3136	0.43723	0.0:0.0735:0.0:0.9265	.	4957	Q9Y6V0-5	.	G	4957	ENSP00000334319:S4957G	ENSP00000334319:S4957G	S	-	1	0	PCLO	82273004	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.221000	0.58574	2.154000	0.67381	0.455000	0.32223	AGC	.	.		0.517	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82435068	T	C	82435068	3	2	234	1	0	0	0	0	1	0	0	0	11592	1522	53	2	579	2	PCLO	7	82435068	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	8644641	82435068	76703595	50	32630										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87175239	87175239	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	atgagttcatcatgatttccTttctccacaatgactccatc	4	12	3	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:87175239T>A	ENST00000265724.3	-	16	2244	c.1827A>T	c.(1825-1827)aaA>aaT	p.K609N	ABCB1_ENST00000543898.1_Missense_Mutation_p.K545N	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	609	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CATGATTTCCTTTCTCCACAA	0.408																																					p.K609N		Atlas-SNP	.											.	ABCB1	263	.	0			c.A1827T						.						159	130	140					7																	87175239		2203	4300	6503	SO:0001583	missense	5243	exon16			ATTTCCTTTCTCC	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.1827A>T	chr7.hg19:g.87175239T>A	ENSP00000265724:p.Lys609Asn	119.0	0.0		140.0	47.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	hg19	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	T	16.94	3.260832	0.59431	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	T;T	0.67171	-0.25;-0.25	5.62	3.25	0.37280	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.624535	0.18300	N	0.145449	T	0.50582	0.1624	N	0.21448	0.665	0.33337	D	0.569323	B;B	0.26120	0.005;0.142	B;B	0.20184	0.004;0.028	T	0.57441	-0.7811	10	0.72032	D	0.01	-1.671	10.2704	0.43479	0.0:0.1341:0.0:0.8659	.	545;609	B5AK60;P08183	.;MDR1_HUMAN	N	390;609;545	ENSP00000265724:K609N;ENSP00000444095:K545N	ENSP00000265724:K609N	K	-	3	2	ABCB1	87013175	0.476000	0.25901	0.922000	0.36590	0.945000	0.59286	0.681000	0.25320	0.504000	0.28082	0.528000	0.53228	AAA	.	.		0.408	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		A	87175239	T	A	87175239	3	1	234	1	0	0	0	0	1	0	0	0	40	1606	56	4	2071	4	ABCB1	7	87175239	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	4740171	87175239	71963424	51	32631										
WASL	8976	hgsc.bcm.edu	37	chr7	123346348	123346348	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	taccagatttcctttgtcgaCggcccaaaaggtctgtaact	8	11	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:123346348C>T	ENST00000223023.4	-	4	751	c.419G>A	c.(418-420)cGt>cAt	p.R140H		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	140	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCTTTGTCGACGGCCCAAAAG	0.363																																					p.R140H		Atlas-SNP	.											.	WASL	70	.	0			c.G419A						.						68	68	68					7																	123346348		2203	4300	6503	SO:0001583	missense	8976	exon4			TGTCGACGGCCCA	D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.419G>A	chr7.hg19:g.123346348C>T	ENSP00000223023:p.Arg140His	90.0	0.0		113.0	40.0	NM_003941	A1JUI9|Q7Z746	Missense_Mutation	SNP	ENST00000223023.4	hg19	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.962656	0.74016	.	.	ENSG00000106299	ENST00000223023	D	0.99511	-6.05	5.77	5.77	0.91146	EVH1 (1);Pleckstrin homology-type (1);	0.052002	0.85682	D	0.000000	D	0.99199	0.9722	L	0.38838	1.175	0.80722	D	1	D	0.64830	0.994	D	0.71870	0.975	D	0.99904	1.1174	10	0.72032	D	0.01	-13.4183	20.3627	0.98863	0.0:1.0:0.0:0.0	.	140	O00401	WASL_HUMAN	H	140	ENSP00000223023:R140H	ENSP00000223023:R140H	R	-	2	0	WASL	123133584	0.993000	0.37304	0.925000	0.36789	0.964000	0.63967	3.476000	0.53143	2.885000	0.99019	0.655000	0.94253	CGT	.	.		0.363	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941		T	123346348	C	T	123346348	3	4	234	1	0	0	0	0	1	0	0	0	17271	536	19	1	1130	1	WASL	7	123346348	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	36171109	123346348	35792315	52	32632										
ZNF800	168850	hgsc.bcm.edu	37	chr7	127031567	127031569	+	In_Frame_Del	DEL	GTG	GTG	-													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ctacctggttcacagcatccGtgatgatggtggtcagtctg					rs138285367|rs559631790		TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	GTG	GTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:127031567_127031569delGTG	ENST00000393313.1	-	2	634_636	c.43_45delCAC	c.(43-45)cacdel	p.H15del	ZNF800_ENST00000393312.1_In_Frame_Del_p.H15del|ZNF800_ENST00000265827.3_In_Frame_Del_p.H15del			Q2TB10	ZN800_HUMAN	zinc finger protein 800	15	Poly-His.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						CACAGCATCCGTGATGATGGTGG	0.488																																					p.15_16del		Atlas-INDEL	.											.	ZNF800	78	.	0			c.44_46del						.																																			SO:0001651	inframe_deletion	168850	exon2			.	AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"Zinc fingers, C2H2-type"	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.43_45delCAC	chr7.hg19:g.127031567_127031569delGTG	ENSP00000376989:p.His15del	116.0	0.0		116.0	47.0	NM_176814	Q9HBN0	In_Frame_Del	DEL	ENST00000393313.1	hg19	CCDS5795.1																																																																																			.	.		0.488	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814		-	127031569	GTG	-	127031567	7	5	234	1	0	1	0	1	0	0	0	0	18184	1136	40	0	1969	0	ZNF800	7	127031567	In_Frame_Del	DEL	GTG	TCGA-DD-AAW1-01A-11D-A40P-10	3685219	127031567	32107096	53	32633										
DENND2A	27147	hgsc.bcm.edu	37	chr7	140223158	140223158	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ctcacaagccagctcgttccTctgttccagaatgtgttcca	7	14	2	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:140223158T>A	ENST00000275884.6	-	16	3031	c.2614A>T	c.(2614-2616)Agg>Tgg	p.R872W	DENND2A_ENST00000537639.1_Missense_Mutation_p.R872W|DENND2A_ENST00000496613.1_Missense_Mutation_p.R872W			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	872					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					AGCTCGTTCCTCTGTTCCAGA	0.602																																					p.R872W		Atlas-SNP	.											.	DENND2A	132	.	0			c.A2614T						.						87	90	89					7																	140223158		2018	4176	6194	SO:0001583	missense	27147	exon15			CGTTCCTCTGTTC	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.2614A>T	chr7.hg19:g.140223158T>A	ENSP00000275884:p.Arg872Trp	62.0	0.0		63.0	26.0	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Missense_Mutation	SNP	ENST00000275884.6	hg19	CCDS43659.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.124893	0.77436	.	.	ENSG00000146966	ENST00000275884;ENST00000537639;ENST00000496613	T;T;T	0.05996	3.36;3.36;3.36	5.49	1.45	0.22620	.	0.527177	0.21485	N	0.073771	T	0.19565	0.0470	M	0.64404	1.975	0.49389	D	0.999786	D	0.76494	0.999	D	0.70935	0.971	T	0.00653	-1.1625	10	0.66056	D	0.02	-26.1182	13.5321	0.61627	0.0:0.0:0.5319:0.4681	.	872	Q9ULE3	DEN2A_HUMAN	W	872	ENSP00000275884:R872W;ENSP00000442245:R872W;ENSP00000419654:R872W	ENSP00000275884:R872W	R	-	1	2	DENND2A	139869627	1.000000	0.71417	0.968000	0.41197	0.867000	0.49689	2.476000	0.45171	0.345000	0.23873	0.459000	0.35465	AGG	.	.		0.602	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		A	140223158	T	A	140223158	3	1	234	1	0	0	0	0	1	0	0	0	4431	1550	54	4	431	4	DENND2A	7	140223158	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	13191591	140223158	18915505	54	32634										
DENND2A	27147	hgsc.bcm.edu	37	chr7	140273641	140273641	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ctcttcttcctgccgttctgTgggtctccaaggttaaagaa	9	11	4	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:140273641T>A	ENST00000275884.6	-	5	1830	c.1413A>T	c.(1411-1413)ccA>ccT	p.P471P	DENND2A_ENST00000537639.1_Silent_p.P471P|DENND2A_ENST00000492720.1_Silent_p.P471P|DENND2A_ENST00000496613.1_Silent_p.P471P			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	471					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					TGCCGTTCTGTGGGTCTCCAA	0.512																																					p.P471P		Atlas-SNP	.											.	DENND2A	132	.	0			c.A1413T						.						198	199	198					7																	140273641		1936	4149	6085	SO:0001819	synonymous_variant	27147	exon4			GTTCTGTGGGTCT	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.1413A>T	chr7.hg19:g.140273641T>A		177.0	0.0		169.0	85.0	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	hg19	CCDS43659.1																																																																																			.	.		0.512	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		A	140273641	T	A	140273641	2	1	234	1	0	0	0	0	0	0	0	1	4431	1683	59	4		4	DENND2A	7	140273641	Silent	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	50483	140273641	18865022	55	32635										
TAS2R38	5726	hgsc.bcm.edu	37	chr7	141673266	141673266	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ggaagtgggtaagctggataGcactcaggaacagcagtcca	14	8	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:141673266G>T	ENST00000547270.1	-	1	307	c.224C>A	c.(223-225)gCt>gAt	p.A75D		NM_176817.4	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	75					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			NS(2)|breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)|stomach(1)	21	Melanoma(164;0.0171)					AAGCTGGATAGCACTCAGGAA	0.512																																					p.A75D		Atlas-SNP	.											.	TAS2R38	51	.	0			c.C224A						.						142	135	138					7																	141673266		2203	4300	6503	SO:0001583	missense	5726	exon1			TGGATAGCACTCA	AF494231	CCDS34765.1	7q34	2012-10-03	2003-05-29	2003-05-30	ENSG00000257138	ENSG00000257138		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	9584	protein-coding gene	gene with protein product		607751	"phenylthiocarbamide tasting"	PTC		12624758, 12584440	Standard	NM_176817		Approved	T2R61	uc003vwx.1	P59533	OTTHUMG00000158374	ENST00000547270.1:c.224C>A	chr7.hg19:g.141673266G>T	ENSP00000448219:p.Ala75Asp	96.0	0.0		97.0	42.0	NM_176817	A4D1U6|P59552|Q2M3E8|Q645W3|Q86UK3	Missense_Mutation	SNP	ENST00000547270.1	hg19	CCDS34765.1	.	.	.	.	.	.	.	.	.	.	G	10.35	1.326344	0.24080	.	.	ENSG00000257138	ENST00000547270	T	0.38722	1.12	5.1	4.2	0.49525	.	0.313947	0.29246	N	0.012719	T	0.44623	0.1302	M	0.70595	2.14	0.23401	N	0.99776	B	0.32968	0.392	B	0.38296	0.27	T	0.45934	-0.9227	10	0.56958	D	0.05	.	9.7331	0.40372	0.096:0.0:0.904:0.0	.	75	P59533	T2R38_HUMAN	D	75	ENSP00000448219:A75D	ENSP00000331291:A75D	A	-	2	0	TAS2R38	141319735	0.135000	0.22499	0.814000	0.32528	0.054000	0.15201	2.645000	0.46621	2.659000	0.90383	0.655000	0.94253	GCT	.	.		0.512	TAS2R38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350810.2	NM_176817		T	141673266	G	T	141673266	3	4	234	1	0	0	0	0	1	0	0	0	15590	971	34	3	781	3	TAS2R38	7	141673266	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	1399625	141673266	17465397	56	32636										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142563322	142563322	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ctcccaacccagcagcccccGtttgcccctgcctggagggc	10	20	0	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr7:142563322G>C	ENST00000392957.2	+	8	1826	c.1039G>C	c.(1039-1041)Gtt>Ctt	p.V347L	EPHB6_ENST00000411471.2_Missense_Mutation_p.V70L|EPHB6_ENST00000442129.1_Missense_Mutation_p.V347L	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	347	Cys-rich.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)	p.V332I(1)		NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					AGCAGCCCCCGTTTGCCCCTG	0.652																																					p.V347L		Atlas-SNP	.											EPHB6,NS,carcinoma,0,1	EPHB6	168	.	1	Substitution - Missense(1)	kidney(1)	c.G1039C						.						36	36	36					7																	142563322		2203	4300	6503	SO:0001583	missense	2051	exon8			GCCCCCGTTTGCC	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1039G>C	chr7.hg19:g.142563322G>C	ENSP00000376684:p.Val347Leu	63.0	0.0		47.0	2.0	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	hg19	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	G	0.209	-1.038157	0.02013	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.70986	-0.48;-0.48;-0.53	5.43	-8.87	0.00792	.	1.203620	0.06175	N	0.678426	T	0.48095	0.1481	N	0.25957	0.775	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.38887	-0.9640	10	0.08837	T	0.75	.	9.4073	0.38469	0.5527:0.2561:0.1912:0.0	.	347	O15197	EPHB6_HUMAN	L	347;347;70	ENSP00000376684:V347L;ENSP00000410789:V347L;ENSP00000409061:V70L	ENSP00000376684:V347L	V	+	1	0	EPHB6	142273444	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.698000	0.05092	-1.875000	0.01132	-1.615000	0.00797	GTT	.	.		0.652	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			C	142563322	G	C	142563322	3	2	234	1	0	0	0	0	1	0	0	0	5180	1145	40	4	1053	4	EPHB6	7	142563322	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	890056	142563322	16575341	57	32637										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110376804	110376804	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	caaataatccccaaagtcacAgaaataatacctaaatatgg	4	9	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr8:110376804A>T	ENST00000378402.5	+	2	206	c.102A>T	c.(100-102)acA>acT	p.T34T		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	34	IPT/TIG 1.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CCAAAGTCACAGAAATAATAC	0.323										HNSCC(38;0.096)																											p.T34T		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A102T						.						52	49	50					8																	110376804		1813	4070	5883	SO:0001819	synonymous_variant	93035	exon2			AGTCACAGAAATA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.102A>T	chr8.hg19:g.110376804A>T		66.0	0.0		141.0	98.0	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.		0.323	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110376804	A	T	110376804	2	4	234	1	0	0	0	0	0	0	0	1	11981	175	7	4		4	PKHD1L1	8	110376804	Silent	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10		110376804	35987218	58	32638										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100080860	100080860	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ggctgaagcatctctgcaccAtctggtatgggcaggagggg	16	9	2	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr9:100080860A>T	ENST00000357054.1	+	24	2559	c.1624A>T	c.(1624-1626)Atc>Ttc	p.I542F	CCDC180_ENST00000411667.2_Missense_Mutation_p.I400F|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000395220.1_Intron|CCDC180_ENST00000375202.2_Missense_Mutation_p.I403F|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Missense_Mutation_p.I403F			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	542						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											TCTCTGCACCATCTGGTATGG	0.607																																					p.I403F		Atlas-SNP	.											.	.	.	.	0			c.A1207T						.						61	52	55					9																	100080860		2203	4300	6503	SO:0001583	missense	0	exon10			TGCACCATCTGGT	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.1624A>T	chr9.hg19:g.100080860A>T	ENSP00000349562:p.Ile542Phe	47.0	0.0		56.0	29.0	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.53	2.264216	0.39995	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	4.61	-2.71	0.05986	.	0.685427	0.13838	N	0.359248	T	0.18425	0.0442	L	0.60455	1.87	0.09310	N	1	B;B;B;B	0.22003	0.063;0.009;0.025;0.009	B;B;B;B	0.19946	0.018;0.016;0.027;0.016	T	0.22487	-1.0215	10	0.40728	T	0.16	-4.2907	2.5815	0.04819	0.2864:0.4495:0.0983:0.1657	.	400;542;403;542	F5H149;B7ZMG3;Q9P1Z9-2;Q9P1Z9	.;.;.;CI174_HUMAN	F	542;403;400;426;403	ENSP00000349562:I542F;ENSP00000364348:I403F;ENSP00000414000:I400F;ENSP00000434727:I403F	ENSP00000349562:I542F	I	+	1	0	C9orf174	99120681	0.006000	0.16342	0.065000	0.19835	0.757000	0.42996	-0.142000	0.10311	-0.254000	0.09500	0.460000	0.39030	ATC	.	.		0.607	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		T	100080860	A	T	100080860	3	4	234	1	0	0	0	0	1	0	0	0	8249	217	8	4	1674	4	KIAA1529	9	100080860	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10		100080860	41132571	59	32639										
OR1L3	26735	hgsc.bcm.edu	37	chr9	125437433	125437434	+	Frame_Shift_Del	DEL	CT	CT	-													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gaatgtccaacctgacaagaCtctctgaatttattctcttg							TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr9:125437433_125437434delCT	ENST00000304820.2	+	1	119_120	c.25_26delCT	c.(25-27)ctcfs	p.L9fs		NM_001005234.1	NP_001005234.1	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L, member 3	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	16						CCTGACAAGACTCTCTGAATTT	0.411																																					p.8_9del		Atlas-INDEL	.											.	OR1L3	51	.	0			c.24_25del						.																																			SO:0001589	frameshift_variant	26735	exon1			.		CCDS35128.1	9q33.2	2013-09-20			ENSG00000171481	ENSG00000171481		"GPCR / Class A : Olfactory receptors"	8215	protein-coding gene	gene with protein product							Standard	NM_001005234		Approved	OR9-D	uc011lzb.2	Q8NH93	OTTHUMG00000020619	ENST00000304820.2:c.25_26delCT	chr9.hg19:g.125437437_125437438delCT	ENSP00000302863:p.Leu9fs	101.0	0.0		73.0	25.0	NM_001005234	B2RNF4|Q6IFN1	Frame_Shift_Del	DEL	ENST00000304820.2	hg19	CCDS35128.1																																																																																			.	.		0.411	OR1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053950.1			-	125437434	CT	-	125437433	7	5	234	1	0	1	0	1	0	0	0	0	10973	565	20	0	27	0	OR1L3	9	125437433	Frame_Shift_Del	DEL	CT	TCGA-DD-AAW1-01A-11D-A40P-10	25356573	125437433	15775998	60	32640										
USP54	159195	hgsc.bcm.edu	37	chr10	75283430	75283448	+	Frame_Shift_Del	DEL	CGAAGTTCCTGTTCCTGCG	CGAAGTTCCTGTTCCTGCG	-													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	actccttctcccgttttcttCgaagttcctgttcctgcgcc					rs199524864|rs370753309|rs199533863	byFrequency	TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	CGAAGTTCCTGTTCCTGCG	CGAAGTTCCTGTTCCTGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr10:75283430_75283448delCGAAGTTCCTGTTCCTGCG	ENST00000339859.4	-	16	2355_2373	c.2255_2273delCGCAGGAACAGGAACTTCG	c.(2254-2274)gcgcaggaacaggaacttcgafs	p.AQEQELR752fs	USP54_ENST00000408019.1_Frame_Shift_Del_p.AQEQELR752fs|USP54_ENST00000497106.1_5'UTR|USP54_ENST00000422491.2_5'UTR|USP54_ENST00000394811.2_5'UTR|USP54_ENST00000428547.1_Frame_Shift_Del_p.AQEQELR602fs			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	752					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					CCGTTTTCTTCGAAGTTCCTGTTCCTGCGCCCTCCTGGC	0.466																																					p.752_758del	Colon(195;880 2046 8854 25025 38456)	Atlas-INDEL	.											.	USP54	178	.	0			c.2256_2274del						.																																			SO:0001589	frameshift_variant	159195	exon15			.	AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"Ubiquitin-specific peptidases"	23513	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 29", "ubiquitin specific protease 54"	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.2255_2273delCGCAGGAACAGGAACTTCG	chr10.hg19:g.75283430_75283448delCGAAGTTCCTGTTCCTGCG	ENSP00000345216:p.Ala752fs	99.0	0.0		85.0	17.0	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Frame_Shift_Del	DEL	ENST00000339859.4	hg19	CCDS7329.2																																																																																			.	.		0.466	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		-	75283448	CGAAGTTCCTGTTCCTGCG	-	75283430	7	5	234	1	0	1	0	1	0	0	0	0	17100	884	31	0	2813	0	USP54	10	75283430	Frame_Shift_Del	DEL	CGAAGTTCCTGTTCCTGCG	TCGA-DD-AAW1-01A-11D-A40P-10		75283430	60251317	61	32641										
FAS	355	hgsc.bcm.edu	37	chr10	90768661	90768661	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tctaggcttagaagtggaaaTaaactgcacccggacccaga	10	10	1	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr10:90768661T>C	ENST00000355279.2	+	4	350	c.350T>C	c.(349-351)aTa>aCa	p.I117T	FAS_ENST00000357339.2_Missense_Mutation_p.I117T|FAS_ENST00000352159.4_Missense_Mutation_p.I117T|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000355740.2_Missense_Mutation_p.I117T			P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	GAAGTGGAAATAAACTGCACC	0.398																																					p.I117T		Atlas-SNP	.											.	FAS	47	.	0			c.T350C						.						223	247	239					10																	90768661		2203	4300	6503	SO:0001583	missense	355	exon4			TGGAAATAAACTG	M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"Tumor necrosis factor receptor superfamily", "CD molecules"	11920	protein-coding gene	gene with protein product	"TNF receptor superfamily member 6"	134637	"tumor necrosis factor receptor superfamily, member 6", "Fas (TNF receptor superfamily, member 6)"	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.350T>C	chr10.hg19:g.90768661T>C	ENSP00000347426:p.Ile117Thr	117.0	0.0		139.0	47.0	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355279.2	hg19	CCDS7395.1	.	.	.	.	.	.	.	.	.	.	T	1.430	-0.570482	0.03910	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000357339;ENST00000355279;ENST00000371875	D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74	4.2	-6.35	0.01975	TNFR/CD27/30/40/95 cysteine-rich region (3);	0.748086	0.12752	N	0.442089	T	0.55893	0.1949	N	0.00308	-1.67	0.09310	N	1	B;B;B	0.15473	0.007;0.013;0.004	B;B;B	0.24701	0.007;0.055;0.009	T	0.66344	-0.5947	10	0.02654	T	1	-5.664	1.1022	0.01686	0.1974:0.3021:0.2936:0.2069	.	117;117;117	P25445-6;Q5T9P3;P25445	.;.;TNR6_HUMAN	T	144;117;117;117;117;117	ENSP00000347979:I117T;ENSP00000345601:I117T;ENSP00000349896:I117T;ENSP00000347426:I117T	ENSP00000345601:I117T	I	+	2	0	FAS	90758641	0.000000	0.05858	0.037000	0.18230	0.220000	0.24768	-0.773000	0.04689	-1.254000	0.02485	-1.437000	0.01076	ATA	.	.		0.398	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2			C	90768661	T	C	90768661	3	2	234	1	0	0	0	0	1	0	0	0	5689	1406	49	2	364	2	FAS	10	90768661	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	15485231	90768661	44766086	62	32642										
TRPM5	29850	hgsc.bcm.edu	37	chr11	2436237	2436237	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tcttctggttcaggtccagcAgccacttctggcccgtgggc	12	14	4	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr11:2436237A>T	ENST00000155858.6	-	10	1528	c.1520T>A	c.(1519-1521)cTg>cAg	p.L507Q	TRPM5_ENST00000528453.1_Missense_Mutation_p.L507Q|TRPM5_ENST00000533060.1_Missense_Mutation_p.L507Q|TRPM5_ENST00000452833.1_Missense_Mutation_p.L509Q	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		CAGGTCCAGCAGCCACTTCTG	0.697																																					p.L507Q	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.T1520A						.						19	26	23					11																	2436237		2167	4262	6429	SO:0001583	missense	29850	exon10			TCCAGCAGCCACT	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"Voltage-gated ion channels / Transient receptor potential cation channels"	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.1520T>A	chr11.hg19:g.2436237A>T	ENSP00000155858:p.Leu507Gln	54.0	0.0		68.0	29.0	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	hg19	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	A	17.32	3.359442	0.61403	.	.	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	3.68	-7.35	0.01422	.	1.962480	0.02611	N	0.102143	T	0.71264	0.3319	L	0.42245	1.32	0.36686	D	0.879339	P;P;P	0.44195	0.809;0.828;0.565	B;P;P	0.47705	0.353;0.555;0.543	T	0.63954	-0.6520	10	0.20519	T	0.43	-1.3285	6.8708	0.24119	0.1962:0.0:0.5473:0.2565	.	507;509;507	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	Q	501;507;509;507;507;507	ENSP00000434383:L501Q;ENSP00000155858:L507Q;ENSP00000387965:L509Q;ENSP00000434121:L507Q;ENSP00000436809:L507Q	ENSP00000155858:L507Q	L	-	2	0	TRPM5	2392813	0.012000	0.17670	0.828000	0.32881	0.990000	0.78478	0.122000	0.15687	-1.643000	0.01519	0.402000	0.26972	CTG	.	.		0.697	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		T	2436237	A	T	2436237	3	4	234	1	0	0	0	0	1	0	0	0	16604	188	7	4	2037	4	TRPM5	11	2436237	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10		2436237	132570279	63	32643										
ANO5	203859	hgsc.bcm.edu	37	chr11	22257809	22257809	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	taacacttactcatctgcctAtccactccatgatgtatgta	4	12	2	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr11:22257809A>G	ENST00000324559.8	+	8	1066	c.749A>G	c.(748-750)tAt>tGt	p.Y250C		NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	250					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCATCTGCCTATCCACTCCAT	0.388																																					p.Y250C		Atlas-SNP	.											.	ANO5	162	.	0			c.A749G						.						125	107	113					11																	22257809		2203	4300	6503	SO:0001583	missense	203859	exon8			CTGCCTATCCACT	AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.749A>G	chr11.hg19:g.22257809A>G	ENSP00000315371:p.Tyr250Cys	111.0	0.0		97.0	41.0	NM_213599		Missense_Mutation	SNP	ENST00000324559.8	hg19	CCDS31444.1	.	.	.	.	.	.	.	.	.	.	A	14.84	2.656247	0.47467	.	.	ENSG00000171714	ENST00000324559	T	0.70631	-0.5	5.64	1.71	0.24356	.	0.222686	0.48286	D	0.000196	D	0.83672	0.5305	M	0.91140	3.18	0.53688	D	0.999979	D	0.63880	0.993	P	0.61275	0.886	D	0.84460	0.0593	10	0.87932	D	0	.	11.1309	0.48347	0.605:0.0:0.0:0.395	.	250	Q75V66	ANO5_HUMAN	C	250	ENSP00000315371:Y250C	ENSP00000315371:Y250C	Y	+	2	0	ANO5	22214385	0.995000	0.38212	0.994000	0.49952	0.616000	0.37450	2.161000	0.42358	0.075000	0.16796	0.455000	0.32223	TAT	.	.		0.388	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599		G	22257809	A	G	22257809	3	3	234	1	0	0	0	0	1	0	0	0	700	449	16	2	779	2	ANO5	11	22257809	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	19821572	22257809	112748707	64	32644										
OR5B21	219968	hgsc.bcm.edu	37	chr11	58274925	58274925	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	atcctctgaatggtgatgcaTatgaagaagtaagaaataag	10	4	1	5	rs146969149		TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr11:58274925T>A	ENST00000360374.2	-	1	653	c.654A>T	c.(652-654)atA>atT	p.I218I		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TGGTGATGCATATGAAGAAGT	0.468																																					p.I218I		Atlas-SNP	.											.	OR5B21	59	.	0			c.A654T						.						73	70	71					11																	58274925		2201	4295	6496	SO:0001819	synonymous_variant	219968	exon1			GATGCATATGAAG		CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"GPCR / Class A : Olfactory receptors"	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.654A>T	chr11.hg19:g.58274925T>A		150.0	0.0		142.0	51.0	NM_001005218		Silent	SNP	ENST00000360374.2	hg19	CCDS31552.1																																																																																			.	T|1.000;C|0.000		0.468	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218		A	58274925	T	A	58274925	2	1	234	1	0	0	0	0	0	0	0	1	11160	1396	49	4		4	OR5B21	11	58274925	Silent	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	36017116	58274925	76731591	65	32645										
MMP10	4319	hgsc.bcm.edu	37	chr11	102650037	102650037	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ttcccagactttcagagcttTctcaatggcagaatcaacag	7	11	3	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr11:102650037T>A	ENST00000279441.4	-	3	439	c.403A>T	c.(403-405)Aaa>Taa	p.K135*		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	135					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	TTCAGAGCTTTCTCAATGGCA	0.408																																					p.K135X		Atlas-SNP	.											.	MMP10	44	.	0			c.A403T						.						157	154	155					11																	102650037		2203	4299	6502	SO:0001587	stop_gained	4319	exon3			GAGCTTTCTCAAT	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"matrix metalloproteinase 10 (stromelysin 2)"	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.403A>T	chr11.hg19:g.102650037T>A	ENSP00000279441:p.Lys135*	134.0	0.0		133.0	48.0	NM_002425	B2R9X9|Q53HH9	Nonsense_Mutation	SNP	ENST00000279441.4	hg19	CCDS8321.1	.	.	.	.	.	.	.	.	.	.	t	13.95	2.388969	0.42308	.	.	ENSG00000166670	ENST00000279441;ENST00000539681	.	.	.	4.38	4.38	0.52667	.	0.815163	0.10845	N	0.627772	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.4803	0.38898	0.1577:0.0:0.0:0.8423	.	.	.	.	X	135	.	ENSP00000279441:K135X	K	-	1	0	MMP10	102155247	0.002000	0.14202	1.000000	0.80357	0.227000	0.25037	1.314000	0.33597	1.961000	0.56991	0.482000	0.46254	AAA	.	.		0.408	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1			A	102650037	T	A	102650037	4	1	234	1	0	0	0	0	0	1	0	0	9658	1792	62	4	1059	4	MMP10	11	102650037	Nonsense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	44375112	102650037	32356479	66	32646										
ZC3H12C	85463	hgsc.bcm.edu	37	chr11	110007788	110007788	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tgaaattttgcaagactttaAacctgaagagtcccagacta	7	8	0	5			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr11:110007788A>C	ENST00000278590.3	+	2	473	c.422A>C	c.(421-423)aAa>aCa	p.K141T	ZC3H12C_ENST00000528673.1_Missense_Mutation_p.K142T|ZC3H12C_ENST00000453089.2_Missense_Mutation_p.K110T	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	141							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		CAAGACTTTAAACCTGAAGAG	0.438																																					p.K141T		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.A422C						.						62	58	59					11																	110007788		1851	4092	5943	SO:0001583	missense	85463	exon2			ACTTTAAACCTGA		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.422A>C	chr11.hg19:g.110007788A>C	ENSP00000278590:p.Lys141Thr	116.0	0.0		82.0	29.0	NM_033390	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	hg19	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	a	13.47	2.246967	0.39697	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.36520	1.25;1.25;1.26	5.63	3.22	0.36961	.	0.805415	0.09259	U	0.826854	T	0.35158	0.0922	M	0.61703	1.905	0.39981	D	0.974919	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.07635	-1.0762	10	0.36615	T	0.2	-8.612	7.3993	0.26954	0.6548:0.2703:0.0749:0.0	.	142;141;141	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	T	141;142;110	ENSP00000278590:K141T;ENSP00000431821:K142T;ENSP00000413094:K110T	ENSP00000278590:K141T	K	+	2	0	ZC3H12C	109512998	0.588000	0.26799	0.999000	0.59377	0.987000	0.75469	1.352000	0.34033	0.372000	0.24591	0.528000	0.53228	AAA	.	.		0.438	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		C	110007788	A	C	110007788	3	2	234	1	0	0	0	0	1	0	0	0	17578	14	1	5	428	5	ZC3H12C	11	110007788	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	7357751	110007788	24998728	67	32647										
MLL	4297	hgsc.bcm.edu	37	chr11	118343010	118343011	+	Frame_Shift_Ins	INS	-	-	A													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aagcaactcttacagagggcINSaaaaaagggggctcaaaaga							TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr11:118343010_118343011insA	ENST00000389506.5	+	3	1136_1137	c.1136_1137insA	c.(1135-1140)gcaaaafs	p.AK379fs	KMT2A_ENST00000534358.1_Frame_Shift_Ins_p.AK379fs|KMT2A_ENST00000354520.4_Frame_Shift_Ins_p.AK379fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	379					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TTACAGAGGGCAAAAAAGGGGG	0.426																																					p.A379fs		Atlas-INDEL	.											.	MLL	548	.	0			c.1136_1137insA						.																																			SO:0001589	frameshift_variant	4297	exon3			.	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.1142dupA	chr11.hg19:g.118343016_118343016dupA	ENSP00000374157:p.Ala379fs	262.0	0.0		261.0	110.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Ins	INS	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.426	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118343011	-	A	118343010	7	5	234	1	0	1	1	0	0	0	0	0	9629	710	25	0	1146	0	MLL	11	118343010	Frame_Shift_Ins	INS	-	TCGA-DD-AAW1-01A-11D-A40P-10	8335222	118343010	16663506	68	32648										
SPA17	53340	hgsc.bcm.edu	37	chr11	124551357	124551357	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	taacaatcatgcattcgaggTatggtcctttgaagctgttg	10	7	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr11:124551357T>C	ENST00000532692.1	+	2	1646		c.e2+2		SPA17_ENST00000524614.1_Splice_Site|SIAE_ENST00000525730.1_Intron|SPA17_ENST00000227135.2_Splice_Site			Q15506	SP17_HUMAN	sperm autoantigenic protein 17						binding of sperm to zona pellucida (GO:0007339)|epithelial cilium movement (GO:0003351)|single fertilization (GO:0007338)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|primary cilium (GO:0072372)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	5	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0223)		GCATTCGAGGTATGGTCCTTT	0.393																																					.		Atlas-SNP	.											.	SPA17	16	.	0			c.225+2T>C						.						104	98	100					11																	124551357		2201	4299	6500	SO:0001630	splice_region_variant	53340	exon3			TCGAGGTATGGTC	AF334735	CCDS8450.1	11q24.2	2009-03-12			ENSG00000064199	ENSG00000064199			11210	protein-coding gene	gene with protein product	"cancer/testis antigen 22"	608621				8688458	Standard	NM_017425		Approved	SP17, CT22	uc001qap.3	Q15506	OTTHUMG00000165927	ENST00000532692.1:c.225+2T>C	chr11.hg19:g.124551357T>C		135.0	0.0		152.0	44.0	NM_017425	B2R4F2|Q9BXF7	Splice_Site	SNP	ENST00000532692.1	hg19	CCDS8450.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.312605	0.60414	.	.	ENSG00000064199	ENST00000227135;ENST00000532692	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1564	0.72746	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SPA17	124056567	1.000000	0.71417	0.998000	0.56505	0.603000	0.37013	5.632000	0.67819	2.221000	0.72209	0.455000	0.32223	.	.	.		0.393	SPA17-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387075.1	NM_017425	Intron	C	124551357	T	C	124551357	5	2	234	1	0	0	0	0	0	0	1	0	14986	1652	57	2	233	2	SPA17	11	124551357	Splice_Site	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	6208347	124551357	10455159	69	32649										
NOP2	4839	hgsc.bcm.edu	37	chr12	6666361	6666361	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tggcccttccaaggggctgaTgatggtccttaggtttcagg	14	9	1	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr12:6666361T>C	ENST00000322166.5	-	16	2358	c.2237A>G	c.(2236-2238)cAt>cGt	p.H746R	NOP2_ENST00000382421.3_Missense_Mutation_p.H779R|IFFO1_ENST00000336604.4_5'Flank|NOP2_ENST00000545200.1_3'UTR|IFFO1_ENST00000356896.4_5'Flank|NOP2_ENST00000541778.1_Missense_Mutation_p.H742R|NOP2_ENST00000399466.2_Missense_Mutation_p.H742R|NOP2_ENST00000537442.1_Missense_Mutation_p.H746R|IFFO1_ENST00000396840.2_5'Flank|NOP2_ENST00000542015.1_5'Flank	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	746					positive regulation of cell proliferation (GO:0008284)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	19						AAGGGGCTGATGATGGTCCTT	0.557																																					p.H779R		Atlas-SNP	.											.	NOP2	44	.	0			c.A2336G						.						141	141	141					12																	6666361		1938	4164	6102	SO:0001583	missense	4839	exon17			GGCTGATGATGGT		CCDS44811.1, CCDS58202.1, CCDS58203.1, CCDS58204.1	12p13	2012-12-10	2012-12-10	2008-10-13	ENSG00000111641	ENSG00000111641		"NOP2/Sun domain containing"	7867	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 1"	164031	"nucleolar protein 1 (120kD)", "nucleolar protein 1, 120kDa", "nucleolar protein 2 homolog (yeast)", "NOP2 nucleolar protein homolog (yeast)"	NOL1		8088812	Standard	NM_006170		Approved	NOP120, NSUN1, p120	uc021qtz.2	P46087	OTTHUMG00000169163	ENST00000322166.5:c.2237A>G	chr12.hg19:g.6666361T>C	ENSP00000313272:p.His746Arg	193.0	0.0		210.0	80.0	NM_001258309	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Missense_Mutation	SNP	ENST00000322166.5	hg19	CCDS58203.1	.	.	.	.	.	.	.	.	.	.	T	4.962	0.178738	0.09443	.	.	ENSG00000111641	ENST00000537442;ENST00000382421;ENST00000399466;ENST00000322166;ENST00000541778	T;T;T;T;T	0.13196	2.61;2.61;2.61;2.61;2.61	4.8	-9.61	0.00550	.	1.957170	0.02489	N	0.089278	T	0.04497	0.0123	N	0.08118	0	0.09310	N	1	B;B	0.14805	0.011;0.008	B;B	0.16289	0.01;0.015	T	0.34254	-0.9836	10	0.15952	T	0.53	7.426	0.546	0.00654	0.2117:0.1569:0.2598:0.3715	.	746;742	P46087;P46087-2	NOP2_HUMAN;.	R	746;779;742;746;742	ENSP00000444437:H746R;ENSP00000371858:H779R;ENSP00000382392:H742R;ENSP00000313272:H746R;ENSP00000443150:H742R	ENSP00000313272:H746R	H	-	2	0	NOP2	6536622	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-3.144000	0.00585	-2.937000	0.00298	0.533000	0.62120	CAT	.	.		0.557	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170		C	6666361	T	C	6666361	3	2	234	1	0	0	0	0	1	0	0	0	10547	1464	51	2	205	2	NOP2	12	6666361	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10		6666361	127185534	70	32650										
TAS2R31	259290	hgsc.bcm.edu	37	chr12	11183213	11183213	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	atatcattatggacagaaagTaaacggcacataacaagagg	9	6	1	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr12:11183213T>A	ENST00000390675.2	-	1	793	c.722A>T	c.(721-723)tAc>tTc	p.Y241F	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	241					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						GGACAGAAAGTAAACGGCACA	0.403																																					p.Y241F		Atlas-SNP	.											.	TAS2R31	24	.	0			c.A722T						.						189	195	193					12																	11183213		2202	4299	6501	SO:0001583	missense	259290	exon1			AGAAAGTAAACGG	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19113	protein-coding gene	gene with protein product		612669	"taste receptor, type 2, member 44"	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.722A>T	chr12.hg19:g.11183213T>A	ENSP00000375093:p.Tyr241Phe	256.0	1.0		274.0	118.0	NM_176885	P59547|Q17R84|Q645X5	Missense_Mutation	SNP	ENST00000390675.2	hg19	CCDS53747.1	.	.	.	.	.	.	.	.	.	.	.	2.379	-0.342482	0.05243	.	.	ENSG00000256436	ENST00000390675	T	0.01172	5.23	2.42	2.42	0.29668	.	.	.	.	.	T	0.01592	0.0051	L	0.41236	1.265	0.09310	N	1	B	0.31581	0.329	B	0.40375	0.327	T	0.49062	-0.8978	9	0.23302	T	0.38	.	6.6665	0.23042	0.0:0.0:0.0:1.0	.	241	P59538	T2R31_HUMAN	F	241	ENSP00000375093:Y241F	ENSP00000375093:Y241F	Y	-	2	0	TAS2R31	11074480	0.001000	0.12720	0.006000	0.13384	0.070000	0.16714	0.679000	0.25291	1.132000	0.42129	0.163000	0.16589	TAC	.	.		0.403	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885		A	11183213	T	A	11183213	3	1	234	1	0	0	0	0	1	0	0	0	15589	1638	57	4	211	4	TAS2R31	12	11183213	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	4516852	11183213	122668682	71	32651										
PPP1R12A	4659	hgsc.bcm.edu	37	chr12	80328602	80328602	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	agacggcgccatcgtcgaacTtcaccttggtcttctggcgc	11	14	3	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr12:80328602T>C	ENST00000450142.2	-	1	376	c.110A>G	c.(109-111)aAg>aGg	p.K37R	PPP1R12A_ENST00000550107.1_Missense_Mutation_p.K37R|PPP1R12A_ENST00000437004.2_Missense_Mutation_p.K37R|RP11-84G21.1_ENST00000552885.1_RNA|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.K37R	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	37					centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						ATCGTCGAACTTCACCTTGGT	0.637																																					p.K37R		Atlas-SNP	.											PPP1R12A,bladder,carcinoma,0,1	PPP1R12A	76	.	0			c.A110G						.						42	48	46					12																	80328602		2042	4202	6244	SO:0001583	missense	4659	exon1			TCGAACTTCACCT	D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7618	protein-coding gene	gene with protein product	"myosin phosphatase-targeting subunit 1", "myosin binding subunit"	602021	"protein phosphatase 1, regulatory (inhibitor) subunit 12A"	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.110A>G	chr12.hg19:g.80328602T>C	ENSP00000389168:p.Lys37Arg	96.0	0.0		89.0	36.0	NM_002480	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	hg19	CCDS44947.1	.	.	.	.	.	.	.	.	.	.	T	7.015	0.557564	0.13436	.	.	ENSG00000058272	ENST00000261207;ENST00000546189;ENST00000360825;ENST00000341878;ENST00000312727;ENST00000450142;ENST00000437004;ENST00000550107;ENST00000547330	T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65	5.01	3.86	0.44501	Ankyrin repeat-containing domain (1);	0.156299	0.56097	D	0.000025	T	0.41743	0.1172	N	0.11284	0.12	0.58432	D	0.999995	P;B;B;P	0.47604	0.855;0.003;0.001;0.898	P;B;B;P	0.61397	0.888;0.021;0.002;0.836	T	0.19224	-1.0312	10	0.19590	T	0.45	.	9.3024	0.37853	0.0:0.0818:0.0:0.9182	.	37;37;37;37	F8W8Q6;O14974-2;O14974-3;O14974	.;.;.;MYPT1_HUMAN	R	37	ENSP00000261207:K37R;ENSP00000389168:K37R;ENSP00000416769:K37R;ENSP00000446855:K37R;ENSP00000446816:K37R	ENSP00000261207:K37R	K	-	2	0	PPP1R12A	78852733	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.139000	0.77314	0.930000	0.37217	0.533000	0.62120	AAG	.	.		0.637	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		C	80328602	T	C	80328602	3	2	234	1	0	0	0	0	1	0	0	0	12366	1609	56	2	3082	2	PPP1R12A	12	80328602	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	69145389	80328602	53523293	72	32652										
STAB2	55576	hgsc.bcm.edu	37	chr12	104149232	104149232	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	gaaatgtgggatgtcttctgCtatcggatgaaaggtaaccg	13	6	2	1	rs375211716		TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr12:104149232C>G	ENST00000388887.2	+	62	7071	c.6867C>G	c.(6865-6867)tgC>tgG	p.C2289W	RP11-341G23.4_ENST00000551299.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						ATGTCTTCTGCTATCGGATGA	0.557																																					p.C2289W		Atlas-SNP	.											.	STAB2	370	.	0			c.C6867G						.						137	117	124					12																	104149232		2203	4300	6503	SO:0001583	missense	55576	exon62			CTTCTGCTATCGG	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.6867C>G	chr12.hg19:g.104149232C>G	ENSP00000373539:p.Cys2289Trp	89.0	0.0		83.0	38.0	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.071949	0.55646	.	.	ENSG00000136011	ENST00000388887;ENST00000258495	T	0.24538	1.85	5.26	1.33	0.21861	C-type lectin fold (1);Link (3);C-type lectin-like (1);FAS1 domain (1);	0.000000	0.85682	D	0.000000	T	0.57095	0.2030	H	0.95365	3.66	0.80722	D	1	D	0.76494	0.999	D	0.71870	0.975	T	0.65236	-0.6217	10	0.87932	D	0	.	9.5713	0.39429	0.0:0.6513:0.0:0.3487	.	2289	Q8WWQ8	STAB2_HUMAN	W	2289;976	ENSP00000373539:C2289W	ENSP00000258495:C976W	C	+	3	2	STAB2	102673362	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.999000	0.29757	0.592000	0.29728	0.650000	0.86243	TGC	.	.		0.557	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			G	104149232	C	G	104149232	3	3	234	1	0	0	0	0	1	0	0	0	15253	805	28	4	7113	4	STAB2	12	104149232	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	23820630	104149232	29702663	73	32653										
ISCU	23479	hgsc.bcm.edu	37	chr12	108960984	108960984	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aggtggaggaagccttgactAtcaaaaacacagatatcgcc	10	9	1	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr12:108960984A>T	ENST00000311893.9	+	4	380	c.358A>T	c.(358-360)Atc>Ttc	p.I120F	ISCU_ENST00000431221.2_Missense_Mutation_p.I120F|ISCU_ENST00000547005.1_Missense_Mutation_p.I120F|ISCU_ENST00000535729.1_Missense_Mutation_p.I120F|ISCU_ENST00000392807.4_Missense_Mutation_p.I95F|ISCU_ENST00000539593.1_Missense_Mutation_p.I120F|ISCU_ENST00000338291.4_Missense_Mutation_p.I95F	NM_213595.2	NP_998760.1	Q9H1K1	ISCU_HUMAN	iron-sulfur cluster assembly enzyme	120					iron-sulfur cluster assembly (GO:0016226)|nitrogen fixation (GO:0009399)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|iron-sulfur cluster binding (GO:0051536)|protein complex scaffold (GO:0032947)			kidney(2)|large_intestine(2)|lung(4)|prostate(2)|urinary_tract(1)	11						AGCCTTGACTATCAAAAACAC	0.488																																					p.I120F		Atlas-SNP	.											.	ISCU	19	.	0			c.A358T						.						147	128	134					12																	108960984		2203	4300	6503	SO:0001583	missense	23479	exon4			TTGACTATCAAAA	U47101	CCDS9118.1, CCDS44966.1, CCDS73518.1	12q24.1	2013-08-05	2013-08-05	2006-10-24	ENSG00000136003	ENSG00000136003			29882	protein-coding gene	gene with protein product		611911	"NifU-like N-terminal domain containing", "IscU iron-sulfur cluster scaffold homolog (E. coli)", "iron-sulfur cluster scaffold homolog (E. coli)"	NIFUN		8875867, 11060020	Standard	XM_005268760		Approved	ISU2, hnifU, IscU	uc010sxc.2	Q9H1K1	OTTHUMG00000168420	ENST00000311893.9:c.358A>T	chr12.hg19:g.108960984A>T	ENSP00000310623:p.Ile120Phe	84.0	0.0		58.0	22.0	NM_213595	Q6P713|Q99617|Q9H1K2	Missense_Mutation	SNP	ENST00000311893.9	hg19	CCDS44966.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.964934	0.92855	.	.	ENSG00000136003	ENST00000535729;ENST00000431221;ENST00000547005;ENST00000311893;ENST00000392807;ENST00000338291;ENST00000539593	T;T;T;T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49;-1.49;-1.49;-1.49	5.59	5.59	0.84812	NIF system FeS cluster assembly, NifU, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91660	0.7364	M	0.92268	3.29	0.80722	D	1	D;D;D;D;D;D	0.71674	0.995;0.998;0.984;0.994;0.986;0.983	D;D;D;D;D;P	0.72075	0.976;0.974;0.935;0.959;0.942;0.904	D	0.93544	0.6880	10	0.87932	D	0	.	14.759	0.69590	1.0:0.0:0.0:0.0	.	120;120;120;120;95;95	B3KQ30;Q9H1K1;B4DNC9;F5H5N2;B1P7G3;Q9H1K1-2	.;ISCU_HUMAN;.;.;.;.	F	120;120;120;120;95;95;120	ENSP00000445598:I120F;ENSP00000411108:I120F;ENSP00000446606:I120F;ENSP00000310623:I120F;ENSP00000376554:I95F;ENSP00000344584:I95F;ENSP00000443272:I120F	ENSP00000310623:I120F	I	+	1	0	ISCU	107485113	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.294000	0.89934	2.137000	0.66172	0.533000	0.62120	ATC	.	.		0.488	ISCU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399693.1	NM_014301		T	108960984	A	T	108960984	3	4	234	1	0	0	0	0	1	0	0	0	7861	449	16	4	297	4	ISCU	12	108960984	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	4811752	108960984	24890911	74	32654										
NAA16	79612	hgsc.bcm.edu	37	chr13	41946367	41946367	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tccattagaggaagccgttaAgttccttatacctcttaaga	7	9	1	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr13:41946367A>T	ENST00000379406.3	+	16	2300	c.1976A>T	c.(1975-1977)aAg>aTg	p.K659M	NAA16_ENST00000497143.1_3'UTR	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	659					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						GAAGCCGTTAAGTTCCTTATA	0.284																																					p.K659M		Atlas-SNP	.											.	NAA16	74	.	0			c.A1976T						.						78	80	80					13																	41946367		2203	4289	6492	SO:0001583	missense	79612	exon16			CCGTTAAGTTCCT	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.1976A>T	chr13.hg19:g.41946367A>T	ENSP00000368716:p.Lys659Met	272.0	0.0		251.0	101.0	NM_024561	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.287525	0.80803	.	.	ENSG00000172766	ENST00000379406	T	0.54866	0.55	5.03	5.03	0.67393	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000001	T	0.74921	0.3780	M	0.86097	2.795	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79543	-0.1760	10	0.62326	D	0.03	-13.1982	14.7201	0.69300	1.0:0.0:0.0:0.0	.	659	Q6N069	NAA16_HUMAN	M	659	ENSP00000368716:K659M	ENSP00000368716:K659M	K	+	2	0	NAA16	40844367	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.654000	0.91092	1.876000	0.54355	0.482000	0.46254	AAG	.	.		0.284	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		T	41946367	A	T	41946367	3	4	234	1	0	0	0	0	1	0	0	0	10128	72	3	4	2071	4	NAA16	13	41946367	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10		41946367	73223511	75	32655										
DLEU7	220107	hgsc.bcm.edu	37	chr13	51417697	51417697	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	cgactggaccgtccccccagCcccactcctgctgcagcagc	9	21	0	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr13:51417697C>T	ENST00000504404.1	-	1	135	c.86G>A	c.(85-87)gGc>gAc	p.G29D	DLEU7-AS1_ENST00000413510.2_RNA|DLEU7_ENST00000400393.3_Missense_Mutation_p.G29D			Q6UYE1	LEU7_HUMAN	deleted in lymphocytic leukemia, 7	29													Acute lymphoblastic leukemia(7;1.03e-07)|Lung NSC(96;0.000818)|Breast(56;0.00122)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.25e-08)		GTCCCCCCAGCCCCACTCCTG	0.741																																					p.G29D		Atlas-SNP	.											.	DLEU7	6	.	0			c.G86A						.						2	3	3					13																	51417697		1396	3132	4528	SO:0001583	missense	220107	exon1			CCCCAGCCCCACT	AK126830	CCDS53869.1	13q14.3	2005-02-22			ENSG00000186047	ENSG00000186047			17567	protein-coding gene	gene with protein product						14706829	Standard	NM_198989		Approved	FLJ44882	uc001vex.2	Q6UYE1	OTTHUMG00000016936	ENST00000504404.1:c.86G>A	chr13.hg19:g.51417697C>T	ENSP00000427177:p.Gly29Asp	26.0	0.0		22.0	12.0	NM_198989	Q2M2E4|Q6ZT82	Missense_Mutation	SNP	ENST00000504404.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.43	2.234208	0.39498	.	.	ENSG00000186047	ENST00000400393;ENST00000504404;ENST00000335465	T;T	0.55413	0.52;0.61	4.11	2.16	0.27623	.	0.277119	0.26203	N	0.025729	T	0.39733	0.1089	L	0.43152	1.355	0.42061	D	0.991166	B;B	0.31413	0.322;0.322	B;B	0.28784	0.065;0.094	T	0.38779	-0.9645	10	0.72032	D	0.01	.	7.2979	0.26403	0.0:0.7541:0.0:0.2459	.	29;29	Q6UYE1;Q6UYE1-2	LEU7_HUMAN;.	D	29	ENSP00000420976:G29D;ENSP00000427177:G29D	ENSP00000439677:G29D	G	-	2	0	DLEU7	50315698	0.992000	0.36948	0.992000	0.48379	0.990000	0.78478	1.189000	0.32114	0.924000	0.37069	0.561000	0.74099	GGC	.	.		0.741	DLEU7-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045005.2	NM_198989		T	51417697	C	T	51417697	3	4	234	1	0	0	0	0	1	0	0	0	4555	739	26	3	404	3	DLEU7	13	51417697	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	9471330	51417697	63752181	76	32656										
DLGAP5	9787	hgsc.bcm.edu	37	chr14	55650384	55650384	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ctcgtttagctttctctctcTgctctttcaatttttgaagt	5	10	4	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr14:55650384T>A	ENST00000247191.2	-	3	542	c.326A>T	c.(325-327)cAg>cTg	p.Q109L	DLGAP5_ENST00000395425.2_Missense_Mutation_p.Q109L	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	109					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TTTCTCTCTCTGCTCTTTCAA	0.368																																					p.Q109L		Atlas-SNP	.											.	DLGAP5	84	.	0			c.A326T						.						87	75	79					14																	55650384		2203	4299	6502	SO:0001583	missense	9787	exon3			TCTCTCTGCTCTT	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.326A>T	chr14.hg19:g.55650384T>A	ENSP00000247191:p.Gln109Leu	172.0	0.0		165.0	62.0	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	hg19	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.631196	0.87660	.	.	ENSG00000126787	ENST00000395425;ENST00000247191;ENST00000557645;ENST00000554067	T;T;T;T	0.46063	2.46;2.46;2.46;0.88	5.55	5.55	0.83447	.	0.139018	0.50627	D	0.000104	T	0.63873	0.2548	M	0.76002	2.32	0.45150	D	0.998169	D;D	0.89917	1.0;1.0	D;D	0.71184	0.972;0.961	T	0.64550	-0.6381	10	0.42905	T	0.14	.	15.6662	0.77230	0.0:0.0:0.0:1.0	.	109;109	A8MTM6;Q15398	.;DLGP5_HUMAN	L	109	ENSP00000378815:Q109L;ENSP00000247191:Q109L;ENSP00000451747:Q109L;ENSP00000452168:Q109L	ENSP00000247191:Q109L	Q	-	2	0	DLGAP5	54720137	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.830000	0.62745	2.243000	0.73865	0.533000	0.62120	CAG	.	.		0.368	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		A	55650384	T	A	55650384	3	1	234	1	0	0	0	0	1	0	0	0	4565	1580	55	4	2377	4	DLGAP5	14	55650384	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10		55650384	51699156	77	32657										
PGF	5228	hgsc.bcm.edu	37	chr14	75412966	75412966	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ctcctcctcttccccctgccCttgggtctcctcctgcaata	5	20	2	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr14:75412966C>T	ENST00000405431.2	-	6	638				PGF_ENST00000238607.6_Silent_p.K144K|PGF_ENST00000555567.1_Silent_p.K145K|PGF_ENST00000553716.1_Intron			P49763	PLGF_HUMAN	placental growth factor						branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|regulation of morphogenesis of a branching structure (GO:0060688)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(234;0.00668)	Aflibercept(DB08885)	TCCCCCTGCCCTTGGGTCTCC	0.657											OREG0022810	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K145K	GBM(127;389 2301 5452 48547)	Atlas-SNP	.											.	PGF	23	.	0			c.G435A						.						103	83	89					14																	75412966		2203	4300	6503	SO:0001627	intron_variant	5228	exon6			CCTGCCCTTGGGT	S72960	CCDS9835.1, CCDS55932.1, CCDS73664.1	14q24.3	2013-02-18	2008-03-20		ENSG00000119630	ENSG00000119630			8893	protein-coding gene	gene with protein product	"placenta growth factor"	601121	"placental growth factor-like", "placental growth factor, vascular endothelial growth factor-related protein"	PGFL		7681160	Standard	NM_002632		Approved	PLGF, PlGF-2, PlGF, SHGC-10760, D12S1900	uc001xqz.3	P49763	OTTHUMG00000171496	ENST00000405431.2:c.638+115G>A	chr14.hg19:g.75412966C>T		66.0	0.0	1160	67.0	27.0	NM_002632	Q07101|Q9BV78|Q9Y6S8	Silent	SNP	ENST00000405431.2	hg19	CCDS9835.1																																																																																			.	.		0.657	PGF-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414064.1	NM_002632		T	75412966	C	T	75412966	1	4	234	0	1	0	0	0	0	0	0	0	11797	680	24	3		3	PGF	14	75412966	Intron	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	19762582	75412966	31936574	78	32658										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51860705	51860705	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	caatttcttttatgagaattTatgcccaagggctcaaatat	6	7	2	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr15:51860705T>A	ENST00000251076.5	-	3	551	c.264A>T	c.(262-264)atA>atT	p.I88I	DMXL2_ENST00000449909.3_Silent_p.I88I|DMXL2_ENST00000543779.2_Silent_p.I88I|DMXL2_ENST00000560421.1_5'UTR	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	88						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TATGAGAATTTATGCCCAAGG	0.269																																					p.I88I		Atlas-SNP	.											.	DMXL2	262	.	0			c.A264T						.						30	30	30					15																	51860705		2186	4273	6459	SO:0001819	synonymous_variant	23312	exon3			AGAATTTATGCCC	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.264A>T	chr15.hg19:g.51860705T>A		503.0	1.0		482.0	214.0	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	hg19	CCDS10141.1																																																																																			.	.		0.269	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		A	51860705	T	A	51860705	2	1	234	1	0	0	0	0	0	0	0	1	4597	1744	61	4		4	DMXL2	15	51860705	Silent	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10		51860705	50670687	79	32659										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54306719	54306720	+	Frame_Shift_Ins	INS	-	-	T													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ctctggcactcacagagtgaINSttttttcactgctaaactta							TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr15:54306719_54306720insT	ENST00000260323.11	+	1	1619_1620	c.1619_1620insT	c.(1618-1623)gattttfs	p.DF540fs	UNC13C_ENST00000537900.1_Frame_Shift_Ins_p.DF540fs|UNC13C_ENST00000545554.1_Frame_Shift_Ins_p.DF540fs	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	540					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCACAGAGTGATTTTTTCACTG	0.366																																					p.D540fs		Atlas-INDEL	.											.,2	UNC13C	674	.	0			c.1619_1620insT						.																																			SO:0001589	frameshift_variant	440279	exon1			.	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.1625dupT	chr15.hg19:g.54306725_54306725dupT	ENSP00000260323:p.Asp540fs	167.0	0.0		146.0	62.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Frame_Shift_Ins	INS	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.366	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54306720	-	T	54306719	7	5	234	1	0	1	1	0	0	0	0	0	17001	333	12	0	1621	0	UNC13C	15	54306719	Frame_Shift_Ins	INS	-	TCGA-DD-AAW1-01A-11D-A40P-10	2446014	54306719	48224673	80	32660										
DYX1C1	161582	hgsc.bcm.edu	37	chr15	55759146	55759146	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	accttttggagcaagatttcTagatgccaaatttctagtaa	7	7	2	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr15:55759146T>A	ENST00000321149.3	-	5	986	c.619A>T	c.(619-621)Aga>Tga	p.R207*	DYX1C1_ENST00000348518.3_Nonsense_Mutation_p.R207*|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000380679.1_Nonsense_Mutation_p.R207*|DYX1C1_ENST00000448430.2_Nonsense_Mutation_p.R207*|DYX1C1_ENST00000457155.2_Nonsense_Mutation_p.R207*	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	207					cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		GCAAGATTTCTAGATGCCAAA	0.269																																					p.R207X		Atlas-SNP	.											.	DYX1C1	54	.	0			c.A619T						.						38	42	41					15																	55759146		2189	4275	6464	SO:0001587	stop_gained	161582	exon5			GATTTCTAGATGC		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"Tetratricopeptide (TTC) repeat domain containing"	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.619A>T	chr15.hg19:g.55759146T>A	ENSP00000323275:p.Arg207*	284.0	0.0		242.0	91.0	NM_001033560	Q6P5Y9|Q8N1S6	Nonsense_Mutation	SNP	ENST00000321149.3	hg19	CCDS10154.1	.	.	.	.	.	.	.	.	.	.	T	14.74	2.626501	0.46840	.	.	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	.	.	.	3.61	3.61	0.41365	.	0.994303	0.08132	U	0.992929	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	8.9152	0.35576	0.0:0.0:0.0:1.0	.	.	.	.	X	207	.	ENSP00000323275:R207X	R	-	1	2	DYX1C1	53546438	0.008000	0.16893	0.003000	0.11579	0.016000	0.09150	1.322000	0.33689	1.873000	0.54277	0.460000	0.39030	AGA	.	.		0.269	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810		A	55759146	T	A	55759146	4	1	234	1	0	0	0	0	0	1	0	0	4864	1530	53	4	770	4	DYX1C1	15	55759146	Nonsense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	1452427	55759146	46772246	81	32661										
C15orf39	56905	hgsc.bcm.edu	37	chr15	75501101	75501101	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aagttactggcgctgcgccaGctgccggacatttaccccga	11	14	0	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr15:75501101G>A	ENST00000360639.2	+	2	3032	c.2712G>A	c.(2710-2712)caG>caA	p.Q904Q	C15orf39_ENST00000394987.4_Silent_p.Q904Q|RP11-69H7.3_ENST00000563568.1_RNA|C15orf39_ENST00000567617.1_Silent_p.Q904Q			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	904						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						CGCTGCGCCAGCTGCCGGACA	0.697																																					p.Q904Q		Atlas-SNP	.											.	C15orf39	64	.	0			c.G2712A						.						26	24	25					15																	75501101		2197	4293	6490	SO:0001819	synonymous_variant	56905	exon2			GCGCCAGCTGCCG	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 38~Name Same As HGNC:28782"				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.2712G>A	chr15.hg19:g.75501101G>A		29.0	0.0		52.0	22.0	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Silent	SNP	ENST00000360639.2	hg19	CCDS10276.1																																																																																			.	.		0.697	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		A	75501101	G	A	75501101	2	1	234	1	0	0	0	0	0	0	0	1	1795	962	34	3		3	C15orf39	15	75501101	Silent	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	19741955	75501101	27030291	82	32662										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86122602	86122602	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aatcttctggaatgcccacaGaccaggagtccctgagcagt	10	12	2	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr15:86122602G>T	ENST00000394518.2	+	7	1398	c.1303G>T	c.(1303-1305)Gac>Tac	p.D435Y	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.D435Y	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	435					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						AATGCCCACAGACCAGGAGTC	0.522																																					p.D435Y	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G1303T						.						58	63	61					15																	86122602		2202	4299	6501	SO:0001583	missense	11214	exon7			CCCACAGACCAGG	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.1303G>T	chr15.hg19:g.86122602G>T	ENSP00000378026:p.Asp435Tyr	179.0	0.0		143.0	56.0	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.648623	0.47258	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.11604	2.76;2.76	5.46	0.979	0.19745	.	.	.	.	.	T	0.08044	0.0201	L	0.27053	0.805	0.09310	N	1	B;B	0.14012	0.005;0.009	B;B	0.14023	0.005;0.01	T	0.32241	-0.9914	9	0.62326	D	0.03	.	8.2193	0.31532	0.0:0.1432:0.3882:0.4686	.	435;435	Q12802;Q12802-2	AKP13_HUMAN;.	Y	435;435;434;434	ENSP00000354718:D435Y;ENSP00000378026:D435Y	ENSP00000354718:D435Y	D	+	1	0	AKAP13	83923606	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.258000	0.18387	0.307000	0.22880	-0.182000	0.12963	GAC	.	.		0.522	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		T	86122602	G	T	86122602	3	4	234	1	0	0	0	0	1	0	0	0	449	942	33	3	1325	3	AKAP13	15	86122602	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	10621501	86122602	16408790	83	32663										
SV2B	9899	hgsc.bcm.edu	37	chr15	91769596	91769596	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aagaagatgcacagagtgatGtcaccgaaggccatgatgag	13	7	1	6			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr15:91769596G>A	ENST00000394232.1	+	2	573	c.103G>A	c.(103-105)Gtc>Atc	p.V35I	SV2B_ENST00000545111.2_Intron|SV2B_ENST00000557291.1_Intron|SV2B_ENST00000330276.4_Missense_Mutation_p.V35I	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	35					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			ACAGAGTGATGTCACCGAAGG	0.532																																					p.V35I		Atlas-SNP	.											.	SV2B	98	.	0			c.G103A						.						145	117	126					15																	91769596		2198	4298	6496	SO:0001583	missense	9899	exon3			AGTGATGTCACCG	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.103G>A	chr15.hg19:g.91769596G>A	ENSP00000377779:p.Val35Ile	81.0	0.0		79.0	38.0	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	hg19	CCDS10370.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.064438	0.55432	.	.	ENSG00000185518	ENST00000394232;ENST00000330276	T;T	0.28666	1.6;1.6	5.71	5.71	0.89125	.	0.097447	0.64402	D	0.000002	T	0.26159	0.0638	N	0.22421	0.69	0.34581	D	0.714444	B	0.26120	0.142	B	0.25759	0.063	T	0.28808	-1.0032	10	0.66056	D	0.02	-22.1591	18.4162	0.90571	0.0:0.0:1.0:0.0	.	35	Q7L1I2	SV2B_HUMAN	I	35	ENSP00000377779:V35I;ENSP00000332818:V35I	ENSP00000332818:V35I	V	+	1	0	SV2B	89570600	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	4.022000	0.57203	2.703000	0.92315	0.563000	0.77884	GTC	.	.		0.532	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		A	91769596	G	A	91769596	3	1	234	1	0	0	0	0	1	0	0	0	15433	1377	48	3	105	3	SV2B	15	91769596	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	5646994	91769596	10761796	84	32664										
LONP2	85320	hgsc.bcm.edu	37	chr16	48278525	48278525	+	Intron	DEL	C	C	-													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	acgcgcaggacctgccgccgCtgcacaggtaggcctggctg							TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr16:48278525delC	ENST00000356608.2	-	1	81				LONP2_ENST00000535754.1_Frame_Shift_Del_p.L76fs|ABCC11_ENST00000537808.1_Intron|LONP2_ENST00000285737.4_Frame_Shift_Del_p.L76fs			Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11						organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CCTGCCGCCGCTGCACAGGTA	0.756																																					p.P75fs		Atlas-INDEL	.											.	LONP2	63	.	0			c.225delG						.						4	3	3					16																	48278525		1393	2779	4172	SO:0001627	intron_variant	83752	exon1			.	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000356608.2:c.17+2699G>-	chr16.hg19:g.48278525delC		43.0	0.0		33.0	14.0	NM_031490	Q8TDJ0|Q96JA6|Q9BX80	Frame_Shift_Del	DEL	ENST00000356608.2	hg19	CCDS10732.1																																																																																			.	.		0.756	ABCC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256843.1	NM_032583		-	48278525	C	-	48278525	6	5	234	0	1	1	0	1	0	0	0	0	8902	796	28	0		0	LONP2	16	48278525	Intron	DEL	C	TCGA-DD-AAW1-01A-11D-A40P-10		48278525	42076228	85	32665										
TAT	6898	hgsc.bcm.edu	37	chr16	71602186	71602186	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tgaaattcgggtactcaaagCactgcaaaaagaagagtctg	10	7	2	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr16:71602186C>A	ENST00000355962.4	-	12	1359	c.1226G>T	c.(1225-1227)tGc>tTc	p.C409F	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	409					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	GTACTCAAAGCACTGCAAAAA	0.502																																					p.C409F	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.G1226T						.						54	45	48					16																	71602186		2198	4300	6498	SO:0001630	splice_region_variant	6898	exon12			TCAAAGCACTGCA		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.1225-1G>T	chr16.hg19:g.71602186C>A		89.0	0.0		92.0	40.0	NM_000353	B2R8I1|D3DWS2	Missense_Mutation	SNP	ENST00000355962.4	hg19	CCDS10903.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.149970	0.57151	.	.	ENSG00000198650	ENST00000355962	D	0.90324	-2.65	6.02	6.02	0.97574	Tyrosine aminotransferase (1);Aminotransferase, class I/classII (1);Tyrosine/nicotianamine aminotransferase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.089128	0.85682	D	0.000000	D	0.96144	0.8743	M	0.88450	2.955	0.80722	D	1	D	0.76494	0.999	D	0.65773	0.938	D	0.95834	0.8860	10	0.66056	D	0.02	-19.3887	20.5407	0.99260	0.0:1.0:0.0:0.0	.	409	P17735	ATTY_HUMAN	F	409	ENSP00000348234:C409F	ENSP00000348234:C409F	C	-	2	0	TAT	70159687	1.000000	0.71417	1.000000	0.80357	0.217000	0.24651	5.165000	0.64959	2.865000	0.98341	0.655000	0.94253	TGC	.	.		0.502	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1		Missense_Mutation	A	71602186	C	A	71602186	5	1	234	1	0	0	0	0	0	0	1	0	15605	724	25	3	142	3	TAT	16	71602186	Splice_Site	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	23323661	71602186	18752567	86	32666										
USP22	23326	hgsc.bcm.edu	37	chr17	20908264	20908264	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ttgtcattgttgagactgtcCgtgggctgctggtactgtcc	13	9	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr17:20908264C>T	ENST00000261497.4	-	11	1565	c.1362G>A	c.(1360-1362)acG>acA	p.T454T	USP22_ENST00000537526.2_Silent_p.T442T|RP11-344E13.3_ENST00000583481.1_RNA|RP11-344E13.3_ENST00000581958.1_RNA|USP22_ENST00000455117.2_Intron	NM_015276.1	NP_056091.1	Q9UPT9	UBP22_HUMAN	ubiquitin specific peptidase 22	454	USP.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|embryo development (GO:0009790)|histone deubiquitination (GO:0016578)|histone H4 acetylation (GO:0043967)|histone ubiquitination (GO:0016574)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deubiquitination (GO:0016579)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	SAGA complex (GO:0000124)	enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|transcription coactivator activity (GO:0003713)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	15						TGAGACTGTCCGTGGGCTGCT	0.542																																					p.T454T		Atlas-SNP	.											.	USP22	45	.	0			c.G1362A						.						239	250	246					17																	20908264		2063	4209	6272	SO:0001819	synonymous_variant	23326	exon11			ACTGTCCGTGGGC	AB028986	CCDS42285.1	17p11.2	2006-11-24	2005-08-08		ENSG00000124422	ENSG00000124422		"Ubiquitin-specific peptidases"	12621	protein-coding gene	gene with protein product		612116	"ubiquitin specific protease 22", "ubiquitin specific peptidase 3-like"	USP3L		12838346	Standard	NM_015276		Approved	KIAA1063	uc002gym.4	Q9UPT9	OTTHUMG00000133621	ENST00000261497.4:c.1362G>A	chr17.hg19:g.20908264C>T		74.0	0.0		109.0	43.0	NM_015276	A0JNS3|Q2NLE2|Q6MZY4|Q8TBS8|Q96IW5	Silent	SNP	ENST00000261497.4	hg19	CCDS42285.1																																																																																			.	.		0.542	USP22-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444169.1			T	20908264	C	T	20908264	2	4	234	1	0	0	0	0	0	0	0	1	17069	639	23	1		1	USP22	17	20908264	Silent	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10		20908264	60286946	87	32667										
C17orf46	124783	hgsc.bcm.edu	37	chr17	43332862	43332862	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	atgggtggcgggagatctgaGgacaggagggggcttggtgc	22	5	1	2	rs373812499		TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr17:43332862G>A	ENST00000331780.4	-	4	782	c.687C>T	c.(685-687)tcC>tcT	p.S229S	MAP3K14-AS1_ENST00000588504.1_RNA|MAP3K14-AS1_ENST00000585346.1_RNA|MAP3K14-AS1_ENST00000591263.1_RNA|MAP3K14-AS1_ENST00000590100.1_RNA|MAP3K14-AS1_ENST00000588160.1_RNA|SPATA32_ENST00000543122.1_Silent_p.S208S|MAP3K14-AS1_ENST00000592422.1_RNA|MAP3K14-AS1_ENST00000588698.1_RNA	NM_152343.2	NP_689556.2	Q96LK8	SPT32_HUMAN	spermatogenesis associated 32	229					spermatogenesis (GO:0007283)	perinuclear region of cytoplasm (GO:0048471)											GGAGATCTGAGGACAGGAGGG	0.612																																					p.S229S		Atlas-SNP	.											.	.	.	.	0			c.C687T						.						89	70	77					17																	43332862		2203	4300	6503	SO:0001819	synonymous_variant	124783	exon4			ATCTGAGGACAGG	AK058143	CCDS32669.1	17q21.31	2013-10-11	2012-10-08	2012-10-08	ENSG00000184361	ENSG00000184361			26349	protein-coding gene	gene with protein product	"acrosome expressed 2"		"chromosome 17 open reading frame 46", "testis expressed 34"	C17orf46, TEX34		18621766	Standard	NM_152343		Approved	FLJ25414, AEP2, VAD1.2	uc002iis.1	Q96LK8	OTTHUMG00000180363	ENST00000331780.4:c.687C>T	chr17.hg19:g.43332862G>A		89.0	0.0		103.0	51.0	NM_152343	Q7Z4U1|Q8N6V6	Silent	SNP	ENST00000331780.4	hg19	CCDS32669.1																																																																																			.	.		0.612	SPATA32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450946.1	NM_152343		A	43332862	G	A	43332862	2	1	234	1	0	0	0	0	0	0	0	1	1859	987	35	3		3	C17orf46	17	43332862	Silent	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10	22424598	43332862	37862348	88	32668										
CA10	56934	hgsc.bcm.edu	37	chr17	49825104	49825104	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ctgtatgtcatgggccctccAgatatgttgaccaagtgctc	10	11	1	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr17:49825104A>T	ENST00000285273.4	-	5	1465	c.354T>A	c.(352-354)tcT>tcA	p.S118S	CA10_ENST00000570565.1_Silent_p.S43S|CA10_ENST00000340813.6_Silent_p.S124S|CA10_ENST00000571918.1_5'UTR|CA10_ENST00000442502.2_Silent_p.S118S|CA10_ENST00000451037.2_Silent_p.S118S	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	118					brain development (GO:0007420)					cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	TGGGCCCTCCAGATATGTTGA	0.552																																					p.S118S		Atlas-SNP	.											.	CA10	84	.	0			c.T354A						.						164	150	154					17																	49825104		2203	4300	6503	SO:0001819	synonymous_variant	56934	exon5			CCCTCCAGATATG	AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"Carbonic anhydrases"	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.354T>A	chr17.hg19:g.49825104A>T		183.0	0.0		303.0	93.0	NM_001082534	B2R7J0|B4DGL6	Silent	SNP	ENST00000285273.4	hg19	CCDS32684.1																																																																																			.	.		0.552	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178		T	49825104	A	T	49825104	2	4	234	1	0	0	0	0	0	0	0	1	2513	175	7	4		4	CA10	17	49825104	Silent	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	6492242	49825104	31370106	89	32669										
ABCA8	10351	hgsc.bcm.edu	37	chr17	66865908	66865908	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	actggcaacttataaaccatCagagaggagtacctgagaga	10	8	1	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr17:66865908C>T	ENST00000269080.2	-	36	4661	c.4524G>A	c.(4522-4524)ctG>ctA	p.L1508L	ABCA8_ENST00000430352.2_Silent_p.L1548L|ABCA8_ENST00000586539.1_Silent_p.L1548L	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1508					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					TATAAACCATCAGAGAGGAGT	0.418																																					p.L1508L		Atlas-SNP	.											.	ABCA8	213	.	0			c.G4524A						.						102	100	100					17																	66865908		2203	4300	6503	SO:0001819	synonymous_variant	10351	exon36			AACCATCAGAGAG	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.4524G>A	chr17.hg19:g.66865908C>T		283.0	0.0		395.0	107.0	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	hg19	CCDS11680.1																																																																																			.	.		0.418	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		T	66865908	C	T	66865908	2	4	234	1	0	0	0	0	0	0	0	1	38	813	29	3		3	ABCA8	17	66865908	Silent	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	17040804	66865908	14329302	90	32670										
DOT1L	84444	hgsc.bcm.edu	37	chr19	2216983	2216983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	caccaaggagaacggccttcCctaccagagccccagcgtgc	10	17	0	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr19:2216983C>T	ENST00000398665.3	+	21	2474	c.2438C>T	c.(2437-2439)cCc>cTc	p.P813L	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	813					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AACGGCCTTCCCTACCAGAGC	0.657																																					p.P813L		Atlas-SNP	.											.	DOT1L	205	.	0			c.C2438T						.						40	44	43					19																	2216983		2109	4208	6317	SO:0001583	missense	84444	exon21			GCCTTCCCTACCA	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.2438C>T	chr19.hg19:g.2216983C>T	ENSP00000381657:p.Pro813Leu	104.0	0.0		120.0	53.0	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.43|11.43	1.635793|1.635793	0.29068|0.29068	.|.	.|.	ENSG00000104885|ENSG00000104885	ENST00000398665;ENST00000221482|ENST00000440640	T|T	0.21932|0.40225	1.98|1.04	4.89|4.89	3.83|3.83	0.44106|0.44106	.|.	0.552403|0.552403	0.19937|0.19937	N|N	0.102737|0.102737	T|T	0.52108|0.52108	0.1714|0.1714	M|M	0.64997|0.64997	1.995|1.995	0.09310|0.09310	N|N	0.999995|0.999995	B;B|.	0.34103|.	0.437;0.169|.	B;B|.	0.32864|.	0.154;0.079|.	T|T	0.48958|0.48958	-0.8988|-0.8988	10|8	0.87932|0.62326	D|D	0|0.03	-17.4826|-17.4826	14.2074|14.2074	0.65744|0.65744	0.0:0.8495:0.1505:0.0|0.0:0.8495:0.1505:0.0	.|.	813;813|.	Q8TEK3;Q8TEK3-2|.	DOT1L_HUMAN;.|.	L|S	813|600	ENSP00000381657:P813L|ENSP00000388276:P600S	ENSP00000221482:P813L|ENSP00000388276:P600S	P|P	+|+	2|1	0|0	DOT1L|DOT1L	2167983|2167983	0.005000|0.005000	0.15991|0.15991	0.093000|0.093000	0.20910|0.20910	0.312000|0.312000	0.27988|0.27988	1.751000|1.751000	0.38339|0.38339	1.030000|1.030000	0.39839|0.39839	0.655000|0.655000	0.94253|0.94253	CCC|CCT	.	.		0.657	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2216983	C	T	2216983	3	4	234	1	0	0	0	0	1	0	0	0	4711	623	22	3	2520	3	DOT1L	19	2216983	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10		2216983	56912000	91	32671										
STAP2	55620	hgsc.bcm.edu	37	chr19	4325516	4325516	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	agacgcaggtgacagcggctTggggccacctgtgcagggtg	18	10	0	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr19:4325516T>A	ENST00000594605.1	-	10	979	c.856A>T	c.(856-858)Aag>Tag	p.K286*	STAP2_ENST00000600324.1_Nonsense_Mutation_p.K286*|STAP2_ENST00000597593.1_5'UTR	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	286	Pro-rich.					cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		GACAGCGGCTTGGGGCCACCT	0.622																																					p.K286X		Atlas-SNP	.											.	STAP2	38	.	0			c.A856T						.						74	82	79					19																	4325516		2203	4300	6503	SO:0001587	stop_gained	55620	exon10			GCGGCTTGGGGCC	AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078			30430	protein-coding gene	gene with protein product		607881				10980601, 11441184	Standard	XM_005259592		Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000594605.1:c.856A>T	chr19.hg19:g.4325516T>A	ENSP00000471052:p.Lys286*	42.0	0.0		64.0	24.0	NM_001013841	A6NKK3|Q9NXI2	Nonsense_Mutation	SNP	ENST00000594605.1	hg19	CCDS45926.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.687924	0.88639	.	.	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	4.66	4.66	0.58398	.	1.536070	0.03701	U	0.248577	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-10.2639	10.5268	0.44954	0.0:0.0:0.0:1.0	.	.	.	.	X	286	.	ENSP00000317912:K286X	K	-	1	0	STAP2	4276516	0.044000	0.20184	0.366000	0.25914	0.089000	0.18198	1.276000	0.33156	1.752000	0.51891	0.393000	0.25936	AAG	.	.		0.622	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841		A	4325516	T	A	4325516	4	1	234	1	0	0	0	0	0	1	0	0	15268	1821	63	4	509	4	STAP2	19	4325516	Nonsense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	2108533	4325516	54803467	92	32672										
MUC16	94025	hgsc.bcm.edu	37	chr19	9075725	9075725	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aagtttatgtccagcgtattCagggtccttaatacactgga	9	8	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr19:9075725C>T	ENST00000397910.4	-	3	11924	c.11721G>A	c.(11719-11721)ctG>ctA	p.L3907L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3908	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCAGCGTATTCAGGGTCCTTA	0.473																																					p.L3907L		Atlas-SNP	.											.	MUC16	4315	.	0			c.G11721A						.						88	81	83					19																	9075725		1919	4120	6039	SO:0001819	synonymous_variant	94025	exon3			CGTATTCAGGGTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11721G>A	chr19.hg19:g.9075725C>T		115.0	0.0		148.0	72.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9075725	C	T	9075725	2	4	234	1	0	0	0	0	0	0	0	1	9982	813	29	3		3	MUC16	19	9075725	Silent	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	4750209	9075725	50053258	93	32673										
OR7G3	390883	hgsc.bcm.edu	37	chr19	9236857	9236857	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ccccagaactaaggtacaccCcaaaccctgttccataaaac	4	16	0	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr19:9236857C>A	ENST00000305444.2	-	1	769	c.770G>T	c.(769-771)gGg>gTg	p.G257V		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	257						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						AAGGTACACCCCAAACCCTGT	0.463																																					p.G257V		Atlas-SNP	.											.	OR7G3	41	.	0			c.G770T						.						94	89	90					19																	9236857		2203	4300	6503	SO:0001583	missense	390883	exon1			TACACCCCAAACC		CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"GPCR / Class A : Olfactory receptors"	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.770G>T	chr19.hg19:g.9236857C>A	ENSP00000302867:p.Gly257Val	192.0	0.0		183.0	91.0	NM_001001958	Q6IFJ6|Q96R99	Missense_Mutation	SNP	ENST00000305444.2	hg19	CCDS32899.1	.	.	.	.	.	.	.	.	.	.	C	10.71	1.427306	0.25726	.	.	ENSG00000170920	ENST00000305444	T	0.00034	8.87	3.74	3.74	0.42951	GPCR, rhodopsin-like superfamily (1);	0.171581	0.27311	U	0.019951	T	0.00271	0.0008	L	0.44542	1.39	0.20703	N	0.999868	D	0.69078	0.997	P	0.61201	0.885	T	0.56475	-0.7973	10	0.66056	D	0.02	.	8.963	0.35858	0.2213:0.7786:0.0:0.0	.	257	Q8NG95	OR7G3_HUMAN	V	257	ENSP00000302867:G257V	ENSP00000302867:G257V	G	-	2	0	OR7G3	9097857	0.000000	0.05858	0.543000	0.28128	0.118000	0.20060	0.749000	0.26320	2.139000	0.66308	0.551000	0.68910	GGG	.	.		0.463	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1			A	9236857	C	A	9236857	3	1	234	1	0	0	0	0	1	0	0	0	11233	623	22	3	171	3	OR7G3	19	9236857	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	161132	9236857	49892126	94	32674										
ZNF578	147660	hgsc.bcm.edu	37	chr19	53014421	53014421	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aaaaacaatataaatttgatAtatgtggcaaagtctttaat	5	3	1	1	rs199506035		TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr19:53014421A>T	ENST00000421239.2	+	6	1031	c.787A>T	c.(787-789)Ata>Tta	p.I263L	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	263					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		TAAATTTGATATATGTGGCAA	0.358																																					p.I263L		Atlas-SNP	.											.	.	.	.	0			c.A787T						.	A	LEU/ILE	0,4396		0,0,2198	91	98	95		787	-2.6	0	19		95	1,8593		0,1,4296	no	missense	ZNF578	NM_001099694.1	5	0,1,6494	TT,TA,AA		0.0116,0.0,0.0077	benign	263/591	53014421	1,12989	2198	4297	6495	SO:0001583	missense	147660	exon6			TTTGATATATGTG	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.787A>T	chr19.hg19:g.53014421A>T	ENSP00000459216:p.Ile263Leu	239.0	0.0		233.0	97.0	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	hg19	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	5.452	0.268581	0.10349	0.0	1.16E-4	ENSG00000258405	ENST00000553364	.	.	.	1.48	-2.63	0.06133	.	.	.	.	.	T	0.15609	0.0376	N	0.16037	0.36	0.09310	N	1	B	0.20671	0.047	B	0.15484	0.013	T	0.26052	-1.0114	7	.	.	.	.	3.5799	0.07949	0.3271:0.2117:0.4612:0.0	.	263	G3V4F6	.	L	263	.	.	I	+	1	0	ZNF578	57706233	0.000000	0.05858	0.002000	0.10522	0.012000	0.07955	-0.394000	0.07296	-0.017000	0.14103	-0.779000	0.03376	ATA	.	.		0.358	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		T	53014421	A	T	53014421	3	4	234	1	0	0	0	0	1	0	0	0	18025	449	16	4	797	4	ZNF578	19	53014421	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	43777564	53014421	6114562	95	32675										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54310876	54310876	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	attggtgcacagggccgctgCcagatgttcactgtaggcgt	14	10	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr19:54310876C>G	ENST00000324134.6	-	4	2284	c.2116G>C	c.(2116-2118)Gca>Cca	p.A706P	NLRP12_ENST00000391773.1_Missense_Mutation_p.A707P|NLRP12_ENST00000345770.5_Missense_Mutation_p.A707P|NLRP12_ENST00000351894.4_Missense_Mutation_p.A706P|NLRP12_ENST00000354278.3_Missense_Mutation_p.A706P|NLRP12_ENST00000391775.3_Missense_Mutation_p.A706P|NLRP12_ENST00000391772.1_Missense_Mutation_p.A707P|NLRP12_ENST00000535162.1_Missense_Mutation_p.A706P	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	706					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		AGGGCCGCTGCCAGATGTTCA	0.562																																					p.L706L		Atlas-SNP	.											.	NLRP12	236	.	0			c.C2116C						.						108	92	97					19																	54310876		2203	4300	6503	SO:0001583	missense	91662	exon4			CCGCTGCCAGATG	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2116G>C	chr19.hg19:g.54310876C>G	ENSP00000319377:p.Ala706Pro	103.0	0.0		126.0	53.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	hg19	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.144639	0.37825	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	D;D;D;D;D;D;D	0.90504	-2.37;-2.37;-2.37;-2.37;-2.37;-2.68;-2.68	3.77	1.26	0.21427	.	0.232869	0.21831	U	0.068479	D	0.91178	0.7221	L	0.57536	1.79	0.21020	N	0.999804	D;D;D;D	0.60160	0.987;0.96;0.978;0.977	P;P;P;P	0.59825	0.827;0.864;0.719;0.864	T	0.82675	-0.0340	10	0.52906	T	0.07	.	7.7211	0.28733	0.4775:0.5225:0.0:0.0	.	707;706;706;706	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	P	706;706;706;706;706;707;707;707	ENSP00000319377:A706P;ENSP00000438030:A706P;ENSP00000340473:A706P;ENSP00000346231:A706P;ENSP00000375655:A706P;ENSP00000375653:A707P;ENSP00000375652:A707P	ENSP00000319377:A706P	A	-	1	0	NLRP12	59002688	0.001000	0.12720	0.008000	0.14137	0.065000	0.16274	-0.337000	0.07852	0.841000	0.35020	0.485000	0.47835	GCA	.	.		0.562	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		G	54310876	C	G	54310876	3	3	234	1	0	0	0	0	1	0	0	0	10483	739	26	4	1193	4	NLRP12	19	54310876	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	1296455	54310876	4818107	96	32676										
ZNF17	7565	hgsc.bcm.edu	37	chr19	57929405	57929405	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tttgcacttttgtcctcagtAggtaaggccctgacacctac	8	12	1	1			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr19:57929405A>G	ENST00000601808.1	+	2	354	c.141A>G	c.(139-141)gtA>gtG	p.V47V	ZNF17_ENST00000595206.1_Intron|ZNF17_ENST00000307658.7_Splice_Site_p.V49V|AC004076.7_ENST00000597410.1_Intron|AC003002.6_ENST00000596400.1_Splice_Site_p.V59V	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	47	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		TGTCCTCAGTAGGTAAGGCCC	0.488																																					p.V47V	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.A141G						.						166	160	162					19																	57929405		2203	4300	6503	SO:0001630	splice_region_variant	7565	exon2			CTCAGTAGGTAAG	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"Zinc fingers, C2H2-type", "-"	12958	protein-coding gene	gene with protein product			"zinc finger protein 17 (HPF3, KOX 10)"			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.142+1A>G	chr19.hg19:g.57929405A>G		124.0	0.0		109.0	46.0	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Silent	SNP	ENST00000601808.1	hg19	CCDS42636.1																																																																																			.	.		0.488	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959	Silent	G	57929405	A	G	57929405	5	3	234	1	0	0	0	0	0	0	1	0	17758	434	15	2	147	2	ZNF17	19	57929405	Splice_Site	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	3618529	57929405	1199578	97	32677										
SRC	6714	hgsc.bcm.edu	37	chr20	36014520	36014520	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	cctctatgactatgagtctaGgacggagacagacctgtcct	10	11	2	4			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr20:36014520G>T	ENST00000373578.2	+	5	642	c.293G>T	c.(292-294)aGg>aTg	p.R98M	SRC_ENST00000358208.4_Missense_Mutation_p.R98M|SRC_ENST00000360723.4_Missense_Mutation_p.R98M|SRC_ENST00000445403.1_Missense_Mutation_p.R98M|SRC_ENST00000373567.2_Missense_Mutation_p.R98M|SRC_ENST00000373558.2_Missense_Mutation_p.R98M	NM_198291.1	NP_938033.1	P12931	SRC_HUMAN	SRC proto-oncogene, non-receptor tyrosine kinase	98	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cellular response to progesterone stimulus (GO:0071393)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|membrane organization (GO:0061024)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of protein homooligomerization (GO:0032463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oogenesis (GO:0048477)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of integrin activation (GO:0033625)|positive regulation of podosome assembly (GO:0071803)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone receptor signaling pathway (GO:0050847)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of bone resorption (GO:0045124)|regulation of caveolin-mediated endocytosis (GO:2001286)|regulation of cell-cell adhesion (GO:0022407)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of epithelial cell migration (GO:0010632)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of protein binding (GO:0043393)|regulation of vascular permeability (GO:0043114)|response to interleukin-1 (GO:0070555)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|T cell costimulation (GO:0031295)|transforming growth factor beta receptor signaling pathway (GO:0007179)|uterus development (GO:0060065)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|growth factor receptor binding (GO:0070851)|heme binding (GO:0020037)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(16)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)			Bosutinib(DB06616)|Dasatinib(DB01254)|Ponatinib(DB08901)	TATGAGTCTAGGACGGAGACA	0.597																																					p.R98M		Atlas-SNP	.											.	SRC	52	.	0			c.G293T						.						196	187	190					20																	36014520		2203	4300	6503	SO:0001583	missense	6714	exon5			AGTCTAGGACGGA	AF077754	CCDS13294.1	20q12-q13	2014-06-25	2014-06-25		ENSG00000197122	ENSG00000197122		"SH2 domain containing"	11283	protein-coding gene	gene with protein product		190090	"v-src avian sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog"	SRC1		2582238	Standard	NM_005417		Approved	ASV, c-src	uc002xgy.3	P12931	OTTHUMG00000032417	ENST00000373578.2:c.293G>T	chr20.hg19:g.36014520G>T	ENSP00000362680:p.Arg98Met	83.0	0.0		108.0	48.0	NM_005417	E1P5V4|Q76P87|Q86VB9|Q9H5A8	Missense_Mutation	SNP	ENST00000373578.2	hg19	CCDS13294.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.143941	0.77888	.	.	ENSG00000197122	ENST00000445403;ENST00000373578;ENST00000360723;ENST00000358208;ENST00000373567;ENST00000373558	T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68	3.99	3.99	0.46301	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.65207	0.2669	M	0.78049	2.395	0.80722	D	1	D	0.64830	0.994	P	0.62491	0.903	T	0.68911	-0.5284	10	0.49607	T	0.09	.	13.9562	0.64150	0.0:0.0:1.0:0.0	.	98	P12931	SRC_HUMAN	M	98	ENSP00000408503:R98M;ENSP00000362680:R98M;ENSP00000353950:R98M;ENSP00000350941:R98M;ENSP00000362668:R98M;ENSP00000362659:R98M	ENSP00000350941:R98M	R	+	2	0	SRC	35447934	1.000000	0.71417	0.845000	0.33349	0.949000	0.60115	9.546000	0.98097	2.222000	0.72286	0.561000	0.74099	AGG	.	.		0.597	SRC-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268142.1	NM_005417		T	36014520	G	T	36014520	3	4	234	1	0	0	0	0	1	0	0	0	15149	1000	35	3	299	3	SRC	20	36014520	Missense_Mutation	SNP	G	TCGA-DD-AAW1-01A-11D-A40P-10		36014520	27011000	98	32678										
PTPRT	11122	hgsc.bcm.edu	37	chr20	41419871	41419871	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	cagaaagtgctgatggcgagCtctgccttcacccagccctc	10	15	2	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr20:41419871C>A	ENST00000373187.1	-	3	449	c.450G>T	c.(448-450)gaG>gaT	p.E150D	PTPRT_ENST00000373198.4_Missense_Mutation_p.E150D|PTPRT_ENST00000356100.2_Missense_Mutation_p.E150D|PTPRT_ENST00000373184.1_Missense_Mutation_p.E150D|PTPRT_ENST00000373193.3_Missense_Mutation_p.E150D|PTPRT_ENST00000373190.1_Missense_Mutation_p.E150D|PTPRT_ENST00000373201.1_Missense_Mutation_p.E150D			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	150	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TGATGGCGAGCTCTGCCTTCA	0.488																																					p.E150D		Atlas-SNP	.											.	PTPRT	372	.	0			c.G450T						.						92	96	95					20																	41419871		2013	4195	6208	SO:0001583	missense	11122	exon3			GGCGAGCTCTGCC	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.450G>T	chr20.hg19:g.41419871C>A	ENSP00000362283:p.Glu150Asp	163.0	0.0		175.0	78.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.780753	0.70222	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.02323	4.34;4.34;4.34;4.34;4.34;4.34;4.34	5.67	2.11	0.27256	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.000000	0.85682	D	0.000000	T	0.14570	0.0352	M	0.85373	2.75	0.46981	D	0.999279	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.997	T	0.00329	-1.1813	10	0.72032	D	0.01	.	10.4604	0.44577	0.0:0.657:0.0:0.343	.	150;150	O14522-1;O14522	.;PTPRT_HUMAN	D	150	ENSP00000362286:E150D;ENSP00000362283:E150D;ENSP00000362289:E150D;ENSP00000348408:E150D;ENSP00000362294:E150D;ENSP00000362280:E150D;ENSP00000362297:E150D	ENSP00000348408:E150D	E	-	3	2	PTPRT	40853285	0.846000	0.29590	1.000000	0.80357	0.997000	0.91878	0.030000	0.13688	0.480000	0.27534	0.561000	0.74099	GAG	.	.		0.488	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	41419871	C	A	41419871	3	1	234	1	0	0	0	0	1	0	0	0	12827	796	28	3	4052	3	PTPRT	20	41419871	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	5405351	41419871	21605649	99	32679										
TPTE	7179	hgsc.bcm.edu	37	chr21	10969094	10969094	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	cctttcactgataggtgacaCccgggctgctcctttaaatt	8	12	1	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr21:10969094C>T	ENST00000361285.4	-	7	483	c.154G>A	c.(154-156)Gtg>Atg	p.V52M	TPTE_ENST00000342420.5_Intron|TPTE_ENST00000415664.2_Intron|TPTE_ENST00000298232.7_Intron	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	52					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ATAGGTGACACCCGGGCTGCT	0.448																																					p.V52M		Atlas-SNP	.											.	TPTE	513	.	0			c.G154A						.						244	227	232					21																	10969094		2203	4300	6503	SO:0001583	missense	7179	exon7			GTGACACCCGGGC	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.154G>A	chr21.hg19:g.10969094C>T	ENSP00000355208:p.Val52Met	96.0	0.0		125.0	22.0	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	C	2.201	-0.382944	0.04966	.	.	ENSG00000166157	ENST00000361285;ENST00000328758	D	0.95412	-3.7	0.558	0.558	0.17266	.	8.382320	0.01685	U	0.026352	D	0.89375	0.6697	N	0.14661	0.345	0.09310	N	1	B	0.30406	0.278	B	0.21917	0.037	T	0.83140	-0.0109	9	0.45353	T	0.12	3.485	.	.	.	.	52	P56180	TPTE_HUMAN	M	52;34	ENSP00000355208:V52M	ENSP00000399471:V34M	V	-	1	0	TPTE	9990965	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.613000	0.02059	0.578000	0.29487	0.400000	0.26472	GTG	.	.		0.448	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			T	10969094	C	T	10969094	3	4	234	1	0	0	0	0	1	0	0	0	16445	507	18	3	1573	3	TPTE	21	10969094	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10		10969094	37160801	100	32680										
GRIK1	2897	hgsc.bcm.edu	37	chr21	30927428	30927428	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	tgaattctccaatagctacaAatacagaaaggaccagtccg	7	10	1	2			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr21:30927428A>T	ENST00000399907.1	-	16	2963	c.2552T>A	c.(2551-2553)tTt>tAt	p.F851Y	GRIK1_ENST00000389125.3_Missense_Mutation_p.F836Y|GRIK1_ENST00000399913.1_Missense_Mutation_p.F851Y|GRIK1_ENST00000309434.7_Missense_Mutation_p.F853Y|GRIK1_ENST00000327783.4_Missense_Mutation_p.F851Y|GRIK1_ENST00000399914.1_Missense_Mutation_p.F836Y|GRIK1_ENST00000399909.1_Missense_Mutation_p.F836Y|GRIK1_ENST00000535441.1_Missense_Mutation_p.F853Y|GRIK1_ENST00000389124.2_Missense_Mutation_p.F851Y	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	851					adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	AATAGCTACAAATACAGAAAG	0.428																																					p.F851Y		Atlas-SNP	.											.	GRIK1	293	.	0			c.T2552A						.						78	78	78					21																	30927428		2203	4300	6503	SO:0001583	missense	2897	exon16			GCTACAAATACAG		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.2552T>A	chr21.hg19:g.30927428A>T	ENSP00000382791:p.Phe851Tyr	72.0	0.0		76.0	37.0	NM_000830	Q13001|Q86SU9	Missense_Mutation	SNP	ENST00000399907.1	hg19	CCDS42913.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.688568	0.88639	.	.	ENSG00000171189	ENST00000327783;ENST00000389125;ENST00000399913;ENST00000399914;ENST00000535441;ENST00000541508;ENST00000389124;ENST00000399907;ENST00000399909;ENST00000309434	T;T;T;T;T;T;T;T;T	0.13196	2.61;2.68;2.67;2.62;2.67;2.64;2.68;2.68;2.68	4.88	4.88	0.63580	.	0.047550	0.85682	D	0.000000	T	0.12008	0.0292	N	0.08118	0	0.80722	D	1	P;P;P;P	0.51449	0.898;0.908;0.898;0.945	P;B;P;P	0.49140	0.493;0.397;0.493;0.601	T	0.14980	-1.0453	10	0.87932	D	0	.	14.5982	0.68422	1.0:0.0:0.0:0.0	.	836;851;851;836	E7EPY9;E9PD61;P39086;P39086-2	.;.;GRIK1_HUMAN;.	Y	851;836;851;836;853;712;851;851;836;853	ENSP00000327687:F851Y;ENSP00000373777:F836Y;ENSP00000382797:F851Y;ENSP00000382798:F836Y;ENSP00000446326:F853Y;ENSP00000373776:F851Y;ENSP00000382791:F851Y;ENSP00000382793:F836Y;ENSP00000311646:F853Y	ENSP00000311646:F853Y	F	-	2	0	GRIK1	29849299	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.257000	0.78362	2.169000	0.68431	0.528000	0.53228	TTT	.	.		0.428	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1			T	30927428	A	T	30927428	3	4	234	1	0	0	0	0	1	0	0	0	6782	14	1	4	372	4	GRIK1	21	30927428	Missense_Mutation	SNP	A	TCGA-DD-AAW1-01A-11D-A40P-10	19958334	30927428	17202467	101	32681										
TOP3B	8940	hgsc.bcm.edu	37	chr22	22322015	22322015	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ttgtcatgtttaaaaacatcTgtgcgatctcccggtcaaac	7	10	4	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr22:22322015T>C	ENST00000398793.2	-	8	1246	c.812A>G	c.(811-813)cAg>cGg	p.Q271R	TOP3B_ENST00000413067.2_5'UTR|TOP3B_ENST00000357179.5_Missense_Mutation_p.Q271R	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	271					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		TAAAAACATCTGTGCGATCTC	0.502																																					p.Q271R		Atlas-SNP	.											.	TOP3B	107	.	0			c.A812G						.						165	139	148					22																	22322015		2203	4300	6503	SO:0001583	missense	8940	exon8			AACATCTGTGCGA	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.812A>G	chr22.hg19:g.22322015T>C	ENSP00000381773:p.Gln271Arg	56.0	0.0		72.0	32.0	NM_003935	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	ENST00000398793.2	hg19	CCDS13797.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.76|12.76	2.035030|2.035030	0.35893|0.35893	.|.	.|.	ENSG00000100038|ENSG00000100038	ENST00000357179;ENST00000398793|ENST00000457270	T;T|.	0.22134|.	1.97;1.97|.	4.71|4.71	4.71|4.71	0.59529|0.59529	DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central (1);|.	0.054213|.	0.85682|.	D|.	0.000000|.	T|T	0.42040|0.42040	0.1185|0.1185	N|N	0.12961|0.12961	0.28|0.28	0.80722|0.80722	D|D	1|1	B|.	0.02656|.	0.0|.	B|.	0.06405|.	0.002|.	T|T	0.31251|0.31251	-0.9950|-0.9950	10|5	0.11485|.	T|.	0.65|.	.|.	14.3402|14.3402	0.66619|0.66619	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	271|.	O95985|.	TOP3B_HUMAN|.	R|G	271|66	ENSP00000349705:Q271R;ENSP00000381773:Q271R|.	ENSP00000349705:Q271R|.	Q|R	-|-	2|1	0|2	TOP3B|TOP3B	20652015|20652015	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	7.699000|7.699000	0.84547|0.84547	1.974000|1.974000	0.57490|0.57490	0.533000|0.533000	0.62120|0.62120	CAG|AGA	.	.		0.502	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935		C	22322015	T	C	22322015	3	2	234	1	0	0	0	0	1	0	0	0	16383	1580	55	2	1820	2	TOP3B	22	22322015	Missense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10		22322015	28982551	102	32682										
ENTHD1	150350	hgsc.bcm.edu	37	chr22	40283506	40283506	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	aactttctttgatccattctTgatgagataatccattaggg	7	7	2	3			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chr22:40283506T>A	ENST00000325157.6	-	2	497	c.247A>T	c.(247-249)Aag>Tag	p.K83*		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	83	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.									breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					GATCCATTCTTGATGAGATAA	0.408																																					p.K83X		Atlas-SNP	.											.	ENTHD1	83	.	0			c.A247T						.						158	160	159					22																	40283506		2203	4300	6503	SO:0001587	stop_gained	150350	exon2			CATTCTTGATGAG	AK093154	CCDS13998.1	22q13.1	2006-06-26			ENSG00000176177	ENSG00000176177			26352	protein-coding gene	gene with protein product						12477932	Standard	NM_152512		Approved	FLJ25421	uc003ayg.3	Q8IYW4	OTTHUMG00000151098	ENST00000325157.6:c.247A>T	chr22.hg19:g.40283506T>A	ENSP00000317431:p.Lys83*	106.0	0.0		114.0	53.0	NM_152512	B0QYD5|Q5H9F7|Q96LK3	Nonsense_Mutation	SNP	ENST00000325157.6	hg19	CCDS13998.1	.	.	.	.	.	.	.	.	.	.	T	39	7.757699	0.98474	.	.	ENSG00000176177	ENST00000325157	.	.	.	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.5867	12.8344	0.57765	0.0:0.0:0.1358:0.8642	.	.	.	.	X	83	.	ENSP00000317431:K83X	K	-	1	0	ENTHD1	38613452	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.257000	0.72480	2.183000	0.69458	0.533000	0.62120	AAG	.	.		0.408	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512		A	40283506	T	A	40283506	4	1	234	1	0	0	0	0	0	1	0	0	5139	1821	63	4	1600	4	ENTHD1	22	40283506	Nonsense_Mutation	SNP	T	TCGA-DD-AAW1-01A-11D-A40P-10	17961491	40283506	11021060	103	32683										
SLC25A6	293	hgsc.bcm.edu	37	chrX	1508319	1508319	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	cgtccgctgccaggcgggttCtggcgaaatccagcgggtac	15	13	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chrX:1508319C>T	ENST00000381401.5	-	2	1127	c.413G>A	c.(412-414)aGa>aAa	p.R138K	SLC25A6_ENST00000475167.1_5'UTR	NM_001636.3	NP_001627.2	P12236	ADT3_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6	138					active induction of host immune response by virus (GO:0046732)|ADP transport (GO:0015866)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|modulation by virus of host morphology or physiology (GO:0019048)|protein targeting to mitochondrion (GO:0006626)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP:ADP antiporter activity (GO:0005471)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(8)|upper_aerodigestive_tract(1)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Clodronate(DB00720)	CAGGCGGGTTCTGGCGAAATC	0.657																																					p.R138K		Atlas-SNP	.											.	SLC25A6	27	.	0			c.G413A						.						110	118	115					X																	1508319		2203	4296	6499	SO:0001583	missense	293	exon2			CGGGTTCTGGCGA	AY007135	CCDS14114.1	Xp22.32 and Yp11.3	2013-05-22			ENSG00000169100	ENSG00000169100		"Pseudoautosomal regions / PAR1", "Solute carriers"	10992	protein-coding gene	gene with protein product		300151, 403000		ANT3			Standard	NM_001636		Approved	ANT3Y, MGC17525	uc004cpt.3	P12236	OTTHUMG00000021058	ENST00000381401.5:c.413G>A	chrX.hg19:g.1508319C>T	ENSP00000370808:p.Arg138Lys	181.0	0.0		202.0	81.0	NM_001636	Q96C49	Missense_Mutation	SNP	ENST00000381401.5	hg19	CCDS14114.1	.	.	.	.	.	.	.	.	.	.	.	18.83	3.706665	0.68615	.	.	ENSG00000169100	ENST00000381401;ENST00000447786	T	0.64991	-0.13	1.85	1.85	0.25348	Mitochondrial carrier domain (2);	0.000000	0.47455	D	0.000230	T	0.71281	0.3321	L	0.52126	1.63	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62812	-0.6775	10	0.87932	D	0	.	12.0543	0.53524	0.0:1.0:0.0:0.0	.	138	P12236	ADT3_HUMAN	K	138	ENSP00000370808:R138K	ENSP00000370808:R138K	R	-	2	0	SLC25A6	1468319	1.000000	0.71417	0.116000	0.21606	0.609000	0.37215	5.896000	0.69822	0.982000	0.38575	0.402000	0.26972	AGA	.	.		0.657	SLC25A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055596.1	NM_001636		T	1508319	C	T	1508319	3	4	234	1	0	0	0	0	1	0	0	0	14528	913	32	3	495	3	SLC25A6	23	1508319	Missense_Mutation	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10		1508319	153762241	104	32684										
AR	367	hgsc.bcm.edu	37	chrX	66765228	66765229	+	Missense_Mutation	DNP	AG	AG	GC													0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	cagcagcagcagcagcagcaAgagactagccccaggcagca							TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chrX:66765228_66765229AG>GC	ENST00000374690.3	+	1	764_765	c.240_241AG>GC	c.(238-243)caAGag>caGCag	p.E81Q	AR_ENST00000396044.3_Missense_Mutation_p.E81Q|AR_ENST00000504326.1_Missense_Mutation_p.E81Q|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	79	Gln-rich.|Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	agcagcagcaagagactagccc	0.644									Androgen Insensitivity Syndrome																												p.Q80Q|p.E81Q		Atlas-SNP	.											.	AR	249	.	0			c.A240G|c.G241C						.																																			SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GCAGCAAGAGACT|CAGCAAGAGACTA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	Exception_encountered	chrX.hg19:g.66765228_66765229delinsGC	ENSP00000363822:p.Glu81Gln	97.0|96.0	0.0		311.0|313.0	16.0|13.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent|Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.		0.644	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		GC	66765229	AG	GC	66765228	3	3	234	1	0	0	0	0	1	0	0	0	836	69	3	2	242	2	AR	23	66765228	Missense_Mutation	DNP	AG	TCGA-DD-AAW1-01A-11D-A40P-10	65256909	66765228	88505332	105	32685										
MPP1	4354	hgsc.bcm.edu	37	chrX	154020561	154020561	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0471698113207547	5	1	1.1283863368669	1.1283863368669	1.1283863368669	0.282051282051282	0.956410256410256	0	ttcaatggatgcgatacagcCtgccaagccaaaacaacaaa	7	11	1	0			TCGA-DD-AAW1-01A-11D-A40P-10	TCGA-DD-AAW1-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e922ce32-e6f6-497a-ae31-ae362055542d	7730846e-e3d4-44d3-a53c-47ab352eaf6e	g.chrX:154020561C>T	ENST00000369534.3	-	2	250		c.e2-1		MPP1_ENST00000462825.1_Intron|MPP1_ENST00000393531.1_Splice_Site|MPP1_ENST00000413259.3_Splice_Site	NM_001166460.1|NM_001166461.1|NM_002436.3	NP_001159932.1|NP_001159933.1|NP_002427.1	Q00013	EM55_HUMAN	membrane protein, palmitoylated 1, 55kDa						nucleotide phosphorylation (GO:0046939)|regulation of neutrophil chemotaxis (GO:0090022)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(9)|ovary(2)|prostate(1)	21	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GCGATACAGCCTGCCAAGCCA	0.517																																					.		Atlas-SNP	.											.	MPP1	52	.	0			c.103-1G>A						.						62	53	56					X																	154020561		2203	4300	6503	SO:0001630	splice_region_variant	4354	exon3			TACAGCCTGCCAA		CCDS14762.1, CCDS55544.1, CCDS55545.1	Xq28	2008-03-04	2002-08-29		ENSG00000130830	ENSG00000130830			7219	protein-coding gene	gene with protein product		305360	"membrane protein, palmitoylated 1 (55kD)"	DXS552E		1713685	Standard	NM_002436		Approved	PEMP	uc004fmp.2	Q00013	OTTHUMG00000024244	ENST00000369534.3:c.103-1G>A	chrX.hg19:g.154020561C>T		56.0	0.0		115.0	95.0	NM_002436	B4DZV5|G3XAI1|Q2TSB6|Q5J7V5	Splice_Site	SNP	ENST00000369534.3	hg19	CCDS14762.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.089769	0.36855	.	.	ENSG00000130830	ENST00000369534;ENST00000413259;ENST00000393531;ENST00000369531	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1399	0.65313	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MPP1	153673755	1.000000	0.71417	0.040000	0.18447	0.009000	0.06853	4.642000	0.61383	2.074000	0.62210	0.513000	0.50165	.	.	.		0.517	MPP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061191.3	NM_002436	Intron	T	154020561	C	T	154020561	5	4	234	1	0	0	0	0	0	0	1	0	9742	695	24	3	1342	3	MPP1	23	154020561	Splice_Site	SNP	C	TCGA-DD-AAW1-01A-11D-A40P-10	87255333	154020561	1249999	106	32686										
ASAP3	55616	hgsc.bcm.edu	37	chr1	23763700	23763700	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tgagcagctttgtgaggtcgTgcggctccccatcatggccg	14	12	1	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr1:23763700T>A	ENST00000336689.3	-	14	1309	c.1265A>T	c.(1264-1266)cAc>cTc	p.H422L	ASAP3_ENST00000437606.2_Missense_Mutation_p.H413L|ASAP3_ENST00000495646.1_5'Flank	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	422					cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						TGTGAGGTCGTGCGGCTCCCC	0.701																																					p.H422L		Atlas-SNP	.											.	ASAP3	65	.	0			c.A1265T						.						16	17	17					1																	23763700		2200	4300	6500	SO:0001583	missense	55616	exon14			AGGTCGTGCGGCT	AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	14987	protein-coding gene	gene with protein product	"centaurin, beta 6"		"development and differentiation enhancing factor-like 1"	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.1265A>T	chr1.hg19:g.23763700T>A	ENSP00000338769:p.His422Leu	123.0	0.0		197.0	72.0	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Missense_Mutation	SNP	ENST00000336689.3	hg19	CCDS235.1	.	.	.	.	.	.	.	.	.	.	T	11.01	1.514166	0.27123	.	.	ENSG00000088280	ENST00000336689;ENST00000437606	T;T	0.52057	0.68;0.68	4.35	2.07	0.26955	.	0.408591	0.24085	N	0.041695	T	0.26774	0.0655	N	0.14661	0.345	0.36068	D	0.84194	B;B;B	0.14805	0.011;0.0;0.006	B;B;B	0.09377	0.004;0.0;0.002	T	0.14531	-1.0469	10	0.44086	T	0.13	.	7.5042	0.27534	0.0:0.207:0.0:0.793	.	413;291;422	Q8TDY4-3;B4DRP2;Q8TDY4	.;.;ASAP3_HUMAN	L	422;413	ENSP00000338769:H422L;ENSP00000408826:H413L	ENSP00000338769:H422L	H	-	2	0	ASAP3	23636287	1.000000	0.71417	0.983000	0.44433	0.136000	0.21042	1.745000	0.38278	0.807000	0.34208	0.391000	0.25812	CAC	.	.		0.701	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		A	23763700	T	A	23763700	3	1	235	1	0	0	0	0	1	0	0	0	1012	1696	59	4	1494	4	ASAP3	1	23763700	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10		23763700	225486921	1	32687										
MKNK1	8569	hgsc.bcm.edu	37	chr1	47048993	47048993	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gatgggaaggggttcgctacTgcccatctctaggagataag	14	8	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr1:47048993T>G	ENST00000371946.4	-	3	206	c.43A>C	c.(43-45)Agt>Cgt	p.S15R	MKNK1_ENST00000371945.4_Missense_Mutation_p.S15R|MKNK1_ENST00000341183.5_Missense_Mutation_p.S15R|MKNK1_ENST00000465783.1_Missense_Mutation_p.S15R|MKNK1_ENST00000545730.1_Missense_Mutation_p.S15R|MKNK1_ENST00000428112.2_Missense_Mutation_p.S15R|MKNK1_ENST00000371944.4_5'UTR|MKNK1_ENST00000525888.1_5'Flank	NM_003684.5	NP_003675.2	Q9BUB5	MKNK1_HUMAN	MAP kinase interacting serine/threonine kinase 1	15					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast growth factor receptor signaling pathway (GO:0008543)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|response to salt stress (GO:0009651)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	13	Acute lymphoblastic leukemia(166;0.155)					GGTTCGCTACTGCCCATCTCT	0.507																																					p.S15R		Atlas-SNP	.											.	MKNK1	36	.	0			c.A43C						.						60	62	61					1																	47048993		2203	4300	6503	SO:0001583	missense	8569	exon3			CGCTACTGCCCAT	AB000409	CCDS538.1, CCDS30705.1, CCDS44134.1	1p33	2008-02-05			ENSG00000079277	ENSG00000079277			7110	protein-coding gene	gene with protein product		606724				9155018	Standard	NM_003684		Approved	MNK1	uc001cqb.4	Q9BUB5	OTTHUMG00000007983	ENST00000371946.4:c.43A>C	chr1.hg19:g.47048993T>G	ENSP00000361014:p.Ser15Arg	50.0	0.0		49.0	18.0	NM_003684	D3DQ20|D3DQ21|O00312|Q5TC06|Q5TC07|Q6V0N6	Missense_Mutation	SNP	ENST00000371946.4	hg19	CCDS538.1	.	.	.	.	.	.	.	.	.	.	T	15.10	2.734135	0.48939	.	.	ENSG00000079277	ENST00000371946;ENST00000371945;ENST00000341183;ENST00000428112;ENST00000532783;ENST00000496619;ENST00000528237;ENST00000545730;ENST00000529170;ENST00000531769;ENST00000465783;ENST00000532110	T;T;T;T;T;T;T;T;T;T;T;T	0.71341	-0.12;-0.51;-0.56;-0.56;-0.23;-0.22;0.07;-0.16;1.44;1.44;1.39;1.3	5.78	5.78	0.91487	.	0.121240	0.85682	D	0.000000	T	0.58652	0.2137	N	0.25485	0.75	0.50039	D	0.999847	B;B;B;B	0.17268	0.011;0.008;0.019;0.021	B;B;B;B	0.16289	0.013;0.009;0.015;0.013	T	0.54289	-0.8316	10	0.33141	T	0.24	.	14.0601	0.64795	0.0:0.0:0.0:1.0	.	15;15;15;15	B4E1V9;Q9BUB5-3;Q9BUB5-2;Q9BUB5	.;.;.;MKNK1_HUMAN	R	15;15;15;15;3;15;9;15;15;15;15;85	ENSP00000361014:S15R;ENSP00000361013:S15R;ENSP00000339573:S15R;ENSP00000411135:S15R;ENSP00000431837:S3R;ENSP00000436709:S15R;ENSP00000432665:S9R;ENSP00000440974:S15R;ENSP00000435163:S15R;ENSP00000434021:S15R;ENSP00000434834:S15R;ENSP00000431985:S85R	ENSP00000339573:S15R	S	-	1	0	MKNK1	46821580	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.352000	0.66028	2.194000	0.70268	0.533000	0.62120	AGT	.	.		0.507	MKNK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021897.2	NM_003684		G	47048993	T	G	47048993	3	3	235	1	0	0	0	0	1	0	0	0	9613	1580	55	5	1402	5	MKNK1	1	47048993	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	23285293	47048993	202201628	2	32688										
MOBKL2C	148932	hgsc.bcm.edu	37	chr1	47075833	47075833	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	actcggaagaggcgggtcagGatcttggtgcagacctgctg	16	9	2	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr1:47075833G>T	ENST00000319928.3	-	3	692	c.462C>A	c.(460-462)atC>atA	p.I154I	MKNK1_ENST00000545730.1_Intron|MOB3C_ENST00000371940.1_Silent_p.I177I|MOB3C_ENST00000271139.8_Silent_p.I206I|MOB3C_ENST00000477318.1_5'UTR	NM_201403.2	NP_958805.1	Q70IA8	MOB3C_HUMAN	MOB kinase activator 3C	154							metal ion binding (GO:0046872)										GGCGGGTCAGGATCTTGGTGC	0.567																																					p.I206I		Atlas-SNP	.											.	MOB3C	1	.	0			c.C618A						.						80	75	77					1																	47075833		2203	4300	6503	SO:0001819	synonymous_variant	148932	exon3			GGTCAGGATCTTG	AK091808	CCDS539.1, CCDS540.1	1p34.1	2011-09-28	2011-09-28	2011-09-28	ENSG00000142961	ENSG00000142961		"MOB kinase activators"	29800	protein-coding gene	gene with protein product			"MOB1, Mps One Binder kinase activator-like 2C (yeast)"	MOBKL2C		12477932	Standard	NM_145279		Approved	MOB1E	uc001cqe.4	Q70IA8	OTTHUMG00000007989	ENST00000319928.3:c.462C>A	chr1.hg19:g.47075833G>T		67.0	0.0		91.0	40.0	NM_145279	D3DQ22|Q0VA98|Q5TC10|Q5TC11|Q8NAZ2|Q8NF28	Silent	SNP	ENST00000319928.3	hg19	CCDS540.1																																																																																			.	.		0.567	MOB3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145279		T	47075833	G	T	47075833	2	4	235	1	0	0	0	0	0	0	0	1	9695	1164	41	3		3	MOBKL2C	1	47075833	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	26840	47075833	202174788	3	32689										
TCHH	7062	hgsc.bcm.edu	37	chr1	152080354	152080354	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gctgttcctccctctcctggCggagctgttcctcctcgcgg	11	17	1	0	rs199599922		TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr1:152080354C>A	ENST00000368804.1	-	2	5338	c.5339G>T	c.(5338-5340)cGc>cTc	p.R1780L		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1780	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTCTCCTGGCGGAGCTGTTC	0.592																																					p.R1780L		Atlas-SNP	.											TCHH,NS,carcinoma,0,1	TCHH	275	.	0			c.G5339T						.						65	66	66					1																	152080354		1903	4116	6019	SO:0001583	missense	7062	exon3			TCCTGGCGGAGCT	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.5339G>T	chr1.hg19:g.152080354C>A	ENSP00000357794:p.Arg1780Leu	58.0	1.0		123.0	77.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	C	9.217	1.032365	0.19590	.	.	ENSG00000159450	ENST00000368804	T	0.10099	2.91	4.03	-3.57	0.04612	.	.	.	.	.	T	0.00815	0.0027	N	0.02225	-0.63	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.46303	-0.9201	9	0.30078	T	0.28	.	1.3741	0.02216	0.4511:0.2437:0.1213:0.1839	.	1780	Q07283	TRHY_HUMAN	L	1780	ENSP00000357794:R1780L	ENSP00000357794:R1780L	R	-	2	0	TCHH	150346978	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.302000	0.02746	-1.171000	0.02765	-1.564000	0.00881	CGC	.	C|0.999;A|0.001		0.592	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		A	152080354	C	A	152080354	3	1	235	1	0	0	0	0	1	0	0	0	15715	768	27	1	496	1	TCHH	1	152080354	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	105004521	152080354	97170267	4	32690										
INTS3	65123	hgsc.bcm.edu	37	chr1	153740305	153740305	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gccctccatctacacagaggTcagtgcctgcatccgtatct	8	15	3	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr1:153740305T>A	ENST00000318967.2	+	21	2812		c.e21+2		INTS3_ENST00000456435.1_Splice_Site|INTS3_ENST00000476843.1_Splice_Site|INTS3_ENST00000512605.1_Splice_Site|INTS3_ENST00000435409.2_Splice_Site	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3						cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TACACAGAGGTCAGTGCCTGC	0.582																																					.		Atlas-SNP	.											.	INTS3	83	.	0			c.2244+2T>A						.						75	63	67					1																	153740305		2203	4300	6503	SO:0001630	splice_region_variant	65123	exon21			CAGAGGTCAGTGC	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"sensor of single-strand DNA complex subunit A"	611347	"chromosome 1 open reading frame 60"	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.2244+2T>A	chr1.hg19:g.153740305T>A		21.0	0.0		66.0	20.0	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Splice_Site	SNP	ENST00000318967.2	hg19	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	T	15.31	2.794223	0.50102	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5963	0.56472	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	INTS3	152006929	1.000000	0.71417	1.000000	0.80357	0.289000	0.27227	7.165000	0.77544	2.234000	0.73211	0.459000	0.35465	.	.	.		0.582	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	Intron	A	153740305	T	A	153740305	5	1	235	1	0	0	0	0	0	0	1	0	7788	1681	58	4	2328	4	INTS3	1	153740305	Splice_Site	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	1659951	153740305	95510316	5	32691										
DCST1	149095	hgsc.bcm.edu	37	chr1	155015937	155015937	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ccggctggagtgggccctggGgctgctgcacgtgctgctct	17	13	1	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr1:155015937G>A	ENST00000295542.1	+	10	1220	c.1124G>A	c.(1123-1125)gGg>gAg	p.G375E	DCST1_ENST00000368419.2_Missense_Mutation_p.G375E|RP11-307C12.11_ENST00000452962.1_RNA|DCST1_ENST00000423025.2_Missense_Mutation_p.G350E|DCST1_ENST00000392480.1_Missense_Mutation_p.G375E	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	375						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			TGGGCCCTGGGGCTGCTGCAC	0.692																																					p.G375E		Atlas-SNP	.											.	DCST1	69	.	0			c.G1124A						.						51	52	52					1																	155015937		2203	4299	6502	SO:0001583	missense	149095	exon10			CCCTGGGGCTGCT	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.1124G>A	chr1.hg19:g.155015937G>A	ENSP00000295542:p.Gly375Glu	68.0	0.0		171.0	56.0	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	hg19	CCDS1083.1	.	.	.	.	.	.	.	.	.	.	g	15.20	2.761967	0.49468	.	.	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.24151	1.89;1.87;1.91;1.87	3.99	2.05	0.26809	.	1.611180	0.04084	N	0.310062	T	0.29588	0.0738	M	0.70595	2.14	0.43259	D	0.995193	D;D;D	0.76494	0.999;0.995;0.999	D;P;D	0.66716	0.946;0.871;0.946	T	0.48514	-0.9029	10	0.23891	T	0.37	-16.1869	5.1654	0.15082	0.1171:0.2121:0.6708:0.0	.	350;400;375	E9PHV3;E9PJX3;Q5T197	.;.;DCST1_HUMAN	E	375;375;350;375	ENSP00000295542:G375E;ENSP00000376271:G375E;ENSP00000387369:G350E;ENSP00000357404:G375E	ENSP00000295542:G375E	G	+	2	0	DCST1	153282561	0.995000	0.38212	0.955000	0.39395	0.721000	0.41392	0.415000	0.21181	0.326000	0.23384	-0.348000	0.07805	GGG	.	.		0.692	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494		A	155015937	G	A	155015937	3	1	235	1	0	0	0	0	1	0	0	0	4304	1232	43	3	1158	3	DCST1	1	155015937	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	1275632	155015937	94234684	6	32692										
LAMC2	3918	hgsc.bcm.edu	37	chr1	183190045	183190045	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	atgggcattcagccagctgcCgcagctctgcagaatacagt	11	12	2	1	rs184817147	byFrequency	TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr1:183190045C>A	ENST00000264144.4	+	5	654	c.589C>A	c.(589-591)Cgc>Agc	p.R197S	LAMC2_ENST00000493293.1_Missense_Mutation_p.R197S	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	197					cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)	p.R197C(1)		breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						AGCCAGCTGCCGCAGCTCTGC	0.468																																					p.R197S		Atlas-SNP	.											LAMC2,caecum,carcinoma,0,1	LAMC2	113	.	1	Substitution - Missense(1)	large_intestine(1)	c.C589A						.						77	79	78					1																	183190045		2203	4300	6503	SO:0001583	missense	3918	exon5			AGCTGCCGCAGCT	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.589C>A	chr1.hg19:g.183190045C>A	ENSP00000264144:p.Arg197Ser	160.0	1.0		323.0	87.0	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	hg19	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	C	6.301	0.423590	0.11928	.	.	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.16073	2.52;2.37	5.41	4.42	0.53409	Growth factor, receptor (1);	0.908562	0.09424	N	0.804096	T	0.06188	0.0160	N	0.02539	-0.55	0.22112	N	0.999353	B;B	0.10296	0.001;0.003	B;B	0.06405	0.001;0.002	T	0.31110	-0.9955	10	0.07325	T	0.83	.	7.7479	0.28879	0.4224:0.4614:0.1162:0.0	.	197;197	Q13753;Q13753-2	LAMC2_HUMAN;.	S	197	ENSP00000432063:R197S;ENSP00000264144:R197S	ENSP00000264144:R197S	R	+	1	0	LAMC2	181456668	0.015000	0.18098	0.974000	0.42286	0.991000	0.79684	0.176000	0.16782	2.529000	0.85273	0.655000	0.94253	CGC	.	C|0.998;T|0.002		0.468	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		A	183190045	C	A	183190045	3	1	235	1	0	0	0	0	1	0	0	0	8624	652	23	1	607	1	LAMC2	1	183190045	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	28174108	183190045	66060576	7	32693										
USH2A	7399	hgsc.bcm.edu	37	chr1	216019200	216019200	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gttgcatgaagtcctgcactGttgatgctgtggactccatt	11	9	0	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr1:216019200G>A	ENST00000307340.3	-	45	9407	c.9021C>T	c.(9019-9021)aaC>aaT	p.N3007N	USH2A_ENST00000366943.2_Silent_p.N3007N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3007	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GTCCTGCACTGTTGATGCTGT	0.443										HNSCC(13;0.011)																											p.N3007N		Atlas-SNP	.											USH2A,NS,carcinoma,0,1	USH2A	1168	.	0			c.C9021T						.						95	88	90					1																	216019200		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon45			TGCACTGTTGATG	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9021C>T	chr1.hg19:g.216019200G>A		151.0	0.0		254.0	76.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.443	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216019200	G	A	216019200	2	1	235	1	0	0	0	0	0	0	0	1	17051	1368	48	3		3	USH2A	1	216019200	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	32829155	216019200	33231421	8	32694										
TBCE	6905	hgsc.bcm.edu	37	chr1	235605132	235605132	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tttgctttcttaaacagaatAtggtgcacctgaagattggg	10	6	1	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr1:235605132A>G	ENST00000366601.3	+	14	1450	c.1274A>G	c.(1273-1275)tAt>tGt	p.Y425C	TBCE_ENST00000472011.1_3'UTR|TBCE_ENST00000543662.1_Missense_Mutation_p.Y476C|TBCE_ENST00000406207.1_Missense_Mutation_p.Y425C			Q15813	TBCE_HUMAN	tubulin folding cofactor E	425					'de novo' posttranslational protein folding (GO:0051084)|adult locomotory behavior (GO:0008344)|cellular protein metabolic process (GO:0044267)|developmental growth (GO:0048589)|microtubule cytoskeleton organization (GO:0000226)|muscle atrophy (GO:0014889)|peripheral nervous system neuron axonogenesis (GO:0048936)|post-chaperonin tubulin folding pathway (GO:0007023)|post-embryonic development (GO:0009791)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	chaperone binding (GO:0051087)			NS(1)|endometrium(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	14	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;2.56e-05)			TAAACAGAATATGGTGCACCT	0.343																																					p.Y425C		Atlas-SNP	.											.	TBCE	40	.	0			c.A1274G						.						89	89	89					1																	235605132		2203	4300	6503	SO:0001583	missense	6905	exon14			CAGAATATGGTGC	U61232	CCDS1605.1, CCDS73052.1	1q42.3	2014-02-04	2006-11-21		ENSG00000116957	ENSG00000116957			11582	protein-coding gene	gene with protein product		604934	"tubulin-specific chaperone e", "Kenny-Caffey syndrome", "hypoparathyroidism, growth and mental retardation, and dysmorphism"	KCS, HRD		8706133, 9806825, 12389028	Standard	NM_001079515		Approved	KCS1, pac2	uc001hxa.1	Q15813	OTTHUMG00000039987	ENST00000366601.3:c.1274A>G	chr1.hg19:g.235605132A>G	ENSP00000355560:p.Tyr425Cys	100.0	0.0		128.0	39.0	NM_003193	A8K8C2|B7Z3P1	Missense_Mutation	SNP	ENST00000366601.3	hg19	CCDS1605.1	.	.	.	.	.	.	.	.	.	.	A	18.92	3.725600	0.68959	.	.	ENSG00000116957	ENST00000366601;ENST00000406207;ENST00000543662	T;T;T	0.47177	0.85;0.85;0.85	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.72771	0.3502	M	0.87456	2.885	0.80722	D	1	D;D;D	0.89917	0.993;1.0;0.981	P;D;P	0.79108	0.811;0.992;0.892	T	0.78465	-0.2193	10	0.87932	D	0	-20.0642	15.6593	0.77169	1.0:0.0:0.0:0.0	.	476;425;425	B7Z3P1;A8K8C2;Q15813	.;.;TBCE_HUMAN	C	425;425;476	ENSP00000355560:Y425C;ENSP00000384571:Y425C;ENSP00000439170:Y476C	ENSP00000355560:Y425C	Y	+	2	0	TBCE	233671755	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	4.364000	0.59479	2.285000	0.76669	0.477000	0.44152	TAT	.	.		0.343	TBCE-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096458.3	NM_003193		G	235605132	A	G	235605132	3	3	235	1	0	0	0	0	1	0	0	0	15649	449	16	2	1324	2	TBCE	1	235605132	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	19585932	235605132	13645489	9	32695										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245851773	245851773	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tgcgggccgggcccgaggcgGaggcgcgcgggggggccctg	24	13	0	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr1:245851773G>A	ENST00000407071.2	+	12	5928	c.5488G>A	c.(5488-5490)Gag>Aag	p.E1830K	KIF26B_ENST00000366518.4_Missense_Mutation_p.E1449K	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1830					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			gcccgaggcggaggcgcgcgg	0.796																																					p.E1830K		Atlas-SNP	.											.	KIF26B	343	.	0			c.G5488A						.						1	1	1					1																	245851773		268	741	1009	SO:0001583	missense	55083	exon12			GAGGCGGAGGCGC	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.5488G>A	chr1.hg19:g.245851773G>A	ENSP00000385545:p.Glu1830Lys	6.0	0.0		32.0	10.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.623293	0.46840	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.78924	-1.22;-1.21	5.12	5.12	0.69794	.	.	.	.	.	T	0.76765	0.4033	L	0.57536	1.79	0.40602	D	0.981596	B;B	0.26318	0.146;0.085	B;B	0.24974	0.057;0.039	T	0.76903	-0.2787	9	0.72032	D	0.01	.	18.5334	0.91000	0.0:0.0:1.0:0.0	.	1449;1830	B7WPD9;Q2KJY2	.;KI26B_HUMAN	K	1830;1449;1446	ENSP00000385545:E1830K;ENSP00000355475:E1449K	ENSP00000355475:E1449K	E	+	1	0	KIF26B	243918396	1.000000	0.71417	0.912000	0.35992	0.103000	0.19146	3.186000	0.50942	2.374000	0.81015	0.407000	0.27541	GAG	.	.		0.796	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245851773	G	A	245851773	3	1	235	1	0	0	0	0	1	0	0	0	8304	1175	41	3	5534	3	KIF26B	1	245851773	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	10246641	245851773	3398848	10	32696										
DDX1	1653	hgsc.bcm.edu	37	chr2	15737583	15737583	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	aaggaaaaacaacaattaaaActggtgcttcaggtaatttt	7	5	1	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:15737583A>C	ENST00000381341.2	+	6	636	c.247A>C	c.(247-249)Act>Cct	p.T83P	DDX1_ENST00000233084.3_Missense_Mutation_p.T83P			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	83	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.|Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Necessary for interaction with HNRNPK.|Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		AACAATTAAAACTGGTGCTTC	0.313																																					p.T83P		Atlas-SNP	.											.	DDX1	70	.	0			c.A247C						.						59	58	58					2																	15737583		2201	4296	6497	SO:0001583	missense	1653	exon5			ATTAAAACTGGTG	X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"DEAD-boxes"	2734	protein-coding gene	gene with protein product		601257	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.247A>C	chr2.hg19:g.15737583A>C	ENSP00000370745:p.Thr83Pro	182.0	0.0		213.0	80.0	NM_004939	B4DME8|B4DPN6	Missense_Mutation	SNP	ENST00000381341.2	hg19	CCDS1686.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.104768	0.37145	.	.	ENSG00000079785	ENST00000381341;ENST00000233084;ENST00000543614	T;T	0.41400	1.0;1.0	5.64	5.64	0.86602	Concanavalin A-like lectin/glucanase (1);DEAD-like helicase (1);B30.2/SPRY domain (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.39226	0.1070	N	0.19112	0.55	0.80722	D	1	D	0.53462	0.96	P	0.51777	0.679	T	0.12268	-1.0554	10	0.20519	T	0.43	-21.2071	15.8545	0.78965	1.0:0.0:0.0:0.0	.	83	Q92499	DDX1_HUMAN	P	83	ENSP00000370745:T83P;ENSP00000233084:T83P	ENSP00000233084:T83P	T	+	1	0	DDX1	15655034	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.806000	0.69150	2.160000	0.67779	0.533000	0.62120	ACT	.	.		0.313	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939		C	15737583	A	C	15737583	3	2	235	1	0	0	0	0	1	0	0	0	4343	43	2	5	265	5	DDX1	2	15737583	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10		15737583	227461790	11	32697										
CRIM1	51232	hgsc.bcm.edu	37	chr2	36749317	36749317	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gaaggggatatattcctggcAgctgagtcctggaagcctga	14	8	0	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:36749317A>T	ENST00000280527.2	+	13	2656	c.2289A>T	c.(2287-2289)gcA>gcT	p.A763A		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	763	VWFC 5. {ECO:0000255|PROSITE- ProRule:PRU00220}.				insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				TATTCCTGGCAGCTGAGTCCT	0.448																																					p.A763A		Atlas-SNP	.											.	CRIM1	88	.	0			c.A2289T						.						177	161	166					2																	36749317		2203	4300	6503	SO:0001819	synonymous_variant	51232	exon13			CCTGGCAGCTGAG	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"cysteine-rich motor neuron 1"	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.2289A>T	chr2.hg19:g.36749317A>T		178.0	0.0		209.0	84.0	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Silent	SNP	ENST00000280527.2	hg19	CCDS1783.1																																																																																			.	.		0.448	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441		T	36749317	A	T	36749317	2	4	235	1	0	0	0	0	0	0	0	1	3875	175	7	4		4	CRIM1	2	36749317	Silent	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	21011734	36749317	206450056	12	32698										
SOS1	6654	hgsc.bcm.edu	37	chr2	39239378	39239378	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tgcttatatgccactcaactGtgggaggtgaactctgaaat	10	8	2	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:39239378G>A	ENST00000426016.1	-	15	2365	c.2279C>T	c.(2278-2280)aCa>aTa	p.T760I	SOS1_ENST00000402219.2_Missense_Mutation_p.T760I|SOS1_ENST00000395038.2_Missense_Mutation_p.T760I			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	760					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				CCACTCAACTGTGGGAGGTGA	0.388									Noonan syndrome																												p.T760I		Atlas-SNP	.											.	SOS1	134	.	0			c.C2279T						.						189	173	178					2																	39239378		2203	4300	6503	SO:0001583	missense	6654	exon14	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TCAACTGTGGGAG	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.2279C>T	chr2.hg19:g.39239378G>A	ENSP00000387784:p.Thr760Ile	105.0	0.0		105.0	8.0	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	hg19	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261711	0.59431	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	T;T;T	0.29655	1.56;1.56;1.56	5.87	4.98	0.66077	Guanine-nucleotide dissociation stimulator CDC25 (1);Ras guanine nucleotide exchange factor, domain (1);	0.280184	0.40385	N	0.001101	T	0.20047	0.0482	N	0.08118	0	0.80722	D	1	B	0.22414	0.069	B	0.18871	0.023	T	0.04281	-1.0963	10	0.72032	D	0.01	.	17.5059	0.87745	0.0:0.1326:0.8674:0.0	.	760	Q07889	SOS1_HUMAN	I	760;760;492;760;760	ENSP00000387784:T760I;ENSP00000384675:T760I;ENSP00000378479:T760I	ENSP00000263879:T760I	T	-	2	0	SOS1	39092882	1.000000	0.71417	0.889000	0.34880	0.985000	0.73830	7.827000	0.86722	1.575000	0.49775	0.655000	0.94253	ACA	.	.		0.388	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		A	39239378	G	A	39239378	3	1	235	1	0	0	0	0	1	0	0	0	14951	1377	48	3	1762	3	SOS1	2	39239378	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	2490061	39239378	203959995	13	32699										
FAM178B	51252	hgsc.bcm.edu	37	chr2	97637903	97637903	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gaaacgtttccccaggtgccTgtatcttgggcttctttggc	11	11	2	0	rs573710266	byFrequency	TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:97637903T>A	ENST00000417561.3	-	7	742	c.743A>T	c.(742-744)cAg>cTg	p.Q248L	FAM178B_ENST00000490605.2_Missense_Mutation_p.Q100L|FAM178B_ENST00000327896.3_Missense_Mutation_p.Q68L			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	248										large_intestine(1)|ovary(1)	2						CCCAGGTGCCTGTATCTTGGG	0.697																																					p.Q100L		Atlas-SNP	.											.	FAM178B	35	.	0			c.A299T						.						7	9	8					2																	97637903		690	1584	2274	SO:0001583	missense	51252	exon3			GGTGCCTGTATCT	AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.743A>T	chr2.hg19:g.97637903T>A	ENSP00000413245:p.Gln248Leu	252.0	0.0		368.0	153.0	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Missense_Mutation	SNP	ENST00000417561.3	hg19		.	.	.	.	.	.	.	.	.	.	T	15.13	2.742564	0.49151	.	.	ENSG00000168754	ENST00000417561;ENST00000327896;ENST00000490605	T;T;T	0.52526	0.66;0.71;0.69	4.22	4.22	0.49857	.	.	.	.	.	T	0.38585	0.1046	N	0.24115	0.695	0.28563	N	0.911001	.	.	.	.	.	.	T	0.28713	-1.0035	7	0.38643	T	0.18	-6.1455	9.9837	0.41828	0.0:0.0:0.0:1.0	.	.	.	.	L	248;68;100	ENSP00000413245:Q248L;ENSP00000333553:Q68L;ENSP00000429896:Q100L	ENSP00000333553:Q68L	Q	-	2	0	FAM178B	97001630	0.980000	0.34600	0.943000	0.38184	0.152000	0.21847	3.093000	0.50217	2.140000	0.66376	0.533000	0.62120	CAG	.	.		0.697	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490		A	97637903	T	A	97637903	3	1	235	1	0	0	0	0	1	0	0	0	5509	1580	55	4	1831	4	FAM178B	2	97637903	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	58398525	97637903	145561470	14	32700										
ANAPC1	64682	hgsc.bcm.edu	37	chr2	112601156	112601156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ttttggcaggataaacttaaTtgcttgcaaacacgtttgta	8	6	0	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:112601156T>C	ENST00000341068.3	-	17	2645	c.1873A>G	c.(1873-1875)Att>Gtt	p.I625V		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	625					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						ATAAACTTAATTGCTTGCAAA	0.373																																					p.I625V		Atlas-SNP	.											.	ANAPC1	116	.	0			c.A1873G						.						60	53	55					2																	112601156		2203	4300	6503	SO:0001583	missense	64682	exon17			ACTTAATTGCTTG	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"Anaphase promoting complex subunits"	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.1873A>G	chr2.hg19:g.112601156T>C	ENSP00000339109:p.Ile625Val	103.0	0.0		140.0	54.0	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	hg19	CCDS2093.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	10.08|10.08	1.253213|1.253213	0.22965|0.22965	.|.	.|.	ENSG00000153107|ENSG00000153107	ENST00000341068|ENST00000427997	.|.	.|.	.|.	4.37|4.37	1.57|1.57	0.23409|0.23409	.|.	0.000000|.	0.36482|.	U|.	0.002569|.	T|T	0.23886|0.23886	0.0578|0.0578	N|N	0.04043|0.04043	-0.29|-0.29	0.35272|0.35272	D|D	0.780557|0.780557	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.22800|0.22800	-1.0206|-1.0206	9|5	0.28530|.	T|.	0.3|.	-15.3506|-15.3506	8.6102|8.6102	0.33797|0.33797	0.0:0.2636:0.0:0.7364|0.0:0.2636:0.0:0.7364	.|.	625|.	Q9H1A4|.	APC1_HUMAN|.	V|S	625|159	.|.	ENSP00000339109:I625V|.	I|N	-|-	1|2	0|0	ANAPC1|ANAPC1	112317627|112317627	0.905000|0.905000	0.30787|0.30787	0.999000|0.999000	0.59377|0.59377	0.962000|0.962000	0.63368|0.63368	0.886000|0.886000	0.28241|0.28241	0.548000|0.548000	0.28955|0.28955	0.445000|0.445000	0.29226|0.29226	ATT|AAT	.	.		0.373	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662		C	112601156	T	C	112601156	3	2	235	1	0	0	0	0	1	0	0	0	598	1493	52	2	4089	2	ANAPC1	2	112601156	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	14963253	112601156	130598217	15	32701										
IFIH1	64135	hgsc.bcm.edu	37	chr2	163139081	163139081	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cggaagagctgttcaactagCagtaccttaaaaaaatgtga	9	7	1	2	rs180798633		TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:163139081C>A	ENST00000263642.2	-	6	1496	c.1101G>T	c.(1099-1101)ctG>ctT	p.L367L		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	367	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						GTTCAACTAGCAGTACCTTAA	0.368																																					p.L367L		Atlas-SNP	.											.	IFIH1	102	.	0			c.G1101T						.						34	33	33					2																	163139081		2200	4299	6499	SO:0001819	synonymous_variant	64135	exon6			AACTAGCAGTACC	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"helicard"	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.1101G>T	chr2.hg19:g.163139081C>A		77.0	0.0		85.0	37.0	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Silent	SNP	ENST00000263642.2	hg19	CCDS2217.1																																																																																			.	C|1.000;G|0.000		0.368	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		A	163139081	C	A	163139081	2	1	235	1	0	0	0	0	0	0	0	1	7529	697	25	3		3	IFIH1	2	163139081	Silent	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	50537925	163139081	80060292	16	32702										
DHRS9	10170	hgsc.bcm.edu	37	chr2	169952088	169952088	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	aaaggcaataaatcctatgtGaacatggacctctctccggt	8	10	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:169952088G>T	ENST00000327239.4	+	8	2275	c.771G>T	c.(769-771)gtG>gtT	p.V257V	DHRS9_ENST00000357546.2_Silent_p.V257V|DHRS9_ENST00000602501.1_Silent_p.V257V|DHRS9_ENST00000421653.1_Silent_p.V110V|DHRS9_ENST00000432060.2_Silent_p.V317V|DHRS9_ENST00000428522.1_Silent_p.V257V|DHRS9_ENST00000412271.1_Silent_p.V257V|DHRS9_ENST00000436483.2_Silent_p.V257V	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	257					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						AATCCTATGTGAACATGGACC	0.433																																					p.V257V		Atlas-SNP	.											.	DHRS9	29	.	0			c.G771T						.						151	149	150					2																	169952088		2203	4300	6503	SO:0001819	synonymous_variant	10170	exon8			CTATGTGAACATG	AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	16888	protein-coding gene	gene with protein product	"NADP-dependent retinol dehydrogenase/reductase", "3-alpha hydroxysteroid dehydrogenase", "retinol dehydrogenase homolog", "short chain dehydrogenase/reductase family 9C, member 4"	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.771G>T	chr2.hg19:g.169952088G>T		274.0	0.0		328.0	125.0	NM_005771	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Silent	SNP	ENST00000327239.4	hg19	CCDS2231.1																																																																																			.	.		0.433	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771		T	169952088	G	T	169952088	2	4	235	1	0	0	0	0	0	0	0	1	4500	1277	45	3		3	DHRS9	2	169952088	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	6813007	169952088	73247285	17	32703										
TTN	7273	hgsc.bcm.edu	37	chr2	179639038	179639038	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ccgtgaggttctgacgtccaCgacgagatgtaattgtatat	11	8	1	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:179639038C>T	ENST00000591111.1	-	30	7177	c.6953G>A	c.(6952-6954)cGt>cAt	p.R2318H	TTN_ENST00000359218.5_Missense_Mutation_p.R2272H|TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.R2318H|TTN_ENST00000589042.1_Missense_Mutation_p.R2318H|TTN_ENST00000342992.6_Missense_Mutation_p.R2318H|RP11-88L24.4_ENST00000582038.2_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R2272H|TTN_ENST00000342175.6_Missense_Mutation_p.R2272H			Q8WZ42	TITIN_HUMAN	titin	12640	Ig-like 12.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGACGTCCACGACGAGATGT	0.403																																					p.R2318H		Atlas-SNP	.											.	TTN	18412	.	0			c.G6953A						.						176	161	166					2																	179639038		2203	4300	6503	SO:0001583	missense	7273	exon30			CGTCCACGACGAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.6953G>A	chr2.hg19:g.179639038C>T	ENSP00000465570:p.Arg2318His	88.0	0.0		132.0	67.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.23	3.065125	0.55432	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	5.6	5.6	0.85130	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56171	0.1967	L	0.29908	0.895	0.39107	D	0.961397	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	T	0.60885	-0.7174	9	0.87932	D	0	.	19.6137	0.95619	0.0:1.0:0.0:0.0	.	2272;2272;2272;2318;2318	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	H	2318;2272;2272;2272;2272;2318	ENSP00000343764:R2318H;ENSP00000434586:R2272H;ENSP00000340554:R2272H;ENSP00000352154:R2272H;ENSP00000354117:R2318H	ENSP00000340554:R2272H	R	-	2	0	TTN	179347283	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.818000	0.86416	2.650000	0.89964	0.557000	0.71058	CGT	.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179639038	C	T	179639038	3	4	235	1	0	0	0	0	1	0	0	0	16750	536	19	1	104367	1	TTN	2	179639038	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	9686950	179639038	63560335	18	32704										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187627077	187627077	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	aaggaaagccctccccgcatCccagagcctggtttgtgtct	10	14	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:187627077C>T	ENST00000304698.5	+	8	2211	c.2008C>T	c.(2008-2010)Ccc>Tcc	p.P670S		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	670						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						CTCCCCGCATCCCAGAGCCTG	0.483																																					p.P670S		Atlas-SNP	.											.	FAM171B	146	.	0			c.C2008T						.						75	83	80					2																	187627077		2203	4300	6503	SO:0001583	missense	165215	exon8			CCGCATCCCAGAG	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.2008C>T	chr2.hg19:g.187627077C>T	ENSP00000304108:p.Pro670Ser	193.0	0.0		213.0	107.0	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.366859	0.82463	.	.	ENSG00000144369	ENST00000304698	T	0.63744	-0.06	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.79191	0.4404	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78974	-0.1992	10	0.87932	D	0	-14.9834	20.547	0.99278	0.0:1.0:0.0:0.0	.	670;671	Q6P995;A8K122	F171B_HUMAN;.	S	670	ENSP00000304108:P670S	ENSP00000304108:P670S	P	+	1	0	FAM171B	187335322	1.000000	0.71417	0.998000	0.56505	0.920000	0.55202	7.460000	0.80816	2.850000	0.98022	0.650000	0.86243	CCC	.	.		0.483	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		T	187627077	C	T	187627077	3	4	235	1	0	0	0	0	1	0	0	0	5496	855	30	3	2038	3	FAM171B	2	187627077	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	7988039	187627077	55572296	19	32705										
USP37	57695	hgsc.bcm.edu	37	chr2	219330793	219330794	+	Frame_Shift_Ins	INS	-	-	A													0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gctcttccctttcacgctccINSatatcatactgctggagcca							TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:219330793_219330794insA	ENST00000258399.3	-	21	2817_2818	c.2405_2406insT	c.(2404-2406)atgfs	p.M802fs	USP37_ENST00000415516.1_Frame_Shift_Ins_p.M708fs|USP37_ENST00000454775.1_Frame_Shift_Ins_p.M802fs|USP37_ENST00000418019.1_Frame_Shift_Ins_p.M802fs	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	802	USP.				G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		TTTCACGCTCCATATCATACTG	0.421																																					p.M802fs		Atlas-INDEL	.											.	USP37	76	.	0			c.2406_2407insT						.																																			SO:0001589	frameshift_variant	57695	exon21			.	AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"Ubiquitin-specific peptidases"	20063	protein-coding gene	gene with protein product			"ubiquitin specific protease 37"			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.2406dupT	chr2.hg19:g.219330794_219330794dupA	ENSP00000258399:p.Met802fs	43.0	0.0		60.0	23.0	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Frame_Shift_Ins	INS	ENST00000258399.3	hg19	CCDS2418.1																																																																																			.	.		0.421	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		A	219330794	-	A	219330793	7	5	235	1	0	1	1	0	0	0	0	0	17083	594	21	0	557	0	USP37	2	219330793	Frame_Shift_Ins	INS	-	TCGA-DD-AAW2-01A-11D-A40P-10	31703716	219330793	23868580	20	32706										
UGT1A1	54658	hgsc.bcm.edu	37	chr2	234669658	234669659	+	Missense_Mutation	DNP	TG	TG	AC													0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	agaattccttcagagagaggTgactgtccaggacctattga							TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:234669658_234669659TG>AC	ENST00000608383.1	+	1	725_726	c.725_726TG>AC	c.(724-726)gTG>gAC	p.V242D	UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A8_ENST00000305208.5_Missense_Mutation_p.V242D|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000360418.3_Missense_Mutation_p.V242D|UGT1A6_ENST00000406651.1_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A3_ENST00000482026.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A5_ENST00000373414.3_Intron			P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	242					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	CAGAGAGAGGTGACTGTCCAGG	0.475																																					p.V242E|p.V242V		Atlas-SNP	.											.	UGT1A1	81	.	0			c.T725A|c.G726C						.																																			SO:0001583	missense	54658	exon1			GAGAGGTGACTGT|AGAGGTGACTGTC	M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"UDP glucuronosyltransferases"	12530	other	complex locus constituent		191740	"UDP glycosyltransferase 1 family, polypeptide A1"	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	Exception_encountered	chr2.hg19:g.234669658_234669659delinsAC	ENSP00000476741:p.Val242Asp	132.0|133.0	0.0		159.0|162.0	65.0|66.0	NM_000463	A6NJC3|B8K286	Missense_Mutation|Silent	SNP	ENST00000608383.1	hg19	CCDS2510.1																																																																																			.	.		0.475	UGT1A1-203	KNOWN	basic|CCDS	protein_coding	protein_coding				AC	234669659	TG	AC	234669658	3	1	235	1	0	0	0	0	1	0	0	0	16959	1696	59	4	727	4	UGT1A1	2	234669658	Missense_Mutation	DNP	TG	TCGA-DD-AAW2-01A-11D-A40P-10	15338865	234669658	8529715	21	32707										
CXCR7	57007	hgsc.bcm.edu	37	chr2	237489983	237489983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cacctgccggctggagcacgCcctcttcacggccctgcatg	11	18	2	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr2:237489983C>T	ENST00000272928.3	+	2	1185	c.875C>T	c.(874-876)gCc>gTc	p.A292V		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	292					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)										CTGGAGCACGCCCTCTTCACG	0.592																																					p.A292V		Atlas-SNP	.											.	CXCR7	72	.	0			c.C875T						.						135	113	121					2																	237489983		2203	4300	6503	SO:0001583	missense	57007	exon2			AGCACGCCCTCTT	BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"CD molecules", "GPCR / Class A : Chemokine receptors : Atypical"	23692	protein-coding gene	gene with protein product		610376	"chemokine orphan receptor 1", "chemokine (C-X-C motif) receptor 7"	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.875C>T	chr2.hg19:g.237489983C>T	ENSP00000272928:p.Ala292Val	41.0	0.0		65.0	24.0	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	hg19	CCDS2516.1	.	.	.	.	.	.	.	.	.	.	C	5.837	0.338691	0.11069	.	.	ENSG00000144476	ENST00000272928	T	0.70164	-0.46	5.41	2.06	0.26882	GPCR, rhodopsin-like superfamily (1);	0.323007	0.32328	N	0.006246	T	0.40347	0.1113	N	0.12637	0.245	0.26746	N	0.970281	B	0.02656	0.0	B	0.04013	0.001	T	0.15578	-1.0432	9	.	.	.	.	5.2762	0.15651	0.0:0.1236:0.184:0.6923	.	292	P25106	CXCR7_HUMAN	V	292	ENSP00000272928:A292V	.	A	+	2	0	CXCR7	237154722	1.000000	0.71417	0.974000	0.42286	0.881000	0.50899	2.115000	0.41921	0.141000	0.18875	-0.176000	0.13171	GCC	.	.		0.592	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		T	237489983	C	T	237489983	3	4	235	1	0	0	0	0	1	0	0	0	4098	739	26	3	877	3	CXCR7	2	237489983	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	2820325	237489983	5709390	22	32708										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4747976	4747976	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tctcagcccgcaatgccgcaCgcagggactctgttctggca	11	15	3	0	rs373619512		TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr3:4747976C>A	ENST00000443694.2	+	34	4738	c.4738C>A	c.(4738-4740)Cgc>Agc	p.R1580S	ITPR1_ENST00000423119.2_Missense_Mutation_p.R1586S|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.R1595S|ITPR1_ENST00000302640.8_Missense_Mutation_p.R1580S|ITPR1_ENST00000357086.4_Missense_Mutation_p.R1586S|ITPR1_ENST00000456211.2_Missense_Mutation_p.R1571S			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1595				AIAIPVDLDSQVNNLFLKSHSIVQK -> HCHSRGPGQPSQ QPLSQVPQHCAE (in Ref. 6; AAD14386). {ECO:0000305}.	activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	CAATGCCGCACGCAGGGACTC	0.537																																					p.R1586S		Atlas-SNP	.											ITPR1_ENST00000357086,colon,carcinoma,0,3	ITPR1	659	.	0			c.C4756A						.						48	51	50					3																	4747976		2030	4186	6216	SO:0001583	missense	3708	exon37			GCCGCACGCAGGG	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.4738C>A	chr3.hg19:g.4747976C>A	ENSP00000401671:p.Arg1580Ser	80.0	1.0		99.0	38.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825180	0.32237	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	T;T;T;T;T;T	0.61627	0.09;0.09;0.09;0.09;0.09;0.09	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.52533	0.1740	L	0.56280	1.765	0.80722	D	1	B;B	0.27679	0.091;0.185	B;B	0.25987	0.033;0.065	T	0.47812	-0.9088	10	0.25751	T	0.34	.	14.9162	0.70798	0.1438:0.8562:0.0:0.0	.	1595;1586	Q14643;G5E9P1	ITPR1_HUMAN;.	S	1595;1580;1595;1586;41;1586;1571;1580	ENSP00000306253:R1580S;ENSP00000346595:R1595S;ENSP00000405934:R1586S;ENSP00000349597:R1586S;ENSP00000397885:R1571S;ENSP00000401671:R1580S	ENSP00000306253:R1580S	R	+	1	0	ITPR1	4722976	0.987000	0.35691	0.570000	0.28473	0.415000	0.31203	2.787000	0.47798	2.609000	0.88269	0.655000	0.94253	CGC	.	.		0.537	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4747976	C	A	4747976	3	1	235	1	0	0	0	0	1	0	0	0	7929	536	19	1	4921	1	ITPR1	3	4747976	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10		4747976	193274454	23	32709										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266124	41266124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gaatccattctggtgccactAccacagctccttctctgagt	7	14	2	1	rs121913412		TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr3:41266124A>G	ENST00000349496.5	+	3	401	c.121A>G	c.(121-123)Acc>Gcc	p.T41A	CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34A|CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41A|CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	41			T -> A (in hepatoblastoma and hepatocellular carcinoma; also in a desmoid tumor; strongly reduces phosphorylation and degradation; abolishes phosphorylation on Ser-33 and Ser-37 and enhances transactivation of target genes). {ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10398436, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10655994, ECO:0000269|PubMed:9927029}.|T -> I (in PTR, hepatocellular carcinoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T41A(550)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41P(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.A39_T42del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGTGCCACTACCACAGCTCC	0.507	T41A(CCK81_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.T41A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	681	Substitution - Missense(559)|Deletion - In frame(96)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)	soft_tissue(387)|liver(158)|large_intestine(61)|endometrium(17)|kidney(11)|stomach(8)|biliary_tract(7)|ovary(6)|small_intestine(4)|lung(4)|prostate(4)|adrenal_gland(3)|haematopoietic_and_lymphoid_tissue(3)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|salivary_gland(1)|pituitary(1)|pancreas(1)	c.A121G						.						89	77	81					3																	41266124		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCCACTACCACAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.121A>G	chr3.hg19:g.41266124A>G	ENSP00000344456:p.Thr41Ala	133.0	0.0		218.0	127.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449381	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.63117	0.2484	M	0.79258	2.445	0.80722	D	1	P	0.50943	0.94	P	0.52267	0.694	T	0.68561	-0.5376	10	0.87932	D	0	-8.9189	16.3453	0.83126	1.0:0.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	A	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34A;ENSP00000385604:T41A;ENSP00000412219:T41A;ENSP00000379486:T41A;ENSP00000344456:T41A;ENSP00000411226:T34A;ENSP00000379488:T41A;ENSP00000409302:T41A;ENSP00000401599:T41A	ENSP00000344456:T41A	T	+	1	0	CTNNB1	41241128	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	ACC	.	.		0.507	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266124	A	G	41266124	3	3	235	1	0	0	0	0	1	0	0	0	4018	391	14	2	127	2	CTNNB1	3	41266124	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	36518148	41266124	156756306	24	32710										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266165	41266165	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ggtaaaggcaatcctgaggaAgaggatgtggatacctccca	13	8	0	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr3:41266165A>C	ENST00000349496.5	+	3	442	c.162A>C	c.(160-162)gaA>gaC	p.E54D	CTNNB1_ENST00000453024.1_Missense_Mutation_p.E47D|CTNNB1_ENST00000405570.1_Missense_Mutation_p.E54D|CTNNB1_ENST00000396183.3_Missense_Mutation_p.E54D|CTNNB1_ENST00000396185.3_Missense_Mutation_p.E54D	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	54					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.Q28_Q61del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ATCCTGAGGAAGAGGATGTGG	0.463		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.E54D	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+2,1	CTNNB1	4904	.	110	Deletion - In frame(88)|Complex - deletion inframe(15)|Unknown(7)	liver(81)|large_intestine(16)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)	c.A162C						.						73	67	69					3																	41266165		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGAGGAAGAGGAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.162A>C	chr3.hg19:g.41266165A>C	ENSP00000344456:p.Glu54Asp	138.0	0.0		206.0	117.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	3.145	-0.175568	0.06421	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.91	-0.768	0.11013	.	0.272597	0.42548	D	0.000690	T	0.10337	0.0253	N	0.02011	-0.69	0.44745	D	0.997743	B	0.02656	0.0	B	0.04013	0.001	T	0.33420	-0.9869	10	0.02654	T	1	-8.2306	2.7296	0.05223	0.3389:0.1297:0.4044:0.127	.	54	P35222	CTNB1_HUMAN	D	47;54;54;54;54;47;54;54;54	ENSP00000400508:E47D;ENSP00000385604:E54D;ENSP00000412219:E54D;ENSP00000379486:E54D;ENSP00000344456:E54D;ENSP00000411226:E47D;ENSP00000379488:E54D;ENSP00000409302:E54D;ENSP00000401599:E54D	ENSP00000344456:E54D	E	+	3	2	CTNNB1	41241169	0.991000	0.36638	0.991000	0.47740	0.997000	0.91878	0.349000	0.20055	-0.081000	0.12662	0.533000	0.62120	GAA	.	.		0.463	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266165	A	C	41266165	3	2	235	1	0	0	0	0	1	0	0	0	4018	69	3	5	168	5	CTNNB1	3	41266165	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	41	41266165	156756265	25	32711										
LZTFL1	54585	hgsc.bcm.edu	37	chr3	45872441	45872441	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tcaagctgtaaatcttgcagTgctttttctagttttgactt	7	7	3	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr3:45872441T>C	ENST00000296135.6	-	7	738	c.564A>G	c.(562-564)gcA>gcG	p.A188A	LZTFL1_ENST00000536047.1_Silent_p.A171A|LZTFL1_ENST00000490463.1_5'UTR|LZTFL1_ENST00000539217.1_Silent_p.A184A	NM_001276378.1|NM_020347.2	NP_001263307.1|NP_065080.1	Q9NQ48	LZTL1_HUMAN	leucine zipper transcription factor-like 1	188	Interaction with BSS9.				establishment of protein localization to organelle (GO:0072594)	BBSome (GO:0034464)|cytoplasm (GO:0005737)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	8				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		AATCTTGCAGTGCTTTTTCTA	0.303																																					p.A188A		Atlas-SNP	.											.	LZTFL1	37	.	0			c.A564G						.						153	148	150					3																	45872441		2201	4299	6500	SO:0001819	synonymous_variant	54585	exon7			TTGCAGTGCTTTT	AJ297351	CCDS2731.1, CCDS63608.1, CCDS63609.1	3p21.3	2014-01-28			ENSG00000163818	ENSG00000163818			6741	protein-coding gene	gene with protein product		606568				11352561, 22510444	Standard	NM_020347		Approved	BBS17	uc003cox.2	Q9NQ48	OTTHUMG00000133452	ENST00000296135.6:c.564A>G	chr3.hg19:g.45872441T>C		96.0	0.0		149.0	40.0	NM_020347	B3KSI9|B4E0K7|Q8TC61|Q9NQ56	Silent	SNP	ENST00000296135.6	hg19	CCDS2731.1	.	.	.	.	.	.	.	.	.	.	T	9.809	1.182699	0.21870	.	.	ENSG00000163818	ENST00000440576	.	.	.	5.78	-4.99	0.03010	.	.	.	.	.	T	0.17959	0.0431	.	.	.	0.25986	N	0.982316	.	.	.	.	.	.	T	0.28235	-1.0050	4	.	.	.	-0.4303	2.3522	0.04286	0.0972:0.2346:0.3008:0.3674	.	.	.	.	A	124	.	.	T	-	1	0	LZTFL1	45847445	0.028000	0.19301	0.001000	0.08648	0.991000	0.79684	-0.961000	0.03845	-0.802000	0.04421	0.533000	0.62120	ACT	.	.		0.303	LZTFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257326.3	NM_020347		C	45872441	T	C	45872441	2	2	235	1	0	0	0	0	0	0	0	1	9145	1683	59	2		2	LZTFL1	3	45872441	Silent	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	4606276	45872441	152149989	26	32712										
TMEM115	11070	hgsc.bcm.edu	37	chr3	50396097	50396097	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ccaaggcgccgtggatacggAcagtgaacaggtagaccagg	15	10	0	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr3:50396097A>C	ENST00000266025.3	-	1	944	c.398T>G	c.(397-399)gTc>gGc	p.V133G	XXcos-LUCA11.5_ENST00000606589.1_Intron	NM_007024.4	NP_008955.1	Q12893	TM115_HUMAN	transmembrane protein 115	133					negative regulation of cell proliferation (GO:0008285)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(1)|lung(1)|prostate(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GTGGATACGGACAGTGAACAG	0.597																																					p.V133G		Atlas-SNP	.											.	TMEM115	20	.	0			c.T398G						.						53	58	56					3																	50396097		2203	4300	6503	SO:0001583	missense	11070	exon1			ATACGGACAGTGA	BC011948	CCDS2828.1	3p21.31	2008-11-04			ENSG00000126062	ENSG00000126062			30055	protein-coding gene	gene with protein product	"placental protein 6"	607069				11085536	Standard	NM_007024		Approved	PL6	uc003dan.1	Q12893	OTTHUMG00000044212	ENST00000266025.3:c.398T>G	chr3.hg19:g.50396097A>C	ENSP00000266025:p.Val133Gly	86.0	0.0		227.0	138.0	NM_007024	A2IDB7|O14568|Q6IAY4|Q9UIX3	Missense_Mutation	SNP	ENST00000266025.3	hg19	CCDS2828.1	.	.	.	.	.	.	.	.	.	.	A	15.93	2.978744	0.53720	.	.	ENSG00000126062	ENST00000266025	.	.	.	5.39	5.39	0.77823	.	0.439891	0.23543	N	0.047046	T	0.61739	0.2371	M	0.74881	2.28	0.80722	D	1	B	0.24186	0.099	B	0.30401	0.115	T	0.59731	-0.7399	9	0.32370	T	0.25	-2.2824	9.0046	0.36104	0.9161:0.0:0.0839:0.0	.	133	Q12893	TM115_HUMAN	G	133	.	ENSP00000266025:V133G	V	-	2	0	TMEM115	50371101	0.993000	0.37304	0.824000	0.32777	0.761000	0.43186	7.406000	0.80017	2.038000	0.60285	0.460000	0.39030	GTC	.	.		0.597	TMEM115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102784.3	NM_007024		C	50396097	A	C	50396097	3	2	235	1	0	0	0	0	1	0	0	0	16044	275	10	5	665	5	TMEM115	3	50396097	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	4523656	50396097	147626333	27	32713										
GNL3	26354	hgsc.bcm.edu	37	chr3	52724657	52724657	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tggctaaattatttgaagaaAgaattgccaacagtggtgtt	10	4	0	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr3:52724657A>C	ENST00000418458.1	+	7	764	c.591A>C	c.(589-591)aaA>aaC	p.K197N	SNORD69_ENST00000391150.1_RNA|GNL3_ENST00000394799.2_Missense_Mutation_p.K185N|SNORD19_ENST00000391191.1_RNA|SNORD19_ENST00000410413.1_RNA|SNORD19B_ENST00000516978.1_RNA|SNORD19B_ENST00000459623.1_RNA	NM_014366.4|NM_206826.1	NP_055181.3|NP_996562.1	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)	197	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				cell proliferation (GO:0008283)|GTP catabolic process (GO:0006184)|regulation of cell proliferation (GO:0042127)|ribosome biogenesis (GO:0042254)	extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|large_intestine(3)|lung(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		ATTTGAAGAAAGAATTGCCAA	0.408																																					p.K197N		Atlas-SNP	.											.	GNL3	37	.	0			c.A591C						.						183	207	199					3																	52724657		2203	4300	6503	SO:0001583	missense	26354	exon7			GAAGAAAGAATTG	AK027514	CCDS2861.1, CCDS43100.1	3p21.1	2005-01-10			ENSG00000163938	ENSG00000163938			29931	protein-coding gene	gene with protein product		608011				11085516, 12464630	Standard	NM_014366		Approved	C77032, E2IG3, MGC800, NS, nucleostemin	uc003dfd.3	Q9BVP2	OTTHUMG00000158752	ENST00000418458.1:c.591A>C	chr3.hg19:g.52724657A>C	ENSP00000395772:p.Lys197Asn	133.0	0.0		206.0	65.0	NM_014366	B2RDC1|Q5PU80|Q96SV6|Q96SV7|Q9UJY0	Missense_Mutation	SNP	ENST00000418458.1	hg19	CCDS2861.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.912593	0.52439	.	.	ENSG00000163938	ENST00000418458;ENST00000394799	T;T	0.14266	2.52;2.52	6.17	1.41	0.22369	.	0.452214	0.27586	N	0.018704	T	0.11281	0.0275	L	0.57536	1.79	0.43467	D	0.995677	B	0.17268	0.021	B	0.16722	0.016	T	0.17868	-1.0355	10	0.14656	T	0.56	.	6.0675	0.19871	0.6025:0.0:0.2784:0.1192	.	197	Q9BVP2	GNL3_HUMAN	N	197;185	ENSP00000395772:K197N;ENSP00000378278:K185N	ENSP00000378278:K185N	K	+	3	2	GNL3	52699697	0.620000	0.27068	0.985000	0.45067	0.999000	0.98932	-0.231000	0.09069	0.019000	0.15079	0.533000	0.62120	AAA	.	.		0.408	GNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352032.1	NM_014366		C	52724657	A	C	52724657	3	2	235	1	0	0	0	0	1	0	0	0	6545	69	3	5	617	5	GNL3	3	52724657	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	2328560	52724657	145297773	28	32714										
ALDH1L1	10840	hgsc.bcm.edu	37	chr3	125833489	125833489	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ggacaccttcttcacgttacTtatggcacagctgcaaggaa	9	11	2	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr3:125833489T>A	ENST00000393434.2	-	18	2342	c.1993A>T	c.(1993-1995)Agt>Tgt	p.S665C	ALDH1L1_ENST00000452905.2_Missense_Mutation_p.S564C|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.S665C|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.S675C|ALDH1L1_ENST00000393431.2_Intron	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	665	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	TTCACGTTACTTATGGCACAG	0.617																																					p.S675C		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.A2023T						.						138	125	129					3																	125833489		2203	4300	6503	SO:0001583	missense	10840	exon18			CGTTACTTATGGC	AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"Aldehyde dehydrogenases"	3978	protein-coding gene	gene with protein product	"cytosolic 10-formyltetrahydrofolate dehydrogenase"	600249	"formyltetrahydrofolate dehydrogenase"	FTHFD			Standard	NM_012190		Approved